#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
PERM1	84808	hgsc.bcm.edu	37	1	915431	915431	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:915431delC	ENST00000341290.2	-	3	672	c.637delG	c.(637-639)gacfs	p.D213fs	C1orf170_ENST00000433179.2_Frame_Shift_Del_p.D233fs			Q5SV97	PERM1_HUMAN		327					regulation of transcription, DNA-templated (GO:0006355)|response to muscle activity (GO:0014850)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCATGTCCCTGTCAGAT	0.597																																					.		Atlas-Indel	.											.	C1orf170	5	.	0			.						PASS	.																																			SO:0001589	frameshift_variant	84808	.			.																												ENST00000341290.2:c.637delG	1.37:g.915431delC	ENSP00000343864:p.Asp213fs	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	190	13	0.0684211	.	Q6ZVZ7|Q9BRF2|S5G239	RNA	DEL	ENST00000341290.2	37																																																																																				.	.	none		0.597	C1orf170-001	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000097943.2		
HLA-B	3106	hgsc.bcm.edu	37	6	31324601	31324602	+	Frame_Shift_Ins	INS	-	-	G	rs41562914|rs41541416|rs9281379	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324601_31324602insG	ENST00000412585.2	-	2	234_235	c.206_207insC	c.(205-207)gagfs	p.E69fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	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.E69fs*30(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCCGCGGCTCCTCTCTCGGACT	0.673									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.E69fs		Atlas-Indel	.											.	HLA-B	54	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.207_208insC						PASS	.			1399,160,2559		395,63,546,25,47,983						0.1	0.1		dbSNP_130	35	1793,477,5714		469,110,745,86,195,2387	no	codingComplex	HLA-B	NM_005514.6		864,173,1291,111,242,3370	A1A1,A1A2,A1R,A2A2,A2R,RR		28.4319,37.8582,31.6394				3192,637,8273				SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	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.206_207insC	6.37:g.31324601_31324602insG	ENSP00000399168:p.Glu69fs	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_005514	Q29764	Frame_Shift_Ins	INS	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.673	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
HERC4	26091	hgsc.bcm.edu	37	10	69785435	69785436	+	Splice_Site	INS	-	-	A	rs397840935|rs3834396	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69785435_69785436insA	ENST00000395198.3	-	8	1025		c.e8-2		HERC4_ENST00000277817.6_Splice_Site|HERC4_ENST00000373700.4_Splice_Site|HERC4_ENST00000395187.2_Splice_Site|HERC4_ENST00000412272.2_Splice_Site	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4						cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.?(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCCACCTTCCTAAAAAAAGACA	0.342													?|AAAAAAA|AAAAAAAA|unsure	984	0.196486	0.1876	0.1744	5008	,	,		18753	0.3889		0.0855	False		,,,				2504	0.1401				.		Pindel,Atlas-Indel	.											.	HERC4	78	.	1	Unknown(1)	pancreas(1)	c.778-2->T						PASS	.		,	756,3508		72,612,1448					,	5.2	1.0		dbSNP_130	89	542,7712		17,508,3602	no	splice-3,splice-3	HERC4	NM_022079.2,NM_015601.3	,	89,1120,5050	A1A1,A1R,RR		6.5665,17.7298,10.3691	,	,		1298,11220				SO:0001630	splice_region_variant	26091	exon9			.	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.778-2->T	10.37:g.69785442_69785442dupA		Somatic	61	.	.		WXS	Illumina HiSeq	Phase_I	42	19	0.452	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Splice_Site	INS	ENST00000395198.3	37	CCDS41533.1																																																																																			-|0.798;A|0.202	0.202	strong		0.342	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	Intron
NUP54	53371	hgsc.bcm.edu	37	4	77065318	77065319	+	In_Frame_Ins	INS	-	-	TGT	rs76406406|rs57577548|rs36024409|rs67608403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77065318_77065319insTGT	ENST00000264883.3	-	3	418_419	c.278_279insACA	c.(277-279)cag>caACAg	p.93_93Q>QQ	NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000514987.1_Intron|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	93	9 X 2 AA repeats of F-G.|Poly-Gln.|Thr-rich.				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 targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.Q93>HK(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GCTGCTGCTGCTGTGTATTAAA	0.411														776	0.154952	0.0567	0.1282	5008	,	,		16499	0.3512		0.1312	False		,,,				2504	0.1288				p.Q93delinsQQ		Pindel,Atlas-Indel	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Complex - insertion inframe(1)	kidney(1)	c.279_280insACA						PASS	.			300,3966		14,272,1847						5.2	1.0		dbSNP_126	211	1244,7010		96,1052,2979	no	coding	NUP54	NM_017426.2		110,1324,4826	A1A1,A1R,RR		15.0715,7.0323,12.3323				1544,10976				SO:0001652	inframe_insertion	53371	exon3			.	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.276_278dupACA	4.37:g.77065319_77065321dupTGT	ENSP00000264883:p.Gln97dup	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	121	26	0.215	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	In_Frame_Ins	INS	ENST00000264883.3	37	CCDS3576.1																																																																																			-|0.827;TGT|0.173	0.173	strong		0.411	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Frame_Shift_Del	DEL	C	C	-	rs386636937|rs542219168|rs71563271|rs2072035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:175129946delC	ENST00000423313.1	-	4	740	c.204delG	c.(202-204)aagfs	p.K75fs	KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.K75fs|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.K75fs	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcttcttcttcttgt	0.498																																					p.K69fs		Atlas-Indel	.											.	KIAA0040	2	.	0			c.205delA						PASS	.						82.0	69.0	73.0					1																	175129946		692	1591	2283	SO:0001589	frameshift_variant	9674	exon5			.	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.204delG	1.37:g.175129946delC	ENSP00000462172:p.Lys75fs	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	113	10	0.0884956	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				-|1.000	.	weak		0.498	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ROBO3	64221	hgsc.bcm.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	CGGAGT	-	rs55725290|rs56085444|rs71859853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CGGAGT	CGGAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124750448_124750453delCGGAGT	ENST00000397801.1	+	27	4285_4290	c.4093_4098delCGGAGT	c.(4093-4098)cggagtdel	p.RS1367del	ROBO3_ENST00000543966.1_In_Frame_Del_p.RS130del|ROBO3_ENST00000538940.1_In_Frame_Del_p.RS1345del|ROBO3_ENST00000525482.1_3'UTR	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	44	.	.		WXS	Illumina HiSeq	Phase_I	59	15	0.254	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	
CFAP74	85452	hgsc.bcm.edu	37	1	1887112	1887112	+	IGR	DEL	C	C	-	rs3838975	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1887112delC								TMEM52 (36400 upstream) : C1orf222 (32450 downstream)																							CCTGGCTTGGCCTGGCAGCCT	0.667													CC|CC|C|deletion	936	0.186901	0.1059	0.232	5008	,	,		12880	0.2292		0.2475	False		,,,				2504	0.1585				p.A732fs		Atlas-Indel	.											.	KIAA1751	92	.	0			c.2195delC						PASS	.			512,3372		50,412,1480	42.0	43.0	43.0			1.2	0.1	1	dbSNP_107	46	2092,5888		286,1520,2184	no	frameshift	KIAA1751	NM_001080484.1		336,1932,3664	A1A1,A1R,RR		26.2155,13.1823,21.9488			1887112	2604,9260	2027	4130	6157	SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887112delC		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				C|0.783;-|0.217	0.217	strong	0	0.667								
RP1L1	94137	hgsc.bcm.edu	37	8	10467673	10467682	+	Frame_Shift_Del	DEL	CCTTCTGTTC	CCTTCTGTTC	-	rs200084961|rs386722181		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CCTTCTGTTC	CCTTCTGTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10467673_10467682delCCTTCTGTTC	ENST00000382483.3	-	4	4149_4158	c.3926_3935delGAACAGAAGG	c.(3925-3936)ggaacagaaggafs	p.GTEG1309fs		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				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)		cagcccttctccttctgttccttcttTAGT	0.481																																					p.1309_1312del		Atlas-Indel	.											.	RP1L1	453	.	0			c.3927_3936del						PASS	.																																			SO:0001589	frameshift_variant	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.3926_3935delGAACAGAAGG	8.37:g.10467673_10467682delCCTTCTGTTC	ENSP00000371923:p.Gly1309fs	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	56	10	0.178571	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Frame_Shift_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.481	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
PYGL	5836	hgsc.bcm.edu	37	14	51378591	51378591	+	Splice_Site	DEL	T	T	-	rs74464749|rs11356035|rs397852066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:51378591delT	ENST00000216392.7	-	16	2160		c.e16-2		PYGL_ENST00000532462.1_Splice_Site|PYGL_ENST00000544180.2_Splice_Site|RP11-218E20.5_ENST00000557343.1_RNA	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	141	.	.		WXS	Illumina HiSeq	Phase_I	144	82	0.569	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
KIAA1211	57482	hgsc.bcm.edu	37	4	57180576	57180577	+	In_Frame_Ins	INS	-	-	GGAGCGGAGGGAGCGGAG	rs71921617|rs138358443|rs11276076	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57180576_57180577insGGAGCGGAGGGAGCGGAG	ENST00000504228.1	+	6	1013_1014	c.908_909insGGAGCGGAGGGAGCGGAG	c.(907-912)gcggag>gcGGAGCGGAGGGAGCGGAGggag	p.304_305insRRERRE	KIAA1211_ENST00000264229.6_In_Frame_Ins_p.304_305insRRERRE|KIAA1211_ENST00000541073.1_In_Frame_Ins_p.297_298insRRERRE			Q6ZU35	K1211_HUMAN	KIAA1211	304	Glu-rich.									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)					TGGGAGGACGCGGAGCGGAGGG	0.733														1350	0.269569	0.2716	0.2781	5008	,	,		14300	0.0694		0.4076	False		,,,				2504	0.3252				p.A303delinsAERRERR		Atlas-Indel	.											.	KIAA1211	178	.	0			c.908_909insGGAGCGGAGGGAGCGGAG						PASS	.			903,2311		258,387,962						-10.2	0.0		dbSNP_130	6	2065,4451		612,841,1805	no	coding	KIAA1211	NM_020722.1		870,1228,2767	A1A1,A1R,RR		31.6912,28.0958,30.5036				2968,6762				SO:0001652	inframe_insertion	57482	exon8			.	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	Exception_encountered	4.37:g.57180576_57180577insGGAGCGGAGGGAGCGGAG	ENSP00000423366:p.Glu304_Arg305insArgArgGluArgArgGlu	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	In_Frame_Ins	INS	ENST00000504228.1	37	CCDS43230.1																																																																																			.	.	strong		0.733	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
ZNF271	10778	hgsc.bcm.edu	37	18	32890334	32890338	+	RNA	DEL	TATTT	TATTT	-	rs144804783|rs376275230	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TATTT	TATTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:32890334_32890338delTATTT	ENST00000399070.3	+	0	4728_4732					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						GTCTAATTAATATTTTAATTTAGCA	0.293														333	0.0664936	0.0605	0.0331	5008	,	,		17383	0.1687		0.0249	False		,,,				2504	0.0358				.		Pindel,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.32890334_32890338delTATTT		Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	126	52	0.413	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	DEL	ENST00000399070.3	37																																																																																				TATTT|0.931;-|0.069	0.069	strong		0.293	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
DNAJC28	54943	hgsc.bcm.edu	37	21	34860750	34860754	+	Frame_Shift_Del	DEL	AATTA	AATTA	-	rs139852262|rs3834674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AATTA	AATTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34860750_34860754delAATTA	ENST00000314399.3	-	2	1385_1389	c.947_951delTAATT	c.(946-951)ttaattfs	p.LI316fs	DNAJC28_ENST00000402202.1_Frame_Shift_Del_p.LI316fs|DNAJC28_ENST00000381947.3_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	119	.	.		WXS	Illumina HiSeq	Phase_I	113	38	0.336	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		
TCEB3CL2	100506888	hgsc.bcm.edu	37	18	44543098	44543099	+	Frame_Shift_Ins	INS	-	-	GC	rs373334809		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:44543098_44543099insGC	ENST00000591973.2	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_001242907.1	NP_001229836.1	A6NLF2	EA3L2_HUMAN	transcription elongation factor B polypeptide 3C-like 2	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)										TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Atlas-Indel	.											.	.	.	.	0			c.1274_1275insGC						PASS	.																																			SO:0001589	frameshift_variant	100506888	exon1			.		CCDS59316.1	18q21.1	2012-10-25			ENSG00000266996	ENSG00000274744			33511	protein-coding gene	gene with protein product							Standard	NM_001242907		Approved		uc021ujk.1	A6NLF2	OTTHUMG00000180382	ENST00000591973.2:c.1272_1273dupGC	18.37:g.44543099_44543100dupGC	ENSP00000468046:p.Gln425fs	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	250	19	0.076	NM_001242907		Frame_Shift_Ins	INS	ENST00000591973.2	37	CCDS59316.1																																																																																			.	.	weak		0.554	TCEB3CL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451070.1	XM_929328	
PRSS3	5646	hgsc.bcm.edu	37	9	33796691	33796693	+	In_Frame_Del	DEL	GAG	GAG	-	rs143332708|rs3831310	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33796691_33796693delGAG	ENST00000361005.5	+	2	262_264	c.262_264delGAG	c.(262-264)gagdel	p.E89del	PRSS3_ENST00000379405.3_In_Frame_Del_p.E32del|PRSS3_ENST00000429677.3_In_Frame_Del_p.E25del|PRSS3_ENST00000342836.4_In_Frame_Del_p.E46del|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	89	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			Missing (in Ref. 1; CAA50484). {ECO:0000305}.	cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			CTACACCTGTGAGGAGAATTCTC	0.537														696	0.138978	0.0484	0.183	5008	,	,		23005	0.0685		0.165	False		,,,				2504	0.2761				p.87_88del		Pindel,Atlas-Indel	.											.	PRSS3	79	.	0			c.261_263del						PASS	.		,,,	293,3971		1,291,1840					,,,	-4.2	0.0		dbSNP_107	166	1418,6836		21,1376,2730	no	coding,coding,coding,coding	PRSS3	NM_007343.3,NM_002771.3,NM_001197098.1,NM_001197097.2	,,,	22,1667,4570	A1A1,A1R,RR		17.1795,6.8715,13.6683	,,,	,,,		1711,10807				SO:0001651	inframe_deletion	5646	exon2			.		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.262_264delGAG	9.37:g.33796694_33796696delGAG	ENSP00000354280:p.Glu89del	Somatic	164	.	.		WXS	Illumina HiSeq	Phase_I	128	33	0.258	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	In_Frame_Del	DEL	ENST00000361005.5	37	CCDS47958.1																																																																																			GAG|0.875;-|0.125	0.125	strong		0.537	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
FAM98B	283742	hgsc.bcm.edu	37	15	38776807	38776815	+	IGR	DEL	GGTGGTGGT	GGTGGTGGT	-	rs201831942|rs374461368		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GGTGGTGGT	GGTGGTGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		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	59	0	0		WXS	Illumina HiSeq	Phase_I	53	10	0.188679	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	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		Atlas-Indel	.											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	30	0	0		WXS	Illumina HiSeq	Phase_I	42	14	0.333333	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	
KRT1	3848	hgsc.bcm.edu	37	12	53069223	53069243	+	In_Frame_Del	DEL	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	-	rs77846840|rs540699806|rs11170232|rs370799361|rs267607656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENST00000252244.3	-	9	1727_1747	c.1669_1689delAGCAGCTACGGCTCCGGAGGT	c.(1669-1689)agcagctacggctccggaggtdel	p.SSYGSGG557del		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	Gly/Ser-rich.|Tail.				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)	p.S557_G563delSSYGSGG(3)		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						catagctgccacctccggagccgtagctgctacctccggag	0.697														1779	0.355232	0.4372	0.3905	5008	,	,		11351	0.1349		0.3459	False		,,,				2504	0.456				p.557_564del		Atlas-Indel	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.1670_1690del						PASS	.			1255,1949		405,445,752						0.8	0.1		dbSNP_130	5	2781,3759		866,1049,1355	no	coding	KRT1	NM_006121.3		1271,1494,2107	A1A1,A1R,RR		42.5229,39.1698,41.4204				4036,5708				SO:0001651	inframe_deletion	3848	exon9			.	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.1669_1689delAGCAGCTACGGCTCCGGAGGT	12.37:g.53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENSP00000252244:p.Ser557_Gly563del	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	In_Frame_Del	DEL	ENST00000252244.3	37	CCDS8836.1																																																																																			.	.	none		0.697	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
ANP32E	81611	hgsc.bcm.edu	37	1	150199040	150199045	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-	rs56692627|rs28594165|rs68136184|rs28460085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150199040_150199045delTCCTCT	ENST00000314136.8	-	5	945_950	c.576_581delAGAGGA	c.(574-582)gaagaggag>gag	p.192_194EEE>E	ANP32E_ENST00000533654.1_In_Frame_Del_p.KR137del|ANP32E_ENST00000369114.5_Intron|ANP32E_ENST00000436748.2_In_Frame_Del_p.151_153EEE>E|ANP32E_ENST00000369116.4_In_Frame_Del_p.60_62EEE>E|ANP32E_ENST00000369115.2_In_Frame_Del_p.60_62EEE>E|ANP32E_ENST00000369119.3_In_Frame_Del_p.144_146EEE>E	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	192	Asp/Glu-rich (highly acidic).				histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-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)			atcctcatcctcctcttcctcttcct	0.437														1756	0.350639	0.1596	0.3559	5008	,	,		19419	0.5446		0.2753	False		,,,				2504	0.4826				p.193_194del		Atlas-Indel	.											.	ANP32E	28	.	0			c.577_582del						PASS	.		,,	627,3639		79,469,1585					,,	-6.5	0.0		dbSNP_130	261	1908,6340		294,1320,2510	no	coding,coding,coding	ANP32E	NM_030920.3,NM_001136479.1,NM_001136478.2	,,	373,1789,4095	A1A1,A1R,RR		23.1329,14.6976,20.2573	,,	,,		2535,9979				SO:0001651	inframe_deletion	81611	exon5			.	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"""ANP32 acidic nuclear phosphoproteins"""	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.576_581delAGAGGA	1.37:g.150199046_150199051delTCCTCT	ENSP00000324074:p.Glu192_Glu193del	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	108	33	0.305556	NM_030920	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	In_Frame_Del	DEL	ENST00000314136.8	37	CCDS946.1																																																																																			TCCTCT|0.685;-|0.315	0.315	strong		0.437	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920	
HCLS1	3059	hgsc.bcm.edu	37	3	121351315	121351316	+	In_Frame_Ins	INS	-	-	GGCTCAGGCTCA	rs150627065|rs372720825|rs80289672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121351315_121351316insGGCTCAGGCTCA	ENST00000314583.3	-	12	1194_1195	c.1103_1104insTGAGCCTGAGCC	c.(1102-1104)ccc>ccTGAGCCTGAGCCc	p.368_368P>PEPEP	HCLS1_ENST00000473883.1_5'UTR|HCLS1_ENST00000428394.2_In_Frame_Ins_p.331_331P>PEPEP	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	368					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)		gctcaggctcgggctcaggctc	0.604														1208	0.241214	0.1573	0.1599	5008	,	,		14710	0.4563		0.2485	False		,,,				2504	0.183				p.P368delinsPEPEP		Atlas-Indel	.											HCLS1,caecum,carcinoma,0,1	HCLS1	78	1	0			c.1104_1105insTGAGCCTGAGCC	GRCh37	CI045897	HCLS1	I	rs80289672	PASS	.																																			SO:0001652	inframe_insertion	3059	exon12			.		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.1092_1103dupTGAGCCTGAGCC	3.37:g.121351315_121351316insGGCTCAGGCTCA	ENSP00000320176:p.GluProGluPro372dup	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	11	0.0982143	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	In_Frame_Ins	INS	ENST00000314583.3	37	CCDS3003.1																																																																																			-|0.731;GGCTCAGGCTCA|0.269	0.269	strong		0.604	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
Unknown	0	hgsc.bcm.edu	37	11	89819888	89819889	+	IGR	INS	-	-	T	rs377696645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89819888_89819889insT								TRIM49C (13330 upstream) : SNORD56 (31669 downstream)																							TTGGCAGACGCTGGCAGCGCAT	0.495													|||unknown(NO_COVERAGE)	1012	0.202077	0.2504	0.1225	5008	,	,		13379	0.127		0.1779	False		,,,				2504	0.2955				p.R257fs		Atlas-Indel	.											.	.	.	.	0			c.771_772insT						PASS	.			674,2076		75,524,776						1.1	0.0			4	1142,4700		184,774,1963	no	frameshift	UBTFL1	NM_001143975.1		259,1298,2739	A1A1,A1R,RR		19.5481,24.5091,21.1359				1816,6776				SO:0001628	intergenic_variant	642623	exon1			.																													11.37:g.89819889_89819889dupT		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_001143975		Frame_Shift_Ins	INS		37																																																																																				.	.	weak	0	0.495								
TAP1	6890	hgsc.bcm.edu	37	6	32814856	32814859	+	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32814856_32814859delTGTT	ENST00000354258.4	-	10	2367_2370	c.2206_2209delAACA	c.(2206-2211)aacagcfs	p.NS736fs	TAP1_ENST00000425148.2_Frame_Shift_Del_p.NS475fs|TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_Intron|PSMB8_ENST00000374881.2_5'Flank	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	736	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	TGTAACTGGCTGTTTGCATCCAGG	0.475																																					p.736_737del		Atlas-Indel	.											.	TAP1	39	.	0			c.2207_2210del						PASS	.																																			SO:0001589	frameshift_variant	6890	exon10			.		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.2206_2209delAACA	6.37:g.32814856_32814859delTGTT	ENSP00000346206:p.Asn736fs	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	10	0.285714	NM_000593	Q16149|Q96CP4	Frame_Shift_Del	DEL	ENST00000354258.4	37	CCDS4758.1																																																																																			.	.	none		0.475	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
OR2B11	127623	hgsc.bcm.edu	37	1	247615262	247615262	+	Frame_Shift_Del	DEL	A	A	-	rs35305980|rs397733455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247615262delA	ENST00000318749.6	-	1	46	c.23delT	c.(22-24)ttcfs	p.F8fs		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	8						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(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-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)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GTCCCCTAAGAAGCTATGGTT	0.473													AA|AA|A|deletion	2249	0.449081	0.2852	0.5274	5008	,	,		21865	0.4762		0.4563	False		,,,				2504	0.5798				p.F8fs		Pindel,Atlas-Indel	.											.	OR2B11	102	.	0			c.24delC						PASS	.			1318,2948		196,926,1011	74.0	72.0	73.0			0.0	0.0	1	dbSNP_131	112	3624,4628		809,2006,1311	no	frameshift	OR2B11	NM_001004492.1		1005,2932,2322	A1A1,A1R,RR		43.9166,30.8955,39.4792			247615262	4942,7576	2167	4183	6350	SO:0001589	frameshift_variant	127623	exon1			.		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.23delT	1.37:g.247615262delA	ENSP00000325682:p.Phe8fs	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	101	62	0.614	NM_001004492	B2RP03	Frame_Shift_Del	DEL	ENST00000318749.6	37	CCDS31090.1																																																																																			A|0.570;-|0.430	0.430	strong		0.473	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
TOX2	84969	hgsc.bcm.edu	37	20	42694558	42694559	+	In_Frame_Ins	INS	-	-	CCG	rs199841880|rs34604629	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42694558_42694559insCCG	ENST00000358131.5	+	6	1321_1322	c.1113_1114insCCG	c.(1114-1116)ccg>CCGccg	p.372_372P>PP	TOX2_ENST00000341197.4_In_Frame_Ins_p.390_390P>PP|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000423191.2_In_Frame_Ins_p.348_348P>PP|TOX2_ENST00000372999.1_In_Frame_Ins_p.348_348P>PP	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	372	Pro-rich.			P -> PP (in Ref. 1; BAF82595). {ECO:0000305}.	female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S347_P348insR(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGTGCGTCCCCGCCGCCGCC	0.713														176	0.0351438	0.0045	0.0648	5008	,	,		13049	0.0		0.1044	False		,,,				2504	0.0204				p.S389delinsSP		Pindel,Atlas-Indel	.											TOX2_ENST00000348077,colon,carcinoma,+2,2	TOX2	158	2	1	Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.1167_1168insCCG						PASS	.		,,,	79,4179		2,75,2052					,,,	1.5	0.1		dbSNP_126	33	928,7320		58,812,3254	no	coding,coding,coding,coding	TOX2	NM_032883.2,NM_001098798.1,NM_001098797.1,NM_001098796.1	,,,	60,887,5306	A1A1,A1R,RR		11.2512,1.8553,8.0521	,,,	,,,		1007,11499				SO:0001652	inframe_insertion	84969	exon7			.	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1120_1122dupCCG	20.37:g.42694565_42694567dupCCG	ENSP00000350849:p.Pro376dup	Somatic	31	.	.		WXS	Illumina HiSeq	Phase_I	54	11	0.204	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	In_Frame_Ins	INS	ENST00000358131.5	37	CCDS42875.1																																																																																			-|0.893;CCG|0.107	0.107	strong		0.713	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887092	+	IGR	DEL	G	G	-	rs3838976|rs139735565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1887092delG								TMEM52 (36380 upstream) : C1orf222 (32470 downstream)																							GGCCCTCACCGCCCGCCCACC	0.632													G|G|-|deletion	942	0.188099	0.1089	0.2334	5008	,	,		13367	0.2292		0.2485	False		,,,				2504	0.1585				p.G739fs		Atlas-Indel	.											.	KIAA1751	92	.	0			c.2215delG						PASS	.						45.0	46.0	46.0					1																	1887092		1963	4068	6031	SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887092delG		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				G|0.777;-|0.223	0.223	strong	0	0.632								
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324229	39324230	+	In_Frame_Ins	INS	-	-	GCAGCAGGTGGTCAG	rs58564583|rs369617852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39324229_39324230insGCAGCAGGTGGTCAG	ENST00000391356.2	-	1	194_195	c.195_196insCTGACCACCTGCTGC	c.(193-198)tgcagg>tgcCTGACCACCTGCTGCagg	p.64_65insCLTTC		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	64	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		C -> CCCLTTCCRTTCCRPSCCISSCCRPSCCISSCCKPS (in allele KAP3-v1).		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			caggtggtcctgcagcagctgg	0.629																																					p.R66delinsLTTCCR		Atlas-Indel	.											.	KRTAP4-3	40	.	0			c.196_197insCTGACCACCTGCTGC						PASS	.			169,589,1746		24,2,119,170,247,690						-9.3	0.0		dbSNP_134	4	951,38,4927		39,1,872,6,25,2015	no	codingComplex	KRTAP4-3	NM_033187.1		63,3,991,176,272,2705	A1A1,A1A2,A1R,A2A2,A2R,RR		16.7174,30.2716,20.7482				1120,627,6673				SO:0001652	inframe_insertion	85290	exon1			.	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.195_196insCTGACCACCTGCTGC	17.37:g.39324229_39324230insGCAGCAGGTGGTCAG	ENSP00000375151:p.Cys64_Cys65insCysLeuThrThrCys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	179	31	0.173184	NM_033187		In_Frame_Ins	INS	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.629	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
ZP3	7784	hgsc.bcm.edu	37	7	76071183	76071184	+	Frame_Shift_Ins	INS	-	-	G	rs375263236		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76071183_76071184insG	ENST00000394857.3	+	8	1143_1144	c.1085_1086insG	c.(1084-1089)gtggggfs	p.VG362fs	ZP3_ENST00000336517.4_Frame_Shift_Ins_p.VG311fs|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Frame_Shift_Ins_p.VG186fs	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	362					binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GATGTCACCGTGGGGCCACTGA	0.545																																					p.V362fs		Atlas-Indel	.											.	ZP3	32	.	0			c.1085_1086insG						PASS	.																																			SO:0001589	frameshift_variant	7784	exon8			.	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1089dupG	7.37:g.76071187_76071187dupG	ENSP00000378326:p.Val362fs	Somatic	435	0	0		WXS	Illumina HiSeq	Phase_I	472	43	0.0911017	NM_001110354	Q06633|Q29RW0	Frame_Shift_Ins	INS	ENST00000394857.3	37	CCDS47618.1																																																																																			.	.	weak		0.545	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
PROSER1	80209	hgsc.bcm.edu	37	13	39588144	39588146	+	In_Frame_Del	DEL	AGC	AGC	-	rs568365521		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:39588144_39588146delAGC	ENST00000352251.3	-	11	2076_2078	c.1243_1245delGCT	c.(1243-1245)gctdel	p.A415del	PROSER1_ENST00000350125.3_In_Frame_Del_p.A393del|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	415	Ser-rich.																TGCTGGTAGAAGCAGCAGAAGAG	0.522																																					p.415_416del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1244_1246del						PASS	.																																			SO:0001651	inframe_deletion	80209	exon11			.	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1243_1245delGCT	13.37:g.39588147_39588149delAGC	ENSP00000332034:p.Ala415del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	113	37	0.327	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	In_Frame_Del	DEL	ENST00000352251.3	37	CCDS9368.2																																																																																			.	.	none		0.522	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
PRKRA	8575	hgsc.bcm.edu	37	2	179315735	179315736	+	Frame_Shift_Del	DEL	GC	GC	-	rs141354030|rs79769305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179315735_179315736delGC	ENST00000325748.4	-	1	222_223	c.22_23delGC	c.(22-24)gccfs	p.A8fs	PRKRA_ENST00000432031.2_5'Flank|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000470200.1_5'UTR|DFNB59_ENST00000375129.4_5'Flank|PRKRA_ENST00000438687.3_5'UTR|PRKRA_ENST00000487082.1_5'Flank	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	8	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CGGGGCCTCGGCGCGGTGCCTG	0.757														1193	0.238219	0.1649	0.3545	5008	,	,		12129	0.123		0.339	False		,,,				2504	0.2699				p.8_8del	Melanoma(200;68 3001 23825 48764)	Atlas-Indel	.											.	PRKRA	56	.	0			c.23_24del						PASS	.			658,2174		225,208,983						-1.9	0.8		dbSNP_134	7	2206,4138		751,704,1717	no	frameshift	PRKRA	NM_003690.4		976,912,2700	A1A1,A1R,RR		34.773,23.2345,31.2119				2864,6312				SO:0001589	frameshift_variant	8575	exon1			.	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.22_23delGC	2.37:g.179315737_179315738delGC	ENSP00000318176:p.Ala8fs	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	37	CCDS2279.1																																																																																			GC|0.847;-|0.153	0.153	strong		0.757	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
APBB2	323	hgsc.bcm.edu	37	4	41016418	41016418	+	Intron	DEL	G	G	-	rs201401961		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:41016418delG	ENST00000295974.8	-	6	649				APBB2_ENST00000506352.1_Intron|APBB2_ENST00000508593.1_Intron|APBB2_ENST00000513140.1_Intron	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2						axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						TGAGTCAGCTGGGGAAAAAAA	0.418																																					.	Ovarian(3;20 75 16686 49997)	Atlas-Indel	.											.	APBB2	61	.	0			c.20-2C>-						PASS	.						42.0	41.0	41.0					4																	41016418		1897	4118	6015	SO:0001627	intron_variant	323	exon7			.	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.20-3C>-	4.37:g.41016418delG		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	12	0.0991736	NM_001166050	B4DSL4|E9PG87|Q8IUI6	Splice_Site	DEL	ENST00000295974.8	37	CCDS54761.1																																																																																			G|0.971;-|0.029	0.029	strong		0.418	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
ACTR8	93973	hgsc.bcm.edu	37	3	53910109	53910110	+	Splice_Site	INS	-	-	G	rs199573495|rs534309799|rs370490982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:53910109_53910110insG	ENST00000335754.3	-	7	879		c.e7-2		ACTR8_ENST00000482349.1_Splice_Site|ACTR8_ENST00000231909.7_Splice_Site	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)						chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		CCACAATCCCTGGGGGGGGAAA	0.515																																					.		Atlas-Indel	.											.	ACTR8	56	.	0			c.779-2->C						PASS	.			3,2297,20,68,1878		0,2,0,0,1,603,12,45,1032,1,1,5,0,22,409						5.7	1.0			52	0,3250,2,40,4962		0,0,0,0,0,603,1,28,2015,0,0,1,0,12,1467	no	intron	ACTR8	NM_022899.4		0,2,0,0,1,1206,13,73,3047,1,1,6,0,34,1876	A1A1,A1A2,A1A3,A1A4,A1R,A2A2,A2A3,A2A4,A2R,A3A3,A3A4,A3R,A4A4,A4R,RR		39.8837,46.1556,45.3674				3,5547,22,108,6840				SO:0001630	splice_region_variant	93973	exon8			.		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.779-2->C	3.37:g.53910117_53910117dupG		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	125	25	0.2	NM_022899	B3KSW7|Q8N566|Q9H663	Splice_Site	INS	ENST00000335754.3	37	CCDS2875.1																																																																																			.	.	weak		0.515	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	Intron
SLAMF8	56833	hgsc.bcm.edu	37	1	159799824	159799825	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:159799824_159799825delCT	ENST00000289707.5	+	2	358_359	c.209_210delCT	c.(208-210)actfs	p.T70fs	SLAMF8_ENST00000368104.4_Intron|SLAMF8_ENST00000471286.1_3'UTR	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	70					cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					TCCCTGGAGACTCTGTACCATT	0.629																																					p.70_70del		Pindel,Atlas-Indel	.											.	SLAMF8	30	.	0			c.208_209del						PASS	.			0,4266		0,0,2133						4.4	1.0			106	3,8249		0,3,4123	no	frameshift	SLAMF8	NM_020125.2		0,3,6256	A1A1,A1R,RR		0.0364,0.0,0.024				3,12515				SO:0001589	frameshift_variant	56833	exon2			.	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.209_210delCT	1.37:g.159799826_159799827delCT	ENSP00000289707:p.Thr70fs	Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	96	42	0.438	NM_020125	Q32MC6|Q5VU15	Frame_Shift_Del	DEL	ENST00000289707.5	37	CCDS1188.1																																																																																			.	.	none		0.629	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125	
RIMBP3	85376	hgsc.bcm.edu	37	22	20460113	20460115	+	In_Frame_Del	DEL	CCG	CCG	-	rs201820173		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20460113_20460115delCCG	ENST00000426804.1	-	1	1671_1673	c.1187_1189delCGG	c.(1186-1191)gcggag>gag	p.A396del		NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	396				A -> E (in Ref. 2; BAB33336). {ECO:0000305}.						breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			TGCTTGTTCTCCGCTTGCAGGGT	0.675																																					p.396_397del		Atlas-Indel	.											.	RIMBP3	42	.	0			c.1188_1190del						PASS	.																																			SO:0001651	inframe_deletion	85376	exon1			.	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.1187_1189delCGG	22.37:g.20460113_20460115delCCG	ENSP00000391564:p.Ala396del	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	30	26	0.866667	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	In_Frame_Del	DEL	ENST00000426804.1	37	CCDS46665.1																																																																																			.	.	alt		0.675	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
LINC00619	414260	hgsc.bcm.edu	37	10	44340783	44340784	+	lincRNA	INS	-	-	C	rs113953295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:44340783_44340784insC	ENST00000374432.3	+	0	30_31					NR_033923.1				long intergenic non-protein coding RNA 619																		GAATCATCCCGCCCCCAGCAGA	0.594													CCCCC|CCCCC|CCCCCC|insertion	662	0.132188	0.4039	0.0922	5008	,	,		17970	0.001		0.0537	False		,,,				2504	0.0092				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																					414260	.			.	BC017939		10q11.21	2012-10-12	2012-07-12	2012-07-12	ENSG00000204187	ENSG00000204187		"""Long non-coding RNAs"""	31657	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 136"""	C10orf136			Standard	NR_033923		Approved	bA168P8.1	uc021ppi.1		OTTHUMG00000018048		10.37:g.44340788_44340788dupC		Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	69	21	0.304	.		RNA	INS	ENST00000374432.3	37																																																																																				-|0.886;C|0.114	0.114	strong		0.594	LINC00619-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000047731.2	NR_033923	
TDRD3	81550	hgsc.bcm.edu	37	13	61102576	61102578	+	In_Frame_Del	DEL	ATA	ATA	-	rs148917045|rs75684327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:61102576_61102578delATA	ENST00000196169.3	+	11	1726_1728	c.938_940delATA	c.(937-942)gataat>gat	p.N315del	TDRD3_ENST00000377894.2_In_Frame_Del_p.N315del|TDRD3_ENST00000377881.2_In_Frame_Del_p.N315del|TDRD3_ENST00000535286.1_In_Frame_Del_p.N408del	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	315					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GGAGTAAAAGATAATAATCATCT	0.384														604	0.120607	0.0325	0.1153	5008	,	,		16312	0.0129		0.1889	False		,,,				2504	0.2843				p.406_406del	Colon(36;164 906 35820 50723)	Pindel,Atlas-Indel	.											TDRD3_ENST00000535286,NS,carcinoma,0,4	TDRD3	123	4	0			c.1216_1218del						PASS	.		,,	224,4040		12,200,1920					,,	6.1	1.0		dbSNP_134	101	1585,6669		152,1281,2694	no	coding,coding,coding	TDRD3	NM_030794.2,NM_001146071.1,NM_001146070.1	,,	164,1481,4614	A1A1,A1R,RR		19.2028,5.2533,14.4512	,,	,,		1809,10709				SO:0001651	inframe_deletion	81550	exon11			.	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"""Tudor domain containing"""	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.938_940delATA	13.37:g.61102579_61102581delATA	ENSP00000196169:p.Asn315del	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	60	14	0.233	NM_001146070	B2MWP9|Q53XA6|Q6P992	In_Frame_Del	DEL	ENST00000196169.3	37	CCDS9441.1																																																																																			ATA|0.894;-|0.106	0.106	strong		0.384	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794	
FAM193A	8603	hgsc.bcm.edu	37	4	2632799	2632800	+	Frame_Shift_Ins	INS	-	-	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2632799_2632800insC	ENST00000324666.5	+	3	419_420	c.68_69insC	c.(67-72)ggcccgfs	p.GP23fs	FAM193A_ENST00000502458.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000505311.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000382839.3_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000545951.1_Frame_Shift_Ins_p.GP23fs	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	23										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GGCCTGCAGGGCCCGCCGCAAG	0.639																																					p.G23fs		Atlas-Indel	.											.	FAM193A	103	.	0			c.68_69insC						PASS	.																																			SO:0001589	frameshift_variant	8603	exon3			.	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.71dupC	4.37:g.2632802_2632802dupC	ENSP00000324587:p.Gly23fs	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	127	12	0.0944882	NM_001256666	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Frame_Shift_Ins	INS	ENST00000324666.5	37	CCDS58875.1																																																																																			.	.	none		0.639	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
BEND7	222389	hgsc.bcm.edu	37	10	13481174	13481175	+	Stop_Codon_Del	DEL	AG	AG	-	rs10590401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13481174_13481175delAG	ENST00000396900.2	-	0	1556_1557				BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Stop_Codon_Del			Q8N7W2	BEND7_HUMAN	BEN domain containing 7							extracellular vesicular exosome (GO:0070062)		p.*469fs?(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						agataatttcagagagagaggc	0.47														227	0.0453275	0.1634	0.0144	5008	,	,		24326	0.0		0.001	False		,,,				2504	0.0				p.469_469del		Pindel,Atlas-Indel	.											.	BEND7	85	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1405_1406del						PASS	.			589,3675		45,499,1588						0.8	0.0		dbSNP_119	108	6,8248		0,6,4121	no	frameshift	BEND7	NM_152751.2		45,505,5709	A1A1,A1R,RR		0.0727,13.8133,4.7532				595,11923				SO:0001567	stop_retained_variant	222389	exon9			.	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	Exception_encountered	10.37:g.13481182_13481183delAG	Exception_encountered	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	150	45	0.300	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Frame_Shift_Del	DEL	ENST00000396900.2	37																																																																																				AG|0.960;-|0.040	0.040	strong		0.470	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
CC2D2A	57545	hgsc.bcm.edu	37	4	15513005	15513007	+	In_Frame_Del	DEL	GAA	GAA	-	rs112367037|rs386833764	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15513005_15513007delGAA	ENST00000503292.1	+	9	856_858	c.676_678delGAA	c.(676-678)gaadel	p.E229del	CC2D2A_ENST00000424120.1_In_Frame_Del_p.E229del|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_In_Frame_Del_p.E229del|CC2D2A_ENST00000389652.5_In_Frame_Del_p.E180del	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	77	21	0.273	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	
PRR25	388199	hgsc.bcm.edu	37	16	863356	863372	+	Frame_Shift_Del	DEL	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC	-	rs367751056|rs199580467|rs371962006|rs200304320|rs138733834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GGACGCCGGACCGACAC	GGACGCCGGACCGACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:863356_863372delGGACGCCGGACCGACAC	ENST00000301698.1	+	3	704_720	c.704_720delGGACGCCGGACCGACAC	c.(703-720)aggacgccggaccgacacfs	p.RTPDRH235fs		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	235										large_intestine(1)|lung(1)|skin(1)	3						GGACCGGCAAGGACGCCGGACCGACACGGCCTCCCCA	0.714														1307	0.260982	0.6876	0.2622	5008	,	,		14975	0.0675		0.0755	False		,,,				2504	0.0736				p.235_240del		Pindel,Atlas-Indel	.											.	PRR25	27	.	0			c.703_719del						PASS	.																																			SO:0001589	frameshift_variant	388199	exon3			.	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.704_720delGGACGCCGGACCGACAC	16.37:g.863356_863372delGGACGCCGGACCGACAC	ENSP00000301698:p.Arg235fs	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	47	12	0.255	NM_001013638		Frame_Shift_Del	DEL	ENST00000301698.1	37	CCDS45372.1																																																																																			GGACGCCGGACCGACAC|0.500;-|0.500	0.500	weak		0.714	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
TP53TG5	27296	hgsc.bcm.edu	37	20	44004156	44004158	+	In_Frame_Del	DEL	ATT	ATT	-	rs562359566|rs76663890|rs10546815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44004156_44004158delATT	ENST00000372726.3	-	4	445_447	c.289_291delAAT	c.(289-291)aatdel	p.N97del	TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000426004.1_3'UTR|TP53TG5_ENST00000537995.1_In_Frame_Del_p.N81del|SYS1-DBNDD2_ENST00000452133.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	97					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						GGAACTCTTCATTATTTTGTTTT	0.493														1936	0.386581	0.1914	0.4452	5008	,	,		18977	0.255		0.659	False		,,,				2504	0.4642				p.97_98del		Pindel,Atlas-Indel	.											.	TP53TG5	36	.	0			c.290_292del						PASS	.		,	1076,3182		141,794,1194					,	-3.1	0.0		dbSNP_119	93	5309,2943		1723,1863,540	no	coding,utr-3	TP53TG5,SYS1	NM_014477.2,NM_001099791.2	,	1864,2657,1734	A1A1,A1R,RR		35.6641,25.2701,48.9608	,	,		6385,6125				SO:0001651	inframe_deletion	27296	exon4			.	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.289_291delAAT	20.37:g.44004159_44004161delATT	ENSP00000361811:p.Asn97del	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	51	35	0.686	NM_014477		In_Frame_Del	DEL	ENST00000372726.3	37	CCDS13352.1																																																																																			ATT|0.574;-|0.426	0.426	strong		0.493	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477	
PNPLA7	375775	hgsc.bcm.edu	37	9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T	rs372921391|rs372038516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	MRPL41_ENST00000371443.5_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					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)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0.0	0.0043	5008	,	,		18178	0.0		0.0099	False		,,,				2504	0.0				p.S8fs		Pindel,Atlas-Indel	.											.	PNPLA7	124	.	0			c.23_24insA						PASS	.		,	12,4252		0,12,2120					,	0.2	0.0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				SO:0001589	frameshift_variant	375775	exon1			.	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.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs	Somatic	42	.	.		WXS	Illumina HiSeq	Phase_I	36	19	0.528	NM_152286	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																			.	.	weak		0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
CHD9	80205	hgsc.bcm.edu	37	16	53338410	53338412	+	In_Frame_Del	DEL	TTC	TTC	-	rs56028815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53338410_53338412delTTC	ENST00000398510.3	+	30	6579_6581	c.6492_6494delTTC	c.(6490-6495)agttct>agt	p.2164_2165SS>S	CHD9_ENST00000566029.1_In_Frame_Del_p.2164_2165SS>S|CHD9_ENST00000447540.1_In_Frame_Del_p.2164_2165SS>S|CHD9_ENST00000564845.1_In_Frame_Del_p.2164_2165SS>S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2164	Ser-rich.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				CAGGCTCTAGttcttcttcatct	0.443														82	0.0163738	0.0	0.0187	5008	,	,		17277	0.0		0.0398	False		,,,				2504	0.0297				p.2164_2165del		Pindel,Atlas-Indel	.											.	CHD9	203	.	0			c.6491_6493del						PASS	.			59,3965		15,29,1968						6.1	1.0		dbSNP_129	133	385,7637		44,297,3670	no	coding	CHD9	NM_025134.4		59,326,5638	A1A1,A1R,RR		4.7993,1.4662,3.6859				444,11602				SO:0001651	inframe_deletion	80205	exon31			.	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6492_6494delTTC	16.37:g.53338416_53338418delTTC	ENSP00000381522:p.Ser2170del	Somatic	233	.	.		WXS	Illumina HiSeq	Phase_I	242	59	0.244	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	In_Frame_Del	DEL	ENST00000398510.3	37																																																																																				TTC|0.986;-|0.014	0.014	strong		0.443	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
SBNO1	55206	hgsc.bcm.edu	37	12	123794283	123794283	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:123794283delT	ENST00000602398.1	-	26	3543	c.3416delA	c.(3415-3417)aatfs	p.N1139fs	SBNO1_ENST00000602750.1_Frame_Shift_Del_p.N1138fs|SBNO1_ENST00000420886.2_Frame_Shift_Del_p.N1139fs|SBNO1_ENST00000267176.4_Frame_Shift_Del_p.N1138fs			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1139					regulation of transcription, DNA-templated (GO:0006355)			p.N1138fs*9(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)		ATATCTTCCATTTTTTTTGGC	0.388																																					p.N1139fs		Atlas-Indel	.											.	SBNO1	138	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3417delT						PASS	.						134.0	131.0	132.0					12																	123794283		2203	4300	6503	SO:0001589	frameshift_variant	55206	exon25			.	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.3416delA	12.37:g.123794283delT	ENSP00000473665:p.Asn1139fs	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	139	11	0.0791367	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Frame_Shift_Del	DEL	ENST00000602398.1	37	CCDS53844.1																																																																																			.	.	none		0.388	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
APOB	338	hgsc.bcm.edu	37	2	21233099	21233101	+	In_Frame_Del	DEL	TCA	TCA	-	rs541497967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21233099_21233101delTCA	ENST00000233242.1	-	26	6766_6768	c.6639_6641delTGA	c.(6637-6642)gatgag>gag	p.D2213del		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2213					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)					ATGATAGTGCTCATCAAGACTTT	0.246														9	0.00179712	0.0	0.0014	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.001				p.2214_2214del		Pindel,Atlas-Indel	.											.	APOB	761	.	0			c.6640_6642del						PASS	.			1,4235		0,1,2117						0.7	0.9		dbSNP_130	33	39,8177		3,33,4072	no	coding	APOB	NM_000384.2		3,34,6189	A1A1,A1R,RR		0.4747,0.0236,0.3212				40,12412				SO:0001651	inframe_deletion	338	exon26			.	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.6639_6641delTGA	2.37:g.21233102_21233104delTCA	ENSP00000233242:p.Asp2213del	Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	46	17	0.370	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	In_Frame_Del	DEL	ENST00000233242.1	37	CCDS1703.1																																																																																			.	.	none		0.246	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470690	24470691	+	Frame_Shift_Ins	INS	-	-	A	rs368539076|rs374759434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24470690_24470691insA	ENST00000335125.6	+	6	755_756	c.629_630insA	c.(628-633)ctgcacfs	p.H211fs	DHRS4L2_ENST00000382755.4_Frame_Shift_Ins_p.H209fs|DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000558753.1_Frame_Shift_Ins_p.H136fs|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Frame_Shift_Ins_p.H136fs|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000534993.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	209						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		GTGAACTGCCTGCACCTGGACT	0.525													A|-|A|deletion	178	0.0355431	0.0076	0.0187	5008	,	,		17571	0.1022		0.0139	False		,,,				2504	0.0389				p.L210fs		Atlas-Indel	.											.	DHRS4L2	29	.	0			c.629_630insA						PASS	.		,,,	146,4000		28,90,1955					,,,	2.5	1.0			148	336,7912		30,276,3818	no	frameshift,frameshift,frameshift,frameshift	DHRS4L2	NM_198083.3,NM_001193637.1,NM_001193636.1,NM_001193635.1	,,,	58,366,5773	A1A1,A1R,RR		4.0737,3.5215,3.889	,,,	,,,		482,11912				SO:0001589	frameshift_variant	317749	exon6			.		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	Exception_encountered	14.37:g.24470690_24470691insA	ENSP00000334801:p.His211fs	Somatic	624	0	0		WXS	Illumina HiSeq	Phase_I	382	35	0.091623	NM_198083	Q3YLD4	Frame_Shift_Ins	INS	ENST00000335125.6	37	CCDS9606.2																																																																																			.	.	weak		0.525	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
NPR2	4882	hgsc.bcm.edu	37	9	35811486	35811497	+	IGR	DEL	CCAGGACCAGAG	CCAGGACCAGAG	-	rs59748329|rs555852229|rs141090907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CCAGGACCAGAG	CCAGGACCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35811486_35811497delCCAGGACCAGAG	ENST00000342694.2	+	0	3686				SPAG8_ENST00000340291.2_In_Frame_Del_p.182_186GSGPG>G|SPAG8_ENST00000479751.1_5'Flank|SPAG8_ENST00000484764.1_In_Frame_Del_p.180_184GSGPG>G|AL133410.1_ENST00000582432.1_RNA|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000396638.2_In_Frame_Del_p.182_186GSGPG>G|HINT2_ENST00000474908.1_5'Flank	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.S183C(2)|p.S183_G186delSGPG(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	agagccatgaccaggaccagagccaggaccag	0.637														1567	0.312899	0.4985	0.2334	5008	,	,		13915	0.379		0.2008	False		,,,				2504	0.1656				p.183_186del		Atlas-Indel	.											.	SPAG8	67	.	3	Substitution - Missense(2)|Deletion - In frame(1)	prostate(2)|upper_aerodigestive_tract(1)	c.547_558del						PASS	.		,	1872,2386		432,1008,689					,	-8.9	0.0		dbSNP_132	42	1635,6615		166,1303,2656	no	coding,coding	SPAG8	NM_172312.1,NM_001039592.1	,	598,2311,3345	A1A1,A1R,RR		19.8182,43.9643,28.0381	,	,		3507,9001				SO:0001628	intergenic_variant	26206	exon2			.	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		9.37:g.35811486_35811497delCCAGGACCAGAG		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	In_Frame_Del	DEL	ENST00000342694.2	37	CCDS6590.1																																																																																			CCAGGACCAGAG|0.500;-|0.500	0.500	weak		0.637	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
SPATA21	374955	hgsc.bcm.edu	37	1	16727305	16727306	+	In_Frame_Ins	INS	-	-	CTT	rs373005990|rs139527123|rs80260069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16727305_16727306insCTT	ENST00000335496.1	-	11	1565_1566	c.1083_1084insAAG	c.(1081-1086)aagctt>aagAAGctt	p.361_362insK	SPATA21_ENST00000540400.1_In_Frame_Ins_p.338_339insK|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	361							calcium ion binding (GO:0005509)	p.K361_L362insK(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)		TTGTAGGGAAGCTTCTGCAACC	0.589														497	0.0992412	0.2247	0.0836	5008	,	,		18406	0.001		0.1074	False		,,,				2504	0.0337				p.L362delinsKL		Pindel,Atlas-Indel	.											SPATA21,NS,carcinoma,+1,1	SPATA21	47	1	1	Insertion - In frame(1)	pancreas(1)	c.1084_1085insAAG						PASS	.			905,3361		92,721,1320						2.0	0.9		dbSNP_131	131	1044,7210		59,926,3142	no	coding	SPATA21	NM_198546.1		151,1647,4462	A1A1,A1R,RR		12.6484,21.2143,15.5671				1949,10571				SO:0001652	inframe_insertion	374955	exon11			.		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.1081_1083dupAAG	1.37:g.16727306_16727308dupCTT	ENSP00000335612:p.Lys361_Lys361dup	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	131	41	0.313	NM_198546	B9EK40|F5GXP5	In_Frame_Ins	INS	ENST00000335496.1	37	CCDS172.1																																																																																			-|0.888;CTT|0.112	0.112	strong		0.589	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458574	39458586	+	Frame_Shift_Del	DEL	GTACAGATGGTTG	GTACAGATGGTTG	-	rs540900200|rs2874235|rs144150438|rs368037290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GTACAGATGGTTG	GTACAGATGGTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39458574_39458586delGTACAGATGGTTG	ENST00000391353.1	-	1	517_529	c.518_530delCAACCATCTGTAC	c.(517-531)ccaaccatctgtacafs	p.PTICT173fs		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	173	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											TGGACTAGCTGTACAGATGGTTGGTAGGCAAGA	0.516														793	0.158347	0.0189	0.1282	5008	,	,		26627	0.3194		0.1869	False		,,,				2504	0.1728				p.173_177del		Atlas-Indel	.											.	KRTAP29-1	2	.	0			c.519_531del						PASS	.																																			SO:0001589	frameshift_variant	100533177	exon1			.		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.518_530delCAACCATCTGTAC	17.37:g.39458574_39458586delGTACAGATGGTTG	ENSP00000375148:p.Pro173fs	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	39	10	0.25641	NM_001257309		Frame_Shift_Del	DEL	ENST00000391353.1	37																																																																																				.	.	strong		0.516	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
ZBTB33	10009	hgsc.bcm.edu	37	X	119387833	119387834	+	In_Frame_Ins	INS	-	-	TGA	rs201958171|rs77815464|rs59686094		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:119387833_119387834insTGA	ENST00000326624.2	+	2	791_792	c.563_564insTGA	c.(562-567)tctgat>tcTGAtgat	p.194_195insD	ZBTB33_ENST00000557385.1_In_Frame_Ins_p.194_195insD	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	194					intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTTACCGATTCtgatgatgatg	0.396														1942	0.514437	0.2065	0.4078	3775	,	,		15520	0.4494		0.5328	False		,,,				2504	0.4059				p.S188delinsSD		Pindel,Atlas-Indel	.											.	ZBTB33	72	.	0			c.563_564insTGA						PASS	.																																			SO:0001652	inframe_insertion	10009	exon2			.	BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.579_581dupTGA	X.37:g.119387840_119387842dupTGA	ENSP00000314153:p.Asp194_Asp194dup	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	89	46	0.517	NM_006777	B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	In_Frame_Ins	INS	ENST00000326624.2	37	CCDS14596.1																																																																																			-|0.437;TGA|0.563	0.563	strong		0.396	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777	
ANLN	54443	hgsc.bcm.edu	37	7	36447349	36447350	+	In_Frame_Ins	INS	-	-	CTT	rs145961275|rs61549495|rs374349756|rs143969069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:36447349_36447350insCTT	ENST00000265748.2	+	5	1101_1102	c.880_881insCTT	c.(880-882)act>aCTTct	p.295_296insS	ANLN_ENST00000396068.2_In_Frame_Ins_p.295_296insS|ANLN_ENST00000495714.1_3'UTR	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	295	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						TCAGAAAGCTACTTCTCCAGTG	0.347														2251	0.449481	0.3374	0.4856	5008	,	,		17344	0.6101		0.3966	False		,,,				2504	0.4642				p.T294delinsTS		Pindel,Atlas-Indel	.											ANLN,caecum,carcinoma,0,2	ANLN	101	2	0			c.880_881insCTT						PASS	.			1485,2779		276,933,923						-7.6	0.1		dbSNP_134	70	3321,4933		668,1985,1474	no	coding	ANLN	NM_018685.2		944,2918,2397	A1A1,A1R,RR		40.235,34.8265,38.3927				4806,7712				SO:0001652	inframe_insertion	54443	exon5			.	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.881_883dupCTT	7.37:g.36447350_36447352dupCTT	ENSP00000265748:p.Ser295_Ser295dup	Somatic	61	.	.		WXS	Illumina HiSeq	Phase_I	110	28	0.255	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	In_Frame_Ins	INS	ENST00000265748.2	37	CCDS5447.1																																																																																			-|0.542;CTT|0.458	0.458	strong		0.347	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
UGDH	7358	hgsc.bcm.edu	37	4	39515807	39515813	+	Intron	DEL	AAAAAGA	AAAAAGA	-	rs201039591|rs372782074|rs151116497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAAAAGA	AAAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:39515807_39515813delAAAAAGA	ENST00000316423.6	-	3	505				UGDH_ENST00000507089.1_Intron|UGDH_ENST00000515398.1_Intron|UGDH_ENST00000506179.1_Intron|UGDH_ENST00000501493.2_Intron	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase						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						AGTCCTGGCTAAAAAGAAAAAAGAAAA	0.3														885	0.176717	0.3737	0.0764	5008	,	,		20050	0.2569		0.0388	False		,,,				2504	0.0409				.		Pindel,Atlas-Indel	.											.	UGDH	52	.	0			.						PASS	.		,,	1365,2775		273,819,978					,,	5.7	1.0		dbSNP_134	47	259,7937		6,247,3845	no	intron,intron,intron	UGDH	NM_003359.3,NM_001184701.1,NM_001184700.1	,,	279,1066,4823	A1A1,A1R,RR		3.1601,32.971,13.1647	,,	,,		1624,10712				SO:0001627	intron_variant	7358	.			.	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.163-3TCTTTTT>-	4.37:g.39515814_39515820delAAAAAGA		Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	75	23	0.307	.	B3KUU2|B4DN25|O60589	Splice_Site	DEL	ENST00000316423.6	37	CCDS3455.1																																																																																			.	.	strong		0.300	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
ENO4	387712	hgsc.bcm.edu	37	10	118609160	118609160	+	Frame_Shift_Del	DEL	G	G	-	rs368456269	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118609160delG	ENST00000409522.1	+	1	138	c.83delG	c.(82-84)cggfs	p.R28fs	RP11-539I5.1_ENST00000453491.1_RNA|ENO4_ENST00000341276.5_Frame_Shift_Del_p.R28fs|RP11-539I5.1_ENST00000434227.1_RNA			A6NNW6	ENO4_HUMAN	enolase family member 4	28					glycolytic process (GO:0006096)	phosphopyruvate hydratase complex (GO:0000015)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			lung(1)	1						GAGTACTACCGGGAGAACGAC	0.612													GGG|GGG|GG|deletion	3	0.000599042	0.0	0.0	5008	,	,		14513	0.0		0.003	False		,,,				2504	0.0				p.R28fs		Pindel,Atlas-Indel	.											.	ENO4	1	.	0			c.82delC						PASS	.																																			SO:0001589	frameshift_variant	387712	exon1			.		CCDS73206.1	10q25.3	2012-04-19	2009-12-15	2009-12-15	ENSG00000188316	ENSG00000188316			31670	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 134"""	C10orf134			Standard	NM_001242699		Approved	AC023283.3	uc021pzj.1	A6NNW6	OTTHUMG00000019113	ENST00000409522.1:c.83delG	10.37:g.118609160delG	ENSP00000387194:p.Arg28fs	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	143	41	0.287	NM_001242699	B8ZZN9	Frame_Shift_Del	DEL	ENST00000409522.1	37																																																																																				.	.	none		0.612	ENO4-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331643.1	NM_001242699	
RP1L1	94137	hgsc.bcm.edu	37	8	10467685	10467686	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10467685_10467686insA	ENST00000382483.3	-	4	4145_4146	c.3922_3923insT	c.(3922-3924)gaafs	p.E1308fs		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				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)		ttctgttccttcttTAGTTTCC	0.49																																					p.E1308fs		Atlas-Indel	.											.	RP1L1	453	.	0			c.3923_3924insT						PASS	.																																			SO:0001589	frameshift_variant	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.3922_3923insT	8.37:g.10467685_10467686insA	ENSP00000371923:p.Glu1308fs	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	64	10	0.15625	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Frame_Shift_Ins	INS	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.490	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
ZNF772	400720	hgsc.bcm.edu	37	19	57988666	57988667	+	In_Frame_Ins	INS	-	-	GCC	rs77164240|rs528587884|rs34678661|rs193920834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57988666_57988667insGCC	ENST00000343280.4	-	1	271_272	c.11_12insGGC	c.(10-12)gct>gcGGCt	p.4_4A>AA	ZNF772_ENST00000601768.1_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000425074.3_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000427512.2_5'UTR|ZNF772_ENST00000356584.3_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000415705.3_5'UTR|AC003005.2_ENST00000595422.1_lincRNA|ZNF772_ENST00000600175.1_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000596831.1_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	176	.	.	1027	WXS	Illumina HiSeq	Phase_I	164	31	0.189	NM_001144068	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	
PCDH12	51294	hgsc.bcm.edu	37	5	141324955	141324956	+	In_Frame_Ins	INS	-	-	CTGCTGCTG	rs5871792|rs200883539|rs59930617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141324955_141324956insCTGCTGCTG	ENST00000231484.3	-	4	4755_4756	c.3545_3546insCAGCAGCAG	c.(3544-3546)agg>agCAGCAGCAGg	p.1181_1182insSSS		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1181	Poly-Ser.			S -> SSSS (in Ref. 4; BAB14837). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCACAGGCACctgctgctgct	0.559														2618	0.522764	0.3064	0.5807	5008	,	,		19761	0.8323		0.4095	False		,,,				2504	0.5716				p.R1182delinsSSSR		Pindel,Atlas-Indel	.											PCDH12,colon,carcinoma,0,1	PCDH12	133	1	0			c.3546_3547insCAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	51294	exon4			.	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3537_3545dupCAGCAGCAG	5.37:g.141324956_141324964dupCTGCTGCTG	ENSP00000231484:p.Ser1179_Ser1181dup	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	75	14	0.187	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	In_Frame_Ins	INS	ENST00000231484.3	37	CCDS4269.1																																																																																			.	.	strong		0.559	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
OR9K2	441639	hgsc.bcm.edu	37	12	55523587	55523587	+	Frame_Shift_Del	DEL	T	T	-	rs398102299|rs58036029|rs200050297	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523587delT	ENST00000305377.5	+	1	123	c.35delT	c.(34-36)attfs	p.I12fs		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	12						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(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CATTTGTATATTTTGCCCTGT	0.363													|||unknown(ALL_OTHER_Ns)	1523	0.304113	0.4085	0.2421	5008	,	,		18883	0.1141		0.334	False		,,,				2504	0.3722				p.I12fs		Pindel,Atlas-Indel	.											.	OR9K2	63	.	0			c.34delA						PASS	.			1650,2614		298,1054,780	93.0	101.0	98.0			2.5	0.8	12	dbSNP_132	145	2679,5575		443,1793,1891	no	frameshift	OR9K2	NM_001005243.1		741,2847,2671	A1A1,A1R,RR		32.457,38.6961,34.5822			55523587	4329,8189	2195	4296	6491	SO:0001589	frameshift_variant	441639	exon1			.	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.35delT	12.37:g.55523587delT	ENSP00000307598:p.Ile12fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	90	26	0.289	NM_001005243	B9EH19|Q6IFD6	Frame_Shift_Del	DEL	ENST00000305377.5	37	CCDS31814.1																																																																																			T|0.711;-|0.289	0.289	strong		0.363	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																					p.Q1128delinsQQQQQ		Pindel,Atlas-Indel	.											.	SHROOM4	171	.	0			c.3384_3385insACAGCAGCAGCA						PASS	.			12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0.0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				SO:0001652	inframe_insertion	57477	exon6			.	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	27	10	0.370	NM_020717	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																			-|0.664;TGCTGCTGCTGT|0.336	0.336	strong		0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
CARD10	29775	hgsc.bcm.edu	37	22	37906309	37906314	+	In_Frame_Del	DEL	CTCCTT	CTCCTT	-	rs113275238|rs60611523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTCCTT	CTCCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37906309_37906314delCTCCTT	ENST00000403299.1	-	5	1030_1035	c.814_819delAAGGAG	c.(814-819)aaggagdel	p.KE272del	CARD10_ENST00000406271.3_5'Flank|CARD10_ENST00000494166.1_5'UTR|CARD10_ENST00000251973.5_In_Frame_Del_p.KE272del			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	272					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CATTGTCTGGctccttctccttctcc	0.631														1551	0.309704	0.4743	0.2536	5008	,	,		16347	0.3036		0.2535	False		,,,				2504	0.1912				p.272_274del		Pindel,Atlas-Indel	.											.	CARD10	55	.	0			c.815_820del						PASS	.																																			SO:0001651	inframe_deletion	29775	exon4			.	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.814_819delAAGGAG	22.37:g.37906315_37906320delCTCCTT	ENSP00000384570:p.Lys272_Glu273del	Somatic	26	.	.		WXS	Illumina HiSeq	Phase_I	23	11	0.478	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	In_Frame_Del	DEL	ENST00000403299.1	37	CCDS13948.1																																																																																			CTCCTT|0.500;-|0.500	0.500	strong		0.631	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
SLC38A10	124565	hgsc.bcm.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617|rs3833102|rs201518560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79219501_79219503delATG	ENST00000374759.3	-	16	3596_3598	c.3213_3215delCAT	c.(3211-3216)atcatt>att	p.1071_1072II>I		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	1071				Missing (in Ref. 5; AAG17235). {ECO:0000305}.	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)			GTTAAGGCCAATGATGACCCCAT	0.685														2114	0.422125	0.025	0.4712	5008	,	,		16375	0.6776		0.4364	False		,,,				2504	0.6462				p.1072_1072del		Pindel,Atlas-Indel	.											.	SLC38A10	133	.	0			c.3214_3216del						PASS	.			353,3595		37,279,1658						-2.8	0.0		dbSNP_119	35	3598,4380		853,1892,1244	no	coding	SLC38A10	NM_001037984.1		890,2171,2902	A1A1,A1R,RR		45.099,8.9412,33.1293				3951,7975				SO:0001651	inframe_deletion	124565	exon16			.	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.3213_3215delCAT	17.37:g.79219504_79219506delATG	ENSP00000363891:p.Ile1072del	Somatic	188	.	.		WXS	Illumina HiSeq	Phase_I	179	85	0.475	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	In_Frame_Del	DEL	ENST00000374759.3	37	CCDS42397.1																																																																																			ATG|0.576;-|0.424	0.424	strong		0.685	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
AK9	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000368948.2_In_Frame_Del_p.E703del|AK9_ENST00000341338.6_5'UTR	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,Atlas-Indel	.											.	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	50	.	.		WXS	Illumina HiSeq	Phase_I	41	16	0.390	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	
ZNRF2	223082	hgsc.bcm.edu	37	7	30329454	30329456	+	Intron	DEL	TGT	TGT	-	rs373052300	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:30329454_30329456delTGT	ENST00000323037.4	+	1	1520				MIR550A1_ENST00000385037.1_RNA	NM_147128.3	NP_667339.1	Q8NHG8	ZNRF2_HUMAN	zinc and ring finger 2							cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|prostate(1)	5						GTAAGAGCCCTGTTGTTGTAAGA	0.493														60	0.0119808	0.0197	0.0159	5008	,	,		16444	0.0		0.0139	False		,,,				2504	0.0092				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			257,3721		19,219,1751						-0.5	0.0			141	846,6652		32,782,2935	no	intron	ZNRF2	NM_147128.3		51,1001,4686	A1A1,A1R,RR		11.283,6.4605,9.6114				1103,10373				SO:0001627	intron_variant	693133	.			.	AF513707	CCDS5426.1	7p15.1	2013-01-09			ENSG00000180233	ENSG00000180233		"""RING-type (C3HC4) zinc fingers"""	22316	protein-coding gene	gene with protein product		612061					Standard	NM_147128		Approved	RNF202	uc003tat.3	Q8NHG8	OTTHUMG00000097759	ENST00000323037.4:c.469+4012TGT>-	7.37:g.30329460_30329462delTGT		Somatic	74	.	.		WXS	Illumina HiSeq	Phase_I	241	39	0.162	.		RNA	DEL	ENST00000323037.4	37	CCDS5426.1																																																																																			.	.	weak		0.493	ZNRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214992.1	NM_147128	
HACE1	57531	hgsc.bcm.edu	37	6	105192108	105192110	+	Intron	DEL	AAC	AAC	-	rs72218235|rs374160571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:105192108_105192110delAAC	ENST00000262903.4	-	22	2719				HACE1_ENST00000369125.2_Intron|HACE1_ENST00000517995.1_Intron	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1						cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.?(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CAGAACCACTAACAACAAGAACA	0.335														967	0.193091	0.4402	0.1441	5008	,	,		17448	0.003		0.1481	False		,,,				2504	0.136				.		Pindel,Atlas-Indel	.											.	HACE1	96	.	1	Unknown(1)	pancreas(1)	.						PASS	.			1754,2510		344,1066,722						4.5	0.9		dbSNP_120	64	1339,6909		107,1125,2892	no	intron	HACE1	NM_020771.3		451,2191,3614	A1A1,A1R,RR		16.2342,41.1351,24.7203				3093,9419				SO:0001627	intron_variant	57531	.			.	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2443-3GTT>-	6.37:g.105192111_105192113delAAC		Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	94	35	0.372	.	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Splice_Site	DEL	ENST00000262903.4	37	CCDS5050.1																																																																																			AAC|0.835;-|0.165	0.165	strong		0.335	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
OR52D1	390066	hgsc.bcm.edu	37	11	5510540	5510541	+	Frame_Shift_Ins	INS	-	-	GGCT	rs146317894|rs576495879|rs190320444|rs36066208|rs377247106	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5510540_5510541insGGCT	ENST00000322641.5	+	1	626_627	c.604_605insGGCT	c.(604-606)gggfs	p.-203fs	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1						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)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TATTGTCTATGGGCTAACTGTG	0.49														471	0.0940495	0.0212	0.1715	5008	,	,		23752	0.0754		0.1779	False		,,,				2504	0.0706				p.G202fs		Pindel,Atlas-Indel	.											.	OR52D1	66	.	0			c.604_605insGGCT						PASS	.			221,4041		4,213,1914						5.5	1.0		dbSNP_130	269	1217,7035		95,1027,3004	no	frameshift	OR52D1	NM_001005163.2		99,1240,4918	A1A1,A1R,RR		14.7479,5.1854,11.4911				1438,11076				SO:0001589	frameshift_variant	390066	exon1			.	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.605_608dupGGCT	11.37:g.5510541_5510544dupGGCT	ENSP00000326232:p.Leu203fs	Somatic	131	.	.		WXS	Illumina HiSeq	Phase_I	106	24	0.226	NM_001005163	B9EGY9|Q6IFI6	Frame_Shift_Ins	INS	ENST00000322641.5	37	CCDS31384.1																																																																																			.	.	strong		0.490	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
DEFB126	81623	hgsc.bcm.edu	37	20	126156	126159	+	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs200807952|rs397788846|rs11467497		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAAA	CAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	119	.	.		WXS	Illumina HiSeq	Phase_I	110	31	0.282	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	
CRACR2B	283229	hgsc.bcm.edu	37	11	831552	831553	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:831552_831553insGC	ENST00000525077.1	+	9	1144_1145	c.1043_1044insGC	c.(1042-1047)ctgcggfs	p.LR348fs	EFCAB4A_ENST00000450448.1_Frame_Shift_Ins_p.A293fs|EFCAB4A_ENST00000528542.2_Frame_Shift_Ins_p.A293fs|CD151_ENST00000397421.1_5'Flank|AP006621.8_ENST00000532946.1_RNA|CD151_ENST00000322008.4_5'Flank|CD151_ENST00000397420.3_5'Flank			Q8N4Y2	EFC4A_HUMAN		348					cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AATACACGGCTGCGGGATGACA	0.673																																					p.A292fs		Pindel,Atlas-Indel	.											.	EFCAB4A	16	.	0			c.876_877insGC						PASS	.			0,3832		0,0,1916						4.1	0.5			34	2,7932		0,2,3965	no	frameshift	EFCAB4A	NM_173584.3		0,2,5881	A1A1,A1R,RR		0.0252,0.0,0.017				2,11764				SO:0001589	frameshift_variant	283229	exon9			.																												ENST00000525077.1:c.1044_1045dupGC	11.37:g.831553_831554dupGC	ENSP00000435299:p.Leu348fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	71	20	0.282	NM_173584	D5LPR2|Q8NBW8	Frame_Shift_Ins	INS	ENST00000525077.1	37																																																																																				.	.	none		0.673	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1		
HOMEZ	57594	hgsc.bcm.edu	37	14	23744801	23744803	+	In_Frame_Del	DEL	CAT	CAT	-	rs148005528		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23744801_23744803delCAT	ENST00000357460.5	-	2	1798_1800	c.1634_1636delATG	c.(1633-1638)gatgtg>gtg	p.D545del	HOMEZ_ENST00000431326.2_In_Frame_Del_p.D547del|HOMEZ_ENST00000561013.1_In_Frame_Del_p.D547del	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	545					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)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGTATGatcacatcatcatcatc	0.438																																					p.545_546del		Pindel,Atlas-Indel	.											.	HOMEZ	80	.	0			c.1635_1637del						PASS	.																																			SO:0001651	inframe_deletion	57594	exon2			.	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1634_1636delATG	14.37:g.23744810_23744812delCAT	ENSP00000350049:p.Asp545del	Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	102	33	0.324	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	In_Frame_Del	DEL	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	strong		0.438	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
CCDC66	285331	hgsc.bcm.edu	37	3	56650051	56650052	+	In_Frame_Ins	INS	-	-	CTT	rs67797937|rs77152637|rs74463118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	.	.		WXS	Illumina HiSeq	Phase_I	109	40	0.367	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	
TMEM87B	84910	hgsc.bcm.edu	37	2	112832536	112832538	+	Splice_Site	DEL	AAT	AAT	-	rs201146763|rs71385858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:112832536_112832538delAAT	ENST00000283206.4	+	5	867_869	c.498_500delAAT	c.(496-501)tcaatg>tcg	p.M167del		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	167						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						AGGAAAGATCAATGGTAAGCAGT	0.3														1297	0.258986	0.2118	0.2954	5008	,	,		17959	0.1835		0.3976	False		,,,				2504	0.2321				p.166_167del		Pindel,Atlas-Indel	.											.	TMEM87B	52	.	0			c.497_499del						PASS	.			915,3343		103,709,1317						3.6	0.8		dbSNP_130	41	3245,4989		636,1973,1508	no	coding-near-splice	TMEM87B	NM_032824.2		739,2682,2825	A1A1,A1R,RR		39.4098,21.489,33.3013				4160,8332				SO:0001630	splice_region_variant	84910	exon5			.	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.501+1AAT>-	2.37:g.112832536_112832538delAAT		Somatic	262	.	.		WXS	Illumina HiSeq	Phase_I	217	42	0.194	NM_032824	A8K2M9|Q1RLN2|Q53R54	In_Frame_Del	DEL	ENST00000283206.4	37	CCDS33275.1																																																																																			AAT|0.722;-|0.278	0.278	strong		0.300	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824	In_Frame_Del
SCRN3	79634	hgsc.bcm.edu	37	2	175292581	175292593	+	Frame_Shift_Del	DEL	TCAAATTTATCAG	TCAAATTTATCAG	-	rs145699077|rs79038555	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCAAATTTATCAG	TCAAATTTATCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:175292581_175292593delTCAAATTTATCAG	ENST00000272732.6	+	8	1315_1327	c.1233_1245delTCAAATTTATCAG	c.(1231-1245)attcaaatttatcagfs	p.IQIYQ411fs	SCRN3_ENST00000548921.1_3'UTR|SCRN3_ENST00000409673.3_Frame_Shift_Del_p.IQIYQ404fs	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	334	.	.		WXS	Illumina HiSeq	Phase_I	263	67	0.255	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	
PSORS1C2	170680	hgsc.bcm.edu	37	6	31105858	31105858	+	Frame_Shift_Del	DEL	G	G	-	rs373592714|rs79153019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31105858delG	ENST00000259845.4	-	2	604	c.281delC	c.(280-282)cctfs	p.P95fs	PSORS1C1_ENST00000259881.9_Intron|PSORS1C1_ENST00000481450.2_5'Flank|PSORS1C1_ENST00000547221.1_Intron	NM_014069.2	NP_054788.2	Q9UIG4	PS1C2_HUMAN	psoriasis susceptibility 1 candidate 2	95						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						AGGCCGGGGAGGTTGAGGAGG	0.652													GG|GG|G|deletion	266	0.053115	0.0272	0.0562	5008	,	,		13538	0.0079		0.1014	False		,,,				2504	0.0828				p.P94fs		Pindel,Atlas-Indel	.											.	PSORS1C2	11	.	0			c.282delT						PASS	.		,	150,3062		13,124,1469	40.0	48.0	45.0		,	4.7	1.0	6	dbSNP_131	48	571,5421		61,449,2486	yes	frameshift,intron	PSORS1C1,PSORS1C2	NM_014069.2,NM_014068.2	,	74,573,3955	A1A1,A1R,RR		9.5294,4.67,7.8336	,	,	31105858	721,8483	1500	2684	4184	SO:0001589	frameshift_variant	170680	exon2			.	AB031480	CCDS4694.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204538	ENSG00000204538			17199	protein-coding gene	gene with protein product		613526	"""chromosome 6 open reading frame 17"""	C6orf17			Standard	NM_014069		Approved	SPR1	uc003nso.4	Q9UIG4	OTTHUMG00000031081	ENST00000259845.4:c.281delC	6.37:g.31105858delG	ENSP00000259845:p.Pro95fs	Somatic	53	.	.		WXS	Illumina HiSeq	Phase_I	53	11	0.208	NM_014069	Q5STD0	Frame_Shift_Del	DEL	ENST00000259845.4	37	CCDS4694.1																																																																																			G|0.946;-|0.054	0.054	strong		0.652	PSORS1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076115.3		
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524657	10524659	+	In_Frame_Del	DEL	GAC	GAC	-	rs56252625|rs75627261|rs571414967|rs113642662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	190	.	.		WXS	Illumina HiSeq	Phase_I	161	81	0.503	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	
UBAC1	10422	hgsc.bcm.edu	37	9	138836942	138836944	+	In_Frame_Del	DEL	CCT	CCT	-	rs66767056|rs140946801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	76	.	.		WXS	Illumina HiSeq	Phase_I	110	35	0.318	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	
MIR205HG	642587	hgsc.bcm.edu	37	1	209605637	209605648	+	lincRNA	DEL	AGCAGCAGCAGC	AGCAGCAGCAGC	-	rs71788170|rs74820836|rs150848171|rs3842530		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGCAGCAGCAGC	AGCAGCAGCAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:209605637_209605648delAGCAGCAGCAGC	ENST00000384891.1	+	0	220					NR_029622.1				MIR205 host gene (non-protein coding)																		ccaccaccgTagcagcagcagcagcagcagca	0.561																																					p.84_88del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.251_262del						PASS	.																																					642587	exon4			.			1q32.2	2014-02-12	2011-11-07		ENSG00000230937	ENSG00000230937		"""Long non-coding RNAs"""	43562	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 510"""						Standard	NM_001104548		Approved	LINC00510	uc009xcn.3		OTTHUMG00000036267		1.37:g.209605637_209605648delAGCAGCAGCAGC		Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	42	11	0.262	NM_001104548		In_Frame_Del	DEL	ENST00000384891.1	37																																																																																				.	.	strong		0.561	MIR205HG-202	KNOWN	basic	miRNA	lincRNA			
PPM1E	22843	hgsc.bcm.edu	37	17	56833457	56833458	+	In_Frame_Ins	INS	-	-	GAACCC	rs3834568|rs201186780|rs74256772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56833457_56833458insGAACCC	ENST00000308249.2	+	1	228_229	c.99_100insGAACCC	c.(100-102)gaa>GAACCCgaa	p.34_34E>EPE		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			agccggagccggaacccgaacc	0.673														1948	0.388978	0.4493	0.2896	5008	,	,		9152	0.3323		0.4036	False		,,,				2504	0.4213				p.P33delinsPEP		Pindel,Atlas-Indel	.											PPM1E,colon,carcinoma,0,1	PPM1E	97	1	0			c.99_100insGAACCC						PASS	.																																			SO:0001652	inframe_insertion	22843	exon1			.	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19322	protein-coding gene	gene with protein product	"""partner of PIX 1"", ""nuclear calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1E (PP2C domain containing)"""			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.124_129dupGAACCC	17.37:g.56833458_56833463dupGAACCC	ENSP00000312411:p.ProGlu44dup	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	105	19	0.181	NM_014906	Q8N8J9|Q96DB8	In_Frame_Ins	INS	ENST00000308249.2	37	CCDS11613.1																																																																																			-|0.417;GAACCC|0.583	0.583	strong		0.673	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906	
FRMPD2	143162	hgsc.bcm.edu	37	10	49379224	49379224	+	Frame_Shift_Del	DEL	T	T	-	rs568453728		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:49379224delT	ENST00000374201.3	-	26	3553	c.3251delA	c.(3250-3252)aagfs	p.K1084fs	FRMPD2_ENST00000407470.4_Frame_Shift_Del_p.K1052fs|FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000305531.3_Frame_Shift_Del_p.K1059fs|FRMPD2_ENST00000474573.1_Frame_Shift_Del_p.K36fs	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	1084	PDZ 3. {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)		ATTGGCATTCTTTTTTAGTTT	0.398																																					p.K1084fs		Atlas-Indel	.											FRMPD2,NS,carcinoma,0,1	FRMPD2	157	1	0			c.3252delG						PASS	.			2,1164		1,0,582	2.0	2.0	2.0			2.4	1.0	10		2	16,1814		7,2,906	no	frameshift	FRMPD2	NM_001018071.3		8,2,1488	A1A1,A1R,RR		0.8743,0.1715,0.6008			49379224	18,2978	812	1396	2208	SO:0001589	frameshift_variant	143162	exon26			.	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.3251delA	10.37:g.49379224delT	ENSP00000363317:p.Lys1084fs	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	214	42	0.196262	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Frame_Shift_Del	DEL	ENST00000374201.3	37	CCDS31195.1																																																																																			.	.	none		0.398	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
DRICH1	51233	hgsc.bcm.edu	37	22	23964283	23964285	+	In_Frame_Del	DEL	CAT	CAT	-	rs66974032|rs142649853|rs10564183|rs200087148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23964283_23964285delCAT	ENST00000317749.5	-	4	674_676	c.377_379delATG	c.(376-381)gatgcc>gcc	p.D126del		NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		126	Asp-rich.							p.D126delD(1)		endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						CTTACCTGGGcatcatcatcatc	0.429														621	0.124002	0.1036	0.0937	5008	,	,		21629	0.1895		0.1133	False		,,,				2504	0.1166				p.126_127del		Pindel,Atlas-Indel	.											.	C22orf43	18	.	1	Deletion - In frame(1)	pancreas(1)	c.378_380del						PASS	.																																			SO:0001651	inframe_deletion	51233	exon4			.																												ENST00000317749.5:c.377_379delATG	22.37:g.23964292_23964294delCAT	ENSP00000316137:p.Asp126del	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	50	10	0.200	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	In_Frame_Del	DEL	ENST00000317749.5	37	CCDS42985.1																																																																																			.	.	weak		0.429	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2		
TCEB3C	162699	hgsc.bcm.edu	37	18	44554940	44554941	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:44554940_44554941insGC	ENST00000330682.2	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Atlas-Indel	.											.	TCEB3C	49	.	0			c.1274_1275insGC						PASS	.																																			SO:0001589	frameshift_variant	162699	exon1			.	AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1272_1273dupGC	18.37:g.44554941_44554942dupGC	ENSP00000328232:p.Gln425fs	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	228	14	0.0614035	NM_145653		Frame_Shift_Ins	INS	ENST00000330682.2	37	CCDS11931.1																																																																																			.	.	none		0.554	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1	NM_145653	
NELFA	7469	hgsc.bcm.edu	37	4	1988188	1988189	+	Intron	INS	-	-	CT	rs35401110|rs3034718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:1988188_1988189insCT	ENST00000411638.2	-	5	650				NELFA_ENST00000542778.1_Intron|NELFA_ENST00000382882.3_Intron|MIR943_ENST00000401286.1_RNA	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A						gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										TCCCCCACCCCGAGCTCAGAAC	0.678														1385	0.276558	0.4629	0.255	5008	,	,		14126	0.2778		0.1928	False		,,,				2504	0.1247				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			1739,0,2511		377,0,985,0,0,763						1.7	0.0		dbSNP_126	28	1828,4,6416		208,1,1411,0,3,2501	no	intron	WHSC2	NM_005663.4		585,1,2396,0,3,3264	A1A1,A1A2,A1R,A2A2,A2R,RR		22.2114,40.9176,28.5726				3567,4,8927				SO:0001627	intron_variant	100126332	.			.	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"""Wolf-Hirschhorn syndrome candidate 2"""	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.635-59->AG	4.37:g.1988188_1988189insCT		Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	92	31	0.337	.	A2A2T1|O95392	RNA	INS	ENST00000411638.2	37																																																																																				CT|1.000;|0.000	1.000	strong		0.678	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
RIMBP3C	150221	hgsc.bcm.edu	37	22	21904075	21904077	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21904075_21904077delCTC	ENST00000433039.1	-	1	1673_1675	c.1189_1191delGAG	c.(1189-1191)gagdel	p.E397del	UBE2L3_ENST00000458578.2_Intron|RIMBP3C_ENST00000331505.5_In_Frame_Del_p.E303del	NM_001128633.1	NP_001122105.1	A6NJZ7	RIM3C_HUMAN	RIMS binding protein 3C	397										large_intestine(1)	1						GCTGCTTGTTCTCCTCTTGCAGG	0.67																																					p.397_398del		Atlas-Indel	.											.	RIMBP3C	6	.	0			c.1190_1192del						PASS	.																																			SO:0001651	inframe_deletion	150221	exon1			.		CCDS46669.1	22q11.21	2008-10-21			ENSG00000183246	ENSG00000183246			33892	protein-coding gene	gene with protein product		612701				17855024	Standard	NM_001128633		Approved		uc002zuq.4	A6NJZ7	OTTHUMG00000150825	ENST00000433039.1:c.1189_1191delGAG	22.37:g.21904078_21904080delCTC	ENSP00000390630:p.Glu397del	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	189	20	0.10582	NM_001128633		In_Frame_Del	DEL	ENST00000433039.1	37	CCDS46669.1																																																																																			.	.	none		0.670	RIMBP3C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_036942	
PI4KB	5298	hgsc.bcm.edu	37	1	151263677	151263678	+	IGR	INS	-	-	ACA	rs145032688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:151263677_151263678insACA	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	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)			GGCTGTTGGGGACAACTAGTCT	0.584														82	0.0163738	0.0023	0.0144	5008	,	,		16222	0.0		0.0547	False		,,,				2504	0.0143				p.D1236delinsDN	Colon(154;765 1838 9854 28443 37492)	Pindel,Atlas-Indel	.											.	ZNF687	94	.	0			c.3706_3707insACA						PASS	.			59,4025		4,51,1987						4.7	1.0		dbSNP_134	30	528,7434		53,422,3506	no	coding	ZNF687	NM_020832.1		57,473,5493	A1A1,A1R,RR		6.6315,1.4447,4.873				587,11459				SO:0001628	intergenic_variant	57592	exon9			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		1.37:g.151263678_151263680dupACA		Somatic	23	.	.		WXS	Illumina HiSeq	Phase_I	27	10	0.370	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	In_Frame_Ins	INS	ENST00000368873.1	37																																																																																				-|0.977;ACA|0.023	0.023	strong		0.584	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651	
WDR63	126820	hgsc.bcm.edu	37	1	85598679	85598680	+	Stop_Codon_Ins	INS	-	-	A	rs145165915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85598679_85598680insA	ENST00000294664.6	+	0	2854_2855				WDR63_ENST00000370596.1_Stop_Codon_Ins|WDR63_ENST00000326813.8_Stop_Codon_Ins|MIR4423_ENST00000580922.1_RNA	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63											NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		GGAGGTGATGTAAAAAAGCTTC	0.386													AAAAAA|AAAAAA|AAAAAAA|insertion	263	0.052516	0.0023	0.0418	5008	,	,		14906	0.1438		0.0676	False		,,,				2504	0.0184				p.X892delinsX		Pindel,Atlas-Indel	.											.	WDR63	91	.	0			c.2674_2675insA						PASS	.			45,4221		0,45,2088						3.8	0.0		dbSNP_134	123	548,7702		15,518,3592	no	frameshift	WDR63	NM_145172.3		15,563,5680	A1A1,A1R,RR		6.6424,1.0549,4.7379				593,11923				SO:0001567	stop_retained_variant	126820	exon23			.		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2679dupA	1.37:g.85598685_85598685dupA		Somatic	30	.	.		WXS	Illumina HiSeq	Phase_I	32	12	0.375	NM_145172	A8K988|Q96L72|Q96NU4	Frame_Shift_Ins	INS	ENST00000294664.6	37	CCDS702.1																																																																																			-|0.938;A|0.062	0.062	strong		0.386	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471753	39471767	+	In_Frame_Del	DEL	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	-	rs373758570|rs74252500|rs572148015|rs386797077|rs577925182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39471753_39471767delGCCCCCGCAGCCAGA	ENST00000334202.3	-	1	180_194	c.136_150delTCTGGCTGCGGGGGC	c.(136-150)tctggctgcgggggcdel	p.SGCGG46del		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	46						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			cgcagcagctgcccccgcagccagagcccccgcag	0.679														1164	0.232428	0.2935	0.1499	5008	,	,		12020	0.3185		0.1829	False		,,,				2504	0.1708				p.46_51del		Pindel,Atlas-Indel	.											.	KRTAP17-1	14	.	0			c.137_151del						PASS	.			1060,2972		251,558,1207						-1.9	0.1		dbSNP_130	17	1435,6399		241,953,2723	no	coding	KRTAP17-1	NM_031964.1		492,1511,3930	A1A1,A1R,RR		18.3176,26.2897,21.0265				2495,9371				SO:0001651	inframe_deletion	83902	exon1			.	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"""Keratin associated proteins"""	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.136_150delTCTGGCTGCGGGGGC	17.37:g.39471753_39471767delGCCCCCGCAGCCAGA	ENSP00000333993:p.Ser46_Gly50del	Somatic	26	.	.		WXS	Illumina HiSeq	Phase_I	44	12	0.273	NM_031964		In_Frame_Del	DEL	ENST00000334202.3	37	CCDS11387.1																																																																																			.	.	none		0.679	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
DDX58	23586	hgsc.bcm.edu	37	9	32457307	32457308	+	Frame_Shift_Ins	INS	-	-	AGAA	rs573952640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32457307_32457308insAGAA	ENST00000379883.2	-	18	2747_2748	c.2590_2591insTTCT	c.(2590-2592)tgtfs	p.C864fs	DDX58_ENST00000542096.1_Frame_Shift_Ins_p.C793fs|DDX58_ENST00000379868.1_Frame_Shift_Ins_p.C661fs|DDX58_ENST00000379882.1_Frame_Shift_Ins_p.C819fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	864	Interaction with ZC3HAV1.|Repressor domain.				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 defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CTGTCGGGCACAGAATATCTTT	0.396														3	0.000599042	0.0	0.0014	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.002				p.C864fs		Pindel,Atlas-Indel	.											.	DDX58	82	.	0			c.2591_2592insTTCT						PASS	.			0,4262		0,0,2131						5.8	1.0			112	13,8241		0,13,4114	no	frameshift	DDX58	NM_014314.3		0,13,6245	A1A1,A1R,RR		0.1575,0.0,0.1039				13,12503				SO:0001589	frameshift_variant	23586	exon18			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2587_2590dupTTCT	9.37:g.32457308_32457311dupAGAA	ENSP00000369213:p.Cys864fs	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	103	33	0.320	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Ins	INS	ENST00000379883.2	37	CCDS6526.1																																																																																			.	.	none		0.396	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
OR2V2	285659	hgsc.bcm.edu	37	5	180582257	180582260	+	Frame_Shift_Del	DEL	TGTC	TGTC	-	rs140598308|rs369545203|rs398109744|rs77629911|rs201952686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:180582257_180582260delTGTC	ENST00000328275.1	+	1	315_318	c.315_318delTGTC	c.(313-318)tttgtcfs	p.FV105fs		NM_206880.1	NP_996763.1	Q96R30	OR2V2_HUMAN	olfactory receptor, family 2, subfamily V, member 2	105						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)|cervix(1)|endometrium(1)|kidney(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(89;8.26e-06)|all_epithelial(37;1.02e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.0103)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0652)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTGGCCTCTTTGTCTGTCTTGTGG	0.51														387	0.0772764	0.1505	0.0476	5008	,	,		23438	0.0159		0.0746	False		,,,				2504	0.0654				p.105_106del		Pindel,Atlas-Indel	.											.	OR2V2	56	.	0			c.314_317del						PASS	.			571,3693		42,487,1603						3.3	1.0		dbSNP_134	108	505,7747		14,477,3635	no	frameshift	OR2V2	NM_206880.1		56,964,5238	A1A1,A1R,RR		6.1197,13.3912,8.597				1076,11440				SO:0001589	frameshift_variant	285659	exon1			.	AL161615	CCDS4461.1	5q35.3	2012-08-09			ENSG00000182613	ENSG00000182613		"""GPCR / Class A : Olfactory receptors"""	15341	protein-coding gene	gene with protein product				OR2V3			Standard	NM_206880		Approved	OST713	uc011dhj.2	Q96R30	OTTHUMG00000130933	ENST00000328275.1:c.315_318delTGTC	5.37:g.180582261_180582264delTGTC	ENSP00000332185:p.Phe105fs	Somatic	198	.	.		WXS	Illumina HiSeq	Phase_I	209	62	0.297	NM_206880	Q6IFL6|Q8NGV1	Frame_Shift_Del	DEL	ENST00000328275.1	37	CCDS4461.1																																																																																			TGTC|0.926;-|0.074	0.074	strong		0.510	OR2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253529.1		
OR2A14	135941	hgsc.bcm.edu	37	7	143826730	143826732	+	In_Frame_Del	DEL	CTT	CTT	-	rs66549240|rs34602346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		Pindel,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	192	.	.		WXS	Illumina HiSeq	Phase_I	146	40	0.274	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		
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650055	+	In_Frame_Ins	INS	-	-	CTC	rs112267342|rs111934125|rs74400129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56650054_56650055insCTC	ENST00000394672.3	+	13	1886_1887	c.1816_1817insCTC	c.(1816-1818)tct>tCTCct	p.606_607insP	CCDC66_ENST00000436465.2_In_Frame_Ins_p.606_607insP|CCDC66_ENST00000326595.7_In_Frame_Ins_p.572_573insP	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)		TTCTACGACTTCTAAGAAGGAT	0.287																																					p.S606delinsSP		Pindel,Atlas-Indel	.											CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	0			c.1816_1817insCTC						PASS	.		,	1614,1970,682		328,715,243,474,307,66					,	4.3	0.6		dbSNP_131	94	983,2804,4449		76,306,525,488,1522,1201	no	codingComplex,codingComplex	CCDC66	NM_001141947.1,NM_001012506.4	,	404,1021,768,962,1829,1267	A1A1,A1A2,A1R,A2A2,A2R,RR		45.9811,53.8209,58.9586	,	,		2597,4774,5131				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	Exception_encountered	3.37:g.56650054_56650055insCTC	ENSP00000378167:p.Ser606_Lys607insPro	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	117	26	0.222	NM_001141947	B3KWL8|Q4VC34|Q8N949	In_Frame_Ins	INS	ENST00000394672.3	37	CCDS46852.1																																																																																			CTC|0.250;CTT|0.750	0.250	strong		0.287	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242149	81242150	+	RNA	DEL	TT	TT	-	rs55980345|rs75398810|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	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		
LAD1	3898	hgsc.bcm.edu	37	1	201356001	201356001	+	Frame_Shift_Del	DEL	C	C	-	rs78190062|rs527771129|rs398053706|rs35016536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201356001delC	ENST00000391967.2	-	3	789	c.488delG	c.(487-489)ggcfs	p.G163fs	LAD1_ENST00000367313.3_Frame_Shift_Del_p.G177fs	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	163						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TGGCTCCCTGCCCACCAAGCT	0.587																																					p.G163fs		Atlas-Indel	.											.	LAD1	42	.	0			c.489delC						PASS	.						46.0	58.0	54.0					1																	201356001		2200	4300	6500	SO:0001589	frameshift_variant	3898	exon3			.	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.488delG	1.37:g.201356001delC	ENSP00000375829:p.Gly163fs	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_005558	O95614|Q96GD8	Frame_Shift_Del	DEL	ENST00000391967.2	37	CCDS1410.1																																																																																			C|0.948;-|0.052	0.052	strong		0.587	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
CLEC17A	388512	hgsc.bcm.edu	37	19	14694175	14694176	+	In_Frame_Ins	INS	-	-	GGA	rs138602183|rs34295949|rs548360441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14694175_14694176insGGA	ENST00000417570.1	+	2	88_89	c.50_51insGGA	c.(49-54)atggag>atGGAggag	p.22_23insE	RN7SL337P_ENST00000462468.2_RNA|CLEC17A_ENST00000547437.1_In_Frame_Ins_p.22_23insE|CLEC17A_ENST00000397439.2_In_Frame_Ins_p.22_23insE	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		Atlas-Indel	.											.	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	193	0	0		WXS	Illumina HiSeq	Phase_I	178	41	0.230337	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	
CDAN1	146059	hgsc.bcm.edu	37	15	43020456	43020457	+	Frame_Shift_Ins	INS	-	-	TGAC			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:43020456_43020457insTGAC	ENST00000356231.3	-	21	2836_2837	c.2813_2814insGTCA	c.(2812-2814)caafs	p.-938fs		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1						chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GGCTCTTCCTTTGACAGAACCT	0.619																																					p.Q938fs		Pindel,Atlas-Indel	.											.	CDAN1	70	.	0			c.2814_2815insGTCA						PASS	.																																			SO:0001589	frameshift_variant	146059	exon21			.	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2810_2813dupGTCA	15.37:g.43020457_43020460dupTGAC	ENSP00000348564:p.Gln938fs	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	60	19	0.317	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Frame_Shift_Ins	INS	ENST00000356231.3	37	CCDS32209.1																																																																																			.	.	none		0.619	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
OR52N1	79473	hgsc.bcm.edu	37	11	5809807	5809807	+	Frame_Shift_Del	DEL	A	A	-	rs142442713	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5809807delA	ENST00000317078.1	-	1	239	c.240delT	c.(238-240)cttfs	p.L80fs	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	80						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)		GAGTGTTGGGAAGGGTGCTGG	0.458													AA|AA|A|deletion	102	0.0203674	0.0015	0.0216	5008	,	,		25345	0.001		0.0447	False		,,,				2504	0.0399				p.P81fs		Pindel,Atlas-Indel	.											.	OR52N1	70	.	0			c.241delC						PASS	.			64,4196		3,58,2069	144.0	125.0	132.0			4.6	0.6	11	dbSNP_134	137	562,7692		17,528,3582	no	frameshift	OR52N1	NM_001001913.1		20,586,5651	A1A1,A1R,RR		6.8088,1.5023,5.0024			5809807	626,11888	2201	4293	6494	SO:0001589	frameshift_variant	79473	exon1			.	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.240delT	11.37:g.5809807delA	ENSP00000322823:p.Leu80fs	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	96	33	0.344	NM_001001913	Q6IFF6	Frame_Shift_Del	DEL	ENST00000317078.1	37	CCDS31398.1																																																																																			A|0.979;-|0.021	0.021	strong		0.458	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
NCOA3	8202	hgsc.bcm.edu	37	20	46279837	46279839	+	In_Frame_Del	DEL	CAG	CAG	-	rs147879509|rs2664555|rs397778717|rs3830809		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000371997.3_In_Frame_Del_p.Q1267del|NCOA3_ENST00000372004.3_In_Frame_Del_p.Q1272del			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	76	0	0		WXS	Illumina HiSeq	Phase_I	75	21	0.28	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	
GPR50	9248	hgsc.bcm.edu	37	X	150349558	150349569	+	In_Frame_Del	DEL	CACCACTGGCCA	CACCACTGGCCA	-	rs377556761|rs199797606|rs68058591|rs200787393		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CACCACTGGCCA	CACCACTGGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150349558_150349569delCACCACTGGCCA	ENST00000218316.3	+	2	1572_1583	c.1503_1514delCACCACTGGCCA	c.(1501-1515)cccaccactggccac>ccc	p.TTGH502del	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	502	Pro-rich.		Missing (lower fasting circulating triglyceride levels). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		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)	p.T502_H505delTTGH(1)		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)					ACCCTAAACCCACCACTGGCCACATCAAGCCA	0.608																																					p.501_505del		Pindel,Atlas-Indel	.											.	GPR50	195	.	1	Deletion - In frame(1)	ovary(1)	c.1502_1513del						PASS	.			1488,2015		315,617,241,554,290						2.6	0.0		dbSNP_130	100	2487,3842		404,1011,668,899,1033	no	coding	GPR50	NM_004224.3		719,1628,909,1453,1323	A1A1,A1R,A1,RR,R		39.2953,42.4779,40.4292				3975,5857				SO:0001651	inframe_deletion	9248	exon2			.	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.1503_1514delCACCACTGGCCA	X.37:g.150349558_150349569delCACCACTGGCCA	ENSP00000218316:p.Thr502_His505del	Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	36	16	0.444	NM_004224	Q0VGG3|Q3ZAR0	In_Frame_Del	DEL	ENST00000218316.3	37	CCDS44012.1																																																																																			CACCACTGGCCA|0.500;-|0.500	0.500	weak		0.608	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
FCN3	8547	hgsc.bcm.edu	37	1	27699671	27699671	+	Frame_Shift_Del	DEL	G	G	-	rs28357092|rs532781899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27699671delG	ENST00000270879.4	-	5	354	c.349delC	c.(349-351)ctcfs	p.L117fs	FCN3_ENST00000354982.2_Frame_Shift_Del_p.L106fs	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	117	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AAGACTGGGAGGGCCCTGCCC	0.632													GGG|GGG|GG|deletion	94	0.01877	0.0242	0.013	5008	,	,		16176	0.0		0.0268	False		,,,				2504	0.0266				p.L117fs		Pindel,Atlas-Indel	.											.	FCN3	30	.	0			c.350delT	GRCh37	CD052457	FCN3	D		PASS	.		,	117,4149		4,109,2020	51.0	57.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	3.1	0.0	1	dbSNP_125	56	147,8107		6,135,3986	no	frameshift,frameshift	FCN3	NM_173452.1,NM_003665.2	,	10,244,6006	A1A1,A1R,RR		1.781,2.7426,2.1086	,	,	27699671	264,12256	2202	4300	6502	SO:0001589	frameshift_variant	8547	exon5			.	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"""Fibrinogen C domain containing"""	3625	protein-coding gene	gene with protein product	"""Hakata antigen"""	604973	"""ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"""			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.349delC	1.37:g.27699671delG	ENSP00000270879:p.Leu117fs	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	175	50	0.286	NM_003665	Q6IBJ5|Q8WW86	Frame_Shift_Del	DEL	ENST00000270879.4	37	CCDS300.1																																																																																			G|0.985;-|0.015	0.015	strong		0.632	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31324604	31324604	+	Frame_Shift_Del	DEL	T	T	-	rs9266179|rs200186034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324604delT	ENST00000412585.2	-	2	232	c.204delA	c.(202-204)agafs	p.R68fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	68	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.E69fs*8(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCGGCTCCTCTCTCGGACTCG	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.E69fs		Atlas-Indel	.											.	HLA-B	54	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.205delG						PASS	.			1993,2105		740,513,796	33.0	33.0	33.0			-6.4	0.0	6	dbSNP_118	34	3347,4625		1272,803,1911	no	frameshift	HLA-B	NM_005514.6		2012,1316,2707	A1A1,A1R,RR		41.9844,48.6335,44.2419			31324604	5340,6730	2015	3950	5965	SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	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.204delA	6.37:g.31324604delT	ENSP00000399168:p.Arg68fs	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.467;-|0.533	0.533	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
CCDC33	80125	hgsc.bcm.edu	37	15	74536401	74536403	+	In_Frame_Del	DEL	AAG	AAG	-	rs397774110|rs201484902|rs10552820|rs201189801|rs35899977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:74536401_74536403delAAG	ENST00000398814.3	+	2	528_530	c.97_99delAAG	c.(97-99)aagdel	p.K34del	CCDC33_ENST00000321288.5_In_Frame_Del_p.K237del	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	237										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						GTCTCCCTCTAAGAAGGAGACCA	0.606														1888	0.376997	0.2685	0.379	5008	,	,		16806	0.3492		0.6093	False		,,,				2504	0.3119				p.32_33del		Pindel,Atlas-Indel	.											.	CCDC33	160	.	0			c.96_98del						PASS	.			1328,2488		280,768,860						-0.4	0.1		dbSNP_119	71	4994,2930		1571,1852,539	no	coding	CCDC33	NM_025055.3		1851,2620,1399	A1A1,A1R,RR		36.9763,34.8008,46.1499				6322,5418				SO:0001651	inframe_deletion	80125	exon2			.	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.97_99delAAG	15.37:g.74536404_74536406delAAG	ENSP00000381795:p.Lys34del	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	80	55	0.688	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	In_Frame_Del	DEL	ENST00000398814.3	37	CCDS42058.1																																																																																			AAG|0.590;-|0.410	0.410	strong		0.606	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
SMEK2	57223	hgsc.bcm.edu	37	2	55777083	55777085	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:55777083_55777085delTTC	ENST00000345102.5	-	17	2813_2815	c.2512_2514delGAA	c.(2512-2514)gaadel	p.E838del	SMEK2_ENST00000407823.3_In_Frame_Del_p.E806del|SMEK2_ENST00000272313.5_In_Frame_Del_p.E753del	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	838	Poly-Glu.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TGGGGGACGATTCTTCTTCTTCA	0.369																																					p.838_839del		Pindel,Atlas-Indel	.											SMEK2_ENST00000345102,colon,carcinoma,+1,4	SMEK2	86	4	0			c.2513_2515del						PASS	.		,	1,4265		0,1,2132					,	3.0	1.0			95	2,8252		0,2,4125	no	coding,coding	SMEK2	NM_020463.2,NM_001122964.1	,	0,3,6257	A1A1,A1R,RR		0.0242,0.0234,0.024	,	,		3,12517				SO:0001651	inframe_deletion	57223	exon17			.	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.2512_2514delGAA	2.37:g.55777092_55777094delTTC	ENSP00000339769:p.Glu838del	Somatic	42	.	.		WXS	Illumina HiSeq	Phase_I	45	15	0.333	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	In_Frame_Del	DEL	ENST00000345102.5	37	CCDS46289.1																																																																																			.	.	none		0.369	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463	
NUP155	9631	hgsc.bcm.edu	37	5	37309372	37309374	+	Intron	DEL	AGA	AGA	-	rs552603277|rs201100022|rs3835198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:37309372_37309374delAGA	ENST00000231498.3	-	24	2832				NUP155_ENST00000502533.1_Intron|NUP155_ENST00000381843.2_Intron|NUP155_ENST00000513532.1_Intron	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa						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)			TCATTTGCCTAGAAGAGGAGATA	0.305														1348	0.269169	0.112	0.3141	5008	,	,		19452	0.3631		0.2952	False		,,,				2504	0.3262				.		Pindel,Atlas-Indel	.											.	NUP155	116	.	0			.						PASS	.		,	601,3665		37,527,1569					,	5.7	1.0		dbSNP_107	61	2403,5851		336,1731,2060	no	intron,intron	NUP155	NM_153485.1,NM_004298.2	,	373,2258,3629	A1A1,A1R,RR		29.1132,14.0881,23.9936	,	,		3004,9516				SO:0001627	intron_variant	9631	.			.	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.2629-3TCT>-	5.37:g.37309375_37309377delAGA		Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	42	27	0.643	.	Q9UBE9|Q9UFL5	Splice_Site	DEL	ENST00000231498.3	37	CCDS3921.1																																																																																			AGA|0.730;-|0.270	0.270	strong		0.305	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
AMBN	258	hgsc.bcm.edu	37	4	71468346	71468348	+	In_Frame_Del	DEL	AGG	AGG	-	rs368655454|rs141384720|rs199556863	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71468346_71468348delAGG	ENST00000322937.6	+	7	640_642	c.537_539delAGG	c.(535-540)ccagga>cca	p.G180del	AMBN_ENST00000449493.2_In_Frame_Del_p.G165del	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	180				G -> R (in Ref. 3; AAG35772 and 4; AAG27036). {ECO:0000305}.	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)			TATAGCTCCCAGGAGTAGATTTT	0.261														603	0.120407	0.1483	0.0749	5008	,	,		15284	0.1577		0.0646	False		,,,				2504	0.1339				p.179_180del		Pindel,Atlas-Indel	.											.	AMBN	73	.	0			c.536_538del						PASS	.			554,3682		46,462,1610						3.3	0.0		dbSNP_134	48	593,7635		24,545,3545	no	coding	AMBN	NM_016519.5		70,1007,5155	A1A1,A1R,RR		7.2071,13.0784,9.2025				1147,11317				SO:0001651	inframe_deletion	258	exon7			.	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.537_539delAGG	4.37:g.71468346_71468348delAGG	ENSP00000313809:p.Gly180del	Somatic	224	.	.		WXS	Illumina HiSeq	Phase_I	199	64	0.322	NM_016519	Q3B862|Q9H2X1|Q9H4L1	In_Frame_Del	DEL	ENST00000322937.6	37	CCDS3543.1																																																																																			AGG|0.889;-|0.111	0.111	strong		0.261	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
MDS2	259283	hgsc.bcm.edu	37	1	23966894	23966895	+	In_Frame_Ins	INS	-	-	AAG	rs371268033|rs3072132|rs5773050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23966894_23966895insAAG	ENST00000374555.3	+	7	865_866	c.278_279insAAG	c.(277-282)gtaaga>gtAAGaaga	p.95_96insR	MDS2_ENST00000477916.1_3'UTR			Q8NDY4	MDS2_HUMAN	myelodysplastic syndrome 2 translocation associated	95						extracellular space (GO:0005615)				breast(1)|ovary(2)	3						Ggtggctttgtaagaagaaaag	0.45			T	ETV6	MDS									1386	0.276757	0.0832	0.4006	5008	,	,		20101	0.4306		0.2505	False		,,,				2504	0.319				.		Pindel,Atlas-Indel	.		Dom	yes		1	1p36	259283	myelodysplastic syndrome 2		L	.	MDS2	4	.	0			.						PASS	.																																			SO:0001652	inframe_insertion	259283	.			.	AJ310434		1p36	2008-02-05			ENSG00000197880	ENSG00000197880			29633	protein-coding gene	gene with protein product		607305				12203785	Standard	NR_027042		Approved		uc001bhi.3	Q8NDY4	OTTHUMG00000002927	ENST00000374555.3:c.282_284dupAAG	1.37:g.23966898_23966900dupAAG	ENSP00000363683:p.Arg95_Arg95dup	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	67	44	0.657	.		RNA	INS	ENST00000374555.3	37																																																																																				-|0.718;AAG|0.282	0.282	strong		0.450	MDS2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008172.1	NM_148895	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140767492	140767497	+	In_Frame_Del	DEL	TGCCAG	TGCCAG	-	rs145222727|rs370380135	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGCCAG	TGCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140767492_140767497delTGCCAG	ENST00000519479.1	+	1	41_46	c.41_46delTGCCAG	c.(40-48)ctgccagtg>ctg	p.PV15del	PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	15					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P15_V16delPV(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGAGAGGCTGCCAGTGCTCTTTCT	0.617											OREG0016859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		166	0.033147	0.0045	0.0476	5008	,	,		16199	0.0		0.0944	False		,,,				2504	0.0327				p.14_15del		Atlas-Indel	.											.	PCDHGB4	125	.	1	Deletion - In frame(1)	prostate(1)	c.40_45del						PASS	.		,,,,,,,,,,,	50,3074		6,38,1518					,,,,,,,,,,,	3.7	0.9		dbSNP_134	6	518,6570		64,390,3090	no	coding,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032098.1,NM_018924.2,NM_018923.2,NM_018922.2,NM_018920.2,NM_018919.2,NM_018918.2,NM_018917.2,NM_018916.3,NM_018915.2,NM_018912.2,NM_003736.2	,,,,,,,,,,,	70,428,4608	A1A1,A1R,RR		7.3081,1.6005,5.5621	,,,,,,,,,,,	,,,,,,,,,,,		568,9644				SO:0001651	inframe_deletion	8641	exon1			.	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.41_46delTGCCAG	5.37:g.140767492_140767497delTGCCAG	ENSP00000428288:p.Pro15_Val16del	Somatic	442	0	0	1658	WXS	Illumina HiSeq	Phase_I	383	46	0.120104	NM_032098	O15099|Q2M267|Q9UN64	In_Frame_Del	DEL	ENST00000519479.1	37	CCDS54928.1																																																																																			.	.	weak		0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
DLX4	1748	hgsc.bcm.edu	37	17	48050500	48050501	+	Frame_Shift_Ins	INS	-	-	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48050500_48050501insC	ENST00000240306.3	+	2	642_643	c.347_348insC	c.(346-351)aagctcfs	p.KL116fs	DLX4_ENST00000411890.2_Frame_Shift_Ins_p.KL44fs|DLX4_ENST00000503410.1_3'UTR	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	116					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CCCGCCAAAAAGCTCCGCAAGC	0.678																																					p.K116fs		Atlas-Indel	.											.	DLX4	25	.	0			c.347_348insC						PASS	.																																			SO:0001589	frameshift_variant	1748	exon2			.		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"""Homeoboxes / ANTP class : NKL subclass"""	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	Exception_encountered	17.37:g.48050500_48050501insC	ENSP00000240306:p.Lys116fs	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	138	10	0.0724638	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Frame_Shift_Ins	INS	ENST00000240306.3	37	CCDS11555.1																																																																																			.	.	none		0.678	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1		
ORC3	23595	hgsc.bcm.edu	37	6	88315742	88315742	+	Intron	DEL	A	A	-	rs397713078|rs2307391|rs201713777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88315742delA	ENST00000392844.3	+	5	475				ORC3_ENST00000417380.2_Intron|ORC3_ENST00000257789.4_Intron|ORC3_ENST00000546266.1_Intron	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3						DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						TTGTCCAGGTAAAAATATAAA	0.363													AAAA|AAAAA|AAAA|insertion	3178	0.634585	0.7526	0.7017	5008	,	,		19964	0.5595		0.5447	False		,,,				2504	0.5971				.		Pindel,Atlas-Indel	.											.	ORC3	51	.	0			c.427+2A>-						PASS	.		,,	3081,1183		1110,861,161	35.0	49.0	44.0		,,	5.4	1.0	6	dbSNP_100	95	4449,3805		1190,2069,868	no	intron,intron,intron	ORC3	NM_181837.2,NM_012381.3,NM_001197259.1	,,	2300,2930,1029	A1A1,A1R,RR		46.0989,27.7439,39.8466	,,	,,	88315742	7530,4988	2201	4298	6499	SO:0001627	intron_variant	23595	exon5			.	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"""origin recognition complex, subunit 3 (yeast homolog)-like"", ""origin recognition complex, subunit 3-like (yeast)"", ""origin recognition complex, subunit 3 honolog (yeast)"""	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.427+3A>-	6.37:g.88315742delA		Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	133	44	0.331	NM_181837	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Splice_Site	DEL	ENST00000392844.3	37	CCDS43486.1																																																																																			A|0.407;-|0.593	0.593	strong		0.363	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2		
Unknown	0	hgsc.bcm.edu	37	7	101988929	101988930	+	IGR	DEL	TG	TG	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:101988929_101988930delTG								Y_RNA (11547 upstream) : PRKRIP1 (15413 downstream)																							ACGGTATAACTGGAACCGACGC	0.569																																					p.315_315del		Atlas-Indel	.											.	SPDYE6	1	.	0			c.944_945del						PASS	.			2,1230		1,0,615							0.0			1	3,2919		1,1,1459	no	frameshift	SPDYE6	NM_001146210.1		2,1,2074	A1A1,A1R,RR		0.1027,0.1623,0.1204				5,4149				SO:0001628	intergenic_variant	729597	exon6			.																													7.37:g.101988929_101988930delTG		Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	686	48	0.0699708	NM_001146210		Frame_Shift_Del	DEL		37																																																																																				.	.	none	0	0.569								
CTSA	5476	hgsc.bcm.edu	37	20	44520238	44520240	+	In_Frame_Del	DEL	CTG	CTG	-	rs3080212|rs11468075|rs10582052|rs397784956|rs397839006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44520238_44520240delCTG	ENST00000372459.2	+	1	224_226	c.31_33delCTG	c.(31-33)ctgdel	p.L19del	NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000372484.3_In_Frame_Del_p.L37del|RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000354880.5_In_Frame_Del_p.L37del|CTSA_ENST00000191018.5_In_Frame_Del_p.L19del			P10619	PPGB_HUMAN	cathepsin A	19				Missing (in Ref. 4; AAH00597). {ECO:0000305}.	glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.L29delL(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				gccgctgttcctgctgctgctgc	0.709														3252	0.649361	0.6868	0.7248	5008	,	,		16739	0.5784		0.6173	False		,,,				2504	0.6513				p.28_29del		Pindel,Atlas-Indel	.											.	CTSA	52	.	1	Deletion - In frame(1)	breast(1)	c.84_86del						PASS	.																																			SO:0001651	inframe_deletion	5476	exon2			.	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.31_33delCTG	20.37:g.44520247_44520249delCTG	ENSP00000361537:p.Leu19del	Somatic	23	.	.		WXS	Illumina HiSeq	Phase_I	40	10	0.250	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	In_Frame_Del	DEL	ENST00000372459.2	37	CCDS46609.1																																																																																			CTG|0.332;-|0.668	0.668	strong		0.709	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73020375	73020376	+	In_Frame_Ins	INS	-	-	CTC	rs113363731|rs79815384|rs376101926|rs139105330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73020375_73020376insCTC	ENST00000263674.3	+	1	1042_1043	c.692_693insCTC	c.(691-696)tgctcc>tgCTCctcc	p.235_236insS	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	235	Poly-Ser.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|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)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CGGGCCTCCTGCTCCTCCTCCT	0.693														1497	0.298922	0.7489	0.1671	5008	,	,		13735	0.0466		0.2068	False		,,,				2504	0.1391				p.C231delinsCS		Pindel,Atlas-Indel	.											.	ARHGEF17	117	.	0			c.692_693insCTC						PASS	.		,	61,2354,1453		19,0,23,836,682,374					,	3.1	1.0		dbSNP_119	18	29,1495,5912		6,0,17,234,1027,2434	no	codingComplex,codingComplex	ARHGEF17,LOC100287837	XM_002343116.2,NM_014786.3	,	25,0,40,1070,1709,2808	A1A1,A1A2,A1R,A2A2,A2R,RR		20.4949,39.1417,34.8461	,	,		90,3849,7365				SO:0001652	inframe_insertion	9828	exon1			.	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.702_704dupCTC	11.37:g.73020382_73020384dupCTC	ENSP00000263674:p.Ser235_Ser235dup	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	162	32	0.198	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	In_Frame_Ins	INS	ENST00000263674.3	37	CCDS8221.1																																																																																			-|0.734;CTC|0.266	0.266	strong		0.693	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
NADK	65220	hgsc.bcm.edu	37	1	1684347	1684348	+	In_Frame_Ins	INS	-	-	CCT	rs139135464|rs71578334|rs150880809		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1684347_1684348insCCT	ENST00000341426.5	-	12	1557_1558	c.1336_1337insAGG	c.(1336-1338)ggc>gAGGgc	p.445_446insE	NADK_ENST00000378625.1_In_Frame_Ins_p.590_591insE|NADK_ENST00000342348.5_In_Frame_Ins_p.413_414insE|NADK_ENST00000341991.3_In_Frame_Ins_p.445_446insE|NADK_ENST00000344463.4_In_Frame_Ins_p.590_591insE	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	445	Poly-Glu.			E -> EE (in Ref. 2; BAB14412). {ECO:0000305}.|G -> EG (in Ref. 3; BAH12420). {ECO:0000305}.	ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		CTTGACCTAGCcctcctcctcc	0.629																																					p.G591delinsEG		Pindel,Atlas-Indel	.											.	NADK	79	.	0			c.1772_1773insAGG						PASS	.																																			SO:0001652	inframe_insertion	65220	exon14			.	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1334_1336dupAGG	1.37:g.1684354_1684356dupCCT	ENSP00000341679:p.Glu445_Glu445dup	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	89	16	0.180	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	In_Frame_Ins	INS	ENST00000341426.5	37	CCDS30565.1																																																																																			.	.	strong		0.629	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
C11orf40	143501	hgsc.bcm.edu	37	11	4594558	4594559	+	Frame_Shift_Ins	INS	-	-	G	rs146711685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4594558_4594559insG	ENST00000307616.1	-	2	284_285	c.285_286insC	c.(283-288)gacaaafs	p.K96fs		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	96										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		CAAGGTCTTTTGTCATCTTCTG	0.485													G|G|GG|insertion	103	0.0205671	0.0015	0.0476	5008	,	,		20680	0.0		0.0547	False		,,,				2504	0.0133				p.K96fs		Pindel,Atlas-Indel	.											.	C11orf40	37	.	0			c.286_287insC						PASS	.			59,4205		2,55,2075						0.3	0.0		dbSNP_134	197	529,7725		20,489,3618	no	frameshift	C11orf40	NM_144663.1		22,544,5693	A1A1,A1R,RR		6.409,1.3837,4.6972				588,11930				SO:0001589	frameshift_variant	143501	exon2			.		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.286dupC	11.37:g.4594559_4594559dupG	ENSP00000302918:p.Lys96fs	Somatic	133	.	.		WXS	Illumina HiSeq	Phase_I	125	41	0.328	NM_144663		Frame_Shift_Ins	INS	ENST00000307616.1	37	CCDS31354.1																																																																																			-|0.969;G|0.031	0.031	strong		0.485	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
OR5K3	403277	hgsc.bcm.edu	37	3	98110406	98110407	+	Frame_Shift_Ins	INS	-	-	A	rs144759043|rs145803525|rs79045298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	30	.	.		WXS	Illumina HiSeq	Phase_I	46	29	0.630	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		
LAD1	3898	hgsc.bcm.edu	37	1	201356005	201356006	+	Frame_Shift_Del	DEL	CC	CC	-	rs552300739|rs148439940|rs386638482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201356005_201356006delCC	ENST00000391967.2	-	3	784_785	c.483_484delGG	c.(481-486)ttggtgfs	p.LV161fs	LAD1_ENST00000367313.3_Frame_Shift_Del_p.LV175fs	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	161						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)	p.V162M(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						TCCCTGCCCACCAAGCTCTCCT	0.584														412	0.0822684	0.1619	0.0144	5008	,	,		14838	0.0486		0.0189	False		,,,				2504	0.1227				p.162_162del		Atlas-Indel	.											LAD1,trunk,malignant_melanoma,-1,1	LAD1	42	1	1	Substitution - Missense(1)	skin(1)	c.484_485del						PASS	.			821,3445		91,639,1403						-10.6	0.0		dbSNP_131	50	704,7548		39,626,3461	no	frameshift	LAD1	NM_005558.3		130,1265,4864	A1A1,A1R,RR		8.5313,19.2452,12.1825				1525,10993				SO:0001589	frameshift_variant	3898	exon3			.	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.483_484delGG	1.37:g.201356005_201356006delCC	ENSP00000375829:p.Leu161fs	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_005558	O95614|Q96GD8	Frame_Shift_Del	DEL	ENST00000391967.2	37	CCDS1410.1																																																																																			.	.	none		0.584	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
TBP	6908	hgsc.bcm.edu	37	6	170871013	170871014	+	In_Frame_Ins	INS	-	-	CAG	rs201732168|rs113202486|rs574714675|rs71010672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:170871013_170871014insCAG	ENST00000392092.2	+	3	468_469	c.189_190insCAG	c.(190-192)cag>CAGcag	p.64_64Q>QQ	TBP_ENST00000230354.6_In_Frame_Ins_p.64_64Q>QQ|TBP_ENST00000540980.1_In_Frame_Ins_p.44_44Q>QQ	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	64	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)	p.Q63_Q64insQ(1)|p.Q63Q(1)		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)		agcaacaacaacagcagcagca	0.55																																					p.Q63delinsQQ		Atlas-Indel	.											TBP,NS,carcinoma,0,5	TBP	58	5	2	Insertion - In frame(1)|Substitution - coding silent(1)	prostate(1)|breast(1)	c.189_190insCAG						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.211_213dupCAG	6.37:g.170871020_170871022dupCAG	ENSP00000375942:p.Gln95dup	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Ins	INS	ENST00000392092.2	37	CCDS5315.1																																																																																			-|0.138;CAG|0.862	0.862	strong		0.550	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560881	160560883	+	In_Frame_Del	DEL	ATG	ATG	-	rs202220802|rs72552763|rs35191146|rs142448543|rs34305973|rs35167514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160560881_160560883delATG	ENST00000366963.4	+	7	1405_1407	c.1258_1260delATG	c.(1258-1260)atgdel	p.M420del	SLC22A1_ENST00000324965.4_In_Frame_Del_p.M420del|SLC22A1_ENST00000457470.2_In_Frame_Del_p.M420del	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	420			Missing (no changes in the MPP uptake. No changes in the MPP uptake; when associated with V-408). {ECO:0000269|PubMed:12439218, ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039}.		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)	CTGCCTCGTCATGATTTTTATCT	0.517														592	0.118211	0.0454	0.2882	5008	,	,		14486	0.005		0.1839	False		,,,				2504	0.1452				p.419_420del		Atlas-Indel	.											SLC22A1,NS,carcinoma,+2,1	SLC22A1	69	1	0			c.1257_1259del	GRCh37	CD072492	SLC22A1	D	rs35191146	PASS	.																																			SO:0001651	inframe_deletion	6580	exon7			.	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.1258_1260delATG	6.37:g.160560881_160560883delATG	ENSP00000355930:p.Met420del	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	47	11	0.234043	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	CCDS5274.1																																																																																			ATG|0.880;-|0.120	0.120	strong		0.517	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937852	88937854	+	In_Frame_Del	DEL	TTT	TTT	-	rs58050565|rs77621374|rs200402481|rs397759922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:88937852_88937854delTTT	ENST00000375963.3	-	13	2983_2985	c.2811_2813delAAA	c.(2809-2814)aaaaat>aat	p.K937del	ZCCHC6_ENST00000277141.6_In_Frame_Del_p.K226del|ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375960.2_In_Frame_Del_p.K814del|ZCCHC6_ENST00000375961.2_In_Frame_Del_p.K937del	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	937				Missing (in Ref. 1; CAI45944/CAH56219). {ECO:0000305}.	RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.N938delN(1)		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						CACAGGTGAATTTTTTTCTTCAC	0.345														2624	0.523962	0.562	0.4899	5008	,	,		19309	0.4792		0.5417	False		,,,				2504	0.5245				p.938_938del		Pindel,Atlas-Indel	.											.	ZCCHC6	105	.	1	Deletion - In frame(1)	large_intestine(1)	c.2812_2814del						PASS	.		,,	2377,1887		665,1047,420					,,	4.1	1.0		dbSNP_129	62	4461,3793		1183,2095,849	no	coding,coding,coding	ZCCHC6	NM_024617.3,NM_001185074.1,NM_001185059.1	,,	1848,3142,1269	A1A1,A1R,RR		45.9535,44.2542,45.3747	,,	,,		6838,5680				SO:0001651	inframe_deletion	79670	exon13			.	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.2811_2813delAAA	9.37:g.88937855_88937857delTTT	ENSP00000365130:p.Lys937del	Somatic	203	.	.		WXS	Illumina HiSeq	Phase_I	176	61	0.347	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	In_Frame_Del	DEL	ENST00000375963.3	37	CCDS35057.1																																																																																			.	.	weak		0.345	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
C10orf85	404216	hgsc.bcm.edu	37	10	122358877	122358878	+	3'UTR	DEL	GA	GA	-	rs71853551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	82	.	.		WXS	Illumina HiSeq	Phase_I	44	29	0.659	.		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		
RBBP6	5930	hgsc.bcm.edu	37	16	24583713	24583718	+	In_Frame_Del	DEL	AAAGAG	AAAGAG	-	rs148143334|rs199567078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAAGAG	AAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24583713_24583718delAAAGAG	ENST00000319715.4	+	18	5758_5763	c.5326_5331delAAAGAG	c.(5326-5331)aaagagdel	p.KE1780del	RBBP6_ENST00000381039.3_In_Frame_Del_p.KE940del|RBBP6_ENST00000348022.2_In_Frame_Del_p.KE1746del	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1780					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		gaacaaagataaagagaaggagaagg	0.311														121	0.0241613	0.0045	0.0375	5008	,	,		24421	0.0		0.0726	False		,,,				2504	0.0164				p.1775_1777del		Atlas-Indel	.											.	RBBP6	158	.	0			c.5325_5330del						PASS	.		,	75,3587		6,63,1762					,	0.7	1.0		dbSNP_134	25	547,6527		74,399,3064	no	coding,coding	RBBP6	NM_018703.3,NM_006910.4	,	80,462,4826	A1A1,A1R,RR		7.7325,2.0481,5.7936	,	,		622,10114				SO:0001651	inframe_deletion	5930	exon18			.		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5326_5331delAAAGAG	16.37:g.24583713_24583718delAAAGAG	ENSP00000317872:p.Lys1780_Glu1781del	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	In_Frame_Del	DEL	ENST00000319715.4	37	CCDS10621.1																																																																																			AAAGAG|0.968;-|0.032	0.032	strong		0.311	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
BPNT1	10380	hgsc.bcm.edu	37	1	220231181	220231181	+	3'UTR	DEL	T	T	-	rs34887640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:220231181delT	ENST00000469520.2	-	0	2381				BPNT1_ENST00000322067.7_3'UTR|BPNT1_ENST00000354807.3_3'UTR			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		TTAAAATTACTGTGAAAAACA	0.318													T|T|-|deletion	1037	0.207069	0.0197	0.2305	5008	,	,		15564	0.2093		0.3588	False		,,,				2504	0.2853				.		Pindel,Atlas-Indel	.											.	BPNT1	29	.	0			.						PASS	.			49,665		19,11,327	1.0	1.0	1.0			1.2	0.0	1	dbSNP_126	1	439,805		197,45,380	no	utr-3	BPNT1	NM_006085.4		216,56,707	A1A1,A1R,RR		35.2894,6.8627,24.9234			220231181	488,1470	244	349	593	SO:0001624	3_prime_UTR_variant	10380	.			.	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.*1005A>-	1.37:g.220231181delT		Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	111	30	0.270	.	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	RNA	DEL	ENST00000469520.2	37	CCDS41469.1																																																																																			T|0.776;-|0.224	0.224	strong		0.318	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085	
ALMS1	7840	hgsc.bcm.edu	37	2	73675227	73675228	+	In_Frame_Ins	INS	-	-	CTC	rs34628045|rs199801824|rs587621330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73675227_73675228insCTC	ENST00000264448.6	+	8	1681_1682	c.1570_1571insCTC	c.(1570-1572)tct>tCTCct	p.524_525insP	ALMS1_ENST00000377715.1_In_Frame_Ins_p.524_525insP|ALMS1_ENST00000409009.1_In_Frame_Ins_p.482_483insP	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	524				S -> SP (in Ref. 1; CAD10391). {ECO:0000305}.	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)		p.S524P(1)		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						GGCTGTAAGTTCTCTAGAAACT	0.421														3007	0.600439	0.2912	0.7046	5008	,	,		17151	0.7847		0.6581	False		,,,				2504	0.6953				p.S524delinsSP		Pindel,Atlas-Indel	.											ALMS1,NS,carcinoma,0,1	ALMS1	384	1	1	Substitution - Missense(1)	pancreas(1)	c.1570_1571insCTC						PASS	.			1351,2331		279,793,769						1.4	0.0		dbSNP_134	97	5015,2861		1592,1831,515	no	coding	ALMS1	NM_015120.4		1871,2624,1284	A1A1,A1R,RR		36.3255,36.692,44.9213				6366,5192				SO:0001652	inframe_insertion	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.1571_1573dupCTC	2.37:g.73675228_73675230dupCTC	ENSP00000264448:p.Ser524_Leu525insPro	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	133	66	0.496	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Ins	INS	ENST00000264448.6	37	CCDS42697.1																																																																																			CTC|1.000;|0.000	1.000	strong		0.421	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106501	31106501	+	Frame_Shift_Del	DEL	C	C	-	rs9278990|rs386698869	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31106501delC	ENST00000259881.9	+	5	401	c.112delC	c.(112-114)cccfs	p.P39fs	PSORS1C1_ENST00000481450.2_Intron|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000547221.1_5'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	39								p.H40fs*3(2)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGAAACTCGTCCCCCCCACGT	0.562														560	0.111821	0.1626	0.1196	5008	,	,		17255	0.0625		0.1491	False		,,,				2504	0.0501				p.R37fs		Pindel,Atlas-Indel	.											.	PSORS1C1	11	.	2	Insertion - Frameshift(2)	ovary(1)|kidney(1)	c.111delT						PASS	.						125.0	129.0	127.0					6																	31106501		1511	2709	4220	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.112delC	6.37:g.31106501delC	ENSP00000259881:p.Pro39fs	Somatic	111	.	.		WXS	Illumina HiSeq	Phase_I	109	43	0.394	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Frame_Shift_Del	DEL	ENST00000259881.9	37	CCDS34390.1																																																																																			.	.	strong		0.562	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
ADM2	79924	hgsc.bcm.edu	37	22	50921149	50921166	+	In_Frame_Del	DEL	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	-	rs559809485|rs72438078|rs3840963|rs199649182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50921149_50921166delACACTCGGGCCCCCGAAG	ENST00000395738.2	+	2	556_573	c.264_281delACACTCGGGCCCCCGAAG	c.(262-282)caacactcgggcccccgaaga>caa	p.HSGPRR95del	ADM2_ENST00000395737.1_In_Frame_Del_p.HSGPRR95del|ADM2_ENST00000362068.2_In_Frame_Del_p.TRAPED6del	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	95					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|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)		GTGGCCGCCAACACTCGGGCCCCCGAAGACACTCGGGC	0.693														589	0.117612	0.0968	0.1686	5008	,	,		17047	0.1915		0.1213	False		,,,				2504	0.0297				p.88_94del		Pindel,Atlas-Indel	.											.	ADM2	15	.	1	Deletion - In frame(1)	breast(1)	c.263_280del						PASS	.			288,3296		54,180,1558						2.4	0.0		dbSNP_130	10	572,6758		74,424,3167	no	coding	ADM2	NM_024866.4		128,604,4725	A1A1,A1R,RR		7.8035,8.0357,7.8798				860,10054				SO:0001651	inframe_deletion	79924	exon3			.	AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"""Endogenous ligands"""	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.264_281delACACTCGGGCCCCCGAAG	22.37:g.50921149_50921166delACACTCGGGCCCCCGAAG	ENSP00000379087:p.His95_Arg100del	Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	105	23	0.219	NM_001253845	Q3LFQ0	In_Frame_Del	DEL	ENST00000395738.2	37	CCDS33682.1																																																																																			ACACTCGGGCCCCCGAAG|0.874;-|0.126	0.126	strong		0.693	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866	
CPNE1	8904	hgsc.bcm.edu	37	20	34215234	34215235	+	Frame_Shift_Ins	INS	-	-	A	rs147019139|rs76294482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34215234_34215235insA	ENST00000317619.3	-	16	1597_1598	c.1203_1204insT	c.(1201-1206)tttgcafs	p.A402fs	CPNE1_ENST00000397445.1_Frame_Shift_Ins_p.A402fs|CPNE1_ENST00000397442.1_Frame_Shift_Ins_p.A402fs|CPNE1_ENST00000397443.1_Frame_Shift_Ins_p.A402fs|CPNE1_ENST00000352393.4_Frame_Shift_Ins_p.A402fs|CPNE1_ENST00000317677.5_Frame_Shift_Ins_p.A407fs|CPNE1_ENST00000397446.1_Frame_Shift_Ins_p.A402fs			Q99829	CPNE1_HUMAN	copine I	402	VWFA.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.A402fs*21(1)		breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GCCTGGGCTGCAAACCTGGCCA	0.589													AAA|AAA|AAAA|insertion	531	0.10603	0.0817	0.1225	5008	,	,		17758	0.0843		0.1014	False		,,,				2504	0.1544				p.A407fs		Pindel,Atlas-Indel	.											.	CPNE1	44	.	1	Insertion - Frameshift(1)	ovary(1)	c.1219_1220insT						PASS	.		,,,,,	385,3879		10,365,1757					,,,,,	5.1	1.0		dbSNP_134	92	873,7381		44,785,3298	yes	frameshift,frameshift,frameshift,frameshift,frameshift,frameshift	CPNE1	NM_152928.2,NM_152927.2,NM_152926.2,NM_152925.2,NM_003915.5,NM_001198863.1	,,,,,	54,1150,5055	A1A1,A1R,RR		10.5767,9.0291,10.0495	,,,,,	,,,,,		1258,11260				SO:0001589	frameshift_variant	8904	exon14			.	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1204dupT	20.37:g.34215237_34215237dupA	ENSP00000326126:p.Ala402fs	Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	76	21	0.276	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Frame_Shift_Ins	INS	ENST00000317619.3	37	CCDS13260.1																																																																																			-|0.911;A|0.089	0.089	strong		0.589	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
ZNF34	80778	hgsc.bcm.edu	37	8	145999617	145999619	+	In_Frame_Del	DEL	TTT	TTT	-	rs3830702|rs79597357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145999617_145999619delTTT	ENST00000343459.4	-	6	780_782	c.715_717delAAA	c.(715-717)aaadel	p.K239del	ZNF34_ENST00000429371.2_In_Frame_Del_p.K218del			Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	239					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11	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)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)		TCTGATCTTCTTTAACAACTAAG	0.389														686	0.136981	0.003	0.1801	5008	,	,		22862	0.3651		0.1004	False		,,,				2504	0.09				p.239_240del		Pindel,Atlas-Indel	.											.	ZNF34	38	.	0			c.716_718del						PASS	.			97,3635		6,85,1775						0.7	0.0		dbSNP_107	57	639,7313		29,581,3366	no	coding	ZNF34	NM_030580.3		35,666,5141	A1A1,A1R,RR		8.0357,2.5991,6.2992				736,10948				SO:0001651	inframe_deletion	80778	exon6			.	BC028136	CCDS47945.1, CCDS69562.1	8q24	2013-01-08	2006-05-11					"""Zinc fingers, C2H2-type"", ""-"""	13098	protein-coding gene	gene with protein product		194526	"""zinc finger protein 34 (KOX 32)"""			8104631, 2014798	Standard	XM_005272349		Approved	KOX32	uc003zdy.4	Q8IZ26		ENST00000343459.4:c.715_717delAAA	8.37:g.145999617_145999619delTTT	ENSP00000341528:p.Lys239del	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	126	40	0.317	NM_030580	D3DWN1|Q9BSZ0	In_Frame_Del	DEL	ENST00000343459.4	37	CCDS47945.1																																																																																			TTT|0.834;-|0.166	0.166	strong		0.389	ZNF34-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382936.1	NM_030580	
NEIL1	79661	hgsc.bcm.edu	37	15	75645966	75645967	+	Intron	DEL	CT	CT	-	rs5745925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75645966_75645967delCT	ENST00000564784.1	+	7	1347				NEIL1_ENST00000355059.4_Intron|MIR631_ENST00000384904.1_RNA|NEIL1_ENST00000569035.1_Intron|RP11-817O13.6_ENST00000563660.1_lincRNA			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)						base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						AGTGTGGCCCCTGACTCAGTCC	0.579								Base excision repair (BER), DNA glycosylases						140	0.0279553	0.0106	0.0476	5008	,	,		19834	0.0		0.0765	False		,,,				2504	0.0164				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			120,4144		1,118,2013						-1.7	0.0		dbSNP_114	92	638,7616		22,594,3511	no	intron	NEIL1	NM_024608.2		23,712,5524	A1A1,A1R,RR		7.7296,2.8143,6.0553				758,11760				SO:0001627	intron_variant	693216	.			.	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.719-113CT>-	15.37:g.75645966_75645967delCT		Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	39	10	0.256	.	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	RNA	DEL	ENST00000564784.1	37	CCDS10278.1																																																																																			CT|0.959;-|0.041	0.041	strong		0.579	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
CACNA1E	777	hgsc.bcm.edu	37	1	181732594	181732594	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:181732594delC	ENST00000367573.2	+	34	4742	c.4742delC	c.(4741-4743)gccfs	p.A1581fs	CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.A1562fs|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.A1513fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.A1581fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.A1188fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.A1532fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.A1562fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1581					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						TTCCGAGCTGCCCGCCTCATA	0.463																																					p.A1581fs		Pindel,Atlas-Indel	.											.	CACNA1E	778	.	0			c.4741delG						PASS	.						84.0	82.0	83.0					1																	181732594		1863	4100	5963	SO:0001589	frameshift_variant	777	exon34			.	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.4742delC	1.37:g.181732594delC	ENSP00000356545:p.Ala1581fs	Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	109	34	0.312	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	37	CCDS55664.1																																																																																			.	.	none		0.463	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
POMZP3	22932	hgsc.bcm.edu	37	7	76240786	76240786	+	Frame_Shift_Del	DEL	A	A	-	rs71819724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76240786delA	ENST00000310842.4	-	6	1244	c.560delT	c.(559-561)ctgfs	p.L187fs	POMZP3_ENST00000275569.4_Intron|UPK3B_ENST00000443097.2_Intron|AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	187										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CTGCGGTTACAGGGAAGCAGA	0.517													-|A|-|insertion	2594	0.517971	0.5333	0.5375	5008	,	,		15695	0.4246		0.5249	False		,,,				2504	0.5726				p.L187fs		Atlas-Indel	.											.	POMZP3	19	.	0			c.561delG						PASS	.		,	2364,1882		761,842,520	51.0	55.0	54.0		,	0.8	0.3	7	dbSNP_130	55	4375,3825		1385,1605,1110	no	intron,frameshift	POMZP3	NM_152992.2,NM_012230.3	,	2146,2447,1630	A1A1,A1R,RR		46.6463,44.3241,45.8541	,	,	76240786	6739,5707	1684	3181	4865	SO:0001589	frameshift_variant	22932	exon6			.	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"""POM-ZP3 fusion protein"", ""POM121/ZP3 fusion protein"""	600587	"""POM (POM121 rat homolog) and ZP3 fusion"", ""POM (POM121 homolog, rat) and ZP3 fusion"""			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.560delT	7.37:g.76240786delA	ENSP00000309233:p.Leu187fs	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_012230	F6STJ3|Q12903|Q9BWB4	Frame_Shift_Del	DEL	ENST00000310842.4	37	CCDS43606.1																																																																																			A|0.541;-|0.459	0.459	strong		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs188283136|rs200434923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37465386_37465390delTGGGG	ENST00000346753.3	-	16	1985		c.e16-2		TMPRSS6_ENST00000381792.2_Splice_Site|TMPRSS6_ENST00000406856.1_Splice_Site|TMPRSS6_ENST00000406725.1_Splice_Site	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						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						GAGGCCATGCtggggtggggtgggg	0.668														2248	0.448882	0.7504	0.2435	5008	,	,		11865	0.4266		0.4036	False		,,,				2504	0.2566				.		Pindel,Atlas-Indel	.											.	TMPRSS6	99	.	0			.						PASS	.			1238,890		571,96,397						5.1	1.0			10	2211,3145		918,375,1385	no	splice-3	TMPRSS6	NM_153609.2		1489,471,1782	A1A1,A1R,RR		41.2808,41.8233,46.085				3449,4035				SO:0001630	splice_region_variant	164656	.			.	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.1869-2CCCCA>-	22.37:g.37465396_37465400delTGGGG		Somatic	51	.	.		WXS	Illumina HiSeq	Phase_I	67	20	0.299	.	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Splice_Site	DEL	ENST00000346753.3	37	CCDS13941.1																																																																																			TGGGG|0.528;-|0.472	0.472	strong		0.668	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	Intron
NBEAL1	65065	hgsc.bcm.edu	37	2	204002925	204002926	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204002925_204002926delAG	ENST00000449802.1	+	29	4852_4853	c.4519_4520delAG	c.(4519-4521)agafs	p.R1507fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1507										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CTCAGAAAACAGAGAAGCAAAA	0.376																																					p.1506_1507del		Pindel,Atlas-Indel	.											.	NBEAL1	266	.	0			c.4518_4519del						PASS	.																																			SO:0001589	frameshift_variant	65065	exon29			.	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.4519_4520delAG	2.37:g.204002927_204002928delAG	ENSP00000399903:p.Arg1507fs	Somatic	165	.	.		WXS	Illumina HiSeq	Phase_I	176	58	0.330	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Del	DEL	ENST00000449802.1	37	CCDS46495.1																																																																																			.	.	none		0.376	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
C14orf23	387978	hgsc.bcm.edu	37	14	29261309	29261310	+	In_Frame_Ins	INS	-	-	AAC	rs79677598|rs71101677|rs56025822|rs151028783	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:29261309_29261310insAAC	ENST00000399387.4	+	3	450_451	c.346_347insAAC	c.(346-348)aaa>aAACaa	p.116_117insQ	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						AGCACTAAAAAAAACAAACAAA	0.381														2112	0.421725	0.3949	0.4683	5008	,	,		16071	0.3998		0.3241	False		,,,				2504	0.5481				.		Pindel,Atlas-Indel	.											.	C14orf23	5	.	0			.						PASS	.																																			SO:0001652	inframe_insertion	387978	.			.			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	Exception_encountered	14.37:g.29261309_29261310insAAC	ENSP00000382318:p.Lys116_Thr117insGln	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	85	17	0.200	.		RNA	INS	ENST00000399387.4	37																																																																																				AAC|1.000	.	strong		0.381	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
MDP1	145553	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610|rs398102305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24683267delA	ENST00000288087.7	-	6	605	c.494delT	c.(493-495)ttgfs	p.L165fs	CHMP4A_ENST00000609024.1_5'Flank|MDP1_ENST00000396833.2_Frame_Shift_Del_p.F118fs|CHMP4A_ENST00000542700.2_5'Flank|MDP1_ENST00000532557.1_5'UTR|TM9SF1_ENST00000556387.1_5'Flank|AL136419.6_ENST00000565988.1_RNA|NEDD8-MDP1_ENST00000604306.1_5'Flank|CHMP4A_ENST00000530996.1_5'Flank|CHMP4A_ENST00000347519.6_5'Flank|TM9SF1_ENST00000530611.1_5'Flank	NM_001199822.1|NM_138476.3	NP_001186751.1|NP_612485.2	Q86V88	MGDP1_HUMAN	magnesium-dependent phosphatase 1	165						extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|large_intestine(2)|lung(3)	7						GCTGGACCTCAAAGGCCCAGT	0.418													AA|AAA|AA|insertion	1020	0.203674	0.4342	0.0807	5008	,	,		23163	0.2123		0.0686	False		,,,				2504	0.1094				p.L182fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.546delG						PASS	.		,,,	1728,2536		344,1040,748	42.0	63.0	56.0		,,,	2.4	0.9	14	dbSNP_134	68	579,7675		25,529,3573	no	frameshift,frameshift,utr-3,frameshift	MDP1,NEDD8-MDP1	NM_138476.3,NM_001199823.1,NM_001199822.1,NM_001199821.1	,,,	369,1569,4321	A1A1,A1R,RR		7.0148,40.5253,18.4295	,,,	,,,	24683267	2307,10211	2162	4299	6461	SO:0001589	frameshift_variant	100528064	exon7			.	BC046912	CCDS9620.1, CCDS55908.1	14q12	2009-07-09			ENSG00000213920	ENSG00000213920			28781	protein-coding gene	gene with protein product	"""fructosamine-6-phosphatase"""					10889041, 16670083	Standard	NM_138476		Approved	MGC5987, FN6Pase		Q86V88	OTTHUMG00000133477	ENST00000288087.7:c.494delT	14.37:g.24683267delA	ENSP00000288087:p.Leu165fs	Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	104	33	0.317	NM_001199823	Q86Y84|Q8NAD9	Frame_Shift_Del	DEL	ENST00000288087.7	37	CCDS9620.1																																																																																			A|0.812;-|0.188	0.188	strong		0.418	MDP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257367.1	NM_138476	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129948	175129955	+	Frame_Shift_Del	DEL	TCTTCTTG	TCTTCTTG	-	rs3208835|rs542219168|rs71563271|rs202239690|rs386636937|rs57794404		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCTTCTTG	TCTTCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:175129948_175129955delTCTTCTTG	ENST00000423313.1	-	4	731_738	c.195_202delCAAGAAGA	c.(193-204)aacaagaagaagfs	p.NKK65fs	KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.NKK65fs|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.NKK65fs	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	ttcttcttcttcttcttgttcttctCTG	0.51																																					p.66_68del		Atlas-Indel	.											.	KIAA0040	2	.	0			c.196_203del						PASS	.																																			SO:0001589	frameshift_variant	9674	exon5			.	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.195_202delCAAGAAGA	1.37:g.175129948_175129955delTCTTCTTG	ENSP00000462172:p.Asn65fs	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	10	0.0884956	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				.	.	none		0.510	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
SETBP1	26040	hgsc.bcm.edu	37	18	42456670	42456671	+	Intron	INS	-	-	TCTT	rs33928380|rs200957852|rs74895636|rs3085861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:42456670_42456671insTCTT	ENST00000282030.5	+	3	836				SETBP1_ENST00000426838.4_Frame_Shift_Ins_p.T228fs	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1							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)		CCGGTTCTCTCACTCTTCCTTT	0.52									Schinzel-Giedion syndrome					2473	0.49381	0.5098	0.4539	5008	,	,		19259	0.4762		0.5616	False		,,,				2504	0.4489				p.L227fs		Pindel,Atlas-Indel	.											.	SETBP1	577	.	0			c.681_682insTCTT						PASS	.		,	1189,1079		386,417,331					,	-7.0	0.0		dbSNP_102	81	2353,2007		767,819,594	no	intron,frameshift	SETBP1	NM_015559.2,NM_001130110.1	,	1153,1236,925	A1A1,A1R,RR		46.0321,47.575,46.56	,	,		3542,3086				SO:0001627	intron_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	.	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.540+7422->TCTT	18.37:g.42456670_42456671insTCTT		Somatic	165	.	.		WXS	Illumina HiSeq	Phase_I	163	51	0.313	NM_001130110	A6H8W5|Q6P6C3|Q9UEF3	Frame_Shift_Ins	INS	ENST00000282030.5	37	CCDS11923.2																																																																																			-|0.500;TCTT|0.500	0.500	strong		0.520	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
LAD1	3898	hgsc.bcm.edu	37	1	201356003	201356006	+	Frame_Shift_Del	DEL	CACC	CACC	-	rs78190062|rs35119736|rs148439940|rs552300739|rs386638482|rs398053706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CACC	CACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201356003_201356006delCACC	ENST00000391967.2	-	3	784_787	c.483_486delGGTG	c.(481-486)ttggtgfs	p.LV161fs	LAD1_ENST00000367313.3_Frame_Shift_Del_p.LV175fs	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	161						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)	p.V162M(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						GCTCCCTGCCCACCAAGCTCTCCT	0.588																																					p.162_163del		Pindel	.											.	LAD1	42	.	1	Substitution - Missense(1)	skin(1)	c.484_487del						PASS	.																																			SO:0001589	frameshift_variant	3898	exon3			.	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.483_486delGGTG	1.37:g.201356003_201356006delCACC	ENSP00000375829:p.Leu161fs	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	141	47	0.333	NM_005558	O95614|Q96GD8	Frame_Shift_Del	DEL	ENST00000391967.2	37	CCDS1410.1																																																																																			.	.	none		0.588	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
CLTCL1	8218	hgsc.bcm.edu	37	22	19189005	19189036	+	Splice_Site	DEL	TACGGATAATAGGGTAGCTCGACTGAGACACT	TACGGATAATAGGGTAGCTCGACTGAGACACT	-	rs375033012|rs368374657|rs1633404|rs202094518|rs367602159|rs144014409|rs200416117|rs546838469|rs368504692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TACGGATAATAGGGTAGCTCGACTGAGACACT	TACGGATAATAGGGTAGCTCGACTGAGACACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19189005_19189036delTACGGATAATAGGGTAGCTCGACTGAGACACT	ENST00000263200.10	-	23	3673		c.e23-1		CLTCL1_ENST00000427926.1_Intron|CLTCL1_ENST00000442042.2_Splice_Site|CLTCL1_ENST00000353891.5_Splice_Site	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1						anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GGTCTCCAACTACGGATAATAGGGTAGCTCGACTGAGACACTCTTCAATGGG	0.483			T	?	ALCL																																.		Pindel	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	8218	.			.		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3601-1AGTGTCTCAGTCGAGCTACCCTATTATCCGTA>-	22.37:g.19189005_19189036delTACGGATAATAGGGTAGCTCGACTGAGACACT		Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	38	12	0.316	.	B7Z7U5|Q14017|Q15808|Q15809	Splice_Site	DEL	ENST00000263200.10	37	CCDS46662.1																																																																																			.	.	none		0.483	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	Intron
ASPN	54829	hgsc.bcm.edu	37	9	95237024	95237025	+	In_Frame_Ins	INS	-	-	TCA	rs113747060|rs71362392|rs111419727|rs3078372|rs397838876|rs376433743|rs557103556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:95237024_95237025insTCA	ENST00000375544.3	-	2	398_399	c.155_156insTGA	c.(154-156)gag>gaTGAg	p.51_52insD	ASPN_ENST00000375543.1_In_Frame_Ins_p.51_52insD|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000395538.3_In_Frame_Ins_p.51_52insD|ASPN_ENST00000450139.2_In_Frame_Ins_p.23_24insD	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	51	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						GAGAGTTGTCCtcatcatcatc	0.396																																					p.E52delinsDE		Pindel	.											.	ASPN	52	.	0			c.156_157insTGA						PASS	.																																			SO:0001652	inframe_insertion	54829	exon2			.	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.153_155dupTGA	9.37:g.95237031_95237033dupTCA	ENSP00000364694:p.Asp52_Asp53dup	Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	111	20	0.180	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	In_Frame_Ins	INS	ENST00000375544.3	37																																																																																				-|0.500;TCA|0.500	0.500	strong		0.396	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129925	175129933	+	In_Frame_Del	DEL	CTTCTTCTT	CTTCTTCTT	-	rs567102553|rs150137790|rs374766108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTTCTTCTT	CTTCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:175129925_175129933delCTTCTTCTT	ENST00000423313.1	-	4	753_761	c.217_225delAAGAAGAAG	c.(217-225)aagaagaagdel	p.KKK73del	KIAA0040_ENST00000545251.2_In_Frame_Del_p.KKK73del|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_In_Frame_Del_p.KKK73del	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	cttcttcatccttcttcttcttcttcttc	0.502																																					p.73_76del		Pindel	.											.	KIAA0040	2	.	0			c.218_226del						PASS	.																																			SO:0001651	inframe_deletion	9674	exon5			.	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.217_225delAAGAAGAAG	1.37:g.175129934_175129942delCTTCTTCTT	ENSP00000462172:p.Lys73_Lys75del	Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	118	21	0.178	NM_001162893	A8K9H6|Q2NKQ0	In_Frame_Del	DEL	ENST00000423313.1	37																																																																																				.	.	strong		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ZNF516	9658	hgsc.bcm.edu	37	18	74090958	74090958	+	Frame_Shift_Del	DEL	G	G	-	rs398079646|rs398033573|rs56087742		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:74090958delG	ENST00000443185.2	-	5	3428	c.3111delC	c.(3109-3111)cccfs	p.P1037fs	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1037					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)		AGTGTAGGACGGGGGGGCGCC	0.652													GGGGGG|GGGGGGG|GGGGGG|insertion	5008	1.0	1.0	1.0	5008	,	,		13278	1.0		1.0	False		,,,				2504	1.0				p.V1038fs		Pindel	.											.	ZNF516	102	.	0			c.3112delG						PASS	.			3517,17		1755,7,5	7.0	7.0	7.0			-0.6	0.0	18	dbSNP_131	33	7701,27		3846,9,9	no	frameshift	ZNF516	NM_014643.3		5601,16,14	A1A1,A1R,RR		0.3494,0.481,0.3907			74090958	11218,44	1730	3829	5559	SO:0001589	frameshift_variant	9658	exon5			.	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.3111delC	18.37:g.74090958delG	ENSP00000394757:p.Pro1037fs	Somatic	19	.	.		WXS	Illumina HiSeq	Phase_I	30	15	0.500	NM_014643		Frame_Shift_Del	DEL	ENST00000443185.2	37																																																																																				G|0.016;-|0.984	0.984	strong		0.652	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
KAT6B	23522	hgsc.bcm.edu	37	10	76781906	76781908	+	In_Frame_Del	DEL	GAA	GAA	-	rs72074375|rs144154275|rs371512199|rs79644703|rs559824889|rs71929101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:76781906_76781908delGAA	ENST00000287239.4	+	16	3778_3780	c.3289_3291delGAA	c.(3289-3291)gaadel	p.E1104del	KAT6B_ENST00000372724.1_In_Frame_Del_p.E812del|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372725.1_In_Frame_Del_p.E812del|KAT6B_ENST00000372711.1_In_Frame_Del_p.E921del|KAT6B_ENST00000372714.1_In_Frame_Del_p.E812del|RP11-77G23.2_ENST00000413431.1_RNA|KAT6B_ENST00000490365.1_3'UTR	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1104	Poly-Glu.				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)	p.E1097E(4)|p.E1097delE(1)									ggaagaagaggaagaagaagaag	0.448											OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2297	0.458666	0.8464	0.2867	5008	,	,		18417	0.373		0.1133	False		,,,				2504	0.5				p.1096_1097del		Pindel	.											MYST4,colon,carcinoma,0,1	.	.	1	5	Substitution - coding silent(4)|Deletion - In frame(1)	ovary(3)|large_intestine(1)|central_nervous_system(1)	c.3288_3290del						PASS	.																																			SO:0001651	inframe_deletion	23522	exon16			.	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.3289_3291delGAA	10.37:g.76781915_76781917delGAA	ENSP00000287239:p.Glu1104del	Somatic	90	.	.	1170	WXS	Illumina HiSeq	Phase_I	105	24	0.229	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	In_Frame_Del	DEL	ENST00000287239.4	37	CCDS7345.1																																																																																			GAA|0.500;-|0.500	0.500	strong		0.448	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
KANK3	256949	hgsc.bcm.edu	37	19	8398950	8398961	+	In_Frame_Del	DEL	TCGCTGTCGCCA	TCGCTGTCGCCA	-	rs111751275|rs199822445|rs201862465|rs6146458|rs200669927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCGCTGTCGCCA	TCGCTGTCGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8398950_8398961delTCGCTGTCGCCA	ENST00000593649.1	-	5	1532_1543	c.1467_1478delTGGCGACAGCGA	c.(1465-1479)gatggcgacagcgag>gag	p.DGDS489del	KANK3_ENST00000330915.3_In_Frame_Del_p.DGDS489del			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	489								p.D489_S492delDGDS(2)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						GCCACCGTTCTCGCTGTCGCCATCGCTGTCGC	0.717														1760	0.351438	0.4085	0.428	5008	,	,		15278	0.2927		0.2962	False		,,,				2504	0.3374				p.490_493del		Pindel	.											.	KANK3	35	.	2	Deletion - In frame(2)	large_intestine(1)|breast(1)	c.1468_1479del						PASS	.			958,2544		287,384,1080						-7.5	0.0		dbSNP_114	6	1402,5766		338,726,2520	no	coding	KANK3	NM_198471.2		625,1110,3600	A1A1,A1R,RR		19.5592,27.3558,22.1181				2360,8310				SO:0001651	inframe_deletion	256949	exon5			.	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.1467_1478delTGGCGACAGCGA	19.37:g.8398950_8398961delTCGCTGTCGCCA	ENSP00000470728:p.Asp489_Ser492del	Somatic	15	.	.		WXS	Illumina HiSeq	Phase_I	11	10	0.909	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	In_Frame_Del	DEL	ENST00000593649.1	37																																																																																				TCGCTGTCGCCA|0.697;-|0.303	0.303	strong		0.717	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
ZFHX3	463	hgsc.bcm.edu	37	16	72822563	72822564	+	In_Frame_Ins	INS	-	-	TGC	rs376311468		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72822563_72822564insTGC	ENST00000268489.5	-	10	10283_10284	c.9611_9612insGCA	c.(9610-9612)caa>caGCAa	p.3204_3204Q>QQ	RP5-991G20.1_ENST00000563328.2_RNA|AC004943.1_ENST00000584072.1_RNA|ZFHX3_ENST00000397992.5_In_Frame_Ins_p.2290_2290Q>QQ|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3204	Poly-Gln.				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)				gcacctgtggttgctgctgctg	0.653																																					p.Q3204delinsQQ		Pindel	.											.	ZFHX3	404	.	0			c.9612_9613insGCA						PASS	.																																			SO:0001652	inframe_insertion	463	exon10			.	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.9609_9611dupGCA	16.37:g.72822570_72822572dupTGC	ENSP00000268489:p.Gln3204dup	Somatic	101	.	.		WXS	Illumina HiSeq	Phase_I	105	16	0.152	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Ins	INS	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	weak		0.653	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																					p.45_45del		Pindel	.											.	KRTAP10-7	41	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.134_134del						PASS	.		,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				SO:0001651	inframe_deletion	386675	exon1			.	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	66	14	0.212	NM_198689	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																				.	.	weak		0.698	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
KDM4A	9682	hgsc.bcm.edu	37	1	44170034	44170035	+	Frame_Shift_Ins	INS	-	-	GGAGTAGGTGCTTCCA			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44170034_44170035insGGAGTAGGTGCTTCCA	ENST00000372396.3	+	22	3322_3323	c.3188_3189insGGAGTAGGTGCTTCCA	c.(3187-3192)atggagfs	p.-1064fs	KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000439057.1_RNA|KDM4A-AS1_ENST00000453015.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A						cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						CGGGCCATCATGGAGTAGGTGC	0.49																																					p.M1063_E1064delinsMEX		Pindel	.											.	KDM4A	74	.	0			c.3188_3189insGGAGTAGGTGCTTCCA						PASS	.																																			SO:0001589	frameshift_variant	9682	exon22			.	AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.3189_3204dupGGAGTAGGTGCTTCCA	1.37:g.44170034_44170035insGGAGTAGGTGCTTCCA	ENSP00000361473:p.Glu1064fs	Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	68	15	0.221	NM_014663	Q5VVB1	Frame_Shift_Ins	INS	ENST00000372396.3	37	CCDS491.1																																																																																			.	.	none		0.490	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663	
OR51B5	282763	hgsc.bcm.edu	37	11	5364542	5364558	+	Frame_Shift_Del	DEL	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	-	rs546965603|rs372207902|rs147062602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364542_5364558delCAGCCCCAGGTCTGTGG	ENST00000300773.2	-	1	251_267	c.197_213delCCACAGACCTGGGGCTG	c.(196-213)gccacagacctggggctgfs	p.ATDLGL66fs	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	66					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)	p.A66fs*48(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGTCAGGGCCAGCCCCAGGTCTGTGGCAGCCAGCAT	0.525														252	0.0503195	0.1377	0.0274	5008	,	,		22155	0.0		0.0457	False		,,,				2504	0.0051				p.66_72del		Pindel	.											.	OR51B5	60	.	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.198_214del						PASS	.			487,3771		28,431,1670						3.6	0.1		dbSNP_134	48	401,7853		15,371,3741	no	frameshift	OR51B5	NM_001005567.2		43,802,5411	A1A1,A1R,RR		4.8583,11.4373,7.0972				888,11624				SO:0001589	frameshift_variant	282763	exon5			.	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.197_213delCCACAGACCTGGGGCTG	11.37:g.5364542_5364558delCAGCCCCAGGTCTGTGG	ENSP00000300773:p.Ala66fs	Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	35	10	0.286	NM_001005567	B2RN59	Frame_Shift_Del	DEL	ENST00000300773.2	37	CCDS31378.1																																																																																			.	.	strong		0.525	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21739333	21739335	+	In_Frame_Del	DEL	GAG	GAG	-	rs201364657		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21739333_21739335delGAG	ENST00000434111.1	+	1	1671_1673	c.1186_1188delGAG	c.(1186-1188)gagdel	p.E397del		NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	397																	TACCCTGCAAGAGGAGAACAAGC	0.665																																					p.395_396del		Pindel	.											.	RIMBP3C	6	.	0			c.1185_1187del						PASS	.																																			SO:0001651	inframe_deletion	150221	exon1			.		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.1186_1188delGAG	22.37:g.21739336_21739338delGAG	ENSP00000407925:p.Glu397del	Somatic	175	.	.		WXS	Illumina HiSeq	Phase_I	177	29	0.164	NM_001128633		In_Frame_Del	DEL	ENST00000434111.1	37	CCDS46668.1																																																																																			GAG|0.990;-|0.010	0.010	strong		0.665	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
ZNF555	148254	hgsc.bcm.edu	37	19	2853905	2853906	+	Frame_Shift_Ins	INS	-	-	GA			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2853905_2853906insGA	ENST00000334241.4	+	4	1980_1981	c.1842_1843insGA	c.(1843-1845)gagfs	p.E615fs	ZNF555_ENST00000591539.1_Frame_Shift_Ins_p.E614fs|AC006130.3_ENST00000589365.1_RNA	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	615					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(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		AGTCACACCAGGAGAGAGATCT	0.391																																					p.Q614fs		Pindel	.											.	ZNF555	61	.	0			c.1842_1843insGA						PASS	.																																			SO:0001589	frameshift_variant	148254	exon4			.	AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"""Zinc fingers, C2H2-type"", ""-"""	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.1849_1850dupGA	19.37:g.2853912_2853913dupGA	ENSP00000334853:p.Glu615fs	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	132	46	0.348	NM_152791	A8KA89|K7EQM2|Q8NA46|Q96MP1	Frame_Shift_Ins	INS	ENST00000334241.4	37	CCDS12096.1																																																																																			.	.	none		0.391	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791	
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-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	ACTCACAGGGGTCACAGACTGATGACCCACAGGGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	116	.	.		WXS	Illumina HiSeq	Phase_I	102	21	0.206	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	
RHBG	57127	hgsc.bcm.edu	37	1	156354348	156354348	+	Frame_Shift_Del	DEL	C	C	-	rs11303415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156354348delC	ENST00000368249.1	+	9	1303	c.1265delC	c.(1264-1266)tccfs	p.S422fs	RHBG_ENST00000368246.2_Splice_Site|RHBG_ENST00000255013.3_Frame_Shift_Del_p.S353fs|RHBG_ENST00000494874.1_Intron|RHBG_ENST00000400992.2_Frame_Shift_Del_p.S390fs	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	72	.	.	1777	WXS	Illumina HiSeq	Phase_I	127	59	0.465	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	
MAP3K1	4214	hgsc.bcm.edu	37	5	56177849	56177851	+	In_Frame_Del	DEL	CAA	CAA	-	rs570353965|rs10552703|rs398064829|rs5868032|rs532800605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:56177849_56177851delCAA	ENST00000399503.3	+	14	2822_2824	c.2822_2824delCAA	c.(2821-2826)tcaaca>tca	p.T949del		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	949	Poly-Thr.				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)		CCTTCTAGTTcaacaacaacaac	0.419																																					p.941_941del		Pindel	.											.	MAP3K1	355	.	0			c.2821_2823del						PASS	.																																			SO:0001651	inframe_deletion	4214	exon14			.	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.2822_2824delCAA	5.37:g.56177858_56177860delCAA	ENSP00000382423:p.Thr949del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	111	25	0.225	NM_005921		In_Frame_Del	DEL	ENST00000399503.3	37	CCDS43318.1																																																																																			CAA|0.500;-|0.500	0.500	strong		0.419	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
ZNF280D	54816	hgsc.bcm.edu	37	15	56946704	56946704	+	Intron	DEL	A	A	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:56946704delA	ENST00000267807.7	-	18	2274				ZNF280D_ENST00000559237.1_Intron|ZNF280D_ENST00000559000.1_Intron	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D						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(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TAATGCCCCTAAAAAAAAAAG	0.284																																					.		Pindel	.											.	ZNF280D	82	.	0			c.2058-2T>-						PASS	.						45.0	44.0	45.0					15																	56946704		2192	4289	6481	SO:0001627	intron_variant	54816	exon19			.	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2058-3T>-	15.37:g.56946704delA		Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	86	13	0.151	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Splice_Site	DEL	ENST00000267807.7	37	CCDS32245.1																																																																																			.	.	none		0.284	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
EFCAB13	124989	hgsc.bcm.edu	37	17	45438887	45438890	+	Splice_Site	DEL	AGTG	AGTG	-	rs10538163|rs201433080|rs55920564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGTG	AGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45438887_45438890delAGTG	ENST00000331493.2	+	10	1216	c.805delAGTG	c.(805-807)agt>gt	p.S269fs	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	269						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										CTATATTGACAGTGAGTTATTTGC	0.328														2236	0.446486	0.5772	0.4135	5008	,	,		17784	0.254		0.5249	False		,,,				2504	0.411				p.268_269del		Pindel	.											.	.	.	.	0			c.804_805del						PASS	.		,	2341,1923		660,1021,451					,	1.8	1.0		dbSNP_119	128	4468,3784		1232,2004,890	no	frameshift-near-splice,intron	C17orf57	NM_152347.4,NM_001195192.1	,	1892,3025,1341	A1A1,A1R,RR		45.8556,45.0985,45.5976	,	,		6809,5707				SO:0001630	splice_region_variant	124989	exon10			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.805+1AGTG>-	17.37:g.45438887_45438890delAGTG		Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	98	28	0.286	NM_152347	G3V128|Q49AG9	Frame_Shift_Del	DEL	ENST00000331493.2	37	CCDS11512.1																																																																																			AGTG|0.561;-|0.439	0.439	strong		0.328	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	Frame_Shift_Del
KDM6B	23135	hgsc.bcm.edu	37	17	7751859	7751864	+	In_Frame_Del	DEL	CACCAC	CACCAC	-	rs59627144|rs377654044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CACCAC	CACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7751859_7751864delCACCAC	ENST00000448097.2	+	11	2584_2589	c.2253_2258delCACCAC	c.(2251-2259)gtcaccacc>gtc	p.TT760del	KDM6B_ENST00000254846.5_In_Frame_Del_p.TT760del			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	760	Pro-rich.|Thr-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						CTGTCGCCGTcaccaccaccaccacc	0.65														750	0.14976	0.0068	0.255	5008	,	,		8183	0.2827		0.0686	False		,,,				2504	0.2147				p.751_753del		Pindel	.											.	KDM6B	95	.	0			c.2252_2257del						PASS	.																																			SO:0001651	inframe_deletion	23135	exon11			.	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.2253_2258delCACCAC	17.37:g.7751865_7751870delCACCAC	ENSP00000412513:p.Thr760_Thr761del	Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	53	12	0.226	NM_001080424	C9IZ40|Q96G33	In_Frame_Del	DEL	ENST00000448097.2	37																																																																																				.	.	weak		0.650	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
POC1B	282809	hgsc.bcm.edu	37	12	89866055	89866064	+	Intron	DEL	AGAAAGAAGA	AGAAAGAAGA	-	rs59139895|rs71082492|rs147832668|rs147021755|rs398055805|rs191378952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGAAAGAAGA	AGAAAGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:89866055_89866064delAGAAAGAAGA	ENST00000313546.3	-	5	581				POC1B_ENST00000549035.1_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000378528.2_Intron	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B						cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						GTGAAAATCTAGAAAGAAGAAGAAAGAAGA	0.367														2704	0.539936	0.6823	0.4784	5008	,	,		11890	0.5456		0.499	False		,,,				2504	0.4274				.		Pindel	.											.	POC1B	41	.	0			.						PASS	.																																			SO:0001627	intron_variant	282809	.			.	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"""WD repeat domain containing"""	30836	protein-coding gene	gene with protein product		614784	"""WD repeat domain 51B"", ""POC1 centriolar protein homolog B (Chlamydomonas)"""	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.453-3TCTTCTTTCT>-	12.37:g.89866065_89866074delAGAAAGAAGA		Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	28	13	0.464	.	G3V1X0	Splice_Site	DEL	ENST00000313546.3	37	CCDS31869.1																																																																																			-|1.000;|0.000	1.000	strong		0.367	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240	
L1TD1	54596	hgsc.bcm.edu	37	1	62675645	62675674	+	In_Frame_Del	DEL	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	-	rs141196718|rs199552452|rs201629799|rs200503897|rs200931139|rs532563709|rs386631745|rs145231033|rs200789118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	CCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62675645_62675674delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	ENST00000498273.1	+	4	1494_1523	c.1199_1228delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	c.(1198-1230)acctcagggctggaggaggaggaggaagagccc>acc	p.SGLEEEEEEP401del	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	401	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						GATGAAGATACCTCAGGGCTggaggaggaggaggaagagccctcagggct	0.535																																					p.400_409del		Pindel	.											L1TD1,NS,carcinoma,-2,1	L1TD1	114	1	0			c.1198_1227del						PASS	.		,	335,3925		13,309,1808					,	-4.7	0.0			50	405,7849		12,381,3734	no	coding,coding	L1TD1	NM_019079.4,NM_001164835.1	,	25,690,5542	A1A1,A1R,RR		4.9067,7.8638,5.9134	,	,		740,11774				SO:0001651	inframe_deletion	54596	exon5			.	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1199_1228delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	1.37:g.62675645_62675674delCCTCAGGGCTGGAGGAGGAGGAGGAAGAGC	ENSP00000419901:p.Ser401_Pro410del	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	80	28	0.350	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	In_Frame_Del	DEL	ENST00000498273.1	37	CCDS619.1																																																																																			.	.	none		0.535	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
ACAA1	30	hgsc.bcm.edu	37	3	38164071	38164073	+	IGR	DEL	ATG	ATG	-	rs398102321|rs144512522|rs61108705|rs199512729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38164071_38164073delATG	ENST00000333167.8	-	0	1785				DLEC1_ENST00000346219.3_In_Frame_Del_p.D1772del|ACAA1_ENST00000480865.1_5'Flank|DLEC1_ENST00000308059.6_3'UTR|Y_RNA_ENST00000365095.1_RNA|DLEC1_ENST00000452631.2_3'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						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)	p.D1772delD(1)		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)		CTAGGCCCTCATGATATGTCCTC	0.527														605	0.120807	0.2549	0.0865	5008	,	,		19346	0.0248		0.1282	False		,,,				2504	0.0552				p.1771_1771del		Pindel	.											.	DLEC1	278	.	1	Deletion - In frame(1)	kidney(1)	c.5311_5313del						PASS	.		,	725,2845		143,439,1203					,	0.7	0.0		dbSNP_129	16	858,6590		127,604,2993	no	coding,utr-3	DLEC1	NM_007337.2,NM_007335.2	,	270,1043,4196	A1A1,A1R,RR		11.5199,20.3081,14.3674	,	,		1583,9435				SO:0001628	intergenic_variant	9940	exon36			.	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		3.37:g.38164071_38164073delATG		Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	32	10	0.312	NM_007337	G5E935|Q96CA6	In_Frame_Del	DEL	ENST00000333167.8	37	CCDS2673.1																																																																																			ATG|0.877;-|0.123	0.123	strong		0.527	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912490	45912492	+	In_Frame_Del	DEL	AAG	AAG	-	rs374686338|rs35729377		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45912490_45912492delAAG	ENST00000309424.3	+	3	1752_1754	c.1264_1266delAAG	c.(1264-1266)aagdel	p.K428del	CD3EAP_ENST00000589804.1_In_Frame_Del_p.K430del|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	428	Poly-Lys.				rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CACATCCACCaagaagaagaaga	0.557																																					p.421_422del		Pindel	.											.	CD3EAP	27	.	0			c.1263_1265del						PASS	.																																			SO:0001651	inframe_deletion	10849	exon3			.	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.1264_1266delAAG	19.37:g.45912499_45912501delAAG	ENSP00000310966:p.Lys428del	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	70	34	0.486	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	In_Frame_Del	DEL	ENST00000309424.3	37	CCDS12661.1																																																																																			.	.	strong		0.557	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
MUC4	4585	hgsc.bcm.edu	37	3	195506713	195506760	+	In_Frame_Del	DEL	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	-	rs62282473|rs550221890|rs62282471|rs200597845|rs201121891|rs9882363|rs192522651|rs62282470|rs554841787|rs201914190|rs200055147|rs181895767|rs374267078|rs199635197|rs201530419|rs200381819|rs201961213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENST00000463781.3	-	2	12150_12197	c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	c.(11689-11739)gcatccacacgtcacgccacccctcttcctgtcaccgacacttcctcagct>gct	p.3897_3913ASTRHATPLPVTDTSSA>A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.3897_3913ASTRHATPLPVTDTSSA>A	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)	p.A3902V(2)|p.P3904S(2)|p.A3902T(1)		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)		ATCTGTGGAAGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGATGCTGAGGAAG	0.593																																					p.3898_3913del		Pindel	.											.	MUC4	1505	.	5	Substitution - Missense(5)	kidney(2)|skin(2)|endometrium(1)	c.11692_11739del						PASS	.		,,	327,1561		144,39,761					,,		0.0			8	1397,2107		610,177,965	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	754,216,1726	A1A1,A1R,RR		39.8687,17.3199,31.9733	,,	,,		1724,3668				SO:0001651	inframe_deletion	4585	exon2			.	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.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	3.37:g.195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENSP00000417498:p.Ala3897_Ser3912del	Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	44	15	0.341	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.593	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SSC5D	284297	hgsc.bcm.edu	37	19	56029616	56029617	+	In_Frame_Ins	INS	-	-	CCA	rs35104581|rs71181782|rs150781976	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		Pindel	.											.	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	54	.	.		WXS	Illumina HiSeq	Phase_I	68	12	0.176	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	
CDCP2	200008	hgsc.bcm.edu	37	1	54605319	54605320	+	Frame_Shift_Ins	INS	-	-	C	rs77544356|rs66812916|rs36013100|rs66537746|rs75306471|rs549857682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:54605319_54605320insC	ENST00000371330.1	-	4	2070_2071	c.1223_1224insG	c.(1222-1224)cccfs	p.P408fs	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_Intron	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	408						extracellular region (GO:0005576)		p.M409fs*>42(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GACCATTCATGGGGGGGGCAGG	0.594													?|-|C|unsure	2403	0.479832	0.3631	0.6614	5008	,	,		16583	0.3889		0.6521	False		,,,				2504	0.4254				p.P408fs		Pindel	.											.	CDCP2	52	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1224_1225insG						PASS	.																																			SO:0001589	frameshift_variant	200008	exon4			.		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.1223_1224insG	1.37:g.54605319_54605320insC	ENSP00000360381:p.Pro408fs	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	66	36	0.545	NM_201546	Q6ZWJ3	Frame_Shift_Ins	INS	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	strong		0.594	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs13005918|rs72362780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENST00000452881.1	+	1	193_219	c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	c.(85-111)cagcagcctagccctgaatccacaccadel	p.QQPSPESTP47del	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000455816.1_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000424440.1_In_Frame_Del_p.QQPSPESTP47del			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	47			Missing.							endometrium(2)|lung(1)	3						TTCCACCTCTCAGCAGCCTAGCCCTGAATCCACACCACAGCAGCCTA	0.564																																					p.28_37del		Pindel	.											.	SPATA3	52	.	0			c.84_110del						PASS	.			924,1842		222,480,681						-8.0	0.0		dbSNP_130	187	2754,2350		871,1012,669	no	coding	SPATA3	NM_139073.3		1093,1492,1350	A1A1,A1R,RR		46.0423,33.4056,46.7344				3678,4192				SO:0001651	inframe_deletion	130560	exon1			.	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.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	2.37:g.231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENSP00000388895:p.Gln47_Pro55del	Somatic	68	.	.		WXS	Illumina HiSeq	Phase_I	58	23	0.397	NM_139073	Q86WX5|Q8N9Y6	In_Frame_Del	DEL	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	strong		0.564	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	IGR	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs3838976|rs199780644|rs3838975|rs562842260|rs139735565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1887092_1887112delGCCCGCCCACCCTGGCTTGGC								TMEM52 (36380 upstream) : C1orf222 (32450 downstream)														p.W736R(1)|p.K733N(1)									GGCCCTCACCGCCCGCCCACCCTGGCTTGGCCTGGCAGCCT	0.643																																					p.732_739del		Pindel	.											.	KIAA1751	92	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.2195_2215del						PASS	.																																			SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887092_1887112delGCCCGCCCACCCTGGCTTGGC		Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	73	14	0.192	NM_001080484		In_Frame_Del	DEL		37																																																																																				-|0.223;G|0.777	0.223	alt	0	0.643								
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280691A>T	ENST00000368799.1	-	3	6706	c.6671T>A	c.(6670-6672)cTg>cAg	p.L2224Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2224	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)			CTGGCCCACCAGTGAGTGTCT	0.542									Ichthyosis				-|||	959	0.191494	0.1936	0.1873	5008	,	,		22319	0.3026		0.0706	False		,,,				2504	0.2014				p.L2224Q		Atlas-SNP	.											FLG,NS,malignant_melanoma,+1,1	FLG	900	1	0			c.T6671A						scavenged	.						260.0	255.0	257.0					1																	152280691		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCACCAGTGAGT	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.6671T>A	1.37:g.152280691A>T	ENSP00000357789:p.Leu2224Gln	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	332	36	0.108434	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	2.028	-0.423196	0.04734	.	.	ENSG00000143631	ENST00000368799	T	0.02656	4.21	0.883	-0.332	0.12675	.	.	.	.	.	T	0.00144	0.0004	N	0.00034	-2.56	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	9	0.08381	T	0.77	.	1.4068	0.02283	0.3248:0.2503:0.0:0.4249	.	2224	P20930	FILA_HUMAN	Q	2224	ENSP00000357789:L2224Q	ENSP00000357789:L2224Q	L	-	2	0	FLG	150547315	0.313000	0.24554	0.000000	0.03702	0.001000	0.01503	-0.556000	0.05992	-0.732000	0.04856	-0.721000	0.03606	CTG	.	.	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ASMTL	8623	hgsc.bcm.edu	37	X	1540706	1540706	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:1540706A>G	ENST00000381317.3	-	9	1122	c.1090T>C	c.(1090-1092)Tac>Cac	p.Y364H	ASMTL_ENST00000381333.4_Missense_Mutation_p.Y348H|ASMTL_ENST00000416733.2_Missense_Mutation_p.Y288H|ASMTL_ENST00000534940.1_Missense_Mutation_p.Y306H	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	364	ASMT-like.			Y -> H (in Ref. 2; BAG63287). {ECO:0000305}.		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)				GATGCCAGGTAGACGTTCGCT	0.498													a|||	401	0.0800719	0.0204	0.0922	5008	,	,		22215	0.0972		0.164	False		,,,				2504	0.0481				p.Y364H		Atlas-SNP	.											.	ASMTL	56	.	0			c.T1090C						PASS	.		HIS/TYR,HIS/TYR,HIS/TYR	164,3892		7,150,1871	348.0	354.0	352.0		916,1042,1090	-1.5	0.0	X	dbSNP_134	352	1313,7073		115,1083,2995	yes	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	83,83,83	122,1233,4866	GG,GA,AA		15.657,4.0434,11.8711	benign,benign,benign	306/564,348/606,364/622	1540706	1477,10965	2028	4193	6221	SO:0001583	missense	8623	exon9			CCAGGTAGACGTT	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.1090T>C	X.37:g.1540706A>G	ENSP00000370718:p.Tyr364His	Somatic	561	1	0.00178253		WXS	Illumina HiSeq	Phase_I	470	467	0.993617	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	230	0.10531135531135531	21	0.042682926829268296	33	0.09116022099447514	65	0.11363636363636363	111	0.14643799472295516	a	4.900	0.167170	0.09339	0.040434	0.15657	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	1.58	-1.51	0.08664	O-methyltransferase, family 2 (1);	0.253860	0.31834	N	0.006989	T	0.00039	0.0001	N	0.25144	0.715	0.09310	N	1	B;B;B	0.22746	0.044;0.074;0.044	B;B;B	0.21360	0.025;0.034;0.024	T	0.34750	-0.9816	10	0.25106	T	0.35	.	6.4899	0.22109	0.8338:0.0:0.1662:0.0	.	288;348;364	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	H	288;306;348;364	ENSP00000410578:Y288H;ENSP00000446410:Y306H;ENSP00000370734:Y348H;ENSP00000370718:Y364H	ENSP00000370718:Y364H	Y	-	1	0	ASMTL	1500706	1.000000	0.71417	0.003000	0.11579	0.028000	0.11728	3.398000	0.52579	-0.341000	0.08376	0.084000	0.15446	TAC	A|0.834;G|0.166	0.166	strong		0.498	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
CHAMP1	283489	hgsc.bcm.edu	37	13	115091399	115091399	+	Silent	SNP	T	T	C	rs9525332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115091399T>C	ENST00000361283.1	+	3	2391	c.2082T>C	c.(2080-2082)tcT>tcC	p.S694S		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	694	Mediates localization to the chromosome and the spindle and negatively regulates chromosome alignment.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CTTTTATCTCTGAAGAGGAGA	0.353													.|||	606	0.121006	0.1452	0.1455	5008	,	,		21177	0.1062		0.0785	False		,,,				2504	0.1299				p.S694S		Atlas-SNP	.											.	.	.	.	0			c.T2082C						PASS	.	C	,,	514,3892	233.9+/-246.9	30,454,1719	80.0	82.0	81.0		2082,2082,2082	0.6	1.0	13	dbSNP_119	81	576,8024	155.2+/-209.3	21,534,3745	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF828	NM_001164144.1,NM_001164145.1,NM_032436.2	,,	51,988,5464	CC,CT,TT		6.6977,11.6659,8.3807	,,	694/813,694/813,694/813	115091399	1090,11916	2203	4300	6503	SO:0001819	synonymous_variant	283489	exon3			TATCTCTGAAGAG	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.2082T>C	13.37:g.115091399T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	37	CCDS9545.1																																																																																			T|0.893;C|0.107	0.107	strong		0.353	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
CCRL2	9034	hgsc.bcm.edu	37	3	46450070	46450070	+	Missense_Mutation	SNP	T	T	A	rs3204849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46450070T>A	ENST00000399036.3	+	2	852	c.500T>A	c.(499-501)tTc>tAc	p.F167Y	CCRL2_ENST00000357392.4_Missense_Mutation_p.F179Y|CCRL2_ENST00000400882.2_Missense_Mutation_p.F167Y|CCRL2_ENST00000400880.3_Missense_Mutation_p.F167Y|RP11-24F11.2_ENST00000451485.1_RNA	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	167			F -> Y (in dbSNP:rs3204849). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16641997, ECO:0000269|PubMed:9473515, ECO:0000269|Ref.2, ECO:0000269|Ref.6}.		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TTGCCTGAATTCGTGGTTTAT	0.478													T|||	1747	0.348842	0.0885	0.379	5008	,	,		20164	0.5615		0.3996	False		,,,				2504	0.408				p.F179Y		Atlas-SNP	.											.	CCRL2	23	.	0			c.T536A						PASS	.	T	TYR/PHE,TYR/PHE	486,3330		23,440,1445	86.0	81.0	83.0		536,500	-7.8	0.0	3	dbSNP_105	83	3245,5035		657,1931,1552	yes	missense,missense	CCRL2	NM_001130910.1,NM_003965.4	22,22	680,2371,2997	AA,AT,TT		39.1908,12.7358,30.8449	benign,benign	179/357,167/345	46450070	3731,8365	1908	4140	6048	SO:0001583	missense	9034	exon2			CTGAATTCGTGGT	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"""GPCR / Class A : Chemokine receptors : Atypical"""	1612	protein-coding gene	gene with protein product	"""atypical chemokine receptor 5"""	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.500T>A	3.37:g.46450070T>A	ENSP00000381994:p.Phe167Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Missense_Mutation	SNP	ENST00000399036.3	37	CCDS43079.1	808	0.36996336996337	52	0.10569105691056911	146	0.40331491712707185	305	0.5332167832167832	305	0.4023746701846966	T	15.21	2.766215	0.49574	0.127358	0.391908	ENSG00000121797	ENST00000399036;ENST00000357392;ENST00000400880;ENST00000433848;ENST00000400882	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	5.4	-7.81	0.01210	GPCR, rhodopsin-like superfamily (1);	1.873720	0.02792	N	0.122158	T	0.00012	0.0000	M	0.67397	2.05	0.80722	P	0.0	P;P	0.40197	0.706;0.642	B;B	0.38954	0.142;0.286	T	0.26710	-1.0095	9	0.87932	D	0	.	3.5343	0.07788	0.1011:0.4167:0.2213:0.2609	rs3204849;rs34060313	179;167	O00421-2;O00421	.;CCRL2_HUMAN	Y	167;179;167;167;167	ENSP00000381994:F167Y;ENSP00000349967:F179Y;ENSP00000383677:F167Y;ENSP00000414957:F167Y;ENSP00000383678:F167Y	ENSP00000349967:F179Y	F	+	2	0	CCRL2	46425074	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.295000	0.19065	-1.990000	0.00978	-0.619000	0.04042	TTC	T|0.631;A|0.369	0.369	strong		0.478	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
ADAM33	80332	hgsc.bcm.edu	37	20	3651742	3651742	+	Silent	SNP	C	C	G	rs528557	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3651742C>G	ENST00000356518.2	-	19	2392	c.2151G>C	c.(2149-2151)ggG>ggC	p.G717G	ADAM33_ENST00000379861.4_Silent_p.G717G|ADAM33_ENST00000350009.2_Silent_p.G691G|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	717					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						CCAGGCCGGCCCCTGGGAGCA	0.672													C|||	1942	0.38778	0.6974	0.1988	5008	,	,		18937	0.25		0.2744	False		,,,				2504	0.362				p.G717G		Atlas-SNP	.											.	ADAM33	76	.	0			c.G2151C						PASS	.	C	,	2757,1639		886,985,327	20.0	24.0	22.0		2151,2073	1.6	0.6	20	dbSNP_83	22	2301,6291		325,1651,2320	no	coding-synonymous,coding-synonymous	ADAM33	NM_025220.2,NM_153202.1	,	1211,2636,2647	GG,GC,CC		26.7807,37.2839,38.9436	,	717/814,691/788	3651742	5058,7930	2198	4296	6494	SO:0001819	synonymous_variant	80332	exon19			GCCGGCCCCTGGG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.2151G>C	20.37:g.3651742C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Silent	SNP	ENST00000356518.2	37	CCDS13058.1																																																																																			C|0.599;G|0.401	0.401	strong		0.672	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
EI24	9538	hgsc.bcm.edu	37	11	125452313	125452313	+	Missense_Mutation	SNP	A	A	G	rs4627097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125452313A>G	ENST00000343678.4	+	10	985	c.743A>G	c.(742-744)cAt>cGt	p.H248R	STT3A-AS1_ENST00000532714.1_RNA|EI24_ENST00000530985.1_3'UTR|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000278903.6_Silent_p.A285A	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	35	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	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	
OR4F4	26682	hgsc.bcm.edu	37	15	102462857	102462857	+	Missense_Mutation	SNP	C	C	T	rs200667206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:102462857C>T	ENST00000326183.3	-	1	441	c.406G>A	c.(406-408)Ggc>Agc	p.G136S		NM_001004195.2	NP_001004195.2	Q96R69	OR4F4_HUMAN	olfactory receptor, family 4, subfamily F, member 4	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			GCCATAATGCCGACACATGCG	0.493													c|||	154	0.0307508	0.0182	0.0187	5008	,	,		39921	0.006		0.0239	False		,,,				2504	0.089				p.G136S		Atlas-SNP	.											OR4F4,NS,carcinoma,0,1	OR4F4	6	1	0			c.G406A						scavenged	.						2.0	2.0	2.0					15																	102462857		514	1891	2405	SO:0001583	missense	26682	exon1			TAATGCCGACACA		CCDS32343.1	15q26.3	2012-08-09			ENSG00000177693	ENSG00000177693		"""GPCR / Class A : Olfactory receptors"""	8301	protein-coding gene	gene with protein product							Standard	NM_001004195		Approved	OR4F18	uc002cdf.1	Q96R69		ENST00000326183.3:c.406G>A	15.37:g.102462857C>T	ENSP00000317482:p.Gly136Ser	Somatic	1380	2	0.00144928		WXS	Illumina HiSeq	Phase_I	1421	155	0.109078	NM_001004195	B2RNI5|Q6IFN9	Missense_Mutation	SNP	ENST00000326183.3	37	CCDS32343.1	.	.	.	.	.	.	.	.	.	.	.	0.556	-0.847333	0.02651	.	.	ENSG00000177693	ENST00000326183	T	0.00063	8.78	2.81	-0.391	0.12446	GPCR, rhodopsin-like superfamily (1);	0.377447	0.19878	N	0.104026	T	0.00073	0.0002	N	0.11341	0.13	0.09310	N	1	B	0.33198	0.401	B	0.25506	0.061	T	0.02721	-1.1119	9	.	.	.	.	4.6638	0.12655	0.3767:0.5061:0.0:0.1172	.	136	Q96R69	OR4F4_HUMAN	S	136	ENSP00000317482:G136S	.	G	-	1	0	OR4F4	100280380	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-2.532000	0.00943	-0.069000	0.12931	0.298000	0.19748	GGC	C|0.972;T|0.028	0.028	strong		0.493	OR4F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417599.1	NM_001004195	
USP10	9100	hgsc.bcm.edu	37	16	84779248	84779248	+	Silent	SNP	T	T	G	rs7185949	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84779248T>G	ENST00000219473.7	+	4	1274	c.1161T>G	c.(1159-1161)gtT>gtG	p.V387V	USP10_ENST00000570191.1_Silent_p.V391V	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	387					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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						TTGTTCCGGTTTCAGAGGATC	0.473													T|||	1163	0.232228	0.0507	0.3948	5008	,	,		20043	0.4038		0.2107	False		,,,				2504	0.2076				p.V391V		Atlas-SNP	.											.	USP10	51	.	0			c.T1173G						PASS	.	T		308,3416		9,290,1563	13.0	14.0	14.0		1161	-4.5	0.7	16	dbSNP_116	14	1783,6445		201,1381,2532	no	coding-synonymous	USP10	NM_005153.2		210,1671,4095	GG,GT,TT		21.6699,8.2707,17.495		387/799	84779248	2091,9861	1862	4114	5976	SO:0001819	synonymous_variant	9100	exon5			TCCGGTTTCAGAG	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.1161T>G	16.37:g.84779248T>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			T|0.769;G|0.231	0.231	strong		0.473	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
PTCHD2	57540	hgsc.bcm.edu	37	1	11561577	11561577	+	Silent	SNP	C	C	T	rs181120200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11561577C>T	ENST00000294484.6	+	2	666	c.528C>T	c.(526-528)ccC>ccT	p.P176P	PTCHD2_ENST00000389575.3_Silent_p.P176P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	176					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)		GCGTCATCCCCGCGGCCTCAC	0.692													C|||	11	0.00219649	0.0015	0.0014	5008	,	,		14434	0.0		0.008	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C528T						PASS	.	C		2,3818		0,2,1908	12.0	15.0	14.0		528	-8.6	0.0	1		14	51,8167		0,51,4058	no	coding-synonymous	PTCHD2	NM_020780.1		0,53,5966	TT,TC,CC		0.6206,0.0524,0.4403		176/1393	11561577	53,11985	1910	4109	6019	SO:0001819	synonymous_variant	57540	exon2			CATCCCCGCGGCC	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.528C>T	1.37:g.11561577C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1																																																																																			C|0.997;T|0.003	0.003	strong		0.692	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
COL4A4	1286	hgsc.bcm.edu	37	2	227946893	227946893	+	Missense_Mutation	SNP	C	C	G	rs1800516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:227946893C>G	ENST00000396625.3	-	23	1841	c.1634G>C	c.(1633-1635)gGt>gCt	p.G545A	COL4A4_ENST00000329662.7_Missense_Mutation_p.G545A	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	545	Triple-helical region.		G -> A (in dbSNP:rs1800516). {ECO:0000269|PubMed:11961012, ECO:0000269|PubMed:9792860}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|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(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCCAGAGGCACCATGCTTTCC	0.413													C|||	103	0.0205671	0.0318	0.0202	5008	,	,		21918	0.0		0.0388	False		,,,				2504	0.0082				p.G545A		Atlas-SNP	.											.	COL4A4	215	.	0			c.G1634C						PASS	.	C	ALA/GLY	125,3751		0,125,1813	208.0	196.0	200.0		1634	5.3	0.9	2	dbSNP_89	200	296,7962		5,286,3838	yes	missense	COL4A4	NM_000092.4	60	5,411,5651	GG,GC,CC		3.5844,3.225,3.4696	probably-damaging	545/1691	227946893	421,11713	1938	4129	6067	SO:0001583	missense	1286	exon23			GAGGCACCATGCT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1634G>C	2.37:g.227946893C>G	ENSP00000379866:p.Gly545Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	58	0.026556776556776556	17	0.034552845528455285	9	0.024861878453038673	0	0.0	32	0.04221635883905013	C	16.55	3.154291	0.57259	0.03225	0.035844	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.99607	-6.27;-6.27	5.34	5.34	0.76211	.	.	.	.	.	D	0.99026	0.9667	H	0.97611	4.04	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	D	0.88502	0.3083	9	0.87932	D	0	.	17.3484	0.87316	0.0:1.0:0.0:0.0	rs1800516;rs52823953	545	P53420	CO4A4_HUMAN	A	545	ENSP00000379866:G545A;ENSP00000328553:G545A	ENSP00000328553:G545A	G	-	2	0	COL4A4	227655137	0.999000	0.42202	0.910000	0.35882	0.164000	0.22412	4.040000	0.57333	2.937000	0.99478	0.650000	0.86243	GGT	C|0.972;G|0.029	0.029	strong		0.413	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
ABRA	137735	hgsc.bcm.edu	37	8	107782065	107782065	+	Silent	SNP	A	A	G	rs13259080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:107782065A>G	ENST00000311955.3	-	1	408	c.354T>C	c.(352-354)taT>taC	p.Y118Y		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			CTCCTCTCTCATAAGTCTTGC	0.522													A|||	930	0.185703	0.0575	0.1859	5008	,	,		18907	0.3581		0.1441	False		,,,				2504	0.2239				p.Y118Y		Atlas-SNP	.											.	ABRA	57	.	0			c.T354C						PASS	.	A		352,4054	180.5+/-208.7	18,316,1869	161.0	143.0	149.0		354	-1.9	1.0	8	dbSNP_121	149	1297,7303	257.2+/-281.3	107,1083,3110	no	coding-synonymous	ABRA	NM_139166.4		125,1399,4979	GG,GA,AA		15.0814,7.9891,12.6788		118/382	107782065	1649,11357	2203	4300	6503	SO:0001819	synonymous_variant	137735	exon1			TCTCTCATAAGTC	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"""striated muscle activator of Rho-dependent signaling"""	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.354T>C	8.37:g.107782065A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																			A|0.847;G|0.153	0.153	strong		0.522	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
HEXDC	284004	hgsc.bcm.edu	37	17	80377690	80377690	+	Silent	SNP	T	T	G	rs1141463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80377690T>G	ENST00000327949.9	+	1	26	c.15T>G	c.(13-15)acT>acG	p.T5T	Y_RNA_ENST00000364369.1_RNA|HEXDC_ENST00000337014.6_Silent_p.T5T|OGFOD3_ENST00000329197.5_5'Flank|HEXDC_ENST00000577944.1_Silent_p.T5T|OGFOD3_ENST00000313056.5_5'Flank			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	5					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)			CAGGTTCCACTCCATTTCAGA	0.438													G|||	2411	0.48143	0.6589	0.3545	5008	,	,		20581	0.7123		0.333	False		,,,				2504	0.2464				p.T5T		Atlas-SNP	.											.	HEXDC	43	.	0			c.T15G						PASS	.	G		2318,1430		723,872,279	90.0	91.0	91.0		15	-8.1	0.0	17	dbSNP_86	91	2446,5726		356,1734,1996	no	coding-synonymous	HEXDC	NM_173620.2		1079,2606,2275	GG,GT,TT		29.9315,38.1537,39.9664		5/586	80377690	4764,7156	1874	4086	5960	SO:0001819	synonymous_variant	284004	exon2			TTCCACTCCATTT	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.15T>G	17.37:g.80377690T>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	214	102	0.476636	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Silent	SNP	ENST00000327949.9	37																																																																																				T|0.535;G|0.465	0.465	strong		0.438	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620	
PTX4	390667	hgsc.bcm.edu	37	16	1536380	1536380	+	Missense_Mutation	SNP	G	G	T	rs2667672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1536380G>T	ENST00000447419.2	-	3	1022	c.997C>A	c.(997-999)Ctg>Atg	p.L333M	PTX4_ENST00000293922.1_Missense_Mutation_p.L328M|PTX4_ENST00000440447.2_Silent_p.P184P			Q96A99	PTX4_HUMAN	pentraxin 4, long	333	Pentaxin.					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						CCGGGCAGCAGGGAGTCTCGG	0.667													G|||	1552	0.309904	0.705	0.1916	5008	,	,		16773	0.0665		0.2306	False		,,,				2504	0.1922				p.L328M		Atlas-SNP	.											.	PTX4	46	.	0			c.C982A						PASS	.	G	MET/LEU	2767,1631	649.8+/-398.9	855,1057,287	50.0	60.0	57.0		982	4.5	0.6	16	dbSNP_100	57	1838,6762	326.9+/-317.6	192,1454,2654	yes	missense	PTX4	NM_001013658.1	15	1047,2511,2941	TT,TG,GG		21.3721,37.085,35.4285	probably-damaging	328/474	1536380	4605,8393	2199	4300	6499	SO:0001583	missense	390667	exon3			GCAGCAGGGAGTC		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.997C>A	16.37:g.1536380G>T	ENSP00000445277:p.Leu333Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		632	0.2893772893772894	336	0.6829268292682927	75	0.20718232044198895	34	0.05944055944055944	187	0.24670184696569922	G	4.294	0.053733	0.08291	0.62915	0.213721	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06294	3.47;3.32	5.5	4.54	0.55810	.	0.426092	0.21261	N	0.077474	T	0.00012	0.0000	M	0.86268	2.805	0.80722	P	0.0	P	0.43826	0.818	B	0.35770	0.21	T	0.06250	-1.0837	9	0.40728	T	0.16	.	9.391	0.38372	0.0:0.1572:0.6798:0.163	rs2667672;rs60531683;rs2667672	328	Q96A99-2	.	M	333;328	ENSP00000445277:L333M;ENSP00000293922:L328M	ENSP00000293922:L328M	L	-	1	2	PTX4	1476381	0.000000	0.05858	0.573000	0.28510	0.006000	0.05464	0.479000	0.22228	1.328000	0.45358	-0.152000	0.13540	CTG	G|0.655;T|0.345	0.345	strong		0.667	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
XYLT2	64132	hgsc.bcm.edu	37	17	48431032	48431032	+	Silent	SNP	G	G	A	rs739990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48431032G>A	ENST00000017003.2	+	2	226	c.177G>A	c.(175-177)gaG>gaA	p.E59E	XYLT2_ENST00000507602.1_Silent_p.E59E	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	59					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					ACCCTGGCGAGGGTTCCAAGG	0.637													G|||	660	0.131789	0.0408	0.2795	5008	,	,		17426	0.0784		0.2147	False		,,,				2504	0.1196				p.E59E		Atlas-SNP	.											XYLT2,NS,carcinoma,0,1	XYLT2	51	1	0			c.G177A						PASS	.	G		317,4071		17,283,1894	16.0	14.0	15.0		177	2.1	1.0	17	dbSNP_86	15	1855,6721		205,1445,2638	no	coding-synonymous	XYLT2	NM_022167.2		222,1728,4532	AA,AG,GG		21.6301,7.2242,16.7541		59/866	48431032	2172,10792	2194	4288	6482	SO:0001819	synonymous_variant	64132	exon2			TGGCGAGGGTTCC	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.177G>A	17.37:g.48431032G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_022167	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	37	CCDS11563.1																																																																																			G|0.851;A|0.149	0.149	strong		0.637	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
PCDHB14	56122	hgsc.bcm.edu	37	5	140605078	140605078	+	Silent	SNP	C	C	T	rs2907322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140605078C>T	ENST00000239449.4	+	1	2001	c.2001C>T	c.(1999-2001)tcC>tcT	p.S667S	PCDHB14_ENST00000515856.2_Silent_p.S514S	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	667	Cadherin 6. {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)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGGCTTCTCCCAGCCCTACC	0.701													c|||	900	0.179712	0.292	0.1412	5008	,	,		12341	0.0933		0.161	False		,,,				2504	0.1636				p.S667S	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C2001T						PASS	.						35.0	41.0	39.0					5																	140605078		2117	4180	6297	SO:0001819	synonymous_variant	56122	exon1			CTTCTCCCAGCCC	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2001C>T	5.37:g.140605078C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.835;T|0.165	0.165	strong		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
C7orf72	100130988	hgsc.bcm.edu	37	7	50173777	50173777	+	Missense_Mutation	SNP	A	A	G	rs998928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:50173777A>G	ENST00000297001.6	+	4	852	c.802A>G	c.(802-804)Acc>Gcc	p.T268A		NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	268				T -> A (in Ref. 2; EAL23902). {ECO:0000305}.				p.T268A(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						ATTGGAAAAAACCGCTGACCC	0.383													G|||	2936	0.586262	0.6702	0.598	5008	,	,		17474	0.745		0.4205	False		,,,				2504	0.4714				p.T268A		Atlas-SNP	.											C7orf72,NS,carcinoma,0,1	C7orf72	26	1	1	Substitution - Missense(1)	kidney(1)	c.A802G						PASS	.	G	ALA/THR	862,522		276,310,106	74.0	66.0	69.0		802	4.8	0.9	7	dbSNP_86	69	1338,1844		283,772,536	yes	missense	C7orf72	NM_001161834.2	58	559,1082,642	GG,GA,AA		42.049,37.7168,48.1822	benign	268/439	50173777	2200,2366	692	1591	2283	SO:0001583	missense	100130988	exon4			GAAAAAACCGCTG		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.802A>G	7.37:g.50173777A>G	ENSP00000297001:p.Thr268Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_001161834	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	37	CCDS47585.1	1284	0.5879120879120879	323	0.6565040650406504	201	0.5552486187845304	431	0.7534965034965035	329	0.4340369393139842	G	0.034	-1.317521	0.01331	0.622832	0.42049	ENSG00000164500	ENST00000297001	.	.	.	5.78	4.79	0.61399	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35425	-0.9789	7	0.08837	T	0.75	.	5.9319	0.19144	0.2545:0.0:0.7455:0.0	rs998928;rs17633607;rs52815494;rs61311333;rs998928	268	A4D263	CG072_HUMAN	A	268	.	ENSP00000297001:T268A	T	+	1	0	C7orf72	50144323	0.935000	0.31712	0.886000	0.34754	0.040000	0.13550	2.477000	0.45180	1.438000	0.47492	-0.128000	0.14901	ACC	A|0.426;G|0.574	0.574	strong		0.383	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
ZNF638	27332	hgsc.bcm.edu	37	2	71654450	71654450	+	Silent	SNP	A	A	G	rs60163900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71654450A>G	ENST00000409544.1	+	24	6081	c.5451A>G	c.(5449-5451)aaA>aaG	p.K1817K	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Silent_p.K757K|ZNF638_ENST00000264447.4_Silent_p.K1817K	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1817					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TGGACACAAAAAAGACAAAAC	0.353													A|||	591	0.118011	0.1369	0.0576	5008	,	,		17859	0.1617		0.0795	False		,,,				2504	0.1299				p.K1817K		Atlas-SNP	.											.	ZNF638	179	.	0			c.A5451G						PASS	.	A	,	621,3785	257.0+/-261.6	46,529,1628	74.0	76.0	75.0		5451,5451	3.3	1.0	2	dbSNP_129	75	782,7818	179.3+/-228.5	41,700,3559	no	coding-synonymous,coding-synonymous	ZNF638	NM_001014972.1,NM_014497.3	,	87,1229,5187	GG,GA,AA		9.093,14.0944,10.7873	,	1817/1979,1817/1979	71654450	1403,11603	2203	4300	6503	SO:0001819	synonymous_variant	27332	exon24			CACAAAAAAGACA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5451A>G	2.37:g.71654450A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			A|0.893;G|0.107	0.107	strong		0.353	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
AKAP13	11214	hgsc.bcm.edu	37	15	86278309	86278309	+	Missense_Mutation	SNP	G	G	A	rs2241268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:86278309G>A	ENST00000394518.2	+	31	7464	c.7369G>A	c.(7369-7371)Ggt>Agt	p.G2457S	AKAP13_ENST00000394510.2_Missense_Mutation_p.G702S|AKAP13_ENST00000361243.2_Missense_Mutation_p.G2461S|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	106	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	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	
MCF2L2	23101	hgsc.bcm.edu	37	3	182897920	182897920	+	Missense_Mutation	SNP	A	A	G	rs35070271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:182897920A>G	ENST00000328913.3	-	28	3341	c.3044T>C	c.(3043-3045)aTg>aCg	p.M1015T	MCF2L2_ENST00000468976.1_5'Flank|MCF2L2_ENST00000473233.1_Missense_Mutation_p.M1015T	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	1015			M -> T (in dbSNP:rs35070271).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AAAGGTGTCCATGGAGCTAAA	0.527													A|||	954	0.190495	0.0953	0.3559	5008	,	,		21609	0.3056		0.171	False		,,,				2504	0.1033				p.M1015T		Atlas-SNP	.											.	MCF2L2	164	.	0			c.T3044C						PASS	.	A	THR/MET	546,3860	247.5+/-255.7	29,488,1686	187.0	186.0	186.0		3044	-4.0	0.0	3	dbSNP_126	186	1164,7436	238.2+/-269.8	81,1002,3217	yes	missense	MCF2L2	NM_015078.2	81	110,1490,4903	GG,GA,AA		13.5349,12.3922,13.1478	benign	1015/1115	182897920	1710,11296	2203	4300	6503	SO:0001583	missense	23101	exon28			GTGTCCATGGAGC	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.3044T>C	3.37:g.182897920A>G	ENSP00000328118:p.Met1015Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	74	0.592	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	486	0.22252747252747251	48	0.0975609756097561	109	0.3011049723756906	189	0.3304195804195804	140	0.18469656992084432	A	7.970	0.748863	0.15710	0.123922	0.135349	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.01725	4.67;4.7	4.3	-3.98	0.04082	.	1.830950	0.02686	N	0.110136	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47262	-0.9131	9	0.13853	T	0.58	.	10.7505	0.46207	0.4031:0.0:0.5969:0.0	rs35070271;rs61750383;rs35070271	1015	Q86YR7	MF2L2_HUMAN	T	1015	ENSP00000328118:M1015T;ENSP00000420070:M1015T	ENSP00000328118:M1015T	M	-	2	0	MCF2L2	184380614	0.000000	0.05858	0.001000	0.08648	0.645000	0.38454	-0.999000	0.03697	-1.047000	0.03242	-0.534000	0.04291	ATG	A|0.833;G|0.167	0.167	strong		0.527	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74206658	74206658	+	Silent	SNP	G	G	A	rs758773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74206658G>A	ENST00000286523.5	-	2	836	c.54C>T	c.(52-54)ttC>ttT	p.F18F	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Silent_p.F18F	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	99	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	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	
KIF27	55582	hgsc.bcm.edu	37	9	86518566	86518566	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:86518566T>C	ENST00000297814.2	-	4	1010	c.867A>G	c.(865-867)tcA>tcG	p.S289S	KIF27_ENST00000413982.1_Silent_p.S289S|KIF27_ENST00000334204.2_Silent_p.S289S	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	289	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						ATGGAATATGTGAACTCTTCC	0.453																																					p.S289S		Atlas-SNP	.											.	KIF27	103	.	0			c.A867G						PASS	.						74.0	79.0	77.0					9																	86518566		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon4			AATATGTGAACTC	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.867A>G	9.37:g.86518566T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	219	96	0.438356	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	37	CCDS6665.1																																																																																			.	.	none		0.453	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
HLA-A	3105	hgsc.bcm.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910693A>G	ENST00000396634.1	+	4	574	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	78	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.Q78R(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGGATAGAGCAGGAGGGGCCG	0.657									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.Q78R		Atlas-SNP	.											HLA-A,bladder,carcinoma,0,8	HLA-A	89	8	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.A233G						scavenged	.						54.0	57.0	56.0					6																	29910693		2203	4299	6502	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TAGAGCAGGAGGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.233A>G	6.37:g.29910693A>G	ENSP00000379873:p.Gln78Arg	Somatic	154	10	0.0649351		WXS	Illumina HiSeq	Phase_I	212	15	0.0707547	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.798	1.179669	0.21787	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00784	5.7;5.7;5.7;5.7	3.72	-4.39	0.03611	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	1.398580	0.06189	N	0.681068	T	0.00815	0.0027	L	0.56280	1.765	0.09310	N	1	B;P;B;P;B	0.42483	0.0;0.781;0.0;0.781;0.0	B;D;B;D;B	0.71184	0.006;0.972;0.01;0.972;0.01	T	0.44952	-0.9294	10	0.87932	D	0	.	0.9552	0.01384	0.3504:0.1689:0.3159:0.1647	rs41559716	78;78;78;78;78	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	78	ENSP00000379873:Q78R;ENSP00000366002:Q78R;ENSP00000366005:Q78R;ENSP00000365998:Q78R	ENSP00000348012:Q78R	Q	+	2	0	HLA-A	30018672	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.990000	0.03732	-0.910000	0.03847	-0.450000	0.05554	CAG	A|0.979;G|0.021	0.021	strong		0.657	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
HLA-C	3107	hgsc.bcm.edu	37	6	31239116	31239116	+	Missense_Mutation	SNP	G	G	A	rs1131119	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31239116G>A	ENST00000376228.5	-	3	367	c.353C>T	c.(352-354)aCc>aTc	p.T118I	HLA-C_ENST00000383329.3_Missense_Mutation_p.T118I	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	118	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						CCTCTGGAGGGTGTGAGACCC	0.687																																					p.T118I		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,6	HLA-C	92	6	0			c.C353T						scavenged	.						17.0	17.0	17.0					6																	31239116		2157	4237	6394	SO:0001583	missense	3107	exon3			TGGAGGGTGTGAG	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.353C>T	6.37:g.31239116G>A	ENSP00000365402:p.Thr118Ile	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	24	7	0.291667	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	423	0.1936813186813187	79	0.16056910569105692	68	0.1878453038674033	152	0.26573426573426573	124	0.16358839050131926	.	9.307	1.054522	0.19907	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00012	9.29;9.29	2.81	1.92	0.25849	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.000000	0.37053	U	0.002274	T	0.00109	0.0003	M	0.88842	2.985	0.58432	P	1.999999999946489E-6	B;B;B;B;B	0.24675	0.109;0.017;0.018;0.046;0.018	P;B;B;B;B	0.45406	0.479;0.25;0.047;0.25;0.047	T	0.03306	-1.1050	9	0.54805	T	0.06	.	9.8074	0.40801	0.0:0.2129:0.787:0.0	rs1131119;rs1131231;rs2308564;rs3177884;rs3177885;rs3190688;rs3190934;rs3177924	118;93;118;118;118	A2AEA4;Q92671;A6H578;A2AEA2;P10321	.;.;.;.;1C07_HUMAN	I	118;118;118;155	ENSP00000365402:T118I;ENSP00000372819:T118I	ENSP00000365402:T118I	T	-	2	0	HLA-C	31347095	0.848000	0.29623	0.562000	0.28370	0.036000	0.12997	2.341000	0.43983	0.732000	0.32470	0.305000	0.20034	ACC	G|0.815;A|0.185	0.185	strong		0.687	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
CD226	10666	hgsc.bcm.edu	37	18	67534642	67534642	+	Missense_Mutation	SNP	C	C	T	rs72481820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:67534642C>T	ENST00000280200.4	-	6	1104	c.836G>A	c.(835-837)aGa>aAa	p.R279K	CD226_ENST00000581982.1_Missense_Mutation_p.R124K|CD226_ENST00000577287.1_Missense_Mutation_p.R124K|CD226_ENST00000582621.1_Missense_Mutation_p.R279K	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	279	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)				CTCTCTCCTTCTCCTTCTGGA	0.353													C|||	363	0.072484	0.0847	0.1009	5008	,	,		16801	0.0288		0.0865	False		,,,				2504	0.0665				p.R279K	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.G836A						PASS	.	C	LYS/ARG	332,4074	173.7+/-203.5	10,312,1881	222.0	220.0	221.0		836	2.8	0.8	18	dbSNP_130	221	622,7978	159.8+/-213.0	23,576,3701	yes	missense	CD226	NM_006566.2	26	33,888,5582	TT,TC,CC		7.2326,7.5352,7.3351	benign	279/337	67534642	954,12052	2203	4300	6503	SO:0001583	missense	10666	exon6			CTCCTTCTCCTTC	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.836G>A	18.37:g.67534642C>T	ENSP00000280200:p.Arg279Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	166	0.076007326007326	45	0.09146341463414634	31	0.0856353591160221	20	0.03496503496503497	70	0.09234828496042216	C	8.882	0.951907	0.18431	0.075352	0.072326	ENSG00000150637	ENST00000280200	T	0.27104	1.69	4.61	2.84	0.33178	.	0.289768	0.31963	N	0.006790	T	0.00468	0.0015	N	0.20986	0.625	0.41481	P	0.01183500000000004	B	0.28900	0.227	B	0.17979	0.02	T	0.17992	-1.0351	9	0.25106	T	0.35	.	8.0181	0.30393	0.0:0.8455:0.0:0.1545	.	279	Q15762	CD226_HUMAN	K	279	ENSP00000280200:R279K	ENSP00000280200:R279K	R	-	2	0	CD226	65685622	0.284000	0.24287	0.818000	0.32626	0.324000	0.28378	0.468000	0.22051	0.886000	0.36113	0.655000	0.94253	AGA	C|0.926;T|0.074	0.074	strong		0.353	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
ACO2	50	hgsc.bcm.edu	37	22	41911525	41911525	+	Silent	SNP	C	C	T	rs1799932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:41911525C>T	ENST00000216254.4	+	5	692	c.670C>T	c.(670-672)Ctg>Ttg	p.L224L	ACO2_ENST00000396512.3_Silent_p.L224L	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	224					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						CCCCTGGGAGCTGAAGTGCCC	0.647													C|||	1354	0.270367	0.1195	0.2767	5008	,	,		14695	0.1994		0.4722	False		,,,				2504	0.3354				p.L224L		Atlas-SNP	.											.	ACO2	58	.	0			c.C670T						PASS	.	C		716,3690	293.0+/-282.3	50,616,1537	33.0	33.0	33.0		670	4.4	1.0	22	dbSNP_89	33	4275,4325	567.6+/-388.9	1094,2087,1119	no	coding-synonymous	ACO2	NM_001098.2		1144,2703,2656	TT,TC,CC		49.7093,16.2506,38.3746		224/781	41911525	4991,8015	2203	4300	6503	SO:0001819	synonymous_variant	50	exon5			TGGGAGCTGAAGT	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"""aconitate hydratase, mitochondrial"""	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.670C>T	22.37:g.41911525C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Silent	SNP	ENST00000216254.4	37	CCDS14017.1																																																																																			C|0.666;T|0.334	0.334	strong		0.647	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098	
PVRL2	5819	hgsc.bcm.edu	37	19	45381649	45381649	+	Intron	SNP	C	C	T	rs373022885		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45381649C>T	ENST00000252483.5	+	6	1042				PVRL2_ENST00000252485.4_Silent_p.D404D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|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)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CCAGTGGCGACGGGGGATTCT	0.612																																					p.D404D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C1212T						PASS	.	C	,	0,4336		0,0,2168	60.0	42.0	48.0		,1212	-2.3	0.0	19		48	1,8497		0,1,4248	no	intron,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	0,1,6416	TT,TC,CC		0.0118,0.0,0.0078	,	,404/480	45381649	1,12833	2168	4249	6417	SO:0001627	intron_variant	5819	exon6			TGGCGACGGGGGA	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1043-3819C>T	19.37:g.45381649C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			.	.	weak		0.612	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
SLC39A4	55630	hgsc.bcm.edu	37	8	145642002	145642002	+	Missense_Mutation	SNP	C	C	T	rs2280838	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145642002C>T	ENST00000301305.3	-	1	277	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	SLC39A4_ENST00000276833.5_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	58			A -> T (in dbSNP:rs2280838). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)			GGCCCGTTGGCGCAGTGCACA	0.692													C|||	2171	0.433506	0.416	0.4236	5008	,	,		14513	0.373		0.5567	False		,,,				2504	0.3998				p.A58T		Atlas-SNP	.											.	SLC39A4	54	.	0			c.G172A						PASS	.	C	THR/ALA	1886,2490		408,1070,710	22.0	21.0	21.0		172	-9.4	0.0	8	dbSNP_100	21	4892,3694		1419,2054,820	yes	missense	SLC39A4	NM_130849.2	58	1827,3124,1530	TT,TC,CC		43.0235,43.0987,47.7087	benign	58/648	145642002	6778,6184	2188	4293	6481	SO:0001583	missense	55630	exon1			CGTTGGCGCAGTG	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.172G>A	8.37:g.145642002C>T	ENSP00000301305:p.Ala58Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	1051	0.48122710622710624	205	0.4166666666666667	172	0.47513812154696133	232	0.40559440559440557	442	0.58311345646438	C	15.35	2.807508	0.50421	0.430987	0.569765	ENSG00000147804	ENST00000301305;ENST00000526658	T;T	0.58652	0.32;0.38	4.71	-9.42	0.00610	.	1.979900	0.02592	N	0.100064	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	0.20907	-1.0261	9	0.10111	T	0.7	-8.2952	5.7065	0.17911	0.1114:0.5786:0.1239:0.1861	rs2280838;rs11553157;rs17855766;rs2280838	58	Q6P5W5	S39A4_HUMAN	T	58	ENSP00000301305:A58T;ENSP00000434512:A58T	ENSP00000301305:A58T	A	-	1	0	SLC39A4	145612810	0.000000	0.05858	0.038000	0.18304	0.845000	0.48019	-2.408000	0.01042	-1.950000	0.01030	-0.683000	0.03753	GCC	C|0.520;T|0.480	0.480	strong		0.692	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
ARID3A	1820	hgsc.bcm.edu	37	19	971949	971949	+	Missense_Mutation	SNP	G	G	A	rs1051505|rs552779877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:971949G>A	ENST00000263620.3	+	9	1993	c.1666G>A	c.(1666-1668)Ggc>Agc	p.G556S		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	556	Gly-rich.|Important for cytoplasmic localization. {ECO:0000250}.		G -> S (in dbSNP:rs1051505). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9780002}.			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)		cggcggcggcggcagcagcag	0.657														3599	0.71865	0.6989	0.6124	5008	,	,		8554	0.5694		0.8618	False		,,,				2504	0.8272				p.G556S	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.G1666A						PASS	.	G	SER/GLY	3346,1052		1274,798,127	24.0	29.0	27.0		1666	-7.2	0.0	19	dbSNP_86	27	7417,1161		3207,1003,79	no	missense	ARID3A	NM_005224.2	56	4481,1801,206	AA,AG,GG		13.5346,23.92,17.0546	benign	556/594	971949	10763,2213	2199	4289	6488	SO:0001583	missense	1820	exon9			GGCGGCGGCAGCA	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.1666G>A	19.37:g.971949G>A	ENSP00000263620:p.Gly556Ser	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	37	CCDS12050.1	1304	0.5970695970695971	298	0.6056910569105691	205	0.5662983425414365	264	0.46153846153846156	537	0.7084432717678101	G	8.079	0.772037	0.16051	0.7608	0.864654	ENSG00000116017	ENST00000263620	T	0.37915	1.17	4.76	-7.15	0.01521	.	0.684797	0.11959	N	0.512882	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30268	-0.9984	9	0.26408	T	0.33	-0.9576	3.7922	0.08726	0.3015:0.115:0.4878:0.0957	rs1051505;rs3170449;rs17846038;rs17857500;rs17859024;rs59930819	556	Q99856	ARI3A_HUMAN	S	556	ENSP00000263620:G556S	ENSP00000263620:G556S	G	+	1	0	ARID3A	922949	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.089000	0.15002	-0.954000	0.03640	-1.439000	0.01073	GGC	G|0.272;A|0.728	0.728	strong		0.657	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
PLXND1	23129	hgsc.bcm.edu	37	3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	rs112755880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:129297255T>C	ENST00000324093.4	-	9	2441	c.2263A>G	c.(2263-2265)Acc>Gcc	p.T755A	PLXND1_ENST00000393239.1_Missense_Mutation_p.T755A	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	755					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						GAGAGCAGGGTCCGGGGGCAG	0.617																																					p.T755A	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2263G						PASS	.	T	ALA/THR	5,4399		0,5,2197	32.0	36.0	35.0		2263	4.6	1.0	3	dbSNP_132	35	30,8566		0,30,4268	yes	missense	PLXND1	NM_015103.2	58	0,35,6465	CC,CT,TT		0.349,0.1135,0.2692	benign	755/1926	129297255	35,12965	2202	4298	6500	SO:0001583	missense	23129	exon9			GCAGGGTCCGGGG	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.2263A>G	3.37:g.129297255T>C	ENSP00000317128:p.Thr755Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	125	81	0.648	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.505945	0.26949	0.001135	0.00349	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33654	1.45;1.4	4.62	4.62	0.57501	.	0.643158	0.13899	N	0.355056	T	0.23572	0.0570	N	0.14661	0.345	0.23581	N	0.997361	B	0.12630	0.006	B	0.06405	0.002	T	0.16600	-1.0397	10	0.87932	D	0	.	10.4209	0.44350	0.0:0.0:0.0:1.0	.	755	Q9Y4D7	PLXD1_HUMAN	A	755	ENSP00000317128:T755A;ENSP00000376931:T755A	ENSP00000317128:T755A	T	-	1	0	PLXND1	130779945	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.729000	0.47327	1.708000	0.51301	0.459000	0.35465	ACC	T|0.997;C|0.003	0.003	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
ANK3	288	hgsc.bcm.edu	37	10	61834573	61834573	+	Silent	SNP	G	G	A	rs17208576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61834573G>A	ENST00000280772.2	-	37	6257	c.6066C>T	c.(6064-6066)gcC>gcT	p.A2022A	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2022					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)			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						TTTCGGAGGCGGCTTTTGCTT	0.418													G|||	158	0.0315495	0.0053	0.049	5008	,	,		19964	0.0		0.1044	False		,,,				2504	0.0123				p.A2022A		Atlas-SNP	.											ANK3,NS,carcinoma,-1,1	ANK3	703	1	0			c.C6066T						PASS	.	G	,,,	85,4321	72.0+/-110.0	3,79,2121	83.0	84.0	84.0		,,,6066	-6.8	0.8	10	dbSNP_123	84	938,7662	207.7+/-249.4	57,824,3419	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	60,903,5540	AA,AG,GG		10.907,1.9292,7.8656	,,,	,,,2022/4378	61834573	1023,11983	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			GGAGGCGGCTTTT	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.6066C>T	10.37:g.61834573G>A		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			G|0.933;A|0.067	0.067	strong		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	32	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	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	
DNAH5	1767	hgsc.bcm.edu	37	5	13900345	13900345	+	Silent	SNP	A	A	G	rs1445823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13900345A>G	ENST00000265104.4	-	15	2333	c.2229T>C	c.(2227-2229)gaT>gaC	p.D743D	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	743	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)					TTTTGTATCTATCTCGTTTCT	0.388									Kartagener syndrome				A|||	3011	0.601238	0.6831	0.5159	5008	,	,		20177	0.8661		0.4493	False		,,,				2504	0.4346				p.D743D		Atlas-SNP	.											.	DNAH5	868	.	0			c.T2229C						PASS	.	A		2887,1519	670.8+/-402.4	953,981,269	81.0	86.0	84.0		2229	-7.2	0.0	5	dbSNP_88	84	3904,4696	544.8+/-384.7	912,2080,1308	no	coding-synonymous	DNAH5	NM_001369.2		1865,3061,1577	GG,GA,AA		45.3953,34.4757,47.7856		743/4625	13900345	6791,6215	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon15	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GTATCTATCTCGT	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.2229T>C	5.37:g.13900345A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.423;G|0.577	0.577	strong		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
B9D2	80776	hgsc.bcm.edu	37	19	41869392	41869392	+	Missense_Mutation	SNP	T	T	C	rs2241714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41869392T>C	ENST00000243578.3	-	2	252	c.33A>G	c.(31-33)atA>atG	p.I11M	CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000413014.2_5'Flank|TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000539627.1_Intron|B9D2_ENST00000601597.1_5'UTR	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	11	B9. {ECO:0000255|PROSITE- ProRule:PRU00713}.		I -> M (in dbSNP:rs2241714). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						CGCTGGCCCCTATGATCTGCC	0.537													C|||	3253	0.649561	0.8608	0.5461	5008	,	,		18734	0.4464		0.675	False		,,,				2504	0.6207				p.I11M		Atlas-SNP	.											.	B9D2	9	.	0			c.A33G						PASS	.	C	MET/ILE	3637,769	310.8+/-291.8	1513,611,79	69.0	58.0	62.0		33	-1.1	0.3	19	dbSNP_98	62	5786,2814	442.9+/-360.2	1943,1900,457	yes	missense	B9D2	NM_030578.3	10	3456,2511,536	CC,CT,TT		32.7209,17.4535,27.5488	benign	11/176	41869392	9423,3583	2203	4300	6503	SO:0001583	missense	80776	exon2			GGCCCCTATGATC	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9		ENST00000243578.3:c.33A>G	19.37:g.41869392T>C	ENSP00000243578:p.Ile11Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_030578		Missense_Mutation	SNP	ENST00000243578.3	37	CCDS12579.1	1421	0.6506410256410257	419	0.8516260162601627	213	0.5883977900552486	276	0.4825174825174825	513	0.6767810026385225	C	11.10	1.538474	0.27475	0.825465	0.672791	ENSG00000123810	ENST00000243578	T	0.69926	-0.44	5.08	-1.13	0.09775	.	0.463445	0.22241	N	0.062693	T	0.00012	0.0000	L	0.55103	1.725	0.36668	P	0.12166299999999997	B	0.06786	0.001	B	0.10450	0.005	T	0.19679	-1.0298	9	0.46703	T	0.11	.	5.3714	0.16142	0.1756:0.4159:0.0:0.4086	rs2241714;rs17856099;rs17856116;rs60400278;rs2241714	11	Q9BPU9	B9D2_HUMAN	M	11	ENSP00000243578:I11M	ENSP00000243578:I11M	I	-	3	3	B9D2	46561232	0.258000	0.24033	0.296000	0.24974	0.829000	0.46940	-0.226000	0.09139	-0.144000	0.11314	-0.320000	0.08662	ATA	T|0.311;C|0.689	0.689	strong		0.537	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578	
COG3	83548	hgsc.bcm.edu	37	13	46067593	46067593	+	Silent	SNP	G	G	A	rs2985959	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:46067593G>A	ENST00000349995.5	+	12	1411	c.1299G>A	c.(1297-1299)gaG>gaA	p.E433E	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	433					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.E433E(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTAAAAATGAGGTGCTTGAAG	0.343													G|||	1805	0.360423	0.1551	0.3818	5008	,	,		15875	0.495		0.4175	False		,,,				2504	0.4254				p.E433E	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											COG3,NS,carcinoma,0,1	COG3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.G1299A						PASS	.	G		996,3410	373.7+/-320.9	117,762,1324	152.0	142.0	145.0		1299	3.7	1.0	13	dbSNP_101	145	3797,4803	538.1+/-383.3	856,2085,1359	no	coding-synonymous	COG3	NM_031431.3		973,2847,2683	AA,AG,GG		44.1512,22.6055,36.8522		433/829	46067593	4793,8213	2203	4300	6503	SO:0001819	synonymous_variant	83548	exon12			AAATGAGGTGCTT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1299G>A	13.37:g.46067593G>A		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																			G|0.624;A|0.376	0.376	strong		0.343	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
MGAM	8972	hgsc.bcm.edu	37	7	141752215	141752215	+	Missense_Mutation	SNP	A	A	C	rs386718585|rs116536012	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141752215A>C	ENST00000549489.2	+	25	3022	c.2927A>C	c.(2926-2928)gAa>gCa	p.E976A	MGAM_ENST00000475668.2_Missense_Mutation_p.E976A	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	976	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				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.E976A(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)	GCTTCTGCCGAAAACTGCACT	0.458													a|||	322	0.0642971	0.1339	0.0706	5008	,	,		18996	0.0198		0.0398	False		,,,				2504	0.0368				p.E976A		Atlas-SNP	.											MGAM_ENST00000473011,NS,carcinoma,0,1	MGAM	767	1	1	Substitution - Missense(1)	stomach(1)	c.A2927C						PASS	.	A	ALA/GLU	347,3559		20,307,1626	74.0	68.0	70.0		2927	0.9	0.0	7	dbSNP_132	70	183,8101		4,175,3963	no	missense	MGAM	NM_004668.2	107	24,482,5589	CC,CA,AA		2.2091,8.8838,4.3478	benign	976/1858	141752215	530,11660	1953	4142	6095	SO:0001583	missense	8972	exon25			CTGCCGAAAACTG	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.2927A>C	7.37:g.141752215A>C	ENSP00000447378:p.Glu976Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	111	0.050824175824175824	55	0.11178861788617886	17	0.04696132596685083	16	0.027972027972027972	23	0.030343007915567283	A	10.88	1.476265	0.26511	0.088838	0.022091	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	T	0.13778	2.56	4.64	0.889	0.19212	P-type trefoil (4);	0.964184	0.08439	N	0.945705	T	0.00178	0.0005	N	0.11313	0.125	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.41270	-0.9518	10	0.30854	T	0.27	.	13.2332	0.59955	0.2851:0.7149:0.0:0.0	.	976	O43451	MGA_HUMAN	A	976;976;853	ENSP00000447378:E976A	ENSP00000316431:E853A	E	+	2	0	MGAM	141398684	0.044000	0.20184	0.001000	0.08648	0.187000	0.23431	0.456000	0.21859	-0.095000	0.12351	0.377000	0.23210	GAA	A|0.956;C|0.044	0.044	strong		0.458	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
RPL36AL	6166	hgsc.bcm.edu	37	14	50085571	50085571	+	Silent	SNP	G	G	A	rs1054427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50085571G>A	ENST00000298289.6	-	2	411	c.252C>T	c.(250-252)gcC>gcT	p.A84A	MGAT2_ENST00000305386.2_5'Flank|RP11-649E7.5_ENST00000555043.1_RNA	NM_001001.4	NP_000992.1	Q969Q0	RL36L_HUMAN	ribosomal protein L36a-like	84					translation (GO:0006412)	ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)					all_epithelial(31;0.0021)|Breast(41;0.0124)					ATCTCTTAATGGCCAGCATCC	0.418													G|||	857	0.171126	0.261	0.3141	5008	,	,		20139	0.0258		0.2286	False		,,,				2504	0.0389				p.Q84H		Atlas-SNP	.											.	RPL36AL	6	.	0			c.A252T						PASS	.	G		1118,3284		139,840,1222	81.0	82.0	82.0		252	2.9	1.0	14	dbSNP_86	82	1868,6730		219,1430,2650	no	coding-synonymous	RPL36AL	NM_001001.3		358,2270,3872	AA,AG,GG		21.726,25.3975,22.9692		84/107	50085571	2986,10014	2201	4299	6500	SO:0001819	synonymous_variant	6166	exon2			CTTAATGGCCAGC	BC000741	CCDS9689.1	14q21	2008-08-29	2002-01-15	2002-01-18	ENSG00000165502	ENSG00000165502		"""L ribosomal proteins"""	10346	protein-coding gene	gene with protein product		180469	"""ribosomal protein L36a"""	RPL36A		1577483	Standard	NM_001001		Approved		uc001wwq.2	Q969Q0	OTTHUMG00000152330	ENST00000298289.6:c.252C>T	14.37:g.50085571G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_001001	Q3B7A5	Missense_Mutation	SNP	ENST00000298289.6	37	CCDS9689.1																																																																																			G|0.250;A|0.750	0.750	weak		0.418	RPL36AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276808.2		
UNC13C	440279	hgsc.bcm.edu	37	15	54919047	54919047	+	Silent	SNP	A	A	G	rs1520411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:54919047A>G	ENST00000260323.11	+	32	6381	c.6381A>G	c.(6379-6381)cgA>cgG	p.R2127R	UNC13C_ENST00000539562.2_Silent_p.R48R|UNC13C_ENST00000537900.1_Silent_p.R2125R|UNC13C_ENST00000545554.1_Silent_p.R2127R	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2127	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AGGAAAATCGACCAGGGGCTT	0.388													A|||	2740	0.547125	0.3033	0.5533	5008	,	,		18490	0.6657		0.664	False		,,,				2504	0.6299				p.R2127R		Atlas-SNP	.											UNC13C_ENST00000260323,NS,carcinoma,+2,2	UNC13C	674	2	0			c.A6381G						PASS	.	A		1368,2308		239,890,709	53.0	46.0	48.0		6381	-3.2	0.7	15	dbSNP_88	48	5319,2833		1740,1839,497	no	coding-synonymous	UNC13C	NM_001080534.1		1979,2729,1206	GG,GA,AA		34.7522,37.2144,43.4647		2127/2215	54919047	6687,5141	1838	4076	5914	SO:0001819	synonymous_variant	440279	exon31			AAATCGACCAGGG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.6381A>G	15.37:g.54919047A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	28	0.277228	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			A|0.436;G|0.564	0.564	strong		0.388	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8792171T>C	ENST00000447110.1	-	10	1057	c.933A>G	c.(931-933)ctA>ctG	p.L311L	PIK3R5_ENST00000581552.1_Silent_p.L311L|PIK3R5_ENST00000584803.1_Silent_p.L311L	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	311				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	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)	p.L311L(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CTGGCTGGAGTAGCTCCTGTT	0.582													C|||	1017	0.203075	0.2995	0.2839	5008	,	,		20122	0.001		0.2843	False		,,,				2504	0.1401				p.L311L	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											PIK3R5,NS,carcinoma,0,1	PIK3R5	79	1	2	Substitution - coding silent(2)	prostate(2)	c.A933G						PASS	.	C	,	1302,3104	692.1+/-405.5	204,894,1105	51.0	56.0	54.0		933,933	3.7	1.0	17	dbSNP_120	54	2695,5905	681.3+/-403.7	418,1859,2023	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	622,2753,3128	CC,CT,TT		31.3372,29.5506,30.732	,	311/881,311/881	8792171	3997,9009	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CTGGAGTAGCTCC	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.933A>G	17.37:g.8792171T>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			T|0.722;C|0.278	0.278	strong		0.582	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
NAGPA	51172	hgsc.bcm.edu	37	16	5075633	5075633	+	Missense_Mutation	SNP	G	G	A	rs7188856	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5075633G>A	ENST00000312251.3	-	10	1413	c.1394C>T	c.(1393-1395)aCt>aTt	p.T465I	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Missense_Mutation_p.T431I	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	465			T -> I (in dbSNP:rs7188856). {ECO:0000269|PubMed:10551838}.		carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	GTTTGCTGCAGTGCTGATCAG	0.642													G|||	1006	0.200879	0.0893	0.2997	5008	,	,		17690	0.1736		0.3419	False		,,,				2504	0.1646				p.T465I		Atlas-SNP	.											.	NAGPA	30	.	0			c.C1394T						PASS	.	G	ILE/THR	586,3806	257.4+/-261.8	30,526,1640	34.0	36.0	36.0		1394	-3.2	0.0	16	dbSNP_116	36	3005,5595	460.3+/-365.1	531,1943,1826	yes	missense	NAGPA	NM_016256.3	89	561,2469,3466	AA,AG,GG		34.9419,13.3424,27.6401	possibly-damaging	465/516	5075633	3591,9401	2196	4300	6496	SO:0001583	missense	51172	exon10			GCTGCAGTGCTGA	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1394C>T	16.37:g.5075633G>A	ENSP00000310998:p.Thr465Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	172	172	1	NM_016256	B2RAS1|Q96EJ8	Missense_Mutation	SNP	ENST00000312251.3	37	CCDS10527.1	498	0.22802197802197802	49	0.09959349593495935	99	0.27348066298342544	94	0.16433566433566432	256	0.33773087071240104	G	0.034	-1.317453	0.01331	0.133424	0.349419	ENSG00000103174	ENST00000312251;ENST00000381955	T;T	0.24151	2.28;1.87	5.18	-3.19	0.05171	.	1.101780	0.06824	N	0.792789	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.37430	-0.9706	9	0.52906	T	0.07	0.3722	11.7169	0.51659	0.5135:0.0:0.4865:0.0	rs7188856;rs17634473;rs7188856	465;431	Q9UK23;Q9UK23-2	NAGPA_HUMAN;.	I	465;431	ENSP00000310998:T465I;ENSP00000371381:T431I	ENSP00000310998:T465I	T	-	2	0	NAGPA	5015634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.505000	0.02273	-1.423000	0.02002	-1.134000	0.01955	ACT	G|0.758;A|0.242	0.242	strong		0.642	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256	
RCBTB1	55213	hgsc.bcm.edu	37	13	50134150	50134150	+	Silent	SNP	A	A	G	rs17073150	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50134150A>G	ENST00000378302.2	-	5	608	c.348T>C	c.(346-348)atT>atC	p.I116I	RCBTB1_ENST00000258646.3_Silent_p.I116I|RCBTB1_ENST00000546015.1_Silent_p.I116I	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	116					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GGACGGGAGCAATGCCTTGGT	0.502													A|||	1517	0.302915	0.4955	0.1311	5008	,	,		16926	0.2768		0.167	False		,,,				2504	0.3313				p.I116I		Atlas-SNP	.											.	RCBTB1	34	.	0			c.T348C						PASS	.	A		1956,2450	553.6+/-378.8	426,1104,673	230.0	224.0	226.0		348	2.5	1.0	13	dbSNP_123	226	1257,7343	249.6+/-276.8	80,1097,3123	no	coding-synonymous	RCBTB1	NM_018191.3		506,2201,3796	GG,GA,AA		14.6163,44.394,24.704		116/532	50134150	3213,9793	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon5			GGGAGCAATGCCT	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.348T>C	13.37:g.50134150A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	153	83	0.542484	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			A|0.751;G|0.249	0.249	strong		0.502	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
RTCB	51493	hgsc.bcm.edu	37	22	32784051	32784051	+	Silent	SNP	T	T	C	rs11635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32784051T>C	ENST00000216038.5	-	12	1544	c.1446A>G	c.(1444-1446)gtA>gtG	p.V482V	RTCB_ENST00000451746.2_3'UTR|RP1-149A16.17_ENST00000444848.1_lincRNA	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		GGCAGGTATTTACCACATCTG	0.443													T|||	817	0.163139	0.0915	0.0893	5008	,	,		19332	0.4593		0.0467	False		,,,				2504	0.1268				p.V482V		Atlas-SNP	.											.	C22orf28	43	.	0			c.A1446G						PASS	.	T		451,3955	212.5+/-232.4	26,399,1778	156.0	130.0	139.0		1446	1.5	1.0	22	dbSNP_52	139	486,8114	140.9+/-197.4	11,464,3825	no	coding-synonymous	C22orf28	NM_014306.4		37,863,5603	CC,CT,TT		5.6512,10.236,7.2044		482/506	32784051	937,12069	2203	4300	6503	SO:0001819	synonymous_variant	51493	exon12			GGTATTTACCACA	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1446A>G	22.37:g.32784051T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	139	78	0.561151	NM_014306		Silent	SNP	ENST00000216038.5	37	CCDS13905.1																																																																																			T|0.883;C|0.117	0.117	strong		0.443	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
PRDM1	639	hgsc.bcm.edu	37	6	106543533	106543533	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106543533G>A	ENST00000369096.4	+	3	569	c.335G>A	c.(334-336)cGt>cAt	p.R112H	PRDM1_ENST00000369091.2_Missense_Mutation_p.R76H	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	112	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		AAGGGCACACGTTTTGGACCC	0.363			"""D, N, Mis, F, S"""		DLBCL																																p.R112H		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	0			c.G335A						PASS	.						97.0	91.0	93.0					6																	106543533		2203	4300	6503	SO:0001583	missense	639	exon3			GCACACGTTTTGG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.335G>A	6.37:g.106543533G>A	ENSP00000358092:p.Arg112His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	6	0.0882353	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	35	5.532045	0.96446	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278	T;T	0.73363	-0.74;-0.74	6.06	6.06	0.98353	SET domain (3);	0.052943	0.85682	D	0.000000	D	0.83968	0.5369	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83781	0.0225	10	0.87932	D	0	-14.1659	20.6208	0.99490	0.0:0.0:1.0:0.0	.	112	O75626	PRDM1_HUMAN	H	76;112;76	ENSP00000358087:R76H;ENSP00000358092:R112H	ENSP00000358087:R76H	R	+	2	0	PRDM1	106650226	1.000000	0.71417	0.890000	0.34922	0.962000	0.63368	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	CGT	.	.	none		0.363	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
ZSWIM3	140831	hgsc.bcm.edu	37	20	44506418	44506418	+	Silent	SNP	G	G	A	rs1045493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44506418G>A	ENST00000255152.2	+	2	1430	c.1221G>A	c.(1219-1221)cgG>cgA	p.R407R	ZSWIM3_ENST00000454862.2_Silent_p.R401R	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	407							zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				GCCTCTTTCGGGAACAGCAGT	0.493													G|||	2389	0.477037	0.3268	0.6441	5008	,	,		22282	0.4573		0.5517	False		,,,				2504	0.5051				p.R407R		Atlas-SNP	.											.	ZSWIM3	96	.	0			c.G1221A						PASS	.	G		1739,2667	519.6+/-370.0	352,1035,816	86.0	69.0	74.0		1221	2.5	0.7	20	dbSNP_86	74	4836,3764	615.5+/-396.4	1367,2102,831	no	coding-synonymous	ZSWIM3	NM_080752.3		1719,3137,1647	AA,AG,GG		43.7674,39.4689,49.4464		407/697	44506418	6575,6431	2203	4300	6503	SO:0001819	synonymous_variant	140831	exon2			CTTTCGGGAACAG	AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"""Zinc fingers, SWIM-type"""	16157	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 174"""		"""chromosome 20 open reading frame 164"""	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.1221G>A	20.37:g.44506418G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_080752	Q9BR13	Silent	SNP	ENST00000255152.2	37	CCDS13381.1																																																																																			G|0.506;A|0.494	0.494	strong		0.493	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752	
OPN4	94233	hgsc.bcm.edu	37	10	88414570	88414570	+	Silent	SNP	G	G	A	rs11202106	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88414570G>A	ENST00000241891.5	+	1	197	c.30G>A	c.(28-30)ccG>ccA	p.P10P	OPN4_ENST00000372071.2_Silent_p.P10P	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	10			P -> L (in dbSNP:rs2675703). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CAAGAGTCCCGCCCAGCCCAA	0.642													G|||	1182	0.236022	0.062	0.1758	5008	,	,		15979	0.2778		0.3022	False		,,,				2504	0.4029				p.P10P		Atlas-SNP	.											OPN4,NS,carcinoma,+1,1	OPN4	61	1	0			c.G30A						PASS	.	G	,	432,3974	207.8+/-229.1	21,390,1792	65.0	66.0	66.0		30,30	-9.3	0.0	10	dbSNP_120	66	2819,5781	443.7+/-360.5	483,1853,1964	no	coding-synonymous,coding-synonymous	OPN4	NM_001030015.2,NM_033282.3	,	504,2243,3756	AA,AG,GG		32.7791,9.8048,24.9962	,	10/490,10/479	88414570	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	94233	exon1			AGTCCCGCCCAGC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.30G>A	10.37:g.88414570G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Silent	SNP	ENST00000241891.5	37	CCDS7376.1																																																																																			G|0.763;A|0.237	0.237	strong		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
GSDMA	284110	hgsc.bcm.edu	37	17	38122686	38122686	+	Missense_Mutation	SNP	G	G	A	rs7212944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38122686G>A	ENST00000301659.4	+	3	506	c.388G>A	c.(388-390)Gag>Aag	p.E130K		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	130			E -> K (in dbSNP:rs7212944). {ECO:0000269|PubMed:17471240}.		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						GACCGTGCAGGAGAGGTGAGA	0.617													G|||	1595	0.31849	0.3389	0.2795	5008	,	,		16891	0.38		0.331	False		,,,				2504	0.2423				p.E130K		Atlas-SNP	.											.	GSDMA	26	.	0			c.G388A						PASS	.	G	LYS/GLU	1364,2680		232,900,890	72.0	81.0	78.0		388	3.0	0.4	17	dbSNP_116	78	2755,5607		443,1869,1869	yes	missense	GSDMA	NM_178171.4	56	675,2769,2759	AA,AG,GG		32.9467,33.729,33.2017	benign	130/446	38122686	4119,8287	2022	4181	6203	SO:0001583	missense	284110	exon3			GTGCAGGAGAGGT	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.388G>A	17.37:g.38122686G>A	ENSP00000301659:p.Glu130Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	767	0.35119047619047616	181	0.3678861788617886	103	0.2845303867403315	230	0.4020979020979021	253	0.3337730870712401	G	9.682	1.149475	0.21288	0.33729	0.329467	ENSG00000167914	ENST00000301659	T	0.21031	2.03	4.97	2.99	0.34606	.	1.021790	0.07809	N	0.957779	T	0.00012	0.0000	N	0.10782	0.045	0.46279	P	0.0010320000000000329	B	0.19583	0.037	B	0.25614	0.062	T	0.47169	-0.9138	9	0.08599	T	0.76	-11.5077	7.4073	0.26998	0.1956:0.0:0.8044:0.0	rs7212944;rs12950665;rs59929480	130	Q96QA5	GSDMA_HUMAN	K	130	ENSP00000301659:E130K	ENSP00000301659:E130K	E	+	1	0	GSDMA	35376212	1.000000	0.71417	0.418000	0.26571	0.493000	0.33554	2.671000	0.46842	0.692000	0.31613	0.563000	0.77884	GAG	G|0.646;A|0.354	0.354	strong		0.617	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
OR52I1	390037	hgsc.bcm.edu	37	11	4616062	4616062	+	Missense_Mutation	SNP	C	C	T	rs61997187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4616062C>T	ENST00000530443.2	+	1	794	c.794C>T	c.(793-795)gCg>gTg	p.A265V	OR52I1_ENST00000450052.2_Missense_Mutation_p.A289V	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	265						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(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCATCTATGCGGCCTGGTTG	0.512													T|||	265	0.0529153	0.1142	0.0548	5008	,	,		21180	0.0		0.0527	False		,,,				2504	0.0235				p.A265V		Atlas-SNP	.											.	OR52I1	29	.	0			c.C794T						PASS	.	T	VAL/ALA	482,3920	781.4+/-414.5	22,438,1741	156.0	152.0	153.0		794	2.6	0.7	11	dbSNP_129	153	522,8074	795.4+/-407.5	21,480,3797	no	missense	OR52I1	NM_001005169.1	64	43,918,5538	TT,TC,CC		6.0726,10.9496,7.7243	benign	265/325	4616062	1004,11994	2201	4298	6499	SO:0001583	missense	390037	exon1			TCTATGCGGCCTG	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.794C>T	11.37:g.4616062C>T	ENSP00000436453:p.Ala265Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	172	88	0.511628	NM_001005169	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	143	0.06547619047619048	78	0.15853658536585366	26	0.0718232044198895	0	0.0	39	0.051451187335092345	T	0.485	-0.878119	0.02550	0.109496	0.060726	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.35048	1.33;1.33	4.96	2.6	0.31112	GPCR, rhodopsin-like superfamily (1);	0.411746	0.17735	N	0.163764	T	0.00039	0.0001	N	0.00504	-1.425	0.19300	P	0.999977	B	0.09022	0.002	B	0.04013	0.001	T	0.16482	-1.0401	9	0.62326	D	0.03	-6.6257	9.7681	0.40574	0.0:0.2656:0.0:0.7344	rs61997187	265	Q8NGK6	O52I1_HUMAN	V	289;265	ENSP00000409094:A289V;ENSP00000436453:A265V	ENSP00000409094:A289V	A	+	2	0	OR52I1	4572638	0.000000	0.05858	0.698000	0.30274	0.003000	0.03518	-1.428000	0.02439	-0.106000	0.12110	-2.692000	0.00139	GCG	C|0.937;T|0.063	0.063	strong		0.512	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713625	32713625	+	Missense_Mutation	SNP	C	C	T	rs116163401		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32713625C>T	ENST00000374940.3	+	3	491	c.389C>T	c.(388-390)aCc>aTc	p.T130I		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	130	Alpha-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)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	CAGCCCAACACCCTCATCTGT	0.507																																					p.T130I		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C389T						PASS	.						233.0	188.0	204.0					6																	32713625		1511	2709	4220	SO:0001583	missense	3118	exon3			CCAACACCCTCAT		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.389C>T	6.37:g.32713625C>T	ENSP00000364076:p.Thr130Ile	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	307	27	0.0879479	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	4.868	0.161426	0.09287	.	.	ENSG00000237541	ENST00000374940	T	0.00646	6.0	3.06	-0.952	0.10366	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.640493	0.14599	N	0.309723	T	0.00271	0.0008	L	0.38649	1.16	0.30248	N	0.79432	B	0.24618	0.107	B	0.32724	0.151	T	0.24941	-1.0146	10	0.26408	T	0.33	.	6.9609	0.24597	0.0:0.3016:0.0:0.6984	.	130	P01906	DQA2_HUMAN	I	130	ENSP00000364076:T130I	ENSP00000364076:T130I	T	+	2	0	HLA-DQA2	32821603	0.587000	0.26791	0.996000	0.52242	0.133000	0.20885	0.068000	0.14531	-0.173000	0.10761	0.174000	0.16983	ACC	C|0.998;T|0.002	0.002	weak		0.507	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
OR8H1	219469	hgsc.bcm.edu	37	11	56058535	56058535	+	Missense_Mutation	SNP	C	C	T	rs11600896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56058535C>T	ENST00000313022.2	-	1	31	c.4G>A	c.(4-6)Ggt>Agt	p.G2S		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	2			G -> S (in dbSNP:rs11600896).			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)					TTTCTTCTACCCATGATGTTC	0.353													c|||	391	0.0780751	0.0053	0.0821	5008	,	,		19107	0.0863		0.1302	False		,,,				2504	0.1115				p.G2S		Atlas-SNP	.											.	OR8H1	89	.	0			c.G4A						PASS	.	C	SER/GLY	117,4285	83.9+/-122.4	3,111,2087	78.0	73.0	75.0		4	-4.6	0.0	11	dbSNP_120	75	1199,7393	239.2+/-270.4	84,1031,3181	yes	missense	OR8H1	NM_001005199.1	56	87,1142,5268	TT,TC,CC		13.9548,2.6579,10.1278	benign	2/312	56058535	1316,11678	2201	4296	6497	SO:0001583	missense	219469	exon1			TTCTACCCATGAT	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.4G>A	11.37:g.56058535C>T	ENSP00000323595:p.Gly2Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	194	0.08882783882783883	7	0.014227642276422764	32	0.08839779005524862	60	0.1048951048951049	95	0.12532981530343007	C	7.524	0.657329	0.14580	0.026579	0.139548	ENSG00000181693	ENST00000313022	T	0.02890	4.12	3.5	-4.63	0.03359	.	1.394090	0.04559	N	0.391311	T	0.00012	0.0000	N	0.04387	-0.21	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48258	-0.9051	9	0.33940	T	0.23	.	3.4625	0.07537	0.107:0.432:0.1067:0.3543	rs11600896;rs52821264;rs11600896	2	Q8NGG4	OR8H1_HUMAN	S	2	ENSP00000323595:G2S	ENSP00000323595:G2S	G	-	1	0	OR8H1	55815111	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.301000	0.08232	-0.758000	0.04690	-0.715000	0.03620	GGT	C|0.902;T|0.098	0.098	strong		0.353	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
NKAIN3	286183	hgsc.bcm.edu	37	8	63659610	63659610	+	Silent	SNP	G	G	A	rs1319275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:63659610G>A	ENST00000523211.1	+	4	525	c.393G>A	c.(391-393)acG>acA	p.T131T	NKAIN3_ENST00000328472.5_Silent_p.T131T|NKAIN3_ENST00000519049.1_3'UTR	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				ACGATTACACGTACGTCTCTG	0.498													G|||	2153	0.429912	0.1914	0.5836	5008	,	,		19706	0.3095		0.6441	False		,,,				2504	0.547				p.T131T		Atlas-SNP	.											NKAIN3,NS,carcinoma,+1,1	NKAIN3	32	1	0			c.G393A						scavenged	.	G		1177,3009		185,807,1101	130.0	131.0	131.0		393	-11.0	0.0	8	dbSNP_88	131	5685,2767		1913,1859,454	no	coding-synonymous	NKAIN3	NM_173688.2		2098,2666,1555	AA,AG,GG		32.7378,28.1175,45.7034		131/198	63659610	6862,5776	2093	4226	6319	SO:0001819	synonymous_variant	286183	exon4			TTACACGTACGTC	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"""Na+/K+ transporting ATPase interacting"""	26829	protein-coding gene	gene with protein product		612872	"""family with sequence similarity 77, member D"""	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.393G>A	8.37:g.63659610G>A		Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_173688		Silent	SNP	ENST00000523211.1	37	CCDS55239.1																																																																																			G|0.548;A|0.452	0.452	strong		0.498	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688	
IGSF5	150084	hgsc.bcm.edu	37	21	41165462	41165462	+	Splice_Site	SNP	C	C	A	rs2837225	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:41165462C>A	ENST00000380588.4	+	8	1153	c.1050C>A	c.(1048-1050)gaC>gaA	p.D350E		NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	350			D -> E (in dbSNP:rs2837225). {ECO:0000269|PubMed:14702039}.		single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.D350E(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CTGTTGCAGACACCGCTTCTC	0.418													A|||	2256	0.450479	0.5265	0.5173	5008	,	,		17880	0.4802		0.333	False		,,,				2504	0.3906				p.D350E		Atlas-SNP	.											IGSF5,NS,carcinoma,0,1	IGSF5	62	1	1	Substitution - Missense(1)	stomach(1)	c.C1050A						PASS	.	A	GLU/ASP	2197,2209	587.7+/-386.8	536,1125,542	125.0	129.0	127.0		1050	-1.0	0.0	21	dbSNP_100	127	2502,6098	694.7+/-404.8	361,1780,2159	yes	missense-near-splice	IGSF5	NM_001080444.1	45	897,2905,2701	AA,AC,CC		29.093,49.8638,36.1295	benign	350/408	41165462	4699,8307	2203	4300	6503	SO:0001630	splice_region_variant	150084	exon8			TGCAGACACCGCT		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.1049-1C>A	21.37:g.41165462C>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	126	42	0.333333	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	975	0.44642857142857145	251	0.5101626016260162	180	0.4972375690607735	281	0.49125874125874125	263	0.3469656992084433	A	0.017	-1.499114	0.01001	0.498638	0.29093	ENSG00000183067	ENST00000380588	T	0.05447	3.44	4.15	-1.03	0.10102	.	2.385660	0.01435	N	0.014860	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	0.43278	-0.9401	9	0.02654	T	1	.	4.5133	0.11923	0.379:0.2986:0.3224:0.0	rs2837225;rs52825047;rs60127372;rs2837225	350	Q9NSI5	IGSF5_HUMAN	E	350	ENSP00000369962:D350E	ENSP00000369962:D350E	D	+	3	2	IGSF5	40087332	0.000000	0.05858	0.006000	0.13384	0.007000	0.05969	-0.700000	0.05081	-0.476000	0.06842	-1.346000	0.01242	GAC	C|0.600;A|0.400	0.400	strong		0.418	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		Missense_Mutation
CCDC141	285025	hgsc.bcm.edu	37	2	179721046	179721046	+	Missense_Mutation	SNP	G	G	A	rs17362588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179721046G>A	ENST00000420890.2	-	18	2920	c.2803C>T	c.(2803-2805)Cgg>Tgg	p.R935W	CCDC141_ENST00000295723.5_Missense_Mutation_p.R360W	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	935			R -> W (in dbSNP:rs17362588).							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)			TTCAGATTCCGAGATTTTTCA	0.294													G|||	179	0.0357428	0.0023	0.0735	5008	,	,		15141	0.0		0.1014	False		,,,				2504	0.0235				p.R935W		Atlas-SNP	.											CCDC141_ENST00000420890,lymph_node,lymphoid_neoplasm,0,2	CCDC141	362	2	0			c.C2803T						PASS	.	G	TRP/ARG	103,4301	80.4+/-118.8	0,103,2099	88.0	86.0	87.0		2803	5.0	1.0	2	dbSNP_123	87	775,7821	184.2+/-232.2	44,687,3567	yes	missense	CCDC141	NM_173648.3	101	44,790,5666	AA,AG,GG		9.0158,2.3388,6.7538	probably-damaging	935/1531	179721046	878,12122	2202	4298	6500	SO:0001583	missense	285025	exon18			GATTCCGAGATTT	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.2803C>T	2.37:g.179721046G>A	ENSP00000395995:p.Arg935Trp	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	183	106	0.579235	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		100	0.045787545787545784	2	0.0040650406504065045	30	0.08287292817679558	0	0.0	68	0.08970976253298153	G	15.90	2.968976	0.53614	0.023388	0.090158	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758	T;T;T;T	0.52057	0.68;1.27;1.27;0.7	5.91	5.03	0.67393	.	0.147330	0.31834	N	0.006986	T	0.04452	0.0122	L	0.34521	1.04	0.35415	P	0.20720300000000003	D	0.89917	1.0	D	0.87578	0.998	T	0.46456	-0.9190	9	0.87932	D	0	-13.8917	14.8021	0.69924	0.0:0.0:0.7375:0.2625	rs17362588;rs52809114;rs59461643;rs17362588	360	Q6ZP82	CC141_HUMAN	W	935;379;360;935	ENSP00000395995:R935W;ENSP00000344627:R379W;ENSP00000295723:R360W;ENSP00000390190:R935W	ENSP00000295723:R360W	R	-	1	2	CCDC141	179429291	1.000000	0.71417	0.998000	0.56505	0.267000	0.26476	1.860000	0.39428	1.477000	0.48234	0.650000	0.86243	CGG	G|0.940;A|0.060	0.060	strong		0.294	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648	
CHIC1	53344	hgsc.bcm.edu	37	X	72797296	72797296	+	Splice_Site	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:72797296A>T	ENST00000373502.5	+	2	427	c.350A>T	c.(349-351)aAg>aTg	p.K117M	CHIC1_ENST00000373504.6_Splice_Site_p.K117M	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	117						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					CTAACAGGGAAGGTAAGTGAG	0.343																																					p.K117M		Atlas-SNP	.											.	CHIC1	13	.	0			c.A350T						PASS	.						225.0	188.0	201.0					X																	72797296		2203	4300	6503	SO:0001630	splice_region_variant	53344	exon2			CAGGGAAGGTAAG	Y11897	CCDS35335.2, CCDS75993.1	Xq13.2	2008-05-14			ENSG00000204116	ENSG00000204116			1934	protein-coding gene	gene with protein product		300922				9321471, 11257495	Standard	NM_001039840		Approved	BRX	uc004ebk.4	Q5VXU3	OTTHUMG00000021835	ENST00000373502.5:c.351+1A>T	X.37:g.72797296A>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Missense_Mutation	SNP	ENST00000373502.5	37	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820831	0.71028	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	4.4	4.4	0.53042	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.76574	2.34	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;0.999;1.0	T	0.79132	-0.1929	9	0.72032	D	0.01	-22.424	11.0475	0.47867	1.0:0.0:0.0:0.0	.	117;117;117	B7Z3I1;Q5VXU3-2;Q5VXU3	.;.;CHIC1_HUMAN	M	117	.	ENSP00000362601:K117M	K	+	2	0	CHIC1	72714021	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.715000	0.91416	1.682000	0.51000	0.437000	0.28790	AAG	.	.	none		0.343	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3		Missense_Mutation
ANKRD66	100287718	hgsc.bcm.edu	37	6	46726500	46726500	+	Missense_Mutation	SNP	C	C	A	rs9472839	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46726500C>A	ENST00000565422.1	+	5	603	c.598C>A	c.(598-600)Cag>Aag	p.Q200K	ANKRD66_ENST00000536046.1_Missense_Mutation_p.Q171K|RP11-268F1.3_ENST00000438738.1_lincRNA	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	200																	CGCTGCCCAGCAGAAGGGGCT	0.537													C|||	506	0.101038	0.2148	0.0865	5008	,	,		17497	0.0		0.1074	False		,,,				2504	0.0552				p.Q200K		Atlas-SNP	.											.	.	.	.	0			c.C598A						PASS	.	C	LYS/GLN	214,1170		15,184,493	38.0	37.0	38.0		598	4.7	0.0	6	dbSNP_119	38	385,2797		31,323,1237	yes	missense	LOC100287718	NM_001162435.2	53	46,507,1730	AA,AC,CC		12.0993,15.4624,13.1187	benign	200/252	46726500	599,3967	692	1591	2283	SO:0001583	missense	100287718	exon5			GCCCAGCAGAAGG	AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.598C>A	6.37:g.46726500C>A	ENSP00000454770:p.Gln200Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_001162435		Missense_Mutation	SNP	ENST00000565422.1	37	CCDS59024.1																																																																																			C|0.903;A|0.097	0.097	strong		0.537	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1	NM_001162435	
BTK	695	hgsc.bcm.edu	37	X	100608191	100608191	+	Silent	SNP	G	G	A	rs1135363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:100608191G>A	ENST00000308731.7	-	18	2062	c.1899C>T	c.(1897-1899)tgC>tgT	p.C633C	BTK_ENST00000372880.1_Silent_p.C457C	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	633	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		C -> Y (in XLA). {ECO:0000269|PubMed:8695804}.		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						CCTCATGCCAGCAACTGTACA	0.438									Agammaglobulinemia, X-linked				A|||	1918	0.508079	0.6679	0.3429	3775	,	,		12888	0.3224		0.1074	False		,,,				2504	0.3722				p.C633C		Atlas-SNP	.											.	BTK	87	.	0			c.C1899T						PASS	.	A		3039,796		1041,511,446,80,125	189.0	173.0	178.0		1899	4.4	1.0	X	dbSNP_86	178	1085,5643		51,668,315,1709,1557	no	coding-synonymous	BTK	NM_000061.2		1092,1179,761,1789,1682	AA,AG,A,GG,G		16.1266,20.7562,39.0419		633/660	100608191	4124,6439	2203	4300	6503	SO:0001819	synonymous_variant	695	exon18	Familial Cancer Database	Bruton Type Agammaglobulinemia	ATGCCAGCAACTG	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.1899C>T	X.37:g.100608191G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_000061	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1	698	0.4207353827606992	218	0.7315436241610739	76	0.26573426573426573	117	0.2647058823529412	61	0.08664772727272728	A	5.609	0.297042	0.10622	0.792438	0.161266	ENSG00000010671	ENST00000395179	.	.	.	5.23	4.36	0.52297	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34900	-0.9810	4	0.87932	D	0	.	15.3099	0.74023	0.0802:0.0:0.9198:0.0	rs1135363;rs3027647;rs3197968;rs17419882;rs3027647	.	.	.	V	158	.	ENSP00000378608:A158V	A	-	2	0	BTK	100494847	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	2.444000	0.44890	0.502000	0.28037	-1.056000	0.02311	GCT	0|0.003;T|0.000;G|0.558;A|0.439	0.439	strong		0.438	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632782	32632782	+	Missense_Mutation	SNP	G	G	A	rs12722115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632782G>A	ENST00000399084.1	-	3	350	c.172C>T	c.(172-174)Ctt>Ttt	p.L58F	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.L58F|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.L58F|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.L58F|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	58	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CTGGTCACAAGACGCACGCGC	0.632									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.L58F	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C172T						PASS	.						28.0	30.0	29.0					6																	32632782		2115	4196	6311	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCACAAGACGCAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.172C>T	6.37:g.32632782G>A	ENSP00000382034:p.Leu58Phe	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	53	14	0.264151	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	691	0.3163919413919414	162	0.32926829268292684	112	0.30939226519337015	223	0.38986013986013984	194	0.2559366754617414	.	0.009	-1.808428	0.00606	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00291	8.27;8.27;8.27;8.27	3.91	-7.81	0.01210	.	1.484940	0.04916	U	0.454080	T	0.00039	0.0001	L	0.28608	0.87	0.80722	P	0.0	P;B;B;B;B	0.49783	0.928;0.204;0.002;0.001;0.0	B;B;B;B;B	0.39738	0.308;0.127;0.009;0.013;0.005	T	0.54906	-0.8223	9	0.02654	T	1	.	3.2276	0.06737	0.4621:0.2728:0.1732:0.0919	rs12722115	68;58;23;58;58	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	F	58	ENSP00000382029:L58F;ENSP00000364080:L58F;ENSP00000407332:L58F;ENSP00000382034:L58F	ENSP00000364080:L58F	L	-	1	0	HLA-DQB1	32740760	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.064000	0.00025	-3.742000	0.00113	-2.356000	0.00241	CTT	G|0.644;C|0.073;A|0.283	0.283	strong		0.632	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
P2RX7	5027	hgsc.bcm.edu	37	12	121622239	121622239	+	Silent	SNP	C	C	T	rs3751144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121622239C>T	ENST00000546057.1	+	13	1565	c.1422C>T	c.(1420-1422)ccC>ccT	p.P474P	P2RX7_ENST00000535250.1_Silent_p.P384P|P2RX7_ENST00000541446.1_Silent_p.P185P|P2RX7_ENST00000328963.5_Silent_p.P304P|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	474					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)					GGGATAGCCCCGTCTGGTGCC	0.617													C|||	808	0.161342	0.1581	0.2608	5008	,	,		16472	0.1558		0.0755	False		,,,				2504	0.1892				p.P474P		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1422T						PASS	.	C		689,3717	289.2+/-280.3	56,577,1570	64.0	60.0	61.0		1422	-10.4	0.0	12	dbSNP_107	61	631,7969	162.6+/-215.3	29,573,3698	no	coding-synonymous	P2RX7	NM_002562.5		85,1150,5268	TT,TC,CC		7.3372,15.6378,10.1492		474/596	121622239	1320,11686	2203	4300	6503	SO:0001819	synonymous_variant	5027	exon13			TAGCCCCGTCTGG	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.1422C>T	12.37:g.121622239C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Silent	SNP	ENST00000546057.1	37	CCDS9213.1																																																																																			C|0.880;T|0.120	0.120	strong		0.617	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
INTS8	55656	hgsc.bcm.edu	37	8	95877787	95877787	+	Silent	SNP	T	T	C	rs713113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:95877787T>C	ENST00000523731.1	+	17	2263	c.2130T>C	c.(2128-2130)agT>agC	p.S710S	INTS8_ENST00000520845.1_Intron|INTS8_ENST00000447247.1_Silent_p.S710S	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	710					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					CTAAAGAAAGTAGACGGACTG	0.388													T|||	2838	0.566693	0.4531	0.6182	5008	,	,		20986	0.6607		0.5388	False		,,,				2504	0.6155				p.S710S		Atlas-SNP	.											.	INTS8	92	.	0			c.T2130C						PASS	.	T		2180,2226	585.7+/-386.3	543,1094,566	146.0	136.0	139.0		2130	3.8	1.0	8	dbSNP_86	139	4421,4179	586.2+/-392.0	1142,2137,1021	no	coding-synonymous	INTS8	NM_017864.2		1685,3231,1587	CC,CT,TT		48.593,49.478,49.2465		710/996	95877787	6601,6405	2203	4300	6503	SO:0001819	synonymous_variant	55656	exon17			AGAAAGTAGACGG	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"""chromosome 8 open reading frame 52"""	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2130T>C	8.37:g.95877787T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	1231	0.5636446886446886	231	0.4695121951219512	233	0.643646408839779	362	0.6328671328671329	405	0.5343007915567283	T	10.18	1.278450	0.23307	0.49478	0.51407	ENSG00000164941	ENST00000520526	.	.	.	4.97	3.81	0.43845	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46748	-0.9169	3	.	.	.	-13.5691	6.4301	0.21792	0.0:0.2736:0.0:0.7264	rs713113;rs713113	.	.	.	A	532	.	.	V	+	2	0	INTS8	95946963	0.976000	0.34144	1.000000	0.80357	0.993000	0.82548	0.095000	0.15127	1.989000	0.58080	0.383000	0.25322	GTA	T|0.462;C|0.538	0.538	strong		0.388	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864	
MRPL9	65005	hgsc.bcm.edu	37	1	151733327	151733327	+	Missense_Mutation	SNP	T	T	C	rs74228558	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:151733327T>C	ENST00000368830.3	-	6	721	c.637A>G	c.(637-639)Atc>Gtc	p.I213V	MRPL9_ENST00000467306.1_5'UTR|MRPL9_ENST00000368829.3_Missense_Mutation_p.I179V|OAZ3_ENST00000321531.5_5'Flank|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|RP11-98D18.15_ENST00000601684.1_RNA|OAZ3_ENST00000479764.1_5'Flank|OAZ3_ENST00000315067.8_5'Flank	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	213					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)			CACCGTGTGATAGGCTCTTCT	0.378													T|||	349	0.0696885	0.0794	0.0605	5008	,	,		15549	0.0228		0.1123	False		,,,				2504	0.0675				p.I213V		Atlas-SNP	.											.	MRPL9	21	.	0			c.A637G						PASS	.	T	VAL/ILE	350,4056	180.8+/-209.0	11,328,1864	93.0	89.0	91.0		637	5.3	1.0	1	dbSNP_130	91	937,7663	207.7+/-249.4	55,827,3418	yes	missense	MRPL9	NM_031420.2	29	66,1155,5282	CC,CT,TT		10.8953,7.9437,9.8954	benign	213/268	151733327	1287,11719	2203	4300	6503	SO:0001583	missense	65005	exon6			GTGTGATAGGCTC	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.637A>G	1.37:g.151733327T>C	ENSP00000357823:p.Ile213Val	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	154	0.07051282051282051	38	0.07723577235772358	23	0.06353591160220995	12	0.02097902097902098	81	0.10686015831134564	T	14.47	2.545365	0.45280	0.079437	0.108953	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.48201	0.82;1.31	5.27	5.27	0.74061	.	0.071468	0.56097	D	0.000025	T	0.29783	0.0744	M	0.65975	2.015	0.27917	P	0.9383854	P	0.40360	0.714	B	0.35039	0.194	T	0.42032	-0.9475	9	0.49607	T	0.09	-11.3137	11.5085	0.50481	0.0:0.0:0.0:1.0	.	213	Q9BYD2	RM09_HUMAN	V	213;179	ENSP00000357823:I213V;ENSP00000357822:I179V	ENSP00000357822:I179V	I	-	1	0	MRPL9	149999951	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	3.736000	0.55052	2.198000	0.70561	0.533000	0.62120	ATC	T|0.909;C|0.091	0.091	strong		0.378	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
SELE	6401	hgsc.bcm.edu	37	1	169696946	169696946	+	Missense_Mutation	SNP	G	G	A	rs5368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169696946G>A	ENST00000333360.7	-	9	1541	c.1402C>T	c.(1402-1404)Cat>Tat	p.H468Y	SELE_ENST00000367776.1_Missense_Mutation_p.H405Y|SELE_ENST00000367779.4_Intron|SELE_ENST00000367782.4_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367775.1_Missense_Mutation_p.H343Y|SELE_ENST00000367780.4_Missense_Mutation_p.H343Y|SELE_ENST00000367781.4_Missense_Mutation_p.H405Y|SELE_ENST00000367774.1_Intron|SELE_ENST00000367777.1_Intron	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	468	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.		H -> Y (in dbSNP:rs5368). {ECO:0000269|PubMed:10391210, ECO:0000269|Ref.4}.		actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.H468Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	GTTGATCCATGTAATTCAAAT	0.488													G|||	756	0.150958	0.0809	0.2349	5008	,	,		18192	0.2113		0.1262	False		,,,				2504	0.1493				p.H468Y		Atlas-SNP	.											SELE,NS,carcinoma,0,1	SELE	84	1	1	Substitution - Missense(1)	stomach(1)	c.C1402T	GRCh37	CM025889	SELE	M	rs5368	PASS	.	G	TYR/HIS	343,4063	178.7+/-207.4	11,321,1871	130.0	124.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1402	5.7	0.0	1	dbSNP_52	126	816,7784	189.7+/-236.4	40,736,3524	yes	missense	SELE	NM_000450.2	83	51,1057,5395	AA,AG,GG		9.4884,7.7848,8.9113	benign	468/611	169696946	1159,11847	2203	4300	6503	SO:0001583	missense	6401	exon9			ATCCATGTAATTC	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1402C>T	1.37:g.169696946G>A	ENSP00000331736:p.His468Tyr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	180	106	0.588889	NM_000450	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	353	0.16163003663003664	38	0.07723577235772358	75	0.20718232044198895	139	0.243006993006993	101	0.13324538258575197	G	12.65	2.001681	0.35320	0.077848	0.094884	ENSG00000007908	ENST00000367781;ENST00000367780;ENST00000333360;ENST00000367775;ENST00000367776	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.67	5.67	0.87782	Complement control module (2);Sushi/SCR/CCP (3);	0.564738	0.14950	N	0.288970	T	0.56514	0.1990	L	0.58669	1.825	0.54753	P	2.0000000000020002E-5	P	0.51240	0.943	P	0.51101	0.659	T	0.54563	-0.8275	9	0.25751	T	0.34	-2.4227	13.4055	0.60911	0.0:0.2572:0.7428:0.0	rs5368;rs56458628;rs57229922;rs5368	468	P16581	LYAM2_HUMAN	Y	405;343;468;343;405	ENSP00000356755:H405Y;ENSP00000356754:H343Y;ENSP00000331736:H468Y;ENSP00000356749:H343Y;ENSP00000356750:H405Y	ENSP00000331736:H468Y	H	-	1	0	SELE	167963570	0.000000	0.05858	0.006000	0.13384	0.914000	0.54420	0.684000	0.25364	2.675000	0.91044	0.650000	0.86243	CAT	G|0.882;A|0.118	0.118	strong		0.488	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
POSTN	10631	hgsc.bcm.edu	37	13	38158992	38158992	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:38158992C>T	ENST00000379747.4	-	8	1086	c.969G>A	c.(967-969)acG>acA	p.T323T	POSTN_ENST00000379743.4_Silent_p.T323T|POSTN_ENST00000541481.1_Silent_p.T323T|POSTN_ENST00000541179.1_Silent_p.T323T|POSTN_ENST00000379742.4_Silent_p.T323T|POSTN_ENST00000379749.4_Silent_p.T323T	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	323	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTCCTTCCAGCGTCTCAAAGA	0.383																																					p.T323T		Atlas-SNP	.											POSTN,NS,carcinoma,-1,3	POSTN	161	3	0			c.G969A						scavenged	.						187.0	165.0	173.0					13																	38158992		2203	4300	6503	SO:0001819	synonymous_variant	10631	exon8			TTCCAGCGTCTCA	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.969G>A	13.37:g.38158992C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	3	0.0186335	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Silent	SNP	ENST00000379747.4	37	CCDS9364.1																																																																																			.	.	none		0.383	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
STKLD1	169436	hgsc.bcm.edu	37	9	136268897	136268897	+	Silent	SNP	G	G	A	rs36079470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136268897G>A	ENST00000371957.3	+	15	1655	c.1548G>A	c.(1546-1548)gcG>gcA	p.A516A	C9orf96_ENST00000371955.1_Silent_p.A49A	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		516							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)		CCTACCCTGCGGATGGGGAAA	0.652													G|||	123	0.0245607	0.0038	0.036	5008	,	,		17206	0.001		0.0686	False		,,,				2504	0.0235				p.A516A		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1548A						PASS	.	G		58,4348	56.8+/-93.2	2,54,2147	43.0	42.0	43.0		1548	-2.4	0.0	9	dbSNP_126	43	669,7931	166.5+/-218.5	35,599,3666	no	coding-synonymous	C9orf96	NM_153710.3		37,653,5813	AA,AG,GG		7.7791,1.3164,5.5897		516/681	136268897	727,12279	2203	4300	6503	SO:0001819	synonymous_variant	169436	exon15			CCCTGCGGATGGG																												ENST00000371957.3:c.1548G>A	9.37:g.136268897G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			G|0.952;A|0.048	0.048	strong		0.652	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
RPS6KA1	6195	hgsc.bcm.edu	37	1	26887592	26887592	+	Silent	SNP	T	T	C	rs1064196	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:26887592T>C	ENST00000374168.2	+	16	1552	c.1398T>C	c.(1396-1398)taT>taC	p.Y466Y	RPS6KA1_ENST00000374162.2_Silent_p.Y374Y|RPS6KA1_ENST00000531382.1_Silent_p.Y475Y|RPS6KA1_ENST00000530003.1_Silent_p.Y450Y|RPS6KA1_ENST00000374166.4_Silent_p.Y455Y|RPS6KA1_ENST00000526792.1_Silent_p.Y374Y	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	75	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	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	
NUF2	83540	hgsc.bcm.edu	37	1	163309219	163309219	+	Silent	SNP	A	A	T	rs1509022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:163309219A>T	ENST00000271452.3	+	8	837	c.558A>T	c.(556-558)ggA>ggT	p.G186G	NUF2_ENST00000367900.3_Silent_p.G186G|NUF2_ENST00000524800.1_Silent_p.G186G	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	186	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					TTTCAGATGGAATTCAGGAGC	0.338													T|||	2146	0.428514	0.32	0.4352	5008	,	,		18185	0.3512		0.4374	False		,,,				2504	0.6411				p.G186G		Atlas-SNP	.											.	NUF2	138	.	0			c.A558T						PASS	.	T	,	1515,2891	672.9+/-402.7	252,1011,940	95.0	93.0	94.0		558,558	-2.7	0.0	1	dbSNP_88	94	3907,4693	605.8+/-395.0	887,2133,1280	no	coding-synonymous,coding-synonymous	NUF2	NM_031423.3,NM_145697.2	,	1139,3144,2220	TT,TA,AA		45.4302,34.3849,41.6885	,	186/465,186/465	163309219	5422,7584	2203	4300	6503	SO:0001819	synonymous_variant	83540	exon8			AGATGGAATTCAG	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.558A>T	1.37:g.163309219A>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Silent	SNP	ENST00000271452.3	37	CCDS1245.1																																																																																			A|0.599;T|0.401	0.401	strong		0.338	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
COL11A2	1302	hgsc.bcm.edu	37	6	33138677	33138677	+	Silent	SNP	G	G	A	rs1799911	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33138677G>A	ENST00000374708.4	-	44	3384	c.3126C>T	c.(3124-3126)ccC>ccT	p.P1042P	COL11A2_ENST00000341947.2_Silent_p.P1128P|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374714.1_Silent_p.P1102P|COL11A2_ENST00000357486.1_Silent_p.P1107P|COL11A2_ENST00000395197.1_Silent_p.P1068P|COL11A2_ENST00000374713.1_Silent_p.P1081P|COL11A2_ENST00000374712.1_Silent_p.P1047P|COL11A2_ENST00000361917.1_Silent_p.P1021P	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1128	Triple-helical region.				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						CCCGAGCTCCGGGCTCCCCAT	0.572													G|||	1231	0.245807	0.1225	0.2579	5008	,	,		17393	0.2431		0.2525	False		,,,				2504	0.3998				p.P1128P	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.C3384T						PASS	.	G	,,	447,2575		34,379,1098	66.0	74.0	71.0		3063,3384,3126	-9.3	0.7	6	dbSNP_89	71	1509,3909		207,1095,1407	yes	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	241,1474,2505	AA,AG,GG		27.8516,14.7915,23.1754	,,	1021/1630,1128/1737,1042/1651	33138677	1956,6484	1511	2709	4220	SO:0001819	synonymous_variant	1302	exon46			AGCTCCGGGCTCC	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	ENST00000374708.4:c.3126C>T	6.37:g.33138677G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			G|0.763;A|0.237	0.237	strong		0.572	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
SVIL	6840	hgsc.bcm.edu	37	10	29759225	29759225	+	Silent	SNP	A	A	G	rs11007607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29759225A>G	ENST00000355867.4	-	32	6575	c.5823T>C	c.(5821-5823)gcT>gcC	p.A1941A	PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000535393.1_Silent_p.A855A|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|SVIL_ENST00000375398.2_Silent_p.A1941A|SVIL_ENST00000375400.3_Silent_p.A1515A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1941					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)	p.A1941A(1)		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)				TCTTGTTCGCAGCGGTCCTTC	0.602													G|||	1238	0.247204	0.2814	0.2839	5008	,	,		19079	0.2391		0.2286	False		,,,				2504	0.2025				p.A1941A		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.T5823C						scavenged	.	G	,	1185,3221	711.7+/-408.0	162,861,1180	180.0	147.0	158.0		4545,5823	-11.2	0.0	10	dbSNP_120	158	1819,6781	731.9+/-406.8	203,1413,2684	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	365,2274,3864	GG,GA,AA		21.1512,26.8951,23.097	,	1515/1789,1941/2215	29759225	3004,10002	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon32			GTTCGCAGCGGTC	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.5823T>C	10.37:g.29759225A>G		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	160	66	0.4125	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.769;G|0.231	0.231	strong		0.602	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
PRPF4B	8899	hgsc.bcm.edu	37	6	4031998	4031998	+	Missense_Mutation	SNP	A	A	G	rs9503893	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:4031998A>G	ENST00000337659.6	+	2	347	c.247A>G	c.(247-249)Att>Gtt	p.I83V	PRPF4B_ENST00000538861.1_Missense_Mutation_p.I69V	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	83	Arg/Lys-rich (basic).		I -> V (in dbSNP:rs9503893). {ECO:0000269|PubMed:11418604, ECO:0000269|PubMed:12077342, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17081983, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:19413330, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692, ECO:0000269|PubMed:9628581}.		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)				aagaaaagaGATTATTGATGC	0.318													G|||	3583	0.715455	0.7368	0.7277	5008	,	,		19812	0.7877		0.6352	False		,,,				2504	0.6861				p.I83V		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A247G						PASS	.	G	VAL/ILE	3286,1120	397.2+/-330.3	1238,810,155	82.0	75.0	77.0		247	2.6	0.3	6	dbSNP_119	77	5747,2853	444.0+/-360.5	1902,1943,455	yes	missense	PRPF4B	NM_003913.4	29	3140,2753,610	GG,GA,AA		33.1744,25.4199,30.5474	benign	83/1008	4031998	9033,3973	2203	4300	6503	SO:0001583	missense	8899	exon2			AAAGAGATTATTG	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.247A>G	6.37:g.4031998A>G	ENSP00000337194:p.Ile83Val	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	1554	0.7115384615384616	357	0.725609756097561	262	0.7237569060773481	445	0.777972027972028	490	0.6464379947229552	G	0.007	-1.937150	0.00484	0.745801	0.668256	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.65916	-0.18;-0.18	5.4	2.64	0.31445	.	0.667598	0.14335	N	0.326098	T	0.13329	0.0323	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15178	-1.0446	9	0.10377	T	0.69	.	7.1493	0.25601	0.2049:0.1237:0.6714:0.0	rs9503893;rs17292762;rs17857033;rs52826967;rs60980650;rs9503893	83	Q13523	PRP4B_HUMAN	V	83;69	ENSP00000337194:I83V;ENSP00000439331:I69V	ENSP00000337194:I83V	I	+	1	0	PRPF4B	3976997	0.518000	0.26234	0.262000	0.24481	0.567000	0.35839	1.462000	0.35266	0.014000	0.14944	-0.355000	0.07637	ATT	A|0.296;G|0.704	0.704	strong		0.318	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
RNF213	57674	hgsc.bcm.edu	37	17	78363033	78363033	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78363033G>A	ENST00000582970.1	+	65	15204	c.15061G>A	c.(15061-15063)Gcc>Acc	p.A5021T	RNF213_ENST00000508628.2_Missense_Mutation_p.A5070T|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000427003.3_3'UTR|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.A3094T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5021			A -> V (variant detected in cases of Moyamoya disease in East Asian populations; dbSNP:rs138130613). {ECO:0000269|PubMed:21799892}.		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)			CTACAGCGATGCCTGTGAAGT	0.537																																					p.A5021T		Atlas-SNP	.											.	RNF213	766	.	0			c.G15061A						PASS	.						141.0	123.0	129.0					17																	78363033		2203	4300	6503	SO:0001583	missense	57674	exon65			AGCGATGCCTGTG	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.15061G>A	17.37:g.78363033G>A	ENSP00000464087:p.Ala5021Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	179	89	0.497207	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	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015431	0.35511	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23950	1.88	5.39	1.87	0.25490	.	0.435749	0.22236	N	0.062742	T	0.26340	0.0643	M	0.72479	2.2	0.25084	N	0.990904	B;B	0.22146	0.031;0.065	B;B	0.14578	0.011;0.01	T	0.19877	-1.0292	10	0.56958	D	0.05	.	9.3461	0.38109	0.3281:0.0:0.6719:0.0	.	5021;3094	D6RI12;Q63HN8	.;RN213_HUMAN	T	5021;5070;3094;371	ENSP00000338218:A3094T	ENSP00000338218:A3094T	A	+	1	0	RNF213	75977628	1.000000	0.71417	0.244000	0.24202	0.451000	0.32288	2.945000	0.49043	0.124000	0.18369	-0.345000	0.07892	GCC	.	.	none		0.537	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
MTSS1	9788	hgsc.bcm.edu	37	8	125565328	125565328	+	Missense_Mutation	SNP	T	T	C	rs3829037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:125565328T>C	ENST00000518547.1	-	14	2646	c.2173A>G	c.(2173-2175)Act>Gct	p.T725A	MTSS1_ENST00000395508.2_Missense_Mutation_p.T499A|MTSS1_ENST00000524090.1_Missense_Mutation_p.T615A|MTSS1_ENST00000378017.3_Missense_Mutation_p.T700A|MTSS1_ENST00000325064.5_Missense_Mutation_p.T729A|MTSS1_ENST00000354184.4_Missense_Mutation_p.T443A|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000431961.2_Missense_Mutation_p.T443A|MTSS1_ENST00000523587.1_5'UTR	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	725	Pro-rich.		T -> A (in dbSNP:rs3829037).		actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CCTTGTGGAGTATCCCTTGGG	0.552													T|||	810	0.161741	0.1573	0.1066	5008	,	,		17079	0.1587		0.2366	False		,,,				2504	0.1329				p.T725A	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.A2173G						PASS	.	T	ALA/THR	657,3749	280.5+/-275.4	47,563,1593	226.0	222.0	223.0		2173	-4.8	0.0	8	dbSNP_107	223	1858,6742	332.1+/-320.0	203,1452,2645	yes	missense	MTSS1	NM_014751.4	58	250,2015,4238	CC,CT,TT		21.6047,14.9115,19.3372	benign	725/756	125565328	2515,10491	2203	4300	6503	SO:0001583	missense	9788	exon14			GTGGAGTATCCCT	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.2173A>G	8.37:g.125565328T>C	ENSP00000429064:p.Thr725Ala	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	37	CCDS6353.1	405|405	0.18543956043956045|0.18543956043956045	87|87	0.17682926829268292|0.17682926829268292	49|49	0.13535911602209943|0.13535911602209943	81|81	0.14160839160839161|0.14160839160839161	188|188	0.24802110817941952|0.24802110817941952	T|T	0.441|0.441	-0.898591|-0.898591	0.02472|0.02472	0.149115|0.149115	0.216047|0.216047	ENSG00000170873|ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090|ENST00000519168	T;T;T;T;T;T;T|.	0.43294|.	0.95;0.95;0.95;0.95;0.95;0.95;0.95|.	6.14|6.14	-4.85|-4.85	0.03142|0.03142	.|.	1.211830|.	0.05330|.	N|.	0.528165|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03324|0.03324	-0.35|-0.35	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.10296|.	0.0;0.001;0.0;0.001;0.0;0.003|.	B;B;B;B;B;B|.	0.09377|.	0.001;0.002;0.002;0.001;0.001;0.004|.	T|T	0.04140|0.04140	-1.0974|-1.0974	9|4	0.10377|.	T|.	0.69|.	0.0464|0.0464	19.5679|19.5679	0.95403|0.95403	0.0:0.8004:0.0:0.1996|0.0:0.8004:0.0:0.1996	rs3829037;rs17370705;rs52798965;rs56454254;rs57272610;rs3829037|rs3829037;rs17370705;rs52798965;rs56454254;rs57272610;rs3829037	615;499;700;725;700;443|.	E7EWW5;B7Z3B6;A5YM41;O43312;O43312-4;O43312-2|.	.;.;.;MTSS1_HUMAN;.;.|.	A|C	700;725;443;499;729;443;615|512	ENSP00000367256:T700A;ENSP00000429064:T725A;ENSP00000346119:T443A;ENSP00000378884:T499A;ENSP00000322804:T729A;ENSP00000393606:T443A;ENSP00000428319:T615A|.	ENSP00000322804:T729A|.	T|Y	-|-	1|2	0|0	MTSS1|MTSS1	125634509|125634509	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.193000|0.193000	0.23685|0.23685	0.096000|0.096000	0.15147|0.15147	-0.882000|-0.882000	0.03987|0.03987	-0.256000|-0.256000	0.11100|0.11100	ACT|TAC	T|0.816;C|0.184	0.184	strong		0.552	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
MICALCL	84953	hgsc.bcm.edu	37	11	12315186	12315186	+	Missense_Mutation	SNP	G	G	A	rs10741578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:12315186G>A	ENST00000256186.2	+	3	499	c.208G>A	c.(208-210)Gta>Ata	p.V70I		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	70	Interaction with MAPK1. {ECO:0000250}.		V -> I (in dbSNP:rs10741578). {ECO:0000269|PubMed:14702039}.		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)		GAGGCGAGCCGTAGCCCAAGG	0.567													A|||	2673	0.533746	0.6377	0.585	5008	,	,		12833	0.5952		0.3658	False		,,,				2504	0.4663				p.V70I		Atlas-SNP	.											.	MICALCL	59	.	0			c.G208A						PASS	.	A	ILE/VAL	2193,1683		622,949,367	140.0	147.0	145.0		208	2.1	0.0	11	dbSNP_120	145	2950,5296		529,1892,1702	yes	missense	MICALCL	NM_032867.2	29	1151,2841,2069	AA,AG,GG		35.7749,43.4211,42.427	benign	70/696	12315186	5143,6979	1938	4123	6061	SO:0001583	missense	84953	exon3			CGAGCCGTAGCCC	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.208G>A	11.37:g.12315186G>A	ENSP00000256186:p.Val70Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	1116	0.510989010989011	292	0.5934959349593496	187	0.5165745856353591	361	0.6311188811188811	276	0.3641160949868074	A	10.32	1.317556	0.23908	0.565789	0.357749	ENSG00000133808	ENST00000256186	T	0.05855	3.38	5.71	2.09	0.27110	.	0.527164	0.15463	N	0.261051	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	0.13791	-1.0496	9	0.12430	T	0.62	.	5.1684	0.15098	0.4295:0.3887:0.1818:0.0	rs10741578;rs56735949;rs10741578	70	Q6ZW33	MICLK_HUMAN	I	70	ENSP00000256186:V70I	ENSP00000256186:V70I	V	+	1	0	MICALCL	12271762	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	0.283000	0.18846	0.095000	0.17434	-0.254000	0.11334	GTA	G|0.506;A|0.494	0.494	strong		0.567	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
NLRP7	199713	hgsc.bcm.edu	37	19	55450746	55450746	+	Missense_Mutation	SNP	C	C	T	rs61747414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55450746C>T	ENST00000590030.1	-	3	1481	c.1441G>A	c.(1441-1443)Gcc>Acc	p.A481T	NLRP7_ENST00000340844.2_Missense_Mutation_p.A481T|NLRP7_ENST00000588756.1_Missense_Mutation_p.A481T|NLRP7_ENST00000446217.1_Missense_Mutation_p.A509T|NLRP7_ENST00000328092.5_Missense_Mutation_p.A481T|NLRP7_ENST00000592784.1_Missense_Mutation_p.A481T|NLRP7_ENST00000448121.2_Missense_Mutation_p.A481T			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	481	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			A -> T (in Ref. 4; AAI09126). {ECO:0000305}.			ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTCTCCAGGGCGTAGAACAGG	0.592													.|||	455	0.0908546	0.1762	0.0865	5008	,	,		18187	0.006		0.1272	False		,,,				2504	0.0286				p.A481T		Atlas-SNP	.											NLRP7_ENST00000328092,NS,carcinoma,+1,2	NLRP7	411	2	0			c.G1441A						scavenged	.	C	THR/ALA,THR/ALA,THR/ALA	691,3715	285.5+/-278.2	60,571,1572	49.0	48.0	48.0		1441,1441,1441	-3.8	0.0	19	dbSNP_129	48	837,7763	192.0+/-238.1	34,769,3497	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	58,58,58	94,1340,5069	TT,TC,CC		9.7326,15.6832,11.7484	benign,benign,benign	481/1038,481/1010,481/981	55450746	1528,11478	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGGGCGTAGAA	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1441G>A	19.37:g.55450746C>T	ENSP00000465520:p.Ala481Thr	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	218	0.09981684981684982	88	0.17886178861788618	35	0.09668508287292818	3	0.005244755244755245	92	0.12137203166226913	C	6.611	0.481139	0.12581	0.156832	0.097326	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.73789	-0.71;-0.71;-0.78;-0.74	1.92	-3.83	0.04269	.	2.124680	0.03209	N	0.175938	T	0.00178	0.0005	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.27140	0.105;0.105;0.169	B;B;B	0.20184	0.022;0.022;0.028	T	0.01269	-1.1400	9	0.29301	T	0.29	.	0.9361	0.01345	0.1512:0.19:0.3005:0.3582	.	509;481;481	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	T	481;481;481;509;248	ENSP00000329568:A481T;ENSP00000409137:A481T;ENSP00000339491:A481T;ENSP00000414273:A509T	ENSP00000329568:A481T	A	-	1	0	NLRP7	60142558	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-2.206000	0.01231	-1.499000	0.01821	-0.379000	0.06801	GCC	C|0.893;T|0.107	0.107	strong		0.592	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
RPA1	6117	hgsc.bcm.edu	37	17	1782957	1782957	+	Silent	SNP	C	C	T	rs2230930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1782957C>T	ENST00000254719.5	+	11	1166	c.1056C>T	c.(1054-1056)tcC>tcT	p.S352S		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	352					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|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)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						TGGACACATCCGGGAAGGTGG	0.522								Nucleotide excision repair (NER)					c|||	1357	0.270966	0.2088	0.2392	5008	,	,		22185	0.4048		0.1779	False		,,,				2504	0.3354				p.S352S		Atlas-SNP	.											.	RPA1	48	.	0			c.C1056T						PASS	.	C		776,3630	313.8+/-293.3	73,630,1500	196.0	190.0	192.0		1056	-11.1	0.1	17	dbSNP_98	192	1342,7258	261.9+/-284.1	104,1134,3062	no	coding-synonymous	RPA1	NM_002945.3		177,1764,4562	TT,TC,CC		15.6047,17.6123,16.2848		352/617	1782957	2118,10888	2203	4300	6503	SO:0001819	synonymous_variant	6117	exon11			CACATCCGGGAAG	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"""replication protein A1 (70kD)"""			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1056C>T	17.37:g.1782957C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	37	CCDS11014.1																																																																																			C|0.802;N|0.000	.	strong		0.522	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	
DAPK1	1612	hgsc.bcm.edu	37	9	90321293	90321293	+	Missense_Mutation	SNP	G	G	A	rs200627640		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:90321293G>A	ENST00000408954.3	+	26	3642	c.3307G>A	c.(3307-3309)Gtc>Atc	p.V1103I	DAPK1_ENST00000469640.2_Missense_Mutation_p.V1128I|DAPK1_ENST00000358077.5_Missense_Mutation_p.V1103I|DAPK1_ENST00000472284.1_Missense_Mutation_p.V1103I|DAPK1_ENST00000491893.1_Missense_Mutation_p.V1037I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1103					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						CATGGTGGACGTCCCAGCCCT	0.647									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	1	0.000199681	0.0	0.0	5008	,	,		18449	0.0		0.001	False		,,,				2504	0.0				p.V1103I		Atlas-SNP	.											.	DAPK1	329	.	0			c.G3307A						PASS	.	G	ILE/VAL	0,4382		0,0,2191	76.0	87.0	84.0		3307	3.4	1.0	9		84	2,8538		0,2,4268	yes	missense	DAPK1	NM_004938.2	29	0,2,6459	AA,AG,GG		0.0234,0.0,0.0155	benign	1103/1431	90321293	2,12920	2191	4270	6461	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GTGGACGTCCCAG	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.3307G>A	9.37:g.90321293G>A	ENSP00000386135:p.Val1103Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	221	99	0.447964	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.630	-0.519121	0.04171	0.0	2.34E-4	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.03	5.59	3.42	0.39159	.	0.243390	0.26366	N	0.024792	T	0.25717	0.0626	N	0.01267	-0.92	0.31840	N	0.623597	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.34900	-0.9810	10	0.02654	T	1	.	8.3592	0.32348	0.8799:0.0:0.1201:0.0	.	1037;1103;1103	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	I	1103;1103;1128;1103;1037	ENSP00000350785:V1103I;ENSP00000417076:V1103I;ENSP00000418885:V1128I;ENSP00000386135:V1103I;ENSP00000419026:V1037I	ENSP00000350785:V1103I	V	+	1	0	DAPK1	89511113	0.992000	0.36948	0.994000	0.49952	0.932000	0.56968	2.244000	0.43124	0.540000	0.28808	0.561000	0.74099	GTC	G|0.999;A|0.001	0.001	strong		0.647	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
MS4A6A	64231	hgsc.bcm.edu	37	11	59945745	59945745	+	Silent	SNP	T	T	C	rs12453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:59945745T>C	ENST00000530839.1	-	5	819	c.327A>G	c.(325-327)ttA>ttG	p.L109L	MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000420732.2_Silent_p.L109L|MS4A6A_ENST00000528851.1_Silent_p.L109L|MS4A6A_ENST00000426738.2_Silent_p.L64L|MS4A6A_ENST00000412309.2_Silent_p.L137L|MS4A6A_ENST00000529054.1_Silent_p.L137L|MS4A6A_ENST00000323961.3_Silent_p.L109L	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	109						integral component of membrane (GO:0016021)		p.L109L(1)		endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAAGCTTGGTTAACCTTTTCT	0.383													T|||	1539	0.307308	0.1581	0.2723	5008	,	,		18602	0.2252		0.4046	False		,,,				2504	0.5184				p.L137L		Atlas-SNP	.											MS4A6A_ENST00000529054,NS,carcinoma,0,3	MS4A6A	85	3	1	Substitution - coding silent(1)	stomach(1)	c.A411G						PASS	.	T	,,	882,3520	343.8+/-307.8	79,724,1398	154.0	143.0	147.0		327,327,327	-5.8	0.0	11	dbSNP_52	147	3431,5159	506.1+/-376.5	702,2027,1566	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	,,	781,2751,2964	CC,CT,TT		39.9418,20.0363,33.1974	,,	109/226,109/179,109/249	59945745	4313,8679	2201	4295	6496	SO:0001819	synonymous_variant	64231	exon5			CTTGGTTAACCTT	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.327A>G	11.37:g.59945745T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1																																																																																			T|0.688;C|0.312	0.312	strong		0.383	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
NPY2R	4887	hgsc.bcm.edu	37	4	156136027	156136027	+	Silent	SNP	C	C	T	rs2880415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156136027C>T	ENST00000329476.3	+	2	1425	c.936C>T	c.(934-936)atC>atT	p.I312I	NPY2R_ENST00000506608.1_Silent_p.I312I	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	312					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TGTTCCACATCATCGCCATGT	0.537													T|||	3290	0.656949	0.823	0.4914	5008	,	,		21230	0.7609		0.5447	False		,,,				2504	0.5583				p.I312I		Atlas-SNP	.											.	NPY2R	87	.	0			c.C936T	GRCh37	CM057404	NPY2R	M	rs2880415	PASS	.	T		3385,1021	375.9+/-321.8	1319,747,137	124.0	98.0	107.0		936	1.1	0.7	4	dbSNP_101	107	4552,4048	557.8+/-387.1	1201,2150,949	no	coding-synonymous	NPY2R	NM_000910.2		2520,2897,1086	TT,TC,CC		47.0698,23.1729,38.9743		312/382	156136027	7937,5069	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			CCACATCATCGCC	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.936C>T	4.37:g.156136027C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.384;T|0.616	0.616	strong		0.537	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
GLG1	2734	hgsc.bcm.edu	37	16	74499589	74499589	+	Silent	SNP	G	G	A	rs2303275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74499589G>A	ENST00000422840.2	-	19	2651	c.2652C>T	c.(2650-2652)tgC>tgT	p.C884C	GLG1_ENST00000447066.2_Silent_p.C873C|GLG1_ENST00000205061.5_Silent_p.C884C|Y_RNA_ENST00000384794.1_RNA	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	884					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TCATCTGCTTGCAGACCCTCA	0.498													G|||	560	0.111821	0.0552	0.1643	5008	,	,		19806	0.1548		0.1382	False		,,,				2504	0.0798				p.C884C		Atlas-SNP	.											.	GLG1	106	.	0			c.C2652T						PASS	.	G	,,	296,4100	162.5+/-194.5	4,288,1906	208.0	201.0	204.0		2619,2652,2652	3.7	1.0	16	dbSNP_100	204	1144,7456	236.1+/-268.4	63,1018,3219	no	coding-synonymous,coding-synonymous,coding-synonymous	GLG1	NM_001145666.1,NM_001145667.1,NM_012201.5	,,	67,1306,5125	AA,AG,GG		13.3023,6.7334,11.0803	,,	873/1193,884/1180,884/1204	74499589	1440,11556	2198	4300	6498	SO:0001819	synonymous_variant	2734	exon19			CTGCTTGCAGACC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2652C>T	16.37:g.74499589G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	70	0.564516	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	37	CCDS45527.1																																																																																			G|0.883;A|0.117	0.117	strong		0.498	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
NID1	4811	hgsc.bcm.edu	37	1	236144951	236144951	+	Silent	SNP	A	A	G	rs3738525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236144951A>G	ENST00000264187.6	-	16	3269	c.3187T>C	c.(3187-3189)Ttg>Ctg	p.L1063L	NID1_ENST00000366595.3_Silent_p.L930L	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1063					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)	GGATTCACCAAGTCAGTCTCA	0.493													G|||	1675	0.334465	0.3555	0.2579	5008	,	,		19135	0.6151		0.1402	False		,,,				2504	0.271				p.L1063L		Atlas-SNP	.											.	NID1	196	.	0			c.T3187C						PASS	.	G		1481,2925	678.6+/-403.6	235,1011,957	92.0	91.0	91.0		3187	-3.7	0.0	1	dbSNP_107	91	1478,7122	749.6+/-407.4	118,1242,2940	no	coding-synonymous	NID1	NM_002508.2		353,2253,3897	GG,GA,AA		17.186,33.6133,22.751		1063/1248	236144951	2959,10047	2203	4300	6503	SO:0001819	synonymous_variant	4811	exon16			TCACCAAGTCAGT	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.3187T>C	1.37:g.236144951A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			A|0.729;G|0.271	0.271	strong		0.493	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
SLC22A18	5002	hgsc.bcm.edu	37	11	2924591	2924591	+	Missense_Mutation	SNP	G	G	A	rs1048046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2924591G>A	ENST00000380574.1	+	2	447	c.16G>A	c.(16-18)Gct>Act	p.A6T	SLC22A18AS_ENST00000455942.2_Intron|SLC22A18_ENST00000312221.5_Missense_Mutation_p.A6T|SLC22A18_ENST00000449793.2_Missense_Mutation_p.A6T|SLC22A18_ENST00000347936.2_Missense_Mutation_p.A6T|SLC22A18AS_ENST00000533594.1_Intron			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	6			A -> T (in dbSNP:rs1048046). {ECO:0000269|PubMed:9520460}.		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)		GGGAGCTCGGGCTCCCAGGGA	0.662													G|||	814	0.16254	0.2678	0.0951	5008	,	,		17337	0.005		0.1928	False		,,,				2504	0.1994				p.A6T		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G16A						PASS	.	G	THR/ALA,,THR/ALA	1163,3241	402.2+/-332.3	153,857,1192	53.0	56.0	55.0		16,,16	0.7	0.0	11	dbSNP_86	55	1545,7053	285.8+/-297.4	130,1285,2884	yes	missense,intron,missense	SLC22A18,SLC22A18AS	NM_002555.5,NM_007105.2,NM_183233.2	58,,58	283,2142,4076	AA,AG,GG		17.9693,26.4078,20.8276	probably-damaging,,probably-damaging	6/425,,6/425	2924591	2708,10294	2202	4299	6501	SO:0001583	missense	5002	exon2			GCTCGGGCTCCCA	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.16G>A	11.37:g.2924591G>A	ENSP00000369948:p.Ala6Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	298	0.13644688644688643	121	0.2459349593495935	32	0.08839779005524862	0	0.0	145	0.19129287598944592	G	11.64	1.699602	0.30142	0.264078	0.179693	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;T	0.55413	0.52;0.52;2.09;0.52;1.41	2.85	0.666	0.17901	.	3.352530	0.00999	N	0.003644	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.18461	0.028;0.028	B;B	0.14023	0.01;0.01	T	0.13361	-1.0512	9	0.46703	T	0.11	.	2.8279	0.05490	0.1605:0.0:0.5638:0.2757	rs1048046;rs3168332	6;6	E9PRM7;Q96BI1	.;S22AI_HUMAN	T	6	ENSP00000307859:A6T;ENSP00000311139:A6T;ENSP00000392072:A6T;ENSP00000369948:A6T;ENSP00000433019:A6T	ENSP00000311139:A6T	A	+	1	0	SLC22A18	2881167	0.001000	0.12720	0.001000	0.08648	0.066000	0.16364	0.426000	0.21363	0.533000	0.28675	0.462000	0.41574	GCT	G|0.814;A|0.186	0.186	strong		0.662	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
SNAP47	116841	hgsc.bcm.edu	37	1	227954742	227954742	+	Silent	SNP	C	C	T	rs34209229	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:227954742C>T	ENST00000366759.4	+	4	1620	c.1206C>T	c.(1204-1206)agC>agT	p.S402S	SNAP47_ENST00000366760.1_Silent_p.S160S|SNAP47_ENST00000315781.5_Silent_p.S402S	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	402	t-SNARE coiled-coil homology 2. {ECO:0000255|PROSITE-ProRule:PRU00202}.				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						TGCAGACAAGCCTGCCAGCCC	0.627													C|||	68	0.0135783	0.0023	0.013	5008	,	,		22181	0.0		0.0447	False		,,,				2504	0.0112				p.S402S		Atlas-SNP	.											.	SNAP47	42	.	0			c.C1206T						PASS	.	C		48,4358	48.2+/-83.0	1,46,2156	85.0	69.0	75.0		1206	-5.2	0.0	1	dbSNP_126	75	342,8258	116.8+/-176.5	7,328,3965	no	coding-synonymous	SNAP47	NM_053052.3		8,374,6121	TT,TC,CC		3.9767,1.0894,2.9986		402/465	227954742	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	116841	exon4			GACAAGCCTGCCA	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.1206C>T	1.37:g.227954742C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Silent	SNP	ENST00000366759.4	37	CCDS1562.1	46	0.021062271062271064	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	39	0.051451187335092345	C	4.676	0.125669	0.08931	0.010894	0.039767	ENSG00000143740	ENST00000418653;ENST00000426344	.	.	.	4.82	-5.18	0.02840	.	.	.	.	.	T	0.02688	0.0081	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21415	-1.0246	4	.	.	.	-12.8612	2.8145	0.05452	0.1232:0.2501:0.1214:0.5054	rs34209229	.	.	.	S	215;394	.	.	P	+	1	0	SNAP47	226021365	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.944000	0.03913	-0.975000	0.03546	0.549000	0.68633	CCT	C|0.975;T|0.025	0.025	strong		0.627	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240781	39240781	+	Missense_Mutation	SNP	C	C	G	rs372960430|rs553572799	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39240781C>G	ENST00000391417.4	+	1	323	c.323C>G	c.(322-324)aCc>aGc	p.T108S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	133	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						tgccagcccacctgctgccgc	0.662																																					p.T108S		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	0			c.C323G						scavenged	.						13.0	15.0	14.0					17																	39240781		1874	3648	5522	SO:0001583	missense	100132476	exon1			AGCCCACCTGCTG	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.323C>G	17.37:g.39240781C>G	ENSP00000375236:p.Thr108Ser	Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	19	2	0.105263	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	1.159	-0.644403	0.03531	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00580	6.43	3.41	1.04	0.20106	.	1.411810	0.05113	N	0.489187	T	0.00356	0.0011	.	.	.	0.19575	N	0.999961	B	0.17268	0.021	B	0.15052	0.012	T	0.35351	-0.9792	9	0.07175	T	0.84	.	7.6942	0.28585	0.1798:0.6442:0.176:0.0	.	108	Q9BYR0	KRA47_HUMAN	S	108;99	ENSP00000375236:T108S	ENSP00000375236:T108S	T	+	2	0	KRTAP4-9;KRTAP4-7	36494307	0.000000	0.05858	0.287000	0.24848	0.438000	0.31896	-2.909000	0.00699	0.494000	0.27859	0.455000	0.32223	ACC	.	.	alt		0.662	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
FGFR4	2264	hgsc.bcm.edu	37	5	176518784	176518784	+	Silent	SNP	C	C	T	rs452885	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176518784C>T	ENST00000292408.4	+	6	947	c.702C>T	c.(700-702)cgC>cgT	p.R234R	FGFR4_ENST00000292410.3_Silent_p.R234R|FGFR4_ENST00000393637.1_Silent_p.R234R|FGFR4_ENST00000502906.1_Silent_p.R234R|FGFR4_ENST00000393648.2_Silent_p.R234R	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	234	Ig-like C2-type 2.				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)	GCAGCATCCGCTATAACTACC	0.617										TSP Lung(9;0.080)			C|||	4042	0.807109	0.6293	0.8271	5008	,	,		22045	1.0		0.7396	False		,,,				2504	0.9039				p.R234R		Atlas-SNP	.											.	FGFR4	174	.	0			c.C702T						PASS	.	C	,,	2911,1495	676.6+/-403.3	952,1007,244	91.0	81.0	84.0		702,702,702	-1.3	1.0	5	dbSNP_80	84	6468,2132	714.9+/-406.0	2424,1620,256	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	,,	3376,2627,500	TT,TC,CC		24.7907,33.931,27.8871	,,	234/803,234/763,234/803	176518784	9379,3627	2203	4300	6503	SO:0001819	synonymous_variant	2264	exon5			CATCCGCTATAAC	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.702C>T	5.37:g.176518784C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	145	76	0.524138	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Silent	SNP	ENST00000292408.4	37	CCDS4410.1																																																																																			C|0.248;T|0.752	0.752	strong		0.617	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
OR6Y1	391112	hgsc.bcm.edu	37	1	158517353	158517353	+	Silent	SNP	G	G	A	rs16840314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	86	0	0		WXS	Illumina HiSeq	Phase_I	100	39	0.39	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	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_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						PASS	.	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	195	0	0		WXS	Illumina HiSeq	Phase_I	262	124	0.473282	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	
FRRS1	391059	hgsc.bcm.edu	37	1	100203693	100203693	+	Silent	SNP	G	G	A	rs7514021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:100203693G>A	ENST00000414213.1	-	7	1309	c.708C>T	c.(706-708)agC>agT	p.S236S	FRRS1_ENST00000287474.5_Silent_p.S236S			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	236	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					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)		TACTGGGGCCGCTCATTTCAA	0.453													A|||	2796	0.558307	0.9402	0.4928	5008	,	,		18333	0.3909		0.3082	False		,,,				2504	0.5184				p.S236S		Atlas-SNP	.											.	FRRS1	50	.	0			c.C708T						PASS	.	A		3680,726	302.1+/-287.2	1536,608,59	117.0	119.0	119.0		708	-7.1	0.5	1	dbSNP_116	119	2915,5685	671.2+/-402.8	505,1905,1890	no	coding-synonymous	FRRS1	NM_001013660.2		2041,2513,1949	AA,AG,GG		33.8953,16.4775,49.2926		236/627	100203693	6595,6411	2203	4300	6503	SO:0001819	synonymous_variant	391059	exon7			GGGGCCGCTCATT	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.708C>T	1.37:g.100203693G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	185	84	0.454054	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	37																																																																																				G|0.486;A|0.514	0.514	strong		0.453	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
PLEKHG6	55200	hgsc.bcm.edu	37	12	6427052	6427052	+	Silent	SNP	C	C	T	rs1468603	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:6427052C>T	ENST00000396988.3	+	10	1277	c.1047C>T	c.(1045-1047)caC>caT	p.H349H	PLEKHG6_ENST00000304581.8_5'Flank|PLEKHG6_ENST00000449001.2_Silent_p.H317H|PLEKHG6_ENST00000536531.1_Silent_p.H349H|PLEKHG6_ENST00000011684.7_Silent_p.H349H	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	349	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						TCCTGCGACACATCAATGGGC	0.637													C|||	1872	0.373802	0.2375	0.353	5008	,	,		17730	0.2817		0.6203	False		,,,				2504	0.4141				p.H349H		Atlas-SNP	.											.	PLEKHG6	62	.	0			c.C1047T						PASS	.	C	,,	1218,3128		206,806,1161	31.0	28.0	29.0		1047,951,1047	3.8	1.0	12	dbSNP_88	29	5153,3401		1591,1971,715	no	coding-synonymous,coding-synonymous,coding-synonymous	PLEKHG6	NM_001144856.1,NM_001144857.1,NM_018173.3	,,	1797,2777,1876	TT,TC,CC		39.7592,28.0258,49.3876	,,	349/791,317/759,349/791	6427052	6371,6529	2173	4277	6450	SO:0001819	synonymous_variant	55200	exon10			GCGACACATCAAT	AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"""Pleckstrin homology (PH) domain containing"""	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.1047C>T	12.37:g.6427052C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001144856	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Silent	SNP	ENST00000396988.3	37	CCDS8541.1																																																																																			C|0.580;T|0.420	0.420	strong		0.637	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173	
HLA-C	3107	hgsc.bcm.edu	37	6	31239114	31239114	+	Missense_Mutation	SNP	G	G	T	rs1071649	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31239114G>T	ENST00000376228.5	-	3	369	c.355C>A	c.(355-357)Ctc>Atc	p.L119I	HLA-C_ENST00000383329.3_Missense_Mutation_p.L119I	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	119	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						ATCCTCTGGAGGGTGTGAGAC	0.687																																					p.L119I		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,4	HLA-C	92	4	0			c.C355A						scavenged	.						18.0	17.0	17.0					6																	31239114		2156	4235	6391	SO:0001583	missense	3107	exon3			TCTGGAGGGTGTG	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.355C>A	6.37:g.31239114G>T	ENSP00000365402:p.Leu119Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	29	7	0.241379	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	446|446	0.2042124542124542|0.2042124542124542	95|95	0.19308943089430894|0.19308943089430894	69|69	0.19060773480662985|0.19060773480662985	150|150	0.26223776223776224|0.26223776223776224	132|132	0.1741424802110818|0.1741424802110818	.|.	3.049|3.049	-0.195727|-0.195727	0.06259|0.06259	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00892|.	5.57;5.57|.	2.65|2.65	-5.3|-5.3	0.02738|0.02738	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.051930|.	0.07715|.	N|.	0.942735|.	T|T	0.04318|0.04318	0.0119|0.0119	N|N	0.12831|0.12831	0.26|0.26	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.25405|.	0.06;0.023;0.023;0.023;0.015|.	T|T	0.23440|0.23440	-1.0188|-1.0188	9|4	0.02654|.	T|.	1|.	.|.	4.4797|4.4797	0.11760|0.11760	0.3595:0.0:0.1581:0.4824|0.3595:0.0:0.1581:0.4824	rs1071649;rs1131234;rs2308565;rs3177925;rs3190687;rs3190937;rs9266154|rs1071649;rs1131234;rs2308565;rs3177925;rs3190687;rs3190937;rs9266154	119;94;119;119;119|.	A2AEA4;Q92671;A6H578;A2AEA2;P10321|.	.;.;.;.;1C07_HUMAN|.	I|H	119;119;119;156|118	ENSP00000365402:L119I;ENSP00000372819:L119I|.	ENSP00000365402:L119I|.	L|P	-|-	1|2	0|0	HLA-C|HLA-C	31347093|31347093	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	-9.628000|-9.628000	0.00010|0.00010	-2.201000|-2.201000	0.00746|0.00746	-2.518000|-2.518000	0.00185|0.00185	CTC|CCT	T|0.197;G|0.798;A|0.005	0.197	strong		0.687	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548632	32548632	+	Splice_Site	SNP	T	T	A	rs1136881	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32548632T>A	ENST00000360004.5	-	4	759	c.654A>T	c.(652-654)agA>agT	p.R218S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	218	Beta-2.				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						CAGACCGTGCTCCTGAGAGAG	0.493										Multiple Myeloma(14;0.17)																											p.R218S		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A654T						PASS	.						74.0	83.0	79.0					6																	32548632		1511	2709	4220	SO:0001630	splice_region_variant	3123	exon4			CCGTGCTCCTGAG	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.653-1A>T	6.37:g.32548632T>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	192	45	0.234375	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	7.979	0.750737	0.15778	.	.	ENSG00000196126	ENST00000360004	T	0.07688	3.17	3.98	1.02	0.19986	Immunoglobulin-like fold (3);	0.645090	0.16985	N	0.191537	T	0.03477	0.0100	M	0.68317	2.08	0.80722	D	1	B;B;P	0.51449	0.011;0.027;0.945	B;B;B	0.37451	0.01;0.05;0.25	T	0.43114	-0.9411	10	0.59425	D	0.04	.	7.0655	0.25149	0.0:0.6544:0.0:0.3456	rs1136881;rs2308782;rs2308820;rs3200532;rs3830124;rs17433989;rs17856139;rs17883227	218;218;218	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	S	218	ENSP00000353099:R218S	ENSP00000353099:R218S	R	-	3	2	HLA-DRB1	32656610	0.000000	0.05858	0.718000	0.30602	0.080000	0.17528	-0.892000	0.04131	-0.038000	0.13624	-0.479000	0.04858	AGA	T|0.711;A|0.289	0.289	strong		0.493	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	Missense_Mutation
OR56A4	120793	hgsc.bcm.edu	37	11	6023818	6023818	+	Silent	SNP	G	G	A	rs10839221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6023818G>A	ENST00000330728.4	-	1	606	c.561C>T	c.(559-561)taC>taT	p.Y187Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	135						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)		TGATAGACGGGTATCTCAATG	0.493													.|||	812	0.162141	0.0582	0.1945	5008	,	,		22200	0.0794		0.2684	False		,,,				2504	0.2556				p.Y187Y		Atlas-SNP	.											.	OR56A4	66	.	0			c.C561T						PASS	.	G		477,3925	223.9+/-240.3	29,419,1753	65.0	58.0	60.0		561	-0.6	0.1	11	dbSNP_120	60	2565,6027	417.8+/-352.5	397,1771,2128	no	coding-synonymous	OR56A4	NM_001005179.2		426,2190,3881	AA,AG,GG		29.8534,10.836,23.4108		187/366	6023818	3042,9952	2201	4296	6497	SO:0001819	synonymous_variant	120793	exon1			AGACGGGTATCTC	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.561C>T	11.37:g.6023818G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			G|0.801;A|0.199	0.199	strong		0.493	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
CA8	767	hgsc.bcm.edu	37	8	61178574	61178574	+	Silent	SNP	T	T	C	rs7464181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:61178574T>C	ENST00000317995.4	-	3	591	c.327A>G	c.(325-327)gaA>gaG	p.E109E		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	109					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	ACAGTTCAAATTCATGCCCTT	0.398													T|||	2509	0.500998	0.8457	0.3977	5008	,	,		17998	0.2669		0.4235	False		,,,				2504	0.4294				p.E109E		Atlas-SNP	.											.	CA8	31	.	0			c.A327G						PASS	.	T		3347,1059	723.8+/-409.4	1266,815,122	71.0	68.0	69.0		327	-4.1	1.0	8	dbSNP_116	69	3523,5077	514.1+/-378.3	699,2125,1476	yes	coding-synonymous	CA8	NM_004056.4		1965,2940,1598	CC,CT,TT		40.9651,24.0354,47.1782		109/291	61178574	6870,6136	2203	4300	6503	SO:0001819	synonymous_variant	767	exon3			TTCAAATTCATGC	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"""Carbonic anhydrases"""	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.327A>G	8.37:g.61178574T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_004056	A8K0A5|B3KQZ7|Q32MY2	Silent	SNP	ENST00000317995.4	37	CCDS6174.1																																																																																			T|0.488;C|0.512	0.512	strong		0.398	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1		
EYA4	2070	hgsc.bcm.edu	37	6	133789728	133789728	+	Missense_Mutation	SNP	G	G	A	rs9493627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:133789728G>A	ENST00000367895.5	+	11	1293	c.829G>A	c.(829-831)Ggc>Agc	p.G277S	EYA4_ENST00000525849.1_Missense_Mutation_p.G254S|EYA4_ENST00000531901.1_Missense_Mutation_p.G277S|EYA4_ENST00000430974.2_Missense_Mutation_p.G223S|EYA4_ENST00000452339.2_Missense_Mutation_p.G223S|EYA4_ENST00000431403.2_Missense_Mutation_p.G277S|EYA4_ENST00000355167.3_Missense_Mutation_p.G277S|EYA4_ENST00000355286.6_Missense_Mutation_p.G254S	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	277			G -> S (in dbSNP:rs9493627). {ECO:0000269|PubMed:9887327}.		anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TACAGCCTTTGGCCAAAACCA	0.388													G|||	2051	0.409545	0.5688	0.3429	5008	,	,		20421	0.3442		0.3111	False		,,,				2504	0.41				p.G277S	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											.	EYA4	196	.	0			c.G829A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	2291,2115	600.2+/-389.4	590,1111,502	124.0	113.0	116.0		829,760,829	5.5	1.0	6	dbSNP_119	116	2690,5910	432.9+/-357.3	453,1784,2063	yes	missense,missense,missense	EYA4	NM_004100.4,NM_172103.3,NM_172105.3	56,56,56	1043,2895,2565	AA,AG,GG		31.2791,48.0027,38.2977	probably-damaging,probably-damaging,probably-damaging	277/640,254/617,277/640	133789728	4981,8025	2203	4300	6503	SO:0001583	missense	2070	exon11			GCCTTTGGCCAAA	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3522	protein-coding gene	gene with protein product		603550	"""eyes absent (Drosophila) homolog 4"", ""eyes absent homolog 4 (Drosophila)"""	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.829G>A	6.37:g.133789728G>A	ENSP00000356870:p.Gly277Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	859	0.3933150183150183	281	0.5711382113821138	121	0.3342541436464088	220	0.38461538461538464	237	0.31266490765171506	G	35	5.550184	0.96501	0.519973	0.312791	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69;-1.69;-1.69;-1.69	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.83769	0.5326	L	0.48935	1.535	0.09310	P	0.99999999960463	D;D;P;P;D;D	0.54964	0.969;0.969;0.865;0.865;0.966;0.969	P;P;B;B;P;P	0.60068	0.828;0.801;0.301;0.301;0.664;0.868	T	0.78909	-0.2018	9	0.21014	T	0.42	-11.1073	19.7445	0.96247	0.0:0.0:1.0:0.0	rs9493627;rs52825718;rs59205496;rs9493627	277;223;223;254;277;277	F2Z2Y1;E7ESD5;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;.;EYA4_HUMAN	S	223;223;277;277;254;277;254;277	ENSP00000395916:G223S;ENSP00000388670:G223S;ENSP00000356870:G277S;ENSP00000347294:G277S;ENSP00000347434:G254S;ENSP00000432770:G277S;ENSP00000433219:G254S;ENSP00000404558:G277S	ENSP00000347294:G277S	G	+	1	0	EYA4	133831421	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.739000	0.93911	0.655000	0.94253	GGC	G|0.600;A|0.400	0.400	strong		0.388	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100	
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412347	105412347	+	Silent	SNP	C	C	T	rs55842266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105412347C>T	ENST00000333244.5	-	7	9560	c.9441G>A	c.(9439-9441)aaG>aaA	p.K3147K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3147						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)			GCATCTTGAACTTGGGCATTT	0.602													.|||	305	0.0609026	0.0106	0.0778	5008	,	,		16789	0.0109		0.1491	False		,,,				2504	0.0777				p.K3147K		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,neuroblastoma,0,1	AHNAK2	719	1	0			c.G9441A						scavenged	.						199.0	143.0	161.0					14																	105412347		1924	4066	5990	SO:0001819	synonymous_variant	113146	exon7			CTTGAACTTGGGC	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.9441G>A	14.37:g.105412347C>T		Somatic	84	2	0.0238095		WXS	Illumina HiSeq	Phase_I	90	7	0.0777778	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	weak		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	179638721	179638721	+	Missense_Mutation	SNP	C	C	T	rs4894048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179638721C>T	ENST00000591111.1	-	31	7398	c.7174G>A	c.(7174-7176)Ggc>Agc	p.G2392S	TTN_ENST00000589042.1_Missense_Mutation_p.G2392S|TTN_ENST00000360870.5_Missense_Mutation_p.G2392S|TTN_ENST00000342992.6_Missense_Mutation_p.G2392S|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G2346S|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G2346S|TTN_ENST00000460472.2_Missense_Mutation_p.G2346S			Q8WZ42	TITIN_HUMAN	titin	12714	Ig-like 13.		G -> S (in dbSNP:rs4894048). {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)			ACTTCTTGGCCGTCTTTCATC	0.443													C|||	438	0.0874601	0.0915	0.1599	5008	,	,		19821	0.0149		0.0358	False		,,,				2504	0.1585				p.G2392S		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,0,6	TTN	18412	6	0			c.G7174A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	419,3987	204.5+/-226.7	16,387,1800	134.0	122.0	126.0		7036,7174,7174,7036,7036	4.9	1.0	2	dbSNP_111	126	190,8410	84.0+/-146.5	3,184,4113	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	56,56,56,56,56	19,571,5913	TT,TC,CC		2.2093,9.5098,4.6825	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	2346/26927,2392/33424,2392/5605,2346/27052,2346/27119	179638721	609,12397	2203	4300	6503	SO:0001583	missense	7273	exon31			CTTGGCCGTCTTT	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.7174G>A	2.37:g.179638721C>T	ENSP00000465570:p.Gly2392Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	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		122	0.055860805860805864	49	0.09959349593495935	45	0.12430939226519337	4	0.006993006993006993	24	0.0316622691292876	C	12.67	2.007823	0.35415	0.095098	0.022093	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.73	4.86	0.63082	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14570	0.0352	M	0.89840	3.065	0.37263	P	0.09292500000000004	D;D;D;D;D	0.76494	0.984;0.984;0.984;0.992;0.999	P;P;P;P;P	0.60609	0.506;0.506;0.506;0.656;0.877	T	0.63616	-0.6597	8	0.87932	D	0	.	15.039	0.71774	0.0:0.9318:0.0:0.0682	rs4894048;rs59411204;rs4894048	2346;2346;2346;2392;2392	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	S	2392;2346;2346;2346;2346;2392	ENSP00000343764:G2392S;ENSP00000434586:G2346S;ENSP00000340554:G2346S;ENSP00000352154:G2346S;ENSP00000354117:G2392S	ENSP00000340554:G2346S	G	-	1	0	TTN	179346966	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	4.101000	0.57769	1.448000	0.47680	-0.133000	0.14855	GGC	C|0.947;T|0.053	0.053	strong		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SLC25A24	29957	hgsc.bcm.edu	37	1	108728484	108728484	+	Silent	SNP	T	T	C	rs862493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:108728484T>C	ENST00000565488.1	-	2	495	c.276A>G	c.(274-276)aaA>aaG	p.K92K	SLC25A24_ENST00000370041.4_Silent_p.K73K	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	92	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				ATP transport (GO:0015867)|cellular response to calcium ion (GO:0071277)|cellular response to oxidative stress (GO:0034599)|mitochondrial transport (GO:0006839)|regulation of cell death (GO:0010941)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP transmembrane transporter activity (GO:0005347)|calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TAAATGCCAATTTCATTTTCT	0.303													T|||	825	0.164736	0.1815	0.1657	5008	,	,		14544	0.0794		0.2157	False		,,,				2504	0.1769				p.K92K		Atlas-SNP	.											.	SLC25A24	65	.	0			c.A276G						PASS	.	T	,	815,3581	315.2+/-294.0	86,643,1469	96.0	91.0	93.0		276,219	0.8	0.9	1	dbSNP_86	93	1794,6794	310.8+/-310.0	193,1408,2693	no	coding-synonymous,coding-synonymous	SLC25A24	NM_013386.3,NM_213651.1	,	279,2051,4162	CC,CT,TT		20.8896,18.5396,20.094	,	92/478,73/459	108728484	2609,10375	2198	4294	6492	SO:0001819	synonymous_variant	29957	exon2			TGCCAATTTCATT	AJ619961	CCDS786.1, CCDS41361.1	1p13.2	2013-05-22			ENSG00000085491	ENSG00000085491		"""Solute carriers"", ""EF-hand domain containing"""	20662	protein-coding gene	gene with protein product		608744				15123600	Standard	NM_013386		Approved	DKFZp586G0123, APC1	uc001dvn.5	Q6NUK1	OTTHUMG00000011013	ENST00000565488.1:c.276A>G	1.37:g.108728484T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_013386	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Silent	SNP	ENST00000565488.1	37	CCDS41361.1																																																																																			C|0.183;N|0.000	0.183	strong		0.303	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386	
OR5R1	219479	hgsc.bcm.edu	37	11	56185689	56185689	+	Missense_Mutation	SNP	A	A	G	rs7931261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56185689A>G	ENST00000312253.1	-	1	19	c.20T>C	c.(19-21)aTt>aCt	p.I7T		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	7			I -> T (in dbSNP:rs7931261).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I7T(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)					AGTGACATAAATGATATTAAC	0.398													G|||	1415	0.282548	0.5386	0.1916	5008	,	,		20124	0.1369		0.2664	False		,,,				2504	0.1677				p.I7T		Atlas-SNP	.											OR5R1,NS,carcinoma,0,1	OR5R1	83	1	1	Substitution - Missense(1)	prostate(1)	c.T20C						PASS	.	G	THR/ILE	2208,2194	580.7+/-385.2	571,1066,564	76.0	87.0	83.0		20	5.7	0.0	11	dbSNP_116	83	2398,6192	693.5+/-404.7	320,1758,2217	yes	missense	OR5R1	NM_001004744.1	89	891,2824,2781	GG,GA,AA		27.9162,49.841,35.4526	benign	7/325	56185689	4606,8386	2201	4295	6496	SO:0001583	missense	219479	exon1			ACATAAATGATAT	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.20T>C	11.37:g.56185689A>G	ENSP00000308595:p.Ile7Thr	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	609	0.27884615384615385	250	0.508130081300813	63	0.17403314917127072	88	0.15384615384615385	208	0.27440633245382584	G	1.234	-0.623366	0.03636	0.50159	0.279162	ENSG00000174942	ENST00000312253	T	0.02863	4.13	5.7	5.7	0.88788	.	0.256774	0.20090	N	0.099479	T	0.00012	0.0000	N	0.00014	-2.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35500	-0.9786	9	0.02654	T	1	-8.0744	9.7118	0.40249	0.076:0.1401:0.7839:0.0	rs7931261;rs52793105;rs60855759;rs7931261	7	Q8NH85	OR5R1_HUMAN	T	7	ENSP00000308595:I7T	ENSP00000308595:I7T	I	-	2	0	OR5R1	55942265	0.000000	0.05858	0.004000	0.12327	0.307000	0.27823	0.400000	0.20932	1.434000	0.47414	-0.695000	0.03696	ATT	A|0.675;G|0.325	0.325	strong		0.398	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
PMF1	11243	hgsc.bcm.edu	37	1	156202173	156202173	+	Missense_Mutation	SNP	A	A	G	rs1052053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156202173A>G	ENST00000368277.3	+	2	233	c.224A>G	c.(223-225)cAa>cGa	p.Q75R	PMF1_ENST00000565805.1_Missense_Mutation_p.Q75R|PMF1-BGLAP_ENST00000368276.4_Missense_Mutation_p.Q75R|PMF1_ENST00000368273.4_Intron|PMF1_ENST00000368279.3_Missense_Mutation_p.Q75R|PMF1-BGLAP_ENST00000490491.1_Missense_Mutation_p.Q75R|PMF1_ENST00000567140.1_Missense_Mutation_p.Q75R|PMF1-BGLAP_ENST00000320139.5_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	117	0	0		WXS	Illumina HiSeq	Phase_I	192	114	0.59375	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	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111519758	111519758	+	Missense_Mutation	SNP	T	T	A	rs75508009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:111519758T>A	ENST00000261486.5	-	18	1853	c.1577A>T	c.(1576-1578)aAc>aTc	p.N526I	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	526						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)		GTCGGCTTGGTTTTTTTCCTT	0.433													T|||	13	0.00259585	0.0	0.0014	5008	,	,		15867	0.0		0.0109	False		,,,				2504	0.001				p.N526I		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.A1577T						PASS	.	T	ILE/ASN	7,3743		0,7,1868	179.0	164.0	169.0		1577	0.7	1.0	5	dbSNP_131	169	72,8138		1,70,4034	yes	missense	EPB41L4A	NM_022140.3	149	1,77,5902	AA,AT,TT		0.877,0.1867,0.6605	benign	526/687	111519758	79,11881	1875	4105	5980	SO:0001583	missense	64097	exon18			GCTTGGTTTTTTT	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.1577A>T	5.37:g.111519758T>A	ENSP00000261486:p.Asn526Ile	Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	252	112	0.444444	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	T	11.56	1.674770	0.29783	0.001867	0.00877	ENSG00000129595	ENST00000261486	D	0.82526	-1.62	6.17	0.661	0.17874	.	0.451085	0.24415	N	0.038736	T	0.55097	0.1899	N	0.14661	0.345	0.31899	N	0.616178	B;B	0.20671	0.047;0.041	B;B	0.21708	0.036;0.032	T	0.51458	-0.8703	10	0.33940	T	0.23	.	3.1856	0.06599	0.1025:0.1248:0.3433:0.4293	.	526;153	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	I	526	ENSP00000261486:N526I	ENSP00000261486:N526I	N	-	2	0	EPB41L4A	111547657	0.686000	0.27661	0.998000	0.56505	0.978000	0.69477	-0.520000	0.06252	0.158000	0.19367	0.533000	0.62120	AAC	T|0.994;A|0.006	0.006	strong		0.433	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
LRIT1	26103	hgsc.bcm.edu	37	10	85992255	85992255	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85992255C>T	ENST00000372105.3	-	4	1321	c.1300G>A	c.(1300-1302)Gtg>Atg	p.V434M		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	434	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						ACCACCTTCACAGACCTCACC	0.587																																					p.V434M		Atlas-SNP	.											.	LRIT1	73	.	0			c.G1300A						PASS	.						107.0	83.0	91.0					10																	85992255		2203	4300	6503	SO:0001583	missense	26103	exon4			CCTTCACAGACCT	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1300G>A	10.37:g.85992255C>T	ENSP00000361177:p.Val434Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	19	0.231707	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303962	0.60305	.	.	ENSG00000148602	ENST00000372105	T	0.60797	0.16	5.58	3.68	0.42216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.124327	0.53938	D	0.000047	T	0.52533	0.1740	L	0.43923	1.385	0.51012	D	0.999902	P	0.37276	0.589	B	0.39935	0.314	T	0.58668	-0.7596	10	0.62326	D	0.03	.	13.8294	0.63370	0.0:0.5725:0.4275:0.0	.	434	Q9P2V4	LRIT1_HUMAN	M	434	ENSP00000361177:V434M	ENSP00000361177:V434M	V	-	1	0	LRIT1	85982235	0.996000	0.38824	0.897000	0.35233	0.451000	0.32288	2.950000	0.49081	1.347000	0.45714	-0.165000	0.13383	GTG	.	.	none		0.587	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
MYOM1	8736	hgsc.bcm.edu	37	18	3188778	3188778	+	Missense_Mutation	SNP	C	C	T	rs139422575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:3188778C>T	ENST00000356443.4	-	4	1072	c.739G>A	c.(739-741)Gaa>Aaa	p.E247K	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000261606.7_Missense_Mutation_p.E247K|MYOM1_ENST00000400569.3_Missense_Mutation_p.E247K	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	247				E -> G (in Ref. 5; CAA48833). {ECO:0000305}.	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						TCTGCCTTTTCTCGAATCACA	0.453													C|||	11	0.00219649	0.0	0.0029	5008	,	,		18216	0.0		0.008	False		,,,				2504	0.001				p.E247K		Atlas-SNP	.											.	MYOM1	192	.	0			c.G739A						PASS	.	C	LYS/GLU,LYS/GLU	7,3885		1,5,1940	93.0	87.0	89.0		739,739	5.8	1.0	18	dbSNP_134	89	46,8218		0,46,4086	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	56,56	1,51,6026	TT,TC,CC		0.5566,0.1799,0.436	possibly-damaging,possibly-damaging	247/1686,247/1590	3188778	53,12103	1946	4132	6078	SO:0001583	missense	8736	exon4			CCTTTTCTCGAAT	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.739G>A	18.37:g.3188778C>T	ENSP00000348821:p.Glu247Lys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	209	126	0.602871	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	34	5.317846	0.95682	0.001799	0.005566	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.51071	0.87;0.85;0.72	5.84	5.84	0.93424	.	0.246709	0.41294	D	0.000913	T	0.42086	0.1187	L	0.38175	1.15	0.50171	D	0.999857	P;D	0.55172	0.939;0.97	P;P	0.53102	0.523;0.718	T	0.20338	-1.0278	10	0.08599	T	0.76	.	19.7351	0.96200	0.0:1.0:0.0:0.0	.	247;247	P52179-2;P52179	.;MYOM1_HUMAN	K	247	ENSP00000348821:E247K;ENSP00000383413:E247K;ENSP00000261606:E247K	ENSP00000261606:E247K	E	-	1	0	MYOM1	3178778	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.205000	0.58466	2.756000	0.94617	0.603000	0.83216	GAA	C|0.995;T|0.005	0.005	strong		0.453	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
SENP8	123228	hgsc.bcm.edu	37	15	72432140	72432140	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72432140C>T	ENST00000542035.2	+	2	509	c.176C>T	c.(175-177)aCc>aTc	p.T59I	RP11-2I17.4_ENST00000568984.1_RNA|SENP8_ENST00000544171.1_Missense_Mutation_p.T59I|SENP8_ENST00000544411.1_Missense_Mutation_p.T59I|SENP8_ENST00000340912.4_Missense_Mutation_p.T59I	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	59	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						CCTGAAGTCACCCAGTTCATC	0.453																																					p.T59I		Atlas-SNP	.											.	SENP8	18	.	0			c.C176T						PASS	.						156.0	135.0	142.0					15																	72432140		2199	4297	6496	SO:0001583	missense	123228	exon2			AAGTCACCCAGTT	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"""NEDD8-specific protease 1"", ""sentrin/SUMO-specific protease SENP8"", ""deneddylase 1"""	608659	"""protease, cysteine, 2 (NEDD8 specific)"", ""SUMO/sentrin specific protease family member 8"""	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.176C>T	15.37:g.72432140C>T	ENSP00000446057:p.Thr59Ile	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	5	0.04	NM_001166340	Q96QA4	Missense_Mutation	SNP	ENST00000542035.2	37	CCDS10240.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747790	0.69533	.	.	ENSG00000166192	ENST00000542035;ENST00000544411;ENST00000340912;ENST00000544171	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.62	4.71	0.59529	.	0.167236	0.52532	D	0.000072	T	0.40347	0.1113	M	0.70903	2.155	0.58432	D	0.999993	P	0.40332	0.713	P	0.45577	0.486	T	0.27606	-1.0069	10	0.42905	T	0.14	-21.7606	11.9463	0.52930	0.137:0.7313:0.1317:0.0	.	59	Q96LD8	SENP8_HUMAN	I	59	ENSP00000446057:T59I;ENSP00000441753:T59I;ENSP00000340505:T59I;ENSP00000439415:T59I	ENSP00000340505:T59I	T	+	2	0	SENP8	70219194	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	5.879000	0.69690	1.517000	0.48917	0.655000	0.94253	ACC	.	.	none		0.453	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204	
F5	2153	hgsc.bcm.edu	37	1	169541513	169541513	+	Missense_Mutation	SNP	C	C	G	rs6019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169541513C>G	ENST00000367797.3	-	3	520	c.319G>C	c.(319-321)Gat>Cat	p.D107H	F5_ENST00000546081.1_5'UTR|F5_ENST00000367796.3_Missense_Mutation_p.D107H	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	107	F5/8 type A 1.|Plastocyanin-like 1.		D -> H (in dbSNP:rs6019). {ECO:0000269|PubMed:10391209, 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)	AAGGGCTTATCTGCCTTATTT	0.333													C|||	638	0.127396	0.4039	0.0605	5008	,	,		20751	0.0		0.0537	False		,,,				2504	0.0082				p.D107H		Atlas-SNP	.											.	F5	301	.	0			c.G319C	GRCh37	CM032890	F5	M	rs6019	PASS	.	C	HIS/ASP	1506,2900	477.7+/-358.0	253,1000,950	72.0	73.0	73.0		319	3.2	1.0	1	dbSNP_52	73	471,8127	138.3+/-195.1	12,447,3840	yes	missense	F5	NM_000130.4	81	265,1447,4790	GG,GC,CC		5.478,34.1807,15.203	benign	107/2225	169541513	1977,11027	2203	4299	6502	SO:0001583	missense	2153	exon3			GCTTATCTGCCTT	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.319G>C	1.37:g.169541513C>G	ENSP00000356771:p.Asp107His	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	236	0.10805860805860806	166	0.33739837398373984	28	0.07734806629834254	0	0.0	42	0.055408970976253295	C	12.83	2.054285	0.36277	0.341807	0.05478	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.99014	-5.33;-5.33	5.35	3.22	0.36961	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.497971	0.22648	N	0.057373	D	0.95239	0.8456	L	0.59967	1.855	0.09310	P	0.9999999999979803	B	0.22003	0.063	B	0.25759	0.063	D	0.92413	0.5939	9	0.48119	T	0.1	-9.9255	3.2793	0.06909	0.0:0.5284:0.2578:0.2138	rs6019;rs52823153;rs6019	107	P12259	FA5_HUMAN	H	107	ENSP00000356771:D107H;ENSP00000356770:D107H	ENSP00000356770:D107H	D	-	1	0	F5	167808137	0.977000	0.34250	1.000000	0.80357	0.992000	0.81027	0.611000	0.24268	1.243000	0.43853	0.563000	0.77884	GAT	C|0.863;G|0.137	0.137	strong		0.333	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ZP2	7783	hgsc.bcm.edu	37	16	21215672	21215672	+	Silent	SNP	A	A	G	rs2075526	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21215672A>G	ENST00000574002.1	-	9	1229	c.747T>C	c.(745-747)ccT>ccC	p.P249P	ZP2_ENST00000574091.1_Silent_p.P249P|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000219593.4_Silent_p.P249P			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	249					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)		CCTTCTGTCCAGGAGATATAA	0.423													A|||	1593	0.318091	0.2352	0.2968	5008	,	,		22553	0.3998		0.2773	False		,,,				2504	0.4029				p.P249P		Atlas-SNP	.											.	ZP2	92	.	0			c.T747C						PASS	.	A		1023,3377	376.6+/-322.1	110,803,1287	104.0	101.0	102.0		747	2.2	0.7	16	dbSNP_96	102	2326,6274	388.4+/-342.6	330,1666,2304	no	coding-synonymous	ZP2	NM_003460.1		440,2469,3591	GG,GA,AA		27.0465,23.25,25.7615		249/746	21215672	3349,9651	2200	4300	6500	SO:0001819	synonymous_variant	7783	exon8			CTGTCCAGGAGAT	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.747T>C	16.37:g.21215672A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Silent	SNP	ENST00000574002.1	37	CCDS10596.1																																																																																			A|0.721;G|0.279	0.279	strong		0.423	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
TNS4	84951	hgsc.bcm.edu	37	17	38645125	38645125	+	Missense_Mutation	SNP	A	A	G	rs3764424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38645125A>G	ENST00000254051.6	-	3	694	c.536T>C	c.(535-537)cTt>cCt	p.L179P		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	179	Ser-rich.		L -> P (in dbSNP:rs3764424). {ECO:0000269|PubMed:12154022}.		apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			ACCACTGCGAAGGGAGCCGAA	0.622													G|||	1744	0.348243	0.3661	0.3343	5008	,	,		17352	0.3601		0.2664	False		,,,				2504	0.4059				p.L179P		Atlas-SNP	.											TNS4,NS,carcinoma,0,2	TNS4	72	2	0			c.T536C						PASS	.	G	PRO/LEU	1479,2925		272,935,995	51.0	62.0	58.0		536	5.8	0.9	17	dbSNP_107	58	2066,6528		264,1538,2495	yes	missense	TNS4	NM_032865.5	98	536,2473,3490	GG,GA,AA		24.04,33.5831,27.2734	benign	179/716	38645125	3545,9453	2202	4297	6499	SO:0001583	missense	84951	exon3			CTGCGAAGGGAGC	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.536T>C	17.37:g.38645125A>G	ENSP00000254051:p.Leu179Pro	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	37	CCDS11368.1	672	0.3076923076923077	163	0.3313008130081301	109	0.3011049723756906	201	0.3513986013986014	199	0.262532981530343	G	1.812	-0.474428	0.04414	0.335831	0.2404	ENSG00000131746	ENST00000377816;ENST00000254051	T	0.14516	2.5	5.77	5.77	0.91146	.	0.533182	0.17309	N	0.178943	T	0.00012	0.0000	N	0.01048	-1.04	0.34228	P	0.32381099999999996	B	0.02656	0.0	B	0.01281	0.0	T	0.40664	-0.9551	9	0.02654	T	1	-8.4726	13.0665	0.59036	0.0749:0.0:0.9251:0.0	rs3764424;rs3764424	179	Q8IZW8	TENS4_HUMAN	P	179	ENSP00000254051:L179P	ENSP00000254051:L179P	L	-	2	0	TNS4	35898651	1.000000	0.71417	0.866000	0.34008	0.285000	0.27093	3.492000	0.53259	1.462000	0.47948	-0.213000	0.12676	CTT	A|0.708;G|0.292	0.292	strong		0.622	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
SCLT1	132320	hgsc.bcm.edu	37	4	129867280	129867280	+	Missense_Mutation	SNP	T	T	A	rs10028124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:129867280T>A	ENST00000281142.5	-	16	1824	c.1321A>T	c.(1321-1323)Agt>Tgt	p.S441C	SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000439369.2_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	441			S -> C (in dbSNP:rs10028124). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		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						CTGTAATCACTCTCATTTCCT	0.348													T|||	3807	0.760184	0.9599	0.7637	5008	,	,		14832	0.7044		0.673	False		,,,				2504	0.635				p.S441C		Atlas-SNP	.											.	SCLT1	136	.	0			c.A1321T						PASS	.	T	CYS/SER	4025,379	788.6+/-414.9	1839,347,16	98.0	91.0	93.0		1321	1.5	1.0	4	dbSNP_119	93	5628,2968	665.6+/-402.3	1866,1896,536	yes	missense	SCLT1	NM_144643.2	112	3705,2243,552	AA,AT,TT		34.5277,8.6058,25.7462	possibly-damaging	441/689	129867280	9653,3347	2202	4298	6500	SO:0001583	missense	132320	exon16			AATCACTCTCATT	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.1321A>T	4.37:g.129867280T>A	ENSP00000281142:p.Ser441Cys	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	1619	0.7413003663003663	465	0.9451219512195121	270	0.7458563535911602	387	0.6765734265734266	497	0.6556728232189973	T	15.55	2.867699	0.51588	0.913942	0.654723	ENSG00000151466	ENST00000281142	T	0.30981	1.51	4.39	1.5	0.22942	.	0.681258	0.15234	N	0.273277	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999618503	D	0.55800	0.973	P	0.53360	0.724	T	0.23048	-1.0199	8	.	.	.	-0.2858	6.1918	0.20528	0.0:0.3324:0.0:0.6676	rs10028124;rs52819094	441	Q96NL6	SCLT1_HUMAN	C	441	ENSP00000281142:S441C	.	S	-	1	0	SCLT1	130086730	0.035000	0.19736	0.999000	0.59377	0.710000	0.40934	0.010000	0.13242	0.594000	0.29761	0.454000	0.30748	AGT	T|0.257;A|0.743	0.743	strong		0.348	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
COL6A2	1292	hgsc.bcm.edu	37	21	47545913	47545913	+	Silent	SNP	G	G	A	rs2839114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47545913G>A	ENST00000300527.4	+	26	2288	c.2184G>A	c.(2182-2184)gtG>gtA	p.V728V	COL6A2_ENST00000409416.1_Silent_p.V728V|COL6A2_ENST00000397763.1_Silent_p.V728V|COL6A2_ENST00000310645.5_Silent_p.V728V|COL6A2_ENST00000357838.4_Silent_p.V728V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	728	Nonhelical region.|VWFA 2. {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)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGTTTGCGGTGGTCATCACGG	0.652													G|||	1613	0.322085	0.1067	0.5548	5008	,	,		14926	0.4226		0.3837	False		,,,				2504	0.2812				p.V728V		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2184A						PASS	.	G	,,	584,3822	256.7+/-261.4	47,490,1666	80.0	77.0	78.0		2184,2184,2184	3.1	1.0	21	dbSNP_100	78	3208,5392	483.3+/-371.1	614,1980,1706	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	661,2470,3372	AA,AG,GG		37.3023,13.2547,29.1558	,,	728/1020,728/919,728/829	47545913	3792,9214	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			TGCGGTGGTCATC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2184G>A	21.37:g.47545913G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			G|0.690;A|0.310	0.310	strong		0.652	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506747	195506747	+	Missense_Mutation	SNP	C	C	T	rs62282470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506747C>T	ENST00000463781.3	-	2	12163	c.11704G>A	c.(11704-11706)Gcc>Acc	p.A3902T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3902T	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)	p.A3902T(1)		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)		AGAGGGGTGGCGTGACGTGTG	0.592													.|||	553	0.110423	0.0287	0.1095	5008	,	,		8458	0.0536		0.2256	False		,,,				2504	0.1616				p.A3902T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	1	Substitution - Missense(1)	endometrium(1)	c.G11704A						PASS	.						10.0	9.0	9.0					3																	195506747		528	1045	1573	SO:0001583	missense	4585	exon2			GGGTGGCGTGACG	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.11704G>A	3.37:g.195506747C>T	ENSP00000417498:p.Ala3902Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	33	24	0.727273	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	205	0.09386446886446886	39	0.07926829268292683	27	0.07458563535911603	37	0.06468531468531469	102	0.1345646437994723	c	7.588	0.670216	0.14776	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.54;1.44	.	.	.	.	.	.	.	.	T	0.00144	0.0004	N	0.19112	0.55	0.09310	N	1	B	0.26975	0.165	B	0.06405	0.002	T	0.18272	-1.0342	7	.	.	.	.	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	rs62282470	3774	E7ESK3	.	T	3902	ENSP00000417498:A3902T;ENSP00000420243:A3902T	.	A	-	1	0	MUC4	196991526	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-2.501000	0.00966	-2.037000	0.00920	-2.088000	0.00374	GCC	C|0.920;T|0.080	0.080	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR4N2	390429	hgsc.bcm.edu	37	14	20295763	20295763	+	Silent	SNP	C	C	T	rs11621854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	254	0	0		WXS	Illumina HiSeq	Phase_I	319	74	0.231975	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		
EPHX1	2052	hgsc.bcm.edu	37	1	226032229	226032229	+	Silent	SNP	C	C	T	rs1051741	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:226032229C>T	ENST00000366837.4	+	8	1267	c.1071C>T	c.(1069-1071)aaC>aaT	p.N357N	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.N357N	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	357					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)	p.N357N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TGCTGACCAACGTCATGCTCT	0.562													C|||	633	0.126398	0.1051	0.0591	5008	,	,		20510	0.1141		0.0895	False		,,,				2504	0.2536				p.N357N		Atlas-SNP	.											EPHX1,NS,carcinoma,0,1	EPHX1	57	1	1	Substitution - coding silent(1)	stomach(1)	c.C1071T						PASS	.	C	,	498,3908	232.0+/-245.7	37,424,1742	133.0	109.0	117.0		1071,1071	2.5	1.0	1	dbSNP_86	117	888,7712	199.6+/-243.6	60,768,3472	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	97,1192,5214	TT,TC,CC		10.3256,11.3028,10.6566	,	357/456,357/456	226032229	1386,11620	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon8			GACCAACGTCATG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.1071C>T	1.37:g.226032229C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			C|0.899;T|0.101	0.101	strong		0.562	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
GFER	2671	hgsc.bcm.edu	37	16	2035868	2035868	+	Splice_Site	SNP	C	C	T	rs1046502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2035868C>T	ENST00000248114.6	+	3	463	c.457C>T	c.(457-459)Ctg>Ttg	p.L153L	GFER_ENST00000569451.1_Splice_Site_p.A87V|AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000567719.1_Splice_Site_p.L78L	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	153	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				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)	CCTACACAGGCTGTGCAGGAA	0.607													C|||	1156	0.230831	0.4221	0.1268	5008	,	,		20246	0.2937		0.1382	False		,,,				2504	0.0767				p.L153L		Atlas-SNP	.											.	GFER	8	.	0			c.C457T						PASS	.	C		1611,2785	497.6+/-363.9	305,1001,892	93.0	98.0	96.0		457	1.8	0.9	16	dbSNP_86	96	1149,7451	235.7+/-268.2	93,963,3244	yes	coding-synonymous-near-splice	GFER	NM_005262.2		398,1964,4136	TT,TC,CC		13.3605,36.647,21.2373		153/206	2035868	2760,10236	2198	4300	6498	SO:0001630	splice_region_variant	2671	exon3			CACAGGCTGTGCA	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.456-1C>T	16.37:g.2035868C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Silent	SNP	ENST00000248114.6	37	CCDS32368.1																																																																																			C|0.785;T|0.215	0.215	strong		0.607	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262	Silent
SYT15	83849	hgsc.bcm.edu	37	10	46965017	46965017	+	Missense_Mutation	SNP	C	C	T	rs200586361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:46965017C>T	ENST00000374321.4	-	6	994	c.928G>A	c.(928-930)Gac>Aac	p.D310N	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000503753.1_Missense_Mutation_p.D310N|SYT15_ENST00000374325.3_Missense_Mutation_p.D310N|SYT15_ENST00000374323.4_Missense_Mutation_p.D363N	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	310	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						ATGCCTCTGTCCTCCTGGAGC	0.612													C|||	11	0.00219649	0.0	0.0043	5008	,	,		40565	0.0		0.008	False		,,,				2504	0.0				p.D310N	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000374328,NS,carcinoma,-1,1	SYT15	165	1	0			c.G928A						PASS	.	C	ASN/ASP,ASN/ASP	6,4270		0,6,2132	53.0	61.0	58.0		928,928	3.2	0.0	10		58	47,8463		0,47,4208	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	23,23	0,53,6340	TT,TC,CC		0.5523,0.1403,0.4145	benign,benign	310/422,310/391	46965017	53,12733	2138	4255	6393	SO:0001583	missense	83849	exon6			CTCTGTCCTCCTG	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.928G>A	10.37:g.46965017C>T	ENSP00000363441:p.Asp310Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	26	0.226087	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	12.54	1.967239	0.34754	0.001403	0.005523	ENSG00000204176	ENST00000416127;ENST00000374328;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.06	3.16	0.36331	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.144113	0.64402	N	0.000009	T	0.45115	0.1326	L	0.35793	1.09	0.21290	N	0.999734	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.005	T	0.39563	-0.9608	10	0.38643	T	0.18	.	9.1541	0.36983	0.0:0.7682:0.1482:0.0836	.	310;310	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	N	310;100;310;310;149;363;310	ENSP00000363448:D100N;ENSP00000363445:D310N;ENSP00000427607:D310N;ENSP00000363443:D363N;ENSP00000363441:D310N	ENSP00000363441:D310N	D	-	1	0	SYT15	46385023	0.254000	0.23992	0.011000	0.14972	0.936000	0.57629	1.068000	0.30629	0.763000	0.33175	0.561000	0.74099	GAC	C|0.998;T|0.002	0.002	weak		0.612	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629755	32629755	+	Missense_Mutation	SNP	G	G	A	rs1130399	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629755G>A	ENST00000399082.3	-	2	424	c.380C>T	c.(379-381)aCc>aTc	p.T127I	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.T217I|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.T217I|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.T217I|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.T217I			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	217	Beta-2.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CCACTCCACGGTGATGGGGCT	0.542									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1274	0.254393	0.2352	0.3689	5008	,	,		16390	0.2956		0.2237	False		,,,				2504	0.1881				p.T217I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C650T						PASS	.	G	ILE/THR	889,3503		76,737,1383	54.0	58.0	57.0		650	0.1	0.0	6	dbSNP_86	57	1475,7113		149,1177,2968	yes	missense	HLA-DQB1	NM_002123.4	89	225,1914,4351	AA,AG,GG		17.1751,20.2413,18.2126	benign	217/262	32629755	2364,10616	2196	4294	6490	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCCACGGTGATGG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.380C>T	6.37:g.32629755G>A	ENSP00000382032:p.Thr127Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	44	14	0.318182	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		584	0.2673992673992674	96	0.1951219512195122	121	0.3342541436464088	188	0.32867132867132864	179	0.23614775725593667	.	3.116	-0.181687	0.06340	0.202413	0.171751	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T;T	0.03035	4.07;4.07;4.07;4.07;4.07	4.52	0.069	0.14372	.	0.465809	0.22797	N	0.055527	T	0.01454	0.0047	L	0.58583	1.82	0.80722	P	0.0	B;B;B;B	0.10296	0.0;0.0;0.003;0.0	B;B;B;B	0.10450	0.005;0.005;0.005;0.005	T	0.35450	-0.9788	9	0.72032	D	0.01	.	5.5181	0.16918	0.2824:0.1407:0.5769:0.0	rs1130399;rs3189186;rs9273919;rs12722379;rs28724253;rs34530092	217;182;217;217	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	I	127;217;217;217;217	ENSP00000382032:T127I;ENSP00000382029:T217I;ENSP00000364080:T217I;ENSP00000407332:T217I;ENSP00000382034:T217I	ENSP00000364080:T217I	T	-	2	0	HLA-DQB1	32737733	0.000000	0.05858	0.001000	0.08648	0.411000	0.31082	-1.209000	0.03002	-0.017000	0.14103	0.313000	0.20887	ACC	G|0.812;A|0.188	0.188	strong		0.542	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
FLT1	2321	hgsc.bcm.edu	37	13	28893642	28893642	+	Silent	SNP	A	A	G	rs2296189	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:28893642A>G	ENST00000282397.4	-	24	3455	c.3204T>C	c.(3202-3204)ccT>ccC	p.P1068P	FLT1_ENST00000540678.1_Silent_p.P286P|FLT1_ENST00000543394.1_Silent_p.P91P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1068	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|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 MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|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)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|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 receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGATAGATTCAGGAGCCATCC	0.478													A|||	1217	0.243011	0.2806	0.1124	5008	,	,		19391	0.1825		0.169	False		,,,				2504	0.4233				p.P1068P		Atlas-SNP	.											.	FLT1	393	.	0			c.T3204C						PASS	.	A		1161,3245	408.6+/-334.7	155,851,1197	67.0	60.0	62.0		3204	-11.0	0.7	13	dbSNP_100	62	1624,6976	298.2+/-303.8	160,1304,2836	no	coding-synonymous	FLT1	NM_002019.4		315,2155,4033	GG,GA,AA		18.8837,26.3504,21.4132		1068/1339	28893642	2785,10221	2203	4300	6503	SO:0001819	synonymous_variant	2321	exon24			AGATTCAGGAGCC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3204T>C	13.37:g.28893642A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			A|0.792;G|0.208	0.208	strong		0.478	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
MTCL1	23255	hgsc.bcm.edu	37	18	8784612	8784612	+	Missense_Mutation	SNP	A	A	G	rs1965665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:8784612A>G	ENST00000306329.11	+	5	2582	c.2582A>G	c.(2581-2583)cAg>cGg	p.Q861R	SOGA2_ENST00000359865.3_Missense_Mutation_p.Q501R|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000400050.3_Missense_Mutation_p.Q501R|SOGA2_ENST00000517570.1_Missense_Mutation_p.Q501R																							GAAGAGGAGCAGGGTGAGGGG	0.652													A|||	1493	0.298123	0.1324	0.4697	5008	,	,		17610	0.2242		0.3628	False		,,,				2504	0.41				p.Q501R		Atlas-SNP	.											.	.	.	.	0			c.A1502G						PASS	.	A	ARG/GLN	801,3605	303.0+/-287.7	81,639,1483	41.0	46.0	44.0		1502	-6.0	0.0	18	dbSNP_92	44	3182,5418	462.1+/-365.6	592,1998,1710	no	missense	CCDC165	NM_015210.3	43	673,2637,3193	GG,GA,AA		37.0,18.1798,30.6243	benign	501/1587	8784612	3983,9023	2203	4300	6503	SO:0001583	missense	23255	exon6			AGGAGCAGGGTGA																												ENST00000306329.11:c.2582A>G	18.37:g.8784612A>G	ENSP00000305027:p.Gln861Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		627	0.28708791208791207	63	0.12804878048780488	147	0.40607734806629836	142	0.24825174825174826	275	0.3627968337730871	A	0.001	-3.784487	0.00004	0.181798	0.37	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.29397	1.57;1.57;1.57	2.99	-5.97	0.02227	.	2.205680	0.03318	N	0.191481	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17653	-1.0362	9	0.17832	T	0.49	.	3.1576	0.06509	0.4067:0.2889:0.2198:0.0846	rs1965665;rs3744980	522;501	A8MQ54;Q9Y4B5-3	.;.	R	522;501;501;501	ENSP00000429556:Q501R;ENSP00000352927:Q501R;ENSP00000382924:Q501R	ENSP00000305027:Q522R	Q	+	2	0	CCDC165	8774612	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.553000	0.00927	-4.169000	0.00068	-4.723000	0.00003	CAG	A|0.697;G|0.303	0.303	strong		0.652	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
GMEB2	26205	hgsc.bcm.edu	37	20	62221766	62221766	+	Silent	SNP	C	C	T	rs2297428	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62221766C>T	ENST00000266068.1	-	9	1747	c.1269G>A	c.(1267-1269)ccG>ccA	p.P423P	GMEB2_ENST00000370077.1_Silent_p.P423P|GMEB2_ENST00000370069.1_Silent_p.P372P			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	28	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	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	
MUC16	94025	hgsc.bcm.edu	37	19	9080462	9080462	+	Missense_Mutation	SNP	C	C	G	rs2547065	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9080462C>G	ENST00000397910.4	-	2	9772	c.9569G>C	c.(9568-9570)aGc>aCc	p.S3190T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3191	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						TGCTGGACTGCTCCCCGTCTC	0.463													G|||	3027	0.604433	0.4304	0.611	5008	,	,		15446	0.8125		0.5994	False		,,,				2504	0.6258				p.S3190T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G9569C						PASS	.	G	THR/SER	1826,2018		446,934,542	132.0	130.0	130.0		9569	0.9	0.0	19	dbSNP_100	130	5021,3205		1526,1969,618	yes	missense	MUC16	NM_024690.2	58	1972,2903,1160	GG,GC,CC		38.9618,47.5026,43.2726	benign	3190/14508	9080462	6847,5223	1922	4113	6035	SO:0001583	missense	94025	exon2			GGACTGCTCCCCG	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.9569G>C	19.37:g.9080462C>G	ENSP00000381008:p.Ser3190Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1360	0.6227106227106227	210	0.4268292682926829	219	0.6049723756906077	474	0.8286713286713286	457	0.6029023746701847	g	1.495	-0.553583	0.03996	0.475026	0.610382	ENSG00000181143	ENST00000397910	T	0.01705	4.68	0.926	0.926	0.19430	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.04915	-1.0918	7	0.87932	D	0	.	4.8195	0.13383	0.0:0.3988:0.6012:0.0	rs2547065;rs3896536;rs2547065	3190	B5ME49	.	T	3190	ENSP00000381008:S3190T	ENSP00000381008:S3190T	S	-	2	0	MUC16	8941462	0.001000	0.12720	0.010000	0.14722	0.015000	0.08874	-0.194000	0.09559	-0.035000	0.13691	-0.647000	0.03941	AGC	C|0.370;G|0.630	0.630	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KIAA0196	9897	hgsc.bcm.edu	37	8	126044527	126044527	+	Silent	SNP	C	C	T	rs11542889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:126044527C>T	ENST00000318410.7	-	27	3640	c.3291G>A	c.(3289-3291)gcG>gcA	p.A1097A	KIAA0196_ENST00000517845.1_Silent_p.A949A	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	1097					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			GGCCAATCAGCGCCAGGAACT	0.537													C|||	685	0.136781	0.4297	0.0591	5008	,	,		20335	0.0		0.0606	False		,,,				2504	0.0153				p.A1097A		Atlas-SNP	.											.	KIAA0196	90	.	0			c.G3291A						PASS	.	C		1592,2814	494.8+/-363.1	282,1028,893	132.0	123.0	126.0		3291	-1.1	1.0	8	dbSNP_120	126	331,8269	115.3+/-175.2	8,315,3977	no	coding-synonymous	KIAA0196	NM_014846.3		290,1343,4870	TT,TC,CC		3.8488,36.1325,14.7855		1097/1160	126044527	1923,11083	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon27			AATCAGCGCCAGG		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.3291G>A	8.37:g.126044527C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1																																																																																			C|0.847;T|0.153	0.153	strong		0.537	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
RGL4	266747	hgsc.bcm.edu	37	22	24036563	24036563	+	Silent	SNP	G	G	A	rs2070447	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:24036563G>A	ENST00000290691.5	+	5	2112	c.942G>A	c.(940-942)tcG>tcA	p.S314S	GUSBP11_ENST00000455485.1_RNA|AP000347.2_ENST00000417194.1_RNA|RGL4_ENST00000401461.1_Silent_p.S178S|KB-1572G7.2_ENST00000421064.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	314	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						ACTTCTCCTCGGTGCACGTCA	0.587													g|||	595	0.11881	0.0113	0.1009	5008	,	,		20074	0.2798		0.0915	False		,,,				2504	0.1391				p.S314S		Atlas-SNP	.											.	RGL4	29	.	0			c.G942A						PASS	.	G		128,4278	93.9+/-132.6	6,116,2081	164.0	108.0	127.0		942	-3.8	0.0	22	dbSNP_96	127	741,7859	178.6+/-228.0	38,665,3597	no	coding-synonymous	RGL4	NM_153615.1		44,781,5678	AA,AG,GG		8.6163,2.9051,6.6815		314/474	24036563	869,12137	2203	4300	6503	SO:0001819	synonymous_variant	266747	exon5			CTCCTCGGTGCAC		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"""RalGDS related oncogene"""	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.942G>A	22.37:g.24036563G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_153615	Q495L8	Silent	SNP	ENST00000290691.5	37	CCDS13811.1																																																																																			G|0.908;A|0.092	0.092	strong		0.587	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615	
KIR2DL3	3804	hgsc.bcm.edu	37	19	55258808	55258808	+	Missense_Mutation	SNP	C	C	T	rs35861855	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55258808C>T	ENST00000342376.3	+	5	717	c.686C>T	c.(685-687)cCt>cTt	p.P229L	KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	229			P -> L (in dbSNP:rs35861855). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8662091, ECO:0000269|PubMed:9234478}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		AATAGTTGGCCTTCACCCACT	0.483													.|||	639	0.127596	0.0166	0.1196	5008	,	,		13576	0.123		0.2843	False		,,,				2504	0.1268				p.P229L		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.C686T						PASS	.						103.0	88.0	93.0					19																	55258808		1479	2625	4104	SO:0001583	missense	3804	exon5			GTTGGCCTTCACC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.686C>T	19.37:g.55258808C>T	ENSP00000342215:p.Pro229Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	141	55	0.390071	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	37	CCDS33107.1	245	0.11217948717948718	3	0.006097560975609756	47	0.1298342541436464	54	0.0944055944055944	141	0.18601583113456466	C	4.633	0.117677	0.08881	.	.	ENSG00000243772	ENST00000342376	T	0.00507	6.92	0.736	-0.473	0.12112	.	.	.	.	.	T	0.00012	0.0000	M	0.84219	2.685	0.80722	P	0.0	B;B;B;B;B	0.27910	0.051;0.009;0.193;0.021;0.021	B;B;B;B;B	0.26614	0.05;0.019;0.071;0.019;0.019	T	0.36311	-0.9753	8	0.72032	D	0.01	.	3.1738	0.06561	0.0:0.6566:0.0:0.3434	rs35861855;rs62122559	229;229;131;229;229	E3NZD7;P43627;P43628-2;P43628;E3NZD8	.;KI2L2_HUMAN;.;KI2L3_HUMAN;.	L	229	ENSP00000342215:P229L	ENSP00000342215:P229L	P	+	2	0	KIR2DL3	59950620	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.003000	0.13083	-0.133000	0.11537	0.184000	0.17185	CCT	C|0.882;T|0.118	0.118	strong		0.483	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
PLEKHA6	22874	hgsc.bcm.edu	37	1	204242838	204242838	+	Silent	SNP	A	A	C	rs33911350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204242838A>C	ENST00000272203.3	-	3	334	c.18T>G	c.(16-18)ggT>ggG	p.G6G	PLEKHA6_ENST00000414478.1_Silent_p.G6G	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	6								p.G6G(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GGCGTTTCCCACCTGTTTTAT	0.522													A|||	1004	0.200479	0.1286	0.2406	5008	,	,		18200	0.2946		0.1769	False		,,,				2504	0.1963				p.G6G		Atlas-SNP	.											PLEKHA6,NS,carcinoma,0,1	PLEKHA6	115	1	1	Substitution - coding silent(1)	stomach(1)	c.T18G						scavenged	.	A		641,3765	270.7+/-269.8	50,541,1612	153.0	139.0	144.0		18	2.1	1.0	1	dbSNP_126	144	1474,7126	276.4+/-292.3	144,1186,2970	no	coding-synonymous	PLEKHA6	NM_014935.2		194,1727,4582	CC,CA,AA		17.1395,14.5483,16.2617		6/1049	204242838	2115,10891	2203	4300	6503	SO:0001819	synonymous_variant	22874	exon3			TTTCCCACCTGTT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.18T>G	1.37:g.204242838A>C		Somatic	97	4	0.0412371		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	37	CCDS1444.1																																																																																			A|0.831;C|0.169	0.169	strong		0.522	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65208026	65208026	+	Silent	SNP	T	T	C	rs229650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:65208026T>C	ENST00000394691.1	+	16	1938	c.1791T>C	c.(1789-1791)tcT>tcC	p.S597S	PLEKHG3_ENST00000484731.2_Silent_p.S102S|PLEKHG3_ENST00000247226.7_Silent_p.S541S|PLEKHG3_ENST00000471182.2_Silent_p.S130S			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	597							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		TGCCACCCTCTGTGCTGGACC	0.617													C|||	1154	0.230431	0.4002	0.1499	5008	,	,		19780	0.0367		0.2147	False		,,,				2504	0.274				p.S541S		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.T1623C						PASS	.	C		1611,2795	659.7+/-400.6	300,1011,892	61.0	57.0	59.0		1623	-6.9	0.4	14	dbSNP_79	59	1978,6622	721.7+/-406.4	214,1550,2536	no	coding-synonymous	PLEKHG3	NM_015549.1		514,2561,3428	CC,CT,TT		23.0,36.5638,27.595		541/1164	65208026	3589,9417	2203	4300	6503	SO:0001819	synonymous_variant	26030	exon14			ACCCTCTGTGCTG	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1791T>C	14.37:g.65208026T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	37																																																																																				T|0.756;C|0.244	0.244	strong		0.617	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
EFR3A	23167	hgsc.bcm.edu	37	8	132999936	132999936	+	Silent	SNP	A	A	G	rs2270875	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:132999936A>G	ENST00000254624.5	+	18	2277	c.2052A>G	c.(2050-2052)gtA>gtG	p.V684V	EFR3A_ENST00000334503.4_Silent_p.V684V|EFR3A_ENST00000519656.1_Silent_p.V648V	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	684						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.V684V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTCCGTATGTACCACAAGTAA	0.353													A|||	662	0.132188	0.034	0.1513	5008	,	,		15583	0.1587		0.1064	False		,,,				2504	0.2505				p.V684V		Atlas-SNP	.											EFR3A,rectum,carcinoma,0,2	EFR3A	96	2	1	Substitution - coding silent(1)	stomach(1)	c.A2052G						PASS	.	A		198,4204	115.4+/-153.4	6,186,2009	93.0	76.0	81.0		2052	-6.3	0.8	8	dbSNP_100	81	1013,7583	201.3+/-244.8	55,903,3340	no	coding-synonymous	EFR3A	NM_015137.4		61,1089,5349	GG,GA,AA		11.7846,4.498,9.3168		684/822	132999936	1211,11787	2201	4298	6499	SO:0001819	synonymous_variant	23167	exon18			GTATGTACCACAA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.2052A>G	8.37:g.132999936A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																			A|0.899;G|0.101	0.101	strong		0.353	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
CLSPN	63967	hgsc.bcm.edu	37	1	36225948	36225948	+	Missense_Mutation	SNP	T	T	C	rs7537203	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:36225948T>C	ENST00000318121.3	-	8	1631	c.1574A>G	c.(1573-1575)aAc>aGc	p.N525S	CLSPN_ENST00000520551.1_Missense_Mutation_p.N525S|CLSPN_ENST00000373220.3_Missense_Mutation_p.N525S|CLSPN_ENST00000251195.5_Missense_Mutation_p.N525S	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	525			N -> S (in dbSNP:rs7537203).		activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ATTACCTCTGTTGGTTTCAGG	0.438													T|||	2272	0.453674	0.674	0.4323	5008	,	,		18733	0.7401		0.1352	False		,,,				2504	0.2035				p.N525S		Atlas-SNP	.											.	CLSPN	248	.	0			c.A1574G						PASS	.	T	SER/ASN,SER/ASN	2607,1799	641.4+/-397.5	778,1051,374	88.0	82.0	84.0		1574,1574	5.1	1.0	1	dbSNP_116	84	1148,7452	235.8+/-268.3	90,968,3242	yes	missense,missense	CLSPN	NM_001190481.1,NM_022111.3	46,46	868,2019,3616	CC,CT,TT		13.3488,40.8307,28.8713	benign,benign	525/1276,525/1340	36225948	3755,9251	2203	4300	6503	SO:0001583	missense	63967	exon8			CCTCTGTTGGTTT	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.1574A>G	1.37:g.36225948T>C	ENSP00000312995:p.Asn525Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_001190481	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	1010	0.4624542124542125	316	0.6422764227642277	143	0.39502762430939226	449	0.784965034965035	102	0.1345646437994723	T	19.48	3.835941	0.71373	0.591693	0.133488	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551;ENST00000544356	T;T;T;T	0.30182	1.62;1.63;1.73;1.54	5.08	5.08	0.68730	.	0.046376	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.25761	P	0.984948	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.994	T	0.15292	-1.0442	9	0.44086	T	0.13	-16.2566	13.4062	0.60915	0.0:0.0:0.0:1.0	rs7537203;rs57440681;rs7537203	525;525	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	S	525	ENSP00000251195:N525S;ENSP00000312995:N525S;ENSP00000362317:N525S;ENSP00000428848:N525S	ENSP00000251195:N525S	N	-	2	0	CLSPN	35998535	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.600000	0.54052	1.907000	0.55213	0.482000	0.46254	AAC	T|0.628;C|0.372	0.372	strong		0.438	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
AMDHD1	144193	hgsc.bcm.edu	37	12	96346594	96346594	+	Silent	SNP	T	T	C	rs1982138	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:96346594T>C	ENST00000266736.2	+	2	343	c.237T>C	c.(235-237)atT>atC	p.I79I		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	79					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)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						GGAAATGTATTCTACCAGGTA	0.343													T|||	1275	0.254593	0.0923	0.1225	5008	,	,		16507	0.4673		0.2455	False		,,,				2504	0.3579				p.I79I		Atlas-SNP	.											.	AMDHD1	56	.	0			c.T237C						PASS	.	T		558,3848	238.0+/-249.6	31,496,1676	63.0	67.0	66.0		237	-0.1	1.0	12	dbSNP_92	66	2072,6522	353.4+/-329.1	245,1582,2470	no	coding-synonymous	AMDHD1	NM_152435.2		276,2078,4146	CC,CT,TT		24.1098,12.6645,20.2308		79/427	96346594	2630,10370	2203	4297	6500	SO:0001819	synonymous_variant	144193	exon2			ATGTATTCTACCA	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.237T>C	12.37:g.96346594T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_152435	A8K463|Q68CI8	Silent	SNP	ENST00000266736.2	37	CCDS9057.1																																																																																			T|0.779;C|0.221	0.221	strong		0.343	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
IGFN1	91156	hgsc.bcm.edu	37	1	201174215	201174215	+	Missense_Mutation	SNP	C	C	A	rs11584104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201174215C>A	ENST00000335211.4	+	11	1052	c.922C>A	c.(922-924)Ccc>Acc	p.P308T	IGFN1_ENST00000451870.2_Missense_Mutation_p.P308T|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	308						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						GGCAGCCATCCCCCCAAGAGT	0.572													C|||	84	0.0167732	0.0023	0.0317	5008	,	,		17748	0.0		0.0427	False		,,,				2504	0.0164				p.P308T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C922A						PASS	.	C	THR/PRO	13,1367		0,13,677	10.0	13.0	12.0		922	4.7	1.0	1	dbSNP_120	12	183,2993		3,177,1408	yes	missense	IGFN1	NM_001164586.1	38	3,190,2085	AA,AC,CC		5.762,0.942,4.302		308/3709	201174215	196,4360	690	1588	2278	SO:0001583	missense	91156	exon11			GCCATCCCCCCAA	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.922C>A	1.37:g.201174215C>A	ENSP00000334714:p.Pro308Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	45	0.020604395604395604	3	0.006097560975609756	10	0.027624309392265192	0	0.0	32	0.04221635883905013	C	12.39	1.923564	0.33908	0.00942	0.05762	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.76316	-1.01;-1.01	4.68	4.68	0.58851	.	.	.	.	.	T	0.46908	0.1417	M	0.75085	2.285	0.80722	D	1	.	.	.	.	.	.	T	0.73672	-0.3909	7	0.72032	D	0.01	.	14.8477	0.70272	0.0:1.0:0.0:0.0	rs11584104	.	.	.	T	308	ENSP00000334714:P308T;ENSP00000398386:P308T	ENSP00000334714:P308T	P	+	1	0	IGFN1	199440838	1.000000	0.71417	0.951000	0.38953	0.035000	0.12851	3.120000	0.50430	2.295000	0.77249	0.655000	0.94253	CCC	C|0.971;A|0.029	0.029	strong		0.572	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
SLC16A7	9194	hgsc.bcm.edu	37	12	60173356	60173356	+	Missense_Mutation	SNP	A	A	T	rs3763980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000552024.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000552432.1_Missense_Mutation_p.T445S|SLC16A7_ENST00000543448.1_Missense_Mutation_p.T346S	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	88	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	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	
CHGA	1113	hgsc.bcm.edu	37	14	93399101	93399101	+	Missense_Mutation	SNP	C	C	T	rs729940	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:93399101C>T	ENST00000216492.5	+	7	1475	c.1195C>T	c.(1195-1197)Cgg>Tgg	p.R399W	CHGA_ENST00000334654.4_Missense_Mutation_p.R248W	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	399			R -> W (in dbSNP:rs729940). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2445752, ECO:0000269|PubMed:8120054}.		regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		GCCATCCTCCCGGGAGGACAG	0.687													C|||	623	0.124401	0.0121	0.2061	5008	,	,		14971	0.2004		0.164	False		,,,				2504	0.0992				p.R399W	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.C1195T						PASS	.	C	TRP/ARG	148,4206		7,134,2036	11.0	13.0	12.0		1195	1.2	0.1	14	dbSNP_86	12	1200,7320		80,1040,3140	no	missense	CHGA	NM_001275.3	101	87,1174,5176	TT,TC,CC		14.0845,3.3992,10.4707	possibly-damaging	399/458	93399101	1348,11526	2177	4260	6437	SO:0001583	missense	1113	exon7			TCCTCCCGGGAGG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"""vasostatin"", ""pancreastatin"", ""parastatin"""	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.1195C>T	14.37:g.93399101C>T	ENSP00000216492:p.Arg399Trp	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	37	CCDS9906.1	332	0.152014652014652	9	0.018292682926829267	84	0.23204419889502761	114	0.1993006993006993	125	0.16490765171503957	C	13.08	2.129737	0.37630	0.033992	0.140845	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.01821	4.62;4.62	4.71	1.2	0.21068	.	0.839077	0.10441	N	0.674355	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	D;D	0.89917	1.0;0.997	D;D	0.70935	0.971;0.913	T	0.45440	-0.9261	9	0.59425	D	0.04	-3.6408	6.2358	0.20762	0.4752:0.2822:0.2426:0.0	rs729940;rs1058460;rs17847003;rs729940	248;399	G5E968;P10645	.;CMGA_HUMAN	W	399;248	ENSP00000216492:R399W;ENSP00000334023:R248W	ENSP00000216492:R399W	R	+	1	2	CHGA	92468854	0.000000	0.05858	0.140000	0.22221	0.387000	0.30353	0.516000	0.22817	0.327000	0.23409	0.555000	0.69702	CGG	C|0.876;T|0.124	0.124	strong		0.687	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275	
CCDC71	64925	hgsc.bcm.edu	37	3	49201140	49201140	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49201140C>T	ENST00000321895.6	-	2	608	c.502G>A	c.(502-504)Ggt>Agt	p.G168S		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	168										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGGTAGACACCTGGATAAAGG	0.587																																					p.G168S		Atlas-SNP	.											.	CCDC71	33	.	0			c.G502A						PASS	.						54.0	58.0	56.0					3																	49201140		2203	4300	6503	SO:0001583	missense	64925	exon2			AGACACCTGGATA	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.502G>A	3.37:g.49201140C>T	ENSP00000319006:p.Gly168Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	76	16	0.210526	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086570	0.55861	.	.	ENSG00000177352	ENST00000321895	T	0.36699	1.24	5.44	4.57	0.56435	.	0.068720	0.56097	D	0.000035	T	0.52533	0.1740	M	0.66939	2.045	0.36735	D	0.881929	D	0.60160	0.987	P	0.57425	0.82	T	0.65080	-0.6255	10	0.72032	D	0.01	-30.1272	14.1305	0.65250	0.0:0.9276:0.0:0.0724	.	168	Q8IV32	CCD71_HUMAN	S	168	ENSP00000319006:G168S	ENSP00000319006:G168S	G	-	1	0	CCDC71	49176144	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.531000	0.53546	1.313000	0.45069	0.585000	0.79938	GGT	.	.	none		0.587	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178608112	178608112	+	Silent	SNP	G	G	A	rs35462609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178608112G>A	ENST00000251582.7	-	5	1037	c.936C>T	c.(934-936)aaC>aaT	p.N312N	ADAMTS2_ENST00000274609.5_Silent_p.N312N	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	312	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)		CCAGGACCACGTTGATGTGGG	0.607													G|||	54	0.0107827	0.0008	0.0173	5008	,	,		18446	0.0		0.0348	False		,,,				2504	0.0061				p.N312N		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C936T						PASS	.	G	,	35,4371	40.8+/-73.8	0,35,2168	143.0	106.0	119.0		936,936	-4.2	0.5	5	dbSNP_126	119	325,8275	114.4+/-174.4	8,309,3983	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	8,344,6151	AA,AG,GG		3.7791,0.7944,2.768	,	312/1212,312/567	178608112	360,12646	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon5			GACCACGTTGATG	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.936C>T	5.37:g.178608112G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			G|0.974;A|0.026	0.026	strong		0.607	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
CA6	765	hgsc.bcm.edu	37	1	9030964	9030964	+	Silent	SNP	C	C	T	rs3737665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9030964C>T	ENST00000377443.2	+	7	772	c.768C>T	c.(766-768)aaC>aaT	p.N256N	CA6_ENST00000476083.1_3'UTR|CA6_ENST00000377442.2_Silent_p.N196N|CA6_ENST00000377436.3_Silent_p.N256N	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	256					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|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;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	ATCACCGCAACAAGACCATCC	0.502													C|||	1445	0.288538	0.1165	0.2983	5008	,	,		19477	0.5357		0.2097	False		,,,				2504	0.3405				p.N256N		Atlas-SNP	.											.	CA6	47	.	0			c.C768T						PASS	.	C		715,3691	298.1+/-285.1	63,589,1551	148.0	136.0	140.0		768	-2.0	0.0	1	dbSNP_107	140	1767,6833	319.2+/-314.1	184,1399,2717	yes	coding-synonymous	CA6	NM_001215.2		247,1988,4268	TT,TC,CC		20.5465,16.2279,19.0835		256/309	9030964	2482,10524	2203	4300	6503	SO:0001819	synonymous_variant	765	exon7			CCGCAACAAGACC	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.768C>T	1.37:g.9030964C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Silent	SNP	ENST00000377443.2	37	CCDS30578.1																																																																																			C|0.763;T|0.237	0.237	strong		0.502	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
GPLD1	2822	hgsc.bcm.edu	37	6	24437458	24437458	+	Missense_Mutation	SNP	T	T	C	rs1042303	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24437458T>C	ENST00000230036.1	-	21	2190	c.2080A>G	c.(2080-2082)Atg>Gtg	p.M694V		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	694			M -> V (in dbSNP:rs1042303). {ECO:0000269|PubMed:11072085}.		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						AGTGCGTACATGCGAGTGGCT	0.577													T|||	1533	0.30611	0.2549	0.3386	5008	,	,		20191	0.253		0.4364	False		,,,				2504	0.273				p.M694V		Atlas-SNP	.											.	GPLD1	91	.	0			c.A2080G						PASS	.	T	VAL/MET	1259,3147	432.0+/-343.1	201,857,1145	137.0	109.0	119.0		2080	0.9	0.1	6	dbSNP_86	119	3979,4621	552.9+/-386.2	915,2149,1236	yes	missense	GPLD1	NM_001503.2	21	1116,3006,2381	CC,CT,TT		46.2674,28.5747,40.2737	benign	694/841	24437458	5238,7768	2203	4300	6503	SO:0001583	missense	2822	exon21			CGTACATGCGAGT	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.2080A>G	6.37:g.24437458T>C	ENSP00000230036:p.Met694Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	715	0.3273809523809524	137	0.2784552845528455	125	0.3453038674033149	130	0.22727272727272727	323	0.4261213720316623	T	3.704	-0.060886	0.07317	0.285747	0.462674	ENSG00000112293	ENST00000230036	T	0.65364	-0.15	4.69	0.898	0.19264	.	0.307417	0.33346	N	0.005014	T	0.18130	0.0435	L	0.28014	0.82	0.24258	P	0.99529279	B	0.02656	0.0	B	0.04013	0.001	T	0.09015	-1.0694	9	0.12103	T	0.63	-21.3146	4.8618	0.13588	0.0:0.2324:0.153:0.6146	rs1042303;rs3181758;rs17306368;rs60071487	694	P80108	PHLD_HUMAN	V	694	ENSP00000230036:M694V	ENSP00000230036:M694V	M	-	1	0	GPLD1	24545437	0.633000	0.27181	0.141000	0.22245	0.010000	0.07245	0.711000	0.25764	0.068000	0.16574	0.460000	0.39030	ATG	T|0.628;C|0.372	0.372	strong		0.577	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
UGGT2	55757	hgsc.bcm.edu	37	13	96506664	96506664	+	Silent	SNP	A	A	G	rs11070154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96506664A>G	ENST00000376747.3	-	35	4144	c.4074T>C	c.(4072-4074)acT>acC	p.T1358T		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1358	Glucosyltransferase.				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)	p.T1358T(1)		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						CACAAAATGGAGTATACCCAT	0.383													A|||	1648	0.329073	0.2526	0.2622	5008	,	,		17269	0.3155		0.4394	False		,,,				2504	0.3804				p.T1358T		Atlas-SNP	.											UGGT2,NS,carcinoma,0,1	UGGT2	127	1	1	Substitution - coding silent(1)	prostate(1)	c.T4074C						scavenged	.	A		1187,3219	414.6+/-336.9	168,851,1184	91.0	87.0	88.0		4074	-4.8	0.9	13	dbSNP_120	88	3582,5018	517.2+/-379.0	764,2054,1482	no	coding-synonymous	UGGT2	NM_020121.3		932,2905,2666	GG,GA,AA		41.6512,26.9405,36.6677		1358/1517	96506664	4769,8237	2203	4300	6503	SO:0001819	synonymous_variant	55757	exon35			AAATGGAGTATAC	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.4074T>C	13.37:g.96506664A>G		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	127	76	0.598425	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Silent	SNP	ENST00000376747.3	37	CCDS9480.1																																																																																			A|0.648;G|0.352	0.352	strong		0.383	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
RBM23	55147	hgsc.bcm.edu	37	14	23371268	23371268	+	Silent	SNP	A	A	G	rs56708790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23371268A>G	ENST00000359890.3	-	12	1362	c.1167T>C	c.(1165-1167)gcT>gcC	p.A389A	RBM23_ENST00000542016.2_Silent_p.A219A|RBM23_ENST00000555209.1_Silent_p.A139A|RBM23_ENST00000399922.2_Silent_p.A373A|RBM23_ENST00000346528.5_Silent_p.A355A	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	389	Ala-rich.				mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		cggcggcggcagcagcagcag	0.552													A|||	195	0.0389377	0.0053	0.0778	5008	,	,		16698	0.0179		0.0676	False		,,,				2504	0.0491				p.A389A		Atlas-SNP	.											RBM23,NS,carcinoma,0,3	RBM23	44	3	0			c.T1167C						PASS	.	A	,,	54,3898		1,52,1923	34.0	35.0	35.0		1167,1065,1119	-2.4	0.4	14	dbSNP_129	35	529,7793		7,515,3639	yes	coding-synonymous,coding-synonymous,coding-synonymous	RBM23	NM_001077351.1,NM_001077352.1,NM_018107.4	,,	8,567,5562	GG,GA,AA		6.3566,1.3664,4.7499	,,	389/440,355/406,373/424	23371268	583,11691	1976	4161	6137	SO:0001819	synonymous_variant	55147	exon12			GGCGGCAGCAGCA	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.1167T>C	14.37:g.23371268A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	11	0.366667	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Silent	SNP	ENST00000359890.3	37	CCDS41921.1	252	0.11538461538461539	8	0.016260162601626018	50	0.13812154696132597	73	0.12762237762237763	121	0.15963060686015831	A	0.768	-0.766868	0.02974	0.013664	0.063566	ENSG00000100461	ENST00000553884	.	.	.	3.36	-2.38	0.06622	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.53005	D	0.999961	.	.	.	.	.	.	T	0.04294	-1.0962	4	.	.	.	.	8.3885	0.32514	0.37:0.0:0.63:0.0	rs56708790;rs61730800	.	.	.	R	164	.	.	C	-	1	0	RBM23	22441108	0.115000	0.22152	0.443000	0.26883	0.195000	0.23768	0.047000	0.14056	-0.453000	0.07076	0.402000	0.26972	TGC	A|0.887;G|0.113	0.113	strong		0.552	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
PDE11A	50940	hgsc.bcm.edu	37	2	178682603	178682603	+	Silent	SNP	T	T	C	rs6720891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:178682603T>C	ENST00000286063.6	-	8	1943	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000389683.3_Silent_p.A98A|PDE11A_ENST00000449286.2_Silent_p.A184A|PDE11A_ENST00000409504.1_Silent_p.A184A|PDE11A_ENST00000358450.4_Silent_p.A292A	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	542	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GTCGTTGATCTGCATCATCAA	0.383									Primary Pigmented Nodular Adrenocortical Disease, Familial				t|||	2094	0.418131	0.7315	0.2622	5008	,	,		16517	0.3056		0.3241	False		,,,				2504	0.318				p.A542A		Atlas-SNP	.											.	PDE11A	283	.	0			c.A1626G						PASS	.	C	,,,	2726,1680	648.8+/-398.8	856,1014,333	84.0	89.0	87.0		294,876,552,1626	-11.6	0.7	2	dbSNP_116	87	2778,5822	436.2+/-358.2	450,1878,1972	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	,,,	1306,2892,2305	CC,CT,TT		32.3023,38.1298,42.3189	,,,	98/490,292/684,184/576,542/934	178682603	5504,7502	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon8	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TTGATCTGCATCA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1626A>G	2.37:g.178682603T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	900	0.41208791208791207	350	0.7113821138211383	110	0.30386740331491713	206	0.36013986013986016	234	0.3087071240105541	t	5.380	0.255377	0.10185	0.618702	0.323023	ENSG00000128655	ENST00000433879	.	.	.	5.82	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999996	.	.	.	.	.	.	T	0.41645	-0.9497	3	.	.	.	.	0.7539	0.00995	0.1939:0.1937:0.2082:0.4043	rs6720891;rs58395732;rs6720891	.	.	.	R	181	.	.	Q	-	2	0	PDE11A	178390849	0.521000	0.26258	0.742000	0.31022	0.633000	0.38033	-0.365000	0.07573	-1.740000	0.01345	-4.221000	0.00009	CAG	T|0.578;C|0.422	0.422	strong		0.383	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1509123G>A	ENST00000382745.4	-	7	1265	c.660C>T	c.(658-660)caC>caT	p.H220H	CLCN7_ENST00000262318.8_Silent_p.H196H|CLCN7_ENST00000448525.1_Silent_p.H196H	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	220					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GCCGCACCACGTGGGGGATCT	0.662													G|||	611	0.122005	0.2352	0.1225	5008	,	,		18275	0.0099		0.1113	False		,,,				2504	0.0951				p.H220H		Atlas-SNP	.											CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	0			c.C660T						PASS	.	G	,	880,3516	332.0+/-302.3	101,678,1419	42.0	45.0	44.0		588,660	-1.5	1.0	16	dbSNP_121	44	1124,7476	228.4+/-263.5	77,970,3253	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	178,1648,4672	AA,AG,GG		13.0698,20.0182,15.4201	,	196/782,220/806	1509123	2004,10992	2198	4300	6498	SO:0001819	synonymous_variant	1186	exon7			CACCACGTGGGGG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.660C>T	16.37:g.1509123G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	142	53	0.373239	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			G|0.854;A|0.146	0.146	strong		0.662	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
AHDC1	27245	hgsc.bcm.edu	37	1	27878162	27878162	+	Silent	SNP	C	C	T	rs112179924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27878162C>T	ENST00000247087.5	-	5	1061	c.465G>A	c.(463-465)ccG>ccA	p.P155P	AHDC1_ENST00000374011.2_Silent_p.P155P			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	155	Pro-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGGTGCAGGCGGGCGGCTCA	0.632													C|||	278	0.0555112	0.0756	0.0432	5008	,	,		12781	0.004		0.1153	False		,,,				2504	0.0286				p.P155P		Atlas-SNP	.											.	AHDC1	98	.	0			c.G465A						PASS	.	C		393,4013	195.0+/-219.7	21,351,1831	100.0	106.0	104.0		465	-8.7	0.2	1	dbSNP_132	104	786,7814	184.6+/-232.5	38,710,3552	no	coding-synonymous	AHDC1	NM_001029882.2		59,1061,5383	TT,TC,CC		9.1395,8.9197,9.065		155/1604	27878162	1179,11827	2203	4300	6503	SO:0001819	synonymous_variant	27245	exon6			TGCAGGCGGGCGG	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.465G>A	1.37:g.27878162C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	37	CCDS30652.1																																																																																			C|0.918;T|0.082	0.082	strong		0.632	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740192	20740192	+	Missense_Mutation	SNP	G	G	A	rs145446071	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:20740192G>A	ENST00000427390.2	-	8	1648	c.1558C>T	c.(1558-1560)Cgg>Tgg	p.R520W		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	520	Gln-rich.|Glu-rich.							p.R520W(2)		NS(3)|endometrium(4)|kidney(1)|skin(3)	11						tcctgctcccgtatcttctcc	0.557													G|||	708	0.141374	0.0371	0.0504	5008	,	,		31663	0.369		0.0706	False		,,,				2504	0.1851				p.R520W		Atlas-SNP	.											GOLGA6L6,NS,carcinoma,0,2	GOLGA6L6	37	2	2	Substitution - Missense(2)	endometrium(2)	c.C1558T						PASS	.	G	TRP/ARG	29,1327		5,19,654	109.0	111.0	110.0		1558		0.0	15	dbSNP_134	110	182,2950		10,162,1394	no	missense	GOLGA6L6	NM_001145004.1	101	15,181,2048	AA,AG,GG		5.811,2.1386,4.7014	probably-damaging	520/751	20740192	211,4277	678	1566	2244	SO:0001583	missense	727832	exon8			GCTCCCGTATCTT	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1558C>T	15.37:g.20740192G>A	ENSP00000398615:p.Arg520Trp	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	242	67	0.276859	NM_001145004	D3YTC0	Missense_Mutation	SNP	ENST00000427390.2	37	CCDS45184.1	320	0.14652014652014653	37	0.07520325203252033	27	0.07458563535911603	196	0.34265734265734266	60	0.079155672823219	G	1.756	-0.488059	0.04352	0.021386	0.05811	ENSG00000215405	ENST00000427390	T	0.10099	2.91	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	D	0.61080	0.989	B	0.34991	0.193	T	0.51450	-0.8704	6	0.66056	D	0.02	.	.	.	.	.	520	A8MZA4	GG6L6_HUMAN	W	520	ENSP00000398615:R520W	ENSP00000398615:R520W	R	-	1	2	GOLGA6L6	19000206	0.067000	0.21026	0.011000	0.14972	0.011000	0.07611	0.035000	0.13797	0.159000	0.19401	0.162000	0.16502	CGG	G|0.854;A|0.146	0.146	strong		0.557	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
PGR	5241	hgsc.bcm.edu	37	11	100933407	100933407	+	Silent	SNP	G	G	A	rs139646398		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:100933407G>A	ENST00000325455.5	-	4	3436	c.1983C>T	c.(1981-1983)ggC>ggT	p.G661G	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Silent_p.G67G	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	661					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)	CATTTGGAACGCCCACTGGCT	0.418													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15046	0.0		0.0	False		,,,				2504	0.0				p.G661G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C1983T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	129.0	112.0	118.0		1983,1491	4.5	0.9	11	dbSNP_134	118	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923	,	661/934,497/770	100933407	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5241	exon4			TGGAACGCCCACT	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.1983C>T	11.37:g.100933407G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.999;A|0.001	0.001	strong		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
SYCP2L	221711	hgsc.bcm.edu	37	6	10964015	10964015	+	Splice_Site	SNP	G	G	A	rs115084361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:10964015G>A	ENST00000283141.6	+	29	2711	c.2415G>A	c.(2413-2415)agG>agA	p.R805R	SYCP2L_ENST00000465872.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	805						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TTTCTTCCAGGTTCAATTCAA	0.358													G|||	49	0.00978435	0.0015	0.0173	5008	,	,		18130	0.0		0.0239	False		,,,				2504	0.0112				p.R805R		Atlas-SNP	.											.	SYCP2L	101	.	0			c.G2415A						PASS	.	G		11,3687		0,11,1838	103.0	96.0	98.0		2415	2.3	0.9	6	dbSNP_132	98	175,8007		1,173,3917	yes	coding-synonymous-near-splice	SYCP2L	NM_001040274.2		1,184,5755	AA,AG,GG		2.1388,0.2975,1.5657		805/813	10964015	186,11694	1849	4091	5940	SO:0001630	splice_region_variant	221711	exon29			TTCCAGGTTCAAT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.2415-1G>A	6.37:g.10964015G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	37	CCDS43423.1																																																																																			G|0.987;A|0.013	0.013	strong		0.358	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	Silent
P4HB	5034	hgsc.bcm.edu	37	17	79805134	79805134	+	Silent	SNP	G	G	A	rs2070871	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79805134G>A	ENST00000331483.4	-	5	936	c.714C>T	c.(712-714)atC>atT	p.I238I	P4HB_ENST00000472244.1_5'UTR|P4HB_ENST00000439918.2_Silent_p.I194I|P4HB_ENST00000576390.1_Intron	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	238					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			CGGTGAACTCGATGACAAGGG	0.602													G|||	489	0.0976438	0.0083	0.2277	5008	,	,		16422	0.0903		0.168	False		,,,				2504	0.0613				p.I238I	Colon(49;444 983 1296 7887 42561)	Atlas-SNP	.											.	P4HB	43	.	0			c.C714T						PASS	.	G		156,4250	106.5+/-144.9	2,152,2049	123.0	126.0	125.0		714	1.0	1.0	17	dbSNP_96	125	1650,6950	304.9+/-307.2	152,1346,2802	no	coding-synonymous	P4HB	NM_000918.3		154,1498,4851	AA,AG,GG		19.186,3.5406,13.8859		238/509	79805134	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	5034	exon5			GAACTCGATGACA	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"""Protein disulfide isomerases"""	8548	protein-coding gene	gene with protein product	"""protein disulfide isomerase-associated 1"", ""protein disulfide isomerase family A, member 1"", ""collagen prolyl 4-hydroxylase beta"""	176790	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"""	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.714C>T	17.37:g.79805134G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	143	78	0.545455	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Silent	SNP	ENST00000331483.4	37	CCDS11787.1	274	0.12545787545787546	5	0.01016260162601626	76	0.20994475138121546	60	0.1048951048951049	133	0.17546174142480211	G	10.50	1.367499	0.24771	0.035406	0.19186	ENSG00000185624	ENST00000415593;ENST00000439918	.	.	.	5.77	1.03	0.20045	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8055	0.13317	0.3599:0.0:0.4252:0.215	rs2070871;rs11558885;rs17778712;rs58659106;rs2070871	.	.	.	X	24;25	.	.	R	-	1	2	P4HB	77398423	0.975000	0.34042	1.000000	0.80357	0.979000	0.70002	0.065000	0.14466	0.379000	0.24794	-0.143000	0.13931	CGA	G|0.869;A|0.131	0.131	strong		0.602	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918	
ALDH9A1	223	hgsc.bcm.edu	37	1	165652273	165652273	+	Silent	SNP	A	A	G	rs1143659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:165652273A>G	ENST00000354775.4	-	3	706	c.402T>C	c.(400-402)atT>atC	p.I134I	ALDH9A1_ENST00000538148.1_Silent_p.I40I|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	110					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					AGGAAATGTCAATGTCCAAGC	0.498													G|||	3737	0.746206	0.6074	0.7723	5008	,	,		19261	0.9881		0.6372	False		,,,				2504	0.7781				p.I134I	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.T402C						PASS	.	G		2776,1630	503.9+/-365.7	882,1012,309	129.0	112.0	118.0		402	-1.6	0.1	1	dbSNP_86	118	5680,2920	455.2+/-363.7	1859,1962,479	no	coding-synonymous	ALDH9A1	NM_000696.3		2741,2974,788	GG,GA,AA		33.9535,36.995,34.9839		134/519	165652273	8456,4550	2203	4300	6503	SO:0001819	synonymous_variant	223	exon3			AATGTCAATGTCC	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.402T>C	1.37:g.165652273A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			A|0.299;G|0.701	0.701	strong		0.498	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
PATL1	219988	hgsc.bcm.edu	37	11	59410479	59410479	+	Silent	SNP	A	A	T	rs77793148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:59410479A>T	ENST00000300146.9	-	16	2007	c.1923T>A	c.(1921-1923)tcT>tcA	p.S641S		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	641	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|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 metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						AGAGAAGGAGAGAGAAGGGAC	0.473													A|||	33	0.00658946	0.0008	0.0029	5008	,	,		20188	0.0		0.0239	False		,,,				2504	0.0061				p.S641S		Atlas-SNP	.											.	PATL1	92	.	0			c.T1923A						PASS	.	A		17,3945		0,17,1964	118.0	112.0	114.0		1923	-0.6	1.0	11	dbSNP_132	114	187,8113		2,183,3965	no	coding-synonymous	PATL1	NM_152716.2		2,200,5929	TT,TA,AA		2.253,0.4291,1.6637		641/771	59410479	204,12058	1981	4150	6131	SO:0001819	synonymous_variant	219988	exon16			AAGGAGAGAGAAG	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1923T>A	11.37:g.59410479A>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Silent	SNP	ENST00000300146.9	37	CCDS44613.1																																																																																			A|0.995;G|0.000;T|0.005	0.005	strong		0.473	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	
FFAR2	2867	hgsc.bcm.edu	37	19	35940721	35940721	+	Silent	SNP	G	G	C	rs117215242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35940721G>C	ENST00000599180.2	+	2	185	c.105G>C	c.(103-105)cgG>cgC	p.R35R	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Silent_p.R35R			O15552	FFAR2_HUMAN	free fatty acid receptor 2	35					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)			TTGTGGGGCGGATCCGCCAGC	0.632													G|||	146	0.0291534	0.0038	0.062	5008	,	,		15113	0.002		0.0626	False		,,,				2504	0.0337				p.R35R	GBM(40;139 809 9833 23358 48736)	Atlas-SNP	.											.	FFAR2	39	.	0			c.G105C						PASS	.	G		37,4369	39.2+/-71.8	0,37,2166	38.0	36.0	37.0		105	-7.8	0.1	19	dbSNP_132	37	584,8016	153.6+/-207.9	17,550,3733	no	coding-synonymous	FFAR2	NM_005306.2		17,587,5899	CC,CG,GG		6.7907,0.8398,4.7747		35/331	35940721	621,12385	2203	4300	6503	SO:0001819	synonymous_variant	2867	exon1			GGGGCGGATCCGC	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.105G>C	19.37:g.35940721G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	37	CCDS12461.1																																																																																			C|0.043;G|0.956;T|0.001	0.043	strong		0.632	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306	
PCLO	27445	hgsc.bcm.edu	37	7	82387960	82387960	+	Silent	SNP	G	G	A	rs62465931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:82387960G>A	ENST00000333891.9	-	25	15697	c.15360C>T	c.(15358-15360)gaC>gaT	p.D5120D		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						GATCCACTTTGTCAAGCCAGA	0.363													G|||	49	0.00978435	0.0106	0.0058	5008	,	,		18086	0.0119		0.0099	False		,,,				2504	0.0092				p.D5120D		Atlas-SNP	.											.	PCLO	1506	.	0			c.C15360T						PASS	.	G		54,3600		1,52,1774	200.0	190.0	193.0		15360	3.7	1.0	7	dbSNP_129	193	205,7951		2,201,3875	no	coding-synonymous	PCLO	NM_033026.5		3,253,5649	AA,AG,GG		2.5135,1.4778,2.1931		5120/5143	82387960	259,11551	1827	4078	5905	SO:0001819	synonymous_variant	27445	exon25			CACTTTGTCAAGC	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.15360C>T	7.37:g.82387960G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			G|0.987;A|0.013	0.013	strong		0.363	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
RFTN1	23180	hgsc.bcm.edu	37	3	16364919	16364919	+	Silent	SNP	A	A	C	rs690216	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:16364919A>C	ENST00000334133.4	-	9	1568	c.1296T>G	c.(1294-1296)ccT>ccG	p.P432P	OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000435829.2_Intron|RFTN1_ENST00000432519.1_Silent_p.P396P|OXNAD1_ENST00000544043.1_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	432					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						GAGGTAGACAAGGTCTCTGAA	0.458													C|||	2891	0.577276	0.7375	0.5375	5008	,	,		20763	0.5149		0.5626	False		,,,				2504	0.4683				p.P432P		Atlas-SNP	.											.	RFTN1	79	.	0			c.T1296G						PASS	.	C		3032,1374	453.6+/-350.4	1050,932,221	111.0	98.0	103.0		1296	-10.7	0.4	3	dbSNP_83	103	4818,3782	537.1+/-383.1	1359,2100,841	no	coding-synonymous	RFTN1	NM_015150.1		2409,3032,1062	CC,CA,AA		43.9767,31.1847,39.6432		432/579	16364919	7850,5156	2203	4300	6503	SO:0001819	synonymous_variant	23180	exon9			TAGACAAGGTCTC	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1296T>G	3.37:g.16364919A>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																			A|0.402;C|0.598	0.598	strong		0.458	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
SIDT1	54847	hgsc.bcm.edu	37	3	113320477	113320477	+	Missense_Mutation	SNP	C	C	T	rs33990195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:113320477C>T	ENST00000264852.4	+	11	1814	c.1088C>T	c.(1087-1089)aCa>aTa	p.T363I	SIDT1_ENST00000393830.3_Missense_Mutation_p.T363I	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	363			T -> I (in dbSNP:rs33990195).		dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GCTGCCAGCACACCCGAAGGG	0.418													C|||	227	0.0453275	0.0068	0.0605	5008	,	,		19620	0.0407		0.0994	False		,,,				2504	0.0358				p.T363I		Atlas-SNP	.											SIDT1,colon,carcinoma,-1,1	SIDT1	99	1	0			c.C1088T						scavenged	.	C	ILE/THR	64,4342	60.5+/-97.4	2,60,2141	118.0	104.0	109.0		1088	6.1	1.0	3	dbSNP_126	109	872,7728	197.6+/-242.2	52,768,3480	yes	missense	SIDT1	NM_017699.2	89	54,828,5621	TT,TC,CC		10.1395,1.4526,7.1967	possibly-damaging	363/828	113320477	936,12070	2203	4300	6503	SO:0001583	missense	54847	exon11			CCAGCACACCCGA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1088C>T	3.37:g.113320477C>T	ENSP00000264852:p.Thr363Ile	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	154	53	0.344156	NM_017699	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	122	0.055860805860805864	6	0.012195121951219513	23	0.06353591160220995	26	0.045454545454545456	67	0.08839050131926121	C	16.59	3.166585	0.57476	0.014526	0.101395	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.23348	1.91;1.91	6.07	6.07	0.98685	.	0.083258	0.52532	D	0.000080	T	0.00666	0.0022	L	0.34521	1.04	0.54753	D	0.999988	B;B	0.30727	0.248;0.292	B;B	0.33846	0.136;0.171	T	0.01993	-1.1233	10	0.32370	T	0.25	-16.7075	20.6593	0.99626	0.0:1.0:0.0:0.0	rs33990195	363;363	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	I	363	ENSP00000264852:T363I;ENSP00000377416:T363I	ENSP00000264852:T363I	T	+	2	0	SIDT1	114803167	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	5.080000	0.64437	2.885000	0.99019	0.655000	0.94253	ACA	C|0.924;T|0.076	0.076	strong		0.418	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
LSP1	4046	hgsc.bcm.edu	37	11	1874404	1874404	+	Silent	SNP	C	C	T	rs2089910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1874404C>T	ENST00000311604.3	+	1	205	c.30C>T	c.(28-30)gcC>gcT	p.A10A		NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	10					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		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;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		ACCCGGGTGCCGAGGAGCGGG	0.657													C|||	1462	0.291933	0.2799	0.2795	5008	,	,		13920	0.4623		0.2654	False		,,,				2504	0.1687				p.A10A		Atlas-SNP	.											LSP1_ENST00000311604,rectum,carcinoma,0,1	LSP1	59	1	0			c.C30T						PASS	.	C		1155,3241	375.1+/-321.5	150,855,1193	65.0	65.0	65.0		30	-5.1	0.0	11	dbSNP_96	65	1971,6619	325.8+/-317.1	236,1499,2560	no	coding-synonymous	LSP1	NM_002339.2		386,2354,3753	TT,TC,CC		22.9453,26.2739,24.0721		10/340	1874404	3126,9860	2198	4295	6493	SO:0001819	synonymous_variant	4046	exon1			GGGTGCCGAGGAG	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.30C>T	11.37:g.1874404C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_002339	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																			C|0.721;T|0.279	0.279	strong		0.657	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
BPIFC	254240	hgsc.bcm.edu	37	22	32810378	32810378	+	Missense_Mutation	SNP	T	T	G	rs35856742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32810378T>G	ENST00000397452.1	-	16	1546	c.1436A>C	c.(1435-1437)gAa>gCa	p.E479A	RTCB_ENST00000451746.2_5'Flank|BPIFC_ENST00000300399.3_Missense_Mutation_p.E479A|BPIFC_ENST00000534972.1_Missense_Mutation_p.E203A|BPIFC_ENST00000432451.2_Missense_Mutation_p.E236A|RTCB_ENST00000216038.5_5'Flank			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	479			E -> A (in dbSNP:rs35856742).			extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TGAGGATGTTTCATACTTCAG	0.493													T|||	296	0.0591054	0.1233	0.0303	5008	,	,		18467	0.0139		0.0527	False		,,,				2504	0.046				p.E479A		Atlas-SNP	.											.	.	.	.	0			c.A1436C						PASS	.	T	ALA/GLU	496,3910	230.4+/-244.6	35,426,1742	144.0	123.0	130.0		1436	4.3	0.8	22	dbSNP_126	130	372,8228	122.2+/-181.2	15,342,3943	yes	missense	BPIFC	NM_174932.2	107	50,768,5685	GG,GT,TT		4.3256,11.2574,6.6738	benign	479/508	32810378	868,12138	2203	4300	6503	SO:0001583	missense	254240	exon15			GATGTTTCATACT	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1436A>C	22.37:g.32810378T>G	ENSP00000380594:p.Glu479Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	129	0.059065934065934064	68	0.13821138211382114	12	0.03314917127071823	4	0.006993006993006993	45	0.059366754617414245	T	14.93	2.681075	0.47886	0.112574	0.043256	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.04917	3.53;3.53;4.28;3.97	5.39	4.29	0.51040	.	0.550764	0.20116	N	0.098913	T	0.00039	0.0001	M	0.68317	2.08	0.80722	P	0.0	B;P	0.35745	0.047;0.518	B;B	0.30401	0.014;0.115	T	0.18967	-1.0320	9	0.10111	T	0.7	-2.8015	9.7286	0.40348	0.0:0.0:0.1729:0.8271	rs35856742	236;479	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	A	479;479;203;236	ENSP00000380594:E479A;ENSP00000300399:E479A;ENSP00000439123:E203A;ENSP00000408920:E236A	ENSP00000300399:E479A	E	-	2	0	BPIFC	31140378	0.939000	0.31865	0.819000	0.32651	0.995000	0.86356	1.613000	0.36900	2.167000	0.68274	0.460000	0.39030	GAA	T|0.936;G|0.064	0.064	strong		0.493	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
GCC1	79571	hgsc.bcm.edu	37	7	127222157	127222157	+	Silent	SNP	G	G	A	rs3735644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:127222157G>A	ENST00000321407.2	-	2	2663	c.2239C>T	c.(2239-2241)Ctg>Ttg	p.L747L	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	747	GRIP. {ECO:0000255|PROSITE- ProRule:PRU00250}.				protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AAGATAGTCAGTATGGCTGTG	0.527													G|||	1357	0.270966	0.0166	0.2147	5008	,	,		22088	0.7034		0.2127	False		,,,				2504	0.2689				p.L747L		Atlas-SNP	.											.	GCC1	83	.	0			c.C2239T						PASS	.	G		239,4167	139.2+/-174.8	5,229,1969	204.0	198.0	200.0		2239	3.0	0.9	7	dbSNP_107	200	1688,6912	310.0+/-309.6	154,1380,2766	no	coding-synonymous	GCC1	NM_024523.5		159,1609,4735	AA,AG,GG		19.6279,5.4244,14.8162		747/776	127222157	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	79571	exon2			TAGTCAGTATGGC	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"""golgi coiled-coil 1"""			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.2239C>T	7.37:g.127222157G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	200	104	0.52	NM_024523	Q9H6N7	Silent	SNP	ENST00000321407.2	37	CCDS5796.1																																																																																			G|0.799;A|0.201	0.201	strong		0.527	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523	
KANK1	23189	hgsc.bcm.edu	37	9	712156	712156	+	Missense_Mutation	SNP	T	T	G	rs912174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:712156T>G	ENST00000382303.1	+	7	2042	c.1390T>G	c.(1390-1392)Tcc>Gcc	p.S464A	KANK1_ENST00000382293.3_Missense_Mutation_p.S306A|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.S464A	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	464	Interaction with KIF21A.		S -> A (in dbSNP:rs912174). {ECO:0000269|PubMed:8724849}.		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.S306A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GACCATAGAATCCTTGAAGGA	0.473													G|||	1024	0.204473	0.2534	0.3084	5008	,	,		22325	0.1935		0.2137	False		,,,				2504	0.0665				p.S464A		Atlas-SNP	.											KANK1,NS,carcinoma,0,1	KANK1	231	1	1	Substitution - Missense(1)	stomach(1)	c.T1390G						PASS	.	G	ALA/SER,ALA/SER	1123,3283	717.7+/-408.7	143,837,1223	86.0	85.0	85.0		1390,916	5.5	0.9	9	dbSNP_86	85	1920,6680	727.5+/-406.6	234,1452,2614	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	99,99	377,2289,3837	GG,GT,TT		22.3256,25.488,23.3969	benign,benign	464/1353,306/1195	712156	3043,9963	2203	4300	6503	SO:0001583	missense	23189	exon7			ATAGAATCCTTGA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1390T>G	9.37:g.712156T>G	ENSP00000371740:p.Ser464Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	473	0.21657509157509158	108	0.21951219512195122	114	0.3149171270718232	96	0.16783216783216784	155	0.20448548812664907	G	3.902	-0.021755	0.07634	0.25488	0.223256	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.32023	1.47;1.47;1.48	5.52	5.52	0.82312	.	0.000000	0.56097	N	0.000029	T	0.00012	0.0000	N	0.00082	-2.215	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41305	-0.9516	9	0.02654	T	1	-14.5643	15.5859	0.76482	0.0:0.0:0.8609:0.1391	rs912174;rs52832305;rs61129314;rs912174	464;464	Q5W0W1;Q14678	.;KANK1_HUMAN	A	464;464;464;306	ENSP00000371740:S464A;ENSP00000371734:S464A;ENSP00000371730:S306A	ENSP00000346479:S464A	S	+	1	0	KANK1	702156	0.997000	0.39634	0.899000	0.35326	0.993000	0.82548	2.358000	0.44134	1.362000	0.46000	-0.121000	0.15023	TCC	T|0.781;G|0.219	0.219	strong		0.473	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
CCDC51	79714	hgsc.bcm.edu	37	3	48474249	48474249	+	Silent	SNP	A	A	G	rs2279077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48474249A>G	ENST00000395694.2	-	4	890	c.805T>C	c.(805-807)Ttg>Ctg	p.L269L	CCDC51_ENST00000442740.1_Silent_p.L160L|PLXNB1_ENST00000296440.6_5'Flank|CCDC51_ENST00000412398.2_Silent_p.L160L|PLXNB1_ENST00000448774.2_5'Flank|CCDC51_ENST00000447018.1_Silent_p.L160L|CCDC51_ENST00000395696.1_Silent_p.L269L	NM_001256964.1	NP_001243893.1	Q96ER9	CCD51_HUMAN	coiled-coil domain containing 51	269						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				endometrium(4)|kidney(4)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AGGCCCCTCAAGTCCACCATG	0.607													A|||	1602	0.319888	0.2413	0.2882	5008	,	,		19801	0.3135		0.4632	False		,,,				2504	0.3078				p.L269L		Atlas-SNP	.											.	CCDC51	34	.	0			c.T805C						PASS	.	A		1061,2881		145,771,1055	70.0	74.0	73.0		805	2.3	1.0	3	dbSNP_100	73	3858,4428		901,2056,1186	no	coding-synonymous	CCDC51	NM_024661.3		1046,2827,2241	GG,GA,AA		46.5605,26.9153,40.2273		269/412	48474249	4919,7309	1971	4143	6114	SO:0001819	synonymous_variant	79714	exon4			CCCTCAAGTCCAC	AK022498	CCDS2766.2, CCDS58830.1	3p21.31	2005-12-30			ENSG00000164051	ENSG00000164051			25714	protein-coding gene	gene with protein product						12477932	Standard	NM_001256964		Approved	FLJ12436	uc003ctc.3	Q96ER9	OTTHUMG00000133534	ENST00000395694.2:c.805T>C	3.37:g.48474249A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_024661	Q9HA01	Silent	SNP	ENST00000395694.2	37	CCDS2766.2																																																																																			A|0.636;G|0.364	0.364	strong		0.607	CCDC51-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344599.2	NM_024661	
FAM175A	84142	hgsc.bcm.edu	37	4	84383810	84383810	+	Missense_Mutation	SNP	C	C	T	rs12642536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:84383810C>T	ENST00000321945.7	-	9	1150	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	MRPS18C_ENST00000509571.1_Intron|FAM175A_ENST00000506553.1_Missense_Mutation_p.A299T	NM_139076.2	NP_620775.2	Q6UWZ7	F175A_HUMAN	family with sequence similarity 175, member A	348			A -> T (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs12642536). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18695986}.		chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	13						AAGTCTAAGGCTTTATGCTTA	0.398													C|||	2098	0.41893	0.1225	0.5259	5008	,	,		19558	0.6756		0.3787	False		,,,				2504	0.5204				p.A348T		Atlas-SNP	.											.	FAM175A	36	.	0			c.G1042A						PASS	.	C	THR/ALA	747,3659	307.7+/-290.2	56,635,1512	240.0	205.0	217.0		1042	2.8	0.1	4	dbSNP_120	217	3509,5091	512.4+/-377.9	712,2085,1503	yes	missense	FAM175A	NM_139076.2	58	768,2720,3015	TT,TC,CC		40.8023,16.9542,32.7234	possibly-damaging	348/410	84383810	4256,8750	2203	4300	6503	SO:0001583	missense	84142	exon9			CTAAGGCTTTATG	AK023676	CCDS3605.2	4q21.23	2008-10-31	2008-07-02	2008-07-02	ENSG00000163322	ENSG00000163322			25829	protein-coding gene	gene with protein product	"""Abraxas protein"""	611143	"""coiled-coil domain containing 98"""	CCDC98		12975309, 17525340	Standard	NM_139076		Approved	FLJ13614, ABRA1	uc003hou.2	Q6UWZ7	OTTHUMG00000130429	ENST00000321945.7:c.1042G>A	4.37:g.84383810C>T	ENSP00000369857:p.Ala348Thr	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	264	263	0.996212	NM_139076	A5JJ07|Q9H8I1|Q9H9N4	Missense_Mutation	SNP	ENST00000321945.7	37	CCDS3605.2	923	0.4226190476190476	72	0.14634146341463414	180	0.4972375690607735	370	0.6468531468531469	301	0.3970976253298153	C	16.97	3.268943	0.59540	0.169542	0.408023	ENSG00000163322	ENST00000321945;ENST00000506553	T;T	0.48522	0.81;0.82	5.61	2.75	0.32379	.	0.357727	0.26079	N	0.026478	T	0.00012	0.0000	L	0.57536	1.79	0.49687	P	1.8600000000001948E-4	P	0.43938	0.822	B	0.43916	0.436	T	0.44251	-0.9340	9	0.66056	D	0.02	-24.7011	10.914	0.47124	0.2669:0.6152:0.1179:0.0	rs12642536;rs52814022;rs12642536	348	Q6UWZ7	F175A_HUMAN	T	348;299	ENSP00000369857:A348T;ENSP00000426763:A299T	ENSP00000369857:A348T	A	-	1	0	FAM175A	84602834	0.270000	0.24152	0.139000	0.22197	0.030000	0.12068	0.499000	0.22546	1.330000	0.45394	-0.293000	0.09583	GCC	C|0.642;T|0.358	0.358	strong		0.398	FAM175A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252818.1	NM_139076	
GPR144	347088	hgsc.bcm.edu	37	9	127215772	127215772	+	Missense_Mutation	SNP	C	C	G	rs72616654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127215772C>G	ENST00000334810.1	+	4	796	c.796C>G	c.(796-798)Cac>Gac	p.H266D				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	266	Pentaxin.				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)			central_nervous_system(1)|endometrium(3)	4						CTCGGTGCGTCACGCCCTCAG	0.761													G|||	2623	0.523762	0.4834	0.6009	5008	,	,		6568	0.4494		0.5726	False		,,,				2504	0.5501				p.H266D		Atlas-SNP	.											.	GPR144	33	.	0			c.C796G						PASS	.						4.0	5.0	4.0					9																	127215772		654	1515	2169	SO:0001583	missense	347088	exon4			GTGCGTCACGCCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.796C>G	9.37:g.127215772C>G	ENSP00000335156:p.His266Asp	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	19	15	0.789474	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1149	0.5260989010989011	257	0.5223577235772358	216	0.5966850828729282	250	0.4370629370629371	426	0.5620052770448549	G	1.281	-0.610443	0.03690	.	.	ENSG00000180264	ENST00000334810	T	0.05996	3.36	3.81	2.9	0.33743	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00707	-1.245	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.21861	-1.0233	8	0.08837	T	0.75	.	7.5506	0.27796	0.0951:0.1682:0.7367:0.0	.	266	Q7Z7M1	GP144_HUMAN	D	266	ENSP00000335156:H266D	ENSP00000335156:H266D	H	+	1	0	GPR144	126255593	0.998000	0.40836	0.052000	0.19188	0.277000	0.26821	3.079000	0.50104	0.133000	0.18654	-0.647000	0.03941	CAC	C|0.491;G|0.509	0.509	strong		0.761	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
APOBR	55911	hgsc.bcm.edu	37	16	28507452	28507452	+	Missense_Mutation	SNP	G	G	T	rs370148393		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:28507452G>T	ENST00000431282.1	+	3	1073	c.1063G>T	c.(1063-1065)Ggg>Tgg	p.G355W	APOBR_ENST00000328423.5_Missense_Mutation_p.G355W|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000564831.1_Missense_Mutation_p.G364W|CLN3_ENST00000567160.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	355	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						GGAGGAGGCCGGGACAGCCTC	0.672																																					p.G364W		Atlas-SNP	.											APOBR,caecum,carcinoma,0,1	APOBR	89	1	0			c.G1090T						scavenged	.						14.0	17.0	16.0					16																	28507452		1944	4097	6041	SO:0001583	missense	55911	exon2			GAGGCCGGGACAG	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.1063G>T	16.37:g.28507452G>T	ENSP00000416094:p.Gly355Trp	Somatic	22	1	0.0454545		WXS	Illumina HiSeq	Phase_I	7	2	0.285714	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	G	11.71	1.718826	0.30503	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.60548	0.18;0.18	3.86	-2.49	0.06403	.	.	.	.	.	T	0.33059	0.0850	N	0.19112	0.55	0.09310	N	1	B	0.33777	0.425	B	0.27715	0.082	T	0.13980	-1.0489	9	0.72032	D	0.01	.	3.7884	0.08710	0.5999:0.0:0.2159:0.1841	.	355	Q9NS13	.	W	355	ENSP00000327669:G355W;ENSP00000416094:G355W	ENSP00000327669:G355W	G	+	1	0	APOBR	28414953	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.825000	0.04433	-0.783000	0.04534	-0.487000	0.04747	GGG	.	.	alt		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
KNDC1	85442	hgsc.bcm.edu	37	10	135012652	135012652	+	Silent	SNP	T	T	C	rs3008388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:135012652T>C	ENST00000304613.3	+	14	2661	c.2640T>C	c.(2638-2640)gaT>gaC	p.D880D	KNDC1_ENST00000368571.2_Silent_p.D815D|KNDC1_ENST00000368572.2_Silent_p.D880D			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	880	Pro-rich.				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)		CCTGCGTGGATGCCTCGCCAC	0.687													C|||	2060	0.411342	0.1203	0.4049	5008	,	,		11469	0.6091		0.4384	False		,,,				2504	0.5777				p.D880D		Atlas-SNP	.											KNDC1,rectum,carcinoma,0,2	KNDC1	155	2	0			c.T2640C						PASS	.						9.0	9.0	9.0					10																	135012652		2159	4223	6382	SO:0001819	synonymous_variant	85442	exon14			CGTGGATGCCTCG	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.2640T>C	10.37:g.135012652T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																			T|0.587;C|0.413	0.413	strong		0.687	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
TTN	7273	hgsc.bcm.edu	37	2	179593352	179593352	+	Missense_Mutation	SNP	C	C	T	rs11888217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179593352C>T	ENST00000591111.1	-	64	18574	c.18350G>A	c.(18349-18351)aGt>aAt	p.S6117N	TTN_ENST00000589042.1_Missense_Mutation_p.S6434N|TTN_ENST00000342992.6_Missense_Mutation_p.S5190N|RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12904	Ig-like 42.				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)			ATTTTCAAAACTCATTGAAAA	0.423													C|||	467	0.0932508	0.087	0.1513	5008	,	,		20407	0.0238		0.0358	False		,,,				2504	0.1912				p.S6434N		Atlas-SNP	.											.	TTN	18412	.	0			c.G19301A						PASS	.	C	ASN/SER,,,	307,3375		8,291,1542	72.0	66.0	68.0		15569,,,	4.7	1.0	2	dbSNP_120	68	202,8004		5,192,3906	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	46,,,	13,483,5448	TT,TC,CC		2.4616,8.3379,4.2816	possibly-damaging,,,	5190/33424,,,	179593352	509,11379	1841	4103	5944	SO:0001583	missense	7273	exon66			TCAAAACTCATTG	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.18350G>A	2.37:g.179593352C>T	ENSP00000465570:p.Ser6117Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	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		107	0.04899267399267399	37	0.07520325203252033	40	0.11049723756906077	4	0.006993006993006993	26	0.03430079155672823	C	9.202	1.028618	0.19512	0.083379	0.024616	ENSG00000155657	ENST00000342992	T	0.68025	-0.3	5.63	4.73	0.59995	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04092	0.0114	M	0.80746	2.51	0.09310	P	0.9999999999998749	P	0.36354	0.549	B	0.37780	0.258	T	0.56763	-0.7925	8	0.87932	D	0	.	16.6664	0.85254	0.0:0.8702:0.1298:0.0	rs11888217;rs52819977;rs57620947;rs11888217	6117	Q8WZ42	TITIN_HUMAN	N	5190	ENSP00000343764:S5190N	ENSP00000343764:S5190N	S	-	2	0	TTN	179301597	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.753000	0.38359	1.467000	0.48044	0.655000	0.94253	AGT	C|0.952;T|0.048	0.048	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CFAP53	220136	hgsc.bcm.edu	37	18	47777244	47777244	+	Missense_Mutation	SNP	C	C	T	rs35193847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:47777244C>T	ENST00000398545.4	-	5	997	c.880G>A	c.(880-882)Gag>Aag	p.E294K		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		TCTATCCTCTCTTGTAGGGCT	0.418													C|||	969	0.19349	0.1036	0.1787	5008	,	,		20837	0.0625		0.3926	False		,,,				2504	0.2556				p.E294K		Atlas-SNP	.											.	CCDC11	59	.	0			c.G880A						PASS	.	C	LYS/GLU	542,3210		43,456,1377	385.0	342.0	356.0		880	4.9	0.8	18	dbSNP_126	356	3112,5114		618,1876,1619	yes	missense	CCDC11	NM_145020.3	56	661,2332,2996	TT,TC,CC		37.8313,14.4456,30.5059	possibly-damaging	294/515	47777244	3654,8324	1876	4113	5989	SO:0001583	missense	220136	exon5			TCCTCTCTTGTAG																												ENST00000398545.4:c.880G>A	18.37:g.47777244C>T	ENSP00000381553:p.Glu294Lys	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	368	200	0.543478	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	441	0.20192307692307693	49	0.09959349593495935	74	0.20441988950276244	39	0.06818181818181818	279	0.36807387862796836	C	12.00	1.807417	0.31961	0.144456	0.378313	ENSG00000172361	ENST00000398545	T	0.11821	2.74	5.81	4.94	0.65067	.	0.524458	0.21054	N	0.080955	T	0.00012	0.0000	L	0.46157	1.445	0.53688	P	2.8000000000028002E-5	P	0.37061	0.58	B	0.37550	0.253	T	0.43669	-0.9377	9	0.11794	T	0.64	-5.5184	8.4953	0.33125	0.0:0.7651:0.1536:0.0813	rs35193847;rs56682575	294	Q96M91	CCD11_HUMAN	K	294	ENSP00000381553:E294K	ENSP00000381553:E294K	E	-	1	0	CCDC11	46031242	0.587000	0.26791	0.806000	0.32338	0.006000	0.05464	2.060000	0.41394	1.471000	0.48121	0.655000	0.94253	GAG	C|0.738;T|0.262	0.262	strong		0.418	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
PABPC1	26986	hgsc.bcm.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	G	A	rs202060459		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:101724606G>A	ENST00000318607.5	-	7	2084	c.956C>T	c.(955-957)aCa>aTa	p.T319I	PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Missense_Mutation_p.T287I|PABPC1_ENST00000519004.1_Missense_Mutation_p.T274I	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	319	RRM 4. {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)	p.T319I(2)		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)			ACTAGTGATTGTACCAAATGG	0.284																																					p.T319I		Atlas-SNP	.											PABPC1,NS,carcinoma,0,2	PABPC1	76	2	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.C956T						scavenged	.						154.0	166.0	162.0					8																	101724606		2203	4298	6501	SO:0001583	missense	26986	exon7			GTGATTGTACCAA	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.956C>T	8.37:g.101724606G>A	ENSP00000313007:p.Thr319Ile	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	176	4	0.0227273	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.8|26.8	4.768189|4.768189	0.90020|0.90020	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.16196	.|2.36;2.36;2.36	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000009	.|T	.|0.37652	.|0.1011	M|M	0.62154|0.62154	1.92|1.92	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.54964	.|0.917;0.784;0.969	.|P;B;P	.|0.56916	.|0.747;0.442;0.809	.|T	.|0.03784	.|-1.1004	.|10	.|0.87932	.|D	.|0	.|.	20.0919|20.0919	0.97823|0.97823	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|287;319;319	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	X|I	188|319;319;274;287	.|ENSP00000313007:T319I;ENSP00000429594:T274I;ENSP00000429395:T287I	.|ENSP00000313007:T319I	Q|T	-|-	1|2	0|0	PABPC1|PABPC1	101793782|101793782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.776000|9.776000	0.99001|0.99001	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CAA|ACA	.	.	weak		0.284	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
HSPH1	10808	hgsc.bcm.edu	37	13	31725260	31725260	+	Silent	SNP	A	A	G	rs11556147	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:31725260A>G	ENST00000320027.5	-	7	1076	c.732T>C	c.(730-732)ttT>ttC	p.F244F	HSPH1_ENST00000380405.4_Silent_p.F244F|HSPH1_ENST00000380406.5_Silent_p.F203F|HSPH1_ENST00000429785.2_Silent_p.F63F|HSPH1_ENST00000445273.2_Silent_p.F246F	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	244					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		ATTCTGCACAAAAATGTTCCA	0.348													A|||	1131	0.225839	0.2451	0.2723	5008	,	,		18635	0.0109		0.4642	False		,,,				2504	0.1431				p.F244F		Atlas-SNP	.											.	HSPH1	65	.	0			c.T732C						PASS	.	A		1261,3145	427.4+/-341.5	171,919,1113	101.0	100.0	100.0		732	-2.6	1.0	13	dbSNP_120	100	4061,4539	553.7+/-386.4	951,2159,1190	no	coding-synonymous	HSPH1	NM_006644.2		1122,3078,2303	GG,GA,AA		47.2209,28.6201,40.9196		244/859	31725260	5322,7684	2203	4300	6503	SO:0001819	synonymous_variant	10808	exon7			TGCACAAAAATGT	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.732T>C	13.37:g.31725260A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Silent	SNP	ENST00000320027.5	37	CCDS9340.1																																																																																			A|0.653;G|0.347	0.347	strong		0.348	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
GTSE1	51512	hgsc.bcm.edu	37	22	46722531	46722531	+	Silent	SNP	C	C	T	rs9615949	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46722531C>T	ENST00000454366.1	+	9	1916	c.1704C>T	c.(1702-1704)ccC>ccT	p.P568P		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	549					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CCTCTGAGCCCCGCAAGAACT	0.567													C|||	233	0.0465256	0.0287	0.0562	5008	,	,		17060	0.001		0.1223	False		,,,				2504	0.0327				p.P568P	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1704T						PASS	.	C		150,4256	103.4+/-141.9	2,146,2055	52.0	48.0	49.0		1704	2.4	0.8	22	dbSNP_119	49	914,7686	200.7+/-244.4	48,818,3434	no	coding-synonymous	GTSE1	NM_016426.6		50,964,5489	TT,TC,CC		10.6279,3.4044,8.1808		568/740	46722531	1064,11942	2203	4300	6503	SO:0001819	synonymous_variant	51512	exon9			TGAGCCCCGCAAG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1704C>T	22.37:g.46722531C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.928;T|0.072	0.072	strong		0.567	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
ALKBH3	221120	hgsc.bcm.edu	37	11	43940644	43940644	+	Silent	SNP	G	G	T	rs1048928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:43940644G>T	ENST00000302708.4	+	9	1137	c.726G>T	c.(724-726)ggG>ggT	p.G242G	ALKBH3-AS1_ENST00000499194.1_RNA|ALKBH3_ENST00000532410.1_3'UTR|ALKBH3-AS1_ENST00000534287.1_RNA|RP11-613D13.4_ENST00000526408.1_RNA|ALKBH3-AS1_ENST00000527960.1_RNA|ALKBH3-AS1_ENST00000528285.1_RNA	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	242	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TGGATCATGGGACCTTGTTAA	0.423								Direct reversal of damage					G|||	3086	0.616214	0.2958	0.6542	5008	,	,		23097	0.8373		0.6243	False		,,,				2504	0.7863				p.G242G		Atlas-SNP	.											.	ALKBH3	33	.	0			c.G726T						PASS	.	G		1596,2810	497.6+/-363.9	288,1020,895	202.0	167.0	179.0		726	2.8	1.0	11	dbSNP_86	179	5368,3232	651.2+/-400.8	1671,2026,603	no	coding-synonymous	ALKBH3	NM_139178.3		1959,3046,1498	TT,TG,GG		37.5814,36.2233,46.4555		242/287	43940644	6964,6042	2203	4300	6503	SO:0001819	synonymous_variant	221120	exon9			TCATGGGACCTTG	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.726G>T	11.37:g.43940644G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	37	CCDS7906.1	1346	0.6163003663003663	144	0.2926829268292683	236	0.6519337016574586	487	0.8513986013986014	479	0.6319261213720316	G	9.945	1.218599	0.22373	0.362233	0.624186	ENSG00000166199	ENST00000532129	.	.	.	5.91	2.83	0.33086	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999711	.	.	.	.	.	.	T	0.13926	-1.0491	3	.	.	.	-24.6034	7.4352	0.27152	0.167:0.1501:0.6829:0.0	rs1048928;rs3188976;rs3740987;rs17499464;rs58267847;rs1048928	.	.	.	Y	112	.	.	D	+	1	0	ALKBH3	43897220	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.148000	0.16224	0.837000	0.34925	0.655000	0.94253	GAC	G|0.420;T|0.580	0.580	strong		0.423	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
C18orf21	83608	hgsc.bcm.edu	37	18	33557466	33557466	+	Missense_Mutation	SNP	A	A	G	rs2276314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	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	
XPO4	64328	hgsc.bcm.edu	37	13	21429776	21429776	+	Missense_Mutation	SNP	T	T	C	rs17320607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21429776T>C	ENST00000255305.6	-	4	517	c.446A>G	c.(445-447)aAt>aGt	p.N149S	XPO4_ENST00000400602.2_Missense_Mutation_p.N149S|XPO4_ENST00000490513.1_5'UTR			Q9C0E2	XPO4_HUMAN	exportin 4	149			N -> S (in dbSNP:rs17320607).		positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		CACAGTGGGATTGCCACTACT	0.308													T|||	69	0.013778	0.0	0.0331	5008	,	,		16423	0.0		0.0318	False		,,,				2504	0.0143				p.N149S		Atlas-SNP	.											.	XPO4	153	.	0			c.A446G						PASS	.	T	SER/ASN	14,3612		0,14,1799	85.0	74.0	77.0		446	3.5	1.0	13	dbSNP_123	77	221,7925		3,215,3855	yes	missense	XPO4	NM_022459.4	46	3,229,5654	CC,CT,TT		2.713,0.3861,1.9963	benign	149/1152	21429776	235,11537	1813	4073	5886	SO:0001583	missense	64328	exon4			GTGGGATTGCCAC	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"""Exportins"""	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.446A>G	13.37:g.21429776T>C	ENSP00000255305:p.Asn149Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Missense_Mutation	SNP	ENST00000255305.6	37	CCDS41872.1	25	0.011446886446886446	0	0.0	8	0.022099447513812154	0	0.0	17	0.022427440633245383	T	15.86	2.958583	0.53400	0.003861	0.02713	ENSG00000132953	ENST00000400602;ENST00000255305	T;T	0.67171	-0.25;-0.25	5.92	3.48	0.39840	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.21718	0.0523	N	0.25647	0.755	0.52501	D	0.999955	B	0.25441	0.126	B	0.18561	0.022	T	0.19321	-1.0309	10	0.02654	T	1	-7.2714	10.4484	0.44507	0.0:0.1317:0.0:0.8683	rs17320607;rs17320607	149	Q9C0E2	XPO4_HUMAN	S	149	ENSP00000383444:N149S;ENSP00000255305:N149S	ENSP00000255305:N149S	N	-	2	0	XPO4	20327776	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.651000	0.61447	0.495000	0.27882	0.383000	0.25322	AAT	T|0.986;C|0.014	0.014	strong		0.308	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	
HMMR	3161	hgsc.bcm.edu	37	5	162909687	162909687	+	Silent	SNP	G	G	A	rs17600938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:162909687G>A	ENST00000358715.3	+	13	1458	c.1422G>A	c.(1420-1422)aaG>aaA	p.K474K	HMMR_ENST00000393915.4_Silent_p.K475K|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000353866.3_Silent_p.K459K|HMMR_ENST00000432118.2_Silent_p.K388K|RP11-80G7.1_ENST00000514724.2_RNA			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	474					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AAGATCTTAAGCTGGAGAACT	0.368													G|||	563	0.11242	0.1377	0.1037	5008	,	,		17292	0.0615		0.1044	False		,,,				2504	0.1452				p.K475K		Atlas-SNP	.											.	HMMR	64	.	0			c.G1425A						PASS	.	G	,,,	598,3808	254.9+/-260.3	36,526,1641	71.0	71.0	71.0		1425,1164,1422,1377	1.7	1.0	5	dbSNP_123	71	952,7648	206.3+/-248.5	60,832,3408	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	,,,	96,1358,5049	AA,AG,GG		11.0698,13.5724,11.9176	,,,	475/726,388/639,474/725,459/710	162909687	1550,11456	2203	4300	6503	SO:0001819	synonymous_variant	3161	exon13			TCTTAAGCTGGAG	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1422G>A	5.37:g.162909687G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	234	111	0.474359	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Silent	SNP	ENST00000358715.3	37	CCDS4362.1																																																																																			G|0.890;A|0.110	0.110	strong		0.368	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
MUC5B	727897	hgsc.bcm.edu	37	11	1272858	1272858	+	Silent	SNP	C	C	T	rs4963059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1272858C>T	ENST00000529681.1	+	31	14806	c.14748C>T	c.(14746-14748)ttC>ttT	p.F4916F	MUC5B_ENST00000447027.1_Silent_p.F4919F|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4916	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)		TGCCAACCTTCAGCGTGTCCA	0.642													C|||	1697	0.338858	0.2141	0.33	5008	,	,		19521	0.6052		0.2853	False		,,,				2504	0.2945				p.F4916F		Atlas-SNP	.											.	MUC5B	473	.	0			c.C14748T						PASS	.	C		833,3505		82,669,1418	58.0	68.0	65.0		14748	0.6	0.0	11	dbSNP_111	65	2509,6001		390,1729,2136	no	coding-synonymous	MUC5B	NM_002458.2		472,2398,3554	TT,TC,CC		29.483,19.2024,26.0118		4916/5763	1272858	3342,9506	2169	4255	6424	SO:0001819	synonymous_variant	727897	exon31			AACCTTCAGCGTG	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.14748C>T	11.37:g.1272858C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.663;T|0.337	0.337	strong		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
RNF169	254225	hgsc.bcm.edu	37	11	74546905	74546905	+	Silent	SNP	G	G	A	rs1125609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:74546905G>A	ENST00000299563.4	+	6	1270	c.1257G>A	c.(1255-1257)caG>caA	p.Q419Q		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	419					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						GAAGCCTGCAGAAGCAGACTT	0.488													G|||	1251	0.2498	0.171	0.1931	5008	,	,		19862	0.2609		0.2087	False		,,,				2504	0.4274				p.Q419Q		Atlas-SNP	.											RNF169,colon,carcinoma,0,1	RNF169	36	1	0			c.G1257A						PASS	.	G		652,3124		59,534,1295	96.0	97.0	97.0		1257	6.0	1.0	11	dbSNP_86	97	1577,6683		120,1337,2673	no	coding-synonymous	RNF169	NM_001098638.1		179,1871,3968	AA,AG,GG		19.092,17.2669,18.5194		419/709	74546905	2229,9807	1888	4130	6018	SO:0001819	synonymous_variant	254225	exon6			CCTGCAGAAGCAG	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"""RING-type (C3HC4) zinc fingers"""	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1257G>A	11.37:g.74546905G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_001098638	Q6N015	Silent	SNP	ENST00000299563.4	37	CCDS41691.1																																																																																			G|0.788;A|0.212	0.212	strong		0.488	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886	
PRB3	5544	hgsc.bcm.edu	37	12	11420904	11420904	+	Silent	SNP	T	T	C	rs541681122		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11420904T>C	ENST00000279573.7	-	3	414	c.279A>G	c.(277-279)ccA>ccG	p.P93P	PRB3_ENST00000538488.1_Silent_p.P93P|PRB3_ENST00000381842.3_Silent_p.P93P|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	93	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CCGGACGAGGTGGGGGACCTT	0.632																																					p.P93P		Atlas-SNP	.											PRB3_ENST00000538488,colon,carcinoma,0,2	PRB3	84	2	0			c.A279G						scavenged	.						144.0	180.0	168.0					12																	11420904		2084	4222	6306	SO:0001819	synonymous_variant	5544	exon3			ACGAGGTGGGGGA			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.279A>G	12.37:g.11420904T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Silent	SNP	ENST00000279573.7	37																																																																																				.	.	none		0.632	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
OR4P4	81300	hgsc.bcm.edu	37	11	55406022	55406022	+	Nonsense_Mutation	SNP	C	C	G	rs76160133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55406022C>G	ENST00000314612.2	+	1	189	c.189C>G	c.(187-189)taC>taG	p.Y63*		NM_001004124.1	NP_001004124.1	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P, member 4	63						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)|central_nervous_system(1)|kidney(4)|large_intestine(4)|lung(28)|ovary(1)|upper_aerodigestive_tract(1)	40						TCCTCAATTACCTCTCACTCT	0.403													c|||	1428	0.285144	0.0968	0.2968	5008	,	,		14249	0.4563		0.165	False		,,,				2504	0.4785				p.Y63X		Atlas-SNP	.											OR4P4,NS,carcinoma,0,1	OR4P4	84	1	0			c.C189G						PASS	.	C	stop/TYR	475,3887		79,317,1785	176.0	151.0	160.0		189	1.1	0.2	11	dbSNP_131	160	1193,6873		309,575,3149	yes	stop-gained	OR4P4	NM_001004124.1		388,892,4934	GG,GC,CC		14.7905,10.8895,13.4213		63/313	55406022	1668,10760	2181	4033	6214	SO:0001587	stop_gained	81300	exon1			CAATTACCTCTCA	AB065775	CCDS31504.1	11q11	2012-08-09			ENSG00000181927	ENSG00000181927		"""GPCR / Class A : Olfactory receptors"""	15180	protein-coding gene	gene with protein product				OR4P3P			Standard	NM_001004124		Approved		uc010rij.2	Q8NGL7	OTTHUMG00000165300	ENST00000314612.2:c.189C>G	11.37:g.55406022C>G	ENSP00000324831:p.Tyr63*	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_001004124		Nonsense_Mutation	SNP	ENST00000314612.2	37	CCDS31504.1	411	0.18818681318681318	36	0.07317073170731707	76	0.20994475138121546	211	0.3688811188811189	88	0.11609498680738786	C	9.130	1.011142	0.19277	0.108895	0.147905	ENSG00000181927	ENST00000314612	.	.	.	5.18	1.15	0.20763	.	0.212673	0.23912	N	0.043330	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.5722	5.6068	0.17385	0.0:0.5623:0.1312:0.3066	.	.	.	.	X	63	.	ENSP00000324831:Y63X	Y	+	3	2	OR4P4	55162598	0.000000	0.05858	0.215000	0.23724	0.045000	0.14185	-1.856000	0.01662	-0.045000	0.13468	-0.170000	0.13304	TAC	C|0.813;G|0.187	0.187	strong		0.403	OR4P4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383356.1	NM_001004124	
TARBP1	6894	hgsc.bcm.edu	37	1	234529552	234529552	+	Silent	SNP	C	C	T	rs2175594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:234529552C>T	ENST00000040877.1	-	27	4274	c.4275G>A	c.(4273-4275)gcG>gcA	p.A1425A	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1425					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)			CGGTCCACTCCGCTTGGTTAT	0.423													C|||	2554	0.509984	0.6225	0.5692	5008	,	,		17424	0.495		0.4384	False		,,,				2504	0.4049				p.A1425A		Atlas-SNP	.											.	TARBP1	111	.	0			c.G4275A						PASS	.	C		2594,1812	636.1+/-396.5	786,1022,395	77.0	82.0	81.0		4275	-7.5	0.0	1	dbSNP_96	81	3737,4863	530.8+/-381.9	806,2125,1369	no	coding-synonymous	TARBP1	NM_005646.3		1592,3147,1764	TT,TC,CC		43.4535,41.1257,48.6775		1425/1622	234529552	6331,6675	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon27			CCACTCCGCTTGG		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.4275G>A	1.37:g.234529552C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			C|0.508;T|0.492	0.492	strong		0.423	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
TMEM89	440955	hgsc.bcm.edu	37	3	48658924	48658924	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48658924C>T	ENST00000330862.3	-	1	364	c.266G>A	c.(265-267)cGg>cAg	p.R89Q		NM_001008269.1	NP_001008270.1	A2RUT3	TMM89_HUMAN	transmembrane protein 89	89						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|lung(1)|stomach(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGAGCGCCGCCGCCCCTGCAG	0.622																																					p.R89Q		Atlas-SNP	.											TMEM89,NS,carcinoma,+1,1	TMEM89	10	1	0			c.G266A						PASS	.						31.0	30.0	30.0					3																	48658924		2203	4299	6502	SO:0001583	missense	440955	exon1			CGCCGCCGCCCCT	AX657016	CCDS33751.1	3p21.31	2005-11-02			ENSG00000183396	ENSG00000183396			32372	protein-coding gene	gene with protein product							Standard	NM_001008269		Approved		uc011bbo.2	A2RUT3	OTTHUMG00000156647	ENST00000330862.3:c.266G>A	3.37:g.48658924C>T	ENSP00000329557:p.Arg89Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	194	108	0.556701	NM_001008269		Missense_Mutation	SNP	ENST00000330862.3	37	CCDS33751.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705879	0.48412	.	.	ENSG00000183396	ENST00000330862	T	0.57107	0.42	4.79	4.79	0.61399	.	0.182364	0.26899	N	0.021928	T	0.51483	0.1677	L	0.36672	1.1	0.09310	N	1	D	0.64830	0.994	P	0.51229	0.663	T	0.47222	-0.9134	10	0.44086	T	0.13	-19.7761	13.2009	0.59767	0.0:1.0:0.0:0.0	.	89	A2RUT3	TMM89_HUMAN	Q	89	ENSP00000329557:R89Q	ENSP00000329557:R89Q	R	-	2	0	TMEM89	48633928	.	.	0.011000	0.14972	0.055000	0.15305	.	.	2.492000	0.84095	0.462000	0.41574	CGG	.	.	none		0.622	TMEM89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345046.1	NM_001008269	
GABRG3	2567	hgsc.bcm.edu	37	15	27772697	27772697	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:27772697C>A	ENST00000333743.6	+	8	1238	c.984C>A	c.(982-984)ttC>ttA	p.F328L	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	328					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|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)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	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)	TGTTTGTCTTCGCCGCGCTGA	0.542																																					p.F328L	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											GABRG3,NS,carcinoma,0,2	GABRG3	115	2	0			c.C984A						PASS	.						124.0	112.0	116.0					15																	27772697		2161	4270	6431	SO:0001583	missense	2567	exon8			TGTCTTCGCCGCG		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.984C>A	15.37:g.27772697C>A	ENSP00000331912:p.Phe328Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	105	37	0.352381	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.45|18.45	3.626426|3.626426	0.66901|0.66901	.|.	.|.	ENSG00000182256|ENSG00000182256	ENST00000333743|ENST00000451330	D|.	0.87029|.	-2.2|.	5.48|5.48	-0.806|-0.806	0.10875|0.10875	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71375|.	0.3332|.	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	D|.	0.79108|.	0.992|.	T|.	0.71290|.	-0.4637|.	10|.	0.87932|.	D|.	0|.	.|.	10.0297|10.0297	0.42092|0.42092	0.0:0.3808:0.0:0.6192|0.0:0.3808:0.0:0.6192	.|.	328|.	Q99928|.	GBRG3_HUMAN|.	L|X	328|91	ENSP00000331912:F328L|.	ENSP00000331912:F328L|.	F|S	+|+	3|2	2|0	GABRG3|GABRG3	25446292|25446292	0.994000|0.994000	0.37717|0.37717	0.988000|0.988000	0.46212|0.46212	0.588000|0.588000	0.36517|0.36517	0.247000|0.247000	0.18179|0.18179	0.045000|0.045000	0.15804|0.15804	-0.251000|-0.251000	0.11542|0.11542	TTC|TCG	.	.	none		0.542	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
DCHS1	8642	hgsc.bcm.edu	37	11	6652618	6652618	+	Silent	SNP	C	C	T	rs2659871	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6652618C>T	ENST00000299441.3	-	8	4107	c.3696G>A	c.(3694-3696)ccG>ccA	p.P1232P	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1232	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAGTGTTCCCGGAGGCACGC	0.542													T|||	2261	0.451478	0.5946	0.415	5008	,	,		22321	0.4325		0.3797	False		,,,				2504	0.3773				p.P1232P		Atlas-SNP	.											DCHS1,colon,carcinoma,0,1	DCHS1	277	1	0			c.G3696A						PASS	.	T		2464,1938	550.9+/-378.2	700,1064,437	159.0	135.0	143.0		3696	4.2	1.0	11	dbSNP_100	143	3321,5271	644.6+/-400.1	637,2047,1612	no	coding-synonymous	DCHS1	NM_003737.2		1337,3111,2049	TT,TC,CC		38.6522,44.0254,44.5205		1232/3299	6652618	5785,7209	2201	4296	6497	SO:0001819	synonymous_variant	8642	exon8			TGTTCCCGGAGGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3696G>A	11.37:g.6652618C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.532;T|0.468	0.468	strong		0.542	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558345	140558345	+	Missense_Mutation	SNP	G	G	C	rs2950844	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	430	0	0		WXS	Illumina HiSeq	Phase_I	325	114	0.350769	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	
ZC3HC1	51530	hgsc.bcm.edu	37	7	129663496	129663496	+	Missense_Mutation	SNP	C	C	T	rs11556924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:129663496C>T	ENST00000358303.4	-	8	1172	c.1088G>A	c.(1087-1089)cGt>cAt	p.R363H	ZC3HC1_ENST00000481503.1_Missense_Mutation_p.R320H|ZC3HC1_ENST00000360708.5_Intron|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.R342H|RP11-306G20.1_ENST00000587038.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	363			R -> H (in dbSNP:rs11556924). {ECO:0000269|PubMed:15489334}.		mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TGGCTCAGGACGGTCAACAGG	0.582													C|||	780	0.155751	0.0265	0.2089	5008	,	,		15956	0.0496		0.3767	False		,,,				2504	0.1748				p.R363H	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											.	ZC3HC1	45	.	0			c.G1088A						PASS	.	C	HIS/ARG	359,4047	185.0+/-212.2	15,329,1859	102.0	89.0	93.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1088	5.5	1.0	7	dbSNP_120	93	3290,5310	493.5+/-373.6	651,1988,1661	yes	missense	ZC3HC1	NM_016478.3	29	666,2317,3520	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	38.2558,8.148,28.0563	probably-damaging	363/503	129663496	3649,9357	2203	4300	6503	SO:0001583	missense	51530	exon8			TCAGGACGGTCAA	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1088G>A	7.37:g.129663496C>T	ENSP00000351052:p.Arg363His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	418	0.19139194139194138	23	0.046747967479674794	78	0.2154696132596685	27	0.0472027972027972	290	0.38258575197889183	C	24.1	4.497150	0.85069	0.08148	0.382558	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	T;T;T	0.51325	1.25;1.28;0.71	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	L	0.57536	1.79	0.25979	P	0.9823921	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.959	T	0.34054	-0.9844	9	0.18276	T	0.48	-14.8822	16.0957	0.81123	0.0:1.0:0.0:0.0	rs11556924;rs12667709;rs17850754;rs11556924	363;320	Q86WB0;C9J0I9	NIPA_HUMAN;.	H	363;342;320	ENSP00000351052:R363H;ENSP00000309301:R342H;ENSP00000418533:R320H	ENSP00000309301:R342H	R	-	2	0	ZC3HC1	129450732	0.994000	0.37717	0.995000	0.50966	0.725000	0.41563	2.567000	0.45956	2.590000	0.87494	0.563000	0.77884	CGT	C|0.777;T|0.223	0.223	strong		0.582	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
PKD1L2	114780	hgsc.bcm.edu	37	16	81248716	81248716	+	RNA	SNP	C	C	T	rs12933806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0	1204	WXS	Illumina HiSeq	Phase_I	103	56	0.543689	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		
TMEM176B	28959	hgsc.bcm.edu	37	7	150490376	150490376	+	Missense_Mutation	SNP	C	C	T	rs2072443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150490376C>T	ENST00000447204.2	-	5	772	c.400G>A	c.(400-402)Gca>Aca	p.A134T	TMEM176B_ENST00000326442.5_Missense_Mutation_p.A134T|TMEM176B_ENST00000450753.2_Missense_Mutation_p.A97T|TMEM176B_ENST00000434545.1_Missense_Mutation_p.A134T|TMEM176B_ENST00000429904.2_Missense_Mutation_p.A134T|TMEM176B_ENST00000492607.1_Missense_Mutation_p.A134T	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	134			A -> T (in dbSNP:rs2072443). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAAAGCCTGCCAGGGTGAGC	0.512													C|||	2041	0.407548	0.2935	0.3357	5008	,	,		20986	0.5278		0.4155	False		,,,				2504	0.4806				p.A134T		Atlas-SNP	.											.	TMEM176B	36	.	0			c.G400A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1374,3032	454.5+/-350.7	215,944,1044	56.0	51.0	53.0		400,400,289,400	2.3	1.0	7	dbSNP_96	53	3590,5010	518.5+/-379.3	757,2076,1467	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	58,58,58,58	972,3020,2511	TT,TC,CC		41.7442,31.1847,38.167	probably-damaging,probably-damaging,probably-damaging,probably-damaging	134/271,134/271,97/234,134/271	150490376	4964,8042	2203	4300	6503	SO:0001583	missense	28959	exon5			AGCCTGCCAGGGT	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.400G>A	7.37:g.150490376C>T	ENSP00000410269:p.Ala134Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	879	0.4024725274725275	134	0.27235772357723576	122	0.3370165745856354	316	0.5524475524475524	307	0.4050131926121372	C	12.50	1.955452	0.34471	0.311847	0.417442	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.02606	4.23;4.23;4.23;4.23;4.23;4.23	4.32	2.33	0.28932	.	1.198300	0.06321	N	0.704539	T	0.00012	0.0000	M	0.71296	2.17	0.33944	P	0.356445	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.979	T	0.48570	-0.9024	9	0.59425	D	0.04	-12.8358	4.8486	0.13526	0.0:0.6576:0.223:0.1194	rs2072443;rs3177188;rs11546675;rs17849842;rs17851205;rs58621392;rs2072443	97;134	E9PAV4;Q3YBM2	.;T176B_HUMAN	T	134;134;134;134;134;97;134	ENSP00000419258:A134T;ENSP00000318409:A134T;ENSP00000410269:A134T;ENSP00000413531:A134T;ENSP00000397810:A134T;ENSP00000404831:A97T	ENSP00000318409:A134T	A	-	1	0	TMEM176B	150121309	0.954000	0.32549	0.994000	0.49952	0.019000	0.09904	0.396000	0.20867	2.139000	0.66308	0.448000	0.29417	GCA	C|0.608;T|0.392	0.392	strong		0.512	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
DCAF7	10238	hgsc.bcm.edu	37	17	61655938	61655938	+	Silent	SNP	C	C	T	rs143007748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:61655938C>T	ENST00000310827.4	+	2	463	c.246C>T	c.(244-246)ggC>ggT	p.G82G	DCAF7_ENST00000415273.2_Intron|DCAF7_ENST00000431926.1_Silent_p.G82G|DCAF7_ENST00000577702.1_3'UTR	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	82					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.G82G(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						ACACAAAAGGCGTCTATCCAG	0.493													C|||	47	0.00938498	0.0	0.049	5008	,	,		21340	0.0129		0.0	False		,,,				2504	0.0				p.G82G		Atlas-SNP	.											DCAF7,colon,carcinoma,0,1	DCAF7	36	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C246T						scavenged	.	C		1,3959		0,1,1979	195.0	189.0	191.0		246	-1.7	1.0	17	dbSNP_134	191	5,8349		0,5,4172	no	coding-synonymous	DCAF7	NM_005828.3		0,6,6151	TT,TC,CC		0.0599,0.0253,0.0487		82/343	61655938	6,12308	1980	4177	6157	SO:0001819	synonymous_variant	10238	exon2			AAAAGGCGTCTAT	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.246C>T	17.37:g.61655938C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Silent	SNP	ENST00000310827.4	37																																																																																				C|0.990;T|0.010	0.010	strong		0.493	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	
MC3R	4159	hgsc.bcm.edu	37	20	54824029	54824029	+	Missense_Mutation	SNP	G	G	A	rs3827103	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:54824029G>A	ENST00000243911.2	+	1	242	c.130G>A	c.(130-132)Gtt>Att	p.V44I		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	44			V -> I (have ligand binding and signaling properties similar to wild-type; dbSNP:rs3827103). {ECO:0000269|PubMed:8463333}.		adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			CAAGCCCGAGGTTTTCCTGTC	0.557													G|||	1263	0.252196	0.4841	0.1009	5008	,	,		21599	0.253		0.0765	False		,,,				2504	0.226				p.V44I		Atlas-SNP	.											.	MC3R	83	.	0			c.G130A	GRCh37	CM053305	MC3R	M	rs3827103	PASS	.	G	ILE/VAL	1845,2561	537.9+/-374.9	396,1053,754	112.0	100.0	104.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	130	4.1	1.0	20	dbSNP_107	104	744,7856	180.2+/-229.2	31,682,3587	yes	missense	MC3R	NM_019888.3	29	427,1735,4341	AA,AG,GG		8.6512,41.8747,19.9062	possibly-damaging	44/324	54824029	2589,10417	2203	4300	6503	SO:0001583	missense	4159	exon1			CCCGAGGTTTTCC		CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"""GPCR / Class A : Melanocortin receptors"""	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.130G>A	20.37:g.54824029G>A	ENSP00000243911:p.Val44Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_019888	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	37	CCDS13449.2	446	0.2042124542124542	217	0.4410569105691057	38	0.10497237569060773	134	0.23426573426573427	57	0.07519788918205805	G	16.85	3.235825	0.58886	0.418747	0.086512	ENSG00000124089	ENST00000243911	T	0.38077	1.16	5.01	4.05	0.47172	.	0.000000	0.64402	D	0.000020	T	0.00012	0.0000	N	0.08118	0	0.22354	P	0.99917716	B	0.33857	0.429	B	0.24006	0.05	T	0.41088	-0.9528	9	0.56958	D	0.05	.	13.4595	0.61219	0.0787:0.0:0.9213:0.0	rs3827103;rs17847260;rs60060922;rs3827103	81	P41968	MC3R_HUMAN	I	44	ENSP00000243911:V44I	ENSP00000243911:V44I	V	+	1	0	MC3R	54257436	1.000000	0.71417	0.999000	0.59377	0.903000	0.53119	6.535000	0.73838	2.317000	0.78254	0.650000	0.86243	GTT	G|0.782;A|0.218	0.218	strong		0.557	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2		
OR56A4	120793	hgsc.bcm.edu	37	11	6023581	6023581	+	Silent	SNP	A	A	G	rs11040248	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	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	
IKBKAP	8518	hgsc.bcm.edu	37	9	111660851	111660851	+	Missense_Mutation	SNP	C	C	T	rs2230792	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111660851C>T	ENST00000374647.5	-	22	2601	c.2294G>A	c.(2293-2295)gGa>gAa	p.G765E	IKBKAP_ENST00000537196.1_Missense_Mutation_p.G416E	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	765			G -> E (in dbSNP:rs2230792).		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						TTCCACATTTCCAAGAAACAC	0.294													T|||	1448	0.289137	0.4493	0.2493	5008	,	,		19511	0.2589		0.1998	False		,,,				2504	0.2239				p.G765E		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G2294A						PASS	.	T	GLU/GLY	1820,2578	625.1+/-394.5	384,1052,763	68.0	71.0	70.0		2294	4.1	1.0	9	dbSNP_98	70	1566,7032	740.3+/-407.1	143,1280,2876	yes	missense	IKBKAP	NM_003640.3	98	527,2332,3639	TT,TC,CC		18.2135,41.3824,26.0542	benign	765/1333	111660851	3386,9610	2199	4299	6498	SO:0001583	missense	8518	exon22			ACATTTCCAAGAA	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.2294G>A	9.37:g.111660851C>T	ENSP00000363779:p.Gly765Glu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	605	0.27701465201465203	208	0.42276422764227645	97	0.26795580110497236	157	0.2744755244755245	143	0.18865435356200527	T	0.014	-1.591131	0.00864	0.413824	0.182135	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.23950	1.88;1.88	5.21	4.05	0.47172	.	0.107189	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00028	-2.63	0.50813	P	1.0399999999999299E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	9	0.02654	T	1	-6.7461	6.8594	0.24058	0.0:0.0809:0.1511:0.768	rs2230792;rs2275629;rs10979601;rs11554113;rs16913664;rs52832678;rs60459262;rs10979601	765	O95163	ELP1_HUMAN	E	765;416	ENSP00000363779:G765E;ENSP00000439367:G416E	ENSP00000363779:G765E	G	-	2	0	IKBKAP	110700672	1.000000	0.71417	0.996000	0.52242	0.120000	0.20174	2.915000	0.48805	0.368000	0.24481	-1.179000	0.01719	GGA	T|0.207;G|0.122;C|0.615;A|0.056	0.207	strong		0.294	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
GRIN2B	2904	hgsc.bcm.edu	37	12	13716638	13716638	+	Silent	SNP	G	G	A	rs1806191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:13716638G>A	ENST00000609686.1	-	13	3743	c.3534C>T	c.(3532-3534)caC>caT	p.H1178H		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1178					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)	CGTGCTTGATGTGAGACCTGT	0.617													G|||	1240	0.247604	0.1558	0.4452	5008	,	,		14952	0.0139		0.497	False		,,,				2504	0.2157				p.H1178H		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C3534T						PASS	.	G		924,3482	354.1+/-312.5	104,716,1383	101.0	90.0	94.0		3534	3.1	1.0	12	dbSNP_92	94	4298,4302	577.3+/-390.5	1093,2112,1095	yes	coding-synonymous	GRIN2B	NM_000834.3		1197,2828,2478	AA,AG,GG		49.9767,20.9714,40.1507		1178/1485	13716638	5222,7784	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			CTTGATGTGAGAC		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.3534C>T	12.37:g.13716638G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.661;A|0.339	0.339	strong		0.617	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
IST1	9798	hgsc.bcm.edu	37	16	71950450	71950450	+	Silent	SNP	C	C	T	rs1049794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:71950450C>T	ENST00000378799.6	+	3	530	c.174C>T	c.(172-174)caC>caT	p.H58H	IST1_ENST00000541571.2_Silent_p.H58H|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000544564.1_Silent_p.H58H|IST1_ENST00000329908.8_Silent_p.H58H|IST1_ENST00000606369.1_Intron|IST1_ENST00000378798.5_Silent_p.H58H|IST1_ENST00000538565.1_Intron|IST1_ENST00000535424.1_Silent_p.H71H|IST1_ENST00000538850.1_Intron			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	58	Interaction with CHMP1A and CHMP1B.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										GTGTGGAGCACATTATCCGGG	0.532													C|||	1020	0.203674	0.0809	0.1268	5008	,	,		20590	0.2708		0.1421	False		,,,				2504	0.4182				p.H71H		Atlas-SNP	.											.	.	.	.	0			c.C213T						PASS	.	C		297,4099	163.3+/-195.1	14,269,1915	122.0	99.0	107.0		174	3.2	1.0	16	dbSNP_86	107	1193,7407	241.1+/-271.6	82,1029,3189	no	coding-synonymous	IST1	NM_014761.2		96,1298,5104	TT,TC,CC		13.8721,6.7561,11.4651		58/361	71950450	1490,11506	2198	4300	6498	SO:0001819	synonymous_variant	9798	exon4			GGAGCACATTATC	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"""KIAA0174"""	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.174C>T	16.37:g.71950450C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Silent	SNP	ENST00000378799.6	37	CCDS59272.1																																																																																			C|0.864;T|0.136	0.136	strong		0.532	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761	
LRRC23	10233	hgsc.bcm.edu	37	12	7023123	7023123	+	3'UTR	SNP	A	A	G	rs710415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7023123A>G	ENST00000007969.8	+	0	1345				LRRC23_ENST00000436789.1_3'UTR|ENO2_ENST00000538763.1_5'Flank|LRRC23_ENST00000323702.5_Missense_Mutation_p.E276G|ENO2_ENST00000229277.1_5'Flank|LRRC23_ENST00000443597.2_3'UTR|ENO2_ENST00000535366.1_5'Flank|LRRC23_ENST00000429740.1_Missense_Mutation_p.N187D|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000544774.1_5'Flank|ENO2_ENST00000541477.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23											NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						TATGACAGAGAACAGAGGATG	0.542													G|||	2393	0.477835	0.8169	0.2896	5008	,	,		-128	0.4732		0.2972	False		,,,				2504	0.3436				p.E276G		Atlas-SNP	.											.	LRRC23	46	.	0			c.A827G						PASS	.	G	,GLY/GLU,	3115,1291	437.8+/-345.1	1117,881,205	137.0	129.0	132.0		,827,	-0.8	0.0	12	dbSNP_86	132	2441,6159	698.0+/-405.0	363,1715,2222	yes	utr-3,missense,utr-3	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	,98,	1480,2596,2427	GG,GA,AA		28.3837,29.301,42.7187	,,	,276/313,	7023123	5556,7450	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10233	exon7			ACAGAGAACAGAG	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.*93A>G	12.37:g.7023123A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_006992	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	989|989	0.45283882783882784|0.45283882783882784	384|384	0.7804878048780488|0.7804878048780488	128|128	0.35359116022099446|0.35359116022099446	254|254	0.44405594405594406|0.44405594405594406	223|223	0.2941952506596306|0.2941952506596306	G|G	10.42|10.42	1.346628|1.346628	0.24426|0.24426	0.70699|0.70699	0.283837|0.283837	ENSG00000010626|ENSG00000010626	ENST00000323702|ENST00000429740	T|T	0.67865|0.37915	-0.29|1.17	2.86|2.86	-0.778|-0.778	0.10977|0.10977	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.21655|0.21655	-1.0239|-1.0239	7|7	0.35671|0.72032	T|D	0.21|0.01	.|.	3.6922|3.6922	0.08350|0.08350	0.4899:0.2031:0.307:0.0|0.4899:0.2031:0.307:0.0	rs710415;rs3168597;rs17788615;rs52833239;rs56597060;rs60356840;rs710415|rs710415;rs3168597;rs17788615;rs52833239;rs56597060;rs60356840;rs710415	276|187	Q53EV4-2|E9PDZ4	.|.	G|D	276|187	ENSP00000317464:E276G|ENSP00000397192:N187D	ENSP00000317464:E276G|ENSP00000397192:N187D	E|N	+|+	2|1	0|0	LRRC23|LRRC23	6893384|6893384	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.005000|-0.005000	0.12855|0.12855	-0.503000|-0.503000	0.06586|0.06586	-0.355000|-0.355000	0.07637|0.07637	GAA|AAC	A|0.551;G|0.449	0.449	strong		0.542	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
SORL1	6653	hgsc.bcm.edu	37	11	121475922	121475922	+	Silent	SNP	T	T	A	rs3824968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:121475922T>A	ENST00000260197.7	+	34	4881	c.4752T>A	c.(4750-4752)gcT>gcA	p.A1584A	SORL1_ENST00000525532.1_Silent_p.A528A|SORL1_ENST00000532694.1_Silent_p.A430A|SORL1_ENST00000534286.1_Silent_p.A494A|SORL1_ENST00000527934.1_Silent_p.A199A	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1584	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TGCCCTCTGCTTCTTGTGTAT	0.433													T|||	1984	0.396166	0.1324	0.4899	5008	,	,		19405	0.5883		0.3032	False		,,,				2504	0.5838				p.A1584A		Atlas-SNP	.											.	SORL1	218	.	0			c.T4752A						PASS	.	T		644,3762	275.7+/-272.7	51,542,1610	139.0	137.0	138.0		4752	-1.7	1.0	11	dbSNP_107	138	2671,5927	430.8+/-356.6	392,1887,2020	no	coding-synonymous	SORL1	NM_003105.5		443,2429,3630	AA,AT,TT		31.0654,14.6164,25.4922		1584/2215	121475922	3315,9689	2203	4299	6502	SO:0001819	synonymous_variant	6653	exon34			CTCTGCTTCTTGT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4752T>A	11.37:g.121475922T>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	37	CCDS8436.1																																																																																			T|0.706;A|0.294	0.294	strong		0.433	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629809	32629809	+	Missense_Mutation	SNP	C	C	T	rs701564|rs9282122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629809C>T	ENST00000399082.3	-	2	370	c.326G>A	c.(325-327)cGt>cAt	p.R109H	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.R199H			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	199	Beta-1.		T -> R (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:06; dbSNP:rs1130392).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.R199H(1)		breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GACATCTCCACGCTGGGGAGT	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1206	0.240815	0.1997	0.2017	5008	,	,		17689	0.3135		0.1809	False		,,,				2504	0.3108				p.R199H	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	1	Substitution - Missense(1)	pancreas(1)	c.G596A						PASS	.	T	HIS/ARG	801,3603		86,629,1487	52.0	56.0	54.0		596	-1.7	0.0	6	dbSNP_86	54	1677,6923		165,1347,2788	no	missense	HLA-DQB1	NM_002123.4	29	251,1976,4275	TT,TC,CC		19.5,18.188,19.0557	benign	199/262	32629809	2478,10526	2202	4300	6502	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCTCCACGCTGGG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.326G>A	6.37:g.32629809C>T	ENSP00000382032:p.Arg109His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		484	0.2216117216117216	96	0.1951219512195122	76	0.20994475138121546	185	0.32342657342657344	127	0.16754617414248021	.	0.734	-0.778745	0.02929	0.18188	0.195	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	4.52	-1.67	0.08238	.	0.285278	0.34932	N	0.003574	T	0.01124	0.0037	.	.	.	0.80722	P	0.0	B;B;B;B	0.12630	0.003;0.006;0.001;0.001	B;B;B;B	0.09377	0.004;0.004;0.003;0.004	T	0.45760	-0.9239	8	0.56958	D	0.05	.	10.0965	0.42478	0.0:0.4447:0.0:0.5553	rs701564;rs9273944;rs9273945;rs17840138;rs34600508	199;164;199;199	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	H	109;199;199;199;199;135	ENSP00000382032:R109H;ENSP00000382029:R199H;ENSP00000364080:R199H;ENSP00000407332:R199H;ENSP00000382034:R199H	ENSP00000364080:R199H	R	-	2	0	HLA-DQB1	32737787	0.000000	0.05858	0.005000	0.12908	0.045000	0.14185	-0.443000	0.06862	-0.872000	0.04037	-1.740000	0.00687	CGT	T|0.225;C|0.775	0.225	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
NEIL1	79661	hgsc.bcm.edu	37	15	75646194	75646194	+	Missense_Mutation	SNP	C	C	T	rs142213781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75646194C>T	ENST00000564784.1	+	7	1462	c.833C>T	c.(832-834)aCc>aTc	p.T278I	NEIL1_ENST00000355059.4_Missense_Mutation_p.T278I|MIR631_ENST00000384904.1_RNA|NEIL1_ENST00000569035.1_Missense_Mutation_p.T278I|RP11-817O13.6_ENST00000563660.1_lincRNA			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	278					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						CATGGCCGTACCATCTGGTTC	0.617								Base excision repair (BER), DNA glycosylases					C|||	3	0.000599042	0.0	0.0	5008	,	,		21794	0.0		0.001	False		,,,				2504	0.002				p.T364I		Atlas-SNP	.											.	NEIL1	36	.	0			c.C1091T						PASS	.	C	ILE/THR	0,4394		0,0,2197	79.0	83.0	81.0		833	5.1	1.0	15	dbSNP_134	81	6,8582	4.3+/-15.6	0,6,4288	yes	missense	NEIL1	NM_024608.2	89	0,6,6485	TT,TC,CC		0.0699,0.0,0.0462	probably-damaging	278/391	75646194	6,12976	2197	4294	6491	SO:0001583	missense	79661	exon6			GCCGTACCATCTG	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.833C>T	15.37:g.75646194C>T	ENSP00000457352:p.Thr278Ile	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	37	CCDS10278.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	26.0	4.695071	0.88830	0.0	6.99E-4	ENSG00000140398	ENST00000355059	T	0.65916	-0.18	5.09	5.09	0.68999	Endonuclease VIII-like 1, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79836	-0.1635	10	0.72032	D	0.01	-31.8003	17.4649	0.87629	0.0:1.0:0.0:0.0	.	278	Q96FI4	NEIL1_HUMAN	I	278	ENSP00000347170:T278I	ENSP00000347170:T278I	T	+	2	0	NEIL1	73433247	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.710000	0.74670	2.375000	0.81037	0.561000	0.74099	ACC	C|0.999;T|0.001	0.001	strong		0.617	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
C16orf71	146562	hgsc.bcm.edu	37	16	4794873	4794873	+	Missense_Mutation	SNP	C	C	T	rs2075469	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4794873C>T	ENST00000299320.5	+	6	1382	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.R316C	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	302			R -> C (in dbSNP:rs2075469). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						ATCCTCAGACCGCATGGTGCC	0.622													C|||	2762	0.551518	0.4334	0.5576	5008	,	,		18321	0.6776		0.6372	False		,,,				2504	0.4888				p.R302C		Atlas-SNP	.											C16orf71,NS,carcinoma,0,1	C16orf71	46	1	0			c.C904T						PASS	.	C	CYS/ARG	2173,2221	566.7+/-382.0	537,1099,561	48.0	44.0	45.0		904	1.8	0.0	16	dbSNP_96	45	5617,2983	646.8+/-400.3	1833,1951,516	yes	missense	C16orf71	NM_139170.2	180	2370,3050,1077	TT,TC,CC		34.686,49.4538,40.0493	possibly-damaging	302/521	4794873	7790,5204	2197	4300	6497	SO:0001583	missense	146562	exon6			TCAGACCGCATGG	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.904C>T	16.37:g.4794873C>T	ENSP00000299320:p.Arg302Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	1321	0.6048534798534798	230	0.46747967479674796	199	0.5497237569060773	407	0.7115384615384616	485	0.6398416886543535	C	12.33	1.904312	0.33628	0.494538	0.65314	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.13778	2.56	4.02	1.82	0.25136	.	1.111810	0.06870	N	0.800580	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P	0.47350	0.894	B	0.39840	0.311	T	0.28964	-1.0027	9	0.49607	T	0.09	-1.7626	4.3239	0.11031	0.3166:0.567:0.0:0.1164	rs2075469;rs17846122;rs17859127;rs59929783;rs2075469	302	Q8IYS4	CP071_HUMAN	C	302;57	ENSP00000299320:R302C	ENSP00000299320:R302C	R	+	1	0	C16orf71	4734874	0.000000	0.05858	0.008000	0.14137	0.076000	0.17211	0.399000	0.20916	0.488000	0.27723	0.561000	0.74099	CGC	C|0.402;N|0.000	.	strong		0.622	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
TSPAN13	27075	hgsc.bcm.edu	37	7	16816000	16816000	+	Silent	SNP	T	T	C	rs2290837	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:16816000T>C	ENST00000262067.4	+	2	661	c.228T>C	c.(226-228)ttT>ttC	p.F76F	TSPAN13_ENST00000466195.1_3'UTR	NM_014399.3	NP_055214.1	O95857	TSN13_HUMAN	tetraspanin 13	76						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				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)		TGTTGCTATTTTTTGTATCCT	0.363													T|||	1694	0.338259	0.4766	0.3487	5008	,	,		18343	0.2024		0.3926	False		,,,				2504	0.228				p.F76F		Atlas-SNP	.											.	TSPAN13	13	.	0			c.T228C						PASS	.	T		2009,2397	555.4+/-379.2	450,1109,644	166.0	150.0	155.0		228	2.5	1.0	7	dbSNP_100	155	3279,5321	482.4+/-370.9	629,2021,1650	no	coding-synonymous	TSPAN13	NM_014399.3		1079,3130,2294	CC,CT,TT		38.1279,45.5969,40.6582		76/205	16816000	5288,7718	2203	4300	6503	SO:0001819	synonymous_variant	27075	exon2			GCTATTTTTTGTA	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.228T>C	7.37:g.16816000T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	222	149	0.671171	NM_014399		Silent	SNP	ENST00000262067.4	37	CCDS5363.1																																																																																			T|0.608;C|0.392	0.392	strong		0.363	TSPAN13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250178.2	NM_014399	
GUCA2A	2980	hgsc.bcm.edu	37	1	42630364	42630364	+	Missense_Mutation	SNP	G	G	A	rs2071499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:42630364G>A	ENST00000357001.2	-	1	25	c.20C>T	c.(19-21)tCc>tTc	p.S7F		NM_033553.2	NP_291031.2	Q02747	GUC2A_HUMAN	guanylate cyclase activator 2A (guanylin)	7			S -> F (in dbSNP:rs2071499). {ECO:0000269|PubMed:1327879, ECO:0000269|PubMed:1409606, ECO:0000269|PubMed:7892222}.			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	guanylate cyclase activator activity (GO:0030250)|hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|pancreas(1)|skin(1)	5	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCACAGTGCGGAGAGCAGGAA	0.657													G|||	1928	0.384984	0.0772	0.572	5008	,	,		17289	0.4028		0.6113	False		,,,				2504	0.4172				p.S7F		Atlas-SNP	.											GUCA2A,trunk,malignant_melanoma,+1,1	GUCA2A	9	1	0			c.C20T						PASS	.	G	PHE/SER	701,3569		82,537,1516	53.0	38.0	43.0		20	2.8	0.1	1	dbSNP_96	43	4969,3361		1532,1905,728	yes	missense	GUCA2A	NM_033553.2	155	1614,2442,2244	AA,AG,GG		40.3481,16.4169,45.0	possibly-damaging	7/116	42630364	5670,6930	2135	4165	6300	SO:0001583	missense	2980	exon1			AGTGCGGAGAGCA	X74322	CCDS465.1	1p35-p34	2014-01-30			ENSG00000197273	ENSG00000197273		"""Endogenous ligands"""	4682	protein-coding gene	gene with protein product	"""prepro-guanylin"""	139392		GUCA2		1327879, 7892222	Standard	NM_033553		Approved	STARA	uc001chd.1	Q02747	OTTHUMG00000007023	ENST00000357001.2:c.20C>T	1.37:g.42630364G>A	ENSP00000349493:p.Ser7Phe	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	NM_033553		Missense_Mutation	SNP	ENST00000357001.2	37	CCDS465.1	998	0.45695970695970695	46	0.09349593495934959	228	0.6298342541436464	254	0.44405594405594406	470	0.6200527704485488	G	8.260	0.811046	0.16537	0.164169	0.596519	ENSG00000197273	ENST00000357001	T	0.47177	0.85	4.7	2.79	0.32731	.	0.431115	0.22442	N	0.060004	T	0.00012	0.0000	M	0.68317	2.08	0.80722	P	0.0	P	0.44877	0.845	B	0.41813	0.367	T	0.45585	-0.9251	9	0.38643	T	0.18	-15.1715	6.1467	0.20289	0.1047:0.2141:0.6812:0.0	rs2071499;rs17368004;rs52817553;rs58257700;rs2071499	7	Q02747	GUC2A_HUMAN	F	7	ENSP00000349493:S7F	ENSP00000349493:S7F	S	-	2	0	GUCA2A	42402951	0.002000	0.14202	0.058000	0.19502	0.120000	0.20174	0.768000	0.26590	0.680000	0.31366	0.491000	0.48974	TCC	G|0.596;A|0.404	0.404	strong		0.657	GUCA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018306.1	NM_033553	
FLG	2312	hgsc.bcm.edu	37	1	152285099	152285099	+	Missense_Mutation	SNP	C	C	T	rs74129461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152285099C>T	ENST00000368799.1	-	3	2298	c.2263G>A	c.(2263-2265)Gaa>Aaa	p.E755K	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	755	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)			TCTGAGTCTTCTGAATGTCCC	0.582									Ichthyosis				-|||	1641	0.327676	0.0681	0.415	5008	,	,		21625	0.6062		0.171	False		,,,				2504	0.4908				p.E755K		Atlas-SNP	.											.	FLG	900	.	0			c.G2263A						PASS	.	C	LYS/GLU	368,4038		15,338,1850	377.0	363.0	368.0		2263	1.0	0.0	1	dbSNP_130	368	1443,7157		124,1195,2981	yes	missense	FLG	NM_002016.1	56	139,1533,4831	TT,TC,CC		16.7791,8.3522,13.9243	probably-damaging	755/4062	152285099	1811,11195	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTCTTCTGAATG	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.2263G>A	1.37:g.152285099C>T	ENSP00000357789:p.Glu755Lys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	620	0.2838827838827839	41	0.08333333333333333	119	0.3287292817679558	330	0.5769230769230769	130	0.17150395778364116	-	9.927	1.213701	0.22289	0.083522	0.167791	ENSG00000143631	ENST00000368799	T	0.00695	5.83	4.25	1.02	0.19986	.	.	.	.	.	T	0.00412	0.0013	M	0.79123	2.44	0.80722	P	0.0	P	0.43477	0.808	B	0.36418	0.224	T	0.47724	-0.9095	8	0.41790	T	0.15	-3.6243	3.5386	0.07803	0.0:0.5395:0.2134:0.2471	.	755	P20930	FILA_HUMAN	K	755	ENSP00000357789:E755K	ENSP00000357789:E755K	E	-	1	0	FLG	150551723	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.308000	0.08156	0.439000	0.26476	0.479000	0.44913	GAA	C|0.815;T|0.185	0.185	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LAMC1	3915	hgsc.bcm.edu	37	1	183105705	183105705	+	Silent	SNP	G	G	A	rs20561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:183105705G>A	ENST00000258341.4	+	25	4556	c.4299G>A	c.(4297-4299)gcG>gcA	p.A1433A	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1433	Domain II and I.				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						AGAGGATCGCGAGCGCTGTCC	0.567													G|||	1762	0.351837	0.1702	0.3833	5008	,	,		16519	0.5109		0.4433	False		,,,				2504	0.317				p.A1433A		Atlas-SNP	.											.	LAMC1	176	.	0			c.G4299A						PASS	.	G		954,3452	345.1+/-308.4	98,758,1347	52.0	54.0	54.0		4299	-1.7	0.8	1	dbSNP_67	54	3712,4888	509.6+/-377.3	798,2116,1386	no	coding-synonymous	LAMC1	NM_002293.3		896,2874,2733	AA,AG,GG		43.1628,21.6523,35.8757		1433/1610	183105705	4666,8340	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon25			GATCGCGAGCGCT	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.4299G>A	1.37:g.183105705G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	139	89	0.640288	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			G|0.636;A|0.364	0.364	strong		0.567	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
WDFY4	57705	hgsc.bcm.edu	37	10	50184949	50184949	+	Silent	SNP	C	C	T	rs2271565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50184949C>T	ENST00000325239.5	+	58	9243	c.9216C>T	c.(9214-9216)tgC>tgT	p.C3072C	WDFY4_ENST00000465910.1_3'UTR|RP11-523O18.5_ENST00000428825.4_RNA|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3072						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						CCATAACCTGCTGCTGCCTGA	0.597													C|||	1674	0.334265	0.062	0.402	5008	,	,		16207	0.3502		0.4871	False		,,,				2504	0.4806				p.C3072C		Atlas-SNP	.											WDFY4,NS,carcinoma,+1,2	WDFY4	205	2	0			c.C9216T						PASS	.	C		184,1200		14,156,522	73.0	76.0	75.0		9216	3.8	1.0	10	dbSNP_100	75	1568,1614		398,772,421	no	coding-synonymous	WDFY4	NM_020945.1		412,928,943	TT,TC,CC		49.2772,13.2948,38.3706		3072/3185	50184949	1752,2814	692	1591	2283	SO:0001819	synonymous_variant	57705	exon59			AACCTGCTGCTGC	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.9216C>T	10.37:g.50184949C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	729	0.33379120879120877	37	0.07520325203252033	147	0.40607734806629836	171	0.29895104895104896	374	0.49340369393139843	C	13.59	2.281938	0.40394	0.132948	0.492772	ENSG00000128815	ENST00000265453	.	.	.	4.74	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49995	-0.8879	3	.	.	.	.	12.3839	0.55322	0.0:0.9184:0.0:0.0816	rs2271565;rs17772905;rs2271565	.	.	.	V	1159	.	.	A	+	2	0	WDFY4	49854955	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	1.643000	0.37217	1.351000	0.45789	-0.251000	0.11542	GCT	C|0.685;T|0.315	0.315	strong		0.597	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
EFCAB6	64800	hgsc.bcm.edu	37	22	44079680	44079680	+	Missense_Mutation	SNP	G	G	A	rs137794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:44079680G>A	ENST00000262726.7	-	12	1451	c.1198C>T	c.(1198-1200)Cac>Tac	p.H400Y	EFCAB6_ENST00000396231.2_Missense_Mutation_p.H248Y|EFCAB6_ENST00000358439.4_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	400			H -> Y (in dbSNP:rs137794). {ECO:0000269|PubMed:14702039}.		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)				TCTTCAGTGTGTCTAAATAAC	0.353													G|||	380	0.0758786	0.0726	0.1254	5008	,	,		23413	0.0119		0.1451	False		,,,				2504	0.0399				p.H400Y		Atlas-SNP	.											.	EFCAB6	177	.	0			c.C1198T						PASS	.	G	TYR/HIS,TYR/HIS	361,4045	185.0+/-212.2	8,345,1850	301.0	271.0	281.0		1198,742	-0.6	0.0	22	dbSNP_78	281	1077,7523	226.4+/-262.1	68,941,3291	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	83,83	76,1286,5141	AA,AG,GG		12.5233,8.1934,11.0564	benign,benign	400/1502,248/1350	44079680	1438,11568	2203	4300	6503	SO:0001583	missense	64800	exon12			CAGTGTGTCTAAA	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.1198C>T	22.37:g.44079680G>A	ENSP00000262726:p.His400Tyr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	215	0.09844322344322344	42	0.08536585365853659	53	0.1464088397790055	9	0.015734265734265736	111	0.14643799472295516	G	4.808	0.150267	0.09185	0.081934	0.125233	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.16073	2.37;2.37	4.74	-0.573	0.11742	.	1.161790	0.06660	N	0.764303	T	0.00039	0.0001	N	0.17474	0.49	0.80722	P	0.0	B;B	0.25609	0.13;0.046	B;B	0.31245	0.126;0.048	T	0.34825	-0.9813	9	0.06494	T	0.89	-0.4667	3.4673	0.07554	0.3564:0.0:0.4715:0.1721	rs137794;rs52804023;rs61194116;rs137794	400;400	Q5THR3-6;Q5THR3	.;EFCB6_HUMAN	Y	248;400	ENSP00000379533:H248Y;ENSP00000262726:H400Y	ENSP00000262726:H400Y	H	-	1	0	EFCAB6	42411013	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.950000	0.29122	-0.083000	0.12618	-1.119000	0.02030	CAC	G|0.899;A|0.101	0.101	strong		0.353	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552072	32552072	+	Missense_Mutation	SNP	T	T	G	rs17879995	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32552072T>G	ENST00000360004.5	-	2	289	c.184A>C	c.(184-186)Aac>Cac	p.N62H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	62	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						TCCTCCTGGTTATAGAAGTAT	0.607										Multiple Myeloma(14;0.17)			T|||	511	0.102037	0.0333	0.1888	5008	,	,		9156	0.1111		0.1441	False		,,,				2504	0.0808				p.N62H		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A184C						PASS	.						34.0	32.0	33.0					6																	32552072		2192	4275	6467	SO:0001583	missense	3123	exon2			CCTGGTTATAGAA	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.184A>C	6.37:g.32552072T>G	ENSP00000353099:p.Asn62His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	276	0.12637362637362637	12	0.024390243902439025	70	0.19337016574585636	75	0.13111888111888112	119	0.15699208443271767	.	11.90	1.775623	0.31411	.	.	ENSG00000196126	ENST00000360004	T	0.00441	7.41	3.52	3.52	0.40303	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);	0.149573	0.56097	D	0.000021	T	0.01029	0.0034	H	0.97659	4.05	0.58432	P	1.0000000000287557E-6	D	0.89917	1.0	D	0.97110	1.0	T	0.04723	-1.0931	9	0.62326	D	0.03	.	10.2994	0.43644	0.0:0.0:0.0:1.0	rs17879995	62	P01911	2B1F_HUMAN	H	62	ENSP00000353099:N62H	ENSP00000353099:N62H	N	-	1	0	HLA-DRB1	32660050	0.887000	0.30362	0.019000	0.16419	0.015000	0.08874	2.002000	0.40835	1.609000	0.50190	0.372000	0.22366	AAC	T|0.871;G|0.129	0.129	strong		0.607	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FLG	2312	hgsc.bcm.edu	37	1	152281290	152281290	+	Silent	SNP	A	A	G	rs80353812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281290A>G	ENST00000368799.1	-	3	6107	c.6072T>C	c.(6070-6072)caT>caC	p.H2024H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2024	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)			AAGCTTGTCCATGCCCAATGC	0.537									Ichthyosis				-|||	1643	0.328075	0.385	0.3343	5008	,	,		28088	0.4355		0.1292	False		,,,				2504	0.3405				p.H2024H		Atlas-SNP	.											.	FLG	900	.	0			c.T6072C						PASS	.	G		1156,3250		0,1156,1047	624.0	521.0	556.0		6072	-6.7	0.0	1	dbSNP_131	556	1085,7515		0,1085,3215	no	coding-synonymous	FLG	NM_002016.1		0,2241,4262	GG,GA,AA		12.6163,26.2369,17.2305		2024/4062	152281290	2241,10765	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGTCCATGCCCA	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.6072T>C	1.37:g.152281290A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	233	94	0.403433	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.974;G|0.026	0.026	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
DNAH12	201625	hgsc.bcm.edu	37	3	57386148	57386148	+	Silent	SNP	C	C	G	rs12053975	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:57386148C>G	ENST00000351747.2	-	45	7215	c.7035G>C	c.(7033-7035)ctG>ctC	p.L2345L	DNAH12_ENST00000344804.4_5'UTR	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2345	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AGGAAAATAACAGCTTGTCCT	0.308													C|||	1389	0.277356	0.0998	0.2997	5008	,	,		16683	0.4028		0.2326	False		,,,				2504	0.4182				p.L2345L		Atlas-SNP	.											.	DNAH12	182	.	0			c.G7035C						PASS	.	C		154,1230		6,142,544	168.0	148.0	154.0		7035	-0.3	0.4	3	dbSNP_120	154	727,2447		83,561,943	no	coding-synonymous	DNAH12	NM_178504.4		89,703,1487	GG,GC,CC		22.9049,11.1272,19.3287		2345/3093	57386148	881,3677	692	1587	2279	SO:0001819	synonymous_variant	201625	exon45			AAATAACAGCTTG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.7035G>C	3.37:g.57386148C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	37		567	0.25961538461538464	57	0.11585365853658537	106	0.292817679558011	229	0.40034965034965037	175	0.23087071240105542	C	7.860	0.725913	0.15439	0.111272	0.229049	ENSG00000174844	ENST00000462199	.	.	.	5.03	-0.26	0.12967	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44922	-0.9296	3	.	.	.	.	5.6157	0.17430	0.1247:0.578:0.0:0.2973	rs12053975;rs12053975	.	.	.	L	36	.	.	V	-	1	0	DNAH12	57361188	0.409000	0.25368	0.407000	0.26434	0.993000	0.82548	-0.253000	0.08794	-0.286000	0.09076	0.557000	0.71058	GTT	C|0.735;G|0.265	0.265	strong		0.308	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
ANKLE2	23141	hgsc.bcm.edu	37	12	133306710	133306710	+	Missense_Mutation	SNP	C	C	T	rs78905764	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133306710C>T	ENST00000357997.5	-	11	2127	c.2038G>A	c.(2038-2040)Gag>Aag	p.E680K	ANKLE2_ENST00000539605.1_Missense_Mutation_p.E618K|ANKLE2_ENST00000542657.1_Missense_Mutation_p.E35K|ANKLE2_ENST00000542282.1_Missense_Mutation_p.E35K|ANKLE2_ENST00000542374.1_Intron	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	680				E -> K (in Ref. 1; BAG52720). {ECO:0000305}.	mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GCCTCCTGCTCCAAGGGGAAG	0.572													c|||	264	0.0527157	0.0015	0.0447	5008	,	,		15971	0.1002		0.0785	False		,,,				2504	0.0521				p.E680K		Atlas-SNP	.											.	ANKLE2	76	.	0			c.G2038A						PASS	.		LYS/GLU	43,3885		0,43,1921	58.0	63.0	61.0		2038	4.7	0.1	12	dbSNP_131	61	593,7689		25,543,3573	yes	missense	ANKLE2	NM_015114.1	56	25,586,5494	TT,TC,CC		7.1601,1.0947,5.2088	possibly-damaging	680/939	133306710	636,11574	1964	4141	6105	SO:0001583	missense	23141	exon11			CCTGCTCCAAGGG	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.2038G>A	12.37:g.133306710C>T	ENSP00000350686:p.Glu680Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	137	0.06272893772893773	2	0.0040650406504065045	18	0.049723756906077346	60	0.1048951048951049	57	0.07519788918205805	C	16.07	3.018310	0.54576	0.010947	0.071601	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000542282;ENST00000542657;ENST00000538766	T;T;T;T;T	0.51071	1.8;1.78;0.73;0.73;0.72	5.53	4.65	0.58169	.	0.525762	0.23266	N	0.050080	T	0.01421	0.0046	L	0.46157	1.445	0.09310	P	0.99999999986259	P	0.48640	0.913	B	0.41813	0.367	T	0.17228	-1.0376	9	0.38643	T	0.18	-11.1214	14.6753	0.68975	0.0:0.9301:0.0:0.0699	.	680	Q86XL3	ANKL2_HUMAN	K	618;680;35;35;35	ENSP00000446268:E618K;ENSP00000350686:E680K;ENSP00000437807:E35K;ENSP00000438551:E35K;ENSP00000445760:E35K	ENSP00000350686:E680K	E	-	1	0	ANKLE2	131816783	0.526000	0.26298	0.080000	0.20451	0.057000	0.15508	4.268000	0.58883	1.483000	0.48342	0.651000	0.88453	GAG	C|0.934;T|0.066	0.066	strong		0.572	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
TMCO4	255104	hgsc.bcm.edu	37	1	20097822	20097822	+	Silent	SNP	G	G	A	rs11551819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	26	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	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	
CARD10	29775	hgsc.bcm.edu	37	22	37900276	37900276	+	Silent	SNP	A	A	G	rs3817803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37900276A>G	ENST00000403299.1	-	10	1767	c.1551T>C	c.(1549-1551)aaT>aaC	p.N517N	CARD10_ENST00000406271.3_Silent_p.N231N|CARD10_ENST00000251973.5_Silent_p.N517N			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	517					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					TGGAGAGCCGATTGATCTCCT	0.637													G|||	655	0.130791	0.0197	0.1441	5008	,	,		17874	0.2688		0.1064	False		,,,				2504	0.1544				p.N517N		Atlas-SNP	.											.	CARD10	55	.	0			c.T1551C						PASS	.	G		84,4294		0,84,2105	61.0	56.0	58.0		1551	2.5	1.0	22	dbSNP_107	58	867,7701		26,815,3443	no	coding-synonymous	CARD10	NM_014550.3		26,899,5548	GG,GA,AA		10.119,1.9187,7.3459		517/1033	37900276	951,11995	2189	4284	6473	SO:0001819	synonymous_variant	29775	exon9			GAGCCGATTGATC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1551T>C	22.37:g.37900276A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.885;G|0.115	0.115	strong		0.637	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
ARAP2	116984	hgsc.bcm.edu	37	4	36152584	36152584	+	Silent	SNP	G	G	T	rs13148785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:36152584G>T	ENST00000303965.4	-	16	3324	c.2835C>A	c.(2833-2835)acC>acA	p.T945T		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	945	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TGATATTAATGGTGCCATTAG	0.343													G|||	275	0.0549121	0.0862	0.0461	5008	,	,		16646	0.0		0.0934	False		,,,				2504	0.0358				p.T945T		Atlas-SNP	.											.	ARAP2	210	.	0			c.C2835A						PASS	.	G		409,3997	201.1+/-224.2	24,361,1818	167.0	172.0	170.0		2835	1.1	1.0	4	dbSNP_121	170	847,7749	193.7+/-239.3	41,765,3492	no	coding-synonymous	ARAP2	NM_015230.3		65,1126,5310	TT,TG,GG		9.8534,9.2828,9.6601		945/1705	36152584	1256,11746	2203	4298	6501	SO:0001819	synonymous_variant	116984	exon16			ATTAATGGTGCCA	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.2835C>A	4.37:g.36152584G>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																			G|0.916;T|0.084	0.084	strong		0.343	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
SPATA13	221178	hgsc.bcm.edu	37	13	24876752	24876752	+	Silent	SNP	T	T	C	rs33990382	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:24876752T>C	ENST00000382095.4	+	12	2207	c.1800T>C	c.(1798-1800)ccT>ccC	p.P600P	SPATA13_ENST00000399949.2_Silent_p.P522P|RP11-307N16.6_ENST00000382141.4_Intron|SPATA13_ENST00000409126.1_Silent_p.P460P|SPATA13_ENST00000424834.2_Silent_p.P1225P|SPATA13_ENST00000343003.6_Silent_p.P544P|SPATA13_ENST00000382108.3_Silent_p.P1225P	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	600	C-terminal tail.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		ACAGGTGCCCTGTGGCCCCAC	0.587													C|||	2264	0.452077	0.4977	0.317	5008	,	,		14020	0.6062		0.34	False		,,,				2504	0.4427				p.P1225P		Atlas-SNP	.											SPATA13,colon,carcinoma,+1,1	SPATA13	92	1	0			c.T3675C						PASS	.	C	,	2070,2336	605.0+/-390.5	510,1050,643	80.0	79.0	79.0		3675,1800	-8.1	0.0	13	dbSNP_126	79	2890,5710	670.6+/-402.8	496,1898,1906	no	coding-synonymous,coding-synonymous	SPATA13	NM_001166271.1,NM_153023.2	,	1006,2948,2549	CC,CT,TT		33.6047,46.9814,38.1362	,	1225/1278,600/653	24876752	4960,8046	2203	4300	6503	SO:0001819	synonymous_variant	221178	exon13			GTGCCCTGTGGCC	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.1800T>C	13.37:g.24876752T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	909	0.41620879120879123	226	0.45934959349593496	120	0.3314917127071823	325	0.5681818181818182	238	0.31398416886543534	C	1.605	-0.525517	0.04141	0.469814	0.336047	ENSG00000182957	ENST00000424834;ENST00000438694	.	.	.	5.83	-8.13	0.01073	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999977786	.	.	.	.	.	.	T	0.41233	-0.9520	3	.	.	.	.	4.2722	0.10792	0.0777:0.2124:0.2634:0.4465	rs33990382	.	.	.	R	1263;548	.	.	C	+	1	0	SPATA13	23774752	0.000000	0.05858	0.001000	0.08648	0.105000	0.19272	-6.924000	0.00049	-1.684000	0.01443	-0.119000	0.15052	TGT	T|0.616;C|0.384	0.384	strong		0.587	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
BTBD8	284697	hgsc.bcm.edu	37	1	92554283	92554283	+	Missense_Mutation	SNP	G	G	A	rs34856868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:92554283G>A	ENST00000342818.3	+	2	414	c.178G>A	c.(178-180)Gtt>Att	p.V60I	BTBD8_ENST00000370382.3_Missense_Mutation_p.V60I|BTBD8_ENST00000540648.1_Missense_Mutation_p.V60I	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	60	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.		V -> I (in dbSNP:rs34856868).			nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		CCATACAGATGTTACCTTCTC	0.323													G|||	41	0.0081869	0.0	0.013	5008	,	,		15123	0.0		0.0298	False		,,,				2504	0.002				p.V60I		Atlas-SNP	.											.	BTBD8	32	.	0			c.G178A						PASS	.	G	ILE/VAL	26,4380	32.6+/-62.9	0,26,2177	96.0	96.0	96.0		178	3.4	0.9	1	dbSNP_126	96	260,8340	101.0+/-162.3	6,248,4046	yes	missense	BTBD8	NM_183242.3	29	6,274,6223	AA,AG,GG		3.0233,0.5901,2.199	benign	60/379	92554283	286,12720	2203	4300	6503	SO:0001583	missense	284697	exon2			ACAGATGTTACCT	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.178G>A	1.37:g.92554283G>A	ENSP00000343686:p.Val60Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_183242	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	37	CCDS737.1	28	0.01282051282051282	0	0.0	5	0.013812154696132596	0	0.0	23	0.030343007915567283	G	13.65	2.301359	0.40694	0.005901	0.030233	ENSG00000189195	ENST00000370382;ENST00000342818;ENST00000540648	T;T;T	0.76316	-1.01;-1.01;-1.01	5.31	3.42	0.39159	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.247350	0.28273	N	0.015951	T	0.54822	0.1882	L	0.59967	1.855	0.23003	N	0.99845	B	0.24963	0.115	B	0.27076	0.076	T	0.49031	-0.8981	10	0.33940	T	0.23	-10.1214	8.3882	0.32512	0.2616:0.0:0.7384:0.0	rs34856868	60	Q5XKL5	BTBD8_HUMAN	I	60	ENSP00000359408:V60I;ENSP00000343686:V60I;ENSP00000443397:V60I	ENSP00000343686:V60I	V	+	1	0	BTBD8	92326871	1.000000	0.71417	0.859000	0.33776	0.832000	0.47134	1.026000	0.30103	0.718000	0.32166	0.591000	0.81541	GTT	G|0.980;A|0.020	0.020	strong		0.323	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	
RNF152	220441	hgsc.bcm.edu	37	18	59483514	59483514	+	Silent	SNP	A	A	G	rs9319985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	57	0	0		WXS	Illumina HiSeq	Phase_I	62	39	0.629032	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	
WDR62	284403	hgsc.bcm.edu	37	19	36594063	36594063	+	Silent	SNP	C	C	T	rs17851502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36594063C>T	ENST00000270301.7	+	29	3453	c.3453C>T	c.(3451-3453)ctC>ctT	p.L1151L	WDR62_ENST00000401500.2_Silent_p.L1156L			O43379	WDR62_HUMAN	WD repeat domain 62	1151					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGCAGGTCCTCGCTGCAGGGA	0.667													C|||	607	0.121206	0.2557	0.072	5008	,	,		20422	0.0		0.1342	False		,,,				2504	0.0859				p.L1156L		Atlas-SNP	.											.	WDR62	102	.	0			c.C3468T						PASS	.	C	,	978,3428	359.6+/-314.9	106,766,1331	46.0	45.0	45.0		3468,3453	-3.1	0.0	19	dbSNP_123	45	885,7715	194.8+/-240.1	52,781,3467	yes	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	158,1547,4798	TT,TC,CC		10.2907,22.197,14.3242	,	1156/1524,1151/1519	36594063	1863,11143	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon29			GGTCCTCGCTGCA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3453C>T	19.37:g.36594063C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.869;T|0.131	0.131	strong		0.667	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
COQ5	84274	hgsc.bcm.edu	37	12	120954490	120954490	+	Missense_Mutation	SNP	C	C	T	rs3742049	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:120954490C>T	ENST00000288532.6	-	3	494	c.454G>A	c.(454-456)Gcc>Acc	p.A152T	COQ5_ENST00000445328.2_Intron	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	152			A -> T (in dbSNP:rs3742049). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TACTCTTTGGCAATTTCTTCC	0.448													C|||	724	0.144569	0.2859	0.1037	5008	,	,		18233	0.0794		0.1083	False		,,,				2504	0.0869				p.A152T		Atlas-SNP	.											COQ5,NS,carcinoma,0,1	COQ5	26	1	0			c.G454A						scavenged	.	C	THR/ALA	1112,3294	399.5+/-331.2	134,844,1225	192.0	193.0	193.0		454	4.5	1.0	12	dbSNP_107	193	927,7673	204.9+/-247.5	43,841,3416	yes	missense	COQ5	NM_032314.3	58	177,1685,4641	TT,TC,CC		10.7791,25.2383,15.6774	benign	152/328	120954490	2039,10967	2203	4300	6503	SO:0001583	missense	84274	exon3			CTTTGGCAATTTC	AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"""2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"""		"""coenzyme Q5 homolog, methyltransferase (yeast)"""				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.454G>A	12.37:g.120954490C>T	ENSP00000288532:p.Ala152Thr	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_032314	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Missense_Mutation	SNP	ENST00000288532.6	37	CCDS31912.1	319	0.14606227106227107	147	0.29878048780487804	40	0.11049723756906077	44	0.07692307692307693	88	0.11609498680738786	C	15.53	2.859622	0.51376	0.252383	0.107791	ENSG00000110871	ENST00000288532;ENST00000552443;ENST00000547943;ENST00000551769	T;T;T;T	0.63913	-0.07;-0.05;0.54;-0.03	5.41	4.48	0.54585	.	0.281692	0.40640	N	0.001047	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	0.9999999999999977	B	0.21071	0.051	B	0.20577	0.03	T	0.08764	-1.0706	9	0.41790	T	0.15	.	7.3994	0.26954	0.3804:0.5411:0.0:0.0785	rs3742049;rs52835442;rs58137205;rs3742049	152	Q5HYK3	COQ5_HUMAN	T	152;71;102;71	ENSP00000288532:A152T;ENSP00000449863:A71T;ENSP00000449874:A102T;ENSP00000450001:A71T	ENSP00000288532:A152T	A	-	1	0	COQ5	119438873	0.999000	0.42202	1.000000	0.80357	0.977000	0.68977	0.640000	0.24705	2.536000	0.85505	0.557000	0.71058	GCC	C|0.846;T|0.154	0.154	strong		0.448	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314	
ZNF468	90333	hgsc.bcm.edu	37	19	53344118	53344118	+	Missense_Mutation	SNP	C	C	G	rs10419826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53344118C>G	ENST00000595646.1	-	4	1549	c.1429G>C	c.(1429-1431)Ggt>Cgt	p.G477R	ZNF468_ENST00000390651.4_Missense_Mutation_p.G424R|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000396409.4_Missense_Mutation_p.G424R|ZNF28_ENST00000594602.1_Intron			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	60	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	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	
EYS	346007	hgsc.bcm.edu	37	6	64498055	64498055	+	Missense_Mutation	SNP	T	T	A	rs66462731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:64498055T>A	ENST00000370621.3	-	39	8192	c.7666A>T	c.(7666-7668)Agt>Tgt	p.S2556C	EYS_ENST00000503581.1_Missense_Mutation_p.S2556C|EYS_ENST00000370616.2_Missense_Mutation_p.S2556C|EYS_ENST00000486069.1_5'UTR			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2556	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		S -> C. {ECO:0000269|PubMed:20333770, ECO:0000269|PubMed:21069908}.		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.S2556C(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						GTGTATTCACTGTAGCCACCT	0.358													T|||	450	0.0898562	0.056	0.1182	5008	,	,		15408	0.1518		0.0696	False		,,,				2504	0.0726				p.S2556C		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	1	Substitution - Missense(1)	stomach(1)	c.A7666T						PASS	.	T	CYS/SER	83,1301		1,81,610	139.0	119.0	125.0		7666	2.9	1.0	6	dbSNP_130	125	268,2914		10,248,1333	yes	missense	EYS	NM_001142800.1	112	11,329,1943	AA,AT,TT		8.4224,5.9971,7.6873	probably-damaging	2556/3145	64498055	351,4215	692	1591	2283	SO:0001583	missense	346007	exon39			ATTCACTGTAGCC		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.7666A>T	6.37:g.64498055T>A	ENSP00000359655:p.Ser2556Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	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		235	0.10760073260073261	32	0.06504065040650407	35	0.09668508287292818	110	0.19230769230769232	58	0.07651715039577836	T	16.15	3.040955	0.55003	0.059971	0.084224	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.78364	-1.17;-1.17;-1.17	4.1	2.92	0.33932	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.467736	0.15613	U	0.253275	T	0.69278	0.3093	L	0.52011	1.625	0.09310	P	0.999999539944	D;D	0.61697	0.99;0.983	P;P	0.57371	0.634;0.819	T	0.66662	-0.5867	9	0.56958	D	0.05	.	5.4837	0.16737	0.0:0.0994:0.1899:0.7107	.	2556;2556	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	C	2556	ENSP00000424243:S2556C;ENSP00000359655:S2556C;ENSP00000359650:S2556C	ENSP00000359650:S2556C	S	-	1	0	EYS	64556014	0.998000	0.40836	0.978000	0.43139	0.959000	0.62525	2.435000	0.44811	0.462000	0.27095	-0.256000	0.11100	AGT	T|0.899;A|0.101	0.101	strong		0.358	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
MROH2B	133558	hgsc.bcm.edu	37	5	41048533	41048533	+	Missense_Mutation	SNP	C	C	T	rs13173930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:41048533C>T	ENST00000399564.4	-	16	2027	c.1577G>A	c.(1576-1578)cGt>cAt	p.R526H	MROH2B_ENST00000506092.2_Missense_Mutation_p.R81H	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	526			R -> H (in dbSNP:rs13173930). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.														ACCAGCCCCACGTAACTCCCC	0.453													C|||	1177	0.235024	0.1573	0.3329	5008	,	,		17651	0.12		0.3787	False		,,,				2504	0.2413				p.R526H		Atlas-SNP	.											.	.	.	.	0			c.G1577A						PASS	.	C	HIS/ARG	701,3041		61,579,1231	88.0	81.0	83.0		1577	3.0	0.1	5	dbSNP_121	83	3138,5060		614,1910,1575	yes	missense	HEATR7B2	NM_173489.4	29	675,2489,2806	TT,TC,CC		38.2776,18.7333,32.1524	probably-damaging	526/1586	41048533	3839,8101	1871	4099	5970	SO:0001583	missense	133558	exon16			GCCCCACGTAACT		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1577G>A	5.37:g.41048533C>T	ENSP00000382476:p.Arg526His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	559	0.25595238095238093	78	0.15853658536585366	124	0.3425414364640884	64	0.11188811188811189	293	0.3865435356200528	C	8.610	0.888946	0.17540	0.187333	0.382776	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.09163	3.01;3.01	4.87	3.03	0.35002	Armadillo-type fold (1);	1.072850	0.07119	N	0.843613	T	0.00012	0.0000	L	0.54323	1.7	0.54753	P	2.0000000000020002E-5	B	0.09022	0.002	B	0.04013	0.001	T	0.43621	-0.9380	9	0.45353	T	0.12	.	5.8829	0.18866	0.2126:0.6886:0.0:0.0988	rs13173930;rs17854770;rs52825689;rs60763656;rs13173930	526	Q7Z745	HTRB2_HUMAN	H	81;230;526	ENSP00000441504:R81H;ENSP00000382476:R526H	ENSP00000296803:R230H	R	-	2	0	HEATR7B2	41084290	0.742000	0.28228	0.096000	0.21009	0.066000	0.16364	1.280000	0.33202	0.714000	0.32081	0.655000	0.94253	CGT	C|0.756;T|0.244	0.244	strong		0.453	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
TTC21B	79809	hgsc.bcm.edu	37	2	166770120	166770120	+	Silent	SNP	A	A	G	rs10176588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:166770120A>G	ENST00000243344.7	-	16	2312	c.2175T>C	c.(2173-2175)ttT>ttC	p.F725F		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	725					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						CAAGGAGAAGAAAAGACCGAG	0.323													A|||	1389	0.277356	0.2587	0.2262	5008	,	,		14542	0.2014		0.3648	False		,,,				2504	0.3272				p.F725F		Atlas-SNP	.											.	TTC21B	130	.	0			c.T2175C						PASS	.	A		1174,3232	408.4+/-334.6	158,858,1187	95.0	98.0	97.0		2175	-1.5	1.0	2	dbSNP_119	97	3346,5254	494.6+/-373.8	639,2068,1593	no	coding-synonymous	TTC21B	NM_024753.3		797,2926,2780	GG,GA,AA		38.907,26.6455,34.7532		725/1317	166770120	4520,8486	2203	4300	6503	SO:0001819	synonymous_variant	79809	exon16			GAGAAGAAAAGAC	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.2175T>C	2.37:g.166770120A>G		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	217	101	0.465438	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			A|0.681;G|0.319	0.319	strong		0.323	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
PYROXD2	84795	hgsc.bcm.edu	37	10	100147060	100147060	+	Silent	SNP	A	A	G	rs4345897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100147060A>G	ENST00000370575.4	-	14	1500	c.1452T>C	c.(1450-1452)ttT>ttC	p.F484F	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	484							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CGATGCAATCAAACACTGGGG	0.468													G|||	2610	0.521166	0.6422	0.4755	5008	,	,		18833	0.5615		0.334	False		,,,				2504	0.5409				p.F484F		Atlas-SNP	.											.	PYROXD2	43	.	0			c.T1452C						PASS	.	G		2574,1832	535.0+/-374.1	747,1080,376	83.0	80.0	81.0		1452	0.4	1.0	10	dbSNP_111	81	3045,5555	662.2+/-401.9	565,1915,1820	no	coding-synonymous	PYROXD2	NM_032709.2		1312,2995,2196	GG,GA,AA		35.407,41.5797,43.2031		484/582	100147060	5619,7387	2203	4300	6503	SO:0001819	synonymous_variant	84795	exon14			GCAATCAAACACT	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1452T>C	10.37:g.100147060A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Silent	SNP	ENST00000370575.4	37	CCDS7474.1																																																																																			A|0.541;G|0.459	0.459	strong		0.468	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	
ZFHX3	463	hgsc.bcm.edu	37	16	72828403	72828403	+	Silent	SNP	A	A	G	rs2229286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72828403A>G	ENST00000268489.5	-	9	8850	c.8178T>C	c.(8176-8178)ctT>ctC	p.L2726L	ZFHX3_ENST00000397992.5_Silent_p.L1812L|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2726					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)				TATGAGCCTCAAGAGCAGTCT	0.567													G|||	553	0.110423	0.0242	0.2795	5008	,	,		20044	0.2937		0.0139	False		,,,				2504	0.0174				p.L2726L		Atlas-SNP	.											ZFHX3,NS,NS,-2,1	ZFHX3	404	1	0			c.T8178C						PASS	.	G	,	124,4272	811.5+/-416.1	1,122,2075	71.0	61.0	64.0		5436,8178	-11.5	0.0	16	dbSNP_98	64	118,8482	811.0+/-407.1	2,114,4184	no	coding-synonymous,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	3,236,6259	GG,GA,AA		1.3721,2.8207,1.8621	,	1812/2790,2726/3704	72828403	242,12754	2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			AGCCTCAAGAGCA	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.8178T>C	16.37:g.72828403A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			A|0.940;G|0.060	0.060	strong		0.567	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SERPINB10	5273	hgsc.bcm.edu	37	18	61602360	61602360	+	Missense_Mutation	SNP	G	G	A	rs35453062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	70	0	0		WXS	Illumina HiSeq	Phase_I	91	57	0.626374	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	
ERI1	90459	hgsc.bcm.edu	37	8	8869199	8869199	+	Silent	SNP	T	T	G	rs9650616	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0		WXS	Illumina HiSeq	Phase_I	54	33	0.611111	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	
RB1CC1	9821	hgsc.bcm.edu	37	8	53558307	53558307	+	Missense_Mutation	SNP	A	A	T	rs34701924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:53558307A>T	ENST00000025008.5	-	16	4465	c.3942T>A	c.(3940-3942)aaT>aaA	p.N1314K	RB1CC1_ENST00000435644.2_Missense_Mutation_p.N1314K|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.N1314K	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1314			N -> K (in dbSNP:rs34701924).		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)				GCATTTCTTCATTCTTTCTTT	0.343													A|||	22	0.00439297	0.0015	0.0	5008	,	,		16444	0.002		0.0129	False		,,,				2504	0.0051				p.N1314K	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T3942A						PASS	.	A	LYS/ASN,LYS/ASN	6,4400	12.9+/-30.5	0,6,2197	85.0	80.0	82.0		3942,3942	4.3	1.0	8	dbSNP_126	82	87,8513	49.8+/-109.6	1,85,4214	yes	missense,missense	RB1CC1	NM_001083617.1,NM_014781.4	94,94	1,91,6411	TT,TA,AA		1.0116,0.1362,0.7151	probably-damaging,probably-damaging	1314/1592,1314/1595	53558307	93,12913	2203	4300	6503	SO:0001583	missense	9821	exon16			TTCTTCATTCTTT	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.3942T>A	8.37:g.53558307A>T	ENSP00000025008:p.Asn1314Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	9	0.011873350923482849	A	16.47	3.132726	0.56828	0.001362	0.010116	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.16743	2.32;2.32;2.32	5.43	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.18087	0.0434	L	0.36672	1.1	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.08493	-1.0719	10	0.06757	T	0.87	-23.2034	10.0886	0.42434	0.8596:0.0:0.1404:0.0	rs34701924;rs52802517	1314;1314	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	K	1314	ENSP00000025008:N1314K;ENSP00000396067:N1314K;ENSP00000445960:N1314K	ENSP00000025008:N1314K	N	-	3	2	RB1CC1	53720860	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.523000	0.22925	0.896000	0.36366	0.533000	0.62120	AAT	A|0.993;T|0.007	0.007	strong		0.343	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
CEP83	51134	hgsc.bcm.edu	37	12	94761875	94761875	+	Missense_Mutation	SNP	T	T	C	rs185058802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:94761875T>C	ENST00000397809.5	-	10	1700	c.1151A>G	c.(1150-1152)aAa>aGa	p.K384R	CCDC41_ENST00000549352.1_5'Flank|CCDC41_ENST00000339839.5_Missense_Mutation_p.K384R|CCDC41_ENST00000397807.2_Missense_Mutation_p.K351R	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		376					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						ACCTTCTTCTTTGGCAGCTTG	0.323													T|||	2	0.000399361	0.0	0.0	5008	,	,		18493	0.0		0.002	False		,,,				2504	0.0				p.K384R		Atlas-SNP	.											.	CCDC41	59	.	0			c.A1151G						PASS	.	T	ARG/LYS,ARG/LYS	0,3684		0,0,1842	114.0	101.0	105.0		1151,1151	3.8	1.0	12		105	5,8173		0,5,4084	yes	missense,missense	CCDC41	NM_016122.2,NM_001042399.1	26,26	0,5,5926	CC,CT,TT		0.0611,0.0,0.0422	benign,benign	384/702,384/702	94761875	5,11857	1842	4089	5931	SO:0001583	missense	51134	exon10			TCTTCTTTGGCAG																												ENST00000397809.5:c.1151A>G	12.37:g.94761875T>C	ENSP00000380911:p.Lys384Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_016122	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	12.33	1.904325	0.33628	0.0	6.11E-4	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807	T;T;T	0.38722	1.27;1.27;1.12	6.07	3.75	0.43078	.	.	.	.	.	T	0.36276	0.0961	L	0.45581	1.43	0.32464	N	0.543696	B;B	0.27559	0.181;0.02	B;B	0.30943	0.122;0.016	T	0.40515	-0.9559	9	0.26408	T	0.33	-10.2743	10.4787	0.44680	0.0:0.1302:0.0:0.8698	.	351;376	Q9Y592-2;Q9Y592	.;CCD41_HUMAN	R	384;384;351	ENSP00000344655:K384R;ENSP00000380911:K384R;ENSP00000380909:K351R	ENSP00000344655:K384R	K	-	2	0	CCDC41	93286006	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.757000	0.38400	0.547000	0.28938	-0.250000	0.11733	AAA	T|0.999;C|0.001	0.001	strong		0.323	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
FLRT3	23767	hgsc.bcm.edu	37	20	14307564	14307564	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:14307564C>T	ENST00000378053.3	-	2	845	c.589G>A	c.(589-591)Ggt>Agt	p.G197S	FLRT3_ENST00000341420.4_Missense_Mutation_p.G197S|MACROD2_ENST00000217246.4_Intron|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	197					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.G197C(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		CTAGTGAGACCTTGAAGAGAT	0.408																																					p.G197S		Atlas-SNP	.											FLRT3,NS,carcinoma,0,2	FLRT3	67	2	1	Substitution - Missense(1)	lung(1)	c.G589A						scavenged	.						84.0	82.0	83.0					20																	14307564		2203	4300	6503	SO:0001583	missense	23767	exon2			TGAGACCTTGAAG	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"""Fibronectin type III domain containing"""	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.589G>A	20.37:g.14307564C>T	ENSP00000367292:p.Gly197Ser	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	248	3	0.0120968	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	37	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.283092	0.59867	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.58940	0.3;0.3	6.16	5.17	0.71159	.	0.116215	0.56097	D	0.000032	T	0.50154	0.1599	L	0.31371	0.925	0.42896	D	0.994214	B	0.11235	0.004	B	0.25884	0.064	T	0.46345	-0.9198	10	0.54805	T	0.06	-12.6363	17.0792	0.86594	0.0:0.8735:0.1265:0.0	.	197	Q9NZU0	FLRT3_HUMAN	S	197	ENSP00000367292:G197S;ENSP00000339912:G197S	ENSP00000339912:G197S	G	-	1	0	FLRT3	14255564	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.934000	0.63491	2.937000	0.99478	0.650000	0.86243	GGT	.	.	none		0.408	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281	
RHBDF2	79651	hgsc.bcm.edu	37	17	74475975	74475975	+	Missense_Mutation	SNP	C	C	A	rs3809694	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74475975C>A	ENST00000313080.4	-	4	472	c.199G>T	c.(199-201)Gca>Tca	p.A67S	RHBDF2_ENST00000591885.1_Intron|RHBDF2_ENST00000592378.1_Intron|RHBDF2_ENST00000389760.4_Intron	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	67				A -> S (in Ref. 2; BAF84824 and 4; AAH16034). {ECO:0000305}.	negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						GTGGTGTGTGCAGCCCAGGTC	0.547													C|||	2285	0.45627	0.2587	0.5764	5008	,	,		9807	0.6052		0.4652	False		,,,				2504	0.4755				p.A67S		Atlas-SNP	.											RHBDF2,colon,carcinoma,+1,1	RHBDF2	57	1	0			c.G199T						PASS	.	C	,SER/ALA	1298,3108	416.3+/-337.5	180,938,1085	31.0	30.0	30.0		,199	-2.0	0.0	17	dbSNP_130	30	3956,4640	517.9+/-379.1	897,2162,1239	yes	intron,missense	RHBDF2	NM_001005498.3,NM_024599.5	,99	1077,3100,2324	AA,AC,CC		46.0214,29.4598,40.4092	,	,67/857	74475975	5254,7748	2203	4298	6501	SO:0001583	missense	79651	exon4			TGTGTGCAGCCCA	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.199G>T	17.37:g.74475975C>A	ENSP00000322775:p.Ala67Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	1015	0.46474358974358976	125	0.2540650406504065	195	0.5386740331491713	346	0.6048951048951049	349	0.4604221635883905	C	8.467	0.856677	0.17106	0.294598	0.460214	ENSG00000129667	ENST00000313080	T	0.54675	0.56	4.23	-2.03	0.07365	.	2.935030	0.01893	N	0.038673	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.41998	-0.9477	9	0.19590	T	0.45	7.7057	10.8665	0.46858	0.0:0.5646:0.301:0.1344	rs3809694	67	Q6PJF5	RHDF2_HUMAN	S	67	ENSP00000322775:A67S	ENSP00000322775:A67S	A	-	1	0	RHBDF2	71987570	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.503000	0.06383	-0.407000	0.07576	-0.955000	0.02649	GCA	C|0.600;A|0.400	0.400	strong		0.547	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599	
GLIS1	148979	hgsc.bcm.edu	37	1	54060016	54060016	+	Missense_Mutation	SNP	G	G	C	rs35227000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:54060016G>C	ENST00000312233.2	-	3	1126	c.560C>G	c.(559-561)gCa>gGa	p.A187G		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						CACCCTGCCTGCCAGGCCCAG	0.697													G|||	1070	0.213658	0.1104	0.1643	5008	,	,		13194	0.1885		0.2962	False		,,,				2504	0.3292				p.A187G		Atlas-SNP	.											.	GLIS1	52	.	0			c.C560G						PASS	.	G	GLY/ALA	547,3825		59,429,1698	14.0	14.0	14.0		560	-1.2	0.2	1	dbSNP_126	14	2796,5746		502,1792,1977	no	missense	GLIS1	NM_147193.2	60	561,2221,3675	CC,CG,GG		32.7324,12.5114,25.8866	benign	187/621	54060016	3343,9571	2186	4271	6457	SO:0001583	missense	148979	exon3			CTGCCTGCCAGGC	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.560C>G	1.37:g.54060016G>C	ENSP00000309653:p.Ala187Gly	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	477	0.2184065934065934	66	0.13414634146341464	67	0.1850828729281768	114	0.1993006993006993	230	0.3034300791556728	G	8.908	0.958011	0.18507	0.125114	0.327324	ENSG00000174332	ENST00000312233	T	0.10860	2.83	4.67	-1.17	0.09648	.	0.628717	0.14183	N	0.335887	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.48352	-0.9043	9	0.24483	T	0.36	.	5.9742	0.19369	0.3294:0.1274:0.5432:0.0	rs35227000	187	Q8NBF1	GLIS1_HUMAN	G	187	ENSP00000309653:A187G	ENSP00000309653:A187G	A	-	2	0	GLIS1	53832604	0.000000	0.05858	0.203000	0.23512	0.475000	0.33008	0.042000	0.13949	-0.010000	0.14271	0.462000	0.41574	GCA	G|0.757;C|0.243	0.243	strong		0.697	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
POLRMT	5442	hgsc.bcm.edu	37	19	619021	619021	+	Silent	SNP	G	G	C	rs14155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:619021G>C	ENST00000588649.2	-	15	3327	c.3243C>G	c.(3241-3243)ccC>ccG	p.P1081P	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1081	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)	p.P1081P(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		CCAGGCGATAGGGCTGGATGA	0.637													C|||	3117	0.622404	0.7352	0.4006	5008	,	,		13997	0.5823		0.5119	False		,,,				2504	0.7822				p.P1081P		Atlas-SNP	.											POLRMT,colon,carcinoma,0,2	POLRMT	91	2	1	Substitution - coding silent(1)	stomach(1)	c.C3243G						PASS	.	C		2965,1429		999,967,231	59.0	50.0	53.0		3243	-2.7	1.0	19	dbSNP_52	53	4220,4378		1005,2210,1084	no	coding-synonymous	POLRMT	NM_005035.3		2004,3177,1315	CC,CG,GG		49.0812,32.5216,44.6967		1081/1231	619021	7185,5807	2197	4299	6496	SO:0001819	synonymous_variant	5442	exon15			GCGATAGGGCTGG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.3243C>G	19.37:g.619021G>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	170	74	0.435294	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.442;C|0.558	0.558	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363395	42363395	+	Missense_Mutation	SNP	C	C	T	rs78165678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363395C>T	ENST00000290472.3	-	17	1896	c.1802G>A	c.(1801-1803)cGc>cAc	p.R601H		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	601	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GTTGGGGCTGCGCTGGTGGAG	0.672													C|||	222	0.0443291	0.0144	0.0749	5008	,	,		15310	0.0		0.1083	False		,,,				2504	0.0429				p.R601H		Atlas-SNP	.											PLA2G4D,NS,carcinoma,-1,1	PLA2G4D	72	1	0			c.G1802A						PASS	.	C	HIS/ARG	166,4238	107.8+/-146.2	1,164,2037	33.0	34.0	33.0		1802	-3.5	0.1	15	dbSNP_132	33	963,7633	200.2+/-244.0	46,871,3381	yes	missense	PLA2G4D	NM_178034.3	29	47,1035,5418	TT,TC,CC		11.2029,3.7693,8.6846	benign	601/819	42363395	1129,11871	2202	4298	6500	SO:0001583	missense	283748	exon17			GGGCTGCGCTGGT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1802G>A	15.37:g.42363395C>T	ENSP00000290472:p.Arg601His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	128	0.05860805860805861	10	0.02032520325203252	31	0.0856353591160221	0	0.0	87	0.11477572559366754	C	7.075	0.569026	0.13560	0.037693	0.112029	ENSG00000159337	ENST00000290472	T	0.10477	2.87	5.27	-3.52	0.04682	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.685896	0.14003	N	0.348007	T	0.00109	0.0003	N	0.02916	-0.46	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.31696	-0.9934	9	0.39692	T	0.17	-0.9758	14.7385	0.69434	0.0:0.2189:0.0:0.7811	.	601	Q86XP0	PA24D_HUMAN	H	601	ENSP00000290472:R601H	ENSP00000290472:R601H	R	-	2	0	PLA2G4D	40150687	0.000000	0.05858	0.052000	0.19188	0.700000	0.40528	0.069000	0.14552	-0.438000	0.07232	-0.345000	0.07892	CGC	C|0.922;T|0.078	0.078	strong		0.672	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604960	33604960	+	Silent	SNP	C	C	T	rs2273115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	29	0	0		WXS	Illumina HiSeq	Phase_I	20	18	0.9	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	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799183	57799183	+	Silent	SNP	C	C	T	rs7123727	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57799183C>T	ENST00000302622.3	+	1	782	c.759C>T	c.(757-759)agC>agT	p.S253S	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTGTGGTGAGCCTCTTCTATG	0.517													C|||	754	0.150559	0.0938	0.1614	5008	,	,		22234	0.1022		0.2823	False		,,,				2504	0.1339				p.S253S		Atlas-SNP	.											.	OR6Q1	58	.	0			c.C759T						PASS	.	C		497,3905	230.4+/-244.6	30,437,1734	183.0	157.0	166.0		759	3.3	0.9	11	dbSNP_116	166	2503,6089	410.7+/-350.2	351,1801,2144	no	coding-synonymous	OR6Q1	NM_001005186.2		381,2238,3878	TT,TC,CC		29.1318,11.2903,23.0876		253/318	57799183	3000,9994	2201	4296	6497	SO:0001819	synonymous_variant	219952	exon1			GGTGAGCCTCTTC	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.759C>T	11.37:g.57799183C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	63	0.434483	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	37	CCDS31541.1																																																																																			C|0.778;T|0.222	0.222	strong		0.517	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
B3GALNT1	8706	hgsc.bcm.edu	37	3	160804167	160804167	+	Missense_Mutation	SNP	C	C	T	rs2231257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:160804167C>T	ENST00000392781.2	-	8	1123	c.376G>A	c.(376-378)Gac>Aac	p.D126N	B3GALNT1_ENST00000392779.2_Missense_Mutation_p.D126N|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.D126N|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000417187.1_Intron	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	126			D -> N (in dbSNP:rs2231257). {ECO:0000269|Ref.8}.		oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			AACATTTTGTCTTCCTTTTCA	0.393													C|||	260	0.0519169	0.0038	0.0591	5008	,	,		20257	0.0417		0.0298	False		,,,				2504	0.1452				p.D126N		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.G376A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	49,4357	48.9+/-83.8	1,47,2155	107.0	103.0	105.0		376,376,376,376,376	5.7	1.0	3	dbSNP_98	105	290,8310	107.8+/-168.5	3,284,4013	yes	missense,missense,missense,missense,missense	B3GALNT1	NM_001038628.1,NM_003781.3,NM_033167.2,NM_033168.2,NM_033169.2	23,23,23,23,23	4,331,6168	TT,TC,CC		3.3721,1.1121,2.6065	benign,benign,benign,benign,benign	126/332,126/332,126/332,126/332,126/332	160804167	339,12667	2203	4300	6503	SO:0001583	missense	8706	exon8			TTTTGTCTTCCTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"""Blood group antigens"", ""Beta 3-glycosyltransferases"""	918	protein-coding gene	gene with protein product	"""globoside synthase"", ""P antigen synthase"""	603094	"""UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)"", ""UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"""	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.376G>A	3.37:g.160804167C>T	ENSP00000376532:p.Asp126Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	79	27	0.341772	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	37	CCDS3193.1	58	0.026556776556776556	4	0.008130081300813009	14	0.03867403314917127	22	0.038461538461538464	18	0.023746701846965697	C	9.800	1.180328	0.21787	0.011121	0.033721	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.73	5.73	0.89815	.	1.905830	0.02222	N	0.064124	T	0.27169	0.0666	L	0.31476	0.935	0.40277	D	0.978357	D	0.71674	0.998	D	0.63113	0.911	T	0.35773	-0.9775	10	0.38643	T	0.18	.	18.8796	0.92351	0.0:1.0:0.0:0.0	rs2231257;rs52824161;rs2231257	126	O75752	B3GL1_HUMAN	N	126	ENSP00000323479:D126N;ENSP00000376530:D126N;ENSP00000376531:D126N;ENSP00000376532:D126N;ENSP00000418226:D126N;ENSP00000420163:D126N	ENSP00000323479:D126N	D	-	1	0	B3GALNT1	162286861	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	4.898000	0.63238	2.701000	0.92244	0.561000	0.74099	GAC	C|0.973;T|0.027	0.027	strong		0.393	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167	
CCSER2	54462	hgsc.bcm.edu	37	10	86131059	86131059	+	Missense_Mutation	SNP	A	A	G	rs3814205	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	162	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	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	
NOBOX	135935	hgsc.bcm.edu	37	7	144096068	144096068	+	Missense_Mutation	SNP	C	C	T	rs2525702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:144096068C>T	ENST00000467773.1	-	8	1443	c.1444G>A	c.(1444-1446)Ggc>Agc	p.G482S	NOBOX_ENST00000483238.1_Missense_Mutation_p.G450S|NOBOX_ENST00000223140.5_Missense_Mutation_p.G365S	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	482	Pro-rich.		G -> S (in dbSNP:rs2525702). {ECO:0000269|PubMed:17701902}.		oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|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)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					CCACAGGGGCCGTCCTTGTGG	0.597													C|||	812	0.162141	0.2413	0.1124	5008	,	,		15514	0.0238		0.1561	False		,,,				2504	0.2393				p.G482S		Atlas-SNP	.											NOBOX_ENST00000467773,NS,carcinoma,0,2	NOBOX	130	2	0			c.G1444A						PASS	.	C	SER/GLY	809,2975		105,599,1188	11.0	11.0	11.0		1444	3.3	0.2	7	dbSNP_100	11	1323,6897		126,1071,2913	yes	missense	NOBOX	NM_001080413.3	56	231,1670,4101	TT,TC,CC		16.0949,21.3795,17.7607	possibly-damaging	482/692	144096068	2132,9872	1892	4110	6002	SO:0001583	missense	135935	exon8			AGGGGCCGTCCTT			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1444G>A	7.37:g.144096068C>T	ENSP00000419457:p.Gly482Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	37		258	0.11813186813186813	91	0.18495934959349594	43	0.11878453038674033	4	0.006993006993006993	120	0.158311345646438	C	12.44	1.937408	0.34189	0.213795	0.160949	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140	T;T;T	0.32988	1.43;1.43;1.43	4.25	3.35	0.38373	.	0.765147	0.12242	N	0.486405	T	0.00039	0.0001	M	0.63843	1.955	0.58432	P	5.999999999950489E-6	B	0.26672	0.156	B	0.17098	0.017	T	0.11494	-1.0585	9	0.28530	T	0.3	-11.259	7.0702	0.25173	0.0:0.8736:0.0:0.1264	rs2525702;rs10370641;rs2525702	482	O60393	NOBOX_HUMAN	S	450;482;365	ENSP00000419565:G450S;ENSP00000419457:G482S;ENSP00000223140:G365S	ENSP00000223140:G365S	G	-	1	0	NOBOX	143727001	0.000000	0.05858	0.164000	0.22755	0.185000	0.23345	0.481000	0.22260	0.974000	0.38366	0.655000	0.94253	GGC	C|0.876;T|0.124	0.124	strong		0.597	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517142	158517142	+	Missense_Mutation	SNP	C	C	T	rs41273491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	103	0	0		WXS	Illumina HiSeq	Phase_I	116	39	0.336207	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	
GABRR1	2569	hgsc.bcm.edu	37	6	89926966	89926966	+	Missense_Mutation	SNP	T	T	C	rs12200969	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:89926966T>C	ENST00000454853.2	-	1	186	c.76A>G	c.(76-78)Atg>Gtg	p.M26V	GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000481493.1_5'UTR|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	168	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	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		
MYH13	8735	hgsc.bcm.edu	37	17	10223793	10223793	+	Silent	SNP	C	C	T	rs35783712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:10223793C>T	ENST00000418404.3	-	24	3295	c.3132G>A	c.(3130-3132)caG>caA	p.Q1044Q	RP11-401O9.3_ENST00000577743.1_RNA|RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Silent_p.Q1044Q			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1044					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						GTTTCTTCTCCTGCTCTAAGG	0.493													C|||	87	0.0173722	0.0023	0.0274	5008	,	,		16884	0.001		0.0567	False		,,,				2504	0.0072				p.Q1044Q		Atlas-SNP	.											.	MYH13	533	.	0			c.G3132A						PASS	.	C		36,3646		0,36,1805	50.0	47.0	48.0		3132	2.8	1.0	17	dbSNP_126	48	466,7714		7,452,3631	no	coding-synonymous	MYH13	NM_003802.2		7,488,5436	TT,TC,CC		5.6968,0.9777,4.232		1044/1939	10223793	502,11360	1841	4090	5931	SO:0001819	synonymous_variant	8735	exon25			CTTCTCCTGCTCT	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.3132G>A	17.37:g.10223793C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			C|0.970;T|0.030	0.030	strong		0.493	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	
FREM1	158326	hgsc.bcm.edu	37	9	14776027	14776027	+	Silent	SNP	C	C	T	rs2131880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:14776027C>T	ENST00000380880.3	-	25	5400	c.4617G>A	c.(4615-4617)gcG>gcA	p.A1539A	FREM1_ENST00000380894.1_Silent_p.A75A|FREM1_ENST00000422223.2_Silent_p.A1539A|FREM1_ENST00000380881.4_Silent_p.A1540A|FREM1_ENST00000486223.1_5'Flank			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	106	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	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	
MRPL39	54148	hgsc.bcm.edu	37	21	26965205	26965205	+	Silent	SNP	T	T	C	rs1057885	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:26965205T>C	ENST00000352957.4	-	8	881	c.840A>G	c.(838-840)gtA>gtG	p.V280V	MRPL39_ENST00000307301.7_Silent_p.V280V	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	280						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						GAACTGCTGATACTTCATACT	0.373													C|||	3668	0.732428	0.7284	0.8199	5008	,	,		16504	0.7153		0.8121	False		,,,				2504	0.6115				p.V280V		Atlas-SNP	.											.	MRPL39	61	.	0			c.A840G						PASS	.	C	,	3308,1098	396.7+/-330.2	1229,850,124	94.0	88.0	90.0		840,840	0.1	1.0	21	dbSNP_86	90	7111,1489	283.7+/-296.3	2954,1203,143	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4183,2053,267	CC,CT,TT		17.314,24.9206,19.8908	,	280/339,280/354	26965205	10419,2587	2203	4300	6503	SO:0001819	synonymous_variant	54148	exon8			TGCTGATACTTCA	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.840A>G	21.37:g.26965205T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			T|0.211;C|0.789	0.789	strong		0.373	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
KIAA0368	23392	hgsc.bcm.edu	37	9	114190337	114190337	+	Silent	SNP	G	G	A	rs16916100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:114190337G>A	ENST00000338205.5	-	9	1254	c.1035C>T	c.(1033-1035)ttC>ttT	p.F345F	KIAA0368_ENST00000259335.4_Silent_p.F523F			Q5VYK3	ECM29_HUMAN	KIAA0368	351					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TGTTGGCTGGGAACGTTTCAG	0.408													G|||	414	0.0826677	0.0015	0.0807	5008	,	,		15655	0.1845		0.0666	False		,,,				2504	0.1053				p.F523F		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C1569T						PASS	.	G		52,3648		0,52,1798	75.0	73.0	73.0		1569	-0.5	1.0	9	dbSNP_123	73	458,7728		16,426,3651	no	coding-synonymous	KIAA0368	NM_001080398.1		16,478,5449	AA,AG,GG		5.5949,1.4054,4.2908		523/2018	114190337	510,11376	1850	4093	5943	SO:0001819	synonymous_variant	23392	exon11			GGCTGGGAACGTT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1035C>T	9.37:g.114190337G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				G|0.910;A|0.090	0.090	strong		0.408	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
LRRC23	10233	hgsc.bcm.edu	37	12	7022085	7022085	+	Missense_Mutation	SNP	T	T	A	rs1057077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7022085T>A	ENST00000007969.8	+	7	1170	c.950T>A	c.(949-951)gTg>gAg	p.V317E	LRRC23_ENST00000436789.1_Intron|ENO2_ENST00000538763.1_5'Flank|LRRC23_ENST00000323702.5_Intron|ENO2_ENST00000229277.1_5'Flank|LRRC23_ENST00000443597.2_Missense_Mutation_p.V317E|ENO2_ENST00000535366.1_5'Flank|LRRC23_ENST00000429740.1_Intron|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000544774.1_5'Flank|ENO2_ENST00000541477.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	317	LRRCT.		V -> E (in dbSNP:rs1057077).							NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						GAGGCTGATGTGATTCGACAG	0.557													A|||	2010	0.401358	0.7141	0.2752	5008	,	,		-128	0.2579		0.2952	False		,,,				2504	0.3252				p.V317E		Atlas-SNP	.											.	LRRC23	46	.	0			c.T950A						PASS	.	A	GLU/VAL,,GLU/VAL	2718,1688	510.6+/-367.6	851,1016,336	157.0	157.0	157.0		950,,950	5.3	1.0	12	dbSNP_86	157	2410,6190	699.6+/-405.1	350,1710,2240	yes	missense,intron,missense	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	121,,121	1201,2726,2576	AA,AT,TT		28.0233,38.3114,39.428	benign,,benign	317/344,,317/344	7022085	5128,7878	2203	4300	6503	SO:0001583	missense	10233	exon7			CTGATGTGATTCG	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.950T>A	12.37:g.7022085T>A	ENSP00000007969:p.Val317Glu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	830	0.38003663003663	340	0.6910569105691057	125	0.3453038674033149	142	0.24825174825174826	223	0.2941952506596306	A	0.372	-0.933309	0.02359	0.616886	0.280233	ENSG00000010626	ENST00000007969;ENST00000443597	T;T	0.52526	0.66;0.66	5.27	5.27	0.74061	.	.	.	.	.	T	0.00012	0.0000	N	0.00082	-2.215	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45279	-0.9272	8	0.02654	T	1	-19.078	11.9037	0.52699	0.8693:0.0:0.0:0.1307	rs1057077;rs3759354;rs52834149;rs1057077	317	Q53EV4	LRC23_HUMAN	E	317	ENSP00000007969:V317E;ENSP00000390932:V317E	ENSP00000007969:V317E	V	+	2	0	LRRC23	6892346	1.000000	0.71417	0.979000	0.43373	0.029000	0.11900	4.721000	0.61951	0.931000	0.37242	-0.376000	0.06991	GTG	T|0.598;A|0.402	0.402	strong		0.557	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
ARHGEF38	54848	hgsc.bcm.edu	37	4	106510470	106510470	+	Missense_Mutation	SNP	A	A	G	rs2276970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:106510470A>G	ENST00000420470.2	+	2	406	c.262A>G	c.(262-264)Atg>Gtg	p.M88V	ARHGEF38_ENST00000265154.2_Missense_Mutation_p.M88V	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	88			M -> V (in dbSNP:rs2276970).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						AGAGCATCATATGAAGAGGAT	0.423													A|||	440	0.0878594	0.0915	0.0793	5008	,	,		17891	0.1091		0.1064	False		,,,				2504	0.0481				p.M88V		Atlas-SNP	.											.	ARHGEF38	52	.	0			c.A262G						PASS	.	A	VAL/MET,VAL/MET	470,3936	220.0+/-237.6	33,404,1766	124.0	123.0	123.0		262,262	0.4	0.0	4	dbSNP_100	123	769,7831	182.2+/-230.7	30,709,3561	yes	missense,missense	ARHGEF38	NM_001242729.1,NM_017700.1	21,21	63,1113,5327	GG,GA,AA		8.9419,10.6673,9.5264	benign,benign	88/778,88/220	106510470	1239,11767	2203	4300	6503	SO:0001583	missense	54848	exon2			CATCATATGAAGA	AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"""Rho guanine nucleotide exchange factors"""	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.262A>G	4.37:g.106510470A>G	ENSP00000416125:p.Met88Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	NM_001242729	C9JIB4	Missense_Mutation	SNP	ENST00000420470.2	37	CCDS56338.1	214	0.09798534798534798	54	0.10975609756097561	30	0.08287292817679558	50	0.08741258741258741	80	0.10554089709762533	A	0.007	-2.001471	0.00431	0.106673	0.089419	ENSG00000236699	ENST00000265154;ENST00000420470	T;T	0.28666	1.6;1.61	5.34	0.4	0.16331	Dbl homology (DH) domain (1);	0.908004	0.09725	N	0.763874	T	0.00328	0.0010	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33828	-0.9853	9	0.12766	T	0.61	1.1522	4.8709	0.13631	0.5162:0.2832:0.2005:0.0	rs2276970;rs17258977;rs61636643;rs2276970	88	Q9NXL2	ARH38_HUMAN	V	88	ENSP00000265154:M88V;ENSP00000416125:M88V	ENSP00000265154:M88V	M	+	1	0	ARHGEF38	106729919	0.000000	0.05858	0.000000	0.03702	0.496000	0.33645	-0.031000	0.12287	-0.146000	0.11274	0.533000	0.62120	ATG	A|0.908;G|0.092	0.092	strong		0.423	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700	
PAK4	10298	hgsc.bcm.edu	37	19	39668381	39668381	+	Missense_Mutation	SNP	G	G	A	rs372098486		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39668381G>A	ENST00000593690.1	+	10	1979	c.1552G>A	c.(1552-1554)Gag>Aag	p.E518K	PAK4_ENST00000360442.3_Missense_Mutation_p.E518K|PAK4_ENST00000599386.1_Missense_Mutation_p.E365K|PAK4_ENST00000358301.3_Missense_Mutation_p.E518K|PAK4_ENST00000321944.4_Missense_Mutation_p.E428K|PAK4_ENST00000599470.1_Missense_Mutation_p.E365K|PAK4_ENST00000435673.2_Missense_Mutation_p.E518K	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	518	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			CTACTTCAACGAGCCACCCCT	0.602																																					p.E518K		Atlas-SNP	.											.	PAK4	40	.	0			c.G1552A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	166.0	134.0	145.0		1552,1552,1093,1093,1552	5.1	1.0	19		145	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	56,56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	518/592,518/592,365/439,365/439,518/592	39668381	1,13005	2203	4300	6503	SO:0001583	missense	10298	exon8			TTCAACGAGCCAC	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.1552G>A	19.37:g.39668381G>A	ENSP00000469413:p.Glu518Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248588	0.80024	0.0	1.16E-4	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.65364	-0.15;-0.15;-0.15	5.07	5.07	0.68467	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	0.64204	0.2577	N	0.12471	0.22	0.80722	D	1	D;P;P	0.76494	0.999;0.782;0.817	D;B;B	0.70716	0.97;0.115;0.276	T	0.71083	-0.4695	10	0.87932	D	0	.	15.9831	0.80127	0.0:0.0:1.0:0.0	.	428;365;518	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	K	518;365;322;274;518;518	ENSP00000351049:E518K;ENSP00000392753:E518K;ENSP00000353625:E518K	ENSP00000326864:E365K	E	+	1	0	PAK4	44360221	1.000000	0.71417	0.979000	0.43373	0.795000	0.44927	9.657000	0.98554	2.629000	0.89072	0.555000	0.69702	GAG	.	.	weak		0.602	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1		
MICALCL	84953	hgsc.bcm.edu	37	11	12315848	12315848	+	Silent	SNP	C	C	T	rs1493952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:12315848C>T	ENST00000256186.2	+	3	1161	c.870C>T	c.(868-870)ggC>ggT	p.G290G		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	290					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)		ACTCTGAAGGCGGGAAGAAGG	0.567																																					p.G290G		Atlas-SNP	.											.	MICALCL	59	.	0			c.C870T						PASS	.	T		2016,1876		518,980,448	52.0	58.0	56.0		870	-1.6	0.0	11	dbSNP_88	56	2614,5620		424,1766,1927	no	coding-synonymous	MICALCL	NM_032867.2		942,2746,2375	TT,TC,CC		31.7464,48.2014,38.1824		290/696	12315848	4630,7496	1946	4117	6063	SO:0001819	synonymous_variant	84953	exon3			TGAAGGCGGGAAG	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.870C>T	11.37:g.12315848C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_032867	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																			C|0.576;T|0.424	0.424	strong		0.567	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287062	44287062	+	Silent	SNP	A	A	G	rs2071884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:44287062A>G	ENST00000597664.1	-	2	435	c.306T>C	c.(304-306)gaT>gaC	p.D102D	PNPLA5_ENST00000381198.2_Intron|PNPLA5_ENST00000216177.4_Silent_p.D102D|PNPLA5_ENST00000593866.1_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	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	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	
APC	324	hgsc.bcm.edu	37	5	112175770	112175770	+	Silent	SNP	G	G	A	rs41115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112175770G>A	ENST00000457016.1	+	16	4859	c.4479G>A	c.(4477-4479)acG>acA	p.T1493T	APC_ENST00000508376.2_Silent_p.T1493T|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.T1493T			P25054	APC_HUMAN	adenomatous polyposis coli	1493	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1494fs*19(3)|p.E1494fs*13(2)|p.?(1)|p.K1454fs*3(1)|p.L1488fs*13(1)|p.K1192fs*3(1)|p.T1493fs*13(1)|p.E1494fs*11(1)|p.T1493fs*17(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATTTTGCCACGGAAAGTACTC	0.438		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			G|||	3333	0.665535	0.5174	0.7161	5008	,	,		19822	0.8165		0.5994	False		,,,				2504	0.7423				p.T1493T	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,NS,carcinoma,0,1	APC	4158	1	12	Deletion - Frameshift(9)|Complex - frameshift(2)|Unknown(1)	large_intestine(8)|thyroid(1)|lung(1)|soft_tissue(1)|skin(1)	c.G4479A						PASS	.	G	,,	2318,2084	573.2+/-383.5	620,1078,503	70.0	72.0	72.0	http://omim.org/entry/114500	4479,4479,4425	2.5	1.0	5	dbSNP_76	72	5304,3296	638.9+/-399.4	1668,1968,664	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2288,3046,1167	AA,AG,GG		38.3256,47.3421,41.3782	,,	1493/2844,1493/2844,1475/2826	112175770	7622,5380	2201	4300	6501	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TGCCACGGAAAGT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4479G>A	5.37:g.112175770G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.379;N|0.000	.	strong		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
OR51A7	119687	hgsc.bcm.edu	37	11	4928841	4928841	+	Missense_Mutation	SNP	T	T	C	rs7108225	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4928841T>C	ENST00000359350.4	+	1	242	c.242T>C	c.(241-243)aTg>aCg	p.M81T	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	81			M -> T (in dbSNP:rs7108225).			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)		CTTCCTACCATGTTGAGGGTC	0.458													T|||	287	0.0573083	0.0295	0.0663	5008	,	,		22110	0.002		0.1193	False		,,,				2504	0.0818				p.M81T		Atlas-SNP	.											OR51A7,colon,carcinoma,0,4	OR51A7	86	4	0			c.T242C						PASS	.	T	THR/MET	231,4171	136.1+/-172.1	5,221,1975	155.0	133.0	141.0		242	3.9	1.0	11	dbSNP_116	141	1037,7559	221.5+/-258.9	63,911,3324	yes	missense	OR51A7	NM_001004749.1	81	68,1132,5299	CC,CT,TT		12.0638,5.2476,9.7553	benign	81/313	4928841	1268,11730	2201	4298	6499	SO:0001583	missense	119687	exon1			CTACCATGTTGAG	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.242T>C	11.37:g.4928841T>C	ENSP00000352305:p.Met81Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	37	CCDS31364.1	126	0.057692307692307696	12	0.024390243902439025	27	0.07458563535911603	1	0.0017482517482517483	86	0.11345646437994723	T	12.31	1.899731	0.33535	0.052476	0.120638	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.05996	3.36	5.02	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.00144	0.0004	L	0.58354	1.805	0.26250	N	0.978736	B	0.24920	0.114	B	0.31869	0.137	T	0.25745	-1.0123	10	0.31617	T	0.26	.	9.9807	0.41811	0.0:0.0826:0.0:0.9173	rs7108225;rs17252300;rs52835214;rs61049276;rs7108225	81	Q8NH64	O51A7_HUMAN	T	81;81;70	ENSP00000352305:M81T	ENSP00000352305:M81T	M	+	2	0	OR51A7	4885417	0.003000	0.15002	0.998000	0.56505	0.856000	0.48823	1.307000	0.33516	2.098000	0.63641	0.533000	0.62120	ATG	T|0.918;C|0.082	0.082	strong		0.458	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
DNAH17	8632	hgsc.bcm.edu	37	17	76482435	76482435	+	Silent	SNP	C	C	T	rs61743860	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76482435C>T	ENST00000585328.1	-	45	7081	c.6957G>A	c.(6955-6957)acG>acA	p.T2319T	RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.T2310T	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2310					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)			GGTACAGAATCGTTTGGATCA	0.572													C|||	413	0.0824681	0.0234	0.0634	5008	,	,		18447	0.1478		0.0924	False		,,,				2504	0.0982				p.T2324T		Atlas-SNP	.											.	DNAH17	347	.	0			c.G6972A						PASS	.	C		158,4196		2,154,2021	76.0	81.0	79.0		6972	-3.9	0.2	17	dbSNP_129	79	778,7764		30,718,3523	no	coding-synonymous	DNAH17	NM_173628.3		32,872,5544	TT,TC,CC		9.1079,3.6288,7.2581		2324/4463	76482435	936,11960	2177	4271	6448	SO:0001819	synonymous_variant	8632	exon45			CAGAATCGTTTGG	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.6957G>A	17.37:g.76482435C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				C|0.909;T|0.091	0.091	strong		0.572	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
TTC38	55020	hgsc.bcm.edu	37	22	46682976	46682976	+	Missense_Mutation	SNP	C	C	T	rs55653327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46682976C>T	ENST00000381031.3	+	10	917	c.841C>T	c.(841-843)Ccc>Tcc	p.P281S	TTC38_ENST00000445282.2_Missense_Mutation_p.P223S	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	281						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CCAGATCCTTCCCAGCCTGCA	0.662													C|||	190	0.0379393	0.003	0.0562	5008	,	,		21954	0.001		0.1133	False		,,,				2504	0.0327				p.P281S		Atlas-SNP	.											.	TTC38	40	.	0			c.C841T						PASS	.	C	SER/PRO	70,4150		1,68,2041	32.0	36.0	35.0		841	4.7	1.0	22	dbSNP_129	35	854,7630		46,762,3434	yes	missense	TTC38	NM_017931.2	74	47,830,5475	TT,TC,CC		10.066,1.6588,7.2733	benign	281/470	46682976	924,11780	2110	4242	6352	SO:0001583	missense	55020	exon10			ATCCTTCCCAGCC		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.841C>T	22.37:g.46682976C>T	ENSP00000370419:p.Pro281Ser	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	114	0.0521978021978022	0	0.0	26	0.0718232044198895	0	0.0	88	0.11609498680738786	C	17.03	3.284063	0.59867	0.016588	0.10066	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.75154	0.88;-0.91	4.7	4.7	0.59300	.	0.245457	0.39985	N	0.001218	T	0.02380	0.0073	L	0.55743	1.74	0.22066	P	0.999385888	B;B	0.32350	0.335;0.366	B;B	0.35688	0.208;0.112	T	0.47509	-0.9112	9	0.09338	T	0.73	0.3381	16.2259	0.82288	0.0:1.0:0.0:0.0	rs55653327	223;281	E7ES35;Q5R3I4	.;TTC38_HUMAN	S	281;223	ENSP00000370419:P281S;ENSP00000393960:P223S	ENSP00000370419:P281S	P	+	1	0	TTC38	45061640	1.000000	0.71417	0.992000	0.48379	0.883000	0.51084	4.894000	0.63206	2.153000	0.67306	0.563000	0.77884	CCC	C|0.941;T|0.059	0.059	strong		0.662	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
OR5AP2	338675	hgsc.bcm.edu	37	11	56409603	56409603	+	Missense_Mutation	SNP	C	C	T	rs11606499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56409603C>T	ENST00000302981.1	-	1	312	c.313G>A	c.(313-315)Gcc>Acc	p.A105T	OR5AP2_ENST00000544374.1_Missense_Mutation_p.A106T	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	105			A -> T (in dbSNP:rs11606499).			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(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						TAGAACTGGGCAGCACATCCA	0.502													C|||	590	0.117812	0.2587	0.1037	5008	,	,		19446	0.0		0.1392	False		,,,				2504	0.0368				p.A105T		Atlas-SNP	.											.	OR5AP2	69	.	0			c.G313A						PASS	.	C	THR/ALA	1179,3223	411.3+/-335.7	148,883,1170	60.0	65.0	64.0		313	3.2	1.0	11	dbSNP_120	64	1199,7393	242.8+/-272.6	95,1009,3192	yes	missense	OR5AP2	NM_001002925.1	58	243,1892,4362	TT,TC,CC		13.9548,26.7833,18.3008	benign	105/317	56409603	2378,10616	2201	4296	6497	SO:0001583	missense	338675	exon1			ACTGGGCAGCACA	AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"""GPCR / Class A : Olfactory receptors"""	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.313G>A	11.37:g.56409603C>T	ENSP00000303111:p.Ala105Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001002925	B2RNM8	Missense_Mutation	SNP	ENST00000302981.1	37	CCDS31534.1	271	0.12408424908424909	130	0.26422764227642276	33	0.09116022099447514	0	0.0	108	0.1424802110817942	C	2.461	-0.324119	0.05350	0.267833	0.139548	ENSG00000172464	ENST00000544374;ENST00000302981	T;T	0.01347	4.99;4.99	5.06	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.278709	0.25708	N	0.028839	T	0.00012	0.0000	N	0.16130	0.375	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.40213	-0.9575	9	0.09084	T	0.74	.	9.4638	0.38800	0.0:0.7584:0.0:0.2416	rs11606499;rs52811029;rs61316262;rs11606499	105	Q8NGF4	O5AP2_HUMAN	T	106;105	ENSP00000442701:A106T;ENSP00000303111:A105T	ENSP00000303111:A105T	A	-	1	0	OR5AP2	56166179	0.000000	0.05858	0.966000	0.40874	0.935000	0.57460	-0.013000	0.12678	0.700000	0.31782	0.637000	0.83480	GCC	C|0.834;T|0.166	0.166	strong		0.502	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925	
ATP2B2	491	hgsc.bcm.edu	37	3	10413601	10413601	+	Silent	SNP	G	G	A	rs2289273	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10413601G>A	ENST00000352432.4	-	11	1620	c.1551C>T	c.(1549-1551)ggC>ggT	p.G517G	ATP2B2_ENST00000383800.4_Silent_p.G472G|ATP2B2_ENST00000397077.1_Silent_p.G472G|ATP2B2_ENST00000360273.2_Silent_p.G517G|ATP2B2_ENST00000343816.4_Silent_p.G503G			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	517				G -> D (in Ref. 2; AAA50877/AAA51893). {ECO:0000305}.	auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.G472G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AGTGGACGTCGCCGACATAGG	0.562													G|||	705	0.140775	0.0053	0.0447	5008	,	,		19274	0.3234		0.1421	False		,,,				2504	0.2025				p.G517G	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											ATP2B2,NS,carcinoma,0,1	ATP2B2	304	1	1	Substitution - coding silent(1)	stomach(1)	c.C1551T						PASS	.	G	,	132,4274	95.3+/-134.0	2,128,2073	199.0	175.0	183.0		1551,1416	-3.8	0.7	3	dbSNP_100	183	1188,7412	241.8+/-272.0	85,1018,3197	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	87,1146,5270	AA,AG,GG		13.814,2.9959,10.1492	,	517/1244,472/1199	10413601	1320,11686	2203	4300	6503	SO:0001819	synonymous_variant	491	exon12			GACGTCGCCGACA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1551C>T	3.37:g.10413601G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	345	205	0.594203	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			G|0.884;A|0.116	0.116	strong		0.562	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
COL22A1	169044	hgsc.bcm.edu	37	8	139609156	139609156	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:139609156G>A	ENST00000303045.6	-	62	4869	c.4423C>T	c.(4423-4425)Cag>Tag	p.Q1475*	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Nonsense_Mutation_p.Q1455*	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1475	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.Q1475K(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CTTTCAAGCTGCTTCCCCAGC	0.507										HNSCC(7;0.00092)																											p.Q1475X		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	1	1	Substitution - Missense(1)	lung(1)	c.C4423T						PASS	.						182.0	182.0	182.0					8																	139609156		2203	4300	6503	SO:0001587	stop_gained	169044	exon62			CAAGCTGCTTCCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4423C>T	8.37:g.139609156G>A	ENSP00000303153:p.Gln1475*	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	92	20	0.217391	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Nonsense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	47	13.734218	0.99760	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	.	.	.	5.06	5.06	0.68205	.	0.000000	0.44688	U	0.000425	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.4049	0.87470	0.0:0.0:1.0:0.0	.	.	.	.	X	1475;1455;1168	.	ENSP00000303153:Q1475X	Q	-	1	0	COL22A1	139678338	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.323000	0.90002	2.349000	0.79799	0.563000	0.77884	CAG	.	.	none		0.507	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
CLK2	1196	hgsc.bcm.edu	37	1	155239302	155239302	+	Missense_Mutation	SNP	G	G	A	rs375441160		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:155239302G>A	ENST00000368361.4	-	3	691	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CLK2_ENST00000361168.5_Missense_Mutation_p.R126W|CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000355560.4_Missense_Mutation_p.R125W|CLK2_ENST00000536801.1_Missense_Mutation_p.R126W			P49760	CLK2_HUMAN	CDC-like kinase 2	126					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTAAATGTCCGGCTGCGCCTC	0.597								Other conserved DNA damage response genes					G|||	1	0.000199681	0.0008	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.R126W		Atlas-SNP	.											.	CLK2	55	.	0			c.C376T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	69.0	63.0	65.0		376	3.0	1.0	1		65	2,8598		0,2,4298	no	missense	CLK2	NM_003993.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	126/499	155239302	2,13004	2203	4300	6503	SO:0001583	missense	1196	exon3			ATGTCCGGCTGCG	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.376C>T	1.37:g.155239302G>A	ENSP00000357345:p.Arg126Trp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	37		.	.	.	.	.	.	.	.	.	.	.	17.04	3.286501	0.59867	0.0	2.33E-4	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.55760	0.51;0.51;0.5;0.51	4.96	3.05	0.35203	.	0.567586	0.20018	N	0.100976	T	0.47893	0.1470	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.69078	0.995;0.997	P;P	0.53401	0.535;0.725	T	0.51980	-0.8636	10	0.56958	D	0.05	.	13.0486	0.58942	0.0:0.0:0.7088:0.2911	.	126;126	P49760;P49760-3	CLK2_HUMAN;.	W	126;126;125;126	ENSP00000354856:R126W;ENSP00000357345:R126W;ENSP00000347759:R125W;ENSP00000441023:R126W	ENSP00000347759:R125W	R	-	1	2	CLK2	153505926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.717000	0.54911	0.671000	0.31185	0.650000	0.86243	CGG	.	.	none		0.597	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	
ZFP91	80829	hgsc.bcm.edu	37	11	58378424	58378424	+	Splice_Site	SNP	A	A	G	rs8373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:58378424A>G	ENST00000316059.6	+	5	790	c.619A>G	c.(619-621)Agt>Ggt	p.S207G	ZFP91-CNTF_ENST00000389919.4_Splice_Site_p.S207G	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	207	Glu-rich.		S -> G (in dbSNP:rs8373). {ECO:0000269|Ref.6}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TATTTTTAGTAGTGAAGAGGA	0.373													A|||	1075	0.214657	0.1626	0.2176	5008	,	,		17003	0.1835		0.2505	False		,,,				2504	0.2781				p.S207G		Atlas-SNP	.											.	ZFP91	66	.	0			c.A619G						PASS	.	A	,GLY/SER	631,3771	270.4+/-269.6	44,543,1614	73.0	65.0	68.0		,619	5.8	1.0	11	dbSNP_52	68	2108,6482	361.1+/-332.2	264,1580,2451	no	splice-3,missense-near-splice	ZFP91	NM_001197051.1,NM_053023.4	,56	308,2123,4065	GG,GA,AA		24.5402,14.3344,21.0822	,probably-damaging	,207/571	58378424	2739,10253	2201	4295	6496	SO:0001630	splice_region_variant	80829	exon5			TTTAGTAGTGAAG	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.618-1A>G	11.37:g.58378424A>G		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	37	CCDS31553.1	488	0.22344322344322345	109	0.22154471544715448	69	0.19060773480662985	114	0.1993006993006993	196	0.25857519788918204	A	17.02	3.282804	0.59867	0.143344	0.245402	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.11930	2.73	5.76	5.76	0.90799	.	2.285560	0.01956	N	0.042984	T	0.00012	0.0000	N	0.24115	0.695	0.30548	P	0.765736	P	0.48764	0.915	B	0.40940	0.344	T	0.17440	-1.0369	9	0.15499	T	0.54	-3.059	8.6083	0.33786	0.9147:0.0:0.0853:0.0	rs8373;rs1129269;rs2275992;rs3177502;rs11541681;rs17016487;rs17489327;rs52827541;rs57129919;rs8373	207	Q96JP5	ZFP91_HUMAN	G	207	ENSP00000339030:S207G	ENSP00000374569:S207G	S	+	1	0	ZFP91	58135000	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	4.471000	0.60182	2.199000	0.70637	0.528000	0.53228	AGT	A|0.780;G|0.220	0.220	strong		0.373	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023	Missense_Mutation
PKDREJ	10343	hgsc.bcm.edu	37	22	46652959	46652959	+	Silent	SNP	A	A	G	rs4508712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46652959A>G	ENST00000253255.5	-	1	6260	c.6261T>C	c.(6259-6261)ccT>ccC	p.P2087P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2087					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GGCAGATGCCAGGGAGGGCAG	0.478													G|||	1855	0.370407	0.9244	0.2147	5008	,	,		20978	0.0516		0.2893	False		,,,				2504	0.1442				p.P2087P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T6261C						PASS	.	G		3673,733	287.8+/-279.5	1544,585,74	36.0	40.0	38.0		6261	-11.8	0.0	22	dbSNP_111	38	2476,6124	689.2+/-404.3	354,1768,2178	no	coding-synonymous	PKDREJ	NM_006071.1		1898,2353,2252	GG,GA,AA		28.7907,16.6364,47.2782		2087/2254	46652959	6149,6857	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			GATGCCAGGGAGG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6261T>C	22.37:g.46652959A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.593;G|0.407;T|0.000	0.407	strong		0.478	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
RASAL3	64926	hgsc.bcm.edu	37	19	15574858	15574858	+	Silent	SNP	C	C	T	rs78677793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:15574858C>T	ENST00000343625.7	-	2	397	c.312G>A	c.(310-312)ccG>ccA	p.P104P		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	104	Pro-rich.				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						CCTCCTGCTCCGGCTCCGGGT	0.647													C|||	474	0.0946486	0.0817	0.085	5008	,	,		13744	0.0694		0.167	False		,,,				2504	0.0706				p.P104P		Atlas-SNP	.											.	RASAL3	49	.	0			c.G312A						PASS	.	C		343,3561		22,299,1631	13.0	15.0	15.0		312	-7.9	0.0	19	dbSNP_132	15	1352,6896		126,1100,2898	no	coding-synonymous	RASAL3	NM_022904.1		148,1399,4529	TT,TC,CC		16.3919,8.7859,13.9483		104/1012	15574858	1695,10457	1952	4124	6076	SO:0001819	synonymous_variant	64926	exon2			CTGCTCCGGCTCC		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.312G>A	19.37:g.15574858C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_022904	Q8N2T9|Q9H735	Silent	SNP	ENST00000343625.7	37	CCDS46006.1																																																																																			C|0.894;T|0.106	0.106	strong		0.647	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541107	133541107	+	Missense_Mutation	SNP	T	T	A	rs16841277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:133541107T>A	ENST00000409261.1	-	14	3650	c.3277A>T	c.(3277-3279)Aat>Tat	p.N1093Y	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.N1093Y|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_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	213	0	0		WXS	Illumina HiSeq	Phase_I	210	98	0.466667	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	
DISP1	84976	hgsc.bcm.edu	37	1	223177574	223177574	+	Silent	SNP	A	A	G	rs2609355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223177574A>G	ENST00000284476.6	+	8	2999	c.2835A>G	c.(2833-2835)aaA>aaG	p.K945K		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	945					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		AGTTTTATAAAGAGGTGGACT	0.463													A|||	1209	0.241414	0.1581	0.3084	5008	,	,		21088	0.2232		0.2793	False		,,,				2504	0.2863				p.K945K		Atlas-SNP	.											.	DISP1	145	.	0			c.A2835G						PASS	.	A		823,3583	327.2+/-299.9	79,665,1459	76.0	70.0	72.0		2835	-6.3	0.0	1	dbSNP_100	72	2582,6018	418.9+/-352.9	390,1802,2108	no	coding-synonymous	DISP1	NM_032890.3		469,2467,3567	GG,GA,AA		30.0233,18.6791,26.1802		945/1525	223177574	3405,9601	2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			TTATAAAGAGGTG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2835A>G	1.37:g.223177574A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																			A|0.752;G|0.248	0.248	strong		0.463	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
GRIK1	2897	hgsc.bcm.edu	37	21	30971183	30971183	+	Silent	SNP	G	G	A	rs363430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:30971183G>A	ENST00000399907.1	-	8	1584	c.1173C>T	c.(1171-1173)gaC>gaT	p.D391D	GRIK1_ENST00000399914.1_Silent_p.D391D|BACH1_ENST00000462262.1_Intron|GRIK1-AS2_ENST00000333765.4_Intron|GRIK1_ENST00000389125.3_Silent_p.D391D|GRIK1_ENST00000399909.1_Silent_p.D391D|GRIK1_ENST00000535441.1_Silent_p.D393D|GRIK1_ENST00000472429.1_5'UTR|GRIK1_ENST00000399913.1_Silent_p.D391D|GRIK1_ENST00000327783.4_Silent_p.D391D|GRIK1_ENST00000309434.7_Silent_p.D393D|GRIK1_ENST00000389124.2_Silent_p.D391D	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	391					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)	p.D391D(1)		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)	GACTAATAATGTCCAGATCAA	0.373													G|||	1108	0.221246	0.1868	0.2767	5008	,	,		18704	0.3512		0.1322	False		,,,				2504	0.1861				p.D391D		Atlas-SNP	.											GRIK1,NS,carcinoma,0,1	GRIK1	293	1	1	Substitution - coding silent(1)	stomach(1)	c.C1173T						PASS	.	G	,	804,3602	320.7+/-296.8	82,640,1481	100.0	99.0	99.0		1173,1173	3.0	1.0	21	dbSNP_79	99	1195,7405	242.6+/-272.5	85,1025,3190	no	coding-synonymous,coding-synonymous	GRIK1	NM_000830.3,NM_175611.2	,	167,1665,4671	AA,AG,GG		13.8953,18.2478,15.3698	,	391/919,391/906	30971183	1999,11007	2203	4300	6503	SO:0001819	synonymous_variant	2897	exon8			AATAATGTCCAGA		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.1173C>T	21.37:g.30971183G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	43	12	0.27907	NM_175611	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	37	CCDS42913.1																																																																																			G|0.820;A|0.180	0.180	strong		0.373	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		
PTCD3	55037	hgsc.bcm.edu	37	2	86352925	86352925	+	Silent	SNP	A	A	G	rs139474497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44.0	49.0	47.0		873	-11.5	0.0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.873A>G	2.37:g.86352925A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37107770	37107770	+	Missense_Mutation	SNP	C	C	T	rs371325582		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:37107770C>T	ENST00000336686.4	-	22	1591	c.1511G>A	c.(1510-1512)cGa>cAa	p.R504Q	LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.R504Q|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	504					Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GAGCATATCTCGCTCATTCCT	0.478																																					p.R504Q		Atlas-SNP	.											LRRFIP2,colon,carcinoma,-1,1	LRRFIP2	71	1	1	Whole gene deletion(1)	ovary(1)	c.G1511A						scavenged	.	C	,GLN/ARG,	1,4405	2.1+/-5.4	0,1,2202	212.0	191.0	198.0		,1511,	6.2	1.0	3		198	0,8600		0,0,4300	no	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,43,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,probably-damaging,	,504/722,	37107770	1,13005	2203	4300	6503	SO:0001583	missense	9209	exon23			ATATCTCGCTCAT	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.1511G>A	3.37:g.37107770C>T	ENSP00000338727:p.Arg504Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	219	3	0.0136986	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	C	36	5.839226	0.97009	2.27E-4	0.0	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.41400	1.0;1.0	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	M	0.75264	2.295	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.56294	-0.8003	10	0.21014	T	0.42	-6.66	20.8794	0.99867	0.0:1.0:0.0:0.0	.	504	Q9Y608	LRRF2_HUMAN	Q	504	ENSP00000392217:R504Q;ENSP00000338727:R504Q	ENSP00000338727:R504Q	R	-	2	0	LRRFIP2	37082774	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.336000	0.79245	2.941000	0.99782	0.655000	0.94253	CGA	.	.	weak		0.478	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68219200	68219200	+	Missense_Mutation	SNP	C	C	T	rs34373049	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:68219200C>T	ENST00000347230.4	-	40	7370	c.7232G>A	c.(7231-7233)cGc>cAc	p.R2411H	RN7SL213P_ENST00000463482.2_RNA|ZFYVE26_ENST00000557306.1_Missense_Mutation_p.R257H	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2411			R -> H (in dbSNP:rs34373049).		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)		CACCAACTGGCGGGCAGCTCT	0.537													C|||	48	0.00958466	0.003	0.0086	5008	,	,		20154	0.0		0.0338	False		,,,				2504	0.0041				p.R2411H		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G7232A						PASS	.	C	HIS/ARG	58,4348	57.4+/-93.9	1,56,2146	96.0	75.0	82.0		7232	4.0	1.0	14	dbSNP_126	82	346,8254	117.7+/-177.3	7,332,3961	yes	missense	ZFYVE26	NM_015346.3	29	8,388,6107	TT,TC,CC		4.0233,1.3164,3.1063	possibly-damaging	2411/2540	68219200	404,12602	2203	4300	6503	SO:0001583	missense	23503	exon40			AACTGGCGGGCAG	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.7232G>A	14.37:g.68219200C>T	ENSP00000251119:p.Arg2411His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	28	0.01282051282051282	0	0.0	3	0.008287292817679558	0	0.0	25	0.032981530343007916	C	19.65	3.867327	0.72065	0.013164	0.040233	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000557306	T;T	0.44482	1.79;0.92	6.04	4.02	0.46733	.	0.196433	0.44285	D	0.000468	T	0.05960	0.0155	N	0.08118	0	0.80722	D	1	P;D	0.60160	0.938;0.987	P;P	0.46299	0.511;0.474	T	0.01059	-1.1465	10	0.39692	T	0.17	-19.97	6.7706	0.23591	0.0:0.6641:0.0:0.3359	rs34373049	257;2411	Q96H43;Q68DK2	.;ZFY26_HUMAN	H	2411;2390;257	ENSP00000251119:R2411H;ENSP00000452142:R257H	ENSP00000251119:R2411H	R	-	2	0	ZFYVE26	67288953	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.530000	0.45641	1.576000	0.49790	0.561000	0.74099	CGC	C|0.973;T|0.027	0.027	strong		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
EMILIN2	84034	hgsc.bcm.edu	37	18	2891847	2891847	+	Silent	SNP	C	C	T	rs3826638	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:2891847C>T	ENST00000254528.3	+	4	1881	c.1722C>T	c.(1720-1722)cgC>cgT	p.R574R		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	574					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGGAAGACCGCGCAGTACGCG	0.483													C|||	734	0.146565	0.0817	0.3012	5008	,	,		20747	0.2103		0.1382	False		,,,				2504	0.0675				p.R574R		Atlas-SNP	.											.	EMILIN2	97	.	0			c.C1722T						PASS	.	C		410,3996	200.4+/-223.7	20,370,1813	68.0	63.0	65.0		1722	-0.7	0.0	18	dbSNP_107	65	1254,7346	250.1+/-277.1	104,1046,3150	no	coding-synonymous	EMILIN2	NM_032048.2		124,1416,4963	TT,TC,CC		14.5814,9.3055,12.7941		574/1054	2891847	1664,11342	2203	4300	6503	SO:0001819	synonymous_variant	84034	exon4			AGACCGCGCAGTA	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1722C>T	18.37:g.2891847C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Silent	SNP	ENST00000254528.3	37	CCDS11828.1																																																																																			C|0.860;T|0.140	0.140	strong		0.483	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
MUC4	4585	hgsc.bcm.edu	37	3	195506750	195506750	+	Missense_Mutation	SNP	G	G	C	rs62282471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506750G>C	ENST00000463781.3	-	2	12160	c.11701C>G	c.(11701-11703)Cac>Gac	p.H3901D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3901D	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)		GGGGTGGCGTGACGTGTGGAT	0.592													.|||	553	0.110423	0.0287	0.1095	5008	,	,		8303	0.0536		0.2256	False		,,,				2504	0.1616				p.H3901D		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11701G						PASS	.						9.0	9.0	9.0					3																	195506750		524	1014	1538	SO:0001583	missense	4585	exon2			TGGCGTGACGTGT	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.11701C>G	3.37:g.195506750G>C	ENSP00000417498:p.His3901Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	31	26	0.83871	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	86	0.039377289377289376	11	0.022357723577235773	16	0.04419889502762431	6	0.01048951048951049	53	0.06992084432717678	g	2.283	-0.364168	0.05103	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.55;1.5	.	.	.	.	.	.	.	.	T	0.00967	0.0032	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.18053	-1.0349	7	.	.	.	.	5.4844	0.16741	1.0E-4:0.348:0.652:0.0	rs62282471	3773	E7ESK3	.	D	3901	ENSP00000417498:H3901D;ENSP00000420243:H3901D	.	H	-	1	0	MUC4	196991529	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-3.212000	0.00555	-2.418000	0.00566	-2.366000	0.00237	CAC	G|0.967;C|0.033	0.033	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TELO2	9894	hgsc.bcm.edu	37	16	1555589	1555589	+	Missense_Mutation	SNP	A	A	G	rs386787714|rs2248128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1555589A>G	ENST00000262319.6	+	16	2300	c.2021A>G	c.(2020-2022)cAg>cGg	p.Q674R	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	674			Q -> R (in dbSNP:rs2248128).		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)				AGCAAGACCCAGCGGCTCTCC	0.672													G|||	2536	0.50639	0.8343	0.3674	5008	,	,		11908	0.5308		0.2256	False		,,,				2504	0.4254				p.Q674R		Atlas-SNP	.											.	TELO2	44	.	0			c.A2021G						PASS	.	G	ARG/GLN	3286,1112	373.4+/-320.8	1249,788,162	31.0	35.0	34.0		2021	4.9	1.0	16	dbSNP_100	34	1936,6662	714.8+/-406.0	208,1520,2571	yes	missense	TELO2	NM_016111.3	43	1457,2308,2733	GG,GA,AA		22.5169,25.2842,40.1816	benign	674/838	1555589	5222,7774	2199	4299	6498	SO:0001583	missense	9894	exon16			AGACCCAGCGGCT	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.2021A>G	16.37:g.1555589A>G	ENSP00000262319:p.Gln674Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	979	0.4482600732600733	403	0.8191056910569106	127	0.35082872928176795	281	0.49125874125874125	168	0.22163588390501318	G	0.221	-1.028930	0.02045	0.747158	0.225169	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.09350	2.99	4.93	4.93	0.64822	.	0.053924	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00015	-2.88	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36187	-0.9758	9	0.02654	T	1	-32.3826	12.7707	0.57419	0.0818:0.0:0.9182:0.0	rs2248128;rs61199481;rs2248128	674	Q9Y4R8	TELO2_HUMAN	R	197;674	ENSP00000262319:Q674R	ENSP00000262319:Q674R	Q	+	2	0	TELO2	1495590	0.996000	0.38824	0.995000	0.50966	0.157000	0.22087	2.923000	0.48868	1.231000	0.43661	-0.374000	0.07098	CAG	A|0.561;G|0.439	0.439	strong		0.672	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73440864	73440864	+	Silent	SNP	C	C	T	rs12931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73440864C>T	ENST00000556143.1	-	11	2745	c.2025G>A	c.(2023-2025)acG>acA	p.T675T	ZFYVE1_ENST00000554145.1_5'Flank|ZFYVE1_ENST00000318876.5_Silent_p.T661T|ZFYVE1_ENST00000553891.1_Silent_p.T675T|ZFYVE1_ENST00000555072.1_Silent_p.T260T|ZFYVE1_ENST00000394207.2_Silent_p.T260T	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	675					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		GAGCAATGAGCGTTCCACCTT	0.537													T|||	2400	0.479233	0.5877	0.4049	5008	,	,		20915	0.371		0.4781	False		,,,				2504	0.498				p.T675T		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.G2025A						PASS	.	T	,	2386,2020	562.1+/-380.9	628,1130,445	157.0	121.0	133.0		2025,780	-9.5	0.2	14	dbSNP_52	133	4175,4425	586.6+/-392.1	1029,2117,1154	yes	coding-synonymous,coding-synonymous	ZFYVE1	NM_021260.2,NM_178441.1	,	1657,3247,1599	TT,TC,CC		48.5465,45.8466,49.5541	,	675/778,260/363	73440864	6561,6445	2203	4300	6503	SO:0001819	synonymous_variant	53349	exon11			AATGAGCGTTCCA	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.2025G>A	14.37:g.73440864C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			C|0.501;T|0.499	0.499	strong		0.537	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
DOCK8	81704	hgsc.bcm.edu	37	9	334337	334337	+	Missense_Mutation	SNP	A	A	G	rs10970979	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	110	110	1	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	
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263898	55263898	+	Missense_Mutation	SNP	G	G	A	rs1049267	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55263898G>A	ENST00000342376.3	+	8	984	c.953G>A	c.(952-954)cGc>cAc	p.R318H	KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	318			R -> H (in dbSNP:rs1049267). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8662091, ECO:0000269|PubMed:9059894, ECO:0000269|PubMed:9430221}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		AAAATCACTCGCCCTTCTCAG	0.498													.|||	1314	0.26238	0.2958	0.2133	5008	,	,		14495	0.1319		0.4135	False		,,,				2504	0.2311				p.R318H		Atlas-SNP	.											KIR2DL3,NS,carcinoma,0,2	KIR2DL3	68	2	0			c.G953A						PASS	.	G	HIS/ARG	1268,2832		409,450,1191	172.0	190.0	184.0		953	-1.8	0.0	19	dbSNP_86	184	3466,4526		1194,1078,1724	no	missense	KIR2DL3	NM_015868.2	29	1603,1528,2915	AA,AG,GG		43.3684,30.9268,39.1499		318/342	55263898	4734,7358	2050	3996	6046	SO:0001583	missense	3804	exon8			TCACTCGCCCTTC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.953G>A	19.37:g.55263898G>A	ENSP00000342215:p.Arg318His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	215	149	0.693023	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	37	CCDS33107.1	621	0.28434065934065933	137	0.2784552845528455	96	0.26519337016574585	69	0.12062937062937062	319	0.420844327176781	g	4.003	-0.002093	0.07819	0.309268	0.433684	ENSG00000243772	ENST00000342376	T	0.00464	7.24	0.909	-1.82	0.07857	.	.	.	.	.	T	0.00012	0.0000	M	0.80028	2.48	0.80722	P	0.0	D;B;B	0.53151	0.958;0.006;0.006	P;B;B	0.48488	0.579;0.002;0.002	T	0.34428	-0.9829	8	0.42905	T	0.14	.	8.3911	0.32528	0.0:0.6188:0.3812:0.0	rs1049267;rs3189371;rs11671789;rs16985912;rs17845997;rs17858981;rs17859525	220;318;318	P43628-2;P43628;E3NZD8	.;KI2L3_HUMAN;.	H	318	ENSP00000342215:R318H	ENSP00000342215:R318H	R	+	2	0	KIR2DL3	59955710	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.002000	0.12924	-2.805000	0.00350	-2.747000	0.00125	CGC	.	.	weak		0.498	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
ABL1	25	hgsc.bcm.edu	37	9	133760029	133760029	+	Silent	SNP	C	C	G	rs2229070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133760029C>G	ENST00000318560.5	+	11	2733	c.2352C>G	c.(2350-2352)ccC>ccG	p.P784P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	784	Pro-rich.				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)	CGCCTCCCCCCAGGCTGGTGA	0.592			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	534	0.106629	0.2821	0.0865	5008	,	,		18610	0.001		0.0696	False		,,,				2504	0.0307				p.P803P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2409G						PASS	.	C	,	985,3415		107,771,1322	26.0	30.0	28.0		2352,2409	1.6	0.2	9	dbSNP_98	28	622,7976		27,568,3704	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	134,1339,5026	GG,GC,CC		7.2342,22.3864,12.3634	,	784/1131,803/1150	133760029	1607,11391	2200	4299	6499	SO:0001819	synonymous_variant	25	exon11			TCCCCCCAGGCTG	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.2352C>G	9.37:g.133760029C>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			C|0.885;G|0.115	0.115	strong		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
LYST	1130	hgsc.bcm.edu	37	1	235955276	235955276	+	Silent	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:235955276G>T	ENST00000389794.3	-	12	4440	c.4266C>A	c.(4264-4266)gcC>gcA	p.A1422A	LYST_ENST00000389793.2_Silent_p.A1422A|LYST_ENST00000536965.1_Intron			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1422					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)			ATAAACCCATGGCCTTACTGT	0.458																																					p.A1422A		Atlas-SNP	.											.	LYST	370	.	0			c.C4266A						PASS	.						152.0	155.0	154.0					1																	235955276		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon12			ACCCATGGCCTTA	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.4266C>A	1.37:g.235955276G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	none		0.458	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
BRCA1	672	hgsc.bcm.edu	37	17	41246481	41246481	+	Missense_Mutation	SNP	T	T	C	rs80357796|rs1799950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:41246481T>C	ENST00000357654.3	-	10	1185	c.1067A>G	c.(1066-1068)cAg>cGg	p.Q356R	BRCA1_ENST00000471181.2_Missense_Mutation_p.Q356R|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.Q60R|BRCA1_ENST00000493795.1_Missense_Mutation_p.Q309R|BRCA1_ENST00000354071.3_Missense_Mutation_p.Q356R|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.Q356R	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	356			Q -> R (common polymorphism; dbSNP:rs1799950). {ECO:0000269|PubMed:7894493, ECO:0000269|Ref.5, 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)		TGGCAGTTTCTGCTTATTCCA	0.408			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			T|||	109	0.0217652	0.003	0.0461	5008	,	,		22610	0.0		0.0596	False		,,,				2504	0.0133				p.Q356R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.A1067G	GRCh37	CM014322	BRCA1	M	rs1799950	PASS	.	T	ARG/GLN,ARG/GLN,,,ARG/GLN	45,4361	47.5+/-82.1	0,45,2158	238.0	222.0	227.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1067,926,,,1067	3.7	0.0	17	dbSNP_89	227	552,8048	151.6+/-206.3	18,516,3766	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	43,43,,,43	18,561,5924	CC,CT,TT		6.4186,1.0213,4.5902	possibly-damaging,possibly-damaging,,,possibly-damaging	356/1864,309/1817,,,356/1885	41246481	597,12409	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		AGTTTCTGCTTAT	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.1067A>G	17.37:g.41246481T>C	ENSP00000350283:p.Gln356Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	61|61	0.027930402930402932|0.027930402930402932	2|2	0.0040650406504065045|0.0040650406504065045	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	41|41	0.05408970976253298|0.05408970976253298	T|T	9.735|9.735	1.163374|1.163374	0.21538|0.21538	0.010213|0.010213	0.064186|0.064186	ENSG00000012048|ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795;ENST00000470026;ENST00000477152;ENST00000497488;ENST00000494123|ENST00000473961	D;D;D;D;D;D;D;D;D;D|.	0.91843|.	-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92;-2.92|.	4.81|4.81	3.71|3.71	0.42584|0.42584	.|.	0.255608|.	0.28247|.	N|.	0.016049|.	T|T	0.29556|0.29556	0.0737|0.0737	H|H	0.95187|0.95187	3.635|3.635	0.09310|0.09310	N|N	1|1	D;D;D;D;D;D|.	0.76494|.	0.997;0.997;0.987;0.999;0.998;0.995|.	D;D;D;D;D;D|.	0.76575|.	0.933;0.933;0.944;0.988;0.988;0.969|.	T|T	0.53344|0.53344	-0.8452|-0.8452	10|5	0.66056|.	D|.	0.02|.	.|.	10.444|10.444	0.44483|0.44483	0.0:0.0:0.1705:0.8295|0.0:0.0:0.1705:0.8295	rs1799950;rs4986851;rs17846597;rs17859679;rs52822238;rs1799950|rs1799950;rs4986851;rs17846597;rs17859679;rs52822238;rs1799950	356;315;356;356;356;356|.	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2|.	.;.;.;.;BRCA1_HUMAN;.|.	R|G	356;356;356;356;60;356;309;356;330;60;356|222	ENSP00000350283:Q356R;ENSP00000326002:Q356R;ENSP00000246907:Q356R;ENSP00000310938:Q60R;ENSP00000418960:Q356R;ENSP00000418775:Q309R;ENSP00000419274:Q356R;ENSP00000419988:Q330R;ENSP00000418986:Q60R;ENSP00000419103:Q356R|.	ENSP00000310938:Q60R|.	Q|R	-|-	2|1	0|2	BRCA1|BRCA1	38500007|38500007	0.996000|0.996000	0.38824|0.38824	0.045000|0.045000	0.18777|0.18777	0.005000|0.005000	0.04900|0.04900	2.364000|2.364000	0.44187|0.44187	0.939000|0.939000	0.37446|0.37446	0.533000|0.533000	0.62120|0.62120	CAG|AGA	T|0.960;C|0.040	0.040	strong		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
TNFRSF10B	8795	hgsc.bcm.edu	37	8	22926313	22926313	+	Missense_Mutation	SNP	G	G	A	rs1129424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22926313G>A	ENST00000276431.4	-	1	379	c.95C>T	c.(94-96)cCc>cTc	p.P32L	RP11-875O11.2_ENST00000501897.1_RNA|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.P32L|RP11-875O11.3_ENST00000520840.1_RNA|TNFRSF10B_ENST00000542226.1_5'UTR	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	32			P -> L (in dbSNP:rs1129424). {ECO:0000269|PubMed:10072170, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9242611, ECO:0000269|PubMed:9285725, ECO:0000269|PubMed:9325248, ECO:0000269|PubMed:9373179, ECO:0000269|PubMed:9430227, ECO:0000269|Ref.11}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)			NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		GGGGACCCGGGGCCCAGGCCT	0.736													A|||	3753	0.749401	0.7753	0.7493	5008	,	,		13116	0.9107		0.5924	False		,,,				2504	0.7096				p.P32L	GBM(94;1064 1342 1839 21060 42553)	Atlas-SNP	.											.	TNFRSF10B	34	.	0			c.C95T						PASS	.	A	LEU/PRO,LEU/PRO	3291,1103		1260,771,166	13.0	16.0	15.0		95,95	0.1	0.0	8	dbSNP_86	15	5180,3384		1603,1974,705	yes	missense,missense	TNFRSF10B	NM_003842.4,NM_147187.2	98,98	2863,2745,871	AA,AG,GG		39.5142,25.1024,34.6273	benign,benign	32/441,32/412	22926313	8471,4487	2197	4282	6479	SO:0001583	missense	8795	exon1			ACCCGGGGCCCAG	AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.95C>T	8.37:g.22926313G>A	ENSP00000276431:p.Pro32Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_147187	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	1624	0.7435897435897436	384	0.7804878048780488	269	0.7430939226519337	520	0.9090909090909091	451	0.5949868073878628	a	0.028	-1.358005	0.01245	0.748976	0.604858	ENSG00000120889	ENST00000276431;ENST00000347739	T;D	0.83163	-1.44;-1.69	1.32	0.126	0.14722	.	0.377447	0.15516	N	0.258310	T	0.00012	0.0000	N	0.00321	-1.65	0.51482	P	7.900000000005125E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30851	-0.9964	9	0.07482	T	0.82	.	4.2483	0.10682	0.4549:0.0:0.5451:0.0	rs1129424;rs1805039;rs3187295;rs17088926;rs17855358;rs57417067	32;32	O14763;O14763-2	TR10B_HUMAN;.	L	32	ENSP00000276431:P32L;ENSP00000317859:P32L	ENSP00000276431:P32L	P	-	2	0	TNFRSF10B	22982258	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.111000	0.10807	-0.291000	0.09012	-0.521000	0.04368	CCC	G|0.295;A|0.705	0.705	strong		0.736	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187	
WDR90	197335	hgsc.bcm.edu	37	16	717544	717544	+	Silent	SNP	G	G	C	rs3752492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:717544G>C	ENST00000293879.4	+	41	5202	c.5202G>C	c.(5200-5202)acG>acC	p.T1734T	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Silent_p.T1736T|WDR90_ENST00000547944.1_Silent_p.T333T|WDR90_ENST00000315764.4_Silent_p.T285T			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1734										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TGCTCTTCACGGCCGCCCGCA	0.647													G|||	1528	0.305112	0.6188	0.1931	5008	,	,		18687	0.3125		0.1153	False		,,,				2504	0.1483				p.T1734T		Atlas-SNP	.											.	WDR90	107	.	0			c.G5202C						PASS	.	G		2112,2106		537,1038,534	47.0	53.0	51.0		5202	-9.8	0.0	16	dbSNP_107	51	1058,7384		59,940,3222	no	coding-synonymous	WDR90	NM_145294.4		596,1978,3756	CC,CG,GG		12.5326,49.9289,25.0395		1734/1749	717544	3170,9490	2109	4221	6330	SO:0001819	synonymous_variant	197335	exon41			CTTCACGGCCGCC	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.5202G>C	16.37:g.717544G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	14	0.28	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1	602	0.27564102564102566	293	0.5955284552845529	55	0.15193370165745856	179	0.3129370629370629	75	0.09894459102902374	G	1.877	-0.458827	0.04508	0.500711	0.125326	ENSG00000161996	ENST00000546896	.	.	.	4.9	-9.79	0.00494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999985302	.	.	.	.	.	.	T	0.39542	-0.9609	4	0.87932	D	0	.	14.463	0.67465	0.1135:0.396:0.4905:0.0	rs3752492;rs3752492	.	.	.	P	37	.	ENSP00000447915:R37P	R	+	2	0	WDR90	657545	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-4.331000	0.00251	-4.010000	0.00082	-1.168000	0.01747	CGG	G|0.777;C|0.223;A|0.001	0.223	strong		0.647	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
ABHD12B	145447	hgsc.bcm.edu	37	14	51370849	51370849	+	Missense_Mutation	SNP	T	T	C	rs7154732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:51370849T>C	ENST00000337334.2	+	12	1015	c.1000T>C	c.(1000-1002)Ttt>Ctt	p.F334L	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Missense_Mutation_p.F227L|ABHD12B_ENST00000353130.1_Missense_Mutation_p.F257L	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	334			F -> L (in dbSNP:rs7154732). {ECO:0000269|PubMed:15489334}.				hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					GATGGTTATCTTTCCTCCTGG	0.448													T|||	267	0.0533147	0.1437	0.0159	5008	,	,		21545	0.001		0.0378	False		,,,				2504	0.0276				p.F334L		Atlas-SNP	.											.	ABHD12B	53	.	0			c.T1000C						PASS	.	T	LEU/PHE,LEU/PHE	559,3847	249.6+/-257.0	28,503,1672	212.0	210.0	211.0		1000,769	4.9	1.0	14	dbSNP_116	211	313,8287	112.0+/-172.2	5,303,3992	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	22,22	33,806,5664	CC,CT,TT		3.6395,12.6872,6.7046	probably-damaging,probably-damaging	334/363,257/286	51370849	872,12134	2203	4300	6503	SO:0001583	missense	145447	exon12			GTTATCTTTCCTC	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.1000T>C	14.37:g.51370849T>C	ENSP00000336693:p.Phe334Leu	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	192	192	1	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	78	0.03571428571428571	44	0.08943089430894309	5	0.013812154696132596	1	0.0017482517482517483	28	0.036939313984168866	T	26.8	4.774555	0.90108	0.126872	0.036395	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.40756	2.19;1.02;2.22	4.94	4.94	0.65067	.	0.052630	0.85682	D	0.000000	T	0.00936	0.0031	L	0.58510	1.815	0.49915	D	0.999836	D;D	0.65815	0.995;0.985	D;P	0.72075	0.976;0.828	T	0.00244	-1.1883	10	0.51188	T	0.08	-27.9703	12.6506	0.56759	0.0:0.0:0.0:1.0	rs7154732;rs52806964;rs58752453;rs7154732	334;257	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	L	257;334;227	ENSP00000343951:F257L;ENSP00000336693:F334L;ENSP00000379101:F227L	ENSP00000336693:F334L	F	+	1	0	ABHD12B	50440599	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.368000	0.59505	2.161000	0.67846	0.533000	0.62120	TTT	T|0.944;C|0.056	0.056	strong		0.448	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
MDH2	4191	hgsc.bcm.edu	37	7	75687382	75687382	+	Missense_Mutation	SNP	G	G	A	rs111879470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:75687382G>A	ENST00000315758.5	+	4	509	c.415G>A	c.(415-417)Gtc>Atc	p.V139I	MDH2_ENST00000432020.2_Missense_Mutation_p.V139I|MDH2_ENST00000443006.1_Missense_Mutation_p.V32I	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	139					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						CATGATCTGCGTCATTGCCAA	0.592													a|||	4	0.000798722	0.0	0.0	5008	,	,		19731	0.0		0.004	False		,,,				2504	0.0				p.V139I		Atlas-SNP	.											.	MDH2	35	.	0			c.G415A						PASS	.	A	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	57.0	47.0	51.0		415	-4.4	0.9	7	dbSNP_132	51	31,8569	21.0+/-64.5	0,31,4269	yes	missense	MDH2	NM_005918.2	29	0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614	benign	139/339	75687382	34,12972	2203	4300	6503	SO:0001583	missense	4191	exon4			ATCTGCGTCATTG		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.415G>A	7.37:g.75687382G>A	ENSP00000327070:p.Val139Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	1.743	-0.491096	0.04322	6.81E-4	0.003605	ENSG00000146701	ENST00000315758;ENST00000443006;ENST00000432020	D;D;D	0.90676	-2.71;-2.71;-2.71	5.56	-4.41	0.03590	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.347793	0.35903	N	0.002909	T	0.63058	0.2479	N	0.02876	-0.465	0.09310	N	0.999998	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.61456	-0.7059	10	0.02654	T	1	-12.2486	12.6346	0.56677	0.6019:0.0:0.3981:0.0	.	139;139	E9PDB2;P40926	.;MDHM_HUMAN	I	139;32;139	ENSP00000327070:V139I;ENSP00000416929:V32I;ENSP00000408649:V139I	ENSP00000327070:V139I	V	+	1	0	MDH2	75525318	0.934000	0.31675	0.889000	0.34880	0.512000	0.34134	0.266000	0.18534	-0.966000	0.03587	-2.037000	0.00419	GTC	G|0.998;A|0.002	0.002	strong		0.592	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
EFCC1	79825	hgsc.bcm.edu	37	3	128755953	128755953	+	Missense_Mutation	SNP	G	G	A	rs3732430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:128755953G>A	ENST00000480450.1	+	6	1583	c.1583G>A	c.(1582-1584)cGg>cAg	p.R528Q	EFCC1_ENST00000436022.2_Missense_Mutation_p.R91Q			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	528			R -> Q (in dbSNP:rs3732430).				calcium ion binding (GO:0005509)										CAGAGGCTCCGGGACCTGGTA	0.642													G|||	1618	0.323083	0.351	0.281	5008	,	,		16082	0.2063		0.4404	False		,,,				2504	0.3149				p.R528Q		Atlas-SNP	.											.	.	.	.	0			c.G1583A						PASS	.	G	GLN/ARG	1637,2767		317,1003,882	25.0	27.0	26.0		1583	3.5	1.0	3	dbSNP_107	26	3587,5013		743,2101,1456	yes	missense	CCDC48	NM_024768.2	43	1060,3104,2338	AA,AG,GG		41.7093,37.1708,40.1723	possibly-damaging	528/599	128755953	5224,7780	2202	4300	6502	SO:0001583	missense	79825	exon6			GGCTCCGGGACCT	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"""EF-hand domain containing"""	25692	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 73"", ""coiled-coil domain containing 48"""	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1583G>A	3.37:g.128755953G>A	ENSP00000420075:p.Arg528Gln	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_024768	A8MYE2	Missense_Mutation	SNP	ENST00000480450.1	37	CCDS3054.2	719	0.3292124542124542	168	0.34146341463414637	116	0.32044198895027626	101	0.17657342657342656	334	0.44063324538258575	G	24.9	4.580993	0.86748	0.371708	0.417093	ENSG00000114654	ENST00000480450;ENST00000436022	T;T	0.58652	0.48;0.32	4.36	3.48	0.39840	.	0.075929	0.46758	D	0.000280	T	0.00012	0.0000	L	0.54323	1.7	0.24098	P	0.99588451	D	0.56287	0.975	B	0.43680	0.427	T	0.44236	-0.9341	9	0.54805	T	0.06	.	10.1031	0.42517	0.0993:0.0:0.9007:0.0	rs3732430;rs60209959;rs3732430	528	Q9HA90	CCD48_HUMAN	Q	528;91	ENSP00000420075:R528Q;ENSP00000414597:R91Q	ENSP00000414597:R91Q	R	+	2	0	CCDC48	130238643	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.647000	0.54403	1.017000	0.39495	0.591000	0.81541	CGG	G|0.653;A|0.347	0.347	strong		0.642	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768	
C20orf96	140680	hgsc.bcm.edu	37	20	259818	259818	+	Silent	SNP	G	G	A	rs6035541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:259818G>A	ENST00000360321.2	-	5	598	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	C20orf96_ENST00000400269.3_Silent_p.L96L|C20orf96_ENST00000382369.5_Silent_p.L119L	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	154										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CTCACCGCCAGGGTGTCCTGC	0.697													G|||	1490	0.297524	0.2088	0.2622	5008	,	,		5208	0.3304		0.3559	False		,,,				2504	0.3487				p.L154L		Atlas-SNP	.											C20orf96,NS,carcinoma,0,1	C20orf96	28	1	0			c.C460T						PASS	.	G	,	1030,3376	370.5+/-319.6	120,790,1293	72.0	53.0	59.0		457,460	-3.6	0.0	20	dbSNP_114	59	3286,5314	473.6+/-368.6	630,2026,1644	no	coding-synonymous,coding-synonymous	C20orf96	NM_080571.1,NM_153269.2	,	750,2816,2937	AA,AG,GG		38.2093,23.3772,33.1847	,	153/363,154/364	259818	4316,8690	2203	4300	6503	SO:0001819	synonymous_variant	140680	exon5			CCGCCAGGGTGTC	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.460C>T	20.37:g.259818G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Silent	SNP	ENST00000360321.2	37	CCDS12994.1																																																																																			G|0.679;A|0.321	0.321	strong		0.697	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269	
SH2D4A	63898	hgsc.bcm.edu	37	8	19218745	19218745	+	Missense_Mutation	SNP	A	A	G	rs35647122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:19218745A>G	ENST00000265807.3	+	6	1037	c.626A>G	c.(625-627)gAa>gGa	p.E209G	SH2D4A_ENST00000518040.1_Missense_Mutation_p.E164G|SH2D4A_ENST00000519207.1_Missense_Mutation_p.E209G	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	209			E -> G (in dbSNP:rs35647122). {ECO:0000269|PubMed:14702039}.		negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AAACAAGATGAAGAAATAAAT	0.343													A|||	180	0.0359425	0.0023	0.0231	5008	,	,		17894	0.1141		0.0398	False		,,,				2504	0.0061				p.E209G		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A626G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU	44,4362	40.8+/-73.8	0,44,2159	54.0	54.0	54.0		626,491,626	5.6	0.9	8	dbSNP_126	54	357,8243	110.0+/-170.5	7,343,3950	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	98,98,98	7,387,6109	GG,GA,AA		4.1512,0.9986,3.0832	probably-damaging,probably-damaging,probably-damaging	209/455,164/410,209/455	19218745	401,12605	2203	4300	6503	SO:0001583	missense	63898	exon6			AAGATGAAGAAAT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.626A>G	8.37:g.19218745A>G	ENSP00000265807:p.Glu209Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	107	0.04899267399267399	3	0.006097560975609756	10	0.027624309392265192	67	0.11713286713286714	27	0.03562005277044855	A	15.96	2.988095	0.53934	0.009986	0.041512	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207;ENST00000523736	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	5.61	5.61	0.85477	.	0.594604	0.17751	N	0.163223	T	0.00637	0.0021	M	0.80847	2.515	0.26366	P	0.9769664	P;D	0.61080	0.877;0.989	B;P	0.55749	0.417;0.783	T	0.11275	-1.0594	9	0.45353	T	0.12	.	12.1915	0.54275	1.0:0.0:0.0:0.0	rs35647122	164;209	B4DDR1;Q9H788	.;SH24A_HUMAN	G	209;164;209;168	ENSP00000265807:E209G;ENSP00000429482:E164G;ENSP00000428684:E209G;ENSP00000428048:E168G	ENSP00000265807:E209G	E	+	2	0	SH2D4A	19263025	1.000000	0.71417	0.928000	0.36995	0.329000	0.28539	4.210000	0.58500	2.133000	0.65898	0.533000	0.62120	GAA	A|0.963;G|0.037	0.037	strong		0.343	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
LRRC16A	55604	hgsc.bcm.edu	37	6	25420350	25420350	+	Silent	SNP	A	A	C	rs41271807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	127	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	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	
ETV6	2120	hgsc.bcm.edu	37	12	11992168	11992168	+	Silent	SNP	G	G	A	rs11611479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11992168G>A	ENST00000396373.4	+	3	532	c.258G>A	c.(256-258)acG>acA	p.T86T		NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	86	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	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 positive regulation of transcription (GO:0001077)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				ACAGCAACACGTTTGAAATGA	0.488			T	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""	"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""								G|||	1066	0.212859	0.23	0.111	5008	,	,		21183	0.2192		0.1093	False		,,,				2504	0.362				p.T86T		Atlas-SNP	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"""L, E, M"""	.	ETV6	91	.	0			c.G258A						PASS	.	G		815,3591	326.9+/-299.8	75,665,1463	114.0	106.0	109.0		258	-6.2	0.6	12	dbSNP_120	109	887,7713	199.3+/-243.4	53,781,3466	no	coding-synonymous	ETV6	NM_001987.4		128,1446,4929	AA,AG,GG		10.314,18.4975,13.0863		86/453	11992168	1702,11304	2203	4300	6503	SO:0001819	synonymous_variant	2120	exon3			CAACACGTTTGAA	BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"""TEL oncogene"""	600618	"""ets variant gene 6 (TEL oncogene)"""			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.258G>A	12.37:g.11992168G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	166	92	0.554217	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Silent	SNP	ENST00000396373.4	37	CCDS8643.1																																																																																			G|0.850;A|0.150	0.150	strong		0.488	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987	
HBQ1	3049	hgsc.bcm.edu	37	16	230578	230578	+	Silent	SNP	A	A	G	rs11863726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:230578A>G	ENST00000199708.2	+	1	127	c.93A>G	c.(91-93)gaA>gaG	p.E31E	Y_RNA_ENST00000384514.1_RNA	NM_005331.4	NP_005322.1	P09105	HBAT_HUMAN	hemoglobin, theta 1	31					oxygen transport (GO:0015671)	hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			large_intestine(1)	1		all_cancers(16;2.03e-06)|all_epithelial(16;5.16e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0138)|all_lung(18;0.0306)				AGGCCCTGGAAAGGTGCGGCA	0.736													G|||	1021	0.203874	0.5522	0.1081	5008	,	,		7023	0.004		0.0974	False		,,,				2504	0.1166				p.E31E		Atlas-SNP	.											.	HBQ1	4	.	0			c.A93G						PASS	.	G		1020,2422		86,848,787	2.0	3.0	3.0		93	2.5	1.0	16	dbSNP_120	3	483,6397		14,455,2971	no	coding-synonymous	HBQ1	NM_005331.4		100,1303,3758	GG,GA,AA		7.0203,29.6339,14.5611		31/143	230578	1503,8819	1721	3440	5161	SO:0001819	synonymous_variant	3049	exon1			CCTGGAAAGGTGC	BC056686	CCDS10400.1	16p13.3	2014-05-19			ENSG00000086506	ENSG00000086506			4833	protein-coding gene	gene with protein product		142240				2649166	Standard	NM_005331		Approved	HBQ	uc002cfz.3	P09105	OTTHUMG00000060727	ENST00000199708.2:c.93A>G	16.37:g.230578A>G		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	15	8	0.533333	NM_005331	Q13723|Q1W6G5	Silent	SNP	ENST00000199708.2	37	CCDS10400.1																																																																																			A|0.830;G|0.170	0.170	strong		0.736	HBQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134226.1	NM_005331	
PHF11	51131	hgsc.bcm.edu	37	13	50080847	50080847	+	Silent	SNP	A	A	G	rs2031532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50080847A>G	ENST00000378319.3	+	2	212	c.171A>G	c.(169-171)ctA>ctG	p.L57L	PHF11_ENST00000488958.1_Silent_p.L18L|PHF11_ENST00000357596.3_Silent_p.L18L	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	57					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		ATAATGTCCTATACTTTGCAC	0.373													G|||	3917	0.782149	0.9145	0.745	5008	,	,		17033	0.873		0.6421	False		,,,				2504	0.68				p.L57L		Atlas-SNP	.											.	PHF11	20	.	0			c.A171G						PASS	.	G	,	3871,535	243.1+/-252.9	1698,475,30	108.0	93.0	98.0	http://www.ncbi.nlm.nih.gov/pubmed?term	171,54	-1.3	0.2	13	dbSNP_94	98	5533,3067	471.2+/-368.0	1800,1933,567	yes	coding-synonymous,coding-synonymous	PHF11	NM_001040443.1,NM_001040444.1	,	3498,2408,597	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	35.6628,12.1425,27.6949	,	57/332,18/293	50080847	9404,3602	2203	4300	6503	SO:0001819	synonymous_variant	51131	exon2			TGTCCTATACTTT	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"""Zinc fingers, PHD-type"""	17024	protein-coding gene	gene with protein product	"""IgE responsiveness (atopic)"""	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.171A>G	13.37:g.50080847A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Silent	SNP	ENST00000378319.3	37	CCDS31975.1																																																																																			A|0.238;G|0.762	0.762	strong		0.373	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549525	32549525	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549525C>G	ENST00000360004.5	-	3	566	c.461G>C	c.(460-462)gGc>gCc	p.G154A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	154	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)|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						TTCAATGCTGCCTGGATAGAA	0.542										Multiple Myeloma(14;0.17)																											p.G154A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G461C						PASS	.						97.0	115.0	109.0					6																	32549525		1511	2709	4220	SO:0001583	missense	3123	exon3			ATGCTGCCTGGAT	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.461G>C	6.37:g.32549525C>G	ENSP00000353099:p.Gly154Ala	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	233	34	0.145923	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	13.63	2.293183	0.40594	.	.	ENSG00000196126	ENST00000360004	T	0.08370	3.1	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.367213	0.29551	N	0.011839	T	0.03011	0.0089	L	0.33137	0.985	0.27655	N	0.947267	B	0.30605	0.287	B	0.33454	0.164	T	0.27806	-1.0063	10	0.87932	D	0	.	9.8873	0.41268	0.0:0.7906:0.2094:0.0	rs1059352;rs1059620;rs3200389	154	P01911	2B1F_HUMAN	A	154	ENSP00000353099:G154A	ENSP00000353099:G154A	G	-	2	0	HLA-DRB1	32657503	0.002000	0.14202	0.957000	0.39632	0.929000	0.56500	1.302000	0.33459	1.883000	0.54544	0.453000	0.30009	GGC	C|0.932;G|0.068	0.068	strong		0.542	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
NIT1	4817	hgsc.bcm.edu	37	1	161088583	161088583	+	Missense_Mutation	SNP	T	T	G	rs41270017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161088583T>G	ENST00000368009.2	+	2	86	c.10T>G	c.(10-12)Ttc>Gtc	p.F4V	NIT1_ENST00000368007.4_Intron|DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000392190.5_5'UTR|PFDN2_ENST00000368010.3_5'Flank|PFDN2_ENST00000468311.1_5'Flank|NIT1_ENST00000368008.1_Missense_Mutation_p.F4V|NIT1_ENST00000496861.1_3'UTR	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	4					nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CAGGCTGGGCTTCATCACCAG	0.483													T|||	465	0.0928514	0.1067	0.0663	5008	,	,		20822	0.0675		0.0736	False		,,,				2504	0.1391				p.F4V		Atlas-SNP	.											.	NIT1	41	.	0			c.T10G						PASS	.	T	VAL/PHE,,,VAL/PHE	510,3896	236.8+/-248.8	35,440,1728	156.0	130.0	139.0		10,,,10	2.5	1.0	1	dbSNP_127	139	681,7919	170.7+/-221.8	32,617,3651	yes	missense,intron,utr-5,missense	NIT1	NM_001185092.1,NM_001185093.1,NM_001185094.1,NM_005600.2	50,,,50	67,1057,5379	GG,GT,TT		7.9186,11.5751,9.1573	benign,,,benign	4/244,,,4/328	161088583	1191,11815	2203	4300	6503	SO:0001583	missense	4817	exon2			CTGGGCTTCATCA	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.10T>G	1.37:g.161088583T>G	ENSP00000356988:p.Phe4Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_001185092	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	37	CCDS1218.1	160	0.07326007326007326	48	0.0975609756097561	21	0.058011049723756904	36	0.06293706293706294	55	0.07255936675461741	T	11.11	1.542148	0.27563	0.115751	0.079186	ENSG00000158793	ENST00000368009;ENST00000368008	T;D	0.81739	-0.94;-1.53	5.0	2.52	0.30459	.	0.719779	0.12631	N	0.452160	T	0.46073	0.1374	N	0.14661	0.345	0.09310	P	0.99999999791456	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10847	-1.0612	9	0.31617	T	0.26	-1.1472	9.2106	0.37316	0.0:0.0:0.3544:0.6456	rs41270017	4;4	B1AQP4;Q86X76	.;NIT1_HUMAN	V	4	ENSP00000356988:F4V;ENSP00000356987:F4V	ENSP00000356987:F4V	F	+	1	0	NIT1	159355207	0.995000	0.38212	1.000000	0.80357	0.969000	0.65631	0.594000	0.24014	0.903000	0.36546	0.533000	0.62120	TTC	T|0.917;G|0.083	0.083	strong		0.483	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1		
SGSM2	9905	hgsc.bcm.edu	37	17	2266799	2266799	+	Missense_Mutation	SNP	G	G	A	rs745400	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2266799G>A	ENST00000426855.2	+	7	888	c.713G>A	c.(712-714)aGg>aAg	p.R238K	SGSM2_ENST00000574563.1_Missense_Mutation_p.R238K|SGSM2_ENST00000268989.3_Missense_Mutation_p.R238K	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	238			R -> K (in dbSNP:rs745400). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17509819}.		late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TCGGAGGACAGGCTGGCTGCC	0.647													G|||	2765	0.552117	0.4962	0.3386	5008	,	,		17006	0.7639		0.4284	False		,,,				2504	0.6881				p.R238K		Atlas-SNP	.											.	SGSM2	60	.	0			c.G713A						PASS	.	G	LYS/ARG,LYS/ARG	2166,2240		549,1068,586	24.0	27.0	26.0		713,713	3.7	1.0	17	dbSNP_86	26	3936,4656		912,2112,1272	yes	missense,missense	SGSM2	NM_001098509.1,NM_014853.2	26,26	1461,3180,1858	AA,AG,GG		45.8101,49.1602,46.9457	benign,benign	238/1007,238/1052	2266799	6102,6896	2203	4296	6499	SO:0001583	missense	9905	exon7			AGGACAGGCTGGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.713G>A	17.37:g.2266799G>A	ENSP00000415107:p.Arg238Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	88	0.977778	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Missense_Mutation	SNP	ENST00000426855.2	37	CCDS45570.1	1135	0.5196886446886447	236	0.4796747967479675	138	0.3812154696132597	426	0.7447552447552448	335	0.4419525065963061	G	16.77	3.215159	0.58452	0.491602	0.458101	ENSG00000141258	ENST00000268989;ENST00000426855	T;T	0.12879	2.64;2.67	5.73	3.73	0.42828	.	0.152619	0.56097	D	0.000035	T	0.00012	0.0000	L	0.31926	0.97	0.26048	P	0.9815136	B;B;B	0.12630	0.004;0.006;0.006	B;B;B	0.14023	0.01;0.005;0.009	T	0.12682	-1.0538	9	0.25106	T	0.35	-20.9523	9.2868	0.37762	0.221:0.0:0.779:0.0	rs745400;rs3815470;rs17857177;rs57385222;rs745400	238;238;238	O43147-5;O43147;O43147-2	.;SGSM2_HUMAN;.	K	238	ENSP00000268989:R238K;ENSP00000415107:R238K	ENSP00000268989:R238K	R	+	2	0	SGSM2	2213549	0.979000	0.34478	0.994000	0.49952	0.823000	0.46562	2.476000	0.45171	1.440000	0.47531	0.655000	0.94253	AGG	G|0.501;A|0.499	0.499	strong		0.647	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
IL34	146433	hgsc.bcm.edu	37	16	70693991	70693991	+	Silent	SNP	C	C	T	rs138439611		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70693991C>T	ENST00000288098.2	+	6	1013	c.630C>T	c.(628-630)acC>acT	p.T210T	IL34_ENST00000429149.2_Silent_p.T210T|IL34_ENST00000566361.1_Silent_p.T185T|FLJ00418_ENST00000597002.1_5'Flank	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	210					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						ATGCGGCCACCCAGCTGTACC	0.652																																					p.T210T		Atlas-SNP	.											.	IL34	26	.	0			c.C630T						PASS	.	C	,,	0,4396		0,0,2198	84.0	94.0	91.0		627,630,630	-1.8	0.0	16	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	,,	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	,,	209/242,210/243,210/243	70693991	2,12994	2198	4300	6498	SO:0001819	synonymous_variant	146433	exon7			GGCCACCCAGCTG	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"""Interleukins and interleukin receptors"""	28529	protein-coding gene	gene with protein product		612081	"""chromosome 16 open reading frame 77"""	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.630C>T	16.37:g.70693991C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	189	65	0.343915	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Silent	SNP	ENST00000288098.2	37	CCDS10895.1																																																																																			C|1.000;T|0.000	0.000	weak		0.652	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
TAF4	6874	hgsc.bcm.edu	37	20	60572663	60572663	+	Silent	SNP	C	C	A	rs2296081	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60572663C>A	ENST00000252996.4	-	14	3032	c.3033G>T	c.(3031-3033)gcG>gcT	p.A1011A		NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	1011					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)			TGGGCCCGATCGCTGCTAGTG	0.547													C|||	2940	0.587061	0.4849	0.5879	5008	,	,		16162	0.6528		0.672	False		,,,				2504	0.5695				p.A1011A		Atlas-SNP	.											TAF4,caecum,carcinoma,0,1	TAF4	84	1	0			c.G3033T						scavenged	.	C		2255,2151	596.2+/-388.6	584,1087,532	142.0	128.0	132.0		3033	-10.1	0.1	20	dbSNP_100	132	5654,2946	668.9+/-402.6	1876,1902,522	no	coding-synonymous	TAF4	NM_003185.3		2460,2989,1054	AA,AC,CC		34.2558,48.8198,39.1896		1011/1086	60572663	7909,5097	2203	4300	6503	SO:0001819	synonymous_variant	6874	exon14			CCCGATCGCTGCT	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.3033G>T	20.37:g.60572663C>A		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Silent	SNP	ENST00000252996.4	37	CCDS33500.1																																																																																			A|0.613;C|0.387;T|0.000	0.613	strong		0.547	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185	
CDHR2	54825	hgsc.bcm.edu	37	5	176004680	176004680	+	Missense_Mutation	SNP	A	A	C	rs34767982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176004680A>C	ENST00000510636.1	+	14	1667	c.1393A>C	c.(1393-1395)Atg>Ctg	p.M465L	CDHR2_ENST00000506348.1_Missense_Mutation_p.M465L|CDHR2_ENST00000261944.5_Missense_Mutation_p.M465L	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	465	Cadherin 4. {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						CTCCGTCGCCATGGTGACCAT	0.632													A|||	98	0.0195687	0.0333	0.0072	5008	,	,		18027	0.0		0.0229	False		,,,				2504	0.0266				p.M465L		Atlas-SNP	.											.	CDHR2	152	.	0			c.A1393C						PASS	.	A	LEU/MET,LEU/MET	129,4277	95.3+/-134.0	0,129,2074	90.0	82.0	85.0		1393,1393	-5.5	0.0	5	dbSNP_126	85	150,8450	73.2+/-135.9	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	15,15	2,275,6226	CC,CA,AA		1.7442,2.9278,2.1452	benign,benign	465/1311,465/1311	176004680	279,12727	2203	4300	6503	SO:0001583	missense	54825	exon14			GTCGCCATGGTGA	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.1393A>C	5.37:g.176004680A>C	ENSP00000424565:p.Met465Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	33	0.01510989010989011	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	13.81	2.349616	0.41599	0.029278	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.59772	0.24;0.24;0.24	4.8	-5.53	0.02552	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.06826	0.0174	N	0.05012	-0.13	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06250	-1.0837	9	0.44086	T	0.13	0.0331	2.189	0.03894	0.446:0.2189:0.0691:0.266	rs34767982;rs62404700	465	Q9BYE9	CDHR2_HUMAN	L	465	ENSP00000424565:M465L;ENSP00000261944:M465L;ENSP00000421078:M465L	ENSP00000261944:M465L	M	+	1	0	CDHR2	175937286	0.063000	0.20901	0.000000	0.03702	0.408000	0.30992	0.800000	0.27042	-1.193000	0.02688	0.391000	0.25812	ATG	A|0.979;C|0.021	0.021	strong		0.632	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
NID1	4811	hgsc.bcm.edu	37	1	236141174	236141174	+	Missense_Mutation	SNP	T	T	C	rs3213190	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236141174T>C	ENST00000264187.6	-	20	3819	c.3737A>G	c.(3736-3738)cAg>cGg	p.Q1246R	NID1_ENST00000366595.3_Missense_Mutation_p.Q1113R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1246			Q -> R (in dbSNP:rs3213190). {ECO:0000269|PubMed:2471408, ECO:0000269|PubMed:2574658, ECO:0000269|PubMed:7557988}.		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)	TCTTCATTTCTGTTCGATACA	0.502													C|||	1724	0.344249	0.385	0.2608	5008	,	,		21512	0.6131		0.1451	False		,,,				2504	0.2761				p.Q1246R		Atlas-SNP	.											.	NID1	196	.	0			c.A3737G						PASS	.	C	ARG/GLN	1539,2867	671.9+/-402.5	257,1025,921	109.0	106.0	107.0		3737	2.8	1.0	1	dbSNP_106	107	1504,7096	748.1+/-407.3	123,1258,2919	yes	missense	NID1	NM_002508.2	43	380,2283,3840	CC,CT,TT		17.4884,34.9296,23.3969	benign	1246/1248	236141174	3043,9963	2203	4300	6503	SO:0001583	missense	4811	exon20			CATTTCTGTTCGA	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.3737A>G	1.37:g.236141174T>C	ENSP00000264187:p.Gln1246Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	712	0.326007326007326	174	0.35365853658536583	86	0.23756906077348067	348	0.6083916083916084	104	0.13720316622691292	C	5.517	0.280385	0.10458	0.349296	0.174884	ENSG00000116962	ENST00000264187;ENST00000366595	T;D	0.86769	-1.48;-2.17	5.67	2.79	0.32731	.	0.054020	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00075	-2.25	0.58432	P	2.9999999999752447E-6	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	.	7.3131	0.26485	0.1194:0.6886:0.0:0.1919	rs3213190;rs3768077;rs60739893;rs3213190	1113;1246	P14543-2;P14543	.;NID1_HUMAN	R	1246;1113	ENSP00000264187:Q1246R;ENSP00000355554:Q1113R	ENSP00000264187:Q1246R	Q	-	2	0	NID1	234207797	0.971000	0.33674	0.953000	0.39169	0.928000	0.56348	0.131000	0.15870	0.072000	0.16694	-0.226000	0.12346	CAG	T|0.706;C|0.293	0.293	strong		0.502	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
CHFR	55743	hgsc.bcm.edu	37	12	133423695	133423695	+	Silent	SNP	A	A	G	rs2306537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133423695A>G	ENST00000432561.2	-	15	1778	c.1705T>C	c.(1705-1707)Ttg>Ctg	p.L569L	CHFR_ENST00000537522.1_Silent_p.L191L|CHFR_ENST00000315585.7_Silent_p.L528L|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000266880.7_Silent_p.L568L|CHFR_ENST00000450056.2_Silent_p.L557L|CHFR_ENST00000541341.1_5'UTR|CHFR_ENST00000443047.2_Silent_p.L477L			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	569					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TTCCATGTCAAACCTCTGGTT	0.458													A|||	713	0.142372	0.0106	0.1571	5008	,	,		19964	0.1736		0.2803	False		,,,				2504	0.136				p.L569L		Atlas-SNP	.											.	CHFR	83	.	0			c.T1705C						PASS	.	A	,,,,	223,4183	136.5+/-172.5	9,205,1989	102.0	104.0	103.0		1705,1702,1669,1429,1582	2.2	1.0	12	dbSNP_100	103	2569,6031	416.9+/-352.3	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GA,AA		29.8721,5.0613,21.467	,,,,	569/665,568/664,557/653,477/573,528/624	133423695	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon15			ATGTCAAACCTCT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1705T>C	12.37:g.133423695A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			A|0.803;G|0.197	0.197	strong		0.458	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
MTR	4548	hgsc.bcm.edu	37	1	237054569	237054569	+	Silent	SNP	A	A	G	rs2229276	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:237054569A>G	ENST00000366577.5	+	29	3538	c.3144A>G	c.(3142-3144)gcA>gcG	p.A1048A	MTR_ENST00000535889.1_Silent_p.A997A	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	1048	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)	ACCTGTACGCAGAGGCTGCTG	0.547													A|||	1619	0.323283	0.149	0.4323	5008	,	,		17877	0.4276		0.3857	False		,,,				2504	0.3098				p.A1048A		Atlas-SNP	.											.	MTR	127	.	0			c.A3144G						PASS	.	A		874,3532	338.6+/-305.4	86,702,1415	110.0	107.0	108.0		3144	-11.0	0.0	1	dbSNP_98	108	3555,5045	516.9+/-378.9	747,2061,1492	no	coding-synonymous	MTR	NM_000254.2		833,2763,2907	GG,GA,AA		41.3372,19.8366,34.0535		1048/1266	237054569	4429,8577	2203	4300	6503	SO:0001819	synonymous_variant	4548	exon29			GTACGCAGAGGCT	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.3144A>G	1.37:g.237054569A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	37	CCDS1614.1																																																																																			A|0.658;G|0.342	0.342	strong		0.547	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
TXLNB	167838	hgsc.bcm.edu	37	6	139564101	139564101	+	Silent	SNP	C	C	T	rs12529180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	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	
CCDC185	164127	hgsc.bcm.edu	37	1	223567803	223567803	+	Missense_Mutation	SNP	G	G	A	rs10907376	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223567803G>A	ENST00000366875.3	+	1	1089	c.986G>A	c.(985-987)gGc>gAc	p.G329D		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		329			G -> D (in dbSNP:rs10907376). {ECO:0000269|PubMed:15489334}.							breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GAGCAGCGCGGCCTGCGGCGG	0.697													G|||	881	0.175919	0.1831	0.1916	5008	,	,		14025	0.1101		0.2734	False		,,,				2504	0.1227				p.G329D		Atlas-SNP	.											C1orf65,NS,carcinoma,0,4	C1orf65	71	4	0			c.G986A						PASS	.	G	ASP/GLY	834,3424		100,634,1395	11.0	10.0	11.0		986	-0.7	0.0	1	dbSNP_120	11	2191,6245		296,1599,2323	no	missense	C1orf65	NM_152610.2	94	396,2233,3718	AA,AG,GG		25.972,19.5867,23.8302	probably-damaging	329/624	223567803	3025,9669	2129	4218	6347	SO:0001583	missense	164127	exon1			AGCGCGGCCTGCG																												ENST00000366875.3:c.986G>A	1.37:g.223567803G>A	ENSP00000355840:p.Gly329Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	448	0.20512820512820512	88	0.17886178861788618	86	0.23756906077348067	72	0.1258741258741259	202	0.26649076517150394	G	5.552	0.286677	0.10513	0.195867	0.25972	ENSG00000178395	ENST00000366875	T	0.23147	1.92	4.71	-0.728	0.11162	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.29432	0.244	B	0.24848	0.056	T	0.42292	-0.9460	8	0.17369	T	0.5	.	1.5099	0.02494	0.1275:0.3469:0.209:0.3166	rs10907376;rs17481328;rs17852895;rs17858889;rs58442298;rs10907376	329	Q8N715	CA065_HUMAN	D	329	ENSP00000355840:G329D	ENSP00000355840:G329D	G	+	2	0	C1orf65	221634426	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.021000	0.12504	-0.055000	0.13244	0.650000	0.86243	GGC	G|0.814;A|0.186	0.186	strong		0.697	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
GLRX3	10539	hgsc.bcm.edu	37	10	131959150	131959150	+	Missense_Mutation	SNP	C	C	T	rs2274217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:131959150C>T	ENST00000368644.1	+	4	389	c.367C>T	c.(367-369)Ccc>Tcc	p.P123S	GLRX3_ENST00000331244.5_Missense_Mutation_p.P123S	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	123			P -> S (in dbSNP:rs2274217). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CTCCTTCCTACCCAGCGCTAA	0.438													C|||	957	0.191094	0.1241	0.1282	5008	,	,		16273	0.1101		0.2853	False		,,,				2504	0.3129				p.P123S		Atlas-SNP	.											TXNL2,colon,carcinoma,0,2	GLRX3	39	2	0			c.C367T						PASS	.	C	SER/PRO,SER/PRO	596,3810	261.9+/-264.6	47,502,1654	114.0	101.0	106.0		367,367	4.4	0.2	10	dbSNP_100	106	2244,6356	381.3+/-340.0	315,1614,2371	yes	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	74,74	362,2116,4025	TT,TC,CC		26.093,13.527,21.8361	benign,benign	123/336,123/336	131959150	2840,10166	2203	4300	6503	SO:0001583	missense	10539	exon4			TTCCTACCCAGCG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.367C>T	10.37:g.131959150C>T	ENSP00000357633:p.Pro123Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	386	0.17673992673992675	64	0.13008130081300814	53	0.1464088397790055	56	0.0979020979020979	213	0.28100263852242746	C	2.176	-0.388811	0.04932	0.13527	0.26093	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.08546	3.08;3.08	4.39	4.39	0.52855	Thioredoxin-like fold (1);	0.372544	0.26227	N	0.025598	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	0.45249	-0.9274	9	0.08381	T	0.77	-2.8796	10.9948	0.47569	0.0:0.6927:0.3073:0.0	rs2274217;rs17297963;rs2274217	123	O76003	GLRX3_HUMAN	S	123	ENSP00000330836:P123S;ENSP00000357633:P123S	ENSP00000330836:P123S	P	+	1	0	GLRX3	131849140	0.090000	0.21635	0.206000	0.23566	0.141000	0.21300	0.666000	0.25097	2.284000	0.76573	0.655000	0.94253	CCC	C|0.799;T|0.201	0.201	strong		0.438	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
TMEM240	339453	hgsc.bcm.edu	37	1	1471126	1471126	+	Silent	SNP	G	G	A	rs114114317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1471126G>A	ENST00000378733.4	-	3	226	c.216C>T	c.(214-216)gaC>gaT	p.D72D	TMEM240_ENST00000425828.1_Silent_p.D72D	NM_001114748.1	NP_001108220.1	Q5SV17	TM240_HUMAN	transmembrane protein 240	72						integral component of membrane (GO:0016021)											TCTCGGAGGCGTCCACCACCG	0.647													G|||	20	0.00399361	0.0015	0.0043	5008	,	,		10251	0.0		0.0149	False		,,,				2504	0.0				p.D72D		Atlas-SNP	.											.	TMEM240	8	.	0			c.C216T						PASS	.	G		2,1382		0,2,690	66.0	69.0	68.0		216	2.5	1.0	1	dbSNP_132	68	37,3145		0,37,1554	no	coding-synonymous	C1orf70	NM_001114748.1		0,39,2244	AA,AG,GG		1.1628,0.1445,0.8541		72/174	1471126	39,4527	692	1591	2283	SO:0001819	synonymous_variant	339453	exon3			GGAGGCGTCCACC		CCDS44040.1	1p36.33	2011-11-25	2011-11-25	2011-11-25	ENSG00000205090	ENSG00000205090			25186	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 70"""	C1orf70			Standard	NM_001114748		Approved		uc009vkf.3	Q5SV17	OTTHUMG00000042193	ENST00000378733.4:c.216C>T	1.37:g.1471126G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_001114748	B9EJG7	Silent	SNP	ENST00000378733.4	37	CCDS44040.1																																																																																			G|0.994;A|0.006	0.006	strong		0.647	TMEM240-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100391.2	NM_001114748	
FBXL19	54620	hgsc.bcm.edu	37	16	30936081	30936081	+	Missense_Mutation	SNP	G	G	A	rs35675346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30936081G>A	ENST00000380310.2	+	1	186	c.28G>A	c.(28-30)Gaa>Aaa	p.E10K	FBXL19_ENST00000471231.2_Intron|FBXL19-AS1_ENST00000563777.1_RNA|FBXL19_ENST00000562319.1_5'UTR|FBXL19_ENST00000565690.1_5'Flank|FBXL19_ENST00000338343.4_Intron	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	10					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						CGGAAAGGGGGAATCTGGGGT	0.632													g|||	1670	0.333466	0.2943	0.3501	5008	,	,		13277	0.0863		0.2505	False		,,,				2504	0.7147				p.E10K		Atlas-SNP	.											.	FBXL19	74	.	0			c.G28A						PASS	.		LYS/GLU	1003,2613		141,721,946	27.0	29.0	28.0		28	3.9	1.0	16	dbSNP_126	28	1843,6301		225,1393,2454	yes	missense	FBXL19	NM_001099784.2	56	366,2114,3400	AA,AG,GG		22.6302,27.7378,24.2007	benign	10/695	30936081	2846,8914	1808	4072	5880	SO:0001583	missense	54620	exon1			AAGGGGGAATCTG	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"""F-boxes / Leucine-rich repeats"""	25300	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1C"""	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.28G>A	16.37:g.30936081G>A	ENSP00000369666:p.Glu10Lys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	37	CCDS45465.1	481	0.22023809523809523	138	0.2804878048780488	113	0.31215469613259667	37	0.06468531468531469	193	0.2546174142480211	g	11.95	1.791506	0.31685	0.277378	0.226302	ENSG00000099364	ENST00000380310	T	0.16457	2.34	3.88	3.88	0.44766	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.45648	P	0.001422999999999952	B	0.23377	0.084	B	0.14023	0.01	T	0.35475	-0.9787	8	0.02654	T	1	.	11.6992	0.51560	0.0:0.0:1.0:0.0	rs35675346;rs35675346	10	Q6PCT2	FXL19_HUMAN	K	10	ENSP00000369666:E10K	ENSP00000369666:E10K	E	+	1	0	FBXL19	30843582	0.435000	0.25577	0.961000	0.40146	0.626000	0.37791	0.240000	0.18042	1.850000	0.53721	0.306000	0.20318	GAA	G|0.772;A|0.228	0.228	strong		0.632	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085	
SLC4A11	83959	hgsc.bcm.edu	37	20	3211235	3211235	+	Silent	SNP	C	C	T	rs6084312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3211235C>T	ENST00000380056.3	-	11	1436	c.1389G>A	c.(1387-1389)acG>acA	p.T463T	SLC4A11_ENST00000488544.1_5'Flank|SLC4A11_ENST00000380059.3_Silent_p.T490T|SLC4A11_ENST00000539553.2_Silent_p.T447T	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	463	Membrane (bicarbonate transporter).				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.T490T(1)|p.T463T(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						TCCACAGGCCCGTCCATGCGT	0.562													C|||	226	0.0451278	0.0174	0.0749	5008	,	,		19253	0.001		0.1352	False		,,,				2504	0.0143				p.T490T	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	2	Substitution - coding silent(2)	lung(2)	c.G1470A						PASS	.	C	,,	174,4232	115.0+/-153.0	4,166,2033	103.0	105.0	104.0		1341,1470,1389	-9.8	0.1	20	dbSNP_114	104	1007,7593	217.0+/-255.8	71,865,3364	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	75,1031,5397	TT,TC,CC		11.7093,3.9492,9.0804	,,	447/876,490/919,463/892	3211235	1181,11825	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon12			CAGGCCCGTCCAT	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.1389G>A	20.37:g.3211235C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			C|0.926;T|0.074	0.074	strong		0.562	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
IQGAP3	128239	hgsc.bcm.edu	37	1	156518379	156518379	+	Missense_Mutation	SNP	G	G	A	rs744224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	101	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	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	
LRRN2	10446	hgsc.bcm.edu	37	1	204587047	204587047	+	Missense_Mutation	SNP	G	G	A	rs11588857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204587047G>A	ENST00000367175.1	-	1	4286	c.2074C>T	c.(2074-2076)Cca>Tca	p.P692S	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367177.3_Missense_Mutation_p.P692S|LRRN2_ENST00000367176.3_Missense_Mutation_p.P692S|LRRN2_ENST00000496057.1_5'Flank			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	97	0	0		WXS	Illumina HiSeq	Phase_I	126	44	0.349206	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	
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	rs549924845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5878458G>A	ENST00000537935.1	-	1	506	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	159						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)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATGTACAGGCTCCTCAGG	0.507													G|||	10	0.00199681	0.0068	0.0	5008	,	,		18808	0.0		0.0	False		,,,				2504	0.001				p.L159L		Atlas-SNP	.											OR52E8,NS,carcinoma,0,1	OR52E8	54	1	0			c.C475T						scavenged	.						135.0	147.0	143.0					11																	5878458		2154	4296	6450	SO:0001819	synonymous_variant	390079	exon1			TGTACAGGCTCCT	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"""GPCR / Class A : Olfactory receptors"""	15217	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily E, member 8 pseudogene"""				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.475C>T	11.37:g.5878458G>A		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	136	8	0.0588235	NM_001005168	B9EH38	Silent	SNP	ENST00000537935.1	37	CCDS31400.1																																																																																			.	.	none		0.507	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33535060	33535060	+	Missense_Mutation	SNP	G	G	A	rs25754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	39	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	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	
RNF32	140545	hgsc.bcm.edu	37	7	156468559	156468559	+	Splice_Site	SNP	T	T	C	rs3823617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:156468559T>C	ENST00000405335.1	+	9	1261		c.e9+2		RNF32_ENST00000317955.5_Splice_Site|RNF32_ENST00000311822.8_Splice_Site|RNF32_ENST00000392743.2_Splice_Site|RNF32_ENST00000343665.4_Splice_Site|LMBR1_ENST00000430825.2_Intron|RNF32_ENST00000432459.2_Splice_Site			Q9H0A6	RNF32_HUMAN	ring finger protein 32							aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		CAAGTGCAGGTAGGTTTGGCT	0.542													T|||	365	0.0728834	0.1324	0.0303	5008	,	,		17816	0.1111		0.0447	False		,,,				2504	0.0123				.		Atlas-SNP	.											.	RNF32	77	.	0			c.852+2T>C						PASS	.	T	,,	453,3953	216.1+/-234.9	27,399,1777	91.0	85.0	87.0		,,	5.2	1.0	7	dbSNP_107	87	264,8336	100.8+/-162.1	3,258,4039	yes	splice-5,splice-5,splice-5	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	,,	30,657,5816	CC,CT,TT		3.0698,10.2814,5.5128	,,	,,	156468559	717,12289	2203	4300	6503	SO:0001630	splice_region_variant	140545	exon8			TGCAGGTAGGTTT		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.852+2T>C	7.37:g.156468559T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_030936	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Splice_Site	SNP	ENST00000405335.1	37	CCDS5944.1	162	0.07417582417582418	47	0.09552845528455285	14	0.03867403314917127	69	0.12062937062937062	32	0.04221635883905013	T	9.898	1.206101	0.22205	0.102814	0.030698	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000311822;ENST00000392743;ENST00000343665	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.782	0.69774	0.0:0.0:0.0:1.0	rs3823617;rs3823617	.	.	.	.	-1	.	.	.	+	.	.	RNF32	156161320	1.000000	0.71417	0.997000	0.53966	0.034000	0.12701	4.903000	0.63272	1.974000	0.57490	0.528000	0.53228	.	T|0.934;C|0.066	0.066	strong		0.542	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	Intron
RUVBL2	10856	hgsc.bcm.edu	37	19	49513273	49513273	+	Silent	SNP	C	C	T	rs1062708	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49513273C>T	ENST00000595090.1	+	8	1077	c.613C>T	c.(613-615)Ctg>Ttg	p.L205L	RUVBL2_ENST00000413176.2_Silent_p.L160L|RUVBL2_ENST00000601968.1_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	84	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	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		
KRT32	3882	hgsc.bcm.edu	37	17	39619093	39619093	+	Silent	SNP	G	G	A	rs2604954|rs386797091|rs70964671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39619093G>A	ENST00000225899.3	-	6	1309	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	402	Coil 2.|Rod.		N -> S (in dbSNP:rs2604955). {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)				TGCAGTCCTCGTTCTCCAGCA	0.617													G|||	3082	0.615415	0.6309	0.5706	5008	,	,		16907	0.6825		0.673	False		,,,				2504	0.498				p.N402N		Atlas-SNP	.											.	KRT32	57	.	0			c.C1206T						PASS	.	G		2717,1689		860,997,346	60.0	62.0	61.0		1206	0.7	1.0	17	dbSNP_100	61	5451,3149		1776,1899,625	no	coding-synonymous	KRT32	NM_002278.3		2636,2896,971	AA,AG,GG		36.6163,38.3341,37.1982		402/449	39619093	8168,4838	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon6			GTCCTCGTTCTCC	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.1206C>T	17.37:g.39619093G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			AC|1.000;|0.000	.	alt		0.617	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
RNF157	114804	hgsc.bcm.edu	37	17	74152366	74152366	+	Silent	SNP	A	A	G	rs881502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74152366A>G	ENST00000269391.6	-	14	1582	c.1450T>C	c.(1450-1452)Ttg>Ctg	p.L484L	RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000592748.1_RNA|RNF157_ENST00000319945.6_Silent_p.L484L|RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000586661.1_RNA	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	87	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	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	
TAS2R50	259296	hgsc.bcm.edu	37	12	11138683	11138683	+	Silent	SNP	C	C	T	rs10772397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11138683C>T	ENST00000506868.1	-	1	828	c.777G>A	c.(775-777)ccG>ccA	p.P259P	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	259					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						CCATGACAACCGGGTCATTCC	0.418													T|||	2740	0.547125	0.1755	0.6009	5008	,	,		21159	0.755		0.6571	False		,,,				2504	0.684				p.P259P		Atlas-SNP	.											.	TAS2R50	37	.	0			c.G777A						PASS	.	T		1076,3330	721.2+/-409.1	134,808,1261	77.0	79.0	79.0		777	-1.6	0.0	12	dbSNP_120	79	5236,3364	499.6+/-375.0	1612,2012,676	no	coding-synonymous	TAS2R50	NM_176890.2		1746,2820,1937	TT,TC,CC		39.1163,24.4212,48.5314		259/300	11138683	6312,6694	2203	4300	6503	SO:0001819	synonymous_variant	259296	exon1			GACAACCGGGTCA	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.777G>A	12.37:g.11138683C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_176890	P59545|Q2M255|Q645Y0	Silent	SNP	ENST00000506868.1	37	CCDS8638.1																																																																																			C|0.483;T|0.517	0.517	strong		0.418	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88913273	88913273	+	Missense_Mutation	SNP	G	G	C	rs867529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:88913273G>C	ENST00000303236.3	-	2	708	c.407C>G	c.(406-408)tCc>tGc	p.S136C	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	136			S -> C (in dbSNP:rs867529). {ECO:0000269|PubMed:10932183, ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TGACACCAAGGAACCGGATCC	0.383													G|||	1405	0.280551	0.0166	0.3343	5008	,	,		16061	0.4851		0.2982	False		,,,				2504	0.3701				p.S136C	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.C407G						PASS	.	G	CYS/SER	256,4150	145.4+/-180.2	8,240,1955	123.0	109.0	114.0		407	5.4	1.0	2	dbSNP_86	114	2324,6276	389.8+/-343.1	313,1698,2289	yes	missense	EIF2AK3	NM_004836.5	112	321,1938,4244	CC,CG,GG		27.0233,5.8103,19.837	benign	136/1117	88913273	2580,10426	2203	4300	6503	SO:0001583	missense	9451	exon2			ACCAAGGAACCGG	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.407C>G	2.37:g.88913273G>C	ENSP00000307235:p.Ser136Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	629	0.288003663003663	10	0.02032520325203252	123	0.3397790055248619	274	0.479020979020979	222	0.2928759894459103	G	14.41	2.527371	0.44969	0.058103	0.270233	ENSG00000172071	ENST00000303236	T	0.30981	1.51	5.38	5.38	0.77491	Quinonprotein alcohol dehydrogenase-like (2);	0.227346	0.46758	D	0.000261	T	0.00012	0.0000	L	0.33245	0.995	0.29294	P	0.8691530000000001	B	0.09022	0.002	B	0.08055	0.003	T	0.49011	-0.8983	9	0.39692	T	0.17	-10.5973	19.1382	0.93436	0.0:0.0:1.0:0.0	rs867529;rs1805163;rs52809782;rs867529	136	Q9NZJ5	E2AK3_HUMAN	C	136	ENSP00000307235:S136C	ENSP00000307235:S136C	S	-	2	0	EIF2AK3	88694388	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.704000	0.68347	2.507000	0.84556	0.655000	0.94253	TCC	G|0.764;C|0.236	0.236	strong		0.383	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
UMOD	7369	hgsc.bcm.edu	37	16	20359831	20359831	+	Silent	SNP	C	C	T	rs13335818	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:20359831C>T	ENST00000570689.1	-	3	938	c.792G>A	c.(790-792)gtG>gtA	p.V264V	UMOD_ENST00000396138.4_Silent_p.V313V|UMOD_ENST00000424589.1_Silent_p.V297V|UMOD_ENST00000396134.2_Silent_p.V297V|UMOD_ENST00000396142.2_Silent_p.V264V|UMOD_ENST00000302509.4_Silent_p.V264V			P07911	UROM_HUMAN	uromodulin	264					cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CACAGGCCTTCACCTGGACGG	0.667													c|||	603	0.120407	0.093	0.1671	5008	,	,		18285	0.0139		0.1998	False		,,,				2504	0.1524				p.V264V		Atlas-SNP	.											.	UMOD	128	.	0			c.G792A						PASS	.		,	441,3961		23,395,1783	17.0	19.0	18.0		792,792	2.7	1.0	16	dbSNP_121	18	1575,7015		153,1269,2873	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	176,1664,4656	TT,TC,CC		18.3353,10.0182,15.5172	,	264/641,264/641	20359831	2016,10976	2201	4295	6496	SO:0001819	synonymous_variant	7369	exon3			GGCCTTCACCTGG	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.792G>A	16.37:g.20359831C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			C|0.866;T|0.134	0.134	strong		0.667	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
SCN3A	6328	hgsc.bcm.edu	37	2	165996107	165996107	+	Silent	SNP	T	T	A	rs1946892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165996107T>A	ENST00000360093.3	-	14	2522	c.2031A>T	c.(2029-2031)acA>acT	p.T677T	SCN3A_ENST00000409101.3_Silent_p.T628T|SCN3A_ENST00000283254.7_Silent_p.T677T	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	677					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTCCGTTTCTGTGGTGGTGC	0.453													A|||	3178	0.634585	0.7277	0.5778	5008	,	,		16901	0.8165		0.4245	False		,,,				2504	0.5777				p.T677T		Atlas-SNP	.											.	SCN3A	544	.	0			c.A2031T						PASS	.	A	,,	2919,1487	476.4+/-357.6	956,1007,240	126.0	110.0	115.0		1884,1884,2031	1.6	1.0	2	dbSNP_92	115	3622,4978	625.1+/-397.7	767,2088,1445	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	1723,3095,1685	AA,AT,TT		42.1163,33.7494,49.7078	,,	628/1952,628/1952,677/2001	165996107	6541,6465	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon14			CGTTTCTGTGGTG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2031A>T	2.37:g.165996107T>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				A|0.544;N|0.000	0.544	strong		0.453	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
MYO3A	53904	hgsc.bcm.edu	37	10	26455090	26455090	+	Missense_Mutation	SNP	G	G	A	rs34918608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:26455090G>A	ENST00000265944.5	+	27	3260	c.3094G>A	c.(3094-3096)Gct>Act	p.A1032T	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1032	Myosin motor.		A -> T (in dbSNP:rs34918608). {ECO:0000269|PubMed:17344846}.		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)			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						CGATAACTGGGCTCTTGGAAA	0.408													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18704	0.0		0.0119	False		,,,				2504	0.0				p.A1032T		Atlas-SNP	.											MYO3A,NS,carcinoma,-1,1	MYO3A	371	1	0			c.G3094A						PASS	.	G	THR/ALA	8,4398	12.9+/-30.5	0,8,2195	96.0	103.0	101.0		3094	5.2	1.0	10	dbSNP_126	101	73,8527	44.0+/-102.2	1,71,4228	yes	missense	MYO3A	NM_017433.4	58	1,79,6423	AA,AG,GG		0.8488,0.1816,0.6228	possibly-damaging	1032/1617	26455090	81,12925	2203	4300	6503	SO:0001583	missense	53904	exon27			AACTGGGCTCTTG	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.3094G>A	10.37:g.26455090G>A	ENSP00000265944:p.Ala1032Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	20.1	3.938089	0.73557	0.001816	0.008488	ENSG00000095777	ENST00000265944	D	0.87256	-2.23	6.07	5.17	0.71159	Myosin head, motor domain (2);	0.231325	0.47455	N	0.000222	D	0.84338	0.5450	M	0.63428	1.95	0.80722	D	1	P	0.43412	0.806	P	0.47705	0.555	D	0.84836	0.0805	10	0.39692	T	0.17	.	12.1062	0.53813	0.1365:0.0:0.8635:0.0	rs34918608;rs61729832	1032	Q8NEV4	MYO3A_HUMAN	T	1032	ENSP00000265944:A1032T	ENSP00000265944:A1032T	A	+	1	0	MYO3A	26495096	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.247000	0.65416	1.586000	0.49944	0.650000	0.86243	GCT	G|0.994;A|0.006	0.006	strong		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:54060248T>C	ENST00000312233.2	-	3	894	c.328A>G	c.(328-330)Acg>Gcg	p.T110A		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						AGATCTCCCGTCAGAGGGGGG	0.657													C|||	1076	0.214856	0.1074	0.1599	5008	,	,		16057	0.1885		0.2962	False		,,,				2504	0.3425				p.T110A		Atlas-SNP	.											GLIS1,NS,carcinoma,0,1	GLIS1	52	1	0			c.A328G						scavenged	.	C	ALA/THR	469,3885		39,391,1747	20.0	25.0	24.0		328	1.8	0.7	1	dbSNP_111	24	2634,5870		442,1750,2060	yes	missense	GLIS1	NM_147193.2	58	481,2141,3807	CC,CT,TT		30.9737,10.7717,24.1328	benign	110/621	54060248	3103,9755	2177	4252	6429	SO:0001583	missense	148979	exon3			CTCCCGTCAGAGG	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.328A>G	1.37:g.54060248T>C	ENSP00000309653:p.Thr110Ala	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	469	0.21474358974358973	59	0.11991869918699187	66	0.18232044198895028	114	0.1993006993006993	230	0.3034300791556728	C	4.520	0.096571	0.08681	0.107717	0.309737	ENSG00000174332	ENST00000312233	T	0.09163	3.01	4.8	1.81	0.25067	.	0.384219	0.22553	N	0.058568	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	0.47649	-0.9101	9	0.05436	T	0.98	.	5.5009	0.16829	0.0701:0.1254:0.5527:0.2518	rs4307514	110	Q8NBF1	GLIS1_HUMAN	A	110	ENSP00000309653:T110A	ENSP00000309653:T110A	T	-	1	0	GLIS1	53832836	0.999000	0.42202	0.685000	0.30070	0.006000	0.05464	0.857000	0.27831	0.041000	0.15688	-1.109000	0.02080	ACG	T|0.751;C|0.249	0.249	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
ATP7B	540	hgsc.bcm.edu	37	13	52520471	52520471	+	Silent	SNP	C	C	T	rs1801247	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52520471C>T	ENST00000242839.4	-	13	3165	c.3009G>A	c.(3007-3009)gcG>gcA	p.A1003A	ATP7B_ENST00000448424.2_Silent_p.A925A|ATP7B_ENST00000400366.3_Silent_p.A892A|ATP7B_ENST00000418097.2_Intron|ATP7B_ENST00000417240.2_Silent_p.A275A|ATP7B_ENST00000400370.3_Silent_p.A573A|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000344297.5_Silent_p.A796A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1003			A -> T (in WD; dbSNP:rs201497300). {ECO:0000269|PubMed:10790207, ECO:0000269|PubMed:15811015, ECO:0000269|PubMed:16207219, ECO:0000269|PubMed:9671269}.|A -> V (in WD). {ECO:0000269|PubMed:10544227}.		cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCCGTTCTGCGCGGCCACCC	0.627									Wilson disease				c|||	185	0.0369409	0.0015	0.0245	5008	,	,		16080	0.0089		0.0547	False		,,,				2504	0.1043				p.A1003A		Atlas-SNP	.											ATP7B,NS,carcinoma,0,1	ATP7B	123	1	0			c.G3009A						PASS	.	T	,	36,3950		0,36,1957	27.0	31.0	30.0		3009,2388	-3.7	0.8	13	dbSNP_89	30	456,7886		11,434,3726	no	coding-synonymous,coding-synonymous	ATP7B	NM_000053.3,NM_001005918.2	,	11,470,5683	TT,TC,CC		5.4663,0.9032,3.9909	,	1003/1466,796/1259	52520471	492,11836	1993	4171	6164	SO:0001819	synonymous_variant	540	exon13	Familial Cancer Database		GTTCTGCGCGGCC	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3009G>A	13.37:g.52520471C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	37	CCDS41892.1																																																																																			C|0.974;T|0.026	0.026	strong		0.627	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
MST1L	11223	hgsc.bcm.edu	37	1	17086941	17086941	+	RNA	SNP	C	C	T	rs28462251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	177	0	0		WXS	Illumina HiSeq	Phase_I	182	13	0.0714286	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	
RC3H1	149041	hgsc.bcm.edu	37	1	173915909	173915909	+	Missense_Mutation	SNP	G	G	C	rs61741479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:173915909G>C	ENST00000367696.2	-	16	3154	c.2803C>G	c.(2803-2805)Cct>Gct	p.P935A	RC3H1_ENST00000258349.4_Missense_Mutation_p.P935A|RC3H1_ENST00000367694.2_Missense_Mutation_p.P935A			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	935					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						CCCTGAGAAGGTATGTTTTGA	0.368													G|||	140	0.0279553	0.0348	0.0274	5008	,	,		18375	0.0		0.0378	False		,,,				2504	0.0378				p.P935A		Atlas-SNP	.											.	RC3H1	110	.	0			c.C2803G						PASS	.	G	ALA/PRO	186,4220	119.6+/-157.3	6,174,2023	74.0	76.0	76.0		2803	4.6	1.0	1	dbSNP_129	76	277,8323	103.8+/-164.8	6,265,4029	yes	missense	RC3H1	NM_172071.2	27	12,439,6052	CC,CG,GG		3.2209,4.2215,3.5599	benign	935/1134	173915909	463,12543	2203	4300	6503	SO:0001583	missense	149041	exon15			GAGAAGGTATGTT	AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	29434	protein-coding gene	gene with protein product	"""KIAA2025 protein"""	609424	"""ring finger and CCCH-type zinc finger domains 1"""			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.2803C>G	1.37:g.173915909G>C	ENSP00000356669:p.Pro935Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	37	CCDS30940.1	59	0.027014652014652016	18	0.036585365853658534	12	0.03314917127071823	0	0.0	29	0.03825857519788918	G	11.44	1.638286	0.29157	0.042215	0.032209	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	T;T;T	0.39997	1.05;1.05;1.05	5.46	4.55	0.56014	.	0.298435	0.39615	N	0.001318	T	0.17619	0.0423	L	0.40543	1.245	0.34323	D	0.686777	B;B;B;B	0.33940	0.307;0.307;0.433;0.307	B;B;B;B	0.33454	0.079;0.079;0.164;0.079	T	0.06917	-1.0800	10	0.37606	T	0.19	-7.5577	9.9156	0.41432	0.0719:0.14:0.7881:0.0	rs61741479	935;935;935;935	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	A	935	ENSP00000356669:P935A;ENSP00000258349:P935A;ENSP00000356667:P935A	ENSP00000258349:P935A	P	-	1	0	RC3H1	172182532	1.000000	0.71417	0.991000	0.47740	0.631000	0.37964	2.632000	0.46511	1.315000	0.45114	-0.122000	0.15005	CCT	G|0.958;C|0.042	0.042	strong		0.368	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071	
HMGCR	3156	hgsc.bcm.edu	37	5	74652199	74652199	+	Missense_Mutation	SNP	A	A	G	rs5908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:74652199A>G	ENST00000287936.4	+	15	2068	c.1912A>G	c.(1912-1914)Ata>Gta	p.I638V	HMGCR_ENST00000511206.1_Missense_Mutation_p.I638V|HMGCR_ENST00000343975.5_Missense_Mutation_p.I585V	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	638	Catalytic.		I -> V (in dbSNP:rs5908). {ECO:0000269|PubMed:10391209}.		aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TCATACAAGTATAGCTGGACG	0.348													A|||	25	0.00499201	0.0	0.0043	5008	,	,		17301	0.0		0.0159	False		,,,				2504	0.0061				p.I638V		Atlas-SNP	.											.	HMGCR	53	.	0			c.A1912G						PASS	.	A	VAL/ILE,VAL/ILE	20,4386	27.2+/-55.0	0,20,2183	91.0	93.0	92.0		1912,1753	-2.0	0.1	5	dbSNP_52	92	163,8437	76.6+/-139.3	0,163,4137	yes	missense,missense	HMGCR	NM_000859.2,NM_001130996.1	29,29	0,183,6320	GG,GA,AA		1.8953,0.4539,1.407	benign,benign	638/889,585/836	74652199	183,12823	2203	4300	6503	SO:0001583	missense	3156	exon15			ACAAGTATAGCTG		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"""hydroxymethylglutaryl-CoA reductase"", ""3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"""	142910	"""3-hydroxy-3-methylglutaryl-Coenzyme A reductase"""				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1912A>G	5.37:g.74652199A>G	ENSP00000287936:p.Ile638Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_000859	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	37	CCDS4027.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	9.059	0.994103	0.19043	0.004539	0.018953	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.43294	0.95;0.95;0.95	6.02	-2.05	0.07321	Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding (2);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.522971	0.23585	N	0.046609	T	0.08403	0.0209	N	0.16743	0.435	0.26226	N	0.979089	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.05716	-1.0868	10	0.26408	T	0.33	-2.7341	0.1633	0.00105	0.3439:0.226:0.177:0.2532	rs5908;rs17648133;rs52793370;rs5908	638;585;638	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	V	638;569;638;585	ENSP00000426745:I638V;ENSP00000287936:I638V;ENSP00000340816:I585V	ENSP00000287936:I638V	I	+	1	0	HMGCR	74687955	0.014000	0.17966	0.142000	0.22268	0.982000	0.71751	-0.342000	0.07801	-0.440000	0.07211	0.529000	0.55759	ATA	A|0.990;G|0.010	0.010	strong		0.348	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2		
HHATL	57467	hgsc.bcm.edu	37	3	42735150	42735150	+	Missense_Mutation	SNP	T	T	C	rs11079	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:42735150T>C	ENST00000441594.1	-	10	1468	c.1207A>G	c.(1207-1209)Atg>Gtg	p.M403V	HHATL_ENST00000310417.5_Missense_Mutation_p.M403V	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	403			M -> V (in dbSNP:rs11079).		negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		AGTTTTTGCATCCAGAGCTCA	0.572													C|||	3251	0.649161	0.6785	0.6787	5008	,	,		17935	0.7113		0.5924	False		,,,				2504	0.5828				p.M403V		Atlas-SNP	.											.	HHATL	49	.	0			c.A1207G						PASS	.		VAL/MET	2878,1528	483.9+/-359.9	934,1010,259	50.0	46.0	47.0		1207	4.3	1.0	3	dbSNP_52	47	5072,3528	513.4+/-378.2	1462,2148,690	yes	missense	HHATL	NM_020707.3	21	2396,3158,949	CC,CT,TT		41.0233,34.68,38.8744	benign	403/505	42735150	7950,5056	2203	4300	6503	SO:0001583	missense	57467	exon10			TTTGCATCCAGAG	AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"""membrane bound O-acyltransferase domain containing 3"""	608116	"""chromosome 3 open reading frame 3"", ""GUP1, glycerol uptake/transporter homolog (yeast)"""	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.1207A>G	3.37:g.42735150T>C	ENSP00000405423:p.Met403Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_020707	Q8TBG3|Q9ULP7	Missense_Mutation	SNP	ENST00000441594.1	37	CCDS2704.1	1409	0.6451465201465202	338	0.6869918699186992	236	0.6519337016574586	393	0.6870629370629371	442	0.58311345646438	c	4.841	0.156349	0.09236	0.6532	0.589767	ENSG00000010282	ENST00000310417;ENST00000441594	T;T	0.72394	-0.65;-0.65	4.35	4.35	0.52113	.	0.060080	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00044	-2.455	0.39949	P	0.025487000000000037	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	9	0.07030	T	0.85	-3.6735	12.4847	0.55866	0.0:0.9175:0.0:0.0825	rs11079;rs1046552;rs3172382;rs17237886;rs60079680;rs11079	403	Q9HCP6	HHATL_HUMAN	V	403	ENSP00000310621:M403V;ENSP00000405423:M403V	ENSP00000310621:M403V	M	-	1	0	HHATL	42710154	1.000000	0.71417	0.999000	0.59377	0.630000	0.37929	3.125000	0.50469	0.827000	0.34685	-0.404000	0.06349	ATG	T|0.381;C|0.619	0.619	strong		0.572	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707	
OR2B3	442184	hgsc.bcm.edu	37	6	29054923	29054923	+	Missense_Mutation	SNP	A	A	G	rs149723131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29054923A>G	ENST00000377173.2	-	1	167	c.103T>C	c.(103-105)Tac>Cac	p.Y35H		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	35						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)|lung(17)|prostate(1)|skin(2)	24						GTGATTGTGTATGATATTAAC	0.408													A|||	10	0.00199681	0.0	0.0	5008	,	,		19983	0.0		0.0099	False		,,,				2504	0.0				p.Y35H		Atlas-SNP	.											OR2B3,NS,carcinoma,+2,1	OR2B3	44	1	0			c.T103C						PASS	.	A	HIS/TYR	15,4391	21.2+/-45.6	0,15,2188	135.0	124.0	128.0		103	2.7	0.0	6	dbSNP_134	128	87,8513	49.8+/-109.6	0,87,4213	yes	missense	OR2B3	NM_001005226.2	83	0,102,6401	GG,GA,AA		1.0116,0.3404,0.7843	probably-damaging	35/314	29054923	102,12904	2203	4300	6503	SO:0001583	missense	442184	exon1			TTGTGTATGATAT		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"""GPCR / Class A : Olfactory receptors"""	8238	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 3 pseudogene"""	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.103T>C	6.37:g.29054923A>G	ENSP00000366378:p.Tyr35His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	37	CCDS34358.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	14.13	2.442681	0.43326	0.003404	0.010116	ENSG00000204703	ENST00000377173	T	0.04654	3.58	3.9	2.72	0.32119	.	0.000000	0.36854	U	0.002376	T	0.15825	0.0381	H	0.95043	3.615	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12041	-1.0563	10	0.87932	D	0	.	8.8277	0.35065	0.9058:0.0:0.0942:0.0	.	35	O76000	OR2B3_HUMAN	H	35	ENSP00000366378:Y35H	ENSP00000366378:Y35H	Y	-	1	0	OR2B3	29162902	0.799000	0.28903	0.011000	0.14972	0.799000	0.45148	4.031000	0.57267	0.370000	0.24538	-0.396000	0.06452	TAC	A|0.993;G|0.007	0.007	strong		0.408	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2		
EYS	346007	hgsc.bcm.edu	37	6	66005888	66005888	+	Missense_Mutation	SNP	C	C	T	rs9342464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:66005888C>T	ENST00000370621.3	-	12	2417	c.1891G>A	c.(1891-1893)Ggt>Agt	p.G631S	EYS_ENST00000503581.1_Missense_Mutation_p.G631S|EYS_ENST00000370616.2_Missense_Mutation_p.G631S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	631			G -> S (in dbSNP:rs9342464). {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)			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						CTTTGCAGACCGCTACAGTTA	0.433													C|||	2980	0.595048	0.2209	0.7161	5008	,	,		13425	0.8948		0.5924	False		,,,				2504	0.7086				p.G631S		Atlas-SNP	.											.	EYS	527	.	0			c.G1891A						PASS	.	C	SER/GLY	416,968		70,276,346	155.0	120.0	131.0		1891	1.7	0.0	6	dbSNP_119	131	1856,1326		535,786,270	yes	missense	EYS	NM_001142800.1	56	605,1062,616	TT,TC,CC		41.6719,30.0578,49.7591	benign	631/3145	66005888	2272,2294	692	1591	2283	SO:0001583	missense	346007	exon12			GCAGACCGCTACA		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.1891G>A	6.37:g.66005888C>T	ENSP00000359655:p.Gly631Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	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		1323	0.6057692307692307	107	0.21747967479674796	254	0.7016574585635359	523	0.9143356643356644	439	0.579155672823219	.	3.705	-0.060638	0.07317	0.300578	0.583281	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.81163	-1.46;-1.46;-1.46	5.48	1.71	0.24356	.	.	.	.	.	T	0.41050	0.1142	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.05289	-1.0894	8	0.72032	D	0.01	.	6.0161	0.19603	0.5668:0.157:0.0:0.2762	rs9342464;rs17411829;rs9342464	631	Q5T1H1-1	.	S	631	ENSP00000424243:G631S;ENSP00000359655:G631S;ENSP00000359650:G631S	ENSP00000359650:G631S	G	-	1	0	EYS	66062609	0.005000	0.15991	0.025000	0.17156	0.010000	0.07245	2.140000	0.42159	0.054000	0.16065	-1.556000	0.00890	GGT	C|0.404;T|0.596	0.596	strong		0.433	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
TBP	6908	hgsc.bcm.edu	37	6	170878793	170878793	+	Silent	SNP	T	T	C	rs1042327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:170878793T>C	ENST00000392092.2	+	6	1050	c.771T>C	c.(769-771)aaT>aaC	p.N257N	TBP_ENST00000230354.6_Silent_p.N257N|TBP_ENST00000540980.1_Silent_p.N237N	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	257					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)		AGATTCAGAATATGGTGGGGA	0.413													C|||	3078	0.614617	0.7103	0.4957	5008	,	,		18434	0.7877		0.5139	False		,,,				2504	0.4949				p.N257N		Atlas-SNP	.											.	TBP	58	.	0			c.T771C						PASS	.	C	,	2894,1512	479.7+/-358.6	949,996,258	112.0	110.0	111.0		711,771	-0.5	1.0	6	dbSNP_86	111	4306,4294	575.7+/-390.3	1082,2142,1076	no	coding-synonymous,coding-synonymous	TBP	NM_001172085.1,NM_003194.4	,	2031,3138,1334	CC,CT,TT		49.9302,34.3168,44.6409	,	237/320,257/340	170878793	7200,5806	2203	4300	6503	SO:0001819	synonymous_variant	6908	exon6			TCAGAATATGGTG	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.771T>C	6.37:g.170878793T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1	1369	0.6268315018315018	331	0.6727642276422764	197	0.5441988950276243	457	0.798951048951049	384	0.5065963060686016	C	10.23	1.291874	0.23564	0.656832	0.500698	ENSG00000112592	ENST00000446829	.	.	.	6.17	-0.493	0.12038	.	.	.	.	.	T	0.43211	0.1237	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42327	-0.9458	3	.	.	.	-13.4621	13.7889	0.63128	0.0:0.3984:0.0:0.6016	rs1042327;rs2230089;rs3173217;rs9366249;rs17655609;rs17860791;rs57185976;rs1042327	.	.	.	H	32	.	.	Y	+	1	0	TBP	170720718	0.993000	0.37304	0.989000	0.46669	0.992000	0.81027	0.387000	0.20718	-0.240000	0.09696	-0.119000	0.15052	TAT	T|0.400;C|0.600	0.600	strong		0.413	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
PLCL1	5334	hgsc.bcm.edu	37	2	198950029	198950029	+	Silent	SNP	A	A	G	rs2228135	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:198950029A>G	ENST00000428675.1	+	2	2186	c.1788A>G	c.(1786-1788)caA>caG	p.Q596Q	PLCL1_ENST00000437704.2_Silent_p.Q498Q	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	596	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	AATCTGTTCAATACAGGGATT	0.413													G|||	1162	0.232029	0.3578	0.1931	5008	,	,		18872	0.248		0.1909	False		,,,				2504	0.1155				p.Q596Q		Atlas-SNP	.											.	PLCL1	358	.	0			c.A1788G						PASS	.	G		1430,2976	654.7+/-399.8	238,954,1011	69.0	72.0	71.0		1788	1.5	1.0	2	dbSNP_98	71	1539,7061	741.3+/-407.1	127,1285,2888	no	coding-synonymous	PLCL1	NM_006226.3		365,2239,3899	GG,GA,AA		17.8953,32.4557,22.8279		596/1096	198950029	2969,10037	2203	4300	6503	SO:0001819	synonymous_variant	5334	exon2			TGTTCAATACAGG	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1788A>G	2.37:g.198950029A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Silent	SNP	ENST00000428675.1	37	CCDS2326.2																																																																																			A|0.767;G|0.233	0.233	strong		0.413	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226	
TBX10	347853	hgsc.bcm.edu	37	11	67399173	67399173	+	Missense_Mutation	SNP	C	C	T	rs146672518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:67399173C>T	ENST00000335385.3	-	8	1148	c.1061G>A	c.(1060-1062)cGg>cAg	p.R354Q	NUDT8_ENST00000376693.2_5'Flank|NUDT8_ENST00000301490.4_5'Flank	NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	354					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						CCTATCAGCCCGGATGTTGGG	0.652													C|||	18	0.00359425	0.0015	0.0058	5008	,	,		15763	0.0		0.0089	False		,,,				2504	0.0031				p.R354Q		Atlas-SNP	.											.	TBX10	25	.	0			c.G1061A	GRCh37	CM055547	TBX10	M	rs146672518	PASS	.	C	GLN/ARG	6,4394		0,6,2194	22.0	20.0	21.0		1061	-6.5	0.0	11	dbSNP_134	21	99,8487		1,97,4195	yes	missense	TBX10	NM_005995.4	43	1,103,6389	TT,TC,CC		1.153,0.1364,0.8086	benign	354/386	67399173	105,12881	2200	4293	6493	SO:0001583	missense	347853	exon8			TCAGCCCGGATGT	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.1061G>A	11.37:g.67399173C>T	ENSP00000335191:p.Arg354Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	4.834	0.155029	0.09236	0.001364	0.01153	ENSG00000167800	ENST00000335385	D	0.85955	-2.05	3.79	-6.47	0.01902	.	5.537720	0.00166	N	0.000011	T	0.55242	0.1908	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.53788	-0.8389	10	0.25106	T	0.35	.	2.5625	0.04775	0.1339:0.1628:0.1338:0.5696	.	354	O75333	TBX10_HUMAN	Q	354	ENSP00000335191:R354Q	ENSP00000335191:R354Q	R	-	2	0	TBX10	67155749	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.708000	0.05035	-0.878000	0.04007	-0.258000	0.10820	CGG	C|0.994;T|0.006	0.006	strong		0.652	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
SPINK5	11005	hgsc.bcm.edu	37	5	147499670	147499670	+	Silent	SNP	C	C	T	rs33920397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:147499670C>T	ENST00000256084.7	+	25	2454	c.2412C>T	c.(2410-2412)ggC>ggT	p.G804G	SPINK5_ENST00000398454.1_Silent_p.G804G|SPINK5_ENST00000359874.3_Silent_p.G804G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	804	Kazal-like 12. {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.G804G(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)			AGACACATGGCAATAAGTGTA	0.393													C|||	2446	0.488419	0.3139	0.634	5008	,	,		20246	0.4821		0.5924	False		,,,				2504	0.5204				p.G804G		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.C2412T						scavenged	.	C	,,	1394,2340		246,902,719	97.0	87.0	90.0		2412,2412,2412	4.7	1.0	5	dbSNP_126	90	5050,3154		1528,1994,580	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1774,2896,1299	TT,TC,CC		38.4447,37.3326,46.0211	,,	804/1095,804/917,804/1065	147499670	6444,5494	1867	4102	5969	SO:0001819	synonymous_variant	11005	exon25			ACATGGCAATAAG	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.2412C>T	5.37:g.147499670C>T		Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			C|0.461;T|0.539	0.539	strong		0.393	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
ADRB2	154	hgsc.bcm.edu	37	5	148207633	148207633	+	Silent	SNP	G	G	A	rs1042720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148207633G>A	ENST00000305988.4	+	1	1478	c.1239G>A	c.(1237-1239)ctG>ctA	p.L413L		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	413					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	ACTCACTGCTGTAAAGCAGTT	0.403													G|||	2548	0.508786	0.5847	0.4438	5008	,	,		15122	0.6429		0.3131	False		,,,				2504	0.5153				p.L413L		Atlas-SNP	.											.	ADRB2	42	.	0			c.G1239A						PASS	.	G		2363,2043	560.0+/-380.4	646,1071,486	51.0	54.0	53.0		1239	1.6	1.0	5	dbSNP_86	53	2810,5788	431.4+/-356.8	453,1904,1942	no	coding-synonymous	ADRB2	NM_000024.5		1099,2975,2428	AA,AG,GG		32.682,46.3686,39.7801		413/414	148207633	5173,7831	2203	4299	6502	SO:0001819	synonymous_variant	154	exon1			ACTGCTGTAAAGC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.1239G>A	5.37:g.148207633G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			A|0.411;G|0.589	0.411	strong		0.403	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
PSME4	23198	hgsc.bcm.edu	37	2	54150237	54150237	+	Silent	SNP	A	A	G	rs3213775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:54150237A>G	ENST00000404125.1	-	16	1982	c.1927T>C	c.(1927-1929)Ttg>Ctg	p.L643L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	643					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)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|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)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AAGAGCTTCAAAGATTCTTCT	0.338													A|||	565	0.112819	0.0189	0.1455	5008	,	,		18276	0.254		0.0746	False		,,,				2504	0.1104				p.L643L		Atlas-SNP	.											.	PSME4	247	.	0			c.T1927C						PASS	.	A		110,4296	83.9+/-122.4	2,106,2095	88.0	96.0	93.0		1927	-1.0	1.0	2	dbSNP_106	93	695,7905	171.4+/-222.4	33,629,3638	no	coding-synonymous	PSME4	NM_014614.2		35,735,5733	GG,GA,AA		8.0814,2.4966,6.1895		643/1844	54150237	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon16			GCTTCAAAGATTC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.1927T>C	2.37:g.54150237A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	153	70	0.457516	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			A|0.911;G|0.089	0.089	strong		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
EDDM3A	10876	hgsc.bcm.edu	37	14	21215997	21215997	+	Silent	SNP	C	C	T	rs11847654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	83	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	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		
CIITA	4261	hgsc.bcm.edu	37	16	11001743	11001743	+	Silent	SNP	G	G	A	rs2229320	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11001743G>A	ENST00000324288.8	+	11	2527	c.2394G>A	c.(2392-2394)ccG>ccA	p.P798P	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	798					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGCTGCAGCCGGGGACACTGC	0.706			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	948	0.189297	0.0129	0.1499	5008	,	,		13143	0.3145		0.2217	False		,,,				2504	0.2935				p.P798P		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G2394A						PASS	.	G		225,4113		12,201,1956	19.0	27.0	25.0		2394	-10.0	0.0	16	dbSNP_98	25	1715,6781		179,1357,2712	no	coding-synonymous	CIITA	NM_000246.3		191,1558,4668	AA,AG,GG		20.186,5.1867,15.1161		798/1131	11001743	1940,10894	2169	4248	6417	SO:0001819	synonymous_variant	4261	exon11			GCAGCCGGGGACA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2394G>A	16.37:g.11001743G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			G|0.820;A|0.180	0.180	strong		0.706	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
CACNA1S	779	hgsc.bcm.edu	37	1	201038687	201038687	+	Silent	SNP	A	A	G	rs7415038	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201038687A>G	ENST00000362061.3	-	18	2629	c.2403T>C	c.(2401-2403)ttT>ttC	p.F801F	CACNA1S_ENST00000367338.3_Silent_p.F801F	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	801					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)	tgaagTTGGTAAACCAGGTGG	0.607													G|||	1473	0.294129	0.5182	0.3012	5008	,	,		20367	0.001		0.4215	False		,,,				2504	0.1575				p.F801F		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T2403C						PASS	.	G		2257,2135		584,1089,523	78.0	56.0	64.0		2403	3.9	1.0	1	dbSNP_116	64	3865,4721		916,2033,1344	no	coding-synonymous	CACNA1S	NM_000069.2		1500,3122,1867	GG,GA,AA		45.0151,48.6111,47.1721		801/1874	201038687	6122,6856	2196	4293	6489	SO:0001819	synonymous_variant	779	exon18			GTTGGTAAACCAG	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.2403T>C	1.37:g.201038687A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			A|0.620;G|0.380	0.380	strong		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713602	32713602	+	Silent	SNP	T	T	C	rs142901825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32713602T>C	ENST00000374940.3	+	3	468	c.366T>C	c.(364-366)ccT>ccC	p.P122P		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	122	Alpha-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)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	CCAAGTTTCCTGTGACGCTGG	0.507													T|||	301	0.0601038	0.0605	0.0677	5008	,	,		23748	0.0873		0.0467	False		,,,				2504	0.0399				p.P122P		Atlas-SNP	.											HLA-DQA2,NS,carcinoma,+1,1	HLA-DQA2	27	1	0			c.T366C						PASS	.						184.0	144.0	159.0					6																	32713602		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			GTTTCCTGTGACG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.366T>C	6.37:g.32713602T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	256	30	0.117188	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			T|0.983;C|0.017	0.017	strong		0.507	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
OR9G4	283189	hgsc.bcm.edu	37	11	56510623	56510623	+	Missense_Mutation	SNP	A	A	G	rs513873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56510623A>G	ENST00000302957.3	-	1	664	c.665T>C	c.(664-666)gTa>gCa	p.V222A		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	222			V -> A (in dbSNP:rs513873).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCTGGAGAGTACTGTGAAGCC	0.468													A|||	945	0.188698	0.2163	0.1599	5008	,	,		21139	0.0853		0.2992	False		,,,				2504	0.1646				p.V222A		Atlas-SNP	.											.	OR9G4	73	.	0			c.T665C						PASS	.	A	ALA/VAL	1052,3350	384.7+/-325.4	118,816,1267	101.0	92.0	95.0		665	5.1	1.0	11	dbSNP_83	95	2745,5847	436.3+/-358.3	444,1857,1995	yes	missense	OR9G4	NM_001005284.1	64	562,2673,3262	GG,GA,AA		31.9483,23.8982,29.2212	possibly-damaging	222/328	56510623	3797,9197	2201	4296	6497	SO:0001583	missense	283189	exon1			GAGAGTACTGTGA	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"""GPCR / Class A : Olfactory receptors"""	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.665T>C	11.37:g.56510623A>G	ENSP00000307515:p.Val222Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	37	CCDS31537.1	445	0.20375457875457875	112	0.22764227642276422	54	0.14917127071823205	46	0.08041958041958042	233	0.3073878627968338	A	14.16	2.452759	0.43531	0.238982	0.319483	ENSG00000172457	ENST00000302957	T	0.38077	1.16	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35772	N	0.002985	T	0.00012	0.0000	L	0.35542	1.07	0.33213	P	0.44635800000000003	D	0.76494	0.999	D	0.80764	0.994	T	0.32188	-0.9916	9	0.19590	T	0.45	-48.116	13.8217	0.63325	1.0:0.0:0.0:0.0	rs513873;rs52807984;rs60956810;rs513873	222	Q8NGQ1	OR9G4_HUMAN	A	222	ENSP00000307515:V222A	ENSP00000307515:V222A	V	-	2	0	OR9G4	56267199	0.047000	0.20315	0.991000	0.47740	0.912000	0.54170	3.072000	0.50049	2.131000	0.65755	0.523000	0.50628	GTA	A|0.748;G|0.252	0.252	strong		0.468	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284	
GLB1L2	89944	hgsc.bcm.edu	37	11	134244123	134244123	+	Silent	SNP	C	C	G	rs3741097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:134244123C>G	ENST00000535456.2	+	17	1868	c.1680C>G	c.(1678-1680)acC>acG	p.T560T	GLB1L2_ENST00000389881.3_Silent_p.T560T|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_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	126	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	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	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28305212	28305212	+	Missense_Mutation	SNP	C	C	T	rs2830585	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:28305212C>T	ENST00000284987.5	-	5	1962	c.1841G>A	c.(1840-1842)cGc>cAc	p.R614H	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	614	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in dbSNP:rs2830585). {ECO:0000269|PubMed:10464288}.		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						ACTGCAGGAGCGGTAGATGGC	0.512													C|||	495	0.0988419	0.0484	0.1138	5008	,	,		18116	0.0992		0.1799	False		,,,				2504	0.0726				p.R614H	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,colon,carcinoma,-1,6	ADAMTS5	184	6	0			c.G1841A						scavenged	.	C	HIS/ARG	319,4087	171.6+/-201.8	10,299,1894	153.0	105.0	121.0		1841	6.0	1.0	21	dbSNP_100	121	1372,7228	266.9+/-287.0	123,1126,3051	yes	missense	ADAMTS5	NM_007038.3	29	133,1425,4945	TT,TC,CC		15.9535,7.2401,13.0017	probably-damaging	614/931	28305212	1691,11315	2203	4300	6503	SO:0001583	missense	11096	exon5			CAGGAGCGGTAGA	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.1841G>A	21.37:g.28305212C>T	ENSP00000284987:p.Arg614His	Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	267	0.12225274725274725	25	0.0508130081300813	41	0.1132596685082873	65	0.11363636363636363	136	0.17941952506596306	C	35	5.473629	0.96291	0.072401	0.159535	ENSG00000154736	ENST00000284987	T	0.55930	0.49	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	M	0.87269	2.87	0.09310	P	0.9999999848425	D	0.89917	1.0	D	0.91635	0.999	T	0.09443	-1.0674	9	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	rs2830585;rs17595455;rs59709407;rs2830585	614	Q9UNA0	ATS5_HUMAN	H	614	ENSP00000284987:R614H	ENSP00000284987:R614H	R	-	2	0	ADAMTS5	27227083	1.000000	0.71417	0.998000	0.56505	0.835000	0.47333	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	CGC	C|0.872;T|0.128	0.128	strong		0.512	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
DOPEY2	9980	hgsc.bcm.edu	37	21	37609571	37609571	+	Silent	SNP	T	T	C	rs2835322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	60	2	0.0333333		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	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	
PTPN7	5778	hgsc.bcm.edu	37	1	202129826	202129826	+	5'Flank	SNP	T	T	C	rs4309039	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202129826T>C	ENST00000308986.5	-	0	0				PTPN7_ENST00000367279.4_5'Flank|PTPN7_ENST00000309017.3_Missense_Mutation_p.Q37R|PTPN7_ENST00000544762.1_5'Flank|PTPN7_ENST00000543735.1_5'Flank|PTPN7_ENST00000492977.1_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						TCTGCCCTCCTGTGCCTGCTG	0.687													T|||	2120	0.423323	0.1006	0.5231	5008	,	,		13966	0.5387		0.4344	False		,,,				2504	0.6585				p.Q37R		Atlas-SNP	.											.	PTPN7	31	.	0			c.A110G						PASS	.	T	,ARG/GLN	171,1191		30,111,540	2.0	2.0	2.0		,110	2.7	1.0	1	dbSNP_131	2	1133,2023		267,599,712	yes	intron,missense	PTPN7	NM_001199797.1,NM_002832.3	,43	297,710,1252	CC,CT,TT		35.8999,12.5551,28.8623	,	,37/466	202129826	1304,3214	681	1578	2259	SO:0001631	upstream_gene_variant	5778	exon1			CCCTCCTGTGCCT	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.202129826T>C	Exception_encountered	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		860	0.39377289377289376	61	0.12398373983739837	164	0.4530386740331492	306	0.534965034965035	329	0.4340369393139842	T	14.98	2.696455	0.48202	0.125551	0.358999	ENSG00000143851	ENST00000309017	T	0.03951	3.75	3.85	2.72	0.32119	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999604934	.	.	.	.	.	.	T	0.24693	-1.0153	6	0.07030	T	0.85	.	5.1132	0.14821	0.0:0.1373:0.0:0.8627	rs4309039	.	.	.	R	37	ENSP00000309116:Q37R	ENSP00000309116:Q37R	Q	-	2	0	PTPN7	200396449	0.294000	0.24380	0.998000	0.56505	0.883000	0.51084	-0.914000	0.04038	1.377000	0.46286	0.260000	0.18958	CAG	.	.	none		0.687	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65157652	65157652	+	Missense_Mutation	SNP	G	G	A	rs76490900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65157652G>A	ENST00000323544.4	+	6	1166	c.1038G>A	c.(1036-1038)atG>atA	p.M346I	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	346	Pro-rich.									NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						TGAATGGCATGGATGACAGTC	0.582													G|||	25	0.00499201	0.0	0.0029	5008	,	,		19023	0.0		0.0229	False		,,,				2504	0.0				p.M346I		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.G1038A						PASS	.	G	ILE/MET,ILE/MET	10,4394	16.8+/-37.8	0,10,2192	66.0	67.0	67.0		888,1038	4.4	1.0	15	dbSNP_131	67	149,8449	72.9+/-135.5	2,145,4152	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	10,10	2,155,6344	AA,AG,GG		1.733,0.2271,1.2229	benign,benign	296/441,346/491	65157652	159,12843	2202	4299	6501	SO:0001583	missense	80301	exon6			TGGCATGGATGAC	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.1038G>A	15.37:g.65157652G>A	ENSP00000326706:p.Met346Ile	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	19	0.0086996336996337	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	6.574	0.474318	0.12521	0.002271	0.01733	ENSG00000241839	ENST00000323544	T	0.29142	1.58	5.42	4.41	0.53225	.	1.143740	0.06177	N	0.678774	T	0.08758	0.0217	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30736	-0.9968	10	0.16420	T	0.52	.	4.3278	0.11048	0.0907:0.1478:0.6092:0.1523	.	296;346	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	I	346	ENSP00000326706:M346I	ENSP00000326706:M346I	M	+	3	0	PLEKHO2	62944705	0.658000	0.27402	0.978000	0.43139	0.866000	0.49608	0.469000	0.22067	1.118000	0.41863	0.655000	0.94253	ATG	G|0.989;A|0.011	0.011	strong		0.582	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
TACSTD2	4070	hgsc.bcm.edu	37	1	59042311	59042311	+	Missense_Mutation	SNP	T	T	G	rs35075952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	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	
PTPMT1	114971	hgsc.bcm.edu	37	11	47587452	47587452	+	Intron	SNP	C	C	T	rs11537751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47587452C>T	ENST00000326674.9	+	2	196				PTPMT1_ENST00000326656.8_Intron|NDUFS3_ENST00000533507.1_Intron|PTPMT1_ENST00000534775.1_Missense_Mutation_p.S93L|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000426530.2_Missense_Mutation_p.S93L	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1						cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						CTCTTTGCCTCGGCAGCTGGT	0.687													C|||	106	0.0211661	0.0038	0.0317	5008	,	,		13087	0.0		0.0586	False		,,,				2504	0.0204				p.S93L		Atlas-SNP	.											.	PTPMT1	17	.	0			c.C278T						PASS	.	C	LEU/SER,	39,4061		0,39,2011	27.0	29.0	28.0		278,	3.7	1.0	11	dbSNP_120	28	411,7973		5,401,3786	yes	missense,intron	PTPMT1	NM_001143984.1,NM_175732.2	145,	5,440,5797	TT,TC,CC		4.9022,0.9512,3.6046	,	93/152,	47587452	450,12034	2050	4192	6242	SO:0001627	intron_variant	114971	exon1			TTGCCTCGGCAGC	BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.175-6C>T	11.37:g.47587452C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_001143984	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	59	0.027014652014652016	6	0.012195121951219513	11	0.03038674033149171	0	0.0	42	0.055408970976253295	C	18.00	3.525647	0.64860	0.009512	0.049022	ENSG00000110536	ENST00000426530;ENST00000534775	.	.	.	4.58	3.67	0.42095	.	.	.	.	.	T	0.11537	0.0281	N	0.22421	0.69	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.64687	0.873;0.928	T	0.26538	-1.0100	8	0.87932	D	0	.	10.1568	0.42827	0.2002:0.7998:0.0:0.0	rs11537751	93;93	E9PAT8;E9PQM0	.;.	L	93	.	ENSP00000410272:S93L	S	+	2	0	PTPMT1	47544028	0.992000	0.36948	0.999000	0.59377	0.952000	0.60782	0.255000	0.18333	0.906000	0.36621	-0.218000	0.12543	TCG	C|0.963;T|0.037	0.037	strong		0.687	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879	
TATDN2	9797	hgsc.bcm.edu	37	3	10311939	10311939	+	Missense_Mutation	SNP	C	C	T	rs2075352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10311939C>T	ENST00000287652.4	+	4	2124	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.P358L	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	358			P -> L (in dbSNP:rs2075352). {ECO:0000269|PubMed:9039502}.		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						TCAGCCGTTCCGGAGCCTTCT	0.532													C|||	898	0.179313	0.2625	0.0778	5008	,	,		19965	0.2768		0.1044	False		,,,				2504	0.1155				p.P358L		Atlas-SNP	.											.	TATDN2	59	.	0			c.C1073T						PASS	.	C	LEU/PRO	1083,3323	393.1+/-328.7	136,811,1256	164.0	159.0	161.0		1073	4.7	0.9	3	dbSNP_96	161	823,7777	189.8+/-236.5	31,761,3508	yes	missense	TATDN2	NM_014760.3	98	167,1572,4764	TT,TC,CC		9.5698,24.5801,14.6548	possibly-damaging	358/762	10311939	1906,11100	2203	4300	6503	SO:0001583	missense	9797	exon4			CCGTTCCGGAGCC	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.1073C>T	3.37:g.10311939C>T	ENSP00000287652:p.Pro358Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	65	0.643564	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	397	0.18177655677655677	133	0.2703252032520325	28	0.07734806629834254	158	0.2762237762237762	78	0.10290237467018469	C	6.013	0.370799	0.11409	0.245801	0.095698	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.46819	0.86;0.86	4.73	4.73	0.59995	.	0.559131	0.13722	N	0.367281	T	0.00012	0.0000	L	0.51422	1.61	0.36618	P	0.12442900000000001	B	0.26602	0.154	B	0.11329	0.006	T	0.08827	-1.0703	9	0.42905	T	0.14	-4.7704	10.8455	0.46741	0.1885:0.8115:0.0:0.0	rs2075352;rs58904160;rs2075352	358	Q93075	TATD2_HUMAN	L	358	ENSP00000287652:P358L;ENSP00000408736:P358L	ENSP00000287652:P358L	P	+	2	0	TATDN2	10286939	0.001000	0.12720	0.936000	0.37596	0.018000	0.09664	0.912000	0.28597	2.353000	0.79882	0.644000	0.83932	CCG	C|0.833;N|0.000	.	strong		0.532	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
PWP2	5822	hgsc.bcm.edu	37	21	45544594	45544594	+	Silent	SNP	T	T	C	rs2187313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45544594T>C	ENST00000291576.7	+	15	2078	c.1951T>C	c.(1951-1953)Ttg>Ctg	p.L651L		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	651					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		CAACCTGTCTTTGGACGCCAT	0.597													C|||	3723	0.743411	0.6316	0.7954	5008	,	,		19406	0.8085		0.835	False		,,,				2504	0.6963				p.L651L		Atlas-SNP	.											.	PWP2	64	.	0			c.T1951C						PASS	.	C		2849,1557	488.5+/-361.2	941,967,295	86.0	68.0	74.0		1951	2.8	0.8	21	dbSNP_96	74	7029,1571	293.5+/-301.4	2889,1251,160	no	coding-synonymous	PWP2	NM_005049.2		3830,2218,455	CC,CT,TT		18.2674,35.3382,24.0504		651/920	45544594	9878,3128	2203	4300	6503	SO:0001819	synonymous_variant	5822	exon15			CTGTCTTTGGACG		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1951T>C	21.37:g.45544594T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_005049	B2RAG8|Q96A77	Silent	SNP	ENST00000291576.7	37	CCDS33579.1																																																																																			A|0.002;C|0.758	0.758	strong		0.597	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
EIF5B	9669	hgsc.bcm.edu	37	2	99995517	99995517	+	Silent	SNP	C	C	T	rs11896520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	86	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	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	
UMODL1	89766	hgsc.bcm.edu	37	21	43531553	43531553	+	Intron	SNP	A	A	C	rs220128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43531553A>C	ENST00000408910.2	+	12	1899				UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000408989.2_Missense_Mutation_p.T741P|UMODL1_ENST00000400427.1_Missense_Mutation_p.T669P|C21orf128_ENST00000329015.2_5'Flank	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						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						CCCGAAGGCTACTGGGTCAAC	0.662													C|||	2084	0.416134	0.1573	0.5101	5008	,	,		16788	0.5357		0.5318	False		,,,				2504	0.4571				p.T741P	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A2221C						PASS	.	C	,PRO/THR,,PRO/THR	907,3045		122,663,1191	49.0	52.0	51.0		,2005,,2221	-0.8	0.0	21	dbSNP_79	51	4259,4025		1116,2027,999	yes	intron,missense,intron,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,38,,38	1238,2690,2190	CC,CA,AA		48.5876,22.9504,42.2197	,benign,,benign	,669/1375,,741/1447	43531553	5166,7070	1976	4142	6118	SO:0001627	intron_variant	89766	exon11			AAGGCTACTGGGT		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.1900-63A>C	21.37:g.43531553A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	988	0.4523809523809524	94	0.1910569105691057	182	0.5027624309392266	290	0.506993006993007	422	0.5567282321899736	C	0.354	-0.943422	0.02322	0.229504	0.514124	ENSG00000177398	ENST00000400427;ENST00000408989	T;T	0.71934	-0.61;-0.61	4.41	-0.782	0.10961	.	0.261743	0.20395	N	0.093165	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	8	0.02654	T	1	-2.7542	3.3896	0.07283	0.2839:0.3702:0.0:0.3459	rs220128;rs481812;rs1153356;rs57873525;rs220128	741	Q5DID0-2	.	P	669;741	ENSP00000383279:T669P;ENSP00000386126:T741P	ENSP00000383279:T669P	T	+	1	0	UMODL1	42404622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.444000	0.06854	-0.579000	0.05952	-1.544000	0.00907	ACT	A|0.568;C|0.432	0.432	strong		0.662	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
METRNL	284207	hgsc.bcm.edu	37	17	81043039	81043039	+	Silent	SNP	A	A	G	rs9908756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:81043039A>G	ENST00000320095.7	+	2	521	c.396A>G	c.(394-396)ccA>ccG	p.P132P	METRNL_ENST00000570778.1_Silent_p.P50P|METRNL_ENST00000571814.1_Silent_p.P50P	NM_001004431.1	NP_001004431.1	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation regulator-like	132					brown fat cell differentiation (GO:0050873)|fat cell differentiation (GO:0045444)|negative regulation of inflammatory response (GO:0050728)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of energy homeostasis (GO:2000507)|response to cold (GO:0009409)|response to muscle activity (GO:0014850)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			TGCTGGTACCAGACGGGGACG	0.637													G|||	3940	0.786741	0.8517	0.7507	5008	,	,		15514	0.9167		0.6213	False		,,,				2504	0.7607				p.P132P		Atlas-SNP	.											METRNL,NS,carcinoma,0,1	METRNL	29	1	0			c.A396G						PASS	.	G		3646,760	298.4+/-285.3	1520,606,77	38.0	48.0	45.0		396	-1.6	0.0	17	dbSNP_119	45	5266,3334	485.5+/-371.6	1630,2006,664	no	coding-synonymous	METRNL	NM_001004431.1		3150,2612,741	GG,GA,AA		38.7674,17.2492,31.4778		132/312	81043039	8912,4094	2203	4300	6503	SO:0001819	synonymous_variant	284207	exon2			GGTACCAGACGGG	AK093748	CCDS32779.1	17q25.3	2004-12-01				ENSG00000176845			27584	protein-coding gene	gene with protein product							Standard	NM_001004431		Approved		uc002kgh.3	Q641Q3		ENST00000320095.7:c.396A>G	17.37:g.81043039A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_001004431	B3KSJ5|Q86VM0	Silent	SNP	ENST00000320095.7	37	CCDS32779.1																																																																																			A|0.262;G|0.738	0.738	strong		0.637	METRNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438902.1	NM_001004431	
MKNK2	2872	hgsc.bcm.edu	37	19	2050823	2050823	+	Missense_Mutation	SNP	G	G	T	rs3746101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2050823G>T	ENST00000591601.1	-	1	63	c.28C>A	c.(28-30)Cag>Aag	p.Q10K	MKNK2_ENST00000541165.1_5'UTR|MKNK2_ENST00000250896.3_Missense_Mutation_p.Q10K|MKNK2_ENST00000309340.7_Missense_Mutation_p.Q10K			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	10			Q -> K (in dbSNP:rs3746101).		cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|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)		TGGAAACCCTGAAGTTCGGCT	0.756													G|||	512	0.102236	0.0038	0.1354	5008	,	,		8725	0.2292		0.0835	False		,,,				2504	0.1002				p.Q10K		Atlas-SNP	.											MKNK2_ENST00000250896,NS,carcinoma,0,2	MKNK2	56	2	0			c.C28A						PASS	.	G	LYS/GLN,LYS/GLN	50,3838		0,50,1894	28.0	26.0	27.0		28,28	1.1	1.0	19	dbSNP_107	27	491,6991		10,471,3260	yes	missense,missense	MKNK2	NM_017572.3,NM_199054.2	53,53	10,521,5154	TT,TG,GG		6.5624,1.286,4.7581	benign,benign	10/415,10/466	2050823	541,10829	1944	3741	5685	SO:0001583	missense	2872	exon2			AACCCTGAAGTTC	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.28C>A	19.37:g.2050823G>T	ENSP00000467811:p.Gln10Lys	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	244	0.11172161172161173	4	0.008130081300813009	54	0.14917127071823205	126	0.2202797202797203	60	0.079155672823219	G	10.13	1.267076	0.23136	0.01286	0.065624	ENSG00000099875	ENST00000309340;ENST00000250896	T;T	0.65549	-0.16;-0.1	3.65	1.11	0.20524	.	0.396627	0.24552	N	0.037552	T	0.00039	0.0001	N	0.12182	0.205	0.09310	P	0.9999999999997805	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08994	-1.0695	9	0.10377	T	0.69	-11.1872	6.6888	0.23160	0.0:0.4262:0.3985:0.1753	rs3746101;rs61662291;rs3746101	10;10	Q9HBH9;Q9HBH9-2	MKNK2_HUMAN;.	K	10	ENSP00000309485:Q10K;ENSP00000250896:Q10K	ENSP00000250896:Q10K	Q	-	1	0	MKNK2	2001823	1.000000	0.71417	1.000000	0.80357	0.531000	0.34715	2.724000	0.47285	0.808000	0.34231	0.306000	0.20318	CAG	G|0.911;T|0.089	0.089	strong		0.756	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	
KIAA1462	57608	hgsc.bcm.edu	37	10	30317949	30317949	+	Silent	SNP	C	C	T	rs2478835	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:30317949C>T	ENST00000375377.1	-	3	1229	c.1128G>A	c.(1126-1128)ccG>ccA	p.P376P		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	376	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						CCTTCTCGGTCGGAGACTGCT	0.627													C|||	1278	0.255192	0.0598	0.4524	5008	,	,		17511	0.1935		0.4254	False		,,,				2504	0.2679				p.P376P		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G1128A						PASS	.	C		484,3638		32,420,1609	78.0	81.0	80.0		1128	-10.5	0.0	10	dbSNP_100	80	3563,4851		759,2045,1403	no	coding-synonymous	KIAA1462	NM_020848.2		791,2465,3012	TT,TC,CC		42.3461,11.7419,32.283		376/1360	30317949	4047,8489	2061	4207	6268	SO:0001819	synonymous_variant	57608	exon3			CTCGGTCGGAGAC	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.1128G>A	10.37:g.30317949C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			C|0.705;N|0.000	.	strong		0.627	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146377	5146377	+	Missense_Mutation	SNP	T	T	C	rs1019747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:5146377T>C	ENST00000274181.7	+	3	448	c.310T>C	c.(310-312)Tcc>Ccc	p.S104P	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.S104P|CTD-2297D10.1_ENST00000514848.1_RNA	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	60	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	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	
PSG8	440533	hgsc.bcm.edu	37	19	43268388	43268388	+	Missense_Mutation	SNP	G	G	A	rs142689447		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43268388G>A	ENST00000306511.4	-	2	207	c.110C>T	c.(109-111)aCg>aTg	p.T37M	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000401467.2_Missense_Mutation_p.T37M|PSG8_ENST00000404209.4_Missense_Mutation_p.T37M	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	37	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				GGCTTCAATCGTGACTTGGGC	0.463													.|||	1	0.000199681	0.0	0.0	5008	,	,		21250	0.0		0.001	False		,,,				2504	0.0				p.T37M		Atlas-SNP	.											.	PSG8	101	.	0			c.C110T						PASS	.	G	MET/THR,,MET/THR	0,4406		0,0,2203	173.0	170.0	171.0		110,,110	1.4	0.0	19	dbSNP_134	171	8,8590	6.4+/-24.3	0,8,4291	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	81,,81	0,8,6494	AA,AG,GG		0.093,0.0,0.0615	benign,,benign	37/420,,37/427	43268388	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon2			TCAATCGTGACTT	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.110C>T	19.37:g.43268388G>A	ENSP00000305005:p.Thr37Met	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	5.019	0.189287	0.09547	0.0	9.3E-4	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.68331	-0.32;-0.32;-0.32	1.35	1.35	0.21983	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72415	0.3457	M	0.77712	2.385	0.09310	N	1	P;B;P;B;B	0.44690	0.841;0.062;0.538;0.174;0.208	P;B;B;B;B	0.52646	0.705;0.063;0.204;0.066;0.109	T	0.60662	-0.7219	9	0.49607	T	0.09	.	6.1568	0.20342	0.0:0.0:1.0:0.0	.	37;37;37;37;37	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	M	37	ENSP00000385869:T37M;ENSP00000386090:T37M;ENSP00000305005:T37M	ENSP00000305005:T37M	T	-	2	0	PSG8	47960228	0.007000	0.16637	0.011000	0.14972	0.031000	0.12232	2.204000	0.42761	1.063000	0.40649	0.184000	0.17185	ACG	G|1.000;A|0.000	0.000	strong		0.463	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
TTN	7273	hgsc.bcm.edu	37	2	179571448	179571448	+	Missense_Mutation	SNP	A	A	G	rs4893852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179571448A>G	ENST00000591111.1	-	100	28426	c.28202T>C	c.(28201-28203)aTt>aCt	p.I9401T	TTN_ENST00000589042.1_Missense_Mutation_p.I9718T|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I8474T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13499	Ig-like 77.				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)			AACTTTTGCAATGAAGGTCGC	0.358													A|||	638	0.127396	0.2231	0.1556	5008	,	,		19539	0.0258		0.0358	False		,,,				2504	0.1769				p.I9718T		Atlas-SNP	.											.	TTN	18412	.	0			c.T29153C						PASS	.	A	,,,THR/ILE	713,2963		61,591,1186	108.0	101.0	104.0		,,,25421	6.2	1.0	2	dbSNP_111	104	213,7935		5,203,3866	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,89	66,794,5052	GG,GA,AA		2.6141,19.3961,7.8315	,,,benign	,,,8474/33424	179571448	926,10898	1838	4074	5912	SO:0001583	missense	7273	exon102			TTTGCAATGAAGG	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.28202T>C	2.37:g.179571448A>G	ENSP00000465570:p.Ile9401Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	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		185	0.08470695970695971	109	0.22154471544715448	46	0.1270718232044199	4	0.006993006993006993	26	0.03430079155672823	A	13.80	2.346021	0.41599	0.193961	0.026141	ENSG00000155657	ENST00000342992	T	0.64085	-0.08	6.16	6.16	0.99307	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00039	0.0001	N	0.00656	-1.285	0.09310	P	1.0	B	0.33171	0.4	B	0.34873	0.191	T	0.23726	-1.0180	8	0.87932	D	0	.	16.8061	0.85666	1.0:0.0:0.0:0.0	rs4893852;rs52805465;rs56946914;rs4893852	9401	Q8WZ42	TITIN_HUMAN	T	8474	ENSP00000343764:I8474T	ENSP00000343764:I8474T	I	-	2	0	TTN	179279693	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.378000	0.73150	2.367000	0.80283	0.528000	0.53228	ATT	A|0.910;G|0.090	0.090	strong		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ELL2	22936	hgsc.bcm.edu	37	5	95236459	95236459	+	Missense_Mutation	SNP	C	C	T	rs3815768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	126	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	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	
PKD2	5311	hgsc.bcm.edu	37	4	88996673	88996673	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88996673G>A	ENST00000508588.1	+	10	1383	c.988G>A	c.(988-990)Gag>Aag	p.E330K	PKD2_ENST00000237596.2_Missense_Mutation_p.E912K|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.E330K			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		AGTACGTGAAGAGTTGGAACG	0.517																																					p.E912K		Atlas-SNP	.											.	PKD2	82	.	0			c.G2734A						PASS	.						157.0	155.0	155.0					4																	88996673		2203	4300	6503	SO:0001583	missense	5311	exon15			CGTGAAGAGTTGG	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.988G>A	4.37:g.88996673G>A	ENSP00000427131:p.Glu330Lys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	20	0.215054	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.343226	0.95783	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.94613	-0.82;-3.47;-3.47	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.96793	0.8953	M	0.68593	2.085	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.97032	0.9751	10	0.59425	D	0.04	-22.2119	18.7273	0.91718	0.0:0.0:1.0:0.0	.	912	Q13563	PKD2_HUMAN	K	912;330;330	ENSP00000237596:E912K;ENSP00000427131:E330K;ENSP00000425289:E330K	ENSP00000237596:E912K	E	+	1	0	PKD2	89215697	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.183000	0.94887	2.409000	0.81822	0.585000	0.79938	GAG	.	.	none		0.517	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297	
WDR4	10785	hgsc.bcm.edu	37	21	44283574	44283574	+	Silent	SNP	C	C	T	rs11911090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:44283574C>T	ENST00000398208.2	-	4	488	c.429G>A	c.(427-429)ggG>ggA	p.G143G	WDR4_ENST00000330317.2_Silent_p.G143G|WDR4_ENST00000492742.1_5'UTR	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		TAGACAGGTGCCCCAGCTCTA	0.612													C|||	386	0.0770767	0.18	0.049	5008	,	,		18189	0.001		0.0606	False		,,,				2504	0.0532				p.G143G		Atlas-SNP	.											.	WDR4	35	.	0			c.G429A						PASS	.	C	,	788,3618	318.2+/-295.5	69,650,1484	149.0	123.0	132.0		429,429	-7.7	0.2	21	dbSNP_120	132	758,7842	181.3+/-230.0	39,680,3581	no	coding-synonymous,coding-synonymous	WDR4	NM_018669.4,NM_033661.3	,	108,1330,5065	TT,TC,CC		8.814,17.8847,11.8868	,	143/413,143/413	44283574	1546,11460	2203	4300	6503	SO:0001819	synonymous_variant	10785	exon4			CAGGTGCCCCAGC	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.429G>A	21.37:g.44283574C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_018669		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																			C|0.895;T|0.105	0.105	strong		0.612	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
PRRC2B	84726	hgsc.bcm.edu	37	9	134351770	134351770	+	Silent	SNP	G	G	A	rs78591540	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134351770G>A	ENST00000357304.4	+	15	4309	c.4254G>A	c.(4252-4254)aaG>aaA	p.K1418K	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1418							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AGCTGGCCAAGAGGAGCTTCT	0.652											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	487	0.0972444	0.1778	0.0735	5008	,	,		13836	0.004		0.163	False		,,,				2504	0.0337				p.K1418K		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4254A						PASS	.	G		504,3354		23,458,1448	15.0	17.0	16.0		4254	4.9	1.0	9	dbSNP_132	16	1094,7126		70,954,3086	no	coding-synonymous	PRRC2B	NM_013318.3		93,1412,4534	AA,AG,GG		13.309,13.0638,13.2307		1418/2230	134351770	1598,10480	1929	4110	6039	SO:0001819	synonymous_variant	84726	exon15			GGCCAAGAGGAGC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4254G>A	9.37:g.134351770G>A		Somatic	52	0	0	1610	WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	219	0.10027472527472528	68	0.13821138211382114	29	0.08011049723756906	1	0.0017482517482517483	121	0.15963060686015831	G	7.262	0.605446	0.14002	0.130638	0.13309	ENSG00000130723	ENST00000451855	.	.	.	5.93	4.94	0.65067	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06463	-1.0825	3	.	.	.	.	12.4476	0.55659	0.1081:0.0:0.8919:0.0	.	.	.	.	K	152	.	.	E	+	1	0	PRRC2B	133341591	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	3.787000	0.55439	2.814000	0.96858	0.655000	0.94253	GAG	A|0.104;C|0.000;G|0.895	0.104	strong		0.652	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ARHGAP33	115703	hgsc.bcm.edu	37	19	36268771	36268771	+	Silent	SNP	C	C	T	rs231228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36268771C>T	ENST00000007510.4	+	3	294	c.150C>T	c.(148-150)gcC>gcT	p.A50A	ARHGAP33_ENST00000314737.5_Silent_p.A50A|ARHGAP33_ENST00000221905.1_3'UTR|ARHGAP33_ENST00000378944.5_5'UTR			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	50					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CTGACTGCGCCCATTTCCACT	0.592													C|||	1450	0.289537	0.3828	0.3674	5008	,	,		17834	0.2907		0.2038	False		,,,				2504	0.1953				p.A50A		Atlas-SNP	.											ARHGAP33,NS,carcinoma,+2,1	ARHGAP33	102	1	0			c.C150T						PASS	.	C	,	1551,2855	487.1+/-360.8	278,995,930	91.0	93.0	92.0		,150	4.0	1.0	19	dbSNP_79	92	1724,6876	316.4+/-312.7	181,1362,2757	no	utr-5,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	459,2357,3687	TT,TC,CC		20.0465,35.202,25.1807	,	,50/1127	36268771	3275,9731	2203	4300	6503	SO:0001819	synonymous_variant	115703	exon3			CTGCGCCCATTTC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.150C>T	19.37:g.36268771C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				C|0.743;T|0.257	0.257	strong		0.592	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
XBP1	7494	hgsc.bcm.edu	37	22	29196306	29196306	+	Silent	SNP	G	G	A	rs2228260	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:29196306G>A	ENST00000216037.6	-	1	279	c.207C>T	c.(205-207)ccC>ccT	p.P69P	XBP1_ENST00000344347.5_Silent_p.P69P|CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000451486.1_RNA|XBP1_ENST00000403532.3_Silent_p.P69P|CTA-292E10.6_ENST00000458080.1_RNA|CTA-292E10.6_ENST00000585003.1_RNA|XBP1_ENST00000405219.3_5'Flank	NM_001079539.1|NM_005080.3	NP_001073007.1|NP_005071.2	P17861	XBP1_HUMAN	X-box binding protein 1	69					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial cell maturation involved in salivary gland development (GO:0060691)|exocrine pancreas development (GO:0031017)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|serotonin secretion, neurotransmission (GO:0060096)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|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)			breast(2)|endometrium(1)|large_intestine(1)|lung(1)	5						CCTTCTCCTCGGGGCTCAGGT	0.751													G|||	275	0.0549121	0.0015	0.0519	5008	,	,		2085	0.0873		0.0338	False		,,,				2504	0.1176				p.P69P		Atlas-SNP	.											.	XBP1	37	.	0			c.C207T						PASS	.	G	,	14,3276		0,14,1631	3.0	3.0	3.0		207,207	-5.9	1.0	22	dbSNP_132	3	76,6620		0,76,3272	no	coding-synonymous,coding-synonymous	XBP1	NM_001079539.1,NM_005080.3	,	0,90,4903	AA,AG,GG		1.135,0.4255,0.9013	,	69/377,69/262	29196306	90,9896	1645	3348	4993	SO:0001819	synonymous_variant	7494	exon1			CTCCTCGGGGCTC	M31627	CCDS13847.1	22q12.1	2013-01-10			ENSG00000100219	ENSG00000100219		"""basic leucine zipper proteins"""	12801	protein-coding gene	gene with protein product		194355		XBP2		1718857, 2196176	Standard	NM_001079539		Approved		uc003aec.3	P17861	OTTHUMG00000151094	ENST00000216037.6:c.207C>T	22.37:g.29196306G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_001079539	Q8WYK6|Q969P1|Q96BD7	Silent	SNP	ENST00000216037.6	37	CCDS13847.1																																																																																			G|0.952;A|0.048	0.048	strong		0.751	XBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321274.1	NM_005080	
ZNF404	342908	hgsc.bcm.edu	37	19	44377205	44377205	+	Missense_Mutation	SNP	T	T	G	rs78264306	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44377205T>G	ENST00000587539.1	-	3	1160	c.1161A>C	c.(1159-1161)gaA>gaC	p.E387D	ZNF404_ENST00000324394.6_Missense_Mutation_p.E385D	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	387					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)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				TCTTCCCACATTCTTTACATT	0.368													T|||	17	0.00339457	0.0	0.0029	5008	,	,		20949	0.0		0.0149	False		,,,				2504	0.0				p.E384D		Atlas-SNP	.											.	ZNF404	46	.	0			c.A1152C						PASS	.	T	ASP/GLU	8,4362		0,8,2177	30.0	33.0	32.0		1161	1.1	1.0	19	dbSNP_131	32	83,8505		0,83,4211	yes	missense	ZNF404	NM_001033719.2	45	0,91,6388	GG,GT,TT		0.9665,0.1831,0.7023	possibly-damaging	387/553	44377205	91,12867	2185	4294	6479	SO:0001583	missense	342908	exon2			CCCACATTCTTTA	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"""Zinc fingers, C2H2-type"", ""-"""	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.1161A>C	19.37:g.44377205T>G	ENSP00000466051:p.Glu387Asp	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	T	8.200	0.797891	0.16327	0.001831	0.009665	ENSG00000176222	ENST00000324394	T	0.07567	3.18	2.17	1.13	0.20643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06234	0.0161	L	0.42008	1.315	0.09310	N	0.999994	P	0.48089	0.905	P	0.56563	0.801	T	0.17531	-1.0366	9	0.44086	T	0.13	.	4.644	0.12563	0.0:0.2878:0.0:0.7122	.	387	Q494X3	ZN404_HUMAN	D	385	ENSP00000319479:E385D	ENSP00000319479:E385D	E	-	3	2	ZNF404	49069045	0.000000	0.05858	0.972000	0.41901	0.096000	0.18686	-1.263000	0.02850	0.984000	0.38629	0.332000	0.21555	GAA	T|0.993;G|0.007	0.007	strong		0.368	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
MMD2	221938	hgsc.bcm.edu	37	7	4959807	4959807	+	Silent	SNP	G	G	A	rs932061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4959807G>A	ENST00000404774.3	-	3	479	c.285C>T	c.(283-285)caC>caT	p.H95H	MMD2_ENST00000401401.3_Silent_p.H95H|MMD2_ENST00000406755.1_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	25	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	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	
HCN2	610	hgsc.bcm.edu	37	19	613898	613898	+	Silent	SNP	T	T	C	rs1054786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:613898T>C	ENST00000251287.2	+	7	1925	c.1872T>C	c.(1870-1872)gcT>gcC	p.A624A	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	624					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		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)		GCGTGCGGGCTGACACCTACT	0.706													c|||	4115	0.821685	0.9796	0.7349	5008	,	,		4851	0.8958		0.5865	False		,,,				2504	0.8354				p.A624A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T1872C						PASS	.	C		4024,366		1851,322,22	28.0	29.0	28.0		1872	-7.7	0.6	19	dbSNP_86	28	4945,3649		1422,2101,774	no	coding-synonymous	HCN2	NM_001194.3		3273,2423,796	CC,CT,TT		42.4599,8.3371,30.9227		624/890	613898	8969,4015	2195	4297	6492	SO:0001819	synonymous_variant	610	exon7			GCGGGCTGACACC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1872T>C	19.37:g.613898T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.274;C|0.726	0.726	strong		0.706	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
ZNF350	59348	hgsc.bcm.edu	37	19	52471872	52471872	+	Missense_Mutation	SNP	A	A	G	rs2278420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52471872A>G	ENST00000243644.4	-	4	424	c.197T>C	c.(196-198)cTg>cCg	p.L66P	ZNF350_ENST00000600703.1_5'UTR|HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> P (in dbSNP:rs2278420). {ECO:0000269|PubMed:11090615, ECO:0000269|PubMed:12872252, ECO:0000269|PubMed:14702039}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		AATTGTCCACAGTTGTTCTCC	0.453													G|||	1337	0.266973	0.3744	0.1801	5008	,	,		16888	0.2371		0.1889	False		,,,				2504	0.2945				p.L66P		Atlas-SNP	.											.	ZNF350	48	.	0			c.T197C						PASS	.	G	PRO/LEU	1654,2752	658.2+/-400.4	302,1050,851	182.0	153.0	163.0		197	0.9	0.0	19	dbSNP_100	163	1340,7260	756.7+/-407.5	102,1136,3062	yes	missense	ZNF350	NM_021632.3	98	404,2186,3913	GG,GA,AA		15.5814,37.5397,23.0201	benign	66/533	52471872	2994,10012	2203	4300	6503	SO:0001583	missense	59348	exon4			GTCCACAGTTGTT	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.197T>C	19.37:g.52471872A>G	ENSP00000243644:p.Leu66Pro	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_021632	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	37	CCDS12845.1	536	0.2454212454212454	201	0.40853658536585363	64	0.17679558011049723	119	0.20804195804195805	152	0.20052770448548812	G	0.001	-3.172985	0.00027	0.375397	0.155814	ENSG00000256683	ENST00000243644	T	0.03982	3.74	3.17	0.908	0.19326	Krueppel-associated box (2);	.	.	.	.	T	0.00012	0.0000	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41645	-0.9497	8	0.02654	T	1	.	2.7498	0.05277	0.2596:0.0:0.5189:0.2215	rs2278420;rs52805889;rs61035367;rs2278420	66	Q9GZX5	ZN350_HUMAN	P	66	ENSP00000243644:L66P	ENSP00000243644:L66P	L	-	2	0	ZNF350	57163684	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-0.105000	0.10907	-0.194000	0.10399	-1.078000	0.02229	CTG	A|0.747;G|0.253	0.253	strong		0.453	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
HID1	283987	hgsc.bcm.edu	37	17	72949649	72949649	+	Silent	SNP	C	C	T	rs2087718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72949649C>T	ENST00000425042.2	-	15	2039	c.1962G>A	c.(1960-1962)ccG>ccA	p.P654P		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	654					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)											CCCCCTTAGCCGGGCTGCCAT	0.672													T|||	728	0.145367	0.0076	0.0879	5008	,	,		15227	0.503		0.0189	False		,,,				2504	0.1339				p.P654P		Atlas-SNP	.											.	.	.	.	0			c.G1962A						PASS	.	T		40,4366	821.8+/-416.4	0,40,2163	54.0	53.0	53.0		1962	-8.9	0.0	17	dbSNP_96	53	204,8396	809.5+/-407.2	5,194,4101	no	coding-synonymous	C17orf28	NM_030630.2		5,234,6264	TT,TC,CC		2.3721,0.9079,1.8761		654/789	72949649	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	283987	exon15			CTTAGCCGGGCTG		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.1962G>A	17.37:g.72949649C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																			C|0.940;T|0.060	0.060	strong		0.672	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
CTBS	1486	hgsc.bcm.edu	37	1	85031630	85031630	+	Silent	SNP	G	G	A	rs2994953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85031630G>A	ENST00000370630.5	-	4	639	c.591C>T	c.(589-591)atC>atT	p.I197I	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	197					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		AAGCATCTGCGATTCCAGTAT	0.368													G|||	1486	0.296725	0.3404	0.2637	5008	,	,		10897	0.2341		0.2455	False		,,,				2504	0.3783				p.I197I		Atlas-SNP	.											.	CTBS	24	.	0			c.C591T						PASS	.	G		1434,2972	466.0+/-354.4	232,970,1001	97.0	91.0	93.0		591	1.6	1.0	1	dbSNP_101	93	2234,6366	378.1+/-338.8	299,1636,2365	no	coding-synonymous	CTBS	NM_004388.2		531,2606,3366	AA,AG,GG		25.9767,32.5465,28.2024		197/386	85031630	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	1486	exon4			ATCTGCGATTCCA	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.591C>T	1.37:g.85031630G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	192	101	0.526042	NM_004388	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																			G|0.720;A|0.280	0.280	strong		0.368	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
FPR1	2357	hgsc.bcm.edu	37	19	52249680	52249680	+	Missense_Mutation	SNP	T	T	A	rs5030880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	38	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	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	
CUBN	8029	hgsc.bcm.edu	37	10	16930419	16930419	+	Missense_Mutation	SNP	C	C	G	rs45569534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:16930419C>G	ENST00000377833.4	-	56	8967	c.8902G>C	c.(8902-8904)Gaa>Caa	p.E2968Q		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2968	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.		E -> Q (in dbSNP:rs45569534).		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)	AACTTACCTTCTAAGTGGAAG	0.313													C|||	30	0.00599042	0.0	0.0144	5008	,	,		18866	0.0		0.0199	False		,,,				2504	0.0				p.E2968Q		Atlas-SNP	.											.	CUBN	515	.	0			c.G8902C						PASS	.	C	GLN/GLU	24,4382	29.9+/-59.1	0,24,2179	103.0	95.0	98.0		8902	5.9	1.0	10	dbSNP_127	98	199,8401	86.3+/-148.7	2,195,4103	yes	missense	CUBN	NM_001081.3	29	2,219,6282	GG,GC,CC		2.314,0.5447,1.7146	probably-damaging	2968/3624	16930419	223,12783	2203	4300	6503	SO:0001583	missense	8029	exon56			TACCTTCTAAGTG	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.8902G>C	10.37:g.16930419C>G	ENSP00000367064:p.Glu2968Gln	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	12.97	2.096307	0.36952	0.005447	0.02314	ENSG00000107611	ENST00000377833	T	0.65916	-0.18	5.89	5.89	0.94794	CUB (5);	0.000000	0.46758	D	0.000271	T	0.55465	0.1922	M	0.84773	2.715	0.80722	D	1	B	0.27264	0.173	B	0.33454	0.164	T	0.66085	-0.6011	10	0.54805	T	0.06	.	16.154	0.81644	0.0:0.8666:0.1334:0.0	rs45569534	2968	O60494	CUBN_HUMAN	Q	2968	ENSP00000367064:E2968Q	ENSP00000367064:E2968Q	E	-	1	0	CUBN	16970425	1.000000	0.71417	1.000000	0.80357	0.309000	0.27889	2.053000	0.41326	2.793000	0.96121	0.561000	0.74099	GAA	C|0.985;G|0.015	0.015	strong		0.313	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
EXOSC5	56915	hgsc.bcm.edu	37	19	41903220	41903220	+	Missense_Mutation	SNP	G	G	A	rs10853751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41903220G>A	ENST00000221233.4	-	1	164	c.14C>T	c.(13-15)aCg>aTg	p.T5M	CTC-435M10.3_ENST00000604424.1_Intron|CTC-435M10.10_ENST00000598988.1_RNA|BCKDHA_ENST00000457836.2_5'Flank|CTC-435M10.3_ENST00000540732.1_Intron|EXOSC5_ENST00000596905.1_Missense_Mutation_p.T5M|BCKDHA_ENST00000595085.1_Intron|BCKDHA_ENST00000269980.2_5'Flank	NM_020158.3	NP_064543.3	Q9NQT4	EXOS5_HUMAN	exosome component 5	5			T -> M (in dbSNP:rs10853751). {ECO:0000269|PubMed:15489334}.		defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|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)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7						GTCAGTATGCGTCTCCTCCTC	0.652													A|||	3077	0.614417	0.8555	0.4798	5008	,	,		16977	0.4315		0.5875	False		,,,				2504	0.6002				p.T5M		Atlas-SNP	.											.	EXOSC5	18	.	0			c.C14T						PASS	.	A	MET/THR	3569,837	332.0+/-302.3	1444,681,78	132.0	113.0	119.0		14	2.6	0.0	19	dbSNP_120	119	5174,3426	504.9+/-376.3	1574,2026,700	yes	missense	EXOSC5	NM_020158.3	81	3018,2707,778	AA,AG,GG		39.8372,18.9968,32.7772	benign	5/236	41903220	8743,4263	2203	4300	6503	SO:0001583	missense	56915	exon1			GTATGCGTCTCCT	AF285785	CCDS12580.1	19q13.1	2008-02-05				ENSG00000077348			24662	protein-coding gene	gene with protein product	"""exosome component Rrp46"""	606492				11110791, 11812149	Standard	NM_020158		Approved	hRrp46p, Rrp46p, RRP46, RRP41B, MGC12901, p12B	uc002oqo.3	Q9NQT4		ENST00000221233.4:c.14C>T	19.37:g.41903220G>A	ENSP00000221233:p.Thr5Met	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_020158	Q32Q81|Q8NG16|Q96I89	Missense_Mutation	SNP	ENST00000221233.4	37	CCDS12580.1	1324	0.6062271062271062	421	0.8556910569105691	203	0.5607734806629834	260	0.45454545454545453	440	0.5804749340369393	A	0.722	-0.783098	0.02907	0.810032	0.601628	ENSG00000077348	ENST00000221233	T	0.31510	1.49	5.16	2.61	0.31194	.	1.239230	0.05254	N	0.514486	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	0.30765	-0.9967	9	0.21540	T	0.41	-4.4381	3.2455	0.06796	0.5662:0.0:0.1814:0.2524	rs10853751;rs17549237;rs17855390;rs52838397;rs59144776;rs10853751	5	Q9NQT4	EXOS5_HUMAN	M	5	ENSP00000221233:T5M	ENSP00000221233:T5M	T	-	2	0	EXOSC5	46595060	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.095000	0.11077	0.204000	0.20548	-0.378000	0.06908	ACG	G|0.354;N|0.000	.	strong		0.652	EXOSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463492.1	NM_020158	
CCDC66	285331	hgsc.bcm.edu	37	3	56650012	56650012	+	Missense_Mutation	SNP	G	G	C	rs4681904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56650012G>C	ENST00000394672.3	+	13	1844	c.1774G>C	c.(1774-1776)Gaa>Caa	p.E592Q	CCDC66_ENST00000436465.2_Missense_Mutation_p.E592Q|CCDC66_ENST00000326595.7_Missense_Mutation_p.E558Q	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	592			E -> K (in dbSNP:rs4681904).		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)		TGATTCTGATGAAATCAGTGG	0.318													G|||	1553	0.310104	0.4138	0.183	5008	,	,		17328	0.375		0.1223	False		,,,				2504	0.3865				p.E592Q		Atlas-SNP	.											.	CCDC66	145	.	0			c.G1774C						PASS	.	G	GLN/GLU,GLN/GLU	1704,2702		347,1010,846	85.0	92.0	89.0		1672,1774	3.7	0.0	3	dbSNP_111	89	1063,7517		116,831,3343	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	29,29	463,1841,4189	CC,CG,GG		12.3893,38.6745,21.3076	benign,benign	558/915,592/949	56650012	2767,10219	2203	4290	6493	SO:0001583	missense	285331	exon13			TCTGATGAAATCA	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.1774G>C	3.37:g.56650012G>C	ENSP00000378167:p.Glu592Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	613	0.2806776556776557	242	0.491869918699187	68	0.1878453038674033	212	0.3706293706293706	91	0.12005277044854881	G	13.09	2.134654	0.37630	0.386745	0.123893	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.24350	1.86;1.89;1.89;1.89	5.59	3.71	0.42584	.	0.486335	0.22939	N	0.053809	T	0.00012	0.0000	L	0.46157	1.445	0.46725	P	8.299999999999974E-4	P	0.35348	0.496	B	0.34242	0.178	T	0.48603	-0.9021	9	0.23891	T	0.37	-2.8591	9.7068	0.40220	0.0801:0.141:0.7789:0.0	rs4681904;rs28506144;rs52797779	592	A2RUB6	CCD66_HUMAN	Q	548;592;558;592	ENSP00000401451:E548Q;ENSP00000378167:E592Q;ENSP00000326050:E558Q;ENSP00000404320:E592Q	ENSP00000326050:E558Q	E	+	1	0	CCDC66	56625052	0.888000	0.30383	0.026000	0.17262	0.558000	0.35554	2.381000	0.44336	1.511000	0.48818	0.591000	0.81541	GAA	A|0.009;C|0.230;G|0.761	0.230	strong		0.318	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
CELA3A	10136	hgsc.bcm.edu	37	1	22336305	22336305	+	Silent	SNP	C	C	T	rs9187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	227	0	0		WXS	Illumina HiSeq	Phase_I	219	90	0.410959	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	
LRRC40	55631	hgsc.bcm.edu	37	1	70616830	70616830	+	Missense_Mutation	SNP	T	T	C	rs3180401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:70616830T>C	ENST00000370952.3	-	13	1577	c.1498A>G	c.(1498-1500)Atc>Gtc	p.I500V		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	500			I -> V (in dbSNP:rs3180401).			membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GAAAGATTGATCGTTTGCAGT	0.294													T|||	18	0.00359425	0.0015	0.0014	5008	,	,		14238	0.0		0.0149	False		,,,				2504	0.0				p.I500V		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1498G						PASS	.	T	VAL/ILE	21,4377	27.2+/-55.0	0,21,2178	58.0	58.0	58.0		1498	5.7	0.9	1	dbSNP_105	58	141,8447	69.0+/-131.5	1,139,4154	yes	missense	LRRC40	NM_017768.4	29	1,160,6332	CC,CT,TT		1.6418,0.4775,1.2475	benign	500/603	70616830	162,12824	2199	4294	6493	SO:0001583	missense	55631	exon13			GATTGATCGTTTG		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1498A>G	1.37:g.70616830T>C	ENSP00000359990:p.Ile500Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	199	94	0.472362	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	T	9.540	1.113220	0.20795	0.004775	0.016418	ENSG00000066557	ENST00000370952	T	0.53640	0.61	5.74	5.74	0.90152	.	0.097488	0.64402	D	0.000001	T	0.21590	0.0520	L	0.37561	1.115	0.38436	D	0.946563	B	0.29805	0.257	B	0.23018	0.043	T	0.14309	-1.0477	10	0.51188	T	0.08	.	10.3913	0.44171	0.0:0.0727:0.0:0.9273	rs3180401;rs3210316;rs17414609;rs52834337;rs3180401	500	Q9H9A6	LRC40_HUMAN	V	500	ENSP00000359990:I500V	ENSP00000359990:I500V	I	-	1	0	LRRC40	70389418	0.993000	0.37304	0.911000	0.35937	0.431000	0.31685	2.354000	0.44098	2.168000	0.68352	0.533000	0.62120	ATC	T|0.991;C|0.009	0.009	strong		0.294	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768	
TATDN2	9797	hgsc.bcm.edu	37	3	10302172	10302172	+	Missense_Mutation	SNP	G	G	A	rs394558	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10302172G>A	ENST00000287652.4	+	3	1817	c.766G>A	c.(766-768)Gtc>Atc	p.V256I	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.V256I	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	256			V -> I (in dbSNP:rs394558). {ECO:0000269|PubMed:15489334}.		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						AACCCCAGAGGTCAGCATGGA	0.552													A|||	2986	0.596246	0.3737	0.4207	5008	,	,		19472	0.9643		0.4304	False		,,,				2504	0.8129				p.V256I		Atlas-SNP	.											.	TATDN2	59	.	0			c.G766A						PASS	.	A	ILE/VAL	1647,2759	657.7+/-400.3	312,1023,868	64.0	60.0	61.0		766	0.8	0.0	3	dbSNP_80	61	3466,5134	635.5+/-399.0	697,2072,1531	yes	missense	TATDN2	NM_014760.3	29	1009,3095,2399	AA,AG,GG		40.3023,37.3808,39.3126	possibly-damaging	256/762	10302172	5113,7893	2203	4300	6503	SO:0001583	missense	9797	exon3			CCAGAGGTCAGCA	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.766G>A	3.37:g.10302172G>A	ENSP00000287652:p.Val256Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	112	66	0.589286	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	1222	0.5595238095238095	195	0.39634146341463417	154	0.425414364640884	559	0.9772727272727273	314	0.41424802110817943	A	3.840	-0.034032	0.07543	0.373808	0.403023	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.25250	1.81;1.81	4.81	0.786	0.18590	.	0.557126	0.13504	N	0.382984	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.18310	0.027	B	0.11329	0.006	T	0.42344	-0.9457	9	0.08837	T	0.75	-7.8544	5.5043	0.16846	0.2461:0.0:0.6091:0.1447	rs394558;rs52804764;rs59440092;rs394558	256	Q93075	TATD2_HUMAN	I	256	ENSP00000287652:V256I;ENSP00000408736:V256I	ENSP00000287652:V256I	V	+	1	0	TATDN2	10277172	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.634000	0.24614	0.055000	0.16094	-1.822000	0.00598	GTC	G|0.518;A|0.482	0.482	strong		0.552	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
SLC52A3	113278	hgsc.bcm.edu	37	20	746197	746197	+	Missense_Mutation	SNP	G	G	C	rs35655964	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:746197G>C	ENST00000217254.7	-	2	463	c.222C>G	c.(220-222)atC>atG	p.I74M	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Missense_Mutation_p.I74M	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	74			I -> M (in dbSNP:rs35655964).		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)										GGGTGAAGATGATGGGCACTT	0.617													G|||	154	0.0307508	0.0023	0.049	5008	,	,		19137	0.005		0.0825	False		,,,				2504	0.0297				p.I74M		Atlas-SNP	.											.	.	.	.	0			c.C222G						PASS	.	G	MET/ILE	83,4317		0,83,2117	52.0	43.0	46.0		222	2.7	0.9	20	dbSNP_126	46	820,7768		48,724,3522	yes	missense	C20orf54	NM_033409.3	10	48,807,5639	CC,CG,GG		9.5482,1.8864,6.9526	benign	74/470	746197	903,12085	2200	4294	6494	SO:0001583	missense	113278	exon2			GAAGATGATGGGC	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.222C>G	20.37:g.746197G>C	ENSP00000217254:p.Ile74Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	88	0.040293040293040296	1	0.0020325203252032522	19	0.052486187845303865	4	0.006993006993006993	64	0.08443271767810026	G	18.06	3.539786	0.65085	0.018864	0.095482	ENSG00000101276	ENST00000217254;ENST00000381944	D;D	0.85629	-2.01;-2.01	5.79	2.69	0.31865	.	0.828599	0.11387	N	0.569168	T	0.12603	0.0306	L	0.28192	0.835	0.34973	D	0.75332	P;P	0.50272	0.933;0.89	P;P	0.54401	0.751;0.472	T	0.55566	-0.8121	10	0.30078	T	0.28	-17.6335	7.4317	0.27131	0.1468:0.2696:0.5835:0.0	rs35655964	74;74	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	M	74	ENSP00000217254:I74M;ENSP00000371370:I74M	ENSP00000217254:I74M	I	-	3	3	C20orf54	694197	0.990000	0.36364	0.873000	0.34254	0.935000	0.57460	0.228000	0.17814	0.334000	0.23590	0.655000	0.94253	ATC	G|0.942;C|0.058	0.058	strong		0.617	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
SMPD2	6610	hgsc.bcm.edu	37	6	109764535	109764535	+	Missense_Mutation	SNP	G	G	T	rs1476387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:109764535G>T	ENST00000258052.3	+	9	1154	c.795G>T	c.(793-795)agG>agT	p.R265S	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000521072.2_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						PASS	.	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	155	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	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		
ZNF254	9534	hgsc.bcm.edu	37	19	24310413	24310413	+	Missense_Mutation	SNP	G	G	C	rs12611425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:24310413G>C	ENST00000357002.4	+	4	1726	c.1611G>C	c.(1609-1611)aaG>aaC	p.K537N	ZNF254_ENST00000342944.6_Missense_Mutation_p.K452N	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	537			K -> N (in dbSNP:rs12611425). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				CTAAACATAAGATAATTCATA	0.363													G|||	209	0.0417332	0.0	0.1167	5008	,	,		19776	0.0526		0.0288	False		,,,				2504	0.047				p.K537N		Atlas-SNP	.											.	ZNF254	88	.	0			c.G1611C						PASS	.	G	ASN/LYS	29,4321		0,29,2146	40.0	43.0	42.0		1611	-1.5	0.1	19	dbSNP_120	42	236,8340		1,234,4053	no	missense	ZNF254	NM_203282.2	94	1,263,6199	CC,CG,GG		2.7519,0.6667,2.0501	possibly-damaging	537/660	24310413	265,12661	2175	4288	6463	SO:0001583	missense	9534	exon4			ACATAAGATAATT	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1611G>C	19.37:g.24310413G>C	ENSP00000349494:p.Lys537Asn	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_203282	A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	37	CCDS32983.1	113	0.051739926739926737	0	0.0	45	0.12430939226519337	43	0.07517482517482517	25	0.032981530343007916	G	9.570	1.120663	0.20877	0.006667	0.027519	ENSG00000213096	ENST00000342944;ENST00000357002	T;T	0.07567	3.18;3.18	1.11	-1.54	0.08584	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00178	0.0005	L	0.46670	1.46	0.19300	N	0.999973	P	0.46621	0.881	P	0.52710	0.707	T	0.20739	-1.0266	9	0.66056	D	0.02	.	2.616	0.04903	0.242:0.3129:0.445:0.0	rs12611425;rs17854259;rs52806233;rs12611425	537	O75437	ZN254_HUMAN	N	452;537	ENSP00000445527:K452N;ENSP00000349494:K537N	ENSP00000445527:K452N	K	+	3	2	ZNF254	24102253	0.000000	0.05858	0.051000	0.19133	0.760000	0.43138	-0.791000	0.04599	-0.454000	0.07066	0.305000	0.20034	AAG	G|0.964;C|0.036	0.036	strong		0.363	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
WDR62	284403	hgsc.bcm.edu	37	19	36583651	36583651	+	Silent	SNP	G	G	A	rs61494900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36583651G>A	ENST00000270301.7	+	19	2271	c.2271G>A	c.(2269-2271)ctG>ctA	p.L757L	WDR62_ENST00000401500.2_Silent_p.L757L			O43379	WDR62_HUMAN	WD repeat domain 62	757					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			AGCACTTGCTGGAGATTGACC	0.597													G|||	615	0.122804	0.2617	0.0735	5008	,	,		19094	0.0		0.1342	False		,,,				2504	0.0849				p.L757L		Atlas-SNP	.											.	WDR62	102	.	0			c.G2271A						PASS	.	G	,	1005,3401	374.4+/-321.2	111,783,1309	93.0	94.0	93.0		2271,2271	2.9	1.0	19	dbSNP_129	93	890,7710	199.7+/-243.7	54,782,3464	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	165,1565,4773	AA,AG,GG		10.3488,22.8098,14.5702	,	757/1524,757/1519	36583651	1895,11111	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon19			CTTGCTGGAGATT	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2271G>A	19.37:g.36583651G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			G|0.864;A|0.136	0.136	strong		0.597	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
AMOTL1	154810	hgsc.bcm.edu	37	11	94533373	94533373	+	Silent	SNP	C	C	T	rs2303960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:94533373C>T	ENST00000433060.2	+	3	1158	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AMOTL1_ENST00000317837.9_Silent_p.P339P|AMOTL1_ENST00000317829.8_Silent_p.P289P	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	339					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				ACCAGCACCCCGGGATGCTCC	0.587													C|||	1309	0.261382	0.0719	0.464	5008	,	,		16586	0.4444		0.1889	False		,,,				2504	0.2597				p.P339P		Atlas-SNP	.											AMOTL1,colon,carcinoma,+2,1	AMOTL1	95	1	0			c.C1017T						PASS	.	C		368,3618		18,332,1643	123.0	124.0	124.0		1017	-10.3	0.1	11	dbSNP_100	124	1729,6613		177,1375,2619	no	coding-synonymous	AMOTL1	NM_130847.2		195,1707,4262	TT,TC,CC		20.7264,9.2323,17.0101		339/957	94533373	2097,10231	1993	4171	6164	SO:0001819	synonymous_variant	154810	exon3			GCACCCCGGGATG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1017C>T	11.37:g.94533373C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			C|0.744;T|0.256	0.256	strong		0.587	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892031	62892031	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62892031C>T	ENST00000584306.1	-	3	1875	c.1345G>A	c.(1345-1347)Gta>Ata	p.V449I	RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000339474.5_Intron|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.V449I|RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	449						integral component of membrane (GO:0016021)		p.V449I(4)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GGAGGTTCTACATCATTACCT	0.542																																					p.V449I		Atlas-SNP	.											LRRC37A3,NS,carcinoma,0,4	LRRC37A3	75	4	4	Substitution - Missense(4)	kidney(4)	c.G1345A						scavenged	.						1.0	1.0	1.0					17																	62892031		69	307	376	SO:0001583	missense	374819	exon3			GTTCTACATCATT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1345G>A	17.37:g.62892031C>T	ENSP00000464535:p.Val449Ile	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	13.61	2.287768	0.40494	.	.	ENSG00000176809	ENST00000319651	T	0.66460	-0.21	2.12	-2.37	0.06643	.	.	.	.	.	T	0.47060	0.1425	L	0.42245	1.32	0.80722	P	0.0	B	0.29716	0.255	B	0.22152	0.038	T	0.37686	-0.9695	8	0.42905	T	0.14	.	0.6971	0.00901	0.2393:0.3528:0.2366:0.1713	.	449	O60309	L37A3_HUMAN	I	449	ENSP00000325713:V449I	ENSP00000325713:V449I	V	-	1	0	LRRC37A3	60322493	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-1.266000	0.02842	-0.164000	0.10927	0.162000	0.16502	GTA	T|1.000;|0.000	1.000	weak		0.542	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
PTX4	390667	hgsc.bcm.edu	37	16	1538363	1538363	+	Intron	SNP	C	C	A	rs1040499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1538363C>A	ENST00000447419.2	-	2	167				PTX4_ENST00000293922.1_Missense_Mutation_p.G36C|PTX4_ENST00000440447.2_Intron			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						CCCGACAGGCCCACAGCACTC	0.652													A|||	2502	0.499601	0.7534	0.3242	5008	,	,		16625	0.5119		0.3897	False		,,,				2504	0.3814				p.G36C		Atlas-SNP	.											.	PTX4	46	.	0			c.G106T						PASS	.	A	CYS/GLY	2988,1410	458.8+/-352.1	998,992,209	63.0	61.0	62.0		106	-0.2	0.0	16	dbSNP_86	62	3259,5341	647.5+/-400.4	589,2081,1630	yes	missense	PTX4	NM_001013658.1	159	1587,3073,1839	AA,AC,CC		37.8953,32.06,48.0612	benign	36/474	1538363	6247,6751	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			ACAGGCCCACAGC		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.142-392G>T	16.37:g.1538363C>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	187	108	0.57754	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		1092	0.5	347	0.7052845528455285	117	0.32320441988950277	315	0.5506993006993007	313	0.4129287598944591	A	6.903	0.536146	0.13188	0.6794	0.378953	ENSG00000251692	ENST00000293922	T	0.08102	3.13	0.943	-0.196	0.13232	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11542	-1.0583	7	0.42905	T	0.14	.	2.4424	0.04498	0.2564:0.3221:0.4215:0.0	rs1040499;rs59677019;rs1040499	36	Q96A99-2	.	C	36	ENSP00000293922:G36C	ENSP00000293922:G36C	G	-	1	0	PTX4	1478364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.524000	0.06222	-0.511000	0.06514	-1.564000	0.00881	GGC	C|0.502;A|0.498	0.498	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
ACOT4	122970	hgsc.bcm.edu	37	14	74058832	74058832	+	Missense_Mutation	SNP	C	C	T	rs3742819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74058832C>T	ENST00000326303.4	+	1	423	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	57			R -> C (in dbSNP:rs3742819). {ECO:0000269|PubMed:15489334}.		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)		CGCCGACGCCCGCGGCGAGCT	0.761													C|||	1988	0.396965	0.1059	0.513	5008	,	,		12914	0.629		0.3926	False		,,,				2504	0.4734				p.R57C		Atlas-SNP	.											.	ACOT4	25	.	0			c.C169T						PASS	.	C	CYS/ARG	496,3446		38,420,1513	6.0	7.0	6.0		169	-9.9	0.0	14	dbSNP_107	6	2402,5202		412,1578,1812	no	missense	ACOT4	NM_152331.3	180	450,1998,3325	TT,TC,CC		31.5886,12.5824,25.0996	possibly-damaging	57/422	74058832	2898,8648	1971	3802	5773	SO:0001583	missense	122970	exon1			GACGCCCGCGGCG	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.169C>T	14.37:g.74058832C>T	ENSP00000323071:p.Arg57Cys	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	873	0.39972527472527475	60	0.12195121951219512	175	0.48342541436464087	366	0.6398601398601399	272	0.35883905013192613	C	13.86	2.362653	0.41902	0.125824	0.315886	ENSG00000177465	ENST00000326303	T	0.70516	-0.49	4.93	-9.85	0.00476	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	2.024500	0.02238	N	0.065442	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	P	0.51351	0.944	P	0.53954	0.738	T	0.48536	-0.9027	9	0.56958	D	0.05	-7.9166	15.5626	0.76262	0.2094:0.6193:0.1713:0.0	rs3742819	57	Q8N9L9	ACOT4_HUMAN	C	57	ENSP00000323071:R57C	ENSP00000323071:R57C	R	+	1	0	ACOT4	73128585	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.196000	0.03041	-2.884000	0.00318	-0.502000	0.04539	CGC	C|0.599;T|0.401	0.401	strong		0.761	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
TENM1	10178	hgsc.bcm.edu	37	X	123514900	123514900	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:123514900T>C	ENST00000371130.3	-	31	7727	c.7664A>G	c.(7663-7665)aAt>aGt	p.N2555S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.N2562S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2555					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)										ATGGGCATTATTGAGAATGGC	0.443																																					p.N2562S		Atlas-SNP	.											.	.	.	.	0			c.A7685G						PASS	.						88.0	79.0	82.0					X																	123514900		2203	4300	6503	SO:0001583	missense	10178	exon32			GCATTATTGAGAA	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.7664A>G	X.37:g.123514900T>C	ENSP00000360171:p.Asn2555Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	18.76	3.692756	0.68271	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87491	-2.26;-2.23	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.91754	0.7392	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.83275	0.97;0.985;0.996	D	0.90007	0.4118	10	0.24483	T	0.36	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2561;2562;2555	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2555;2562	ENSP00000360171:N2555S;ENSP00000403954:N2562S	ENSP00000360171:N2555S	N	-	2	0	ODZ1	123342581	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	AAT	.	.	none		0.443	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
CCDC180	100499483	hgsc.bcm.edu	37	9	100070351	100070351	+	Silent	SNP	G	G	C	rs12683119	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100070351G>C	ENST00000357054.1	+	16	1490	c.555G>C	c.(553-555)tcG>tcC	p.S185S	CCDC180_ENST00000411667.2_Silent_p.S46S|CCDC180_ENST00000395220.1_Silent_p.S185S|CCDC180_ENST00000529487.1_Silent_p.S46S|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Silent_p.S46S			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	185						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CCAAGATGTCGTCAGTGGGGA	0.592													G|||	687	0.137181	0.0356	0.2003	5008	,	,		14826	0.0575		0.2038	False		,,,				2504	0.2434				p.S46S		Atlas-SNP	.											.	.	.	.	0			c.G138C						PASS	.	G		320,4086	170.5+/-200.9	14,292,1897	72.0	65.0	67.0		138	-6.0	0.0	9	dbSNP_120	67	2362,6238	393.9+/-344.5	312,1738,2250	no	coding-synonymous	C9orf174	NM_020893.2		326,2030,4147	CC,CG,GG		27.4651,7.2628,20.6213		46/1702	100070351	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			GATGTCGTCAGTG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.555G>C	9.37:g.100070351G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				G|0.813;C|0.187	0.187	strong		0.592	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
COL10A1	1300	hgsc.bcm.edu	37	6	116446576	116446576	+	Missense_Mutation	SNP	A	A	G	rs1064583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116446576A>G	ENST00000327673.4	-	1	487	c.80T>C	c.(79-81)aTg>aCg	p.M27T	COL10A1_ENST00000243222.4_Missense_Mutation_p.M27T|NT5DC1_ENST00000319550.4_Intron			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	27	Nonhelical region (NC2).		M -> T (in dbSNP:rs1064583). {ECO:0000269|PubMed:15880705, ECO:0000269|PubMed:1764025}.		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)		GCCTGTGGGCATTTGGTATCG	0.398													G|||	2231	0.445487	0.736	0.3329	5008	,	,		16919	0.2579		0.3956	False		,,,				2504	0.3773				p.M27T		Atlas-SNP	.											.	COL10A1	51	.	0			c.T80C						PASS	.	G	,THR/MET	3084,1322	444.5+/-347.4	1096,892,215	261.0	243.0	249.0		,80	6.1	0.9	6	dbSNP_86	249	3384,5216	641.0+/-399.6	645,2094,1561	yes	intron,missense	COL10A1,NT5DC1	NM_152729.2,NM_000493.3	,81	1741,2986,1776	GG,GA,AA		39.3488,30.0045,49.7309	,benign	,27/681	116446576	6468,6538	2203	4300	6503	SO:0001583	missense	1300	exon2			GTGGGCATTTGGT		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.80T>C	6.37:g.116446576A>G	ENSP00000327368:p.Met27Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	37	CCDS5105.1	924	0.4230769230769231	346	0.7032520325203252	135	0.3729281767955801	144	0.2517482517482518	299	0.3944591029023747	G	0.013	-1.633148	0.00806	0.699955	0.393488	ENSG00000123500	ENST00000243222;ENST00000327673;ENST00000452729;ENST00000418500	D;D;D;T	0.89552	-2.53;-2.53;-2.51;-0.36	6.06	6.06	0.98353	.	0.435749	0.22816	N	0.055291	T	0.45276	0.1334	N	0.00268	-1.735	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38650	-0.9651	9	0.26408	T	0.33	.	8.6061	0.33773	0.076:0.0:0.7387:0.1853	rs1064583;rs52830706;rs59696986;rs1064583	27	Q03692	COAA1_HUMAN	T	27	ENSP00000243222:M27T;ENSP00000327368:M27T;ENSP00000411285:M27T;ENSP00000392712:M27T	ENSP00000243222:M27T	M	-	2	0	COL10A1	116553269	0.995000	0.38212	0.876000	0.34364	0.004000	0.04260	2.657000	0.46724	1.593000	0.50029	-0.119000	0.15052	ATG	A|0.536;G|0.464	0.464	strong		0.398	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1		
LNP1	348801	hgsc.bcm.edu	37	3	100170600	100170600	+	Missense_Mutation	SNP	A	A	T	rs386663873|rs76354691|rs71132521	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100170600A>T	ENST00000383693.3	+	3	1474	c.194A>T	c.(193-195)cAt>cTt	p.H65L	LNP1_ENST00000489752.1_Missense_Mutation_p.H78L	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	65										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						TCTGACTGCCATCCTAGAAGG	0.443																																					p.H65L		Atlas-SNP	.											.	LNP1	26	.	0			c.A194T						PASS	.						80.0	73.0	75.0					3																	100170600		1875	4103	5978	SO:0001583	missense	348801	exon3			ACTGCCATCCTAG		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.194A>T	3.37:g.100170600A>T	ENSP00000373191:p.His65Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	148	18	0.121622	NM_001085451	B7ZLT3	Missense_Mutation	SNP	ENST00000383693.3	37	CCDS43120.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547645	0.45383	.	.	ENSG00000206535	ENST00000383693;ENST00000489752	.	.	.	4.83	0.838	0.18902	.	0.744655	0.11980	N	0.510844	T	0.28366	0.0701	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.23976	-1.0173	9	0.72032	D	0.01	-12.6805	7.7915	0.29123	0.4966:0.0:0.0:0.5034	.	65	A1A4G5	LNP1_HUMAN	L	65;78	.	ENSP00000373191:H65L	H	+	2	0	LNP1	101653290	0.001000	0.12720	0.004000	0.12327	0.041000	0.13682	1.079000	0.30766	-0.004000	0.14419	-0.691000	0.03719	CAT	A|0.818;T|0.182	0.182	strong		0.443	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
SGSM1	129049	hgsc.bcm.edu	37	22	25251372	25251372	+	Missense_Mutation	SNP	C	C	T	rs56123612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:25251372C>T	ENST00000400359.4	+	7	651	c.644C>T	c.(643-645)tCg>tTg	p.S215L	SGSM1_ENST00000400358.4_Missense_Mutation_p.S215L	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	215						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						CGGCAGGACTCGCCCACCAAG	0.602													C|||	21	0.00419329	0.0008	0.0072	5008	,	,		18332	0.0		0.0139	False		,,,				2504	0.001				p.S215L		Atlas-SNP	.											.	SGSM1	150	.	0			c.C644T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	12,4156		0,12,2072	26.0	29.0	28.0		644,644,644,644	4.2	1.0	22	dbSNP_129	28	148,8278		0,148,4065	yes	missense,missense,missense,missense	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	145,145,145,145	0,160,6137	TT,TC,CC		1.7565,0.2879,1.2704	probably-damaging,probably-damaging,probably-damaging,probably-damaging	215/1149,215/1094,215/1033,215/1088	25251372	160,12434	2084	4213	6297	SO:0001583	missense	129049	exon7			AGGACTCGCCCAC	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.644C>T	22.37:g.25251372C>T	ENSP00000383212:p.Ser215Leu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	16	0.007326007326007326	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	26.2	4.716015	0.89205	0.002879	0.017565	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.08807	3.06;3.05	4.2	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.14960	0.0361	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;1.0;0.997;0.994	D;D;D;P;P	0.81914	0.995;0.953;0.991;0.758;0.885	T	0.01397	-1.1365	10	0.72032	D	0.01	-2.0118	15.9207	0.79570	0.0:1.0:0.0:0.0	rs56123612;rs61744442	215;190;348;215;190	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1;B9A6J4	.;.;.;SGSM1_HUMAN;.	L	190;215;215	ENSP00000383211:S215L;ENSP00000383212:S215L	ENSP00000383211:S215L	S	+	2	0	SGSM1	23581372	1.000000	0.71417	0.999000	0.59377	0.728000	0.41692	7.712000	0.84684	2.054000	0.61138	0.478000	0.44815	TCG	C|0.991;T|0.009	0.009	strong		0.602	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
SCN7A	6332	hgsc.bcm.edu	37	2	167284444	167284444	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:167284444G>A	ENST00000409855.1	-	17	2833	c.2707C>T	c.(2707-2709)Cgc>Tgc	p.R903C		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	903					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)	GAAGATCCGCGTCTGCAACCT	0.383																																					p.R903C		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,+1,6	SCN7A	410	6	0			c.C2707T						PASS	.						90.0	83.0	85.0					2																	167284444		1856	4093	5949	SO:0001583	missense	6332	exon17			ATCCGCGTCTGCA	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.2707C>T	2.37:g.167284444G>A	ENSP00000386796:p.Arg903Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	24	0.25	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.428994	0.43122	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.84730	-1.89	5.2	3.32	0.38043	Sodium ion transport-associated (1);	1.098480	0.06996	N	0.822524	D	0.87700	0.6243	M	0.80616	2.505	0.09310	N	1	D	0.61697	0.99	P	0.51101	0.659	T	0.71537	-0.4563	10	0.33141	T	0.24	.	4.2946	0.10895	0.0858:0.1551:0.5991:0.16	.	903	Q01118	SCN7A_HUMAN	C	903	ENSP00000386796:R903C	ENSP00000259060:R903C	R	-	1	0	SCN7A	166992690	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.174000	0.09839	0.630000	0.30394	0.591000	0.81541	CGC	.	.	none		0.383	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
TRIM39	56658	hgsc.bcm.edu	37	6	30297505	30297505	+	Silent	SNP	C	C	T	rs1264581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30297505C>T	ENST00000396547.1	+	2	571	c.411C>T	c.(409-411)gcC>gcT	p.A137A	HCG18_ENST00000413358.2_RNA|TRIM39_ENST00000396548.1_Silent_p.A137A|HCG18_ENST00000412685.2_RNA|TRIM39_ENST00000540416.1_Silent_p.A137A|TRIM39-RPP21_ENST00000513556.1_Silent_p.A49A|TRIM39_ENST00000376659.5_Silent_p.A137A|HCG18_ENST00000426882.1_RNA|TRIM39_ENST00000396551.3_Silent_p.A137A|TRIM39_ENST00000376656.4_Silent_p.A137A			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	137				A -> P (in Ref. 1; BAB16374). {ECO:0000305}.	apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCCACCGGGCCCACACCGTTG	0.557													C|||	248	0.0495208	0.0053	0.0331	5008	,	,		20139	0.0258		0.0835	False		,,,				2504	0.1104				p.A137A		Atlas-SNP	.											.	TRIM39	56	.	0			c.C411T						PASS	.	C	,,	49,2967		0,49,1459	68.0	72.0	70.0		411,411,411	1.2	1.0	6	dbSNP_87	70	400,5014		11,378,2318	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	11,427,3777	TT,TC,CC		7.3883,1.6247,5.3262	,,	137/504,137/519,137/489	30297505	449,7981	1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			CCGGGCCCACACC	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.411C>T	6.37:g.30297505C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1	81	0.03708791208791209	3	0.006097560975609756	13	0.03591160220994475	7	0.012237762237762238	58	0.07651715039577836	C	10.30	1.312291	0.23908	0.016247	0.073883	ENSG00000204599	ENST00000420746	.	.	.	5.35	1.24	0.21308	.	.	.	.	.	T	0.36717	0.0977	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20207	-1.0282	4	.	.	.	.	5.82	0.18522	0.0:0.592:0.1461:0.2619	rs1264581;rs6939888;rs17188498;rs17850231;rs17853355;rs58793944;rs1264581	.	.	.	L	67	.	.	P	+	2	0	TRIM39	30405484	0.841000	0.29509	0.998000	0.56505	0.990000	0.78478	0.240000	0.18042	0.380000	0.24823	0.555000	0.69702	CCC	C|0.951;T|0.049	0.049	strong		0.557	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
DLK1	8788	hgsc.bcm.edu	37	14	101200860	101200860	+	Missense_Mutation	SNP	G	G	A	rs1058009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	43	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	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		
LMBR1	64327	hgsc.bcm.edu	37	7	156518192	156518192	+	Silent	SNP	G	G	A	rs60299355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:156518192G>A	ENST00000353442.5	-	14	1331	c.1095C>T	c.(1093-1095)ggC>ggT	p.G365G	LMBR1_ENST00000354505.4_Silent_p.G406G|LMBR1_ENST00000540390.1_Silent_p.G344G|LMBR1_ENST00000359422.4_Silent_p.G213G	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	365					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		GGCTATAGAAGCCGACAACAG	0.413													G|||	485	0.096845	0.1536	0.0605	5008	,	,		18036	0.1369		0.0437	False		,,,				2504	0.0593				p.G365G		Atlas-SNP	.											LMBR1,lower_third,carcinoma,-2,1	LMBR1	35	1	0			c.C1095T						PASS	.	G		595,3811	260.7+/-263.8	57,481,1665	99.0	103.0	102.0		1095	-2.3	1.0	7	dbSNP_129	102	275,8325	104.0+/-165.0	6,263,4031	no	coding-synonymous	LMBR1	NM_022458.3		63,744,5696	AA,AG,GG		3.1977,13.5043,6.6892		365/491	156518192	870,12136	2203	4300	6503	SO:0001819	synonymous_variant	64327	exon14			ATAGAAGCCGACA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.1095C>T	7.37:g.156518192G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Silent	SNP	ENST00000353442.5	37	CCDS5945.1																																																																																			A|0.073;C|0.000;G|0.927	0.073	strong		0.413	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
CLSTN3	9746	hgsc.bcm.edu	37	12	7287956	7287956	+	Silent	SNP	C	C	T	rs34933247	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7287956C>T	ENST00000266546.6	+	4	867	c.417C>T	c.(415-417)aaC>aaT	p.N139N	CLSTN3_ENST00000537408.1_Silent_p.N151N	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	139	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						ACGATGTGAACGAGTTTGCCC	0.547													C|||	592	0.118211	0.0847	0.049	5008	,	,		-128	0.124		0.0676	False		,,,				2504	0.2587				p.N139N		Atlas-SNP	.											.	CLSTN3	84	.	0			c.C417T						PASS	.	C		407,3999	200.4+/-223.7	21,365,1817	220.0	130.0	160.0		417	-8.4	0.6	12	dbSNP_126	160	722,7878	176.2+/-226.1	24,674,3602	no	coding-synonymous	CLSTN3	NM_014718.3		45,1039,5419	TT,TC,CC		8.3953,9.2374,8.6806		139/957	7287956	1129,11877	2203	4300	6503	SO:0001819	synonymous_variant	9746	exon4			TGTGAACGAGTTT	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.417C>T	12.37:g.7287956C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	207	110	0.531401	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	37	CCDS8575.1																																																																																			C|0.917;T|0.083	0.083	strong		0.547	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
CHDH	55349	hgsc.bcm.edu	37	3	53857676	53857676	+	Silent	SNP	C	C	T	rs17053532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	10	0	0		WXS	Illumina HiSeq	Phase_I	23	19	0.826087	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	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386358	56386358	+	Silent	SNP	T	T	A	rs2526360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56386358T>A	ENST00000343736.4	-	22	4438	c.4275A>T	c.(4273-4275)cgA>cgT	p.R1425R	BZRAP1_ENST00000355701.3_Silent_p.R1425R|BZRAP1_ENST00000268893.6_Silent_p.R1365R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1425						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCAGTGTTCTCGGGGATCTG	0.662													A|||	1407	0.28095	0.2973	0.2709	5008	,	,		15887	0.25		0.332	False		,,,				2504	0.2454				p.R1425R		Atlas-SNP	.											BZRAP1_ENST00000355701,NS,carcinoma,0,2	BZRAP1	287	2	0			c.A4275T						scavenged	.	A	,	1205,3139		177,851,1144	47.0	57.0	54.0		4275,4095	-9.9	0.9	17	dbSNP_100	54	2502,5968		398,1706,2131	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	575,2557,3275	AA,AT,TT		29.5396,27.7394,28.9293	,	1425/1858,1365/1798	56386358	3707,9107	2172	4235	6407	SO:0001819	synonymous_variant	9256	exon22			GTGTTCTCGGGGA	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4275A>T	17.37:g.56386358T>A		Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			T|0.704;A|0.296	0.296	strong		0.662	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
ZBBX	79740	hgsc.bcm.edu	37	3	167023738	167023738	+	Splice_Site	SNP	G	G	C	rs13096767	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167023738G>C	ENST00000392766.2	-	17	1758	c.1418C>G	c.(1417-1419)gCa>gGa	p.A473G	ZBBX_ENST00000455345.2_Splice_Site_p.A473G|ZBBX_ENST00000392767.2_Splice_Site_p.A473G|ZBBX_ENST00000307529.5_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	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	98	98	1	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
LRRC16B	90668	hgsc.bcm.edu	37	14	24533539	24533539	+	Missense_Mutation	SNP	C	C	A	rs10146906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24533539C>A	ENST00000342740.5	+	32	3218	c.3064C>A	c.(3064-3066)Ctg>Atg	p.L1022M	LRRC16B_ENST00000334420.7_Missense_Mutation_p.L118M	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1022			L -> M (in dbSNP:rs10146906).			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)		CCGAAGGGTCCTGGAGGAAAG	0.587													A|||	1746	0.348642	0.4955	0.4553	5008	,	,		17869	0.0437		0.4632	False		,,,				2504	0.271				p.L1022M		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3064A						PASS	.	A	MET/LEU	2144,2262	587.6+/-386.7	530,1084,589	66.0	54.0	58.0		3064	5.3	1.0	14	dbSNP_119	58	3899,4701	596.6+/-393.6	866,2167,1267	yes	missense	LRRC16B	NM_138360.3	15	1396,3251,1856	AA,AC,CC		45.3372,48.6609,46.4632	benign	1022/1373	24533539	6043,6963	2203	4300	6503	SO:0001583	missense	90668	exon32			AGGGTCCTGGAGG	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.3064C>A	14.37:g.24533539C>A	ENSP00000340467:p.Leu1022Met	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	785	0.35943223443223443	237	0.4817073170731707	161	0.4447513812154696	25	0.043706293706293704	362	0.47757255936675463	A	11.50	1.658049	0.29425	0.486609	0.453372	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.43688	0.94;0.94	5.28	5.28	0.74379	.	0.000000	0.52532	N	0.000075	T	0.00012	0.0000	N	0.05383	-0.06	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45629	-0.9248	9	0.11794	T	0.64	-6.5815	9.8541	0.41075	0.6661:0.3338:0.0:0.0	rs10146906;rs52794133;rs56948275;rs10146906	118;1022	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	M	1022;118	ENSP00000340467:L1022M;ENSP00000334701:L118M	ENSP00000334701:L118M	L	+	1	2	LRRC16B	23603379	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.101000	0.41787	0.852000	0.35287	-0.256000	0.11100	CTG	C|0.593;A|0.407	0.407	strong		0.587	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
ARSK	153642	hgsc.bcm.edu	37	5	94939193	94939193	+	Missense_Mutation	SNP	A	A	G	rs17084927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:94939193A>G	ENST00000380009.4	+	8	1779	c.1574A>G	c.(1573-1575)cAg>cGg	p.Q525R		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	525			Q -> R (in dbSNP:rs17084927). {ECO:0000269|PubMed:14702039}.		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 region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		GCAATTGATCAGTGGCTTAAA	0.318													A|||	365	0.0728834	0.0363	0.0591	5008	,	,		17206	0.1081		0.0567	False		,,,				2504	0.1125				p.Q525R		Atlas-SNP	.											.	ARSK	29	.	0			c.A1574G						PASS	.	A	ARG/GLN	145,4261	95.3+/-134.0	1,143,2059	43.0	43.0	43.0		1574	-2.6	0.1	5	dbSNP_123	43	361,8239	118.6+/-178.1	7,347,3946	yes	missense	ARSK	NM_198150.2	43	8,490,6005	GG,GA,AA		4.1977,3.291,3.8905	benign	525/537	94939193	506,12500	2203	4300	6503	SO:0001583	missense	153642	exon8			TTGATCAGTGGCT		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"""Arylsulfatase family"""	25239	protein-coding gene	gene with protein product		610011	"""arylsulfatase K"""			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1574A>G	5.37:g.94939193A>G	ENSP00000369346:p.Gln525Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	37	CCDS4073.1	146	0.06684981684981685	18	0.036585365853658534	17	0.04696132596685083	69	0.12062937062937062	42	0.055408970976253295	A	0.603	-0.828377	0.02734	0.03291	0.041977	ENSG00000164291	ENST00000380009	D	0.98150	-4.75	5.61	-2.58	0.06228	.	0.901912	0.09787	N	0.755883	T	0.13457	0.0326	N	0.04880	-0.145	0.53688	P	2.199999999996649E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.69888	-0.5023	9	0.05620	T	0.96	0.0645	8.0072	0.30332	0.4756:0.0:0.4189:0.1055	rs17084927;rs52832124;rs17084927	525	Q6UWY0	ARSK_HUMAN	R	525	ENSP00000369346:Q525R	ENSP00000369346:Q525R	Q	+	2	0	ARSK	94964949	0.000000	0.05858	0.086000	0.20670	0.377000	0.30045	0.254000	0.18314	-0.355000	0.08199	0.533000	0.62120	CAG	A|0.948;G|0.052	0.052	strong		0.318	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150	
VSIG10L	147645	hgsc.bcm.edu	37	19	51837171	51837171	+	Silent	SNP	A	A	G	rs7255306	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51837171A>G	ENST00000335624.4	-	9	2447	c.2448T>C	c.(2446-2448)ccT>ccC	p.P816P		NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	816						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CCAAGGTAGAAGGATGCTTCT	0.522													G|||	2184	0.436102	0.8449	0.2493	5008	,	,		18798	0.249		0.2992	False		,,,				2504	0.3497				p.P816P		Atlas-SNP	.											.	VSIG10L	40	.	0			c.T2448C						PASS	.	G		1078,306		415,248,29	54.0	59.0	57.0		2448	-7.8	0.0	19	dbSNP_116	57	936,2246		142,652,797	no	coding-synonymous	VSIG10L	NM_001163922.1		557,900,826	GG,GA,AA		29.4155,22.1098,44.1086		816/868	51837171	2014,2552	692	1591	2283	SO:0001819	synonymous_variant	147645	exon9			GGTAGAAGGATGC		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.2448T>C	19.37:g.51837171A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_001163922		Silent	SNP	ENST00000335624.4	37	CCDS54300.1																																																																																			A|0.563;G|0.437	0.437	strong		0.522	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
ERICH6B	220081	hgsc.bcm.edu	37	13	46115731	46115731	+	Missense_Mutation	SNP	C	C	A	rs1536207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:46115731C>A	ENST00000298738.2	-	15	2121	c.1957G>T	c.(1957-1959)Gtc>Ttc	p.V653F	FAM194B_ENST00000504261.1_Intron	NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		653			V -> F (in dbSNP:rs1536207).							breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						CCCAGAAGGACCCGGATCTTC	0.507													C|||	1845	0.368411	0.1626	0.3631	5008	,	,		18039	0.5645		0.3608	False		,,,				2504	0.456				p.V653F		Atlas-SNP	.											.	FAM194B	42	.	0			c.G1957T						PASS	.						170.0	160.0	163.0					13																	46115731		692	1591	2283	SO:0001583	missense	220081	exon15			GAAGGACCCGGAT																												ENST00000298738.2:c.1957G>T	13.37:g.46115731C>A	ENSP00000298738:p.Val653Phe	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	175	91	0.52	NM_182542	Q96MB5	Missense_Mutation	SNP	ENST00000298738.2	37	CCDS45045.1	827	0.37866300366300365	97	0.19715447154471544	133	0.3674033149171271	329	0.5751748251748252	268	0.35356200527704484	C	12.56	1.974839	0.34848	.	.	ENSG00000165837	ENST00000298738	T	0.11930	2.73	4.89	-4.76	0.03229	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	D	0.57899	0.981	P	0.54026	0.74	T	0.32322	-0.9911	8	0.87932	D	0	-4.4035	12.9301	0.58282	0.0:0.7089:0.0:0.2911	rs1536207;rs61562259;rs1536207	653	Q5W0A0	F194B_HUMAN	F	653	ENSP00000298738:V653F	ENSP00000298738:V653F	V	-	1	0	FAM194B	45013732	0.002000	0.14202	0.334000	0.25495	0.122000	0.20287	-0.714000	0.05002	-0.620000	0.05641	-0.904000	0.02843	GTC	C|0.626;A|0.374	0.374	strong		0.507	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
OR10J1	26476	hgsc.bcm.edu	37	1	159409884	159409884	+	Missense_Mutation	SNP	G	G	A	rs12118628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:159409884G>A	ENST00000423932.3	+	1	373	c.336G>A	c.(334-336)atG>atA	p.M112I	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	112			M -> I (in dbSNP:rs12118628).		G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|stomach(1)	25	all_hematologic(112;0.0429)					CCACACAGATGTTCTTTTTTG	0.478													G|||	637	0.127196	0.0189	0.1772	5008	,	,		22012	0.252		0.1004	False		,,,				2504	0.137				p.M112I		Atlas-SNP	.											.	OR10J1	118	.	0			c.G336A						PASS	.	G	ILE/MET	190,4216	120.8+/-158.4	7,176,2020	100.0	82.0	88.0		336	1.8	1.0	1	dbSNP_120	88	1079,7521	226.6+/-262.3	75,929,3296	yes	missense	OR10J1	NM_012351.2	10	82,1105,5316	AA,AG,GG		12.5465,4.3123,9.757	benign	112/321	159409884	1269,11737	2203	4300	6503	SO:0001583	missense	26476	exon1			ACAGATGTTCTTT	X64995	CCDS1185.1	1q23.2	2012-08-09			ENSG00000196184	ENSG00000196184		"""GPCR / Class A : Olfactory receptors"""	8175	protein-coding gene	gene with protein product						1370859	Standard	NM_012351		Approved	HGMP07J, HSHGMP07J	uc010piv.2	P30954	OTTHUMG00000022737	ENST00000423932.3:c.336G>A	1.37:g.159409884G>A	ENSP00000399078:p.Met112Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	138	51	0.369565	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Missense_Mutation	SNP	ENST00000423932.3	37	CCDS1185.1	293	0.13415750915750915	8	0.016260162601626018	62	0.1712707182320442	142	0.24825174825174826	81	0.10686015831134564	G	11.57	1.677382	0.29783	0.043123	0.125465	ENSG00000196184	ENST00000423932	T	0.02015	4.5	4.48	1.82	0.25136	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.00875	0.0029	L	0.37897	1.145	0.38688	P	0.047294999999999976	B	0.23128	0.08	B	0.24006	0.05	T	0.47394	-0.9121	9	0.62326	D	0.03	.	10.0842	0.42408	0.249:0.0:0.751:0.0	rs12118628;rs52818896;rs61045534;rs12118628	112	P30954	O10J1_HUMAN	I	112	ENSP00000399078:M112I	ENSP00000399078:M112I	M	+	3	0	OR10J1	157676508	0.260000	0.24053	0.973000	0.42090	0.792000	0.44763	0.022000	0.13511	0.026000	0.15269	-0.797000	0.03246	ATG	G|0.887;A|0.113	0.113	strong		0.478	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351	
CDH19	28513	hgsc.bcm.edu	37	18	64176365	64176365	+	Silent	SNP	G	G	T	rs1055335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:64176365G>T	ENST00000262150.2	-	11	1987	c.1695C>A	c.(1693-1695)acC>acA	p.T565T	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1840	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)				GGATGGTAAGGGTGTTTGTAC	0.453													G|||	1264	0.252396	0.0651	0.2795	5008	,	,		16004	0.2331		0.3529	False		,,,				2504	0.4029				p.T565T		Atlas-SNP	.											.	CDH19	141	.	0			c.C1695A						PASS	.	G		529,3877	240.3+/-251.1	34,461,1708	212.0	179.0	190.0		1695	-0.1	1.0	18	dbSNP_86	190	3261,5339	489.9+/-372.7	632,1997,1671	no	coding-synonymous	CDH19	NM_021153.2		666,2458,3379	TT,TG,GG		37.9186,12.0064,29.1404		565/773	64176365	3790,9216	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			GGTAAGGGTGTTT	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.1695C>A	18.37:g.64176365G>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	253	91	0.359684	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			G|0.731;T|0.269	0.269	strong		0.453	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
XPC	7508	hgsc.bcm.edu	37	3	14193889	14193889	+	Silent	SNP	C	C	T	rs2227998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:14193889C>T	ENST00000285021.7	-	11	2275	c.2061G>A	c.(2059-2061)agG>agA	p.R687R	XPC_ENST00000449060.2_Silent_p.R650R	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	687	DNA-binding; preference for heteroduplex DNA.|Interaction with RAD23B.|Minimal sensor domain involved in damage recognition.				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						GCCACGTGTCCCTGGAATGCA	0.572			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	1179	0.235423	0.3343	0.2637	5008	,	,		20346	0.0327		0.2396	False		,,,				2504	0.2863				p.R687R		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.G2061A						PASS	.	C	,	1164,2980		169,826,1077	102.0	108.0	106.0		1950,2061	5.1	1.0	3	dbSNP_98	106	2178,6250		292,1594,2328	no	coding-synonymous,coding-synonymous	XPC	NM_001145769.1,NM_004628.4	,	461,2420,3405	TT,TC,CC		25.8424,28.0888,26.5829	,	650/904,687/941	14193889	3342,9230	2072	4214	6286	SO:0001819	synonymous_variant	7508	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CGTGTCCCTGGAA		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.2061G>A	3.37:g.14193889C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Silent	SNP	ENST00000285021.7	37	CCDS46763.1	470	0.21520146520146521	176	0.35772357723577236	97	0.26795580110497236	17	0.02972027972027972	180	0.23746701846965698	C	3.544	-0.093045	0.07053	0.280888	0.258424	ENSG00000154767	ENST00000538683	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28459	-1.0043	3	.	.	.	-14.0125	13.3993	0.60872	0.1573:0.8427:0.0:0.0	rs2227998;rs3731151;rs17562799;rs17851403	.	.	.	R	130	.	.	G	-	1	0	XPC	14168890	0.996000	0.38824	1.000000	0.80357	0.388000	0.30384	2.326000	0.43849	2.342000	0.79632	0.563000	0.77884	GGA	T|0.221;G|0.000;C|0.778	0.221	strong		0.572	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
SMC1B	27127	hgsc.bcm.edu	37	22	45749983	45749983	+	Missense_Mutation	SNP	G	G	T	rs5764698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45749983G>T	ENST00000357450.4	-	21	3147	c.3148C>A	c.(3148-3150)Ctg>Atg	p.L1050M	SMC1B_ENST00000404354.3_Missense_Mutation_p.L1050M	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1050			L -> M (in dbSNP:rs5764698). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		TGCCTACACAGTCTGGCTTCC	0.383													T|||	1443	0.288139	0.0477	0.4654	5008	,	,		16415	0.2946		0.492	False		,,,				2504	0.271				p.L1050M		Atlas-SNP	.											.	SMC1B	215	.	0			c.C3148A						PASS	.	T	MET/LEU	425,3289		27,371,1459	163.0	143.0	149.0		3148	2.4	0.8	22	dbSNP_114	149	4234,3950		1085,2064,943	yes	missense	SMC1B	NM_148674.3	15	1112,2435,2402	TT,TG,GG		48.2649,11.4432,39.1578	benign	1050/1236	45749983	4659,7239	1857	4092	5949	SO:0001583	missense	27127	exon21			TACACAGTCTGGC	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.3148C>A	22.37:g.45749983G>T	ENSP00000350036:p.Leu1050Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	758	0.34706959706959706	31	0.06300813008130081	154	0.425414364640884	191	0.3339160839160839	382	0.503957783641161	T	11.54	1.670439	0.29693	0.114432	0.517351	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.79141	-1.24;-1.04	5.74	2.38	0.29361	.	0.712653	0.13384	N	0.391884	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.40021	-0.9585	9	0.46703	T	0.11	.	2.7414	0.05254	0.1118:0.1276:0.347:0.4136	rs5764698;rs17639107;rs5764698	1050;1050	Q8NDV3-2;Q8NDV3-3	.;.	M	1050	ENSP00000350036:L1050M;ENSP00000385902:L1050M	ENSP00000350036:L1050M	L	-	1	2	SMC1B	44128647	0.249000	0.23941	0.776000	0.31678	0.951000	0.60555	0.418000	0.21230	0.107000	0.17824	-0.346000	0.07831	CTG	G|0.641;N|0.000	.	strong		0.383	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
WDR24	84219	hgsc.bcm.edu	37	16	735921	735921	+	Silent	SNP	T	T	C	rs763053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:735921T>C	ENST00000248142.6	-	9	1910	c.1911A>G	c.(1909-1911)gcA>gcG	p.A637A	JMJD8_ENST00000412368.2_5'Flank|WDR24_ENST00000293883.4_Silent_p.A507A|JMJD8_ENST00000454700.1_5'Flank|JMJD8_ENST00000562111.1_5'Flank|JMJD8_ENST00000562824.1_5'Flank|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000609261.1_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	637										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TGTCGCTCCGTGCATCTCCTT	0.637													t|||	2517	0.502596	0.6278	0.4236	5008	,	,		14641	0.7123		0.2674	False		,,,				2504	0.4151				p.A507A		Atlas-SNP	.											.	WDR24	111	.	0			c.A1521G						PASS	.			2394,2006	609.7+/-391.4	645,1104,451	118.0	114.0	115.0		1521	-6.7	0.5	16	dbSNP_86	115	1958,6640	343.7+/-325.0	214,1530,2555	no	coding-synonymous	WDR24	NM_032259.2		859,2634,3006	CC,CT,TT		22.7727,45.5909,33.4821		507/791	735921	4352,8646	2200	4299	6499	SO:0001819	synonymous_variant	84219	exon5			GCTCCGTGCATCT	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"""WD repeat domain containing"""	20852	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 21"""	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.1911A>G	16.37:g.735921T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	37																																																																																				T|0.601;C|0.399	0.399	strong		0.637	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259	
ZP2	7783	hgsc.bcm.edu	37	16	21213101	21213101	+	Missense_Mutation	SNP	T	T	C	rs201054139		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21213101T>C	ENST00000574002.1	-	14	1912	c.1430A>G	c.(1429-1431)aAc>aGc	p.N477S	ZP2_ENST00000574091.1_Missense_Mutation_p.N468S|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000219593.4_Missense_Mutation_p.N477S			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	477	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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)		GCTTTCAACGTTGATGTTTAG	0.418													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.N477S		Atlas-SNP	.											.	ZP2	92	.	0			c.A1430G						PASS	.						166.0	151.0	156.0					16																	21213101		2200	4300	6500	SO:0001583	missense	7783	exon13			TCAACGTTGATGT	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.1430A>G	16.37:g.21213101T>C	ENSP00000460971:p.Asn477Ser	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	208	104	0.5	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	4.765	0.142318	0.09083	.	.	ENSG00000103310	ENST00000219593	D	0.81499	-1.5	5.64	-0.5	0.12012	Zona pellucida sperm-binding protein (3);	0.414857	0.24343	N	0.039351	T	0.68970	0.3059	L	0.33245	0.995	0.09310	N	1	B;B	0.25105	0.118;0.1	B;B	0.32090	0.14;0.088	T	0.54768	-0.8244	10	0.21540	T	0.41	-4.7459	11.0072	0.47641	0.0:0.3295:0.0:0.6705	.	468;477	Q4VAP1;Q05996	.;ZP2_HUMAN	S	477	ENSP00000219593:N477S	ENSP00000219593:N477S	N	-	2	0	ZP2	21120602	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	0.162000	0.16501	-0.387000	0.07809	-0.326000	0.08463	AAC	T|1.000;C|0.000	0.000	strong		0.418	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
CD163L1	283316	hgsc.bcm.edu	37	12	7585971	7585971	+	Splice_Site	SNP	A	A	G	rs10845159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7585971A>G	ENST00000313599.3	-	3	501	c.444T>C	c.(442-444)taT>taC	p.Y148Y	CD163L1_ENST00000416109.2_Silent_p.Y148Y|CD163L1_ENST00000396630.1_Splice_Site_p.Y148Y			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	148	SRCR 1. {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						GACTCTTACCATAACAGTTCA	0.438													A|||	1437	0.286941	0.0242	0.3458	5008	,	,		-128	0.3413		0.5457	False		,,,				2504	0.2781				p.Y148Y		Atlas-SNP	.											.	CD163L1	238	.	0			c.T444C						PASS	.	A		502,3904	230.7+/-244.8	42,418,1743	102.0	94.0	97.0		444	-4.4	0.0	12	dbSNP_120	97	4725,3875	608.2+/-395.4	1311,2103,886	yes	coding-synonymous-near-splice	CD163L1	NM_174941.4		1353,2521,2629	GG,GA,AA		45.0581,11.3936,40.1891		148/1454	7585971	5227,7779	2203	4300	6503	SO:0001630	splice_region_variant	283316	exon3			CTTACCATAACAG	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.445+1T>C	12.37:g.7585971A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			A|0.625;G|0.375	0.375	strong		0.438	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	Silent
BCR	613	hgsc.bcm.edu	37	22	23627256	23627256	+	Silent	SNP	G	G	A	rs35727393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23627256G>A	ENST00000305877.8	+	10	3025	c.2274G>A	c.(2272-2274)ccG>ccA	p.P758P	BCR_ENST00000359540.3_Silent_p.P758P	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	758	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)	GGTACATTCCGCTCACGGATC	0.537			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""								G|||	89	0.0177716	0.0363	0.0086	5008	,	,		22214	0.0		0.0288	False		,,,				2504	0.0061				p.P758P		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.G2274A						PASS	.	G	,	171,4235	114.2+/-152.2	5,161,2037	121.0	92.0	101.0		2274,2274	-4.0	1.0	22	dbSNP_126	101	217,8383	92.3+/-154.4	4,209,4087	no	coding-synonymous,coding-synonymous	BCR	NM_004327.3,NM_021574.2	,	9,370,6124	AA,AG,GG		2.5233,3.8811,2.9832	,	758/1272,758/1228	23627256	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	613	exon10			CATTCCGCTCACG		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.2274G>A	22.37:g.23627256G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			G|0.975;A|0.025	0.025	strong		0.537	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
FAM118A	55007	hgsc.bcm.edu	37	22	45723920	45723920	+	Silent	SNP	C	C	T	rs111386114		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45723920C>T	ENST00000216214.3	+	5	1332	c.498C>T	c.(496-498)tcC>tcT	p.S166S	FAM118A_ENST00000405673.1_Silent_p.S166S|FAM118A_ENST00000441876.2_Silent_p.S166S|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	166						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)		CCATGGAGTCCCTGGACTTGA	0.617																																					p.S166S		Atlas-SNP	.											FAM118A,brain,glioma,0,1	FAM118A	32	1	0			c.C498T						scavenged	.						11.0	10.0	10.0					22																	45723920		2198	4293	6491	SO:0001819	synonymous_variant	55007	exon4			GGAGTCCCTGGAC	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.498C>T	22.37:g.45723920C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	88	25	0.284091	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			C|0.500;T|0.500	0.500	weak		0.617	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31107648	31107648	+	Missense_Mutation	SNP	C	C	T	rs1063646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31107648C>T	ENST00000259881.9	+	6	687	c.398C>T	c.(397-399)cCa>cTa	p.P133L	PSORS1C1_ENST00000481450.2_Missense_Mutation_p.P70L|PSORS1C2_ENST00000259845.4_5'Flank|PSORS1C1_ENST00000547221.1_Missense_Mutation_p.P85L	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	133			P -> L (in dbSNP:rs1063646). {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ACCTTGGCTCCAACTCTATTG	0.567													C|||	708	0.141374	0.1566	0.1354	5008	,	,		17740	0.0952		0.172	False		,,,				2504	0.1411				p.P133L		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.C398T						PASS	.	C	LEU/PRO	519,2503		36,447,1028	252.0	223.0	233.0		398	-0.1	0.0	6	dbSNP_86	233	899,4519		78,743,1888	yes	missense	PSORS1C1	NM_014068.2	98	114,1190,2916	TT,TC,CC		16.5928,17.1741,16.8009	probably-damaging	133/153	31107648	1418,7022	1511	2709	4220	SO:0001583	missense	170679	exon6			TGGCTCCAACTCT	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.398C>T	6.37:g.31107648C>T	ENSP00000259881:p.Pro133Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	229	118	0.515284	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	301	0.13782051282051283	77	0.1565040650406504	53	0.1464088397790055	58	0.10139860139860139	113	0.14907651715039577	C	7.648	0.682212	0.14907	0.171741	0.165928	ENSG00000204540	ENST00000259881;ENST00000547221;ENST00000481450	T;T;T	0.16457	2.34;2.34;2.34	1.84	-0.116	0.13555	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.80722	P	0.0	B;B	0.28850	0.225;0.225	B;B	0.17979	0.02;0.02	T	0.45175	-0.9279	8	0.08381	T	0.77	.	3.1931	0.06624	0.0:0.4996:0.3096:0.1909	rs1063646;rs3173368;rs1063646	82;133	Q9UIG5-2;Q9UIG5	.;PS1C1_HUMAN	L	133;85;70	ENSP00000259881:P133L;ENSP00000449471:P85L;ENSP00000447158:P70L	ENSP00000259881:P133L	P	+	2	0	PSORS1C1	31215627	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.033000	0.13754	-0.045000	0.13468	0.478000	0.44815	CCA	C|0.847;N|0.000	.	strong		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
TNC	3371	hgsc.bcm.edu	37	9	117826096	117826096	+	Missense_Mutation	SNP	G	G	T	rs113301777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:117826096G>T	ENST00000350763.4	-	12	4150	c.3739C>A	c.(3739-3741)Ctc>Atc	p.L1247I	TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000346706.3_Intron|TNC_ENST00000341037.4_Missense_Mutation_p.L1247I|TNC_ENST00000542877.1_Intron|TNC_ENST00000423613.2_Missense_Mutation_p.L1247I|TNC_ENST00000535648.1_Intron|TNC_ENST00000340094.3_Intron	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1247	Fibronectin type-III 7. {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						TCAACAGAGAGAGGGGTTGTG	0.507													G|||	33	0.00658946	0.0023	0.0115	5008	,	,		20840	0.0		0.0179	False		,,,				2504	0.0041				p.L1247I		Atlas-SNP	.											.	TNC	282	.	0			c.C3739A						PASS	.	G	ILE/LEU	17,4389	24.3+/-50.5	0,17,2186	126.0	130.0	128.0		3739	4.0	1.0	9	dbSNP_132	128	175,8425	81.5+/-144.1	1,173,4126	yes	missense	TNC	NM_002160.3	5	1,190,6312	TT,TG,GG		2.0349,0.3858,1.4762	benign	1247/2202	117826096	192,12814	2203	4300	6503	SO:0001583	missense	3371	exon12			CAGAGAGAGGGGT		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.3739C>A	9.37:g.117826096G>T	ENSP00000265131:p.Leu1247Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	16	0.007326007326007326	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	3.812	-0.039607	0.07497	0.003858	0.020349	ENSG00000041982	ENST00000350763;ENST00000341037;ENST00000423613	T;T;T	0.04758	3.56;3.56;3.56	5.84	3.95	0.45737	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.323443	0.23866	N	0.043799	T	0.03178	0.0093	L	0.51422	1.61	0.80722	D	1	P;B	0.38473	0.633;0.058	B;B	0.42163	0.378;0.208	T	0.43572	-0.9383	10	0.23891	T	0.37	.	11.3137	0.49379	0.0664:0.2508:0.6828:0.0	.	1247;1247	E9PC84;P24821	.;TENA_HUMAN	I	1247	ENSP00000265131:L1247I;ENSP00000339553:L1247I;ENSP00000411406:L1247I	ENSP00000339553:L1247I	L	-	1	0	TNC	116865917	1.000000	0.71417	0.963000	0.40424	0.263000	0.26337	2.368000	0.44222	0.760000	0.33108	0.655000	0.94253	CTC	G|0.985;T|0.015	0.015	strong		0.507	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
ATAD3B	83858	hgsc.bcm.edu	37	1	1431165	1431165	+	Missense_Mutation	SNP	C	C	T	rs9792879		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1431165C>T	ENST00000308647.7	+	16	2031	c.1915C>T	c.(1915-1917)Ccg>Tcg	p.P639S		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	639						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)	p.P639S(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	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)		TGGCGGTCGGCCGTTCTGCCC	0.647																																					p.P639S		Atlas-SNP	.											ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	1	Substitution - Missense(1)	skin(1)	c.C1915T						PASS	.						33.0	33.0	33.0					1																	1431165		2202	4300	6502	SO:0001583	missense	83858	exon16			GGTCGGCCGTTCT	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1915C>T	1.37:g.1431165C>T	ENSP00000311766:p.Pro639Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	476	0.21794871794871795	147	0.29878048780487804	60	0.16574585635359115	170	0.2972027972027972	99	0.13060686015831136	c	11.49	1.652810	0.29336	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93811	-3.29	1.39	0.415	0.16411	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	8.000000000008E-6	B;B	0.22604	0.072;0.024	B;B	0.12156	0.007;0.002	T	0.11324	-1.0592	8	0.87932	D	0	.	3.748	0.08555	0.0:0.7411:0.0:0.2589	rs9792879	593;639	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	S	473;639	ENSP00000311766:P639S	ENSP00000311766:P639S	P	+	1	0	ATAD3B	1421028	0.034000	0.19679	0.001000	0.08648	0.022000	0.10575	0.000000	0.12993	0.145000	0.18977	0.194000	0.17425	CCG	C|0.782;T|0.218	0.218	strong		0.647	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
SPNS3	201305	hgsc.bcm.edu	37	17	4337283	4337283	+	Silent	SNP	G	G	A	rs35751906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4337283G>A	ENST00000355530.2	+	1	301	c.21G>A	c.(19-21)gcG>gcA	p.A7A	SPNS3_ENST00000576069.1_3'UTR|SPNS3_ENST00000333476.2_5'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	7					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GGATGTCAGCGGAGTGCCCTG	0.667													G|||	561	0.112021	0.1846	0.0865	5008	,	,		15916	0.0		0.162	False		,,,				2504	0.0961				p.A7A		Atlas-SNP	.											SPNS3,NS,carcinoma,0,2	SPNS3	52	2	0			c.G21A						PASS	.	G		772,3632		74,624,1504	21.0	22.0	22.0		21	-8.3	0.0	17	dbSNP_126	22	1511,7085		127,1257,2914	no	coding-synonymous	SPNS3	NM_182538.4		201,1881,4418	AA,AG,GG		17.5779,17.5295,17.5615		7/513	4337283	2283,10717	2202	4298	6500	SO:0001819	synonymous_variant	201305	exon1			GTCAGCGGAGTGC		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.21G>A	17.37:g.4337283G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	22	0.328358	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			G|0.847;A|0.153	0.153	strong		0.667	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
KAT6A	7994	hgsc.bcm.edu	37	8	41791283	41791283	+	Silent	SNP	G	G	A	rs3739365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:41791283G>A	ENST00000396930.3	-	18	4998	c.4455C>T	c.(4453-4455)tcC>tcT	p.S1485S	KAT6A_ENST00000406337.1_Silent_p.S1485S|KAT6A_ENST00000265713.2_Silent_p.S1485S	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1485					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)										GAGACTGAACGGAGGAGATAG	0.567													A|||	812	0.162141	0.0953	0.183	5008	,	,		21777	0.2321		0.0716	False		,,,				2504	0.2587				p.S1485S		Atlas-SNP	.											.	.	.	.	0			c.C4455T						PASS	.	A	,,	440,3966	785.9+/-414.8	20,400,1783	132.0	106.0	115.0		4455,4455,4455	-5.8	0.6	8	dbSNP_107	115	633,7967	790.6+/-407.6	22,589,3689	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	42,989,5472	AA,AG,GG		7.3605,9.9864,8.25	,,	1485/2005,1485/2005,1485/2005	41791283	1073,11933	2203	4300	6503	SO:0001819	synonymous_variant	7994	exon18			CTGAACGGAGGAG	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.4455C>T	8.37:g.41791283G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			G|0.888;A|0.112	0.112	strong		0.567	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
CA6	765	hgsc.bcm.edu	37	1	9017204	9017204	+	Missense_Mutation	SNP	A	A	G	rs2274333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9017204A>G	ENST00000377443.2	+	3	272	c.268A>G	c.(268-270)Agc>Ggc	p.S90G	CA6_ENST00000476083.1_Intron|CA6_ENST00000377442.2_Missense_Mutation_p.S30G|CA6_ENST00000377436.3_Missense_Mutation_p.S90G	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	90			S -> G (in dbSNP:rs2274333). {ECO:0000269|PubMed:1899030, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|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;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	AGTGCAGATCAGCCTGCCCTC	0.597													A|||	1722	0.34385	0.1135	0.3919	5008	,	,		20770	0.5575		0.2913	False		,,,				2504	0.455				p.S90G		Atlas-SNP	.											.	CA6	47	.	0			c.A268G	GRCh37	CM065045	CA6	M	rs2274333	PASS	.	A	GLY/SER	701,3705	293.3+/-282.5	57,587,1559	64.0	51.0	56.0		268	-0.4	0.0	1	dbSNP_100	56	2548,6052	412.5+/-350.8	361,1826,2113	yes	missense	CA6	NM_001215.2	56	418,2413,3672	GG,GA,AA		29.6279,15.9101,24.9808	probably-damaging	90/309	9017204	3249,9757	2203	4300	6503	SO:0001583	missense	765	exon3			CAGATCAGCCTGC	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.268A>G	1.37:g.9017204A>G	ENSP00000366662:p.Ser90Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	708	0.3241758241758242	51	0.10365853658536585	126	0.34806629834254144	310	0.541958041958042	221	0.29155672823219	A	19.96	3.924134	0.73213	0.159101	0.296279	ENSG00000131686	ENST00000549778;ENST00000377443;ENST00000377436;ENST00000377442	T;T;T;T	0.68025	0.64;-0.3;-0.3;-0.3	5.22	-0.413	0.12363	Carbonic anhydrase, alpha-class, catalytic domain (4);	1.408090	0.04044	N	0.303668	T	0.00012	0.0000	M	0.65975	2.015	0.45883	P	0.0012699999999999934	D;D	0.58970	0.984;0.971	P;P	0.55999	0.713;0.789	T	0.28902	-1.0029	9	0.44086	T	0.13	.	1.5577	0.02588	0.4778:0.1497:0.0836:0.2889	rs2274333;rs61422202;rs2274333	30;90	E7EMQ1;P23280	.;CAH6_HUMAN	G	58;90;90;30	ENSP00000447108:S58G;ENSP00000366662:S90G;ENSP00000366654:S90G;ENSP00000366661:S30G	ENSP00000366654:S90G	S	+	1	0	CA6	8939791	0.000000	0.05858	0.042000	0.18584	0.647000	0.38526	0.016000	0.13377	-0.257000	0.09459	0.455000	0.32223	AGC	A|0.712;G|0.288	0.288	strong		0.597	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
KCNU1	157855	hgsc.bcm.edu	37	8	36692303	36692303	+	Splice_Site	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:36692303G>T	ENST00000399881.3	+	12	1249		c.e12-1			NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1						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)		TTGAAGGGTAGGTGGAATCTG	0.408																																					.		Atlas-SNP	.											KCNU1_ENST00000399881,colon,carcinoma,0,2	KCNU1	359	2	0			c.1213-1G>T						PASS	.						103.0	100.0	101.0					8																	36692303		1871	4112	5983	SO:0001630	splice_region_variant	157855	exon12			AGGGTAGGTGGAA	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.1213-1G>T	8.37:g.36692303G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_001031836		Splice_Site	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.865287	0.32977	.	.	ENSG00000215262	ENST00000399881	.	.	.	5.9	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9023	0.63812	0.0733:0.0:0.9266:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNU1	36811461	1.000000	0.71417	0.998000	0.56505	0.080000	0.17528	8.882000	0.92420	1.499000	0.48617	0.650000	0.86243	.	.	.	none		0.408	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	Intron
MUC16	94025	hgsc.bcm.edu	37	19	9076991	9076991	+	Silent	SNP	C	C	T	rs2591595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076991C>T	ENST00000397910.4	-	3	10658	c.10455G>A	c.(10453-10455)gcG>gcA	p.A3485A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3486	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						TGACAGATGACGCAGAGCTTG	0.507													T|||	1243	0.248203	0.2005	0.2118	5008	,	,		24293	0.249		0.3121	False		,,,				2504	0.272				p.A3485A		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,-1,2	MUC16	4315	2	0			c.G10455A						PASS	.	T		875,3293		103,669,1312	117.0	113.0	115.0		10455	-3.9	0.0	19	dbSNP_100	115	2435,5991		350,1735,2128	no	coding-synonymous	MUC16	NM_024690.2		453,2404,3440	TT,TC,CC		28.8986,20.9933,26.2824		3485/14508	9076991	3310,9284	2084	4213	6297	SO:0001819	synonymous_variant	94025	exon3			AGATGACGCAGAG	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.10455G>A	19.37:g.9076991C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.750;T|0.250	0.250	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NME4	4833	hgsc.bcm.edu	37	16	449659	449659	+	Silent	SNP	G	G	A	rs14293	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:449659G>A	ENST00000219479.2	+	4	374	c.360G>A	c.(358-360)tcG>tcA	p.S120S	DECR2_ENST00000397710.1_5'Flank|DECR2_ENST00000219481.5_5'Flank|NME4_ENST00000382940.4_Silent_p.S128S|DECR2_ENST00000424398.2_5'Flank|NME4_ENST00000397722.1_Silent_p.S50S|NME4_ENST00000450036.1_Silent_p.S50S	NM_005009.2	NP_005000.1	O00746	NDKM_HUMAN	NME/NM23 nucleoside diphosphate kinase 4	120					CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.S120S(1)		NS(1)|lung(1)|stomach(1)|urinary_tract(1)	4		Hepatocellular(16;0.00015)				TCCGCGCCTCGAGGGCCATGA	0.612													g|||	2213	0.441893	0.5598	0.4251	5008	,	,		19812	0.3671		0.3648	False		,,,				2504	0.4509				p.S120S		Atlas-SNP	.											NME4,NS,carcinoma,0,1	NME4	9	1	1	Substitution - coding silent(1)	stomach(1)	c.G360A						PASS	.	A		2418,1986	614.5+/-392.4	655,1108,439	105.0	102.0	103.0		360	-9.4	0.0	16	dbSNP_52	103	3421,5179	504.0+/-376.0	661,2099,1540	no	coding-synonymous	NME4	NM_005009.2		1316,3207,1979	AA,AG,GG		39.7791,45.0954,44.9016		120/188	449659	5839,7165	2202	4300	6502	SO:0001819	synonymous_variant	4833	exon4			CGCCTCGAGGGCC	Y07604	CCDS10408.1, CCDS66886.1, CCDS73797.1	16p13.3	2013-04-29	2012-05-18		ENSG00000103202	ENSG00000103202			7852	protein-coding gene	gene with protein product		601818	"""non-metastatic cells 4, protein expressed in"""			9099850, 19852809	Standard	NM_005009		Approved	nm23-H4, NM23H4, NDPKD	uc002cgz.3	O00746	OTTHUMG00000047995	ENST00000219479.2:c.360G>A	16.37:g.449659G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_005009	A2IDD0|Q5U0M9	Silent	SNP	ENST00000219479.2	37	CCDS10408.1	943	0.4317765567765568	300	0.6097560975609756	144	0.39779005524861877	222	0.3881118881118881	277	0.3654353562005277	g	0.088	-1.171406	0.01660	0.549046	0.397791	ENSG00000103202	ENST00000433358	.	.	.	4.7	-9.4	0.00616	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22779	P	0.99874316	.	.	.	.	.	.	T	0.36553	-0.9743	3	.	.	.	-14.0168	3.1609	0.06520	0.3082:0.1507:0.4248:0.1162	rs14293;rs1044211;rs3169386;rs11538882;rs17356176;rs17845527;rs17858422;rs59659280	.	.	.	K	116	.	.	E	+	1	0	NME4	389660	0.000000	0.05858	0.029000	0.17559	0.006000	0.05464	-3.108000	0.00601	-2.144000	0.00802	-4.346000	0.00007	GAG	G|0.557;A|0.443	0.443	strong		0.612	NME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109256.2	NM_005009	
WDR90	197335	hgsc.bcm.edu	37	16	701656	701656	+	Missense_Mutation	SNP	C	C	T	rs11642546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	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	
POU5F1	5460	hgsc.bcm.edu	37	6	31138371	31138371	+	Silent	SNP	G	G	A	rs1265160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31138371G>A	ENST00000259915.8	-	1	99	c.27C>T	c.(25-27)ttC>ttT	p.F9F	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	9					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)	GCGAGAAGGCGAAATCCGAAG	0.667			T	EWSR1	sarcoma								G|||	937	0.187101	0.1528	0.2305	5008	,	,		12955	0.3145		0.1302	False		,,,				2504	0.1299				p.F9F		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	POU5F1,caecum,carcinoma,0,1	POU5F1	25	1	0			c.C27T						PASS	.	G		266,2524		4,258,1133	4.0	4.0	4.0		27	-8.4	0.3	6	dbSNP_87	4	427,4481		12,403,2039	no	coding-synonymous	POU5F1	NM_002701.4		16,661,3172	AA,AG,GG		8.7001,9.5341,9.0023		9/361	31138371	693,7005	1395	2454	3849	SO:0001819	synonymous_variant	5460	exon1			GAAGGCGAAATCC	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.27C>T	6.37:g.31138371G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			G|0.822;A|0.178	0.178	strong		0.667	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
WBSCR17	64409	hgsc.bcm.edu	37	7	71142219	71142219	+	Silent	SNP	C	C	T	rs61740246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:71142219C>T	ENST00000333538.5	+	9	2062	c.1428C>T	c.(1426-1428)gaC>gaT	p.D476D	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	476	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				AGGCAAAAGACGTCTGCTTGG	0.542													C|||	235	0.0469249	0.0045	0.0735	5008	,	,		17946	0.001		0.1133	False		,,,				2504	0.0644				p.D476D		Atlas-SNP	.											WBSCR17,NS,carcinoma,+2,1	WBSCR17	208	1	0			c.C1428T						PASS	.	C		107,4299	82.9+/-121.4	1,105,2097	234.0	232.0	232.0		1428	-5.5	0.8	7	dbSNP_129	232	1054,7546	222.3+/-259.4	47,960,3293	no	coding-synonymous	WBSCR17	NM_022479.1		48,1065,5390	TT,TC,CC		12.2558,2.4285,8.9266		476/599	71142219	1161,11845	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon9			AAAAGACGTCTGC	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1428C>T	7.37:g.71142219C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																			C|0.917;T|0.083	0.083	strong		0.542	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
AGMAT	79814	hgsc.bcm.edu	37	1	15905501	15905501	+	Silent	SNP	G	G	A	rs41270261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15905501G>A	ENST00000375826.3	-	4	715	c.573C>T	c.(571-573)acC>acT	p.T191T	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	191					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCCTTGTCGGTCGTGTCCG	0.642													G|||	462	0.0922524	0.087	0.1124	5008	,	,		16216	0.0308		0.1421	False		,,,				2504	0.0971				p.T191T	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											AGMAT,colon,carcinoma,0,1	AGMAT	25	1	0			c.C573T						PASS	.	G		401,4005	201.5+/-224.5	22,357,1824	63.0	60.0	61.0		573	-11.7	0.0	1	dbSNP_127	61	1212,7388	244.2+/-273.5	81,1050,3169	no	coding-synonymous	AGMAT	NM_024758.4		103,1407,4993	AA,AG,GG		14.093,9.1012,12.402		191/353	15905501	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	79814	exon4			CTTGTCGGTCGTG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.573C>T	1.37:g.15905501G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_024758	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	37	CCDS160.1																																																																																			G|0.883;A|0.117	0.117	strong		0.642	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
GZF1	64412	hgsc.bcm.edu	37	20	23350290	23350290	+	Missense_Mutation	SNP	G	G	A	rs144872945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23350290G>A	ENST00000338121.5	+	5	1774	c.1697G>A	c.(1696-1698)cGc>cAc	p.R566H	GZF1_ENST00000377051.2_Missense_Mutation_p.R566H|GZF1_ENST00000544236.1_Missense_Mutation_p.R90H|GZF1_ENST00000542987.1_Missense_Mutation_p.R75H			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	566					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	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)|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 negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					CAGCGCCACCGCCGCATCCAC	0.632													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18962	0.0		0.004	False		,,,				2504	0.0				p.R566H		Atlas-SNP	.											GZF1,NS,adenocarcinoma,0,1	GZF1	61	1	0			c.G1697A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	85.0	88.0		1697	3.7	1.0	20	dbSNP_134	88	12,8588	9.1+/-34.3	0,12,4288	yes	missense	GZF1	NM_022482.3	29	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign	566/712	23350290	13,12993	2203	4300	6503	SO:0001583	missense	64412	exon4			GCCACCGCCGCAT	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1697G>A	20.37:g.23350290G>A	ENSP00000338290:p.Arg566His	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.792	1.178312	0.21787	2.27E-4	0.001395	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.37584	3.17;1.19;3.17;1.19	5.95	3.74	0.42951	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.205916	0.32055	N	0.006644	T	0.15739	0.0379	N	0.26092	0.79	0.35685	D	0.814363	B	0.06786	0.001	B	0.06405	0.002	T	0.16129	-1.0413	10	0.16896	T	0.51	.	7.9996	0.30288	0.8298:0.0:0.1702:0.0	.	566	Q9H116	GZF1_HUMAN	H	90;566;75;566	ENSP00000445458:R90H;ENSP00000338290:R566H;ENSP00000445118:R75H;ENSP00000366250:R566H	ENSP00000338290:R566H	R	+	2	0	GZF1	23298290	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	6.157000	0.71846	0.545000	0.28902	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.632	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
MYO5C	55930	hgsc.bcm.edu	37	15	52534344	52534344	+	Silent	SNP	G	G	A	rs3751631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52534344G>A	ENST00000261839.7	-	20	2618	c.2457C>T	c.(2455-2457)cgC>cgT	p.R819R	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	819	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		CAAGATACCCGCGGCAGTGCT	0.498													G|||	1918	0.382987	0.1415	0.6167	5008	,	,		21504	0.0417		0.8171	False		,,,				2504	0.4489				p.R819R		Atlas-SNP	.											MYO5C,colon,carcinoma,0,1	MYO5C	162	1	0			c.C2457T						PASS	.	G		1127,2871		161,805,1033	264.0	266.0	266.0		2457	-10.3	0.0	15	dbSNP_107	266	6795,1557		2766,1263,147	no	coding-synonymous	MYO5C	NM_018728.3		2927,2068,1180	AA,AG,GG		18.6422,28.1891,35.8543		819/1743	52534344	7922,4428	1999	4176	6175	SO:0001819	synonymous_variant	55930	exon20			ATACCCGCGGCAG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2457C>T	15.37:g.52534344G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	37	CCDS42036.1																																																																																			G|0.534;A|0.466	0.466	strong		0.498	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
FKBP15	23307	hgsc.bcm.edu	37	9	115932012	115932012	+	Missense_Mutation	SNP	G	G	T	rs57348436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115932012G>T	ENST00000238256.3	-	26	3094	c.2977C>A	c.(2977-2979)Ccg>Acg	p.P993T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	993			P -> T (in dbSNP:rs57348436).		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						GGAGGCAACGGGACAGCTTCC	0.592													G|||	307	0.0613019	0.0363	0.0317	5008	,	,		17489	0.0387		0.0467	False		,,,				2504	0.1544				p.P993T		Atlas-SNP	.											.	FKBP15	128	.	0			c.C2977A						PASS	.	G	THR/PRO	190,3968		5,180,1894	44.0	49.0	47.0		2977	2.7	0.0	9	dbSNP_129	47	532,7884		15,502,3691	yes	missense	FKBP15	NM_015258.1	38	20,682,5585	TT,TG,GG		6.3213,4.5695,5.742	possibly-damaging	993/1220	115932012	722,11852	2079	4208	6287	SO:0001583	missense	23307	exon26			GCAACGGGACAGC	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.2977C>A	9.37:g.115932012G>T	ENSP00000238256:p.Pro993Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	79	0.036172161172161175	22	0.044715447154471545	12	0.03314917127071823	11	0.019230769230769232	34	0.044854881266490766	G	9.749	1.167001	0.21621	0.045695	0.063213	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.29142	1.58;1.6	4.61	2.72	0.32119	.	.	.	.	.	T	0.03095	0.0091	L	0.51422	1.61	0.09310	N	1	B;B	0.29646	0.253;0.02	B;B	0.31337	0.128;0.018	T	0.11743	-1.0575	9	0.56958	D	0.05	0.0131	6.2186	0.20669	0.2382:0.0:0.7618:0.0	rs57348436	574;993	B4DVS2;Q5T1M5	.;FKB15_HUMAN	T	1018;993	ENSP00000416158:P1018T;ENSP00000238256:P993T	ENSP00000238256:P993T	P	-	1	0	FKBP15	114971833	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-0.337000	0.07852	0.532000	0.28657	0.491000	0.48974	CCG	G|0.954;T|0.046	0.046	strong		0.592	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
RREB1	6239	hgsc.bcm.edu	37	6	7211818	7211818	+	Missense_Mutation	SNP	G	G	A	rs1334576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7211818G>A	ENST00000349384.6	+	8	897	c.583G>A	c.(583-585)Ggg>Agg	p.G195R	RREB1_ENST00000379938.2_Missense_Mutation_p.G195R|RREB1_ENST00000379933.3_Missense_Mutation_p.G195R|RREB1_ENST00000334984.6_Missense_Mutation_p.G195R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	195			G -> R (in dbSNP:rs1334576). {ECO:0000269|PubMed:15067362, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21703425}.		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)				GGTAGAAGACGGGCAGTCAGG	0.458													G|||	2292	0.457668	0.32	0.4308	5008	,	,		16453	0.5327		0.4076	False		,,,				2504	0.637				p.G195R		Atlas-SNP	.											.	RREB1	242	.	0			c.G583A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1475,2931	475.9+/-357.4	243,989,971	121.0	113.0	116.0		583,583,583,583	2.9	0.0	6	dbSNP_88	116	3451,5149	506.6+/-376.6	687,2077,1536	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	125,125,125,125	930,3066,2507	AA,AG,GG		40.1279,33.4771,37.8748	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/1688,195/1743,195/1477,195/1688	7211818	4926,8080	2203	4300	6503	SO:0001583	missense	6239	exon8			GAAGACGGGCAGT	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.583G>A	6.37:g.7211818G>A	ENSP00000305560:p.Gly195Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	927	0.42445054945054944	172	0.34959349593495936	154	0.425414364640884	292	0.5104895104895105	309	0.4076517150395778	G	12.02	1.811580	0.32053	0.334771	0.401279	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T	0.11385	2.9;2.85;2.9;2.78;2.89	6.06	2.93	0.34026	.	0.599517	0.15531	N	0.257488	T	0.07369	0.0186	L	0.51422	1.61	0.80722	P	0.0	D;D;B	0.71674	0.997;0.998;0.139	P;P;B	0.59546	0.859;0.823;0.027	T	0.23904	-1.0175	9	0.23302	T	0.38	-50.4784	1.897	0.03260	0.1631:0.1215:0.4717:0.2437	rs1334576;rs17672663;rs17846344;rs17859378;rs52793584;rs60410842;rs1334576	195;195;195	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	195	ENSP00000369265:G195R;ENSP00000369270:G195R;ENSP00000305560:G195R;ENSP00000335574:G195R;ENSP00000419511:G195R	ENSP00000335574:G195R	G	+	1	0	RREB1	7156817	0.133000	0.22466	0.039000	0.18376	0.029000	0.11900	0.911000	0.28584	1.580000	0.49851	0.655000	0.94253	GGG	G|0.596;N|0.000	.	strong		0.458	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
RAB8B	51762	hgsc.bcm.edu	37	15	63548787	63548787	+	Silent	SNP	G	G	A	rs10851726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:63548787G>A	ENST00000321437.4	+	5	564	c.408G>A	c.(406-408)ggG>ggA	p.G136G	RAB8B_ENST00000448330.2_Silent_p.G136G	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	136					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						AAGAAAGAGGGGAGAAGGTAA	0.333													G|||	1375	0.274561	0.1452	0.2089	5008	,	,		19289	0.4663		0.1521	False		,,,				2504	0.4243				p.G136G		Atlas-SNP	.											.	RAB8B	23	.	0			c.G408A						PASS	.	G		606,3800	263.8+/-265.7	42,522,1639	103.0	97.0	99.0		408	-8.6	0.6	15	dbSNP_120	99	1200,7400	240.7+/-271.3	91,1018,3191	no	coding-synonymous	RAB8B	NM_016530.2		133,1540,4830	AA,AG,GG		13.9535,13.754,13.8859		136/208	63548787	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	51762	exon5			AAGAGGGGAGAAG	AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"""RAB, member RAS oncogene"""	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.408G>A	15.37:g.63548787G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_016530	Q5JPC4|Q9P293	Silent	SNP	ENST00000321437.4	37	CCDS10183.1																																																																																			G|0.814;A|0.186	0.186	strong		0.333	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1	NM_016530	
EXOSC10	5394	hgsc.bcm.edu	37	1	11150682	11150682	+	Silent	SNP	C	C	T	rs3737621	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11150682C>T	ENST00000376936.4	-	6	736	c.687G>A	c.(685-687)gaG>gaA	p.E229E	EXOSC10_ENST00000544779.1_Silent_p.E229E|EXOSC10_ENST00000304457.7_Silent_p.E229E	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	229					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E229E(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CGTCCAAGTCCTCAGGACGAT	0.502													C|||	563	0.11242	0.1384	0.072	5008	,	,		19085	0.1577		0.0258	False		,,,				2504	0.1483				p.E229E	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											EXOSC10,NS,carcinoma,0,1	EXOSC10	59	1	1	Substitution - coding silent(1)	stomach(1)	c.G687A						PASS	.	C	,	496,3910	227.5+/-242.7	26,444,1733	60.0	52.0	55.0		687,687	3.8	1.0	1	dbSNP_107	55	201,8399	85.6+/-148.0	5,191,4104	no	coding-synonymous,coding-synonymous	EXOSC10	NM_001001998.1,NM_002685.2	,	31,635,5837	TT,TC,CC		2.3372,11.2574,5.3591	,	229/886,229/861	11150682	697,12309	2203	4300	6503	SO:0001819	synonymous_variant	5394	exon6			CAAGTCCTCAGGA	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.687G>A	1.37:g.11150682C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	37	CCDS30584.1																																																																																			C|0.940;T|0.060	0.060	strong		0.502	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325325	77325325	+	Missense_Mutation	SNP	G	G	T	rs35478105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:77325325G>T	ENST00000282849.5	-	21	3658	c.3240C>A	c.(3238-3240)agC>agA	p.S1080R	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1080	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> R (in dbSNP:rs35478105). {ECO:0000269|PubMed:14702039}.		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)	p.S1080R(1)		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						AGCCCTTCTCGCTGCACTTCA	0.498													G|||	1141	0.227835	0.0303	0.245	5008	,	,		21167	0.1101		0.5159	False		,,,				2504	0.3078				p.S1080R		Atlas-SNP	.											ADAMTS18,NS,carcinoma,0,1	ADAMTS18	270	1	1	Substitution - Missense(1)	stomach(1)	c.C3240A						PASS	.	G	ARG/SER	525,3871	238.7+/-250.0	33,459,1706	211.0	213.0	213.0		3240	-4.8	0.9	16	dbSNP_126	213	4260,4340	573.4+/-389.9	1045,2170,1085	yes	missense	ADAMTS18	NM_199355.2	110	1078,2629,2791	TT,TG,GG		49.5349,11.9427,36.819	possibly-damaging	1080/1222	77325325	4785,8211	2198	4300	6498	SO:0001583	missense	170692	exon21			CTTCTCGCTGCAC	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.3240C>A	16.37:g.77325325G>T	ENSP00000282849:p.Ser1080Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	597	0.2733516483516483	19	0.03861788617886179	103	0.2845303867403315	79	0.1381118881118881	396	0.5224274406332454	G	16.99	3.274610	0.59649	0.119427	0.495349	ENSG00000140873	ENST00000282849	T	0.53857	0.6	5.8	-4.75	0.03239	.	0.275715	0.40469	N	0.001099	T	0.00012	0.0000	N	0.13198	0.31	0.45704	P	0.0013840000000000519	B	0.27765	0.188	B	0.31191	0.125	T	0.39702	-0.9601	9	0.14656	T	0.56	.	10.3361	0.43850	0.6058:0.0983:0.2959:0.0	rs35478105;rs61749043	1080	Q8TE60	ATS18_HUMAN	R	1080	ENSP00000282849:S1080R	ENSP00000282849:S1080R	S	-	3	2	ADAMTS18	75882826	0.036000	0.19791	0.928000	0.36995	0.846000	0.48090	-0.545000	0.06069	-0.629000	0.05575	-0.253000	0.11424	AGC	G|0.665;T|0.335	0.335	strong		0.498	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
DCK	1633	hgsc.bcm.edu	37	4	71888176	71888176	+	Silent	SNP	C	C	T	rs11544786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71888176C>T	ENST00000286648.5	+	3	697	c.300C>T	c.(298-300)gcC>gcT	p.A100A	DCK_ENST00000504730.1_Silent_p.A100A|DCK_ENST00000504952.1_Silent_p.A100A	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	100					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	AAACATATGCCTGTCTCAGTC	0.393													C|||	160	0.0319489	0.0023	0.0447	5008	,	,		18473	0.0		0.0815	False		,,,				2504	0.045				p.A100A		Atlas-SNP	.											.	DCK	23	.	0			c.C300T						PASS	.	C		61,4345	58.7+/-95.3	0,61,2142	128.0	126.0	127.0		300	2.0	1.0	4	dbSNP_120	127	526,8074	148.3+/-203.6	17,492,3791	no	coding-synonymous	DCK	NM_000788.2		17,553,5933	TT,TC,CC		6.1163,1.3845,4.5133		100/261	71888176	587,12419	2203	4300	6503	SO:0001819	synonymous_variant	1633	exon3			ATATGCCTGTCTC	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.300C>T	4.37:g.71888176C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Silent	SNP	ENST00000286648.5	37	CCDS3548.1																																																																																			C|0.956;T|0.044	0.044	strong		0.393	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2		
OR2S2	56656	hgsc.bcm.edu	37	9	35957355	35957355	+	Silent	SNP	G	G	A	rs2233568	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35957355G>A	ENST00000341959.2	-	1	796	c.741C>T	c.(739-741)acC>acT	p.T247T		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	247					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)	p.T237T(1)		central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			CGATCACCACGGTGAGGTGGG	0.498													A|||	1722	0.34385	0.4902	0.2968	5008	,	,		24532	0.2986		0.2793	False		,,,				2504	0.2924				p.T247T	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											OR2S2,NS,carcinoma,0,1	OR2S2	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C741T						PASS	.	A		2030,2376	611.7+/-391.8	445,1140,618	100.0	102.0	101.0		741	-3.0	0.6	9	dbSNP_98	101	2836,5764	675.0+/-403.2	508,1820,1972	no	coding-synonymous	OR2S2	NM_019897.2		953,2960,2590	AA,AG,GG		32.9767,46.0735,37.4135		247/320	35957355	4866,8140	2203	4300	6503	SO:0001819	synonymous_variant	56656	exon1			CACCACGGTGAGG	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.741C>T	9.37:g.35957355G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_019897	Q2M3L0|Q6IF19|Q96R42	Silent	SNP	ENST00000341959.2	37	CCDS6596.2																																																																																			G|0.634;A|0.366	0.366	strong		0.498	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
OR2M2	391194	hgsc.bcm.edu	37	1	248343543	248343543	+	Silent	SNP	C	C	T	rs9435919|rs386641960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248343543C>T	ENST00000359682.2	+	1	256	c.256C>T	c.(256-258)Ctg>Ttg	p.L86L		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	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)			CTTCAACTACCTGTCTGGCAG	0.493													c|||	2897	0.578474	0.6188	0.6052	5008	,	,		20890	0.4306		0.6382	False		,,,				2504	0.5961				p.L86L		Atlas-SNP	.											.	OR2M2	149	.	0			c.C256T						PASS	.	C		2728,1678	654.4+/-399.7	843,1042,318	212.0	217.0	216.0		256	-4.1	0.0	1	dbSNP_119	216	5583,3015	664.4+/-402.2	1825,1933,541	no	coding-synonymous	OR2M2	NM_001004688.1		2668,2975,859	TT,TC,CC		35.0663,38.0844,36.0889		86/348	248343543	8311,4693	2203	4299	6502	SO:0001819	synonymous_variant	391194	exon1			AACTACCTGTCTG	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.256C>T	1.37:g.248343543C>T		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	186	182	0.978495	NM_001004688	A3KFT4	Silent	SNP	ENST00000359682.2	37	CCDS31106.1																																																																																			C|0.384;T|0.616	0.616	strong		0.493	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
OR1A2	26189	hgsc.bcm.edu	37	17	3101590	3101590	+	Missense_Mutation	SNP	C	C	T	rs2469791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3101590C>T	ENST00000381951.1	+	1	778	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	260			R -> C (in dbSNP:rs2469791). {ECO:0000269|PubMed:15489334}.		positive regulation of cytokinesis (GO:0032467)	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)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						CATGTATTTCCGCCCTCTGAC	0.438													C|||	740	0.147764	0.2194	0.1571	5008	,	,		18666	0.001		0.2406	False		,,,				2504	0.1002				p.R260C		Atlas-SNP	.											.	OR1A2	52	.	0			c.C778T						PASS	.	C	CYS/ARG	932,3474	356.4+/-313.5	100,732,1371	115.0	110.0	112.0		778	-0.6	0.0	17	dbSNP_100	112	2170,6430	370.0+/-335.7	279,1612,2409	yes	missense	OR1A2	NM_012352.1	180	379,2344,3780	TT,TC,CC		25.2326,21.153,23.8505	probably-damaging	260/310	3101590	3102,9904	2203	4300	6503	SO:0001583	missense	26189	exon1			TATTTCCGCCCTC	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"""GPCR / Class A : Olfactory receptors"""	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.778C>T	17.37:g.3101590C>T	ENSP00000371377:p.Arg260Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	37	CCDS11021.1	338	0.15476190476190477	104	0.21138211382113822	61	0.1685082872928177	0	0.0	173	0.22823218997361477	C	1.569	-0.534700	0.04082	0.21153	0.252326	ENSG00000172150	ENST00000381951	T	0.35789	1.29	4.0	-0.599	0.11645	GPCR, rhodopsin-like superfamily (1);	0.135982	0.34268	N	0.004118	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	P	0.36535	0.557	B	0.34093	0.175	T	0.28713	-1.0035	9	0.23302	T	0.38	.	4.6096	0.12395	0.157:0.5721:0.0:0.2709	rs2469791;rs52812308;rs56722735;rs2469791	260	Q9Y585	OR1A2_HUMAN	C	260	ENSP00000371377:R260C	ENSP00000371377:R260C	R	+	1	0	OR1A2	3048340	0.000000	0.05858	0.012000	0.15200	0.177000	0.22998	-1.119000	0.03276	-0.147000	0.11254	0.543000	0.68304	CGC	C|0.791;T|0.209	0.209	strong		0.438	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352	
SPNS3	201305	hgsc.bcm.edu	37	17	4337412	4337412	+	Silent	SNP	C	C	G	rs3809853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4337412C>G	ENST00000355530.2	+	1	430	c.150C>G	c.(148-150)gtC>gtG	p.V50V	SPNS3_ENST00000576069.1_3'UTR|SPNS3_ENST00000333476.2_5'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	50					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						CTGCCGCCGTCCTCTGCTACA	0.647													G|||	1162	0.232029	0.407	0.1585	5008	,	,		17785	0.125		0.2396	False		,,,				2504	0.1503				p.V50V		Atlas-SNP	.											.	SPNS3	52	.	0			c.C150G						PASS	.	G		1639,2767	657.5+/-400.2	307,1025,871	75.0	75.0	75.0		150	-6.1	0.2	17	dbSNP_107	75	2183,6417	710.3+/-405.8	268,1647,2385	no	coding-synonymous	SPNS3	NM_182538.4		575,2672,3256	GG,GC,CC		25.3837,37.1993,29.3864		50/513	4337412	3822,9184	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon1			CGCCGTCCTCTGC		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.150C>G	17.37:g.4337412C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			C|0.722;G|0.278	0.278	strong		0.647	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
EID2	163126	hgsc.bcm.edu	37	19	40030704	40030704	+	Missense_Mutation	SNP	C	C	T	rs7252027	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	55	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	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	
CPVL	54504	hgsc.bcm.edu	37	7	29160604	29160604	+	Missense_Mutation	SNP	C	C	T	rs34219043	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:29160604C>T	ENST00000409850.1	-	6	720	c.74G>A	c.(73-75)cGc>cAc	p.R25H	CPVL_ENST00000265394.5_Missense_Mutation_p.R25H|CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Missense_Mutation_p.R25H			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	25			R -> H (in dbSNP:rs34219043). {ECO:0000269|Ref.2}.			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						GTATAGGGAGCGAAACAGCCC	0.493													C|||	366	0.0730831	0.0219	0.1138	5008	,	,		14887	0.0327		0.172	False		,,,				2504	0.0532				p.R25H		Atlas-SNP	.											CPVL,NS,malignant_melanoma,-1,1	CPVL	60	1	0			c.G74A						PASS	.	C	HIS/ARG,HIS/ARG	239,4167	139.6+/-175.2	7,225,1971	98.0	90.0	93.0		74,74	0.6	0.0	7	dbSNP_126	93	1728,6872	315.3+/-312.2	180,1368,2752	yes	missense,missense	CPVL	NM_019029.2,NM_031311.3	29,29	187,1593,4723	TT,TC,CC		20.093,5.4244,15.1238	benign,benign	25/477,25/477	29160604	1967,11039	2203	4300	6503	SO:0001583	missense	54504	exon2			AGGGAGCGAAACA	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.74G>A	7.37:g.29160604C>T	ENSP00000387164:p.Arg25His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	186	63	0.33871	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	204	0.09340659340659341	18	0.036585365853658534	40	0.11049723756906077	13	0.022727272727272728	133	0.17546174142480211	C	8.292	0.817846	0.16607	0.054244	0.20093	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000409850;ENST00000449801;ENST00000455544	T;T;T;T;T	0.41758	2.5;2.5;2.5;1.14;0.99	5.58	0.593	0.17478	.	2.246760	0.01807	N	0.033217	T	0.00039	0.0001	N	0.11064	0.09	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.13764	-1.0497	9	0.27785	T	0.31	-12.872	8.7206	0.34439	0.0:0.608:0.0:0.392	rs34219043	25	Q9H3G5	CPVL_HUMAN	H	25	ENSP00000265394:R25H;ENSP00000379572:R25H;ENSP00000387164:R25H;ENSP00000413287:R25H;ENSP00000412857:R25H	ENSP00000265394:R25H	R	-	2	0	CPVL	29127129	0.680000	0.27605	0.016000	0.15963	0.459000	0.32528	0.188000	0.17018	-0.176000	0.10707	0.563000	0.77884	CGC	C|0.863;G|0.000;T|0.137	0.137	strong		0.493	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
FLG	2312	hgsc.bcm.edu	37	1	152285621	152285621	+	Missense_Mutation	SNP	T	T	A	rs145627745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152285621T>A	ENST00000368799.1	-	3	1776	c.1741A>T	c.(1741-1743)Acc>Tcc	p.T581S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	581	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)			GAGTGCCTGGTGCCGTCTCCT	0.567									Ichthyosis				-|||	15	0.00299521	0.0	0.0014	5008	,	,		18116	0.0		0.0089	False		,,,				2504	0.0051				p.T581S		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A1741T						PASS	.	A	SER/THR	13,4393		0,13,2190	392.0	368.0	376.0		1741	-4.3	0.0	1	dbSNP_134	376	101,8499		2,97,4201	no	missense	FLG	NM_002016.1	58	2,110,6391	AA,AT,TT		1.1744,0.2951,0.8765	benign	581/4062	152285621	114,12892	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCCTGGTGCCGTC	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.1741A>T	1.37:g.152285621T>A	ENSP00000357789:p.Thr581Ser	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	247	96	0.388664	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	1.132	-0.652029	0.03506	0.002951	0.011744	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01548	4.78	2.15	-4.3	0.03710	.	.	.	.	.	T	0.00109	0.0003	N	0.00265	-1.74	0.09310	N	1	B	0.23316	0.083	B	0.28139	0.086	T	0.37361	-0.9709	9	0.06365	T	0.9	.	0.4631	0.00519	0.1939:0.3015:0.2321:0.2724	.	581	P20930	FILA_HUMAN	S	581;113	ENSP00000357789:T581S	ENSP00000357789:T581S	T	-	1	0	FLG	150552245	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.125000	0.00079	-3.882000	0.00095	-1.828000	0.00595	ACC	T|0.993;A|0.007	0.007	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EVC	2121	hgsc.bcm.edu	37	4	5749961	5749961	+	Silent	SNP	G	G	C	rs4688962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	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		
FYCO1	79443	hgsc.bcm.edu	37	3	46008790	46008790	+	Missense_Mutation	SNP	G	G	A	rs3796375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46008790G>A	ENST00000296137.2	-	8	2241	c.2036C>T	c.(2035-2037)gCg>gTg	p.A679V	FYCO1_ENST00000535325.1_Missense_Mutation_p.A679V	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	679			A -> V (in dbSNP:rs3796375). {ECO:0000269|PubMed:17974005}.		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)		CAGCAAGCTCGCCTCCATCTG	0.617													G|||	1979	0.395168	0.093	0.5648	5008	,	,		18181	0.6607		0.4314	False		,,,				2504	0.3722				p.A679V		Atlas-SNP	.											.	FYCO1	115	.	0			c.C2036T						PASS	.	G	VAL/ALA	626,3780	268.6+/-268.5	47,532,1624	67.0	72.0	71.0		2036	3.5	0.9	3	dbSNP_107	71	3706,4892	521.8+/-380.0	808,2090,1401	yes	missense	FYCO1	NM_024513.2	64	855,2622,3025	AA,AG,GG		43.103,14.2079,33.3128	possibly-damaging	679/1479	46008790	4332,8672	2203	4299	6502	SO:0001583	missense	79443	exon8			AAGCTCGCCTCCA	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.2036C>T	3.37:g.46008790G>A	ENSP00000296137:p.Ala679Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	933	0.4271978021978022	45	0.09146341463414634	198	0.5469613259668509	363	0.6346153846153846	327	0.4313984168865435	G	15.03	2.711650	0.48517	0.142079	0.43103	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21031	2.03;2.03	5.53	3.55	0.40652	.	0.182612	0.45867	N	0.000338	T	0.00012	0.0000	L	0.57536	1.79	0.37551	P	0.08129600000000003	D;D	0.60160	0.984;0.987	B;B	0.43155	0.41;0.356	T	0.35475	-0.9787	9	0.33141	T	0.24	-16.3376	6.1101	0.20096	0.0989:0.0:0.5877:0.3134	rs3796375;rs57674943;rs3796375	679;679	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	V	679	ENSP00000296137:A679V;ENSP00000441178:A679V	ENSP00000296137:A679V	A	-	2	0	FYCO1	45983794	0.998000	0.40836	0.871000	0.34182	0.819000	0.46315	2.820000	0.48057	1.331000	0.45412	0.655000	0.94253	GCG	G|0.650;A|0.350	0.350	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
TMEM244	253582	hgsc.bcm.edu	37	6	130152479	130152479	+	Silent	SNP	T	T	C	rs7758540	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:130152479T>C	ENST00000368143.1	-	5	454	c.372A>G	c.(370-372)tcA>tcG	p.S124S	TMEM244_ENST00000438392.1_Silent_p.S124S	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	124						integral component of membrane (GO:0016021)											CAAGCAATTTTGATATACCTA	0.269													C|||	2301	0.459465	0.6074	0.3934	5008	,	,		16994	0.1399		0.6193	False		,,,				2504	0.4714				p.S124S		Atlas-SNP	.											C6orf191,NS,carcinoma,-1,1	.	.	1	0			c.A372G						PASS	.	C		2708,1698	507.6+/-366.7	837,1034,332	61.0	59.0	59.0		372	-1.2	0.0	6	dbSNP_116	59	5563,3037	462.4+/-365.7	1802,1959,539	no	coding-synonymous	C6orf191	NM_001010876.1		2639,2993,871	CC,CT,TT		35.314,38.5384,36.4063		124/129	130152479	8271,4735	2203	4300	6503	SO:0001819	synonymous_variant	253582	exon5			CAATTTTGATATA		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.372A>G	6.37:g.130152479T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_001010876		Silent	SNP	ENST00000368143.1	37	CCDS34536.1																																																																																			T|0.428;C|0.572	0.572	strong		0.269	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
DPP6	1804	hgsc.bcm.edu	37	7	154561188	154561188	+	Silent	SNP	C	C	T	rs56091483	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:154561188C>T	ENST00000377770.3	+	9	1086	c.945C>T	c.(943-945)taC>taT	p.Y315Y	DPP6_ENST00000332007.3_Silent_p.Y253Y|DPP6_ENST00000427557.1_Silent_p.Y208Y|DPP6_ENST00000404039.1_Silent_p.Y251Y			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	315					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)			GACTCGCCTACGCCGCCATCA	0.522													C|||	485	0.096845	0.1104	0.0533	5008	,	,		18877	0.12		0.0964	False		,,,				2504	0.0859				p.Y315Y	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C945T						PASS	.	C	,,	422,3630		26,370,1630	75.0	79.0	78.0		399,318,318	-4.7	0.9	7	dbSNP_129	78	671,7673		27,617,3528	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	53,987,5158	TT,TC,CC		8.0417,10.4146,8.8174	,,	133/684,106/657,106/657	154561188	1093,11303	2026	4172	6198	SO:0001819	synonymous_variant	1804	exon9			CGCCTACGCCGCC	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.945C>T	7.37:g.154561188C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				C|0.910;T|0.090	0.090	strong		0.522	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
TEKT4	150483	hgsc.bcm.edu	37	2	95539833	95539833	+	Silent	SNP	C	C	T	rs111469930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:95539833C>T	ENST00000295201.4	+	3	830	c.693C>T	c.(691-693)taC>taT	p.Y231Y	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	231					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CTCATCCGTACTCCACCACCT	0.662													.|||	28	0.00559105	0.0015	0.0101	5008	,	,		14386	0.0		0.0149	False		,,,				2504	0.0041				p.Y231Y		Atlas-SNP	.											.	TEKT4	72	.	0			c.C693T						PASS	.	C		14,4392		0,14,2189	73.0	70.0	71.0		693	2.2	0.0	2	dbSNP_132	71	177,8423		1,175,4124	no	coding-synonymous	TEKT4	NM_144705.2		1,189,6313	TT,TC,CC		2.0581,0.3177,1.4686		231/436	95539833	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	150483	exon3			TCCGTACTCCACC	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.693C>T	2.37:g.95539833C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			C|0.988;T|0.012	0.012	strong		0.662	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
FSCB	84075	hgsc.bcm.edu	37	14	44973866	44973866	+	Silent	SNP	C	C	T	rs200610473		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:44973866C>T	ENST00000340446.4	-	1	2616	c.2325G>A	c.(2323-2325)tcG>tcA	p.S775S	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	775			S -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CCAAAACAACCGATCCTAATT	0.418																																					p.S775S		Atlas-SNP	.											FSCB,colon,carcinoma,0,8	FSCB	173	8	0			c.G2325A						scavenged	.						82.0	89.0	87.0					14																	44973866		2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			AACAACCGATCCT	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2325G>A	14.37:g.44973866C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	2	0.0173913	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			C|0.999;G|0.001	.	alt		0.418	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
DMXL2	23312	hgsc.bcm.edu	37	15	51868373	51868373	+	Silent	SNP	A	A	G	rs2414105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51868373A>G	ENST00000251076.5	-	2	380	c.93T>C	c.(91-93)taT>taC	p.Y31Y	DMXL2_ENST00000560421.1_5'UTR|DMXL2_ENST00000449909.3_Silent_p.Y31Y|DMXL2_ENST00000543779.2_Silent_p.Y31Y	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	31						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AGCCTGATCCATATGCCTaaa	0.299													a|||	2250	0.449281	0.4463	0.4942	5008	,	,		10234	0.4018		0.5149	False		,,,				2504	0.4029				p.Y31Y		Atlas-SNP	.											.	DMXL2	262	.	0			c.T93C						PASS	.	G	,,	2059,2331	565.7+/-381.7	493,1073,629	81.0	72.0	75.0		93,93,93	1.9	1.0	15	dbSNP_100	75	4336,4250	577.8+/-390.6	1105,2126,1062	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1598,3199,1691	GG,GA,AA		49.4992,46.9021,49.2833	,,	31/3038,31/2401,31/3037	51868373	6395,6581	2195	4293	6488	SO:0001819	synonymous_variant	23312	exon2			TGATCCATATGCC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.93T>C	15.37:g.51868373A>G		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			A|0.512;G|0.488	0.488	strong		0.299	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
PIGQ	9091	hgsc.bcm.edu	37	16	624114	624114	+	Missense_Mutation	SNP	A	A	G	rs2071979	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:624114A>G	ENST00000026218.5	+	2	128	c.40A>G	c.(40-42)Acg>Gcg	p.T14A	PIGQ_ENST00000470411.2_Missense_Mutation_p.T14A|PIGQ_ENST00000409527.2_Missense_Mutation_p.T14A|PIGQ_ENST00000321878.5_Missense_Mutation_p.T14A	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	14			T -> A (in dbSNP:rs2071979). {ECO:0000269|PubMed:11157797, ECO:0000269|PubMed:15489334}.		C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CTGCGTCTCGACGGACAGCGG	0.672													G|||	2664	0.531949	0.4871	0.4914	5008	,	,		17009	0.6359		0.4264	False		,,,				2504	0.6227				p.T14A		Atlas-SNP	.											.	PIGQ	43	.	0			c.A40G						PASS	.	G	ALA/THR,ALA/THR	2107,2295	592.7+/-387.9	516,1075,610	58.0	50.0	53.0		40,40	5.2	0.0	16	dbSNP_96	53	3507,5093	627.8+/-398.0	716,2075,1509	yes	missense,missense	PIGQ	NM_004204.3,NM_148920.1	58,58	1232,3150,2119	GG,GA,AA		40.7791,47.8646,43.178	benign,benign	14/582,14/761	624114	5614,7388	2201	4300	6501	SO:0001583	missense	9091	exon2			GTCTCGACGGACA	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.40A>G	16.37:g.624114A>G	ENSP00000026218:p.Thr14Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	1138	0.5210622710622711	255	0.5182926829268293	182	0.5027624309392266	360	0.6293706293706294	341	0.449868073878628	G	1.577	-0.532487	0.04112	0.478646	0.407791	ENSG00000007541	ENST00000293874;ENST00000409527;ENST00000409439;ENST00000422307;ENST00000321878;ENST00000439574;ENST00000026218;ENST00000470411	T;T;T;T;T;T;T;T	0.32753	1.49;1.69;1.51;1.58;1.69;1.44;2.65;1.49	5.17	5.17	0.71159	.	0.210963	0.49305	N	0.000156	T	0.00012	0.0000	N	0.00159	-1.955	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38067	-0.9678	9	0.08837	T	0.75	-10.5149	13.0251	0.58810	0.0783:0.0:0.9217:0.0	rs2071979;rs59323214;rs2071979	28;14;14;14	E7ERP4;Q9BRB3;Q9BRB3-2;Q9BRB3-3	.;PIGQ_HUMAN;.;.	A	14	ENSP00000293874:T14A;ENSP00000386760:T14A;ENSP00000386554:T14A;ENSP00000413753:T14A;ENSP00000326674:T14A;ENSP00000387820:T14A;ENSP00000026218:T14A;ENSP00000439650:T14A	ENSP00000026218:T14A	T	+	1	0	PIGQ	564115	1.000000	0.71417	0.002000	0.10522	0.085000	0.17905	7.784000	0.85713	1.192000	0.43071	-0.282000	0.10007	ACG	A|0.533;G|0.467	0.467	strong		0.672	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
PMFBP1	83449	hgsc.bcm.edu	37	16	72158675	72158675	+	Silent	SNP	G	G	A	rs34831115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72158675G>A	ENST00000537792.1	-	1	77	c.78C>T	c.(76-78)gaC>gaT	p.D26D	PMFBP1_ENST00000355636.6_Silent_p.D715D|PMFBP1_ENST00000537465.1_Silent_p.D865D|PMFBP1_ENST00000237353.10_Silent_p.D860D			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	865						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)				CCTCCTTATCGTCCTCAAGGA	0.572											OREG0023927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	23	0.00459265	0.0	0.0029	5008	,	,		19816	0.0		0.0159	False		,,,				2504	0.0051				p.D860D		Atlas-SNP	.											PMFBP1,NS,carcinoma,-2,1	PMFBP1	101	1	0			c.C2580T						PASS	.	G	,	7,4389	12.9+/-30.5	0,7,2191	148.0	132.0	137.0		2145,2580	-10.2	0.0	16	dbSNP_126	137	129,8471	65.6+/-127.9	1,127,4172	no	coding-synonymous,coding-synonymous	PMFBP1	NM_001160213.1,NM_031293.2	,	1,134,6363	AA,AG,GG		1.5,0.1592,1.0465	,	715/883,860/1008	72158675	136,12860	2198	4300	6498	SO:0001819	synonymous_variant	83449	exon17			CTTATCGTCCTCA	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.78C>T	16.37:g.72158675G>A		Somatic	61	0	0	1135	WXS	Illumina HiSeq	Phase_I	62	39	0.629032	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Silent	SNP	ENST00000537792.1	37																																																																																				G|0.990;A|0.010	0.010	strong		0.572	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293	
UBE3C	9690	hgsc.bcm.edu	37	7	157000176	157000176	+	Silent	SNP	T	T	C	rs2301914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	146	0	0		WXS	Illumina HiSeq	Phase_I	143	52	0.363636	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	
MMS19	64210	hgsc.bcm.edu	37	10	99225645	99225645	+	Missense_Mutation	SNP	G	G	A	rs12360068	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99225645G>A	ENST00000438925.2	-	18	2008	c.1673C>T	c.(1672-1674)gCc>gTc	p.A558V	MMS19_ENST00000327277.7_Missense_Mutation_p.A194V|MMS19_ENST00000370782.2_Missense_Mutation_p.A558V|MMS19_ENST00000355839.6_Missense_Mutation_p.A515V|MMS19_ENST00000327238.10_Missense_Mutation_p.A460V	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	558			A -> V (in dbSNP:rs12360068). {ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AGCTGACAAGGCTTGCAGACA	0.502								Direct reversal of damage					G|||	79	0.0157748	0.0038	0.0331	5008	,	,		20802	0.0		0.0467	False		,,,				2504	0.0041				p.A558V		Atlas-SNP	.											.	MMS19	36	.	0			c.C1673T						PASS	.	G	VAL/ALA	33,4373	39.2+/-71.8	0,33,2170	180.0	166.0	171.0		1673	4.6	1.0	10	dbSNP_120	171	370,8230	123.1+/-182.0	7,356,3937	yes	missense	MMS19	NM_022362.4	64	7,389,6107	AA,AG,GG		4.3023,0.749,3.0986	benign	558/1031	99225645	403,12603	2203	4300	6503	SO:0001583	missense	64210	exon18			GACAAGGCTTGCA	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.1673C>T	10.37:g.99225645G>A	ENSP00000412698:p.Ala558Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	54|54	0.024725274725274724|0.024725274725274724	6|6	0.012195121951219513|0.012195121951219513	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	34|34	0.044854881266490766|0.044854881266490766	G|G	20.5|20.5	3.995419|3.995419	0.74703|0.74703	0.00749|0.00749	0.043023|0.043023	ENSG00000155229|ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000327277;ENST00000327253;ENST00000355839|ENST00000434538	T;T;T;T;T|.	0.30981|.	1.51;1.51;1.51;1.51;1.51|.	5.54|5.54	4.64|4.64	0.57946|0.57946	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.102590|.	0.64402|.	D|.	0.000003|.	T|T	0.43277|0.43277	0.1240|0.1240	M|M	0.74258|0.74258	2.255|2.255	0.46131|0.46131	D|D	0.998881|0.998881	D;D;D;P;D|.	0.89917|.	0.994;1.0;1.0;0.584;0.994|.	D;D;D;B;D|.	0.91635|.	0.917;0.999;0.999;0.213;0.917|.	T|T	0.63097|0.63097	-0.6713|-0.6713	10|5	0.23891|.	T|.	0.37|.	.|.	14.2368|14.2368	0.65932|0.65932	0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0	rs12360068;rs52809901;rs12360068|rs12360068;rs52809901;rs12360068	579;460;515;558;515|.	B4DQX2;Q96T76-5;F8W9Y2;Q96T76;B4E2I3|.	.;.;.;MMS19_HUMAN;.|.	V|S	558;558;460;537;194;143;515|133	ENSP00000412698:A558V;ENSP00000359818:A558V;ENSP00000320059:A460V;ENSP00000322236:A194V;ENSP00000348097:A515V|.	ENSP00000320059:A460V|.	A|P	-|-	2|1	0|0	MMS19|MMS19	99215635|99215635	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.638000|4.638000	0.61353|0.61353	1.330000|1.330000	0.45394|0.45394	0.561000|0.561000	0.74099|0.74099	GCC|CCT	G|0.974;A|0.026	0.026	strong		0.502	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
C14orf159	80017	hgsc.bcm.edu	37	14	91666131	91666131	+	Silent	SNP	C	C	T	rs28481732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666131C>T	ENST00000523771.1	+	11	1914	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	C14orf159_ENST00000521077.2_Silent_p.A442A|C14orf159_ENST00000428926.2_Silent_p.A437A|C14orf159_ENST00000523816.1_Silent_p.A437A|C14orf159_ENST00000412671.2_Silent_p.A442A|C14orf159_ENST00000518868.1_Silent_p.A442A|C14orf159_ENST00000256324.10_Silent_p.A442A|C14orf159_ENST00000525393.2_Silent_p.A313A|C14orf159_ENST00000522322.1_Silent_p.A437A|C14orf159_ENST00000520328.1_Silent_p.A425A			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	437						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)		TAGAGCGTGCCGGAAGAGCTG	0.512													C|||	121	0.0241613	0.0658	0.0303	5008	,	,		19104	0.0		0.0089	False		,,,				2504	0.0041				p.A442A		Atlas-SNP	.											.	C14orf159	57	.	0			c.C1326T						PASS	.	C	,,,,	223,4183	134.9+/-171.1	8,207,1988	125.0	119.0	121.0		1311,1311,1326,1275,1311	-9.8	0.0	14	dbSNP_125	121	112,8488	59.5+/-121.1	0,112,4188	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	,,,,	8,319,6176	TT,TC,CC		1.3023,5.0613,2.5757	,,,,	437/617,437/617,442/622,425/565,437/617	91666131	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon11			GCGTGCCGGAAGA	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.1311C>T	14.37:g.91666131C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	41	0.018772893772893772	24	0.04878048780487805	11	0.03038674033149171	0	0.0	6	0.0079155672823219	C	0.268	-0.994827	0.02145	0.050613	0.013023	ENSG00000133943	ENST00000522816	.	.	.	5.05	-9.84	0.00479	.	.	.	.	.	T	0.05686	0.0149	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33979	-0.9847	4	.	.	.	.	0.4736	0.00536	0.1844:0.1765:0.3025:0.3367	rs28481732	.	.	.	L	38	.	.	P	+	2	0	C14orf159	90735884	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.872000	0.01639	-2.087000	0.00862	-2.357000	0.00240	CCG	C|0.977;T|0.023	0.023	strong		0.512	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
CCDC38	120935	hgsc.bcm.edu	37	12	96288860	96288860	+	Missense_Mutation	SNP	T	T	C	rs10859974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:96288860T>C	ENST00000344280.3	-	8	1236	c.679A>G	c.(679-681)Atg>Gtg	p.M227V	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	227			M -> V (in dbSNP:rs10859974).							breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTGGAGACATTTGCAGCAGA	0.333													T|||	1228	0.245208	0.2738	0.1282	5008	,	,		13669	0.4236		0.1988	False		,,,				2504	0.1534				p.M227V		Atlas-SNP	.											.	CCDC38	45	.	0			c.A679G						PASS	.	T	VAL/MET	1194,3208	417.2+/-337.8	166,862,1173	211.0	204.0	206.0		679	-1.6	1.0	12	dbSNP_120	206	1489,7109	283.3+/-296.1	124,1241,2934	yes	missense	CCDC38	NM_182496.2	21	290,2103,4107	CC,CT,TT		17.318,27.124,20.6385	benign	227/564	96288860	2683,10317	2201	4299	6500	SO:0001583	missense	120935	exon8			GAGACATTTGCAG	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.679A>G	12.37:g.96288860T>C	ENSP00000345470:p.Met227Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	550	0.2518315018315018	122	0.24796747967479674	41	0.1132596685082873	224	0.3916083916083916	163	0.21503957783641162	T	7.320	0.616850	0.14129	0.27124	0.17318	ENSG00000165972	ENST00000344280	T	0.09073	3.02	5.23	-1.62	0.08372	.	0.164203	0.40385	N	0.001117	T	0.00012	0.0000	N	0.00841	-1.15	0.09310	P	0.999999986606	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.32370	T	0.25	-8.8723	0.3596	0.00362	0.3028:0.1429:0.2707:0.2835	rs10859974;rs56430645;rs59112589;rs10859974	227	Q502W7	CCD38_HUMAN	V	227	ENSP00000345470:M227V	ENSP00000345470:M227V	M	-	1	0	CCDC38	94812991	0.738000	0.28186	0.987000	0.45799	0.355000	0.29361	-0.095000	0.11077	-0.122000	0.11766	-0.536000	0.04276	ATG	T|0.772;C|0.228	0.228	strong		0.333	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
ABCA13	154664	hgsc.bcm.edu	37	7	48506566	48506566	+	Missense_Mutation	SNP	A	A	G	rs4917152	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:48506566A>G	ENST00000435803.1	+	44	12853	c.12829A>G	c.(12829-12831)Aac>Gac	p.N4277D	ABCA13_ENST00000544596.1_Intron	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4277			N -> D (in dbSNP:rs4917152).		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						TGGGGGCGACAACTTGGACCT	0.498													G|||	1156	0.230831	0.3525	0.2608	5008	,	,		16829	0.2163		0.1491	False		,,,				2504	0.1442				p.N4277D		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A12829G						PASS	.	G	ASP/ASN	1219,2921		166,887,1017	107.0	116.0	113.0		12829	1.5	0.0	7	dbSNP_111	113	1020,7400		55,910,3245	yes	missense	ABCA13	NM_152701.3	23	221,1797,4262	GG,GA,AA		12.114,29.4444,17.8264	benign	4277/5059	48506566	2239,10321	2070	4210	6280	SO:0001583	missense	154664	exon44			GGCGACAACTTGG	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.12829A>G	7.37:g.48506566A>G	ENSP00000411096:p.Asn4277Asp	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	154	49	0.318182	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	493	0.22573260073260074	156	0.3170731707317073	91	0.2513812154696133	128	0.22377622377622378	118	0.15567282321899736	G	0.065	-1.215318	0.01542	0.294444	0.12114	ENSG00000179869	ENST00000435803	D	0.85013	-1.93	5.29	1.49	0.22878	.	0.841374	0.10012	N	0.727113	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.05649	-1.0872	9	0.02654	T	1	.	8.1325	0.31035	0.4133:0.0:0.5867:0.0	rs4917152;rs10358914;rs17132360;rs52799285;rs4917152	1979;4277	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	D	4277	ENSP00000411096:N4277D	ENSP00000411096:N4277D	N	+	1	0	ABCA13	48477112	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	1.337000	0.33862	-0.123000	0.11745	-1.551000	0.00897	AAC	A|0.777;G|0.223	0.223	strong		0.498	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
TPRKB	51002	hgsc.bcm.edu	37	2	73957124	73957124	+	Silent	SNP	A	A	G	rs7210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73957124A>G	ENST00000272424.5	-	5	580	c.474T>C	c.(472-474)atT>atC	p.I158I	TPRKB_ENST00000409716.2_Silent_p.I197I|TPRKB_ENST00000485758.1_5'UTR|TPRKB_ENST00000318190.7_Silent_p.I197I	NM_016058.2	NP_057142.1	Q9Y3C4	TPRKB_HUMAN	TP53RK binding protein	158					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			lung(2)|ovary(1)|skin(1)	4						ATAATGTCCCAATACTTTCTT	0.269													a|||	2858	0.570687	0.292	0.5821	5008	,	,		16898	0.6954		0.6899	False		,,,				2504	0.6881				p.I158I		Atlas-SNP	.											.	TPRKB	20	.	0			c.T474C						PASS	.	A		1686,2690		339,1008,841	43.0	41.0	42.0		474	1.4	0.8	2	dbSNP_52	42	5643,2921		1848,1947,487	no	coding-synonymous	TPRKB	NM_016058.2		2187,2955,1328	GG,GA,AA		34.1079,38.5283,43.3617		158/176	73957124	7329,5611	2188	4282	6470	SO:0001819	synonymous_variant	51002	exon5			TGTCCCAATACTT	AY157986	CCDS1927.1	2p24.3-p24.1	2008-02-05			ENSG00000144034	ENSG00000144034			24259	protein-coding gene	gene with protein product		608680				10810093, 12659830	Standard	NM_016058		Approved	CGI-121	uc002sjn.2	Q9Y3C4	OTTHUMG00000129815	ENST00000272424.5:c.474T>C	2.37:g.73957124A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_016058	D6W5H6|Q8IWR6|Q8IWR7|Q9H3K4	Silent	SNP	ENST00000272424.5	37	CCDS1927.1																																																																																			A|0.429;G|0.571	0.571	strong		0.269	TPRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252046.2	NM_016058	
AK9	221264	hgsc.bcm.edu	37	6	109885475	109885475	+	Missense_Mutation	SNP	G	G	A	rs10499052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	49	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	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	
ZNF98	148198	hgsc.bcm.edu	37	19	22575777	22575777	+	Missense_Mutation	SNP	T	T	C	rs200167484	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22575777T>C	ENST00000357774.5	-	4	381	c.260A>G	c.(259-261)tAt>tGt	p.Y87C		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AAAATAAGAATATACAACTGA	0.274																																					p.Y87C		Atlas-SNP	.											.	ZNF98	230	.	0			c.A260G						PASS	.						22.0	18.0	20.0					19																	22575777		1824	4100	5924	SO:0001583	missense	148198	exon4			TAAGAATATACAA		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.260A>G	19.37:g.22575777T>C	ENSP00000350418:p.Tyr87Cys	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	13	0.232143	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.067335	0.00036	.	.	ENSG00000197360	ENST00000357774	T	0.06371	3.31	1.63	-1.74	0.08056	.	.	.	.	.	T	0.01800	0.0057	N	0.01464	-0.85	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43065	-0.9414	9	0.14252	T	0.57	.	3.4345	0.07441	0.0:0.4227:0.2165:0.3608	.	87	A6NK75	ZNF98_HUMAN	C	87	ENSP00000350418:Y87C	ENSP00000350418:Y87C	Y	-	2	0	ZNF98	22367617	0.007000	0.16637	0.011000	0.14972	0.027000	0.11550	-0.524000	0.06222	-1.771000	0.01293	-2.179000	0.00317	TAT	C|0.005;G|0.039;T|0.955	0.005	strong		0.274	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
PEBP4	157310	hgsc.bcm.edu	37	8	22584718	22584718	+	Missense_Mutation	SNP	T	T	C	rs1129474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22584718T>C	ENST00000256404.6	-	5	464	c.373A>G	c.(373-375)Aaa>Gaa	p.K125E	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	125			K -> E (in dbSNP:rs1129474). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)		p.K125E(1)		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)		ATCTTCCCTTTCTTCAGGTCG	0.552													T|||	2497	0.498602	0.7458	0.5749	5008	,	,		18949	0.2798		0.4672	False		,,,				2504	0.3681				p.K125E		Atlas-SNP	.											PEBP4,NS,carcinoma,0,1	PEBP4	23	1	1	Substitution - Missense(1)	stomach(1)	c.A373G						PASS	.	T	GLU/LYS	2792,1180		984,824,178	64.0	71.0	69.0		373	3.3	0.2	8	dbSNP_86	69	3985,4303		951,2083,1110	yes	missense	PEBP4	NM_144962.2	56	1935,2907,1288	CC,CT,TT		48.0816,29.708,44.7227	benign	125/228	22584718	6777,5483	1986	4144	6130	SO:0001583	missense	157310	exon5			TCCCTTTCTTCAG	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.373A>G	8.37:g.22584718T>C	ENSP00000256404:p.Lys125Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	1052	0.4816849816849817	362	0.7357723577235772	202	0.5580110497237569	141	0.2465034965034965	347	0.4577836411609499	T	11.80	1.747447	0.30955	0.70292	0.480816	ENSG00000134020	ENST00000256404	T	0.40756	1.02	4.47	3.31	0.37934	.	1.360170	0.04715	N	0.418228	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B	0.22146	0.065	B	0.18561	0.022	T	0.45116	-0.9283	9	0.39692	T	0.17	-2.3351	6.1388	0.20249	0.0:0.1147:0.0:0.8853	rs1129474;rs2271529;rs57266891;rs1129474	125	Q96S96	PEBP4_HUMAN	E	125	ENSP00000256404:K125E	ENSP00000256404:K125E	K	-	1	0	PEBP4	22640663	0.018000	0.18449	0.210000	0.23637	0.019000	0.09904	0.388000	0.20735	1.783000	0.52377	0.482000	0.46254	AAA	T|0.516;C|0.484	0.484	strong		0.552	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
CFAP46	54777	hgsc.bcm.edu	37	10	134736026	134736026	+	Silent	SNP	G	G	A	rs4880286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	79	0	0		WXS	Illumina HiSeq	Phase_I	83	83	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		
ANKLE1	126549	hgsc.bcm.edu	37	19	17392894	17392894	+	Missense_Mutation	SNP	G	G	A	rs8100241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17392894G>A	ENST00000394458.3	+	2	367	c.91G>A	c.(91-93)Gcg>Acg	p.A31T	ANKLE1_ENST00000598347.1_Missense_Mutation_p.A31T|ANKLE1_ENST00000433424.2_Missense_Mutation_p.A85T|ANKLE1_ENST00000594072.1_Missense_Mutation_p.A20T|ANKLE1_ENST00000404085.1_Missense_Mutation_p.A53T|CTD-2278I10.6_ENST00000596542.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	31			A -> T (in dbSNP:rs8100241). {ECO:0000269|Ref.1}.							large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GCGCTGCGGCGCGGACCCTAA	0.736													G|||	2140	0.427316	0.3865	0.3761	5008	,	,		10836	0.3115		0.5716	False		,,,				2504	0.4898				p.A31T		Atlas-SNP	.											FLJ39369,NS,carcinoma,0,4	ANKLE1	27	4	0			c.G91A						PASS	.	G	THR/ALA	1171,2027		272,627,700	4.0	6.0	6.0		91	1.6	0.3	19	dbSNP_116	6	2712,3014		694,1324,845	yes	missense	ANKLE1	NM_152363.4	58	966,1951,1545	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	47.3629,36.6166,43.5119	probably-damaging	31/616	17392894	3883,5041	1599	2863	4462	SO:0001583	missense	126549	exon2			TGCGGCGCGGACC	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.91G>A	19.37:g.17392894G>A	ENSP00000377971:p.Ala31Thr	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	947	0.4336080586080586	186	0.3780487804878049	156	0.430939226519337	163	0.28496503496503495	442	0.58311345646438	G	15.15	2.747219	0.49257	0.366166	0.473629	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.70869	-0.52;-0.52;-0.52	4.06	1.65	0.23941	Ankyrin repeat-containing domain (4);	0.076309	0.50627	D	0.000109	T	0.00012	0.0000	M	0.87456	2.885	0.48762	P	2.910000000000412E-4	P;D;D	0.89917	0.634;1.0;0.998	B;D;P	0.87578	0.302;0.998;0.884	T	0.47446	-0.9117	9	0.48119	T	0.1	-10.2519	6.5304	0.22324	0.0:0.1999:0.5941:0.2059	rs8100241;rs61305143;rs8100241	31;17;31	E7ETZ9;Q8NAG6-1;Q8NAG6	.;.;ANKL1_HUMAN	T	31;85;53;20;31	ENSP00000384753:A31T;ENSP00000394460:A85T;ENSP00000384008:A53T	ENSP00000377971:A20T	A	+	1	0	ANKLE1	17253894	0.981000	0.34729	0.273000	0.24645	0.084000	0.17831	5.063000	0.64332	0.873000	0.35799	0.484000	0.47621	GCG	G|0.574;A|0.426	0.426	strong		0.736	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
HPS1	3257	hgsc.bcm.edu	37	10	100183570	100183570	+	Missense_Mutation	SNP	G	G	C	rs2296434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100183570G>C	ENST00000325103.6	-	15	1705	c.1472C>G	c.(1471-1473)cCc>cGc	p.P491R	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Missense_Mutation_p.P491R	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	491			P -> R (in dbSNP:rs2296434).		blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TCCCCTGCTGGGGGCTGTGGT	0.657									Hermansky-Pudlak syndrome				G|||	623	0.124401	0.1369	0.1614	5008	,	,		17591	0.1716		0.1123	False		,,,				2504	0.045				p.P491R		Atlas-SNP	.											.	HPS1	65	.	0			c.C1472G						PASS	.	G	ARG/PRO	484,3922	224.6+/-240.7	21,442,1740	45.0	51.0	49.0		1472	5.5	0.1	10	dbSNP_100	49	727,7873	176.5+/-226.3	33,661,3606	yes	missense	HPS1	NM_000195.3	103	54,1103,5346	CC,CG,GG		8.4535,10.985,9.3111	probably-damaging	491/701	100183570	1211,11795	2203	4300	6503	SO:0001583	missense	3257	exon15	Familial Cancer Database	HPS, HPS1-8	CTGCTGGGGGCTG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1472C>G	10.37:g.100183570G>C	ENSP00000326649:p.Pro491Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	51	0.593023	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	37	CCDS7475.1	309	0.14148351648351648	79	0.16056910569105692	49	0.13535911602209943	93	0.16258741258741258	88	0.11609498680738786	G	19.71	3.878892	0.72294	0.10985	0.084535	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891;ENST00000359632	T;T;T	0.30182	1.54;1.54;1.54	5.51	5.51	0.81932	.	0.071871	0.64402	D	0.000008	T	0.00328	0.0010	M	0.73962	2.25	0.09310	P	1.0	D;D;D;D	0.76494	0.995;0.999;0.997;0.995	D;D;D;D	0.70016	0.939;0.967;0.939;0.933	T	0.01228	-1.1412	9	0.72032	D	0.01	.	14.9208	0.70835	0.0:0.0:1.0:0.0	rs2296434;rs59912963;rs2296434	129;458;491;491	Q658M9;Q92902-2;Q8WXE5;D3DR62	.;.;.;.	R	491;491;458;286	ENSP00000326649:P491R;ENSP00000355310:P491R;ENSP00000352652:P286R	ENSP00000326649:P491R	P	-	2	0	HPS1	100173560	0.980000	0.34600	0.106000	0.21319	0.016000	0.09150	4.548000	0.60718	2.581000	0.87130	0.555000	0.69702	CCC	.	.	none		0.657	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
CARD8	22900	hgsc.bcm.edu	37	19	48737706	48737706	+	Nonsense_Mutation	SNP	A	A	T	rs2043211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48737706A>T	ENST00000359009.4	-	3	342	c.30T>A	c.(28-30)tgT>tgA	p.C10*	CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000519940.1_Missense_Mutation_p.F102I|CARD8_ENST00000520153.1_Missense_Mutation_p.F52I|CARD8_ENST00000521613.1_Missense_Mutation_p.F52I|CARD8_ENST00000447740.2_Missense_Mutation_p.F52I|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000520753.1_Missense_Mutation_p.F102I|CARD8_ENST00000391898.3_Missense_Mutation_p.F102I|CARD8_ENST00000520015.1_Missense_Mutation_p.F102I			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	10					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|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)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		ACAGCACGGAACAATAATGGC	0.458													A|||	1585	0.316494	0.1808	0.2709	5008	,	,		19304	0.5069		0.332	False		,,,				2504	0.32				p.F102I		Atlas-SNP	.											.	CARD8	53	.	0			c.T304A						PASS	.	A	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	919,3487	354.4+/-312.6	106,707,1390	162.0	134.0	144.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	304,154,304,304,154	-2.4	0.0	19	dbSNP_94	144	2829,5771	446.4+/-361.2	498,1833,1969	yes	missense,missense,missense,missense,missense	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	21,21,21,21,21	604,2540,3359	TT,TA,AA		32.8953,20.8579,28.8175	,,,,	102/538,52/488,102/393,102/393,52/488	48737706	3748,9258	2203	4300	6503	SO:0001587	stop_gained	22900	exon3			CACGGAACAATAA	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.30T>A	19.37:g.48737706A>T	ENSP00000351901:p.Cys10*	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Missense_Mutation	SNP	ENST00000359009.4	37		722|722	0.3305860805860806|0.3305860805860806	98|98	0.1991869918699187|0.1991869918699187	102|102	0.281767955801105|0.281767955801105	265|265	0.4632867132867133|0.4632867132867133	257|257	0.3390501319261214|0.3390501319261214	A|A	16.67|16.67	3.186927|3.186927	0.57909|0.57909	0.208579|0.208579	0.328953|0.328953	ENSG00000105483|ENSG00000105483	ENST00000359009|ENST00000447740;ENST00000391898;ENST00000520753;ENST00000520153;ENST00000520015;ENST00000521613;ENST00000519940	.|T;T;T;T;T;T;T	.|0.19394	.|2.53;2.43;2.15;2.53;2.15;2.53;2.43	1.21|1.21	-2.42|-2.42	0.06542|0.06542	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	N|N	0.08118|0.08118	0|0	0.09310|0.09310	P|P	0.99999999792962|0.99999999792962	.|B;P;B	.|0.39157	.|0.271;0.662;0.11	.|B;B;B	.|0.24006	.|0.015;0.05;0.023	.|T	.|0.45220	.|-0.9276	.|8	0.02654|0.56958	T|D	1|0.05	.|.	0.3286|0.3286	0.00315|0.00315	0.1977:0.2982:0.1876:0.3165|0.1977:0.2982:0.1876:0.3165	rs2043211;rs59690382;rs2043211|rs2043211;rs59690382;rs2043211	.|102;102;52	.|E9PEM7;Q9Y2G2-3;G3XAM9	.|.;.;.	X|I	10|52;102;102;52;102;52;102	.|ENSP00000391248:F52I;ENSP00000375767:F102I;ENSP00000429839:F102I;ENSP00000428736:F52I;ENSP00000430747:F102I;ENSP00000427858:F52I;ENSP00000428883:F102I	ENSP00000351901:C10X|ENSP00000375767:F102I	C|F	-|-	3|1	2|0	CARD8|CARD8	53429518|53429518	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.316000|-1.316000	0.02710|0.02710	-2.374000|-2.374000	0.00599|0.00599	-0.871000|-0.871000	0.02989|0.02989	TGT|TTC	A|0.691;T|0.309	0.309	strong		0.458	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
SPRED2	200734	hgsc.bcm.edu	37	2	65540905	65540905	+	Silent	SNP	C	C	G	rs8827	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:65540905C>G	ENST00000356388.4	-	6	1176	c.987G>C	c.(985-987)gcG>gcC	p.A329A	SPRED2_ENST00000474228.1_5'Flank|SPRED2_ENST00000443619.2_Silent_p.A326A	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	329	SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						CGGAGTCGGGCGCGTCCTGGC	0.647													C|||	1980	0.395367	0.112	0.4784	5008	,	,		17430	0.755		0.2505	False		,,,				2504	0.498				p.A329A		Atlas-SNP	.											SPRED2,colon,carcinoma,0,1	SPRED2	70	1	0			c.G987C						PASS	.	C	,	670,3736	273.1+/-271.2	53,564,1586	82.0	81.0	81.0		978,987	-6.7	0.9	2	dbSNP_52	81	2208,6390	354.6+/-329.6	291,1626,2382	no	coding-synonymous,coding-synonymous	SPRED2	NM_001128210.1,NM_181784.2	,	344,2190,3968	GG,GC,CC		25.6804,15.2065,22.1317	,	326/416,329/419	65540905	2878,10126	2203	4299	6502	SO:0001819	synonymous_variant	200734	exon6			GTCGGGCGCGTCC	AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.987G>C	2.37:g.65540905C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Silent	SNP	ENST00000356388.4	37	CCDS33211.1																																																																																			C|0.713;G|0.287	0.287	strong		0.647	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
EIF4EBP2	1979	hgsc.bcm.edu	37	10	72179746	72179746	+	Silent	SNP	C	C	T	rs1043098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:72179746C>T	ENST00000373218.4	+	2	245	c.222C>T	c.(220-222)caC>caT	p.H74H		NM_004096.4	NP_004087.1	Q13542	4EBP2_HUMAN	eukaryotic translation initiation factor 4E binding protein 2	74					cAMP-mediated signaling (GO:0019933)|insulin receptor signaling pathway (GO:0008286)|negative regulation of translational initiation (GO:0045947)|translation (GO:0006412)					large_intestine(1)	1						CACCCTGCCACCTGCCCAATA	0.448													T|||	2568	0.51278	0.4266	0.4712	5008	,	,		17456	0.7272		0.4612	False		,,,				2504	0.4908				p.H74H		Atlas-SNP	.											.	EIF4EBP2	7	.	0			c.C222T						PASS	.	T		1858,2548	633.8+/-396.1	400,1058,745	85.0	84.0	84.0		222	1.3	1.0	10	dbSNP_86	84	4213,4387	583.0+/-391.5	1028,2157,1115	no	coding-synonymous	EIF4EBP2	NM_004096.4		1428,3215,1860	TT,TC,CC		48.9884,42.1698,46.6785		74/121	72179746	6071,6935	2203	4300	6503	SO:0001819	synonymous_variant	1979	exon2			CTGCCACCTGCCC		CCDS7303.1	10q21-q22	2008-08-01			ENSG00000148730	ENSG00000148730			3289	protein-coding gene	gene with protein product		602224				7935836, 8975712	Standard	NM_004096		Approved		uc001jrb.3	Q13542	OTTHUMG00000018409	ENST00000373218.4:c.222C>T	10.37:g.72179746C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_004096		Silent	SNP	ENST00000373218.4	37	CCDS7303.1																																																																																			C|0.528;T|0.472	0.472	strong		0.448	EIF4EBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048513.1	NM_004096	
ATAD3A	55210	hgsc.bcm.edu	37	1	1455652	1455652	+	Missense_Mutation	SNP	G	G	T	rs2767471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1455652G>T	ENST00000378755.5	+	6	884	c.790G>T	c.(790-792)Gcc>Tcc	p.A264S	ATAD3A_ENST00000378756.3_Missense_Mutation_p.A216S|ATAD3A_ENST00000536055.1_Missense_Mutation_p.A137S	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	264					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.A264S(4)		endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	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;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCTGAAGGCGGCCGAGCACCG	0.682																																					p.A264S		Atlas-SNP	.											ATAD3A,NS,carcinoma,0,4	ATAD3A	35	4	4	Substitution - Missense(4)	kidney(4)	c.G790T						scavenged	.						53.0	52.0	52.0					1																	1455652		2203	4300	6503	SO:0001583	missense	55210	exon6			AAGGCGGCCGAGC	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.790G>T	1.37:g.1455652G>T	ENSP00000368030:p.Ala264Ser	Somatic	171	3	0.0175439		WXS	Illumina HiSeq	Phase_I	278	37	0.133094	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	9.081|9.081	0.999324|0.999324	0.19121|0.19121	.|.	.|.	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055;ENST00000429957|ENST00000339113	D;T;D|.	0.94457|.	-2.51;1.42;-3.43|.	4.43|4.43	3.44|3.44	0.39384|0.39384	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);|.	0.054326|.	0.64402|.	D|.	0.000001|.	T|T	0.48333|0.48333	0.1494|0.1494	N|N	0.20766|0.20766	0.605|0.605	0.52501|0.52501	D|D	0.999956|0.999956	B;B|.	0.14805|.	0.0;0.011|.	B;B|.	0.18263|.	0.007;0.021|.	T|T	0.40997|0.40997	-0.9533|-0.9533	10|5	0.07990|.	T|.	0.79|.	.|.	13.2731|13.2731	0.60172|0.60172	0.0:0.0:0.8418:0.1582|0.0:0.0:0.8418:0.1582	rs2767471|rs2767471	216;264|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	S|V	216;264;137;98|201	ENSP00000368031:A216S;ENSP00000368030:A264S;ENSP00000439290:A137S|.	ENSP00000368030:A264S|.	A|G	+|+	1|2	0|0	ATAD3A|ATAD3A	1445515|1445515	1.000000|1.000000	0.71417|0.71417	0.501000|0.501000	0.27601|0.27601	0.170000|0.170000	0.22686|0.22686	7.461000|7.461000	0.80834|0.80834	2.162000|2.162000	0.67917|0.67917	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.	weak		0.682	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
XPO7	23039	hgsc.bcm.edu	37	8	21846586	21846586	+	Silent	SNP	G	G	C	rs2306646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:21846586G>C	ENST00000252512.9	+	16	1960	c.1860G>C	c.(1858-1860)ctG>ctC	p.L620L	XPO7_ENST00000433566.4_Silent_p.L621L|XPO7_ENST00000434536.1_Silent_p.L629L	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	620					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TCAATGACCTGTCCATTGGAT	0.438													C|||	2900	0.579073	0.764	0.4352	5008	,	,		18527	0.5238		0.6014	False		,,,				2504	0.4652				p.L620L		Atlas-SNP	.											.	XPO7	79	.	0			c.G1860C						PASS	.	C		2808,1032		1041,726,153	97.0	104.0	102.0		1860	2.0	1.0	8	dbSNP_100	102	4557,3707		1263,2031,838	no	coding-synonymous	XPO7	NM_015024.4		2304,2757,991	CC,CG,GG		44.8572,26.875,39.1523		620/1088	21846586	7365,4739	1920	4132	6052	SO:0001819	synonymous_variant	23039	exon16			TGACCTGTCCATT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1860G>C	8.37:g.21846586G>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	37	CCDS47818.1																																																																																			G|0.405;C|0.595	0.595	strong		0.438	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65236875	65236875	+	Silent	SNP	T	T	C	rs2414865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65236875T>C	ENST00000380230.3	+	12	1121	c.1092T>C	c.(1090-1092)gcT>gcC	p.A364A	ANKDD1A_ENST00000395723.1_Intron|ANKDD1A_ENST00000395720.1_Silent_p.A364A|ANKDD1A_ENST00000357698.3_Intron	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	364					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TGGCAGTGGCTGTCCGCAGCA	0.517													C|||	2769	0.552915	0.7489	0.3573	5008	,	,		19859	0.3909		0.4463	False		,,,				2504	0.7035				p.A364A		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.T1092C						PASS	.	C		3150,1254	429.9+/-342.4	1130,890,182	77.0	68.0	71.0		1092	-3.0	0.9	15	dbSNP_100	71	3963,4635	600.8+/-394.3	930,2103,1266	no	coding-synonymous	ANKDD1A	NM_182703.3		2060,2993,1448	CC,CT,TT		46.0921,28.4741,45.293		364/523	65236875	7113,5889	2202	4299	6501	SO:0001819	synonymous_variant	348094	exon12			AGTGGCTGTCCGC		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.1092T>C	15.37:g.65236875T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	37	CCDS10197.2																																																																																			T|0.460;C|0.540	0.540	strong		0.517	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
HIVEP3	59269	hgsc.bcm.edu	37	1	42046613	42046613	+	Silent	SNP	G	G	T	rs12132697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:42046613G>T	ENST00000372583.1	-	4	4741	c.3856C>A	c.(3856-3858)Cgg>Agg	p.R1286R	HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Silent_p.R1286R|HIVEP3_ENST00000247584.5_Silent_p.R1286R|HIVEP3_ENST00000429157.2_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						PASS	.	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	54	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	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	
KCNU1	157855	hgsc.bcm.edu	37	8	36788479	36788479	+	Missense_Mutation	SNP	A	A	G	rs16885577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:36788479A>G	ENST00000399881.3	+	25	2784	c.2747A>G	c.(2746-2748)aAt>aGt	p.N916S	KCNU1_ENST00000518904.1_Silent_p.Q27Q	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	916			N -> S (in dbSNP:rs16885577).		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)		GCCTTCTACAATTATCATGTC	0.443													A|||	1067	0.213059	0.2526	0.1599	5008	,	,		18427	0.1786		0.1322	False		,,,				2504	0.316				p.N916S		Atlas-SNP	.											.	KCNU1	359	.	0			c.A2747G						PASS	.	A	SER/ASN	997,2895		136,725,1085	73.0	65.0	68.0		2747	5.6	1.0	8	dbSNP_123	68	1337,6967		107,1123,2922	yes	missense	KCNU1	NM_001031836.2	46	243,1848,4007	GG,GA,AA		16.1007,25.6166,19.1374	probably-damaging	916/1150	36788479	2334,9862	1946	4152	6098	SO:0001583	missense	157855	exon25			TCTACAATTATCA	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.2747A>G	8.37:g.36788479A>G	ENSP00000382770:p.Asn916Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	405	0.18543956043956045	117	0.23780487804878048	65	0.17955801104972377	114	0.1993006993006993	109	0.1437994722955145	A	10.57	1.388271	0.25118	0.256166	0.161007	ENSG00000215262	ENST00000399881	T	0.41400	1.0	5.58	5.58	0.84498	.	0.000000	0.40728	U	0.001031	T	0.00012	0.0000	M	0.79123	2.44	0.09310	P	1.0	D	0.89917	1.0	D	0.78314	0.991	T	0.03240	-1.1057	9	0.87932	D	0	-0.0157	13.117	0.59305	1.0:0.0:0.0:0.0	rs16885577;rs56708487;rs16885577	916	A8MYU2	KCNU1_HUMAN	S	916	ENSP00000382770:N916S	ENSP00000382770:N916S	N	+	2	0	KCNU1	36907637	1.000000	0.71417	0.984000	0.44739	0.602000	0.36980	4.563000	0.60823	2.121000	0.65114	0.528000	0.53228	AAT	A|0.799;G|0.201	0.201	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733050	52733050	+	Missense_Mutation	SNP	T	T	A	rs12335014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Missense_Mutation_p.N312I	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	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	159	141	0.886792	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	
CASZ1	54897	hgsc.bcm.edu	37	1	10709441	10709441	+	Silent	SNP	C	C	T	rs284299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10709441C>T	ENST00000377022.3	-	14	3251	c.2934G>A	c.(2932-2934)gcG>gcA	p.A978A	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.A978A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	978					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)		GGCTCCCCTCCGCTTCCGCCT	0.647													C|||	1567	0.312899	0.5416	0.1427	5008	,	,		16270	0.2321		0.1839	False		,,,				2504	0.3405				p.A978A		Atlas-SNP	.											CASZ1,NS,carcinoma,0,1	CASZ1	150	1	0			c.G2934A						PASS	.	C	,	1958,2436		448,1062,687	20.0	23.0	22.0		2934,2934	-9.6	0.0	1	dbSNP_79	22	1520,7080		140,1240,2920	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	588,2302,3607	TT,TC,CC		17.6744,44.5608,26.7662	,	978/1760,978/1167	10709441	3478,9516	2197	4300	6497	SO:0001819	synonymous_variant	54897	exon14			CCCCTCCGCTTCC	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.2934G>A	1.37:g.10709441C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			T|0.279;C|0.721	0.279	strong		0.647	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617105	183617105	+	Missense_Mutation	SNP	A	A	G	rs1174658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	337	0	0		WXS	Illumina HiSeq	Phase_I	416	411	0.987981	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	
FXR2	9513	hgsc.bcm.edu	37	17	7496411	7496411	+	Silent	SNP	G	G	A	rs61730843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7496411G>A	ENST00000250113.7	-	13	1753	c.1419C>T	c.(1417-1419)ccC>ccT	p.P473P	FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000250055.2_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	473						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)		CTCGGGTTGGGGGATCCCTGT	0.627													G|||	29	0.00579073	0.0	0.0101	5008	,	,		13144	0.0		0.0119	False		,,,				2504	0.0102				p.P473P		Atlas-SNP	.											.	FXR2	44	.	0			c.C1419T						PASS	.	G		6,3684		0,6,1839	19.0	19.0	19.0		1419	1.9	1.0	17	dbSNP_129	19	66,8118		0,66,4026	no	coding-synonymous	FXR2	NM_004860.3		0,72,5865	AA,AG,GG		0.8065,0.1626,0.6064		473/674	7496411	72,11802	1845	4092	5937	SO:0001819	synonymous_variant	9513	exon13			GGTTGGGGGATCC	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.1419C>T	17.37:g.7496411G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Silent	SNP	ENST00000250113.7	37	CCDS45604.1																																																																																			G|0.995;A|0.005	0.005	strong		0.627	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
HDX	139324	hgsc.bcm.edu	37	X	83591866	83591866	+	Silent	SNP	C	C	T	rs5922966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:83591866C>T	ENST00000297977.5	-	7	1794	c.1683G>A	c.(1681-1683)ccG>ccA	p.P561P	HDX_ENST00000373177.2_Silent_p.P561P|HDX_ENST00000506585.2_Silent_p.P503P	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	21	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	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	
PKD1	5310	hgsc.bcm.edu	37	16	2161097	2161097	+	Silent	SNP	C	C	A	rs145737766	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2161097C>A	ENST00000262304.4	-	15	4279	c.4071G>T	c.(4069-4071)ctG>ctT	p.L1357L	PKD1_ENST00000423118.1_Silent_p.L1357L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1357	PKD 8. {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						GCACCAGCGCCAGGGGGAACG	0.652													c|||	19	0.00379393	0.0015	0.0086	5008	,	,		17499	0.0		0.008	False		,,,				2504	0.0031				p.L1357L		Atlas-SNP	.											.	PKD1	184	.	0			c.G4071T						PASS	.	C	,	11,4371	17.9+/-39.9	0,11,2180	33.0	35.0	35.0		4071,4071	3.5	0.4	16	dbSNP_134	35	77,8515	41.7+/-99.0	1,75,4220	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	1,86,6400	AA,AC,CC		0.8962,0.251,0.6783	,	1357/4303,1357/4304	2161097	88,12886	2191	4296	6487	SO:0001819	synonymous_variant	5310	exon15			CAGCGCCAGGGGG	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.4071G>T	16.37:g.2161097C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	48	0.592593	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			C|0.993;A|0.007	0.007	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
WDR49	151790	hgsc.bcm.edu	37	3	167217964	167217964	+	Missense_Mutation	SNP	A	A	G	rs13060964	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167217964A>G	ENST00000308378.3	-	14	2257	c.1952T>C	c.(1951-1953)cTg>cCg	p.L651P	WDR49_ENST00000476376.1_Missense_Mutation_p.L476P|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Missense_Mutation_p.L616P	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	651			L -> P (in dbSNP:rs13060964).							breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CGGGGCCTCCAGAATTTGGGG	0.433													G|||	1807	0.360823	0.2632	0.3429	5008	,	,		16385	0.4812		0.3519	False		,,,				2504	0.3906				p.L651P		Atlas-SNP	.											.	WDR49	188	.	0			c.T1952C						PASS	.	G	PRO/LEU	1191,3215	707.3+/-407.5	165,861,1177	128.0	146.0	140.0		1952	3.3	0.1	3	dbSNP_121	140	2999,5601	664.5+/-402.2	539,1921,1840	yes	missense	WDR49	NM_178824.3	98	704,2782,3017	GG,GA,AA		34.8721,27.0313,32.2159	benign	651/698	167217964	4190,8816	2203	4300	6503	SO:0001583	missense	151790	exon14			GCCTCCAGAATTT	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1952T>C	3.37:g.167217964A>G	ENSP00000311343:p.Leu651Pro	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	798|798	0.36538461538461536|0.36538461538461536	145|145	0.29471544715447157|0.29471544715447157	122|122	0.3370165745856354|0.3370165745856354	264|264	0.46153846153846156|0.46153846153846156	267|267	0.35224274406332456|0.35224274406332456	G|G	0.623|0.623	-0.820174|-0.820174	0.02755|0.02755	0.270313|0.270313	0.348721|0.348721	ENSG00000174776|ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925|ENST00000472600	T;T;T|.	0.52295|.	0.67;1.97;1.03|.	5.13|5.13	3.29|3.29	0.37713|0.37713	.|.	0.401030|.	0.22481|.	N|.	0.059486|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00170|0.00170	-1.935|-1.935	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	0.45906|0.45906	-0.9229|-0.9229	9|4	0.46703|.	T|.	0.11|.	.|.	6.7493|6.7493	0.23477|0.23477	0.328:0.0:0.672:0.0|0.328:0.0:0.672:0.0	rs13060964;rs52834126;rs58923964;rs13060964|rs13060964;rs52834126;rs58923964;rs13060964	616;651|.	E7EQK3;Q8IV35|.	.;WDR49_HUMAN|.	P|R	651;476;616|628	ENSP00000311343:L651P;ENSP00000420508:L476P;ENSP00000410863:L616P|.	ENSP00000311343:L651P|.	L|W	-|-	2|1	0|0	WDR49|WDR49	168700658|168700658	0.130000|0.130000	0.22417|0.22417	0.090000|0.090000	0.20809|0.20809	0.002000|0.002000	0.02628|0.02628	1.406000|1.406000	0.34646|0.34646	1.165000|1.165000	0.42670|0.42670	-0.349000|-0.349000	0.07799|0.07799	CTG|TGG	A|0.662;G|0.338	0.338	strong		0.433	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168004	161168004	+	Silent	SNP	C	C	T	rs33941127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161168004C>T	ENST00000367996.5	-	1	842	c.414G>A	c.(412-414)tcG>tcA	p.S138S	ADAMTS4_ENST00000367995.3_Silent_p.S138S|ADAMTS4_ENST00000478394.1_5'Flank|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	138					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GAGATGCCACCGACTCCGGAT	0.632													C|||	1828	0.365016	0.4145	0.3141	5008	,	,		17741	0.4494		0.2087	False		,,,				2504	0.408				p.S138S		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.G414A						PASS	.	C		1587,2819	489.4+/-361.5	271,1045,887	62.0	62.0	62.0		414	-6.8	0.9	1	dbSNP_126	62	1776,6824	320.1+/-314.5	175,1426,2699	no	coding-synonymous	ADAMTS4	NM_005099.4		446,2471,3586	TT,TC,CC		20.6512,36.0191,25.8573		138/838	161168004	3363,9643	2203	4300	6503	SO:0001819	synonymous_variant	9507	exon1			TGCCACCGACTCC	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.414G>A	1.37:g.161168004C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	72	0.699029	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Silent	SNP	ENST00000367996.5	37	CCDS1223.1																																																																																			C|0.720;T|0.280	0.280	strong		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
TTN	7273	hgsc.bcm.edu	37	2	179606538	179606538	+	Missense_Mutation	SNP	G	G	A	rs2627037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179606538G>A	ENST00000591111.1	-	46	10695	c.10471C>T	c.(10471-10473)Cca>Tca	p.P3491S	TTN_ENST00000589042.1_Missense_Mutation_p.P3808S|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P3637S|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P3570S|TTN_ENST00000460472.2_Missense_Mutation_p.P3445S			Q8WZ42	TITIN_HUMAN	titin	13810			P -> S. {ECO:0000269|PubMed:10850961, ECO:0000269|PubMed:11717165, 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)			AATTTAGTTGGGTAAACTGGA	0.398													A|||	1368	0.273163	0.4531	0.3602	5008	,	,		14879	0.2133		0.0875	False		,,,				2504	0.2209				p.P3808S		Atlas-SNP	.											.	TTN	18412	.	0			c.C11422T						PASS	.	A	SER/PRO,,SER/PRO,SER/PRO	1541,2121		341,859,631	62.0	58.0	59.0		10333,,10708,10909	6.1	1.0	2	dbSNP_100	59	597,7563		27,543,3510	yes	missense,intron,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,,74,74	368,1402,4141	AA,AG,GG		7.3162,42.0808,18.0849	,,,	3445/26927,,3570/27052,3637/27119	179606538	2138,9684	1831	4080	5911	SO:0001583	missense	7273	exon48			TAGTTGGGTAAAC	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.10471C>T	2.37:g.179606538G>A	ENSP00000465570:p.Pro3491Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	26	0.295455	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		491	0.22481684981684982	206	0.4186991869918699	98	0.27071823204419887	124	0.21678321678321677	63	0.08311345646437995	A	13.60	2.284320	0.40394	0.420808	0.073162	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.56776	0.47;0.54;0.44	6.07	6.07	0.98685	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.38951	P	0.04164500000000004	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36212	-0.9757	8	0.87932	D	0	.	12.4038	0.55428	0.9347:0.0:0.0653:0.0	rs2627037;rs52826161;rs58316879;rs2627037	3445;3570;3637	D3DPF9;E7EQE6;E7ET18	.;.;.	S	3445;3637;3570;3445	ENSP00000434586:P3445S;ENSP00000340554:P3637S;ENSP00000352154:P3570S	ENSP00000340554:P3637S	P	-	1	0	TTN	179314783	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.370000	0.59517	1.120000	0.41904	-0.352000	0.07741	CCA	G|0.778;A|0.222	0.222	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PLBD2	196463	hgsc.bcm.edu	37	12	113825679	113825679	+	Missense_Mutation	SNP	C	C	T	rs12425042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:113825679C>T	ENST00000280800.3	+	11	1601	c.1570C>T	c.(1570-1572)Cgt>Tgt	p.R524C	PLBD2_ENST00000545182.2_Missense_Mutation_p.R492C	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	524			R -> C (in dbSNP:rs12425042).		lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						CCAGGCCCTGCGTCAGCGCTC	0.637													C|||	344	0.0686901	0.0469	0.0836	5008	,	,		18279	0.001		0.1332	False		,,,				2504	0.091				p.R524C		Atlas-SNP	.											.	PLBD2	33	.	0			c.C1570T						PASS	.	C	CYS/ARG,CYS/ARG	328,4078	173.4+/-203.2	18,292,1893	135.0	134.0	134.0		1474,1570	2.0	0.5	12	dbSNP_120	134	1271,7329	253.2+/-279.0	101,1069,3130	yes	missense,missense	PLBD2	NM_001159727.1,NM_173542.3	180,180	119,1361,5023	TT,TC,CC		14.7791,7.4444,12.2943	possibly-damaging,possibly-damaging	492/558,524/590	113825679	1599,11407	2203	4300	6503	SO:0001583	missense	196463	exon11			GCCCTGCGTCAGC	BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"""PLB homolog 2 (Dictyostelium)"", ""mannose-6-phosphate protein associated protein p76"""					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.1570C>T	12.37:g.113825679C>T	ENSP00000280800:p.Arg524Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_173542	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	37	CCDS9168.1	167	0.07646520146520147	27	0.054878048780487805	33	0.09116022099447514	1	0.0017482517482517483	106	0.13984168865435356	C	14.72	2.618394	0.46736	0.074444	0.147791	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.19806	2.12;2.12	4.93	2.01	0.26516	.	0.688265	0.14858	N	0.294242	T	0.00210	0.0006	M	0.68952	2.095	0.38881	P	0.04308299999999998	D;D	0.65815	0.995;0.971	P;P	0.58970	0.711;0.849	T	0.04885	-1.0920	9	0.56958	D	0.05	-1.4107	8.2799	0.31894	0.1286:0.7279:0.0:0.1436	rs12425042;rs57493511;rs12425042	492;524	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	C	492;524	ENSP00000443463:R492C;ENSP00000280800:R524C	ENSP00000280800:R524C	R	+	1	0	PLBD2	112310062	0.001000	0.12720	0.528000	0.27938	0.526000	0.34562	-0.094000	0.11094	0.579000	0.29504	-0.266000	0.10368	CGT	C|0.896;T|0.104	0.104	strong		0.637	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542	
GPR87	53836	hgsc.bcm.edu	37	3	151012639	151012639	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:151012639A>G	ENST00000260843.4	-	3	859	c.395T>C	c.(394-396)cTt>cCt	p.L132P	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	132					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TATCAGCCCAAGGAACACGAT	0.418																																					p.L132P		Atlas-SNP	.											GPR87,NS,carcinoma,+1,1	GPR87	52	1	0			c.T395C						scavenged	.						99.0	90.0	93.0					3																	151012639		2203	4300	6503	SO:0001583	missense	53836	exon3			AGCCCAAGGAACA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.395T>C	3.37:g.151012639A>G	ENSP00000260843:p.Leu132Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	2	0.0322581	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.050620	0.75960	.	.	ENSG00000138271	ENST00000260843	D	0.81659	-1.52	5.56	5.56	0.83823	GPCR, rhodopsin-like superfamily (1);	0.153130	0.45126	D	0.000392	D	0.90345	0.6979	M	0.85777	2.775	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.91893	0.5525	10	0.87932	D	0	-13.4027	15.6607	0.77186	1.0:0.0:0.0:0.0	.	132	Q9BY21	GPR87_HUMAN	P	132	ENSP00000260843:L132P	ENSP00000260843:L132P	L	-	2	0	GPR87	152495329	1.000000	0.71417	0.781000	0.31783	0.968000	0.65278	8.905000	0.92613	2.241000	0.73720	0.533000	0.62120	CTT	.	.	none		0.418	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4510560	4510560	+	Missense_Mutation	SNP	C	C	T	rs7251858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4510560C>T	ENST00000301286.3	-	3	3369	c.3370G>A	c.(3370-3372)Gcc>Acc	p.A1124T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1124			A -> T (in dbSNP:rs7251858). {ECO:0000269|PubMed:11572484}.			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						TGTGTGGTGGCCAAAAGCCCC	0.657													C|||	1776	0.354633	0.27	0.304	5008	,	,		15490	0.5645		0.3091	False		,,,				2504	0.3354				p.A1124T		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G3370A						PASS	.	C	THR/ALA	1202,3044		173,856,1094	38.0	44.0	42.0		3370	1.5	0.0	19	dbSNP_116	42	2576,5880		397,1782,2049	yes	missense	PLIN4	NM_001080400.1	58	570,2638,3143	TT,TC,CC		30.4636,28.309,29.7433	possibly-damaging	1124/1358	4510560	3778,8924	2123	4228	6351	SO:0001583	missense	729359	exon3			TGGTGGCCAAAAG	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.3370G>A	19.37:g.4510560C>T	ENSP00000301286:p.Ala1124Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	792	0.3626373626373626	121	0.2459349593495935	119	0.3287292817679558	322	0.5629370629370629	230	0.3034300791556728	C	15.40	2.823443	0.50739	0.28309	0.304636	ENSG00000167676	ENST00000301286	T	0.10763	2.84	2.67	1.51	0.23008	.	0.243249	0.21268	N	0.077365	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.47762	0.9	P	0.44518	0.452	T	0.31052	-0.9957	9	0.27082	T	0.32	.	3.8559	0.08974	0.0:0.7687:0.0:0.2313	rs7251858;rs61171079;rs7251858	1124	Q96Q06	PLIN4_HUMAN	T	1124	ENSP00000301286:A1124T	ENSP00000301286:A1124T	A	-	1	0	PLIN4	4461560	0.000000	0.05858	0.015000	0.15790	0.007000	0.05969	0.396000	0.20867	1.353000	0.45828	0.511000	0.50034	GCC	C|0.660;T|0.340	0.340	strong		0.657	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
RDH8	50700	hgsc.bcm.edu	37	19	10132290	10132290	+	Silent	SNP	C	C	T	rs747574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10132290C>T	ENST00000171214.1	+	6	1050	c.801C>T	c.(799-801)ctC>ctT	p.L267L	RDH8_ENST00000591589.1_Silent_p.L287L	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	267					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)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGACCACGCTCAAAACCGTGG	0.602													C|||	1068	0.213259	0.0688	0.1974	5008	,	,		18015	0.3938		0.1451	False		,,,				2504	0.3037				p.L287L		Atlas-SNP	.											.	RDH8	51	.	0			c.C861T						PASS	.	C		403,4003	200.1+/-223.5	17,369,1817	109.0	103.0	105.0		801	2.1	0.5	19	dbSNP_86	105	1278,7322	254.6+/-279.8	90,1098,3112	no	coding-synonymous	RDH8	NM_015725.2		107,1467,4929	TT,TC,CC		14.8605,9.1466,12.9248		267/312	10132290	1681,11325	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon6			CACGCTCAAAACC	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.801C>T	19.37:g.10132290C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				C|0.835;T|0.165	0.165	strong		0.602	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
GPC1	2817	hgsc.bcm.edu	37	2	241404317	241404317	+	Silent	SNP	C	C	T	rs2229458	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	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	
PDCD11	22984	hgsc.bcm.edu	37	10	105177645	105177645	+	Missense_Mutation	SNP	G	G	T	rs11598673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:105177645G>T	ENST00000369797.3	+	14	1961	c.1867G>T	c.(1867-1869)Gca>Tca	p.A623S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	623			A -> S (in dbSNP:rs11598673).		mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GAAAGAGCCTGCAGGACACAG	0.478													G|||	134	0.0267572	0.0068	0.0663	5008	,	,		20481	0.0		0.0557	False		,,,				2504	0.0235				p.A623S		Atlas-SNP	.											.	PDCD11	160	.	0			c.G1867T						PASS	.	G	SER/ALA	79,4327	69.2+/-107.0	0,79,2124	154.0	138.0	143.0		1867	2.2	0.0	10	dbSNP_120	143	598,8002	157.7+/-211.4	22,554,3724	yes	missense	PDCD11	NM_014976.1	99	22,633,5848	TT,TG,GG		6.9535,1.793,5.2053	benign	623/1872	105177645	677,12329	2203	4300	6503	SO:0001583	missense	22984	exon14			GAGCCTGCAGGAC	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.1867G>T	10.37:g.105177645G>T	ENSP00000358812:p.Ala623Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	70	0.03205128205128205	3	0.006097560975609756	29	0.08011049723756906	0	0.0	38	0.05013192612137203	G	11.18	1.561328	0.27915	0.01793	0.069535	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.10192	2.9	5.28	2.15	0.27550	Nucleic acid-binding, OB-fold-like (1);	1.245640	0.05180	N	0.501217	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.36237	-0.9756	10	0.09338	T	0.73	0.2355	6.3238	0.21232	0.2411:0.1436:0.6154:0.0	rs11598673;rs52837777;rs57202852;rs11598673	623	Q14690	RRP5_HUMAN	S	623	ENSP00000358812:A623S	ENSP00000358812:A623S	A	+	1	0	PDCD11	105167635	0.000000	0.05858	0.001000	0.08648	0.949000	0.60115	0.046000	0.14035	1.161000	0.42604	0.462000	0.41574	GCA	G|0.954;T|0.046	0.046	strong		0.478	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
AKAP13	11214	hgsc.bcm.edu	37	15	86123170	86123170	+	Missense_Mutation	SNP	G	G	T	rs745191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	116	0	0		WXS	Illumina HiSeq	Phase_I	93	93	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	
HPS5	11234	hgsc.bcm.edu	37	11	18319180	18319180	+	Missense_Mutation	SNP	G	G	T	rs7128017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18319180G>T	ENST00000349215.3	-	11	1526	c.1249C>A	c.(1249-1251)Ctg>Atg	p.L417M	HPS5_ENST00000438420.2_Missense_Mutation_p.L303M|HPS5_ENST00000531848.1_Missense_Mutation_p.L303M|HPS5_ENST00000352460.3_5'Flank|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	90	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	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	
SLC36A2	153201	hgsc.bcm.edu	37	5	150696496	150696496	+	Missense_Mutation	SNP	G	G	A	rs10042608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150696496G>A	ENST00000335244.4	-	10	1463	c.1334C>T	c.(1333-1335)gCc>gTc	p.A445V	SLC36A2_ENST00000450886.1_Missense_Mutation_p.A169V	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	445			A -> V (in dbSNP:rs10042608).		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)	GCTGATCAGGGCGTCCTTGAA	0.612													G|||	333	0.0664936	0.1808	0.0331	5008	,	,		15056	0.001		0.0417	False		,,,				2504	0.0286				p.A445V		Atlas-SNP	.											.	SLC36A2	71	.	0			c.C1334T						PASS	.	G	VAL/ALA	700,3706	291.8+/-281.7	61,578,1564	80.0	71.0	74.0		1334	-0.9	0.9	5	dbSNP_119	74	336,8264	116.1+/-175.8	3,330,3967	no	missense	SLC36A2	NM_181776.2	64	64,908,5531	AA,AG,GG		3.907,15.8874,7.9656	benign	445/484	150696496	1036,11970	2203	4300	6503	SO:0001583	missense	153201	exon10			ATCAGGGCGTCCT	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.1334C>T	5.37:g.150696496G>A	ENSP00000334223:p.Ala445Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	143	0.06547619047619048	98	0.1991869918699187	15	0.04143646408839779	0	0.0	30	0.0395778364116095	G	9.961	1.222784	0.22457	0.158874	0.03907	ENSG00000186335	ENST00000335244;ENST00000450886	T;T	0.01963	4.53;4.53	4.92	-0.909	0.10514	.	0.567303	0.18762	N	0.131880	T	0.00012	0.0000	N	0.01686	-0.76	0.45239	P	0.0017559999999999798	B	0.02656	0.0	B	0.06405	0.002	T	0.45086	-0.9285	9	0.28530	T	0.3	-5.571	9.8733	0.41189	0.7231:0.0:0.2769:0.0	rs10042608;rs60920031	445	Q495M3	S36A2_HUMAN	V	445;169	ENSP00000334223:A445V;ENSP00000399479:A169V	ENSP00000334223:A445V	A	-	2	0	SLC36A2	150676689	0.081000	0.21417	0.921000	0.36526	0.975000	0.68041	2.432000	0.44784	-0.093000	0.12396	0.650000	0.86243	GCC	G|0.928;A|0.072	0.072	strong		0.612	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
PTPRJ	5795	hgsc.bcm.edu	37	11	48145375	48145375	+	Missense_Mutation	SNP	A	A	C	rs1566734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:48145375A>C	ENST00000418331.2	+	5	1179	c.827A>C	c.(826-828)cAa>cCa	p.Q276P	PTPRJ_ENST00000440289.2_Missense_Mutation_p.Q276P	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	276	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> P (in a colon cancer sample; somatic mutation; dbSNP:rs1566734). {ECO:0000269|PubMed:12089527, ECO:0000269|PubMed:15378013}.		contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|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 platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.Q276P(3)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TATCTTCTACAATCAAATAAG	0.468													A|||	951	0.189896	0.1051	0.1239	5008	,	,		17537	0.3185		0.161	False		,,,				2504	0.2485				p.Q276P		Atlas-SNP	.											PTPRJ_ENST00000418331,NS,carcinoma,0,2	PTPRJ	225	2	3	Substitution - Missense(3)	prostate(3)	c.A827C	GRCh37	CM043071	PTPRJ	M	rs1566734	PASS	.	A	PRO/GLN,PRO/GLN	528,3874	240.9+/-251.5	33,462,1706	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	827,827	1.5	0.0	11	dbSNP_88	69	1389,7207	267.8+/-287.5	107,1175,3016	yes	missense,missense	PTPRJ	NM_001098503.1,NM_002843.3	76,76	140,1637,4722	CC,CA,AA		16.1587,11.9945,14.7484	benign,benign	276/540,276/1338	48145375	1917,11081	2201	4298	6499	SO:0001583	missense	5795	exon5			TTCTACAATCAAA	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.827A>C	11.37:g.48145375A>C	ENSP00000400010:p.Gln276Pro	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	364	0.16666666666666666	46	0.09349593495934959	46	0.1270718232044199	150	0.26223776223776224	122	0.16094986807387862	A	10.21	1.286333	0.23478	0.119945	0.161587	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.35973	2.56;1.28	5.31	1.54	0.23209	Fibronectin, type III (2);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;P	0.37500	0.001;0.597	B;B	0.32624	0.002;0.149	T	0.34453	-0.9828	8	0.45353	T	0.12	.	3.8559	0.08974	0.6593:0.0:0.1756:0.1651	rs1566734;rs17791465;rs61316421;rs1566734	276;276	Q12913;Q6P4H4	PTPRJ_HUMAN;.	P	276	ENSP00000400010:Q276P;ENSP00000409733:Q276P	ENSP00000278456:Q276P	Q	+	2	0	PTPRJ	48101951	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.077000	0.14738	0.062000	0.16340	0.528000	0.53228	CAA	C|0.161;N|0.000	0.161	strong		0.468	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
DPY19L1	23333	hgsc.bcm.edu	37	7	34979905	34979905	+	Missense_Mutation	SNP	C	C	A	rs1637696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:34979905C>A	ENST00000310974.4	-	19	1649	c.1505G>T	c.(1504-1506)gGt>gTt	p.G502V	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	502			G -> V (in dbSNP:rs1637696).			integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						CACAATAGCACCAGGATGTAC	0.373													C|||	1028	0.205272	0.1589	0.255	5008	,	,		11564	0.129		0.2982	False		,,,				2504	0.2157				p.G502V		Atlas-SNP	.											.	DPY19L1	56	.	0			c.G1505T						PASS	.	C	VAL/GLY	672,3044		61,550,1247	84.0	71.0	75.0		1505	5.2	1.0	7	dbSNP_89	75	2726,5462		436,1854,1804	yes	missense	DPY19L1	NM_015283.1	109	497,2404,3051	AA,AC,CC		33.2926,18.084,28.545	benign	502/676	34979905	3398,8506	1858	4094	5952	SO:0001583	missense	23333	exon19			ATAGCACCAGGAT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1505G>T	7.37:g.34979905C>A	ENSP00000308695:p.Gly502Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	78	54	0.692308	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	37	CCDS43567.1	488	0.22344322344322345	96	0.1951219512195122	91	0.2513812154696133	77	0.1346153846153846	224	0.2955145118733509	C	11.25	1.582436	0.28180	0.18084	0.332926	ENSG00000173852	ENST00000310974	T	0.55588	0.51	5.24	5.24	0.73138	.	0.555807	0.20240	N	0.096314	T	0.00012	0.0000	N	0.19112	0.55	0.21915	P	0.999475072	P	0.36354	0.549	B	0.36534	0.227	T	0.34601	-0.9822	9	0.27082	T	0.32	-13.4767	7.3913	0.26911	0.0:0.7346:0.1721:0.0933	rs1637696;rs9655360;rs10349593;rs17792208;rs1637696	502	Q2PZI1	D19L1_HUMAN	V	502	ENSP00000308695:G502V	ENSP00000308695:G502V	G	-	2	0	DPY19L1	34946430	0.968000	0.33430	1.000000	0.80357	0.967000	0.64934	0.945000	0.29056	2.619000	0.88677	0.655000	0.94253	GGT	C|0.758;A|0.242	0.242	strong		0.373	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
TFR2	7036	hgsc.bcm.edu	37	7	100225031	100225031	+	Silent	SNP	G	G	A	rs2075674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100225031G>A	ENST00000462107.1	-	17	2138	c.1851C>T	c.(1849-1851)gcC>gcT	p.A617A	TFR2_ENST00000544242.1_Silent_p.A158A|TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000223051.3_Silent_p.A617A			Q9UP52	TFR2_HUMAN	transferrin receptor 2	617					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	CCTGGGCCACGGCGGGCAGGC	0.672													G|||	651	0.129992	0.087	0.17	5008	,	,		15358	0.12		0.1839	False		,,,				2504	0.1145				p.A617A		Atlas-SNP	.											.	TFR2	53	.	0			c.C1851T						PASS	.	G	,	418,3964		25,368,1798	26.0	23.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1338,1851	-4.8	1.0	7	dbSNP_96	24	1695,6881		175,1345,2768	no	coding-synonymous,coding-synonymous	TFR2	NM_001206855.1,NM_003227.3	,	200,1713,4566	AA,AG,GG		19.7645,9.539,16.3065	,	446/631,617/802	100225031	2113,10845	2191	4288	6479	SO:0001819	synonymous_variant	7036	exon16			GGCCACGGCGGGC	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1851C>T	7.37:g.100225031G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																			G|0.856;A|0.144	0.144	strong		0.672	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497914	32497914	+	Missense_Mutation	SNP	C	C	T	rs76748970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32497914C>T	ENST00000374975.3	-	1	150	c.88G>A	c.(88-90)Ggg>Agg	p.G30R		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						CGGGTGTCCCCAGCCAAAGCC	0.547																																					p.G30R		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G88A						PASS	.						103.0	105.0	104.0					6																	32497914		2203	4300	6503	SO:0001583	missense	3127	exon1			TGTCCCCAGCCAA		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.88G>A	6.37:g.32497914C>T	ENSP00000364114:p.Gly30Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	154	61	0.396104	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	404	0.184981684981685	40	0.08130081300813008	78	0.2154696132596685	126	0.2202797202797203	160	0.21108179419525067	.	5.421	0.262764	0.10294	.	.	ENSG00000198502	ENST00000374975	T	0.00220	8.52	4.54	2.07	0.26955	MHC classes I/II-like antigen recognition protein (1);	1.862590	0.02449	N	0.085362	T	0.00039	0.0001	N	0.03903	-0.33	0.80722	P	0.0	B	0.15719	0.014	B	0.25987	0.065	T	0.12016	-1.0564	9	0.02654	T	1	.	5.9769	0.19385	0.0:0.2201:0.0:0.7799	.	30	Q30154	DRB5_HUMAN	R	30	ENSP00000364114:G30R	ENSP00000364114:G30R	G	-	1	0	HLA-DRB5	32605892	0.227000	0.23707	0.001000	0.08648	0.062000	0.15995	0.527000	0.22987	0.253000	0.21552	-0.350000	0.07774	GGG	C|0.842;T|0.158	0.158	strong		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
UMOD	7369	hgsc.bcm.edu	37	16	20359633	20359633	+	Silent	SNP	C	C	T	rs28544423	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:20359633C>T	ENST00000570689.1	-	4	1031	c.885G>A	c.(883-885)ggG>ggA	p.G295G	UMOD_ENST00000396138.4_Silent_p.G344G|UMOD_ENST00000424589.1_Silent_p.G328G|UMOD_ENST00000396134.2_Silent_p.G328G|UMOD_ENST00000396142.2_Silent_p.G295G|UMOD_ENST00000302509.4_Silent_p.G295G			P07911	UROM_HUMAN	uromodulin	295					cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CCTCACACGTCCCCTCCACGG	0.567													c|||	580	0.115815	0.0673	0.1599	5008	,	,		20928	0.0129		0.1998	False		,,,				2504	0.1697				p.G295G		Atlas-SNP	.											.	UMOD	128	.	0			c.G885A						PASS	.		,	337,4069	175.5+/-204.9	17,303,1883	196.0	177.0	183.0		885,885	-4.2	0.5	16	dbSNP_125	183	1626,6974	301.8+/-305.6	154,1318,2828	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	171,1621,4711	TT,TC,CC		18.907,7.6487,15.093	,	295/641,295/641	20359633	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	7369	exon4			ACACGTCCCCTCC	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.885G>A	16.37:g.20359633C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			C|0.858;T|0.142	0.142	strong		0.567	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31239776	31239776	+	Splice_Site	SNP	A	A	C	rs2074493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31239776A>C	ENST00000376228.5	-	1	87	c.73T>G	c.(73-75)Tgc>Ggc	p.C25G	HLA-C_ENST00000383329.3_Splice_Site_p.C25G	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	25	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						CCGCACTCACAGGCCCAGGTC	0.736													N|||	1529	0.305312	0.4047	0.3314	5008	,	,		11801	0.3095		0.2773	False		,,,				2504	0.1769				p.C25G		Atlas-SNP	.											.	HLA-C	92	.	0			c.T73G						PASS	.	C	GLY/CYS	995,2019		180,635,692	15.0	17.0	16.0		73	2.4	0.3	6	dbSNP_96	16	1335,4081		166,1003,1539	no	missense-near-splice	HLA-C	NM_002117.5	159	346,1638,2231	CC,CA,AA		24.6492,33.0126,27.6394	benign	25/367	31239776	2330,6100	1507	2708	4215	SO:0001630	splice_region_variant	3107	exon1			ACTCACAGGCCCA	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.73+1T>G	6.37:g.31239776A>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	700|700	0.32051282051282054|0.32051282051282054	193|193	0.39227642276422764|0.39227642276422764	117|117	0.32320441988950277|0.32320441988950277	180|180	0.3146853146853147|0.3146853146853147	210|210	0.2770448548812665|0.2770448548812665	-|-	6.538|6.538	0.467500|0.467500	0.12402|0.12402	0.330126|0.330126	0.246492|0.246492	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00659|.	5.94;5.94|.	3.24|3.24	2.36|2.36	0.29203|0.29203	MHC class I-like antigen recognition (1);|.	.|.	.|.	.|.	.|.	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.00000|0.00000	-4.495|-4.495	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-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|T	0.47761|0.47761	-0.9092|-0.9092	8|4	0.02654|.	T|.	1|.	.|.	4.2289|4.2289	0.10594|0.10594	0.224:0.6494:0.0:0.1266|0.224:0.6494:0.0:0.1266	rs2074493;rs2308532;rs17880133|rs2074493;rs2308532;rs17880133	25;25;25;25|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	G|R	25|24	ENSP00000365402:C25G;ENSP00000372819:C25G|.	ENSP00000365402:C25G|.	C|L	-|-	1|2	0|0	HLA-C|HLA-C	31347755|31347755	0.000000|0.000000	0.05858|0.05858	0.333000|0.333000	0.25482|0.25482	0.006000|0.006000	0.05464|0.05464	-0.609000|-0.609000	0.05635|0.05635	0.222000|0.222000	0.20900|0.20900	-1.818000|-1.818000	0.00600|0.00600	TGC;TGC;TGC;TGT|CTG	A|0.719;C|0.281	0.281	strong		0.736	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	Missense_Mutation
THBS2	7058	hgsc.bcm.edu	37	6	169637763	169637763	+	Silent	SNP	G	G	C	rs9766671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:169637763G>C	ENST00000366787.3	-	9	1506	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	419	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GTGTCTGGATGGAGGGCCCCA	0.662													g|||	1270	0.253594	0.2526	0.2478	5008	,	,		17747	0.2679		0.1968	False		,,,				2504	0.3027				p.S419S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	0			c.C1257G						PASS	.			1069,3337	387.5+/-326.5	123,823,1257	87.0	79.0	81.0		1257	2.5	1.0	6	dbSNP_119	81	1601,6999	295.8+/-302.6	167,1267,2866	no	coding-synonymous	THBS2	NM_003247.2		290,2090,4123	CC,CG,GG		18.6163,24.2624,20.529		419/1173	169637763	2670,10336	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon9			CTGGATGGAGGGC		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1257C>G	6.37:g.169637763G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	50	0.595238	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.786;C|0.214	0.214	strong		0.662	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879366	39879366	+	Silent	SNP	T	T	C	rs604316	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:39879366T>C	ENST00000530275.1	+	1	3216	c.3021T>C	c.(3019-3021)ccT>ccC	p.P1007P	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000289893.4_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1007	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGAGGAGCCTGCCTTCCCAG	0.706													t|||	1994	0.398163	0.7194	0.3329	5008	,	,		9912	0.3294		0.2833	False		,,,				2504	0.1994				p.P1143P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.T3429C						PASS	.	C	,,	2233,1537		716,801,368	11.0	15.0	14.0		,3429,	2.9	0.0	1	dbSNP_83	14	2427,5783		394,1639,2072	no	intron,coding-synonymous,intron	MACF1,KIAA0754	NM_012090.4,NM_015038.1,NM_033044.3	,,	1110,2440,2440	CC,CT,TT		29.5615,40.7692,38.8982	,,	,1143/1428,	39879366	4660,7320	1885	4105	5990	SO:0001819	synonymous_variant	643314	exon1			GGAGCCTGCCTTC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3021T>C	1.37:g.39879366T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				T|0.605;C|0.395	0.395	strong		0.706	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
CACNA1E	777	hgsc.bcm.edu	37	1	181759657	181759657	+	Missense_Mutation	SNP	G	G	A	rs704326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:181759657G>A	ENST00000367573.2	+	44	5863	c.5863G>A	c.(5863-5865)Gcc>Acc	p.A1955T	CACNA1E_ENST00000360108.3_Missense_Mutation_p.A1936T|CACNA1E_ENST00000358338.5_Missense_Mutation_p.A1887T|CACNA1E_ENST00000367570.1_Missense_Mutation_p.A1955T|CACNA1E_ENST00000367567.4_Missense_Mutation_p.A1562T|CACNA1E_ENST00000357570.5_Missense_Mutation_p.A1906T|CACNA1E_ENST00000526775.1_Missense_Mutation_p.A1936T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1955			A -> T (in dbSNP:rs704326). {ECO:0000269|PubMed:7536609}.		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						TATGGACCCCGCCGATGACGG	0.483													G|||	1384	0.276358	0.1203	0.3242	5008	,	,		18450	0.3879		0.4314	False		,,,				2504	0.1789				p.A1955T		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G5863A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	591,3217		55,481,1368	81.0	92.0	89.0		5863,5863,5806	-1.5	0.0	1	dbSNP_86	89	3736,4484		850,2036,1224	yes	missense,missense,missense	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	58,58,58	905,2517,2592	AA,AG,GG		45.4501,15.52,35.9744	benign,benign,benign	1955/2271,1955/2314,1936/2252	181759657	4327,7701	1904	4110	6014	SO:0001583	missense	777	exon44			GACCCCGCCGATG	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.5863G>A	1.37:g.181759657G>A	ENSP00000356545:p.Ala1955Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	171	94	0.549708	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	784	0.358974358974359	58	0.11788617886178862	139	0.3839779005524862	254	0.44405594405594406	333	0.4393139841688654	G	1.618	-0.522134	0.04171	0.1552	0.454501	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96365	-3.92;-3.92;-3.83;-3.92;-3.99;-3.84;-3.83	5.54	-1.5	0.08691	.	1.620940	0.02678	N	0.109393	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.31336	-0.9947	9	0.14656	T	0.56	.	11.663	0.51358	0.5216:0.0:0.4784:0.0	rs704326;rs56466668;rs60254499;rs704326	1936;1955	Q15878-2;Q15878-3	.;.	T	1955;1936;1906;1887;1562;1936;1955	ENSP00000356542:A1955T;ENSP00000434814:A1936T;ENSP00000350183:A1906T;ENSP00000351101:A1887T;ENSP00000356539:A1562T;ENSP00000353222:A1936T;ENSP00000356545:A1955T	ENSP00000350183:A1906T	A	+	1	0	CACNA1E	180026280	0.000000	0.05858	0.002000	0.10522	0.463000	0.32649	0.331000	0.19733	-0.148000	0.11234	-0.768000	0.03414	GCC	G|0.652;T|0.008	.	strong		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
KIAA1217	56243	hgsc.bcm.edu	37	10	24813282	24813282	+	Silent	SNP	G	G	C	rs2297329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24813282G>C	ENST00000376454.3	+	13	2517	c.2487G>C	c.(2485-2487)acG>acC	p.T829T	KIAA1217_ENST00000376462.1_Silent_p.T749T|KIAA1217_ENST00000307544.6_Silent_p.T512T|KIAA1217_ENST00000376452.3_Silent_p.T794T|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000396446.1_Silent_p.T512T|KIAA1217_ENST00000396445.1_Silent_p.T512T|KIAA1217_ENST00000376451.2_Silent_p.T512T|KIAA1217_ENST00000458595.1_Silent_p.T794T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	829				T -> M (in Ref. 3; BX648451). {ECO:0000305}.	embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TGAAAGGCACGGACGCAGCCC	0.562													G|||	714	0.142572	0.2791	0.0951	5008	,	,		19110	0.1468		0.0308	False		,,,				2504	0.1022				p.T829T		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G2487C						PASS	.	G	,,	1081,3325	391.4+/-328.1	137,807,1259	77.0	78.0	77.0		2247,2382,2487	-11.2	0.0	10	dbSNP_100	77	325,8275	113.5+/-173.5	5,315,3980	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	142,1122,5239	CC,CG,GG		3.7791,24.5347,10.8104	,,	749/1265,794/1310,829/1944	24813282	1406,11600	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon13			AGGCACGGACGCA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2487G>C	10.37:g.24813282G>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			G|0.889;C|0.111	0.111	strong		0.562	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
HECTD1	25831	hgsc.bcm.edu	37	14	31647241	31647241	+	Silent	SNP	G	G	A	rs2274201	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31647241G>A	ENST00000399332.1	-	3	848	c.360C>T	c.(358-360)gcC>gcT	p.A120A	HECTD1_ENST00000553700.1_Silent_p.A120A	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	120					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CACACTGTTCGGCTAAGTCTC	0.388													A|||	2794	0.557907	0.7496	0.6081	5008	,	,		16639	0.4405		0.4175	False		,,,				2504	0.5286				p.A120A		Atlas-SNP	.											.	HECTD1	159	.	0			c.C360T						PASS	.	A		2498,1272		832,834,219	147.0	144.0	145.0		360	4.3	1.0	14	dbSNP_100	145	3245,4983		637,1971,1506	no	coding-synonymous	HECTD1	NM_015382.2		1469,2805,1725	AA,AG,GG		39.4385,33.7401,47.8663		120/2611	31647241	5743,6255	1885	4114	5999	SO:0001819	synonymous_variant	25831	exon3			CTGTTCGGCTAAG	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.360C>T	14.37:g.31647241G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			G|0.486;A|0.514	0.514	strong		0.388	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
MICAL3	57553	hgsc.bcm.edu	37	22	18300594	18300594	+	Silent	SNP	G	G	A	rs11704160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	106	65	0.613208	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		
UNC45B	146862	hgsc.bcm.edu	37	17	33513337	33513337	+	Missense_Mutation	SNP	T	T	A	rs11654824	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33513337T>A	ENST00000268876.5	+	20	2652	c.2555T>A	c.(2554-2556)aTc>aAc	p.I852N	RP11-799D4.2_ENST00000590144.1_RNA|UNC45B_ENST00000394570.2_Missense_Mutation_p.I850N|UNC45B_ENST00000433649.1_Missense_Mutation_p.I850N|UNC45B_ENST00000591048.1_Missense_Mutation_p.I771N|UNC45B_ENST00000378449.1_Missense_Mutation_p.I771N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	852			I -> N (in dbSNP:rs11654824).		cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGGTTGGAGATCCTCCAGCGG	0.567													T|||	169	0.033746	0.0053	0.0317	5008	,	,		19749	0.0		0.0905	False		,,,				2504	0.0501				p.I852N		Atlas-SNP	.											.	UNC45B	133	.	0			c.T2555A						PASS	.	T	ASN/ILE,ASN/ILE	65,4341	61.1+/-98.1	2,61,2140	82.0	82.0	82.0		2549,2555	6.0	1.0	17	dbSNP_120	82	627,7973	163.0+/-215.7	13,601,3686	yes	missense,missense	UNC45B	NM_001033576.1,NM_173167.2	149,149	15,662,5826	AA,AT,TT		7.2907,1.4753,5.3206	possibly-damaging,possibly-damaging	850/930,852/932	33513337	692,12314	2203	4300	6503	SO:0001583	missense	146862	exon20			TGGAGATCCTCCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2555T>A	17.37:g.33513337T>A	ENSP00000268876:p.Ile852Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	24	0.328767	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	102	0.046703296703296704	5	0.01016260162601626	16	0.04419889502762431	0	0.0	81	0.10686015831134564	T	17.96	3.516186	0.64634	0.014753	0.072907	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51574	0.7;1.45;0.7	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.03564	0.0102	M	0.75615	2.305	0.09310	P	0.999999791172	D;D;P	0.89917	0.999;1.0;0.93	D;D;P	0.91635	0.997;0.999;0.496	T	0.39961	-0.9588	9	0.87932	D	0	-26.2242	15.7258	0.77756	0.0:0.0:0.0:1.0	rs11654824;rs52819819;rs11654824	771;850;852	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	N	852;852;850;771	ENSP00000268876:I852N;ENSP00000412840:I850N;ENSP00000367710:I771N	ENSP00000268876:I852N	I	+	2	0	UNC45B	30537450	1.000000	0.71417	0.958000	0.39756	0.992000	0.81027	7.886000	0.87288	2.311000	0.77944	0.533000	0.62120	ATC	T|0.948;A|0.052	0.052	strong		0.567	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
AGBL4	84871	hgsc.bcm.edu	37	1	49511424	49511424	+	Silent	SNP	A	A	G	rs3934240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:49511424A>G	ENST00000371839.1	-	5	542	c.426T>C	c.(424-426)caT>caC	p.H142H	AGBL4_ENST00000371836.1_Silent_p.H142H|AGBL4_ENST00000371838.1_Silent_p.H142H|RP11-141A19.1_ENST00000456002.1_RNA	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	100	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	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	
L1TD1	54596	hgsc.bcm.edu	37	1	62676091	62676091	+	Missense_Mutation	SNP	C	C	A	rs11207933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62676091C>A	ENST00000498273.1	+	4	1940	c.1645C>A	c.(1645-1647)Ccc>Acc	p.P549T	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	549			P -> T (in dbSNP:rs11207933).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						AACTGGCACACCCTGTCTGAC	0.463													C|||	944	0.188498	0.1876	0.1196	5008	,	,		19633	0.2798		0.1183	False		,,,				2504	0.2168				p.P549T		Atlas-SNP	.											.	L1TD1	114	.	0			c.C1645A						PASS	.	C	THR/PRO,THR/PRO	718,3688	293.8+/-282.8	59,600,1544	76.0	75.0	75.0		1645,1645	0.6	0.0	1	dbSNP_120	75	1059,7541	223.0+/-259.9	64,931,3305	yes	missense,missense	L1TD1	NM_001164835.1,NM_019079.4	38,38	123,1531,4849	AA,AC,CC		12.314,16.296,13.6629	possibly-damaging,possibly-damaging	549/866,549/866	62676091	1777,11229	2203	4300	6503	SO:0001583	missense	54596	exon5			GGCACACCCTGTC	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1645C>A	1.37:g.62676091C>A	ENSP00000419901:p.Pro549Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	359	0.16437728937728938	96	0.1951219512195122	38	0.10497237569060773	133	0.23251748251748253	92	0.12137203166226913	C	6.397	0.441377	0.12164	0.16296	0.12314	ENSG00000240563	ENST00000498273	T	0.15834	2.39	2.59	0.605	0.17553	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.28419	0.211	B	0.33890	0.172	T	0.43081	-0.9413	8	0.51188	T	0.08	.	3.759	0.08596	0.0:0.5901:0.2567:0.1533	rs11207933;rs52794473;rs11207933	549	Q5T7N2	LITD1_HUMAN	T	549	ENSP00000419901:P549T	ENSP00000419901:P549T	P	+	1	0	L1TD1	62448679	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.318000	0.19504	0.176000	0.19873	0.543000	0.68304	CCC	C|0.857;A|0.143	0.143	strong		0.463	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
SAMD4A	23034	hgsc.bcm.edu	37	14	55243209	55243209	+	Silent	SNP	G	G	A	rs1951438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:55243209G>A	ENST00000554335.1	+	11	2658	c.1995G>A	c.(1993-1995)tcG>tcA	p.S665S	SAMD4A_ENST00000392067.3_Silent_p.S665S|SAMD4A_ENST00000555192.1_Silent_p.S256S|SAMD4A_ENST00000251091.5_Silent_p.S577S|SAMD4A_ENST00000357634.3_Silent_p.S664S			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	665					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						GGACCCGCTCGCTGCCCGTGC	0.602													G|||	152	0.0303514	0.0204	0.0245	5008	,	,		16495	0.001		0.0447	False		,,,				2504	0.0634				p.S665S		Atlas-SNP	.											.	SAMD4A	68	.	0			c.G1995A						PASS	.	G	,,	91,4315	76.2+/-114.5	1,89,2113	102.0	111.0	108.0		1728,768,1992	0.1	1.0	14	dbSNP_92	108	355,8245	118.6+/-178.1	7,341,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	SAMD4A	NM_001161576.2,NM_001161577.1,NM_015589.5	,,	8,430,6065	AA,AG,GG		4.1279,2.0654,3.4292	,,	576/630,256/346,664/718	55243209	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	23034	exon10			CCGCTCGCTGCCC	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1995G>A	14.37:g.55243209G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	34	26	0.764706	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Silent	SNP	ENST00000554335.1	37	CCDS32084.2																																																																																			G|0.970;A|0.030	0.030	strong		0.602	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
TRIM56	81844	hgsc.bcm.edu	37	7	100731184	100731184	+	Silent	SNP	C	C	T	rs36064566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100731184C>T	ENST00000306085.6	+	3	888	c.591C>T	c.(589-591)caC>caT	p.H197H		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	197					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					TAGACCCCCACCTGGACCACC	0.692													C|||	135	0.0269569	0.0053	0.0461	5008	,	,		13054	0.001		0.0726	False		,,,				2504	0.0225				p.H197H	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.C591T						PASS	.	C		34,4100		0,34,2033	15.0	21.0	19.0		591	2.0	1.0	7	dbSNP_126	19	423,7997		7,409,3794	no	coding-synonymous	TRIM56	NM_030961.1		7,443,5827	TT,TC,CC		5.0238,0.8224,3.6403		197/756	100731184	457,12097	2067	4210	6277	SO:0001819	synonymous_variant	81844	exon3			CCCCCACCTGGAC	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19028	protein-coding gene	gene with protein product			"""tripartite motif-containing 56"""				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.591C>T	7.37:g.100731184C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			C|0.964;T|0.036	0.036	strong		0.692	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
SLC24A3	57419	hgsc.bcm.edu	37	20	19261623	19261623	+	Missense_Mutation	SNP	G	G	A	rs1569767	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:19261623G>A	ENST00000328041.6	+	2	360	c.163G>A	c.(163-165)Gta>Ata	p.V55I	RP5-1027G4.3_ENST00000319682.2_RNA	NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	55			V -> I (in dbSNP:rs1569767). {ECO:0000269|PubMed:11294880}.		ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CATGGACCTCGTAGGGGAAGA	0.557													A|||	2164	0.432109	0.3298	0.5375	5008	,	,		20396	0.5188		0.4175	False		,,,				2504	0.4213				p.V55I		Atlas-SNP	.											.	SLC24A3	92	.	0			c.G163A						PASS	.	A	ILE/VAL	1440,2966	682.4+/-404.1	246,948,1009	133.0	105.0	114.0		163	1.9	0.9	20	dbSNP_88	114	3725,4875	617.4+/-396.6	827,2071,1402	yes	missense	SLC24A3	NM_020689.3	29	1073,3019,2411	AA,AG,GG		43.314,32.6827,39.7124	benign	55/645	19261623	5165,7841	2203	4300	6503	SO:0001583	missense	57419	exon2			GACCTCGTAGGGG	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"""Solute carriers"""	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.163G>A	20.37:g.19261623G>A	ENSP00000333519:p.Val55Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	134	57	0.425373	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Missense_Mutation	SNP	ENST00000328041.6	37	CCDS13140.1	947	0.4336080586080586	136	0.2764227642276423	196	0.5414364640883977	303	0.5297202797202797	312	0.41160949868073876	A	10.25	1.299700	0.23650	0.326827	0.43314	ENSG00000185052	ENST00000328041	T	0.60920	0.15	5.39	1.86	0.25419	.	0.881058	0.09758	N	0.759602	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	0.46911	-0.9157	8	.	.	.	.	2.3173	0.04201	0.4409:0.3294:0.0849:0.1448	rs1569767;rs3790175;rs17349471;rs52833581;rs59389417;rs1569767	55	Q9HC58	NCKX3_HUMAN	I	55	ENSP00000333519:V55I	.	V	+	1	0	SLC24A3	19209623	0.462000	0.25791	0.908000	0.35775	0.996000	0.88848	-0.057000	0.11768	-0.085000	0.12573	-0.254000	0.11334	GTA	G|0.578;A|0.422	0.422	strong		0.557	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	
TOX3	27324	hgsc.bcm.edu	37	16	52478215	52478215	+	Silent	SNP	C	C	T	rs3743797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:52478215C>T	ENST00000219746.9	-	6	1244	c.960G>A	c.(958-960)gcG>gcA	p.A320A	TOX3_ENST00000407228.3_Silent_p.A315A	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	320					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)	p.A320A(2)|p.A315A(1)		NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CCCTGTATGCCGCCAGGGCCT	0.463													C|||	506	0.101038	0.0522	0.0749	5008	,	,		15360	0.1488		0.0984	False		,,,				2504	0.1391				p.A320A		Atlas-SNP	.											TOX3_ENST00000407228,NS,carcinoma,0,3	TOX3	121	3	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.G960A						PASS	.	C	,	208,3428		4,200,1614	49.0	47.0	48.0		960,945	-5.3	0.6	16	dbSNP_107	48	623,7555		26,571,3492	yes	coding-synonymous,coding-synonymous	TOX3	NM_001080430.2,NM_001146188.1	,	30,771,5106	TT,TC,CC		7.618,5.7206,7.034	,	320/577,315/572	52478215	831,10983	1818	4089	5907	SO:0001819	synonymous_variant	27324	exon6			GTATGCCGCCAGG	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.960G>A	16.37:g.52478215C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001080430	B4DRD0|B5MCW4	Silent	SNP	ENST00000219746.9	37	CCDS54009.1																																																																																			C|0.891;T|0.109	0.109	strong		0.463	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
COL27A1	85301	hgsc.bcm.edu	37	9	117033022	117033022	+	Silent	SNP	T	T	C	rs4143245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:117033022T>C	ENST00000356083.3	+	36	3961	c.3570T>C	c.(3568-3570)ctT>ctC	p.L1190L	COL27A1_ENST00000477421.2_3'UTR	NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1190	Pro-rich.|Triple-helical region.				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						AGCCAGGCCTTGAGGGTGACA	0.617													C|||	1957	0.390775	0.4213	0.4942	5008	,	,		20384	0.3175		0.4185	False		,,,				2504	0.3231				p.L1190L		Atlas-SNP	.											.	COL27A1	200	.	0			c.T3570C						PASS	.	C		1692,2714	653.6+/-399.6	304,1084,815	97.0	89.0	92.0		3570	-9.7	0.1	9	dbSNP_110	92	3498,5102	634.1+/-398.8	716,2066,1518	no	coding-synonymous	COL27A1	NM_032888.2		1020,3150,2333	CC,CT,TT		40.6744,38.4022,39.9047		1190/1861	117033022	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon36			AGGCCTTGAGGGT	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.3570T>C	9.37:g.117033022T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			T|0.601;C|0.399	0.399	strong		0.617	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
KLHL25	64410	hgsc.bcm.edu	37	15	86311695	86311695	+	Silent	SNP	G	G	A	rs1978391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:86311695G>A	ENST00000337975.5	-	2	1621	c.1347C>T	c.(1345-1347)ttC>ttT	p.F449F	KLHL25_ENST00000536947.1_Silent_p.F449F|MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	449					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						TGGTTCCTCCGAAAACAAAGA	0.602													G|||	626	0.125	0.0106	0.2291	5008	,	,		19969	0.0188		0.2883	False		,,,				2504	0.1472				p.F449F		Atlas-SNP	.											.	KLHL25	58	.	0			c.C1347T						PASS	.	G		200,4204	124.1+/-161.4	7,186,2009	88.0	77.0	81.0		1347	-2.1	0.2	15	dbSNP_92	81	2337,6261	389.7+/-343.0	349,1639,2311	no	coding-synonymous	KLHL25	NM_022480.3		356,1825,4320	AA,AG,GG		27.1807,4.5413,19.5124		449/590	86311695	2537,10465	2202	4299	6501	SO:0001819	synonymous_variant	64410	exon2			TCCTCCGAAAACA		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.1347C>T	15.37:g.86311695G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_022480	B2RDH2|B3KRT7	Silent	SNP	ENST00000337975.5	37	CCDS10339.1																																																																																			G|0.822;A|0.178	0.178	strong		0.602	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56735015	56735015	+	Silent	SNP	T	T	C	rs4801692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56735015T>C	ENST00000587340.1	-	5	1268	c.573A>G	c.(571-573)gcA>gcG	p.A191A	ZSCAN5A_ENST00000592355.1_Silent_p.A191A|ZSCAN5A_ENST00000254165.3_Silent_p.A74A|ZSCAN5A_ENST00000587492.1_Silent_p.A45A|ZSCAN5A_ENST00000391713.1_Silent_p.A191A			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	191					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)			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						TCCTGGACAATGCAGGGACCC	0.612													T|||	226	0.0451278	0.0946	0.0562	5008	,	,		17867	0.0		0.0457	False		,,,				2504	0.0164				p.A191A		Atlas-SNP	.											.	ZSCAN5A	118	.	0			c.A573G						PASS	.	T		451,3955	212.8+/-232.6	27,397,1779	49.0	45.0	47.0		573	-5.6	0.0	19	dbSNP_111	47	433,8167	131.2+/-189.0	9,415,3876	no	coding-synonymous	ZSCAN5A	NM_024303.1		36,812,5655	CC,CT,TT		5.0349,10.236,6.7969		191/497	56735015	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	79149	exon3			GGACAATGCAGGG	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.573A>G	19.37:g.56735015T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Silent	SNP	ENST00000587340.1	37	CCDS12941.1																																																																																			T|0.937;C|0.063	0.063	strong		0.612	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
IMMP1L	196294	hgsc.bcm.edu	37	11	31482246	31482246	+	Missense_Mutation	SNP	T	T	C	rs370083551		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:31482246T>C	ENST00000278200.1	-	4	316	c.121A>G	c.(121-123)Atg>Gtg	p.M41V	IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000528161.1_Intron|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000532287.1_Missense_Mutation_p.M41V	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	41					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					GTAGGCTCCATTGATGGTCCA	0.279																																					p.M41V		Atlas-SNP	.											.	IMMP1L	16	.	0			c.A121G						PASS	.	T	VAL/MET	0,4404		0,0,2202	69.0	72.0	71.0		121	5.6	1.0	11		71	1,8585	1.2+/-3.3	0,1,4292	no	missense	IMMP1L	NM_144981.1	21	0,1,6494	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	41/167	31482246	1,12989	2202	4293	6495	SO:0001583	missense	196294	exon4			GCTCCATTGATGG		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.121A>G	11.37:g.31482246T>C	ENSP00000278200:p.Met41Val	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.083575	0.76642	0.0	1.16E-4	ENSG00000148950	ENST00000532287;ENST00000278200;ENST00000529749;ENST00000530023	.	.	.	5.58	5.58	0.84498	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.000000	0.85682	D	0.000000	D	0.86997	0.6068	H	0.95043	3.615	0.80722	D	1	D;P	0.53885	0.963;0.873	D;P	0.69824	0.966;0.687	D	0.90553	0.4510	9	0.66056	D	0.02	-8.7493	16.0334	0.80603	0.0:0.0:0.0:1.0	.	41;41	E9PIG6;Q96LU5	.;IMP1L_HUMAN	V	41	.	ENSP00000278200:M41V	M	-	1	0	IMMP1L	31438822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.023000	0.76437	2.243000	0.73865	0.533000	0.62120	ATG	.	.	weak		0.279	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103082558	103082558	+	Silent	SNP	A	A	G	rs17394217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:103082558A>G	ENST00000375735.2	+	54	8724	c.8580A>G	c.(8578-8580)gaA>gaG	p.E2860E	DYNC2H1_ENST00000398093.3_Silent_p.E2860E|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	2860	AAA 4. {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)		TAATCCATGAATCTTGTAAAG	0.264													A|||	389	0.0776757	0.0023	0.0922	5008	,	,		14624	0.0923		0.1243	False		,,,				2504	0.1063				p.E2860E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A8580G						PASS	.	A	,	85,3421		2,81,1670	29.0	26.0	27.0		8580,8580	-3.2	1.0	11	dbSNP_123	27	847,7065		40,767,3149	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	42,848,4819	GG,GA,AA		10.7053,2.4244,8.1626	,	2860/4315,2860/4308	103082558	932,10486	1753	3956	5709	SO:0001819	synonymous_variant	79659	exon54			CCATGAATCTTGT	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.8580A>G	11.37:g.103082558A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			A|0.913;G|0.087	0.087	strong		0.264	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
UTP20	27340	hgsc.bcm.edu	37	12	101767224	101767224	+	Silent	SNP	C	C	T	rs112278934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:101767224C>T	ENST00000261637.4	+	53	7098	c.6924C>T	c.(6922-6924)gcC>gcT	p.A2308A		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2308					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AAATGATCGCCTATCTCTTTG	0.463													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.001				p.A2308A		Atlas-SNP	.											.	UTP20	222	.	0			c.C6924T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	88.0	88.0	88.0		6924	-3.3	0.6	12	dbSNP_132	88	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	UTP20	NM_014503.2		0,9,6494	TT,TC,CC		0.093,0.0227,0.0692		2308/2786	101767224	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon53			GATCGCCTATCTC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6924C>T	12.37:g.101767224C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.998;T|0.002	0.002	strong		0.463	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
RBMS3	27303	hgsc.bcm.edu	37	3	30032626	30032626	+	Silent	SNP	C	C	G	rs114278295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:30032626C>G	ENST00000383767.2	+	14	1569	c.1233C>G	c.(1231-1233)acC>acG	p.T411T	RBMS3_ENST00000434693.2_Silent_p.T410T|RBMS3_ENST00000383766.2_Silent_p.T393T|RBMS3_ENST00000273139.9_Silent_p.T395T|RBMS3_ENST00000456853.1_Silent_p.T408T|RBMS3_ENST00000396583.3_Silent_p.T408T|RBMS3_ENST00000473799.1_3'UTR|RBMS3_ENST00000452462.1_Silent_p.T395T			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	186	0	0		WXS	Illumina HiSeq	Phase_I	196	112	0.571429	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	
RCBTB1	55213	hgsc.bcm.edu	37	13	50141345	50141345	+	Missense_Mutation	SNP	G	G	A	rs4942848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50141345G>A	ENST00000378302.2	-	3	331	c.71C>T	c.(70-72)gCg>gTg	p.A24V	RCBTB1_ENST00000258646.3_Missense_Mutation_p.A24V|RCBTB1_ENST00000546015.1_Missense_Mutation_p.A24V	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	24			A -> V (in dbSNP:rs4942848). {ECO:0000269|PubMed:11306461, ECO:0000269|PubMed:14565662, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GAAGACACACGCCTTCCGAAT	0.468													G|||	2635	0.526158	0.3177	0.7305	5008	,	,		18492	0.6131		0.6561	False		,,,				2504	0.4397				p.A24V		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C71T						PASS	.	G	VAL/ALA	1660,2746	507.4+/-366.7	304,1052,847	124.0	111.0	115.0		71	5.8	1.0	13	dbSNP_111	115	5887,2713	682.2+/-403.8	2041,1805,454	yes	missense	RCBTB1	NM_018191.3	64	2345,2857,1301	AA,AG,GG		31.5465,37.6759,41.9729	benign	24/532	50141345	7547,5459	2203	4300	6503	SO:0001583	missense	55213	exon3			ACACACGCCTTCC	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.71C>T	13.37:g.50141345G>A	ENSP00000367552:p.Ala24Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_018191	Q8IY29|Q969U9	Missense_Mutation	SNP	ENST00000378302.2	37	CCDS9418.1	1284	0.5879120879120879	162	0.32926829268292684	245	0.6767955801104972	366	0.6398601398601399	511	0.6741424802110818	G	23.9	4.468169	0.84533	0.376759	0.684535	ENSG00000136144	ENST00000258646;ENST00000378302;ENST00000546015	T;T;T	0.77098	1.34;1.34;-1.07	5.84	5.84	0.93424	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.42744	1.35	0.09310	P	0.999999999232834	D	0.89917	1.0	D	0.91635	0.999	T	0.45338	-0.9268	9	0.02654	T	1	-16.71	20.1466	0.98079	0.0:0.0:1.0:0.0	rs4942848;rs17857155;rs57157356;rs4942848	24	Q8NDN9	RCBT1_HUMAN	V	24	ENSP00000258646:A24V;ENSP00000367552:A24V;ENSP00000443293:A24V	ENSP00000258646:A24V	A	-	2	0	RCBTB1	49039346	1.000000	0.71417	0.989000	0.46669	0.904000	0.53231	9.358000	0.97109	2.779000	0.95612	0.591000	0.81541	GCG	G|0.431;A|0.568	0.568	strong		0.468	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
SSTR3	6753	hgsc.bcm.edu	37	22	37603390	37603390	+	Silent	SNP	C	C	T	rs86582	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37603390C>T	ENST00000328544.3	-	2	986	c.453G>A	c.(451-453)tcG>tcA	p.S151S	SSTR3_ENST00000402501.1_Silent_p.S151S	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	151					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)	GCCAGCGGGCCGAGCGGGTGG	0.667													C|||	1956	0.390575	0.4811	0.3343	5008	,	,		16771	0.5863		0.2217	False		,,,				2504	0.2802				p.S151S		Atlas-SNP	.											.	SSTR3	42	.	0			c.G453A						PASS	.	C		1910,2496	540.1+/-375.4	400,1110,693	69.0	65.0	66.0		453	-11.3	0.2	22	dbSNP_79	66	1784,6814	318.7+/-313.8	188,1408,2703	no	coding-synonymous	SSTR3	NM_001051.2		588,2518,3396	TT,TC,CC		20.749,43.35,28.4066		151/419	37603390	3694,9310	2203	4299	6502	SO:0001819	synonymous_variant	6753	exon2			GCGGGCCGAGCGG		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.453G>A	22.37:g.37603390C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	NM_001051	A8K550|Q53ZR7	Silent	SNP	ENST00000328544.3	37	CCDS13944.1																																																																																			C|0.663;T|0.337	0.337	strong		0.667	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
KRT40	125115	hgsc.bcm.edu	37	17	39138712	39138712	+	Silent	SNP	G	G	A	rs4243257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	34	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	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	
MRTO4	51154	hgsc.bcm.edu	37	1	19584004	19584004	+	Silent	SNP	G	G	A	rs1042380	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	37	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	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	
B4GALT3	8703	hgsc.bcm.edu	37	1	161145005	161145005	+	Silent	SNP	C	C	T	rs3813620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161145005C>T	ENST00000319769.5	-	4	489	c.267G>A	c.(265-267)tcG>tcA	p.S89S	B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Silent_p.S89S	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	89					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	TAAAGGACACCGACACAGGAC	0.572													C|||	456	0.0910543	0.1044	0.0663	5008	,	,		19458	0.0675		0.0736	False		,,,				2504	0.1329				p.S89S		Atlas-SNP	.											.	B4GALT3	39	.	0			c.G267A						PASS	.	C	,,	510,3896	234.2+/-247.1	34,442,1727	46.0	45.0	45.0		267,267,267	-1.7	1.0	1	dbSNP_107	45	680,7920	169.3+/-220.7	31,618,3651	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	,,	65,1060,5378	TT,TC,CC		7.907,11.5751,9.1496	,,	89/394,89/394,89/394	161145005	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	8703	exon4			GGACACCGACACA	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.267G>A	1.37:g.161145005C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Silent	SNP	ENST00000319769.5	37	CCDS1222.1																																																																																			C|0.918;T|0.082	0.082	strong		0.572	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
CMYA5	202333	hgsc.bcm.edu	37	5	79030045	79030045	+	Silent	SNP	A	A	G	rs4639193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79030045A>G	ENST00000446378.2	+	2	5488	c.5457A>G	c.(5455-5457)gtA>gtG	p.V1819V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1819					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)		ACCTCCTTGTAGAACAAAAAA	0.378													G|||	2926	0.584265	0.885	0.4193	5008	,	,		20073	0.6468		0.3917	False		,,,				2504	0.4284				p.V1819V		Atlas-SNP	.											.	CMYA5	643	.	0			c.A5457G						PASS	.	G		2994,692		1228,538,77	69.0	67.0	68.0		5457	-1.9	0.0	5	dbSNP_111	68	3231,4959		658,1915,1522	yes	coding-synonymous	CMYA5	NM_153610.3		1886,2453,1599	GG,GA,AA		39.4505,18.7737,47.5834		1819/4070	79030045	6225,5651	1843	4095	5938	SO:0001819	synonymous_variant	202333	exon2			CCTTGTAGAACAA	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.5457A>G	5.37:g.79030045A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			A|0.395;G|0.605	0.605	strong		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
KDM4C	23081	hgsc.bcm.edu	37	9	7011719	7011719	+	Missense_Mutation	SNP	T	T	C	rs34369202		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:7011719T>C	ENST00000381309.3	+	13	2373	c.1808T>C	c.(1807-1809)aTt>aCt	p.I603T	KDM4C_ENST00000442236.2_Missense_Mutation_p.I348T|KDM4C_ENST00000381306.3_Missense_Mutation_p.I603T|KDM4C_ENST00000536108.1_Missense_Mutation_p.I422T|KDM4C_ENST00000543771.1_Missense_Mutation_p.I603T|KDM4C_ENST00000428870.2_Missense_Mutation_p.I290T|KDM4C_ENST00000535193.1_Missense_Mutation_p.I625T	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	603					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						GTTCTGTCCATTGAGGAGGAA	0.463													T|||	1	0.000199681	0.0	0.0	5008	,	,		21962	0.0		0.0	False		,,,				2504	0.001				p.I625T		Atlas-SNP	.											.	KDM4C	186	.	0			c.T1874C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	99.0	97.0	98.0		1808,1808,1874,1808	0.8	0.0	9	dbSNP_126	98	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	89,89,89,89	0,10,6493	CC,CT,TT		0.1163,0.0,0.0769	benign,benign,benign,benign	603/1048,603/814,625/836,603/1057	7011719	10,12996	2203	4300	6503	SO:0001583	missense	23081	exon13			TGTCCATTGAGGA	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.1808T>C	9.37:g.7011719T>C	ENSP00000370710:p.Ile603Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	T	1.169	-0.641475	0.03531	0.0	0.001163	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.76	0.841	0.18918	.	0.988395	0.08268	N	0.971876	T	0.40791	0.1131	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.003;0.002;0.001;0.001	T	0.27468	-1.0073	10	0.20046	T	0.44	.	5.1095	0.14802	0.1283:0.3276:0.0:0.544	rs34369202	348;603;625;603;603	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	T	625;603;603;603;348;422;290	ENSP00000442382:I625T;ENSP00000445427:I603T;ENSP00000370710:I603T;ENSP00000370707:I603T;ENSP00000409353:I348T;ENSP00000440656:I422T;ENSP00000405739:I290T	ENSP00000370707:I603T	I	+	2	0	KDM4C	7001719	0.000000	0.05858	0.027000	0.17364	0.458000	0.32498	0.834000	0.27518	-0.091000	0.12440	-0.333000	0.08304	ATT	T|0.999;C|0.001	0.001	strong		0.463	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
GEMIN6	79833	hgsc.bcm.edu	37	2	39008949	39008949	+	Missense_Mutation	SNP	G	G	A	rs1056104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:39008949G>A	ENST00000281950.3	+	3	535	c.419G>A	c.(418-420)gGt>gAt	p.G140D	GEMIN6_ENST00000409011.1_3'UTR|GEMIN6_ENST00000409566.1_3'UTR	NM_024775.9	NP_079051.9	Q8WXD5	GEMI6_HUMAN	gem (nuclear organelle) associated protein 6	140			G -> D (in dbSNP:rs1056104). {ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				kidney(1)|large_intestine(3)|pancreas(1)	5		all_hematologic(82;0.21)				CCACCATATGGTCCAGAAAAT	0.483													G|||	577	0.115216	0.003	0.1138	5008	,	,		18334	0.253		0.0765	False		,,,				2504	0.1656				p.G140D		Atlas-SNP	.											.	GEMIN6	13	.	0			c.G419A						PASS	.	G	ASP/GLY	80,4326	69.8+/-107.6	2,76,2125	89.0	91.0	90.0		419	4.0	0.0	2	dbSNP_86	90	668,7932	168.8+/-220.3	26,616,3658	yes	missense	GEMIN6	NM_024775.9	94	28,692,5783	AA,AG,GG		7.7674,1.8157,5.7512	probably-damaging	140/168	39008949	748,12258	2203	4300	6503	SO:0001583	missense	79833	exon3			CATATGGTCCAGA	AF453443	CCDS1799.1	2p22.1	2014-05-14			ENSG00000152147	ENSG00000152147			20044	protein-coding gene	gene with protein product		607006				11748230	Standard	NM_024775		Approved	FLJ23459	uc002rrc.3	Q8WXD5	OTTHUMG00000128588	ENST00000281950.3:c.419G>A	2.37:g.39008949G>A	ENSP00000281950:p.Gly140Asp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_024775	B2RDP8|Q53SI5|Q8WVB4|Q9H5G6	Missense_Mutation	SNP	ENST00000281950.3	37	CCDS1799.1	265	0.12133699633699634	1	0.0020325203252032522	39	0.10773480662983426	165	0.28846153846153844	60	0.079155672823219	G	15.96	2.985870	0.53934	0.018157	0.077674	ENSG00000152147	ENST00000281950	T	0.40756	1.02	5.78	3.95	0.45737	.	0.306608	0.40469	N	0.001096	T	0.00012	0.0000	L	0.45581	1.43	0.09310	P	0.9999999999999967	B	0.18610	0.029	B	0.23275	0.045	T	0.18903	-1.0322	9	0.40728	T	0.16	-5.9046	10.9809	0.47494	0.0712:0.1344:0.7944:0.0	rs1056104;rs3196717;rs3821134;rs17845579;rs17858478;rs52834272;rs61267155;rs1056104	140	Q8WXD5	GEMI6_HUMAN	D	140	ENSP00000281950:G140D	ENSP00000281950:G140D	G	+	2	0	GEMIN6	38862453	1.000000	0.71417	0.033000	0.17914	0.728000	0.41692	5.920000	0.70017	0.769000	0.33313	-0.229000	0.12294	GGT	G|0.901;A|0.099	0.099	strong		0.483	GEMIN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250441.3		
FASTKD1	79675	hgsc.bcm.edu	37	2	170411698	170411698	+	Missense_Mutation	SNP	C	C	G	rs12618227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170411698C>G	ENST00000453153.2	-	7	1496	c.1150G>C	c.(1150-1152)Gaa>Caa	p.E384Q	FASTKD1_ENST00000453929.2_Missense_Mutation_p.E384Q	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	384			E -> Q (in dbSNP:rs12618227).		cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.E384*(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AAAGTTAATTCTTGAGTTATC	0.299													C|||	175	0.0349441	0.0008	0.0086	5008	,	,		20027	0.1111		0.0288	False		,,,				2504	0.0276				p.E384Q		Atlas-SNP	.											FASTKD1,colon,carcinoma,0,1	FASTKD1	86	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1150C						PASS	.	C	GLN/GLU	31,4371	37.6+/-69.7	0,31,2170	73.0	78.0	76.0		1150	3.0	0.6	2	dbSNP_120	76	302,8298	108.8+/-169.4	4,294,4002	yes	missense	FASTKD1	NM_024622.3	29	4,325,6172	GG,GC,CC		3.5116,0.7042,2.5611	benign	384/848	170411698	333,12669	2201	4300	6501	SO:0001583	missense	79675	exon7			TTAATTCTTGAGT	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1150G>C	2.37:g.170411698C>G	ENSP00000400513:p.Glu384Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	85	0.03891941391941392	1	0.0020325203252032522	5	0.013812154696132596	58	0.10139860139860139	21	0.027704485488126648	C	9.994	1.231609	0.22626	0.007042	0.035116	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.17370	2.28;2.28	4.84	3.04	0.35103	.	0.408805	0.27946	N	0.017214	T	0.00241	0.0007	N	0.08118	0	0.80722	P	0.0	B;B	0.24132	0.098;0.059	B;B	0.28305	0.088;0.04	T	0.19095	-1.0316	9	0.42905	T	0.14	-9.8948	4.3534	0.11167	0.1921:0.6197:0.0:0.1882	rs12618227	384;384	Q53R41-2;Q53R41	.;FAKD1_HUMAN	Q	384	ENSP00000400513:E384Q;ENSP00000403229:E384Q	ENSP00000400513:E384Q	E	-	1	0	FASTKD1	170119944	0.321000	0.24625	0.556000	0.28293	0.504000	0.33889	0.243000	0.18106	0.629000	0.30376	0.650000	0.86243	GAA	C|0.969;G|0.031	0.031	strong		0.299	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
Unknown	0	hgsc.bcm.edu	37	1	16133987	16133987	+	IGR	SNP	T	T	C	rs7417535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16133987T>C								FBLIM1 (20898 upstream) : RP11-169K16.9 (26572 downstream)																							ATGCTCATCATAGAGCTCTAG	0.502													C|||	733	0.146366	0.3646	0.0965	5008	,	,		16739	0.0099		0.0994	False		,,,				2504	0.0757				p.Y53C		Atlas-SNP	.											.	.	.	.	0			c.A158G						PASS	.	C	CYS/TYR	1490,2916	675.8+/-403.1	268,954,981	113.0	123.0	120.0		158	1.9	0.0	1	dbSNP_116	120	1031,7569	772.0+/-407.7	63,905,3332	no	missense	UQCRHL	NM_001089591.1	194	331,1859,4313	CC,CT,TT		11.9884,33.8175,19.3834	probably-damaging	53/92	16133987	2521,10485	2203	4300	6503	SO:0001628	intergenic_variant	0	exon1			TCATCATAGAGCT																													1.37:g.16133987T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_001089591		Missense_Mutation	SNP		37																																																																																				T|0.874;C|0.126	0.126	strong	0	0.502								
RP1	6101	hgsc.bcm.edu	37	8	55533805	55533805	+	Silent	SNP	G	G	T	rs144293929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55533805G>T	ENST00000220676.1	+	2	427	c.279G>T	c.(277-279)acG>acT	p.T93T		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	93	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ACAGCATCACGCGCCTGGAGG	0.617													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		13894	0.0		0.001	False		,,,				2504	0.0041				p.T93T	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G279T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	83.0	71.0	75.0		279	-6.7	0.1	8	dbSNP_134	75	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous	RP1	NM_006269.1		0,23,6480	TT,TG,GG		0.2442,0.0454,0.1768		93/2157	55533805	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon2			CATCACGCGCCTG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.279G>T	8.37:g.55533805G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	27	0.627907	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			G|0.998;T|0.002	0.002	strong		0.617	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
GOLGA3	2802	hgsc.bcm.edu	37	12	133393323	133393323	+	Missense_Mutation	SNP	C	C	T	rs2291256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133393323C>T	ENST00000450791.2	-	2	392	c.209G>A	c.(208-210)gGg>gAg	p.G70E	GOLGA3_ENST00000456883.2_Missense_Mutation_p.G70E|GOLGA3_ENST00000537452.1_Missense_Mutation_p.G70E|GOLGA3_ENST00000204726.3_Missense_Mutation_p.G70E|GOLGA3_ENST00000545875.1_Missense_Mutation_p.G70E			Q08378	GOGA3_HUMAN	golgin A3	70	Pro-rich.		G -> E (in dbSNP:rs2291256).		intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TGGCGTTGGCCCGTTCTGACA	0.627													C|||	291	0.058107	0.0	0.0634	5008	,	,		17764	0.129		0.0696	False		,,,				2504	0.0481				p.G70E		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G209A						PASS	.	C	GLU/GLY,GLU/GLY	64,4342	62.3+/-99.4	0,64,2139	91.0	91.0	91.0		209,209	5.0	0.9	12	dbSNP_100	91	737,7863	178.3+/-227.7	35,667,3598	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	98,98	35,731,5737	TT,TC,CC		8.5698,1.4526,6.1587	probably-damaging,probably-damaging	70/1135,70/1499	133393323	801,12205	2203	4300	6503	SO:0001583	missense	2802	exon3			GTTGGCCCGTTCT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.209G>A	12.37:g.133393323C>T	ENSP00000410378:p.Gly70Glu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	153	0.07005494505494506	0	0.0	19	0.052486187845303865	77	0.1346153846153846	57	0.07519788918205805	C	19.99	3.928431	0.73327	0.014526	0.085698	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.62232	0.57;0.57;0.55;0.04;0.04	5.91	5.02	0.67125	.	0.048742	0.85682	N	0.000000	T	0.01387	0.0045	M	0.66939	2.045	0.09310	P	1.0	P;B;B	0.38078	0.617;0.36;0.36	B;B;B	0.42959	0.403;0.181;0.181	T	0.43278	-0.9401	9	0.87932	D	0	.	14.9478	0.71047	0.0:0.9316:0.0:0.0684	rs2291256;rs52803888;rs56627172;rs60184311;rs2291256	70;70;70	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	E	70	ENSP00000204726:G70E;ENSP00000410378:G70E;ENSP00000409303:G70E;ENSP00000442143:G70E;ENSP00000442603:G70E	ENSP00000204726:G70E	G	-	2	0	GOLGA3	131903396	1.000000	0.71417	0.950000	0.38849	0.253000	0.25986	2.565000	0.45939	1.498000	0.48600	0.462000	0.41574	GGG	C|0.932;T|0.068	0.068	strong		0.627	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
MUC2	4583	hgsc.bcm.edu	37	11	1092953	1092953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1092953C>T	ENST00000441003.2	+	30	4799	c.4772C>T	c.(4771-4773)aCg>aTg	p.T1591M	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Splice_Site_p.T1592M|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1592M(1)|p.T1591M(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)	accaccactacggtgacccca	0.627																																					p.T1591M		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,-1,4	MUC2	614	4	2	Substitution - Missense(2)	endometrium(2)	c.C4772T						scavenged	.						54.0	86.0	74.0					11																	1092953		1812	3313	5125	SO:0001583	missense	4583	exon30			CCACTACGGTGAC	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.4772C>T	11.37:g.1092953C>T	ENSP00000415183:p.Thr1591Met	Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	39	5	0.128205	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.179	-0.168424	0.06461	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.16743	2.32;2.56	1.75	-0.619	0.11572	.	6.725620	0.00827	U	0.001636	T	0.08846	0.0219	.	.	.	0.09310	N	1	D	0.60575	0.988	B	0.34489	0.184	T	0.24548	-1.0157	9	0.32370	T	0.25	.	3.3423	0.07123	0.2481:0.5888:0.0:0.163	.	1591	E7EUV1	.	M	1591;1592	ENSP00000415183:T1591M;ENSP00000351956:T1592M	ENSP00000351956:T1592M	T	+	2	0	MUC2	1082953	0.064000	0.20934	0.000000	0.03702	0.189000	0.23516	1.615000	0.36922	-0.313000	0.08728	0.121000	0.15741	ACG	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OCA2	4948	hgsc.bcm.edu	37	15	28117060	28117060	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28117060T>A	ENST00000354638.3	-	20	2243	c.2088A>T	c.(2086-2088)gcA>gcT	p.A696A	OCA2_ENST00000353809.5_Silent_p.A672A	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	696					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		AGTGGAGATGTGCCAATGCCT	0.338									Oculocutaneous Albinism																												p.A696A		Atlas-SNP	.											.	OCA2	173	.	0			c.A2088T						PASS	.						112.0	116.0	115.0					15																	28117060		2203	4300	6503	SO:0001819	synonymous_variant	4948	exon20	Familial Cancer Database		GAGATGTGCCAAT		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2088A>T	15.37:g.28117060T>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	36	6	0.166667	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			.	.	none		0.338	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T|TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7.0	9.0	9.0		1366	-6.4	0.0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
MAST2	23139	hgsc.bcm.edu	37	1	46493460	46493460	+	Missense_Mutation	SNP	T	T	G	rs1707336	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	133	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	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	
CCDC6	8030	hgsc.bcm.edu	37	10	61665886	61665886	+	Silent	SNP	C	C	A	rs1171830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61665886C>A	ENST00000263102.6	-	1	528	c.297G>T	c.(295-297)gtG>gtT	p.V99V		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	99						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		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)		TCACGATGGTCACGCTGGCTT	0.657			T	RET	NSCLC								C|||	1880	0.375399	0.0393	0.4726	5008	,	,		12230	0.627		0.4523	False		,,,				2504	0.4223				p.V99V		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.G297T						PASS	.	C		501,3905	230.4+/-244.6	46,409,1748	58.0	55.0	56.0		297	2.5	1.0	10	dbSNP_87	56	4054,4546	556.5+/-386.9	955,2144,1201	no	coding-synonymous	CCDC6	NM_005436.4		1001,2553,2949	AA,AC,CC		47.1395,11.3709,35.0223		99/475	61665886	4555,8451	2203	4300	6503	SO:0001819	synonymous_variant	8030	exon1			GATGGTCACGCTG	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.297G>T	10.37:g.61665886C>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_005436	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																			C|0.638;A|0.362	0.362	strong		0.657	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
FMN1	342184	hgsc.bcm.edu	37	15	33359370	33359370	+	Intron	SNP	C	C	T	rs11072170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:33359370C>T	ENST00000559047.1	-	3	2043				FMN1_ENST00000561249.1_Intron|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.G239E|FMN1_ENST00000334528.9_Missense_Mutation_p.G239E			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	72	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	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	
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276626G>C	ENST00000368799.1	-	3	10771	c.10736C>G	c.(10735-10737)aCg>aGg	p.T3579R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3579	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)			GTGATGGGACGTGGGGTGTCT	0.567									Ichthyosis				C|||	2393	0.477835	0.6074	0.4395	5008	,	,		15943	0.6498		0.1561	False		,,,				2504	0.4836				p.T3579R		Atlas-SNP	.											FLG,colon,carcinoma,-1,1	FLG	900	1	0			c.C10736G						scavenged	.	C	ARG/THR	1117,3267		429,259,1504	128.0	213.0	184.0		10736	-2.5	0.0	1	dbSNP_103	184	149,8435		32,85,4175	no	missense	FLG	NM_002016.1	71	461,344,5679	CC,CG,GG		1.7358,25.479,9.7625	benign	3579/4062	152276626	1266,11702	2192	4292	6484	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGTGGGGT	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.10736C>G	1.37:g.152276626G>C	ENSP00000357789:p.Thr3579Arg	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	169	44	0.260355	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	619	0.2834249084249084	182	0.3699186991869919	94	0.2596685082872928	272	0.4755244755244755	71	0.09366754617414248	C	1.750	-0.489390	0.04352	0.25479	0.017358	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.29	-2.52	0.06346	.	.	.	.	.	T	0.00178	0.0005	N	0.00538	-1.39	0.09310	N	1	B	0.14438	0.01	B	0.01281	0.0	T	0.26189	-1.0110	9	0.12430	T	0.62	.	4.0484	0.09783	0.0:0.2359:0.3609:0.4032	rs3126075;rs12072880;rs60733655	3579	P20930	FILA_HUMAN	R	3579	ENSP00000357789:T3579R	ENSP00000357789:T3579R	T	-	2	0	FLG	150543250	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.448000	0.00121	-0.991000	0.03476	-0.521000	0.04368	ACG	G|0.716;C|0.284	0.284	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4945196T>G	ENST00000321961.2	-	1	441	c.374A>C	c.(373-375)tAc>tCc	p.Y125S	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	125			Y -> S (in dbSNP:rs1378739). {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)|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)		GACGGCCACGTAGCGGTCAAT	0.507													T|||	3292	0.657348	0.7231	0.6484	5008	,	,		22751	0.7222		0.5686	False		,,,				2504	0.5992				p.Y125S		Atlas-SNP	.											.	OR51G1	74	.	0			c.A374C						PASS	.	T	SER/TYR	3078,1324	695.5+/-405.9	1059,960,182	110.0	98.0	102.0		374	3.0	1.0	11	dbSNP_88	102	4985,3611	625.5+/-397.7	1451,2083,764	yes	missense	OR51G1	NM_001005237.1	144	2510,3043,946	GG,GT,TT		42.0079,30.0772,37.9674	probably-damaging	125/322	4945196	8063,4935	2201	4298	6499	SO:0001583	missense	79324	exon1			GCCACGTAGCGGT	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.374A>C	11.37:g.4945196T>G	ENSP00000322546:p.Tyr125Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	1442	0.6602564102564102	372	0.7560975609756098	244	0.6740331491712708	410	0.7167832167832168	416	0.5488126649076517	T	9.340	1.062863	0.19987	0.699228	0.579921	ENSG00000176879	ENST00000321961	T	0.57436	0.4	4.2	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	0.227317	0.22524	U	0.058922	T	0.00012	0.0000	M	0.86953	2.85	0.30227	P	0.796256	P	0.41748	0.761	B	0.37346	0.247	T	0.38542	-0.9656	9	0.87932	D	0	.	9.0162	0.36170	0.1644:0.0:0.0:0.8356	rs1378739;rs17337943	125	Q8NGK1	O51G1_HUMAN	S	125	ENSP00000322546:Y125S	ENSP00000322546:Y125S	Y	-	2	0	OR51G1	4901772	0.085000	0.21516	0.996000	0.52242	0.061000	0.15899	0.375000	0.20518	1.760000	0.52011	0.455000	0.32223	TAC	T|0.355;G|0.645	0.645	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115004914C>T	ENST00000356221.3	+	5	438	c.330C>T	c.(328-330)gaC>gaT	p.D110D	CDC16_ENST00000360383.3_Silent_p.D110D|CDC16_ENST00000375312.3_Silent_p.D16D|CDC16_ENST00000375308.1_Silent_p.D16D|CDC16_ENST00000375310.1_Silent_p.D16D|CDC16_ENST00000252457.5_Silent_p.D109D|CDC16_ENST00000252458.6_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	45	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	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	
H6PD	9563	hgsc.bcm.edu	37	1	9307138	9307138	+	Silent	SNP	T	T	C	rs11121350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	106	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	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	
KIAA1217	56243	hgsc.bcm.edu	37	10	24833137	24833137	+	Silent	SNP	C	C	T	rs2250411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24833137C>T	ENST00000376454.3	+	19	4968	c.4938C>T	c.(4936-4938)atC>atT	p.I1646I	KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Silent_p.I1329I|KIAA1217_ENST00000458595.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1646					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AGCCCAGCATCGAGAGTACAT	0.458													C|||	1308	0.261182	0.2542	0.3141	5008	,	,		20086	0.1419		0.3956	False		,,,				2504	0.2178				p.I1646I		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C4938T						PASS	.	C	,,	1213,3193	421.3+/-339.3	165,883,1155	99.0	97.0	98.0		,,4938	-10.9	0.0	10	dbSNP_100	98	3300,5300	492.9+/-373.4	633,2034,1633	no	intron,intron,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	798,2917,2788	TT,TC,CC		38.3721,27.5306,34.6994	,,	,,1646/1944	24833137	4513,8493	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			CAGCATCGAGAGT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4938C>T	10.37:g.24833137C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			C|0.698;T|0.302	0.302	strong		0.458	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
FUT7	2529	hgsc.bcm.edu	37	9	139925927	139925927	+	Silent	SNP	G	G	C	rs1139444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139925927G>C	ENST00000314412.6	-	2	1282	c.264C>G	c.(262-264)gcC>gcG	p.A88A	C9orf139_ENST00000314330.2_Intron	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	88					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CCACGGCGTCGGCGCTGGCCA	0.731													g|||	418	0.0834665	0.1437	0.0922	5008	,	,		13090	0.0317		0.0994	False		,,,				2504	0.0327				p.A88A		Atlas-SNP	.											.	FUT7	24	.	0			c.C264G						PASS	.		,	615,3547		51,513,1517	21.0	19.0	20.0		264,	-9.7	0.0	9	dbSNP_86	20	643,7531		18,607,3462	no	coding-synonymous,intron	FUT7,C9orf139	NM_004479.3,NM_207511.1	,	69,1120,4979	CC,CG,GG		7.8664,14.7765,10.1978	,	88/343,	139925927	1258,11078	2081	4087	6168	SO:0001819	synonymous_variant	2529	exon2			GGCGTCGGCGCTG	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"""Fucosyltransferases"""	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.264C>G	9.37:g.139925927G>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_004479	B2R7U7|Q6DK54	Silent	SNP	ENST00000314412.6	37	CCDS7022.1																																																																																			G|0.916;C|0.084	0.084	strong		0.731	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479	
NCOA3	8202	hgsc.bcm.edu	37	20	46264888	46264888	+	Missense_Mutation	SNP	G	G	C	rs2230782	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:46264888G>C	ENST00000371998.3	+	12	1949	c.1758G>C	c.(1756-1758)caG>caC	p.Q586H	NCOA3_ENST00000341724.6_Missense_Mutation_p.Q596H|NCOA3_ENST00000371997.3_Missense_Mutation_p.Q596H|NCOA3_ENST00000372004.3_Missense_Mutation_p.Q586H			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	586	Ser-rich.		Q -> H (in dbSNP:rs2230782). {ECO:0000269|Ref.5}.		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)			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						CAATGTGTCAGTCAAATAGCA	0.423													G|||	198	0.0395367	0.003	0.0634	5008	,	,		19974	0.0218		0.1153	False		,,,				2504	0.0123				p.Q596H		Atlas-SNP	.											.	NCOA3	156	.	0			c.G1788C	GRCh37	CM051113	NCOA3	M	rs2230782	PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	98,4308	78.3+/-116.7	0,98,2105	65.0	63.0	64.0		1758,1788,1758,1758	2.4	1.0	20	dbSNP_98	64	812,7788	188.3+/-235.3	31,750,3519	yes	missense,missense,missense,missense	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	24,24,24,24	31,848,5624	CC,CG,GG		9.4419,2.2242,6.9968	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	586/1424,596/1416,586/1421,586/1425	46264888	910,12096	2203	4300	6503	SO:0001583	missense	8202	exon12			GTGTCAGTCAAAT	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.1758G>C	20.37:g.46264888G>C	ENSP00000361066:p.Gln586His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	126	0.057692307692307696	1	0.0020325203252032522	27	0.07458563535911603	14	0.024475524475524476	84	0.11081794195250659	G	14.27	2.484933	0.44147	0.022242	0.094419	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.49	2.41	0.29592	.	0.359607	0.26546	N	0.023774	T	0.00440	0.0014	L	0.37750	1.13	0.27719	P	0.9451862	B;D;P;P;D;P	0.54397	0.249;0.963;0.939;0.939;0.966;0.881	B;P;P;P;P;P	0.61003	0.064;0.807;0.707;0.615;0.882;0.615	T	0.08289	-1.0729	9	0.24483	T	0.36	-1.1094	10.7536	0.46223	0.3206:0.0:0.6794:0.0	rs2230782;rs17726736;rs52816651;rs2230782	586;596;590;586;586;586	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	H	586;596;586;586;596	ENSP00000342123:Q596H;ENSP00000361073:Q586H;ENSP00000361066:Q586H;ENSP00000361065:Q596H	ENSP00000345671:Q586H	Q	+	3	2	NCOA3	45698295	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.398000	0.20899	0.659000	0.30945	0.655000	0.94253	CAG	G|0.934;C|0.066	0.066	strong		0.423	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
ANKMY2	57037	hgsc.bcm.edu	37	7	16666759	16666759	+	Silent	SNP	G	G	C	rs11531477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:16666759G>C	ENST00000306999.2	-	3	420	c.177C>G	c.(175-177)ctC>ctG	p.L59L	ANKMY2_ENST00000421746.1_5'UTR	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	59						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TGCACATATCGAGTTTTCCTT	0.368													G|||	701	0.139976	0.093	0.2075	5008	,	,		16035	0.1438		0.2187	False		,,,				2504	0.0706				p.L59L		Atlas-SNP	.											.	ANKMY2	46	.	0			c.C177G						PASS	.	G		418,3988	204.1+/-226.4	16,386,1801	96.0	83.0	87.0		177	-11.5	0.6	7	dbSNP_120	87	1835,6765	327.5+/-317.9	198,1439,2663	no	coding-synonymous	ANKMY2	NM_020319.2		214,1825,4464	CC,CG,GG		21.3372,9.4871,17.3228		59/442	16666759	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	57037	exon3			CATATCGAGTTTT	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.177C>G	7.37:g.16666759G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																			G|0.823;C|0.177	0.177	strong		0.368	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
PROKR1	10887	hgsc.bcm.edu	37	2	68873071	68873071	+	Missense_Mutation	SNP	A	A	G	rs7570797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68873071A>G	ENST00000303786.3	+	2	538	c.118A>G	c.(118-120)Agc>Ggc	p.S40G	PROKR1_ENST00000394342.2_Missense_Mutation_p.S40G			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	40			S -> G (in dbSNP:rs7570797).		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						CTTCAGCTACAGCGACTATGA	0.498													G|||	791	0.157947	0.4697	0.0476	5008	,	,		24402	0.0417		0.0497	False		,,,				2504	0.046				p.S40G		Atlas-SNP	.											.	PROKR1	69	.	0			c.A118G						PASS	.	G	GLY/SER	1741,2665	646.9+/-398.4	373,995,835	252.0	224.0	234.0		118	3.2	0.0	2	dbSNP_116	234	446,8154	799.5+/-407.4	13,420,3867	yes	missense	PROKR1	NM_138964.2	56	386,1415,4702	GG,GA,AA		5.186,39.5143,16.8153	benign	40/394	68873071	2187,10819	2203	4300	6503	SO:0001583	missense	10887	exon1			AGCTACAGCGACT	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.118A>G	2.37:g.68873071A>G	ENSP00000303775:p.Ser40Gly	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	229	115	0.502183	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	291	0.13324175824175824	216	0.43902439024390244	16	0.04419889502762431	24	0.04195804195804196	35	0.04617414248021108	G	0.003	-2.508885	0.00153	0.395143	0.05186	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.72615	-0.67;-0.67	5.03	3.21	0.36854	.	0.300619	0.42420	N	0.000712	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	0.42085	-0.9472	9	0.14252	T	0.57	.	4.6472	0.12577	0.18:0.0:0.6467:0.1733	rs7570797;rs52822714;rs59745452;rs7570797	40	Q8TCW9	PKR1_HUMAN	G	40	ENSP00000303775:S40G;ENSP00000377874:S40G	ENSP00000303775:S40G	S	+	1	0	PROKR1	68726575	0.970000	0.33590	0.022000	0.16811	0.000000	0.00434	1.623000	0.37008	0.399000	0.25367	-0.847000	0.03039	AGC	A|0.839;G|0.161	0.161	strong		0.498	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
SCAPER	49855	hgsc.bcm.edu	37	15	77176158	77176158	+	Start_Codon_SNP	SNP	T	T	C	rs3812908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:77176158T>C	ENST00000563290.1	-	2	96	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	SCAPER_ENST00000324767.7_Start_Codon_SNP_p.M1V			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1				M -> V (in Ref. 1; AAK29205). {ECO:0000305}.		endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						CTTACCATCATTCTTTAAATT	0.284													T|||	2092	0.417732	0.3434	0.3256	5008	,	,		17908	0.5774		0.3101	False		,,,				2504	0.5297				p.M1V		Atlas-SNP	.											.	SCAPER	160	.	0			c.A1G						PASS	.	T	VAL/MET	1148,2456		188,772,842	102.0	106.0	105.0		1	3.9	1.0	15	dbSNP_107	105	2329,5803		333,1663,2070	yes	missense	SCAPER	NM_020843.2	21	521,2435,2912	CC,CT,TT		28.6399,31.8535,29.6268	benign	1/1401	77176158	3477,8259	1802	4066	5868	SO:0001582	initiator_codon_variant	49855	exon1			CCATCATTCTTTA	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1A>G	15.37:g.77176158T>C	ENSP00000454973:p.Met1Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	808|808	0.36996336996337|0.36996336996337	145|145	0.29471544715447157|0.29471544715447157	125|125	0.3453038674033149|0.3453038674033149	311|311	0.5437062937062938|0.5437062937062938	227|227	0.2994722955145119|0.2994722955145119	T|T	9.550|9.550	1.115590|1.115590	0.20795|0.20795	0.318535|0.318535	0.286399|0.286399	ENSG00000140386|ENSG00000140386	ENST00000324767|ENST00000303521	T|.	0.21031|.	2.03|.	3.87|3.87	3.87|3.87	0.44632|0.44632	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.36073|0.36073	P|P	0.157763|0.157763	P|.	0.43578|.	0.811|.	P|.	0.57846|.	0.828|.	T|T	0.52109|0.52109	-0.8619|-0.8619	7|4	0.40728|0.46703	T|T	0.16|0.11	.|.	9.3739|9.3739	0.38270|0.38270	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs3812908;rs60428850;rs3812908|rs3812908;rs60428850;rs3812908	1|.	Q6NSF1|.	.|.	V|S	1|55	ENSP00000326924:M1V|.	ENSP00000326924:M1V|ENSP00000303560:N55S	M|N	-|-	1|2	0|0	SCAPER|SCAPER	74963213|74963213	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.971000|0.971000	0.66376|0.66376	2.645000|2.645000	0.46621|0.46621	1.990000|1.990000	0.58119|0.58119	0.528000|0.528000	0.53228|0.53228	ATG|AAT	T|0.628;C|0.372	0.372	strong		0.284	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	Missense_Mutation
HELZ2	85441	hgsc.bcm.edu	37	20	62200576	62200576	+	Missense_Mutation	SNP	G	G	A	rs6090457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62200576G>A	ENST00000467148.1	-	4	1082	c.1013C>T	c.(1012-1014)tCa>tTa	p.S338L	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_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	26	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	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	
TXNDC5	81567	hgsc.bcm.edu	37	6	7910865	7910865	+	Missense_Mutation	SNP	G	G	A	rs183777097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7910865G>A	ENST00000379757.4	-	1	182	c.145C>T	c.(145-147)Ccc>Tcc	p.P49S	TXNDC5_ENST00000473453.1_5'Flank|TXNDC5_ENST00000539054.1_Intron|BLOC1S5-TXNDC5_ENST00000439343.2_Intron	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	49	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					GCCGCGGGGGGCCCGTccgcc	0.771													g|||	70	0.0139776	0.0023	0.0187	5008	,	,		3218	0.001		0.0408	False		,,,				2504	0.0123				p.P49S	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C145T						PASS	.		SER/PRO	31,3679		1,29,1825	11.0	11.0	11.0		145	-5.6	0.0	6		11	258,6904		3,252,3326	no	missense	TXNDC5	NM_030810.3	74	4,281,5151	AA,AG,GG		3.6023,0.8356,2.6582	benign	49/433	7910865	289,10583	1855	3581	5436	SO:0001583	missense	81567	exon1			CGGGGGGCCCGTC	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"""Protein disulfide isomerases"""	21073	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 15"""		"""thioredoxin domain containing 5"""				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.145C>T	6.37:g.7910865G>A	ENSP00000369081:p.Pro49Ser	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	37	CCDS4505.1	73	0.033424908424908424	19	0.03861788617886179	8	0.022099447513812154	2	0.0034965034965034965	44	0.05804749340369393	.	0.221	-1.028982	0.02045	0.008356	0.036023	ENSG00000239264	ENST00000379757	T	0.03441	3.93	2.8	-5.61	0.02489	Thioredoxin-like fold (1);	0.991997	0.08180	N	0.985621	T	0.00468	0.0015	N	0.11201	0.11	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.45527	-0.9255	10	0.22109	T	0.4	.	5.4918	0.16781	0.3092:0.4165:0.2743:0.0	.	49	Q8NBS9	TXND5_HUMAN	S	49	ENSP00000369081:P49S	ENSP00000369081:P49S	P	-	1	0	TXNDC5	7855864	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.769000	0.04710	-3.133000	0.00235	-1.338000	0.01255	CCC	G|0.966;A|0.034	0.034	strong		0.771	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810	
OR52B6	340980	hgsc.bcm.edu	37	11	5602605	5602605	+	Missense_Mutation	SNP	G	G	A	rs2341433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602605G>A	ENST00000345043.2	+	1	499	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	167			A -> T (in dbSNP:rs2341433).			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)		CGTCACTGCCGCCCTGAGCCA	0.507													G|||	2831	0.565296	0.6142	0.562	5008	,	,		24980	0.7659		0.331	False		,,,				2504	0.5358				p.A167T		Atlas-SNP	.											.	OR52B6	37	.	0			c.G499A						PASS	.	G	THR/ALA	2408,1994	582.3+/-385.5	657,1094,450	191.0	200.0	196.0		499	1.6	0.0	11	dbSNP_100	196	2694,5898	421.6+/-353.8	427,1840,2029	yes	missense	OR52B6	NM_001005162.2	58	1084,2934,2479	AA,AG,GG		31.3547,45.2976,39.2643	benign	167/336	5602605	5102,7892	2201	4296	6497	SO:0001583	missense	340980	exon1			ACTGCCGCCCTGA	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.499G>A	11.37:g.5602605G>A	ENSP00000341581:p.Ala167Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	73	0.960526	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	1182	0.5412087912087912	298	0.6056910569105691	191	0.5276243093922652	436	0.7622377622377622	257	0.3390501319261214	G	3.422	-0.117846	0.06838	0.547024	0.313547	ENSG00000187747	ENST00000345043	T	0.37584	1.19	5.15	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	0.372331	0.19199	N	0.120223	T	0.00012	0.0000	N	0.25789	0.76	0.80722	P	0.0	B	0.15473	0.013	B	0.18561	0.022	T	0.34179	-0.9839	9	0.09338	T	0.73	.	8.4941	0.33117	0.679:0.0:0.321:0.0	rs2341433;rs16933207;rs60635257;rs2341433	167	Q8NGF0	O52B6_HUMAN	T	167	ENSP00000341581:A167T	ENSP00000341581:A167T	A	+	1	0	OR52B6	5559181	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.549000	0.06041	0.101000	0.17610	-1.656000	0.00753	GCC	G|0.494;A|0.506	0.506	strong		0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
ZNF93	81931	hgsc.bcm.edu	37	19	20044041	20044041	+	Missense_Mutation	SNP	G	G	T	rs12151060	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:20044041G>T	ENST00000343769.5	+	4	305	c.277G>T	c.(277-279)Gat>Tat	p.D93Y	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	93			D -> Y (in dbSNP:rs12151060). {ECO:0000269|PubMed:14702039}.		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)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GAACATAAAAGATTCTTTCCA	0.328													g|||	940	0.1877	0.0809	0.17	5008	,	,		18208	0.4415		0.1531	False		,,,				2504	0.1186				p.D93Y		Atlas-SNP	.											.	ZNF93	81	.	0			c.G277T						PASS	.	G	TYR/ASP	457,3947	202.8+/-225.5	28,401,1773	56.0	59.0	58.0		277	0.9	0.3	19	dbSNP_120	58	1452,7148	271.6+/-289.6	119,1214,2967	no	missense	ZNF93	NM_031218.3	160	147,1615,4740	TT,TG,GG		16.8837,10.3769,14.6801	benign	93/621	20044041	1909,11095	2202	4300	6502	SO:0001583	missense	81931	exon4			ATAAAAGATTCTT	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.277G>T	19.37:g.20044041G>T	ENSP00000342002:p.Asp93Tyr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	489	0.2239010989010989	42	0.08536585365853659	50	0.13812154696132597	269	0.47027972027972026	128	0.16886543535620052	g	13.15	2.150834	0.37923	0.103769	0.168837	ENSG00000184635	ENST00000343769;ENST00000427325;ENST00000430434	T	0.05513	3.43	0.85	0.85	0.18980	.	.	.	.	.	T	0.00012	0.0000	M	0.84326	2.69	0.44268	P	0.0028719999999999857	P	0.37573	0.6	B	0.36922	0.236	T	0.40553	-0.9557	8	0.62326	D	0.03	.	4.7959	0.13272	0.0:0.0:1.0:0.0	rs12151060;rs52830493;rs12151060	93	P35789	ZNF93_HUMAN	Y	93;93;24	ENSP00000342002:D93Y	ENSP00000342002:D93Y	D	+	1	0	ZNF93	19905041	0.000000	0.05858	0.257000	0.24404	0.256000	0.26092	-2.231000	0.01206	0.192000	0.20272	0.195000	0.17529	GAT	G|0.821;T|0.179	0.179	strong		0.328	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
TDGF1	6997	hgsc.bcm.edu	37	3	46620614	46620614	+	Missense_Mutation	SNP	T	T	C	rs11130097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46620614T>C	ENST00000296145.5	+	2	798	c.65T>C	c.(64-66)gTc>gCc	p.V22A	TDGF1_ENST00000542931.1_Missense_Mutation_p.V6A|LRRC2_ENST00000296144.3_Intron	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	169	0	0		WXS	Illumina HiSeq	Phase_I	197	196	0.994924	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	
ZNF777	27153	hgsc.bcm.edu	37	7	149153057	149153057	+	Silent	SNP	G	G	C	rs73166027	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:149153057G>C	ENST00000247930.4	-	2	380	c.57C>G	c.(55-57)acC>acG	p.T19T		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	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)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CCTGACGTAAGGTTTCTTCTT	0.522													G|||	101	0.0201677	0.003	0.013	5008	,	,		16684	0.0		0.0417	False		,,,				2504	0.047				p.T19T		Atlas-SNP	.											.	ZNF777	63	.	0			c.C57G						PASS	.	G		36,3818		0,36,1891	62.0	66.0	65.0		57	-0.4	0.0	7	dbSNP_130	65	438,7810		12,414,3698	no	coding-synonymous	ZNF777	NM_015694.2		12,450,5589	CC,CG,GG		5.3104,0.9341,3.9167		19/832	149153057	474,11628	1927	4124	6051	SO:0001819	synonymous_variant	27153	exon2			ACGTAAGGTTTCT	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.57C>G	7.37:g.149153057G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_015694	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	37	CCDS43675.1																																																																																			G|0.961;C|0.039	0.039	strong		0.522	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554562	140554562	+	Missense_Mutation	SNP	A	A	T	rs2910314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	127	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	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	
ZBTB40	9923	hgsc.bcm.edu	37	1	22835677	22835677	+	Missense_Mutation	SNP	A	A	G	rs209729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22835677A>G	ENST00000375647.4	+	9	1991	c.1784A>G	c.(1783-1785)tAc>tGc	p.Y595C	ZBTB40_ENST00000374651.4_Missense_Mutation_p.Y483C|ZBTB40_ENST00000404138.1_Missense_Mutation_p.Y595C	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	595			Y -> C (in dbSNP:rs209729). {ECO:0000269|PubMed:9455484}.		bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|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(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		AAGATTGAGTACAAGCTCTTT	0.473													G|||	4119	0.822484	0.9395	0.8429	5008	,	,		17714	0.8929		0.7167	False		,,,				2504	0.6861				p.Y595C		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A1784G						PASS	.	G	CYS/TYR,CYS/TYR	3983,423	204.8+/-226.9	1808,367,28	134.0	134.0	134.0		1784,1784	0.9	0.0	1	dbSNP_79	134	6185,2415	401.6+/-347.2	2231,1723,346	yes	missense,missense	ZBTB40	NM_001083621.1,NM_014870.3	194,194	4039,2090,374	GG,GA,AA		28.0814,9.6005,21.8207	benign,benign	595/1240,595/1240	22835677	10168,2838	2203	4300	6503	SO:0001583	missense	9923	exon10			TTGAGTACAAGCT	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.1784A>G	1.37:g.22835677A>G	ENSP00000364798:p.Tyr595Cys	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	1831	0.8383699633699634	460	0.9349593495934959	298	0.8232044198895028	520	0.9090909090909091	553	0.7295514511873351	G	9.371	1.070475	0.20147	0.903995	0.719186	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.40476	1.03;1.03;1.03	5.95	0.925	0.19424	.	0.817059	0.10496	N	0.667812	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	0.13656	-1.0501	9	0.33141	T	0.24	0.3201	2.8661	0.05602	0.2256:0.0705:0.3909:0.313	rs209729;rs535560;rs17277764;rs52789802;rs61611872;rs209729	483;595	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	C	595;595;483	ENSP00000384527:Y595C;ENSP00000364798:Y595C;ENSP00000363782:Y483C	ENSP00000363782:Y483C	Y	+	2	0	ZBTB40	22708264	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.223000	0.17719	-0.333000	0.08476	-1.068000	0.02270	TAC	G|0.812;N|0.000	0.812	strong		0.473	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
COL18A1	80781	hgsc.bcm.edu	37	21	46911188	46911188	+	Missense_Mutation	SNP	C	C	G	rs79980197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46911188C>G	ENST00000359759.4	+	21	3383	c.3362C>G	c.(3361-3363)cCc>cGc	p.P1121R	COL18A1_ENST00000400337.2_Missense_Mutation_p.P706R|COL18A1_ENST00000355480.5_Missense_Mutation_p.P886R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1121	Triple-helical region 4 (COL4).		P -> R (in dbSNP:rs79980197). {ECO:0000269|PubMed:14695535, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:8188291}.		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)		CCTGGCCCCCCCGGACCCCCG	0.682													C|||	345	0.0688898	0.0227	0.0303	5008	,	,		10479	0.0873		0.0895	False		,,,				2504	0.1186				p.P886R		Atlas-SNP	.											.	COL18A1	129	.	0			c.C2657G						PASS	.	C	ARG/PRO,ARG/PRO	125,3713		2,121,1796	19.0	25.0	23.0		2657,2117	3.8	0.9	21	dbSNP_131	23	594,7590		18,558,3516	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	103,103	20,679,5312	GG,GC,CC		7.2581,3.2569,5.9807	probably-damaging,probably-damaging	886/1520,706/1340	46911188	719,11303	1919	4092	6011	SO:0001583	missense	80781	exon21			GCCCCCCCGGACC		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.3362C>G	21.37:g.46911188C>G	ENSP00000352798:p.Pro1121Arg	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	169	80	0.473373	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		129	0.059065934065934064	16	0.032520325203252036	13	0.03591160220994475	28	0.04895104895104895	72	0.09498680738786279	C	14.33	2.503088	0.44558	0.032569	0.072581	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	D;D;D;D	0.95447	-3.09;-3.09;-3.09;-3.71	3.85	3.85	0.44370	.	0.073580	0.56097	D	0.000037	T	0.62380	0.2423	L	0.52266	1.64	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75243	-0.3386	10	0.27785	T	0.31	.	13.6811	0.62487	0.0:1.0:0.0:0.0	.	1121;886;706	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	R	706;706;886;1121;1121;53	ENSP00000383191:P706R;ENSP00000347665:P886R;ENSP00000352798:P1121R;ENSP00000339118:P53R	ENSP00000339118:P53R	P	+	2	0	COL18A1	45735616	0.222000	0.23652	0.916000	0.36221	0.128000	0.20619	3.287000	0.51732	2.159000	0.67721	0.561000	0.74099	CCC	C|0.938;G|0.062	0.062	strong		0.682	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
LSG1	55341	hgsc.bcm.edu	37	3	194387300	194387300	+	Splice_Site	SNP	C	C	T	rs1675943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:194387300C>T	ENST00000265245.5	-	3	542	c.228G>A	c.(226-228)gaG>gaA	p.E76E	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	76					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)		TATTAAGTTTCTCTGTTCAAA	0.358													C|||	2129	0.42512	0.2587	0.4481	5008	,	,		17143	0.4405		0.5348	False		,,,				2504	0.5051				p.E76E		Atlas-SNP	.											.	LSG1	38	.	0			c.G228A						PASS	.	C		1332,3074	415.2+/-337.1	212,908,1083	54.0	55.0	54.0		228	3.5	1.0	3	dbSNP_89	54	4540,4060	571.5+/-389.6	1223,2094,983	yes	coding-synonymous-near-splice	LSG1	NM_018385.2		1435,3002,2066	TT,TC,CC		47.2093,30.2315,45.1484		76/659	194387300	5872,7134	2203	4300	6503	SO:0001630	splice_region_variant	55341	exon3			AAGTTTCTCTGTT		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.227-1G>A	3.37:g.194387300C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1																																																																																			C|0.573;T|0.427	0.427	strong		0.358	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	Silent
CLSTN1	22883	hgsc.bcm.edu	37	1	9804693	9804693	+	Missense_Mutation	SNP	C	C	T	rs7550295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9804693C>T	ENST00000377298.4	-	8	1786	c.994G>A	c.(994-996)Gcg>Acg	p.A332T	CLSTN1_ENST00000377288.3_Missense_Mutation_p.A332T|CLSTN1_ENST00000361311.4_Missense_Mutation_p.A322T	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	332			A -> T (in dbSNP:rs7550295).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GCAGTGCCCGCGGCCGCACCT	0.632													C|||	992	0.198083	0.2723	0.1628	5008	,	,		14632	0.1508		0.0497	False		,,,				2504	0.3241				p.A332T		Atlas-SNP	.											.	CLSTN1	88	.	0			c.G994A						PASS	.	C	THR/ALA,THR/ALA	1026,3380		122,782,1299	33.0	25.0	28.0		994,964	-6.0	0.0	1	dbSNP_116	28	438,8160		19,400,3880	yes	missense,missense	CLSTN1	NM_001009566.1,NM_014944.3	58,58	141,1182,5179	TT,TC,CC		5.0942,23.2864,11.2581	benign,benign	332/982,322/972	9804693	1464,11540	2203	4299	6502	SO:0001583	missense	22883	exon8			TGCCCGCGGCCGC	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.994G>A	1.37:g.9804693C>T	ENSP00000366513:p.Ala332Thr	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	37	CCDS30580.1	322	0.14743589743589744	134	0.27235772357723576	53	0.1464088397790055	101	0.17657342657342656	34	0.044854881266490766	C	12.45	1.943043	0.34283	0.232864	0.050942	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.8	-6.0	0.02206	Concanavalin A-like lectin/glucanase (1);	0.397427	0.31041	N	0.008379	T	0.00012	0.0000	N	0.01352	-0.895	0.48511	P	3.3199999999999896E-4	B;B;B	0.32071	0.242;0.355;0.242	B;B;B	0.30401	0.054;0.115;0.054	T	0.41342	-0.9514	9	0.23891	T	0.37	-4.2631	2.0135	0.03493	0.4898:0.1173:0.2463:0.1466	rs7550295;rs60924364;rs7550295	332;322;332	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	T	332;322;152;332;332	ENSP00000366513:A332T;ENSP00000354997:A322T;ENSP00000401934:A152T;ENSP00000366502:A332T	ENSP00000354997:A322T	A	-	1	0	CLSTN1	9727280	0.002000	0.14202	0.000000	0.03702	0.014000	0.08584	-0.104000	0.10923	-1.301000	0.02338	-1.229000	0.01577	GCG	C|0.864;T|0.136	0.136	strong		0.632	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
TINAG	27283	hgsc.bcm.edu	37	6	54219326	54219326	+	Missense_Mutation	SNP	G	G	A	rs3195579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:54219326G>A	ENST00000259782.4	+	9	1238	c.1142G>A	c.(1141-1143)cGt>cAt	p.R381H		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	381				R -> H (in Ref. 1; BAA84949). {ECO:0000305}.	cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			ATGCAAGTCCGTGAAGATTTC	0.333													G|||	573	0.114417	0.1074	0.1124	5008	,	,		16355	0.0327		0.1839	False		,,,				2504	0.138				p.R381H		Atlas-SNP	.											TINAG,mucosal,malignant_melanoma,+1,1	TINAG	102	1	0			c.G1142A						PASS	.	G	HIS/ARG	515,3889	233.9+/-246.9	22,471,1709	109.0	106.0	107.0		1142	2.8	0.6	6	dbSNP_105	107	1643,6953	301.7+/-305.6	140,1363,2795	yes	missense	TINAG	NM_014464.3	29	162,1834,4504	AA,AG,GG		19.1135,11.6939,16.6	benign	381/477	54219326	2158,10842	2202	4298	6500	SO:0001583	missense	27283	exon9			AAGTCCGTGAAGA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1142G>A	6.37:g.54219326G>A	ENSP00000259782:p.Arg381His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	257	0.11767399267399267	56	0.11382113821138211	50	0.13812154696132597	15	0.026223776223776224	136	0.17941952506596306	G	2.469	-0.322348	0.05350	0.116939	0.191135	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.83755	-1.76	5.4	2.85	0.33270	Peptidase C1A, papain C-terminal (2);	0.544853	0.19170	N	0.120955	T	0.24774	0.0601	N	0.00496	-1.435	0.09310	P	0.9999999999999998	B	0.02656	0.0	B	0.04013	0.001	T	0.10177	-1.0641	9	0.05721	T	0.95	.	8.295	0.31980	0.8322:0.0:0.1678:0.0	rs3195579;rs10498796;rs17418879;rs17681573;rs60554247;rs10498796	381	Q9UJW2	TINAG_HUMAN	H	240;381;60	ENSP00000259782:R381H	ENSP00000259782:R381H	R	+	2	0	TINAG	54327285	0.998000	0.40836	0.594000	0.28785	0.988000	0.76386	3.531000	0.53546	0.421000	0.25980	-0.290000	0.09829	CGT	A|0.135;C|0.000;G|0.865	0.135	strong		0.333	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464	
PWP2	5822	hgsc.bcm.edu	37	21	45540919	45540919	+	Silent	SNP	A	A	G	rs2071143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45540919A>G	ENST00000291576.7	+	13	1699	c.1572A>G	c.(1570-1572)acA>acG	p.T524T		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	524					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GGGACAAGACAGTGCGCCTAT	0.587													G|||	2913	0.581669	0.2769	0.6772	5008	,	,		19329	0.6994		0.8211	False		,,,				2504	0.5583				p.T524T		Atlas-SNP	.											.	PWP2	64	.	0			c.A1572G						PASS	.	G		1538,2868	672.4+/-402.6	277,984,942	103.0	84.0	90.0		1572	-10.2	0.1	21	dbSNP_96	90	6948,1652	304.9+/-307.2	2827,1294,179	no	coding-synonymous	PWP2	NM_005049.2		3104,2278,1121	GG,GA,AA		19.2093,34.9069,34.7532		524/920	45540919	8486,4520	2203	4300	6503	SO:0001819	synonymous_variant	5822	exon13			CAAGACAGTGCGC		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1572A>G	21.37:g.45540919A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_005049	B2RAG8|Q96A77	Silent	SNP	ENST00000291576.7	37	CCDS33579.1																																																																																			A|0.362;G|0.638	0.638	strong		0.587	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
APBB2	323	hgsc.bcm.edu	37	4	41015742	41015742	+	Silent	SNP	T	T	C	rs11942640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:41015742T>C	ENST00000295974.8	-	6	1322	c.693A>G	c.(691-693)gaA>gaG	p.E231E	APBB2_ENST00000506352.1_Silent_p.E231E|APBB2_ENST00000508593.1_Silent_p.E231E|APBB2_ENST00000513140.1_Silent_p.E231E	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	231					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CCTTCTTGGTTTCTGGGCTGG	0.562													C|||	231	0.0461262	0.1362	0.036	5008	,	,		16665	0.001		0.0179	False		,,,				2504	0.0072				p.E231E	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A693G						PASS	.	C	,,	470,3614		24,422,1596	384.0	382.0	383.0		693,693,693	5.9	1.0	4	dbSNP_120	383	117,8257		2,113,4072	no	coding-synonymous,coding-synonymous,coding-synonymous	APBB2	NM_001166050.1,NM_004307.1,NM_173075.4	,,	26,535,5668	CC,CT,TT		1.3972,11.5083,4.7118	,,	231/759,231/760,231/737	41015742	587,11871	2042	4187	6229	SO:0001819	synonymous_variant	323	exon6			CTTGGTTTCTGGG	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.693A>G	4.37:g.41015742T>C		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	289	134	0.463668	NM_173075	B4DSL4|E9PG87|Q8IUI6	Silent	SNP	ENST00000295974.8	37	CCDS54761.1	90	0.04120879120879121	63	0.12804878048780488	13	0.03591160220994475	0	0.0	14	0.018469656992084433	C	7.090	0.572023	0.13623	0.115083	0.013972	ENSG00000163697	ENST00000513611	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01762	-1.1279	4	.	.	.	-33.8325	15.3626	0.74492	0.0:0.9334:0.0:0.0666	rs11942640;rs11942640	.	.	.	D	221	.	.	N	-	1	0	APBB2	40710499	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	3.310000	0.51911	1.531000	0.49152	-0.349000	0.07799	AAC	T|0.953;C|0.047	0.047	strong		0.562	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
DACT1	51339	hgsc.bcm.edu	37	14	59112732	59112732	+	Missense_Mutation	SNP	C	C	T	rs17832998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:59112732C>T	ENST00000335867.4	+	4	1415	c.1391C>T	c.(1390-1392)gCt>gTt	p.A464V	DACT1_ENST00000541264.2_Missense_Mutation_p.A183V|DACT1_ENST00000556859.1_Missense_Mutation_p.A183V|DACT1_ENST00000395153.3_Missense_Mutation_p.A427V			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	24	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	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	
TMEM132C	92293	hgsc.bcm.edu	37	12	129189702	129189702	+	Missense_Mutation	SNP	C	C	G	rs12426596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:129189702C>G	ENST00000435159.2	+	9	2189	c.2189C>G	c.(2188-2190)aCc>aGc	p.T730S	TMEM132C_ENST00000315208.8_Missense_Mutation_p.T346S|TMEM132C_ENST00000537538.1_Missense_Mutation_p.T115S	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	730			T -> S (in dbSNP:rs12426596).			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						ATCTACGACACCAAGGACTTC	0.627													C|||	304	0.0607029	0.0	0.0836	5008	,	,		17150	0.1181		0.0308	False		,,,				2504	0.0982				p.T730S		Atlas-SNP	.											.	TMEM132C	142	.	0			c.C2189G						PASS	.	C	SER/THR	8,1376		0,8,684	56.0	57.0	56.0		2189	3.0	1.0	12	dbSNP_120	56	54,3128		1,52,1538	yes	missense	TMEM132C	NM_001136103.2	58	1,60,2222	GG,GC,CC		1.697,0.578,1.3579	benign	730/1109	129189702	62,4504	692	1591	2283	SO:0001583	missense	92293	exon9			ACGACACCAAGGA	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.2189C>G	12.37:g.129189702C>G	ENSP00000410852:p.Thr730Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		129	0.059065934065934064	0	0.0	35	0.09668508287292818	72	0.1258741258741259	22	0.029023746701846966	C	8.069	0.769854	0.15983	0.00578	0.01697	ENSG00000181234	ENST00000435159;ENST00000315208;ENST00000537538	T;T;T	0.13307	2.6;2.6;2.6	4.84	2.95	0.34219	.	0.672434	0.13554	N	0.379300	T	0.00039	0.0001	N	0.01705	-0.755	0.22675	N	0.998866	B	0.09022	0.002	B	0.09377	0.004	T	0.41233	-0.9520	10	0.02654	T	1	.	10.022	0.42048	0.1464:0.5708:0.2828:0.0	rs12426596;rs12426596	730	Q8N3T6	T132C_HUMAN	S	730;346;115	ENSP00000410852:T730S;ENSP00000324458:T346S;ENSP00000438477:T115S	ENSP00000324458:T346S	T	+	2	0	TMEM132C	127755655	0.020000	0.18652	0.952000	0.39060	0.931000	0.56810	2.396000	0.44468	0.418000	0.25898	-0.165000	0.13383	ACC	C|0.942;G|0.058	0.058	strong		0.627	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
FAM184A	79632	hgsc.bcm.edu	37	6	119327632	119327632	+	Missense_Mutation	SNP	C	C	T	rs17827619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:119327632C>T	ENST00000338891.7	-	7	2238	c.1795G>A	c.(1795-1797)Gat>Aat	p.D599N	RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000352896.5_Missense_Mutation_p.D479N|FAM184A_ENST00000522284.1_Missense_Mutation_p.D479N|FAM184A_ENST00000368475.4_Missense_Mutation_p.D479N|FAM184A_ENST00000521531.1_Missense_Mutation_p.D599N	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	599			D -> N (in dbSNP:rs17827619).			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						AATAGAGCATCCTTGGTCTCC	0.388													C|||	404	0.0806709	0.028	0.0879	5008	,	,		16906	0.0704		0.1014	False		,,,				2504	0.136				p.D599N		Atlas-SNP	.											.	FAM184A	109	.	0			c.G1795A						PASS	.	C	ASN/ASP,ASN/ASP	169,3529		4,161,1684	109.0	103.0	105.0		1435,1795	5.8	1.0	6	dbSNP_123	105	1062,7108		68,926,3091	yes	missense,missense	FAM184A	NM_001100411.1,NM_024581.4	23,23	72,1087,4775	TT,TC,CC		12.9988,4.57,10.3724	benign,benign	479/972,599/1141	119327632	1231,10637	1849	4085	5934	SO:0001583	missense	79632	exon7			GAGCATCCTTGGT	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.1795G>A	6.37:g.119327632C>T	ENSP00000342604:p.Asp599Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	168	0.07692307692307693	14	0.028455284552845527	39	0.10773480662983426	35	0.06118881118881119	80	0.10554089709762533	C	11.06	1.528683	0.27387	0.0457	0.129988	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.23950	2.5;2.51;1.95;1.94;1.88	5.85	5.85	0.93711	.	0.101830	0.64402	D	0.000003	T	0.10252	0.0251	N	0.17082	0.46	0.22050	P	0.999398441	B;B;B	0.13594	0.006;0.003;0.008	B;B;B	0.17433	0.018;0.005;0.015	T	0.10660	-1.0620	9	0.26408	T	0.33	-14.7958	20.1731	0.98165	0.0:1.0:0.0:0.0	rs17827619;rs52823165;rs17827619	599;479;599	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	N	599;479;479;599;479	ENSP00000342604:D599N;ENSP00000326608:D479N;ENSP00000357460:D479N;ENSP00000430442:D599N;ENSP00000429826:D479N	ENSP00000342604:D599N	D	-	1	0	FAM184A	119369331	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	2.811000	0.47986	2.768000	0.95171	0.655000	0.94253	GAT	C|0.913;T|0.087	0.087	strong		0.388	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7504982	7504982	+	Silent	SNP	C	C	T	rs10422503	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7504982C>T	ENST00000359920.6	+	1	409	c.156C>T	c.(154-156)ggC>ggT	p.G52G	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	52					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GAGCCCCGGGCGCGAACATGG	0.652													C|||	1727	0.344848	0.211	0.4078	5008	,	,		11852	0.4196		0.326	False		,,,				2504	0.4233				p.G52G		Atlas-SNP	.											ARHGEF18_ENST00000359920,colon,carcinoma,0,2	ARHGEF18	129	2	0			c.C156T						PASS	.						17.0	19.0	18.0					19																	7504982		692	1591	2283	SO:0001819	synonymous_variant	23370	exon1			CCCGGGCGCGAAC	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.156C>T	19.37:g.7504982C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	37	CCDS45946.1																																																																																			C|0.677;T|0.323	0.323	strong		0.652	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
LDLRAD3	143458	hgsc.bcm.edu	37	11	36103228	36103228	+	Silent	SNP	A	A	G	rs1138807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	107	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	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	
GPC1	2817	hgsc.bcm.edu	37	2	241402836	241402836	+	Missense_Mutation	SNP	G	G	A	rs150681136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241402836G>A	ENST00000264039.2	+	4	1038	c.790G>A	c.(790-792)Ggc>Agc	p.G264S		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	264					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)		GGGAGTCCCCGGCGCCAGGCC	0.662													G|||	141	0.028155	0.0106	0.0115	5008	,	,		16141	0.0069		0.0268	False		,,,				2504	0.0869				p.G264S		Atlas-SNP	.											.	GPC1	32	.	0			c.G790A						PASS	.	G	SER/GLY	39,4365	44.6+/-78.6	0,39,2163	76.0	80.0	79.0		790	2.0	0.5	2	dbSNP_134	79	242,8358	96.3+/-158.1	3,236,4061	yes	missense	GPC1	NM_002081.2	56	3,275,6224	AA,AG,GG		2.814,0.8856,2.1609	benign	264/559	241402836	281,12723	2202	4300	6502	SO:0001583	missense	2817	exon4			GTCCCCGGCGCCA	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.790G>A	2.37:g.241402836G>A	ENSP00000264039:p.Gly264Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	178	89	0.5	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	33|33	0.01510989010989011|0.01510989010989011	4|4	0.008130081300813009|0.008130081300813009	4|4	0.011049723756906077|0.011049723756906077	3|3	0.005244755244755245|0.005244755244755245	22|22	0.029023746701846966|0.029023746701846966	G|G	0.511|0.511	-0.866682|-0.866682	0.02590|0.02590	0.008856|0.008856	0.02814|0.02814	ENSG00000063660|ENSG00000063660	ENST00000264039|ENST00000420138;ENST00000455111	T|.	0.43688|.	0.94|.	3.88|3.88	2.04|2.04	0.26737|0.26737	Glypican, conserved site (1);|.	0.158468|.	0.56097|.	D|.	0.000034|.	T|T	0.05456|0.05456	0.0144|0.0144	N|N	0.05383|0.05383	-0.06|-0.06	0.09310|0.09310	N|N	1|1	B|.	0.15719|.	0.014|.	B|.	0.16722|.	0.016|.	T|T	0.19451|0.19451	-1.0305|-1.0305	10|5	0.06625|.	T|.	0.88|.	-22.2779|-22.2779	5.2272|5.2272	0.15401|0.15401	0.3467:0.0:0.6533:0.0|0.3467:0.0:0.6533:0.0	.|.	264|.	P35052|.	GPC1_HUMAN|.	S|Q	264|303;8	ENSP00000264039:G264S|.	ENSP00000264039:G264S|.	G|R	+|+	1|2	0|0	GPC1|GPC1	241051509|241051509	0.652000|0.652000	0.27349|0.27349	0.493000|0.493000	0.27502|0.27502	0.588000|0.588000	0.36517|0.36517	1.994000|1.994000	0.40757|0.40757	0.979000|0.979000	0.38497|0.38497	0.484000|0.484000	0.47621|0.47621	GGC|CGG	G|0.981;A|0.019	0.019	strong		0.662	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
SLC7A2	6542	hgsc.bcm.edu	37	8	17396415	17396415	+	Intron	SNP	G	G	C	rs13259978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17396415G>C	ENST00000494857.1	+	3	196				SLC7A2_ENST00000398090.3_Missense_Mutation_p.D28H|SLC7A2_ENST00000470360.1_Missense_Mutation_p.D28H|SLC7A2_ENST00000004531.10_Missense_Mutation_p.D28H|SLC7A2_ENST00000522656.1_Intron	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	ACCGGTTTGCGACAGCAAGTT	0.413													G|||	967	0.193091	0.295	0.1744	5008	,	,		17605	0.1141		0.2038	False		,,,				2504	0.1391				p.D28H		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G82C						PASS	.	G	,HIS/ASP,HIS/ASP	1012,2652		143,726,963	99.0	89.0	92.0		,82,82	-1.8	0.0	8	dbSNP_121	92	1725,6447		238,1249,2599	yes	intron,missense,missense	SLC7A2	NM_001008539.3,NM_001164771.1,NM_003046.5	,81,81	381,1975,3562	CC,CG,GG		21.1087,27.6201,23.1244	,benign,benign	,28/699,28/698	17396415	2737,9099	1832	4086	5918	SO:0001627	intron_variant	6542	exon1			GTTTGCGACAGCA	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.-22-4412G>C	8.37:g.17396415G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	395	0.18086080586080586	124	0.25203252032520324	66	0.18232044198895028	58	0.10139860139860139	147	0.19393139841688653	G	7.037	0.561770	0.13498	0.276201	0.211087	ENSG00000003989	ENST00000470360;ENST00000004531;ENST00000398090	D;D;D	0.89343	-2.5;-2.36;-2.5	3.54	-1.78	0.07957	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09487	-1.0672	7	0.49607	T	0.09	.	0.5525	0.00665	0.1741:0.3011:0.1787:0.3461	rs13259978	28;28	P52569-3;P52569-2	.;.	H	28	ENSP00000419873:D28H;ENSP00000004531:D28H;ENSP00000381164:D28H	ENSP00000004531:D28H	D	+	1	0	SLC7A2	17440794	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.069000	0.11542	-0.398000	0.07679	-0.256000	0.11100	GAC	A|0.011;C|0.200;G|0.789	0.200	strong		0.413	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
C17orf80	55028	hgsc.bcm.edu	37	17	71239087	71239087	+	Silent	SNP	G	G	T	rs1566290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:71239087G>T	ENST00000535032.2	+	4	1787	c.1674G>T	c.(1672-1674)acG>acT	p.T558T	RP11-661C3.2_ENST00000579037.1_RNA|C17orf80_ENST00000582793.1_Silent_p.T27T|C17orf80_ENST00000359042.2_Silent_p.T558T|C17orf80_ENST00000426147.2_Silent_p.T558T|C17orf80_ENST00000255557.4_Silent_p.T522T|C17orf80_ENST00000268942.8_Silent_p.T522T|C17orf80_ENST00000577615.1_Silent_p.T522T			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	558						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T558T(1)		kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			GTGGCATCACGATGCTCTTCA	0.463													G|||	1103	0.220248	0.0408	0.3761	5008	,	,		17952	0.1558		0.331	False		,,,				2504	0.3047				p.T558T		Atlas-SNP	.											C17orf80,colon,carcinoma,+1,2	C17orf80	37	2	1	Substitution - coding silent(1)	stomach(1)	c.G1674T						scavenged	.	G	,,	415,3991	206.5+/-228.1	18,379,1806	200.0	146.0	165.0		1566,1674,1674	-11.8	0.0	17	dbSNP_88	165	3138,5462	476.9+/-369.5	598,1942,1760	no	coding-synonymous,coding-synonymous,coding-synonymous	C17orf80	NM_001100621.1,NM_001100622.1,NM_017941.4	,,	616,2321,3566	TT,TG,GG		36.4884,9.419,27.3182	,,	522/574,558/584,558/610	71239087	3553,9453	2203	4300	6503	SO:0001819	synonymous_variant	55028	exon5			CATCACGATGCTC	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"""sperm-expressed protein 1"", ""migration-inducing protein 3"""					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.1674G>T	17.37:g.71239087G>T		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_017941	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Silent	SNP	ENST00000535032.2	37	CCDS11694.1																																																																																			G|0.750;T|0.250	0.250	strong		0.463	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941	
FLG	2312	hgsc.bcm.edu	37	1	152281534	152281534	+	Missense_Mutation	SNP	A	A	T	rs113544881	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281534A>T	ENST00000368799.1	-	3	5863	c.5828T>A	c.(5827-5829)cTt>cAt	p.L1943H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1943	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)			AGCAGATCCAAGATGGTTTCT	0.562									Ichthyosis				-|||	1570	0.313498	0.3336	0.3285	5008	,	,		24124	0.4335		0.1302	False		,,,				2504	0.3405				p.L1943H		Atlas-SNP	.											.	FLG	900	.	0			c.T5828A						PASS	.						240.0	230.0	233.0					1																	152281534		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCCAAGATGGT	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.5828T>A	1.37:g.152281534A>T	ENSP00000357789:p.Leu1943His	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	398	122	0.306533	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	2.070	-0.413379	0.04799	.	.	ENSG00000143631	ENST00000368799	T	0.00808	5.67	2.69	0.209	0.15226	.	.	.	.	.	T	0.00073	0.0002	N	0.00210	-1.845	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	9	0.36615	T	0.2	0.0549	0.4679	0.00527	0.2155:0.1344:0.2221:0.428	.	1943	P20930	FILA_HUMAN	H	1943	ENSP00000357789:L1943H	ENSP00000357789:L1943H	L	-	2	0	FLG	150548158	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.730000	0.00805	-0.267000	0.09325	-1.521000	0.00933	CTT	A|0.949;T|0.051	0.051	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17118730	17118730	+	Silent	SNP	A	A	G	rs113662142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17118730A>G	ENST00000265970.7	-	26	4199	c.4200T>C	c.(4198-4200)ggT>ggC	p.G1400G	PIK3C2A_ENST00000540361.1_Silent_p.G1020G|PIK3C2A_ENST00000531428.1_5'UTR	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1400					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TAGAAGGAAGACCAGAAAAAC	0.358													A|||	27	0.00539137	0.0023	0.0	5008	,	,		19765	0.0		0.0089	False		,,,				2504	0.0153				p.G1400G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4200C						PASS	.	A		12,4388	19.1+/-41.9	0,12,2188	116.0	111.0	113.0		4200	0.9	1.0	11	dbSNP_132	113	80,8506	45.8+/-104.6	1,78,4214	no	coding-synonymous	PIK3C2A	NM_002645.2		1,90,6402	GG,GA,AA		0.9317,0.2727,0.7085		1400/1687	17118730	92,12894	2200	4293	6493	SO:0001819	synonymous_variant	5286	exon26			AGGAAGACCAGAA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.4200T>C	11.37:g.17118730A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																			A|0.992;G|0.008	0.008	strong		0.358	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
VN1R1	57191	hgsc.bcm.edu	37	19	57967133	57967133	+	Missense_Mutation	SNP	G	G	A	rs28649880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57967133G>A	ENST00000321039.3	-	1	721	c.722C>T	c.(721-723)tCc>tTc	p.S241F	AC004076.9_ENST00000415705.3_Intron|AC004076.9_ENST00000596831.1_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						scavenged	.	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	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	197	103	0.522843	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	
DSCAM	1826	hgsc.bcm.edu	37	21	42064785	42064785	+	Silent	SNP	C	C	T	rs79669041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:42064785C>T	ENST00000400454.1	-	3	936	c.459G>A	c.(457-459)gcG>gcA	p.A153A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	153	Ig-like C2-type 2.				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)				CAGTGATGTACGCCTCCACCG	0.527													c|||	23	0.00459265	0.0	0.0072	5008	,	,		20320	0.0		0.0159	False		,,,				2504	0.002				p.A153A	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G459A						PASS	.	T		9,4065		0,9,2028	136.0	134.0	134.0		459	-1.4	1.0	21	dbSNP_132	134	88,8274		0,88,4093	no	coding-synonymous	DSCAM	NM_001389.3		0,97,6121	TT,TC,CC		1.0524,0.2209,0.78		153/2013	42064785	97,12339	2037	4181	6218	SO:0001819	synonymous_variant	1826	exon3			GATGTACGCCTCC	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.459G>A	21.37:g.42064785C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
ATXN7	6314	hgsc.bcm.edu	37	3	63981635	63981635	+	Silent	SNP	C	C	T	rs3733125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:63981635C>T	ENST00000295900.6	+	12	2687	c.2137C>T	c.(2137-2139)Ctg>Ttg	p.L713L	ATXN7_ENST00000398590.3_Silent_p.L713L|ATXN7_ENST00000484332.1_Silent_p.L568L|ATXN7_ENST00000487717.1_Silent_p.L713L|ATXN7_ENST00000538065.1_Silent_p.L713L	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	713	Ser-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.L713L(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		CAGTTCCCCACTGTTGGTTCA	0.498													C|||	453	0.0904553	0.0061	0.0548	5008	,	,		18163	0.1925		0.1272	False		,,,				2504	0.0869				p.L713L		Atlas-SNP	.											ATXN7,NS,carcinoma,0,1	ATXN7	126	1	1	Substitution - coding silent(1)	stomach(1)	c.C2137T						PASS	.	C	,,	82,4234		2,78,2078	59.0	71.0	67.0		2137,1702,2137	2.2	0.1	3	dbSNP_107	67	888,7670		42,804,3433	no	coding-synonymous,coding-synonymous,coding-synonymous	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	,,	44,882,5511	TT,TC,CC		10.3763,1.8999,7.5346	,,	713/893,568/748,713/946	63981635	970,11904	2158	4279	6437	SO:0001819	synonymous_variant	6314	exon12			TCCCCACTGTTGG	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2137C>T	3.37:g.63981635C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Silent	SNP	ENST00000295900.6	37	CCDS43102.1																																																																																			C|0.892;T|0.108	0.108	strong		0.498	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
HERC3	8916	hgsc.bcm.edu	37	4	89607905	89607905	+	Silent	SNP	A	A	G	rs3737488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:89607905A>G	ENST00000402738.1	+	22	2765	c.2526A>G	c.(2524-2526)ttA>ttG	p.L842L	RNU6-33P_ENST00000384793.1_RNA|HERC3_ENST00000264345.3_Silent_p.L842L|HERC3_ENST00000543130.1_Silent_p.L286L	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	842					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		AAGAGCTTTTAGATTACCCCG	0.438													A|||	653	0.130391	0.059	0.1599	5008	,	,		16831	0.1964		0.159	False		,,,				2504	0.1084				p.L842L		Atlas-SNP	.											.	HERC3	82	.	0			c.A2526G						PASS	.	A		297,4109	161.8+/-193.9	10,277,1916	114.0	105.0	108.0		2526	1.2	1.0	4	dbSNP_107	108	1348,7252	263.5+/-285.0	117,1114,3069	no	coding-synonymous	HERC3	NM_014606.1		127,1391,4985	GG,GA,AA		15.6744,6.7408,12.648		842/1051	89607905	1645,11361	2203	4300	6503	SO:0001819	synonymous_variant	8916	exon22			GCTTTTAGATTAC	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.2526A>G	4.37:g.89607905A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_014606	A8K1S5|Q8IXX3	Silent	SNP	ENST00000402738.1	37	CCDS34028.1																																																																																			A|0.874;G|0.126	0.126	strong		0.438	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
CECR1	51816	hgsc.bcm.edu	37	22	17690430	17690430	+	Silent	SNP	C	C	G	rs7289141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:17690430C>G	ENST00000399839.1	-	2	408	c.138G>C	c.(136-138)ctG>ctC	p.L46L	CECR1_ENST00000399837.2_Silent_p.L46L|CECR1_ENST00000449907.2_Silent_p.L4L|CECR1_ENST00000262607.3_Silent_p.L46L	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	46	Dimerization.				adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.L46L(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GCCGCCCCCCCAGCCGCATCA	0.532													C|||	917	0.183107	0.0734	0.1527	5008	,	,		16629	0.3214		0.1173	False		,,,				2504	0.2781				p.L46L		Atlas-SNP	.											CECR1,NS,carcinoma,0,1	CECR1	77	1	1	Substitution - coding silent(1)	stomach(1)	c.G138C						PASS	.	C		339,4067	171.2+/-201.5	19,301,1883	36.0	36.0	36.0		138	-8.9	0.0	22	dbSNP_116	36	964,7636	199.2+/-243.3	54,856,3390	no	coding-synonymous	CECR1	NM_017424.2		73,1157,5273	GG,GC,CC		11.2093,7.6941,10.0185		46/512	17690430	1303,11703	2203	4300	6503	SO:0001819	synonymous_variant	51816	exon1			CCCCCCCAGCCGC	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.138G>C	22.37:g.17690430C>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																			C|0.869;G|0.131	0.131	strong		0.532	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
BCAS1	8537	hgsc.bcm.edu	37	20	52561469	52561469	+	Missense_Mutation	SNP	A	A	G	rs1055246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:52561469A>G	ENST00000395961.3	-	12	1913	c.1747T>C	c.(1747-1749)Tcc>Ccc	p.S583P	AC005220.3_ENST00000450473.1_RNA|BCAS1_ENST00000434986.2_Missense_Mutation_p.S249P|BCAS1_ENST00000371435.2_Missense_Mutation_p.S505P|BCAS1_ENST00000371440.3_Missense_Mutation_p.S592P	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	583			S -> P (in dbSNP:rs1055246). {ECO:0000269|PubMed:9671742}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.S583P(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GTTTACTTGGATTTGCCAACT	0.488													A|||	651	0.129992	0.1021	0.0836	5008	,	,		20005	0.0804		0.1481	False		,,,				2504	0.2331				p.S583P		Atlas-SNP	.											BCAS1,NS,carcinoma,0,1	BCAS1	77	1	1	Substitution - Missense(1)	prostate(1)	c.T1747C						PASS	.	A	PRO/SER	410,3996	202.5+/-225.2	17,376,1810	361.0	317.0	332.0		1747	4.1	1.0	20	dbSNP_86	332	1161,7439	238.1+/-269.7	77,1007,3216	yes	missense	BCAS1	NM_003657.2	74	94,1383,5026	GG,GA,AA		13.5,9.3055,12.079	probably-damaging	583/585	52561469	1571,11435	2203	4300	6503	SO:0001583	missense	8537	exon12			ACTTGGATTTGCC	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.1747T>C	20.37:g.52561469A>G	ENSP00000379290:p.Ser583Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	246	0.11263736263736264	47	0.09552845528455285	34	0.09392265193370165	47	0.08216783216783216	118	0.15567282321899736	A	20.1	3.935346	0.73442	0.093055	0.135	ENSG00000064787	ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	T;T;T;T;T	0.49720	1.43;1.68;1.58;1.47;0.77	5.21	4.08	0.47627	.	0.186396	0.39759	N	0.001262	T	0.00210	0.0006	N	0.08118	0	0.09310	P	0.9999999999999993	D;D;D;D;D	0.89917	1.0;0.996;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.953;0.994;0.999;0.999	T	0.18429	-1.0337	9	0.49607	T	0.09	.	10.1213	0.42623	0.8318:0.1682:0.0:0.0	rs1055246;rs3195743;rs52836527;rs58678039;rs1055246	249;592;505;583;583	B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363	.;.;.;.;BCAS1_HUMAN	P	454;592;383;583;505;249	ENSP00000396361:S454P;ENSP00000360495:S592P;ENSP00000379290:S583P;ENSP00000360490:S505P;ENSP00000409956:S249P	ENSP00000360490:S505P	S	-	1	0	BCAS1	51994876	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.298000	0.33412	0.783000	0.33636	0.459000	0.35465	TCC	T|0.006;G|0.117	0.117	strong		0.488	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	
RNF213	57674	hgsc.bcm.edu	37	17	78354661	78354661	+	Silent	SNP	C	C	T	rs4889848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78354661C>T	ENST00000582970.1	+	56	13814	c.13671C>T	c.(13669-13671)caC>caT	p.H4557H	RNF213_ENST00000508628.2_Silent_p.H4606H|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Silent_p.H2630H	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4557					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)			AGACCGGCCACGTGCTGGGCA	0.602													T|||	3803	0.759385	0.9879	0.6311	5008	,	,		18393	0.5794		0.8419	False		,,,				2504	0.6421				p.H4557H		Atlas-SNP	.											.	RNF213	766	.	0			c.C13671T						PASS	.	T		4221,185	118.4+/-156.1	2021,179,3	147.0	149.0	148.0		13818	-2.9	1.0	17	dbSNP_111	148	7247,1353	265.3+/-286.1	3057,1133,110	no	coding-synonymous	RNF213	NM_020914.4		5078,1312,113	TT,TC,CC		15.7326,4.1988,11.8253		4606/5257	78354661	11468,1538	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon56			CGGCCACGTGCTG	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.13671C>T	17.37:g.78354661C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	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|0.163;T|0.837	0.837	strong		0.602	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
NPVF	64111	hgsc.bcm.edu	37	7	25266400	25266400	+	Silent	SNP	G	G	A	rs2717851	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:25266400G>A	ENST00000222674.2	-	2	430	c.384C>T	c.(382-384)ccC>ccT	p.P128P		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	128					negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						CAAACCTTTGGGGCAGGTTAG	0.473													G|||	1394	0.278355	0.3722	0.3184	5008	,	,		19591	0.1468		0.2773	False		,,,				2504	0.2597				p.P128P		Atlas-SNP	.											.	NPVF	36	.	0			c.C384T						PASS	.	G		1581,2825	493.6+/-362.7	276,1029,898	214.0	201.0	206.0		384	1.0	1.0	7	dbSNP_100	206	2424,6176	401.8+/-347.3	341,1742,2217	no	coding-synonymous	NPVF	NM_022150.3		617,2771,3115	AA,AG,GG		28.186,35.8829,30.7935		128/197	25266400	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	64111	exon2			CCTTTGGGGCAGG	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.384C>T	7.37:g.25266400G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	305	186	0.609836	NM_022150	A4D164|Q7LE27|Q96PI9	Silent	SNP	ENST00000222674.2	37	CCDS5395.1																																																																																			G|0.702;A|0.298	0.298	strong		0.473	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	
ZNF468	90333	hgsc.bcm.edu	37	19	53344701	53344701	+	Silent	SNP	A	A	G	rs10420793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53344701A>G	ENST00000595646.1	-	4	966	c.846T>C	c.(844-846)caT>caC	p.H282H	ZNF468_ENST00000390651.4_Silent_p.H229H|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000396409.4_Silent_p.H229H|ZNF28_ENST00000594602.1_Intron			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	282					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.H282H(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)		GGGATGAATTATGACCAAAGG	0.418													-|||	1803	0.360024	0.562	0.2752	5008	,	,		21073	0.1101		0.2674	False		,,,				2504	0.5				p.H282H		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	1	1	Substitution - coding silent(1)	stomach(1)	c.T846C						PASS	.	G	,	2294,2112		583,1128,492	125.0	116.0	119.0		846,687	-3.5	0.0	19	dbSNP_119	119	2537,6063		380,1777,2143	no	coding-synonymous,coding-synonymous	ZNF468	NM_001008801.1,NM_199132.1	,	963,2905,2635	GG,GA,AA		29.5,47.9346,37.1444	,	282/523,229/470	53344701	4831,8175	2203	4300	6503	SO:0001819	synonymous_variant	90333	exon4			TGAATTATGACCA	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.846T>C	19.37:g.53344701A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Silent	SNP	ENST00000595646.1	37	CCDS33094.1																																																																																			A|0.649;G|0.351	0.351	strong		0.418	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
ZBP1	81030	hgsc.bcm.edu	37	20	56191475	56191475	+	Silent	SNP	C	C	T	rs16981188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:56191475C>T	ENST00000371173.3	-	2	261	c.84G>A	c.(82-84)ccG>ccA	p.P28P	ZBP1_ENST00000343535.4_Silent_p.P28P|ZBP1_ENST00000538947.1_5'UTR|ZBP1_ENST00000541799.1_Silent_p.P28P|ZBP1_ENST00000340462.4_Silent_p.P28P|ZBP1_ENST00000395822.3_Intron	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	28					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CAAGTTTCACCGGGGAGCCAG	0.577													C|||	98	0.0195687	0.028	0.0317	5008	,	,		18817	0.0		0.0308	False		,,,				2504	0.0082				p.P28P		Atlas-SNP	.											.	ZBP1	65	.	0			c.G84A						PASS	.	C	,,,	158,4248	108.2+/-146.6	0,158,2045	95.0	94.0	94.0		84,,84,84	-7.3	0.0	20	dbSNP_123	94	318,8282	112.9+/-173.0	5,308,3987	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	ZBP1	NM_001160417.1,NM_001160418.1,NM_001160419.1,NM_030776.2	,,,	5,466,6032	TT,TC,CC		3.6977,3.586,3.6598	,,,	28/429,,28/249,28/430	56191475	476,12530	2203	4300	6503	SO:0001819	synonymous_variant	81030	exon2			TTTCACCGGGGAG	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.84G>A	20.37:g.56191475C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
LGMN	5641	hgsc.bcm.edu	37	14	93170993	93170993	+	Silent	SNP	C	C	T	rs9791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:93170993C>T	ENST00000393218.2	-	14	1588	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	LGMN_ENST00000557434.1_Silent_p.P360P|LGMN_ENST00000555699.1_Intron|LGMN_ENST00000334869.4_Silent_p.P417P	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	417					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		ACCTGTGAAGCGGATACGGCT	0.473													C|||	1412	0.281949	0.2678	0.5519	5008	,	,		20858	0.0754		0.4245	False		,,,				2504	0.1759				p.P417P		Atlas-SNP	.											.	LGMN	28	.	0			c.G1251A						PASS	.	C	,	1264,3142	432.6+/-343.3	185,894,1124	188.0	179.0	182.0		1251,1251	-10.0	0.0	14	dbSNP_52	182	3540,5060	514.7+/-378.4	722,2096,1482	no	coding-synonymous,coding-synonymous	LGMN	NM_001008530.2,NM_005606.6	,	907,2990,2606	TT,TC,CC		41.1628,28.6882,36.9368	,	417/434,417/434	93170993	4804,8202	2203	4300	6503	SO:0001819	synonymous_variant	5641	exon13			GTGAAGCGGATAC	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1251G>A	14.37:g.93170993C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																			C|0.681;T|0.319	0.319	strong		0.473	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
ZBTB3	79842	hgsc.bcm.edu	37	11	62519565	62519565	+	Missense_Mutation	SNP	G	G	C	rs544641	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:62519565G>C	ENST00000394807.3	-	2	1847	c.1722C>G	c.(1720-1722)atC>atG	p.I574M		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	574			I -> M (in dbSNP:rs544641).		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(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						TGCTCCCTTAGATGTTAGTTT	0.527													G|||	565	0.112819	0.2504	0.0303	5008	,	,		17043	0.1518		0.0189	False		,,,				2504	0.0419				p.I574M		Atlas-SNP	.											.	ZBTB3	47	.	0			c.C1722G						PASS	.	G	MET/ILE	909,3495	350.8+/-311.0	106,697,1399	74.0	68.0	70.0		1722	3.2	0.0	11	dbSNP_83	70	195,8403	85.8+/-148.2	1,193,4105	yes	missense	ZBTB3	NM_024784.3	10	107,890,5504	CC,CG,GG		2.268,20.6403,8.491	benign	574/575	62519565	1104,11898	2202	4299	6501	SO:0001583	missense	79842	exon2			CCCTTAGATGTTA	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.1722C>G	11.37:g.62519565G>C	ENSP00000378286:p.Ile574Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	37	CCDS8034.1	224|224	0.10256410256410256|0.10256410256410256	119|119	0.241869918699187|0.241869918699187	10|10	0.027624309392265192|0.027624309392265192	78|78	0.13636363636363635|0.13636363636363635	17|17	0.022427440633245383|0.022427440633245383	G|G	10.98|10.98	1.505033|1.505033	0.26949|0.26949	0.206403|0.206403	0.02268|0.02268	ENSG00000185670|ENSG00000185670	ENST00000394807|ENST00000530112	T|.	0.14266|.	2.52|.	4.15|4.15	3.24|3.24	0.37175|0.37175	.|.	.|.	.|.	.|.	.|.	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|.	0.25169|.	0.119|.	B|.	0.21917|.	0.037|.	T|T	0.33854|0.33854	-0.9852|-0.9852	8|4	0.51188|.	T|.	0.08|.	.|.	7.9669|7.9669	0.30104|0.30104	0.117:0.0:0.883:0.0|0.117:0.0:0.883:0.0	rs544641;rs3881260;rs17652170;rs544641|rs544641;rs3881260;rs17652170;rs544641	574|.	Q9H5J0|.	ZBTB3_HUMAN|.	M|V	574|3	ENSP00000378286:I574M|.	ENSP00000378286:I574M|.	I|L	-|-	3|1	3|2	ZBTB3|ZBTB3	62276141|62276141	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.858000|0.858000	0.48976|0.48976	0.116000|0.116000	0.15561|0.15561	0.874000|0.874000	0.35823|0.35823	0.561000|0.561000	0.74099|0.74099	ATC|CTA	G|0.908;C|0.092	0.092	strong		0.527	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
SMCR8	140775	hgsc.bcm.edu	37	17	18221010	18221010	+	Missense_Mutation	SNP	A	A	G	rs12449313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18221010A>G	ENST00000406438.3	+	1	2387	c.1907A>G	c.(1906-1908)aAc>aGc	p.N636S	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	636			N -> S (in dbSNP:rs12449313).			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						GAAAATGCCAACCCTTCTTCC	0.587													A|||	1075	0.214657	0.1452	0.2421	5008	,	,		20342	0.3185		0.2425	False		,,,				2504	0.1534				p.N636S		Atlas-SNP	.											.	SMCR8	62	.	0			c.A1907G						PASS	.	A	SER/ASN	683,3723	288.7+/-280.0	64,555,1584	67.0	64.0	65.0		1907	-7.7	0.0	17	dbSNP_120	65	2197,6403	372.7+/-336.7	284,1629,2387	yes	missense	SMCR8	NM_144775.2	46	348,2184,3971	GG,GA,AA		25.5465,15.5016,22.1436	benign	636/938	18221010	2880,10126	2203	4300	6503	SO:0001583	missense	140775	exon1			ATGCCAACCCTTC	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.1907A>G	17.37:g.18221010A>G	ENSP00000385025:p.Asn636Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	527	0.2413003663003663	81	0.16463414634146342	86	0.23756906077348067	167	0.291958041958042	193	0.2546174142480211	A	0.006	-2.101022	0.00360	0.155016	0.255465	ENSG00000176994	ENST00000406438	T	0.38240	1.15	5.87	-7.65	0.01281	.	1.269400	0.05095	N	0.486016	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	0.30650	-0.9971	9	0.13108	T	0.6	-32.4624	20.8995	0.99940	0.3953:0.0:0.6047:0.0	rs12449313;rs52833335;rs58781335;rs12449313	636	Q8TEV9	SMCR8_HUMAN	S	636	ENSP00000385025:N636S	ENSP00000385025:N636S	N	+	2	0	SMCR8	18161735	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.038000	0.03553	-2.092000	0.00857	-1.139000	0.01908	AAC	A|0.770;G|0.229	0.229	strong		0.587	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
NLRC5	84166	hgsc.bcm.edu	37	16	57060724	57060724	+	Silent	SNP	G	G	A	rs13339199	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:57060724G>A	ENST00000262510.6	+	6	2094	c.1869G>A	c.(1867-1869)caG>caA	p.Q623Q	NLRC5_ENST00000539144.1_Silent_p.Q623Q|NLRC5_ENST00000436936.1_Silent_p.Q623Q|NLRC5_ENST00000308149.7_Silent_p.Q623Q	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	623					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)				ATGAGACACAGGAGCCTGAGC	0.577													G|||	543	0.108427	0.2958	0.0461	5008	,	,		19707	0.0		0.0487	False		,,,				2504	0.0726				p.Q623Q		Atlas-SNP	.											.	NLRC5	186	.	0			c.G1869A						PASS	.	G		1047,3349	385.8+/-325.9	127,793,1278	116.0	87.0	97.0		1869	5.5	1.0	16	dbSNP_121	97	434,8166	132.5+/-190.1	11,412,3877	no	coding-synonymous	NLRC5	NM_032206.3		138,1205,5155	AA,AG,GG		5.0465,23.8171,11.3958		623/1867	57060724	1481,11515	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon5			GACACAGGAGCCT	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.1869G>A	16.37:g.57060724G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	200	0.09157509157509157	144	0.2926829268292683	15	0.04143646408839779	3	0.005244755244755245	38	0.05013192612137203	G	6.139	0.393896	0.11638	0.238171	0.050465	ENSG00000140853	ENST00000538805	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33240	-0.9876	3	.	.	.	.	8.0878	0.30782	0.1725:0.0:0.8275:0.0	rs13339199;rs13339199	.	.	.	R	376	.	.	G	+	1	0	NLRC5	55618225	1.000000	0.71417	0.972000	0.41901	0.756000	0.42949	3.034000	0.49751	2.594000	0.87642	0.561000	0.74099	GGA	G|0.895;A|0.105	0.105	strong		0.577	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
KATNAL2	83473	hgsc.bcm.edu	37	18	44626630	44626630	+	Silent	SNP	T	T	G	rs2289130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:44626630T>G	ENST00000245121.5	+	14	1358	c.1164T>G	c.(1162-1164)acT>acG	p.T388T	KATNAL2_ENST00000356157.7_Silent_p.T460T	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TTCAGGAGACTGAGGGCTACT	0.512											OREG0024959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	359	0.0716853	0.0348	0.0533	5008	,	,		18539	0.1458		0.0775	False		,,,				2504	0.0521				p.T388T		Atlas-SNP	.											.	KATNAL2	64	.	0			c.T1164G						PASS	.	T		188,4218	120.0+/-157.7	5,178,2020	90.0	77.0	81.0		1164	-11.4	0.6	18	dbSNP_100	81	589,8011	157.0+/-210.8	17,555,3728	no	coding-synonymous	KATNAL2	NM_031303.2		22,733,5748	GG,GT,TT		6.8488,4.2669,5.9742		388/467	44626630	777,12229	2203	4300	6503	SO:0001819	synonymous_variant	83473	exon14			GGAGACTGAGGGC	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.1164T>G	18.37:g.44626630T>G		Somatic	42	0	0	925	WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_031303		Silent	SNP	ENST00000245121.5	37	CCDS32828.1																																																																																			T|0.929;G|0.071	0.071	strong		0.512	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363012	42363012	+	Missense_Mutation	SNP	G	G	C	rs17690899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363012G>C	ENST00000290472.3	-	18	2040	c.1946C>G	c.(1945-1947)gCc>gGc	p.A649G		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	649	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		A -> G (in dbSNP:rs17690899).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GATGAAGTAGGCGGCGTCCAC	0.627													C|||	222	0.0443291	0.0144	0.0749	5008	,	,		18384	0.0		0.1083	False		,,,				2504	0.0429				p.A649G		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.C1946G						PASS	.	C	GLY/ALA	158,4246	779.9+/-414.4	2,154,2046	77.0	71.0	73.0		1946	1.2	0.3	15	dbSNP_123	73	908,7690	744.4+/-407.2	42,824,3433	yes	missense	PLA2G4D	NM_178034.3	60	44,978,5479	CC,CG,GG		10.5606,3.5876,8.1987	benign	649/819	42363012	1066,11936	2202	4299	6501	SO:0001583	missense	283748	exon18			AAGTAGGCGGCGT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1946C>G	15.37:g.42363012G>C	ENSP00000290472:p.Ala649Gly	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	128	0.05860805860805861	10	0.02032520325203252	31	0.0856353591160221	0	0.0	87	0.11477572559366754	C	0.007	-1.995943	0.00435	0.035876	0.105606	ENSG00000159337	ENST00000290472	T	0.01197	5.19	4.46	1.22	0.21188	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.514594	0.16305	N	0.220291	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47235	-0.9133	9	0.02654	T	1	-6.1083	18.0458	0.89331	0.0:0.3887:0.6113:0.0	rs17690899;rs52796698;rs17690899	649	Q86XP0	PA24D_HUMAN	G	649	ENSP00000290472:A649G	ENSP00000290472:A649G	A	-	2	0	PLA2G4D	40150304	0.001000	0.12720	0.279000	0.24732	0.183000	0.23260	-0.065000	0.11617	0.218000	0.20820	-0.216000	0.12614	GCC	G|0.931;C|0.069	0.069	strong		0.627	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471778	39471778	+	Missense_Mutation	SNP	C	C	T	rs78413710|rs386797077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39471778C>T	ENST00000334202.3	-	1	169	c.125G>A	c.(124-126)gGc>gAc	p.G42D		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	42						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			gcccccgcagccagagccccc	0.687													C|||	941	0.187899	0.1354	0.1354	5008	,	,		9853	0.3165		0.1809	False		,,,				2504	0.1708				p.G42D		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.G125A						PASS	.						10.0	13.0	12.0					17																	39471778		2170	4250	6420	SO:0001583	missense	83902	exon1			CCGCAGCCAGAGC	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"""Keratin associated proteins"""	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.125G>A	17.37:g.39471778C>T	ENSP00000333993:p.Gly42Asp	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_031964		Missense_Mutation	SNP	ENST00000334202.3	37	CCDS11387.1	399	0.18269230769230768	62	0.12601626016260162	49	0.13535911602209943	159	0.27797202797202797	129	0.17018469656992086	C	5.391	0.257268	0.10239	.	.	ENSG00000186860	ENST00000334202	.	.	.	4.26	3.29	0.37713	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.46586	P	8.879999999999999E-4	B	0.15930	0.015	B	0.17433	0.018	T	0.15809	-1.0424	7	0.87932	D	0	-10.805	7.6767	0.28490	0.0:0.8845:0.0:0.1155	.	42	Q9BYP8	KR171_HUMAN	D	42	.	ENSP00000333993:G42D	G	-	2	0	KRTAP17-1	36725304	0.664000	0.27457	0.310000	0.25168	0.312000	0.27988	1.496000	0.35638	1.004000	0.39156	0.462000	0.41574	GGC	C|0.818;T|0.182	0.182	strong		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
TEP1	7011	hgsc.bcm.edu	37	14	20859205	20859205	+	Silent	SNP	C	C	T	rs872074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20859205C>T	ENST00000262715.5	-	14	2188	c.2148G>A	c.(2146-2148)gcG>gcA	p.A716A	TEP1_ENST00000556935.1_Silent_p.A608A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	716					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)	p.A716A(1)		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)		CCACCTGCTCCGCCCTCGTGA	0.537													C|||	802	0.160144	0.2685	0.1297	5008	,	,		21203	0.0317		0.1819	False		,,,				2504	0.1452				p.A716A		Atlas-SNP	.											TEP1,rectum,carcinoma,0,2	TEP1	224	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2148A						scavenged	.	C		1066,3340	389.6+/-327.4	114,838,1251	114.0	92.0	100.0		2148	-11.0	0.1	14	dbSNP_86	100	1515,7085	285.1+/-297.0	135,1245,2920	no	coding-synonymous	TEP1	NM_007110.4		249,2083,4171	TT,TC,CC		17.6163,24.1943,19.8447		716/2628	20859205	2581,10425	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon14			CTGCTCCGCCCTC		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.2148G>A	14.37:g.20859205C>T		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			C|0.822;T|0.178	0.178	strong		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
PTPRQ	374462	hgsc.bcm.edu	37	12	80936026	80936026	+	Missense_Mutation	SNP	A	A	G	rs17713202	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	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	
CDH13	1012	hgsc.bcm.edu	37	16	83065664	83065664	+	Silent	SNP	G	G	A	rs6565105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:83065664G>A	ENST00000566620.1	+	3	497	c.207G>A	c.(205-207)tcG>tcA	p.S69S	CDH13_ENST00000268613.10_Silent_p.S116S|CDH13_ENST00000446376.2_Silent_p.S69S|CDH13_ENST00000431540.3_Silent_p.S69S|CDH13_ENST00000565636.1_Silent_p.S69S|CDH13_ENST00000569454.1_3'UTR|CDH13_ENST00000428848.3_Silent_p.S69S	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	69					adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		ATGAGGTCTCGAGCCCATACT	0.507													G|||	2675	0.534145	0.559	0.5821	5008	,	,		21576	0.4573		0.5298	False		,,,				2504	0.5501				p.S116S		Atlas-SNP	.											.	CDH13	97	.	0			c.G348A						PASS	.	G	,,,,,	2229,1811		639,951,430	71.0	69.0	70.0		348,207,,207,207,207	-2.0	1.0	16	dbSNP_116	70	4635,3727		1288,2059,834	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001220491.1,NM_001220492.1,NM_001257.4	,,,,,	1927,3010,1264	AA,AG,GG		44.5707,44.8267,44.6541	,,,,,	116/761,69/675,,69/191,69/176,69/714	83065664	6864,5538	2020	4181	6201	SO:0001819	synonymous_variant	1012	exon4			GGTCTCGAGCCCA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.207G>A	16.37:g.83065664G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			A|0.532;C|0.000;G|0.467	0.532	strong		0.507	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
TRIB3	57761	hgsc.bcm.edu	37	20	368905	368905	+	Missense_Mutation	SNP	A	A	G	rs2295490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:368905A>G	ENST00000217233.3	+	2	804	c.251A>G	c.(250-252)cAg>cGg	p.Q84R	TRIB3_ENST00000422053.2_Missense_Mutation_p.Q111R	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	84	Interaction with DDIT3/CHOP.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> R (in dbSNP:rs2295490). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cellular lipid metabolic process (GO:0044255)|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)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		CGGGCCTACCAGGCCCTGCAC	0.667													G|||	997	0.199081	0.1641	0.0836	5008	,	,		17047	0.1865		0.1441	False		,,,				2504	0.3978				p.Q84R	Melanoma(101;421 2374 19538)	Atlas-SNP	.											.	TRIB3	50	.	0			c.A251G	GRCh37	CM052928	TRIB3	M	rs2295490	PASS	.	G	ARG/GLN	706,3700	730.6+/-410.2	59,588,1556	34.0	36.0	35.0		251	4.5	0.5	20	dbSNP_100	35	1334,7262	727.5+/-406.6	117,1100,3081	yes	missense	TRIB3	NM_021158.3	43	176,1688,4637	GG,GA,AA		15.5188,16.0236,15.6899	benign	84/359	368905	2040,10962	2203	4298	6501	SO:0001583	missense	57761	exon2			CCTACCAGGCCCT	AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"""chromosome 20 open reading frame 97"", ""tribbles homolog 3 (Drosophila)"""	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.251A>G	20.37:g.368905A>G	ENSP00000217233:p.Gln84Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Missense_Mutation	SNP	ENST00000217233.3	37	CCDS12997.1	338	0.15476190476190477	75	0.1524390243902439	31	0.0856353591160221	125	0.21853146853146854	107	0.14116094986807387	G	5.585	0.292770	0.10567	0.160236	0.155188	ENSG00000101255	ENST00000217233;ENST00000449710;ENST00000422053	T;T;T	0.18338	2.22;2.24;2.22	4.49	4.49	0.54785	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.253277	0.20459	N	0.091939	T	0.00012	0.0000	N	0.00175	-1.925	0.50039	P	1.5699999999996272E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34378	-0.9831	9	0.17369	T	0.5	-10.8277	10.4874	0.44731	0.0958:0.0:0.9042:0.0	rs2295490;rs17856768;rs2295490	111;84	B4DMM9;Q96RU7	.;TRIB3_HUMAN	R	84;84;111	ENSP00000217233:Q84R;ENSP00000391873:Q84R;ENSP00000415416:Q111R	ENSP00000217233:Q84R	Q	+	2	0	TRIB3	316905	1.000000	0.71417	0.489000	0.27452	0.548000	0.35241	5.142000	0.64820	1.119000	0.41883	-0.215000	0.12644	CAG	A|0.840;G|0.160	0.160	strong		0.667	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158	
FAM209B	388799	hgsc.bcm.edu	37	20	55108617	55108617	+	Missense_Mutation	SNP	C	C	A	rs3209183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	187	0	0		WXS	Illumina HiSeq	Phase_I	191	107	0.560209	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		
PIGS	94005	hgsc.bcm.edu	37	17	26888506	26888506	+	Missense_Mutation	SNP	G	G	C	rs140545278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26888506G>C	ENST00000308360.7	-	6	985	c.610C>G	c.(610-612)Ctg>Gtg	p.L204V	PIGS_ENST00000543734.1_Missense_Mutation_p.L143V|PIGS_ENST00000395346.2_Missense_Mutation_p.L196V|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	204					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					TGGTCAGCCAGAGCAGCAGCA	0.602																																					p.L204V		Atlas-SNP	.											.	PIGS	42	.	0			c.C610G						PASS	.	G	VAL/LEU	0,4406		0,0,2203	83.0	66.0	72.0		610	2.2	0.9	17	dbSNP_134	72	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PIGS	NM_033198.3	32	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	204/556	26888506	4,13002	2203	4300	6503	SO:0001583	missense	94005	exon6			CAGCCAGAGCAGC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.610C>G	17.37:g.26888506G>C	ENSP00000309430:p.Leu204Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454766	0.63290	0.0	4.65E-4	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.49139	0.86;0.86;0.79	5.68	2.21	0.28008	.	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	M	0.72479	2.2	0.52099	D	0.99994	D;D	0.63880	0.993;0.991	D;P	0.66084	0.941;0.862	T	0.55218	-0.8175	10	0.17832	T	0.49	-12.9026	10.0958	0.42475	0.2491:0.0:0.7509:0.0	.	204;196	Q96S52;Q96S52-2	PIGS_HUMAN;.	V	196;204;143	ENSP00000378755:L196V;ENSP00000309430:L204V;ENSP00000438447:L143V	ENSP00000309430:L204V	L	-	1	2	PIGS	23912633	1.000000	0.71417	0.939000	0.37840	0.997000	0.91878	2.033000	0.41136	0.191000	0.20236	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.602	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198	
ITGB3	3690	hgsc.bcm.edu	37	17	45364540	45364540	+	Silent	SNP	T	T	C	rs5919	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45364540T>C	ENST00000559488.1	+	6	898	c.882T>C	c.(880-882)ccT>ccC	p.P294P	ITGB3_ENST00000560629.1_Nonstop_Mutation_p.*283Q|ITGB3_ENST00000435993.2_Silent_p.P247P|ITGB3_ENST00000571680.1_Silent_p.P294P	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	294	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TTGTCCAGCCTAATGACGGGC	0.488													C|||	721	0.14397	0.1498	0.0908	5008	,	,		22457	0.2262		0.0765	False		,,,				2504	0.1585				p.P294P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T882C						PASS	.	C		636,3770	767.4+/-413.5	51,534,1618	175.0	119.0	138.0		882	3.1	1.0	17	dbSNP_52	138	641,7959	790.2+/-407.6	23,595,3682	no	coding-synonymous	ITGB3	NM_000212.2		74,1129,5300	CC,CT,TT		7.4535,14.4349,9.8185		294/789	45364540	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	3690	exon6			CCAGCCTAATGAC		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.882T>C	17.37:g.45364540T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			T|0.878;C|0.122	0.122	strong		0.488	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
MAP3K1	4214	hgsc.bcm.edu	37	5	56178217	56178217	+	Silent	SNP	A	A	C	rs832583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:56178217A>C	ENST00000399503.3	+	14	3190	c.3190A>C	c.(3190-3192)Aga>Cga	p.R1064R		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1064					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)		AAAGCCATCTAGACCTACCCC	0.438													C|||	3547	0.708267	0.7126	0.6527	5008	,	,		23224	0.5704		0.8052	False		,,,				2504	0.7843				p.R1064R		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A3190C						PASS	.	C		2817,951		1053,711,120	79.0	75.0	76.0		3190	5.9	1.0	5	dbSNP_86	76	6759,1451		2785,1189,131	no	coding-synonymous	MAP3K1	NM_005921.1		3838,1900,251	CC,CA,AA		17.6736,25.2389,20.0534		1064/1513	56178217	9576,2402	1884	4105	5989	SO:0001819	synonymous_variant	4214	exon14			CCATCTAGACCTA	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.3190A>C	5.37:g.56178217A>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			A|0.275;C|0.725	0.725	strong		0.438	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
TTC14	151613	hgsc.bcm.edu	37	3	180325487	180325487	+	Silent	SNP	T	T	C	rs9858483	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:180325487T>C	ENST00000296015.4	+	10	1356	c.1224T>C	c.(1222-1224)gcT>gcC	p.A408A	TTC14_ENST00000382584.4_Silent_p.A408A|TTC14_ENST00000412756.2_Silent_p.A408A	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	408							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			ATAAGAAAGCTTTGGCTTTGG	0.289													T|||	349	0.0696885	0.0787	0.1167	5008	,	,		16148	0.0		0.1044	False		,,,				2504	0.0603				p.A408A		Atlas-SNP	.											.	TTC14	112	.	0			c.T1224C						PASS	.	T	,	307,4095	143.5+/-178.5	12,283,1906	60.0	67.0	65.0		1224,1224	3.0	1.0	3	dbSNP_119	65	832,7748	182.0+/-230.6	43,746,3501	no	coding-synonymous,coding-synonymous	TTC14	NM_001042601.2,NM_133462.3	,	55,1029,5407	CC,CT,TT		9.697,6.9741,8.7737	,	408/440,408/771	180325487	1139,11843	2201	4290	6491	SO:0001819	synonymous_variant	151613	exon10			GAAAGCTTTGGCT	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"""Tetratricopeptide (TTC) repeat domain containing"""	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1224T>C	3.37:g.180325487T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	63	0.65625	NM_001042601	G5E9X0|Q6UWJ7|Q8TF22	Silent	SNP	ENST00000296015.4	37	CCDS3237.1																																																																																			T|0.915;C|0.085	0.085	strong		0.289	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462	
HRNR	388697	hgsc.bcm.edu	37	1	152190945	152190945	+	Missense_Mutation	SNP	C	C	T	rs77376932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152190945C>T	ENST00000368801.2	-	3	3235	c.3160G>A	c.(3160-3162)Gag>Aag	p.E1054K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1054					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGCGAGACTCTCGGTGACCT	0.552													C|||	1483	0.296126	0.0242	0.3905	5008	,	,		28894	0.619		0.1402	False		,,,				2504	0.4243				p.E1054K		Atlas-SNP	.											.	HRNR	403	.	0			c.G3160A						PASS	.	C	LYS/GLU	209,4197	126.1+/-163.2	8,193,2002	88.0	100.0	96.0		3160	1.4	0.0	1	dbSNP_131	96	1239,7355	245.3+/-274.2	99,1041,3157	no	missense	HRNR	NM_001009931.1	56	107,1234,5159	TT,TC,CC		14.417,4.7435,11.1385	possibly-damaging	1054/2851	152190945	1448,11552	2203	4297	6500	SO:0001583	missense	388697	exon3			GAGACTCTCGGTG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3160G>A	1.37:g.152190945C>T	ENSP00000357791:p.Glu1054Lys	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	275	157	0.570909	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	569	0.26053113553113555	13	0.026422764227642278	115	0.31767955801104975	330	0.5769230769230769	111	0.14643799472295516	C	8.047	0.765129	0.15914	0.047435	0.14417	ENSG00000197915	ENST00000368801	T	0.02631	4.22	2.38	1.39	0.22231	.	.	.	.	.	T	0.00496	0.0016	N	0.22421	0.69	0.80722	P	0.0	P	0.37233	0.588	B	0.30943	0.122	T	0.36237	-0.9756	8	0.06365	T	0.9	.	7.4102	0.27014	0.0:0.8495:0.0:0.1505	.	1054	Q86YZ3	HORN_HUMAN	K	1054	ENSP00000357791:E1054K	ENSP00000357791:E1054K	E	-	1	0	HRNR	150457569	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.190000	0.09615	0.300000	0.22699	0.306000	0.20318	GAG	C|0.852;T|0.148	0.148	strong		0.552	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
JSRP1	126306	hgsc.bcm.edu	37	19	2255311	2255311	+	Start_Codon_SNP	SNP	C	C	G	rs7250822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2255311C>G	ENST00000300961.6	-	2	67	c.3G>C	c.(1-3)atG>atC	p.M1I	JSRP1_ENST00000586471.2_Start_Codon_SNP_p.M1I	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	1					protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				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)		TTGTCATGGACATGGCTGGAG	0.662													G|||	1176	0.234824	0.475	0.1326	5008	,	,		15298	0.2728		0.0239	False		,,,				2504	0.1605				p.M1I		Atlas-SNP	.											.	JSRP1	18	.	0			c.G3C						PASS	.	G	ILE/MET	1817,2579		378,1061,759	20.0	26.0	24.0		3	1.7	0.2	19	dbSNP_116	24	209,8381		4,201,4090	yes	missense	JSRP1	NM_144616.3	10	382,1262,4849	GG,GC,CC		2.4331,41.333,15.6014	benign	1/332	2255311	2026,10960	2198	4295	6493	SO:0001582	initiator_codon_variant	126306	exon2			CATGGACATGGCT	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.3G>C	19.37:g.2255311C>G	ENSP00000300961:p.Met1Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	401	0.18360805860805862	201	0.40853658536585363	36	0.09944751381215469	147	0.256993006993007	17	0.022427440633245383	G	0.003	-2.464928	0.00171	0.41333	0.024331	ENSG00000167476	ENST00000300961	T	0.16897	2.31	3.87	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46775	-0.9167	7	0.35671	T	0.21	.	4.0592	0.09831	0.2189:0.1962:0.5849:0.0	rs7250822;rs7250822	1	Q96MG2	JSPR1_HUMAN	I	1	ENSP00000300961:M1I	ENSP00000300961:M1I	M	-	3	0	JSRP1	2206311	0.002000	0.14202	0.246000	0.24233	0.034000	0.12701	-0.003000	0.12901	0.096000	0.17463	-0.357000	0.07601	ATG	C|0.836;G|0.164	0.164	strong		0.662	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	Missense_Mutation
DNAH3	55567	hgsc.bcm.edu	37	16	20974740	20974740	+	Missense_Mutation	SNP	C	C	T	rs111539520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:20974740C>T	ENST00000261383.3	-	53	10465	c.10466G>A	c.(10465-10467)cGg>cAg	p.R3489Q	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3489	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)			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)		AATGAACTCCCGGACCGCTGG	0.507													C|||	40	0.00798722	0.0015	0.0173	5008	,	,		22273	0.0		0.0229	False		,,,				2504	0.0031				p.R3489Q		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,-1,2	DNAH3	1142	2	0			c.G10466A						PASS	.	C	GLN/ARG	44,4358	46.0+/-80.4	0,44,2157	94.0	84.0	87.0		10466	0.9	0.0	16	dbSNP_132	87	344,8256	116.8+/-176.5	6,332,3962	yes	missense	DNAH3	NM_017539.1	43	6,376,6119	TT,TC,CC		4.0,0.9995,2.9842	benign	3489/4117	20974740	388,12614	2201	4300	6501	SO:0001583	missense	55567	exon53			AACTCCCGGACCG	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.10466G>A	16.37:g.20974740C>T	ENSP00000261383:p.Arg3489Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	30	0.013736263736263736	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	22	0.029023746701846966	C	2.749	-0.260560	0.05791	0.009995	0.04	ENSG00000158486	ENST00000261383	T	0.08807	3.05	5.52	0.898	0.19264	Dynein heavy chain (1);	0.139369	0.48286	N	0.000189	T	0.00384	0.0012	N	0.00321	-1.65	0.21627	N	0.999615	B	0.14012	0.009	B	0.08055	0.003	T	0.46020	-0.9221	10	0.02654	T	1	.	7.0178	0.24897	0.0:0.3119:0.0:0.6881	.	3489	Q8TD57	DYH3_HUMAN	Q	3489	ENSP00000261383:R3489Q	ENSP00000261383:R3489Q	R	-	2	0	DNAH3	20882241	0.013000	0.17824	0.007000	0.13788	0.003000	0.03518	1.007000	0.29860	0.290000	0.22444	-0.136000	0.14681	CGG	C|0.977;T|0.023	0.023	strong		0.507	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56763316	56763316	+	Silent	SNP	G	G	A	rs1565376	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56763316G>A	ENST00000296315.3	-	10	1731	c.1563C>T	c.(1561-1563)caC>caT	p.H521H	ARHGEF3_ENST00000497267.1_Silent_p.H492H|ARHGEF3_ENST00000338458.4_Silent_p.H553H|ARHGEF3_ENST00000496106.1_Silent_p.H527H|ARHGEF3_ENST00000413728.2_Silent_p.H527H	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	521					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)		TACTTTCACCGTGCCTGCTGT	0.507													A|||	3657	0.730232	0.8805	0.6585	5008	,	,		22435	0.8542		0.4235	False		,,,				2504	0.7658				p.H553H		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.C1659T						PASS	.	A	,,	3624,782	316.3+/-294.6	1489,646,68	198.0	146.0	164.0		1659,1581,1563	-4.0	0.0	3	dbSNP_88	164	3606,4994	626.5+/-397.9	729,2148,1423	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	2218,2794,1491	AA,AG,GG		41.9302,17.7485,44.4103	,,	553/559,527/533,521/527	56763316	7230,5776	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon13			TTCACCGTGCCTG	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.1563C>T	3.37:g.56763316G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	198	197	0.99495	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			G|0.420;A|0.580	0.580	strong		0.507	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
MACF1	23499	hgsc.bcm.edu	37	1	39908506	39908506	+	Missense_Mutation	SNP	G	G	A	rs587404	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:39908506G>A	ENST00000372915.3	+	77	19009	c.18922G>A	c.(18922-18924)Gcc>Acc	p.A6308T	MACF1_ENST00000564288.1_Missense_Mutation_p.A6409T|MACF1_ENST00000361689.2_Missense_Mutation_p.A4350T|MACF1_ENST00000545844.1_Missense_Mutation_p.A4350T|MACF1_ENST00000567887.1_Missense_Mutation_p.A6446T|MACF1_ENST00000317713.7_Missense_Mutation_p.A4350T|MACF1_ENST00000539005.1_Missense_Mutation_p.A4220T|MACF1_ENST00000289893.4_Missense_Mutation_p.A4852T			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6308			A -> T (in dbSNP:rs587404).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CCGTTTGGAAGCCATGAACCA	0.502													A|||	1723	0.34405	0.5106	0.3156	5008	,	,		20152	0.3462		0.2823	False		,,,				2504	0.2004				p.A4350T		Atlas-SNP	.											MACF1_ENST00000361689,NS,carcinoid-endocrine_tumour,-1,2	MACF1	909	2	0			c.G13048A						PASS	.	A	THR/ALA,THR/ALA	2069,2337	607.1+/-390.9	472,1125,606	63.0	54.0	57.0		14554,13048	5.8	1.0	1	dbSNP_83	57	2637,5963	686.1+/-404.1	418,1801,2081	yes	missense,missense	MACF1	NM_033044.3,NM_012090.4	58,58	890,2926,2687	AA,AG,GG		30.6628,46.9587,36.1833	benign,benign	4852/5939,4350/5431	39908506	4706,8300	2203	4300	6503	SO:0001583	missense	23499	exon75			TTGGAAGCCATGA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18922G>A	1.37:g.39908506G>A	ENSP00000362006:p.Ala6308Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		770|770	0.3525641025641026|0.3525641025641026	259|259	0.5264227642276422|0.5264227642276422	117|117	0.32320441988950277|0.32320441988950277	192|192	0.3356643356643357|0.3356643356643357	202|202	0.26649076517150394|0.26649076517150394	A|A	8.201|8.201	0.798095|0.798095	0.16397|0.16397	0.469587|0.469587	0.306628|0.306628	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.51574|.	1.3;0.7;1.3;1.3;1.3;0.7|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.195229|.	0.36066|.	N|.	0.002819|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01874|0.01874	-0.695|-0.695	0.40421|0.40421	P|P	0.02015699999999998|0.02015699999999998	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.41822|0.41822	-0.9487|-0.9487	9|4	0.02654|.	T|.	1|.	.|.	9.6911|9.6911	0.40129|0.40129	0.8135:0.0:0.1865:0.0|0.8135:0.0:0.1865:0.0	rs587404;rs52831614;rs58672434;rs587404|rs587404;rs52831614;rs58672434;rs587404	6308;4350|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	T|N	4350;6308;4350;4350;4220;4852|3353	ENSP00000439537:A4350T;ENSP00000362006:A6308T;ENSP00000354573:A4350T;ENSP00000313438:A4350T;ENSP00000444364:A4220T;ENSP00000289893:A4852T|.	ENSP00000289893:A4852T|.	A|S	+|+	1|2	0|0	MACF1|MACF1	39681093|39681093	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.976000|0.976000	0.68499|0.68499	1.859000|1.859000	0.39418|0.39418	1.035000|1.035000	0.39972|0.39972	-0.254000|-0.254000	0.11334|0.11334	GCC|AGC	G|0.640;A|0.360	0.360	strong		0.502	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
APOB	338	hgsc.bcm.edu	37	2	21225753	21225753	+	Missense_Mutation	SNP	C	C	T	rs1042031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21225753C>T	ENST00000233242.1	-	29	12668	c.12541G>A	c.(12541-12543)Gaa>Aaa	p.E4181K	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4181			E -> K (in dbSNP:rs1042031). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2994225, ECO:0000269|PubMed:3030729, ECO:0000269|PubMed:3464946, ECO:0000269|PubMed:3763409, ECO:0000269|PubMed:3841481}.		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)					ATATGGAATTCTTGAGTAACT	0.463													C|||	640	0.127796	0.1611	0.1196	5008	,	,		19930	0.0446		0.2127	False		,,,				2504	0.0869				p.E4181K		Atlas-SNP	.											.	APOB	761	.	0			c.G12541A						PASS	.	C	LYS/GLU	652,3754	277.5+/-273.7	34,584,1585	66.0	64.0	64.0		12541	0.2	0.0	2	dbSNP_86	64	1508,7092	283.9+/-296.4	137,1234,2929	yes	missense	APOB	NM_000384.2	56	171,1818,4514	TT,TC,CC		17.5349,14.798,16.6077	benign	4181/4564	21225753	2160,10846	2203	4300	6503	SO:0001583	missense	338	exon29			GGAATTCTTGAGT	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.12541G>A	2.37:g.21225753C>T	ENSP00000233242:p.Glu4181Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	333	0.15247252747252749	97	0.19715447154471544	58	0.16022099447513813	21	0.03671328671328671	157	0.20712401055408972	C	13.89	2.373145	0.42105	0.14798	0.175349	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00737	5.76	5.99	0.147	0.14838	.	0.748815	0.12158	N	0.494257	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	8.000000000008E-6	B	0.15141	0.012	B	0.13407	0.009	T	0.33085	-0.9882	9	0.27082	T	0.32	.	5.4344	0.16472	0.0:0.5218:0.1308:0.3473	rs1042031;rs3181511;rs17247312;rs17398356;rs52807383;rs60017641;rs1042031	4181	P04114	APOB_HUMAN	K	4181	ENSP00000233242:E4181K	ENSP00000233242:E4181K	E	-	1	0	APOB	21079258	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.080000	0.11339	-0.260000	0.09418	-0.140000	0.14226	GAA	C|0.848;T|0.152	0.152	strong		0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
TJP3	27134	hgsc.bcm.edu	37	19	3747891	3747891	+	Missense_Mutation	SNP	G	G	A	rs144472063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3747891G>A	ENST00000541714.2	+	19	2884	c.2422G>A	c.(2422-2424)Gag>Aag	p.E808K	TJP3_ENST00000539908.2_Missense_Mutation_p.E772K|TJP3_ENST00000589378.1_Missense_Mutation_p.E817K|TJP3_ENST00000382008.3_Missense_Mutation_p.E822K|TJP3_ENST00000262968.9_Missense_Mutation_p.E841K|TJP3_ENST00000587686.1_Missense_Mutation_p.E827K	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	808					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCGACTACGAGACGGACGG	0.677													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		16795	0.0		0.0	False		,,,				2504	0.0				p.E817K		Atlas-SNP	.											.	TJP3	79	.	0			c.G2449A						PASS	.	G	LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	35.0	30.0	32.0		2521	4.5	0.8	19	dbSNP_134	32	0,8596		0,0,4298	no	missense	TJP3	NM_014428.1	56	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	841/953	3747891	1,12999	2202	4298	6500	SO:0001583	missense	27134	exon19			GACTACGAGACGG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2422G>A	19.37:g.3747891G>A	ENSP00000439278:p.Glu808Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.2	4.114574	0.77210	2.27E-4	0.0	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.76;2.93;2.74;2.81	4.54	4.54	0.55810	.	0.112463	0.64402	D	0.000016	T	0.39410	0.1077	M	0.77820	2.39	0.51482	D	0.999924	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;P;D	0.76575	0.946;0.988;0.771;0.946	T	0.40850	-0.9541	10	0.87932	D	0	.	16.2624	0.82553	0.0:0.0:1.0:0.0	.	827;841;822;808	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	K	808;772;822;841	ENSP00000439278:E808K;ENSP00000439991:E772K;ENSP00000371438:E822K;ENSP00000262968:E841K	ENSP00000262968:E841K	E	+	1	0	TJP3	3698891	1.000000	0.71417	0.841000	0.33234	0.048000	0.14542	7.375000	0.79646	2.062000	0.61559	0.561000	0.74099	GAG	G|1.000;A|0.000	0.000	strong		0.677	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
ZSWIM4	65249	hgsc.bcm.edu	37	19	13941597	13941597	+	Silent	SNP	C	C	T	rs112676900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13941597C>T	ENST00000254323.2	+	13	2892	c.2703C>T	c.(2701-2703)gcC>gcT	p.A901A	ZSWIM4_ENST00000440752.2_Silent_p.A735A	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	901							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)			CACGCCGGGCCGCCAAGCCAC	0.682													C|||	465	0.0928514	0.1142	0.0591	5008	,	,		10708	0.0645		0.0646	False		,,,				2504	0.1462				p.A901A		Atlas-SNP	.											ZSWIM4,NS,carcinoma,0,1	ZSWIM4	69	1	0			c.C2703T						scavenged	.	C		409,3935		21,367,1784	17.0	22.0	20.0		2703	-8.7	0.0	19	dbSNP_132	20	513,7955		11,491,3732	no	coding-synonymous	ZSWIM4	NM_023072.2		32,858,5516	TT,TC,CC		6.0581,9.4153,7.1964		901/990	13941597	922,11890	2172	4234	6406	SO:0001819	synonymous_variant	65249	exon13			CCGGGCCGCCAAG	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.2703C>T	19.37:g.13941597C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_023072		Silent	SNP	ENST00000254323.2	37	CCDS32924.1																																																																																			C|0.927;T|0.073	0.073	strong		0.682	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
OR2V1	26693	hgsc.bcm.edu	37	5	180551937	180551937	+	Missense_Mutation	SNP	C	C	T	rs10073017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:180551937C>T	ENST00000329365.2	-	1	367	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_001258283.1	NP_001245212.1	Q8NHB1	OR2V1_HUMAN	olfactory receptor, family 2, subfamily V, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(4)	4						GGCCACGTAGCGGTCATAAGC	0.512													c|||	560	0.111821	0.3154	0.0677	5008	,	,		21207	0.001		0.0626	False		,,,				2504	0.0327				p.R123H		Atlas-SNP	.											.	OR2V1	20	.	0			c.G368A						PASS	.																																			SO:0001583	missense	26693	exon1			ACGTAGCGGTCAT	AB065465	CCDS58992.1	5q35.3	2012-08-09		2004-03-10	ENSG00000185372	ENSG00000185372		"""GPCR / Class A : Olfactory receptors"""	8280	protein-coding gene	gene with protein product				OR2V1P			Standard	NM_001258283		Approved	OST265	uc031smg.1	Q8NHB1	OTTHUMG00000162118	ENST00000329365.2:c.368G>A	5.37:g.180551937C>T	ENSP00000404102:p.Arg123His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001258283		Missense_Mutation	SNP	ENST00000329365.2	37	CCDS58992.1	245	0.11217948717948718	168	0.34146341463414637	29	0.08011049723756906	0	0.0	48	0.0633245382585752	.	15.66	2.900509	0.52227	.	.	ENSG00000185372	ENST00000329365	T	0.77489	-1.1	4.8	3.94	0.45596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.28991	P	0.88806	.	.	.	.	.	.	T	0.00686	-1.1610	5	0.72032	D	0.01	.	11.1029	0.48186	0.0:0.9093:0.0:0.0907	rs10073017;rs59710711;rs10073017	.	.	.	H	123	ENSP00000404102:R123H	ENSP00000404102:R123H	R	-	2	0	OR2V1	180484543	0.999000	0.42202	0.821000	0.32701	0.801000	0.45260	2.905000	0.48727	1.241000	0.43820	0.436000	0.28706	CGC	C|0.880;T|0.120	0.120	strong		0.512	OR2V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367367.1		
ITIH6	347365	hgsc.bcm.edu	37	X	54781530	54781530	+	Missense_Mutation	SNP	C	C	G	rs17316491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:54781530C>G	ENST00000218436.6	-	9	3151	c.3122G>C	c.(3121-3123)tGg>tCg	p.W1041S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1041			W -> S (in dbSNP:rs17316491).		hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATTGCCATCCCAGTTTGGACT	0.493													C|||	131	0.034702	0.0045	0.0389	3775	,	,		13733	0.0		0.0875	False		,,,				2504	0.0102				p.W1041S		Atlas-SNP	.											.	.	.	.	0			c.G3122C						PASS	.	C	SER/TRP	48,3787		0,43,5,1589,566	92.0	76.0	81.0		3122	1.6	0.1	X	dbSNP_123	81	639,6089		21,413,184,1994,1688	yes	missense	ITIH5L	NM_198510.2	177	21,456,189,3583,2254	GG,GC,G,CC,C		9.4976,1.2516,6.5038	probably-damaging	1041/1314	54781530	687,9876	2203	4300	6503	SO:0001583	missense	347365	exon9			CCATCCCAGTTTG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3122G>C	X.37:g.54781530C>G	ENSP00000218436:p.Trp1041Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	97	0.05846895720313442	5	0.010245901639344262	11	0.031073446327683617	0	0.0	54	0.07563025210084033	C	3.999	-0.002876	0.07773	0.012516	0.094976	ENSG00000102313	ENST00000218436	T	0.02323	4.34	1.58	1.58	0.23477	.	0.763532	0.10135	U	0.711568	T	0.00109	0.0003	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	P	0.48694	0.914	B	0.35240	0.198	T	0.48559	-0.9025	9	0.22706	T	0.39	.	6.0319	0.19684	0.0:1.0:0.0:0.0	rs17316491;rs52814299;rs17316491	1041	Q6UXX5	ITH5L_HUMAN	S	1041	ENSP00000218436:W1041S	ENSP00000218436:W1041S	W	-	2	0	ITIH5L	54798255	0.713000	0.27926	0.062000	0.19696	0.473000	0.32948	2.380000	0.44327	1.069000	0.40788	0.287000	0.19450	TGG	C|0.935;0|0.004	.	strong		0.493	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
CDKN1A	1026	hgsc.bcm.edu	37	6	36652228	36652228	+	Missense_Mutation	SNP	G	G	A	rs148679597		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:36652228G>A	ENST00000405375.1	+	2	585	c.350G>A	c.(349-351)tGt>tAt	p.C117Y	CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.C117Y|CDKN1A_ENST00000448526.2_Missense_Mutation_p.C151Y|CDKN1A_ENST00000244741.5_Missense_Mutation_p.C117Y	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	117					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						TCACTGTCTTGTACCCTTGTG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.C117Y		Atlas-SNP	.											.	CDKN1A	27	.	0			c.G350A						PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS	3,4403	6.2+/-15.9	0,3,2200	45.0	44.0	44.0		350,350,350,350	5.2	1.0	6	dbSNP_134	44	30,8570	19.8+/-62.0	0,30,4270	yes	missense,missense,missense,missense	CDKN1A	NM_000389.4,NM_001220777.1,NM_001220778.1,NM_078467.2	194,194,194,194	0,33,6470	AA,AG,GG		0.3488,0.0681,0.2537	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	117/165,117/165,117/165,117/165	36652228	33,12973	2203	4300	6503	SO:0001583	missense	1026	exon2			TGTCTTGTACCCT	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.350G>A	6.37:g.36652228G>A	ENSP00000384849:p.Cys117Tyr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441009	0.43326	6.81E-4	0.003488	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000010	T	0.81240	0.4781	L	0.49126	1.545	0.48040	D	0.999578	D;D;D	0.69078	0.997;0.995;0.997	D;D;D	0.73380	0.98;0.916;0.956	T	0.81911	-0.0716	10	0.56958	D	0.05	-36.2508	14.1752	0.65537	0.0:0.0:1.0:0.0	.	151;117;117	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Y	151;117;117;117	ENSP00000409259:C151Y;ENSP00000244741:C117Y;ENSP00000384849:C117Y;ENSP00000362815:C117Y	ENSP00000244741:C117Y	C	+	2	0	CDKN1A	36760206	0.127000	0.22367	0.981000	0.43875	0.040000	0.13550	1.857000	0.39399	2.724000	0.93272	0.561000	0.74099	TGT	G|0.998;A|0.002	0.002	strong		0.642	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
SLC52A3	113278	hgsc.bcm.edu	37	20	745963	745963	+	Silent	SNP	G	G	A	rs3746807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:745963G>A	ENST00000217254.7	-	2	697	c.456C>T	c.(454-456)ccC>ccT	p.P152P	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Silent_p.P152P	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	152					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)										CCACCAGGGCGGGCAAGAGGC	0.597													A|||	491	0.0980431	0.0968	0.0663	5008	,	,		17870	0.1637		0.0924	False		,,,				2504	0.0603				p.P152P		Atlas-SNP	.											.	.	.	.	0			c.C456T						PASS	.	A		494,3912	780.3+/-414.4	22,450,1731	68.0	65.0	66.0		456	0.1	1.0	20	dbSNP_107	66	888,7712	778.5+/-407.7	60,768,3472	no	coding-synonymous	C20orf54	NM_033409.3		82,1218,5203	AA,AG,GG		10.3256,11.212,10.6259		152/470	745963	1382,11624	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon2			CAGGGCGGGCAAG	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.456C>T	20.37:g.745963G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.885;A|0.115	0.115	strong		0.597	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
NUAK2	81788	hgsc.bcm.edu	37	1	205273142	205273142	+	Silent	SNP	G	G	C	rs41264881	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:205273142G>C	ENST00000367157.3	-	7	1449	c.1323C>G	c.(1321-1323)ccC>ccG	p.P441P		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			TGGGGAGCAGGGGGGCAGCCT	0.627													G|||	382	0.076278	0.0461	0.1571	5008	,	,		16405	0.001		0.1501	False		,,,				2504	0.0613				p.P441P		Atlas-SNP	.											NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	0			c.C1323G						PASS	.	G		321,4085	160.3+/-192.7	10,301,1892	39.0	39.0	39.0		1323	3.1	0.5	1	dbSNP_127	39	1318,7282	246.1+/-274.7	97,1124,3079	no	coding-synonymous	NUAK2	NM_030952.1		107,1425,4971	CC,CG,GG		15.3256,7.2855,12.6019		441/629	205273142	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			GAGCAGGGGGGCA	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1323C>G	1.37:g.205273142G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	109	68	0.623853	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.874;C|0.126	0.126	strong		0.627	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
EVI5L	115704	hgsc.bcm.edu	37	19	7913974	7913974	+	Silent	SNP	T	T	C	rs555609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7913974T>C	ENST00000270530.4	+	4	691	c.495T>C	c.(493-495)caT>caC	p.H165H	EVI5L_ENST00000538904.2_Silent_p.H165H	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	165	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						ACCCGGAACATGAGTTCTTCA	0.622													C|||	3514	0.701677	0.5719	0.8141	5008	,	,		19492	0.5923		0.7565	False		,,,				2504	0.8538				p.H165H		Atlas-SNP	.											.	EVI5L	43	.	0			c.T495C						PASS	.	C	,	2741,1665	482.3+/-359.4	847,1047,309	31.0	28.0	29.0		495,495	-4.0	0.9	19	dbSNP_83	29	6565,2035	333.2+/-320.4	2510,1545,245	no	coding-synonymous,coding-synonymous	EVI5L	NM_001159944.1,NM_145245.3	,	3357,2592,554	CC,CT,TT		23.6628,37.7894,28.4484	,	165/806,165/795	7913974	9306,3700	2203	4300	6503	SO:0001819	synonymous_variant	115704	exon3			GGAACATGAGTTC	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.495T>C	19.37:g.7913974T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			T|0.304;C|0.695	0.695	strong		0.622	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245	
ZNF480	147657	hgsc.bcm.edu	37	19	52825235	52825235	+	Silent	SNP	A	A	G	rs8102373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52825235A>G	ENST00000595962.1	+	5	798	c.732A>G	c.(730-732)tcA>tcG	p.S244S	ZNF480_ENST00000490272.1_3'UTR|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000334564.7_Silent_p.S201S|ZNF480_ENST00000335090.6_Silent_p.S167S	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		GTCGCAATTCACACCTTGCAG	0.368													A|||	2636	0.526358	0.5371	0.5101	5008	,	,		20260	0.3998		0.6123	False		,,,				2504	0.5654				p.S244S		Atlas-SNP	.											ZNF480_ENST00000468240,NS,carcinoma,+1,2	ZNF480	123	2	0			c.A732G						PASS	.	A		2320,2086	586.1+/-386.4	622,1076,505	41.0	41.0	41.0		732	-2.0	0.0	19	dbSNP_116	41	5037,3563	616.4+/-396.5	1472,2093,735	no	coding-synonymous	ZNF480	NM_144684.2		2094,3169,1240	GG,GA,AA		41.4302,47.3445,43.4338		244/536	52825235	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	147657	exon5			CAATTCACACCTT	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.732A>G	19.37:g.52825235A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Silent	SNP	ENST00000595962.1	37	CCDS12850.2																																																																																			A|0.449;G|0.551	0.551	strong		0.368	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
PPP1R36	145376	hgsc.bcm.edu	37	14	65054858	65054858	+	Silent	SNP	T	T	C	rs723594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:65054858T>C	ENST00000298705.1	+	11	1023	c.927T>C	c.(925-927)gcT>gcC	p.A309A	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	309					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTAAAAAAGCTATCAACATGC	0.428													C|||	213	0.0425319	0.0469	0.0461	5008	,	,		21889	0.0129		0.0845	False		,,,				2504	0.0215				p.A309A		Atlas-SNP	.											.	.	.	.	0			c.T927C						PASS	.	C		198,4208	808.1+/-415.9	4,190,2009	100.0	99.0	99.0		927	3.2	1.0	14	dbSNP_86	99	670,7930	788.6+/-407.6	30,610,3660	no	coding-synonymous	C14orf50	NM_172365.1		34,800,5669	CC,CT,TT		7.7907,4.4939,6.6738		309/423	65054858	868,12138	2203	4300	6503	SO:0001819	synonymous_variant	145376	exon11			AAAAGCTATCAAC		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.927T>C	14.37:g.65054858T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_172365	Q6NTH6	Silent	SNP	ENST00000298705.1	37	CCDS9767.1																																																																																			T|0.940;C|0.060	0.060	strong		0.428	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
UROC1	131669	hgsc.bcm.edu	37	3	126219627	126219627	+	Silent	SNP	G	G	A	rs34025926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	117	37	0.316239	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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607299	84607299	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84607299C>T	ENST00000344803.2	+	4	1961	c.1914C>T	c.(1912-1914)ggC>ggT	p.G638G		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	638					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G638G(2)									GTTTGTGGGGCTTACCCTCTG	0.478																																					p.G638G		Atlas-SNP	.											FAM75D4,right_upper_lobe,carcinoma,0,2	.	.	2	2	Substitution - coding silent(2)	lung(2)	c.C1914T						scavenged	.						101.0	97.0	99.0					9																	84607299		1860	4112	5972	SO:0001819	synonymous_variant	389763	exon4			GTGGGGCTTACCC		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.1914C>T	9.37:g.84607299C>T		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	105	4	0.0380952	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			.	.	none		0.478	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
TRUB2	26995	hgsc.bcm.edu	37	9	131084628	131084628	+	Silent	SNP	C	C	A	rs11539570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131084628C>A	ENST00000372890.4	-	1	393	c.60G>T	c.(58-60)ggG>ggT	p.G20G	COQ4_ENST00000609948.1_5'Flank|TRUB2_ENST00000460320.1_5'UTR|COQ4_ENST00000608951.1_5'Flank|COQ4_ENST00000300452.3_5'Flank|TRUB2_ENST00000546104.1_5'Flank|COQ4_ENST00000372875.3_5'Flank	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	20					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						TCCATTTTAGCCCCGGGGGCT	0.577													C|||	39	0.00778754	0.0	0.0086	5008	,	,		16888	0.0		0.0129	False		,,,				2504	0.0204				p.G20G		Atlas-SNP	.											.	TRUB2	26	.	0			c.G60T						PASS	.	C		16,4390	22.3+/-47.3	0,16,2187	82.0	82.0	82.0		60	-1.1	0.7	9	dbSNP_120	82	125,8475	63.5+/-125.6	1,123,4176	no	coding-synonymous	TRUB2	NM_015679.1		1,139,6363	AA,AC,CC		1.4535,0.3631,1.0841		20/332	131084628	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	26995	exon1			TTTTAGCCCCGGG	AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"""TruB pseudouridine (psi) synthase homolog 2 (E. coli)"""			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.60G>T	9.37:g.131084628C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_015679	B7Z7G5	Silent	SNP	ENST00000372890.4	37	CCDS6897.1																																																																																			T|0.008;C|0.982;A|0.010	0.010	strong		0.577	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181393	19181393	+	Missense_Mutation	SNP	T	T	C	rs35874116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19181393T>C	ENST00000375371.3	-	3	592	c.571A>G	c.(571-573)Atc>Gtc	p.I191V	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	191			I -> V (in dbSNP:rs35874116). {ECO:0000269|PubMed:11917125}.		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ATGGCCTCGATGTGGTGGTCG	0.612													C|||	1337	0.266973	0.3389	0.2695	5008	,	,		20996	0.1042		0.3241	False		,,,				2504	0.2771				p.I191V		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,1	TAS1R2	134	1	0			c.A571G						PASS	.	C	VAL/ILE	1349,3057	684.6+/-404.4	206,937,1060	42.0	42.0	42.0		571	-4.1	0.0	1	dbSNP_126	42	2845,5755	666.6+/-402.4	461,1923,1916	yes	missense	TAS1R2	NM_152232.2	29	667,2860,2976	CC,CT,TT		33.0814,30.6173,32.2467	benign	191/840	19181393	4194,8812	2203	4300	6503	SO:0001583	missense	80834	exon3			CCTCGATGTGGTG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.571A>G	1.37:g.19181393T>C	ENSP00000364520:p.Ile191Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	581	0.266025641025641	167	0.3394308943089431	112	0.30939226519337015	57	0.09965034965034965	245	0.3232189973614776	C	0.004	-2.354529	0.00217	0.306173	0.330814	ENSG00000179002	ENST00000375371	D	0.82526	-1.62	4.9	-4.08	0.03963	Extracellular ligand-binding receptor (1);	1.331270	0.05169	N	0.499177	T	0.00012	0.0000	N	0.04245	-0.25	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.10405	-1.0631	9	0.02654	T	1	.	10.7064	0.45958	0.0:0.5932:0.1201:0.2867	rs35874116	191	Q8TE23	TS1R2_HUMAN	V	191	ENSP00000364520:I191V	ENSP00000364520:I191V	I	-	1	0	TAS1R2	19053980	0.000000	0.05858	0.012000	0.15200	0.008000	0.06430	-0.421000	0.07053	-1.020000	0.03354	-2.680000	0.00142	ATC	T|0.700;C|0.300	0.300	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
EIF2B3	8891	hgsc.bcm.edu	37	1	45340342	45340342	+	Intron	SNP	A	A	C	rs77068026	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45340342A>C	ENST00000360403.2	-	10	1329				EIF2B3_ENST00000372183.3_Missense_Mutation_p.S404A	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa						cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|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)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					GTACAGGGGGAAACATACCCT	0.408													A|||	78	0.0155751	0.0	0.0807	5008	,	,		19961	0.001		0.0129	False		,,,				2504	0.0082				p.S404A	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.T1210G						PASS	.	A	ALA/SER,	21,4385	28.1+/-56.4	0,21,2182	114.0	105.0	108.0		1210,	2.5	0.5	1	dbSNP_131	108	128,8472	65.6+/-127.9	0,128,4172	yes	missense,intron	EIF2B3	NM_001166588.1,NM_020365.3	99,	0,149,6354	CC,CA,AA		1.4884,0.4766,1.1456	,	404/413,	45340342	149,12857	2203	4300	6503	SO:0001627	intron_variant	8891	exon10			AGGGGGAAACATA	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"""eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"""			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.1202+7T>G	1.37:g.45340342A>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001166588	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	37	CCDS517.1	31	0.014194139194139194	0	0.0	17	0.04696132596685083	1	0.0017482517482517483	13	0.017150395778364115	A	10.25	1.299497	0.23650	0.004766	0.014884	ENSG00000070785	ENST00000372183	D	0.88896	-2.44	4.79	2.49	0.30216	.	.	.	.	.	T	0.44726	0.1307	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58482	-0.7629	8	0.46703	T	0.11	.	2.5858	0.04830	0.6116:0.1448:0.0851:0.1584	.	404	Q9NR50-2	.	A	404	ENSP00000361257:S404A	ENSP00000361257:S404A	S	-	1	0	EIF2B3	45112929	0.919000	0.31177	0.458000	0.27068	0.510000	0.34073	1.679000	0.37597	0.921000	0.36994	0.533000	0.62120	TCC	A|0.985;C|0.015	0.015	strong		0.408	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365	
IGFN1	91156	hgsc.bcm.edu	37	1	201183402	201183402	+	Silent	SNP	T	T	C	rs1568810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201183402T>C	ENST00000335211.4	+	13	8956	c.8826T>C	c.(8824-8826)ccT>ccC	p.P2942P	IGFN1_ENST00000451870.2_Silent_p.P485P|IGFN1_ENST00000295591.8_Silent_p.P102P	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	58	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	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	
LRRC16B	90668	hgsc.bcm.edu	37	14	24526206	24526206	+	Silent	SNP	T	T	C	rs45484702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	87	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	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	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892271	62892271	+	Missense_Mutation	SNP	A	A	T	rs62071406		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62892271A>T	ENST00000584306.1	-	3	1635	c.1105T>A	c.(1105-1107)Tct>Act	p.S369T	RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000339474.5_Intron|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.S369T|RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	369						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TCCCTAGAAGACTCAGAAGGC	0.537																																					p.S369T		Atlas-SNP	.											LRRC37A3,NS,haematopoietic_neoplasm,0,1	LRRC37A3	75	1	0			c.T1105A						scavenged	.						25.0	32.0	30.0					17																	62892271		1973	4078	6051	SO:0001583	missense	374819	exon3			TAGAAGACTCAGA	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1105T>A	17.37:g.62892271A>T	ENSP00000464535:p.Ser369Thr	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	473	204	0.43129	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	3.342	-0.134342	0.06711	.	.	ENSG00000176809	ENST00000319651	T	0.58506	0.33	2.69	-3.39	0.04868	.	.	.	.	.	T	0.43010	0.1228	L	0.31294	0.92	0.09310	N	1	P	0.52061	0.95	P	0.46718	0.525	T	0.36890	-0.9729	9	0.56958	D	0.05	.	3.9507	0.09368	0.5048:0.1903:0.3049:0.0	.	369	O60309	L37A3_HUMAN	T	369	ENSP00000325713:S369T	ENSP00000325713:S369T	S	-	1	0	LRRC37A3	60322733	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.093000	0.03362	-0.631000	0.05560	0.234000	0.17832	TCT	.	.	weak		0.537	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
SH3BP1	23616	hgsc.bcm.edu	37	22	38046718	38046718	+	Silent	SNP	A	A	G	rs762987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38046718A>G	ENST00000357436.4	+	16	1897	c.1584A>G	c.(1582-1584)gcA>gcG	p.A528A	SH3BP1_ENST00000599616.1_Silent_p.A464A|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	528					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)					TGGCTTCAGCAGCTACCAAGG	0.642													G|||	778	0.155351	0.3759	0.0735	5008	,	,		15112	0.0149		0.0626	False		,,,				2504	0.1554				p.A528A		Atlas-SNP	.											.	SH3BP1	41	.	0			c.A1584G						PASS	.	G		1518,2888		272,974,957	27.0	31.0	30.0		1584	-0.9	0.0	22	dbSNP_86	30	654,7946		29,596,3675	no	coding-synonymous	SH3BP1	NM_018957.3		301,1570,4632	GG,GA,AA		7.6047,34.453,16.7		528/702	38046718	2172,10834	2203	4300	6503	SO:0001819	synonymous_variant	23616	exon16			TTCAGCAGCTACC		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.1584A>G	22.37:g.38046718A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			A|0.859;G|0.141	0.141	strong		0.642	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
PERP	64065	hgsc.bcm.edu	37	6	138413269	138413269	+	Silent	SNP	A	A	G	rs648396	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:138413269A>G	ENST00000421351.3	-	3	662	c.492T>C	c.(490-492)atT>atC	p.I164I		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	164					activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		AGGCACAGCCAATCAGGATAA	0.522													G|||	3166	0.632188	0.5545	0.5288	5008	,	,		18524	0.7232		0.5775	False		,,,				2504	0.773				p.I164I		Atlas-SNP	.											.	PERP	15	.	0			c.T492C						PASS	.	G		2342,2064	569.5+/-382.6	628,1086,489	83.0	78.0	80.0		492	-10.2	0.1	6	dbSNP_83	80	4752,3848	541.9+/-384.1	1313,2126,861	no	coding-synonymous	PERP	NM_022121.4		1941,3212,1350	GG,GA,AA		44.7442,46.8452,45.4559		164/194	138413269	7094,5912	2203	4300	6503	SO:0001819	synonymous_variant	64065	exon3			ACAGCCAATCAGG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.492T>C	6.37:g.138413269A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Silent	SNP	ENST00000421351.3	37	CCDS5188.1																																																																																			A|0.435;G|0.565	0.565	strong		0.522	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
POMT1	10585	hgsc.bcm.edu	37	9	134385435	134385435	+	Nonsense_Mutation	SNP	C	C	T	rs386738991|rs3887873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134385435C>T	ENST00000372228.3	+	8	930	c.751C>T	c.(751-753)Cag>Tag	p.Q251*	POMT1_ENST00000404875.2_Intron|POMT1_ENST00000402686.3_Intron|POMT1_ENST00000541219.1_Intron|POMT1_ENST00000354713.4_Intron|POMT1_ENST00000341012.7_Intron|POMT1_ENST00000419118.2_Intron|POMT1_ENST00000423007.1_Intron	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	251			Q -> R (in dbSNP:rs2296949). {ECO:0000269|PubMed:10366449, ECO:0000269|PubMed:14702039}.|Q -> W (requires 2 nucleotide substitutions; dbSNP:rs3887873).		carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GGGGCAGATGCAGATGTCACA	0.572													C|||	394	0.0786741	0.1248	0.0793	5008	,	,		19038	0.001		0.1461	False		,,,				2504	0.0266				p.Q251X		Atlas-SNP	.											.	POMT1	59	.	0			c.C751T						PASS	.	C	,,,,stop/GLN	395,4011		22,351,1830	72.0	61.0	65.0		,,,,751	-1.1	0.0	9	dbSNP_108	65	871,7729		65,741,3494	yes	intron,intron,intron,intron,stop-gained	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	87,1092,5324	TT,TC,CC		10.1279,8.965,9.734	,,,,	,,,,251/748	134385435	1266,11740	2203	4300	6503	SO:0001587	stop_gained	10585	exon8			CAGATGCAGATGT	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.751C>T	9.37:g.134385435C>T	ENSP00000361302:p.Gln251*	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Nonsense_Mutation	SNP	ENST00000372228.3	37	CCDS6943.1	147	0.0673076923076923	34	0.06910569105691057	29	0.08011049723756906	1	0.0017482517482517483	83	0.10949868073878628	C	12.05	1.821679	0.32237	0.08965	0.101279	ENSG00000130714	ENST00000441334;ENST00000372228;ENST00000448212	.	.	.	2.2	-1.1	0.09872	.	4.494090	0.00649	U	0.000543	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2385	2.8102	0.05440	0.3724:0.2516:0.376:0.0	rs3887873;rs52806687;rs57618284;rs3887873	.	.	.	X	134;251;197	.	.	Q	+	1	0	POMT1	133375256	0.274000	0.24191	0.001000	0.08648	0.049000	0.14656	-0.097000	0.11042	-0.288000	0.09051	-0.234000	0.12200	CAG	C|0.904;T|0.096	0.096	strong		0.572	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
WSCD2	9671	hgsc.bcm.edu	37	12	108618630	108618630	+	Missense_Mutation	SNP	C	C	T	rs3764002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:108618630C>T	ENST00000332082.4	+	6	1615	c.797C>T	c.(796-798)aCt>aTt	p.T266I	WSCD2_ENST00000547525.1_Missense_Mutation_p.T266I|WSCD2_ENST00000261400.3_Missense_Mutation_p.T266I|WSCD2_ENST00000549903.1_Missense_Mutation_p.T266I			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	266	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.		T -> I (in dbSNP:rs3764002). {ECO:0000269|PubMed:15489334}.			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						GACTTCTGCACTGAGAAGGTG	0.592													C|||	1287	0.256989	0.0144	0.1657	5008	,	,		22314	0.5476		0.2594	False		,,,				2504	0.3476				p.T266I		Atlas-SNP	.											.	WSCD2	125	.	0			c.C797T						PASS	.	C	ILE/THR	193,3799		3,187,1806	62.0	61.0	61.0		797	5.4	1.0	12	dbSNP_107	61	2151,6217		310,1531,2343	yes	missense	WSCD2	NM_014653.2	89	313,1718,4149	TT,TC,CC		25.7051,4.8347,18.9644	probably-damaging	266/566	108618630	2344,10016	1996	4184	6180	SO:0001583	missense	9671	exon5			TCTGCACTGAGAA		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.797C>T	12.37:g.108618630C>T	ENSP00000331933:p.Thr266Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	568	0.2600732600732601	8	0.016260162601626018	62	0.1712707182320442	287	0.5017482517482518	211	0.2783641160949868	C	23.7	4.443960	0.83993	0.048347	0.257051	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000551638;ENST00000332082;ENST00000549903	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	5.39	5.39	0.77823	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	0.99999999374288	D;D	0.76494	0.997;0.999	D;D	0.85130	0.91;0.997	T	0.48937	-0.8990	9	0.35671	T	0.21	-20.9307	17.8977	0.88893	0.0:1.0:0.0:0.0	rs3764002;rs52812734;rs57199422;rs3764002	266;266	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	I	266;266;113;266;266	ENSP00000448047:T266I;ENSP00000261400:T266I;ENSP00000446744:T113I;ENSP00000331933:T266I;ENSP00000447272:T266I	ENSP00000261400:T266I	T	+	2	0	WSCD2	107142760	1.000000	0.71417	0.967000	0.41034	0.953000	0.61014	7.560000	0.82277	2.804000	0.96469	0.655000	0.94253	ACT	C|0.745;T|0.255	0.255	strong		0.592	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
FANCF	2188	hgsc.bcm.edu	37	11	22646532	22646532	+	Silent	SNP	C	C	T	rs36045913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:22646532C>T	ENST00000327470.3	-	1	855	c.825G>A	c.(823-825)ctG>ctA	p.L275L	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	275					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						TTAGCAGACCCAGATAGACAG	0.547			"""N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	34	0.00678914	0.0008	0.013	5008	,	,		17436	0.0		0.0219	False		,,,				2504	0.002				p.L275L		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"""Fanconi anemia, complementation group F"""		L	.	FANCF	24	.	0			c.G825A						PASS	.	C		17,4389	23.3+/-48.9	0,17,2186	54.0	61.0	58.0		825	4.5	0.0	11	dbSNP_126	58	200,8400	87.1+/-149.5	1,198,4101	no	coding-synonymous	FANCF	NM_022725.3		1,215,6287	TT,TC,CC		2.3256,0.3858,1.6685		275/375	22646532	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAGACCCAGATAG		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"""Fanconi anemia, complementation groups"""	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.825G>A	11.37:g.22646532C>T		Somatic	62	0	0	757	WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_022725	Q52LM0	Silent	SNP	ENST00000327470.3	37	CCDS7857.1																																																																																			C|0.985;T|0.015	0.015	strong		0.547	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725	
ZNF638	27332	hgsc.bcm.edu	37	2	71631109	71631109	+	Missense_Mutation	SNP	A	A	G	rs3732235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71631109A>G	ENST00000409544.1	+	17	3569	c.2939A>G	c.(2938-2940)aAc>aGc	p.N980S	ZNF638_ENST00000355812.3_Missense_Mutation_p.N980S|ZNF638_ENST00000264447.4_Missense_Mutation_p.N980S	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	980			N -> S (in dbSNP:rs3732235). {ECO:0000269|PubMed:11149944}.		regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GCTCCTGAAAACATGAATATA	0.313													A|||	575	0.114816	0.1256	0.0576	5008	,	,		17380	0.1577		0.0805	False		,,,				2504	0.1319				p.N980S		Atlas-SNP	.											.	ZNF638	179	.	0			c.A2939G						PASS	.	A	SER/ASN,SER/ASN	579,3827	254.9+/-260.3	38,503,1662	124.0	141.0	135.0		2939,2939	2.7	1.0	2	dbSNP_107	135	784,7812	184.6+/-232.5	41,702,3555	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	46,46	79,1205,5217	GG,GA,AA		9.1205,13.1412,10.483	benign,benign	980/1979,980/1979	71631109	1363,11639	2203	4298	6501	SO:0001583	missense	27332	exon17			CTGAAAACATGAA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2939A>G	2.37:g.71631109A>G	ENSP00000386433:p.Asn980Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	223	0.1021062271062271	54	0.10975609756097561	28	0.07734806629834254	77	0.1346153846153846	64	0.08443271767810026	A	8.614	0.889830	0.17540	0.131412	0.091205	ENSG00000075292	ENST00000394137;ENST00000355812;ENST00000264447;ENST00000409544	T;T;T	0.55052	0.54;1.53;1.53	5.12	2.67	0.31697	.	0.527792	0.17196	N	0.183314	T	0.00412	0.0013	L	0.44542	1.39	0.31384	P	0.67868	B;B;B;B	0.27791	0.094;0.152;0.152;0.189	B;B;B;B	0.24394	0.039;0.053;0.037;0.039	T	0.07693	-1.0759	9	0.22109	T	0.4	0.0015	4.2706	0.10785	0.7283:0.0:0.0958:0.1758	rs3732235;rs52803566;rs56671072;rs3732235	980;980;980;980	A8K583;Q14966-4;Q14966-3;Q14966	.;.;.;ZN638_HUMAN	S	559;980;980;980	ENSP00000348066:N980S;ENSP00000264447:N980S;ENSP00000386433:N980S	ENSP00000264447:N980S	N	+	2	0	ZNF638	71484617	0.971000	0.33674	0.963000	0.40424	0.985000	0.73830	3.352000	0.52239	0.262000	0.21774	0.528000	0.53228	AAC	A|0.891;G|0.109	0.109	strong		0.313	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
IL1RL2	8808	hgsc.bcm.edu	37	2	102851496	102851496	+	Silent	SNP	C	C	T	rs35960329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:102851496C>T	ENST00000264257.2	+	11	1563	c.1437C>T	c.(1435-1437)gaC>gaT	p.D479D	IL1RL2_ENST00000441515.2_Silent_p.D361D|IL1RL2_ENST00000539491.1_Silent_p.D479D|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	479	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)	p.D479D(1)|p.D361D(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TGATCCAGGACGGGATGAAGG	0.502													C|||	27	0.00539137	0.0015	0.0086	5008	,	,		20745	0.0		0.008	False		,,,				2504	0.0112				p.D479D		Atlas-SNP	.											IL1RL2_ENST00000441515,NS,carcinoma,0,2	IL1RL2	118	2	2	Substitution - coding silent(2)	lung(2)	c.C1437T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	147.0	129.0	135.0		1437	-10.4	0.2	2	dbSNP_126	135	158,8442	76.3+/-139.0	0,158,4142	no	coding-synonymous	IL1RL2	NM_003854.2		0,175,6328	TT,TC,CC		1.8372,0.3858,1.3455		479/576	102851496	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	8808	exon11			CCAGGACGGGATG	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1437C>T	2.37:g.102851496C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Silent	SNP	ENST00000264257.2	37	CCDS2056.1																																																																																			C|0.988;T|0.012	0.012	strong		0.502	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
SCNN1D	6339	hgsc.bcm.edu	37	1	1226757	1226757	+	Missense_Mutation	SNP	G	G	A	rs6690013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1226757G>A	ENST00000338555.2	+	15	2828	c.1684G>A	c.(1684-1686)Ggc>Agc	p.G562S	SCNN1D_ENST00000400928.3_Missense_Mutation_p.G562S|SCNN1D_ENST00000325425.8_Missense_Mutation_p.G628S|SCNN1D_ENST00000379116.5_Missense_Mutation_p.G726S			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	562			G -> S (in dbSNP:rs6690013). {ECO:0000269|PubMed:14702039}.		ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	GGTGCTAGGCGGCCGCCGGCT	0.701													G|||	549	0.109625	0.1392	0.085	5008	,	,		13307	0.1478		0.0437	False		,,,				2504	0.1155				p.G726S		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G2176A						PASS	.	G	SER/GLY	402,3900		14,374,1763	17.0	15.0	16.0		2176	1.9	0.0	1	dbSNP_116	16	324,8136		3,318,3909	yes	missense	SCNN1D	NM_001130413.3	56	17,692,5672	AA,AG,GG		3.8298,9.3445,5.6888	benign	726/803	1226757	726,12036	2151	4230	6381	SO:0001583	missense	6339	exon18			CTAGGCGGCCGCC	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.1684G>A	1.37:g.1226757G>A	ENSP00000339504:p.Gly562Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	126	73	0.579365	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		231	0.10576923076923077	80	0.16260162601626016	41	0.1132596685082873	75	0.13111888111888112	35	0.04617414248021108	G	10.62	1.401579	0.25291	0.093445	0.038298	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928	T;T;T;T	0.68181	-0.31;-0.26;-0.29;-0.26	4.25	1.92	0.25849	.	.	.	.	.	T	0.00178	0.0005	N	0.19112	0.55	0.80722	P	0.0	B;P;P	0.43633	0.429;0.682;0.813	B;B;B	0.28305	0.052;0.088;0.088	T	0.03413	-1.1039	8	0.22109	T	0.4	.	5.198	0.15249	0.0:0.0972:0.1916:0.7112	rs6690013	384;562;726	B1AMF2;P51172;A6NNF7	.;SCNND_HUMAN;.	S	593;726;562;628;562	ENSP00000368411:G726S;ENSP00000339504:G562S;ENSP00000321594:G628S;ENSP00000383717:G562S	ENSP00000321594:G628S	G	+	1	0	SCNN1D	1216620	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.091000	0.15046	0.219000	0.20840	-0.516000	0.04426	GGC	G|0.926;A|0.074	0.074	strong		0.701	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144909956	144909956	+	Silent	SNP	G	G	A	rs638260	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:144909956G>A	ENST00000369354.3	-	17	2421	c.2232C>T	c.(2230-2232)gaC>gaT	p.D744D	PDE4DIP_ENST00000369359.4_Silent_p.D881D|PDE4DIP_ENST00000524974.1_5'Flank|PDE4DIP_ENST00000530740.1_Silent_p.D881D|PDE4DIP_ENST00000369356.4_Silent_p.D744D|PDE4DIP_ENST00000313382.9_Silent_p.D810D|PDE4DIP_ENST00000529945.1_Silent_p.D907D|PDE4DIP_ENST00000369349.3_Silent_p.D744D|PDE4DIP_ENST00000479408.2_Silent_p.D531D|PDE4DIP_ENST00000313431.9_Silent_p.D907D|PDE4DIP_ENST00000369351.3_Silent_p.D744D			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	744					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)		CTGTGTCCAAGTCTCCTAAAA	0.363			T	PDGFRB	MPD																																p.D907D		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C2721T						PASS	.	C	,,,,	985,3421		0,985,1218	88.0	89.0	88.0		2721,2232,2430,2232,2232	0.0	0.1	1	dbSNP_83	88	1948,6652		0,1948,2352	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	,,,,	0,2933,3570	AA,AG,GG		22.6512,22.3559,22.5511	,,,,	907/1133,744/970,810/2241,744/2363,744/2347	144909956	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	9659	exon13			GTCCAAGTCTCCT	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.2232C>T	1.37:g.144909956G>A		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	257	57	0.22179	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|0.701	0.001	strong		0.363	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
F5	2153	hgsc.bcm.edu	37	1	169510348	169510348	+	Missense_Mutation	SNP	T	T	C	rs1800595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169510348T>C	ENST00000367797.3	-	13	4181	c.3980A>G	c.(3979-3981)cAt>cGt	p.H1327R	F5_ENST00000367796.3_Missense_Mutation_p.H1332R	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1327	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.		H -> R (in dbSNP:rs1800595). {ECO:0000269|PubMed:10942390, ECO:0000269|PubMed:8713778}.		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)	AAGGGTTGTATGGCTGAGGTC	0.522													T|||	228	0.0455272	0.0045	0.0922	5008	,	,		21634	0.0327		0.0616	False		,,,				2504	0.0644				p.H1327R		Atlas-SNP	.											.	F5	301	.	0			c.A3980G	GRCh37	CM970468	F5	M	rs1800595	PASS	.	T	ARG/HIS	45,4361	46.7+/-81.2	0,45,2158	216.0	239.0	231.0		3980	2.2	0.0	1	dbSNP_89	231	544,8056	150.0+/-205.0	18,508,3774	no	missense	F5	NM_000130.4	29	18,553,5932	CC,CT,TT		6.3256,1.0213,4.5287	benign	1327/2225	169510348	589,12417	2203	4300	6503	SO:0001583	missense	2153	exon13			GTTGTATGGCTGA	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.3980A>G	1.37:g.169510348T>C	ENSP00000356771:p.His1327Arg	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	360	123	0.341667	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	105	0.04807692307692308	5	0.01016260162601626	32	0.08839779005524862	19	0.033216783216783216	49	0.06464379947229551	T	8.796	0.931762	0.18131	0.010213	0.063256	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.32515	1.45;1.45	4.62	2.19	0.27852	.	0.873235	0.10101	N	0.716004	T	0.10165	0.0249	L	0.50333	1.59	0.21355	N	0.999715	B	0.26318	0.146	B	0.19148	0.024	T	0.26710	-1.0095	9	0.15066	T	0.55	0.3176	10.0654	0.42299	0.0:0.0:0.3248:0.6752	rs1800595;rs13306333	1327	P12259	FA5_HUMAN	R	1327;1332	ENSP00000356771:H1327R;ENSP00000356770:H1332R	ENSP00000356770:H1332R	H	-	2	0	F5	167776972	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	0.544000	0.23253	0.223000	0.20920	-0.367000	0.07326	CAT	T|0.953;C|0.047	0.047	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43861012	43861012	+	Missense_Mutation	SNP	C	C	T	rs530378867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:43861012C>T	ENST00000377564.3	+	13	2279	c.1886C>T	c.(1885-1887)gCg>gTg	p.A629V		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	629	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						GCAGACTCCGCGTGGACGGTG	0.647													C|||	19	0.00379393	0.0	0.0	5008	,	,		17105	0.0		0.0119	False		,,,				2504	0.0072				p.A629V		Atlas-SNP	.											.	CNTNAP3B	37	.	0			c.C1886T						PASS	.																																			SO:0001583	missense	728577	exon13			ACTCCGCGTGGAC	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.1886C>T	9.37:g.43861012C>T	ENSP00000366787:p.Ala629Val	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.700|5.700	0.313777|0.313777	0.10789|0.10789	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377564;ENST00000341990;ENST00000403166|ENST00000377561	T|.	0.21361|.	2.01|.	1.94|1.94	1.94|1.94	0.25998|0.25998	.|.	.|.	.|.	.|.	.|.	T|T	0.31949|0.31949	0.0813|0.0813	L|L	0.27975|0.27975	0.815|0.815	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21143|0.21143	-1.0254|-1.0254	7|5	0.02654|.	T|.	1|.	.|.	9.4766|9.4766	0.38875|0.38875	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|C	629;629;535|678	ENSP00000366787:A629V|.	ENSP00000340890:A629V|.	A|R	+|+	2|1	0|0	CNTNAP3B|CNTNAP3B	43801008|43801008	0.004000|0.004000	0.15560|0.15560	0.008000|0.008000	0.14137|0.14137	0.015000|0.015000	0.08874|0.08874	1.729000|1.729000	0.38115|0.38115	1.408000|1.408000	0.46895|0.46895	0.423000|0.423000	0.28283|0.28283	GCG|CGT	.	.	none		0.647	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
HLA-A	3105	hgsc.bcm.edu	37	6	29910378	29910378	+	Silent	SNP	C	C	T	rs41546314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910378C>T	ENST00000396634.1	+	3	389	c.48C>T	c.(46-48)gcC>gcT	p.A16A	HLA-A_ENST00000376806.5_Silent_p.A16A|HLA-A_ENST00000376809.5_Silent_p.A16A|HLA-A_ENST00000376802.2_Silent_p.A16A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCTCGGGGGCCCTGGCCCTGA	0.711									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	1224	0.244409	0.1755	0.3357	5008	,	,		14832	0.2917		0.3141	False		,,,				2504	0.1524				p.A16A		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.C48T						PASS	.	C		793,3603		72,649,1477	28.0	31.0	30.0		48	-3.8	0.0	6	dbSNP_131	30	2397,6193		349,1699,2247	no	coding-synonymous	HLA-A	NM_002116.7		421,2348,3724	TT,TC,CC		27.9045,18.0391,24.5649		16/366	29910378	3190,9796	2198	4295	6493	SO:0001819	synonymous_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGGGGCCCTGGCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.48C>T	6.37:g.29910378C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.769;T|0.231	0.231	strong		0.711	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4442818	4442818	+	Silent	SNP	G	G	A	rs73335853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4442818G>A	ENST00000254718.4	-	26	4185	c.3879C>T	c.(3877-3879)tcC>tcT	p.S1293S	MYBBP1A_ENST00000381556.2_Silent_p.S1293S			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1293	Required for nuclear and nucleolar localization. {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						GTGCCAGCGCGGACAGTGGTG	0.582													G|||	320	0.0638978	0.1959	0.0216	5008	,	,		14164	0.0268		0.0129	False		,,,				2504	0.0061				p.S1293S		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C3879T						PASS	.	G	,,	806,3600	324.5+/-298.6	86,634,1483	170.0	169.0	169.0		3879,,3879	-7.8	0.0	17	dbSNP_130	169	50,8550	31.7+/-84.0	0,50,4250	no	coding-synonymous,utr-3,coding-synonymous	MYBBP1A,SPNS2	NM_001105538.1,NM_001124758.1,NM_014520.3	,,	86,684,5733	AA,AG,GG		0.5814,18.2932,6.5816	,,	1293/1333,,1293/1329	4442818	856,12150	2203	4300	6503	SO:0001819	synonymous_variant	10514	exon26			CAGCGCGGACAGT	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.3879C>T	17.37:g.4442818G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			G|0.941;A|0.059	0.059	strong		0.582	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
COL18A1	80781	hgsc.bcm.edu	37	21	46899842	46899842	+	Silent	SNP	C	C	T	rs1131100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46899842C>T	ENST00000359759.4	+	9	2541	c.2520C>T	c.(2518-2520)ccC>ccT	p.P840P	COL18A1_ENST00000400337.2_Silent_p.P425P|COL18A1_ENST00000355480.5_Silent_p.P605P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	840	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)		AAGGCTTCCCCGGGACTCCAG	0.677													C|||	817	0.163139	0.2965	0.0922	5008	,	,		16956	0.1101		0.0696	False		,,,				2504	0.184				p.P605P		Atlas-SNP	.											COL18A1_ENST00000359759,NS,carcinoma,0,2	COL18A1	129	2	0			c.C1815T						PASS	.	C	,	1059,2899		144,771,1064	52.0	63.0	59.0		1815,1275	-8.0	0.2	21	dbSNP_86	59	546,7746		18,510,3618	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	162,1281,4682	TT,TC,CC		6.5847,26.7559,13.102	,	605/1520,425/1340	46899842	1605,10645	1979	4146	6125	SO:0001819	synonymous_variant	80781	exon9			CTTCCCCGGGACT		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.2520C>T	21.37:g.46899842C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.882;T|0.118	0.118	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238155	31238155	+	Missense_Mutation	SNP	G	G	A	rs1050328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238155G>A	ENST00000376228.5	-	4	741	c.727C>T	c.(727-729)Cgg>Tgg	p.R243W	HLA-C_ENST00000383329.3_Missense_Mutation_p.R243W	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	243	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						TCCCCATCCCGCTGCCAGGTC	0.632													G|||	1934	0.386182	0.3714	0.428	5008	,	,		14977	0.5675		0.327	False		,,,				2504	0.2505				p.R243W		Atlas-SNP	.											HLA-C,colon,carcinoma,+1,1	HLA-C	92	1	0			c.C727T						PASS	.	G	TRP/ARG	1452,2948		276,900,1024	38.0	37.0	37.0		727	0.7	1.0	6	dbSNP_86	37	2279,6297		360,1559,2369	no	missense	HLA-C	NM_002117.5	101	636,2459,3393	AA,AG,GG		26.5742,33.0,28.7531	probably-damaging	243/367	31238155	3731,9245	2200	4288	6488	SO:0001583	missense	3107	exon4			CATCCCGCTGCCA	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.727C>T	6.37:g.31238155G>A	ENSP00000365402:p.Arg243Trp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	832	0.38095238095238093	157	0.31910569105691056	140	0.3867403314917127	306	0.534965034965035	229	0.3021108179419525	.	3.864	-0.029320	0.07589	0.33	0.265742	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.03181	4.02;4.02	2.67	0.7	0.18099	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.232985	0.21532	U	0.073034	T	0.01835	0.0058	M	0.83953	2.67	0.46609	P	8.749999999999591E-4	B;B;B;B	0.10296	0.003;0.0;0.001;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.24977	-1.0145	9	0.48119	T	0.1	.	2.7344	0.05236	0.1696:0.0:0.5518:0.2786	rs1050328;rs2308614;rs3177868;rs3190622;rs12721973;rs17840005	243;243;243;243	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	W	243;243;243;280	ENSP00000365402:R243W;ENSP00000372819:R243W	ENSP00000365402:R243W	R	-	1	2	HLA-C	31346134	0.000000	0.05858	0.987000	0.45799	0.454000	0.32378	-0.406000	0.07187	0.168000	0.19655	0.298000	0.19748	CGG	G|0.695;A|0.305	0.305	strong		0.632	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FTO	79068	hgsc.bcm.edu	37	16	53860253	53860253	+	Missense_Mutation	SNP	G	G	A	rs150450891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53860253G>A	ENST00000471389.1	+	3	823	c.601G>A	c.(601-603)Gta>Ata	p.V201I	FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	201	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						AGCATACAACGTAACTTTGCT	0.453																																					p.V201I		Atlas-SNP	.											.	FTO	51	.	0			c.G601A						PASS	.	G	ILE/VAL	0,4396		0,0,2198	158.0	139.0	145.0		601	3.1	0.9	16	dbSNP_134	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FTO	NM_001080432.2	29	0,7,6491	AA,AG,GG		0.0814,0.0,0.0539	benign	201/506	53860253	7,12989	2198	4300	6498	SO:0001583	missense	79068	exon3			TACAACGTAACTT	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.601G>A	16.37:g.53860253G>A	ENSP00000418823:p.Val201Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861372	0.51482	0.0	8.14E-4	ENSG00000140718	ENST00000471389	T	0.80994	-1.44	5.32	3.09	0.35607	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	0.170382	0.49916	D	0.000131	T	0.74981	0.3788	M	0.64404	1.975	0.80722	D	1	P	0.39576	0.679	B	0.35114	0.196	T	0.76868	-0.2800	10	0.62326	D	0.03	-8.3027	10.9439	0.47289	0.0:0.1016:0.6004:0.298	.	201	Q9C0B1	FTO_HUMAN	I	201	ENSP00000418823:V201I	ENSP00000418823:V201I	V	+	1	0	FTO	52417754	0.751000	0.28327	0.911000	0.35937	0.981000	0.71138	0.893000	0.28336	1.196000	0.43129	0.655000	0.94253	GTA	G|0.999;A|0.001	0.001	strong		0.453	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
PELP1	27043	hgsc.bcm.edu	37	17	4574751	4574751	+	Missense_Mutation	SNP	T	T	A	rs9436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4574751T>A	ENST00000574876.1	-	17	3393	c.3376A>T	c.(3376-3378)Aca>Tca	p.T1126S	PELP1_ENST00000301396.4_Missense_Mutation_p.T1270S|PELP1_ENST00000269230.7_Missense_Mutation_p.T1036S|PELP1_ENST00000572293.1_Missense_Mutation_p.T1176S|PELP1_ENST00000436683.2_Missense_Mutation_p.T902S			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	77	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	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	
DCDC2	51473	hgsc.bcm.edu	37	6	24357796	24357796	+	Silent	SNP	G	G	A	rs33943110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24357796G>A	ENST00000378454.3	-	1	484	c.183C>T	c.(181-183)gcC>gcT	p.A61A	KAAG1_ENST00000274766.1_5'UTR	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	61	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TGTTCCTGACGGCCCCAAAGG	0.622													G|||	161	0.0321486	0.0068	0.0605	5008	,	,		16785	0.002		0.0606	False		,,,				2504	0.0481				p.A61A		Atlas-SNP	.											.	DCDC2	53	.	0			c.C183T						PASS	.	G	,,	58,4348		1,56,2146	38.0	38.0	38.0		183,183,	-11.1	0.0	6	dbSNP_126	38	573,8027		23,527,3750	no	coding-synonymous,coding-synonymous,utr-5	DCDC2,KAAG1	NM_001195610.1,NM_016356.3,NM_181337.3	,,	24,583,5896	AA,AG,GG		6.6628,1.3164,4.8516	,,	61/477,61/477,	24357796	631,12375	2203	4300	6503	SO:0001819	synonymous_variant	51473	exon2			CCTGACGGCCCCA	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.183C>T	6.37:g.24357796G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	23	0.69697	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1	67	0.030677655677655676	3	0.006097560975609756	19	0.052486187845303865	2	0.0034965034965034965	43	0.05672823218997362	G	6.402	0.442341	0.12164	0.013164	0.066628	ENSG00000146038	ENST00000436313	.	.	.	5.56	-11.1	0.00147	.	.	.	.	.	T	0.23370	0.0565	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51593	-0.8686	4	.	.	.	-12.4188	6.3844	0.21552	0.2367:0.4667:0.1801:0.1165	rs33943110;rs33943110	.	.	.	L	29	.	.	P	-	2	0	DCDC2	24465775	0.000000	0.05858	0.027000	0.17364	0.687000	0.40016	-3.787000	0.00366	-3.168000	0.00226	-1.692000	0.00727	CCG	G|0.955;A|0.045	0.045	strong		0.622	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
CPVL	54504	hgsc.bcm.edu	37	7	29152416	29152416	+	Silent	SNP	G	G	A	rs2011337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:29152416G>A	ENST00000409850.1	-	7	838	c.192C>T	c.(190-192)ggC>ggT	p.G64G	CPVL_ENST00000265394.5_Silent_p.G64G|CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Silent_p.G64G			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	64						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						CTGGGAAAGGGCCGACCAAAC	0.438													A|||	492	0.0982428	0.2171	0.085	5008	,	,		16606	0.0337		0.0984	False		,,,				2504	0.0133				p.G64G		Atlas-SNP	.											.	CPVL	60	.	0			c.C192T						PASS	.	A	,	851,3555	745.5+/-411.7	80,691,1432	80.0	76.0	77.0		192,192	0.9	0.0	7	dbSNP_92	77	1017,7583	772.7+/-407.7	65,887,3348	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	145,1578,4780	AA,AG,GG		11.8256,19.3146,14.3626	,	64/477,64/477	29152416	1868,11138	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon3			GAAAGGGCCGACC	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.192C>T	7.37:g.29152416G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	187	42	0.224599	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			G|0.869;A|0.131	0.131	strong		0.438	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
DTX2	113878	hgsc.bcm.edu	37	7	76112060	76112060	+	Silent	SNP	C	C	T	rs1638074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76112060C>T	ENST00000324432.5	+	5	1014	c.504C>T	c.(502-504)ttC>ttT	p.F168F	DTX2_ENST00000446600.1_Silent_p.F77F|DTX2_ENST00000430490.2_Silent_p.F168F|DTX2_ENST00000307569.8_Silent_p.F168F|DTX2_ENST00000446820.2_Silent_p.F168F|DTX2_ENST00000413936.2_Silent_p.F168F	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	168	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.				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						CTTCCAGCTTCTGCCGCAGCG	0.657													.|||	2953	0.589657	0.6369	0.5893	5008	,	,		16482	0.5526		0.507	False		,,,				2504	0.6493				p.F168F		Atlas-SNP	.											.	DTX2	64	.	0			c.C504T						PASS	.	C	,,,	2779,1627		896,987,320	56.0	49.0	51.0		504,504,504,504	2.7	1.0	7	dbSNP_89	51	4346,4254		1110,2126,1064	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	2006,3113,1384	TT,TC,CC		49.4651,36.9269,45.2176	,,,	168/623,168/623,168/576,168/623	76112060	7125,5881	2203	4300	6503	SO:0001819	synonymous_variant	113878	exon2			CAGCTTCTGCCGC		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.504C>T	7.37:g.76112060C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	173	97	0.560694	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			C|0.449;T|0.551	0.551	strong		0.657	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
RASSF5	83593	hgsc.bcm.edu	37	1	206757857	206757857	+	Silent	SNP	C	C	A	rs4845112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:206757857C>A	ENST00000355294.4	+	4	886	c.829C>A	c.(829-831)Cgg>Agg	p.R277R	RASSF5_ENST00000491368.1_3'UTR|RASSF5_ENST00000367117.3_Silent_p.R277R|RASSF5_ENST00000304534.8_Silent_p.R124R|EIF2D_ENST00000472709.2_Intron	NM_182663.2	NP_872604.1	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family member 5	277	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein localization to nucleus (GO:1900180)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	8	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CACGGACAAGCGGACATCCTT	0.592													C|||	539	0.107628	0.1422	0.0951	5008	,	,		17694	0.1508		0.0626	False		,,,				2504	0.0716				p.R277R	GBM(162;656 1984 11916 22872 31529)	Atlas-SNP	.											.	RASSF5	54	.	0			c.C829A						PASS	.	C	,,	556,3850	251.2+/-258.0	29,498,1676	149.0	140.0	143.0		829,829,370	2.8	1.0	1	dbSNP_111	143	487,8113	141.1+/-197.5	14,459,3827	yes	coding-synonymous,coding-synonymous,coding-synonymous	RASSF5	NM_182663.2,NM_182664.2,NM_182665.2	,,	43,957,5503	AA,AC,CC		5.6628,12.6192,8.0194	,,	277/419,277/337,124/266	206757857	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	83593	exon4			GACAAGCGGACAT	BC004270	CCDS1463.1, CCDS1464.1, CCDS30998.1	1q31	2014-04-10	2008-02-22		ENSG00000136653	ENSG00000266094			17609	protein-coding gene	gene with protein product		607020				11978988, 11965544	Standard	NM_182663		Approved	Maxp1, NORE1, RAPL	uc001hed.3	Q8WWW0	OTTHUMG00000184616	ENST00000355294.4:c.829C>A	1.37:g.206757857C>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_182663	A8K1E6|Q5SY32|Q8WWV9|Q8WXF4|Q9BT99	Silent	SNP	ENST00000355294.4	37	CCDS30998.1																																																																																			C|0.905;A|0.095	0.095	strong		0.592	RASSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088469.1	NM_031437	
LAPTM4A	9741	hgsc.bcm.edu	37	2	20240668	20240668	+	Silent	SNP	C	C	A	rs3731673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:20240668C>A	ENST00000175091.4	-	2	723	c.216G>T	c.(214-216)tcG>tcT	p.S72S		NM_014713.4	NP_055528.1	Q15012	LAP4A_HUMAN	lysosomal protein transmembrane 4 alpha	72					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTCTCAGACGAATAGTAAT	0.373													C|||	846	0.16893	0.0136	0.1988	5008	,	,		16753	0.3056		0.174	False		,,,				2504	0.2117				p.S72S	Ovarian(90;1240 1386 7711 14384 46863)	Atlas-SNP	.											.	LAPTM4A	18	.	0			c.G216T						PASS	.	C		219,4187	131.4+/-167.9	4,211,1988	127.0	121.0	123.0		216	-9.1	0.9	2	dbSNP_107	123	1601,6999	298.7+/-304.1	135,1331,2834	no	coding-synonymous	LAPTM4A	NM_014713.4		139,1542,4822	AA,AC,CC		18.6163,4.9705,13.9935		72/234	20240668	1820,11186	2203	4300	6503	SO:0001819	synonymous_variant	9741	exon2			CTCAGACGAATAG	D14696	CCDS1696.1	2p24.1	2008-08-11	2008-08-11		ENSG00000068697	ENSG00000068697			6924	protein-coding gene	gene with protein product			"""lysosomal-associated protein transmembrane 4 alpha"""	MBNT		8621662, 7788527	Standard	NM_014713		Approved	HUMORF13, KIAA0108, Mtrp, LAPTM4	uc002rdm.3	Q15012	OTTHUMG00000090750	ENST00000175091.4:c.216G>T	2.37:g.20240668C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_014713	Q6UW22	Silent	SNP	ENST00000175091.4	37	CCDS1696.1																																																																																			C|0.849;A|0.151	0.151	strong		0.373	LAPTM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207494.1	NM_014713	
CNN1	1264	hgsc.bcm.edu	37	19	11660519	11660519	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11660519A>G	ENST00000252456.2	+	7	1014	c.803A>G	c.(802-804)tAc>tGc	p.Y268C	CNN1_ENST00000544952.1_Missense_Mutation_p.Y248C|CNN1_ENST00000592923.1_Missense_Mutation_p.Y218C|CNN1_ENST00000535659.2_Missense_Mutation_p.Y218C	NM_001299.4	NP_001290.2	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle	268					actomyosin structure organization (GO:0031032)|regulation of smooth muscle contraction (GO:0006940)	cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9						CGCCAGGTCTACGACCCCAAG	0.617																																					p.Y268C		Atlas-SNP	.											CNN1,colon,carcinoma,-1,2	CNN1	34	2	0			c.A803G						scavenged	.						79.0	69.0	73.0					19																	11660519		2203	4300	6503	SO:0001583	missense	1264	exon7			AGGTCTACGACCC	U37019	CCDS12263.1	19p13.2-p13.1	2008-07-16				ENSG00000130176			2155	protein-coding gene	gene with protein product		600806				8526917, 9332369	Standard	XM_005259741		Approved	SMCC, Sm-Calp	uc002msc.1	P51911		ENST00000252456.2:c.803A>G	19.37:g.11660519A>G	ENSP00000252456:p.Tyr268Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_001299	B2R868|B4DUX6|O00638|Q15416|Q8IY93|Q99438	Missense_Mutation	SNP	ENST00000252456.2	37	CCDS12263.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.685308	0.47991	.	.	ENSG00000130176	ENST00000252456;ENST00000535659;ENST00000544952	T;T;T	0.54675	0.56;0.56;0.56	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.55924	0.1951	M	0.74881	2.28	0.58432	D	0.999999	B	0.28552	0.215	B	0.33196	0.159	T	0.59300	-0.7480	10	0.49607	T	0.09	-52.2324	13.4048	0.60906	1.0:0.0:0.0:0.0	.	268	P51911	CNN1_HUMAN	C	268;218;248	ENSP00000252456:Y268C;ENSP00000442031:Y218C;ENSP00000437470:Y248C	ENSP00000252456:Y268C	Y	+	2	0	CNN1	11521519	1.000000	0.71417	0.972000	0.41901	0.754000	0.42855	5.521000	0.67086	2.013000	0.59113	0.443000	0.29094	TAC	.	.	none		0.617	CNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458854.1	NM_001299	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106489	31106489	+	Missense_Mutation	SNP	G	G	A	rs1265096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31106489G>A	ENST00000259881.9	+	5	389	c.100G>A	c.(100-102)Gag>Aag	p.E34K	PSORS1C1_ENST00000481450.2_Intron|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000547221.1_5'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	34			E -> K (in dbSNP:rs1265096). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:12930300}.|E -> Q. {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TCCCAGCTCCGAGGAAACTCG	0.567													G|||	85	0.0169728	0.0053	0.0115	5008	,	,		16762	0.0		0.0656	False		,,,				2504	0.0041				p.E34K		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.G100A						PASS	.	G	LYS/GLU,	50,2972		0,50,1461	141.0	142.0	142.0		100,	0.3	0.0	6	dbSNP_87	142	361,5057		14,333,2362	yes	missense,intron	PSORS1C1,PSORS1C2	NM_014068.2,NM_014069.2	56,	14,383,3823	AA,AG,GG		6.663,1.6545,4.8697	benign,	34/153,	31106489	411,8029	1511	2709	4220	SO:0001583	missense	170679	exon5			AGCTCCGAGGAAA	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.100G>A	6.37:g.31106489G>A	ENSP00000259881:p.Glu34Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	64	0.029304029304029304	3	0.006097560975609756	4	0.011049723756906077	0	0.0	57	0.07519788918205805	G	10.18	1.278140	0.23307	0.016545	0.06663	ENSG00000204540	ENST00000259881	T	0.14266	2.52	2.33	0.351	0.16042	.	.	.	.	.	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	P	0.44578	0.838	B	0.29353	0.101	T	0.44375	-0.9332	9	0.26408	T	0.33	.	4.9377	0.13948	0.3537:0.0:0.6463:0.0	rs1265096;rs3912054;rs1265096	34	Q9UIG5	PS1C1_HUMAN	K	34	ENSP00000259881:E34K	ENSP00000259881:E34K	E	+	1	0	PSORS1C1	31214468	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.035000	0.01423	-0.095000	0.12351	0.297000	0.19635	GAG	G|0.960;A|0.040	0.040	strong		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
MUC16	94025	hgsc.bcm.edu	37	19	9061559	9061559	+	Silent	SNP	C	C	G	rs1423052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9061559C>G	ENST00000397910.4	-	3	26090	c.25887G>C	c.(25885-25887)acG>acC	p.T8629T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8631	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						TGACTTCAGACGTGGCTAATA	0.453													N|||	1919	0.383187	0.3472	0.4006	5008	,	,		22669	0.5933		0.2525	False		,,,				2504	0.3374				p.T8629T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G25887C						PASS	.			1265,2617		198,869,874	146.0	138.0	140.0		25887	-4.2	0.0	19	dbSNP_88	140	2154,6140		270,1614,2263	no	coding-synonymous	MUC16	NM_024690.2		468,2483,3137	GG,GC,CC		25.9706,32.5863,28.0798		8629/14508	9061559	3419,8757	1941	4147	6088	SO:0001819	synonymous_variant	94025	exon3			TTCAGACGTGGCT	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.25887G>C	19.37:g.9061559C>G		Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	305	148	0.485246	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.616;G|0.384	0.384	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GRIPAP1	56850	hgsc.bcm.edu	37	X	48847497	48847497	+	Silent	SNP	T	T	C	rs11545861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:48847497T>C	ENST00000376441.1	-	7	517	c.483A>G	c.(481-483)gaA>gaG	p.E161E	GRIPAP1_ENST00000376425.3_Silent_p.E161E|GRIPAP1_ENST00000376444.3_Silent_p.E116E|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376423.4_Silent_p.E108E	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	161						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ACTTCCCGGCTTCTTTCCCAT	0.617													t|||	957	0.25351	0.0144	0.3444	3775	,	,		13768	0.1825		0.3698	False		,,,				2504	0.1462				p.E161E		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.A483G						PASS	.	T	,	288,3545		12,218,46,1401,525	27.0	24.0	25.0		483,324	2.4	0.9	X	dbSNP_120	25	2989,3734		491,1171,836,765,1033	no	coding-synonymous,coding-synonymous	GRIPAP1	NM_020137.3,NM_207672.1	,	503,1389,882,2166,1558	CC,CT,C,TT,T		44.4593,7.5137,31.044	,	161/842,108/626	48847497	3277,7279	2202	4296	6498	SO:0001819	synonymous_variant	56850	exon7			CCCGGCTTCTTTC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.483A>G	X.37:g.48847497T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	CCDS35248.1																																																																																			T|0.713;C|0.287	0.287	strong		0.617	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
IFRD1	3475	hgsc.bcm.edu	37	7	112112892	112112892	+	Silent	SNP	G	G	A	rs11542468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:112112892G>A	ENST00000403825.3	+	11	1503	c.1242G>A	c.(1240-1242)acG>acA	p.T414T	IFRD1_ENST00000535603.1_Silent_p.T364T|IFRD1_ENST00000005558.4_Silent_p.T414T	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	414					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						CGCTTAAAACGATGAAGATTT	0.378													G|||	227	0.0453275	0.0287	0.0375	5008	,	,		18284	0.0		0.0785	False		,,,				2504	0.0859				p.T414T		Atlas-SNP	.											.	IFRD1	46	.	0			c.G1242A						PASS	.	G	,,,	151,4255	104.3+/-142.8	3,145,2055	129.0	131.0	130.0		1242,1092,1092,1242	-11.6	0.6	7	dbSNP_120	130	700,7900	172.7+/-223.4	23,654,3623	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFRD1	NM_001007245.2,NM_001197079.1,NM_001197080.1,NM_001550.3	,,,	26,799,5678	AA,AG,GG		8.1395,3.4271,6.5431	,,,	414/452,364/402,364/402,414/452	112112892	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	3475	exon12			TAAAACGATGAAG	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1242G>A	7.37:g.112112892G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	37	CCDS34736.1																																																																																			G|0.940;A|0.060	0.060	strong		0.378	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
GIMAP8	155038	hgsc.bcm.edu	37	7	150163837	150163837	+	Silent	SNP	A	A	G	rs2140595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	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	
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650054	+	Missense_Mutation	SNP	T	T	C	rs112267342|rs111934125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56650054T>C	ENST00000394672.3	+	13	1886	c.1816T>C	c.(1816-1818)Tct>Cct	p.S606P	CCDC66_ENST00000436465.2_Missense_Mutation_p.S606P|CCDC66_ENST00000326595.7_Missense_Mutation_p.S572P	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)		TTCTACGACTTCTAAGAAGGA	0.289																																					p.S606P		Atlas-SNP	.											CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	0			c.T1816C						PASS	.						86.0	99.0	94.0					3																	56650054		2203	4291	6494	SO:0001583	missense	285331	exon13			ACGACTTCTAAGA	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.1816T>C	3.37:g.56650054T>C	ENSP00000378167:p.Ser606Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	116	8	0.0689655	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.676847	0.29783	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.19105	2.17;2.28;2.28;2.28	5.5	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	M	0.72894	2.215	0.80722	D	1	D	0.58268	0.982	P	0.57911	0.829	T	0.40924	-0.9537	10	0.02654	T	1	-4.7355	10.7191	0.46030	0.0:0.0:0.1601:0.8399	.	606	A2RUB6	CCD66_HUMAN	P	562;606;572;606	ENSP00000401451:S562P;ENSP00000378167:S606P;ENSP00000326050:S572P;ENSP00000404320:S606P	ENSP00000326050:S572P	S	+	1	0	CCDC66	56625094	0.993000	0.37304	0.582000	0.28627	0.363000	0.29612	2.520000	0.45554	1.007000	0.39238	0.482000	0.46254	TCT	C|1.000;|0.000	1.000	weak		0.289	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
RADIL	55698	hgsc.bcm.edu	37	7	4876057	4876057	+	Missense_Mutation	SNP	C	C	T	rs3763384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4876057C>T	ENST00000399583.3	-	3	902	c.715G>A	c.(715-717)Gac>Aac	p.D239N	RADIL_ENST00000538469.1_5'UTR|RADIL_ENST00000536091.1_Missense_Mutation_p.D239N	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	38	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	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	
STRA6	64220	hgsc.bcm.edu	37	15	74488424	74488424	+	Silent	SNP	G	G	A	rs11857410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:74488424G>A	ENST00000323940.5	-	5	576	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L	STRA6_ENST00000535552.1_Silent_p.L148L|STRA6_ENST00000395105.4_Silent_p.L111L|STRA6_ENST00000574278.1_Silent_p.L126L|STRA6_ENST00000563965.1_Silent_p.L150L|STRA6_ENST00000416286.3_Silent_p.L111L|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000423167.2_Silent_p.L102L|STRA6_ENST00000432245.2_Silent_p.L111L|STRA6_ENST00000449139.2_Silent_p.L111L	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	111					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						AGGGAGCTCAGGAGGACCATG	0.637													A|||	309	0.0617013	0.0333	0.072	5008	,	,		17589	0.0		0.1809	False		,,,				2504	0.0337				p.L150L		Atlas-SNP	.											.	STRA6	66	.	0			c.C448T						PASS	.	A	,,,,,,,	290,4106	792.7+/-415.2	10,270,1918	94.0	77.0	83.0		331,331,304,331,442,376,448,331	4.1	1.0	15	dbSNP_120	83	1841,6753	728.8+/-406.7	191,1459,2647	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STRA6	NM_001142617.1,NM_001142618.1,NM_001142619.1,NM_001142620.1,NM_001199040.1,NM_001199041.1,NM_001199042.1,NM_022369.3	,,,,,,,	201,1729,4565	AA,AG,GG		21.4219,6.5969,16.4049	,,,,,,,	111/668,111/668,102/659,111/160,148/705,126/683,150/707,111/668	74488424	2131,10859	2198	4297	6495	SO:0001819	synonymous_variant	64220	exon5			AGCTCAGGAGGAC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.331C>T	15.37:g.74488424G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Silent	SNP	ENST00000323940.5	37	CCDS10261.1																																																																																			G|0.878;A|0.122	0.122	strong		0.637	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
POLR1B	84172	hgsc.bcm.edu	37	2	113309473	113309473	+	Missense_Mutation	SNP	C	C	T	rs1545133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113309473C>T	ENST00000263331.5	+	6	1464	c.884C>T	c.(883-885)tCg>tTg	p.S295L	POLR1B_ENST00000417433.2_Missense_Mutation_p.S239L|POLR1B_ENST00000409894.3_Missense_Mutation_p.S295L|POLR1B_ENST00000537335.1_Missense_Mutation_p.S84L|POLR1B_ENST00000541869.1_Missense_Mutation_p.S333L	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	295			S -> L (in dbSNP:rs1545133). {ECO:0000269|PubMed:15489334}.		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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						GAGGGTTGTTCGACACAAAAA	0.413													c|||	2245	0.448283	0.3449	0.5014	5008	,	,		17373	0.4028		0.5726	False		,,,				2504	0.4693				p.S295L	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											.	POLR1B	95	.	0			c.C884T						PASS	.	T	LEU/SER,LEU/SER	1838,2568	534.2+/-373.9	399,1040,764	143.0	134.0	137.0		716,884	-2.6	0.8	2	dbSNP_88	137	5129,3471	635.6+/-399.0	1544,2041,715	yes	missense,missense	POLR1B	NM_001137604.1,NM_019014.4	145,145	1943,3081,1479	TT,TC,CC		40.3605,41.7158,46.4324	benign,benign	239/1080,295/1136	113309473	6967,6039	2203	4300	6503	SO:0001583	missense	84172	exon6			GTTGTTCGACACA	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.884C>T	2.37:g.113309473C>T	ENSP00000263331:p.Ser295Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	1003	0.4592490842490842	178	0.3617886178861789	196	0.5414364640883977	201	0.3513986013986014	428	0.5646437994722955	c	9.660	1.143968	0.21205	0.417158	0.596395	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	5.21	-2.63	0.06133	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.889113	0.10118	N	0.713739	T	0.00012	0.0000	N	0.04203	-0.255	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.14438	0.0;0.01;0.0;0.0	B;B;B;B	0.11329	0.001;0.006;0.001;0.001	T	0.44636	-0.9315	9	0.13108	T	0.6	-0.8701	5.5742	0.17215	0.2207:0.3025:0.0:0.4768	rs1545133;rs52823536;rs59317394;rs1545133	333;295;239;295	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	L	295;333;295;84;239	ENSP00000263331:S295L;ENSP00000444136:S333L;ENSP00000387143:S295L;ENSP00000437914:S84L;ENSP00000405358:S239L	ENSP00000263331:S295L	S	+	2	0	POLR1B	113025944	0.000000	0.05858	0.761000	0.31378	0.581000	0.36288	-0.090000	0.11163	-0.479000	0.06813	-0.930000	0.02707	TCG	C|0.497;T|0.503	0.503	strong		0.413	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
ATP12A	479	hgsc.bcm.edu	37	13	25265139	25265139	+	Silent	SNP	T	T	C	rs2071490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25265139T>C	ENST00000381946.3	+	8	986	c.819T>C	c.(817-819)gtT>gtC	p.V273V	ATP12A_ENST00000218548.6_Silent_p.V279V			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	273					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CCGGCATGGTTATCAACACGG	0.562													C|||	1480	0.295527	0.1755	0.3617	5008	,	,		22367	0.4762		0.1899	False		,,,				2504	0.3333				p.V279V	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.T837C						PASS	.	C	,	775,3631	753.4+/-412.4	68,639,1496	166.0	149.0	155.0		837,819	4.2	1.0	13	dbSNP_96	155	1883,6717	728.7+/-406.7	225,1433,2642	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	293,2072,4138	CC,CT,TT		21.8953,17.5897,20.4367	,	279/1046,273/1040	25265139	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	479	exon8			CATGGTTATCAAC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.819T>C	13.37:g.25265139T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			T|0.751;C|0.249	0.249	strong		0.562	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
INPP5B	3633	hgsc.bcm.edu	37	1	38338795	38338795	+	Missense_Mutation	SNP	A	A	G	rs11488569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38338795A>G	ENST00000373026.1	-	18	2234	c.2234T>C	c.(2233-2235)aTg>aCg	p.M745T	INPP5B_ENST00000373024.3_Missense_Mutation_p.M665T|INPP5B_ENST00000373023.2_Missense_Mutation_p.M745T|INPP5B_ENST00000373027.1_Missense_Mutation_p.M501T			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	745	ASH. {ECO:0000250}.		M -> T (in dbSNP:rs11488569). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1718960, ECO:0000269|PubMed:7721860}.		in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGTAGCTGTCATCTTATTTAC	0.438													G|||	2622	0.523562	0.298	0.5994	5008	,	,		19866	0.4752		0.7266	False		,,,				2504	0.6155				p.M665T		Atlas-SNP	.											.	INPP5B	76	.	0			c.T1994C						PASS	.	G	THR/MET	1395,2291		262,871,710	167.0	150.0	155.0		1994	2.6	0.4	1	dbSNP_120	155	5766,2428		2006,1754,337	yes	missense	INPP5B	NM_005540.2	81	2268,2625,1047	GG,GA,AA		29.6314,37.8459,39.7222	benign	665/914	38338795	7161,4719	1843	4097	5940	SO:0001583	missense	3633	exon19			GCTGTCATCTTAT	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.2234T>C	1.37:g.38338795A>G	ENSP00000362117:p.Met745Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		1237	0.5663919413919414	166	0.33739837398373984	215	0.5939226519337016	293	0.5122377622377622	563	0.7427440633245382	G	0.015	-1.564422	0.00903	0.378459	0.703686	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	D;D;D;D	0.92699	-3.09;-2.92;-2.92;-2.92	5.59	2.59	0.31030	.	0.979230	0.08449	N	0.944196	T	0.00012	0.0000	N	0.00325	-1.645	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41592	-0.9500	9	0.11485	T	0.65	.	5.429	0.16442	0.0649:0.1192:0.4463:0.3696	rs11488569;rs17855745;rs17857480;rs11488569	745;665	P32019;P32019-2	I5P2_HUMAN;.	T	501;745;745;745;665	ENSP00000362118:M501T;ENSP00000362114:M745T;ENSP00000362117:M745T;ENSP00000362115:M665T	ENSP00000362114:M745T	M	-	2	0	INPP5B	38111382	0.489000	0.26004	0.403000	0.26384	0.963000	0.63663	1.586000	0.36611	0.026000	0.15269	-0.844000	0.03045	ATG	A|0.436;G|0.564	0.564	strong		0.438	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
SEMA6A	57556	hgsc.bcm.edu	37	5	115782493	115782493	+	Missense_Mutation	SNP	T	T	G	rs200578077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:115782493T>G	ENST00000343348.6	-	19	3696	c.2909A>C	c.(2908-2910)cAg>cCg	p.Q970P	SEMA6A_ENST00000282394.6_Missense_Mutation_p.Q447P|SEMA6A_ENST00000513137.1_Missense_Mutation_p.Q397P|SEMA6A_ENST00000257414.8_Missense_Mutation_p.Q987P|CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000512128.1_RNA|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.Q970P|SEMA6A_ENST00000503865.1_Missense_Mutation_p.Q349P	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	970					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		GCTGTGCACCTGGATGGAGTC	0.617																																					p.Q970P		Atlas-SNP	.											.	SEMA6A	93	.	0			c.A2909C						PASS	.	T	PRO/GLN	5,4167		0,5,2081	24.0	27.0	26.0		2909	4.3	1.0	5		26	62,8402		0,62,4170	yes	missense	SEMA6A	NM_020796.3	76	0,67,6251	GG,GT,TT		0.7325,0.1198,0.5302	probably-damaging	970/1031	115782493	67,12569	2086	4232	6318	SO:0001583	missense	57556	exon19			TGCACCTGGATGG	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.2909A>C	5.37:g.115782493T>G	ENSP00000345512:p.Gln970Pro	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	37	CCDS47256.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	15.45	2.836504	0.50951	0.001198	0.007325	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263	T;T;T;T;T;T	0.50001	2.11;2.1;0.76;2.59;0.79;2.11	4.27	4.27	0.50696	.	1.559450	0.04430	N	0.369061	T	0.51109	0.1655	L	0.46157	1.445	0.58432	D	0.999996	P;P;D;D;D;D	0.62365	0.936;0.874;0.991;0.974;0.965;0.965	P;B;P;P;P;P	0.55161	0.571;0.439;0.77;0.663;0.567;0.663	T	0.40739	-0.9547	10	0.59425	D	0.04	.	11.7765	0.51989	0.0:0.0:0.0:1.0	.	349;970;514;987;447;397	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01	.;SEM6A_HUMAN;.;.;.;.	P	970;987;397;447;349;970	ENSP00000345512:Q970P;ENSP00000257414:Q987P;ENSP00000422997:Q397P;ENSP00000282394:Q447P;ENSP00000425364:Q349P;ENSP00000424388:Q970P	ENSP00000257414:Q987P	Q	-	2	0	SEMA6A	115810392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.512000	0.81728	1.793000	0.52555	0.379000	0.24179	CAG	T|0.997;G|0.003	0.003	strong		0.617	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
ANO8	57719	hgsc.bcm.edu	37	19	17441909	17441909	+	Silent	SNP	T	T	G	rs61734355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17441909T>G	ENST00000159087.4	-	7	977	c.819A>C	c.(817-819)acA>acC	p.T273T		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	273					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)	p.T273T(1)		autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GATCAGCCTCTGTGAATGTGT	0.542													t|||	243	0.0485224	0.0522	0.0504	5008	,	,		19317	0.001		0.1054	False		,,,				2504	0.0327				p.T273T		Atlas-SNP	.											ANO8,NS,carcinoma,0,1	ANO8	67	1	1	Substitution - coding silent(1)	pancreas(1)	c.A819C						PASS	.	T		240,4166	140.4+/-175.9	6,228,1969	94.0	99.0	98.0		819	-9.6	0.0	19	dbSNP_129	98	941,7659	206.8+/-248.7	55,831,3414	no	coding-synonymous	ANO8	NM_020959.2		61,1059,5383	GG,GT,TT		10.9419,5.4471,9.0804		273/1233	17441909	1181,11825	2203	4300	6503	SO:0001819	synonymous_variant	57719	exon7			AGCCTCTGTGAAT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.819A>C	19.37:g.17441909T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	37	CCDS32949.1																																																																																			T|0.922;G|0.078	0.078	strong		0.542	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	73	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	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	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602865	138602865	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:138602865T>G	ENST00000422774.1	-	2	1555	c.1507A>C	c.(1507-1509)Acg>Ccg	p.T503P	KIAA1549_ENST00000242365.4_Missense_Mutation_p.T453P|KIAA1549_ENST00000440172.1_Missense_Mutation_p.T503P			Q9HCM3	K1549_HUMAN	KIAA1549	503	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCAACACTCGTCTCTGAGATT	0.502			O	BRAF	pilocytic astrocytoma																																p.T503P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.A1507C						PASS	.						34.0	34.0	34.0					7																	138602865		1944	4154	6098	SO:0001583	missense	57670	exon2			CACTCGTCTCTGA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1507A>C	7.37:g.138602865T>G	ENSP00000416040:p.Thr503Pro	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.264426	0.23136	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25912	1.77;1.77;1.77	4.24	-8.13	0.01073	.	2.614330	0.01241	N	0.008611	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14587	-1.0467	10	0.18276	T	0.48	.	5.0234	0.14372	0.2255:0.5515:0.1044:0.1186	.	503;503	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	P	503;453;503	ENSP00000406661:T503P;ENSP00000242365:T453P;ENSP00000416040:T503P	ENSP00000242365:T453P	T	-	1	0	KIAA1549	138253405	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.452000	0.06787	-1.529000	0.01754	-0.290000	0.09829	ACG	.	.	none		0.502	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
TLN2	83660	hgsc.bcm.edu	37	15	62990971	62990971	+	Silent	SNP	C	C	T	rs12905981	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:62990971C>T	ENST00000561311.1	+	15	1722	c.1492C>T	c.(1492-1494)Ctg>Ttg	p.L498L	TLN2_ENST00000306829.6_Silent_p.L498L			Q9Y4G6	TLN2_HUMAN	talin 2	498					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)	p.L498L(1)		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						CCAGCAGGCCCTGATGGGGAC	0.552													C|||	1755	0.350439	0.1899	0.3718	5008	,	,		19202	0.6855		0.2942	False		,,,				2504	0.2648				p.L498L		Atlas-SNP	.											TLN2,rectum,carcinoma,0,1	TLN2	253	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1492T						PASS	.	C		929,3477	353.3+/-312.1	94,741,1368	73.0	63.0	67.0		1492	5.0	1.0	15	dbSNP_121	67	2729,5871	432.8+/-357.2	420,1889,1991	no	coding-synonymous	TLN2	NM_015059.2		514,2630,3359	TT,TC,CC		31.7326,21.0849,28.1255		498/2543	62990971	3658,9348	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon13			CAGGCCCTGATGG	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.1492C>T	15.37:g.62990971C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.701;T|0.299	0.299	strong		0.552	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
CELSR1	9620	hgsc.bcm.edu	37	22	46760086	46760086	+	Missense_Mutation	SNP	C	C	T	rs35364389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46760086C>T	ENST00000262738.3	-	34	8841	c.8842G>A	c.(8842-8844)Ggc>Agc	p.G2948S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2948			G -> S (in dbSNP:rs35364389).		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)		CGGAGCCGGCCCTTCAGCGTC	0.642													C|||	899	0.179513	0.4576	0.1081	5008	,	,		15696	0.002		0.166	False		,,,				2504	0.0511				p.G2948S		Atlas-SNP	.											.	CELSR1	242	.	0			c.G8842A						PASS	.	C	SER/GLY	1704,2700	465.1+/-354.1	337,1030,835	39.0	47.0	44.0		8842	-0.1	0.3	22	dbSNP_126	44	1241,7351	234.4+/-267.4	87,1067,3142	yes	missense	CELSR1	NM_014246.1	56	424,2097,3977	TT,TC,CC		14.4437,38.6921,22.6608	benign	2948/3015	46760086	2945,10051	2202	4296	6498	SO:0001583	missense	9620	exon34			GCCGGCCCTTCAG	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.8842G>A	22.37:g.46760086C>T	ENSP00000262738:p.Gly2948Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	71	47	0.661972	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	390	0.17857142857142858	218	0.44308943089430897	46	0.1270718232044199	3	0.005244755244755245	123	0.16226912928759896	C	8.608	0.888398	0.17540	0.386921	0.144437	ENSG00000075275	ENST00000262738	T	0.65549	-0.16	4.85	-0.0792	0.13711	.	5.751230	0.01890	N	0.038451	T	0.00012	0.0000	N	0.02011	-0.69	0.09310	P	0.999999999478815	B	0.12630	0.006	B	0.04013	0.001	T	0.31052	-0.9957	9	0.02654	T	1	.	4.0661	0.09861	0.3067:0.2609:0.0:0.4324	rs35364389;rs59097028	2948	Q9NYQ6	CELR1_HUMAN	S	2948	ENSP00000262738:G2948S	ENSP00000262738:G2948S	G	-	1	0	CELSR1	45138750	1.000000	0.71417	0.252000	0.24328	0.974000	0.67602	2.559000	0.45888	-0.074000	0.12820	0.563000	0.77884	GGC	C|0.794;T|0.206	0.206	strong		0.642	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
MSLN	10232	hgsc.bcm.edu	37	16	818559	818559	+	Missense_Mutation	SNP	A	A	G	rs1135210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:818559A>G	ENST00000382862.3	+	16	1896	c.1801A>G	c.(1801-1803)Atg>Gtg	p.M601V	MSLN_ENST00000545450.2_Missense_Mutation_p.M593V|MSLN_ENST00000566549.1_Missense_Mutation_p.M593V|MIR662_ENST00000384847.1_RNA|MSLN_ENST00000563941.1_Missense_Mutation_p.M593V	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	601			M -> V (in dbSNP:rs1135210). {ECO:0000269|PubMed:10500211, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15616553, ECO:0000269|PubMed:15897581, ECO:0000269|PubMed:7665620, ECO:0000269|PubMed:8552591}.		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)				AGACCTCAGCATGCAAGGTGG	0.706													G|||	1770	0.353435	0.6059	0.2968	5008	,	,		10967	0.3115		0.1978	False		,,,				2504	0.2556				p.M601V		Atlas-SNP	.											MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	0			c.A1801G						scavenged	.	G	VAL/MET,VAL/MET,VAL/MET	2203,2121		564,1075,523	15.0	16.0	16.0		1777,1777,1801	-6.5	0.0	16	dbSNP_86	16	1921,6613		222,1477,2568	no	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	21,21,21	786,2552,3091	GG,GA,AA		22.51,49.0518,32.0734	benign,benign,benign	593/623,593/623,601/631	818559	4124,8734	2162	4267	6429	SO:0001583	missense	10232	exon16			CTCAGCATGCAAG	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.1801A>G	16.37:g.818559A>G	ENSP00000372313:p.Met601Val	Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	719	0.3292124542124542	305	0.6199186991869918	92	0.2541436464088398	174	0.3041958041958042	148	0.19525065963060687	G	0.008	-1.869221	0.00547	0.509482	0.2251	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.08896	3.04;3.04	3.27	-6.54	0.01860	.	1.419940	0.04960	N	0.461970	T	0.00012	0.0000	N	0.00347	-1.61	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	0.42207	-0.9465	9	0.10111	T	0.7	0.374	3.2179	0.06705	0.2108:0.0953:0.5431:0.1508	rs1135210;rs1803988;rs2272906;rs3178838;rs3197756;rs11558321;rs17143768;rs17855368;rs60036829;rs1135210	592;601;593	Q13421-4;Q13421;Q13421-3	.;MSLN_HUMAN;.	V	601;593;593;601	ENSP00000442965:M593V;ENSP00000372313:M601V	ENSP00000372313:M601V	M	+	1	0	MSLN	758560	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.235000	0.09016	-1.745000	0.01337	-2.568000	0.00172	ATG	A|0.678;G|0.322	0.322	strong		0.706	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
SMOX	54498	hgsc.bcm.edu	37	20	4164283	4164283	+	Silent	SNP	A	A	G	rs1741327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4164283A>G	ENST00000305958.4	+	6	1737	c.1512A>G	c.(1510-1512)acA>acG	p.T504T	SMOX_ENST00000379460.2_Silent_p.T504T|SMOX_ENST00000278795.3_Silent_p.T451T|SMOX_ENST00000346595.2_Intron|SMOX_ENST00000339123.6_Silent_p.T451T	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	504				T -> A (in Ref. 2; AAK55764). {ECO:0000305}.	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)	TGCCGTACACAGAGAGCTCAA	0.617													G|||	3478	0.694489	0.798	0.7219	5008	,	,		13512	0.7192		0.6889	False		,,,				2504	0.5153				p.T504T		Atlas-SNP	.											.	SMOX	119	.	0			c.A1512G						PASS	.	G	,,,	3497,905		1404,689,108	35.0	39.0	38.0		1512,1353,,1353	-10.4	0.1	20	dbSNP_89	38	5932,2664		2064,1804,430	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	SMOX	NM_175839.1,NM_175840.1,NM_175841.1,NM_175842.1	,,,	3468,2493,538	GG,GA,AA		30.9912,20.5588,27.4581	,,,	504/556,451/503,,451/533	4164283	9429,3569	2201	4298	6499	SO:0001819	synonymous_variant	54498	exon6			GTACACAGAGAGC	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.1512A>G	20.37:g.4164283A>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	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																																																																																			A|0.284;G|0.716	0.716	strong		0.617	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842	
KANK1	23189	hgsc.bcm.edu	37	9	712052	712052	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:712052C>T	ENST00000382303.1	+	7	1938	c.1286C>T	c.(1285-1287)aCa>aTa	p.T429I	KANK1_ENST00000382293.3_Missense_Mutation_p.T271I|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.T429I	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	429	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GCTGTAGGGACACTTGTTGAG	0.532																																					p.T429I		Atlas-SNP	.											.	KANK1	231	.	0			c.C1286T						PASS	.						118.0	101.0	107.0					9																	712052		2203	4300	6503	SO:0001583	missense	23189	exon7			TAGGGACACTTGT	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1286C>T	9.37:g.712052C>T	ENSP00000371740:p.Thr429Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010448	0.35511	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.43294	0.95;0.95;0.96	5.73	3.89	0.44902	.	0.112785	0.40728	N	0.001035	T	0.56277	0.1974	M	0.74258	2.255	0.80722	D	1	P;P	0.51147	0.942;0.865	P;P	0.56563	0.801;0.71	T	0.55976	-0.8055	10	0.44086	T	0.13	-15.3443	11.3529	0.49598	0.0:0.8043:0.127:0.0687	.	429;429	Q5W0W1;Q14678	.;KANK1_HUMAN	I	429;429;429;271	ENSP00000371740:T429I;ENSP00000371734:T429I;ENSP00000371730:T271I	ENSP00000346479:T429I	T	+	2	0	KANK1	702052	0.995000	0.38212	0.133000	0.22050	0.124000	0.20399	3.732000	0.55021	0.781000	0.33589	0.655000	0.94253	ACA	.	.	none		0.532	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056072	26056072	+	Silent	SNP	G	G	C	rs8384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	155	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	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	
USP45	85015	hgsc.bcm.edu	37	6	99956560	99956560	+	Missense_Mutation	SNP	T	T	C	rs7744845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:99956560T>C	ENST00000327681.6	-	3	731	c.199A>G	c.(199-201)Aaa>Gaa	p.K67E	USP45_ENST00000500704.2_Missense_Mutation_p.K67E|USP45_ENST00000369231.3_Missense_Mutation_p.K67E|USP45_ENST00000472914.2_Missense_Mutation_p.K67E|USP45_ENST00000369232.2_5'UTR|USP45_ENST00000392738.2_5'UTR|USP45_ENST00000369233.2_Missense_Mutation_p.K67E|USP45_ENST00000329966.6_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						scavenged	.	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	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	80	50	0.625	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	
KIAA0020	9933	hgsc.bcm.edu	37	9	2828742	2828742	+	Missense_Mutation	SNP	C	C	A	rs2270891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:2828742C>A	ENST00000397885.2	-	9	1095	c.889G>T	c.(889-891)Gta>Tta	p.V297L	KIAA0020_ENST00000469168.1_5'UTR	NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	297	HA-8.|PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.		V -> L (in allele HA-8PL; dbSNP:rs2270891).			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)		TCTGGCTGTACCTCTAACACT	0.333													C|||	244	0.048722	0.0499	0.0576	5008	,	,		16884	0.0615		0.0427	False		,,,				2504	0.0337				p.V297L		Atlas-SNP	.											.	KIAA0020	56	.	0			c.G889T						PASS	.	C	LEU/VAL	218,4184	130.2+/-166.9	2,214,1985	154.0	145.0	148.0		889	0.7	0.3	9	dbSNP_100	148	341,8259	116.3+/-176.0	4,333,3963	yes	missense	KIAA0020	NM_014878.4	32	6,547,5948	AA,AC,CC		3.9651,4.9523,4.2993	benign	297/649	2828742	559,12443	2201	4300	6501	SO:0001583	missense	9933	exon9			GCTGTACCTCTAA	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.889G>T	9.37:g.2828742C>A	ENSP00000380982:p.Val297Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	50	0.657895	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	111	0.050824175824175824	20	0.04065040650406504	16	0.04419889502762431	44	0.07692307692307693	31	0.040897097625329816	C	13.37	2.216896	0.39201	0.049523	0.039651	ENSG00000080608	ENST00000397885	T	0.12039	2.72	5.72	0.669	0.17918	Armadillo-like helical (1);Armadillo-type fold (1);	0.564178	0.18984	N	0.125797	T	0.00356	0.0011	N	0.14661	0.345	0.22771	N	0.998757	B	0.02656	0.0	B	0.01281	0.0	T	0.39099	-0.9630	10	0.28530	T	0.3	-33.3817	7.6286	0.28226	0.0:0.6455:0.1081:0.2463	rs2270891;rs58094561;rs2270891	297	Q15397	K0020_HUMAN	L	297	ENSP00000380982:V297L	ENSP00000380982:V297L	V	-	1	0	KIAA0020	2818742	0.265000	0.24102	0.265000	0.24526	0.961000	0.63080	0.634000	0.24614	-0.063000	0.13065	0.650000	0.86243	GTA	C|0.954;A|0.046	0.046	strong		0.333	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
SEC16A	9919	hgsc.bcm.edu	37	9	139370217	139370217	+	Silent	SNP	G	G	A	rs76562693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139370217G>A	ENST00000371706.3	-	1	1350	c.1317C>T	c.(1315-1317)caC>caT	p.H439H	SEC16A_ENST00000313050.7_Silent_p.H617H|SEC16A_ENST00000290037.6_Silent_p.H439H|SEC16A_ENST00000431893.2_Silent_p.H439H			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	439					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)				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)		CCCCAACTAAGTGAGATTTTA	0.547													G|||	136	0.0271565	0.003	0.0447	5008	,	,		18314	0.0		0.0696	False		,,,				2504	0.0317				p.H617H		Atlas-SNP	.											SEC16A_NM_014866.1,NS,haematopoietic_neoplasm,0,2	SEC16A	249	2	0			c.C1851T						PASS	.	G		63,4083		0,63,2010	37.0	38.0	38.0		1851	1.2	0.3	9	dbSNP_132	38	592,7816		15,562,3627	yes	coding-synonymous	SEC16A	NM_014866.1		15,625,5637	AA,AG,GG		7.0409,1.5195,5.2175		617/2358	139370217	655,11899	2073	4204	6277	SO:0001819	synonymous_variant	9919	exon3			AACTAAGTGAGAT	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.1317C>T	9.37:g.139370217G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.965;A|0.035	0.035	strong		0.547	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
GLYATL3	389396	hgsc.bcm.edu	37	6	49489397	49489397	+	Missense_Mutation	SNP	C	C	A	rs9369905	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:49489397C>A	ENST00000371197.4	+	5	466	c.353C>A	c.(352-354)gCc>gAc	p.A118D		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	118						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.A118D(3)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						AAAGCGGTTGCCAATTCAAAG	0.363													C|||	889	0.177516	0.0212	0.1931	5008	,	,		18692	0.2073		0.3439	False		,,,				2504	0.1759				p.A118D		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,3	GLYATL3	19	3	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.C353A						PASS	.						209.0	173.0	184.0					6																	49489397		692	1591	2283	SO:0001583	missense	389396	exon5			CGGTTGCCAATTC		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.353C>A	6.37:g.49489397C>A	ENSP00000360240:p.Ala118Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	437	0.2000915750915751	15	0.03048780487804878	75	0.20718232044198895	97	0.16958041958041958	250	0.32981530343007914	C	15.38	2.816761	0.50633	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.20738	2.05;2.05	5.9	5.9	0.94986	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	.	.	.	.	T	0.19644	0.0472	M	0.81341	2.54	0.27018	P	0.9645316	B	0.28470	0.213	B	0.32022	0.139	T	0.03335	-1.1047	8	0.36615	T	0.2	.	15.7685	0.78146	0.0:1.0:0.0:0.0	rs9369905;rs52815318;rs57040541;rs9369905	118	Q5SZD4	GLYL3_HUMAN	D	118	ENSP00000360240:A118D;ENSP00000440029:A118D	ENSP00000360240:A118D	A	+	2	0	GLYATL3	49597356	0.993000	0.37304	0.971000	0.41717	0.620000	0.37586	3.899000	0.56288	2.800000	0.96347	0.591000	0.81541	GCC	C|0.805;A|0.195	0.195	strong		0.363	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
TMEM230	29058	hgsc.bcm.edu	37	20	5086918	5086918	+	Silent	SNP	G	G	A	rs147693982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:5086918G>A	ENST00000379286.2	-	4	558	c.138C>T	c.(136-138)atC>atT	p.I46I	TMEM230_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000202834.7_Silent_p.I46I|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000342308.5_Silent_p.I109I|TMEM230_ENST00000379283.2_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	46						integral component of membrane (GO:0016021)											TGGCAAGTGCGATGGCCTTAT	0.443													G|||	21	0.00419329	0.0	0.0058	5008	,	,		15312	0.0		0.0169	False		,,,				2504	0.0				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.C327T						PASS	.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	63.0	62.0	62.0		327,138,138,138	-5.4	0.7	20	dbSNP_134	62	156,8444	74.5+/-137.1	2,152,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	2,178,6323	AA,AG,GG		1.814,0.5901,1.3994	,,,	109/184,46/121,46/121,46/121	5086918	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			AAGTGCGATGGCC	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.138C>T	20.37:g.5086918G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
PCNXL2	80003	hgsc.bcm.edu	37	1	233134086	233134086	+	Missense_Mutation	SNP	C	C	T	rs56231757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:233134086C>T	ENST00000258229.9	-	32	5936	c.5702G>A	c.(5701-5703)aGt>aAt	p.S1901N	PCNXL2_ENST00000344698.2_Missense_Mutation_p.S553N	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1901			S -> N (in dbSNP:rs56231757). {ECO:0000269|PubMed:9455477}.			integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GCTGCCACCACTCGGGGCATT	0.627													C|||	919	0.183506	0.2542	0.1657	5008	,	,		18270	0.12		0.2147	False		,,,				2504	0.1339				p.S1901N		Atlas-SNP	.											.	PCNXL2	204	.	0			c.G5702A						PASS	.	C	ASN/SER	1011,3043		106,799,1122	47.0	48.0	48.0		5702	3.8	0.0	1	dbSNP_129	48	1921,6477		222,1477,2500	yes	missense	PCNXL2	NM_014801.3	46	328,2276,3622	TT,TC,CC		22.8745,24.9383,23.5464	benign	1901/2138	233134086	2932,9520	2027	4199	6226	SO:0001583	missense	80003	exon32			CCACCACTCGGGG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5702G>A	1.37:g.233134086C>T	ENSP00000258229:p.Ser1901Asn	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	434	0.1987179487179487	132	0.2682926829268293	67	0.1850828729281768	75	0.13111888111888112	160	0.21108179419525067	C	13.99	2.402301	0.42613	0.249383	0.228745	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.23754	1.89;3.06	5.71	3.82	0.43975	.	0.900119	0.09944	N	0.735589	T	0.00012	0.0000	L	0.31294	0.92	0.41241	P	0.01335900000000001	B;B	0.11235	0.0;0.004	B;B	0.09377	0.002;0.004	T	0.29027	-1.0025	9	0.44086	T	0.13	.	9.345	0.38102	0.0:0.7795:0.0:0.2205	rs56231757;rs61738804	1901;553	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	N	553;1901	ENSP00000340759:S553N;ENSP00000258229:S1901N	ENSP00000258229:S1901N	S	-	2	0	PCNXL2	231200709	0.003000	0.15002	0.009000	0.14445	0.119000	0.20118	1.895000	0.39778	0.757000	0.33036	0.563000	0.77884	AGT	C|0.789;T|0.211	0.211	strong		0.627	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
FAM196B	100131897	hgsc.bcm.edu	37	5	169310606	169310606	+	Silent	SNP	A	A	T	rs145002054	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169310606A>T	ENST00000377365.3	-	2	1678	c.297T>A	c.(295-297)acT>acA	p.T99T	DOCK2_ENST00000256935.8_Intron|FAM196B_ENST00000523970.1_5'Flank|DOCK2_ENST00000520908.1_Intron|DOCK2_ENST00000540750.1_Intron|DOCK2_ENST00000523351.1_Intron	NM_001129891.1	NP_001123363.1	A6NMK8	F196B_HUMAN	family with sequence similarity 196, member B	99										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|skin(1)	5						GACTGGGGGAAGTTTGGATTG	0.547																																					p.T99T		Atlas-SNP	.											.	FAM196B	28	.	0			c.T297A						PASS	.	A	,	3,1381		0,3,689	83.0	82.0	82.0		297,	-3.8	1.0	5	dbSNP_134	82	77,3105		0,77,1514	no	coding-synonymous,intron	DOCK2,FAM196B	NM_001129891.1,NM_004946.2	,	0,80,2203	TT,TA,AA		2.4199,0.2168,1.7521	,	99/536,	169310606	80,4486	692	1591	2283	SO:0001819	synonymous_variant	100131897	exon2			GGGGGAAGTTTGG		CCDS47336.1	5q35.1	2010-02-17	2009-09-11	2009-09-11	ENSG00000204767	ENSG00000204767			37271	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 57"""	C5orf57			Standard	NM_001129891		Approved		uc003mag.2	A6NMK8	OTTHUMG00000163083	ENST00000377365.3:c.297T>A	5.37:g.169310606A>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001129891		Silent	SNP	ENST00000377365.3	37	CCDS47336.1																																																																																			A|0.987;T|0.013	0.013	strong		0.547	FAM196B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371629.1	NM_001129891	
MUC16	94025	hgsc.bcm.edu	37	19	9059159	9059159	+	Missense_Mutation	SNP	T	T	G	rs12462651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9059159T>G	ENST00000397910.4	-	3	28490	c.28287A>C	c.(28285-28287)aaA>aaC	p.K9429N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9431	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						GAGGGCTGTTTTTTTCCACAG	0.512													T|||	733	0.146366	0.087	0.1787	5008	,	,		20089	0.2669		0.0865	False		,,,				2504	0.1411				p.K9429N		Atlas-SNP	.											.	MUC16	4315	.	0			c.A28287C						PASS	.	T	ASN/LYS	387,3645		23,341,1652	107.0	107.0	107.0		28287	-1.8	0.0	19	dbSNP_120	107	644,7720		25,594,3563	yes	missense	MUC16	NM_024690.2	94	48,935,5215	GG,GT,TT		7.6997,9.5982,8.3172	possibly-damaging	9429/14508	9059159	1031,11365	2016	4182	6198	SO:0001583	missense	94025	exon3			GCTGTTTTTTTCC	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.28287A>C	19.37:g.9059159T>G	ENSP00000381008:p.Lys9429Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	334	0.15293040293040294	39	0.07926829268292683	56	0.15469613259668508	169	0.29545454545454547	70	0.09234828496042216	t	5.225	0.227014	0.09916	0.095982	0.076997	ENSG00000181143	ENST00000397910	T	0.27557	1.66	2.14	-1.81	0.07882	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	P	0.34977	0.478	B	0.34385	0.181	T	0.38265	-0.9669	8	0.87932	D	0	.	4.2523	0.10700	0.0:0.1647:0.5186:0.3167	rs12462651;rs52830069;rs12462651	9429	B5ME49	.	N	9429	ENSP00000381008:K9429N	ENSP00000381008:K9429N	K	-	3	2	MUC16	8920159	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.820000	0.04457	-0.484000	0.06763	0.255000	0.18592	AAA	T|0.854;G|0.146	0.146	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MAN2B2	23324	hgsc.bcm.edu	37	4	6600012	6600012	+	Missense_Mutation	SNP	A	A	G	rs2301790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:6600012A>G	ENST00000285599.3	+	9	1372	c.1336A>G	c.(1336-1338)Atg>Gtg	p.M446V	MAN2B2_ENST00000504248.1_Missense_Mutation_p.M395V	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	446			M -> V (in dbSNP:rs2301790). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.		mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						GATGCTGGGCATGCGCAAGCT	0.657													G|||	2501	0.499401	0.4372	0.5101	5008	,	,		19379	0.6141		0.4483	False		,,,				2504	0.5102				p.M446V		Atlas-SNP	.											MAN2B2,NS,carcinoma,0,2	MAN2B2	80	2	0			c.A1336G						PASS	.	G	VAL/MET	2005,2401	613.3+/-392.2	465,1075,663	77.0	69.0	71.0		1336	4.0	0.0	4	dbSNP_100	71	4036,4564	595.9+/-393.5	933,2170,1197	yes	missense	MAN2B2	NM_015274.1	21	1398,3245,1860	GG,GA,AA		46.9302,45.5061,46.4478	benign	446/1010	6600012	6041,6965	2203	4300	6503	SO:0001583	missense	23324	exon9			CTGGGCATGCGCA	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1336A>G	4.37:g.6600012A>G	ENSP00000285599:p.Met446Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	1098	0.5027472527472527	211	0.42886178861788615	185	0.511049723756906	357	0.6241258741258742	345	0.4551451187335092	G	0.009	-1.853728	0.00558	0.455061	0.469302	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.73575	-0.76;-0.76	4.86	4.02	0.46733	Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.49213	P	2.3399999999995647E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43393	-0.9394	9	0.07175	T	0.84	-24.7393	10.3179	0.43747	0.1656:0.0:0.8344:0.0	rs2301790;rs59126677;rs2301790	395;446;446	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	V	446;395	ENSP00000285599:M446V;ENSP00000423129:M395V	ENSP00000285599:M446V	M	+	1	0	MAN2B2	6650913	0.996000	0.38824	0.022000	0.16811	0.003000	0.03518	3.887000	0.56197	0.465000	0.27167	-0.735000	0.03563	ATG	G|0.474;A|0.526	0.474	strong		0.657	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48142636	48142636	+	Missense_Mutation	SNP	C	C	T	rs12422983	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:48142636C>T	ENST00000449771.2	-	11	1208	c.1120G>A	c.(1120-1122)Ggc>Agc	p.G374S	RAPGEF3_ENST00000549151.1_Missense_Mutation_p.G332S|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.G374S|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.G332S|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.G332S|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.G332S|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.G374S			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	374			G -> S (in dbSNP:rs12422983).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CGGGAAGGGCCGGCGCCCTGA	0.592													C|||	452	0.0902556	0.0998	0.1354	5008	,	,		16760	0.0298		0.1451	False		,,,				2504	0.0511				p.G374S		Atlas-SNP	.											RAPGEF3,colon,carcinoma,+1,1	RAPGEF3	98	1	0			c.G1120A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	488,3918	227.8+/-242.9	27,434,1742	165.0	152.0	156.0		1120,994,994	3.3	0.0	12	dbSNP_120	156	1253,7347	251.5+/-278.0	78,1097,3125	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	56,56,56	105,1531,4867	TT,TC,CC		14.5698,11.0758,13.3861	possibly-damaging,possibly-damaging,possibly-damaging	374/924,332/882,332/882	48142636	1741,11265	2203	4300	6503	SO:0001583	missense	10411	exon11			AAGGGCCGGCGCC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1120G>A	12.37:g.48142636C>T	ENSP00000395708:p.Gly374Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	221	0.10119047619047619	52	0.10569105691056911	56	0.15469613259668508	16	0.027972027972027972	97	0.1279683377308707	C	9.169	1.020728	0.19433	0.110758	0.145698	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	T;T;T;T;T;T;T	0.69806	-0.26;-0.26;-0.26;-0.26;-0.26;-0.43;-0.32	4.19	3.3	0.37823	Ras guanine nucleotide exchange factor, domain (1);	1.144270	0.06284	N	0.698024	T	0.00524	0.0017	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	P;D	0.63880	0.627;0.993	B;P	0.52793	0.034;0.709	T	0.10870	-1.0611	9	0.37606	T	0.19	.	5.7708	0.18251	0.0:0.7053:0.0:0.2947	rs12422983;rs52812325;rs12422983	386;374	B7Z5J6;O95398	.;RPGF3_HUMAN	S	332;374;21;332;332;332;374;386;332;374	ENSP00000384521:G332S;ENSP00000395708:G374S;ENSP00000448619:G332S;ENSP00000171000:G332S;ENSP00000373864:G374S;ENSP00000448480:G332S;ENSP00000378764:G374S	ENSP00000171000:G332S	G	-	1	0	RAPGEF3	46428903	0.000000	0.05858	0.023000	0.16930	0.065000	0.16274	0.404000	0.20999	1.349000	0.45751	0.650000	0.86243	GGC	C|0.880;T|0.120	0.120	strong		0.592	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
HRNR	388697	hgsc.bcm.edu	37	1	152188999	152188999	+	Silent	SNP	G	G	A	rs149648668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152188999G>A	ENST00000368801.2	-	3	5181	c.5106C>T	c.(5104-5106)caC>caT	p.H1702H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1702					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.H1702H(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTGTCGGCCGTGGCCCGAAG	0.632																																					p.H1702H		Atlas-SNP	.											HRNR,NS,carcinoma,0,2	HRNR	403	2	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C5106T						scavenged	.	G		87,3097		0,87,1505	50.0	74.0	66.0		5106	-6.0	0.0	1	dbSNP_134	66	354,5964		0,354,2805	no	coding-synonymous	HRNR	NM_001009931.1		0,441,4310	AA,AG,GG		5.603,2.7324,4.6411		1702/2851	152188999	441,9061	1592	3159	4751	SO:0001819	synonymous_variant	388697	exon3			TCGGCCGTGGCCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5106C>T	1.37:g.152188999G>A		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	160	23	0.14375	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.947;A|0.053	0.053	strong		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ITIH2	3698	hgsc.bcm.edu	37	10	7774397	7774397	+	Missense_Mutation	SNP	A	A	G	rs141156651		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:7774397A>G	ENST00000358415.4	+	14	1910	c.1744A>G	c.(1744-1746)Aaa>Gaa	p.K582E	ITIH2_ENST00000379587.4_Missense_Mutation_p.K571E	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	582					hyaluronan metabolic process (GO:0030212)|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)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TTTCACCAGGAAACTGTGGGC	0.493																																					p.K582E		Atlas-SNP	.											.	ITIH2	144	.	0			c.A1744G						PASS	.	A	GLU/LYS	0,4406		0,0,2203	101.0	91.0	95.0		1744	5.3	0.8	10	dbSNP_134	95	6,8594	5.7+/-21.5	0,6,4294	yes	missense	ITIH2	NM_002216.2	56	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	possibly-damaging	582/947	7774397	6,13000	2203	4300	6503	SO:0001583	missense	3698	exon14			ACCAGGAAACTGT	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1744A>G	10.37:g.7774397A>G	ENSP00000351190:p.Lys582Glu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202257	0.79127	0.0	6.98E-4	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.30714	1.52;1.52	5.32	5.32	0.75619	.	0.054094	0.85682	D	0.000000	T	0.40619	0.1124	M	0.76838	2.35	0.41456	D	0.988014	P	0.45902	0.868	P	0.45167	0.472	T	0.47724	-0.9095	10	0.87932	D	0	-28.5342	11.323	0.49433	0.848:0.152:0.0:0.0	.	582	P19823	ITIH2_HUMAN	E	582;571	ENSP00000351190:K582E;ENSP00000368906:K571E	ENSP00000351190:K582E	K	+	1	0	ITIH2	7814403	1.000000	0.71417	0.827000	0.32855	0.967000	0.64934	6.049000	0.71053	2.022000	0.59522	0.523000	0.50628	AAA	A|1.000;G|0.000	0.000	weak		0.493	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
IMPG1	3617	hgsc.bcm.edu	37	6	76640803	76640803	+	Missense_Mutation	SNP	G	G	A	rs10943299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:76640803G>A	ENST00000369950.3	-	15	2299	c.2110C>T	c.(2110-2112)Cgg>Tgg	p.R704W	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TCCTCAGTCCGTTCGTTCTTT	0.542													g|||	450	0.0898562	0.0862	0.0821	5008	,	,		19099	0.003		0.1402	False		,,,				2504	0.138				p.R704W	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C2110T						PASS	.	A	TRP/ARG	419,3987	204.5+/-226.7	21,377,1805	88.0	71.0	77.0		2110	-7.6	0.0	6	dbSNP_120	77	1243,7357	249.0+/-276.5	81,1081,3138	yes	missense	IMPG1	NM_001563.2	101	102,1458,4943	AA,AG,GG		14.4535,9.5098,12.7787	benign	704/798	76640803	1662,11344	2203	4300	6503	SO:0001583	missense	3617	exon15			CAGTCCGTTCGTT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2110C>T	6.37:g.76640803G>A	ENSP00000358966:p.Arg704Trp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	189	0.08653846153846154	49	0.09959349593495935	28	0.07734806629834254	0	0.0	112	0.14775725593667546	g	0.009	-1.809098	0.00606	0.095098	0.144535	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.15834	2.41;2.39	5.45	-7.59	0.01308	Epidermal growth factor-like, type 3 (1);	0.900030	0.09563	N	0.785241	T	0.00666	0.0022	N	0.00510	-1.415	0.36734	P	0.11815600000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.33445	-0.9868	9	0.02654	T	1	.	8.3239	0.32145	0.3945:0.2022:0.4034:0.0	rs10943299;rs52822464;rs10943299	704	Q17R60	IMPG1_HUMAN	W	704;65	ENSP00000358966:R704W;ENSP00000358968:R65W	ENSP00000358966:R704W	R	-	1	2	IMPG1	76697523	0.200000	0.23398	0.001000	0.08648	0.029000	0.11900	0.417000	0.21214	-2.374000	0.00599	-2.927000	0.00089	CGG	G|0.883;A|0.117	0.117	strong		0.542	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
XPO7	23039	hgsc.bcm.edu	37	8	21862551	21862551	+	Silent	SNP	A	A	G	rs1058486	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:21862551A>G	ENST00000252512.9	+	28	3316	c.3216A>G	c.(3214-3216)tcA>tcG	p.S1072S	XPO7_ENST00000433566.4_Silent_p.S1073S|XPO7_ENST00000434536.1_Silent_p.S1081S	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	1072					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TCAACGACTCAATGAAGAATT	0.522													G|||	2894	0.577875	0.7632	0.4352	5008	,	,		19393	0.5268		0.5994	False		,,,				2504	0.4591				p.S1072S		Atlas-SNP	.											.	XPO7	79	.	0			c.A3216G						PASS	.	G		2957,1095		1097,763,166	150.0	151.0	151.0		3216	-1.1	1.0	8	dbSNP_86	151	4638,3738		1290,2058,840	no	coding-synonymous	XPO7	NM_015024.4		2387,2821,1006	GG,GA,AA		44.6275,27.0237,38.888		1072/1088	21862551	7595,4833	2026	4188	6214	SO:0001819	synonymous_variant	23039	exon28			CGACTCAATGAAG	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.3216A>G	8.37:g.21862551A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	37	CCDS47818.1																																																																																			A|0.407;G|0.593	0.593	strong		0.522	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
MICAL1	64780	hgsc.bcm.edu	37	6	109767930	109767930	+	Missense_Mutation	SNP	G	G	T	rs552227069|rs9320288|rs35260632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:109767930G>T	ENST00000358807.3	-	18	2584	c.2273C>A	c.(2272-2274)gCg>gAg	p.A758E	MICAL1_ENST00000358577.3_Missense_Mutation_p.A672E|MICAL1_ENST00000368952.4_Missense_Mutation_p.A777E	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	758			A -> E (in dbSNP:rs9320288).|A -> K (requires 2 nucleotide substitutions; dbSNP:rs35260632). {ECO:0000269|PubMed:11827972, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|A -> S (in dbSNP:rs59056467).|A -> T (in dbSNP:rs59056467).		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)		GCTGCCTTCCGCTTTGTGGTC	0.572													T|||	2790	0.557109	0.7579	0.4971	5008	,	,		18500	0.4514		0.4453	False		,,,				2504	0.5521				p.A758E		Atlas-SNP	.											.	MICAL1	79	.	0			c.C2273A						PASS	.	T	GLU/ALA,GLU/ALA	3013,1393		1086,841,276	77.0	68.0	71.0		2015,2273	2.2	0.0	6	dbSNP_119	71	3274,5326		825,1624,1851	no	missense,missense	MICAL1	NM_001159291.1,NM_022765.3	107,107	1911,2465,2127	TT,TG,GG		38.0698,31.616,48.3392	benign,benign	672/982,758/1068	109767930	6287,6719	2203	4300	6503	SO:0001583	missense	64780	exon18			CCTTCCGCTTTGT	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.2273C>A	6.37:g.109767930G>T	ENSP00000351664:p.Ala758Glu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	181	92	0.508287	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	37	CCDS5076.1	1108	0.5073260073260073	358	0.7276422764227642	171	0.4723756906077348	268	0.46853146853146854	311	0.4102902374670185	T	0.142	-1.100897	0.01843	0.68384	0.380698	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577;ENST00000368957	T;T;T	0.50277	0.76;0.75;0.76	4.88	2.24	0.28232	.	0.685752	0.13980	N	0.349545	T	0.03095	0.0091	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	0.43048	-0.9415	9	0.02654	T	1	.	10.2069	0.43118	0.0:0.0:0.5225:0.4775	rs9320288;rs61598792	672;758	Q8TDZ2-2;Q8TDZ2	.;MICA1_HUMAN	E	758;777;672;282	ENSP00000351664:A758E;ENSP00000357948:A777E;ENSP00000351385:A672E	ENSP00000351385:A672E	A	-	2	0	MICAL1	109874623	0.007000	0.16637	0.001000	0.08648	0.000000	0.00434	1.565000	0.36386	0.400000	0.25396	-1.489000	0.00976	GCG	G|0.502;T|0.498	0.498	strong		0.572	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
FEZ2	9637	hgsc.bcm.edu	37	2	36810586	36810586	+	Silent	SNP	T	T	C	rs14291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:36810586T>C	ENST00000405912.3	-	3	401	c.402A>G	c.(400-402)acA>acG	p.T134T	FEZ2_ENST00000379245.4_Silent_p.T134T|FEZ2_ENST00000305852.7_5'UTR	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	134					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)				CATCATCTGATGTATCAAAGA	0.403													C|||	2147	0.428714	0.4478	0.5144	5008	,	,		21080	0.4147		0.4115	False		,,,				2504	0.3742				p.T134T		Atlas-SNP	.											.	FEZ2	13	.	0			c.A402G						PASS	.	C	,	1709,2153		369,971,591	132.0	125.0	127.0		402,402	-11.3	0.0	2	dbSNP_52	127	3043,5251		542,1959,1646	yes	coding-synonymous,coding-synonymous	FEZ2	NM_001042548.1,NM_005102.2	,	911,2930,2237	CC,CT,TT		36.6892,44.2517,39.0918	,	134/381,134/354	36810586	4752,7404	1931	4147	6078	SO:0001819	synonymous_variant	9637	exon3			ATCTGATGTATCA	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.402A>G	2.37:g.36810586T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_001042548	Q5EBN3|Q76LN0|Q99690	Silent	SNP	ENST00000405912.3	37	CCDS46257.1																																																																																			T|0.567;C|0.433	0.433	strong		0.403	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1		
NPS	594857	hgsc.bcm.edu	37	10	129347785	129347785	+	Missense_Mutation	SNP	C	C	T	rs990310	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:129347785C>T	ENST00000398023.1	+	2	61	c.41C>T	c.(40-42)tCg>tTg	p.S14L		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	14			S -> L (in dbSNP:rs990310).		neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						CTAGTTCTGTCGCTGTCCACA	0.363													C|||	681	0.135982	0.3245	0.0476	5008	,	,		18800	0.0546		0.0477	False		,,,				2504	0.1186				p.S14L		Atlas-SNP	.											.	NPS	14	.	0			c.C41T						PASS	.	C	LEU/SER	1039,2823		147,745,1039	258.0	243.0	248.0		41	-9.2	0.0	10	dbSNP_86	248	332,7932		9,314,3809	yes	missense	NPS	NM_001030013.1	145	156,1059,4848	TT,TC,CC		4.0174,26.9032,11.3063	benign	14/90	129347785	1371,10755	1931	4132	6063	SO:0001583	missense	594857	exon2			TTCTGTCGCTGTC	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"""Endogenous ligands"""	33940	protein-coding gene	gene with protein product	"""prepro-neuropeptide S"""	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.41C>T	10.37:g.129347785C>T	ENSP00000381105:p.Ser14Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	155	84	0.541936	NM_001030013		Missense_Mutation	SNP	ENST00000398023.1	37	CCDS41577.1	235	0.10760073260073261	153	0.31097560975609756	22	0.06077348066298342	26	0.045454545454545456	34	0.044854881266490766	C	2.573	-0.299248	0.05532	0.269032	0.040174	ENSG00000214285	ENST00000398023	T	0.31769	1.48	5.72	-9.24	0.00669	.	0.726816	0.10555	N	0.660992	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.32107	-0.9919	8	0.02654	T	1	1.1698	11.0046	0.47626	0.0:0.1362:0.2648:0.599	rs990310;rs990310	14	P0C0P6	NPS_HUMAN	L	14	ENSP00000381105:S14L	ENSP00000381105:S14L	S	+	2	0	NPS	129237775	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.888000	0.04148	-1.435000	0.01972	-0.812000	0.03155	TCG	C|0.892;T|0.108	0.108	strong		0.363	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013	
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36157740C>T	ENST00000222275.2	+	1	26	c.26C>T	c.(25-27)gCc>gTc	p.A9V	UPK1A_ENST00000379013.2_Missense_Mutation_p.A9V|RN7SL765P_ENST00000580260.1_RNA|UPK1A-AS1_ENST00000443196.1_RNA	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	9					epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCAGCGGAGGCCGAGAAGGGA	0.612													C|||	764	0.152556	0.2753	0.0562	5008	,	,		17149	0.0278		0.1123	False		,,,				2504	0.2249				p.A9V		Atlas-SNP	.											.	UPK1A	23	.	0			c.C26T						PASS	.	C	VAL/ALA	1011,3395	375.1+/-321.5	123,765,1315	147.0	136.0	139.0		26	-3.1	0.0	19	dbSNP_129	139	949,7651	209.6+/-250.7	53,843,3404	yes	missense	UPK1A	NM_007000.2	64	176,1608,4719	TT,TC,CC		11.0349,22.946,15.07	benign	9/259	36157740	1960,11046	2203	4300	6503	SO:0001583	missense	11045	exon1			CGGAGGCCGAGAA	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"""Tetraspanins"""	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.26C>T	19.37:g.36157740C>T	ENSP00000222275:p.Ala9Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	154	64	0.415584	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	259	0.11858974358974358	130	0.26422764227642276	27	0.07458563535911603	14	0.024475524475524476	88	0.11609498680738786	C	13.21	2.167807	0.38315	0.22946	0.110349	ENSG00000105668	ENST00000222275;ENST00000379013	T;T	0.06849	3.43;3.25	4.23	-3.14	0.05250	.	1.673270	0.03514	N	0.219987	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	0.08055	0.003;0.0	T	0.46965	-0.9153	9	0.30854	T	0.27	.	1.2775	0.02033	0.1348:0.2769:0.1798:0.4085	rs61741212	9;9	O00322-2;O00322	.;UPK1A_HUMAN	V	9	ENSP00000222275:A9V;ENSP00000368298:A9V	ENSP00000222275:A9V	A	+	2	0	UPK1A	40849580	0.000000	0.05858	0.002000	0.10522	0.060000	0.15804	-1.225000	0.02956	-0.417000	0.07461	0.655000	0.94253	GCC	C|0.856;T|0.144	0.144	strong		0.612	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
SLC27A6	28965	hgsc.bcm.edu	37	5	128301885	128301885	+	Missense_Mutation	SNP	T	T	G	rs2526247	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:128301885T>G	ENST00000262462.4	+	1	1065	c.55T>G	c.(55-57)Ttg>Gtg	p.L19V	SLC27A6_ENST00000395266.1_Missense_Mutation_p.L19V|SLC27A6_ENST00000506176.1_Missense_Mutation_p.L19V			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	19			L -> V (in dbSNP:rs2526247). {ECO:0000269|PubMed:15489334}.		long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		CCTGCACTTCTTGCAGAAACT	0.507													G|||	1037	0.207069	0.1853	0.2522	5008	,	,		18107	0.0585		0.3668	False		,,,				2504	0.1933				p.L19V		Atlas-SNP	.											.	SLC27A6	112	.	0			c.T55G						PASS	.	G	VAL/LEU,VAL/LEU	972,3434	730.0+/-410.1	92,788,1323	80.0	78.0	79.0		55,55	-8.9	0.0	5	dbSNP_100	79	3234,5366	647.5+/-400.4	618,1998,1684	yes	missense,missense	SLC27A6	NM_001017372.1,NM_014031.3	32,32	710,2786,3007	GG,GT,TT		37.6047,22.0608,32.3389	benign,benign	19/620,19/620	128301885	4206,8800	2203	4300	6503	SO:0001583	missense	28965	exon1			CACTTCTTGCAGA	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.55T>G	5.37:g.128301885T>G	ENSP00000262462:p.Leu19Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	529	0.24221611721611722	103	0.20934959349593496	114	0.3149171270718232	38	0.06643356643356643	274	0.36147757255936674	G	2.764	-0.257268	0.05791	0.220608	0.376047	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.53640	0.61;0.61;0.61	4.45	-8.9	0.00782	.	1.067860	0.07158	N	0.850299	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.20940	-1.0260	9	0.13108	T	0.6	-17.7733	2.4377	0.04487	0.1714:0.3601:0.1558:0.3126	rs2526247;rs3734163;rs17857261;rs56951819;rs2526247	19	Q9Y2P4	S27A6_HUMAN	V	19	ENSP00000262462:L19V;ENSP00000378684:L19V;ENSP00000421024:L19V	ENSP00000262462:L19V	L	+	1	2	SLC27A6	128329784	0.000000	0.05858	0.000000	0.03702	0.606000	0.37113	-6.036000	0.00084	-3.239000	0.00207	-1.023000	0.02433	TTG	T|0.717;G|0.283	0.283	strong		0.507	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
RNF43	54894	hgsc.bcm.edu	37	17	56438301	56438301	+	Missense_Mutation	SNP	G	G	A	rs2680701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56438301G>A	ENST00000584437.1	-	6	2647	c.692C>T	c.(691-693)cCg>cTg	p.P231L	RNF43_ENST00000581868.1_Missense_Mutation_p.P104L|RNF43_ENST00000577625.1_Missense_Mutation_p.P104L|RNF43_ENST00000577716.1_Missense_Mutation_p.P231L|RNF43_ENST00000500597.2_Missense_Mutation_p.P190L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Missense_Mutation_p.P231L|RNF43_ENST00000583753.1_Missense_Mutation_p.P190L			Q68DV7	RNF43_HUMAN	ring finger protein 43	231			P -> L (in dbSNP:rs2680701). {ECO:0000269|PubMed:14702039}.		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)					CTGCTGAAGCGGATCCTGGGA	0.642													G|||	413	0.0824681	0.0227	0.1297	5008	,	,		18621	0.001		0.2197	False		,,,				2504	0.0726				p.P231L		Atlas-SNP	.											.	RNF43	157	.	0			c.C692T						PASS	.	G	LEU/PRO	212,4194	128.2+/-165.1	7,198,1998	36.0	36.0	36.0		692	3.7	1.0	17	dbSNP_100	36	1740,6860	315.1+/-312.1	173,1394,2733	yes	missense	RNF43	NM_017763.4	98	180,1592,4731	AA,AG,GG		20.2326,4.8116,15.0085	probably-damaging	231/784	56438301	1952,11054	2203	4300	6503	SO:0001583	missense	54894	exon7			TGAAGCGGATCCT		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.692C>T	17.37:g.56438301G>A	ENSP00000463069:p.Pro231Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	224	0.10256410256410256	13	0.026422764227642278	59	0.16298342541436464	0	0.0	152	0.20052770448548812	G	16.66	3.184208	0.57800	0.048116	0.202326	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.08984	3.18;3.03	4.64	3.65	0.41850	.	0.860402	0.10142	N	0.710769	T	0.00012	0.0000	L	0.29908	0.895	0.19575	P	0.9999681561	B;D;P	0.53312	0.056;0.959;0.76	B;B;B	0.39617	0.012;0.305;0.054	T	0.41034	-0.9531	9	0.10636	T	0.68	-4.0077	12.1401	0.53993	0.0852:0.0:0.9148:0.0	rs2680701;rs17762921;rs52810433;rs60964304;rs2680701	190;231;231	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	L	231;190	ENSP00000385328:P231L;ENSP00000441969:P190L	ENSP00000385328:P231L	P	-	2	0	RNF43	53793300	1.000000	0.71417	0.992000	0.48379	0.880000	0.50808	7.333000	0.79214	0.939000	0.37446	0.313000	0.20887	CCG	G|0.875;A|0.125	0.125	strong		0.642	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
INADL	10207	hgsc.bcm.edu	37	1	62456014	62456014	+	Missense_Mutation	SNP	G	G	A	rs1134767	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62456014G>A	ENST00000371158.2	+	28	3959	c.3845G>A	c.(3844-3846)cGt>cAt	p.R1282H	INADL_ENST00000543708.1_Missense_Mutation_p.R66H|INADL_ENST00000316485.6_Missense_Mutation_p.R1282H|INADL_ENST00000545929.1_5'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1282	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> H (in dbSNP:rs1134767). {ECO:0000269|PubMed:11374908, ECO:0000269|PubMed:9280290}.		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						GGACGAATGCGTATTGGAGAT	0.458													A|||	2378	0.47484	0.553	0.3199	5008	,	,		14762	0.4683		0.4066	False		,,,				2504	0.5562				p.R1282H		Atlas-SNP	.											.	INADL	179	.	0			c.G3845A						PASS	.	A	HIS/ARG	2162,2244	593.7+/-388.1	566,1030,607	78.0	75.0	76.0		3845	-1.2	0.0	1	dbSNP_86	76	3630,4970	625.1+/-397.7	782,2066,1452	yes	missense	INADL	NM_176877.2	29	1348,3096,2059	AA,AG,GG		42.2093,49.0695,44.5333	benign	1282/1802	62456014	5792,7214	2203	4300	6503	SO:0001583	missense	10207	exon28			GAATGCGTATTGG	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.3845G>A	1.37:g.62456014G>A	ENSP00000360200:p.Arg1282His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	944	0.43223443223443225	265	0.5386178861788617	134	0.3701657458563536	239	0.4178321678321678	306	0.40369393139841686	A	1.458	-0.563118	0.03939	0.490695	0.422093	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.73	-1.21	0.09524	PDZ/DHR/GLGF (4);	0.336176	0.26200	N	0.025758	T	0.00012	0.0000	L	0.37897	1.145	0.26059	P	0.981374	B;B;B;B;B	0.09022	0.002;0.001;0.0;0.002;0.0	B;B;B;B;B	0.10450	0.005;0.003;0.002;0.003;0.001	T	0.46775	-0.9167	9	0.16896	T	0.51	.	7.2394	0.26088	0.4461:0.0:0.4453:0.1086	rs1134767;rs3197112;rs3762448;rs58675169;rs1134767	66;741;1282;1282;1282	B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;INADL_HUMAN;.	H	1282;1282;1282;1282;66;66	ENSP00000360200:R1282H;ENSP00000326199:R1282H;ENSP00000307496:R66H;ENSP00000445790:R66H	ENSP00000307496:R66H	R	+	2	0	INADL	62228602	0.000000	0.05858	0.044000	0.18714	0.004000	0.04260	-0.174000	0.09839	-0.098000	0.12285	-1.632000	0.00781	CGT	G|0.547;A|0.453	0.453	strong		0.458	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
NOX4	50507	hgsc.bcm.edu	37	11	89060002	89060002	+	Silent	SNP	G	G	A	rs28517716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89060002G>A	ENST00000263317.4	-	18	1897	c.1659C>T	c.(1657-1659)tcC>tcT	p.S553S	NOX4_ENST00000343727.5_Silent_p.S529S|NOX4_ENST00000535633.1_Silent_p.S529S|NOX4_ENST00000528341.1_Silent_p.S528S|NOX4_ENST00000413594.2_Silent_p.S574S|NOX4_ENST00000375979.3_Silent_p.S246S|NOX4_ENST00000527626.1_Silent_p.S366S|NOX4_ENST00000527956.1_Silent_p.S529S|NOX4_ENST00000532825.1_Silent_p.S489S|NOX4_ENST00000531342.1_Silent_p.S206S|NOX4_ENST00000542487.1_Silent_p.S529S|NOX4_ENST00000534731.1_Silent_p.S513S|NOX4_ENST00000424319.1_Silent_p.S529S|NOX4_ENST00000525196.1_Silent_p.S317S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	553	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAAGAGTCTTGGATAGTGAAT	0.368													G|||	660	0.131789	0.2405	0.0418	5008	,	,		16825	0.1429		0.0507	False		,,,				2504	0.1207				p.S553S		Atlas-SNP	.											NOX4,NS,carcinoma,-1,1	NOX4	101	1	0			c.C1659T						PASS	.	G	,,	791,3611	299.6+/-285.9	68,655,1478	89.0	89.0	89.0		1539,1587,1659	2.4	1.0	11	dbSNP_125	89	347,8251	115.5+/-175.4	5,337,3957	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX4	NM_001143836.1,NM_001143837.1,NM_016931.3	,,	73,992,5435	AA,AG,GG		4.0358,17.9691,8.7538	,,	513/539,529/555,553/579	89060002	1138,11862	2201	4299	6500	SO:0001819	synonymous_variant	50507	exon18			AGTCTTGGATAGT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1659C>T	11.37:g.89060002G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	37	CCDS8285.1																																																																																			G|0.912;A|0.088	0.088	strong		0.368	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
DCHS2	54798	hgsc.bcm.edu	37	4	155298536	155298536	+	Missense_Mutation	SNP	C	C	T	rs149005474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:155298536C>T	ENST00000357232.4	-	3	294	c.295G>A	c.(295-297)Gga>Aga	p.G99R	DCHS2_ENST00000339452.1_Missense_Mutation_p.G705R	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	99	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)		CTCAGGAATCCATCATAAAGA	0.468																																					p.G705R		Atlas-SNP	.											.	DCHS2	594	.	0			c.G2113A						PASS	.	C	ARG/GLY,ARG/GLY	0,4406		0,0,2203	94.0	90.0	91.0		2113,295	5.6	1.0	4	dbSNP_134	91	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	DCHS2	NM_001142552.1,NM_017639.3	125,125	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	705/1370,99/2917	155298536	4,13002	2203	4300	6503	SO:0001583	missense	54798	exon2			GGAATCCATCATA	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.295G>A	4.37:g.155298536C>T	ENSP00000349768:p.Gly99Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.787331	0.70337	0.0	4.65E-4	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.66460	-0.21;0.42	5.64	5.64	0.86602	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000013	T	0.81375	0.4809	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.83054	-0.0151	10	0.72032	D	0.01	.	13.6208	0.62136	0.0:0.9248:0.0:0.0752	.	705;99	E9PC11;Q6V1P9	.;PCD23_HUMAN	R	99;705;705	ENSP00000349768:G99R;ENSP00000345062:G705R	ENSP00000345062:G705R	G	-	1	0	DCHS2	155517986	1.000000	0.71417	0.997000	0.53966	0.613000	0.37349	4.520000	0.60524	2.664000	0.90586	0.561000	0.74099	GGA	C|1.000;T|0.000	0.000	strong		0.468	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
NAA38	84316	hgsc.bcm.edu	37	17	7760704	7760704	+	Silent	SNP	A	A	G	rs8522	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7760704A>G	ENST00000335155.5	-	1	77	c.78T>C	c.(76-78)gcT>gcC	p.A26A	LSMD1_ENST00000575208.1_Intron|LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000575071.1_5'UTR|LSMD1_ENST00000576384.1_5'Flank|CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000570446.1_5'Flank|LSMD1_ENST00000333775.5_Missense_Mutation_p.L13P|LSMD1_ENST00000576861.1_Intron|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000575771.1_5'UTR			Q9BRA0	LSMD1_HUMAN		26					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				TGCTAACCCCAGCACTGGAGC	0.637													G|||	2185	0.436302	0.388	0.3905	5008	,	,		15269	0.7956		0.1948	False		,,,				2504	0.4121				p.L13P	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											.	LSMD1	8	.	0			c.T38C						PASS	.	G	PRO/LEU	1544,2862	641.0+/-397.4	272,1000,931	42.0	52.0	49.0		38	-5.0	0.9	17	dbSNP_52	49	1882,6718	711.5+/-405.8	209,1464,2627	yes	missense	LSMD1	NM_032356.3	98	481,2464,3558	GG,GA,AA		21.8837,35.0431,26.3417	benign	13/174	7760704	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	84316	exon1			AACCCCAGCACTG																												ENST00000335155.5:c.78T>C	17.37:g.7760704A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_032356	Q8N4M0	Missense_Mutation	SNP	ENST00000335155.5	37		874	0.4001831501831502	148	0.3008130081300813	127	0.35082872928176795	465	0.8129370629370629	134	0.17678100263852242	G	0.844	-0.740751	0.03088	0.350431	0.218837	ENSG00000183011	ENST00000333775	T	0.56444	0.46	5.65	-5.02	0.02982	.	0.196677	0.25469	N	0.030450	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999877715	B	0.02656	0.0	B	0.01281	0.0	T	0.32161	-0.9917	8	0.11794	T	0.64	.	3.8358	0.08893	0.5487:0.1141:0.2209:0.1162	rs8522;rs1129549;rs3826332;rs11551746;rs17855012;rs52822583;rs58072623;rs8522	13	Q9BRA0-2	.	P	13	ENSP00000332103:L13P	ENSP00000332103:L13P	L	-	2	0	LSMD1	7701429	0.911000	0.30947	0.947000	0.38551	0.581000	0.36288	-0.339000	0.07832	-0.670000	0.05282	-0.916000	0.02749	CTG	A|0.678;G|0.322	0.322	strong		0.637	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
COL27A1	85301	hgsc.bcm.edu	37	9	116930194	116930194	+	Missense_Mutation	SNP	A	A	G	rs2567706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:116930194A>G	ENST00000356083.3	+	3	750	c.359A>G	c.(358-360)cAg>cGg	p.Q120R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	120	Laminin G-like.		Q -> R (in dbSNP:rs2567706).		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						GTCCGCAGCCAGAAACGCAAG	0.662													G|||	1060	0.211661	0.3033	0.17	5008	,	,		16427	0.1329		0.2883	False		,,,				2504	0.1196				p.Q120R		Atlas-SNP	.											.	COL27A1	200	.	0			c.A359G						PASS	.	G	ARG/GLN	1367,3037	682.0+/-404.1	209,949,1044	60.0	61.0	61.0		359	2.2	1.0	9	dbSNP_100	61	2356,6244	692.5+/-404.6	317,1722,2261	yes	missense	COL27A1	NM_032888.2	43	526,2671,3305	GG,GA,AA		27.3953,31.04,28.6297	benign	120/1861	116930194	3723,9281	2202	4300	6502	SO:0001583	missense	85301	exon3			GCAGCCAGAAACG	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.359A>G	9.37:g.116930194A>G	ENSP00000348385:p.Gln120Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	496	0.2271062271062271	155	0.3150406504065041	69	0.19060773480662985	69	0.12062937062937062	203	0.2678100263852243	G	8.628	0.893086	0.17613	0.3104	0.273953	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.02067	4.47;4.47	5.14	2.19	0.27852	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.00538	-1.39	0.53688	P	2.5000000000052758E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	8	0.02654	T	1	.	4.1964	0.10445	0.3302:0.0:0.5205:0.1493	rs2567706;rs17801114;rs52832119;rs60803978;rs2567706	120	Q8IZC6	CORA1_HUMAN	R	120;120;67;67	ENSP00000348385:Q120R;ENSP00000391328:Q67R	ENSP00000348385:Q120R	Q	+	2	0	COL27A1	115970015	0.940000	0.31905	0.997000	0.53966	0.805000	0.45488	0.676000	0.25247	0.213000	0.20722	-1.700000	0.00722	CAG	A|0.748;G|0.252	0.252	strong		0.662	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
CSF3R	1441	hgsc.bcm.edu	37	1	36937065	36937065	+	Silent	SNP	A	A	G	rs3917980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:36937065A>G	ENST00000373106.1	-	10	1801	c.1254T>C	c.(1252-1254)cgT>cgC	p.R418R	CSF3R_ENST00000373104.1_Silent_p.R418R|CSF3R_ENST00000338937.5_Silent_p.R418R|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000331941.5_Silent_p.R418R|CSF3R_ENST00000373103.1_Silent_p.R418R|CSF3R_ENST00000418048.2_Silent_p.R418R|CSF3R_ENST00000440588.2_Silent_p.R418R|CSF3R_ENST00000361632.4_Silent_p.R418R	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	418	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	CCGGAGTGGGACGAGAGGTCC	0.592													A|||	1234	0.246406	0.1717	0.2003	5008	,	,		17736	0.13		0.338	False		,,,				2504	0.4059				p.R418R		Atlas-SNP	.											CSF3R_ENST00000373104,NS,carcinoma,-1,2	CSF3R	157	2	0			c.T1254C						scavenged	.	A	,,	899,3507	339.4+/-305.8	92,715,1396	100.0	108.0	105.0		1254,1254,1254	-8.3	0.0	1	dbSNP_108	105	2999,5601	455.9+/-363.9	539,1921,1840	no	coding-synonymous,coding-synonymous,coding-synonymous	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	,,	631,2636,3236	GG,GA,AA		34.8721,20.404,29.9708	,,	418/837,418/864,418/784	36937065	3898,9108	2203	4300	6503	SO:0001819	synonymous_variant	1441	exon10			AGTGGGACGAGAG	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1254T>C	1.37:g.36937065A>G		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_156039		Silent	SNP	ENST00000373106.1	37	CCDS413.1	467	0.21382783882783882	68	0.13821138211382114	88	0.2430939226519337	57	0.09965034965034965	254	0.33509234828496043	A	0.623	-0.820494	0.02755	0.20404	0.348721	ENSG00000119535	ENST00000464465	.	.	.	5.3	-8.29	0.01009	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27884	P	0.9395732	.	.	.	.	.	.	T	0.37314	-0.9711	3	.	.	.	3.4373	4.0217	0.09668	0.2191:0.2359:0.4396:0.1053	rs3917980;rs17444611	.	.	.	A	4	.	.	V	-	2	0	CSF3R	36709652	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-2.296000	0.01142	-1.460000	0.01911	0.459000	0.35465	GTC	A|0.732;G|0.268	0.268	strong		0.592	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
QSOX2	169714	hgsc.bcm.edu	37	9	139118673	139118673	+	Missense_Mutation	SNP	T	T	C	rs12380852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139118673T>C	ENST00000358701.5	-	2	413	c.376A>G	c.(376-378)Aag>Gag	p.K126E		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	126	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		K -> E (in dbSNP:rs12380852).		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)		GCCTGGTTCTTCTCTTCCATG	0.572											OREG0019616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	490	0.0978435	0.034	0.0893	5008	,	,		20846	0.1915		0.1243	False		,,,				2504	0.0665				p.K126E		Atlas-SNP	.											.	QSOX2	63	.	0			c.A376G						PASS	.	T	GLU/LYS	197,4209	122.9+/-160.3	6,185,2012	275.0	229.0	245.0		376	2.2	0.6	9	dbSNP_120	245	1006,7594	216.7+/-255.6	58,890,3352	yes	missense	QSOX2	NM_181701.3	56	64,1075,5364	CC,CT,TT		11.6977,4.4712,9.2496	benign	126/699	139118673	1203,11803	2203	4300	6503	SO:0001583	missense	169714	exon2			GGTTCTTCTCTTC	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.376A>G	9.37:g.139118673T>C	ENSP00000351536:p.Lys126Glu	Somatic	100	0	0	1646	WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	37	CCDS35178.1	271	0.12408424908424909	27	0.054878048780487805	41	0.1132596685082873	112	0.1958041958041958	91	0.12005277044854881	T	0.595	-0.831311	0.02713	0.044712	0.116977	ENSG00000165661	ENST00000358701;ENST00000389471	T	0.64803	-0.12	4.91	2.18	0.27775	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.301070	0.34338	N	0.004045	T	0.00039	0.0001	N	0.04297	-0.235	0.40128	P	0.023313000000000028	B	0.09022	0.002	B	0.10450	0.005	T	0.09079	-1.0691	9	0.06099	T	0.92	-15.2089	5.0026	0.14271	0.0:0.4884:0.0:0.5116	rs12380852	126	Q6ZRP7	QSOX2_HUMAN	E	126;4	ENSP00000351536:K126E	ENSP00000351536:K126E	K	-	1	0	QSOX2	138258494	0.718000	0.27976	0.615000	0.29064	0.045000	0.14185	1.187000	0.32090	0.807000	0.34208	0.455000	0.32223	AAG	T|0.895;C|0.105	0.105	strong		0.572	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	
PBRM1	55193	hgsc.bcm.edu	37	3	52637631	52637631	+	Silent	SNP	T	T	C	rs34341044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52637631T>C	ENST00000296302.7	-	17	2686	c.2685A>G	c.(2683-2685)acA>acG	p.T895T	PBRM1_ENST00000337303.4_Silent_p.T895T|PBRM1_ENST00000409767.1_Silent_p.T910T|PBRM1_ENST00000409057.1_Silent_p.T895T|PBRM1_ENST00000409114.3_Silent_p.T910T|PBRM1_ENST00000410007.1_Silent_p.T895T|PBRM1_ENST00000356770.4_Silent_p.T863T|PBRM1_ENST00000394830.3_Silent_p.T895T			Q86U86	PB1_HUMAN	polybromo 1	895			T -> S (found in a lung cancer 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)	p.H897fs*4(2)|p.H865fs*4(1)		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)		GCAAATGTTTTGTGGTATAGC	0.348			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	47	0.00938498	0.0008	0.0144	5008	,	,		17909	0.0		0.0348	False		,,,				2504	0.001				p.T895T		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	3	Insertion - Frameshift(3)	kidney(3)	c.A2685G						PASS	.	T	,,	30,4376	36.8+/-68.6	0,30,2173	76.0	75.0	75.0		2589,2685,2685	0.6	1.0	3	dbSNP_126	75	313,8285	111.4+/-171.7	5,303,3991	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	5,333,6164	CC,CT,TT		3.6404,0.6809,2.6376	,,	863/1603,895/1583,895/1583	52637631	343,12661	2203	4299	6502	SO:0001819	synonymous_variant	55193	exon18			ATGTTTTGTGGTA	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.2685A>G	3.37:g.52637631T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.975;C|0.025	0.025	strong		0.348	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
ZNF264	9422	hgsc.bcm.edu	37	19	57723007	57723007	+	Missense_Mutation	SNP	G	G	C	rs2074858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57723007G>C	ENST00000263095.6	+	4	956	c.542G>C	c.(541-543)aGa>aCa	p.R181T	ZNF264_ENST00000536056.1_Missense_Mutation_p.R181T	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	181			R -> T (in dbSNP:rs2074858).		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(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		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;0.0135)		CCAGGAGATAGAGTCCGTAGC	0.438													.|||	3113	0.621605	0.8427	0.6369	5008	,	,		22133	0.3125		0.6481	False		,,,				2504	0.6033				p.R181T		Atlas-SNP	.											.	ZNF264	65	.	0			c.G542C						PASS	.	C	THR/ARG	3599,807	322.9+/-297.8	1474,651,78	96.0	86.0	89.0		542	1.0	0.0	19	dbSNP_96	89	5197,3403	503.0+/-375.8	1571,2055,674	yes	missense	ZNF264	NM_003417.4	71	3045,2706,752	CC,CG,GG		39.5698,18.3159,32.3697	benign	181/628	57723007	8796,4210	2203	4300	6503	SO:0001583	missense	9422	exon4			GAGATAGAGTCCG	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"""Zinc fingers, C2H2-type"", ""-"""	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.542G>C	19.37:g.57723007G>C	ENSP00000263095:p.Arg181Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_003417	A8K8Y9|Q9P1V0	Missense_Mutation	SNP	ENST00000263095.6	37	CCDS33127.1	1306	0.597985347985348	412	0.8373983739837398	232	0.6408839779005525	172	0.3006993006993007	490	0.6464379947229552	C	0.379	-0.929639	0.02359	0.816841	0.604302	ENSG00000083844	ENST00000263095;ENST00000536056	T;T	0.20598	2.06;2.06	2.04	0.985	0.19779	.	.	.	.	.	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08046	-1.0741	8	0.54805	T	0.06	.	4.7159	0.12894	0.0:0.6328:0.2246:0.1426	rs2074858;rs2074858	181	O43296	ZN264_HUMAN	T	181	ENSP00000263095:R181T;ENSP00000440376:R181T	ENSP00000263095:R181T	R	+	2	0	ZNF264	62414819	0.003000	0.15002	0.008000	0.14137	0.013000	0.08279	-0.779000	0.04659	0.034000	0.15491	-1.001000	0.02504	AGA	G|0.358;C|0.642	0.642	strong		0.438	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1		
CPEB2	132864	hgsc.bcm.edu	37	4	15005604	15005604	+	5'UTR	SNP	G	G	A	rs112476821	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15005604G>A	ENST00000507071.1	+	0	83				CPEB2_ENST00000442003.2_Missense_Mutation_p.S436N|CPEB2_ENST00000541112.1_Missense_Mutation_p.S436N|CPEB2_ENST00000538197.1_Missense_Mutation_p.S436N|CPEB2_ENST00000382401.3_5'UTR|CPEB2_ENST00000345451.3_5'UTR|RP11-665G4.1_ENST00000502344.1_RNA|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000382395.3_5'UTR|CPEB2_ENST00000259997.5_5'UTR			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2						cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						GGCTCGCTCAGCGCCATGCCG	0.756													g|||	2367	0.472644	0.3253	0.5922	5008	,	,		2747	0.7292		0.5258	False		,,,				2504	0.2679				p.S436N		Atlas-SNP	.											.	CPEB2	77	.	0			c.G1307A						PASS	.		ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	1000,2112		207,586,763	3.0	4.0	4.0		1307,1307,1307,1307,1307,1307	0.3	0.9	4	dbSNP_132	4	2948,3446		796,1356,1045	no	missense,missense,missense,missense,missense,missense	CPEB2	NM_001177381.1,NM_001177382.1,NM_001177383.1,NM_001177384.1,NM_182485.2,NM_182646.2	46,46,46,46,46,46	1003,1942,1808	AA,AG,GG		46.1057,32.1337,41.5317	,,,,,	436/1008,436/1035,436/1005,436/1000,436/1027,436/997	15005604	3948,5558	1556	3197	4753	SO:0001623	5_prime_UTR_variant	132864	exon1			CGCTCAGCGCCAT	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"""RNA binding motif (RRM) containing"""	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.-5G>A	4.37:g.15005604G>A		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_001177381	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	37		1222	0.5595238095238095	170	0.34552845528455284	202	0.5580110497237569	441	0.7709790209790209	409	0.5395778364116095	g	0.683	-0.797424	0.02862	0.321337	0.461057	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003	D;T;T	0.82433	-1.61;0.79;0.8	1.29	0.336	0.15958	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52501	P	4.499999999996174E-5	.	.	.	.	.	.	T	0.38351	-0.9665	6	0.27082	T	0.32	.	2.7676	0.05324	0.2146:0.3084:0.477:0.0	.	.	.	.	N	436	ENSP00000443985:S436N;ENSP00000437884:S436N;ENSP00000414270:S436N	ENSP00000414270:S436N	S	+	2	0	CPEB2	14614702	.	.	0.933000	0.37362	0.034000	0.12701	.	.	-0.171000	0.10797	-1.037000	0.02385	AGC	G|0.440;A|0.560	0.560	strong		0.756	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607	
UGT1A3	54659	hgsc.bcm.edu	37	2	234637912	234637912	+	Missense_Mutation	SNP	T	T	C	rs6431625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234637912T>C	ENST00000482026.1	+	1	159	c.140T>C	c.(139-141)gTc>gCc	p.V47A	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.V47A|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	47			V -> A (in dbSNP:rs6431625). {ECO:0000269|PubMed:19204906}.		cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	ATGCGGGAGGTCTTGCGGGAG	0.567													C|||	2174	0.434105	0.7322	0.4294	5008	,	,		20161	0.126		0.3469	False		,,,				2504	0.4417				p.V47A		Atlas-SNP	.											UGT1A3,colon,carcinoma,0,1	UGT1A3	91	1	0			c.T140C	GRCh37	CM042130	UGT1A3	M	rs6431625	scavenged	.	C	,,,,,,ALA/VAL,,	2908,1498		965,978,260	68.0	68.0	68.0		,,,,,,140,,	-6.8	0.0	2	dbSNP_116	68	3367,5233		651,2065,1584	no	intron,intron,intron,intron,intron,intron,missense,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,64,,	1616,3043,1844	CC,CT,TT		39.1512,33.9991,48.247	,,,,,,,,	,,,,,,47/535,,	234637912	6275,6731	2203	4300	6503	SO:0001583	missense	54659	exon1			GGGAGGTCTTGCG	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.140T>C	2.37:g.234637912T>C	ENSP00000418532:p.Val47Ala	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	37	CCDS2509.1	804	0.36813186813186816	342	0.6951219512195121	143	0.39502762430939226	68	0.11888111888111888	251	0.3311345646437995	N	5.019	0.189247	0.09547	0.660009	0.391512	ENSG00000243135	ENST00000482026	T	0.62788	-0.0	4.35	-6.82	0.01698	.	.	.	.	.	T	0.00012	0.0000	L	0.52823	1.66	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.005	T	0.24584	-1.0156	8	0.49607	T	0.09	.	19.0734	0.93150	0.0:0.0973:0.0:0.9027	rs6431625;rs17864457;rs61313666	47;47	Q5DT01;P35503	.;UD13_HUMAN	A	47	ENSP00000418532:V47A	ENSP00000418532:V47A	V	+	2	0	UGT1A3	234302651	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.181000	0.16880	-2.173000	0.00773	-1.952000	0.00485	GTC	T|0.573;C|0.427	0.427	strong		0.567	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
RBM34	23029	hgsc.bcm.edu	37	1	235324298	235324298	+	Silent	SNP	T	T	C	rs2295815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:235324298T>C	ENST00000408888.3	-	2	368	c.138A>G	c.(136-138)gaA>gaG	p.E46E	RBM34_ENST00000366606.3_Silent_p.E41E			P42696	RBM34_HUMAN	RNA binding motif protein 34	46						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			TGGAATGGTGTTCGCCGCGAA	0.577													C|||	840	0.167732	0.4009	0.121	5008	,	,		14732	0.0208		0.1233	False		,,,				2504	0.0828				p.E46E		Atlas-SNP	.											.	RBM34	41	.	0			c.A138G						PASS	.	C	,	1487,2415		281,925,745	41.0	47.0	45.0		138,138	3.3	0.0	1	dbSNP_100	45	1064,7222		65,934,3144	yes	coding-synonymous,coding-synonymous	RBM34	NM_001161533.1,NM_015014.2	,	346,1859,3889	CC,CT,TT		12.8409,38.1087,20.9304	,	46/226,46/431	235324298	2551,9637	1951	4143	6094	SO:0001819	synonymous_variant	23029	exon2			ATGGTGTTCGCCG		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"""RNA binding motif (RRM) containing"""	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.138A>G	1.37:g.235324298T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001161533	A8K8J7|Q8N2Z8|Q9H5A1	Silent	SNP	ENST00000408888.3	37	CCDS41477.2																																																																																			T|0.850;C|0.150	0.150	strong		0.577	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014	
IL4R	3566	hgsc.bcm.edu	37	16	27373972	27373972	+	Silent	SNP	T	T	C	rs2234900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000170630.2_Silent_p.L433L|IL4R_ENST00000543915.2_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	64	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	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		
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956196	18956196	+	Missense_Mutation	SNP	C	C	T	rs78179510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18956196C>T	ENST00000302797.3	-	1	360	c.136G>A	c.(136-138)Gca>Aca	p.A46T	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	46					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A46T(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AGCACAACTGCGTTTCCTGTC	0.582																																					p.A46T		Atlas-SNP	.											MRGPRX1,caecum,carcinoma,0,3	MRGPRX1	84	3	1	Substitution - Missense(1)	stomach(1)	c.G136A						PASS	.	C	THR/ALA	708,3680		4,700,1490	170.0	161.0	164.0		136	-0.9	0.0	11	dbSNP_131	164	1289,7285		4,1281,3002	no	missense	MRGPRX1	NM_147199.3	58	8,1981,4492	TT,TC,CC		15.0338,16.1349,15.4066	possibly-damaging	46/323	18956196	1997,10965	2194	4287	6481	SO:0001583	missense	259249	exon1			CAACTGCGTTTCC		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.136G>A	11.37:g.18956196C>T	ENSP00000305766:p.Ala46Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	150	48	0.32	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	380	0.17399267399267399	86	0.17479674796747968	73	0.20165745856353592	104	0.18181818181818182	117	0.15435356200527706	.	14.50	2.554820	0.45487	0.161349	0.150338	ENSG00000170255	ENST00000302797	T	0.09350	2.99	2.43	-0.872	0.10638	GPCR, rhodopsin-like superfamily (1);	0.959312	0.08638	N	0.915990	T	0.00012	0.0000	L	0.55213	1.73	0.80722	P	0.0	D	0.60575	0.988	P	0.54238	0.746	T	0.34104	-0.9842	9	0.31617	T	0.26	.	7.0239	0.24930	0.0:0.6214:0.0:0.3786	.	46	Q96LB2	MRGX1_HUMAN	T	46	ENSP00000305766:A46T	ENSP00000305766:A46T	A	-	1	0	MRGPRX1	18912772	0.000000	0.05858	0.004000	0.12327	0.047000	0.14425	-0.160000	0.10041	-0.190000	0.10465	0.491000	0.48974	GCA	C|0.842;T|0.158	0.158	strong		0.582	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
RBFOX3	146713	hgsc.bcm.edu	37	17	77111732	77111732	+	Silent	SNP	G	G	A	rs80198744	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:77111732G>A	ENST00000453134.2	-	5	578	c.66C>T	c.(64-66)taC>taT	p.Y22Y	RBFOX3_ENST00000415831.1_Silent_p.Y22Y|RBFOX3_ENST00000583458.1_Silent_p.Y22Y|RBFOX3_ENST00000584778.1_Silent_p.Y22Y|RBFOX3_ENST00000582043.1_Silent_p.Y22Y|RBFOX3_ENST00000580155.1_Silent_p.Y22Y			A6NFN3	RFOX3_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 3	22	Pro-rich.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perikaryon (GO:0043204)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)	2						GGGGCGGGGCGTACTCGGCAG	0.706													G|||	944	0.188498	0.1974	0.1398	5008	,	,		7226	0.2649		0.1511	False		,,,				2504	0.1708				p.F22F		Atlas-SNP	.											.	RBFOX3	10	.	0			c.T66T						PASS	.	G		269,1115		29,211,452	56.0	47.0	50.0		66	-8.5	0.6	17	dbSNP_131	50	519,2663		40,439,1112	no	coding-synonymous	RBFOX3	NM_001082575.1		69,650,1564	AA,AG,GG		16.3105,19.4364,17.258		22/313	77111732	788,3778	692	1591	2283	SO:0001819	synonymous_variant	146713	exon5			CGGGGCGTACTCG		CCDS45805.1	17q25.3	2013-02-12			ENSG00000167281	ENSG00000167281		"""RNA binding motif (RRM) containing"""	27097	protein-coding gene	gene with protein product	"""neuronal nuclei"", ""hexaribonucleotide binding protein 3"""					16260614	Standard	NM_001082575		Approved	FOX-3, NeuN, HRNBP3	uc010dhs.4	A6NFN3	OTTHUMG00000150183	ENST00000453134.2:c.66C>T	17.37:g.77111732G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_001082575	B4DEG6|B4DF29	Silent	SNP	ENST00000453134.2	37	CCDS45805.1																																																																																			G|0.804;A|0.196	0.196	strong		0.706	RBFOX3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437658.1	NM_001082575	
CAPZA3	93661	hgsc.bcm.edu	37	12	18891966	18891966	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:18891966T>C	ENST00000317658.3	+	1	922	c.764T>C	c.(763-765)aTt>aCt	p.I255T	PLCZ1_ENST00000447925.2_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	255					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTGAGAAAAATTCTACGAAGG	0.418																																					p.I255T		Atlas-SNP	.											.	CAPZA3	51	.	0			c.T764C						PASS	.						48.0	51.0	50.0					12																	18891966		2203	4299	6502	SO:0001583	missense	93661	exon1			GAAAAATTCTACG	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.764T>C	12.37:g.18891966T>C	ENSP00000326238:p.Ile255Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	T	8.214	0.801016	0.16397	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.63	2.16	0.27623	F-actin capping protein, alpha subunit, conserved site (1);	0.428352	0.23132	N	0.051565	T	0.21841	0.0526	N	0.16478	0.41	0.31847	N	0.622758	B	0.10296	0.003	B	0.11329	0.006	T	0.08722	-1.0708	9	0.39692	T	0.17	-16.7227	3.7138	0.08430	0.3352:0.0947:0.0:0.5702	.	255	Q96KX2	CAZA3_HUMAN	T	255	.	ENSP00000326238:I255T	I	+	2	0	CAPZA3	18783233	0.896000	0.30565	0.969000	0.41365	0.943000	0.58893	0.619000	0.24388	0.781000	0.33589	0.379000	0.24179	ATT	.	.	none		0.418	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
HPR	3250	hgsc.bcm.edu	37	16	72110948	72110948	+	Missense_Mutation	SNP	C	C	G	rs12646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72110948C>G	ENST00000540303.2	+	5	1047	c.1015C>G	c.(1015-1017)Cac>Gac	p.H339D	HPR_ENST00000561690.1_3'UTR|HPR_ENST00000356967.5_Missense_Mutation_p.H339D|HPR_ENST00000228226.8_Missense_Mutation_p.H376D	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	339	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> D (in dbSNP:rs12646). {ECO:0000269|PubMed:1478675, ECO:0000269|PubMed:2987228, ECO:0000269|PubMed:4018023}.			blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)	p.H339D(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				TTCCATCCAGCACTGGGTTCA	0.542																																					p.H339D		Atlas-SNP	.											.	HPR	43	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C1015G						PASS	.	G	ASP/HIS	1169,2855		357,455,1200	204.0	127.0	152.0		1015	2.6	0.5	16	dbSNP_52	152	2459,5863		536,1387,2238	no	missense	HPR	NM_020995.3	81	893,1842,3438	GG,GC,CC		29.5482,29.0507,29.386	benign	339/349	72110948	3628,8718	2012	4161	6173	SO:0001583	missense	3250	exon5			ATCCAGCACTGGG	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.1015C>G	16.37:g.72110948C>G	ENSP00000441828:p.His339Asp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Missense_Mutation	SNP	ENST00000540303.2	37	CCDS42193.1	634	0.2902930402930403	170	0.34552845528455284	100	0.27624309392265195	151	0.263986013986014	213	0.28100263852242746	G	0	-2.720080	0.00092	0.290507	0.295482	ENSG00000257017	ENST00000356967;ENST00000540303;ENST00000228226	D;D;D	0.90788	-2.73;-2.73;-2.73	2.64	2.64	0.31445	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.349704	0.30989	N	0.008477	T	0.00012	0.0000	N	0.00020	-2.76	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	9	0.02654	T	1	.	10.297	0.43629	0.0:0.204:0.796:0.0	rs12646;rs593960;rs647237;rs3190322;rs12934886;rs16973684;rs28609419;rs59126784	339	P00739	HPTR_HUMAN	D	339;339;376	ENSP00000349451:H339D;ENSP00000441828:H339D;ENSP00000228226:H376D	ENSP00000228226:H376D	H	+	1	0	HP	70668449	1.000000	0.71417	0.478000	0.27316	0.019000	0.09904	3.354000	0.52254	0.437000	0.26423	-0.477000	0.04895	CAC	.	.	weak		0.542	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995	
TM4SF19	116211	hgsc.bcm.edu	37	3	196050862	196050862	+	Silent	SNP	A	A	G	rs36016914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196050862A>G	ENST00000273695.3	-	5	581	c.456T>C	c.(454-456)taT>taC	p.Y152Y	TM4SF19_ENST00000446879.1_Missense_Mutation_p.I151T|TM4SF19-AS1_ENST00000420226.1_RNA|TM4SF19_ENST00000454715.1_Silent_p.Y126Y|TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000442633.1_Silent_p.Y152Y|TM4SF19-AS1_ENST00000444939.1_RNA	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	152						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GGTCATACAGATAATTCCTAT	0.552													A|||	32	0.00638978	0.0008	0.0259	5008	,	,		20131	0.0		0.0129	False		,,,				2504	0.0				p.I151T		Atlas-SNP	.											.	TM4SF19	21	.	0			c.T452C						PASS	.	A	THR/ILE,,	14,4392	20.2+/-43.8	0,14,2189	54.0	52.0	53.0		452,378,456	-0.1	0.6	3	dbSNP_126	53	114,8486	61.3+/-123.2	2,110,4188	yes	missense,coding-synonymous,coding-synonymous	TM4SF19	NM_001204897.1,NM_001204898.1,NM_138461.3	89,,	2,124,6377	GG,GA,AA		1.3256,0.3177,0.9842	,,	151/243,126/184,152/210	196050862	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	116211	exon5			ATACAGATAATTC	BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.456T>C	3.37:g.196050862A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	76	22	0.289474	NM_001204897	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	A|A	6.649|6.649	0.488243|0.488243	0.12641|0.12641	0.003177|0.003177	0.013256|0.013256	ENSG00000145107|ENSG00000145107	ENST00000446879|ENST00000440822	T|.	0.27402|.	1.67|.	5.13|5.13	-0.105|-0.105	0.13601|0.13601	.|.	.|.	.|.	.|.	.|.	T|T	0.29945|0.29945	0.0749|0.0749	.|.	.|.	.|.	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.24132|.	0.098|.	B|.	0.26094|.	0.066|.	T|T	0.27365|0.27365	-1.0076|-1.0076	8|4	0.27082|.	T|.	0.32|.	-5.5124|-5.5124	7.8335|7.8335	0.29358|0.29358	0.5849:0.0:0.415:0.0|0.5849:0.0:0.415:0.0	rs36016914;rs62409180|rs36016914;rs62409180	151|.	C9JCD5|.	.|.	T|P	151|19	ENSP00000395280:I151T|.	ENSP00000395280:I151T|.	I|S	-|-	2|1	0|0	TM4SF19|TM4SF19	197535259|197535259	0.355000|0.355000	0.24921|0.24921	0.565000|0.565000	0.28409|0.28409	0.176000|0.176000	0.22953|0.22953	0.361000|0.361000	0.20267|0.20267	0.002000|0.002000	0.14630|0.14630	0.460000|0.460000	0.39030|0.39030	ATC|TCT	A|0.989;G|0.011	0.011	strong		0.552	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461	
PNMAL2	57469	hgsc.bcm.edu	37	19	46997522	46997522	+	Intron	SNP	C	C	T	rs3745790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46997522C>T	ENST00000377655.2	-	1	734				AC011484.1_ENST00000377652.3_5'Flank|PNMAL2_ENST00000599531.1_Missense_Mutation_p.V401I|PNMAL2_ENST00000594749.1_Intron			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TTGCGCAGGACCACGGCGTCC	0.677													C|||	760	0.151757	0.1225	0.1441	5008	,	,		13657	0.3353		0.0775	False		,,,				2504	0.0838				p.V401I		Atlas-SNP	.											.	PNMAL2	44	.	0			c.G1201A						PASS	.	C	,ILE/VAL	469,3433		23,423,1505	13.0	16.0	15.0		,1201	2.6	0.5	19	dbSNP_107	15	757,7469		38,681,3394	yes	intron,missense	PNMAL2,LOC100506012	NM_001205281.1,NM_020709.1	,29	61,1104,4899	TT,TC,CC		9.2025,12.0195,10.1088	,possibly-damaging	,401/636	46997522	1226,10902	1951	4113	6064	SO:0001627	intron_variant	57469	exon1			GCAGGACCACGGC	AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"""Paraneoplastic Ma antigens"""	29206	protein-coding gene	gene with protein product			"""PNMA-like 2"""			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.734+466G>A	19.37:g.46997522C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_020709	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37																																																																																				C|0.848;T|0.152	0.152	strong		0.677	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709	
CSMD1	64478	hgsc.bcm.edu	37	8	3072107	3072107	+	Silent	SNP	G	G	C	rs73183587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:3072107G>C	ENST00000520002.1	-	31	5337	c.4782C>G	c.(4780-4782)ggC>ggG	p.G1594G	CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Silent_p.G1594G|CSMD1_ENST00000602723.1_Silent_p.G1594G|CSMD1_ENST00000537824.1_Silent_p.G1593G|CSMD1_ENST00000539096.1_Silent_p.G1593G|CSMD1_ENST00000542608.1_Silent_p.G1593G|CSMD1_ENST00000400186.3_Silent_p.G1594G			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	178	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	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	
PTH2R	5746	hgsc.bcm.edu	37	2	209358262	209358262	+	Missense_Mutation	SNP	G	G	A	rs140566891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209358262G>A	ENST00000272847.2	+	13	1744	c.1531G>A	c.(1531-1533)Gag>Aag	p.E511K	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	511					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	CTCTTTCCACGAGGAGACCAA	0.527													G|||	2	0.000399361	0.0	0.0	5008	,	,		20843	0.0		0.001	False		,,,				2504	0.001				p.E511K		Atlas-SNP	.											.	PTH2R	92	.	0			c.G1531A						PASS	.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	84.0	77.0	80.0		1531	4.4	0.3	2	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PTH2R	NM_005048.2	56	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	probably-damaging	511/551	209358262	12,12994	2203	4300	6503	SO:0001583	missense	5746	exon13			TTCCACGAGGAGA	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"""GPCR / Class B : Parathyroid hormone receptors"""	9609	protein-coding gene	gene with protein product		601469	"""parathyroid hormone receptor 2"""	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1531G>A	2.37:g.209358262G>A	ENSP00000272847:p.Glu511Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	179	96	0.536313	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.8	4.050399	0.75960	2.27E-4	0.001279	ENSG00000144407	ENST00000272847	T	0.58060	0.36	5.31	4.43	0.53597	.	0.000000	0.36740	U	0.002436	T	0.48750	0.1517	M	0.73962	2.25	0.31256	N	0.693435	P;P	0.51240	0.892;0.943	B;B	0.37144	0.178;0.242	T	0.62358	-0.6871	9	.	.	.	.	11.6752	0.51425	0.0868:0.0:0.9132:0.0	.	400;511	B4DFN8;P49190	.;PTH2R_HUMAN	K	511	ENSP00000272847:E511K	.	E	+	1	0	PTH2R	209066507	1.000000	0.71417	0.276000	0.24689	0.027000	0.11550	4.221000	0.58574	1.236000	0.43740	0.591000	0.81541	GAG	G|0.999;A|0.001	0.001	strong		0.527	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
NUB1	51667	hgsc.bcm.edu	37	7	151074296	151074296	+	Silent	SNP	A	A	G	rs2159158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151074296A>G	ENST00000355851.4	+	15	1910	c.1833A>G	c.(1831-1833)gcA>gcG	p.A611A	NUB1_ENST00000568733.1_Silent_p.A635A|WDR86_ENST00000463000.1_Intron|NUB1_ENST00000566856.1_Silent_p.A597A|NUB1_ENST00000413040.2_Silent_p.A621A	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	611					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGAAGTCAGCAACAAAGAAAA	0.333													A|||	1667	0.332867	0.1233	0.4035	5008	,	,		20987	0.4603		0.5249	False		,,,				2504	0.2372				p.A635A		Atlas-SNP	.											.	NUB1	31	.	0			c.A1905G						PASS	.	A		639,3053		58,523,1265	29.0	27.0	28.0		1791	1.1	0.1	7	dbSNP_96	28	4187,3983		1062,2063,960	no	coding-synonymous	NUB1	NM_016118.4		1120,2586,2225	GG,GA,AA		48.7515,17.3077,40.6845		597/602	151074296	4826,7036	1846	4085	5931	SO:0001819	synonymous_variant	51667	exon15			GTCAGCAACAAAG	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1833A>G	7.37:g.151074296A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001243351	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37		932	0.4267399267399267	75	0.1524390243902439	164	0.4530386740331492	294	0.513986013986014	399	0.5263852242744064	A	0.352	-0.944139	0.02322	0.173077	0.512485	ENSG00000013374	ENST00000460712	.	.	.	5.11	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.8000000000048004E-5	.	.	.	.	.	.	T	0.48811	-0.9002	3	.	.	.	-18.3438	7.6126	0.28139	0.3371:0.5744:0.0885:0.0	rs2159158;rs3207510;rs10369514;rs11550340;rs2159158	.	.	.	R	198	.	.	Q	+	2	0	NUB1	150705229	0.005000	0.15991	0.118000	0.21660	0.142000	0.21351	0.018000	0.13422	0.019000	0.15079	0.482000	0.46254	CAA	A|0.597;G|0.403	0.403	strong		0.333	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
KIRREL2	84063	hgsc.bcm.edu	37	19	36349752	36349752	+	Missense_Mutation	SNP	G	G	A	rs404299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36349752G>A	ENST00000360202.5	+	4	706	c.508G>A	c.(508-510)Gcc>Acc	p.A170T	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.A170T|KIRREL2_ENST00000262625.7_Missense_Mutation_p.A170T|KIRREL2_ENST00000347900.6_Missense_Mutation_p.A120T	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	170	Ig-like C2-type 2.		A -> T (in dbSNP:rs404299).		cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTTGGATGGAGCCACCTTCCA	0.562													A|||	765	0.152756	0.4342	0.062	5008	,	,		18561	0.0744		0.0258	False		,,,				2504	0.0481				p.A170T		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G508A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA	1646,2760	658.7+/-400.4	309,1028,866	104.0	100.0	102.0		508,358,508	3.4	1.0	19	dbSNP_80	102	309,8291	805.8+/-407.3	2,305,3993	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	58,58,58	311,1333,4859	AA,AG,GG		3.593,37.3581,15.0315	benign,benign,benign	170/634,120/584,170/709	36349752	1955,11051	2203	4300	6503	SO:0001583	missense	84063	exon4			GATGGAGCCACCT	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.508G>A	19.37:g.36349752G>A	ENSP00000353331:p.Ala170Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	152	65	0.427632	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	263	0.12042124542124542	173	0.3516260162601626	26	0.0718232044198895	44	0.07692307692307693	20	0.026385224274406333	A	15.04	2.716294	0.48622	0.373581	0.03593	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.77098	-1.07;-1.07;-1.07	5.69	3.36	0.38483	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.794047	0.10947	N	0.616505	T	0.00012	0.0000	N	0.17474	0.49	0.52501	P	4.300000000001525E-5	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.08055	0.003;0.003;0.001;0.003;0.001	T	0.20806	-1.0264	9	0.25751	T	0.34	-3.2746	6.4145	0.21710	0.4597:0.0:0.5403:0.0	rs404299;rs52823047;rs57040740;rs404299	170;170;170;120;170	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	T	170;120;170;170	ENSP00000262625:A170T;ENSP00000345067:A120T;ENSP00000353331:A170T	ENSP00000262625:A170T	A	+	1	0	KIRREL2	41041592	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	2.662000	0.46766	0.166000	0.19597	-0.260000	0.10688	GCC	G|0.863;A|0.137	0.137	strong		0.562	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
TTK	7272	hgsc.bcm.edu	37	6	80718167	80718167	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:80718167G>A	ENST00000369798.2	+	4	538	c.427G>A	c.(427-429)Gct>Act	p.A143T	TTK_ENST00000230510.3_Missense_Mutation_p.A143T|TTK_ENST00000509894.1_Missense_Mutation_p.A143T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	143					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CAAGAAATTTGCTTTTGTTCA	0.299																																					p.A143T		Atlas-SNP	.											.	TTK	199	.	0			c.G427A						PASS	.						77.0	70.0	73.0					6																	80718167		2203	4299	6502	SO:0001583	missense	7272	exon4			AAATTTGCTTTTG		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.427G>A	6.37:g.80718167G>A	ENSP00000358813:p.Ala143Thr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	10	0.212766	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	32	5.165323	0.94768	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000511260;ENST00000504040	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	6.16	5.27	0.74061	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	M	0.66939	2.045	0.49213	D	0.999764	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.93231	0.6617	10	0.62326	D	0.03	.	15.8123	0.78573	0.0:0.0:0.8632:0.1368	.	143;143	P33981;A8K8U5	TTK_HUMAN;.	T	143	ENSP00000422936:A143T;ENSP00000230510:A143T;ENSP00000358813:A143T;ENSP00000421636:A143T;ENSP00000427483:A143T	ENSP00000230510:A143T	A	+	1	0	TTK	80774886	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.619000	0.67729	1.557000	0.49525	0.650000	0.86243	GCT	.	.	none		0.299	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
MUC4	4585	hgsc.bcm.edu	37	3	195509939	195509939	+	Missense_Mutation	SNP	G	G	T	rs202039836	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195509939G>T	ENST00000463781.3	-	2	8971	c.8512C>A	c.(8512-8514)Cct>Act	p.P2838T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2838T	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)	p.P2838T(3)		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)		GCTGAGGAAGGGATGGTGACA	0.592													.|||	318	0.0634984	0.0045	0.0432	5008	,	,		7871	0.0417		0.1521	False		,,,				2504	0.089				p.P2838T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	kidney(3)	c.C8512A						PASS	.						102.0	63.0	75.0					3																	195509939		690	1569	2259	SO:0001583	missense	4585	exon2			AGGAAGGGATGGT	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.8512C>A	3.37:g.195509939G>T	ENSP00000417498:p.Pro2838Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	148	9	0.0608108	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	3.466	-0.108992	0.06924	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	P	0.38110	0.618	B	0.28638	0.092	T	0.19386	-1.0307	7	.	.	.	.	4.5444	0.12074	0.0:0.4166:0.5833:0.0	.	2710	E7ESK3	.	T	2838	ENSP00000417498:P2838T;ENSP00000420243:P2838T	.	P	-	1	0	MUC4	196994718	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.690000	0.00392	-0.000000	0.14550	0.000000	0.15137	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MAP1S	55201	hgsc.bcm.edu	37	19	17837512	17837512	+	Missense_Mutation	SNP	G	G	A	rs12983721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17837512G>A	ENST00000324096.4	+	5	1470	c.1319G>A	c.(1318-1320)tGc>tAc	p.C440Y	MAP1S_ENST00000544059.2_Missense_Mutation_p.C414Y|MAP1S_ENST00000597681.1_Intron|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	440	Necessary for the microtubule-organizing center localization.			C -> Y (in Ref. 4; CAD38911). {ECO:0000305}.	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						CCGCCCGCCTGCCTCCTGGAC	0.736													G|||	693	0.138379	0.0182	0.1614	5008	,	,		11854	0.0149		0.2843	False		,,,				2504	0.2618				p.C440Y		Atlas-SNP	.											.	MAP1S	74	.	0			c.G1319A						PASS	.	G	TYR/CYS	193,3737		13,167,1785	4.0	5.0	5.0		1319	3.9	0.8	19	dbSNP_121	5	2036,5818		304,1428,2195	yes	missense	MAP1S	NM_018174.4	194	317,1595,3980	AA,AG,GG		25.9231,4.9109,18.9155	benign	440/1060	17837512	2229,9555	1965	3927	5892	SO:0001583	missense	55201	exon5			CCGCCTGCCTCCT	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.1319G>A	19.37:g.17837512G>A	ENSP00000325313:p.Cys440Tyr	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	310	0.14194139194139194	18	0.036585365853658534	66	0.18232044198895028	5	0.008741258741258742	221	0.29155672823219	G	8.946	0.966997	0.18659	0.049109	0.259231	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.02682	4.2;4.2	3.88	3.88	0.44766	.	0.135987	0.33916	N	0.004423	T	0.00012	0.0000	N	0.22421	0.69	0.40783	P	0.016803000000000012	B;B;B	0.31989	0.35;0.35;0.173	B;B;B	0.31495	0.131;0.131;0.093	T	0.50381	-0.8835	9	0.72032	D	0.01	-15.1875	7.4603	0.27291	0.1228:0.0:0.8772:0.0	rs12983721	414;440;440	B4DH53;A8K940;Q66K74	.;.;MAP1S_HUMAN	Y	440;414	ENSP00000325313:C440Y;ENSP00000439243:C414Y	ENSP00000325313:C440Y	C	+	2	0	MAP1S	17698512	1.000000	0.71417	0.793000	0.32043	0.003000	0.03518	5.139000	0.64801	1.700000	0.51204	0.491000	0.48974	TGC	G|0.856;A|0.144	0.144	strong		0.736	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
AKAP6	9472	hgsc.bcm.edu	37	14	33292743	33292743	+	Silent	SNP	A	A	C	rs2239647	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:33292743A>C	ENST00000280979.4	+	13	5894	c.5724A>C	c.(5722-5724)ggA>ggC	p.G1908G	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1908					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)		GGCAAAAGGGAAAACCGAATG	0.353													C|||	3562	0.711262	0.9092	0.683	5008	,	,		22521	0.6696		0.5427	False		,,,				2504	0.68				p.G1908G	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A5724C						PASS	.	C		3783,623	260.7+/-263.8	1631,521,51	62.0	64.0	63.0		5724	2.2	0.0	14	dbSNP_98	63	4679,3921	542.1+/-384.1	1229,2221,850	no	coding-synonymous	AKAP6	NM_004274.4		2860,2742,901	CC,CA,AA		45.593,14.1398,34.9377		1908/2320	33292743	8462,4544	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon13			AAAGGGAAAACCG	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.5724A>C	14.37:g.33292743A>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			A|0.319;C|0.681	0.681	strong		0.353	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
SERPINF1	5176	hgsc.bcm.edu	37	17	1673276	1673276	+	Missense_Mutation	SNP	C	C	T	rs1136287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1673276C>T	ENST00000254722.4	+	3	378	c.215C>T	c.(214-216)aCg>aTg	p.T72M	SERPINF1_ENST00000571870.1_3'UTR	NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	72			T -> M (polymorphism confirmed at protein level; dbSNP:rs1136287). {ECO:0000269|PubMed:10398730, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:22028381, ECO:0000269|PubMed:8434014, ECO:0000269|PubMed:8473338, ECO:0000269|PubMed:9238088, ECO:0000269|Ref.10, ECO:0000269|Ref.3, ECO:0000269|Ref.5, ECO:0000269|Ref.8}.		aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						CGATCCAGCACGAGCCCCACG	0.627													T|||	3136	0.626198	0.8759	0.5893	5008	,	,		18941	0.4871		0.6541	False		,,,				2504	0.4294				p.T72M		Atlas-SNP	.											SERPINF1,colon,carcinoma,0,1	SERPINF1	31	1	0			c.C215T	GRCh37	CM081434	SERPINF1	M	rs1136287	PASS	.	T	MET/THR	3652,754	308.0+/-290.3	1516,620,67	94.0	84.0	88.0		215	-11.3	0.0	17	dbSNP_86	88	5606,2994	462.4+/-365.7	1838,1930,532	yes	missense	SERPINF1	NM_002615.5	81	3354,2550,599	TT,TC,CC		34.814,17.113,28.8175	benign	72/419	1673276	9258,3748	2203	4300	6503	SO:0001583	missense	5176	exon3			CCAGCACGAGCCC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"""Serine (or cysteine) peptidase inhibitors"""	8824	protein-coding gene	gene with protein product	"""pigment epithelium-derived factor"", ""proliferation-inducing protein 35"""	172860	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"""	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.215C>T	17.37:g.1673276C>T	ENSP00000254722:p.Thr72Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Missense_Mutation	SNP	ENST00000254722.4	37	CCDS11012.1	1414	0.6474358974358975	423	0.8597560975609756	224	0.6187845303867403	287	0.5017482517482518	480	0.633245382585752	T	9.272	1.045905	0.19748	0.82887	0.65186	ENSG00000132386	ENST00000254722	D	0.84589	-1.87	5.67	-11.3	0.00108	Serpin domain (3);	2.927490	0.00589	N	0.000341	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.0000000000287557E-6	B	0.12013	0.005	B	0.11329	0.006	T	0.40608	-0.9554	9	0.38643	T	0.18	.	5.2065	0.15293	0.4348:0.3488:0.1331:0.0833	rs1136287;rs1804144;rs3199567;rs16951641;rs17352972;rs17845405;rs17858264;rs58553017;rs1136287	72	P36955	PEDF_HUMAN	M	72	ENSP00000254722:T72M	ENSP00000254722:T72M	T	+	2	0	SERPINF1	1620026	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-0.750000	0.04808	-2.772000	0.00364	-0.260000	0.10688	ACG	C|0.316;T|0.684	0.684	strong		0.627	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
ENOSF1	55556	hgsc.bcm.edu	37	18	712568	712568	+	Missense_Mutation	SNP	G	G	A	rs3786349	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:712568G>A	ENST00000251101.7	-	1	108	c.20C>T	c.(19-21)tCc>tTc	p.S7F	ENOSF1_ENST00000539164.1_Missense_Mutation_p.S7F|ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000580982.1_Missense_Mutation_p.S7F|ENOSF1_ENST00000340116.7_5'Flank	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	7					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						CGAGAGCCGGGAGATCCTGCC	0.766													G|||	601	0.120008	0.0265	0.0778	5008	,	,		9725	0.2748		0.1412	False		,,,				2504	0.0951				p.S7F		Atlas-SNP	.											.	ENOSF1	44	.	0			c.C20T						PASS	.	G	,PHE/SER	105,3179		1,103,1538	5.0	5.0	5.0		,20	-1.5	0.0	18	dbSNP_107	5	546,5710		15,516,2597	no	utr-5,missense	ENOSF1	NM_001126123.3,NM_017512.5	,155	16,619,4135	AA,AG,GG		8.7276,3.1973,6.8239	,benign	,7/444	712568	651,8889	1642	3128	4770	SO:0001583	missense	55556	exon1			AGCCGGGAGATCC	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.20C>T	18.37:g.712568G>A	ENSP00000251101:p.Ser7Phe	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	19	18	0.947368	NM_017512	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	37	CCDS11822.1	329	0.15064102564102563	28	0.056910569105691054	34	0.09392265193370165	161	0.28146853146853146	106	0.13984168865435356	G	10.32	1.318029	0.23994	0.031973	0.087276	ENSG00000132199	ENST00000251101;ENST00000539164	T;T	0.42131	0.98;0.98	4.19	-1.5	0.08691	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.30455	0.28	B	0.25506	0.061	T	0.26018	-1.0115	8	0.42905	T	0.14	.	10.165	0.42875	0.083:0.5405:0.3765:0.0	rs3786349	7	Q7L5Y1	ENOF1_HUMAN	F	7	ENSP00000251101:S7F;ENSP00000446321:S7F	ENSP00000251101:S7F	S	-	2	0	ENOSF1	702568	0.079000	0.21365	0.023000	0.16930	0.684000	0.39900	0.057000	0.14279	-0.433000	0.07286	0.313000	0.20887	TCC	G|0.851;A|0.149	0.149	strong		0.766	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24458236	24458236	+	Missense_Mutation	SNP	G	G	A	rs55795553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24458236G>A	ENST00000335125.6	+	1	206	c.80G>A	c.(79-81)cGg>cAg	p.R27Q	DHRS4L2_ENST00000382755.4_Missense_Mutation_p.R25Q|DHRS4L2_ENST00000545240.1_Missense_Mutation_p.R27Q|DHRS4L2_ENST00000558753.1_Missense_Mutation_p.R27Q|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Missense_Mutation_p.R27Q|DHRS4L2_ENST00000397071.1_Missense_Mutation_p.R27Q|DHRS4L2_ENST00000534993.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	25						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		ATGACCCGCCGGGACCCGCTC	0.637													g|||	139	0.0277556	0.0613	0.0216	5008	,	,		16799	0.0		0.0358	False		,,,				2504	0.0072				p.R27Q		Atlas-SNP	.											.	DHRS4L2	29	.	0			c.G80A						PASS	.	G	,,,GLN/ARG	234,4166	128.2+/-165.1	9,216,1975	52.0	53.0	52.0		,,,80	-3.3	0.0	14	dbSNP_129	52	290,8310	101.0+/-162.3	7,276,4017	no	intron,intron,intron,missense	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,43	16,492,5992	AA,AG,GG		3.3721,5.3182,4.0308	,,,	,,,27/233	24458236	524,12476	2200	4300	6500	SO:0001583	missense	317749	exon1			CCCGCCGGGACCC		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.80G>A	14.37:g.24458236G>A	ENSP00000334801:p.Arg27Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_198083	Q3YLD4	Missense_Mutation	SNP	ENST00000335125.6	37	CCDS9606.2	63	0.028846153846153848	28	0.056910569105691054	11	0.03038674033149171	0	0.0	24	0.0316622691292876	G	11.69	1.712640	0.30413	0.053182	0.033721	ENSG00000187630	ENST00000397071;ENST00000335125;ENST00000537912;ENST00000545240;ENST00000382755	T;T;T;T;D	0.82803	1.72;0.71;0.71;2.48;-1.65	2.83	-3.28	0.05033	NAD(P)-binding domain (1);	0.823536	0.10893	N	0.622534	T	0.15869	0.0382	N	0.17082	0.46	0.09310	N	0.999995	B;B	0.28820	0.224;0.062	B;B	0.19148	0.024;0.001	T	0.20174	-1.0283	10	0.12766	T	0.61	.	7.9605	0.30068	0.6921:0.0:0.3079:0.0	rs55795553	27;25	F6TD35;Q6PKH6	.;DR4L2_HUMAN	Q	27;27;27;27;25	ENSP00000380261:R27Q;ENSP00000334801:R27Q;ENSP00000439942:R27Q;ENSP00000437883:R27Q;ENSP00000372203:R25Q	ENSP00000334801:R27Q	R	+	2	0	DHRS4L2	23528076	0.000000	0.05858	0.001000	0.08648	0.098000	0.18820	-0.979000	0.03774	-0.740000	0.04803	0.411000	0.27672	CGG	G|0.962;A|0.038	0.038	strong		0.637	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
GLI3	2737	hgsc.bcm.edu	37	7	42088232	42088232	+	Silent	SNP	G	G	A	rs3898405	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:42088232G>A	ENST00000395925.3	-	5	621	c.537C>T	c.(535-537)caC>caT	p.H179H	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	179					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TGGGGTTCCGGTGTGGGGAGA	0.537									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	167	0.0333466	0.0061	0.0389	5008	,	,		18645	0.0		0.1133	False		,,,				2504	0.0184				p.H179H		Atlas-SNP	.											.	GLI3	312	.	0			c.C537T						PASS	.	G		93,4313	76.8+/-115.0	1,91,2111	112.0	117.0	115.0		537	2.7	1.0	7	dbSNP_108	115	816,7784	189.4+/-236.2	38,740,3522	no	coding-synonymous	GLI3	NM_000168.5		39,831,5633	AA,AG,GG		9.4884,2.1108,6.9891		179/1581	42088232	909,12097	2203	4300	6503	SO:0001819	synonymous_variant	2737	exon5	Familial Cancer Database	;	GTTCCGGTGTGGG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.537C>T	7.37:g.42088232G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	182	123	0.675824	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.934;A|0.066	0.066	strong		0.537	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
POLRMT	5442	hgsc.bcm.edu	37	19	621712	621712	+	Silent	SNP	A	A	G	rs2238547	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:621712A>G	ENST00000588649.2	-	10	2070	c.1986T>C	c.(1984-1986)gcT>gcC	p.A662A	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	662					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		TGAGCAGGAAAGCACCAGAGT	0.682													G|||	3105	0.620008	0.7398	0.3905	5008	,	,		11355	0.5813		0.504	False		,,,				2504	0.7802				p.A662A		Atlas-SNP	.											POLRMT,NS,carcinoma,0,1	POLRMT	91	1	0			c.T1986C						PASS	.						16.0	19.0	18.0					19																	621712		2191	4288	6479	SO:0001819	synonymous_variant	5442	exon10			CAGGAAAGCACCA		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1986T>C	19.37:g.621712A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			A|0.472;G|0.528	0.528	strong		0.682	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
HOXB6	3216	hgsc.bcm.edu	37	17	46675240	46675240	+	Silent	SNP	G	G	T	rs34438598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:46675240G>T	ENST00000484302.2	-	2	895	c.273C>A	c.(271-273)tcC>tcA	p.S91S	HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB6_ENST00000225648.3_Silent_p.S91S|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000480872.1_RNA			P17509	HXB6_HUMAN	homeobox B6	91					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGTCGGCGCCGGAGAGTGCGC	0.711													G|||	154	0.0307508	0.003	0.049	5008	,	,		11019	0.002		0.0815	False		,,,				2504	0.0327				p.S91S		Atlas-SNP	.											.	HOXB6	13	.	0			c.C273A						PASS	.	G		78,4274		1,76,2099	10.0	9.0	9.0		273	-6.3	0.9	17	dbSNP_126	9	693,7829		17,659,3585	no	coding-synonymous	HOXB6	NM_018952.4		18,735,5684	TT,TG,GG		8.1319,1.7923,5.9888		91/225	46675240	771,12103	2176	4261	6437	SO:0001819	synonymous_variant	3216	exon3			GGCGCCGGAGAGT		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"""Homeoboxes / ANTP class : HOXL subclass"""	5117	protein-coding gene	gene with protein product		142961	"""homeo box B6"""	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.273C>A	17.37:g.46675240G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Silent	SNP	ENST00000484302.2	37	CCDS11531.1																																																																																			G|0.956;T|0.044	0.044	strong		0.711	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2		
OR1L1	26737	hgsc.bcm.edu	37	9	125424507	125424507	+	Silent	SNP	A	A	C	rs70156	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	105	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	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			
VN1R4	317703	hgsc.bcm.edu	37	19	53770764	53770764	+	Missense_Mutation	SNP	G	G	A	rs74429916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53770764G>A	ENST00000311170.4	-	1	208	c.155C>T	c.(154-156)gCc>gTc	p.A52V	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	52			A -> V (in allele VN1R4*3; dbSNP:rs112711591). {ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			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)		TAAGAAGTTGGCTACAATCAG	0.453										HNSCC(26;0.072)																											p.A52V		Atlas-SNP	.											VN1R4,NS,carcinoma,-1,1	VN1R4	65	1	0			c.C155T						scavenged	.	G	VAL/ALA	1197,3209		125,947,1131	43.0	44.0	44.0		155	0.1	0.1	19	dbSNP_132	44	1999,6597		219,1561,2518	no	missense	VN1R4	NM_173857.2	64	344,2508,3649	AA,AG,GG		23.255,27.1675,24.5808	probably-damaging	52/302	53770764	3196,9806	2203	4298	6501	SO:0001583	missense	317703	exon1			AAGTTGGCTACAA	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.155C>T	19.37:g.53770764G>A	ENSP00000310856:p.Ala52Val	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	452	0.20695970695970695	155	0.3150406504065041	74	0.20441988950276244	48	0.08391608391608392	175	0.23087071240105542	G	14.88	2.666556	0.47677	0.271675	0.23255	ENSG00000228567	ENST00000311170	T	0.46451	0.87	2.49	0.0798	0.14418	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33346	U	0.005015	T	0.00012	0.0000	L	0.56199	1.76	0.49915	P	1.6899999999997473E-4	D	0.65815	0.995	D	0.63877	0.919	T	0.14420	-1.0473	9	0.72032	D	0.01	.	4.7929	0.13257	0.1357:0.4481:0.4162:0.0	.	52	Q7Z5H5	VN1R4_HUMAN	V	52	ENSP00000310856:A52V	ENSP00000310856:A52V	A	-	2	0	VN1R4	58462576	0.827000	0.29292	0.104000	0.21259	0.028000	0.11728	0.705000	0.25675	0.118000	0.18165	0.545000	0.68477	GCC	.	.	weak		0.453	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
MICAL1	64780	hgsc.bcm.edu	37	6	109767931	109767931	+	Missense_Mutation	SNP	C	C	T	rs59056467|rs35260632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:109767931C>T	ENST00000358807.3	-	18	2583	c.2272G>A	c.(2272-2274)Gcg>Acg	p.A758T	MICAL1_ENST00000358577.3_Missense_Mutation_p.A672T|MICAL1_ENST00000368952.4_Missense_Mutation_p.A777T	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	758			A -> E (in dbSNP:rs9320288).|A -> K (requires 2 nucleotide substitutions; dbSNP:rs35260632). {ECO:0000269|PubMed:11827972, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|A -> S (in dbSNP:rs59056467).|A -> T (in dbSNP:rs59056467).		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)		CTGCCTTCCGCTTTGTGGTCT	0.577													C|||	1559	0.311302	0.1936	0.3156	5008	,	,		18659	0.3482		0.3519	False		,,,				2504	0.3875				p.A758T		Atlas-SNP	.											.	MICAL1	79	.	0			c.G2272A						PASS	.	C	THR/ALA,THR/ALA	728,3678		104,520,1579	76.0	67.0	70.0		2014,2272	2.4	0.0	6	dbSNP_129	70	2206,6394		492,1222,2586	yes	missense,missense	MICAL1	NM_001159291.1,NM_022765.3	58,58	596,1742,4165	TT,TC,CC		25.6512,16.5229,22.5588	benign,benign	672/982,758/1068	109767931	2934,10072	2203	4300	6503	SO:0001583	missense	64780	exon18			CTTCCGCTTTGTG	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.2272G>A	6.37:g.109767931C>T	ENSP00000351664:p.Ala758Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	180	92	0.511111	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	37	CCDS5076.1	672	0.3076923076923077	84	0.17073170731707318	113	0.31215469613259667	225	0.39335664335664333	250	0.32981530343007914	C	8.656	0.899389	0.17686	0.165229	0.256512	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577;ENST00000368957	T;T;T	0.51574	0.7;0.7;0.7	4.23	2.43	0.29744	.	0.685752	0.13980	N	0.349545	T	0.08358	0.0208	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.04013	0.001;0.0	T	0.27640	-1.0068	9	0.18276	T	0.48	.	5.1073	0.14790	0.205:0.6896:0.0:0.1054	rs59056467;rs61742212	672;758	Q8TDZ2-2;Q8TDZ2	.;MICA1_HUMAN	T	758;777;672;282	ENSP00000351664:A758T;ENSP00000357948:A777T;ENSP00000351385:A672T	ENSP00000351385:A672T	A	-	1	0	MICAL1	109874624	0.003000	0.15002	0.001000	0.08648	0.000000	0.00434	0.504000	0.22626	0.720000	0.32209	-0.314000	0.08810	GCG	C|0.695;G|0.000;T|0.305	0.305	strong		0.577	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
BAGE2	85319	hgsc.bcm.edu	37	21	11049623	11049623	+	RNA	SNP	T	T	C	rs28537865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11049623T>C	ENST00000470054.1	-	0	487							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								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)		CTTCCTTCGCTATAATTAACA	0.368													t|||	470	0.0938498	0.1558	0.0533	5008	,	,		112925	0.0268		0.0626	False		,,,				2504	0.1401				.		Atlas-SNP	.											.	.	.	.	0			c.280-2A>G						PASS	.						140.0	100.0	112.0					21																	11049623		692	1591	2283			85319	exon5			CTTCGCTATAATT	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049623T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	335	40	0.119403	NM_182482	A8K925|Q08ER0	Splice_Site	SNP	ENST00000470054.1	37																																																																																				T|0.643;C|0.357	0.357	strong		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726772	32726772	+	Silent	SNP	G	G	A	rs200147031		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32726772G>A	ENST00000437316.2	-	3	564	c.501C>T	c.(499-501)gcC>gcT	p.A167A	HLA-DQB2_ENST00000435145.2_Silent_p.A167A|HLA-DQB2_ENST00000411527.1_Silent_p.A167A			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	171	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|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)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACACAACACCGGCTGTCTCCT	0.547																																					p.A167A		Atlas-SNP	.											HLA-DQB2,NS,carcinoma,-2,4	HLA-DQB2	22	4	0			c.C501T						scavenged	.																																			SO:0001819	synonymous_variant	3120	exon3			AACACCGGCTGTC	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.501C>T	6.37:g.32726772G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	10	0.078125	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Silent	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	G	1.934	-0.445141	0.04604	.	.	ENSG00000232629	ENST00000427449	.	.	.	3.43	-4.55	0.03441	.	.	.	.	.	T	0.10035	0.0246	.	.	.	0.28648	N	0.906781	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	.	4.9433	0.13976	0.3541:0.3084:0.3376:0.0	.	.	.	.	L	166	.	.	P	-	2	0	HLA-DQB2	32834750	0.000000	0.05858	0.601000	0.28877	0.295000	0.27426	-1.774000	0.01784	-0.898000	0.03906	-0.339000	0.08088	CCG	.	.	weak		0.547	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
GPRC5B	51704	hgsc.bcm.edu	37	16	19883364	19883364	+	Silent	SNP	G	G	A	rs61742688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19883364G>A	ENST00000300571.2	-	2	995	c.804C>T	c.(802-804)aaC>aaT	p.N268N	GPRC5B_ENST00000569479.1_Silent_p.N268N|GPRC5B_ENST00000535671.1_Silent_p.N268N|GPRC5B_ENST00000569847.1_Silent_p.N268N|GPRC5B_ENST00000537135.1_Silent_p.N294N	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	268					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						AGGTGGGGTCGTTCCAGGCAT	0.617													G|||	331	0.0660942	0.0908	0.0663	5008	,	,		18744	0.0		0.1252	False		,,,				2504	0.0399				p.N268N		Atlas-SNP	.											.	GPRC5B	54	.	0			c.C804T						PASS	.	G		356,4038	183.6+/-211.2	21,314,1862	77.0	83.0	81.0		804	-3.3	1.0	16	dbSNP_129	81	1228,7372	247.6+/-275.6	104,1020,3176	no	coding-synonymous	GPRC5B	NM_016235.1		125,1334,5038	AA,AG,GG		14.2791,8.102,12.1902		268/404	19883364	1584,11410	2197	4300	6497	SO:0001819	synonymous_variant	51704	exon2			GGGGTCGTTCCAG	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.804C>T	16.37:g.19883364G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_016235	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																			A|0.107;C|0.000;G|0.893	0.107	strong		0.617	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1		
ARID3A	1820	hgsc.bcm.edu	37	19	971933	971933	+	Silent	SNP	A	A	G	rs1051504|rs201340870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:971933A>G	ENST00000263620.3	+	9	1977	c.1650A>G	c.(1648-1650)ggA>ggG	p.G550G		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	550	Gly-rich.|Important for cytoplasmic localization. {ECO:0000250}.					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)		CCAACAAAGGAggcggcggcg	0.652													.|||	2979	0.594848	0.6248	0.549	5008	,	,		9555	0.4871		0.7674	False		,,,				2504	0.5204				p.G550G	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.A1650G						PASS	.	A		2821,1573		931,959,307	28.0	37.0	34.0		1650	-9.8	0.0	19	dbSNP_86	34	6635,1943		2582,1471,236	no	coding-synonymous	ARID3A	NM_005224.2		3513,2430,543	GG,GA,AA		22.651,35.7988,27.1045		550/594	971933	9456,3516	2197	4289	6486	SO:0001819	synonymous_variant	1820	exon9			CAAAGGAGGCGGC	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.1650A>G	19.37:g.971933A>G		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	37	CCDS12050.1																																																																																			A|0.328;G|0.672	0.672	strong		0.652	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717256	2717256	+	Silent	SNP	C	C	G	rs3745812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2717256C>G	ENST00000323469.4	-	2	732	c.549G>C	c.(547-549)ggG>ggC	p.G183G	DIRAS1_ENST00000585334.1_Silent_p.G183G	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	183					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				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)		TCTTCTGCTTCCCGGAGCGCT	0.652													C|||	988	0.197284	0.0166	0.2277	5008	,	,		11924	0.494		0.1362	False		,,,				2504	0.1769				p.G183G		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G549C						PASS	.	C		193,4213	122.5+/-159.9	4,185,2014	110.0	104.0	106.0		549	-0.1	1.0	19	dbSNP_107	106	1276,7320	250.8+/-277.5	87,1102,3109	no	coding-synonymous	DIRAS1	NM_145173.3		91,1287,5123	GG,GC,CC		14.8441,4.3804,11.2983		183/199	2717256	1469,11533	2203	4298	6501	SO:0001819	synonymous_variant	148252	exon2			CTGCTTCCCGGAG	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.549G>C	19.37:g.2717256C>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_145173		Silent	SNP	ENST00000323469.4	37	CCDS12092.1																																																																																			C|0.851;G|0.149	0.149	strong		0.652	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55179184	55179184	+	Silent	SNP	T	T	C	rs142100665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55179184T>C	ENST00000391736.1	+	13	1455	c.1140T>C	c.(1138-1140)tcT>tcC	p.S380S	LILRB4_ENST00000430952.2_Silent_p.S379S|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000270452.2_Silent_p.S380S|LILRB4_ENST00000391733.3_Silent_p.S381S	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	380					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)		CCCCACTGTCTGGGGAATTCC	0.587													T|||	47	0.00938498	0.025	0.0029	5008	,	,		18397	0.0		0.005	False		,,,				2504	0.0072				p.S380S		Atlas-SNP	.											.	LILRB4	86	.	0			c.T1140C						PASS	.						68.0	68.0	68.0					19																	55179184		2201	4297	6498	SO:0001819	synonymous_variant	11006	exon11			ACTGTCTGGGGAA	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.1140T>C	19.37:g.55179184T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	214	22	0.102804	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Silent	SNP	ENST00000391736.1	37	CCDS12902.1																																																																																			T|0.633;C|0.367	0.367	strong		0.587	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
ZIM3	114026	hgsc.bcm.edu	37	19	57649900	57649900	+	Missense_Mutation	SNP	C	C	T	rs2370134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57649900C>T	ENST00000269834.1	-	3	467	c.82G>A	c.(82-84)Gaa>Aaa	p.E28K		NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		E -> K (in dbSNP:rs2370134).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTTCTCTGTTCGGGATTCAGC	0.512													C|||	696	0.138978	0.0144	0.2161	5008	,	,		16919	0.247		0.161	False		,,,				2504	0.1186				p.E28K		Atlas-SNP	.											.	ZIM3	107	.	0			c.G82A						PASS	.	C	LYS/GLU	214,4192	129.4+/-166.1	9,196,1998	98.0	87.0	91.0		82	-1.3	0.0	19	dbSNP_100	91	1569,7031	294.3+/-301.8	153,1263,2884	no	missense	ZIM3	NM_052882.1	56	162,1459,4882	TT,TC,CC		18.2442,4.857,13.7091	benign	28/473	57649900	1783,11223	2203	4300	6503	SO:0001583	missense	114026	exon3			TCTGTTCGGGATT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.82G>A	19.37:g.57649900C>T	ENSP00000269834:p.Glu28Lys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	346	0.15842490842490842	15	0.03048780487804878	67	0.1850828729281768	152	0.26573426573426573	112	0.14775725593667546	C	10.87	1.473521	0.26423	0.04857	0.182442	ENSG00000141946	ENST00000269834	T	0.01705	4.68	2.72	-1.33	0.09172	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	P	0.37914	0.611	B	0.23716	0.048	T	0.47971	-0.9075	8	0.72032	D	0.01	.	0.2325	0.00182	0.2046:0.2664:0.2019:0.3271	rs2370134;rs17207663;rs52794544;rs61460479;rs2370134	28	Q96PE6	ZIM3_HUMAN	K	28	ENSP00000269834:E28K	ENSP00000269834:E28K	E	-	1	0	ZIM3	62341712	0.000000	0.05858	0.000000	0.03702	0.309000	0.27889	-2.790000	0.00767	0.277000	0.22141	0.205000	0.17691	GAA	C|0.856;T|0.143	0.143	strong		0.512	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
AKR1C4	1109	hgsc.bcm.edu	37	10	5260682	5260682	+	Splice_Site	SNP	C	C	G	rs17134592	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5260682C>G	ENST00000380448.1	+	11	1184	c.931C>G	c.(931-933)Ctt>Gtt	p.L311V	AKR1C4_ENST00000263126.1_Splice_Site_p.L311V			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	311			L -> V (in dbSNP:rs17134592). {ECO:0000269|PubMed:10634139}.		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.L311V(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						TCTTTTCAGTCTTATGGACCA	0.388													C|||	513	0.102436	0.025	0.2017	5008	,	,		18168	0.1111		0.1203	False		,,,				2504	0.1094				p.L311V		Atlas-SNP	.											AKR1C4,NS,carcinoma,0,1	AKR1C4	57	1	1	Substitution - Missense(1)	stomach(1)	c.C931G	GRCh37	CM995179	AKR1C4	M	rs17134592	PASS	.	C	VAL/LEU	185,4221	116.7+/-154.6	4,177,2022	156.0	133.0	141.0		931	-5.7	0.0	10	dbSNP_123	141	1301,7299	258.1+/-281.9	94,1113,3093	yes	missense-near-splice	AKR1C4	NM_001818.3	32	98,1290,5115	GG,GC,CC		15.1279,4.1988,11.4255	benign	311/324	5260682	1486,11520	2203	4300	6503	SO:0001630	splice_region_variant	1109	exon9			TTCAGTCTTATGG	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.930-1C>G	10.37:g.5260682C>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	226	0.10347985347985347	5	0.01016260162601626	61	0.1685082872928177	60	0.1048951048951049	100	0.13192612137203166	C	0.808	-0.753018	0.03041	0.041988	0.151279	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.50813	0.73;0.73	2.83	-5.67	0.02444	NADP-dependent oxidoreductase domain (2);	3.044690	0.01760	N	0.030534	T	0.00073	0.0002	N	0.16266	0.395	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06899	-1.0801	9	0.15066	T	0.55	.	5.379	0.16181	0.0:0.1334:0.2328:0.6338	rs17134592;rs52836437;rs17134592	311	P17516	AK1C4_HUMAN	V	311	ENSP00000369814:L311V;ENSP00000263126:L311V	ENSP00000263126:L311V	L	+	1	0	AKR1C4	5250682	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.365000	0.00496	-0.332000	0.08489	-0.657000	0.03884	CTT	C|0.890;G|0.110	0.110	strong		0.388	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	Missense_Mutation
POLQ	10721	hgsc.bcm.edu	37	3	121207449	121207449	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121207449A>C	ENST00000264233.5	-	16	4457	c.4329T>G	c.(4327-4329)aaT>aaG	p.N1443K		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1443					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)		GAAGAAAACTATTTAATTGTG	0.348								DNA polymerases (catalytic subunits)																													p.N1443K	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T4329G						PASS	.						44.0	46.0	45.0					3																	121207449		2201	4296	6497	SO:0001583	missense	10721	exon16			AAAACTATTTAAT	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.4329T>G	3.37:g.121207449A>C	ENSP00000264233:p.Asn1443Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	19	0.17757	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.118039	0.56505	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.50548	0.74	6.11	3.38	0.38709	.	0.230437	0.44688	D	0.000425	T	0.48804	0.1520	L	0.34521	1.04	0.28458	N	0.916	D;D	0.67145	0.996;0.975	P;P	0.62740	0.906;0.781	T	0.40608	-0.9554	10	0.54805	T	0.06	.	5.3884	0.16229	0.5847:0.1381:0.2772:0.0	.	1443;615	O75417;O75417-2	DPOLQ_HUMAN;.	K	1066;1443;1579	ENSP00000264233:N1443K	ENSP00000264233:N1443K	N	-	3	2	POLQ	122690139	0.943000	0.32029	1.000000	0.80357	0.899000	0.52679	-0.042000	0.12063	0.392000	0.25172	0.533000	0.62120	AAT	.	.	none		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
RHOT2	89941	hgsc.bcm.edu	37	16	722331	722331	+	Missense_Mutation	SNP	C	C	T	rs3177338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	40	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	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	
TTLL5	23093	hgsc.bcm.edu	37	14	76368544	76368544	+	Missense_Mutation	SNP	T	T	C	rs1133834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:76368544T>C	ENST00000298832.9	+	31	4005	c.3800T>C	c.(3799-3801)tTt>tCt	p.F1267S		NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1267			F -> S (in dbSNP:rs1133834). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:17116691}.		fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		CCTGCAGCCTTTGTGCCCATC	0.562													T|||	2131	0.425519	0.5832	0.366	5008	,	,		19061	0.494		0.1928	False		,,,				2504	0.4233				p.F1267S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T3800C						PASS	.	T	SER/PHE	2238,2168	594.9+/-388.3	570,1098,535	85.0	77.0	80.0		3800	1.5	0.3	14	dbSNP_86	80	1537,7063	286.6+/-297.8	137,1263,2900	yes	missense	TTLL5	NM_015072.4	155	707,2361,3435	CC,CT,TT		17.8721,49.2056,29.0251	benign	1267/1282	76368544	3775,9231	2203	4300	6503	SO:0001583	missense	23093	exon31			CAGCCTTTGTGCC	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.3800T>C	14.37:g.76368544T>C	ENSP00000298832:p.Phe1267Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	835	0.3823260073260073	292	0.5934959349593496	125	0.3453038674033149	277	0.48426573426573427	141	0.18601583113456466	T	13.21	2.170428	0.38315	0.507944	0.178721	ENSG00000119685	ENST00000286653;ENST00000298832	T	0.02763	4.17	5.43	1.48	0.22813	.	2.780490	0.00890	N	0.002234	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.38972	-0.9636	9	0.09590	T	0.72	.	1.2609	0.02001	0.1796:0.1055:0.1866:0.5283	rs1133834;rs2272583;rs3195915;rs52790173;rs61039434;rs1133834	341;1267	F8W7N3;Q6EMB2	.;TTLL5_HUMAN	S	341;1267	ENSP00000298832:F1267S	ENSP00000286653:F341S	F	+	2	0	TTLL5	75438297	0.014000	0.17966	0.310000	0.25168	0.975000	0.68041	0.410000	0.21098	0.346000	0.23899	-0.316000	0.08728	TTT	C|0.345;N|0.000	0.345	strong		0.562	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
Unknown	0	hgsc.bcm.edu	37	11	5989293	5989293	+	IGR	SNP	G	G	A	rs7113548	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5989293G>A								OR56A3 (19702 upstream) : OR52L1 (17828 downstream)																							CAGCCCTAGCGACAAATTGAT	0.483													.|||	1143	0.228235	0.1989	0.2233	5008	,	,		22002	0.2133		0.2883	False		,,,				2504	0.2249				p.V144V		Atlas-SNP	.											.	.	.	.	0			c.C432T						PASS	.	G		297,1087		30,237,425	70.0	63.0	65.0		432	-3.5	0.0	11	dbSNP_116	65	887,2295		131,625,835	no	coding-synonymous	OR56A5	NM_001146033.1		161,862,1260	AA,AG,GG		27.8755,21.4595,25.9308		144/314	5989293	1184,3382	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			CCTAGCGACAAAT																													11.37:g.5989293G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_001146033		Silent	SNP		37																																																																																				G|0.755;A|0.245	0.245	strong	0	0.483								
OCA2	4948	hgsc.bcm.edu	37	15	28230318	28230318	+	Missense_Mutation	SNP	C	C	T	rs1800407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28230318C>T	ENST00000354638.3	-	13	1411	c.1256G>A	c.(1255-1257)cGg>cAg	p.R419Q	OCA2_ENST00000353809.5_Missense_Mutation_p.R395Q|OCA2_ENST00000382996.2_Missense_Mutation_p.R419Q	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	419			R -> Q (polymorphism associated with green/hazel eye color; dbSNP:rs1800407). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:12163334, ECO:0000269|PubMed:15889046, ECO:0000269|PubMed:18252222, ECO:0000269|PubMed:7601462}.|R -> W (in OCA2; dbSNP:rs143218168).		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CACCCGTCCCCGGGAGAGCCG	0.567									Oculocutaneous Albinism				C|||	127	0.0253594	0.0015	0.0317	5008	,	,		19816	0.001		0.0755	False		,,,				2504	0.0266				p.R419Q		Atlas-SNP	.											.	OCA2	173	.	0			c.G1256A	GRCh37	CM025432	OCA2	M	rs1800407	PASS	.	C	GLN/ARG	54,4352	52.9+/-88.7	0,54,2149	95.0	73.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1256	4.4	0.2	15	dbSNP_89	80	669,7931	166.2+/-218.2	27,615,3658	yes	missense	OCA2	NM_000275.2	43	27,669,5807	TT,TC,CC		7.7791,1.2256,5.559	probably-damaging	419/839	28230318	723,12283	2203	4300	6503	SO:0001583	missense	4948	exon13	Familial Cancer Database		CGTCCCCGGGAGA		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1256G>A	15.37:g.28230318C>T	ENSP00000346659:p.Arg419Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	76	0.0347985347985348	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	60	0.079155672823219	C	21.8	4.202313	0.79127	0.012256	0.077791	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.85955	-2.05;-2.05;-2.05	5.35	4.44	0.53790	Divalent ion symporter (1);	0.000000	0.85682	D	0.000000	T	0.39358	0.1075	L	0.45470	1.425	0.29970	P	0.818602	D;D	0.89917	0.994;1.0	P;D	0.75484	0.879;0.986	T	0.72953	-0.4135	9	0.36615	T	0.2	-17.4895	13.4028	0.60893	0.0:0.9242:0.0:0.0758	rs1800407;rs52791072;rs1800407	395;419	Q04671-2;Q04671	.;P_HUMAN	Q	419;395;419	ENSP00000346659:R419Q;ENSP00000261276:R395Q;ENSP00000372457:R419Q	ENSP00000261276:R395Q	R	-	2	0	OCA2	25903913	1.000000	0.71417	0.152000	0.22495	0.788000	0.44548	7.083000	0.76859	1.384000	0.46424	-0.136000	0.14681	CGG	C|0.952;T|0.048	0.048	strong		0.567	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
BIRC7	79444	hgsc.bcm.edu	37	20	61870727	61870727	+	Missense_Mutation	SNP	G	G	C	rs1077019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61870727G>C	ENST00000217169.3	+	6	881	c.667G>C	c.(667-669)Gag>Cag	p.E223Q	NKAIN4_ENST00000466885.1_5'Flank|BIRC7_ENST00000342412.6_Intron|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000395306.1_Intron	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	223			E -> Q (in dbSNP:rs1077019). {ECO:0000269|PubMed:15489334}.		activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					CAGTCCAGCCGAGGCCCAGAG	0.682													C|||	1235	0.246605	0.2753	0.183	5008	,	,		14175	0.377		0.174	False		,,,				2504	0.1933				p.E223Q		Atlas-SNP	.											BIRC7,NS,carcinoma,0,1	BIRC7	25	1	0			c.G667C						PASS	.	C	,GLN/GLU	1167,3239	697.2+/-406.2	150,867,1186	41.0	47.0	45.0		,667	1.4	0.0	20	dbSNP_86	45	1398,7200	747.0+/-407.3	107,1184,3008	yes	intron,missense	BIRC7	NM_022161.2,NM_139317.1	,29	257,2051,4194	CC,CG,GG		16.2596,26.4866,19.7247	,benign	,223/299	61870727	2565,10439	2203	4299	6502	SO:0001583	missense	79444	exon6			CCAGCCGAGGCCC	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	13702	protein-coding gene	gene with protein product	"""melanoma inhibitor of apoptosis protein"", ""kidney inhibitor of apoptosis protein"", ""livin inhibitor-of-apoptosis"", ""livin"""	605737	"""baculoviral IAP repeat-containing 7"""			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.667G>C	20.37:g.61870727G>C	ENSP00000217169:p.Glu223Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Missense_Mutation	SNP	ENST00000217169.3	37	CCDS13513.1	527	0.2413003663003663	133	0.2703252032520325	66	0.18232044198895028	200	0.34965034965034963	128	0.16886543535620052	C	0.171	-1.071505	0.01918	0.264866	0.162596	ENSG00000101197	ENST00000217169	T	0.52295	0.67	2.35	1.36	0.22044	.	5.807070	0.00923	N	0.002613	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	0.31223	-0.9951	9	0.15066	T	0.55	.	3.2184	0.06707	0.0:0.5395:0.2817:0.1788	rs1077019;rs2273491;rs17845421;rs17858287;rs1077019	223	Q96CA5	BIRC7_HUMAN	Q	223	ENSP00000217169:E223Q	ENSP00000217169:E223Q	E	+	1	0	BIRC7	61341172	0.000000	0.05858	0.003000	0.11579	0.057000	0.15508	-0.427000	0.06999	0.092000	0.17331	-0.352000	0.07741	GAG	G|0.802;C|0.198	0.198	strong		0.682	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317	
LMF1	64788	hgsc.bcm.edu	37	16	929711	929711	+	Silent	SNP	C	C	T	rs2076425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:929711C>T	ENST00000262301.11	-	6	774	c.756G>A	c.(754-756)gcG>gcA	p.A252A	LMF1_ENST00000399843.2_Silent_p.A252A|LMF1_ENST00000543238.1_Silent_p.A15A|LMF1_ENST00000568268.1_5'UTR|LMF1_ENST00000568897.1_Silent_p.A35A	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	252					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				GCAGGTAGTACGCCACAGGAT	0.657													C|||	887	0.177117	0.208	0.0735	5008	,	,		14626	0.3026		0.1113	False		,,,				2504	0.1472				p.A252A		Atlas-SNP	.											LMF1,colon,carcinoma,-1,1	LMF1	42	1	0			c.G756A						scavenged	.	C		796,3524		69,658,1433	58.0	70.0	66.0		756	3.1	1.0	16	dbSNP_96	66	881,7623		44,793,3415	no	coding-synonymous	LMF1	NM_022773.2		113,1451,4848	TT,TC,CC		10.3598,18.4259,13.077		252/568	929711	1677,11147	2160	4252	6412	SO:0001819	synonymous_variant	64788	exon6			GTAGTACGCCACA	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.756G>A	16.37:g.929711C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	155	60	0.387097	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.827;T|0.173	0.173	strong		0.657	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
NIPA1	123606	hgsc.bcm.edu	37	15	23052632	23052632	+	Silent	SNP	T	T	C	rs11263683	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:23052632T>C	ENST00000337435.4	-	4	465	c.441A>G	c.(439-441)acA>acG	p.T147T	NIPA1_ENST00000538684.1_5'UTR|NIPA1_ENST00000561183.1_Silent_p.T72T|NIPA1_ENST00000437912.2_Silent_p.T72T	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	147					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		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;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		CAGCCTGAGTTGTCACACTCT	0.493													C|||	3526	0.704073	0.4478	0.8098	5008	,	,		17610	0.8026		0.7157	False		,,,				2504	0.862				p.T147T		Atlas-SNP	.											.	NIPA1	26	.	0			c.A441G						PASS	.	C	,	2179,2227	592.1+/-387.7	556,1067,580	150.0	140.0	144.0		216,441	-7.4	0.0	15	dbSNP_120	144	6323,2277	385.7+/-341.6	2330,1663,307	no	coding-synonymous,coding-synonymous	NIPA1	NM_001142275.1,NM_144599.4	,	2886,2730,887	CC,CT,TT		26.4767,49.4553,34.6302	,	72/255,147/330	23052632	8502,4504	2203	4300	6503	SO:0001819	synonymous_variant	123606	exon4			CTGAGTTGTCACA	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"""spastic paraplegia 6 (autosomal dominant)"""	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.441A>G	15.37:g.23052632T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_144599	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Silent	SNP	ENST00000337435.4	37	CCDS10011.1																																																																																			T|0.325;C|0.675	0.675	strong		0.493	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599	
PZP	5858	hgsc.bcm.edu	37	12	9303296	9303296	+	Missense_Mutation	SNP	A	A	T	rs10842971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:9303296A>T	ENST00000261336.2	-	34	4356	c.4328T>A	c.(4327-4329)aTc>aAc	p.I1443N	PZP_ENST00000381997.2_Missense_Mutation_p.I1229N	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1443			I -> N (in dbSNP:rs10842971).		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.I1229N(1)|p.I1443N(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						TCCTACTGGGATGTCTTGCAG	0.398													A|||	954	0.190495	0.1172	0.3458	5008	,	,		-128	0.0655		0.2823	False		,,,				2504	0.2137				p.I1443N	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,0,2	PZP	422	2	2	Substitution - Missense(2)	stomach(2)	c.T4328A						PASS	.	A	ASN/ILE	625,3781	270.4+/-269.6	40,545,1618	130.0	123.0	125.0		4328	4.2	0.0	12	dbSNP_120	125	2559,6041	416.9+/-352.3	388,1783,2129	yes	missense	PZP	NM_002864.2	149	428,2328,3747	TT,TA,AA		29.7558,14.1852,24.481	probably-damaging	1443/1483	9303296	3184,9822	2203	4300	6503	SO:0001583	missense	5858	exon34			ACTGGGATGTCTT	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.4328T>A	12.37:g.9303296A>T	ENSP00000261336:p.Ile1443Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	435	0.19917582417582416	53	0.10772357723577236	117	0.32320441988950277	34	0.05944055944055944	231	0.30474934036939316	A	9.854	1.194413	0.22037	0.141852	0.297558	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.23950	1.88;1.88	4.18	4.18	0.49190	Alpha-macroglobulin, receptor-binding (3);	0.289408	0.27311	U	0.019954	T	0.00012	0.0000	L	0.57536	1.79	0.52099	P	5.100000000002325E-5	P;D	0.76494	0.899;0.999	P;D	0.69824	0.491;0.966	T	0.30297	-0.9983	9	0.40728	T	0.16	.	12.7098	0.57083	1.0:0.0:0.0:0.0	rs10842971;rs17803568;rs10842971	1229;1443	P20742-2;P20742	.;PZP_HUMAN	N	1443;1229	ENSP00000261336:I1443N;ENSP00000371427:I1229N	ENSP00000261336:I1443N	I	-	2	0	PZP	9194563	0.334000	0.24739	0.040000	0.18447	0.161000	0.22273	4.995000	0.63908	1.817000	0.53016	0.460000	0.39030	ATC	A|0.782;T|0.218	0.218	strong		0.398	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
CCHCR1	54535	hgsc.bcm.edu	37	6	31118511	31118511	+	Missense_Mutation	SNP	T	T	G	rs130067	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31118511T>G	ENST00000376266.5	-	6	947	c.825A>C	c.(823-825)gaA>gaC	p.E275D	CCHCR1_ENST00000396268.3_Missense_Mutation_p.E364D|CCHCR1_ENST00000396263.2_Missense_Mutation_p.E275D|CCHCR1_ENST00000451521.2_Missense_Mutation_p.E328D|CCHCR1_ENST00000480060.1_Intron	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	275			E -> D (in dbSNP:rs130067). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14702039, 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						CCTGCATGGTTTCCAGAAGCT	0.537													T|||	1277	0.254992	0.1899	0.3329	5008	,	,		21952	0.3462		0.2087	False		,,,				2504	0.2413				p.E364D		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A1092C						PASS	.		ASP/GLU,ASP/GLU,ASP/GLU	580,2442		55,470,986	261.0	237.0	246.0	http://www.ncbi.nlm.nih.gov/pubmed?term	984,1092,825	-1.1	0.7	6	dbSNP_78	246	1069,4349		109,851,1749	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	45,45,45	164,1321,2735	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	19.7305,19.1926,19.5379	benign,benign,benign	328/836,364/872,275/783	31118511	1649,6791	1511	2709	4220	SO:0001583	missense	54535	exon6			CATGGTTTCCAGA	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.825A>C	6.37:g.31118511T>G	ENSP00000365442:p.Glu275Asp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	533	0.24404761904761904	94	0.1910569105691057	114	0.3149171270718232	167	0.291958041958042	158	0.20844327176781002	t	7.582	0.668930	0.14776	0.191926	0.197305	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.03330	3.97;3.97;3.97;3.97	4.61	-1.08	0.09936	.	0.906802	0.09417	N	0.804971	T	0.00637	0.0021	N	0.20685	0.6	0.58432	P	1.999999999946489E-6	B;B;B;B;B	0.10296	0.0;0.0;0.0;0.003;0.003	B;B;B;B;B	0.13407	0.004;0.001;0.004;0.007;0.009	T	0.48747	-0.9008	9	0.26408	T	0.33	-0.2533	0.579	0.00709	0.1777:0.2813:0.2658:0.2752	rs130067;rs3204905;rs17400880;rs52813182;rs59178150;rs130067	275;275;275;328;364	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	D	364;275;275;275;328	ENSP00000379566:E364D;ENSP00000365442:E275D;ENSP00000379561:E275D;ENSP00000401039:E328D	ENSP00000365442:E275D	E	-	3	2	CCHCR1	31226490	0.025000	0.19082	0.723000	0.30687	0.112000	0.19704	-0.444000	0.06854	-0.132000	0.11557	0.228000	0.17796	GAA	T|0.787;G|0.213	0.213	strong		0.537	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:113508839G>C	ENST00000487903.1	+	19	2326	c.2238G>C	c.(2236-2238)ctG>ctC	p.L746L	ATP11A_ENST00000283558.8_Silent_p.L746L|ATP11A_ENST00000375645.3_Silent_p.L746L|ATP11A_ENST00000375630.2_Silent_p.L746L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	746					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)				GAGACAACCTGTCCGGGTAGG	0.652													C|||	3487	0.696286	0.9644	0.7262	5008	,	,		15382	0.6567		0.6044	False		,,,				2504	0.4479				p.L746L		Atlas-SNP	.											.	ATP11A	225	.	0			c.G2238C						PASS	.	C	,	4036,368		1849,338,15	38.0	39.0	38.0		2238,2238	2.8	0.8	13	dbSNP_119	38	5293,3307		1625,2043,632	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	3474,2381,647	CC,CG,GG		38.4535,8.356,28.2605	,	746/1135,746/1192	113508839	9329,3675	2202	4300	6502	SO:0001819	synonymous_variant	23250	exon19			CAACCTGTCCGGG	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.2238G>C	13.37:g.113508839G>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1	1540	0.7051282051282052	473	0.9613821138211383	258	0.712707182320442	356	0.6223776223776224	453	0.5976253298153035	C	0.639	-0.814080	0.02798	0.91644	0.615465	ENSG00000068650	ENST00000418678	.	.	.	4.66	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999997	.	.	.	.	.	.	T	0.16897	-1.0387	3	.	.	.	.	10.7428	0.46162	0.0:0.5688:0.3611:0.0701	rs9549573;rs60929322;rs9549573	.	.	.	S	721	.	.	C	+	2	0	ATP11A	112556840	1.000000	0.71417	0.764000	0.31436	0.011000	0.07611	2.234000	0.43035	0.391000	0.25143	-0.223000	0.12442	TGT	G|0.292;C|0.708	0.708	strong		0.652	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
TTN	7273	hgsc.bcm.edu	37	2	179631214	179631214	+	Silent	SNP	T	T	C	rs2291312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179631214T>C	ENST00000591111.1	-	41	9821	c.9597A>G	c.(9595-9597)gaA>gaG	p.E3199E	TTN_ENST00000589042.1_Silent_p.E3199E|TTN_ENST00000360870.5_Silent_p.E3199E|TTN_ENST00000342992.6_Silent_p.E3199E|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.E3153E|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Silent_p.E3153E|TTN_ENST00000460472.2_Silent_p.E3153E			Q8WZ42	TITIN_HUMAN	titin	13529					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)			GGATTCTTCTTTCCACTACAT	0.418													C|||	840	0.167732	0.0772	0.3271	5008	,	,		19941	0.2143		0.0845	False		,,,				2504	0.2147				p.E3199E		Atlas-SNP	.											.	TTN	18412	.	0			c.A9597G						PASS	.	C	,,,,	383,4023	791.5+/-415.1	17,349,1837	170.0	156.0	161.0		9459,9597,9597,9459,9459	1.3	1.0	2	dbSNP_100	161	574,8026	793.5+/-407.5	23,528,3749	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	40,877,5586	CC,CT,TT		6.6744,8.6927,7.3581	,,,,	3153/26927,3199/33424,3199/5605,3153/27052,3153/27119	179631214	957,12049	2203	4300	6503	SO:0001819	synonymous_variant	7273	exon41			TCTTCTTTCCACT	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.9597A>G	2.37:g.179631214T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	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|0.898;C|0.102	0.102	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PALM3	342979	hgsc.bcm.edu	37	19	14164629	14164629	+	Missense_Mutation	SNP	C	C	T	rs75841596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14164629C>T	ENST00000340790.4	-	6	1809	c.1810G>A	c.(1810-1812)Gat>Aat	p.D604N		NM_001145028.1	NP_001138500.1	A6NDB9	PALM3_HUMAN	paralemmin 3	604					negative regulation of cytokine-mediated signaling pathway (GO:0001960)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)			endometrium(1)|kidney(2)|pancreas(1)|skin(1)	5						GGTGTGGCATCCCCCAAGGGG	0.672													c|||	58	0.0115815	0.003	0.0274	5008	,	,		15582	0.0		0.0278	False		,,,				2504	0.0072				p.D604N		Atlas-SNP	.											.	PALM3	26	.	0			c.G1810A						PASS	.						39.0	41.0	40.0					19																	14164629		692	1591	2283	SO:0001583	missense	342979	exon6			TGGCATCCCCCAA		CCDS46001.1	19p13.12	2010-04-15			ENSG00000187867	ENSG00000187867			33274	protein-coding gene	gene with protein product							Standard	NM_001145028		Approved		uc010xnk.1	A6NDB9		ENST00000340790.4:c.1810G>A	19.37:g.14164629C>T	ENSP00000344996:p.Asp604Asn	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_001145028		Missense_Mutation	SNP	ENST00000340790.4	37	CCDS46001.1	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	N	19.45	3.830302	0.71258	.	.	ENSG00000187867	ENST00000340790	T	0.38401	1.14	4.5	4.5	0.54988	.	.	.	.	.	T	0.27169	0.0666	L	0.43152	1.355	0.20074	N	0.999931	D	0.71674	0.998	D	0.66351	0.943	T	0.19095	-1.0316	9	0.66056	D	0.02	.	15.1641	0.72807	0.0:1.0:0.0:0.0	.	604	A6NDB9	PALM3_HUMAN	N	604	ENSP00000344996:D604N	ENSP00000344996:D604N	D	-	1	0	PALM3	14025629	0.041000	0.20044	0.041000	0.18516	0.734000	0.41952	0.917000	0.28665	2.248000	0.74166	0.291000	0.19559	GAT	C|0.982;T|0.018	0.018	strong		0.672	PALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458540.1	NM_001145028	
C6orf47	57827	hgsc.bcm.edu	37	6	31627449	31627449	+	Missense_Mutation	SNP	C	C	G	rs2242655	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31627449C>G	ENST00000375911.1	-	1	1100	c.276G>C	c.(274-276)aaG>aaC	p.K92N	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	92			K -> N (in dbSNP:rs2242655).			cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						GCTGGTCCCACTTGAGGGAAT	0.567													C|||	636	0.126997	0.0756	0.1873	5008	,	,		17694	0.131		0.163	False		,,,				2504	0.1125				p.K92N		Atlas-SNP	.											.	C6orf47	15	.	0			c.G276C						PASS	.	C	ASN/LYS	257,2763		12,233,1265	63.0	67.0	65.0		276	3.5	0.9	6	dbSNP_98	65	724,4694		52,620,2037	yes	missense	C6orf47	NM_021184.3	94	64,853,3302	GG,GC,CC		13.3629,8.5099,11.626	possibly-damaging	92/295	31627449	981,7457	1510	2709	4219	SO:0001583	missense	57827	exon1			GTCCCACTTGAGG	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.276G>C	6.37:g.31627449C>G	ENSP00000365076:p.Lys92Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Missense_Mutation	SNP	ENST00000375911.1	37	CCDS34399.1	339	0.15521978021978022	33	0.06707317073170732	66	0.18232044198895028	103	0.18006993006993008	137	0.18073878627968337	C	13.06	2.125104	0.37533	0.085099	0.133629	ENSG00000204439	ENST00000375911;ENST00000538106	T	0.35236	1.32	5.44	3.53	0.40419	.	0.283163	0.25151	N	0.032743	T	0.29190	0.0726	L	0.54323	1.7	0.38932	P	0.04203599999999996	D	0.57257	0.979	P	0.54270	0.747	T	0.23332	-1.0191	9	0.72032	D	0.01	-7.2804	6.587	0.22626	0.0:0.7876:0.0:0.2124	rs2242655;rs17558921;rs58544317;rs2242655	92	O95873	CF047_HUMAN	N	92	ENSP00000365076:K92N	ENSP00000365076:K92N	K	-	3	2	C6orf47	31735428	0.307000	0.24500	0.857000	0.33713	0.849000	0.48306	0.439000	0.21575	1.541000	0.49316	0.655000	0.94253	AAG	C|0.866;G|0.134	0.134	strong		0.567	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184	
IGFN1	91156	hgsc.bcm.edu	37	1	201187764	201187764	+	Silent	SNP	T	T	C	rs10920144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201187764T>C	ENST00000335211.4	+	18	10006	c.9876T>C	c.(9874-9876)gcT>gcC	p.A3292A	IGFN1_ENST00000295591.8_Silent_p.A452A	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	835						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						CATCGGATGCTGTCTTTGCTC	0.632													C|||	4656	0.929712	0.9592	0.8501	5008	,	,		12560	0.998		0.8946	False		,,,				2504	0.9121				p.A3292A		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,+1,2	IGFN1	220	2	0			c.T9876C						PASS	.	C		4185,221	133.3+/-169.7	1988,209,6	44.0	42.0	43.0		9876	-8.1	0.0	1	dbSNP_120	43	7537,1063	221.5+/-258.9	3299,939,62	no	coding-synonymous	IGFN1	NM_001164586.1		5287,1148,68	CC,CT,TT		12.3605,5.0159,9.8724		3292/3709	201187764	11722,1284	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon18			GGATGCTGTCTTT	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.9876T>C	1.37:g.201187764T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	2031	0.929945054945055	473	0.9613821138211383	309	0.8535911602209945	570	0.9965034965034965	679	0.895778364116095	C	7.575	0.667577	0.14710	0.949841	0.876395	ENSG00000163395	ENST00000412892	.	.	.	4.9	-8.1	0.01086	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26135	P	0.9803556	.	.	.	.	.	.	T	0.14924	-1.0455	3	.	.	.	.	10.5584	0.45131	0.0:0.1687:0.0983:0.7331	rs10920144;rs58401488	.	.	.	R	710	.	.	C	+	1	0	IGFN1	199454387	0.000000	0.05858	0.020000	0.16555	0.008000	0.06430	-2.244000	0.01193	-1.316000	0.02295	-1.814000	0.00607	TGT	C|0.912;G|0.000;T|0.088	0.912	strong		0.632	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TPRA1	131601	hgsc.bcm.edu	37	3	127295857	127295857	+	Silent	SNP	C	C	G	rs75067887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:127295857C>G	ENST00000355552.3	-	4	697	c.321G>C	c.(319-321)tcG>tcC	p.S107S	TPRA1_ENST00000465915.1_5'Flank|TPRA1_ENST00000489960.1_Silent_p.S107S|TPRA1_ENST00000296210.7_Silent_p.S107S|TPRA1_ENST00000450633.2_Silent_p.S107S	NM_001136053.1	NP_001129525.1	Q86W33	TPRA1_HUMAN	transmembrane protein, adipocyte asscociated 1	107					aging (GO:0007568)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	9						TTGCAGCGTTCGAGGTGCTCA	0.657													C|||	121	0.0241613	0.0635	0.0072	5008	,	,		19863	0.0		0.002	False		,,,				2504	0.0307				p.S107S		Atlas-SNP	.											TPRA1,NS,carcinoma,0,1	TPRA1	21	1	0			c.G321C						PASS	.	C	,,	258,4148	147.3+/-181.8	6,246,1951	76.0	78.0	77.0		321,321,321	-6.8	0.2	3	dbSNP_131	77	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	TPRA1	NM_001136053.1,NM_001142646.1,NM_016372.2	,,	6,252,6245	GG,GC,CC		0.0698,5.8557,2.0298	,,	107/374,107/294,107/374	127295857	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	131601	exon4			AGCGTTCGAGGTG	AK056759	CCDS3042.1, CCDS46899.1	3q21.2	2012-08-22	2009-07-08	2009-07-08	ENSG00000163870	ENSG00000163870		"""GPCR / Unclassified : 7TM orphan receptors"""	30413	protein-coding gene	gene with protein product	"""transmembrane protein 227"""	608336	"""G protein-coupled receptor 175"""	GPR175		10342878	Standard	NM_001136053		Approved	TPRA40, FLJ32197, TMEM227	uc003ejn.3	Q86W33	OTTHUMG00000159639	ENST00000355552.3:c.321G>C	3.37:g.127295857C>G		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	276	184	0.666667	NM_001142646	A8MVB8|D3DNA9|Q8WZ24|Q96AJ6|Q9P2R4	Silent	SNP	ENST00000355552.3	37	CCDS3042.1																																																																																			C|0.981;G|0.019	0.019	strong		0.657	TPRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356624.1	NM_016372	
HTR3C	170572	hgsc.bcm.edu	37	3	183774762	183774762	+	Missense_Mutation	SNP	C	C	A	rs6766410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	141	0	0		WXS	Illumina HiSeq	Phase_I	166	64	0.385542	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	
CASP9	842	hgsc.bcm.edu	37	1	15844615	15844615	+	Silent	SNP	A	A	G	rs1132312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15844615A>G	ENST00000333868.5	-	2	502	c.408T>C	c.(406-408)ttT>ttC	p.F136F	CASP9_ENST00000348549.5_Silent_p.F136F|CASP9_ENST00000546424.1_Silent_p.F136F|CASP9_ENST00000375890.4_Silent_p.F53F|CASP9_ENST00000469637.1_5'Flank	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	136			F -> L (in dbSNP:rs1820204).		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)	p.F136F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CGACATCACCAAATCCTCCAG	0.507													G|||	2929	0.584864	0.739	0.4986	5008	,	,		18823	0.6538		0.5149	False		,,,				2504	0.4387				p.F136F		Atlas-SNP	.											CASP9,NS,carcinoma,0,1	CASP9	40	1	1	Substitution - coding silent(1)	stomach(1)	c.T408C						PASS	.	G	,	3099,1307	441.8+/-346.5	1100,899,204	113.0	101.0	105.0		408,159	-3.0	0.0	1	dbSNP_92	105	4542,4058	559.4+/-387.4	1215,2112,973	no	coding-synonymous,coding-synonymous	CASP9	NM_001229.3,NM_032996.2	,	2315,3011,1177	GG,GA,AA		47.186,29.6641,41.2502	,	136/417,53/334	15844615	7641,5365	2203	4300	6503	SO:0001819	synonymous_variant	842	exon2			ATCACCAAATCCT	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.408T>C	1.37:g.15844615A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Silent	SNP	ENST00000333868.5	37	CCDS158.1																																																																																			G|0.589;A|0.411	0.589	strong		0.507	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
CLSTN2	64084	hgsc.bcm.edu	37	3	140178485	140178485	+	Missense_Mutation	SNP	G	G	A	rs7632885	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:140178485G>A	ENST00000458420.3	+	7	1286	c.1096G>A	c.(1096-1098)Gtc>Atc	p.V366I	RP11-68L1.2_ENST00000503357.1_RNA|RP11-68L1.1_ENST00000483759.2_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	366			V -> I (in dbSNP:rs7632885). {ECO:0000269|PubMed:12498782, ECO:0000269|PubMed:12972431, ECO:0000269|Ref.5}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GGGTGCCAAAGTCCCCGATGG	0.577										HNSCC(16;0.037)			A|||	2666	0.532348	0.6112	0.4265	5008	,	,		19051	0.502		0.5944	False		,,,				2504	0.4683				p.V366I	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G1096A						PASS	.	A	ILE/VAL	2582,1824	533.3+/-373.7	744,1094,365	82.0	70.0	74.0		1096	4.2	1.0	3	dbSNP_116	74	5209,3391	501.9+/-375.6	1606,1997,697	yes	missense	CLSTN2	NM_022131.2	29	2350,3091,1062	AA,AG,GG		39.4302,41.3981,40.0969	benign	366/956	140178485	7791,5215	2203	4300	6503	SO:0001583	missense	64084	exon7			GCCAAAGTCCCCG	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.1096G>A	3.37:g.140178485G>A	ENSP00000402460:p.Val366Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	1202	0.5503663003663004	295	0.5995934959349594	162	0.44751381215469616	293	0.5122377622377622	452	0.5963060686015831	A	2.739	-0.262611	0.05754	0.586019	0.605698	ENSG00000158258	ENST00000458420	T	0.74209	-0.82	5.4	4.25	0.50352	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.178921	0.47852	N	0.000210	T	0.00012	0.0000	N	0.03917	-0.325	0.48040	P	4.210000000000047E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47018	-0.9149	9	0.10902	T	0.67	-15.312	8.393	0.32540	0.8373:0.0:0.1627:0.0	rs7632885;rs13090511;rs16850312;rs52798163;rs60628243;rs7632885	366	Q9H4D0	CSTN2_HUMAN	I	366	ENSP00000402460:V366I	ENSP00000402460:V366I	V	+	1	0	CLSTN2	141661175	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	2.225000	0.42954	0.369000	0.24510	-0.269000	0.10298	GTC	G|0.425;A|0.574	0.574	strong		0.577	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
ZFHX3	463	hgsc.bcm.edu	37	16	72984668	72984668	+	Silent	SNP	C	C	T	rs2228200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72984668C>T	ENST00000268489.5	-	3	3588	c.2916G>A	c.(2914-2916)tcG>tcA	p.S972S	ZFHX3_ENST00000397992.5_Silent_p.S58S	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	972					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)				ACTCGTCCTCCGACAGGCTGC	0.602													C|||	107	0.0213658	0.0045	0.0375	5008	,	,		20737	0.0		0.0656	False		,,,				2504	0.0092				p.S972S		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G2916A						PASS	.	C	,	57,4339	56.8+/-93.2	0,57,2141	109.0	95.0	100.0		174,2916	-10.4	0.6	16	dbSNP_98	100	682,7918	170.0+/-221.2	21,640,3639	no	coding-synonymous,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	21,697,5780	TT,TC,CC		7.9302,1.2966,5.6864	,	58/2790,972/3704	72984668	739,12257	2198	4300	6498	SO:0001819	synonymous_variant	463	exon3			GTCCTCCGACAGG	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.2916G>A	16.37:g.72984668C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			C|0.953;T|0.047	0.047	strong		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
FBXO24	26261	hgsc.bcm.edu	37	7	100197690	100197690	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100197690G>A	ENST00000241071.6	+	9	1565	c.1243G>A	c.(1243-1245)Ggc>Agc	p.G415S	FBXO24_ENST00000468962.1_Missense_Mutation_p.G403S|PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000427939.2_Missense_Mutation_p.G453S|PCOLCE_ENST00000223061.5_5'Flank|FBXO24_ENST00000360609.2_3'UTR|PCOLCE-AS1_ENST00000442166.2_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	415					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CCTGTGGTGCGGCCTCAACCA	0.692																																					p.G453S		Atlas-SNP	.											.	FBXO24	125	.	0			c.G1357A						PASS	.						27.0	29.0	28.0					7																	100197690		2203	4300	6503	SO:0001583	missense	26261	exon9			TGGTGCGGCCTCA	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"""F-boxes /  ""other"""""	13595	protein-coding gene	gene with protein product		609097	"""F-box only protein 24"""			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.1243G>A	7.37:g.100197690G>A	ENSP00000241071:p.Gly415Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	185	49	0.264865	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477965	0.63849	.	.	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	D;D;D	0.98028	-4.67;-4.67;-4.67	4.76	4.76	0.60689	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.52532	D	0.000065	D	0.98317	0.9442	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.76575	0.982;0.988;0.982	D	0.98525	1.0625	10	0.44086	T	0.13	-19.8922	15.2622	0.73634	0.0:0.0:1.0:0.0	.	403;453;415	B4DY42;B4DX91;O75426	.;.;FBX24_HUMAN	S	415;403;453	ENSP00000241071:G415S;ENSP00000420239:G403S;ENSP00000416558:G453S	ENSP00000241071:G415S	G	+	1	0	FBXO24	100035626	1.000000	0.71417	0.988000	0.46212	0.549000	0.35272	5.078000	0.64425	2.199000	0.70637	0.442000	0.29010	GGC	.	.	none		0.692	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1		
ARHGEF15	22899	hgsc.bcm.edu	37	17	8215534	8215534	+	Silent	SNP	C	C	T	rs3744651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8215534C>T	ENST00000361926.3	+	2	287	c.177C>T	c.(175-177)acC>acT	p.T59T	ARHGEF15_ENST00000421050.1_Silent_p.T59T	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	59	Pro-rich.				negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CAATGTGCACCCCCATCTTCT	0.617													C|||	2088	0.416933	0.4062	0.4424	5008	,	,		11137	0.6468		0.3211	False		,,,				2504	0.2751				p.T59T		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.C177T						PASS	.	C	,	1667,2739	508.6+/-367.0	313,1041,849	93.0	95.0	94.0		177,177	2.1	1.0	17	dbSNP_107	94	2855,5745	447.6+/-361.6	465,1925,1910	no	coding-synonymous,coding-synonymous	ARHGEF15	NM_025014.1,NM_173728.3	,	778,2966,2759	TT,TC,CC		33.1977,37.8348,34.7686	,	59/842,59/842	8215534	4522,8484	2203	4300	6503	SO:0001819	synonymous_variant	22899	exon2			GTGCACCCCCATC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.177C>T	17.37:g.8215534C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	260	132	0.507692	NM_025014	A8K6G1|Q8N449|Q9H8B4	Silent	SNP	ENST00000361926.3	37	CCDS11139.1	977	0.44734432234432236	210	0.4268292682926829	153	0.42265193370165743	369	0.6451048951048951	245	0.3232189973614776	c	7.455	0.643538	0.14451	0.378348	0.331977	ENSG00000198844	ENST00000455564	.	.	.	5.14	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999378766	.	.	.	.	.	.	T	0.41431	-0.9509	4	0.66056	D	0.02	-14.1856	5.1653	0.15082	0.0:0.6475:0.1706:0.182	rs3744651;rs61574661;rs3744651	.	.	.	L	21	.	ENSP00000413324:P21L	P	+	2	0	ARHGEF15	8156259	0.001000	0.12720	0.998000	0.56505	0.894000	0.52154	-0.282000	0.08445	0.358000	0.24211	-0.126000	0.14955	CCC	C|0.620;T|0.380	0.380	strong		0.617	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
MOV10L1	54456	hgsc.bcm.edu	37	22	50584130	50584130	+	Missense_Mutation	SNP	G	G	A	rs55747387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50584130G>A	ENST00000262794.5	+	19	2601	c.2518G>A	c.(2518-2520)Gcc>Acc	p.A840T	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000545383.1_Missense_Mutation_p.A840T|MOV10L1_ENST00000395858.3_Missense_Mutation_p.A840T|MOV10L1_ENST00000540615.1_Missense_Mutation_p.A820T	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	840					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)		AGTTATTGACGCCGTCAAACC	0.473													g|||	39	0.00778754	0.0	0.0072	5008	,	,		18260	0.0		0.0139	False		,,,				2504	0.0204				p.A840T		Atlas-SNP	.											.	MOV10L1	238	.	0			c.G2518A						PASS	.		THR/ALA,THR/ALA,THR/ALA	29,4377	33.5+/-64.1	0,29,2174	112.0	109.0	110.0		2518,2458,2518	0.9	0.0	22	dbSNP_129	110	226,8374	93.8+/-155.7	5,216,4079	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	58,58,58	5,245,6253	AA,AG,GG		2.6279,0.6582,1.9606	benign,benign,benign	840/1166,820/1166,840/1212	50584130	255,12751	2203	4300	6503	SO:0001583	missense	54456	exon19			ATTGACGCCGTCA	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.2518G>A	22.37:g.50584130G>A	ENSP00000262794:p.Ala840Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	g	7.682	0.689253	0.14973	0.006582	0.026279	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.78	0.859	0.19036	.	0.515088	0.24145	N	0.041125	T	0.43656	0.1257	L	0.27053	0.805	0.20638	N	0.999875	B;B;B	0.27316	0.145;0.175;0.175	B;B;B	0.19946	0.016;0.027;0.027	T	0.36962	-0.9726	10	0.15499	T	0.54	-9.7106	9.903	0.41359	0.4224:0.0:0.5776:0.0	rs55747387	820;840;840	F5H403;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	T	840;840;840;820	ENSP00000438978:A840T;ENSP00000262794:A840T;ENSP00000379199:A840T;ENSP00000438542:A820T	ENSP00000262794:A840T	A	+	1	0	MOV10L1	48926257	0.016000	0.18221	0.009000	0.14445	0.002000	0.02628	1.111000	0.31159	0.324000	0.23333	-0.162000	0.13425	GCC	G|0.984;A|0.016	0.016	strong		0.473	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
MUC16	94025	hgsc.bcm.edu	37	19	9074950	9074950	+	Missense_Mutation	SNP	G	G	T	rs2591591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9074950G>T	ENST00000397910.4	-	3	12699	c.12496C>A	c.(12496-12498)Cat>Aat	p.H4166N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4168	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						GTTGTAGCATGGATAGGTACC	0.502													G|||	1195	0.238618	0.1649	0.2104	5008	,	,		21932	0.249		0.3121	False		,,,				2504	0.272				p.H4166N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12496A						PASS	.	G	ASN/HIS	718,3230		67,584,1323	157.0	146.0	149.0		12496	-2.4	0.0	19	dbSNP_100	149	2408,5922		347,1714,2104	yes	missense	MUC16	NM_024690.2	68	414,2298,3427	TT,TG,GG		28.9076,18.1864,25.4602	possibly-damaging	4166/14508	9074950	3126,9152	1974	4165	6139	SO:0001583	missense	94025	exon3			TAGCATGGATAGG	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.12496C>A	19.37:g.9074950G>T	ENSP00000381008:p.His4166Asn	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	534	0.2445054945054945	92	0.18699186991869918	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	5.100	0.204049	0.09704	0.181864	0.289076	ENSG00000181143	ENST00000397910	T	0.21031	2.03	1.49	-2.4	0.06583	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	.	.	.	P	0.34977	0.478	B	0.23716	0.048	T	0.43114	-0.9411	8	0.87932	D	0	.	5.1886	0.15197	0.5643:0.0:0.4357:0.0	rs2591591;rs59166931;rs2591591	4166	B5ME49	.	N	4166	ENSP00000381008:H4166N	ENSP00000381008:H4166N	H	-	1	0	MUC16	8935950	0.000000	0.05858	0.000000	0.03702	0.408000	0.30992	-0.296000	0.08287	-0.632000	0.05553	0.313000	0.20887	CAT	G|0.758;T|0.242	0.242	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
COL5A3	50509	hgsc.bcm.edu	37	19	10106936	10106936	+	Silent	SNP	G	G	C	rs1559186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10106936G>C	ENST00000264828.3	-	14	1510	c.1425C>G	c.(1423-1425)ctC>ctG	p.L475L	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	475	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTTTCATAGAGAGCTGGAAAG	0.597													G|||	1978	0.394968	0.6256	0.3689	5008	,	,		16292	0.3403		0.3221	False		,,,				2504	0.2331				p.L475L		Atlas-SNP	.											.	COL5A3	243	.	0			c.C1425G						PASS	.	G		2545,1855		749,1047,404	20.0	24.0	23.0		1425	-11.3	0.1	19	dbSNP_88	23	2898,5686		493,1912,1887	no	coding-synonymous	COL5A3	NM_015719.3		1242,2959,2291	CC,CG,GG		33.7605,42.1591,41.9208		475/1746	10106936	5443,7541	2200	4292	6492	SO:0001819	synonymous_variant	50509	exon14			CATAGAGAGCTGG	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1425C>G	19.37:g.10106936G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			G|0.601;C|0.399	0.399	strong		0.597	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
FRMPD1	22844	hgsc.bcm.edu	37	9	37729786	37729786	+	Missense_Mutation	SNP	C	C	T	rs1359590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:37729786C>T	ENST00000539465.1	+	8	1267	c.674C>T	c.(673-675)gCc>gTc	p.A225V	FRMPD1_ENST00000541302.1_Missense_Mutation_p.A94V|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000536622.1_Missense_Mutation_p.A47V|FRMPD1_ENST00000377765.3_Missense_Mutation_p.A225V			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	225	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		A -> V (in dbSNP:rs1359590).			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)		TTTGCACTGGCCCTGGAAGAG	0.567													C|||	1042	0.208067	0.2224	0.1311	5008	,	,		23758	0.1855		0.2137	False		,,,				2504	0.2607				p.A225V		Atlas-SNP	.											FRMPD1,colon,carcinoma,-1,1	FRMPD1	237	1	0			c.C674T						PASS	.	C	VAL/ALA	866,3540	338.9+/-305.5	92,682,1429	121.0	98.0	106.0		674	0.3	1.0	9	dbSNP_88	106	1768,6832	319.9+/-314.4	186,1396,2718	yes	missense	FRMPD1	NM_014907.2	64	278,2078,4147	TT,TC,CC		20.5581,19.655,20.2522	benign	225/1579	37729786	2634,10372	2203	4300	6503	SO:0001583	missense	22844	exon8			CACTGGCCCTGGA	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.674C>T	9.37:g.37729786C>T	ENSP00000444411:p.Ala225Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	11	0.23913	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	437	0.2000915750915751	132	0.2682926829268293	55	0.15193370165745856	88	0.15384615384615385	162	0.21372031662269128	C	5.809	0.333501	0.11013	0.19655	0.205581	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	5.64	0.349	0.16032	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.378196	0.29544	N	0.011852	T	0.00012	0.0000	N	0.00991	-1.07	0.20703	P	0.999861752	B;B	0.11235	0.002;0.004	B;B	0.12156	0.007;0.007	T	0.15867	-1.0422	9	0.02654	T	1	-1.9553	8.8058	0.34936	0.0:0.567:0.0:0.433	rs1359590;rs52793782;rs59936264;rs1359590	94;225	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	V	225;225;47;94	ENSP00000366995:A225V;ENSP00000444411:A225V;ENSP00000437762:A47V;ENSP00000444804:A94V	ENSP00000366995:A225V	A	+	2	0	FRMPD1	37719786	0.032000	0.19561	0.987000	0.45799	0.980000	0.70556	0.034000	0.13776	0.009000	0.14813	-0.136000	0.14681	GCC	T|0.202;G|0.004	0.202	strong		0.567	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
AHRR	57491	hgsc.bcm.edu	37	5	422858	422858	+	Missense_Mutation	SNP	C	C	G	rs562253075		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:422858C>G	ENST00000505113.1	+	6	512	c.468C>G	c.(466-468)caC>caG	p.H156Q	AHRR_ENST00000512529.1_Missense_Mutation_p.H2Q|AHRR_ENST00000506456.1_Missense_Mutation_p.H12Q|AHRR_ENST00000316418.5_Missense_Mutation_p.H156Q	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	156	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			ATGTAATGCACCAGAACATTT	0.522																																					p.H156Q		Atlas-SNP	.											.	AHRR	67	.	0			c.C468G						PASS	.						92.0	98.0	96.0					5																	422858		1997	4152	6149	SO:0001583	missense	57491	exon6			AATGCACCAGAAC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.468C>G	5.37:g.422858C>G	ENSP00000424601:p.His156Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070730	0.36566	.	.	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000514523;ENST00000510400;ENST00000506456	T;T;T;T;T	0.36878	2.32;2.32;1.3;2.32;1.23	4.76	0.128	0.14733	PAS (2);PAS fold (1);	0.047043	0.85682	D	0.000000	T	0.51787	0.1695	M	0.72576	2.205	0.58432	D	0.999991	D;D;D	0.76494	0.999;0.993;0.99	D;D;D	0.74023	0.982;0.954;0.923	T	0.49744	-0.8907	10	0.87932	D	0	.	8.2783	0.31885	0.0:0.4437:0.0:0.5563	.	12;156;156	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	Q	156;156;2;2;152;12	ENSP00000424601:H156Q;ENSP00000323816:H156Q;ENSP00000424880:H2Q;ENSP00000428893:H152Q;ENSP00000426932:H12Q	ENSP00000323816:H156Q	H	+	3	2	AHRR	475858	0.862000	0.29867	0.994000	0.49952	0.918000	0.54935	-0.009000	0.12765	-0.051000	0.13334	0.655000	0.94253	CAC	.	.	none		0.522	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
WDR61	80349	hgsc.bcm.edu	37	15	78585106	78585106	+	Silent	SNP	C	C	T	rs2280364	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:78585106C>T	ENST00000267973.2	-	5	442	c.171G>A	c.(169-171)caG>caA	p.Q57Q	RP11-762H8.1_ENST00000560057.1_RNA|WDR61_ENST00000558459.1_Intron|WDR61_ENST00000558311.1_Silent_p.Q57Q			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	67	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	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	
RGS3	5998	hgsc.bcm.edu	37	9	116356529	116356529	+	Intron	SNP	C	C	G	rs10817493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:116356529C>G	ENST00000374140.2	+	23	3289				RGS3_ENST00000394646.3_Intron|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.C110W	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|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)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GACCAATCTGCGGCCCCAAGG	0.652													C|||	4186	0.835863	0.8048	0.8127	5008	,	,		13828	0.9881		0.7376	False		,,,				2504	0.8384				p.C110W		Atlas-SNP	.											.	RGS3	251	.	0			c.C330G						PASS	.	C	,,,,TRP/CYS	3452,950		1378,696,127	32.0	41.0	38.0		,,,,330	-3.7	0.0	9	dbSNP_120	38	6233,2363		2275,1683,340	yes	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,215	3653,2379,467	GG,GC,CC		27.4895,21.5811,25.4885	,,,,	,,,,110/312	116356529	9685,3313	2201	4298	6499	SO:0001627	intron_variant	5998	exon1			AATCTGCGGCCCC	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-181C>G	9.37:g.116356529C>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	1816	0.8315018315018315	404	0.8211382113821138	291	0.8038674033149171	568	0.993006993006993	553	0.7295514511873351	C	0	-2.721434	0.00092	0.784189	0.725105	ENSG00000138835	ENST00000462403	T	0.59364	0.27	5.02	-3.7	0.04437	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	8	0.49607	T	0.09	.	0.4211	0.00456	0.2748:0.2263:0.2827:0.2162	rs10817493;rs60929919	110	Q5VZ06	.	W	110	ENSP00000436168:C110W	ENSP00000436168:C110W	C	+	3	2	RGS3	115396350	0.413000	0.25400	0.009000	0.14445	0.043000	0.13939	0.721000	0.25911	-0.367000	0.08052	-1.109000	0.02080	TGC	C|0.230;G|0.770	0.770	strong		0.652	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
OXA1L	5018	hgsc.bcm.edu	37	14	23236524	23236524	+	Missense_Mutation	SNP	C	C	T	rs8572	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23236524C>T	ENST00000604262.1	+	2	154	c.131C>T	c.(130-132)gCa>gTa	p.A44V	CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA|OXA1L_ENST00000358043.5_Missense_Mutation_p.A28V|OXA1L_ENST00000285848.5_Missense_Mutation_p.A104V|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000412791.1_Missense_Mutation_p.A44V			Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	44			V -> A (in dbSNP:rs8572). {ECO:0000269|Ref.3}.		aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		CTATTCCCAGCAGCCCCGTGC	0.597													c|||	3865	0.771765	0.553	0.9121	5008	,	,		16631	0.869		0.8489	False		,,,				2504	0.7883				p.A104V		Atlas-SNP	.											.	OXA1L	49	.	0			c.C311T						PASS	.	T	VAL/ALA	2719,1687	652.8+/-399.5	855,1009,339	40.0	39.0	39.0		311	1.4	0.0	14	dbSNP_52	39	7292,1308	754.3+/-407.5	3088,1116,96	yes	missense	OXA1L	NM_005015.3	64	3943,2125,435	TT,TC,CC		15.2093,38.2887,23.0278	benign	104/496	23236524	10011,2995	2203	4300	6503	SO:0001583	missense	5018	exon2			TCCCAGCAGCCCC		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000604262.1:c.131C>T	14.37:g.23236524C>T	ENSP00000474623:p.Ala44Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	53	50	0.943396	NM_005015	B4DPA2	Missense_Mutation	SNP	ENST00000604262.1	37		1740	0.7967032967032966	297	0.6036585365853658	324	0.8950276243093923	477	0.833916083916084	642	0.8469656992084432	c	13.10	2.136213	0.37728	0.617113	0.847907	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.33216	1.42;1.51;1.48	5.2	1.35	0.21983	.	0.667119	0.14099	N	0.341522	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06807	-1.0806	8	0.59425	D	0.04	-0.7083	5.4078	0.16330	0.1344:0.6132:0.0:0.2524	rs8572;rs712426;rs2070221;rs2228663;rs3197053;rs57253098;rs8572	44	E7EVY0	.	V	104;44;28	ENSP00000285848:A104V;ENSP00000387601:A44V;ENSP00000350740:A28V	ENSP00000285848:A104V	A	+	2	0	OXA1L	22306364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.034000	0.12225	-0.041000	0.13558	-1.551000	0.00897	GCA	C|0.216;T|0.784	0.784	strong		0.597	OXA1L-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468876.1	NM_005015	
LECT1	11061	hgsc.bcm.edu	37	13	53282749	53282749	+	Silent	SNP	G	G	A	rs61959654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:53282749G>A	ENST00000377962.3	-	6	789	c.711C>T	c.(709-711)ggC>ggT	p.G237G	LECT1_ENST00000448904.2_Silent_p.G237G			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	237					cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		GTCTTCCAGCGCCTGGGTTGC	0.443													G|||	136	0.0271565	0.0113	0.0216	5008	,	,		16589	0.0079		0.0388	False		,,,				2504	0.0603				p.G237G		Atlas-SNP	.											.	LECT1	44	.	0			c.C711T						PASS	.	G	,	87,4319	73.6+/-111.7	0,87,2116	201.0	177.0	185.0		711,711	-1.7	0.0	13	dbSNP_129	185	434,8166	133.5+/-191.0	12,410,3878	no	coding-synonymous,coding-synonymous	LECT1	NM_001011705.1,NM_007015.2	,	12,497,5994	AA,AG,GG		5.0465,1.9746,4.0058	,	237/334,237/335	53282749	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	11061	exon6			TCCAGCGCCTGGG	AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"""BRICHOS domain containing"""	17005	protein-coding gene	gene with protein product	"""BRICHOS domain containing 3"""	605147	"""multiple myeloma tumor suppressor 1"""	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.711C>T	13.37:g.53282749G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	211	97	0.459716	NM_007015	Q5TAM4|Q8TAY6|Q9UM18	Silent	SNP	ENST00000377962.3	37	CCDS9437.1																																																																																			G|0.965;A|0.035	0.035	strong		0.443	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045110.3		
OBSL1	23363	hgsc.bcm.edu	37	2	220427395	220427395	+	Splice_Site	SNP	G	G	A	rs3183099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220427395G>A	ENST00000404537.1	-	8	2738	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	OBSL1_ENST00000289656.3_Splice_Site_p.D481D|OBSL1_ENST00000603926.1_Splice_Site_p.D894D|OBSL1_ENST00000373873.4_Splice_Site_p.D894D|OBSL1_ENST00000265318.4_Splice_Site_p.D894D|OBSL1_ENST00000373876.1_Splice_Site_p.D894D	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	894					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACGAGGAGACGTCTGGAGGAC	0.647													G|||	822	0.164137	0.0772	0.2608	5008	,	,		17765	0.2123		0.2386	False		,,,				2504	0.0869				p.D894D		Atlas-SNP	.											.	OBSL1	120	.	0			c.C2682T						PASS	.	G	,,	461,3787		40,381,1703	18.0	22.0	21.0		2682,2682,2682	-7.6	0.4	2	dbSNP_105	21	1962,6404		251,1460,2472	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	,,	291,1841,4175	AA,AG,GG		23.4521,10.8522,19.2088	,,	894/1026,894/1544,894/1897	220427395	2423,10191	2124	4183	6307	SO:0001630	splice_region_variant	23363	exon8			GGAGACGTCTGGA	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2681-1C>T	2.37:g.220427395G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			G|0.802;A|0.198	0.198	strong		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		Silent
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57077464	57077464	+	Silent	SNP	T	T	C	rs10896602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57077464T>C	ENST00000532437.1	-	5	3032	c.2721A>G	c.(2719-2721)caA>caG	p.Q907Q	TNKS1BP1_ENST00000530920.1_5'UTR|TNKS1BP1_ENST00000358252.3_Silent_p.Q907Q			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	135	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	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	
RGS12	6002	hgsc.bcm.edu	37	4	3344680	3344680	+	Missense_Mutation	SNP	G	G	A	rs61748736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3344680G>A	ENST00000344733.5	+	3	2802	c.1898G>A	c.(1897-1899)cGg>cAg	p.R633Q	RGS12_ENST00000382788.3_Missense_Mutation_p.R633Q|RGS12_ENST00000306648.7_Missense_Mutation_p.R31Q|RGS12_ENST00000336727.3_Missense_Mutation_p.R633Q|RGS12_ENST00000543385.1_Missense_Mutation_p.R633Q	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	633					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AAATTTGGGCGGGGAACTGGA	0.453													G|||	221	0.0441294	0.0371	0.0216	5008	,	,		17346	0.0228		0.0477	False		,,,				2504	0.0879				p.R633Q		Atlas-SNP	.											RGS12,NS,carcinoma,+1,2	RGS12	128	2	0			c.G1898A						PASS	.	G	GLN/ARG,GLN/ARG	130,4276	93.4+/-132.2	1,128,2074	132.0	131.0	131.0		1898,1898	1.9	0.1	4	dbSNP_129	131	392,8208	126.5+/-185.0	10,372,3918	yes	missense,missense	RGS12	NM_002926.3,NM_198229.2	43,43	11,500,5992	AA,AG,GG		4.5581,2.9505,4.0135	possibly-damaging,possibly-damaging	633/1377,633/1448	3344680	522,12484	2203	4300	6503	SO:0001583	missense	6002	exon3			TTGGGCGGGGAAC	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.1898G>A	4.37:g.3344680G>A	ENSP00000339381:p.Arg633Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	76	0.0347985347985348	21	0.042682926829268296	4	0.011049723756906077	11	0.019230769230769232	40	0.052770448548812667	G	18.35	3.605735	0.66445	0.029505	0.045581	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648	T;T;T;T;T	0.36699	1.33;1.53;1.54;1.54;1.24	4.92	1.94	0.25998	.	0.372941	0.24412	N	0.038760	T	0.04770	0.0129	L	0.54323	1.7	0.09310	N	1	P;P;P;D	0.52996	0.856;0.856;0.929;0.957	B;B;B;P	0.44860	0.122;0.05;0.272;0.462	T	0.06698	-1.0812	10	0.24483	T	0.36	-11.3791	2.5637	0.04778	0.1058:0.186:0.5157:0.1925	rs61748736	31;633;633;633	Q8WX95;Q8WX97;O14924;O14924-4	.;.;RGS12_HUMAN;.	Q	633;633;633;633;31	ENSP00000440566:R633Q;ENSP00000339381:R633Q;ENSP00000338509:R633Q;ENSP00000372238:R633Q;ENSP00000304459:R31Q	ENSP00000304459:R31Q	R	+	2	0	RGS12	3314478	0.000000	0.05858	0.084000	0.20598	0.539000	0.34962	0.633000	0.24598	2.277000	0.76020	0.655000	0.94253	CGG	G|0.961;A|0.039	0.039	strong		0.453	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
IGSF5	150084	hgsc.bcm.edu	37	21	41137507	41137507	+	Missense_Mutation	SNP	G	G	C	rs2205204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:41137507G>C	ENST00000380588.4	+	3	249	c.146G>C	c.(145-147)aGa>aCa	p.R49T	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	49	Ig-like V-type 1.		R -> T (in dbSNP:rs2205204). {ECO:0000269|PubMed:14702039}.		single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CAAAATGCAAGAGTCCTGAAG	0.502													C|||	3303	0.659545	0.4274	0.7507	5008	,	,		19828	0.7292		0.7396	False		,,,				2504	0.7546				p.R49T		Atlas-SNP	.											.	IGSF5	62	.	0			c.G146C						PASS	.	C	THR/ARG	2034,2372	609.2+/-391.3	463,1108,632	59.0	57.0	58.0		146	4.1	0.0	21	dbSNP_96	58	6355,2245	380.0+/-339.5	2365,1625,310	yes	missense	IGSF5	NM_001080444.1	71	2828,2733,942	CC,CG,GG		26.1047,46.1643,35.499	benign	49/408	41137507	8389,4617	2203	4300	6503	SO:0001583	missense	150084	exon3			ATGCAAGAGTCCT		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.146G>C	21.37:g.41137507G>C	ENSP00000369962:p.Arg49Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	1466	0.6712454212454212	203	0.41260162601626016	267	0.7375690607734806	432	0.7552447552447552	564	0.7440633245382586	C	0.007	-2.009370	0.00426	0.461643	0.738953	ENSG00000183067	ENST00000380588	T	0.65549	-0.16	4.05	4.05	0.47172	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.056707	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00074	-2.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45145	-0.9281	9	0.02654	T	1	-9.7601	12.9111	0.58181	0.0:0.8363:0.1637:0.0	rs2205204;rs2205204	49	Q9NSI5	IGSF5_HUMAN	T	49	ENSP00000369962:R49T	ENSP00000369962:R49T	R	+	2	0	IGSF5	40059377	0.997000	0.39634	0.007000	0.13788	0.001000	0.01503	2.825000	0.48096	1.026000	0.39733	-0.127000	0.14921	AGA	G|0.344;C|0.656	0.656	strong		0.502	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53726039	53726039	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53726039A>G	ENST00000379925.3	-	4	518	c.468T>C	c.(466-468)cgT>cgC	p.R156R	RPGRIP1L_ENST00000563746.1_Silent_p.R156R|RPGRIP1L_ENST00000262135.4_Silent_p.R156R|RPGRIP1L_ENST00000564374.1_Silent_p.R156R	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	156					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)				CAGTGTTAATACGAGATTGTA	0.373																																					p.R156R		Atlas-SNP	.											RPGRIP1L,NS,carcinoma,-2,2	RPGRIP1L	118	2	0			c.T468C						scavenged	.						273.0	252.0	259.0					16																	53726039		2198	4300	6498	SO:0001819	synonymous_variant	23322	exon4			GTTAATACGAGAT		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.468T>C	16.37:g.53726039A>G		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	311	4	0.0128617	NM_001127897	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	37	CCDS32447.1																																																																																			.	.	none		0.373	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
XPO7	23039	hgsc.bcm.edu	37	8	21833965	21833965	+	Silent	SNP	C	C	T	rs2306641	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:21833965C>T	ENST00000252512.9	+	7	796	c.696C>T	c.(694-696)atC>atT	p.I232I	XPO7_ENST00000518017.1_3'UTR|XPO7_ENST00000433566.4_Silent_p.I233I|XPO7_ENST00000434536.1_Silent_p.I241I	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	232					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TTGACTTCATCGGCACTTCCA	0.478													C|||	1473	0.294129	0.2186	0.2104	5008	,	,		18198	0.4008		0.4563	False		,,,				2504	0.1789				p.I232I		Atlas-SNP	.											.	XPO7	79	.	0			c.C696T						PASS	.	C		1090,2952		163,764,1094	153.0	150.0	151.0		696	0.8	1.0	8	dbSNP_100	151	3545,4903		757,2031,1436	no	coding-synonymous	XPO7	NM_015024.4		920,2795,2530	TT,TC,CC		41.9626,26.9668,37.1097		232/1088	21833965	4635,7855	2021	4224	6245	SO:0001819	synonymous_variant	23039	exon7			CTTCATCGGCACT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.696C>T	8.37:g.21833965C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	37	CCDS47818.1																																																																																			C|0.655;T|0.345	0.345	strong		0.478	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
SCEL	8796	hgsc.bcm.edu	37	13	78188078	78188078	+	Missense_Mutation	SNP	A	A	G	rs8002725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:78188078A>G	ENST00000349847.3	+	24	1523	c.1439A>G	c.(1438-1440)aAa>aGa	p.K480R	SCEL_ENST00000377246.3_Missense_Mutation_p.K460R|SCEL_ENST00000469982.1_3'UTR|SCEL_ENST00000535157.1_Missense_Mutation_p.K438R	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	480	16 X approximate tandem repeats.		K -> R (in dbSNP:rs8002725).		embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AAAGCTGTCAAAAACACTGAT	0.328													A|||	1081	0.215855	0.3903	0.1729	5008	,	,		17587	0.1409		0.1183	False		,,,				2504	0.1881				p.K480R		Atlas-SNP	.											.	SCEL	85	.	0			c.A1439G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	1565,2841	489.0+/-361.4	284,997,922	182.0	174.0	177.0		1313,1379,1439	3.9	1.0	13	dbSNP_116	177	1284,7316	254.1+/-279.5	110,1064,3126	yes	missense,missense,missense	SCEL	NM_001160706.1,NM_003843.3,NM_144777.2	26,26,26	394,2061,4048	GG,GA,AA		14.9302,35.5197,21.9053	possibly-damaging,possibly-damaging,possibly-damaging	438/647,460/669,480/689	78188078	2849,10157	2203	4300	6503	SO:0001583	missense	8796	exon24			CTGTCAAAAACAC	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1439A>G	13.37:g.78188078A>G	ENSP00000302579:p.Lys480Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	37	CCDS9459.1	413	0.1891025641025641	176	0.35772357723577236	68	0.1878453038674033	82	0.14335664335664336	87	0.11477572559366754	A	8.124	0.781687	0.16120	0.355197	0.149302	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	D;T;D	0.81579	-1.51;1.84;-1.51	5.14	3.93	0.45458	.	0.112463	0.40144	N	0.001165	T	0.00012	0.0000	L	0.55103	1.725	0.42313	P	0.007777999999999952	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.14578	0.01;0.011;0.01	T	0.16512	-1.0400	9	0.15952	T	0.53	-18.9715	8.1757	0.31281	0.9068:0.0:0.0932:0.0	rs8002725;rs52813774;rs61017956;rs8002725	438;460;480	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	R	438;460;480	ENSP00000437895:K438R;ENSP00000366454:K460R;ENSP00000302579:K480R	ENSP00000302579:K480R	K	+	2	0	SCEL	77086079	0.958000	0.32768	0.980000	0.43619	0.070000	0.16714	1.211000	0.32382	0.883000	0.36040	0.454000	0.30748	AAA	A|0.790;G|0.209	0.209	strong		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
ETS2	2114	hgsc.bcm.edu	37	21	40190408	40190408	+	Missense_Mutation	SNP	C	C	A	rs61735785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:40190408C>A	ENST00000360214.3	+	8	1109	c.649C>A	c.(649-651)Ctc>Atc	p.L217I	ETS2_ENST00000360938.3_Missense_Mutation_p.L217I	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	217					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				CAAAGGCGGCCTCCTGGACAG	0.567													C|||	17	0.00339457	0.0	0.0086	5008	,	,		17462	0.0		0.0089	False		,,,				2504	0.002				p.L357I		Atlas-SNP	.											.	ETS2	87	.	0			c.C1069A						PASS	.	C	ILE/LEU	4,4402	8.1+/-20.4	0,4,2199	149.0	155.0	153.0		649	5.3	0.9	21	dbSNP_129	153	103,8497	56.4+/-117.6	1,101,4198	yes	missense	ETS2	NM_005239.4	5	1,105,6397	AA,AC,CC		1.1977,0.0908,0.8227	probably-damaging	217/470	40190408	107,12899	2203	4300	6503	SO:0001583	missense	2114	exon8			GGCGGCCTCCTGG		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.649C>A	21.37:g.40190408C>A	ENSP00000353344:p.Leu217Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	13.05	2.120236	0.37436	9.08E-4	0.011977	ENSG00000157557	ENST00000360214;ENST00000360938;ENST00000456966	T;T;T	0.41400	2.48;2.48;1.0	6.16	5.28	0.74379	.	2.205300	0.02436	N	0.084067	T	0.42832	0.1220	M	0.69823	2.125	0.42985	D	0.994471	P;D	0.54397	0.908;0.966	B;P	0.46144	0.277;0.505	T	0.54649	-0.8262	10	0.07990	T	0.79	.	12.2106	0.54377	0.1305:0.7322:0.1373:0.0	rs61735785	217;217	P15036;C9JAG2	ETS2_HUMAN;.	I	217	ENSP00000353344:L217I;ENSP00000354194:L217I;ENSP00000411086:L217I	ENSP00000353344:L217I	L	+	1	0	ETS2	39112278	0.976000	0.34144	0.916000	0.36221	0.114000	0.19823	2.340000	0.43974	1.609000	0.50190	0.650000	0.86243	CTC	C|0.993;A|0.007	0.007	strong		0.567	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
MUC16	94025	hgsc.bcm.edu	37	19	9076083	9076083	+	Missense_Mutation	SNP	G	G	A	rs2547072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076083G>A	ENST00000397910.4	-	3	11566	c.11363C>T	c.(11362-11364)aCa>aTa	p.T3788I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3789	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						TGCAGCTGGTGTGACTGCACT	0.522													G|||	1243	0.248203	0.2005	0.2118	5008	,	,		21894	0.249		0.3121	False		,,,				2504	0.272				p.T3788I		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.C11363T						PASS	.	G	ILE/THR	843,3259		99,645,1307	170.0	165.0	167.0		11363	-3.8	0.0	19	dbSNP_100	167	2422,5998		346,1730,2134	yes	missense	MUC16	NM_024690.2	89	445,2375,3441	AA,AG,GG		28.7648,20.551,26.0741	benign	3788/14508	9076083	3265,9257	2051	4210	6261	SO:0001583	missense	94025	exon3			GCTGGTGTGACTG	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.11363C>T	19.37:g.9076083G>A	ENSP00000381008:p.Thr3788Ile	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	2.614	-0.290069	0.05568	0.20551	0.287648	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.93	-3.8	0.04307	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.23540	0.087	B	0.26416	0.069	T	0.48364	-0.9042	8	0.87932	D	0	.	2.3025	0.04165	0.302:0.0:0.2829:0.4151	rs2547072;rs17418366;rs60517166;rs2547072	3788	B5ME49	.	I	3788	ENSP00000381008:T3788I	ENSP00000381008:T3788I	T	-	2	0	MUC16	8937083	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	-0.039000	0.12124	-0.874000	0.04027	0.313000	0.20887	ACA	G|0.750;A|0.250	0.250	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR13G1	441933	hgsc.bcm.edu	37	1	247835908	247835908	+	Missense_Mutation	SNP	T	T	A	rs28556931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247835908T>A	ENST00000359688.2	-	1	457	c.436A>T	c.(436-438)Atg>Ttg	p.M146L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	146			M -> L (in dbSNP:rs28556931).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	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)			GCAATAGCCATGACCATGCTG	0.473													T|||	1654	0.330272	0.2995	0.2392	5008	,	,		23615	0.376		0.3519	False		,,,				2504	0.3671				p.M146L		Atlas-SNP	.											.	OR13G1	78	.	0			c.A436T						PASS	.	T	LEU/MET	1324,3082	443.9+/-347.2	192,940,1071	103.0	83.0	90.0		436	-1.1	0.1	1	dbSNP_125	90	3098,5502	474.3+/-368.8	562,1974,1764	yes	missense	OR13G1	NM_001005487.1	15	754,2914,2835	AA,AT,TT		36.0233,30.0499,33.9997	possibly-damaging	146/308	247835908	4422,8584	2203	4300	6503	SO:0001583	missense	441933	exon1			TAGCCATGACCAT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.436A>T	1.37:g.247835908T>A	ENSP00000352717:p.Met146Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	677	0.309981684981685	139	0.28252032520325204	88	0.2430939226519337	185	0.32342657342657344	265	0.3496042216358839	T	10.64	1.406508	0.25378	0.300499	0.360233	ENSG00000197437	ENST00000359688	T	0.34859	1.34	4.2	-1.12	0.09808	GPCR, rhodopsin-like superfamily (1);	0.246896	0.28600	N	0.014777	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.18741	0.03	B	0.25759	0.063	T	0.46569	-0.9182	9	0.66056	D	0.02	-26.0996	0.9164	0.01305	0.156:0.2813:0.1606:0.4022	rs28556931;rs60481591	146	Q8NGZ3	O13G1_HUMAN	L	146	ENSP00000352717:M146L	ENSP00000352717:M146L	M	-	1	0	OR13G1	245902531	0.000000	0.05858	0.085000	0.20634	0.536000	0.34869	0.305000	0.19254	-0.302000	0.08869	0.460000	0.39030	ATG	T|0.665;A|0.335	0.335	strong		0.473	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
POTEC	388468	hgsc.bcm.edu	37	18	14542916	14542916	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:14542916G>T	ENST00000358970.5	-	1	229	c.230C>A	c.(229-231)aCg>aAg	p.T77K	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	77										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						CACGTTGCTCGTGCCGCTCCC	0.577																																					p.T77K		Atlas-SNP	.											POTEC,NS,carcinoma,+1,1	POTEC	129	1	0			c.C230A						scavenged	.						42.0	51.0	48.0					18																	14542916		692	1591	2283	SO:0001583	missense	388468	exon1			TTGCTCGTGCCGC	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.230C>A	18.37:g.14542916G>T	ENSP00000351856:p.Thr77Lys	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	287	6	0.0209059	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.707401	0.00096	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.22743	1.94	0.429	-0.857	0.10693	.	.	.	.	.	T	0.03827	0.0108	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	8	0.02654	T	1	.	.	.	.	.	77	B2RU33	POTEC_HUMAN	K	77	ENSP00000351856:T77K	ENSP00000351856:T77K	T	-	2	0	POTEC	14532916	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.710000	0.01888	-2.489000	0.00518	-1.883000	0.00544	ACG	G|1.000;|0.000	.	weak		0.577	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
LYPD2	137797	hgsc.bcm.edu	37	8	143833856	143833856	+	Missense_Mutation	SNP	C	C	T	rs11778314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143833856C>T	ENST00000359228.3	-	1	96	c.14G>A	c.(13-15)cGg>cAg	p.R5Q		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	5			R -> Q (in dbSNP:rs11778314).	RLA -> QLV (in Ref. 3; AAI19020). {ECO:0000305}.		anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GAGCGCCAGCCGCGTCCCCCG	0.692													C|||	1175	0.234625	0.149	0.1585	5008	,	,		13084	0.4038		0.1899	False		,,,				2504	0.2761				p.R5Q		Atlas-SNP	.											LYPD2,caecum,carcinoma,0,2	LYPD2	18	2	0			c.G14A						PASS	.	C	GLN/ARG	699,3703	284.0+/-277.4	44,611,1546	41.0	47.0	45.0		14	-2.4	0.0	8	dbSNP_120	45	1540,7056	283.5+/-296.1	140,1260,2898	no	missense	LYPD2	NM_205545.1	43	184,1871,4444	TT,TC,CC		17.9153,15.8791,17.2257	probably-damaging	5/126	143833856	2239,10759	2201	4298	6499	SO:0001583	missense	137797	exon1			GCCAGCCGCGTCC	AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.14G>A	8.37:g.143833856C>T	ENSP00000352163:p.Arg5Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	183	178	0.972678	NM_205545	A8K2R6|Q0VD64|Q0VF31	Missense_Mutation	SNP	ENST00000359228.3	37	CCDS6388.1	501	0.22939560439560439	70	0.14227642276422764	58	0.16022099447513813	225	0.39335664335664333	148	0.19525065963060687	C	10.68	1.417549	0.25552	0.158791	0.179153	ENSG00000197353	ENST00000359228	T	0.73681	-0.77	4.29	-2.4	0.06583	.	0.804858	0.09861	N	0.746178	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B	0.14438	0.01	B	0.04013	0.001	T	0.27365	-1.0076	9	0.45353	T	0.12	.	5.4003	0.16293	0.1554:0.2681:0.0:0.5765	rs11778314;rs58429093	5	Q6UXB3	LYPD2_HUMAN	Q	5	ENSP00000352163:R5Q	ENSP00000352163:R5Q	R	-	2	0	LYPD2	143830858	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.279000	0.08479	-0.285000	0.09089	-0.145000	0.13849	CGG	C|0.808;T|0.192	0.192	strong		0.692	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545	
BACE1	23621	hgsc.bcm.edu	37	11	117186506	117186506	+	Silent	SNP	G	G	A	rs28917234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:117186506G>A	ENST00000313005.6	-	1	466	c.6C>T	c.(4-6)gcC>gcT	p.A2A	BACE1_ENST00000513780.1_Silent_p.A2A|AP000892.4_ENST00000504906.1_RNA|BACE1_ENST00000445823.2_Silent_p.A2A|BACE1_ENST00000428381.2_Silent_p.A2A|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Silent_p.A2A	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	2					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)		GCAGGGCTTGGGCCATGGTGG	0.746													G|||	92	0.0183706	0.0023	0.0159	5008	,	,		10280	0.0		0.0378	False		,,,				2504	0.0409				p.A2A		Atlas-SNP	.											.	BACE1	33	.	0			c.C6T						PASS	.	G	,,,	14,2658		0,14,1322	2.0	3.0	3.0		6,6,6,6	0.6	0.9	11	dbSNP_125	3	131,5129		1,129,2500	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,	1,143,3822	AA,AG,GG		2.4905,0.524,1.828	,,,	2/502,2/458,2/477,2/433	117186506	145,7787	1336	2630	3966	SO:0001819	synonymous_variant	23621	exon1			GGCTTGGGCCATG	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.6C>T	11.37:g.117186506G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1																																																																																			G|0.979;A|0.021	0.021	strong		0.746	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
TSC2	7249	hgsc.bcm.edu	37	16	2138269	2138269	+	Silent	SNP	T	T	C	rs137854091|rs1748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2138269T>C	ENST00000219476.3	+	41	5832	c.5202T>C	c.(5200-5202)gaT>gaC	p.D1734D	TSC2_ENST00000439673.2_Silent_p.D1631D|TSC2_ENST00000401874.2_Silent_p.D1667D|TSC2_ENST00000353929.4_Silent_p.D1691D|TSC2_ENST00000382538.6_Silent_p.D1619D|TSC2_ENST00000568454.1_Silent_p.D1678D|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000350773.4_Silent_p.D1711D	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1734	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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)				ACCCCACCGATATCTACCCCT	0.652			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	1384	0.276358	0.7481	0.1988	5008	,	,		14957	0.0		0.1839	False		,,,				2504	0.0736				p.D1734D		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.T5202C						PASS	.	C	,,	2789,1607	496.0+/-363.4	885,1019,294	96.0	103.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5202,5001,5133	3.2	1.0	16	dbSNP_36	101	1531,7067	745.9+/-407.3	140,1251,2908	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	1025,2270,3202	CC,CT,TT		17.8065,36.556,33.2461	,,	1734/1808,1667/1741,1711/1785	2138269	4320,8674	2198	4299	6497	SO:0001819	synonymous_variant	7249	exon41	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CACCGATATCTAC	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.5202T>C	16.37:g.2138269T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			T|0.695;G|0.000;C|0.305;A|0.000	0.305	strong		0.652	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
A4GNT	51146	hgsc.bcm.edu	37	3	137849888	137849888	+	Missense_Mutation	SNP	C	C	T	rs79791762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137849888C>T	ENST00000236709.3	-	2	412	c.211G>A	c.(211-213)Gta>Ata	p.V71I		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	71					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						GCAGACTCTACGGAACAGGAG	0.537													C|||	61	0.0121805	0.0038	0.0216	5008	,	,		18589	0.004		0.0318	False		,,,				2504	0.0051				p.V71I		Atlas-SNP	.											.	A4GNT	42	.	0			c.G211A						PASS	.	C	ILE/VAL	34,4372	39.2+/-71.8	0,34,2169	105.0	105.0	105.0		211	4.6	1.0	3	dbSNP_132	105	238,8362	95.9+/-157.7	3,232,4065	yes	missense	A4GNT	NM_016161.2	29	3,266,6234	TT,TC,CC		2.7674,0.7717,2.0913	possibly-damaging	71/341	137849888	272,12734	2203	4300	6503	SO:0001583	missense	51146	exon2			ACTCTACGGAACA	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.211G>A	3.37:g.137849888C>T	ENSP00000236709:p.Val71Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	151	51	0.337748	NM_016161	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	ENST00000236709.3	37	CCDS3097.1	40	0.018315018315018316	4	0.008130081300813009	10	0.027624309392265192	1	0.0017482517482517483	25	0.032981530343007916	C	13.69	2.312966	0.40895	0.007717	0.027674	ENSG00000118017	ENST00000236709	T	0.74737	-0.87	5.42	4.55	0.56014	Glycosyltransferase, DXD sugar-binding motif (1);	0.118011	0.37437	N	0.002089	T	0.45875	0.1364	L	0.43152	1.355	0.34686	D	0.725269	D	0.63880	0.993	P	0.49708	0.62	T	0.65565	-0.6137	10	0.12430	T	0.62	-2.3222	10.3309	0.43823	0.0:0.8505:0.0:0.1495	.	71	Q9UNA3	A4GCT_HUMAN	I	71	ENSP00000236709:V71I	ENSP00000236709:V71I	V	-	1	0	A4GNT	139332578	0.997000	0.39634	0.994000	0.49952	0.407000	0.30961	3.791000	0.55469	1.281000	0.44480	0.561000	0.74099	GTA	C|0.980;T|0.020	0.020	strong		0.537	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120303	38120303	+	Silent	SNP	C	C	A	rs79945262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38120303C>A	ENST00000406386.3	+	7	1995	c.1740C>A	c.(1738-1740)gcC>gcA	p.A580A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	580					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)					CATCCTGTGCCCAGCGGGACA	0.587													-|||	288	0.057508	0.0862	0.0389	5008	,	,		26787	0.001		0.0358	False		,,,				2504	0.1125				p.A580A		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C1740A						PASS	.						82.0	131.0	115.0					22																	38120303		1929	4162	6091	SO:0001819	synonymous_variant	11078	exon7			CTGTGCCCAGCGG	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.1740C>A	22.37:g.38120303C>A		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.966;A|0.034	0.034	strong		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
AKAP11	11215	hgsc.bcm.edu	37	13	42877265	42877265	+	Silent	SNP	G	G	C	rs9315906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42877265G>C	ENST00000025301.2	+	8	4558	c.4383G>C	c.(4381-4383)ctG>ctC	p.L1461L		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1461				LDPYRNEVSQLYSFSTSLVHSITKDA -> CGPSVELSPWK WQTRCGREGNSWKRE (in Ref. 5; BAA92117). {ECO:0000305}.	intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CAACCTCTCTGGTTCACAGCA	0.373													C|||	675	0.134784	0.0424	0.1297	5008	,	,		21744	0.1716		0.1282	False		,,,				2504	0.2321				p.L1461L		Atlas-SNP	.											.	AKAP11	146	.	0			c.G4383C						PASS	.	C		282,4124	779.6+/-414.4	13,256,1934	69.0	74.0	72.0		4383	-8.3	0.2	13	dbSNP_119	72	1322,7278	754.2+/-407.5	95,1132,3073	no	coding-synonymous	AKAP11	NM_016248.3		108,1388,5007	CC,CG,GG		15.3721,6.4004,12.3328		1461/1902	42877265	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			CTCTCTGGTTCAC	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4383G>C	13.37:g.42877265G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			G|0.878;C|0.122	0.122	strong		0.373	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4901385A>C	ENST00000404991.1	-	1	240	c.54T>G	c.(52-54)aaT>aaG	p.N18K	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	18					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		CGCCGTAGCGATTCGGCGGCG	0.672													C|||	2479	0.495008	0.708	0.3689	5008	,	,		13116	0.4117		0.341	False		,,,				2504	0.5409				p.N19K		Atlas-SNP	.											.	PAPOLB	93	.	0			c.T57G						PASS	.	C	,LYS/ASN	2462,1420		806,850,285	10.0	11.0	11.0		,57	3.2	0.2	7	dbSNP_107	11	3180,5066		607,1966,1550	yes	intron,missense	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,94	1413,2816,1835	CC,CA,AA		38.5642,36.5791,46.5204	,benign	,19/638	4901385	5642,6486	1941	4123	6064	SO:0001583	missense	56903	exon1			GTAGCGATTCGGC	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.54T>G	7.37:g.4901385A>C	ENSP00000384700:p.Asn18Lys	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	64	17	0.265625	NM_020144	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	37		948	0.4340659340659341	356	0.7235772357723578	128	0.35359116022099446	208	0.36363636363636365	256	0.33773087071240104	C	0.005	-2.186441	0.00305	0.634209	0.385642	ENSG00000218823	ENST00000404991	.	.	.	4.13	3.25	0.37280	.	.	.	.	.	T	0.00012	0.0000	N	0.00025	-2.685	0.47621	P	5.300000000000304E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42015	-0.9476	7	0.02654	T	1	.	3.8434	0.08925	0.1922:0.6117:0.0:0.1961	rs3750009;rs9655434;rs57255641;rs3750009	19	A4D1Z6	.	K	18	.	ENSP00000384700:N18K	N	-	3	2	PAPOLB	4867911	1.000000	0.71417	0.189000	0.23252	0.003000	0.03518	0.699000	0.25586	0.718000	0.32166	-0.121000	0.15023	AAT	A|0.534;C|0.466	0.466	strong		0.672	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
HECTD4	283450	hgsc.bcm.edu	37	12	112622244	112622244	+	Missense_Mutation	SNP	A	A	G	rs369692553		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112622244A>G	ENST00000430131.2	-	60	10405	c.9260T>C	c.(9259-9261)gTg>gCg	p.V3087A	HECTD4_ENST00000377560.5_Missense_Mutation_p.V3337A|HECTD4_ENST00000550722.1_Missense_Mutation_p.V3363A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3087					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)										CAGCGGATCCACAGAGAGGTC	0.677																																					p.V3375A		Atlas-SNP	.											.	.	.	.	0			c.T10124C						PASS	.	A	ALA/VAL	0,4366		0,0,2183	20.0	26.0	24.0		10010	2.1	0.7	12		24	1,8559		0,1,4279	no	missense	C12orf51	NM_001109662.2	64	0,1,6462	GG,GA,AA		0.0117,0.0,0.0077	benign	3337/4247	112622244	1,12925	2183	4280	6463	SO:0001583	missense	283450	exon61			GGATCCACAGAGA	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.9260T>C	12.37:g.112622244A>G	ENSP00000404379:p.Val3087Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	A	9.809	1.182707	0.21870	0.0	1.17E-4	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51325	0.71;0.71;0.71	5.82	2.06	0.26882	.	.	.	.	.	T	0.27866	0.0686	N	0.14661	0.345	0.29651	N	0.843934	B	0.02656	0.0	B	0.01281	0.0	T	0.18429	-1.0337	9	0.42905	T	0.14	.	6.5643	0.22503	0.7294:0.1299:0.1406:0.0	.	3087	Q9Y4D8	K0614_HUMAN	A	3337;3087;3363	ENSP00000366783:V3337A;ENSP00000404379:V3087A;ENSP00000449784:V3363A	ENSP00000366783:V3337A	V	-	2	0	C12orf51	111106627	0.368000	0.25031	0.678000	0.29963	0.067000	0.16453	3.175000	0.50855	0.479000	0.27511	0.533000	0.62120	GTG	.	.	weak		0.677	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
NIPBL	25836	hgsc.bcm.edu	37	5	36985274	36985274	+	Silent	SNP	C	C	T	rs116049172		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:36985274C>T	ENST00000282516.8	+	10	2491	c.1992C>T	c.(1990-1992)aaC>aaT	p.N664N	NIPBL_ENST00000448238.2_Silent_p.N664N|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	664					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)			GCAAACAAAACGAGAGCACCA	0.338													C|||	1	0.000199681	0.0	0.0	5008	,	,		20570	0.0		0.001	False		,,,				2504	0.0				p.N664N		Atlas-SNP	.											.	NIPBL	513	.	0			c.C1992T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	97.0	96.0	96.0		1992,1992	0.7	0.9	5	dbSNP_132	96	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	664/2698,664/2805	36985274	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAACGAGAGC	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.1992C>T	5.37:g.36985274C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			C|1.000;T|0.000	0.000	strong		0.338	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
CLCA1	1179	hgsc.bcm.edu	37	1	86965419	86965419	+	Silent	SNP	T	T	C	rs1882753	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:86965419T>C	ENST00000234701.3	+	15	2787	c.2436T>C	c.(2434-2436)acT>acC	p.T812T	CLCA1_ENST00000394711.1_Silent_p.T812T			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	812					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)		TGAATACTACTGCTCTCATCC	0.343													T|||	1766	0.352636	0.2837	0.2291	5008	,	,		18120	0.5446		0.2604	False		,,,				2504	0.4305				p.T812T		Atlas-SNP	.											.	CLCA1	109	.	0			c.T2436C						PASS	.	T		1173,3231	395.6+/-329.7	162,849,1191	89.0	92.0	91.0		2436	-4.7	0.0	1	dbSNP_92	91	2238,6362	375.2+/-337.7	316,1606,2378	no	coding-synonymous	CLCA1	NM_001285.3		478,2455,3569	CC,CT,TT		26.0233,26.6349,26.2304		812/915	86965419	3411,9593	2202	4300	6502	SO:0001819	synonymous_variant	1179	exon14			TACTACTGCTCTC		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.2436T>C	1.37:g.86965419T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																			T|0.690;C|0.310	0.310	strong		0.343	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
NRIP1	8204	hgsc.bcm.edu	37	21	16339348	16339348	+	Missense_Mutation	SNP	A	A	G	rs77402452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:16339348A>G	ENST00000400202.1	-	3	1878	c.1166T>C	c.(1165-1167)aTa>aCa	p.I389T	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000400199.1_Missense_Mutation_p.I389T|NRIP1_ENST00000318948.4_Missense_Mutation_p.I389T			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	389	Interaction with ZNF366.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TGGCTTAGGTATAGTCTGGCT	0.353													A|||	50	0.00998403	0.0015	0.0043	5008	,	,		24788	0.0		0.0119	False		,,,				2504	0.0337				p.I389T		Atlas-SNP	.											.	NRIP1	103	.	0			c.T1166C						PASS	.	A	THR/ILE	17,4389	24.3+/-50.5	0,17,2186	189.0	180.0	183.0		1166	3.7	1.0	21	dbSNP_131	183	128,8470	65.6+/-127.9	2,124,4173	yes	missense	NRIP1	NM_003489.3	89	2,141,6359	GG,GA,AA		1.4887,0.3858,1.115	benign	389/1159	16339348	145,12859	2203	4299	6502	SO:0001583	missense	8204	exon4			TTAGGTATAGTCT	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.1166T>C	21.37:g.16339348A>G	ENSP00000383063:p.Ile389Thr	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	243	118	0.485597	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	A	1.706	-0.500263	0.04291	0.003858	0.014887	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.07800	3.16;3.16;3.16	6.02	3.66	0.41972	.	0.580040	0.18443	N	0.141077	T	0.03651	0.0104	N	0.25647	0.755	0.30132	N	0.804713	B	0.02656	0.0	B	0.01281	0.0	T	0.26573	-1.0099	10	0.18710	T	0.47	-23.0024	7.328	0.26566	0.6676:0.0:0.3324:0.0	.	389	P48552	NRIP1_HUMAN	T	389	ENSP00000383060:I389T;ENSP00000383063:I389T;ENSP00000327213:I389T	ENSP00000327213:I389T	I	-	2	0	NRIP1	15261219	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	2.377000	0.44300	1.123000	0.41961	0.524000	0.50904	ATA	A|0.991;G|0.009	0.009	strong		0.353	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41351321C>T	ENST00000301141.5	-	7	1059	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	347					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|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)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGCATCTTGGCCCGGTCCTCA	0.537																																					p.A347T		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G1039A						PASS	.						115.0	104.0	108.0					19																	41351321		2203	4300	6503	SO:0001583	missense	1548	exon7			TCTTGGCCCGGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1039G>A	19.37:g.41351321C>T	ENSP00000301141:p.Ala347Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	248	11	0.0443548	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	4.025	0.002161	0.07819	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.76	-2.87	0.05700	.	0.614141	0.16066	U	0.231229	T	0.43853	0.1266	L	0.31120	0.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.17319	-1.0373	10	0.22706	T	0.39	.	4.9051	0.13795	0.0:0.2915:0.1649:0.5436	.	347;347	Q13120;P11509	.;CP2A6_HUMAN	T	347	ENSP00000301141:A347T	ENSP00000301141:A347T	A	-	1	0	CYP2A6	46043161	0.000000	0.05858	0.011000	0.14972	0.659000	0.38960	-1.191000	0.03055	-0.603000	0.05767	-0.912000	0.02778	GCC	C|0.500;T|0.500	0.500	strong		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
RASGRF1	5923	hgsc.bcm.edu	37	15	79296172	79296172	+	Silent	SNP	G	G	A	rs1562008	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79296172G>A	ENST00000419573.3	-	16	2743	c.2469C>T	c.(2467-2469)ccC>ccT	p.P823P	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Silent_p.P807P|RASGRF1_ENST00000394745.3_Silent_p.P39P	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	823					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						AAGGGTCTTCGGGCTTCTCAG	0.627													G|||	626	0.125	0.0272	0.1556	5008	,	,		18455	0.0942		0.2316	False		,,,				2504	0.1575				p.P823P		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2469T						PASS	.	G	,,	271,4121	149.2+/-183.4	12,247,1937	52.0	45.0	47.0		2421,2469,117	-3.4	0.3	15	dbSNP_88	47	2028,6558	338.3+/-322.7	245,1538,2510	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	257,1785,4447	AA,AG,GG		23.6198,6.1703,17.7146	,,	807/1258,823/1274,39/490	79296172	2299,10679	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon16			GTCTTCGGGCTTC	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.2469C>T	15.37:g.79296172G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			G|0.849;A|0.151	0.151	strong		0.627	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
CROCC	9696	hgsc.bcm.edu	37	1	17273444	17273444	+	Silent	SNP	G	G	A	rs7545185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17273444G>A	ENST00000375541.5	+	17	2541	c.2472G>A	c.(2470-2472)acG>acA	p.T824T	CROCC_ENST00000467938.1_3'UTR	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)		AGCTCCCCACGCTGCGCCATG	0.701																																					p.T824T		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.G2472A						PASS	.	G		183,4075		0,183,1946	9.0	9.0	9.0		2472	-5.3	0.0	1	dbSNP_116	9	1201,7057		4,1193,2932	no	coding-synonymous	CROCC	NM_014675.3		4,1376,4878	AA,AG,GG		14.5435,4.2978,11.0578		824/2018	17273444	1384,11132	2129	4129	6258	SO:0001819	synonymous_variant	9696	exon17			CCCCACGCTGCGC	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.2472G>A	1.37:g.17273444G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	14	0.197183	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			G|0.809;A|0.191	0.191	strong		0.701	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
MDH1B	130752	hgsc.bcm.edu	37	2	207603221	207603221	+	Missense_Mutation	SNP	T	T	C	rs2287632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	113	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	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	
ATP6AP1	537	hgsc.bcm.edu	37	X	153657083	153657083	+	Silent	SNP	A	A	G	rs28497482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153657083A>G	ENST00000369762.2	+	1	106	c.45A>G	c.(43-45)cgA>cgG	p.R15R		NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	15					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-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)					TGGGGCCGCGATGCGCCCAGG	0.721											OREG0003604	type=REGULATORY REGION|Gene=BC009467|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	3373	0.89351	0.6838	0.6542	3775	,	,		7559	0.7103		0.7028	False		,,,				2504	0.6053				p.R15R		Atlas-SNP	.											.	ATP6AP1	46	.	0			c.A45G						PASS	.	G		2818,273		1150,220,298,9,35	7.0	9.0	9.0		45	-0.2	0.0	X	dbSNP_125	9	4664,511		1583,354,1144,7,143	no	coding-synonymous	ATP6AP1	NM_001183.4		2733,574,1442,16,178	GG,GA,G,AA,A		9.8744,8.8321,9.4846		15/471	153657083	7482,784	1712	3231	4943	SO:0001819	synonymous_variant	537	exon1			GCCGCGATGCGCC	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"""	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.45A>G	X.37:g.153657083A>G		Somatic	0	0	.	1757	WXS	Illumina HiSeq	Phase_I	11	11	1	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Silent	SNP	ENST00000369762.2	37	CCDS35451.1																																																																																			A|0.090;G|0.910	0.910	strong		0.721	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183	
PAK2	5062	hgsc.bcm.edu	37	3	196530013	196530013	+	Silent	SNP	A	A	G	rs73205842	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196530013A>G	ENST00000327134.3	+	4	736	c.414A>G	c.(412-414)aaA>aaG	p.K138K		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	138					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGAAGCAGAAATATCTGAGCT	0.418																																					p.K138K		Atlas-SNP	.											PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	0			c.A414G						scavenged	.						92.0	84.0	87.0					3																	196530013		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			GCAGAAATATCTG	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.414A>G	3.37:g.196530013A>G		Somatic	50	2	0.04		WXS	Illumina HiSeq	Phase_I	106	18	0.169811	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			A|0.970;G|0.030	0.030	strong		0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
ZNF599	148103	hgsc.bcm.edu	37	19	35250448	35250448	+	Nonsense_Mutation	SNP	C	C	A	rs112895297	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35250448C>A	ENST00000329285.8	-	4	1631	c.1258G>T	c.(1258-1260)Gag>Tag	p.E420*		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	420					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(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AAGGGCTTCTCTCCGGTATGG	0.473													C|||	3	0.000599042	0.0	0.0	5008	,	,		20006	0.0		0.003	False		,,,				2504	0.0				p.E420X		Atlas-SNP	.											ZNF599,right_upper_lobe,carcinoma,0,1	ZNF599	72	1	0			c.G1258T						scavenged	.	C	stop/GLU	2,4404	4.2+/-10.8	0,2,2201	56.0	54.0	55.0		1258	2.5	1.0	19	dbSNP_132	55	44,8556	30.1+/-81.4	1,42,4257	yes	stop-gained	ZNF599	NM_001007248.2		1,44,6458	AA,AC,CC		0.5116,0.0454,0.3537		420/589	35250448	46,12960	2203	4300	6503	SO:0001587	stop_gained	148103	exon4			GCTTCTCTCCGGT	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"""Zinc fingers, C2H2-type"", ""-"""	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1258G>T	19.37:g.35250448C>A	ENSP00000333802:p.Glu420*	Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_001007248	Q569K0|Q5PRG1	Nonsense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	39	7.703439	0.98444	4.54E-4	0.005116	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	.	.	.	2.53	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	8.6882	0.34251	0.0:1.0:0.0:0.0	.	.	.	.	X	419;420;194	.	ENSP00000333802:E420X	E	-	1	0	ZNF599	39942288	0.925000	0.31364	1.000000	0.80357	0.969000	0.65631	3.255000	0.51484	1.735000	0.51646	0.491000	0.48974	GAG	C|0.997;A|0.003	0.003	strong		0.473	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046	
DFNB59	494513	hgsc.bcm.edu	37	2	179325735	179325735	+	Missense_Mutation	SNP	C	C	T	rs17304212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179325735C>T	ENST00000409117.3	+	7	1149	c.793C>T	c.(793-795)Cgt>Tgt	p.R265C	DFNB59_ENST00000375129.4_Missense_Mutation_p.R265C	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	265			R -> C (in dbSNP:rs17304212).		sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TGTCATTTCTCGTTCACAGCT	0.338													C|||	144	0.028754	0.003	0.0519	5008	,	,		18996	0.0		0.0865	False		,,,				2504	0.0174				p.R265C		Atlas-SNP	.											DFNB59,lymph_node,lymphoid_neoplasm,0,1	DFNB59	37	1	0			c.C793T	GRCh37	CM074142|CM074143	DFNB59	M	rs17304212	PASS	.	C	CYS/ARG	65,3655		0,65,1795	215.0	190.0	198.0		793	6.0	1.0	2	dbSNP_123	198	687,7517		55,577,3470	yes	missense	DFNB59	NM_001042702.3	180	55,642,5265	TT,TC,CC		8.374,1.7473,6.3066	probably-damaging	265/353	179325735	752,11172	1860	4102	5962	SO:0001583	missense	494513	exon7			ATTTCTCGTTCAC	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.793C>T	2.37:g.179325735C>T	ENSP00000386647:p.Arg265Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246908	0.80024	0.017473	0.08374	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.60672	0.17;0.17	6.04	6.04	0.98038	.	0.089808	0.45606	U	0.000358	T	0.06142	0.0159	L	0.29908	0.895	0.37759	D	0.926253	D	0.60575	0.988	P	0.51777	0.679	T	0.31861	-0.9928	10	0.72032	D	0.01	-28.2832	14.3944	0.67001	0.2446:0.7554:0.0:0.0	rs17304212;rs17304212	265	Q0ZLH3	PJVK_HUMAN	C	265	ENSP00000386647:R265C;ENSP00000364271:R265C	ENSP00000364271:R265C	R	+	1	0	DFNB59	179033981	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.135000	0.42112	2.873000	0.98535	0.563000	0.77884	CGT	C|0.932;G|0.038;T|0.030	0.030	strong		0.338	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
EMILIN2	84034	hgsc.bcm.edu	37	18	2909700	2909700	+	Missense_Mutation	SNP	C	C	T	rs56288451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:2909700C>T	ENST00000254528.3	+	7	2866	c.2707C>T	c.(2707-2709)Cct>Tct	p.P903S	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	903	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		P -> S (in dbSNP:rs56288451). {ECO:0000269|PubMed:11278945}.		cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		AGCTCCGGTGCCTTCTCTGGT	0.587													C|||	507	0.101238	0.1581	0.1412	5008	,	,		19834	0.0942		0.0447	False		,,,				2504	0.0613				p.P903S		Atlas-SNP	.											.	EMILIN2	97	.	0			c.C2707T						PASS	.	C	SER/PRO	612,3794	266.5+/-267.3	45,522,1636	99.0	98.0	98.0		2707	1.7	0.1	18	dbSNP_129	98	403,8197	128.2+/-186.4	7,389,3904	yes	missense	EMILIN2	NM_032048.2	74	52,911,5540	TT,TC,CC		4.686,13.8901,7.8041	benign	903/1054	2909700	1015,11991	2203	4300	6503	SO:0001583	missense	84034	exon7			CCGGTGCCTTCTC	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.2707C>T	18.37:g.2909700C>T	ENSP00000254528:p.Pro903Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	168	71	0.422619	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	244	0.11172161172161173	95	0.19308943089430894	51	0.1408839779005525	59	0.10314685314685315	39	0.051451187335092345	C	9.047	0.991147	0.18966	0.138901	0.04686	ENSG00000132205	ENST00000254528;ENST00000308080	T	0.01629	4.72	5.8	1.68	0.24146	Tumour necrosis factor-like (1);Complement C1q protein (1);	0.163547	0.42420	D	0.000711	T	0.00012	0.0000	N	0.25332	0.735	0.80722	P	0.0	B	0.31485	0.325	B	0.21917	0.037	T	0.49862	-0.8894	9	0.21014	T	0.42	-12.4802	4.3023	0.10930	0.1152:0.4082:0.3496:0.127	rs56288451;rs61743706	903	Q9BXX0	EMIL2_HUMAN	S	903;180	ENSP00000254528:P903S	ENSP00000254528:P903S	P	+	1	0	EMILIN2	2899700	0.004000	0.15560	0.081000	0.20488	0.398000	0.30690	0.292000	0.19011	0.746000	0.32786	0.655000	0.94253	CCT	C|0.917;T|0.083	0.083	strong		0.587	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048	
R3HDM4	91300	hgsc.bcm.edu	37	19	899444	899444	+	Silent	SNP	C	C	T	rs2965284	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:899444C>T	ENST00000361574.5	-	7	772	c.699G>A	c.(697-699)tcG>tcA	p.S233S	R3HDM4_ENST00000587975.1_Silent_p.S212S	NM_138774.3	NP_620129.2	Q96D70	R3HD4_HUMAN	R3H domain containing 4	233	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)										ACTTACTGGCCGAGATGAGGT	0.657													C|||	408	0.0814696	0.0159	0.1081	5008	,	,		12934	0.0109		0.1809	False		,,,				2504	0.1217				p.S233S		Atlas-SNP	.											C19orf22,NS,carcinoma,0,1	.	.	1	0			c.G699A						PASS	.	C		177,4229	114.6+/-152.6	5,167,2031	46.0	47.0	47.0		699	-7.7	1.0	19	dbSNP_101	47	1656,6944	300.6+/-305.0	170,1316,2814	no	coding-synonymous	C19orf22	NM_138774.3		175,1483,4845	TT,TC,CC		19.2558,4.0172,14.0935		233/269	899444	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	91300	exon7			ACTGGCCGAGATG	BC012775	CCDS12048.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000198858	ENSG00000198858			28270	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 22"""	C19orf22		12477932	Standard	NM_138774		Approved	MGC16353	uc002lqg.2	Q96D70		ENST00000361574.5:c.699G>A	19.37:g.899444C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_138774		Silent	SNP	ENST00000361574.5	37	CCDS12048.1																																																																																			C|0.877;T|0.123	0.123	strong		0.657	R3HDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458209.1	NM_138774	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12862170	12862170	+	Silent	SNP	C	C	T	rs3213687	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:12862170C>T	ENST00000379672.5	+	16	1779	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	ARHGAP44_ENST00000340825.3_Silent_p.S493S|ARHGAP44_ENST00000262444.9_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	65	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	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	
TLK2	11011	hgsc.bcm.edu	37	17	60683503	60683503	+	Silent	SNP	A	A	G	rs8078132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:60683503A>G	ENST00000326270.9	+	21	2206	c.1938A>G	c.(1936-1938)ccA>ccG	p.P646P	TLK2_ENST00000582809.1_Silent_p.P475P|TLK2_ENST00000346027.5_Silent_p.P624P|TLK2_ENST00000343388.7_Silent_p.P592P|TLK2_ENST00000542523.1_Silent_p.P592P	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	646	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						ATTTACCACCAGAGTGTTTTG	0.333													A|||	2636	0.526358	0.18	0.5086	5008	,	,		16721	0.8135		0.6153	False		,,,				2504	0.6196				p.P624P		Atlas-SNP	.											.	TLK2	223	.	0			c.A1872G						PASS	.	A	,	1162,3244	405.1+/-333.4	145,872,1186	72.0	66.0	68.0		1776,1872	4.9	1.0	17	dbSNP_116	68	5207,3393	637.4+/-399.2	1565,2077,658	no	coding-synonymous,coding-synonymous	TLK2	NM_001112707.1,NM_006852.3	,	1710,2949,1844	GG,GA,AA		39.4535,26.3731,48.9697	,	592/719,624/751	60683503	6369,6637	2203	4300	6503	SO:0001819	synonymous_variant	11011	exon20			ACCACCAGAGTGT	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1938A>G	17.37:g.60683503A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Silent	SNP	ENST00000326270.9	37																																																																																				A|0.486;G|0.514	0.514	strong		0.333	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940191	70940191	+	Silent	SNP	C	C	T	rs2292192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70940191C>T	ENST00000359655.4	+	1	204	c.144C>T	c.(142-144)gcC>gcT	p.A48A	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	48					ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTGCCACCGCCTCCTCCTCTG	0.662													C|||	734	0.146565	0.3548	0.0548	5008	,	,		18083	0.1339		0.0109	False		,,,				2504	0.0828				p.A48A		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C144T						PASS	.	C		1425,2981	460.0+/-352.4	255,915,1033	58.0	65.0	62.0		144	1.5	0.1	10	dbSNP_100	62	134,8466	67.3+/-129.8	1,132,4167	no	coding-synonymous	SUPV3L1	NM_003171.3		256,1047,5200	TT,TC,CC		1.5581,32.3423,11.9868		48/787	70940191	1559,11447	2203	4300	6503	SO:0001819	synonymous_variant	6832	exon1			CACCGCCTCCTCC	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.144C>T	10.37:g.70940191C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	37	CCDS7287.1																																																																																			C|0.884;T|0.116	0.116	strong		0.662	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
SLC22A16	85413	hgsc.bcm.edu	37	6	110760008	110760008	+	Missense_Mutation	SNP	A	A	G	rs12210538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:110760008A>G	ENST00000368919.3	-	5	1292	c.1226T>C	c.(1225-1227)aTg>aCg	p.M409T	SLC22A16_ENST00000330550.4_Missense_Mutation_p.M375T|RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000439654.1_Missense_Mutation_p.M409T	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	409			M -> T (in dbSNP:rs12210538). {ECO:0000269|PubMed:12372408, ECO:0000269|PubMed:12384147, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15963465}.		acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GACCTTGTCCATGGCGATGCA	0.542													A|||	458	0.0914537	0.0121	0.1527	5008	,	,		14934	0.0		0.2445	False		,,,				2504	0.092				p.M409T		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T1226C						PASS	.	A	THR/MET	225,4181	133.7+/-170.0	4,217,1982	152.0	115.0	128.0		1226	5.0	0.0	6	dbSNP_120	128	2091,6509	360.9+/-332.1	287,1517,2496	yes	missense	SLC22A16	NM_033125.2	81	291,1734,4478	GG,GA,AA		24.314,5.1067,17.8072	possibly-damaging	409/578	110760008	2316,10690	2203	4300	6503	SO:0001583	missense	85413	exon5			TTGTCCATGGCGA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1226T>C	6.37:g.110760008A>G	ENSP00000357915:p.Met409Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	247	0.1130952380952381	9	0.018292682926829267	49	0.13535911602209943	0	0.0	189	0.24934036939313983	A	18.24	3.580325	0.65992	0.051067	0.24314	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.086812	0.85682	D	0.000000	T	0.76856	0.4046	M	0.70595	2.14	0.09310	P	1.0	D;P	0.53312	0.959;0.949	P;P	0.55749	0.783;0.743	T	0.80448	-0.1378	9	0.52906	T	0.07	.	14.6674	0.68918	1.0:0.0:0.0:0.0	rs12210538;rs17494155;rs12210538	409;375	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	T	409;326;375;409;239	ENSP00000357915:M409T;ENSP00000395642:M326T;ENSP00000328583:M375T;ENSP00000408799:M409T;ENSP00000409306:M239T	ENSP00000328583:M375T	M	-	2	0	SLC22A16	110866701	1.000000	0.71417	0.005000	0.12908	0.006000	0.05464	6.101000	0.71479	1.877000	0.54381	0.519000	0.50382	ATG	A|0.851;G|0.149	0.149	strong		0.542	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
KLHL30	377007	hgsc.bcm.edu	37	2	239059578	239059578	+	Missense_Mutation	SNP	G	G	A	rs369686635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239059578G>A	ENST00000409223.1	+	8	1716	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N	KLHL30_ENST00000305959.4_Missense_Mutation_p.D519N			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	537										lung(4)	4		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)		GGAGGCCTACGACACGGTTCG	0.672													G|||	2	0.000399361	0.0	0.0014	5008	,	,		11838	0.001		0.0	False		,,,				2504	0.0				p.D537N		Atlas-SNP	.											.	KLHL30	79	.	0			c.G1609A						PASS	.	G	ASN/ASP	1,4305		0,1,2152	19.0	27.0	24.0		1609	4.7	0.9	2		24	0,8462		0,0,4231	no	missense	KLHL30	NM_198582.3	23	0,1,6383	AA,AG,GG		0.0,0.0232,0.0078	possibly-damaging	537/579	239059578	1,12767	2153	4231	6384	SO:0001583	missense	377007	exon8			GCCTACGACACGG		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1609G>A	2.37:g.239059578G>A	ENSP00000386389:p.Asp537Asn	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192615	0.38707	2.32E-4	0.0	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.70869	-0.52;-0.52	4.66	4.66	0.58398	Kelch-type beta propeller (1);	0.075656	0.64402	D	0.000008	T	0.61825	0.2378	L	0.52011	1.625	0.41539	D	0.988502	P	0.47841	0.901	B	0.34652	0.187	T	0.67620	-0.5624	10	0.39692	T	0.17	.	16.4605	0.84033	0.0:0.0:1.0:0.0	.	537	Q0D2K2	KLH30_HUMAN	N	537;519	ENSP00000386389:D537N;ENSP00000302386:D519N	ENSP00000302386:D519N	D	+	1	0	KLHL30	238724317	1.000000	0.71417	0.923000	0.36655	0.269000	0.26545	3.349000	0.52217	2.423000	0.82170	0.561000	0.74099	GAC	.	.	weak		0.672	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
PTPN7	5778	hgsc.bcm.edu	37	1	202129895	202129895	+	5'Flank	SNP	G	G	A	rs3935295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202129895G>A	ENST00000308986.5	-	0	0				PTPN7_ENST00000367279.4_5'Flank|PTPN7_ENST00000309017.3_Missense_Mutation_p.T14M|PTPN7_ENST00000544762.1_5'Flank|PTPN7_ENST00000543735.1_5'Flank|PTPN7_ENST00000492977.1_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	51	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	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	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399064	204399064	+	Silent	SNP	G	G	A	rs2271420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204399064G>A	ENST00000367187.3	-	30	4939	c.4383C>T	c.(4381-4383)ccC>ccT	p.P1461P	PIK3C2B_ENST00000424712.2_Silent_p.P1433P|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1461	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|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)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCACCTCAGGGGGTGCGTGGA	0.667													G|||	690	0.13778	0.2784	0.1037	5008	,	,		16736	0.0774		0.1113	False		,,,				2504	0.0613				p.P1461P		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4383T						PASS	.	G		117,4289		49,19,2135	88.0	78.0	81.0		4383	1.9	1.0	1	dbSNP_100	81	33,8567		10,13,4277	no	coding-synonymous	PIK3C2B	NM_002646.3		59,32,6412	AA,AG,GG		0.3837,2.6555,1.1533		1461/1635	204399064	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon30			CTCAGGGGGTGCG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4383C>T	1.37:g.204399064G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.866;A|0.134	0.134	strong		0.667	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
TBC1D1	23216	hgsc.bcm.edu	37	4	38054737	38054737	+	Intron	SNP	C	C	T	rs58983546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	246	0	0		WXS	Illumina HiSeq	Phase_I	245	111	0.453061	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	
TTN	7273	hgsc.bcm.edu	37	2	179632496	179632496	+	Missense_Mutation	SNP	T	T	C	rs4893853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179632496T>C	ENST00000591111.1	-	40	9685	c.9461A>G	c.(9460-9462)aAg>aGg	p.K3154R	TTN_ENST00000589042.1_Missense_Mutation_p.K3154R|TTN_ENST00000360870.5_Missense_Mutation_p.K3154R|TTN_ENST00000342992.6_Missense_Mutation_p.K3154R|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K3108R|TTN_ENST00000359218.5_Missense_Mutation_p.K3108R|TTN_ENST00000460472.2_Missense_Mutation_p.K3108R			Q8WZ42	TITIN_HUMAN	titin	13486			K -> R. {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)			CTGAACCTCCTTTTTAATACT	0.363													T|||	431	0.0860623	0.0749	0.1542	5008	,	,		21137	0.0208		0.0348	False		,,,				2504	0.1728				p.K3154R		Atlas-SNP	.											.	TTN	18412	.	0			c.A9461G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	317,4089	153.7+/-187.2	8,301,1894	114.0	119.0	117.0		9323,9323,9461,9461,9323	2.1	1.0	2	dbSNP_111	117	182,8418	72.0+/-134.6	3,176,4121	yes	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	26,26,26,26,26	11,477,6015	CC,CT,TT		2.1163,7.1947,3.8367	benign,benign,benign,benign,benign	3108/27119,3108/27052,3154/5605,3154/33424,3108/26927	179632496	499,12507	2203	4300	6503	SO:0001583	missense	7273	exon40			ACCTCCTTTTTAA	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.9461A>G	2.37:g.179632496T>C	ENSP00000465570:p.Lys3154Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	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		103	0.04716117216117216	33	0.06707317073170732	41	0.1132596685082873	5	0.008741258741258742	24	0.0316622691292876	T	12.22	1.872880	0.33069	0.071947	0.021163	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	6.03	2.14	0.27477	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01558	0.0050	L	0.31752	0.955	0.46241	P	0.0010599999999999499	B;B;B;B;B	0.18863	0.0;0.0;0.0;0.0;0.031	B;B;B;B;B	0.19666	0.004;0.004;0.007;0.007;0.026	T	0.28332	-1.0047	8	0.87932	D	0	.	10.1377	0.42717	0.0:0.2014:0.0:0.7986	rs4893853;rs17452923;rs52829052;rs4893853	3108;3108;3108;3154;3154	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	R	3154;3108;3108;3108;3108;3154	ENSP00000343764:K3154R;ENSP00000434586:K3108R;ENSP00000340554:K3108R;ENSP00000352154:K3108R;ENSP00000354117:K3154R	ENSP00000340554:K3108R	K	-	2	0	TTN	179340741	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	1.539000	0.36104	0.458000	0.26988	0.533000	0.62120	AAG	T|0.956;C|0.044	0.044	strong		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ABHD8	79575	hgsc.bcm.edu	37	19	17412366	17412366	+	Silent	SNP	G	G	A	rs11086066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17412366G>A	ENST00000247706.3	-	2	299	c.60C>T	c.(58-60)gcC>gcT	p.A20A	MRPL34_ENST00000594999.1_5'Flank|MRPL34_ENST00000595444.1_Intron|MRPL34_ENST00000600434.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	20							hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						GTGGCCCCACGGCGTTGGGGG	0.652													G|||	1187	0.237021	0.1286	0.2277	5008	,	,		15353	0.1319		0.325	False		,,,				2504	0.408				p.A20A	Ovarian(156;1368 2543 15275 41187)	Atlas-SNP	.											.	ABHD8	26	.	0			c.C60T						PASS	.	G		707,3643		62,583,1530	23.0	25.0	24.0		60	-10.5	0.7	19	dbSNP_120	24	2448,6010		382,1684,2163	no	coding-synonymous	ABHD8	NM_024527.4		444,2267,3693	AA,AG,GG		28.943,16.2529,24.633		20/440	17412366	3155,9653	2175	4229	6404	SO:0001819	synonymous_variant	79575	exon2			CCCCACGGCGTTG	AK021805	CCDS12355.1	19p13.12	2010-12-09			ENSG00000127220	ENSG00000127220		"""Abhydrolase domain containing"""	23759	protein-coding gene	gene with protein product						12477932	Standard	NM_024527		Approved	FLJ11743, MGC14280, MGC2512	uc002ngb.4	Q96I13		ENST00000247706.3:c.60C>T	19.37:g.17412366G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_024527	Q9HAE9	Silent	SNP	ENST00000247706.3	37	CCDS12355.1																																																																																			G|0.784;A|0.216	0.216	strong		0.652	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	NM_024527	
CES5A	221223	hgsc.bcm.edu	37	16	55907811	55907811	+	Missense_Mutation	SNP	C	C	T	rs2397965	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:55907811C>T	ENST00000290567.9	-	2	333	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	CES5A_ENST00000521992.1_Missense_Mutation_p.R100Q|CES5A_ENST00000520435.1_Missense_Mutation_p.R71Q|CES5A_ENST00000541580.1_Intron|CES5A_ENST00000319165.9_Missense_Mutation_p.R71Q|CES5A_ENST00000518005.1_5'UTR	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	78	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	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	
GUF1	60558	hgsc.bcm.edu	37	4	44682465	44682465	+	Missense_Mutation	SNP	T	T	C	rs6447368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:44682465T>C	ENST00000281543.5	+	2	367	c.173T>C	c.(172-174)cTt>cCt	p.L58P	GUF1_ENST00000506793.1_Intron	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)									p.L58P(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						TAGGAAAAACTTGACATGTCT	0.338													T|||	2205	0.440296	0.2897	0.5202	5008	,	,		14515	0.4018		0.6014	False		,,,				2504	0.4611				p.L58P		Atlas-SNP	.											GUF1,NS,carcinoma,0,1	GUF1	72	1	1	Substitution - Missense(1)	stomach(1)	c.T173C						PASS	.	T	PRO/LEU	1523,2883	461.5+/-352.9	267,989,947	56.0	54.0	54.0		173	2.8	0.4	4	dbSNP_116	54	5468,3132	637.2+/-399.2	1747,1974,579	yes	missense	GUF1	NM_021927.2	98	2014,2963,1526	CC,CT,TT		36.4186,34.5665,46.2479	benign	58/670	44682465	6991,6015	2203	4300	6503	SO:0001583	missense	60558	exon2			AAAAACTTGACAT		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.173T>C	4.37:g.44682465T>C	ENSP00000281543:p.Leu58Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	1004	0.4597069597069597	144	0.2926829268292683	188	0.5193370165745856	226	0.3951048951048951	446	0.5883905013192612	T	9.377	1.072042	0.20147	0.345665	0.635814	ENSG00000151806	ENST00000281543	T	0.70045	-0.45	5.17	2.83	0.33086	.	1.148940	0.06297	N	0.700199	T	0.00012	0.0000	N	0.08118	0	0.47094	P	6.840000000000179E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.46762	-0.9168	9	0.49607	T	0.09	-0.1341	7.0188	0.24902	0.0:0.2122:0.0:0.7878	rs6447368;rs11556168;rs6447368	58	Q8N442	GUF1_HUMAN	P	58	ENSP00000281543:L58P	ENSP00000281543:L58P	L	+	2	0	GUF1	44377222	0.824000	0.29247	0.358000	0.25811	0.746000	0.42486	4.783000	0.62403	0.412000	0.25729	-0.388000	0.06559	CTT	T|0.484;C|0.516	0.516	strong		0.338	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	
INPP1	3628	hgsc.bcm.edu	37	2	191224981	191224981	+	Silent	SNP	G	G	T	rs4656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:191224981G>T	ENST00000322522.4	+	2	609	c.153G>T	c.(151-153)acG>acT	p.T51T	INPP1_ENST00000392329.2_Silent_p.T51T|INPP1_ENST00000417336.1_3'UTR|INPP1_ENST00000541441.1_Silent_p.T51T	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	51					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			ACTTCAAGACGCTGGCTGATG	0.458													G|||	2252	0.449681	0.7194	0.3329	5008	,	,		20345	0.4901		0.3012	False		,,,				2504	0.2791				p.T51T	Melanoma(130;184 1743 2185 19805 38428)	Atlas-SNP	.											.	INPP1	29	.	0			c.G153T						PASS	.	G	,	2896,1510	674.4+/-402.9	967,962,274	80.0	86.0	84.0		153,153	-9.7	0.5	2	dbSNP_52	84	2600,6000	420.1+/-353.3	388,1824,2088	no	coding-synonymous,coding-synonymous	INPP1	NM_001128928.1,NM_002194.3	,	1355,2786,2362	TT,TG,GG		30.2326,34.2714,42.2574	,	51/400,51/400	191224981	5496,7510	2203	4300	6503	SO:0001819	synonymous_variant	3628	exon2			CAAGACGCTGGCT		CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.153G>T	2.37:g.191224981G>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_002194		Silent	SNP	ENST00000322522.4	37	CCDS2305.1																																																																																			G|0.559;T|0.441	0.441	strong		0.458	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2		
UGT1A3	54659	hgsc.bcm.edu	37	2	234638249	234638249	+	Silent	SNP	A	A	G	rs7574296	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234638249A>G	ENST00000482026.1	+	1	496	c.477A>G	c.(475-477)gcA>gcG	p.A159A	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Silent_p.A159A|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	159					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	TCTGCGCGGCAGTGCTGGCTA	0.473													G|||	2870	0.573083	0.8336	0.5216	5008	,	,		21211	0.3571		0.4155	False		,,,				2504	0.6421				p.A159A		Atlas-SNP	.											UGT1A3,NS,carcinoma,+2,1	UGT1A3	91	1	0			c.A477G						PASS	.	G	,,,,,,,,	3294,1112		1241,812,150	186.0	193.0	191.0		,,,,,,477,,	-8.7	0.0	2	dbSNP_116	191	3870,4730		842,2186,1272	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,	2083,2998,1422	GG,GA,AA		45.0,25.2383,44.9177	,,,,,,,,	,,,,,,159/535,,	234638249	7164,5842	2203	4300	6503	SO:0001819	synonymous_variant	54659	exon1			CGCGGCAGTGCTG	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.477A>G	2.37:g.234638249A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	203	113	0.55665	NM_019093	B8K287	Silent	SNP	ENST00000482026.1	37	CCDS2509.1																																																																																			A|0.477;G|0.523	0.523	strong		0.473	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
STARD6	147323	hgsc.bcm.edu	37	18	51880889	51880889	+	Nonsense_Mutation	SNP	G	G	A	rs17292725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:51880889G>A	ENST00000581310.1	-	4	428	c.55C>T	c.(55-57)Cga>Tga	p.R19*	STARD6_ENST00000577499.1_Nonsense_Mutation_p.R19*|STARD6_ENST00000584040.1_Nonsense_Mutation_p.R19*|STARD6_ENST00000580990.2_5'Flank|STARD6_ENST00000307844.3_Nonsense_Mutation_p.R19*			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	19	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)	8				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		GATGTATCTCGATTATAACCT	0.308													G|||	73	0.0145767	0.0015	0.0187	5008	,	,		15856	0.0		0.0328	False		,,,				2504	0.0256				p.R19X		Atlas-SNP	.											.	STARD6	19	.	0			c.C55T						PASS	.	G	stop/ARG	30,4376	35.2+/-66.4	0,30,2173	74.0	76.0	76.0		55	5.6	1.0	18	dbSNP_123	76	342,8258	116.8+/-176.5	8,326,3966	yes	stop-gained	STARD6	NM_139171.1		8,356,6139	AA,AG,GG		3.9767,0.6809,2.8602		19/221	51880889	372,12634	2203	4300	6503	SO:0001587	stop_gained	147323	exon1			TATCTCGATTATA	AF480305	CCDS11955.1	18q21.2	2011-09-12	2007-08-16		ENSG00000174448	ENSG00000174448		"""StAR-related lipid transfer (START) domain containing"""	18066	protein-coding gene	gene with protein product		607051	"""START domain containing 6"""			12011452	Standard	NM_139171		Approved		uc010xdt.2	P59095	OTTHUMG00000132702	ENST00000581310.1:c.55C>T	18.37:g.51880889G>A	ENSP00000462349:p.Arg19*	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	267	76	0.284644	NM_139171		Nonsense_Mutation	SNP	ENST00000581310.1	37	CCDS11955.1	36	0.016483516483516484	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	24	0.0316622691292876	G	14.62	2.589686	0.46214	0.006809	0.039767	ENSG00000174448	ENST00000307844	.	.	.	5.58	5.58	0.84498	.	0.282468	0.30901	N	0.008646	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	16.4978	0.84250	0.0:0.0:1.0:0.0	rs17292725;rs52836398;rs17292725	.	.	.	X	19	.	ENSP00000310814:R19X	R	-	1	2	STARD6	50134887	1.000000	0.71417	0.992000	0.48379	0.011000	0.07611	4.047000	0.57383	2.616000	0.88540	0.460000	0.39030	CGA	G|0.974;A|0.026	0.026	strong		0.308	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171	
HOPX	84525	hgsc.bcm.edu	37	4	57516896	57516896	+	Intron	SNP	G	G	A	rs4371677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57516896G>A	ENST00000337881.7	-	3	801				HOPX_ENST00000508121.1_Intron|HOPX_ENST00000317745.7_Intron|HOPX_ENST00000381260.3_Missense_Mutation_p.P76L|HOPX_ENST00000503639.3_Intron|HOPX_ENST00000554144.1_Missense_Mutation_p.P94L|HOPX_ENST00000556614.2_Intron|HOPX_ENST00000553379.2_Intron|HOPX_ENST00000420433.1_Intron|HOPX_ENST00000556376.2_Intron|HOPX_ENST00000555760.2_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	86	0	0		WXS	Illumina HiSeq	Phase_I	103	37	0.359223	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		
DDOST	1650	hgsc.bcm.edu	37	1	20982631	20982631	+	Silent	SNP	G	G	A	rs4704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20982631G>A	ENST00000375048.3	-	3	471	c.366C>T	c.(364-366)ggC>ggT	p.G122G	DDOST_ENST00000602624.2_Silent_p.G105G|DDOST_ENST00000415136.2_Silent_p.G85G	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	122					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-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;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CACTGCCTCCGCCGTCAATAA	0.557													A|||	2941	0.58726	0.7579	0.5908	5008	,	,		21225	0.4117		0.6292	False		,,,				2504	0.4918				p.G122G		Atlas-SNP	.											.	DDOST	30	.	0			c.C366T						PASS	.	A		3208,1198	421.3+/-339.3	1161,886,156	115.0	96.0	102.0		366	-6.5	0.8	1	dbSNP_52	102	5249,3351	497.3+/-374.5	1628,1993,679	no	coding-synonymous	DDOST	NM_005216.4		2789,2879,835	AA,AG,GG		38.9651,27.1902,34.9762		122/457	20982631	8457,4549	2203	4300	6503	SO:0001819	synonymous_variant	1650	exon3			GCCTCCGCCGTCA	D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.366C>T	1.37:g.20982631G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																			G|0.379;A|0.621	0.621	strong		0.557	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
EMR2	30817	hgsc.bcm.edu	37	19	14854338	14854338	+	Missense_Mutation	SNP	C	C	T	rs117617387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14854338C>T	ENST00000315576.3	-	20	2808	c.2357G>A	c.(2356-2358)cGg>cAg	p.R786Q	EMR2_ENST00000353005.1_Missense_Mutation_p.R644Q|EMR2_ENST00000346057.1_Missense_Mutation_p.R737Q|EMR2_ENST00000594076.1_Missense_Mutation_p.R693Q|EMR2_ENST00000353876.1_Missense_Mutation_p.R693Q|EMR2_ENST00000596991.2_Missense_Mutation_p.R775Q|EMR2_ENST00000392965.3_Missense_Mutation_p.R728Q|EMR2_ENST00000392967.2_Missense_Mutation_p.R775Q|EMR2_ENST00000595839.1_Missense_Mutation_p.R644Q|EMR2_ENST00000594294.1_Missense_Mutation_p.R737Q|EMR2_ENST00000601345.1_Missense_Mutation_p.R775Q	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	786					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						ATATTGCTCCCGGACCTGCAG	0.547													c|||	36	0.0071885	0.0015	0.0086	5008	,	,		20652	0.0		0.0089	False		,,,				2504	0.0194				p.R786Q		Atlas-SNP	.											EMR2,NS,carcinoma,+1,1	EMR2	99	1	0			c.G2357A						scavenged	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	17,4389	22.3+/-47.3	0,17,2186	304.0	290.0	295.0		2357,2210,2078,1931,2324,2177,2045	-3.3	0.0	19	dbSNP_132	295	155,8445	74.2+/-136.8	2,151,4147	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	43,43,43,43,43,43,43	2,168,6333	TT,TC,CC		1.8023,0.3858,1.3225	benign,benign,benign,benign,benign,benign,benign	786/824,737/775,693/731,644/682,775/813,726/764,682/720	14854338	172,12834	2203	4300	6503	SO:0001583	missense	30817	exon20			TGCTCCCGGACCT	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.2357G>A	19.37:g.14854338C>T	ENSP00000319883:p.Arg786Gln	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	190	99	0.521053	NM_013447	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	11	0.005036630036630037	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	6	0.0079155672823219	c	15.15	2.747296	0.49257	0.003858	0.018023	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41	5.02	-3.26	0.05064	.	.	.	.	.	T	0.27313	0.0670	L	0.43923	1.385	0.09310	N	0.999996	B;B;B;P;B;B;B;B	0.46952	0.026;0.107;0.014;0.887;0.289;0.238;0.054;0.045	B;B;B;P;B;B;B;B	0.45794	0.006;0.08;0.011;0.493;0.141;0.103;0.022;0.099	T	0.35599	-0.9782	9	0.23891	T	0.37	.	9.6794	0.40061	0.0:0.4651:0.0:0.5349	.	728;693;786;644;737;786;786;775	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	Q	786;775;737;693;644;728	ENSP00000319883:R786Q;ENSP00000376694:R775Q;ENSP00000263380:R737Q;ENSP00000319454:R693Q;ENSP00000319838:R644Q;ENSP00000376692:R728Q	ENSP00000319883:R786Q	R	-	2	0	EMR2	14715338	0.007000	0.16637	0.033000	0.17914	0.247000	0.25773	0.266000	0.18534	-0.410000	0.07542	-0.205000	0.12727	CGG	C|0.989;T|0.011	0.011	strong		0.547	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
PSAPL1	768239	hgsc.bcm.edu	37	4	7436239	7436239	+	Missense_Mutation	SNP	C	C	T	rs56402179	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7436239C>T	ENST00000319098.4	-	1	461	c.368G>A	c.(367-369)cGt>cAt	p.R123H	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	123	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CGGGGCCCCACGGAGCATGCT	0.642													C|||	518	0.103435	0.0151	0.1282	5008	,	,		15529	0.0764		0.1909	False		,,,				2504	0.1431				p.R123H		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G368A						PASS	.	C	HIS/ARG,	160,3918		3,154,1882	21.0	22.0	22.0		368,	-2.8	0.0	4	dbSNP_129	22	1577,6775		145,1287,2744	no	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	29,	148,1441,4626	TT,TC,CC		18.8817,3.9235,13.9743	benign,	123/522,	7436239	1737,10693	2039	4176	6215	SO:0001583	missense	768239	exon1			GCCCCACGGAGCA	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.368G>A	4.37:g.7436239C>T	ENSP00000317445:p.Arg123His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	237	0.10851648351648352	10	0.02032520325203252	52	0.143646408839779	33	0.057692307692307696	142	0.18733509234828497	C	8.082	0.772668	0.16051	0.039235	0.188817	ENSG00000178597	ENST00000319098	D	0.84442	-1.85	3.21	-2.82	0.05787	Saposin-like (2);Saposin B (2);	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02132	-1.1208	8	0.41790	T	0.15	.	1.7598	0.02989	0.1384:0.4234:0.1367:0.3015	rs56402179;rs61734836	123	Q6NUJ1	SAPL1_HUMAN	H	123	ENSP00000317445:R123H	ENSP00000317445:R123H	R	-	2	0	PSAPL1	7487140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.605000	0.02074	-1.445000	0.01948	-2.630000	0.00154	CGT	C|0.882;T|0.118	0.118	strong		0.642	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
MUC16	94025	hgsc.bcm.edu	37	19	9020153	9020153	+	Missense_Mutation	SNP	C	C	T	rs75217292|rs386806634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9020153C>T	ENST00000397910.4	-	21	37545	c.37342G>A	c.(37342-37344)Gag>Aag	p.E12448K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12450	SEA 3. {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						CCATCCTTCTCAGACCTGGGG	0.507													-|||	449	0.0896565	0.0098	0.1282	5008	,	,		19938	0.0982		0.1083	False		,,,				2504	0.1421				p.E12448K		Atlas-SNP	.											.	MUC16	4315	.	0			c.G37342A						PASS	.	C	LYS/GLU	99,3725		2,95,1815	94.0	82.0	86.0		37342	-0.4	0.0	19	dbSNP_131	86	864,7388		36,792,3298	no	missense	MUC16	NM_024690.2	56	38,887,5113	TT,TC,CC		10.4702,2.5889,7.9745	benign	12448/14508	9020153	963,11113	1912	4126	6038	SO:0001583	missense	94025	exon21			CCTTCTCAGACCT	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.37342G>A	19.37:g.9020153C>T	ENSP00000381008:p.Glu12448Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	154	0.07051282051282051	6	0.012195121951219513	43	0.11878453038674033	46	0.08041958041958042	59	0.07783641160949868	.	7.743	0.701679	0.15172	0.025889	0.104702	ENSG00000181143	ENST00000397910	T	0.43688	0.94	3.21	-0.36	0.12568	.	.	.	.	.	T	0.00496	0.0016	L	0.51914	1.62	.	.	.	B	0.14438	0.01	B	0.19946	0.027	T	0.11299	-1.0593	8	0.87932	D	0	.	6.1032	0.20059	0.0:0.616:0.0:0.3839	.	12448	B5ME49	.	K	12448	ENSP00000381008:E12448K	ENSP00000381008:E12448K	E	-	1	0	MUC16	8881153	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.494000	0.06451	-0.111000	0.12001	-1.022000	0.02435	GAG	C|0.917;T|0.083	0.083	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRPC3	7222	hgsc.bcm.edu	37	4	122872719	122872719	+	Silent	SNP	G	G	A	rs1396082	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:122872719G>A	ENST00000379645.3	-	1	190	c.117C>T	c.(115-117)ggC>ggT	p.G39G		NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	0					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						CGCCCCTCCAGCCCCGGCGGC	0.751													G|||	1898	0.378994	0.093	0.4193	5008	,	,		7272	0.5179		0.5318	False		,,,				2504	0.4366				p.G39G		Atlas-SNP	.											.	TRPC3	201	.	0			c.C117T						PASS	.						3.0	4.0	4.0					4																	122872719		586	1410	1996	SO:0001819	synonymous_variant	7222	exon1			CCTCCAGCCCCGG	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.117C>T	4.37:g.122872719G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																			G|0.558;A|0.442	0.442	strong		0.751	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
PSG11	5680	hgsc.bcm.edu	37	19	43519442	43519442	+	Missense_Mutation	SNP	T	T	C	rs10414166	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43519442T>C	ENST00000401740.1	-	4	893	c.790A>G	c.(790-792)Aac>Gac	p.N264D	PSG11_ENST00000403486.1_Missense_Mutation_p.N142D|PSG11_ENST00000320078.7_Missense_Mutation_p.N264D|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_Missense_Mutation_p.N142D			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	261	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				GGGTTAGAGTTTGCGAAGCAG	0.443													.|||	4289	0.85643	0.9803	0.7594	5008	,	,		20114	0.999		0.6789	False		,,,				2504	0.7935				p.N264D		Atlas-SNP	.											.	PSG11	57	.	0			c.A790G						PASS	.	C	ASP/ASN,ASP/ASN,ASP/ASN	4100,300	163.3+/-195.1	1925,250,25	142.0	150.0	147.0		424,790,424	-2.3	0.0	19	dbSNP_119	147	5841,2755	439.2+/-359.1	2028,1785,485	yes	missense,missense,missense	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	23,23,23	3953,2035,510	CC,CT,TT		32.0498,6.8182,23.5072	,,	142/214,264/336,142/214	43519442	9941,3055	2200	4298	6498	SO:0001583	missense	5680	exon4			TAGAGTTTGCGAA	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.790A>G	19.37:g.43519442T>C	ENSP00000384995:p.Asn264Asp	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	1839	0.842032967032967	476	0.967479674796748	270	0.7458563535911602	571	0.9982517482517482	522	0.6886543535620053	c	0.210	-1.037745	0.02013	0.931818	0.679502	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	1.3	-2.28	0.06826	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02181	-0.65	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27739	-1.0065	8	0.02654	T	1	.	5.6087	0.17394	0.0:0.4336:0.0:0.5664	rs10414166;rs52794850;rs58631477;rs10414166	142;264	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	D	264;142;142;264	ENSP00000319140:N264D;ENSP00000385427:N142D;ENSP00000304913:N142D;ENSP00000384995:N264D	ENSP00000304913:N142D	N	-	1	0	PSG11	48211282	0.003000	0.15002	0.001000	0.08648	0.012000	0.07955	-0.180000	0.09754	-1.524000	0.01764	-1.160000	0.01791	AAC	T|0.203;C|0.797	0.797	strong		0.443	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
IGFALS	3483	hgsc.bcm.edu	37	16	1840853	1840853	+	Silent	SNP	C	C	T	rs2230053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1840853C>T	ENST00000215539.3	-	2	1676	c.1566G>A	c.(1564-1566)acG>acA	p.T522T	IGFALS_ENST00000415638.3_Silent_p.T560T			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	522					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						GGGGCTGCGGCGTGAAGGTCC	0.677													C|||	158	0.0315495	0.0076	0.0014	5008	,	,		15143	0.1121		0.008	False		,,,				2504	0.0266				p.T560T		Atlas-SNP	.											.	IGFALS	29	.	0			c.G1680A						PASS	.	C	,	31,4213		0,31,2091	15.0	14.0	14.0		1680,1566	1.7	0.1	16	dbSNP_98	14	48,8362		1,46,4158	no	coding-synonymous,coding-synonymous	IGFALS	NM_001146006.1,NM_004970.2	,	1,77,6249	TT,TC,CC		0.5707,0.7304,0.6243	,	560/644,522/606	1840853	79,12575	2122	4205	6327	SO:0001819	synonymous_variant	3483	exon2			CTGCGGCGTGAAG	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.1566G>A	16.37:g.1840853C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_001146006	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			T|0.022;C|0.978	0.022	strong		0.677	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
IL4R	3566	hgsc.bcm.edu	37	16	27373872	27373872	+	Missense_Mutation	SNP	A	A	C	rs1805011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000170630.2_Missense_Mutation_p.E400A|IL4R_ENST00000543915.2_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	60	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	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		
LNP1	348801	hgsc.bcm.edu	37	3	100170634	100170634	+	Silent	SNP	T	T	C	rs9848109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100170634T>C	ENST00000383693.3	+	3	1508	c.228T>C	c.(226-228)ttT>ttC	p.F76F	LNP1_ENST00000489752.1_Silent_p.F89F	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	76										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						ACCAAGAATTTCGATGCCGTA	0.433																																					p.F76F		Atlas-SNP	.											LNP1,caecum,carcinoma,0,2	LNP1	26	2	0			c.T228C						PASS	.						98.0	90.0	92.0					3																	100170634		1871	4098	5969	SO:0001819	synonymous_variant	348801	exon3			AGAATTTCGATGC		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.228T>C	3.37:g.100170634T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	115	26	0.226087	NM_001085451	B7ZLT3	Silent	SNP	ENST00000383693.3	37	CCDS43120.1																																																																																			T|0.500;C|0.500	0.500	strong		0.433	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
FITM1	161247	hgsc.bcm.edu	37	14	24600828	24600828	+	Missense_Mutation	SNP	C	C	T	rs147792464		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24600828C>T	ENST00000267426.5	+	1	345	c.56C>T	c.(55-57)gCa>gTa	p.A19V	RP11-468E2.6_ENST00000558325.1_Silent_p.G206G|FITM1_ENST00000559294.1_5'Flank	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	19					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CGAATCCAGGCACTGCTGGGC	0.672																																					p.A19V		Atlas-SNP	.											.	FITM1	25	.	0			c.C56T						PASS	.	C	VAL/ALA	0,4406		0,0,2203	18.0	23.0	21.0		56	1.6	0.9	14	dbSNP_134	21	6,8592		0,6,4293	yes	missense	FITM1	NM_203402.2	64	0,6,6496	TT,TC,CC		0.0698,0.0,0.0461	benign	19/293	24600828	6,12998	2203	4299	6502	SO:0001583	missense	161247	exon1			TCCAGGCACTGCT		CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"""fat-inducing transcript 1"""	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.56C>T	14.37:g.24600828C>T	ENSP00000267426:p.Ala19Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_203402	Q8IUQ7	Missense_Mutation	SNP	ENST00000267426.5	37	CCDS9611.1	.	.	.	.	.	.	.	.	.	.	c	7.996	0.754445	0.15778	0.0	6.98E-4	ENSG00000139914	ENST00000267426	.	.	.	4.6	1.58	0.23477	.	0.188323	0.32655	N	0.005818	T	0.13030	0.0316	N	0.03608	-0.345	0.25699	N	0.985606	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.21540	T	0.41	-7.9479	5.6671	0.17700	0.0:0.6485:0.0:0.3515	.	19	A5D6W6	FITM1_HUMAN	V	19	.	ENSP00000267426:A19V	A	+	2	0	FITM1	23670668	0.001000	0.12720	0.860000	0.33809	0.460000	0.32559	0.514000	0.22786	0.567000	0.29293	-0.369000	0.07265	GCA	C|1.000;T|0.000	0.000	weak		0.672	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1	NM_203402	
STKLD1	169436	hgsc.bcm.edu	37	9	136268952	136268952	+	Splice_Site	SNP	G	G	T	rs33919837	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136268952G>T	ENST00000371957.3	+	15	1710	c.1603G>T	c.(1603-1605)Ggc>Tgc	p.G535C	C9orf96_ENST00000371955.1_Splice_Site_p.G68C	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		535							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)		GTCCCTGCTGGGTGAGCTGGG	0.677													G|||	162	0.0323482	0.0045	0.0403	5008	,	,		15964	0.0188		0.0825	False		,,,				2504	0.0266				p.G535C		Atlas-SNP	.											.	C9orf96	77	.	0			c.G1603T						PASS	.	G	CYS/GLY	76,4330	65.8+/-103.3	1,74,2128	32.0	35.0	34.0		1603	4.6	0.9	9	dbSNP_126	34	723,7877	172.7+/-223.4	36,651,3613	yes	missense-near-splice	C9orf96	NM_153710.3	159	37,725,5741	TT,TG,GG		8.407,1.7249,6.1433	probably-damaging	535/681	136268952	799,12207	2203	4300	6503	SO:0001630	splice_region_variant	169436	exon15			CTGCTGGGTGAGC																												ENST00000371957.3:c.1603+1G>T	9.37:g.136268952G>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	97	0.044413919413919416	3	0.006097560975609756	16	0.04419889502762431	12	0.02097902097902098	66	0.0870712401055409	G	17.20	3.329732	0.60743	0.017249	0.08407	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51817	0.69;0.72	4.6	4.6	0.57074	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.06050	0.0157	L	0.61218	1.895	0.09310	P	0.99999999878625	D	0.89917	1.0	D	0.91635	0.999	T	0.52726	-0.8537	9	0.87932	D	0	-33.6075	12.7755	0.57445	0.0:0.0:1.0:0.0	rs33919837	535	Q8NE28	SGK71_HUMAN	C	535;68	ENSP00000361025:G535C;ENSP00000361023:G68C	ENSP00000361023:G68C	G	+	1	0	C9orf96	135258773	1.000000	0.71417	0.942000	0.38095	0.418000	0.31294	4.743000	0.62110	2.354000	0.79902	0.561000	0.74099	GGC	G|0.944;T|0.056	0.056	strong		0.677	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		Missense_Mutation
SBNO2	22904	hgsc.bcm.edu	37	19	1122147	1122147	+	Silent	SNP	G	G	A	rs2072280	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	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	
ZNF536	9745	hgsc.bcm.edu	37	19	31039669	31039669	+	Missense_Mutation	SNP	C	C	T	rs77238711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039669C>T	ENST00000355537.3	+	4	3290	c.3143C>T	c.(3142-3144)gCg>gTg	p.A1048V		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1048					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCCCGGGAGGCGAGTAAGATG	0.537													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		19387	0.005		0.0338	False		,,,				2504	0.135				p.A1048V		Atlas-SNP	.											.	ZNF536	424	.	0			c.C3143T						PASS	.	C	VAL/ALA	161,4245	108.6+/-147.0	2,157,2044	79.0	73.0	75.0		3143	0.6	0.1	19	dbSNP_131	75	288,8312	107.0+/-167.8	5,278,4017	yes	missense	ZNF536	NM_014717.1	64	7,435,6061	TT,TC,CC		3.3488,3.6541,3.4523	benign	1048/1301	31039669	449,12557	2203	4300	6503	SO:0001583	missense	9745	exon4			GGGAGGCGAGTAA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3143C>T	19.37:g.31039669C>T	ENSP00000347730:p.Ala1048Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	22	0.628571	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	50	0.022893772893772892	15	0.03048780487804878	8	0.022099447513812154	0	0.0	27	0.03562005277044855	C	0.303	-0.972510	0.02215	0.036541	0.033488	ENSG00000198597	ENST00000355537	T	0.09538	2.97	5.74	0.614	0.17603	.	0.308174	0.30383	N	0.009750	T	0.01156	0.0038	N	0.14661	0.345	0.23492	N	0.99756	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.37619	-0.9698	10	0.36615	T	0.2	-16.6787	8.9777	0.35946	0.0:0.6367:0.1064:0.2569	.	1048;1048	A7E228;O15090	.;ZN536_HUMAN	V	1048	ENSP00000347730:A1048V	ENSP00000347730:A1048V	A	+	2	0	ZNF536	35731509	0.146000	0.22672	0.080000	0.20451	0.020000	0.10135	0.203000	0.17315	0.337000	0.23665	-0.768000	0.03414	GCG	C|0.970;T|0.030	0.030	strong		0.537	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
PCDH12	51294	hgsc.bcm.edu	37	5	141337126	141337126	+	Silent	SNP	C	C	T	rs164076	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141337126C>T	ENST00000231484.3	-	1	1501	c.291G>A	c.(289-291)ctG>ctA	p.L97L	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	97	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGTCGGCACAGCTGCTCTC	0.587													T|||	2964	0.591853	0.348	0.6369	5008	,	,		16000	0.8492		0.508	False		,,,				2504	0.7106				p.L97L		Atlas-SNP	.											.	PCDH12	133	.	0			c.G291A						PASS	.	T		1656,2750	656.9+/-400.1	305,1046,852	60.0	64.0	62.0		291	-8.6	0.9	5	dbSNP_79	62	4196,4404	585.1+/-391.8	1044,2108,1148	no	coding-synonymous	PCDH12	NM_016580.2		1349,3154,2000	TT,TC,CC		48.7907,37.5851,44.9946		97/1185	141337126	5852,7154	2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			TCGGCACAGCTGC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.291G>A	5.37:g.141337126C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																			C|0.497;T|0.503	0.503	strong		0.587	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
HERC1	8925	hgsc.bcm.edu	37	15	63918307	63918307	+	Silent	SNP	G	G	C	rs1140422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:63918307G>C	ENST00000443617.2	-	71	13239	c.13152C>G	c.(13150-13152)ccC>ccG	p.P4384P		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4384					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCCCATACTGGGGGGGCACTG	0.557													G|||	368	0.0734824	0.0189	0.1873	5008	,	,		19519	0.003		0.161	False		,,,				2504	0.0491				p.P4384P		Atlas-SNP	.											.	HERC1	624	.	0			c.C13152G						PASS	.	G		169,3791		3,163,1814	38.0	40.0	39.0		13152	-7.7	0.6	15	dbSNP_86	39	1430,6864		129,1172,2846	no	coding-synonymous	HERC1	NM_003922.3		132,1335,4660	CC,CG,GG		17.2414,4.2677,13.0488		4384/4862	63918307	1599,10655	1980	4147	6127	SO:0001819	synonymous_variant	8925	exon71			ATACTGGGGGGGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13152C>G	15.37:g.63918307G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																			G|0.899;C|0.101	0.101	strong		0.557	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
FLG	2312	hgsc.bcm.edu	37	1	152281479	152281479	+	Missense_Mutation	SNP	G	G	T	rs3126079	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281479G>T	ENST00000368799.1	-	3	5918	c.5883C>A	c.(5881-5883)caC>caA	p.H1961Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1961	Ser-rich.		H -> Q (in dbSNP:rs3126079).		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)			CTCTGTCTTCGTGATGGGACC	0.572									Ichthyosis				-|||	2695	0.538139	0.7897	0.4683	5008	,	,		26201	0.6607		0.1759	False		,,,				2504	0.4939				p.H1961Q		Atlas-SNP	.											.	FLG	900	.	0			c.C5883A						PASS	.	T	GLN/HIS	3032,1374	454.4+/-350.6	1056,920,227	293.0	278.0	283.0		5883	-4.8	0.0	1	dbSNP_103	283	1480,7120	749.5+/-407.4	129,1222,2949	no	missense	FLG	NM_002016.1	24	1185,2142,3176	TT,TG,GG		17.2093,31.1847,34.6917	benign	1961/4062	152281479	4512,8494	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTTCGTGATGG	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.5883C>A	1.37:g.152281479G>T	ENSP00000357789:p.His1961Gln	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	509	397	0.779961	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1005	0.46016483516483514	366	0.7439024390243902	142	0.39226519337016574	362	0.6328671328671329	135	0.17810026385224276	t	0.268	-0.994755	0.02145	0.688153	0.172093	ENSG00000143631	ENST00000368799	T	0.00949	5.51	2.37	-4.75	0.03239	.	.	.	.	.	T	0.00144	0.0004	N	0.12746	0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40757	-0.9546	8	0.13470	T	0.59	-0.1204	2.7757	0.05347	0.1149:0.1132:0.4273:0.3447	rs3126079;rs28567722;rs35290811	1961	P20930	FILA_HUMAN	Q	1961	ENSP00000357789:H1961Q	ENSP00000357789:H1961Q	H	-	3	2	FLG	150548103	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.708000	0.00196	-3.868000	0.00097	-4.206000	0.00009	CAC	A|0.000;G|0.622;T|0.378	0.378	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FBXO18	84893	hgsc.bcm.edu	37	10	5979117	5979117	+	Silent	SNP	T	T	C	rs2274033	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5979117T>C	ENST00000362091.4	+	21	3121	c.3006T>C	c.(3004-3006)tgT>tgC	p.C1002C	RP11-536K7.3_ENST00000397264.4_RNA|FBXO18_ENST00000397269.3_Silent_p.C506C|FBXO18_ENST00000379999.5_Silent_p.C1053C	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	1002					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						GCCACTCCTGTGCGGAGCAGC	0.597													C|||	360	0.071885	0.0333	0.0389	5008	,	,		17143	0.1558		0.0358	False		,,,				2504	0.0982				p.C1053C		Atlas-SNP	.											.	FBXO18	108	.	0			c.T3159C						PASS	.	C	,	157,4249		0,157,2046	37.0	43.0	41.0		3159,3006	-5.3	0.0	10	dbSNP_100	41	291,8309		1,289,4010	no	coding-synonymous,coding-synonymous	FBXO18	NM_032807.3,NM_178150.1	,	1,446,6056	CC,CT,TT		3.3837,3.5633,3.4446	,	1053/1095,1002/1044	5979117	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	84893	exon22			CTCCTGTGCGGAG	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.3006T>C	10.37:g.5979117T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	37	CCDS7072.1																																																																																			T|0.958;C|0.042	0.042	strong		0.597	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
LAMB4	22798	hgsc.bcm.edu	37	7	107743664	107743664	+	Silent	SNP	A	A	G	rs402113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:107743664A>G	ENST00000388781.3	-	10	1088	c.1005T>C	c.(1003-1005)aaT>aaC	p.N335N	LAMB4_ENST00000388780.3_Silent_p.N335N|LAMB4_ENST00000205386.4_Silent_p.N335N|LAMB4_ENST00000418464.1_Silent_p.N335N|LAMB4_ENST00000414450.2_Silent_p.N335N	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	335	Laminin EGF-like 2. {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						TGGAGTGGCTATTACAGCTGC	0.612													G|||	1517	0.302915	0.2322	0.3674	5008	,	,		15081	0.2639		0.3777	False		,,,				2504	0.316				p.N335N		Atlas-SNP	.											.	LAMB4	253	.	0			c.T1005C						PASS	.	G		1148,3248		179,790,1229	23.0	18.0	20.0		1005	-0.6	0.0	7	dbSNP_80	20	3349,5225		712,1925,1650	no	coding-synonymous	LAMB4	NM_007356.2		891,2715,2879	GG,GA,AA		39.0599,26.1146,34.6723		335/1762	107743664	4497,8473	2198	4287	6485	SO:0001819	synonymous_variant	22798	exon10			GTGGCTATTACAG	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.1005T>C	7.37:g.107743664A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			A|0.701;G|0.299	0.299	strong		0.612	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
CPXM2	119587	hgsc.bcm.edu	37	10	125521533	125521533	+	Silent	SNP	G	G	A	rs10794566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:125521533G>A	ENST00000241305.3	-	11	1786	c.1632C>T	c.(1630-1632)gaC>gaT	p.D544D	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	544					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		ACACGTGGTCGTCGGGGGTGG	0.677													G|||	3037	0.60643	0.4614	0.7277	5008	,	,		15724	0.5655		0.7684	False		,,,				2504	0.592				p.D544D		Atlas-SNP	.											.	CPXM2	120	.	0			c.C1632T						PASS	.	G		2241,2165	588.1+/-386.8	569,1103,531	62.0	63.0	63.0		1632	-1.4	1.0	10	dbSNP_120	63	6445,2155	711.9+/-405.9	2435,1575,290	no	coding-synonymous	CPXM2	NM_198148.2		3004,2678,821	AA,AG,GG		25.0581,49.1375,33.2154		544/757	125521533	8686,4320	2203	4300	6503	SO:0001819	synonymous_variant	119587	exon11			GTGGTCGTCGGGG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1632C>T	10.37:g.125521533G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	37	CCDS7637.1																																																																																			G|0.352;A|0.648	0.648	strong		0.677	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
EFCAB13	124989	hgsc.bcm.edu	37	17	45468858	45468858	+	Nonsense_Mutation	SNP	T	T	G	rs118004742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45468858T>G	ENST00000331493.2	+	15	2049	c.1638T>G	c.(1636-1638)taT>taG	p.Y546*	EFCAB13_ENST00000517484.1_Nonsense_Mutation_p.Y450*	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	546	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.Y546*(1)									ATGTGGATTATGAGGATCTAA	0.303													T|||	116	0.0231629	0.0045	0.0634	5008	,	,		11984	0.0		0.0547	False		,,,				2504	0.0112				p.Y546X		Atlas-SNP	.											C17orf57,NS,carcinoma,0,1	.	.	1	1	Substitution - Nonsense(1)	pancreas(1)	c.T1638G						PASS	.	T	stop/TYR,stop/TYR	65,4341	58.7+/-95.3	0,65,2138	58.0	62.0	61.0		1350,1638	2.1	0.0	17	dbSNP_132	61	511,8085	143.7+/-199.7	14,483,3801	yes	stop-gained,stop-gained	C17orf57	NM_001195192.1,NM_152347.4	,	14,548,5939	GG,GT,TT		5.9446,1.4753,4.4301	,	450/785,546/974	45468858	576,12426	2203	4298	6501	SO:0001587	stop_gained	124989	exon15			GGATTATGAGGAT	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1638T>G	17.37:g.45468858T>G	ENSP00000332111:p.Tyr546*	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	186	97	0.521505	NM_152347	G3V128|Q49AG9	Nonsense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	64	0.029304029304029304	2	0.0040650406504065045	29	0.08011049723756906	0	0.0	33	0.04353562005277045	T	12.68	2.009891	0.35415	0.014753	0.059446	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176;ENST00000523842	.	.	.	3.2	2.06	0.26882	.	1.357670	0.05230	N	0.510165	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.6206	5.4591	0.16607	0.0:0.1345:0.0:0.8655	.	.	.	.	X	546;450;498;72	.	ENSP00000332111:Y546X	Y	+	3	2	C17orf57	42823857	0.002000	0.14202	0.004000	0.12327	0.878000	0.50629	0.671000	0.25172	0.539000	0.28788	0.383000	0.25322	TAT	T|0.958;G|0.042	0.042	strong		0.303	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
DOCK5	80005	hgsc.bcm.edu	37	8	25149612	25149612	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:25149612C>T	ENST00000276440.7	+	6	438	c.394C>T	c.(394-396)Ctg>Ttg	p.L132L	DOCK5_ENST00000481100.1_Silent_p.L132L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	132					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			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)		GTCCCAGATCCTGTCTGGGAC	0.493																																					p.L132L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C394T						PASS	.						37.0	34.0	35.0					8																	25149612		2203	4298	6501	SO:0001819	synonymous_variant	80005	exon6			CAGATCCTGTCTG		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.394C>T	8.37:g.25149612C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	69	16	0.231884	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			.	.	none		0.493	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989187	60989187	+	Missense_Mutation	SNP	G	G	T	rs45514096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	28	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	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	
MTNR1A	4543	hgsc.bcm.edu	37	4	187454951	187454951	+	Silent	SNP	T	T	C	rs8192551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187454951T>C	ENST00000307161.5	-	2	1146	c.945A>G	c.(943-945)acA>acG	p.T315T	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	315					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	ACACCCTGGCTGTACAGAGCG	0.448													T|||	334	0.0666933	0.1135	0.049	5008	,	,		20852	0.0784		0.0408	False		,,,				2504	0.0307				p.T315T		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A945G						PASS	.	T		473,3933	223.9+/-240.3	22,429,1752	137.0	136.0	136.0		945	-1.6	0.1	4	dbSNP_117	136	387,8213	125.6+/-184.2	15,357,3928	no	coding-synonymous	MTNR1A	NM_005958.3		37,786,5680	CC,CT,TT		4.5,10.7354,6.6123		315/351	187454951	860,12146	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			CCTGGCTGTACAG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.945A>G	4.37:g.187454951T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			T|0.936;C|0.064	0.064	strong		0.448	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
SVIL	6840	hgsc.bcm.edu	37	10	29821089	29821089	+	Silent	SNP	C	C	T	rs17756919	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29821089C>T	ENST00000355867.4	-	9	2603	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V	SVIL_ENST00000375398.2_Silent_p.V617V|SVIL_ENST00000375400.3_Intron	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	48	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	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		
CDHR1	92211	hgsc.bcm.edu	37	10	85958847	85958847	+	Silent	SNP	C	C	T	rs148125234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85958847C>T	ENST00000372117.3	+	5	511	c.408C>T	c.(406-408)atC>atT	p.I136I	CDHR1_ENST00000440770.2_5'Flank|CDHR1_ENST00000332904.3_Silent_p.I136I	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	136	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCAGGTTCATCCAGGAGCCTT	0.597													C|||	5	0.000998403	0.0008	0.0	5008	,	,		17525	0.0		0.004	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CDHR1	122	.	0			c.C408T						PASS	.	C	,	1,4047		0,1,2023	95.0	77.0	83.0		408,408	3.3	0.9	10	dbSNP_134	83	15,7755		0,15,3870	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	0,16,5893	TT,TC,CC		0.1931,0.0247,0.1354	,	136/746,136/860	85958847	16,11802	2024	3885	5909	SO:0001819	synonymous_variant	92211	exon5			GTTCATCCAGGAG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.408C>T	10.37:g.85958847C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
FLG	2312	hgsc.bcm.edu	37	1	152283236	152283236	+	Missense_Mutation	SNP	T	T	C	rs11581433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152283236T>C	ENST00000368799.1	-	3	4161	c.4126A>G	c.(4126-4128)Aga>Gga	p.R1376G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1376	Ser-rich.		R -> G (in dbSNP:rs11581433).		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)			GAAGCTTGTCTGTGCCCAATG	0.532									Ichthyosis				C|||	1718	0.343051	0.1218	0.4236	5008	,	,		21937	0.6062		0.171	False		,,,				2504	0.4908				p.R1376G		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A4126G						scavenged	.	C	GLY/ARG	607,3799	768.9+/-413.6	43,521,1639	411.0	383.0	392.0		4126	-4.5	0.0	1	dbSNP_120	392	1436,7160	750.9+/-407.4	123,1190,2985	no	missense	FLG	NM_002016.1	125	166,1711,4624	CC,CT,TT		16.7054,13.7767,15.713	benign	1376/4062	152283236	2043,10959	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTCTGTGCCC	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.4126A>G	1.37:g.152283236T>C	ENSP00000357789:p.Arg1376Gly	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	131	85	0.648855	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	588	0.2692307692307692	51	0.10365853658536585	109	0.3011049723756906	317	0.5541958041958042	111	0.14643799472295516	C	6.987	0.552125	0.13374	0.137767	0.167054	ENSG00000143631	ENST00000368799	T	0.02032	4.49	4.29	-4.46	0.03536	.	.	.	.	.	T	0.00178	0.0005	N	0.00642	-1.3	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39663	-0.9603	8	0.02654	T	1	.	8.0818	0.30750	0.0:0.1976:0.1306:0.6718	rs11581433	1376	P20930	FILA_HUMAN	G	1376	ENSP00000357789:R1376G	ENSP00000357789:R1376G	R	-	1	2	FLG	150549860	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.374000	0.01072	-0.955000	0.03636	-0.949000	0.02662	AGA	T|0.807;C|0.193	0.193	strong		0.532	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs386643884|rs1041968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21232804G>A	ENST00000233242.1	-	26	7063	c.6936C>T	c.(6934-6936)gaC>gaT	p.D2312D		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2312					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)					GCTCAAGAATGTCATTTATTC	0.348													G|||	1248	0.249201	0.2095	0.3775	5008	,	,		20035	0.0615		0.4423	False		,,,				2504	0.2065				p.D2312D		Atlas-SNP	.											APOB,NS,malignant_melanoma,-2,1	APOB	761	1	0			c.C6936T						PASS	.	G		1032,3374		139,754,1310	116.0	119.0	118.0		6936	-2.2	0.0	2	dbSNP_86	118	4118,4482		1092,1934,1274	no	coding-synonymous	APOB	NM_000384.2		1231,2688,2584	AA,AG,GG		47.8837,23.4226,39.5971		2312/4564	21232804	5150,7856	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			AAGAATGTCATTT	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.6936C>T	2.37:g.21232804G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.640;A|0.360	0.360	strong		0.348	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
THBS2	7058	hgsc.bcm.edu	37	6	169632219	169632219	+	Silent	SNP	G	G	A	rs35935937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:169632219G>A	ENST00000366787.3	-	14	2256	c.2007C>T	c.(2005-2007)ggC>ggT	p.G669G	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	669	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.G669G(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGCTGAAGTGGCCCAGGTAGA	0.632													G|||	960	0.191693	0.1218	0.2161	5008	,	,		16580	0.2679		0.17	False		,,,				2504	0.2127				p.G669G	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	1	Substitution - coding silent(1)	stomach(1)	c.C2007T						PASS	.	G		538,3868	241.2+/-251.7	41,456,1706	205.0	177.0	187.0		2007	-0.2	1.0	6	dbSNP_126	187	1347,7253	263.1+/-284.8	124,1099,3077	no	coding-synonymous	THBS2	NM_003247.2		165,1555,4783	AA,AG,GG		15.6628,12.2106,14.4933		669/1173	169632219	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon14			GAAGTGGCCCAGG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2007C>T	6.37:g.169632219G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	116	50	0.431034	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.839;C|0.000;A|0.161	0.161	strong		0.632	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
ZNF440	126070	hgsc.bcm.edu	37	19	11942615	11942615	+	Silent	SNP	A	A	C	rs394416	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	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	
DNAH12	201625	hgsc.bcm.edu	37	3	57414434	57414434	+	Missense_Mutation	SNP	A	A	G	rs4462937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:57414434A>G	ENST00000351747.2	-	34	5290	c.5110T>C	c.(5110-5112)Tat>Cat	p.Y1704H		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1704			Y -> H (in dbSNP:rs4462937).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AGAGCTTGATATTCTGGTTCA	0.403													A|||	1502	0.29992	0.1218	0.3127	5008	,	,		19134	0.4187		0.2416	False		,,,				2504	0.4693				p.Y1704H		Atlas-SNP	.											.	DNAH12	182	.	0			c.T5110C						PASS	.	A	HIS/TYR	195,1189		14,167,511	125.0	106.0	112.0		5110	-1.9	0.0	3	dbSNP_111	112	759,2423		91,577,923	yes	missense	DNAH12	NM_178504.4	83	105,744,1434	GG,GA,AA		23.8529,14.0896,20.8936	benign	1704/3093	57414434	954,3612	692	1591	2283	SO:0001583	missense	201625	exon34			CTTGATATTCTGG	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5110T>C	3.37:g.57414434A>G	ENSP00000295937:p.Tyr1704His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		594	0.27197802197802196	62	0.12601626016260162	111	0.30662983425414364	239	0.4178321678321678	182	0.24010554089709762	A	0.006	-2.027775	0.00410	0.140896	0.238529	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.23147	1.92;1.92	5.76	-1.92	0.07618	.	.	.	.	.	T	0.00012	0.0000	N	0.00360	-1.595	0.51482	P	7.100000000004325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43940	-0.9360	8	0.02654	T	1	.	5.2318	0.15426	0.2915:0.0:0.4287:0.2798	rs4462937;rs4462937	1704	Q6ZR08	DYH12_HUMAN	H	1704;1727	ENSP00000295937:Y1704H;ENSP00000418137:Y1727H	ENSP00000295937:Y1704H	Y	-	1	0	DNAH12	57389474	0.015000	0.18098	0.001000	0.08648	0.016000	0.09150	0.114000	0.15520	-0.118000	0.11851	-0.789000	0.03336	TAT	A|0.728;G|0.272	0.272	strong		0.403	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
DNAH7	56171	hgsc.bcm.edu	37	2	196822004	196822004	+	Missense_Mutation	SNP	A	A	G	rs62623378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:196822004A>G	ENST00000312428.6	-	19	3159	c.3059T>C	c.(3058-3060)aTa>aCa	p.I1020T		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1020	Stem. {ECO:0000250}.			I -> T (in Ref. 2; BAA76788). {ECO:0000305}.	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						ACTTCTCATTATATCTCTCCA	0.388													A|||	239	0.0477236	0.0068	0.0778	5008	,	,		20305	0.001		0.1074	False		,,,				2504	0.0685				p.I1020T		Atlas-SNP	.											.	DNAH7	512	.	0			c.T3059C						PASS	.	A	THR/ILE	77,3669		1,75,1797	120.0	108.0	111.0		3059	4.4	0.9	2	dbSNP_129	111	972,7268		59,854,3207	yes	missense	DNAH7	NM_018897.2	89	60,929,5004	GG,GA,AA		11.7961,2.0555,8.7519	benign	1020/4025	196822004	1049,10937	1873	4120	5993	SO:0001583	missense	56171	exon19			CTCATTATATCTC	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.3059T>C	2.37:g.196822004A>G	ENSP00000311273:p.Ile1020Thr	Somatic	352	1	0.00284091		WXS	Illumina HiSeq	Phase_I	344	343	0.997093	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	110	0.05036630036630037	2	0.0040650406504065045	33	0.09116022099447514	1	0.0017482517482517483	74	0.09762532981530343	A	8.570	0.879782	0.17467	0.020555	0.117961	ENSG00000118997	ENST00000312428	T	0.64085	-0.08	5.57	4.41	0.53225	Dynein heavy chain, domain-2 (1);	0.529435	0.20211	N	0.096913	T	0.00998	0.0033	L	0.38692	1.165	0.20563	P	0.999884684	B	0.12013	0.005	B	0.16722	0.016	T	0.15665	-1.0429	9	0.40728	T	0.16	.	11.7773	0.51993	0.9308:0.0:0.0692:0.0	rs62623378	1020	Q8WXX0	DYH7_HUMAN	T	1020	ENSP00000311273:I1020T	ENSP00000311273:I1020T	I	-	2	0	DNAH7	196530249	0.507000	0.26146	0.939000	0.37840	0.485000	0.33311	2.482000	0.45224	1.044000	0.40200	0.533000	0.62120	ATA	A|0.921;G|0.079	0.079	strong		0.388	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PTPRB	5787	hgsc.bcm.edu	37	12	70925864	70925864	+	Missense_Mutation	SNP	C	C	G	rs17226367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:70925864C>G	ENST00000261266.5	-	30	5830	c.5801G>C	c.(5800-5802)gGa>gCa	p.G1934A	RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000451516.2_Missense_Mutation_p.G1844A|RP11-588H23.3_ENST00000547656.1_RNA|RP11-588H23.3_ENST00000549460.1_RNA|PTPRB_ENST00000550358.1_Missense_Mutation_p.G2064A|RP11-588H23.3_ENST00000548687.1_RNA|PTPRB_ENST00000550857.1_Missense_Mutation_p.G1844A|PTPRB_ENST00000538708.1_Missense_Mutation_p.G1844A|RP11-588H23.3_ENST00000546836.1_RNA|PTPRB_ENST00000334414.6_Missense_Mutation_p.G2152A	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1934	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		G -> A (in dbSNP:rs17226367).		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)			GTGCACTGCTCCATAAATGTC	0.493													C|||	111	0.0221645	0.0008	0.0202	5008	,	,		14445	0.0		0.0775	False		,,,				2504	0.0184				p.G2152A		Atlas-SNP	.											.	PTPRB	676	.	0			c.G6455C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY	43,3839		1,41,1899	136.0	130.0	132.0		6455,5531,5531,5801	5.5	1.0	12	dbSNP_123	132	496,7788		16,464,3662	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	60,60,60,60	17,505,5561	GG,GC,CC		5.9874,1.1077,4.4304	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	2152/2216,1844/1908,1844/1908,1934/1998	70925864	539,11627	1941	4142	6083	SO:0001583	missense	5787	exon32			ACTGCTCCATAAA	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.5801G>C	12.37:g.70925864C>G	ENSP00000261266:p.Gly1934Ala	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	64	0.029304029304029304	0	0.0	9	0.024861878453038673	0	0.0	55	0.07255936675461741	C	14.83	2.652199	0.47362	0.011077	0.059874	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77	5.53	5.53	0.82687	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.105660	0.64402	D	0.000005	T	0.01254	0.0041	L	0.28649	0.875	0.80722	D	1	D;P;D;D;D	0.76494	0.976;0.78;0.999;0.989;0.96	P;P;P;P;P	0.56042	0.683;0.568;0.79;0.681;0.496	T	0.00321	-1.1819	10	0.56958	D	0.05	.	16.3458	0.83132	0.0:0.8594:0.1406:0.0	rs17226367;rs52813184;rs17226367	1844;1844;2152;1934;2064	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	A	2152;1844;2064;1844;1844;1934	ENSP00000334928:G2152A;ENSP00000393028:G1844A;ENSP00000448058:G2064A;ENSP00000438927:G1844A;ENSP00000447302:G1844A;ENSP00000261266:G1934A	ENSP00000261266:G1934A	G	-	2	0	PTPRB	69212131	1.000000	0.71417	1.000000	0.80357	0.403000	0.30841	3.907000	0.56348	2.770000	0.95276	0.655000	0.94253	GGA	C|0.968;G|0.032	0.032	strong		0.493	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
PDYN	5173	hgsc.bcm.edu	37	20	1961298	1961298	+	Missense_Mutation	SNP	T	T	G	rs77155664	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1961298T>G	ENST00000217305.2	-	4	661	c.436A>C	c.(436-438)Atg>Ctg	p.M146L	PDYN_ENST00000539905.1_Missense_Mutation_p.M146L|PDYN_ENST00000540134.1_Missense_Mutation_p.M146L|RP4-684O24.5_ENST00000446562.1_RNA	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	146					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCATCCCTCATCAGCTCAGAC	0.557													T|||	6	0.00119808	0.0008	0.0029	5008	,	,		18495	0.0		0.003	False		,,,				2504	0.0				p.M146L		Atlas-SNP	.											.	PDYN	74	.	0			c.A436C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET,LEU/MET,LEU/MET	4,4402	8.1+/-20.4	0,4,2199	117.0	110.0	112.0		436,436,436,436,436	-9.4	0.0	20	dbSNP_131	112	64,8536	39.8+/-96.3	0,64,4236	yes	missense,missense,missense,missense,missense	PDYN	NM_001190892.1,NM_001190898.2,NM_001190899.2,NM_001190900.1,NM_024411.4	15,15,15,15,15	0,68,6435	GG,GT,TT		0.7442,0.0908,0.5228	benign,benign,benign,benign,benign	146/255,146/255,146/255,146/255,146/255	1961298	68,12938	2203	4300	6503	SO:0001583	missense	5173	exon4			CCCTCATCAGCTC		CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"""Endogenous ligands"""	8820	protein-coding gene	gene with protein product	"""preproenkephalin B"", ""rimorphin"", ""beta-neoendorphin"", ""dynorphin"", ""leu-enkephalin"", ""leumorphin"", ""neoendorphin-dynorphin-enkephalin prepropeptide"""	131340	"""spinocerebellar ataxia 23"""	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.436A>C	20.37:g.1961298T>G	ENSP00000217305:p.Met146Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_001190898	A8K0Q3	Missense_Mutation	SNP	ENST00000217305.2	37	CCDS13023.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	9.719	1.159229	0.21454	9.08E-4	0.007442	ENSG00000101327	ENST00000539905;ENST00000540134;ENST00000217305	T;T;T	0.79247	-1.25;-1.25;-1.25	4.71	-9.42	0.00610	.	1.585980	0.02994	N	0.147212	T	0.47173	0.1431	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47156	-0.9139	10	0.10377	T	0.69	0.1214	3.3855	0.07270	0.1334:0.3827:0.3142:0.1696	.	146	P01213	PDYN_HUMAN	L	146	ENSP00000440185:M146L;ENSP00000442259:M146L;ENSP00000217305:M146L	ENSP00000217305:M146L	M	-	1	0	PDYN	1909298	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-2.498000	0.00968	-2.359000	0.00611	-0.608000	0.04076	ATG	T|0.997;G|0.003	0.003	strong		0.557	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2		
STXBP3	6814	hgsc.bcm.edu	37	1	109338861	109338861	+	Silent	SNP	G	G	C	rs1127635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:109338861G>C	ENST00000370008.3	+	14	1166	c.1116G>C	c.(1114-1116)ctG>ctC	p.L372L		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	372					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TTAAGGACCTGGCACTTGGAA	0.353													G|||	1650	0.329473	0.2731	0.3213	5008	,	,		18139	0.1925		0.4334	False		,,,				2504	0.4458				p.L372L		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1116C						PASS	.	G		1335,3071	440.4+/-346.0	212,911,1080	57.0	57.0	57.0		1116	4.9	1.0	1	dbSNP_86	57	3818,4782	536.8+/-383.1	825,2168,1307	no	coding-synonymous	STXBP3	NM_007269.2		1037,3079,2387	CC,CG,GG		44.3953,30.2996,39.6202		372/593	109338861	5153,7853	2203	4300	6503	SO:0001819	synonymous_variant	6814	exon14			GGACCTGGCACTT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1116G>C	1.37:g.109338861G>C		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	233	112	0.480687	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	37	CCDS790.1																																																																																			G|0.624;C|0.375	0.375	strong		0.353	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	
NLRP9	338321	hgsc.bcm.edu	37	19	56249672	56249672	+	Silent	SNP	A	A	G	rs56211941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	150	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	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	
LPPR1	54886	hgsc.bcm.edu	37	9	104032338	104032338	+	Silent	SNP	C	C	T	rs7847596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104032338C>T	ENST00000374874.3	+	3	679	c.240C>T	c.(238-240)acC>acT	p.T80T	LPPR1_ENST00000395056.2_Silent_p.T80T	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		80					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										TGGCTGCCACCCCAACTGCTA	0.443													C|||	86	0.0171725	0.003	0.0187	5008	,	,		19611	0.001		0.0417	False		,,,				2504	0.0266				p.T80T		Atlas-SNP	.											.	.	.	.	0			c.C240T						PASS	.	C	,	32,4374	34.3+/-65.2	0,32,2171	83.0	81.0	82.0		240,240	-1.7	1.0	9	dbSNP_116	82	342,8258	112.7+/-172.9	5,332,3963	no	coding-synonymous,coding-synonymous	LPPR1	NM_017753.2,NM_207299.1	,	5,364,6134	TT,TC,CC		3.9767,0.7263,2.8756	,	80/326,80/326	104032338	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGCCACCCCAACT																												ENST00000374874.3:c.240C>T	9.37:g.104032338C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	61	0.554545	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	37	CCDS6751.1																																																																																			C|0.973;T|0.027	0.027	strong		0.443	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
ATP2B1	490	hgsc.bcm.edu	37	12	90028901	90028901	+	Silent	SNP	T	T	C	rs1050395	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:90028901T>C	ENST00000428670.3	-	4	990	c.534A>G	c.(532-534)gaA>gaG	p.E178E	ATP2B1_ENST00000359142.3_Silent_p.E178E|ATP2B1_ENST00000348959.3_Silent_p.E178E|ATP2B1_ENST00000261173.2_Silent_p.E178E			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	178					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|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)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TAAACTGTTTTTCCTTACTCC	0.438													T|||	605	0.120807	0.1505	0.1455	5008	,	,		17520	0.0317		0.1928	False		,,,				2504	0.0808				p.E178E		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A534G						PASS	.	T	,	715,3691	296.7+/-284.4	51,613,1539	133.0	111.0	118.0		534,534	-0.9	1.0	12	dbSNP_86	118	1674,6926	304.6+/-307.0	164,1346,2790	no	coding-synonymous,coding-synonymous	ATP2B1	NM_001001323.1,NM_001682.2	,	215,1959,4329	CC,CT,TT		19.4651,16.2279,18.3684	,	178/1177,178/1221	90028901	2389,10617	2203	4300	6503	SO:0001819	synonymous_variant	490	exon3			CTGTTTTTCCTTA	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.534A>G	12.37:g.90028901T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000428670.3	37	CCDS9035.1																																																																																			T|0.837;C|0.163	0.163	strong		0.438	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
EBLN2	55096	hgsc.bcm.edu	37	3	73111809	73111809	+	Missense_Mutation	SNP	A	A	G	rs2231926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:73111809A>G	ENST00000533473.1	+	1	1000	c.577A>G	c.(577-579)Att>Gtt	p.I193V	PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	193										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						TTTGATAGGCATTGCGGCTGG	0.448													G|||	2635	0.526158	0.618	0.3689	5008	,	,		22330	0.4504		0.508	False		,,,				2504	0.6104				p.I193V		Atlas-SNP	.											.	EBLN2	18	.	0			c.A577G						PASS	.	G	VAL/ILE,	2504,1466		792,920,273	71.0	72.0	72.0		577,	-0.6	0.0	3	dbSNP_98	72	4270,4038		1096,2078,980	yes	missense,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	29,	1888,2998,1253	GG,GA,AA		48.6038,36.927,44.8281	benign,	193/273,	73111809	6774,5504	1985	4154	6139	SO:0001583	missense	55096	exon1			ATAGGCATTGCGG		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.577A>G	3.37:g.73111809A>G	ENSP00000432104:p.Ile193Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	1072	0.4908424908424908	301	0.6117886178861789	143	0.39502762430939226	248	0.43356643356643354	380	0.5013192612137203	G	0	-2.810176	0.00074	0.63073	0.513962	ENSG00000255423	ENST00000533473	.	.	.	0.468	-0.603	0.11630	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	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	0.43097	-0.9412	6	0.02654	T	1	.	.	.	.	rs2231926;rs3821377;rs52822828;rs2231926	193	Q6P2I7	EBLN2_HUMAN	V	193	.	ENSP00000432104:I193V	I	+	1	0	EBLN2	73194499	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-2.665000	0.00848	-1.385000	0.02101	-1.383000	0.01170	ATT	A|0.500;G|0.500	0.500	strong		0.448	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
C14orf159	80017	hgsc.bcm.edu	37	14	91666248	91666248	+	Splice_Site	SNP	T	T	C	rs28715808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	476						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)		TCTCATCAACTGGTAAGTATG	0.458													T|||	181	0.0361422	0.1067	0.0346	5008	,	,		22154	0.0		0.0109	False		,,,				2504	0.0051				p.T481T		Atlas-SNP	.											.	C14orf159	57	.	0			c.T1443C						PASS	.	T	,,,,	337,4069	176.9+/-206.0	16,305,1882	151.0	142.0	145.0		1428,1428,1443,1392,1428	-2.7	0.1	14	dbSNP_125	145	117,8483	61.0+/-122.8	0,117,4183	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	16,422,6065	CC,CT,TT		1.3605,7.6487,3.4907	,,,,	476/617,476/617,481/622,464/565,476/617	91666248	454,12552	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon11			ATCAACTGGTAAG	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.1429+1T>C	14.37:g.91666248T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	60	0.027472527472527472	41	0.08333333333333333	12	0.03314917127071823	0	0.0	7	0.009234828496042216	T	0.894	-0.724442	0.03158	0.076487	0.013605	ENSG00000133943	ENST00000522816	.	.	.	5.1	-2.71	0.05986	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22173	-1.0224	3	.	.	.	.	2.29	0.04136	0.3649:0.0777:0.3565:0.2009	rs28715808	.	.	.	P	77	.	.	L	+	2	0	C14orf159	90736001	0.990000	0.36364	0.051000	0.19133	0.053000	0.15095	0.237000	0.17985	-0.360000	0.08138	-0.461000	0.05368	CTG	T|0.967;C|0.033	0.033	strong		0.458	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Silent
C2orf44	80304	hgsc.bcm.edu	37	2	24262060	24262060	+	Missense_Mutation	SNP	G	G	A	rs3731620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:24262060G>A	ENST00000295148.4	-	2	362	c.305C>T	c.(304-306)aCg>aTg	p.T102M	C2orf44_ENST00000406895.3_Missense_Mutation_p.T102M	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	102			T -> M (in dbSNP:rs3731620).						C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTCTGAGACGTCAGCCATTT	0.507			T	ALK	NSCLC								G|||	493	0.0984425	0.0772	0.0533	5008	,	,		23586	0.0367		0.1402	False		,,,				2504	0.18				p.T102M		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.C305T						PASS	.	G	MET/THR,MET/THR	332,4074	174.4+/-204.0	11,310,1882	97.0	89.0	92.0		305,305	2.7	0.5	2	dbSNP_107	92	1213,7387	244.4+/-273.7	85,1043,3172	yes	missense,missense	C2orf44	NM_001142319.1,NM_025203.2	81,81	96,1353,5054	AA,AG,GG		14.1047,7.5352,11.8791	benign,benign	102/623,102/722	24262060	1545,11461	2203	4300	6503	SO:0001583	missense	80304	exon2			TGAGACGTCAGCC	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.305C>T	2.37:g.24262060G>A	ENSP00000295148:p.Thr102Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	187	0.08562271062271062	32	0.06504065040650407	29	0.08011049723756906	19	0.033216783216783216	107	0.14116094986807387	G	2.674	-0.276795	0.05679	0.075352	0.141047	ENSG00000163026	ENST00000295148;ENST00000406895;ENST00000443232	T;T;T	0.40225	1.04;1.04;1.04	5.24	2.72	0.32119	WD40/YVTN repeat-like-containing domain (1);	0.460245	0.27214	N	0.020393	T	0.00073	0.0002	N	0.00237	-1.79	0.45490	P	0.0015420000000000433	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13629	-1.0502	9	0.22706	T	0.39	-7.9865	9.37	0.38248	0.8524:0.0:0.1476:0.0	rs3731620;rs17356692;rs52809153;rs60551542;rs3731620	102;102	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	M	102	ENSP00000295148:T102M;ENSP00000385816:T102M;ENSP00000413426:T102M	ENSP00000295148:T102M	T	-	2	0	C2orf44	24115564	1.000000	0.71417	0.543000	0.28128	0.115000	0.19883	3.141000	0.50593	0.405000	0.25532	-0.290000	0.09829	ACG	G|0.898;N|0.000	.	strong		0.507	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
WASF1	8936	hgsc.bcm.edu	37	6	110448742	110448742	+	Silent	SNP	G	G	A	rs55817927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:110448742G>A	ENST00000392589.1	-	4	899	c.63C>T	c.(61-63)ggC>ggT	p.G21G	WASF1_ENST00000392588.1_Silent_p.G21G|WASF1_ENST00000392587.2_Silent_p.G21G|WASF1_ENST00000359451.2_Silent_p.G21G|WASF1_ENST00000392586.1_Silent_p.G21G	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	21					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		CATTCTTAATGCCTCTAGGCA	0.373													G|||	286	0.0571086	0.1127	0.0591	5008	,	,		18823	0.0		0.0557	False		,,,				2504	0.0409				p.G21G		Atlas-SNP	.											.	WASF1	35	.	0			c.C63T						PASS	.	G	,,,	488,3918	226.5+/-242.0	39,410,1754	101.0	99.0	99.0		63,63,63,63	1.1	1.0	6	dbSNP_129	99	429,8171	132.0+/-189.7	12,405,3883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WASF1	NM_001024934.1,NM_001024935.1,NM_001024936.1,NM_003931.2	,,,	51,815,5637	AA,AG,GG		4.9884,11.0758,7.0506	,,,	21/560,21/560,21/560,21/560	110448742	917,12089	2203	4300	6503	SO:0001819	synonymous_variant	8936	exon3			CTTAATGCCTCTA	D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"""A-kinase anchor proteins"""	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.63C>T	6.37:g.110448742G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_001024935	E1P5F2|Q5SZK7	Silent	SNP	ENST00000392589.1	37	CCDS5080.1																																																																																			G|0.929;A|0.071	0.071	strong		0.373	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931	
SENP7	57337	hgsc.bcm.edu	37	3	101066717	101066717	+	Splice_Site	SNP	T	T	A	rs2433031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:101066717T>A	ENST00000394095.2	-	13	1889	c.1836A>T	c.(1834-1836)caA>caT	p.Q612H	SENP7_ENST00000314261.7_Splice_Site_p.Q546H|SENP7_ENST00000348610.3_Splice_Site_p.Q579H|SENP7_ENST00000358203.3_Splice_Site_p.Q448H|SENP7_ENST00000394091.1_Splice_Site_p.Q448H|SENP7_ENST00000394094.2_Splice_Site_p.Q547H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	612			Q -> H (in dbSNP:rs2433031). {ECO:0000269|PubMed:11214970}.			intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.Q546H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TATACTCACATTGCTGGCTTA	0.294													T|||	1508	0.301118	0.177	0.2767	5008	,	,		13620	0.3403		0.3827	False		,,,				2504	0.362				p.Q612H		Atlas-SNP	.											SENP7,NS,carcinoma,0,1	SENP7	170	1	1	Substitution - Missense(1)	prostate(1)	c.A1836T						PASS	.	T	HIS/GLN,HIS/GLN	989,3417	356.4+/-313.5	98,793,1312	66.0	67.0	67.0		1641,1836	1.1	1.0	3	dbSNP_100	67	3167,5431	468.5+/-367.3	596,1975,1728	yes	missense-near-splice,missense-near-splice	SENP7	NM_001077203.1,NM_020654.3	24,24	694,2768,3040	AA,AT,TT		36.8341,22.4467,31.9594	possibly-damaging,possibly-damaging	547/986,612/1051	101066717	4156,8848	2203	4299	6502	SO:0001630	splice_region_variant	57337	exon13			CTCACATTGCTGG		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1837+1A>T	3.37:g.101066717T>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	46	0.351145	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	678|678	0.31043956043956045|0.31043956043956045	81|81	0.16463414634146342|0.16463414634146342	103|103	0.2845303867403315|0.2845303867403315	192|192	0.3356643356643357|0.3356643356643357	302|302	0.39841688654353563|0.39841688654353563	T|T	13.81|13.81	2.347976|2.347976	0.41599|0.41599	0.224467|0.224467	0.368341|0.368341	ENSG00000138468|ENSG00000138468	ENST00000366089|ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	.|T;T;T;T;T;T	.|0.19532	.|2.14;2.16;2.16;2.16;2.16;2.14	5.69|5.69	1.12|1.12	0.20585|0.20585	.|.	.|0.239918	.|0.33938	.|N	.|0.004414	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.43271|0.43271	P|P	0.0047719999999999985|0.0047719999999999985	.|D;D;D;D	.|0.67145	.|0.995;0.996;0.991;0.993	.|P;P;D;P	.|0.63192	.|0.871;0.878;0.912;0.753	T|T	0.38243|0.38243	-0.9670|-0.9670	4|9	.|0.15066	.|T	.|0.55	-2.9468|-2.9468	5.1706|5.1706	0.15108|0.15108	0.0:0.2965:0.1434:0.5601|0.0:0.2965:0.1434:0.5601	rs2433031;rs52806065;rs2433031|rs2433031;rs52806065;rs2433031	.|448;546;579;612	.|Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.|.;.;.;SENP7_HUMAN	I|H	14|612;547;546;448;448;579	.|ENSP00000377655:Q612H;ENSP00000377654:Q547H;ENSP00000313624:Q546H;ENSP00000377651:Q448H;ENSP00000350936:Q448H;ENSP00000342159:Q579H	.|ENSP00000313624:Q546H	N|Q	-|-	2|3	0|2	SENP7|SENP7	102549407|102549407	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.862000|0.862000	0.49288|0.49288	0.454000|0.454000	0.21827|0.21827	-0.055000|-0.055000	0.13244|0.13244	-0.417000|-0.417000	0.06048|0.06048	AAT|CAA	T|0.679;A|0.321	0.321	strong		0.294	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	Missense_Mutation
PLD2	5338	hgsc.bcm.edu	37	17	4721376	4721376	+	Missense_Mutation	SNP	A	A	G	rs17854914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4721376A>G	ENST00000263088.6	+	18	2026	c.1895A>G	c.(1894-1896)gAg>gGg	p.E632G	PLD2_ENST00000572940.1_Missense_Mutation_p.E632G	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	632	Catalytic.		E -> G (in dbSNP:rs17854914). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		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)	p.E632G(1)		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)	ACCATCAGGGAGAGCCAGCAC	0.572													A|||	380	0.0758786	0.0234	0.0836	5008	,	,		19234	0.0675		0.163	False		,,,				2504	0.0603				p.E632G		Atlas-SNP	.											PLD2,NS,carcinoma,0,1	PLD2	138	1	1	Substitution - Missense(1)	stomach(1)	c.A1895G						PASS	.	A	GLY/GLU	162,4244	105.6+/-144.1	2,158,2043	84.0	65.0	72.0		1895	4.8	1.0	17	dbSNP_123	72	1242,7358	243.9+/-273.3	106,1030,3164	yes	missense	PLD2	NM_002663.4	98	108,1188,5207	GG,GA,AA		14.4419,3.6768,10.795	possibly-damaging	632/934	4721376	1404,11602	2203	4300	6503	SO:0001583	missense	5338	exon18			TCAGGGAGAGCCA	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.1895A>G	17.37:g.4721376A>G	ENSP00000263088:p.Glu632Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	200	0.09157509157509157	8	0.016260162601626018	36	0.09944751381215469	41	0.07167832167832168	115	0.1517150395778364	A	14.76	2.631171	0.46944	0.036768	0.144419	ENSG00000129219	ENST00000263088	T	0.30182	1.54	4.77	4.77	0.60923	.	0.170853	0.51477	D	0.000095	T	0.00144	0.0004	N	0.26042	0.785	0.27570	P	0.9499091	B;B;P	0.35139	0.033;0.057;0.486	B;B;B	0.40329	0.022;0.064;0.326	T	0.21484	-1.0244	9	0.31617	T	0.26	-15.9283	12.2194	0.54425	1.0:0.0:0.0:0.0	rs17854914	489;632;632	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	G	632	ENSP00000263088:E632G	ENSP00000263088:E632G	E	+	2	0	PLD2	4668342	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	3.862000	0.56009	1.787000	0.52448	0.454000	0.30748	GAG	A|0.896;G|0.104	0.104	strong		0.572	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
CST11	140880	hgsc.bcm.edu	37	20	23432528	23432528	+	Silent	SNP	A	A	G	rs2236021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23432528A>G	ENST00000377009.3	-	2	291	c.258T>C	c.(256-258)aaT>aaC	p.N86N	CST11_ENST00000377007.3_Intron	NM_130794.1	NP_570612.1	Q9H112	CST11_HUMAN	cystatin 11	86					defense response to bacterium (GO:0042742)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(2)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	14	Colorectal(13;0.0431)|Lung NSC(19;0.235)					GCATTTCCACATTCAGGTGAT	0.572													G|||	1384	0.276358	0.6044	0.1744	5008	,	,		17088	0.3006		0.0457	False		,,,				2504	0.1176				p.N86N		Atlas-SNP	.											.	CST11	27	.	0			c.T258C						PASS	.	G	,	2195,2211	590.3+/-387.3	561,1073,569	114.0	98.0	103.0		,258	-3.6	0.0	20	dbSNP_98	103	521,8079	796.3+/-407.5	17,487,3796	no	intron,coding-synonymous	CST11	NM_080830.2,NM_130794.1	,	578,1560,4365	GG,GA,AA		6.0581,49.8184,20.8827	,	,86/139	23432528	2716,10290	2203	4300	6503	SO:0001819	synonymous_variant	140880	exon2			TTCCACATTCAGG	AL096677	CCDS13154.1, CCDS13155.1	20p11.21	2012-08-14			ENSG00000125831	ENSG00000125831			15959	protein-coding gene	gene with protein product		609731		CST8L		20565543	Standard	NM_080830		Approved	dJ322G13.6, CTES2	uc002wtf.1	Q9H112	OTTHUMG00000032060	ENST00000377009.3:c.258T>C	20.37:g.23432528A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_130794	Q0VAF2|Q0VAF3|Q8WXU5|Q8WXU6|Q9H113	Silent	SNP	ENST00000377009.3	37	CCDS13155.1																																																																																			A|0.763;G|0.237	0.237	strong		0.572	CST11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078314.1	NM_130794	
UAP1L1	91373	hgsc.bcm.edu	37	9	139973820	139973820	+	Missense_Mutation	SNP	C	C	T	rs7037849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	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	
F5	2153	hgsc.bcm.edu	37	1	169529826	169529826	+	Silent	SNP	C	C	A	rs6022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169529826C>A	ENST00000367797.3	-	4	753	c.552G>T	c.(550-552)tcG>tcT	p.S184S	F5_ENST00000546081.1_Silent_p.S47S|F5_ENST00000367796.3_Silent_p.S184S	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	102	0	0		WXS	Illumina HiSeq	Phase_I	179	69	0.385475	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	
EVPL	2125	hgsc.bcm.edu	37	17	74014628	74014628	+	Silent	SNP	G	G	A	rs2071193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74014628G>A	ENST00000301607.3	-	12	1591	c.1338C>T	c.(1336-1338)caC>caT	p.H446H	EVPL_ENST00000586740.1_Silent_p.H446H	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	446	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						CGACCCAGGCGTGCGGGTCAG	0.677													G|||	2508	0.500799	0.3646	0.4885	5008	,	,		14719	0.751		0.4006	False		,,,				2504	0.5389				p.H446H		Atlas-SNP	.											.	EVPL	155	.	0			c.C1338T						PASS	.	G		1824,2582		401,1022,780	21.0	24.0	23.0		1338	3.0	1.0	17	dbSNP_96	23	3666,4934		767,2132,1401	no	coding-synonymous	EVPL	NM_001988.2		1168,3154,2181	AA,AG,GG		42.6279,41.3981,42.2113		446/2034	74014628	5490,7516	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon12			CCAGGCGTGCGGG	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.1338C>T	17.37:g.74014628G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			T|0.000;G|0.562;C|0.000;A|0.438	0.438	strong		0.677	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
FOLH1	2346	hgsc.bcm.edu	37	11	49197416	49197416	+	Silent	SNP	A	A	G	rs144950409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49197416A>G	ENST00000256999.2	-	8	1274	c.1014T>C	c.(1012-1014)tcT>tcC	p.S338S	FOLH1_ENST00000340334.7_Silent_p.S323S|FOLH1_ENST00000533034.1_Silent_p.S323S|FOLH1_ENST00000525629.1_5'UTR|FOLH1_ENST00000343844.4_Silent_p.S30S|FOLH1_ENST00000356696.3_Silent_p.S338S	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	338	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TTAACTGTGTAGAAAAGTTTC	0.363													A|||	705	0.140775	0.0477	0.1441	5008	,	,		16671	0.1548		0.0895	False		,,,				2504	0.3027				p.S338S		Atlas-SNP	.											.	FOLH1	141	.	0			c.T1014C						PASS	.	A	,,,,	214,4188	131.0+/-167.6	5,204,1992	71.0	71.0	71.0		1014,969,969,90,1014	2.0	1.0	11	dbSNP_134	71	781,7815	183.6+/-231.8	38,705,3555	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	,,,,	43,909,5547	GG,GA,AA		9.0856,4.8614,7.655	,,,,	338/720,323/736,323/705,30/443,338/751	49197416	995,12003	2201	4298	6499	SO:0001819	synonymous_variant	2346	exon8			CTGTGTAGAAAAG	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.1014T>C	11.37:g.49197416A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	25	0.352113	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																			A|0.914;G|0.086	0.086	strong		0.363	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
WDR90	197335	hgsc.bcm.edu	37	16	703648	703648	+	Missense_Mutation	SNP	A	A	G	rs143047488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:703648A>G	ENST00000293879.4	+	12	1357	c.1357A>G	c.(1357-1359)Atg>Gtg	p.M453V	WDR90_ENST00000549091.1_Missense_Mutation_p.M453V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	453										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCGGAGCCCAATGCACGTTGT	0.637													A|||	7	0.00139776	0.0	0.0014	5008	,	,		18008	0.001		0.004	False		,,,				2504	0.001				p.M453V		Atlas-SNP	.											.	WDR90	107	.	0			c.A1357G						PASS	.	A	VAL/MET	1,4113		0,1,2056	55.0	61.0	59.0		1357	-5.9	0.0	16	dbSNP_134	59	14,8368		0,14,4177	yes	missense	WDR90	NM_145294.4	21	0,15,6233	GG,GA,AA		0.167,0.0243,0.12	benign	453/1749	703648	15,12481	2057	4191	6248	SO:0001583	missense	197335	exon12			AGCCCAATGCACG	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.1357A>G	16.37:g.703648A>G	ENSP00000293879:p.Met453Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0	-2.592739	0.00126	2.43E-4	0.00167	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.01265	5.08;5.08	4.74	-5.88	0.02290	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.312485	0.23962	N	0.042850	T	0.00440	0.0014	N	0.00560	-1.38	0.19300	N	0.999974	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44997	-0.9291	10	0.20519	T	0.43	.	7.8237	0.29303	0.3658:0.2096:0.4247:0.0	.	453;454;453	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	V	453	ENSP00000448122:M453V;ENSP00000293879:M453V	ENSP00000293879:M453V	M	+	1	0	WDR90	643649	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.485000	0.06520	-1.101000	0.03027	-1.545000	0.00906	ATG	A|0.997;G|0.003	0.003	strong		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
GRM7	2917	hgsc.bcm.edu	37	3	7620382	7620382	+	Silent	SNP	C	C	T	rs7614915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:7620382C>T	ENST00000357716.4	+	8	2063	c.1789C>T	c.(1789-1791)Ctg>Ttg	p.L597L	GRM7_ENST00000389336.4_Silent_p.L597L|GRM7_ENST00000402647.2_Silent_p.L597L|GRM7_ENST00000486284.1_Silent_p.L597L|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000403881.1_Silent_p.L597L	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	597					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TCCTGTCTTCCTGGCAATGTT	0.542													C|||	853	0.170327	0.0552	0.2565	5008	,	,		19511	0.1379		0.2932	False		,,,				2504	0.1718				p.L597L		Atlas-SNP	.											.	GRM7	223	.	0			c.C1789T						PASS	.	C	,	371,4035	187.1+/-213.8	16,339,1848	96.0	101.0	99.0		1789,1789	3.9	1.0	3	dbSNP_116	99	2397,6203	399.4+/-346.4	339,1719,2242	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	355,2058,4090	TT,TC,CC		27.8721,8.4203,21.2825	,	597/916,597/923	7620382	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			GTCTTCCTGGCAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1789C>T	3.37:g.7620382C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	132	77	0.583333	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			C|0.804;T|0.196	0.196	strong		0.542	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632781	32632781	+	Missense_Mutation	SNP	A	A	T	rs1049066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632781A>T	ENST00000399084.1	-	3	351	c.173T>A	c.(172-174)cTt>cAt	p.L58H	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.L58H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.L58H|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.L58H|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	58	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCTGGTCACAAGACGCACGCG	0.632									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.L58H	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T173A						PASS	.						28.0	30.0	30.0					6																	32632781		2120	4206	6326	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTCACAAGACGCA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.173T>A	6.37:g.32632781A>T	ENSP00000382034:p.Leu58His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	53	14	0.264151	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	0.044	-1.273457	0.01421	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00357	7.89;7.89;7.89;7.89	3.91	-7.81	0.01210	.	1.484940	0.04916	U	0.454080	T	0.00073	0.0002	L	0.55213	1.73	0.09310	N	1	B;B;B;B;B	0.19200	0.034;0.002;0.001;0.002;0.0	B;B;B;B;B	0.17722	0.013;0.009;0.009;0.019;0.005	T	0.27434	-1.0074	10	0.54805	T	0.06	.	2.9111	0.05737	0.1916:0.3895:0.0766:0.3423	rs1049066;rs3189145;rs12722116	68;58;23;58;58	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	H	58	ENSP00000382029:L58H;ENSP00000364080:L58H;ENSP00000407332:L58H;ENSP00000382034:L58H	ENSP00000364080:L58H	L	-	2	0	HLA-DQB1	32740759	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.691000	0.00057	-2.933000	0.00300	-0.878000	0.02970	CTT	CCC|1.000;|0.000	.	alt		0.632	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
PCMTD1	115294	hgsc.bcm.edu	37	8	52746153	52746153	+	Silent	SNP	C	C	T	rs9298462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Silent_p.V169V	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	59	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	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	
CHIA	27159	hgsc.bcm.edu	37	1	111862074	111862074	+	Silent	SNP	C	C	T	rs2820092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111862074C>T	ENST00000369740.1	+	11	1264	c.1161C>T	c.(1159-1161)ctC>ctT	p.L387L	CHIA_ENST00000353665.6_Silent_p.L226L|CHIA_ENST00000343320.6_Silent_p.L387L|CHIA_ENST00000451398.2_Silent_p.L226L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Silent_p.L226L|CHIA_ENST00000430615.1_Silent_p.L279L	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	387					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)		AGAAGGCCCTCGGCCTGCAGA	0.542													C|||	876	0.17492	0.354	0.1037	5008	,	,		19741	0.0923		0.0994	False		,,,				2504	0.1462				p.L387L		Atlas-SNP	.											.	CHIA	115	.	0			c.C1161T						PASS	.	C	,	1351,3055	451.2+/-349.6	207,937,1059	68.0	63.0	65.0		837,1161	-8.3	0.0	1	dbSNP_100	65	934,7666	206.1+/-248.3	49,836,3415	no	coding-synonymous,coding-synonymous	CHIA	NM_021797.2,NM_201653.2	,	256,1773,4474	TT,TC,CC		10.8605,30.6627,17.5688	,	279/369,387/477	111862074	2285,10721	2203	4300	6503	SO:0001819	synonymous_variant	27159	exon11			GGCCCTCGGCCTG	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.1161C>T	1.37:g.111862074C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																			C|0.834;T|0.166	0.166	strong		0.542	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
FOCAD	54914	hgsc.bcm.edu	37	9	20953049	20953049	+	Missense_Mutation	SNP	A	A	G	rs3206852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:20953049A>G	ENST00000380249.1	+	37	4481	c.4117A>G	c.(4117-4119)Aca>Gca	p.T1373A	FOCAD_ENST00000338382.6_Missense_Mutation_p.T1373A|FOCAD_ENST00000605086.1_Missense_Mutation_p.T809A	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1373			T -> A (in dbSNP:rs3206852). {ECO:0000269|PubMed:14702039}.|T -> P (in dbSNP:rs3206852).|T -> S (in dbSNP:rs3206852).			focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.T1373A(1)									CTTCTTCATTACAGGAGGAAA	0.373													A|||	1681	0.335663	0.2405	0.2695	5008	,	,		19170	0.4355		0.4006	False		,,,				2504	0.3415				p.T1373A		Atlas-SNP	.											KIAA1797,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A4117G						PASS	.	A	ALA/THR	1256,3150	428.9+/-342.0	163,930,1110	111.0	108.0	109.0		4117	3.7	1.0	9	dbSNP_105	109	3578,5022	516.7+/-378.9	753,2072,1475	yes	missense	KIAA1797	NM_017794.3	58	916,3002,2585	GG,GA,AA		41.6047,28.5066,37.1675	benign	1373/1802	20953049	4834,8172	2203	4300	6503	SO:0001583	missense	54914	exon37			TTCATTACAGGAG	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.4117A>G	9.37:g.20953049A>G	ENSP00000369599:p.Thr1373Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	772	0.3534798534798535	136	0.2764227642276423	101	0.27900552486187846	227	0.3968531468531469	308	0.40633245382585753	A	10.14	1.267734	0.23136	0.285066	0.416047	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.21932	1.98;1.98	6.07	3.73	0.42828	.	0.342483	0.31145	N	0.008168	T	0.00012	0.0000	L	0.44542	1.39	0.43740	P	0.0037679999999999936	B	0.02656	0.0	B	0.04013	0.001	T	0.47497	-0.9113	9	0.28530	T	0.3	-2.0043	2.4306	0.04470	0.5373:0.0:0.2603:0.2024	rs3206852;rs3739935;rs17759648;rs58774393;rs3206852	1373	Q5VW36	K1797_HUMAN	A	1373	ENSP00000369599:T1373A;ENSP00000344307:T1373A	ENSP00000344307:T1373A	T	+	1	0	KIAA1797	20943049	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.718000	0.38001	1.107000	0.41642	0.533000	0.62120	ACA	G|0.351;A|0.649	0.351	strong		0.373	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
COL18A1	80781	hgsc.bcm.edu	37	21	46908355	46908355	+	Silent	SNP	T	T	C	rs11702425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46908355T>C	ENST00000359759.4	+	17	3186	c.3165T>C	c.(3163-3165)ctT>ctC	p.L1055L	COL18A1_ENST00000400337.2_Silent_p.L640L|COL18A1_ENST00000355480.5_Silent_p.L820L			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1055	Triple-helical region 4 (COL4).				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)		TGCCGGGACTTAAGGTCAGTG	0.607													C|||	1602	0.319888	0.3797	0.3084	5008	,	,		15666	0.254		0.3131	False		,,,				2504	0.3221				p.L820L		Atlas-SNP	.											.	COL18A1	129	.	0			c.T2460C						PASS	.	C	,	1382,2586		232,918,834	90.0	98.0	96.0		2460,1920	0.3	0.2	21	dbSNP_120	96	2445,5819		350,1745,2037	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	582,2663,2871	CC,CT,TT		29.5862,34.8286,31.2868	,	820/1520,640/1340	46908355	3827,8405	1984	4132	6116	SO:0001819	synonymous_variant	80781	exon17			GGGACTTAAGGTC		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.3165T>C	21.37:g.46908355T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				T|0.680;C|0.320	0.320	strong		0.607	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13700783	13700783	+	Missense_Mutation	SNP	C	C	G	rs374221053		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13700783C>G	ENST00000265104.4	-	78	13793	c.13689G>C	c.(13687-13689)ttG>ttC	p.L4563F		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4563					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)					TGACAGGCATCAACTCAAAGA	0.413									Kartagener syndrome																												p.L4563F		Atlas-SNP	.											.	DNAH5	868	.	0			c.G13689C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	183.0	176.0	178.0		13689	2.1	0.8	5		178	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH5	NM_001369.2	22	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	4563/4625	13700783	1,13005	2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGCATCAACTCA	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.13689G>C	5.37:g.13700783C>G	ENSP00000265104:p.Leu4563Phe	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405974	0.42715	0.0	1.16E-4	ENSG00000039139	ENST00000265104	T	0.08896	3.04	5.95	2.1	0.27182	Dynein heavy chain (1);	0.167558	0.46758	D	0.000275	T	0.14013	0.0339	M	0.73430	2.235	0.36463	D	0.866823	P	0.37612	0.602	P	0.45474	0.482	T	0.04427	-1.0952	10	0.51188	T	0.08	.	5.1797	0.15154	0.0:0.4605:0.2582:0.2813	.	4563	Q8TE73	DYH5_HUMAN	F	4563	ENSP00000265104:L4563F	ENSP00000265104:L4563F	L	-	3	2	DNAH5	13753783	0.427000	0.25514	0.788000	0.31933	0.528000	0.34623	0.101000	0.15251	0.095000	0.17434	-0.182000	0.12963	TTG	.	.	weak		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ACTR3C	653857	hgsc.bcm.edu	37	7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	rs117425825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:149981856G>A	ENST00000539352.1	-	6	801	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	ACTR3C_ENST00000252071.4_Missense_Mutation_p.R184C	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	184						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										TACAGCGGACGCCGCACATCG	0.403													G|||	105	0.0209665	0.003	0.0187	5008	,	,		13887	0.0		0.0457	False		,,,				2504	0.0429				p.R184C		Atlas-SNP	.											.	.	.	.	0			c.C550T						PASS	.	G	CYS/ARG,CYS/ARG	13,1371		0,13,679	85.0	73.0	77.0		550,550	2.2	0.9	7	dbSNP_132	77	125,3057		1,123,1467	yes	missense,missense	ACTR3C	NM_001164458.1,NM_001164459.1	180,180	1,136,2146	AA,AG,GG		3.9283,0.9393,3.0223	probably-damaging,probably-damaging	184/211,184/211	149981856	138,4428	692	1591	2283	SO:0001583	missense	653857	exon6			GCGGACGCCGCAC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.550C>T	7.37:g.149981856G>A	ENSP00000440990:p.Arg184Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	43	0.019688644688644688	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	32	0.04221635883905013	G	13.83	2.352944	0.41700	0.009393	0.039283	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352	T;T;T	0.09350	2.99;2.99;2.99	2.16	2.16	0.27623	.	0.221425	0.28151	N	0.016416	T	0.14141	0.0342	H	0.97587	4.035	0.39214	D	0.963377	D	0.89917	1.0	D	0.68943	0.961	T	0.52961	-0.8505	9	.	.	.	.	10.4552	0.44546	0.0:0.0:1.0:0.0	.	184	Q9C0K3	ARP3C_HUMAN	C	182;184;184	ENSP00000417426:R182C;ENSP00000252071:R184C;ENSP00000440990:R184C	.	R	-	1	0	ACTR3C	149612789	1.000000	0.71417	0.896000	0.35187	0.654000	0.38779	4.696000	0.61774	1.511000	0.48818	0.398000	0.26397	CGT	G|0.976;A|0.024	0.024	strong		0.403	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
CYP2D6	1565	hgsc.bcm.edu	37	22	42525132	42525132	+	Silent	SNP	G	G	C	rs1058164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42525132G>C	ENST00000360608.5	-	3	522	c.408C>G	c.(406-408)gtC>gtG	p.V136V	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.V136V|NDUFA6-AS1_ENST00000608288.1_RNA|CYP2D6_ENST00000359033.4_Intron	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	136					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)	GCAAGGTGGAGACGGAGAAGC	0.687													C|||	2008	0.400958	0.3275	0.5274	5008	,	,		17302	0.2907		0.4563	False		,,,				2504	0.4673				p.V136V		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C408G						PASS	.	C	,	1385,2681		296,793,944	23.0	28.0	26.0		408,	-1.1	0.2	22	dbSNP_86	26	3482,4840		824,1834,1503	no	coding-synonymous,intron	CYP2D6	NM_000106.4,NM_001025161.1	,	1120,2627,2447	CC,CG,GG		41.8409,34.063,39.288	,	136/498,	42525132	4867,7521	2033	4161	6194	SO:0001819	synonymous_variant	1565	exon3			GGTGGAGACGGAG	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.408C>G	22.37:g.42525132G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	72	23	0.319444	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																			G|0.414;C|0.586	0.586	strong		0.687	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
PKP3	11187	hgsc.bcm.edu	37	11	403980	403980	+	Silent	SNP	G	G	A	rs11748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	51	35	0.686275	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	
SLC6A5	9152	hgsc.bcm.edu	37	11	20623023	20623023	+	Silent	SNP	C	C	T	rs2241941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	26	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	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	
ME3	10873	hgsc.bcm.edu	37	11	86159223	86159223	+	Silent	SNP	C	C	T	rs34662182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:86159223C>T	ENST00000393324.3	-	10	1459	c.1206G>A	c.(1204-1206)gtG>gtA	p.V402V	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Silent_p.V402V|ME3_ENST00000543262.1_Silent_p.V402V	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	402					aerobic respiration (GO:0009060)|malate metabolic process (GO:0006108)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|pyruvate metabolic process (GO:0006090)	mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|skin(3)|stomach(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)				CCAGCCTCACCACCTCCTCCA	0.552													C|||	180	0.0359425	0.003	0.0591	5008	,	,		18896	0.001		0.0855	False		,,,				2504	0.0491				p.V402V		Atlas-SNP	.											ME3,NS,carcinoma,0,1	ME3	70	1	0			c.G1206A						PASS	.	C	,,	68,4336	62.3+/-99.4	1,66,2135	149.0	106.0	121.0		1206,1206,1206	3.7	1.0	11	dbSNP_126	121	684,7914	170.4+/-221.6	23,638,3638	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	24,704,5773	TT,TC,CC		7.9553,1.5441,5.7837	,,	402/605,402/605,402/605	86159223	752,12250	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon11			CCTCACCACCTCC	X79440	CCDS8277.1	11q14.2	2012-09-20			ENSG00000151376	ENSG00000151376	1.1.1.40		6985	protein-coding gene	gene with protein product		604626				7818469	Standard	NM_001161586		Approved		uc001pbz.3	Q16798	OTTHUMG00000167217	ENST00000393324.3:c.1206G>A	11.37:g.86159223C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	81	48	0.592593	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			C|0.946;T|0.054	0.054	strong		0.552	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
SMARCA4	6597	hgsc.bcm.edu	37	19	11105608	11105608	+	Silent	SNP	T	T	C	rs7935	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11105608T>C	ENST00000429416.3	+	10	1805	c.1524T>C	c.(1522-1524)caT>caC	p.H508H	SMARCA4_ENST00000358026.2_Silent_p.H508H|SMARCA4_ENST00000589677.1_Silent_p.H508H|SMARCA4_ENST00000590574.1_Silent_p.H508H|SMARCA4_ENST00000444061.3_Silent_p.H508H|SMARCA4_ENST00000413806.3_Silent_p.H508H|SMARCA4_ENST00000541122.2_Silent_p.H508H|SMARCA4_ENST00000344626.4_Silent_p.H508H|SMARCA4_ENST00000450717.3_Silent_p.H508H	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	508	HSA. {ECO:0000255|PROSITE- ProRule:PRU00549}.				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)				CCACGTACCATGCCAACACGG	0.537			"""F, N, Mis"""		NSCLC								C|||	1560	0.311502	0.3109	0.2133	5008	,	,		19701	0.2639		0.3519	False		,,,				2504	0.3896				p.H508H		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.T1524C						PASS	.	C	,,,,,,	1338,3068	693.3+/-405.7	203,932,1068	133.0	104.0	114.0		1524,1524,1524,1524,1524,1524,1524	-6.9	0.9	19	dbSNP_52	114	2932,5668	668.8+/-402.6	510,1912,1878	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	,,,,,,	713,2844,2946	CC,CT,TT		34.093,30.3677,32.831	,,,,,,	508/1648,508/1618,508/1617,508/1615,508/1614,508/1680,508/1648	11105608	4270,8736	2203	4300	6503	SO:0001819	synonymous_variant	6597	exon9			GTACCATGCCAAC	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.1524T>C	19.37:g.11105608T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			C|0.324;N|0.001	0.324	strong		0.537	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
FLNB	2317	hgsc.bcm.edu	37	3	58112488	58112488	+	Splice_Site	SNP	C	C	T	rs2362904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000429972.2_Splice_Site_p.P1407P|FLNB_ENST00000493452.1_Splice_Site_p.P1238P|FLNB_ENST00000419752.2_Splice_Site_p.P1238P|FLNB_ENST00000358537.3_Splice_Site_p.P1407P|FLNB_ENST00000357272.4_Splice_Site_p.P1407P|FLNB_ENST00000348383.5_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	111	0	0		WXS	Illumina HiSeq	Phase_I	112	40	0.357143	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
CHAMP1	283489	hgsc.bcm.edu	37	13	115090193	115090193	+	Silent	SNP	G	G	A	rs3813133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115090193G>A	ENST00000361283.1	+	3	1185	c.876G>A	c.(874-876)ccG>ccA	p.P292P		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	292	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CTTGGAAGCCGTTCCCTGCTG	0.612													A|||	603	0.120407	0.1452	0.1427	5008	,	,		17573	0.1062		0.0775	False		,,,				2504	0.1299				p.P292P		Atlas-SNP	.											.	.	.	.	0			c.G876A						PASS	.	A	,,	511,3895	776.6+/-414.2	29,453,1721	51.0	59.0	56.0		876,876,876	-1.7	0.9	13	dbSNP_107	56	572,8028	792.9+/-407.5	21,530,3749	yes	coding-synonymous,coding-synonymous,coding-synonymous	ZNF828	NM_001164144.1,NM_001164145.1,NM_032436.2	,,	50,983,5470	AA,AG,GG		6.6512,11.5978,8.3269	,,	292/813,292/813,292/813	115090193	1083,11923	2203	4300	6503	SO:0001819	synonymous_variant	283489	exon3			GAAGCCGTTCCCT	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.876G>A	13.37:g.115090193G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	41	0.672131	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	37	CCDS9545.1																																																																																			G|0.893;A|0.107	0.107	strong		0.612	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
GPATCH8	23131	hgsc.bcm.edu	37	17	42475983	42475983	+	Silent	SNP	G	G	C	rs936019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:42475983G>C	ENST00000591680.1	-	8	3492	c.3462C>G	c.(3460-3462)acC>acG	p.T1154T	GPATCH8_ENST00000434000.1_Silent_p.T1076T	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1154							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TGGGCTTTCGGGTAGCTGGGA	0.562													G|||	2462	0.491613	0.4009	0.5937	5008	,	,		18050	0.497		0.6014	False		,,,				2504	0.4233				p.T1154T		Atlas-SNP	.											GPATCH8,NS,adenoma,0,1	GPATCH8	114	1	0			c.C3462G						PASS	.	G		1816,2588	505.6+/-366.2	383,1050,769	134.0	140.0	138.0		3462	1.7	1.0	17	dbSNP_86	138	5354,3246	638.5+/-399.3	1659,2036,605	no	coding-synonymous	GPATCH8	NM_001002909.2		2042,3086,1374	CC,CG,GG		37.7442,41.2352,44.8631		1154/1503	42475983	7170,5834	2202	4300	6502	SO:0001819	synonymous_variant	23131	exon8			CTTTCGGGTAGCT	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.3462C>G	17.37:g.42475983G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_001002909	B9EGP9|O60300|Q8TB99	Silent	SNP	ENST00000591680.1	37	CCDS32666.1																																																																																			G|0.435;C|0.565	0.565	strong		0.562	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
DDX11	1663	hgsc.bcm.edu	37	12	31242869	31242869	+	Silent	SNP	G	G	A	rs201738430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:31242869G>A	ENST00000407793.2	+	9	1181	c.930G>A	c.(928-930)gaG>gaA	p.E310E	DDX11_ENST00000545668.1_Silent_p.E310E|DDX11_ENST00000228264.6_Silent_p.E284E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Silent_p.E310E|DDX11_ENST00000350437.4_Silent_p.E310E	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	310	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)					GGAGGCAGGAGAAGCAGGCAG	0.582										Multiple Myeloma(12;0.14)																											p.E310E		Atlas-SNP	.											DDX11_ENST00000407793,NS,carcinoma,0,16	DDX11	188	16	0			c.G930A						scavenged	.						4.0	6.0	6.0					12																	31242869		2012	4018	6030	SO:0001819	synonymous_variant	1663	exon9			GCAGGAGAAGCAG	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.930G>A	12.37:g.31242869G>A		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	421	124	0.294537	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			G|0.889;A|0.111	0.111	strong		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
C8orf44	56260	hgsc.bcm.edu	37	8	67592152	67592152	+	Missense_Mutation	SNP	T	T	C	rs1057463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:67592152T>C	ENST00000519561.1	+	3	594	c.443T>C	c.(442-444)tTc>tCc	p.F148S	C8orf44-SGK3_ENST00000519289.1_5'UTR|C8orf44-SGK3_ENST00000520044.1_3'UTR|C8orf44_ENST00000518860.1_3'UTR|C8orf44_ENST00000390159.3_Missense_Mutation_p.F148S	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	48	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	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	
TREX1	11277	hgsc.bcm.edu	37	3	48508585	48508585	+	Silent	SNP	C	C	T	rs11797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48508585C>T	ENST00000422277.2	+	1	1357	c.696C>T	c.(694-696)taC>taT	p.Y232Y	SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000444177.1_Silent_p.Y167Y|TREX1_ENST00000492235.1_3'UTR|TREX1_ENST00000436480.2_Silent_p.Y177Y|TREX1_ENST00000433541.1_Silent_p.Y38Y|TREX1_ENST00000296443.9_Silent_p.Y177Y|TREX1_ENST00000456089.1_Silent_p.Y38Y	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	232					cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGAAGAGCTACAGCCTAGGCA	0.607													C|||	1569	0.313299	0.2383	0.2853	5008	,	,		21572	0.3125		0.4433	False		,,,				2504	0.3016				p.Y232Y		Atlas-SNP	.											.	TREX1	17	.	0			c.C696T						PASS	.	C	,	1210,3196	421.9+/-339.5	170,870,1163	62.0	63.0	63.0		696,531	2.7	1.0	3	dbSNP_52	63	3903,4697	544.3+/-384.6	894,2115,1291	no	coding-synonymous,coding-synonymous	TREX1	NM_016381.3,NM_033629.2	,	1064,2985,2454	TT,TC,CC		45.3837,27.4626,39.3126	,	232/370,177/315	48508585	5113,7893	2203	4300	6503	SO:0001819	synonymous_variant	11277	exon1			GAGCTACAGCCTA	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"""Aicardi-Goutieres syndrome 1"""	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.696C>T	3.37:g.48508585C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	93	0.615894	NM_016381	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Silent	SNP	ENST00000422277.2	37	CCDS43086.1																																																																																			C|0.642;T|0.358	0.358	strong		0.607	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381	
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12209752T>C	ENST00000491614.1	-	10	1004	c.609A>G	c.(607-609)gcA>gcG	p.A203A	NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000537776.1_Silent_p.A203A|NUDT5_ENST00000378937.3_Silent_p.A216A|SEC61A2_ENST00000304267.8_Intron|SEC61A2_ENST00000495368.1_3'UTR			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	203					D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CATGTTTCAGTGCTAGAGCGT	0.448													C|||	2315	0.46226	0.4251	0.5245	5008	,	,		20633	0.5575		0.4821	False		,,,				2504	0.3497				p.A203A		Atlas-SNP	.											.	NUDT5	10	.	0			c.A609G						PASS	.	C	,	1985,2421	615.9+/-392.7	459,1067,677	163.0	148.0	153.0		,609	-10.3	0.0	10	dbSNP_52	153	4282,4318	578.9+/-390.8	1067,2148,1085	no	intron,coding-synonymous	NUDT5,SEC61A2	NM_001142627.1,NM_014142.2	,	1526,3215,1762	CC,CT,TT		49.7907,45.0522,48.1855	,	,203/220	12209752	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	11164	exon10			TTTCAGTGCTAGA	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.609A>G	10.37:g.12209752T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	37	CCDS7089.1																																																																																			T|0.523;C|0.477	0.477	strong		0.448	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
C1orf112	55732	hgsc.bcm.edu	37	1	169773317	169773317	+	Silent	SNP	G	G	A	rs11590604	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169773317G>A	ENST00000286031.6	+	6	1114	c.414G>A	c.(412-414)ctG>ctA	p.L138L	C1orf112_ENST00000413811.2_Silent_p.L109L|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.L138L|C1orf112_ENST00000456684.1_Silent_p.L196L	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	138								p.L138L(1)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TAATGGAACTGCTGGACATGG	0.388													G|||	732	0.146166	0.087	0.2378	5008	,	,		17145	0.1677		0.1113	False		,,,				2504	0.1748				p.L138L		Atlas-SNP	.											C1orf112,NS,carcinoma,0,1	C1orf112	74	1	1	Substitution - coding silent(1)	stomach(1)	c.G414A						PASS	.	G		358,4048	184.0+/-211.4	17,324,1862	136.0	133.0	134.0		414	-2.3	0.9	1	dbSNP_120	134	835,7765	192.7+/-238.6	37,761,3502	no	coding-synonymous	C1orf112	NM_018186.2		54,1085,5364	AA,AG,GG		9.7093,8.1253,9.1727		138/854	169773317	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	55732	exon6			GGAACTGCTGGAC	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.414G>A	1.37:g.169773317G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	202	120	0.594059	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			G|0.890;A|0.110	0.110	strong		0.388	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
ABT1	29777	hgsc.bcm.edu	37	6	26598188	26598188	+	Silent	SNP	A	A	G	rs3800303	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26598188A>G	ENST00000274849.1	+	2	319	c.288A>G	c.(286-288)ggA>ggG	p.G96G		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	96	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGCCGGAGGAAAAAAGCGGT	0.587													a|||	2585	0.516174	0.4917	0.5144	5008	,	,		18490	0.6667		0.3787	False		,,,				2504	0.5368				p.G96G		Atlas-SNP	.											.	ABT1	39	.	0			c.A288G						PASS	.	G		2101,2305	554.9+/-379.1	499,1103,601	50.0	47.0	48.0		288	-10.5	0.5	6	dbSNP_107	48	3611,4989	499.0+/-374.9	794,2023,1483	no	coding-synonymous	ABT1	NM_013375.3		1293,3126,2084	GG,GA,AA		41.9884,47.685,43.9182		96/273	26598188	5712,7294	2203	4300	6503	SO:0001819	synonymous_variant	29777	exon2			CGGAGGAAAAAAG	AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.288A>G	6.37:g.26598188A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_013375		Silent	SNP	ENST00000274849.1	37	CCDS4616.1																																																																																			A|0.536;G|0.464	0.464	strong		0.587	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1		
POLA2	23649	hgsc.bcm.edu	37	11	65064690	65064690	+	Missense_Mutation	SNP	G	G	A	rs487989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65064690G>A	ENST00000265465.3	+	18	2278	c.1747G>A	c.(1747-1749)Ggg>Agg	p.G583R	POLA2_ENST00000534785.1_3'UTR	NM_002689.2	NP_002680.2	Q14181	DPOA2_HUMAN	polymerase (DNA directed), alpha 2, accessory subunit	583			G -> R (in dbSNP:rs487989).		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)|protein import into nucleus, translocation (GO:0000060)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|protein heterodimerization activity (GO:0046982)			endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	11					Dacarbazine(DB00851)	GGCAGCGGACGGGGCAGAGAG	0.612													G|||	752	0.15016	0.1846	0.1326	5008	,	,		17961	0.0645		0.1382	False		,,,				2504	0.2168				p.G583R		Atlas-SNP	.											.	POLA2	75	.	0			c.G1747A						PASS	.	G	ARG/GLY	769,3633	311.9+/-292.3	56,657,1488	71.0	74.0	73.0		1747	-0.8	0.0	11	dbSNP_83	73	1218,7376	246.4+/-274.8	80,1058,3159	yes	missense	POLA2	NM_002689.2	125	136,1715,4647	AA,AG,GG		14.1727,17.4693,15.2893	benign	583/599	65064690	1987,11009	2201	4297	6498	SO:0001583	missense	23649	exon18			GCGGACGGGGCAG	BC002990	CCDS8098.1	11q13	2012-05-18	2012-05-18		ENSG00000014138	ENSG00000014138		"""DNA polymerases"""	30073	protein-coding gene	gene with protein product	"""DNA polymerase alpha subunit B"", ""DNA polymerase alpha 70 kDa subunit"""		"""polymerase (DNA directed), alpha 2 (70kD subunit)"""			8223465, 11433027	Standard	NM_002689		Approved	FLJ21662	uc001odj.3	Q14181	OTTHUMG00000165951	ENST00000265465.3:c.1747G>A	11.37:g.65064690G>A	ENSP00000265465:p.Gly583Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_002689	B4DNB4|Q9BPV3	Missense_Mutation	SNP	ENST00000265465.3	37	CCDS8098.1	268	0.1227106227106227	73	0.1483739837398374	54	0.14917127071823205	44	0.07692307692307693	97	0.1279683377308707	G	12.79	2.042383	0.35989	0.174693	0.141727	ENSG00000014138	ENST00000265465	T	0.23552	1.9	4.94	-0.784	0.10954	.	1.136850	0.06344	N	0.708516	T	0.00039	0.0001	L	0.59436	1.845	0.80722	P	0.0	P	0.34892	0.474	B	0.22386	0.039	T	0.21759	-1.0236	9	0.21540	T	0.41	-0.4999	1.0441	0.01565	0.1687:0.262:0.2986:0.2708	rs487989;rs1211593;rs3881265;rs57424239;rs487989	583	Q14181	DPOA2_HUMAN	R	583	ENSP00000265465:G583R	ENSP00000265465:G583R	G	+	1	0	POLA2	64821266	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.736000	0.26130	0.040000	0.15660	0.655000	0.94253	GGG	A|0.140;C|0.005	0.140	strong		0.612	POLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387223.1	NM_002689	
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:31250830C>G	ENST00000407793.2	+	18	2025	c.1774C>G	c.(1774-1776)Cag>Gag	p.Q592E	DDX11_ENST00000539673.1_3'UTR|DDX11_ENST00000545668.1_Missense_Mutation_p.Q592E|DDX11_ENST00000228264.6_Missense_Mutation_p.Q566E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.Q592E|DDX11_ENST00000350437.4_Missense_Mutation_p.Q592E	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	592					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)	p.Q592E(1)		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)					CAGCCTCAGTCAGAGCACCCT	0.582										Multiple Myeloma(12;0.14)																											p.Q592E		Atlas-SNP	.											DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	1	Substitution - Missense(1)	skin(1)	c.C1774G						scavenged	.						81.0	80.0	81.0					12																	31250830		2203	4300	6503	SO:0001583	missense	1663	exon18			CTCAGTCAGAGCA	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.1774C>G	12.37:g.31250830C>G	ENSP00000384703:p.Gln592Glu	Somatic	137	4	0.0291971		WXS	Illumina HiSeq	Phase_I	140	16	0.114286	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	C	5.933	0.356089	0.11239	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	3.23	3.23	0.37069	.	0.250227	0.40728	N	0.001040	T	0.21550	0.0519	L	0.54965	1.715	0.80722	D	1	B;B;B;B	0.22909	0.048;0.077;0.023;0.048	B;B;B;B	0.18871	0.023;0.017;0.015;0.023	T	0.04481	-1.0948	10	0.11794	T	0.64	.	12.0234	0.53356	0.0:1.0:0.0:0.0	rs2911826	566;592;592;592	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	E	592;592;317;566;592;592	ENSP00000443426:Q592E;ENSP00000384703:Q592E;ENSP00000228264:Q566E;ENSP00000440402:Q592E;ENSP00000309965:Q592E	ENSP00000228264:Q566E	Q	+	1	0	DDX11	31142097	1.000000	0.71417	0.998000	0.56505	0.511000	0.34104	3.091000	0.50199	1.632000	0.50472	0.505000	0.49811	CAG	.	.	weak		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
MUC4	4585	hgsc.bcm.edu	37	3	195513365	195513365	+	Missense_Mutation	SNP	G	G	A	rs62282501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195513365G>A	ENST00000463781.3	-	2	5545	c.5086C>T	c.(5086-5088)Cgt>Tgt	p.R1696C	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R1696C	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)		ACAGGAAGACGGGTGGTGTCA	0.602													.|||	681	0.135982	0.118	0.1758	5008	,	,		25005	0.0476		0.2127	False		,,,				2504	0.1442				p.R1696C		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5086T						PASS	.						40.0	43.0	42.0					3																	195513365		689	1582	2271	SO:0001583	missense	4585	exon2			GAAGACGGGTGGT	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.5086C>T	3.37:g.195513365G>A	ENSP00000417498:p.Arg1696Cys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	317	107	0.337539	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	273	0.125	36	0.07317073170731707	56	0.15469613259668508	36	0.06293706293706294	145	0.19129287598944592	-	4.772	0.143509	0.09134	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.43	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.01281	0.0	T	0.35674	-0.9779	6	.	.	.	.	2.8509	0.05558	3.0E-4:2.0E-4:0.5024:0.497	.	1696	E7ESK3	.	C	1696	ENSP00000417498:R1696C;ENSP00000420243:R1696C	.	R	-	1	0	MUC4	196997760	0.002000	0.14202	0.006000	0.13384	0.006000	0.05464	0.009000	0.13219	0.088000	0.17205	0.089000	0.15464	CGT	G|0.863;A|0.137	0.137	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AQP12B	653437	hgsc.bcm.edu	37	2	241621869	241621869	+	Missense_Mutation	SNP	G	G	A	rs74882485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241621869G>A	ENST00000407834.3	-	1	448	c.386C>T	c.(385-387)aCg>aTg	p.T129M		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	117						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)		GCAGAGGCGCGTCAGGGTGCA	0.697																																					p.T129M		Atlas-SNP	.											AQP12B,rectum,carcinoma,0,2	AQP12B	33	2	0			c.C386T						scavenged	.						24.0	24.0	24.0					2																	241621869		2196	4279	6475	SO:0001583	missense	653437	exon1			AGGCGCGTCAGGG	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.386C>T	2.37:g.241621869G>A	ENSP00000384894:p.Thr129Met	Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	69	23	0.333333	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	.	.	.	.	.	.	.	.	.	.	.	7.337	0.620131	0.14193	.	.	ENSG00000185176	ENST00000407834	T	0.15017	2.46	2.84	1.94	0.25998	.	0.293024	0.38492	N	0.001671	T	0.26810	0.0656	.	.	.	0.80722	P	0.0	D	0.71674	0.998	P	0.61592	0.891	T	0.30995	-0.9959	8	0.28530	T	0.3	-0.0254	8.3053	0.32038	0.1286:0.0:0.8714:0.0	.	129	A6NM10-2	.	M	129	ENSP00000384894:T129M	ENSP00000384894:T129M	T	-	2	0	AQP12B	241270542	0.997000	0.39634	0.002000	0.10522	0.132000	0.20833	5.268000	0.65536	0.748000	0.32831	0.473000	0.43528	ACG	G|0.972;A|0.028	0.028	strong		0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
CNTN3	5067	hgsc.bcm.edu	37	3	74344356	74344356	+	Silent	SNP	T	T	G	rs10490832	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:74344356T>G	ENST00000263665.6	-	18	2460	c.2433A>C	c.(2431-2433)gcA>gcC	p.A811A		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	811	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)		ATAGGCTATTTGCAGAGACTT	0.388													T|||	445	0.0888578	0.0068	0.0706	5008	,	,		18103	0.0288		0.1421	False		,,,				2504	0.2198				p.A811A		Atlas-SNP	.											.	CNTN3	174	.	0			c.A2433C						PASS	.	T		139,4267	98.0+/-136.7	4,131,2068	100.0	93.0	95.0		2433	-2.5	0.2	3	dbSNP_119	95	1410,7190	270.5+/-289.0	131,1148,3021	yes	coding-synonymous	CNTN3	NM_020872.1		135,1279,5089	GG,GT,TT		16.3953,3.1548,11.9099		811/1029	74344356	1549,11457	2203	4300	6503	SO:0001819	synonymous_variant	5067	exon18			GCTATTTGCAGAG	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.2433A>C	3.37:g.74344356T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_020872	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																			T|0.912;G|0.088	0.088	strong		0.388	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
SSPO	23145	hgsc.bcm.edu	37	7	149481994	149481994	+	RNA	SNP	G	G	T	rs73168055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:149481994G>T	ENST00000378016.2	+	0	2782							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CAGGGAGCTTGTCTATGCCCC	0.617													G|||	106	0.0211661	0.0053	0.0317	5008	,	,		20160	0.0		0.0626	False		,,,				2504	0.0143				p.V928F		Atlas-SNP	.											.	.	.	.	0			c.G2782T						PASS	.	G		37,4031		0,37,1997	51.0	55.0	54.0		2786	0.7	0.6	7	dbSNP_130	54	473,7875		10,453,3711	yes	coding-notMod3	SSPO	NM_198455.2		10,490,5708	TT,TG,GG		5.666,0.9095,4.1076			149481994	510,11906	2034	4174	6208			23145	exon20			GAGCTTGTCTATG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149481994G>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.966;T|0.034	0.034	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GLDN	342035	hgsc.bcm.edu	37	15	51689772	51689772	+	Missense_Mutation	SNP	G	G	A	rs17648128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	128	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	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	
MASP2	10747	hgsc.bcm.edu	37	1	11090897	11090897	+	Missense_Mutation	SNP	A	A	G	rs2273346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11090897A>G	ENST00000400897.3	-	9	1145	c.1130T>C	c.(1129-1131)gTg>gCg	p.V377A	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	377	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> A (associated with reduced MASP2 levels in plasma; dbSNP:rs2273346). {ECO:0000269|PubMed:11426320, ECO:0000269|PubMed:17252003}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		GATGTACTCCACTCGGCCACT	0.463													A|||	593	0.118411	0.171	0.0461	5008	,	,		19371	0.1984		0.0199	False		,,,				2504	0.1176				p.V377A	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.T1130C	GRCh37	CM073193	MASP2	M	rs2273346	PASS	.	A	ALA/VAL	564,3842	253.7+/-259.5	35,494,1674	97.0	82.0	87.0		1130	2.8	0.0	1	dbSNP_100	87	156,8444	74.8+/-137.4	0,156,4144	yes	missense	MASP2	NM_006610.3	64	35,650,5818	GG,GA,AA		1.814,12.8007,5.5359	possibly-damaging	377/687	11090897	720,12286	2203	4300	6503	SO:0001583	missense	10747	exon9			TACTCCACTCGGC	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1130T>C	1.37:g.11090897A>G	ENSP00000383690:p.Val377Ala	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	196	0.08974358974358974	66	0.13414634146341464	18	0.049723756906077346	101	0.17657342657342656	11	0.014511873350923483	A	7.202	0.593678	0.13875	0.128007	0.01814	ENSG00000009724	ENST00000400897	T	0.67345	-0.26	5.38	2.81	0.32909	Complement control module (2);Sushi/SCR/CCP (3);	0.493902	0.18977	N	0.125992	T	0.00241	0.0007	M	0.74389	2.26	0.50039	P	1.5100000000001224E-4	B	0.09022	0.002	B	0.22386	0.039	T	0.14172	-1.0482	9	0.62326	D	0.03	.	8.3873	0.32508	0.8296:0.0:0.1704:0.0	rs2273346;rs9430345;rs52825556;rs57237765;rs2273346	377	O00187	MASP2_HUMAN	A	377	ENSP00000383690:V377A	ENSP00000383690:V377A	V	-	2	0	MASP2	11013484	0.002000	0.14202	0.001000	0.08648	0.021000	0.10359	1.715000	0.37971	0.269000	0.21961	-0.375000	0.07067	GTG	A|0.916;G|0.084	0.084	strong		0.463	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
BLK	640	hgsc.bcm.edu	37	8	11406593	11406593	+	Silent	SNP	T	T	C	rs3816668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11406593T>C	ENST00000259089.4	+	5	922	c.330T>C	c.(328-330)agT>agC	p.S110S	BLK_ENST00000529894.1_Silent_p.S39S	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	110	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		ATGTGCCCAGTAACTTTGTGG	0.577													C|||	2088	0.416933	0.5424	0.3905	5008	,	,		19482	0.0784		0.5666	False		,,,				2504	0.4611				p.S110S		Atlas-SNP	.											.	BLK	78	.	0			c.T330C						PASS	.	C		2212,2194	574.0+/-383.7	566,1080,557	114.0	91.0	99.0		330	3.2	1.0	8	dbSNP_107	99	4417,4183	556.0+/-386.8	1108,2201,991	no	coding-synonymous	BLK	NM_001715.2		1674,3281,1548	CC,CT,TT		48.6395,49.7957,49.0312		110/506	11406593	6629,6377	2203	4300	6503	SO:0001819	synonymous_variant	640	exon5			GCCCAGTAACTTT	BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.330T>C	8.37:g.11406593T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_001715	Q16291|Q96IN1	Silent	SNP	ENST00000259089.4	37	CCDS5982.1																																																																																			T|0.538;C|0.462	0.462	strong		0.577	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
TBC1D2	55357	hgsc.bcm.edu	37	9	100995721	100995721	+	Missense_Mutation	SNP	A	A	G	rs879369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100995721A>G	ENST00000375064.1	-	4	796	c.758T>C	c.(757-759)tTg>tCg	p.L253S	TBC1D2_ENST00000342112.5_Missense_Mutation_p.L35S|TBC1D2_ENST00000375066.5_Missense_Mutation_p.L253S	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	253			L -> S (in dbSNP:rs879369). {ECO:0000269|PubMed:11785977, ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GTCAGAGGCCAAGGGCTGCTC	0.622													G|||	2065	0.41234	0.8011	0.3372	5008	,	,		19660	0.1756		0.339	False		,,,				2504	0.2597				p.L253S		Atlas-SNP	.											.	TBC1D2	70	.	0			c.T758C						PASS	.	G	SER/LEU	3240,1166	410.4+/-335.4	1196,848,159	104.0	93.0	97.0		758	-6.0	0.0	9	dbSNP_86	97	2730,5870	681.8+/-403.7	425,1880,1995	yes	missense	TBC1D2	NM_018421.3	145	1621,2728,2154	GG,GA,AA		31.7442,26.4639,45.9019	benign	253/918	100995721	5970,7036	2203	4300	6503	SO:0001583	missense	55357	exon4			GAGGCCAAGGGCT	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.758T>C	9.37:g.100995721A>G	ENSP00000364205:p.Leu253Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		882	0.40384615384615385	382	0.7764227642276422	130	0.35911602209944754	99	0.17307692307692307	271	0.3575197889182058	G	0.006	-2.118793	0.00346	0.735361	0.317442	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112	T;T;T	0.13196	2.61;3.15;2.61	4.95	-5.96	0.02234	.	1.754710	0.02901	N	0.135376	T	0.00012	0.0000	L	0.35723	1.085	0.80722	P	0.0	B;B	0.11235	0.003;0.004	B;B	0.06405	0.001;0.002	T	0.34104	-0.9842	9	0.18710	T	0.47	.	15.9903	0.80199	0.7218:0.0:0.2782:0.0	rs879369;rs17761260;rs61283010;rs879369	253;253	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	S	253;253;35	ENSP00000364205:L253S;ENSP00000364207:L253S;ENSP00000341567:L35S	ENSP00000341567:L35S	L	-	2	0	TBC1D2	100035542	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.964000	0.01512	-2.065000	0.00887	-2.930000	0.00088	TTG	T|0.000;G|0.439;C|0.000;A|0.561	0.439	strong		0.622	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
ARGFX	503582	hgsc.bcm.edu	37	3	121304933	121304933	+	Missense_Mutation	SNP	G	G	A	rs9813391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121304933G>A	ENST00000334384.3	+	4	444	c.434G>A	c.(433-435)cGa>cAa	p.R145Q		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	145			R -> Q (in dbSNP:rs9813391).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		GCAAAGCAACGAAACCAGATC	0.502													G|||	857	0.171126	0.1127	0.4438	5008	,	,		19879	0.0506		0.2545	False		,,,				2504	0.0951				p.R145Q		Atlas-SNP	.											.	ARGFX	36	.	0			c.G434A						PASS	.	G	GLN/ARG	613,3793	263.1+/-265.3	38,537,1628	123.0	113.0	116.0		434	-0.9	0.0	3	dbSNP_119	116	2371,6229	390.0+/-343.1	324,1723,2253	yes	missense	ARGFX	NM_001012659.1	43	362,2260,3881	AA,AG,GG		27.5698,13.9128,22.9433	benign	145/316	121304933	2984,10022	2203	4300	6503	SO:0001583	missense	503582	exon5			AGCAACGAAACCA		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"""Homeoboxes / PRD class"""	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.434G>A	3.37:g.121304933G>A	ENSP00000335578:p.Arg145Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001012659		Missense_Mutation	SNP	ENST00000334384.3	37	CCDS33834.1	440	0.20146520146520147	64	0.13008130081300814	142	0.39226519337016574	30	0.05244755244755245	204	0.2691292875989446	G	0.150	-1.091973	0.01858	0.139128	0.275698	ENSG00000186103	ENST00000334384	D	0.88354	-2.37	3.32	-0.937	0.10415	.	1.246050	0.06010	N	0.649304	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.16396	0.017	B	0.04013	0.001	T	0.04165	-1.0972	9	0.10111	T	0.7	-0.0198	2.7093	0.05170	0.1684:0.3796:0.344:0.108	rs9813391;rs17741793;rs52830852;rs9813391	145	A6NJG6	ARGFX_HUMAN	Q	145	ENSP00000335578:R145Q	ENSP00000335578:R145Q	R	+	2	0	ARGFX	122787623	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.293000	0.08320	-0.190000	0.10465	-0.270000	0.10280	CGA	G|0.786;A|0.214	0.214	strong		0.502	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659	
MERTK	10461	hgsc.bcm.edu	37	2	112686988	112686988	+	Missense_Mutation	SNP	G	G	A	rs13027171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:112686988G>A	ENST00000295408.4	+	2	610	c.353G>A	c.(352-354)aGt>aAt	p.S118N	MERTK_ENST00000409780.1_Intron|MERTK_ENST00000421804.2_Missense_Mutation_p.S118N|RN7SL297P_ENST00000483161.2_RNA			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	118	Ig-like C2-type 1.		S -> N (in dbSNP:rs13027171). {ECO:0000269|PubMed:11062461, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8086340}.		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						TGCTCAATCAGTGTACCTAAT	0.403													G|||	842	0.168131	0.0219	0.1844	5008	,	,		15437	0.1726		0.2853	False		,,,				2504	0.229				p.S118N		Atlas-SNP	.											.	MERTK	112	.	0			c.G353A						PASS	.	G	ASN/SER	307,4099	165.4+/-196.9	12,283,1908	119.0	109.0	112.0		353	-4.0	0.0	2	dbSNP_121	112	2579,6021	418.8+/-352.9	387,1805,2108	yes	missense	MERTK	NM_006343.2	46	399,2088,4016	AA,AG,GG		29.9884,6.9678,22.1898	benign	118/1000	112686988	2886,10120	2203	4300	6503	SO:0001583	missense	10461	exon2			CAATCAGTGTACC	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.353G>A	2.37:g.112686988G>A	ENSP00000295408:p.Ser118Asn	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	230	121	0.526087	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	350	0.16025641025641027	10	0.02032520325203252	80	0.22099447513812154	69	0.12062937062937062	191	0.2519788918205805	G	1.417	-0.574024	0.03882	0.069678	0.299884	ENSG00000153208	ENST00000295408;ENST00000421804	T;T	0.68624	-0.34;-0.34	4.13	-3.98	0.04082	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.749006	0.10916	N	0.620055	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.21211	-1.0252	9	0.21540	T	0.41	-3.733	11.6222	0.51124	0.4288:0.0:0.5712:0.0	rs13027171;rs28381988;rs52818700;rs59349003;rs13027171	118	Q12866	MERTK_HUMAN	N	118	ENSP00000295408:S118N;ENSP00000389152:S118N	ENSP00000295408:S118N	S	+	2	0	MERTK	112403459	0.003000	0.15002	0.020000	0.16555	0.460000	0.32559	-0.287000	0.08388	-0.649000	0.05430	-0.484000	0.04775	AGT	G|0.804;A|0.196	0.196	strong		0.403	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
FBXW5	54461	hgsc.bcm.edu	37	9	139835558	139835558	+	Missense_Mutation	SNP	C	C	T	rs45559439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139835558C>T	ENST00000325285.3	-	9	1602	c.1523G>A	c.(1522-1524)cGg>cAg	p.R508Q	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	508				R -> Q (in Ref. 5; BAD92963). {ECO:0000305}.	centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		ATCCTCGTGCCGCAGCCTGGC	0.677													C|||	49	0.00978435	0.0	0.0245	5008	,	,		15182	0.0		0.0298	False		,,,				2504	0.002				p.R508Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1523A						PASS	.	C	GLN/ARG	22,4320		0,22,2149	66.0	61.0	62.0		1523	2.2	1.0	9	dbSNP_127	62	215,8361		3,209,4076	yes	missense	FBXW5	NM_018998.2	43	3,231,6225	TT,TC,CC		2.507,0.5067,1.8346	benign	508/567	139835558	237,12681	2171	4288	6459	SO:0001583	missense	54461	exon9			TCGTGCCGCAGCC	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1523G>A	9.37:g.139835558C>T	ENSP00000313034:p.Arg508Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	C	10.25	1.298726	0.23650	0.005067	0.02507	ENSG00000159069	ENST00000325285	T	0.65549	-0.16	4.05	2.21	0.28008	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1);	0.432182	0.22954	N	0.053633	T	0.11922	0.0290	N	0.04705	-0.18	0.35200	D	0.774171	B	0.06786	0.001	B	0.04013	0.001	T	0.09122	-1.0689	10	0.09338	T	0.73	-16.5307	4.2639	0.10754	0.0:0.5978:0.19:0.2122	rs45559439	508	Q969U6	FBXW5_HUMAN	Q	508	ENSP00000313034:R508Q	ENSP00000313034:R508Q	R	-	2	0	FBXW5	138955379	0.994000	0.37717	1.000000	0.80357	0.857000	0.48899	1.227000	0.32576	0.403000	0.25479	-0.265000	0.10407	CGG	C|0.985;T|0.015	0.015	strong		0.677	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
SI	6476	hgsc.bcm.edu	37	3	164783165	164783165	+	Missense_Mutation	SNP	T	T	C	rs9283633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	138	0	0		WXS	Illumina HiSeq	Phase_I	186	104	0.55914	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	
KRT40	125115	hgsc.bcm.edu	37	17	39137104	39137104	+	Missense_Mutation	SNP	A	A	G	rs9908389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	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	
MUC4	4585	hgsc.bcm.edu	37	3	195517124	195517124	+	Silent	SNP	G	G	A	rs1806440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195517124G>A	ENST00000463781.3	-	2	1786	c.1327C>T	c.(1327-1329)Cta>Tta	p.L443L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.L443L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448					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)		TTTGGAGGTAGAGAACTGGGG	0.493													N|||	637	0.127196	0.1679	0.0951	5008	,	,		19914	0.0456		0.173	False		,,,				2504	0.1319				p.L443L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C1327T						PASS	.		,,	554,3356		46,462,1447	218.0	214.0	215.0		,1327,	-0.1	0.0	3	dbSNP_92	215	1424,6882		124,1176,2853	yes	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	170,1638,4300	AA,AG,GG		17.1442,14.1688,16.1919	,,	,443/5413,	195517124	1978,10238	1955	4153	6108	SO:0001819	synonymous_variant	4585	exon2			GAGGTAGAGAACT	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.1327C>T	3.37:g.195517124G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	198	79	0.39899	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.871;A|0.129	0.129	strong		0.493	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RP1L1	94137	hgsc.bcm.edu	37	8	10470068	10470068	+	Missense_Mutation	SNP	C	C	T	rs74990397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	17	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	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		
UMPS	7372	hgsc.bcm.edu	37	3	124462808	124462808	+	Silent	SNP	C	C	T	rs13146	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124462808C>T	ENST00000232607.2	+	6	1426	c.1320C>T	c.(1318-1320)ggC>ggT	p.G440G	UMPS_ENST00000536109.1_Silent_p.G348G|UMPS_ENST00000538242.1_Silent_p.G262G|UMPS_ENST00000413078.2_Silent_p.G165G	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	440	OMPdecase.				'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	AAGTTATTGGCAAACGAGGTT	0.418													C|||	932	0.186102	0.1505	0.2622	5008	,	,		17453	0.1677		0.1511	False		,,,				2504	0.2352				p.G440G		Atlas-SNP	.											.	UMPS	43	.	0			c.C1320T						PASS	.	C		681,3725	287.2+/-279.2	57,567,1579	152.0	139.0	144.0		1320	-0.3	0.6	3	dbSNP_52	144	1471,7129	280.8+/-294.7	123,1225,2952	no	coding-synonymous	UMPS	NM_000373.3		180,1792,4531	TT,TC,CC		17.1047,15.4562,16.5462		440/481	124462808	2152,10854	2203	4300	6503	SO:0001819	synonymous_variant	7372	exon6			TATTGGCAAACGA		CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"""orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"""	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.1320C>T	3.37:g.124462808C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	152	57	0.375	NM_000373	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	Silent	SNP	ENST00000232607.2	37	CCDS3029.1																																																																																			C|0.830;A|0.001	.	strong		0.418	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373	
OR4D11	219986	hgsc.bcm.edu	37	11	59271637	59271637	+	Missense_Mutation	SNP	T	T	C	rs7120079	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	286	1	0.0034965		WXS	Illumina HiSeq	Phase_I	337	164	0.486647	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	
TM7SF2	7108	hgsc.bcm.edu	37	11	64880743	64880743	+	Missense_Mutation	SNP	C	C	T	rs11539360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64880743C>T	ENST00000279263.7	+	4	518	c.356C>T	c.(355-357)gCg>gTg	p.A119V	AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000531029.1_3'UTR|TM7SF2_ENST00000345348.5_Missense_Mutation_p.A119V|TM7SF2_ENST00000540748.1_Missense_Mutation_p.A3V	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	119			A -> V (in dbSNP:rs11539360).		cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGGATGTCAGCGGGGCTGCCT	0.652											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	140	0.0279553	0.003	0.0389	5008	,	,		15608	0.0655		0.0348	False		,,,				2504	0.0082				p.A119V		Atlas-SNP	.											.	TM7SF2	30	.	0			c.C356T						PASS	.	C	VAL/ALA	24,3984		0,24,1980	20.0	25.0	23.0		356	-5.6	0.0	11	dbSNP_120	23	274,8018		3,268,3875	yes	missense	TM7SF2	NM_003273.2	64	3,292,5855	TT,TC,CC		3.3044,0.5988,2.4228	benign	119/419	64880743	298,12002	2004	4146	6150	SO:0001583	missense	7108	exon4			TGTCAGCGGGGCT	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"""delta(14)-sterol reductase"""	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.356C>T	11.37:g.64880743C>T	ENSP00000279263:p.Ala119Val	Somatic	22	0	0	134	WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	37	CCDS41669.1	74	0.03388278388278388	8	0.016260162601626018	15	0.04143646408839779	21	0.03671328671328671	30	0.0395778364116095	C	8.231	0.804716	0.16467	0.005988	0.033044	ENSG00000149809	ENST00000279263;ENST00000524986;ENST00000540748;ENST00000525385;ENST00000345348;ENST00000529414	D;D;D;D;D;D	0.98075	-4.7;-4.7;-4.66;-4.7;-4.7;-4.7	4.81	-5.63	0.02474	.	1.058010	0.07252	N	0.866091	T	0.77391	0.4123	N	0.16266	0.395	0.09310	N	1	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.13407	0.003;0.005;0.009	T	0.80650	-0.1288	10	0.17369	T	0.5	-8.2347	7.4336	0.27141	0.0:0.1618:0.3499:0.4882	rs11539360	3;119;119	F5GYV3;O76062-2;O76062	.;.;ERG24_HUMAN	V	119;90;3;90;119;119	ENSP00000279263:A119V;ENSP00000435972:A90V;ENSP00000441215:A3V;ENSP00000433325:A90V;ENSP00000329520:A119V;ENSP00000433275:A119V	ENSP00000279263:A119V	A	+	2	0	TM7SF2	64637319	0.000000	0.05858	0.000000	0.03702	0.394000	0.30568	-0.725000	0.04942	-0.920000	0.03799	-1.080000	0.02220	GCG	C|0.967;T|0.033	0.033	strong		0.652	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
ZNF765	91661	hgsc.bcm.edu	37	19	53911510	53911510	+	Silent	SNP	G	G	A	rs8182488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53911510G>A	ENST00000396408.3	+	4	819	c.702G>A	c.(700-702)caG>caA	p.Q234Q	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	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)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		GGAAACATCAGTTAATCCATT	0.383													.|||	1140	0.227636	0.0522	0.3775	5008	,	,		22745	0.1042		0.3201	False		,,,				2504	0.3906				p.Q234Q		Atlas-SNP	.											.	ZNF765	61	.	0			c.G702A						PASS	.	G		420,3980	195.0+/-219.7	24,372,1804	76.0	76.0	76.0		702	0.4	0.0	19	dbSNP_117	76	2840,5756	440.4+/-359.5	474,1892,1932	no	coding-synonymous	ZNF765	NM_001040185.1		498,2264,3736	AA,AG,GG		33.0386,9.5455,25.0846		234/524	53911510	3260,9736	2200	4298	6498	SO:0001819	synonymous_variant	91661	exon4			ACATCAGTTAATC	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"""Zinc fingers, C2H2-type"", ""-"""	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.702G>A	19.37:g.53911510G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Silent	SNP	ENST00000396408.3	37	CCDS46171.1																																																																																			G|0.796;A|0.204	0.204	strong		0.383	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
MUC2	4583	hgsc.bcm.edu	37	11	1087972	1087972	+	Silent	SNP	C	C	T	rs10902088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1087972C>T	ENST00000441003.2	+	25	3474	c.3447C>T	c.(3445-3447)aaC>aaT	p.N1149N	MUC2_ENST00000359061.5_Silent_p.N1149N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1149					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)	GGACCATCAACGGCATCCACT	0.622													C|||	1641	0.327676	0.3759	0.3631	5008	,	,		15887	0.3899		0.2167	False		,,,				2504	0.2873				p.N1149N		Atlas-SNP	.											.	MUC2	614	.	0			c.C3447T						PASS	.			1440,2836		247,946,945	56.0	61.0	60.0		3447	-2.9	0.0	11	dbSNP_120	60	1693,6791		174,1345,2723	no	coding-synonymous	MUC2	NM_002457.2		421,2291,3668	TT,TC,CC		19.9552,33.6763,24.5533		1149/2813	1087972	3133,9627	2138	4242	6380	SO:0001819	synonymous_variant	4583	exon25			CATCAACGGCATC	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.3447C>T	11.37:g.1087972C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.712;T|0.288	0.288	strong		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF805	390980	hgsc.bcm.edu	37	19	57764770	57764770	+	Missense_Mutation	SNP	G	G	A	rs10421632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57764770G>A	ENST00000414468.2	+	4	583	c.583G>A	c.(583-585)Gtt>Att	p.V195I	ZNF805_ENST00000535550.1_Missense_Mutation_p.V62I|ZNF805_ENST00000354309.4_Missense_Mutation_p.V62I	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	195					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)|kidney(3)|lung(1)|stomach(1)	9						TAAAAATCCAGTTATTCAGGA	0.413													.|||	1831	0.365615	0.2421	0.4481	5008	,	,		22087	0.1766		0.5746	False		,,,				2504	0.454				p.V195I		Atlas-SNP	.											.	ZNF805	30	.	0			c.G583A						PASS	.	A	ILE/VAL,ILE/VAL	375,1009		49,277,366	122.0	105.0	110.0		583,184	-8.7	0.0	19	dbSNP_119	110	1647,1535		429,789,373	yes	missense,missense	ZNF805	NM_001023563.3,NM_001145078.1	29,29	478,1066,739	AA,AG,GG		48.2401,27.0954,44.2838	benign,benign	195/628,62/495	57764770	2022,2544	692	1591	2283	SO:0001583	missense	390980	exon4			AATCCAGTTATTC	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.583G>A	19.37:g.57764770G>A	ENSP00000412999:p.Val195Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	848	0.3882783882783883	129	0.2621951219512195	174	0.48066298342541436	112	0.1958041958041958	433	0.5712401055408971	g	6.573	0.474080	0.12521	0.270954	0.517599	ENSG00000204524	ENST00000535550;ENST00000414468;ENST00000354309	T;T;T	0.06371	3.31;3.47;3.31	4.35	-8.7	0.00851	.	.	.	.	.	T	0.00012	0.0000	N	0.05050	-0.12	0.80722	P	0.0	B	0.18166	0.026	B	0.12837	0.008	T	0.43702	-0.9375	8	0.54805	T	0.06	.	2.344	0.04267	0.3727:0.0955:0.3431:0.1887	rs10421632;rs52822092;rs10421632	195	Q5CZA5	ZN805_HUMAN	I	62;195;62	ENSP00000440067:V62I;ENSP00000412999:V195I;ENSP00000365414:V62I	ENSP00000365414:V62I	V	+	1	0	ZNF805	62456582	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.992000	0.00657	-3.127000	0.00237	-2.384000	0.00231	GTT	G|0.634;A|0.366	0.366	strong		0.413	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
KDM5A	5927	hgsc.bcm.edu	37	12	406292	406292	+	Silent	SNP	G	G	A	rs2229351	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:406292G>A	ENST00000399788.2	-	25	4511	c.4149C>T	c.(4147-4149)tcC>tcT	p.S1383S	KDM5A_ENST00000382815.4_Silent_p.S1383S	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1383					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CCACCTCCTCGGATTTGATGG	0.418			T	NUP98	AML								G|||	1766	0.352636	0.3306	0.3199	5008	,	,		18093	0.5109		0.2326	False		,,,				2504	0.3661				p.S1383S		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	KDM5A_ENST00000399788,trunk,malignant_melanoma,-1,2	KDM5A	307	2	0			c.C4149T						PASS	.	G		1187,2579		201,785,897	65.0	64.0	64.0		4149	-3.8	1.0	12	dbSNP_98	64	2087,6129		276,1535,2297	no	coding-synonymous	KDM5A	NM_001042603.1		477,2320,3194	AA,AG,GG		25.4017,31.5189,27.3243		1383/1691	406292	3274,8708	1883	4108	5991	SO:0001819	synonymous_variant	5927	exon25			CTCCTCGGATTTG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4149C>T	12.37:g.406292G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Silent	SNP	ENST00000399788.2	37	CCDS41736.1																																																																																			T|0.139;G|0.444;C|0.211;A|0.206	0.206	strong		0.418	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
PPP1R1C	151242	hgsc.bcm.edu	37	2	182981968	182981968	+	Silent	SNP	A	A	G	rs1882212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:182981968A>G	ENST00000409137.3	+	5	519	c.276A>G	c.(274-276)gcA>gcG	p.A92A	PPP1R1C_ENST00000452904.1_Silent_p.A92A|PPP1R1C_ENST00000280295.3_Silent_p.A99A|PPP1R1C_ENST00000475249.1_Intron|PPP1R1C_ENST00000409702.1_Silent_p.A92A	NM_001261424.1|NM_001261425.1	NP_001248353.1|NP_001248354.1	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1C	92					cell cycle (GO:0007049)|cell division (GO:0051301)|negative regulation of catalytic activity (GO:0043086)|positive regulation of cell growth (GO:0030307)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			ATGAATCAGCATTCCCTGAAG	0.378													a|||	1704	0.340256	0.5983	0.2219	5008	,	,		18159	0.2183		0.2048	False		,,,				2504	0.3405				p.A99A		Atlas-SNP	.											.	PPP1R1C	14	.	0			c.A297G						PASS	.	G		1949,1799		507,935,432	51.0	51.0	51.0		276	-6.1	0.9	2	dbSNP_92	51	1779,6421		206,1367,2527	no	coding-synonymous	PPP1R1C	NM_001080545.1		713,2302,2959	GG,GA,AA		21.6951,47.9989,31.2019		92/110	182981968	3728,8220	1874	4100	5974	SO:0001819	synonymous_variant	151242	exon5			ATCAGCATTCCCT	AF494535, BC017943	CCDS46468.1, CCDS58740.1	2q31.3	2012-04-17			ENSG00000150722	ENSG00000150722		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14940	protein-coding gene	gene with protein product		613240				11948623	Standard	NM_001261424		Approved	Inhibitor-1-like	uc010frm.2	Q8WVI7	OTTHUMG00000154326	ENST00000409137.3:c.276A>G	2.37:g.182981968A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	231	125	0.541126	NM_001261424	Q5HYJ5|Q8TD54	Silent	SNP	ENST00000409137.3	37	CCDS46468.1																																																																																			A|0.704;G|0.296	0.296	strong		0.378	PPP1R1C-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334874.1	NM_001080545	
EIF2A	83939	hgsc.bcm.edu	37	3	150285520	150285520	+	Silent	SNP	T	T	C	rs2293151	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:150285520T>C	ENST00000460851.1	+	7	625	c.516T>C	c.(514-516)gaT>gaC	p.D172D	SERP1_ENST00000490945.1_Intron|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000487799.1_Silent_p.D147D|EIF2A_ENST00000406576.3_Silent_p.D111D|EIF2A_ENST00000273435.5_Silent_p.D167D|EIF2A_ENST00000383043.3_5'Flank			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	172					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AAATTAATGATTTTGTATTAT	0.279													T|||	597	0.119209	0.1619	0.1441	5008	,	,		20121	0.0208		0.1581	False		,,,				2504	0.1053				p.D172D		Atlas-SNP	.											.	EIF2A	59	.	0			c.T516C						PASS	.	T		531,3049		33,465,1292	72.0	63.0	65.0		516	3.6	1.0	3	dbSNP_100	65	1227,6867		110,1007,2930	no	coding-synonymous	EIF2A	NM_032025.3		143,1472,4222	CC,CT,TT		15.1594,14.8324,15.0591		172/586	150285520	1758,9916	1790	4047	5837	SO:0001819	synonymous_variant	83939	exon7			TAATGATTTTGTA	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.516T>C	3.37:g.150285520T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	222	135	0.608108	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			T|0.885;C|0.115	0.115	strong		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
MAP9	79884	hgsc.bcm.edu	37	4	156289917	156289917	+	Missense_Mutation	SNP	G	G	A	rs3733391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156289917G>A	ENST00000311277.4	-	5	792	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	AC097467.2_ENST00000597831.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.R177W|MAP9_ENST00000379248.2_Missense_Mutation_p.R104W|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000596165.1_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	391	0	0		WXS	Illumina HiSeq	Phase_I	311	149	0.4791	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	
FLG	2312	hgsc.bcm.edu	37	1	152280782	152280782	+	Missense_Mutation	SNP	A	A	G	rs2184953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280782A>G	ENST00000368799.1	-	3	6615	c.6580T>C	c.(6580-6582)Tat>Cat	p.Y2194H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2194	Ser-rich.		Y -> H (in dbSNP:rs2184953).		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)			TCCTTGTCATATGTTTTTCTG	0.547									Ichthyosis				-|||	2703	0.539736	0.7897	0.4683	5008	,	,		29126	0.6607		0.1759	False		,,,				2504	0.502				p.Y2194H		Atlas-SNP	.											.	FLG	900	.	0			c.T6580C						PASS	.						483.0	407.0	432.0					1																	152280782		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGTCATATGTTTT	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.6580T>C	1.37:g.152280782A>G	ENSP00000357789:p.Tyr2194His	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	362	270	0.745856	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1006	0.4606227106227106	366	0.7439024390243902	142	0.39226519337016574	362	0.6328671328671329	136	0.17941952506596306	g	2.593	-0.294672	0.05568	.	.	ENSG00000143631	ENST00000368799	T	0.01665	4.7	2.99	-5.98	0.02220	.	.	.	.	.	T	0.00241	0.0007	N	0.02011	-0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.45673	-0.9245	8	0.45353	T	0.12	.	4.3415	0.11112	0.287:0.0:0.31:0.403	rs2184953;rs2184953	2194	P20930	FILA_HUMAN	H	2194	ENSP00000357789:Y2194H	ENSP00000357789:Y2194H	Y	-	1	0	FLG	150547406	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.749000	0.00793	-2.890000	0.00315	-2.627000	0.00155	TAT	A|0.483;G|0.517	0.517	strong		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CHPF2	54480	hgsc.bcm.edu	37	7	150935430	150935430	+	Missense_Mutation	SNP	G	G	C	rs3748098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150935430G>C	ENST00000035307.2	+	4	3495	c.1982G>C	c.(1981-1983)gGg>gCg	p.G661A	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.G653A	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	661					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						GCTCCTATAGGGGGGAGATTT	0.701													G|||	207	0.0413339	0.0061	0.111	5008	,	,		13688	0.0149		0.0666	False		,,,				2504	0.0409				p.G661A		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1982C						PASS	.	G	ALA/GLY	72,4294		1,70,2112	9.0	12.0	11.0		1982	3.0	0.2	7	dbSNP_107	11	694,7842		27,640,3601	yes	missense	CHPF2	NM_019015.1	60	28,710,5713	CC,CG,GG		8.1303,1.6491,5.9371	possibly-damaging	661/773	150935430	766,12136	2183	4268	6451	SO:0001583	missense	54480	exon4			CTATAGGGGGGAG	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.1982G>C	7.37:g.150935430G>C	ENSP00000035307:p.Gly661Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	107	0.04899267399267399	6	0.012195121951219513	43	0.11878453038674033	10	0.017482517482517484	48	0.0633245382585752	G	3.215	-0.160799	0.06502	0.016491	0.081303	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.24350	1.86;1.86	4.81	3.03	0.35002	.	0.177071	0.50627	N	0.000115	T	0.00109	0.0003	N	0.00347	-1.61	0.38178	D	0.939527	P;P	0.43024	0.798;0.759	B;B	0.43838	0.433;0.306	T	0.30208	-0.9986	10	0.07175	T	0.84	-25.0544	11.6931	0.51527	0.0:0.3371:0.6629:0.0	rs3748098	661;653	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	A	653;661	ENSP00000418914:G653A;ENSP00000035307:G661A	ENSP00000035307:G661A	G	+	2	0	CHPF2	150566363	1.000000	0.71417	0.185000	0.23176	0.116000	0.19942	1.235000	0.32671	0.654000	0.30846	-0.719000	0.03609	GGG	G|0.948;C|0.052	0.052	strong		0.701	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
OR5H1	26341	hgsc.bcm.edu	37	3	97851968	97851968	+	Missense_Mutation	SNP	C	C	T	rs139235176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	414	2	0.00483092		WXS	Illumina HiSeq	Phase_I	484	48	0.0991736	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	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549424	32549424	+	Missense_Mutation	SNP	C	C	T	rs112116022		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549424C>T	ENST00000360004.5	-	3	667	c.562G>A	c.(562-564)Gtg>Atg	p.V188M		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	188	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)|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						TCCAGCATCACCAGGGTCTGG	0.557										Multiple Myeloma(14;0.17)																											p.V188M		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G562A						PASS	.						145.0	156.0	152.0					6																	32549424		1511	2709	4220	SO:0001583	missense	3123	exon3			GCATCACCAGGGT	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.562G>A	6.37:g.32549424C>T	ENSP00000353099:p.Val188Met	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	249	20	0.0803213	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	17.39	3.377277	0.61735	.	.	ENSG00000196126	ENST00000360004	T	0.03094	4.05	3.87	3.87	0.44632	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.249924	0.40554	N	0.001065	T	0.14830	0.0358	M	0.90309	3.105	0.38652	D	0.951871	D;D;D;D	0.89917	0.996;1.0;0.998;1.0	P;D;P;D	0.87578	0.88;0.998;0.88;0.983	T	0.02661	-1.1127	10	0.87932	D	0	.	13.682	0.62491	0.0:1.0:0.0:0.0	.	188;188;188;188	P04229;P01912;Q29974;P01911	2B11_HUMAN;2B13_HUMAN;2B1G_HUMAN;2B1F_HUMAN	M	188	ENSP00000353099:V188M	ENSP00000353099:V188M	V	-	1	0	HLA-DRB1	32657402	1.000000	0.71417	0.991000	0.47740	0.791000	0.44710	3.253000	0.51469	1.883000	0.54544	0.453000	0.30009	GTG	C|0.500;T|0.500	0.500	weak		0.557	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
MTRF1L	54516	hgsc.bcm.edu	37	6	153316326	153316326	+	Silent	SNP	A	A	G	rs3734467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:153316326A>G	ENST00000367233.5	-	3	467	c.468T>C	c.(466-468)taT>taC	p.Y156Y	MTRF1L_ENST00000367230.1_Intron|MTRF1L_ENST00000367231.5_Silent_p.Y156Y|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	156						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)	p.Y156Y(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		TAAATGCAGCATATTGCTGAT	0.348													A|||	735	0.146765	0.1475	0.1081	5008	,	,		16505	0.131		0.1083	False		,,,				2504	0.229				p.Y156Y		Atlas-SNP	.											MTRF1L,NS,carcinoma,0,1	MTRF1L	21	1	1	Substitution - coding silent(1)	stomach(1)	c.T468C						PASS	.	A	,	556,3850	231.4+/-245.2	37,482,1684	37.0	35.0	36.0		468,468	1.4	1.0	6	dbSNP_107	36	958,7634	205.9+/-248.2	61,836,3399	no	coding-synonymous,coding-synonymous	MTRF1L	NM_001114184.1,NM_019041.5	,	98,1318,5083	GG,GA,AA		11.1499,12.6192,11.6479	,	156/272,156/381	153316326	1514,11484	2203	4296	6499	SO:0001819	synonymous_variant	54516	exon3			TGCAGCATATTGC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.468T>C	6.37:g.153316326A>G		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	199	88	0.442211	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Silent	SNP	ENST00000367233.5	37	CCDS5243.1																																																																																			A|0.888;G|0.112	0.112	strong		0.348	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
GDAP1	54332	hgsc.bcm.edu	37	8	75274141	75274141	+	Silent	SNP	T	T	G	rs11554166	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:75274141T>G	ENST00000220822.7	+	4	587	c.507T>G	c.(505-507)tcT>tcG	p.S169S	GDAP1_ENST00000521096.1_3'UTR|GDAP1_ENST00000434412.2_Silent_p.S101S	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	169	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			ACACAGAGTCTGAGCTGAAGA	0.378													T|||	1098	0.219249	0.093	0.1787	5008	,	,		19465	0.3026		0.3569	False		,,,				2504	0.1912				p.S169S		Atlas-SNP	.											.	GDAP1	36	.	0			c.T507G						PASS	.	T	,	564,3842	252.4+/-258.8	27,510,1666	108.0	102.0	104.0		303,507	0.1	1.0	8	dbSNP_120	104	2736,5864	436.4+/-358.3	437,1862,2001	no	coding-synonymous,coding-synonymous	GDAP1	NM_001040875.1,NM_018972.2	,	464,2372,3667	GG,GT,TT		31.814,12.8007,25.3729	,	101/291,169/359	75274141	3300,9706	2203	4300	6503	SO:0001819	synonymous_variant	54332	exon4			AGAGTCTGAGCTG		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"""Charcot-Marie-Tooth neuropathy 4A"""	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.507T>G	8.37:g.75274141T>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_018972	A8K957|E7FJF3|E7FJF4	Silent	SNP	ENST00000220822.7	37	CCDS34911.1																																																																																			T|0.753;G|0.247	0.247	strong		0.378	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972	
GLB1L3	112937	hgsc.bcm.edu	37	11	134147600	134147600	+	Silent	SNP	T	T	C	rs76849136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:134147600T>C	ENST00000431683.2	+	3	156	c.156T>C	c.(154-156)aaT>aaC	p.N52N	GLB1L3_ENST00000389887.5_Silent_p.N52N	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	52					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CCAGGTTTAATTGGTCTCATC	0.562													T|||	51	0.0101837	0.0015	0.0101	5008	,	,		17048	0.003		0.0368	False		,,,				2504	0.002				p.N52N		Atlas-SNP	.											.	GLB1L3	102	.	0			c.T156C						PASS	.	T		37,4025		0,37,1994	29.0	31.0	30.0		156	-10.1	0.0	11	dbSNP_132	30	221,8203		1,219,3992	no	coding-synonymous	GLB1L3	NM_001080407.2		1,256,5986	CC,CT,TT		2.6235,0.9109,2.0663		52/654	134147600	258,12228	2031	4212	6243	SO:0001819	synonymous_variant	112937	exon3			GTTTAATTGGTCT		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.156T>C	11.37:g.134147600T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Silent	SNP	ENST00000431683.2	37	CCDS44780.1																																																																																			T|0.981;C|0.019	0.019	strong		0.562	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	
IFI44	10561	hgsc.bcm.edu	37	1	79115905	79115905	+	Missense_Mutation	SNP	T	T	C	rs2070123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:79115905T>C	ENST00000370747.4	+	2	110	c.25T>C	c.(25-27)Tgg>Cgg	p.W9R	IFI44_ENST00000545124.1_Intron|IFI44_ENST00000495254.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	9			W -> R (in dbSNP:rs2070123). {ECO:0000269|PubMed:15489334}.		response to virus (GO:0009615)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						TCGTTTGACATGGTTGCACGA	0.353													T|||	610	0.121805	0.1346	0.1138	5008	,	,		17255	0.131		0.0775	False		,,,				2504	0.1462				p.W9R		Atlas-SNP	.											IFI44,NS,carcinoma,-1,1	IFI44	55	1	0			c.T25C						PASS	.	T	ARG/TRP	590,3816	261.9+/-264.6	40,510,1653	102.0	96.0	98.0		25	-0.7	0.0	1	dbSNP_96	98	703,7897	172.7+/-223.4	27,649,3624	yes	missense	IFI44	NM_006417.4	101	67,1159,5277	CC,CT,TT		8.1744,13.3908,9.9416	possibly-damaging	9/445	79115905	1293,11713	2203	4300	6503	SO:0001583	missense	10561	exon2			TTGACATGGTTGC	D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 5"""	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.25T>C	1.37:g.79115905T>C	ENSP00000359783:p.Trp9Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_006417	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	37	CCDS688.1	237	0.10851648351648352	58	0.11788617886178862	48	0.13259668508287292	73	0.12762237762237763	58	0.07651715039577836	T	4.491	0.091066	0.08632	0.133908	0.081744	ENSG00000137965	ENST00000370747	T	0.08193	3.12	3.32	-0.723	0.11181	.	0.879816	0.09828	N	0.750596	T	0.04272	0.0118	M	0.68952	2.095	0.80722	P	0.0	P;P	0.50272	0.933;0.933	P;P	0.45881	0.496;0.496	T	0.30966	-0.9960	9	0.40728	T	0.16	-0.3873	4.5869	0.12287	0.1923:0.0:0.3963:0.4114	rs2070123;rs2070602;rs17852121;rs52832822;rs2070123	9;9	B7ZB11;Q8TCB0	.;IFI44_HUMAN	R	9	ENSP00000359783:W9R	ENSP00000359783:W9R	W	+	1	0	IFI44	78888493	0.078000	0.21339	0.004000	0.12327	0.003000	0.03518	0.111000	0.15458	-0.137000	0.11455	-0.661000	0.03856	TGG	T|0.891;C|0.109	0.109	strong		0.353	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417	
WWC3	55841	hgsc.bcm.edu	37	X	10085602	10085602	+	Silent	SNP	A	A	C	rs56130457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085602A>C	ENST00000380861.4	+	11	1894	c.1503A>C	c.(1501-1503)gcA>gcC	p.A501A	WWC3_ENST00000454666.1_Silent_p.A501A	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	501					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)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GACTGCGGGCACACGCCTCGG	0.716													A|||	8	0.00211921	0.0008	0.0014	3775	,	,		11380	0.0		0.006	False		,,,				2504	0.0				p.A501A		Atlas-SNP	.											.	WWC3	142	.	0			c.A1503C						PASS	.	A		8,3752		0,6,2,1607,532	7.0	7.0	7.0		1503	-10.9	0.0	X	dbSNP_129	7	85,6535		0,60,25,2350,1775	no	coding-synonymous	WWC3	NM_015691.3		0,66,27,3957,2307	CC,CA,C,AA,A		1.284,0.2128,0.896		501/1093	10085602	93,10287	2147	4210	6357	SO:0001819	synonymous_variant	55841	exon11			GCGGGCACACGCC	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1503A>C	X.37:g.10085602A>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			A|0.995;C|0.005	0.005	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
MAGEC1	9947	hgsc.bcm.edu	37	X	140994517	140994517	+	Missense_Mutation	SNP	C	C	G	rs62611966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:140994517C>G	ENST00000285879.4	+	4	1613	c.1327C>G	c.(1327-1329)Ctc>Gtc	p.L443V	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	443								p.L443I(1)		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)					CCAGTCTCCTCTCCAGATTCC	0.453										HNSCC(15;0.026)			-||||-|||	289|289	0.0765563|0.0765563	0.0401|0.0401	0.0533|0.0533	3775|3775	,|,	,|,		13812|13812	0.0337|0.0337		0.0636|0.0636	False|False		,,,|,,,				2504|2504	0.1033|0.1033				p.L443V		Atlas-SNP	.											.	MAGEC1	317	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1327G						PASS	.	C	VAL/LEU	196,3636		12,139,33,1481,535	98.0	107.0	104.0		1327	0.1	0.0	X	dbSNP_129	104	668,6052		32,430,174,1966,1690	no	missense	MAGEC1	NM_005462.4	32	44,569,207,3447,2225	GG,GC,G,CC,C		9.9405,5.1148,8.188	possibly-damaging	443/1143	140994517	864,9688	2200	4292	6492	SO:0001583	missense	9947	exon4			TCTCCTCTCCAGA	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.1327C>G	X.37:g.140994517C>G	ENSP00000285879:p.Leu443Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	111	0.06690777576853527	19	0.03991596638655462	11	0.03197674418604651	10	0.017793594306049824	33	0.045454545454545456	c	1.155	-0.645395	0.03531	0.051148	0.099405	ENSG00000155495	ENST00000285879	T	0.02216	4.39	0.131	0.131	0.14755	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.199999999996649E-5	P	0.46912	0.886	B	0.34138	0.176	T	0.52888	-0.8515	8	0.87932	D	0	.	5.9545	0.19265	0.0:0.9994:0.0:6.0E-4	rs62611966	443	O60732	MAGC1_HUMAN	V	443	ENSP00000285879:L443V	ENSP00000285879:L443V	L	+	1	0	MAGEC1	140822183	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	0.065000	0.14466	0.157000	0.19338	0.158000	0.16466	CTC	C|0.929;G|0.071	0.071	strong		0.453	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
MROH7	374977	hgsc.bcm.edu	37	1	55119637	55119637	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55119637C>G	ENST00000421030.2	+	3	1323	c.1038C>G	c.(1036-1038)agC>agG	p.S346R	MROH7_ENST00000395690.2_Missense_Mutation_p.S346R|MROH7_ENST00000339553.5_Missense_Mutation_p.S346R|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000409996.1_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S346R|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000472987.1_3'UTR	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	346	Ser-rich.					extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TCCTGTTCAGCGACACCTCCA	0.562																																					p.S346R		Atlas-SNP	.											.	.	.	.	0			c.C1038G						PASS	.						99.0	98.0	98.0					1																	55119637		2139	4231	6370	SO:0001583	missense	374977	exon3			GTTCAGCGACACC	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.1038C>G	1.37:g.55119637C>G	ENSP00000396622:p.Ser346Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	147	77	0.52381	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152800	0.21371	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.04454	3.62;3.62;3.62	3.89	-7.78	0.01223	.	0.164918	0.29113	N	0.013103	T	0.09818	0.0241	L	0.27053	0.805	0.31997	N	0.603917	D;D;D	0.89917	0.996;0.989;1.0	D;P;D	0.75484	0.944;0.875;0.986	T	0.34104	-0.9842	10	0.87932	D	0	.	19.0946	0.93244	0.0:0.7723:0.0:0.2277	.	346;346;346	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	R	346	ENSP00000396622:S346R;ENSP00000343211:S346R;ENSP00000379044:S346R	ENSP00000343211:S346R	S	+	3	2	HEATR8	54892225	0.000000	0.05858	0.261000	0.24466	0.379000	0.30106	-7.901000	0.00028	-2.926000	0.00302	-1.916000	0.00518	AGC	.	.	none		0.562	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
MYO9B	4650	hgsc.bcm.edu	37	19	17301935	17301935	+	Silent	SNP	G	G	A	rs55959020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17301935G>A	ENST00000594824.1	+	20	2865	c.2718G>A	c.(2716-2718)ctG>ctA	p.L906L	MYO9B_ENST00000397274.2_Silent_p.L906L|MYO9B_ENST00000595618.1_Silent_p.L906L			Q13459	MYO9B_HUMAN	myosin IXB	906	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						AGGTGCTCCTGCCCAAGGATG	0.532													G|||	58	0.0115815	0.0015	0.0159	5008	,	,		20194	0.0		0.0417	False		,,,				2504	0.0031				p.L906L		Atlas-SNP	.											.	MYO9B	264	.	0			c.G2718A						PASS	.	G	,	19,3935		0,19,1958	62.0	63.0	63.0		2718,2718	-1.9	1.0	19	dbSNP_129	63	308,7996		8,292,3852	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	8,311,5810	AA,AG,GG		3.7091,0.4805,2.6676	,	906/2023,906/2158	17301935	327,11931	1977	4152	6129	SO:0001819	synonymous_variant	4650	exon20			GCTCCTGCCCAAG		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2718G>A	19.37:g.17301935G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				G|0.975;A|0.025	0.025	strong		0.532	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
MPPE1	65258	hgsc.bcm.edu	37	18	11886563	11886563	+	Missense_Mutation	SNP	C	C	G	rs662515	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:11886563C>G	ENST00000588072.1	-	9	2023	c.802G>C	c.(802-804)Gca>Cca	p.A268P	MPPE1_ENST00000309976.9_Intron|MPPE1_ENST00000317235.7_Intron|MPPE1_ENST00000592755.1_5'Flank|MPPE1_ENST00000399978.2_Missense_Mutation_p.A269P|MPPE1_ENST00000344987.7_Missense_Mutation_p.A246P	NM_023075.5	NP_075563.3	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1	268			A -> P (in dbSNP:rs662515). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15498874, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						CTTTCCTCTGCAGGAGCAGCG	0.512													G|||	2517	0.502596	0.7995	0.3069	5008	,	,		20961	0.5744		0.3022	False		,,,				2504	0.3722				p.A268P		Atlas-SNP	.											.	MPPE1	21	.	0			c.G802C						PASS	.	G	,PRO/ALA	3149,1257	430.6+/-342.6	1134,881,188	129.0	98.0	108.0		,802	4.7	0.0	18	dbSNP_83	108	2306,6294	705.9+/-405.5	313,1680,2307	no	intron,missense	MPPE1	NM_001242904.1,NM_023075.5	,27	1447,2561,2495	GG,GC,CC		26.814,28.5293,41.9422	,benign	,268/397	11886563	5455,7551	2203	4300	6503	SO:0001583	missense	65258	exon9			CCTCTGCAGGAGC	BC002877	CCDS11853.1, CCDS56054.1	18p11.21	2004-04-30			ENSG00000154889	ENSG00000154889			15988	protein-coding gene	gene with protein product		611900				11978971	Standard	NM_001242904		Approved		uc002kqf.3	Q53F39	OTTHUMG00000131661	ENST00000588072.1:c.802G>C	18.37:g.11886563C>G	ENSP00000465894:p.Ala268Pro	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	118	0.614583	NM_023075	B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4	Missense_Mutation	SNP	ENST00000588072.1	37	CCDS11853.1	1065	0.4876373626373626	370	0.7520325203252033	120	0.3314917127071823	349	0.6101398601398601	226	0.29815303430079154	G	5.153	0.213902	0.09810	0.714707	0.26814	ENSG00000154889	ENST00000309976;ENST00000317251;ENST00000344987;ENST00000399978	T;T	0.17528	2.27;2.27	5.54	4.66	0.58398	Calcineurin-like phosphoesterase superfamily domain (1);	0.267639	0.43260	N	0.000587	T	0.00012	0.0000	N	0.00538	-1.39	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	0.21211	-1.0252	9	0.14656	T	0.56	-10.6476	16.2476	0.82454	0.0:0.2512:0.7487:0.0	rs662515;rs52835677;rs60714545;rs662515	269;171;268;268	Q53F39-3;B3KNP1;Q53F39-2;Q53F39	.;.;.;MPPE1_HUMAN	P	268;171;269;269	ENSP00000312935:A171P;ENSP00000382860:A269P	ENSP00000311200:A268P	A	-	1	0	MPPE1	11876563	0.998000	0.40836	0.001000	0.08648	0.003000	0.03518	3.353000	0.52247	0.706000	0.31912	-0.120000	0.15030	GCA	C|0.545;G|0.455	0.455	strong		0.512	MPPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254562.2	NM_023075	
GRB14	2888	hgsc.bcm.edu	37	2	165476253	165476253	+	Missense_Mutation	SNP	A	A	T	rs61748245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165476253A>T	ENST00000263915.3	-	2	806	c.268T>A	c.(268-270)Ttt>Att	p.F90I		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	90			F -> I (in dbSNP:rs61748245). {ECO:0000269|PubMed:21220648, ECO:0000269|PubMed:8647858}.		blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						ACAGATGTAAATGGAGAACAG	0.348													A|||	2219	0.443091	0.1838	0.7392	5008	,	,		14271	0.3571		0.6769	False		,,,				2504	0.4315				p.F90I		Atlas-SNP	.											GRB14,trunk,malignant_melanoma,+1,1	GRB14	73	1	0			c.T268A						PASS	.	A	ILE/PHE	1177,3229	412.6+/-336.2	166,845,1192	141.0	142.0	142.0		268	4.3	1.0	2	dbSNP_129	142	5636,2964	666.6+/-402.4	1883,1870,547	yes	missense	GRB14	NM_004490.2	21	2049,2715,1739	TT,TA,AA		34.4651,26.7136,47.6165	benign	90/541	165476253	6813,6193	2203	4300	6503	SO:0001583	missense	2888	exon2			ATGTAAATGGAGA		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.268T>A	2.37:g.165476253A>T	ENSP00000263915:p.Phe90Ile	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	239	238	0.995816	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	1083	0.4958791208791209	109	0.22154471544715448	253	0.6988950276243094	208	0.36363636363636365	513	0.6767810026385225	A	11.79	1.743698	0.30865	0.267136	0.655349	ENSG00000115290	ENST00000263915;ENST00000446413;ENST00000424693	T;T;T	0.41400	2.02;1.61;1.0	5.45	4.3	0.51218	.	0.195453	0.36932	N	0.002332	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999999769	B	0.17465	0.022	B	0.19946	0.027	T	0.33929	-0.9849	9	0.20519	T	0.43	-2.7772	8.9411	0.35731	0.9131:0.0:0.0869:0.0	rs61748245	90	Q14449	GRB14_HUMAN	I	90;45;32	ENSP00000263915:F90I;ENSP00000416786:F45I;ENSP00000401702:F32I	ENSP00000263915:F90I	F	-	1	0	GRB14	165184499	0.975000	0.34042	1.000000	0.80357	0.999000	0.98932	1.690000	0.37711	0.913000	0.36797	0.533000	0.62120	TTT	A|0.485;T|0.515	0.515	strong		0.348	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
RNF20	56254	hgsc.bcm.edu	37	9	104324545	104324545	+	Silent	SNP	G	G	A	rs10521057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104324545G>A	ENST00000389120.3	+	20	2859	c.2769G>A	c.(2767-2769)ccG>ccA	p.P923P		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	923					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)		TGACCTGTCCGTGCTGTAACA	0.418													G|||	928	0.185304	0.0038	0.0865	5008	,	,		20396	0.3562		0.1938	False		,,,				2504	0.316				p.P923P		Atlas-SNP	.											RNF20,NS,carcinoma,0,1	RNF20	110	1	0			c.G2769A						PASS	.	G		179,4227	117.1+/-155.0	3,173,2027	157.0	143.0	148.0		2769	-11.7	0.5	9	dbSNP_119	148	1583,7017	296.3+/-302.9	145,1293,2862	no	coding-synonymous	RNF20	NM_019592.5		148,1466,4889	AA,AG,GG		18.407,4.0626,13.5476		923/976	104324545	1762,11244	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon20			CTGTCCGTGCTGT	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.2769G>A	9.37:g.104324545G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	37	CCDS35084.1																																																																																			G|0.836;A|0.164	0.164	strong		0.418	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
MUC16	94025	hgsc.bcm.edu	37	19	9059181	9059181	+	Missense_Mutation	SNP	G	G	A	rs12459532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9059181G>A	ENST00000397910.4	-	3	28468	c.28265C>T	c.(28264-28266)cCa>cTa	p.P9422L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9424	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						CAGCGGGCTTGGCCATGACAC	0.512													G|||	182	0.0363419	0.0008	0.1153	5008	,	,		20341	0.0099		0.0189	False		,,,				2504	0.0736				p.P9422L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C28265T						PASS	.	G	LEU/PRO	23,4023		0,23,2000	118.0	117.0	117.0		28265	0.8	0.0	19	dbSNP_120	117	177,8189		3,171,4009	yes	missense	MUC16	NM_024690.2	98	3,194,6009	AA,AG,GG		2.1157,0.5685,1.6113	benign	9422/14508	9059181	200,12212	2023	4183	6206	SO:0001583	missense	94025	exon3			GGGCTTGGCCATG	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.28265C>T	19.37:g.9059181G>A	ENSP00000381008:p.Pro9422Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	53	0.024267399267399268	0	0.0	35	0.09668508287292818	4	0.006993006993006993	14	0.018469656992084433	g	4.312	0.057126	0.08339	0.005685	0.021157	ENSG00000181143	ENST00000397910	T	0.21031	2.03	1.95	0.802	0.18686	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	.	.	.	B	0.27625	0.183	B	0.30943	0.122	T	0.21999	-1.0229	8	0.87932	D	0	.	5.1883	0.15195	0.0:0.0:0.6334:0.3666	rs12459532;rs12459532	9422	B5ME49	.	L	9422	ENSP00000381008:P9422L	ENSP00000381008:P9422L	P	-	2	0	MUC16	8920181	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.068000	0.11561	0.328000	0.23435	0.306000	0.20318	CCA	G|0.977;A|0.023	0.023	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TAS2R9	50835	hgsc.bcm.edu	37	12	10962115	10962115	+	Missense_Mutation	SNP	A	A	G	rs3741845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10962115A>G	ENST00000240691.2	-	1	652	c.560T>C	c.(559-561)gTg>gCg	p.V187A	TAS2R8_ENST00000240615.2_5'Flank	NM_023917.2	NP_076406.1	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	187			V -> A (in dbSNP:rs3741845). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15744053}.		detection of chemical stimulus involved in sensory perception of taste (GO:0050912)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	taste receptor activity (GO:0008527)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GGGAACCATCACCCCCAGGTT	0.398													a|||	2659	0.53095	0.1982	0.5749	5008	,	,		20313	0.7183		0.6839	False		,,,				2504	0.5992				p.V187A		Atlas-SNP	.											.	TAS2R9	39	.	0			c.T560C						PASS	.	C	ALA/VAL	1148,3258	405.1+/-333.4	160,828,1215	77.0	76.0	76.0		560	-3.4	0.0	12	dbSNP_107	76	5268,3332	642.4+/-399.8	1626,2016,658	yes	missense	TAS2R9	NM_023917.2	64	1786,2844,1873	GG,GA,AA		38.7442,26.0554,49.3311	benign	187/313	10962115	6416,6590	2203	4300	6503	SO:0001583	missense	50835	exon1			ACCATCACCCCCA	AF227135	CCDS8633.1	12p13	2012-08-22			ENSG00000121381	ENSG00000121381		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14917	protein-coding gene	gene with protein product		604795				10761934, 10766242	Standard	NM_023917		Approved	T2R9, TRB6	uc001qyx.3	Q9NYW1	OTTHUMG00000168507	ENST00000240691.2:c.560T>C	12.37:g.10962115A>G	ENSP00000240691:p.Val187Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_023917	Q502V7|Q50KT0|Q50KT1|Q645W9	Missense_Mutation	SNP	ENST00000240691.2	37	CCDS8633.1	1258	0.576007326007326	122	0.24796747967479674	217	0.5994475138121547	402	0.7027972027972028	517	0.6820580474934037	a	0.846	-0.740210	0.03088	0.260554	0.612558	ENSG00000121381	ENST00000240691	T	0.38077	1.16	3.94	-3.44	0.04796	GPCR, rhodopsin-like superfamily (1);	0.963080	0.08410	N	0.950106	T	0.00012	0.0000	N	0.00991	-1.07	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37957	-0.9683	9	0.07030	T	0.85	.	7.5536	0.27812	0.2663:0.5366:0.1971:0.0	rs3741845;rs52807644;rs57707743;rs3741845	187	Q9NYW1	TA2R9_HUMAN	A	187	ENSP00000240691:V187A	ENSP00000240691:V187A	V	-	2	0	TAS2R9	10853382	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.109000	0.00600	-0.834000	0.04239	-2.499000	0.00192	GTG	G|0.526;N|0.001	0.526	strong		0.398	TAS2R9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399933.1		
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	42	42	1	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	
ATF5	22809	hgsc.bcm.edu	37	19	50436115	50436115	+	Silent	SNP	C	C	T	rs61742136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50436115C>T	ENST00000423777.2	+	3	992	c.615C>T	c.(613-615)acC>acT	p.T205T	MIR4751_ENST00000578027.1_RNA|ATF5_ENST00000595125.1_Silent_p.T205T|CTC-326K19.6_ENST00000451973.1_Intron	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	205	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|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)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	ATCCTGCCACCACCCGAGGGG	0.672													C|||	196	0.0391374	0.0772	0.0159	5008	,	,		10442	0.0		0.0249	False		,,,				2504	0.0593				p.T205T	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.C615T						PASS	.	C	,	265,4131		5,255,1938	32.0	25.0	27.0		615,615	1.7	0.0	19	dbSNP_129	27	200,8396		1,198,4099	no	coding-synonymous,coding-synonymous	ATF5	NM_001193646.1,NM_012068.5	,	6,453,6037	TT,TC,CC		2.3267,6.0282,3.5791	,	205/283,205/283	50436115	465,12527	2198	4298	6496	SO:0001819	synonymous_variant	22809	exon4			TGCCACCACCCGA	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.615C>T	19.37:g.50436115C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	37	CCDS12789.1																																																																																			C|0.967;T|0.033	0.033	strong		0.672	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
DAGLA	747	hgsc.bcm.edu	37	11	61511133	61511133	+	Silent	SNP	G	G	A	rs3741251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:61511133G>A	ENST00000257215.5	+	20	2417	c.2301G>A	c.(2299-2301)gcG>gcA	p.A767A	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	767					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)		AGCGGCTGGCGGCGGAGCTGC	0.716													G|||	902	0.180112	0.0772	0.2176	5008	,	,		9840	0.1478		0.163	False		,,,				2504	0.3436				p.A767A		Atlas-SNP	.											.	DAGLA	109	.	0			c.G2301A						PASS	.	G		307,3765		11,285,1740	17.0	22.0	20.0		2301	-6.2	0.0	11	dbSNP_107	20	1129,6939		80,969,2985	no	coding-synonymous	DAGLA	NM_006133.2		91,1254,4725	AA,AG,GG		13.9936,7.5393,11.8287		767/1043	61511133	1436,10704	2036	4034	6070	SO:0001819	synonymous_variant	747	exon20			GCTGGCGGCGGAG	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.2301G>A	11.37:g.61511133G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.868;A|0.132	0.132	strong		0.716	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
ZNF91	7644	hgsc.bcm.edu	37	19	23557502	23557502	+	Missense_Mutation	SNP	G	G	A	rs141062920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23557502G>A	ENST00000300619.7	-	2	300	c.95C>T	c.(94-96)aCt>aTt	p.T32I	ZNF91_ENST00000599743.1_Missense_Mutation_p.T32I|ZNF91_ENST00000397082.2_Missense_Mutation_p.T32I	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CTGCTGTGCAGTGTCCAGACA	0.388													G|||	429	0.0856629	0.09	0.0317	5008	,	,		15505	0.1012		0.0636	False		,,,				2504	0.1247				p.T32I		Atlas-SNP	.											.	ZNF91	349	.	0			c.C95T						PASS	.	G	ILE/THR	370,4036	180.5+/-208.7	15,340,1848	90.0	99.0	96.0		95	0.2	0.0	19	dbSNP_134	96	456,8144	136.4+/-193.5	9,438,3853	no	missense	ZNF91	NM_003430.2	89	24,778,5701	AA,AG,GG		5.3023,8.3976,6.3509	possibly-damaging	32/1192	23557502	826,12180	2203	4300	6503	SO:0001583	missense	7644	exon2			TGTGCAGTGTCCA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.95C>T	19.37:g.23557502G>A	ENSP00000300619:p.Thr32Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	163	0.07463369963369963	42	0.08536585365853659	12	0.03314917127071823	58	0.10139860139860139	51	0.06728232189973615	G	2.575	-0.298822	0.05532	0.083976	0.053023	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.01767	4.65;4.65	0.149	0.149	0.14863	Krueppel-associated box (4);	.	.	.	.	T	0.00109	0.0003	M	0.70275	2.135	0.80722	P	0.0	B;B	0.24132	0.004;0.098	B;B	0.23419	0.002;0.046	T	0.16630	-1.0396	7	0.51188	T	0.08	.	.	.	.	.	32;32	Q05481-2;Q05481	.;ZNF91_HUMAN	I	32	ENSP00000300619:T32I;ENSP00000380272:T32I	ENSP00000300619:T32I	T	-	2	0	ZNF91	23349342	0.000000	0.05858	0.049000	0.19019	0.050000	0.14768	-0.411000	0.07142	0.192000	0.20272	0.195000	0.17529	ACT	G|0.932;A|0.068	0.068	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
PPP1R12C	54776	hgsc.bcm.edu	37	19	55624113	55624113	+	Silent	SNP	G	G	A	rs34521018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55624113G>A	ENST00000263433.3	-	2	387	c.372C>T	c.(370-372)ggC>ggT	p.G124G	PPP1R12C_ENST00000376393.2_Silent_p.G124G|PPP1R12C_ENST00000435544.2_Silent_p.G50G	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)		TCACAGTGGCGCCCTGCTCCA	0.657													G|||	770	0.153754	0.1051	0.1254	5008	,	,		17342	0.1101		0.1362	False		,,,				2504	0.3027				p.G124G		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.C372T						PASS	.	G		468,3938	222.3+/-239.2	18,432,1753	82.0	72.0	76.0		372	-9.4	0.2	19	dbSNP_126	76	1019,7581	218.4+/-256.8	70,879,3351	no	coding-synonymous	PPP1R12C	NM_017607.2		88,1311,5104	AA,AG,GG		11.8488,10.6219,11.4332		124/783	55624113	1487,11519	2203	4300	6503	SO:0001819	synonymous_variant	54776	exon2			AGTGGCGCCCTGC	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.372C>T	19.37:g.55624113G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			G|0.877;A|0.123	0.123	strong		0.657	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	163	0	0		WXS	Illumina HiSeq	Phase_I	162	144	0.888889	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	
KANK1	23189	hgsc.bcm.edu	37	9	740901	740901	+	Silent	SNP	C	C	T	rs2296049	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:740901C>T	ENST00000382303.1	+	13	4315	c.3663C>T	c.(3661-3663)ttC>ttT	p.F1221F	KANK1_ENST00000382293.3_Silent_p.F1063F|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Silent_p.F1221F	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1221	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.F1063F(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AAGAACTCTTCGGCTGTGGGG	0.572													T|||	1332	0.265974	0.413	0.317	5008	,	,		19213	0.1716		0.2117	False		,,,				2504	0.184				p.F1221F		Atlas-SNP	.											KANK1,NS,carcinoma,0,1	KANK1	231	1	1	Substitution - coding silent(1)	stomach(1)	c.C3663T						scavenged	.	T	,	1741,2665	521.4+/-370.5	354,1033,816	155.0	127.0	136.0		3663,3189	-5.9	0.3	9	dbSNP_100	136	1891,6709	334.6+/-321.1	223,1445,2632	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	577,2478,3448	TT,TC,CC		21.9884,39.5143,27.9256	,	1221/1353,1063/1195	740901	3632,9374	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon13			ACTCTTCGGCTGT	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3663C>T	9.37:g.740901C>T		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			C|0.732;T|0.268	0.268	strong		0.572	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
P2RX7	5027	hgsc.bcm.edu	37	12	121622419	121622419	+	Silent	SNP	G	G	T	rs3751142|rs199840038	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121622419G>T	ENST00000546057.1	+	13	1745	c.1602G>T	c.(1600-1602)ctG>ctT	p.L534L	P2RX7_ENST00000535250.1_Silent_p.L444L|P2RX7_ENST00000541446.1_Silent_p.L245L|P2RX7_ENST00000328963.5_Silent_p.L364L|RP11-340F14.5_ENST00000569999.1_RNA|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	534					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)					AGCCCTTGCTGGCGCTGGATG	0.622													G|||	813	0.16234	0.1589	0.2608	5008	,	,		17910	0.1597		0.0755	False		,,,				2504	0.1892				p.L534L		Atlas-SNP	.											.	P2RX7	53	.	0			c.G1602T						PASS	.	G		687,3719		55,577,1571	24.0	21.0	22.0		1602	4.3	1.0	12	dbSNP_107	22	631,7967		29,573,3697	no	coding-synonymous	P2RX7	NM_002562.5		84,1150,5268	TT,TG,GG		7.3389,15.5924,10.1353		534/596	121622419	1318,11686	2203	4299	6502	SO:0001819	synonymous_variant	5027	exon13			CTTGCTGGCGCTG	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.1602G>T	12.37:g.121622419G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Silent	SNP	ENST00000546057.1	37	CCDS9213.1																																																																																			G|0.883;T|0.117	0.117	strong		0.622	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TMEM232	642987	hgsc.bcm.edu	37	5	109954164	109954164	+	Missense_Mutation	SNP	C	C	T	rs61978570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:109954164C>T	ENST00000455884.2	-	8	918	c.868G>A	c.(868-870)Gtc>Atc	p.V290I	TMEM232_ENST00000429839.2_Missense_Mutation_p.V290I|TMEM232_ENST00000515518.2_5'UTR			C9JQI7	TM232_HUMAN	transmembrane protein 232	290						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						TTATGGAAGACGAGATGTTCA	0.393													C|||	83	0.0165735	0.0219	0.0216	5008	,	,		16329	0.0079		0.0278	False		,,,				2504	0.0031				p.V290I		Atlas-SNP	.											.	TMEM232	57	.	0			c.G868A						PASS	.	C	ILE/VAL	42,1342		0,42,650	132.0	105.0	113.0		868	-8.7	0.0	5	dbSNP_129	113	58,3124		0,58,1533	yes	missense	TMEM232	NM_001039763.3	29	0,100,2183	TT,TC,CC		1.8228,3.0347,2.1901	benign	290/658	109954164	100,4466	692	1591	2283	SO:0001583	missense	642987	exon8			GGAAGACGAGATG	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.868G>A	5.37:g.109954164C>T	ENSP00000401477:p.Val290Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	46	0.021062271062271064	12	0.024390243902439025	10	0.027624309392265192	6	0.01048951048951049	18	0.023746701846965697	C	0.387	-0.925431	0.02377	0.030347	0.018228	ENSG00000186952	ENST00000429839;ENST00000455884	.	.	.	5.97	-8.69	0.00855	.	1.308790	0.05193	N	0.503539	T	0.01835	0.0058	N	0.00246	-1.78	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42430	-0.9452	8	.	.	.	0.2126	10.7866	0.46409	0.0788:0.0627:0.6199:0.2386	rs61978570	290;290;172	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	I	290	.	.	V	-	1	0	TMEM232	109982063	0.015000	0.18098	0.019000	0.16419	0.490000	0.33462	-0.534000	0.06150	-0.777000	0.04572	-1.333000	0.01266	GTC	C|0.980;T|0.020	0.020	strong		0.393	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
CHTF18	63922	hgsc.bcm.edu	37	16	840378	840378	+	Missense_Mutation	SNP	A	A	G	rs3765263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:840378A>G	ENST00000262315.9	+	6	794	c.731A>G	c.(730-732)aAg>aGg	p.K244R	RPUSD1_ENST00000561734.1_5'Flank|CHTF18_ENST00000455171.2_Missense_Mutation_p.K272R|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR|RPUSD1_ENST00000565809.1_5'Flank|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.K441R	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						PASS	.	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	72	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	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	
OR13G1	441933	hgsc.bcm.edu	37	1	247836207	247836207	+	Missense_Mutation	SNP	T	T	A	rs28711149	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247836207T>A	ENST00000359688.2	-	1	158	c.137A>T	c.(136-138)aAa>aTa	p.K46I	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	46			K -> I (in dbSNP:rs28711149).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	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)			GTTATAGATTTTGGCAATGAT	0.438													A|||	1650	0.329473	0.2965	0.2392	5008	,	,		23955	0.376		0.3519	False		,,,				2504	0.3671				p.K46I		Atlas-SNP	.											.	OR13G1	78	.	0			c.A137T						PASS	.	A	ILE/LYS	1312,3094	697.4+/-406.2	188,936,1079	90.0	74.0	80.0		137	3.2	0.0	1	dbSNP_125	80	3098,5502	658.3+/-401.6	562,1974,1764	yes	missense	OR13G1	NM_001005487.1	102	750,2910,2843	AA,AT,TT		36.0233,29.7776,33.9074	benign	46/308	247836207	4410,8596	2203	4300	6503	SO:0001583	missense	441933	exon1			TAGATTTTGGCAA	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.137A>T	1.37:g.247836207T>A	ENSP00000352717:p.Lys46Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	676	0.30952380952380953	138	0.2804878048780488	88	0.2430939226519337	185	0.32342657342657344	265	0.3496042216358839	A	1.436	-0.568925	0.03910	0.297776	0.360233	ENSG00000197437	ENST00000359688	T	0.01240	5.12	4.33	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.164771	0.27591	N	0.018682	T	0.00012	0.0000	N	0.00000	-4.03	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38023	-0.9680	9	0.02654	T	1	-29.134	4.9356	0.13939	0.7438:0.0:0.0927:0.1635	rs28711149	46	Q8NGZ3	O13G1_HUMAN	I	46	ENSP00000352717:K46I	ENSP00000352717:K46I	K	-	2	0	OR13G1	245902830	0.030000	0.19436	0.006000	0.13384	0.001000	0.01503	3.177000	0.50871	0.297000	0.22615	-0.257000	0.10917	AAA	T|0.663;A|0.337	0.337	strong		0.438	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
PKD1L2	114780	hgsc.bcm.edu	37	16	81211496	81211496	+	RNA	SNP	C	C	A	rs9935113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81211496C>A	ENST00000527937.1	-	0	319				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA			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						AGAACGGTGCCCTCCTCTGGG	0.597													C|||	1042	0.208067	0.2791	0.1744	5008	,	,		17905	0.1052		0.171	False		,,,				2504	0.2802				p.G785C		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G2353T						PASS	.	C	CYS/GLY,CYS/GLY	1011,3087		126,759,1164	79.0	81.0	80.0		2353,2353	4.9	0.6	16	dbSNP_119	80	1412,6976		122,1168,2904	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	159,159	248,1927,4068	AA,AC,CC		16.8336,24.6706,19.4057	probably-damaging,probably-damaging	785/992,785/2460	81211496	2423,10063	2049	4194	6243			114780	exon14			CGGTGCCCTCCTC	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.81211496C>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		368|368	0.1684981684981685|0.1684981684981685	132|132	0.2682926829268293|0.2682926829268293	59|59	0.16298342541436464|0.16298342541436464	53|53	0.09265734265734266|0.09265734265734266	124|124	0.16358839050131926|0.16358839050131926	C|C	14.11|14.11	2.437976|2.437976	0.43326|0.43326	0.246706|0.246706	0.168336|0.168336	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114|ENST00000526632	D;D|.	0.85629|.	-2.01;-2.01|.	4.89|4.89	4.89|4.89	0.63831|0.63831	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);|.	0.067594|0.067594	0.64402|0.64402	D|D	0.000012|0.000012	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.33815|0.33815	P|P	0.37165400000000004|0.37165400000000004	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.997;0.998|.	T|T	0.01290|0.01290	-1.1394|-1.1394	8|4	0.87932|.	D|.	0|.	-13.2573|-13.2573	15.0685|15.0685	0.72014|0.72014	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs9935113;rs52837465;rs57029035;rs9935113|rs9935113;rs52837465;rs57029035;rs9935113	785;785|.	Q7Z442-3;Q7Z442|.	.;PK1L2_HUMAN|.	C|V	100;785|312	ENSP00000436309:G100C;ENSP00000337397:G785C|.	ENSP00000337397:G785C|.	G|G	-|-	1|2	0|0	PKD1L2|PKD1L2	79768997|79768997	1.000000|1.000000	0.71417|0.71417	0.603000|0.603000	0.28903|0.28903	0.040000|0.040000	0.13550|0.13550	3.894000|3.894000	0.56250|0.56250	2.289000|2.289000	0.77006|0.77006	0.549000|0.549000	0.68633|0.68633	GGC|GGG	C|0.823;A|0.177	0.177	strong		0.597	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
PARL	55486	hgsc.bcm.edu	37	3	183580581	183580581	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183580581C>T	ENST00000317096.4	-	4	531	c.471G>A	c.(469-471)aaG>aaA	p.K157K	PARL_ENST00000311101.5_Silent_p.K157K|PARL_ENST00000435888.1_Silent_p.K157K	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	157					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TATTCCACCACTTGTTAATCT	0.393																																					p.K157K		Atlas-SNP	.											.	PARL	32	.	0			c.G471A						PASS	.						108.0	95.0	100.0					3																	183580581		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon4			CCACCACTTGTTA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.471G>A	3.37:g.183580581C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	C	9.171	1.021044	0.19433	.	.	ENSG00000175193	ENST00000449306	.	.	.	5.45	4.51	0.55191	.	.	.	.	.	T	0.61476	0.2350	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57774	-0.7753	4	.	.	.	-19.1355	10.6799	0.45809	0.1449:0.7143:0.1408:0.0	.	.	.	.	M	71	.	.	V	-	1	0	PARL	185063275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.931000	0.28871	2.690000	0.91761	0.557000	0.71058	GTG	.	.	none		0.393	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
C17orf53	78995	hgsc.bcm.edu	37	17	42225547	42225547	+	Missense_Mutation	SNP	A	A	C	rs227584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:42225547A>C	ENST00000319977.4	+	3	613	c.376A>C	c.(376-378)Aca>Cca	p.T126P	C17orf53_ENST00000245382.6_Missense_Mutation_p.T126P|C17orf53_ENST00000585683.1_Missense_Mutation_p.T126P	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	126			T -> P (in dbSNP:rs227584). {ECO:0000269|PubMed:15489334}.							NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GCTCAGAGAGACAGCAAGACC	0.522													C|||	2887	0.576478	0.9047	0.4582	5008	,	,		20956	0.7589		0.2992	False		,,,				2504	0.3139				p.T126P		Atlas-SNP	.											.	C17orf53	59	.	0			c.A376C						PASS	.	C	PRO/THR,PRO/THR	3497,909	350.8+/-311.0	1401,695,107	130.0	136.0	134.0	http://www.ncbi.nlm.nih.gov/pubmed?term	376,376	1.5	0.7	17	dbSNP_79	134	2666,5934	685.3+/-404.0	417,1832,2051	yes	missense,missense	C17orf53	NM_001171251.1,NM_024032.3	38,38	1818,2527,2158	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.0,20.631,47.3858	benign,benign	126/647,126/648	42225547	6163,6843	2203	4300	6503	SO:0001583	missense	78995	exon3			AGAGAGACAGCAA	AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.376A>C	17.37:g.42225547A>C	ENSP00000313500:p.Thr126Pro	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	1253	0.5737179487179487	445	0.9044715447154471	149	0.4116022099447514	424	0.7412587412587412	235	0.3100263852242744	C	0.355	-0.942870	0.02322	0.79369	0.31	ENSG00000125319	ENST00000319977;ENST00000245382	T;T	0.42513	0.97;0.97	4.61	1.5	0.22942	.	0.782162	0.11770	N	0.531181	T	0.00012	0.0000	N	0.00308	-1.67	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	0.33343	-0.9872	9	0.02654	T	1	-1.4987	3.1789	0.06578	0.319:0.4178:0.0:0.2632	rs227584;rs3744431;rs17844825;rs17857536;rs57825870;rs227584	126;126;126	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	P	126	ENSP00000313500:T126P;ENSP00000245382:T126P	ENSP00000245382:T126P	T	+	1	0	C17orf53	39581073	0.082000	0.21442	0.737000	0.30932	0.059000	0.15707	0.105000	0.15333	0.023000	0.15187	-0.217000	0.12591	ACA	T|0.004;G|0.002	.	strong		0.522	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
PCNXL2	80003	hgsc.bcm.edu	37	1	233122127	233122127	+	Missense_Mutation	SNP	C	C	T	rs41309639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:233122127C>T	ENST00000258229.9	-	33	6185	c.5951G>A	c.(5950-5952)cGg>cAg	p.R1984Q	PCNXL2_ENST00000344698.2_Missense_Mutation_p.R636Q	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1984	Ser-rich.		R -> Q (in dbSNP:rs41309639).			integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CAAGGAGAGCCGGCTGCCCGA	0.677													C|||	863	0.172324	0.2163	0.1254	5008	,	,		15104	0.1667		0.2008	False		,,,				2504	0.1227				p.R1984Q		Atlas-SNP	.											PCNXL2,NS,carcinoma,0,2	PCNXL2	204	2	0			c.G5951A						PASS	.	C	GLN/ARG	941,3155		122,697,1229	18.0	25.0	23.0		5951	1.6	1.0	1	dbSNP_127	23	1981,6397		239,1503,2447	yes	missense	PCNXL2	NM_014801.3	43	361,2200,3676	TT,TC,CC		23.6453,22.9736,23.4247	benign	1984/2138	233122127	2922,9552	2048	4189	6237	SO:0001583	missense	80003	exon33			GAGAGCCGGCTGC	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5951G>A	1.37:g.233122127C>T	ENSP00000258229:p.Arg1984Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	436	0.19963369963369965	107	0.21747967479674796	55	0.15193370165745856	117	0.20454545454545456	157	0.20712401055408972	C	1.460	-0.562604	0.03939	0.229736	0.236453	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.19806	2.12;3.33	5.85	1.57	0.23409	.	0.260739	0.32624	N	0.005850	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	1.0	B;B	0.15473	0.003;0.013	B;B	0.10450	0.002;0.005	T	0.40496	-0.9560	9	0.02654	T	1	.	3.1769	0.06571	0.1857:0.3746:0.0:0.4397	rs41309639;rs61731485	1984;636	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	Q	636;1984	ENSP00000340759:R636Q;ENSP00000258229:R1984Q	ENSP00000258229:R1984Q	R	-	2	0	PCNXL2	231188750	1.000000	0.71417	0.999000	0.59377	0.110000	0.19582	1.388000	0.34442	0.318000	0.23185	-0.258000	0.10820	CGG	C|0.800;T|0.200	0.200	strong		0.677	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
MUC4	4585	hgsc.bcm.edu	37	3	195511364	195511364	+	Missense_Mutation	SNP	T	T	A	rs75187745		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195511364T>A	ENST00000463781.3	-	2	7546	c.7087A>T	c.(7087-7089)Aca>Tca	p.T2363S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2363S	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)		GTGTCACCTGTGGATACTGAG	0.587																																					p.T2363S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.A7087T						scavenged	.						23.0	21.0	21.0					3																	195511364		689	1583	2272	SO:0001583	missense	4585	exon2			CACCTGTGGATAC	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.7087A>T	3.37:g.195511364T>A	ENSP00000417498:p.Thr2363Ser	Somatic	65	2	0.0307692		WXS	Illumina HiSeq	Phase_I	173	11	0.0635838	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	.	.	.	.	.	.	.	.	.	.	T	5.115	0.206928	0.09704	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49720	0.77;1.01	.	.	.	.	.	.	.	.	T	0.29321	0.0730	N	0.19112	0.55	0.09310	N	1	P	0.34587	0.458	B	0.39152	0.292	T	0.18272	-1.0342	7	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2363	E7ESK3	.	S	2363	ENSP00000417498:T2363S;ENSP00000420243:T2363S	.	T	-	1	0	MUC4	196995759	0.007000	0.16637	0.008000	0.14137	0.111000	0.19643	-2.023000	0.01438	0.408000	0.25621	0.055000	0.15244	ACA	T|0.500;A|0.500	0.500	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7110548C>T	ENST00000306904.5	+	1	384	c.197C>T	c.(196-198)gCc>gTc	p.A66V		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	66	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.		A -> V (in dbSNP:rs11041170). {ECO:0000269|PubMed:10958650}.			nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCGCCGCCAGAGACATG	0.647													C|||	759	0.151558	0.2337	0.1628	5008	,	,		9247	0.0139		0.2316	False		,,,				2504	0.092				p.A66V		Atlas-SNP	.											.	RBMXL2	47	.	0			c.C197T						PASS	.	C	VAL/ALA	998,3396		105,788,1304	22.0	21.0	21.0		197	-0.5	1.0	11	dbSNP_120	21	1993,6599		240,1513,2543	no	missense	RBMXL2	NM_014469.4	64	345,2301,3847	TT,TC,CC		23.196,22.7128,23.0325	benign	66/393	7110548	2991,9995	2197	4296	6493	SO:0001583	missense	27288	exon1			CCGCCGCCAGAGA	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.197C>T	11.37:g.7110548C>T	ENSP00000304139:p.Ala66Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	364	0.16666666666666666	119	0.241869918699187	62	0.1712707182320442	11	0.019230769230769232	172	0.22691292875989447	C	10.62	1.401357	0.25291	0.227128	0.23196	ENSG00000170748	ENST00000306904	T	0.13778	2.56	2.51	-0.49	0.12049	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.068562	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00707	-1.245	0.29091	P	0.882081	B	0.06786	0.001	B	0.13407	0.009	T	0.46076	-0.9217	9	0.36615	T	0.2	.	6.1131	0.20112	0.0:0.4557:0.0:0.5443	rs11041170	66	O75526	HNRGT_HUMAN	V	66	ENSP00000304139:A66V	ENSP00000304139:A66V	A	+	2	0	RBMXL2	7067124	0.996000	0.38824	0.978000	0.43139	0.984000	0.73092	1.429000	0.34903	-0.131000	0.11578	-0.463000	0.05309	GCC	C|0.795;T|0.205	0.205	strong		0.647	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
ELFN1	392617	hgsc.bcm.edu	37	7	1785738	1785738	+	Silent	SNP	G	G	A	rs61236605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1785738G>A	ENST00000424383.2	+	3	1993	c.1506G>A	c.(1504-1506)gcG>gcA	p.A502A	ELFN1_ENST00000561626.1_Silent_p.A502A|ELFN1_ENST00000541472.1_Silent_p.A502A			P0C7U0	ELFN1_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 1	502					negative regulation of phosphatase activity (GO:0010923)|synapse organization (GO:0050808)	dendrite (GO:0030425)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)	1						ACCTGCCTGCGGCCGGCGAGG	0.711													G|||	684	0.136581	0.0325	0.1138	5008	,	,		13818	0.1042		0.2018	False		,,,				2504	0.2597				p.A502A		Atlas-SNP	.											.	ELFN1	22	.	0			c.G1506A						PASS	.						32.0	37.0	35.0					7																	1785738		692	1591	2283	SO:0001819	synonymous_variant	392617	exon2			GCCTGCGGCCGGC		CCDS59046.1	7p22.3	2013-02-11	2011-10-27	2011-10-27	ENSG00000225968	ENSG00000225968		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	33154	protein-coding gene	gene with protein product		614964	"""extracellular leucine-rich repeat and fibronectin type III containing 1"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 1"", ""protein phosphatase 1, regulatory subunit 28"""	PPP1R28		17868438	Standard	NM_001128636		Approved		uc010ksg.2	P0C7U0	OTTHUMG00000151495	ENST00000424383.2:c.1506G>A	7.37:g.1785738G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	26	21	0.807692	NM_001128636	H3BS57	Silent	SNP	ENST00000424383.2	37	CCDS59046.1																																																																																			G|0.868;A|0.132	0.132	strong		0.711	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322893.2	NM_001128636	
MDH1B	130752	hgsc.bcm.edu	37	2	207619779	207619779	+	Silent	SNP	A	A	G	rs59358632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207619779A>G	ENST00000374412.3	-	5	1139	c.864T>C	c.(862-864)ggT>ggC	p.G288G	MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000454776.2_Silent_p.G288G|MDH1B_ENST00000449792.1_Silent_p.G190G	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	288					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)		CTTTCGCTTCACCTTCCACCC	0.428													A|||	573	0.114417	0.2595	0.0548	5008	,	,		19768	0.0526		0.0586	False		,,,				2504	0.0818				p.G288G	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.T864C						PASS	.	A		1059,3347	386.5+/-326.1	130,799,1274	92.0	85.0	87.0		864	-5.9	0.0	2	dbSNP_129	87	649,7951	165.8+/-217.9	31,587,3682	no	coding-synonymous	MDH1B	NM_001039845.1		161,1386,4956	GG,GA,AA		7.5465,24.0354,13.1324		288/519	207619779	1708,11298	2203	4300	6503	SO:0001819	synonymous_variant	130752	exon5			CGCTTCACCTTCC		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.864T>C	2.37:g.207619779A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	118	66	0.559322	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Silent	SNP	ENST00000374412.3	37	CCDS33365.1																																																																																			A|0.884;G|0.116	0.116	strong		0.428	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
AGMAT	79814	hgsc.bcm.edu	37	1	15905471	15905471	+	Missense_Mutation	SNP	G	G	T	rs116813534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15905471G>T	ENST00000375826.3	-	4	745	c.603C>A	c.(601-603)caC>caA	p.H201Q	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	201					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCGCCCCGTGGTAGAGCT	0.627																																					p.H201Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.C603A						PASS	.						66.0	64.0	64.0					1																	15905471		2203	4300	6503	SO:0001583	missense	79814	exon4			CGCCCCGTGGTAG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.603C>A	1.37:g.15905471G>T	ENSP00000364986:p.His201Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	51	0.607143	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029886	0.75504	.	.	ENSG00000116771	ENST00000375826	D	0.88354	-2.37	5.87	-5.21	0.02815	Ureohydrolase domain (1);	0.000000	0.85682	D	0.000000	D	0.96281	0.8787	H	0.99312	4.51	0.50813	D	0.999893	D	0.89917	1.0	D	0.97110	1.0	D	0.95290	0.8394	10	0.87932	D	0	-29.7251	16.7644	0.85521	0.7501:0.0:0.2499:0.0	.	201	Q9BSE5	SPEB_HUMAN	Q	201	ENSP00000364986:H201Q	ENSP00000364986:H201Q	H	-	3	2	AGMAT	15778058	0.088000	0.21588	0.767000	0.31495	0.884000	0.51177	-0.576000	0.05854	-1.114000	0.02977	-0.142000	0.14014	CAC	A|0.007;G|0.993;T|0.000	0.000	strong		0.627	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
C9orf139	401563	hgsc.bcm.edu	37	9	139929435	139929435	+	Missense_Mutation	SNP	A	A	G	rs12337910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	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	
SERPINA10	51156	hgsc.bcm.edu	37	14	94756750	94756750	+	Missense_Mutation	SNP	T	T	C	rs941591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:94756750T>C	ENST00000393096.1	-	2	646	c.181A>G	c.(181-183)Agt>Ggt	p.S61G	SERPINA10_ENST00000554723.1_Missense_Mutation_p.S101G|SERPINA10_ENST00000261994.4_Missense_Mutation_p.S61G|SERPINA10_ENST00000554173.1_Missense_Mutation_p.S61G	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	61			S -> G (in dbSNP:rs941591). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S61G(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		TCTTCCTCACTGGCCTTCTCC	0.592													T|||	1727	0.344848	0.4614	0.1513	5008	,	,		20023	0.6052		0.166	False		,,,				2504	0.2403				p.S61G		Atlas-SNP	.											SERPINA10,NS,carcinoma,0,1	SERPINA10	83	1	1	Substitution - Missense(1)	stomach(1)	c.A181G						PASS	.	T	GLY/SER,GLY/SER	1748,2658	520.2+/-370.2	366,1016,821	55.0	51.0	52.0		181,181	-2.3	0.0	14	dbSNP_86	52	1414,7186	271.7+/-289.7	124,1166,3010	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	56,56	490,2182,3831	CC,CT,TT		16.4419,39.6732,24.3119	benign,benign	61/445,61/445	94756750	3162,9844	2203	4300	6503	SO:0001583	missense	51156	exon2			CCTCACTGGCCTT	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.181A>G	14.37:g.94756750T>C	ENSP00000376809:p.Ser61Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	766	0.3507326007326007	242	0.491869918699187	56	0.15469613259668508	341	0.5961538461538461	127	0.16754617414248021	T	0.007	-2.006494	0.00426	0.396732	0.164419	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.85629	-2.01;-1.97;-1.97;-1.97	1.16	-2.32	0.06745	Serpin domain (1);	.	.	.	.	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	0.35847	-0.9772	8	0.26408	T	0.33	.	6.1543	0.20328	0.0:0.5275:0.0:0.4725	rs941591;rs52819624;rs60013744;rs941591	61	Q9UK55	ZPI_HUMAN	G	101;61;61;61	ENSP00000450896:S101G;ENSP00000376809:S61G;ENSP00000261994:S61G;ENSP00000450971:S61G	ENSP00000261994:S61G	S	-	1	0	SERPINA10	93826503	0.000000	0.05858	0.005000	0.12908	0.013000	0.08279	-4.369000	0.00245	-2.725000	0.00387	-2.748000	0.00125	AGT	T|0.700;C|0.300	0.300	strong		0.592	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
FAM135B	51059	hgsc.bcm.edu	37	8	139164570	139164570	+	Silent	SNP	C	C	T	rs3750307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	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	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305956	39305956	+	Missense_Mutation	SNP	G	G	A	rs1497383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39305956G>A	ENST00000343246.4	-	1	98	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	22	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		R -> C (in dbSNP:rs1497383). {ECO:0000269|PubMed:11279113}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGTTC	0.632													G|||	2209	0.441094	0.3699	0.5144	5008	,	,		16738	0.3532		0.4861	False		,,,				2504	0.5297				p.R22C		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.C64T						PASS	.	G	CYS/ARG	1658,2746		319,1020,863	30.0	34.0	33.0		64	1.5	0.5	17	dbSNP_88	33	4137,4449		994,2149,1150	yes	missense	KRTAP4-5	NM_033188.3	180	1313,3169,2013	AA,AG,GG		48.1831,37.6476,44.6112	benign	22/182	39305956	5795,7195	2202	4293	6495	SO:0001583	missense	85289	exon1			TGGGGCGGCAGCA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.64C>T	17.37:g.39305956G>A	ENSP00000340546:p.Arg22Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	954	0.4368131868131868	186	0.3780487804878049	187	0.5165745856353591	216	0.3776223776223776	365	0.4815303430079156	.	4.323	0.059209	0.08339	0.376476	0.481831	ENSG00000198271	ENST00000343246	T	0.01446	4.88	3.52	1.46	0.22682	.	0.915314	0.08847	U	0.884953	T	0.00012	0.0000	M	0.72576	2.205	0.41445	P	0.012055999999999956	B	0.21753	0.06	B	0.15484	0.013	T	0.35624	-0.9781	9	0.49607	T	0.09	.	2.1325	0.03754	0.1118:0.1821:0.4821:0.224	rs1497383;rs6503605;rs1497383	22	Q9BYR2	KRA45_HUMAN	C	22	ENSP00000340546:R22C	ENSP00000340546:R22C	R	-	1	0	KRTAP4-5	36559482	0.022000	0.18835	0.504000	0.27639	0.011000	0.07611	-0.126000	0.10563	0.421000	0.25980	-0.254000	0.11334	CGC	G|0.556;A|0.444	0.444	strong		0.632	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
LDB3	11155	hgsc.bcm.edu	37	10	88466465	88466465	+	Silent	SNP	C	C	T	rs45459491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88466465C>T	ENST00000361373.4	+	7	1095	c.1074C>T	c.(1072-1074)gcC>gcT	p.A358A	LDB3_ENST00000458213.2_Intron|LDB3_ENST00000429277.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CAAGTCCTGCCGACAGCCCAA	0.672													C|||	101	0.0201677	0.0008	0.0159	5008	,	,		18021	0.0		0.0368	False		,,,				2504	0.0532				p.A358A		Atlas-SNP	.											.	LDB3	164	.	0			c.C1074T						PASS	.	C	,,	34,4366		1,32,2167	29.0	22.0	25.0		,,1074	-0.1	0.0	10	dbSNP_127	25	317,8279		5,307,3986	no	intron,intron,coding-synonymous	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	,,	6,339,6153	TT,TC,CC		3.6878,0.7727,2.7008	,,	,,358/728	88466465	351,12645	2200	4298	6498	SO:0001819	synonymous_variant	11155	exon7			TCCTGCCGACAGC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1074C>T	10.37:g.88466465C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	164	71	0.432927	NM_007078		Silent	SNP	ENST00000361373.4	37	CCDS7377.1																																																																																			C|0.976;T|0.024	0.024	strong		0.672	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2		
LAMP2	3920	hgsc.bcm.edu	37	X	119576455	119576455	+	Splice_Site	SNP	G	G	A	rs73219144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:119576455G>A	ENST00000200639.4	-	7	1063	c.927C>T	c.(925-927)tcC>tcT	p.S309S	LAMP2_ENST00000538785.1_Splice_Site_p.S198S|LAMP2_ENST00000371335.4_Splice_Site_p.S309S|LAMP2_ENST00000434600.2_Splice_Site_p.S309S|LAMP2_ENST00000540603.1_Splice_Site_p.S262S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	309	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTGCTTACCGGAGCCATTAA	0.358													G|||	50	0.013245	0.0	0.0072	3775	,	,		13506	0.0		0.0398	False		,,,				2504	0.0051				p.S309S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C927T						PASS	.	G	,,	29,3806		0,24,5,1608,566	254.0	242.0	246.0		927,927,927	0.9	1.0	X	dbSNP_130	246	274,6454		6,187,75,2235,1797	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	6,211,80,3843,2363	AA,AG,A,GG,G		4.0725,0.7562,2.8685	,,	309/412,309/411,309/411	119576455	303,10260	2203	4300	6503	SO:0001630	splice_region_variant	3920	exon7			CTTACCGGAGCCA	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"""CD molecules"""	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.928+1C>T	X.37:g.119576455G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	36	0.947368	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.358	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		Silent
FUT6	2528	hgsc.bcm.edu	37	19	5832209	5832209	+	Missense_Mutation	SNP	G	G	A	rs778805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5832209G>A	ENST00000318336.4	-	3	1564	c.370C>T	c.(370-372)Ccg>Tcg	p.P124S	FUT6_ENST00000527106.1_Missense_Mutation_p.P124S|FUT6_ENST00000286955.5_Missense_Mutation_p.P124S|FUT6_ENST00000592563.1_Missense_Mutation_p.P124S|FUT6_ENST00000524754.1_Missense_Mutation_p.P124S	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	124			P -> S (found in alpha(1,3)- fucosyltransferase-deficient individuals; results in partial enzyme inactivation; complete enzyme inactivation when associated with V-244 and G-303; dbSNP:rs778805). {ECO:0000269|PubMed:11102976, ECO:0000269|Ref.4}.		fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|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)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						TGCCGCCTCGGGGAGCGTGGG	0.607													G|||	2480	0.495208	0.643	0.4928	5008	,	,		16047	0.6121		0.3131	False		,,,				2504	0.364				p.P124S		Atlas-SNP	.											FUT6,NS,carcinoma,+1,1	FUT6	30	1	0			c.C370T	GRCh37	CM940794	FUT6	M	rs778805	scavenged	.	G	SER/PRO,SER/PRO	2612,1794	638.8+/-397.0	766,1080,357	71.0	60.0	64.0		370,370	2.1	0.0	19	dbSNP_86	64	2849,5751	447.3+/-361.5	453,1943,1904	yes	missense,missense	FUT6	NM_000150.2,NM_001040701.1	74,74	1219,3023,2261	AA,AG,GG		33.1279,40.7172,41.9883	possibly-damaging,possibly-damaging	124/360,124/360	5832209	5461,7545	2203	4300	6503	SO:0001583	missense	2528	exon3			GCCTCGGGGAGCG		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"""Fucosyltransferases"""	4017	protein-coding gene	gene with protein product	"""alpha-(1,3)-fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.370C>T	19.37:g.5832209G>A	ENSP00000313398:p.Pro124Ser	Somatic	121	2	0.0165289		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	1053	0.48214285714285715	319	0.6483739837398373	168	0.46408839779005523	329	0.5751748251748252	237	0.31266490765171506	G	10.20	1.286073	0.23478	0.592828	0.331279	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	3.17	2.11	0.27256	.	0.206719	0.32970	N	0.005421	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B	0.19331	0.035;0.006	B;B	0.29440	0.102;0.063	T	0.32295	-0.9912	9	0.41790	T	0.15	.	12.3946	0.55378	0.0:0.0:0.8278:0.1722	rs778805;rs4041472;rs17205925;rs17855738;rs58152597;rs778805	124;124	C9J8A2;P51993	.;FUT6_HUMAN	S	124	ENSP00000431708:P124S;ENSP00000432954:P124S;ENSP00000313398:P124S;ENSP00000286955:P124S;ENSP00000436547:P124S	ENSP00000286955:P124S	P	-	1	0	FUT6	5783209	0.573000	0.26676	0.000000	0.03702	0.000000	0.00434	1.907000	0.39897	0.145000	0.18977	-2.014000	0.00435	CCG	G|0.555;A|0.445	0.445	strong		0.607	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150	
FCGBP	8857	hgsc.bcm.edu	37	19	40392360	40392360	+	Missense_Mutation	SNP	G	G	A	rs200977347	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40392360G>A	ENST00000221347.6	-	16	8151	c.8144C>T	c.(8143-8145)gCa>gTa	p.A2715V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2715						extracellular vesicular exosome (GO:0070062)		p.A2715V(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)			GCCTCCAGCTGCCTGGCAAGC	0.587													G|||	1248	0.249201	0.1619	0.3876	5008	,	,		13881	0.1935		0.33	False		,,,				2504	0.2434				p.A2715V		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.C8144T						scavenged	.						5.0	6.0	6.0					19																	40392360		1980	3956	5936	SO:0001583	missense	8857	exon16			CCAGCTGCCTGGC	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.8144C>T	19.37:g.40392360G>A	ENSP00000221347:p.Ala2715Val	Somatic	405	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082846	0.36758	.	.	ENSG00000090920	ENST00000221347	T	0.77620	-1.11	2.58	-0.163	0.13363	Uncharacterised domain, cysteine-rich (2);	0.292022	0.32244	N	0.006362	D	0.82323	0.5012	M	0.76574	2.34	0.23331	N	0.997894	D	0.76494	0.999	D	0.79108	0.992	T	0.69347	-0.5169	10	0.33940	T	0.23	.	5.3676	0.16123	0.0:0.1728:0.3161:0.5111	.	2715	Q9Y6R7	FCGBP_HUMAN	V	2715	ENSP00000221347:A2715V	ENSP00000221347:A2715V	A	-	2	0	FCGBP	45084200	0.000000	0.05858	0.984000	0.44739	0.668000	0.39293	-0.272000	0.08560	0.383000	0.24910	0.298000	0.19748	GCA	.	.	weak		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MLN	4295	hgsc.bcm.edu	37	6	33768897	33768897	+	Missense_Mutation	SNP	A	A	G	rs2281820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33768897A>G	ENST00000430124.2	-	2	109	c.44T>C	c.(43-45)gTa>gCa	p.V15A	MLN_ENST00000266003.5_Missense_Mutation_p.V15A|MLN_ENST00000507738.1_Missense_Mutation_p.V15A	NM_001040109.1|NM_001184698.1|NM_002418.2	NP_001035198.1|NP_001171627.1|NP_002409.1	P12872	MOTI_HUMAN	motilin	15			V -> A (in dbSNP:rs2281820). {ECO:0000269|PubMed:15489334}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)	receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)	6						CATGGCAGCTACATGCACCAC	0.577													G|||	3163	0.631589	0.4932	0.5216	5008	,	,		20036	0.8562		0.5368	False		,,,				2504	0.7628				p.V15A		Atlas-SNP	.											.	MLN	16	.	0			c.T44C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL	2229,2177	585.3+/-386.2	560,1109,534	98.0	86.0	90.0		44,44,44	-1.1	0.0	6	dbSNP_100	90	4994,3606	520.8+/-379.8	1460,2074,766	yes	missense,missense,missense	MLN	NM_001040109.1,NM_001184698.1,NM_002418.2	64,64,64	2020,3183,1300	GG,GA,AA		41.9302,49.4099,44.4641	benign,benign,benign	15/115,15/109,15/116	33768897	7223,5783	2203	4300	6503	SO:0001583	missense	4295	exon2			GCAGCTACATGCA		CCDS4786.1, CCDS47412.1, CCDS54993.1	6p21.31	2014-01-30			ENSG00000096395	ENSG00000096395		"""Endogenous ligands"""	7141	protein-coding gene	gene with protein product	"""prepromotilin"""	158270					Standard	NM_001184698		Approved		uc003off.1	P12872	OTTHUMG00000014536	ENST00000430124.2:c.44T>C	6.37:g.33768897A>G	ENSP00000388825:p.Val15Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_002418	B7ZLR7|E9PDN2|J3KN51|Q2M1L2|Q5T975|Q6NSY7	Missense_Mutation	SNP	ENST00000430124.2	37	CCDS4786.1	1328	0.608058608058608	256	0.5203252032520326	185	0.511049723756906	475	0.8304195804195804	412	0.5435356200527705	G	0.628	-0.818365	0.02776	0.505901	0.580698	ENSG00000096395	ENST00000430124;ENST00000266003;ENST00000507738	T;T;T	0.51325	0.71;0.71;0.71	5.43	-1.12	0.09808	.	1.272520	0.05417	N	0.543508	T	0.11067	0.0270	L	0.28115	0.83	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12682	-1.0538	9	0.10636	T	0.68	0.251	7.2176	0.25969	0.4771:0.12:0.4029:0.0	rs2281820;rs52813189;rs61381966;rs2281820	15;15	E9PDN2;P12872	.;MOTI_HUMAN	A	15	ENSP00000388825:V15A;ENSP00000266003:V15A;ENSP00000425467:V15A	ENSP00000266003:V15A	V	-	2	0	MLN	33876875	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.753000	0.04792	-0.651000	0.05415	-0.812000	0.03155	GTA	A|0.403;G|0.597	0.597	strong		0.577	MLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040211.4		
OR7C1	26664	hgsc.bcm.edu	37	19	14910321	14910321	+	Missense_Mutation	SNP	A	A	G	rs16979912	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	75	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	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		
OR51I1	390063	hgsc.bcm.edu	37	11	5462255	5462255	+	Missense_Mutation	SNP	C	C	G	rs11037445	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5462255C>G	ENST00000380211.1	-	1	489	c.490G>C	c.(490-492)Gtg>Ctg	p.V164L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	164			V -> L (in dbSNP:rs11037445).		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)		CGTTTCACCACAAAAGGGAAA	0.463													G|||	1275	0.254593	0.2148	0.2493	5008	,	,		23310	0.373		0.2296	False		,,,				2504	0.2157				p.V164L		Atlas-SNP	.											.	OR51I1	66	.	0			c.G490C						PASS	.	G	LEU/VAL	905,3497	740.0+/-411.1	79,747,1375	102.0	86.0	92.0		490	3.6	1.0	11	dbSNP_120	92	1811,6783	732.4+/-406.8	201,1409,2687	yes	missense	OR51I1	NM_001005288.2	32	280,2156,4062	GG,GC,CC		21.0728,20.5588,20.8987	benign	164/315	5462255	2716,10280	2201	4297	6498	SO:0001583	missense	390063	exon1			TCACCACAAAAGG	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.490G>C	11.37:g.5462255C>G	ENSP00000369559:p.Val164Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	526	0.24084249084249085	83	0.16869918699186992	90	0.24861878453038674	188	0.32867132867132864	165	0.21767810026385223	G	0.528	-0.859342	0.02610	0.205588	0.210728	ENSG00000167359	ENST00000317283;ENST00000321307;ENST00000380211	T	0.00678	5.87	5.47	3.61	0.41365	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	N	0.000420	T	0.00012	0.0000	N	0.00009	-3.075	0.51767	P	6.899999999998574E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.28267	-1.0049	9	0.02654	T	1	.	8.2374	0.31634	0.1436:0.1295:0.7269:0.0	rs11037445;rs57956763;rs11037445	164	Q9H343	O51I1_HUMAN	L	149;161;164	ENSP00000369559:V164L	ENSP00000348350:V149L	V	-	1	0	OR51I1	5418831	0.005000	0.15991	0.996000	0.52242	0.785000	0.44390	0.780000	0.26760	0.315000	0.23110	-1.028000	0.02416	GTG	C|0.771;G|0.229	0.229	strong		0.463	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
FZD6	8323	hgsc.bcm.edu	37	8	104312432	104312432	+	Missense_Mutation	SNP	A	A	G	rs827528	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:104312432A>G	ENST00000358755.4	+	2	414	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	RP11-318M2.2_ENST00000523614.2_RNA|RP11-318M2.2_ENST00000521383.1_RNA|FZD6_ENST00000523739.1_Start_Codon_SNP_p.M1V|FZD6_ENST00000540287.1_5'UTR|RP11-318M2.2_ENST00000522856.1_RNA|FZD6_ENST00000522566.1_Missense_Mutation_p.M33V	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	33	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		M -> V (in dbSNP:rs827528). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:22045688}.		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)			TCCCAGATGTATGAAAATGGC	0.423													A|||	852	0.170128	0.2156	0.1657	5008	,	,		20348	0.0129		0.2704	False		,,,				2504	0.1708				p.M33V		Atlas-SNP	.											FZD6,colon,carcinoma,0,1	FZD6	61	1	0			c.A97G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	930,3476	356.4+/-313.5	95,740,1368	200.0	177.0	185.0		97,1,97	-0.7	1.0	8	dbSNP_86	185	2279,6321	385.2+/-341.4	294,1691,2315	yes	missense,missense,missense	FZD6	NM_001164615.1,NM_001164616.1,NM_003506.3	21,21,21	389,2431,3683	GG,GA,AA		26.5,21.1076,24.6732	benign,benign,benign	33/707,1/675,33/707	104312432	3209,9797	2203	4300	6503	SO:0001583	missense	8323	exon2			AGATGTATGAAAA	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.97A>G	8.37:g.104312432A>G	ENSP00000351605:p.Met33Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	188	100	0.531915	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	375	0.1717032967032967	96	0.1951219512195122	72	0.19889502762430938	5	0.008741258741258742	202	0.26649076517150394	A	11.83	1.756296	0.31137	0.211076	0.265	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739	T;T;T	0.75938	-0.93;-0.93;-0.98	5.93	-0.683	0.11335	Frizzled domain (5);	0.614894	0.19147	N	0.121550	T	0.00012	0.0000	L	0.28400	0.85	0.09310	P	0.9999999135129	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04307	-1.0961	9	0.38643	T	0.18	.	2.9794	0.05948	0.4952:0.1098:0.2875:0.1075	rs827528;rs57692859;rs827528	33;33	B2R9H9;O60353	.;FZD6_HUMAN	V	33;33;1	ENSP00000429055:M33V;ENSP00000351605:M33V;ENSP00000429528:M1V	ENSP00000351605:M33V	M	+	1	0	FZD6	104381608	0.093000	0.21703	0.954000	0.39281	0.985000	0.73830	-0.195000	0.09546	-0.097000	0.12307	-0.256000	0.11100	ATG	A|0.785;G|0.215;T|0.000	0.215	strong		0.423	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
MUC16	94025	hgsc.bcm.edu	37	19	9058942	9058942	+	Missense_Mutation	SNP	C	C	T	rs1833778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9058942C>T	ENST00000397910.4	-	3	28707	c.28504G>A	c.(28504-28506)Gct>Act	p.A9502T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9504	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						GCTTTAGAAGCGGCCAGACTC	0.478													c|||	2201	0.439497	0.2829	0.487	5008	,	,		21053	0.5546		0.4742	False		,,,				2504	0.4632				p.A9502T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G28504A						PASS	.	C	THR/ALA	1242,2732		191,860,936	161.0	157.0	158.0		28504	-4.6	0.0	19	dbSNP_92	158	3928,4420		946,2036,1192	yes	missense	MUC16	NM_024690.2	58	1137,2896,2128	TT,TC,CC		47.0532,31.2531,41.9575	benign	9502/14508	9058942	5170,7152	1987	4174	6161	SO:0001583	missense	94025	exon3			TAGAAGCGGCCAG	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.28504G>A	19.37:g.9058942C>T	ENSP00000381008:p.Ala9502Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1022	0.46794871794871795	166	0.33739837398373984	179	0.494475138121547	321	0.5611888111888111	356	0.46965699208443273	c	2.488	-0.318202	0.05386	0.312531	0.470532	ENSG00000181143	ENST00000397910	T	0.19105	2.17	2.29	-4.58	0.03410	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.42207	-0.9465	7	0.87932	D	0	.	2.0581	0.03586	0.5546:0.1062:0.1212:0.218	rs1833778;rs1833778	9502	B5ME49	.	T	9502	ENSP00000381008:A9502T	ENSP00000381008:A9502T	A	-	1	0	MUC16	8919942	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.608000	0.00887	-3.882000	0.00095	-1.013000	0.02462	GCT	C|0.535;T|0.465	0.465	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942047	12942047	+	Missense_Mutation	SNP	C	C	T	rs199749044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12942047C>T	ENST00000235349.5	-	3	573	c.503G>A	c.(502-504)tGc>tAc	p.C168Y		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	168					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)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		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)		TAGAAGGAGGCAGGTGAGGTA	0.483																																					p.C168Y		Atlas-SNP	.											PRAMEF4,NS,carcinoma,+1,1	PRAMEF4	62	1	0			c.G503A						scavenged	.						29.0	37.0	34.0					1																	12942047		1442	2626	4068	SO:0001583	missense	400735	exon3			AGGAGGCAGGTGA		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.503G>A	1.37:g.12942047C>T	ENSP00000235349:p.Cys168Tyr	Somatic	44	2	0.0454545		WXS	Illumina HiSeq	Phase_I	49	4	0.0816327	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-3.193621	0.00026	.	.	ENSG00000243073	ENST00000235349	T	0.04015	3.73	1.48	-2.96	0.05547	.	0.745300	0.12225	N	0.488004	T	0.01222	0.0040	N	0.01446	-0.86	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.35450	-0.9788	10	0.02654	T	1	.	3.4864	0.07620	0.185:0.1969:0.0:0.6181	.	168	O60810	PRAM4_HUMAN	Y	168	ENSP00000235349:C168Y	ENSP00000235349:C168Y	C	-	2	0	PRAMEF4	12864634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.422000	0.07043	-1.840000	0.01184	-3.148000	0.00058	TGC	T|1.000;|0.000	1.000	weak		0.483	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
CCDC150	284992	hgsc.bcm.edu	37	2	197541296	197541296	+	Silent	SNP	G	G	A	rs17271281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:197541296G>A	ENST00000389175.4	+	12	1416	c.1281G>A	c.(1279-1281)gaG>gaA	p.E427E	CCDC150_ENST00000423093.2_Silent_p.E95E|CCDC150_ENST00000472405.2_3'UTR|CCDC150_ENST00000272831.7_Silent_p.E95E	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	427										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TAATCCTTGAGCATAACCAGT	0.368													G|||	356	0.0710863	0.0968	0.0879	5008	,	,		20424	0.006		0.1322	False		,,,				2504	0.0286				p.E427E		Atlas-SNP	.											.	CCDC150	96	.	0			c.G1281A						PASS	.	G		347,3351		14,319,1516	55.0	53.0	53.0		1281	3.2	1.0	2	dbSNP_123	53	1099,7097		79,941,3078	no	coding-synonymous	CCDC150	NM_001080539.1		93,1260,4594	AA,AG,GG		13.409,9.3835,12.1574		427/1102	197541296	1446,10448	1849	4098	5947	SO:0001819	synonymous_variant	284992	exon12			CCTTGAGCATAAC		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.1281G>A	2.37:g.197541296G>A		Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	279	125	0.448029	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Silent	SNP	ENST00000389175.4	37	CCDS46478.1																																																																																			G|0.912;A|0.088	0.088	strong		0.368	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
SYT8	90019	hgsc.bcm.edu	37	11	1857762	1857762	+	Silent	SNP	C	C	T	rs3741230	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1857762C>T	ENST00000381968.3	+	6	794	c.666C>T	c.(664-666)acC>acT	p.T222T	TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000535046.1_3'UTR|SYT8_ENST00000341958.3_Silent_p.T208T	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	222					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)		CACTGGGCACCGTGGATCTGC	0.657													C|||	457	0.091254	0.0507	0.0749	5008	,	,		14854	0.0724		0.1223	False		,,,				2504	0.1452				p.T222T		Atlas-SNP	.											.	SYT8	29	.	0			c.C666T						PASS	.	C		229,4171		9,211,1980	25.0	30.0	28.0		666	-4.5	0.0	11	dbSNP_107	28	1000,7590		58,884,3353	no	coding-synonymous	SYT8	NM_138567.3		67,1095,5333	TT,TC,CC		11.6414,5.2045,9.4611		222/402	1857762	1229,11761	2200	4295	6495	SO:0001819	synonymous_variant	90019	exon6			GGGCACCGTGGAT	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.666C>T	11.37:g.1857762C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_138567	A6NFJ4|Q9NSV9	Silent	SNP	ENST00000381968.3	37	CCDS7726.2	200	0.09157509157509157	33	0.06707317073170732	31	0.0856353591160221	48	0.08391608391608392	88	0.11609498680738786	c	10.60	1.396992	0.25205	0.052045	0.116414	ENSG00000149043	ENST00000381978	.	.	.	3.28	-4.52	0.03472	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.23904	-1.0175	3	.	.	.	.	0.2565	0.00212	0.2237:0.2566:0.2221:0.2976	rs3741230	.	.	.	C	221	.	.	R	+	1	0	SYT8	1814338	0.000000	0.05858	0.002000	0.10522	0.572000	0.35998	-2.531000	0.00943	-0.771000	0.04608	0.313000	0.20887	CGT	C|0.910;T|0.090	0.090	strong		0.657	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
OR7D4	125958	hgsc.bcm.edu	37	19	9325252	9325252	+	Missense_Mutation	SNP	G	G	A	rs61729907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9325252G>A	ENST00000308682.2	-	1	290	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	88			R -> W (impaired response to androstenone and androstadienone; when associated with M-133; dbSNP:rs61729907). {ECO:0000269|PubMed:17873857}.			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(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TCTTTGCTCCGTGCCTGGATG	0.493													G|||	739	0.147564	0.0567	0.1066	5008	,	,		23181	0.2163		0.2008	False		,,,				2504	0.1738				p.R88W		Atlas-SNP	.											.	OR7D4	66	.	0			c.C262T						PASS	.	G	TRP/ARG	350,4056	181.2+/-209.3	7,336,1860	80.0	72.0	74.0		262	0.4	0.0	19	dbSNP_129	74	1572,7028	291.5+/-300.3	137,1298,2865	no	missense	OR7D4	NM_001005191.2	101	144,1634,4725	AA,AG,GG		18.2791,7.9437,14.7778	probably-damaging	88/313	9325252	1922,11084	2203	4300	6503	SO:0001583	missense	125958	exon1			TGCTCCGTGCCTG		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.262C>T	19.37:g.9325252G>A	ENSP00000310488:p.Arg88Trp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	37	CCDS32901.1	341	0.15613553113553114	22	0.044715447154471545	38	0.10497237569060773	130	0.22727272727272727	151	0.19920844327176782	G	7.331	0.619028	0.14129	0.079437	0.182791	ENSG00000174667	ENST00000308682	T	0.05447	3.44	4.0	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	1.279690	0.05122	N	0.490958	T	0.00012	0.0000	L	0.39633	1.23	0.80722	P	0.0	P	0.44659	0.84	B	0.38562	0.276	T	0.47749	-0.9093	9	0.72032	D	0.01	.	8.2617	0.31788	0.0867:0.2955:0.6177:0.0	.	88	Q8NG98	OR7D4_HUMAN	W	88	ENSP00000310488:R88W	ENSP00000310488:R88W	R	-	1	2	OR7D4	9186252	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.901000	0.01597	0.095000	0.17434	0.436000	0.28706	CGG	G|0.845;A|0.155	0.155	strong		0.493	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
PRPF8	10594	hgsc.bcm.edu	37	17	1584324	1584324	+	Silent	SNP	A	A	G	rs7503397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	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		
CCDC116	164592	hgsc.bcm.edu	37	22	21988602	21988602	+	Missense_Mutation	SNP	C	C	T	rs861853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21988602C>T	ENST00000292779.3	+	3	525	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	CCDC116_ENST00000607942.1_Missense_Mutation_p.R122W	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	122			R -> W (in dbSNP:rs861853).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AAGTGGTGGACGGCGGGCACA	0.662													C|||	672	0.134185	0.2421	0.1066	5008	,	,		15625	0.003		0.1889	False		,,,				2504	0.0869				p.R122W		Atlas-SNP	.											.	CCDC116	56	.	0			c.C364T						PASS	.	C	TRP/ARG	1015,3391	371.7+/-320.1	109,797,1297	90.0	84.0	86.0		364	2.0	0.0	22	dbSNP_86	86	1526,7074	286.1+/-297.5	138,1250,2912	no	missense	CCDC116	NM_152612.2	101	247,2047,4209	TT,TC,CC		17.7442,23.0368,19.5371	probably-damaging	122/614	21988602	2541,10465	2203	4300	6503	SO:0001583	missense	164592	exon3			GGTGGACGGCGGG	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.364C>T	22.37:g.21988602C>T	ENSP00000292779:p.Arg122Trp	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	322	0.14743589743589744	126	0.25609756097560976	43	0.11878453038674033	2	0.0034965034965034965	151	0.19920844327176782	C	12.66	2.004421	0.35320	0.230368	0.177442	ENSG00000161180	ENST00000292779	T	0.23552	1.9	4.42	2.05	0.26809	.	1.322430	0.05338	N	0.529573	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	D;D	0.89917	1.0;0.999	D;D	0.68483	0.958;0.942	T	0.22347	-1.0219	8	.	.	.	-30.0854	6.6824	0.23127	0.2055:0.5952:0.1992:0.0	rs861853;rs1647700	122;122	B7Z7H5;Q8IYX3-2	.;.	W	122	ENSP00000292779:R122W	.	R	+	1	2	CCDC116	20318602	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	0.357000	0.20199	1.150000	0.42419	0.491000	0.48974	CGG	C|0.817;T|0.183	0.183	strong		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
RNF17	56163	hgsc.bcm.edu	37	13	25367301	25367301	+	Silent	SNP	C	C	T	rs1158061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25367301C>T	ENST00000255324.5	+	10	1109	c.1057C>T	c.(1057-1059)Cta>Tta	p.L353L	RNF17_ENST00000255325.6_Silent_p.L353L|RNF17_ENST00000381921.1_Silent_p.L353L|RNF17_ENST00000255326.4_3'UTR	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	54	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	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	
ECSIT	51295	hgsc.bcm.edu	37	19	11617073	11617073	+	Missense_Mutation	SNP	C	C	T	rs35513404	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11617073C>T	ENST00000270517.7	-	8	1357	c.1222G>A	c.(1222-1224)Gag>Aag	p.E408K	ECSIT_ENST00000591104.1_3'UTR|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000252440.7_3'UTR|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000417981.2_Missense_Mutation_p.E194K|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000588998.1_3'UTR|ZNF653_ENST00000593191.1_5'Flank	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	408					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						GGCGGCTCCTCCAGCCCTGCA	0.697													C|||	66	0.0131789	0.0023	0.0159	5008	,	,		14958	0.0		0.0477	False		,,,				2504	0.0041				p.E408K		Atlas-SNP	.											.	ECSIT	32	.	0			c.G1222A						PASS	.	C	,LYS/GLU,LYS/GLU	31,4361		1,29,2166	28.0	30.0	29.0		,580,1222	4.5	0.3	19	dbSNP_126	29	298,8264		8,282,3991	yes	utr-3,missense,missense	ECSIT	NM_001142464.2,NM_001142465.2,NM_016581.4	,56,56	9,311,6157	TT,TC,CC		3.4805,0.7058,2.5398	,probably-damaging,probably-damaging	,194/218,408/432	11617073	329,12625	2196	4281	6477	SO:0001583	missense	51295	exon8			GCTCCTCCAGCCC	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.1222G>A	19.37:g.11617073C>T	ENSP00000270517:p.Glu408Lys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_016581	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	43	0.019688644688644688	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	37	0.048812664907651716	C	15.26	2.781666	0.49891	0.007058	0.034805	ENSG00000130159	ENST00000270517;ENST00000417981	T;T	0.32272	1.46;1.48	5.6	4.53	0.55603	.	0.770776	0.12165	N	0.493617	T	0.05777	0.0151	L	0.60455	1.87	0.25877	N	0.983634	P;P	0.47962	0.903;0.728	B;B	0.43052	0.406;0.138	T	0.04467	-1.0949	10	0.11182	T	0.66	-22.674	12.5994	0.56489	0.0:0.8343:0.1657:0.0	rs35513404;rs35513404	194;408	E9PAN9;Q9BQ95	.;ECSIT_HUMAN	K	408;194	ENSP00000270517:E408K;ENSP00000412712:E194K	ENSP00000270517:E408K	E	-	1	0	ECSIT	11478073	0.000000	0.05858	0.261000	0.24466	0.089000	0.18198	0.234000	0.17930	2.650000	0.89964	0.585000	0.79938	GAG	C|0.978;T|0.022	0.022	strong		0.697	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
FGFR4	2264	hgsc.bcm.edu	37	5	176520243	176520243	+	Missense_Mutation	SNP	G	G	A	rs351855	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176520243G>A	ENST00000292408.4	+	9	1407	c.1162G>A	c.(1162-1164)Ggg>Agg	p.G388R	FGFR4_ENST00000292410.3_Intron|FGFR4_ENST00000393637.1_Intron|FGFR4_ENST00000502906.1_Missense_Mutation_p.G388R|FGFR4_ENST00000393648.2_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	388			G -> R (prolonged FGFR4 activity, increased cell motility and tumor cell invasion, possibly due to increased stability of the protease MMP14; dbSNP:rs351855). {ECO:0000269|PubMed:11781352, 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)	GCTGCTGGCCGGGCTGTATCG	0.711										TSP Lung(9;0.080)			G|||	1500	0.299521	0.1097	0.3098	5008	,	,		12765	0.4633		0.2942	False		,,,				2504	0.3855				p.G388R		Atlas-SNP	.											FGFR4_ENST00000292408,rectum,carcinoma,0,1	FGFR4	174	1	0			c.G1162A	GRCh37	CM023917	FGFR4	M	rs351855	PASS	.	G	ARG/GLY,,ARG/GLY	567,3839	240.9+/-251.5	34,499,1670	35.0	32.0	33.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1162,,1162	4.3	0.9	5	dbSNP_79	33	2583,6011	393.4+/-344.3	429,1725,2143	yes	missense,intron,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	125,,125	463,2224,3813	AA,AG,GG		30.0559,12.8688,24.2308	possibly-damaging,,possibly-damaging	388/803,,388/803	176520243	3150,9850	2203	4297	6500	SO:0001583	missense	2264	exon9			CTGGCCGGGCTGT	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.1162G>A	5.37:g.176520243G>A	ENSP00000292408:p.Gly388Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	661|661	0.30265567765567764|0.30265567765567764	61|61	0.12398373983739837|0.12398373983739837	123|123	0.3397790055248619|0.3397790055248619	258|258	0.45104895104895104|0.45104895104895104	219|219	0.28891820580474936|0.28891820580474936	G|G	19.01|19.01	3.743077|3.743077	0.69418|0.69418	0.128688|0.128688	0.300559|0.300559	ENSG00000160867|ENSG00000160867	ENST00000292408;ENST00000502906;ENST00000377207|ENST00000511076	D;D|.	0.82984|.	-1.67;-1.67|.	4.29|4.29	4.29|4.29	0.51040|0.51040	.|.	0.316526|.	0.32753|.	N|.	0.005687|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	P|P	1.0|1.0	D|.	0.71674|.	0.998|.	P|.	0.52481|.	0.7|.	T|T	0.50338|0.50338	-0.8840|-0.8840	9|4	0.59425|.	D|.	0.04|.	.|.	11.2123|11.2123	0.48806|0.48806	0.0906:0.0:0.9094:0.0|0.0906:0.0:0.9094:0.0	rs351855;rs56695235;rs351855|rs351855;rs56695235;rs351855	388|.	P22455|.	FGFR4_HUMAN|.	R|Q	388;388;616|23	ENSP00000292408:G388R;ENSP00000424960:G388R|.	ENSP00000292408:G388R|.	G|R	+|+	1|2	0|0	FGFR4|FGFR4	176452849|176452849	0.995000|0.995000	0.38212|0.38212	0.911000|0.911000	0.35937|0.35937	0.721000|0.721000	0.41392|0.41392	4.235000|4.235000	0.58666|0.58666	2.233000|2.233000	0.73108|0.73108	0.561000|0.561000	0.74099|0.74099	GGG|CGG	G|0.732;T|0.008	.	strong		0.711	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
CDC16	8881	hgsc.bcm.edu	37	13	115002275	115002275	+	Splice_Site	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115002275A>G	ENST00000356221.3	+	3	213	c.105A>G	c.(103-105)gaA>gaG	p.E35E	CDC16_ENST00000360383.3_Splice_Site_p.E35E|CDC16_ENST00000375312.3_5'UTR|CDC16_ENST00000375308.1_Splice_Site|CDC16_ENST00000375310.1_Splice_Site|CDC16_ENST00000252457.5_Splice_Site|CDC16_ENST00000252458.6_Splice_Site			Q13042	CDC16_HUMAN	cell division cycle 16	35					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)			TCCCTCCAGAAGAACCCCAGG	0.413																																					p.E35E		Atlas-SNP	.											.	CDC16	50	.	0			c.A105G						PASS	.						135.0	135.0	135.0					13																	115002275		2203	4300	6503	SO:0001630	splice_region_variant	8881	exon3			TCCAGAAGAACCC	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.104-1A>G	13.37:g.115002275A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	A	9.067	0.995900	0.19043	.	.	ENSG00000130177	ENST00000252457	.	.	.	5.43	2.58	0.30949	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6961	0.40158	0.2981:0.0:0.7019:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC16	114020377	1.000000	0.71417	0.999000	0.59377	0.274000	0.26718	1.778000	0.38614	0.864000	0.35578	-0.146000	0.13790	.	.	.	none		0.413	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	Silent
COMT	1312	hgsc.bcm.edu	37	22	19950235	19950235	+	Silent	SNP	C	C	T	rs4633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19950235C>T	ENST00000361682.6	+	3	568	c.186C>T	c.(184-186)caC>caT	p.H62H	COMT_ENST00000403184.1_Silent_p.H62H|MIR4761_ENST00000585066.1_RNA|COMT_ENST00000407537.1_Silent_p.H12H|COMT_ENST00000403710.1_Silent_p.H62H|COMT_ENST00000406520.3_Silent_p.H62H|COMT_ENST00000449653.1_Silent_p.H12H	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	62					cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)	p.H62H(1)		kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	TCCTGAACCACGTGCTGCAGC	0.622													C|||	1861	0.371605	0.2935	0.3804	5008	,	,		17719	0.2698		0.499	False		,,,				2504	0.4448				p.H62H		Atlas-SNP	.											COMT,NS,carcinoma,0,1	COMT	10	1	1	Substitution - coding silent(1)	stomach(1)	c.C186T						PASS	.	C	,,,	1486,2918	474.1+/-356.9	245,996,961	73.0	65.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	186,186,186,36	-11.0	0.0	22	dbSNP_52	68	4497,4103	589.2+/-392.5	1174,2149,977	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	1419,3145,1938	TT,TC,CC		47.7093,33.7421,46.0089	,,,	62/272,62/272,62/272,12/222	19950235	5983,7021	2202	4300	6502	SO:0001819	synonymous_variant	1312	exon3			GAACCACGTGCTG		CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	2.1.1.6		2228	protein-coding gene	gene with protein product		116790				1572656	Standard	NM_000754		Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.186C>T	22.37:g.19950235C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			C|0.586;T|0.414	0.414	strong		0.622	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754	
ZMYND15	84225	hgsc.bcm.edu	37	17	4641755	4641755	+	5'Flank	SNP	C	C	T	rs1050997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4641755C>T	ENST00000433935.1	+	0	0				ZMYND15_ENST00000573751.2_5'Flank|ZMYND15_ENST00000592813.1_5'Flank|CXCL16_ENST00000293778.6_Silent_p.G102G|CXCL16_ENST00000574412.1_Silent_p.G102G|CXCL16_ENST00000576153.1_5'Flank|ZMYND15_ENST00000269289.6_5'Flank	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15						negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.G102G(1)		endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						CCTTGTTGCCCCCACACACGC	0.572													C|||	3125	0.624002	0.3828	0.6816	5008	,	,		17955	0.6944		0.7913	False		,,,				2504	0.6646				p.G102G		Atlas-SNP	.											CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	1	Substitution - coding silent(1)	stomach(1)	c.G306A						PASS	.	C	,	2010,2396	561.9+/-380.8	468,1074,661	107.0	84.0	92.0		306,306	-2.7	0.1	17	dbSNP_86	92	6654,1946	723.9+/-406.5	2562,1530,208	no	coding-synonymous,coding-synonymous	CXCL16	NM_001100812.1,NM_022059.2	,	3030,2604,869	TT,TC,CC		22.6279,45.6196,33.3846	,	102/274,102/274	4641755	8664,4342	2203	4300	6503	SO:0001631	upstream_gene_variant	58191	exon3			GTTGCCCCCACAC	AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"""Zinc fingers, MYND-type"""	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760		17.37:g.4641755C>T	Exception_encountered	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_022059	B4DXY5|I3L296	Silent	SNP	ENST00000433935.1	37	CCDS45584.1																																																																																			C|0.322;T|0.678	0.678	strong		0.572	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265	
LNP1	348801	hgsc.bcm.edu	37	3	100170596	100170596	+	Missense_Mutation	SNP	T	T	C	rs386663873|rs75122231	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100170596T>C	ENST00000383693.3	+	3	1470	c.190T>C	c.(190-192)Tgc>Cgc	p.C64R	LNP1_ENST00000489752.1_Missense_Mutation_p.C77R	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	64										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						ATCATCTGACTGCCATCCTAG	0.438																																					p.C64R		Atlas-SNP	.											.	LNP1	26	.	0			c.T190C						PASS	.						77.0	70.0	72.0					3																	100170596		1876	4104	5980	SO:0001583	missense	348801	exon3			TCTGACTGCCATC		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.190T>C	3.37:g.100170596T>C	ENSP00000373191:p.Cys64Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	146	16	0.109589	NM_001085451	B7ZLT3	Missense_Mutation	SNP	ENST00000383693.3	37	CCDS43120.1	.	.	.	.	.	.	.	.	.	.	C	1.974	-0.435728	0.04636	.	.	ENSG00000206535	ENST00000383693;ENST00000489752	.	.	.	5.36	-4.39	0.03611	.	0.901104	0.09540	N	0.788361	T	0.14227	0.0344	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27123	-1.0083	9	0.15499	T	0.54	-3.57	2.218	0.03965	0.1129:0.3736:0.1713:0.3422	.	64	A1A4G5	LNP1_HUMAN	R	64;77	.	ENSP00000373191:C64R	C	+	1	0	LNP1	101653286	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.213000	0.17521	-1.009000	0.03400	-2.905000	0.00092	TGC	A|0.001;C|0.044;T|0.955	0.044	strong		0.438	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
CACNA1C	775	hgsc.bcm.edu	37	12	2558186	2558186	+	Silent	SNP	G	G	A	rs1544514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:2558186G>A	ENST00000347598.4	+	4	522	c.522G>A	c.(520-522)gcG>gcA	p.A174A	CACNA1C_ENST00000402845.3_Silent_p.A174A|CACNA1C_ENST00000399595.1_Silent_p.A174A|CACNA1C_ENST00000399603.1_Silent_p.A174A|CACNA1C_ENST00000399617.1_Silent_p.A174A|CACNA1C_ENST00000399597.1_Silent_p.A174A|CACNA1C_ENST00000406454.3_Silent_p.A174A|CACNA1C_ENST00000399621.1_Silent_p.A174A|CACNA1C_ENST00000399591.1_Silent_p.A174A|CACNA1C_ENST00000399601.1_Silent_p.A174A|CACNA1C_ENST00000327702.7_Silent_p.A174A|CACNA1C_ENST00000399649.1_Silent_p.A174A|CACNA1C_ENST00000399634.1_Silent_p.A174A|CACNA1C_ENST00000344100.3_Silent_p.A174A|CACNA1C_ENST00000399638.1_Silent_p.A174A|CACNA1C_ENST00000399637.1_Silent_p.A174A|CACNA1C_ENST00000335762.5_Silent_p.A174A|CACNA1C_ENST00000399644.1_Silent_p.A174A|CACNA1C_ENST00000399629.1_Silent_p.A174A|CACNA1C_ENST00000399606.1_Silent_p.A174A|CACNA1C_ENST00000399655.1_Silent_p.A174A|CACNA1C_ENST00000399641.1_Silent_p.A174A|CACNA1C_ENST00000480911.1_Silent_p.A174A	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	174					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)	CGGTGGAAGCGTTTTTAAAAG	0.403													G|||	603	0.120407	0.0756	0.147	5008	,	,		17828	0.0655		0.1928	False		,,,				2504	0.1442				p.A174A		Atlas-SNP	.											CACNA1C_ENST00000344100,colon,carcinoma,+1,2	CACNA1C	1023	2	0			c.G522A						PASS	.	G	,,,,,,,,,,,,,,,,,,,,,,	326,3334		21,284,1525	90.0	84.0	86.0		522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522	-0.1	1.0	12	dbSNP_88	86	1749,6401		192,1365,2518	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	,,,,,,,,,,,,,,,,,,,,,,	213,1649,4043	AA,AG,GG		21.4601,8.9071,17.5699	,,,,,,,,,,,,,,,,,,,,,,	174/2139,174/2187,174/2180,174/2174,174/2167,174/2159,174/2158,174/2158,174/2158,174/2156,174/2147,174/2147,174/2145,174/2139,174/2139,174/2139,174/2139,174/2136,174/2128,174/2139,174/2174,174/2199,174/2222	2558186	2075,9735	1830	4075	5905	SO:0001819	synonymous_variant	775	exon4			GGAAGCGTTTTTA	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.522G>A	12.37:g.2558186G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	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																																																																																			G|0.860;A|0.140	0.140	strong		0.403	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
PSME4	23198	hgsc.bcm.edu	37	2	54197829	54197829	+	Missense_Mutation	SNP	C	C	A	rs78645734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:54197829C>A	ENST00000404125.1	-	1	148	c.93G>T	c.(91-93)gaG>gaT	p.E31D	ACYP2_ENST00000606082.1_5'Flank|ACYP2_ENST00000607452.1_5'Flank|ACYP2_ENST00000422521.2_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	31					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)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|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)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TGTAGACGATCTCCTTCTGCG	0.721													C|||	114	0.0227636	0.003	0.0591	5008	,	,		7936	0.001		0.0308	False		,,,				2504	0.0378				p.E31D		Atlas-SNP	.											.	PSME4	247	.	0			c.G93T						PASS	.	C	ASP/GLU	7,1377		0,7,685	10.0	11.0	11.0		93	2.0	1.0	2	dbSNP_131	11	122,3052		1,120,1466	yes	missense	PSME4	NM_014614.2	45	1,127,2151	AA,AC,CC		3.8437,0.5058,2.8302	benign	31/1844	54197829	129,4429	692	1587	2279	SO:0001583	missense	23198	exon1			GACGATCTCCTTC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.93G>T	2.37:g.54197829C>A	ENSP00000384211:p.Glu31Asp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	38	0.0173992673992674	2	0.0040650406504065045	19	0.052486187845303865	1	0.0017482517482517483	16	0.021108179419525065	c	14.47	2.543979	0.45280	0.005058	0.038437	ENSG00000068878	ENST00000404125	T	0.25912	1.77	3.79	1.98	0.26296	.	.	.	.	.	T	0.02610	0.0079	L	0.38953	1.18	0.80722	D	1	B	0.25390	0.125	B	0.22753	0.041	T	0.08269	-1.0730	9	0.33141	T	0.24	.	7.5316	0.27687	0.0:0.7274:0.0:0.2726	.	31	Q14997	PSME4_HUMAN	D	31	ENSP00000384211:E31D	ENSP00000374643:E31D	E	-	3	2	PSME4	54051333	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.804000	0.38873	0.276000	0.22118	-1.045000	0.02358	GAG	C|0.982;A|0.018	0.018	strong		0.721	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
DIDO1	11083	hgsc.bcm.edu	37	20	61528306	61528306	+	Missense_Mutation	SNP	A	A	G	rs1883848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61528306A>G	ENST00000266070.4	-	7	1956	c.1631T>C	c.(1630-1632)aTg>aCg	p.M544T	DIDO1_ENST00000395335.2_Missense_Mutation_p.M544T|DIDO1_ENST00000395343.1_Missense_Mutation_p.M544T|DIDO1_ENST00000395340.1_Missense_Mutation_p.M544T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	544			M -> T (in dbSNP:rs1883848). {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)			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)					TGAGGCTGCCATGGCTGCCGC	0.567													G|||	2438	0.486821	0.4395	0.5014	5008	,	,		17658	0.629		0.3877	False		,,,				2504	0.4959				p.M544T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,0,1	DIDO1	321	1	0			c.T1631C						PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET	1888,2518		409,1070,724	24.0	26.0	25.0		1631,1631,1631,1631	-1.2	0.0	20	dbSNP_92	25	3549,5045		754,2041,1502	yes	missense,missense,missense,missense	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	81,81,81,81	1163,3111,2226	GG,GA,AA		41.2963,42.8507,41.8231	benign,benign,benign,benign	544/2241,544/1190,544/2241,544/1190	61528306	5437,7563	2203	4297	6500	SO:0001583	missense	11083	exon7			GCTGCCATGGCTG	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.1631T>C	20.37:g.61528306A>G	ENSP00000266070:p.Met544Thr	Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	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	1026	0.4697802197802198	209	0.4247967479674797	189	0.5220994475138122	353	0.6171328671328671	275	0.3627968337730871	G	4.197	0.035244	0.08148	0.428507	0.412963	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.10477	3.23;3.23;2.87;2.87	5.12	-1.16	0.09678	.	1.282380	0.05904	N	0.630433	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	0.38329	-0.9666	9	0.14656	T	0.56	-1.5461	10.4843	0.44713	0.5041:0.0:0.4959:0.0	rs1883848;rs58247654;rs1883848	544;544	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	T	544	ENSP00000266070:M544T;ENSP00000378752:M544T;ENSP00000378749:M544T;ENSP00000378744:M544T	ENSP00000266070:M544T	M	-	2	0	DIDO1	60998751	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.881000	0.28173	-0.468000	0.06922	-0.213000	0.12676	ATG	A|0.551;G|0.449	0.449	strong		0.567	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
HERC6	55008	hgsc.bcm.edu	37	4	89300241	89300241	+	Silent	SNP	C	C	A	rs61978650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:89300241C>A	ENST00000264346.7	+	1	227	c.168C>A	c.(166-168)ggC>ggA	p.G56G	HERC6_ENST00000380265.5_Silent_p.G56G|HERC6_ENST00000273960.3_Silent_p.G56G	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	56					hematopoietic progenitor cell differentiation (GO:0002244)|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)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GTCAGCTGGGCCGCAGGGGCG	0.721													C|||	518	0.103435	0.0938	0.1297	5008	,	,		12109	0.0357		0.1799	False		,,,				2504	0.089				p.G56G		Atlas-SNP	.											.	HERC6	104	.	0			c.C168A						PASS	.						3.0	4.0	3.0					4																	89300241		1638	3675	5313	SO:0001819	synonymous_variant	55008	exon1			GCTGGGCCGCAGG	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.168C>A	4.37:g.89300241C>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	24	14	0.583333	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Silent	SNP	ENST00000264346.7	37	CCDS47098.1	266	0.12179487179487179	55	0.11178861788617886	53	0.1464088397790055	17	0.02972027972027972	141	0.18601583113456466	C	4.468	0.086782	0.08583	.	.	ENSG00000138642	ENST00000502870	.	.	.	3.8	1.98	0.26296	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999903432	.	.	.	.	.	.	T	0.06917	-1.0800	3	.	.	.	.	12.2098	0.54373	0.0:0.6693:0.3307:0.0	rs61978650	.	.	.	D	9	.	.	A	+	2	0	HERC6	89519265	0.957000	0.32711	0.630000	0.29268	0.289000	0.27227	1.715000	0.37971	0.244000	0.21351	0.313000	0.20887	GCC	C|0.875;A|0.125	0.125	strong		0.721	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
SVIL	6840	hgsc.bcm.edu	37	10	29839787	29839787	+	Missense_Mutation	SNP	A	A	G	rs10160013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29839787A>G	ENST00000355867.4	-	6	1318	c.566T>C	c.(565-567)gTg>gCg	p.V189A	SVIL_ENST00000375398.2_Missense_Mutation_p.V189A|SVIL_ENST00000375400.3_Missense_Mutation_p.V189A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	189			V -> A (in dbSNP:rs10160013). {ECO:0000269|PubMed:12711699, ECO:0000269|PubMed:9867483}.		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)	p.V189A(1)		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)				GCCGTCACCCACATGGAGGGC	0.592													C|||	1542	0.307907	0.4228	0.2651	5008	,	,		18277	0.3462		0.2386	False		,,,				2504	0.2147				p.V189A		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - Missense(1)	stomach(1)	c.T566C						PASS	.	C	ALA/VAL,ALA/VAL	1833,2573		375,1083,745	91.0	92.0	92.0		566,566	-0.7	0.0	10	dbSNP_119	92	2246,6354		293,1660,2347	yes	missense,missense	SVIL	NM_003174.3,NM_021738.2	64,64	668,2743,3092	GG,GA,AA		26.1163,41.6024,31.3624	benign,benign	189/1789,189/2215	29839787	4079,8927	2203	4300	6503	SO:0001583	missense	6840	exon8			TCACCCACATGGA	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.566T>C	10.37:g.29839787A>G	ENSP00000348128:p.Val189Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	672	0.3076923076923077	201	0.40853658536585363	98	0.27071823204419887	190	0.3321678321678322	183	0.24142480211081793	C	5.753	0.323264	0.10900	0.416024	0.261163	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.40476	1.03;1.03;1.03	4.89	-0.679	0.11350	.	1.309280	0.04659	N	0.408500	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	0.42378	-0.9455	8	.	.	.	0.0556	2.3037	0.04169	0.1303:0.1857:0.4323:0.2516	rs10160013;rs56604844;rs57764178;rs10160013	189;189	O95425-2;O95425	.;SVIL_HUMAN	A	189	ENSP00000364549:V189A;ENSP00000364547:V189A;ENSP00000348128:V189A	.	V	-	2	0	SVIL	29879793	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.415000	0.07106	-0.477000	0.06832	-0.187000	0.12897	GTG	A|0.692;G|0.308	0.308	strong		0.592	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SH2D4A	63898	hgsc.bcm.edu	37	8	19190491	19190491	+	Silent	SNP	A	A	G	rs1574288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:19190491A>G	ENST00000265807.3	+	3	618	c.207A>G	c.(205-207)aaA>aaG	p.K69K	SH2D4A_ENST00000518040.1_Silent_p.K24K|SH2D4A_ENST00000519207.1_Silent_p.K69K	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	69					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TTCATTGGAAACTTGGAGCTG	0.398													G|||	1117	0.223043	0.3858	0.1527	5008	,	,		15903	0.1438		0.2266	False		,,,				2504	0.1309				p.K69K		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A207G						PASS	.	G	,,	1590,2816	665.4+/-401.5	301,988,914	168.0	160.0	163.0		207,72,207	-3.0	1.0	8	dbSNP_88	163	2056,6544	719.1+/-406.2	252,1552,2496	no	coding-synonymous,coding-synonymous,coding-synonymous	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	,,	553,2540,3410	GG,GA,AA		23.907,36.0872,28.0332	,,	69/455,24/410,69/455	19190491	3646,9360	2203	4300	6503	SO:0001819	synonymous_variant	63898	exon3			TTGGAAACTTGGA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.207A>G	8.37:g.19190491A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	37	CCDS6009.1																																																																																			A|0.739;G|0.261	0.261	strong		0.398	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125872293	125872293	+	Silent	SNP	G	G	A	rs16837178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:125872293G>A	ENST00000393434.2	-	7	1201	c.852C>T	c.(850-852)gaC>gaT	p.D284D	ALDH1L1_ENST00000413612.1_5'UTR|ALDH1L1_ENST00000472186.1_Silent_p.D284D|ALDH1L1_ENST00000452905.2_Silent_p.D183D|ALDH1L1_ENST00000393431.2_Silent_p.D284D|ALDH1L1_ENST00000455064.2_Silent_p.D109D|ALDH1L1_ENST00000273450.3_Silent_p.D294D	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	284					10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	TTACCATTTTGTCATCATTCC	0.597													G|||	285	0.0569089	0.1324	0.062	5008	,	,		17660	0.0		0.0437	False		,,,				2504	0.0235				p.D294D		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.C882T						PASS	.	G		547,3859	245.3+/-254.3	30,487,1686	102.0	98.0	99.0		852	3.4	1.0	3	dbSNP_123	99	491,8109	142.3+/-198.5	18,455,3827	no	coding-synonymous	ALDH1L1	NM_012190.2		48,942,5513	AA,AG,GG		5.7093,12.4149,7.9809		284/903	125872293	1038,11968	2203	4300	6503	SO:0001819	synonymous_variant	10840	exon7			CATTTTGTCATCA	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.852C>T	3.37:g.125872293G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																			G|0.922;A|0.078	0.078	strong		0.597	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197176	39197176	+	Silent	SNP	G	G	A	rs3815561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39197176G>A	ENST00000306271.4	-	1	537	c.474C>T	c.(472-474)taC>taT	p.Y158Y		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	158						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)			ACTGTCCACAGTAGGATGGGC	0.627													g|||	1112	0.222045	0.1967	0.2622	5008	,	,		17623	0.2817		0.1332	False		,,,				2504	0.2577				p.Y158Y		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.C474T						PASS	.	G		725,3381		53,619,1381	31.0	35.0	34.0		474	5.1	1.0	17	dbSNP_107	34	1275,7081		98,1079,3001	no	coding-synonymous	KRTAP1-1	NM_030967.2		151,1698,4382	AA,AG,GG		15.2585,17.6571,16.0488		158/178	39197176	2000,10462	2053	4178	6231	SO:0001819	synonymous_variant	81851	exon1			TCCACAGTAGGAT	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.474C>T	17.37:g.39197176G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			G|1.000;|0.000	.	weak		0.627	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
ROBO1	6091	hgsc.bcm.edu	37	3	78676523	78676523	+	Silent	SNP	A	A	G	rs62260386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:78676523A>G	ENST00000464233.1	-	26	3936	c.3823T>C	c.(3823-3825)Tta>Cta	p.L1275L	ROBO1_ENST00000467549.1_Silent_p.L1175L|ROBO1_ENST00000436010.2_Silent_p.L1236L|ROBO1_ENST00000495273.1_Silent_p.L1230L	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1275					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		CAATCCTGTAACATGGGCTGG	0.532													A|||	12	0.00239617	0.0008	0.0014	5008	,	,		18854	0.0		0.006	False		,,,				2504	0.0041				p.L1275L		Atlas-SNP	.											.	ROBO1	833	.	0			c.T3823C						PASS	.	A	,,	10,4316		0,10,2153	53.0	61.0	58.0		3523,3823,3688	-1.6	1.0	3	dbSNP_129	58	97,8443		1,95,4174	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	1,105,6327	GG,GA,AA		1.1358,0.2312,0.8316	,,	1175/1552,1275/1652,1230/1607	78676523	107,12759	2163	4270	6433	SO:0001819	synonymous_variant	6091	exon26			CCTGTAACATGGG	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3823T>C	3.37:g.78676523A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	186	113	0.607527	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			A|0.997;G|0.003	0.003	strong		0.532	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
MGLL	11343	hgsc.bcm.edu	37	3	127540635	127540635	+	Silent	SNP	C	C	T	rs11538698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:127540635C>T	ENST00000434178.2	-	2	923	c.27G>A	c.(25-27)cgG>cgA	p.R9R	MGLL_ENST00000398104.1_Silent_p.R9R|MGLL_ENST00000265052.5_Silent_p.R19R|MGLL_ENST00000453507.2_Silent_p.R19R			Q99685	MGLL_HUMAN	monoglyceride lipase	9					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						TCTGCGGGGTCCGCCTGGGGG	0.522													C|||	78	0.0155751	0.0	0.0216	5008	,	,		15700	0.0		0.0507	False		,,,				2504	0.0123				p.R19R		Atlas-SNP	.											.	MGLL	19	.	0			c.G57A						PASS	.	C	,	32,3730		0,32,1849	113.0	119.0	117.0		27,57	2.0	1.0	3	dbSNP_120	117	345,7867		8,329,3769	no	coding-synonymous,coding-synonymous	MGLL	NM_001003794.1,NM_007283.5	,	8,361,5618	TT,TC,CC		4.2012,0.8506,3.1485	,	9/304,19/314	127540635	377,11597	1881	4106	5987	SO:0001819	synonymous_variant	11343	exon2			CGGGGTCCGCCTG	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.27G>A	3.37:g.127540635C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	151	81	0.536424	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	37	CCDS43148.1																																																																																			T|0.033;G|0.000;C|0.967	0.033	strong		0.522	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
CLASP1	23332	hgsc.bcm.edu	37	2	122182786	122182786	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:122182786G>A	ENST00000263710.4	-	22	2530	c.2141C>T	c.(2140-2142)tCa>tTa	p.S714L	CLASP1_ENST00000545861.1_Missense_Mutation_p.S490L|CLASP1_ENST00000397587.3_Missense_Mutation_p.S722L|CLASP1_ENST00000541377.1_Missense_Mutation_p.S721L|CLASP1_ENST00000455322.2_Missense_Mutation_p.S714L|CLASP1_ENST00000409078.3_Missense_Mutation_p.S714L|CLASP1_ENST00000541859.1_Missense_Mutation_p.S483L	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	714	Interaction with microtubules, MAPRE1 and MAPRE3.|Ser-rich.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TCGCTTTTCTGAAGACGGTGT	0.512																																					p.S722L		Atlas-SNP	.											CLASP1,bladder,carcinoma,0,1	CLASP1	135	1	0			c.C2165T						scavenged	.						113.0	111.0	111.0					2																	122182786		1857	4092	5949	SO:0001583	missense	23332	exon23			TTTTCTGAAGACG	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2141C>T	2.37:g.122182786G>A	ENSP00000263710:p.Ser714Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	151	2	0.013245	NM_001142273	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	G	19.47	3.833428	0.71258	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861;ENST00000463621	T;T;T;T;T;T	0.45668	2.2;2.16;2.22;2.21;0.89;2.19	5.83	5.83	0.93111	Armadillo-type fold (1);	0.152670	0.45361	D	0.000371	T	0.44993	0.1320	L	0.56769	1.78	0.47659	D	0.99948	B;B;B;B	0.26845	0.1;0.161;0.1;0.148	B;B;B;B	0.21708	0.014;0.033;0.036;0.031	T	0.34850	-0.9812	10	0.56958	D	0.05	-8.0939	20.1047	0.97888	0.0:0.0:1.0:0.0	.	714;722;721;714	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	L	714;714;722;721;483;714;490;55	ENSP00000263710:S714L;ENSP00000389372:S714L;ENSP00000380717:S722L;ENSP00000441625:S721L;ENSP00000441770:S483L;ENSP00000386442:S714L	ENSP00000263710:S714L	S	-	2	0	CLASP1	121899256	1.000000	0.71417	0.998000	0.56505	0.829000	0.46940	9.624000	0.98398	2.762000	0.94881	0.655000	0.94253	TCA	.	.	none		0.512	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
FAM131B	9715	hgsc.bcm.edu	37	7	143053723	143053723	+	Missense_Mutation	SNP	C	C	T	rs17854363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000409578.1_Missense_Mutation_p.A323T|FAM131B_ENST00000409222.3_Missense_Mutation_p.A307T|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	74	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	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	
NARFL	64428	hgsc.bcm.edu	37	16	781633	781633	+	Silent	SNP	G	G	A	rs3829492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:781633G>A	ENST00000251588.2	-	9	982	c.966C>T	c.(964-966)caC>caT	p.H322H	NARFL_ENST00000301694.5_3'UTR|NARFL_ENST00000568545.1_Silent_p.H220H|NARFL_ENST00000562862.1_5'UTR|NARFL_ENST00000540986.1_Silent_p.H220H	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	322					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCCGGAACACGTGCTCCAGGT	0.657													G|||	1908	0.38099	0.1271	0.4539	5008	,	,		18429	0.7599		0.2147	False		,,,				2504	0.453				p.H322H		Atlas-SNP	.											NARFL,NS,adenoma,0,1	NARFL	31	1	0			c.C966T						PASS	.	G		476,3844		18,440,1702	32.0	27.0	29.0		966	-4.5	0.9	16	dbSNP_107	29	1536,7010		136,1264,2873	no	coding-synonymous	NARFL	NM_022493.1		154,1704,4575	AA,AG,GG		17.9733,11.0185,15.6381		322/477	781633	2012,10854	2160	4273	6433	SO:0001819	synonymous_variant	64428	exon9			GAACACGTGCTCC	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.966C>T	16.37:g.781633G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	20	6	0.3	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1																																																																																			G|0.714;A|0.286	0.286	strong		0.657	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
SMCHD1	23347	hgsc.bcm.edu	37	18	2750477	2750477	+	Silent	SNP	A	A	G	rs2304859	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	69	0	0		WXS	Illumina HiSeq	Phase_I	113	39	0.345133	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		
UMODL1	89766	hgsc.bcm.edu	37	21	43522349	43522349	+	Silent	SNP	T	T	C	rs220109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43522349T>C	ENST00000408910.2	+	8	1260	c.1260T>C	c.(1258-1260)agT>agC	p.S420S	UMODL1_ENST00000400424.2_Silent_p.S348S|UMODL1_ENST00000408989.2_Silent_p.S420S|UMODL1_ENST00000400427.1_Silent_p.S348S|C21orf128_ENST00000329015.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	420	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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						ACCGCAGCAGTGTGGAGTACC	0.438													C|||	2716	0.542332	0.4516	0.6484	5008	,	,		20187	0.5813		0.5358	False		,,,				2504	0.5562				p.S420S	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T1260C						PASS	.	C	,,,	1858,1970		454,950,510	90.0	89.0	89.0		1260,1044,1044,1260	1.1	0.1	21	dbSNP_79	89	4490,3774		1235,2020,877	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	1689,2970,1387	CC,CT,TT		45.668,48.5371,47.5025	,,,	420/1319,348/1375,348/1247,420/1447	43522349	6348,5744	1914	4132	6046	SO:0001819	synonymous_variant	89766	exon8			CAGCAGTGTGGAG		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.1260T>C	21.37:g.43522349T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			T|0.458;C|0.542	0.542	strong		0.438	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
OR52N2	390077	hgsc.bcm.edu	37	11	5841778	5841778	+	Silent	SNP	T	T	A	rs73394374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5841778T>A	ENST00000317037.2	+	1	235	c.213T>A	c.(211-213)acT>acA	p.T71T	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	71						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)		TCTCCTTCACTGATGTCACCT	0.532													T|||	204	0.0407348	0.0749	0.0259	5008	,	,		22577	0.001		0.0467	False		,,,				2504	0.0399				p.T71T		Atlas-SNP	.											.	OR52N2	58	.	0			c.T213A						PASS	.	T		338,4064	178.0+/-206.8	9,320,1872	169.0	146.0	154.0		213	-5.6	0.3	11	dbSNP_130	154	576,8016	154.8+/-208.9	16,544,3736	no	coding-synonymous	OR52N2	NM_001005174.1		25,864,5608	AA,AT,TT		6.7039,7.6783,7.034		71/322	5841778	914,12080	2201	4296	6497	SO:0001819	synonymous_variant	390077	exon1			CTTCACTGATGTC	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.213T>A	11.37:g.5841778T>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_001005174	Q6IFF9	Silent	SNP	ENST00000317037.2	37	CCDS31399.1																																																																																			T|0.939;A|0.061	0.061	strong		0.532	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
MAP4	4134	hgsc.bcm.edu	37	3	47958037	47958037	+	Missense_Mutation	SNP	G	G	T	rs1060407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:47958037G>T	ENST00000360240.6	-	7	1798	c.1280C>A	c.(1279-1281)tCc>tAc	p.S427Y	MAP4_ENST00000383737.4_Intron|MAP4_ENST00000426837.2_Missense_Mutation_p.S444Y|MAP4_ENST00000395734.3_Missense_Mutation_p.S427Y	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	427	17 X 14 AA tandem repeats.		S -> Y (in dbSNP:rs1060407). {ECO:0000269|PubMed:1718985}.		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TATTTCTGTGGATGATATAAT	0.483													G|||	1261	0.251797	0.1165	0.3458	5008	,	,		21315	0.2629		0.2992	False		,,,				2504	0.3078				p.S427Y		Atlas-SNP	.											.	MAP4	176	.	0			c.C1280A						PASS	.	G	TYR/SER,TYR/SER	591,3815	257.0+/-261.6	36,519,1648	124.0	111.0	116.0		1280,1280	4.1	0.1	3	dbSNP_86	116	2660,5940	426.6+/-355.3	420,1820,2060	yes	missense,missense	MAP4	NM_001134364.1,NM_002375.4	144,144	456,2339,3708	TT,TG,GG		30.9302,13.4135,24.9962	benign,benign	427/1136,427/1153	47958037	3251,9755	2203	4300	6503	SO:0001583	missense	4134	exon7			TCTGTGGATGATA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1280C>A	3.37:g.47958037G>T	ENSP00000353375:p.Ser427Tyr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	220	137	0.622727	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	506	0.2316849816849817	46	0.09349593495934959	108	0.2983425414364641	131	0.229020979020979	221	0.29155672823219	G	13.11	2.140525	0.37825	0.134135	0.309302	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.08807	3.12;3.05;3.13	4.09	4.09	0.47781	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.23277	P	0.99799361	P;B;B	0.45827	0.867;0.27;0.319	B;B;B	0.42062	0.374;0.151;0.073	T	0.48502	-0.9030	8	0.87932	D	0	-1.8424	14.6207	0.68582	0.0:0.0:1.0:0.0	rs1060407;rs3201295;rs3821448;rs17382401;rs61068109;rs1060407	404;427;427	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	Y	427;444;427	ENSP00000379083:S427Y;ENSP00000407602:S444Y;ENSP00000353375:S427Y	ENSP00000353375:S427Y	S	-	2	0	MAP4	47933041	0.200000	0.23398	0.112000	0.21494	0.006000	0.05464	1.868000	0.39509	2.560000	0.86352	0.561000	0.74099	TCC	G|0.754;T|0.246	0.246	strong		0.483	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
ADH7	131	hgsc.bcm.edu	37	4	100349669	100349669	+	Missense_Mutation	SNP	C	C	G	rs543158429|rs1573496	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:100349669C>G	ENST00000209665.4	-	3	515	c.275G>C	c.(274-276)gGa>gCa	p.G92A	ADH7_ENST00000476959.1_Missense_Mutation_p.G100A|ADH7_ENST00000482593.1_Missense_Mutation_p.G23A|ADH7_ENST00000437033.2_Missense_Mutation_p.G80A	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	92			G -> A (in dbSNP:rs1573496).		ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TGTAGTCACTCCTTCTCCAAT	0.423																																					p.G100A		Atlas-SNP	.											ADH7_ENST00000476959,NS,malignant_melanoma,-1,2	ADH7	76	2	0			c.G299C						PASS	.	C	ALA/GLY,ALA/GLY	80,4326	68.7+/-106.4	3,74,2126	260.0	214.0	230.0	http://omim.org/entry/103720	275,299	3.4	0.5	4	dbSNP_88	230	950,7650	208.4+/-249.9	62,826,3412	yes	missense,missense	ADH7	NM_000673.4,NM_001166504.1	60,60	65,900,5538	GG,GC,CC		11.0465,1.8157,7.9194	possibly-damaging,possibly-damaging	92/387,100/395	100349669	1030,11976	2203	4300	6503	SO:0001583	missense	131	exon3			GTCACTCCTTCTC	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.275G>C	4.37:g.100349669C>G	ENSP00000209665:p.Gly92Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Missense_Mutation	SNP	ENST00000209665.4	37	CCDS34034.1	127	0.05815018315018315	0	0.0	39	0.10773480662983426	0	0.0	88	0.11609498680738786	C	18.53	3.644194	0.67244	0.018157	0.110465	ENSG00000196344	ENST00000437033;ENST00000209665;ENST00000482593;ENST00000476959;ENST00000474027	T;T;T;T;T	0.04049	3.72;3.72;3.72;3.72;3.72	4.24	3.39	0.38822	GroES-like (1);Alcohol dehydrogenase GroES-like (1);Alcohol dehydrogenase, zinc-type, conserved site (1);	0.296303	0.36338	N	0.002660	T	0.00210	0.0006	M	0.62266	1.93	0.18873	P	0.9999810684	D	0.55800	0.973	D	0.63033	0.91	T	0.04115	-1.0976	9	0.87932	D	0	-16.7579	10.8069	0.46522	0.0:0.8377:0.0:0.1623	rs1573496;rs52814989;rs56770102;rs1573496	92	P40394	ADH7_HUMAN	A	80;92;23;100;23	ENSP00000414254:G80A;ENSP00000209665:G92A;ENSP00000420613:G23A;ENSP00000420269:G100A;ENSP00000420300:G23A	ENSP00000209665:G92A	G	-	2	0	ADH7	100568692	0.904000	0.30761	0.496000	0.27539	0.945000	0.59286	3.253000	0.51469	0.973000	0.38340	0.655000	0.94253	GGA	C|0.933;G|0.067	0.067	strong		0.423	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136301982	136301982	+	Missense_Mutation	SNP	C	C	G	rs2301612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136301982C>G	ENST00000371929.3	+	12	1786	c.1342C>G	c.(1342-1344)Caa>Gaa	p.Q448E	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.Q417E|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.Q120E|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.Q448E	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	448	Cysteine-rich.		Q -> E (does not affect protein secretion; normal proteolytic activity; dbSNP:rs2301612). {ECO:0000269|PubMed:11586351, ECO:0000269|PubMed:12181489, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14512317, ECO:0000269|PubMed:14563640, ECO:0000269|PubMed:17003922, ECO:0000269|PubMed:19055667, 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)		GTTCATGTCGCAACAGTGCGC	0.697													G|||	1360	0.271565	0.0408	0.389	5008	,	,		12424	0.1835		0.4254	False		,,,				2504	0.4325				p.Q448E		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C1342G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	421,3969		32,357,1806	15.0	12.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1342,1249,1342	4.2	0.6	9	dbSNP_100	13	3485,5089		725,2035,1527	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	29,29,29	757,2392,3333	GG,GC,CC		40.6461,9.59,30.1296	benign,benign,benign	448/1428,417/1341,448/1372	136301982	3906,9058	2195	4287	6482	SO:0001583	missense	11093	exon12			ATGTCGCAACAGT	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.1342C>G	9.37:g.136301982C>G	ENSP00000360997:p.Gln448Glu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	600	0.27472527472527475	28	0.056910569105691054	132	0.36464088397790057	108	0.1888111888111888	332	0.43799472295514513	G	0.692	-0.794038	0.02862	0.0959	0.406461	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.67345	-0.21;-0.26;-0.23;3.91	5.17	4.25	0.50352	.	.	.	.	.	T	0.00012	0.0000	N	0.00754	-1.215	0.53005	P	3.2999999999949736E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35992	-0.9766	8	0.02654	T	1	.	13.5897	0.61953	0.0:0.297:0.703:0.0	rs2301612;rs17662628;rs36220238;rs2301612	448;417;448	Q76LX8;Q76LX8-3;Q76LX8-2	ATS13_HUMAN;.;.	E	448;448;417;120	ENSP00000360997:Q448E;ENSP00000347927:Q448E;ENSP00000348997:Q417E;ENSP00000444504:Q120E	ENSP00000347927:Q448E	Q	+	1	0	ADAMTS13	135291803	1.000000	0.71417	0.600000	0.28864	0.317000	0.28152	3.711000	0.54868	0.678000	0.31325	-0.223000	0.12442	CAA	C|0.735;G|0.265	0.265	strong		0.697	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SIM1	6492	hgsc.bcm.edu	37	6	100868721	100868721	+	Missense_Mutation	SNP	G	G	A	rs3734355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:100868721G>A	ENST00000369208.3	-	10	1894	c.1112C>T	c.(1111-1113)gCc>gTc	p.A371V	SIM1_ENST00000262901.4_Missense_Mutation_p.A371V			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	371	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		A -> V (in dbSNP:rs3734355).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A371V(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CCGGGATTTGGCCCCCTTTCT	0.517													G|||	894	0.178514	0.0053	0.2089	5008	,	,		15370	0.4067		0.1471	False		,,,				2504	0.1881				p.A371V		Atlas-SNP	.											SIM1,NS,carcinoma,0,1	SIM1	173	1	1	Substitution - Missense(1)	stomach(1)	c.C1112T						PASS	.	G	VAL/ALA	139,4267	97.6+/-136.3	2,135,2066	111.0	104.0	106.0		1112	2.9	1.0	6	dbSNP_107	106	1172,7428	239.3+/-270.5	62,1048,3190	yes	missense	SIM1	NM_005068.2	64	64,1183,5256	AA,AG,GG		13.6279,3.1548,10.08	benign	371/767	100868721	1311,11695	2203	4300	6503	SO:0001583	missense	6492	exon9			GATTTGGCCCCCT	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1112C>T	6.37:g.100868721G>A	ENSP00000358210:p.Ala371Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	432	0.1978021978021978	7	0.014227642276422764	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	15.06	2.722664	0.48728	0.031548	0.136279	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.33438	1.41;1.41	5.8	2.86	0.33363	Single-minded, C-terminal (2);	0.916570	0.09543	N	0.788056	T	0.06645	0.0170	N	0.19112	0.55	0.35594	P	0.19266700000000003	B	0.10296	0.003	B	0.12156	0.007	T	0.30592	-0.9973	9	0.27785	T	0.31	.	4.3759	0.11270	0.0874:0.3246:0.4629:0.1251	rs3734355;rs3734355	371	P81133	SIM1_HUMAN	V	371	ENSP00000358210:A371V;ENSP00000262901:A371V	ENSP00000262901:A371V	A	-	2	0	SIM1	100975442	0.941000	0.31946	1.000000	0.80357	0.987000	0.75469	1.394000	0.34509	1.466000	0.48025	-0.157000	0.13467	GCC	G|0.857;A|0.143	0.143	strong		0.517	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552115	178552115	+	Silent	SNP	G	G	A	rs201215425		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178552115G>A	ENST00000251582.7	-	19	2918	c.2817C>T	c.(2815-2817)tcC>tcT	p.S939S		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	939	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		TGCAGCGCACGGAGCGCACCT	0.692																																					p.S939S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C2817T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107.0	106.0	107.0		2817	-9.1	0.4	5		107	0,8600		0,0,4300	yes	coding-synonymous	ADAMTS2	NM_014244.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		939/1212	178552115	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon19			GCGCACGGAGCGC	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.2817C>T	5.37:g.178552115G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	169	70	0.414201	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16525657	16525657	+	Missense_Mutation	SNP	A	A	G	rs148325785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16525657A>G	ENST00000270747.3	-	15	2375	c.2239T>C	c.(2239-2241)Tgg>Cgg	p.W747R	ARHGEF19-AS1_ENST00000457809.1_RNA|ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	747	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		TCACTGGTCCAGGTCCTCACT	0.562													A|||	25	0.00499201	0.0	0.0115	5008	,	,		19556	0.0		0.0159	False		,,,				2504	0.001				p.W747R		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.T2239C						PASS	.	A	ARG/TRP	11,4395	17.9+/-39.9	0,11,2192	125.0	98.0	107.0		2239	-0.1	1.0	1	dbSNP_134	107	106,8494	57.9+/-119.4	1,104,4195	yes	missense	ARHGEF19	NM_153213.3	101	1,115,6387	GG,GA,AA		1.2326,0.2497,0.8996	benign	747/803	16525657	117,12889	2203	4300	6503	SO:0001583	missense	128272	exon15			TGGTCCAGGTCCT	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.2239T>C	1.37:g.16525657A>G	ENSP00000270747:p.Trp747Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	A	4.292	0.053391	0.08291	0.002497	0.012326	ENSG00000142632	ENST00000270747	T	0.43294	0.95	4.57	-0.0683	0.13756	Src homology-3 domain (4);	0.268702	0.27604	N	0.018633	T	0.03011	0.0089	N	0.00170	-1.935	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28933	-1.0028	10	0.06236	T	0.91	.	4.4685	0.11701	0.2021:0.0:0.4709:0.327	.	747	Q8IW93	ARHGJ_HUMAN	R	747	ENSP00000270747:W747R	ENSP00000270747:W747R	W	-	1	0	ARHGEF19	16398244	0.005000	0.15991	0.963000	0.40424	0.929000	0.56500	0.455000	0.21843	0.151000	0.19162	-0.366000	0.07423	TGG	A|0.991;G|0.009	0.009	strong		0.562	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105885961	105885961	+	Missense_Mutation	SNP	T	T	C	rs2241797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:105885961T>C	ENST00000393359.2	-	11	2600	c.2174A>G	c.(2173-2175)cAt>cGt	p.H725R	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.H725R			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	725			H -> R (in dbSNP:rs2241797). {ECO:0000269|PubMed:9545258, ECO:0000269|Ref.4}.		intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GGGGCCAGCATGCAGGTAGAT	0.657													T|||	2519	0.502995	0.4697	0.6383	5008	,	,		16692	0.2827		0.66	False		,,,				2504	0.5174				p.H725R	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.A2174G						PASS	.	T	ARG/HIS,ARG/HIS	2155,2251		551,1053,599	26.0	29.0	28.0		2174,2174	-7.0	0.0	2	dbSNP_98	28	5562,3036		1787,1988,524	yes	missense,missense	TGFBRAP1	NM_001142621.1,NM_004257.4	29,29	2338,3041,1123	CC,CT,TT		35.3105,48.9106,40.6567	benign,benign	725/861,725/861	105885961	7717,5287	2203	4299	6502	SO:0001583	missense	9392	exon11			CCAGCATGCAGGT	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2174A>G	2.37:g.105885961T>C	ENSP00000377027:p.His725Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	182	74	0.406593	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	1113	0.5096153846153846	240	0.4878048780487805	223	0.6160220994475138	154	0.2692307692307692	496	0.6543535620052771	T	0.297	-0.976266	0.02215	0.489106	0.646895	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.40476	1.03;1.03	5.66	-6.99	0.01605	.	1.789210	0.02336	N	0.074427	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	0.06405	0.0;0.002	T	0.37663	-0.9696	9	0.11182	T	0.66	-0.1023	11.5638	0.50794	0.0:0.144:0.1815:0.6745	rs2241797;rs52789328;rs59139027;rs2241797	180;725	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	R	725;725;180	ENSP00000377027:H725R;ENSP00000258449:H725R	ENSP00000258449:H725R	H	-	2	0	TGFBRAP1	105252393	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.176000	0.09811	-1.005000	0.03417	-1.156000	0.01807	CAT	T|0.465;C|0.535	0.535	strong		0.657	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
KIAA1211	57482	hgsc.bcm.edu	37	4	57190356	57190356	+	Silent	SNP	G	G	A	rs7695701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57190356G>A	ENST00000504228.1	+	8	3570	c.3465G>A	c.(3463-3465)agG>agA	p.R1155R	KIAA1211_ENST00000264229.6_Silent_p.R1155R|KIAA1211_ENST00000541073.1_Silent_p.R1148R			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						PASS	.	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	239	0	0		WXS	Illumina HiSeq	Phase_I	250	248	0.992	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	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653398	121653398	+	Missense_Mutation	SNP	G	G	A	rs1147504	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:121653398G>A	ENST00000393386.2	+	12	4709	c.4298G>A	c.(4297-4299)gGt>gAt	p.G1433D	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	1433			G -> D (in dbSNP:rs1147504). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:1323835, ECO:0000269|Ref.5}.		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						gatgaCAGAGGTAGTGATGGC	0.428													A|||	3404	0.679712	0.9327	0.5663	5008	,	,		21180	0.6478		0.4672	False		,,,				2504	0.6697				p.G1433D		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4298A						PASS	.	A	,,ASP/GLY	3849,557	247.8+/-255.9	1684,481,38	80.0	73.0	75.0		,,4298	3.2	0.9	7	dbSNP_87	75	4459,4141	564.5+/-388.3	1147,2165,988	yes	intron,intron,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,94	2831,2646,1026	AA,AG,GG		48.1512,12.6419,36.1218	,,benign	,,1433/2316	121653398	8308,4698	2203	4300	6503	SO:0001583	missense	5803	exon12			ACAGAGGTAGTGA	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.4298G>A	7.37:g.121653398G>A	ENSP00000377047:p.Gly1433Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	1382	0.6327838827838828	458	0.9308943089430894	204	0.56353591160221	379	0.6625874125874126	341	0.449868073878628	A	2.951	-0.216791	0.06101	0.873581	0.518488	ENSG00000106278	ENST00000393386	T	0.37915	1.17	5.61	3.22	0.36961	.	0.407826	0.21036	N	0.081258	T	0.00012	0.0000	N	0.00197	-1.87	0.18873	P	0.9999875516	B	0.02656	0.0	B	0.01281	0.0	T	0.33445	-0.9868	9	0.02654	T	1	.	5.9064	0.19004	0.7168:0.14:0.1431:0.0	rs1147504;rs1725065;rs52812647;rs57155850;rs1147504	1433	P23471	PTPRZ_HUMAN	D	1433	ENSP00000377047:G1433D	ENSP00000377047:G1433D	G	+	2	0	PTPRZ1	121440634	0.997000	0.39634	0.927000	0.36925	0.907000	0.53573	1.465000	0.35299	0.476000	0.27440	-0.269000	0.10298	GGT	G|0.353;A|0.647	0.647	strong		0.428	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
NPAS2	4862	hgsc.bcm.edu	37	2	101541736	101541736	+	Missense_Mutation	SNP	G	G	C	rs138995271		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:101541736G>C	ENST00000335681.5	+	3	446	c.161G>C	c.(160-162)gGa>gCa	p.G54A	NPAS2_ENST00000542504.1_Missense_Mutation_p.G119A|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	54	Sufficient for heterodimer formation with ARNTL/BMAL1, E-box binding and for the effect of NADPH. {ECO:0000250|UniProtKB:P97460}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGGTCATCGGATTTTTGCAG	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		20410	0.0		0.001	False		,,,				2504	0.0				p.G54A		Atlas-SNP	.											.	NPAS2	88	.	0			c.G161C						PASS	.	G	ALA/GLY	0,4406		0,0,2203	108.0	101.0	104.0		161	5.7	1.0	2	dbSNP_134	104	10,8590	7.7+/-29.5	0,10,4290	yes	missense	NPAS2	NM_002518.3	60	0,10,6493	CC,CG,GG		0.1163,0.0,0.0769	benign	54/825	101541736	10,12996	2203	4300	6503	SO:0001583	missense	4862	exon3			TCATCGGATTTTT	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.161G>C	2.37:g.101541736G>C	ENSP00000338283:p.Gly54Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	11.83|11.83	1.756142|1.756142	0.31137|0.31137	0.0|0.0	0.001163|0.001163	ENSG00000170485|ENSG00000170485	ENST00000427413|ENST00000335681;ENST00000542504;ENST00000451740	.|D;D;D	.|0.97710	.|-4.5;-4.5;-4.5	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Helix-loop-helix DNA-binding (5);	.|0.055781	.|0.64402	.|D	.|0.000001	D|D	0.93680|0.93680	0.7981|0.7981	N|N	0.02751|0.02751	-0.505|-0.505	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.37370	.|0.537;0.592	.|B;B	.|0.41174	.|0.237;0.349	D|D	0.93572|0.93572	0.6905|0.6905	5|10	.|0.41790	.|T	.|0.15	.|.	19.7272|19.7272	0.96168|0.96168	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|119;54	.|F5H027;Q99743	.|.;NPAS2_HUMAN	H|A	120|54;119;38	.|ENSP00000338283:G54A;ENSP00000438428:G119A;ENSP00000395265:G38A	.|ENSP00000338283:G54A	D|G	+|+	1|2	0|0	NPAS2|NPAS2	100908168|100908168	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.994000|0.994000	0.84299|0.84299	6.750000|6.750000	0.74888|0.74888	2.646000|2.646000	0.89796|0.89796	0.655000|0.655000	0.94253|0.94253	GAT|GGA	G|0.999;C|0.001	0.001	strong		0.498	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
LILRB4	11006	hgsc.bcm.edu	37	19	55174498	55174498	+	Missense_Mutation	SNP	T	T	C	rs28366008	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000270452.2_Missense_Mutation_p.F5L|LILRB4_ENST00000391733.3_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	26	0	0	1005	WXS	Illumina HiSeq	Phase_I	26	14	0.538462	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		
ODAM	54959	hgsc.bcm.edu	37	4	71062426	71062426	+	Silent	SNP	C	C	T	rs17704351	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71062426C>T	ENST00000396094.2	+	2	117	c.69C>T	c.(67-69)ctC>ctT	p.L23L		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	23					biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						CACAGCGTCTCATGTCTGCCA	0.343													T|||	1445	0.288538	0.1641	0.2032	5008	,	,		16862	0.2996		0.2753	False		,,,				2504	0.5194				p.L23L		Atlas-SNP	.											.	ODAM	38	.	0			c.C69T						PASS	.	T		711,2935		73,565,1185	65.0	59.0	61.0		69	-0.4	0.0	4	dbSNP_123	61	2316,5846		329,1658,2094	no	coding-synonymous	ODAM	NM_017855.3		402,2223,3279	TT,TC,CC		28.3754,19.5008,25.6352		23/280	71062426	3027,8781	1823	4081	5904	SO:0001819	synonymous_variant	54959	exon2			GCGTCTCATGTCT	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.69C>T	4.37:g.71062426C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	175	76	0.434286	NM_017855	Q8WWE5|Q9NWZ9	Silent	SNP	ENST00000396094.2	37	CCDS3536.2																																																																																			C|0.741;T|0.259	0.259	strong		0.343	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855	
ZNF773	374928	hgsc.bcm.edu	37	19	58017758	58017758	+	Missense_Mutation	SNP	G	G	C	rs55823456	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58017758G>C	ENST00000282292.4	+	4	435	c.295G>C	c.(295-297)Gct>Cct	p.A99P	ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.A98P	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	75	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	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	
WDR90	197335	hgsc.bcm.edu	37	16	716971	716971	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:716971C>T	ENST00000293879.4	+	40	5071	c.5071C>T	c.(5071-5073)Ctg>Ttg	p.L1691L	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Silent_p.L1693L|WDR90_ENST00000547944.1_Silent_p.L290L|WDR90_ENST00000315764.4_Silent_p.L242L			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1691										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GACCCACCTCCTGGCTGTTGG	0.617																																					p.L1691L		Atlas-SNP	.											.	WDR90	107	.	0			c.C5071T						PASS	.						69.0	73.0	72.0					16																	716971		2108	4232	6340	SO:0001819	synonymous_variant	197335	exon40			CACCTCCTGGCTG	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.5071C>T	16.37:g.716971C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	none		0.617	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
NOL9	79707	hgsc.bcm.edu	37	1	6614535	6614535	+	Missense_Mutation	SNP	G	G	A	rs4908923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6614535G>A	ENST00000377705.5	-	1	60	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	TAS1R1_ENST00000328191.4_5'Flank|TAS1R1_ENST00000333172.6_5'Flank|TAS1R1_ENST00000351136.3_5'Flank	NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	10			R -> W (in dbSNP:rs4908923). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		CAGGAACCCCGCTTTAGCAGC	0.731													G|||	3617	0.722244	0.4266	0.8473	5008	,	,		10220	0.7927		0.8608	False		,,,				2504	0.818				p.R10W		Atlas-SNP	.											.	NOL9	49	.	0			c.C28T						PASS	.	G	TRP/ARG	1563,1181		454,655,263	9.0	11.0	11.0		28	2.2	0.2	1	dbSNP_111	11	5290,676		2366,558,59	yes	missense	NOL9	NM_024654.4	101	2820,1213,322	AA,AG,GG		11.3309,43.0394,21.3203	probably-damaging	10/703	6614535	6853,1857	1372	2983	4355	SO:0001583	missense	79707	exon1			AACCCCGCTTTAG	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"""polynucleotide 5'-kinase"""					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.28C>T	1.37:g.6614535G>A	ENSP00000366934:p.Arg10Trp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	37	CCDS80.1	1640	0.7509157509157509	215	0.4369918699186992	303	0.8370165745856354	461	0.8059440559440559	661	0.8720316622691293	G	18.08	3.544878	0.65198	0.569606	0.886691	ENSG00000162408	ENST00000377705	T	0.22336	1.96	4.22	2.15	0.27550	.	0.359620	0.20473	N	0.091646	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.89917	1.0	D	0.64410	0.925	T	0.05178	-1.0901	9	0.87932	D	0	-23.1595	6.7366	0.23413	0.0:0.1971:0.5992:0.2036	rs4908923;rs11557042;rs60306735;rs4908923	10	Q5SY16	NOL9_HUMAN	W	10	ENSP00000366934:R10W	ENSP00000366934:R10W	R	-	1	2	NOL9	6537122	0.003000	0.15002	0.211000	0.23655	0.006000	0.05464	0.459000	0.21908	1.112000	0.41740	0.561000	0.74099	CGG	G|0.274;A|0.726	0.726	strong		0.731	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654	
GABRB3	2562	hgsc.bcm.edu	37	15	26812780	26812780	+	Silent	SNP	C	C	T	rs76812964	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:26812780C>T	ENST00000311550.5	-	7	894	c.783G>A	c.(781-783)tcG>tcA	p.S261S	GABRB3_ENST00000541819.2_Silent_p.S317S|GABRB3_ENST00000299267.4_Silent_p.S261S|GABRB3_ENST00000545868.1_Silent_p.S176S|GABRB3_ENST00000400188.3_Silent_p.S190S	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	261					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|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)|GABA-A receptor complex (GO:1902711)|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)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	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)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGGACACCCACGACAGAATCG	0.408													C|||	66	0.0131789	0.0015	0.0202	5008	,	,		21102	0.0		0.0447	False		,,,				2504	0.0051				p.S261S		Atlas-SNP	.											.	GABRB3	338	.	0			c.G783A						PASS	.	C	,,,	38,4368	42.3+/-75.8	1,36,2166	128.0	110.0	116.0		783,528,570,783	-12.1	0.0	15	dbSNP_131	116	291,8309	107.4+/-168.2	6,279,4015	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	7,315,6181	TT,TC,CC		3.3837,0.8625,2.5296	,,,	261/474,176/389,190/403,261/474	26812780	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon7			CACCCACGACAGA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.783G>A	15.37:g.26812780C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			C|0.975;T|0.025	0.025	strong		0.408	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
ARSG	22901	hgsc.bcm.edu	37	17	66364770	66364770	+	Silent	SNP	G	G	A	rs146307895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66364770G>A	ENST00000448504.2	+	7	1582	c.786G>A	c.(784-786)gcG>gcA	p.A262A	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Silent_p.A98A	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	262					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)			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)			TACCAGCAGCGCCACGGGGCA	0.577													G|||	15	0.00299521	0.0	0.0043	5008	,	,		18986	0.0		0.0119	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											.	ARSG	55	.	0			c.G786A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	99.0	96.0	97.0		786	-1.9	0.0	17	dbSNP_134	97	89,8511	49.8+/-109.6	0,89,4211	no	coding-synonymous	ARSG	NM_014960.3		0,94,6409	AA,AG,GG		1.0349,0.1135,0.7227		262/526	66364770	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon7			AGCAGCGCCACGG	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.786G>A	17.37:g.66364770G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			G|0.993;A|0.007	0.007	strong		0.577	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:22775185C>T	ENST00000361524.3	-	5	3745	c.3597G>A	c.(3595-3597)aaG>aaA	p.K1199K	ZNF521_ENST00000538137.2_Silent_p.K1199K|ZNF521_ENST00000584787.1_Silent_p.K979K	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	77	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	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	
GOLGB1	2804	hgsc.bcm.edu	37	3	121414061	121414061	+	Missense_Mutation	SNP	C	C	T	rs1127412	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121414061C>T	ENST00000340645.5	-	13	5419	c.5294G>A	c.(5293-5295)gGt>gAt	p.G1765D	GOLGB1_ENST00000393667.3_Missense_Mutation_p.G1770D	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1765			G -> D (in dbSNP:rs1127412). {ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:7511208, ECO:0000269|PubMed:8198703}.		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)		AGATACATTACCTTCTATCTG	0.383													C|||	1253	0.2502	0.1649	0.1614	5008	,	,		23338	0.4841		0.2515	False		,,,				2504	0.1861				p.G1770D		Atlas-SNP	.											.	GOLGB1	319	.	0			c.G5309A						PASS	.	C	ASP/GLY	708,3698	292.7+/-282.2	54,600,1549	259.0	242.0	248.0		5294	-9.9	0.0	3	dbSNP_86	248	2114,6486	365.4+/-333.9	278,1558,2464	yes	missense	GOLGB1	NM_004487.3	94	332,2158,4013	TT,TC,CC		24.5814,16.069,21.6977	benign	1765/3260	121414061	2822,10184	2203	4300	6503	SO:0001583	missense	2804	exon13			ACATTACCTTCTA	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.5294G>A	3.37:g.121414061C>T	ENSP00000341848:p.Gly1765Asp	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	306	117	0.382353	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	610	0.2793040293040293	79	0.16056910569105692	71	0.19613259668508287	267	0.46678321678321677	193	0.2546174142480211	C	1.818	-0.473049	0.04445	0.16069	0.245814	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.13089	2.62;2.62	5.8	-9.92	0.00455	.	2.277780	0.01577	N	0.020871	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.44267	-0.9339	9	0.15066	T	0.55	.	1.5861	0.02644	0.1697:0.1956:0.1763:0.4583	rs1127412;rs52834346;rs56608721;rs1127412	1690;1770;1765	F1T0J2;E7EP74;Q14789	.;.;GOGB1_HUMAN	D	1765;1770	ENSP00000341848:G1765D;ENSP00000377275:G1770D	ENSP00000341848:G1765D	G	-	2	0	GOLGB1	122896751	0.000000	0.05858	0.000000	0.03702	0.385000	0.30292	-0.790000	0.04604	-1.808000	0.01234	-0.311000	0.09066	GGT	C|0.760;T|0.240	0.240	strong		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
VEGFC	7424	hgsc.bcm.edu	37	4	177650866	177650866	+	Missense_Mutation	SNP	C	C	T	rs41278571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:177650866C>T	ENST00000280193.2	-	2	597	c.182G>A	c.(181-183)cGg>cAg	p.R61Q	VEGFC_ENST00000507638.1_5'Flank	NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	61					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)	p.R61P(1)		biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		GGACACAGACCGTAACTGCTC	0.408													C|||	18	0.00359425	0.0008	0.0	5008	,	,		16512	0.0		0.0169	False		,,,				2504	0.0				p.R61Q		Atlas-SNP	.											VEGFC,caecum,carcinoma,-1,2	VEGFC	94	2	1	Substitution - Missense(1)	prostate(1)	c.G182A						PASS	.	C	GLN/ARG	13,3819		0,13,1903	89.0	82.0	84.0		182	4.9	0.8	4	dbSNP_127	84	84,8180		0,84,4048	yes	missense	VEGFC	NM_005429.2	43	0,97,5951	TT,TC,CC		1.0165,0.3392,0.8019	probably-damaging	61/421	177650866	97,11999	1916	4132	6048	SO:0001583	missense	7424	exon2			ACAGACCGTAACT	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"""vascular endothelial growth factor-related protein"""	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.182G>A	4.37:g.177650866C>T	ENSP00000280193:p.Arg61Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	14	0.00641025641025641	0	0.0	0	0.0	0	0.0	14	0.018469656992084433	C	32	5.131400	0.94473	0.003392	0.010165	ENSG00000150630	ENST00000280193	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.67505	0.2900	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78342	-0.2241	9	0.87932	D	0	-14.0043	18.5048	0.90893	0.0:1.0:0.0:0.0	rs41278571;rs61731224	61	P49767	VEGFC_HUMAN	Q	61	.	ENSP00000280193:R61Q	R	-	2	0	VEGFC	177887860	1.000000	0.71417	0.774000	0.31636	0.915000	0.54546	7.141000	0.77330	2.466000	0.83321	0.484000	0.47621	CGG	C|0.992;T|0.008	0.008	strong		0.408	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429	
CDH20	28316	hgsc.bcm.edu	37	18	59195294	59195294	+	Missense_Mutation	SNP	A	A	G	rs35923922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:59195294A>G	ENST00000262717.4	+	7	1510	c.1112A>G	c.(1111-1113)cAg>cGg	p.Q371R	CDH20_ENST00000536675.2_Missense_Mutation_p.Q371R|CDH20_ENST00000538374.1_Missense_Mutation_p.Q371R			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	371	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> R (in dbSNP:rs35923922).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GGCCCATTTCAGGACACAACA	0.498													A|||	43	0.00858626	0.0287	0.0058	5008	,	,		18645	0.0		0.001	False		,,,				2504	0.0				p.Q371R		Atlas-SNP	.											CDH20,NS,carcinoma,+1,1	CDH20	117	1	0			c.A1112G						PASS	.	A	ARG/GLN	88,4318	74.1+/-112.3	2,84,2117	132.0	124.0	127.0		1112	5.9	1.0	18	dbSNP_126	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CDH20	NM_031891.2	43	2,86,6415	GG,GA,AA		0.0233,1.9973,0.692	benign	371/802	59195294	90,12916	2203	4300	6503	SO:0001583	missense	28316	exon6			CATTTCAGGACAC	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1112A>G	18.37:g.59195294A>G	ENSP00000262717:p.Gln371Arg	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	185	113	0.610811	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	16	0.007326007326007326	12	0.024390243902439025	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.09	1.535027	0.27475	0.019973	2.33E-4	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.51325	0.71;0.71;0.71	5.88	5.88	0.94601	Cadherin (4);Cadherin-like (1);	0.452719	0.25270	N	0.031885	T	0.12475	0.0303	N	0.04805	-0.155	0.27597	N	0.94909	B	0.02656	0.0	B	0.06405	0.002	T	0.04400	-1.0954	10	0.33940	T	0.23	.	6.32	0.21213	0.8101:0.0:0.1899:0.0	rs35923922	371	Q9HBT6	CAD20_HUMAN	R	371	ENSP00000444767:Q371R;ENSP00000442226:Q371R;ENSP00000262717:Q371R	ENSP00000262717:Q371R	Q	+	2	0	CDH20	57346274	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.994000	0.56994	2.252000	0.74401	0.529000	0.55759	CAG	A|0.992;G|0.008	0.008	strong		0.498	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779032	88779032	+	IGR	SNP	G	G	C	rs2290896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88779032G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.V65V|CTU2_ENST00000453996.2_Silent_p.V152V|CTU2_ENST00000567949.1_Silent_p.V223V|CTU2_ENST00000312060.5_Silent_p.V152V	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						CCCGGAAGGTGTTCAGCCTGC	0.692													G|||	474	0.0946486	0.0318	0.1556	5008	,	,		12054	0.127		0.1243	False		,,,				2504	0.0726				p.V152V		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,2	CTU2	66	2	0			c.G456C						PASS	.	G	,	212,4180		4,204,1988	27.0	33.0	31.0		456,456	3.1	1.0	16	dbSNP_100	31	1191,7405		74,1043,3181	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	78,1247,5169	CC,CG,GG		13.8553,4.827,10.8023	,	152/516,152/486	88779032	1403,11585	2196	4298	6494	SO:0001628	intergenic_variant	348180	exon7			GAAGGTGTTCAGC	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		16.37:g.88779032G>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	175	85	0.485714	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			G|0.895;C|0.105	0.105	strong		0.692	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
RDH5	5959	hgsc.bcm.edu	37	12	56115585	56115585	+	Silent	SNP	C	C	T	rs3138142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56115585C>T	ENST00000257895.5	+	3	575	c.423C>T	c.(421-423)atC>atT	p.I141I	RP11-644F5.10_ENST00000550412.1_3'UTR|RDH5_ENST00000548082.1_Silent_p.I141I|RDH5_ENST00000547072.1_Silent_p.I44I|RDH5_ENST00000553160.1_Intron	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	141					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)	TGGGTCCCATCGGGGTCACCC	0.622													C|||	765	0.152756	0.0098	0.1023	5008	,	,		17734	0.12		0.1899	False		,,,				2504	0.3773				p.I141I		Atlas-SNP	.											.	RDH5	25	.	0			c.C423T						PASS	.	C	,	219,4187	131.0+/-167.6	8,203,1992	46.0	43.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	423,423	-2.2	0.8	12	dbSNP_104	44	1828,6772	323.7+/-316.1	214,1400,2686	no	coding-synonymous,coding-synonymous	RDH5	NM_001199771.1,NM_002905.3	,	222,1603,4678	TT,TC,CC		21.2558,4.9705,15.7389	,	141/319,141/319	56115585	2047,10959	2203	4300	6503	SO:0001819	synonymous_variant	5959	exon3			TCCCATCGGGGTC	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.423C>T	12.37:g.56115585C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_001199771	O00179|Q8TAI2	Silent	SNP	ENST00000257895.5	37	CCDS31829.1																																																																																			C|0.865;T|0.135	0.135	strong		0.622	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905	
GAK	2580	hgsc.bcm.edu	37	4	882643	882643	+	Silent	SNP	G	G	A	rs2279181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:882643G>A	ENST00000314167.4	-	11	1307	c.1197C>T	c.(1195-1197)tcC>tcT	p.S399S	GAK_ENST00000511163.1_Silent_p.S320S	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	399	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				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)		ACTTAGCGACGGACTGGATGA	0.637													G|||	601	0.120008	0.0946	0.0634	5008	,	,		16076	0.0992		0.1183	False		,,,				2504	0.2178				p.S399S		Atlas-SNP	.											.	GAK	104	.	0			c.C1197T						PASS	.	G		374,4018		10,354,1832	89.0	70.0	77.0		1197	-4.0	0.6	4	dbSNP_100	77	909,7673		54,801,3436	no	coding-synonymous	GAK	NM_005255.2		64,1155,5268	AA,AG,GG		10.5919,8.5155,9.889		399/1312	882643	1283,11691	2196	4291	6487	SO:0001819	synonymous_variant	2580	exon11			AGCGACGGACTGG	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.1197C>T	4.37:g.882643G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1																																																																																			G|0.901;A|0.099	0.099	strong		0.637	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
TSPAN8	7103	hgsc.bcm.edu	37	12	71533534	71533534	+	Missense_Mutation	SNP	C	C	G	rs3763978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:71533534C>G	ENST00000393330.2	-	7	770	c.218G>C	c.(217-219)gGa>gCa	p.G73A	TSPAN8_ENST00000247829.3_Missense_Mutation_p.G73A|TSPAN8_ENST00000552128.1_5'Flank|TSPAN8_ENST00000546561.1_Missense_Mutation_p.G73A|TSPAN8_ENST00000552786.1_5'Flank			P19075	TSN8_HUMAN	tetraspanin 8	73			G -> A (in dbSNP:rs3763978). {ECO:0000269|PubMed:15489334}.		negative regulation of blood coagulation (GO:0030195)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(7)|skin(3)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			ACCGCAGCATCCCAGGAAGCC	0.473													C|||	1137	0.227037	0.0378	0.2233	5008	,	,		18058	0.2847		0.3956	False		,,,				2504	0.2526				p.G73A		Atlas-SNP	.											TSPAN8,colon,carcinoma,0,1	TSPAN8	30	1	0			c.G218C						PASS	.	C	ALA/GLY	483,3923	224.9+/-240.9	27,429,1747	186.0	178.0	181.0		218	5.1	1.0	12	dbSNP_107	181	3526,5074	513.3+/-378.1	729,2068,1503	yes	missense	TSPAN8	NM_004616.2	60	756,2497,3250	GG,GC,CC		41.0,10.9623,30.8242	probably-damaging	73/238	71533534	4009,8997	2203	4300	6503	SO:0001583	missense	7103	exon4			CAGCATCCCAGGA	M35252	CCDS8999.1	12q14.1-q21.1	2013-02-14	2005-03-21	2005-03-21		ENSG00000127324		"""Tetraspanins"""	11855	protein-coding gene	gene with protein product		600769	"""transmembrane 4 superfamily member 3"""	TM4SF3		2395876	Standard	NM_004616		Approved	CO-029	uc001swj.1	P19075		ENST00000393330.2:c.218G>C	12.37:g.71533534C>G	ENSP00000377003:p.Gly73Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_004616	B2R7T7|Q9BS78	Missense_Mutation	SNP	ENST00000393330.2	37	CCDS8999.1	591	0.2706043956043956	28	0.056910569105691054	91	0.2513812154696133	177	0.3094405594405594	295	0.3891820580474934	C	19.74	3.884505	0.72410	0.109623	0.41	ENSG00000127324	ENST00000393330;ENST00000247829;ENST00000546561	D;D;D	0.94793	-3.52;-3.52;-3.52	5.09	5.09	0.68999	Tetraspanin, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94847	3.59	0.09310	P	1.0	D	0.76494	0.999	D	0.77004	0.989	T	0.00000	-1.6730	9	0.72032	D	0.01	.	16.3635	0.83296	0.0:1.0:0.0:0.0	rs3763978;rs17849951;rs52802585;rs3763978	73	P19075	TSN8_HUMAN	A	73	ENSP00000377003:G73A;ENSP00000247829:G73A;ENSP00000447160:G73A	ENSP00000247829:G73A	G	-	2	0	TSPAN8	69819801	0.999000	0.42202	1.000000	0.80357	0.509000	0.34042	4.362000	0.59467	2.525000	0.85131	0.655000	0.94253	GGA	C|0.707;G|0.293	0.293	strong		0.473	TSPAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404737.1	NM_004616	
INSR	3643	hgsc.bcm.edu	37	19	7184518	7184518	+	Silent	SNP	G	G	A	rs891087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7184518G>A	ENST00000302850.5	-	3	925	c.783C>T	c.(781-783)gaC>gaT	p.D261D	INSR_ENST00000341500.5_Silent_p.D261D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	261	Cys-rich.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CACACCTGCCGTCCAGGTAGA	0.627													G|||	694	0.138578	0.2262	0.085	5008	,	,		12759	0.0486		0.0726	False		,,,				2504	0.2188				p.D261D		Atlas-SNP	.											.	INSR	265	.	0			c.C783T						PASS	.	G	,	885,3521	334.7+/-303.5	91,703,1409	43.0	38.0	39.0		783,783	-8.6	0.5	19	dbSNP_86	39	747,7853	176.2+/-226.1	28,691,3581	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	119,1394,4990	AA,AG,GG		8.686,20.0862,12.5481	,	261/1383,261/1371	7184518	1632,11374	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon3			CCTGCCGTCCAGG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.783C>T	19.37:g.7184518G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			A|0.117;C|0.000;G|0.883;T|0.000	0.117	strong		0.627	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
NUB1	51667	hgsc.bcm.edu	37	7	151064064	151064064	+	Silent	SNP	C	C	T	rs386956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151064064C>T	ENST00000355851.4	+	9	917	c.840C>T	c.(838-840)taC>taT	p.Y280Y	NUB1_ENST00000568733.1_Silent_p.Y304Y|NUB1_ENST00000566856.1_Silent_p.Y280Y|NUB1_ENST00000413040.2_Silent_p.Y304Y	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	280					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGGATAACTACGCCGTCCTCC	0.458													C|||	1925	0.384385	0.1634	0.4553	5008	,	,		19414	0.4603		0.6302	False		,,,				2504	0.3016				p.Y304Y		Atlas-SNP	.											NUB1,caecum,carcinoma,0,1	NUB1	31	1	0			c.C912T						PASS	.	C		867,3207		101,665,1271	75.0	74.0	74.0		840	-9.4	0.1	7	dbSNP_80	74	5179,3203		1574,2031,586	no	coding-synonymous	NUB1	NM_016118.4		1675,2696,1857	TT,TC,CC		38.2128,21.2813,48.5389		280/602	151064064	6046,6410	2037	4191	6228	SO:0001819	synonymous_variant	51667	exon9			TAACTACGCCGTC	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.840C>T	7.37:g.151064064C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37																																																																																				C|0.538;T|0.462	0.462	strong		0.458	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
LRRC8E	80131	hgsc.bcm.edu	37	19	7964616	7964616	+	Silent	SNP	G	G	C	rs45603833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7964616G>C	ENST00000306708.6	+	3	1310	c.1209G>C	c.(1207-1209)acG>acC	p.T403T	AC010336.1_ENST00000539278.1_Silent_p.G217G|RN7SL115P_ENST00000392196.5_RNA	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	403					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						ACGAGTGGACGCCCGAGAAGC	0.617													G|||	460	0.091853	0.0151	0.2046	5008	,	,		16322	0.001		0.2485	False		,,,				2504	0.0481				p.T403T		Atlas-SNP	.											.	LRRC8E	67	.	0			c.G1209C						PASS	.	G		217,4189	126.6+/-163.6	6,205,1992	49.0	44.0	45.0		1209	-9.3	0.0	19	dbSNP_127	45	2053,6547	341.3+/-324.0	242,1569,2489	no	coding-synonymous	LRRC8E	NM_025061.3		248,1774,4481	CC,CG,GG		23.8721,4.9251,17.4535		403/797	7964616	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	80131	exon4			GTGGACGCCCGAG		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1209G>C	19.37:g.7964616G>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	CCDS12189.1																																																																																			G|0.834;C|0.166	0.166	strong		0.617	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
CKM	1158	hgsc.bcm.edu	37	19	45818835	45818835	+	Silent	SNP	A	A	G	rs1133190	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45818835A>G	ENST00000221476.3	-	4	543	c.369T>C	c.(367-369)ccT>ccC	p.P123P		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	123					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.P123P(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	GCACGTAGTTAGGGTCCAGGT	0.682													G|||	2039	0.407149	0.3011	0.3372	5008	,	,		15644	0.2381		0.6342	False		,,,				2504	0.5409				p.P123P		Atlas-SNP	.											CKM,colon,carcinoma,0,1	CKM	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T369C						PASS	.	G		1562,2844	658.0+/-400.3	276,1010,917	38.0	38.0	38.0		369	2.6	1.0	19	dbSNP_86	38	5416,3184	475.0+/-369.0	1738,1940,622	no	coding-synonymous	CKM	NM_001824.3		2014,2950,1539	GG,GA,AA		37.0233,35.4517,46.3478		123/382	45818835	6978,6028	2203	4300	6503	SO:0001819	synonymous_variant	1158	exon4			GTAGTTAGGGTCC	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.369T>C	19.37:g.45818835A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_001824	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																			A|0.522;G|0.478	0.478	strong		0.682	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
DIAPH3	81624	hgsc.bcm.edu	37	13	60240961	60240961	+	Silent	SNP	C	C	T	rs9538494	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:60240961C>T	ENST00000400324.4	-	28	3559	c.3339G>A	c.(3337-3339)ttG>ttA	p.L1113L	DIAPH3_ENST00000400330.1_Silent_p.L1113L|DIAPH3_ENST00000400320.1_Silent_p.L1067L|DIAPH3_ENST00000400319.1_Silent_p.L1043L|DIAPH3_ENST00000377908.2_Silent_p.L1102L	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1113					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ACCCTTCTGTCAACTGCACTT	0.368													C|||	736	0.146965	0.0242	0.2147	5008	,	,		17183	0.1071		0.2594	False		,,,				2504	0.1902				p.L1113L		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G3339A						PASS	.	C		241,3523		9,223,1650	110.0	101.0	104.0		3339	4.1	1.0	13	dbSNP_119	104	2196,6046		292,1612,2217	no	coding-synonymous	DIAPH3	NM_001042517.1		301,1835,3867	TT,TC,CC		26.644,6.4028,20.2982		1113/1194	60240961	2437,9569	1882	4121	6003	SO:0001819	synonymous_variant	81624	exon28			TTCTGTCAACTGC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3339G>A	13.37:g.60240961C>T		Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	230	230	1	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																			C|0.820;T|0.180	0.180	strong		0.368	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
TMEM171	134285	hgsc.bcm.edu	37	5	72419287	72419287	+	Silent	SNP	C	C	T	rs35987724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:72419287C>T	ENST00000454765.2	+	2	560	c.87C>T	c.(85-87)ggC>ggT	p.G29G	TMEM171_ENST00000287773.5_Silent_p.G29G			Q8WVE6	TM171_HUMAN	transmembrane protein 171	29						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)		TTGTCTTCGGCGCCGTCTTGT	0.582													C|||	75	0.014976	0.0045	0.0216	5008	,	,		17833	0.001		0.0408	False		,,,				2504	0.0123				p.G29G	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.C87T						PASS	.	C	,	34,4372	38.4+/-70.7	0,34,2169	125.0	118.0	120.0		87,87	-10.2	0.1	5	dbSNP_126	120	372,8228	122.7+/-181.7	6,360,3934	no	coding-synonymous,coding-synonymous	TMEM171	NM_001161342.1,NM_173490.6	,	6,394,6103	TT,TC,CC		4.3256,0.7717,3.1216	,	29/324,29/325	72419287	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	134285	exon2			CTTCGGCGCCGTC	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.87C>T	5.37:g.72419287C>T		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	271	145	0.535055	NM_173490	Q8N0S1|Q8TDT7	Silent	SNP	ENST00000454765.2	37	CCDS4017.1																																																																																			C|0.972;T|0.028	0.028	strong		0.582	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
ADCY9	115	hgsc.bcm.edu	37	16	4164364	4164364	+	Silent	SNP	C	C	T	rs2230738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4164364C>T	ENST00000294016.3	-	2	1618	c.1080G>A	c.(1078-1080)agG>agA	p.R360R		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	360					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)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGGTGGCATGCCTCTTGACAG	0.468													C|||	1624	0.324281	0.0234	0.3199	5008	,	,		20673	0.6111		0.2575	False		,,,				2504	0.5072				p.R360R		Atlas-SNP	.											.	ADCY9	151	.	0			c.G1080A						PASS	.	C		236,4158	138.8+/-174.5	11,214,1972	168.0	158.0	162.0		1080	3.0	1.0	16	dbSNP_98	162	2198,6402	374.2+/-337.3	285,1628,2387	no	coding-synonymous	ADCY9	NM_001116.3		296,1842,4359	TT,TC,CC		25.5581,5.371,18.7317		360/1354	4164364	2434,10560	2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			GGCATGCCTCTTG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1080G>A	16.37:g.4164364C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			C|0.761;T|0.239	0.239	strong		0.468	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
CELSR1	9620	hgsc.bcm.edu	37	22	46785301	46785301	+	Silent	SNP	C	C	T	rs11090875	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46785301C>T	ENST00000262738.3	-	18	6440	c.6441G>A	c.(6439-6441)acG>acA	p.T2147T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2147					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)		TGCCAAAGAGCGTGCCCGTGT	0.662													C|||	359	0.0716853	0.1399	0.0476	5008	,	,		15237	0.0		0.0954	False		,,,				2504	0.046				p.T2147T		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	1	0			c.G6441A						PASS	.	C		513,3893	228.8+/-243.5	24,465,1714	48.0	41.0	43.0		6441	0.2	0.1	22	dbSNP_120	43	749,7851	177.5+/-227.1	26,697,3577	no	coding-synonymous	CELSR1	NM_014246.1		50,1162,5291	TT,TC,CC		8.7093,11.6432,9.7032		2147/3015	46785301	1262,11744	2203	4300	6503	SO:0001819	synonymous_variant	9620	exon18			AAAGAGCGTGCCC	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.6441G>A	22.37:g.46785301C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	76	0.603175	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.908;T|0.092	0.092	strong		0.662	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
MS4A10	341116	hgsc.bcm.edu	37	11	60565921	60565921	+	Missense_Mutation	SNP	C	C	T	rs12419635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60565921C>T	ENST00000308287.1	+	7	752	c.656C>T	c.(655-657)cCg>cTg	p.P219L		NM_206893.3	NP_996776.2	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member 10	219			P -> L (in dbSNP:rs12419635).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|skin(2)	21						AAAGGCCTGCCGGTGGAGCCC	0.567													C|||	286	0.0571086	0.0666	0.0548	5008	,	,		18992	0.001		0.0964	False		,,,				2504	0.0634				p.P219L		Atlas-SNP	.											.	MS4A10	38	.	0			c.C656T						PASS	.	C	LEU/PRO	236,4170	136.9+/-172.8	9,218,1976	99.0	92.0	95.0		656	0.9	0.0	11	dbSNP_120	95	829,7769	191.7+/-237.8	42,745,3512	yes	missense	MS4A10	NM_206893.3	98	51,963,5488	TT,TC,CC		9.6418,5.3563,8.1898	possibly-damaging	219/268	60565921	1065,11939	2203	4299	6502	SO:0001583	missense	341116	exon7			GCCTGCCGGTGGA	AK122633	CCDS7992.1	11q12.2	2008-02-05				ENSG00000172689			13368	protein-coding gene	gene with protein product		608403				11486273, 11401424	Standard	NM_206893		Approved	CD20L7, MS4A9	uc001npz.1	Q96PG2		ENST00000308287.1:c.656C>T	11.37:g.60565921C>T	ENSP00000311862:p.Pro219Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_206893	B2RP45|Q96PG3	Missense_Mutation	SNP	ENST00000308287.1	37	CCDS7992.1	115	0.052655677655677656	26	0.052845528455284556	23	0.06353591160220995	1	0.0017482517482517483	65	0.08575197889182058	C	8.476	0.858621	0.17178	0.053563	0.096418	ENSG00000172689	ENST00000308287	T	0.24350	1.86	2.88	0.925	0.19424	.	.	.	.	.	T	0.00356	0.0011	N	0.19112	0.55	0.80722	P	0.0	B	0.19331	0.035	B	0.09377	0.004	T	0.15350	-1.0440	8	0.56958	D	0.05	-0.5622	4.3628	0.11210	0.0:0.6326:0.2315:0.1359	rs12419635;rs12419635	219	Q96PG2	M4A10_HUMAN	L	219	ENSP00000311862:P219L	ENSP00000311862:P219L	P	+	2	0	MS4A10	60322497	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.094000	0.11094	0.260000	0.21731	0.467000	0.42956	CCG	C|0.926;T|0.074	0.074	strong		0.567	MS4A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395619.1	NM_206893	
OR8B4	283162	hgsc.bcm.edu	37	11	124294213	124294213	+	Missense_Mutation	SNP	C	C	A	rs61736181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124294213C>A	ENST00000356130.3	-	1	576	c.555G>T	c.(553-555)caG>caT	p.Q185H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	185						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(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		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;0.0279)		TGCAGGAGAGCTGCAAGAGGG	0.502													C|||	41	0.0081869	0.0023	0.013	5008	,	,		22316	0.0		0.0249	False		,,,				2504	0.0041				p.Q185H		Atlas-SNP	.											.	OR8B4	60	.	0			c.G555T						PASS	.	C	HIS/GLN	23,4379	29.9+/-59.1	0,23,2178	82.0	58.0	66.0		555	3.1	1.0	11	dbSNP_129	66	220,8378	92.3+/-154.4	3,214,4082	yes	missense	OR8B4	NM_001005196.1	24	3,237,6260	AA,AC,CC		2.5587,0.5225,1.8692	possibly-damaging	185/310	124294213	243,12757	2201	4299	6500	SO:0001583	missense	283162	exon1			GGAGAGCTGCAAG	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.555G>T	11.37:g.124294213C>A	ENSP00000348449:p.Gln185His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	28	0.01282051282051282	3	0.006097560975609756	6	0.016574585635359115	0	0.0	19	0.025065963060686015	c	14.77	2.635013	0.47049	0.005225	0.025587	ENSG00000198657	ENST00000356130	T	0.00137	8.68	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.495221	0.17506	N	0.171789	T	0.00109	0.0003	L	0.43757	1.38	0.32996	D	0.525657	D	0.57899	0.981	D	0.64877	0.93	T	0.68322	-0.5439	10	0.87932	D	0	.	6.7728	0.23602	0.0:0.6864:0.0:0.3136	.	185	Q96RC9	OR8B4_HUMAN	H	185	ENSP00000348449:Q185H	ENSP00000348449:Q185H	Q	-	3	2	OR8B4	123799423	0.000000	0.05858	0.994000	0.49952	0.955000	0.61496	-1.016000	0.03633	1.219000	0.43474	0.650000	0.86243	CAG	C|0.982;A|0.018	0.018	strong		0.502	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
RAB36	9609	hgsc.bcm.edu	37	22	23503170	23503170	+	Missense_Mutation	SNP	A	A	G	rs5759612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23503170A>G	ENST00000263116.2	+	10	962	c.922A>G	c.(922-924)Aat>Gat	p.N308D	RAB36_ENST00000341989.4_Missense_Mutation_p.N286D	NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	308			N -> D (in dbSNP:rs5759612). {ECO:0000269|PubMed:9920784}.		protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		CCAGGTCGGCAATGGAGACCT	0.607													G|||	2781	0.555312	0.5265	0.4654	5008	,	,		21125	0.6448		0.5119	False		,,,				2504	0.6104				p.N308D		Atlas-SNP	.											.	RAB36	26	.	0			c.A922G						PASS	.	G	ASP/ASN	2404,2002	559.6+/-380.3	661,1082,460	85.0	69.0	74.0		922	3.6	1.0	22	dbSNP_114	74	4288,4312	578.0+/-390.6	1088,2112,1100	yes	missense	RAB36	NM_004914.2	23	1749,3194,1560	GG,GA,AA		49.8605,45.438,48.5468	benign	308/334	23503170	6692,6314	2203	4300	6503	SO:0001583	missense	9609	exon10			GTCGGCAATGGAG	AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228		"""RAB, member RAS oncogene"""	9775	protein-coding gene	gene with protein product		605662				9920784, 10591208	Standard	NM_004914		Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.922A>G	22.37:g.23503170A>G	ENSP00000263116:p.Asn308Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_004914	Q2M390|Q7Z4A9|Q9UHP5	Missense_Mutation	SNP	ENST00000263116.2	37	CCDS13805.1	1182	0.5412087912087912	261	0.5304878048780488	179	0.494475138121547	359	0.6276223776223776	383	0.5052770448548812	G	1.563	-0.536108	0.04082	0.54562	0.498605	ENSG00000100228	ENST00000263116;ENST00000341989	T;T	0.63096	-0.02;0.38	5.67	3.59	0.41128	.	0.419531	0.24851	N	0.035086	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	0.47548	-0.9109	9	0.02654	T	1	-13.2367	9.9112	0.41406	0.2244:0.0:0.7756:0.0	rs5759612;rs58963192;rs5759612	286;308	O95755-2;O95755	.;RAB36_HUMAN	D	308;286	ENSP00000263116:N308D;ENSP00000343494:N286D	ENSP00000263116:N308D	N	+	1	0	RAB36	21833170	0.332000	0.24722	0.980000	0.43619	0.283000	0.27025	0.812000	0.27211	0.457000	0.26962	-0.119000	0.15052	AAT	A|0.466;G|0.534	0.534	strong		0.607	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319046.1	NM_004914	
APOBEC4	403314	hgsc.bcm.edu	37	1	183616926	183616926	+	Missense_Mutation	SNP	T	T	C	rs1174657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:183616926T>C	ENST00000308641.4	-	2	1262	c.991A>G	c.(991-993)Aag>Gag	p.K331E	APOBEC4_ENST00000481562.1_5'UTR|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)	331			K -> E (in dbSNP:rs1174657). {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						CCAAGGTCCTTGGTTTCCTGG	0.443													C|||	1854	0.370208	0.4932	0.3473	5008	,	,		21494	0.244		0.4006	False		,,,				2504	0.319				p.K331E		Atlas-SNP	.											.	APOBEC4	45	.	0			c.A991G						PASS	.	C	,GLU/LYS	2068,2338	606.6+/-390.8	487,1094,622	151.0	146.0	148.0		,991	-0.5	0.0	1	dbSNP_87	148	3401,5199	640.6+/-399.6	679,2043,1578	yes	intron,missense	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,56	1166,3137,2200	CC,CT,TT		39.5465,46.936,42.0498	,benign	,331/368	183616926	5469,7537	2203	4300	6503	SO:0001583	missense	403314	exon2			GGTCCTTGGTTTC	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.991A>G	1.37:g.183616926T>C	ENSP00000310622:p.Lys331Glu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	224	223	0.995536	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	C	0.043	-1.278574	0.01410	0.46936	0.395465	ENSG00000173627	ENST00000308641	T	0.13420	2.59	5.15	-0.467	0.12150	.	0.863067	0.09808	N	0.753250	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	0.46062	-0.9218	9	0.07175	T	0.84	-23.8613	6.984	0.24718	0.0:0.2167:0.117:0.6663	rs1174657;rs17489759;rs52808143;rs59101056;rs1174657	331	Q8WW27	ABEC4_HUMAN	E	331	ENSP00000310622:K331E	ENSP00000310622:K331E	K	-	1	0	APOBEC4	181883549	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.073000	0.14640	-0.238000	0.09724	-2.030000	0.00424	AAG	T|0.608;C|0.392	0.392	strong		0.443	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
PTPRQ	374462	hgsc.bcm.edu	37	12	80936082	80936082	+	Silent	SNP	C	C	T	rs11114503	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	94	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	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	
DNAH10	196385	hgsc.bcm.edu	37	12	124330311	124330311	+	Missense_Mutation	SNP	C	C	T	rs34934281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124330311C>T	ENST00000409039.3	+	30	5196	c.5171C>T	c.(5170-5172)aCg>aTg	p.T1724M		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1724	Stem. {ECO:0000250}.		T -> M (in dbSNP:rs34934281).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAGTTGGTAACGCGCATCACC	0.463													c|||	255	0.0509185	0.0091	0.0865	5008	,	,		19892	0.001		0.1322	False		,,,				2504	0.0501				p.T1724M		Atlas-SNP	.											.	DNAH10	888	.	0			c.C5171T						PASS	.	T	MET/THR	97,4027		1,95,1966	111.0	120.0	117.0		5171	4.9	0.5	12	dbSNP_126	117	982,7410		54,874,3268	yes	missense	DNAH10	NM_207437.3	81	55,969,5234	TT,TC,CC		11.7016,2.3521,8.621	possibly-damaging	1724/4472	124330311	1079,11437	2062	4196	6258	SO:0001583	missense	196385	exon30			TGGTAACGCGCAT	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.5171C>T	12.37:g.124330311C>T	ENSP00000386770:p.Thr1724Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	131	0.059981684981684984	6	0.012195121951219513	34	0.09392265193370165	1	0.0017482517482517483	90	0.11873350923482849	c	8.486	0.860907	0.17178	0.023521	0.117016	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.77	4.89	0.63831	.	0.164918	0.39020	U	0.001488	T	0.00440	0.0014	M	0.79926	2.475	0.28587	P	0.9098119	P	0.34909	0.475	B	0.26416	0.069	T	0.08106	-1.0738	9	0.51188	T	0.08	.	15.0778	0.72090	0.0:0.9323:0.0:0.0677	rs34934281	1724	Q8IVF4	DYH10_HUMAN	M	1724	ENSP00000386770:T1724M	ENSP00000386770:T1724M	T	+	2	0	DNAH10	122896264	0.947000	0.32204	0.462000	0.27118	0.042000	0.13812	2.540000	0.45727	1.459000	0.47892	-0.215000	0.12644	ACG	C|0.933;T|0.067	0.067	strong		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:2092803A>G	ENST00000262113.4	+	37	4437	c.4296A>G	c.(4294-4296)acA>acG	p.T1432T	MYOM2_ENST00000520298.1_3'UTR|MYOM2_ENST00000523438.1_Silent_p.T857T	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1432	Ig-like C2-type 5.				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)		TCGACGTGACAGTGAGCGTGT	0.587													G|||	1206	0.240815	0.2481	0.2435	5008	,	,		13751	0.2292		0.2883	False		,,,				2504	0.1922				p.T1432T		Atlas-SNP	.											.	MYOM2	251	.	0			c.A4296G						PASS	.	G		1137,3269	716.8+/-408.6	130,877,1196	108.0	92.0	98.0		4296	-9.3	0.1	8	dbSNP_86	98	2274,6326	707.3+/-405.6	301,1672,2327	no	coding-synonymous	MYOM2	NM_003970.2		431,2549,3523	GG,GA,AA		26.4419,25.8057,26.2264		1432/1466	2092803	3411,9595	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon37			CGTGACAGTGAGC		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.4296A>G	8.37:g.2092803A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			A|0.741;G|0.259	0.259	strong		0.587	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
NUTM1	256646	hgsc.bcm.edu	37	15	34649631	34649631	+	Missense_Mutation	SNP	G	G	A	rs2279685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:34649631G>A	ENST00000333756.4	+	7	3493	c.3338G>A	c.(3337-3339)cGt>cAt	p.R1113H	NUTM1_ENST00000438749.3_Missense_Mutation_p.R1131H|NUTM1_ENST00000537011.1_Missense_Mutation_p.R1141H	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1113			R -> H (in dbSNP:rs2279685).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCACAGCCTCGTAAAAGGCGG	0.582													G|||	610	0.121805	0.0091	0.2277	5008	,	,		18445	0.2907		0.0586	False		,,,				2504	0.09				p.R1113H		Atlas-SNP	.											.	C15orf55	110	.	0			c.G3338A						PASS	.	G	HIS/ARG	94,4308	75.7+/-113.9	0,94,2107	67.0	69.0	69.0		3338	4.2	0.3	15	dbSNP_100	69	632,7964	161.9+/-214.7	17,598,3683	yes	missense	C15orf55	NM_175741.1	29	17,692,5790	AA,AG,GG		7.3523,2.1354,5.5855	probably-damaging	1113/1133	34649631	726,12272	2201	4298	6499	SO:0001583	missense	256646	exon7			AGCCTCGTAAAAG	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3338G>A	15.37:g.34649631G>A	ENSP00000329448:p.Arg1113His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	296	0.13553113553113552	7	0.014227642276422764	78	0.2154696132596685	169	0.29545454545454547	42	0.055408970976253295	G	15.29	2.791151	0.50102	0.021354	0.073523	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.47177	0.85;0.85;0.85	6.08	4.22	0.49857	.	0.515823	0.18218	N	0.147984	T	0.00012	0.0000	M	0.70595	2.14	0.42195	P	0.008257999999999988	B;B;D	0.89917	0.159;0.247;1.0	B;B;P	0.62885	0.037;0.082;0.908	T	0.08973	-1.0696	9	0.72032	D	0.01	.	9.1913	0.37200	0.1643:0.0:0.8357:0.0	rs2279685;rs57129363;rs2279685	1131;1141;1113	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	H	1141;1131;1113	ENSP00000444896:R1141H;ENSP00000407031:R1131H;ENSP00000329448:R1113H	ENSP00000329448:R1113H	R	+	2	0	C15orf55	32436923	0.999000	0.42202	0.301000	0.25044	0.855000	0.48748	2.130000	0.42064	0.921000	0.36994	0.655000	0.94253	CGT	G|0.915;A|0.085	0.085	strong		0.582	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
NEDD9	4739	hgsc.bcm.edu	37	6	11190215	11190215	+	Silent	SNP	G	G	A	rs35719173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:11190215G>A	ENST00000379446.5	-	5	2053	c.1887C>T	c.(1885-1887)taC>taT	p.Y629Y	NEDD9_ENST00000504387.1_Silent_p.Y629Y|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	629					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)				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)			GGACGTAATCGTAGTCATCCA	0.542													G|||	41	0.0081869	0.0045	0.0058	5008	,	,		21782	0.0		0.0139	False		,,,				2504	0.0174				p.Y629Y		Atlas-SNP	.											.	NEDD9	191	.	0			c.C1887T						PASS	.	G	,	15,4391	23.3+/-48.9	0,15,2188	130.0	122.0	124.0		1887,1887	2.1	1.0	6	dbSNP_126	124	185,8415	82.6+/-145.2	1,183,4116	no	coding-synonymous,coding-synonymous	NEDD9	NM_001142393.1,NM_006403.3	,	1,198,6304	AA,AG,GG		2.1512,0.3404,1.5378	,	629/835,629/835	11190215	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	4739	exon6			GTAATCGTAGTCA	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.1887C>T	6.37:g.11190215G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	CCDS4520.1																																																																																			G|0.986;A|0.014	0.014	strong		0.542	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
KLHL30	377007	hgsc.bcm.edu	37	2	239049928	239049928	+	Missense_Mutation	SNP	G	G	A	rs112962843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239049928G>A	ENST00000409223.1	+	2	640	c.533G>A	c.(532-534)cGg>cAg	p.R178Q	KLHL30_ENST00000305959.4_Missense_Mutation_p.R160Q			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	178	BACK.			R -> Q (in Ref. 4; AAI05697). {ECO:0000305}.						lung(4)	4		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)		CCCCGAGAGCGGCTGGTCACT	0.677													g|||	165	0.0329473	0.003	0.0576	5008	,	,		17702	0.0605		0.0437	False		,,,				2504	0.0164				p.R178Q		Atlas-SNP	.											.	KLHL30	79	.	0			c.G533A						PASS	.		GLN/ARG	50,4118		2,46,2036	15.0	18.0	17.0		533	5.8	1.0	2	dbSNP_132	17	339,8075		10,319,3878	yes	missense	KLHL30	NM_198582.3	43	12,365,5914	AA,AG,GG		4.029,1.1996,3.0917	possibly-damaging	178/579	239049928	389,12193	2084	4207	6291	SO:0001583	missense	377007	exon2			GAGAGCGGCTGGT		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.533G>A	2.37:g.239049928G>A	ENSP00000386389:p.Arg178Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	89	0.04075091575091575	4	0.008130081300813009	22	0.06077348066298342	26	0.045454545454545456	37	0.048812664907651716	G	26.3	4.728791	0.89390	0.011996	0.04029	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.66995	-0.24;-0.24	5.82	5.82	0.92795	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.20455	0.0492	N	0.16368	0.405	0.48135	D	0.999593	D	0.89917	1.0	D	0.97110	1.0	T	0.49916	-0.8888	10	0.02654	T	1	.	18.862	0.92276	0.0:0.0:1.0:0.0	.	178	Q0D2K2	KLH30_HUMAN	Q	178;160	ENSP00000386389:R178Q;ENSP00000302386:R160Q	ENSP00000302386:R160Q	R	+	2	0	KLHL30	238714667	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.496000	0.66918	2.753000	0.94483	0.651000	0.88453	CGG	G|0.959;A|0.041	0.041	strong		0.677	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
ITGAE	3682	hgsc.bcm.edu	37	17	3654980	3654980	+	Silent	SNP	A	A	G	rs11652878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3654980A>G	ENST00000263087.4	-	15	1955	c.1857T>C	c.(1855-1857)aaT>aaC	p.N619N		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	619					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CCCAGTGTCCATTGTAGATAT	0.592													G|||	708	0.141374	0.1694	0.0908	5008	,	,		14885	0.1687		0.1093	False		,,,				2504	0.1442				p.N619N	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.T1857C						PASS	.	G		705,3701	760.6+/-413.0	61,583,1559	71.0	77.0	75.0		1857	-7.1	0.4	17	dbSNP_120	75	847,7753	780.3+/-407.7	35,777,3488	no	coding-synonymous	ITGAE	NM_002208.4		96,1360,5047	GG,GA,AA		9.8488,16.0009,11.933		619/1180	3654980	1552,11454	2203	4300	6503	SO:0001819	synonymous_variant	3682	exon15			GTGTCCATTGTAG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.1857T>C	17.37:g.3654980A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_002208	Q17RS6|Q9NZU9	Silent	SNP	ENST00000263087.4	37	CCDS32531.1																																																																																			A|0.864;G|0.136	0.136	strong		0.592	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
DSCAM	1826	hgsc.bcm.edu	37	21	41725625	41725625	+	Missense_Mutation	SNP	C	C	T	rs41395652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:41725625C>T	ENST00000400454.1	-	5	1178	c.701G>A	c.(700-702)cGc>cAc	p.R234H		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	234	Ig-like C2-type 3.				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)				CATGGCTTTGCGATGGTCAAA	0.537													C|||	57	0.0113818	0.0008	0.0216	5008	,	,		17831	0.0		0.0388	False		,,,				2504	0.002				p.R234H	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G701A						PASS	.	C	HIS/ARG	40,3756		0,40,1858	25.0	25.0	25.0		701	3.5	1.0	21	dbSNP_127	25	362,7904		6,350,3777	yes	missense	DSCAM	NM_001389.3	29	6,390,5635	TT,TC,CC		4.3794,1.0537,3.3328	benign	234/2013	41725625	402,11660	1898	4133	6031	SO:0001583	missense	1826	exon5			GCTTTGCGATGGT	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.701G>A	21.37:g.41725625C>T	ENSP00000383303:p.Arg234His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	35	0.016025641025641024	0	0.0	8	0.022099447513812154	0	0.0	27	0.03562005277044855	C	15.30	2.791214	0.50102	0.010537	0.043794	ENSG00000171587	ENST00000400454	T	0.66995	-0.24	5.31	3.5	0.40072	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.057726	0.64402	N	0.000001	T	0.19406	0.0466	L	0.34521	1.04	0.42295	D	0.992155	B	0.29766	0.256	B	0.22753	0.041	T	0.18335	-1.0340	10	0.40728	T	0.16	.	9.1538	0.36980	0.0:0.7766:0.0:0.2234	rs41395652	234	O60469	DSCAM_HUMAN	H	234	ENSP00000383303:R234H	ENSP00000383303:R234H	R	-	2	0	DSCAM	40647495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.992000	0.49417	0.727000	0.32360	0.650000	0.86243	CGC	C|0.978;T|0.022	0.022	strong		0.537	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
KIF26A	26153	hgsc.bcm.edu	37	14	104640098	104640098	+	Silent	SNP	G	G	A	rs61745565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17.0	24.0	22.0		1923	-2.2	0.0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	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.1923G>A	14.37:g.104640098G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
C10orf53	282966	hgsc.bcm.edu	37	10	50901938	50901938	+	Splice_Site	SNP	C	C	T	rs1133837	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50901938C>T	ENST00000374111.3	+	2	228	c.216C>T	c.(214-216)ttC>ttT	p.F72F	C10orf53_ENST00000374112.3_Splice_Site_p.F72F|C10orf53_ENST00000374113.3_Silent_p.F72F|C10orf53_ENST00000535836.1_Splice_Site_p.F72F	NM_001042427.1	NP_001035892.1	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53	72										endometrium(1)|lung(6)	7		all_neural(218;0.107)				ACTTGGAGTTCGGTAAGCCCT	0.453													C|||	1768	0.353035	0.3707	0.3732	5008	,	,		23180	0.1389		0.4761	False		,,,				2504	0.409				p.F72F		Atlas-SNP	.											.	C10orf53	19	.	0			c.C216T						PASS	.	C	,	1676,2730	508.9+/-367.1	324,1028,851	169.0	155.0	160.0		216,216	-1.3	1.0	10	dbSNP_86	160	4053,4547	559.2+/-387.4	939,2175,1186	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	C10orf53	NM_001042427.1,NM_182554.2	,	1263,3203,2037	TT,TC,CC		47.1279,38.039,44.0489	,	72/94,72/158	50901938	5729,7277	2203	4300	6503	SO:0001630	splice_region_variant	282966	exon2			GGAGTTCGGTAAG	BC028127	CCDS31202.1, CCDS41521.1	10q11.23	2012-05-24			ENSG00000178645	ENSG00000178645			27421	protein-coding gene	gene with protein product						12477932	Standard	NM_182554		Approved	Em:AC069546.1	uc001jid.1	Q8N6V4	OTTHUMG00000018199	ENST00000374111.3:c.217+1C>T	10.37:g.50901938C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_182554	A6NI81|A6NLE0|B9ZVK6	Silent	SNP	ENST00000374111.3	37	CCDS41521.1																																																																																			C|0.595;T|0.405	0.405	strong		0.453	C10orf53-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048005.1	NM_182554	Silent
ELK4	2005	hgsc.bcm.edu	37	1	205589574	205589574	+	Silent	SNP	C	C	T	rs1064406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:205589574C>T	ENST00000357992.4	-	3	939	c.600G>A	c.(598-600)ccG>ccA	p.P200P	ELK4_ENST00000468523.1_5'Flank|ELK4_ENST00000289703.4_Silent_p.P200P	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)	200					cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|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 cofactor activity (GO:0003712)		SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CAGGTTCAACCGGTGGCTTTT	0.463			T	SLC45A3	prostate								C|||	981	0.195887	0.146	0.1153	5008	,	,		19202	0.37		0.0706	False		,,,				2504	0.2699				p.P200P		Atlas-SNP	.		Dom	yes		1	1q32	2005	"""ELK4, ETS-domain protein (SRF accessory protein 1)"""		E	.	ELK4	45	.	0			c.G600A						PASS	.	C	,	574,3832	257.0+/-261.6	45,484,1674	73.0	75.0	75.0		600,600	-5.2	0.0	1	dbSNP_86	75	780,7820	184.2+/-232.2	37,706,3557	no	coding-synonymous,coding-synonymous	ELK4	NM_001973.3,NM_021795.2	,	82,1190,5231	TT,TC,CC		9.0698,13.0277,10.4106	,	200/432,200/406	205589574	1354,11652	2203	4300	6503	SO:0001819	synonymous_variant	2005	exon3			TTCAACCGGTGGC	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.600G>A	1.37:g.205589574C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	187	115	0.614973	NM_021795	P28323|Q6GSJ2	Silent	SNP	ENST00000357992.4	37	CCDS1456.1																																																																																			C|0.873;T|0.127	0.127	strong		0.463	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795	
WNT7A	7476	hgsc.bcm.edu	37	3	13896140	13896140	+	Silent	SNP	A	A	G	rs3762719	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13896140A>G	ENST00000285018.4	-	3	763	c.459T>C	c.(457-459)tcT>tcC	p.S153S		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	153					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						GGATGTCGGCAGAGCAGCCAC	0.607													A|||	1256	0.250799	0.1293	0.2061	5008	,	,		18627	0.5813		0.17	False		,,,				2504	0.1892				p.S153S		Atlas-SNP	.											.	WNT7A	70	.	0			c.T459C						PASS	.	A		775,3631	311.1+/-291.9	70,635,1498	113.0	110.0	111.0		459	-9.5	0.9	3	dbSNP_107	111	1567,7033	293.0+/-301.1	135,1297,2868	no	coding-synonymous	WNT7A	NM_004625.3		205,1932,4366	GG,GA,AA		18.2209,17.5897,18.0071		153/350	13896140	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	7476	exon3			GTCGGCAGAGCAG	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.459T>C	3.37:g.13896140A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	37	CCDS2616.1																																																																																			A|0.795;G|0.205	0.205	strong		0.607	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
MYOG	4656	hgsc.bcm.edu	37	1	203054651	203054651	+	Missense_Mutation	SNP	G	G	A	rs61745017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:203054651G>A	ENST00000241651.4	-	1	513	c.439C>T	c.(439-441)Cgc>Tgc	p.R147C		NM_002479.5	NP_002470.2	P15173	MYOG_HUMAN	myogenin (myogenic factor 4)	147					cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lithium ion (GO:0071285)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|negative regulation of cell proliferation (GO:0008285)|ossification (GO:0001503)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of muscle atrophy (GO:0014737)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myoblast fusion (GO:1901739)|regulation of satellite cell proliferation (GO:0014842)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|skeletal muscle fiber development (GO:0048741)|skeletal muscle tissue development (GO:0007519)|striated muscle atrophy (GO:0014891)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|E-box binding (GO:0070888)|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)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|urinary_tract(1)	12						CCCCGGTAGCGGAGGTCACGC	0.701													G|||	60	0.0119808	0.003	0.0202	5008	,	,		15296	0.0		0.0378	False		,,,				2504	0.0041				p.R147C		Atlas-SNP	.											.	MYOG	28	.	0			c.C439T						PASS	.	G	CYS/ARG	32,4374	35.2+/-66.4	0,32,2171	23.0	26.0	25.0		439	4.4	1.0	1	dbSNP_129	25	268,8332	99.9+/-161.4	5,258,4037	yes	missense	MYOG	NM_002479.4	180	5,290,6208	AA,AG,GG		3.1163,0.7263,2.3066	probably-damaging	147/225	203054651	300,12706	2203	4300	6503	SO:0001583	missense	4656	exon1			GGTAGCGGAGGTC	BC053899	CCDS1433.1	1q31-q41	2013-05-21			ENSG00000122180	ENSG00000122180		"""Basic helix-loop-helix proteins"""	7612	protein-coding gene	gene with protein product		159980		MYF4		10329008	Standard	NM_002479		Approved	bHLHc3	uc001gzd.4	P15173	OTTHUMG00000042127	ENST00000241651.4:c.439C>T	1.37:g.203054651G>A	ENSP00000241651:p.Arg147Cys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	138	82	0.594203	NM_002479	Q53XW6	Missense_Mutation	SNP	ENST00000241651.4	37	CCDS1433.1	42	0.019230769230769232	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	31	0.040897097625329816	G	18.45	3.626906	0.66901	0.007263	0.031163	ENSG00000122180	ENST00000241651	D	0.98585	-5.01	5.32	4.36	0.52297	Helix-loop-helix DNA-binding (1);	0.215520	0.47852	D	0.000208	D	0.87688	0.6240	L	0.46157	1.445	0.45567	D	0.998512	D	0.58620	0.983	B	0.38296	0.27	D	0.89363	0.3669	10	0.62326	D	0.03	-7.4351	15.9767	0.80071	0.0:0.1461:0.8539:0.0	.	147	P15173	MYOG_HUMAN	C	147	ENSP00000241651:R147C	ENSP00000241651:R147C	R	-	1	0	MYOG	201321274	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	5.946000	0.70234	2.486000	0.83907	0.563000	0.77884	CGC	G|0.979;A|0.021	0.021	strong		0.701	MYOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100279.1	NM_002479	
SLC22A12	116085	hgsc.bcm.edu	37	11	64360274	64360274	+	Silent	SNP	T	T	C	rs11231825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64360274T>C	ENST00000377574.1	+	2	1173	c.426T>C	c.(424-426)caT>caC	p.H142H	SLC22A12_ENST00000377567.2_Silent_p.H142H|SLC22A12_ENST00000336464.7_Silent_p.H142H|SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377572.1_Silent_p.H142H	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	142					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	GTGACTCTCATGCTCTGAAGC	0.632													T|||	1933	0.385982	0.0953	0.4323	5008	,	,		18361	0.2212		0.7058	False		,,,				2504	0.5869				p.H142H		Atlas-SNP	.											.	SLC22A12	68	.	0			c.T426C	GRCh37	CM063145	SLC22A12	M	rs11231825	PASS	.	T	,	872,3530	339.1+/-305.6	88,696,1417	161.0	134.0	143.0		426,	0.5	0.0	11	dbSNP_120	143	6096,2498	694.6+/-404.7	2167,1762,368	no	coding-synonymous,utr-5	SLC22A12	NM_144585.2,NM_153378.1	,	2255,2458,1785	CC,CT,TT		29.0668,19.8092,46.3835	,	142/554,	64360274	6968,6028	2201	4297	6498	SO:0001819	synonymous_variant	116085	exon2			CTCTCATGCTCTG	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"""Solute carriers"""	17989	protein-coding gene	gene with protein product		607096	"""solute carrier family 22 (organic anion/cation transporter), member 12"""			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.426T>C	11.37:g.64360274T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	37	CCDS8075.1																																																																																			T|0.525;C|0.475	0.475	strong		0.632	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
DRD5	1816	hgsc.bcm.edu	37	4	9783905	9783905	+	Silent	SNP	C	C	T	rs2227848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:9783905C>T	ENST00000304374.2	+	1	648	c.252C>T	c.(250-252)gcC>gcT	p.A84A		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	84					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	TGTCTCTGGCCGTGTCAGACC	0.642																																					p.A84A		Atlas-SNP	.											DRD5,colon,carcinoma,+1,1	DRD5	119	1	0			c.C252T						scavenged	.						54.0	47.0	49.0					4																	9783905		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			TCTGGCCGTGTCA	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.252C>T	4.37:g.9783905C>T		Somatic	131	5	0.0381679		WXS	Illumina HiSeq	Phase_I	146	11	0.0753425	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			C|0.963;T|0.037	0.037	strong		0.642	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
CHRD	8646	hgsc.bcm.edu	37	3	184106493	184106493	+	Silent	SNP	T	T	G	rs2293606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184106493T>G	ENST00000204604.1	+	21	2919	c.2673T>G	c.(2671-2673)ccT>ccG	p.P891P	CHRD_ENST00000450923.1_Silent_p.P891P|CHRD_ENST00000348986.3_Silent_p.P851P|CHRD_ENST00000545352.1_Silent_p.P433P|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	891	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	p.P891P(1)		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)			CAGTGCCCCCTTTTGGAGAGA	0.632													T|||	559	0.111621	0.1641	0.134	5008	,	,		18024	0.1062		0.0596	False		,,,				2504	0.0838				p.P891P		Atlas-SNP	.											CHRD,NS,carcinoma,0,1	CHRD	149	1	1	Substitution - coding silent(1)	breast(1)	c.T2673G						PASS	.	T		659,3747	279.9+/-275.1	56,547,1600	77.0	79.0	78.0		2673	1.1	1.0	3	dbSNP_100	78	450,8150	135.6+/-192.8	12,426,3862	no	coding-synonymous	CHRD	NM_003741.2		68,973,5462	GG,GT,TT		5.2326,14.9569,8.5268		891/956	184106493	1109,11897	2203	4300	6503	SO:0001819	synonymous_variant	8646	exon21			GCCCCCTTTTGGA	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.2673T>G	3.37:g.184106493T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	61	0.592233	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			T|0.904;G|0.096	0.096	strong		0.632	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
MAML2	84441	hgsc.bcm.edu	37	11	95825362	95825362	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:95825362C>T	ENST00000524717.1	-	2	3117	c.1833G>A	c.(1831-1833)caG>caA	p.Q611Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	611					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)	p.Q611Q(2)	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)				gctgttgctgctgctgctgct	0.542			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q611Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,NS,carcinoma,0,4	MAML2	94	4	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.G1833A						scavenged	.						39.0	44.0	42.0					11																	95825362		2057	4042	6099	SO:0001819	synonymous_variant	84441	exon2			TTGCTGCTGCTGC	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.1833G>A	11.37:g.95825362C>T		Somatic	106	5	0.0471698		WXS	Illumina HiSeq	Phase_I	79	5	0.0632911	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	none		0.542	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
NAGA	4668	hgsc.bcm.edu	37	22	42463814	42463814	+	Silent	SNP	C	C	T	rs133369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42463814C>T	ENST00000396398.3	-	3	811	c.279G>A	c.(277-279)ccG>ccA	p.P93P	NAGA_ENST00000403363.1_Silent_p.P93P|NAGA_ENST00000402937.1_Silent_p.P93P	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	93					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GCTTGGGATCCGGCATCAGGC	0.612													T|||	3390	0.676917	0.5726	0.6772	5008	,	,		18255	0.8532		0.668	False		,,,				2504	0.6452				p.P93P		Atlas-SNP	.											.	NAGA	26	.	0			c.G279A						PASS	.	T		2633,1773	525.4+/-371.6	765,1103,335	137.0	120.0	126.0		279	-9.3	0.0	22	dbSNP_78	126	5724,2876	452.6+/-363.0	1923,1878,499	no	coding-synonymous	NAGA	NM_000262.2		2688,2981,834	TT,TC,CC		33.4419,40.2406,35.745		93/412	42463814	8357,4649	2203	4300	6503	SO:0001819	synonymous_variant	4668	exon3			GGGATCCGGCATC		CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.279G>A	22.37:g.42463814C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_000262		Silent	SNP	ENST00000396398.3	37	CCDS14030.1																																																																																			C|0.347;T|0.653	0.653	strong		0.612	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1		
ZBED8	63920	hgsc.bcm.edu	37	5	159820931	159820931	+	Missense_Mutation	SNP	C	C	A	rs10515808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:159820931C>A	ENST00000408953.3	-	2	2074	c.1567G>T	c.(1567-1569)Gca>Tca	p.A523S	C5orf54_ENST00000523213.1_Missense_Mutation_p.A523S	NM_022090.3	NP_071373.2														breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						tttggaaatgctgtgaattgg	0.378													C|||	259	0.0517173	0.0242	0.0692	5008	,	,		18533	0.001		0.1143	False		,,,				2504	0.0644				p.A523S		Atlas-SNP	.											C5orf54,NS,carcinoma,+1,1	C5orf54	46	1	0			c.G1567T						PASS	.	C	SER/ALA	176,4230	112.9+/-151.0	1,174,2028	98.0	91.0	93.0		1567	1.0	1.0	5	dbSNP_119	93	881,7719	198.9+/-243.1	45,791,3464	yes	missense	C5orf54	NM_022090.3	99	46,965,5492	AA,AC,CC		10.2442,3.9946,8.127	benign	523/595	159820931	1057,11949	2203	4300	6503	SO:0001583	missense	63920	exon2			GAAATGCTGTGAA																												ENST00000408953.3:c.1567G>T	5.37:g.159820931C>A	ENSP00000386184:p.Ala523Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	133	52	0.390977	NM_022090		Missense_Mutation	SNP	ENST00000408953.3	37	CCDS34283.1	123	0.05631868131868132	12	0.024390243902439025	25	0.06906077348066299	1	0.0017482517482517483	85	0.11213720316622691	C	0.955	-0.705164	0.03255	0.039946	0.102442	ENSG00000221886	ENST00000408953;ENST00000523213	T;T	0.20881	2.04;2.04	2.82	1.03	0.20045	.	.	.	.	.	T	0.00109	0.0003	N	0.01576	-0.805	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40384	-0.9566	8	0.02654	T	1	.	5.1216	0.14863	0.0:0.7156:0.0:0.2844	rs10515808;rs17475306;rs52822306;rs10515808	523	Q8IZ13	CE054_HUMAN	S	523	ENSP00000386184:A523S;ENSP00000428831:A523S	ENSP00000386184:A523S	A	-	1	0	C5orf54	159753509	0.924000	0.31332	0.959000	0.39883	0.725000	0.41563	0.468000	0.22051	0.261000	0.21753	-0.137000	0.14449	GCA	C|0.943;A|0.057	0.057	strong		0.378	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1		
CHL1	10752	hgsc.bcm.edu	37	3	407785	407785	+	Missense_Mutation	SNP	A	A	G	rs143907501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:407785A>G	ENST00000256509.2	+	15	2380	c.1738A>G	c.(1738-1740)Aca>Gca	p.T580A	CHL1-AS1_ENST00000608098.1_RNA|CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.T564A	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					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)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AATTAATGGCACAGAAGATGG	0.363																																					p.T580A		Atlas-SNP	.											.	CHL1	242	.	0			c.A1738G						PASS	.	A	ALA/THR	0,4406		0,0,2203	115.0	111.0	112.0		1738	4.9	0.8	3	dbSNP_134	112	3,8597	3.0+/-9.4	0,3,4297	no	missense	CHL1	NM_006614.2	58	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign	580/1225	407785	3,13003	2203	4300	6503	SO:0001583	missense	10752	exon13			AATGGCACAGAAG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1738A>G	3.37:g.407785A>G	ENSP00000256509:p.Thr580Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	93	60	0.645161	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535747	0.45176	0.0	3.49E-4	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.13778	2.56;2.56	4.94	4.94	0.65067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.056117	0.64402	D	0.000001	T	0.19208	0.0461	L	0.55103	1.725	0.37538	D	0.918193	B;B;B	0.26363	0.003;0.004;0.147	B;B;B	0.35727	0.026;0.016;0.209	T	0.08534	-1.0717	10	0.59425	D	0.04	.	13.1152	0.59295	1.0:0.0:0.0:0.0	.	564;564;580	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	A	580;564	ENSP00000256509:T580A;ENSP00000380628:T564A	ENSP00000256509:T580A	T	+	1	0	CHL1	382785	1.000000	0.71417	0.824000	0.32777	0.973000	0.67179	4.982000	0.63825	1.980000	0.57719	0.460000	0.39030	ACA	A|1.000;G|0.000	0.000	strong		0.363	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
RARA	5914	hgsc.bcm.edu	37	17	38508756	38508756	+	Silent	SNP	C	C	T	rs41283421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38508756C>T	ENST00000254066.5	+	6	1259	c.804C>T	c.(802-804)atC>atT	p.I268I	RARA_ENST00000394081.3_Silent_p.I263I|RARA_ENST00000425707.3_Silent_p.I171I|RARA_ENST00000394086.3_Silent_p.I284I|RARA_ENST00000420042.1_3'UTR|RARA_ENST00000394089.2_Silent_p.I268I	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	268	Ligand-binding.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GCCTGGACATCCTGGTGAGGG	0.607			T	"""PML, ZNF145, TIF1, NUMA1, NPM1"""	APL								C|||	39	0.00778754	0.0008	0.0187	5008	,	,		20175	0.0		0.0249	False		,,,				2504	0.0				p.I268I		Atlas-SNP	.		Dom	yes		17	17q12	5914	"""retinoic acid receptor, alpha"""		L	.	RARA	52	.	0			c.C804T						PASS	.	C	,,,	24,4382	30.8+/-60.4	0,24,2179	59.0	45.0	50.0		804,789,804,513	3.5	1.0	17	dbSNP_127	50	147,8453	70.7+/-133.2	3,141,4156	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RARA	NM_000964.3,NM_001024809.3,NM_001145301.2,NM_001145302.2	,,,	3,165,6335	TT,TC,CC		1.7093,0.5447,1.3148	,,,	268/463,263/458,268/463,171/366	38508756	171,12835	2203	4300	6503	SO:0001819	synonymous_variant	5914	exon6			GGACATCCTGGTG	X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"""Nuclear hormone receptors"""	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.804C>T	17.37:g.38508756C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_000964	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Silent	SNP	ENST00000254066.5	37	CCDS11366.1																																																																																			C|0.987;T|0.013	0.013	strong		0.607	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2		
SBF2	81846	hgsc.bcm.edu	37	11	9879838	9879838	+	Missense_Mutation	SNP	C	C	T	rs7102464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9879838C>T	ENST00000256190.8	-	18	2172	c.2035G>A	c.(2035-2037)Gaa>Aaa	p.E679K	RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	679			E -> K (in dbSNP:rs7102464).		cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CGAACCTGTTCCTGCACTGCA	0.468													C|||	164	0.0327476	0.0023	0.0519	5008	,	,		19098	0.0		0.1163	False		,,,				2504	0.0082				p.E679K		Atlas-SNP	.											.	SBF2	146	.	0			c.G2035A						PASS	.	C	LYS/GLU	102,4300	81.9+/-120.4	1,100,2100	211.0	191.0	198.0		2035	4.3	1.0	11	dbSNP_116	198	918,7670	203.8+/-246.7	64,790,3440	yes	missense	SBF2	NM_030962.3	56	65,890,5540	TT,TC,CC		10.6893,2.3171,7.8522	benign	679/1850	9879838	1020,11970	2201	4294	6495	SO:0001583	missense	81846	exon18			CCTGTTCCTGCAC	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2035G>A	11.37:g.9879838C>T	ENSP00000256190:p.Glu679Lys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	122|122	0.055860805860805864|0.055860805860805864	3|3	0.006097560975609756|0.006097560975609756	20|20	0.055248618784530384|0.055248618784530384	0|0	0.0|0.0	99|99	0.13060686015831136|0.13060686015831136	C|C	10.67|10.67	1.415362|1.415362	0.25552|0.25552	0.023171|0.023171	0.106893|0.106893	ENSG00000133812|ENSG00000133812	ENST00000256190|ENST00000420722	T|.	0.41400|.	1.0|.	5.36|5.36	4.34|4.34	0.51931|0.51931	.|.	0.157913|.	0.56097|.	D|.	0.000034|.	T|T	0.00144|0.00144	0.0004|0.0004	N|N	0.01705|0.01705	-0.755|-0.755	0.35399|0.35399	D|D	0.791393|0.791393	B|.	0.02656|.	0.0|.	B|.	0.09377|.	0.004|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|5	0.09084|.	T|.	0.74|.	.|.	3.53|3.53	0.07773|0.07773	0.0:0.6334:0.0:0.3666|0.0:0.6334:0.0:0.3666	rs7102464;rs17354351;rs52819750;rs61100799;rs7102464|rs7102464;rs17354351;rs52819750;rs61100799;rs7102464	679|.	Q86WG5|.	MTMRD_HUMAN|.	K|E	679|285	ENSP00000256190:E679K|.	ENSP00000256190:E679K|.	E|G	-|-	1|2	0|0	SBF2|SBF2	9836414|9836414	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.946000|4.946000	0.63576|0.63576	2.523000|2.523000	0.85059|0.85059	0.552000|0.552000	0.68991|0.68991	GAA|GGA	C|0.933;T|0.067	0.067	strong		0.468	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
FAM208A	23272	hgsc.bcm.edu	37	3	56703746	56703746	+	Silent	SNP	A	A	C	rs13094666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	76	0	0		WXS	Illumina HiSeq	Phase_I	162	93	0.574074	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	
OR2T34	127068	hgsc.bcm.edu	37	1	248737734	248737734	+	Missense_Mutation	SNP	G	G	A	rs139616012		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248737734G>A	ENST00000328782.2	-	1	346	c.325C>T	c.(325-327)Cac>Tac	p.H109Y		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(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)			AGGGTCAGGTGGAAGAACATC	0.542																																					p.H109Y		Atlas-SNP	.											OR2T34,NS,carcinoma,0,4	OR2T34	72	4	0			c.C325T						scavenged	.						120.0	109.0	112.0					1																	248737734		2163	4276	6439	SO:0001583	missense	127068	exon1			TCAGGTGGAAGAA	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.325C>T	1.37:g.248737734G>A	ENSP00000330904:p.His109Tyr	Somatic	373	4	0.0107239		WXS	Illumina HiSeq	Phase_I	433	12	0.0277136	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	296	0.13553113553113552	69	0.1402439024390244	61	0.1685082872928177	71	0.12412587412587413	95	0.12532981530343007	.	0.011	-1.710055	0.00712	.	.	ENSG00000183310	ENST00000328782	T	0.01304	5.03	2.34	-0.481	0.12082	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00109	-2.105	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38908	-0.9639	8	0.02654	T	1	.	4.2299	0.10597	0.597:0.1723:0.2307:0.0	.	109	Q8NGX1	O2T34_HUMAN	Y	109	ENSP00000330904:H109Y	ENSP00000330904:H109Y	H	-	1	0	OR2T34	246804357	0.001000	0.12720	0.040000	0.18447	0.392000	0.30506	0.697000	0.25556	-0.366000	0.08064	-1.344000	0.01245	CAC	.	.	weak		0.542	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
ZNF615	284370	hgsc.bcm.edu	37	19	52497943	52497943	+	Missense_Mutation	SNP	G	G	A	rs10500311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52497943G>A	ENST00000602063.1	-	6	735	c.386C>T	c.(385-387)aCg>aTg	p.T129M	ZNF615_ENST00000391795.3_Missense_Mutation_p.T134M|ZNF615_ENST00000376716.5_Missense_Mutation_p.T129M|ZNF615_ENST00000594083.1_Missense_Mutation_p.T140M|ZNF615_ENST00000598071.1_Missense_Mutation_p.T140M			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	129			T -> M (in dbSNP:rs10500311). {ECO:0000269|PubMed:14702039, 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)	p.T129M(1)|p.T140M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TAAGTCAAACGTATCACAATC	0.348													G|||	2388	0.476837	0.6074	0.3977	5008	,	,		18054	0.3929		0.3121	False		,,,				2504	0.6125				p.T140M		Atlas-SNP	.											ZNF615,NS,carcinoma,0,2	ZNF615	111	2	2	Substitution - Missense(2)	stomach(2)	c.C419T						PASS	.	G	MET/THR,MET/THR	2555,1851	614.9+/-392.5	720,1115,368	44.0	45.0	45.0		419,386	1.3	0.0	19	dbSNP_119	45	2392,6208	383.3+/-340.7	324,1744,2232	yes	missense,missense	ZNF615	NM_001199324.1,NM_198480.3	81,81	1044,2859,2600	AA,AG,GG		27.814,42.0109,38.0363	benign,benign	140/743,129/732	52497943	4947,8059	2203	4300	6503	SO:0001583	missense	284370	exon7			TCAAACGTATCAC	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.386C>T	19.37:g.52497943G>A	ENSP00000473089:p.Thr129Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	893	0.4088827838827839	297	0.6036585365853658	145	0.4005524861878453	204	0.35664335664335667	247	0.3258575197889182	G	2.565	-0.300886	0.05495	0.579891	0.27814	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.08102	3.15;3.13	2.33	1.3	0.21679	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.12013	0.005;0.005;0.003	B;B;B	0.09377	0.004;0.004;0.001	T	0.23404	-1.0189	8	0.35671	T	0.21	.	4.1627	0.10291	0.6351:0.0:0.3649:0.0	rs10500311;rs57600563;rs10500311	136;140;129	Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;ZN615_HUMAN	M	129;139;134;139	ENSP00000365906:T129M;ENSP00000375672:T134M	ENSP00000347019:T139M	T	-	2	0	ZNF615	57189755	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	0.558000	0.23469	0.341000	0.23771	-0.302000	0.09304	ACG	G|0.596;A|0.404	0.404	strong		0.348	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
TTN	7273	hgsc.bcm.edu	37	2	179611875	179611875	+	Intron	SNP	A	A	G	rs61233923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611875A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.Y5084Y|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGGTGTGGAATATCTCTCTA	0.547													a|||	199	0.0397364	0.1407	0.013	5008	,	,		14705	0.0		0.003	False		,,,				2504	0.001				p.Y5084Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15252C						PASS	.	G	,,,,	406,4000	178.7+/-207.4	27,352,1824	62.0	73.0	69.0		,,15252,,	-7.1	0.0	2	dbSNP_129	69	6,8592	1.2+/-3.3	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	27,358,6117	GG,GA,AA		0.0698,9.2147,3.1683	,,,,	,,5084/5605,,	179611875	412,12592	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TGTGGAATATCTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5227T>C	2.37:g.179611875A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	162	20	0.123457	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.963;G|0.037	0.037	strong		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NDN	4692	hgsc.bcm.edu	37	15	23931507	23931507	+	Silent	SNP	G	G	A	rs2192206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:23931507G>A	ENST00000331837.4	-	1	943	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	286	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGGCCTGGGGGTCTTTCTTAA	0.602									Prader-Willi syndrome				G|||	949	0.189497	0.0083	0.3026	5008	,	,		16558	0.3482		0.2107	False		,,,				2504	0.1687				p.D286D		Atlas-SNP	.											.	NDN	79	.	0			c.C858T						PASS	.	G		198,4204		8,182,2011	28.0	32.0	30.0		858	-1.8	1.0	15	dbSNP_96	30	1867,6727		206,1455,2636	no	coding-synonymous	NDN	NM_002487.2		214,1637,4647	AA,AG,GG		21.7245,4.498,15.8895		286/322	23931507	2065,10931	2201	4297	6498	SO:0001819	synonymous_variant	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	CTGGGGGTCTTTC	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"""Prader-Willi syndrome chromosome region"""	602117	"""necdin (mouse) homolog"", ""necdin homolog (mouse)"""			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.858C>T	15.37:g.23931507G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_002487	B2R6Z5	Silent	SNP	ENST00000331837.4	37	CCDS10014.1																																																																																			G|0.810;A|0.190	0.190	strong		0.602	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487	
GABRA3	2556	hgsc.bcm.edu	37	X	151358333	151358333	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:151358333T>C	ENST00000370314.4	-	9	1250	c.1012A>G	c.(1012-1014)Atg>Gtg	p.M338V	GABRA3_ENST00000497894.1_5'UTR|GABRA3_ENST00000535043.1_Missense_Mutation_p.M338V	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	338					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)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				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)|Zolpidem(DB00425)|Zopiclone(DB01198)	AACCAGTCCATGGCCGTCGCA	0.478																																					p.M338V	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.A1012G						PASS	.						86.0	81.0	83.0					X																	151358333		2203	4300	6503	SO:0001583	missense	2556	exon9			AGTCCATGGCCGT		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4077	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 3"""	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.1012A>G	X.37:g.151358333T>C	ENSP00000359337:p.Met338Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	NM_000808	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	37	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089013	0.76756	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	D;D;D	0.85955	-2.05;-2.05;-2.05	5.56	5.56	0.83823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	N	0.19112	0.55	0.58432	D	0.999993	B	0.18166	0.026	B	0.22880	0.042	T	0.73972	-0.3814	10	0.87932	D	0	.	12.5432	0.56184	0.0:0.0:0.0:1.0	.	338	P34903	GBRA3_HUMAN	V	338	ENSP00000359337:M338V;ENSP00000359334:M338V;ENSP00000443527:M338V	ENSP00000359334:M338V	M	-	1	0	GABRA3	151108989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.989000	0.88205	1.868000	0.54150	0.483000	0.47432	ATG	.	.	none		0.478	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808	
CHRNA1	1134	hgsc.bcm.edu	37	2	175614716	175614716	+	Silent	SNP	G	G	A	rs2229957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:175614716G>A	ENST00000261007.5	-	8	1101	c.1035C>T	c.(1033-1035)caC>caT	p.H345H	CHRNA1_ENST00000348749.5_Silent_p.H320H|CHRNA1_ENST00000409219.1_Silent_p.H320H|CHRNA1_ENST00000409542.1_Silent_p.H238H|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	345					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|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)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TGGGTGAGCGGTGGTGTGTGT	0.562													G|||	614	0.122604	0.1808	0.0519	5008	,	,		18200	0.0565		0.0706	False		,,,				2504	0.2157				p.H345H		Atlas-SNP	.											.	CHRNA1	92	.	0			c.C1035T						PASS	.	G	,	697,3709	291.3+/-281.4	56,585,1562	189.0	145.0	160.0		960,1035	5.4	1.0	2	dbSNP_98	160	569,8031	154.3+/-208.6	15,539,3746	no	coding-synonymous,coding-synonymous	CHRNA1	NM_000079.3,NM_001039523.2	,	71,1124,5308	AA,AG,GG		6.6163,15.8193,9.734	,	320/458,345/483	175614716	1266,11740	2203	4300	6503	SO:0001819	synonymous_variant	1134	exon8			TGAGCGGTGGTGT	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.1035C>T	2.37:g.175614716G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	72	0.631579	NM_001039523	B4DRV6|D3DPE8	Silent	SNP	ENST00000261007.5	37	CCDS33331.1																																																																																			T|0.025;G|0.730;C|0.169;A|0.077	0.077	strong		0.562	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
PCNX	22990	hgsc.bcm.edu	37	14	71444788	71444788	+	Silent	SNP	G	G	A	rs3814871	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:71444788G>A	ENST00000304743.2	+	6	2180	c.1734G>A	c.(1732-1734)agG>agA	p.R578R	PCNX_ENST00000238570.5_Silent_p.R578R|PCNX_ENST00000439984.3_Silent_p.R578R	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	578						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)		GCCGGCATAGGGACTATGTTT	0.468													G|||	2035	0.40635	0.4009	0.4164	5008	,	,		21529	0.6131		0.3539	False		,,,				2504	0.2474				p.R578R		Atlas-SNP	.											PCNX,NS,carcinoma,0,1	PCNX	198	1	0			c.G1734A						PASS	.	G		1680,2726	508.3+/-366.9	334,1012,857	109.0	107.0	107.0		1734	5.0	1.0	14	dbSNP_107	107	3002,5598	463.4+/-366.0	544,1914,1842	no	coding-synonymous	PCNX	NM_014982.2		878,2926,2699	AA,AG,GG		34.907,38.1298,35.9988		578/2342	71444788	4682,8324	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			GCATAGGGACTAT	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.1734G>A	14.37:g.71444788G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1																																																																																			G|0.604;A|0.396	0.396	strong		0.468	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229702	87229702	+	Silent	SNP	A	A	G	rs4546639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:87229702A>G	ENST00000297524.3	-	3	1279	c.1176T>C	c.(1174-1176)taT>taC	p.Y392Y	SLC7A13_ENST00000520624.1_5'Flank|SLC7A13_ENST00000419776.2_Silent_p.Y383Y	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	392						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						ATTTTACCTTATAAGGTATAG	0.289													A|||	1014	0.202476	0.0688	0.1974	5008	,	,		17572	0.3383		0.1372	False		,,,				2504	0.3139				p.Y392Y		Atlas-SNP	.											.	SLC7A13	97	.	0			c.T1176C						PASS	.	A		394,3954		20,354,1800	21.0	23.0	22.0		1176	5.0	1.0	8	dbSNP_111	22	1098,7456		81,936,3260	no	coding-synonymous	SLC7A13	NM_138817.2		101,1290,5060	GG,GA,AA		12.8361,9.0616,11.5641		392/471	87229702	1492,11410	2174	4277	6451	SO:0001819	synonymous_variant	157724	exon3			TACCTTATAAGGT	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.1176T>C	8.37:g.87229702A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																			A|0.858;G|0.142	0.142	strong		0.289	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
MYOM3	127294	hgsc.bcm.edu	37	1	24406647	24406647	+	Silent	SNP	G	G	A	rs4649175	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24406647G>A	ENST00000374434.3	-	20	2607	c.2445C>T	c.(2443-2445)gcC>gcT	p.A815A	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000475306.1_5'Flank|MYOM3_ENST00000329601.7_Silent_p.A815A|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Silent_p.A816A	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	815	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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)		CCAGGGATGTGGCCCGCACCT	0.607													G|||	1774	0.354233	0.3238	0.3444	5008	,	,		18648	0.4276		0.4423	False		,,,				2504	0.2362				p.A815A		Atlas-SNP	.											.	MYOM3	131	.	0			c.C2445T						PASS	.	G		1246,2752		209,828,962	47.0	53.0	51.0		2445	4.5	1.0	1	dbSNP_111	51	3538,4792		746,2046,1373	yes	coding-synonymous	MYOM3	NM_152372.3		955,2874,2335	AA,AG,GG		42.473,31.1656,38.806		815/1438	24406647	4784,7544	1999	4165	6164	SO:0001819	synonymous_variant	127294	exon20			GGATGTGGCCCGC	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.2445C>T	1.37:g.24406647G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			G|0.639;A|0.361	0.361	strong		0.607	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
C19orf57	79173	hgsc.bcm.edu	37	19	14000870	14000870	+	Missense_Mutation	SNP	C	C	T	rs2305775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14000870C>T	ENST00000586783.1	-	5	798	c.799G>A	c.(799-801)Gga>Aga	p.G267R	C19orf57_ENST00000346736.2_Missense_Mutation_p.G267R|C19orf57_ENST00000454313.1_Missense_Mutation_p.G267R|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	267			G -> R (in dbSNP:rs2305775). {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)			TGGGGCCCTCCAGGCAGGCCA	0.647													C|||	1915	0.382388	0.7005	0.232	5008	,	,		17154	0.3075		0.2117	False		,,,				2504	0.3119				p.G267R		Atlas-SNP	.											.	C19orf57	34	.	0			c.G799A						PASS	.	C	ARG/GLY	2723,1683	642.6+/-397.7	843,1037,323	45.0	44.0	45.0		799	1.7	0.0	19	dbSNP_100	45	1838,6762	325.4+/-316.9	193,1452,2655	yes	missense	C19orf57	NM_024323.3	125	1036,2489,2978	TT,TC,CC		21.3721,38.1979,35.0684	probably-damaging	267/638	14000870	4561,8445	2203	4300	6503	SO:0001583	missense	79173	exon6			GCCCTCCAGGCAG	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.799G>A	19.37:g.14000870C>T	ENSP00000465822:p.Gly267Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		767	0.35119047619047616	330	0.6707317073170732	81	0.22375690607734808	195	0.3409090909090909	161	0.21240105540897097	C	13.44	2.236897	0.39498	0.618021	0.213721	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.30981	1.51;1.51	2.86	1.72	0.24424	.	1.545910	0.04576	N	0.394047	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P	0.51791	0.22;0.948	B;P	0.54140	0.028;0.743	T	0.43877	-0.9364	9	0.13108	T	0.6	3.3121	7.3728	0.26810	0.0:0.7258:0.2742:0.0	rs2305775;rs59881652;rs2305775	267;267	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	R	267	ENSP00000404382:G267R;ENSP00000254336:G267R	ENSP00000254336:G267R	G	-	1	0	C19orf57	13861870	0.000000	0.05858	0.004000	0.12327	0.174000	0.22865	-0.199000	0.09491	0.464000	0.27142	0.313000	0.20887	GGA	C|0.657;T|0.343	0.343	strong		0.647	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461062	141461062	+	Silent	SNP	G	G	A	rs3735803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461062G>A	ENST00000438773.2	-	2	544	c.411C>T	c.(409-411)aaC>aaT	p.N137N	TRAPPC9_ENST00000389327.3_Silent_p.N137N|TRAPPC9_ENST00000389328.4_Silent_p.N235N	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	53	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	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	
MX1	4599	hgsc.bcm.edu	37	21	42824733	42824733	+	Silent	SNP	G	G	A	rs469304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:42824733G>A	ENST00000398600.2	+	18	2720	c.1695G>A	c.(1693-1695)caG>caA	p.Q565Q	MX1_ENST00000455164.2_Silent_p.Q565Q|MX1_ENST00000398598.3_Silent_p.Q565Q|MX1_ENST00000288383.6_Silent_p.Q542Q	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	565	Stalk.				apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				GGGCTTTCCAGTCCAGCTCGG	0.517													G|||	1337	0.266973	0.1641	0.3127	5008	,	,		18892	0.006		0.5348	False		,,,				2504	0.3671				p.Q565Q		Atlas-SNP	.											.	MX1	58	.	0			c.G1695A						PASS	.	G	,,	964,3442	365.1+/-317.3	100,764,1339	181.0	189.0	186.0		1695,1695,1695	-6.9	0.0	21	dbSNP_80	186	4700,3900	605.8+/-395.0	1268,2164,868	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	1368,2928,2207	AA,AG,GG		45.3488,21.8793,43.5491	,,	565/663,565/663,565/663	42824733	5664,7342	2203	4300	6503	SO:0001819	synonymous_variant	4599	exon18			TTTCCAGTCCAGC		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.1695G>A	21.37:g.42824733G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																			G|0.620;A|0.380	0.380	strong		0.517	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
MAP3K4	4216	hgsc.bcm.edu	37	6	161507618	161507618	+	Silent	SNP	C	C	T	rs145569434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:161507618C>T	ENST00000392142.4	+	9	2623	c.2475C>T	c.(2473-2475)gaC>gaT	p.D825D	MAP3K4_ENST00000348824.7_Silent_p.D825D|MAP3K4_ENST00000366920.2_Silent_p.D825D|MAP3K4_ENST00000366919.2_Silent_p.D825D	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	825					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GATCCTAGGACCTGGAAATAG	0.353													C|||	32	0.00638978	0.0008	0.0346	5008	,	,		19983	0.0		0.006	False		,,,				2504	0.001				p.D825D		Atlas-SNP	.											.	MAP3K4	364	.	0			c.C2475T						PASS	.	C	,	15,4391	22.3+/-47.3	0,15,2188	71.0	69.0	70.0		2475,2475	4.4	1.0	6	dbSNP_134	70	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	MAP3K4	NM_005922.2,NM_006724.2	,	0,80,6423	TT,TC,CC		0.7558,0.3404,0.6151	,	825/1609,825/1559	161507618	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	4216	exon9			CTAGGACCTGGAA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2475C>T	6.37:g.161507618C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																			C|0.994;T|0.006	0.006	strong		0.353	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
ASCL3	56676	hgsc.bcm.edu	37	11	8959370	8959370	+	Silent	SNP	G	G	A	rs2742505	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	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		
INADL	10207	hgsc.bcm.edu	37	1	62483599	62483599	+	Silent	SNP	G	G	A	rs34726576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62483599G>A	ENST00000371158.2	+	29	4053	c.3939G>A	c.(3937-3939)aaG>aaA	p.K1313K	INADL_ENST00000543708.1_Silent_p.K97K|INADL_ENST00000316485.6_Silent_p.K1313K|INADL_ENST00000545929.1_Intron	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1313	PDZ 7. {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						CCCCATCAAAGGTCAAGCTGG	0.363													G|||	537	0.107228	0.0424	0.147	5008	,	,		16837	0.002		0.2416	False		,,,				2504	0.137				p.K1313K		Atlas-SNP	.											.	INADL	179	.	0			c.G3939A						PASS	.	G		298,4108	164.7+/-196.3	10,278,1915	151.0	137.0	142.0		3939	-1.0	0.2	1	dbSNP_126	142	2210,6390	375.7+/-337.9	278,1654,2368	no	coding-synonymous	INADL	NM_176877.2		288,1932,4283	AA,AG,GG		25.6977,6.7635,19.2834		1313/1802	62483599	2508,10498	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon29			ATCAAAGGTCAAG	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.3939G>A	1.37:g.62483599G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.818;A|0.182	0.182	strong		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
CDHR2	54825	hgsc.bcm.edu	37	5	176005481	176005481	+	Missense_Mutation	SNP	G	G	A	rs61743422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176005481G>A	ENST00000510636.1	+	16	1964	c.1690G>A	c.(1690-1692)Ggg>Agg	p.G564R	CDHR2_ENST00000506348.1_Missense_Mutation_p.G564R|CDHR2_ENST00000261944.5_Missense_Mutation_p.G564R	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	564	Cadherin 5. {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						CACAGACGGCGGGAACCTGTC	0.617													G|||	53	0.0105831	0.0038	0.0043	5008	,	,		19440	0.0		0.0189	False		,,,				2504	0.0266				p.G564R		Atlas-SNP	.											.	CDHR2	152	.	0			c.G1690A						PASS	.	G	ARG/GLY,ARG/GLY	21,4385	29.0+/-57.7	0,21,2182	80.0	61.0	67.0		1690,1690	5.3	0.1	5	dbSNP_129	67	150,8450	72.9+/-135.5	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	125,125	2,167,6334	AA,AG,GG		1.7442,0.4766,1.3148	probably-damaging,probably-damaging	564/1311,564/1311	176005481	171,12835	2203	4300	6503	SO:0001583	missense	54825	exon16			GACGGCGGGAACC	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.1690G>A	5.37:g.176005481G>A	ENSP00000424565:p.Gly564Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	G	15.92	2.975766	0.53720	0.004766	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	5.33	0.75918	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.70474	0.3228	M	0.79693	2.465	0.48452	D	0.999658	D	0.89917	1.0	D	0.70935	0.971	T	0.79969	-0.1579	9	0.72032	D	0.01	-27.052	14.6072	0.68489	0.0:0.1456:0.8544:0.0	rs61743422	564	Q9BYE9	CDHR2_HUMAN	R	564	ENSP00000424565:G564R;ENSP00000261944:G564R;ENSP00000421078:G564R	ENSP00000261944:G564R	G	+	1	0	CDHR2	175938087	1.000000	0.71417	0.098000	0.21074	0.041000	0.13682	5.345000	0.65987	2.504000	0.84457	0.542000	0.68232	GGG	G|0.987;A|0.013	0.013	strong		0.617	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
ACO1	48	hgsc.bcm.edu	37	9	32433803	32433803	+	Silent	SNP	C	C	A	rs61752944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32433803C>A	ENST00000309951.6	+	16	2067	c.1929C>A	c.(1927-1929)atC>atA	p.I643I	ACO1_ENST00000541043.1_Silent_p.I544I|ACO1_ENST00000379923.1_Silent_p.I643I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	643					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		CTACGTATATCAAATCACCAC	0.328													C|||	2	0.000399361	0.0	0.0	5008	,	,		17515	0.0		0.002	False		,,,				2504	0.0				p.I643I		Atlas-SNP	.											.	ACO1	149	.	0			c.C1929A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	107.0	107.0	107.0		1929	1.2	0.8	9	dbSNP_129	107	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	ACO1	NM_002197.2		0,17,6486	AA,AC,CC		0.1744,0.0454,0.1307		643/890	32433803	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	48	exon16			GTATATCAAATCA	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1929C>A	9.37:g.32433803C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			C|0.999;A|0.001	0.001	strong		0.328	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
OR1N1	138883	hgsc.bcm.edu	37	9	125289033	125289033	+	Silent	SNP	A	A	G	rs41277122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:125289033A>G	ENST00000304880.2	-	1	539	c.540T>C	c.(538-540)acT>acC	p.T180T		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	180						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)|large_intestine(2)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						TCAGGACAGGAGTGATGTCAC	0.493													A|||	241	0.048123	0.0098	0.0677	5008	,	,		21902	0.001		0.1163	False		,,,				2504	0.0644				p.T180T		Atlas-SNP	.											.	OR1N1	38	.	0			c.T540C						PASS	.	A		83,4323	71.4+/-109.4	1,81,2121	91.0	81.0	84.0		540	-1.9	0.0	9	dbSNP_127	84	954,7646	208.9+/-250.2	54,846,3400	no	coding-synonymous	OR1N1	NM_012363.1		55,927,5521	GG,GA,AA		11.093,1.8838,7.9732		180/312	125289033	1037,11969	2203	4300	6503	SO:0001819	synonymous_variant	138883	exon1			GACAGGAGTGATG	U86216	CCDS6844.1	9q34.11	2012-08-09			ENSG00000171505	ENSG00000171505		"""GPCR / Class A : Olfactory receptors"""	8221	protein-coding gene	gene with protein product				OR1N3		9500546	Standard	NM_012363		Approved	OR1-26	uc004bmn.1	Q8NGS0	OTTHUMG00000020608	ENST00000304880.2:c.540T>C	9.37:g.125289033A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_012363	A3KFM1|O43870|Q6IF16|Q96R93	Silent	SNP	ENST00000304880.2	37	CCDS6844.1																																																																																			A|0.931;G|0.069	0.069	strong		0.493	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1		
THSD1	55901	hgsc.bcm.edu	37	13	52952680	52952680	+	Silent	SNP	G	G	A	rs9536043	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52952680G>A	ENST00000258613.4	-	5	1603	c.1425C>T	c.(1423-1425)cgC>cgT	p.R475R	THSD1_ENST00000544466.1_Silent_p.R96R|THSD1_ENST00000349258.4_Silent_p.R422R	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	475					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		AGAAGCTCCCGCGCTGCTCGC	0.652													G|||	281	0.0561102	0.1135	0.0274	5008	,	,		14836	0.0079		0.0388	False		,,,				2504	0.0665				p.R475R		Atlas-SNP	.											THSD1,NS,carcinoma,-1,1	THSD1	89	1	0			c.C1425T						PASS	.	G	,	395,4011	195.0+/-219.7	16,363,1824	44.0	50.0	48.0		1425,1266	-12.1	0.0	13	dbSNP_119	48	442,8158	133.5+/-191.0	12,418,3870	no	coding-synonymous,coding-synonymous	THSD1	NM_018676.3,NM_199263.2	,	28,781,5694	AA,AG,GG		5.1395,8.965,6.4355	,	475/853,422/800	52952680	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	55901	exon5			GCTCCCGCGCTGC	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1425C>T	13.37:g.52952680G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Silent	SNP	ENST00000258613.4	37	CCDS9432.1																																																																																			G|0.948;A|0.052	0.052	strong		0.652	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
SHROOM3	57619	hgsc.bcm.edu	37	4	77662125	77662125	+	Silent	SNP	C	C	T	rs36036308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77662125C>T	ENST00000296043.6	+	5	3752	c.2799C>T	c.(2797-2799)tcC>tcT	p.S933S		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	933	ASD1. {ECO:0000255|PROSITE- ProRule:PRU00637}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ACGCACAGTCCCGTGTCTTGG	0.721													C|||	187	0.0373403	0.031	0.0375	5008	,	,		11231	0.004		0.0895	False		,,,				2504	0.0266				p.S933S		Atlas-SNP	.											.	SHROOM3	134	.	0			c.C2799T						PASS	.	C		133,4161		2,129,2016	9.0	10.0	10.0		2799	2.3	1.0	4	dbSNP_126	10	719,7635		31,657,3489	no	coding-synonymous	SHROOM3	NM_020859.3		33,786,5505	TT,TC,CC		8.6067,3.0973,6.7362		933/1997	77662125	852,11796	2147	4177	6324	SO:0001819	synonymous_variant	57619	exon5			ACAGTCCCGTGTC	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.2799C>T	4.37:g.77662125C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			C|0.951;T|0.049	0.049	strong		0.721	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
MKI67	4288	hgsc.bcm.edu	37	10	129902368	129902368	+	Missense_Mutation	SNP	T	T	A	rs79661992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:129902368T>A	ENST00000368654.3	-	13	8111	c.7736A>T	c.(7735-7737)gAc>gTc	p.D2579V	MKI67_ENST00000368653.3_Missense_Mutation_p.D2219V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2579	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)	p.D2579V(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)				TGTGTTTTTGTCAATAGTCAT	0.478													T|||	204	0.0407348	0.0643	0.0375	5008	,	,		19458	0.0188		0.0586	False		,,,				2504	0.0153				p.D2579V		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	pancreas(1)	c.A7736T						PASS	.	T	VAL/ASP,VAL/ASP	208,4198	127.4+/-164.3	6,196,2001	91.0	92.0	92.0		6656,7736	-2.9	0.0	10	dbSNP_131	92	480,8120	140.0+/-196.6	14,452,3834	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	152,152	20,648,5835	AA,AT,TT		5.5814,4.7208,5.2899	probably-damaging,probably-damaging	2219/2897,2579/3257	129902368	688,12318	2203	4300	6503	SO:0001583	missense	4288	exon13			TTTTTGTCAATAG	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.7736A>T	10.37:g.129902368T>A	ENSP00000357643:p.Asp2579Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	106	0.048534798534798536	31	0.06300813008130081	18	0.049723756906077346	9	0.015734265734265736	48	0.0633245382585752	T	10.98	1.504090	0.26949	0.047208	0.055814	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01745	4.79;4.66	2.62	-2.94	0.05581	.	.	.	.	.	T	0.00178	0.0005	L	0.40543	1.245	0.09310	N	1	P;B;B	0.37101	0.582;0.22;0.296	B;B;B	0.31614	0.133;0.042;0.041	T	0.44711	-0.9310	9	0.26408	T	0.33	.	3.244	0.06791	0.2094:0.4109:0.0:0.3796	.	2578;2219;2579	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	2579;2219;2578	ENSP00000357643:D2579V;ENSP00000357642:D2219V	ENSP00000357642:D2219V	D	-	2	0	MKI67	129792358	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.003000	0.01463	-0.713000	0.04981	-0.371000	0.07208	GAC	T|0.949;A|0.051	0.051	strong		0.478	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152283862G>C	ENST00000368799.1	-	3	3535	c.3500C>G	c.(3499-3501)gCa>gGa	p.A1167G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1167	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)			CCCCGGGTGTGCACGAATGGT	0.597									Ichthyosis				g|||	2675	0.534145	0.7806	0.4611	5008	,	,		20510	0.6577		0.1759	False		,,,				2504	0.4939				p.A1167G		Atlas-SNP	.											FLG,brain,glioma,0,1	FLG	900	1	0			c.C3500G						PASS	.	C	GLY/ALA	2642,1764	599.0+/-389.2	734,1174,295	291.0	346.0	328.0		3500	-5.5	0.0	1	dbSNP_129	328	1392,7208	258.1+/-281.9	103,1186,3011	no	missense	FLG	NM_002016.1	60	837,2360,3306	CC,CG,GG		16.186,40.0363,31.0165	benign	1167/4062	152283862	4034,8972	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGGTGTGCACGAA	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.3500C>G	1.37:g.152283862G>C	ENSP00000357789:p.Ala1167Gly	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	229	134	0.585153	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	814	0.3727106227106227	262	0.532520325203252	123	0.3397790055248619	315	0.5506993006993007	114	0.1503957783641161	g	3.006	-0.204867	0.06180	0.599637	0.16186	ENSG00000143631	ENST00000368799	T	0.03920	3.76	2.76	-5.53	0.02552	.	.	.	.	.	T	0.00271	0.0008	N	0.00049	-2.42	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.48269	-0.9050	8	0.21540	T	0.41	.	10.7783	0.46363	0.0:0.1887:0.7027:0.1086	rs58001094	1167	P20930	FILA_HUMAN	G	1167	ENSP00000357789:A1167G	ENSP00000357789:A1167G	A	-	2	0	FLG	150550486	.	.	0.000000	0.03702	0.008000	0.06430	.	.	-1.865000	0.01147	-1.429000	0.01096	GCA	G|0.640;C|0.360	0.360	strong		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PCNT	5116	hgsc.bcm.edu	37	21	47773103	47773103	+	Silent	SNP	C	C	A	rs2249057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47773103C>A	ENST00000359568.5	+	10	1649	c.1542C>A	c.(1540-1542)tcC>tcA	p.S514S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	514	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)		p.S514S(1)		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)					AGCATGAGTCCGAACTGGAGC	0.483													C|||	1450	0.289537	0.2141	0.1988	5008	,	,		20023	0.3839		0.3449	False		,,,				2504	0.3016				p.S514S		Atlas-SNP	.											PCNT,NS,carcinoma,0,1	PCNT	283	1	1	Substitution - coding silent(1)	prostate(1)	c.C1542A						PASS	.	C		1035,3371	379.4+/-323.3	115,805,1283	66.0	71.0	69.0		1542	-9.5	0.0	21	dbSNP_100	69	2844,5756	448.4+/-361.8	464,1916,1920	no	coding-synonymous	PCNT	NM_006031.5		579,2721,3203	AA,AC,CC		33.0698,23.4907,29.8247		514/3337	47773103	3879,9127	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon10			TGAGTCCGAACTG	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.1542C>A	21.37:g.47773103C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	19	0.333333	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.694;A|0.306	0.306	strong		0.483	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
AIFM3	150209	hgsc.bcm.edu	37	22	21328568	21328568	+	Missense_Mutation	SNP	G	G	A	rs56179977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21328568G>A	ENST00000399167.2	+	6	733	c.493G>A	c.(493-495)Gtc>Atc	p.V165I	AIFM3_ENST00000333607.6_Missense_Mutation_p.V165I|AIFM3_ENST00000399163.2_Missense_Mutation_p.V165I|AIFM3_ENST00000405089.1_Missense_Mutation_p.V171I|AIFM3_ENST00000335375.5_Missense_Mutation_p.V153I|AIFM3_ENST00000440238.2_Missense_Mutation_p.V165I	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	97	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	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	
BTNL2	56244	hgsc.bcm.edu	37	6	32370835	32370835	+	Missense_Mutation	SNP	T	T	C	rs2076523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32370835T>C	ENST00000374993.1	-	3	585	c.586A>G	c.(586-588)Aaa>Gaa	p.K196E	BTNL2_ENST00000374995.3_Intron|BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.K196E|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000544175.1_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	141	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	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	
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280614C>G	ENST00000368799.1	-	3	6783	c.6748G>C	c.(6748-6750)Gag>Cag	p.E2250Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2250	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)			GAGTGTCCCTCACTGTCACTG	0.592									Ichthyosis																												p.E2250Q		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,+2,1	FLG	900	1	0			c.G6748C						scavenged	.						203.0	203.0	203.0					1																	152280614		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	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.6748G>C	1.37:g.152280614C>G	ENSP00000357789:p.Glu2250Gln	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	256	24	0.09375	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	6.497	0.459945	0.12342	.	.	ENSG00000143631	ENST00000368799	T	0.08008	3.14	3.75	0.494	0.16884	.	.	.	.	.	T	0.01454	0.0047	N	0.13043	0.29	0.09310	N	1	P	0.43542	0.81	B	0.39503	0.301	T	0.47100	-0.9143	9	0.30078	T	0.28	.	6.151	0.20313	0.1996:0.4103:0.3901:0.0	.	2250	P20930	FILA_HUMAN	Q	2250	ENSP00000357789:E2250Q	ENSP00000357789:E2250Q	E	-	1	0	FLG	150547238	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	-0.121000	0.10643	0.707000	0.31934	-0.447000	0.05616	GAG	C|0.996;G|0.003;T|0.001	0.003	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LAMA5	3911	hgsc.bcm.edu	37	20	60887581	60887581	+	Missense_Mutation	SNP	G	G	A	rs944895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60887581G>A	ENST00000252999.3	-	68	9301	c.9235C>T	c.(9235-9237)Cgg>Tgg	p.R3079W		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3079	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		R -> W (in dbSNP:rs944895). {ECO:0000269|PubMed:11821406, ECO:0000269|PubMed:9271224, ECO:0000269|PubMed:9628581}.		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)			GGGAAGAGCCGTCGCAGGCTG	0.677													.|||	3391	0.677117	0.5666	0.6988	5008	,	,		15366	0.7411		0.6431	False		,,,				2504	0.7802				p.R3079W		Atlas-SNP	.											LAMA5,NS,carcinoma,0,1	LAMA5	268	1	0			c.C9235T						PASS	.		TRP/ARG	2500,1886	594.1+/-388.1	703,1094,396	31.0	29.0	30.0		9235	3.4	0.1	20	dbSNP_86	30	5600,2988	634.2+/-398.8	1810,1980,504	yes	missense	LAMA5	NM_005560.3	101	2513,3074,900	AA,AG,GG		34.7927,43.0005,37.5674	probably-damaging	3079/3696	60887581	8100,4874	2193	4294	6487	SO:0001583	missense	3911	exon68			AGAGCCGTCGCAG	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.9235C>T	20.37:g.60887581G>A	ENSP00000252999:p.Arg3079Trp	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1458	0.6675824175824175	280	0.5691056910569106	257	0.7099447513812155	425	0.743006993006993	496	0.6543535620052771	g	9.192	1.026390	0.19512	0.569995	0.652073	ENSG00000130702	ENST00000252999	T	0.78481	-1.18	4.36	3.38	0.38709	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	1.920180	0.02454	N	0.085827	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.58620	0.983	P	0.47376	0.545	T	0.48547	-0.9026	9	0.72032	D	0.01	.	3.2954	0.06964	0.0954:0.1438:0.5475:0.2134	rs944895;rs58677971;rs944895	3079	O15230	LAMA5_HUMAN	W	3079	ENSP00000252999:R3079W	ENSP00000252999:R3079W	R	-	1	2	LAMA5	60320976	0.000000	0.05858	0.064000	0.19789	0.038000	0.13279	-0.605000	0.05661	2.269000	0.75478	0.556000	0.70494	CGG	G|0.358;A|0.642	0.642	strong		0.677	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZNF768	79724	hgsc.bcm.edu	37	16	30536672	30536672	+	Silent	SNP	A	A	G	rs3751847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	76	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	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	
MAN2B2	23324	hgsc.bcm.edu	37	4	6594947	6594947	+	Missense_Mutation	SNP	A	A	C	rs2301796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:6594947A>C	ENST00000285599.3	+	6	764	c.728A>C	c.(727-729)cAa>cCa	p.Q243P	MAN2B2_ENST00000504248.1_Missense_Mutation_p.Q243P	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	243			Q -> P (in dbSNP:rs2301796). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.		mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						AAGCCTCCCCAAGATGGGGTG	0.597													C|||	2173	0.433906	0.1762	0.4841	5008	,	,		20214	0.6141		0.4543	False		,,,				2504	0.5399				p.Q243P		Atlas-SNP	.											MAN2B2,NS,carcinoma,0,1	MAN2B2	80	1	0			c.A728C						PASS	.	C	PRO/GLN	1016,3390	727.4+/-409.8	112,792,1299	128.0	108.0	115.0		728	-9.4	0.0	4	dbSNP_100	115	4016,4584	594.7+/-393.3	926,2164,1210	yes	missense	MAN2B2	NM_015274.1	76	1038,2956,2509	CC,CA,AA		46.6977,23.0595,38.6898	benign	243/1010	6594947	5032,7974	2203	4300	6503	SO:0001583	missense	23324	exon6			CTCCCCAAGATGG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.728A>C	4.37:g.6594947A>C	ENSP00000285599:p.Gln243Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	72	0.972973	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	985|985	0.451007326007326|0.451007326007326	101|101	0.20528455284552846|0.20528455284552846	177|177	0.4889502762430939|0.4889502762430939	356|356	0.6223776223776224|0.6223776223776224	351|351	0.4630606860158311|0.4630606860158311	C|C	6.607|6.607	0.480416|0.480416	0.12581|0.12581	0.230595|0.230595	0.466977|0.466977	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|T;T	.|0.73789	.|2.2;-0.78	4.7|4.7	-9.4|-9.4	0.00616|0.00616	.|Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	.|0.608375	.|0.16823	.|N	.|0.198079	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02158|0.02158	-0.66|-0.66	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	0.37776|0.37776	-0.9691|-0.9691	4|9	.|0.27785	.|T	.|0.31	-0.3197|-0.3197	3.2177|3.2177	0.06705|0.06705	0.4679:0.1136:0.2867:0.1318|0.4679:0.1136:0.2867:0.1318	rs2301796;rs60868849;rs2301796|rs2301796;rs60868849;rs2301796	.|243;243;243	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	Q|P	242|243	.|ENSP00000285599:Q243P;ENSP00000423129:Q243P	.|ENSP00000285599:Q243P	K|Q	+|+	1|2	0|0	MAN2B2|MAN2B2	6645848|6645848	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.361000|0.361000	0.29550|0.29550	0.375000|0.375000	0.20518|0.20518	-2.218000|-2.218000	0.00730|0.00730	-0.232000|-0.232000	0.12228|0.12228	AAG|CAA	C|0.413;A|0.587	0.413	strong		0.597	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
JRK	8629	hgsc.bcm.edu	37	8	143746050	143746050	+	RNA	SNP	C	C	T	rs2976399	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143746050C>T	ENST00000507178.2	-	0	1760							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ggatctcctccgccgtcctgg	0.657													C|||	2208	0.440895	0.466	0.2925	5008	,	,		17155	0.4841		0.3469	False		,,,				2504	0.5644				p.G476R		Atlas-SNP	.											.	.	.	.	0			c.G1426A						PASS	.	C	ARG/GLY,ARG/GLY	1797,2389		398,1001,694	19.0	23.0	22.0		1428,1428	2.0	0.0	8	dbSNP_101	22	2759,5647		478,1803,1922	no	missense,missense	JRK	NM_001077527.1,NM_003724.2	125,125	876,2804,2616	TT,TC,CC		32.8218,42.9288,36.1817	benign,benign	476/557,476/569	143746050	4556,8036	2093	4203	6296			8629	exon3			CTCCTCCGCCGTC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746050C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				C|0.577;T|0.423	0.423	strong		0.657	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
LNP1	348801	hgsc.bcm.edu	37	3	100174722	100174722	+	Silent	SNP	G	G	A	rs1132022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100174722G>A	ENST00000383693.3	+	4	1769	c.489G>A	c.(487-489)gaG>gaA	p.E163E	LNP1_ENST00000489752.1_Silent_p.E176E	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	163										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						GGAAAGAAGAGCATGGAGAAG	0.428													A|||	2426	0.484425	0.3759	0.4409	5008	,	,		19498	0.7222		0.4205	False		,,,				2504	0.4826				p.E163E		Atlas-SNP	.											.	LNP1	26	.	0			c.G489A						PASS	.	A		1324,2444		238,848,798	128.0	128.0	128.0		489	-7.3	0.0	3	dbSNP_86	128	3333,4897		687,1959,1469	no	coding-synonymous	LNP1	NM_001085451.1		925,2807,2267	AA,AG,GG		40.4982,35.138,38.8148		163/179	100174722	4657,7341	1884	4115	5999	SO:0001819	synonymous_variant	348801	exon4			AGAAGAGCATGGA		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.489G>A	3.37:g.100174722G>A		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	386	248	0.642487	NM_001085451	B7ZLT3	Silent	SNP	ENST00000383693.3	37	CCDS43120.1																																																																																			G|0.515;A|0.485	0.485	strong		0.428	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
MOCS2	4338	hgsc.bcm.edu	37	5	52397311	52397311	+	Silent	SNP	T	T	C	rs2233216	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52397311T>C	ENST00000396954.3	-	5	932	c.255A>G	c.(253-255)aaA>aaG	p.K85K	MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000510818.2_3'UTR|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000361377.4_Intron	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				TAATGACTTTTTTCCCTTCAA	0.318													T|||	182	0.0363419	0.0151	0.0548	5008	,	,		15502	0.0665		0.0368	False		,,,				2504	0.0204				p.K85K		Atlas-SNP	.											.	MOCS2	28	.	0			c.A255G						PASS	.	T	,	89,4317	63.5+/-100.7	0,89,2114	183.0	190.0	188.0		255,	0.9	1.0	5	dbSNP_98	188	298,8302	97.7+/-159.3	6,286,4008	no	coding-synonymous,utr-3	MOCS2	NM_004531.3,NM_176806.2	,	6,375,6122	CC,CT,TT		3.4651,2.02,2.9755	,	85/189,	52397311	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	4338	exon5			GACTTTTTTCCCT	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.255A>G	5.37:g.52397311T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_004531		Silent	SNP	ENST00000396954.3	37	CCDS3958.1																																																																																			T|0.959;C|0.041	0.041	strong		0.318	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418	
OXR1	55074	hgsc.bcm.edu	37	8	107754473	107754473	+	Silent	SNP	G	G	A	rs1681904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:107754473G>A	ENST00000442977.2	+	14	2442	c.2343G>A	c.(2341-2343)gaG>gaA	p.E781E	OXR1_ENST00000521592.1_Silent_p.E26E|OXR1_ENST00000452423.2_Silent_p.E201E|OXR1_ENST00000445937.1_Silent_p.E753E|OXR1_ENST00000312046.6_Silent_p.E746E|OXR1_ENST00000517566.2_Silent_p.E780E|OXR1_ENST00000449762.2_Silent_p.E123E|OXR1_ENST00000297447.6_Silent_p.E150E|OXR1_ENST00000531443.1_Silent_p.E753E	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	781	TLD.				adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TAGCATCTGAGCCACTGAAAG	0.343													G|||	1911	0.381589	0.2057	0.5216	5008	,	,		16724	0.3492		0.4433	False		,,,				2504	0.4898				p.E781E		Atlas-SNP	.											.	OXR1	190	.	0			c.G2343A						PASS	.	G	,,,,,	1065,3341	388.4+/-326.9	123,819,1261	194.0	180.0	185.0		2343,2340,450,369,2259,2238	4.3	1.0	8	dbSNP_89	185	3733,4867	530.5+/-381.8	804,2125,1371	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OXR1	NM_001198532.1,NM_001198533.1,NM_001198534.1,NM_001198535.1,NM_018002.3,NM_181354.4	,,,,,	927,2944,2632	AA,AG,GG		43.407,24.1716,36.8907	,,,,,	781/875,780/874,150/244,123/217,753/847,746/840	107754473	4798,8208	2203	4300	6503	SO:0001819	synonymous_variant	55074	exon14			ATCTGAGCCACTG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.2343G>A	8.37:g.107754473G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1	838	0.3836996336996337	100	0.2032520325203252	181	0.5	213	0.3723776223776224	344	0.45382585751978893	G	8.497	0.863313	0.17250	0.241716	0.43407	ENSG00000164830	ENST00000519415	.	.	.	5.46	4.35	0.52113	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51834	-0.8655	3	.	.	.	-12.3073	6.9569	0.24576	0.2445:0.0:0.7555:0.0	rs1681904;rs11538335;rs17351853;rs1681904	.	.	.	N	425	.	.	S	+	2	0	OXR1	107823649	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.822000	0.39052	2.715000	0.92844	0.563000	0.77884	AGC	G|0.627;A|0.373	0.373	strong		0.343	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
A4GALT	53947	hgsc.bcm.edu	37	22	43089833	43089833	+	Missense_Mutation	SNP	A	A	G	rs148881382		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43089833A>G	ENST00000401850.1	-	2	614	c.125T>C	c.(124-126)gTt>gCt	p.V42A	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000249005.2_Missense_Mutation_p.V42A|A4GALT_ENST00000381278.3_Missense_Mutation_p.V42A			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	42					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						CTCTCCCACAACGTGCCAGTA	0.622																																					p.V42A		Atlas-SNP	.											.	A4GALT	35	.	0			c.T125C						PASS	.	A	ALA/VAL	0,4404		0,0,2202	28.0	20.0	23.0		125	2.3	0.0	22	dbSNP_134	23	4,8592		0,4,4294	yes	missense	A4GALT	NM_017436.4	64	0,4,6496	GG,GA,AA		0.0465,0.0,0.0308	benign	42/354	43089833	4,12996	2202	4298	6500	SO:0001583	missense	53947	exon3			CCCACAACGTGCC		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.125T>C	22.37:g.43089833A>G	ENSP00000384794:p.Val42Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	37	CCDS14041.1	.	.	.	.	.	.	.	.	.	.	A	9.301	1.053038	0.19907	0.0	4.65E-4	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.80393	-1.37;-1.37;-1.37	4.49	2.33	0.28932	.	0.613294	0.12950	U	0.425919	T	0.60932	0.2307	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.47611	-0.9104	10	0.29301	T	0.29	-9.9823	8.3249	0.32151	0.8269:0.0:0.1731:0.0	.	42	Q9NPC4	A4GAT_HUMAN	A	42	ENSP00000384794:V42A;ENSP00000249005:V42A;ENSP00000370678:V42A	ENSP00000249005:V42A	V	-	2	0	A4GALT	41419777	0.020000	0.18652	0.000000	0.03702	0.056000	0.15407	2.025000	0.41059	0.324000	0.23333	-0.464000	0.05259	GTT	A|1.000;G|0.000	0.000	weak		0.622	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
LINGO3	645191	hgsc.bcm.edu	37	19	2290870	2290870	+	Silent	SNP	G	G	C	rs8111892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2290870G>C	ENST00000585527.1	-	1	1153	c.906C>G	c.(904-906)gcC>gcG	p.A302A	LINGO3_ENST00000404279.1_Silent_p.A302A			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	302						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCAGGGCCCCGGCCAGGTGCA	0.687													G|||	1212	0.242013	0.3828	0.2781	5008	,	,		14359	0.2421		0.1183	False		,,,				2504	0.1534				p.A302A		Atlas-SNP	.											.	LINGO3	19	.	0			c.C906G						PASS	.	G		1256,2676		198,860,908	12.0	15.0	14.0		906	-9.0	0.2	19	dbSNP_116	14	848,7400		46,756,3322	no	coding-synonymous	LINGO3	NM_001101391.1		244,1616,4230	CC,CG,GG		10.2813,31.943,17.2742		302/593	2290870	2104,10076	1966	4124	6090	SO:0001819	synonymous_variant	645191	exon2			GGCCCCGGCCAGG	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"""Immunoglobulin superfamily / I-set domain containing"""	21206	protein-coding gene	gene with protein product		609792	"""leucine rich repeat neuronal 6B"""	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.906C>G	19.37:g.2290870G>C		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001101391		Silent	SNP	ENST00000585527.1	37	CCDS45905.1																																																																																			G|0.803;C|0.197	0.197	strong		0.687	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391	
EPB41L4B	54566	hgsc.bcm.edu	37	9	111938926	111938926	+	Silent	SNP	C	C	T	rs10979729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111938926C>T	ENST00000374566.3	-	25	3055	c.2538G>A	c.(2536-2538)ccG>ccA	p.P846P		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	846					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTGGGATCAGCGGGGAAGTCG	0.527													C|||	372	0.0742812	0.0076	0.1643	5008	,	,		19661	0.1052		0.0606	False		,,,				2504	0.0828				p.P846P		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.G2538A						PASS	.	C		66,3834		0,66,1884	67.0	71.0	70.0		2538	-6.5	0.7	9	dbSNP_120	70	438,7856		8,422,3717	no	coding-synonymous	EPB41L4B	NM_019114.3		8,488,5601	TT,TC,CC		5.2809,1.6923,4.1332		846/901	111938926	504,11690	1950	4147	6097	SO:0001819	synonymous_variant	54566	exon25			GATCAGCGGGGAA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.2538G>A	9.37:g.111938926C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	37	CCDS43859.1																																																																																			C|0.923;T|0.077	0.077	strong		0.527	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	
EDARADD	128178	hgsc.bcm.edu	37	1	236645609	236645609	+	Missense_Mutation	SNP	C	C	T	rs114632254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236645609C>T	ENST00000334232.4	+	6	475	c.308C>T	c.(307-309)tCc>tTc	p.S103F	EDARADD_ENST00000359362.5_Missense_Mutation_p.S93F	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	103			S -> F (in dbSNP:rs114632254). {ECO:0000269|PubMed:18231121}.		cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGTACTTGTTCCTCCTGCTTG	0.483													C|||	65	0.0129792	0.0008	0.0245	5008	,	,		16925	0.0		0.0398	False		,,,				2504	0.0072				p.S103F		Atlas-SNP	.											.	EDARADD	31	.	0			c.C308T						PASS	.	C	PHE/SER,PHE/SER	21,4385	29.0+/-57.7	0,21,2182	90.0	86.0	87.0		278,308	5.2	0.4	1	dbSNP_132	87	236,8364	96.1+/-157.9	2,232,4066	yes	missense,missense	EDARADD	NM_080738.3,NM_145861.2	155,155	2,253,6248	TT,TC,CC		2.7442,0.4766,1.976	possibly-damaging,possibly-damaging	93/206,103/216	236645609	257,12749	2203	4300	6503	SO:0001583	missense	128178	exon6			CTTGTTCCTCCTG	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.308C>T	1.37:g.236645609C>T	ENSP00000335076:p.Ser103Phe	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	37	CCDS1610.1	43	0.019688644688644688	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	32	0.04221635883905013	C	27.0	4.788745	0.90367	0.004766	0.027442	ENSG00000186197	ENST00000439430;ENST00000334232;ENST00000359362	T;T;D	0.82081	0.39;-0.99;-1.57	5.22	5.22	0.72569	.	0.214130	0.23215	U	0.050639	T	0.60353	0.2262	L	0.59436	1.845	0.23926	N	0.996444	P;P	0.49447	0.924;0.924	P;P	0.48030	0.564;0.564	T	0.70443	-0.4870	10	0.66056	D	0.02	.	14.5705	0.68208	0.0:0.8542:0.1458:0.0	.	93;103	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	F	81;103;93	ENSP00000405815:S81F;ENSP00000335076:S103F;ENSP00000352320:S93F	ENSP00000335076:S103F	S	+	2	0	EDARADD	234712232	0.985000	0.35326	0.417000	0.26559	0.852000	0.48524	2.573000	0.46007	2.720000	0.93068	0.655000	0.94253	TCC	C|0.980;T|0.020	0.020	strong		0.483	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861	
ELAVL1	1994	hgsc.bcm.edu	37	19	8028544	8028544	+	Silent	SNP	A	A	G	rs14394	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8028544A>G	ENST00000407627.2	-	6	933	c.804T>C	c.(802-804)ggT>ggC	p.G268G	ELAVL1_ENST00000593807.1_3'UTR|ELAVL1_ENST00000596459.1_Silent_p.G268G|ELAVL1_ENST00000351593.5_Silent_p.G295G	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	268	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TGGTGACGGCACCAAACGGCC	0.547													G|||	763	0.152356	0.1634	0.1585	5008	,	,		18524	0.0456		0.3101	False		,,,				2504	0.0808				p.G268G		Atlas-SNP	.											.	ELAVL1	44	.	0			c.T804C						PASS	.	G		871,3535	743.3+/-411.4	87,697,1419	135.0	115.0	121.0		804	-5.1	0.3	19	dbSNP_52	121	2454,6146	697.0+/-404.9	337,1780,2183	no	coding-synonymous	ELAVL1	NM_001419.2		424,2477,3602	GG,GA,AA		28.5349,19.7685,25.5651		268/327	8028544	3325,9681	2203	4300	6503	SO:0001819	synonymous_variant	1994	exon6			GACGGCACCAAAC	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.804T>C	19.37:g.8028544A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Silent	SNP	ENST00000407627.2	37	CCDS12193.1																																																																																			A|0.776;G|0.224	0.224	strong		0.547	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
RXRG	6258	hgsc.bcm.edu	37	1	165377552	165377552	+	Silent	SNP	G	G	A	rs2134095	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:165377552G>A	ENST00000359842.5	-	8	1352	c.1050C>T	c.(1048-1050)gtC>gtT	p.V350V	RXRG_ENST00000470566.1_5'Flank	NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	350	Ligand-binding. {ECO:0000250}.				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)	GCTCAGTTAGGACTCTGTTAA	0.433													A|||	2398	0.478834	0.2284	0.6023	5008	,	,		19617	0.5079		0.671	False		,,,				2504	0.502				p.V350V		Atlas-SNP	.											.	RXRG	91	.	0			c.C1050T						PASS	.	A		1364,3042	690.9+/-405.3	214,936,1053	121.0	107.0	112.0		1050	-4.1	0.5	1	dbSNP_96	112	5847,2753	436.9+/-358.5	1990,1867,443	no	coding-synonymous	RXRG	NM_006917.4		2204,2803,1496	AA,AG,GG		32.0116,30.9578,44.5564		350/464	165377552	7211,5795	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon8			AGTTAGGACTCTG	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.1050C>T	1.37:g.165377552G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	129	49	0.379845	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			G|0.486;A|0.514	0.514	strong		0.433	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
TBX4	9496	hgsc.bcm.edu	37	17	59557600	59557600	+	Missense_Mutation	SNP	C	C	T	rs3744438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59557600C>T	ENST00000240335.1	+	7	986	c.941C>T	c.(940-942)gCg>gTg	p.A314V	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Missense_Mutation_p.A314V	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	314			A -> V (in dbSNP:rs3744438).		angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TCACAGCTCGCGGAGCCGCAG	0.647													C|||	1068	0.213259	0.4402	0.134	5008	,	,		13484	0.1111		0.1213	False		,,,				2504	0.1626				p.A314V		Atlas-SNP	.											TBX4,mouth,carcinoma,-1,1	TBX4	69	1	0			c.C941T						PASS	.	C	VAL/ALA	1822,2584	528.6+/-372.4	381,1060,762	61.0	55.0	57.0		941	5.8	0.0	17	dbSNP_107	57	1070,7530	222.2+/-259.3	66,938,3296	yes	missense	TBX4	NM_018488.2	64	447,1998,4058	TT,TC,CC		12.4419,41.3527,22.2359	possibly-damaging	314/546	59557600	2892,10114	2203	4300	6503	SO:0001583	missense	9496	exon7			AGCTCGCGGAGCC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.941C>T	17.37:g.59557600C>T	ENSP00000240335:p.Ala314Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	374	0.17124542124542125	190	0.3861788617886179	43	0.11878453038674033	63	0.11013986013986014	78	0.10290237467018469	C	14.31	2.496648	0.44352	0.413527	0.124419	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.81499	-1.5;-1.5	5.84	5.84	0.93424	.	0.374762	0.29876	N	0.010974	T	0.00012	0.0000	L	0.36672	1.1	0.45979	P	0.0012090000000000156	P;P	0.46020	0.871;0.85	B;B	0.35240	0.198;0.041	T	0.25152	-1.0140	8	.	.	.	.	19.1261	0.93384	0.0:1.0:0.0:0.0	rs3744438;rs57055977;rs3744438	314;314	A5PKU7;P57082	.;TBX4_HUMAN	V	314	ENSP00000377435:A314V;ENSP00000240335:A314V	.	A	+	2	0	TBX4	56912382	0.289000	0.24334	0.011000	0.14972	0.022000	0.10575	4.496000	0.60360	2.779000	0.95612	0.655000	0.94253	GCG	C|0.789;T|0.211	0.211	strong		0.647	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
PAK7	57144	hgsc.bcm.edu	37	20	9543622	9543622	+	Missense_Mutation	SNP	C	C	T	rs2297345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	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		
MYOM3	127294	hgsc.bcm.edu	37	1	24413159	24413159	+	Silent	SNP	T	T	C	rs6424152	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24413159T>C	ENST00000374434.3	-	15	1935	c.1773A>G	c.(1771-1773)gaA>gaG	p.E591E	MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Silent_p.E591E|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Silent_p.E592E	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	591	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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)		AGGCGATGGGTTCGCTGGGCT	0.627													C|||	1877	0.3748	0.3646	0.353	5008	,	,		16925	0.4623		0.4463	False		,,,				2504	0.2403				p.E591E		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1773G						PASS	.	C		1365,2533		253,859,837	55.0	58.0	57.0		1773	-0.2	1.0	1	dbSNP_116	57	3544,4742		750,2044,1349	no	coding-synonymous	MYOM3	NM_152372.3		1003,2903,2186	CC,CT,TT		42.7709,35.018,40.2905		591/1438	24413159	4909,7275	1949	4143	6092	SO:0001819	synonymous_variant	127294	exon15			GATGGGTTCGCTG	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.1773A>G	1.37:g.24413159T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			T|0.602;C|0.398	0.398	strong		0.627	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
HIF1A	3091	hgsc.bcm.edu	37	14	62207553	62207553	+	Silent	SNP	G	G	A	rs34005929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:62207553G>A	ENST00000337138.4	+	12	2005	c.1740G>A	c.(1738-1740)ttG>ttA	p.L580L	HIF1A_ENST00000557538.1_Silent_p.L521L|HIF1A_ENST00000539097.1_Silent_p.L604L|HIF1A_ENST00000323441.6_Silent_p.L580L|HIF1A-AS2_ENST00000554254.1_lincRNA|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000394997.1_Silent_p.L581L	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	580	ID.|ODD.				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)	TCGATCAGTTGTCACCATTAG	0.423													G|||	7	0.00139776	0.0	0.0043	5008	,	,		19279	0.0		0.002	False		,,,				2504	0.002				p.L604L		Atlas-SNP	.											.	HIF1A	120	.	0			c.G1812A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	151.0	141.0	144.0		1740,1740	2.6	1.0	14	dbSNP_126	144	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous	HIF1A	NM_001530.3,NM_181054.2	,	0,29,6474	AA,AG,GG		0.3256,0.0227,0.223	,	580/827,580/736	62207553	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	3091	exon12			TCAGTTGTCACCA	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.1740G>A	14.37:g.62207553G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Silent	SNP	ENST00000337138.4	37	CCDS9753.1																																																																																			G|0.998;A|0.002	0.002	strong		0.423	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530	
SLC5A1	6523	hgsc.bcm.edu	37	22	32506050	32506050	+	Missense_Mutation	SNP	C	C	G	rs33954001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32506050C>G	ENST00000266088.4	+	15	2095	c.1845C>G	c.(1843-1845)caC>caG	p.H615Q	SLC5A1_ENST00000543737.1_Missense_Mutation_p.H488Q	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	615					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TAGAGCAGCACGGTGCACCCA	0.463													G|||	111	0.0221645	0.003	0.0259	5008	,	,		20384	0.0		0.0606	False		,,,				2504	0.0286				p.H615Q		Atlas-SNP	.											.	SLC5A1	80	.	0			c.C1845G	GRCh37	CM961339	SLC5A1	M	rs33954001	PASS	.	G	GLN/HIS	61,4345	820.7+/-416.4	0,61,2142	173.0	145.0	154.0		1845	2.9	0.6	22	dbSNP_126	154	601,7999	792.5+/-407.5	20,561,3719	yes	missense	SLC5A1	NM_000343.3	24	20,622,5861	GG,GC,CC		6.9884,1.3845,5.09	benign	615/665	32506050	662,12344	2203	4300	6503	SO:0001583	missense	6523	exon15			GCAGCACGGTGCA		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1845C>G	22.37:g.32506050C>G	ENSP00000266088:p.His615Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	37	CCDS13902.1	65	0.02976190476190476	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	53	0.06992084432717678	G	0.014	-1.579169	0.00879	0.013845	0.069884	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.87103	-1.87;-2.21	5.2	2.94	0.34122	.	0.847000	0.11120	N	0.597485	T	0.09247	0.0228	N	0.00436	-1.5	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.31641	-0.9936	10	0.09084	T	0.74	.	4.8205	0.13389	0.0742:0.2303:0.5061:0.1893	rs33954001;rs45589234	615	P13866	SC5A1_HUMAN	Q	615;488	ENSP00000266088:H615Q;ENSP00000444898:H488Q	ENSP00000266088:H615Q	H	+	3	2	SLC5A1	30836050	0.775000	0.28604	0.622000	0.29159	0.170000	0.22686	0.052000	0.14163	0.073000	0.16731	-0.127000	0.14921	CAC	C|0.953;G|0.047	0.047	strong		0.463	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23049292	23049292	+	Missense_Mutation	SNP	C	C	T	rs2230229	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:23049292C>T	ENST00000221132.3	-	10	1386	c.1322G>A	c.(1321-1323)aGa>aAa	p.R441K	RP11-1149O23.2_ENST00000518308.1_RNA	NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	441	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.		R -> K (in dbSNP:rs2230229). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9082980, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)			NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		AATCTTCTCTCTTGCATGTCT	0.488													T|||	4570	0.91254	0.8759	0.902	5008	,	,		14055	0.9772		0.8628	False		,,,				2504	0.954				p.R441K		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.G1322A						PASS	.	T	LYS/ARG	3773,633	273.1+/-271.2	1614,545,44	137.0	121.0	127.0		1322	-2.6	0.0	8	dbSNP_98	127	7273,1327	261.0+/-283.6	3079,1115,106	yes	missense	TNFRSF10A	NM_003844.3	26	4693,1660,150	TT,TC,CC		15.4302,14.3668,15.07	benign	441/469	23049292	11046,1960	2203	4300	6503	SO:0001583	missense	8797	exon10			TTCTCTCTTGCAT	U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.1322G>A	8.37:g.23049292C>T	ENSP00000221132:p.Arg441Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1965	0.8997252747252747	437	0.8882113821138211	321	0.8867403314917127	558	0.9755244755244755	649	0.8562005277044855	T	0.546	-0.851516	0.02651	0.856332	0.845698	ENSG00000104689	ENST00000221132	D	0.85556	-2.0	3.43	-2.61	0.06171	Death (3);DEATH-like (2);	0.681612	0.12988	N	0.422740	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32214	-0.9915	9	0.02654	T	1	.	6.4331	0.21809	0.2135:0.6077:0.0:0.1788	rs2230229;rs17856410;rs52803224;rs59918525;rs2230229	441	O00220	TR10A_HUMAN	K	441	ENSP00000221132:R441K	ENSP00000221132:R441K	R	-	2	0	TNFRSF10A	23105237	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.512000	0.06313	-0.983000	0.03511	-0.521000	0.04368	AGA	C|0.120;T|0.880	0.880	strong		0.488	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
CCDC7	79741	hgsc.bcm.edu	37	10	32780886	32780886	+	Missense_Mutation	SNP	T	T	C	rs145255525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32780886T>C	ENST00000362006.5	+	10	1376	c.833T>C	c.(832-834)aTg>aCg	p.M278T	CCDC7_ENST00000489718.1_3'UTR|CCDC7_ENST00000535327.1_Intron|CCDC7_ENST00000277657.6_Missense_Mutation_p.M278T|CCDC7_ENST00000539197.1_Intron|CCDC7_ENST00000545067.1_Intron|CCDC7_ENST00000537047.1_3'UTR	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	278										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				TTTAATGCCATGTTGAAAGTA	0.249																																					p.M278T		Atlas-SNP	.											.	CCDC7	47	.	0			c.T833C						PASS	.	T	THR/MET,THR/MET	0,4406		0,0,2203	76.0	85.0	82.0		833,833	4.1	0.5	10	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense,missense	CCDC7	NM_001026383.1,NM_145023.4	81,81	0,4,6494	CC,CT,TT		0.0466,0.0,0.0308	possibly-damaging,possibly-damaging	278/487,278/487	32780886	4,12992	2203	4295	6498	SO:0001583	missense	221016	exon10			ATGCCATGTTGAA	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.833T>C	10.37:g.32780886T>C	ENSP00000355078:p.Met278Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248137	0.39697	0.0	4.66E-4	ENSG00000216937	ENST00000277657;ENST00000362006	T;T	0.38077	1.16;1.16	4.13	4.13	0.48395	.	.	.	.	.	T	0.40322	0.1112	L	0.36672	1.1	0.80722	D	1	D	0.54964	0.969	P	0.55087	0.768	T	0.28202	-1.0051	9	0.72032	D	0.01	-22.3335	9.8398	0.40991	0.0:0.0:0.0:1.0	.	278	Q96M83	CCDC7_HUMAN	T	278	ENSP00000277657:M278T;ENSP00000355078:M278T	ENSP00000277657:M278T	M	+	2	0	CCDC7	32820892	0.994000	0.37717	0.468000	0.27192	0.520000	0.34377	2.364000	0.44187	2.098000	0.63641	0.459000	0.35465	ATG	T|1.000;C|0.000	0.000	strong		0.249	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
MYOM3	127294	hgsc.bcm.edu	37	1	24393563	24393563	+	Missense_Mutation	SNP	C	C	T	rs16829071	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24393563C>T	ENST00000374434.3	-	28	3533	c.3371G>A	c.(3370-3372)cGg>cAg	p.R1124Q	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000329601.7_Missense_Mutation_p.R1124Q|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000338909.5_5'Flank|MYOM3_ENST00000330966.7_Missense_Mutation_p.R1127Q	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1124	Ig-like C2-type 3.		R -> Q (in dbSNP:rs16829071). {ECO:0000269|PubMed:15489334}.			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)		CTGCAACGGCCGCTCAAAATA	0.637													T|||	1404	0.280351	0.4871	0.1599	5008	,	,		16492	0.1964		0.1421	False		,,,				2504	0.3149				p.R1124Q		Atlas-SNP	.											.	MYOM3	131	.	0			c.G3371A						PASS	.	T	GLN/ARG	1438,2592		264,910,841	19.0	21.0	20.0		3371	5.5	0.8	1	dbSNP_123	20	1155,7167		85,985,3091	yes	missense	MYOM3	NM_152372.3	43	349,1895,3932	TT,TC,CC		13.8789,35.6824,20.9926	benign	1124/1438	24393563	2593,9759	2015	4161	6176	SO:0001583	missense	127294	exon28			AACGGCCGCTCAA	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.3371G>A	1.37:g.24393563C>T	ENSP00000363557:p.Arg1124Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	469	0.21474358974358973	196	0.3983739837398374	61	0.1685082872928177	109	0.19055944055944055	103	0.1358839050131926	T	14.02	2.411762	0.42817	0.356824	0.138789	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.54071	0.64;0.59;0.64	5.53	5.53	0.82687	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.166494	0.52532	N	0.000073	T	0.00012	0.0000	N	0.08118	0	0.58432	P	9.000000000036756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34900	-0.9810	9	0.54805	T	0.06	.	11.5382	0.50651	0.0:0.0703:0.0:0.9297	rs16829071;rs52795219;rs16829071	1124;1124	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	Q	1124;1127;1124	ENSP00000363557:R1124Q;ENSP00000332670:R1127Q;ENSP00000328415:R1124Q	ENSP00000328415:R1124Q	R	-	2	0	MYOM3	24266150	1.000000	0.71417	0.793000	0.32043	0.105000	0.19272	5.362000	0.66098	0.941000	0.37499	-0.490000	0.04691	CGG	C|0.765;T|0.235	0.235	strong		0.637	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273293	56273293	+	Missense_Mutation	SNP	G	G	A	rs2019946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	378	1	0.0026455		WXS	Illumina HiSeq	Phase_I	455	71	0.156044	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	
KYNU	8942	hgsc.bcm.edu	37	2	143798189	143798189	+	Missense_Mutation	SNP	A	A	G	rs9013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:143798189A>G	ENST00000264170.4	+	13	1492	c.1234A>G	c.(1234-1236)Aaa>Gaa	p.K412E	KYNU_ENST00000409512.1_Missense_Mutation_p.K412E	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TGTTCCAAACAAAGATGTTTT	0.398													A|||	880	0.175719	0.1422	0.0908	5008	,	,		19752	0.2738		0.1879	False		,,,				2504	0.1677				p.K412E		Atlas-SNP	.											.	KYNU	110	.	0			c.A1234G						PASS	.	A	GLU/LYS,GLU/LYS	614,3792	265.3+/-266.6	52,510,1641	50.0	47.0	48.0		1234,1234	4.4	0.0	2	dbSNP_52	48	1481,7119	278.7+/-293.6	133,1215,2952	yes	missense,missense	KYNU	NM_001199241.1,NM_003937.2	56,56	185,1725,4593	GG,GA,AA		17.2209,13.9355,16.108	benign,benign	412/466,412/466	143798189	2095,10911	2203	4300	6503	SO:0001583	missense	8942	exon14			CCAAACAAAGATG	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"""L-kynurenine hydrolase"""	605197	"""kynureninase (L-kynurenine hydrolase)"""			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.1234A>G	2.37:g.143798189A>G	ENSP00000264170:p.Lys412Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001199241		Missense_Mutation	SNP	ENST00000264170.4	37	CCDS2183.1	401	0.18360805860805862	68	0.13821138211382114	41	0.1132596685082873	161	0.28146853146853146	131	0.17282321899736147	A	0.005	-2.138038	0.00335	0.139355	0.172209	ENSG00000115919	ENST00000264170;ENST00000409512	T;T	0.53206	0.63;0.63	5.54	4.36	0.52297	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.537909	0.21696	N	0.070493	T	0.00012	0.0000	L	0.33189	0.99	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.13019	-1.0525	9	0.02654	T	1	.	12.6349	0.56677	0.8614:0.1386:0.0:0.0	rs9013;rs1058039;rs2070091;rs3204588;rs11548541;rs17342017;rs17349746;rs61368383;rs9013	412	Q16719	KYNU_HUMAN	E	412	ENSP00000264170:K412E;ENSP00000386731:K412E	ENSP00000264170:K412E	K	+	1	0	KYNU	143514659	0.043000	0.20138	0.001000	0.08648	0.063000	0.16089	1.857000	0.39399	0.904000	0.36572	-0.435000	0.05868	AAA	A|0.832;G|0.168	0.168	strong		0.398	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998	
NLRP2	55655	hgsc.bcm.edu	37	19	55494188	55494188	+	Silent	SNP	C	C	T	rs3826883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55494188C>T	ENST00000543010.1	+	6	1265	c.1122C>T	c.(1120-1122)gaC>gaT	p.D374D	NLRP2_ENST00000427260.2_Silent_p.D351D|NLRP2_ENST00000448584.2_Silent_p.D374D|NLRP2_ENST00000538819.1_Silent_p.D350D|NLRP2_ENST00000391721.4_Silent_p.D350D|NLRP2_ENST00000263437.6_Silent_p.D371D|NLRP2_ENST00000339757.7_Silent_p.D352D|NLRP2_ENST00000537859.1_Silent_p.D352D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	374	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		ACTTTGGAGACGAGGACCAAG	0.622													C|||	546	0.109026	0.0794	0.1412	5008	,	,		18151	0.0516		0.2386	False		,,,				2504	0.0521				p.D374D		Atlas-SNP	.											.	NLRP2	161	.	0			c.C1122T						PASS	.	C	,,,	459,3947	208.8+/-229.8	28,403,1772	25.0	25.0	25.0		1122,1056,1053,1122	-3.3	0.0	19	dbSNP_107	25	1926,6662	317.0+/-313.0	221,1484,2589	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	249,1887,4361	TT,TC,CC		22.4266,10.4176,18.3546	,,,	374/1063,352/1041,351/1040,374/1063	55494188	2385,10609	2203	4294	6497	SO:0001819	synonymous_variant	55655	exon6			TGGAGACGAGGAC	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.1122C>T	19.37:g.55494188C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			C|0.833;T|0.167	0.167	strong		0.622	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
CPSF1	29894	hgsc.bcm.edu	37	8	145634452	145634452	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145634452C>T	ENST00000349769.3	-	2	185	c.91G>A	c.(91-93)Gta>Ata	p.V31I	GS1-393G12.14_ENST00000607491.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	31					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCGGCCACTACCAGGTTGCGC	0.652																																					p.V31I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G91A						PASS	.						132.0	126.0	128.0					8																	145634452		2203	4300	6503	SO:0001583	missense	29894	exon2			CCACTACCAGGTT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.91G>A	8.37:g.145634452C>T	ENSP00000339353:p.Val31Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	37	6.015090	0.97205	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	T	0.55760	0.5	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000003	T	0.60856	0.2301	L	0.57536	1.79	0.80722	D	1	P;P	0.47545	0.675;0.897	B;P	0.51945	0.254;0.685	T	0.57894	-0.7732	10	0.31617	T	0.26	-0.1634	16.1609	0.81704	0.0:1.0:0.0:0.0	.	31;31	B4DEF4;Q10570	.;CPSF1_HUMAN	I	31	ENSP00000339353:V31I	ENSP00000339353:V31I	V	-	1	0	CPSF1	145605260	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.070000	0.76763	2.415000	0.81967	0.561000	0.74099	GTA	.	.	none		0.652	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
SGSM2	9905	hgsc.bcm.edu	37	17	2266812	2266812	+	Silent	SNP	T	T	C	rs2003968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2266812T>C	ENST00000426855.2	+	7	901	c.726T>C	c.(724-726)tgT>tgC	p.C242C	SGSM2_ENST00000574563.1_Silent_p.C242C|SGSM2_ENST00000268989.3_Silent_p.C242C	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	242					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TGGCTGCCTGTGCCCGCGAGT	0.642													C|||	2836	0.566294	0.5431	0.3444	5008	,	,		16364	0.7639		0.4314	False		,,,				2504	0.6902				p.C242C		Atlas-SNP	.											SGSM2,rectum,carcinoma,0,1	SGSM2	60	1	0			c.T726C						PASS	.	C	,	2372,2034		640,1092,471	25.0	28.0	27.0		726,726	-11.5	0.1	17	dbSNP_92	27	3921,4677		893,2135,1271	yes	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	1533,3227,1742	CC,CT,TT		45.6036,46.1643,48.3928	,	242/1007,242/1052	2266812	6293,6711	2203	4299	6502	SO:0001819	synonymous_variant	9905	exon7			TGCCTGTGCCCGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.726T>C	17.37:g.2266812T>C		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																			C|0.502;T|0.498	0.502	strong		0.642	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
KLHL38	340359	hgsc.bcm.edu	37	8	124658210	124658210	+	Silent	SNP	C	C	T	rs16898671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:124658210C>T	ENST00000325995.7	-	3	1538	c.1515G>A	c.(1513-1515)gcG>gcA	p.A505A	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	505										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CTTTCATGTCCGCACATTTGA	0.512													c|||	805	0.160743	0.2133	0.0821	5008	,	,		20655	0.1637		0.1014	False		,,,				2504	0.2035				p.A505A		Atlas-SNP	.											KLHL38,NS,carcinoma,-1,2	KLHL38	81	2	0			c.G1515A						PASS	.	T		802,3380		70,662,1359	82.0	89.0	87.0		1515	-5.2	1.0	8	dbSNP_123	87	1000,7460		51,898,3281	no	coding-synonymous	KLHL38	NM_001081675.2		121,1560,4640	TT,TC,CC		11.8203,19.1774,14.2541		505/582	124658210	1802,10840	2091	4230	6321	SO:0001819	synonymous_variant	340359	exon3			CATGTCCGCACAT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1515G>A	8.37:g.124658210C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			C|0.859;T|0.141	0.141	strong		0.512	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
CLCNKA	1187	hgsc.bcm.edu	37	1	16360137	16360137	+	Missense_Mutation	SNP	C	C	T	rs12746751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16360137C>T	ENST00000331433.4	+	20	2067	c.2048C>T	c.(2047-2049)cCg>cTg	p.P683L	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.P682L|CLCNKA_ENST00000439316.2_Missense_Mutation_p.P640L|CLCNKA_ENST00000420078.1_Missense_Mutation_p.P682L			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	683	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.		P -> L (in dbSNP:rs12746751).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	CTGACAAATCCGCCAGCTCCA	0.567													C|||	303	0.0605032	0.1036	0.0504	5008	,	,		13686	0.006		0.0775	False		,,,				2504	0.0481				p.P683L		Atlas-SNP	.											.	CLCNKA	56	.	0			c.C2048T						PASS	.	C	LEU/PRO,LEU/PRO	513,3893	227.8+/-242.9	29,455,1719	83.0	83.0	83.0		2045,2048	3.7	0.3	1	dbSNP_121	83	807,7793	184.7+/-232.6	37,733,3530	no	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	98,98	66,1188,5249	TT,TC,CC		9.3837,11.6432,10.1492	possibly-damaging,possibly-damaging	682/687,683/688	16360137	1320,11686	2203	4300	6503	SO:0001583	missense	1187	exon20			CAAATCCGCCAGC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.2048C>T	1.37:g.16360137C>T	ENSP00000332771:p.Pro683Leu	Somatic	339	1	0.00294985		WXS	Illumina HiSeq	Phase_I	259	107	0.413127	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	129	0.059065934065934064	48	0.0975609756097561	21	0.058011049723756904	4	0.006993006993006993	56	0.07387862796833773	c	14.68	2.606533	0.46527	0.116432	0.093837	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.84370	-1.79;-1.79;-1.84;-1.79	3.73	3.73	0.42828	Cystathionine beta-synthase, core (1);	0.135063	0.48286	D	0.000186	T	0.16342	0.0393	M	0.76838	2.35	0.21020	P	0.999802966	D;D;D	0.89917	1.0;0.999;0.999	D;P;P	0.77004	0.989;0.866;0.866	T	0.67118	-0.5751	9	0.72032	D	0.01	.	11.1831	0.48640	0.0:1.0:0.0:0.0	rs12746751	640;682;683	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	L	682;682;640;683	ENSP00000364844:P682L;ENSP00000410353:P682L;ENSP00000414445:P640L;ENSP00000332771:P683L	ENSP00000332771:P683L	P	+	2	0	CLCNKA	16232724	0.868000	0.29978	0.272000	0.24630	0.024000	0.10985	3.811000	0.55620	2.060000	0.61445	0.313000	0.20887	CCG	C|0.917;T|0.083	0.083	strong		0.567	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257352	68257352	+	Missense_Mutation	SNP	T	T	A	rs17192170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:68257352T>A	ENST00000347230.4	-	15	2830	c.2692A>T	c.(2692-2694)Acc>Tcc	p.T898S	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T898S	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	898			T -> S (in dbSNP:rs17192170).		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)		CTCCGAATGGTGCTGCTACCC	0.547													T|||	215	0.0429313	0.0061	0.0648	5008	,	,		20189	0.0		0.1153	False		,,,				2504	0.047				p.T898S		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A2692T						PASS	.	T	SER/THR	122,4284	91.6+/-130.3	4,114,2085	149.0	118.0	128.0		2692	2.4	1.0	14	dbSNP_123	128	1032,7568	219.9+/-257.8	61,910,3329	yes	missense	ZFYVE26	NM_015346.3	58	65,1024,5414	AA,AT,TT		12.0,2.769,8.8728	benign	898/2540	68257352	1154,11852	2203	4300	6503	SO:0001583	missense	23503	exon15			GAATGGTGCTGCT	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.2692A>T	14.37:g.68257352T>A	ENSP00000251119:p.Thr898Ser	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	218	106	0.486239	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	102	0.046703296703296704	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	74	0.09762532981530343	T	12.54	1.967920	0.34754	0.02769	0.12	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.28895	1.73;1.59	5.95	2.38	0.29361	.	0.540708	0.19473	N	0.113394	T	0.00300	0.0009	M	0.65975	2.015	0.34490	P	0.29508900000000005	B;B	0.23128	0.041;0.08	B;B	0.19946	0.027;0.023	T	0.18461	-1.0336	9	0.06494	T	0.89	-15.8916	2.4765	0.04577	0.1242:0.1348:0.1296:0.6114	rs17192170;rs52807491;rs17192170	898;898	G3V2D8;Q68DK2	.;ZFY26_HUMAN	S	898;877;898	ENSP00000251119:T898S;ENSP00000450603:T898S	ENSP00000251119:T898S	T	-	1	0	ZFYVE26	67327105	1.000000	0.71417	0.991000	0.47740	0.836000	0.47400	1.256000	0.32921	0.504000	0.28082	-0.336000	0.08194	ACC	T|0.932;A|0.068	0.068	strong		0.547	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
OR10A4	283297	hgsc.bcm.edu	37	11	6898663	6898663	+	Missense_Mutation	SNP	G	G	A	rs10839635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6898663G>A	ENST00000379829.2	+	1	808	c.785G>A	c.(784-786)cGa>cAa	p.R262Q		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	262			R -> Q (in dbSNP:rs10839635). {ECO:0000269|PubMed:15489334}.		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)		ACGTATTTCCGACCCCAATCC	0.522													G|||	1548	0.309105	0.2042	0.2882	5008	,	,		19605	0.3988		0.325	False		,,,				2504	0.3569				p.R262Q		Atlas-SNP	.											OR10A4,NS,carcinoma,-1,1	OR10A4	65	1	0			c.G785A						PASS	.		GLN/ARG	1040,3362	382.5+/-324.5	134,772,1295	171.0	140.0	150.0		785	4.0	0.9	11	dbSNP_120	150	2442,6150	402.8+/-347.6	362,1718,2216	yes	missense	OR10A4	NM_207186.2	43	496,2490,3511	AA,AG,GG		28.4218,23.6256,26.797	possibly-damaging	262/316	6898663	3482,9512	2201	4296	6497	SO:0001583	missense	283297	exon1			ATTTCCGACCCCA	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.785G>A	11.37:g.6898663G>A	ENSP00000369157:p.Arg262Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_207186	B2RNP5|B9EH36|Q96R20	Missense_Mutation	SNP	ENST00000379829.2	37	CCDS7774.1	649	0.29716117216117216	95	0.19308943089430894	102	0.281767955801105	202	0.3531468531468531	250	0.32981530343007914	g	9.692	1.152108	0.21371	0.236256	0.284218	ENSG00000170782	ENST00000379829	T	0.37235	1.21	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37530	N	0.002055	T	0.00012	0.0000	N	0.20357	0.565	0.39828	P	0.027078999999999964	P	0.48230	0.907	P	0.49953	0.627	T	0.35674	-0.9779	9	0.15952	T	0.53	.	7.8776	0.29603	0.1097:0.0:0.8903:0.0	rs10839635;rs52822008;rs60284173;rs10839635	262	Q9H209	O10A4_HUMAN	Q	262	ENSP00000369157:R262Q	ENSP00000369157:R262Q	R	+	2	0	OR10A4	6855239	0.001000	0.12720	0.916000	0.36221	0.131000	0.20780	0.803000	0.27083	2.554000	0.86153	0.651000	0.88453	CGA	G|0.724;A|0.276	0.276	strong		0.522	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186	
PRB4	5545	hgsc.bcm.edu	37	12	11461802	11461802	+	Nonsense_Mutation	SNP	G	G	A	rs12829245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11461802G>A	ENST00000535904.1	-	3	148	c.115C>T	c.(115-117)Cga>Tga	p.R39*	PRB4_ENST00000445719.2_Nonsense_Mutation_p.R39*|PRB4_ENST00000279575.1_Nonsense_Mutation_p.R39*			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	39	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.			LISGKPEGR -> IIPPKPPG (in Ref. 5; AA sequence). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TGTGGGCGTCGTCCTTCTGGC	0.547										HNSCC(22;0.051)			G|||	377	0.0752796	0.0113	0.1787	5008	,	,		23181	0.002		0.1839	False		,,,				2504	0.0521				p.R39X		Atlas-SNP	.											.	PRB4	59	.	0			c.C115T						PASS	.	G	stop/ARG	178,4216		2,174,2021	187.0	200.0	196.0		115	-0.7	0.0	12	dbSNP_121	196	1578,7006		48,1482,2762	no	stop-gained	PRB4	NM_002723.3		50,1656,4783	AA,AG,GG		18.383,4.051,13.5306		39/248	11461802	1756,11222	2197	4292	6489	SO:0001587	stop_gained	5545	exon3			GGCGTCGTCCTTC		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.115C>T	12.37:g.11461802G>A	ENSP00000442834:p.Arg39*	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	18	0.290323	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Nonsense_Mutation	SNP	ENST00000535904.1	37	CCDS8641.1	217	0.09935897435897435	9	0.018292682926829267	64	0.17679558011049723	2	0.0034965034965034965	142	0.18733509234828497	.	10.92	1.485680	0.26686	0.04051	0.18383	ENSG00000230657	ENST00000279575;ENST00000535904;ENST00000445719	.	.	.	0.419	-0.661	0.11417	.	.	.	.	.	.	.	.	.	.	.	0.23016	P	0.99842989	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	.	.	.	rs12829245	.	.	.	X	39	.	ENSP00000279575:R39X	R	-	1	2	PRB4	11353069	0.000000	0.05858	0.015000	0.15790	0.098000	0.18820	-1.823000	0.01710	-0.433000	0.07286	0.195000	0.17529	CGA	G|0.900;A|0.100	0.100	strong		0.547	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
EMC1	23065	hgsc.bcm.edu	37	1	19565338	19565338	+	Missense_Mutation	SNP	C	C	T	rs709682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19565338C>T	ENST00000477853.1	-	10	1082	c.1040G>A	c.(1039-1041)aGt>aAt	p.S347N	EMC1_ENST00000375208.3_Missense_Mutation_p.S325N|EMC1_ENST00000375199.3_Missense_Mutation_p.S346N|RP1-43E13.2_ENST00000437898.1_RNA	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	347			S -> N (in dbSNP:rs709682). {ECO:0000269|PubMed:16303743}.			ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)		p.S347N(1)									ATCTTCAGAACTGCTACTTTT	0.468													T|||	852	0.170128	0.3162	0.098	5008	,	,		18740	0.124		0.1173	False		,,,				2504	0.1258				p.S347N		Atlas-SNP	.											KIAA0090,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G1040A						PASS	.	T	ASN/SER	1304,3102	697.9+/-406.3	204,896,1103	124.0	132.0	129.0		1040	-0.3	0.5	1	dbSNP_86	129	1192,7408	764.2+/-407.6	96,1000,3204	yes	missense	KIAA0090	NM_015047.1	46	300,1896,4307	TT,TC,CC		13.8605,29.596,19.1911	benign	347/994	19565338	2496,10510	2203	4300	6503	SO:0001583	missense	23065	exon10			TCAGAACTGCTAC		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.1040G>A	1.37:g.19565338C>T	ENSP00000420608:p.Ser347Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_001271428	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	376	0.17216117216117216	177	0.3597560975609756	36	0.09944751381215469	66	0.11538461538461539	97	0.1279683377308707	T	11.32	1.602931	0.28534	0.29596	0.138605	ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208	T;T;T	0.24151	1.9;1.87;1.89	6.17	-0.272	0.12919	.	0.884235	0.10526	N	0.664347	T	0.00012	0.0000	L	0.36672	1.1	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.0	T	0.48410	-0.9038	9	0.17832	T	0.49	0.3363	6.7827	0.23654	0.1082:0.5551:0.0:0.3367	rs709682;rs52798866;rs59494929;rs709682	325;346;347;347	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.;.;.;K0090_HUMAN	N	347;346;325	ENSP00000420608:S347N;ENSP00000364345:S346N;ENSP00000364354:S325N	ENSP00000364345:S346N	S	-	2	0	KIAA0090	19437925	0.013000	0.17824	0.478000	0.27316	0.893000	0.52053	-0.513000	0.06305	-0.571000	0.06014	-0.254000	0.11334	AGT	C|0.816;T|0.184	0.184	strong		0.468	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
VN1R1	57191	hgsc.bcm.edu	37	19	57967049	57967049	+	Missense_Mutation	SNP	G	G	T	rs61744949	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57967049G>T	ENST00000321039.3	-	1	805	c.806C>A	c.(805-807)gCc>gAc	p.A269D	AC004076.9_ENST00000415705.3_5'UTR|AC004076.9_ENST00000596831.1_Missense_Mutation_p.P107T	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	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	241	118	0.489627	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	
EME1	146956	hgsc.bcm.edu	37	17	48455985	48455985	+	Silent	SNP	A	A	T	rs2189712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48455985A>T	ENST00000338165.4	+	4	1015	c.933A>T	c.(931-933)acA>acT	p.T311T	EME1_ENST00000511648.2_Silent_p.T311T|EME1_ENST00000393271.2_Silent_p.T311T	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	311					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)	p.T311T(1)		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)			AGGAGCCAACAGTACTGGTGT	0.587								Direct reversal of damage;Homologous recombination					A|||	715	0.142772	0.0416	0.2911	5008	,	,		18564	0.0794		0.2465	False		,,,				2504	0.1329				p.T311T		Atlas-SNP	.											EME1,NS,carcinoma,0,1	EME1	39	1	1	Substitution - coding silent(1)	stomach(1)	c.A933T						PASS	.	A	,	356,4050	184.0+/-211.4	21,314,1868	150.0	148.0	149.0		933,933	-1.3	0.1	17	dbSNP_96	149	2244,6356	380.3+/-339.6	297,1650,2353	no	coding-synonymous,coding-synonymous	EME1	NM_001166131.1,NM_152463.2	,	318,1964,4221	TT,TA,AA		26.093,8.0799,19.9908	,	311/584,311/571	48455985	2600,10406	2203	4300	6503	SO:0001819	synonymous_variant	146956	exon4			GCCAACAGTACTG	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.933A>T	17.37:g.48455985A>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_152463	Q96N62	Silent	SNP	ENST00000338165.4	37	CCDS11565.1	340	0.15567765567765568	19	0.03861788617886179	94	0.2596685082872928	43	0.07517482517482517	184	0.24274406332453827	A	2.611	-0.290728	0.05568	0.080799	0.26093	ENSG00000154920	ENST00000511519	T	0.19394	2.15	5.32	-1.3	0.09259	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41124	-0.9526	5	0.87932	D	0	-20.2006	0.2198	0.00167	0.331:0.212:0.2412:0.2157	rs2189712;rs2189712	.	.	.	C	153	ENSP00000423029:S153C	ENSP00000423029:S153C	S	+	1	0	EME1	45810984	0.000000	0.05858	0.071000	0.20095	0.004000	0.04260	-0.478000	0.06575	0.137000	0.18759	-0.366000	0.07423	AGT	A|0.812;T|0.188	0.188	strong		0.587	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
PRKRA	8575	hgsc.bcm.edu	37	2	179300971	179300971	+	Silent	SNP	G	G	A	rs62176107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179300971G>A	ENST00000325748.4	-	7	885	c.685C>T	c.(685-687)Ctg>Ttg	p.L229L	AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000432031.2_Silent_p.L218L|PRKRA_ENST00000438687.3_Silent_p.L116L|AC009948.5_ENST00000436616.2_RNA|PRKRA_ENST00000487082.1_Silent_p.L204L	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	229	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CTTCTTTTCAGTAAGTTGATC	0.353																																					p.L229L	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,colon,carcinoma,0,1	PRKRA	56	1	0			c.C685T						PASS	.						156.0	180.0	172.0					2																	179300971		2203	4300	6503	SO:0001819	synonymous_variant	8575	exon7			TTTTCAGTAAGTT	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.685C>T	2.37:g.179300971G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	32	0.333333	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Silent	SNP	ENST00000325748.4	37	CCDS2279.1																																																																																			G|0.775;A|0.225	0.225	strong		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
CROCC	9696	hgsc.bcm.edu	37	1	17263290	17263290	+	Missense_Mutation	SNP	G	G	A	rs57442576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17263290G>A	ENST00000375541.5	+	9	1184	c.1115G>A	c.(1114-1116)cGg>cAg	p.R372Q	CROCC_ENST00000467938.1_3'UTR	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)		GAGCAGCTGCGGGACAAGGTG	0.682													g|||	464	0.0926518	0.152	0.0677	5008	,	,		25223	0.0377		0.1024	False		,,,				2504	0.0767				p.R372Q		Atlas-SNP	.											.	CROCC	185	.	0			c.G1115A						PASS	.	G	GLN/ARG	659,3745		4,651,1547	37.0	34.0	35.0		1115	-2.8	0.1	1	dbSNP_129	35	749,7845		2,745,3550	no	missense	CROCC	NM_014675.3	43	6,1396,5097	AA,AG,GG		8.7154,14.9637,10.8324	benign	372/2018	17263290	1408,11590	2202	4297	6499	SO:0001583	missense	9696	exon9			AGCTGCGGGACAA	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.1115G>A	1.37:g.17263290G>A	ENSP00000364691:p.Arg372Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	92	28	0.304348	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	182	0.08333333333333333	71	0.1443089430894309	23	0.06353591160220995	18	0.03146853146853147	70	0.09234828496042216	G	12.85	2.062876	0.36373	0.149637	0.087154	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11169	2.8	4.1	-2.84	0.05751	.	.	.	.	.	T	0.00039	0.0001	L	0.28458	0.855	0.46317	P	0.0010109999999999841	B;B;B	0.25809	0.135;0.068;0.002	B;B;B	0.14023	0.01;0.005;0.002	T	0.45629	-0.9248	8	0.15499	T	0.54	.	10.356	0.43964	0.5601:0.0:0.4399:0.0	rs57442576	235;235;372	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	Q	372;253	ENSP00000364691:R372Q	ENSP00000364691:R372Q	R	+	2	0	CROCC	17135877	1.000000	0.71417	0.053000	0.19242	0.481000	0.33189	0.626000	0.24492	-0.699000	0.05077	-0.362000	0.07510	CGG	G|0.924;A|0.076	0.076	strong		0.682	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SEC16B	89866	hgsc.bcm.edu	37	1	177933344	177933344	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177933344A>G	ENST00000308284.6	-	5	693	c.604T>C	c.(604-606)Ttt>Ctt	p.F202L	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000464631.2_Missense_Mutation_p.F202L	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	202	Required for endoplasmic reticulum localization.				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						CTCCCTGGAAACAGCTCCCCC	0.557																																					p.F202L		Atlas-SNP	.											.	SEC16B	92	.	0			c.T604C						PASS	.						50.0	53.0	52.0					1																	177933344		1948	4130	6078	SO:0001583	missense	89866	exon5			CTGGAAACAGCTC	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.604T>C	1.37:g.177933344A>G	ENSP00000308339:p.Phe202Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	A	0.430	-0.903732	0.02453	.	.	ENSG00000120341	ENST00000308284;ENST00000464631	T;T	0.39229	2.65;1.09	4.91	-4.56	0.03431	.	1.235800	0.05332	N	0.528496	T	0.20455	0.0492	N	0.15975	0.35	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	0.21008	-1.0258	10	0.11485	T	0.65	2.0E-4	6.3453	0.21345	0.4249:0.0:0.4488:0.1264	.	202;202;202	E9PK14;B1AM08;Q96JE7	.;.;SC16B_HUMAN	L	202	ENSP00000308339:F202L;ENSP00000431727:F202L	ENSP00000308339:F202L	F	-	1	0	AL359075.1	176199967	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.207000	0.09384	-0.739000	0.04809	-0.290000	0.09829	TTT	.	.	none		0.557	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
ZNF773	374928	hgsc.bcm.edu	37	19	58018618	58018618	+	Silent	SNP	A	A	G	rs2074064	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58018618A>G	ENST00000282292.4	+	4	1295	c.1155A>G	c.(1153-1155)aaA>aaG	p.K385K	ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Silent_p.K384K	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	62	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	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	
TTC39A	22996	hgsc.bcm.edu	37	1	51754619	51754619	+	Missense_Mutation	SNP	T	T	C	rs138509677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:51754619T>C	ENST00000447632.2	-	17	1658	c.1610A>G	c.(1609-1611)aAg>aGg	p.K537R	TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000371750.5_Missense_Mutation_p.K502R|TTC39A_ENST00000530004.1_Missense_Mutation_p.K145R|TTC39A_ENST00000413473.2_Missense_Mutation_p.K505R|TTC39A_ENST00000451380.1_Missense_Mutation_p.K501R|TTC39A_ENST00000262675.7_Missense_Mutation_p.K474R			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	537								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						ATATTTAATCTTCTTTTCACT	0.488													T|||	4	0.000798722	0.0	0.0029	5008	,	,		21512	0.0		0.001	False		,,,				2504	0.001				p.K505R		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1514G						PASS	.	T	ARG/LYS,ARG/LYS	2,3792		0,2,1895	44.0	45.0	45.0		1505,1514	4.6	1.0	1	dbSNP_134	45	26,8194		0,26,4084	yes	missense,missense	TTC39A	NM_001080494.2,NM_001144832.1	26,26	0,28,5979	CC,CT,TT		0.3163,0.0527,0.2331	benign,benign	502/579,505/582	51754619	28,11986	1897	4110	6007	SO:0001583	missense	22996	exon17			TTAATCTTCTTTT	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.1610A>G	1.37:g.51754619T>C	ENSP00000393952:p.Lys537Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	70	0.538462	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	10.05	1.242909	0.22796	5.27E-4	0.003163	ENSG00000085831	ENST00000530004;ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750	T;T;T;T;T;T	0.63580	-0.05;0.73;0.75;0.76;0.75;0.75	5.75	4.57	0.56435	Tetratricopeptide-like helical (1);	0.146555	0.64402	N	0.000009	T	0.43144	0.1234	N	0.24115	0.695	0.33034	D	0.530583	B;B;B;B;B	0.09022	0.0;0.002;0.002;0.001;0.002	B;B;B;B;B	0.12837	0.003;0.003;0.008;0.006;0.007	T	0.46034	-0.9220	10	0.16420	T	0.52	-26.6932	8.059	0.30623	0.0:0.1678:0.0:0.8322	.	505;501;474;537;502	Q5SRH9-4;E7EQY9;D3DQ30;Q5SRH9;G3XAF8	.;.;.;TT39A_HUMAN;.	R	145;537;505;474;501;502	ENSP00000431228:K145R;ENSP00000393952:K537R;ENSP00000406144:K505R;ENSP00000262675:K474R;ENSP00000397207:K501R;ENSP00000360815:K502R	ENSP00000262675:K474R	K	-	2	0	TTC39A	51527207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.926000	0.56491	0.938000	0.37419	0.533000	0.62120	AAG	T|0.999;C|0.001	0.001	strong		0.488	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
HS3ST1	9957	hgsc.bcm.edu	37	4	11401012	11401012	+	Silent	SNP	A	A	G	rs1047385	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	57	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	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	
HRNR	388697	hgsc.bcm.edu	37	1	152186042	152186042	+	Missense_Mutation	SNP	A	A	G	rs12751022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152186042A>G	ENST00000368801.2	-	3	8138	c.8063T>C	c.(8062-8064)tTg>tCg	p.L2688S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2688				L -> S (in Ref. 1; BAC57496). {ECO:0000305}.	establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.L2688S(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGAGTGACCCAAGCGAGACTC	0.582													G|||	2279	0.455072	0.3336	0.5908	5008	,	,		10987	0.6181		0.3718	False		,,,				2504	0.4407				p.L2688S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	1	Substitution - Missense(1)	prostate(1)	c.T8063C						scavenged	.						30.0	26.0	28.0					1																	152186042		1929	3848	5777	SO:0001583	missense	388697	exon3			TGACCCAAGCGAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.8063T>C	1.37:g.152186042A>G	ENSP00000357791:p.Leu2688Ser	Somatic	49	3	0.0612245		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	1136	0.5201465201465202	216	0.43902439024390244	226	0.6243093922651933	348	0.6083916083916084	346	0.45646437994722955	G	3.703	-0.061145	0.07317	.	.	ENSG00000197915	ENST00000368801	T	0.01484	4.84	2.89	1.85	0.25348	.	.	.	.	.	T	0.00178	0.0005	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14755	-1.0461	8	0.08381	T	0.77	.	5.4214	0.16402	0.4598:0.0:0.5402:0.0	rs12751022	2688	Q86YZ3	HORN_HUMAN	S	2688	ENSP00000357791:L2688S	ENSP00000357791:L2688S	L	-	2	0	HRNR	150452666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.091000	0.11146	0.047000	0.15862	-0.291000	0.09656	TTG	A|0.478;G|0.522	0.522	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
MBIP	51562	hgsc.bcm.edu	37	14	36784062	36784062	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:36784062C>G	ENST00000416007.4	-	3	396	c.309G>C	c.(307-309)gaG>gaC	p.E103D	MBIP_ENST00000603913.1_5'Flank|MBIP_ENST00000359527.7_Missense_Mutation_p.E103D|MBIP_ENST00000318473.7_Missense_Mutation_p.E103D	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	103					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|inactivation of MAPK activity involved in osmosensory signaling pathway (GO:0000173)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein kinase inhibitor activity (GO:0004860)			breast(2)|large_intestine(1)|lung(5)	8	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)		TTCTTCCTATCTCTTCAACAG	0.378																																					p.E103D		Atlas-SNP	.											.	MBIP	25	.	0			c.G309C						PASS	.						131.0	120.0	124.0					14																	36784062		2201	4300	6501	SO:0001583	missense	51562	exon3			TCCTATCTCTTCA	BC016821	CCDS9658.1, CCDS45096.1	14q13.2	2005-01-10			ENSG00000151332	ENSG00000151332			20427	protein-coding gene	gene with protein product		609431				10801814	Standard	NM_016586		Approved		uc001wtm.2	Q9NS73	OTTHUMG00000140222	ENST00000416007.4:c.309G>C	14.37:g.36784062C>G	ENSP00000399718:p.Glu103Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	148	57	0.385135	NM_016586	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Missense_Mutation	SNP	ENST00000416007.4	37	CCDS9658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.648|6.648	0.488059|0.488059	0.12641|0.12641	.|.	.|.	ENSG00000151332|ENSG00000151332	ENST00000553977|ENST00000416007;ENST00000318473;ENST00000359527;ENST00000396329;ENST00000553298;ENST00000553549;ENST00000556427	.|T;T;T	.|0.46063	.|0.88;0.88;0.88	6.17|6.17	0.564|0.564	0.17302|0.17302	.|.	.|0.715788	.|0.14682	.|N	.|0.304691	T|T	0.24275|0.24275	0.0588|0.0588	L|L	0.36672|0.36672	1.1|1.1	0.25366|0.25366	N|N	0.988744|0.988744	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.15752|0.15752	-1.0426|-1.0426	5|10	.|0.21014	.|T	.|0.42	-2.0398|-2.0398	1.586|1.586	0.02644|0.02644	0.2059:0.402:0.2295:0.1626|0.2059:0.402:0.2295:0.1626	.|.	.|103;103;103	.|Q9NS73-5;Q9NS73-3;Q9NS73	.|.;.;MBIP1_HUMAN	H|D	100|103;103;103;110;63;82;61	.|ENSP00000399718:E103D;ENSP00000324444:E103D;ENSP00000352517:E103D	.|ENSP00000324444:E103D	D|E	-|-	1|3	0|2	MBIP|MBIP	35853813|35853813	0.597000|0.597000	0.26874|0.26874	0.995000|0.995000	0.50966|0.50966	0.821000|0.821000	0.46438|0.46438	0.313000|0.313000	0.19415|0.19415	0.089000|0.089000	0.17243|0.17243	-0.211000|-0.211000	0.12701|0.12701	GAT|GAG	.	.	none		0.378	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586	
GPR50	9248	hgsc.bcm.edu	37	X	150349649	150349649	+	Missense_Mutation	SNP	A	A	G	rs561077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150349649A>G	ENST00000218316.3	+	2	1663	c.1594A>G	c.(1594-1596)Act>Gct	p.T532A	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	532	Pro-rich.		T -> A (higher fasting circulating triglyceride levels; dbSNP:rs561077). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		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)	p.N532D(1)|p.T532A(1)		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)					CCCTAAGCCCACTGCTGCTGA	0.617													G|||	1620	0.429139	0.3986	0.4121	3775	,	,		15435	0.1984		0.335	False		,,,				2504	0.2761				p.T532A		Atlas-SNP	.											.	GPR50	195	.	2	Substitution - Missense(2)	stomach(2)	c.A1594G						PASS	.	G	ALA/THR	1892,1897		427,748,290,434,281	77.0	88.0	84.0		1594	-3.2	0.0	X	dbSNP_83	84	2782,3903		455,1129,743,836,1102	yes	missense	GPR50	NM_004224.3	58	882,1877,1033,1270,1383	GG,GA,G,AA,A		41.6156,49.934,44.6248	benign	532/618	150349649	4674,5800	2180	4265	6445	SO:0001583	missense	9248	exon2			AAGCCCACTGCTG	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.1594A>G	X.37:g.150349649A>G	ENSP00000218316:p.Thr532Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	743	0.4478601567209162	138	0.3812154696132597	114	0.3986013986013986	81	0.16598360655737704	184	0.30976430976430974	G	3.343	-0.134242	0.06711	0.49934	0.416156	ENSG00000102195	ENST00000218316	T	0.73897	-0.79	2.63	-3.21	0.05140	.	1.162070	0.06802	N	0.788946	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	0.18935	-1.0321	9	0.05721	T	0.95	-0.0027	6.6426	0.22917	0.2539:0.0:0.5933:0.1528	rs561077;rs3827433;rs561077	532	Q13585	MTR1L_HUMAN	A	532	ENSP00000218316:T532A	ENSP00000218316:T532A	T	+	1	0	GPR50	150100307	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.842000	0.01681	-1.307000	0.02321	-2.432000	0.00214	ACT	A|0.574;G|0.426	0.426	strong		0.617	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105268104	105268104	+	Silent	SNP	G	G	A	rs10141867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105268104G>A	ENST00000342537.7	+	1	855	c.570G>A	c.(568-570)ctG>ctA	p.L190L	ZBTB42_ENST00000555360.1_Silent_p.L190L	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	190	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CCCTGGACCTGTCGTTGAAGT	0.677													G|||	1092	0.218051	0.3064	0.2406	5008	,	,		17283	0.1022		0.2684	False		,,,				2504	0.1503				p.L190L		Atlas-SNP	.											ZBTB42_ENST00000342537,NS,carcinoma,0,2	ZBTB42	10	2	0			c.G570A						PASS	.	G		427,957		76,275,341	18.0	24.0	23.0		570	3.4	1.0	14	dbSNP_119	23	880,2288		123,634,827	no	coding-synonymous	ZBTB42	NM_001137601.1		199,909,1168	AA,AG,GG		27.7778,30.8526,28.7127		190/423	105268104	1307,3245	692	1584	2276	SO:0001819	synonymous_variant	100128927	exon2			GGACCTGTCGTTG	AX721091	CCDS45174.1	14q32.33	2013-01-09				ENSG00000179627		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	32550	protein-coding gene	gene with protein product		613915					Standard	NM_001137601		Approved	ZNF925	uc001ypp.3	B2RXF5		ENST00000342537.7:c.570G>A	14.37:g.105268104G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_001137601	B7ZW21	Silent	SNP	ENST00000342537.7	37	CCDS45174.1																																																																																			G|0.771;A|0.229	0.229	strong		0.677	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:137323213G>A	ENST00000316649.5	-	7	1379	c.1144C>T	c.(1144-1146)Ctc>Ttc	p.L382F	IL20RA_ENST00000541547.1_Missense_Mutation_p.L333F|IL20RA_ENST00000367748.1_Missense_Mutation_p.L271F|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000468393.1_5'Flank	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	382			L -> F (in dbSNP:rs1342642). {ECO:0000269|Ref.1}.		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TGCTGGGTGAGAGAAGTACCT	0.463													G|||	1000	0.199681	0.2383	0.183	5008	,	,		19502	0.0714		0.2594	False		,,,				2504	0.2301				p.L382F		Atlas-SNP	.											.	IL20RA	54	.	0			c.C1144T						PASS	.	G	PHE/LEU	977,3429	366.4+/-317.8	118,741,1344	79.0	74.0	76.0		1144	0.2	0.0	6	dbSNP_88	76	2322,6278	387.8+/-342.3	319,1684,2297	yes	missense	IL20RA	NM_014432.2	22	437,2425,3641	AA,AG,GG		27.0,22.1743,25.3652	possibly-damaging	382/554	137323213	3299,9707	2203	4300	6503	SO:0001583	missense	53832	exon7			GGGTGAGAGAAGT	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"""Interleukins and interleukin receptors"""	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1144C>T	6.37:g.137323213G>A	ENSP00000314976:p.Leu382Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	450	0.20604395604395603	137	0.2784552845528455	69	0.19060773480662985	47	0.08216783216783216	197	0.2598944591029024	G	15.12	2.740564	0.49045	0.221743	0.27	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.62232	0.3;1.76;0.04	5.76	0.246	0.15516	.	6.474150	0.00914	N	0.002515	T	0.48150	0.1484	L	0.56769	1.78	0.80722	P	0.0	P;P	0.49961	0.899;0.93	P;B	0.48840	0.592;0.38	T	0.18745	-1.0327	9	0.46703	T	0.11	-0.0228	6.7229	0.23340	0.0755:0.4712:0.3326:0.1207	rs1342642;rs17310128;rs52809262;rs61018497;rs1342642	271;382	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	F	382;271;333	ENSP00000314976:L382F;ENSP00000356722:L271F;ENSP00000437843:L333F	ENSP00000314976:L382F	L	-	1	0	IL20RA	137364906	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.732000	0.26072	0.013000	0.14918	0.655000	0.94253	CTC	G|0.794;N|0.001	.	strong		0.463	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432	
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:47093864C>T	ENST00000261292.4	+	3	610	c.332C>T	c.(331-333)aCa>aTa	p.T111I	LIPG_ENST00000580036.1_Missense_Mutation_p.T111I|LIPG_ENST00000577628.1_Missense_Mutation_p.T147I|LIPG_ENST00000427224.2_Missense_Mutation_p.T111I	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	111			T -> I (in dbSNP:rs2000813). {ECO:0000269|PubMed:12966036}.		cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						GCCCTGCACACAAGAGAGAAA	0.493													C|||	1205	0.240615	0.0673	0.2277	5008	,	,		16337	0.3274		0.3022	False		,,,				2504	0.3313				p.T111I	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C332T	GRCh37	CM077882	LIPG	M	rs2000813	PASS	.	C	ILE/THR	473,3933	225.2+/-241.2	20,433,1750	88.0	75.0	79.0		332	-3.7	0.2	18	dbSNP_92	79	2506,6094	410.5+/-350.2	364,1778,2158	yes	missense	LIPG	NM_006033.2	89	384,2211,3908	TT,TC,CC		29.1395,10.7354,22.9048	benign	111/501	47093864	2979,10027	2203	4300	6503	SO:0001583	missense	9388	exon3			TGCACACAAGAGA	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.332C>T	18.37:g.47093864C>T	ENSP00000261292:p.Thr111Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Missense_Mutation	SNP	ENST00000261292.4	37	CCDS11938.1	532	0.24358974358974358	29	0.05894308943089431	101	0.27900552486187846	182	0.3181818181818182	220	0.29023746701846964	C	10.03	1.238711	0.22711	0.107354	0.291395	ENSG00000101670	ENST00000261292;ENST00000427224	D;D	0.90444	-2.67;-2.67	5.13	-3.65	0.04502	Lipase, N-terminal (1);	0.762883	0.13306	N	0.397833	T	0.00012	0.0000	N	0.12853	0.265	0.80722	P	0.0	B;B;B	0.12013	0.005;0.003;0.002	B;B;B	0.11329	0.006;0.006;0.004	T	0.07539	-1.0767	9	0.49607	T	0.09	-23.8984	5.0178	0.14345	0.372:0.2221:0.0:0.4059	rs2000813;rs3786250;rs52802490;rs56604138;rs58046713;rs2000813	111;111;111	B4DTR8;Q9Y5X9;Q9Y5X9-2	.;LIPE_HUMAN;.	I	111	ENSP00000261292:T111I;ENSP00000387978:T111I	ENSP00000261292:T111I	T	+	2	0	LIPG	45347862	0.013000	0.17824	0.170000	0.22879	0.332000	0.28634	0.406000	0.21032	-0.342000	0.08363	0.561000	0.74099	ACA	C|0.760;T|0.240	0.240	strong		0.493	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
TNRC18	84629	hgsc.bcm.edu	37	7	5396715	5396715	+	Missense_Mutation	SNP	T	T	C	rs35508364	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5396715T>C	ENST00000430969.1	-	16	5374	c.5026A>G	c.(5026-5028)Aac>Gac	p.N1676D	TNRC18_ENST00000399537.4_Missense_Mutation_p.N1676D	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1676							chromatin binding (GO:0003682)	p.N1676D(1)|p.N731D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCCTTCCTGTTCTTCCCCAGC	0.567													C|||	1865	0.372404	0.4939	0.3156	5008	,	,		15116	0.1597		0.4791	False		,,,				2504	0.3579				p.N1676D		Atlas-SNP	.											TNRC18_ENST00000430969,NS,carcinoma,0,2	TNRC18	311	2	2	Substitution - Missense(2)	stomach(2)	c.A5026G						PASS	.	C	ASP/ASN	679,705		183,313,196	57.0	51.0	53.0		5026	4.6	1.0	7	dbSNP_126	53	1477,1705		340,797,454	yes	missense	TNRC18	NM_001080495.2	23	523,1110,650	CC,CT,TT		46.4173,49.0607,47.2186	benign	1676/2969	5396715	2156,2410	692	1591	2283	SO:0001583	missense	84629	exon16			TCCTGTTCTTCCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5026A>G	7.37:g.5396715T>C	ENSP00000395538:p.Asn1676Asp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	203	143	0.704434	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	809	0.37042124542124544	235	0.47764227642276424	120	0.3314917127071823	70	0.12237762237762238	384	0.5065963060686016	c	4.760	0.141296	0.09083	0.490607	0.464173	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.39229	2.89;2.89;1.09	5.52	4.64	0.57946	.	0.000000	0.47093	N	0.000245	T	0.00012	0.0000	N	0.00289	-1.7	0.58432	P	8.000000000008E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44982	-0.9292	9	0.07325	T	0.83	.	7.7425	0.28849	0.0:0.7244:0.1333:0.1423	rs35508364;rs59846759;rs61745137	731;1676	A8MSW5;O15417	.;TNC18_HUMAN	D	1676;1676;731;166	ENSP00000382452:N1676D;ENSP00000395538:N1676D;ENSP00000395990:N166D	ENSP00000382452:N1676D	N	-	1	0	TNRC18	5363241	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	1.454000	0.35178	0.724000	0.32296	-0.215000	0.12644	AAC	T|0.609;C|0.391	0.391	strong		0.567	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
GRM7	2917	hgsc.bcm.edu	37	3	7620168	7620168	+	Silent	SNP	A	A	G	rs34373930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:7620168A>G	ENST00000357716.4	+	8	1849	c.1575A>G	c.(1573-1575)ctA>ctG	p.L525L	GRM7_ENST00000389336.4_Silent_p.L525L|GRM7_ENST00000402647.2_Silent_p.L525L|GRM7_ENST00000486284.1_Silent_p.L525L|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000403881.1_Silent_p.L525L	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	525					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TGTGCACACTACCATGTAAGC	0.463													A|||	854	0.170527	0.0552	0.2565	5008	,	,		19770	0.1379		0.2932	False		,,,				2504	0.1728				p.L525L		Atlas-SNP	.											.	GRM7	223	.	0			c.A1575G						PASS	.	A	,	371,4035	187.1+/-213.8	16,339,1848	104.0	100.0	102.0		1575,1575	0.8	0.2	3	dbSNP_126	102	2397,6203	399.2+/-346.4	339,1719,2242	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	355,2058,4090	GG,GA,AA		27.8721,8.4203,21.2825	,	525/916,525/923	7620168	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			CACACTACCATGT	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1575A>G	3.37:g.7620168A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	185	105	0.567568	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			A|0.788;G|0.212	0.212	strong		0.463	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
PCDH15	65217	hgsc.bcm.edu	37	10	55955444	55955444	+	Splice_Site	SNP	T	T	G	rs4935502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:55955444T>G	ENST00000320301.6	-	11	1698	c.1304A>C	c.(1303-1305)gAt>gCt	p.D435A	PCDH15_ENST00000395430.1_Splice_Site_p.D435A|PCDH15_ENST00000373957.3_Splice_Site_p.D413A|PCDH15_ENST00000395445.1_Splice_Site_p.D435A|PCDH15_ENST00000395438.1_Splice_Site_p.D435A|PCDH15_ENST00000395433.1_Splice_Site_p.D413A|PCDH15_ENST00000395440.1_Splice_Site_p.D435A|PCDH15_ENST00000395446.1_Splice_Site_p.D435A|PCDH15_ENST00000361849.3_Splice_Site_p.D435A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Splice_Site_p.D39A|PCDH15_ENST00000373955.1_Splice_Site_p.D435A|PCDH15_ENST00000437009.1_Splice_Site_p.D435A|PCDH15_ENST00000395432.2_Splice_Site_p.D398A|PCDH15_ENST00000414778.1_Splice_Site_p.D440A|PCDH15_ENST00000373965.2_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	61	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	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
RP1	6101	hgsc.bcm.edu	37	8	55539057	55539057	+	Missense_Mutation	SNP	G	G	A	rs444772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55539057G>A	ENST00000220676.1	+	4	2763	c.2615G>A	c.(2614-2616)cGt>cAt	p.R872H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	872			R -> H (in dbSNP:rs444772). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:15933747, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CAGAAAAAACGTAAAGGGGAT	0.358													G|||	1363	0.272165	0.1407	0.3055	5008	,	,		16799	0.4415		0.2714	False		,,,				2504	0.2526				p.R872H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											RP1,caecum,carcinoma,0,1	RP1	429	1	0			c.G2615A						PASS	.	G	HIS/ARG	743,3653		64,615,1519	36.0	38.0	37.0		2615	1.4	1.0	8	dbSNP_80	37	2330,6262		305,1720,2271	yes	missense	RP1	NM_006269.1	29	369,2335,3790	AA,AG,GG		27.1182,16.9017,23.6603	benign	872/2157	55539057	3073,9915	2198	4296	6494	SO:0001583	missense	6101	exon4			AAAAACGTAAAGG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2615G>A	8.37:g.55539057G>A	ENSP00000220676:p.Arg872His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	657	0.3008241758241758	102	0.2073170731707317	109	0.3011049723756906	250	0.4370629370629371	196	0.25857519788918204	G	11.43	1.636342	0.29068	0.169017	0.271182	ENSG00000104237	ENST00000220676	T	0.43294	0.95	5.44	1.42	0.22433	.	0.938342	0.08875	N	0.881013	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.29253	0.239	B	0.22880	0.042	T	0.44997	-0.9291	9	0.56958	D	0.05	.	8.4605	0.32925	0.5628:0.37:0.0671:0.0	rs444772;rs52805057;rs57776921;rs444772	872	P56715	RP1_HUMAN	H	872	ENSP00000220676:R872H	ENSP00000220676:R872H	R	+	2	0	RP1	55701610	0.998000	0.40836	0.994000	0.49952	0.827000	0.46813	1.804000	0.38873	0.327000	0.23409	-0.294000	0.09567	CGT	G|0.735;A|0.265	0.265	strong		0.358	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
DCHS1	8642	hgsc.bcm.edu	37	11	6644600	6644600	+	Silent	SNP	C	C	T	rs72911011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6644600C>T	ENST00000299441.3	-	21	8718	c.8307G>A	c.(8305-8307)gcG>gcA	p.A2769A	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2769	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGGCACTCGCGCACGCAACT	0.597													T|||	624	0.124601	0.0908	0.1571	5008	,	,		19220	0.0754		0.2117	False		,,,				2504	0.1084				p.A2769A		Atlas-SNP	.											.	DCHS1	277	.	0			c.G8307A						PASS	.	T		481,3919		36,409,1755	52.0	47.0	48.0		8307	2.7	1.0	11	dbSNP_130	48	1715,6877		167,1381,2748	no	coding-synonymous	DCHS1	NM_003737.2		203,1790,4503	TT,TC,CC		19.9604,10.9318,16.9027		2769/3299	6644600	2196,10796	2200	4296	6496	SO:0001819	synonymous_variant	8642	exon21			CACTCGCGCACGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8307G>A	11.37:g.6644600C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.839;T|0.161	0.161	strong		0.597	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
CPNE1	8904	hgsc.bcm.edu	37	20	34219480	34219480	+	Silent	SNP	G	G	A	rs2230219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34219480G>A	ENST00000317619.3	-	10	1042	c.648C>T	c.(646-648)gaC>gaT	p.D216D	CPNE1_ENST00000397445.1_Silent_p.D216D|CPNE1_ENST00000397442.1_Silent_p.D216D|CPNE1_ENST00000397443.1_Silent_p.D216D|CPNE1_ENST00000352393.4_Silent_p.D216D|CPNE1_ENST00000317677.5_Silent_p.D221D|CPNE1_ENST00000397446.1_Silent_p.D216D			Q99829	CPNE1_HUMAN	copine I	216	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			ACCCGTCACTGTCATAATCGG	0.557													G|||	237	0.0473243	0.0008	0.0202	5008	,	,		20674	0.002		0.0507	False		,,,				2504	0.1728				p.D221D		Atlas-SNP	.											.	CPNE1	44	.	0			c.C663T						PASS	.	G	,,,,,	37,4369	41.6+/-74.8	0,37,2166	70.0	51.0	57.0		648,663,648,648,648,648	3.5	1.0	20	dbSNP_98	57	418,8182	130.2+/-188.1	14,390,3896	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,	14,427,6062	AA,AG,GG		4.8605,0.8398,3.4984	,,,,,	216/537,221/543,216/538,216/538,216/538,216/538	34219480	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	8904	exon8			GTCACTGTCATAA	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.648C>T	20.37:g.34219480G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Silent	SNP	ENST00000317619.3	37	CCDS13260.1																																																																																			G|0.969;A|0.031	0.031	strong		0.557	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
STK31	56164	hgsc.bcm.edu	37	7	23775477	23775477	+	Missense_Mutation	SNP	G	G	T	rs10264967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23775477G>T	ENST00000355870.3	+	7	923	c.804G>T	c.(802-804)aaG>aaT	p.K268N	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.K245N|STK31_ENST00000354639.3_Missense_Mutation_p.K245N|STK31_ENST00000433467.2_Missense_Mutation_p.K268N	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	268			K -> N (in dbSNP:rs10264967). {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						TTGACTTGAAGGATGAAAATG	0.408													g|||	449	0.0896565	0.0772	0.1196	5008	,	,		18423	0.0308		0.173	False		,,,				2504	0.0603				p.K268N		Atlas-SNP	.											.	STK31	175	.	0			c.G804T						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS	404,4002	197.4+/-221.5	18,368,1817	68.0	71.0	70.0		735,804,735	4.7	1.0	7	dbSNP_119	70	1622,6978	299.5+/-304.5	133,1356,2811	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	94,94,94	151,1724,4628	TT,TG,GG		18.8605,9.1693,15.5774	probably-damaging,probably-damaging,probably-damaging	245/997,268/1020,245/997	23775477	2026,10980	2203	4300	6503	SO:0001583	missense	56164	exon7			CTTGAAGGATGAA	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.804G>T	7.37:g.23775477G>T	ENSP00000348132:p.Lys268Asn	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	64	43	0.671875	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	243	0.11126373626373626	43	0.08739837398373984	55	0.15193370165745856	15	0.026223776223776224	130	0.17150395778364116	g	12.88	2.070656	0.36566	0.091693	0.188605	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.20598	2.06;2.06;2.06;2.06	4.71	4.71	0.59529	.	0.135740	0.47455	D	0.000236	T	0.00039	0.0001	M	0.62723	1.935	0.35467	P	0.20294199999999996	D;D	0.60575	0.988;0.988	P;P	0.53912	0.737;0.737	T	0.04900	-1.0919	9	0.54805	T	0.06	-6.4717	11.1853	0.48653	0.0908:0.0:0.9092:0.0	rs10264967;rs10264967	268;268	B4DZ06;Q9BXU1	.;STK31_HUMAN	N	268;268;245;245	ENSP00000348132:K268N;ENSP00000411852:K268N;ENSP00000346660:K245N;ENSP00000406146:K245N	ENSP00000346660:K245N	K	+	3	2	STK31	23742002	1.000000	0.71417	0.994000	0.49952	0.023000	0.10783	3.548000	0.53670	2.332000	0.79248	0.467000	0.42956	AAG	G|0.862;T|0.138	0.138	strong		0.408	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	0	0		WXS	Illumina HiSeq	Phase_I	92	89	0.967391	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	
VTN	7448	hgsc.bcm.edu	37	17	26694861	26694861	+	Missense_Mutation	SNP	G	G	A	rs704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26694861G>A	ENST00000226218.4	-	7	1817	c.1199C>T	c.(1198-1200)aCg>aTg	p.T400M	TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|VTN_ENST00000438614.1_De_novo_Start_OutOfFrame|CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.T58M|VTN_ENST00000536498.1_De_novo_Start_OutOfFrame|VTN_ENST00000431468.1_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	400			T -> M (in dbSNP:rs704). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GGACAGCCACGTGGCGCGGGA	0.577													G|||	2780	0.555112	0.6097	0.5389	5008	,	,		20006	0.7083		0.4493	False		,,,				2504	0.4438				p.T400M		Atlas-SNP	.											.	VTN	45	.	0			c.C1199T						PASS	.	G	MET/THR	2493,1913	624.5+/-394.3	699,1095,409	67.0	58.0	61.0		1199	-8.9	0.0	17	dbSNP_36	61	4134,4466	564.2+/-388.3	993,2148,1159	yes	missense	VTN	NM_000638.3	81	1692,3243,1568	AA,AG,GG		48.0698,43.4181,49.0466	possibly-damaging	400/479	26694861	6627,6379	2203	4300	6503	SO:0001583	missense	7448	exon7			AGCCACGTGGCGC	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.1199C>T	17.37:g.26694861G>A	ENSP00000226218:p.Thr400Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_000638	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	1260|1260	0.5769230769230769|0.5769230769230769	285|285	0.5792682926829268|0.5792682926829268	200|200	0.5524861878453039|0.5524861878453039	438|438	0.7657342657342657|0.7657342657342657	337|337	0.4445910290237467|0.4445910290237467	G|G	12.13|12.13	1.846907|1.846907	0.32606|0.32606	0.565819|0.565819	0.480698|0.480698	ENSG00000258852|ENSG00000255604	ENST00000555059|ENST00000226218	.|T	.|0.04234	.|3.67	4.47|4.47	-8.94|-8.94	0.00768|0.00768	.|Hemopexin/matrixin (1);	.|2.881560	.|0.01033	.|N	.|0.004177	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.51240	.|0.943	.|B	.|0.30401	.|0.115	T|T	0.48559|0.48559	-0.9025|-0.9025	4|9	.|0.34782	.|T	.|0.22	1.9295|1.9295	6.4258|6.4258	0.21768|0.21768	0.615:0.1722:0.1319:0.0809|0.615:0.1722:0.1319:0.0809	rs704;rs3203620;rs17849906;rs56842307;rs704|rs704;rs3203620;rs17849906;rs56842307;rs704	.|400	.|P04004	.|VTNC_HUMAN	C|M	10|400	.|ENSP00000226218:T400M	.|ENSP00000226218:T400M	R|T	-|-	1|2	0|0	CTB-96E2.2|AC002094.1	23718988|23718988	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.133000|-3.133000	0.00589|0.00589	-2.112000|-2.112000	0.00835|0.00835	-0.964000|-0.964000	0.02622|0.02622	CGT|ACG	G|0.469;A|0.531	0.531	strong		0.577	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
EMP2	2013	hgsc.bcm.edu	37	16	10631912	10631912	+	Silent	SNP	C	C	T	rs2279868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	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	
C10orf53	282966	hgsc.bcm.edu	37	10	50916542	50916542	+	Missense_Mutation	SNP	C	C	T	rs4838554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50916542C>T	ENST00000374112.3	+	3	365	c.353C>T	c.(352-354)aCt>aTt	p.T118I	C10orf53_ENST00000535836.1_Missense_Mutation_p.T118I	NM_182554.2	NP_872360.2	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53	0										endometrium(1)|lung(6)	7		all_neural(218;0.107)				ctgacttgtactgtattggcc	0.488													T|||	1958	0.390974	0.4365	0.4611	5008	,	,		20401	0.1548		0.495	False		,,,				2504	0.4162				p.T118I		Atlas-SNP	.											.	C10orf53	19	.	0			c.C353T						PASS	.	T	ILE/THR	1995,2411	616.3+/-392.7	454,1087,662	167.0	162.0	163.0		353	-0.5	0.0	10	dbSNP_111	163	4151,4449	588.1+/-392.3	978,2195,1127	yes	missense	C10orf53	NM_182554.2	89	1432,3282,1789	TT,TC,CC		48.2674,45.2792,47.2551	benign	118/158	50916542	6146,6860	2203	4300	6503	SO:0001583	missense	282966	exon3			CTTGTACTGTATT	BC028127	CCDS31202.1, CCDS41521.1	10q11.23	2012-05-24			ENSG00000178645	ENSG00000178645			27421	protein-coding gene	gene with protein product						12477932	Standard	NM_182554		Approved	Em:AC069546.1	uc001jid.1	Q8N6V4	OTTHUMG00000018199	ENST00000374112.3:c.353C>T	10.37:g.50916542C>T	ENSP00000363226:p.Thr118Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_182554	A6NI81|A6NLE0|B9ZVK6	Missense_Mutation	SNP	ENST00000374112.3	37	CCDS31202.1	834	0.38186813186813184	221	0.4491869918699187	152	0.4198895027624309	80	0.13986013986013987	381	0.5026385224274407	T	0.003	-2.454822	0.00173	0.452792	0.482674	ENSG00000178645	ENST00000374112;ENST00000535836	.	.	.	0.818	-0.507	0.11985	.	.	.	.	.	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	0.46775	-0.9167	7	0.12103	T	0.63	.	4.4657	0.11687	0.0:0.5365:0.0:0.4635	rs4838554;rs17856787;rs52809141;rs59677133;rs4838554	118	B9ZVK6	.	I	118	.	ENSP00000363226:T118I	T	+	2	0	C10orf53	50586548	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.916000	0.04029	-0.926000	0.03770	-1.140000	0.01884	ACT	C|0.571;T|0.429	0.429	strong		0.488	C10orf53-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048006.1	NM_182554	
ANK1	286	hgsc.bcm.edu	37	8	41525914	41525914	+	Silent	SNP	C	C	T	rs750625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:41525914C>T	ENST00000347528.4	-	39	5348	c.5265G>A	c.(5263-5265)gtG>gtA	p.V1755V	RP11-930P14.1_ENST00000522388.1_RNA|ANK1_ENST00000396945.1_Silent_p.V1755V|ANK1_ENST00000352337.4_Silent_p.V1755V|ANK1_ENST00000396942.1_Silent_p.V1755V|ANK1_ENST00000265709.8_Silent_p.V1796V|ANK1_ENST00000289734.7_Silent_p.V1755V|ANK1_ENST00000379758.2_Silent_p.V1755V	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1755	55 kDa regulatory domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CACTTACAGACACCAGGACCT	0.592													C|||	975	0.194688	0.1936	0.2147	5008	,	,		20886	0.1409		0.2406	False		,,,				2504	0.1902				p.V1796V		Atlas-SNP	.											.	ANK1	497	.	0			c.G5388A						PASS	.	C	,,,,	900,3506	347.2+/-309.4	91,718,1394	148.0	113.0	125.0		5265,5388,5265,5265,4779	2.3	0.0	8	dbSNP_86	125	2107,6493	364.6+/-333.6	269,1569,2462	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	360,2287,3856	TT,TC,CC		24.5,20.4267,23.1201	,,,,	1755/1881,1796/1898,1755/1857,1755/1882,1593/1720	41525914	3007,9999	2203	4300	6503	SO:0001819	synonymous_variant	286	exon40			TACAGACACCAGG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.5265G>A	8.37:g.41525914C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	439	0.20100732600732601	102	0.2073170731707317	94	0.2596685082872928	81	0.14160839160839161	162	0.21372031662269128	C	0.035	-1.311843	0.01342	0.204267	0.245	ENSG00000029534	ENST00000520299	T	0.67171	-0.25	4.17	2.34	0.29019	.	1.106060	0.06943	N	0.813257	T	0.00012	0.0000	.	.	.	0.53688	P	2.999999999997449E-5	.	.	.	.	.	.	T	0.05435	-1.0885	6	0.42905	T	0.14	.	7.2806	0.26310	0.0:0.7369:0.1698:0.0933	rs750625;rs17659714;rs750625	.	.	.	I	915	ENSP00000430174:V915I	ENSP00000430174:V915I	V	-	1	0	ANK1	41645071	0.693000	0.27728	0.007000	0.13788	0.026000	0.11368	1.235000	0.32671	0.532000	0.28657	0.313000	0.20887	GTC	C|0.778;A|0.001	.	strong		0.592	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190632	209190632	+	Missense_Mutation	SNP	T	T	G	rs999890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209190632T>G	ENST00000264380.4	+	20	3255	c.3097T>G	c.(3097-3099)Tcc>Gcc	p.S1033A		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1033			S -> A (in dbSNP:rs999890).		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						GGAAGTCACCTCCTCTGAAGA	0.433													T|||	496	0.0990415	0.1513	0.1081	5008	,	,		20723	0.0089		0.1282	False		,,,				2504	0.0849				p.S1033A		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T3097G						PASS	.	T	ALA/SER	629,3777	270.4+/-269.6	39,551,1613	98.0	101.0	100.0		3097	-0.5	0.0	2	dbSNP_86	100	1207,7393	244.7+/-273.8	76,1055,3169	yes	missense	PIKFYVE	NM_015040.3	99	115,1606,4782	GG,GT,TT		14.0349,14.276,14.1166	probably-damaging	1033/2099	209190632	1836,11170	2203	4300	6503	SO:0001583	missense	200576	exon20			GTCACCTCCTCTG	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.3097T>G	2.37:g.209190632T>G	ENSP00000264380:p.Ser1033Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	200	0.09157509157509157	67	0.13617886178861788	38	0.10497237569060773	2	0.0034965034965034965	93	0.12269129287598944	T	6.037	0.375195	0.11409	0.14276	0.140349	ENSG00000115020	ENST00000264380;ENST00000392200;ENST00000452564	T;T	0.31769	1.48;1.61	6.17	-0.478	0.12093	.	0.293705	0.33438	N	0.004919	T	0.00178	0.0005	M	0.71581	2.175	0.19575	P	0.9999630138	B;B	0.23650	0.089;0.0	B;B	0.25506	0.061;0.001	T	0.20538	-1.0272	9	0.10377	T	0.69	-0.8691	2.5622	0.04774	0.1093:0.1811:0.1141:0.5956	rs999890;rs16840965;rs52825237;rs58476487;rs999890	1033;977	Q9Y2I7;E9PDH4	FYV1_HUMAN;.	A	1033;609;977	ENSP00000264380:S1033A;ENSP00000405736:S977A	ENSP00000264380:S1033A	S	+	1	0	PIKFYVE	208898877	0.997000	0.39634	0.019000	0.16419	0.075000	0.17131	2.824000	0.48088	-0.287000	0.09064	-0.290000	0.09829	TCC	T|0.884;G|0.116	0.116	strong		0.433	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
IMPDH1	3614	hgsc.bcm.edu	37	7	128034629	128034629	+	Silent	SNP	C	C	T	rs2228075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:128034629C>T	ENST00000480861.1	-	12	1382	c.1305G>A	c.(1303-1305)gcG>gcA	p.A435A	IMPDH1_ENST00000348127.6_Silent_p.A489A|IMPDH1_ENST00000378717.4_Silent_p.A456A|IMPDH1_ENST00000496200.1_Silent_p.A415A|IMPDH1_ENST00000470772.1_Silent_p.A439A|IMPDH1_ENST00000354269.5_Silent_p.A515A|IMPDH1_ENST00000419067.2_Silent_p.A492A|IMPDH1_ENST00000338791.6_Silent_p.A525A|IMPDH1_ENST00000343214.4_Silent_p.A415A	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						AGACACCCTGCGCGATCTTCA	0.587													C|||	1390	0.277556	0.2239	0.2651	5008	,	,		19268	0.3839		0.2724	False		,,,				2504	0.2546				p.A525A		Atlas-SNP	.											.	IMPDH1	38	.	0			c.G1575A						PASS	.	C	,,,,,,	893,3513	347.2+/-309.4	97,699,1407	75.0	73.0	74.0		1575,1545,1320,1305,1245,1476,1467	-10.4	0.1	7	dbSNP_98	74	2232,6368	378.1+/-338.8	298,1636,2366	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IMPDH1	NM_000883.3,NM_001102605.1,NM_001142573.1,NM_001142574.1,NM_001142575.1,NM_001142576.1,NM_183243.2	,,,,,,	395,2335,3773	TT,TC,CC		25.9535,20.2678,24.0274	,,,,,,	525/600,515/590,440/515,435/510,415/490,492/567,489/564	128034629	3125,9881	2203	4300	6503	SO:0001819	synonymous_variant	3614	exon15			ACCCTGCGCGATC		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1305G>A	7.37:g.128034629C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_000883		Silent	SNP	ENST00000480861.1	37	CCDS55161.1																																																																																			T|0.249;G|0.000;C|0.750	0.249	strong		0.587	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883	
ZNF488	118738	hgsc.bcm.edu	37	10	48370595	48370595	+	Silent	SNP	G	G	A	rs11204210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:48370595G>A	ENST00000395702.2	+	2	290	c.63G>A	c.(61-63)ggG>ggA	p.G21G	ZNF488_ENST00000494156.1_Silent_p.G21G|ZNF488_ENST00000586537.1_5'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	21					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|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)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						TGGCAGCTGGGAAGGGAGCCC	0.612													g|||	1837	0.366813	0.3396	0.2421	5008	,	,		18570	0.4812		0.329	False		,,,				2504	0.4131				p.G21G		Atlas-SNP	.											ZNF488,NS,carcinoma,0,2	ZNF488	38	2	0			c.G63A						PASS	.	G		1512,2892		262,988,952	54.0	60.0	58.0		63	0.1	0.0	10	dbSNP_120	58	2876,5720		490,1896,1912	no	coding-synonymous	ZNF488	NM_153034.2		752,2884,2864	AA,AG,GG		33.4574,34.3324,33.7538		21/341	48370595	4388,8612	2202	4298	6500	SO:0001819	synonymous_variant	118738	exon2			AGCTGGGAAGGGA	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"""Zinc fingers, C2H2-type"""	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.63G>A	10.37:g.48370595G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_153034	Q05CE0	Silent	SNP	ENST00000395702.2	37	CCDS7217.1																																																																																			G|0.644;A|0.356	0.356	strong		0.612	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111611076	111611076	+	Silent	SNP	A	A	G	rs12521830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	133	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	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		
KIF7	374654	hgsc.bcm.edu	37	15	90188392	90188392	+	Silent	SNP	A	A	T	rs72750755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90188392A>T	ENST00000394412.3	-	10	2119	c.2043T>A	c.(2041-2043)gtT>gtA	p.V681V		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	681	Sufficient for interaction with NPHP1.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			TGCTCCCACCAACTGCTGCAA	0.667													a|||	90	0.0179712	0.0	0.0187	5008	,	,		16240	0.0		0.0338	False		,,,				2504	0.044				p.V681V		Atlas-SNP	.											.	KIF7	130	.	0			c.T2043A						PASS	.			33,4367	37.6+/-69.7	0,33,2167	27.0	31.0	30.0		2043	-3.7	0.0	15	dbSNP_130	30	364,8234	116.5+/-176.2	5,354,3940	no	coding-synonymous	KIF7	NM_198525.2		5,387,6107	TT,TA,AA		4.2335,0.75,3.0543		681/1344	90188392	397,12601	2200	4299	6499	SO:0001819	synonymous_variant	374654	exon10			CCCACCAACTGCT	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.2043T>A	15.37:g.90188392A>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Silent	SNP	ENST00000394412.3	37	CCDS32325.2																																																																																			A|0.976;T|0.024	0.024	strong		0.667	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
KIF13A	63971	hgsc.bcm.edu	37	6	17834198	17834198	+	Silent	SNP	T	T	G	rs4716189	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17834198T>G	ENST00000259711.6	-	12	1365	c.1260A>C	c.(1258-1260)atA>atC	p.I420I	KIF13A_ENST00000378843.2_Silent_p.I420I|KIF13A_ENST00000378826.2_Silent_p.I420I|KIF13A_ENST00000378814.5_Silent_p.I420I|KIF13A_ENST00000378816.5_Silent_p.I420I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	420					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)			CTACCTGTGCTATCTCTTCTG	0.378													G|||	2187	0.436701	0.2988	0.5144	5008	,	,		17599	0.4018		0.496	False		,,,				2504	0.5429				p.I420I		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1260C						PASS	.	G	,,,	1238,2446		214,810,818	144.0	133.0	137.0		1260,1260,1260,1260	-2.6	0.9	6	dbSNP_111	137	3953,4239		950,2053,1093	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	1164,2863,1911	GG,GT,TT		48.2544,33.6048,43.71	,,,	420/1771,420/1758,420/1750,420/1806	17834198	5191,6685	1842	4096	5938	SO:0001819	synonymous_variant	63971	exon12			CTGTGCTATCTCT	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.1260A>C	6.37:g.17834198T>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			T|0.583;G|0.417	0.417	strong		0.378	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
ADAM18	8749	hgsc.bcm.edu	37	8	39496029	39496029	+	Silent	SNP	T	T	C	rs12708194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:39496029T>C	ENST00000265707.5	+	10	918	c.873T>C	c.(871-873)acT>acC	p.T291T	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Silent_p.T267T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	291	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTCCTGGCACTGTATGCAATA	0.279													C|||	2947	0.588458	0.736	0.5994	5008	,	,		14168	0.251		0.6431	False		,,,				2504	0.6728				p.T291T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T873C						PASS	.	C		3289,1117	398.3+/-330.8	1236,817,150	116.0	112.0	113.0		873	-4.8	0.0	8	dbSNP_121	113	5733,2855	447.4+/-361.5	1918,1897,479	no	coding-synonymous	ADAM18	NM_014237.2		3154,2714,629	CC,CT,TT		33.2441,25.3518,30.568		291/740	39496029	9022,3972	2203	4294	6497	SO:0001819	synonymous_variant	8749	exon10			TGGCACTGTATGC	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.873T>C	8.37:g.39496029T>C		Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	188	187	0.994681	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	37	CCDS6113.1																																																																																			T|0.346;C|0.654	0.654	strong		0.279	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
SSU72	29101	hgsc.bcm.edu	37	1	1479333	1479333	+	Silent	SNP	A	A	G	rs7533	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1479333A>G	ENST00000291386.3	-	4	710	c.399T>C	c.(397-399)ccT>ccC	p.P133P		NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	133					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CCACGTGCACAGGCTGGCAGG	0.567													a|||	3474	0.69369	0.91	0.5634	5008	,	,		18035	0.8671		0.3062	False		,,,				2504	0.7137				p.P133P		Atlas-SNP	.											.	SSU72	15	.	0			c.T399C						PASS	.	G		3599,807	320.2+/-296.5	1474,651,78	109.0	99.0	103.0		399	-9.5	0.0	1	dbSNP_52	103	2537,6063	692.7+/-404.6	364,1809,2127	no	coding-synonymous	SSU72	NM_014188.2		1838,2460,2205	GG,GA,AA		29.5,18.3159,47.1782		133/195	1479333	6136,6870	2203	4300	6503	SO:0001819	synonymous_variant	29101	exon4			GTGCACAGGCTGG	AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"""Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"""			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.399T>C	1.37:g.1479333A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_014188	Q9BZS6|Q9H933	Silent	SNP	ENST00000291386.3	37	CCDS32.1																																																																																			A|0.488;G|0.512	0.512	strong		0.567	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12252955	12252955	+	Missense_Mutation	SNP	T	T	G	rs1061622	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12252955T>G	ENST00000376259.3	+	6	676	c.587T>G	c.(586-588)aTg>aGg	p.M196R	TNFRSF1B_ENST00000492361.1_3'UTR|MIR4632_ENST00000584158.1_RNA	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	196			M -> R (frequent polymorphism; seems to be associated with hyperandrogenism, polycystic ovary syndrome (PCOS) and systemic lupus erythematosus; dbSNP:rs1061622). {ECO:0000269|PubMed:11197692, ECO:0000269|PubMed:11762942, ECO:0000269|PubMed:12161545, ECO:0000269|PubMed:2166946, ECO:0000269|PubMed:2172983, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)	p.M196R(1)		central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	AATGCAAGCATGGATGCAGTC	0.637													T|||	975	0.194688	0.1868	0.1268	5008	,	,		15660	0.1498		0.2177	False		,,,				2504	0.2761				p.M196R		Atlas-SNP	.											TNFRSF1B,NS,carcinoma,0,1	TNFRSF1B	28	1	1	Substitution - Missense(1)	stomach(1)	c.T587G	GRCh37	CM022071	TNFRSF1B	M	rs1061622	scavenged	.	T	ARG/MET	929,3477	349.8+/-310.5	94,741,1368	134.0	100.0	112.0		587	-4.1	0.0	1	dbSNP_86	112	2069,6531	355.3+/-329.8	275,1519,2506	yes	missense	TNFRSF1B	NM_001066.2	91	369,2260,3874	GG,GT,TT		24.0581,21.0849,23.0509	benign	196/462	12252955	2998,10008	2203	4300	6503	SO:0001583	missense	7133	exon6			CAAGCATGGATGC	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.587T>G	1.37:g.12252955T>G	ENSP00000365435:p.Met196Arg	Somatic	31	1	0.0322581		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	430	0.19688644688644688	104	0.21138211382113822	56	0.15469613259668508	95	0.1660839160839161	175	0.23087071240105542	T	10.29	1.310596	0.23821	0.210849	0.240581	ENSG00000028137	ENST00000376259;ENST00000400863	T	0.60548	0.18	4.15	-4.13	0.03904	TNFR/CD27/30/40/95 cysteine-rich region (1);	1.471100	0.03493	N	0.216872	T	0.00012	0.0000	N	0.13198	0.31	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.07947	-1.0746	9	0.38643	T	0.18	-9.0951	7.0833	0.25244	0.0:0.5369:0.1669:0.2962	rs1061622;rs1681698;rs2228492;rs13306722;rs17037789;rs17883437;rs52797629;rs60195947;rs1061622	196	P20333	TNR1B_HUMAN	R	196	ENSP00000365435:M196R	ENSP00000365435:M196R	M	+	2	0	TNFRSF1B	12175542	0.000000	0.05858	0.000000	0.03702	0.905000	0.53344	-1.738000	0.01842	-0.694000	0.05113	0.482000	0.46254	ATG	T|0.792;G|0.208	0.208	strong		0.637	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
GRHL1	29841	hgsc.bcm.edu	37	2	10126330	10126330	+	Missense_Mutation	SNP	G	G	A	rs2303920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10126330G>A	ENST00000324907.9	+	9	1325	c.1189G>A	c.(1189-1191)Gtt>Att	p.V397I	GRHL1_ENST00000405379.2_Missense_Mutation_p.V397I|GRHL1_ENST00000324883.5_Missense_Mutation_p.V208I	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	397			V -> I (in dbSNP:rs2303920). {ECO:0000269|PubMed:15489334}.		cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V208I(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		TAACATTCAAGTTGATACCTA	0.488													A|||	1316	0.26278	0.3064	0.402	5008	,	,		12735	0.2599		0.2316	False		,,,				2504	0.1401				p.V397I		Atlas-SNP	.											GRHL1,NS,carcinoma,0,1	GRHL1	95	1	1	Substitution - Missense(1)	stomach(1)	c.G1189A						PASS	.	A	ILE/VAL	1374,3032	689.5+/-405.1	222,930,1051	204.0	208.0	207.0		1189	5.5	0.4	2	dbSNP_100	207	1832,6768	731.2+/-406.8	199,1434,2667	yes	missense	GRHL1	NM_198182.2	29	421,2364,3718	AA,AG,GG		21.3023,31.1847,24.6502	benign	397/619	10126330	3206,9800	2203	4300	6503	SO:0001583	missense	29841	exon9			ATTCAAGTTGATA	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"""transcription factor CP2-like 2"""	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.1189G>A	2.37:g.10126330G>A	ENSP00000324693:p.Val397Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	625	0.28617216117216115	168	0.34146341463414637	142	0.39226519337016574	143	0.25	172	0.22691292875989447	A	8.514	0.867179	0.17250	0.311847	0.213023	ENSG00000134317	ENST00000405379;ENST00000324883;ENST00000324907	T;T;T	0.15487	2.42;2.42;2.42	5.49	5.49	0.81192	CP2 transcription factor (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00465	-1.465	0.47659	P	5.159999999999609E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45041	-0.9288	9	0.02654	T	1	-2.9841	11.4774	0.50306	0.9295:0.0:0.0705:0.0	rs2303920;rs52812320;rs59250653;rs2303920	208;397	Q9NZI5-2;Q9NZI5	.;GRHL1_HUMAN	I	397;208;397	ENSP00000384209:V397I;ENSP00000324494:V208I;ENSP00000324693:V397I	ENSP00000324494:V208I	V	+	1	0	GRHL1	10043781	1.000000	0.71417	0.392000	0.26245	0.930000	0.56654	6.326000	0.72905	0.922000	0.37019	-0.490000	0.04691	GTT	G|0.743;A|0.257	0.257	strong		0.488	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
PFKL	5211	hgsc.bcm.edu	37	21	45732116	45732116	+	Silent	SNP	C	C	T	rs1057034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45732116C>T	ENST00000349048.4	+	4	421	c.366C>T	c.(364-366)ctC>ctT	p.L122L	PFKL_ENST00000496824.1_3'UTR|PFKL_ENST00000403390.1_Silent_p.L169L	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	122	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		ATGGCAGCCTCACAGGTGCCA	0.672													C|||	2296	0.458466	0.2852	0.5231	5008	,	,		14177	0.38		0.5755	False		,,,				2504	0.6074				p.L122L		Atlas-SNP	.											.	PFKL	65	.	0			c.C366T						PASS	.	C		1316,3064		194,928,1068	27.0	21.0	23.0		366	2.1	1.0	21	dbSNP_86	23	4925,3659		1428,2069,795	no	coding-synonymous	PFKL	NM_002626.4		1622,2997,1863	TT,TC,CC		42.6258,30.0457,48.141		122/781	45732116	6241,6723	2190	4292	6482	SO:0001819	synonymous_variant	5211	exon4			CAGCCTCACAGGT		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.366C>T	21.37:g.45732116C>T		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	204	198	0.970588	NM_002626	Q96A64|Q96IH4|Q9BR91	Silent	SNP	ENST00000349048.4	37	CCDS33582.1																																																																																			C|0.555;T|0.445	0.445	strong		0.672	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1		
MAST2	23139	hgsc.bcm.edu	37	1	46498375	46498375	+	Silent	SNP	A	A	G	rs1622208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46498375A>G	ENST00000361297.2	+	26	3805	c.3522A>G	c.(3520-3522)gtA>gtG	p.V1174V	MAST2_ENST00000372009.2_Silent_p.V1081V	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)					CGGAGGTGGTAGAGCTGATCC	0.587													G|||	3444	0.6877	0.7534	0.6441	5008	,	,		19107	0.7073		0.7346	False		,,,				2504	0.5613				p.V1174V		Atlas-SNP	.											.	MAST2	136	.	0			c.A3522G						PASS	.	G		3303,1101	369.1+/-318.9	1237,829,136	111.0	114.0	113.0		3522	0.9	1.0	1	dbSNP_89	113	6106,2494	396.6+/-345.4	2176,1754,370	yes	coding-synonymous	MAST2	NM_015112.2		3413,2583,506	GG,GA,AA		29.0,25.0,27.6453		1174/1799	46498375	9409,3595	2202	4300	6502	SO:0001819	synonymous_variant	23139	exon26			GGTGGTAGAGCTG	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.3522A>G	1.37:g.46498375A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			A|0.293;G|0.707	0.707	strong		0.587	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
PAPLN	89932	hgsc.bcm.edu	37	14	73716774	73716774	+	Silent	SNP	G	G	A	rs177393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73716774G>A	ENST00000554301.1	+	5	580	c.417G>A	c.(415-417)acG>acA	p.T139T	PAPLN_ENST00000427855.1_Silent_p.T139T|PAPLN_ENST00000555445.1_Silent_p.T139T|PAPLN_ENST00000381166.3_Silent_p.T139T|PAPLN_ENST00000340738.5_Silent_p.T139T			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	139						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TTGATGGGACGCCCTGCGAGC	0.637													G|||	1679	0.335264	0.4576	0.2925	5008	,	,		17768	0.1458		0.3042	False		,,,				2504	0.4274				p.T139T		Atlas-SNP	.											.	PAPLN	180	.	0			c.G417A						PASS	.	G		1913,2493	541.0+/-375.7	395,1123,685	104.0	78.0	87.0		417	-9.7	0.6	14	dbSNP_79	87	2771,5829	434.6+/-357.8	460,1851,1989	no	coding-synonymous	PAPLN	NM_173462.3		855,2974,2674	AA,AG,GG		32.2209,43.4181,36.0141		139/1252	73716774	4684,8322	2203	4300	6503	SO:0001819	synonymous_variant	89932	exon6			TGGGACGCCCTGC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.417G>A	14.37:g.73716774G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	75	0.9375	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																				G|0.667;A|0.333	0.333	strong		0.637	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
ELF3	1999	hgsc.bcm.edu	37	1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	rs55729978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D|ELF3_ENST00000367284.5_Missense_Mutation_p.G162D|RP11-465N4.4_ENST00000419190.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CCAGACCAGGGCAGCCCCTTT	0.642													G|||	364	0.0726837	0.2421	0.0159	5008	,	,		14680	0.0		0.0229	False		,,,				2504	0.0102				p.G162D		Atlas-SNP	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	0			c.G485A						PASS	.	G	ASP/GLY,ASP/GLY	690,3716		51,588,1564	28.0	34.0	32.0		485,485	3.3	1.0	1	dbSNP_129	32	147,8451		1,145,4153	yes	missense,missense	ELF3	NM_001114309.1,NM_004433.4	94,94	52,733,5717	AA,AG,GG		1.7097,15.6605,6.4365	benign,benign	162/372,162/372	201981774	837,12167	2203	4299	6502	SO:0001583	missense	1999	exon5			ACCAGGGCAGCCC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.485G>A	1.37:g.201981774G>A	ENSP00000352673:p.Gly162Asp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	157	0.07188644688644688	129	0.2621951219512195	9	0.024861878453038673	0	0.0	19	0.025065963060686015	G	10.76	1.441663	0.25900	0.156605	0.017097	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	T;T;T;T	0.56103	2.47;2.47;2.47;0.48	5.2	3.29	0.37713	.	0.821186	0.11026	N	0.607832	T	0.00012	0.0000	L	0.37561	1.115	0.27380	P	0.9554544	B	0.10296	0.003	B	0.09377	0.004	T	0.09796	-1.0658	9	0.37606	T	0.19	.	7.8653	0.29533	0.0862:0.164:0.7499:0.0	rs55729978	162	P78545	ELF3_HUMAN	D	162;162;162;162;160	ENSP00000352673:G162D;ENSP00000356253:G162D;ENSP00000356252:G162D;ENSP00000405162:G160D	ENSP00000311348:G162D	G	+	2	0	ELF3	200248397	0.174000	0.23070	0.988000	0.46212	0.681000	0.39784	0.316000	0.19469	1.168000	0.42723	0.655000	0.94253	GGC	G|0.938;A|0.062	0.062	strong		0.642	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
DLEC1	9940	hgsc.bcm.edu	37	3	38136476	38136476	+	Missense_Mutation	SNP	G	G	A	rs34290809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38136476G>A	ENST00000308059.6	+	13	2047	c.2026G>A	c.(2026-2028)Gag>Aag	p.E676K	DLEC1_ENST00000346219.3_Missense_Mutation_p.E676K|DLEC1_ENST00000452631.2_Missense_Mutation_p.E676K					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)		CCCCGACAAGGAGACTGCCTT	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		23233	0.0		0.004	False		,,,				2504	0.0				p.E676K		Atlas-SNP	.											.	DLEC1	278	.	0			c.G2026A						PASS	.	G	LYS/GLU,LYS/GLU	1,4115		0,1,2057	84.0	91.0	89.0		2026,2026	5.4	0.0	3	dbSNP_126	89	21,8383		0,21,4181	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	56,56	0,22,6238	AA,AG,GG		0.2499,0.0243,0.1757	possibly-damaging,possibly-damaging	676/1756,676/1779	38136476	22,12498	2058	4202	6260	SO:0001583	missense	9940	exon13			GACAAGGAGACTG	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.2026G>A	3.37:g.38136476G>A	ENSP00000308597:p.Glu676Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	142	55	0.387324	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.20	1.569663	0.28003	2.43E-4	0.002499	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05513	3.45;3.43;3.67	5.39	5.39	0.77823	.	0.244689	0.40908	D	0.000992	T	0.13841	0.0335	M	0.67953	2.075	0.09310	N	1	P;D;P	0.53745	0.804;0.962;0.804	P;P;P	0.52481	0.485;0.7;0.485	T	0.13495	-1.0507	10	0.54805	T	0.06	-14.4509	8.3585	0.32344	0.1685:0.0:0.8315:0.0	rs34290809	676;676;676	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	K	676	ENSP00000308597:E676K;ENSP00000315914:E676K;ENSP00000410427:E676K	ENSP00000308597:E676K	E	+	1	0	DLEC1	38111480	0.996000	0.38824	0.037000	0.18230	0.085000	0.17905	2.689000	0.46993	2.506000	0.84524	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.552	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
NCAPG2	54892	hgsc.bcm.edu	37	7	158449369	158449369	+	Missense_Mutation	SNP	G	G	A	rs61752310	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:158449369G>A	ENST00000409423.1	-	19	2261	c.2089C>T	c.(2089-2091)Cgg>Tgg	p.R697W	NCAPG2_ENST00000449727.2_Missense_Mutation_p.R697W|NCAPG2_ENST00000356309.3_Missense_Mutation_p.R697W|NCAPG2_ENST00000541468.1_Missense_Mutation_p.R198W|NCAPG2_ENST00000275830.10_Missense_Mutation_p.R489W|NCAPG2_ENST00000409339.3_Missense_Mutation_p.R697W	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	697					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		CCCTCCTCCCGGCTTCTCAGC	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		18903	0.0		0.002	False		,,,				2504	0.0				p.R697W		Atlas-SNP	.											.	NCAPG2	80	.	0			c.C2089T						PASS	.		TRP/ARG	8,3888		0,8,1940	38.0	40.0	39.0		2089	5.6	1.0	7	dbSNP_129	39	42,8254		0,42,4106	yes	missense	NCAPG2	NM_017760.5	101	0,50,6046	AA,AG,GG		0.5063,0.2053,0.4101	possibly-damaging	697/1144	158449369	50,12142	1948	4148	6096	SO:0001583	missense	54892	exon18			CCTCCCGGCTTCT	BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"""leucine zipper protein 5"""	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.2089C>T	7.37:g.158449369G>A	ENSP00000386569:p.Arg697Trp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	37	CCDS43686.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.88	2.368740	0.42003	0.002053	0.005063	ENSG00000146918	ENST00000541468;ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000545393;ENST00000449727	T;T;T;T;T;T	0.30448	1.53;1.54;1.54;1.54;1.53;1.53	5.63	5.63	0.86233	.	0.249547	0.40144	N	0.001171	T	0.18923	0.0454	N	0.08118	0	0.20821	N	0.999843	D;D;P;D	0.64830	0.988;0.994;0.669;0.977	P;P;B;P	0.56612	0.526;0.802;0.04;0.657	T	0.10989	-1.0606	10	0.37606	T	0.19	-14.9982	8.9354	0.35697	0.0755:0.0:0.7658:0.1587	rs61752310	697;140;489;697	Q86XI2-2;B4DHE5;E7EUH9;Q86XI2	.;.;.;CNDG2_HUMAN	W	198;697;697;489;697;140;697	ENSP00000442337:R198W;ENSP00000348657:R697W;ENSP00000386569:R697W;ENSP00000275830:R489W;ENSP00000387007:R697W;ENSP00000388326:R697W	ENSP00000275830:R489W	R	-	1	2	NCAPG2	158142130	1.000000	0.71417	0.989000	0.46669	0.515000	0.34225	2.869000	0.48444	2.652000	0.90054	0.655000	0.94253	CGG	G|0.997;A|0.003	0.003	strong		0.532	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760	
TTN	7273	hgsc.bcm.edu	37	2	179578704	179578704	+	Missense_Mutation	SNP	G	G	A	rs13398235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179578704G>A	ENST00000591111.1	-	90	25954	c.25730C>T	c.(25729-25731)cCg>cTg	p.P8577L	TTN_ENST00000589042.1_Missense_Mutation_p.P8894L|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P7650L|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12741	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)			ACTGTCACTCGGTGCTACATT	0.428													G|||	558	0.111422	0.1649	0.1527	5008	,	,		20072	0.0258		0.0358	False		,,,				2504	0.1759				p.P8894L		Atlas-SNP	.											.	TTN	18412	.	0			c.C26681T						PASS	.	G	,,,LEU/PRO	531,3273		33,465,1404	162.0	154.0	157.0		,,,22949	6.1	0.3	2	dbSNP_121	157	211,8045		5,201,3922	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,98	38,666,5326	AA,AG,GG		2.5557,13.959,6.1526	,,,benign	,,,7650/33424	179578704	742,11318	1902	4128	6030	SO:0001583	missense	7273	exon92			TCACTCGGTGCTA	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.25730C>T	2.37:g.179578704G>A	ENSP00000465570:p.Pro8577Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	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		156	0.07142857142857142	82	0.16666666666666666	44	0.12154696132596685	4	0.006993006993006993	26	0.03430079155672823	G	9.357	1.067043	0.20067	0.13959	0.025557	ENSG00000155657	ENST00000342992	T	0.39592	1.07	6.07	6.07	0.98685	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.02854	-0.475	0.09310	P	0.99999999986044	B	0.22211	0.066	B	0.14578	0.011	T	0.01961	-1.1239	8	0.87932	D	0	.	9.1292	0.36835	0.0774:0.0:0.7749:0.1477	rs13398235;rs52837389;rs13398235	8577	Q8WZ42	TITIN_HUMAN	L	7650	ENSP00000343764:P7650L	ENSP00000343764:P7650L	P	-	2	0	TTN	179286949	0.992000	0.36948	0.349000	0.25694	0.362000	0.29581	2.783000	0.47766	2.884000	0.98904	0.655000	0.94253	CCG	G|0.920;A|0.080	0.080	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PTPRR	5801	hgsc.bcm.edu	37	12	71078528	71078528	+	Missense_Mutation	SNP	C	C	T	rs35390084	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:71078528C>T	ENST00000283228.2	-	9	1767	c.1315G>A	c.(1315-1317)Gta>Ata	p.V439I	PTPRR_ENST00000549308.1_Missense_Mutation_p.V194I|PTPRR_ENST00000378778.1_Missense_Mutation_p.V233I|PTPRR_ENST00000342084.4_Missense_Mutation_p.V327I|PTPRR_ENST00000440835.2_Missense_Mutation_p.V194I	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	439	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		V -> I (in dbSNP:rs35390084).		ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		GAATCGGTTACATTTTTTGGT	0.308													C|||	81	0.0161741	0.0008	0.0086	5008	,	,		19603	0.0		0.0457	False		,,,				2504	0.0286				p.V439I		Atlas-SNP	.											.	PTPRR	109	.	0			c.G1315A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	42,4364	45.3+/-79.5	0,42,2161	89.0	95.0	93.0		979,697,1315,580	0.6	1.0	12	dbSNP_126	93	447,8147	134.7+/-192.1	13,421,3863	yes	missense,missense,missense,missense	PTPRR	NM_001207015.1,NM_001207016.1,NM_002849.3,NM_130846.2	29,29,29,29	13,463,6024	TT,TC,CC		5.2013,0.9532,3.7615	benign,benign,benign,benign	327/546,233/452,439/658,194/413	71078528	489,12511	2203	4297	6500	SO:0001583	missense	5801	exon9			CGGTTACATTTTT	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1315G>A	12.37:g.71078528C>T	ENSP00000283228:p.Val439Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	46	0.021062271062271064	0	0.0	4	0.011049723756906077	0	0.0	42	0.055408970976253295	C	12.80	2.046178	0.36085	0.009532	0.052013	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308;ENST00000550661	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;2.29	5.74	0.559	0.17272	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	1.045190	0.07619	N	0.926709	T	0.02342	0.0072	N	0.25890	0.77	0.20638	N	0.999879	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	0.20438	-1.0275	10	0.27785	T	0.31	-4.7236	11.36	0.49638	0.0:0.4899:0.409:0.1011	rs35390084;rs52820438	288;327;233;439	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	I	194;439;233;327;194;194	ENSP00000391750:V194I;ENSP00000283228:V439I;ENSP00000368054:V233I;ENSP00000339605:V327I;ENSP00000446943:V194I;ENSP00000449616:V194I	ENSP00000283228:V439I	V	-	1	0	PTPRR	69364795	0.220000	0.23631	0.994000	0.49952	0.993000	0.82548	-0.423000	0.07034	0.147000	0.19030	0.563000	0.77884	GTA	C|0.965;T|0.035	0.035	strong		0.308	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
STAB2	55576	hgsc.bcm.edu	37	12	104056737	104056737	+	Silent	SNP	G	G	A	rs148397037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104056737G>A	ENST00000388887.2	+	18	2187	c.1983G>A	c.(1981-1983)ctG>ctA	p.L661L		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						TCCCGATTCTGCCCCATCGAT	0.458													G|||	30	0.00599042	0.0008	0.0202	5008	,	,		20909	0.0		0.0109	False		,,,				2504	0.0041				p.L661L		Atlas-SNP	.											.	STAB2	370	.	0			c.G1983A						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	135.0	131.0	133.0		1983	0.9	1.0	12	dbSNP_134	133	113,8487	60.6+/-122.4	0,113,4187	no	coding-synonymous	STAB2	NM_017564.9		0,126,6377	AA,AG,GG		1.314,0.2951,0.9688		661/2552	104056737	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon18			GATTCTGCCCCAT	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.1983G>A	12.37:g.104056737G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			G|0.993;A|0.007	0.007	strong		0.458	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
FOLH1	2346	hgsc.bcm.edu	37	11	49227620	49227620	+	Splice_Site	SNP	A	A	G	rs202676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49227620A>G	ENST00000256999.2	-	2	483	c.223T>C	c.(223-225)Tat>Cat	p.Y75H	FOLH1_ENST00000340334.7_Splice_Site_p.Y60H|FOLH1_ENST00000533034.1_Splice_Site_p.Y60H|FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000356696.3_Splice_Site_p.Y75H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	75			Y -> H (in dbSNP:rs202676). {ECO:0000269|PubMed:9838072}.		folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGTACTTACTATAAGAACTTC	0.294													A|||	1935	0.386382	0.6021	0.2896	5008	,	,		16366	0.3155		0.2256	False		,,,				2504	0.4018				p.Y75H		Atlas-SNP	.											.	FOLH1	141	.	0			c.T223C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,,HIS/TYR	2305,2095	599.3+/-389.2	593,1119,488	68.0	68.0	68.0		223,178,178,,223	1.9	0.9	11	dbSNP_79	68	1924,6662	337.1+/-322.1	206,1512,2575	yes	missense-near-splice,missense-near-splice,missense-near-splice,utr-5,missense-near-splice	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	83,83,83,,83	799,2631,3063	GG,GA,AA		22.4086,47.6136,32.5658	benign,benign,benign,,benign	75/720,60/736,60/705,,75/751	49227620	4229,8757	2200	4293	6493	SO:0001630	splice_region_variant	2346	exon2			CTTACTATAAGAA	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.224+1T>C	11.37:g.49227620A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	755	0.3456959706959707	288	0.5853658536585366	96	0.26519337016574585	197	0.34440559440559443	174	0.22955145118733508	A	0.951	-0.706256	0.03255	0.523864	0.224086	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724;ENST00000529117	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	4.29	1.93	0.25924	.	0.293789	0.24436	N	0.038558	T	0.00012	0.0000	N	0.11724	0.165	0.09310	P	0.9999999999994258	B;B;B;B;B	0.13145	0.007;0.0;0.0;0.004;0.0	B;B;B;B;B	0.17722	0.019;0.002;0.0;0.012;0.0	T	0.43163	-0.9408	9	0.41790	T	0.15	.	7.8033	0.29187	0.7216:0.0:0.2784:0.0	rs202676;rs7937199;rs52836105;rs58342698;rs202676	60;60;60;75;75	Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609	.;.;.;.;FOLH1_HUMAN	H	75;75;60;60;75;18	ENSP00000256999:Y75H;ENSP00000349129:Y75H;ENSP00000344131:Y60H;ENSP00000431463:Y60H;ENSP00000431577:Y18H	ENSP00000256999:Y75H	Y	-	1	0	FOLH1	49184196	0.800000	0.28916	0.906000	0.35671	0.393000	0.30537	0.183000	0.16919	0.011000	0.14865	-1.186000	0.01703	TAT	A|0.657;G|0.343	0.343	strong		0.294	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	Missense_Mutation
ALDH1B1	219	hgsc.bcm.edu	37	9	38396065	38396065	+	Missense_Mutation	SNP	G	G	T	rs2073478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:38396065G>T	ENST00000377698.3	+	2	473	c.320G>T	c.(319-321)cGc>cTc	p.R107L		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	107			L -> R (in allele ALDHA1B1*3; dbSNP:rs2073478). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15164053, 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)		CTGCTGAACCGCCTGGCAGAC	0.627													G|||	1978	0.394968	0.2572	0.3646	5008	,	,		17971	0.3036		0.6093	False		,,,				2504	0.4765				p.R107L		Atlas-SNP	.											ALDH1B1,colon,carcinoma,0,1	ALDH1B1	50	1	0			c.G320T						PASS	.	G	LEU/ARG	1354,3052	450.6+/-349.4	214,926,1063	80.0	89.0	86.0		320	2.8	1.0	9	dbSNP_96	86	5192,3408	639.3+/-399.4	1574,2044,682	yes	missense	ALDH1B1	NM_000692.4	102	1788,2970,1745	TT,TG,GG		39.6279,30.7308,49.6694	benign	107/518	38396065	6546,6460	2203	4300	6503	SO:0001583	missense	219	exon2			TGAACCGCCTGGC	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.320G>T	9.37:g.38396065G>T	ENSP00000366927:p.Arg107Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	917	0.4198717948717949	140	0.2845528455284553	156	0.430939226519337	167	0.291958041958042	454	0.5989445910290238	G	17.79	3.476510	0.63737	0.307308	0.603721	ENSG00000137124	ENST00000377698	T	0.78246	-1.16	5.61	2.79	0.32731	.	0.182441	0.37761	N	0.001953	T	0.00012	0.0000	.	.	.	0.23563	P	0.99740854	.	.	.	.	.	.	T	0.48758	-0.9007	6	0.72032	D	0.01	.	7.7413	0.28843	0.1173:0.0:0.7444:0.1383	rs2073478;rs17844915;rs17857639;rs56596067;rs60107705;rs2073478	.	.	.	L	107	ENSP00000366927:R107L	ENSP00000366927:R107L	R	+	2	0	ALDH1B1	38386065	0.493000	0.26035	0.990000	0.47175	0.995000	0.86356	2.228000	0.42981	0.332000	0.23536	0.655000	0.94253	CGC	A|0.003;C|0.003	.	strong		0.627	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
C11orf16	56673	hgsc.bcm.edu	37	11	8942942	8942942	+	Missense_Mutation	SNP	C	C	T	rs2653601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	144	2	0.0138889		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	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	
ZNF350	59348	hgsc.bcm.edu	37	19	52468587	52468587	+	Silent	SNP	G	G	T	rs3764538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52468587G>T	ENST00000243644.4	-	5	1346	c.1119C>A	c.(1117-1119)ccC>ccA	p.P373P	ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	373					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		TACATTCAAAGGGTTTCTCTC	0.428													G|||	880	0.175719	0.1029	0.1297	5008	,	,		21165	0.2331		0.1471	False		,,,				2504	0.2771				p.P373P		Atlas-SNP	.											.	ZNF350	48	.	0			c.C1119A						PASS	.	G		630,3776	272.8+/-271.0	52,526,1625	64.0	61.0	62.0		1119	-2.0	0.9	19	dbSNP_107	62	1096,7504	228.4+/-263.5	72,952,3276	no	coding-synonymous	ZNF350	NM_021632.3		124,1478,4901	TT,TG,GG		12.7442,14.2987,13.2708		373/533	52468587	1726,11280	2203	4300	6503	SO:0001819	synonymous_variant	59348	exon5			TTCAAAGGGTTTC	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1119C>A	19.37:g.52468587G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	37	CCDS12845.1																																																																																			G|0.855;T|0.145	0.145	strong		0.428	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821467	100821467	+	Silent	SNP	G	G	A	rs7496640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:100821467G>A	ENST00000268070.4	-	4	861	c.756C>T	c.(754-756)gcC>gcT	p.A252A		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	252	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)		ACCTCTGGGCGGCCTCGGCCC	0.642													G|||	2504	0.5	0.5	0.5605	5008	,	,		14806	0.505		0.3499	False		,,,				2504	0.6063				p.A252A		Atlas-SNP	.											ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	0			c.C756T						PASS	.	G		2145,2261	572.9+/-383.4	517,1111,575	64.0	70.0	68.0		756	-9.6	0.9	15	dbSNP_116	68	2862,5738	445.9+/-361.1	447,1968,1885	no	coding-synonymous	ADAMTS17	NM_139057.2		964,3079,2460	AA,AG,GG		33.2791,48.6836,38.4976		252/1096	100821467	5007,7999	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon4			CTGGGCGGCCTCG	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.756C>T	15.37:g.100821467G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			G|0.576;A|0.424	0.424	strong		0.642	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
LRP2	4036	hgsc.bcm.edu	37	2	170053505	170053505	+	Missense_Mutation	SNP	C	C	T	rs2228171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	38	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	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	
ERI2	112479	hgsc.bcm.edu	37	16	20810067	20810067	+	Missense_Mutation	SNP	T	T	C	rs3213646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:20810067T>C	ENST00000357967.4	-	9	1097	c.1055A>G	c.(1054-1056)tAt>tGt	p.Y352C	ERI2_ENST00000563117.1_Missense_Mutation_p.Y259C|ERI2_ENST00000389345.5_Missense_Mutation_p.Y87C|ERI2_ENST00000564349.1_Missense_Mutation_p.Y259C|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000569729.1_Intron	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	352				Y -> C (in Ref. 4; BAA96028). {ECO:0000305}.			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						CTTTTGCATATAGATAGGTGA	0.383													T|||	1602	0.319888	0.0915	0.5014	5008	,	,		20635	0.1528		0.5805	False		,,,				2504	0.4039				p.Y352C		Atlas-SNP	.											.	ERI2	50	.	0			c.A1055G						PASS	.	T	CYS/TYR,	245,1139		18,209,465	105.0	90.0	95.0		1055,	-4.4	0.0	16	dbSNP_106	95	1820,1362		509,802,280	yes	missense,intron	ERI2	NM_001142725.1,NM_080663.2	194,	527,1011,745	CC,CT,TT		42.8033,17.7023,45.2256	benign,	352/692,	20810067	2065,2501	692	1591	2283	SO:0001583	missense	112479	exon9			TGCATATAGATAG	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.1055A>G	16.37:g.20810067T>C	ENSP00000350651:p.Tyr352Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	747	0.34203296703296704	54	0.10975609756097561	168	0.46408839779005523	88	0.15384615384615385	437	0.5765171503957783	T	7.807	0.714797	0.15306	0.177023	0.571967	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.19105	2.21;2.17	4.94	-4.38	0.03622	.	2.213460	0.01814	N	0.033658	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	9	0.40728	T	0.16	1.6145	4.0005	0.09577	0.1145:0.2589:0.4658:0.1609	rs3213646;rs17690686;rs52837000;rs58027232;rs3213646	352	A8K979	ERI2_HUMAN	C	352;87	ENSP00000350651:Y352C;ENSP00000373996:Y87C	ENSP00000350651:Y352C	Y	-	2	0	ERI2	20717568	0.000000	0.05858	0.001000	0.08648	0.733000	0.41908	-0.080000	0.11339	-0.792000	0.04480	0.533000	0.62120	TAT	T|0.674;C|0.326	0.326	strong		0.383	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
TMCO4	255104	hgsc.bcm.edu	37	1	20009737	20009737	+	Silent	SNP	G	G	A	rs10917514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20009737G>A	ENST00000294543.6	-	16	1942	c.1701C>T	c.(1699-1701)tcC>tcT	p.S567S	TMCO4_ENST00000375122.2_Silent_p.S527S|TMCO4_ENST00000489814.1_5'UTR|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	165	0	0		WXS	Illumina HiSeq	Phase_I	201	84	0.41791	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	
ZSCAN22	342945	hgsc.bcm.edu	37	19	58850357	58850357	+	Missense_Mutation	SNP	G	G	A	rs138944686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58850357G>A	ENST00000329665.4	+	3	1288	c.1141G>A	c.(1141-1143)Gag>Aag	p.E381K		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	381					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(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		GCGGCCCTACGAGTGTGACGC	0.607													G|||	69	0.013778	0.025	0.0202	5008	,	,		19277	0.0		0.0209	False		,,,				2504	0.001				p.E381K		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G1141A						PASS	.	G	LYS/GLU	69,4337	63.5+/-100.7	1,67,2135	68.0	64.0	65.0		1141	0.3	0.2	19	dbSNP_134	65	87,8513	51.1+/-111.2	1,85,4214	no	missense	ZSCAN22	NM_181846.2	56	2,152,6349	AA,AG,GG		1.0116,1.566,1.1994	possibly-damaging	381/492	58850357	156,12850	2203	4300	6503	SO:0001583	missense	342945	exon3			CCCTACGAGTGTG	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"""-"", ""Zinc fingers, C2H2-type"""	4929	protein-coding gene	gene with protein product	"""oncogene HKR2"""	165260	"""zinc finger protein 50"", ""GLI-Kruppel family member HKR2"""	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.1141G>A	19.37:g.58850357G>A	ENSP00000332433:p.Glu381Lys	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	37	CCDS12975.1	39	0.017857142857142856	14	0.028455284552845527	8	0.022099447513812154	0	0.0	17	0.022427440633245383	G	8.214	0.801043	0.16397	0.01566	0.010116	ENSG00000182318	ENST00000329665	T	0.06608	3.28	3.72	0.353	0.16058	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00580	0.0019	N	0.01284	-0.91	0.09310	N	1	B	0.27117	0.168	B	0.15052	0.012	T	0.44375	-0.9332	9	0.27082	T	0.32	.	0.7237	0.00945	0.2251:0.1908:0.3878:0.1963	.	381	P10073	ZSC22_HUMAN	K	381	ENSP00000332433:E381K	ENSP00000332433:E381K	E	+	1	0	ZSCAN22	63542169	0.000000	0.05858	0.163000	0.22734	0.372000	0.29890	-2.584000	0.00904	0.344000	0.23847	-0.300000	0.09419	GAG	G|0.986;A|0.014	0.014	strong		0.607	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
ASTN1	460	hgsc.bcm.edu	37	1	176992676	176992676	+	Silent	SNP	C	C	T	rs10798496	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:176992676C>T	ENST00000367654.3	-	7	1513	c.1302G>A	c.(1300-1302)caG>caA	p.Q434Q	ASTN1_ENST00000367657.3_Silent_p.Q434Q|ASTN1_ENST00000424564.2_Silent_p.Q434Q|ASTN1_ENST00000361833.2_Silent_p.Q434Q|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	434					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TGGCATCCAGCTGGCTCCCCT	0.607													C|||	1187	0.237021	0.264	0.2248	5008	,	,		18455	0.003		0.4364	False		,,,				2504	0.2454				p.Q434Q		Atlas-SNP	.											.	ASTN1	314	.	0			c.G1302A						PASS	.	C	,	1212,3194	414.6+/-336.9	177,858,1168	41.0	38.0	39.0		1302,1302	2.7	1.0	1	dbSNP_120	39	3682,4918	520.5+/-379.7	777,2128,1395	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	954,2986,2563	TT,TC,CC		42.814,27.5079,37.6288	,	434/1295,434/1217	176992676	4894,8112	2203	4300	6503	SO:0001819	synonymous_variant	460	exon7			ATCCAGCTGGCTC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1302G>A	1.37:g.176992676C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	129	49	0.379845	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				C|0.677;T|0.323	0.323	strong		0.607	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610009	32610009	+	Missense_Mutation	SNP	C	C	G	rs2308891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32610009C>G	ENST00000343139.5	+	3	694	c.592C>G	c.(592-594)Cag>Gag	p.Q198E	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.Q198E|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.Q198E	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	197	Alpha-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)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGGCCTGGACCAGCCTCTTCT	0.448													.|||	1501	0.29972	0.2073	0.3977	5008	,	,		13880	0.3304		0.3191	False		,,,				2504	0.3037				p.Q198E		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C592G						PASS	.	G	GLU/GLN	1002,2012		326,350,831	101.0	105.0	103.0		592	-7.1	0.0	6	dbSNP_123	103	2297,3115		753,791,1162	no	missense	HLA-DQA1	NM_002122.3	29	1079,1141,1993	GG,GC,CC		42.4427,33.2449,39.1526	benign	198/256	32610009	3299,5127	1507	2706	4213	SO:0001583	missense	3117	exon3			CTGGACCAGCCTC		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.592C>G	6.37:g.32610009C>G	ENSP00000339398:p.Gln198Glu	Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	121	98	0.809917	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	971	0.44459706959706957	155	0.3150406504065041	201	0.5552486187845304	278	0.486013986013986	337	0.4445910290237467	.	0.004	-2.328993	0.00229	0.332449	0.424427	ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	T;T;T;T	0.02552	4.25;4.25;4.25;4.25	4.08	-7.11	0.01542	.	0.770143	0.11459	N	0.561938	T	0.00271	0.0008	N	0.03016	-0.435	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38415	-0.9662	9	0.02654	T	1	.	7.9996	0.30288	0.5421:0.3066:0.1513:0.0	rs2308891;rs5020391;rs9272753;rs9272754	204;198	Q59F33;G4XQK2	.;.	E	198	ENSP00000339398:Q198E;ENSP00000378767:Q198E;ENSP00000437302:Q198E;ENSP00000364087:Q198E	ENSP00000339398:Q198E	Q	+	1	0	HLA-DQA1	32717987	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-2.454000	0.01004	-2.029000	0.00930	-0.763000	0.03452	CAG	A|0.077;C|0.499;G|0.424	0.424	strong		0.448	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
MET	4233	hgsc.bcm.edu	37	7	116436022	116436022	+	Silent	SNP	G	G	A	rs2023748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	179	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	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		
PTGS1	5742	hgsc.bcm.edu	37	9	125143792	125143792	+	Silent	SNP	C	C	A	rs5788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:125143792C>A	ENST00000362012.2	+	6	644	c.639C>A	c.(637-639)ggC>ggA	p.G213G	PTGS1_ENST00000223423.4_Silent_p.G213G|PTGS1_ENST00000373698.5_Silent_p.G104G|PTGS1_ENST00000540753.1_Silent_p.G188G	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	213					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.G213G(1)		large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAACTTCTGGCAAGATGGGTC	0.542													C|||	1356	0.270767	0.6876	0.2406	5008	,	,		19091	0.0407		0.1402	False		,,,				2504	0.1002				p.G213G		Atlas-SNP	.											PTGS1,NS,carcinoma,0,1	PTGS1	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C639A						scavenged	.	C	,	2612,1794	640.2+/-397.3	804,1004,395	65.0	71.0	69.0		639,639	1.9	1.0	9	dbSNP_52	69	1130,7470	233.0+/-266.5	70,990,3240	no	coding-synonymous,coding-synonymous	PTGS1	NM_000962.2,NM_080591.1	,	874,1994,3635	AA,AC,CC		13.1395,40.7172,28.7713	,	213/600,213/563	125143792	3742,9264	2203	4300	6503	SO:0001819	synonymous_variant	5742	exon6			TTCTGGCAAGATG	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.639C>A	9.37:g.125143792C>A		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	132	78	0.590909	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Silent	SNP	ENST00000362012.2	37	CCDS6842.1																																																																																			C|0.722;A|0.278	0.278	strong		0.542	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548628	32548628	+	Missense_Mutation	SNP	G	G	A	rs34624872	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32548628G>A	ENST00000360004.5	-	4	763	c.658C>T	c.(658-660)Cgg>Tgg	p.R220W		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	220	Beta-2.				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						GATTCAGACCGTGCTCCTGAG	0.483										Multiple Myeloma(14;0.17)																											p.R220W		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C658T						PASS	.						77.0	86.0	83.0					6																	32548628		1511	2709	4220	SO:0001583	missense	3123	exon4			CAGACCGTGCTCC	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.658C>T	6.37:g.32548628G>A	ENSP00000353099:p.Arg220Trp	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	196	51	0.260204	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.70	2.016010	0.35606	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	3.98	0.46160	Immunoglobulin-like fold (3);	0.849923	0.10912	N	0.620484	T	0.00580	0.0019	L	0.56769	1.78	0.24665	N	0.993446	B;B;D	0.71674	0.007;0.007;0.998	B;B;P	0.47430	0.0;0.001;0.547	T	0.53995	-0.8359	10	0.66056	D	0.02	.	10.0825	0.42399	0.0:0.2056:0.7944:0.0	rs34624872	220;220;220	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	W	220	ENSP00000353099:R220W	ENSP00000353099:R220W	R	-	1	2	HLA-DRB1	32656606	0.013000	0.17824	0.747000	0.31113	0.149000	0.21700	1.804000	0.38873	1.943000	0.56356	0.453000	0.30009	CGG	G|0.814;A|0.185	0.185	strong		0.483	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
HECTD1	25831	hgsc.bcm.edu	37	14	31582526	31582526	+	Silent	SNP	T	T	C	rs2273483	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31582526T>C	ENST00000399332.1	-	33	6509	c.6021A>G	c.(6019-6021)ctA>ctG	p.L2007L	HECTD1_ENST00000553700.1_Silent_p.L2007L	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2007					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CAACTATATATAGAATACGCA	0.373													C|||	2673	0.533746	0.7549	0.5	5008	,	,		14301	0.376		0.4215	False		,,,				2504	0.5368				p.L2007L		Atlas-SNP	.											HECTD1,rectum,carcinoma,0,1	HECTD1	159	1	0			c.A6021G						PASS	.	C		2479,1217		830,819,199	123.0	118.0	119.0		6021	3.0	1.0	14	dbSNP_100	119	3329,4851		682,1965,1443	no	coding-synonymous	HECTD1	NM_015382.2		1512,2784,1642	CC,CT,TT		40.6968,32.9275,48.9054		2007/2611	31582526	5808,6068	1848	4090	5938	SO:0001819	synonymous_variant	25831	exon33			TATATATAGAATA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6021A>G	14.37:g.31582526T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1	1078	0.4935897435897436	375	0.7621951219512195	183	0.505524861878453	206	0.36013986013986016	314	0.41424802110817943	C	0.183	-1.060382	0.01950	0.670725	0.406968	ENSG00000092148	ENST00000554882	.	.	.	5.94	3.05	0.35203	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25293	-1.0136	3	.	.	.	-4.2389	4.2472	0.10677	0.117:0.5125:0.2434:0.127	rs2273483;rs61584938;rs2273483	.	.	.	C	373	.	.	Y	-	2	0	HECTD1	30652277	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	0.790000	0.26900	0.424000	0.26061	-0.755000	0.03482	TAT	T|0.505;C|0.495	0.495	strong		0.373	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
SAMD15	161394	hgsc.bcm.edu	37	14	77845121	77845121	+	Missense_Mutation	SNP	A	A	G	rs2193595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77845121A>G	ENST00000216471.4	+	1	1646	c.1360A>G	c.(1360-1362)Aaa>Gaa	p.K454E	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	454			K -> E (in dbSNP:rs2193595).					p.K454E(1)		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						ACTAAGTGACAAATTTAGAAA	0.373													G|||	2569	0.512979	0.888	0.4841	5008	,	,		21569	0.0883		0.497	False		,,,				2504	0.4806				p.K454E		Atlas-SNP	.											SAMD15,NS,carcinoma,0,1	SAMD15	60	1	1	Substitution - Missense(1)	stomach(1)	c.A1360G						PASS	.	G	GLU/LYS	3626,780	313.0+/-292.9	1499,628,76	74.0	73.0	73.0		1360	-2.4	0.0	14	dbSNP_96	73	4023,4577	597.9+/-393.8	955,2113,1232	yes	missense	SAMD15	NM_001010860.1	56	2454,2741,1308	GG,GA,AA		46.7791,17.7031,41.1887	benign	454/675	77845121	7649,5357	2203	4300	6503	SO:0001583	missense	161394	exon1			AGTGACAAATTTA	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.1360A>G	14.37:g.77845121A>G	ENSP00000216471:p.Lys454Glu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	1051	0.48122710622710624	436	0.8861788617886179	197	0.5441988950276243	43	0.07517482517482517	375	0.4947229551451187	G	0.019	-1.454591	0.01071	0.822969	0.467791	ENSG00000100583	ENST00000216471	T	0.34275	1.37	2.27	-2.42	0.06542	.	.	.	.	.	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35500	-0.9786	8	0.02654	T	1	.	3.7904	0.08718	0.4507:0.1975:0.3518:0.0	rs2193595;rs3742735;rs52827749;rs57272414;rs2193595	454	Q9P1V8	SAM15_HUMAN	E	454	ENSP00000216471:K454E	ENSP00000216471:K454E	K	+	1	0	SAMD15	76914874	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.968000	0.03817	-0.675000	0.05246	-0.227000	0.12334	AAA	A|0.451;G|0.549	0.549	strong		0.373	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
BSG	682	hgsc.bcm.edu	37	19	580665	580665	+	Silent	SNP	T	T	C	rs4682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:580665T>C	ENST00000333511.3	+	5	745	c.675T>C	c.(673-675)gcT>gcC	p.A225A	BSG_ENST00000545507.2_Silent_p.A16A|BSG_ENST00000353555.4_Silent_p.A109A|BSG_ENST00000346916.4_Silent_p.A45A	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	225	Ig-like V-type.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		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)		GAGTGAAGGCTGTGAAGTCGT	0.637													T|||	1635	0.326478	0.3275	0.2853	5008	,	,		16585	0.4563		0.1899	False		,,,				2504	0.3609				p.A225A		Atlas-SNP	.											BSG_ENST00000346916,NS,carcinoma,0,4	BSG	48	4	0			c.T675C						PASS	.	T	,,	1289,3113	431.0+/-342.8	202,885,1114	60.0	60.0	60.0		675,327,135	-8.2	0.0	19	dbSNP_52	60	1845,6755	328.2+/-318.2	199,1447,2654	no	coding-synonymous,coding-synonymous,coding-synonymous	BSG	NM_001728.2,NM_198589.1,NM_198591.1	,,	401,2332,3768	CC,CT,TT		21.4535,29.2821,24.104	,,	225/386,109/270,45/206	580665	3134,9868	2201	4300	6501	SO:0001819	synonymous_variant	682	exon5			GAAGGCTGTGAAG	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.675T>C	19.37:g.580665T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	37	CCDS12033.1																																																																																			T|0.744;C|0.256	0.256	strong		0.637	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
BRF1	2972	hgsc.bcm.edu	37	14	105688082	105688082	+	Silent	SNP	C	C	T	rs28406206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105688082C>T	ENST00000546474.1	-	11	16177	c.1218G>A	c.(1216-1218)ccG>ccA	p.P406P	BRF1_ENST00000327359.3_Silent_p.P291P|BRF1_ENST00000440513.3_Silent_p.P291P|BRF1_ENST00000392557.4_Silent_p.P202P|BRF1_ENST00000551787.1_Intron|BRF1_ENST00000549044.1_5'Flank|BRF1_ENST00000547530.1_5'UTR|BRF1_ENST00000379932.4_Intron|BRF1_ENST00000446501.2_Silent_p.P168P|BRF1_ENST00000379937.2_Silent_p.P379P	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	406					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ACCCCAGGGCCGGAGGTCTGC	0.672													C|||	245	0.0489217	0.0719	0.0476	5008	,	,		15085	0.0		0.0905	False		,,,				2504	0.0266				p.P406P		Atlas-SNP	.											.	BRF1	102	.	0			c.G1218A						PASS	.	C	,,,,,	350,4044		18,314,1865	14.0	18.0	17.0		873,873,1137,504,1218,606	-9.3	0.0	14	dbSNP_125	17	751,7829		34,683,3573	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRF1	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001242789.1,NM_001519.3,NM_145685.2	,,,,,	52,997,5438	TT,TC,CC		8.7529,7.9654,8.4862	,,,,,	291/585,291/563,379/651,168/440,406/678,202/474	105688082	1101,11873	2197	4290	6487	SO:0001819	synonymous_variant	2972	exon11			CAGGGCCGGAGGT	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.1218G>A	14.37:g.105688082C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1																																																																																			C|0.927;T|0.073	0.073	strong		0.672	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
MMP9	4318	hgsc.bcm.edu	37	20	44640225	44640225	+	Missense_Mutation	SNP	A	A	G	rs17576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44640225A>G	ENST00000372330.3	+	6	855	c.836A>G	c.(835-837)cAg>cGg	p.Q279R	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	279			Q -> R (common polymorphism; may be associated with susceptibility to IDD; dbSNP:rs17576). {ECO:0000269|PubMed:10598806, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2551898, ECO:0000269|Ref.4}.		collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CTCTACACCCAGGACGGCAAT	0.582											OREG0025989	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2281	0.455471	0.3442	0.2277	5008	,	,		18346	0.7391		0.3807	False		,,,				2504	0.5521				p.Q279R		Atlas-SNP	.											.	MMP9	84	.	0			c.A836G	GRCh37	CM062877	MMP9	M	rs17576	PASS	.	A	ARG/GLN	1533,2873	483.2+/-359.6	267,999,937	100.0	92.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	836	2.7	1.0	20	dbSNP_63	95	2991,5609	463.4+/-366.0	518,1955,1827	yes	missense	MMP9	NM_004994.2	43	785,2954,2764	GG,GA,AA		34.7791,34.7935,34.7839	benign	279/708	44640225	4524,8482	2203	4300	6503	SO:0001583	missense	4318	exon6			ACACCCAGGACGG		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.836A>G	20.37:g.44640225A>G	ENSP00000361405:p.Gln279Arg	Somatic	61	0	0	925	WXS	Illumina HiSeq	Phase_I	46	46	1	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	983	0.4500915750915751	172	0.34959349593495936	103	0.2845303867403315	413	0.722027972027972	295	0.3891820580474934	A	11.82	1.753923	0.31046	0.347935	0.347791	ENSG00000100985	ENST00000372330	T	0.08984	3.03	3.92	2.71	0.32032	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (1);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.648390	0.14719	N	0.302456	T	0.00012	0.0000	N	0.11560	0.145	0.41443	P	0.012062000000000017	B	0.11235	0.004	B	0.14023	0.01	T	0.13124	-1.0521	9	0.30078	T	0.28	.	9.3516	0.38142	0.8401:0.0:0.0:0.1599	rs17576;rs2664538;rs17845069;rs17857851;rs52800421;rs61231474;rs17576	279	P14780	MMP9_HUMAN	R	279	ENSP00000361405:Q279R	ENSP00000361405:Q279R	Q	+	2	0	MMP9	44073632	0.132000	0.22450	1.000000	0.80357	0.949000	0.60115	2.309000	0.43699	1.778000	0.52293	0.459000	0.35465	CAG	A|0.578;G|0.422	0.422	strong		0.582	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
NID2	22795	hgsc.bcm.edu	37	14	52534758	52534758	+	Missense_Mutation	SNP	C	C	G	rs61734508	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52534758C>G	ENST00000216286.5	-	2	351	c.352G>C	c.(352-354)Ggc>Cgc	p.G118R	NID2_ENST00000541773.1_Missense_Mutation_p.G65R	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	118	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				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)					CGGCCTCTGCCGTGGCTCGTG	0.652													C|||	41	0.0081869	0.0008	0.0144	5008	,	,		16613	0.0		0.0219	False		,,,				2504	0.0082				p.G118R		Atlas-SNP	.											.	NID2	201	.	0			c.G352C						PASS	.	C	ARG/GLY	25,4379	28.1+/-56.4	0,25,2177	27.0	32.0	30.0		352	4.7	0.8	14	dbSNP_129	30	193,8405	82.3+/-144.9	3,187,4109	yes	missense	NID2	NM_007361.3	125	3,212,6286	GG,GC,CC		2.2447,0.5677,1.6767	probably-damaging	118/1376	52534758	218,12784	2202	4299	6501	SO:0001583	missense	22795	exon2			CTCTGCCGTGGCT	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.352G>C	14.37:g.52534758C>G	ENSP00000216286:p.Gly118Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	35	5.438062	0.96168	0.005677	0.022447	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.37584	1.19;1.19	5.58	4.68	0.58851	Nidogen, extracellular domain (2);	0.044802	0.85682	D	0.000000	T	0.33904	0.0879	M	0.76170	2.325	0.35775	D	0.821189	D;D;D	0.89917	1.0;1.0;0.989	D;D;P	0.69307	0.963;0.959;0.901	T	0.65294	-0.6203	10	0.87932	D	0	.	13.5203	0.61563	0.0:0.9239:0.0:0.0761	rs61734508	65;120;118	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	R	118;118;65;120	ENSP00000216286:G118R;ENSP00000443730:G65R	ENSP00000216286:G118R	G	-	1	0	NID2	51604508	0.997000	0.39634	0.785000	0.31869	0.991000	0.79684	4.395000	0.59678	1.327000	0.45338	0.563000	0.77884	GGC	C|0.977;G|0.023	0.023	strong		0.652	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
IGFN1	91156	hgsc.bcm.edu	37	1	201183424	201183424	+	Missense_Mutation	SNP	G	G	A	rs41304263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201183424G>A	ENST00000335211.4	+	13	8978	c.8848G>A	c.(8848-8850)Gtc>Atc	p.V2950I	IGFN1_ENST00000451870.2_Missense_Mutation_p.V493I|IGFN1_ENST00000295591.8_Missense_Mutation_p.V110I	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	493						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						TAAGGATGGCGTCAAGGTACT	0.577													G|||	97	0.019369	0.0076	0.0389	5008	,	,		17684	0.0		0.0437	False		,,,				2504	0.0164				p.V2950I		Atlas-SNP	.											.	IGFN1	220	.	0			c.G8848A						PASS	.	G	ILE/VAL	80,4326	65.3+/-102.7	0,80,2123	66.0	51.0	56.0		8848	2.8	1.0	1	dbSNP_127	56	522,8078	142.2+/-198.4	16,490,3794	yes	missense	IGFN1	NM_001164586.1	29	16,570,5917	AA,AG,GG		6.0698,1.8157,4.6286	benign	2950/3709	201183424	602,12404	2203	4300	6503	SO:0001583	missense	91156	exon13			GATGGCGTCAAGG	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.8848G>A	1.37:g.201183424G>A	ENSP00000334714:p.Val2950Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	57|57	0.0260989010989011|0.0260989010989011	11|11	0.022357723577235773|0.022357723577235773	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	32|32	0.04221635883905013|0.04221635883905013	G|G	12.91|12.91	2.079584|2.079584	0.36662|0.36662	0.018157|0.018157	0.060698|0.060698	ENSG00000163395|ENSG00000163395	ENST00000412892|ENST00000335211;ENST00000451870;ENST00000295591	.|T;T;T	.|0.66815	.|-0.23;-0.23;-0.23	3.66|3.66	2.75|2.75	0.32379|0.32379	.|.	.|0.540943	.|0.16807	.|N	.|0.198737	T|T	0.14700|0.14700	0.0355|0.0355	M|M	0.64567|0.64567	1.98|1.98	0.20926|0.20926	N|N	0.999824|0.999824	.|B	.|0.33940	.|0.433	.|B	.|0.38954	.|0.286	T|T	0.38090|0.38090	-0.9677|-0.9677	5|10	.|0.44086	.|T	.|0.13	.|.	2.1086|2.1086	0.03697|0.03697	0.1078:0.1664:0.4439:0.2819|0.1078:0.1664:0.4439:0.2819	rs41304263;rs61739654|rs41304263;rs61739654	.|2950	.|F8WAI1	.|.	H|I	367|2950;493;110	.|ENSP00000334714:V2950I;ENSP00000398386:V493I;ENSP00000295591:V110I	.|ENSP00000295591:V110I	R|V	+|+	2|1	0|0	IGFN1|IGFN1	199450047|199450047	0.136000|0.136000	0.22515|0.22515	0.996000|0.996000	0.52242|0.52242	0.611000|0.611000	0.37282|0.37282	0.563000|0.563000	0.23547|0.23547	0.748000|0.748000	0.32831|0.32831	0.462000|0.462000	0.41574|0.41574	CGT|GTC	G|0.960;A|0.040	0.040	strong		0.577	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
OR51B6	390058	hgsc.bcm.edu	37	11	5373311	5373311	+	Missense_Mutation	SNP	T	T	C	rs201581003|rs386750142|rs5006883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373311T>C	ENST00000380219.1	+	1	574	c.574T>C	c.(574-576)Ttc>Ctc	p.F192L	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	192			F -> L (in dbSNP:rs5006883). {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)			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)		TGACATCACCTTCAACCGTCT	0.438													T|||	1172	0.234026	0.3275	0.2349	5008	,	,		23945	0.0863		0.2644	False		,,,				2504	0.228				p.F192L		Atlas-SNP	.											OR51B6,NS,carcinoma,-1,1	OR51B6	53	1	0			c.T574C						PASS	.	T	LEU/PHE	973,3429		172,629,1400	218.0	193.0	202.0		574	5.2	1.0	11	dbSNP_113	202	1931,6663		302,1327,2668	yes	missense	OR51B6	NM_001004750.1	22	474,1956,4068	CC,CT,TT		22.4692,22.1036,22.3453	possibly-damaging	192/313	5373311	2904,10092	2201	4297	6498	SO:0001583	missense	390058	exon1			ATCACCTTCAACC		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.574T>C	11.37:g.5373311T>C	ENSP00000369568:p.Phe192Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	180	80	0.444444	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	473	0.21657509157509158	160	0.3252032520325203	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	T	14.91	2.677503	0.47886	0.221036	0.224692	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00021	9.02	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000030	T	0.00012	0.0000	L	0.45422	1.42	0.33219	P	0.44557800000000003	D	0.89917	1.0	D	0.91635	0.999	T	0.48570	-0.9024	9	0.40728	T	0.16	.	5.3614	0.16089	0.0:0.0883:0.1795:0.7322	rs5006883;rs52793310;rs59096293;rs5006883	192	Q9H340	O51B6_HUMAN	L	191;192	ENSP00000369568:F192L	ENSP00000369568:F192L	F	+	1	0	OR51B6	5329887	0.000000	0.05858	0.998000	0.56505	0.555000	0.35460	-1.108000	0.03313	2.157000	0.67596	0.455000	0.32223	TTC	T|0.772;C|0.228	0.228	strong		0.438	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
CSMD3	114788	hgsc.bcm.edu	37	8	113960093	113960093	+	Silent	SNP	A	A	C	rs61753740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:113960093A>C	ENST00000297405.5	-	9	1678	c.1434T>G	c.(1432-1434)ggT>ggG	p.G478G	CSMD3_ENST00000455883.2_Silent_p.G374G|CSMD3_ENST00000352409.3_Silent_p.G478G|CSMD3_ENST00000343508.3_Silent_p.G438G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	478						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						CTGTTTTAATACCTCCCTCAT	0.294										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	4	0.000798722	0.0	0.0	5008	,	,		12495	0.0		0.003	False		,,,				2504	0.001				p.G478G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T1434G						PASS	.	A	,,	2,4404	4.2+/-10.8	0,2,2201	81.0	82.0	82.0		1122,1434,1314	3.9	1.0	8	dbSNP_129	82	34,8564	22.2+/-67.0	0,34,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,36,6466	CC,CA,AA		0.3954,0.0454,0.2768	,,	374/3539,478/3708,438/3668	113960093	36,12968	2203	4299	6502	SO:0001819	synonymous_variant	114788	exon9			TTTAATACCTCCC	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.1434T>G	8.37:g.113960093A>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.997;C|0.003	0.003	strong		0.294	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
AKR1C4	1109	hgsc.bcm.edu	37	10	5247784	5247784	+	Missense_Mutation	SNP	C	C	G	rs3829125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5247784C>G	ENST00000380448.1	+	6	687	c.434C>G	c.(433-435)tCt>tGt	p.S145C	AKR1C4_ENST00000263126.1_Missense_Mutation_p.S145C			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	145			S -> C (in dbSNP:rs3829125). {ECO:0000269|PubMed:10634139}.		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)			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						GTGGATCTCTCTGCCACATGG	0.438													G|||	515	0.102835	0.025	0.2017	5008	,	,		20850	0.1111		0.1203	False		,,,				2504	0.1115				p.S145C		Atlas-SNP	.											.	AKR1C4	57	.	0			c.C434G						PASS	.	G	CYS/SER	185,4221	809.9+/-416.0	4,177,2022	128.0	112.0	117.0		434	3.2	0.1	10	dbSNP_107	117	1302,7298	758.2+/-407.5	95,1112,3093	yes	missense	AKR1C4	NM_001818.3	112	99,1289,5115	GG,GC,CC		15.1395,4.1988,11.4332	benign	145/324	5247784	1487,11519	2203	4300	6503	SO:0001583	missense	1109	exon4			ATCTCTCTGCCAC	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.434C>G	10.37:g.5247784C>G	ENSP00000369814:p.Ser145Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	166	95	0.572289	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	226	0.10347985347985347	5	0.01016260162601626	61	0.1685082872928177	60	0.1048951048951049	100	0.13192612137203166	G	0.001	-3.174814	0.00027	0.041988	0.151395	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.25085	1.82;1.82	3.16	3.16	0.36331	NADP-dependent oxidoreductase domain (3);	0.126528	0.43747	N	0.000535	T	0.00039	0.0001	N	0.05050	-0.12	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33727	-0.9857	9	0.02654	T	1	.	10.1844	0.42988	0.0:0.2064:0.7936:0.0	rs3829125;rs3829125	145	P17516	AK1C4_HUMAN	C	145	ENSP00000369814:S145C;ENSP00000263126:S145C	ENSP00000263126:S145C	S	+	2	0	AKR1C4	5237784	0.906000	0.30813	0.071000	0.20095	0.093000	0.18481	1.318000	0.33643	0.432000	0.26286	-0.647000	0.03941	TCT	C|0.890;G|0.110	0.110	strong		0.438	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
ASPH	444	hgsc.bcm.edu	37	8	62489334	62489334	+	Silent	SNP	C	C	T	rs16927574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:62489334C>T	ENST00000379454.4	-	16	1333	c.1146G>A	c.(1144-1146)gcG>gcA	p.A382A	ASPH_ENST00000541428.1_Silent_p.A353A	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	382					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|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 inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	AGAATACCTGCGCCTTCCCAT	0.383													C|||	654	0.130591	0.1551	0.0994	5008	,	,		16528	0.2371		0.0795	False		,,,				2504	0.0624				p.A382A		Atlas-SNP	.											.	ASPH	87	.	0			c.G1146A						PASS	.	C	,	587,3819	259.2+/-262.9	43,501,1659	171.0	153.0	159.0		1059,1146	-9.1	0.9	8	dbSNP_123	159	557,8043	153.0+/-207.5	13,531,3756	no	coding-synonymous,coding-synonymous	ASPH	NM_001164750.1,NM_004318.3	,	56,1032,5415	TT,TC,CC		6.4767,13.3227,8.7959	,	353/730,382/759	62489334	1144,11862	2203	4300	6503	SO:0001819	synonymous_variant	444	exon16			TACCTGCGCCTTC	AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"""junctin"", ""humbug"", ""junctate"""	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.1146G>A	8.37:g.62489334C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_004318	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Silent	SNP	ENST00000379454.4	37	CCDS34898.1																																																																																			C|0.883;N|0.000	.	strong		0.383	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318	
ERCC5	2073	hgsc.bcm.edu	37	13	103528002	103528002	+	Missense_Mutation	SNP	G	G	C	rs17655	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:103528002G>C	ENST00000355739.4	+	15	4733	c.3310G>C	c.(3310-3312)Gat>Cat	p.D1104H	ERCC5_ENST00000472247.1_3'UTR|ERCC5_ENST00000375954.1_Missense_Mutation_p.D337H	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	1104			D -> H (in dbSNP:rs17655). {ECO:0000269|PubMed:8483504}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTCAAGTGAAGATGCTGAAAG	0.428			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1810	0.361422	0.5008	0.2709	5008	,	,		19196	0.4623		0.2495	False		,,,				2504	0.2485				p.D1558H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.G4672C	GRCh37	CM063964	ERCC5	M	rs17655	PASS	.	G	HIS/ASP,HIS/ASP	2009,2397	558.4+/-380.0	460,1089,654	53.0	55.0	54.0		3310,4672	4.1	0.0	13	dbSNP_63	54	1968,6632	344.4+/-325.3	237,1494,2569	yes	missense,missense	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	81,81	697,2583,3223	CC,CG,GG		22.8837,45.5969,30.5782	,	1104/1187,1558/1641	103528002	3977,9029	2203	4300	6503	SO:0001583	missense	0	exon23	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTGAAGATGCTG	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.3310G>C	13.37:g.103528002G>C	ENSP00000347978:p.Asp1104His	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	823	0.3768315018315018	245	0.49796747967479676	98	0.27071823204419887	283	0.49475524475524474	197	0.2598944591029024	G	18.44	3.624019	0.66901	0.455969	0.228837	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.08807	3.27;3.05	4.96	4.11	0.48088	.	0.687220	0.14782	N	0.298701	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	1.0	D	0.65815	0.995	P	0.57371	0.819	T	0.48514	-0.9029	9	0.40728	T	0.16	-12.1551	13.3474	0.60582	0.0764:0.0:0.9236:0.0	rs17655;rs3188002;rs3825521;rs16960665;rs52825398;rs17655	1104	P28715	ERCC5_HUMAN	H	1529;1104;936;337	ENSP00000347978:D1104H;ENSP00000365121:D337H	ENSP00000347978:D1104H	D	+	1	0	ERCC5	102326003	1.000000	0.71417	0.047000	0.18901	0.012000	0.07955	3.757000	0.55212	1.221000	0.43506	0.650000	0.86243	GAT	G|0.655;C|0.345	0.345	strong		0.428	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
SMC1B	27127	hgsc.bcm.edu	37	22	45748339	45748339	+	Silent	SNP	A	A	G	rs5765275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45748339A>G	ENST00000357450.4	-	22	3416	c.3417T>C	c.(3415-3417)gcT>gcC	p.A1139A	SMC1B_ENST00000404354.3_Intron	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1139	Ala/Asp-rich (DA-box).				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)		ACCTGTGCACAGCAAACAGGA	0.438													G|||	1451	0.289736	0.0499	0.4683	5008	,	,		16723	0.2946		0.494	False		,,,				2504	0.272				p.A1139A		Atlas-SNP	.											SMC1B_ENST00000357450,colon,carcinoma,-1,2	SMC1B	215	2	0			c.T3417C						scavenged	.	G		436,3384		27,382,1501	75.0	74.0	74.0		3417	-1.2	1.0	22	dbSNP_114	74	4259,3963		1097,2065,949	no	coding-synonymous	SMC1B	NM_148674.3		1124,2447,2450	GG,GA,AA		48.2,11.4136,38.9885		1139/1236	45748339	4695,7347	1910	4111	6021	SO:0001819	synonymous_variant	27127	exon22			GTGCACAGCAAAC	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.3417T>C	22.37:g.45748339A>G		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.638;G|0.361	0.361	strong		0.438	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
GABRR1	2569	hgsc.bcm.edu	37	6	89926962	89926962	+	Missense_Mutation	SNP	T	T	C	rs1186902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:89926962T>C	ENST00000454853.2	-	1	190	c.80A>G	c.(79-81)cAc>cGc	p.H27R	GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000481493.1_5'UTR|GABRR1_ENST00000435811.1_Missense_Mutation_p.H27R	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	27			H -> R (in dbSNP:rs1186902).		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)	p.H21R(1)		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)	TCCGGGCCAGTGCATTCTGCT	0.458													T|||	1156	0.230831	0.0711	0.3069	5008	,	,		18130	0.2857		0.2644	False		,,,				2504	0.3016				p.H27R		Atlas-SNP	.											GABRR1,NS,carcinoma,0,1	GABRR1	63	1	1	Substitution - Missense(1)	stomach(1)	c.A80G						PASS	.	T	ARG/HIS	472,3934	222.0+/-238.9	26,420,1757	96.0	79.0	85.0		80	1.8	1.0	6	dbSNP_87	85	2313,6287	387.8+/-342.3	324,1665,2311	yes	missense	GABRR1	NM_002042.3	29	350,2085,4068	CC,CT,TT		26.8953,10.7127,21.4132	benign	27/480	89926962	2785,10221	2203	4300	6503	SO:0001583	missense	2569	exon1			GGCCAGTGCATTC		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.80A>G	6.37:g.89926962T>C	ENSP00000412673:p.His27Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001256703	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	37	CCDS5019.2	513	0.2348901098901099	33	0.06707317073170732	113	0.31215469613259667	164	0.2867132867132867	203	0.2678100263852243	T	9.648	1.140726	0.21205	0.107127	0.268953	ENSG00000146276	ENST00000454853;ENST00000435811	T;T	0.37235	1.21;1.21	5.75	1.76	0.24704	.	0.481200	0.20662	N	0.088011	T	0.09730	0.0239	N	0.24115	0.695	0.38563	P	0.05025400000000002	B;B	0.19445	0.036;0.021	B;B	0.23018	0.043;0.019	T	0.18304	-1.0341	8	.	.	.	-20.5204	12.327	0.55018	0.0:0.0:0.4083:0.5917	rs1186902;rs1998819;rs60344424;rs1186902	27;27	P24046-2;P24046	.;GBRR1_HUMAN	R	27	ENSP00000412673:H27R;ENSP00000394687:H27R	.	H	-	2	0	GABRR1	89983681	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	2.229000	0.42990	0.056000	0.16144	0.528000	0.53228	CAC	T|0.779;C|0.221	0.221	strong		0.458	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
SCN1B	6324	hgsc.bcm.edu	37	19	35524944	35524944	+	Intron	SNP	G	G	C	rs67486287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35524944G>C	ENST00000262631.5	+	3	585				CTD-2527I21.9_ENST00000601692.1_RNA|SCN1B_ENST00000595652.1_Intron|SCN1B_ENST00000596348.1_Intron|SCN1B_ENST00000415950.3_Missense_Mutation_p.R250T	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit						axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	ctgagccaaagggttgtcctg	0.557													G|||	597	0.119209	0.0582	0.1297	5008	,	,		21167	0.1825		0.1461	False		,,,				2504	0.1012				p.R250T		Atlas-SNP	.											.	SCN1B	32	.	0			c.G749C						PASS	.	G	,THR/ARG	136,2124		5,126,999	91.0	102.0	99.0		,749	1.8	0.0	19	dbSNP_130	99	639,3757		42,555,1601	yes	intron,missense	SCN1B	NM_001037.4,NM_199037.3	,71	47,681,2600	CC,CG,GG		14.5359,6.0177,11.6436	,benign	,250/269	35524944	775,5881	1130	2198	3328	SO:0001627	intron_variant	6324	exon3			GCCAAAGGGTTGT		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10586	protein-coding gene	gene with protein product		600235	"""sodium channel, voltage-gated, type I, beta polypeptide"", ""sodium channel, voltage-gated, type I, beta"""			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.448+301G>C	19.37:g.35524944G>C		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	189	97	0.513228	NM_199037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	37	CCDS12441.1	282	0.12912087912087913	24	0.04878048780487805	49	0.13535911602209943	93	0.16258741258741258	116	0.15303430079155672	G	11.85	1.761724	0.31228	0.060177	0.145359	ENSG00000105711	ENST00000415950	D	0.90004	-2.6	2.9	1.84	0.25277	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.80722	P	0.0	B	0.28636	0.218	B	0.25140	0.058	T	0.24870	-1.0148	6	.	.	.	.	5.1292	0.14901	0.1738:0.0:0.8262:0.0	.	250	Q07699-2	.	T	250	ENSP00000396915:R250T	.	R	+	2	0	SCN1B	40216784	0.034000	0.19679	0.007000	0.13788	0.021000	0.10359	0.862000	0.27899	0.750000	0.32877	0.549000	0.68633	AGG	G|0.870;C|0.130	0.130	strong		0.557	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1		
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628948	1628948	+	Missense_Mutation	SNP	G	G	A	rs117085626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1628948G>A	ENST00000399685.1	-	1	745	c.668C>T	c.(667-669)tCc>tTc	p.S223F		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	223	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)		GGACTGGGAGGAGCAGGGCTT	0.602													g|||	312	0.0623003	0.0061	0.1138	5008	,	,		19294	0.002		0.1352	False		,,,				2504	0.089				p.S223F		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C668T						PASS	.	G	PHE/SER	122,4282	89.7+/-128.4	4,114,2084	157.0	162.0	160.0		668	2.1	0.6	11	dbSNP_132	160	1066,7532	224.5+/-260.9	64,938,3297	no	missense	KRTAP5-3	NM_001012708.2	155	68,1052,5381	AA,AG,GG		12.3982,2.7702,9.1371	possibly-damaging	223/239	1628948	1188,11814	2202	4299	6501	SO:0001583	missense	387266	exon1			TGGGAGGAGCAGG	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.668C>T	11.37:g.1628948G>A	ENSP00000382592:p.Ser223Phe	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001012708	Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	37	CCDS41591.1	147	0.0673076923076923	3	0.006097560975609756	51	0.1408839779005525	0	0.0	93	0.12269129287598944	G	4.922	0.171317	0.09391	0.027702	0.123982	ENSG00000196224	ENST00000399685	T	0.00995	5.46	3.02	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41921	P	0.00948300000000002	P	0.36249	0.545	B	0.35607	0.206	T	0.54629	-0.8265	8	0.56958	D	0.05	.	10.0527	0.42225	0.0:0.7914:0.2086:0.0	.	223	Q6L8H2	KRA53_HUMAN	F	223	ENSP00000382592:S223F	ENSP00000382592:S223F	S	-	2	0	KRTAP5-3	1585524	0.997000	0.39634	0.623000	0.29173	0.119000	0.20118	0.255000	0.18333	0.608000	0.30000	-0.748000	0.03510	TCC	G|0.917;A|0.083	0.083	strong		0.602	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
PRKRIP1	79706	hgsc.bcm.edu	37	7	102036877	102036877	+	Missense_Mutation	SNP	T	T	G	rs6951185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102036877T>G	ENST00000496391.1	+	5	1329	c.19T>G	c.(19-21)Tcc>Gcc	p.S7A	PRKRIP1_ENST00000397912.3_Missense_Mutation_p.S7A|PRKRIP1_ENST00000354783.4_5'Flank|PRKRIP1_ENST00000482465.1_Intron|PRKRIP1_ENST00000462601.1_Intron			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	7	Interaction with EIF2AK2. {ECO:0000250}.		S -> A (in dbSNP:rs6951185).		negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						CCCAGCCGCCTCCTCGGTGCG	0.662													T|||	245	0.0489217	0.0908	0.0476	5008	,	,		12427	0.002		0.0686	False		,,,				2504	0.0215				p.S7A		Atlas-SNP	.											.	PRKRIP1	25	.	0			c.T19G						PASS	.	T	ALA/SER	308,3994		15,278,1858	8.0	10.0	10.0		19	-4.7	0.0	7	dbSNP_116	10	446,8002		10,426,3788	yes	missense	PRKRIP1	NM_024653.3	99	25,704,5646	GG,GT,TT		5.2794,7.1595,5.9137	benign	7/185	102036877	754,11996	2151	4224	6375	SO:0001583	missense	79706	exon1			GCCGCCTCCTCGG	AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563		"""Zinc fingers, C2H2-type"", ""-"""	21894	protein-coding gene	gene with protein product	"""likely ortholog of mouse C114 dsRNA-binding protein"", ""KRAB box domain containing 3"""					12679338	Standard	NM_024653		Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	ENST00000496391.1:c.19T>G	7.37:g.102036877T>G	ENSP00000419270:p.Ser7Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_024653	B4DGM2|Q8NDM6|Q96CF8	Missense_Mutation	SNP	ENST00000496391.1	37	CCDS34714.1	120	0.054945054945054944	45	0.09146341463414634	25	0.06906077348066299	1	0.0017482517482517483	49	0.06464379947229551	t	17.54	3.415228	0.62511	0.071595	0.052794	ENSG00000128563	ENST00000496391;ENST00000397912	T;T	0.28255	1.62;1.62	5.17	-4.72	0.03269	.	0.816710	0.12034	N	0.505733	T	0.00328	0.0010	N	0.08118	0	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	9	0.06891	T	0.86	-13.1401	0.8194	0.01109	0.2447:0.1563:0.3454:0.2535	rs6951185;rs11556161;rs6951185	7	Q9H875	PKRI1_HUMAN	A	7	ENSP00000419270:S7A;ENSP00000381010:S7A	ENSP00000381010:S7A	S	+	1	0	PRKRIP1	101823882	0.000000	0.05858	0.001000	0.08648	0.455000	0.32408	-0.205000	0.09411	-1.009000	0.03400	0.450000	0.29827	TCC	T|0.938;G|0.062	0.062	strong		0.662	PRKRIP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349489.1	NM_024653	
PAPLN	89932	hgsc.bcm.edu	37	14	73726151	73726151	+	Missense_Mutation	SNP	A	A	G	rs17182244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73726151A>G	ENST00000554301.1	+	15	2046	c.1883A>G	c.(1882-1884)cAc>cGc	p.H628R	PAPLN_ENST00000427855.1_Missense_Mutation_p.H628R|PAPLN_ENST00000555445.1_Missense_Mutation_p.H628R|PAPLN_ENST00000381166.3_Missense_Mutation_p.H628R|PAPLN_ENST00000340738.5_Missense_Mutation_p.H601R			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	628			H -> R (in dbSNP:rs17182244).			basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TCAGGGCCCCACGACTGCAGA	0.711													A|||	55	0.0109824	0.0015	0.0115	5008	,	,		15850	0.0		0.0408	False		,,,				2504	0.0041				p.H601R		Atlas-SNP	.											.	PAPLN	180	.	0			c.A1802G						PASS	.	A	ARG/HIS	33,4373		0,33,2170	20.0	24.0	23.0		1802	-5.5	0.0	14	dbSNP_123	23	320,8268		4,312,3978	yes	missense	PAPLN	NM_173462.3	29	4,345,6148	GG,GA,AA		3.7261,0.749,2.7166	benign	601/1252	73726151	353,12641	2203	4294	6497	SO:0001583	missense	89932	exon15			GGCCCCACGACTG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1883A>G	14.37:g.73726151A>G	ENSP00000451803:p.His628Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		41	0.018772893772893772	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	33	0.04353562005277045	A	4.734	0.136524	0.09032	0.00749	0.037261	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.61627	0.09;0.09;0.39;0.09;0.23	4.23	-5.49	0.02584	.	.	.	.	.	T	0.03871	0.0109	N	0.00436	-1.5	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.31081	-0.9956	9	0.11182	T	0.66	.	8.8397	0.35135	0.6381:0.1121:0.2498:0.0	rs17182244;rs17182244	628;628;601	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	R	601;628;628;628;628	ENSP00000345395:H601R;ENSP00000403403:H628R;ENSP00000370558:H628R;ENSP00000451803:H628R;ENSP00000451729:H628R	ENSP00000216658:H628R	H	+	2	0	PAPLN	72795904	0.000000	0.05858	0.000000	0.03702	0.737000	0.42083	-1.238000	0.02919	-0.688000	0.05155	0.379000	0.24179	CAC	A|0.976;G|0.024	0.024	strong		0.711	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
XIRP1	165904	hgsc.bcm.edu	37	3	39226114	39226114	+	Missense_Mutation	SNP	G	G	A	rs34810344	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:39226114G>A	ENST00000340369.3	-	2	5051	c.4823C>T	c.(4822-4824)gCa>gTa	p.A1608V	XIRP1_ENST00000396251.1_3'UTR|XIRP1_ENST00000421646.1_Missense_Mutation_p.A291V	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1608			A -> V (in dbSNP:rs34810344).		cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GTTCTTGACTGCAGTTTGACC	0.562													G|||	458	0.0914537	0.0507	0.098	5008	,	,		20993	0.0367		0.166	False		,,,				2504	0.1217				p.A1608V		Atlas-SNP	.											.	XIRP1	173	.	0			c.C4823T						PASS	.	G	,VAL/ALA	313,4093	168.7+/-199.5	11,291,1901	211.0	192.0	198.0		,4823	-3.4	0.0	3	dbSNP_126	198	1551,7049	290.8+/-300.0	144,1263,2893	yes	utr-3,missense	XIRP1	NM_001198621.1,NM_194293.2	,64	155,1554,4794	AA,AG,GG		18.0349,7.1039,14.3318	,benign	,1608/1844	39226114	1864,11142	2203	4300	6503	SO:0001583	missense	165904	exon2			TTGACTGCAGTTT	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.4823C>T	3.37:g.39226114G>A	ENSP00000343140:p.Ala1608Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	53	0.616279	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	207	0.09478021978021978	24	0.04878048780487805	33	0.09116022099447514	19	0.033216783216783216	131	0.17282321899736147	G	1.329	-0.597404	0.03771	0.071039	0.180349	ENSG00000168334	ENST00000340369;ENST00000421646	T;T	0.18810	3.92;2.19	4.06	-3.42	0.04825	.	0.570073	0.15883	U	0.239960	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	0.35599	-0.9782	9	0.24483	T	0.36	.	1.9548	0.03374	0.3307:0.1235:0.4199:0.1259	rs34810344	1608	Q702N8	XIRP1_HUMAN	V	1608;291	ENSP00000343140:A1608V;ENSP00000391645:A291V	ENSP00000343140:A1608V	A	-	2	0	XIRP1	39201118	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.069000	0.11542	-0.874000	0.04027	-0.150000	0.13652	GCA	G|0.874;A|0.126	0.126	strong		0.562	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
KMT2D	8085	hgsc.bcm.edu	37	12	49426818	49426818	+	Silent	SNP	G	G	A	rs376471354		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49426818G>A	ENST00000301067.7	-	39	11669	c.11670C>T	c.(11668-11670)agC>agT	p.S3890S	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3890	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)										TGGGCTGAGCGCTCAGTTTGG	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.S3890S		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11670T						PASS	.	G		0,3580		0,0,1790	22.0	27.0	25.0		11670	-9.3	0.0	12		25	3,6691		0,3,3344	no	coding-synonymous	MLL2	NM_003482.3		0,3,5134	AA,AG,GG		0.0448,0.0,0.0292		3890/5538	49426818	3,10271	1790	3347	5137	SO:0001819	synonymous_variant	8085	exon39			CTGAGCGCTCAGT	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.11670C>T	12.37:g.49426818G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KTI12	112970	hgsc.bcm.edu	37	1	52498370	52498370	+	Silent	SNP	C	C	T	rs2809917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:52498370C>T	ENST00000371614.1	-	1	1118	c.1064G>A	c.(1063-1065)tGa>tAa	p.*355*	RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000371626.4_Intron	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						scavenged	.	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	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	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	
UNC80	285175	hgsc.bcm.edu	37	2	210685100	210685100	+	Silent	SNP	G	G	A	rs13432185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:210685100G>A	ENST00000439458.1	+	13	2108	c.2028G>A	c.(2026-2028)gcG>gcA	p.A676A	UNC80_ENST00000272845.6_Silent_p.A676A	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	676					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A676A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						GTGACGTGGCGCTAAACATTG	0.403													g|||	604	0.120607	0.1838	0.1225	5008	,	,		19110	0.2381		0.006	False		,,,				2504	0.0307				p.A676A		Atlas-SNP	.											UNC80_ENST00000439458,colon,carcinoma,0,2	UNC80	280	2	1	Substitution - coding silent(1)	stomach(1)	c.G2028A						scavenged	.	A	,	241,1143		24,193,475	220.0	195.0	203.0		2028,2028	-11.5	0.0	2	dbSNP_121	203	3,3179		0,3,1588	no	coding-synonymous,coding-synonymous	UNC80	NM_032504.1,NM_182587.3	,	24,196,2063	AA,AG,GG		0.0943,17.4133,5.3438	,	676/3259,676/3235	210685100	244,4322	692	1591	2283	SO:0001819	synonymous_variant	285175	exon13			CGTGGCGCTAAAC	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.2028G>A	2.37:g.210685100G>A		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_182587	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	37	CCDS46504.1																																																																																			G|0.897;A|0.103	0.103	strong		0.403	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465389	39465389	+	Silent	SNP	T	T	A	rs12451604	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39465389T>A	ENST00000391352.1	-	1	116	c.117A>T	c.(115-117)acA>acT	p.T39T		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	39						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CCAGCTGCCATGTCTGGCTCT	0.602													T|||	1153	0.230232	0.2806	0.147	5008	,	,		22564	0.3204		0.1849	False		,,,				2504	0.1748				p.T39T		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.A117T						PASS	.																																			SO:0001819	synonymous_variant	100505753	exon1			CTGCCATGTCTGG	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.117A>T	17.37:g.39465389T>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_001146182		Silent	SNP	ENST00000391352.1	37	CCDS56032.1																																																																																			T|0.764;A|0.236	0.236	strong		0.602	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
TAS2R38	5726	hgsc.bcm.edu	37	7	141672604	141672604	+	Missense_Mutation	SNP	T	T	C	rs10246939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141672604T>C	ENST00000547270.1	-	1	969	c.886A>G	c.(886-888)Atc>Gtc	p.I296V		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	296			I -> V (in dbSNP:rs10246939). {ECO:0000269|PubMed:12595690}.		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)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					GAGATCAGGATGGCTGCATGC	0.537													C|||	2607	0.520567	0.4766	0.6873	5008	,	,		18774	0.6766		0.4612	False		,,,				2504	0.362				p.I296V		Atlas-SNP	.											.	TAS2R38	51	.	0			c.A886G	GRCh37	CM031370	TAS2R38	M	rs10246939	PASS	.	C	VAL/ILE	2106,2300	602.7+/-390.0	487,1132,584	80.0	70.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	886	1.0	0.1	7	dbSNP_119	74	3918,4682	604.5+/-394.8	884,2150,1266	yes	missense	TAS2R38	NM_176817.4	29	1371,3282,1850	CC,CT,TT		45.5581,47.7985,46.3171	probably-damaging	296/334	141672604	6024,6982	2203	4300	6503	SO:0001583	missense	5726	exon1			TCAGGATGGCTGC	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	9584	protein-coding gene	gene with protein product		607751	"""phenylthiocarbamide tasting"""	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.886A>G	7.37:g.141672604T>C	ENSP00000448219:p.Ile296Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Missense_Mutation	SNP	ENST00000547270.1	37	CCDS34765.1	1198	0.5485347985347986	254	0.516260162601626	230	0.6353591160220995	370	0.6468531468531469	344	0.45382585751978893	C	8.017	0.758746	0.15846	0.477985	0.455581	ENSG00000257138	ENST00000547270	T	0.52057	0.68	5.01	0.982	0.19762	.	0.155819	0.42420	N	0.000713	T	0.00012	0.0000	L	0.52905	1.665	0.80722	P	0.0	P	0.41366	0.747	P	0.54706	0.759	T	0.45571	-0.9252	9	0.33141	T	0.24	.	8.7971	0.34885	0.0:0.2497:0.0:0.7503	rs10246939;rs17712734;rs52837199;rs57237947;rs10246939	296	P59533	T2R38_HUMAN	V	296	ENSP00000448219:I296V	ENSP00000331291:I296V	I	-	1	0	TAS2R38	141319073	0.000000	0.05858	0.100000	0.21137	0.012000	0.07955	-2.380000	0.01066	-0.099000	0.12263	-2.030000	0.00424	ATC	T|0.495;C|0.505	0.505	strong		0.537	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817	
POTEE	445582	hgsc.bcm.edu	37	2	132021658	132021658	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:132021658G>A	ENST00000356920.5	+	15	2724	c.2630G>A	c.(2629-2631)cGc>cAc	p.R877H	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	877	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCCACCCTGCGCCTAGACCTG	0.612																																					p.R877H		Atlas-SNP	.											ENSG00000188219,right_upper_lobe,carcinoma,-1,1	.	.	1	0			c.G2630A						scavenged	.						28.0	30.0	29.0					2																	132021658		2171	4240	6411	SO:0001583	missense	445582	exon15			CCCTGCGCCTAGA	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.2630G>A	2.37:g.132021658G>A	ENSP00000439189:p.Arg877His	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	220	3	0.0136364	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	11.54	1.670073	0.29693	.	.	ENSG00000188219	ENST00000356920	D	0.94966	-3.57	.	.	.	.	.	.	.	.	D	0.92067	0.7486	M	0.87900	2.915	0.80722	D	1	D	0.62365	0.991	B	0.36885	0.235	D	0.88086	0.2810	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	877	Q6S8J3	POTEE_HUMAN	H	877	ENSP00000439189:R877H	ENSP00000439189:R877H	R	+	2	0	AC131180.1	131738128	1.000000	0.71417	0.094000	0.20943	0.095000	0.18619	6.504000	0.73704	0.119000	0.18210	0.121000	0.15741	CGC	.	.	none		0.612	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
NIN	51199	hgsc.bcm.edu	37	14	51237126	51237126	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:51237126G>A	ENST00000382041.3	-	12	1604	c.1414C>T	c.(1414-1416)Cgc>Tgc	p.R472C	NIN_ENST00000389868.3_Missense_Mutation_p.R472C|NIN_ENST00000530997.2_Missense_Mutation_p.R472C|NIN_ENST00000245441.5_Missense_Mutation_p.R472C|NIN_ENST00000453196.1_Missense_Mutation_p.R472C|NIN_ENST00000382043.4_Missense_Mutation_p.R472C|NIN_ENST00000324330.9_Missense_Mutation_p.R472C	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	472					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)					AGGGCAAGGCGGTCCCGGATA	0.478			T	PDGFRB	MPD																																p.R472C		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	NIN_ENST00000382041,colon,carcinoma,+1,3	NIN	475	3	0			c.C1414T						scavenged	.						173.0	153.0	160.0					14																	51237126		2203	4300	6503	SO:0001583	missense	51199	exon12			CAAGGCGGTCCCG	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.1414C>T	14.37:g.51237126G>A	ENSP00000371472:p.Arg472Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	g	28.6	4.931882	0.92389	.	.	ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97	5.64	5.64	0.86602	.	0.047406	0.85682	D	0.000000	T	0.44767	0.1309	M	0.65975	2.015	0.58432	D	0.999992	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.999;0.987;0.997	T	0.33854	-0.9852	10	0.87932	D	0	-9.6817	13.6682	0.62409	0.0:0.0:0.8457:0.1543	.	478;472;472;472;472	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7	.;.;NIN_HUMAN;.;.	C	472;472;472;472;478;472;472;472	ENSP00000245441:R472C;ENSP00000374518:R472C;ENSP00000371474:R472C;ENSP00000371472:R472C;ENSP00000324210:R472C;ENSP00000412391:R472C	ENSP00000245441:R472C	R	-	1	0	NIN	50306876	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.186000	0.65082	2.668000	0.90789	0.645000	0.84053	CGC	.	.	none		0.478	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
NELFB	25920	hgsc.bcm.edu	37	9	140147152	140147152	+	5'Flank	SNP	C	C	G	rs28376526	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140147152C>G	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Silent_p.P177P|C9orf173_ENST00000412566.1_Silent_p.P177P	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCAGCCGGCCCGCCTTCCCCG	0.706													C|||	3054	0.609824	0.4924	0.7608	5008	,	,		10116	0.4772		0.7237	False		,,,				2504	0.681				p.P177P		Atlas-SNP	.											.	C9orf173	19	.	0			c.C531G						PASS	.	C		2055,1687		610,835,426	5.0	6.0	6.0		531	-3.2	0.0	9	dbSNP_125	6	6011,1957		2391,1229,364	no	coding-synonymous	C9orf173	NM_001004353.2		3001,2064,790	GG,GC,CC		24.5607,45.0828,31.1187		177/309	140147152	8066,3644	1871	3984	5855	SO:0001631	upstream_gene_variant	441476	exon5			CCGGCCCGCCTTC	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		9.37:g.140147152C>G	Exception_encountered	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																			C|0.388;G|0.612	0.612	strong		0.706	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
SP100	6672	hgsc.bcm.edu	37	2	231327184	231327184	+	Silent	SNP	C	C	T	rs35985492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231327184C>T	ENST00000264052.5	+	10	1363	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	SP100_ENST00000409824.1_Silent_p.D311D|SP100_ENST00000340126.4_Silent_p.D336D|SP100_ENST00000409897.1_Silent_p.D301D|SP100_ENST00000341950.4_Silent_p.D336D|SP100_ENST00000409112.1_Silent_p.D336D|SP100_ENST00000409341.1_Silent_p.D336D|SP100_ENST00000427101.2_Silent_p.D311D	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	336	Sufficient to mediate interaction with ETS1.				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)		GATCCACTGACGTTGATGAGC	0.493													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19642	0.0		0.0089	False		,,,				2504	0.0031				p.D336D		Atlas-SNP	.											.	SP100	167	.	0			c.C1008T						PASS	.	C	,,,,,	11,4395	17.9+/-39.9	0,11,2192	126.0	110.0	115.0		1008,1008,1008,933,903,1008	-4.5	0.0	2	dbSNP_126	115	121,8479	62.8+/-124.8	1,119,4180	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	,,,,,	1,130,6372	TT,TC,CC		1.407,0.2497,1.0149	,,,,,	336/886,336/689,336/481,311/453,301/446,336/880	231327184	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	6672	exon10			CACTGACGTTGAT	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.1008C>T	2.37:g.231327184C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	54	0.435484	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	37	CCDS2477.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	2.308	-0.358494	0.05138	0.002497	0.01407	ENSG00000067066	ENST00000413284	.	.	.	4.09	-4.5	0.03493	.	.	.	.	.	T	0.15176	0.0366	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	5.3685	0.16127	0.0:0.3668:0.307:0.3261	rs35985492	.	.	.	M	12	.	.	T	+	2	0	SP100	231035428	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.439000	0.02414	-0.840000	0.04206	-2.265000	0.00278	ACG	C|0.992;T|0.008	0.008	strong		0.493	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
HLA-G	3135	hgsc.bcm.edu	37	6	29796369	29796369	+	Silent	SNP	A	A	T	rs3873252	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29796369A>T	ENST00000360323.6	+	3	417	c.393A>T	c.(391-393)ggA>ggT	p.G131G	HLA-G_ENST00000428701.1_Silent_p.G131G|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376828.2_Silent_p.G136G			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	131	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)|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)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						GGTCCGACGGACGCCTCCTCC	0.682													a|||	439	0.0876597	0.0008	0.0375	5008	,	,		14207	0.1954		0.0596	False		,,,				2504	0.1585				p.G131G		Atlas-SNP	.											.	HLA-G	90	.	0			c.A393T						PASS	.	A		43,2977		0,43,1467	103.0	106.0	105.0		393	-2.6	0.0	6	dbSNP_108	105	341,5077		15,311,2383	no	coding-synonymous	HLA-G	NM_002127.5		15,354,3850	TT,TA,AA		6.2938,1.4238,4.5508		131/339	29796369	384,8054	1510	2709	4219	SO:0001819	synonymous_variant	3135	exon4			CGACGGACGCCTC		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.393A>T	6.37:g.29796369A>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			A|0.942;T|0.058	0.058	strong		0.682	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
PRSS35	167681	hgsc.bcm.edu	37	6	84234144	84234144	+	Silent	SNP	C	C	T	rs3812141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	51	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	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	
MTRF1L	54516	hgsc.bcm.edu	37	6	153323594	153323594	+	Missense_Mutation	SNP	C	C	T	rs3818123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:153323594C>T	ENST00000367233.5	-	1	226	c.227G>A	c.(226-228)cGg>cAg	p.R76Q	MTRF1L_ENST00000367230.1_Missense_Mutation_p.R76Q|MTRF1L_ENST00000367231.5_Missense_Mutation_p.R76Q|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	76			R -> Q (in dbSNP:rs3818123). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.			mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		CCGCAGCTCCCGCTCCTTCTC	0.607																																					p.R76Q		Atlas-SNP	.											.	MTRF1L	21	.	0			c.G227A						PASS	.	T	GLN/ARG,GLN/ARG	3126,1280	424.0+/-340.3	1107,912,184	30.0	31.0	31.0		227,227	-1.8	0.9	6	dbSNP_107	31	5858,2742	422.0+/-353.9	1985,1888,427	no	missense,missense	MTRF1L	NM_001114184.1,NM_019041.5	43,43	3092,2800,611	TT,TC,CC		31.8837,29.0513,30.9242	benign,benign	76/272,76/381	153323594	8984,4022	2203	4300	6503	SO:0001583	missense	54516	exon1			AGCTCCCGCTCCT	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.227G>A	6.37:g.153323594C>T	ENSP00000356202:p.Arg76Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	37	CCDS5243.1	1432	0.6556776556776557	355	0.7215447154471545	265	0.7320441988950276	284	0.4965034965034965	528	0.6965699208443272	T	0.672	-0.801645	0.02841	0.709487	0.681163	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230	T;T;T	0.11063	2.81;2.81;2.81	4.9	-1.77	0.07982	.	0.714789	0.13448	N	0.387104	T	0.01156	0.0038	N	0.08118	0	0.39769	P	0.02786299999999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.47886	-0.9082	9	0.02654	T	1	-1.2935	13.1372	0.59415	0.0:0.6449:0.0:0.3551	rs3818123;rs9397576;rs17856379	76;76;76	Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;RF1ML_HUMAN	Q	76	ENSP00000356202:R76Q;ENSP00000356200:R76Q;ENSP00000356199:R76Q	ENSP00000356199:R76Q	R	-	2	0	MTRF1L	153365287	0.001000	0.12720	0.935000	0.37517	0.007000	0.05969	-2.545000	0.00933	-0.841000	0.04200	-0.972000	0.02603	CGG	C|0.314;T|0.686	0.686	strong		0.607	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
DNHD1	144132	hgsc.bcm.edu	37	11	6578004	6578004	+	Silent	SNP	G	G	A	rs11600179	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6578004G>A	ENST00000527990.2	+	23	7479	c.7479G>A	c.(7477-7479)acG>acA	p.T2493T	DNHD1_ENST00000254579.6_Silent_p.T2493T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2493					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)		AACTGCAGACGCTGCAGCCTA	0.587													A|||	923	0.184305	0.4448	0.1484	5008	,	,		21654	0.0169		0.0915	False		,,,				2504	0.1258				p.T2493T		Atlas-SNP	.											.	DNHD1	198	.	0			c.G7479A						PASS	.	A		605,779		128,349,215	68.0	64.0	65.0		7479	-11.8	0.1	11	dbSNP_120	65	354,2828		18,318,1255	yes	coding-synonymous	DNHD1	NM_144666.2		146,667,1470	AA,AG,GG		11.1251,43.7139,21.0031		2493/4754	6578004	959,3607	692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			GCAGACGCTGCAG	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.7479G>A	11.37:g.6578004G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
METTL5	29081	hgsc.bcm.edu	37	2	170678476	170678476	+	Silent	SNP	G	G	A	rs35417312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170678476G>A	ENST00000260953.5	-	2	517	c.201C>T	c.(199-201)atC>atT	p.I67I	METTL5_ENST00000409837.1_Silent_p.I67I|METTL5_ENST00000409965.1_Silent_p.I67I|METTL5_ENST00000410097.1_Silent_p.I67I|METTL5_ENST00000308099.3_Silent_p.I67I|METTL5_ENST00000392640.2_Silent_p.I67I|METTL5_ENST00000409340.1_Intron	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5	67							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						TTGCAGTTCCGATGCTAAGTA	0.363													G|||	123	0.0245607	0.0227	0.0187	5008	,	,		19258	0.0179		0.0318	False		,,,				2504	0.0307				p.I67I		Atlas-SNP	.											.	METTL5	24	.	0			c.C201T						PASS	.	G		121,4285	90.2+/-128.9	1,119,2083	183.0	158.0	166.0		201	-1.8	1.0	2	dbSNP_126	166	329,8271	115.9+/-175.7	7,315,3978	no	coding-synonymous	METTL5	NM_014168.2		8,434,6061	AA,AG,GG		3.8256,2.7463,3.4599		67/210	170678476	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	29081	exon2			AGTTCCGATGCTA	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.201C>T	2.37:g.170678476G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_014168	D3DPC9|Q9NVX1	Silent	SNP	ENST00000260953.5	37	CCDS33320.1																																																																																			G|0.965;A|0.035	0.035	strong		0.363	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	
COL5A2	1290	hgsc.bcm.edu	37	2	189923577	189923577	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:189923577T>C	ENST00000374866.3	-	32	2402	c.2128A>G	c.(2128-2130)Aga>Gga	p.R710G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	710					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)			ATACTTACTCTAGGTCCTAAC	0.343																																					p.R710G		Atlas-SNP	.											COL5A2,rectum,carcinoma,+1,1	COL5A2	230	1	0			c.A2128G						scavenged	.						43.0	44.0	44.0					2																	189923577		2203	4300	6503	SO:0001583	missense	1290	exon32			TTACTCTAGGTCC	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.2128A>G	2.37:g.189923577T>C	ENSP00000364000:p.Arg710Gly	Somatic	242	2	0.00826446		WXS	Illumina HiSeq	Phase_I	259	3	0.011583	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.857739	0.51376	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.93426	-3.22	5.52	-1.79	0.07932	.	0.000000	0.53938	D	0.000055	D	0.95604	0.8571	M	0.74647	2.275	0.80722	D	1	D;P	0.57899	0.981;0.95	D;D	0.71656	0.966;0.974	D	0.93903	0.7190	9	.	.	.	.	17.2118	0.86932	0.0:0.0:0.5674:0.4326	.	350;710	Q5PR22;P05997	.;CO5A2_HUMAN	G	710;350	ENSP00000364000:R710G	.	R	-	1	2	COL5A2	189631822	0.992000	0.36948	0.997000	0.53966	0.906000	0.53458	2.137000	0.42130	-0.221000	0.09973	-0.460000	0.05396	AGA	.	.	none		0.343	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
TAF10	6881	hgsc.bcm.edu	37	11	6632450	6632450	+	Silent	SNP	C	C	T	rs12451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6632450C>T	ENST00000299424.4	-	4	1014	c.537G>A	c.(535-537)acG>acA	p.T179T	TAF10_ENST00000531760.1_5'UTR|RP11-732A19.2_ENST00000527398.1_RNA	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa	179					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)		TGCCGGAGGCCGTGCCCTTCA	0.498													T|||	708	0.141374	0.0825	0.1974	5008	,	,		21101	0.0833		0.2406	False		,,,				2504	0.1391				p.T179T		Atlas-SNP	.											.	TAF10	9	.	0			c.G537A						PASS	.	T		553,3849	771.8+/-413.8	34,485,1682	69.0	72.0	71.0		537	2.5	1.0	11	dbSNP_52	71	2054,6538	717.7+/-406.2	246,1562,2488	no	coding-synonymous	TAF10	NM_006284.3		280,2047,4170	TT,TC,CC		23.906,12.5625,20.0631		179/219	6632450	2607,10387	2201	4296	6497	SO:0001819	synonymous_variant	6881	exon4			GGAGGCCGTGCCC	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	ENST00000299424.4:c.537G>A	11.37:g.6632450C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	160	90	0.5625	NM_006284	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																			C|0.817;T|0.183	0.183	strong		0.498	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41383134A>G	ENST00000301146.4	-	7	1663	c.1122T>C	c.(1120-1122)gtT>gtC	p.V374V	CYP2A7_ENST00000291764.3_Silent_p.V323V|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	374						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGTCCTTTTTAACCCTGCGGG	0.537													.|||	60	0.0119808	0.0	0.0144	5008	,	,		18790	0.002		0.0457	False		,,,				2504	0.002				p.V374V		Atlas-SNP	.											.	CYP2A7	71	.	0			c.T1122C						PASS	.	A	,	24,4382	27.2+/-55.0	0,24,2179	102.0	90.0	94.0		1122,969	-2.4	0.0	19	dbSNP_134	94	294,8304	99.5+/-161.0	15,264,4020	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	15,288,6199	GG,GA,AA		3.4194,0.5447,2.4454	,	374/495,323/444	41383134	318,12686	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			CTTTTTAACCCTG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1122T>C	19.37:g.41383134A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			A|0.978;G|0.022	0.022	strong		0.537	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
HSPBP1	23640	hgsc.bcm.edu	37	19	55790902	55790902	+	Silent	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55790902C>G	ENST00000255631.5	-	3	385	c.75G>C	c.(73-75)ggG>ggC	p.G25G	HSPBP1_ENST00000433386.2_Silent_p.G25G|BRSK1_ENST00000590333.1_5'Flank|HSPBP1_ENST00000587922.1_Silent_p.G25G|HSPBP1_ENST00000376343.3_Silent_p.G25G	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	25	Gly-rich.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9830037, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CGCCGCCGCCCCCTGAAGAGC	0.692																																					p.G25G		Atlas-SNP	.											HSPBP1,NS,carcinoma,-1,1	HSPBP1	24	1	0			c.G75C						scavenged	.						7.0	10.0	9.0					19																	55790902		1738	3706	5444	SO:0001819	synonymous_variant	23640	exon2			GCCGCCCCCTGAA		CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"""hsp70 interacting protein"", ""Hsp70 binding protein 1"""	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.75G>C	19.37:g.55790902C>G		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	3	0.1875	NM_012267	B3KQP0|B4DG11|O95351|Q6ZNU5	Silent	SNP	ENST00000255631.5	37	CCDS33111.1																																																																																			.	.	none		0.692	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267	
PHC1	1911	hgsc.bcm.edu	37	12	9086553	9086553	+	Silent	SNP	G	G	A	rs1805773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:9086553G>A	ENST00000543824.1	+	10	2318	c.1986G>A	c.(1984-1986)aaG>aaA	p.K662K	PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000544916.1_Silent_p.K662K|PHC1_ENST00000536844.1_Silent_p.K268K|PHC1_ENST00000433083.2_Silent_p.K617K			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	148	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	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	
PTPN21	11099	hgsc.bcm.edu	37	14	88945591	88945591	+	Silent	SNP	A	A	G	rs879932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88945591A>G	ENST00000556564.1	-	13	2468	c.2184T>C	c.(2182-2184)ccT>ccC	p.P728P	PTPN21_ENST00000328736.3_Silent_p.P728P	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	728					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						CACGTGCAGGAGGCGCCCGGG	0.711													G|||	1981	0.395567	0.5234	0.2781	5008	,	,		12795	0.38		0.2962	False		,,,				2504	0.4243				p.P728P		Atlas-SNP	.											.	PTPN21	113	.	0			c.T2184C						PASS	.	G		2216,2188		559,1098,545	23.0	25.0	24.0		2184	-1.8	0.0	14	dbSNP_86	24	2902,5686		492,1918,1884	no	coding-synonymous	PTPN21	NM_007039.3		1051,3016,2429	GG,GA,AA		33.7913,49.6821,39.3935		728/1175	88945591	5118,7874	2202	4294	6496	SO:0001819	synonymous_variant	11099	exon13			TGCAGGAGGCGCC	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.2184T>C	14.37:g.88945591A>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	18	14	0.777778	NM_007039		Silent	SNP	ENST00000556564.1	37	CCDS9884.1																																																																																			A|0.604;G|0.396	0.396	strong		0.711	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
COPS7B	64708	hgsc.bcm.edu	37	2	232653358	232653358	+	Silent	SNP	C	C	T	rs11557625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:232653358C>T	ENST00000350033.3	+	2	219	c.78C>T	c.(76-78)gcC>gcT	p.A26A	COPS7B_ENST00000410017.1_Silent_p.A26A|COPS7B_ENST00000373608.3_Silent_p.A26A|COPS7B_ENST00000410024.1_Silent_p.A26A|COPS7B_ENST00000409091.1_Intron|COPS7B_ENST00000409295.1_Intron	NM_001282949.1|NM_022730.1	NP_001269878.1|NP_073567.1	Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	26					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTGGCTCAGCCCTCACTGCTC	0.507													C|||	31	0.0061901	0.0	0.0086	5008	,	,		16814	0.0		0.0239	False		,,,				2504	0.001				p.A26A		Atlas-SNP	.											.	COPS7B	14	.	0			c.C78T						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	84.0	86.0	85.0		78	1.2	1.0	2	dbSNP_120	85	195,8405	85.8+/-148.2	2,191,4107	no	coding-synonymous	COPS7B	NM_022730.1		2,218,6283	TT,TC,CC		2.2674,0.6128,1.7069		26/265	232653358	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	64708	exon2			CTCAGCCCTCACT	AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524			16760	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B"", ""COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)"""			9707402	Standard	NM_001282950		Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000350033.3:c.78C>T	2.37:g.232653358C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_022730	Q53S22|Q5BJG3|Q9H7V6	Silent	SNP	ENST00000350033.3	37	CCDS2488.1																																																																																			C|0.988;T|0.012	0.012	strong		0.507	COPS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256964.2	NM_022730	
JRK	8629	hgsc.bcm.edu	37	8	143746365	143746365	+	RNA	SNP	G	G	A	rs3802234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143746365G>A	ENST00000507178.2	-	0	1445							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tagggactgcgttccaggcac	0.602													G|||	119	0.023762	0.0174	0.0173	5008	,	,		18772	0.0288		0.0437	False		,,,				2504	0.0112				p.N371N		Atlas-SNP	.											.	.	.	.	0			c.C1113T						PASS	.	G	,	75,4109		0,75,2017	10.0	11.0	11.0		1113,1113	-2.6	0.0	8	dbSNP_107	11	408,8048		6,396,3826	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	6,471,5843	AA,AG,GG		4.825,1.7925,3.8212	,	371/557,371/569	143746365	483,12157	2092	4228	6320			8629	exon2			GACTGCGTTCCAG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746365G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				G|0.972;A|0.028	0.028	strong		0.602	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
ASAP3	55616	hgsc.bcm.edu	37	1	23759743	23759743	+	Missense_Mutation	SNP	G	G	T	rs140136454	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23759743G>T	ENST00000336689.3	-	22	2194	c.2150C>A	c.(2149-2151)gCc>gAc	p.A717D	ASAP3_ENST00000437606.2_Missense_Mutation_p.A708D|ASAP3_ENST00000495646.1_Missense_Mutation_p.A221D	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	717					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						GTGAGCCTGGGCCGGGAGCTT	0.652													G|||	13	0.00259585	0.0008	0.0029	5008	,	,		17511	0.0		0.0089	False		,,,				2504	0.001				p.A717D		Atlas-SNP	.											.	ASAP3	65	.	0			c.C2150A						PASS	.	G	ASP/ALA,ASP/ALA	7,4397	9.9+/-24.2	0,7,2195	47.0	52.0	50.0		2123,2150	3.8	1.0	1	dbSNP_134	50	64,8530	37.4+/-92.8	0,64,4233	yes	missense,missense	ASAP3	NM_001143778.1,NM_017707.3	126,126	0,71,6428	TT,TG,GG		0.7447,0.1589,0.5462	possibly-damaging,possibly-damaging	708/895,717/904	23759743	71,12927	2202	4297	6499	SO:0001583	missense	55616	exon22			GCCTGGGCCGGGA	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	14987	protein-coding gene	gene with protein product	"""centaurin, beta 6"""		"""development and differentiation enhancing factor-like 1"""	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.2150C>A	1.37:g.23759743G>T	ENSP00000338769:p.Ala717Asp	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	37	CCDS235.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	9.640	1.138839	0.21123	0.001589	0.007447	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000465372;ENST00000437606	T;T;T	0.54279	1.99;0.58;0.59	4.69	3.77	0.43336	.	5.644720	0.00687	N	0.000719	T	0.45955	0.1368	L	0.27053	0.805	0.28882	N	0.894374	D;B;B;P	0.59357	0.985;0.009;0.024;0.883	P;B;B;B	0.48704	0.587;0.013;0.006;0.368	T	0.53114	-0.8484	10	0.25106	T	0.35	.	15.1191	0.72429	0.0785:0.0:0.9215:0.0	.	708;607;240;717	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	D	240;221;717;44;708	ENSP00000436150:A221D;ENSP00000338769:A717D;ENSP00000408826:A708D	ENSP00000338769:A717D	A	-	2	0	ASAP3	23632330	0.999000	0.42202	0.968000	0.41197	0.006000	0.05464	4.079000	0.57613	0.712000	0.32039	-1.134000	0.01955	GCC	G|0.995;T|0.005	0.005	strong		0.652	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
RCN2	5955	hgsc.bcm.edu	37	15	77241542	77241542	+	Silent	SNP	T	T	C	rs15939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:77241542T>C	ENST00000394885.3	+	7	1156	c.933T>C	c.(931-933)taT>taC	p.Y311Y	RCN2_ENST00000320963.5_Silent_p.Y329Y|RCN2_ENST00000394883.3_Silent_p.Y210Y	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	311						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						ATGATGACTATTTCTATCATG	0.393													T|||	249	0.0497204	0.0045	0.0706	5008	,	,		14638	0.0		0.1272	False		,,,				2504	0.0675				p.Y329Y		Atlas-SNP	.											.	RCN2	16	.	0			c.T987C						PASS	.	T		106,4286	82.9+/-121.4	1,104,2091	98.0	98.0	98.0		933	-3.5	1.0	15	dbSNP_52	98	948,7640	207.9+/-249.5	41,866,3387	no	coding-synonymous	RCN2	NM_002902.2		42,970,5478	CC,CT,TT		11.0387,2.4135,8.1202		311/318	77241542	1054,11926	2196	4294	6490	SO:0001819	synonymous_variant	5955	exon8			TGACTATTTCTAT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"""EF-hand domain containing"""	9935	protein-coding gene	gene with protein product	"""Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"""	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.933T>C	15.37:g.77241542T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Silent	SNP	ENST00000394885.3	37	CCDS10291.1																																																																																			T|0.927;C|0.073	0.073	strong		0.393	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902	
PXMP2	5827	hgsc.bcm.edu	37	12	133272470	133272470	+	Splice_Site	SNP	G	G	T	rs74727297	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133272470G>T	ENST00000317479.3	+	3	302	c.237G>T	c.(235-237)ggG>ggT	p.G79G	PXMP2_ENST00000539093.1_Intron|PXMP2_ENST00000545677.1_Intron|RP13-672B3.2_ENST00000537262.1_Intron|PXMP2_ENST00000428960.2_5'UTR|PXMP2_ENST00000543589.1_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	85	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	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
ZNF653	115950	hgsc.bcm.edu	37	19	11598288	11598288	+	Silent	SNP	G	G	C	rs145806085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11598288G>C	ENST00000293771.5	-	4	1126	c.990C>G	c.(988-990)ctC>ctG	p.L330L	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CCTCGGCCGTGAGAGCGTCGT	0.672													G|||	7	0.00139776	0.0	0.0	5008	,	,		17152	0.0		0.007	False		,,,				2504	0.0				p.L330L	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C990G						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	65.0	60.0	61.0		990	1.8	0.9	19	dbSNP_134	61	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous	ZNF653	NM_138783.3		0,13,6490	CC,CG,GG		0.1395,0.0227,0.1		330/616	11598288	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	115950	exon4			GGCCGTGAGAGCG	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.990C>G	19.37:g.11598288G>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887433	9887433	+	Silent	SNP	A	A	G	rs2240907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:9887433A>G	ENST00000306084.6	+	2	1156	c.957A>G	c.(955-957)gaA>gaG	p.E319E	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Silent_p.E252E	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	319	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						AGTCCCCAGAAGAAGCCATCC	0.592													A|||	1247	0.249002	0.3472	0.1787	5008	,	,		20422	0.1508		0.2952	False		,,,				2504	0.2198				p.E319E		Atlas-SNP	.											.	TXNDC2	168	.	0			c.A957G						PASS	.	A	,	863,3541		192,479,1531	116.0	114.0	115.0		957,756	-1.1	0.0	18	dbSNP_98	115	1637,6961		282,1073,2944	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	474,1552,4475	GG,GA,AA		19.0393,19.5958,19.2278	,	319/554,252/487	9887433	2500,10502	2202	4299	6501	SO:0001819	synonymous_variant	84203	exon2			CCCAGAAGAAGCC	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.957A>G	18.37:g.9887433A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			A|0.791;G|0.209	0.209	strong		0.592	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
TPRX1	284355	hgsc.bcm.edu	37	19	48305674	48305674	+	Silent	SNP	T	T	C	rs78381908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48305674T>C	ENST00000322175.3	-	2	749	c.594A>G	c.(592-594)ccA>ccG	p.P198P	TPRX1_ENST00000543508.1_Silent_p.P188P|TPRX1_ENST00000535759.1_Silent_p.P295P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	198	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		ggactgagattgggcctggga	0.657													T|||	683	0.136382	0.174	0.0893	5008	,	,		12887	0.1994		0.0547	False		,,,				2504	0.138				p.P198P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.A594G						PASS	.	T		400,3106		25,350,1378	14.0	11.0	12.0		594	-0.8	0.0	19	dbSNP_131	12	308,6188		8,292,2948	no	coding-synonymous	TPRX1	NM_198479.2		33,642,4326	CC,CT,TT		4.7414,11.409,7.0786		198/412	48305674	708,9294	1753	3248	5001	SO:0001819	synonymous_variant	284355	exon2			TGAGATTGGGCCT		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.594A>G	19.37:g.48305674T>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			T|0.885;C|0.115	0.115	strong		0.657	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
ZIM3	114026	hgsc.bcm.edu	37	19	57647015	57647015	+	Silent	SNP	A	A	G	rs7251328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57647015A>G	ENST00000269834.1	-	5	1075	c.690T>C	c.(688-690)aaT>aaC	p.N230N	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GCTTGTAGGCATTTCCACAGT	0.413													G|||	3252	0.649361	0.652	0.6225	5008	,	,		18142	0.7649		0.5507	False		,,,				2504	0.6472				p.N230N		Atlas-SNP	.											.	ZIM3	107	.	0			c.T690C						PASS	.	G		2867,1539	486.4+/-360.6	939,989,275	142.0	139.0	140.0		690	-0.3	0.3	19	dbSNP_116	140	4776,3824	539.0+/-383.5	1363,2050,887	no	coding-synonymous	ZIM3	NM_052882.1		2302,3039,1162	GG,GA,AA		44.4651,34.9296,41.2348		230/473	57647015	7643,5363	2203	4300	6503	SO:0001819	synonymous_variant	114026	exon5			GTAGGCATTTCCA	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.690T>C	19.37:g.57647015A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_052882	Q14CA6	Silent	SNP	ENST00000269834.1	37	CCDS33125.1																																																																																			A|0.387;G|0.613	0.613	strong		0.413	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
WDR90	197335	hgsc.bcm.edu	37	16	700644	700644	+	Missense_Mutation	SNP	G	G	C	rs13337278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656511	46656511	+	Silent	SNP	A	A	G	rs9627324	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46656511A>G	ENST00000253255.5	-	1	2708	c.2709T>C	c.(2707-2709)atT>atC	p.I903I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	903	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACATTGTAGAAATGGGACCAT	0.408													A|||	1229	0.245407	0.6785	0.134	5008	,	,		21872	0.001		0.16	False		,,,				2504	0.0787				p.I903I		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2709C						PASS	.	A		2655,1751	638.7+/-397.0	794,1067,342	97.0	100.0	99.0		2709	-10.7	0.0	22	dbSNP_119	99	1259,7341	250.5+/-277.4	88,1083,3129	no	coding-synonymous	PKDREJ	NM_006071.1		882,2150,3471	GG,GA,AA		14.6395,39.7413,30.0938		903/2254	46656511	3914,9092	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TGTAGAAATGGGA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2709T>C	22.37:g.46656511A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.733;G|0.267	0.267	strong		0.408	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
FAM151A	338094	hgsc.bcm.edu	37	1	55080475	55080475	+	Missense_Mutation	SNP	C	C	T	rs150113940	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55080475C>T	ENST00000302250.2	-	4	633	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	FAM151A_ENST00000371304.2_Missense_Mutation_p.R158Q|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	158						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R158Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						TGTCAGCTGCCGCAGGAGGTC	0.557													C|||	3	0.000599042	0.0	0.0	5008	,	,		18449	0.0		0.003	False		,,,				2504	0.0				p.R158Q		Atlas-SNP	.											FAM151A,NS,carcinoma,0,1	FAM151A	58	1	1	Substitution - Missense(1)	lung(1)	c.G473A						PASS	.	C	,GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	90.0	79.0	82.0		,473	3.6	0.9	1	dbSNP_134	82	25,8575	19.2+/-60.6	0,25,4275	yes	intron,missense	ACOT11,FAM151A	NM_015547.3,NM_176782.2	,43	0,31,6472	TT,TC,CC		0.2907,0.1362,0.2384	,probably-damaging	,158/586	55080475	31,12975	2203	4300	6503	SO:0001583	missense	338094	exon4			AGCTGCCGCAGGA	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.473G>A	1.37:g.55080475C>T	ENSP00000306888:p.Arg158Gln	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	37	CCDS594.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	11.04	1.520558	0.27211	0.001362	0.002907	ENSG00000162391	ENST00000302250;ENST00000371304;ENST00000294370	T;T	0.12039	2.72;2.72	3.6	3.6	0.41247	.	0.444374	0.19958	N	0.102273	T	0.13841	0.0335	M	0.67953	2.075	0.20563	N	0.999885	B	0.31581	0.329	B	0.25140	0.058	T	0.12400	-1.0549	10	0.22109	T	0.4	-29.7803	10.9205	0.47161	0.0:1.0:0.0:0.0	.	158	Q8WW52	F151A_HUMAN	Q	158	ENSP00000306888:R158Q;ENSP00000360353:R158Q	ENSP00000294370:R158Q	R	-	2	0	FAM151A	54853063	0.000000	0.05858	0.932000	0.37286	0.919000	0.55068	0.062000	0.14389	1.993000	0.58246	0.462000	0.41574	CGG	C|0.998;T|0.002	0.002	strong		0.557	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
NR0B1	190	hgsc.bcm.edu	37	X	30327367	30327367	+	Silent	SNP	G	G	A	rs6150	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:30327367G>A	ENST00000378970.4	-	1	348	c.114C>T	c.(112-114)tgC>tgT	p.C38C	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Silent_p.C38C	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	38	4 X 67 AA tandem repeats.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|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)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	AACAGCCCCAGCACTGATCCA	0.657													G|||	361	0.0956291	0.0182	0.0764	3775	,	,		9344	0.0893		0.1441	False		,,,				2504	0.0501				p.C38C		Atlas-SNP	.											.	NR0B1	61	.	0			c.C114T						PASS	.	G		154,3607		4,125,21,1480,522	10.0	11.0	10.0		114	2.5	1.0	X	dbSNP_52	10	1325,5296		104,755,362,1548,1445	no	coding-synonymous	NR0B1	NM_000475.4		108,880,383,3028,1967	AA,AG,A,GG,G		20.0121,4.0947,14.2458		38/471	30327367	1479,8903	2152	4214	6366	SO:0001819	synonymous_variant	190	exon1			GCCCCAGCACTGA	S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"""Nuclear hormone receptors"""	7960	protein-coding gene	gene with protein product		300473	"""dosage-sensitive sex reversal"""	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.114C>T	X.37:g.30327367G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_000475	Q96F69	Silent	SNP	ENST00000378970.4	37	CCDS14223.1																																																																																			G|0.887;A|0.113	0.113	strong		0.657	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475	
TF	7018	hgsc.bcm.edu	37	3	133475722	133475722	+	Silent	SNP	C	C	T	rs1799852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133475722C>T	ENST00000402696.3	+	7	1224	c.739C>T	c.(739-741)Ctg>Ttg	p.L247L	TF_ENST00000264998.3_Silent_p.L120L|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	247	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				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)	GCTGCTTTGCCTGGACAACAC	0.577													C|||	714	0.142572	0.0499	0.1398	5008	,	,		18772	0.2232		0.1362	False		,,,				2504	0.1933				p.L247L		Atlas-SNP	.											.	TF	116	.	0			c.C739T						PASS	.	C		281,4125	155.5+/-188.7	10,261,1932	104.0	106.0	105.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	739	-0.9	0.0	3	dbSNP_89	105	826,7774	190.1+/-236.7	39,748,3513	yes	coding-synonymous	TF	NM_001063.3		49,1009,5445	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	9.6047,6.3777,8.5115		247/699	133475722	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon7			CTTTGCCTGGACA		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.739C>T	3.37:g.133475722C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	165	104	0.630303	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.895;T|0.105	0.105	strong		0.577	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
SPAM1	6677	hgsc.bcm.edu	37	7	123594206	123594206	+	Silent	SNP	G	G	A	rs2285996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:123594206G>A	ENST00000439500.1	+	4	1195	c.582G>A	c.(580-582)aaG>aaA	p.K194K	SPAM1_ENST00000402183.2_Silent_p.K194K|SPAM1_ENST00000340011.5_Silent_p.K194K|SPAM1_ENST00000460182.1_Silent_p.K194K|SPAM1_ENST00000223028.7_Silent_p.K194K	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	194					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AATTTGAAAAGGCAGGGAAGG	0.373													G|||	1237	0.247005	0.1271	0.379	5008	,	,		18479	0.3006		0.2753	False		,,,				2504	0.2311				p.K194K		Atlas-SNP	.											.	SPAM1	195	.	0			c.G582A						PASS	.	G	,,,,	694,3712	273.4+/-271.3	61,572,1570	66.0	70.0	69.0		582,582,582,582,582	0.8	0.1	7	dbSNP_100	69	2407,6193	390.9+/-343.5	325,1757,2218	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPAM1	NM_001174044.1,NM_001174045.1,NM_001174046.1,NM_003117.4,NM_153189.2	,,,,	386,2329,3788	AA,AG,GG		27.9884,15.7512,23.8428	,,,,	194/510,194/510,194/510,194/512,194/510	123594206	3101,9905	2203	4300	6503	SO:0001819	synonymous_variant	6677	exon3			TGAAAAGGCAGGG	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.582G>A	7.37:g.123594206G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_153189	Q8TC30	Silent	SNP	ENST00000439500.1	37	CCDS5791.1																																																																																			G|0.754;T|0.001	.	strong		0.373	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1		
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689166	41689166	+	Missense_Mutation	SNP	C	C	A	rs3204853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41689166C>A	ENST00000260361.4	-	2	473	c.92G>T	c.(91-93)cGc>cTc	p.R31L		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	31			R -> L (in dbSNP:rs3204853). {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)		CTCTGCAAAGCGAATACCCAA	0.443													C|||	581	0.116014	0.0091	0.1585	5008	,	,		17407	0.0079		0.2714	False		,,,				2504	0.182				p.R31L		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G92T						PASS	.	C	LEU/ARG	223,4183	128.2+/-165.1	9,205,1989	52.0	53.0	53.0		92	-4.1	0.0	15	dbSNP_105	53	2242,6356	365.7+/-334.0	277,1688,2334	yes	missense	NDUFAF1	NM_016013.2	102	286,1893,4323	AA,AC,CC		26.0758,5.0613,18.9557	benign	31/328	41689166	2465,10539	2203	4299	6502	SO:0001583	missense	51103	exon2			GCAAAGCGAATAC	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.92G>T	15.37:g.41689166C>A	ENSP00000260361:p.Arg31Leu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	137	77	0.562044	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	275	0.1259157509157509	6	0.012195121951219513	66	0.18232044198895028	3	0.005244755244755245	200	0.2638522427440633	C	10.60	1.394920	0.25205	0.050613	0.260758	ENSG00000137806	ENST00000260361	T	0.59224	0.28	5.23	-4.12	0.03916	.	1.787450	0.02174	N	0.059935	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11397	-1.0589	9	0.40728	T	0.16	-16.936	6.8289	0.23898	0.146:0.363:0.0:0.491	rs3204853;rs52836078;rs3204853	31	Q9Y375	CIA30_HUMAN	L	31	ENSP00000260361:R31L	ENSP00000260361:R31L	R	-	2	0	NDUFAF1	39476458	0.000000	0.05858	0.000000	0.03702	0.868000	0.49771	-0.952000	0.03881	-0.576000	0.05974	-0.261000	0.10672	CGC	C|0.839;A|0.161	0.161	strong		0.443	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21232195G>A	ENST00000233242.1	-	26	7672	c.7545C>T	c.(7543-7545)acC>acT	p.T2515T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2515					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)					TATCTTCTAGGGTCTCTCGGA	0.438													G|||	1257	0.250998	0.2095	0.3775	5008	,	,		21485	0.0615		0.4423	False		,,,				2504	0.2157				p.T2515T		Atlas-SNP	.											.	APOB	761	.	0			c.C7545T						PASS	.	G		1082,3324	391.4+/-328.1	140,802,1261	128.0	107.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7545	3.2	0.9	2	dbSNP_36	114	4301,4299	577.5+/-390.6	1092,2117,1091	no	coding-synonymous	APOB	NM_000384.2		1232,2919,2352	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.9884,24.5574,41.3886		2515/4564	21232195	5383,7623	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTCTAGGGTCTCT	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.7545C>T	2.37:g.21232195G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	152	65	0.427632	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.665;N|0.000	.	strong		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
PLEKHA3	65977	hgsc.bcm.edu	37	2	179358665	179358665	+	Silent	SNP	A	A	G	rs2303536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	203	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	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	
SRMS	6725	hgsc.bcm.edu	37	20	62172281	62172281	+	Missense_Mutation	SNP	C	C	T	rs310655	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62172281C>T	ENST00000217188.1	-	8	1397	c.1357G>A	c.(1357-1359)Gcg>Acg	p.A453T		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	453	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs310655). {ECO:0000269|PubMed:17344846}.		peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			TAGACCTCCGCCGGGCAGGCA	0.692													C|||	1058	0.211262	0.4387	0.0749	5008	,	,		16230	0.0327		0.0616	False		,,,				2504	0.3384				p.A453T		Atlas-SNP	.											.	SRMS	48	.	0			c.G1357A						PASS	.	C	THR/ALA	1589,2813	472.2+/-356.3	281,1027,893	63.0	66.0	65.0		1357	2.1	0.0	20	dbSNP_79	65	460,8134	133.5+/-191.0	10,440,3847	yes	missense	SRMS	NM_080823.2	58	291,1467,4740	TT,TC,CC		5.3526,36.0972,15.7664	benign	453/489	62172281	2049,10947	2201	4297	6498	SO:0001583	missense	6725	exon8			CCTCCGCCGGGCA		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1357G>A	20.37:g.62172281C>T	ENSP00000217188:p.Ala453Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	313	0.1433150183150183	221	0.4491869918699187	24	0.06629834254143646	20	0.03496503496503497	48	0.0633245382585752	C	6.541	0.468081	0.12461	0.360972	0.053526	ENSG00000125508	ENST00000217188	D	0.82803	-1.65	5.17	2.06	0.26882	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.476218	0.19288	N	0.117983	T	0.00012	0.0000	L	0.31526	0.94	0.80722	P	0.0	B	0.19200	0.034	B	0.17979	0.02	T	0.31166	-0.9953	9	0.41790	T	0.15	.	7.6184	0.28171	0.0:0.602:0.214:0.1841	rs310655;rs311539;rs1757733;rs57083542;rs310655	453	Q9H3Y6	SRMS_HUMAN	T	453	ENSP00000217188:A453T	ENSP00000217188:A453T	A	-	1	0	SRMS	61642725	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.099000	0.15210	0.596000	0.29794	-0.768000	0.03414	GCG	C|0.826;T|0.174	0.174	strong		0.692	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
KIAA1522	57648	hgsc.bcm.edu	37	1	33231380	33231380	+	Missense_Mutation	SNP	T	T	G	rs6694085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:33231380T>G	ENST00000373480.1	+	1	113	c.10T>G	c.(10-12)Ttc>Gtc	p.F4V	KIAA1522_ENST00000401073.2_Intron|KIAA1522_ENST00000373481.3_Intron|KIAA1522_ENST00000294521.3_Missense_Mutation_p.F4V	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	4										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)				CATGGTGGTGTTCGTTGGCCG	0.637													T|||	708	0.141374	0.0113	0.1023	5008	,	,		12710	0.2262		0.1849	False		,,,				2504	0.2127				p.F4V		Atlas-SNP	.											KIAA1522_ENST00000373480,rectum,carcinoma,0,1	KIAA1522	68	1	0			c.T10G						scavenged	.																																			SO:0001583	missense	57648	exon1			GTGGTGTTCGTTG	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.10T>G	1.37:g.33231380T>G	ENSP00000362579:p.Phe4Val	Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001198972	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	320	0.14652014652014653	10	0.02032520325203252	38	0.10497237569060773	129	0.22552447552447552	143	0.18865435356200527	T	15.56	2.870690	0.51695	.	.	ENSG00000162522	ENST00000294521;ENST00000373480	T;T	0.42900	0.96;2.17	4.1	1.74	0.24563	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.40146	P	0.023108000000000017	B;B	0.33612	0.16;0.419	B;B	0.30646	0.037;0.118	T	0.11941	-1.0567	8	0.87932	D	0	.	5.5376	0.17020	0.0:0.2322:0.0:0.7678	rs6694085;rs61533893;rs6694085	4;4	B4DQU8;Q9P206	.;K1522_HUMAN	V	4	ENSP00000294521:F4V;ENSP00000362579:F4V	ENSP00000294521:F4V	F	+	1	0	KIAA1522	33003967	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	1.509000	0.35780	0.258000	0.21686	0.397000	0.26171	TTC	T|0.857;G|0.143	0.143	strong		0.637	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
CRELD2	79174	hgsc.bcm.edu	37	22	50315952	50315952	+	Intron	SNP	C	C	T	rs377640443|rs7410276|rs386822607|rs386822606|rs71805922|rs386822608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50315952C>T	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Silent_p.T200T|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000444954.1_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		CAGTCAGGACCGGCCTCTCCG	0.632													T|||	1115	0.222644	0.4592	0.0908	5008	,	,		13528	0.0833		0.0825	False		,,,				2504	0.2843				p.T200T		Atlas-SNP	.											.	CRELD2	57	.	0			c.C600T						PASS	.	T	,	1260,1822		329,602,610	25.0	29.0	28.0		600,	-3.0	0.0	22	dbSNP_116	28	718,6430		49,620,2905	no	coding-synonymous,intron	CRELD2	NM_001135101.1,NM_024324.3	,	378,1222,3515	TT,TC,CC		10.0448,40.8825,19.3353	,	200/403,	50315952	1978,8252	1541	3574	5115	SO:0001627	intron_variant	79174	exon6			CAGGACCGGCCTC	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-308C>T	22.37:g.50315952C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Silent	SNP	ENST00000328268.4	37	CCDS14082.1																																																																																			C|0.827;T|0.173	0.173	strong		0.632	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
TAS2R8	50836	hgsc.bcm.edu	37	12	10959031	10959031	+	Silent	SNP	C	C	T	rs1548803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10959031C>T	ENST00000240615.2	-	1	861	c.549G>A	c.(547-549)ttG>ttA	p.L183L		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	183					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)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TAAAGAGAGTCAAGGGTTCAA	0.323													C|||	2524	0.503994	0.1641	0.5692	5008	,	,		19896	0.6448		0.6789	False		,,,				2504	0.592				p.L183L		Atlas-SNP	.											.	TAS2R8	42	.	0			c.G549A						PASS	.	C		1026,3380	377.8+/-322.6	124,778,1301	149.0	133.0	138.0		549	-3.5	0.0	12	dbSNP_88	138	5190,3410	636.6+/-399.1	1578,2034,688	no	coding-synonymous	TAS2R8	NM_023918.1		1702,2812,1989	TT,TC,CC		39.6512,23.2864,47.7933		183/310	10959031	6216,6790	2203	4300	6503	SO:0001819	synonymous_variant	50836	exon1			GAGAGTCAAGGGT	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.549G>A	12.37:g.10959031C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_023918	Q4KN29|Q645Y2	Silent	SNP	ENST00000240615.2	37	CCDS8632.1																																																																																			C|0.498;T|0.502	0.502	strong		0.323	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
FAM78B	149297	hgsc.bcm.edu	37	1	166039512	166039512	+	Missense_Mutation	SNP	C	C	G	rs138713518		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:166039512C>G	ENST00000338353.3	-	3	1341	c.752G>C	c.(751-753)cGg>cCg	p.R251P	FAM78B_ENST00000354422.3_Missense_Mutation_p.R251P			Q5VT40	FA78B_HUMAN	family with sequence similarity 78, member B	251										central_nervous_system(1)|endometrium(5)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					AGGTGGCCCCCGCTTGGGCCT	0.597																																					p.R251P		Atlas-SNP	.											FAM78B,NS,carcinoma,+1,1	FAM78B	51	1	0			c.G752C						PASS	.						91.0	91.0	91.0					1																	166039512		2203	4300	6503	SO:0001583	missense	149297	exon2			GGCCCCCGCTTGG	AL626787	CCDS30931.1	1q24.1	2008-02-05			ENSG00000188859	ENSG00000188859			13495	protein-coding gene	gene with protein product							Standard	NM_001017961		Approved		uc021pee.1	Q5VT40	OTTHUMG00000034705	ENST00000338353.3:c.752G>C	1.37:g.166039512C>G	ENSP00000339681:p.Arg251Pro	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	285	51	0.178947	NM_001017961	B7Z693	Missense_Mutation	SNP	ENST00000338353.3	37	CCDS30931.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.883574	0.51908	.	.	ENSG00000188859	ENST00000354422;ENST00000338353	D;D	0.94330	-3.4;-3.4	5.96	3.94	0.45596	.	0.049142	0.85682	D	0.000000	D	0.89072	0.6611	L	0.44542	1.39	0.53688	D	0.999975	D	0.53745	0.962	P	0.50049	0.629	D	0.87304	0.2307	9	0.27785	T	0.31	-16.1405	14.0529	0.64749	0.0:0.7123:0.2877:0.0	.	251	Q5VT40	FA78B_HUMAN	P	251	ENSP00000346404:R251P;ENSP00000339681:R251P	ENSP00000339681:R251P	R	-	2	0	FAM78B	164306136	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	4.646000	0.61411	1.471000	0.48121	0.650000	0.86243	CGG	C|1.000;T|0.000	.	alt		0.597	FAM78B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343108.1	NM_001017961	
SEC16B	89866	hgsc.bcm.edu	37	1	177901658	177901658	+	Silent	SNP	C	C	T	rs7554597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177901658C>T	ENST00000308284.6	-	24	3068	c.2979G>A	c.(2977-2979)gcG>gcA	p.A993A	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	993					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						CCCCAGCGCCCGCAGCTGCTC	0.652													C|||	1141	0.227835	0.2655	0.2622	5008	,	,		16820	0.1052		0.2604	False		,,,				2504	0.2454				p.A993A		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2979A						PASS	.	C		1084,3004		158,768,1118	11.0	15.0	13.0		2979	-1.3	0.0	1	dbSNP_116	13	1743,6483		202,1339,2572	no	coding-synonymous	SEC16B	NM_033127.2		360,2107,3690	TT,TC,CC		21.1889,26.5166,22.9576		993/1061	177901658	2827,9487	2044	4113	6157	SO:0001819	synonymous_variant	89866	exon24			AGCGCCCGCAGCT	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.2979G>A	1.37:g.177901658C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	116	31	0.267241	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			C|0.785;T|0.215	0.215	strong		0.652	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
C2orf74	339804	hgsc.bcm.edu	37	2	61389737	61389737	+	Missense_Mutation	SNP	T	T	G	rs1729674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:61389737T>G	ENST00000432605.1	+	1	109	c.109T>G	c.(109-111)Tat>Gat	p.Y37D	C2orf74_ENST00000426997.1_Intron|RP11-493E12.1_ENST00000605902.1_lincRNA	NM_001143959.1	NP_001137431.1	A8MZ97	CB074_HUMAN	chromosome 2 open reading frame 74	37						integral component of membrane (GO:0016021)				endometrium(1)	1						GGTTTTTTTATATAAATGGTA	0.318													T|||	1972	0.39377	0.4455	0.389	5008	,	,		20712	0.3968		0.4533	False		,,,				2504	0.2628				p.Y37D		Atlas-SNP	.											.	C2orf74	22	.	0			c.T109G						PASS	.						218.0	173.0	187.0					2																	61389737		692	1591	2283	SO:0001583	missense	339804	exon1			TTTTTATATAAAT			2p15	2012-08-06			ENSG00000237651	ENSG00000237651			34439	protein-coding gene	gene with protein product							Standard	NM_001143959		Approved	LOC339804	uc010ypm.1	A8MZ97		ENST00000432605.1:c.109T>G	2.37:g.61389737T>G	ENSP00000402915:p.Tyr37Asp	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001143959	C9JP62	Missense_Mutation	SNP	ENST00000432605.1	37		938	0.42948717948717946	210	0.4268292682926829	158	0.43646408839779005	223	0.38986013986013984	347	0.4577836411609499	T	12.42	1.933117	0.34096	.	.	ENSG00000237651	ENST00000432605	.	.	.	4.9	2.31	0.28768	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.0000000000287557E-6	D	0.54207	0.965	P	0.54312	0.748	T	0.45190	-0.9278	7	0.87932	D	0	.	1.6236	0.02719	0.1687:0.0969:0.1747:0.5597	rs1729674;rs52790424;rs56837693;rs1729674	37	A8MZ97	CB074_HUMAN	D	37	.	ENSP00000402915:Y37D	Y	+	1	0	C2orf74	61243241	0.829000	0.29322	0.939000	0.37840	0.582000	0.36321	1.552000	0.36244	0.831000	0.34780	0.254000	0.18369	TAT	T|0.583;G|0.417	0.417	strong		0.318	C2orf74-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001143959	
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:69221510C>G	ENST00000336278.4	+	1	479	c.441C>G	c.(439-441)ccC>ccG	p.P147P		NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	147	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		AGATCTTCCCCGGGCTGGCTG	0.716													G|||	905	0.180711	0.3003	0.1671	5008	,	,		5567	0.0417		0.2296	False		,,,				2504	0.1217				p.P147P	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.C441G						PASS	.	G		1114,3104		166,782,1161	7.0	9.0	8.0		441	2.9	1.0	16	dbSNP_52	8	1807,6475		241,1325,2575	no	coding-synonymous	SNTB2	NM_006750.3		407,2107,3736	GG,GC,CC		21.8184,26.4106,23.368		147/541	69221510	2921,9579	2109	4141	6250	SO:0001819	synonymous_variant	6645	exon1			CTTCCCCGGGCTG	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"""syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"""	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.441C>G	16.37:g.69221510C>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_006750	Q9BY09	Silent	SNP	ENST00000336278.4	37	CCDS10873.1	400	0.18315018315018314	144	0.2926829268292683	62	0.1712707182320442	30	0.05244755244755245	164	0.21635883905013192	G	13.11	2.137905	0.37728	0.264106	0.218184	ENSG00000168807	ENST00000525632;ENST00000360496	T	0.31510	1.49	4.91	2.86	0.33363	.	0.067858	0.64402	N	0.000013	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17992	-1.0351	6	0.87932	D	0	3.495	8.6306	0.33917	0.1548:0.1286:0.7166:0.0	rs10650;rs1136061;rs1136064;rs3169308;rs17354236	.	.	.	R	16;8	ENSP00000432201:P16R	ENSP00000353686:P8R	P	+	2	0	SNTB2	67779011	0.942000	0.31987	1.000000	0.80357	0.953000	0.61014	0.499000	0.22546	0.564000	0.29238	-0.215000	0.12644	CCG	C|0.815;G|0.185	0.185	strong		0.716	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		
LMBR1	64327	hgsc.bcm.edu	37	7	156518195	156518195	+	Silent	SNP	G	G	A	rs59912051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:156518195G>A	ENST00000353442.5	-	14	1328	c.1092C>T	c.(1090-1092)gtC>gtT	p.V364V	LMBR1_ENST00000354505.4_Silent_p.V405V|LMBR1_ENST00000540390.1_Silent_p.V343V|LMBR1_ENST00000359422.4_Silent_p.V212V	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	364					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		TATAGAAGCCGACAACAGAGG	0.413													G|||	676	0.134984	0.1596	0.0908	5008	,	,		18069	0.1518		0.0865	False		,,,				2504	0.1656				p.V364V		Atlas-SNP	.											.	LMBR1	35	.	0			c.C1092T						PASS	.	G		646,3760	276.6+/-273.2	61,524,1618	95.0	98.0	97.0		1092	-5.1	0.9	7	dbSNP_129	97	642,7958	164.1+/-216.5	25,592,3683	no	coding-synonymous	LMBR1	NM_022458.3		86,1116,5301	AA,AG,GG		7.4651,14.6618,9.9031		364/491	156518195	1288,11718	2203	4300	6503	SO:0001819	synonymous_variant	64327	exon14			GAAGCCGACAACA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.1092C>T	7.37:g.156518195G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Silent	SNP	ENST00000353442.5	37	CCDS5945.1																																																																																			G|0.897;A|0.103	0.103	strong		0.413	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
ISLR	3671	hgsc.bcm.edu	37	15	74467796	74467796	+	Silent	SNP	C	C	T	rs11854957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:74467796C>T	ENST00000249842.3	+	2	954	c.597C>T	c.(595-597)gcC>gcT	p.A199A	ISLR_ENST00000395118.1_Silent_p.A199A|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	199	LRRCT.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						TGACCACGGCCGTGTCCATCC	0.667													C|||	284	0.0567093	0.0098	0.0764	5008	,	,		18723	0.0		0.1859	False		,,,				2504	0.0317				p.A199A		Atlas-SNP	.											.	ISLR	49	.	0			c.C597T						PASS	.	C	,	183,4213	118.4+/-156.1	5,173,2020	59.0	50.0	53.0		597,597	-8.1	0.0	15	dbSNP_120	53	1840,6754	326.0+/-317.2	188,1464,2645	no	coding-synonymous,coding-synonymous	ISLR	NM_005545.3,NM_201526.1	,	193,1637,4665	TT,TC,CC		21.4103,4.1629,15.5735	,	199/429,199/429	74467796	2023,10967	2198	4297	6495	SO:0001819	synonymous_variant	3671	exon2			CACGGCCGTGTCC	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.597C>T	15.37:g.74467796C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_201526		Silent	SNP	ENST00000249842.3	37	CCDS10260.1																																																																																			A|0.000;C|0.870;T|0.130	0.130	strong		0.667	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
HAUS6	54801	hgsc.bcm.edu	37	9	19058425	19058425	+	Silent	SNP	G	G	A	rs11515236	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19058425G>A	ENST00000380502.3	-	16	2807	c.2340C>T	c.(2338-2340)ctC>ctT	p.L780L	HAUS6_ENST00000380496.1_Silent_p.L644L	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	780					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)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTTCTTCCGGGAGAGTTTCGT	0.358													A|||	1605	0.320487	0.6074	0.1729	5008	,	,		18434	0.1776		0.2734	False		,,,				2504	0.2331				p.L780L		Atlas-SNP	.											.	HAUS6	66	.	0			c.C2340T						PASS	.						31.0	43.0	39.0					9																	19058425		2159	4288	6447	SO:0001819	synonymous_variant	54801	exon16			TTCCGGGAGAGTT	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.2340C>T	9.37:g.19058425G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			G|0.250;A|0.750	0.750	weak		0.358	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
OVGP1	5016	hgsc.bcm.edu	37	1	111957583	111957583	+	Missense_Mutation	SNP	A	A	G	rs1126656|rs376377993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	121	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	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	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29908433	29908433	+	Missense_Mutation	SNP	C	C	G	rs11649499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:29908433C>G	ENST00000308713.5	-	3	748	c.221G>C	c.(220-222)cGg>cCg	p.R74P	SEZ6L2_ENST00000562159.1_5'UTR|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.R74P|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.R30P|SEZ6L2_ENST00000350527.3_Intron	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	74	Pro-rich.		R -> P (in dbSNP:rs11649499). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGTGGGGTCCCGATCAGATCC	0.667													G|||	3761	0.750998	0.9932	0.7464	5008	,	,		9668	0.6052		0.827	False		,,,				2504	0.499				p.R74P		Atlas-SNP	.											SEZ6L2,NS,carcinoma,0,1	SEZ6L2	137	1	0			c.G221C						scavenged	.	G	,PRO/ARG,,PRO/ARG	4084,194		1951,182,6	7.0	10.0	9.0		,221,,221	2.8	1.0	16	dbSNP_120	9	7159,1331		3016,1127,102	yes	intron,missense,intron,missense	SEZ6L2	NM_001114099.2,NM_001114100.2,NM_012410.3,NM_201575.3	,103,,103	4967,1309,108	GG,GC,CC		15.6773,4.5348,11.9439	,benign,,benign	,74/810,,74/911	29908433	11243,1525	2139	4245	6384	SO:0001583	missense	26470	exon3			GGGTCCCGATCAG	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.221G>C	16.37:g.29908433C>G	ENSP00000312550:p.Arg74Pro	Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	1718	0.7866300366300366	484	0.983739837398374	282	0.7790055248618785	322	0.5629370629370629	630	0.8311345646437994	G	0.009	-1.806021	0.00606	0.954652	0.843227	ENSG00000174938	ENST00000308713;ENST00000346932;ENST00000537485	T;T;T	0.45276	0.9;0.9;0.9	5.17	2.85	0.33270	.	0.128667	0.35436	N	0.003211	T	0.00012	0.0000	N	0.03608	-0.345	0.50632	P	1.1099999999997223E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30621	-0.9972	8	.	.	.	.	7.5026	0.27526	0.1787:0.1431:0.6783:0.0	rs11649499;rs60390109;rs11649499	30;74	F5H293;Q6UXD5	.;SE6L2_HUMAN	P	74;74;30	ENSP00000312550:R74P;ENSP00000319215:R74P;ENSP00000439412:R30P	.	R	-	2	0	SEZ6L2	29815934	0.685000	0.27652	1.000000	0.80357	0.050000	0.14768	0.504000	0.22626	0.600000	0.29862	-0.998000	0.02512	CGG	C|0.218;G|0.782	0.782	strong		0.667	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
BACH2	60468	hgsc.bcm.edu	37	6	90642358	90642358	+	Silent	SNP	G	G	A	rs3798789	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:90642358G>A	ENST00000257749.4	-	9	3002	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	BACH2_ENST00000537989.1_Silent_p.N765N|BACH2_ENST00000343122.3_Silent_p.N765N	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	765						cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		AGCAGGGCACGTTTTCCCCCA	0.637													A|||	518	0.103435	0.152	0.0692	5008	,	,		16614	0.0704		0.1074	False		,,,				2504	0.092				p.N765N		Atlas-SNP	.											.	BACH2	224	.	0			c.C2295T						PASS	.	A	,	593,3813	769.3+/-413.7	42,509,1652	42.0	44.0	44.0		2295,2295	-5.0	0.0	6	dbSNP_107	44	1029,7571	770.4+/-407.7	51,927,3322	no	coding-synonymous,coding-synonymous	BACH2	NM_001170794.1,NM_021813.2	,	93,1436,4974	AA,AG,GG		11.9651,13.4589,12.4712	,	765/842,765/842	90642358	1622,11384	2203	4300	6503	SO:0001819	synonymous_variant	60468	exon7			GGGCACGTTTTCC	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.2295C>T	6.37:g.90642358G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			G|0.877;A|0.123	0.123	strong		0.637	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
RRP12	23223	hgsc.bcm.edu	37	10	99139140	99139140	+	Silent	SNP	G	G	A	rs41300217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99139140G>A	ENST00000370992.4	-	15	1819	c.1708C>T	c.(1708-1710)Ctg>Ttg	p.L570L	RRP12_ENST00000414986.1_Silent_p.L509L|RRP12_ENST00000536831.1_Silent_p.L288L|RRP12_ENST00000315563.6_Silent_p.L470L	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	570						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.L570L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		ATGACAGGCAGCAGCCAGCTC	0.542													G|||	299	0.0597045	0.0219	0.0648	5008	,	,		20958	0.1131		0.0487	False		,,,				2504	0.0634				p.L570L		Atlas-SNP	.											RRP12,NS,carcinoma,0,1	RRP12	97	1	1	Substitution - coding silent(1)	stomach(1)	c.C1708T						PASS	.	G	,	106,4300	82.4+/-120.9	4,98,2101	124.0	123.0	124.0		1525,1708	4.8	1.0	10	dbSNP_127	124	533,8067	149.7+/-204.7	12,509,3779	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	16,607,5880	AA,AG,GG		6.1977,2.4058,4.9131	,	509/1237,570/1298	99139140	639,12367	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon15			CAGGCAGCAGCCA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1708C>T	10.37:g.99139140G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	42	25	0.595238	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.951;A|0.049	0.049	strong		0.542	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
JRK	8629	hgsc.bcm.edu	37	8	143746069	143746069	+	RNA	SNP	T	T	C	rs3735999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143746069T>C	ENST00000507178.2	-	0	1741							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ggtcagcttttggagtctttt	0.672													C|||	2666	0.532348	0.7171	0.3213	5008	,	,		16647	0.5188		0.3926	False		,,,				2504	0.59				p.P469P		Atlas-SNP	.											.	.	.	.	0			c.A1407G						PASS	.	C	,	2527,1527		799,929,299	19.0	22.0	21.0		1409,1409	-2.2	0.0	8	dbSNP_107	21	3154,5166		626,1902,1632	yes	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	1425,2831,1931	CC,CT,TT		37.9087,37.6665,45.9108	,	469/557,469/569	143746069	5681,6693	2027	4160	6187			8629	exon3			AGCTTTTGGAGTC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746069T>C		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				T|0.479;C|0.521	0.521	strong		0.672	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
GOLGA3	2802	hgsc.bcm.edu	37	12	133384864	133384864	+	Missense_Mutation	SNP	G	G	A	rs3741486	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133384864G>A	ENST00000450791.2	-	4	974	c.791C>T	c.(790-792)cCg>cTg	p.P264L	GOLGA3_ENST00000456883.2_Missense_Mutation_p.P264L|GOLGA3_ENST00000537452.1_Missense_Mutation_p.P264L|GOLGA3_ENST00000204726.3_Missense_Mutation_p.P264L|GOLGA3_ENST00000545875.1_Missense_Mutation_p.P264L			Q08378	GOGA3_HUMAN	golgin A3	264			P -> L (in dbSNP:rs3741486).		intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		ATCGGGAGCCGGGACATTTCC	0.527													G|||	711	0.141973	0.0106	0.1571	5008	,	,		15064	0.1736		0.2813	False		,,,				2504	0.1329				p.P264L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C791T						PASS	.	G	LEU/PRO,LEU/PRO	225,4181	138.0+/-173.8	9,207,1987	134.0	148.0	143.0		791,791	0.8	0.0	12	dbSNP_107	143	2559,6041	416.7+/-352.2	385,1789,2126	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	98,98	394,1996,4113	AA,AG,GG		29.7558,5.1067,21.4055	benign,benign	264/1135,264/1499	133384864	2784,10222	2203	4300	6503	SO:0001583	missense	2802	exon5			GGAGCCGGGACAT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.791C>T	12.37:g.133384864G>A	ENSP00000410378:p.Pro264Leu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	167	77	0.461078	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	394	0.1804029304029304	8	0.016260162601626018	59	0.16298342541436464	105	0.18356643356643357	222	0.2928759894459103	G	1.008	-0.688716	0.03328	0.051067	0.297558	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.23	0.791	0.18619	.	1.119980	0.06397	N	0.718094	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	B;B;B	0.14805	0.011;0.006;0.006	B;B;B	0.06405	0.002;0.002;0.001	T	0.35919	-0.9769	9	0.66056	D	0.02	.	9.7493	0.40466	0.4088:0.0:0.5912:0.0	rs3741486;rs52796197;rs60613371;rs3741486	264;264;264	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	L	264	ENSP00000204726:P264L;ENSP00000410378:P264L;ENSP00000409303:P264L;ENSP00000442143:P264L;ENSP00000442603:P264L	ENSP00000204726:P264L	P	-	2	0	GOLGA3	131894937	0.000000	0.05858	0.002000	0.10522	0.034000	0.12701	0.439000	0.21575	0.310000	0.22990	0.585000	0.79938	CCG	G|0.802;A|0.198	0.198	strong		0.527	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
OR2B2	81697	hgsc.bcm.edu	37	6	27879551	27879551	+	Missense_Mutation	SNP	C	C	G	rs9368537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27879551C>G	ENST00000303324.2	-	1	623	c.547G>C	c.(547-549)Gct>Cct	p.A183P		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	183			A -> P (in dbSNP:rs9368537).			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(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						TTGAGCAGAGCAGGGACTTCA	0.438													C|||	291	0.058107	0.0265	0.111	5008	,	,		20677	0.0853		0.0119	False		,,,				2504	0.0828				p.A183P		Atlas-SNP	.											OR2B2,colon,carcinoma,0,1	OR2B2	54	1	0			c.G547C						PASS	.	C	PRO/ALA	98,4308	79.3+/-117.8	1,96,2106	103.0	95.0	98.0		547	4.3	1.0	6	dbSNP_119	98	228,8372	93.3+/-155.3	3,222,4075	yes	missense	OR2B2	NM_033057.2	27	4,318,6181	GG,GC,CC		2.6512,2.2242,2.5065	probably-damaging	183/358	27879551	326,12680	2203	4300	6503	SO:0001583	missense	81697	exon1			GCAGAGCAGGGAC	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.547G>C	6.37:g.27879551C>G	ENSP00000304419:p.Ala183Pro	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	51	0.414634	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	113	0.051739926739926737	14	0.028455284552845527	39	0.10773480662983426	53	0.09265734265734266	7	0.009234828496042216	C	14.45	2.540423	0.45176	0.022242	0.026512	ENSG00000168131	ENST00000303324	T	0.00029	8.91	4.32	4.32	0.51571	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38959	U	0.001514	T	0.00109	0.0003	N	0.20610	0.595	0.80722	P	0.0	D	0.89917	1.0	D	0.79108	0.992	T	0.78600	-0.2141	9	0.52906	T	0.07	.	11.0304	0.47769	0.0:0.8099:0.1901:0.0	rs9368537;rs52831196;rs9368537	183	Q9GZK3	OR2B2_HUMAN	P	183	ENSP00000304419:A183P	ENSP00000304419:A183P	A	-	1	0	OR2B2	27987530	0.297000	0.24408	0.962000	0.40283	0.845000	0.48019	0.938000	0.28965	2.311000	0.77944	0.563000	0.77884	GCT	C|0.966;G|0.034	0.034	strong		0.438	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
PRSS54	221191	hgsc.bcm.edu	37	16	58314598	58314598	+	Missense_Mutation	SNP	C	C	T	rs1052276	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:58314598C>T	ENST00000219301.4	-	7	1112	c.718G>A	c.(718-720)Gtc>Atc	p.V240I	CCDC113_ENST00000219299.4_3'UTR|PRSS54_ENST00000567164.1_Missense_Mutation_p.V240I|PRSS54_ENST00000543437.1_Missense_Mutation_p.V141I|CCDC113_ENST00000443128.2_3'UTR	NM_001080492.1	NP_001073961.1	Q6PEW0	PRS54_HUMAN	protease, serine, 54	240	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> I (in dbSNP:rs1052276). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			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						AAGTTCAGGACTCCTCTCAGA	0.532													C|||	473	0.0944489	0.0673	0.1513	5008	,	,		18873	0.1032		0.1074	False		,,,				2504	0.0685				p.V240I		Atlas-SNP	.											.	PRSS54	48	.	0			c.G718A						PASS	.	C	ILE/VAL,,	332,4064	174.8+/-204.3	7,318,1873	65.0	62.0	63.0		718,,	-10.9	0.0	16	dbSNP_86	63	916,7684	204.5+/-247.2	50,816,3434	yes	missense,utr-3,utr-3	CCDC113,PRSS54	NM_001080492.1,NM_001142302.1,NM_014157.3	29,,	57,1134,5307	TT,TC,CC		10.6512,7.5523,9.603	benign,,	240/396,,	58314598	1248,11748	2198	4300	6498	SO:0001583	missense	221191	exon7			TCAGGACTCCTCT	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.718G>A	16.37:g.58314598C>T	ENSP00000219301:p.Val240Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001080492	Q96LN9|Q9NT77	Missense_Mutation	SNP	ENST00000219301.4	37	CCDS32463.1	212	0.09706959706959707	38	0.07723577235772358	42	0.11602209944751381	52	0.09090909090909091	80	0.10554089709762533	C	5.061	0.196935	0.09599	0.075523	0.106512	ENSG00000103023	ENST00000219301;ENST00000543437	D;D	0.87334	-2.24;-2.24	5.77	-10.9	0.00192	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.353490	0.04775	N	0.428687	T	0.01523	0.0049	N	0.03209	-0.39	0.80722	P	0.0	B	0.25272	0.122	B	0.27380	0.079	T	0.34625	-0.9821	9	0.02654	T	1	-3.9884	5.8642	0.18765	0.0917:0.4863:0.2235:0.1986	rs1052276;rs3169291;rs17846560;rs17859635;rs52811089;rs57343894;rs1052276	240	Q6PEW0	PRS54_HUMAN	I	240;141	ENSP00000219301:V240I;ENSP00000437705:V141I	ENSP00000219301:V240I	V	-	1	0	PRSS54	56872099	0.000000	0.05858	0.002000	0.10522	0.110000	0.19582	-1.992000	0.01476	-1.858000	0.01158	-0.302000	0.09304	GTC	C|0.905;T|0.095	0.095	strong		0.532	PRSS54-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422556.1	NM_001080492	
CEP250	11190	hgsc.bcm.edu	37	20	34090519	34090519	+	Missense_Mutation	SNP	G	G	A	rs3748433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34090519G>A	ENST00000397527.1	+	30	5042	c.4322G>A	c.(4321-4323)cGg>cAg	p.R1441Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1385Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1441	Gln/Glu-rich.		R -> Q (in dbSNP:rs3748433).		centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GAGACTCTGCGGGGACAAATC	0.542													G|||	692	0.138179	0.1596	0.1052	5008	,	,		20568	0.1359		0.0954	False		,,,				2504	0.1789				p.R1441Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G4322A						PASS	.	G	GLN/ARG	714,3692	290.4+/-280.9	53,608,1542	47.0	54.0	52.0		4322	-3.2	0.4	20	dbSNP_107	52	752,7848	180.6+/-229.5	36,680,3584	yes	missense	CEP250	NM_007186.3	43	89,1288,5126	AA,AG,GG		8.7442,16.2052,11.2717	benign	1441/2443	34090519	1466,11540	2203	4300	6503	SO:0001583	missense	11190	exon30			CTCTGCGGGGACA	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.4322G>A	20.37:g.34090519G>A	ENSP00000380661:p.Arg1441Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	254	0.1163003663003663	73	0.1483739837398374	40	0.11049723756906077	76	0.13286713286713286	65	0.08575197889182058	G	0	-2.638637	0.00112	0.162052	0.087442	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.08102	3.13;3.13	4.33	-3.22	0.05125	.	0.369326	0.23254	N	0.050211	T	0.00012	0.0000	N	0.05383	-0.06	0.80722	P	0.0	B	0.12630	0.006	B	0.08055	0.003	T	0.39860	-0.9593	9	0.02654	T	1	.	7.3033	0.26432	0.4577:0.0:0.4304:0.1119	rs3748433;rs52789825;rs60773845;rs3748433	1441	Q9BV73	CP250_HUMAN	Q	1441;1385	ENSP00000380661:R1441Q;ENSP00000341541:R1385Q	ENSP00000341541:R1385Q	R	+	2	0	CEP250	33553933	0.957000	0.32711	0.404000	0.26397	0.012000	0.07955	0.802000	0.27069	-1.014000	0.03379	-2.303000	0.00259	CGG	G|0.880;N|0.000	.	strong		0.542	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
GRIK1	2897	hgsc.bcm.edu	37	21	30925928	30925928	+	Missense_Mutation	SNP	A	A	G	rs363504	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:30925928A>G	ENST00000399907.1	-	17	3116	c.2705T>C	c.(2704-2706)tTa>tCa	p.L902S	GRIK1_ENST00000399914.1_Intron|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000399909.1_Missense_Mutation_p.L887S|GRIK1_ENST00000535441.1_Intron|GRIK1_ENST00000399913.1_Intron|GRIK1_ENST00000327783.4_Intron|GRIK1_ENST00000309434.7_Missense_Mutation_p.L904S|GRIK1_ENST00000389124.2_Intron	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	902			L -> S (in dbSNP:rs363504). {ECO:0000269|PubMed:11702055}.		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)	CTCTCGAATTAATTTACCACA	0.353													A|||	550	0.109824	0.2186	0.134	5008	,	,		15478	0.0853		0.0368	False		,,,				2504	0.046				p.L902S		Atlas-SNP	.											.	GRIK1	293	.	0			c.T2705C	GRCh37	CM067678	GRIK1	M	rs363504	PASS	.	A	SER/LEU,	637,3021		43,551,1235	113.0	115.0	115.0		2705,	4.2	1.0	21	dbSNP_79	115	363,7809		6,351,3729	yes	missense,intron	GRIK1	NM_000830.3,NM_175611.2	145,	49,902,4964	GG,GA,AA		4.442,17.4139,8.4531	benign,	902/919,	30925928	1000,10830	1829	4086	5915	SO:0001583	missense	2897	exon17			CGAATTAATTTAC		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.2705T>C	21.37:g.30925928A>G	ENSP00000382791:p.Leu902Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	37	CCDS42913.1	223	0.1021062271062271	107	0.21747967479674796	45	0.12430939226519337	44	0.07692307692307693	27	0.03562005277044855	A	15.36	2.810171	0.50421	0.174139	0.04442	ENSG00000171189	ENST00000399907;ENST00000399909;ENST00000309434	T;T;T	0.12879	2.69;2.64;2.69	5.4	4.25	0.50352	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.38545	P	0.050674	B	0.29862	0.259	B	0.25759	0.063	T	0.34403	-0.9830	8	0.05959	T	0.93	.	10.9814	0.47497	0.9265:0.0:0.0735:0.0	rs363504;rs52810048;rs60803631;rs363504	902	P39086	GRIK1_HUMAN	S	902;887;904	ENSP00000382791:L902S;ENSP00000382793:L887S;ENSP00000311646:L904S	ENSP00000311646:L904S	L	-	2	0	GRIK1	29847799	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.194000	0.65125	1.065000	0.40693	0.533000	0.62120	TTA	T|0.000;G|0.095	0.095	strong		0.353	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		
CNGA2	1260	hgsc.bcm.edu	37	X	150908168	150908168	+	Missense_Mutation	SNP	G	G	T	rs144366408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150908168G>T	ENST00000329903.4	+	3	371	c.338G>T	c.(337-339)gGc>gTc	p.G113V		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	113					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)					GAGGGGGATGGCAAAGGCGAC	0.542													G|||	13	0.00344371	0.0015	0.0029	3775	,	,		14551	0.0		0.005	False		,,,				2504	0.0041				p.G113V		Atlas-SNP	.											.	CNGA2	136	.	0			c.G338T						PASS	.	G	VAL/GLY	2,3833		0,2,0,1630,571	128.0	96.0	107.0		338	2.8	1.0	X	dbSNP_134	107	55,6673		0,36,19,2392,1853	yes	missense	CNGA2	NM_005140.1	109	0,38,19,4022,2424	TT,TG,T,GG,G		0.8175,0.0522,0.5396	benign	113/665	150908168	57,10506	2203	4300	6503	SO:0001583	missense	1260	exon4			GGGATGGCAAAGG	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.338G>T	X.37:g.150908168G>T	ENSP00000328478:p.Gly113Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	7	0.004219409282700422	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.003968253968253968	G	9.795	1.178974	0.21787	5.22E-4	0.008175	ENSG00000183862	ENST00000329903	D	0.97328	-4.34	5.58	2.75	0.32379	.	0.401066	0.26948	N	0.021695	D	0.88991	0.6588	L	0.31926	0.97	0.58432	D	0.999997	B	0.15473	0.013	B	0.16289	0.015	T	0.79567	-0.1750	10	0.20519	T	0.43	.	2.2593	0.04063	0.1718:0.1496:0.5206:0.1579	.	113	Q16280	CNGA2_HUMAN	V	113	ENSP00000328478:G113V	ENSP00000328478:G113V	G	+	2	0	CNGA2	150658824	0.971000	0.33674	0.998000	0.56505	0.632000	0.37999	0.882000	0.28186	0.138000	0.18790	-0.343000	0.07986	GGC	G|0.994;T|0.006	0.006	strong		0.542	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
DOCK2	1794	hgsc.bcm.edu	37	5	169267784	169267784	+	Silent	SNP	G	G	A	rs261623	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169267784G>A	ENST00000256935.8	+	27	2807	c.2727G>A	c.(2725-2727)caG>caA	p.Q909Q	DOCK2_ENST00000520908.1_Silent_p.Q401Q|DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	909					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCATATCCAGGAGATCATGG	0.468													G|||	1980	0.395367	0.6415	0.389	5008	,	,		21508	0.1577		0.4155	False		,,,				2504	0.2914				p.Q909Q		Atlas-SNP	.											.	DOCK2	389	.	0			c.G2727A						PASS	.	G		2658,1748	646.1+/-398.3	798,1062,343	137.0	113.0	121.0		2727	0.3	1.0	5	dbSNP_79	121	3542,5058	514.7+/-378.5	713,2116,1471	no	coding-synonymous	DOCK2	NM_004946.2		1511,3178,1814	AA,AG,GG		41.186,39.6732,47.6703		909/1831	169267784	6200,6806	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon27			TATCCAGGAGATC	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.2727G>A	5.37:g.169267784G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			G|0.557;A|0.443	0.443	strong		0.468	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
ZP3	7784	hgsc.bcm.edu	37	7	76069902	76069902	+	Missense_Mutation	SNP	G	G	C	rs1804905		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76069902G>C	ENST00000394857.3	+	7	1092	c.1034G>C	c.(1033-1035)aGg>aCg	p.R345T	ZP3_ENST00000336517.4_Missense_Mutation_p.R294T|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.R169T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	345				R -> T (in Ref. 2; CAA40095). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						CAGTGGTCCAGGTCTGCTTCC	0.537																																					p.R345T		Atlas-SNP	.											.	ZP3	32	.	0			c.G1034C						PASS	.						135.0	127.0	130.0					7																	76069902		2203	4300	6503	SO:0001583	missense	7784	exon7			GGTCCAGGTCTGC	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1034G>C	7.37:g.76069902G>C	ENSP00000378326:p.Arg345Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	202	28	0.138614	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	8.608|8.608	0.888351|0.888351	0.17540|0.17540	.|.	.|.	ENSG00000188372|ENSG00000188372	ENST00000394860|ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	.|T;T;T	.|0.25250	.|2.41;2.63;1.81	4.64|4.64	-8.56|-8.56	0.00904|0.00904	.|.	.|0.754812	.|0.12103	.|U	.|0.499355	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.28115|0.28115	0.83|0.83	0.09310|0.09310	N|N	1|1	.|B;B	.|0.19817	.|0.002;0.039	.|B;B	.|0.17722	.|0.004;0.019	T|T	0.33292|0.33292	-0.9874|-0.9874	5|10	.|0.13108	.|T	.|0.6	-0.2921|-0.2921	12.2107|12.2107	0.54377|0.54377	0.1994:0.1279:0.6727:0.0|0.1994:0.1279:0.6727:0.0	rs1804905|rs1804905	.|294;345	.|P21754-3;P21754	.|.;ZP3_HUMAN	R|T	179|294;345;345;169	.|ENSP00000337310:R294T;ENSP00000378326:R345T;ENSP00000411955:R169T	.|ENSP00000337310:R294T	G|R	+|+	1|2	0|0	ZP3|ZP3	75907838|75907838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.592000|-0.592000	0.05747|0.05747	-1.616000|-1.616000	0.01572|0.01572	-0.291000|-0.291000	0.09656|0.09656	GGT|AGG	G|0.500;C|0.500	0.500	weak		0.537	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
ADCK3	56997	hgsc.bcm.edu	37	1	227174210	227174210	+	Silent	SNP	T	T	C	rs3738725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:227174210T>C	ENST00000366779.1	+	20	4487	c.1716T>C	c.(1714-1716)tcT>tcC	p.S572S	ADCK3_ENST00000433743.2_Silent_p.S246S|ADCK3_ENST00000366778.1_Silent_p.S520S|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000366777.3_Silent_p.S572S|ADCK3_ENST00000458507.2_Silent_p.S293S			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	572					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						CCTTCGCCTCTGATGAGCCTT	0.582													C|||	1572	0.313898	0.2882	0.3127	5008	,	,		17137	0.2133		0.494	False		,,,				2504	0.2679				p.S572S		Atlas-SNP	.											.	ADCK3	77	.	0			c.T1716C						PASS	.	C		1405,3001	687.2+/-404.8	222,961,1020	98.0	97.0	97.0		1716	-11.7	0.0	1	dbSNP_107	97	4346,4254	574.0+/-390.0	1088,2170,1042	no	coding-synonymous	ADCK3	NM_020247.4		1310,3131,2062	CC,CT,TT		49.4651,31.8883,44.2181		572/648	227174210	5751,7255	2203	4300	6503	SO:0001819	synonymous_variant	56997	exon15			CGCCTCTGATGAG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"""coenzyme Q8 homolog (yeast)"""	606980	"""chaperone-ABC1 (activity of bc1 complex, S.pombe)-like"", ""chaperone, ABC1 activity of bc1 complex like (S. pombe)"", ""chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"""	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1716T>C	1.37:g.227174210T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Silent	SNP	ENST00000366779.1	37	CCDS1557.1																																																																																			T|0.607;C|0.393	0.393	strong		0.582	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247	
FMNL1	752	hgsc.bcm.edu	37	17	43316360	43316360	+	Silent	SNP	G	G	A	rs12940312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:43316360G>A	ENST00000331495.3	+	11	1344	c.1008G>A	c.(1006-1008)tcG>tcA	p.S336S	CTD-2020K17.3_ENST00000393507.2_RNA|FMNL1_ENST00000592006.1_3'UTR|CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000328118.3_Silent_p.S336S|FMNL1_ENST00000587489.1_5'Flank	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	336	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TGGTACATTCGGTGGAGAACA	0.537													G|||	565	0.112819	0.0061	0.0879	5008	,	,		23216	0.1339		0.1083	False		,,,				2504	0.2577				p.S336S	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.G1008A						PASS	.	G		90,4316	75.7+/-113.9	1,88,2114	219.0	154.0	176.0		1008	-8.5	0.3	17	dbSNP_121	176	917,7683	204.8+/-247.4	50,817,3433	no	coding-synonymous	FMNL1	NM_005892.3		51,905,5547	AA,AG,GG		10.6628,2.0427,7.7426		336/1101	43316360	1007,11999	2203	4300	6503	SO:0001819	synonymous_variant	752	exon11			ACATTCGGTGGAG	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.1008G>A	17.37:g.43316360G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	210	88	0.419048	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Silent	SNP	ENST00000331495.3	37	CCDS11497.1																																																																																			G|0.919;A|0.081	0.081	strong		0.537	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	
IFNLR1	163702	hgsc.bcm.edu	37	1	24496085	24496085	+	Silent	SNP	G	G	A	rs34654982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24496085G>A	ENST00000327535.1	-	3	201	c.189C>T	c.(187-189)ccC>ccT	p.P63P	IFNLR1_ENST00000327575.2_Silent_p.P63P|IFNLR1_ENST00000374421.3_Silent_p.P63P|IFNLR1_ENST00000374419.1_5'UTR|IFNLR1_ENST00000374418.3_Silent_p.P63P	NM_170743.3|NM_173064.2	NP_734464.1|NP_775087.1	Q8IU57	INLR1_HUMAN	interferon, lambda receptor 1	63	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mucosal immune response (GO:0002385)|negative regulation of cell proliferation (GO:0008285)|regulation of defense response to virus by host (GO:0050691)|response to type III interferon (GO:0034342)	integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)											GTCTACGGGTGGGAGAGCTGG	0.552													G|||	582	0.116214	0.289	0.0432	5008	,	,		21000	0.0327		0.0417	False		,,,				2504	0.0971				p.P63P		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.	G	,,	1063,3343	387.5+/-326.5	126,811,1266	62.0	62.0	62.0		189,189,189	-4.2	0.0	1	dbSNP_126	62	315,8285	112.3+/-172.5	3,309,3988	no	coding-synonymous,coding-synonymous,coding-synonymous	IL28RA	NM_170743.3,NM_173064.2,NM_173065.2	,,	129,1120,5254	AA,AG,GG		3.6628,24.1262,10.5951	,,	63/521,63/492,63/245	24496085	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	163702	exon3			ACGGGTGGGAGAG	AY129153	CCDS248.1, CCDS249.1, CCDS250.1	1p36.11	2012-11-27	2012-11-26	2012-11-26	ENSG00000185436	ENSG00000185436		"""Interferons"""	18584	protein-coding gene	gene with protein product	"""interferon lambda receptor 1"""	607404	"""interleukin 28 receptor, alpha"", ""interleukin 28 receptor, alpha (interferon, lambda receptor)"""	IL28RA			Standard	NM_173064		Approved	CRF2/12, IFNLR, IL-28R1	uc001bis.3	Q8IU57	OTTHUMG00000003036	ENST00000327535.1:c.189C>T	1.37:g.24496085G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_170743	Q5VTX5|Q5VTX7|Q5VTX8|Q6ZML8|Q8IV66|Q8IZI7|Q8IZI8	Silent	SNP	ENST00000327535.1	37	CCDS248.1																																																																																			G|0.897;A|0.103	0.103	strong		0.552	IFNLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008402.1	NM_170743	
ZFR2	23217	hgsc.bcm.edu	37	19	3831709	3831709	+	Missense_Mutation	SNP	C	C	T	rs2240234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3831709C>T	ENST00000262961.4	-	4	557	c.547G>A	c.(547-549)Gtg>Atg	p.V183M	ZFR2_ENST00000591965.1_5'UTR	NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	183			V -> M (in dbSNP:rs2240234). {ECO:0000269|PubMed:10470851}.				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		TAGGAGGTCACGATGGAAGCT	0.662													C|||	1294	0.258387	0.23	0.1643	5008	,	,		11909	0.2609		0.1998	False		,,,				2504	0.4213				p.V183M		Atlas-SNP	.											.	ZFR2	63	.	0			c.G547A						PASS	.	C	MET/VAL	774,3496		71,632,1432	22.0	26.0	25.0		547	-2.6	0.0	19	dbSNP_98	25	1621,6847		164,1293,2777	yes	missense	ZFR2	NM_015174.1	21	235,1925,4209	TT,TC,CC		19.1427,18.1265,18.802	possibly-damaging	183/940	3831709	2395,10343	2135	4234	6369	SO:0001583	missense	23217	exon4			AGGTCACGATGGA	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.547G>A	19.37:g.3831709C>T	ENSP00000262961:p.Val183Met	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	37	CCDS45921.1	450	0.20604395604395603	114	0.23170731707317074	65	0.17955801104972377	120	0.2097902097902098	151	0.19920844327176782	C	10.93	1.489829	0.26686	0.181265	0.191427	ENSG00000105278	ENST00000262961;ENST00000438164	T;T	0.16196	3.13;2.36	2.75	-2.61	0.06171	.	0.960602	0.08492	N	0.937889	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.31318	0.319	B	0.20577	0.03	T	0.42749	-0.9433	9	0.36615	T	0.2	-2.2124	4.3181	0.11003	0.0:0.2878:0.2342:0.478	rs2240234;rs52792083;rs59294651;rs2240234	183	Q9UPR6	ZFR2_HUMAN	M	183	ENSP00000262961:V183M;ENSP00000388974:V183M	ENSP00000262961:V183M	V	-	1	0	ZFR2	3782709	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.114000	0.15520	-0.426000	0.07360	-0.266000	0.10368	GTG	C|0.782;T|0.218	0.218	strong		0.662	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174	
SLC6A5	9152	hgsc.bcm.edu	37	11	20673902	20673902	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:20673902G>A	ENST00000525748.1	+	15	2411	c.2138G>A	c.(2137-2139)tGg>tAg	p.W713*	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	713					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)	TATCCTAACTGGTCCATGGTG	0.468																																					p.W713X		Atlas-SNP	.											SLC6A5,NS,carcinoma,+1,1	SLC6A5	151	1	0			c.G2138A						scavenged	.						238.0	214.0	222.0					11																	20673902		2203	4300	6503	SO:0001587	stop_gained	9152	exon15			CTAACTGGTCCAT	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.2138G>A	11.37:g.20673902G>A	ENSP00000434364:p.Trp713*	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	111	2	0.018018	NM_004211	O95288|Q4VAM7|Q9BX77	Nonsense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	G	42	9.584418	0.99211	.	.	ENSG00000165970	ENST00000525748	.	.	.	5.88	5.88	0.94601	.	0.114954	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.3017	0.98615	0.0:0.0:1.0:0.0	.	.	.	.	X	713	.	ENSP00000434364:W713X	W	+	2	0	SLC6A5	20630478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.404000	0.97306	2.800000	0.96347	0.650000	0.86243	TGG	.	.	none		0.468	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
ZNF714	148206	hgsc.bcm.edu	37	19	21300462	21300462	+	Missense_Mutation	SNP	A	A	G	rs2884554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:21300462A>G	ENST00000596143.1	+	5	1317	c.992A>G	c.(991-993)aAa>aGa	p.K331R	ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	331			K -> R (in dbSNP:rs2884554). {ECO:0000269|PubMed:14702039, 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)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ACAAAACATAAAAGAATTCAT	0.348													.|||	3353	0.669529	0.2035	0.8084	5008	,	,		20909	0.8611		0.8191	False		,,,				2504	0.8497				p.K331R		Atlas-SNP	.											.	ZNF714	121	.	0			c.A992G						PASS	.	A	ARG/LYS	1513,2791		267,979,906	33.0	36.0	35.0		992	1.0	0.8	19	dbSNP_101	35	7198,1358		3030,1138,110	yes	missense	ZNF714	NM_182515.3	26	3297,2117,1016	GG,GA,AA		15.8719,35.1533,32.2628	benign	331/555	21300462	8711,4149	2152	4278	6430	SO:0001583	missense	148206	exon5			AACATAAAAGAAT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.992A>G	19.37:g.21300462A>G	ENSP00000472368:p.Lys331Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	1519	0.6955128205128205	120	0.24390243902439024	287	0.7928176795580111	503	0.8793706293706294	609	0.8034300791556728	.	11.58	1.680248	0.29872	0.351533	0.841281	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	.	.	.	.	.	T	0.00012	0.0000	N	0.10972	0.075	0.53005	P	3.6000000000036E-5	D	0.76494	0.999	D	0.70487	0.969	T	0.38351	-0.9665	7	0.39692	T	0.17	.	4.6997	0.12822	0.6729:0.3271:0.0:0.0	rs2884554;rs52821377;rs2884554	331	A6NEM4	.	R	331	.	ENSP00000291770:K331R	K	+	2	0	ZNF714	21092302	0.000000	0.05858	0.766000	0.31476	0.755000	0.42902	0.131000	0.15870	0.378000	0.24764	0.369000	0.22263	AAA	A|0.264;G|0.736	0.736	strong		0.348	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
KDM3B	51780	hgsc.bcm.edu	37	5	137733891	137733891	+	Silent	SNP	A	A	G	rs17294563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:137733891A>G	ENST00000314358.5	+	10	3056	c.2856A>G	c.(2854-2856)gtA>gtG	p.V952V	KDM3B_ENST00000394866.1_Silent_p.V608V|KDM3B_ENST00000542866.1_5'UTR	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	952					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						GAAAAGGGGTACTCCGTGTGG	0.483													A|||	559	0.111621	0.0091	0.1037	5008	,	,		19992	0.0228		0.171	False		,,,				2504	0.2863				p.V952V		Atlas-SNP	.											.	KDM3B	177	.	0			c.A2856G						PASS	.	A		194,4212	122.1+/-159.5	4,186,2013	106.0	100.0	102.0		2856	0.2	1.0	5	dbSNP_123	102	1546,7054	290.5+/-299.9	141,1264,2895	no	coding-synonymous	KDM3B	NM_016604.3		145,1450,4908	GG,GA,AA		17.9767,4.4031,13.3784		952/1762	137733891	1740,11266	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon10			AGGGGTACTCCGT	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.2856A>G	5.37:g.137733891A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			A|0.883;G|0.117	0.117	strong		0.483	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
PRG3	10394	hgsc.bcm.edu	37	11	57146225	57146225	+	Missense_Mutation	SNP	A	A	G	rs34108746	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57146225A>G	ENST00000287143.2	-	4	545	c.436T>C	c.(436-438)Tat>Cat	p.Y146H		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						TGAATGCGATAGTTGAAGTTG	0.502													A|||	152	0.0303514	0.0068	0.0288	5008	,	,		19253	0.001		0.1064	False		,,,				2504	0.0153				p.Y146H	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.T436C						PASS	.	A	HIS/TYR	59,4343	56.8+/-93.2	0,59,2142	255.0	242.0	247.0		436	-9.8	0.0	11	dbSNP_126	247	667,7925	168.7+/-220.2	32,603,3661	yes	missense	PRG3	NM_006093.3	83	32,662,5803	GG,GA,AA		7.763,1.3403,5.5872	benign	146/226	57146225	726,12268	2201	4296	6497	SO:0001583	missense	10394	exon4			TGCGATAGTTGAA	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.436T>C	11.37:g.57146225A>G	ENSP00000287143:p.Tyr146His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_006093	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	37	CCDS7954.1	96	0.04395604395604396	5	0.01016260162601626	14	0.03867403314917127	0	0.0	77	0.10158311345646438	A	12.32	1.902968	0.33628	0.013403	0.07763	ENSG00000156575	ENST00000287143	T	0.18174	2.23	5.27	-9.75	0.00506	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	3.747700	0.00424	N	0.000069	T	0.00384	0.0012	L	0.55103	1.725	0.09310	N	1	B	0.28470	0.213	B	0.31751	0.135	T	0.06899	-1.0801	10	0.22109	T	0.4	2.6185	6.0565	0.19815	0.1861:0.0:0.359:0.4549	rs34108746;rs52794566	146	Q9Y2Y8	PRG3_HUMAN	H	146	ENSP00000287143:Y146H	ENSP00000287143:Y146H	Y	-	1	0	PRG3	56902801	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.855000	0.00729	-1.949000	0.01031	-0.516000	0.04426	TAT	A|0.947;G|0.053	0.053	strong		0.502	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
CCDC78	124093	hgsc.bcm.edu	37	16	775236	775236	+	Splice_Site	SNP	C	C	T	rs138669350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:775236C>T	ENST00000293889.6	-	5	598		c.e5+1		HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000564537.1_5'Flank|HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000549114.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78						cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				TGCACACTCACGCCGCTCCCC	0.642													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17690	0.0		0.003	False		,,,				2504	0.001				.		Atlas-SNP	.											.	CCDC78	26	.	0			c.492+1G>A						PASS	.	C		7,4383	11.4+/-27.6	0,7,2188	63.0	74.0	70.0			-0.3	0.0	16	dbSNP_134	70	13,8577	9.8+/-36.6	0,13,4282	yes	splice-5	CCDC78	NM_001031737.2		0,20,6470	TT,TC,CC		0.1513,0.1595,0.1541			775236	20,12960	2195	4295	6490	SO:0001630	splice_region_variant	124093	exon6			CACTCACGCCGCT	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.492+1G>A	16.37:g.775236C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001031737	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Splice_Site	SNP	ENST00000293889.6	37	CCDS32353.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	4.939	0.174544	0.09391	0.001595	0.001513	ENSG00000162004	ENST00000345165;ENST00000293889	.	.	.	3.84	-0.34	0.12643	.	.	.	.	.	.	.	.	.	.	.	0.21325	N	0.999729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3859	0.21559	0.0:0.5601:0.0:0.4399	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC78	715237	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.394000	0.07296	-0.010000	0.14271	0.561000	0.74099	.	C|0.998;T|0.002	0.002	strong		0.642	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476	Intron
FCAR	2204	hgsc.bcm.edu	37	19	55401170	55401170	+	Missense_Mutation	SNP	A	A	G	rs16986050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55401170A>G	ENST00000355524.3	+	5	815	c.805A>G	c.(805-807)Agc>Ggc	p.S269G	FCAR_ENST00000353758.4_Missense_Mutation_p.S160G|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000359272.4_Missense_Mutation_p.S257G|FCAR_ENST00000391726.3_Missense_Mutation_p.S161G|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000391725.3_Missense_Mutation_p.S247G|FCAR_ENST00000345937.4_Missense_Mutation_p.S173G|FCAR_ENST00000391724.3_Missense_Mutation_p.S235G|CTB-61M7.2_ENST00000594721.1_lincRNA	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	269			S -> G (in dbSNP:rs16986050). {ECO:0000269|PubMed:17548632}.		immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		ACCGAGCTGGAGCCAACAGAT	0.547													.|||	778	0.155351	0.3434	0.1081	5008	,	,		18910	0.0198		0.1839	False		,,,				2504	0.045				p.S269G		Atlas-SNP	.											FCAR,NS,carcinoma,-2,1	FCAR	110	1	0			c.A805G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,,GLY/SER,GLY/SER	1384,3022	454.9+/-350.8	206,972,1025	154.0	155.0	155.0		805,739,517,769,481,,478,703	0.9	0.0	19	dbSNP_123	155	1522,7078	287.7+/-298.4	135,1252,2913	yes	missense,missense,missense,missense,missense,utr-3,missense,missense	FCAR	NM_002000.2,NM_133269.2,NM_133271.2,NM_133272.2,NM_133273.2,NM_133274.2,NM_133277.2,NM_133278.2	56,56,56,56,56,,56,56	341,2224,3938	GG,GA,AA		17.6977,31.4117,22.3435	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	269/288,247/266,173/192,257/276,161/180,,160/179,235/254	55401170	2906,10100	2203	4300	6503	SO:0001583	missense	2204	exon5			AGCTGGAGCCAAC	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.805A>G	19.37:g.55401170A>G	ENSP00000347714:p.Ser269Gly	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	363	0.1662087912087912	170	0.34552845528455284	48	0.13259668508287292	10	0.017482517482517484	135	0.17810026385224276	A	9.725	1.160659	0.21538	0.314117	0.176977	ENSG00000186431	ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391724	T;T;T;T;T;T;T	0.04406	3.63;6.77;6.35;4.65;6.45;6.61;6.22	2.95	0.854	0.19007	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B;B;B	0.34372	0.451;0.307;0.101;0.0;0.199;0.053;0.311	B;B;B;B;B;B;B	0.30179	0.112;0.097;0.039;0.003;0.097;0.021;0.103	T	0.49062	-0.8978	8	0.34782	T	0.22	.	4.7474	0.13043	0.7178:0.0:0.2822:0.0	rs16986050;rs52827522;rs60168829;rs16986050	160;235;161;257;247;173;269	Q92592;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071	.;.;.;.;.;.;FCAR_HUMAN	G	161;269;247;173;160;257;235	ENSP00000375606:S161G;ENSP00000347714:S269G;ENSP00000375605:S247G;ENSP00000338257:S173G;ENSP00000338058:S160G;ENSP00000352218:S257G;ENSP00000375604:S235G	ENSP00000338257:S173G	S	+	1	0	FCAR	60092982	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.154000	0.31688	0.108000	0.17862	-0.379000	0.06801	AGC	A|0.795;G|0.205	0.205	strong		0.547	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
IFT140	9742	hgsc.bcm.edu	37	16	1573890	1573890	+	Missense_Mutation	SNP	G	G	A	rs2235638	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1573890G>A	ENST00000426508.2	-	25	3572	c.3209C>T	c.(3208-3210)gCg>gTg	p.A1070V	IFT140_ENST00000361339.5_Missense_Mutation_p.A264V	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1070			A -> V (in dbSNP:rs2235638). {ECO:0000269|PubMed:9628581}.		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				GTATCGGGCCGCCTCGATCAT	0.667													G|||	417	0.0832668	0.0023	0.1945	5008	,	,		15491	0.1825		0.0487	False		,,,				2504	0.047				p.A1070V		Atlas-SNP	.											.	IFT140	128	.	0			c.C3209T						PASS	.	G	VAL/ALA	60,4338	58.7+/-95.3	0,60,2139	69.0	56.0	60.0		3209	2.7	0.2	16	dbSNP_98	60	427,8173	130.7+/-188.6	10,407,3883	yes	missense	IFT140	NM_014714.3	64	10,467,6022	AA,AG,GG		4.9651,1.3643,3.7467	benign	1070/1463	1573890	487,12511	2199	4300	6499	SO:0001583	missense	9742	exon25			CGGGCCGCCTCGA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.3209C>T	16.37:g.1573890G>A	ENSP00000406012:p.Ala1070Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	197	0.0902014652014652	1	0.0020325203252032522	58	0.16022099447513813	101	0.17657342657342656	37	0.048812664907651716	G	11.79	1.744161	0.30865	0.013643	0.049651	ENSG00000187535	ENST00000397417;ENST00000361339;ENST00000426508	T;T	0.54866	0.55;0.55	5.71	2.68	0.31781	.	0.184300	0.47852	N	0.000203	T	0.00073	0.0002	L	0.43152	1.355	0.18873	P	0.9999875837	B;B	0.19817	0.023;0.039	B;B	0.21917	0.01;0.037	T	0.11591	-1.0581	9	0.10902	T	0.67	.	9.164	0.37041	0.1324:0.1214:0.7462:0.0	rs2235638;rs57949177;rs2235638	1070;757	Q96RY7;B4DR58	IF140_HUMAN;.	V	1070;264;1070	ENSP00000354895:A264V;ENSP00000406012:A1070V	ENSP00000354895:A264V	A	-	2	0	IFT140	1513891	1.000000	0.71417	0.183000	0.23137	0.635000	0.38103	4.875000	0.63072	0.347000	0.23924	-0.137000	0.14449	GCG	G|0.941;A|0.059	0.059	strong		0.667	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
ASTL	431705	hgsc.bcm.edu	37	2	96789787	96789787	+	Silent	SNP	T	T	C	rs893173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	58	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	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		
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:68773403G>A	ENST00000309099.6	-	3	757	c.375C>T	c.(373-375)tgC>tgT	p.C125C	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Silent_p.C125C	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	125						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TAAGGAACATGCAGAGCCCCA	0.687													G|||	1164	0.232428	0.2065	0.1354	5008	,	,		14674	0.2272		0.2694	False		,,,				2504	0.3037				p.C125C		Atlas-SNP	.											.	MRGPRF	22	.	0			c.C375T						PASS	.	G	,	885,3459		100,685,1387	21.0	21.0	21.0		375,375	2.7	0.8	11	dbSNP_120	21	2185,6331		295,1595,2368	no	coding-synonymous,coding-synonymous	MRGPRF	NM_001098515.1,NM_145015.4	,	395,2280,3755	AA,AG,GG		25.6576,20.3729,23.8725	,	125/344,125/344	68773403	3070,9790	2172	4258	6430	SO:0001819	synonymous_variant	116535	exon3			GAACATGCAGAGC	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.375C>T	11.37:g.68773403G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001098515	B3KV43|Q8NBK8	Silent	SNP	ENST00000309099.6	37	CCDS8188.1																																																																																			G|0.763;A|0.237	0.237	strong		0.687	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
CD300A	11314	hgsc.bcm.edu	37	17	72469966	72469966	+	Missense_Mutation	SNP	G	G	A	rs2272111	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72469966G>A	ENST00000360141.3	+	2	620	c.332G>A	c.(331-333)cGa>cAa	p.R111Q	CD300A_ENST00000310828.5_Intron|CD300A_ENST00000577511.1_5'UTR|CD300A_ENST00000392625.3_Intron|CD300A_ENST00000361933.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	111	Ig-like V-type.		R -> Q (in dbSNP:rs2272111). {ECO:0000269|PubMed:12483297, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						CCATGGCTCCGAGACTTTCAT	0.567													G|||	1731	0.345647	0.705	0.2161	5008	,	,		17525	0.1964		0.1978	False		,,,				2504	0.2577				p.R111Q		Atlas-SNP	.											.	CD300A	40	.	0			c.G332A						PASS	.	G	GLN/ARG	2763,1643	659.8+/-400.6	875,1013,315	125.0	131.0	129.0		332	-2.2	0.0	17	dbSNP_100	129	1761,6839	319.5+/-314.2	187,1387,2726	no	missense	CD300A	NM_007261.2	43	1062,2400,3041	AA,AG,GG		20.4767,37.2901,34.7839	benign	111/300	72469966	4524,8482	2203	4300	6503	SO:0001583	missense	11314	exon2			GGCTCCGAGACTT	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19319	protein-coding gene	gene with protein product		606790	"""CD300a antigen"""			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.332G>A	17.37:g.72469966G>A	ENSP00000353259:p.Arg111Gln	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_007261	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Missense_Mutation	SNP	ENST00000360141.3	37	CCDS32720.1	652	0.29853479853479853	334	0.6788617886178862	71	0.19613259668508287	107	0.18706293706293706	140	0.18469656992084432	G	0.945	-0.708406	0.03230	0.627099	0.204767	ENSG00000167851	ENST00000360141	T	0.02863	4.13	1.13	-2.22	0.06952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.16368	0.405	0.58432	P	1.999999999946489E-6	B	0.15473	0.013	B	0.16289	0.015	T	0.11717	-1.0576	8	0.12103	T	0.63	.	4.3704	0.11244	0.4976:0.0:0.5024:0.0	rs2272111;rs11869780;rs59752364;rs2272111	111	Q9UGN4	CLM8_HUMAN	Q	111	ENSP00000353259:R111Q	ENSP00000353259:R111Q	R	+	2	0	CD300A	69981561	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.049000	0.00629	-0.558000	0.06118	-1.277000	0.01392	CGA	.	.	weak		0.567	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261	
POGLUT1	56983	hgsc.bcm.edu	37	3	119196166	119196166	+	Silent	SNP	T	T	C	rs3732420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:119196166T>C	ENST00000295588.4	+	4	411	c.327T>C	c.(325-327)agT>agC	p.S109S		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	109					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						ACAGGTGTAGTGGTGTTGAGC	0.468													T|||	596	0.11901	0.0136	0.2305	5008	,	,		21369	0.123		0.169	False		,,,				2504	0.1268				p.S109S		Atlas-SNP	.											.	POGLUT1	32	.	0			c.T327C						PASS	.	T		188,4218	118.0+/-155.7	6,176,2021	183.0	178.0	180.0		327	1.6	1.0	3	dbSNP_107	180	1636,6964	303.2+/-306.3	163,1310,2827	no	coding-synonymous	POGLUT1	NM_152305.2		169,1486,4848	CC,CT,TT		19.0233,4.2669,14.0243		109/393	119196166	1824,11182	2203	4300	6503	SO:0001819	synonymous_variant	56983	exon4			GTGTAGTGGTGTT	BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"""KDELC family like 1"""	615618	"""chromosome 3 open reading frame 9"", ""KTEL (Lys-Tyr-Glu-Leu) containing 1"""	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.327T>C	3.37:g.119196166T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	184	69	0.375	NM_152305	B2RD13|Q53GJ4|Q8N2T1	Silent	SNP	ENST00000295588.4	37	CCDS2988.1	279	0.12774725274725274	10	0.02032520325203252	65	0.17955801104972377	79	0.1381118881118881	125	0.16490765171503957	T	10.66	1.412246	0.25465	0.042669	0.190233	ENSG00000163389	ENST00000476573	.	.	.	5.26	1.57	0.23409	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11108	-1.0601	3	.	.	.	-7.4987	6.8594	0.24058	0.0:0.2755:0.0:0.7245	rs3732420;rs17852786;rs3732420	.	.	.	R	96	.	.	W	+	1	0	POGLUT1	120678856	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.215000	0.32431	0.479000	0.27511	0.533000	0.62120	TGG	T|0.860;C|0.140	0.140	strong		0.468	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305	
C10orf111	221060	hgsc.bcm.edu	37	10	15138615	15138615	+	Missense_Mutation	SNP	C	C	T	rs7896053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:15138615C>T	ENST00000378207.3	-	2	482	c.209G>A	c.(208-210)aGg>aAg	p.R70K	RPP38_ENST00000378202.5_5'Flank|RPP38_ENST00000378197.4_5'Flank	NM_153244.1	NP_694976.1	Q8N326	CJ111_HUMAN	chromosome 10 open reading frame 111	70			R -> K (in dbSNP:rs7896053).			integral component of membrane (GO:0016021)				lung(5)|upper_aerodigestive_tract(1)	6						CGATGGTAGCCTGAGTCTCCA	0.502													T|||	1194	0.238419	0.6649	0.1182	5008	,	,		16927	0.0625		0.1113	False		,,,				2504	0.0593				p.R70K		Atlas-SNP	.											.	C10orf111	11	.	0			c.G209A						PASS	.	T	LYS/ARG	2472,1934	549.9+/-377.9	678,1116,409	141.0	138.0	139.0		209	-1.9	0.0	10	dbSNP_116	139	923,7677	776.9+/-407.7	51,821,3428	yes	missense	C10orf111	NM_153244.1	26	729,1937,3837	TT,TC,CC		10.7326,43.8947,26.1033	benign	70/156	15138615	3395,9611	2203	4300	6503	SO:0001583	missense	221060	exon2			GGTAGCCTGAGTC	BC029034	CCDS7107.1	10p13	2004-04-20			ENSG00000176236	ENSG00000176236			28582	protein-coding gene	gene with protein product						12477932	Standard	NM_153244		Approved	MGC35468, bA455B2.4	uc001inw.3	Q8N326	OTTHUMG00000017727	ENST00000378207.3:c.209G>A	10.37:g.15138615C>T	ENSP00000367449:p.Arg70Lys	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	72	0.441718	NM_153244	B2RAC4	Missense_Mutation	SNP	ENST00000378207.3	37	CCDS7107.1	497	0.22756410256410256	327	0.6646341463414634	52	0.143646408839779	32	0.055944055944055944	86	0.11345646437994723	T	8.664	0.901234	0.17760	0.561053	0.107326	ENSG00000176236	ENST00000378207	T	0.53857	0.6	2.83	-1.94	0.07571	.	.	.	.	.	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	0.41233	-0.9520	8	0.87932	D	0	.	4.5021	0.11869	0.1568:0.5125:0.0:0.3307	rs7896053;rs52818153;rs58141984;rs7896053	70	Q8N326	CJ111_HUMAN	K	70	ENSP00000367449:R70K	ENSP00000367449:R70K	R	-	2	0	C10orf111	15178621	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.525000	0.00221	-0.731000	0.04862	-2.791000	0.00116	AGG	C|0.740;T|0.260	0.260	strong		0.502	C10orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046975.1	NM_153244	
FAM161A	84140	hgsc.bcm.edu	37	2	62065759	62065759	+	Intron	SNP	C	C	T	rs6545910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:62065759C>T	ENST00000405894.3	-	3	1685				FAM161A_ENST00000404929.1_Silent_p.L555L	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A						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						GGAGTTTCTGCAATTCTTTCA	0.373													C|||	500	0.0998403	0.0061	0.2104	5008	,	,		12908	0.1696		0.1034	False		,,,				2504	0.0726				p.L555L		Atlas-SNP	.											.	FAM161A	200	.	0			c.G1665A						PASS	.	C	,	37,1715		0,37,839	150.0	151.0	151.0		1665,	3.3	1.0	2	dbSNP_116	151	459,3523		31,397,1563	no	coding-synonymous,intron	FAM161A	NM_001201543.1,NM_032180.2	,	31,434,2402	TT,TC,CC		11.5269,2.1119,8.6502	,	555/717,	62065759	496,5238	876	1991	2867	SO:0001627	intron_variant	84140	exon4			TTTCTGCAATTCT		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.1583+796G>A	2.37:g.62065759C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	192	84	0.4375	NM_001201543	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																			C|0.876;T|0.124	0.124	strong		0.373	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
FLG	2312	hgsc.bcm.edu	37	1	152280347	152280347	+	Missense_Mutation	SNP	C	C	T	rs139476473	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280347C>T	ENST00000368799.1	-	3	7050	c.7015G>A	c.(7015-7017)Gac>Aac	p.D2339N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2339	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.D2339N(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)			CTGGAGCTGTCTGCTGACTGC	0.557									Ichthyosis																												p.D2339N		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - Missense(1)	stomach(1)	c.G7015A						scavenged	.	C	ASN/ASP	81,4309		0,81,2114	193.0	265.0	240.0		7015	4.1	0.1	1	dbSNP_134	240	282,8314		22,238,4038	no	missense	FLG	NM_002016.1	23	22,319,6152	TT,TC,CC		3.2806,1.8451,2.7953	probably-damaging	2339/4062	152280347	363,12623	2195	4298	6493	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGCTGTCTGCTGA	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.7015G>A	1.37:g.152280347C>T	ENSP00000357789:p.Asp2339Asn	Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	162	61	0.376543	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	432	0.1978021978021978	6	0.012195121951219513	90	0.24861878453038674	245	0.42832167832167833	91	0.12005277044854881	C	13.82	2.350104	0.41599	0.018451	0.032806	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.08008	3.14	4.12	4.12	0.48240	.	.	.	.	.	T	0.14570	0.0352	M	0.62723	1.935	0.80722	P	0.0	D	0.69078	0.997	D	0.66196	0.942	T	0.00619	-1.1641	8	0.66056	D	0.02	.	12.0996	0.53776	0.0:1.0:0.0:0.0	.	2339	P20930	FILA_HUMAN	N	2339;249	ENSP00000357789:D2339N	ENSP00000271820:D249N	D	-	1	0	FLG	150546971	0.223000	0.23663	0.097000	0.21041	0.004000	0.04260	1.691000	0.37721	2.287000	0.76781	0.430000	0.28490	GAC	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NLRP4	147945	hgsc.bcm.edu	37	19	56369593	56369593	+	Silent	SNP	T	T	C	rs421810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56369593T>C	ENST00000301295.6	+	3	1256	c.834T>C	c.(832-834)gcT>gcC	p.A278A	NLRP4_ENST00000587891.1_Silent_p.A203A|NLRP4_ENST00000346986.5_Silent_p.A278A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	278	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)		TGCTCATCGCTATCAAACCCG	0.552													C|||	2661	0.53135	0.4523	0.4841	5008	,	,		16520	0.6657		0.4274	False		,,,				2504	0.6401				p.A278A		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+2,1	NLRP4	331	1	0			c.T834C						PASS	.	C		1956,2450	618.8+/-393.2	434,1088,681	68.0	75.0	72.0		834	-8.2	0.0	19	dbSNP_80	72	3589,5011	627.5+/-398.0	754,2081,1465	no	coding-synonymous	NLRP4	NM_134444.4		1188,3169,2146	CC,CT,TT		41.7326,44.394,42.6342		278/995	56369593	5545,7461	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			CATCGCTATCAAA	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.834T>C	19.37:g.56369593T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	96	0.979592	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			T|0.545;C|0.454	0.454	strong		0.552	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
CASP9	842	hgsc.bcm.edu	37	1	15850613	15850613	+	Missense_Mutation	SNP	G	G	A	rs1052571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15850613G>A	ENST00000333868.5	-	1	177	c.83C>T	c.(82-84)gCc>gTc	p.A28V	CASP9_ENST00000348549.5_Missense_Mutation_p.A28V|CASP9_ENST00000546424.1_Missense_Mutation_p.A28V|DNAJC16_ENST00000375838.1_5'Flank|DNAJC16_ENST00000375849.1_5'Flank|CASP9_ENST00000375890.4_Intron|DNAJC16_ENST00000375847.3_5'Flank|CASP9_ENST00000469637.1_Intron	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	28	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		A -> V (in dbSNP:rs1052571). {ECO:0000269|PubMed:16780893, ECO:0000269|PubMed:8663294, ECO:0000269|PubMed:9890966, ECO:0000269|Ref.9}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		GCTCAGCAGGGCGTCCCAGAG	0.711													G|||	2928	0.584665	0.739	0.4986	5008	,	,		5756	0.6538		0.5149	False		,,,				2504	0.4376				p.A28V		Atlas-SNP	.											.	CASP9	40	.	0			c.C83T						PASS	.						8.0	10.0	10.0					1																	15850613		2109	4166	6275	SO:0001583	missense	842	exon1			AGCAGGGCGTCCC	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.83C>T	1.37:g.15850613G>A	ENSP00000330237:p.Ala28Val	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	1291	0.5911172161172161	350	0.7113821138211383	179	0.494475138121547	358	0.6258741258741258	404	0.5329815303430079	G	15.45	2.836320	0.50951	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000440484	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.59	1.33	0.21861	DEATH-like (2);Caspase Recruitment (3);	0.919308	0.09391	N	0.808563	T	0.00012	0.0000	M	0.63428	1.95	0.21290	P	0.999735974	P;B;B	0.42908	0.793;0.009;0.029	B;B;B	0.39562	0.303;0.015;0.015	T	0.33394	-0.9870	9	0.22109	T	0.4	.	4.6003	0.12350	0.2169:0.0:0.6031:0.18	rs1052571;rs3192982;rs59045053;rs1052571	28;28;28	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	V	28	ENSP00000449584:A28V;ENSP00000330237:A28V;ENSP00000255256:A28V;ENSP00000411304:A28V	ENSP00000330237:A28V	A	-	2	0	CASP9	15723200	0.277000	0.24220	0.926000	0.36857	0.713000	0.41058	0.257000	0.18369	0.500000	0.27991	0.305000	0.20034	GCC	G|0.387;A|0.613	0.613	strong		0.711	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
MRS2	57380	hgsc.bcm.edu	37	6	24415380	24415380	+	Silent	SNP	G	G	A	rs3761788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24415380G>A	ENST00000378386.3	+	6	801	c.708G>A	c.(706-708)caG>caA	p.Q236Q	MRS2_ENST00000443868.2_Silent_p.Q239Q|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.Q186Q|MRS2_ENST00000378353.1_Silent_p.Q236Q|MRS2_ENST00000274747.7_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	236						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						TTTTACTACAGAATGGCAAAA	0.348													G|||	110	0.0219649	0.003	0.0418	5008	,	,		19207	0.001		0.0706	False		,,,				2504	0.0051				p.Q236Q		Atlas-SNP	.											.	MRS2	31	.	0			c.G708A						PASS	.	G		57,4349	56.8+/-93.2	0,57,2146	75.0	70.0	71.0		708	-1.4	1.0	6	dbSNP_107	71	639,7961	164.1+/-216.5	24,591,3685	no	coding-synonymous	MRS2	NM_020662.2		24,648,5831	AA,AG,GG		7.4302,1.2937,5.3514		236/444	24415380	696,12310	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon6			ACTACAGAATGGC	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.708G>A	6.37:g.24415380G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1																																																																																			G|0.954;A|0.046	0.046	strong		0.348	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
PTPN21	11099	hgsc.bcm.edu	37	14	88938652	88938652	+	Missense_Mutation	SNP	A	A	G	rs2274736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88938652A>G	ENST00000556564.1	-	15	3091	c.2807T>C	c.(2806-2808)gTg>gCg	p.V936A	PTPN21_ENST00000328736.3_Missense_Mutation_p.V936A	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	936	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		V -> A (in dbSNP:rs2274736). {ECO:0000269|PubMed:7519780}.		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						CTCCACTCTCACATCATCATA	0.428													G|||	1982	0.395767	0.5227	0.2781	5008	,	,		17688	0.38		0.2962	False		,,,				2504	0.4264				p.V936A		Atlas-SNP	.											.	PTPN21	113	.	0			c.T2807C						PASS	.	G	ALA/VAL	2230,2176	585.1+/-386.2	555,1120,528	208.0	181.0	190.0		2807	5.9	0.1	14	dbSNP_100	190	2933,5667	668.9+/-402.6	490,1953,1857	yes	missense	PTPN21	NM_007039.3	64	1045,3073,2385	GG,GA,AA		34.1047,49.3872,39.6971	benign	936/1175	88938652	5163,7843	2203	4300	6503	SO:0001583	missense	11099	exon15			ACTCTCACATCAT	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.2807T>C	14.37:g.88938652A>G	ENSP00000452414:p.Val936Ala	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	799	0.3658424908424908	258	0.524390243902439	103	0.2845303867403315	205	0.3583916083916084	233	0.3073878627968338	G	10.25	1.298031	0.23650	0.506128	0.341047	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.12774	2.65;2.65	5.86	5.86	0.93980	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.169720	0.52532	N	0.000078	T	0.00012	0.0000	N	0.01048	-1.04	0.52099	P	5.100000000002325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43245	-0.9403	9	0.28530	T	0.3	.	15.2622	0.73634	0.067:0.0:0.933:0.0	rs2274736;rs60443733;rs2274736	936	Q16825	PTN21_HUMAN	A	936	ENSP00000330276:V936A;ENSP00000452414:V936A	ENSP00000330276:V936A	V	-	2	0	PTPN21	88008405	1.000000	0.71417	0.050000	0.19076	0.315000	0.28087	3.948000	0.56660	1.502000	0.48669	-0.119000	0.15052	GTG	G|0.389;N|0.000	0.389	strong		0.428	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					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(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	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)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85.0	91.0	89.0		2392,2392	5.0	1.0	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
MROH2B	133558	hgsc.bcm.edu	37	5	41054934	41054934	+	Silent	SNP	A	A	G	rs325874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:41054934A>G	ENST00000399564.4	-	11	1492	c.1042T>C	c.(1042-1044)Ttg>Ctg	p.L348L	MROH2B_ENST00000506092.2_Intron	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	348																	TGATCCCTCAACCTGGGCTCT	0.383													A|||	1074	0.214457	0.2095	0.1585	5008	,	,		18279	0.2222		0.2286	False		,,,				2504	0.2382				p.L348L		Atlas-SNP	.											.	.	.	.	0			c.T1042C						PASS	.	A		771,2899		83,605,1147	112.0	105.0	107.0		1042	-0.9	0.0	5	dbSNP_79	107	1831,6327		192,1447,2440	no	coding-synonymous	HEATR7B2	NM_173489.4		275,2052,3587	GG,GA,AA		22.4442,21.0082,21.9986		348/1586	41054934	2602,9226	1835	4079	5914	SO:0001819	synonymous_variant	133558	exon11			CCCTCAACCTGGG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1042T>C	5.37:g.41054934A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			A|0.778;G|0.222	0.222	strong		0.383	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
PCDHA3	56145	hgsc.bcm.edu	37	5	140181614	140181614	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140181614G>A	ENST00000522353.2	+	1	832	c.832G>A	c.(832-834)Gcg>Acg	p.A278T	PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.A278T|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	278	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(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)			TAAGGATATCGCGTATTCTTT	0.393																																					p.A278T		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,-2,4	PCDHA3	396	4	0			c.G832A						scavenged	.						91.0	89.0	90.0					5																	140181614		2203	4300	6503	SO:0001583	missense	56145	exon1			GATATCGCGTATT	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.832G>A	5.37:g.140181614G>A	ENSP00000429808:p.Ala278Thr	Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	73	2	0.0273973	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.868748	0.00547	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.50813	0.73;0.73	4.79	-0.699	0.11277	Cadherin (4);Cadherin-like (1);	1.311480	0.05755	N	0.603847	T	0.12263	0.0298	N	0.00385	-1.57	0.09310	N	1	B;B	0.12013	0.005;0.002	B;B	0.04013	0.001;0.0	T	0.34129	-0.9841	10	0.02654	T	1	.	4.893	0.13737	0.3825:0.0:0.4219:0.1956	.	278;278	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	T	278	ENSP00000429808:A278T;ENSP00000434086:A278T	ENSP00000429808:A278T	A	+	1	0	PCDHA3	140161798	0.000000	0.05858	0.004000	0.12327	0.014000	0.08584	-3.927000	0.00332	0.148000	0.19059	-0.373000	0.07131	GCG	.	.	none		0.393	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
F5	2153	hgsc.bcm.edu	37	1	169519894	169519894	+	Silent	SNP	G	G	A	rs6015	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169519894G>A	ENST00000367797.3	-	9	1581	c.1380C>T	c.(1378-1380)aaC>aaT	p.N460N	F5_ENST00000546081.1_Silent_p.N323N|F5_ENST00000367796.3_Silent_p.N460N	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	460	F5/8 type A 2.|Plastocyanin-like 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)	TGAAAGAAGAGTTGACTTCAT	0.433													G|||	255	0.0509185	0.0053	0.1023	5008	,	,		15812	0.0298		0.0736	False		,,,				2504	0.0746				p.N460N		Atlas-SNP	.											.	F5	301	.	0			c.C1380T						PASS	.	G		58,4348	55.5+/-91.7	1,56,2146	92.0	90.0	91.0		1380	3.2	1.0	1	dbSNP_52	91	672,7928	168.8+/-220.3	25,622,3653	no	coding-synonymous	F5	NM_000130.4		26,678,5799	AA,AG,GG		7.814,1.3164,5.6128		460/2225	169519894	730,12276	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon9			AGAAGAGTTGACT	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.1380C>T	1.37:g.169519894G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.946;A|0.054	0.054	strong		0.433	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ENTPD5	957	hgsc.bcm.edu	37	14	74444009	74444009	+	Silent	SNP	G	G	A	rs143835358	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74444009G>A	ENST00000334696.6	-	7	829	c.510C>T	c.(508-510)tcC>tcT	p.S170S	ENTPD5_ENST00000557325.1_Silent_p.S170S	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	170					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CACCTTCGTCGGATCCATCCA	0.453													G|||	5	0.000998403	0.0	0.0	5008	,	,		17509	0.0		0.005	False		,,,				2504	0.0				p.S170S		Atlas-SNP	.											.	ENTPD5	26	.	0			c.C510T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	113.0	99.0	103.0		510	2.5	1.0	14	dbSNP_134	103	17,8583	11.9+/-42.8	1,15,4284	no	coding-synonymous	ENTPD5	NM_001249.2		1,17,6485	AA,AG,GG		0.1977,0.0454,0.1461		170/429	74444009	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	957	exon7			TTCGTCGGATCCA	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.510C>T	14.37:g.74444009G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	37	CCDS9825.1																																																																																			G|0.998;A|0.002	0.002	strong		0.453	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
OR2C3	81472	hgsc.bcm.edu	37	1	247694958	247694958	+	Silent	SNP	G	G	A	rs6702695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247694958G>A	ENST00000366487.3	-	2	1217	c.856C>T	c.(856-858)Ctg>Ttg	p.L286L	GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366490.3_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	286						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(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-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)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			AGTGGGTTCAGCGCAGGAGTG	0.547													G|||	925	0.184704	0.1036	0.1268	5008	,	,		21934	0.1994		0.2107	False		,,,				2504	0.2935				p.L286L		Atlas-SNP	.											.	OR2C3	92	.	0			c.C856T						PASS	.	G		514,3892	236.1+/-248.4	35,444,1724	101.0	87.0	92.0		856	2.0	0.1	1	dbSNP_116	92	1645,6955	304.6+/-307.0	153,1339,2808	no	coding-synonymous	OR2C3	NM_198074.4		188,1783,4532	AA,AG,GG		19.1279,11.6659,16.6		286/321	247694958	2159,10847	2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			GGTTCAGCGCAGG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.856C>T	1.37:g.247694958G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	37	CCDS1634.2																																																																																			G|0.830;A|0.170	0.170	strong		0.547	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
OR51B6	390058	hgsc.bcm.edu	37	11	5373334	5373334	+	Silent	SNP	A	A	G	rs5006882	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373334A>G	ENST00000380219.1	+	1	597	c.597A>G	c.(595-597)gtA>gtG	p.V199V	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	199					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)		ATCCAGTTGTAGTTTTATTTG	0.438													A|||	1170	0.233626	0.326	0.2349	5008	,	,		23806	0.0863		0.2644	False		,,,				2504	0.228				p.V199V		Atlas-SNP	.											OR51B6,NS,carcinoma,+2,1	OR51B6	53	1	0			c.A597G						PASS	.	A		1286,3116	439.2+/-345.6	173,940,1088	242.0	217.0	226.0		597	-0.1	0.9	11	dbSNP_113	226	2270,6324	382.6+/-340.4	310,1650,2337	no	coding-synonymous	OR51B6	NM_001004750.1		483,2590,3425	GG,GA,AA		26.4138,29.214,27.3623		199/313	5373334	3556,9440	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			AGTTGTAGTTTTA		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.597A>G	11.37:g.5373334A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			A|0.757;G|0.243	0.243	strong		0.438	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
SORL1	6653	hgsc.bcm.edu	37	11	121367626	121367626	+	Silent	SNP	T	T	C	rs12364988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:121367626T>C	ENST00000260197.7	+	6	936	c.807T>C	c.(805-807)caT>caC	p.H269H	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	269					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.H269H(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TTGAACGACATGAACCCTCTG	0.408													T|||	2222	0.44369	0.4902	0.5101	5008	,	,		20039	0.3115		0.495	False		,,,				2504	0.4172				p.H269H		Atlas-SNP	.											SORL1,NS,carcinoma,0,1	SORL1	218	1	1	Substitution - coding silent(1)	stomach(1)	c.T807C						PASS	.	T		2210,2196	590.2+/-387.3	545,1120,538	87.0	81.0	83.0		807	-8.8	0.6	11	dbSNP_120	83	4471,4127	586.4+/-392.0	1201,2069,1029	no	coding-synonymous	SORL1	NM_003105.5		1746,3189,1567	CC,CT,TT		47.9995,49.8411,48.6235		269/2215	121367626	6681,6323	2203	4299	6502	SO:0001819	synonymous_variant	6653	exon6			ACGACATGAACCC	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.807T>C	11.37:g.121367626T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	37	CCDS8436.1																																																																																			T|0.511;C|0.489	0.489	strong		0.408	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
FREM2	341640	hgsc.bcm.edu	37	13	39430314	39430314	+	Missense_Mutation	SNP	C	C	T	rs9548509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	43	43	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	
WNT16	51384	hgsc.bcm.edu	37	7	120969825	120969825	+	Silent	SNP	C	C	A	rs17143291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:120969825C>A	ENST00000222462.2	+	2	590	c.300C>A	c.(298-300)acC>acA	p.T100T	WNT16_ENST00000361301.2_Silent_p.T90T	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	100					bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					CCGCCACTACCGCCCCGATGG	0.662													C|||	53	0.0105831	0.0212	0.0216	5008	,	,		13952	0.0		0.0089	False		,,,				2504	0.001				p.T100T		Atlas-SNP	.											.	WNT16	97	.	0			c.C300A						PASS	.	C	,	79,4315		0,79,2118	22.0	25.0	24.0		270,300	2.1	0.2	7	dbSNP_123	24	48,8512		0,48,4232	no	coding-synonymous,coding-synonymous	WNT16	NM_016087.2,NM_057168.1	,	0,127,6350	AA,AC,CC		0.5607,1.7979,0.9804	,	90/356,100/366	120969825	127,12827	2197	4280	6477	SO:0001819	synonymous_variant	51384	exon2			CACTACCGCCCCG	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"""Wingless-type MMTV integration sites"""	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.300C>A	7.37:g.120969825C>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_057168	Q2M3G1|Q9Y5C0	Silent	SNP	ENST00000222462.2	37	CCDS5781.1																																																																																			C|0.988;A|0.012	0.012	strong		0.662	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
KRT71	112802	hgsc.bcm.edu	37	12	52946543	52946543	+	Missense_Mutation	SNP	C	C	T	rs665522	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	104	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	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	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605274	32605274	+	Silent	SNP	T	T	C	rs1130034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32605274T>C	ENST00000343139.5	+	1	141	c.39T>C	c.(37-39)gcT>gcC	p.A13A	HLA-DQA1_ENST00000374949.2_Silent_p.A13A|HLA-DQA1_ENST00000395363.1_Silent_p.A13A	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	13					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGGCCCTCGCTCTGACCACCG	0.517													.|||	2809	0.560903	0.5166	0.7104	5008	,	,		15087	0.5446		0.5964	False		,,,				2504	0.4949				p.A13A		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.T39C						PASS	.	C		2107,2299		611,885,707	74.0	67.0	69.0		39	-0.1	0.0	6	dbSNP_86	69	4718,3882		1512,1694,1094	no	coding-synonymous	HLA-DQA1	NM_002122.3		2123,2579,1801	CC,CT,TT		45.1395,47.8212,47.5242		13/256	32605274	6825,6181	2203	4300	6503	SO:0001819	synonymous_variant	3117	exon1			CCTCGCTCTGACC		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.39T>C	6.37:g.32605274T>C		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			A|0.000;C|0.568;G|0.000;T|0.431	0.568	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
GTSE1	51512	hgsc.bcm.edu	37	22	46704676	46704676	+	Missense_Mutation	SNP	A	A	G	rs6008600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46704676A>G	ENST00000454366.1	+	4	810	c.598A>G	c.(598-600)Acc>Gcc	p.T200A		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	181			A -> V (in dbSNP:rs34404175).		DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GGCCCGCCTCACCCGGGCGCC	0.692													G|||	735	0.146765	0.3858	0.085	5008	,	,		13128	0.001		0.1233	False		,,,				2504	0.0419				p.T200A	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.A598G						PASS	.	G	ALA/THR	1491,2909		273,945,982	40.0	51.0	47.0		598	-6.7	0.0	22	dbSNP_114	47	902,7688		48,806,3441	no	missense	GTSE1	NM_016426.6	58	321,1751,4423	GG,GA,AA		10.5006,33.8864,18.4219	benign	200/740	46704676	2393,10597	2200	4295	6495	SO:0001583	missense	51512	exon4			CGCCTCACCCGGG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.598A>G	22.37:g.46704676A>G	ENSP00000415430:p.Thr200Ala	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	16	6	0.375	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	313	0.1433150183150183	181	0.3678861788617886	36	0.09944751381215469	0	0.0	96	0.1266490765171504	G	3.517	-0.098507	0.07010	0.338864	0.105006	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07216	3.21	5.02	-6.73	0.01749	.	1.573020	0.03335	N	0.193924	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	0.46034	-0.9220	9	0.07325	T	0.83	0.9441	4.0771	0.09909	0.3281:0.1372:0.4497:0.085	rs6008600;rs60205302	181	Q9NYZ3	GTSE1_HUMAN	A	200;160	ENSP00000415430:T200A	ENSP00000354634:T160A	T	+	1	0	GTSE1	45083340	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.181000	0.00568	-1.072000	0.03141	-2.228000	0.00293	ACC	A|0.826;G|0.174	0.174	strong		0.692	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
CATSPER1	117144	hgsc.bcm.edu	37	11	65789004	65789004	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65789004G>A	ENST00000312106.5	-	4	1791	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	552					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						CTCAGGGCCCGCAGGCTCTTG	0.627																																					p.R552W		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C1654T						PASS	.						60.0	64.0	63.0					11																	65789004		2201	4296	6497	SO:0001583	missense	117144	exon4			GGGCCCGCAGGCT	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.1654C>T	11.37:g.65789004G>A	ENSP00000309052:p.Arg552Trp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.378231	0.42207	.	.	ENSG00000175294	ENST00000312106	D	0.98633	-5.04	4.99	3.08	0.35506	Ion transport (1);	0.000000	0.30565	U	0.009357	D	0.99211	0.9726	H	0.95917	3.74	0.23331	N	0.997892	D	0.89917	1.0	D	0.97110	1.0	D	0.96270	0.9198	10	0.87932	D	0	-21.6854	6.1104	0.20097	0.0968:0.0:0.7178:0.1855	.	552	Q8NEC5	CTSR1_HUMAN	W	552	ENSP00000309052:R552W	ENSP00000309052:R552W	R	-	1	2	CATSPER1	65545580	1.000000	0.71417	0.893000	0.35052	0.020000	0.10135	1.757000	0.38400	0.495000	0.27882	0.561000	0.74099	CGG	.	.	none		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
C1D	10438	hgsc.bcm.edu	37	2	68270068	68270068	+	Missense_Mutation	SNP	A	A	G	rs10444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68270068A>G	ENST00000355848.3	-	5	426	c.379T>C	c.(379-381)Tcg>Ccg	p.S127P	C1D_ENST00000410067.3_Missense_Mutation_p.S127P|C1D_ENST00000407324.1_Missense_Mutation_p.S166P|C1D_ENST00000409302.1_Missense_Mutation_p.S127P			Q13901	C1D_HUMAN	C1D nuclear receptor corepressor	127	Interaction with NCOR1 and NCOR2. {ECO:0000250}.		S -> P (in dbSNP:rs10444).		apoptotic process (GO:0006915)|maturation of 5.8S rRNA (GO:0000460)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)			lung(2)|urinary_tract(1)	3						GCATTTTTCGATTTTGGTTCC	0.388													G|||	1579	0.315296	0.5023	0.1455	5008	,	,		13251	0.2976		0.1789	False		,,,				2504	0.3415				p.S127P		Atlas-SNP	.											C1D,NS,carcinoma,+1,1	C1D	11	1	0			c.T379C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER,PRO/SER	1768,2626		405,958,834	23.0	27.0	26.0		379,379,379,379	1.4	0.2	2	dbSNP_52	26	1304,7286		134,1036,3125	no	missense,missense,missense,missense	C1D	NM_001190263.1,NM_001190265.1,NM_006333.3,NM_173177.2	74,74,74,74	539,1994,3959	GG,GA,AA		15.1804,40.2367,23.6599	benign,benign,benign,benign	127/142,127/142,127/142,127/142	68270068	3072,9912	2197	4295	6492	SO:0001583	missense	10438	exon6			TTTTCGATTTTGG		CCDS1883.1	2p13-p12	2010-06-10	2010-06-10		ENSG00000197223	ENSG00000197223			29911	protein-coding gene	gene with protein product	"""small unique nuclear receptor co-repressor"""	606997	"""C1D nuclear receptor co-repressor"""			9469821, 17599775, 17412707, 11801738, 9405624	Standard	NM_006333		Approved	SUNCOR, SUN-CoR, LRP1	uc002seb.3	Q13901	OTTHUMG00000129564	ENST00000355848.3:c.379T>C	2.37:g.68270068A>G	ENSP00000348107:p.Ser127Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	145	51	0.351724	NM_001190263	A8K336|D6W5F8|Q05D64	Missense_Mutation	SNP	ENST00000355848.3	37	CCDS1883.1	491	0.22481684981684982	174	0.35365853658536583	45	0.12430939226519337	170	0.2972027972027972	102	0.1345646437994723	G	0	-2.632687	0.00115	0.402367	0.151804	ENSG00000197223	ENST00000355848;ENST00000407324;ENST00000410067;ENST00000409302	T;T;T;T	0.46819	0.91;0.86;0.91;0.91	5.33	1.37	0.22104	.	0.466924	0.26055	N	0.026605	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46938	-0.9155	9	0.26408	T	0.33	.	6.3353	0.21292	0.2575:0.3386:0.4039:0.0	rs10444;rs1044990;rs3174545;rs60579062	127	Q13901	C1D_HUMAN	P	127;166;127;127	ENSP00000348107:S127P;ENSP00000384304:S166P;ENSP00000386468:S127P;ENSP00000386779:S127P	ENSP00000348107:S127P	S	-	1	0	C1D	68123572	0.000000	0.05858	0.236000	0.24074	0.075000	0.17131	-0.176000	0.09811	0.040000	0.15660	-0.349000	0.07799	TCG	.	.	weak		0.388	C1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251757.3	NM_006333	
SPTLC3	55304	hgsc.bcm.edu	37	20	13053035	13053035	+	Silent	SNP	A	A	G	rs243888	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:13053035A>G	ENST00000399002.2	+	3	709	c.435A>G	c.(433-435)tcA>tcG	p.S145S	SPTLC3_ENST00000378194.4_Silent_p.S145S	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	145					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						AGAGGGTATCAGACGACTATA	0.448													G|||	3274	0.653754	0.7973	0.6542	5008	,	,		18548	0.6052		0.6491	False		,,,				2504	0.5143				p.S145S		Atlas-SNP	.											.	SPTLC3	78	.	0			c.A435G						PASS	.	G		2765,905		1047,671,117	200.0	204.0	203.0		435	-11.0	0.0	20	dbSNP_79	203	5089,3095		1590,1909,593	no	coding-synonymous	SPTLC3	NM_018327.2		2637,2580,710	GG,GA,AA		37.8177,24.6594,33.7439		145/553	13053035	7854,4000	1835	4092	5927	SO:0001819	synonymous_variant	55304	exon3			GGTATCAGACGAC	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.435A>G	20.37:g.13053035A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2																																																																																			A|0.332;G|0.668	0.668	strong		0.448	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
ABCA7	10347	hgsc.bcm.edu	37	19	1051214	1051214	+	Silent	SNP	A	A	G	rs3752240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1051214A>G	ENST00000263094.6	+	20	2976	c.2745A>G	c.(2743-2745)gtA>gtG	p.V915V	ABCA7_ENST00000435683.2_Silent_p.V777V|ABCA7_ENST00000433129.1_Silent_p.V915V	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	915	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		GTGCCGCTGTAGTGGGCCCCG	0.647													G|||	1448	0.289137	0.3676	0.4107	5008	,	,		16484	0.1101		0.3509	False		,,,				2504	0.2178				p.V915V		Atlas-SNP	.											.	ABCA7	174	.	0			c.A2745G						PASS	.	G		1639,2733	648.0+/-398.6	306,1027,853	57.0	55.0	55.0		2745	-9.0	0.0	19	dbSNP_107	55	3093,5483	656.0+/-401.3	577,1939,1772	no	coding-synonymous	ABCA7	NM_019112.3		883,2966,2625	GG,GA,AA		36.0658,37.4886,36.5462		915/2147	1051214	4732,8216	2186	4288	6474	SO:0001819	synonymous_variant	10347	exon20			CGCTGTAGTGGGC	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.2745A>G	19.37:g.1051214A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.653;G|0.347	0.347	strong		0.647	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
CCDC116	164592	hgsc.bcm.edu	37	22	21988524	21988524	+	Missense_Mutation	SNP	C	C	T	rs861854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21988524C>T	ENST00000292779.3	+	3	447	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C	CCDC116_ENST00000607942.1_Missense_Mutation_p.R96C	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	96			R -> C (in dbSNP:rs861854).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCGACTGAGCGCATGGCTGC	0.627													C|||	504	0.100639	0.1203	0.0965	5008	,	,		18553	0.003		0.1889	False		,,,				2504	0.0869				p.R96C		Atlas-SNP	.											CCDC116,NS,carcinoma,-1,1	CCDC116	56	1	0			c.C286T						PASS	.	C	CYS/ARG	591,3815	259.5+/-263.1	35,521,1647	106.0	95.0	99.0		286	1.0	0.0	22	dbSNP_86	99	1525,7075	288.0+/-298.5	137,1251,2912	yes	missense	CCDC116	NM_152612.2	180	172,1772,4559	TT,TC,CC		17.7326,13.4135,16.2694	benign	96/614	21988524	2116,10890	2203	4300	6503	SO:0001583	missense	164592	exon3			ACTGAGCGCATGG	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.286C>T	22.37:g.21988524C>T	ENSP00000292779:p.Arg96Cys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	257	0.11767399267399267	66	0.13414634146341464	38	0.10497237569060773	2	0.0034965034965034965	151	0.19920844327176782	C	17.04	3.286187	0.59867	0.134135	0.177326	ENSG00000161180	ENST00000292779	T	0.24908	1.83	4.55	0.993	0.19825	.	0.657051	0.13333	N	0.395798	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B	0.33549	0.128;0.417	B;B	0.25759	0.029;0.063	T	0.33701	-0.9858	8	.	.	.	-64.5118	3.7257	0.08474	0.1921:0.5996:0.0:0.2083	rs861854;rs1647699;rs58992651;rs861854	96;96	B7Z7H5;Q8IYX3-2	.;.	C	96	ENSP00000292779:R96C	.	R	+	1	0	CCDC116	20318524	0.444000	0.25649	0.028000	0.17463	0.878000	0.50629	0.664000	0.25068	0.629000	0.30376	0.585000	0.79938	CGC	C|0.855;T|0.145	0.145	strong		0.627	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
AGT	183	hgsc.bcm.edu	37	1	230845977	230845977	+	Missense_Mutation	SNP	G	G	A	rs4762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:230845977G>A	ENST00000366667.4	-	2	834	c.620C>T	c.(619-621)aCg>aTg	p.T207M	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	207			T -> M (associated with hypertension; dbSNP:rs4762). {ECO:0000269|PubMed:1394429}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCCCACCACCGTGGACAGCAG	0.662													G|||	509	0.101637	0.0545	0.1268	5008	,	,		19740	0.1071		0.1302	False		,,,				2504	0.1125				p.T207M		Atlas-SNP	.											.	AGT	62	.	0			c.C620T	GRCh37	CM920009	AGT	M	rs4762	PASS	.	G	MET/THR	291,4115	151.8+/-185.6	13,265,1925	32.0	33.0	33.0		620	4.1	0.8	1	dbSNP_52	33	1130,7470	222.9+/-259.8	71,988,3241	yes	missense	AGT	NM_000029.3	81	84,1253,5166	AA,AG,GG		13.1395,6.6046,10.9257	probably-damaging	207/486	230845977	1421,11585	2203	4300	6503	SO:0001583	missense	183	exon2			ACCACCGTGGACA	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.620C>T	1.37:g.230845977G>A	ENSP00000355627:p.Thr207Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	227	0.10393772893772894	17	0.034552845528455285	45	0.12430939226519337	58	0.10139860139860139	107	0.14116094986807387	G	11.57	1.679313	0.29783	0.066046	0.131395	ENSG00000135744	ENST00000366667	D	0.84223	-1.82	5.01	4.08	0.47627	Serpin domain (3);	0.157526	0.56097	D	0.000038	T	0.05960	0.0155	M	0.66939	2.045	0.26682	P	0.9715215	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.997	T	0.65364	-0.6186	9	0.72032	D	0.01	.	4.3912	0.11341	0.081:0.121:0.5566:0.2414	rs4762;rs3182294;rs16852387;rs52830531;rs60395225;rs4762	207;207;207	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	M	207	ENSP00000355627:T207M	ENSP00000355627:T207M	T	-	2	0	AGT	228912600	0.992000	0.36948	0.834000	0.33040	0.033000	0.12548	2.300000	0.43620	1.201000	0.43203	0.591000	0.81541	ACG	G|0.900;A|0.100	0.100	strong		0.662	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
PTPN12	5782	hgsc.bcm.edu	37	7	77256713	77256713	+	Missense_Mutation	SNP	A	A	G	rs3750050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:77256713A>G	ENST00000248594.6	+	13	1989	c.1717A>G	c.(1717-1719)Aca>Gca	p.T573A	PTPN12_ENST00000415482.2_Missense_Mutation_p.T454A|PTPN12_ENST00000435495.2_Missense_Mutation_p.T443A	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	573			T -> A (in dbSNP:rs3750050). {ECO:0000269|PubMed:14702039}.		protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						ACCAAGTCCTACAACACAAGT	0.403													A|||	1828	0.365016	0.2171	0.4366	5008	,	,		22259	0.6905		0.16	False		,,,				2504	0.3896				p.T573A		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1717G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	949,3457	358.6+/-314.5	116,717,1370	167.0	152.0	157.0		1360,1327,1717	-0.4	0.0	7	dbSNP_107	157	1303,7297	256.8+/-281.1	106,1091,3103	yes	missense,missense,missense	PTPN12	NM_001131008.1,NM_001131009.1,NM_002835.3	58,58,58	222,1808,4473	GG,GA,AA		15.1512,21.5388,17.3151	benign,benign,benign	454/662,443/651,573/781	77256713	2252,10754	2203	4300	6503	SO:0001583	missense	5782	exon13			AGTCCTACAACAC		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1717A>G	7.37:g.77256713A>G	ENSP00000248594:p.Thr573Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	749	0.34294871794871795	93	0.18902439024390244	150	0.4143646408839779	387	0.6765734265734266	119	0.15699208443271767	A	4.040	0.005088	0.07866	0.215388	0.151512	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495;ENST00000407343	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	6.04	-0.387	0.12463	.	0.428092	0.25765	N	0.028452	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.42241	-0.9463	9	0.13470	T	0.59	.	1.0381	0.01553	0.4387:0.1514:0.2294:0.1805	rs3750050;rs11540138;rs60753265;rs3750050	573	Q05209	PTN12_HUMAN	A	573;454;454;443;81	ENSP00000248594:T573A;ENSP00000392429:T454A;ENSP00000397991:T443A;ENSP00000385079:T81A	ENSP00000248594:T573A	T	+	1	0	PTPN12	77094649	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.275000	0.08525	-0.319000	0.08652	-1.961000	0.00478	ACA	A|0.745;G|0.255	0.255	strong		0.403	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
PHIP	55023	hgsc.bcm.edu	37	6	79679577	79679577	+	Silent	SNP	A	A	G	rs7742431	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:79679577A>G	ENST00000275034.4	-	27	3347	c.3180T>C	c.(3178-3180)gaT>gaC	p.D1060D	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1060	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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TGTATTTTGCATCATCAAATT	0.308													G|||	2763	0.551717	0.4395	0.4813	5008	,	,		17734	0.6855		0.4901	False		,,,				2504	0.6789				p.D1060D		Atlas-SNP	.											.	PHIP	177	.	0			c.T3180C						PASS	.	G		1835,2571	631.0+/-395.6	398,1039,766	122.0	110.0	114.0		3180	-7.2	0.3	6	dbSNP_116	114	4327,4273	572.9+/-389.8	1086,2155,1059	no	coding-synonymous	PHIP	NM_017934.5		1484,3194,1825	GG,GA,AA		49.686,41.6478,47.3781		1060/1822	79679577	6162,6844	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon27			TTTTGCATCATCA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3180T>C	6.37:g.79679577A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			A|0.506;G|0.494	0.494	strong		0.308	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
RABGGTA	5875	hgsc.bcm.edu	37	14	24736961	24736961	+	Missense_Mutation	SNP	T	T	C	rs729421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24736961T>C	ENST00000399409.3	-	13	1741	c.1258A>G	c.(1258-1260)Acg>Gcg	p.T420A	RABGGTA_ENST00000560777.1_Missense_Mutation_p.T29A|RABGGTA_ENST00000216840.6_Missense_Mutation_p.T420A|RABGGTA_ENST00000559586.1_5'Flank	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	420			T -> A (in dbSNP:rs729421). {ECO:0000269|PubMed:14702039}.		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)		TCCAGATACGTTGCCCGCATG	0.607													C|||	3017	0.602436	0.7663	0.5519	5008	,	,		21713	0.6181		0.3837	False		,,,				2504	0.6258				p.T420A		Atlas-SNP	.											.	RABGGTA	43	.	0			c.A1258G						PASS	.	C	ALA/THR,ALA/THR	3015,1329		1060,895,217	56.0	60.0	59.0		1258,1258	3.7	0.6	14	dbSNP_86	59	3175,5357		589,1997,1680	yes	missense,missense	RABGGTA	NM_004581.3,NM_182836.1	58,58	1649,2892,1897	CC,CT,TT		37.2128,30.5939,48.0739	benign,benign	420/568,420/568	24736961	6190,6686	2172	4266	6438	SO:0001583	missense	5875	exon13			GATACGTTGCCCG		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.1258A>G	14.37:g.24736961T>C	ENSP00000382341:p.Thr420Ala	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_004581	A8K5N2|D3DS69	Missense_Mutation	SNP	ENST00000399409.3	37	CCDS45088.1	1214	0.5558608058608059	372	0.7560975609756098	187	0.5165745856353591	355	0.6206293706293706	300	0.39577836411609496	C	2.403	-0.337163	0.05278	0.694061	0.372128	ENSG00000100949	ENST00000216840;ENST00000399409	T;T	0.40756	1.02;1.02	5.67	3.66	0.41972	Protein prenyltransferase (1);	0.222293	0.36555	N	0.002530	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	0.41998	-0.9477	9	0.02654	T	1	-5.2527	7.889	0.29667	0.1403:0.701:0.0:0.1587	rs729421;rs59249478;rs729421	420	Q92696	PGTA_HUMAN	A	420	ENSP00000216840:T420A;ENSP00000382341:T420A	ENSP00000216840:T420A	T	-	1	0	RABGGTA	23806801	0.937000	0.31787	0.647000	0.29507	0.860000	0.49131	1.958000	0.40402	0.768000	0.33290	-0.213000	0.12676	ACG	T|0.432;C|0.568	0.568	strong		0.607	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836	
RHO	6010	hgsc.bcm.edu	37	3	129247936	129247936	+	Splice_Site	SNP	C	C	T	rs79765751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:129247936C>T	ENST00000296271.3	+	1	454	c.360C>T	c.(358-360)ggC>ggT	p.G120G		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	120	Retinal chromophore binding. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CCACCCTGGGCGGTATGAGCC	0.637													C|||	7	0.00139776	0.0	0.0	5008	,	,		17167	0.001		0.006	False		,,,				2504	0.0				p.G120G	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.C360T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	69.0	72.0	71.0		360	-8.9	0.8	3	dbSNP_132	71	39,8561	25.7+/-73.6	0,39,4261	yes	coding-synonymous-near-splice	RHO	NM_000539.3		0,47,6456	TT,TC,CC		0.4535,0.1816,0.3614		120/349	129247936	47,12959	2203	4300	6503	SO:0001630	splice_region_variant	6010	exon1			CCTGGGCGGTATG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.361+1C>T	3.37:g.129247936C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																			C|0.996;T|0.004	0.004	strong		0.637	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	Silent
C14orf159	80017	hgsc.bcm.edu	37	14	91681888	91681888	+	Silent	SNP	G	G	A	rs34424078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91681888G>A	ENST00000523771.1	+	13	2292	c.1689G>A	c.(1687-1689)ccG>ccA	p.P563P	C14orf159_ENST00000521077.2_Silent_p.P528P|C14orf159_ENST00000428926.2_Silent_p.P563P|C14orf159_ENST00000523816.1_Silent_p.P563P|C14orf159_ENST00000412671.2_Silent_p.P568P|C14orf159_ENST00000518868.1_Silent_p.P568P|C14orf159_ENST00000256324.10_Silent_p.P568P|C14orf159_ENST00000525393.2_Silent_p.P439P|C14orf159_ENST00000522322.1_Silent_p.P563P|C14orf159_ENST00000520328.1_Silent_p.P511P			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	39	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	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	
SLC26A8	116369	hgsc.bcm.edu	37	6	35980121	35980121	+	Missense_Mutation	SNP	C	C	T	rs743923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	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		
MUC16	94025	hgsc.bcm.edu	37	19	9088722	9088722	+	Silent	SNP	G	G	A	rs17000948	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9088722G>A	ENST00000397910.4	-	1	3296	c.3093C>T	c.(3091-3093)ggC>ggT	p.G1031G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1031	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						CAGCCATAGAGCCTGGGCCAT	0.478													G|||	720	0.14377	0.1437	0.1124	5008	,	,		22388	0.2282		0.0855	False		,,,				2504	0.1391				p.G1031G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C3093T						PASS	.	G		509,3445		39,431,1507	158.0	152.0	154.0		3093	1.5	0.0	19	dbSNP_123	154	628,7686		25,578,3554	no	coding-synonymous	MUC16	NM_024690.2		64,1009,5061	AA,AG,GG		7.5535,12.873,9.268		1031/14508	9088722	1137,11131	1977	4157	6134	SO:0001819	synonymous_variant	94025	exon1			CATAGAGCCTGGG	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.3093C>T	19.37:g.9088722G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.860;A|0.140	0.140	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136290672	136290672	+	Silent	SNP	G	G	A	rs28571612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136290672G>A	ENST00000371929.3	+	4	798	c.354G>A	c.(352-354)ccG>ccA	p.P118P	ADAMTS13_ENST00000356589.2_Silent_p.P118P|ADAMTS13_ENST00000371911.3_Silent_p.P118P|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_Silent_p.P118P|ADAMTS13_ENST00000355699.2_Silent_p.P118P	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	118	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)		TTCGGGACCCGTCCCTGGGGG	0.627													G|||	130	0.0259585	0.0045	0.0403	5008	,	,		17635	0.001		0.0726	False		,,,				2504	0.0225				p.P118P		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G354A						PASS	.	G	,,	75,4331	66.4+/-103.9	1,73,2129	50.0	43.0	46.0		354,354,354	-9.1	0.4	9	dbSNP_125	46	708,7892	173.9+/-224.3	36,636,3628	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	37,709,5757	AA,AG,GG		8.2326,1.7022,6.0203	,,	118/1428,118/1341,118/1372	136290672	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon4			GGACCCGTCCCTG	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.354G>A	9.37:g.136290672G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			G|0.945;A|0.055	0.055	strong		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711853	140711853	+	Silent	SNP	G	G	A	rs17097187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140711853G>A	ENST00000517417.1	+	1	1602	c.1602G>A	c.(1600-1602)gcG>gcA	p.A534A	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Silent_p.A534A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	534	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(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)			AAGTGATGGCGCGGGACAGTG	0.597													G|||	175	0.0349441	0.0408	0.0519	5008	,	,		18545	0.001		0.0746	False		,,,				2504	0.0092				p.A534A		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.G1602A						PASS	.	G	,	197,4209	122.1+/-159.5	1,195,2007	185.0	198.0	193.0		1602,1602	-7.6	0.0	5	dbSNP_123	193	613,7987	160.7+/-213.8	28,557,3715	no	coding-synonymous,coding-synonymous	PCDHGA1	NM_018912.2,NM_031993.1	,	29,752,5722	AA,AG,GG		7.1279,4.4712,6.2279	,	534/932,534/824	140711853	810,12196	2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			GATGGCGCGGGAC	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.1602G>A	5.37:g.140711853G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			G|0.946;A|0.054	0.054	strong		0.597	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
SMG6	23293	hgsc.bcm.edu	37	17	2203167	2203167	+	Missense_Mutation	SNP	T	T	G	rs216195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2203167T>G	ENST00000263073.6	-	2	930	c.880A>C	c.(880-882)Aag>Cag	p.K294Q	SMG6_ENST00000544865.1_Missense_Mutation_p.K263Q	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	294	Interaction with telomeric DNA.		K -> Q (in dbSNP:rs216195).		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						GACACTTGCTTCTTCAGTCGT	0.537													T|||	2010	0.401358	0.3222	0.2205	5008	,	,		17706	0.6736		0.2813	False		,,,				2504	0.4796				p.K294Q	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A880C						PASS	.	T	GLN/LYS,GLN/LYS	1550,2856	490.1+/-361.7	267,1016,920	89.0	79.0	83.0		787,880	5.3	1.0	17	dbSNP_79	83	2510,6090	410.5+/-350.2	357,1796,2147	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	53,53	624,2812,3067	GG,GT,TT		29.186,35.1793,31.2164	probably-damaging,probably-damaging	263/1389,294/1420	2203167	4060,8946	2203	4300	6503	SO:0001583	missense	23293	exon2			CTTGCTTCTTCAG	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.880A>C	17.37:g.2203167T>G	ENSP00000263073:p.Lys294Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	826	0.3782051282051282	160	0.3252032520325203	79	0.21823204419889503	371	0.6486013986013986	216	0.2849604221635884	T	14.92	2.679107	0.47886	0.351793	0.29186	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.08807	3.05;3.05	5.35	5.35	0.76521	.	0.329730	0.32416	N	0.006125	T	0.00012	0.0000	L	0.29908	0.895	0.34437	P	0.300809	B	0.31077	0.307	B	0.22152	0.038	T	0.08249	-1.0731	9	0.39692	T	0.17	-10.2096	11.93	0.52841	0.0:0.0:0.1452:0.8548	rs216195;rs3826336;rs58625577;rs216195	294	Q86US8	EST1A_HUMAN	Q	294;263	ENSP00000263073:K294Q;ENSP00000443920:K263Q	ENSP00000263073:K294Q	K	-	1	0	SMG6	2149917	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.662000	0.46766	2.015000	0.59207	0.533000	0.62120	AAG	T|0.655;G|0.345	0.345	strong		0.537	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
ANKRD35	148741	hgsc.bcm.edu	37	1	145555699	145555699	+	Missense_Mutation	SNP	G	G	A	rs141350599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145555699G>A	ENST00000355594.4	+	2	134	c.47G>A	c.(46-48)aGa>aAa	p.R16K	ANKRD35_ENST00000544626.1_Missense_Mutation_p.R16K	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	16										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)					CAGGTGGAGAGATGGAACCGC	0.562													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18080	0.0		0.005	False		,,,				2504	0.0				p.R16K	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G47A						PASS	.	G	LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	56.0	52.0	54.0		47	0.3	1.0	1	dbSNP_134	54	42,8558	26.3+/-74.7	0,42,4258	yes	missense	ANKRD35	NM_144698.3	26	0,43,6460	AA,AG,GG		0.4884,0.0227,0.3306	benign	16/1002	145555699	43,12963	2203	4300	6503	SO:0001583	missense	148741	exon2			TGGAGAGATGGAA	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.47G>A	1.37:g.145555699G>A	ENSP00000347802:p.Arg16Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	10.69	1.420552	0.25639	2.27E-4	0.004884	ENSG00000198483	ENST00000355594;ENST00000544626	T;T	0.63417	-0.04;2.52	5.99	0.277	0.15668	.	0.660459	0.13934	N	0.352680	T	0.13157	0.0319	N	0.02011	-0.69	0.19775	N	0.999952	B	0.10296	0.003	B	0.10450	0.005	T	0.34800	-0.9814	10	0.30854	T	0.27	-4.0648	8.8959	0.35465	0.4511:0.0:0.5489:0.0	.	16	Q8N283	ANR35_HUMAN	K	16	ENSP00000347802:R16K;ENSP00000442671:R16K	ENSP00000347802:R16K	R	+	2	0	ANKRD35	144267056	0.998000	0.40836	0.999000	0.59377	0.978000	0.69477	0.259000	0.18405	0.126000	0.18424	0.655000	0.94253	AGA	G|0.998;A|0.002	0.002	strong		0.562	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
MMRN2	79812	hgsc.bcm.edu	37	10	88696622	88696622	+	Missense_Mutation	SNP	C	C	G	rs34587013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88696622C>G	ENST00000372027.5	-	7	3049	c.2728G>C	c.(2728-2730)Gtc>Ctc	p.V910L		NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	910	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		V -> L (in dbSNP:rs34587013).		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						ATGGCAAAGACCGTTGCTGTG	0.572													C|||	483	0.0964457	0.1301	0.0562	5008	,	,		20865	0.0675		0.0666	False		,,,				2504	0.1401				p.V910L		Atlas-SNP	.											.	MMRN2	49	.	0			c.G2728C						PASS	.	C	LEU/VAL	487,3919	227.5+/-242.7	33,421,1749	178.0	183.0	182.0		2728	0.7	0.0	10	dbSNP_126	182	705,7895	174.6+/-224.8	30,645,3625	yes	missense	MMRN2	NM_024756.2	32	63,1066,5374	GG,GC,CC		8.1977,11.0531,9.165	benign	910/950	88696622	1192,11814	2203	4300	6503	SO:0001583	missense	79812	exon7			CAAAGACCGTTGC	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.2728G>C	10.37:g.88696622C>G	ENSP00000361097:p.Val910Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_024756	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	189	0.08653846153846154	80	0.16260162601626016	27	0.07458563535911603	34	0.05944055944055944	48	0.0633245382585752	C	4.458	0.084782	0.08583	0.110531	0.081977	ENSG00000173269	ENST00000372027;ENST00000443699	T	0.74842	-0.88	4.34	0.706	0.18133	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.674810	0.13481	N	0.384715	T	0.00271	0.0008	N	0.14661	0.345	0.80722	P	0.0	B;B	0.32010	0.351;0.016	B;B	0.29440	0.065;0.102	T	0.02728	-1.1118	9	0.30078	T	0.28	-16.7327	3.9598	0.09405	0.1461:0.2616:0.0:0.5923	rs34587013	688;910	E7EN39;Q9H8L6	.;MMRN2_HUMAN	L	910;688	ENSP00000361097:V910L	ENSP00000361097:V910L	V	-	1	0	MMRN2	88686602	0.228000	0.23718	0.005000	0.12908	0.012000	0.07955	0.347000	0.20014	-0.034000	0.13713	-0.484000	0.04775	GTC	C|0.912;G|0.088	0.088	strong		0.572	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
ZNF526	116115	hgsc.bcm.edu	37	19	42728836	42728836	+	Missense_Mutation	SNP	T	T	C	rs3810151	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:42728836T>C	ENST00000301215.3	+	3	506	c.281T>C	c.(280-282)gTt>gCt	p.V94A		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	94			V -> A (in dbSNP:rs3810151).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				ACACAGAATGTTGGCCTGGAG	0.617													T|||	438	0.0874601	0.0068	0.1066	5008	,	,		20397	0.0863		0.0905	False		,,,				2504	0.181				p.V94A		Atlas-SNP	.											.	ZNF526	51	.	0			c.T281C						PASS	.	T	ALA/VAL	78,4328	67.6+/-105.2	2,74,2127	65.0	63.0	63.0		281	1.7	0.0	19	dbSNP_107	63	865,7735	197.3+/-242.0	43,779,3478	yes	missense	ZNF526	NM_133444.1	64	45,853,5605	CC,CT,TT		10.0581,1.7703,7.2505	benign	94/671	42728836	943,12063	2203	4300	6503	SO:0001583	missense	116115	exon3			AGAATGTTGGCCT	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"""Zinc fingers, C2H2-type"""	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.281T>C	19.37:g.42728836T>C	ENSP00000301215:p.Val94Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	37	CCDS12598.1	166	0.076007326007326	6	0.012195121951219513	45	0.12430939226519337	46	0.08041958041958042	69	0.09102902374670185	T	0.016	-1.526062	0.00959	0.017703	0.100581	ENSG00000167625	ENST00000301215	T	0.08720	3.06	4.06	1.66	0.24008	.	0.811457	0.10617	N	0.653825	T	0.00073	0.0002	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46359	-0.9197	8	.	.	.	0.354	5.8756	0.18826	0.4808:0.423:0.0:0.0962	rs3810151;rs3810151	94	Q8TF50	ZN526_HUMAN	A	94	ENSP00000301215:V94A	.	V	+	2	0	ZNF526	47420676	0.000000	0.05858	0.000000	0.03702	0.412000	0.31113	-0.444000	0.06854	0.593000	0.29745	-0.624000	0.04008	GTT	T|0.923;C|0.077	0.077	strong		0.617	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401	
SPG11	80208	hgsc.bcm.edu	37	15	44890486	44890486	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44890486G>C	ENST00000261866.7	-	23	3994	c.3978C>G	c.(3976-3978)agC>agG	p.S1326R	SPG11_ENST00000535302.2_Missense_Mutation_p.S1326R|SPG11_ENST00000558319.1_Missense_Mutation_p.S1326R|SPG11_ENST00000427534.2_Missense_Mutation_p.S1326R	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1326					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)				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)		GTTGCTGAATGCTGTTCCATG	0.378																																					p.S1326R		Atlas-SNP	.											.	SPG11	207	.	0			c.C3978G						PASS	.						152.0	131.0	138.0					15																	44890486		2198	4298	6496	SO:0001583	missense	80208	exon23			CTGAATGCTGTTC		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.3978C>G	15.37:g.44890486G>C	ENSP00000261866:p.Ser1326Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.725352	0.48833	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.80304	-1.36;-1.36;-1.36	5.77	1.3	0.21679	.	0.489617	0.24520	N	0.037813	T	0.74550	0.3731	L	0.51422	1.61	0.80722	D	1	P;P;P	0.50443	0.773;0.935;0.773	B;P;B	0.48815	0.414;0.591;0.332	T	0.67288	-0.5708	10	0.19590	T	0.45	.	6.1682	0.20402	0.315:0.0:0.5586:0.1264	.	1326;1326;1326	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	R	1326	ENSP00000261866:S1326R;ENSP00000445278:S1326R;ENSP00000396110:S1326R	ENSP00000261866:S1326R	S	-	3	2	SPG11	42677778	0.423000	0.25482	0.999000	0.59377	0.899000	0.52679	0.278000	0.18753	0.373000	0.24621	0.655000	0.94253	AGC	.	.	none		0.378	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
NOSIP	51070	hgsc.bcm.edu	37	19	50059982	50059982	+	Silent	SNP	C	C	G	rs4594362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50059982C>G	ENST00000596358.1	-	7	607	c.549G>C	c.(547-549)gtG>gtC	p.V183V	NOSIP_ENST00000339093.3_Silent_p.V186V|NOSIP_ENST00000391853.3_Silent_p.V183V	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	183					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		TGGGGCAGGTCACCGTGCGGG	0.692													C|||	397	0.0792732	0.003	0.0418	5008	,	,		13510	0.0198		0.0974	False		,,,				2504	0.2515				p.V183V		Atlas-SNP	.											.	NOSIP	28	.	0			c.G549C						PASS	.	C		70,4326		0,70,2128	22.0	19.0	20.0		549	2.4	1.0	19	dbSNP_111	20	864,7728		39,786,3471	no	coding-synonymous	NOSIP	NM_015953.3		39,856,5599	GG,GC,CC		10.0559,1.5924,7.1913		183/302	50059982	934,12054	2198	4296	6494	SO:0001819	synonymous_variant	51070	exon8			GCAGGTCACCGTG	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.549G>C	19.37:g.50059982C>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	19	0.351852	NM_015953	Q96FD2	Silent	SNP	ENST00000596358.1	37	CCDS12772.1																																																																																			C|0.940;G|0.060	0.060	strong		0.692	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1		
CTSS	1520	hgsc.bcm.edu	37	1	150727539	150727539	+	Missense_Mutation	SNP	G	G	A	rs2230061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150727539G>A	ENST00000368985.3	-	4	597	c.337C>T	c.(337-339)Cgg>Tgg	p.R113W	CTSS_ENST00000448301.2_Intron|CTSS_ENST00000480760.1_5'UTR	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	113			R -> W (in dbSNP:rs2230061). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|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-independent (GO:0002480)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.R113W(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|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;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			GGCAATATCCGATTAGGGTTT	0.433													G|||	1915	0.382388	0.261	0.4366	5008	,	,		20296	0.3532		0.3698	False		,,,				2504	0.5511				p.R113W		Atlas-SNP	.											CTSS,NS,carcinoma,0,1	CTSS	31	1	1	Substitution - Missense(1)	stomach(1)	c.C337T						PASS	.	G	,TRP/ARG	1229,3177	426.4+/-341.1	167,895,1141	214.0	206.0	209.0		,337	1.2	0.0	1	dbSNP_98	209	3052,5548	470.0+/-367.7	551,1950,1799	yes	intron,missense	CTSS	NM_001199739.1,NM_004079.4	,101	718,2845,2940	AA,AG,GG		35.4884,27.8938,32.9156	,possibly-damaging	,113/332	150727539	4281,8725	2203	4300	6503	SO:0001583	missense	1520	exon4			ATATCCGATTAGG	M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	3.4.22.27	"""Cathepsins"""	2545	protein-coding gene	gene with protein product		116845				1373132	Standard	NM_001199739		Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.337C>T	1.37:g.150727539G>A	ENSP00000357981:p.Arg113Trp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	167	53	0.317365	NM_004079	B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	Missense_Mutation	SNP	ENST00000368985.3	37	CCDS968.1	768	0.3516483516483517	133	0.2703252032520325	156	0.430939226519337	202	0.3531468531468531	277	0.3654353562005277	G	9.045	0.990707	0.18966	0.278938	0.354884	ENSG00000163131	ENST00000368985	T	0.22539	1.95	5.47	1.23	0.21249	.	3.731250	0.00357	N	0.000022	T	0.05868	0.0153	L	0.37697	1.125	0.80722	P	0.0	P	0.48016	0.904	B	0.38655	0.278	T	0.14448	-1.0472	9	0.40728	T	0.16	.	4.546	0.12081	0.0765:0.1336:0.5144:0.2756	rs2230061;rs10888390;rs17357778;rs17607024;rs17849640;rs52835690;rs60119206;rs10888390	113	P25774	CATS_HUMAN	W	113	ENSP00000357981:R113W	ENSP00000357981:R113W	R	-	1	2	CTSS	148994163	0.004000	0.15560	0.009000	0.14445	0.359000	0.29487	0.427000	0.21379	-0.025000	0.13918	0.591000	0.81541	CGG	T|0.068;G|0.534;C|0.117;N|0.000;A|0.281	0.281	strong		0.433	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084737.1	NM_004079	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84608900	84608900	+	Missense_Mutation	SNP	C	C	T	rs75742550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84608900C>T	ENST00000344803.2	+	4	3562	c.3515C>T	c.(3514-3516)aCa>aTa	p.T1172I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1172					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGCTCACTGACAAATGTGAAA	0.408													C|||	30	0.00599042	0.0	0.0043	5008	,	,		21271	0.005		0.0149	False		,,,				2504	0.0072				p.T1172I		Atlas-SNP	.											.	.	.	.	0			c.C3515T						PASS	.	C	ILE/THR	15,3741		0,15,1863	53.0	51.0	51.0		3515	-6.1	0.0	9	dbSNP_132	51	76,8174		1,74,4050	yes	missense	FAM75D1	NM_001001670.2	89	1,89,5913	TT,TC,CC		0.9212,0.3994,0.758	possibly-damaging	1172/1577	84608900	91,11915	1878	4125	6003	SO:0001583	missense	389763	exon4			CACTGACAAATGT		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.3515C>T	9.37:g.84608900C>T	ENSP00000341988:p.Thr1172Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	17	0.007783882783882784	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	14	0.018469656992084433	C	0.004	-2.302874	0.00240	0.003994	0.009212	ENSG00000214929	ENST00000344803	T	0.04015	3.73	3.05	-6.11	0.02131	.	.	.	.	.	T	0.00784	0.0026	N	0.04508	-0.205	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.43245	-0.9403	9	0.27082	T	0.32	.	0.1448	0.00087	0.2811:0.1577:0.2358:0.3254	.	1172	Q6ZQQ2	F75D1_HUMAN	I	1172	ENSP00000341988:T1172I	ENSP00000341988:T1172I	T	+	2	0	FAM75D1	83798720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.244000	0.00542	-2.594000	0.00455	-1.379000	0.01178	ACA	C|0.993;T|0.007	0.007	strong		0.408	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
SH3TC2	79628	hgsc.bcm.edu	37	5	148388512	148388512	+	Missense_Mutation	SNP	C	C	T	rs139192433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148388512C>T	ENST00000515425.1	-	15	3481	c.3380G>A	c.(3379-3381)cGg>cAg	p.R1127Q	SH3TC2_ENST00000512049.1_Missense_Mutation_p.R1120Q|SH3TC2_ENST00000538184.1_Missense_Mutation_p.R674Q|SH3TC2_ENST00000502274.1_5'Flank	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1127					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)			ATTGAAAATCCGGAGCTCAGT	0.522													C|||	2	0.000399361	0.0	0.0	5008	,	,		21382	0.0		0.002	False		,,,				2504	0.0				p.R1127Q		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G3380A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	134.0	133.0	133.0		3380	5.2	1.0	5	dbSNP_134	133	19,8581	14.0+/-48.4	0,19,4281	yes	missense	SH3TC2	NM_024577.3	43	0,21,6482	TT,TC,CC		0.2209,0.0454,0.1615	probably-damaging	1127/1289	148388512	21,12985	2203	4300	6503	SO:0001583	missense	79628	exon15			AAAATCCGGAGCT	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.3380G>A	5.37:g.148388512C>T	ENSP00000423660:p.Arg1127Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	33	5.223428	0.95139	4.54E-4	0.002209	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	T;T;T	0.75821	-0.97;-0.97;-0.95	6.03	5.16	0.70880	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	D	0.86083	0.5848	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.87067	0.2157	10	0.52906	T	0.07	-21.7677	17.3176	0.87228	0.0:0.8748:0.1252:0.0	.	1120;1127;1127	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	Q	674;1127;1120	ENSP00000441427:R674Q;ENSP00000423660:R1127Q;ENSP00000421860:R1120Q	ENSP00000425627:R1127Q	R	-	2	0	SH3TC2	148368705	0.978000	0.34361	0.959000	0.39883	0.995000	0.86356	7.275000	0.78548	1.530000	0.49136	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.522	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
LAMA5	3911	hgsc.bcm.edu	37	20	60897721	60897721	+	Missense_Mutation	SNP	C	C	T	rs3737137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60897721C>T	ENST00000252999.3	-	46	6224	c.6158G>A	c.(6157-6159)cGc>cAc	p.R2053H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2053	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.		R -> H (in dbSNP:rs3737137).		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)			TACCTGGCAGCGGTCACAGCG	0.682													.|||	749	0.149561	0.0091	0.1571	5008	,	,		8221	0.127		0.2425	False		,,,				2504	0.2618				p.R2053H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6158A						PASS	.	C	HIS/ARG	173,3877		11,151,1863	6.0	6.0	6.0		6158	-4.9	0.9	20	dbSNP_107	6	1643,6367		144,1355,2506	yes	missense	LAMA5	NM_005560.3	29	155,1506,4369	TT,TC,CC		20.5119,4.2716,15.058	benign	2053/3696	60897721	1816,10244	2025	4005	6030	SO:0001583	missense	3911	exon46			TGGCAGCGGTCAC	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.6158G>A	20.37:g.60897721C>T	ENSP00000252999:p.Arg2053His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	317	0.14514652014652016	9	0.018292682926829267	64	0.17679558011049723	64	0.11188811188811189	180	0.23746701846965698	c	9.823	1.186240	0.21870	0.042716	0.205119	ENSG00000130702	ENST00000252999	T	0.37058	1.22	4.12	-4.95	0.03048	EGF-like, laminin (4);	0.294485	0.33691	N	0.004660	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	B	0.21452	0.056	B	0.17433	0.018	T	0.15093	-1.0449	9	0.42905	T	0.14	.	7.5599	0.27845	0.1022:0.4074:0.0:0.4904	rs3737137;rs60521636;rs3737137	2053	O15230	LAMA5_HUMAN	H	2053	ENSP00000252999:R2053H	ENSP00000252999:R2053H	R	-	2	0	LAMA5	60331116	0.806000	0.28996	0.855000	0.33649	0.027000	0.11550	0.110000	0.15437	-0.895000	0.03920	-1.199000	0.01669	CGC	C|0.858;T|0.142	0.142	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632820	32632820	+	Missense_Mutation	SNP	C	C	G	rs1130375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632820C>G	ENST00000399084.1	-	3	312	c.134G>C	c.(133-135)gGc>gCc	p.G45A	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G45A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G45A|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G45A|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	45	Beta-1.		A -> G (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:05, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:15, allele DQB1*03:17, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; dbSNP:rs1130375). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GTAGCACATGCCCTTAAACTG	0.652									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				c|||	1300	0.259585	0.2216	0.2147	5008	,	,		7556	0.3234		0.1998	False		,,,				2504	0.3384				p.G45A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G134C						PASS	.	C	ALA/GLY	656,3586		71,514,1536	24.0	24.0	24.0		134	2.3	0.0	6	dbSNP_86	24	1516,6910		184,1148,2881	yes	missense	HLA-DQB1	NM_002123.4	60	255,1662,4417	GG,GC,CC		17.9919,15.4644,17.1456	benign	45/262	32632820	2172,10496	2121	4213	6334	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CACATGCCCTTAA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.134G>C	6.37:g.32632820C>G	ENSP00000382034:p.Gly45Ala	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	484	0.2216117216117216	93	0.18902439024390244	72	0.19889502762430938	191	0.3339160839160839	128	0.16886543535620052	.	4.079	0.012574	0.07912	0.154644	0.179919	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00235	8.48;8.48;8.48;8.48	4.13	2.26	0.28386	.	0.340862	0.12493	N	0.464088	T	0.00039	0.0001	.	.	.	0.39429	P	0.03294699999999995	B;B;B;B	0.26775	0.159;0.005;0.001;0.001	B;B;B;B	0.32149	0.141;0.012;0.009;0.009	T	0.00000	-1.3101	8	0.12103	T	0.63	.	11.998	0.53214	0.0:0.5934:0.4066:0.0	rs1130375;rs3189158;rs12722109;rs17416204	55;45;45;45	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	A	45	ENSP00000382029:G45A;ENSP00000364080:G45A;ENSP00000407332:G45A;ENSP00000382034:G45A	ENSP00000364080:G45A	G	-	2	0	HLA-DQB1	32740798	0.000000	0.05858	0.040000	0.18447	0.076000	0.17211	-4.545000	0.00218	0.344000	0.23847	0.305000	0.20034	GGC	G|0.228;C|0.772	0.228	strong		0.652	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
SPHK2	56848	hgsc.bcm.edu	37	19	49129486	49129486	+	Silent	SNP	G	G	A	rs61748787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49129486G>A	ENST00000245222.4	+	3	744	c.378G>A	c.(376-378)ggG>ggA	p.G126G	SPHK2_ENST00000598088.1_Silent_p.G126G|SPHK2_ENST00000340932.3_Silent_p.G90G|SPHK2_ENST00000443164.1_Silent_p.G188G|SPHK2_ENST00000599029.1_Silent_p.G90G|SPHK2_ENST00000599748.1_Silent_p.G90G|AC022154.7_ENST00000594850.1_RNA|SPHK2_ENST00000600537.1_Silent_p.G67G|SPHK2_ENST00000599033.1_3'UTR|AC022154.7_ENST00000600303.1_RNA|SPHK2_ENST00000601712.1_Silent_p.G90G|AC022154.7_ENST00000598735.1_RNA	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	126	Required for binding to sulfatide and phosphoinositides and for membrane localization.				blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		gccggcgcggggcccggcgcA	0.706													G|||	148	0.0295527	0.0008	0.036	5008	,	,		13429	0.0		0.0785	False		,,,				2504	0.044				p.G126G		Atlas-SNP	.											.	SPHK2	62	.	0			c.G378A						PASS	.	G	,,,	50,4160		0,50,2055	9.0	10.0	10.0		201,378,270,378	2.6	1.0	19	dbSNP_129	10	480,7874		13,454,3710	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	13,504,5765	AA,AG,GG		5.7458,1.1876,4.2184	,,,	67/596,126/655,90/619,126/655	49129486	530,12034	2105	4177	6282	SO:0001819	synonymous_variant	56848	exon3			GCGCGGGGCCCGG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.378G>A	19.37:g.49129486G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	14	5	0.357143	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.962;A|0.038	0.038	strong		0.706	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
FCRL1	115350	hgsc.bcm.edu	37	1	157768000	157768000	+	Silent	SNP	G	G	C	rs3811024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:157768000G>C	ENST00000368176.3	-	8	1132	c.1065C>G	c.(1063-1065)acC>acG	p.T355T	FCRL1_ENST00000358292.3_Silent_p.T316T|FCRL1_ENST00000491942.1_Silent_p.T355T|FCRL1_ENST00000489998.1_5'UTR	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	355						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGTTGAGGTAGGTGAACTCTT	0.493													G|||	1158	0.23123	0.3434	0.2032	5008	,	,		20568	0.1855		0.2406	False		,,,				2504	0.137				p.T355T	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.C1065G						PASS	.	G	,,	1381,3025	456.3+/-351.3	216,949,1038	116.0	111.0	112.0		948,1065,1065	-0.7	0.0	1	dbSNP_107	112	2098,6502	362.6+/-332.8	252,1594,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	468,2543,3492	CC,CG,GG		24.3953,31.3436,26.7492	,,	316/367,355/429,355/430	157768000	3479,9527	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon8			GAGGTAGGTGAAC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1065C>G	1.37:g.157768000G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	164	59	0.359756	NM_001159398	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			G|0.747;C|0.253	0.253	strong		0.493	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44618187	44618187	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:44618187C>T	ENST00000576629.1	+	8	3488	c.2993C>T	c.(2992-2994)aCg>aTg	p.T998M	ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000337845.7_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.T998M|ARL17A_ENST00000445552.2_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	998						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)		ATGGGAACAACGCTAGTCCCA	0.328																																					p.T998M		Atlas-SNP	.											LRRC37A2,NS,carcinoma,-1,1	LRRC37A2	37	1	0			c.C2993T						scavenged	.						1.0	1.0	1.0					17																	44618187		65	196	261	SO:0001583	missense	474170	exon7			GAACAACGCTAGT	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.2993C>T	17.37:g.44618187C>T	ENSP00000459551:p.Thr998Met	Somatic	747	0	0		WXS	Illumina HiSeq	Phase_I	571	2	0.00350263	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	C	5.625	0.300049	0.10622	.	.	ENSG00000238083	ENST00000333412	D	0.83914	-1.78	3.43	2.45	0.29901	.	.	.	.	.	D	0.87665	0.6234	M	0.71036	2.16	0.20196	N	0.999922	D	0.89917	1.0	D	0.64776	0.929	T	0.76244	-0.3030	9	0.72032	D	0.01	.	7.1058	0.25362	0.0:0.8704:0.0:0.1296	.	998	A6NM11	L37A2_HUMAN	M	998	ENSP00000333071:T998M	ENSP00000333071:T998M	T	+	2	0	LRRC37A2	41973503	0.889000	0.30405	0.011000	0.14972	0.004000	0.04260	2.100000	0.41777	0.800000	0.34041	-0.791000	0.03333	ACG	.	.	none		0.328	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
FBXO24	26261	hgsc.bcm.edu	37	7	100198386	100198386	+	Missense_Mutation	SNP	C	C	T	rs11768465	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100198386C>T	ENST00000241071.6	+	10	1929	c.1607C>T	c.(1606-1608)aCg>aTg	p.T536M	FBXO24_ENST00000468962.1_Missense_Mutation_p.T524M|PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000427939.2_Missense_Mutation_p.T574M|PCOLCE_ENST00000223061.5_5'Flank|FBXO24_ENST00000360609.2_3'UTR|PCOLCE-AS1_ENST00000442166.2_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	536					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CAGGACCGCACGGAGAAGATG	0.642													T|||	1081	0.215855	0.379	0.2089	5008	,	,		17640	0.0188		0.2107	False		,,,				2504	0.2086				p.T574M		Atlas-SNP	.											.	FBXO24	125	.	0			c.C1721T						PASS	.	T	MET/THR,MET/THR,MET/THR	1502,2904	675.6+/-403.1	257,988,958	83.0	76.0	78.0		1571,1721,1607	3.1	1.0	7	dbSNP_120	78	2001,6599	722.8+/-406.4	244,1513,2543	yes	missense,missense,missense	FBXO24	NM_001163499.1,NM_012172.4,NM_033506.2	81,81,81	501,2501,3501	TT,TC,CC		23.2674,34.0899,26.9337	benign,benign,benign	524/569,574/619,536/581	100198386	3503,9503	2203	4300	6503	SO:0001583	missense	26261	exon10			ACCGCACGGAGAA	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"""F-boxes /  ""other"""""	13595	protein-coding gene	gene with protein product		609097	"""F-box only protein 24"""			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.1607C>T	7.37:g.100198386C>T	ENSP00000241071:p.Thr536Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	454	0.2078754578754579	197	0.40040650406504064	91	0.2513812154696133	4	0.006993006993006993	162	0.21372031662269128	t	11.94	1.789266	0.31685	0.340899	0.232674	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	T;T;T	0.12569	2.67;2.67;2.68	4.22	3.06	0.35304	.	0.091005	0.45867	N	0.000324	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.99999999461126	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.48906	-0.8993	9	0.02654	T	1	-5.1182	7.1574	0.25645	0.0:0.1952:0.0:0.8048	rs11768465;rs56642930;rs59987023;rs11768465	524;574;536;536	B4DY42;B4DX91;A4D2D3;O75426	.;.;.;FBX24_HUMAN	M	536;524;574	ENSP00000241071:T536M;ENSP00000420239:T524M;ENSP00000416558:T574M	ENSP00000241071:T536M	T	+	2	0	FBXO24	100036322	1.000000	0.71417	0.998000	0.56505	0.790000	0.44656	3.163000	0.50763	0.190000	0.20209	-0.593000	0.04111	ACG	C|0.761;T|0.239	0.239	strong		0.642	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1		
PTPRF	5792	hgsc.bcm.edu	37	1	44072018	44072018	+	Silent	SNP	C	C	T	rs1065772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000372413.3_Silent_p.T1188T|PTPRF_ENST00000438120.1_Silent_p.T1188T|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.T545T	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	83	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	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		
MUC4	4585	hgsc.bcm.edu	37	3	195506760	195506760	+	Silent	SNP	T	T	A	rs62282473	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506760T>A	ENST00000463781.3	-	2	12150	c.11691A>T	c.(11689-11691)gcA>gcT	p.A3897A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.A3897A	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)		GACGTGTGGATGCTGAGGAAG	0.592													.|||	492	0.0982428	0.0166	0.0994	5008	,	,		8412	0.0526		0.2008	False		,,,				2504	0.1493				p.A3897A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A11691T						PASS	.						9.0	8.0	8.0					3																	195506760		534	1118	1652	SO:0001819	synonymous_variant	4585	exon2			TGTGGATGCTGAG	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.11691A>T	3.37:g.195506760T>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	35	28	0.8	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			T|0.967;A|0.033	0.033	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ROBO4	54538	hgsc.bcm.edu	37	11	124766128	124766128	+	Silent	SNP	A	A	G	rs4078313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124766128A>G	ENST00000306534.3	-	4	1130	c.645T>C	c.(643-645)caT>caC	p.H215H	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Silent_p.H70H	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	120	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	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	
FLG	2312	hgsc.bcm.edu	37	1	152281008	152281008	+	Silent	SNP	A	A	G	rs7512554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281008A>G	ENST00000368799.1	-	3	6389	c.6354T>C	c.(6352-6354)caT>caC	p.H2118H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2118	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)			CCTGATCATAATGGGATCCTT	0.572									Ichthyosis				-|||	1641	0.327676	0.3843	0.3357	5008	,	,		29299	0.4355		0.1282	False		,,,				2504	0.3395				p.H2118H		Atlas-SNP	.											.	FLG	900	.	0			c.T6354C						PASS	.	G		1446,2960		0,1446,757	349.0	263.0	292.0		6354	-0.6	0.0	1	dbSNP_116	292	1083,7517		0,1083,3217	no	coding-synonymous	FLG	NM_002016.1		0,2529,3974	GG,GA,AA		12.593,32.8189,19.4449		2118/4062	152281008	2529,10477	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATCATAATGGGAT	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.6354T>C	1.37:g.152281008A>G		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	427	176	0.412178	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.500;G|0.500	0.500	weak		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
IGFN1	91156	hgsc.bcm.edu	37	1	201184275	201184275	+	Silent	SNP	C	C	T	rs2275673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201184275C>T	ENST00000335211.4	+	14	9118	c.8988C>T	c.(8986-8988)acC>acT	p.T2996T	IGFN1_ENST00000451870.2_Silent_p.T539T|IGFN1_ENST00000295591.8_Silent_p.T156T	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	162	0	0		WXS	Illumina HiSeq	Phase_I	211	124	0.587678	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	
C3orf35	339883	hgsc.bcm.edu	37	3	37458758	37458758	+	Start_Codon_SNP	SNP	A	A	C	rs113724034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000452017.2_Start_Codon_SNP_p.M1L|C3orf35_ENST00000481400.1_Intron|C3orf35_ENST00000426078.1_Start_Codon_SNP_p.M1L|C3orf35_ENST00000425564.2_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	39	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	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
HIVEP3	59269	hgsc.bcm.edu	37	1	41976529	41976529	+	Missense_Mutation	SNP	C	C	T	rs11809423	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41976529C>T	ENST00000372583.1	-	9	7699	c.6814G>A	c.(6814-6816)Ggg>Agg	p.G2272R	HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Missense_Mutation_p.G2271R|HIVEP3_ENST00000247584.5_Missense_Mutation_p.G2272R|HIVEP3_ENST00000429157.2_Missense_Mutation_p.G2271R	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2272			G -> R (in dbSNP:rs11809423). {ECO:0000269|PubMed:11161801}.		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)				GGGTAGTCCCCGCCCTCCAGC	0.677													T|||	502	0.10024	0.2352	0.036	5008	,	,		14383	0.0149		0.0249	False		,,,				2504	0.1288				p.G2272R		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G6814A						PASS	.	T	ARG/GLY,ARG/GLY	909,3497	718.5+/-408.8	95,719,1389	28.0	32.0	30.0		6811,6814	2.6	1.0	1	dbSNP_120	30	370,8228	790.1+/-407.6	5,360,3934	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	125,125	100,1079,5323	TT,TC,CC		4.3033,20.631,9.8354	benign,benign	2271/2406,2272/2407	41976529	1279,11725	2203	4299	6502	SO:0001583	missense	59269	exon9			AGTCCCCGCCCTC	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.6814G>A	1.37:g.41976529C>T	ENSP00000361664:p.Gly2272Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	146	0.06684981684981685	109	0.22154471544715448	14	0.03867403314917127	4	0.006993006993006993	19	0.025065963060686015	T	2.703	-0.270621	0.05716	0.20631	0.043033	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05258	3.48;3.47;3.47;3.48	4.9	2.59	0.31030	.	0.133081	0.34603	N	0.003833	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.48210	-0.9055	9	0.02654	T	1	-3.8396	7.6365	0.28270	0.0:0.2453:0.0:0.7547	rs11809423;rs52805193;rs58390647;rs11809423	2271;2272	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	R	2271;2272;2272;2271	ENSP00000361665:G2271R;ENSP00000361664:G2272R;ENSP00000247584:G2272R;ENSP00000410828:G2271R	ENSP00000247584:G2272R	G	-	1	0	HIVEP3	41749116	0.043000	0.20138	0.977000	0.42913	0.966000	0.64601	0.293000	0.19029	0.068000	0.16574	-0.361000	0.07541	GGG	C|0.909;T|0.091	0.091	strong		0.677	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
HPGD	3248	hgsc.bcm.edu	37	4	175443156	175443156	+	Silent	SNP	C	C	T	rs1050145	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:175443156C>T	ENST00000296522.6	-	2	602	c.156G>A	c.(154-156)caG>caA	p.Q52Q	HPGD_ENST00000504433.1_Silent_p.Q52Q|HPGD_ENST00000510901.1_5'UTR|HPGD_ENST00000542498.1_Silent_p.Q52Q|HPGD_ENST00000422112.2_Silent_p.Q52Q|HPGD_ENST00000296521.7_Silent_p.Q52Q|RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000541923.1_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	69	0	0		WXS	Illumina HiSeq	Phase_I	66	19	0.287879	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		
JRK	8629	hgsc.bcm.edu	37	8	143747097	143747097	+	RNA	SNP	C	C	T	rs34800931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143747097C>T	ENST00000507178.2	-	0	713							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				acacgcagggctcagtgagct	0.592													C|||	120	0.0239617	0.0174	0.0173	5008	,	,		19670	0.0298		0.0437	False		,,,				2504	0.0112				p.E127E		Atlas-SNP	.											.	.	.	.	0			c.G381A						PASS	.	C	,	64,4076		0,64,2006	24.0	28.0	27.0		381,381	2.2	1.0	8	dbSNP_126	27	395,7947		6,383,3782	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	6,447,5788	TT,TC,CC		4.7351,1.5459,3.6773	,	127/557,127/569	143747097	459,12023	2070	4171	6241			8629	exon2			GCAGGGCTCAGTG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143747097C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				C|0.968;T|0.032	0.032	strong		0.592	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
FLG	2312	hgsc.bcm.edu	37	1	152286367	152286367	+	Missense_Mutation	SNP	C	C	A	rs41267154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152286367C>A	ENST00000368799.1	-	3	1030	c.995G>T	c.(994-996)gGc>gTc	p.G332V	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	332	Ser-rich.		G -> V (in dbSNP:rs41267154).		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)			GTGTCTGGAGCCATCTCTTGA	0.567									Ichthyosis				-|||	1706	0.340655	0.115	0.4193	5008	,	,		19207	0.6062		0.171	False		,,,				2504	0.4908				p.G332V		Atlas-SNP	.											.	FLG	900	.	0			c.G995T						PASS	.	C	VAL/GLY	582,3824		39,504,1660	195.0	196.0	196.0		995	1.2	0.0	1	dbSNP_127	196	1444,7156		124,1196,2980	no	missense	FLG	NM_002016.1	109	163,1700,4640	AA,AC,CC		16.7907,13.2093,15.5774	probably-damaging	332/4062	152286367	2026,10980	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGAGCCATCTC	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.995G>T	1.37:g.152286367C>A	ENSP00000357789:p.Gly332Val	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	288	184	0.638889	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	676	0.30952380952380953	64	0.13008130081300814	125	0.3453038674033149	355	0.6206293706293706	132	0.1741424802110818	-	9.095	1.002721	0.19121	0.132093	0.167907	ENSG00000143631	ENST00000368799	T	0.01685	4.69	3.14	1.2	0.21068	.	.	.	.	.	T	0.02571	0.0078	M	0.70595	2.14	0.80722	P	0.0	D	0.89917	1.0	D	0.81914	0.995	T	0.46247	-0.9205	8	0.33141	T	0.24	0.3437	5.3802	0.16187	0.0:0.7225:0.0:0.2775	rs41267154	332	P20930	FILA_HUMAN	V	332	ENSP00000357789:G332V	ENSP00000357789:G332V	G	-	2	0	FLG	150552991	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.020000	0.03618	0.200000	0.20447	0.400000	0.26472	GGC	C|0.793;A|0.207	0.207	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NUP205	23165	hgsc.bcm.edu	37	7	135269655	135269655	+	Missense_Mutation	SNP	T	T	C	rs58392569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135269655T>C	ENST00000285968.6	+	8	1144	c.1118T>C	c.(1117-1119)aTg>aCg	p.M373T	NUP205_ENST00000440390.2_Missense_Mutation_p.M167T	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	373					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTGTTCCTCATGGAATCTGTA	0.393													C|||	250	0.0499201	0.034	0.0504	5008	,	,		16380	0.0516		0.0457	False		,,,				2504	0.0736				p.M373T		Atlas-SNP	.											.	NUP205	198	.	0			c.T1118C						PASS	.	C	THR/MET	109,4297	801.6+/-415.6	2,105,2096	81.0	72.0	75.0		1118	3.7	0.7	7	dbSNP_129	75	226,8374	791.2+/-407.6	4,218,4078	yes	missense	NUP205	NM_015135.2	81	6,323,6174	CC,CT,TT		2.6279,2.4739,2.5757	benign	373/2013	135269655	335,12671	2203	4300	6503	SO:0001583	missense	23165	exon8			TCCTCATGGAATC	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1118T>C	7.37:g.135269655T>C	ENSP00000285968:p.Met373Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	79	0.036172161172161175	11	0.022357723577235773	16	0.04419889502762431	29	0.050699300699300696	23	0.030343007915567283	C	6.524	0.464871	0.12402	0.024739	0.026279	ENSG00000155561	ENST00000285968;ENST00000440390	T;T	0.28666	1.6;1.6	5.53	3.68	0.42216	.	0.144073	0.64402	N	0.000008	T	0.01222	0.0040	N	0.00538	-1.39	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.13388	-1.0511	9	0.18710	T	0.47	-28.4751	10.9304	0.47215	0.0:0.6812:0.2514:0.0673	rs58392569;rs61751961	373	Q92621	NU205_HUMAN	T	373;167	ENSP00000285968:M373T;ENSP00000401983:M167T	ENSP00000285968:M373T	M	+	2	0	NUP205	134920195	0.985000	0.35326	0.749000	0.31150	0.907000	0.53573	2.702000	0.47102	0.273000	0.22049	-0.186000	0.12905	ATG	T|0.960;C|0.040	0.040	strong		0.393	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
PLIN3	10226	hgsc.bcm.edu	37	19	4859937	4859937	+	Missense_Mutation	SNP	T	T	C	rs8289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4859937T>C	ENST00000221957.4	-	3	342	c.166A>G	c.(166-168)Atc>Gtc	p.I56V	PLIN3_ENST00000585479.1_Missense_Mutation_p.I56V|PLIN3_ENST00000592528.1_Missense_Mutation_p.I56V	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	56			I -> V (in dbSNP:rs8289). {ECO:0000269|PubMed:10393528, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9590177, ECO:0000269|PubMed:9874244}.		vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	ACAGTCTTGATGTGCGGGTAG	0.642													C|||	3174	0.633786	0.6437	0.6254	5008	,	,		18806	0.5129		0.661	False		,,,				2504	0.7229				p.I56V		Atlas-SNP	.											PLIN3,NS,carcinoma,0,1	PLIN3	36	1	0			c.A166G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE	2949,1457	468.7+/-355.2	987,975,241	78.0	65.0	70.0		166,166,166	1.3	0.0	19	dbSNP_52	70	6262,2338	392.0+/-343.8	2293,1676,331	yes	missense,missense,missense	PLIN3	NM_001164189.1,NM_001164194.1,NM_005817.4	29,29,29	3280,2651,572	CC,CT,TT		27.186,33.0685,29.1788	benign,benign,benign	56/434,56/423,56/435	4859937	9211,3795	2203	4300	6503	SO:0001583	missense	10226	exon3			TCTTGATGTGCGG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.166A>G	19.37:g.4859937T>C	ENSP00000221957:p.Ile56Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	1298	0.5943223443223443	293	0.5955284552845529	204	0.56353591160221	301	0.5262237762237763	500	0.6596306068601583	C	0.005	-2.137034	0.00335	0.669315	0.72814	ENSG00000105355	ENST00000221957	T	0.04654	3.58	4.76	1.26	0.21427	.	0.273464	0.30840	N	0.008766	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	0.08868	-1.0701	9	0.08599	T	0.76	-24.4028	5.0884	0.14694	0.0:0.3555:0.2614:0.383	rs8289;rs3196414;rs17856053;rs17856214;rs59152954;rs8289	56;56	O60664-3;O60664	.;PLIN3_HUMAN	V	56	ENSP00000221957:I56V	ENSP00000221957:I56V	I	-	1	0	PLIN3	4810937	0.016000	0.18221	0.001000	0.08648	0.014000	0.08584	-0.510000	0.06328	0.073000	0.16731	-0.355000	0.07637	ATC	T|0.343;C|0.657	0.657	strong		0.642	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
CNTNAP1	8506	hgsc.bcm.edu	37	17	40839829	40839829	+	Missense_Mutation	SNP	G	G	A	rs375309204		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40839829G>A	ENST00000264638.4	+	8	1353	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	379					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)		GGTTTCCCACGCCGTGGCCGC	0.637																																					p.R379H		Atlas-SNP	.											.	CNTNAP1	116	.	0			c.G1136A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	96.0	88.0	90.0		1136	5.0	0.2	17		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTNAP1	NM_003632.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	379/1385	40839829	1,13005	2203	4300	6503	SO:0001583	missense	8506	exon8			TCCCACGCCGTGG	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.1136G>A	17.37:g.40839829G>A	ENSP00000264638:p.Arg379His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	23	0.267442	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634266	0.47049	0.0	1.16E-4	ENSG00000108797	ENST00000264638	T	0.79247	-1.25	5.02	5.02	0.67125	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.187385	0.37955	N	0.001877	T	0.80773	0.4687	L	0.43152	1.355	0.44927	D	0.997946	D	0.76494	0.999	P	0.59643	0.861	T	0.80410	-0.1394	10	0.42905	T	0.14	.	13.3172	0.60413	0.0:0.0:0.8419:0.1581	.	379	P78357	CNTP1_HUMAN	H	379	ENSP00000264638:R379H	ENSP00000264638:R379H	R	+	2	0	CNTNAP1	38093355	1.000000	0.71417	0.248000	0.24265	0.483000	0.33249	7.263000	0.78421	2.302000	0.77476	0.655000	0.94253	CGC	.	.	weak		0.637	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
SDHA	6389	hgsc.bcm.edu	37	5	256470	256470	+	Missense_Mutation	SNP	G	G	A	rs3211483		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:256470G>A	ENST00000264932.6	+	15	2045	c.1930G>A	c.(1930-1932)Gtg>Atg	p.V644M	SDHA_ENST00000504309.1_Missense_Mutation_p.V563M|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000510361.1_Missense_Mutation_p.V596M	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	644					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)	ATATAGACCCGTGATCGACAA	0.428									Familial Paragangliomas																												p.V644M		Atlas-SNP	.											SDHA,NS,adenocarcinoma,0,2	SDHA	80	2	0			c.G1930A						scavenged	.						91.0	104.0	99.0					5																	256470		2203	4300	6503	SO:0001583	missense	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	AGACCCGTGATCG	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.1930G>A	5.37:g.256470G>A	ENSP00000264932:p.Val644Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	107	2	0.0186916	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	15.71|15.71	2.915077|2.915077	0.52546|0.52546	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000515815|ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	.|D;D;D	.|0.84730	.|-1.89;-1.89;-1.89	4.12|4.12	4.12|4.12	0.48240|0.48240	.|Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	.|0.000000	.|0.64402	.|U	.|0.000002	D|D	0.94056|0.94056	0.8095|0.8095	H|H	0.94582|0.94582	3.555|3.555	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.999;1.0	.|D;D;D;D	.|0.97110	.|1.0;0.997;0.993;0.997	D|D	0.95511|0.95511	0.8586|0.8586	5|10	.|0.87932	.|D	.|0	.|.	13.8591|13.8591	0.63548|0.63548	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs3211483;rs17415232|rs3211483;rs17415232	.|596;238;563;644	.|E9PBJ5;B3KYA5;D6RFM5;P31040	.|.;.;.;DHSA_HUMAN	H|M	126|644;499;563;596	.|ENSP00000264932:V644M;ENSP00000426514:V563M;ENSP00000427703:V596M	.|ENSP00000264932:V644M	R|V	+|+	2|1	0|0	SDHA|SDHA	309470|309470	1.000000|1.000000	0.71417|0.71417	0.642000|0.642000	0.29436|0.29436	0.242000|0.242000	0.25591|0.25591	8.735000|8.735000	0.91549|0.91549	1.861000|1.861000	0.53984|0.53984	0.305000|0.305000	0.20034|0.20034	CGT|GTG	G|1.000;|0.000	.	weak		0.428	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
NUBP2	10101	hgsc.bcm.edu	37	16	1836796	1836796	+	Silent	SNP	C	C	A	rs2235648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1836796C>A	ENST00000262302.9	+	3	294	c.174C>A	c.(172-174)atC>atA	p.I58I	NUBP2_ENST00000568706.1_Intron|NUBP2_ENST00000565134.1_Silent_p.I58I|NUBP2_ENST00000543305.1_Intron|NUBP2_ENST00000565987.1_5'UTR	NM_001284501.1|NM_012225.2	NP_001271430.1|NP_036357.1			nucleotide binding protein 2											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						GCCCCAGTATCCCCCGCATGC	0.701													C|||	2474	0.49401	0.5477	0.6095	5008	,	,		15131	0.4097		0.5885	False		,,,				2504	0.3292				p.I58I		Atlas-SNP	.											NUBP2,colon,carcinoma,0,2	NUBP2	25	2	0			c.C174A						PASS	.	C		2414,1974	596.3+/-388.6	656,1102,436	44.0	42.0	42.0		174	-4.4	0.9	16	dbSNP_98	42	5192,3402	622.6+/-397.3	1577,2038,682	no	coding-synonymous	NUBP2	NM_012225.2		2233,3140,1118	AA,AC,CC		39.5858,44.9863,41.4112		58/272	1836796	7606,5376	2194	4297	6491	SO:0001819	synonymous_variant	10101	exon3			CAGTATCCCCCGC	AF118394	CCDS10445.1, CCDS66898.1	16p13.3	2011-05-19	2011-05-19		ENSG00000095906	ENSG00000095906			8042	protein-coding gene	gene with protein product		610779	"""nucleotide binding protein 2 (E.coli MinD like)"", ""nucleotide binding protein 2 (MinD homolog, E. coli)"""			10486206	Standard	XM_005255025		Approved	CFD1	uc002cmw.4	Q9Y5Y2	OTTHUMG00000128639	ENST00000262302.9:c.174C>A	16.37:g.1836796C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_012225		Silent	SNP	ENST00000262302.9	37	CCDS10445.1																																																																																			C|0.448;A|0.552	0.552	strong		0.701	NUBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250510.1	NM_012225	
NDNF	79625	hgsc.bcm.edu	37	4	121957559	121957559	+	Silent	SNP	G	G	A	rs34766411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:121957559G>A	ENST00000379692.4	-	4	2093	c.1567C>T	c.(1567-1569)Ctg>Ttg	p.L523L	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	523	Fibronectin type-III 2.				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						GCTTTCTGCAGGTTTTGACTG	0.418													G|||	1234	0.246406	0.1755	0.3429	5008	,	,		19471	0.2351		0.2058	False		,,,				2504	0.3272				p.L523L		Atlas-SNP	.											.	NDNF	72	.	0			c.C1567T						PASS	.	G		828,3578	328.3+/-300.5	83,662,1458	149.0	141.0	144.0		1567	4.0	1.0	4	dbSNP_126	144	1807,6793	325.2+/-316.8	190,1427,2683	no	coding-synonymous	NDNF	NM_024574.3		273,2089,4141	AA,AG,GG		21.0116,18.7926,20.2599		523/569	121957559	2635,10371	2203	4300	6503	SO:0001819	synonymous_variant	79625	exon4			TCTGCAGGTTTTG	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.1567C>T	4.37:g.121957559G>A		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	316	158	0.5	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			G|0.789;A|0.211	0.211	strong		0.418	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
SLFN14	342618	hgsc.bcm.edu	37	17	33880003	33880003	+	Silent	SNP	C	C	G	rs28498569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33880003C>G	ENST00000415846.3	-	3	1685	c.1650G>C	c.(1648-1650)gtG>gtC	p.V550V	RP11-1094M14.12_ENST00000588445.1_RNA	NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	550							ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						ACAGGGAGACCACCACCAGAG	0.527													C|||	1164	0.232428	0.3782	0.2046	5008	,	,		15105	0.2976		0.0964	False		,,,				2504	0.1278				p.V550V		Atlas-SNP	.											.	SLFN14	43	.	0			c.G1650C						PASS	.	C		420,964		61,298,333	142.0	136.0	138.0		1650	-5.5	0.0	17	dbSNP_125	138	281,2901		11,259,1321	no	coding-synonymous	SLFN14	NM_001129820.1		72,557,1654	GG,GC,CC		8.8309,30.3468,15.3526		550/913	33880003	701,3865	692	1591	2283	SO:0001819	synonymous_variant	342618	exon3			GGAGACCACCACC		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.1650G>C	17.37:g.33880003C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_001129820	B2RTW9	Silent	SNP	ENST00000415846.3	37	CCDS45650.1																																																																																			C|0.765;G|0.235	0.235	strong		0.527	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
LITAF	9516	hgsc.bcm.edu	37	16	11647492	11647492	+	Missense_Mutation	SNP	T	T	C	rs4280262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11647492T>C	ENST00000571688.1	-	3	504	c.274A>G	c.(274-276)Atc>Gtc	p.I92V	LITAF_ENST00000381810.3_Missense_Mutation_p.I92V|LITAF_ENST00000571459.1_Intron|LITAF_ENST00000413364.2_Missense_Mutation_p.I92V|LITAF_ENST00000572255.1_5'UTR|LITAF_ENST00000574763.1_Missense_Mutation_p.I92V|LITAF_ENST00000571976.1_Missense_Mutation_p.I92V|LITAF_ENST00000570904.1_Missense_Mutation_p.I92V|LITAF_ENST00000339430.5_Missense_Mutation_p.I92V|LITAF_ENST00000576036.1_Missense_Mutation_p.I92V	NM_001136472.1	NP_001129944.1	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF factor	92			I -> V (in dbSNP:rs4280262). {ECO:0000269|PubMed:15776429, ECO:0000269|PubMed:15786462}.		aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cytokine production (GO:0001817)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			endometrium(1)|large_intestine(1)|liver(1)|lung(3)|skin(1)	7						CACATTTGGATAGGGCGGTCC	0.552													C|||	514	0.102636	0.0393	0.1513	5008	,	,		19842	0.0625		0.2058	False		,,,				2504	0.089				p.I92V		Atlas-SNP	.											.	LITAF	16	.	0			c.A274G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE	318,4076	796.0+/-415.3	10,298,1889	113.0	72.0	86.0		274,274,274	1.1	0.1	16	dbSNP_111	86	1831,6769	731.2+/-406.8	184,1463,2653	yes	missense,missense,missense	LITAF	NM_001136472.1,NM_001136473.1,NM_004862.3	29,29,29	194,1761,4542	CC,CT,TT		21.2907,7.2371,16.5384	benign,benign,benign	92/162,92/153,92/162	11647492	2149,10845	2197	4300	6497	SO:0001583	missense	9516	exon3			TTTGGATAGGGCG	AB034747	CCDS32386.1, CCDS45411.1	16p13.3-p12	2014-09-17							16841	protein-coding gene	gene with protein product		603795				9305847, 10200294	Standard	NM_004862		Approved	PIG7, SIMPLE, FLJ38636, TP53I7	uc002dbb.3	Q99732		ENST00000571688.1:c.274A>G	16.37:g.11647492T>C	ENSP00000459533:p.Ile92Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_001136473	D3DUG1|G5E9K0|Q05DW0|Q9C0L6	Missense_Mutation	SNP	ENST00000571688.1	37	CCDS32386.1	281	0.12866300366300365	24	0.04878048780487805	56	0.15469613259668508	40	0.06993006993006994	161	0.21240105540897097	C	0.007	-2.004687	0.00431	0.072371	0.212907	ENSG00000189067	ENST00000339430;ENST00000413364;ENST00000381810	D;D;D	0.85702	-2.02;-2.02;-2.02	5.38	1.12	0.20585	LPS-induced tumor necrosis factor alpha factor (2);	0.145452	0.44902	N	0.000408	T	0.00039	0.0001	N	0.00327	-1.64	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.18053	-1.0349	9	0.02654	T	1	-9.3056	9.8475	0.41037	0.0:0.6357:0.0:0.3643	rs4280262;rs17605605;rs56421922;rs4280262	92;92	G5E9K0;Q99732	.;LITAF_HUMAN	V	92	ENSP00000340118:I92V;ENSP00000397958:I92V;ENSP00000371231:I92V	ENSP00000340118:I92V	I	-	1	0	LITAF	11554993	0.046000	0.20272	0.100000	0.21137	0.028000	0.11728	0.244000	0.18124	0.009000	0.14813	-0.119000	0.15052	ATC	T|0.859;C|0.141	0.141	strong		0.552	LITAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436794.2	NM_004862	
POM121	9883	hgsc.bcm.edu	37	7	72413423	72413423	+	Missense_Mutation	SNP	C	C	T	rs71554686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000358357.3_Missense_Mutation_p.P699L|POM121_ENST00000257622.4_Missense_Mutation_p.P699L|POM121_ENST00000395270.1_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						PASS	.						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	293	0	0		WXS	Illumina HiSeq	Phase_I	242	52	0.214876	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		
MATN2	4147	hgsc.bcm.edu	37	8	98943446	98943446	+	Silent	SNP	T	T	C	rs2290470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:98943446T>C	ENST00000520016.1	+	2	532	c.408T>C	c.(406-408)acT>acC	p.T136T	MATN2_ENST00000521689.1_Silent_p.T136T|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000254898.5_Silent_p.T136T|MATN2_ENST00000524308.1_Silent_p.T136T			O00339	MATN2_HUMAN	matrilin 2	136	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)			GCACCATGACTGGGCTGGCCA	0.577													G|||	2139	0.427117	0.2443	0.2896	5008	,	,		21591	0.7808		0.3419	False		,,,				2504	0.4949				p.T136T		Atlas-SNP	.											.	MATN2	165	.	0			c.T408C						PASS	.	G	,	1052,3166		160,732,1217	44.0	49.0	47.0		408,408	-11.9	0.2	8	dbSNP_100	47	2824,5676		470,1884,1896	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	630,2616,3113	CC,CT,TT		33.2235,24.9407,30.4765	,	136/957,136/938	98943446	3876,8842	2109	4250	6359	SO:0001819	synonymous_variant	4147	exon3			CATGACTGGGCTG	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.408T>C	8.37:g.98943446T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1																																																																																			C|0.399;T|0.601	0.399	strong		0.577	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
OR2A2	442361	hgsc.bcm.edu	37	7	143807515	143807515	+	Missense_Mutation	SNP	T	T	G	rs2961149	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	108	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	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		
CRLF1	9244	hgsc.bcm.edu	37	19	18710496	18710496	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18710496G>A	ENST00000392386.3	-	2	469	c.276C>T	c.(274-276)aaC>aaT	p.N92N		NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	92	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						AGGTGGAGGCGTTGAGTACAC	0.692																																					p.N92N		Atlas-SNP	.											.	CRLF1	32	.	0			c.C276T						PASS	.						24.0	23.0	23.0					19																	18710496		2200	4298	6498	SO:0001819	synonymous_variant	9244	exon2			GGAGGCGTTGAGT	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.276C>T	19.37:g.18710496G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_004750	Q9UHH5	Silent	SNP	ENST00000392386.3	37	CCDS32962.1																																																																																			.	.	none		0.692	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1		
VENTX	27287	hgsc.bcm.edu	37	10	135051562	135051562	+	Silent	SNP	A	A	G	rs2998143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:135051562A>G	ENST00000325980.9	+	1	655	c.144A>G	c.(142-144)ccA>ccG	p.P48P		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	48					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		TCCCTGGCCCAGGCCAGACAT	0.706													G|||	3991	0.796925	0.8268	0.6643	5008	,	,		12276	0.994		0.6054	False		,,,				2504	0.8446				p.P48P		Atlas-SNP	.											VENTX,NS,carcinoma,0,1	VENTX	24	1	0			c.A144G						PASS	.	G		3080,772		1299,482,145	4.0	6.0	6.0		144	-3.6	0.0	10	dbSNP_101	6	4807,3287		1548,1711,788	no	coding-synonymous	VENTX	NM_014468.2		2847,2193,933	GG,GA,AA		40.6103,20.0415,33.9779		48/259	135051562	7887,4059	1926	4047	5973	SO:0001819	synonymous_variant	27287	exon1			TGGCCCAGGCCAG	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"""Homeoboxes / ANTP class : NKL subclass"""	13639	protein-coding gene	gene with protein product		607158	"""VENT-like homeobox 2"", ""VENT homeobox homolog (Xenopus laevis)"""	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.144A>G	10.37:g.135051562A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_014468	Q32MZ3	Silent	SNP	ENST00000325980.9	37	CCDS7675.1																																																																																			A|0.248;G|0.752	0.752	strong		0.706	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733209	52733209	+	Missense_Mutation	SNP	A	A	G	rs202074278		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Missense_Mutation_p.I259T	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	147	2	0.0136054		WXS	Illumina HiSeq	Phase_I	153	4	0.0261438	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	
OR1D5	8386	hgsc.bcm.edu	37	17	2966173	2966173	+	Silent	SNP	G	G	C	rs2676565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2966173G>C	ENST00000575751.1	-	1	728	c.729C>G	c.(727-729)tcC>tcG	p.S243S		NM_014566.1	NP_055381.1	P58170	OR1D5_HUMAN	olfactory receptor, family 1, subfamily D, member 5	243					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|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(1)|lung(10)	11						CACCCAAATGGGAGGCACAGG	0.493													g|||	1334	0.266374	0.3638	0.2954	5008	,	,		29376	0.0228		0.334	False		,,,				2504	0.2955				p.S243S		Atlas-SNP	.											.	OR1D5	33	.	0			c.C729G						PASS	.						91.0	101.0	98.0					17																	2966173		2195	4300	6495	SO:0001819	synonymous_variant	8386	exon1			CAAATGGGAGGCA	AF087923	CCDS58499.1	17p13.3	2012-10-09			ENSG00000262628	ENSG00000262628		"""GPCR / Class A : Olfactory receptors"""	8186	protein-coding gene	gene with protein product						10673334	Standard	NM_014566		Approved	OR17-31	uc021tns.1	P58170	OTTHUMG00000177676	ENST00000575751.1:c.729C>G	17.37:g.2966173G>C		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	427	129	0.302108	NM_014566	Q96RA6	Silent	SNP	ENST00000575751.1	37	CCDS58499.1																																																																																			G|0.162;C|0.837	0.837	strong		0.493	OR1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438410.2	NM_014566	
RPS16	6217	hgsc.bcm.edu	37	19	39923952	39923952	+	Silent	SNP	G	G	A	rs17627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39923952G>A	ENST00000251453.3	-	5	454	c.402C>T	c.(400-402)ggC>ggT	p.G134G	RPS16_ENST00000339471.4_3'UTR|RPS16_ENST00000601655.1_Silent_p.G117G|RPS16_ENST00000599539.1_3'UTR	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	116	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	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	
UPF3A	65110	hgsc.bcm.edu	37	13	115047305	115047305	+	Missense_Mutation	SNP	G	G	A	rs3752105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115047305G>A	ENST00000375299.3	+	1	247	c.191G>A	c.(190-192)aGg>aAg	p.R64K	UPF3A_ENST00000351487.5_Missense_Mutation_p.R64K	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	64			R -> K (in dbSNP:rs3752105).		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)		GAGGAGAAGAGGACGGCCCTG	0.721													g|||	1524	0.304313	0.5416	0.17	5008	,	,		6771	0.1032		0.2584	False		,,,				2504	0.3333				p.R64K		Atlas-SNP	.											UPF3A,NS,carcinoma,0,1	UPF3A	47	1	0			c.G191A						PASS	.		LYS/ARG,LYS/ARG	1665,2487		352,961,763	6.0	7.0	6.0		191,191	0.4	0.3	13	dbSNP_107	6	1559,6677		178,1203,2737	yes	missense,missense	UPF3A	NM_023011.3,NM_080687.2	26,26	530,2164,3500	AA,AG,GG		18.9291,40.1012,26.0252	benign,benign	64/477,64/444	115047305	3224,9164	2076	4118	6194	SO:0001583	missense	65110	exon1			AGAAGAGGACGGC	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.191G>A	13.37:g.115047305G>A	ENSP00000364448:p.Arg64Lys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_080687	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Missense_Mutation	SNP	ENST00000375299.3	37	CCDS9543.1	596	0.27289377289377287	268	0.5447154471544715	69	0.19060773480662985	67	0.11713286713286714	192	0.2532981530343008	g	0.059	-1.228239	0.01518	0.401012	0.189291	ENSG00000169062	ENST00000375299;ENST00000351487	T;T	0.61980	0.06;0.06	3.1	0.383	0.16239	Regulator of nonsense-mediated decay, UPF3 (1);	0.193157	0.44902	N	0.000402	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B;B;B	0.18461	0.001;0.004;0.028	B;B;B	0.18263	0.006;0.006;0.021	T	0.45833	-0.9234	8	.	.	.	-6.5893	7.2758	0.26283	0.425:0.0:0.575:0.0	rs3752105	64;64;64	B4DGE0;Q9H1J1-2;Q9H1J1	.;.;REN3A_HUMAN	K	64	ENSP00000364448:R64K;ENSP00000329592:R64K	.	R	+	2	0	UPF3A	114065407	0.085000	0.21516	0.350000	0.25708	0.233000	0.25261	0.005000	0.13129	0.041000	0.15688	0.479000	0.44913	AGG	G|0.728;A|0.272	0.272	strong		0.721	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
SERPINA4	5267	hgsc.bcm.edu	37	14	95033356	95033356	+	Silent	SNP	C	C	T	rs5510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95033356C>T	ENST00000557004.1	+	3	1120	c.699C>T	c.(697-699)ttC>ttT	p.F233F	SERPINA4_ENST00000555095.1_Silent_p.F233F|SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Silent_p.F233F			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	233					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		CCAAAGACTTCTATGTTGATG	0.507													C|||	1505	0.300519	0.3434	0.1787	5008	,	,		20522	0.2867		0.2565	False		,,,				2504	0.3885				p.F233F		Atlas-SNP	.											.	SERPINA4	81	.	0			c.C699T						PASS	.	C		1375,3031	455.7+/-351.1	222,931,1050	112.0	103.0	106.0		699	2.6	0.4	14	dbSNP_52	106	2131,6469	366.6+/-334.4	260,1611,2429	no	coding-synonymous	SERPINA4	NM_006215.2		482,2542,3479	TT,TC,CC		24.7791,31.2074,26.9568		233/428	95033356	3506,9500	2203	4300	6503	SO:0001819	synonymous_variant	5267	exon3			AGACTTCTATGTT	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"""Serine (or cysteine) peptidase inhibitors"""	8948	protein-coding gene	gene with protein product		147935	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"""	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.699C>T	14.37:g.95033356C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	37	CCDS9927.1																																																																																			C|0.718;T|0.282	0.282	strong		0.507	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215	
HSD17B12	51144	hgsc.bcm.edu	37	11	43876698	43876698	+	Missense_Mutation	SNP	C	C	T	rs11555762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:43876698C>T	ENST00000278353.4	+	11	958	c.839C>T	c.(838-840)tCg>tTg	p.S280L	RP11-613D13.5_ENST00000530450.1_RNA	NM_016142.2	NP_057226.1	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	280			S -> L (in dbSNP:rs11555762). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)			endometrium(2)|large_intestine(4)|lung(4)	10						CCCTAGGGCTCGATAATCTCA	0.328													C|||	1798	0.359026	0.4236	0.464	5008	,	,		17419	0.256		0.3211	False		,,,				2504	0.3425				p.S280L	Ovarian(58;548 1143 13948 16572 34258)	Atlas-SNP	.											.	HSD17B12	25	.	0			c.C839T						PASS	.	C	LEU/SER	1835,2571	530.8+/-373.0	371,1093,739	113.0	115.0	114.0		839	0.4	0.0	11	dbSNP_120	114	2661,5939	427.2+/-355.5	385,1891,2024	yes	missense	HSD17B12	NM_016142.2	145	756,2984,2763	TT,TC,CC		30.9419,41.6478,34.5687	benign	280/313	43876698	4496,8510	2203	4300	6503	SO:0001583	missense	51144	exon11			AGGGCTCGATAAT	AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18646	protein-coding gene	gene with protein product	"""3-ketoacyl-CoA reductase"", ""short chain dehydrogenase/reductase family 12C, member 1"""	609574				12482854, 19027726	Standard	NM_016142		Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000278353.4:c.839C>T	11.37:g.43876698C>T	ENSP00000278353:p.Ser280Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_016142	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	Missense_Mutation	SNP	ENST00000278353.4	37	CCDS7905.1	711	0.32554945054945056	207	0.42073170731707316	162	0.44751381215469616	110	0.19230769230769232	232	0.30606860158311344	C	2.602	-0.292759	0.05568	0.416478	0.309419	ENSG00000149084	ENST00000278353	T	0.45668	0.89	5.63	0.382	0.16234	NAD(P)-binding domain (1);	1.871760	0.02473	N	0.087729	T	0.00012	0.0000	N	0.21097	0.63	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.38542	-0.9656	9	0.09590	T	0.72	2.0097	7.7993	0.29166	0.0:0.4083:0.3545:0.2373	rs11555762;rs12576296;rs52827594;rs60391800;rs11555762	280	Q53GQ0	DHB12_HUMAN	L	280	ENSP00000278353:S280L	ENSP00000278353:S280L	S	+	2	0	HSD17B12	43833274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.692000	0.25482	-0.122000	0.11766	-2.389000	0.00228	TCG	C|0.665;T|0.335	0.335	strong		0.328	HSD17B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389594.1		
B3GNT7	93010	hgsc.bcm.edu	37	2	232263127	232263127	+	Missense_Mutation	SNP	G	G	A	rs2290130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:232263127G>A	ENST00000287590.5	+	2	958	c.697G>A	c.(697-699)Gtc>Atc	p.V233I		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	233			V -> I (in dbSNP:rs2290130).		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|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)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		CTGCCCCCACGTCCCCTTCAT	0.557													G|||	1168	0.233227	0.1551	0.2378	5008	,	,		17143	0.2381		0.2833	False		,,,				2504	0.2791				p.V233I		Atlas-SNP	.											.	B3GNT7	38	.	0			c.G697A						PASS	.	G	ILE/VAL	642,3600		55,532,1534	102.0	110.0	108.0		697	3.8	0.4	2	dbSNP_100	108	2069,6407		260,1549,2429	yes	missense	B3GNT7	NM_145236.2	29	315,2081,3963	AA,AG,GG		24.4101,15.1344,21.3162	benign	233/402	232263127	2711,10007	2121	4238	6359	SO:0001583	missense	93010	exon2			CCCCACGTCCCCT	AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"""Beta 3-glycosyltransferases"""	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.697G>A	2.37:g.232263127G>A	ENSP00000287590:p.Val233Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_145236	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	519	0.23763736263736263	90	0.18292682926829268	77	0.212707182320442	132	0.23076923076923078	220	0.29023746701846964	G	13.31	2.200387	0.38905	0.151344	0.244101	ENSG00000156966	ENST00000287590	T	0.41065	1.01	4.71	3.84	0.44239	.	0.343906	0.30168	N	0.010260	T	0.00012	0.0000	L	0.52126	1.63	0.50632	P	1.1399999999994748E-4	P	0.52577	0.954	B	0.39339	0.297	T	0.30851	-0.9964	9	0.36615	T	0.2	.	10.276	0.43510	0.167:0.0:0.833:0.0	rs2290130;rs17612615;rs52793391;rs58977067;rs2290130	233	Q8NFL0	B3GN7_HUMAN	I	233	ENSP00000287590:V233I	ENSP00000287590:V233I	V	+	1	0	B3GNT7	231971371	1.000000	0.71417	0.374000	0.26016	0.925000	0.55904	4.133000	0.57983	0.988000	0.38734	0.655000	0.94253	GTC	G|0.763;A|0.237	0.237	strong		0.557	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236	
ZFP28	140612	hgsc.bcm.edu	37	19	57058998	57058998	+	Missense_Mutation	SNP	C	C	G	rs34136271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57058998C>G	ENST00000301318.3	+	3	493	c.422C>G	c.(421-423)tCg>tGg	p.S141W	ZFP28_ENST00000591844.1_Missense_Mutation_p.S141W|AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	141	KRAB 1. {ECO:0000255|PROSITE- ProRule:PRU00119}.		S -> W (in dbSNP:rs34136271).		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(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		AACCTGGCATCGCTGGGTAAG	0.552													C|||	583	0.116414	0.0567	0.1441	5008	,	,		16068	0.0675		0.1779	False		,,,				2504	0.1646				p.S141W	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C422G						PASS	.	C	TRP/SER	346,4060	180.1+/-208.5	15,316,1872	113.0	105.0	108.0		422	1.6	0.0	19	dbSNP_126	108	1625,6975	300.9+/-305.2	142,1341,2817	yes	missense	ZFP28	NM_020828.1	177	157,1657,4689	GG,GC,CC		18.8953,7.8529,15.1545	probably-damaging	141/869	57058998	1971,11035	2203	4300	6503	SO:0001583	missense	140612	exon3			TGGCATCGCTGGG		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.422C>G	19.37:g.57058998C>G	ENSP00000301318:p.Ser141Trp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	269	0.12316849816849818	26	0.052845528455284556	65	0.17955801104972377	45	0.07867132867132867	133	0.17546174142480211	C	15.08	2.726692	0.48833	0.078529	0.188953	ENSG00000196867	ENST00000301318	T	0.03386	3.95	3.8	1.65	0.23941	Krueppel-associated box (4);	0.000000	0.32593	N	0.005896	T	0.00012	0.0000	M	0.79123	2.44	0.58432	P	5.000000000032756E-6	D	0.61697	0.99	D	0.64237	0.923	T	0.11036	-1.0604	9	0.66056	D	0.02	.	7.8272	0.29322	0.0:0.8098:0.0:0.1902	rs34136271	141	Q8NHY6	ZFP28_HUMAN	W	141	ENSP00000301318:S141W	ENSP00000301318:S141W	S	+	2	0	ZFP28	61750810	0.069000	0.21087	0.005000	0.12908	0.481000	0.33189	1.402000	0.34600	0.403000	0.25479	-1.008000	0.02478	TCG	C|0.859;G|0.141	0.141	strong		0.552	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
SESTD1	91404	hgsc.bcm.edu	37	2	179986553	179986553	+	Silent	SNP	T	T	C	rs56336305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179986553T>C	ENST00000428443.3	-	13	1702	c.1386A>G	c.(1384-1386)aaA>aaG	p.K462K		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	462							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|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)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			CCACATTTTCTTTATTTTCAA	0.383													T|||	56	0.0111821	0.0	0.0159	5008	,	,		17677	0.0		0.0278	False		,,,				2504	0.0174				p.K462K		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1386G						PASS	.	T		25,4381	32.6+/-62.9	0,25,2178	110.0	105.0	107.0		1386	2.8	1.0	2	dbSNP_129	107	198,8402	86.9+/-149.2	0,198,4102	no	coding-synonymous	SESTD1	NM_178123.4		0,223,6280	CC,CT,TT		2.3023,0.5674,1.7146		462/697	179986553	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon13			ATTTTCTTTATTT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1386A>G	2.37:g.179986553T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.982;C|0.018	0.018	strong		0.383	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44630768	44630768	+	Missense_Mutation	SNP	A	A	G	rs200445221		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:44630768A>G	ENST00000576629.1	+	12	5307	c.4812A>G	c.(4810-4812)atA>atG	p.I1604M	ARL17A_ENST00000329240.4_Intron|ARL17A_ENST00000570550.1_Intron|ARL17A_ENST00000337845.7_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.I1604M|ARL17A_ENST00000573185.1_Intron|ARL17A_ENST00000445552.2_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1604						integral component of membrane (GO:0016021)		p.I1604M(2)		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)		TAAAACAGATATGTTGTCACC	0.338																																					p.I1604M		Atlas-SNP	.											LRRC37A2,NS,carcinoma,0,2	LRRC37A2	37	2	2	Substitution - Missense(2)	prostate(2)	c.A4812G						scavenged	.						66.0	120.0	102.0					17																	44630768		2198	4293	6491	SO:0001583	missense	474170	exon11			ACAGATATGTTGT	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.4812A>G	17.37:g.44630768A>G	ENSP00000459551:p.Ile1604Met	Somatic	1504	14	0.00930851		WXS	Illumina HiSeq	Phase_I	606	7	0.0115512	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	a	11.80	1.747925	0.30955	.	.	ENSG00000238083	ENST00000333412	T	0.53857	0.6	2.45	1.28	0.21552	.	.	.	.	.	T	0.60792	0.2296	L	0.53249	1.67	0.20307	N	0.999911	D;D	0.89917	1.0;0.997	D;D	0.80764	0.994;0.916	T	0.48958	-0.8988	9	0.87932	D	0	.	3.1223	0.06395	0.2434:0.0:0.2508:0.5058	.	565;1604	B3KRJ4;A6NM11	.;L37A2_HUMAN	M	1604	ENSP00000333071:I1604M	ENSP00000333071:I1604M	I	+	3	3	LRRC37A2	41986084	0.009000	0.17119	0.240000	0.24138	0.009000	0.06853	-0.890000	0.04140	-0.033000	0.13736	-1.974000	0.00461	ATA	.	.	alt		0.338	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
TTI2	80185	hgsc.bcm.edu	37	8	33369944	33369944	+	Missense_Mutation	SNP	T	T	C	rs2304748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:33369944T>C	ENST00000431156.2	-	2	806	c.188A>G	c.(187-189)gAa>gGa	p.E63G	TTI2_ENST00000519356.1_5'Flank|SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000520636.1_Missense_Mutation_p.E63G|TTI2_ENST00000360742.5_Missense_Mutation_p.E63G	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	63			E -> G (in dbSNP:rs2304748). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.														CCTATCAAATTCTGTGGCTTC	0.527													T|||	2538	0.506789	0.4463	0.4654	5008	,	,		16481	0.5556		0.6252	False		,,,				2504	0.4458				p.E63G		Atlas-SNP	.											C8orf41,NS,carcinoma,-1,1	.	.	1	0			c.A188G						PASS	.	T	GLY/GLU,GLY/GLU	2032,2374	563.2+/-381.1	479,1074,650	71.0	74.0	73.0		188,188	3.3	0.0	8	dbSNP_100	73	5312,3288	643.2+/-399.9	1639,2034,627	yes	missense,missense	TTI2	NM_001102401.1,NM_025115.2	98,98	2118,3108,1277	CC,CT,TT		38.2326,46.1189,43.5338	benign,benign	63/509,63/509	33369944	7344,5662	2203	4300	6503	SO:0001583	missense	80185	exon2			TCAAATTCTGTGG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.188A>G	8.37:g.33369944T>C	ENSP00000411169:p.Glu63Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	1176	0.5384615384615384	220	0.44715447154471544	171	0.4723756906077348	319	0.5576923076923077	466	0.6147757255936676	T	14.07	2.425243	0.43020	0.461189	0.617674	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397;ENST00000523305	T;T;T;T	0.59772	0.26;0.26;0.24;0.6	4.53	3.34	0.38264	.	0.258590	0.29822	N	0.011110	T	0.00012	0.0000	M	0.76838	2.35	0.58432	P	1.0000000000287557E-6	P;B;B	0.39809	0.689;0.437;0.437	B;B;B	0.34590	0.186;0.115;0.115	T	0.45977	-0.9224	9	0.52906	T	0.07	-14.6433	8.882	0.35380	0.0:0.0:0.1894:0.8106	rs2304748;rs17845116;rs17857909;rs52822961;rs59743233;rs2304748	63;63;63	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	G	63	ENSP00000353971:E63G;ENSP00000411169:E63G;ENSP00000428401:E63G;ENSP00000428569:E63G	ENSP00000353971:E63G	E	-	2	0	C8orf41	33489486	0.126000	0.22350	0.010000	0.14722	0.011000	0.07611	0.768000	0.26590	0.735000	0.32537	0.533000	0.62120	GAA	C|0.548;N|0.000	0.548	strong		0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
SIRT1	23411	hgsc.bcm.edu	37	10	69644820	69644820	+	Missense_Mutation	SNP	C	C	A	rs182199697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69644820C>A	ENST00000212015.6	+	1	394	c.341C>A	c.(340-342)cCa>cAa	p.P114Q	SIRT1_ENST00000432464.1_5'Flank	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	114	Interaction with CLOCK. {ECO:0000250|UniProtKB:Q923E4}.|Interaction with HIST1H1E.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						TCTCGGGAGCCACCGCTGGCC	0.721													C|||	8	0.00159744	0.0	0.0043	5008	,	,		9467	0.0		0.005	False		,,,				2504	0.0				p.P114Q		Atlas-SNP	.											.	SIRT1	38	.	0			c.C341A						PASS	.	C	GLN/PRO	3,3319		0,3,1658	3.0	4.0	4.0		341	3.0	0.9	10		4	24,6694		0,24,3335	yes	missense	SIRT1	NM_012238.4	76	0,27,4993	AA,AC,CC		0.3572,0.0903,0.2689	benign	114/748	69644820	27,10013	1661	3359	5020	SO:0001583	missense	23411	exon1			GGGAGCCACCGCT	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.341C>A	10.37:g.69644820C>A	ENSP00000212015:p.Pro114Gln	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	43	27	0.627907	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1	23	0.010531135531135532	11	0.022357723577235773	4	0.011049723756906077	0	0.0	8	0.010554089709762533	c	9.153	1.016794	0.19355	9.03E-4	0.003572	ENSG00000096717	ENST00000212015	T	0.36157	1.27	3.91	3.0	0.34707	.	1.246700	0.05789	N	0.609970	T	0.18718	0.0449	L	0.44542	1.39	0.80722	D	1	P	0.36733	0.567	B	0.37387	0.248	T	0.03000	-1.1084	10	0.35671	T	0.21	0.1106	7.5885	0.28006	0.0:0.8736:0.0:0.1264	.	114	Q96EB6	SIRT1_HUMAN	Q	114	ENSP00000212015:P114Q	ENSP00000212015:P114Q	P	+	2	0	SIRT1	69314826	0.994000	0.37717	0.940000	0.37924	0.069000	0.16628	0.498000	0.22530	0.746000	0.32786	0.556000	0.70494	CCA	C|0.989;A|0.011	0.011	strong		0.721	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
OXA1L	5018	hgsc.bcm.edu	37	14	23235808	23235808	+	Silent	SNP	G	G	A	rs1957374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23235808G>A	ENST00000285848.5	+	1	78	c.78G>A	c.(76-78)ctG>ctA	p.L26L	OXA1L_ENST00000604262.1_5'Flank|CTD-2555K7.2_ENST00000553792.1_RNA|CTD-2555K7.2_ENST00000554857.1_RNA|OXA1L_ENST00000358043.5_5'Flank|CTD-2555K7.2_ENST00000554730.1_RNA|OXA1L_ENST00000412791.1_5'Flank	NM_005015.3	NP_005006.3	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	0					aerobic respiration (GO:0009060)|mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex I biogenesis (GO:0097031)|negative regulation of ATPase activity (GO:0032780)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|protein complex assembly (GO:0006461)|protein insertion into membrane (GO:0051205)|protein tetramerization (GO:0051262)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	mitochondrial ribosome binding (GO:0097177)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|skin(2)	19	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		CGCCTGATCTGCGGCTACAAT	0.522													G|||	1969	0.393171	0.0507	0.5965	5008	,	,		19117	0.6776		0.4662	False		,,,				2504	0.3436				p.L26L		Atlas-SNP	.											.	OXA1L	49	.	0			c.G78A						PASS	.	G		545,3861	246.8+/-255.3	32,481,1690	112.0	119.0	117.0		78	-3.8	0.0	14	dbSNP_92	117	3856,4744	542.3+/-384.2	860,2136,1304	no	coding-synonymous	OXA1L	NM_005015.3		892,2617,2994	AA,AG,GG		44.8372,12.3695,33.8382		26/496	23235808	4401,8605	2203	4300	6503	SO:0001819	synonymous_variant	5018	exon1			TGATCTGCGGCTA		CCDS9573.1	14q11.2	2009-05-26			ENSG00000155463	ENSG00000155463			8526	protein-coding gene	gene with protein product		601066				8586451, 19349278	Standard	NM_005015		Approved	MGC133129, OXA1	uc001wgn.2	Q15070	OTTHUMG00000028691	ENST00000285848.5:c.78G>A	14.37:g.23235808G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_005015	B4DPA2	Silent	SNP	ENST00000285848.5	37	CCDS9573.1																																																																																			G|0.629;A|0.371	0.371	strong		0.522	OXA1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071630.2	NM_005015	
TYW3	127253	hgsc.bcm.edu	37	1	75214441	75214441	+	Missense_Mutation	SNP	A	A	G	rs1133891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:75214441A>G	ENST00000370867.3	+	4	450	c.361A>G	c.(361-363)Atg>Gtg	p.M121V	TYW3_ENST00000479111.1_Start_Codon_SNP_p.M1V|TYW3_ENST00000421739.2_Intron|TYW3_ENST00000457880.2_Missense_Mutation_p.M88V	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	121			M -> V (in dbSNP:rs1133891). {ECO:0000269|PubMed:14702039}.		tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						ACAGCATTCCATGGCAATAGA	0.348													A|||	1799	0.359225	0.2496	0.317	5008	,	,		18562	0.7063		0.1262	False		,,,				2504	0.4192				p.M121V		Atlas-SNP	.											.	TYW3	36	.	0			c.A361G						PASS	.	A	VAL/MET,VAL/MET	987,3419	369.8+/-319.3	108,771,1324	109.0	110.0	110.0		262,361	5.0	1.0	1	dbSNP_86	110	962,7638	209.0+/-250.3	49,864,3387	yes	missense,missense	TYW3	NM_001162916.1,NM_138467.2	21,21	157,1635,4711	GG,GA,AA		11.186,22.4013,14.9854	benign,benign	88/227,121/260	75214441	1949,11057	2203	4300	6503	SO:0001583	missense	127253	exon4			CATTCCATGGCAA	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"""chromosome 1 open reading frame 171"""	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.361A>G	1.37:g.75214441A>G	ENSP00000359904:p.Met121Val	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	211	82	0.388626	NM_138467	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	37	CCDS666.1	717	0.3282967032967033	110	0.22357723577235772	99	0.27348066298342544	402	0.7027972027972028	106	0.13984168865435356	A	0.319	-0.962859	0.02249	0.224013	0.11186	ENSG00000162623	ENST00000457880;ENST00000370867	T;T	0.24723	1.84;1.84	5.94	5.03	0.67393	tRNA wybutosine-synthesizing protein (2);	0.105878	0.64402	N	0.000005	T	0.01421	0.0046	N	0.00086	-2.195	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40117	-0.9580	9	0.02654	T	1	-5.3508	14.4234	0.67200	0.072:0.0:0.928:0.0	rs11538280	88;121	E9PGR7;Q6IPR3	.;TYW3_HUMAN	V	88;121	ENSP00000407025:M88V;ENSP00000359904:M121V	ENSP00000359904:M121V	M	+	1	0	TYW3	74987029	1.000000	0.71417	0.997000	0.53966	0.248000	0.25809	5.631000	0.67812	1.528000	0.49103	-0.252000	0.11476	ATG	A|0.763;G|0.237	0.237	strong		0.348	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467	
FLG	2312	hgsc.bcm.edu	37	1	152279841	152279841	+	Missense_Mutation	SNP	G	G	C	rs3126074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152279841G>C	ENST00000368799.1	-	3	7556	c.7521C>G	c.(7519-7521)caC>caG	p.H2507Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2507	Ser-rich.		H -> Q (in dbSNP:rs3126074).		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)			TGGATCCTGAGTGCCCATGGG	0.552									Ichthyosis				C|||	2315	0.46226	0.5189	0.451	5008	,	,		20836	0.6548		0.172	False		,,,				2504	0.4939				p.H2507Q		Atlas-SNP	.											.	FLG	900	.	0			c.C7521G						PASS	.	C	GLN/HIS	2053,2353	607.9+/-391.1	471,1111,621	342.0	327.0	332.0		7521	-4.9	0.0	1	dbSNP_103	332	1456,7144	750.9+/-407.4	126,1204,2970	no	missense	FLG	NM_002016.1	24	597,2315,3591	CC,CG,GG		16.9302,46.5956,26.9799	benign	2507/4062	152279841	3509,9497	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCTGAGTGCCCA	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.7521C>G	1.37:g.152279841G>C	ENSP00000357789:p.His2507Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	246	172	0.699187	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	865	0.39606227106227104	239	0.48577235772357724	136	0.3756906077348066	358	0.6258741258741258	132	0.1741424802110818	C	2.091	-0.408310	0.04832	0.465956	0.169302	ENSG00000143631	ENST00000368799	T	0.04015	3.73	2.43	-4.87	0.03123	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43814	-0.9368	8	0.11794	T	0.64	.	8.373	0.32425	0.1409:0.2981:0.5611:0.0	rs3126074	2507	P20930	FILA_HUMAN	Q	2507	ENSP00000357789:H2507Q	ENSP00000357789:H2507Q	H	-	3	2	FLG	150546465	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-7.955000	0.00027	-1.444000	0.01950	-2.178000	0.00318	CAC	G|0.693;C|0.307	0.307	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CD6	923	hgsc.bcm.edu	37	11	60776209	60776209	+	Missense_Mutation	SNP	C	C	T	rs11230563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60776209C>T	ENST00000313421.7	+	4	859	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	CD6_ENST00000344028.5_Missense_Mutation_p.R225W|CD6_ENST00000352009.5_Missense_Mutation_p.R225W|CD6_ENST00000545105.1_Intron|CD6_ENST00000346437.4_Missense_Mutation_p.R225W|CD6_ENST00000452451.2_Missense_Mutation_p.R225W	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	225	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		R -> W (in dbSNP:rs11230563).		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GCCTATCCACCGGGACCAGGT	0.711													C|||	1754	0.35024	0.612	0.2968	5008	,	,		13804	0.1706		0.3579	False		,,,				2504	0.2117				p.R225W	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C673T						PASS	.	C	TRP/ARG	2381,2019		684,1013,503	17.0	18.0	18.0		673	1.2	0.4	11	dbSNP_120	18	2855,5731		483,1889,1921	yes	missense	CD6	NM_006725.3	101	1167,2902,2424	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	33.2518,45.8864,40.3203	benign	225/669	60776209	5236,7750	2200	4293	6493	SO:0001583	missense	923	exon4			ATCCACCGGGACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.673C>T	11.37:g.60776209C>T	ENSP00000323280:p.Arg225Trp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	763	0.34935897435897434	288	0.5853658536585366	126	0.34806629834254144	92	0.16083916083916083	257	0.3390501319261214	C	11.21	1.572893	0.28092	0.541136	0.332518	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34	4.21	1.17	0.20885	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.340153	0.20669	N	0.087870	T	0.00012	0.0000	N	0.16478	0.41	0.37772	P	0.07327799999999995	B;P;B;B;B	0.38642	0.434;0.641;0.173;0.371;0.443	B;B;B;B;B	0.32533	0.087;0.109;0.055;0.133;0.147	T	0.41431	-0.9509	9	0.59425	D	0.04	.	4.6963	0.12806	0.1512:0.6004:0.0:0.2484	rs11230563;rs57136002;rs11230563	225;225;225;225;225	E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.;.;.;CD6_HUMAN;.	W	225	ENSP00000344108:R225W;ENSP00000345566:R225W;ENSP00000323280:R225W;ENSP00000440055:R225W;ENSP00000410638:R225W;ENSP00000390676:R225W;ENSP00000340628:R225W	ENSP00000323280:R225W	R	+	1	2	CD6	60532785	0.439000	0.25610	0.353000	0.25747	0.098000	0.18820	1.031000	0.30165	0.412000	0.25729	0.655000	0.94253	CGG	C|0.622;T|0.378	0.378	strong		0.711	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
SRCIN1	80725	hgsc.bcm.edu	37	17	36704829	36704829	+	Silent	SNP	G	G	A	rs56321748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:36704829G>A	ENST00000264659.7	-	17	3458	c.3234C>T	c.(3232-3234)gaC>gaT	p.D1078D	SRCIN1_ENST00000398579.4_5'UTR|SRCIN1_ENST00000578925.1_Silent_p.D1112D	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	950					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CGTCATCCTCGTCCTTGATGG	0.667													G|||	541	0.108027	0.0477	0.062	5008	,	,		15350	0.1429		0.1402	False		,,,				2504	0.1534				p.D1078D		Atlas-SNP	.											.	SRCIN1	66	.	0			c.C3234T						PASS	.	G		232,3976		4,224,1876	82.0	86.0	85.0		3234	-5.2	1.0	17	dbSNP_129	85	1107,7313		66,975,3169	no	coding-synonymous	SRCIN1	NM_025248.2		70,1199,5045	AA,AG,GG		13.1473,5.5133,10.6034		1078/1184	36704829	1339,11289	2104	4210	6314	SO:0001819	synonymous_variant	80725	exon17			ATCCTCGTCCTTG		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.3234C>T	17.37:g.36704829G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_025248	Q75T46|Q8N4W8	Silent	SNP	ENST00000264659.7	37	CCDS45660.1																																																																																			G|0.883;A|0.117	0.117	strong		0.667	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
ATP2C2	9914	hgsc.bcm.edu	37	16	84476200	84476200	+	Missense_Mutation	SNP	A	A	T	rs247897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84476200A>T	ENST00000262429.4	+	15	1485	c.1396A>T	c.(1396-1398)Atg>Ttg	p.M466L	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Missense_Mutation_p.M466L	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	466			M -> L (in dbSNP:rs247897). {ECO:0000269|PubMed:14702039}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						GGCCCTGGCGATGAAGGTAGG	0.582													A|||	2044	0.408147	0.4713	0.3401	5008	,	,		15905	0.4226		0.3499	False		,,,				2504	0.4162				p.M466L		Atlas-SNP	.											.	ATP2C2	75	.	0			c.A1396T						PASS	.	A	LEU/MET	1590,2186		322,946,620	112.0	117.0	115.0		1396	3.8	0.9	16	dbSNP_79	115	3082,5134		589,1904,1615	yes	missense	ATP2C2	NM_014861.2	15	911,2850,2235	TT,TA,AA		37.5122,42.1081,38.9593	benign	466/947	84476200	4672,7320	1888	4108	5996	SO:0001583	missense	9914	exon15			CTGGCGATGAAGG	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1396A>T	16.37:g.84476200A>T	ENSP00000262429:p.Met466Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	879	0.4024725274725275	252	0.5121951219512195	129	0.356353591160221	235	0.41083916083916083	263	0.3469656992084433	A	10.78	1.446866	0.25987	0.421081	0.375122	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	D;D	0.95342	-3.68;-3.68	4.92	3.8	0.43715	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.057448	0.64402	D	0.000001	T	0.00012	0.0000	N	0.11154	0.105	0.23010	P	0.99843986	B;B;B;B	0.27910	0.043;0.022;0.034;0.193	B;B;B;B	0.32533	0.102;0.051;0.091;0.147	T	0.29088	-1.0023	9	0.25751	T	0.34	.	11.1725	0.48579	0.8452:0.1548:0.0:0.0	rs247897;rs497275;rs56485429;rs57635635;rs247897	466;315;483;466	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	L	466;466;315	ENSP00000397925:M466L;ENSP00000262429:M466L	ENSP00000262429:M466L	M	+	1	0	ATP2C2	83033701	1.000000	0.71417	0.883000	0.34634	0.277000	0.26821	6.632000	0.74281	0.794000	0.33899	0.402000	0.26972	ATG	A|0.597;T|0.403	0.403	strong		0.582	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
ITGA2	3673	hgsc.bcm.edu	37	5	52351413	52351413	+	Silent	SNP	G	G	A	rs1062535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	88	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	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	
BMS1	9790	hgsc.bcm.edu	37	10	43292647	43292647	+	Missense_Mutation	SNP	A	A	G	rs787795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:43292647A>G	ENST00000374518.5	+	10	2018	c.1955A>G	c.(1954-1956)aAg>aGg	p.K652R		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	652			K -> R (in dbSNP:rs787795).		ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAAGATTACAAGGAAGAAAAT	0.393													A|||	904	0.180511	0.1725	0.2392	5008	,	,		20648	0.1835		0.1571	False		,,,				2504	0.1708				p.K652R		Atlas-SNP	.											.	BMS1	132	.	0			c.A1955G						PASS	.	A	ARG/LYS	724,3566		68,588,1489	39.0	40.0	40.0		1955	2.6	1.0	10	dbSNP_86	40	1381,7161		131,1119,3021	yes	missense	BMS1	NM_014753.3	26	199,1707,4510	GG,GA,AA		16.1672,16.8765,16.4043	benign	652/1283	43292647	2105,10727	2145	4271	6416	SO:0001583	missense	9790	exon10			ATTACAAGGAAGA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.1955A>G	10.37:g.43292647A>G	ENSP00000363642:p.Lys652Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	385	0.1762820512820513	79	0.16056910569105692	72	0.19889502762430938	115	0.20104895104895104	119	0.15699208443271767	A	8.696	0.908575	0.17833	0.168765	0.161672	ENSG00000165733	ENST00000374518	T	0.26518	1.73	5.02	2.61	0.31194	.	0.519373	0.19428	N	0.114529	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.30387	-0.9980	9	0.18276	T	0.48	.	7.5141	0.27590	0.7816:0.1438:0.0747:0.0	rs787795;rs3740330;rs52813958;rs60228399;rs787795	652	Q14692	BMS1_HUMAN	R	652	ENSP00000363642:K652R	ENSP00000363642:K652R	K	+	2	0	BMS1	42612653	0.985000	0.35326	0.988000	0.46212	0.817000	0.46193	1.212000	0.32394	0.851000	0.35264	0.519000	0.50382	AAG	A|0.810;C|0.002	.	strong		0.393	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
ANO8	57719	hgsc.bcm.edu	37	19	17435851	17435851	+	Silent	SNP	G	G	T	rs755124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17435851G>T	ENST00000159087.4	-	17	3164	c.3006C>A	c.(3004-3006)gcC>gcA	p.A1002A		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1002					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)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						TGGTGGCTCCGGCCCCTGCAG	0.632													G|||	224	0.0447284	0.0371	0.0519	5008	,	,		13390	0.001		0.1054	False		,,,				2504	0.0327				p.A1002A		Atlas-SNP	.											.	ANO8	67	.	0			c.C3006A						PASS	.	G		178,4226		4,170,2028	56.0	69.0	65.0		3006	-7.7	0.0	19	dbSNP_86	65	917,7681		56,805,3438	no	coding-synonymous	ANO8	NM_020959.2		60,975,5466	TT,TG,GG		10.6653,4.0418,8.4218		1002/1233	17435851	1095,11907	2202	4299	6501	SO:0001819	synonymous_variant	57719	exon17			GGCTCCGGCCCCT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.3006C>A	19.37:g.17435851G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	37	CCDS32949.1																																																																																			G|0.933;T|0.067	0.067	strong		0.632	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
MAPT	4137	hgsc.bcm.edu	37	17	44067382	44067382	+	Missense_Mutation	SNP	T	T	C	rs2258689	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:44067382T>C	ENST00000571987.1	+	7	1321	c.1321T>C	c.(1321-1323)Tac>Cac	p.Y441H	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.Y441H|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.Y441H|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.Y441H|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	441			Y -> H (in dbSNP:rs2258689). {ECO:0000269|PubMed:1420178, ECO:0000269|PubMed:15365985, 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)	p.H441Y(1)|p.Y441H(1)		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)	CTCTCCTAAATACGTCTCTTC	0.542													T|||	1567	0.312899	0.146	0.2867	5008	,	,		17087	0.628		0.2117	False		,,,				2504	0.3364				p.Y441H		Atlas-SNP	.											MAPT_ENST00000344290,NS,adenoma,-2,3	MAPT	135	3	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.T1321C						PASS	.	T	HIS/TYR,,,,,,HIS/TYR,	651,3755	278.7+/-274.4	39,573,1591	160.0	161.0	161.0		1321,,,,,,1321,	1.8	1.0	17	dbSNP_100	161	1707,6893	312.9+/-311.0	174,1359,2767	no	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	83,,,,,,83,	213,1932,4358	CC,CT,TT		19.8488,14.7753,18.1301	benign,,,,,,benign,	441/777,,,,,,441/759,	44067382	2358,10648	2203	4300	6503	SO:0001583	missense	4137	exon8			CCTAAATACGTCT	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.1321T>C	17.37:g.44067382T>C	ENSP00000458742:p.Tyr441His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	707	0.32371794871794873	66	0.13414634146341464	112	0.30939226519337015	359	0.6276223776223776	170	0.22427440633245382	T	4.814	0.151267	0.09185	0.147753	0.198488	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.28069	1.63;1.63;1.63	4.96	1.82	0.25136	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999784324	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.35574	-0.9783	8	0.31617	T	0.26	-2.8969	6.8926	0.24238	0.0:0.7086:0.0:0.2914	rs2258689;rs17572963;rs52834697;rs59032677;rs2258689	441;441	P10636-9;P10636	.;TAU_HUMAN	H	441	ENSP00000340820:Y441H;ENSP00000262410:Y441H;ENSP00000410838:Y441H	ENSP00000262410:Y441H	Y	+	1	0	MAPT	41423219	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.139000	0.31504	0.254000	0.21573	-0.415000	0.06103	TAC	A|0.134;C|0.198	0.198	strong		0.542	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
DSG1	1828	hgsc.bcm.edu	37	18	28898294	28898294	+	Missense_Mutation	SNP	A	A	G	rs1426310	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:28898294A>G	ENST00000257192.4	+	1	243	c.31A>G	c.(31-33)Atg>Gtg	p.M11V		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	11			M -> V (in dbSNP:rs1426310). {ECO:0000269|PubMed:1711210, ECO:0000269|PubMed:1770008}.		apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			AGTAGTTGCAATGCTGTTCAT	0.383													G|||	1816	0.36262	0.4349	0.2997	5008	,	,		19378	0.0694		0.4911	False		,,,				2504	0.4796				p.M11V		Atlas-SNP	.											.	DSG1	176	.	0			c.A31G						PASS	.	G	VAL/MET	2051,2355	608.7+/-391.2	475,1101,627	190.0	169.0	176.0		31	4.3	0.1	18	dbSNP_88	176	4191,4409	585.3+/-391.9	1010,2171,1119	yes	missense	DSG1	NM_001942.2	21	1485,3272,1746	GG,GA,AA		48.7326,46.5502,47.9932	benign	11/1050	28898294	6242,6764	2203	4300	6503	SO:0001583	missense	1828	exon1			GTTGCAATGCTGT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.31A>G	18.37:g.28898294A>G	ENSP00000257192:p.Met11Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	85	27	0.317647	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	755	0.3456959706959707	214	0.4349593495934959	125	0.3453038674033149	37	0.06468531468531469	379	0.5	G	2.884	-0.231213	0.05983	0.465502	0.487326	ENSG00000134760	ENST00000257192	T	0.54071	0.59	6.16	4.32	0.51571	.	0.683152	0.13353	N	0.394257	T	0.00012	0.0000	N	0.00538	-1.39	0.29189	P	0.876017	B	0.02656	0.0	B	0.01281	0.0	T	0.46442	-0.9191	9	0.06891	T	0.86	.	6.0664	0.19866	0.0691:0.2287:0.5715:0.1307	rs1426310;rs58912989;rs1426310	11	Q02413	DSG1_HUMAN	V	11	ENSP00000257192:M11V	ENSP00000257192:M11V	M	+	1	0	DSG1	27152292	0.767000	0.28508	0.081000	0.20488	0.895000	0.52256	1.404000	0.34623	0.446000	0.26666	-0.128000	0.14901	ATG	A|0.579;G|0.421	0.421	strong		0.383	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629891	32629891	+	Missense_Mutation	SNP	C	C	T	rs386699585|rs1063323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629891C>T	ENST00000399082.3	-	2	288	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.A172T			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	172	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACAACGCCGGCTGTCTCCTCC	0.547									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1979	0.395168	0.3154	0.5447	5008	,	,		15401	0.4782		0.3946	False		,,,				2504	0.3119				p.A172T	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,colon,carcinoma,+1,1	HLA-DQB1	15	1	0			c.G514A						PASS	.	T	THR/ALA	1264,3120		198,868,1126	45.0	47.0	47.0		514	1.8	0.0	6	dbSNP_86	47	3012,5578		578,1856,1861	no	missense	HLA-DQB1	NM_002123.4	58	776,2724,2987	TT,TC,CC		35.064,28.8321,32.9582	benign	172/262	32629891	4276,8698	2192	4295	6487	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CGCCGGCTGTCTC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.244G>A	6.37:g.32629891C>T	ENSP00000382032:p.Ala82Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		927	0.42445054945054944	152	0.3089430894308943	189	0.5220994475138122	281	0.49125874125874125	305	0.4023746701846966	.	0.892	-0.725235	0.03158	0.288321	0.35064	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02812	4.15;4.15;4.15;4.15;4.15	4.52	1.78	0.24846	.	0.459394	0.20863	N	0.084310	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	B;B;B;B	0.13594	0.002;0.001;0.008;0.0	B;B;B;B	0.12837	0.003;0.003;0.008;0.003	T	0.48969	-0.8987	8	0.31617	T	0.26	.	8.6058	0.33773	0.0:0.7426:0.0:0.2574	rs1063323;rs3204390;rs9280014;rs17840143;rs28724256;rs34109183	172;137;172;172	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	T	82;172;172;172;172;108	ENSP00000382032:A82T;ENSP00000382029:A172T;ENSP00000364080:A172T;ENSP00000407332:A172T;ENSP00000382034:A172T	ENSP00000364080:A172T	A	-	1	0	HLA-DQB1	32737869	0.000000	0.05858	0.034000	0.17996	0.001000	0.01503	0.431000	0.21444	0.057000	0.16193	-1.922000	0.00515	GCC	C|0.587;T|0.413	0.413	strong		0.547	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
DND1	373863	hgsc.bcm.edu	37	5	140052271	140052271	+	Silent	SNP	A	A	G	rs2563333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140052271A>G	ENST00000542735.1	-	3	406	c.363T>C	c.(361-363)caT>caC	p.H121H		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	121	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)			GCCGCAGCGGATGGTTGTGCA	0.701													G|||	2562	0.511581	0.6989	0.415	5008	,	,		11028	0.4524		0.4493	False		,,,				2504	0.4519				p.H121H		Atlas-SNP	.											.	DND1	15	.	0			c.T363C						PASS	.						5.0	7.0	6.0					5																	140052271		2040	4039	6079	SO:0001819	synonymous_variant	373863	exon3			CAGCGGATGGTTG	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.363T>C	5.37:g.140052271A>G		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			A|0.513;G|0.487	0.487	strong		0.701	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
TTC27	55622	hgsc.bcm.edu	37	2	32961858	32961858	+	Missense_Mutation	SNP	A	A	G	rs2273660	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	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	
TOPBP1	11073	hgsc.bcm.edu	37	3	133356790	133356790	+	Missense_Mutation	SNP	G	G	A	rs17301766	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133356790G>A	ENST00000260810.5	-	14	2581	c.2450C>T	c.(2449-2451)tCg>tTg	p.S817L		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	817			S -> L (in dbSNP:rs17301766).		cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CAGGTGTAACGAGGGCTCCTT	0.498								Other conserved DNA damage response genes					G|||	406	0.0810703	0.0681	0.121	5008	,	,		19159	0.001		0.1829	False		,,,				2504	0.0481				p.S817L	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.C2450T						PASS	.	G	LEU/SER	293,3721		9,275,1723	209.0	214.0	212.0		2450	5.2	0.7	3	dbSNP_123	212	1628,6724		173,1282,2721	yes	missense	TOPBP1	NM_007027.3	145	182,1557,4444	AA,AG,GG		19.4923,7.2995,15.5345	possibly-damaging	817/1523	133356790	1921,10445	2007	4176	6183	SO:0001583	missense	11073	exon14			TGTAACGAGGGCT	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.2450C>T	3.37:g.133356790G>A	ENSP00000260810:p.Ser817Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	134	37	0.276119	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	228	0.1043956043956044	36	0.07317073170731707	52	0.143646408839779	1	0.0017482517482517483	139	0.18337730870712401	G	16.89	3.246578	0.59103	0.072995	0.194923	ENSG00000163781	ENST00000260810	T	0.21191	2.02	6.03	5.16	0.70880	.	0.281133	0.35207	N	0.003379	T	0.00039	0.0001	L	0.48362	1.52	0.22684	P	0.99885029	B	0.32467	0.372	B	0.23150	0.044	T	0.14420	-1.0473	9	0.46703	T	0.11	.	15.2571	0.73593	0.0668:0.0:0.9332:0.0	rs17301766;rs52819963;rs17301766	817	Q92547	TOPB1_HUMAN	L	817	ENSP00000260810:S817L	ENSP00000260810:S817L	S	-	2	0	TOPBP1	134839480	1.000000	0.71417	0.656000	0.29637	0.910000	0.53928	5.412000	0.66392	1.559000	0.49555	0.655000	0.94253	TCG	G|0.890;A|0.110	0.110	strong		0.498	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110534512	110534512	+	Silent	SNP	G	G	A	rs1563578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:110534512G>A	ENST00000378402.5	+	74	12233	c.12129G>A	c.(12127-12129)tcG>tcA	p.S4043S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4043					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)			TTAACATTTCGTCCATGTCTA	0.388										HNSCC(38;0.096)			G|||	1429	0.285343	0.3464	0.3991	5008	,	,		17113	0.3244		0.1412	False		,,,				2504	0.2301				p.S4043S		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	0			c.G12129A						PASS	.	G		1209,2491		198,813,839	84.0	81.0	82.0		12129	0.8	1.0	8	dbSNP_88	82	1326,6866		117,1092,2887	no	coding-synonymous	PKHD1L1	NM_177531.4		315,1905,3726	AA,AG,GG		16.1865,32.6757,21.3169		4043/4244	110534512	2535,9357	1850	4096	5946	SO:0001819	synonymous_variant	93035	exon74			CATTTCGTCCATG	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.12129G>A	8.37:g.110534512G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.740;A|0.260	0.260	strong		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
ZNF773	374928	hgsc.bcm.edu	37	19	58017754	58017754	+	Silent	SNP	A	A	G	rs386811330|rs61737910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58017754A>G	ENST00000282292.4	+	4	431	c.291A>G	c.(289-291)gcA>gcG	p.A97A	ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Silent_p.A96A	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	75	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	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	
FIG4	9896	hgsc.bcm.edu	37	6	110146303	110146303	+	Silent	SNP	G	G	A	rs1127771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:110146303G>A	ENST00000230124.3	+	23	2683	c.2559G>A	c.(2557-2559)tcG>tcA	p.S853S	RP1-249I4.2_ENST00000458693.1_lincRNA|FIG4_ENST00000441478.2_Silent_p.S547S	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	853					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		CACCCATCTCGGCTTTCTCGC	0.453													g|||	1982	0.395767	0.0915	0.451	5008	,	,		19345	0.5595		0.4205	False		,,,				2504	0.5736				p.S853S		Atlas-SNP	.											.	FIG4	77	.	0			c.G2559A						PASS	.	G		652,3754	275.2+/-272.4	52,548,1603	106.0	103.0	104.0		2559	-9.5	0.9	6	dbSNP_119	104	3529,5071	513.3+/-378.1	743,2043,1514	no	coding-synonymous	FIG4	NM_014845.5		795,2591,3117	AA,AG,GG		41.0349,14.798,32.1467		853/908	110146303	4181,8825	2203	4300	6503	SO:0001819	synonymous_variant	9896	exon23			CATCTCGGCTTTC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.2559G>A	6.37:g.110146303G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_014845	Q53H49|Q5TCS6	Silent	SNP	ENST00000230124.3	37	CCDS5078.1																																																																																			G|0.652;A|0.348	0.348	strong		0.453	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
CCDC180	100499483	hgsc.bcm.edu	37	9	100087345	100087345	+	Silent	SNP	A	A	G	rs3747496	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100087345A>G	ENST00000357054.1	+	28	2900	c.1965A>G	c.(1963-1965)tcA>tcG	p.S655S	CCDC180_ENST00000411667.2_Silent_p.S513S|CCDC180_ENST00000395220.1_Missense_Mutation_p.H627R|CCDC180_ENST00000529487.1_Silent_p.S516S|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Silent_p.S516S			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	655						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.S655S(1)									GGCAGAGTTCACACCTCTTCA	0.562													G|||	2995	0.598043	0.7587	0.6671	5008	,	,		18972	0.5843		0.3956	False		,,,				2504	0.5542				p.S516S		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A1548G						PASS	.	G		3229,1177	412.2+/-336.0	1184,861,158	52.0	50.0	51.0		1548	-10.3	0.0	9	dbSNP_107	51	3985,4615	598.9+/-394.0	916,2153,1231	no	coding-synonymous	C9orf174	NM_020893.2		2100,3014,1389	GG,GA,AA		46.3372,26.7136,44.5333		516/1702	100087345	7214,5792	2203	4300	6503	SO:0001819	synonymous_variant	0	exon14			GAGTTCACACCTC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.1965A>G	9.37:g.100087345A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37		1225	0.5608974358974359	357	0.725609756097561	224	0.6187845303867403	341	0.5961538461538461	303	0.3997361477572559	G	2.270	-0.367181	0.05069	0.732864	0.463372	ENSG00000197816	ENST00000395220	T	0.24350	1.86	5.39	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.26155	-1.0111	5	0.16420	T	0.52	3.1745	6.5357	0.22352	0.308:0.0946:0.504:0.0934	rs3747496;rs58149924;rs3747496	.	.	.	R	627	ENSP00000378646:H627R	ENSP00000378646:H627R	H	+	2	0	C9orf174	99127166	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.804000	0.04535	-2.480000	0.00523	-2.236000	0.00289	CAC	A|0.437;G|0.563	0.563	strong		0.562	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
RAD52	5893	hgsc.bcm.edu	37	12	1039288	1039288	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:1039288C>T	ENST00000358495.3	-	4	347	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	RAD52_ENST00000430095.2_Missense_Mutation_p.R70Q|RAD52_ENST00000544742.1_Missense_Mutation_p.R70Q|RAD52_ENST00000539046.1_5'UTR|RAD52_ENST00000545564.1_Missense_Mutation_p.R70Q|RAD52_ENST00000541619.1_Missense_Mutation_p.R70Q|RAD52_ENST00000536177.1_Missense_Mutation_p.R70Q	NM_134424.2	NP_602296.2	P43351	RAD52_HUMAN	RAD52 homolog (S. cerevisiae)	70			R -> W (in dbSNP:rs11571421). {ECO:0000269|Ref.6}.		DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			ATTAATTACCCGATGACCCTC	0.413								Homologous recombination																													p.R70Q		Atlas-SNP	.											RAD52,NS,carcinoma,0,1	RAD52	27	1	0			c.G209A						scavenged	.						119.0	97.0	105.0					12																	1039288		2203	4300	6503	SO:0001583	missense	5893	exon4			ATTACCCGATGAC		CCDS8507.2	12p13-p12.2	2008-08-05	2001-11-28		ENSG00000002016	ENSG00000002016			9824	protein-coding gene	gene with protein product		600392	"""RAD52 (S. cerevisiae) homolog"""			7774919, 18313388	Standard	XM_005253721		Approved		uc001qis.1	P43351	OTTHUMG00000090361	ENST00000358495.3:c.209G>A	12.37:g.1039288C>T	ENSP00000351284:p.Arg70Gln	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	163	2	0.0122699	NM_134424	Q13205|Q9Y5T7|Q9Y5T8|Q9Y5T9	Missense_Mutation	SNP	ENST00000358495.3	37	CCDS8507.2	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466546	0.63625	.	.	ENSG00000002016	ENST00000358495;ENST00000430095;ENST00000536177;ENST00000545564;ENST00000542785;ENST00000397230;ENST00000544742;ENST00000541619	T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	4.89	2.97	0.34412	.	0.191520	0.49916	D	0.000133	T	0.26955	0.0660	L	0.31526	0.94	0.40478	D	0.980417	P;D;D	0.62365	0.953;0.957;0.991	B;B;P	0.48654	0.338;0.404;0.585	T	0.02581	-1.1138	10	0.48119	T	0.1	-13.6929	9.7892	0.40695	0.0:0.833:0.0:0.167	.	70;70;70	F5GX32;Q9Y5T7;P43351	.;.;RAD52_HUMAN	Q	70	ENSP00000351284:R70Q;ENSP00000387901:R70Q;ENSP00000440486:R70Q;ENSP00000440268:R70Q;ENSP00000441073:R70Q;ENSP00000380407:R70Q;ENSP00000443254:R70Q;ENSP00000438965:R70Q	ENSP00000351284:R70Q	R	-	2	0	RAD52	909549	1.000000	0.71417	0.913000	0.36048	0.482000	0.33219	1.404000	0.34623	0.531000	0.28639	0.305000	0.20034	CGG	.	.	none		0.413	RAD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206733.2	NM_134424	
TRIM48	79097	hgsc.bcm.edu	37	11	55032500	55032500	+	Missense_Mutation	SNP	C	C	T	rs141034048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55032500C>T	ENST00000417545.2	+	2	255	c.169C>T	c.(169-171)Ctc>Ttc	p.L57F		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	41						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.L41F(1)|p.L57F(1)		endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CTGTTTCTACCTCAACTGGCA	0.463																																					p.L57F		Atlas-SNP	.											TRIM48_ENST00000417545,extremity,malignant_melanoma,0,2	TRIM48	149	2	2	Substitution - Missense(2)	skin(2)	c.C169T						scavenged	.	C	PHE/LEU	1,4367	2.1+/-5.4	0,1,2183	75.0	78.0	77.0		169	0.6	0.0	11	dbSNP_134	77	7,8517	4.3+/-15.6	0,7,4255	no	missense	TRIM48	NM_024114.3	22	0,8,6438	TT,TC,CC		0.0821,0.0229,0.0621	benign	57/225	55032500	8,12884	2184	4262	6446	SO:0001583	missense	79097	exon2			TTCTACCTCAACT	AF521869	CCDS7947.2	11q12	2013-01-09	2011-01-25		ENSG00000150244	ENSG00000150244		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19021	protein-coding gene	gene with protein product			"""tripartite motif-containing 48"""				Standard	NM_024114		Approved	RNF101	uc010rid.2	Q8IWZ4	OTTHUMG00000157011	ENST00000417545.2:c.169C>T	11.37:g.55032500C>T	ENSP00000402414:p.Leu57Phe	Somatic	570	0	0		WXS	Illumina HiSeq	Phase_I	283	16	0.0565371	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	.	.	.	.	.	.	.	.	.	.	c	8.067	0.769474	0.15983	2.29E-4	8.21E-4	ENSG00000150244	ENST00000417545	D	0.84223	-1.82	0.596	0.596	0.17496	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	.	.	.	.	T	0.81987	0.4939	L	0.52905	1.665	0.09310	N	1	B	0.18013	0.025	B	0.33750	0.169	T	0.73385	-0.3999	9	0.49607	T	0.09	.	7.1377	0.25537	0.0:0.9999:0.0:1.0E-4	.	41	Q8IWZ4	TRI48_HUMAN	F	57	ENSP00000402414:L57F	ENSP00000402414:L57F	L	+	1	0	TRIM48	54789076	0.001000	0.12720	0.010000	0.14722	0.006000	0.05464	0.051000	0.14141	0.629000	0.30376	0.413000	0.27773	CTC	C|0.997;T|0.003	0.003	strong		0.463	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1		
ATP10D	57205	hgsc.bcm.edu	37	4	47570876	47570876	+	Missense_Mutation	SNP	G	G	A	rs17462252	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:47570876G>A	ENST00000273859.3	+	16	3145	c.2876G>A	c.(2875-2877)aGc>aAc	p.S959N		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	959			S -> N (in dbSNP:rs17462252).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|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(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						ATGCTGATGAGCACAATTTTG	0.468													G|||	98	0.0195687	0.003	0.0216	5008	,	,		18790	0.001		0.0656	False		,,,				2504	0.0123				p.S959N		Atlas-SNP	.											.	ATP10D	168	.	0			c.G2876A						PASS	.	G	ASN/SER	41,4365	43.1+/-76.7	0,41,2162	68.0	70.0	69.0		2876	1.8	0.9	4	dbSNP_123	69	586,8014	156.0+/-209.9	20,546,3734	yes	missense	ATP10D	NM_020453.3	46	20,587,5896	AA,AG,GG		6.814,0.9305,4.8209	benign	959/1427	47570876	627,12379	2203	4300	6503	SO:0001583	missense	57205	exon16			TGATGAGCACAAT	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.2876G>A	4.37:g.47570876G>A	ENSP00000273859:p.Ser959Asn	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	67	0.030677655677655676	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	55	0.07255936675461741	G	3.395	-0.123382	0.06795	0.009305	0.06814	ENSG00000145246	ENST00000273859	D	0.82893	-1.66	6.07	1.84	0.25277	HAD-like domain (1);	0.684805	0.15746	N	0.246645	T	0.09512	0.0234	N	0.03224	-0.385	0.38349	D	0.944294	B	0.02656	0.0	B	0.06405	0.002	T	0.33803	-0.9854	10	0.02654	T	1	-2.4303	10.3286	0.43809	0.4361:0.0:0.5639:0.0	rs17462252;rs52835435;rs17462252	959	Q9P241	AT10D_HUMAN	N	959	ENSP00000273859:S959N	ENSP00000273859:S959N	S	+	2	0	ATP10D	47265633	0.729000	0.28090	0.929000	0.37066	0.951000	0.60555	0.903000	0.28475	0.421000	0.25980	0.655000	0.94253	AGC	G|0.961;A|0.039	0.039	strong		0.468	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
OR52K1	390036	hgsc.bcm.edu	37	11	4510587	4510587	+	Missense_Mutation	SNP	C	C	T	rs331510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	192	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	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	
DNHD1	144132	hgsc.bcm.edu	37	11	6585007	6585007	+	Missense_Mutation	SNP	G	G	A	rs11040923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6585007G>A	ENST00000527990.2	+	29	9937	c.9937G>A	c.(9937-9939)Gat>Aat	p.D3313N	DNHD1_ENST00000254579.6_Missense_Mutation_p.D3313N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3313					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)		AGGTATGGACGATGCAGCCCT	0.572													G|||	2182	0.435703	0.0734	0.4654	5008	,	,		20999	0.7212		0.4742	False		,,,				2504	0.5706				p.D3313N		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9937A						PASS	.	G	ASN/ASP	193,1191		8,177,507	51.0	47.0	48.0		9937	1.9	0.0	11	dbSNP_120	48	1552,1630		380,792,419	yes	missense	DNHD1	NM_144666.2	23	388,969,926	AA,AG,GG		48.7744,13.9451,38.2173	benign	3313/4754	6585007	1745,2821	692	1591	2283	SO:0001583	missense	144132	exon31			ATGGACGATGCAG	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.9937G>A	11.37:g.6585007G>A	ENSP00000436180:p.Asp3313Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	972	0.44505494505494503	49	0.09959349593495935	169	0.46685082872928174	386	0.6748251748251748	368	0.48548812664907653	G	6.557	0.471037	0.12461	0.139451	0.487744	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000526486	T;T	0.74106	-0.81;-0.81	4.87	1.89	0.25635	Dynein heavy chain, coiled coil stalk (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18863	0.031	B	0.18871	0.023	T	0.42649	-0.9439	8	0.40728	T	0.16	.	4.8015	0.13299	0.1976:0.1778:0.6246:0.0	rs11040923;rs17245815;rs58851054;rs11040923	3313	Q96M86	DNHD1_HUMAN	N	3313;3313;225	ENSP00000254579:D3313N;ENSP00000436180:D3313N	ENSP00000254579:D3313N	D	+	1	0	DNHD1	6541583	0.088000	0.21588	0.001000	0.08648	0.071000	0.16799	1.110000	0.31147	0.108000	0.17862	0.313000	0.20887	GAT	G|0.573;A|0.427	0.427	strong		0.572	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
KIF20B	9585	hgsc.bcm.edu	37	10	91522548	91522548	+	Missense_Mutation	SNP	A	A	G	rs34354493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91522548A>G	ENST00000371728.3	+	29	5010	c.4945A>G	c.(4945-4947)Aag>Gag	p.K1649E	KIF20B_ENST00000394289.2_Missense_Mutation_p.K1649E|KIF20B_ENST00000416354.1_Missense_Mutation_p.K1679E|KIF20B_ENST00000260753.4_Missense_Mutation_p.K1609E|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1649	Interaction with PIN1.			K -> E (in Ref. 2; CAB55962 and 3; BAB15194). {ECO:0000305}.	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						AGTGACAGTTAAGATTCCCAA	0.373													A|||	533	0.10643	0.0098	0.1801	5008	,	,		19128	0.001		0.2276	False		,,,				2504	0.1687				p.K1609E		Atlas-SNP	.											.	KIF20B	191	.	0			c.A4825G						PASS	.	A	GLU/LYS	228,4178	135.7+/-171.8	4,220,1979	61.0	57.0	59.0		4825	6.1	1.0	10	dbSNP_126	59	2012,6588	352.1+/-328.5	237,1538,2525	yes	missense	KIF20B	NM_016195.2	56	241,1758,4504	GG,GA,AA		23.3953,5.1748,17.2228	benign	1609/1781	91522548	2240,10766	2203	4300	6503	SO:0001583	missense	9585	exon29			ACAGTTAAGATTC	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.4945A>G	10.37:g.91522548A>G	ENSP00000360793:p.Lys1649Glu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	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		257	0.11767399267399267	8	0.016260162601626018	71	0.19613259668508287	1	0.0017482517482517483	177	0.23350923482849603	A	29.6	5.019322	0.93462	0.051748	0.233953	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	6.06	6.06	0.98353	.	0.114668	0.39341	N	0.001382	T	0.00073	0.0002	M	0.68952	2.095	0.09310	P	0.99999348147	P;D	0.55385	0.952;0.971	P;P	0.57152	0.656;0.814	T	0.00475	-1.1717	9	0.87932	D	0	-12.4306	15.5919	0.76537	1.0:0.0:0.0:0.0	rs34354493	1649;1609	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	E	1609;1679;1649;1649	ENSP00000260753:K1609E;ENSP00000411545:K1679E;ENSP00000377830:K1649E;ENSP00000360793:K1649E	ENSP00000260753:K1609E	K	+	1	0	KIF20B	91512528	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.147000	0.89628	2.324000	0.78689	0.533000	0.62120	AAG	A|0.845;G|0.155	0.155	strong		0.373	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
VMO1	284013	hgsc.bcm.edu	37	17	4689572	4689572	+	Missense_Mutation	SNP	T	T	C	rs4790706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4689572T>C	ENST00000328739.5	-	1	155	c.76A>G	c.(76-78)Aca>Gca	p.T26A	VMO1_ENST00000354194.4_Missense_Mutation_p.T26A|GLTPD2_ENST00000331264.7_5'Flank|VMO1_ENST00000416307.2_Missense_Mutation_p.T26A|VMO1_ENST00000441199.2_Missense_Mutation_p.T26A	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	26			T -> A (in dbSNP:rs4790706). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						CGGCCATCTGTCTGTGCACAT	0.642													C|||	2672	0.533546	0.407	0.4957	5008	,	,		15997	0.5516		0.5348	False		,,,				2504	0.7117				p.T26A		Atlas-SNP	.											.	VMO1	19	.	0			c.A76G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR,ALA/THR	1970,2436		435,1100,668	25.0	28.0	27.0		76,76,76,76	-3.6	0.0	17	dbSNP_111	27	4576,4022		1212,2152,935	yes	missense,missense,missense,missense	VMO1	NM_001144939.1,NM_001144940.1,NM_001144941.1,NM_182566.2	58,58,58,58	1647,3252,1603	CC,CT,TT		46.7783,44.7118,49.6616	benign,benign,benign,benign	26/115,26/103,26/71,26/203	4689572	6546,6458	2203	4299	6502	SO:0001583	missense	284013	exon1			CATCTGTCTGTGC	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.76A>G	17.37:g.4689572T>C	ENSP00000328397:p.Thr26Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	37	CCDS11055.1	1109	0.5077838827838828	207	0.42073170731707316	184	0.5082872928176796	290	0.506993006993007	428	0.5646437994722955	C	2.909	-0.225681	0.06022	0.447118	0.532217	ENSG00000182853	ENST00000328739;ENST00000416307;ENST00000354194;ENST00000441199	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.57	-3.6	0.04570	.	1.617020	0.03169	N	0.170489	T	0.00012	0.0000	N	0.01576	-0.805	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	0.42258	-0.9462	9	0.13108	T	0.6	2.7273	1.4357	0.02343	0.2336:0.2382:0.3445:0.1837	rs4790706;rs17177719;rs17846231;rs17859248;rs60321209;rs4790706	26;26;26;26	C9JQ15;E9PAU9;E9PGP4;Q7Z5L0	.;.;.;VMO1_HUMAN	A	26	ENSP00000328397:T26A;ENSP00000390450:T26A;ENSP00000346133:T26A;ENSP00000408166:T26A	ENSP00000328397:T26A	T	-	1	0	VMO1	4636312	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.070000	0.14573	-0.778000	0.04566	-1.096000	0.02151	ACA	T|0.502;C|0.498	0.498	strong		0.642	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
ATP2B2	491	hgsc.bcm.edu	37	3	10413715	10413715	+	Silent	SNP	G	G	A	rs2289274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10413715G>A	ENST00000352432.4	-	11	1506	c.1437C>T	c.(1435-1437)aaC>aaT	p.N479N	ATP2B2_ENST00000383800.4_Silent_p.N434N|ATP2B2_ENST00000397077.1_Silent_p.N434N|ATP2B2_ENST00000360273.2_Silent_p.N479N|ATP2B2_ENST00000343816.4_Silent_p.N465N			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	479					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.N434N(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GGCGTACCAGGTTGTTGTCCT	0.582													G|||	1387	0.276957	0.1324	0.3256	5008	,	,		19783	0.3323		0.3002	False		,,,				2504	0.3569				p.N479N	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											ATP2B2_ENST00000360273,right_lower_lobe,carcinoma,-1,3	ATP2B2	304	3	1	Substitution - coding silent(1)	stomach(1)	c.C1437T						PASS	.	G	,	698,3708	291.8+/-281.7	58,582,1563	141.0	121.0	128.0		1437,1302	3.8	1.0	3	dbSNP_100	128	2656,5944	427.2+/-355.5	432,1792,2076	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	490,2374,3639	AA,AG,GG		30.8837,15.842,25.7881	,	479/1244,434/1199	10413715	3354,9652	2203	4300	6503	SO:0001819	synonymous_variant	491	exon12			TACCAGGTTGTTG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1437C>T	3.37:g.10413715G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	258	143	0.554264	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			G|0.752;A|0.248	0.248	strong		0.582	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
SASH1	23328	hgsc.bcm.edu	37	6	148841011	148841011	+	Silent	SNP	C	C	T	rs13196292	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:148841011C>T	ENST00000367467.3	+	10	1666	c.1191C>T	c.(1189-1191)ctC>ctT	p.L397L		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	397					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)		AGAAGGGTCTCGGGTCCCTAA	0.567													C|||	410	0.081869	0.0862	0.0403	5008	,	,		17258	0.0903		0.0736	False		,,,				2504	0.1053				p.L397L		Atlas-SNP	.											SASH1,NS,carcinoma,0,2	SASH1	123	2	0			c.C1191T						scavenged	.	C		349,4051		13,323,1864	12.0	14.0	13.0		1191	-2.3	0.4	6	dbSNP_121	13	694,7886		31,632,3627	no	coding-synonymous	SASH1	NM_015278.3		44,955,5491	TT,TC,CC		8.0886,7.9318,8.0354		397/1248	148841011	1043,11937	2200	4290	6490	SO:0001819	synonymous_variant	23328	exon10			GGGTCTCGGGTCC	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.1191C>T	6.37:g.148841011C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																			C|0.926;T|0.074	0.074	strong		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
ELL	8178	hgsc.bcm.edu	37	19	18583657	18583657	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18583657T>C	ENST00000262809.4	-	2	242	c.171A>G	c.(169-171)caA>caG	p.Q57Q	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	57					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		CTTGGCTTCCTTGAAATCGGA	0.398			T	MLL	AL																																p.Q57Q		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.A171G						PASS	.						108.0	99.0	102.0					19																	18583657		2203	4300	6503	SO:0001819	synonymous_variant	8178	exon2			GCTTCCTTGAAAT	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.171A>G	19.37:g.18583657T>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			.	.	none		0.398	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
VPS8	23355	hgsc.bcm.edu	37	3	184550501	184550501	+	Missense_Mutation	SNP	A	A	G	rs9830734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184550501A>G	ENST00000437079.3	+	4	418	c.247A>G	c.(247-249)Att>Gtt	p.I83V	VPS8_ENST00000436792.2_Missense_Mutation_p.I83V|VPS8_ENST00000287546.4_Missense_Mutation_p.I83V|VPS8_ENST00000446204.2_Missense_Mutation_p.I83V|VPS8_ENST00000424463.2_Missense_Mutation_p.I83V	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	83			I -> V (in dbSNP:rs9830734). {ECO:0000269|PubMed:17974005}.				zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TGAGTCTTTTATTCTTGAGGA	0.348													G|||	2774	0.553914	0.7103	0.4452	5008	,	,		18685	0.6657		0.3151	False		,,,				2504	0.5501				p.I83V		Atlas-SNP	.											.	VPS8	109	.	0			c.A247G						PASS	.	G	VAL/ILE,VAL/ILE	2431,1327		802,827,250	125.0	114.0	117.0		247,247	3.0	1.0	3	dbSNP_119	117	2377,5857		366,1645,2106	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	29,29	1168,2472,2356	GG,GA,AA		28.8681,35.3113,40.0934	benign,benign	83/1429,83/1427	184550501	4808,7184	1879	4117	5996	SO:0001583	missense	23355	exon4			TCTTTTATTCTTG	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.247A>G	3.37:g.184550501A>G	ENSP00000397879:p.Ile83Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	226	128	0.566372	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	1121	0.5132783882783882	336	0.6829268292682927	171	0.4723756906077348	365	0.6381118881118881	249	0.32849604221635886	G	1.030	-0.682044	0.03353	0.646887	0.288681	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204;ENST00000422105;ENST00000424463;ENST00000441141;ENST00000445089	T;T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.7	2.98	0.34508	.	0.257195	0.38959	N	0.001503	T	0.00012	0.0000	N	0.08118	0	0.46376	P	9.829999999999561E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.22068	-1.0227	9	0.20519	T	0.43	-3.4649	8.947	0.35764	0.358:0.0:0.642:0.0	rs9830734;rs61289304;rs9830734	83;83;83	Q8N3P4-2;C9JP71;Q8N3P4-3	.;.;.	V	83	ENSP00000287546:I83V;ENSP00000397879:I83V;ENSP00000404704:I83V;ENSP00000405483:I83V;ENSP00000415161:I83V;ENSP00000389480:I83V;ENSP00000409957:I83V;ENSP00000416150:I83V	ENSP00000287546:I83V	I	+	1	0	VPS8	186033195	1.000000	0.71417	0.995000	0.50966	0.886000	0.51366	0.871000	0.28023	0.093000	0.17368	-1.861000	0.00560	ATT	A|0.480;G|0.520	0.520	strong		0.348	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236097	67236097	+	Missense_Mutation	SNP	A	A	T	rs1060575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:67236097A>T	ENST00000282670.2	+	3	275	c.147A>T	c.(145-147)gaA>gaT	p.E49D	TCTEX1D1_ENST00000491611.1_3'UTR	NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	49			E -> D (in dbSNP:rs1060575).							large_intestine(2)|lung(10)|skin(1)	13						CTTATATGGAAGAACCCAGTC	0.328													T|||	664	0.132588	0.0862	0.1023	5008	,	,		19085	0.1488		0.1511	False		,,,				2504	0.181				p.E49D		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.A147T						PASS	.	T	ASP/GLU	378,4028	792.1+/-415.1	18,342,1843	180.0	175.0	177.0		147	2.5	1.0	1	dbSNP_86	177	1188,7412	763.8+/-407.6	85,1018,3197	yes	missense	TCTEX1D1	NM_152665.2	45	103,1360,5040	TT,TA,AA		13.814,8.5792,12.0406	benign	49/180	67236097	1566,11440	2203	4300	6503	SO:0001583	missense	200132	exon3			TATGGAAGAACCC	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.147A>T	1.37:g.67236097A>T	ENSP00000282670:p.Glu49Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	37	CCDS633.1	266	0.12179487179487179	37	0.07520325203252033	42	0.11602209944751381	82	0.14335664335664336	105	0.13852242744063326	T	0.109	-1.141193	0.01728	0.085792	0.13814	ENSG00000152760	ENST00000282670	T	0.13901	2.55	6.06	2.55	0.30701	.	0.147752	0.64402	N	0.000016	T	0.00524	0.0017	N	0.00151	-1.98	0.46609	P	8.709999999999551E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42378	-0.9455	9	0.02654	T	1	-10.0546	4.7902	0.13245	0.1273:0.2766:0.0:0.596	rs1060575;rs1498353;rs3201482;rs17441805;rs52832612;rs1060575	49	Q8N7M0	TC1D1_HUMAN	D	49	ENSP00000282670:E49D	ENSP00000282670:E49D	E	+	3	2	TCTEX1D1	67008685	1.000000	0.71417	0.990000	0.47175	0.008000	0.06430	1.263000	0.33004	-0.032000	0.13758	-1.091000	0.02175	GAA	A|0.878;N|0.000	.	strong		0.328	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	
FAM71B	153745	hgsc.bcm.edu	37	5	156589585	156589585	+	Missense_Mutation	SNP	A	A	G	rs31208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:156589585A>G	ENST00000302938.4	-	2	1786	c.1691T>C	c.(1690-1692)aTg>aCg	p.M564T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	564			M -> T (in dbSNP:rs31208). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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)			CTTCTCCACCATCTTAGCCAC	0.502													A|||	574	0.114617	0.2436	0.0922	5008	,	,		19806	0.0139		0.1243	False		,,,				2504	0.0501				p.M564T		Atlas-SNP	.											.	FAM71B	145	.	0			c.T1691C						PASS	.	A	THR/MET	1034,3372	382.5+/-324.5	125,784,1294	281.0	274.0	276.0		1691	0.9	0.0	5	dbSNP_76	276	1165,7435	238.2+/-269.8	76,1013,3211	yes	missense	FAM71B	NM_130899.2	81	201,1797,4505	GG,GA,AA		13.5465,23.468,16.9076	benign	564/606	156589585	2199,10807	2203	4300	6503	SO:0001583	missense	153745	exon2			TCCACCATCTTAG		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.1691T>C	5.37:g.156589585A>G	ENSP00000305596:p.Met564Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	172	73	0.424419	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	254	0.1163003663003663	123	0.25	30	0.08287292817679558	10	0.017482517482517484	91	0.12005277044854881	A	0.005	-2.137566	0.00335	0.23468	0.135465	ENSG00000170613	ENST00000302938	T	0.17691	2.26	3.87	0.954	0.19595	.	1.609550	0.03833	N	0.269439	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35773	-0.9775	9	0.02654	T	1	-0.7755	2.6679	0.05058	0.2627:0.0:0.5112:0.2261	rs31208;rs17851963;rs17852269;rs52832622;rs59767396;rs31208	564	Q8TC56	FA71B_HUMAN	T	564	ENSP00000305596:M564T	ENSP00000305596:M564T	M	-	2	0	FAM71B	156522163	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.172000	0.16704	0.170000	0.19704	-0.242000	0.12053	ATG	A|0.858;G|0.142	0.142	strong		0.502	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237974	239237974	+	Silent	SNP	T	T	C	rs17854985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239237974T>C	ENST00000373327.4	+	5	1128	c.906T>C	c.(904-906)ccT>ccC	p.P302P	TRAF3IP1_ENST00000391993.3_Silent_p.P302P|TRAF3IP1_ENST00000391994.2_Silent_p.P302P	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	302	Abolishes microtubules-binding when missing.|DISC1-interaction domain.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		ATGACAAACCTGAGAAAAAGG	0.483													C|||	767	0.153155	0.3283	0.0821	5008	,	,		20141	0.0992		0.0586	False		,,,				2504	0.1196				p.P302P		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.T906C						PASS	.	C	,	1092,3292		147,798,1247	58.0	68.0	65.0		906,906	-7.3	0.0	2	dbSNP_123	65	336,8212		2,332,3940	no	coding-synonymous,coding-synonymous	TRAF3IP1	NM_001139490.1,NM_015650.3	,	149,1130,5187	CC,CT,TT		3.9307,24.9088,11.0424	,	302/626,302/692	239237974	1428,11504	2192	4274	6466	SO:0001819	synonymous_variant	26146	exon5			CAAACCTGAGAAA	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.906T>C	2.37:g.239237974T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Silent	SNP	ENST00000373327.4	37	CCDS33415.1																																																																																			T|0.883;C|0.117	0.117	strong		0.483	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
NFASC	23114	hgsc.bcm.edu	37	1	204966428	204966428	+	Missense_Mutation	SNP	C	C	G	rs2802808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204966428C>G	ENST00000401399.1	+	24	3112	c.2913C>G	c.(2911-2913)atC>atG	p.I971M	NFASC_ENST00000513543.1_Intron|NFASC_ENST00000367172.4_Missense_Mutation_p.I1078M|NFASC_ENST00000367171.4_Missense_Mutation_p.I1063M|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000495396.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000339876.6_Missense_Mutation_p.I971M|NFASC_ENST00000367170.4_Intron|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000338515.6_Missense_Mutation_p.I1078M|NFASC_ENST00000338586.6_Intron			O94856	NFASC_HUMAN	neurofascin	1078	Fibronectin type-III 4. {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)			CTaccaccatcgccaccacca	0.617													C|||	1555	0.310503	0.208	0.2867	5008	,	,		17209	0.4345		0.2545	False		,,,				2504	0.3957				p.I971M		Atlas-SNP	.											NFASC_ENST00000339876,caecum,carcinoma,0,2	NFASC	396	2	0			c.C2913G						PASS	.	C	,,,MET/ILE	676,2456		87,502,977	242.0	289.0	275.0		,,,2913	0.4	0.9	1	dbSNP_100	275	2031,5129		293,1445,1842	yes	intron,intron,intron,missense	NFASC	NM_001160331.1,NM_001160332.1,NM_015090.3,NM_001005388.2	,,,10	380,1947,2819	GG,GC,CC		28.3659,21.5837,26.302	,,,benign	,,,971/1241	204966428	2707,7585	1566	3580	5146	SO:0001583	missense	23114	exon25			CACCATCGCCACC	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.2913C>G	1.37:g.204966428C>G	ENSP00000385637:p.Ile971Met	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	187	118	0.631016	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	677	0.309981684981685	103	0.20934959349593496	104	0.287292817679558	266	0.46503496503496505	204	0.2691292875989446	C	11.69	1.712468	0.30322	0.215837	0.283659	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000338515;ENST00000339876;ENST00000401399;ENST00000447819	T;T;T;T;T;T	0.78481	-0.14;0.99;-0.12;-0.09;-0.09;-1.18	4.59	0.388	0.16264	.	1.599380	0.03805	N	0.265054	T	0.00012	0.0000	.	.	.	0.30560	P	0.764566	B;B	0.28801	0.223;0.002	B;B	0.19946	0.027;0.004	T	0.23797	-1.0178	8	0.52906	T	0.07	.	5.0857	0.14680	0.0:0.4819:0.3275:0.1906	rs2802808;rs52830695;rs2802808	1078;971	O94856-7;O94856-9	.;.	M	1078;1063;1078;971;971;39	ENSP00000356140:I1078M;ENSP00000356139:I1063M;ENSP00000342128:I1078M;ENSP00000344786:I971M;ENSP00000385637:I971M;ENSP00000416891:I39M	ENSP00000342128:I1078M	I	+	3	3	NFASC	203233051	0.001000	0.12720	0.922000	0.36590	0.994000	0.84299	-0.198000	0.09505	0.162000	0.19483	0.655000	0.94253	ATC	C|0.678;G|0.322	0.322	strong		0.617	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
PEX6	5190	hgsc.bcm.edu	37	6	42933526	42933526	+	Splice_Site	SNP	C	C	T	rs2274515	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:42933526C>T	ENST00000304611.8	-	13	2433	c.2364G>A	c.(2362-2364)gtG>gtA	p.V788V	PEX6_ENST00000244546.4_Splice_Site_p.C706Y	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	788					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)			CCCTGGCAAACACTGAAGAGA	0.577													C|||	549	0.109625	0.0582	0.1671	5008	,	,		15330	0.1379		0.0437	False		,,,				2504	0.1769				p.V788V		Atlas-SNP	.											.	PEX6	44	.	0			c.G2364A						PASS	.	C		250,4156	138.4+/-174.2	9,232,1962	57.0	66.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2364	3.1	1.0	6	dbSNP_100	63	384,8216	121.7+/-180.7	5,374,3921	yes	coding-synonymous-near-splice	PEX6	NM_000287.3		14,606,5883	TT,TC,CC		4.4651,5.6741,4.8747		788/981	42933526	634,12372	2203	4300	6503	SO:0001630	splice_region_variant	5190	exon13			GGCAAACACTGAA	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.2363-1G>A	6.37:g.42933526C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Silent	SNP	ENST00000304611.8	37	CCDS4877.1	192	0.08791208791208792	24	0.04878048780487805	52	0.143646408839779	80	0.13986013986013987	36	0.047493403693931395	C	14.26	2.482455	0.44147	0.056741	0.044651	ENSG00000124587	ENST00000244546	D	0.94966	-3.57	5.86	3.11	0.35812	.	.	.	.	.	D	0.92417	0.7593	.	.	.	0.38098	P	0.062832	.	.	.	.	.	.	D	0.90084	0.4172	5	0.87932	D	0	.	8.7772	0.34769	0.0:0.7383:0.1252:0.1364	rs2274515;rs17854562;rs52825508;rs2274515	.	.	.	Y	706	ENSP00000244546:C706Y	ENSP00000244546:C706Y	C	-	2	0	PEX6	43041504	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.952000	0.29149	0.378000	0.24764	0.563000	0.77884	TGT	C|0.937;T|0.063	0.063	strong		0.577	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	Silent
PRR12	57479	hgsc.bcm.edu	37	19	50097784	50097784	+	Silent	SNP	T	T	C	rs10414643	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50097784T>C	ENST00000418929.2	+	3	285	c.273T>C	c.(271-273)ctT>ctC	p.L91L		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TCATGAACCTTATCTCGGCCC	0.667													C|||	1791	0.357628	0.5499	0.2954	5008	,	,		14010	0.1915		0.2247	False		,,,				2504	0.4499				p.L91L		Atlas-SNP	.											PRR12_ENST00000418929,NS,carcinoma,0,1	PRR12	157	1	0			c.T273C						PASS	.	C		1892,1904		466,960,472	40.0	49.0	46.0		273	3.6	1.0	19	dbSNP_119	46	1962,6220		219,1524,2348	no	coding-synonymous	PRR12	NM_020719.1		685,2484,2820	CC,CT,TT		23.9795,49.8419,32.1757		91/2037	50097784	3854,8124	1898	4091	5989	SO:0001819	synonymous_variant	57479	exon3			GAACCTTATCTCG	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.273T>C	19.37:g.50097784T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			T|0.712;C|0.288	0.288	strong		0.667	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
AKAP17A	8227	hgsc.bcm.edu	37	X	1719897	1719897	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	21	0	0		WXS	Illumina HiSeq	Phase_I	12	12	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	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777268	18777268	+	Missense_Mutation	SNP	C	C	T	rs117786774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:18777268C>T	ENST00000380548.4	+	19	3380	c.3041C>T	c.(3040-3042)gCc>gTc	p.A1014V		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1014						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)		CGGGGCCTGGCCGCCAACCCG	0.706													C|||	80	0.0159744	0.0008	0.0216	5008	,	,		13184	0.001		0.0358	False		,,,				2504	0.0276				p.A1014V		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.C3041T						PASS	.	C	VAL/ALA	33,3623		0,33,1795	7.0	10.0	9.0		3041	3.8	0.0	9	dbSNP_132	9	356,7646		6,344,3651	yes	missense	ADAMTSL1	NM_001040272.5	64	6,377,5446	TT,TC,CC		4.4489,0.9026,3.3368	benign	1014/1763	18777268	389,11269	1828	4001	5829	SO:0001583	missense	92949	exon19			GCCTGGCCGCCAA	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.3041C>T	9.37:g.18777268C>T	ENSP00000369921:p.Ala1014Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	39	0.017857142857142856	0	0.0	9	0.024861878453038673	3	0.005244755244755245	27	0.03562005277044855	C	6.265	0.417010	0.11870	0.009026	0.044489	ENSG00000178031	ENST00000380548	T	0.62498	0.02	5.75	3.8	0.43715	.	0.000000	0.08080	U	1.000000	T	0.11537	0.0281	N	0.08118	0	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.09357	-1.0678	10	0.29301	T	0.29	.	3.1534	0.06495	0.1923:0.5276:0.0:0.2802	.	1014	Q8N6G6	ATL1_HUMAN	V	1014	ENSP00000369921:A1014V	ENSP00000369921:A1014V	A	+	2	0	ADAMTSL1	18767268	0.000000	0.05858	0.002000	0.10522	0.660000	0.38997	0.853000	0.27777	1.438000	0.47492	0.455000	0.32223	GCC	C|0.982;T|0.018	0.018	strong		0.706	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
TCHH	7062	hgsc.bcm.edu	37	1	152083325	152083325	+	Missense_Mutation	SNP	A	A	T	rs11803731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152083325A>T	ENST00000368804.1	-	2	2367	c.2368T>A	c.(2368-2370)Ttg>Atg	p.L790M		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	790			L -> M (in dbSNP:rs11803731).		keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTCCCGCAATGGGGGCCTG	0.692													a|||	364	0.0726837	0.0045	0.0937	5008	,	,		13411	0.001		0.2286	False		,,,				2504	0.0634				p.L790M		Atlas-SNP	.											.	TCHH	275	.	0			c.T2368A						PASS	.		MET/LEU	145,3885		1,143,1871	24.0	30.0	28.0	http://omim.org/entry/139450|http://www.ncbi.nlm.nih.gov/pubmed?term	2368	-0.6	0.0	1	dbSNP_120	28	1494,6884		131,1232,2826	yes	missense	TCHH	NM_007113.2	15	132,1375,4697	TT,TA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	17.8324,3.598,13.2092	probably-damaging	790/1944	152083325	1639,10769	2015	4189	6204	SO:0001583	missense	7062	exon3			CCCGCAATGGGGG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2368T>A	1.37:g.152083325A>T	ENSP00000357794:p.Leu790Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	62	0.652632	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	222	0.10164835164835165	3	0.006097560975609756	51	0.1408839779005525	1	0.0017482517482517483	167	0.22031662269129287	a	0.520	-0.862595	0.02610	0.03598	0.178324	ENSG00000159450	ENST00000368804	T	0.08370	3.1	2.41	-0.583	0.11706	.	.	.	.	.	T	0.02929	0.0087	N	0.24115	0.695	0.80722	P	0.0	D	0.61080	0.989	P	0.53912	0.737	T	0.35624	-0.9781	8	0.51188	T	0.08	1.1016	1.5277	0.02529	0.4732:0.0:0.2233:0.3034	rs11803731;rs11803731	790	Q07283	TRHY_HUMAN	M	790	ENSP00000357794:L790M	ENSP00000357794:L790M	L	-	1	2	TCHH	150349949	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	-0.142000	0.10311	0.140000	0.18849	0.255000	0.18592	TTG	A|0.890;T|0.110	0.110	strong		0.692	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
SPTA1	6708	hgsc.bcm.edu	37	1	158612236	158612236	+	Missense_Mutation	SNP	A	A	G	rs863931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158612236A>G	ENST00000368147.4	-	33	4882	c.4702T>C	c.(4702-4704)Tgt>Cgt	p.C1568R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1568			C -> R (in dbSNP:rs863931). {ECO:0000269|PubMed:1689726, ECO:0000269|PubMed:3000887}.		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)					CAAGCGCTACACTCAATCAGG	0.468													G|||	2975	0.59405	0.6853	0.5605	5008	,	,		13150	0.6359		0.5865	False		,,,				2504	0.4591				p.C1568R		Atlas-SNP	.											.	SPTA1	720	.	0			c.T4702C						PASS	.	G	ARG/CYS	2688,1274		915,858,208	105.0	105.0	105.0		4702	1.0	0.2	1	dbSNP_86	105	4689,3653		1346,1997,828	yes	missense	SPTA1	NM_003126.2	180	2261,2855,1036	GG,GA,AA		43.7905,32.1555,40.0439	benign	1568/2420	158612236	7377,4927	1981	4171	6152	SO:0001583	missense	6708	exon33			CGCTACACTCAAT	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.4702T>C	1.37:g.158612236A>G	ENSP00000357129:p.Cys1568Arg	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	385	149	0.387013	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	1362	0.6236263736263736	362	0.7357723577235772	199	0.5497237569060773	347	0.6066433566433567	454	0.5989445910290238	G	0.005	-2.205016	0.00296	0.678445	0.562095	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46451	0.87;0.87	5.26	1.01	0.19927	.	0.000000	0.30879	N	0.008681	T	0.02610	0.0079	N	0.00210	-1.845	0.44042	P	0.0032240000000000046	B	0.02656	0.0	B	0.01281	0.0	T	0.42224	-0.9464	9	0.10377	T	0.69	.	10.0752	0.42355	0.0669:0.0:0.4509:0.4822	rs863931;rs2230860;rs17687023;rs34131035;rs61640254;rs863931	1568	P02549	SPTA1_HUMAN	R	1568	ENSP00000357130:C1568R;ENSP00000357129:C1568R	ENSP00000357129:C1568R	C	-	1	0	SPTA1	156878860	0.752000	0.28338	0.175000	0.22980	0.097000	0.18754	0.863000	0.27913	0.084000	0.17077	-0.119000	0.15052	TGT	A|0.379;G|0.621	0.621	strong		0.468	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212510	149212510	+	Missense_Mutation	SNP	C	C	A	rs11959820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:149212510C>A	ENST00000309241.5	+	5	906	c.874C>A	c.(874-876)Cgc>Agc	p.R292S	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.R253S|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.R292S|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.R228S	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	292			R -> S (in dbSNP:rs11959820). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15863669}.		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)			GCAACTCATACGCTACATGCA	0.657													C|||	525	0.104832	0.1997	0.0461	5008	,	,		16955	0.128		0.0308	False		,,,				2504	0.0706				p.R292S		Atlas-SNP	.											PPARGC1B,NS,carcinoma,0,1	PPARGC1B	74	1	0			c.C874A						scavenged	.	C	SER/ARG,SER/ARG,SER/ARG	776,3630	307.5+/-290.0	63,650,1490	48.0	57.0	54.0		757,682,874	5.8	1.0	5	dbSNP_120	54	292,8308	106.0+/-166.9	5,282,4013	yes	missense,missense,missense	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	110,110,110	68,932,5503	AA,AC,CC		3.3953,17.6123,8.2116	probably-damaging,probably-damaging,probably-damaging	253/985,228/960,292/1024	149212510	1068,11938	2203	4300	6503	SO:0001583	missense	133522	exon5			CTCATACGCTACA	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.874C>A	5.37:g.149212510C>A	ENSP00000312649:p.Arg292Ser	Somatic	115	2	0.0173913		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	196	0.08974358974358974	89	0.18089430894308944	16	0.04419889502762431	66	0.11538461538461539	25	0.032981530343007916	C	20.6	4.011421	0.75046	0.176123	0.033953	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.12465	2.69;2.78;2.79;2.68	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.61703	1.905	0.26653	P	0.9720632	D;D;D;D;D	0.76494	0.999;0.994;0.999;0.999;0.998	D;P;D;P;D	0.67382	0.951;0.879;0.951;0.894;0.95	T	0.00004	-1.2558	9	0.56958	D	0.05	-22.9034	19.976	0.97309	0.0:1.0:0.0:0.0	rs11959820;rs52793886;rs58815357;rs11959820	271;271;253;292;292	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	S	253;292;292;228	ENSP00000353638:R253S;ENSP00000377855:R292S;ENSP00000312649:R292S;ENSP00000384403:R228S	ENSP00000312649:R292S	R	+	1	0	PPARGC1B	149192703	1.000000	0.71417	0.986000	0.45419	0.947000	0.59692	4.437000	0.59955	2.713000	0.92767	0.655000	0.94253	CGC	C|0.912;A|0.087	0.087	strong		0.657	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
LRRN2	10446	hgsc.bcm.edu	37	1	204588140	204588140	+	Silent	SNP	G	G	A	rs3747630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204588140G>A	ENST00000367175.1	-	1	3193	c.981C>T	c.(979-981)caC>caT	p.H327H	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367177.3_Silent_p.H327H|LRRN2_ENST00000367176.3_Silent_p.H327H|LRRN2_ENST00000496057.1_5'Flank			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	97	0	0		WXS	Illumina HiSeq	Phase_I	106	32	0.301887	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	
AP1G2	8906	hgsc.bcm.edu	37	14	24033027	24033027	+	Missense_Mutation	SNP	G	G	A	rs12897422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24033027G>A	ENST00000308724.5	-	11	1885	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	AP1G2_ENST00000556277.1_5'Flank|AP1G2_ENST00000397120.3_Missense_Mutation_p.S377F|RP11-66N24.3_ENST00000555968.1_RNA	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	74	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	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	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74203789	74203789	+	Missense_Mutation	SNP	G	G	A	rs17782124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74203789G>A	ENST00000286523.5	-	3	2443	c.1661C>T	c.(1660-1662)cCt>cTt	p.P554L	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Missense_Mutation_p.P554L	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	70	0	0		WXS	Illumina HiSeq	Phase_I	93	48	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	
F5	2153	hgsc.bcm.edu	37	1	169512093	169512093	+	Silent	SNP	A	A	G	rs6017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169512093A>G	ENST00000367797.3	-	13	2436	c.2235T>C	c.(2233-2235)aaT>aaC	p.N745N	F5_ENST00000367796.3_Silent_p.N750N	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	745	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)	CTTCTTCCTGATTCAATGATG	0.393													A|||	1316	0.26278	0.1679	0.3948	5008	,	,		21864	0.248		0.2535	False		,,,				2504	0.3221				p.N745N		Atlas-SNP	.											.	F5	301	.	0			c.T2235C						PASS	.	A		812,3594	320.7+/-296.8	68,676,1459	216.0	202.0	206.0		2235	-1.3	0.0	1	dbSNP_52	206	2355,6245	393.9+/-344.5	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2433,3703	GG,GA,AA		27.3837,18.4294,24.3503		745/2225	169512093	3167,9839	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TTCCTGATTCAAT	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.2235T>C	1.37:g.169512093A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	149	87	0.583893	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			A|0.760;G|0.240	0.240	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447640	10447640	+	Missense_Mutation	SNP	A	A	G	rs10016702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:10447640A>G	ENST00000326756.3	-	3	751	c.313T>C	c.(313-315)Tcc>Ccc	p.S105P		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	105			S -> P (in dbSNP:rs10016702). {ECO:0000269|PubMed:11214970}.		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.S105P(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GTCGCACTGGAATTATTGCTC	0.413													G|||	1054	0.210463	0.4274	0.1196	5008	,	,		20274	0.1696		0.0924	False		,,,				2504	0.1452				p.S105P		Atlas-SNP	.											ZNF518B,NS,carcinoma,0,1	ZNF518B	116	1	1	Substitution - Missense(1)	stomach(1)	c.T313C						PASS	.	G	PRO/SER	1689,2717	652.6+/-399.4	333,1023,847	101.0	106.0	104.0		313	0.5	0.0	4	dbSNP_119	104	867,7733	779.6+/-407.7	46,775,3479	yes	missense	ZNF518B	NM_053042.2	74	379,1798,4326	GG,GA,AA		10.0814,38.3341,19.6525	benign	105/1075	10447640	2556,10450	2203	4300	6503	SO:0001583	missense	85460	exon3			CACTGGAATTATT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.313T>C	4.37:g.10447640A>G	ENSP00000317614:p.Ser105Pro	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	433	0.19826007326007325	217	0.4410569105691057	49	0.13535911602209943	94	0.16433566433566432	73	0.09630606860158311	G	3.972	-0.008261	0.07727	0.383341	0.100814	ENSG00000178163	ENST00000326756	T	0.01560	4.77	5.76	0.517	0.17025	.	0.862050	0.09828	N	0.750635	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	0.21042	-1.0257	9	0.23891	T	0.37	-0.0895	3.5717	0.07920	0.2131:0.4421:0.2393:0.1056	rs10016702;rs52819764;rs59445573;rs10016702	105	Q9C0D4	Z518B_HUMAN	P	105	ENSP00000317614:S105P	ENSP00000317614:S105P	S	-	1	0	ZNF518B	10056738	0.000000	0.05858	0.000000	0.03702	0.302000	0.27658	0.016000	0.13377	-0.161000	0.10983	-0.128000	0.14901	TCC	A|0.793;G|0.207	0.207	strong		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
SON	6651	hgsc.bcm.edu	37	21	34924243	34924243	+	Silent	SNP	T	T	C	rs16990760	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000381679.4_Silent_p.D902D|SON_ENST00000290239.6_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						scavenged	.	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	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	200	86	0.43	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	
OR51G2	81282	hgsc.bcm.edu	37	11	4936608	4936608	+	Missense_Mutation	SNP	C	C	G	rs12419598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4936608C>G	ENST00000322013.3	-	1	314	c.286G>C	c.(286-288)Gaa>Caa	p.E96Q	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	96			E -> Q (in dbSNP:rs12419598).			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)		TGGCTAATTTCTCGTGCTCCA	0.502													C|||	261	0.0521166	0.0053	0.072	5008	,	,		21521	0.002		0.1223	False		,,,				2504	0.0808				p.E96Q		Atlas-SNP	.											.	OR51G2	70	.	0			c.G286C						PASS	.	C	GLN/GLU	124,4278	90.2+/-128.9	1,122,2078	91.0	82.0	85.0		286	5.5	0.1	11	dbSNP_120	85	1034,7562	220.5+/-258.2	62,910,3326	yes	missense	OR51G2	NM_001005238.1	29	63,1032,5404	GG,GC,CC		12.0289,2.8169,8.9091	benign	96/315	4936608	1158,11840	2201	4298	6499	SO:0001583	missense	81282	exon1			TAATTTCTCGTGC	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.286G>C	11.37:g.4936608C>G	ENSP00000322593:p.Glu96Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	123	0.05631868131868132	5	0.01016260162601626	29	0.08011049723756906	1	0.0017482517482517483	88	0.11609498680738786	C	6.592	0.477565	0.12521	0.028169	0.120289	ENSG00000176893	ENST00000322013	T	0.00554	6.64	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.529639	0.17116	N	0.186427	T	0.00039	0.0001	M	0.67569	2.06	0.09310	N	1	B	0.32717	0.381	B	0.34301	0.179	T	0.48375	-0.9041	10	0.59425	D	0.04	.	18.052	0.89353	0.0:1.0:0.0:0.0	rs12419598;rs17252531	96	Q8NGK0	O51G2_HUMAN	Q	96	ENSP00000322593:E96Q	ENSP00000322593:E96Q	E	-	1	0	OR51G2	4893184	0.000000	0.05858	0.077000	0.20336	0.018000	0.09664	-0.312000	0.08113	2.847000	0.97988	0.655000	0.94253	GAA	C|0.921;G|0.079	0.079	strong		0.502	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156941607	156941607	+	Intron	SNP	C	C	T	rs537664586		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156941607C>T	ENST00000361409.2	-	8	1325				ARHGEF11_ENST00000368194.3_Splice_Site_p.R195H	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|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(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTCACAGATACGCTAGGGATG	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		17391	0.0		0.0	False		,,,				2504	0.001				p.R195H		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G584A						PASS	.						46.0	48.0	47.0					1																	156941607		2203	4300	6503	SO:0001627	intron_variant	9826	exon8			CAGATACGCTAGG	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.583-1772G>A	1.37:g.156941607C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461360	0.26248	.	.	ENSG00000132694	ENST00000368194	T	0.66460	-0.21	5.32	1.87	0.25490	.	0.440313	0.21740	N	0.069832	T	0.32376	0.0827	.	.	.	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.13629	-1.0502	9	0.33141	T	0.24	-4.1001	7.6746	0.28478	0.0:0.5815:0.0:0.4185	.	195	O15085-2	.	H	195	ENSP00000357177:R195H	ENSP00000357177:R195H	R	-	2	0	ARHGEF11	155208231	0.878000	0.30173	1.000000	0.80357	0.995000	0.86356	0.424000	0.21330	0.622000	0.30249	0.655000	0.94253	CGT	.	.	none		0.567	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
C2orf70	339778	hgsc.bcm.edu	37	2	26799031	26799031	+	Silent	SNP	G	G	A	rs2272464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26799031G>A	ENST00000329615.3	+	2	367	c.336G>A	c.(334-336)acG>acA	p.T112T	C2orf70_ENST00000409392.1_Missense_Mutation_p.E100K	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	112						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						CAGAGCTTACGAATTTCTACC	0.657													G|||	1802	0.359824	0.1785	0.232	5008	,	,		18685	0.623		0.336	False		,,,				2504	0.4489				p.T112T		Atlas-SNP	.											.	C2orf70	26	.	0			c.G336A						PASS	.	G		736,3246		71,594,1326	54.0	57.0	56.0		336	-9.6	0.0	2	dbSNP_100	56	2481,5851		350,1781,2035	no	coding-synonymous	C2orf70	NM_001105519.1		421,2375,3361	AA,AG,GG		29.7768,18.4832,26.1247		112/202	26799031	3217,9097	1991	4166	6157	SO:0001819	synonymous_variant	339778	exon2			GCTTACGAATTTC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"""hypothetical protein LOC339778"""						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.336G>A	2.37:g.26799031G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001105519		Silent	SNP	ENST00000329615.3	37	CCDS42661.1	771|771	0.35302197802197804|0.35302197802197804	100|100	0.2032520325203252|0.2032520325203252	76|76	0.20994475138121546|0.20994475138121546	341|341	0.5961538461538461|0.5961538461538461	254|254	0.33509234828496043|0.33509234828496043	G|G	8.134|8.134	0.783761|0.783761	0.16189|0.16189	0.184832|0.184832	0.297768|0.297768	ENSG00000173557|ENSG00000173557	ENST00000409392|ENST00000453368	.|.	.|.	.|.	4.8|4.8	-9.61|-9.61	0.00550|0.00550	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30621|0.30621	-0.9972|-0.9972	4|3	0.87932|.	D|.	0|.	0.6775|0.6775	1.4254|1.4254	0.02322|0.02322	0.1944:0.2379:0.3479:0.2198|0.1944:0.2379:0.3479:0.2198	rs2272464;rs57992066;rs2272464|rs2272464;rs57992066;rs2272464	.|.	.|.	.|.	K|Q	100|13	.|.	ENSP00000386615:E100K|.	E|R	+|+	1|2	0|0	C2orf70|C2orf70	26652535|26652535	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-3.581000|-3.581000	0.00424|0.00424	-3.293000|-3.293000	0.00194|0.00194	-1.621000|-1.621000	0.00791|0.00791	GAA|CGA	G|0.672;A|0.328	0.328	strong		0.657	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519	
DNAH10	196385	hgsc.bcm.edu	37	12	124355003	124355003	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124355003C>T	ENST00000409039.3	+	43	7281	c.7256C>T	c.(7255-7257)gCc>gTc	p.A2419V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2419	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TATATTCATGCCCCCGAGAGG	0.433																																					p.A2419V		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7256T						PASS	.						81.0	77.0	78.0					12																	124355003		1865	4114	5979	SO:0001583	missense	196385	exon43			TTCATGCCCCCGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7256C>T	12.37:g.124355003C>T	ENSP00000386770:p.Ala2419Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863422	0.32884	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.06	-6.26	0.02033	.	5.622030	0.00939	U	0.002819	T	0.08935	0.0221	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.16512	-1.0400	10	0.39692	T	0.17	.	0.4362	0.00479	0.3524:0.2407:0.1472:0.2597	.	2419	Q8IVF4	DYH10_HUMAN	V	2419	ENSP00000386770:A2419V	ENSP00000386770:A2419V	A	+	2	0	DNAH10	122920956	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.150000	0.10189	-0.924000	0.03780	-0.137000	0.14449	GCC	.	.	none		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ZNF879	345462	hgsc.bcm.edu	37	5	178455114	178455114	+	Missense_Mutation	SNP	A	A	G	rs146216019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178455114A>G	ENST00000444149.2	+	4	430	c.242A>G	c.(241-243)cAa>cGa	p.Q81R	ZNF879_ENST00000519896.1_Silent_p.P92P	NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	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)			endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						GGAGTTCCCCAAGGCGCACAT	0.532													A|||	17	0.00339457	0.0008	0.0043	5008	,	,		19179	0.0		0.0089	False		,,,				2504	0.0041				p.Q81R		Atlas-SNP	.											.	ZNF879	41	.	0			c.A242G						PASS	.	A	ARG/GLN	4,1380		0,4,688	84.0	80.0	81.0		242	-0.3	0.0	5	dbSNP_134	81	49,3133		0,49,1542	yes	missense	ZNF879	NM_001136116.1	43	0,53,2230	GG,GA,AA		1.5399,0.289,1.1608	benign	81/564	178455114	53,4513	692	1591	2283	SO:0001583	missense	345462	exon4			TTCCCCAAGGCGC	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.242A>G	5.37:g.178455114A>G	ENSP00000414887:p.Gln81Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	0.237	-1.016524	0.02078	0.00289	0.015399	ENSG00000234284	ENST00000444149;ENST00000522442	T;T	0.05447	3.44;6.0	4.55	-0.285	0.12866	Krueppel-associated box (1);	.	.	.	.	T	0.01061	0.0035	N	0.03891	-0.335	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45556	-0.9253	9	0.05351	T	0.99	-9.1498	8.0252	0.30434	0.623:0.0:0.377:0.0	.	81	B4DU55	ZN879_HUMAN	R	81	ENSP00000414887:Q81R;ENSP00000428477:Q81R	ENSP00000414887:Q81R	Q	+	2	0	ZNF879	178387720	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.314000	0.08092	0.064000	0.16427	0.482000	0.46254	CAA	A|0.996;G|0.004	0.004	strong		0.532	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
CFAP44	55779	hgsc.bcm.edu	37	3	113135374	113135374	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:113135374C>T	ENST00000295868.2	-	6	833	c.671G>A	c.(670-672)cGa>cAa	p.R224Q	WDR52_ENST00000393845.2_Missense_Mutation_p.R224Q|WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA	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						GGACTCACCTCGAAGGACTCT	0.353																																					p.R224Q		Atlas-SNP	.											WDR52,NS,carcinoma,-1,1	WDR52	151	1	0			c.G671A						scavenged	.						48.0	49.0	49.0					3																	113135374		2203	4297	6500	SO:0001583	missense	55779	exon6			TCACCTCGAAGGA																												ENST00000295868.2:c.671G>A	3.37:g.113135374C>T	ENSP00000295868:p.Arg224Gln	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	290	4	0.0137931	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.899955	0.33535	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.06449	5.05;3.3	4.87	-0.511	0.11970	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.04861	0.0131	L	0.37561	1.115	0.80722	D	1	B	0.27625	0.183	B	0.17433	0.018	T	0.43686	-0.9376	9	0.22706	T	0.39	.	10.5017	0.44810	0.0:0.5101:0.0:0.4899	.	224	Q96MT7	WDR52_HUMAN	Q	224	ENSP00000377428:R224Q;ENSP00000295868:R224Q	ENSP00000295868:R224Q	R	-	2	0	WDR52	114618064	0.963000	0.33076	0.986000	0.45419	0.978000	0.69477	0.119000	0.15626	-0.210000	0.10140	0.557000	0.71058	CGA	.	.	none		0.353	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
MSTN	2660	hgsc.bcm.edu	37	2	190925077	190925077	+	Missense_Mutation	SNP	T	T	C	rs1805086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:190925077T>C	ENST00000260950.4	-	2	590	c.458A>G	c.(457-459)aAg>aGg	p.K153R	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	153			K -> R (in dbSNP:rs1805086). {ECO:0000269|PubMed:17186467}.		cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			TAGTTGGGCCTTTACTACTTT	0.353													T|||	356	0.0710863	0.2194	0.0504	5008	,	,		17180	0.001		0.0288	False		,,,				2504	0.001				p.K153R		Atlas-SNP	.											.	MSTN	46	.	0			c.A458G						PASS	.	T	ARG/LYS	906,3500	324.2+/-298.5	99,708,1396	85.0	83.0	83.0		458	5.8	1.0	2	dbSNP_89	83	141,8457	66.3+/-128.7	2,137,4160	yes	missense	MSTN	NM_005259.2	26	101,845,5556	CC,CT,TT		1.6399,20.5629,8.0514	probably-damaging	153/376	190925077	1047,11957	2203	4299	6502	SO:0001583	missense	2660	exon2			TGGGCCTTTACTA	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"""growth differentiation factor 8"""	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.458A>G	2.37:g.190925077T>C	ENSP00000260950:p.Lys153Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	37	CCDS2303.1	134	0.06135531135531135	99	0.20121951219512196	19	0.052486187845303865	0	0.0	16	0.021108179419525065	T	8.860	0.946745	0.18356	0.205629	0.016399	ENSG00000138379	ENST00000260950	T	0.64991	-0.13	5.76	5.76	0.90799	Transforming growth factor-beta, N-terminal (1);	0.092591	0.64402	D	0.000001	T	0.00039	0.0001	N	0.20530	0.585	0.27314	P	0.9572201	B	0.06786	0.001	B	0.13407	0.009	T	0.05767	-1.0865	9	0.13853	T	0.58	-7.3207	16.0697	0.80914	0.0:0.0:0.0:1.0	rs1805086;rs52812921;rs1805086	153	O14793	GDF8_HUMAN	R	153	ENSP00000260950:K153R	ENSP00000260950:K153R	K	-	2	0	MSTN	190633322	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.322000	0.52007	2.194000	0.70268	0.528000	0.53228	AAG	T|0.932;C|0.068	0.068	strong		0.353	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259	
KIAA1731	85459	hgsc.bcm.edu	37	11	93454524	93454524	+	Silent	SNP	T	T	C	rs17651231	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:93454524T>C	ENST00000325212.6	+	19	5958	c.5796T>C	c.(5794-5796)taT>taC	p.Y1932Y	SCARNA9_ENST00000530422.1_RNA|KIAA1731_ENST00000531700.1_Silent_p.Y112Y|SCARNA9_ENST00000362805.1_RNA|Y_RNA_ENST00000363005.1_RNA|SCARNA9_ENST00000364329.1_RNA|KIAA1731_ENST00000344196.4_Silent_p.Y112Y|KIAA1731_ENST00000411936.1_Silent_p.Y1932Y			Q9C0D2	K1731_HUMAN	KIAA1731	1932						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGTTAAGTTATGCTGTGGAGG	0.368													T|||	136	0.0271565	0.0038	0.0476	5008	,	,		20492	0.0		0.0855	False		,,,				2504	0.0123				p.Y1932Y		Atlas-SNP	.											.	KIAA1731	173	.	0			c.T5796C						PASS	.	T		23,1361		0,23,669	371.0	306.0	325.0		5796	1.4	0.0	11	dbSNP_123	325	295,2887		13,269,1309	no	coding-synonymous	KIAA1731	NM_033395.1		13,292,1978	CC,CT,TT		9.2709,1.6618,6.9645		1932/2602	93454524	318,4248	692	1591	2283	SO:0001819	synonymous_variant	85459	exon19			AAGTTATGCTGTG	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.5796T>C	11.37:g.93454524T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	193	87	0.450777	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																			T|0.957;C|0.043	0.043	strong		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
SLC5A1	6523	hgsc.bcm.edu	37	22	32506143	32506143	+	Silent	SNP	C	C	T	rs33954397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32506143C>T	ENST00000266088.4	+	15	2188	c.1938C>T	c.(1936-1938)aaC>aaT	p.N646N	SLC5A1_ENST00000543737.1_Silent_p.N519N	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	646					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	CAGTGTTGAACGTCAATGGCA	0.493													C|||	111	0.0221645	0.003	0.0259	5008	,	,		20879	0.0		0.0606	False		,,,				2504	0.0286				p.N646N		Atlas-SNP	.											.	SLC5A1	80	.	0			c.C1938T						PASS	.	C		61,4345	58.1+/-94.6	0,61,2142	328.0	243.0	272.0		1938	2.4	1.0	22	dbSNP_126	272	602,7998	157.9+/-211.5	20,562,3718	no	coding-synonymous	SLC5A1	NM_000343.3		20,623,5860	TT,TC,CC		7.0,1.3845,5.0976		646/665	32506143	663,12343	2203	4300	6503	SO:0001819	synonymous_variant	6523	exon15			GTTGAACGTCAAT		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1938C>T	22.37:g.32506143C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	224	120	0.535714	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Silent	SNP	ENST00000266088.4	37	CCDS13902.1																																																																																			C|0.952;T|0.048	0.048	strong		0.493	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
OR4B1	119765	hgsc.bcm.edu	37	11	48239182	48239182	+	Missense_Mutation	SNP	C	C	A	rs7130086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:48239182C>A	ENST00000309562.2	+	1	839	c.821C>A	c.(820-822)aCg>aAg	p.T274K		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	274						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(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GTATTCTACACGGTCATCACC	0.453													c|||	1313	0.262181	0.1293	0.1844	5008	,	,		21194	0.3869		0.174	False		,,,				2504	0.4591				p.T274K		Atlas-SNP	.											.	OR4B1	52	.	0			c.C821A						PASS	.	C	LYS/THR	620,3782	269.8+/-269.2	41,538,1622	113.0	92.0	99.0		821	4.6	1.0	11	dbSNP_116	99	1460,7136	277.1+/-292.7	142,1176,2980	yes	missense	OR4B1	NM_001005470.1	78	183,1714,4602	AA,AC,CC		16.9846,14.0845,16.0025	probably-damaging	274/310	48239182	2080,10918	2201	4298	6499	SO:0001583	missense	119765	exon1			TCTACACGGTCAT	AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"""GPCR / Class A : Olfactory receptors"""	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.821C>A	11.37:g.48239182C>A	ENSP00000311605:p.Thr274Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001005470	Q6IF75|Q96R64	Missense_Mutation	SNP	ENST00000309562.2	37	CCDS31485.1	466	0.21336996336996336	67	0.13617886178861788	65	0.17955801104972377	192	0.3356643356643357	142	0.18733509234828497	C	13.26	2.184673	0.38609	0.140845	0.169846	ENSG00000175619	ENST00000309562	T	0.00265	8.39	5.54	4.63	0.57726	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000035	T	0.00012	0.0000	H	0.97896	4.1	0.32621	P	0.523358	D	0.64830	0.994	D	0.67548	0.952	T	0.14392	-1.0474	9	0.87932	D	0	.	12.4818	0.55847	0.0:0.9185:0.0:0.0815	rs7130086	274	Q8NGF8	OR4B1_HUMAN	K	274	ENSP00000311605:T274K	ENSP00000311605:T274K	T	+	2	0	OR4B1	48195758	0.195000	0.23338	0.953000	0.39169	0.088000	0.18126	1.092000	0.30927	1.347000	0.45714	-0.302000	0.09304	ACG	A|0.186;C|0.806;T|0.008	0.186	strong		0.453	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470	
CDRT1	374286	hgsc.bcm.edu	37	17	15498089	15498089	+	Missense_Mutation	SNP	C	C	T	rs201107040		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:15498089C>T	ENST00000395906.3	-	10	1819	c.1820G>A	c.(1819-1821)cGc>cAc	p.R607H	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.R917H|CDRT1_ENST00000354433.3_Missense_Mutation_p.R107H|CDRT1_ENST00000583965.1_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	607										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		CATCAGGCAGCGCTCGTACTT	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		17002	0.0		0.001	False		,,,				2504	0.0				p.R607H		Atlas-SNP	.											ENSG00000251537,colon,carcinoma,-1,4	CDRT1	83	4	0			c.G1820A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	58.0	60.0	60.0		1820	5.0	1.0	17		60	5,8591	4.3+/-15.6	0,5,4293	no	missense	CDRT1	NM_006382.3	29	0,6,6495	TT,TC,CC		0.0582,0.0227,0.0461	probably-damaging	607/753	15498089	6,12996	2203	4298	6501	SO:0001583	missense	374286	exon10			AGGCAGCGCTCGT	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1820G>A	17.37:g.15498089C>T	ENSP00000379242:p.Arg607His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.09|14.09	2.432384|2.432384	0.43224|0.43224	2.27E-4|2.27E-4	5.82E-4|5.82E-4	ENSG00000251537|ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000455584|ENST00000354433;ENST00000261644;ENST00000395906	.|T;T	.|0.19532	.|2.14;2.14	4.99|4.99	4.99|4.99	0.66335|0.66335	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.314339	.|0.20931	.|N	.|0.083091	T|T	0.39835|0.39835	0.1093|0.1093	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.68621	.|0.925;0.959	T|T	0.06023|0.06023	-1.0850|-1.0850	5|10	.|0.46703	.|T	.|0.11	.|.	10.7364|10.7364	0.46128|0.46128	0.0:0.912:0.0:0.088|0.0:0.912:0.0:0.088	.|.	.|607;931	.|O95170;Q59EB2	.|CDRT1_HUMAN;.	T|H	932|107;637;607	.|ENSP00000346416:R107H;ENSP00000379242:R607H	.|ENSP00000346416:R107H	A|R	-|-	1|2	0|0	RP11-385D13.1|CDRT1;RP11-385D13.1	15438814|15438814	0.967000|0.967000	0.33354|0.33354	0.996000|0.996000	0.52242|0.52242	0.995000|0.995000	0.86356|0.86356	1.971000|1.971000	0.40530|0.40530	2.595000|2.595000	0.87683|0.87683	0.585000|0.585000	0.79938|0.79938	GCT|CGC	C|0.999;T|0.001	0.001	weak		0.572	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
SERPINA3	12	hgsc.bcm.edu	37	14	95080803	95080803	+	Missense_Mutation	SNP	G	G	A	rs4934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95080803G>A	ENST00000467132.1	+	2	1173	c.25G>A	c.(25-27)Gct>Act	p.A9T	SERPINA3_ENST00000393078.3_Missense_Mutation_p.A9T|SERPINA3_ENST00000393080.4_Missense_Mutation_p.A9T|RP11-986E7.7_ENST00000553947.1_3'UTR			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	9			A -> T (in dbSNP:rs4934). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		ACCTCTCCTGGCTCTGGGGCT	0.582													G|||	2000	0.399361	0.2133	0.2781	5008	,	,		18889	0.62		0.4871	False		,,,				2504	0.4192				p.A9T		Atlas-SNP	.											.	SERPINA3	78	.	0			c.G25A	GRCh37	CM950001	SERPINA3	M	rs4934	PASS	.	G	THR/ALA	1129,3277	400.6+/-331.6	146,837,1220	66.0	65.0	65.0		25	-0.7	0.0	14	dbSNP_52	65	4102,4498	560.5+/-387.6	1007,2088,1205	yes	missense	SERPINA3	NM_001085.4	58	1153,2925,2425	AA,AG,GG		47.6977,25.6241,40.2199	possibly-damaging	9/424	95080803	5231,7775	2203	4300	6503	SO:0001583	missense	12	exon2			CTCCTGGCTCTGG	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"""Serine (or cysteine) peptidase inhibitors"""	16	protein-coding gene	gene with protein product		107280	"""alpha-1-antichymotrypsin"", ""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"""	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.25G>A	14.37:g.95080803G>A	ENSP00000450540:p.Ala9Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	37	CCDS32150.1	952	0.4358974358974359	100	0.2032520325203252	108	0.2983425414364641	371	0.6486013986013986	373	0.4920844327176781	G	14.13	2.443510	0.43429	0.256241	0.476977	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132;ENST00000380354	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	4.61	-0.687	0.11320	Serpin domain (1);	1.376250	0.04847	N	0.441646	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.30851	0.121;0.297	B;B	0.31751	0.019;0.135	T	0.37430	-0.9706	9	0.23891	T	0.37	.	0.7578	0.01001	0.3256:0.1603:0.3502:0.1639	rs4934;rs7399;rs1065214;rs1065661;rs3168981;rs17753472;rs52816435;rs59552549;rs4934	9;34	P01011;G3V5I3	AACT_HUMAN;.	T	34;9;9;9;9;9	ENSP00000452367:A34T;ENSP00000376793:A9T;ENSP00000376795:A9T;ENSP00000450540:A9T	ENSP00000369712:A9T	A	+	1	0	SERPINA3	94150556	0.002000	0.14202	0.006000	0.13384	0.579000	0.36224	-0.060000	0.11712	-0.020000	0.14032	-0.258000	0.10820	GCT	G|0.587;A|0.413	0.413	strong		0.582	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085	
HECW2	57520	hgsc.bcm.edu	37	2	197208397	197208397	+	Silent	SNP	C	C	T	rs61741962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:197208397C>T	ENST00000260983.3	-	3	566	c.384G>A	c.(382-384)ggG>ggA	p.G128G	HECW2_ENST00000409111.1_5'UTR	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	128					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						TGAAATAGGGCCCAGGCTCAA	0.363													C|||	30	0.00599042	0.0	0.0086	5008	,	,		16772	0.0		0.0219	False		,,,				2504	0.002				p.G128G		Atlas-SNP	.											.	HECW2	239	.	0			c.G384A						PASS	.	C		18,4388	24.3+/-50.5	0,18,2185	182.0	198.0	193.0		384	4.2	1.0	2	dbSNP_129	193	190,8410	83.4+/-145.9	1,188,4111	yes	coding-synonymous	HECW2	NM_020760.1		1,206,6296	TT,TC,CC		2.2093,0.4085,1.5993		128/1573	197208397	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	57520	exon3			ATAGGGCCCAGGC	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.384G>A	2.37:g.197208397C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	24	0.352941	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																			C|0.984;T|0.016	0.016	strong		0.363	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
FTCD	10841	hgsc.bcm.edu	37	21	47571845	47571845	+	Silent	SNP	C	C	T	rs61729391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47571845C>T	ENST00000291670.5	-	4	460	c.417G>A	c.(415-417)ccG>ccA	p.P139P	FTCD_ENST00000397748.1_Silent_p.P139P|FTCD_ENST00000397746.3_Silent_p.P139P|FTCD_ENST00000355384.2_Silent_p.P139P|FTCD_ENST00000359679.2_Silent_p.P139P|FTCD_ENST00000397743.1_Silent_p.P139P|FTCD_ENST00000498355.2_5'UTR|FTCD-AS1_ENST00000446649.1_RNA	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	139	Formiminotransferase N-subdomain. {ECO:0000250}.				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)	CCCGGATGGCCGGCAGGGTCC	0.711													C|||	443	0.0884585	0.0507	0.0504	5008	,	,		14418	0.0853		0.0905	False		,,,				2504	0.1677				p.P139P		Atlas-SNP	.											FTCD,caecum,carcinoma,0,1	FTCD	59	1	0			c.G417A						PASS	.	C	,	265,4015		9,247,1884	6.0	9.0	8.0		417,417	-7.3	0.5	21	dbSNP_129	8	582,7850		18,546,3652	no	coding-synonymous,coding-synonymous	FTCD	NM_006657.2,NM_206965.1	,	27,793,5536	TT,TC,CC		6.9023,6.1916,6.663	,	139/542,139/542	47571845	847,11865	2140	4216	6356	SO:0001819	synonymous_variant	10841	exon4			GATGGCCGGCAGG	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.417G>A	21.37:g.47571845C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Silent	SNP	ENST00000291670.5	37	CCDS13731.1																																																																																			C|0.926;T|0.074	0.074	strong		0.711	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	
LUZP2	338645	hgsc.bcm.edu	37	11	25098938	25098938	+	Missense_Mutation	SNP	G	G	C	rs7930185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:25098938G>C	ENST00000336930.6	+	11	988	c.922G>C	c.(922-924)Gag>Cag	p.E308Q	LUZP2_ENST00000533227.1_Missense_Mutation_p.E222Q			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	308			E -> Q (in dbSNP:rs7930185).			extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						TGCAGAAACCGAGCCTATCCC	0.333													G|||	2195	0.438299	0.1195	0.4712	5008	,	,		12587	0.7808		0.4553	False		,,,				2504	0.4755				p.E308Q		Atlas-SNP	.											.	LUZP2	90	.	0			c.G922C						PASS	.	G	GLN/GLU	741,3665	304.4+/-288.4	65,611,1527	142.0	142.0	142.0		922	3.1	0.0	11	dbSNP_116	142	3621,4979	522.4+/-380.1	766,2089,1445	yes	missense	LUZP2	NM_001009909.2	29	831,2700,2972	CC,CG,GG		42.1047,16.818,33.5384	benign	308/347	25098938	4362,8644	2203	4300	6503	SO:0001583	missense	338645	exon11			GAAACCGAGCCTA	AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.922G>C	11.37:g.25098938G>C	ENSP00000336817:p.Glu308Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	72	0.972973	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Missense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	1042	0.47710622710622713	56	0.11382113821138211	169	0.46685082872928174	468	0.8181818181818182	349	0.4604221635883905	G	6.284	0.420420	0.11928	0.16818	0.421047	ENSG00000187398	ENST00000336930;ENST00000533227	T;T	0.51574	0.71;0.7	5.05	3.09	0.35607	.	0.612081	0.15151	N	0.277731	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;B	0.42556	0.783;0.325	B;B	0.41723	0.365;0.133	T	0.11665	-1.0578	9	0.48119	T	0.1	-0.1151	6.8141	0.23820	0.0972:0.1785:0.7243:0.0	rs7930185;rs17235288;rs52806551;rs7930185	222;308	E9PN53;Q86TE4	.;LUZP2_HUMAN	Q	308;222	ENSP00000336817:E308Q;ENSP00000432952:E222Q	ENSP00000336817:E308Q	E	+	1	0	LUZP2	25055514	0.000000	0.05858	0.005000	0.12908	0.269000	0.26545	0.240000	0.18042	0.581000	0.29539	0.551000	0.68910	GAG	G|0.600;C|0.400	0.400	strong		0.333	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909	
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	188	0	0		WXS	Illumina HiSeq	Phase_I	145	142	0.97931	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	
TTC37	9652	hgsc.bcm.edu	37	5	94826655	94826655	+	Missense_Mutation	SNP	C	C	A	rs2303650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:94826655C>A	ENST00000358746.2	-	37	4186	c.3888G>T	c.(3886-3888)agG>agT	p.R1296S		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1296			R -> S (in dbSNP:rs2303650).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						ATAAATCTATCCTCTTTGGCT	0.388													C|||	1139	0.227436	0.4024	0.1787	5008	,	,		16608	0.12		0.165	False		,,,				2504	0.2004				p.R1296S		Atlas-SNP	.											.	TTC37	128	.	0			c.G3888T						PASS	.	C	SER/ARG	1648,2758	505.4+/-366.1	324,1000,879	98.0	88.0	91.0		3888	3.2	1.0	5	dbSNP_100	91	1367,7233	265.8+/-286.4	123,1121,3056	yes	missense	TTC37	NM_014639.3	110	447,2121,3935	AA,AC,CC		15.8953,37.4035,23.1816	probably-damaging	1296/1565	94826655	3015,9991	2203	4300	6503	SO:0001583	missense	9652	exon37			ATCTATCCTCTTT	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.3888G>T	5.37:g.94826655C>A	ENSP00000351596:p.Arg1296Ser	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	268	116	0.432836	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	454	0.2078754578754579	186	0.3780487804878049	71	0.19613259668508287	72	0.1258741258741259	125	0.16490765171503957	C	15.45	2.836743	0.50951	0.374035	0.158953	ENSG00000198677	ENST00000358746	T	0.78481	-1.18	6.04	3.23	0.37069	.	0.084053	0.85682	N	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.29078	P	0.882896	P	0.40144	0.704	B	0.36719	0.231	T	0.31530	-0.9940	9	0.18276	T	0.48	.	5.8838	0.18870	0.0:0.6167:0.1386:0.2447	rs2303650;rs52800045;rs57022049;rs2303650	1296	Q6PGP7	TTC37_HUMAN	S	1296	ENSP00000351596:R1296S	ENSP00000351596:R1296S	R	-	3	2	TTC37	94852411	0.960000	0.32886	0.999000	0.59377	0.831000	0.47069	1.310000	0.33551	0.398000	0.25338	0.561000	0.74099	AGG	C|0.776;A|0.224	0.224	strong		0.388	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599571	161599571	+	Intron	SNP	T	T	C	rs2290834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161599571T>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000367964.2_Missense_Mutation_p.I106V|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.I106V|FCGR3B_ENST00000531221.1_Missense_Mutation_p.I142V|FCGR2B_ENST00000367960.5_Intron			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	284	0	0		WXS	Illumina HiSeq	Phase_I	102	53	0.519608	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	
LRRC17	10234	hgsc.bcm.edu	37	7	102574920	102574920	+	Missense_Mutation	SNP	G	G	C	rs1057066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102574920G>C	ENST00000339431.4	+	2	855	c.560G>C	c.(559-561)gGg>gCg	p.G187A	LRRC17_ENST00000249377.4_Missense_Mutation_p.G187A|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000455112.2_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	187	LRRCT 1.		G -> A (in dbSNP:rs1057066). {ECO:0000269|PubMed:8982252}.		bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						CGGAATTTGGGGAACTACGCC	0.408													G|||	964	0.192492	0.1793	0.1657	5008	,	,		18592	0.2837		0.1014	False		,,,				2504	0.229				p.G187A		Atlas-SNP	.											.	LRRC17	45	.	0			c.G560C						PASS	.	G	ALA/GLY,,ALA/GLY,	747,3659	302.4+/-287.4	60,627,1516	87.0	90.0	89.0		560,,560,	5.3	1.0	7	dbSNP_86	89	987,7613	212.7+/-252.9	63,861,3376	yes	missense,intron,missense,intron	LRRC17,FBXL13	NM_001031692.2,NM_001111038.1,NM_005824.2,NM_145032.3	60,,60,	123,1488,4892	CC,CG,GG		11.4767,16.9542,13.3323	probably-damaging,,probably-damaging,	187/442,,187/314,	102574920	1734,11272	2203	4300	6503	SO:0001583	missense	10234	exon2			ATTTGGGGAACTA	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.560G>C	7.37:g.102574920G>C	ENSP00000344242:p.Gly187Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	CCDS34721.1	376	0.17216117216117216	85	0.17276422764227642	49	0.13535911602209943	163	0.28496503496503495	79	0.10422163588390501	G	21.4	4.138569	0.77775	0.169542	0.114767	ENSG00000128606	ENST00000339431;ENST00000249377	T;D	0.89810	3.4;-2.57	5.28	5.28	0.74379	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.56097	D	0.000031	T	0.00073	0.0002	L	0.46670	1.46	0.09310	P	0.9999999713712	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.00012	-1.2428	9	0.40728	T	0.16	-23.4069	19.2694	0.94003	0.0:0.0:1.0:0.0	rs1057066;rs3735213;rs52819539;rs59783455;rs1057066	187;187	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	A	187	ENSP00000344242:G187A;ENSP00000249377:G187A	ENSP00000249377:G187A	G	+	2	0	LRRC17	102362156	1.000000	0.71417	0.999000	0.59377	0.860000	0.49131	5.506000	0.66993	2.617000	0.88574	0.563000	0.77884	GGG	G|0.848;C|0.152	0.152	strong		0.408	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824	
THBS2	7058	hgsc.bcm.edu	37	6	169622490	169622490	+	Silent	SNP	G	G	A	rs9505895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:169622490G>A	ENST00000366787.3	-	20	3324	c.3075C>T	c.(3073-3075)gcC>gcT	p.A1025A	THBS2_ENST00000488355.1_5'UTR|XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1025	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.A1025A(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AGACGAAGCCGGCATAGTCGT	0.547													g|||	1108	0.221246	0.2821	0.2205	5008	,	,		17516	0.1518		0.2048	False		,,,				2504	0.228				p.A1025A	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	1	Substitution - coding silent(1)	stomach(1)	c.C3075T						PASS	.	T		1085,3321	391.7+/-328.2	143,799,1261	86.0	79.0	82.0		3075	-8.2	0.0	6	dbSNP_119	82	1739,6861	315.1+/-312.1	175,1389,2736	no	coding-synonymous	THBS2	NM_003247.2		318,2188,3997	AA,AG,GG		20.2209,24.6255,21.7131		1025/1173	169622490	2824,10182	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon20			GAAGCCGGCATAG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3075C>T	6.37:g.169622490G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.783;A|0.217	0.217	strong		0.547	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
FBXW12	285231	hgsc.bcm.edu	37	3	48422235	48422235	+	Missense_Mutation	SNP	T	T	A	rs6784322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48422235T>A	ENST00000296438.5	+	8	1004	c.818T>A	c.(817-819)gTt>gAt	p.V273D	RN7SL321P_ENST00000581742.1_RNA|FBXW12_ENST00000468158.1_3'UTR|FBXW12_ENST00000436231.1_Missense_Mutation_p.V116D|FBXW12_ENST00000415155.1_Missense_Mutation_p.V203D|FBXW12_ENST00000445170.1_Missense_Mutation_p.V254D	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	273			V -> D (in dbSNP:rs6784322). {ECO:0000269|PubMed:15040455, ECO:0000269|PubMed:15489334}.							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)		GAAGGCAGTGTTCCTCTGTCT	0.488													t|||	1772	0.353834	0.3018	0.3703	5008	,	,		19337	0.3373		0.4702	False		,,,				2504	0.3098				p.V273D		Atlas-SNP	.											.	FBXW12	44	.	0			c.T818A						PASS	.	T	ASP/VAL,ASP/VAL,ASP/VAL	1465,2941	473.0+/-356.5	237,991,975	102.0	99.0	100.0		608,761,818	-6.8	0.0	3	dbSNP_116	100	4066,4534	558.7+/-387.3	966,2134,1200	yes	missense,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	152,152,152	1203,3125,2175	AA,AT,TT		47.2791,33.2501,42.5265	benign,benign,benign	203/395,254/446,273/465	48422235	5531,7475	2203	4300	6503	SO:0001583	missense	285231	exon8			GCAGTGTTCCTCT	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.818T>A	3.37:g.48422235T>A	ENSP00000296438:p.Val273Asp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	153	90	0.588235	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	803	0.3676739926739927	135	0.27439024390243905	135	0.3729281767955801	186	0.32517482517482516	347	0.4577836411609499	t	8.943	0.966403	0.18659	0.332501	0.472791	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.63096	2.05;-0.02;1.63;3.5	4.38	-6.75	0.01738	Quinoprotein amine dehydrogenase, beta chain-like (1);	1.814540	0.02661	N	0.107520	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B;B;B	0.19817	0.039;0.039;0.023;0.023	B;B;B;B	0.23716	0.048;0.029;0.013;0.021	T	0.13388	-1.0511	9	0.22706	T	0.39	-0.7478	2.7167	0.05189	0.1117:0.1654:0.2368:0.4861	rs6784322;rs56511515;rs6784322	172;254;203;273	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	D	172;273;116;254;203	ENSP00000296438:V273D;ENSP00000413866:V116D;ENSP00000406139:V254D;ENSP00000414683:V203D	ENSP00000296438:V273D	V	+	2	0	FBXW12	48397239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.749000	0.04813	-1.581000	0.01642	-0.821000	0.03111	GTT	T|0.600;A|0.400	0.400	strong		0.488	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102	
ARVCF	421	hgsc.bcm.edu	37	22	19969106	19969106	+	Missense_Mutation	SNP	A	A	G	rs2240717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19969106A>G	ENST00000263207.3	-	5	815	c.524T>C	c.(523-525)gTg>gCg	p.V175A	ARVCF_ENST00000406259.1_Missense_Mutation_p.V175A|ARVCF_ENST00000406522.1_Missense_Mutation_p.V112A|ARVCF_ENST00000401994.1_Missense_Mutation_p.V112A|ARVCF_ENST00000344269.3_Missense_Mutation_p.V112A|ARVCF_ENST00000487793.1_5'UTR	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	175			V -> A (in dbSNP:rs2240717).		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)					GAGTGTGGCCACTGGGCCACC	0.687													G|||	2101	0.419529	0.5983	0.366	5008	,	,		14994	0.2302		0.3459	False		,,,				2504	0.4867				p.V175A		Atlas-SNP	.											.	ARVCF	54	.	0			c.T524C						PASS	.	G	ALA/VAL	2258,1978		656,946,516	17.0	21.0	20.0		524	0.0	0.0	22	dbSNP_98	20	2834,5496		579,1676,1910	yes	missense	ARVCF	NM_001670.2	64	1235,2622,2426	GG,GA,AA		34.0216,46.695,40.522	benign	175/963	19969106	5092,7474	2118	4165	6283	SO:0001583	missense	421	exon5			GTGGCCACTGGGC		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.524T>C	22.37:g.19969106A>G	ENSP00000263207:p.Val175Ala	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	819	0.375	287	0.5833333333333334	131	0.36187845303867405	132	0.23076923076923078	269	0.3548812664907652	G	2.063	-0.414989	0.04766	0.53305	0.340216	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	4.43	0.00231	0.14049	.	1.179390	0.05906	N	0.630796	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	0.45644	-0.9247	8	.	.	.	2.2165	8.9895	0.36014	0.4449:0.0:0.5551:0.0	rs2240717;rs2240717	175	O00192	ARVC_HUMAN	A	175;112;112;112;175	ENSP00000263207:V175A;ENSP00000342042:V112A;ENSP00000384341:V112A;ENSP00000384732:V112A;ENSP00000385444:V175A	.	V	-	2	0	ARVCF	18349106	0.793000	0.28825	0.003000	0.11579	0.004000	0.04260	1.447000	0.35101	-0.211000	0.10124	-2.027000	0.00425	GTG	T|0.008;G|0.350	0.350	strong		0.687	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
STARD13	90627	hgsc.bcm.edu	37	13	33704154	33704154	+	Silent	SNP	C	C	T	rs596742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:33704154C>T	ENST00000336934.5	-	5	776	c.660G>A	c.(658-660)ccG>ccA	p.P220P	STARD13_ENST00000255486.4_Silent_p.P212P|STARD13_ENST00000399365.3_Silent_p.P102P	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	220					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)		CCAGCATGACCGGGTTGTCTG	0.627													C|||	534	0.106629	0.2315	0.049	5008	,	,		16990	0.001		0.0875	False		,,,				2504	0.1074				p.P220P		Atlas-SNP	.											.	STARD13	100	.	0			c.G660A						PASS	.	C	,,	815,3591	323.4+/-298.1	71,673,1459	44.0	48.0	47.0		306,660,636	-1.1	0.0	13	dbSNP_83	47	705,7895	175.0+/-225.2	31,643,3626	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	102,1316,5085	TT,TC,CC		8.1977,18.4975,11.6869	,,	102/996,220/1114,212/1106	33704154	1520,11486	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			CATGACCGGGTTG	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.660G>A	13.37:g.33704154C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.894;T|0.106	0.106	strong		0.627	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
MST1L	11223	hgsc.bcm.edu	37	1	17085006	17085006	+	RNA	SNP	C	C	T	rs201784242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17085006C>T	ENST00000455405.2	-	0	182							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CGGATGGCCCCCAGCCACGCG	0.607																																					p.G490E		Atlas-SNP	.											.	.	.	.	0			c.G1469A						PASS	.																																					11223	exon11			TGGCCCCCAGCCA	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.17085006C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	240	26	0.108333	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	11.84	1.758278	0.31137	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.000000	0.42964	D	0.000638	T	0.62636	0.2444	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.65524	-0.6147	6	0.35671	T	0.21	.	6.8326	0.23919	0.0:0.9999:0.0:1.0E-4	.	490;490	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	E	459;490;490	.	ENSP00000439273:G490E	G	-	2	0	MST1P9	16957593	0.982000	0.34865	0.000000	0.03702	0.000000	0.00434	2.313000	0.43735	-0.000000	0.14550	0.000000	0.15137	GGG	C|0.987;T|0.013	0.013	strong		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
GJA4	2701	hgsc.bcm.edu	37	1	35260769	35260769	+	Missense_Mutation	SNP	C	C	T	rs1764391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35260769C>T	ENST00000342280.4	+	2	1043	c.955C>T	c.(955-957)Ccc>Tcc	p.P319S		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	319			P -> S (in allele CX37*2; dbSNP:rs1764391). {ECO:0000269|PubMed:10447790, ECO:0000269|PubMed:10728596, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGGCCAAAAACCCCCAAGTCG	0.577													T|||	1671	0.333666	0.5847	0.2723	5008	,	,		17834	0.1726		0.332	False		,,,				2504	0.2055				p.P319S		Atlas-SNP	.											.	GJA4	25	.	0			c.C955T	GRCh37	CM994122	GJA4	M	rs1764391	PASS	.	T	SER/PRO	2315,2091	563.5+/-381.2	610,1095,498	43.0	41.0	42.0		955	0.0	0.9	1	dbSNP_89	42	2603,5997	677.2+/-403.4	395,1813,2092	yes	missense	GJA4	NM_002060.2	74	1005,2908,2590	TT,TC,CC		30.2674,47.458,37.8133	benign	319/334	35260769	4918,8088	2203	4300	6503	SO:0001583	missense	2701	exon2			CAAAAACCCCCAA	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.955C>T	1.37:g.35260769C>T	ENSP00000343676:p.Pro319Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	CCDS30669.1	730	0.3342490842490842	264	0.5365853658536586	109	0.3011049723756906	106	0.1853146853146853	251	0.3311345646437995	T	0.051	-1.249319	0.01469	0.52542	0.302674	ENSG00000187513	ENST00000342280	D	0.97114	-4.25	5.25	0.0125	0.14092	.	2.066470	0.02474	N	0.087865	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	0.42816	-0.9429	9	0.36615	T	0.2	.	5.8617	0.18752	0.0:0.4496:0.296:0.2544	rs1764391;rs16837028;rs52823203;rs1764391	319	P35212	CXA4_HUMAN	S	319	ENSP00000343676:P319S	ENSP00000343676:P319S	P	+	1	0	GJA4	35033356	0.000000	0.05858	0.865000	0.33974	0.202000	0.24057	0.155000	0.16362	0.237000	0.21200	-0.361000	0.07541	CCC	C|0.634;T|0.366	0.366	strong		0.577	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
RFPL3	10738	hgsc.bcm.edu	37	22	32756407	32756407	+	Missense_Mutation	SNP	A	A	G	rs5749408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32756407A>G	ENST00000249007.4	+	2	747	c.542A>G	c.(541-543)tAc>tGc	p.Y181C	RFPL3_ENST00000397468.1_Missense_Mutation_p.Y152C|RFPL3S_ENST00000400234.1_3'UTR|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.Y152C|RFPL3S_ENST00000382084.4_3'UTR	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	181	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Y -> C (in dbSNP:rs5749408).				zinc ion binding (GO:0008270)	p.Y152C(1)|p.Y181C(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGCCGCCACTACTGGGAGGTG	0.562													a|||	851	0.169928	0.1059	0.1124	5008	,	,		18743	0.4583		0.0467	False		,,,				2504	0.1268				p.Y181C		Atlas-SNP	.											RFPL3_ENST00000249007,NS,carcinoma,0,2	RFPL3	91	2	2	Substitution - Missense(2)	stomach(2)	c.A542G						scavenged	.	A	CYS/TYR,CYS/TYR	499,3907	228.1+/-243.1	40,419,1744	85.0	86.0	85.0		542,455	0.7	0.2	22	dbSNP_114	85	479,8117	140.3+/-196.8	11,457,3830	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	194,194	51,876,5574	GG,GA,AA		5.5724,11.3255,7.5219	benign,benign	181/318,152/289	32756407	978,12024	2203	4298	6501	SO:0001583	missense	10738	exon2			GCCACTACTGGGA	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.542A>G	22.37:g.32756407A>G	ENSP00000249007:p.Tyr181Cys	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	386	0.17673992673992675	52	0.10569105691056911	46	0.1270718232044199	254	0.44405594405594406	34	0.044854881266490766	A	8.527	0.870091	0.17322	0.113255	0.055724	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.74947	-0.89;-0.89;-0.89	0.704	0.704	0.18121	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.00012	0.0000	M	0.81497	2.545	0.09310	P	0.999999999404185	B	0.33413	0.411	B	0.28709	0.093	T	0.22556	-1.0213	8	0.54805	T	0.06	.	5.601	0.17353	0.9999:0.0:1.0E-4:0.0	rs5749408	181	O75679	RFPL3_HUMAN	C	152;181;152	ENSP00000380609:Y152C;ENSP00000249007:Y181C;ENSP00000371520:Y152C	ENSP00000249007:Y181C	Y	+	2	0	RFPL3	31086407	0.989000	0.36119	0.246000	0.24233	0.050000	0.14768	1.786000	0.38694	0.528000	0.28580	0.172000	0.16884	TAC	A|0.959;G|0.041	0.041	strong		0.562	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
MED9	55090	hgsc.bcm.edu	37	17	17394611	17394611	+	Silent	SNP	G	G	A	rs1242489	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	26	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	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	
OR51B6	390058	hgsc.bcm.edu	37	11	5373242	5373242	+	Missense_Mutation	SNP	T	T	G	rs5006885	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373242T>G	ENST00000380219.1	+	1	505	c.505T>G	c.(505-507)Tcc>Gcc	p.S169A	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	169			S -> A (in dbSNP:rs5006885). {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)			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)		CTACTGTCGATCCCATGTACT	0.468													T|||	1191	0.237819	0.3366	0.2392	5008	,	,		22723	0.0863		0.2684	False		,,,				2504	0.228				p.S169A		Atlas-SNP	.											.	OR51B6	53	.	0			c.T505G						PASS	.	T	ALA/SER	1320,3082	445.9+/-347.8	185,950,1066	238.0	194.0	209.0		505	2.8	0.1	11	dbSNP_113	209	2281,6313	383.9+/-340.9	310,1661,2326	yes	missense	OR51B6	NM_001004750.1	99	495,2611,3392	GG,GT,TT		26.5418,29.9864,27.7085	possibly-damaging	169/313	5373242	3601,9395	2201	4297	6498	SO:0001583	missense	390058	exon1			TGTCGATCCCATG		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.505T>G	11.37:g.5373242T>G	ENSP00000369568:p.Ser169Ala	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	163	68	0.417178	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	488	0.22344322344322345	169	0.3434959349593496	94	0.2596685082872928	30	0.05244755244755245	195	0.25725593667546176	T	13.44	2.238074	0.39598	0.299864	0.265418	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00115	8.71	5.15	2.77	0.32553	GPCR, rhodopsin-like superfamily (1);	0.250277	0.28647	N	0.014606	T	0.00012	0.0000	L	0.49571	1.57	0.80722	P	0.0	D	0.65815	0.995	D	0.63192	0.912	T	0.52946	-0.8507	9	0.44086	T	0.13	.	9.095	0.36634	0.4264:0.0:0.0:0.5736	rs5006885;rs58324903;rs5006885	169	Q9H340	O51B6_HUMAN	A	168;169	ENSP00000369568:S169A	ENSP00000369568:S169A	S	+	1	0	OR51B6	5329818	0.000000	0.05858	0.066000	0.19879	0.759000	0.43091	-0.362000	0.07602	0.394000	0.25230	0.455000	0.32223	TCC	T|0.751;G|0.249	0.249	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230440	23230440	+	Splice_Site	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230440G>A	ENST00000526893.1	+	1	480		c.e1+1		hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Splice_Site|IGLL5_ENST00000531372.1_Splice_Site	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGTGGGGCAGGTAAGGGGCAA	0.627																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.100+1G>A						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGCAGGTAAGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.206+1G>A	22.37:g.23230440G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	NM_001256296		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271539	0.23221	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.74	0.51788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21560440	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.700000	0.37815	2.481000	0.83766	0.643000	0.83706	.	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron
MYO15A	51168	hgsc.bcm.edu	37	17	18064730	18064730	+	Silent	SNP	C	C	T	rs8077577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18064730C>T	ENST00000205890.5	+	57	9824	c.9486C>T	c.(9484-9486)gaC>gaT	p.D3162D	MYO15A_ENST00000451725.2_Silent_p.D54D|MYO15A_ENST00000418233.3_Silent_p.D426D	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3162	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|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)					TCCTCCAAGACGTGAGCCGGA	0.632													C|||	789	0.157548	0.2231	0.1758	5008	,	,		18343	0.0149		0.2038	False		,,,				2504	0.1554				p.D3162D		Atlas-SNP	.											.	MYO15A	268	.	0			c.C9486T						PASS	.	C		873,3373		104,665,1354	75.0	80.0	78.0		9486	-5.0	0.0	17	dbSNP_116	78	1733,6747		173,1387,2680	no	coding-synonymous	MYO15A	NM_016239.3		277,2052,4034	TT,TC,CC		20.4363,20.5605,20.4778		3162/3531	18064730	2606,10120	2123	4240	6363	SO:0001819	synonymous_variant	51168	exon56			CCAAGACGTGAGC	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.9486C>T	17.37:g.18064730C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.806;T|0.194	0.194	strong		0.632	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
TBCD	6904	hgsc.bcm.edu	37	17	80863857	80863857	+	Missense_Mutation	SNP	T	T	C	rs2292971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80863857T>C	ENST00000355528.4	+	20	1980	c.1850T>C	c.(1849-1851)aTg>aCg	p.M617T	TBCD_ENST00000397466.2_Missense_Mutation_p.M231T|TBCD_ENST00000539345.2_Missense_Mutation_p.M617T	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	617			M -> T (in dbSNP:rs2292971). {ECO:0000269|PubMed:15489334}.		'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GATCTTCACATGAGGCATGGG	0.567													C|||	2434	0.486022	0.6989	0.3703	5008	,	,		21227	0.2609		0.4573	False		,,,				2504	0.5419				p.M617T		Atlas-SNP	.											.	TBCD	94	.	0			c.T1850C						PASS	.	C	THR/MET	2857,1383		969,919,232	92.0	94.0	94.0		1850	1.9	0.1	17	dbSNP_100	94	3645,4813		789,2067,1373	yes	missense	TBCD	NM_005993.4	81	1758,2986,1605	CC,CT,TT		43.0953,32.6179,48.7951	benign	617/1193	80863857	6502,6196	2120	4229	6349	SO:0001583	missense	6904	exon20			TTCACATGAGGCA	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.1850T>C	17.37:g.80863857T>C	ENSP00000347719:p.Met617Thr	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	988	0.4523809523809524	344	0.6991869918699187	148	0.4088397790055249	151	0.263986013986014	345	0.4551451187335092	C	0	-2.677429	0.00102	0.673821	0.430953	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000397466;ENST00000536182	T;T	0.66995	-0.24;-0.24	5.18	1.93	0.25924	Armadillo-like helical (1);Armadillo-type fold (1);	0.483859	0.21986	N	0.066222	T	0.00012	0.0000	N	0.00859	-1.14	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	0.41538	-0.9503	8	.	.	.	.	3.3001	0.06980	0.14:0.5663:0.1357:0.1579	rs2292971;rs17846260;rs17859282;rs59603092;rs2292971	617;617;617	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	T	617;368;231;617	ENSP00000347719:M617T;ENSP00000380608:M231T	.	M	+	2	0	TBCD	78457146	0.010000	0.17322	0.053000	0.19242	0.000000	0.00434	0.028000	0.13644	-0.066000	0.12998	-0.735000	0.03563	ATG	T|0.550;C|0.450	0.450	strong		0.567	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
ANLN	54443	hgsc.bcm.edu	37	7	36445855	36445855	+	Silent	SNP	A	A	C	rs386712160|rs61737563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:36445855A>C	ENST00000265748.2	+	4	774	c.553A>C	c.(553-555)Aga>Cga	p.R185R	ANLN_ENST00000396068.2_Silent_p.R185R	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	185	Nuclear localization.		R -> K (in dbSNP:rs197367). {ECO:0000269|PubMed:10931866, ECO:0000269|PubMed:16964243}.		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						TTCCCCTCCCAGACCTCTGCT	0.468													A|||	238	0.047524	0.0431	0.0677	5008	,	,		18777	0.002		0.1064	False		,,,				2504	0.0256				p.R185R		Atlas-SNP	.											.	ANLN	101	.	0			c.A553C						PASS	.																																			SO:0001819	synonymous_variant	54443	exon4			CCTCCCAGACCTC	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.553A>C	7.37:g.36445855A>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	146	41	0.280822	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	37	CCDS5447.1																																																																																			A|0.929;C|0.071	0.071	strong		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
SVIL	6840	hgsc.bcm.edu	37	10	29769647	29769647	+	Silent	SNP	G	G	A	rs10763720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29769647G>A	ENST00000355867.4	-	29	5948	c.5196C>T	c.(5194-5196)gtC>gtT	p.V1732V	PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000535393.1_Silent_p.V646V|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000538146.1_Silent_p.V524V|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375398.2_Silent_p.V1732V|SVIL_ENST00000375400.3_Silent_p.V1306V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1732					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)				AGCCACGGCCGACGTTCACTC	0.567													G|||	253	0.0505192	0.0371	0.0533	5008	,	,		16755	0.001		0.1362	False		,,,				2504	0.0297				p.V1732V		Atlas-SNP	.											.	SVIL	226	.	0			c.C5196T						PASS	.	G	,	223,4183	133.3+/-169.7	0,223,1980	174.0	148.0	157.0		3918,5196	-8.8	0.2	10	dbSNP_120	157	1131,7469	233.7+/-266.9	81,969,3250	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	81,1192,5230	AA,AG,GG		13.1512,5.0613,10.4106	,	1306/1789,1732/2215	29769647	1354,11652	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon29			ACGGCCGACGTTC	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.5196C>T	10.37:g.29769647G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.917;A|0.083	0.083	strong		0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
DOPEY1	23033	hgsc.bcm.edu	37	6	83880167	83880167	+	IGR	SNP	C	C	T	rs473267	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:83880167C>T	ENST00000349129.2	+	0	8210				PGM3_ENST00000512866.1_Missense_Mutation_p.D466N|PGM3_ENST00000513973.1_Missense_Mutation_p.D466N|DOPEY1_ENST00000484282.1_3'UTR|PGM3_ENST00000283977.4_Missense_Mutation_p.D385N|PGM3_ENST00000506587.1_Missense_Mutation_p.D494N	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	158	0	0		WXS	Illumina HiSeq	Phase_I	162	87	0.537037	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	
MYOM3	127294	hgsc.bcm.edu	37	1	24416133	24416133	+	Silent	SNP	C	C	T	rs4276859	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24416133C>T	ENST00000374434.3	-	14	1671	c.1509G>A	c.(1507-1509)ccG>ccA	p.P503P	MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Silent_p.P503P|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Silent_p.P504P	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	503	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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)		CATTGGTTGGCGGTGAGGGGA	0.597													C|||	871	0.173922	0.1876	0.1254	5008	,	,		18991	0.1845		0.1143	False		,,,				2504	0.2403				p.P503P		Atlas-SNP	.											MYOM3,caecum,carcinoma,0,1	MYOM3	131	1	0			c.G1509A						PASS	.	C		619,3447		51,517,1465	35.0	40.0	38.0		1509	-3.8	0.0	1	dbSNP_111	38	899,7463		48,803,3330	no	coding-synonymous	MYOM3	NM_152372.3		99,1320,4795	TT,TC,CC		10.751,15.2238,12.2144		503/1438	24416133	1518,10910	2033	4181	6214	SO:0001819	synonymous_variant	127294	exon14			GGTTGGCGGTGAG	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.1509G>A	1.37:g.24416133C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			C|0.855;T|0.145	0.145	strong		0.597	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
C8orf34	116328	hgsc.bcm.edu	37	8	69434195	69434195	+	Silent	SNP	T	T	C	rs2289831	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:69434195T>C	ENST00000539993.1	+	6	1218	c.669T>C	c.(667-669)agT>agC	p.S223S	C8orf34_ENST00000518698.1_Silent_p.S309S|C8orf34_ENST00000348340.2_Silent_p.S223S|C8orf34_ENST00000337103.4_Silent_p.S198S			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	223										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			GTGGCTCTAGTCCTGCAGGAA	0.403													C|||	1038	0.207268	0.4077	0.1455	5008	,	,		16810	0.1121		0.1392	False		,,,				2504	0.1483				p.S309S		Atlas-SNP	.											.	C8orf34	170	.	0			c.T927C						PASS	.	C	,	1597,2809	664.7+/-401.4	286,1025,892	94.0	91.0	92.0		927,927	-0.8	0.9	8	dbSNP_100	92	1171,7429	765.0+/-407.6	79,1013,3208	no	coding-synonymous,coding-synonymous	C8orf34	NM_001195639.1,NM_052958.2	,	365,2038,4100	CC,CT,TT		13.6163,36.246,21.2825	,	309/374,309/539	69434195	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	116328	exon6			CTCTAGTCCTGCA	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"""vestibule 1"""						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.669T>C	8.37:g.69434195T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Silent	SNP	ENST00000539993.1	37																																																																																				T|0.788;C|0.212	0.212	strong		0.403	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	
MEPE	56955	hgsc.bcm.edu	37	4	88767008	88767008	+	Missense_Mutation	SNP	G	G	A	rs17013285	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88767008G>A	ENST00000424957.3	+	4	1061	c.988G>A	c.(988-990)Gtt>Att	p.V330I	MEPE_ENST00000497649.2_Missense_Mutation_p.V306I|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000560249.1_Missense_Mutation_p.V217I|MEPE_ENST00000395102.4_Missense_Mutation_p.V361I|MEPE_ENST00000540395.1_Missense_Mutation_p.V217I|MEPE_ENST00000361056.3_Missense_Mutation_p.V330I	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	330			V -> I (in dbSNP:rs17013285).		biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		GGCAGATGCTGTTGATGTCAG	0.458													G|||	863	0.172324	0.0484	0.1801	5008	,	,		20635	0.2827		0.164	False		,,,				2504	0.229				p.V330I		Atlas-SNP	.											.	MEPE	86	.	0			c.G988A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	286,4120	158.1+/-190.9	8,270,1925	65.0	64.0	64.0		988,649,649,649,988	0.4	0.0	4	dbSNP_123	64	1468,7132	274.2+/-291.1	134,1200,2966	yes	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	29,29,29,29,29	142,1470,4891	AA,AG,GG		17.0698,6.4911,13.4861	benign,benign,benign,benign,benign	330/526,217/413,217/413,217/413,330/526	88767008	1754,11252	2203	4300	6503	SO:0001583	missense	56955	exon4			GATGCTGTTGATG	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.988G>A	4.37:g.88767008G>A	ENSP00000416984:p.Val330Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	385	0.1762820512820513	25	0.0508130081300813	54	0.14917127071823205	171	0.29895104895104896	135	0.17810026385224276	G	9.102	1.004490	0.19199	0.064911	0.170698	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.95;0.94	4.68	0.436	0.16549	.	0.506936	0.16629	N	0.206152	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.15719	0.014	B	0.10450	0.005	T	0.34650	-0.9820	9	0.31617	T	0.26	-0.3551	3.377	0.07241	0.3818:0.2037:0.4145:0.0	rs17013285;rs52799941;rs17013285	330	Q9NQ76	MEPE_HUMAN	I	330;361;306;217;330	ENSP00000416984:V330I;ENSP00000378534:V361I;ENSP00000422747:V306I;ENSP00000443491:V217I;ENSP00000354341:V330I	ENSP00000354341:V330I	V	+	1	0	MEPE	88986032	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.389000	0.20751	0.161000	0.19458	0.655000	0.94253	GTT	G|0.854;A|0.146	0.146	strong		0.458	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
LAMC3	10319	hgsc.bcm.edu	37	9	133963008	133963008	+	Splice_Site	SNP	G	G	A	rs4740412	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133963008G>A	ENST00000361069.4	+	26	4509	c.4376G>A	c.(4375-4377)cGg>cAg	p.R1459Q	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1459	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GAAGCTGAGCGGGTACGTTTG	0.657													G|||	818	0.163339	0.0635	0.2435	5008	,	,		18447	0.0833		0.2714	False		,,,				2504	0.2127				p.R1459Q		Atlas-SNP	.											LAMC3,NS,carcinoma,-1,1	LAMC3	167	1	0			c.G4376A						PASS	.	G	GLN/ARG	359,4047	184.0+/-211.4	15,329,1859	66.0	72.0	70.0		4376	-4.3	0.1	9	dbSNP_111	70	2287,6313	383.0+/-340.6	301,1685,2314	yes	missense-near-splice	LAMC3	NM_006059.3	43	316,2014,4173	AA,AG,GG		26.593,8.148,20.3445	benign	1459/1576	133963008	2646,10360	2203	4300	6503	SO:0001630	splice_region_variant	10319	exon26			CTGAGCGGGTACG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.4377+1G>A	9.37:g.133963008G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	374|374	0.17124542124542125|0.17124542124542125	39|39	0.07926829268292683|0.07926829268292683	94|94	0.2596685082872928|0.2596685082872928	41|41	0.07167832167832168|0.07167832167832168	200|200	0.2638522427440633|0.2638522427440633	G|G	0.779|0.779	-0.763118|-0.763118	0.02996|0.02996	0.08148|0.08148	0.26593|0.26593	ENSG00000050555|ENSG00000050555	ENST00000355452|ENST00000361069;ENST00000355048	.|T	.|0.26518	.|1.73	4.62|4.62	-4.34|-4.34	0.03666|0.03666	.|.	.|1.674320	.|0.03126	.|N	.|0.164480	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00823|0.00823	-1.155|-1.155	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.34403|0.34403	-0.9830|-0.9830	4|9	.|0.14656	.|T	.|0.56	.|.	8.3932|8.3932	0.32542|0.32542	0.2491:0.0:0.6052:0.1457|0.2491:0.0:0.6052:0.1457	rs4740412;rs17453122;rs52815542;rs4740412|rs4740412;rs17453122;rs52815542;rs4740412	.|140;1459	.|Q9UF61;Q9Y6N6	.|.;LAMC3_HUMAN	R|Q	141|1459;1471	.|ENSP00000354360:R1459Q	.|ENSP00000347156:R1471Q	G|R	+|+	1|2	0|0	LAMC3|LAMC3	132952829|132952829	0.001000|0.001000	0.12720|0.12720	0.080000|0.080000	0.20451|0.20451	0.126000|0.126000	0.20510|0.20510	-0.404000|-0.404000	0.07205|0.07205	-0.993000|-0.993000	0.03467|0.03467	-1.595000|-1.595000	0.00837|0.00837	GGG|CGG	G|0.817;A|0.183	0.183	strong		0.657	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation
SORL1	6653	hgsc.bcm.edu	37	11	121498410	121498410	+	Missense_Mutation	SNP	G	G	A	rs146742626		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:121498410G>A	ENST00000260197.7	+	47	6640	c.6511G>A	c.(6511-6513)Gcc>Acc	p.A2171T	SORL1_ENST00000525532.1_Missense_Mutation_p.A1115T|SORL1_ENST00000532694.1_Missense_Mutation_p.A1017T|SORL1_ENST00000534286.1_Missense_Mutation_p.A1081T|SORL1_ENST00000527934.1_Missense_Mutation_p.A786T	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	2171					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CAGCTTCACCGCCTTCGCCAA	0.607																																					p.A2171T		Atlas-SNP	.											.	SORL1	218	.	0			c.G6511A						PASS	.	G	THR/ALA	0,4404		0,0,2202	59.0	52.0	54.0		6511	6.0	0.2	11	dbSNP_134	54	1,8597	1.2+/-3.3	0,1,4298	no	missense	SORL1	NM_003105.5	58	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	2171/2215	121498410	1,13001	2202	4299	6501	SO:0001583	missense	6653	exon47			TTCACCGCCTTCG	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.6511G>A	11.37:g.121498410G>A	ENSP00000260197:p.Ala2171Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610245	0.87258	0.0	1.16E-4	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	D;D;D;D;D	0.91464	-2.85;-2.59;-2.23;-2.26;-2.13	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.93058	0.7790	L	0.59436	1.845	0.58432	D	0.99999	D;D	0.62365	0.983;0.991	B;P	0.54629	0.397;0.757	D	0.91897	0.5528	10	0.44086	T	0.13	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	786;2171	E9PKB0;Q92673	.;SORL_HUMAN	T	2171;1115;1017;1081;786	ENSP00000260197:A2171T;ENSP00000434634:A1115T;ENSP00000432131:A1017T;ENSP00000436447:A1081T;ENSP00000435405:A786T	ENSP00000260197:A2171T	A	+	1	0	SORL1	121003620	1.000000	0.71417	0.204000	0.23530	0.947000	0.59692	5.412000	0.66392	2.826000	0.97356	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.607	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381826	39381826	+	Missense_Mutation	SNP	A	A	G	rs2076109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39381826A>G	ENST00000333467.3	+	3	229	c.184A>G	c.(184-186)Aag>Gag	p.K62E	APOBEC3B_ENST00000402182.3_Missense_Mutation_p.K62E|APOBEC3B_ENST00000407298.3_Missense_Mutation_p.K62E	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	62			K -> E (in dbSNP:rs2076109). {ECO:0000269|PubMed:15461802}.		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)					GGTGTATTTCAAGCCTCAGTA	0.587													C|||	3211	0.641174	0.6762	0.5259	5008	,	,		13686	0.628		0.5974	False		,,,				2504	0.7342				p.K62E		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.A184G						PASS	.	C	GLU/LYS	3020,1374		1091,838,268	107.0	92.0	97.0		184	-1.1	0.0	22	dbSNP_96	97	4829,3735		1532,1765,985	no	missense	APOBEC3B	NM_004900.3	56	2623,2603,1253	GG,GA,AA		43.6128,31.2699,39.4274	benign	62/383	39381826	7849,5109	2197	4282	6479	SO:0001583	missense	9582	exon3			TATTTCAAGCCTC	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.184A>G	22.37:g.39381826A>G	ENSP00000327459:p.Lys62Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Missense_Mutation	SNP	ENST00000333467.3	37	CCDS13982.1	1367	0.6259157509157509	332	0.6747967479674797	185	0.511049723756906	379	0.6625874125874126	471	0.6213720316622692	.	5.287	0.238307	0.10023	0.687301	0.563872	ENSG00000179750	ENST00000407298;ENST00000402182;ENST00000333467	T;T;T	0.65178	-0.14;-0.14;-0.14	0.575	-1.15	0.09709	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.25992	0.78	0.80722	P	0.0	B;B	0.18968	0.032;0.0	B;B	0.13407	0.009;0.007	T	0.48514	-0.9029	7	0.19147	T	0.46	.	.	.	.	rs2076109;rs17000716;rs17857431;rs57140217;rs2076109	62;62	B0QYD2;Q9UH17	.;ABC3B_HUMAN	E	62	ENSP00000385068:K62E;ENSP00000385060:K62E;ENSP00000327459:K62E	ENSP00000327459:K62E	K	+	1	0	APOBEC3B	37711772	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.983000	0.01488	-2.941000	0.00297	-2.942000	0.00086	AAG	A|0.388;G|0.612	0.612	strong		0.587	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
KIF19	124602	hgsc.bcm.edu	37	17	72350412	72350412	+	Missense_Mutation	SNP	G	G	A	rs2271535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	16	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	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	
BCL2L13	23786	hgsc.bcm.edu	37	22	18165995	18165995	+	Missense_Mutation	SNP	T	T	G	rs2587070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:18165995T>G	ENST00000317582.5	+	3	484	c.137T>G	c.(136-138)aTa>aGa	p.I46R	BCL2L13_ENST00000337612.5_De_novo_Start_OutOfFrame|BCL2L13_ENST00000543133.1_De_novo_Start_OutOfFrame|BCL2L13_ENST00000538149.1_Intron|BCL2L13_ENST00000493680.1_Missense_Mutation_p.I46R|BCL2L13_ENST00000399782.1_Missense_Mutation_p.I46R|BCL2L13_ENST00000418951.2_Missense_Mutation_p.I46R|BCL2L13_ENST00000355028.3_Missense_Mutation_p.I46R	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	46			I -> R (in dbSNP:rs2587070). {ECO:0000269|PubMed:18669648}.|I -> T (in dbSNP:rs2587070).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		CAACTAGATATAGCTTCACAA	0.294													T|||	356	0.0710863	0.0204	0.1326	5008	,	,		16986	0.004		0.173	False		,,,				2504	0.0603				p.I70R		Atlas-SNP	.											.	BCL2L13	27	.	0			c.T209G						PASS	.	T	ARG/ILE	244,4160	131.8+/-168.3	18,208,1976	40.0	42.0	41.0		137	-2.2	0.0	22	dbSNP_100	41	1737,6853	305.7+/-307.6	168,1401,2726	yes	missense	BCL2L13	NM_015367.2	97	186,1609,4702	GG,GT,TT		20.2212,5.5404,15.2455	benign	46/486	18165995	1981,11013	2202	4295	6497	SO:0001583	missense	23786	exon2			TAGATATAGCTTC	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.137T>G	22.37:g.18165995T>G	ENSP00000318883:p.Ile46Arg	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	192	87	0.453125	NM_001270726	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Missense_Mutation	SNP	ENST00000317582.5	37	CCDS13746.1	207	0.09478021978021978	13	0.026422764227642278	50	0.13812154696132597	2	0.0034965034965034965	142	0.18733509234828497	T	1.782	-0.481591	0.04383	0.055404	0.202212	ENSG00000099968	ENST00000399782;ENST00000317582;ENST00000493680;ENST00000355028;ENST00000418951	T;T;T;T;T	0.04083	3.71;3.71;3.71;3.71;3.71	5.56	-2.15	0.07102	.	1.863950	0.02420	N	0.082536	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B;B	0.26400	0.148;0.09;0.006	B;B;B	0.24394	0.053;0.047;0.008	T	0.45804	-0.9236	9	0.24483	T	0.36	-0.1026	7.6672	0.28439	0.1134:0.4482:0.0:0.4384	rs2587070;rs17741846;rs52795605	46;46;46	E9PDD6;Q9BXK5;Q9BXK5-2	.;B2L13_HUMAN;.	R	46	ENSP00000382682:I46R;ENSP00000318883:I46R;ENSP00000434764:I46R;ENSP00000347133:I46R;ENSP00000410019:I46R	ENSP00000318883:I46R	I	+	2	0	BCL2L13	16545995	0.000000	0.05858	0.013000	0.15412	0.170000	0.22686	-2.225000	0.01212	-0.403000	0.07622	-1.128000	0.01989	ATA	C|0.000;G|0.131;T|0.869	0.131	strong		0.294	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367	
SMC1B	27127	hgsc.bcm.edu	37	22	45750920	45750920	+	Silent	SNP	A	A	G	rs61748560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45750920A>G	ENST00000357450.4	-	20	3036	c.3037T>C	c.(3037-3039)Tta>Cta	p.L1013L	SMC1B_ENST00000404354.3_Silent_p.L1013L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1013					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)		GTTTTCAGTAAGATATCTTCC	0.443													A|||	17	0.00339457	0.0	0.0043	5008	,	,		18176	0.0		0.0129	False		,,,				2504	0.001				p.L1013L		Atlas-SNP	.											.	SMC1B	215	.	0			c.T3037C						PASS	.	A		6,3840		0,6,1917	206.0	194.0	197.0		3037	-0.4	0.0	22	dbSNP_129	197	87,8191		0,87,4052	no	coding-synonymous	SMC1B	NM_148674.3		0,93,5969	GG,GA,AA		1.051,0.156,0.7671		1013/1236	45750920	93,12031	1923	4139	6062	SO:0001819	synonymous_variant	27127	exon20			TCAGTAAGATATC	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.3037T>C	22.37:g.45750920A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	170	85	0.5	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.989;G|0.011	0.011	strong		0.443	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
PCDH12	51294	hgsc.bcm.edu	37	5	141336264	141336264	+	Missense_Mutation	SNP	G	G	T	rs164075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141336264G>T	ENST00000231484.3	-	1	2363	c.1153C>A	c.(1153-1155)Cac>Aac	p.H385N	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	385	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		H -> N (in dbSNP:rs164075). {ECO:0000269|PubMed:14702039}.	HN -> KD (in Ref. 4; BAB55016). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACCATTGTGTCCTGAATCC	0.502																																					p.H385N		Atlas-SNP	.											.	PCDH12	133	.	0			c.C1153A						PASS	.	T	ASN/HIS	3793,613	264.4+/-266.0	1645,503,55	123.0	116.0	118.0		1153	2.5	1.0	5	dbSNP_79	118	4438,4162	567.3+/-388.8	1160,2118,1022	yes	missense	PCDH12	NM_016580.2	68	2805,2621,1077	TT,TG,GG		48.3953,13.9128,36.7138	benign	385/1185	141336264	8231,4775	2203	4300	6503	SO:0001583	missense	51294	exon1			CATTGTGTCCTGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1153C>A	5.37:g.141336264G>T	ENSP00000231484:p.His385Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	1587	0.7266483516483516	456	0.926829268292683	241	0.6657458563535912	492	0.8601398601398601	398	0.525065963060686	T	2.403	-0.337136	0.05278	0.860872	0.516047	ENSG00000113555	ENST00000231484	T	0.49720	0.77	4.92	2.48	0.30137	Cadherin (4);Cadherin-like (1);	0.431228	0.26522	N	0.023902	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	0.27905	-1.0060	9	0.12103	T	0.63	.	6.3241	0.21234	0.0:0.0967:0.5217:0.3815	rs164075;rs675911;rs3747722;rs17526249;rs17857273;rs17857422;rs56617655;rs58315115;rs164075	385	Q9NPG4	PCD12_HUMAN	N	385	ENSP00000231484:H385N	ENSP00000231484:H385N	H	-	1	0	PCDH12	141316448	0.004000	0.15560	0.999000	0.59377	0.935000	0.57460	0.360000	0.20250	0.358000	0.24211	-0.363000	0.07495	CAC	G|0.313;T|0.686	0.686	strong		0.502	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
DSE	29940	hgsc.bcm.edu	37	6	116720514	116720514	+	Missense_Mutation	SNP	C	C	T	rs35548455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116720514C>T	ENST00000331677.3	+	3	545	c.101C>T	c.(100-102)cCc>cTc	p.P34L	DSE_ENST00000359564.2_Missense_Mutation_p.P34L|DSE_ENST00000452085.3_Missense_Mutation_p.P34L|DSE_ENST00000537543.1_Missense_Mutation_p.P53L|DSE_ENST00000540275.1_3'UTR			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	34			P -> L (in dbSNP:rs35548455).		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)		GTTATGATTCCCTTCACCAAT	0.532													C|||	110	0.0219649	0.0023	0.049	5008	,	,		18805	0.0		0.0477	False		,,,				2504	0.0256				p.P34L		Atlas-SNP	.											.	DSE	98	.	0			c.C101T						PASS	.	C	LEU/PRO,LEU/PRO	70,4336	63.5+/-100.7	0,70,2133	90.0	77.0	81.0		101,101	5.7	1.0	6	dbSNP_126	81	583,8017	156.4+/-210.3	20,543,3737	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	98,98	20,613,5870	TT,TC,CC		6.7791,1.5887,5.0208	possibly-damaging,possibly-damaging	34/959,34/959	116720514	653,12353	2203	4300	6503	SO:0001583	missense	29940	exon2			TGATTCCCTTCAC	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.101C>T	6.37:g.116720514C>T	ENSP00000332151:p.Pro34Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	61	0.027930402930402932	1	0.0020325203252032522	20	0.055248618784530384	0	0.0	40	0.052770448548812667	C	22.8	4.341742	0.81911	0.015887	0.067791	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.65	5.65	0.86999	.	0.112000	0.64402	D	0.000007	T	0.16938	0.0407	L	0.44542	1.39	0.80722	D	1	P;P	0.36535	0.557;0.557	B;B	0.34242	0.178;0.178	T	0.02417	-1.1162	10	0.59425	D	0.04	-19.329	19.9142	0.97043	0.0:1.0:0.0:0.0	rs35548455	53;34	B7Z765;Q9UL01	.;DSE_HUMAN	L	34;34;53;34;34	ENSP00000397597:P34L;ENSP00000404049:P34L;ENSP00000441152:P53L;ENSP00000332151:P34L;ENSP00000352567:P34L	ENSP00000332151:P34L	P	+	2	0	DSE	116827207	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.454000	0.66651	2.941000	0.99782	0.655000	0.94253	CCC	C|0.955;T|0.045	0.045	strong		0.532	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
ITIH4	3700	hgsc.bcm.edu	37	3	52860936	52860936	+	Silent	SNP	C	C	T	rs2276817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52860936C>T	ENST00000266041.4	-	4	486	c.390G>A	c.(388-390)gtG>gtA	p.V130V	ITIH4_ENST00000485816.1_Silent_p.V130V|ITIH4_ENST00000406595.1_Silent_p.V130V|ITIH4_ENST00000346281.5_Silent_p.V130V|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000434759.3_Silent_p.V42V|RP5-966M1.6_ENST00000513520.1_5'Flank|ITIH4-AS1_ENST00000478366.1_RNA	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	130	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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)		CACTGACCGACACCTGGAACT	0.607													C|||	1227	0.245008	0.1989	0.379	5008	,	,		20931	0.3175		0.2584	False		,,,				2504	0.1237				p.V130V		Atlas-SNP	.											.	ITIH4	74	.	0			c.G390A						PASS	.	C	,	948,3458	361.9+/-315.9	89,770,1344	86.0	87.0	87.0		390,390	2.7	1.0	3	dbSNP_100	87	2004,6596	350.2+/-327.8	265,1474,2561	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	354,2244,3905	TT,TC,CC		23.3023,21.5161,22.6972	,	130/901,130/931	52860936	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon4			GACCGACACCTGG	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.390G>A	3.37:g.52860936C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	58	0.597938	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1																																																																																			C|0.753;T|0.247	0.247	strong		0.607	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
STON1	11037	hgsc.bcm.edu	37	2	48809629	48809629	+	Silent	SNP	G	G	T	rs17397707	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48809629G>T	ENST00000406226.1	+	3	2052	c.1857G>T	c.(1855-1857)gtG>gtT	p.V619V	STON1-GTF2A1L_ENST00000394754.1_Silent_p.V619V|STON1-GTF2A1L_ENST00000402114.2_Silent_p.V619V|STON1-GTF2A1L_ENST00000405008.1_Silent_p.V619V|STON1-GTF2A1L_ENST00000394751.3_Silent_p.V619V|STON1-GTF2A1L_ENST00000309827.2_Silent_p.V619V|STON1_ENST00000309835.3_Silent_p.V619V|STON1_ENST00000404752.1_Silent_p.V619V	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	619	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				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)			AAGTCACTGTGGGGTCAGCAA	0.443													G|||	136	0.0271565	0.0015	0.0375	5008	,	,		20270	0.0		0.1024	False		,,,				2504	0.0051				p.V619V		Atlas-SNP	.											.	STON1	100	.	0			c.G1857T						PASS	.	G	,,,,	89,4317	74.7+/-112.8	2,85,2116	59.0	57.0	58.0		1857,1857,1857,1857,1857	4.8	1.0	2	dbSNP_123	58	787,7813	183.7+/-231.9	33,721,3546	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	35,806,5662	TT,TG,GG		9.1512,2.02,6.7354	,,,,	619/1159,619/1136,619/736,619/736,619/1183	48809629	876,12130	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			CACTGTGGGGTCA	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.1857G>T	2.37:g.48809629G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			G|0.941;T|0.059	0.059	strong		0.443	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
MIPEP	4285	hgsc.bcm.edu	37	13	24443512	24443512	+	Missense_Mutation	SNP	T	T	G	rs149856612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:24443512T>G	ENST00000382172.3	-	7	960	c.862A>C	c.(862-864)Agc>Cgc	p.S288R		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	288					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		AGATCTCTGCTGCTGAGCAAT	0.403													T|||	5	0.000998403	0.0	0.0014	5008	,	,		17922	0.0		0.002	False		,,,				2504	0.002				p.S288R		Atlas-SNP	.											.	MIPEP	53	.	0			c.A862C						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	88.0	89.0	89.0		862	3.4	0.0	13	dbSNP_134	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MIPEP	NM_005932.3	110	0,4,6499	GG,GT,TT		0.0349,0.0227,0.0308	possibly-damaging	288/714	24443512	4,13002	2203	4300	6503	SO:0001583	missense	4285	exon7			CTCTGCTGCTGAG		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.862A>C	13.37:g.24443512T>G	ENSP00000371607:p.Ser288Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	55	37	0.672727	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	11.52	1.662789	0.29515	2.27E-4	3.49E-4	ENSG00000027001	ENST00000382172	T	0.07688	3.17	5.9	3.38	0.38709	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.354147	0.38605	N	0.001630	T	0.13329	0.0323	L	0.54323	1.7	0.09310	N	0.999996	P	0.41498	0.752	P	0.45794	0.493	T	0.03473	-1.1033	10	0.44086	T	0.13	.	12.8495	0.57850	0.0:0.0:0.2573:0.7427	.	288	Q99797	MIPEP_HUMAN	R	288	ENSP00000371607:S288R	ENSP00000371607:S288R	S	-	1	0	MIPEP	23341512	0.998000	0.40836	0.010000	0.14722	0.350000	0.29205	3.528000	0.53524	0.442000	0.26555	0.459000	0.35465	AGC	T|1.000;G|0.000	0.000	strong		0.403	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
C9orf57	138240	hgsc.bcm.edu	37	9	74671719	74671719	+	Silent	SNP	T	T	C	rs13295099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	24	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	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	
PDGFRL	5157	hgsc.bcm.edu	37	8	17500223	17500223	+	Silent	SNP	T	T	C	rs4705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17500223T>C	ENST00000541323.1	+	7	1486	c.1041T>C	c.(1039-1041)ttT>ttC	p.F347F	PDGFRL_ENST00000251630.6_Silent_p.F347F|PDGFRL_ENST00000523248.1_Intron|PDGFRL_ENST00000398074.3_Silent_p.F347F	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	347	Ig-like C2-type 2.				G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		TGGAAGACTTTGAGACGATTG	0.463													T|||	2038	0.406949	0.2012	0.4135	5008	,	,		20472	0.4593		0.5825	False		,,,				2504	0.4458				p.F347F		Atlas-SNP	.											.	PDGFRL	27	.	0			c.T1041C						PASS	.	T		1206,3200	418.5+/-338.3	161,884,1158	121.0	103.0	109.0		1041	-3.7	1.0	8	dbSNP_52	109	4890,3710	619.5+/-396.9	1384,2122,794	no	coding-synonymous	PDGFRL	NM_006207.2		1545,3006,1952	CC,CT,TT		43.1395,27.3718,46.8707		347/376	17500223	6096,6910	2203	4300	6503	SO:0001819	synonymous_variant	5157	exon7			AGACTTTGAGACG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.1041T>C	8.37:g.17500223T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	25	0.362319	NM_006207	A8K085|Q6FH04	Silent	SNP	ENST00000541323.1	37	CCDS6003.1																																																																																			T|0.548;C|0.452	0.452	strong		0.463	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
SLC39A4	55630	hgsc.bcm.edu	37	8	145639726	145639726	+	Missense_Mutation	SNP	T	T	C	rs2272662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145639726T>C	ENST00000301305.3	-	6	1174	c.1069A>G	c.(1069-1071)Acc>Gcc	p.T357A	SLC39A4_ENST00000276833.5_Missense_Mutation_p.T332A|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	357			T -> A (in dbSNP:rs2272662). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039}.		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)	p.T357A(1)		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)			ATGTAGTGGGTGACCCCCCTG	0.657													T|||	1971	0.39357	0.0711	0.4669	5008	,	,		16204	0.4861		0.5686	False		,,,				2504	0.502				p.T357A		Atlas-SNP	.											SLC39A4,NS,carcinoma,0,1	SLC39A4	54	1	1	Substitution - Missense(1)	prostate(1)	c.A1069G						PASS	.	T	ALA/THR,ALA/THR	644,3742		61,522,1610	47.0	40.0	42.0		994,1069	-1.0	0.2	8	dbSNP_100	42	4952,3634		1443,2066,784	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	58,58	1504,2588,2394	CC,CT,TT		42.3247,14.6831,43.1391	benign,benign	332/623,357/648	145639726	5596,7376	2193	4293	6486	SO:0001583	missense	55630	exon6			AGTGGGTGACCCC	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.1069A>G	8.37:g.145639726T>C	ENSP00000301305:p.Thr357Ala	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	259	113	0.436293	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	926	0.423992673992674	39	0.07926829268292683	162	0.44751381215469616	285	0.4982517482517482	440	0.5804749340369393	T	8.761	0.923532	0.18056	0.146831	0.576753	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.46063	0.88;0.88	5.03	-0.978	0.10279	.	0.621523	0.17481	N	0.172725	T	0.00012	0.0000	L	0.28504	0.86	0.46113	P	0.0011229999999999851	B;B	0.26002	0.012;0.139	B;B	0.28305	0.011;0.088	T	0.42832	-0.9428	9	0.41790	T	0.15	-18.2025	3.8096	0.08791	0.4831:0.1973:0.0:0.3196	rs2272662;rs17232582;rs2272662	357;332	Q6P5W5;A6NDY5	S39A4_HUMAN;.	A	332;357	ENSP00000276833:T332A;ENSP00000301305:T357A	ENSP00000276833:T332A	T	-	1	0	SLC39A4	145610534	0.768000	0.28519	0.183000	0.23137	0.175000	0.22909	1.314000	0.33597	-0.019000	0.14055	0.467000	0.42956	ACC	T|0.606;C|0.394	0.394	strong		0.657	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
GSX2	170825	hgsc.bcm.edu	37	4	54966919	54966919	+	Silent	SNP	T	T	C	rs549077093|rs1132998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:54966919T>C	ENST00000326902.2	+	1	722	c.408T>C	c.(406-408)caT>caC	p.H136H	AC110298.1_ENST00000408292.1_RNA|GSX2_ENST00000503800.1_Intron|FIP1L1_ENST00000507166.1_Intron	NM_133267.2	NP_573574.1	Q9BZM3	GSX2_HUMAN	GS homeobox 2	136	Poly-His.				forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|hindbrain morphogenesis (GO:0021575)|neuron fate specification (GO:0048665)|olfactory bulb interneuron differentiation (GO:0021889)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|spinal cord association neuron differentiation (GO:0021527)|subpallium neuron fate commitment (GO:0060163)|telencephalon regionalization (GO:0021978)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(2)|lung(2)	6	all_cancers(7;0.00671)|Lung NSC(11;0.0154)|all_neural(26;0.0209)|Glioma(25;0.08)|all_epithelial(27;0.147)		LUSC - Lung squamous cell carcinoma(32;0.00216)			agcaccaccatcaccatcatc	0.716													T|||	3005	0.60004	0.2859	0.7219	5008	,	,		10117	0.8423		0.6133	False		,,,				2504	0.6748				p.H136H		Atlas-SNP	.											GSX2,NS,carcinoma,0,2	GSX2	27	2	0			c.T408C						PASS	.	T		1314,1784		296,722,531	5.0	4.0	4.0		408	1.3	1.0	4	dbSNP_86	4	3784,1884		1366,1052,416	no	coding-synonymous	GSX2	NM_133267.2		1662,1774,947	CC,CT,TT		33.2392,42.4145,41.8435		136/305	54966919	5098,3668	1549	2834	4383	SO:0001819	synonymous_variant	170825	exon1			CCACCATCACCAT		CCDS3494.1	4q12	2012-03-09			ENSG00000180613	ENSG00000180613		"""Homeoboxes / ANTP class : HOXL subclass"""	24959	protein-coding gene	gene with protein product						11861295, 12205114	Standard	NM_133267		Approved	Gsh2	uc010igp.1	Q9BZM3	OTTHUMG00000128696	ENST00000326902.2:c.408T>C	4.37:g.54966919T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_133267		Silent	SNP	ENST00000326902.2	37	CCDS3494.1																																																																																			T|0.388;C|0.612	0.612	strong		0.716	GSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250595.1	NM_133267	
PCGF2	7703	hgsc.bcm.edu	37	17	36894839	36894839	+	Silent	SNP	G	G	A	rs1138349	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:36894839G>A	ENST00000580830.1	-	9	1136	c.435C>T	c.(433-435)gaC>gaT	p.D145D	PCGF2_ENST00000360797.2_Silent_p.D145D|PCGF2_ENST00000585100.1_Nonsense_Mutation_p.R147*|PCGF2_ENST00000581345.1_Silent_p.D145D|PCGF2_ENST00000579882.1_Nonsense_Mutation_p.R147*|PCGF2_ENST00000578109.1_Nonsense_Mutation_p.R93*			P35227	PCGF2_HUMAN	polycomb group ring finger 2	145					anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CCTTCTTCTCGTCCCGGTCCC	0.602													G|||	2172	0.433706	0.5121	0.4179	5008	,	,		17528	0.2758		0.4284	False		,,,				2504	0.5072				p.D145D		Atlas-SNP	.											.	PCGF2	24	.	0			c.C435T						PASS	.	G		2286,2120	598.7+/-389.1	597,1092,514	70.0	71.0	71.0		435	-5.6	0.8	17	dbSNP_86	71	3914,4686	546.1+/-384.9	910,2094,1296	no	coding-synonymous	PCGF2	NM_007144.2		1507,3186,1810	AA,AG,GG		45.5116,48.1162,47.6703		145/345	36894839	6200,6806	2203	4300	6503	SO:0001819	synonymous_variant	7703	exon8			CTTCTCGTCCCGG	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	12929	protein-coding gene	gene with protein product		600346	"""ring finger protein 110"""	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.435C>T	17.37:g.36894839G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_007144	A6NGD8	Silent	SNP	ENST00000580830.1	37	CCDS32638.1																																																																																			G|0.545;A|0.455	0.455	strong		0.602	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144	
NLRP2	55655	hgsc.bcm.edu	37	19	55494740	55494740	+	Silent	SNP	T	T	C	rs10412915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55494740T>C	ENST00000543010.1	+	6	1817	c.1674T>C	c.(1672-1674)ttT>ttC	p.F558F	NLRP2_ENST00000427260.2_Silent_p.F535F|NLRP2_ENST00000448584.2_Silent_p.F558F|NLRP2_ENST00000538819.1_Silent_p.F534F|NLRP2_ENST00000391721.4_Silent_p.F534F|NLRP2_ENST00000263437.6_Silent_p.F555F|NLRP2_ENST00000339757.7_Silent_p.F536F|NLRP2_ENST00000537859.1_Silent_p.F536F	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	558					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)		ACTACTCCTTTGGCCTCGCTA	0.552													C|||	1428	0.285144	0.2655	0.3141	5008	,	,		19437	0.3085		0.3211	False		,,,				2504	0.2301				p.F558F		Atlas-SNP	.											.	NLRP2	161	.	0			c.T1674C						PASS	.	C	,,,	1118,3288	399.2+/-331.1	137,844,1222	78.0	72.0	74.0		1674,1608,1605,1674	-3.6	0.0	19	dbSNP_119	74	2520,6080	413.3+/-351.1	371,1778,2151	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	508,2622,3373	CC,CT,TT		29.3023,25.3745,27.9717	,,,	558/1063,536/1041,535/1040,558/1063	55494740	3638,9368	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon6			CTCCTTTGGCCTC	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.1674T>C	19.37:g.55494740T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.710;C|0.290	0.290	strong		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
PPP2R3B	28227	hgsc.bcm.edu	37	X	299360	299360	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:299360G>A	ENST00000390665.3	-	12	1574	c.1556C>T	c.(1555-1557)gCg>gTg	p.A519V		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	519			A -> V (in dbSNP:rs1133520). {ECO:0000269|PubMed:15489334}.		cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(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)				GGGCTCTCCCGCAGTCTCCTC	0.692													G|||	1043	0.208267	0.1135	0.2133	5008	,	,		11088	0.2222		0.3012	False		,,,				2504	0.2229				p.A519V		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.C1556T						PASS	.	G	VAL/ALA	680,3680		59,562,1559	74.0	66.0	69.0		1556	0.9	0.0	X	dbSNP_134	69	2514,6044		372,1770,2137	no	missense	PPP2R3B	NM_013239.4	64	431,2332,3696	AA,AG,GG		29.376,15.5963,24.7252	possibly-damaging	519/576	299360	3194,9724	2180	4279	6459	SO:0001583	missense	28227	exon12			TCTCCCGCAGTCT	AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"""Pseudoautosomal regions / PAR1"", ""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	13417	protein-coding gene	gene with protein product		300339	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"""	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.1556C>T	X.37:g.299360G>A	ENSP00000375080:p.Ala519Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Missense_Mutation	SNP	ENST00000390665.3	37	CCDS14104.1	504	0.23076923076923078	56	0.11382113821138211	87	0.24033149171270718	129	0.22552447552447552	232	0.30606860158311344	G	13.72	2.322172	0.41096	0.155963	0.29376	ENSG00000167393	ENST00000390665	T	0.47528	0.84	1.87	0.895	0.19247	.	0.000000	0.64402	U	0.000001	T	0.00012	0.0000	L	0.56769	1.78	0.09310	N	0.999999	D	0.61697	0.99	P	0.55112	0.769	T	0.01711	-1.1290	10	0.66056	D	0.02	.	7.588	0.28004	0.1538:0.0:0.8462:0.0	.	519	Q9Y5P8	P2R3B_HUMAN	V	519	ENSP00000375080:A519V	ENSP00000375080:A519V	A	-	2	0	PPP2R3B	219360	1.000000	0.71417	0.004000	0.12327	0.040000	0.13550	2.464000	0.45067	0.487000	0.27698	0.174000	0.16983	GCG	G|0.755;A|0.245	0.245	strong		0.692	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239	
TSC22D4	81628	hgsc.bcm.edu	37	7	100064719	100064719	+	Silent	SNP	A	A	G	rs7806537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100064719A>G	ENST00000300181.2	-	5	1805	c.1051T>C	c.(1051-1053)Ttg>Ctg	p.L351L	TSC22D4_ENST00000496728.1_Intron|TSC22D4_ENST00000393991.1_Silent_p.L112L|C7orf61_ENST00000332375.3_5'Flank	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	351	Leucine-zipper.				negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGCTCCGCCAATTCCCGGATC	0.692													G|||	1684	0.336262	0.4478	0.2651	5008	,	,		16634	0.0972		0.3956	False		,,,				2504	0.4213				p.L351L		Atlas-SNP	.											TSC22D4,NS,carcinoma,0,1	TSC22D4	28	1	0			c.T1051C						PASS	.	G		1922,2484	624.6+/-394.4	428,1066,709	50.0	51.0	51.0		1051	3.3	1.0	7	dbSNP_116	51	3333,5267	643.3+/-399.9	640,2053,1607	no	coding-synonymous	TSC22D4	NM_030935.3		1068,3119,2316	GG,GA,AA		38.7558,43.6223,40.4044		351/396	100064719	5255,7751	2203	4300	6503	SO:0001819	synonymous_variant	81628	exon5			CCGCCAATTCCCG	BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.1051T>C	7.37:g.100064719A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_030935	A4D2C3|A8MWR6|D6W5V9	Silent	SNP	ENST00000300181.2	37	CCDS5695.1																																																																																			A|0.644;G|0.356	0.356	strong		0.692	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1	NM_030935	
DCHS2	54798	hgsc.bcm.edu	37	4	155256177	155256177	+	Silent	SNP	A	A	G	rs6858157	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	110	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	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	
WDR86	349136	hgsc.bcm.edu	37	7	151097323	151097323	+	Silent	SNP	A	A	G	rs11767693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151097323A>G	ENST00000334493.6	-	2	598	c.168T>C	c.(166-168)caT>caC	p.H56H	WDR86_ENST00000477459.1_5'UTR|WDR86_ENST00000469830.2_Silent_p.H56H	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	56										breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATAGCTTTCATGTCCTGCAG	0.557													G|||	3543	0.707468	0.6611	0.7522	5008	,	,		21371	0.8194		0.7227	False		,,,				2504	0.6074				p.H56H		Atlas-SNP	.											.	WDR86	35	.	0			c.T168C						PASS	.	G		2971,1339		1047,877,231	37.0	38.0	38.0		168	-2.4	0.9	7	dbSNP_120	38	6155,2333		2219,1717,308	no	coding-synonymous	WDR86	NM_198285.2		3266,2594,539	GG,GA,AA		27.4859,31.0673,28.692		56/377	151097323	9126,3672	2155	4244	6399	SO:0001819	synonymous_variant	349136	exon2			GCTTTCATGTCCT	AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"""WD repeat domain containing"""	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.168T>C	7.37:g.151097323A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_198285	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Silent	SNP	ENST00000334493.6	37	CCDS5925.2																																																																																			A|0.267;G|0.733	0.733	strong		0.557	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285	
KLHL6	89857	hgsc.bcm.edu	37	3	183212026	183212026	+	Silent	SNP	C	C	T	rs2256061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183212026C>T	ENST00000341319.3	-	5	1226	c.1191G>A	c.(1189-1191)tcG>tcA	p.S397S		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	397					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			ACTTGTTGATCGAAGAATTAT	0.418													C|||	755	0.150759	0.2436	0.1225	5008	,	,		22548	0.0069		0.1819	False		,,,				2504	0.1616				p.S397S		Atlas-SNP	.											KLHL6,colon,carcinoma,-1,2	KLHL6	100	2	0			c.G1191A						PASS	.	C		995,3411	372.5+/-320.4	114,767,1322	154.0	151.0	152.0		1191	-11.9	0.0	3	dbSNP_100	152	1750,6850	319.2+/-314.1	173,1404,2723	no	coding-synonymous	KLHL6	NM_130446.2		287,2171,4045	TT,TC,CC		20.3488,22.5828,21.1056		397/622	183212026	2745,10261	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon5			GTTGATCGAAGAA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1191G>A	3.37:g.183212026C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			C|0.818;T|0.182	0.182	strong		0.418	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
GATA3	2625	hgsc.bcm.edu	37	10	8100647	8100647	+	Silent	SNP	C	C	T	rs1778076|rs2229359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:8100647C>T	ENST00000346208.3	+	3	1076	c.621C>T	c.(619-621)gcC>gcT	p.A207A	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.A207A			P23771	GATA3_HUMAN	GATA binding protein 3	207					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|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)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|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 core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						GCATGACCGCCCTGGGTGGAG	0.677			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""						C|||	102	0.0203674	0.0015	0.0288	5008	,	,		14000	0.0		0.0716	False		,,,				2504	0.0082				p.A207A		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C621T						PASS	.	C	,	66,4340	59.9+/-96.7	1,64,2138	81.0	73.0	76.0		621,621	0.3	1.0	10	dbSNP_98	76	649,7951	164.2+/-216.6	28,593,3679	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	29,657,5817	TT,TC,CC		7.5465,1.498,5.4975	,	207/445,207/444	8100647	715,12291	2203	4300	6503	SO:0001819	synonymous_variant	2625	exon3			GACCGCCCTGGGT	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.621C>T	10.37:g.8100647C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																			C|0.956;T|0.044	0.044	strong		0.677	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955744	18955744	+	Silent	SNP	C	C	T	rs11599929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18955744C>T	ENST00000302797.3	-	1	812	c.588G>A	c.(586-588)ctG>ctA	p.L196L	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	196					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L196L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TCAGCAGGACCAGGCTGGACC	0.522													C|||	1479	0.295327	0.2769	0.2695	5008	,	,		24177	0.3879		0.2237	False		,,,				2504	0.317				p.L196L		Atlas-SNP	.											MRGPRX1,NS,carcinoma,0,1	MRGPRX1	84	1	1	Substitution - coding silent(1)	stomach(1)	c.G588A						PASS	.	C		1209,3179		61,1087,1046	118.0	101.0	107.0		588	1.4	0.3	11	dbSNP_120	107	1862,6710		49,1764,2473	no	coding-synonymous	MRGPRX1	NM_147199.3		110,2851,3519	TT,TC,CC		21.7219,27.5524,23.696		196/323	18955744	3071,9889	2194	4286	6480	SO:0001819	synonymous_variant	259249	exon1			CAGGACCAGGCTG		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.588G>A	11.37:g.18955744C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																			C|0.741;T|0.259	0.259	strong		0.522	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
G6PC2	57818	hgsc.bcm.edu	37	2	169764546	169764546	+	Missense_Mutation	SNP	C	C	G	rs2232328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:169764546C>G	ENST00000375363.3	+	5	1117	c.1025C>G	c.(1024-1026)tCt>tGt	p.S342C	G6PC2_ENST00000461586.1_3'UTR|SPC25_ENST00000472216.2_Intron	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	342			S -> C (in dbSNP:rs2232328).		carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.S342C(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						ATTCCCTACTCTGTTCATATG	0.433													G|||	1059	0.211462	0.6029	0.1888	5008	,	,		20427	0.0169		0.0875	False		,,,				2504	0.0266				p.S342C		Atlas-SNP	.											G6PC2,NS,carcinoma,0,1	G6PC2	44	1	1	Substitution - Missense(1)	stomach(1)	c.C1025G						PASS	.	G	,CYS/SER	2210,2196	587.9+/-386.8	570,1070,563	140.0	140.0	140.0		,1025	4.9	1.0	2	dbSNP_98	140	788,7812	783.6+/-407.6	38,712,3550	yes	utr-3,missense	G6PC2	NM_001081686.1,NM_021176.2	,112	608,1782,4113	GG,GC,CC		9.1628,49.8411,23.0509	,benign	,342/356	169764546	2998,10008	2203	4300	6503	SO:0001583	missense	57818	exon5			CCTACTCTGTTCA	AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"""islet specific glucose 6 phosphatase catalytic subunit related protein"""	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.1025C>G	2.37:g.169764546C>G	ENSP00000364512:p.Ser342Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_021176	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	ENST00000375363.3	37	CCDS2230.1	451	0.2065018315018315	308	0.6260162601626016	66	0.18232044198895028	11	0.019230769230769232	66	0.0870712401055409	G	0.007	-1.986502	0.00443	0.501589	0.091628	ENSG00000152254	ENST00000375363	T	0.74209	-0.82	5.76	4.89	0.63831	.	0.061431	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00064	-2.31	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46582	-0.9181	9	0.02654	T	1	-2.6082	10.5611	0.45146	0.0696:0.132:0.7984:0.0	rs2232328;rs3770569;rs52803996;rs58257436;rs2232328	342	Q9NQR9	G6PC2_HUMAN	C	342	ENSP00000364512:S342C	ENSP00000364512:S342C	S	+	2	0	G6PC2	169472792	1.000000	0.71417	0.997000	0.53966	0.082000	0.17680	3.922000	0.56462	0.809000	0.34255	-0.701000	0.03672	TCT	C|0.776;G|0.224	0.224	strong		0.433	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176	
NAA38	84316	hgsc.bcm.edu	37	17	7760397	7760397	+	Silent	SNP	G	G	A	rs4724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7760397G>A	ENST00000335155.5	-	2	200	c.201C>T	c.(199-201)ttC>ttT	p.F67F	LSMD1_ENST00000575208.1_Silent_p.F15F|LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000575071.1_Silent_p.F15F|LSMD1_ENST00000576384.1_Silent_p.F15F|CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000570446.1_5'Flank|LSMD1_ENST00000333775.5_Silent_p.F115F|LSMD1_ENST00000576861.1_Silent_p.F41F|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000575771.1_Silent_p.F15F			Q9BRA0	LSMD1_HUMAN		67					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				CAGTGCAGAGGAAGCAGCCGA	0.627											OREG0024146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1267	0.252995	0.3336	0.2882	5008	,	,		16927	0.2748		0.0924	False		,,,				2504	0.2618				p.F115F	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											LSMD1,NS,carcinoma,0,2	LSMD1	8	2	0			c.C345T						PASS	.	G		1287,3119	431.0+/-342.8	187,913,1103	110.0	108.0	109.0		345	4.4	1.0	17	dbSNP_52	109	956,7644	208.9+/-250.2	46,864,3390	no	coding-synonymous	LSMD1	NM_032356.3		233,1777,4493	AA,AG,GG		11.1163,29.2102,17.2459		115/174	7760397	2243,10763	2203	4300	6503	SO:0001819	synonymous_variant	84316	exon1			GCAGAGGAAGCAG																												ENST00000335155.5:c.201C>T	17.37:g.7760397G>A		Somatic	89	0	0	644	WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_032356	Q8N4M0	Silent	SNP	ENST00000335155.5	37																																																																																				G|0.831;A|0.169	0.169	strong		0.627	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
YPEL5	51646	hgsc.bcm.edu	37	2	30381505	30381505	+	Silent	SNP	T	T	C	rs1137288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:30381505T>C	ENST00000379520.3	+	5	666	c.162T>C	c.(160-162)agT>agC	p.S54S	YPEL5_ENST00000261353.4_Silent_p.S54S|YPEL5_ENST00000402003.3_Silent_p.S54S|YPEL5_ENST00000402708.1_Silent_p.S54S|YPEL5_ENST00000379519.3_Silent_p.S54S|YPEL5_ENST00000495673.1_3'UTR	NM_001127401.1	NP_001120873.1	P62699	YPEL5_HUMAN	yippee-like 5 (Drosophila)	54										NS(1)|endometrium(1)|kidney(1)|lung(3)|prostate(1)	7	Acute lymphoblastic leukemia(172;0.155)					TGCAGTACAGTGAAGTTCAAG	0.418													T|||	2348	0.46885	0.2776	0.4135	5008	,	,		21493	0.7401		0.4503	False		,,,				2504	0.5061				p.S54S		Atlas-SNP	.											.	YPEL5	16	.	0			c.T162C						PASS	.	T	,,,	1472,2934		260,952,991	109.0	99.0	102.0		162,162,162,162	5.6	1.0	2	dbSNP_86	102	4032,4568		925,2182,1193	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YPEL5	NM_001127399.1,NM_001127400.1,NM_001127401.1,NM_016061.2	,,,	1185,3134,2184	CC,CT,TT		46.8837,33.409,42.3189	,,,	54/122,54/122,54/122,54/122	30381505	5504,7502	2203	4300	6503	SO:0001819	synonymous_variant	51646	exon4			GTACAGTGAAGTT	AF135161	CCDS1771.1	2p23	2004-06-28			ENSG00000119801	ENSG00000119801			18329	protein-coding gene	gene with protein product		609726					Standard	NM_016061		Approved	CGI-127	uc002rmz.4	P62699	OTTHUMG00000097839	ENST00000379520.3:c.162T>C	2.37:g.30381505T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_001127400	D6W568|Q65Z97|Q8R174|Q9D6M1|Q9UMX7|Q9Y3C9	Silent	SNP	ENST00000379520.3	37	CCDS1771.1																																																																																			T|0.549;C|0.451	0.451	strong		0.418	YPEL5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215128.1	NM_016061	
ZNF229	7772	hgsc.bcm.edu	37	19	44932704	44932704	+	Missense_Mutation	SNP	T	T	C	rs375182987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44932704T>C	ENST00000588931.1	-	6	2685	c.2252A>G	c.(2251-2253)cAg>cGg	p.Q751R	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.Q745R|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	751					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)				ATGTGAGCTCTGACTATAGCC	0.512																																					p.Q751R		Atlas-SNP	.											.	ZNF229	123	.	0			c.A2252G						PASS	.	T	ARG/GLN	0,4404		0,0,2202	73.0	81.0	79.0		2252	0.6	0.0	19		79	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF229	NM_014518.2	43	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	benign	751/826	44932704	2,13002	2202	4300	6502	SO:0001583	missense	7772	exon6			GAGCTCTGACTAT	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.2252A>G	19.37:g.44932704T>C	ENSP00000466519:p.Gln751Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	173	88	0.508671	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497781	0.44455	0.0	2.33E-4	ENSG00000167383	ENST00000291187	.	.	.	4.04	0.594	0.17485	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11196	0.0273	N	0.03294	-0.36	0.09310	N	1	P	0.39216	0.664	B	0.37267	0.245	T	0.25152	-1.0140	8	0.10902	T	0.67	.	7.7713	0.29010	0.0:0.2711:0.0:0.7289	.	751	Q9UJW7	ZN229_HUMAN	R	751	.	ENSP00000291187:Q751R	Q	-	2	0	ZNF229	49624544	0.000000	0.05858	0.000000	0.03702	0.755000	0.42902	-2.022000	0.01439	-0.284000	0.09102	0.496000	0.49642	CAG	.	.	weak		0.512	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
GRHL1	29841	hgsc.bcm.edu	37	2	10101468	10101468	+	Missense_Mutation	SNP	A	A	G	rs16867256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10101468A>G	ENST00000324907.9	+	4	708	c.572A>G	c.(571-573)aAt>aGt	p.N191S	GRHL1_ENST00000405379.2_Missense_Mutation_p.N191S|GRHL1_ENST00000324883.5_Missense_Mutation_p.I28V	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	191			N -> S (in dbSNP:rs16867256). {ECO:0000269|PubMed:15489334}.		cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CGGAATCTCAATACTGACCAG	0.542													G|||	883	0.176318	0.438	0.1052	5008	,	,		18383	0.0119		0.1461	False		,,,				2504	0.0736				p.N191S		Atlas-SNP	.											.	GRHL1	95	.	0			c.A572G						PASS	.	G	SER/ASN	1597,2809	664.3+/-401.3	279,1039,885	121.0	118.0	119.0		572	-8.9	0.0	2	dbSNP_123	119	1160,7440	765.5+/-407.6	74,1012,3214	yes	missense	GRHL1	NM_198182.2	46	353,2051,4099	GG,GA,AA		13.4884,36.246,21.1979	benign	191/619	10101468	2757,10249	2203	4300	6503	SO:0001583	missense	29841	exon4			ATCTCAATACTGA	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"""transcription factor CP2-like 2"""	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.572A>G	2.37:g.10101468A>G	ENSP00000324693:p.Asn191Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	339|339	0.15521978021978022|0.15521978021978022	195|195	0.39634146341463417|0.39634146341463417	36|36	0.09944751381215469|0.09944751381215469	4|4	0.006993006993006993|0.006993006993006993	104|104	0.13720316622691292|0.13720316622691292	G|G	0.388|0.388	-0.924831|-0.924831	0.02377|0.02377	0.36246|0.36246	0.134884|0.134884	ENSG00000134317|ENSG00000134317	ENST00000324883|ENST00000405379;ENST00000324907	T|T;T	0.16743|0.11169	2.32|2.8;2.8	5.5|5.5	-8.89|-8.89	0.00785|0.00785	.|.	.|0.571760	.|0.20829	.|N	.|0.084921	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	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.40887|0.40887	-0.9539|-0.9539	8|9	0.07482|0.15952	T|T	0.82|0.53	.|.	10.4728|10.4728	0.44646|0.44646	0.3294:0.2381:0.4325:0.0|0.3294:0.2381:0.4325:0.0	rs16867256;rs52810082;rs16867256|rs16867256;rs52810082;rs16867256	28|191	Q9NZI5-2|Q9NZI5	.|GRHL1_HUMAN	V|S	28|191	ENSP00000324494:I28V|ENSP00000384209:N191S;ENSP00000324693:N191S	ENSP00000324494:I28V|ENSP00000324693:N191S	I|N	+|+	1|2	0|0	GRHL1|GRHL1	10018919|10018919	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.440000|0.440000	0.31957|0.31957	-0.411000|-0.411000	0.07142|0.07142	-2.729000|-2.729000	0.00385|0.00385	-1.945000|-1.945000	0.00491|0.00491	ATA|AAT	A|0.801;G|0.199	0.199	strong		0.542	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
CEP55	55165	hgsc.bcm.edu	37	10	95278683	95278683	+	Missense_Mutation	SNP	G	G	A	rs75139274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:95278683G>A	ENST00000371485.3	+	7	1347	c.1043G>A	c.(1042-1044)aGg>aAg	p.R348K	CEP55_ENST00000496302.1_3'UTR	NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	348					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)				GAACAAACAAGGGTAGCTCTG	0.408													G|||	170	0.0339457	0.0008	0.0504	5008	,	,		21704	0.001		0.1034	False		,,,				2504	0.0297				p.R348K		Atlas-SNP	.											.	CEP55	35	.	0			c.G1043A						PASS	.	G	LYS/ARG,LYS/ARG	94,4312	75.2+/-113.4	1,92,2110	193.0	161.0	172.0		1043,1043	5.0	0.7	10	dbSNP_132	172	876,7724	183.9+/-232.0	39,798,3463	yes	missense,missense	CEP55	NM_001127182.1,NM_018131.4	26,26	40,890,5573	AA,AG,GG		10.186,2.1335,7.4581	benign,benign	348/465,348/465	95278683	970,12036	2203	4300	6503	SO:0001583	missense	55165	exon7			AAACAAGGGTAGC	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.1043G>A	10.37:g.95278683G>A	ENSP00000360540:p.Arg348Lys	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	225	101	0.448889	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	116|116	0.05311355311355311|0.05311355311355311	2|2	0.0040650406504065045|0.0040650406504065045	26|26	0.0718232044198895|0.0718232044198895	0|0	0.0|0.0	88|88	0.11609498680738786|0.11609498680738786	G|G	15.90|15.90	2.968022|2.968022	0.53507|0.53507	0.021335|0.021335	0.10186|0.10186	ENSG00000138180|ENSG00000138180	ENST00000445435|ENST00000371485;ENST00000358339	.|T	.|0.20738	.|2.05	5.88|5.88	4.97|4.97	0.65823|0.65823	.|.	.|0.130357	.|0.64402	.|D	.|0.000001	T|T	0.00241|0.00241	0.0007|0.0007	L|L	0.38531|0.38531	1.155|1.155	0.23572|0.23572	P|P	0.99738673|0.99738673	.|B	.|0.28512	.|0.214	.|B	.|0.24269	.|0.052	T|T	0.07271|0.07271	-1.0781|-1.0781	4|9	.|0.37606	.|T	.|0.19	-10.4322|-10.4322	11.4386|11.4386	0.50083|0.50083	0.1379:0.0:0.8621:0.0|0.1379:0.0:0.8621:0.0	.|.	.|348	.|Q53EZ4	.|CEP55_HUMAN	R|K	188|348	.|ENSP00000360540:R348K	.|ENSP00000351102:R348K	G|R	+|+	1|2	0|0	CEP55|CEP55	95268673|95268673	1.000000|1.000000	0.71417|0.71417	0.654000|0.654000	0.29608|0.29608	0.813000|0.813000	0.45954|0.45954	2.379000|2.379000	0.44318|0.44318	2.778000|2.778000	0.95560|0.95560	0.655000|0.655000	0.94253|0.94253	GGG|AGG	G|0.931;A|0.069	0.069	strong		0.408	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
DIDO1	11083	hgsc.bcm.edu	37	20	61528271	61528271	+	Missense_Mutation	SNP	C	C	T	rs1883847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61528271C>T	ENST00000266070.4	-	7	1991	c.1666G>A	c.(1666-1668)Gcg>Acg	p.A556T	DIDO1_ENST00000395335.2_Missense_Mutation_p.A556T|DIDO1_ENST00000395343.1_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	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	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	
MCF2L	23263	hgsc.bcm.edu	37	13	113733009	113733009	+	Silent	SNP	C	C	T	rs35155188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:113733009C>T	ENST00000375608.3	+	16	1912	c.1854C>T	c.(1852-1854)cgC>cgT	p.R618R	MCF2L_ENST00000375601.3_Silent_p.R592R|MCF2L_ENST00000434480.2_Silent_p.R594R|MCF2L_ENST00000535094.2_Silent_p.R588R|MCF2L_ENST00000421756.1_Silent_p.R592R|MCF2L_ENST00000397030.1_Silent_p.R621R|MCF2L_ENST00000375597.4_Silent_p.R586R|MCF2L_ENST00000375604.2_Silent_p.R645R|MCF2L_ENST00000442652.2_Silent_p.R618R|MCF2L_ENST00000423482.2_Silent_p.R586R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	618					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	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_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GGCAGGGCCGCGGCTCAGCGG	0.657													c|||	321	0.0640974	0.0651	0.072	5008	,	,		15873	0.005		0.1014	False		,,,				2504	0.0798				p.R588R		Atlas-SNP	.											.	MCF2L	182	.	0			c.C1764T						PASS	.	C	,	328,4072	169.4+/-200.1	13,302,1885	27.0	31.0	29.0		1764,1758	2.2	0.0	13	dbSNP_126	29	904,7694	193.7+/-239.3	52,800,3447	no	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	65,1102,5332	TT,TC,CC		10.5141,7.4545,9.4784	,	588/1126,586/1124	113733009	1232,11766	2200	4299	6499	SO:0001819	synonymous_variant	23263	exon15			GGGCCGCGGCTCA	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1854C>T	13.37:g.113733009C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		139	0.06364468864468864	37	0.07520325203252033	25	0.06906077348066299	4	0.006993006993006993	73	0.09630606860158311	C	0.481	-0.879868	0.02530	0.074545	0.105141	ENSG00000126217	ENST00000397017	T	0.43688	0.94	4.26	2.25	0.28309	.	0.054435	0.64402	D	0.000001	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.12837	-1.0532	6	0.72032	D	0.01	.	2.654	0.05007	0.227:0.5119:0.0:0.2611	rs35155188	.	.	.	W	249	ENSP00000380212:R249W	ENSP00000380212:R249W	R	+	1	2	MCF2L	112781010	0.001000	0.12720	0.007000	0.13788	0.111000	0.19643	-0.015000	0.12634	0.944000	0.37579	0.561000	0.74099	CGG	C|0.916;T|0.084	0.084	strong		0.657	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
DENND1A	57706	hgsc.bcm.edu	37	9	126520068	126520068	+	Silent	SNP	T	T	C	rs9785285	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:126520068T>C	ENST00000373624.2	-	5	417	c.216A>G	c.(214-216)acA>acG	p.T72T	DENND1A_ENST00000394219.3_Silent_p.T40T|DENND1A_ENST00000373618.1_Silent_p.T40T|DENND1A_ENST00000373620.3_Silent_p.T72T|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394215.2_Silent_p.T42T	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	80	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	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	
PKDCC	91461	hgsc.bcm.edu	37	2	42275819	42275819	+	Silent	SNP	T	T	C	rs11897440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:42275819T>C	ENST00000294964.5	+	1	660	c.480T>C	c.(478-480)ggT>ggC	p.G160G		NM_138370.2	NP_612379.2			protein kinase domain containing, cytoplasmic											breast(2)|kidney(1)|lung(5)	8						TGCCCGGCGGTGCCGCGGTGG	0.731													C|||	2998	0.598642	0.8623	0.6196	5008	,	,		9651	0.505		0.3897	False		,,,				2504	0.5389				p.G160G		Atlas-SNP	.											.	PKDCC	21	.	0			c.T480C						PASS	.	C		1041,283		419,203,40	5.0	7.0	7.0		480	3.2	1.0	2	dbSNP_120	7	1311,1805		320,671,567	no	coding-synonymous	PKDCC	NM_138370.2		739,874,607	CC,CT,TT		42.0732,21.3746,47.027		160/494	42275819	2352,2088	662	1558	2220	SO:0001819	synonymous_variant	91461	exon1			CGGCGGTGCCGCG		CCDS33186.2	2p21	2014-01-28	2012-12-07		ENSG00000162878	ENSG00000162878			25123	protein-coding gene	gene with protein product	"""vertebrate lonesome kinase"""	614150	"""protein kinase domain containing, cytoplasmic homolog (mouse)"""			19097194, 19465597	Standard	NM_138370		Approved	SgK493, Vlk	uc002rsg.3	Q504Y2	OTTHUMG00000152303	ENST00000294964.5:c.480T>C	2.37:g.42275819T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_138370		Silent	SNP	ENST00000294964.5	37	CCDS33186.2																																																																																			T|0.448;C|0.552	0.552	strong		0.731	PKDCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325745.3		
SIK1	150094	hgsc.bcm.edu	37	21	44846016	44846016	+	Missense_Mutation	SNP	C	C	T	rs3746951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	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	
PARD3	56288	hgsc.bcm.edu	37	10	34408636	34408636	+	Silent	SNP	T	T	C	rs11009651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:34408636T>C	ENST00000374789.3	-	24	3907	c.3582A>G	c.(3580-3582)cgA>cgG	p.R1194R	PARD3_ENST00000350537.4_Silent_p.R1148R|PARD3_ENST00000374788.3_Silent_p.R1191R|PARD3_ENST00000545260.1_Silent_p.R1104R|PARD3_ENST00000346874.4_Silent_p.R1157R|PARD3_ENST00000374794.3_Silent_p.R1082R|PARD3_ENST00000545693.1_Silent_p.R1178R|PARD3_ENST00000374790.3_Silent_p.R1134R	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	1194					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				ACACCGAGTGTCGCCCGCTCT	0.607													C|||	975	0.194688	0.3563	0.1945	5008	,	,		13606	0.003		0.2495	False		,,,				2504	0.1176				p.R1194R		Atlas-SNP	.											PARD3,NS,carcinoma,0,1	PARD3	131	1	0			c.A3582G						PASS	.	C	,,,,,,,	1385,3017		211,963,1027	25.0	23.0	23.0		3573,3534,3471,3444,3333,3312,3246,3582	-0.5	1.0	10	dbSNP_120	23	2210,6382		288,1634,2374	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_019619.3	,,,,,,,	499,2597,3401	CC,CT,TT		25.7216,31.463,27.6666	,,,,,,,	1191/1354,1178/1341,1157/1320,1148/1311,1111/1274,1104/1267,1082/1245,1194/1357	34408636	3595,9399	2201	4296	6497	SO:0001819	synonymous_variant	56288	exon24			CGAGTGTCGCCCG	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.3582A>G	10.37:g.34408636T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_019619	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			T|0.750;C|0.250	0.250	strong		0.607	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
MUC4	4585	hgsc.bcm.edu	37	3	195515194	195515194	+	Missense_Mutation	SNP	G	G	C	rs201370057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195515194G>C	ENST00000463781.3	-	2	3716	c.3257C>G	c.(3256-3258)aCc>aGc	p.T1086S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1086S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	518					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T1086S(1)		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)		AAGAGGGGTGGTGTCACCTGT	0.572													.|||	109	0.0217652	0.0582	0.0072	5008	,	,		18106	0.0159		0.0099	False		,,,				2504	0.001				p.T1086S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	endometrium(1)	c.C3257G						scavenged	.						18.0	14.0	15.0					3																	195515194		685	1579	2264	SO:0001583	missense	4585	exon2			GGGGTGGTGTCAC	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.3257C>G	3.37:g.195515194G>C	ENSP00000417498:p.Thr1086Ser	Somatic	48	4	0.0833333		WXS	Illumina HiSeq	Phase_I	91	10	0.10989	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	.	.	.	.	.	.	.	.	.	.	-	3.733	-0.055087	0.07362	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.34	0.814	0.814	0.18756	.	.	.	.	.	T	0.34279	0.0892	N	0.19112	0.55	0.09310	N	1	D	0.60160	0.987	D	0.65684	0.937	T	0.14309	-1.0477	8	.	.	.	.	3.1761	0.06569	0.3046:0.0:0.6954:0.0	.	1086	E7ESK3	.	S	1086	ENSP00000417498:T1086S;ENSP00000420243:T1086S	.	T	-	2	0	MUC4	196999589	0.000000	0.05858	0.011000	0.14972	0.090000	0.18270	0.417000	0.21214	0.776000	0.33473	0.064000	0.15345	ACC	G|0.939;C|0.061	0.061	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CATSPER1	117144	hgsc.bcm.edu	37	11	65790527	65790527	+	Silent	SNP	G	G	T	rs2845570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65790527G>T	ENST00000312106.5	-	2	1359	c.1222C>A	c.(1222-1224)Cgg>Agg	p.R408R		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	408					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						CGCTGGAGCCGGCCGGCTGAA	0.597											OREG0021092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2163	0.431909	0.1906	0.3847	5008	,	,		17874	0.377		0.5616	False		,,,				2504	0.7147				p.R408R		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C1222A						PASS	.	G		1056,3346	385.8+/-325.9	129,798,1274	59.0	61.0	60.0		1222	-2.9	0.0	11	dbSNP_100	60	4850,3742	617.1+/-396.6	1349,2152,795	no	coding-synonymous	CATSPER1	NM_053054.3		1478,2950,2069	TT,TG,GG		43.5521,23.9891,45.4517		408/781	65790527	5906,7088	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon2			GGAGCCGGCCGGC	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.1222C>A	11.37:g.65790527G>T		Somatic	51	0	0	1086	WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.549;T|0.451	0.451	strong		0.597	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
ABCA12	26154	hgsc.bcm.edu	37	2	215876371	215876371	+	Silent	SNP	T	T	C	rs10198064	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:215876371T>C	ENST00000272895.7	-	17	2343	c.2124A>G	c.(2122-2124)gcA>gcG	p.A708A	ABCA12_ENST00000389661.4_Silent_p.A390A	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	708					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)		TTCTGTACATTGCCTGTGAGA	0.373													T|||	1399	0.279353	0.6982	0.2752	5008	,	,		17328	0.0456		0.0845	False		,,,				2504	0.1575				p.A708A	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,-1,1	ABCA12	368	1	0			c.A2124G						PASS	.	T	,	2641,1765	644.0+/-397.9	786,1069,348	145.0	139.0	141.0		1170,2124	-4.7	0.6	2	dbSNP_119	141	785,7815	185.7+/-233.4	33,719,3548	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	819,1788,3896	CC,CT,TT		9.1279,40.059,26.3417	,	390/2278,708/2596	215876371	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon17			GTACATTGCCTGT	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.2124A>G	2.37:g.215876371T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			T|0.734;C|0.266	0.266	strong		0.373	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
ADCY10	55811	hgsc.bcm.edu	37	1	167825485	167825485	+	Missense_Mutation	SNP	T	T	C	rs2071921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:167825485T>C	ENST00000367851.4	-	17	2273	c.2089A>G	c.(2089-2091)Att>Gtt	p.I697V	ADCY10_ENST00000545172.1_Missense_Mutation_p.I544V|ADCY10_ENST00000367848.1_Missense_Mutation_p.I605V	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	253	0	0		WXS	Illumina HiSeq	Phase_I	320	157	0.490625	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	
CRISP3	10321	hgsc.bcm.edu	37	6	49696473	49696473	+	Silent	SNP	G	G	T	rs488132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:49696473G>T	ENST00000393666.1	-	7	714	c.708C>A	c.(706-708)gcC>gcA	p.A236A	CRISP3_ENST00000423399.2_Silent_p.A146A|CRISP3_ENST00000263045.4_Silent_p.A249A|CRISP3_ENST00000433368.2_Silent_p.A259A|CRISP3_ENST00000371159.4_Silent_p.A267A			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	61	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	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	
CIC	23152	hgsc.bcm.edu	37	19	42799049	42799049	+	Silent	SNP	C	C	T	rs1052023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:42799049C>T	ENST00000575354.2	+	20	4573	c.4533C>T	c.(4531-4533)atC>atT	p.I1511I	CIC_ENST00000160740.3_Silent_p.I1509I|CIC_ENST00000572681.2_Silent_p.I2417I	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	21	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	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		
NFKB1	4790	hgsc.bcm.edu	37	4	103518700	103518700	+	Missense_Mutation	SNP	A	A	G	rs4648072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:103518700A>G	ENST00000505458.1	+	15	1793	c.1516A>G	c.(1516-1518)Atg>Gtg	p.M506V	NFKB1_ENST00000600343.1_Missense_Mutation_p.M326V|NFKB1_ENST00000226574.4_Missense_Mutation_p.M507V|NFKB1_ENST00000394820.4_Missense_Mutation_p.M506V			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	506	Interaction with CFLAR.		M -> V (in dbSNP:rs4648072). {ECO:0000269|Ref.8}.		apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|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 calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|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)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|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)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|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)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	AGAGAAGGCTATGCAGCTTGC	0.483													A|||	69	0.013778	0.0424	0.0072	5008	,	,		22523	0.0		0.008	False		,,,				2504	0.0				p.M507V		Atlas-SNP	.											.	NFKB1	78	.	0			c.A1519G						PASS	.	A	VAL/MET,VAL/MET	181,4225	118.0+/-155.7	4,173,2026	111.0	101.0	104.0		1516,1519	-4.9	0.0	4	dbSNP_111	104	69,8531	41.7+/-99.0	0,69,4231	yes	missense,missense	NFKB1	NM_001165412.1,NM_003998.3	21,21	4,242,6257	GG,GA,AA		0.8023,4.108,1.9222	benign,benign	506/969,507/970	103518700	250,12756	2203	4300	6503	SO:0001583	missense	4790	exon15			AAGGCTATGCAGC	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1516A>G	4.37:g.103518700A>G	ENSP00000424790:p.Met506Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	26	0.011904761904761904	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	7.891	0.732244	0.15507	0.04108	0.008023	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.36157	1.28;1.27;1.27	4.57	-4.88	0.03113	.	0.299368	0.33327	N	0.005038	T	0.07369	0.0186	L	0.56769	1.78	0.18873	N	0.999983	B;B;B	0.20052	0.011;0.011;0.041	B;B;B	0.20955	0.021;0.021;0.032	T	0.10245	-1.0638	10	0.48119	T	0.1	.	10.0045	0.41949	0.2584:0.6027:0.1389:0.0	rs4648072;rs4648072	326;506;507	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	V	507;506;506	ENSP00000226574:M507V;ENSP00000378297:M506V;ENSP00000424790:M506V	ENSP00000226574:M507V	M	+	1	0	NFKB1	103737738	0.037000	0.19845	0.034000	0.17996	0.916000	0.54674	0.284000	0.18864	-1.114000	0.02977	0.533000	0.62120	ATG	A|0.984;G|0.016	0.016	strong		0.483	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
TOPBP1	11073	hgsc.bcm.edu	37	3	133371471	133371471	+	Missense_Mutation	SNP	G	G	A	rs55633281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133371471G>A	ENST00000260810.5	-	8	1056	c.925C>T	c.(925-927)Cgt>Tgt	p.R309C	TOPBP1_ENST00000511439.1_Intron	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	309					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						GAAAGAGTACGACCTACATAT	0.303								Other conserved DNA damage response genes					G|||	196	0.0391374	0.0461	0.0591	5008	,	,		19753	0.001		0.0765	False		,,,				2504	0.0164				p.R309C	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											TOPBP1_ENST00000260810,colon,carcinoma,0,4	TOPBP1	218	4	0			c.C925T	GRCh37	CM067798	TOPBP1	M	rs55633281	scavenged	.	G	CYS/ARG	158,3480		3,152,1664	76.0	73.0	74.0		925	3.9	1.0	3	dbSNP_129	74	621,7519		19,583,3468	yes	missense	TOPBP1	NM_007027.3	180	22,735,5132	AA,AG,GG		7.629,4.343,6.614	benign	309/1523	133371471	779,10999	1819	4070	5889	SO:0001583	missense	11073	exon8			GAGTACGACCTAC	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.925C>T	3.37:g.133371471G>A	ENSP00000260810:p.Arg309Cys	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	100	0.045787545787545784	21	0.042682926829268296	25	0.06906077348066299	1	0.0017482517482517483	53	0.06992084432717678	G	14.89	2.669114	0.47677	0.04343	0.07629	ENSG00000163781	ENST00000260810	T	0.12879	2.64	5.7	3.9	0.45041	.	0.273790	0.41294	N	0.000920	T	0.00608	0.0020	L	0.50333	1.59	0.25291	P	0.9893591	P	0.35174	0.488	B	0.26864	0.074	T	0.12553	-1.0543	9	0.54805	T	0.06	.	12.9326	0.58294	0.1344:0.0:0.8656:0.0	rs55633281;rs61748110	309	Q92547	TOPB1_HUMAN	C	309	ENSP00000260810:R309C	ENSP00000260810:R309C	R	-	1	0	TOPBP1	134854161	1.000000	0.71417	0.960000	0.40013	0.938000	0.57974	3.469000	0.53093	1.426000	0.47256	0.655000	0.94253	CGT	G|0.947;A|0.053	0.053	strong		0.303	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
FLT4	2324	hgsc.bcm.edu	37	5	180046344	180046344	+	Missense_Mutation	SNP	G	G	C	rs448012	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:180046344G>C	ENST00000261937.6	-	19	2748	c.2670C>G	c.(2668-2670)caC>caG	p.H890Q	FLT4_ENST00000393347.3_Missense_Mutation_p.H890Q|FLT4_ENST00000424276.2_5'Flank|FLT4_ENST00000502649.1_Missense_Mutation_p.H890Q	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> Q (in dbSNP:rs448012). {ECO:0000269|PubMed:11807987, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8386825, ECO:0000269|Ref.7}.		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)	TCAGCGCGCGGTGCTCGCTGG	0.697													G|||	2918	0.582668	0.5144	0.7464	5008	,	,		9644	0.497		0.6531	False		,,,				2504	0.5746				p.H890Q	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											FLT4_ENST00000261937,NS,carcinoma,0,2	FLT4	356	2	0			c.C2670G						scavenged	.	G	GLN/HIS,GLN/HIS	2398,1998	588.0+/-386.8	655,1088,455	38.0	35.0	36.0		2670,2670	1.2	1.0	5	dbSNP_80	36	5356,3236	622.5+/-397.3	1691,1974,631	no	missense,missense	FLT4	NM_002020.4,NM_182925.4	24,24	2346,3062,1086	CC,CG,GG		37.6629,45.4504,40.2987	benign,benign	890/1299,890/1364	180046344	7754,5234	2198	4296	6494	SO:0001583	missense	2324	exon19			CGCGCGGTGCTCG	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.2670C>G	5.37:g.180046344G>C	ENSP00000261937:p.His890Gln	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	1150	0.5265567765567766	227	0.4613821138211382	233	0.643646408839779	251	0.4388111888111888	439	0.579155672823219	G	16.09	3.023122	0.54683	0.545496	0.623371	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649	D;D;D	0.81821	-1.54;-1.54;-1.54	4.0	1.22	0.21188	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.04018	-0.295	0.18873	P	0.9999871816	B;B	0.27498	0.18;0.18	B;B	0.38921	0.285;0.285	T	0.48080	-0.9066	8	0.29301	T	0.29	.	8.8325	0.35093	0.2491:0.0:0.7509:0.0	rs448012;rs1130377;rs2447732	890;890	E9PD35;P35916	.;VGFR3_HUMAN	Q	890	ENSP00000261937:H890Q;ENSP00000377016:H890Q;ENSP00000426057:H890Q	ENSP00000261937:H890Q	H	-	3	2	FLT4	179978950	1.000000	0.71417	0.987000	0.45799	0.929000	0.56500	3.431000	0.52814	0.126000	0.18424	0.455000	0.32223	CAC	G|0.426;C|0.574	0.574	strong		0.697	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
GTPBP10	85865	hgsc.bcm.edu	37	7	89982132	89982132	+	Silent	SNP	T	T	C	rs6972561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:89982132T>C	ENST00000222511.6	+	2	102	c.36T>C	c.(34-36)taT>taC	p.Y12Y	GTPBP10_ENST00000257659.8_Silent_p.Y12Y	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	12					ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						TTTTTAAGTATGGAAATTTCA	0.368											OREG0003797	type=REGULATORY REGION|Gene=BC021573|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1370	0.273562	0.3979	0.2536	5008	,	,		15695	0.244		0.2366	False		,,,				2504	0.1881				p.Y12Y		Atlas-SNP	.											.	GTPBP10	31	.	0			c.T36C						PASS	.	T	,	1521,2885	481.0+/-359.0	269,983,951	81.0	82.0	82.0		36,36	6.1	1.0	7	dbSNP_116	82	1671,6929	307.2+/-308.3	156,1359,2785	no	coding-synonymous,coding-synonymous	GTPBP10	NM_001042717.2,NM_033107.3	,	425,2342,3736	CC,CT,TT		19.4302,34.5211,24.5425	,	12/309,12/388	89982132	3192,9814	2203	4300	6503	SO:0001819	synonymous_variant	85865	exon2			TAAGTATGGAAAT		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.36T>C	7.37:g.89982132T>C		Somatic	41	0	0	1271	WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_001042717	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Silent	SNP	ENST00000222511.6	37	CCDS5617.1																																																																																			T|0.731;C|0.269	0.269	strong		0.368	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821576	100821576	+	Missense_Mutation	SNP	G	G	A	rs7496668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:100821576G>A	ENST00000268070.4	-	4	752	c.647C>T	c.(646-648)tCg>tTg	p.S216L		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	216			S -> L (in dbSNP:rs7496668). {ECO:0000269|PubMed:19836009}.			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)		CCAGTCCCGCGAAGGCCTGCC	0.597													G|||	2427	0.484625	0.447	0.5504	5008	,	,		16139	0.505		0.3489	False		,,,				2504	0.6074				p.S216L		Atlas-SNP	.											ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	0			c.C647T						PASS	.	G	LEU/SER	1873,2497		409,1055,721	29.0	27.0	28.0		647	3.6	0.0	15	dbSNP_116	28	2807,5731		446,1915,1908	yes	missense	ADAMTS17	NM_139057.2	145	855,2970,2629	AA,AG,GG		32.8766,42.8604,36.2566	benign	216/1096	100821576	4680,8228	2185	4269	6454	SO:0001583	missense	170691	exon4			TCCCGCGAAGGCC	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.647C>T	15.37:g.100821576G>A	ENSP00000268070:p.Ser216Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	958	0.43864468864468864	236	0.4796747967479675	184	0.5082872928176796	280	0.48951048951048953	258	0.3403693931398417	G	14.09	2.430321	0.43122	0.428604	0.328766	ENSG00000140470	ENST00000268070	T	0.61980	0.06	4.51	3.57	0.40892	.	0.752556	0.12004	N	0.508584	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.14012	0.009	B	0.06405	0.002	T	0.45101	-0.9284	9	0.25106	T	0.35	.	12.6923	0.56982	0.0:0.166:0.834:0.0	rs7496668;rs60305285;rs7496668	216	Q8TE56	ATS17_HUMAN	L	216	ENSP00000268070:S216L	ENSP00000268070:S216L	S	-	2	0	ADAMTS17	98639099	0.000000	0.05858	0.002000	0.10522	0.107000	0.19398	0.272000	0.18644	0.852000	0.35287	0.462000	0.41574	TCG	G|0.589;A|0.411	0.411	strong		0.597	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
SOHLH2	54937	hgsc.bcm.edu	37	13	36744800	36744800	+	Silent	SNP	G	G	A	rs2296967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:36744800G>A	ENST00000379881.3	-	10	1213	c.1125C>T	c.(1123-1125)taC>taT	p.Y375Y	CCDC169-SOHLH2_ENST00000511166.1_Silent_p.Y452Y|SOHLH2_ENST00000554962.1_Silent_p.Y452Y	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	375					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)	p.Y375Y(1)		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)		CAGTTGCATCGTAGGAAGGGG	0.448													G|||	374	0.0746805	0.003	0.085	5008	,	,		19637	0.0794		0.1014	False		,,,				2504	0.1319				p.Y452Y		Atlas-SNP	.											SOHLH2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1356T						scavenged	.	G	,	114,4292	87.8+/-126.4	0,114,2089	161.0	147.0	152.0		1356,1125	1.0	0.0	13	dbSNP_100	152	1028,7572	218.1+/-256.6	62,904,3334	no	coding-synonymous,coding-synonymous	SOHLH2,CCDC169-SOHLH2	NM_001198910.1,NM_017826.2	,	62,1018,5423	AA,AG,GG		11.9535,2.5874,8.7806	,	452/503,375/426	36744800	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	100526761	exon15			TGCATCGTAGGAA	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.1125C>T	13.37:g.36744800G>A		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																			G|0.916;A|0.084	0.084	strong		0.448	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
ITGAE	3682	hgsc.bcm.edu	37	17	3664361	3664361	+	Missense_Mutation	SNP	T	T	C	rs140947594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3664361T>C	ENST00000263087.4	-	6	642	c.544A>G	c.(544-546)Aag>Gag	p.K182E		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	182	Glu-rich (acidic).|X-domain (extra domain).				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		tcctcctccttctccAGAGCC	0.567													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		19977	0.0		0.0119	False		,,,				2504	0.001				p.K182E	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.A544G						PASS	.	T	GLU/LYS	3,4403	6.2+/-15.9	0,3,2200	127.0	131.0	130.0		544	-6.0	0.0	17	dbSNP_134	130	49,8551	28.5+/-78.6	0,49,4251	yes	missense	ITGAE	NM_002208.4	56	0,52,6451	CC,CT,TT		0.5698,0.0681,0.3998	benign	182/1180	3664361	52,12954	2203	4300	6503	SO:0001583	missense	3682	exon6			CCTCCTTCTCCAG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.544A>G	17.37:g.3664361T>C	ENSP00000263087:p.Lys182Glu	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	3.041	-0.197461	0.06259	6.81E-4	0.005698	ENSG00000083457	ENST00000263087	T	0.59772	0.24	3.57	-6.0	0.02206	.	.	.	.	.	T	0.18425	0.0442	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31724	-0.9933	9	0.02654	T	1	.	5.5585	0.17129	0.0:0.215:0.2778:0.5073	.	182	P38570	ITAE_HUMAN	E	182	ENSP00000263087:K182E	ENSP00000263087:K182E	K	-	1	0	ITGAE	3611110	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-1.083000	0.03397	-1.253000	0.02488	-0.534000	0.04291	AAG	T|0.996;C|0.004	0.004	strong		0.567	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
PRKCB	5579	hgsc.bcm.edu	37	16	24046861	24046861	+	Silent	SNP	T	T	C	rs116345778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24046861T>C	ENST00000321728.7	+	5	697	c.522T>C	c.(520-522)atT>atC	p.I174I	PRKCB_ENST00000303531.7_Silent_p.I174I	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	174	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)	ACGTCCTCATTGTCCTCGGTA	0.647													T|||	48	0.00958466	0.0174	0.0029	5008	,	,		13772	0.0		0.005	False		,,,				2504	0.0184				p.I174I		Atlas-SNP	.											.	PRKCB	383	.	0			c.T522C						PASS	.	T	,	68,4326	63.5+/-100.7	1,66,2130	74.0	69.0	71.0		522,522	-4.3	0.6	16	dbSNP_132	71	16,8584	11.2+/-40.8	0,16,4284	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	1,82,6414	CC,CT,TT		0.186,1.5476,0.6465	,	174/674,174/672	24046861	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon5			CCTCATTGTCCTC	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.522T>C	16.37:g.24046861T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			T|0.993;C|0.007	0.007	strong		0.647	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
LRP2	4036	hgsc.bcm.edu	37	2	170147502	170147502	+	Missense_Mutation	SNP	C	C	G	rs34693334	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170147502C>G	ENST00000263816.3	-	8	1060	c.775G>C	c.(775-777)Ggt>Cgt	p.G259R	LRP2_ENST00000443831.1_Missense_Mutation_p.G259R	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	259			G -> R (in dbSNP:rs34693334).		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)"""	TCATGAGGACCGCTTTCTGTG	0.448													T|||	202	0.0403355	0.0113	0.0476	5008	,	,		18320	0.002		0.0805	False		,,,				2504	0.0726				p.G259R		Atlas-SNP	.											.	LRP2	751	.	0			c.G775C						PASS	.	T	ARG/GLY	112,4294		1,110,2092	92.0	92.0	92.0		775	2.7	0.4	2	dbSNP_126	92	608,7992		23,562,3715	yes	missense	LRP2	NM_004525.2	125	24,672,5807	GG,GC,CC		7.0698,2.542,5.5359	benign	259/4656	170147502	720,12286	2203	4300	6503	SO:0001583	missense	4036	exon8			GAGGACCGCTTTC		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.775G>C	2.37:g.170147502C>G	ENSP00000263816:p.Gly259Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	79	0.036172161172161175	4	0.008130081300813009	17	0.04696132596685083	0	0.0	58	0.07651715039577836	T	2.005	-0.428422	0.04701	0.02542	0.070698	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.94457	-2.55;-3.43	5.39	2.67	0.31697	.	0.903087	0.09356	N	0.813489	T	0.36110	0.0955	N	0.16708	0.43	0.09310	N	1	B;B	0.21071	0.051;0.013	B;B	0.17722	0.019;0.018	T	0.59284	-0.7483	9	.	.	.	.	8.0514	0.30581	0.0:0.4174:0.0:0.5826	rs34693334	259;259	E9PC35;P98164	.;LRP2_HUMAN	R	259	ENSP00000263816:G259R;ENSP00000409813:G259R	.	G	-	1	0	LRP2	169855748	0.061000	0.20836	0.357000	0.25798	0.078000	0.17371	0.617000	0.24359	0.419000	0.25927	-0.254000	0.11334	GGT	C|0.944;G|0.056	0.056	strong		0.448	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
KMT2E	55904	hgsc.bcm.edu	37	7	104747899	104747899	+	Missense_Mutation	SNP	G	G	T	rs117986340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:104747899G>T	ENST00000311117.3	+	22	3540	c.2995G>T	c.(2995-2997)Ggt>Tgt	p.G999C	CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000257745.4_Missense_Mutation_p.G999C|KMT2E_ENST00000334914.7_Missense_Mutation_p.G54C|KMT2E_ENST00000334877.4_Missense_Mutation_p.G999C	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	999					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AAAGACTATTGGTTATACGAG	0.433													G|||	77	0.0153754	0.0023	0.0274	5008	,	,		17573	0.0		0.0507	False		,,,				2504	0.0041				p.G999C		Atlas-SNP	.											.	MLL5	173	.	0			c.G2995T						PASS	.	G	CYS/GLY,CYS/GLY	28,4378	31.7+/-61.6	0,28,2175	83.0	87.0	85.0		2995,2995	6.0	1.0	7	dbSNP_132	85	399,8201	127.2+/-185.5	8,383,3909	yes	missense,missense	MLL5	NM_018682.3,NM_182931.2	159,159	8,411,6084	TT,TG,GG		4.6395,0.6355,3.2831	probably-damaging,probably-damaging	999/1859,999/1859	104747899	427,12579	2203	4300	6503	SO:0001583	missense	55904	exon21			ACTATTGGTTATA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2995G>T	7.37:g.104747899G>T	ENSP00000312379:p.Gly999Cys	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	51	0.023351648351648352	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	40	0.052770448548812667	G	24.2	4.502636	0.85176	0.006355	0.046395	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.96168	-3.93;-3.11;-3.93;-0.21	6.03	6.03	0.97812	.	0.062767	0.64402	D	0.000006	D	0.85566	0.5726	L	0.29908	0.895	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.88825	0.3301	10	0.62326	D	0.03	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	999	Q8IZD2	MLL5_HUMAN	C	999;999;999;919;999;54	ENSP00000312379:G999C;ENSP00000335599:G999C;ENSP00000257745:G999C;ENSP00000333986:G54C	ENSP00000257745:G999C	G	+	1	0	MLL5	104535135	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.239000	0.78182	2.854000	0.98071	0.655000	0.94253	GGT	G|0.969;T|0.031	0.031	strong		0.433	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
TMEM135	65084	hgsc.bcm.edu	37	11	87032287	87032287	+	Missense_Mutation	SNP	G	G	C	rs11235097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:87032287G>C	ENST00000305494.5	+	15	1328	c.1289G>C	c.(1288-1290)gGt>gCt	p.G430A	TMEM135_ENST00000340353.7_Missense_Mutation_p.G408A|TMEM135_ENST00000532959.1_Missense_Mutation_p.G301A|TMEM135_ENST00000535167.1_Missense_Mutation_p.G291A	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	430			G -> A (in dbSNP:rs11235097).		peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTTGGTACTGGTGCATCTAAA	0.343													G|||	318	0.0634984	0.0333	0.0115	5008	,	,		16365	0.1617		0.0169	False		,,,				2504	0.0879				p.G430A		Atlas-SNP	.											.	TMEM135	40	.	0			c.G1289C						PASS	.	G	ALA/GLY,ALA/GLY	89,4313	75.2+/-113.4	1,87,2113	101.0	96.0	98.0		1223,1289	2.4	1.0	11	dbSNP_120	98	207,8391	88.9+/-151.2	3,201,4095	yes	missense,missense	TMEM135	NM_001168724.1,NM_022918.3	60,60	4,288,6208	CC,CG,GG		2.4075,2.0218,2.2769	benign,benign	408/437,430/459	87032287	296,12704	2201	4299	6500	SO:0001583	missense	65084	exon15			GTACTGGTGCATC	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.1289G>C	11.37:g.87032287G>C	ENSP00000306344:p.Gly430Ala	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Missense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	135	0.061813186813186816	20	0.04065040650406504	3	0.008287292817679558	102	0.17832167832167833	10	0.013192612137203167	G	7.385	0.629618	0.14257	0.020218	0.024075	ENSG00000166575	ENST00000340353;ENST00000544294;ENST00000532959;ENST00000305494;ENST00000535167	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.63	2.41	0.29592	.	0.386804	0.31301	N	0.007890	T	0.00039	0.0001	N	0.08118	0	0.38656	P	0.04803599999999997	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.006	T	0.20672	-1.0268	8	.	.	.	-11.8363	5.2898	0.15721	0.5155:0.0:0.4845:0.0	rs11235097;rs17820109;rs52793217;rs61431591;rs11235097	408;430	Q86UB9-2;Q86UB9	.;TM135_HUMAN	A	408;267;301;430;291	ENSP00000345513:G408A;ENSP00000436179:G301A;ENSP00000306344:G430A;ENSP00000439525:G291A	.	G	+	2	0	TMEM135	86709935	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	2.735000	0.47377	0.754000	0.32968	-0.143000	0.13931	GGT	G|0.958;C|0.042	0.042	strong		0.343	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	
R3HDML	140902	hgsc.bcm.edu	37	20	42966025	42966025	+	Silent	SNP	T	T	C	rs1884612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42966025T>C	ENST00000217043.2	+	1	400	c.228T>C	c.(226-228)agT>agC	p.S76S		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	76	SCP.					extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TCCGGGCCAGTGTGTACCCAC	0.607													C|||	1236	0.246805	0.2519	0.3516	5008	,	,		17546	0.0982		0.2962	False		,,,				2504	0.2679				p.S76S		Atlas-SNP	.											.	R3HDML	33	.	0			c.T228C						PASS	.	C		1187,3219	708.5+/-407.6	176,835,1192	57.0	54.0	55.0		228	0.6	1.0	20	dbSNP_92	55	2476,6124	694.4+/-404.7	346,1784,2170	no	coding-synonymous	R3HDML	NM_178491.2		522,2619,3362	CC,CT,TT		28.7907,26.9405,28.1639		76/254	42966025	3663,9343	2203	4300	6503	SO:0001819	synonymous_variant	140902	exon1			GGCCAGTGTGTAC	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.228T>C	20.37:g.42966025T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_178491		Silent	SNP	ENST00000217043.2	37	CCDS13329.1																																																																																			T|0.730;C|0.270	0.270	strong		0.607	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
TRIM38	10475	hgsc.bcm.edu	37	6	25967068	25967068	+	Silent	SNP	C	C	T	rs2009610	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	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		
ZNF492	57615	hgsc.bcm.edu	37	19	22846601	22846601	+	Splice_Site	SNP	G	G	T	rs71355985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22846601G>T	ENST00000456783.2	+	4	374		c.e4-1		CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492						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(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATTTCTTTCAGTTGTATGTTC	0.299													N|||	190	0.0379393	0.0295	0.0187	5008	,	,		14644	0.0813		0.0398	False		,,,				2504	0.0164				.		Atlas-SNP	.											.	ZNF492	129	.	0			c.131-1G>T						PASS	.						14.0	15.0	15.0					19																	22846601		1803	4084	5887	SO:0001630	splice_region_variant	57615	exon4			CTTTCAGTTGTAT	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.131-1G>T	19.37:g.22846601G>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_020855	Q08EI7|Q08EI8	Splice_Site	SNP	ENST00000456783.2	37	CCDS46032.1	109	0.04990842490842491	17	0.034552845528455285	10	0.027624309392265192	53	0.09265734265734266	29	0.03825857519788918	.	8.371	0.835363	0.16820	.	.	ENSG00000229676	ENST00000456783	.	.	.	1.12	1.12	0.20585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2552	0.15544	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF492	22638441	0.029000	0.19370	0.383000	0.26132	0.378000	0.30076	0.233000	0.17911	0.269000	0.21961	0.274000	0.19336	.	G|0.955;T|0.045	0.045	strong		0.299	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	Intron
TOPORS	10210	hgsc.bcm.edu	37	9	32543801	32543801	+	Missense_Mutation	SNP	G	G	A	rs41272913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32543801G>A	ENST00000360538.2	-	3	838	c.722C>T	c.(721-723)aCg>aTg	p.T241M	TOPORS_ENST00000379858.1_Missense_Mutation_p.T176M	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	241	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TTCATCTGCCGTAGTTGGCCT	0.378													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.T241M		Atlas-SNP	.											.	TOPORS	127	.	0			c.C722T						PASS	.	G	MET/THR,MET/THR	6,4400	11.4+/-27.6	0,6,2197	112.0	116.0	115.0		527,722	3.2	0.0	9	dbSNP_127	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	81,81	0,9,6494	AA,AG,GG		0.0349,0.1362,0.0692	probably-damaging,probably-damaging	176/981,241/1046	32543801	9,12997	2203	4300	6503	SO:0001583	missense	10210	exon3			TCTGCCGTAGTTG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.722C>T	9.37:g.32543801G>A	ENSP00000353735:p.Thr241Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	13.72	2.322059	0.41096	0.001362	3.49E-4	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15256	2.44;2.45	5.2	3.18	0.36537	.	0.543306	0.16954	N	0.192770	T	0.07188	0.0182	N	0.08118	0	0.09310	N	1	P	0.42010	0.768	B	0.33521	0.165	T	0.18085	-1.0348	10	0.52906	T	0.07	-1.9948	8.0253	0.30434	0.0:0.1386:0.467:0.3944	rs41272913	241	Q9NS56	TOPRS_HUMAN	M	241;176	ENSP00000353735:T241M;ENSP00000369187:T176M	ENSP00000353735:T241M	T	-	2	0	TOPORS	32533801	0.003000	0.15002	0.009000	0.14445	0.458000	0.32498	1.039000	0.30266	1.478000	0.48253	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
FLG	2312	hgsc.bcm.edu	37	1	152281039	152281039	+	Missense_Mutation	SNP	G	G	A	rs7522925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281039G>A	ENST00000368799.1	-	3	6358	c.6323C>T	c.(6322-6324)gCg>gTg	p.A2108V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2108	Ser-rich.		A -> V (in dbSNP:rs7522925).		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)			AGTGCTGGGCGCAGACTGTCC	0.567									Ichthyosis																												p.A2108V		Atlas-SNP	.											.	FLG	900	.	0			c.C6323T						PASS	.	G	VAL/ALA	1572,2834		0,1572,631	307.0	228.0	255.0		6323	-6.7	0.0	1	dbSNP_116	255	1153,7447		0,1153,3147	yes	missense	FLG	NM_002016.1	64	0,2725,3778	AA,AG,GG		13.407,35.6786,20.9519	benign	2108/4062	152281039	2725,10281	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGGCGCAGACT	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.6323C>T	1.37:g.152281039G>A	ENSP00000357789:p.Ala2108Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	430	167	0.388372	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	635	0.2907509157509158	187	0.3800813008130081	109	0.3011049723756906	241	0.42132867132867136	98	0.12928759894459102	c	6.463	0.453669	0.12283	0.356786	0.13407	ENSG00000143631	ENST00000368799	T	0.01725	4.67	3.37	-6.74	0.01743	.	.	.	.	.	T	0.00384	0.0012	L	0.29908	0.895	0.09310	N	1	B	0.31459	0.324	B	0.18263	0.021	T	0.44757	-0.9307	9	0.28530	T	0.3	.	6.0989	0.20035	0.0:0.1746:0.3926:0.4328	rs7522925;rs7522925	2108	P20930	FILA_HUMAN	V	2108	ENSP00000357789:A2108V	ENSP00000357789:A2108V	A	-	2	0	FLG	150547663	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.796000	0.00364	-1.346000	0.02211	-1.980000	0.00456	GCG	G|0.716;A|0.284	0.284	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
C1orf100	200159	hgsc.bcm.edu	37	1	244552296	244552296	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:244552296G>A	ENST00000308105.4	+	5	482	c.369G>A	c.(367-369)ccG>ccA	p.P123P	C1orf100_ENST00000470211.1_3'UTR|RP11-518L10.5_ENST00000417765.1_RNA|C1orf100_ENST00000366537.1_Silent_p.P91P	NM_001012970.1	NP_001012988.1	Q5SVJ3	CA100_HUMAN	chromosome 1 open reading frame 100	123										endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)	7	all_cancers(71;3.94e-05)|all_epithelial(71;0.000138)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|all_lung(81;0.0736)|Ovarian(71;0.0761)|Lung NSC(105;0.103)		all cancers(7;8.19e-08)|GBM - Glioblastoma multiforme(7;2.05e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.000984)			ATCCTCGACCGCTTAATTCAC	0.353																																					p.A66T		Atlas-SNP	.											C1orf100,brain,glioma,+1,1	C1orf100	30	1	0			c.G196A						scavenged	.						94.0	94.0	94.0					1																	244552296		2203	4300	6503	SO:0001819	synonymous_variant	200159	exon4			TCGACCGCTTAAT	BC054479	CCDS31079.1, CCDS60465.1	1q44	2008-02-05			ENSG00000173728	ENSG00000173728			30435	protein-coding gene	gene with protein product							Standard	NM_001276348		Approved		uc001iah.4	Q5SVJ3	OTTHUMG00000040104	ENST00000308105.4:c.369G>A	1.37:g.244552296G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	227	3	0.0132159	NM_001276349	Q5SVJ4	Missense_Mutation	SNP	ENST00000308105.4	37	CCDS31079.1																																																																																			.	.	none		0.353	C1orf100-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096712.1	NM_001012970	
THUMPD3	25917	hgsc.bcm.edu	37	3	9426224	9426224	+	Missense_Mutation	SNP	G	G	A	rs1129174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9426224G>A	ENST00000345094.3	+	10	1710	c.1376G>A	c.(1375-1377)cGa>cAa	p.R459Q	SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000515662.2_Missense_Mutation_p.R459Q|SETD5-AS1_ENST00000521609.1_RNA|SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000520629.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.R459Q	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	459			R -> Q (in dbSNP:rs1129174). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		TCTGGAATGCGACACGTATGG	0.418													G|||	525	0.104832	0.0401	0.2248	5008	,	,		20841	0.0605		0.1879	False		,,,				2504	0.0675				p.R459Q		Atlas-SNP	.											THUMPD3,caecum,carcinoma,0,1	THUMPD3	46	1	0			c.G1376A						PASS	.	G	GLN/ARG,GLN/ARG	290,4116	158.5+/-191.2	6,278,1919	388.0	344.0	359.0		1376,1376	4.8	1.0	3	dbSNP_86	359	1274,7326	254.7+/-279.9	85,1104,3111	yes	missense,missense	THUMPD3	NM_001114092.1,NM_015453.2	43,43	91,1382,5030	AA,AG,GG		14.814,6.5819,12.0252	benign,benign	459/508,459/508	9426224	1564,11442	2203	4300	6503	SO:0001583	missense	25917	exon10			GAATGCGACACGT	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1376G>A	3.37:g.9426224G>A	ENSP00000339532:p.Arg459Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	152	55	0.361842	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	37	CCDS2573.1	293	0.13415750915750915	26	0.052845528455284556	82	0.2265193370165746	43	0.07517482517482517	142	0.18733509234828497	G	14.07	2.424325	0.43020	0.065819	0.14814	ENSG00000134077	ENST00000452837;ENST00000345094;ENST00000515662	T;T;T	0.42513	0.97;0.97;0.97	5.67	4.8	0.61643	Putative RNA methylase (1);	0.147419	0.64402	D	0.000009	T	0.00012	0.0000	N	0.04724	-0.175	0.35024	P	0.24185800000000002	B	0.21452	0.056	B	0.18561	0.022	T	0.16188	-1.0411	9	0.31617	T	0.26	-21.4693	14.2841	0.66235	0.072:0.0:0.928:0.0	rs1129174;rs3177483;rs3186769;rs3816407;rs52834451;rs61368596;rs1129174	459	Q9BV44	THUM3_HUMAN	Q	459	ENSP00000395893:R459Q;ENSP00000339532:R459Q;ENSP00000424064:R459Q	ENSP00000339532:R459Q	R	+	2	0	THUMPD3	9401224	1.000000	0.71417	0.996000	0.52242	0.254000	0.26022	5.388000	0.66249	1.415000	0.47037	0.555000	0.69702	CGA	G|0.880;A|0.120	0.120	strong		0.418	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
CTNNA3	29119	hgsc.bcm.edu	37	10	69281701	69281701	+	Missense_Mutation	SNP	A	A	T	rs61749223	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69281701A>T	ENST00000433211.2	-	5	652	c.478T>A	c.(478-480)Tct>Act	p.S160T	CTNNA3_ENST00000373744.4_Missense_Mutation_p.S160T|CTNNA3_ENST00000545309.1_Missense_Mutation_p.S160T	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						TTTTTGAGAGACTCAAATGTC	0.378													A|||	57	0.0113818	0.0008	0.0101	5008	,	,		19674	0.0		0.0229	False		,,,				2504	0.0266				p.S160T		Atlas-SNP	.											.	CTNNA3	401	.	0			c.T478A						PASS	.	A	THR/SER,THR/SER	12,4394	20.2+/-43.8	0,12,2191	91.0	90.0	90.0		478,478	5.2	1.0	10	dbSNP_129	90	218,8382	91.6+/-153.7	3,212,4085	yes	missense,missense	CTNNA3	NM_001127384.1,NM_013266.2	58,58	3,224,6276	TT,TA,AA		2.5349,0.2724,1.7684	benign,benign	160/896,160/896	69281701	230,12776	2203	4300	6503	SO:0001583	missense	29119	exon5			TGAGAGACTCAAA	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.478T>A	10.37:g.69281701A>T	ENSP00000389714:p.Ser160Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	19	0.025065963060686015	A	14.51	2.556647	0.45487	0.002724	0.025349	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309;ENST00000330298;ENST00000540598	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.19	5.19	0.71726	.	0.131595	0.34986	N	0.003526	T	0.14960	0.0361	N	0.04959	-0.14	0.30220	N	0.796892	D;D;B;D	0.57257	0.979;0.979;0.002;0.963	D;D;B;D	0.71414	0.973;0.973;0.008;0.95	T	0.16453	-1.0402	10	0.45353	T	0.12	-9.4118	11.4391	0.50086	1.0:0.0:0.0:0.0	rs61749223	160;160;160;160	A8K141;F2Z2R0;Q9UI47-2;Q9UI47	.;.;.;CTNA3_HUMAN	T	160	ENSP00000389714:S160T;ENSP00000362849:S160T;ENSP00000441444:S160T;ENSP00000330570:S160T	ENSP00000330570:S160T	S	-	1	0	CTNNA3	68951707	0.997000	0.39634	0.975000	0.42487	0.930000	0.56654	3.845000	0.55880	1.967000	0.57214	0.383000	0.25322	TCT	A|0.981;T|0.019	0.019	strong		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
PRG4	10216	hgsc.bcm.edu	37	1	186276411	186276411	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:186276411G>A	ENST00000445192.2	+	7	1605	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	PRG4_ENST00000367483.4_Silent_p.K479K|PRG4_ENST00000367485.4_Silent_p.K427K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.K477K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	520	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACTCCCAAGGAGCCTGCAC	0.632																																					p.K520K		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	0			c.G1560A						scavenged	.						129.0	118.0	122.0					1																	186276411		2203	4299	6502	SO:0001819	synonymous_variant	10216	exon7			TCCCAAGGAGCCT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1560G>A	1.37:g.186276411G>A		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	77	3	0.038961	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.632	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
THADA	63892	hgsc.bcm.edu	37	2	43805739	43805739	+	Silent	SNP	C	C	T	rs61754256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43805739C>T	ENST00000405006.4	-	9	1080	c.729G>A	c.(727-729)ctG>ctA	p.L243L	THADA_ENST00000402360.2_Silent_p.L243L|THADA_ENST00000404790.1_Silent_p.L243L|THADA_ENST00000403856.1_Silent_p.L243L|THADA_ENST00000415080.2_5'UTR|THADA_ENST00000405975.2_Silent_p.L243L|THADA_ENST00000330266.7_5'Flank	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	243										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)				CAGTCTGTAACAGATCATCTA	0.393													T|||	790	0.157748	0.3487	0.0922	5008	,	,		19141	0.0069		0.1064	False		,,,				2504	0.1544				p.L243L		Atlas-SNP	.											.	THADA	131	.	0			c.G729A						PASS	.	T	,	1074,2590		155,764,913	64.0	64.0	64.0		729,729	-2.6	0.6	2	dbSNP_129	64	1108,7072		80,948,3062	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	235,1712,3975	TT,TC,CC		13.5452,29.3122,18.4228	,	243/1954,243/1954	43805739	2182,9662	1832	4090	5922	SO:0001819	synonymous_variant	63892	exon9			CTGTAACAGATCA	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.729G>A	2.37:g.43805739C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1																																																																																			C|0.866;T|0.134	0.134	strong		0.393	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
NACAD	23148	hgsc.bcm.edu	37	7	45124465	45124465	+	Missense_Mutation	SNP	A	A	T	rs3735495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45124465A>T	ENST00000490531.2	-	2	1333	c.1314T>A	c.(1312-1314)gaT>gaA	p.D438E		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	438			D -> E (in dbSNP:rs3735495).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						ACACAGTCCCATCCTGAGCCT	0.612													T|||	1391	0.277756	0.1573	0.402	5008	,	,		20664	0.2857		0.334	False		,,,				2504	0.2863				p.D438E		Atlas-SNP	.											.	NACAD	44	.	0			c.T1314A						PASS	.	T	GLU/ASP	290,1094		23,244,425	18.0	20.0	20.0		1314	-5.2	0.0	7	dbSNP_107	20	1116,2066		188,740,663	yes	missense	NACAD	NM_001146334.1	45	211,984,1088	TT,TA,AA		35.0723,20.9538,30.7928	benign	438/1563	45124465	1406,3160	692	1591	2283	SO:0001583	missense	23148	exon2			AGTCCCATCCTGA	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1314T>A	7.37:g.45124465A>T	ENSP00000420477:p.Asp438Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	133	34	0.255639	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	639	0.2925824175824176	94	0.1910569105691057	141	0.38950276243093923	150	0.26223776223776224	254	0.33509234828496043	T	0.037	-1.301109	0.01364	0.209538	0.350723	ENSG00000136274	ENST00000490531	T	0.10382	2.88	2.6	-5.2	0.02823	.	.	.	.	.	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	0.42882	-0.9425	8	0.02654	T	1	.	0.0621	0.00016	0.3137:0.1922:0.2349:0.2592	rs3735495;rs9639906;rs3735495	438	O15069	NACAD_HUMAN	E	438	ENSP00000420477:D438E	ENSP00000420477:D438E	D	-	3	2	NACAD	45090990	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.322000	0.02695	-2.714000	0.00392	-1.400000	0.01143	GAT	A|0.707;T|0.293	0.293	strong		0.612	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45700409	45700409	+	Missense_Mutation	SNP	C	C	T	rs61741592	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	241	0	0		WXS	Illumina HiSeq	Phase_I	218	108	0.495413	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		
KIAA0895L	653319	hgsc.bcm.edu	37	16	67210741	67210741	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:67210741C>T	ENST00000290881.7	-	8	2315	c.1389G>A	c.(1387-1389)gcG>gcA	p.A463A	KIAA0895L_ENST00000563831.2_5'UTR|KIAA0895L_ENST00000561621.1_3'UTR|KIAA0895L_ENST00000563902.1_Silent_p.A463A			Q68EN5	K895L_HUMAN	KIAA0895-like	463										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GACCCAGCTCCGCCTCATCCA	0.612																																					p.A463A		Atlas-SNP	.											KIAA0895L,NS,carcinoma,0,1	KIAA0895L	32	1	0			c.G1389A						scavenged	.						74.0	81.0	79.0					16																	67210741		2089	4242	6331	SO:0001819	synonymous_variant	653319	exon7			CAGCTCCGCCTCA	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.1389G>A	16.37:g.67210741C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	118	2	0.0169492	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Silent	SNP	ENST00000290881.7	37	CCDS42177.1																																																																																			.	.	none		0.612	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715	
BCR	613	hgsc.bcm.edu	37	22	23631801	23631801	+	Silent	SNP	T	T	C	rs2227939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	117	0	0	765	WXS	Illumina HiSeq	Phase_I	112	53	0.473214	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	
MUC16	94025	hgsc.bcm.edu	37	19	9014551	9014551	+	Silent	SNP	T	T	C	rs12459127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9014551T>C	ENST00000397910.4	-	31	38627	c.38424A>G	c.(38422-38424)agA>agG	p.R12808R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12810	SEA 5. {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						AGAGACTGTTTCTGTCCAGGG	0.552													-|||	1572	0.313898	0.2126	0.353	5008	,	,		18595	0.3095		0.3787	False		,,,				2504	0.3609				p.R12808R		Atlas-SNP	.											.	MUC16	4315	.	0			c.A38424G						PASS	.	C		746,3130		98,550,1290	196.0	156.0	168.0		38424	-2.3	0.0	19	dbSNP_120	168	2833,5437		549,1735,1851	no	coding-synonymous	MUC16	NM_024690.2		647,2285,3141	CC,CT,TT		34.2563,19.2466,29.4665		12808/14508	9014551	3579,8567	1938	4135	6073	SO:0001819	synonymous_variant	94025	exon31			ACTGTTTCTGTCC	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.38424A>G	19.37:g.9014551T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.673;C|0.327	0.327	strong		0.552	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR5P2	120065	hgsc.bcm.edu	37	11	7818471	7818471	+	Missense_Mutation	SNP	C	C	T	rs1482804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7818471C>T	ENST00000329434.2	-	1	49	c.19G>A	c.(19-21)Ggg>Agg	p.G7R	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	7			G -> R (in dbSNP:rs1482804).			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)|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)		GTGTGATTCCCGTCCTTCAGG	0.423													C|||	422	0.0842652	0.1989	0.0418	5008	,	,		15921	0.0109		0.0447	False		,,,				2504	0.0757				p.G7R		Atlas-SNP	.											.	OR5P2	68	.	0			c.G19A						PASS	.	C	ARG/GLY	856,3336		220,416,1460	50.0	58.0	56.0		19	0.4	0.0	11	dbSNP_88	56	462,8122		30,402,3860	yes	missense	OR5P2	NM_153444.1	125	250,818,5320	TT,TC,CC		5.3821,20.4198,10.3162	benign	7/323	7818471	1318,11458	2096	4292	6388	SO:0001583	missense	120065	exon1			GATTCCCGTCCTT	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.19G>A	11.37:g.7818471C>T	ENSP00000331823:p.Gly7Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	151	0.06913919413919414	97	0.19715447154471544	18	0.049723756906077346	9	0.015734265734265736	27	0.03562005277044855	C	10.95	1.496322	0.26861	0.204198	0.053821	ENSG00000183303	ENST00000329434	T	0.19532	2.14	5.5	0.423	0.16463	.	0.613891	0.16516	N	0.211029	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.21381	0.055	B	0.20184	0.028	T	0.38156	-0.9674	9	0.22109	T	0.4	1.1225	4.1703	0.10326	0.1521:0.5167:0.0:0.3312	rs1482804;rs1482804	7	Q8WZ92	OR5P2_HUMAN	R	7	ENSP00000331823:G7R	ENSP00000331823:G7R	G	-	1	0	OR5P2	7775047	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-0.080000	0.11339	0.153000	0.19213	-0.300000	0.09419	GGG	C|0.918;T|0.082	0.082	strong		0.423	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
NBEA	26960	hgsc.bcm.edu	37	13	35756572	35756572	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:35756572C>T	ENST00000400445.3	+	29	5272	c.4738C>T	c.(4738-4740)Cgt>Tgt	p.R1580C	NBEA_ENST00000310336.4_Missense_Mutation_p.R1580C|NBEA_ENST00000540320.1_Missense_Mutation_p.R1580C|NBEA_ENST00000379939.2_Missense_Mutation_p.R1577C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1580					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTCCAAGTATCGTGACATATT	0.388																																					p.R1580C		Atlas-SNP	.											NBEA,NS,carcinoma,-1,1	NBEA	340	1	0			c.C4738T						scavenged	.						134.0	124.0	127.0					13																	35756572		1837	4088	5925	SO:0001583	missense	26960	exon29			AAGTATCGTGACA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4738C>T	13.37:g.35756572C>T	ENSP00000383295:p.Arg1580Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668553	0.88348	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.69561	-0.41;-0.4;-0.41;-0.41	5.63	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.82024	0.4947	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.84850	0.0813	10	0.87932	D	0	.	15.8808	0.79205	0.1366:0.8634:0.0:0.0	.	1580;1577	Q8NFP9;Q5T321	NBEA_HUMAN;.	C	1580;1580;1577;1580;239	ENSP00000440951:R1580C;ENSP00000383295:R1580C;ENSP00000369271:R1577C;ENSP00000308534:R1580C	ENSP00000308534:R1580C	R	+	1	0	NBEA	34654572	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	6.050000	0.71063	1.354000	0.45846	0.467000	0.42956	CGT	.	.	none		0.388	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
PARD3B	117583	hgsc.bcm.edu	37	2	205990353	205990353	+	Silent	SNP	C	C	T	rs2276676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:205990353C>T	ENST00000406610.2	+	10	1533	c.1326C>T	c.(1324-1326)acC>acT	p.T442T	PARD3B_ENST00000358768.2_Silent_p.T442T|PARD3B_ENST00000351153.1_Silent_p.T442T|PARD3B_ENST00000462231.1_Silent_p.T442T|PARD3B_ENST00000349953.3_Silent_p.T442T	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	442	PDZ 2. {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)		GAGATGTCACCGGACGAACCC	0.473													C|||	1538	0.307109	0.1097	0.4942	5008	,	,		19117	0.4167		0.3032	False		,,,				2504	0.3323				p.T442T		Atlas-SNP	.											.	PARD3B	314	.	0			c.C1326T						PASS	.	C	,,	541,3443		32,477,1483	104.0	104.0	104.0		1326,1326,1326	-3.8	0.9	2	dbSNP_100	104	2656,5698		437,1782,1958	no	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	469,2259,3441	TT,TC,CC		31.7932,13.5793,25.9118	,,	442/1137,442/1144,442/1105	205990353	3197,9141	1992	4177	6169	SO:0001819	synonymous_variant	117583	exon10			TGTCACCGGACGA	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.1326C>T	2.37:g.205990353C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				T|0.294;C|0.706	0.294	strong		0.473	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
SLC36A3	285641	hgsc.bcm.edu	37	5	150666843	150666843	+	Silent	SNP	A	A	G	rs6579846	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150666843A>G	ENST00000335230.3	-	6	1083	c.672T>C	c.(670-672)ctT>ctC	p.L224L	SLC36A3_ENST00000377713.3_Silent_p.L265L	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	224						integral component of membrane (GO:0016021)		p.L224L(1)		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)			CCATGCTCCCAAGGGTGGTGA	0.512													C|||	500	0.0998403	0.295	0.0403	5008	,	,		21417	0.0		0.0408	False		,,,				2504	0.0419				p.L265L		Atlas-SNP	.											SLC36A3,NS,carcinoma,0,1	SLC36A3	54	1	1	Substitution - coding silent(1)	stomach(1)	c.T795C						PASS	.	C	,	1542,2864		510,522,1171	122.0	113.0	116.0		795,672	2.1	1.0	5	dbSNP_116	116	415,8185		39,337,3924	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	549,859,5095	GG,GA,AA		4.8256,34.9977,15.0469	,	265/512,224/471	150666843	1957,11049	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon7			GCTCCCAAGGGTG	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.672T>C	5.37:g.150666843A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			A|0.800;C|0.190;G|0.010	0.010	strong		0.512	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
OR8S1	341568	hgsc.bcm.edu	37	12	48919796	48919796	+	Missense_Mutation	SNP	C	C	T	rs12425460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:48919796C>T	ENST00000310194.1	+	1	382	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	128			R -> C (in dbSNP:rs12425460).			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						TGCCATCTGCCGCCCACTACT	0.547													C|||	2899	0.578874	0.4879	0.6599	5008	,	,		20053	0.6895		0.5139	False		,,,				2504	0.5971				p.R128C		Atlas-SNP	.											.	OR8S1	47	.	0			c.C382T						PASS	.	C	CYS/ARG	2183,2223	586.1+/-386.4	519,1145,539	133.0	121.0	125.0		382	3.1	1.0	12	dbSNP_120	125	4568,4032	597.4+/-393.8	1210,2148,942	yes	missense	OR8S1	NM_001005203.2	180	1729,3293,1481	TT,TC,CC		46.8837,49.5461,48.0932	benign	128/360	48919796	6751,6255	2203	4300	6503	SO:0001583	missense	341568	exon1			ATCTGCCGCCCAC		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.382C>T	12.37:g.48919796C>T	ENSP00000310632:p.Arg128Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	1296	0.5934065934065934	238	0.483739837398374	237	0.6546961325966851	409	0.715034965034965	412	0.5435356200527705	C	11.62	1.691514	0.30052	0.495461	0.531163	ENSG00000197376	ENST00000310194	T	0.01347	4.99	5.03	3.07	0.35406	GPCR, rhodopsin-like superfamily (1);	0.165039	0.29139	N	0.013025	T	0.00012	0.0000	L	0.33485	1.01	0.33610	P	0.396579	B	0.10296	0.003	B	0.08055	0.003	T	0.11372	-1.0590	9	0.72032	D	0.01	-31.9331	8.0558	0.30604	0.1665:0.7433:0.0:0.0902	rs12425460;rs56692529;rs12425460	128	Q8NH09	OR8S1_HUMAN	C	128	ENSP00000310632:R128C	ENSP00000310632:R128C	R	+	1	0	OR8S1	47206063	0.000000	0.05858	1.000000	0.80357	0.771000	0.43674	-0.820000	0.04457	1.345000	0.45676	-0.137000	0.14449	CGC	C|0.456;T|0.544	0.544	strong		0.547	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
NCOR2	9612	hgsc.bcm.edu	37	12	124856618	124856618	+	Silent	SNP	A	A	G	rs7961196	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124856618A>G	ENST00000405201.1	-	20	2757	c.2757T>C	c.(2755-2757)gcT>gcC	p.A919A	NCOR2_ENST00000404121.2_Silent_p.A472A|NCOR2_ENST00000397355.1_Silent_p.A902A|NCOR2_ENST00000356219.3_Silent_p.A919A|NCOR2_ENST00000429285.2_Silent_p.A901A|NCOR2_ENST00000404621.1_Silent_p.A901A			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	919					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)		CACTGCAGGTAGCACTGGAGT	0.677													G|||	1578	0.315096	0.4728	0.2709	5008	,	,		13115	0.0843		0.34	False		,,,				2504	0.3456				p.A919A		Atlas-SNP	.											NCOR2_ENST00000405201,NS,carcinoma,0,2	NCOR2	475	2	0			c.T2757C						scavenged	.	G	,,	1791,2433		394,1003,715	34.0	43.0	40.0		2703,2703,2757	4.0	1.0	12	dbSNP_116	40	2793,5671		480,1833,1919	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	874,2836,2634	GG,GA,AA		32.9986,42.4006,36.1286	,,	901/2459,901/2505,919/2515	124856618	4584,8104	2112	4232	6344	SO:0001819	synonymous_variant	9612	exon22			GCAGGTAGCACTG	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.2757T>C	12.37:g.124856618A>G		Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			A|0.698;G|0.302	0.302	strong		0.677	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
OSBPL1A	114876	hgsc.bcm.edu	37	18	21891975	21891975	+	Silent	SNP	A	A	G	rs2337961	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21891975A>G	ENST00000319481.3	-	13	1271	c.1065T>C	c.(1063-1065)tcT>tcC	p.S355S	OSBPL1A_ENST00000357041.4_5'Flank	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	355					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					GGTCTGCAGCAGAAACCGTAT	0.408													a|||	1172	0.234026	0.4455	0.1527	5008	,	,		19330	0.0625		0.2336	False		,,,				2504	0.183				p.S355S		Atlas-SNP	.											OSBPL1A,colon,carcinoma,0,1	OSBPL1A	94	1	0			c.T1065C						PASS	.	G		1789,2617	528.2+/-372.3	372,1045,786	201.0	195.0	197.0		1065	-2.5	0.1	18	dbSNP_100	197	1940,6660	340.5+/-323.6	211,1518,2571	no	coding-synonymous	OSBPL1A	NM_080597.3		583,2563,3357	GG,GA,AA		22.5581,40.6037,28.6714		355/951	21891975	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	114876	exon13			TGCAGCAGAAACC	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1065T>C	18.37:g.21891975A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	120	78	0.65	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			A|0.731;G|0.269	0.269	strong		0.408	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305800	39305800	+	Missense_Mutation	SNP	T	T	A	rs141998775		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39305800T>A	ENST00000343246.4	-	1	254	c.220A>T	c.(220-222)Agc>Tgc	p.S74C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	74	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			cggcagcagctggattcacag	0.657																																					p.S74C		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,4	KRTAP4-5	34	4	0			c.A220T						scavenged	.						12.0	18.0	16.0					17																	39305800		2056	4148	6204	SO:0001583	missense	85289	exon1			AGCAGCTGGATTC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.220A>T	17.37:g.39305800T>A	ENSP00000340546:p.Ser74Cys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	40	4	0.1	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	12.46	1.946118	0.34377	.	.	ENSG00000198271	ENST00000343246	T	0.00633	6.08	3.65	2.55	0.30701	.	.	.	.	.	T	0.01287	0.0042	N	0.25957	0.775	0.22412	N	0.999125	D	0.76494	0.999	D	0.63703	0.917	T	0.57015	-0.7883	9	0.59425	D	0.04	.	7.2679	0.26239	0.0:0.1123:0.0:0.8877	.	74	Q9BYR2	KRA45_HUMAN	C	74	ENSP00000340546:S74C	ENSP00000340546:S74C	S	-	1	0	KRTAP4-5	36559326	0.004000	0.15560	0.084000	0.20598	0.021000	0.10359	-0.223000	0.09177	0.555000	0.29079	0.358000	0.22013	AGC	.	.	none		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
KMT2C	58508	hgsc.bcm.edu	37	7	151945225	151945225	+	Missense_Mutation	SNP	T	T	C	rs202098135		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151945225T>C	ENST00000262189.6	-	14	2512	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	KMT2C_ENST00000355193.2_Missense_Mutation_p.E765G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	765					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)	p.E765G(2)									TGACTCTGTCTCAGATGATAA	0.423																																					p.E765G		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,0,2	MLL3	1564	2	2	Substitution - Missense(2)	skin(2)	c.A2294G						scavenged	.																																			SO:0001583	missense	58508	exon14			TCTGTCTCAGATG	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.2294A>G	7.37:g.151945225T>C	ENSP00000262189:p.Glu765Gly	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	269	17	0.063197	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	9.954	1.221036	0.22457	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85088	-1.93;-1.94	5.68	4.53	0.55603	.	0.000000	0.46758	D	0.000267	T	0.75700	0.3885	L	0.34521	1.04	0.80722	D	1	B	0.21753	0.06	B	0.17433	0.018	T	0.67753	-0.5589	10	0.30078	T	0.28	.	8.7934	0.34866	0.0:0.1446:0.0:0.8554	.	765	Q8NEZ4	MLL3_HUMAN	G	765	ENSP00000262189:E765G;ENSP00000347325:E765G	ENSP00000262189:E765G	E	-	2	0	MLL3	151576158	0.998000	0.40836	0.463000	0.27130	0.101000	0.19017	2.545000	0.45769	0.983000	0.38602	0.528000	0.53228	GAG	T|0.700;C|0.300	0.300	strong		0.423	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
SEC31B	25956	hgsc.bcm.edu	37	10	102265847	102265847	+	Missense_Mutation	SNP	A	A	C	rs2295774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102265847A>C	ENST00000370345.3	-	9	1091	c.994T>G	c.(994-996)Tct>Gct	p.S332A	SEC31B_ENST00000370329.5_Missense_Mutation_p.S335A|SEC31B_ENST00000451524.1_Missense_Mutation_p.S332A|SEC31B_ENST00000535773.1_Missense_Mutation_p.S175A	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	332			S -> A (in dbSNP:rs2295774). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCCATCACAGAGTACAAACTG	0.542													A|||	751	0.14996	0.0719	0.1744	5008	,	,		19627	0.1319		0.1909	False		,,,				2504	0.2147				p.S332A		Atlas-SNP	.											SEC31B,colon,carcinoma,0,1	SEC31B	84	1	0			c.T994G						PASS	.	A	ALA/SER	340,4066	181.5+/-209.5	13,314,1876	158.0	156.0	157.0		994	5.9	1.0	10	dbSNP_100	157	1888,6712	335.8+/-321.6	216,1456,2628	yes	missense	SEC31B	NM_015490.3	99	229,1770,4504	CC,CA,AA		21.9535,7.7167,17.1306	probably-damaging	332/1180	102265847	2228,10778	2203	4300	6503	SO:0001583	missense	25956	exon9			TCACAGAGTACAA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.994T>G	10.37:g.102265847A>C	ENSP00000359370:p.Ser332Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	338	0.15476190476190477	19	0.03861788617886179	66	0.18232044198895028	94	0.16433566433566432	159	0.20976253298153033	A	32	5.124589	0.94429	0.077167	0.219535	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000535773;ENST00000370329	T;T;T;T	0.71817	1.47;1.47;-0.6;1.47	5.94	5.94	0.96194	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.050373	0.85682	D	0.000000	T	0.00300	0.0009	M	0.92169	3.28	0.09310	P	0.9999999837421	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.979;0.994;0.979;0.987	T	0.01566	-1.1323	9	0.72032	D	0.01	-11.7028	15.579	0.76418	1.0:0.0:0.0:0.0	rs2295774;rs2295774	332;335;331;332;332	A8KAL6;B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;.;SC31B_HUMAN	A	332;332;175;335	ENSP00000359370:S332A;ENSP00000391178:S332A;ENSP00000442621:S175A;ENSP00000359354:S335A	ENSP00000359354:S335A	S	-	1	0	SEC31B	102255837	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.334000	0.79224	2.279000	0.76181	0.459000	0.35465	TCT	A|0.836;C|0.164	0.164	strong		0.542	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
ERICH1	157697	hgsc.bcm.edu	37	8	623593	623593	+	Silent	SNP	G	G	A	rs55783038	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:623593G>A	ENST00000262109.7	-	4	836	c.759C>T	c.(757-759)gcC>gcT	p.A253A	ERICH1_ENST00000522706.1_Silent_p.A159A|ERICH1_ENST00000518277.1_5'Flank	NM_207332.1	NP_997215.1	Q86X53	ERIC1_HUMAN	glutamate-rich 1	253	Glu-rich.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)	20		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		CTTCCTCACTGGCGTCCGCAC	0.632													G|||	989	0.197484	0.0371	0.2435	5008	,	,		17962	0.0675		0.4066	False		,,,				2504	0.3006				p.A253A		Atlas-SNP	.											.	ERICH1	50	.	0			c.C759T						PASS	.	G		398,4008	197.7+/-221.8	17,364,1822	109.0	102.0	104.0		759	0.1	0.0	8	dbSNP_129	104	3438,5162	505.0+/-376.3	677,2084,1539	no	coding-synonymous	ERICH1	NM_207332.1		694,2448,3361	AA,AG,GG		39.9767,9.0331,29.4941		253/444	623593	3836,9170	2203	4300	6503	SO:0001819	synonymous_variant	157697	exon4			CTCACTGGCGTCC		CCDS5955.1	8p23.3	2005-09-01			ENSG00000104714	ENSG00000104714			27234	protein-coding gene	gene with protein product							Standard	NM_207332		Approved		uc003wph.3	Q86X53	OTTHUMG00000129163	ENST00000262109.7:c.759C>T	8.37:g.623593G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_207332	A8K2J9|Q9P063	Silent	SNP	ENST00000262109.7	37	CCDS5955.1	462	0.21153846153846154	12	0.024390243902439025	116	0.32044198895027626	35	0.06118881118881119	299	0.3944591029023747	G	3.781	-0.045708	0.07452	0.090331	0.399767	ENSG00000104714	ENST00000522893	.	.	.	1.05	0.0893	0.14458	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44620	-0.9316	3	.	.	.	.	1.7477	0.02965	0.2453:0.0:0.4267:0.3279	rs55783038;rs61743224	.	.	.	L	22	.	.	P	-	2	0	ERICH1	613593	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.004000	0.13106	0.005000	0.14708	0.543000	0.68304	CCA	G|0.717;A|0.283	0.283	strong		0.632	ERICH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251228.3	NM_207332	
TCFL5	10732	hgsc.bcm.edu	37	20	61488785	61488785	+	Silent	SNP	T	T	C	rs2294996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	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	
PRDM15	63977	hgsc.bcm.edu	37	21	43236176	43236176	+	Silent	SNP	G	G	A	rs4075967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43236176G>A	ENST00000269844.3	-	26	3485	c.3375C>T	c.(3373-3375)caC>caT	p.H1125H	PRDM15_ENST00000398548.1_Silent_p.H796H|PRDM15_ENST00000447207.2_Silent_p.H759H|PRDM15_ENST00000422911.1_Silent_p.H816H|PRDM15_ENST00000538201.1_Silent_p.H779H	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GGCGCAGCGCGTGCTTGGTCT	0.637													g|||	886	0.176917	0.1324	0.2248	5008	,	,		18307	0.2054		0.1879	False		,,,				2504	0.1626				p.H1125H		Atlas-SNP	.											.	PRDM15	110	.	0			c.C3375T						PASS	.		,	679,3727	286.0+/-278.5	51,577,1575	146.0	104.0	118.0		2388,3375	0.6	1.0	21	dbSNP_108	118	1998,6602	350.1+/-327.7	230,1538,2532	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	281,2115,4107	AA,AG,GG		23.2326,15.4108,20.5828	,	796/1179,1125/1508	43236176	2677,10329	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon26			CAGCGCGTGCTTG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3375C>T	21.37:g.43236176G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			G|0.802;A|0.198	0.198	strong		0.637	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
OR52N1	79473	hgsc.bcm.edu	37	11	5809477	5809477	+	Silent	SNP	A	A	G	rs10838637	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5809477A>G	ENST00000317078.1	-	1	569	c.570T>C	c.(568-570)tcT>tcC	p.S190S	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	190						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)		CATTACCACAAGATATCTTGG	0.473													A|||	1611	0.321685	0.4576	0.2738	5008	,	,		22466	0.2004		0.332	False		,,,				2504	0.2863				p.S190S		Atlas-SNP	.											OR52N1,colon,carcinoma,-1,1	OR52N1	70	1	0			c.T570C						PASS	.	A		1897,2505	544.2+/-376.5	399,1099,703	155.0	130.0	139.0		570	2.5	1.0	11	dbSNP_120	139	2640,5952	425.0+/-354.8	396,1848,2052	no	coding-synonymous	OR52N1	NM_001001913.1		795,2947,2755	GG,GA,AA		30.7263,43.094,34.9161		190/321	5809477	4537,8457	2201	4296	6497	SO:0001819	synonymous_variant	79473	exon1			ACCACAAGATATC	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.570T>C	11.37:g.5809477A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001001913	Q6IFF6	Silent	SNP	ENST00000317078.1	37	CCDS31398.1																																																																																			A|0.672;G|0.328	0.328	strong		0.473	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
HIVEP2	3097	hgsc.bcm.edu	37	6	143092754	143092754	+	Missense_Mutation	SNP	G	G	A	rs34875559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:143092754G>A	ENST00000367604.1	-	4	3761	c.3122C>T	c.(3121-3123)gCg>gTg	p.A1041V	HIVEP2_ENST00000367603.2_Missense_Mutation_p.A1041V|HIVEP2_ENST00000012134.2_Missense_Mutation_p.A1041V			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1041			A -> V (in dbSNP:rs34875559).		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)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TGGGACTTCCGCTGGGTGAGG	0.552													G|||	79	0.0157748	0.0	0.0216	5008	,	,		19973	0.0109		0.0219	False		,,,				2504	0.0317				p.A1041V	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.C3122T						PASS	.	G	VAL/ALA	16,3954		0,16,1969	49.0	50.0	49.0		3122	4.9	0.0	6	dbSNP_126	49	147,8217		1,145,4036	yes	missense	HIVEP2	NM_006734.3	64	1,161,6005	AA,AG,GG		1.7575,0.403,1.3216	benign	1041/2447	143092754	163,12171	1985	4182	6167	SO:0001583	missense	3097	exon5			ACTTCCGCTGGGT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.3122C>T	6.37:g.143092754G>A	ENSP00000356576:p.Ala1041Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	4	0.006993006993006993	18	0.023746701846965697	G	13.47	2.245434	0.39697	0.00403	0.017575	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.13538	2.58;2.58;2.58	5.8	4.94	0.65067	.	0.495910	0.25487	N	0.030329	T	0.05502	0.0145	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.22068	-1.0227	10	0.72032	D	0.01	-12.0601	14.6293	0.68645	0.0696:0.0:0.9304:0.0	rs34875559	1041	P31629	ZEP2_HUMAN	V	1041	ENSP00000356576:A1041V;ENSP00000356575:A1041V;ENSP00000012134:A1041V	ENSP00000012134:A1041V	A	-	2	0	HIVEP2	143134447	0.978000	0.34361	0.003000	0.11579	0.592000	0.36648	5.811000	0.69187	1.470000	0.48102	0.655000	0.94253	GCG	G|0.982;A|0.018	0.018	strong		0.552	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
DDX58	23586	hgsc.bcm.edu	37	9	32480251	32480251	+	Missense_Mutation	SNP	A	A	T	rs17217280	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32480251A>T	ENST00000379883.2	-	12	1897	c.1740T>A	c.(1738-1740)gaT>gaA	p.D580E	DDX58_ENST00000545044.1_Missense_Mutation_p.D377E|DDX58_ENST00000542096.1_Missense_Mutation_p.D509E|DDX58_ENST00000379868.1_Missense_Mutation_p.D377E|DDX58_ENST00000379882.1_Missense_Mutation_p.D535E	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	580	Interaction with ZC3HAV1.		D -> E (in dbSNP:rs17217280). {ECO:0000269|PubMed:11890704, ECO:0000269|Ref.1}.		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 defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GCTCAATCTCATCGAATCCTG	0.428													A|||	284	0.0567093	0.0068	0.1009	5008	,	,		19368	0.0129		0.1362	False		,,,				2504	0.0562				p.D580E		Atlas-SNP	.											.	DDX58	82	.	0			c.T1740A						PASS	.	A	GLU/ASP	142,4264	99.8+/-138.5	2,138,2063	154.0	135.0	141.0		1740	4.7	1.0	9	dbSNP_123	141	1268,7332	251.8+/-278.1	93,1082,3125	yes	missense	DDX58	NM_014314.3	45	95,1220,5188	TT,TA,AA		14.7442,3.2229,10.8412	possibly-damaging	580/926	32480251	1410,11596	2203	4300	6503	SO:0001583	missense	23586	exon12			AATCTCATCGAAT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.1740T>A	9.37:g.32480251A>T	ENSP00000369213:p.Asp580Glu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	169	0.07738095238095238	6	0.012195121951219513	47	0.1298342541436464	11	0.019230769230769232	105	0.13852242744063326	A	21.6	4.172154	0.78452	0.032229	0.147442	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.67	4.67	0.58626	.	0.144833	0.46758	D	0.000261	T	0.00440	0.0014	M	0.79011	2.435	0.24770	P	0.99287946	D;P;B;P	0.55800	0.973;0.886;0.037;0.818	P;P;B;B	0.55011	0.766;0.489;0.037;0.215	T	0.12502	-1.0545	9	0.21014	T	0.42	-18.2098	13.7947	0.63164	1.0:0.0:0.0:0.0	rs17217280;rs17217280	377;535;509;580	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	E	535;580;377;509;377	ENSP00000369212:D535E;ENSP00000369213:D580E;ENSP00000369197:D377E;ENSP00000442160:D509E;ENSP00000443055:D377E	ENSP00000369197:D377E	D	-	3	2	DDX58	32470251	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.645000	0.37238	2.051000	0.60960	0.533000	0.62120	GAT	A|0.906;T|0.094	0.094	strong		0.428	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
ZBTB32	27033	hgsc.bcm.edu	37	19	36207510	36207510	+	Silent	SNP	G	G	A	rs1052491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36207510G>A	ENST00000392197.2	+	7	1638	c.1320G>A	c.(1318-1320)ctG>ctA	p.L440L	KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|ZBTB32_ENST00000262630.3_Silent_p.L440L|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000607650.1_RNA			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	440					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTCCCAGCCTGGCCTCCATGC	0.701											OREG0025433	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	209	0.0417332	0.0068	0.0591	5008	,	,		16742	0.0		0.1272	False		,,,				2504	0.0317				p.L440L		Atlas-SNP	.											.	ZBTB32	33	.	0			c.G1320A						PASS	.	G		144,4262	101.2+/-139.8	4,136,2063	59.0	56.0	57.0		1320	2.6	1.0	19	dbSNP_86	57	1235,7363	246.7+/-275.0	95,1045,3159	no	coding-synonymous	ZBTB32	NM_014383.1		99,1181,5222	AA,AG,GG		14.3638,3.2683,10.6044		440/488	36207510	1379,11625	2203	4299	6502	SO:0001819	synonymous_variant	27033	exon6			CAGCCTGGCCTCC	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.1320G>A	19.37:g.36207510G>A		Somatic	35	0	0	861	WXS	Illumina HiSeq	Phase_I	50	32	0.64	NM_014383	Q8WVP2	Silent	SNP	ENST00000392197.2	37	CCDS12471.1																																																																																			G|0.910;A|0.090	0.090	strong		0.701	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
SERPINI2	5276	hgsc.bcm.edu	37	3	167170788	167170788	+	Silent	SNP	G	G	A	rs61750373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167170788G>A	ENST00000476257.1	-	7	1198	c.900C>T	c.(898-900)gaC>gaT	p.D300D	SERPINI2_ENST00000461846.1_Silent_p.D300D|SERPINI2_ENST00000264677.4_Silent_p.D300D|SERPINI2_ENST00000471111.1_Silent_p.D300D			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	300					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						AATACAAAACGTCTTTGAAGT	0.279													G|||	7	0.00139776	0.0015	0.0	5008	,	,		15704	0.0		0.004	False		,,,				2504	0.001				p.D310D		Atlas-SNP	.											.	SERPINI2	85	.	0			c.C930T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	64.0	61.0	62.0		900	1.5	1.0	3	dbSNP_129	62	66,8532	39.8+/-96.3	1,64,4234	no	coding-synonymous	SERPINI2	NM_006217.3		1,73,6428	AA,AG,GG		0.7676,0.2043,0.5767		300/406	167170788	75,12929	2203	4299	6502	SO:0001819	synonymous_variant	5276	exon7			CAAAACGTCTTTG	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.900C>T	3.37:g.167170788G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	204	75	0.367647	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			G|0.996;A|0.004	0.004	strong		0.279	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
P2RX2	22953	hgsc.bcm.edu	37	12	133196596	133196596	+	Silent	SNP	T	T	C	rs7964634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133196596T>C	ENST00000389110.3	+	5	505	c.468T>C	c.(466-468)acT>acC	p.T156T	P2RX2_ENST00000348800.5_Silent_p.T156T|P2RX2_ENST00000449132.2_Intron|P2RX2_ENST00000351222.4_Silent_p.T64T|P2RX2_ENST00000350048.5_Silent_p.T132T|P2RX2_ENST00000343948.4_Silent_p.T156T|P2RX2_ENST00000352418.4_Silent_p.T84T	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	156					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|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)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		GCCTGAGGACTGGGCGCTGTG	0.692													C|||	3570	0.712859	0.8449	0.7522	5008	,	,		9375	0.7808		0.5616	False		,,,				2504	0.592				p.T156T		Atlas-SNP	.											P2RX2,NS,carcinoma,0,1	P2RX2	49	1	0			c.T468C						PASS	.	C	,,,,,	3486,890		1422,642,124	11.0	11.0	11.0		252,396,468,468,192,468	-6.3	0.2	12	dbSNP_116	11	4981,3583		1468,2045,769	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	P2RX2	NM_012226.3,NM_016318.2,NM_170682.2,NM_170683.2,NM_174872.1,NM_174873.1	,,,,,	2890,2687,893	CC,CT,TT		41.8379,20.3382,34.5672	,,,,,	84/400,132/448,156/472,156/498,64/380,156/405	133196596	8467,4473	2188	4282	6470	SO:0001819	synonymous_variant	22953	exon5			GAGGACTGGGCGC	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	15459	protein-coding gene	gene with protein product		600844	"""deafness, autosomal dominant 41"""	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.468T>C	12.37:g.133196596T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Silent	SNP	ENST00000389110.3	37	CCDS31931.1	1536	0.7032967032967034	399	0.8109756097560976	265	0.7320441988950276	449	0.784965034965035	423	0.558047493403694	C	1.836	-0.468560	0.04445	0.796618	0.581621	ENSG00000187848	ENST00000542301;ENST00000536121;ENST00000535910	.	.	.	4.99	-6.26	0.02033	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33701	-0.9858	3	.	.	.	-23.5422	1.2958	0.02069	0.1936:0.1398:0.2356:0.431	rs7964634;rs57252153	.	.	.	P	167;142;112	.	.	L	+	2	0	P2RX2	131706669	0.000000	0.05858	0.232000	0.24009	0.080000	0.17528	-8.920000	0.00015	-1.059000	0.03193	-1.163000	0.01768	CTG	T|0.323;C|0.677	0.677	strong		0.692	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609105	32609105	+	Missense_Mutation	SNP	G	G	A	rs1129740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609105G>A	ENST00000343139.5	+	2	203	c.101G>A	c.(100-102)tGt>tAt	p.C34Y	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.C34Y|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.C34Y	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	34	Alpha-1.		Y -> C (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06 and allele DQA1*01:07; dbSNP:rs1129740).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GTTGCCTCTTGTGGTGTAAAC	0.473													.|||	2620	0.523163	0.503	0.6758	5008	,	,		16991	0.4623		0.5547	False		,,,				2504	0.4724				p.C34Y		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G101A						PASS	.	A	TYR/CYS	1866,2540		609,648,946	147.0	124.0	131.0		101	-0.3	0.0	6	dbSNP_86	131	3996,4590		1509,978,1806	yes	missense	HLA-DQA1	NM_002122.3	194	2118,1626,2752	AA,AG,GG		46.5409,42.3513,45.1201	benign	34/256	32609105	5862,7130	2203	4293	6496	SO:0001583	missense	3117	exon2			CCTCTTGTGGTGT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.101G>A	6.37:g.32609105G>A	ENSP00000339398:p.Cys34Tyr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	1155|1155	0.5288461538461539|0.5288461538461539	219|219	0.4451219512195122|0.4451219512195122	236|236	0.6519337016574586|0.6519337016574586	300|300	0.5244755244755245|0.5244755244755245	400|400	0.5277044854881267|0.5277044854881267	.|.	0.005|0.005	-2.227569|-2.227569	0.00280|0.00280	0.423513|0.423513	0.465409|0.465409	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.00627|.	6.12;6.12;6.12;6.12|.	3.84|3.84	-0.275|-0.275	0.12906|0.12906	.|.	1.206650|.	0.05915|.	N|.	0.632490|.	T|T	0.00784|0.00784	0.0026|0.0026	N|N	0.00067|0.00067	-2.295|-2.295	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.11235|.	0.004;0.001|.	B;B|.	0.16289|.	0.015;0.002|.	T|T	0.39035|0.39035	-0.9633|-0.9633	9|4	0.02654|.	T|.	1|.	.|.	1.0863|1.0863	0.01654|0.01654	0.4832:0.1399:0.1032:0.2736|0.4832:0.1399:0.1032:0.2736	rs1129740;rs1142321;rs3187980;rs3205982;rs9272689;rs12722045;rs17412265|rs1129740;rs1142321;rs3187980;rs3205982;rs9272689;rs12722045;rs17412265	40;34|.	Q59F33;G4XQK2|.	.;.|.	Y|M	34|7	ENSP00000339398:C34Y;ENSP00000378767:C34Y;ENSP00000437302:C34Y;ENSP00000364087:C34Y|.	ENSP00000339398:C34Y|.	C|V	+|+	2|1	0|0	HLA-DQA1|HLA-DQA1	32717083|32717083	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.118000|0.118000	0.15605|0.15605	-0.454000|-0.454000	0.07066|0.07066	-1.852000|-1.852000	0.00566|0.00566	TGT|GTG	G|0.446;A|0.554	0.554	strong		0.473	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
MUC16	94025	hgsc.bcm.edu	37	19	9056982	9056982	+	Missense_Mutation	SNP	G	G	A	rs11670318	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9056982G>A	ENST00000397910.4	-	3	30667	c.30464C>T	c.(30463-30465)aCa>aTa	p.T10155I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10157	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						CTCAAATCCTGTGGTCTCAAA	0.468													G|||	1241	0.247804	0.1543	0.2161	5008	,	,		22860	0.2391		0.336	False		,,,				2504	0.3149				p.T10155I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C30464T						PASS	.	G	ILE/THR	691,3181		64,563,1309	81.0	78.0	79.0		30464	0.5	0.0	19	dbSNP_120	79	2676,5598		418,1840,1879	yes	missense	MUC16	NM_024690.2	89	482,2403,3188	AA,AG,GG		32.3423,17.8461,27.7211	probably-damaging	10155/14508	9056982	3367,8779	1936	4137	6073	SO:0001583	missense	94025	exon3			AATCCTGTGGTCT	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.30464C>T	19.37:g.9056982G>A	ENSP00000381008:p.Thr10155Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	549	0.25137362637362637	89	0.18089430894308944	90	0.24861878453038674	119	0.20804195804195805	251	0.3311345646437995	g	4.903	0.167900	0.09339	0.178461	0.323423	ENSG00000181143	ENST00000397910	T	0.28666	1.6	2.78	0.467	0.16721	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	D	0.69078	0.997	D	0.63793	0.918	T	0.36625	-0.9740	8	0.87932	D	0	.	5.0713	0.14608	0.0:0.2366:0.5203:0.2431	rs11670318;rs60325742	10155	B5ME49	.	I	10155	ENSP00000381008:T10155I	ENSP00000381008:T10155I	T	-	2	0	MUC16	8917982	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.151000	0.10175	0.193000	0.20303	0.563000	0.77884	ACA	G|0.740;A|0.260	0.260	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	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	
C6orf118	168090	hgsc.bcm.edu	37	6	165713961	165713961	+	Missense_Mutation	SNP	A	A	C	rs510579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:165713961A>C	ENST00000230301.8	-	3	788	c.768T>G	c.(766-768)atT>atG	p.I256M	C6orf118_ENST00000543069.1_Missense_Mutation_p.I152M	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	256			I -> M (in dbSNP:rs510579).							breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		TGCACGTGCAAATTTTCTGGA	0.443													A|||	2422	0.483626	0.8207	0.4395	5008	,	,		15414	0.2073		0.3757	False		,,,				2504	0.455				p.I256M		Atlas-SNP	.											.	C6orf118	116	.	0			c.T768G						PASS	.	A	MET/ILE	3290,1116	716.3+/-408.6	1241,808,154	120.0	138.0	132.0		768	-10.0	0.0	6	dbSNP_83	132	2999,5601	462.9+/-365.8	536,1927,1837	yes	missense	C6orf118	NM_144980.3	10	1777,2735,1991	CC,CA,AA		34.8721,25.3291,48.3546	benign	256/470	165713961	6289,6717	2203	4300	6503	SO:0001583	missense	168090	exon3			CGTGCAAATTTTC		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.768T>G	6.37:g.165713961A>C	ENSP00000230301:p.Ile256Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	995	0.4555860805860806	413	0.8394308943089431	153	0.42265193370165743	134	0.23426573426573427	295	0.3891820580474934	A	4.334	0.061360	0.08339	0.746709	0.348721	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.14766	2.48;2.48	5.02	-10.0	0.00425	.	0.793262	0.10664	N	0.648383	T	0.07234	0.0183	L	0.47716	1.5	0.80722	P	0.0	D	0.63880	0.993	P	0.60682	0.878	T	0.12477	-1.0546	9	0.38643	T	0.18	.	7.8459	0.29424	0.082:0.4184:0.3904:0.1092	rs510579;rs1134555;rs3196777;rs11553362;rs17858772;rs52834728;rs56421334;rs58722559;rs510579	256	Q5T5N4	CF118_HUMAN	M	256;152	ENSP00000230301:I256M;ENSP00000439288:I152M	ENSP00000230301:I256M	I	-	3	3	C6orf118	165633951	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.096000	0.01349	-3.147000	0.00231	-2.324000	0.00251	ATT	A|0.515;C|0.485	0.485	strong		0.443	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
EVI5L	115704	hgsc.bcm.edu	37	19	7916620	7916620	+	Silent	SNP	A	A	G	rs580790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7916620A>G	ENST00000270530.4	+	8	1147	c.951A>G	c.(949-951)gcA>gcG	p.A317A	EVI5L_ENST00000538904.2_Silent_p.A317A	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	317					negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						TGAACCAGGCAGAGCTGATGC	0.682													G|||	3845	0.767772	0.6346	0.8473	5008	,	,		16562	0.7014		0.8429	False		,,,				2504	0.8824				p.A317A		Atlas-SNP	.											.	EVI5L	43	.	0			c.A951G						PASS	.	G	,	3002,1404	460.3+/-352.6	1020,962,221	48.0	44.0	45.0		951,951	-3.2	0.4	19	dbSNP_83	45	7311,1289	255.9+/-280.6	3106,1099,95	no	coding-synonymous,coding-synonymous	EVI5L	NM_001159944.1,NM_145245.3	,	4126,2061,316	GG,GA,AA		14.9884,31.8656,20.7058	,	317/806,317/795	7916620	10313,2693	2203	4300	6503	SO:0001819	synonymous_variant	115704	exon7			CCAGGCAGAGCTG	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.951A>G	19.37:g.7916620A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			A|0.216;G|0.784	0.784	strong		0.682	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256729	140256729	+	Missense_Mutation	SNP	G	G	A	rs543806401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256729G>A	ENST00000398631.2	+	1	1672	c.1672G>A	c.(1672-1674)Gag>Aag	p.E558K	PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	558	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)			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)			CGTGCTGGACGAGAACGACAA	0.701													.|||	2	0.000399361	0.0	0.0	5008	,	,		17343	0.0		0.0	False		,,,				2504	0.002				p.E558K	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G1672A						PASS	.						144.0	149.0	147.0					5																	140256729		2203	4299	6502	SO:0001583	missense	56137	exon1			CTGGACGAGAACG	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.1672G>A	5.37:g.140256729G>A	ENSP00000381628:p.Glu558Lys	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023113	0.54683	.	.	ENSG00000251664	ENST00000398631	T	0.60920	0.15	4.92	4.05	0.47172	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.65698	0.2716	M	0.70108	2.13	0.24151	N	0.995691	D;D	0.60575	0.988;0.983	P;B	0.53760	0.734;0.284	T	0.57585	-0.7786	9	0.62326	D	0.03	.	8.9151	0.35576	0.1715:0.0:0.8285:0.0	.	558;558	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	K	558	ENSP00000381628:E558K	ENSP00000381628:E558K	E	+	1	0	PCDHA12	140236913	0.033000	0.19621	0.956000	0.39512	0.208000	0.24298	0.499000	0.22546	1.060000	0.40578	0.561000	0.74099	GAG	.	.	none		0.701	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
S100A5	6276	hgsc.bcm.edu	37	1	153509890	153509890	+	Missense_Mutation	SNP	T	T	C	rs3795393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:153509890T>C	ENST00000368718.1	-	4	442	c.161A>G	c.(160-162)gAc>gGc	p.D54G	S100A6_ENST00000368719.4_5'Flank|BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000496817.1_5'Flank|S100A5_ENST00000359215.1_Missense_Mutation_p.D72G|S100A5_ENST00000368717.2_Missense_Mutation_p.D54G|S100A6_ENST00000368720.2_5'Flank	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	104	2	0.0192308		WXS	Illumina HiSeq	Phase_I	156	95	0.608974	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	
IFT140	9742	hgsc.bcm.edu	37	16	1616201	1616201	+	Missense_Mutation	SNP	C	C	T	rs11648609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1616201C>T	ENST00000426508.2	-	16	2225	c.1862G>A	c.(1861-1863)cGg>cAg	p.R621Q	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	621			R -> Q (in dbSNP:rs11648609).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CGTCTCTCTCCGATCAATTTG	0.418													C|||	357	0.0712859	0.0113	0.1916	5008	,	,		22031	0.1329		0.0427	False		,,,				2504	0.0327				p.R621Q		Atlas-SNP	.											.	IFT140	128	.	0			c.G1862A						PASS	.	C	GLN/ARG	74,4324	67.0+/-104.6	1,72,2126	208.0	200.0	202.0		1862	-8.2	0.0	16	dbSNP_120	202	419,8181	129.0+/-187.1	8,403,3889	yes	missense	IFT140	NM_014714.3	43	9,475,6015	TT,TC,CC		4.8721,1.6826,3.7929	benign	621/1463	1616201	493,12505	2199	4300	6499	SO:0001583	missense	9742	exon16			TCTCTCCGATCAA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1862G>A	16.37:g.1616201C>T	ENSP00000406012:p.Arg621Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	169	0.07738095238095238	6	0.012195121951219513	54	0.14917127071823205	78	0.13636363636363635	31	0.040897097625329816	C	7.243	0.601619	0.13939	0.016826	0.048721	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.61859	0.07	5.29	-8.21	0.01041	.	0.395863	0.27549	N	0.018867	T	0.00178	0.0005	N	0.24115	0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.18999	-1.0319	9	0.09338	T	0.73	.	10.3675	0.44033	0.0:0.6097:0.1016:0.2887	rs11648609;rs52820135;rs59302511;rs11648609	621;346	Q96RY7;B4DR58	IF140_HUMAN;.	Q	621	ENSP00000406012:R621Q	ENSP00000380562:R621Q	R	-	2	0	IFT140	1556202	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.556000	0.05992	-1.140000	0.02877	-0.948000	0.02665	CGG	C|0.946;T|0.054	0.054	strong		0.418	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
FSTL5	56884	hgsc.bcm.edu	37	4	162307312	162307312	+	Missense_Mutation	SNP	C	C	A	rs3749598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:162307312C>A	ENST00000306100.5	-	16	2567	c.2131G>T	c.(2131-2133)Gat>Tat	p.D711Y	FSTL5_ENST00000427802.2_Missense_Mutation_p.D701Y|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000379164.4_Missense_Mutation_p.D710Y|FSTL5_ENST00000536695.1_Missense_Mutation_p.D710Y	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	711			D -> Y (in dbSNP:rs3749598).			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)		CCTTTCACATCATTAATGCTG	0.433													C|||	456	0.0910543	0.0628	0.121	5008	,	,		20320	0.0704		0.1203	False		,,,				2504	0.0992				p.D711Y		Atlas-SNP	.											.	FSTL5	207	.	0			c.G2131T						PASS	.	C	TYR/ASP,TYR/ASP,TYR/ASP	296,4110	164.0+/-195.7	17,262,1924	112.0	104.0	107.0		2128,2101,2131	4.0	0.0	4	dbSNP_107	107	833,7767	192.4+/-238.4	46,741,3513	yes	missense,missense,missense	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	160,160,160	63,1003,5437	AA,AC,CC		9.686,6.7181,8.6806	probably-damaging,probably-damaging,probably-damaging	710/847,701/838,711/848	162307312	1129,11877	2203	4300	6503	SO:0001583	missense	56884	exon16			TCACATCATTAAT	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.2131G>T	4.37:g.162307312C>A	ENSP00000305334:p.Asp711Tyr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	205	0.09386446886446886	37	0.07520325203252033	38	0.10497237569060773	36	0.06293706293706294	94	0.12401055408970976	C	16.08	3.021450	0.54576	0.067181	0.09686	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.7	3.98	0.46160	WD40/YVTN repeat-like-containing domain (1);	0.044086	0.85682	D	0.000000	T	0.00936	0.0031	M	0.64997	1.995	0.09310	P	0.99999974501	D;D;D	0.89917	1.0;0.964;0.972	D;P;P	0.72075	0.976;0.785;0.786	T	0.14896	-1.0456	9	0.72032	D	0.01	.	11.5272	0.50586	0.0:0.8673:0.0:0.1327	rs3749598;rs17337120;rs52795466;rs60151024;rs3749598	701;710;711	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	Y	711;710;701;710	ENSP00000305334:D711Y;ENSP00000368462:D710Y;ENSP00000389270:D701Y;ENSP00000440409:D710Y	ENSP00000305334:D711Y	D	-	1	0	FSTL5	162526762	1.000000	0.71417	0.009000	0.14445	0.893000	0.52053	4.524000	0.60552	0.771000	0.33359	0.655000	0.94253	GAT	C|0.914;A|0.086	0.086	strong		0.433	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
PRDM10	56980	hgsc.bcm.edu	37	11	129794950	129794950	+	Missense_Mutation	SNP	T	T	C	rs2241571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:129794950T>C	ENST00000360871.3	-	12	1936	c.1705A>G	c.(1705-1707)Aca>Gca	p.T569A	PRDM10_ENST00000526082.1_Missense_Mutation_p.T487A|PRDM10_ENST00000528746.1_Missense_Mutation_p.T543A|PRDM10_ENST00000423662.2_Missense_Mutation_p.T487A|PRDM10_ENST00000358825.5_Missense_Mutation_p.T573A|PRDM10_ENST00000304538.6_Missense_Mutation_p.T483A	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	573				F -> L (in Ref. 4; BX648944). {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)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TCCAAGGATGTGCTGCTGATG	0.507													C|||	2121	0.423522	0.4773	0.3977	5008	,	,		19557	0.3988		0.3907	False		,,,				2504	0.4284				p.T573A		Atlas-SNP	.											.	PRDM10	120	.	0			c.A1717G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR,ALA/THR	1995,2407	614.6+/-392.4	430,1135,636	192.0	189.0	190.0		1447,1459,1705,1717	0.8	0.1	11	dbSNP_98	190	3392,5202	639.6+/-399.5	641,2110,1546	yes	missense,missense,missense,missense	PRDM10	NM_199439.1,NM_199438.1,NM_199437.1,NM_020228.2	58,58,58,58	1071,3245,2182	CC,CT,TT		39.4694,45.3203,41.4512	benign,benign,benign,benign	483/1024,487/1062,569/1157,573/1161	129794950	5387,7609	2201	4297	6498	SO:0001583	missense	56980	exon13			AGGATGTGCTGCT	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.1705A>G	11.37:g.129794950T>C	ENSP00000354118:p.Thr569Ala	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	913	0.41804029304029305	227	0.4613821138211382	145	0.4005524861878453	238	0.4160839160839161	303	0.3997361477572559	C	6.919	0.539222	0.13250	0.453203	0.394694	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	T;T;T;T;T;T;T	0.07114	3.22;3.22;3.22;3.22;3.22;3.22;3.22	5.71	0.816	0.18768	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.450530	0.25711	N	0.028802	T	0.00012	0.0000	N	0.11870	0.19	0.80722	P	0.0	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.0	B;B;B;B;B	0.12156	0.001;0.007;0.0;0.003;0.0	T	0.44802	-0.9304	9	0.21540	T	0.41	-10.1967	6.2641	0.20917	0.1179:0.3856:0.0:0.4965	rs2241571;rs59538863;rs2241571	569;573;487;483;487	G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;PRD10_HUMAN;.;.;.	A	573;483;569;487;543;487;286	ENSP00000351686:T573A;ENSP00000302669:T483A;ENSP00000354118:T569A;ENSP00000398431:T487A;ENSP00000431262:T543A;ENSP00000432237:T487A;ENSP00000435940:T286A	ENSP00000302669:T483A	T	-	1	0	PRDM10	129300160	0.003000	0.15002	0.068000	0.19968	0.849000	0.48306	-0.590000	0.05760	-0.030000	0.13804	-0.726000	0.03593	ACA	T|0.578;C|0.421	0.421	strong		0.507	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
ZNF512B	57473	hgsc.bcm.edu	37	20	62597694	62597694	+	Silent	SNP	T	T	G	rs817329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62597694T>G	ENST00000450537.1	-	5	894	c.834A>C	c.(832-834)gtA>gtC	p.V278V	ZNF512B_ENST00000369888.1_Silent_p.V278V|ZNF512B_ENST00000217130.3_Silent_p.V278V			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	278					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.V278V(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)					CAAGCTTTGTTACCGTAATGG	0.577													G|||	2456	0.490415	0.7504	0.428	5008	,	,		20355	0.0546		0.5676	False		,,,				2504	0.5532				p.V278V		Atlas-SNP	.											ZNF512B,NS,carcinoma,0,1	ZNF512B	72	1	1	Substitution - coding silent(1)	prostate(1)	c.A834C						PASS	.	G		3223,1183	415.0+/-337.0	1197,829,177	299.0	300.0	300.0		834	-0.8	0.0	20	dbSNP_86	300	4905,3695	528.5+/-381.4	1405,2095,800	no	coding-synonymous	ZNF512B	NM_020713.1		2602,2924,977	GG,GT,TT		42.9651,26.8498,37.5058		278/893	62597694	8128,4878	2203	4300	6503	SO:0001819	synonymous_variant	57473	exon5			CTTTGTTACCGTA	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.834A>C	20.37:g.62597694T>G		Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	295	142	0.481356	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			T|0.446;G|0.554	0.554	strong		0.577	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
POR	5447	hgsc.bcm.edu	37	7	75609677	75609677	+	Silent	SNP	A	A	G	rs1135612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:75609677A>G	ENST00000461988.1	+	5	492	c.387A>G	c.(385-387)ccA>ccG	p.P129P	POR_ENST00000394893.1_Silent_p.P129P|POR_ENST00000545601.1_5'UTR|POR_ENST00000419840.1_5'UTR|POR_ENST00000475509.1_3'UTR|POR_ENST00000439269.1_5'Flank|POR_ENST00000450476.1_5'Flank	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	126	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCAGCCTGCCAGAGATCGACA	0.627													A|||	1249	0.249401	0.0552	0.4035	5008	,	,		18095	0.4504		0.2445	False		,,,				2504	0.2004				p.P129P		Atlas-SNP	.											POR,NS,carcinoma,0,1	POR	46	1	0			c.A387G						PASS	.	A		313,3791		20,273,1759	53.0	59.0	57.0		387	-9.6	0.0	7	dbSNP_86	57	2101,6263		264,1573,2345	yes	coding-synonymous	POR	NM_000941.2		284,1846,4104	GG,GA,AA		25.1196,7.6267,19.3616		129/681	75609677	2414,10054	2052	4182	6234	SO:0001819	synonymous_variant	5447	exon5			CCTGCCAGAGATC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.387A>G	7.37:g.75609677A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	623	0.28525641025641024	26	0.052845528455284556	143	0.39502762430939226	255	0.4458041958041958	199	0.262532981530343	A	0.957	-0.704665	0.03255	0.076267	0.251196	ENSG00000127948	ENST00000447222	.	.	.	4.81	-9.62	0.00547	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999194	.	.	.	.	.	.	T	0.28038	-1.0056	3	.	.	.	-13.7498	0.1049	0.00051	0.2682:0.2151:0.1846:0.3322	rs1135612;rs2228102;rs2286818;rs3178962;rs3198391;rs11540671;rs12669302;rs61690444	.	.	.	G	102	.	.	R	+	1	2	POR	75447613	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-5.483000	0.00119	-3.832000	0.00101	-1.215000	0.01618	AGA	A|0.715;G|0.284;T|0.000	0.284	strong		0.627	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
OSGEP	55644	hgsc.bcm.edu	37	14	20920250	20920250	+	Silent	SNP	T	T	C	rs2275007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20920250T>C	ENST00000206542.4	-	3	715	c.294A>G	c.(292-294)caA>caG	p.Q98Q	OSGEP_ENST00000554249.1_5'Flank|OSGEP_ENST00000555656.1_5'Flank|RP11-203M5.7_ENST00000555435.1_RNA|OSGEP_ENST00000556252.1_5'UTR	NM_017807.3	NP_060277.1			O-sialoglycoprotein endopeptidase											endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(4)|stomach(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)		TATTCCACAGTTGGGCCACAG	0.532													T|||	2770	0.553115	0.6286	0.451	5008	,	,		16968	0.4514		0.6282	False		,,,				2504	0.5511				p.Q98Q		Atlas-SNP	.											.	OSGEP	31	.	0			c.A294G						PASS	.	T		2678,1728	648.8+/-398.8	814,1050,339	56.0	55.0	55.0		294	-4.4	0.1	14	dbSNP_100	55	5190,3410	638.1+/-399.3	1561,2068,671	no	coding-synonymous	OSGEP	NM_017807.3		2375,3118,1010	CC,CT,TT		39.6512,39.2192,39.5048		98/336	20920250	7868,5138	2203	4300	6503	SO:0001819	synonymous_variant	55644	exon3			CCACAGTTGGGCC	AB050442	CCDS9549.1	14q12	2010-03-19			ENSG00000092094	ENSG00000092094	3.4.24.57		18028	protein-coding gene	gene with protein product		610107				12039036	Standard	NM_017807		Approved	PRSMG1, GCPL1, OSGEP1, KAE1	uc001vxf.3	Q9NPF4	OTTHUMG00000029543	ENST00000206542.4:c.294A>G	14.37:g.20920250T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	60	0.571429	NM_017807		Silent	SNP	ENST00000206542.4	37	CCDS9549.1																																																																																			T|0.408;C|0.592	0.592	strong		0.532	OSGEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073635.3	NM_017807	
ZUFSP	221302	hgsc.bcm.edu	37	6	116973182	116973182	+	Missense_Mutation	SNP	T	T	C	rs4946188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116973182T>C	ENST00000368576.3	-	6	1378	c.1135A>G	c.(1135-1137)Aac>Gac	p.N379D	ZUFSP_ENST00000368573.1_3'UTR|ZUFSP_ENST00000471919.1_5'UTR	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	379			N -> D (in dbSNP:rs4946188). {ECO:0000269|PubMed:14702039}.				metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		AAGCAATCGTTGTAAGCATCA	0.323													C|||	2030	0.405351	0.5076	0.4928	5008	,	,		19570	0.3056		0.2932	False		,,,				2504	0.4233				p.N379D		Atlas-SNP	.											ZUFSP,NS,carcinoma,0,1	ZUFSP	46	1	0			c.A1135G						PASS	.	C	ASP/ASN	2088,2318	603.5+/-390.1	475,1138,590	117.0	121.0	120.0		1135	1.5	0.4	6	dbSNP_111	120	2404,6196	699.1+/-405.1	321,1762,2217	yes	missense	ZUFSP	NM_145062.2	23	796,2900,2807	CC,CT,TT		27.9535,47.3899,34.5379	benign	379/579	116973182	4492,8514	2203	4300	6503	SO:0001583	missense	221302	exon6			AATCGTTGTAAGC	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"""Zinc fingers, C2H2-type"""	21224	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 113"""	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1135A>G	6.37:g.116973182T>C	ENSP00000357565:p.Asn379Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	31	0.645833	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	37	CCDS5110.1	807	0.3695054945054945	242	0.491869918699187	164	0.4530386740331492	172	0.3006993006993007	229	0.3021108179419525	C	3.231	-0.157533	0.06544	0.473899	0.279535	ENSG00000153975	ENST00000368576	T	0.41400	1.0	5.83	1.52	0.23074	.	0.579616	0.20593	N	0.089307	T	0.07098	0.0180	N	0.19112	0.55	0.43304	P	0.004693999999999976	B	0.02656	0.0	B	0.06405	0.002	T	0.32798	-0.9893	9	0.08837	T	0.75	6.0687	5.3231	0.15891	0.0:0.2902:0.1594:0.5504	rs4946188;rs52824326;rs57266096;rs4946188	379	Q96AP4	ZUFSP_HUMAN	D	379	ENSP00000357565:N379D	ENSP00000357565:N379D	N	-	1	0	ZUFSP	117079875	0.957000	0.32711	0.356000	0.25785	0.915000	0.54546	0.628000	0.24522	0.108000	0.17862	-0.757000	0.03467	AAC	T|0.640;C|0.360	0.360	strong		0.323	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062	
DCTN1	1639	hgsc.bcm.edu	37	2	74596527	74596527	+	Missense_Mutation	SNP	C	C	T	rs17721059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:74596527C>T	ENST00000361874.3	-	14	1801	c.1484G>A	c.(1483-1485)cGg>cAg	p.R495Q	DCTN1_ENST00000409567.3_Missense_Mutation_p.R475Q|DCTN1_ENST00000394003.3_Missense_Mutation_p.R488Q|DCTN1_ENST00000407639.2_Missense_Mutation_p.R361Q|DCTN1_ENST00000409240.1_Missense_Mutation_p.R458Q|DCTN1_ENST00000409868.1_Missense_Mutation_p.R478Q|DCTN1_ENST00000409438.1_Missense_Mutation_p.R361Q|DCTN1_ENST00000495643.1_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	495			R -> Q (in dbSNP:rs17721059).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CTCACGAACCCGCGCGCCTGC	0.597													C|||	39	0.00778754	0.0	0.0187	5008	,	,		16682	0.0		0.0239	False		,,,				2504	0.002				p.R495Q		Atlas-SNP	.											.	DCTN1	110	.	0			c.G1484A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	19,4387	25.3+/-52.1	0,19,2184	89.0	90.0	90.0		1424,1082,1373,1463,1484,1082	5.0	1.0	2	dbSNP_123	90	160,8440	73.2+/-135.9	1,158,4141	yes	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	43,43,43,43,43,43	1,177,6325	TT,TC,CC		1.8605,0.4312,1.3763	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	475/1254,361/1140,458/1237,488/1272,495/1279,361/1145	74596527	179,12827	2203	4300	6503	SO:0001583	missense	1639	exon14			CGAACCCGCGCGC		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1484G>A	2.37:g.74596527C>T	ENSP00000354791:p.Arg495Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	15.10	2.731990	0.48939	0.004312	0.018605	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-0.71;-1.03	5.91	5.03	0.67393	.	0.203082	0.24587	N	0.037257	T	0.43500	0.1250	N	0.25144	0.715	0.50632	D	0.99988	B;P;P;B;B;P	0.46578	0.176;0.88;0.804;0.016;0.136;0.876	B;B;B;B;B;B	0.34138	0.022;0.122;0.123;0.008;0.04;0.176	T	0.54833	-0.8234	10	0.14252	T	0.57	-6.5169	14.0459	0.64704	0.0:0.9269:0.0:0.0731	rs17721059;rs17721059	475;458;495;488;361;361	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	Q	495;488;478;361;361;458;478;475	ENSP00000354791:R495Q;ENSP00000377571:R488Q;ENSP00000384844:R361Q;ENSP00000387270:R361Q;ENSP00000386406:R458Q;ENSP00000387327:R478Q;ENSP00000386843:R475Q	ENSP00000354791:R495Q	R	-	2	0	DCTN1	74450035	0.991000	0.36638	0.970000	0.41538	0.394000	0.30568	3.179000	0.50887	1.507000	0.48752	0.655000	0.94253	CGG	C|0.985;T|0.015	0.015	strong		0.597	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	rs142399667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:21318826G>A	ENST00000583088.1	+	3	1067	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A58T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	58					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)	CATTGAGTTCGCCAACATGGA	0.597										Prostate(3;0.18)																											p.A58T		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.G172A						PASS	.	G	THR/ALA	69,4337	52.3+/-87.9	0,69,2134	197.0	131.0	153.0		172	5.3	1.0	17	dbSNP_134	153	62,8538	26.8+/-75.7	0,62,4238	yes	missense	KCNJ12	NM_021012.4	58	0,131,6372	AA,AG,GG		0.7209,1.566,1.0072	benign	58/434	21318826	131,12875	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGTTCGCCAACA	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.172G>A	17.37:g.21318826G>A	ENSP00000463778:p.Ala58Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	192	26	0.135417	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692589	0.30052	0.01566	0.007209	ENSG00000184185	ENST00000331718	D	0.93859	-3.3	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.248894	0.40908	D	0.000997	T	0.77631	0.4159	N	0.16233	0.39	0.36661	D	0.877951	B	0.12630	0.006	B	0.18263	0.021	T	0.80009	-0.1562	10	0.32370	T	0.25	.	10.2342	0.43273	0.1224:0.0:0.8776:0.0	.	58	Q14500	IRK12_HUMAN	T	58	ENSP00000328150:A58T	ENSP00000328150:A58T	A	+	1	0	KCNJ12	21259419	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	2.230000	0.42999	2.506000	0.84524	0.591000	0.81541	GCC	G|0.993;A|0.007	0.007	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140856349	140856349	+	Silent	SNP	A	A	G	rs115808055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140856349A>G	ENST00000308177.3	+	1	770	c.666A>G	c.(664-666)ccA>ccG	p.P222P	PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	222	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGGACCCCAGCTCTCTCCG	0.627													A|||	20	0.00399361	0.0008	0.0014	5008	,	,		15671	0.0		0.0179	False		,,,				2504	0.0				p.P222P		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.A666G						PASS	.	A	,,,,,,,,,,,,,,,,,,,,,,	17,4389	23.3+/-48.9	0,17,2186	37.0	29.0	32.0		666,,,,,,,,,,,,,,,,,,,,,666,	-2.9	0.7	5	dbSNP_132	32	100,8500	51.5+/-111.7	2,96,4202	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,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_032092.1,NM_032402.1,NM_032403.1	,,,,,,,,,,,,,,,,,,,,,,	2,113,6388	GG,GA,AA		1.1628,0.3858,0.8996	,,,,,,,,,,,,,,,,,,,,,,	222/935,,,,,,,,,,,,,,,,,,,,,222/864,	140856349	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GACCCCAGCTCTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.666A>G	5.37:g.140856349A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	23	16	0.695652	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			A|0.990;G|0.010	0.010	strong		0.627	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
GRXCR2	643226	hgsc.bcm.edu	37	5	145246085	145246085	+	Missense_Mutation	SNP	T	T	G	rs2569006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:145246085T>G	ENST00000377976.1	-	2	542	c.543A>C	c.(541-543)ttA>ttC	p.L181F		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	181			L -> F (in dbSNP:rs2569006).			cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						GGTTTTGGGGTAATGTGCTTT	0.537													G|||	3778	0.754393	0.9032	0.732	5008	,	,		15944	0.7262		0.5845	False		,,,				2504	0.773				p.L181F		Atlas-SNP	.											.	GRXCR2	32	.	0			c.A543C						PASS	.	G	PHE/LEU	3695,711	295.3+/-283.6	1555,585,63	146.0	141.0	143.0		543	0.1	0.0	5	dbSNP_100	143	4987,3613	522.1+/-380.0	1461,2065,774	yes	missense	GRXCR2	NM_001080516.1	22	3016,2650,837	GG,GT,TT		42.0116,16.1371,33.2462	benign	181/249	145246085	8682,4324	2203	4300	6503	SO:0001583	missense	643226	exon2			TTGGGGTAATGTG		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.543A>C	5.37:g.145246085T>G	ENSP00000367214:p.Leu181Phe	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	37	CCDS34263.1	1535	0.7028388278388278	446	0.9065040650406504	251	0.6933701657458563	402	0.7027972027972028	436	0.575197889182058	G	3.586	-0.084576	0.07097	0.838629	0.579884	ENSG00000204928	ENST00000377976	T	0.56941	0.43	5.02	0.0768	0.14405	.	0.665541	0.15774	N	0.245277	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	0.33828	-0.9853	9	0.02654	T	1	-8.7431	6.4314	0.21798	0.4419:0.0:0.4365:0.1216	rs2569006;rs17423587;rs58884732;rs2569006	181	A6NFK2	GRCR2_HUMAN	F	181	ENSP00000367214:L181F	ENSP00000367214:L181F	L	-	3	2	GRXCR2	145226278	0.000000	0.05858	0.038000	0.18304	0.026000	0.11368	-0.877000	0.04197	-0.154000	0.11118	-0.358000	0.07595	TTA	T|0.304;G|0.696	0.696	strong		0.537	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2		
ARHGAP44	9912	hgsc.bcm.edu	37	17	12852459	12852459	+	Silent	SNP	A	A	G	rs2072254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:12852459A>G	ENST00000379672.5	+	11	1164	c.864A>G	c.(862-864)ggA>ggG	p.G288G	ARHGAP44_ENST00000340825.3_Silent_p.G288G|ARHGAP44_ENST00000262444.9_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	16	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	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	
NELFB	25920	hgsc.bcm.edu	37	9	140167022	140167022	+	Silent	SNP	G	G	A	rs3204123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140167022G>A	ENST00000343053.4	+	12	1888	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	517					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GGGTGGCCCCGTCTAAGCTGG	0.687													g|||	3081	0.615216	0.5129	0.7608	5008	,	,		16657	0.4782		0.7276	False		,,,				2504	0.6759				p.P517P		Atlas-SNP	.											COBRA1,NS,carcinoma,0,2	.	.	2	0			c.G1551A						PASS	.			2391,2011		661,1069,471	21.0	20.0	21.0		1551	-9.5	0.0	9	dbSNP_105	21	6529,2065		2500,1529,268	no	coding-synonymous	COBRA1	NM_015456.3		3161,2598,739	AA,AG,GG		24.0284,45.6838,31.3635		517/581	140167022	8920,4076	2201	4297	6498	SO:0001819	synonymous_variant	25920	exon12			GGCCCCGTCTAAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.1551G>A	9.37:g.140167022G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	77	0.55	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																			A|0.666;C|0.000;G|0.333;T|0.000	0.666	strong		0.687	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
L3MBTL4	91133	hgsc.bcm.edu	37	18	5956238	5956238	+	Missense_Mutation	SNP	C	C	T	rs3737353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000317931.7_Missense_Mutation_p.G609D|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.G618D|L3MBTL4_ENST00000535782.1_Missense_Mutation_p.G422D	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	120	0	0		WXS	Illumina HiSeq	Phase_I	141	87	0.617021	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	
UGGT2	55757	hgsc.bcm.edu	37	13	96638651	96638651	+	Missense_Mutation	SNP	C	C	T	rs12863903	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96638651C>T	ENST00000376747.3	-	9	1037	c.967G>A	c.(967-969)Gct>Act	p.A323T	UGGT2_ENST00000376714.3_3'UTR|UGGT2_ENST00000397618.3_Missense_Mutation_p.A323T|UGGT2_ENST00000467305.1_5'UTR	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	323			A -> T (in dbSNP:rs12863903). {ECO:0000269|PubMed:10694380}.		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						TAAACTGGAGCGGACATTATT	0.313													c|||	381	0.0760783	0.0166	0.1009	5008	,	,		15082	0.0337		0.1789	False		,,,				2504	0.0767				p.A323T		Atlas-SNP	.											.	UGGT2	127	.	0			c.G967A						PASS	.	C	THR/ALA	196,4210	121.7+/-159.2	4,188,2011	76.0	77.0	77.0		967	2.8	1.0	13	dbSNP_121	77	1389,7201	265.8+/-286.4	127,1135,3033	yes	missense	UGGT2	NM_020121.3	58	131,1323,5044	TT,TC,CC		16.17,4.4485,12.1961	benign	323/1517	96638651	1585,11411	2203	4295	6498	SO:0001583	missense	55757	exon9			CTGGAGCGGACAT	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.967G>A	13.37:g.96638651C>T	ENSP00000365938:p.Ala323Thr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	50	0.961538	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	208	0.09523809523809523	4	0.008130081300813009	54	0.14917127071823205	17	0.02972027972027972	133	0.17546174142480211	c	9.920	1.212009	0.22289	0.044485	0.1617	ENSG00000102595	ENST00000376747;ENST00000397618	T;T	0.44881	0.91;0.91	5.54	2.79	0.32731	.	0.332788	0.36591	N	0.002512	T	0.00039	0.0001	N	0.05414	-0.055	0.09310	P	0.9999999999876714	B;B;B	0.12630	0.003;0.003;0.006	B;B;B	0.08055	0.003;0.003;0.002	T	0.20075	-1.0286	9	0.16896	T	0.51	-13.5618	8.4809	0.33043	0.0:0.231:0.0:0.769	rs12863903;rs17268651;rs12863903	323;323;323	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	T	323	ENSP00000365938:A323T;ENSP00000380743:A323T	ENSP00000365938:A323T	A	-	1	0	UGGT2	95436652	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.673000	0.25203	0.906000	0.36621	-0.285000	0.09966	GCT	C|0.894;T|0.106	0.106	strong		0.313	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
KIAA0922	23240	hgsc.bcm.edu	37	4	154387597	154387597	+	Silent	SNP	G	G	C	rs71620317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:154387597G>C	ENST00000409663.3	+	1	100	c.48G>C	c.(46-48)gcG>gcC	p.A16A	KIAA0922_ENST00000440693.1_Silent_p.A16A|KIAA0922_ENST00000409959.3_Silent_p.A16A	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	16						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)				GCCGCACCGCGGCGGCCGTGA	0.741													-|||	2539	0.506989	0.848	0.2839	5008	,	,		5547	0.3254		0.3887	False		,,,				2504	0.5133				p.A16A		Atlas-SNP	.											.	KIAA0922	214	.	0			c.G48C						PASS	.						2.0	4.0	4.0					4																	154387597		533	1352	1885	SO:0001819	synonymous_variant	23240	exon1			CACCGCGGCGGCC	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.48G>C	4.37:g.154387597G>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			G|0.548;C|0.452	0.452	strong		0.741	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
RRP1	8568	hgsc.bcm.edu	37	21	45209559	45209559	+	Silent	SNP	C	C	T	rs78489660	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45209559C>T	ENST00000497547.1	+	1	166	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L		NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		GGCTCAGCGCCTGGCGGGGAA	0.697													C|||	331	0.0660942	0.0159	0.0259	5008	,	,		12101	0.0863		0.0457	False		,,,				2504	0.1626				p.L17L		Atlas-SNP	.											.	RRP1	23	.	0			c.C49T						PASS	.	C		90,3924		2,86,1919	10.0	16.0	14.0		49	4.4	0.9	21	dbSNP_131	14	467,7841		14,439,3701	yes	coding-synonymous	RRP1	NM_003683.5		16,525,5620	TT,TC,CC		5.6211,2.2422,4.5204		17/462	45209559	557,11765	2007	4154	6161	SO:0001819	synonymous_variant	8568	exon1			CAGCGCCTGGCGG	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.49C>T	21.37:g.45209559C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	53	0.420635	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			C|0.949;T|0.051	0.051	strong		0.697	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
NMS	129521	hgsc.bcm.edu	37	2	101096960	101096960	+	Silent	SNP	C	C	T	rs1519654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:101096960C>T	ENST00000376865.1	+	7	346	c.339C>T	c.(337-339)ggC>ggT	p.G113G		NM_001011717.1	NP_001011717.1	Q5H8A3	NMS_HUMAN	neuromedin S	113					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				breast(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)	14						CCTTGCAGGGCTCGGGGACTG	0.542													T|||	4025	0.803714	0.9183	0.6859	5008	,	,		18499	1.0		0.5	False		,,,				2504	0.8425				p.G113G		Atlas-SNP	.											NMS,colon,carcinoma,0,3	NMS	26	3	0			c.C339T						scavenged	.	T		3751,655	280.5+/-275.4	1612,527,64	122.0	115.0	118.0		339	-1.5	0.0	2	dbSNP_88	118	4226,4374	583.1+/-391.5	1049,2128,1123	no	coding-synonymous	NMS	NM_001011717.1		2661,2655,1187	TT,TC,CC		49.1395,14.8661,38.6668		113/154	101096960	7977,5029	2203	4300	6503	SO:0001819	synonymous_variant	129521	exon7			GCAGGGCTCGGGG	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.339C>T	2.37:g.101096960C>T		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_001011717		Silent	SNP	ENST00000376865.1	37	CCDS33259.1																																																																																			C|0.321;T|0.679	0.679	strong		0.542	NMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329737.1	NM_001011717	
PEX12	5193	hgsc.bcm.edu	37	17	33902881	33902881	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33902881T>C	ENST00000225873.4	-	3	1607	c.1000A>G	c.(1000-1002)Agg>Ggg	p.R334G	SNORD7_ENST00000384567.1_RNA|RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	334					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGTGACTCCTCACATAATGA	0.453																																					p.R334G		Atlas-SNP	.											PEX12,NS,carcinoma,+1,1	PEX12	36	1	0			c.A1000G						scavenged	.						191.0	171.0	178.0					17																	33902881		2203	4300	6503	SO:0001583	missense	5193	exon3			GACTCCTCACATA	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.1000A>G	17.37:g.33902881T>C	ENSP00000225873:p.Arg334Gly	Somatic	184	2	0.0108696		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_000286	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	37	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.453836	0.43531	.	.	ENSG00000108733	ENST00000225873	D	0.86297	-2.1	5.64	4.5	0.54988	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);	0.048037	0.85682	D	0.000000	T	0.81427	0.4820	L	0.39245	1.2	0.40745	D	0.982864	B	0.25007	0.116	B	0.24006	0.05	T	0.79769	-0.1664	10	0.46703	T	0.11	-8.823	11.717	0.51659	0.0:0.0:0.1474:0.8526	.	334	O00623	PEX12_HUMAN	G	334	ENSP00000225873:R334G	ENSP00000225873:R334G	R	-	1	2	PEX12	30926994	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.733000	0.68571	2.147000	0.66899	0.533000	0.62120	AGG	.	.	none		0.453	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286	
ZNF418	147686	hgsc.bcm.edu	37	19	58437767	58437767	+	Missense_Mutation	SNP	C	C	A	rs199612939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58437767C>A	ENST00000396147.1	-	4	2073	c.1782G>T	c.(1780-1782)agG>agT	p.R594S	ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000599852.1_Missense_Mutation_p.R509S|ZNF418_ENST00000425570.3_Missense_Mutation_p.R615S|ZNF418_ENST00000595830.1_Missense_Mutation_p.R594S	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	594					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)		TTCCACATTCCCTGCATTCAT	0.448																																					p.R594S		Atlas-SNP	.											.	ZNF418	76	.	0			c.G1782T						PASS	.	C	SER/ARG	8,4390		0,8,2191	86.0	89.0	88.0		1782	-5.5	0.0	19		88	87,8513		1,85,4214	yes	missense	ZNF418	NM_133460.1	110	1,93,6405	AA,AC,CC		1.0116,0.1819,0.7309	benign	594/677	58437767	95,12903	2199	4300	6499	SO:0001583	missense	147686	exon4			ACATTCCCTGCAT	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.1782G>T	19.37:g.58437767C>A	ENSP00000379451:p.Arg594Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	53	8	0.150943	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	37	CCDS42642.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	.	0	-2.840553	0.00068	0.001819	0.010116	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.16457	2.34;2.34	2.76	-5.51	0.02568	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11203	-1.0597	9	0.07813	T	0.8	.	1.0134	0.01502	0.1849:0.1646:0.3013:0.3492	.	594	Q8TF45	ZN418_HUMAN	S	594;615;560	ENSP00000379451:R594S;ENSP00000407039:R615S	ENSP00000379451:R594S	R	-	3	2	ZNF418	63129579	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-10.328000	0.00007	-4.068000	0.00076	-1.399000	0.01144	AGG	C|0.989;A|0.011	0.011	strong		0.448	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
UBOX5	22888	hgsc.bcm.edu	37	20	3090884	3090884	+	Silent	SNP	C	C	A	rs34606078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3090884C>A	ENST00000217173.2	-	5	1965	c.1494G>T	c.(1492-1494)ccG>ccT	p.P498P	UBOX5-AS1_ENST00000454019.1_RNA|UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Silent_p.P444P	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						GCTGGTACACCGGCTCCTTTT	0.602													c|||	40	0.00798722	0.0	0.0115	5008	,	,		17312	0.002		0.0189	False		,,,				2504	0.0112				p.G497C		Atlas-SNP	.											.	UBOX5	47	.	0			c.G1489T						PASS	.	T	,	13,4393	20.2+/-43.8	0,13,2190	69.0	78.0	75.0		1494,1332	-10.1	0.0	20	dbSNP_126	75	149,8451	72.3+/-134.9	0,149,4151	no	coding-synonymous,coding-synonymous	UBOX5	NM_014948.2,NM_199415.1	,	0,162,6341	AA,AC,CC		1.7326,0.2951,1.2456	,	498/542,444/488	3090884	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	22888	exon5			GTACACCGGCTCC	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"""RING-type (C3HC4) zinc fingers"", ""U-box domain containing"""	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.1494G>T	20.37:g.3090884C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001267584		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1																																																																																			C|0.990;A|0.010	0.010	strong		0.602	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948	
TCTN3	26123	hgsc.bcm.edu	37	10	97447373	97447373	+	Silent	SNP	A	A	T	rs10786229	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:97447373A>T	ENST00000371217.5	-	4	626	c.603T>A	c.(601-603)acT>acA	p.T201T	TCTN3_ENST00000371209.5_Silent_p.T201T|TCTN3_ENST00000430368.2_Intron|TCTN3_ENST00000265993.9_Silent_p.T219T			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	62	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	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	
NRP2	8828	hgsc.bcm.edu	37	2	206590686	206590686	+	Silent	SNP	T	T	C	rs2228639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:206590686T>C	ENST00000357785.5	+	6	901	c.870T>C	c.(868-870)aaT>aaC	p.N290N	NRP2_ENST00000357118.4_Silent_p.N290N|NRP2_ENST00000360409.3_Silent_p.N290N|NRP2_ENST00000417189.1_Silent_p.N290N|NRP2_ENST00000540841.1_Silent_p.N290N|NRP2_ENST00000355117.4_Silent_p.N290N|NRP2_ENST00000412873.2_Silent_p.N290N|NRP2_ENST00000272849.3_Silent_p.N290N|NRP2_ENST00000540178.1_Silent_p.N290N			Q99435	NELL2_HUMAN	neuropilin 2	0	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.					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						GGATTGCTAATGAACAGATCA	0.527													T|||	199	0.0397364	0.0333	0.0461	5008	,	,		20497	0.001		0.0964	False		,,,				2504	0.0256				p.N290N		Atlas-SNP	.											.	NRP2	179	.	0			c.T870C						PASS	.	T	,,,,,	197,4209	125.7+/-162.9	2,193,2008	148.0	122.0	131.0		870,870,870,870,870,870	3.7	1.0	2	dbSNP_98	131	825,7775	191.0+/-237.3	43,739,3518	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRP2	NM_003872.2,NM_018534.3,NM_201264.1,NM_201266.1,NM_201267.1,NM_201279.1	,,,,,	45,932,5526	CC,CT,TT		9.593,4.4712,7.8579	,,,,,	290/927,290/907,290/556,290/932,290/902,290/910	206590686	1022,11984	2203	4300	6503	SO:0001819	synonymous_variant	8828	exon6			TGCTAATGAACAG	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.870T>C	2.37:g.206590686T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_201279	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																			T|0.932;C|0.068	0.068	strong		0.527	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
CTTN	2017	hgsc.bcm.edu	37	11	70253475	70253475	+	Silent	SNP	C	C	T	rs2298397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70253475C>T	ENST00000301843.8	+	3	278	c.72C>T	c.(70-72)acC>acT	p.T24T	CTTN_ENST00000346329.3_Silent_p.T24T|CTTN_ENST00000376561.3_Silent_p.T24T|CTTN_ENST00000527622.1_3'UTR	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	24					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		ACTGGGAGACCGACCCTGATT	0.572													C|||	706	0.140974	0.0325	0.2651	5008	,	,		16440	0.1062		0.2376	False		,,,				2504	0.136				p.T24T		Atlas-SNP	.											.	CTTN	162	.	0			c.C72T						PASS	.	C	,,	356,4002		15,326,1838	21.0	23.0	22.0		72,72,72	-11.0	0.1	11	dbSNP_100	22	1849,6689		197,1455,2617	no	coding-synonymous,coding-synonymous,coding-synonymous	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	,,	212,1781,4455	TT,TC,CC		21.6561,8.1689,17.0983	,,	24/635,24/551,24/514	70253475	2205,10691	2179	4269	6448	SO:0001819	synonymous_variant	2017	exon3			GGAGACCGACCCT	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.72C>T	11.37:g.70253475C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_001184740	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1	356	0.163003663003663	20	0.04065040650406504	89	0.24585635359116023	67	0.11713286713286714	180	0.23746701846965698	C	4.787	0.146369	0.09134	0.081689	0.216561	ENSG00000085733	ENST00000415461	.	.	.	5.48	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999998	.	.	.	.	.	.	T	0.11767	-1.0574	3	.	.	.	-39.5588	1.2588	0.01997	0.271:0.1249:0.1798:0.4243	rs2298397;rs3209200;rs11546011;rs17334986;rs17410320;rs2298397	.	.	.	L	6	.	.	P	+	2	0	CTTN	69931123	0.000000	0.05858	0.084000	0.20598	0.566000	0.35808	-4.692000	0.00198	-3.381000	0.00175	-0.749000	0.03505	CCG	C|0.847;T|0.153	0.153	strong		0.572	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
OR13H1	347468	hgsc.bcm.edu	37	X	130678467	130678467	+	Silent	SNP	A	A	G	rs499030	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	114	0	0		WXS	Illumina HiSeq	Phase_I	91	91	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		
DCC	1630	hgsc.bcm.edu	37	18	50432602	50432602	+	Missense_Mutation	SNP	C	C	G	rs2229080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:50432602C>G	ENST00000442544.2	+	3	1217	c.601C>G	c.(601-603)Cga>Gga	p.R201G	DCC_ENST00000412726.1_Missense_Mutation_p.R49G	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	201	Ig-like C2-type 2.		R -> G (in dbSNP:rs2229080). {ECO:0000269|PubMed:8187090}.		anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GCAGATCAGCCGACTCCAACC	0.507													C|||	2391	0.477436	0.3427	0.4813	5008	,	,		15703	0.5387		0.4155	False		,,,				2504	0.6575				p.R201G		Atlas-SNP	.											.	DCC	360	.	0			c.C601G	GRCh37	CM973390	DCC	M	rs2229080	PASS	.	C	GLY/ARG	1517,2889	480.3+/-358.8	261,995,947	81.0	76.0	78.0		601	-0.5	1.0	18	dbSNP_98	78	3157,5443	479.9+/-370.2	579,1999,1722	yes	missense	DCC	NM_005215.3	125	840,2994,2669	GG,GC,CC		36.7093,34.4303,35.9373	possibly-damaging	201/1448	50432602	4674,8332	2203	4300	6503	SO:0001583	missense	1630	exon3			ATCAGCCGACTCC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.601C>G	18.37:g.50432602C>G	ENSP00000389140:p.Arg201Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	997	0.4565018315018315	194	0.3943089430894309	159	0.43922651933701656	326	0.5699300699300699	318	0.41952506596306066	C	12.26	1.883736	0.33255	0.344303	0.367093	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.38887	1.11;1.11	5.71	-0.494	0.12034	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.075429	0.51477	D	0.000098	T	0.00012	0.0000	N	0.21545	0.675	0.09310	P	0.999999999852581	B;P	0.43024	0.083;0.798	B;P	0.45506	0.057;0.483	T	0.47222	-0.9134	9	0.62326	D	0.03	.	17.8242	0.88660	0.3349:0.6651:0.0:0.0	rs2229080;rs52797535;rs2229080	49;201	E7EQM8;P43146	.;DCC_HUMAN	G	201;134;49	ENSP00000389140:R201G;ENSP00000397322:R49G	ENSP00000304146:R134G	R	+	1	2	DCC	48686600	0.840000	0.29493	0.972000	0.41901	0.924000	0.55760	-0.023000	0.12456	-0.304000	0.08843	0.655000	0.94253	CGA	C|0.604;G|0.396	0.396	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
LRIT2	340745	hgsc.bcm.edu	37	10	85984723	85984723	+	Silent	SNP	G	G	A	rs11200928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85984723G>A	ENST00000372113.4	-	2	263	c.258C>T	c.(256-258)ctC>ctT	p.L86L	LRIT2_ENST00000538192.1_Silent_p.L86L	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	86						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						TGTTAAAATTGAGCCAGAGGT	0.463													G|||	1042	0.208067	0.0522	0.2925	5008	,	,		18577	0.3452		0.2346	False		,,,				2504	0.1902				p.L86L		Atlas-SNP	.											.	LRIT2	81	.	0			c.C258T						PASS	.	G		386,4020	196.0+/-220.5	12,362,1829	114.0	114.0	114.0		258	1.6	1.0	10	dbSNP_120	114	1937,6663	341.4+/-324.0	199,1539,2562	no	coding-synonymous	LRIT2	NM_001017924.2		211,1901,4391	AA,AG,GG		22.5233,8.7608,17.861		86/551	85984723	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon2			AAAATTGAGCCAG		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.258C>T	10.37:g.85984723G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			G|0.807;A|0.193	0.193	strong		0.463	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
KLHL30	377007	hgsc.bcm.edu	37	2	239059610	239059610	+	Silent	SNP	C	C	T	rs61736173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239059610C>T	ENST00000409223.1	+	8	1748	c.1641C>T	c.(1639-1641)ggC>ggT	p.G547G	KLHL30_ENST00000305959.4_Silent_p.G529G			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	547										lung(4)	4		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)		CCCGCCACGGCGCCCTGCCCC	0.682													c|||	172	0.034345	0.0711	0.0317	5008	,	,		13240	0.0		0.0517	False		,,,				2504	0.0041				p.G547G		Atlas-SNP	.											.	KLHL30	79	.	0			c.C1641T						PASS	.	T		255,3769		9,237,1766	8.0	14.0	12.0		1641	-0.5	1.0	2	dbSNP_129	12	387,7855		11,365,3745	no	coding-synonymous	KLHL30	NM_198582.3		20,602,5511	TT,TC,CC		4.6955,6.337,5.234		547/579	239059610	642,11624	2012	4121	6133	SO:0001819	synonymous_variant	377007	exon8			CCACGGCGCCCTG		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1641C>T	2.37:g.239059610C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_198582	Q6ZUS1	Silent	SNP	ENST00000409223.1	37	CCDS46555.2																																																																																			C|0.961;T|0.039	0.039	strong		0.682	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
OR52E6	390078	hgsc.bcm.edu	37	11	5862780	5862780	+	Silent	SNP	T	T	C	rs4362172	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5862780T>C	ENST00000329322.5	-	1	347	c.348A>G	c.(346-348)gtA>gtG	p.V116V	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Silent_p.V120V	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	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)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGCCACCAATACGATGCTCT	0.453													C|||	1924	0.384185	0.3782	0.3184	5008	,	,		22675	0.4603		0.3728	False		,,,				2504	0.3722				p.V116V		Atlas-SNP	.											.	OR52E6	70	.	0			c.A348G						PASS	.	C		1620,2782	661.0+/-400.8	294,1032,875	189.0	177.0	181.0		348	-1.0	0.0	11	dbSNP_111	181	3009,5583	664.5+/-402.2	533,1943,1820	no	coding-synonymous	OR52E6	NM_001005167.1		827,2975,2695	CC,CT,TT		35.0209,36.8015,35.6241		116/314	5862780	4629,8365	2201	4296	6497	SO:0001819	synonymous_variant	390078	exon1			CACCAATACGATG	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.348A>G	11.37:g.5862780T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_001005167	Q6IFF8	Silent	SNP	ENST00000329322.5	37	CCDS53597.1																																																																																			T|0.607;C|0.393	0.393	strong		0.453	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
PTPLA	9200	hgsc.bcm.edu	37	10	17659131	17659131	+	Missense_Mutation	SNP	C	C	A	rs11254692		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:17659131C>A	ENST00000361271.3	-	1	245	c.208G>T	c.(208-210)Gtc>Ttc	p.V70F	PTPLA_ENST00000326961.6_Missense_Mutation_p.V70F	NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	70			V -> F (in dbSNP:rs11254692). {ECO:0000269|PubMed:11054553, ECO:0000269|PubMed:15489334}.		fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						GTGGCCAAGACCCCCAGGCGC	0.786													A|||	5008	1.0	1.0	1.0	5008	,	,		6615	1.0		1.0	False		,,,				2504	1.0				p.V70F		Atlas-SNP	.											.	PTPLA	34	.	0			c.G208T						PASS	.						3.0	4.0	4.0					10																	17659131		1418	2520	3938	SO:0001583	missense	9200	exon1			CCAAGACCCCCAG	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.208G>T	10.37:g.17659131C>A	ENSP00000355308:p.Val70Phe	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	2101	0.961996336996337	463	0.9410569105691057	352	0.9723756906077348	542	0.9475524475524476	744	0.9815303430079155	A	3.143	-0.175883	0.06421	.	.	ENSG00000165996	ENST00000361271;ENST00000326961	T;T	0.19532	2.72;2.14	3.35	-3.22	0.05125	.	0.992513	0.08174	N	0.986484	T	0.00012	0.0000	N	0.14661	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;0.0;0.001	T	0.14504	-1.0470	9	0.17369	T	0.5	-25.4183	5.6815	0.17778	0.3895:0.4093:0.2012:0.0	rs11254692;rs12765300;rs17856331	70;70;70	A6NP58;B0YJ81-2;B0YJ81	.;.;HACD1_HUMAN	F	70	ENSP00000355308:V70F;ENSP00000322923:V70F	ENSP00000322923:V70F	V	-	1	0	PTPLA	17699137	0.175000	0.23083	0.002000	0.10522	0.001000	0.01503	0.509000	0.22707	-1.288000	0.02378	-2.813000	0.00110	GTC	C|0.038;A|0.962	0.962	strong		0.786	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
UGT2B17	7367	hgsc.bcm.edu	37	4	69416556	69416556	+	Silent	SNP	T	T	C	rs13102139		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69416556T>C	ENST00000317746.2	-	5	1194	c.1152A>G	c.(1150-1152)gcA>gcG	p.A384A		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	384					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	CATGGTAGATTGCCTCATAGA	0.428																																					p.A384A	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.A1152G						PASS	.						143.0	105.0	118.0					4																	69416556		2108	3990	6098	SO:0001819	synonymous_variant	7367	exon5			GTAGATTGCCTCA	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1152A>G	4.37:g.69416556T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	229	73	0.318777	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			T|0.250;C|0.750	0.750	weak		0.428	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
USP43	124739	hgsc.bcm.edu	37	17	9586165	9586165	+	Silent	SNP	C	C	T	rs12453943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:9586165C>T	ENST00000285199.7	+	7	1227	c.1131C>T	c.(1129-1131)tcC>tcT	p.S377S	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Silent_p.S377S	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	377	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						TGTCGGCCTCCCCACGCCTGG	0.552													C|||	2254	0.45008	0.5234	0.3112	5008	,	,		15519	0.6488		0.2306	False		,,,				2504	0.4703				p.S377S		Atlas-SNP	.											.	USP43	65	.	0			c.C1131T						PASS	.	C		1815,2129		427,961,584	82.0	85.0	84.0		1131	1.6	0.9	17	dbSNP_120	84	1865,6449		225,1415,2517	no	coding-synonymous	USP43	NM_153210.3		652,2376,3101	TT,TC,CC		22.432,46.0193,30.0212		377/1124	9586165	3680,8578	1972	4157	6129	SO:0001819	synonymous_variant	124739	exon7			GGCCTCCCCACGC	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1131C>T	17.37:g.9586165C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Silent	SNP	ENST00000285199.7	37	CCDS45610.1																																																																																			C|0.627;T|0.373	0.373	strong		0.552	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
CNTN3	5067	hgsc.bcm.edu	37	3	74349062	74349062	+	Missense_Mutation	SNP	T	T	C	rs626578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:74349062T>C	ENST00000263665.6	-	16	2150	c.2123A>G	c.(2122-2124)aAt>aGt	p.N708S		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	708	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		N -> S (in dbSNP:rs626578). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.N708S(1)		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)		GCCTCCTCCATTGACTTCAGA	0.428													T|||	613	0.122404	0.1225	0.072	5008	,	,		15596	0.2331		0.0726	False		,,,				2504	0.0951				p.N708S		Atlas-SNP	.											CNTN3,NS,carcinoma,0,1	CNTN3	174	1	1	Substitution - Missense(1)	stomach(1)	c.A2123G						PASS	.	T	SER/ASN	465,3941	221.0+/-238.3	24,417,1762	89.0	78.0	82.0		2123	2.7	0.9	3	dbSNP_83	82	473,8127	138.9+/-195.6	17,439,3844	yes	missense	CNTN3	NM_020872.1	46	41,856,5606	CC,CT,TT		5.5,10.5538,7.2121	benign	708/1029	74349062	938,12068	2203	4300	6503	SO:0001583	missense	5067	exon16			CCTCCATTGACTT	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.2123A>G	3.37:g.74349062T>C	ENSP00000263665:p.Asn708Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	261	0.11950549450549451	49	0.09959349593495935	27	0.07458563535911603	136	0.23776223776223776	49	0.06464379947229551	T	4.681	0.126704	0.08931	0.105538	0.055	ENSG00000113805	ENST00000263665	T	0.54071	0.59	5.86	2.67	0.31697	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.143004	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00841	-1.15	0.42217	P	0.008164999999999978	B	0.02656	0.0	B	0.04013	0.001	T	0.28396	-1.0045	9	0.02654	T	1	.	8.4371	0.32793	0.0:0.7099:0.0:0.2901	rs626578;rs52819645;rs626578	708	Q9P232	CNTN3_HUMAN	S	708	ENSP00000263665:N708S	ENSP00000263665:N708S	N	-	2	0	CNTN3	74431752	1.000000	0.71417	0.940000	0.37924	0.998000	0.95712	3.493000	0.53266	0.209000	0.20645	0.528000	0.53228	AAT	T|0.910;C|0.090	0.090	strong		0.428	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
ZNF385A	25946	hgsc.bcm.edu	37	12	54767812	54767812	+	Silent	SNP	G	G	A	rs2887875	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:54767812G>A	ENST00000338010.5	-	4	419	c.366C>T	c.(364-366)gaC>gaT	p.D122D	ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000352268.6_Silent_p.D122D|ZNF385A_ENST00000551771.1_Silent_p.D102D|ZNF385A_ENST00000546970.1_Silent_p.D102D|ZNF385A_ENST00000394313.2_Silent_p.D102D|RP11-753H16.3_ENST00000550474.1_RNA|ZNF385A_ENST00000551109.1_Silent_p.D102D|RP11-753H16.5_ENST00000552785.1_RNA	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	122					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						GGGGAGCTGGGTCTCCAGGTT	0.587													G|||	1202	0.240016	0.1029	0.3674	5008	,	,		16152	0.3075		0.165	False		,,,				2504	0.3425				p.D122D		Atlas-SNP	.											.	ZNF385A	45	.	0			c.C366T						PASS	.	G	,,	570,3836	254.3+/-259.9	42,486,1675	84.0	74.0	78.0		366,366,306	0.9	1.0	12	dbSNP_101	78	1534,7066	289.2+/-299.1	133,1268,2899	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF385A	NM_001130967.1,NM_001130968.1,NM_015481.1	,,	175,1754,4574	AA,AG,GG		17.8372,12.9369,16.1771	,,	122/387,122/306,102/367	54767812	2104,10902	2203	4300	6503	SO:0001819	synonymous_variant	25946	exon4			AGCTGGGTCTCCA	AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"""zinc finger protein 385"""	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.366C>T	12.37:g.54767812G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001130967	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Silent	SNP	ENST00000338010.5	37	CCDS44911.1																																																																																			G|0.827;C|0.000;A|0.173	0.173	strong		0.587	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481	
OGG1	4968	hgsc.bcm.edu	37	3	9798773	9798773	+	Missense_Mutation	SNP	C	C	G	rs1052133|rs1052134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9798773C>G	ENST00000344629.7	+	7	1320	c.977C>G	c.(976-978)tCc>tGc	p.S326C	OGG1_ENST00000302036.7_Intron|OGG1_ENST00000302003.7_Missense_Mutation_p.P332A|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000339511.5_3'UTR|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Intron			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	326			S -> C (common polymorphism in the Japanese population; dbSNP:rs1052133). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.13}.		acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					CTGCGCCAATCCCGCCATGCT	0.597								Base excision repair (BER), DNA glycosylases					C|||	1513	0.302117	0.1551	0.2939	5008	,	,		18217	0.5476		0.2028	False		,,,				2504	0.3558				p.P332A		Atlas-SNP	.											.	OGG1	57	.	0			c.C994G	GRCh37	CM993185	OGG1	M	rs1052133	PASS	.	C	CYS/SER,,ALA/PRO,,,,,	767,3639	311.1+/-291.9	74,619,1510	106.0	115.0	112.0		977,,994,,,,,	-1.3	0.0	3	dbSNP_86	112	1979,6621	346.1+/-326.1	235,1509,2556	yes	missense,utr-3,missense,intron,intron,intron,intron,intron	OGG1	NM_002542.5,NM_016819.3,NM_016820.3,NM_016821.2,NM_016826.2,NM_016827.2,NM_016828.2,NM_016829.2	112,,27,,,,,	309,2128,4066	GG,GC,CC		23.0116,17.4081,21.1133	benign,,benign,,,,,	326/346,,332/411,,,,,	9798773	2746,10260	2203	4300	6503	SO:0001583	missense	4968	exon7			GCCAATCCCGCCA	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"""8-hydroxyguanine DNA glycosylase"", ""OGG1 type 1e"", ""OGG1 type 1d"", ""OGG1 type 1g"", ""OGG1 type 1h"""	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.977C>G	3.37:g.9798773C>G	ENSP00000342851:p.Ser326Cys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	94	57	0.606383	NM_016820	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	652|652|652	0.29853479853479853|0.29853479853479853|0.29853479853479853	79|79|79	0.16056910569105692|0.16056910569105692|0.16056910569105692	108|108|108	0.2983425414364641|0.2983425414364641|0.2983425414364641	311|311|311	0.5437062937062938|0.5437062937062938|0.5437062937062938	154|154|154	0.20316622691292877|0.20316622691292877|0.20316622691292877	C|C|C	4.259|4.259|4.259	0.047094|0.047094|0.047094	0.08243|0.08243|0.08243	0.174081|0.174081|0.174081	0.230116|0.230116|0.230116	ENSG00000114026|ENSG00000114026|ENSG00000114026	ENST00000416333|ENST00000302003;ENST00000339542|ENST00000344629	.|T|T	.|0.59502|0.50813	.|0.26|0.73	5.05|5.05|5.05	-1.32|-1.32|-1.32	0.09201|0.09201|0.09201	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	0.00012|0.00012|0.00012	0.0000|0.0000|0.0000	L|L|L	0.39898|0.39898|0.39898	1.24|1.24|1.24	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	.|B;B;B;B|B;B	.|0.29481|0.25235	.|0.228;0.245;0.103;0.035|0.121;0.121	.|B;B;B;B|B;B	.|0.31946|0.39660	.|0.121;0.138;0.085;0.027|0.306;0.306	T|T|T	0.48536|0.48536|0.48536	-0.9027|-0.9027|-0.9027	4|8|8	.|0.07990|0.56958	.|T|D	.|0.79|0.05	.|.|.	3.5612|3.5612|3.5612	0.07882|0.07882|0.07882	0.4329:0.3147:0.0:0.2523|0.4329:0.3147:0.0:0.2523|0.4329:0.3147:0.0:0.2523	rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133|rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133|rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133	.|119;103;332;332|326;326	.|F8WA07;Q9HCR8;O15527-3;E5KPN0|E5KPN1;O15527	.|.;.;.;.|.;OGG1_HUMAN	M|A|C	98|332;119|326	.|ENSP00000305584:P332A|ENSP00000342851:S326C	.|ENSP00000305584:P332A|ENSP00000342851:S326C	I|P|S	+|+|+	3|1|2	3|0|0	OGG1|OGG1|OGG1	9773773|9773773|9773773	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.006000|0.006000|0.006000	0.05464|0.05464|0.05464	0.037000|0.037000|0.037000	0.13840|0.13840|0.13840	-0.141000|-0.141000|-0.141000	0.11374|0.11374|0.11374	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	ATC|CCC|TCC	C|1.000;|0.000	.	weak		0.597	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821	
RYR1	6261	hgsc.bcm.edu	37	19	38949904	38949904	+	Silent	SNP	C	C	T	rs3745847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	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		
GJB4	127534	hgsc.bcm.edu	37	1	35226963	35226963	+	Silent	SNP	C	C	T	rs142720849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35226963C>T	ENST00000339480.1	+	2	478	c.108C>T	c.(106-108)taC>taT	p.Y36Y	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	36					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGCTGGTGTACGTGGTGGCAG	0.582													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		23419	0.001		0.003	False		,,,				2504	0.0				p.Y36Y		Atlas-SNP	.											GJB4,NS,carcinoma,0,1	GJB4	51	1	0			c.C108T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	235.0	160.0	186.0		108	0.9	1.0	1	dbSNP_134	186	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous	GJB4	NM_153212.2		0,55,6448	TT,TC,CC		0.6163,0.0454,0.4229		36/267	35226963	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			GGTGTACGTGGTG		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.108C>T	1.37:g.35226963C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.996;T|0.004	0.004	strong		0.582	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
TAF1C	9013	hgsc.bcm.edu	37	16	84213114	84213114	+	Silent	SNP	C	C	T	rs2230130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84213114C>T	ENST00000567759.1	-	14	2225	c.2043G>A	c.(2041-2043)gtG>gtA	p.V681V	TAF1C_ENST00000378541.4_Silent_p.V681V|TAF1C_ENST00000570117.1_Silent_p.V349V|TAF1C_ENST00000566732.1_Silent_p.V655V|TAF1C_ENST00000541676.1_Silent_p.V588V|TAF1C_ENST00000341690.6_Silent_p.V587V	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	681					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						CCTTGCGGAGCACACCCAGCC	0.687													C|||	1436	0.286741	0.1256	0.4135	5008	,	,		15010	0.371		0.3469	False		,,,				2504	0.2658				p.V681V		Atlas-SNP	.											.	TAF1C	60	.	0			c.G2043A						PASS	.	C	,	749,3647		65,619,1514	24.0	25.0	24.0		2043,1761	-2.0	0.0	16	dbSNP_98	24	3086,5510		583,1920,1795	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	648,2539,3309	TT,TC,CC		35.9004,17.0382,29.5182	,	681/870,587/776	84213114	3835,9157	2198	4298	6496	SO:0001819	synonymous_variant	9013	exon14			GCGGAGCACACCC	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.2043G>A	16.37:g.84213114C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			C|0.709;T|0.291	0.291	strong		0.687	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
TAS2R42	353164	hgsc.bcm.edu	37	12	11339020	11339020	+	Missense_Mutation	SNP	T	T	A	rs35969491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11339020T>A	ENST00000334266.1	-	1	523	c.524A>T	c.(523-525)tAt>tTt	p.Y175F		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	175			Y -> F (in dbSNP:rs35969491). {ECO:0000269|PubMed:16541075}.		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)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			GAGTTTATCATAGAGAGTTTT	0.294													T|||	2708	0.540735	0.1596	0.6167	5008	,	,		17187	0.7569		0.6521	False		,,,				2504	0.6646				p.Y175F	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A524T						PASS	.	T	PHE/TYR	926,3392		119,688,1352	35.0	38.0	37.0		524	1.5	0.0	12	dbSNP_126	37	5079,3457		1541,1997,730	yes	missense	TAS2R42	NM_181429.1	22	1660,2685,2082	AA,AT,TT		40.4991,21.4451,46.717	benign	175/315	11339020	6005,6849	2159	4268	6427	SO:0001583	missense	353164	exon1			TTATCATAGAGAG	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.524A>T	12.37:g.11339020T>A	ENSP00000334050:p.Tyr175Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	1242	0.5686813186813187	91	0.18495934959349594	232	0.6408839779005525	426	0.7447552447552448	493	0.6503957783641161	T	12.24	1.877526	0.33162	0.214451	0.595009	ENSG00000186136	ENST00000334266	T	0.37411	1.2	2.66	1.48	0.22813	GPCR, rhodopsin-like superfamily (1);	0.755692	0.11404	U	0.567508	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	D	0.69078	0.997	D	0.72625	0.978	T	0.36138	-0.9760	9	0.52906	T	0.07	.	4.4507	0.11619	0.0:0.1616:0.0:0.8384	rs35969491	175	Q7RTR8	T2R42_HUMAN	F	175	ENSP00000334050:Y175F	ENSP00000334050:Y175F	Y	-	2	0	TAS2R42	11230287	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.328000	0.19681	0.451000	0.26802	0.260000	0.18958	TAT	T|0.472;A|0.528	0.528	strong		0.294	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
OSBPL3	26031	hgsc.bcm.edu	37	7	24905795	24905795	+	Missense_Mutation	SNP	C	C	T	rs201132926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:24905795C>T	ENST00000313367.2	-	6	894	c.443G>A	c.(442-444)cGt>cAt	p.R148H	OSBPL3_ENST00000431825.2_Missense_Mutation_p.R148H|OSBPL3_ENST00000352860.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000396431.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000409069.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000396429.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000353930.1_Missense_Mutation_p.R148H	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	148					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TTCATTCTGACGATACATTCT	0.398													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20987	0.0		0.0	False		,,,				2504	0.001				p.R148H		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G443A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	164.0	135.0	145.0		443,443,443,443	5.6	1.0	7		145	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	OSBPL3	NM_015550.2,NM_145320.1,NM_145321.1,NM_145322.1	29,29,29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	148/888,148/857,148/852,148/821	24905795	2,13004	2203	4300	6503	SO:0001583	missense	26031	exon6			TTCTGACGATACA	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.443G>A	7.37:g.24905795C>T	ENSP00000315410:p.Arg148His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	135	39	0.288889	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425170	0.96131	2.27E-4	1.16E-4	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.55588	1.89;0.51;0.57;1.85;0.51;0.57;1.85	5.63	5.63	0.86233	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	M	0.78637	2.42	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;1.0;1.0;0.999	T	0.74771	-0.3552	10	0.51188	T	0.08	-2.461	20.0499	0.97621	0.0:1.0:0.0:0.0	.	148;148;148;148	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	H	148	ENSP00000315410:R148H;ENSP00000315331:R148H;ENSP00000315277:R148H;ENSP00000389779:R148H;ENSP00000379708:R148H;ENSP00000379706:R148H;ENSP00000386953:R148H	ENSP00000315410:R148H	R	-	2	0	OSBPL3	24872320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.752000	0.85141	2.798000	0.96311	0.655000	0.94253	CGT	.	.	weak		0.398	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
MUC16	94025	hgsc.bcm.edu	37	19	9076278	9076278	+	Missense_Mutation	SNP	G	G	A	rs953551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076278G>A	ENST00000397910.4	-	3	11371	c.11168C>T	c.(11167-11169)aCg>aTg	p.T3723M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3724	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						GGACAGGGGCGTATTTGGGTC	0.473													A|||	1282	0.25599	0.2035	0.2161	5008	,	,		21497	0.254		0.335	False		,,,				2504	0.2761				p.T3723M		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.C11168T						PASS	.	A	MET/THR	853,3105		98,657,1224	129.0	127.0	128.0		11168	-1.1	0.0	19	dbSNP_86	128	2580,5764		389,1802,1981	yes	missense	MUC16	NM_024690.2	81	487,2459,3205	AA,AG,GG		30.9204,21.5513,27.906	benign	3723/14508	9076278	3433,8869	1979	4172	6151	SO:0001583	missense	94025	exon3			AGGGGCGTATTTG	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.11168C>T	19.37:g.9076278G>A	ENSP00000381008:p.Thr3723Met	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	573	0.2623626373626374	110	0.22357723577235772	88	0.2430939226519337	126	0.2202797202797203	249	0.32849604221635886	a	1.415	-0.574322	0.03882	0.215513	0.309204	ENSG00000181143	ENST00000397910	T	0.02579	4.24	1.65	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.01281	0.0	T	0.47129	-0.9141	8	0.87932	D	0	.	2.4527	0.04522	0.3366:0.0:0.413:0.2504	rs953551;rs17516069;rs52791023;rs59907804;rs953551	3723	B5ME49	.	M	3723	ENSP00000381008:T3723M	ENSP00000381008:T3723M	T	-	2	0	MUC16	8937278	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.808000	0.01732	-0.903000	0.03881	-0.817000	0.03123	ACG	G|0.739;A|0.261	0.261	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GABRR1	2569	hgsc.bcm.edu	37	6	89913209	89913209	+	Intron	SNP	C	C	T	rs4590242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:89913209C>T	ENST00000454853.2	-	2	233				GABRR1_ENST00000369451.3_Intron|GABRR1_ENST00000481493.1_5'Flank|GABRR1_ENST00000435811.1_Intron	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1						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)	TGGGGCCTACCATGAACATTA	0.438													T|||	3716	0.742013	0.674	0.7896	5008	,	,		17811	0.9286		0.6531	False		,,,				2504	0.6994				.		Atlas-SNP	.											.	GABRR1	63	.	0			.						PASS	.	T		3020,1386	458.0+/-351.8	1039,942,222	253.0	214.0	227.0			-0.0	0.0	6	dbSNP_111	227	5629,2971	461.9+/-365.5	1849,1931,520	no	intron	GABRR1	NM_002042.3		2888,2873,742	TT,TC,CC		34.5465,31.4571,33.4999			89913209	8649,4357	2203	4300	6503	SO:0001627	intron_variant	2569	.			GCCTACCATGAAC		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.123-5G>A	6.37:g.89913209C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	.	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Splice_Site	SNP	ENST00000454853.2	37	CCDS5019.2																																																																																			C|0.295;T|0.705	0.705	strong		0.438	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
PRNP	5621	hgsc.bcm.edu	37	20	4680251	4680251	+	Missense_Mutation	SNP	A	A	G	rs1799990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4680251A>G	ENST00000379440.4	+	2	672	c.385A>G	c.(385-387)Atg>Gtg	p.M129V	PRNP_ENST00000430350.2_Missense_Mutation_p.M129V	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	0						integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)		p.M129V(2)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						TGGCGGCTACATGCTGGGAAG	0.547													A|||	1335	0.266573	0.3525	0.4063	5008	,	,		16338	0.0248		0.325	False		,,,				2504	0.2403				p.M129V		Atlas-SNP	.											PRNP,face,carcinoma,0,4	PRNP	31	4	2	Substitution - Missense(2)	central_nervous_system(1)|skin(1)	c.A385G	GRCh37	CM890104	PRNP	M	rs1799990	PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	1504,2902	476.6+/-357.7	261,982,960	72.0	56.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	385,385,385,385,385	2.9	1.0	20	dbSNP_89	62	2889,5711	452.0+/-362.8	486,1917,1897	yes	missense,missense,missense,missense,missense	PRNP	NM_000311.3,NM_001080121.1,NM_001080122.1,NM_001080123.1,NM_183079.2	21,21,21,21,21	747,2899,2857	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.593,34.1353,33.7767	benign,benign,benign,benign,benign	129/254,129/254,129/254,129/254,129/254	4680251	4393,8613	2203	4300	6503	SO:0001583	missense	5621	exon2			GGCTACATGCTGG	M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"""CD molecules"""	9449	protein-coding gene	gene with protein product	"""Creutzfeldt-Jakob disease"", ""Gerstmann-Strausler-Scheinker syndrome"", ""fatal familial insomnia"", ""p27-30"""	176640	"""prion protein (p27-30)"""	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.385A>G	20.37:g.4680251A>G	ENSP00000368752:p.Met129Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_000311		Missense_Mutation	SNP	ENST00000379440.4	37	CCDS13080.1	576	0.26373626373626374	172	0.34959349593495936	140	0.3867403314917127	12	0.02097902097902098	252	0.3324538258575198	A	11.91	1.778679	0.31502	0.341353	0.33593	ENSG00000171867	ENST00000379440;ENST00000430350;ENST00000424424;ENST00000444805;ENST00000457586	D;D;D;T	0.91996	-2.95;-2.95;-2.95;-1.42	5.3	2.93	0.34026	Prion/Doppel protein, beta-ribbon domain (2);	0.219208	0.38720	N	0.001589	T	0.00012	0.0000	L	0.47716	1.5	0.30001	P	0.8160000000000001	B;B;B	0.25235	0.009;0.082;0.121	B;B;B	0.22601	0.012;0.036;0.04	T	0.04693	-1.0933	9	0.66056	D	0.02	-2.3944	5.8372	0.18613	0.6585:0.1745:0.0:0.167	rs1799990;rs17850971;rs17858648;rs52800775;rs1799990	129;129;161	B2NI04;P04156;O75942	.;PRIO_HUMAN;.	V	129;129;129;68;129	ENSP00000368752:M129V;ENSP00000399376:M129V;ENSP00000411599:M129V;ENSP00000415284:M129V	ENSP00000368752:M129V	M	+	1	0	PRNP	4628251	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.521000	0.22893	0.281000	0.22233	0.533000	0.62120	ATG	A|0.700;G|0.300	0.300	strong		0.547	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311	
FLG	2312	hgsc.bcm.edu	37	1	152279019	152279019	+	Silent	SNP	G	G	A	rs57670307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152279019G>A	ENST00000368799.1	-	3	8378	c.8343C>T	c.(8341-8343)gaC>gaT	p.D2781D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2781	Ser-rich.		D -> Y (in dbSNP:rs2065958).		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)			TGTCCTGACCGTCTTGGGATG	0.607									Ichthyosis																												p.D2781D		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.C8343T						PASS	.	C		87,4307		0,87,2110	459.0	597.0	550.0		8343	-6.8	0.0	1	dbSNP_129	550	660,7940		0,660,3640	no	coding-synonymous	FLG	NM_002016.1		0,747,5750	AA,AG,GG		7.6744,1.98,5.7488		2781/4062	152279019	747,12247	2197	4300	6497	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGTCTTGG	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.8343C>T	1.37:g.152279019G>A		Somatic	508	0	0		WXS	Illumina HiSeq	Phase_I	693	161	0.232323	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			G|0.939;A|0.061	0.061	strong		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NLRP1	22861	hgsc.bcm.edu	37	17	5436263	5436263	+	Missense_Mutation	SNP	C	C	T	rs2301582	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:5436263C>T	ENST00000572272.1	-	11	3174	c.3175G>A	c.(3175-3177)Gtg>Atg	p.V1059M	NLRP1_ENST00000269280.4_Missense_Mutation_p.V1059M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V1059M|NLRP1_ENST00000577119.1_Missense_Mutation_p.V1029M|NLRP1_ENST00000262467.5_Missense_Mutation_p.V1063M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V1029M|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1059			V -> M (in dbSNP:rs2301582).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GGAGAAGGCACGCACAAGAGT	0.607													C|||	923	0.184305	0.0787	0.3573	5008	,	,		17458	0.0228		0.3738	False		,,,				2504	0.1759				p.V1063M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G3187A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	567,3839	254.6+/-260.1	35,497,1671	89.0	78.0	82.0		3187,3175,3175,3085,3085	0.8	0.0	17	dbSNP_100	82	3421,5179	504.5+/-376.2	664,2093,1543	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	699,2590,3214	TT,TC,CC		39.7791,12.8688,30.6628	benign,benign,benign,benign,benign	1063/1376,1059/1430,1059/1474,1029/1444,1029/1400	5436263	3988,9018	2203	4300	6503	SO:0001583	missense	22861	exon11			AAGGCACGCACAA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3175G>A	17.37:g.5436263C>T	ENSP00000460475:p.Val1059Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	464	0.21245421245421245	46	0.09349593495934959	123	0.3397790055248619	16	0.027972027972027972	279	0.36807387862796836	C	8.966	0.971710	0.18736	0.128688	0.397791	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.71817	-0.6;-0.6;-0.58;-0.48;-0.58	3.94	0.836	0.18891	.	1.178250	0.06625	N	0.758189	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P;P;P;P;B	0.42039	0.434;0.769;0.769;0.658;0.769;0.095	B;B;B;B;B;B	0.24701	0.055;0.037;0.037;0.017;0.037;0.01	T	0.17653	-1.0362	9	0.49607	T	0.09	.	6.2112	0.20630	0.1028:0.3672:0.53:0.0	rs2301582;rs17765850;rs52830015;rs56943859;rs2301582	325;1029;1029;1059;1059;1063	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	1063;1063;1059;1029;1059;325	ENSP00000442029:V1063M;ENSP00000262467:V1063M;ENSP00000269280:V1059M;ENSP00000346390:V1029M;ENSP00000324366:V1059M	ENSP00000262467:V1063M	V	-	1	0	NLRP1	5376987	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.977000	0.03782	0.255000	0.21593	-0.236000	0.12185	GTG	C|0.738;T|0.262	0.262	strong		0.607	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
SPATA3	130560	hgsc.bcm.edu	37	2	231865144	231865144	+	Missense_Mutation	SNP	G	G	C	rs12105962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231865144G>C	ENST00000452881.1	+	2	473	c.365G>C	c.(364-366)tGc>tCc	p.C122S	SPATA3_ENST00000409956.1_Intron|SPATA3_ENST00000433428.2_Missense_Mutation_p.C122S|SPATA3_ENST00000455816.1_Missense_Mutation_p.C122S|SPATA3_ENST00000424440.1_Missense_Mutation_p.C122S			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	122										endometrium(2)|lung(1)	3						AGCTCCGCTTGCTGGCGTCGT	0.652													G|||	1085	0.216653	0.1876	0.3256	5008	,	,		17115	0.1736		0.2565	False		,,,				2504	0.182				p.C122S		Atlas-SNP	.											.	SPATA3	52	.	0			c.G365C						PASS	.	G	SER/CYS	251,1133		19,213,460	37.0	35.0	36.0		365	4.2	1.0	2	dbSNP_120	36	817,2365		99,619,873	yes	missense	SPATA3	NM_139073.3	112	118,832,1333	CC,CG,GG		25.6757,18.1358,23.3903	probably-damaging	122/193	231865144	1068,3498	692	1591	2283	SO:0001583	missense	130560	exon2			CCGCTTGCTGGCG	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.365G>C	2.37:g.231865144G>C	ENSP00000388895:p.Cys122Ser	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_139073	Q86WX5|Q8N9Y6	Missense_Mutation	SNP	ENST00000452881.1	37	CCDS2481.1	513	0.2348901098901099	94	0.1910569105691057	119	0.3287292817679558	106	0.1853146853146853	194	0.2559366754617414	G	10.64	1.405615	0.25378	0.181358	0.256757	ENSG00000173699	ENST00000424440;ENST00000452881;ENST00000433428;ENST00000455816;ENST00000355662	.	.	.	4.25	4.25	0.50352	.	0.000000	0.49916	D	0.000135	T	0.00012	0.0000	L	0.34521	1.04	0.26558	P	0.9737856	D	0.89917	1.0	D	0.87578	0.998	T	0.16335	-1.0406	8	0.66056	D	0.02	-27.4861	12.4701	0.55781	0.0:0.0:1.0:0.0	rs12105962;rs59056322	113	Q8NHX4	SPTA3_HUMAN	S	122;122;122;122;113	.	ENSP00000347884:C113S	C	+	2	0	SPATA3	231573388	1.000000	0.71417	1.000000	0.80357	0.527000	0.34593	3.817000	0.55668	2.657000	0.90304	0.655000	0.94253	TGC	G|0.771;C|0.229	0.229	strong		0.652	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
FKBP15	23307	hgsc.bcm.edu	37	9	115933980	115933980	+	Missense_Mutation	SNP	C	C	A	rs1128116|rs386737766	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115933980C>A	ENST00000238256.3	-	24	2656	c.2539G>T	c.(2539-2541)Gcc>Tcc	p.A847S		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	847			A -> S (in dbSNP:rs1128116).		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						GCCTGGAGGGCTAAACACTGC	0.502													C|||	399	0.0796725	0.0991	0.0389	5008	,	,		11879	0.0387		0.0477	False		,,,				2504	0.1575				p.A847S		Atlas-SNP	.											.	FKBP15	128	.	0			c.G2539T						PASS	.	C	SER/ALA	387,3373		14,359,1507	80.0	82.0	81.0		2539	4.7	0.8	9	dbSNP_86	81	511,7709		15,481,3614	yes	missense	FKBP15	NM_015258.1	99	29,840,5121	AA,AC,CC		6.2165,10.2926,7.4958	probably-damaging	847/1220	115933980	898,11082	1880	4110	5990	SO:0001583	missense	23307	exon24			GGAGGGCTAAACA	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.2539G>T	9.37:g.115933980C>A	ENSP00000238256:p.Ala847Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	115	0.052655677655677656	54	0.10975609756097561	15	0.04143646408839779	11	0.019230769230769232	35	0.04617414248021108	C	21.1	4.099307	0.76983	0.102926	0.062165	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.25749	1.78;1.79	5.62	4.71	0.59529	.	.	.	.	.	T	0.00784	0.0026	L	0.41824	1.3	0.22880	N	0.998611	D;D	0.69078	0.997;0.996	D;P	0.64042	0.921;0.787	T	0.01124	-1.1444	9	0.33141	T	0.24	-11.7822	11.9909	0.53173	0.1729:0.8271:0.0:0.0	rs1128116;rs3184696;rs17405802	428;847	B4DVS2;Q5T1M5	.;FKB15_HUMAN	S	872;847	ENSP00000416158:A872S;ENSP00000238256:A847S	ENSP00000238256:A847S	A	-	1	0	FKBP15	114973801	0.966000	0.33281	0.809000	0.32408	0.922000	0.55478	2.091000	0.41691	1.348000	0.45733	0.655000	0.94253	GCC	C|0.940;A|0.060	0.060	strong		0.502	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
OVCH1	341350	hgsc.bcm.edu	37	12	29649191	29649191	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:29649191C>T	ENST00000318184.5	-	3	203	c.204G>A	c.(202-204)gaG>gaA	p.E68E		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	68	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					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)					AGAAGTGGTGCTCATCTGATT	0.448																																					p.E68E		Atlas-SNP	.											.	OVCH1	195	.	0			c.G204A						PASS	.						67.0	67.0	67.0					12																	29649191		1951	4150	6101	SO:0001819	synonymous_variant	341350	exon3			GTGGTGCTCATCT	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.204G>A	12.37:g.29649191C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	7	0.189189	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				.	.	none		0.448	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
CYTH4	27128	hgsc.bcm.edu	37	22	37699377	37699377	+	Silent	SNP	T	T	C	rs2239822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37699377T>C	ENST00000248901.6	+	8	817	c.630T>C	c.(628-630)ttT>ttC	p.F210F		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	210	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						GGCCGCCTTTTGAGCGCTTTG	0.632													C|||	3758	0.750399	0.8026	0.7637	5008	,	,		18013	0.7183		0.6312	False		,,,				2504	0.8262				p.F210F		Atlas-SNP	.											.	CYTH4	51	.	0			c.T630C						PASS	.	C		3455,951	361.6+/-315.8	1361,733,109	81.0	69.0	73.0		630	-0.6	1.0	22	dbSNP_98	73	5339,3261	490.1+/-372.8	1648,2043,609	no	coding-synonymous	CYTH4	NM_013385.3		3009,2776,718	CC,CT,TT		37.9186,21.5842,32.3851		210/395	37699377	8794,4212	2203	4300	6503	SO:0001819	synonymous_variant	27128	exon8			GCCTTTTGAGCGC	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.630T>C	22.37:g.37699377T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_013385	Q5R3F9|Q9UGT6	Silent	SNP	ENST00000248901.6	37	CCDS13946.1																																																																																			C|0.686;N|0.000	0.686	strong		0.632	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
BRAF	673	hgsc.bcm.edu	37	7	140453155	140453155	+	Missense_Mutation	SNP	C	C	T	rs397516896		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140453155C>T	ENST00000288602.6	-	15	1840	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in NHL). {ECO:0000269|PubMed:14612909}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D594N(9)|p.D594H(2)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AGACCAAAATCACCTATTTTT	0.378		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.D594N	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,rectum,carcinoma,0,77	BRAF	36346	77	11	Substitution - Missense(11)	skin(6)|large_intestine(2)|lung(2)|haematopoietic_and_lymphoid_tissue(1)	c.G1780A						PASS	.						106.0	100.0	102.0					7																	140453155		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	CAAAATCACCTAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1780G>A	7.37:g.140453155C>T	ENSP00000288602:p.Asp594Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	20	0.28169	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	C	36	5.616687	0.96649	.	.	ENSG00000157764	ENST00000288602	D	0.99849	-7.15	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96728	0.9537	10	0.87932	D	0	.	19.7917	0.96461	0.0:1.0:0.0:0.0	.	594	P15056	BRAF_HUMAN	N	594	ENSP00000288602:D594N	ENSP00000288602:D594N	D	-	1	0	BRAF	140099624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.686000	0.91538	0.650000	0.86243	GAT	.	.	none		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
UBR3	130507	hgsc.bcm.edu	37	2	170780657	170780657	+	Silent	SNP	C	C	T	rs61744354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170780657C>T	ENST00000272793.5	+	13	2046	c.1996C>T	c.(1996-1998)Cta>Tta	p.L666L	UBR3_ENST00000418381.1_Silent_p.L666L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	666					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						GTTAATGAAACTAATGATTCA	0.294													C|||	136	0.0271565	0.0189	0.0274	5008	,	,		15661	0.0		0.0567	False		,,,				2504	0.0358				p.L666L		Atlas-SNP	.											.	UBR3	182	.	0			c.C1996T						PASS	.	C		39,1345		0,39,653	44.0	39.0	41.0		1996	4.1	1.0	2	dbSNP_129	41	170,2986		5,160,1413	no	coding-synonymous	UBR3	NM_172070.3		5,199,2066	TT,TC,CC		5.3866,2.8179,4.6035		666/1889	170780657	209,4331	692	1578	2270	SO:0001819	synonymous_variant	130507	exon13			ATGAAACTAATGA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1996C>T	2.37:g.170780657C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				C|0.960;T|0.040	0.040	strong		0.294	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65676617T>C	ENST00000352385.2	-	20	3692	c.3483A>G	c.(3481-3483)ccA>ccG	p.P1161P	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CAGGAGCCTCTGGAGGCAGGG	0.627													C|||	2605	0.520168	0.5976	0.5994	5008	,	,		19120	0.6687		0.3926	False		,,,				2504	0.3374				p.P1161P		Atlas-SNP	.											IGDCC4,caecum,carcinoma,-1,1	IGDCC4	95	1	0			c.A3483G						scavenged	.	C		2490,1912	520.4+/-370.3	709,1072,420	34.0	37.0	36.0		3483	-2.3	0.0	15	dbSNP_100	36	3477,5121	611.3+/-395.8	690,2097,1512	no	coding-synonymous	IGDCC4	NM_020962.1		1399,3169,1932	CC,CT,TT		40.4396,43.4348,45.9		1161/1251	65676617	5967,7033	2201	4299	6500	SO:0001819	synonymous_variant	57722	exon20			AGCCTCTGGAGGC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.3483A>G	15.37:g.65676617T>C		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_020962	Q9HCE4	Silent	SNP	ENST00000352385.2	37	CCDS10206.1																																																																																			T|0.516;C|0.484	0.484	strong		0.627	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629935	32629935	+	Missense_Mutation	SNP	C	C	G	rs1063322		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629935C>G	ENST00000399082.3	-	2	244	c.200G>C	c.(199-201)gGc>gCc	p.G67A	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G157A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G157A|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G157A|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.G157A			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	157	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TTTGATCTGGCCTGGATAGAA	0.567									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.G157A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G470C						PASS	.						30.0	29.0	29.0					6																	32629935		2014	4198	6212	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	ATCTGGCCTGGAT		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.200G>C	6.37:g.32629935C>G	ENSP00000382032:p.Gly67Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		.	.	.	.	.	.	.	.	.	.	.	1.163	-0.643227	0.03531	.	.	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02682	4.2;4.2;4.2;4.2;4.2	4.52	0.489	0.16854	.	1.197420	0.06155	N	0.674887	T	0.01124	0.0037	.	.	.	0.80722	P	0.0	B;B;B;B	0.10296	0.002;0.003;0.003;0.002	B;B;B;B	0.19391	0.025;0.025;0.025;0.025	T	0.45381	-0.9265	8	0.59425	D	0.04	.	9.8117	0.40826	0.0:0.3076:0.6022:0.0902	rs1063322;rs3204388;rs9274000;rs9282126;rs17840187	157;122;157;157	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	A	67;157;157;157;157;93	ENSP00000382032:G67A;ENSP00000382029:G157A;ENSP00000364080:G157A;ENSP00000407332:G157A;ENSP00000382034:G157A	ENSP00000364080:G157A	G	-	2	0	HLA-DQB1	32737913	0.000000	0.05858	0.038000	0.18304	0.240000	0.25518	0.233000	0.17911	-0.243000	0.09653	-0.676000	0.03789	GGC	C|0.500;G|0.500	0.500	weak		0.567	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
THAP4	51078	hgsc.bcm.edu	37	2	242573211	242573211	+	Missense_Mutation	SNP	T	T	C	rs7424328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	69	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	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	
C10orf67	256815	hgsc.bcm.edu	37	10	23633566	23633566	+	Silent	SNP	C	C	A	rs2036917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:23633566C>A	ENST00000323327.4	-	1	208	c.141G>T	c.(139-141)cgG>cgT	p.R47R	RP11-371A19.2_ENST00000443224.1_RNA	NM_153714.2	NP_714925.2	Q8IYJ2	CJ067_HUMAN	chromosome 10 open reading frame 67	47										central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5						CGCAGCAGACCCGCAGCTCGG	0.612													C|||	3379	0.67472	0.7277	0.6599	5008	,	,		14886	0.8562		0.4771	False		,,,				2504	0.6299				p.R47R		Atlas-SNP	.											C10orf67,NS,carcinoma,0,1	C10orf67	21	1	0			c.G141T						PASS	.	C		2741,1125		992,757,184	22.0	24.0	23.0		141	-2.6	0.0	10	dbSNP_94	23	4020,4234		998,2024,1105	no	coding-synonymous	C10orf67	NM_153714.2		1990,2781,1289	AA,AC,CC		48.7037,29.0998,44.2162		47/186	23633566	6761,5359	1933	4127	6060	SO:0001819	synonymous_variant	256815	exon1			GCAGACCCGCAGC	BC035732	CCDS44365.1	10p12.31	2012-05-31			ENSG00000179133	ENSG00000179133			28716	protein-coding gene	gene with protein product						12477932	Standard	NM_153714		Approved	MGC46732	uc010qcx.2	Q8IYJ2	OTTHUMG00000017818	ENST00000323327.4:c.141G>T	10.37:g.23633566C>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_153714	A8MUP9|Q5SWD4	Silent	SNP	ENST00000323327.4	37	CCDS44365.1																																																																																			C|0.343;A|0.657	0.657	strong		0.612	C10orf67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047213.1	NM_153714	
PTPRG	5793	hgsc.bcm.edu	37	3	61975387	61975387	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:61975387G>A	ENST00000474889.1	+	3	656	c.279G>A	c.(277-279)gcG>gcA	p.A93A	PTPRG_ENST00000295874.10_Silent_p.A93A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	93	Alpha-carbonic anhydrase.				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)		ACCAGTATGCGCGTGTTGGGG	0.483																																					p.A93A		Atlas-SNP	.											PTPRG,NS,carcinoma,0,1	PTPRG	153	1	0			c.G279A						PASS	.						117.0	107.0	111.0					3																	61975387		2203	4300	6503	SO:0001819	synonymous_variant	5793	exon3			GTATGCGCGTGTT	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.279G>A	3.37:g.61975387G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																			.	.	none		0.483	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
OR4S2	219431	hgsc.bcm.edu	37	11	55418659	55418659	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55418659G>A	ENST00000312422.2	+	1	280	c.280G>A	c.(280-282)Ggg>Agg	p.G94R		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	94						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)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				CTCCTATGTGGGGTGCATGTT	0.423																																					p.G94R		Atlas-SNP	.											OR4S2,face,carcinoma,-1,1	OR4S2	89	1	0			c.G280A						scavenged	.						234.0	194.0	208.0					11																	55418659		2184	4043	6227	SO:0001583	missense	219431	exon1			TATGTGGGGTGCA	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"""GPCR / Class A : Olfactory receptors"""	15183	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily S, member 2 pseudogene"""	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.280G>A	11.37:g.55418659G>A	ENSP00000310337:p.Gly94Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	283	3	0.0106007	NM_001004059	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.073805	0.55646	.	.	ENSG00000174982	ENST00000312422	T	0.09817	2.94	5.36	2.27	0.28462	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000046	T	0.26629	0.0651	M	0.78916	2.43	0.09310	N	1	D	0.76494	0.999	D	0.67382	0.951	T	0.01608	-1.1313	10	0.66056	D	0.02	.	7.0689	0.25167	0.1555:0.0:0.7044:0.14	.	94	Q8NH73	OR4S2_HUMAN	R	94	ENSP00000310337:G94R	ENSP00000310337:G94R	G	+	1	0	OR4S2	55175235	0.000000	0.05858	0.342000	0.25602	0.974000	0.67602	0.480000	0.22244	1.233000	0.43693	0.549000	0.68633	GGG	.	.	none		0.423	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5200281	5200281	+	Silent	SNP	C	C	T	rs6555335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:5200281C>T	ENST00000274181.7	+	9	1488	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	ADAMTS16_ENST00000511368.1_Silent_p.C450C	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	450	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						GGAACATGTGCAAAAAGTCCG	0.443													C|||	3632	0.72524	0.5651	0.8314	5008	,	,		19242	0.8026		0.7396	False		,,,				2504	0.772				p.C450C		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C1350T						PASS	.	C		2409,1511		739,931,290	60.0	62.0	61.0		1350	3.2	1.0	5	dbSNP_116	61	6227,2101		2330,1567,267	no	coding-synonymous	ADAMTS16	NM_139056.2		3069,2498,557	TT,TC,CC		25.2281,38.5459,29.4905		450/1225	5200281	8636,3612	1960	4164	6124	SO:0001819	synonymous_variant	170690	exon9			CATGTGCAAAAAG	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.1350C>T	5.37:g.5200281C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			C|0.270;T|0.730	0.730	strong		0.443	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278203	126278203	+	Splice_Site	SNP	T	T	C	rs2298475	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126278203T>C	ENST00000526727.1	+	7	813	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	ST3GAL4_ENST00000534457.1_Splice_Site_p.L142L|ST3GAL4_ENST00000534083.1_Splice_Site_p.L147L|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000444328.2_Splice_Site_p.L147L|ST3GAL4_ENST00000227495.6_Splice_Site_p.L143L|ST3GAL4_ENST00000392669.2_Splice_Site_p.L147L|ST3GAL4_ENST00000449406.2_Splice_Site_p.L136L|ST3GAL4_ENST00000532243.1_Splice_Site_p.L146L|ST3GAL4_ENST00000530591.1_Splice_Site_p.L143L|ST3GAL4_ENST00000356132.4_Splice_Site_p.L153L			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						scavenged	.	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	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	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
IKBKAP	8518	hgsc.bcm.edu	37	9	111679872	111679872	+	Silent	SNP	G	G	A	rs12340246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	101	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	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		
CHST13	166012	hgsc.bcm.edu	37	3	126261345	126261345	+	Missense_Mutation	SNP	G	G	A	rs1056522	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:126261345G>A	ENST00000319340.2	+	3	1000	c.950G>A	c.(949-951)cGg>cAg	p.R317Q		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	317			R -> Q (in dbSNP:rs1056522). {ECO:0000269|PubMed:15489334}.		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)		TTCTACCAGCGGCGCCTCTTC	0.687													G|||	1612	0.321885	0.4622	0.3444	5008	,	,		9648	0.2569		0.2992	False		,,,				2504	0.2065				p.R317Q		Atlas-SNP	.											.	CHST13	21	.	0			c.G950A						PASS	.	G	GLN/ARG	1519,2051		338,843,604	11.0	11.0	11.0		950	2.0	1.0	3	dbSNP_86	11	2065,5231		339,1387,1922	yes	missense	CHST13	NM_152889.2	43	677,2230,2526	AA,AG,GG		28.3032,42.549,32.9836	probably-damaging	317/342	126261345	3584,7282	1785	3648	5433	SO:0001583	missense	166012	exon3			ACCAGCGGCGCCT	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.950G>A	3.37:g.126261345G>A	ENSP00000317404:p.Arg317Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	127	74	0.582677	NM_152889	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	37	CCDS3039.1	738	0.33791208791208793	232	0.4715447154471545	126	0.34806629834254144	151	0.263986013986014	229	0.3021108179419525	G	7.729	0.698807	0.15106	0.42549	0.283032	ENSG00000180767	ENST00000319340	T	0.72942	-0.7	3.89	1.96	0.26148	.	0.134719	0.44688	U	0.000428	T	0.00012	0.0000	L	0.41824	1.3	0.09310	P	0.99999902818	B	0.28419	0.211	B	0.28011	0.085	T	0.45041	-0.9288	9	0.26408	T	0.33	-22.0086	7.5408	0.27737	0.2353:0.0:0.7647:0.0	rs1056522;rs3172309;rs59933474;rs1056522	317	Q8NET6	CHSTD_HUMAN	Q	317	ENSP00000317404:R317Q	ENSP00000317404:R317Q	R	+	2	0	CHST13	127744035	1.000000	0.71417	0.995000	0.50966	0.060000	0.15804	1.832000	0.39151	0.102000	0.17638	0.313000	0.20887	CGG	G|0.655;A|0.345	0.345	strong		0.687	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
PIEZO1	9780	hgsc.bcm.edu	37	16	88791458	88791458	+	Missense_Mutation	SNP	G	G	A	rs11645197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	97	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	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	
TRIM77	390231	hgsc.bcm.edu	37	11	89443808	89443808	+	Silent	SNP	A	A	C	rs11018745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89443808A>C	ENST00000398290.3	+	1	342	c.342A>C	c.(340-342)ctA>ctC	p.L114L		NM_001146162.1	NP_001139634.1	I1YAP6	TRI77_HUMAN	tripartite motif containing 77	114						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										TGTGTTTTCTATGCTCTCAAT	0.443													C|||	1300	0.259585	0.1188	0.281	5008	,	,		17154	0.3264		0.3738	False		,,,				2504	0.2485				p.L114L		Atlas-SNP	.											.	.	.	.	0			c.A342C						PASS	.						51.0	42.0	45.0					11																	89443808		692	1589	2281	SO:0001819	synonymous_variant	390231	exon1			TTTTCTATGCTCT		CCDS60929.1	11q14.3	2014-02-17	2013-01-14	2013-01-14	ENSG00000214414	ENSG00000214414		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	34228	protein-coding gene	gene with protein product			"""tripartite motif-containing 77"", ""tripartite motif containing 77, pseudogene"""	TRIM77P			Standard	NM_001146162		Approved		uc010rtw.2	I1YAP6	OTTHUMG00000167624	ENST00000398290.3:c.342A>C	11.37:g.89443808A>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_001146162		Silent	SNP	ENST00000398290.3	37																																																																																				A|0.705;C|0.295	0.295	strong		0.443	TRIM77-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146162	
LCT	3938	hgsc.bcm.edu	37	2	136561557	136561557	+	Silent	SNP	G	G	A	rs2304371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:136561557G>A	ENST00000264162.2	-	11	4616	c.4606C>T	c.(4606-4608)Ctg>Ttg	p.L1536L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1536	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGCTCATTCAGCGTGATCCAA	0.522													G|||	3306	0.660144	0.4047	0.7507	5008	,	,		20923	0.7758		0.7485	False		,,,				2504	0.7311				p.L1536L		Atlas-SNP	.											.	LCT	309	.	0			c.C4606T						PASS	.	G		2172,2234	585.3+/-386.2	536,1100,567	142.0	108.0	120.0		4606	2.8	0.7	2	dbSNP_100	120	6875,1725	737.2+/-407.0	2785,1305,210	no	coding-synonymous	LCT	NM_002299.2		3321,2405,777	AA,AG,GG		20.0581,49.2964,30.4398		1536/1928	136561557	9047,3959	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon11			CATTCAGCGTGAT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4606C>T	2.37:g.136561557G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.327;A|0.673	0.673	strong		0.522	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
GRXCR1	389207	hgsc.bcm.edu	37	4	42895308	42895308	+	Missense_Mutation	SNP	G	G	A	rs78136490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:42895308G>A	ENST00000399770.2	+	1	25	c.25G>A	c.(25-27)Gaa>Aaa	p.E9K	RN7SKP82_ENST00000516786.1_RNA	NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	9			E -> K (in dbSNP:rs78136490). {ECO:0000269|PubMed:20137778}.		auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GATGAAGCCAGAAAGTGACAG	0.517													G|||	617	0.123203	0.2307	0.0648	5008	,	,		20255	0.1567		0.0716	False		,,,				2504	0.0378				p.E9K		Atlas-SNP	.											.	GRXCR1	78	.	0			c.G25A						PASS	.	G	LYS/GLU	732,3324		67,598,1363	91.0	99.0	96.0		25	5.0	0.9	4	dbSNP_131	96	548,7810		13,522,3644	yes	missense	GRXCR1	NM_001080476.2	56	80,1120,5007	AA,AG,GG		6.5566,18.0473,10.3109	possibly-damaging	9/291	42895308	1280,11134	2028	4179	6207	SO:0001583	missense	389207	exon1			AAGCCAGAAAGTG		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 88"""	613283	"""deafness, autosomal recessive 25"""	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.25G>A	4.37:g.42895308G>A	ENSP00000382670:p.Glu9Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	37	CCDS43225.1	276	0.12637362637362637	117	0.23780487804878048	23	0.06353591160220995	80	0.13986013986013987	56	0.07387862796833773	G	11.87	1.769118	0.31320	0.180473	0.065566	ENSG00000215203	ENST00000399770	T	0.36878	1.23	5.83	4.99	0.66335	.	0.209202	0.40554	U	0.001072	T	0.00012	0.0000	L	0.50333	1.59	0.23376	P	0.99780957	B	0.26635	0.155	B	0.15870	0.014	T	0.14980	-1.0453	9	0.23302	T	0.38	-2.6283	16.1478	0.81583	0.0:0.1334:0.8666:0.0	.	9	A8MXD5	GRCR1_HUMAN	K	9	ENSP00000382670:E9K	ENSP00000382670:E9K	E	+	1	0	GRXCR1	42590065	0.995000	0.38212	0.896000	0.35187	0.018000	0.09664	5.087000	0.64480	1.451000	0.47736	0.650000	0.86243	GAA	G|0.906;A|0.094	0.094	strong		0.517	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656073	167656073	+	Silent	SNP	C	C	T	rs1057377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:167656073C>T	ENST00000357154.3	-	12	1447	c.1310G>A	c.(1309-1311)tGa>tAa	p.*437*	SPOCK3_ENST00000510741.1_Silent_p.*394*|SPOCK3_ENST00000504953.1_Silent_p.*434*|SPOCK3_ENST00000512681.1_Silent_p.*339*|SPOCK3_ENST00000534949.1_Silent_p.*341*|SPOCK3_ENST00000541637.1_Silent_p.*339*|SPOCK3_ENST00000511531.1_Silent_p.*437*|SPOCK3_ENST00000421836.2_Silent_p.*386*|SPOCK3_ENST00000541354.1_Silent_p.*317*|SPOCK3_ENST00000511269.1_Silent_p.*434*|SPOCK3_ENST00000535728.1_Silent_p.*305*|SPOCK3_ENST00000357545.4_Silent_p.*434*|SPOCK3_ENST00000506886.1_Silent_p.*437*|SPOCK3_ENST00000502330.1_Silent_p.*437*|SPOCK3_ENST00000507137.1_5'UTR	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	252	0	0		WXS	Illumina HiSeq	Phase_I	239	131	0.548117	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		
MTG2	26164	hgsc.bcm.edu	37	20	60768615	60768615	+	Missense_Mutation	SNP	G	G	A	rs6062133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60768615G>A	ENST00000370823.3	+	2	157	c.139G>A	c.(139-141)Ggc>Agc	p.G47S	MTG2_ENST00000436421.2_Missense_Mutation_p.G47S|MTG2_ENST00000536470.1_Intron	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	89	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	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	
RP1L1	94137	hgsc.bcm.edu	37	8	10467636	10467636	+	Silent	SNP	T	T	C	rs386722179|rs4840500		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10467636T>C	ENST00000382483.3	-	4	4195	c.3972A>G	c.(3970-3972)gaA>gaG	p.E1324E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1340	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		E -> G (in allele RP1L1-3; dbSNP:rs4240659).		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)		ctgttttagtttcctctaact	0.463																																					p.E1324E		Atlas-SNP	.											.	RP1L1	453	.	0			c.A3972G						PASS	.						134.0	131.0	132.0					8																	10467636		1937	4124	6061	SO:0001819	synonymous_variant	94137	exon4			TTTAGTTTCCTCT	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.3972A>G	8.37:g.10467636T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	88	17	0.193182	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	weak		0.463	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
FNBP1	23048	hgsc.bcm.edu	37	9	132662786	132662786	+	Missense_Mutation	SNP	C	C	T	rs1023000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:132662786C>T	ENST00000446176.2	-	14	1655	c.1469G>A	c.(1468-1470)aGc>aAc	p.S490N	FNBP1_ENST00000443566.2_Missense_Mutation_p.S118N|FNBP1_ENST00000420781.1_Missense_Mutation_p.S481N|FNBP1_ENST00000478129.1_5'UTR|FNBP1_ENST00000355681.3_Missense_Mutation_p.S461N	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	490	Interaction with RND2. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.		S -> N (in dbSNP:rs1023000). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		CGCCTGCTCGCTGCGTGCTGG	0.622			T	MLL	AML								c|||	3179	0.634784	0.5787	0.6527	5008	,	,		16546	0.7927		0.507	False		,,,				2504	0.6667				p.S490N		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	FNBP1_ENST00000372416,NS,carcinoma,0,2	FNBP1	51	2	0			c.G1469A						PASS	.	T	ASN/SER	2340,1616		694,952,332	27.0	30.0	29.0		1469	2.2	0.0	9	dbSNP_86	29	4354,3952		1131,2092,930	yes	missense	FNBP1	NM_015033.2	46	1825,3044,1262	TT,TC,CC		47.5801,40.8493,45.4086	benign	490/618	132662786	6694,5568	1978	4153	6131	SO:0001583	missense	23048	exon14			TGCTCGCTGCGTG	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.1469G>A	9.37:g.132662786C>T	ENSP00000413625:p.Ser490Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	37	CCDS48040.1	1334|1334	0.6108058608058609|0.6108058608058609	308|308	0.6260162601626016|0.6260162601626016	218|218	0.6022099447513812|0.6022099447513812	433|433	0.756993006993007|0.756993006993007	375|375	0.4947229551451187|0.4947229551451187	c|c	0.609|0.609	-0.825795|-0.825795	0.02734|0.02734	0.591507|0.591507	0.524199|0.524199	ENSG00000187239|ENSG00000187239	ENST00000449089|ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000443566;ENST00000355681	.|T;T;T;T	.|0.73681	.|-0.77;-0.77;-0.77;-0.77	4.02|4.02	2.15|2.15	0.27550|0.27550	.|.	.|1.265410	.|0.05157	.|N	.|0.497001	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25144|0.25144	0.715|0.715	0.80722|0.80722	P|P	0.0|0.0	.|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	.|0.15052	.|0.001;0.001;0.002;0.001;0.003;0.012;0.003;0.001	T|T	0.46679|0.46679	-0.9174|-0.9174	4|9	.|0.45353	.|T	.|0.12	-4.9808|-4.9808	5.5861|5.5861	0.17275|0.17275	0.0:0.5641:0.1482:0.2878|0.0:0.5641:0.1482:0.2878	rs1023000;rs3208771;rs17407396;rs58921965;rs1023000|rs1023000;rs3208771;rs17407396;rs58921965;rs1023000	.|485;480;118;424;461;441;485;490	.|B7ZL12;B7ZL13;E7EPB7;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3	.|.;.;.;.;.;.;.;FNBP1_HUMAN	T|N	442|490;490;481;490;118;461	.|ENSP00000413625:S490N;ENSP00000407548:S481N;ENSP00000389117:S118N;ENSP00000347907:S461N	.|ENSP00000347907:S461N	A|S	-|-	1|2	0|0	FNBP1|FNBP1	131702607|131702607	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.351000|0.351000	0.29236|0.29236	0.438000|0.438000	0.21559|0.21559	0.131000|0.131000	0.18576|0.18576	-1.924000|-1.924000	0.00514|0.00514	GCG|AGC	C|0.386;T|0.614	0.614	strong		0.622	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2		
WDR72	256764	hgsc.bcm.edu	37	15	53907948	53907948	+	Missense_Mutation	SNP	G	G	A	rs17730281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:53907948G>A	ENST00000396328.1	-	15	2694	c.2455C>T	c.(2455-2457)Ctc>Ttc	p.L819F	WDR72_ENST00000559418.1_Missense_Mutation_p.L829F|WDR72_ENST00000360509.5_Missense_Mutation_p.L819F|WDR72_ENST00000557913.1_Missense_Mutation_p.L816F	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	819			L -> F (in dbSNP:rs17730281).							NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		AAAATATTGAGGTGCTTAATG	0.373													G|||	1337	0.266973	0.1248	0.3804	5008	,	,		18191	0.4851		0.2018	False		,,,				2504	0.2209				p.L819F		Atlas-SNP	.											.	WDR72	177	.	0			c.C2455T						PASS	.	G	PHE/LEU	692,3694	282.8+/-276.7	56,580,1557	103.0	105.0	104.0		2455	5.7	1.0	15	dbSNP_123	104	1896,6690	324.5+/-316.5	195,1506,2592	yes	missense	WDR72	NM_182758.2	22	251,2086,4149	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.0825,15.7775,19.9507	probably-damaging	819/1103	53907948	2588,10384	2193	4293	6486	SO:0001583	missense	256764	exon15			TATTGAGGTGCTT	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.2455C>T	15.37:g.53907948G>A	ENSP00000379619:p.Leu819Phe	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	611	0.27976190476190477	65	0.13211382113821138	121	0.3342541436464088	276	0.4825174825174825	149	0.19656992084432717	G	18.65	3.669478	0.67814	0.157775	0.220825	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.69561	-0.41;-0.41	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	M	0.80616	2.505	0.23168	P	0.99818646	D	0.76494	0.999	D	0.68765	0.96	T	0.51108	-0.8747	9	0.87932	D	0	.	10.4234	0.44363	0.1487:0.0:0.8513:0.0	rs17730281;rs52809867;rs17730281	819	Q3MJ13	WDR72_HUMAN	F	819	ENSP00000379619:L819F;ENSP00000353699:L819F	ENSP00000353699:L819F	L	-	1	0	WDR72	51695240	0.991000	0.36638	1.000000	0.80357	0.973000	0.67179	2.006000	0.40874	2.703000	0.92315	0.655000	0.94253	CTC	G|0.773;A|0.227	0.227	strong		0.373	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
SUMF1	285362	hgsc.bcm.edu	37	3	4508742	4508742	+	Missense_Mutation	SNP	C	C	T	rs2819590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:4508742C>T	ENST00000272902.5	-	1	223	c.188G>A	c.(187-189)aGt>aAt	p.S63N	SUMF1_ENST00000458465.2_Missense_Mutation_p.S63N|SUMF1_ENST00000534863.1_Missense_Mutation_p.S63N|SUMF1_ENST00000383843.5_Missense_Mutation_p.S63N|SUMF1_ENST00000405420.2_Missense_Mutation_p.S63N	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	63			S -> N (in dbSNP:rs2819590). {ECO:0000269|PubMed:12757705, ECO:0000269|PubMed:12975309}.		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)		GGCTGCCGAACTGCCATGGGC	0.726													C|||	584	0.116613	0.0386	0.1859	5008	,	,		11781	0.002		0.3022	False		,,,				2504	0.1002				p.S63N		Atlas-SNP	.											.	SUMF1	23	.	0			c.G188A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	218,3086		23,172,1457	3.0	4.0	4.0		188,188,188	3.0	1.0	3	dbSNP_100	4	1828,5392		262,1304,2044	no	missense,missense,missense	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	46,46,46	285,1476,3501	TT,TC,CC		25.3186,6.5981,19.4413	possibly-damaging,possibly-damaging,possibly-damaging	63/350,63/355,63/375	4508742	2046,8478	1652	3610	5262	SO:0001583	missense	285362	exon1			GCCGAACTGCCAT	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.188G>A	3.37:g.4508742C>T	ENSP00000272902:p.Ser63Asn	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	43	33	0.767442	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	37	CCDS2564.1	311	0.1423992673992674	17	0.034552845528455285	68	0.1878453038674033	1	0.0017482517482517483	225	0.29683377308707126	C	23.3	4.402650	0.83230	0.065981	0.253186	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000458465;ENST00000405420	D;D;D;D;D	0.92805	-2.65;-3.11;-3.07;-2.29;-3.11	3.95	3.04	0.35103	.	0.756838	0.13236	N	0.403262	T	0.00039	0.0001	L	0.51422	1.61	0.38220	P	0.059289999999999954	D;P;P;P	0.54601	0.967;0.902;0.956;0.704	P;P;P;B	0.60682	0.878;0.677;0.468;0.236	T	0.00002	-1.2618	9	0.27785	T	0.31	-20.9529	9.4883	0.38944	0.0:0.7843:0.2157:0.0	rs2819590;rs17706014;rs2819590	63;63;63;63	E9PF05;G5E9B0;E9PGL0;Q8NBK3	.;.;.;SUMF1_HUMAN	N	63	ENSP00000440421:S63N;ENSP00000272902:S63N;ENSP00000373355:S63N;ENSP00000410060:S63N;ENSP00000384977:S63N	ENSP00000272902:S63N	S	-	2	0	SUMF1	4483742	0.859000	0.29813	0.991000	0.47740	0.843000	0.47879	0.513000	0.22770	1.196000	0.43129	0.585000	0.79938	AGT	C|0.867;T|0.133	0.133	strong		0.726	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
SNX31	169166	hgsc.bcm.edu	37	8	101586133	101586133	+	Missense_Mutation	SNP	T	T	C	rs2022923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:101586133T>C	ENST00000311812.2	-	14	1433	c.1283A>G	c.(1282-1284)gAt>gGt	p.D428G	SNX31_ENST00000428383.2_Missense_Mutation_p.D329G	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	428			D -> G (in dbSNP:rs2022923). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			AACGCAGTCATCTTTAGCTAT	0.343													T|||	2063	0.411941	0.5514	0.3689	5008	,	,		19008	0.2778		0.4364	False		,,,				2504	0.3671				p.D428G		Atlas-SNP	.											SNX31,NS,carcinoma,0,1	SNX31	66	1	0			c.A1283G						PASS	.	T	GLY/ASP	2346,2058	605.4+/-390.5	623,1100,479	128.0	127.0	127.0		1283	-11.0	0.0	8	dbSNP_94	127	3688,4908	527.2+/-381.1	783,2122,1393	yes	missense	SNX31	NM_152628.3	94	1406,3222,1872	CC,CT,TT		42.9037,46.7302,46.4154	benign	428/441	101586133	6034,6966	2202	4298	6500	SO:0001583	missense	169166	exon14			CAGTCATCTTTAG		CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"""Sorting nexins"""	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.1283A>G	8.37:g.101586133T>C	ENSP00000312368:p.Asp428Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	35	0.37234	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	942|942	0.43131868131868134|0.43131868131868134	304|304	0.6178861788617886|0.6178861788617886	140|140	0.3867403314917127|0.3867403314917127	158|158	0.2762237762237762|0.2762237762237762	340|340	0.44854881266490765|0.44854881266490765	T|T	7.650|7.650	0.682808|0.682808	0.14907|0.14907	0.532698|0.532698	0.429037|0.429037	ENSG00000174226|ENSG00000174226	ENST00000311812;ENST00000428383|ENST00000518342	T;T|.	0.23348|.	2.24;1.91|.	5.51|5.51	-11.0|-11.0	0.00169|0.00169	.|.	1.819920|.	0.02970|.	N|.	0.144295|.	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|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|T	0.36212|0.36212	-0.9757|-0.9757	9|4	0.11794|.	T|.	0.64|.	6.6358|6.6358	3.7682|3.7682	0.08630|0.08630	0.1019:0.3636:0.3892:0.1454|0.1019:0.3636:0.3892:0.1454	rs2022923;rs17845950;rs17858931;rs52797088;rs60518312;rs2022923|rs2022923;rs17845950;rs17858931;rs52797088;rs60518312;rs2022923	329;428|.	Q8N9S9-2;Q8N9S9|.	.;SNX31_HUMAN|.	G|V	428;329|36	ENSP00000312368:D428G;ENSP00000405024:D329G|.	ENSP00000312368:D428G|.	D|M	-|-	2|1	0|0	SNX31|SNX31	101655309|101655309	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.851000|0.851000	0.48451|0.48451	-0.575000|-0.575000	0.05861|0.05861	-2.690000|-2.690000	0.00404|0.00404	-0.472000|-0.472000	0.04984|0.04984	GAT|ATG	T|0.551;C|0.449	0.449	strong		0.343	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628	
TK1	7083	hgsc.bcm.edu	37	17	76178748	76178748	+	Silent	SNP	T	T	C	rs1143697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76178748T>C	ENST00000301634.7	-	4	463	c.225A>G	c.(223-225)gcA>gcG	p.A75A	TK1_ENST00000590430.1_Intron|TK1_ENST00000405273.1_Silent_p.A75A|TK1_ENST00000590862.1_Silent_p.A75A|TK1_ENST00000588734.1_Silent_p.A75A	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	75					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)	p.A75A(1)		endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	AGGCGGGCAGTGCCTCCATGG	0.632													C|||	3416	0.682109	0.8707	0.6686	5008	,	,		14475	0.622		0.4523	False		,,,				2504	0.7352				p.A75A		Atlas-SNP	.											TK1_ENST00000301634,NS,carcinoma,0,1	TK1	23	1	1	Substitution - coding silent(1)	stomach(1)	c.A225G						scavenged	.	C		3616,782		1501,614,84	44.0	30.0	35.0		225	-11.0	0.1	17	dbSNP_86	35	3810,4784		851,2108,1338	no	coding-synonymous	TK1	NM_003258.4		2352,2722,1422	CC,CT,TT		44.3333,17.7808,42.8417		75/235	76178748	7426,5566	2199	4297	6496	SO:0001819	synonymous_variant	7083	exon4			GGGCAGTGCCTCC		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.225A>G	17.37:g.76178748T>C		Somatic	19	3	0.157895		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_003258	B2RC58|Q969V0|Q9UMG9	Silent	SNP	ENST00000301634.7	37	CCDS11754.1																																																																																			T|0.400;G|0.007	.	strong		0.632	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258	
EMID1	129080	hgsc.bcm.edu	37	22	29630337	29630337	+	Splice_Site	SNP	G	G	A	rs3950176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	62	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	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
UNC13A	23025	hgsc.bcm.edu	37	19	17766900	17766900	+	Missense_Mutation	SNP	C	C	T	rs34752754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17766900C>T	ENST00000519716.2	-	10	1074	c.1075G>A	c.(1075-1077)Gcc>Acc	p.A359T	UNC13A_ENST00000552293.1_Missense_Mutation_p.A359T|UNC13A_ENST00000550896.1_Missense_Mutation_p.A359T|UNC13A_ENST00000551649.1_Missense_Mutation_p.A359T|UNC13A_ENST00000252773.7_Missense_Mutation_p.A359T|UNC13A_ENST00000428389.2_Missense_Mutation_p.A447T	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	359			A -> T (in dbSNP:rs34752754).		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						TCACGCTGGGCATAGCTGCCC	0.627													C|||	1216	0.242812	0.121	0.2939	5008	,	,		18688	0.0685		0.4732	False		,,,				2504	0.3139				p.A359T		Atlas-SNP	.											.	UNC13A	299	.	0			c.G1075A						PASS	.	C	THR/ALA	649,3625		79,491,1567	34.0	40.0	38.0		1075	-7.9	0.0	19	dbSNP_126	38	3649,4737		880,1889,1424	yes	missense	UNC13A	NM_001080421.2	58	959,2380,2991	TT,TC,CC		43.513,15.1848,33.9494	benign	359/1704	17766900	4298,8362	2137	4193	6330	SO:0001583	missense	23025	exon10			GCTGGGCATAGCT	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.1075G>A	19.37:g.17766900C>T	ENSP00000429562:p.Ala359Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	588	0.2692307692307692	81	0.16463414634146342	115	0.31767955801104975	31	0.05419580419580419	361	0.4762532981530343	C	13.78	2.339705	0.41398	0.151848	0.43513	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	4.03	-7.87	0.01183	.	7739.210000	0.00166	U	0.000007	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	0.11012	-1.0605	9	0.09843	T	0.71	.	4.8204	0.13387	0.2613:0.2535:0.0:0.4852	rs34752754;rs62121693	359	Q9UPW8	UN13A_HUMAN	T	359;447;359;359;359;359	ENSP00000429562:A359T;ENSP00000400409:A447T;ENSP00000252773:A359T;ENSP00000447236:A359T;ENSP00000447572:A359T;ENSP00000446831:A359T	ENSP00000252773:A359T	A	-	1	0	UNC13A	17627900	0.000000	0.05858	0.000000	0.03702	0.700000	0.40528	-0.345000	0.07770	-1.077000	0.03121	0.491000	0.48974	GCC	C|0.720;T|0.280	0.280	strong		0.627	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
TTC23	64927	hgsc.bcm.edu	37	15	99762041	99762041	+	Missense_Mutation	SNP	C	C	T	rs78534478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:99762041C>T	ENST00000394132.2	-	6	1026	c.209G>A	c.(208-210)cGt>cAt	p.R70H	TTC23_ENST00000558613.1_Missense_Mutation_p.R70H|TTC23_ENST00000262074.4_Missense_Mutation_p.R70H|TTC23_ENST00000558663.1_Missense_Mutation_p.R70H|TTC23_ENST00000394136.1_Missense_Mutation_p.R70H|TTC23_ENST00000394130.1_Missense_Mutation_p.R70H|TTC23_ENST00000394135.3_Missense_Mutation_p.R70H|TTC23_ENST00000394129.2_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	70	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	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	
NLRP2	55655	hgsc.bcm.edu	37	19	55481398	55481398	+	Silent	SNP	G	G	A	rs269912	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55481398G>A	ENST00000543010.1	+	2	158	c.15G>A	c.(13-15)gcG>gcA	p.A5A	NLRP2_ENST00000427260.2_Silent_p.A5A|NLRP2_ENST00000448584.2_Silent_p.A5A|NLRP2_ENST00000538819.1_Silent_p.A5A|NLRP2_ENST00000391721.4_Silent_p.A5A|NLRP2_ENST00000263437.6_Silent_p.A5A|NLRP2_ENST00000339757.7_Silent_p.A5A|NLRP2_ENST00000537859.1_Silent_p.A5A	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	5	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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)		TGTCTTCGGCGCAGATGGGCT	0.552													.|||	425	0.0848642	0.0212	0.1182	5008	,	,		21209	0.0417		0.2177	False		,,,				2504	0.0552				p.A5A		Atlas-SNP	.											.	NLRP2	161	.	0			c.G15A						PASS	.	G	,,,	180,4226	116.7+/-154.6	3,174,2026	83.0	74.0	77.0		15,15,15,15	-2.1	0.0	19	dbSNP_79	77	1705,6895	312.6+/-310.9	185,1335,2780	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	188,1509,4806	AA,AG,GG		19.8256,4.0853,14.4933	,,,	5/1063,5/1041,5/1040,5/1063	55481398	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon2			TTCGGCGCAGATG	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.15G>A	19.37:g.55481398G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001174082	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			G|0.872;A|0.128	0.128	strong		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
CREBRF	153222	hgsc.bcm.edu	37	5	172550204	172550204	+	Splice_Site	SNP	C	C	T	rs1129146	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:172550204C>T	ENST00000296953.2	+	8	2122	c.1803C>T	c.(1801-1803)ctC>ctT	p.L601L	CREBRF_ENST00000540014.1_Splice_Site_p.L603L	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	601					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAGATACTCTCGGTAAGAAGA	0.353													C|||	768	0.153355	0.3517	0.0749	5008	,	,		17090	0.0139		0.0736	False		,,,				2504	0.1667				p.L601L		Atlas-SNP	.											.	.	.	.	0			c.C1803T						PASS	.	C		1249,3157	425.7+/-340.9	180,889,1134	74.0	85.0	82.0		1803	-4.9	1.0	5	dbSNP_119	82	622,7978	160.8+/-213.9	22,578,3700	yes	coding-synonymous-near-splice	C5orf41	NM_153607.2		202,1467,4834	TT,TC,CC		7.2326,28.3477,14.3857		601/640	172550204	1871,11135	2203	4300	6503	SO:0001630	splice_region_variant	153222	exon8			TACTCTCGGTAAG	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"""luman/CREB3 recruitment factor"""		"""chromosome 5 open reading frame 41"""	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1804+1C>T	5.37:g.172550204C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_153607	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Silent	SNP	ENST00000296953.2	37	CCDS34293.1																																																																																			C|0.868;T|0.132	0.132	strong		0.353	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607	Silent
HERC4	26091	hgsc.bcm.edu	37	10	69773841	69773841	+	Silent	SNP	G	G	A	rs866255	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69773841G>A	ENST00000395198.3	-	9	1258	c.1011C>T	c.(1009-1011)agC>agT	p.S337S	HERC4_ENST00000277817.6_Silent_p.S227S|HERC4_ENST00000373700.4_Silent_p.S337S|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000412272.2_Silent_p.S337S	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	337					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						CAGTAAAGGGGCTTTTCCTGT	0.418													A|||	2601	0.519369	0.4039	0.4741	5008	,	,		16334	0.8413		0.331	False		,,,				2504	0.5695				p.S337S		Atlas-SNP	.											.	HERC4	78	.	0			c.C1011T						PASS	.	A	,	1694,2712	652.8+/-399.5	332,1030,841	104.0	99.0	101.0		1011,1011	2.1	1.0	10	dbSNP_86	101	2830,5770	675.1+/-403.2	460,1910,1930	no	coding-synonymous,coding-synonymous	HERC4	NM_015601.3,NM_022079.2	,	792,2940,2771	AA,AG,GG		32.907,38.4476,34.7839	,	337/1050,337/1058	69773841	4524,8482	2203	4300	6503	SO:0001819	synonymous_variant	26091	exon9			AAAGGGGCTTTTC	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.1011C>T	10.37:g.69773841G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Silent	SNP	ENST00000395198.3	37	CCDS41533.1																																																																																			G|0.595;A|0.405	0.405	strong		0.418	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
GDF5	8200	hgsc.bcm.edu	37	20	34022387	34022387	+	Missense_Mutation	SNP	A	A	C	rs224331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34022387A>C	ENST00000374372.1	-	4	1329	c.826T>G	c.(826-828)Tcc>Gcc	p.S276A	GDF5_ENST00000374369.3_Missense_Mutation_p.S276A|GDF5OS_ENST00000374375.1_Missense_Mutation_p.E144A			P43026	GDF5_HUMAN	growth differentiation factor 5	276			S -> A (in dbSNP:rs224331). {ECO:0000269|PubMed:7961761, ECO:0000269|Ref.4}.		cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			TCCAGCAAGGAGGCCGGCTGC	0.682													C|||	1923	0.383986	0.466	0.2608	5008	,	,		13219	0.2857		0.3539	False		,,,				2504	0.4928				p.S276A		Atlas-SNP	.											GDF5OS_ENST00000374375,NS,carcinoma,0,3	GDF5	66	3	0			c.T826G						PASS	.	C	ALA/SER	1790,2526		429,932,797	11.0	14.0	13.0		826	3.5	1.0	20	dbSNP_79	13	2951,5579		595,1761,1909	yes	missense	GDF5	NM_000557.2	99	1024,2693,2706	CC,CA,AA		34.5955,41.4736,36.9064	benign	276/502	34022387	4741,8105	2158	4265	6423	SO:0001583	missense	8200	exon2			GCAAGGAGGCCGG	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.826T>G	20.37:g.34022387A>C	ENSP00000363492:p.Ser276Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	733|733	0.3356227106227106|0.3356227106227106	221|221	0.4491869918699187|0.4491869918699187	105|105	0.2900552486187845|0.2900552486187845	137|137	0.2395104895104895|0.2395104895104895	270|270	0.3562005277044855|0.3562005277044855	C|C	8.146|8.146	0.786387|0.786387	0.16189|0.16189	0.414736|0.414736	0.345955|0.345955	ENSG00000204183|ENSG00000125965	ENST00000374375|ENST00000374369;ENST00000374372	.|T;T	.|0.64438	.|-0.1;-0.1	4.56|4.56	3.54|3.54	0.40534|0.40534	.|Transforming growth factor-beta, N-terminal (1);	.|0.399875	.|0.24606	.|N	.|0.037095	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	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.43442|0.43442	-0.9391|-0.9391	5|9	0.87932|0.09338	D|T	0|0.73	.|.	1.8889|1.8889	0.03243|0.03243	0.3052:0.4336:0.0:0.2612|0.3052:0.4336:0.0:0.2612	rs224331;rs3748436;rs224331|rs224331;rs3748436;rs224331	.|276	.|P43026	.|GDF5_HUMAN	A|A	144|276	.|ENSP00000363489:S276A;ENSP00000363492:S276A	ENSP00000363495:E144A|ENSP00000363489:S276A	E|S	+|-	2|1	0|0	GDF5OS|GDF5	33485801|33485801	0.974000|0.974000	0.33945|0.33945	1.000000|1.000000	0.80357|0.80357	0.917000|0.917000	0.54804|0.54804	1.594000|1.594000	0.36697|0.36697	1.145000|1.145000	0.42336|0.42336	-0.323000|-0.323000	0.08544|0.08544	GAG|TCC	A|0.641;C|0.359	0.359	strong		0.682	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
TMEM245	23731	hgsc.bcm.edu	37	9	111868885	111868885	+	Silent	SNP	G	G	A	rs2271878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111868885G>A	ENST00000374586.3	-	3	733	c.702C>T	c.(700-702)tcC>tcT	p.S234S		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	234						integral component of membrane (GO:0016021)											AGCCAGCCAGGGATGCTGCAA	0.353													G|||	990	0.197684	0.0166	0.3256	5008	,	,		13020	0.2937		0.2803	False		,,,				2504	0.1677				p.S234S		Atlas-SNP	.											.	.	.	.	0			c.C702T						PASS	.	G		192,3446		9,174,1636	47.0	42.0	43.0		702	0.9	1.0	9	dbSNP_100	43	2273,5879		299,1675,2102	no	coding-synonymous	C9orf5	NM_032012.3		308,1849,3738	AA,AG,GG		27.8827,5.2776,20.9075		234/880	111868885	2465,9325	1819	4076	5895	SO:0001819	synonymous_variant	23731	exon3			AGCCAGGGATGCT	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.702C>T	9.37:g.111868885G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	69	0.621622	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	37	CCDS43858.1																																																																																			G|0.789;A|0.211	0.211	strong		0.353	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
CLNK	116449	hgsc.bcm.edu	37	4	10502936	10502936	+	Missense_Mutation	SNP	G	G	A	rs190441710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:10502936G>A	ENST00000226951.6	-	18	1323	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C	CLNK_ENST00000515667.1_Missense_Mutation_p.R100C	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	362	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TCCAGGAAGCGTATTTTTACA	0.468													G|||	7	0.00139776	0.0	0.0	5008	,	,		19909	0.0		0.007	False		,,,				2504	0.0				p.R362C	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C1084T						PASS	.						82.0	78.0	79.0					4																	10502936		1884	4125	6009	SO:0001583	missense	116449	exon18			GGAAGCGTATTTT	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.1084C>T	4.37:g.10502936G>A	ENSP00000226951:p.Arg362Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	25.4	4.637615	0.87760	.	.	ENSG00000109684	ENST00000226951;ENST00000515667;ENST00000429087	D;D	0.89196	-2.48;-2.48	5.39	5.39	0.77823	SH2 motif (4);	0.000000	0.64402	D	0.000001	D	0.91439	0.7298	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92357	0.5894	10	0.87932	D	0	-20.0915	16.6639	0.85247	0.0:0.0:1.0:0.0	.	362	Q7Z7G1	CLNK_HUMAN	C	362;100;326	ENSP00000226951:R362C;ENSP00000427256:R100C	ENSP00000226951:R362C	R	-	1	0	CLNK	10112034	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.149000	0.89632	2.515000	0.84797	0.650000	0.86243	CGC	G|0.998;A|0.002	0.002	strong		0.468	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964	
GPM6A	2823	hgsc.bcm.edu	37	4	176573028	176573028	+	Silent	SNP	T	T	C	rs72702639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:176573028T>C	ENST00000280187.7	-	5	543	c.498A>G	c.(496-498)acA>acG	p.T166T	GPM6A_ENST00000393658.2_Silent_p.T166T|GPM6A_ENST00000515090.1_Silent_p.T159T|GPM6A_ENST00000506894.1_Silent_p.T155T	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	166					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CCTCCACTAATGTGGTGTTCC	0.458													T|||	138	0.0275559	0.0008	0.0072	5008	,	,		18223	0.0		0.0308	False		,,,				2504	0.1033				p.T166T		Atlas-SNP	.											.	GPM6A	70	.	0			c.A498G						PASS	.	T	,,	18,4388	25.3+/-52.1	1,16,2186	142.0	131.0	134.0		498,498,465	-11.2	0.0	4	dbSNP_130	134	174,8426	78.6+/-141.3	4,166,4130	no	coding-synonymous,coding-synonymous,coding-synonymous	GPM6A	NM_005277.3,NM_201591.1,NM_201592.1	,,	5,182,6316	CC,CT,TT		2.0233,0.4085,1.4762	,,	166/279,166/279,155/268	176573028	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	2823	exon4			CACTAATGTGGTG		CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.498A>G	4.37:g.176573028T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_201591	B7Z642|E9PHI5|Q92602	Silent	SNP	ENST00000280187.7	37	CCDS3824.1																																																																																			T|0.986;C|0.014	0.014	strong		0.458	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1		
ALS2CL	259173	hgsc.bcm.edu	37	3	46729757	46729757	+	Missense_Mutation	SNP	C	C	G	rs7642448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46729757C>G	ENST00000318962.4	-	3	216	c.133G>C	c.(133-135)Gag>Cag	p.E45Q	ALS2CL_ENST00000415953.1_Missense_Mutation_p.E45Q	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	45			E -> Q (in dbSNP:rs7642448). {ECO:0000269|PubMed:17974005}.		endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCAGGCACTCTCTGCCCCAG	0.617													C|||	2246	0.448482	0.736	0.3991	5008	,	,		20682	0.3046		0.3161	False		,,,				2504	0.3793				p.E45Q		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G133C						PASS	.	C	GLN/GLU,GLN/GLU	2839,1567	657.0+/-400.2	921,997,285	36.0	37.0	37.0		133,133	4.4	0.6	3	dbSNP_116	37	2641,5959	418.8+/-352.9	400,1841,2059	yes	missense,missense	ALS2CL	NM_001190707.1,NM_147129.3	29,29	1321,2838,2344	GG,GC,CC		30.7093,35.5651,42.1344	possibly-damaging,possibly-damaging	45/954,45/954	46729757	5480,7526	2203	4300	6503	SO:0001583	missense	259173	exon3			GGCACTCTCTGCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.133G>C	3.37:g.46729757C>G	ENSP00000313670:p.Glu45Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	875	0.40064102564102566	337	0.6849593495934959	146	0.40331491712707185	159	0.27797202797202797	233	0.3073878627968338	C	11.66	1.703594	0.30232	0.644349	0.307093	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.56275	0.47;0.47	4.36	4.36	0.52297	.	0.111814	0.39407	N	0.001379	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.9999999999980187	D	0.60575	0.988	P	0.52109	0.69	T	0.40739	-0.9547	9	0.39692	T	0.17	.	12.5671	0.56316	0.0:1.0:0.0:0.0	rs7642448;rs59127538;rs7642448	45	Q60I27	AL2CL_HUMAN	Q	45	ENSP00000313670:E45Q;ENSP00000413223:E45Q	ENSP00000313670:E45Q	E	-	1	0	ALS2CL	46704761	0.845000	0.29573	0.643000	0.29450	0.182000	0.23217	3.504000	0.53347	2.413000	0.81919	0.591000	0.81541	GAG	C|0.587;G|0.413	0.413	strong		0.617	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
MRPL39	54148	hgsc.bcm.edu	37	21	26969703	26969703	+	Silent	SNP	T	T	C	rs1135618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:26969703T>C	ENST00000352957.4	-	6	653	c.612A>G	c.(610-612)aaA>aaG	p.K204K	MRPL39_ENST00000307301.7_Silent_p.K204K	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	204						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						CATGAGCATCTTTTGTGAAGG	0.333													C|||	3670	0.732827	0.7284	0.8199	5008	,	,		16021	0.7153		0.8141	False		,,,				2504	0.6115				p.K204K		Atlas-SNP	.											.	MRPL39	61	.	0			c.A612G						PASS	.	C	,	3308,1092		1232,844,124	51.0	48.0	49.0		612,612	-1.6	1.0	21	dbSNP_86	49	7124,1476		2975,1174,151	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4207,2018,275	CC,CT,TT		17.1628,24.8182,19.7538	,	204/339,204/354	26969703	10432,2568	2200	4300	6500	SO:0001819	synonymous_variant	54148	exon6			AGCATCTTTTGTG	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.612A>G	21.37:g.26969703T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			T|0.220;C|0.780	0.780	strong		0.333	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
PIR	8544	hgsc.bcm.edu	37	X	15415583	15415583	+	Silent	SNP	C	C	T	rs8094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	128	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	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	
IFIT2	3433	hgsc.bcm.edu	37	10	91066460	91066460	+	Silent	SNP	T	T	A	rs954439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	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	
ZNF212	7988	hgsc.bcm.edu	37	7	148936878	148936878	+	Missense_Mutation	SNP	G	G	T	rs11548535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:148936878G>T	ENST00000335870.2	+	1	137	c.9G>T	c.(7-9)gaG>gaT	p.E3D		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	3					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)			endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			CCATGGCGGAGTCGGCGCCTG	0.736													G|||	343	0.0684904	0.0234	0.062	5008	,	,		11880	0.003		0.1352	False		,,,				2504	0.1329				p.E3D		Atlas-SNP	.											.	ZNF212	28	.	0			c.G9T						PASS	.	G	ASP/GLU	133,4113		4,125,1994	9.0	12.0	11.0		9	3.8	1.0	7	dbSNP_130	11	1070,7270		62,946,3162	no	missense	ZNF212	NM_012256.3	45	66,1071,5156	TT,TG,GG		12.8297,3.1324,9.5582	benign	3/496	148936878	1203,11383	2123	4170	6293	SO:0001583	missense	7988	exon1			GGCGGAGTCGGCG	U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"""Zinc fingers, C2H2-type"", ""-"""	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.9G>T	7.37:g.148936878G>T	ENSP00000338572:p.Glu3Asp	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	37	CCDS5896.1	141	0.06456043956043957	14	0.028455284552845527	22	0.06077348066298342	3	0.005244755244755245	102	0.1345646437994723	G	15.69	2.908566	0.52439	0.031324	0.128297	ENSG00000170260	ENST00000335870	T	0.09445	2.98	4.66	3.76	0.43208	.	0.000000	0.45867	D	0.000326	T	0.00073	0.0002	N	0.19112	0.55	0.32824	P	0.49688299999999996	B	0.22080	0.064	B	0.17979	0.02	T	0.33803	-0.9854	9	0.30854	T	0.27	-10.8146	10.8729	0.46894	0.0:0.1903:0.8097:0.0	.	3	Q9UDV6	ZN212_HUMAN	D	3	ENSP00000338572:E3D	ENSP00000338572:E3D	E	+	3	2	ZNF212	148567811	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.277000	0.51654	1.291000	0.44653	0.655000	0.94253	GAG	G|0.935;T|0.065	0.065	strong		0.736	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256	
LAMA4	3910	hgsc.bcm.edu	37	6	112457383	112457383	+	Missense_Mutation	SNP	G	G	C	rs1050349	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:112457383G>C	ENST00000230538.7	-	25	3753	c.3356C>G	c.(3355-3357)cCt>cGt	p.P1119R	LAMA4_ENST00000522006.1_Missense_Mutation_p.P1112R|LAMA4_ENST00000389463.4_Missense_Mutation_p.P1112R|LAMA4_ENST00000424408.2_Missense_Mutation_p.P1112R	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1119	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		P -> R (in dbSNP:rs1050349). {ECO:0000269|PubMed:7781776, ECO:0000269|PubMed:7959779, ECO:0000269|PubMed:8706685}.		blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AAGATGCACAGGGCCACCGCT	0.363													G|||	1054	0.210463	0.1233	0.2104	5008	,	,		19414	0.3601		0.2316	False		,,,				2504	0.1524				p.P1119R		Atlas-SNP	.											.	LAMA4	227	.	0			c.C3356G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO	649,3757	278.1+/-274.1	45,559,1599	131.0	118.0	123.0		3356,3335,3335	5.9	1.0	6	dbSNP_86	123	2239,6361	380.5+/-339.7	275,1689,2336	yes	missense,missense,missense	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	103,103,103	320,2248,3935	CC,CG,GG		26.0349,14.7299,22.2051	probably-damaging,probably-damaging,probably-damaging	1119/1824,1112/1817,1112/1817	112457383	2888,10118	2203	4300	6503	SO:0001583	missense	3910	exon25			TGCACAGGGCCAC		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.3356C>G	6.37:g.112457383G>C	ENSP00000230538:p.Pro1119Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	508	0.2326007326007326	65	0.13211382113821138	78	0.2154696132596685	200	0.34965034965034963	165	0.21767810026385223	G	18.62	3.663396	0.67700	0.147299	0.260349	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.103908	0.64402	D	0.000003	D	0.85340	0.5674	L	0.52573	1.65	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.989	T	0.81739	-0.0795	9	0.34782	T	0.22	.	20.3368	0.98748	0.0:0.0:1.0:0.0	rs1050349	1119;1112	Q16363;Q16363-2	LAMA4_HUMAN;.	R	1119;1112;1112;1112	ENSP00000230538:P1119R;ENSP00000429488:P1112R;ENSP00000374114:P1112R;ENSP00000416470:P1112R	ENSP00000230538:P1119R	P	-	2	0	LAMA4	112564076	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	9.026000	0.93700	2.805000	0.96524	0.655000	0.94253	CCT	G|0.773;C|0.227	0.227	strong		0.363	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
OR2L5	81466	hgsc.bcm.edu	37	1	248185951	248185951	+	Silent	SNP	A	A	G	rs12753585	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248185951A>G	ENST00000355281.1	+	1	702	c.702A>G	c.(700-702)aaA>aaG	p.K234K	OR2L13_ENST00000366478.2_Intron	NM_001258284.1	NP_001245213.1	Q8NG80	OR2L5_HUMAN	olfactory receptor, family 2, subfamily L, member 5	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										AAGGGAGGAAAAAGGCCTATT	0.498													N|||	39	0.00778754	0.0	0.0072	5008	,	,		23120	0.0		0.0239	False		,,,				2504	0.0102				p.K234K		Atlas-SNP	.											.	.	.	.	0			c.A702G						PASS	.																																			SO:0001819	synonymous_variant	81466	exon1			GAGGAAAAAGGCC		CCDS58068.1	1q44	2012-08-09		2004-03-10	ENSG00000197454	ENSG00000197454		"""GPCR / Class A : Olfactory receptors"""	15011	protein-coding gene	gene with protein product				OR2L11, OR2L5P			Standard	NM_001258284		Approved		uc031psy.1	Q8NG80	OTTHUMG00000040194	ENST00000355281.1:c.702A>G	1.37:g.248185951A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_001258284	Q6IF04	Silent	SNP	ENST00000355281.1	37	CCDS58068.1																																																																																			A|0.981;G|0.019	0.019	strong		0.498	OR2L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096851.1		
COL4A4	1286	hgsc.bcm.edu	37	2	227872995	227872995	+	Silent	SNP	T	T	C	rs2228555	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:227872995T>C	ENST00000396625.3	-	47	4755	c.4548A>G	c.(4546-4548)gtA>gtG	p.V1516V	COL4A4_ENST00000329662.7_Silent_p.V1513V	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1516	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|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(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCGTGCTAAATACGGGAAGGC	0.587													C|||	3208	0.640575	0.7761	0.5432	5008	,	,		20423	0.5982		0.5199	False		,,,				2504	0.6943				p.V1516V		Atlas-SNP	.											.	COL4A4	215	.	0			c.A4548G						PASS	.	C		3066,1150		1125,816,167	50.0	58.0	55.0		4548	2.2	0.1	2	dbSNP_98	55	4342,4090		1139,2064,1013	no	coding-synonymous	COL4A4	NM_000092.4		2264,2880,1180	CC,CT,TT		48.5057,27.277,41.4295		1516/1691	227872995	7408,5240	2108	4216	6324	SO:0001819	synonymous_variant	1286	exon47			GCTAAATACGGGA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4548A>G	2.37:g.227872995T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			T|0.294;G|0.193	.	strong		0.587	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
WDR18	57418	hgsc.bcm.edu	37	19	984533	984533	+	Silent	SNP	T	T	C	rs2301810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:984533T>C	ENST00000251289.5	+	1	203	c.180T>C	c.(178-180)aaT>aaC	p.N60N	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.N60N	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	37	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	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		
LRG1	116844	hgsc.bcm.edu	37	19	4538599	4538599	+	Missense_Mutation	SNP	G	G	A	rs966384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4538599G>A	ENST00000306390.6	-	2	857	c.397C>T	c.(397-399)Ccg>Tcg	p.P133S	LRG1_ENST00000586883.1_5'UTR|CTB-50L17.14_ENST00000586020.1_Intron	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	133			P -> S (in dbSNP:rs966384). {ECO:0000269|PubMed:15489334}.		brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGGCCCGGGGGCAGCCCG	0.632													G|||	1604	0.320288	0.0862	0.4467	5008	,	,		16078	0.5308		0.3618	False		,,,				2504	0.2873				p.P133S		Atlas-SNP	.											.	LRG1	25	.	0			c.C397T						PASS	.	G	SER/PRO	566,3826		41,484,1671	24.0	30.0	28.0		397	0.9	0.0	19	dbSNP_86	28	2767,5779		455,1857,1961	yes	missense	LRG1	NM_052972.2	74	496,2341,3632	AA,AG,GG		32.3777,12.8871,25.7613	benign	133/348	4538599	3333,9605	2196	4273	6469	SO:0001583	missense	116844	exon2			GGCCCGGGGGCAG		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"""leucine rich alpha 2 glycoprotein"""	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.397C>T	19.37:g.4538599G>A	ENSP00000302621:p.Pro133Ser	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_052972	Q8N4F5|Q96QZ4	Missense_Mutation	SNP	ENST00000306390.6	37	CCDS12130.1	770	0.3525641025641026	39	0.07926829268292683	168	0.46408839779005523	290	0.506993006993007	273	0.36015831134564646	.	4.933	0.173269	0.09391	0.128871	0.323777	ENSG00000171236	ENST00000306390	T	0.03524	3.9	4.71	0.948	0.19561	.	0.000000	0.40469	N	0.001098	T	0.00012	0.0000	L	0.38733	1.17	0.80722	P	0.0	B	0.30068	0.267	B	0.30495	0.116	T	0.32214	-0.9915	9	0.22109	T	0.4	-22.3111	6.9139	0.24349	0.0:0.3445:0.4527:0.2027	rs966384;rs17846084;rs17859086;rs57205193;rs966384	133	P02750	A2GL_HUMAN	S	133	ENSP00000302621:P133S	ENSP00000302621:P133S	P	-	1	0	LRG1	4489599	0.091000	0.21658	0.009000	0.14445	0.001000	0.01503	0.022000	0.13511	0.527000	0.28560	0.655000	0.94253	CCG	G|0.705;A|0.295	0.295	strong		0.632	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188603	32188603	+	Silent	SNP	C	C	T	rs520803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	119	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	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		
POTEF	728378	hgsc.bcm.edu	37	2	130872871	130872871	+	Silent	SNP	C	C	T	rs199770435		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:130872871C>T	ENST00000409914.2	-	4	951	c.552G>A	c.(550-552)ggG>ggA	p.G184G	POTEF_ENST00000361163.4_Silent_p.G184G|POTEF_ENST00000360967.5_Silent_p.G184G|POTEF_ENST00000357462.5_Silent_p.G184G	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	184					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G184G(2)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CTTCTGAATTCCCATTGGCAG	0.423																																					p.G184G		Atlas-SNP	.											POTEF,NS,carcinoma,0,5	POTEF	140	5	2	Substitution - coding silent(2)	prostate(2)	c.G552A						scavenged	.						45.0	53.0	50.0					2																	130872871		2105	4041	6146	SO:0001819	synonymous_variant	728378	exon4			TGAATTCCCATTG	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.552G>A	2.37:g.130872871C>T		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	361	29	0.0803324	NM_001099771	A6NC34	Silent	SNP	ENST00000409914.2	37	CCDS46409.1																																																																																			C|0.998;T|0.002	0.002	weak		0.423	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
HELQ	113510	hgsc.bcm.edu	37	4	84361121	84361121	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:84361121A>G	ENST00000295488.3	-	8	1865	c.1703T>C	c.(1702-1704)gTa>gCa	p.V568A	HELQ_ENST00000510985.1_Missense_Mutation_p.V501A	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	568	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						CACCAATGCTACCAAGTGATC	0.338								Other identified genes with known or suspected DNA repair function																													p.V568A		Atlas-SNP	.											HELQ,NS,carcinoma,-1,1	HELQ	95	1	0			c.T1703C						scavenged	.						93.0	92.0	92.0					4																	84361121		2203	4298	6501	SO:0001583	missense	113510	exon8			AATGCTACCAAGT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1703T>C	4.37:g.84361121A>G	ENSP00000295488:p.Val568Ala	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	349	5	0.0143266	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.558755	0.65538	.	.	ENSG00000163312	ENST00000295488;ENST00000510985	T;D	0.90563	-0.5;-2.69	5.79	4.61	0.57282	Helicase, C-terminal (1);	0.167823	0.52532	N	0.000075	D	0.90345	0.6979	L	0.59436	1.845	0.48040	D	0.999578	D;B	0.53885	0.963;0.034	P;B	0.50825	0.651;0.027	D	0.87474	0.2416	10	0.27082	T	0.32	.	11.5039	0.50454	0.9303:0.0:0.0697:0.0	.	501;568	E3W980;Q8TDG4	.;HELQ_HUMAN	A	568;501	ENSP00000295488:V568A;ENSP00000424539:V501A	ENSP00000295488:V568A	V	-	2	0	HELQ	84580145	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.310000	0.96267	1.026000	0.39733	0.533000	0.62120	GTA	.	.	none		0.338	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
OTUB2	78990	hgsc.bcm.edu	37	14	94510964	94510964	+	Silent	SNP	T	T	C	rs2273226	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:94510964T>C	ENST00000203664.5	+	5	545	c.336T>C	c.(334-336)gaT>gaC	p.D112D		NM_023112.3	NP_075601.1	Q96DC9	OTUB2_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 2	112	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				cellular amino acid metabolic process (GO:0006520)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)	5		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		TAGAGAAGGATGGCTCAGTGT	0.617													C|||	2455	0.490216	0.6853	0.5288	5008	,	,		18338	0.4306		0.4076	False		,,,				2504	0.3456				p.D112D		Atlas-SNP	.											.	OTUB2	10	.	0			c.T336C						PASS	.	C		2918,1488	475.9+/-357.4	954,1010,239	108.0	91.0	97.0		336	-1.3	0.9	14	dbSNP_100	97	3614,4986	626.2+/-397.8	770,2074,1456	no	coding-synonymous	OTUB2	NM_023112.3		1724,3084,1695	CC,CT,TT		42.0233,33.7721,49.777		112/235	94510964	6532,6474	2203	4300	6503	SO:0001819	synonymous_variant	78990	exon5			GAAGGATGGCTCA	AF318378	CCDS9917.1	14q32.13-q32.2	2014-02-24	2014-02-24	2004-05-28		ENSG00000089723		"""OTU domain containing"""	20351	protein-coding gene	gene with protein product		608338	"""chromosome 14 open reading frame 137"", ""OTU domain, ubiquitin aldehyde binding 2"""	C14orf137		12704427, 19996094	Standard	NM_023112		Approved	FLJ21916, MGC3102	uc001ych.4	Q96DC9		ENST00000203664.5:c.336T>C	14.37:g.94510964T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_023112	Q6IA10|Q9H6T1	Silent	SNP	ENST00000203664.5	37	CCDS9917.1																																																																																			T|0.488;C|0.512	0.512	strong		0.617	OTUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412855.1		
NMD3	51068	hgsc.bcm.edu	37	3	160956548	160956548	+	Silent	SNP	A	A	G	rs11539155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:160956548A>G	ENST00000460469.1	+	8	1142	c.687A>G	c.(685-687)caA>caG	p.Q229Q	NMD3_ENST00000472947.1_Silent_p.Q229Q|NMD3_ENST00000351193.2_Silent_p.Q229Q			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	229					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			TGATCTCTCAAGATATCCATA	0.294													A|||	275	0.0549121	0.0061	0.0591	5008	,	,		17776	0.0516		0.0308	False		,,,				2504	0.1462				p.Q229Q		Atlas-SNP	.											.	NMD3	49	.	0			c.A687G						PASS	.	A		48,4354	48.2+/-83.0	1,46,2154	100.0	100.0	100.0		687	-3.4	1.0	3	dbSNP_120	100	298,8296	107.6+/-168.3	5,288,4004	no	coding-synonymous	NMD3	NM_015938.3		6,334,6158	GG,GA,AA		3.4675,1.0904,2.6624		229/504	160956548	346,12650	2201	4297	6498	SO:0001819	synonymous_variant	51068	exon9			CTCTCAAGATATC	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.687A>G	3.37:g.160956548A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	305	110	0.360656	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	37	CCDS3194.1																																																																																			A|0.972;G|0.028	0.028	strong		0.294	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938	
SDHAF1	644096	hgsc.bcm.edu	37	19	36486509	36486509	+	Silent	SNP	C	C	G	rs76336581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36486509C>G	ENST00000378887.2	+	1	420	c.333C>G	c.(331-333)cgC>cgG	p.R111R		NM_001042631.2	NP_001036096			succinate dehydrogenase complex assembly factor 1																		CGGAGACCCGCCCCGACGGAC	0.721													G|||	234	0.0467252	0.0582	0.0562	5008	,	,		14200	0.0109		0.0517	False		,,,				2504	0.0562				p.R111R		Atlas-SNP	.											.	.	.	.	0			c.C333G						PASS	.	G		134,3692		1,132,1780	3.0	4.0	4.0		333	-2.9	0.0	19	dbSNP_132	4	249,7165		3,243,3461	no	coding-synonymous	SDHAF1	NM_001042631.2		4,375,5241	GG,GC,CC		3.3585,3.5024,3.4075		111/116	36486509	383,10857	1913	3707	5620	SO:0001819	synonymous_variant	644096	exon1			GACCCGCCCCGAC		CCDS32999.1	19q13.12	2014-06-05			ENSG00000205138	ENSG00000205138		"""Mitochondrial respiratory chain complex assembly factors"", ""LYR motif containing"""	33867	protein-coding gene	gene with protein product	"""LYR motif containing 8"""	612848				19465911	Standard	NM_001042631		Approved	LYRM8	uc002ocp.3	A6NFY7		ENST00000378887.2:c.333C>G	19.37:g.36486509C>G		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_001042631		Silent	SNP	ENST00000378887.2	37	CCDS32999.1																																																																																			C|0.958;G|0.042	0.042	strong		0.721	SDHAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457409.2	NM_001042631	
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:22038525G>T	ENST00000303532.1	-	1	350	c.351C>A	c.(349-351)acC>acA	p.T117T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	117						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)		AGGCCATTAGGGTGTAGAGGA	0.527													G|||	1822	0.363818	0.5371	0.2277	5008	,	,		21719	0.2966		0.3072	False		,,,				2504	0.3538				p.T117T		Atlas-SNP	.											.	OR10G3	40	.	0			c.C351A						PASS	.	G		2158,2248	583.6+/-385.9	549,1060,594	58.0	56.0	56.0		351	-3.3	0.1	14	dbSNP_120	56	2429,6171	401.1+/-347.0	347,1735,2218	no	coding-synonymous	OR10G3	NM_001005465.1		896,2795,2812	TT,TG,GG		28.2442,48.9787,35.2683		117/314	22038525	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			CATTAGGGTGTAG		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.351C>A	14.37:g.22038525G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			G|0.656;T|0.344	0.344	strong		0.527	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.L27L|IGLL5_ENST00000531372.1_Silent_p.L27L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>T	22.37:g.23230312C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	125	43	0.344	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
SLC25A5	292	hgsc.bcm.edu	37	X	118603844	118603844	+	Missense_Mutation	SNP	T	T	G	rs371749	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:118603844T>G	ENST00000317881.8	+	2	448	c.332T>G	c.(331-333)cTc>cGc	p.L111R	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	111			L -> R (in dbSNP:rs371749). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2168878, ECO:0000269|PubMed:3031073, ECO:0000269|PubMed:8918809}.		adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	CAGTTTTGGCTCTACTTTGCA	0.517													G|||	3064	0.811656	0.7489	0.5735	3775	,	,		10941	0.5188		0.5686	False		,,,				2504	0.5941				p.L111R		Atlas-SNP	.											.	SLC25A5	33	.	0			c.T332G						PASS	.						105.0	104.0	104.0					X																	118603844		2203	4300	6503	SO:0001583	missense	292	exon2			TTTGGCTCTACTT	BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"""Solute carriers"""	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.332T>G	X.37:g.118603844T>G	ENSP00000360671:p.Leu111Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	63	0.828947	NM_001152	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	37	CCDS14578.1	1274	0.7679324894514767	268	0.9370629370629371	145	0.6359649122807017	187	0.4844559585492228	302	0.5992063492063492	G	4.239	0.043209	0.08196	.	.	ENSG00000005022	ENST00000317881	T	0.80304	-1.36	4.35	4.35	0.52113	Mitochondrial carrier domain (2);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00427	-1.505	0.39232	P	0.036302999999999974	B	0.02656	0.0	B	0.01281	0.0	T	0.42832	-0.9428	9	0.02654	T	1	.	12.2673	0.54684	0.0:0.0:0.8282:0.1717	rs371749;rs3190903;rs17848741;rs17857454;rs58026331;rs371749	111	P05141	ADT2_HUMAN	R	111	ENSP00000360671:L111R	ENSP00000360671:L111R	L	+	2	0	SLC25A5	118487872	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.542000	0.82095	0.940000	0.37473	-0.253000	0.11424	CTC	T|0.185;G|0.815	0.815	strong		0.517	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152	
CDKN2D	1032	hgsc.bcm.edu	37	19	10676681	10676681	+	IGR	SNP	T	T	C	rs3218222	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10676681T>C	ENST00000393599.2	-	0	1422				KRI1_ENST00000361821.5_5'UTR|KRI1_ENST00000312962.6_Missense_Mutation_p.T5A|KRI1_ENST00000537964.1_5'UTR	NM_001800.3|NM_079421.2	NP_001791.1|NP_524145.1	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)						autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to retinoic acid (GO:0032526)|response to UV (GO:0009411)|response to vitamin D (GO:0033280)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)			endometrium(3)|lung(2)|ovary(1)	6			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			GGCATGGCGGTTCTGTGGCCC	0.706													C|||	3026	0.604233	0.7474	0.4741	5008	,	,		10642	0.3353		0.7773	False		,,,				2504	0.6022				p.T5A		Atlas-SNP	.											.	KRI1	65	.	0			c.A13G						PASS	.	C	ALA/THR	2546,602		1026,494,54	2.0	3.0	3.0		13	3.3	0.1	19	dbSNP_106	3	4779,1197		1926,927,135	yes	missense	KRI1	NM_023008.3	58	2952,1421,189	CC,CT,TT		20.0301,19.1233,19.7172	benign	5/710	10676681	7325,1799	1574	2988	4562	SO:0001628	intergenic_variant	65095	exon1			TGGCGGTTCTGTG		CCDS12244.1	19p13	2013-01-10				ENSG00000129355		"""Ankyrin repeat domain containing"""	1790	protein-coding gene	gene with protein product		600927				8575754	Standard	NM_079421		Approved	INK4D, p19	uc002mpa.3	P55273			19.37:g.10676681T>C		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_023008	Q13102|Q6FGE9	Missense_Mutation	SNP	ENST00000393599.2	37	CCDS12244.1	1350	0.6181318681318682	374	0.7601626016260162	193	0.5331491712707183	189	0.3304195804195804	594	0.783641160949868	N	0.054	-1.242595	0.01481	0.808767	0.799699	ENSG00000129347	ENST00000312962;ENST00000541101	T	0.05580	3.42	4.38	3.34	0.38264	.	0.806907	0.10336	N	0.686893	T	0.00012	0.0000	N	0.00237	-1.79	0.43326	P	0.004641000000000006	B	0.02656	0.0	B	0.01281	0.0	T	0.11348	-1.0591	8	.	.	.	-5.9339	6.3743	0.21499	0.0:0.6913:0.0:0.3087	rs3218222;rs3745243;rs58608125;rs3218222	5	Q8N9T8	KRI1_HUMAN	A	5	ENSP00000320917:T5A	.	T	-	1	0	KRI1	10537681	0.010000	0.17322	0.067000	0.19924	0.165000	0.22458	0.892000	0.28322	0.486000	0.27676	-0.338000	0.08134	ACC	T|0.386;C|0.614	0.614	strong		0.706	CDKN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452030.1	NM_079421	
KRT40	125115	hgsc.bcm.edu	37	17	39137154	39137154	+	Missense_Mutation	SNP	C	C	G	rs721958	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	81	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	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	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209816	84209816	+	Missense_Mutation	SNP	T	T	C	rs2288022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84209816T>C	ENST00000378553.5	+	11	2100	c.1976T>C	c.(1975-1977)cTa>cCa	p.L659P	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						TCTGGCCAGCTACTGATGCCC	0.562													C|||	1339	0.267372	0.0613	0.4049	5008	,	,		17071	0.375		0.3439	False		,,,				2504	0.2587				p.L659P		Atlas-SNP	.											.	DNAAF1	81	.	0			c.T1976C						PASS	.	C	PRO/LEU	480,3920	773.9+/-414.0	32,416,1752	36.0	33.0	34.0		1976	2.3	0.0	16	dbSNP_100	34	3017,5583	653.0+/-401.0	558,1901,1841	yes	missense	DNAAF1	NM_178452.4	98	590,2317,3593	CC,CT,TT		35.0814,10.9091,26.9	benign	659/726	84209816	3497,9503	2200	4300	6500	SO:0001583	missense	123872	exon11			GCCAGCTACTGAT	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.1976T>C	16.37:g.84209816T>C	ENSP00000367815:p.Leu659Pro	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	658	0.30128205128205127	36	0.07317073170731707	124	0.3425414364640884	237	0.4143356643356643	261	0.34432717678100266	C	0.017	-1.499376	0.01001	0.109091	0.350814	ENSG00000154099	ENST00000378553	T	0.19394	2.15	4.67	2.33	0.28932	.	1.269100	0.05886	N	0.627428	T	0.00012	0.0000	N	0.00583	-1.355	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45745	-0.9240	9	0.02654	T	1	1.8768	6.3052	0.21135	0.0:0.594:0.0:0.406	rs2288022;rs17845737;rs17858687	423;659	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	P	659	ENSP00000367815:L659P	ENSP00000367815:L659P	L	+	2	0	DNAAF1	82767317	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.001000	0.13038	0.156000	0.19299	-0.355000	0.07637	CTA	A|0.000;C|0.285;T|0.715	0.285	strong		0.562	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
CECR1	51816	hgsc.bcm.edu	37	22	17669306	17669306	+	Missense_Mutation	SNP	T	T	C	rs2231495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:17669306T>C	ENST00000399839.1	-	7	1274	c.1004A>G	c.(1003-1005)cAt>cGt	p.H335R	CECR1_ENST00000399837.2_Missense_Mutation_p.H335R|CECR1_ENST00000449907.2_Missense_Mutation_p.H293R|CECR1_ENST00000262607.3_Missense_Mutation_p.H335R|CECR1_ENST00000330232.4_Missense_Mutation_p.H94R|CECR1_ENST00000480276.1_5'Flank	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	335			H -> R (in dbSNP:rs2231495). {ECO:0000269|PubMed:10756095, ECO:0000269|PubMed:14702039}.		adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CTTGTAGTCATGCAAGGAGTG	0.612													T|||	1826	0.364617	0.5696	0.3156	5008	,	,		18402	0.2262		0.3211	False		,,,				2504	0.3098				p.H335R		Atlas-SNP	.											.	CECR1	77	.	0			c.A1004G						PASS	.	T	ARG/HIS,ARG/HIS	2411,1995	615.3+/-392.5	659,1093,451	84.0	68.0	73.0		1004,281	0.3	0.0	22	dbSNP_98	73	2864,5736	449.2+/-362.0	478,1908,1914	yes	missense,missense	CECR1	NM_017424.2,NM_177405.1	29,29	1137,3001,2365	CC,CT,TT		33.3023,45.2792,40.5582	benign,benign	335/512,94/271	17669306	5275,7731	2203	4300	6503	SO:0001583	missense	51816	exon6			TAGTCATGCAAGG	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1004A>G	22.37:g.17669306T>C	ENSP00000382733:p.His335Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	728	0.3333333333333333	258	0.524390243902439	99	0.27348066298342544	121	0.21153846153846154	250	0.32981530343007914	T	2.455	-0.325573	0.05350	0.547208	0.333023	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	4.24	0.283	0.15696	Adenosine/AMP deaminase (1);	0.345183	0.32640	N	0.005837	T	0.00012	0.0000	N	0.03948	-0.315	0.54753	P	1.3000000000040757E-5	B;B	0.29212	0.237;0.001	B;B	0.16289	0.015;0.0	T	0.46428	-0.9192	9	0.25751	T	0.34	.	2.3977	0.04394	0.5396:0.1884:0.0:0.272	rs2231495;rs61542193;rs2231495	335;94	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	R	335;94;335;293;335	ENSP00000382733:H335R;ENSP00000332871:H94R;ENSP00000262607:H335R;ENSP00000406443:H293R;ENSP00000382731:H335R	ENSP00000262607:H335R	H	-	2	0	CECR1	16049306	0.974000	0.33945	0.000000	0.03702	0.005000	0.04900	2.520000	0.45554	0.033000	0.15463	-0.527000	0.04329	CAT	T|0.627;C|0.373	0.373	strong		0.612	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
CUL2	8453	hgsc.bcm.edu	37	10	35321414	35321414	+	Silent	SNP	C	C	T	rs16935840	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:35321414C>T	ENST00000374748.1	-	13	1432	c.1119G>A	c.(1117-1119)acG>acA	p.T373T	CUL2_ENST00000374746.1_Silent_p.T373T|CUL2_ENST00000374749.3_Silent_p.T373T|CUL2_ENST00000602371.1_Silent_p.T316T|CUL2_ENST00000537177.1_Silent_p.T392T|CUL2_ENST00000374742.1_Silent_p.T373T|CUL2_ENST00000374751.3_Silent_p.T373T			Q13617	CUL2_HUMAN	cullin 2	373					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TTACAACTGACGTAAGGGCCT	0.363													C|||	748	0.149361	0.0348	0.1945	5008	,	,		15135	0.255		0.1849	False		,,,				2504	0.1268				p.T392T		Atlas-SNP	.											.	CUL2	63	.	0			c.G1176A						PASS	.	C	,,,	217,4189	131.8+/-168.3	7,203,1993	80.0	82.0	82.0		1119,1176,1158,1119	-6.1	0.9	10	dbSNP_123	82	1431,7169	274.3+/-291.2	117,1197,2986	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUL2	NM_001198777.1,NM_001198778.1,NM_001198779.1,NM_003591.3	,,,	124,1400,4979	TT,TC,CC		16.6395,4.9251,12.6711	,,,	373/746,392/765,386/759,373/746	35321414	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	8453	exon12			AACTGACGTAAGG	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1119G>A	10.37:g.35321414C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Silent	SNP	ENST00000374748.1	37	CCDS7179.1																																																																																			C|0.867;T|0.133	0.133	strong		0.363	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591	
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40627845G>A	ENST00000559313.1	-	11	1134	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	C15orf52_ENST00000397536.2_Silent_p.S163S	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	373							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GCTCCATCCCGCTCTGCTTCT	0.647													G|||	733	0.146366	0.0855	0.1686	5008	,	,		17103	0.0278		0.2803	False		,,,				2504	0.1973				p.S373S		Atlas-SNP	.											.	C15orf52	47	.	0			c.C1119T						PASS	.	G		443,3913		25,393,1760	43.0	44.0	44.0		1119	0.1	0.0	15	dbSNP_129	44	2221,6283		313,1595,2344	no	coding-synonymous	C15orf52	NM_207380.2		338,1988,4104	AA,AG,GG		26.1171,10.1699,20.7154		373/535	40627845	2664,10196	2178	4252	6430	SO:0001819	synonymous_variant	388115	exon11			CATCCCGCTCTGC	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.1119C>T	15.37:g.40627845G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Silent	SNP	ENST00000559313.1	37	CCDS10055.2																																																																																			G|0.836;A|0.164	0.164	strong		0.647	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
TAB2	23118	hgsc.bcm.edu	37	6	149730846	149730846	+	Silent	SNP	G	G	A	rs652921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:149730846G>A	ENST00000367456.1	+	8	2650	c.2073G>A	c.(2071-2073)agG>agA	p.R691R	TAB2_ENST00000536230.1_Silent_p.R659R|TAB2_ENST00000286332.5_Silent_p.R691R|TAB2_ENST00000538427.1_Silent_p.R691R			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	691					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|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)|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 protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|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)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						AGATGCCAAGGCATTTCTGAG	0.428													G|||	1089	0.217452	0.0552	0.2507	5008	,	,		19114	0.5496		0.0944	False		,,,				2504	0.1973				p.R691R		Atlas-SNP	.											.	TAB2	55	.	0			c.G2073A						PASS	.	G		276,4130	155.9+/-189.0	7,262,1934	153.0	143.0	146.0		2073	5.9	1.0	6	dbSNP_83	146	909,7691	203.0+/-246.1	53,803,3444	no	coding-synonymous	TAB2	NM_015093.4		60,1065,5378	AA,AG,GG		10.5698,6.2642,9.1112		691/694	149730846	1185,11821	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon9			GCCAAGGCATTTC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.2073G>A	6.37:g.149730846G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	55	0.572917	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			G|0.850;A|0.150	0.150	strong		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
WDR63	126820	hgsc.bcm.edu	37	1	85594392	85594392	+	Splice_Site	SNP	T	T	C	rs2305930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85594392T>C	ENST00000294664.6	+	21	2499	c.2319T>C	c.(2317-2319)tcT>tcC	p.S773S	WDR63_ENST00000370596.1_Splice_Site_p.S734S|WDR63_ENST00000326813.8_Splice_Site_p.S734S	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	773										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		AATTTTCAGCTAAACAGCAAT	0.333													T|||	263	0.052516	0.0023	0.0418	5008	,	,		19327	0.1429		0.0686	False		,,,				2504	0.0184				p.S773S		Atlas-SNP	.											.	WDR63	91	.	0			c.T2319C						PASS	.	T		44,4360	45.3+/-79.5	0,44,2158	58.0	58.0	58.0		2319	0.2	1.0	1	dbSNP_100	58	569,8029	152.8+/-207.3	16,537,3746	yes	coding-synonymous-near-splice	WDR63	NM_145172.3		16,581,5904	CC,CT,TT		6.6178,0.9991,4.7147		773/892	85594392	613,12389	2202	4299	6501	SO:0001630	splice_region_variant	126820	exon21			TTCAGCTAAACAG		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2318-1T>C	1.37:g.85594392T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_145172	A8K988|Q96L72|Q96NU4	Silent	SNP	ENST00000294664.6	37	CCDS702.1																																																																																			T|0.947;C|0.053	0.053	strong		0.333	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	Silent
GDI2	2665	hgsc.bcm.edu	37	10	5808086	5808086	+	Silent	SNP	G	G	A	rs1129614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5808086G>A	ENST00000380191.4	-	11	1511	c.1221C>T	c.(1219-1221)acC>acT	p.T407T	GDI2_ENST00000380181.3_Silent_p.T362T|GDI2_ENST00000479928.1_5'UTR|GDI2_ENST00000380132.4_Silent_p.T411T	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	407					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						CAAAATGAGTGGTGGCATCAT	0.393													G|||	687	0.137181	0.0719	0.2378	5008	,	,		21975	0.1389		0.1879	False		,,,				2504	0.1002				p.T407T		Atlas-SNP	.											.	GDI2	26	.	0			c.C1221T						PASS	.	G	,	340,4066	178.7+/-207.4	14,312,1877	154.0	138.0	143.0		1086,1221	2.1	1.0	10	dbSNP_86	143	1791,6809	322.6+/-315.6	191,1409,2700	no	coding-synonymous,coding-synonymous	GDI2	NM_001115156.1,NM_001494.3	,	205,1721,4577	AA,AG,GG		20.8256,7.7167,16.3847	,	362/401,407/446	5808086	2131,10875	2203	4300	6503	SO:0001819	synonymous_variant	2665	exon11			ATGAGTGGTGGCA	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"""rab GDP-dissociation"""	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.1221C>T	10.37:g.5808086G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	181	101	0.558011	NM_001494	O43928|Q5SX88|Q9UQM6	Silent	SNP	ENST00000380191.4	37	CCDS7071.1	367	0.16804029304029305	37	0.07520325203252033	91	0.2513812154696133	96	0.16783216783216784	143	0.18865435356200527	G	7.169	0.587236	0.13812	0.077167	0.208256	ENSG00000057608	ENST00000380153;ENST00000447751	.	.	.	5.78	2.06	0.26882	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.07065	-1.0792	4	0.87932	D	0	-16.8514	10.1725	0.42920	0.0:0.0728:0.5546:0.3727	rs1129614;rs2230284;rs17143301;rs61630631;rs1129614	.	.	.	L	192;187	.	ENSP00000369498:P192L	P	-	2	0	GDI2	5848092	0.932000	0.31603	0.998000	0.56505	0.089000	0.18198	-0.116000	0.10724	0.099000	0.17552	-0.474000	0.04947	CCA	G|0.842;A|0.158	0.158	strong		0.393	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494	
TMEM189-UBE2V1	387522	hgsc.bcm.edu	37	20	48746189	48746189	+	Silent	SNP	C	C	T	rs6122878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:48746189C>T	ENST00000341698.2	-	4	371	c.372G>A	c.(370-372)ccG>ccA	p.P124P	TMEM189_ENST00000371650.5_Silent_p.P121P|TMEM189_ENST00000371656.2_Silent_p.P49P|TMEM189_ENST00000371652.4_Silent_p.P124P|TMEM189_ENST00000557021.1_Silent_p.P124P	NM_001257399.1	NP_001244328.1			TMEM189-UBE2V1 readthrough											breast(1)|endometrium(4)|large_intestine(6)|lung(6)	17			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			TGATAGCTGTCGGGTCAATGT	0.597													C|||	1438	0.287141	0.3238	0.255	5008	,	,		18263	0.25		0.2863	False		,,,				2504	0.2996				p.P124P		Atlas-SNP	.											.	TMEM189	15	.	0			c.G372A						PASS	.	C	,,	1335,3071	447.3+/-348.3	205,925,1073	219.0	182.0	195.0		363,372,372	-10.5	0.5	20	dbSNP_114	195	2336,6264	392.2+/-343.9	337,1662,2301	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM189,TMEM189-UBE2V1	NM_001162505.1,NM_199129.2,NM_199203.2	,,	542,2587,3374	TT,TC,CC		27.1628,30.2996,28.2254	,,	121/268,124/271,124/371	48746189	3671,9335	2203	4300	6503	SO:0001819	synonymous_variant	387521	exon4			AGCTGTCGGGTCA	U39361	CCDS13424.1	20q13.13	2011-05-31			ENSG00000124208	ENSG00000124208			33521	other	readthrough						11076860	Standard	NM_199203		Approved	Kua-UEV, CROC-1B	uc002xvf.3		OTTHUMG00000033085	ENST00000341698.2:c.372G>A	20.37:g.48746189C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	51	0.927273	NM_199129		Silent	SNP	ENST00000341698.2	37	CCDS13424.1																																																																																			C|0.712;T|0.288	0.288	strong		0.597	TMEM189-UBE2V1-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000080532.5		
EEF2	1938	hgsc.bcm.edu	37	19	3983184	3983184	+	Silent	SNP	A	A	G	rs2230560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3983184A>G	ENST00000309311.6	-	3	412	c.324T>C	c.(322-324)caT>caC	p.H108H	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	108	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)	p.H108H(1)		endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAAGTCGACATGCCCGGGGG	0.592													G|||	1280	0.255591	0.6566	0.1009	5008	,	,		19536	0.0615		0.1034	False		,,,				2504	0.18				p.H108H	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											EEF2,NS,carcinoma,0,2	EEF2	57	2	1	Substitution - coding silent(1)	stomach(1)	c.T324C						PASS	.	G		2482,1924	546.6+/-377.1	709,1064,430	109.0	108.0	109.0		324	-2.8	0.1	19	dbSNP_98	109	846,7754	780.5+/-407.7	37,772,3491	no	coding-synonymous	EEF2	NM_001961.3		746,1836,3921	GG,GA,AA		9.8372,43.6677,25.5882		108/859	3983184	3328,9678	2203	4300	6503	SO:0001819	synonymous_variant	1938	exon3			GTCGACATGCCCG	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.324T>C	19.37:g.3983184A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			T|0.000;G|0.239;C|0.000;A|0.760	0.239	strong		0.592	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549428	32549428	+	Silent	SNP	G	G	T	rs113663708	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549428G>T	ENST00000360004.5	-	3	663	c.558C>A	c.(556-558)acC>acA	p.T186T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	186	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)|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						GCATCACCAGGGTCTGGAAGG	0.562										Multiple Myeloma(14;0.17)																											p.T186T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C558A						PASS	.						144.0	157.0	153.0					6																	32549428		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			CACCAGGGTCTGG	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.558C>A	6.37:g.32549428G>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	251	20	0.0796813	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.989;T|0.011	0.011	strong		0.562	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PPEF2	5470	hgsc.bcm.edu	37	4	76811175	76811175	+	Missense_Mutation	SNP	G	G	T	rs28436183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:76811175G>T	ENST00000286719.7	-	5	708	c.352C>A	c.(352-354)Cgc>Agc	p.R118S	PPEF2_ENST00000510607.1_5'Flank	NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	118				R -> S (in Ref. 1; AAB82796/AAB82797). {ECO:0000305}.	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)			AAGGAGAGGCGTGGCCCCGTG	0.537													G|||	486	0.0970447	0.1301	0.0937	5008	,	,		20469	0.0079		0.1571	False		,,,				2504	0.0849				p.R118S	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.C352A						PASS	.	G	SER/ARG	458,3948	218.4+/-236.5	41,376,1786	248.0	216.0	227.0		352	4.8	1.0	4	dbSNP_125	227	1456,7144	277.8+/-293.0	135,1186,2979	yes	missense	PPEF2	NM_006239.2	110	176,1562,4765	TT,TG,GG		16.9302,10.3949,14.7163	probably-damaging	118/754	76811175	1914,11092	2203	4300	6503	SO:0001583	missense	5470	exon5			AGAGGCGTGGCCC	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.352C>A	4.37:g.76811175G>T	ENSP00000286719:p.Arg118Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	229	0.10485347985347986	73	0.1483739837398374	33	0.09116022099447514	6	0.01048951048951049	117	0.15435356200527706	G	20.1	3.938625	0.73557	0.103949	0.169302	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.48522	0.81	4.8	4.8	0.61643	Serine/threonine phosphatase, PPP5 (1);	0.315459	0.35436	N	0.003216	T	0.00300	0.0009	M	0.84948	2.725	0.25320	P	0.9891248	B;P	0.45902	0.427;0.868	B;P	0.47075	0.171;0.536	T	0.17561	-1.0365	9	0.72032	D	0.01	-1.5701	15.3613	0.74478	0.0:0.0:1.0:0.0	rs28436183	118;118	O14830-2;O14830	.;PPE2_HUMAN	S	118	ENSP00000286719:R118S	ENSP00000286719:R118S	R	-	1	0	PPEF2	77030199	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	9.230000	0.95299	2.227000	0.72691	0.313000	0.20887	CGC	G|0.859;T|0.141	0.141	strong		0.537	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983483	2983483	+	Silent	SNP	C	C	G	rs2074362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2983483C>G	ENST00000253928.9	+	5	1554	c.1149C>G	c.(1147-1149)ctC>ctG	p.L383L	FLYWCH1_ENST00000416288.2_Silent_p.L382L|FLYWCH1_ENST00000399667.2_Silent_p.L383L			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	59	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	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	
IL33	90865	hgsc.bcm.edu	37	9	6254467	6254467	+	Missense_Mutation	SNP	G	G	A	rs148943384		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:6254467G>A	ENST00000381434.3	+	6	539	c.526G>A	c.(526-528)Ggt>Agt	p.G176S	IL33_ENST00000417746.2_Missense_Mutation_p.G50S|IL33_ENST00000456383.2_Missense_Mutation_p.G134S	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	176					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		GTAAGGTGACGGTGTTGATGG	0.333																																					p.G176S		Atlas-SNP	.											.	IL33	27	.	0			c.G526A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	73.0	69.0	71.0		400,148,526	1.6	0.0	9	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	IL33	NM_001199640.1,NM_001199641.1,NM_033439.3	56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	134/229,50/145,176/271	6254467	1,13005	2203	4300	6503	SO:0001583	missense	90865	exon7			GGTGACGGTGTTG	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.526G>A	9.37:g.6254467G>A	ENSP00000370842:p.Gly176Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919265	0.52546	0.0	1.16E-4	ENSG00000137033	ENST00000417746;ENST00000456383;ENST00000381434	T;T;T	0.51817	0.69;0.69;0.69	4.47	1.57	0.23409	.	2.047450	0.01906	N	0.039500	T	0.35653	0.0939	L	0.29908	0.895	0.80722	D	1	B;B;B	0.26602	0.06;0.154;0.06	B;B;B	0.13407	0.005;0.009;0.009	T	0.33727	-0.9857	10	0.72032	D	0.01	0.2295	3.6079	0.08049	0.2088:0.0:0.5934:0.1978	.	50;134;176	B4DJ35;B4E1Q9;O95760	.;.;IL33_HUMAN	S	50;134;176	ENSP00000394039:G50S;ENSP00000414238:G134S;ENSP00000370842:G176S	ENSP00000370842:G176S	G	+	1	0	IL33	6244467	0.020000	0.18652	0.000000	0.03702	0.032000	0.12392	0.634000	0.24614	0.227000	0.20999	0.655000	0.94253	GGT	G|1.000;A|0.000	0.000	weak		0.333	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
FGD6	55785	hgsc.bcm.edu	37	12	95502303	95502303	+	Silent	SNP	G	G	A	rs11107896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:95502303G>A	ENST00000343958.4	-	10	3391	c.3168C>T	c.(3166-3168)caC>caT	p.H1056H	FGD6_ENST00000549499.1_Silent_p.H1056H|FGD6_ENST00000546711.1_Silent_p.H1056H	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1056	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|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)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TGTCATTGGCGTGGTTGGCTA	0.428													G|||	524	0.104633	0.0862	0.1484	5008	,	,		21293	0.1488		0.0577	False		,,,				2504	0.1012				p.H1056H		Atlas-SNP	.											.	FGD6	127	.	0			c.C3168T						PASS	.	G		343,4063	179.0+/-207.6	14,315,1874	164.0	129.0	141.0		3168	-0.4	1.0	12	dbSNP_120	141	633,7967	163.2+/-215.8	24,585,3691	no	coding-synonymous	FGD6	NM_018351.3		38,900,5565	AA,AG,GG		7.3605,7.7848,7.5042		1056/1431	95502303	976,12030	2203	4300	6503	SO:0001819	synonymous_variant	55785	exon10			ATTGGCGTGGTTG	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3168C>T	12.37:g.95502303G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	71	0.581967	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			G|0.906;A|0.094	0.094	strong		0.428	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
OLFM2	93145	hgsc.bcm.edu	37	19	9968434	9968434	+	Missense_Mutation	SNP	C	C	T	rs2303100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9968434C>T	ENST00000264833.4	-	3	502	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	OLFM2_ENST00000590841.1_Missense_Mutation_p.R28Q	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	106			R -> Q (in dbSNP:rs2303100). {ECO:0000269|Ref.1}.		protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						TGCCCGGAGCCGCGCATCCAG	0.597													C|||	1555	0.310503	0.0401	0.5403	5008	,	,		19097	0.3095		0.5427	False		,,,				2504	0.2751				p.R106Q		Atlas-SNP	.											.	OLFM2	42	.	0			c.G317A	GRCh37	CM066940	OLFM2	M	rs2303100	PASS	.	C	GLN/ARG	564,3842	250.6+/-257.6	43,478,1682	45.0	47.0	47.0		317	3.9	0.9	19	dbSNP_100	47	4718,3882	605.1+/-394.9	1298,2122,880	yes	missense	OLFM2	NM_058164.2	43	1341,2600,2562	TT,TC,CC		45.1395,12.8007,40.612	possibly-damaging	106/455	9968434	5282,7724	2203	4300	6503	SO:0001583	missense	93145	exon3			CGGAGCCGCGCAT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.317G>A	19.37:g.9968434C>T	ENSP00000264833:p.Arg106Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	66	0.970588	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1	816	0.37362637362637363	26	0.052845528455284556	195	0.5386740331491713	180	0.3146853146853147	415	0.5474934036939314	C	15.68	2.904240	0.52333	0.128007	0.548605	ENSG00000105088	ENST00000264833	T	0.46063	0.88	3.92	3.92	0.45320	.	0.063680	0.64402	D	0.000012	T	0.00012	0.0000	L	0.36672	1.1	0.37247	P	0.09359600000000001	P	0.51147	0.942	B	0.40444	0.329	T	0.48681	-0.9014	8	.	.	.	.	7.3267	0.26560	0.0:0.8818:0.0:0.1182	rs2303100;rs12983966;rs17795374;rs2303100	106	O95897	NOE2_HUMAN	Q	106	ENSP00000264833:R106Q	.	R	-	2	0	OLFM2	9829434	0.761000	0.28439	0.942000	0.38095	0.791000	0.44710	1.246000	0.32803	2.025000	0.59659	0.313000	0.20887	CGG	C|0.622;T|0.378	0.378	strong		0.597	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
HDAC10	83933	hgsc.bcm.edu	37	22	50686371	50686371	+	Missense_Mutation	SNP	C	C	T	rs34402301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50686371C>T	ENST00000216271.5	-	13	1637	c.1285G>A	c.(1285-1287)Gtc>Atc	p.V429I	TUBGCP6_ENST00000439308.2_5'Flank|HDAC10_ENST00000498366.1_5'UTR|HDAC10_ENST00000349505.4_Missense_Mutation_p.V409I|HDAC10_ENST00000448072.1_Missense_Mutation_p.V379I|MAPK12_ENST00000497036.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	429			V -> I (in dbSNP:rs34402301).		chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|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)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		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)		TGTTGGATGACGTCAGGGGGC	0.657													C|||	96	0.0191693	0.003	0.0432	5008	,	,		20936	0.0		0.0557	False		,,,				2504	0.0061				p.V429I		Atlas-SNP	.											.	HDAC10	29	.	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	48,4358	47.5+/-82.1	0,48,2155	40.0	37.0	38.0		1225,1285	1.1	0.0	22	dbSNP_126	38	516,8084	143.6+/-199.6	21,474,3805	yes	missense,missense	HDAC10	NM_001159286.1,NM_032019.5	29,29	21,522,5960	TT,TC,CC		6.0,1.0894,4.3365	probably-damaging,probably-damaging	409/650,429/670	50686371	564,12442	2203	4300	6503	SO:0001583	missense	83933	exon13			GGATGACGTCAGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1285G>A	22.37:g.50686371C>T	ENSP00000216271:p.Val429Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	64	0.029304029304029304	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	44	0.05804749340369393	C	13.95	2.388992	0.42308	0.010894	0.06	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.29397	1.57;1.57;1.57	4.33	1.1	0.20463	.	1.989150	0.03993	N	0.295219	T	0.05777	0.0151	M	0.76574	2.34	0.20403	N	0.99991	D;P;D;D;D	0.61697	0.99;0.928;0.969;0.957;0.982	P;B;P;B;B	0.47705	0.555;0.225;0.453;0.399;0.352	T	0.09684	-1.0663	10	0.23891	T	0.37	-16.585	6.0518	0.19789	0.0:0.6718:0.0:0.3282	rs34402301	409;419;379;429;429	Q969S8-2;E2QRD2;C9J8B8;Q969S8-4;Q969S8	.;.;.;.;HDA10_HUMAN	I	429;379;409	ENSP00000216271:V429I;ENSP00000397542:V379I;ENSP00000343540:V409I	ENSP00000216271:V429I	V	-	1	0	HDAC10	49028498	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.055000	0.14229	0.204000	0.20548	0.591000	0.81541	GTC	C|0.961;T|0.039	0.039	strong		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
RYR3	6263	hgsc.bcm.edu	37	15	34137131	34137131	+	Silent	SNP	G	G	A	rs118177681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:34137131G>A	ENST00000389232.4	+	93	13435	c.13365G>A	c.(13363-13365)gaG>gaA	p.E4455E	RYR3_ENST00000415757.3_Silent_p.E4450E	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4455					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)		TTAATGACGAGGAAGAGGAAG	0.463													G|||	42	0.00838658	0.0	0.013	5008	,	,		19806	0.0		0.006	False		,,,				2504	0.0276				p.E4455E		Atlas-SNP	.											.	RYR3	760	.	0			c.G13365A						PASS	.	G		11,3879		0,11,1934	135.0	126.0	129.0		13365	-0.3	1.0	15	dbSNP_132	129	88,8196		0,88,4054	no	coding-synonymous	RYR3	NM_001036.3		0,99,5988	AA,AG,GG		1.0623,0.2828,0.8132		4455/4871	34137131	99,12075	1945	4142	6087	SO:0001819	synonymous_variant	6263	exon93			TGACGAGGAAGAG		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.13365G>A	15.37:g.34137131G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.993;A|0.007	0.007	strong		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
C21orf33	8209	hgsc.bcm.edu	37	21	45553596	45553596	+	Missense_Mutation	SNP	T	T	C	rs968714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45553596T>C	ENST00000291577.6	+	1	110	c.17T>C	c.(16-18)gTc>gCc	p.V6A	C21orf33_ENST00000427803.2_Missense_Mutation_p.V6A|C21orf33_ENST00000493883.1_3'UTR|C21orf33_ENST00000348499.5_Missense_Mutation_p.V6A	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	6			V -> A (in dbSNP:rs968714). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8753807, ECO:0000269|PubMed:8975701, ECO:0000269|PubMed:9150728}.			mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		GCTGTGAGGGTCCTGGTGGCC	0.692													C|||	2964	0.591853	0.3139	0.6816	5008	,	,		13909	0.7004		0.8211	False		,,,				2504	0.5562				p.V6A		Atlas-SNP	.											C21orf33,NS,carcinoma,0,1	C21orf33	23	1	0			c.T17C						scavenged	.	C	ALA/VAL,ALA/VAL	1627,2771		334,959,906	29.0	23.0	25.0		17,17	-1.3	0.0	21	dbSNP_86	25	6925,1665		2843,1239,213	yes	missense,missense	C21orf33	NM_198155.3,NM_004649.6	64,64	3177,2198,1119	CC,CT,TT		19.383,36.9941,34.1546	benign,benign	6/238,6/269	45553596	8552,4436	2199	4295	6494	SO:0001583	missense	8209	exon1			TGAGGGTCCTGGT	Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.17T>C	21.37:g.45553596T>C	ENSP00000291577:p.Val6Ala	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	164	60	0.365854	NM_198155	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	37	CCDS33580.1	1441	0.6597985347985348	166	0.33739837398373984	255	0.7044198895027625	403	0.7045454545454546	617	0.8139841688654353	C	2.537	-0.307097	0.05458	0.369941	0.80617	ENSG00000160221	ENST00000291577;ENST00000427803;ENST00000348499	T;T;T	0.35048	1.87;1.33;1.85	3.96	-1.32	0.09201	.	0.993292	0.08177	N	0.986026	T	0.00012	0.0000	N	0.02142	-0.665	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37361	-0.9709	9	0.02654	T	1	-0.2574	8.8345	0.35104	0.0:0.348:0.0:0.652	rs968714;rs17844987;rs17856059;rs17857746;rs58914271;rs968714	6;6	P30042-2;P30042	.;ES1_HUMAN	A	6	ENSP00000291577:V6A;ENSP00000396655:V6A;ENSP00000344901:V6A	ENSP00000291577:V6A	V	+	2	0	C21orf33	44378024	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.246000	0.02896	-0.466000	0.06943	-0.974000	0.02594	GTC	T|0.378;C|0.622	0.622	strong		0.692	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649	
FGD2	221472	hgsc.bcm.edu	37	6	36988364	36988364	+	Silent	SNP	C	C	T	rs831504	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:36988364C>T	ENST00000274963.8	+	10	1341	c.1170C>T	c.(1168-1170)tcC>tcT	p.S390S		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	390	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						TCCTGGTGTCCGGGAAGCAGC	0.642													C|||	2793	0.557708	0.612	0.5548	5008	,	,		16624	0.4831		0.492	False		,,,				2504	0.6309				p.S390S		Atlas-SNP	.											.	FGD2	65	.	0			c.C1170T						PASS	.	C		2604,1802	611.4+/-391.8	773,1058,372	33.0	31.0	32.0		1170	-10.9	0.2	6	dbSNP_86	32	4259,4341	548.0+/-385.3	1058,2143,1099	no	coding-synonymous	FGD2	NM_173558.3		1831,3201,1471	TT,TC,CC		49.5233,40.8988,47.232		390/656	36988364	6863,6143	2203	4300	6503	SO:0001819	synonymous_variant	221472	exon10			GGTGTCCGGGAAG	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.1170C>T	6.37:g.36988364C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	37	CCDS4829.1																																																																																			C|0.467;T|0.533	0.533	strong		0.642	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56771251	56771251	+	Missense_Mutation	SNP	A	A	C	rs3772219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56771251A>C	ENST00000296315.3	-	8	1171	c.1003T>G	c.(1003-1005)Ttg>Gtg	p.L335V	ARHGEF3_ENST00000495373.1_Missense_Mutation_p.L335V|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.L306V|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.L367V|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.L341V|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.L341V	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	335	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		L -> V (in dbSNP:rs3772219). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		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)		TGACAACACAAGACTCGAGAG	0.468													A|||	2077	0.414736	0.5688	0.487	5008	,	,		17361	0.4206		0.2863	False		,,,				2504	0.2812				p.L367V		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.T1099G						PASS	.	A	VAL/LEU,VAL/LEU,VAL/LEU	2309,2097	603.2+/-390.1	593,1123,487	112.0	106.0	108.0		1099,1021,1003	0.5	1.0	3	dbSNP_107	108	2611,5989	423.7+/-354.4	405,1801,2094	yes	missense,missense,missense	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	32,32,32	998,2924,2581	CC,CA,AA		30.3605,47.5942,37.8287	benign,benign,benign	367/559,341/533,335/527	56771251	4920,8086	2203	4300	6503	SO:0001583	missense	50650	exon11			AACACAAGACTCG	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.1003T>G	3.37:g.56771251A>C	ENSP00000296315:p.Leu335Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	886	0.4056776556776557	261	0.5304878048780488	160	0.4419889502762431	234	0.4090909090909091	231	0.30474934036939316	A	16.61	3.170374	0.57584	0.524058	0.303605	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49	5.93	0.518	0.17030	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.75615	2.305	0.20489	P	0.99989088	B;B;B;B;P;B;B	0.37500	0.316;0.206;0.309;0.092;0.597;0.206;0.443	B;B;B;B;B;B;B	0.44224	0.191;0.191;0.351;0.125;0.444;0.191;0.351	T	0.44513	-0.9323	9	0.59425	D	0.04	-3.1857	6.604	0.22716	0.3714:0.167:0.4617:0.0	rs3772219;rs17665523;rs52814186;rs59143147;rs3772219	341;306;133;335;367;335;341	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	V	335;367;341;341;306;335	ENSP00000296315:L335V;ENSP00000341071:L367V;ENSP00000410922:L341V;ENSP00000420420:L341V;ENSP00000418826:L306V;ENSP00000417986:L335V	ENSP00000296315:L335V	L	-	1	2	ARHGEF3	56746291	0.970000	0.33590	0.996000	0.52242	0.995000	0.86356	0.940000	0.28992	0.023000	0.15187	0.454000	0.30748	TTG	C|0.390;N|0.000	0.390	strong		0.468	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
NUGGC	389643	hgsc.bcm.edu	37	8	27886903	27886903	+	Silent	SNP	C	C	T	rs9314357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:27886903C>T	ENST00000413272.2	-	17	2176	c.2034G>A	c.(2032-2034)acG>acA	p.T678T	NUGGC_ENST00000341513.6_Silent_p.T678T	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	678					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)										CTTTTTTGCCCGTGATCTGAG	0.547													C|||	1628	0.32508	0.4251	0.2939	5008	,	,		20199	0.1181		0.4274	False		,,,				2504	0.32				p.T678T		Atlas-SNP	.											.	.	.	.	0			c.G2034A						PASS	.	C		1663,2325		346,971,677	53.0	53.0	53.0		2034	-7.5	0.9	8	dbSNP_119	53	3648,4688		822,2004,1342	no	coding-synonymous	C8orf80	NM_001010906.1		1168,2975,2019	TT,TC,CC		43.762,41.7001,43.0948		678/797	27886903	5311,7013	1994	4168	6162	SO:0001819	synonymous_variant	389643	exon17			TTTGCCCGTGATC	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.2034G>A	8.37:g.27886903C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			C|0.663;T|0.337	0.337	strong		0.547	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
SH3BP1	23616	hgsc.bcm.edu	37	22	38039128	38039128	+	Silent	SNP	A	A	G	rs74516928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38039128A>G	ENST00000357436.4	+	6	733	c.420A>G	c.(418-420)aaA>aaG	p.K140K	SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000442465.2_Silent_p.K140K|SH3BP1_ENST00000336738.5_Silent_p.K140K|SH3BP1_ENST00000599616.1_Silent_p.K76K|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	140	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				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)					CCATCCTCAAACACAAGAAAA	0.627											OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	473	0.0944489	0.1641	0.0591	5008	,	,		13756	0.0139		0.0616	False		,,,				2504	0.1421				p.K140K		Atlas-SNP	.											SH3BP1,NS,carcinoma,0,1	SH3BP1	41	1	0			c.A420G						PASS	.	G		685,3717	733.1+/-410.4	53,579,1569	29.0	31.0	31.0		420	4.2	1.0	22	dbSNP_131	31	647,7949	768.5+/-407.6	29,589,3680	no	coding-synonymous	SH3BP1	NM_018957.3		82,1168,5249	GG,GA,AA		7.5268,15.5611,10.2477		140/702	38039128	1332,11666	2201	4298	6499	SO:0001819	synonymous_variant	23616	exon6			CCTCAAACACAAG		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.420A>G	22.37:g.38039128A>G		Somatic	31	0	0	875	WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			A|0.907;G|0.093	0.093	strong		0.627	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
ASAH1	427	hgsc.bcm.edu	37	8	17942204	17942204	+	5'Flank	SNP	C	C	T	rs13263632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17942204C>T	ENST00000262097.6	-	0	0				CTD-2547L16.1_ENST00000505114.2_RNA|CTD-2547L16.1_ENST00000499554.2_RNA|ASAH1_ENST00000381733.4_Missense_Mutation_p.S36N|CTD-2547L16.1_ENST00000521775.1_RNA|CTD-2547L16.1_ENST00000517798.1_RNA|ASAH1_ENST00000520781.1_5'Flank|ASAH1_ENST00000417108.2_5'Flank|ASAH1_ENST00000314146.10_Missense_Mutation_p.S36N|ASAH1_ENST00000520051.1_5'UTR|CTD-2547L16.1_ENST00000517747.1_RNA	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1						cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		CACAGCAAAGCTGCCAAATCC	0.587											OREG0018581	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	348	0.0694888	0.1536	0.0317	5008	,	,		16475	0.0298		0.0348	False		,,,				2504	0.0593				p.S36N		Atlas-SNP	.											.	ASAH1	71	.	0			c.G107A						PASS	.	C	ASN/SER,ASN/SER	640,3766		45,550,1608	50.0	50.0	50.0		107,107	0.2	0.0	8	dbSNP_121	50	416,8184		9,398,3893	yes	missense,missense	ASAH1	NM_001127505.1,NM_004315.4	46,46	54,948,5501	TT,TC,CC		4.8372,14.5256,8.1193	,	36/390,36/412	17942204	1056,11950	2203	4300	6503	SO:0001631	upstream_gene_variant	427	exon1			GCAAAGCTGCCAA	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997		8.37:g.17942204C>T	Exception_encountered	Somatic	40	0	0	721	WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	137	0.06272893772893773	76	0.15447154471544716	13	0.03591160220994475	17	0.02972027972027972	31	0.040897097625329816	.	8.884	0.952250	0.18431	0.145256	0.048372	ENSG00000104763	ENST00000381733;ENST00000314146	T;T	0.71461	-0.45;-0.57	3.11	0.221	0.15283	.	35.164000	0.00166	N	0.000000	T	0.00328	0.0010	N	0.08118	0	0.58432	P	4.000000000004E-6	B;B	0.13145	0.005;0.007	B;B	0.11329	0.002;0.006	T	0.03717	-1.1010	9	0.15952	T	0.53	-6.1906	3.2332	0.06756	0.0:0.5083:0.2265:0.2652	rs13263632;rs17436114;rs52832668;rs13263632	36;36	E9PDS0;Q13510-2	.;.	N	36	ENSP00000371152:S36N;ENSP00000326970:S36N	ENSP00000326970:S36N	S	-	2	0	ASAH1	17986484	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.267000	0.08619	0.029000	0.15352	0.563000	0.77884	AGC	C|0.924;T|0.076	0.076	strong		0.587	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
FOLH1B	219595	hgsc.bcm.edu	37	11	89413781	89413781	+	RNA	SNP	C	C	G	rs10830339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89413781C>G	ENST00000532352.1	+	0	1266							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						TTTCAGGAAACTACACTCTGA	0.299													C|||	1130	0.225639	0.1619	0.2478	5008	,	,		17371	0.1319		0.3718	False		,,,				2504	0.2423				p.N151K		Atlas-SNP	.											.	FOLH1B	93	.	0			c.C453G						PASS	.	C	LYS/ASN	939,3463	318.5+/-295.7	88,763,1350	33.0	34.0	34.0		453	3.2	1.0	11	dbSNP_120	34	3199,5385	442.5+/-360.1	587,2025,1680	no	missense	FOLH1B	NM_153696.2	94	675,2788,3030	GG,GC,CC		37.267,21.3312,31.8651	possibly-damaging	151/443	89413781	4138,8848	2201	4292	6493			219595	exon8			AGGAAACTACACT	AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89413781C>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	168	56	0.333333	NM_153696		Missense_Mutation	SNP	ENST00000532352.1	37																																																																																				C|0.717;G|0.283	0.283	strong		0.299	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696	
NDNF	79625	hgsc.bcm.edu	37	4	121958691	121958691	+	Silent	SNP	T	T	C	rs3733559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:121958691T>C	ENST00000379692.4	-	4	961	c.435A>G	c.(433-435)ttA>ttG	p.L145L	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	145					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						CCAACTGATATAAACCGGATG	0.408													T|||	1127	0.22504	0.0998	0.3357	5008	,	,		19003	0.2351		0.2038	False		,,,				2504	0.3272				p.L145L		Atlas-SNP	.											NDNF,colon,carcinoma,-2,1	NDNF	72	1	0			c.A435G						PASS	.	T		445,3451		28,389,1531	139.0	133.0	135.0		435	-8.0	0.0	4	dbSNP_107	135	1732,6590		179,1374,2608	no	coding-synonymous	NDNF	NM_024574.3		207,1763,4139	CC,CT,TT		20.8123,11.422,17.818		145/569	121958691	2177,10041	1948	4161	6109	SO:0001819	synonymous_variant	79625	exon4			CTGATATAAACCG	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.435A>G	4.37:g.121958691T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			T|0.796;C|0.204	0.204	strong		0.408	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
TRIO	7204	hgsc.bcm.edu	37	5	14397238	14397238	+	Silent	SNP	T	T	C	rs30774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:14397238T>C	ENST00000344204.4	+	29	4422	c.4398T>C	c.(4396-4398)gaT>gaC	p.D1466D	TRIO_ENST00000509967.2_Silent_p.D1417D|TRIO_ENST00000537187.1_Silent_p.D1466D	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1466	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GAGCCAATGATGCCATGCACC	0.498													C|||	1970	0.393371	0.6974	0.3761	5008	,	,		19858	0.0982		0.334	False		,,,				2504	0.3599				p.D1466D		Atlas-SNP	.											TRIO,NS,carcinoma,0,1	TRIO	305	1	0			c.T4398C						PASS	.	C		2842,1564	475.7+/-357.4	918,1006,279	97.0	87.0	90.0		4398	-7.6	0.2	5	dbSNP_76	90	2907,5691	654.6+/-401.2	511,1885,1903	no	coding-synonymous	TRIO	NM_007118.2		1429,2891,2182	CC,CT,TT		33.8102,35.497,44.2095		1466/3098	14397238	5749,7255	2203	4299	6502	SO:0001819	synonymous_variant	7204	exon29			CAATGATGCCATG	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.4398T>C	5.37:g.14397238T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			T|0.590;C|0.410	0.410	strong		0.498	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
FBXO7	25793	hgsc.bcm.edu	37	22	32871383	32871383	+	Intron	SNP	T	T	G	rs8137714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32871383T>G	ENST00000266087.7	+	1	449				FBXO7_ENST00000382058.3_Missense_Mutation_p.L12R|FBXO7_ENST00000397426.1_5'UTR	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7						cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGTCCCCTCCTCGGTGAGTCA	0.617													T|||	776	0.154952	0.1233	0.2161	5008	,	,		12429	0.1567		0.1928	False		,,,				2504	0.1135				p.L12R		Atlas-SNP	.											FBXO7_ENST00000382058,NS,carcinoma,0,1	FBXO7	131	1	0			c.T35G						scavenged	.	T	ARG/LEU,	537,3099		39,459,1320	25.0	31.0	29.0		35,	-6.1	0.0	22	dbSNP_116	29	1668,6478		161,1346,2566	yes	missense,intron	FBXO7	NM_001033024.1,NM_012179.3	102,	200,1805,3886	GG,GT,TT		20.4763,14.769,18.715	,	12/444,	32871383	2205,9577	1818	4073	5891	SO:0001627	intron_variant	25793	exon1			CCCTCCTCGGTGA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.122+272T>G	22.37:g.32871383T>G		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001033024	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	383	0.17536630036630035	53	0.10772357723577236	85	0.23480662983425415	95	0.1660839160839161	150	0.19788918205804748	T	4.156	0.027415	0.08054	0.14769	0.204763	ENSG00000100225	ENST00000452138;ENST00000382058	T;T	0.65364	0.81;-0.15	3.07	-6.13	0.02118	.	.	.	.	.	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	0.09015	-1.0694	8	0.40728	T	0.16	.	0.5836	0.00716	0.3068:0.276:0.1109:0.3063	rs8137714;rs11538370	12	Q9Y3I1-2	.	R	12	ENSP00000388547:L12R;ENSP00000371490:L12R	ENSP00000371490:L12R	L	+	2	0	FBXO7	31201383	0.003000	0.15002	0.002000	0.10522	0.001000	0.01503	-0.257000	0.08745	-1.638000	0.01529	-0.441000	0.05720	CTC	A|0.000;C|0.000;G|0.179;T|0.820	0.179	strong		0.617	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
ZNF638	27332	hgsc.bcm.edu	37	2	71654175	71654175	+	Missense_Mutation	SNP	G	G	A	rs1804020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71654175G>A	ENST00000409544.1	+	24	5806	c.5176G>A	c.(5176-5178)Gtg>Atg	p.V1726M	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Missense_Mutation_p.V666M|ZNF638_ENST00000264447.4_Missense_Mutation_p.V1726M	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1726			V -> M (in dbSNP:rs1804020). {ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTCTTCTCAGGTGCCCGAAGA	0.383													A|||	1719	0.343251	0.2262	0.2435	5008	,	,		19941	0.7034		0.2376	False		,,,				2504	0.3098				p.V1726M		Atlas-SNP	.											ZNF638,tonsil,carcinoma,0,1	ZNF638	179	1	0			c.G5176A						scavenged	.	A	MET/VAL,MET/VAL	1105,3301	720.2+/-409.0	146,813,1244	122.0	125.0	124.0		5176,5176	3.3	1.0	2	dbSNP_89	124	2047,6553	719.4+/-406.3	260,1527,2513	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	21,21	406,2340,3757	AA,AG,GG		23.8023,25.0794,24.235	benign,benign	1726/1979,1726/1979	71654175	3152,9854	2203	4300	6503	SO:0001583	missense	27332	exon24			TCTCAGGTGCCCG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5176G>A	2.37:g.71654175G>A	ENSP00000386433:p.Val1726Met	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	753	0.3447802197802198	101	0.20528455284552846	93	0.2569060773480663	376	0.6573426573426573	183	0.24142480211081793	A	1.046	-0.677433	0.03378	0.250794	0.238023	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.30448	1.53;1.53;1.94	5.85	3.35	0.38373	.	0.089095	0.49916	N	0.000133	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.99999999834298	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37220	-0.9715	9	0.19590	T	0.45	-6.9875	5.2117	0.15320	0.6696:0.1557:0.1747:0.0	rs1804020;rs3198783;rs57778009;rs1804020	1726;1726	Q14966-3;Q14966	.;ZN638_HUMAN	M	1726;1726;666	ENSP00000264447:V1726M;ENSP00000386433:V1726M;ENSP00000386813:V666M	ENSP00000264447:V1726M	V	+	1	0	ZNF638	71507683	0.993000	0.37304	1.000000	0.80357	0.957000	0.61999	0.199000	0.17237	1.048000	0.40298	-0.254000	0.11334	GTG	G|0.710;A|0.290	0.290	strong		0.383	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
NUP155	9631	hgsc.bcm.edu	37	5	37294473	37294473	+	Silent	SNP	T	T	C	rs1045908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:37294473T>C	ENST00000231498.3	-	33	4091	c.3888A>G	c.(3886-3888)ttA>ttG	p.L1296L	NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Silent_p.L1237L|NUP155_ENST00000513532.1_Silent_p.L1232L	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1296					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)	p.L1296L(1)		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)			GTAGTCTAGGTAATGGTACTC	0.308													T|||	1388	0.277157	0.112	0.3156	5008	,	,		15068	0.3829		0.2972	False		,,,				2504	0.3436				p.L1296L		Atlas-SNP	.											NUP155,NS,carcinoma,0,1	NUP155	116	1	1	Substitution - coding silent(1)	stomach(1)	c.A3888G						PASS	.	T	,	636,3770	270.7+/-269.8	41,554,1608	52.0	48.0	49.0		3711,3888	1.6	1.0	5	dbSNP_86	49	2519,6081	409.4+/-349.8	354,1811,2135	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	395,2365,3743	CC,CT,TT		29.2907,14.4349,24.258	,	1237/1333,1296/1392	37294473	3155,9851	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon33			TCTAGGTAATGGT	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.3888A>G	5.37:g.37294473T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			T|0.750;C|0.250	0.250	strong		0.308	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
ZFHX3	463	hgsc.bcm.edu	37	16	72992269	72992269	+	Silent	SNP	G	G	A	rs11075951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72992269G>A	ENST00000268489.5	-	2	2448	c.1776C>T	c.(1774-1776)gaC>gaT	p.D592D	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	592					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)				TGGCACTTTCGTCAGCGAAGT	0.552													G|||	128	0.0255591	0.0053	0.0476	5008	,	,		18384	0.0		0.0795	False		,,,				2504	0.0082				p.D592D		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1776T						PASS	.	G	,	76,4320	68.1+/-105.8	1,74,2123	108.0	104.0	105.0		,1776	-1.9	1.0	16	dbSNP_120	105	849,7751	193.9+/-239.5	38,773,3489	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	39,847,5612	AA,AG,GG		9.8721,1.7288,7.1176	,	,592/3704	72992269	925,12071	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			ACTTTCGTCAGCG	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.1776C>T	16.37:g.72992269G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			A|0.058;C|0.000;G|0.941	0.058	strong		0.552	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SURF6	6838	hgsc.bcm.edu	37	9	136199466	136199466	+	Missense_Mutation	SNP	G	G	A	rs886089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136199466G>A	ENST00000372022.4	-	4	789	c.524C>T	c.(523-525)aCg>aTg	p.T175M	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	175			T -> M (in dbSNP:rs886089).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		CTGGGCCTCCGTGGCCTCCTC	0.657													G|||	1407	0.28095	0.0386	0.3501	5008	,	,		15252	0.2986		0.3569	False		,,,				2504	0.4632				p.T175M		Atlas-SNP	.											SURF6,rectum,carcinoma,0,1	SURF6	32	1	0			c.C524T						PASS	.	G	MET/THR	372,4034	184.0+/-211.4	20,332,1851	88.0	92.0	90.0		524	-8.3	0.0	9	dbSNP_86	90	3017,5583	460.5+/-365.2	543,1931,1826	yes	missense	SURF6	NM_006753.4	81	563,2263,3677	AA,AG,GG		35.0814,8.443,26.0572	possibly-damaging	175/362	136199466	3389,9617	2203	4300	6503	SO:0001583	missense	6838	exon4			GCCTCCGTGGCCT	AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.524C>T	9.37:g.136199466G>A	ENSP00000361092:p.Thr175Met	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_006753	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	584	0.2673992673992674	31	0.06300813008130081	122	0.3370165745856354	154	0.2692307692307692	277	0.3654353562005277	G	8.549	0.875047	0.17395	0.08443	0.350814	ENSG00000148296	ENST00000372022	T	0.14516	2.5	4.14	-8.28	0.01013	.	1.762280	0.02976	N	0.145022	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.31191	0.125	T	0.25847	-1.0120	9	0.48119	T	0.1	.	1.6707	0.02811	0.2994:0.1487:0.0953:0.4565	rs886089;rs886089	175	O75683	SURF6_HUMAN	M	175	ENSP00000361092:T175M	ENSP00000361092:T175M	T	-	2	0	SURF6	135189287	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.892000	0.01610	-3.813000	0.00104	-1.250000	0.01514	ACG	A|0.255;C|0.000;G|0.745	0.255	strong		0.657	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
LRWD1	222229	hgsc.bcm.edu	37	7	102108263	102108263	+	Missense_Mutation	SNP	A	A	G	rs35310665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102108263A>G	ENST00000292616.5	+	5	823	c.671A>G	c.(670-672)aAg>aGg	p.K224R	MIR5090_ENST00000582533.1_RNA|ALKBH4_ENST00000292566.3_5'Flank	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	224					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						GCTGCCCACAAGCCCAGGGTG	0.642													A|||	182	0.0363419	0.0461	0.0418	5008	,	,		17800	0.0		0.0706	False		,,,				2504	0.0215				p.K224R		Atlas-SNP	.											.	LRWD1	41	.	0			c.A671G						PASS	.	A	ARG/LYS	159,3947		2,155,1896	21.0	26.0	24.0		671	-0.9	0.2	7	dbSNP_126	24	472,7608		13,446,3581	yes	missense	LRWD1	NM_152892.1	26	15,601,5477	GG,GA,AA		5.8416,3.8724,5.1781	benign	224/648	102108263	631,11555	2053	4040	6093	SO:0001583	missense	222229	exon5			CCCACAAGCCCAG	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.671A>G	7.37:g.102108263A>G	ENSP00000292616:p.Lys224Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	37	CCDS34715.1	91	0.041666666666666664	17	0.034552845528455285	19	0.052486187845303865	0	0.0	55	0.07255936675461741	A	3.314	-0.140203	0.06669	0.038724	0.058416	ENSG00000161036	ENST00000292616	T	0.60920	0.15	4.37	-0.919	0.10478	.	1.134180	0.06202	N	0.683498	T	0.03220	0.0094	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04811	-1.0925	10	0.11794	T	0.64	-17.7258	3.8487	0.08945	0.4978:0.1921:0.3101:0.0	rs35310665	224	Q9UFC0	LRWD1_HUMAN	R	224	ENSP00000292616:K224R	ENSP00000292616:K224R	K	+	2	0	LRWD1	101895268	0.652000	0.27349	0.186000	0.23195	0.555000	0.35460	1.268000	0.33062	0.042000	0.15717	-0.475000	0.04921	AAG	A|0.958;G|0.042	0.042	strong		0.642	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
MROH9	80133	hgsc.bcm.edu	37	1	170959088	170959088	+	Silent	SNP	C	C	T	rs28634500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:170959088C>T	ENST00000367758.3	+	11	1071	c.972C>T	c.(970-972)tgC>tgT	p.C324C	MROH9_ENST00000367759.4_Silent_p.C324C	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	324																	TGTTGACATGCACTTCACCCA	0.458													T|||	1109	0.221446	0.4614	0.1902	5008	,	,		20280	0.001		0.2227	False		,,,				2504	0.1452				p.C324C		Atlas-SNP	.											.	.	.	.	0			c.C972T						PASS	.	T	,	1558,2326		317,924,701	141.0	135.0	136.0		972,972	-10.4	0.0	1	dbSNP_125	136	1712,6574		185,1342,2616	no	coding-synonymous,coding-synonymous	C1orf129	NM_001163629.1,NM_025063.2	,	502,2266,3317	TT,TC,CC		20.6614,40.1133,26.8694	,	324/862,324/574	170959088	3270,8900	1942	4143	6085	SO:0001819	synonymous_variant	80133	exon11			GACATGCACTTCA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.972C>T	1.37:g.170959088C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	179	109	0.608939	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																			C|0.791;T|0.209	0.209	strong		0.458	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
PML	5371	hgsc.bcm.edu	37	15	74328141	74328141	+	Intron	SNP	G	G	T	rs743581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:74328141G>T	ENST00000268058.3	+	7	1806				PML_ENST00000435786.2_3'UTR|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.G780V|PML_ENST00000565898.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000354026.6_Missense_Mutation_p.G732V|PML_ENST00000395132.2_Intron|PML_ENST00000563500.1_3'UTR|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000564428.1_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|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)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CTTGGAGCAGGTGTTCCCCCT	0.582			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	1759	0.351238	0.298	0.4481	5008	,	,		15253	0.4018		0.3837	False		,,,				2504	0.2689				p.G780V		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2339T						PASS	.	G	,,VAL/GLY,,,,,,VAL/GLY	1412,2984	428.5+/-341.9	230,952,1016	52.0	62.0	59.0		,,2339,,,,,,2195	-2.4	0.0	15	dbSNP_86	59	3088,5506	456.0+/-363.9	540,2008,1749	yes	intron,intron,missense,utr-3,utr-3,intron,intron,intron,missense	PML	NM_002675.3,NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3,NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2	,,109,,,,,,109	770,2960,2765	TT,TG,GG		35.932,32.1201,34.642	,,,,,,,,	,,780/830,,,,,,732/782	74328141	4500,8490	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GAGCAGGTGTTCC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1270G>T	15.37:g.74328141G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	846	0.3873626373626374	151	0.30691056910569103	141	0.38950276243093923	253	0.4423076923076923	301	0.3970976253298153	G	3.117	-0.181346	0.06380	0.321201	0.35932	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.24	-2.39	0.06602	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.22909	0.077;0.077	B;B	0.19391	0.025;0.025	T	0.47711	-0.9096	6	0.32370	T	0.25	.	1.2769	0.02032	0.2141:0.3451:0.282:0.1587	rs743581;rs17855994;rs17856628	732;780	P29590-13;P29590-8	.;.	V	780;732	.	ENSP00000268059:G780V	G	+	2	0	PML	72115194	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.312000	0.19397	-0.518000	0.06452	-0.502000	0.04539	GGT	A|0.000;G|0.653;T|0.347	0.347	strong		0.582	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
GABRA6	2559	hgsc.bcm.edu	37	5	161128627	161128627	+	Missense_Mutation	SNP	C	C	T	rs34907804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:161128627C>T	ENST00000274545.5	+	9	1643	c.1210C>T	c.(1210-1212)Ccc>Tcc	p.P404S	GABRA6_ENST00000523217.1_Missense_Mutation_p.P394S			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	404			P -> S (in dbSNP:rs34907804).		gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|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)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		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)	ACCTGTCACACCCCCACCACT	0.473										TCGA Ovarian(5;0.080)			C|||	365	0.0728834	0.1369	0.085	5008	,	,		16777	0.0		0.0765	False		,,,				2504	0.0491				p.P404S		Atlas-SNP	.											GABRA6,lower_third,carcinoma,-2,1	GABRA6	139	1	0			c.C1210T						PASS	.	C	SER/PRO	541,3865	239.6+/-250.7	29,483,1691	109.0	103.0	105.0		1210	5.2	1.0	5	dbSNP_126	105	666,7934	167.1+/-218.9	28,610,3662	yes	missense	GABRA6	NM_000811.2	74	57,1093,5353	TT,TC,CC		7.7442,12.2787,9.2803	benign	404/454	161128627	1207,11799	2203	4300	6503	SO:0001583	missense	2559	exon9			GTCACACCCCCAC		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1210C>T	5.37:g.161128627C>T	ENSP00000274545:p.Pro404Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	158	0.07234432234432235	62	0.12601626016260162	40	0.11049723756906077	0	0.0	56	0.07387862796833773	C	8.391	0.839816	0.16891	0.122787	0.077442	ENSG00000145863	ENST00000274545;ENST00000523217	D;D	0.83335	-1.71;-1.71	5.16	5.16	0.70880	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.345405	0.34484	N	0.003927	T	0.01765	0.0056	L	0.29908	0.895	0.35992	P	0.16322899999999996	B	0.12013	0.005	B	0.06405	0.002	T	0.39014	-0.9634	9	0.20519	T	0.43	.	9.2591	0.37601	0.0:0.7619:0.1583:0.0798	rs34907804;rs52809327;rs61306367	404	Q16445	GBRA6_HUMAN	S	404;394	ENSP00000274545:P404S;ENSP00000430527:P394S	ENSP00000274545:P404S	P	+	1	0	GABRA6	161061205	0.998000	0.40836	0.990000	0.47175	0.451000	0.32288	3.751000	0.55165	2.571000	0.86741	0.655000	0.94253	CCC	C|0.915;T|0.085	0.085	strong		0.473	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
CPXM2	119587	hgsc.bcm.edu	37	10	125521590	125521590	+	Silent	SNP	G	G	A	rs10794567	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:125521590G>A	ENST00000241305.3	-	11	1729	c.1575C>T	c.(1573-1575)taC>taT	p.Y525Y	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	525					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GGTCGTAGGGGTACGCCACCA	0.642													G|||	3255	0.64996	0.6112	0.7435	5008	,	,		15544	0.5665		0.7744	False		,,,				2504	0.5941				p.Y525Y		Atlas-SNP	.											.	CPXM2	120	.	0			c.C1575T						PASS	.	G		2759,1647	655.5+/-399.9	870,1019,314	78.0	79.0	79.0		1575	4.3	1.0	10	dbSNP_120	79	6475,2125	713.7+/-406.0	2455,1565,280	no	coding-synonymous	CPXM2	NM_198148.2		3325,2584,594	AA,AG,GG		24.7093,37.3808,29.002		525/757	125521590	9234,3772	2203	4300	6503	SO:0001819	synonymous_variant	119587	exon11			GTAGGGGTACGCC	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1575C>T	10.37:g.125521590G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	37	CCDS7637.1																																																																																			G|0.303;A|0.697	0.697	strong		0.642	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
SDC2	6383	hgsc.bcm.edu	37	8	97614661	97614661	+	Missense_Mutation	SNP	T	T	A	rs1042381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:97614661T>A	ENST00000302190.4	+	3	1132	c.211T>A	c.(211-213)Tct>Act	p.S71T	SDC2_ENST00000522911.1_Missense_Mutation_p.S42T|SDC2_ENST00000519914.1_Missense_Mutation_p.S42T|SDC2_ENST00000518385.1_Missense_Mutation_p.S35T	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	71			S -> T (in dbSNP:rs1042381). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2523388}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.S71T(1)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	GCTGACAACATCTCGACCACT	0.453													T|||	1180	0.235623	0.385	0.1643	5008	,	,		20513	0.2282		0.17	False		,,,				2504	0.1595				p.S71T		Atlas-SNP	.											SDC2,NS,carcinoma,0,1	SDC2	33	1	1	Substitution - Missense(1)	stomach(1)	c.T211A						PASS	.	T	THR/SER	1674,2732	509.1+/-367.1	337,1000,866	187.0	170.0	176.0		211	3.8	0.9	8	dbSNP_86	176	1568,7032	293.4+/-301.3	168,1232,2900	yes	missense	SDC2	NM_002998.3	58	505,2232,3766	AA,AT,TT		18.2326,37.9936,24.927	benign	71/202	97614661	3242,9764	2203	4300	6503	SO:0001583	missense	6383	exon3			ACAACATCTCGAC	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"""Proteoglycans / Cell Surface : Syndecans"", ""CD molecules"""	10659	protein-coding gene	gene with protein product	"""syndecan proteoglycan 2"""	142460	"""heparan sulfate proteoglycan 1, cell surface-associated"""	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.211T>A	8.37:g.97614661T>A	ENSP00000307046:p.Ser71Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	32	0.323232	NM_002998	B3KQA3|Q6PIS6|Q9H6V1	Missense_Mutation	SNP	ENST00000302190.4	37	CCDS6272.1	483	0.22115384615384615	169	0.3434959349593496	63	0.17403314917127072	128	0.22377622377622378	123	0.16226912928759896	T	15.30	2.793196	0.50102	0.379936	0.182326	ENSG00000169439	ENST00000302190;ENST00000518385;ENST00000545117;ENST00000546193;ENST00000522911;ENST00000519914;ENST00000521590;ENST00000523877	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.03	3.79	0.43588	.	0.356619	0.30850	N	0.008754	T	0.00012	0.0000	L	0.56769	1.78	0.26421	P	0.9760966	P	0.40578	0.722	B	0.42625	0.393	T	0.42172	-0.9467	9	0.13470	T	0.59	-18.4812	6.6506	0.22959	0.0:0.0823:0.1548:0.7629	rs1042381;rs3181837;rs16894877;rs17846449;rs17859499;rs52818651;rs1042381	71	P34741	SDC2_HUMAN	T	71;35;71;61;42;42;42;42	ENSP00000307046:S71T;ENSP00000429045:S35T;ENSP00000427784:S42T;ENSP00000428256:S42T;ENSP00000429121:S42T	ENSP00000307046:S71T	S	+	1	0	SDC2	97683837	1.000000	0.71417	0.900000	0.35374	0.998000	0.95712	2.297000	0.43593	2.025000	0.59659	0.533000	0.62120	TCT	T|0.760;A|0.240	0.240	strong		0.453	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998	
SPEG	10290	hgsc.bcm.edu	37	2	220348751	220348751	+	Missense_Mutation	SNP	C	C	T	rs10755037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220348751C>T	ENST00000312358.7	+	30	6698	c.6566C>T	c.(6565-6567)cCt>cTt	p.P2189L	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2189	Pro-rich.		P -> L (in dbSNP:rs10755037).		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)		CCCAGTACCCCTAAGTCTGCA	0.662													C|||	1430	0.285543	0.289	0.2738	5008	,	,		13041	0.1448		0.2694	False		,,,				2504	0.4509				p.P2189L		Atlas-SNP	.											SPEG,NS,carcinoma,0,2	SPEG	272	2	0			c.C6566T						PASS	.	C	LEU/PRO	1072,3052		152,768,1142	39.0	49.0	46.0		6566	1.9	0.0	2	dbSNP_120	46	2065,6317		271,1523,2397	yes	missense	SPEG	NM_005876.4	98	423,2291,3539	TT,TC,CC		24.6361,25.9942,25.084	benign	2189/3268	220348751	3137,9369	2062	4191	6253	SO:0001583	missense	10290	exon30			GTACCCCTAAGTC	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.6566C>T	2.37:g.220348751C>T	ENSP00000311684:p.Pro2189Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	529	0.24221611721611722	129	0.2621951219512195	107	0.2955801104972376	92	0.16083916083916083	201	0.26517150395778366	C	0.010	-1.750379	0.00669	0.259942	0.246361	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.64991	-0.13	3.72	1.85	0.25348	.	0.416002	0.17647	N	0.166837	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.16837	-1.0389	9	0.51188	T	0.08	.	10.7058	0.45954	0.0:0.8205:0.0:0.1795	rs10755037	2189	Q15772	SPEG_HUMAN	L	2189	ENSP00000311684:P2189L	ENSP00000265327:P2189L	P	+	2	0	SPEG	220056995	0.482000	0.25948	0.008000	0.14137	0.002000	0.02628	2.969000	0.49232	0.351000	0.24027	-1.901000	0.00528	CCT	A|0.000;C|0.753;G|0.000;T|0.247	0.247	strong		0.662	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701116	8701116	+	Silent	SNP	G	G	A	rs2242374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8701116G>A	ENST00000329805.4	-	1	1551	c.1323C>T	c.(1321-1323)ctC>ctT	p.L441L		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	441						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						GCTGCCCAGCGAGGCAGCTCA	0.572													G|||	971	0.19389	0.2625	0.1484	5008	,	,		19332	0.2748		0.0845	False		,,,				2504	0.1626				p.L441L		Atlas-SNP	.											.	MFSD6L	46	.	0			c.C1323T						PASS	.	G		949,3457	353.3+/-312.1	111,727,1365	89.0	101.0	97.0		1323	-7.4	0.1	17	dbSNP_98	97	850,7750	193.8+/-239.4	34,782,3484	no	coding-synonymous	MFSD6L	NM_152599.3		145,1509,4849	AA,AG,GG		9.8837,21.5388,13.8321		441/587	8701116	1799,11207	2203	4300	6503	SO:0001819	synonymous_variant	162387	exon1			CCCAGCGAGGCAG	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1323C>T	17.37:g.8701116G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_152599	Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																			G|0.836;A|0.164	0.164	strong		0.572	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
Unknown	0	hgsc.bcm.edu	37	11	5989223	5989223	+	IGR	SNP	G	G	A	rs61730422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5989223G>A								OR56A3 (19632 upstream) : OR52L1 (17898 downstream)																							TATCTGAGTCGAGAAGAAAGT	0.448													.|||	154	0.0307508	0.0076	0.036	5008	,	,		22511	0.0139		0.0755	False		,,,				2504	0.0297				p.R168X		Atlas-SNP	.											.	.	.	.	0			c.C502T						PASS	.	G	stop/ARG	27,1357		0,27,665	92.0	78.0	82.0		502	-2.7	0.0	11	dbSNP_129	82	275,2907		9,257,1325	yes	stop-gained	OR56A5	NM_001146033.1		9,284,1990	AA,AG,GG		8.6424,1.9509,6.6141		168/314	5989223	302,4264	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TGAGTCGAGAAGA																													11.37:g.5989223G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001146033		Nonsense_Mutation	SNP		37																																																																																				G|0.951;A|0.049	0.049	strong	0	0.448								
FAM171A2	284069	hgsc.bcm.edu	37	17	42437000	42437000	+	Missense_Mutation	SNP	G	G	A	rs71371993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	28	0	0		WXS	Illumina HiSeq	Phase_I	27	17	0.62963	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	
ALK	238	hgsc.bcm.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	T	C	rs1881420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29416481T>C	ENST00000389048.3	-	29	5378	c.4472A>G	c.(4471-4473)aAg>aGg	p.K1491R	ALK_ENST00000431873.1_Missense_Mutation_p.K321R	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1491			K -> R (in dbSNP:rs1881420). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9053841, ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K1491R(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TCCGTGGACCTTGTGCAACTC	0.532			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				T|||	2079	0.415136	0.2405	0.4467	5008	,	,		18547	0.7312		0.2336	False		,,,				2504	0.4898				p.K1491R		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - Missense(1)	prostate(1)	c.A4472G						PASS	.		ARG/LYS	1068,3338	389.1+/-327.2	147,774,1282	113.0	118.0	116.0		4472	1.9	0.4	2	dbSNP_92	116	1837,6763	330.1+/-319.0	216,1405,2679	yes	missense	ALK	NM_004304.4	26	363,2179,3961	CC,CT,TT		21.3605,24.2397,22.3358	benign	1491/1621	29416481	2905,10101	2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGACCTTGTGCA	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4472A>G	2.37:g.29416481T>C	ENSP00000373700:p.Lys1491Arg	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	290	146	0.503448	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	863	0.39514652014652013	114	0.23170731707317074	151	0.4171270718232044	415	0.7255244755244755	183	0.24142480211081793	t	13.96	2.391818	0.42410	0.242397	0.213605	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.77489	-1.1;2.84	5.64	1.9	0.25705	.	0.124743	0.35349	U	0.003264	T	0.00012	0.0000	L	0.60455	1.87	0.51233	P	8.500000000000174E-5	B	0.02656	0.0	B	0.08055	0.003	T	0.44467	-0.9326	9	0.23302	T	0.38	.	6.8496	0.24008	0.0:0.1336:0.1271:0.7393	rs1881420;rs3738871;rs56441963;rs59805402;rs1881420	1491	Q9UM73	ALK_HUMAN	R	1491;321	ENSP00000373700:K1491R;ENSP00000414027:K321R	ENSP00000373700:K1491R	K	-	2	0	ALK	29269985	1.000000	0.71417	0.353000	0.25747	0.942000	0.58702	2.447000	0.44917	0.089000	0.17243	0.454000	0.30748	AAG	T|0.684;G|0.005	.	strong		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
NUTM2A	728118	hgsc.bcm.edu	37	10	88992641	88992641	+	Missense_Mutation	SNP	G	G	A	rs145500179	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88992641G>A	ENST00000381707.2	+	5	2016	c.1633G>A	c.(1633-1635)Ggc>Agc	p.G545S	NUTM2A_ENST00000381689.4_Missense_Mutation_p.G545S|NUTM2A-AS1_ENST00000451940.2_RNA|NUTM2A-AS1_ENST00000456104.1_RNA	NM_001099338.1	NP_001092808.1	Q8IVF1	NTM2A_HUMAN	NUT family member 2A	545																	ACGGGAAGAGGGCGAAGTGAA	0.617													.|||	3976	0.79393	0.6974	0.8256	5008	,	,		17238	0.9563		0.7734	False		,,,				2504	0.7556				p.G545S		Atlas-SNP	.											FAM22D,colon,carcinoma,-2,2	FAM22A	20	2	0			c.G1633A						scavenged	.						7.0	9.0	8.0					10																	88992641		1545	3107	4652	SO:0001583	missense	728118	exon5			GAAGAGGGCGAAG		CCDS44452.1	10q23.2	2013-03-15	2013-03-14	2013-03-14	ENSG00000184923	ENSG00000184923			23438	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member A"""	FAM22A			Standard	NM_001099338		Approved		uc001kek.3	Q8IVF1	OTTHUMG00000018670	ENST00000381707.2:c.1633G>A	10.37:g.88992641G>A	ENSP00000371126:p.Gly545Ser	Somatic	35	1	0.0285714		WXS	Illumina HiSeq	Phase_I	241	210	0.871369	NM_001099338	A6NMX5|C9JDI1|Q5VZW1	Missense_Mutation	SNP	ENST00000381707.2	37	CCDS44452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	8.454|8.454	0.853843|0.853843	0.17106|0.17106	.|.	.|.	ENSG00000184923|ENSG00000184923	ENST00000451286|ENST00000381689;ENST00000381707;ENST00000416901;ENST00000432986	.|T;T	.|0.24723	.|1.84;2.64	1.18|1.18	1.18|1.18	0.20946|0.20946	.|Nuclear Testis protein, C-terminal (1);	1.216050|1.216050	0.05733|0.05733	N|N	0.599879|0.599879	T|T	0.26085|0.26085	0.0636|0.0636	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.43287	.|0.802	.|B	.|0.42959	.|0.403	T|T	0.31558|0.31558	-0.9939|-0.9939	5|9	.|0.37606	.|T	.|0.19	.|.	5.8963|5.8963	0.18941|0.18941	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|545	.|Q8IVF1	.|FA22A_HUMAN	E|S	322|545;545;472;22	.|ENSP00000371107:G545S;ENSP00000371126:G545S	.|ENSP00000371107:G545S	G|G	+|+	2|1	0|0	FAM22A|FAM22A	88982621|88982621	0.007000|0.007000	0.16637|0.16637	0.006000|0.006000	0.13384|0.13384	0.008000|0.008000	0.06430|0.06430	2.120000|2.120000	0.41968|0.41968	1.015000|1.015000	0.39444|0.39444	0.374000|0.374000	0.22700|0.22700	GGG|GGC	G|0.250;A|0.750	0.750	strong		0.617	NUTM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049198.2	NM_001099338	
LRFN3	79414	hgsc.bcm.edu	37	19	36430798	36430798	+	Silent	SNP	A	A	G	rs1057265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36430798A>G	ENST00000588831.1	+	3	1525	c.471A>G	c.(469-471)acA>acG	p.T157T	LRFN3_ENST00000246529.3_Silent_p.T157T			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	157					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GTGCCGAGACACTGGAGGACC	0.667													G|||	800	0.159744	0.3865	0.1009	5008	,	,		14187	0.127		0.0268	False		,,,				2504	0.0654				p.T157T		Atlas-SNP	.											LRFN3,NS,carcinoma,0,1	LRFN3	43	1	0			c.A471G						PASS	.	G		1420,2986		224,972,1007	48.0	45.0	46.0		471	-8.7	0.5	19	dbSNP_86	46	306,8288		2,302,3993	no	coding-synonymous	LRFN3	NM_024509.1		226,1274,5000	GG,GA,AA		3.5606,32.2288,13.2769		157/629	36430798	1726,11274	2203	4297	6500	SO:0001819	synonymous_variant	79414	exon2			CGAGACACTGGAG	BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28370	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 1"""	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.471A>G	19.37:g.36430798A>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	25	11	0.44	NM_024509	Q6UY10	Silent	SNP	ENST00000588831.1	37	CCDS12483.1																																																																																			A|0.872;G|0.128	0.128	strong		0.667	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509	
RANBP17	64901	hgsc.bcm.edu	37	5	170626735	170626735	+	Silent	SNP	A	A	G	rs35724654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	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	
WDR90	197335	hgsc.bcm.edu	37	16	717523	717523	+	Silent	SNP	G	G	T	rs3752493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:717523G>T	ENST00000293879.4	+	41	5181	c.5181G>T	c.(5179-5181)ccG>ccT	p.P1727P	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Silent_p.P1729P|WDR90_ENST00000547944.1_Silent_p.P326P|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						PASS	.	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	48	0	0		WXS	Illumina HiSeq	Phase_I	57	57	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	
MGA	23269	hgsc.bcm.edu	37	15	41991315	41991315	+	Missense_Mutation	SNP	A	A	T	rs2178004	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41991315A>T	ENST00000570161.1	+	4	2146	c.2146A>T	c.(2146-2148)Act>Tct	p.T716S	MGA_ENST00000566586.1_Missense_Mutation_p.T716S|MGA_ENST00000389936.4_Missense_Mutation_p.T716S|MGA_ENST00000545763.1_Missense_Mutation_p.T716S|MGA_ENST00000219905.7_Missense_Mutation_p.T716S			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGATTTGAAGACTTTGCGGCA	0.353													T|||	3803	0.759385	0.5083	0.8256	5008	,	,		17381	0.8909		0.835	False		,,,				2504	0.8384				p.T716S		Atlas-SNP	.											.	MGA	264	.	0			c.A2146T						PASS	.	T	SER/THR,SER/THR	2070,1604		579,912,346	70.0	68.0	69.0		2146,2146	-0.2	1.0	15	dbSNP_96	69	6758,1400		2803,1152,124	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	58,58	3382,2064,470	TT,TA,AA		17.1611,43.6581,25.3888	benign,benign	716/2857,716/3066	41991315	8828,3004	1837	4079	5916	SO:0001583	missense	23269	exon5			TTGAAGACTTTGC	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.2146A>T	15.37:g.41991315A>T	ENSP00000457035:p.Thr716Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	153	150	0.980392	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	1683	0.7706043956043956	246	0.5	295	0.8149171270718232	504	0.8811188811188811	638	0.841688654353562	T	1.588	-0.529880	0.04112	0.563419	0.828389	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.39406	1.08;1.08;1.08	4.95	-0.188	0.13264	.	4.216510	0.00604	N	0.000390	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.42716	-0.9435	8	0.02654	T	1	.	1.6685	0.02807	0.4295:0.0866:0.143:0.3409	rs2178004;rs52809171;rs57181707;rs2178004	716;716	F5H7K2;E7ENI0	.;.	S	716	ENSP00000219905:T716S;ENSP00000374586:T716S;ENSP00000442467:T716S	ENSP00000219905:T716S	T	+	1	0	MGA	39778607	0.994000	0.37717	0.994000	0.49952	0.593000	0.36681	0.756000	0.26419	-0.227000	0.09884	-0.364000	0.07487	ACT	A|0.216;T|0.784	0.784	strong		0.353	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
TNS1	7145	hgsc.bcm.edu	37	2	218686643	218686643	+	Missense_Mutation	SNP	T	T	A	rs112371945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:218686643T>A	ENST00000171887.4	-	23	3532	c.3080A>T	c.(3079-3081)gAg>gTg	p.E1027V	TNS1_ENST00000419504.1_Missense_Mutation_p.E1014V|TNS1_ENST00000430930.1_Missense_Mutation_p.E1006V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1027					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)		TGCCACAGACTCCACATAGCT	0.627													T|||	3	0.000599042	0.0	0.0	5008	,	,		17582	0.0		0.003	False		,,,				2504	0.0				p.E1027V		Atlas-SNP	.											.	TNS1	251	.	0			c.A3080T						PASS	.	T	VAL/GLU	0,4400		0,0,2200	16.0	18.0	17.0		3080	4.1	1.0	2	dbSNP_132	17	12,8582		0,12,4285	yes	missense	TNS1	NM_022648.4	121	0,12,6485	AA,AT,TT		0.1396,0.0,0.0924	probably-damaging	1027/1736	218686643	12,12982	2200	4297	6497	SO:0001583	missense	7145	exon23			ACAGACTCCACAT	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.3080A>T	2.37:g.218686643T>A	ENSP00000171887:p.Glu1027Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	22	0.010073260073260074	6	0.012195121951219513	2	0.0055248618784530384	6	0.01048951048951049	8	0.010554089709762533	T	22.7	4.320848	0.81469	0.0	0.001396	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.93859	-3.3;1.79;-3.19;-3.12	4.11	4.11	0.48088	.	0.793281	0.11520	N	0.555860	D	0.92675	0.7672	L	0.32530	0.975	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.984	D;D;P	0.85130	0.997;0.994;0.844	D	0.91199	0.4990	10	0.62326	D	0.03	.	13.4292	0.61044	0.0:0.0:0.0:1.0	.	1027;1006;1014	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	V	1027;165;1014;1006	ENSP00000171887:E1027V;ENSP00000394171:E165V;ENSP00000408724:E1014V;ENSP00000406016:E1006V	ENSP00000171887:E1027V	E	-	2	0	TNS1	218394888	1.000000	0.71417	0.994000	0.49952	0.792000	0.44763	7.653000	0.83643	1.631000	0.50456	0.459000	0.35465	GAG	T|0.996;A|0.004	0.004	strong		0.627	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
OR2M2	391194	hgsc.bcm.edu	37	1	248343990	248343990	+	Missense_Mutation	SNP	T	T	C	rs4916104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248343990T>C	ENST00000359682.2	+	1	703	c.703T>C	c.(703-705)Tgc>Cgc	p.C235R		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	235			C -> R (in dbSNP:rs4916104).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	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)			AGAGGGTCGTTGCAAAGCTTT	0.478													C|||	2903	0.579673	0.6142	0.6052	5008	,	,		20359	0.4415		0.6382	False		,,,				2504	0.5971				p.C235R		Atlas-SNP	.											OR2M2,NS,carcinoma,-1,1	OR2M2	149	1	0			c.T703C						PASS	.	C	ARG/CYS	2517,1889		810,897,496	176.0	155.0	162.0		703	1.1	0.0	1	dbSNP_111	162	5393,3205		1825,1743,731	no	missense	OR2M2	NM_001004688.1	180	2635,2640,1227	CC,CT,TT		37.2761,42.8734,39.1726	benign	235/348	248343990	7910,5094	2203	4299	6502	SO:0001583	missense	391194	exon1			GGTCGTTGCAAAG	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.703T>C	1.37:g.248343990T>C	ENSP00000352710:p.Cys235Arg	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	151	147	0.97351	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	1105	0.5059523809523809	252	0.5121951219512195	202	0.5580110497237569	227	0.3968531468531469	424	0.5593667546174143	N	0.011	-1.736827	0.00681	0.571266	0.627239	ENSG00000198601	ENST00000359682	T	0.00036	8.86	2.03	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	1.321480	0.05860	N	0.622788	T	0.00012	0.0000	N	0.00132	-2.035	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23013	-1.0200	9	0.25106	T	0.35	.	6.5264	0.22303	0.1664:0.7098:0.0:0.1238	rs4916104	235	Q96R28	OR2M2_HUMAN	R	235	ENSP00000352710:C235R	ENSP00000352710:C235R	C	+	1	0	OR2M2	246410613	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.939000	0.01545	-0.143000	0.11334	-1.498000	0.00962	TGC	T|0.447;C|0.553	0.553	strong		0.478	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461266	141461266	+	Silent	SNP	A	A	G	rs3735801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461266A>G	ENST00000438773.2	-	2	340	c.207T>C	c.(205-207)ggT>ggC	p.G69G	TRAPPC9_ENST00000389327.3_Silent_p.G69G|TRAPPC9_ENST00000389328.4_Silent_p.G167G	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	56	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	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	
FAM47E	100129583	hgsc.bcm.edu	37	4	77192868	77192868	+	Missense_Mutation	SNP	G	G	A	rs3733250	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77192868G>A	ENST00000424749.2	+	5	823	c.817G>A	c.(817-819)Gag>Aag	p.E273K	FAM47E-STBD1_ENST00000539752.1_5'UTR|FAM47E_ENST00000510197.1_Missense_Mutation_p.E175K|FAM47E_ENST00000339906.6_Missense_Mutation_p.E175K|FAM47E_ENST00000515604.1_Missense_Mutation_p.E273K	NM_001136570.2	NP_001130042.1	Q6ZV65	FA47E_HUMAN	family with sequence similarity 47, member E	273				E -> K (in Ref. 1; BAC85998). {ECO:0000305}.													TAAACTGCAGGAGACAGAGTT	0.463													G|||	1603	0.320088	0.1717	0.428	5008	,	,		18148	0.3224		0.4076	False		,,,				2504	0.3517				p.E273K		Atlas-SNP	.											.	.	.	.	0			c.G817A						PASS	.	G	LYS/GLU	311,1073		38,235,419	103.0	87.0	92.0		817	0.5	0.0	4	dbSNP_107	92	1317,1865		273,771,547	yes	missense	FAM47E	NM_001136570.2	56	311,1006,966	AA,AG,GG		41.3891,22.4711,35.6548	benign	273/394	77192868	1628,2938	692	1591	2283	SO:0001583	missense	0	exon5			CTGCAGGAGACAG	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.817G>A	4.37:g.77192868G>A	ENSP00000409423:p.Glu273Lys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_001242939	D6R8Y4	Missense_Mutation	SNP	ENST00000424749.2	37	CCDS47081.1	761	0.3484432234432234	109	0.22154471544715448	140	0.3867403314917127	197	0.34440559440559443	315	0.4155672823218997	G	12.22	1.873593	0.33069	0.224711	0.413891	ENSG00000189157	ENST00000510197;ENST00000339906;ENST00000515604;ENST00000509377;ENST00000424749;ENST00000514140	T;T;T;T	0.47869	0.83;0.83;1.39;1.42	4.74	0.488	0.16848	.	0.797101	0.10624	N	0.652981	T	0.00012	0.0000	M	0.62088	1.915	0.58432	P	9.000000000036756E-6	B;P;B;B;B	0.35656	0.11;0.514;0.154;0.015;0.041	B;B;B;B;B	0.29862	0.018;0.108;0.078;0.028;0.011	T	0.36792	-0.9733	9	0.54805	T	0.06	-1.7053	3.9358	0.09305	0.3515:0.1752:0.4734:0.0	rs3733250;rs17236563;rs52802996;rs56884110;rs3733250	120;273;273;273;175	D6RCS4;Q6ZV65-1;Q6ZV65;C9JTC9;Q6ZV65-2	.;.;FA47E_HUMAN;.;.	K	175;175;273;120;273;81	ENSP00000422262:E175K;ENSP00000340401:E175K;ENSP00000422067:E273K;ENSP00000409423:E273K	ENSP00000340401:E175K	E	+	1	0	FAM47E	77411892	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.138000	0.16016	-0.049000	0.13379	0.655000	0.94253	GAG	G|0.650;A|0.350	0.350	strong		0.463	FAM47E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362528.2	NM_001136570	
SORBS2	8470	hgsc.bcm.edu	37	4	186536235	186536235	+	Silent	SNP	G	G	A	rs373495088		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186536235G>A	ENST00000284776.7	-	16	3227	c.2718C>T	c.(2716-2718)caC>caT	p.H906H	SORBS2_ENST00000449407.2_Silent_p.H450H|SORBS2_ENST00000431808.1_Silent_p.H906H|SORBS2_ENST00000319471.9_Silent_p.H537H|SORBS2_ENST00000355634.5_Silent_p.H1006H|SORBS2_ENST00000393528.3_Silent_p.H472H|SORBS2_ENST00000437304.2_Silent_p.H630H|SORBS2_ENST00000448662.2_Silent_p.H467H|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000418609.1_Silent_p.H810H	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	906	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		CCACTCTCCCGTGGTGTTCTC	0.468																																					p.H1006H	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C3018T						PASS	.	G	,,,,,,,	0,4406		0,0,2203	145.0	134.0	138.0		1350,1611,1401,1890,2430,894,1416,2718	-6.9	0.3	4		138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,,	450/645,537/732,467/662,630/825,810/1005,298/493,472/667,906/1101	186536235	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8470	exon19			TCTCCCGTGGTGT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2718C>T	4.37:g.186536235G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																			.	.	weak		0.468	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
SVEP1	79987	hgsc.bcm.edu	37	9	113212454	113212454	+	Missense_Mutation	SNP	A	A	T	rs10817021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:113212454A>T	ENST00000401783.2	-	24	4324	c.3988T>A	c.(3988-3990)Ttg>Atg	p.L1330M	SVEP1_ENST00000374469.1_Missense_Mutation_p.L1307M|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Missense_Mutation_p.L1330M	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1330	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> M (in dbSNP:rs10817021).		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						CATTTGCACAAGAATCCCCCA	0.473													A|||	512	0.102236	0.0061	0.0951	5008	,	,		18786	0.0327		0.1531	False		,,,				2504	0.2566				p.L1330M		Atlas-SNP	.											.	SVEP1	326	.	0			c.T3988A						PASS	.	A	MET/LEU	120,3630		1,118,1756	191.0	179.0	183.0		3988	0.5	1.0	9	dbSNP_120	183	1400,6820		125,1150,2835	yes	missense	SVEP1	NM_153366.3	15	126,1268,4591	TT,TA,AA		17.0316,3.2,12.6984	benign	1330/3572	113212454	1520,10450	1875	4110	5985	SO:0001583	missense	79987	exon24			TGCACAAGAATCC	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.3988T>A	9.37:g.113212454A>T	ENSP00000384917:p.Leu1330Met	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	170	0.07783882783882784	6	0.012195121951219513	34	0.09392265193370165	17	0.02972027972027972	113	0.14907651715039577	A	11.24	1.579014	0.28180	0.032	0.170316	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.61274	0.12;0.12;0.12	5.74	0.456	0.16655	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.102910	0.06717	N	0.774184	T	0.00109	0.0003	N	0.17082	0.46	0.50632	P	1.1799999999995148E-4	B;B	0.19445	0.036;0.012	B;B	0.21360	0.034;0.013	T	0.08086	-1.0739	9	0.46703	T	0.11	.	1.629	0.02729	0.4634:0.1333:0.2752:0.1282	rs10817021;rs52835013;rs10817021	1330;1330	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	M	1330;1307;1330	ENSP00000384917:L1330M;ENSP00000363593:L1307M;ENSP00000304118:L1330M	ENSP00000304118:L1330M	L	-	1	2	SVEP1	112252275	0.003000	0.15002	0.997000	0.53966	0.752000	0.42762	0.033000	0.13754	0.108000	0.17862	-0.334000	0.08254	TTG	A|0.904;T|0.096	0.096	strong		0.473	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
POTEF	728378	hgsc.bcm.edu	37	2	130832389	130832389	+	Missense_Mutation	SNP	G	G	T	rs199761904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:130832389G>T	ENST00000409914.2	-	17	3055	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	POTEF_ENST00000357462.5_Missense_Mutation_p.P886T	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	886	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						AGGTAGTCAGGCAGTTCCCGC	0.587																																					p.P886T		Atlas-SNP	.											POTEF,NS,carcinoma,0,1	POTEF	140	1	0			c.C2656A						scavenged	.						20.0	28.0	25.0					2																	130832389		1902	3994	5896	SO:0001583	missense	728378	exon17			AGTCAGGCAGTTC	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.2656C>A	2.37:g.130832389G>T	ENSP00000386786:p.Pro886Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	11	0.0909091	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.840460	0.00573	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	T;T	0.04360	3.64;3.64	.	.	.	.	.	.	.	.	T	0.00241	0.0007	N	0.00000	-5.41	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59364	-0.7468	8	0.02654	T	1	.	4.0871	0.09951	0.0:1.0E-4:0.3502:0.6498	.	886	A5A3E0	POTEF_HUMAN	T	886	ENSP00000350052:P886T;ENSP00000386786:P886T	ENSP00000350052:P886T	P	-	1	0	POTEF	130548859	1.000000	0.71417	0.050000	0.19076	0.050000	0.14768	3.856000	0.55964	-2.076000	0.00875	-2.150000	0.00334	CCT	.	.	weak		0.587	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	rs73365341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F|AFAP1L2_ENST00000491814.1_5'Flank			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	412	PH 2. {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)		AAGGAGTAGAGGTGGTCGGGG	0.682													G|||	531	0.10603	0.354	0.0375	5008	,	,		12908	0.0		0.0199	False		,,,				2504	0.0174				p.L412F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1234T						PASS	.	G	PHE/LEU,PHE/LEU	1464,2940	461.5+/-352.9	257,950,995	39.0	38.0	38.0		1234,1234	5.3	1.0	10	dbSNP_130	38	165,8435	76.3+/-139.0	3,159,4138	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	22,22	260,1109,5133	AA,AG,GG		1.9186,33.2425,12.5269	probably-damaging,probably-damaging	412/819,412/815	116064528	1629,11375	2202	4300	6502	SO:0001583	missense	84632	exon11			AGTAGAGGTGGTC	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.1234C>T	10.37:g.116064528G>A	ENSP00000303042:p.Leu412Phe	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	24	14	0.583333	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	224	0.10256410256410256	195	0.39634146341463417	15	0.04143646408839779	0	0.0	14	0.018469656992084433	G	26.3	4.722438	0.89298	0.332425	0.019186	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.75589	-0.95;-0.95;-0.95	5.3	5.3	0.74995	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.999999814385	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.984;0.998;1.0	T	0.02104	-1.1213	9	0.45353	T	0.12	-16.927	18.9486	0.92632	0.0:0.0:1.0:0.0	.	465;466;440;412;412	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	F	412;412;439;465	ENSP00000358276:L412F;ENSP00000303042:L412F;ENSP00000444511:L465F	ENSP00000303042:L412F	L	-	1	0	AFAP1L2	116054518	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.973000	0.88032	2.470000	0.83445	0.563000	0.77884	CTC	G|0.884;A|0.116	0.116	strong		0.682	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
ITGA2	3673	hgsc.bcm.edu	37	5	52351377	52351377	+	Silent	SNP	T	T	C	rs1139484	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52351377T>C	ENST00000296585.5	+	8	932	c.789T>C	c.(787-789)gcT>gcC	p.A263A		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	263	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)				GAAAATATGCTTATTCAGCAG	0.358													T|||	489	0.0976438	0.1717	0.0605	5008	,	,		18641	0.0317		0.0895	False		,,,				2504	0.1002				p.A263A		Atlas-SNP	.											.	ITGA2	211	.	0			c.T789C						PASS	.	T		701,3705	290.4+/-280.9	51,599,1553	96.0	95.0	96.0		789	1.4	1.0	5	dbSNP_86	96	822,7778	189.0+/-235.8	38,746,3516	no	coding-synonymous	ITGA2	NM_002203.3		89,1345,5069	CC,CT,TT		9.5581,15.9101,11.71		263/1182	52351377	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon8			ATATGCTTATTCA		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.789T>C	5.37:g.52351377T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|0.107;G|0.000;T|0.893	0.107	strong		0.358	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
SEC24B	10427	hgsc.bcm.edu	37	4	110384790	110384790	+	Silent	SNP	A	A	G	rs33911248	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:110384790A>G	ENST00000265175.5	+	2	922	c.867A>G	c.(865-867)ccA>ccG	p.P289P	SEC24B_ENST00000399100.2_Silent_p.P289P|SEC24B_ENST00000504968.2_Silent_p.P320P	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	289					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACAACAACCCAACCATTACTG	0.413													A|||	355	0.0708866	0.1051	0.0591	5008	,	,		21905	0.0		0.0934	False		,,,				2504	0.0828				p.P289P		Atlas-SNP	.											SEC24B_ENST00000265175,rectum,carcinoma,+1,2	SEC24B	186	2	0			c.A867G						PASS	.	A	,	484,3528		30,424,1552	64.0	63.0	64.0		867,867	-3.8	0.0	4	dbSNP_126	64	892,7488		42,808,3340	no	coding-synonymous,coding-synonymous	SEC24B	NM_001042734.1,NM_006323.2	,	72,1232,4892	GG,GA,AA		10.6444,12.0638,11.1039	,	289/1234,289/1269	110384790	1376,11016	2006	4190	6196	SO:0001819	synonymous_variant	10427	exon2			CAACCCAACCATT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.867A>G	4.37:g.110384790A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	CCDS47124.1																																																																																			A|0.915;G|0.085	0.085	strong		0.413	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
HS3ST6	64711	hgsc.bcm.edu	37	16	1961866	1961866	+	Silent	SNP	G	G	A	rs61742747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1961866G>A	ENST00000293937.3	-	2	753	c.754C>T	c.(754-756)Ctg>Ttg	p.L252L	HS3ST6_ENST00000454677.2_Silent_p.L269L|HS3ST6_ENST00000443547.1_Silent_p.L221L			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	252					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						TCGCTGACCAGACGCTCCCCG	0.667													g|||	315	0.0628994	0.1921	0.0331	5008	,	,		14253	0.0		0.0348	False		,,,				2504	0.0031				p.L221L		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C661T						PASS	.	A		704,3682	271.6+/-270.3	56,592,1545	48.0	58.0	55.0		661	3.9	1.0	16	dbSNP_129	55	266,8328	100.3+/-161.8	3,260,4034	no	coding-synonymous	HS3ST6	NM_001009606.2		59,852,5579	AA,AG,GG		3.0952,16.0511,7.473		221/312	1961866	970,12010	2193	4297	6490	SO:0001819	synonymous_variant	64711	exon2			TGACCAGACGCTC			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"""Sulfotransferases, membrane-bound"""	14178	protein-coding gene	gene with protein product			"""heparan sulfate (glucosamine) 3-O-sulfotransferase 5"""	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.754C>T	16.37:g.1961866G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	42	0.7	NM_001009606	Q96RX7	Silent	SNP	ENST00000293937.3	37																																																																																				G|0.953;A|0.047	0.047	strong		0.667	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32975257	32975257	+	Silent	SNP	C	C	T	rs365066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	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	
SPEG	10290	hgsc.bcm.edu	37	2	220356520	220356520	+	Silent	SNP	G	G	T	rs12473286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220356520G>T	ENST00000312358.7	+	39	9522	c.9390G>T	c.(9388-9390)ccG>ccT	p.P3130P	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	3130	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TGTCAGCTCCGGAGATGGTGA	0.627													G|||	1406	0.280751	0.267	0.2723	5008	,	,		16932	0.1458		0.2744	False		,,,				2504	0.4509				p.P3130P		Atlas-SNP	.											.	SPEG	272	.	0			c.G9390T						PASS	.	G		1007,3087		131,745,1171	51.0	59.0	56.0		9390	3.3	1.0	2	dbSNP_120	56	2196,6178		299,1598,2290	no	coding-synonymous	SPEG	NM_005876.4		430,2343,3461	TT,TG,GG		26.224,24.597,25.6898		3130/3268	220356520	3203,9265	2047	4187	6234	SO:0001819	synonymous_variant	10290	exon39			AGCTCCGGAGATG	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.9390G>T	2.37:g.220356520G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.755;T|0.245	0.245	strong		0.627	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
AKAP6	9472	hgsc.bcm.edu	37	14	33292914	33292914	+	Silent	SNP	A	A	C	rs2239648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:33292914A>C	ENST00000280979.4	+	13	6065	c.5895A>C	c.(5893-5895)ccA>ccC	p.P1965P	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1965					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)		AGAAATGTCCAAATCACCACC	0.378													A|||	1333	0.266174	0.4864	0.1499	5008	,	,		20480	0.251		0.1113	False		,,,				2504	0.226				p.P1965P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A5895C						PASS	.	A		1861,2545	529.5+/-372.7	406,1049,748	70.0	71.0	71.0		5895	0.5	0.6	14	dbSNP_98	71	893,7707	196.5+/-241.4	35,823,3442	no	coding-synonymous	AKAP6	NM_004274.4		441,1872,4190	CC,CA,AA		10.3837,42.2379,21.1748		1965/2320	33292914	2754,10252	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon13			ATGTCCAAATCAC	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.5895A>C	14.37:g.33292914A>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			A|0.767;C|0.233	0.233	strong		0.378	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
ACSL1	2180	hgsc.bcm.edu	37	4	185686032	185686032	+	Silent	SNP	C	C	T	rs2292898	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:185686032C>T	ENST00000515030.1	-	15	1732	c.1407G>A	c.(1405-1407)ctG>ctA	p.L469L	ACSL1_ENST00000454703.2_Silent_p.L298L|ACSL1_ENST00000437665.3_Silent_p.L298L|ACSL1_ENST00000507295.1_Silent_p.L435L|ACSL1_ENST00000504342.1_Silent_p.L469L|ACSL1_ENST00000513317.1_Silent_p.L469L|ACSL1_ENST00000281455.2_Silent_p.L469L			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	469					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CAGGCATGGTCAGGCAGCACC	0.473													C|||	4164	0.83147	0.9546	0.8242	5008	,	,		20689	0.9306		0.6511	False		,,,				2504	0.7536				p.L469L		Atlas-SNP	.											.	ACSL1	77	.	0			c.G1407A						PASS	.	C		4037,369	792.4+/-415.1	1847,343,13	69.0	63.0	65.0		1407	2.9	0.6	4	dbSNP_100	65	5660,2940	668.7+/-402.6	1851,1958,491	no	coding-synonymous	ACSL1	NM_001995.2		3698,2301,504	TT,TC,CC		34.186,8.3749,25.4421		469/699	185686032	9697,3309	2203	4300	6503	SO:0001819	synonymous_variant	2180	exon15			CATGGTCAGGCAG	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"""Acyl-CoA synthetase family"""	3569	protein-coding gene	gene with protein product	"""lignoceroyl-CoA synthase"", ""long-chain fatty-acid-coenzyme A ligase 1"""	152425	"""fatty-acid-Coenzyme A ligase, long-chain 2"""	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.1407G>A	4.37:g.185686032C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Silent	SNP	ENST00000515030.1	37	CCDS3839.1																																																																																			C|0.220;T|0.780	0.780	strong		0.473	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
KIAA1217	56243	hgsc.bcm.edu	37	10	24833407	24833407	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24833407T>C	ENST00000376454.3	+	19	5238	c.5208T>C	c.(5206-5208)cgT>cgC	p.R1736R	KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Silent_p.R1419R|KIAA1217_ENST00000458595.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1736					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CAGCTTCACGTAAGGTATCTT	0.493																																					p.R1736R		Atlas-SNP	.											KIAA1217,colon,carcinoma,+1,1	KIAA1217	235	1	0			c.T5208C						scavenged	.						45.0	45.0	45.0					10																	24833407		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			TTCACGTAAGGTA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5208T>C	10.37:g.24833407T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	65	3	0.0461538	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435797	7435797	+	Silent	SNP	G	G	A	rs34136551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7435797G>A	ENST00000319098.4	-	1	903	c.810C>T	c.(808-810)gaC>gaT	p.D270D	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	270					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						AGGGGACCCCGTCCATGGCCA	0.612													G|||	109	0.0217652	0.0068	0.0403	5008	,	,		18247	0.0		0.0626	False		,,,				2504	0.0092				p.D270D		Atlas-SNP	.											.	PSAPL1	51	.	0			c.C810T						PASS	.	G	,	52,4024		0,52,1986	43.0	48.0	46.0		810,	-6.7	0.0	4	dbSNP_126	46	387,7991		7,373,3809	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	7,425,5795	AA,AG,GG		4.6192,1.2758,3.525	,	270/522,	7435797	439,12015	2038	4189	6227	SO:0001819	synonymous_variant	768239	exon1			GACCCCGTCCATG	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.810C>T	4.37:g.7435797G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.963;A|0.037	0.037	strong		0.612	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
VCPKMT	79609	hgsc.bcm.edu	37	14	50583083	50583083	+	Missense_Mutation	SNP	G	G	T	rs11157729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50583083G>T	ENST00000395860.2	-	1	192	c.188C>A	c.(187-189)gCc>gAc	p.A63D	VCPKMT_ENST00000395859.2_Missense_Mutation_p.A63D	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	63			A -> D (in dbSNP:rs11157729).		peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										CAGCGCGTGGGCCCCGTCGCC	0.667													G|||	1252	0.25	0.2216	0.245	5008	,	,		12014	0.4603		0.1461	False		,,,				2504	0.182				p.A63D		Atlas-SNP	.											.	METTL21D	11	.	0			c.C188A						PASS	.	G	ASP/ALA,ASP/ALA	876,3530	312.2+/-292.5	86,704,1413	22.0	27.0	25.0		188,188	4.2	0.4	14	dbSNP_120	25	1343,7257	252.3+/-278.5	107,1129,3064	yes	missense,missense	METTL21D	NM_001040662.1,NM_024558.2	126,126	193,1833,4477	TT,TG,GG		15.6163,19.882,17.0614	benign,benign	63/195,63/230	50583083	2219,10787	2203	4300	6503	SO:0001583	missense	79609	exon1			GCGTGGGCCCCGT	AK023982	CCDS9696.2, CCDS41951.1	14q21.3	2013-09-30	2013-09-30	2013-09-30	ENSG00000100483	ENSG00000100483			20352	protein-coding gene	gene with protein product		615260	"""chromosome 14 open reading frame 138"", ""methyltransferase like 21D"""	C14orf138, METTL21D		22948820	Standard	NR_049738		Approved	VCP-KMT	uc001wxo.1	Q9H867	OTTHUMG00000029531	ENST00000395860.2:c.188C>A	14.37:g.50583083G>T	ENSP00000379201:p.Ala63Asp	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	37	CCDS9696.2	527	0.2413003663003663	93	0.18902439024390244	72	0.19889502762430938	252	0.4405594405594406	110	0.14511873350923482	G	13.02	2.111626	0.37242	0.19882	0.156163	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.06933	3.24;3.24	6.06	4.2	0.49525	.	0.741259	0.12068	N	0.502470	T	0.00012	0.0000	L	0.35288	1.05	0.80722	P	0.0	B;B	0.21381	0.055;0.055	B;B	0.21546	0.023;0.035	T	0.42582	-0.9443	9	0.15499	T	0.54	0.0014	6.6147	0.22771	0.0678:0.1304:0.6662:0.1355	rs11157729;rs57168136	63;63	B7ZLA4;Q9H867	.;MT21D_HUMAN	D	63	ENSP00000379200:A63D;ENSP00000379201:A63D	ENSP00000379200:A63D	A	-	2	0	METTL21D	49652833	0.008000	0.16893	0.394000	0.26270	0.985000	0.73830	0.585000	0.23879	0.849000	0.35215	0.650000	0.86243	GCC	G|0.812;T|0.188	0.188	strong		0.667	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558	
MAP4	4134	hgsc.bcm.edu	37	3	47956424	47956424	+	Missense_Mutation	SNP	C	C	T	rs1137524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:47956424C>T	ENST00000360240.6	-	8	2400	c.1882G>A	c.(1882-1884)Gtc>Atc	p.V628I	MAP4_ENST00000383737.4_Intron|MAP4_ENST00000426837.2_Missense_Mutation_p.V645I|MAP4_ENST00000395734.3_Missense_Mutation_p.V628I	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	628			V -> I (in dbSNP:rs1137524). {ECO:0000269|PubMed:1718985, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:20068231}.		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	GTTCCTGTGACGGTTTCTAAA	0.443													C|||	1947	0.388778	0.5628	0.3963	5008	,	,		18715	0.2847		0.3002	False		,,,				2504	0.3466				p.V628I		Atlas-SNP	.											.	MAP4	176	.	0			c.G1882A						PASS	.	C	ILE/VAL,ILE/VAL	2353,2053	607.5+/-391.0	627,1099,477	127.0	132.0	130.0		1882,1882	0.4	0.0	3	dbSNP_86	130	2696,5904	431.8+/-356.9	429,1838,2033	yes	missense,missense	MAP4	NM_001134364.1,NM_002375.4	29,29	1056,2937,2510	TT,TC,CC		31.3488,46.5956,38.8205	probably-damaging,probably-damaging	628/1136,628/1153	47956424	5049,7957	2203	4300	6503	SO:0001583	missense	4134	exon8			CTGTGACGGTTTC		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1882G>A	3.37:g.47956424C>T	ENSP00000353375:p.Val628Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	65	0.670103	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	736	0.336996336996337	242	0.491869918699187	129	0.356353591160221	144	0.2517482517482518	221	0.29155672823219	C	6.223	0.409250	0.11812	0.534044	0.313488	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.10192	3.1;2.9;3.1	4.42	0.416	0.16416	.	.	.	.	.	T	0.00012	0.0000	M	0.72118	2.19	0.80722	P	0.0	B;B;P	0.35208	0.137;0.216;0.49	B;B;B	0.22152	0.017;0.024;0.038	T	0.40496	-0.9560	8	0.34782	T	0.22	-1.0291	1.6979	0.02866	0.1672:0.4786:0.1625:0.1917	rs1137524;rs2230170;rs3201296;rs6442089;rs11548143;rs17434449;rs52792140;rs59940954;rs6442089	605;628;628	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	I	628;645;628	ENSP00000379083:V628I;ENSP00000407602:V645I;ENSP00000353375:V628I	ENSP00000353375:V628I	V	-	1	0	MAP4	47931428	0.019000	0.18553	0.014000	0.15608	0.015000	0.08874	-0.083000	0.11286	-0.054000	0.13266	-1.067000	0.02272	GTC	T|0.303;G|0.116;C|0.511;N|0.000;A|0.069	0.303	strong		0.443	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
HDAC4	9759	hgsc.bcm.edu	37	2	240036848	240036848	+	Silent	SNP	C	C	T	rs114495208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240036848C>T	ENST00000345617.3	-	13	2468	c.1677G>A	c.(1675-1677)aaG>aaA	p.K559K	HDAC4_ENST00000541256.1_Silent_p.K533K|HDAC4_ENST00000543185.1_Silent_p.K143K	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	559					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)		TGGGCTCCTGCTTCACCTGCA	0.687													C|||	13	0.00259585	0.0	0.0072	5008	,	,		16655	0.0		0.007	False		,,,				2504	0.001				p.K559K		Atlas-SNP	.											.	HDAC4	127	.	0			c.G1677A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	66.0	73.0	71.0		1677	2.3	1.0	2	dbSNP_132	71	44,8554	29.0+/-79.6	0,44,4255	no	coding-synonymous	HDAC4	NM_006037.3		0,49,6453	TT,TC,CC		0.5117,0.1135,0.3768		559/1085	240036848	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	9759	exon13			CTCCTGCTTCACC	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.1677G>A	2.37:g.240036848C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
ZNF683	257101	hgsc.bcm.edu	37	1	26688181	26688181	+	Silent	SNP	G	G	C	rs11583897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:26688181G>C	ENST00000436292.1	-	7	1656	c.1536C>G	c.(1534-1536)gcC>gcG	p.A512A	ZNF683_ENST00000403843.1_Silent_p.A512A|ZNF683_ENST00000349618.3_Silent_p.A492A|ZNF683_ENST00000374204.1_Silent_p.A492A			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	512					natural killer cell differentiation (GO:0001779)|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(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-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;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		GGGGAGTCCCGGCACTGCTCA	0.522													G|||	407	0.08127	0.1346	0.0533	5008	,	,		21791	0.0278		0.0875	False		,,,				2504	0.0777				p.A492A		Atlas-SNP	.											.	ZNF683	51	.	0			c.C1476G						PASS	.	G	,	494,3912	227.8+/-242.9	18,458,1727	135.0	132.0	133.0		1476,1476	-0.2	0.0	1	dbSNP_120	133	788,7812	184.2+/-232.2	33,722,3545	no	coding-synonymous,coding-synonymous	ZNF683	NM_001114759.1,NM_173574.2	,	51,1180,5272	CC,CG,GG		9.1628,11.212,9.857	,	492/505,492/505	26688181	1282,11724	2203	4300	6503	SO:0001819	synonymous_variant	257101	exon6			AGTCCCGGCACTG	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.1536C>G	1.37:g.26688181G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Silent	SNP	ENST00000436292.1	37																																																																																				G|0.907;C|0.093	0.093	strong		0.522	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
HRNR	388697	hgsc.bcm.edu	37	1	152185750	152185750	+	Silent	SNP	G	G	A	rs12729662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152185750G>A	ENST00000368801.2	-	3	8430	c.8355C>T	c.(8353-8355)taC>taT	p.Y2785Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2785					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGTTGGCCGTAGCTGGAAG	0.562													G|||	1716	0.342652	0.1172	0.415	5008	,	,		15303	0.6181		0.17	False		,,,				2504	0.4898				p.Y2785Y		Atlas-SNP	.											HRNR,colon,carcinoma,0,1	HRNR	403	1	0			c.C8355T						PASS	.						92.0	83.0	86.0					1																	152185750		2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			TTGGCCGTAGCTG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.8355C>T	1.37:g.152185750G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	168	131	0.779762	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.723;A|0.277	0.277	strong		0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
MVK	4598	hgsc.bcm.edu	37	12	110013879	110013879	+	Missense_Mutation	SNP	G	G	A	rs104895327|rs7957619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:110013879G>A	ENST00000228510.3	+	3	231	c.155G>A	c.(154-156)aGc>aAc	p.S52N	MVK_ENST00000535044.1_3'UTR|MMAB_ENST00000266839.5_5'Flank|MVK_ENST00000539575.1_Missense_Mutation_p.S52N|MVK_ENST00000541384.1_5'UTR|MMAB_ENST00000545712.2_5'Flank|MVK_ENST00000539696.1_Intron|MMAB_ENST00000540016.1_5'Flank|MVK_ENST00000392727.3_Missense_Mutation_p.S52N	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	52			S -> N (in dbSNP:rs7957619). {ECO:0000269|PubMed:11313769, ECO:0000269|PubMed:15536479}.		cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						GTGGACCTCAGCTTACCCAAC	0.502													G|||	380	0.0758786	0.1029	0.098	5008	,	,		19049	0.0		0.1471	False		,,,				2504	0.0286				p.S52N		Atlas-SNP	.											.	MVK	42	.	0			c.G155A						PASS	.	G	ASN/SER,ASN/SER	392,4014	194.0+/-219.0	18,356,1829	86.0	76.0	79.0		155,155	-4.1	0.0	12	dbSNP_116	79	1119,7481	231.4+/-265.4	69,981,3250	yes	missense,missense	MVK	NM_000431.2,NM_001114185.1	46,46	87,1337,5079	AA,AG,GG		13.0116,8.897,11.6177	benign,benign	52/397,52/397	110013879	1511,11495	2203	4300	6503	SO:0001583	missense	4598	exon3			ACCTCAGCTTACC	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"""LH receptor mRNA-binding protein"", ""mevalonic aciduria"""	251170	"""mevalonate kinase (mevalonic aciduria)"""			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.155G>A	12.37:g.110013879G>A	ENSP00000228510:p.Ser52Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_000431		Missense_Mutation	SNP	ENST00000228510.3	37	CCDS9132.1	204	0.09340659340659341	51	0.10365853658536585	43	0.11878453038674033	0	0.0	110	0.14511873350923482	G	0.024	-1.393647	0.01175	0.08897	0.130116	ENSG00000110921	ENST00000539335;ENST00000546277;ENST00000228510;ENST00000392727;ENST00000539575	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.25	-4.11	0.03928	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.464242	0.25596	N	0.029591	T	0.00754	0.0025	N	0.00991	-1.07	0.20307	P	0.99991635	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.0	T	0.46541	-0.9184	9	0.12103	T	0.63	-3.8097	7.7576	0.28933	0.3512:0.0:0.5294:0.1194	rs7957619;rs52800176;rs58148787;rs7957619	52;52	F5H8H2;Q03426	.;KIME_HUMAN	N	52	ENSP00000440379:S52N;ENSP00000438153:S52N;ENSP00000228510:S52N;ENSP00000376487:S52N;ENSP00000443551:S52N	ENSP00000228510:S52N	S	+	2	0	MVK	108498262	0.103000	0.21917	0.020000	0.16555	0.177000	0.22998	0.118000	0.15605	-0.505000	0.06568	-0.471000	0.05019	AGC	G|0.892;A|0.108	0.108	strong		0.502	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431	
SLC35E2	9906	hgsc.bcm.edu	37	1	1666167	1666167	+	Missense_Mutation	SNP	C	C	T	rs146479779		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1666167C>T	ENST00000246421.4	-	5	1109	c.694G>A	c.(694-696)Gta>Ata	p.V232I	SLC35E2_ENST00000400924.1_Missense_Mutation_p.V232I|SLC35E2_ENST00000475229.1_5'UTR|SLC35E2_ENST00000355439.2_Missense_Mutation_p.V232I|RP1-283E3.4_ENST00000417099.1_RNA|RP1-283E3.8_ENST00000598846.1_RNA	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	232						integral component of membrane (GO:0016021)		p.V232I(1)		endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGAGGGCGTACGCCGTGACGC	0.552																																					p.V232I		Atlas-SNP	.											SLC35E2,NS,carcinoid-endocrine_tumour,0,1	SLC35E2	13	1	1	Substitution - Missense(1)	pancreas(1)	c.G694A						scavenged	.						40.0	25.0	30.0					1																	1666167		2201	4275	6476	SO:0001583	missense	9906	exon5			GGCGTACGCCGTG	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"""Solute carriers"""	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.694G>A	1.37:g.1666167C>T	ENSP00000246421:p.Val232Ile	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	187	47	0.251337	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Missense_Mutation	SNP	ENST00000246421.4	37	CCDS33.1	.	.	.	.	.	.	.	.	.	.	c	14.26	2.482855	0.44147	.	.	ENSG00000215790	ENST00000355439;ENST00000400924;ENST00000246421	.	.	.	3.0	-2.18	0.07037	.	0.382752	0.21835	U	0.068420	T	0.13884	0.0336	N	0.08118	0	0.20975	N	0.999815	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.20240	-1.0281	9	0.20046	T	0.44	-9.892	7.073	0.25189	0.0:0.3883:0.2627:0.349	.	232;232	P0CK97;P0CK97-2	S35E2_HUMAN;.	I	232	.	ENSP00000246421:V232I	V	-	1	0	SLC35E2	1656027	0.667000	0.27484	0.932000	0.37286	0.364000	0.29643	-0.354000	0.07681	-0.661000	0.05345	-0.701000	0.03672	GTA	C|0.500;T|0.500	0.500	weak		0.552	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733	
ELF3	1999	hgsc.bcm.edu	37	1	201981218	201981218	+	Silent	SNP	C	C	G	rs11543979	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201981218C>G	ENST00000359651.3	+	2	3489	c.297C>G	c.(295-297)ggC>ggG	p.G99G	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Silent_p.G99G|ELF3_ENST00000367284.5_Silent_p.G99G|ELF3_ENST00000495848.1_3'UTR|RP11-465N4.4_ENST00000419190.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.G99G(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						ACATGGATGGCGCCACCCTCT	0.577													G|||	1694	0.338259	0.5424	0.2363	5008	,	,		20658	0.3363		0.2396	False		,,,				2504	0.2382				p.G99G		Atlas-SNP	.											ELF3,NS,carcinoma,0,1	ELF3	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C297G						scavenged	.	G	,	1965,2441	620.6+/-393.6	423,1119,661	88.0	80.0	83.0		297,297	-1.9	1.0	1	dbSNP_120	83	1879,6721	728.9+/-406.7	194,1491,2615	no	coding-synonymous,coding-synonymous	ELF3	NM_001114309.1,NM_004433.4	,	617,2610,3276	GG,GC,CC		21.8488,44.5983,29.5556	,	99/372,99/372	201981218	3844,9162	2203	4300	6503	SO:0001819	synonymous_variant	1999	exon3			GGATGGCGCCACC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.297C>G	1.37:g.201981218C>G		Somatic	107	2	0.0186916		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_001114309		Silent	SNP	ENST00000359651.3	37	CCDS1419.1																																																																																			C|0.695;G|0.305	0.305	strong		0.577	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
ATAD3C	219293	hgsc.bcm.edu	37	1	1387764	1387764	+	Missense_Mutation	SNP	G	G	A	rs9793256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1387764G>A	ENST00000378785.2	+	3	1167	c.172G>A	c.(172-174)Ggg>Agg	p.G58R		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	58							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)		CACCTTGTTTGGGGAAGGATT	0.567													N|||	1402	0.279952	0.1967	0.3314	5008	,	,		20431	0.3849		0.1571	False		,,,				2504	0.3742				p.G58R		Atlas-SNP	.											.	ATAD3C	23	.	0			c.G172A						PASS	.	G	ARG/GLY	238,1146		17,204,471	128.0	110.0	116.0		172	2.2	1.0	1	dbSNP_119	116	515,2667		57,401,1133	no	missense	ATAD3C	NM_001039211.2	125	74,605,1604	AA,AG,GG		16.1848,17.1965,16.4915	probably-damaging	58/412	1387764	753,3813	692	1591	2283	SO:0001583	missense	219293	exon3			TTGTTTGGGGAAG	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.172G>A	1.37:g.1387764G>A	ENSP00000368062:p.Gly58Arg	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	214	109	0.509346	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	556	0.25457875457875456	122	0.24796747967479674	99	0.27348066298342544	217	0.3793706293706294	118	0.15567282321899736	.	6.701	0.497956	0.12762	0.171965	0.161848	ENSG00000215915	ENST00000378785	D	0.94687	-3.49	2.18	2.18	0.27775	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.80616	2.505	0.09310	P	0.9999999850473	D	0.76494	0.999	D	0.77557	0.99	T	0.00000	-1.5390	9	0.59425	D	0.04	.	11.6938	0.51532	0.0:0.0:1.0:0.0	rs9793256	58	Q5T2N8	ATD3C_HUMAN	R	58	ENSP00000368062:G58R	ENSP00000368062:G58R	G	+	1	0	ATAD3C	1377627	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	7.824000	0.86668	1.224000	0.43551	0.194000	0.17425	GGG	G|0.744;A|0.256	0.256	strong		0.567	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
CR2	1380	hgsc.bcm.edu	37	1	207653395	207653395	+	Missense_Mutation	SNP	C	C	A	rs17617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:207653395C>A	ENST00000367058.3	+	17	3197	c.3008C>A	c.(3007-3009)gCa>gAa	p.A1003E	CR2_ENST00000367057.3_Missense_Mutation_p.A1062E|CR2_ENST00000367059.3_Missense_Mutation_p.A941E|CR2_ENST00000458541.2_Missense_Mutation_p.A976E	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	1003			A -> E (in dbSNP:rs6540433). {ECO:0000269|PubMed:2563370, ECO:0000269|PubMed:2827171}.		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						AAACACAGAGCACGGTAAGTT	0.373													A|||	4722	0.942891	0.9962	0.9121	5008	,	,		21110	1.0		0.837	False		,,,				2504	0.9427				p.A1062E		Atlas-SNP	.											.	CR2	164	.	0			c.C3185A						PASS	.	A	GLU/ALA,GLU/ALA	4299,107	85.3+/-124.0	2100,99,4	167.0	156.0	160.0		3185,3008	-2.1	0.8	1	dbSNP_116	160	7127,1469	280.2+/-294.4	2963,1201,134	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	107,107	5063,1300,138	AA,AC,CC		17.0893,2.4285,12.1212	benign,benign	1062/1093,1003/1034	207653395	11426,1576	2203	4298	6501	SO:0001583	missense	1380	exon18			ACAGAGCACGGTA	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.3008C>A	1.37:g.207653395C>A	ENSP00000356025:p.Ala1003Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	2026	0.9276556776556777	489	0.9939024390243902	324	0.8950276243093923	572	1.0	641	0.8456464379947229	A	0.039	-1.292762	0.01375	0.975715	0.829107	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.30714	1.59;1.52;1.64;1.57	4.74	-2.09	0.07232	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	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	0.40701	-0.9549	8	0.02654	T	1	.	0.2783	0.00241	0.3287:0.1429:0.2513:0.2771	rs6540433;rs17258989;rs52807086;rs60854041;rs6540433	941;1003;1062	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	E	1003;1062;941;976	ENSP00000356025:A1003E;ENSP00000356024:A1062E;ENSP00000356026:A941E;ENSP00000404222:A976E	ENSP00000356024:A1062E	A	+	2	0	CR2	205720018	0.848000	0.29623	0.759000	0.31340	0.308000	0.27856	-0.173000	0.09854	-0.826000	0.04284	-0.494000	0.04653	GCA	C|0.103;A|0.897	0.897	strong		0.373	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
SNRNP200	23020	hgsc.bcm.edu	37	2	96944553	96944553	+	Silent	SNP	G	G	A	rs772175	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	165	0	0		WXS	Illumina HiSeq	Phase_I	149	82	0.550336	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	
SNAP29	9342	hgsc.bcm.edu	37	22	21213416	21213416	+	Silent	SNP	A	A	G	rs1061064	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21213416A>G	ENST00000215730.7	+	1	146	c.18A>G	c.(16-18)aaA>aaG	p.K6K	PI4KA_ENST00000255882.6_5'Flank|PI4KA_ENST00000572273.1_5'Flank	NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	6					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|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;0.000592)|Lung(15;0.0117)			CTTACCCTAAAAGCTACAATC	0.731													A|||	2021	0.403554	0.1604	0.4323	5008	,	,		12279	0.372		0.5249	False		,,,				2504	0.6196				p.K6K		Atlas-SNP	.											SNAP29,NS,carcinoma,0,1	SNAP29	22	1	0			c.A18G						PASS	.	A		909,3459		120,669,1395	10.0	12.0	12.0		18	-2.2	0.2	22	dbSNP_86	12	4457,4057		1243,1971,1043	no	coding-synonymous	SNAP29	NM_004782.3		1363,2640,2438	GG,GA,AA		47.6509,20.8104,41.655		6/259	21213416	5366,7516	2184	4257	6441	SO:0001819	synonymous_variant	9342	exon1			CCCTAAAAGCTAC	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.18A>G	22.37:g.21213416A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_004782		Silent	SNP	ENST00000215730.7	37	CCDS13784.1																																																																																			A|0.600;G|0.400	0.400	strong		0.731	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
KDM5B	10765	hgsc.bcm.edu	37	1	202715288	202715288	+	Missense_Mutation	SNP	G	G	A	rs144876400		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202715288G>A	ENST00000367265.3	-	15	3344	c.2180C>T	c.(2179-2181)cCt>cTt	p.P727L	KDM5B_ENST00000367264.2_Missense_Mutation_p.P763L	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	727					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						ATATTTGTAAGGAGGACAGGA	0.388																																					p.P727L		Atlas-SNP	.											.	KDM5B	166	.	0			c.C2180T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	122.0	106.0	112.0		2180	5.1	0.9	1	dbSNP_134	112	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KDM5B	NM_006618.3	98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	727/1545	202715288	2,13004	2203	4300	6503	SO:0001583	missense	10765	exon15			TTGTAAGGAGGAC	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.2180C>T	1.37:g.202715288G>A	ENSP00000356234:p.Pro727Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	130	52	0.4	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916623	0.33815	0.0	2.33E-4	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790;ENST00000543924	D;D;D	0.88201	-2.35;-2.35;-2.35	5.97	5.06	0.68205	Zinc finger, C5HC2-type (1);	0.356049	0.34555	N	0.003863	D	0.85106	0.5621	L	0.52905	1.665	0.42064	D	0.991176	B;B	0.16396	0.017;0.005	B;B	0.19148	0.011;0.024	T	0.79704	-0.1692	10	0.34782	T	0.22	-10.6553	10.7795	0.46369	0.1402:0.0:0.8598:0.0	.	763;727	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	L	727;569;763;569;96	ENSP00000356234:P727L;ENSP00000356233:P763L;ENSP00000235790:P569L	ENSP00000235790:P569L	P	-	2	0	KDM5B	200981911	0.987000	0.35691	0.930000	0.37139	0.965000	0.64279	3.717000	0.54911	2.836000	0.97738	0.655000	0.94253	CCT	G|1.000;A|0.000	0.000	weak		0.388	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
CDCA2	157313	hgsc.bcm.edu	37	8	25364834	25364834	+	Missense_Mutation	SNP	A	A	T	rs3829009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:25364834A>T	ENST00000330560.3	+	15	3129	c.2652A>T	c.(2650-2652)agA>agT	p.R884S	CDCA2_ENST00000521098.2_3'UTR|CDCA2_ENST00000380665.3_Missense_Mutation_p.R869S	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	36	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	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	
ANKRD50	57182	hgsc.bcm.edu	37	4	125592065	125592065	+	Silent	SNP	C	C	A	rs10018651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:125592065C>A	ENST00000504087.1	-	4	3404	c.2367G>T	c.(2365-2367)gcG>gcT	p.A789A	ANKRD50_ENST00000515641.1_Silent_p.A610A	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	789										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GACCCATAGACGCTGCTGCTA	0.458													A|||	1436	0.286741	0.3918	0.2233	5008	,	,		24284	0.2619		0.2107	False		,,,				2504	0.2935				p.A789A		Atlas-SNP	.											.	ANKRD50	136	.	0			c.G2367T						PASS	.	A	,	1568,2838	668.5+/-402.0	259,1050,894	141.0	131.0	134.0		1830,2367	-0.4	0.9	4	dbSNP_119	134	1800,6800	732.8+/-406.9	201,1398,2701	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	460,2448,3595	AA,AC,CC		20.9302,35.5878,25.8957	,	610/1251,789/1430	125592065	3368,9638	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			CATAGACGCTGCT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2367G>T	4.37:g.125592065C>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	65	0.408805	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			C|0.743;A|0.257	0.257	strong		0.458	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
VEZT	55591	hgsc.bcm.edu	37	12	95693943	95693943	+	Missense_Mutation	SNP	G	G	A	rs17344738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:95693943G>A	ENST00000436874.1	+	12	1939	c.1834G>A	c.(1834-1836)Gtg>Atg	p.V612M	VEZT_ENST00000261219.6_Missense_Mutation_p.V564M|VEZT_ENST00000356859.4_3'UTR	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	612			V -> M (in dbSNP:rs17344738). {ECO:0000269|PubMed:17974005}.		chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						atttGAAGCCGTGTTGAAATC	0.299													G|||	352	0.0702875	0.0174	0.1297	5008	,	,		15706	0.0417		0.0696	False		,,,				2504	0.1299				p.V612M		Atlas-SNP	.											.	VEZT	106	.	0			c.G1834A						PASS	.	G	MET/VAL	66,3394		0,66,1664	13.0	11.0	12.0		1834	4.4	1.0	12	dbSNP_123	12	454,7410		10,434,3488	no	missense	VEZT	NM_017599.3	21	10,500,5152	AA,AG,GG		5.7731,1.9075,4.592	possibly-damaging	612/780	95693943	520,10804	1730	3932	5662	SO:0001583	missense	55591	exon12			GAAGCCGTGTTGA	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.1834G>A	12.37:g.95693943G>A	ENSP00000410083:p.Val612Met	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	14	0.736842	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	37	CCDS44954.1	136	0.06227106227106227	9	0.018292682926829267	42	0.11602209944751381	27	0.0472027972027972	58	0.07651715039577836	G	14.51	2.556863	0.45590	0.019075	0.057731	ENSG00000028203	ENST00000436874;ENST00000261219;ENST00000397792;ENST00000397796	T;T;T	0.18016	2.25;2.24;2.26	6.16	4.37	0.52481	.	0.194341	0.47852	D	0.000209	T	0.00210	0.0006	L	0.50333	1.59	0.38142	D	0.938482	P	0.43938	0.822	B	0.26864	0.074	T	0.11916	-1.0568	10	0.62326	D	0.03	-31.7729	13.7008	0.62608	0.1121:0.0:0.8879:0.0	rs17344738;rs52799363;rs17344738	612	Q9HBM0	VEZA_HUMAN	M	612;564;568;612	ENSP00000410083:V612M;ENSP00000261219:V564M;ENSP00000380894:V568M	ENSP00000261219:V564M	V	+	1	0	VEZT	94218074	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	4.425000	0.59875	0.952000	0.37798	-0.808000	0.03180	GTG	G|0.947;A|0.053	0.053	strong		0.299	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595831	140595831	+	Silent	SNP	G	G	T	rs145378952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140595831G>T	ENST00000341948.4	+	1	2323	c.2136G>T	c.(2134-2136)cgG>cgT	p.R712R		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	712					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)			TGGCGGTGCGGCTGTGTAGGA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		15801	0.0		0.001	False		,,,				2504	0.0				p.R712R		Atlas-SNP	.											.	PCDHB13	142	.	0			c.G2136T						PASS	.	G		0,4402		0,0,2201	88.0	97.0	94.0		2136	0.2	0.8	5	dbSNP_134	94	4,8580		0,4,4288	no	coding-synonymous	PCDHB13	NM_018933.2		0,4,6489	TT,TG,GG		0.0466,0.0,0.0308		712/799	140595831	4,12982	2201	4292	6493	SO:0001819	synonymous_variant	56123	exon1			GGTGCGGCTGTGT	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.2136G>T	5.37:g.140595831G>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			G|1.000;T|0.000	0.000	strong		0.662	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
SALL1	6299	hgsc.bcm.edu	37	16	51173559	51173559	+	Silent	SNP	G	G	A	rs1965024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:51173559G>A	ENST00000251020.4	-	2	2607	c.2574C>T	c.(2572-2574)ctC>ctT	p.L858L	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Silent_p.L761L|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	858					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)	p.L858L(1)		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)			TCGACATCTCGAGGGGCAAAG	0.527													G|||	2698	0.538738	0.1006	0.634	5008	,	,		21471	0.7173		0.6223	False		,,,				2504	0.7935				p.L858L	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,NS,carcinoma,0,1	SALL1	301	1	1	Substitution - coding silent(1)	prostate(1)	c.C2574T						PASS	.	G	,	890,3506	343.8+/-307.8	97,696,1405	96.0	94.0	95.0		2283,2574	-10.7	0.7	16	dbSNP_92	95	5503,3097	659.0+/-401.6	1761,1981,558	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	1858,2677,1963	AA,AG,GG		36.0116,20.2457,49.1921	,	761/1228,858/1325	51173559	6393,6603	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			CATCTCGAGGGGC	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.2574C>T	16.37:g.51173559G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			.	.	weak		0.527	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
WDFY4	57705	hgsc.bcm.edu	37	10	50186415	50186415	+	Missense_Mutation	SNP	C	C	T	rs2292584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50186415C>T	ENST00000325239.5	+	59	9380	c.9353C>T	c.(9352-9354)cCg>cTg	p.P3118L	WDFY4_ENST00000465910.1_3'UTR|RP11-523O18.5_ENST00000428825.4_RNA|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3118				P -> L (in Ref. 3; AAH47574 and 5; BAB13433). {ECO:0000305}.		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						GAGGAGCCCCCGGCTCAGCCT	0.617													C|||	2099	0.419129	0.3616	0.438	5008	,	,		19919	0.3512		0.4901	False		,,,				2504	0.4806				p.P3118L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C9353T						PASS	.	C	LEU/PRO	521,863		105,311,276	67.0	75.0	72.0		9353	-1.0	0.0	10	dbSNP_100	72	1572,1610		400,772,419	yes	missense	WDFY4	NM_020945.1	98	505,1083,695	TT,TC,CC		49.4029,37.6445,45.8388	benign	3118/3185	50186415	2093,2473	692	1591	2283	SO:0001583	missense	57705	exon60			AGCCCCCGGCTCA	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.9353C>T	10.37:g.50186415C>T	ENSP00000320563:p.Pro3118Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	31	0.688889	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	871|871	0.39880952380952384|0.39880952380952384	162|162	0.32926829268292684|0.32926829268292684	163|163	0.45027624309392267|0.45027624309392267	171|171	0.29895104895104896|0.29895104895104896	375|375	0.4947229551451187|0.4947229551451187	C|C	0.687|0.687	-0.796110|-0.796110	0.02862|0.02862	0.376445|0.376445	0.494029|0.494029	ENSG00000128815|ENSG00000128815	ENST00000325239;ENST00000544136|ENST00000265453	T|.	0.55413|.	0.52|.	4.77|4.77	-0.999|-0.999	0.10208|0.10208	WD40 repeat-like-containing domain (1);|.	.|.	.|.	.|.	.|.	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	0.47535|0.47535	-0.9110|-0.9110	7|4	.|.	.|.	.|.	.|.	2.2603|2.2603	0.04065|0.04065	0.1328:0.3971:0.2906:0.1794|0.1328:0.3971:0.2906:0.1794	rs2292584;rs58993406;rs2292584|rs2292584;rs58993406;rs2292584	3118|.	Q6ZS81|.	WDFY4_HUMAN|.	L|W	3118;581|1205	ENSP00000320563:P3118L|.	.|.	P|R	+|+	2|1	0|2	WDFY4|WDFY4	49856421|49856421	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.005000|0.005000	0.04900|0.04900	-0.189000|-0.189000	0.09629|0.09629	-0.062000|-0.062000	0.13088|0.13088	-0.254000|-0.254000	0.11334|0.11334	CCG|CGG	C|0.598;T|0.402	0.402	strong		0.617	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ANO7	50636	hgsc.bcm.edu	37	2	242144308	242144308	+	Silent	SNP	G	G	A	rs139761441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242144308G>A	ENST00000274979.8	+	10	1183	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A	ANO7_ENST00000402430.3_Silent_p.A359A	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	360					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						TCCTGCCAGCGGCAGTGGTGG	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		16608	0.0		0.004	False		,,,				2504	0.0				p.A360A		Atlas-SNP	.											.	ANO7	136	.	0			c.G1080A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	52.0	55.0	54.0		1080	-5.1	0.1	2	dbSNP_134	54	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	ANO7	NM_001001891.3		0,25,6478	AA,AG,GG		0.2674,0.0454,0.1922		360/934	242144308	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	50636	exon10			GCCAGCGGCAGTG	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.1080G>A	2.37:g.242144308G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.998;A|0.002	0.002	strong		0.632	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
UBE3D	90025	hgsc.bcm.edu	37	6	83667045	83667045	+	Missense_Mutation	SNP	C	C	T	rs7739323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	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	
TAS1R3	83756	hgsc.bcm.edu	37	1	1268462	1268462	+	Silent	SNP	G	G	A	rs138915131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1268462G>A	ENST00000339381.5	+	4	1469	c.1437G>A	c.(1435-1437)agG>agA	p.R479R		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	479					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		GCAGCCTCAGGACAGAGCGCC	0.667													g|||	17	0.00339457	0.0015	0.0058	5008	,	,		15673	0.0		0.0109	False		,,,				2504	0.0				p.R479R		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G1437A						PASS	.	G		6,4396	14.3+/-33.2	0,6,2195	48.0	45.0	46.0		1437	-1.7	0.0	1	dbSNP_134	46	113,8475	58.7+/-120.3	0,113,4181	no	coding-synonymous	TAS1R3	NM_152228.1		0,119,6376	AA,AG,GG		1.3158,0.1363,0.9161		479/853	1268462	119,12871	2201	4294	6495	SO:0001819	synonymous_variant	83756	exon4			CCTCAGGACAGAG	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1437G>A	1.37:g.1268462G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_152228	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																			G|0.994;A|0.006	0.006	strong		0.667	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113209195	113209195	+	Missense_Mutation	SNP	T	T	G	rs1889323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:113209195T>G	ENST00000401783.2	-	25	4582	c.4246A>C	c.(4246-4248)Aaa>Caa	p.K1416Q	SVEP1_ENST00000374469.1_Missense_Mutation_p.K1393Q|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Missense_Mutation_p.K1416Q	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1416	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		K -> Q (in dbSNP:rs1889323).		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						TCACACCTTTTGCCTGAAAAT	0.343													T|||	568	0.113419	0.0401	0.1037	5008	,	,		19021	0.0327		0.1561	False		,,,				2504	0.2587				p.K1416Q		Atlas-SNP	.											.	SVEP1	326	.	0			c.A4246C						PASS	.	T	GLN/LYS	152,2988		5,142,1423	87.0	79.0	82.0		4246	4.8	1.0	9	dbSNP_92	82	1038,5840		81,876,2482	yes	missense	SVEP1	NM_153366.3	53	86,1018,3905	GG,GT,TT		15.0916,4.8408,11.8786	benign	1416/3572	113209195	1190,8828	1570	3439	5009	SO:0001583	missense	79987	exon25			ACCTTTTGCCTGA	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.4246A>C	9.37:g.113209195T>G	ENSP00000384917:p.Lys1416Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	185	0.08470695970695971	17	0.034552845528455285	36	0.09944751381215469	17	0.02972027972027972	115	0.1517150395778364	T	13.99	2.401177	0.42613	0.048408	0.150916	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	D;D;D	0.86562	-2.14;-2.14;-2.14	5.95	4.8	0.61643	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.351938	0.39407	N	0.001370	T	0.01661	0.0053	L	0.42744	1.35	0.40196	P	0.022534000000000054	B;B	0.15719	0.014;0.007	B;B	0.18871	0.023;0.003	T	0.50206	-0.8855	9	0.13108	T	0.6	.	13.096	0.59192	0.0:0.0:0.1385:0.8615	rs1889323;rs52835560;rs57327200;rs1889323	1416;1416	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	Q	1416;1393;1416	ENSP00000384917:K1416Q;ENSP00000363593:K1393Q;ENSP00000304118:K1416Q	ENSP00000304118:K1416Q	K	-	1	0	SVEP1	112249016	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.923000	0.56469	1.057000	0.40506	0.533000	0.62120	AAA	T|0.902;G|0.098	0.098	strong		0.343	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CD200	4345	hgsc.bcm.edu	37	3	112066562	112066562	+	Silent	SNP	G	G	A	rs1050572	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:112066562G>A	ENST00000315711.8	+	4	636	c.579G>A	c.(577-579)acG>acA	p.T193T	CD200_ENST00000473539.1_Silent_p.T218T|CD200_ENST00000383681.3_Silent_p.T119T	NM_005944.5	NP_005935.4	P41217	OX2G_HUMAN	CD200 molecule	193	Ig-like C2-type.				regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.T218T(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				ATGGGACCACGTCTGTTACCA	0.557													G|||	1072	0.214058	0.3132	0.0677	5008	,	,		729	0.255		0.0746	False		,,,				2504	0.2853				p.T218T		Atlas-SNP	.											CD200,NS,carcinoma,0,1	CD200	33	1	1	Substitution - coding silent(1)	stomach(1)	c.G654A						scavenged	.	G	,	1219,3187	424.0+/-340.3	151,917,1135	128.0	125.0	126.0		654,579	-9.3	0.4	3	dbSNP_86	126	657,7943	166.4+/-218.3	24,609,3667	no	coding-synonymous,coding-synonymous	CD200	NM_001004196.2,NM_005944.5	,	175,1526,4802	AA,AG,GG		7.6395,27.6668,14.4241	,	218/295,193/270	112066562	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	4345	exon5			GACCACGTCTGTT		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7203	protein-coding gene	gene with protein product		155970	"""antigen identified by monoclonal antibody MRC OX-2"", ""CD200 antigen"""	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000315711.8:c.579G>A	3.37:g.112066562G>A		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Silent	SNP	ENST00000315711.8	37	CCDS2965.1																																																																																			G|0.836;A|0.164	0.164	strong		0.557	CD200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354078.1		
FLG	2312	hgsc.bcm.edu	37	1	152282917	152282917	+	Missense_Mutation	SNP	G	G	T	rs11204978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152282917G>T	ENST00000368799.1	-	3	4480	c.4445C>A	c.(4444-4446)tCc>tAc	p.S1482Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1482	Ser-rich.		S -> Y (in dbSNP:rs11204978).		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)			ACCGTCTTGGGATGCTGAGTG	0.572									Ichthyosis				G|||	1438	0.287141	0.0113	0.3905	5008	,	,		21395	0.5823		0.1421	False		,,,				2504	0.4315				p.S1482Y		Atlas-SNP	.											.	FLG	900	.	0			c.C4445A						PASS	.	G	TYR/SER	161,4245	108.2+/-146.6	2,157,2044	367.0	352.0	357.0		4445	0.7	0.0	1	dbSNP_120	357	1240,7360	249.0+/-276.5	97,1046,3157	no	missense	FLG	NM_002016.1	144	99,1203,5201	TT,TG,GG		14.4186,3.6541,10.772	possibly-damaging	1482/4062	152282917	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTTGGGATGCTG	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.4445C>A	1.37:g.152282917G>T	ENSP00000357789:p.Ser1482Tyr	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	227	145	0.638767	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	572	0.2619047619047619	9	0.018292682926829267	118	0.3259668508287293	333	0.5821678321678322	112	0.14775725593667546	G	8.364	0.833852	0.16820	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.03801	3.8	2.75	0.67	0.17923	.	.	.	.	.	T	0.01800	0.0057	M	0.81682	2.555	0.80722	P	0.0	P	0.41978	0.767	B	0.40825	0.341	T	0.36890	-0.9729	8	0.02654	T	1	.	4.9552	0.14035	0.0:0.24:0.5137:0.2463	rs11204978;rs52811516;rs11204978	1482	P20930	FILA_HUMAN	Y	1482	ENSP00000357789:S1482Y	ENSP00000357789:S1482Y	S	-	2	0	FLG	150549541	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.247000	0.18179	0.192000	0.20272	0.556000	0.70494	TCC	G|0.836;T|0.164	0.164	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR51B6	390058	hgsc.bcm.edu	37	11	5373562	5373562	+	Missense_Mutation	SNP	C	C	A	rs5024042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373562C>A	ENST00000380219.1	+	1	825	c.825C>A	c.(823-825)agC>agA	p.S275R	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	275			S -> R (in dbSNP:rs5024042). {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)			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)		TCACAATGAGCTACATCCACT	0.393													C|||	1164	0.232428	0.326	0.2349	5008	,	,		23831	0.0863		0.2644	False		,,,				2504	0.2219				p.S275R		Atlas-SNP	.											.	OR51B6	53	.	0			c.C825A						PASS	.	C	ARG/SER	1287,3115	438.8+/-345.5	173,941,1087	199.0	181.0	187.0		825	2.3	1.0	11	dbSNP_113	187	2270,6324	382.2+/-340.3	310,1650,2337	yes	missense	OR51B6	NM_001004750.1	110	483,2591,3424	AA,AC,CC		26.4138,29.2367,27.37	probably-damaging	275/313	5373562	3557,9439	2201	4297	6498	SO:0001583	missense	390058	exon1			AATGAGCTACATC		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.825C>A	11.37:g.5373562C>A	ENSP00000369568:p.Ser275Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	162	73	0.450617	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	C	15.09	2.730424	0.48939	0.292367	0.264138	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00262	8.4	5.13	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	0.091548	0.48286	D	0.000198	T	0.00012	0.0000	M	0.90759	3.145	0.39650	P	0.02954599999999996	D	0.89917	1.0	D	0.97110	1.0	T	0.46498	-0.9187	9	0.72032	D	0.01	.	9.0581	0.36419	0.0:0.7606:0.0:0.2394	rs5024042;rs52807625;rs58117426;rs5024042	275	Q9H340	O51B6_HUMAN	R	274;275	ENSP00000369568:S275R	ENSP00000369568:S275R	S	+	3	2	OR51B6	5330138	0.000000	0.05858	0.967000	0.41034	0.805000	0.45488	-0.398000	0.07259	0.347000	0.23924	-0.142000	0.14014	AGC	C|0.767;A|0.233	0.233	strong		0.393	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
GALNT12	79695	hgsc.bcm.edu	37	9	101570336	101570336	+	Missense_Mutation	SNP	A	A	T	rs1137654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:101570336A>T	ENST00000375011.3	+	1	356	c.356A>T	c.(355-357)gAg>gTg	p.E119V		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	119			E -> V (in dbSNP:rs1137654). {ECO:0000269|PubMed:12135769, ECO:0000269|PubMed:19617566}.		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)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				CGCCTGCCCGAGCGCTGGAAC	0.677													A|||	143	0.0285543	0.0061	0.0389	5008	,	,		9421	0.001		0.0865	False		,,,				2504	0.0204				p.E119V		Atlas-SNP	.											.	GALNT12	37	.	0			c.A356T						PASS	.		VAL/GLU	68,4208		0,68,2070	6.0	7.0	7.0		356	3.7	1.0	9	dbSNP_120	7	664,7712		19,626,3543	yes	missense	GALNT12	NM_024642.4	121	19,694,5613	TT,TA,AA		7.9274,1.5903,5.7856	possibly-damaging	119/582	101570336	732,11920	2138	4188	6326	SO:0001583	missense	79695	exon1			TGCCCGAGCGCTG	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19877	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 12"""	610290	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"""			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.356A>T	9.37:g.101570336A>T	ENSP00000364150:p.Glu119Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Missense_Mutation	SNP	ENST00000375011.3	37	CCDS6737.1	82	0.037545787545787544	6	0.012195121951219513	14	0.03867403314917127	0	0.0	62	0.08179419525065963	a	19.38	3.817277	0.70912	0.015903	0.079274	ENSG00000119514	ENST00000375011	T	0.60548	0.18	3.74	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.05090	0.0136	M	0.76838	2.35	0.52501	D	0.999955	P	0.42827	0.791	B	0.35240	0.198	T	0.22800	-1.0206	10	0.87932	D	0	.	8.9953	0.36048	1.0:0.0:0.0:0.0	rs1137654	119	Q8IXK2	GLT12_HUMAN	V	119	ENSP00000364150:E119V	ENSP00000364150:E119V	E	+	2	0	GALNT12	100610157	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.587000	0.82613	1.679000	0.50963	0.375000	0.23000	GAG	A|0.957;T|0.043	0.043	strong		0.677	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642	
HEATR4	399671	hgsc.bcm.edu	37	14	73969610	73969610	+	Silent	SNP	G	G	A	rs11626122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73969610G>A	ENST00000553558.1	-	11	2415	c.2094C>T	c.(2092-2094)caC>caT	p.H698H	HEATR4_ENST00000560393.1_Silent_p.H651H|HEATR4_ENST00000334988.2_Silent_p.H698H	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	698										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)		TGATTATGTCGTGCACCTCTT	0.493													G|||	926	0.184904	0.0787	0.268	5008	,	,		19315	0.2867		0.174	False		,,,				2504	0.1759				p.H698H		Atlas-SNP	.											.	HEATR4	126	.	0			c.C2094T						PASS	.	G	,	427,3979	209.5+/-230.2	20,387,1796	164.0	142.0	150.0		2094,2094	1.4	0.8	14	dbSNP_120	150	1174,7426	239.3+/-270.5	86,1002,3212	no	coding-synonymous,coding-synonymous	HEATR4	NM_001220484.1,NM_203309.2	,	106,1389,5008	AA,AG,GG		13.6512,9.6913,12.3097	,	698/1027,698/1027	73969610	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	399671	exon10			TATGTCGTGCACC	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.2094C>T	14.37:g.73969610G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	37	CCDS9815.2																																																																																			G|0.841;A|0.159	0.159	strong		0.493	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39465094C>T	ENST00000391352.1	-	1	411	c.412G>A	c.(412-414)Gtt>Att	p.V138I		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	138	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GGCTCACAAACGGTGGCCTCA	0.562													T|||	1153	0.230232	0.2806	0.147	5008	,	,		24905	0.3204		0.1849	False		,,,				2504	0.1748				p.V138I		Atlas-SNP	.											KRTAP16-1,NS,carcinoma,+2,1	KRTAP16-1	12	1	0			c.G412A						PASS	.																																			SO:0001583	missense	100505753	exon1			CACAAACGGTGGC	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.412G>A	17.37:g.39465094C>T	ENSP00000375147:p.Val138Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	158	84	0.531646	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	493	0.22573260073260074	124	0.25203252032520324	56	0.15469613259668508	175	0.30594405594405594	138	0.1820580474934037	T	0.005	-2.230228	0.00280	.	.	ENSG00000212657	ENST00000391352	T	0.01335	5.0	3.88	-7.76	0.01232	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	.	.	.	.	.	.	T	0.51395	-0.8711	6	0.39692	T	0.17	.	10.9678	0.47422	0.0:0.6171:0.225:0.1579	rs12453338;rs12453338	.	.	.	I	138	ENSP00000375147:V138I	ENSP00000375147:V138I	V	-	1	0	KRTAP16-1	36718620	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.707000	0.01893	-2.488000	0.00518	-1.265000	0.01443	GTT	C|0.771;T|0.229	0.229	strong		0.562	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
MASP1	5648	hgsc.bcm.edu	37	3	186953808	186953808	+	Intron	SNP	C	C	T	rs850312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186953808C>T	ENST00000337774.5	-	10	1693				MASP1_ENST00000392472.2_Silent_p.L504L|MASP1_ENST00000495249.1_5'UTR|MASP1_ENST00000296280.6_Silent_p.L617L	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)						complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.L617L(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TGACATACTGCAGGACATCTG	0.562													C|||	1061	0.211861	0.0265	0.3473	5008	,	,		21420	0.2034		0.3479	False		,,,				2504	0.2352				p.L617L		Atlas-SNP	.											MASP1_ENST00000296280,NS,carcinoma,0,1	MASP1	240	1	1	Substitution - coding silent(1)	stomach(1)	c.G1851A						PASS	.	C	,	299,4107	164.0+/-195.7	15,269,1919	109.0	94.0	99.0		,1851	-6.7	0.3	3	dbSNP_86	99	2918,5682	456.7+/-364.1	497,1924,1879	no	intron,coding-synonymous	MASP1	NM_001879.5,NM_139125.3	,	512,2193,3798	TT,TC,CC		33.9302,6.7862,24.7347	,	,617/729	186953808	3217,9789	2203	4300	6503	SO:0001627	intron_variant	5648	exon11			ATACTGCAGGACA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1303+5460G>A	3.37:g.186953808C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	91	59	0.648352	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																			T|0.232;G|0.004	0.232	strong		0.562	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
MEGF6	1953	hgsc.bcm.edu	37	1	3425183	3425183	+	Silent	SNP	G	G	A	rs61735125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3425183G>A	ENST00000356575.4	-	13	1825	c.1599C>T	c.(1597-1599)tgC>tgT	p.C533C	MEGF6_ENST00000294599.4_Silent_p.C428C	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	533	EGF-like 9. {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)		GGCCCAGGAGGCAGGTCCCTC	0.642													G|||	325	0.0648962	0.028	0.0519	5008	,	,		17150	0.1032		0.0507	False		,,,				2504	0.0992				p.C533C	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C1599T						PASS	.	G		145,4025		4,137,1944	47.0	54.0	52.0		1599	3.5	0.9	1	dbSNP_129	52	502,7904		12,478,3713	no	coding-synonymous	MEGF6	NM_001409.3		16,615,5657	AA,AG,GG		5.9719,3.4772,5.1447		533/1542	3425183	647,11929	2085	4203	6288	SO:0001819	synonymous_variant	1953	exon13			CAGGAGGCAGGTC	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.1599C>T	1.37:g.3425183G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	287	146	0.508711	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			G|0.940;A|0.060	0.060	strong		0.642	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
ZNF439	90594	hgsc.bcm.edu	37	19	11978828	11978828	+	Missense_Mutation	SNP	G	G	T	rs112352083	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11978828G>T	ENST00000304030.2	+	3	1144	c.944G>T	c.(943-945)aGa>aTa	p.R315I	ZNF439_ENST00000455282.1_Missense_Mutation_p.R179I|ZNF439_ENST00000592534.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	315					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						TATGTTCGTAGACATGAAAGG	0.413													g|||	69	0.013778	0.0023	0.0173	5008	,	,		22307	0.0		0.0447	False		,,,				2504	0.0092				p.R315I		Atlas-SNP	.											.	ZNF439	67	.	0			c.G944T						PASS	.	G	ILE/ARG	42,4364	44.6+/-78.6	0,42,2161	128.0	126.0	126.0		944	-1.1	0.0	19	dbSNP_132	126	368,8232	121.3+/-180.4	3,362,3935	no	missense	ZNF439	NM_152262.2	97	3,404,6096	TT,TG,GG		4.2791,0.9532,3.1524	benign	315/500	11978828	410,12596	2203	4300	6503	SO:0001583	missense	90594	exon3			TTCGTAGACATGA	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.944G>T	19.37:g.11978828G>T	ENSP00000305077:p.Arg315Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	42	0.019230769230769232	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	34	0.044854881266490766	g	2.769	-0.256159	0.05829	0.009532	0.042791	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.26223	1.75;1.75	0.575	-1.15	0.09709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03305	0.0096	L	0.44542	1.39	0.09310	N	0.999996	B	0.02656	0.0	B	0.09377	0.004	T	0.34030	-0.9845	9	0.13470	T	0.59	.	2.7752	0.05345	0.2309:0.0:0.477:0.2921	.	315	Q8NDP4	ZN439_HUMAN	I	179;315	ENSP00000395632:R179I;ENSP00000305077:R315I	ENSP00000305077:R315I	R	+	2	0	ZNF439	11839828	0.000000	0.05858	0.007000	0.13788	0.218000	0.24690	-2.442000	0.01014	-0.470000	0.06901	0.194000	0.17425	AGA	G|0.972;T|0.028	0.028	strong		0.413	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67243024	67243024	+	Missense_Mutation	SNP	C	C	A	rs2133173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:67243024C>A	ENST00000282670.2	+	5	555	c.427C>A	c.(427-429)Ctt>Att	p.L143I		NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	143			L -> I (in dbSNP:rs2133173). {ECO:0000269|PubMed:15489334}.							large_intestine(2)|lung(10)|skin(1)	13						GCAGAGCATACTTATTGGAAG	0.383													C|||	990	0.197684	0.205	0.2219	5008	,	,		17572	0.1012		0.2932	False		,,,				2504	0.1718				p.L143I		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.C427A						PASS	.	C	ILE/LEU	1034,3372	379.9+/-323.5	109,816,1278	164.0	170.0	168.0		427	1.9	0.8	1	dbSNP_96	168	2542,6058	415.5+/-351.8	397,1748,2155	yes	missense	TCTEX1D1	NM_152665.2	5	506,2564,3433	AA,AC,CC		29.5581,23.468,27.495	benign	143/180	67243024	3576,9430	2203	4300	6503	SO:0001583	missense	200132	exon5			AGCATACTTATTG	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.427C>A	1.37:g.67243024C>A	ENSP00000282670:p.Leu143Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	37	CCDS633.1	490	0.22435897435897437	104	0.21138211382113822	92	0.2541436464088398	60	0.1048951048951049	234	0.3087071240105541	C	5.444	0.267048	0.10294	0.23468	0.295581	ENSG00000152760	ENST00000282670	T	0.29655	1.56	5.93	1.91	0.25777	.	0.696895	0.15165	N	0.276948	T	0.11793	0.0287	L	0.59436	1.845	0.53688	P	2.8999999999945736E-5	B	0.20368	0.044	B	0.25759	0.063	T	0.15925	-1.0420	9	0.22109	T	0.4	1.5115	7.868	0.29549	0.0:0.6817:0.1202:0.1981	rs2133173;rs17495194;rs52837318;rs59922194;rs2133173	143	Q8N7M0	TC1D1_HUMAN	I	143	ENSP00000282670:L143I	ENSP00000282670:L143I	L	+	1	0	TCTEX1D1	67015612	0.160000	0.22878	0.828000	0.32881	0.190000	0.23558	1.313000	0.33585	0.105000	0.17753	0.655000	0.94253	CTT	C|0.762;N|0.000	.	strong		0.383	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	
CNN2	1265	hgsc.bcm.edu	37	19	1032689	1032689	+	Silent	SNP	G	G	T	rs1141534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1032689G>T	ENST00000263097.4	+	4	747	c.384G>T	c.(382-384)gcG>gcT	p.A128A	CNN2_ENST00000562958.2_Silent_p.A128A|CNN2_ENST00000348419.3_Silent_p.A128A|CNN2_ENST00000565096.2_Intron|CNN2_ENST00000606983.1_3'UTR	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	128	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		tcgccctggcggggaaggtga	0.572													G|||	636	0.126997	0.028	0.1354	5008	,	,		20053	0.1429		0.1948	False		,,,				2504	0.1687				p.A128A		Atlas-SNP	.											.	CNN2	26	.	0			c.G384T						PASS	.	G	,	259,4143		9,241,1951	24.0	20.0	21.0		384,384	-8.1	0.6	19	dbSNP_86	21	1763,6833		184,1395,2719	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	193,1636,4670	TT,TG,GG		20.5095,5.8837,15.5562	,	128/310,128/271	1032689	2022,10976	2201	4298	6499	SO:0001819	synonymous_variant	1265	exon4			CCTGGCGGGGAAG	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.384G>T	19.37:g.1032689G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_201277	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			G|0.862;T|0.138	0.138	strong		0.572	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
APLF	200558	hgsc.bcm.edu	37	2	68729992	68729992	+	Missense_Mutation	SNP	A	A	G	rs11902811	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68729992A>G	ENST00000303795.4	+	3	469	c.298A>G	c.(298-300)Att>Gtt	p.I100V		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	100	FHA-like.		I -> V (in dbSNP:rs11902811).		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						CATTTTCCGCATTCTCTCTAT	0.373													G|||	804	0.160543	0.4841	0.0461	5008	,	,		16152	0.0357		0.0497	False		,,,				2504	0.047				p.I100V		Atlas-SNP	.											.	APLF	69	.	0			c.A298G						PASS	.	G	VAL/ILE	1877,2529		439,999,765	137.0	138.0	137.0		298	5.1	0.8	2	dbSNP_120	137	456,8144		14,428,3858	yes	missense	APLF	NM_173545.2	29	453,1427,4623	GG,GA,AA		5.3023,42.601,17.9379	benign	100/512	68729992	2333,10673	2203	4300	6503	SO:0001583	missense	200558	exon3			TTCCGCATTCTCT	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.298A>G	2.37:g.68729992A>G	ENSP00000307004:p.Ile100Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	167	72	0.431138	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	310	0.14194139194139194	240	0.4878048780487805	15	0.04143646408839779	20	0.03496503496503497	35	0.04617414248021108	N	0.018	-1.473098	0.01044	0.42601	0.053023	ENSG00000169621	ENST00000303795	T	0.18502	2.21	5.09	5.09	0.68999	SMAD/FHA domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00413	-1.525	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44081	-0.9351	9	0.02654	T	1	.	11.3629	0.49655	0.0866:0.0:0.9134:0.0	rs11902811;rs57585915;rs11902811	100;100	F8WET0;Q8IW19	.;APLF_HUMAN	V	100	ENSP00000307004:I100V	ENSP00000307004:I100V	I	+	1	0	APLF	68583496	0.999000	0.42202	0.847000	0.33407	0.004000	0.04260	2.004000	0.40854	1.283000	0.44513	-0.213000	0.12676	ATT	A|0.831;G|0.169	0.169	strong		0.373	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
OR52M1	119772	hgsc.bcm.edu	37	11	4567335	4567335	+	Missense_Mutation	SNP	C	C	G	rs2657167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4567335C>G	ENST00000360213.1	+	1	915	c.915C>G	c.(913-915)agC>agG	p.S305R		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	305			S -> R (in dbSNP:rs2657167).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S305R(1)		endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCGAGAGAGCCTTCTCCAAA	0.438													G|||	2131	0.425519	0.584	0.268	5008	,	,		21751	0.3046		0.3827	False		,,,				2504	0.4918				p.S305R		Atlas-SNP	.											OR52M1,NS,carcinoma,0,1	OR52M1	53	1	1	Substitution - Missense(1)	stomach(1)	c.C915G						PASS	.	G	ARG/SER	2358,2044	562.1+/-380.9	633,1092,476	89.0	85.0	86.0		915	-2.9	0.0	11	dbSNP_100	86	3417,5179	634.9+/-398.9	671,2075,1552	yes	missense	OR52M1	NM_001004137.1	110	1304,3167,2028	GG,GC,CC		39.751,46.4334,44.4299	benign	305/318	4567335	5775,7223	2201	4298	6499	SO:0001583	missense	119772	exon1			AGAGAGCCTTCTC	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.915C>G	11.37:g.4567335C>G	ENSP00000353343:p.Ser305Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	37	CCDS31353.1	856	0.39194139194139194	287	0.5833333333333334	109	0.3011049723756906	193	0.3374125874125874	267	0.35224274406332456	G	0	-2.710022	0.00094	0.535666	0.39751	ENSG00000197790	ENST00000360213	T	0.36520	1.25	4.91	-2.88	0.05682	.	0.000000	0.51477	N	0.000090	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	0.22626	-1.0211	9	0.02654	T	1	.	2.3754	0.04340	0.4729:0.1261:0.2719:0.1291	rs2657167;rs57297503;rs2657167	305	Q8NGK5	O52M1_HUMAN	R	305	ENSP00000353343:S305R	ENSP00000353343:S305R	S	+	3	2	OR52M1	4523911	0.000000	0.05858	0.007000	0.13788	0.202000	0.24057	-0.773000	0.04689	-1.036000	0.03287	-0.729000	0.03580	AGC	C|0.521;G|0.479	0.479	strong		0.438	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
ASPHD2	57168	hgsc.bcm.edu	37	22	26830316	26830316	+	Silent	SNP	G	G	A	rs11705277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26830316G>A	ENST00000215906.5	+	2	1173	c.735G>A	c.(733-735)agG>agA	p.R245R		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	245					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						GGAACTGTAGGAAGTGCCCAC	0.562													G|||	311	0.0621006	0.0401	0.0576	5008	,	,		20689	0.0169		0.1372	False		,,,				2504	0.0644				p.R245R		Atlas-SNP	.											.	ASPHD2	42	.	0			c.G735A						PASS	.	G		312,4094	167.3+/-198.3	10,292,1901	134.0	126.0	129.0		735	2.7	1.0	22	dbSNP_120	129	1439,7161	276.8+/-292.5	125,1189,2986	no	coding-synonymous	ASPHD2	NM_020437.4		135,1481,4887	AA,AG,GG		16.7326,7.0813,13.463		245/370	26830316	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	57168	exon2			CTGTAGGAAGTGC	AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.735G>A	22.37:g.26830316G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Silent	SNP	ENST00000215906.5	37	CCDS13834.2																																																																																			G|0.880;A|0.120	0.120	strong		0.562	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
SOS2	6655	hgsc.bcm.edu	37	14	50585248	50585248	+	Silent	SNP	C	C	T	rs2227276	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50585248C>T	ENST00000216373.5	-	23	4087	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	SOS2_ENST00000543680.1_Silent_p.P1238P|VCPKMT_ENST00000395859.2_5'Flank|VCPKMT_ENST00000395860.2_5'Flank	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1271					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					AGCATCGACGCGGTACCCTTG	0.517													C|||	1218	0.243211	0.2201	0.2435	5008	,	,		17245	0.4315		0.1461	False		,,,				2504	0.18				p.P1271P		Atlas-SNP	.											.	SOS2	195	.	0			c.G3813A						PASS	.	C		883,3523	342.8+/-307.3	89,705,1409	145.0	120.0	128.0		3813	-3.7	1.0	14	dbSNP_98	128	1355,7245	264.9+/-285.8	113,1129,3058	no	coding-synonymous	SOS2	NM_006939.2		202,1834,4467	TT,TC,CC		15.7558,20.0409,17.2074		1271/1333	50585248	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon23			TCGACGCGGTACC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3813G>A	14.37:g.50585248C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			T|0.202;C|0.798	0.202	strong		0.517	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
ANKRD16	54522	hgsc.bcm.edu	37	10	5926034	5926034	+	Silent	SNP	T	T	C	rs3750656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5926034T>C	ENST00000380094.5	-	4	1128	c.585A>G	c.(583-585)caA>caG	p.Q195Q	ANKRD16_ENST00000191063.8_Silent_p.Q195Q|ANKRD16_ENST00000380092.4_Silent_p.Q195Q	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	195								p.Q195Q(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						CTGGTTCATATTGGCACCTAG	0.522													T|||	318	0.0634984	0.0008	0.0346	5008	,	,		20222	0.1577		0.0368	False		,,,				2504	0.0992				p.Q195Q		Atlas-SNP	.											ANKRD16,NS,carcinoma,0,1	ANKRD16	32	1	1	Substitution - coding silent(1)	stomach(1)	c.A585G						PASS	.	T	,,	49,4357	49.6+/-84.7	0,49,2154	111.0	88.0	96.0		585,585,585	0.4	1.0	10	dbSNP_107	96	301,8299	109.0+/-169.6	1,299,4000	no	coding-synonymous,coding-synonymous,coding-synonymous	ANKRD16	NM_001009941.2,NM_001009943.2,NM_019046.2	,,	1,348,6154	CC,CT,TT		3.5,1.1121,2.6911	,,	195/362,195/305,195/362	5926034	350,12656	2203	4300	6503	SO:0001819	synonymous_variant	54522	exon4			TTCATATTGGCAC	AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"""Ankyrin repeat domain containing"""	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.585A>G	10.37:g.5926034T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_001009943	A6NEF0|F8WEI4|Q9NT01	Silent	SNP	ENST00000380094.5	37	CCDS31136.1																																																																																			T|0.961;C|0.039	0.039	strong		0.522	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138	
GSDMB	55876	hgsc.bcm.edu	37	17	38062217	38062217	+	Missense_Mutation	SNP	C	C	T	rs2305479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38062217C>T	ENST00000394179.1	-	8	1025	c.895G>A	c.(895-897)Ggg>Agg	p.G299R	GSDMB_ENST00000394175.2_Missense_Mutation_p.G282R|GSDMB_ENST00000520542.1_Missense_Mutation_p.G295R|GSDMB_ENST00000360317.3_Missense_Mutation_p.G304R|GSDMB_ENST00000309481.7_Missense_Mutation_p.G291R|GSDMB_ENST00000418519.1_Missense_Mutation_p.G304R			Q8TAX9	GSDMB_HUMAN	gasdermin B	299			G -> R (in dbSNP:rs2305479). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.G282R(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						TGTAGCTCCCCGGAAATCAGG	0.537													c|||	1558	0.311102	0.1422	0.3646	5008	,	,		17374	0.2817		0.502	False		,,,				2504	0.3354				p.G304R		Atlas-SNP	.											GSDMB_ENST00000418519,colon,carcinoma,+1,3	GSDMB	87	3	1	Substitution - Missense(1)	stomach(1)	c.G910A						PASS	.	T	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	811,3595	323.7+/-298.2	71,669,1463	73.0	69.0	70.0		871,910,883,844	-2.5	0.0	17	dbSNP_100	70	4139,4461	562.4+/-387.9	975,2189,1136	yes	missense,missense,missense,missense	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	125,125,125,125	1046,2858,2599	TT,TC,CC		48.1279,18.4067,38.0594	probably-damaging,probably-damaging,probably-damaging,probably-damaging	291/404,304/417,295/408,282/395	38062217	4950,8056	2203	4300	6503	SO:0001583	missense	55876	exon9			GCTCCCCGGAAAT	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.895G>A	17.37:g.38062217C>T	ENSP00000377733:p.Gly299Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	115	111	0.965217	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Missense_Mutation	SNP	ENST00000394179.1	37		769	0.35210622710622713	64	0.13008130081300814	137	0.3784530386740331	180	0.3146853146853147	388	0.5118733509234829	c	12.85	2.060971	0.36373	0.184067	0.481279	ENSG00000073605	ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	3.64	-2.46	0.06461	.	1.125150	0.07152	N	0.849236	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	D;D;D;B;B	0.89917	1.0;1.0;1.0;0.055;0.055	D;D;D;B;B	0.91635	0.995;0.999;0.993;0.013;0.013	T	0.37776	-0.9691	9	0.54805	T	0.06	.	5.3214	0.15883	0.0:0.433:0.144:0.423	rs2305479;rs17608794;rs17845768;rs17858728;rs52797128;rs2305479	295;304;299;291;282	B4DKK7;Q8TAX9-4;Q8TAX9;Q8TAX9-3;Q8TAX9-2	.;.;GSDMB_HUMAN;.;.	R	299;282;291;295;304;299	ENSP00000377729:G282R;ENSP00000312584:G291R;ENSP00000430157:G295R;ENSP00000415049:G304R;ENSP00000377733:G299R	ENSP00000312584:G291R	G	-	1	0	GSDMB	35315743	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.110000	0.15437	-0.954000	0.03640	-2.010000	0.00438	GGG	C|0.645;T|0.355	0.355	strong		0.537	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
WNT16	51384	hgsc.bcm.edu	37	7	120979089	120979089	+	Missense_Mutation	SNP	C	C	T	rs2707466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:120979089C>T	ENST00000222462.2	+	4	1078	c.788C>T	c.(787-789)aCa>aTa	p.T263I	WNT16_ENST00000361301.2_Missense_Mutation_p.T253I	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	263			T -> I (in dbSNP:rs2707466). {ECO:0000269|PubMed:11095990}.		bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					TCAGACAAAACAAAGAGGAAA	0.363													T|||	2519	0.502995	0.9017	0.4063	5008	,	,		22765	0.1716		0.4404	False		,,,				2504	0.4387				p.T263I		Atlas-SNP	.											.	WNT16	97	.	0			c.C788T						PASS	.	T	ILE/THR,ILE/THR	3624,782	316.9+/-294.8	1493,638,72	75.0	77.0	76.0		758,788	2.7	1.0	7	dbSNP_100	76	3922,4678	606.5+/-395.1	912,2098,1290	yes	missense,missense	WNT16	NM_016087.2,NM_057168.1	89,89	2405,2736,1362	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	45.6047,17.7485,41.9806	benign,benign	253/356,263/366	120979089	7546,5460	2203	4300	6503	SO:0001583	missense	51384	exon4			ACAAAACAAAGAG	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"""Wingless-type MMTV integration sites"""	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.788C>T	7.37:g.120979089C>T	ENSP00000222462:p.Thr263Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_057168	Q2M3G1|Q9Y5C0	Missense_Mutation	SNP	ENST00000222462.2	37	CCDS5781.1	1030	0.4716117216117216	442	0.8983739837398373	158	0.43646408839779005	100	0.17482517482517482	330	0.43535620052770446	T	11.32	1.602926	0.28534	0.822515	0.456047	ENSG00000002745	ENST00000361301;ENST00000222462	T;T	0.76186	-1.0;-1.0	5.51	2.66	0.31614	.	.	.	.	.	T	0.00012	0.0000	N	0.25060	0.705	0.51233	P	8.699999999994823E-5	B;B	0.10296	0.003;0.003	B;B	0.09377	0.004;0.004	T	0.31833	-0.9929	8	0.29301	T	0.29	.	9.1866	0.37174	0.0:0.2482:0.0:0.7518	rs2707466;rs52828976;rs56918180;rs2707466	263;253	Q9UBV4;E9PH60	WNT16_HUMAN;.	I	253;263	ENSP00000355065:T253I;ENSP00000222462:T263I	ENSP00000222462:T263I	T	+	2	0	WNT16	120766325	1.000000	0.71417	0.977000	0.42913	0.979000	0.70002	2.782000	0.47758	0.021000	0.15133	-0.254000	0.11334	ACA	C|0.462;T|0.538	0.538	strong		0.363	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
OVCH2	341277	hgsc.bcm.edu	37	11	7717233	7717233	+	RNA	SNP	G	G	A	rs62624491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7717233G>A	ENST00000533663.1	-	0	0				OVCH2_ENST00000454689.1_RNA|OVCH2_ENST00000534193.2_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		aaTGGATGAAGGGAGGCTTTC	0.408													G|||	174	0.0347444	0.0113	0.0403	5008	,	,		11986	0.001		0.0437	False		,,,				2504	0.0879				p.P389L		Atlas-SNP	.											.	OVCH2	47	.	0			c.C1166T						PASS	.	G	LEU/PRO	20,1798		0,20,889	40.0	37.0	38.0		1166	0.4	0.0	11	dbSNP_129	38	191,3947		5,181,1883	yes	missense-near-splice	OVCH2	NM_198185.2	98	5,201,2772	AA,AG,GG		4.6158,1.1001,3.5426	possibly-damaging	389/565	7717233	211,5745	909	2069	2978			341277	exon11			GATGAAGGGAGGC	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7717233G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_198185		Missense_Mutation	SNP	ENST00000533663.1	37		58	0.026556776556776556	13	0.026422764227642278	14	0.03867403314917127	1	0.0017482517482517483	30	0.0395778364116095	G	9.689	1.151433	0.21371	0.011001	0.046158	ENSG00000183378	ENST00000454689	T	0.26957	1.7	3.49	0.451	0.16629	CUB (5);	0.882429	0.09172	U	0.838758	T	0.06280	0.0162	M	0.88640	2.97	0.09310	N	1	P	0.35793	0.521	B	0.36845	0.234	T	0.16129	-1.0413	10	0.48119	T	0.1	0.9252	4.0851	0.09943	0.2006:0.2025:0.5969:0.0	rs62624491	389	Q7RTZ1	OVCH2_HUMAN	L	389	ENSP00000407158:P389L	ENSP00000407158:P389L	P	-	2	0	OVCH2	7673809	0.948000	0.32251	0.000000	0.03702	0.060000	0.15804	1.361000	0.34136	0.109000	0.17891	0.655000	0.94253	CCT	G|0.966;A|0.034	0.034	strong		0.408	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108098	17108098	+	Silent	SNP	C	C	T	rs112680414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	156	53	0.339744	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	
FBXO42	54455	hgsc.bcm.edu	37	1	16641797	16641797	+	Silent	SNP	C	C	T	rs61753288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16641797C>T	ENST00000375592.3	-	2	333	c.117G>A	c.(115-117)gaG>gaA	p.E39E	FBXO42_ENST00000478089.1_5'UTR	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	39										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GTCTAGTCTCCTCAGCCTCCA	0.502													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17411	0.0		0.0119	False		,,,				2504	0.0				p.E39E		Atlas-SNP	.											.	FBXO42	53	.	0			c.G117A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	120.0	100.0	107.0		117	-3.5	0.0	1	dbSNP_129	107	115,8485	60.2+/-122.0	0,115,4185	no	coding-synonymous	FBXO42	NM_018994.1		0,123,6380	TT,TC,CC		1.3372,0.1816,0.9457		39/718	16641797	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon2			AGTCTCCTCAGCC	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.117G>A	1.37:g.16641797C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	246	110	0.447154	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			C|0.993;T|0.007	0.007	strong		0.502	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
CYP8B1	1582	hgsc.bcm.edu	37	3	42916618	42916618	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:42916618G>A	ENST00000316161.4	-	1	1015	c.691C>T	c.(691-693)Cga>Tga	p.R231*	KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Nonsense_Mutation_p.R231*	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	231					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|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)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)	p.R231*(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CGCTGGAGTCGGCCCACTTCT	0.552																																					p.R231X		Atlas-SNP	.											CYP8B1,NS,carcinoma,0,1	CYP8B1	59	1	1	Substitution - Nonsense(1)	prostate(1)	c.C691T						scavenged	.						25.0	27.0	26.0					3																	42916618		2200	4296	6496	SO:0001587	stop_gained	1582	exon1			GGAGTCGGCCCAC	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.691C>T	3.37:g.42916618G>A	ENSP00000318867:p.Arg231*	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Nonsense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755840	0.89843	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	.	.	.	5.34	3.33	0.38152	.	0.717261	0.12781	N	0.439655	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-9.0149	12.7401	0.57246	0.0:0.0:0.5821:0.4179	.	.	.	.	X	231	.	ENSP00000318867:R231X	R	-	1	2	CYP8B1	42891622	0.213000	0.23551	0.372000	0.25991	0.789000	0.44602	0.664000	0.25068	1.257000	0.44085	0.549000	0.68633	CGA	.	.	none		0.552	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
HERC2	8924	hgsc.bcm.edu	37	15	28412872	28412872	+	Silent	SNP	G	G	A	rs61756152	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28412872G>A	ENST00000261609.7	-	68	10623	c.10515C>T	c.(10513-10515)gcC>gcT	p.A3505A		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)		TGATGCTTGCGGCTCCCAGGT	0.498													G|||	864	0.172524	0.0908	0.2305	5008	,	,		18732	0.2946		0.1074	False		,,,				2504	0.183				p.A3505A		Atlas-SNP	.											.	HERC2	501	.	0			c.C10515T						PASS	.	G		431,3975	209.2+/-230.0	16,399,1788	83.0	88.0	86.0		10515	1.1	1.0	15	dbSNP_129	86	723,7877	175.5+/-225.5	30,663,3607	no	coding-synonymous	HERC2	NM_004667.4		46,1062,5395	AA,AG,GG		8.407,9.7821,8.8728		3505/4835	28412872	1154,11852	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon68			GCTTGCGGCTCCC	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.10515C>T	15.37:g.28412872G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.885;A|0.115	0.115	strong		0.498	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
TAS2R4	50832	hgsc.bcm.edu	37	7	141478800	141478800	+	Missense_Mutation	SNP	G	G	A	rs2234002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141478800G>A	ENST00000247881.2	+	1	559	c.512G>A	c.(511-513)aGt>aAt	p.S171N	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	171			S -> N (in dbSNP:rs2234002).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		TTTAATATCAGTGAGGGCATC	0.423													g|||	2461	0.491414	0.1929	0.5663	5008	,	,		22114	0.745		0.4722	False		,,,				2504	0.6002				p.S171N		Atlas-SNP	.											.	TAS2R4	25	.	0			c.G512A						PASS	.	A	ASN/SER	1106,3300	398.5+/-330.9	147,812,1244	263.0	256.0	259.0		512	-8.9	0.0	7	dbSNP_98	259	4271,4329	574.9+/-390.1	1053,2165,1082	yes	missense	TAS2R4	NM_016944.1	46	1200,2977,2326	AA,AG,GG		49.6628,25.1021,41.3425	benign	171/300	141478800	5377,7629	2203	4300	6503	SO:0001583	missense	50832	exon1			ATATCAGTGAGGG	AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.512G>A	7.37:g.141478800G>A	ENSP00000247881:p.Ser171Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	1081	0.49496336996337	103	0.20934959349593496	198	0.5469613259668509	427	0.7465034965034965	353	0.4656992084432718	g	0.003	-2.486927	0.00161	0.251021	0.496628	ENSG00000127364	ENST00000247881	T	0.00768	5.72	5.06	-8.91	0.00778	.	1.458410	0.03642	N	0.239661	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.43294	-0.9400	9	0.02654	T	1	.	10.909	0.47097	0.2401:0.2116:0.5482:0.0	rs2234002;rs3735277;rs17523587;rs52816893;rs60480904;rs2234002	171	Q9NYW5	TA2R4_HUMAN	N	171	ENSP00000247881:S171N	ENSP00000247881:S171N	S	+	2	0	TAS2R4	141125269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.744000	0.04839	-1.732000	0.01359	-0.508000	0.04489	AGT	G|0.543;A|0.457	0.457	strong		0.423	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
PEAR1	375033	hgsc.bcm.edu	37	1	156873727	156873727	+	Silent	SNP	G	G	A	rs12407843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156873727G>A	ENST00000338302.3	+	3	234	c.9G>A	c.(7-9)ccG>ccA	p.P3P	PEAR1_ENST00000292357.7_Silent_p.P3P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	3					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CAATGTCACCGCCTCTGTGTC	0.637													g|||	974	0.194489	0.146	0.1499	5008	,	,		17619	0.3442		0.1113	False		,,,				2504	0.2229				p.P3P		Atlas-SNP	.											.	PEAR1	118	.	0			c.G9A						PASS	.			638,3768	274.3+/-271.8	57,524,1622	112.0	100.0	104.0		9	-4.5	0.0	1	dbSNP_120	104	974,7626	212.1+/-252.5	61,852,3387	no	coding-synonymous	PEAR1	NM_001080471.1		118,1376,5009	AA,AG,GG		11.3256,14.4803,12.3943		3/1038	156873727	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon2			GTCACCGCCTCTG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.9G>A	1.37:g.156873727G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			G|0.842;A|0.158	0.158	strong		0.637	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
SP110	3431	hgsc.bcm.edu	37	2	231077112	231077112	+	Missense_Mutation	SNP	G	G	A	rs28930679	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231077112G>A	ENST00000358662.4	-	5	695	c.617C>T	c.(616-618)gCg>gTg	p.A206V	SP110_ENST00000258382.5_Missense_Mutation_p.A206V|SP110_ENST00000486146.2_5'UTR|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000392048.3_Missense_Mutation_p.A206V|SP110_ENST00000540870.1_Missense_Mutation_p.A212V|SP110_ENST00000258381.6_Missense_Mutation_p.A206V	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	177	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	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	
PRPF18	8559	hgsc.bcm.edu	37	10	13639490	13639490	+	Silent	SNP	C	C	T	rs2502213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13639490C>T	ENST00000378572.3	+	2	259	c.99C>T	c.(97-99)ctC>ctT	p.L33L		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	33					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GTAGTGAGCTCGCCAAAAAAG	0.284													C|||	136	0.0271565	0.0968	0.0072	5008	,	,		16174	0.001		0.0	False		,,,				2504	0.002				p.L33L		Atlas-SNP	.											.	PRPF18	32	.	0			c.C99T						PASS	.	C		399,4007	198.7+/-222.5	17,365,1821	92.0	93.0	93.0		99	-1.6	0.9	10	dbSNP_100	93	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	PRPF18	NM_003675.3		17,371,6115	TT,TC,CC		0.0698,9.0558,3.1139		33/343	13639490	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon2			TGAGCTCGCCAAA	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.99C>T	10.37:g.13639490C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			C|0.972;T|0.028	0.028	strong		0.284	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
SIDT1	54847	hgsc.bcm.edu	37	3	113286405	113286405	+	Silent	SNP	C	C	T	rs2292511	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:113286405C>T	ENST00000264852.4	+	3	1089	c.363C>T	c.(361-363)aaC>aaT	p.N121N	SIDT1_ENST00000393830.3_Silent_p.N121N	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	121					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GGAGCTACAACTATCAAGAAG	0.478													C|||	1617	0.322883	0.267	0.2565	5008	,	,		18650	0.5873		0.2326	False		,,,				2504	0.2658				p.N121N		Atlas-SNP	.											SIDT1,NS,carcinoma,0,1	SIDT1	99	1	0			c.C363T						PASS	.	C		1182,3224	416.7+/-337.7	158,866,1179	87.0	82.0	84.0		363	4.2	1.0	3	dbSNP_100	84	1759,6841	318.2+/-313.6	166,1427,2707	no	coding-synonymous	SIDT1	NM_017699.2		324,2293,3886	TT,TC,CC		20.4535,26.8271,22.6126		121/828	113286405	2941,10065	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon3			CTACAACTATCAA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.363C>T	3.37:g.113286405C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	115	68	0.591304	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			C|0.717;T|0.283	0.283	strong		0.478	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
GUSB	2990	hgsc.bcm.edu	37	7	65429359	65429359	+	Silent	SNP	G	G	A	rs1061361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:65429359G>A	ENST00000304895.4	-	11	1870	c.1740C>T	c.(1738-1740)taC>taT	p.Y580Y	GUSB_ENST00000421103.1_Silent_p.Y434Y|GUSB_ENST00000345660.6_Silent_p.Y529Y	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	580					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						CTCCAACCACGTATTTTCTGC	0.453													G|||	712	0.142173	0.0825	0.2147	5008	,	,		20195	0.1468		0.1064	False		,,,				2504	0.2035				p.Y580Y		Atlas-SNP	.											.	GUSB	52	.	0			c.C1740T						PASS	.	G		309,4097	168.0+/-198.9	10,289,1904	101.0	83.0	89.0		1740	-1.4	0.9	7	dbSNP_86	89	966,7630	207.6+/-249.3	59,848,3391	no	coding-synonymous	GUSB	NM_000181.3		69,1137,5295	AA,AG,GG		11.2378,7.0132,9.8062		580/652	65429359	1275,11727	2203	4298	6501	SO:0001819	synonymous_variant	2990	exon11			AACCACGTATTTT	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.1740C>T	7.37:g.65429359G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	37	CCDS5530.1																																																																																			G|1.000;|0.000	.	weak		0.453	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
CATSPER4	378807	hgsc.bcm.edu	37	1	26524520	26524520	+	Silent	SNP	G	G	A	rs61776651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:26524520G>A	ENST00000456354.2	+	5	697	c.630G>A	c.(628-630)tcG>tcA	p.S210S		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	210					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)		TCCTGCAGTCGGTGCCTGACA	0.637													G|||	180	0.0359425	0.0045	0.0389	5008	,	,		16368	0.0		0.1292	False		,,,				2504	0.0174				p.S210S		Atlas-SNP	.											.	CATSPER4	59	.	0			c.G630A						PASS	.	G		120,4286	88.7+/-127.4	3,114,2086	179.0	162.0	168.0		630	-4.7	1.0	1	dbSNP_129	168	1102,7498	229.7+/-264.3	78,946,3276	no	coding-synonymous	CATSPER4	NM_198137.1		81,1060,5362	AA,AG,GG		12.814,2.7236,9.3957		210/473	26524520	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon5			GCAGTCGGTGCCT	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.630G>A	1.37:g.26524520G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	72	0.541353	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			G|0.917;A|0.083	0.083	strong		0.637	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
OR2M2	391194	hgsc.bcm.edu	37	1	248343945	248343945	+	Missense_Mutation	SNP	C	C	G	rs4244171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248343945C>G	ENST00000359682.2	+	1	658	c.658C>G	c.(658-660)Cga>Gga	p.R220G		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	220			R -> G (in dbSNP:rs4244171).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	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)			TTCCTATGCTCGAGTTATTCT	0.438													c|||	2878	0.574681	0.6051	0.6037	5008	,	,		22034	0.4306		0.6382	False		,,,				2504	0.5961				p.R220G		Atlas-SNP	.											OR2M2,NS,adenoma,0,1	OR2M2	149	1	0			c.C658G						PASS	.	C	GLY/ARG	2575,1831		801,973,429	199.0	183.0	189.0		658	-2.0	0.0	1	dbSNP_111	189	5443,3155		1823,1797,679	no	missense	OR2M2	NM_001004688.1	125	2624,2770,1108	GG,GC,CC		36.6946,41.557,38.342	probably-damaging	220/348	248343945	8018,4986	2203	4299	6502	SO:0001583	missense	391194	exon1			TATGCTCGAGTTA	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.658C>G	1.37:g.248343945C>G	ENSP00000352710:p.Arg220Gly	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	1111	0.5086996336996337	250	0.508130081300813	201	0.5552486187845304	220	0.38461538461538464	440	0.5804749340369393	c	6.844	0.524908	0.13066	0.58443	0.633054	ENSG00000198601	ENST00000359682	T	0.00123	8.7	2.03	-2.0	0.07433	GPCR, rhodopsin-like superfamily (1);	1.563310	0.05152	U	0.496260	T	0.00012	0.0000	M	0.70275	2.135	0.80722	P	0.0	D	0.55385	0.971	P	0.58391	0.838	T	0.16217	-1.0410	9	0.26408	T	0.33	.	3.4291	0.07421	0.1778:0.45:0.0:0.3722	rs4244171;rs59366045	220	Q96R28	OR2M2_HUMAN	G	220	ENSP00000352710:R220G	ENSP00000352710:R220G	R	+	1	2	OR2M2	246410568	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.965000	0.03829	-0.160000	0.11002	0.454000	0.30748	CGA	C|0.400;G|0.600	0.600	strong		0.438	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
NUP85	79902	hgsc.bcm.edu	37	17	73230856	73230856	+	Silent	SNP	C	C	T	rs9988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73230856C>T	ENST00000245544.4	+	17	1811	c.1740C>T	c.(1738-1740)gaC>gaT	p.D580D	NUP85_ENST00000541827.1_Silent_p.D534D|NUP85_ENST00000447371.2_Silent_p.D412D|NUP85_ENST00000540768.1_Silent_p.D183D|NUP85_ENST00000579298.1_Silent_p.D535D|NUP85_ENST00000579324.1_Silent_p.D468D	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	580					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|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)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			TGCTGACAGACGCCTTGCCCC	0.527													T|||	4427	0.883986	0.879	0.8833	5008	,	,		19130	0.9306		0.8022	False		,,,				2504	0.9274				p.D580D		Atlas-SNP	.											.	NUP85	44	.	0			c.C1740T						PASS	.	T		3857,549	247.8+/-255.9	1694,469,40	181.0	166.0	171.0		1740	-5.0	0.7	17	dbSNP_52	171	7015,1585	295.4+/-302.4	2869,1277,154	no	coding-synonymous	NUP85	NM_024844.3		4563,1746,194	TT,TC,CC		18.4302,12.4603,16.4078		580/657	73230856	10872,2134	2203	4300	6503	SO:0001819	synonymous_variant	79902	exon17			GACAGACGCCTTG	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.1740C>T	17.37:g.73230856C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Silent	SNP	ENST00000245544.4	37	CCDS32730.1																																																																																			C|0.149;T|0.851	0.851	strong		0.527	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
TEP1	7011	hgsc.bcm.edu	37	14	20872881	20872881	+	Missense_Mutation	SNP	G	G	T	rs1760898	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20872881G>T	ENST00000262715.5	-	5	961	c.921C>A	c.(919-921)aaC>aaA	p.N307K	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	307	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.		N -> K (in dbSNP:rs1760898).		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)		TGGCCAAGATGTTATTGGCCA	0.557													T|||	1827	0.364816	0.4894	0.2781	5008	,	,		21010	0.4167		0.2247	False		,,,				2504	0.3487				p.N307K		Atlas-SNP	.											.	TEP1	224	.	0			c.C921A						PASS	.	T	LYS/ASN	1989,2417	616.8+/-392.8	467,1055,681	78.0	73.0	74.0		921	-1.0	0.0	14	dbSNP_89	74	1865,6735	729.4+/-406.7	206,1453,2641	yes	missense	TEP1	NM_007110.4	94	673,2508,3322	TT,TG,GG		21.686,45.143,29.6325	benign	307/2628	20872881	3854,9152	2203	4300	6503	SO:0001583	missense	7011	exon5			CAAGATGTTATTG		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.921C>A	14.37:g.20872881G>T	ENSP00000262715:p.Asn307Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	737	0.3374542124542125	230	0.46747967479674796	106	0.292817679558011	221	0.38636363636363635	180	0.23746701846965698	T	10.03	1.237915	0.22711	0.45143	0.21686	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.14022	2.54	5.55	-0.961	0.10337	TROVE (2);	1.009720	0.07938	N	0.978726	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	0.45469	-0.9259	9	0.10377	T	0.69	0.7568	2.53	0.04701	0.1169:0.3087:0.3471:0.2273	rs1760898;rs59063415;rs1760898	307	Q99973	TEP1_HUMAN	K	307	ENSP00000262715:N307K	ENSP00000262715:N307K	N	-	3	2	TEP1	19942721	0.017000	0.18338	0.001000	0.08648	0.936000	0.57629	0.083000	0.14871	-0.293000	0.08986	-0.256000	0.11100	AAC	G|0.682;T|0.318	0.318	strong		0.557	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
HLA-A	3105	hgsc.bcm.edu	37	6	29911207	29911207	+	Missense_Mutation	SNP	G	G	A	rs1059520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29911207G>A	ENST00000396634.1	+	5	847	c.506G>A	c.(505-507)cGc>cAc	p.R169H	HLA-A_ENST00000376806.5_Missense_Mutation_p.R169H|HLA-A_ENST00000376809.5_Missense_Mutation_p.R169H|HLA-A_ENST00000376802.2_Missense_Mutation_p.R169H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	169	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ATCACCAAGCGCAAGTGGGAG	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.R169H		Atlas-SNP	.											.	HLA-A	89	.	0			c.G506A						PASS	.						34.0	26.0	29.0					6																	29911207		1508	2704	4212	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCAAGCGCAAGTG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.506G>A	6.37:g.29911207G>A	ENSP00000379873:p.Arg169His	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	136	58	0.426471	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	710|710	0.3250915750915751|0.3250915750915751	149|149	0.30284552845528456|0.30284552845528456	124|124	0.3425414364640884|0.3425414364640884	164|164	0.2867132867132867|0.2867132867132867	273|273	0.36015831134564646|0.36015831134564646	.|.	2.879|2.879	-0.232306|-0.232306	0.05983|0.05983	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000355767|ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	.|T;T;T;T	.|0.00856	.|5.61;5.61;5.61;5.61	3.78|3.78	0.89|0.89	0.19218|0.19218	.|MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	.|0.211148	.|0.20683	.|U	.|0.087616	T|T	0.00784|0.00784	0.0026|0.0026	.|.	.|.	.|.	0.51233|0.51233	P|P	8.900000000000574E-5|8.900000000000574E-5	.|D;B;P;B;P;B;B	.|0.61080	.|0.989;0.0;0.936;0.0;0.829;0.0;0.0	.|P;B;P;B;P;B;B	.|0.61874	.|0.895;0.001;0.638;0.001;0.486;0.001;0.001	T|T	0.55933|0.55933	-0.8062|-0.8062	4|8	0.72032|0.29301	D|T	0.01|0.29	.|.	3.0116|3.0116	0.06046|0.06046	0.322:0.0:0.4849:0.1931|0.322:0.0:0.4849:0.1931	rs1059520;rs2975061;rs3179200;rs3200220;rs16896012;rs41540321|rs1059520;rs2975061;rs3179200;rs3200220;rs16896012;rs41540321	.|48;169;169;169;169;169;169	.|B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.|.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	T|H	144|169	.|ENSP00000379873:R169H;ENSP00000366002:R169H;ENSP00000366005:R169H;ENSP00000365998:R169H	ENSP00000348012:A144T|ENSP00000365998:R169H	A|R	+|+	1|2	0|0	HLA-A|HLA-A	30019186|30019186	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.034000|0.034000	0.12701|0.12701	0.075000|0.075000	0.14686|0.14686	0.052000|0.052000	0.16007|0.16007	-0.515000|-0.515000	0.04445|0.04445	GCA|CGC	A|0.308;G|0.692	0.308	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DENND1B	163486	hgsc.bcm.edu	37	1	197482049	197482049	+	IGR	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:197482049C>A								CRB1 (34464 upstream) : DENND1B (39335 downstream)																							ATATAGAGCACCATCAAGGCT	0.368																																					p.G517V		Atlas-SNP	.											.	DENND1B	108	.	0			c.G1550T						PASS	.						115.0	99.0	105.0					1																	197482049		2203	4299	6502	SO:0001628	intergenic_variant	163486	exon21			AGAGCACCATCAA																													1.37:g.197482049C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	124	90	0.725806	NM_001195215		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	6.634	0.485376	0.12641	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.32023	1.47	5.2	5.2	0.72013	.	0.398495	0.23317	U	0.049495	T	0.19248	0.0462	L	0.33189	0.99	0.19575	N	0.999965	B	0.21753	0.06	B	0.23574	0.047	T	0.16660	-1.0395	10	0.16896	T	0.51	.	4.781	0.13202	0.1539:0.6157:0.1487:0.0817	.	517	Q6P3S1-5	.	V	157;517;497	ENSP00000375839:G157V	ENSP00000375839:G157V	G	-	2	0	DENND1B	195748672	0.000000	0.05858	0.053000	0.19242	0.125000	0.20455	0.676000	0.25247	2.578000	0.87016	0.655000	0.94253	GGT	.	.	none	0	0.368								
ABCG8	64241	hgsc.bcm.edu	37	2	44071743	44071743	+	Missense_Mutation	SNP	A	A	G	rs4148211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:44071743A>G	ENST00000272286.2	+	2	251	c.161A>G	c.(160-162)tAc>tGc	p.Y54C		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	54	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		Y -> C (in dbSNP:rs4148211). {ECO:0000269|PubMed:11099417, 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)	GACCTCAACTACCAGGTAGAG	0.577													A|||	2177	0.434704	0.1293	0.3501	5008	,	,		16941	0.8512		0.3708	False		,,,				2504	0.544				p.Y54C		Atlas-SNP	.											.	ABCG8	98	.	0			c.A161G	GRCh37	CM075964	ABCG8	M	rs4148211	PASS	.	A	CYS/TYR	860,3546	335.7+/-304.0	80,700,1423	51.0	43.0	46.0		161	4.1	1.0	2	dbSNP_110	46	3313,5287	495.2+/-374.0	621,2071,1608	yes	missense	ABCG8	NM_022437.2	194	701,2771,3031	GG,GA,AA		38.5233,19.5188,32.0852	benign	54/674	44071743	4173,8833	2203	4300	6503	SO:0001583	missense	64241	exon2			TCAACTACCAGGT	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.161A>G	2.37:g.44071743A>G	ENSP00000272286:p.Tyr54Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	963	0.4409340659340659	57	0.11585365853658537	115	0.31767955801104975	494	0.8636363636363636	297	0.391820580474934	A	15.11	2.737366	0.49045	0.195188	0.385233	ENSG00000143921	ENST00000272286	D	0.88431	-2.38	5.27	4.12	0.48240	ABC transporter-like (1);	0.184905	0.49305	N	0.000154	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.9999999685781	B;B	0.31383	0.321;0.215	B;B	0.34873	0.191;0.093	T	0.42999	-0.9418	9	0.54805	T	0.06	.	10.9764	0.47469	0.927:0.0:0.073:0.0	rs4148211;rs17424080;rs59500626;rs4148211	54;54	Q9H221-2;Q9H221	.;ABCG8_HUMAN	C	54	ENSP00000272286:Y54C	ENSP00000272286:Y54C	Y	+	2	0	ABCG8	43925247	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.345000	0.65987	0.856000	0.35383	0.523000	0.50628	TAC	A|0.626;G|0.374	0.374	strong		0.577	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854272	12854272	+	Missense_Mutation	SNP	T	T	C	rs61775050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12854272T>C	ENST00000332296.7	+	3	599	c.496T>C	c.(496-498)Tac>Cac	p.Y166H	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	166					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)		ATGCCTGAGATACCTCTTCCA	0.463																																					p.Y166H		Atlas-SNP	.											.	PRAMEF1	78	.	0			c.T496C						PASS	.	T	HIS/TYR	77,4317		0,77,2120	110.0	112.0	111.0		496	1.7	0.0	1	dbSNP_129	111	150,8412		0,150,4131	no	missense	PRAMEF1	NM_023013.2	83	0,227,6251	CC,CT,TT		1.7519,1.7524,1.7521	probably-damaging	166/475	12854272	227,12729	2197	4281	6478	SO:0001583	missense	65121	exon3			CTGAGATACCTCT	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.496T>C	1.37:g.12854272T>C	ENSP00000332134:p.Tyr166His	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	231	48	0.207792	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	54	0.024725274725274724	27	0.054878048780487805	3	0.008287292817679558	4	0.006993006993006993	20	0.026385224274406333	.	5.291	0.239042	0.10023	0.017524	0.017519	ENSG00000116721	ENST00000332296	T	0.05319	3.46	1.74	1.74	0.24563	.	0.514588	0.18857	N	0.129221	T	0.00784	0.0026	L	0.39397	1.21	0.09310	N	0.999996	B	0.12013	0.005	B	0.17098	0.017	T	0.34179	-0.9839	10	0.51188	T	0.08	.	5.5397	0.17031	0.0:0.0:0.0:1.0	rs61775050	166	O95521	PRAM1_HUMAN	H	166	ENSP00000332134:Y166H	ENSP00000332134:Y166H	Y	+	1	0	PRAMEF1	12776859	0.001000	0.12720	0.004000	0.12327	0.002000	0.02628	1.259000	0.32956	1.048000	0.40298	0.443000	0.29094	TAC	T|0.500;C|0.500	0.500	weak		0.463	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455800	5455800	+	Missense_Mutation	SNP	G	G	A	rs2240745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	29	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	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	
HLA-B	3106	hgsc.bcm.edu	37	6	31324602	31324602	+	Missense_Mutation	SNP	T	T	G	rs41562914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324602T>G	ENST00000412585.2	-	2	234	c.206A>C	c.(205-207)gAg>gCg	p.E69A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	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.E69fs*30(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCGCGGCTCCTCTCTCGGACT	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1344	0.268371	0.3222	0.2666	5008	,	,		7700	0.1677		0.2008	False		,,,				2504	0.3701				p.E69A		Atlas-SNP	.											.	HLA-B	54	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.A206C						PASS	.						34.0	34.0	34.0					6																	31324602		2056	4023	6079	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GGCTCCTCTCTCG	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.206A>C	6.37:g.31324602T>G	ENSP00000399168:p.Glu69Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	0.012	-1.657841	0.00779	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00007	9.68;9.68	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);	4.848800	0.01913	U	0.040001	T	0.00039	0.0001	N	0.16833	0.445	0.09310	N	1	B;B;B	0.21309	0.002;0.001;0.054	B;B;P	0.44772	0.007;0.005;0.46	T	0.32052	-0.9921	10	0.20519	T	0.43	.	8.9744	0.35926	0.1185:0.0:0.2387:0.6428	rs9281379	69;69;44	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	A	69;80	ENSP00000399168:E69A;ENSP00000405931:E80A	ENSP00000399168:E69A	E	-	2	0	HLA-B	31432581	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.912000	0.00171	-4.011000	0.00082	-0.641000	0.03968	GAG	T|0.638;G|0.265;C|0.001;A|0.096	0.265	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
FRY	10129	hgsc.bcm.edu	37	13	32811974	32811974	+	Missense_Mutation	SNP	C	C	T	rs73169136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:32811974C>T	ENST00000380250.3	+	44	6765	c.6269C>T	c.(6268-6270)gCa>gTa	p.A2090V		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2090						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)		AAACTCCAGGCACAGCTGAAG	0.527													C|||	39	0.00778754	0.0	0.0346	5008	,	,		18641	0.0		0.0129	False		,,,				2504	0.002				p.A2090V		Atlas-SNP	.											.	FRY	312	.	0			c.C6269T						PASS	.	C	VAL/ALA	6,3982		0,6,1988	61.0	65.0	63.0		6269	4.3	0.9	13	dbSNP_130	63	95,8227		0,95,4066	yes	missense	FRY	NM_023037.2	64	0,101,6054	TT,TC,CC		1.1416,0.1505,0.8205	benign	2090/3014	32811974	101,12209	1994	4161	6155	SO:0001583	missense	10129	exon44			TCCAGGCACAGCT	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.6269C>T	13.37:g.32811974C>T	ENSP00000369600:p.Ala2090Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	24	0.01098901098901099	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	10	0.013192612137203167	C	15.28	2.786075	0.49997	0.001505	0.011416	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.23950	1.88	6.03	4.26	0.50523	.	0.390654	0.30850	N	0.008748	T	0.07234	0.0183	L	0.50333	1.59	0.80722	D	1	B	0.11235	0.004	B	0.19666	0.026	T	0.02805	-1.1108	10	0.52906	T	0.07	.	16.0022	0.80301	0.0:0.623:0.377:0.0	.	2090	Q5TBA9	FRY_HUMAN	V	2090;927	ENSP00000369600:A2090V	ENSP00000369600:A2090V	A	+	2	0	FRY	31709974	0.424000	0.25490	0.926000	0.36857	0.984000	0.73092	0.907000	0.28531	1.543000	0.49345	0.655000	0.94253	GCA	C|0.990;T|0.010	0.010	strong		0.527	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
OR10X1	128367	hgsc.bcm.edu	37	1	158549264	158549264	+	Silent	SNP	G	G	A	rs863360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158549264G>A	ENST00000368150.1	-	1	425	c.426C>T	c.(424-426)atC>atT	p.I142I		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	142						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(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GAGGGTTACAGATGGCCAGGA	0.458													G|||	2516	0.502396	0.5741	0.4135	5008	,	,		22554	0.5853		0.4732	False		,,,				2504	0.4131				p.I142I		Atlas-SNP	.											OR10X1,NS,carcinoma,0,1	OR10X1	96	1	0			c.C426T						PASS	.	G		2499,1907	627.1+/-394.8	679,1141,383	75.0	76.0	75.0		426	2.1	1.0	1	dbSNP_86	75	3826,4774	538.9+/-383.5	877,2072,1351	no	coding-synonymous	OR10X1	NM_001004477.1		1556,3213,1734	AA,AG,GG		44.4884,43.2819,48.6314		142/327	158549264	6325,6681	2203	4300	6503	SO:0001819	synonymous_variant	128367	exon1			GTTACAGATGGCC	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.426C>T	1.37:g.158549264G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	284	108	0.380282	NM_001004477	Q6IFR8	Silent	SNP	ENST00000368150.1	37	CCDS30900.1																																																																																			G|0.489;A|0.511	0.511	strong		0.458	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
GZMB	3002	hgsc.bcm.edu	37	14	25100282	25100282	+	Missense_Mutation	SNP	A	A	G	rs2236338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:25100282A>G	ENST00000216341.4	-	5	845	c.739T>C	c.(739-741)Tac>Cac	p.Y247H	RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Missense_Mutation_p.Y202H|GZMB_ENST00000415355.3_Missense_Mutation_p.Y235H|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Missense_Mutation_p.Y281H			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	247			Y -> H (in dbSNP:rs2236338). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Y247H(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		TGTAGTTAGTAGCGTTTCATG	0.478													G|||	1462	0.291933	0.3298	0.2075	5008	,	,		18111	0.2986		0.2495	False		,,,				2504	0.3374				p.Y247H		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - Missense(1)	stomach(1)	c.T739C	GRCh37	CM033777	GZMB	M	rs2236338	PASS	.	G	HIS/TYR	1401,3005	688.4+/-405.0	213,975,1015	234.0	227.0	229.0		739	-1.6	0.0	14	dbSNP_98	229	2050,6550	719.9+/-406.3	255,1540,2505	yes	missense	GZMB	NM_004131.4	83	468,2515,3520	GG,GA,AA		23.8372,31.7975,26.5339	benign	247/248	25100282	3451,9555	2203	4300	6503	SO:0001583	missense	3002	exon5			GTTAGTAGCGTTT	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.739T>C	14.37:g.25100282A>G	ENSP00000216341:p.Tyr247His	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	221	219	0.99095	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	585	0.26785714285714285	163	0.3313008130081301	82	0.2265193370165746	148	0.25874125874125875	192	0.2532981530343008	G	0.858	-0.736322	0.03111	0.317975	0.238372	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000382539	D;D;D;D	0.90261	-2.55;-2.53;-2.6;-2.64	4.88	-1.58	0.08479	.	1.357460	0.05613	N	0.578444	T	0.00012	0.0000	N	0.20986	0.625	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.02758	-1.1114	9	0.39692	T	0.17	.	3.5013	0.07674	0.3485:0.0:0.2432:0.4082	rs2236338;rs17856857;rs52792984;rs56781976;rs2236338	235;247	Q6XGZ4;P10144	.;GRAB_HUMAN	H	235;247;281;202;152	ENSP00000387385:Y235H;ENSP00000216341:Y247H;ENSP00000371982:Y281H;ENSP00000371980:Y202H	ENSP00000216341:Y247H	Y	-	1	0	GZMB	24170122	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.197000	0.09518	-0.409000	0.07553	-0.119000	0.15052	TAC	A|0.729;G|0.271	0.271	strong		0.478	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
CD5	921	hgsc.bcm.edu	37	11	60886913	60886913	+	Missense_Mutation	SNP	C	C	T	rs2241002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60886913C>T	ENST00000347785.3	+	5	837	c.671C>T	c.(670-672)cCa>cTa	p.P224L		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	224	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		P -> L (in dbSNP:rs2241002). {ECO:0000269|PubMed:14702039}.		apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		GCCCAAGACCCAGGGGAGCCA	0.562													C|||	861	0.171925	0.3064	0.1369	5008	,	,		19463	0.0625		0.1491	False		,,,				2504	0.1513				p.P224L		Atlas-SNP	.											.	CD5	52	.	0			c.C671T						PASS	.	C	LEU/PRO	1223,3183	422.1+/-339.6	171,881,1151	59.0	59.0	59.0		671	1.3	0.0	11	dbSNP_98	59	1505,7093	283.2+/-296.0	136,1233,2930	yes	missense	CD5	NM_014207.3	98	307,2114,4081	TT,TC,CC		17.5041,27.7576,20.9782	probably-damaging	224/496	60886913	2728,10276	2203	4299	6502	SO:0001583	missense	921	exon5			AAGACCCAGGGGA	X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"""CD molecules"""	1685	protein-coding gene	gene with protein product		153340	"""CD5 antigen (p56-62)"""	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.671C>T	11.37:g.60886913C>T	ENSP00000342681:p.Pro224Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_014207	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	348	0.15934065934065933	168	0.34146341463414637	56	0.15469613259668508	32	0.055944055944055944	92	0.12137203166226913	C	10.38	1.333753	0.24167	0.277576	0.175041	ENSG00000110448	ENST00000347785	T	0.29917	1.55	4.3	1.32	0.21799	Speract/scavenger receptor (1);	0.275244	0.25456	N	0.030547	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	2.9999999999752447E-6	B	0.15473	0.013	B	0.08055	0.003	T	0.41052	-0.9530	9	0.46703	T	0.11	-2.5347	6.9155	0.24357	0.0:0.6873:0.0:0.3127	rs2241002;rs2241002	224	P06127	CD5_HUMAN	L	224	ENSP00000342681:P224L	ENSP00000342681:P224L	P	+	2	0	CD5	60643489	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.782000	0.26788	0.294000	0.22547	-0.908000	0.02827	CCA	C|0.799;T|0.201	0.201	strong		0.562	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207	
MUC17	140453	hgsc.bcm.edu	37	7	100677279	100677279	+	Missense_Mutation	SNP	G	G	C	rs76184171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100677279G>C	ENST00000306151.4	+	3	2646	c.2582G>C	c.(2581-2583)aGt>aCt	p.S861T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	861	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)	p.S861T(3)		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)					TCAACTTATAGTGAAGGAAGA	0.483																																					p.S861T		Atlas-SNP	.											MUC17,colon,carcinoma,+1,9	MUC17	804	9	3	Substitution - Missense(3)	breast(3)	c.G2582C						PASS	.	G	THR/SER	792,3614		0,792,1411	299.0	284.0	289.0		2582	-1.5	0.0	7	dbSNP_131	289	690,7910		0,690,3610	no	missense	MUC17	NM_001040105.1	58	0,1482,5021	CC,CG,GG		8.0233,17.9755,11.3947	benign	861/4494	100677279	1482,11524	2203	4300	6503	SO:0001583	missense	140453	exon3			CTTATAGTGAAGG	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.2582G>C	7.37:g.100677279G>C	ENSP00000302716:p.Ser861Thr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	1.778	-0.482778	0.04383	0.179755	0.080233	ENSG00000169876	ENST00000306151	T	0.02498	4.27	1.14	-1.5	0.08691	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42749	-0.9433	9	0.06891	T	0.86	.	3.7128	0.08427	0.0:0.532:0.2629:0.2051	.	861	Q685J3	MUC17_HUMAN	T	861	ENSP00000302716:S861T	ENSP00000302716:S861T	S	+	2	0	MUC17	100463999	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.197000	0.09518	-0.462000	0.06984	0.196000	0.17591	AGT	G|0.992;C|0.008	0.008	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
C9orf129	445577	hgsc.bcm.edu	37	9	96097673	96097673	+	Silent	SNP	G	G	A	rs62574460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:96097673G>A	ENST00000375419.1	-	3	711	c.348C>T	c.(346-348)ggC>ggT	p.G116G		NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	116										endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						CCCCTCCGCTGCCCTCGTCGT	0.642													G|||	1348	0.269169	0.1082	0.1052	5008	,	,		17992	0.3601		0.1909	False		,,,				2504	0.59				p.G116G		Atlas-SNP	.											.	C9orf129	18	.	0			c.C348T						PASS	.						15.0	17.0	16.0					9																	96097673		2198	4269	6467	SO:0001819	synonymous_variant	445577	exon3			TCCGCTGCCCTCG		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.348C>T	9.37:g.96097673G>A		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	339	143	0.421829	NM_001098808		Silent	SNP	ENST00000375419.1	37	CCDS43850.1																																																																																			G|0.804;A|0.196	0.196	strong		0.642	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808	
MUC16	94025	hgsc.bcm.edu	37	19	9060656	9060656	+	Silent	SNP	C	C	T	rs2216663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9060656C>T	ENST00000397910.4	-	3	26993	c.26790G>A	c.(26788-26790)gaG>gaA	p.E8930E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8932	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)		p.E8930E(2)|p.E4563E(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						GCTGAATTGCCTCTGTCTCCA	0.493													c|||	1050	0.209665	0.0628	0.2003	5008	,	,		21414	0.249		0.3101	False		,,,				2504	0.271				p.E8930E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - coding silent(3)	stomach(3)	c.G26790A						PASS	.	C		425,3671		24,377,1647	180.0	170.0	173.0		26790	-0.2	0.0	19	dbSNP_96	173	2415,6013		342,1731,2141	no	coding-synonymous	MUC16	NM_024690.2		366,2108,3788	TT,TC,CC		28.6545,10.376,22.6765		8930/14508	9060656	2840,9684	2048	4214	6262	SO:0001819	synonymous_variant	94025	exon3			AATTGCCTCTGTC	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.26790G>A	19.37:g.9060656C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			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	
ZNF333	84449	hgsc.bcm.edu	37	19	14829749	14829749	+	Missense_Mutation	SNP	C	C	T	rs3764626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	79	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	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	
RAB5C	5878	hgsc.bcm.edu	37	17	40280291	40280291	+	Silent	SNP	G	G	A	rs2230326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40280291G>A	ENST00000346213.4	-	4	641	c.429C>T	c.(427-429)gcC>gcT	p.A143A	RAB5C_ENST00000547517.1_Silent_p.A176A|CTD-2132N18.3_ENST00000592574.1_Silent_p.A143A|RAB5C_ENST00000393860.3_Silent_p.A143A	NM_004583.3	NP_004574.2	P51148	RAB5C_HUMAN	RAB5C, member RAS oncogene family	143					endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)|skin(1)	7		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GGAATTCCACGGCTCTCTTGC	0.627													G|||	1261	0.251797	0.4743	0.1513	5008	,	,		17879	0.1657		0.1769	False		,,,				2504	0.1881				p.A176A		Atlas-SNP	.											.	RAB5C	20	.	0			c.C528T						PASS	.	G	,	1796,2610	529.5+/-372.7	382,1032,789	122.0	103.0	109.0		429,429	-4.5	1.0	17	dbSNP_98	109	1409,7191	272.3+/-290.0	114,1181,3005	no	coding-synonymous,coding-synonymous	RAB5C	NM_004583.2,NM_201434.1	,	496,2213,3794	AA,AG,GG		16.3837,40.7626,24.6425	,	143/217,143/217	40280291	3205,9801	2203	4300	6503	SO:0001819	synonymous_variant	5878	exon5			TTCCACGGCTCTC	U18420	CCDS11419.1, CCDS58551.1	17q21.2	2013-02-15			ENSG00000108774	ENSG00000108774		"""RAB, member RAS oncogene"""	9785	protein-coding gene	gene with protein product	"""RAB, member of RAS oncogene family-like"", ""RAB5C, member of RAS oncogene family"""	604037		RABL		8646882	Standard	NM_004583		Approved	RAB5CL	uc010cxx.3	P51148	OTTHUMG00000169703	ENST00000346213.4:c.429C>T	17.37:g.40280291G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_001252039	F8W1H5|Q6FH55|Q9P0Y5	Silent	SNP	ENST00000346213.4	37	CCDS11419.1																																																																																			G|0.619;T|0.051	.	strong		0.627	RAB5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405509.1	NM_004583	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111870037	111870037	+	Silent	SNP	T	T	C	rs2296354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:111870037T>C	ENST00000375741.2	+	6	793	c.543T>C	c.(541-543)gaT>gaC	p.D181D	ARHGEF7_ENST00000375737.5_Silent_p.D78D|ARHGEF7_ENST00000370623.3_Silent_p.D88D|ARHGEF7_ENST00000317133.5_Silent_p.D160D|ARHGEF7_ENST00000375736.4_Silent_p.D3D|ARHGEF7_ENST00000375739.2_Silent_p.D131D|ARHGEF7_ENST00000426073.2_Silent_p.D3D|ARHGEF7_ENST00000375723.1_Silent_p.D3D|ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000218789.5_Silent_p.D3D	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	181					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ACATGACCGATAATAGCAACA	0.388													T|||	1246	0.248802	0.025	0.1225	5008	,	,		18731	0.6825		0.174	False		,,,				2504	0.271				p.D181D		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T543C						PASS	.	T	,,,,	223,4183	134.5+/-170.7	3,217,1983	115.0	109.0	111.0		543,393,9,9,480	-3.1	0.4	13	dbSNP_100	111	1437,7163	276.7+/-292.4	115,1207,2978	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF7	NM_001113511.1,NM_001113512.1,NM_001113513.1,NM_003899.3,NM_145735.2	,,,,	118,1424,4961	CC,CT,TT		16.7093,5.0613,12.7633	,,,,	181/804,131/754,3/647,3/647,160/783	111870037	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	8874	exon6			GACCGATAATAGC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.543T>C	13.37:g.111870037T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	157	73	0.464968	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																			T|0.807;C|0.193	0.193	strong		0.388	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
FAT1	2195	hgsc.bcm.edu	37	4	187522528	187522528	+	Silent	SNP	C	C	T	rs2289550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187522528C>T	ENST00000441802.2	-	21	11744	c.11535G>A	c.(11533-11535)acG>acA	p.T3845T	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3845	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTTCATTTTCCGTCAGACGGT	0.413										HNSCC(5;0.00058)			C|||	279	0.0557109	0.0023	0.1052	5008	,	,		17244	0.1558		0.0348	False		,,,				2504	0.0112				p.T3845T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,-1,3	FAT1	500	3	0			c.G11535A						PASS	.	C		32,3780		0,32,1874	139.0	137.0	137.0		11535	2.7	0.8	4	dbSNP_100	137	247,7991		3,241,3875	no	coding-synonymous	FAT1	NM_005245.3		3,273,5749	TT,TC,CC		2.9983,0.8395,2.3154		3845/4589	187522528	279,11771	1906	4119	6025	SO:0001819	synonymous_variant	2195	exon21			ATTTTCCGTCAGA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11535G>A	4.37:g.187522528C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			C|0.934;T|0.066	0.066	strong		0.413	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
SAAL1	113174	hgsc.bcm.edu	37	11	18108512	18108512	+	Missense_Mutation	SNP	T	T	C	rs35525096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18108512T>C	ENST00000524803.1	-	9	992	c.943A>G	c.(943-945)Att>Gtt	p.I315V	SAAL1_ENST00000300013.4_Missense_Mutation_p.I315V|SAAL1_ENST00000529318.1_Missense_Mutation_p.I315V|SAAL1_ENST00000533851.1_5'Flank			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	315			I -> V (in dbSNP:rs35525096).							breast(2)|large_intestine(5)|lung(8)	15						TCTTGAAGAATGATGGGTGGA	0.398													T|||	426	0.0850639	0.1589	0.0519	5008	,	,		15367	0.0119		0.0885	False		,,,				2504	0.0808				p.I315V		Atlas-SNP	.											.	SAAL1	34	.	0			c.A943G						PASS	.	T	VAL/ILE	578,3822	255.5+/-260.7	33,512,1655	106.0	102.0	103.0		943	3.4	0.9	11	dbSNP_126	103	819,7767	189.4+/-236.2	59,701,3533	yes	missense	SAAL1	NM_138421.2	29	92,1213,5188	CC,CT,TT		9.5388,13.1364,10.7577	possibly-damaging	315/475	18108512	1397,11589	2200	4293	6493	SO:0001583	missense	113174	exon9			GAAGAATGATGGG	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.943A>G	11.37:g.18108512T>C	ENSP00000432487:p.Ile315Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	NM_138421	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	37	CCDS31439.1	175	0.08012820512820513	82	0.16666666666666666	18	0.049723756906077346	8	0.013986013986013986	67	0.08839050131926121	T	13.16	2.154880	0.38021	0.131364	0.095388	ENSG00000166788	ENST00000524803;ENST00000300013;ENST00000531751;ENST00000529318	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.68	3.36	0.38483	Armadillo-like helical (1);	0.229621	0.41938	N	0.000783	T	0.00073	0.0002	L	0.45581	1.43	0.28340	P	0.9213964	P;P;P	0.40619	0.724;0.724;0.724	B;B;B	0.39152	0.292;0.292;0.292	T	0.08126	-1.0737	9	0.45353	T	0.12	-5.7964	9.7489	0.40464	0.0:0.14:0.0:0.86	rs35525096	315;315;315	E9PRZ1;G1UCX3;Q96ER3	.;.;SAAL1_HUMAN	V	315;315;204;315	ENSP00000432487:I315V;ENSP00000300013:I315V;ENSP00000436031:I204V;ENSP00000432216:I315V	ENSP00000300013:I315V	I	-	1	0	SAAL1	18065088	1.000000	0.71417	0.909000	0.35828	0.985000	0.73830	3.280000	0.51677	0.441000	0.26529	0.467000	0.42956	ATT	T|0.903;C|0.097	0.097	strong		0.398	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
BMP1	649	hgsc.bcm.edu	37	8	22067022	22067022	+	Silent	SNP	C	C	A	rs77242743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22067022C>A	ENST00000306385.5	+	19	3310	c.2640C>A	c.(2638-2640)ggC>ggA	p.G880G	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	880	CUB 5. {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)		CCCAGTTTGGCGACAACAACT	0.617													C|||	176	0.0351438	0.003	0.0605	5008	,	,		18109	0.0198		0.0895	False		,,,				2504	0.0204				p.G880G		Atlas-SNP	.											.	BMP1	131	.	0			c.C2640A						PASS	.	C		112,4294	85.8+/-124.5	1,110,2092	260.0	204.0	223.0		2640	-9.5	0.2	8	dbSNP_132	223	989,7611	214.2+/-253.9	52,885,3363	no	coding-synonymous	BMP1	NM_006129.4		53,995,5455	AA,AC,CC		11.5,2.542,8.4653		880/987	22067022	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	649	exon19			GTTTGGCGACAAC		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.2640C>A	8.37:g.22067022C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.929;A|0.071	0.071	strong		0.617	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
MYH9	4627	hgsc.bcm.edu	37	22	36700175	36700175	+	Silent	SNP	A	A	G	rs9619601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36700175A>G	ENST00000216181.5	-	19	2486	c.2256T>C	c.(2254-2256)aaT>aaC	p.N752N		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	752	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						TGCGGTACAGATTGCTGTCGA	0.592			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				G|||	302	0.0603035	0.0477	0.0231	5008	,	,		3469	0.0962		0.0477	False		,,,				2504	0.0798				p.N752N		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.T2256C						PASS	.	G		154,4252	810.6+/-416.0	4,146,2053	70.0	64.0	66.0		2256	1.9	1.0	22	dbSNP_119	66	429,8171	799.3+/-407.4	7,415,3878	no	coding-synonymous	MYH9	NM_002473.4		11,561,5931	GG,GA,AA		4.9884,3.4952,4.4825		752/1961	36700175	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon19	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GTACAGATTGCTG		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.2256T>C	22.37:g.36700175A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			A|0.951;G|0.049	0.049	strong		0.592	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
SLC2A14	144195	hgsc.bcm.edu	37	12	7966975	7966975	+	Silent	SNP	C	C	T	rs10845982		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7966975C>T	ENST00000543909.1	-	16	2259	c.1500G>A	c.(1498-1500)ggG>ggA	p.G500G	SLC2A14_ENST00000539924.1_Silent_p.G515G|SLC2A14_ENST00000542505.1_Silent_p.G141G|SLC2A14_ENST00000396589.2_Silent_p.G500G|SLC2A14_ENST00000431042.2_Silent_p.G477G|SLC2A14_ENST00000542546.1_Silent_p.G391G|SLC2A14_ENST00000340749.5_Silent_p.G477G|SLC2A14_ENST00000535295.1_Silent_p.G391G			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	500					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)		CGCCGTCCTTCCCAGATCTAT	0.557																																					p.G500G		Atlas-SNP	.											SLC2A14,NS,carcinoma,-2,1	SLC2A14	78	1	0			c.G1500A						scavenged	.						218.0	142.0	167.0					12																	7966975		2203	4299	6502	SO:0001819	synonymous_variant	144195	exon12			GTCCTTCCCAGAT	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.1500G>A	12.37:g.7966975C>T		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																			T|1.000;|0.000	1.000	weak		0.557	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
HLA-C	3107	hgsc.bcm.edu	37	6	31238875	31238875	+	Silent	SNP	G	G	A	rs1131104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238875G>A	ENST00000376228.5	-	3	608	c.594C>T	c.(592-594)aaC>aaT	p.N198N	HLA-C_ENST00000383329.3_Silent_p.N198N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	198	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						TCTCCTTCCCGTTCTCCAGGT	0.662																																					p.N198N		Atlas-SNP	.											.	HLA-C	92	.	0			c.C594T						PASS	.						53.0	44.0	47.0					6																	31238875		2202	4299	6501	SO:0001819	synonymous_variant	3107	exon3			CTTCCCGTTCTCC	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.594C>T	6.37:g.31238875G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	99	23	0.232323	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	251	0.11492673992673992	26	0.052845528455284556	32	0.08839779005524862	111	0.19405594405594406	82	0.10817941952506596	.	8.202	0.798445	0.16397	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.55	-1.69	0.08186	.	.	.	.	.	T	0.33440	0.0863	.	.	.	0.09310	P	0.99999187897	.	.	.	.	.	.	T	0.29549	-1.0008	3	.	.	.	.	12.2664	0.54681	0.0:0.543:0.457:0.0	rs1131104;rs3177876;rs3190654;rs17362029	.	.	.	W	198	.	.	R	-	1	2	HLA-C	31346854	0.000000	0.05858	0.199000	0.23439	0.105000	0.19272	-2.752000	0.00791	-0.422000	0.07405	0.305000	0.20034	CGG	G|0.912;A|0.088	0.088	strong		0.662	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ITPR2	3709	hgsc.bcm.edu	37	12	26732987	26732987	+	Silent	SNP	G	G	A	rs2230376	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:26732987G>A	ENST00000381340.3	-	33	4898	c.4482C>T	c.(4480-4482)ccC>ccT	p.P1494P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1494					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGAAAAGGGAGAATTAA	0.363													G|||	935	0.186701	0.0923	0.2248	5008	,	,		16444	0.0744		0.332	False		,,,				2504	0.2536				p.P1494P		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4482T						PASS	.	G		475,3141		30,415,1363	116.0	104.0	108.0		4482	-10.1	0.0	12	dbSNP_98	108	2587,5565		428,1731,1917	no	coding-synonymous	ITPR2	NM_002223.2		458,2146,3280	AA,AG,GG		31.7345,13.1361,26.0197		1494/2702	26732987	3062,8706	1808	4076	5884	SO:0001819	synonymous_variant	3709	exon33			TGAAAAGGGAGAA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4482C>T	12.37:g.26732987G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.794;A|0.206	0.206	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ASB6	140459	hgsc.bcm.edu	37	9	132400480	132400480	+	Silent	SNP	G	G	A	rs3739851	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:132400480G>A	ENST00000277458.4	-	6	1020	c.855C>T	c.(853-855)gcC>gcT	p.A285A	ASB6_ENST00000277459.4_3'UTR|RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000450050.2_Silent_p.A206A	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	22	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	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	
AMER3	205147	hgsc.bcm.edu	37	2	131520178	131520178	+	Missense_Mutation	SNP	C	C	G	rs77687733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:131520178C>G	ENST00000423981.1	+	2	643	c.533C>G	c.(532-534)gCg>gGg	p.A178G	AMER3_ENST00000321420.4_Missense_Mutation_p.A178G	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	178					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										GCCTCGCTGGCGGCCGAGGGG	0.642													C|||	628	0.125399	0.0083	0.2839	5008	,	,		17094	0.1379		0.1879	False		,,,				2504	0.0941				p.A178G		Atlas-SNP	.											FAM123C,caecum,carcinoma,0,1	.	.	1	0			c.C533G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	158,4246		2,154,2046	44.0	49.0	47.0		533,533,533,533	-4.1	0.0	2	dbSNP_131	47	1442,7146		136,1170,2988	yes	missense,missense,missense,missense	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	60,60,60,60	138,1324,5034	GG,GC,CC		16.7909,3.5876,12.3153	benign,benign,benign,benign	178/862,178/862,178/862,178/862	131520178	1600,11392	2202	4294	6496	SO:0001583	missense	205147	exon2			CGCTGGCGGCCGA	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.533C>G	2.37:g.131520178C>G	ENSP00000392700:p.Ala178Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	334	0.15293040293040294	4	0.008130081300813009	102	0.281767955801105	84	0.14685314685314685	144	0.18997361477572558	C	5.497	0.276733	0.10403	0.035876	0.167909	ENSG00000178171	ENST00000321420;ENST00000458606;ENST00000423981	T;T	0.47528	0.84;0.84	5.21	-4.14	0.03892	.	1.080390	0.07081	N	0.837120	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.43169	0.8	B	0.39904	0.313	T	0.07028	-1.0794	9	0.27785	T	0.31	.	4.3062	0.10947	0.5233:0.1686:0.0:0.3081	.	178	Q8N944	F123C_HUMAN	G	178	ENSP00000314914:A178G;ENSP00000392700:A178G	ENSP00000314914:A178G	A	+	2	0	FAM123C	131236648	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	-0.631000	0.05560	-0.310000	0.09108	GCG	C|0.866;G|0.134	0.134	strong		0.642	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33548175	33548175	+	Silent	SNP	T	T	C	rs41304751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33548175T>C	ENST00000290943.6	+	9	1299	c.1203T>C	c.(1201-1203)aaT>aaC	p.N401N		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	401										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						AACAGCTTAATGATCTGAAAG	0.338													.|||	434	0.0866613	0.0734	0.0821	5008	,	,		18892	0.0556		0.0994	False		,,,				2504	0.1268				p.N400N		Atlas-SNP	.											ANKRD18B,NS,carcinoma,+1,1	ANKRD18B	46	1	0			c.T1200C						PASS	.																																			SO:0001819	synonymous_variant	441459	exon9			GCTTAATGATCTG			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.1203T>C	9.37:g.33548175T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|0.917;C|0.083	0.083	strong		0.338	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
DRC1	92749	hgsc.bcm.edu	37	2	26667130	26667130	+	Missense_Mutation	SNP	A	A	G	rs3795958	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26667130A>G	ENST00000288710.2	+	9	1143	c.1069A>G	c.(1069-1071)Aag>Gag	p.K357E	DRC1_ENST00000483675.1_3'UTR	NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	357			K -> E (in dbSNP:rs3795958). {ECO:0000269|PubMed:17974005}.		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)											AAAATATGCCAAGCAAATAAA	0.408													A|||	807	0.161142	0.0053	0.1931	5008	,	,		23665	0.2421		0.1918	False		,,,				2504	0.2342				p.K357E		Atlas-SNP	.											.	CCDC164	84	.	0			c.A1069G						PASS	.	A	GLU/LYS	156,4250	106.0+/-144.5	1,154,2048	110.0	100.0	104.0		1069	4.2	0.7	2	dbSNP_107	104	1473,7127	280.9+/-294.7	133,1207,2960	yes	missense	CCDC164	NM_145038.2	56	134,1361,5008	GG,GA,AA		17.1279,3.5406,12.525	possibly-damaging	357/741	26667130	1629,11377	2203	4300	6503	SO:0001583	missense	92749	exon9			TATGCCAAGCAAA	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.1069A>G	2.37:g.26667130A>G	ENSP00000288710:p.Lys357Glu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	345	0.15796703296703296	3	0.006097560975609756	76	0.20994475138121546	114	0.1993006993006993	152	0.20052770448548812	A	22.0	4.225716	0.79576	0.035406	0.171279	ENSG00000157856	ENST00000288710	T	0.15952	2.38	5.39	4.2	0.49525	.	0.367187	0.32093	N	0.006596	T	0.00012	0.0000	L	0.49699	1.58	0.32998	P	0.474106	P	0.49253	0.921	P	0.48524	0.58	T	0.35001	-0.9806	9	0.20046	T	0.44	-22.0796	10.739	0.46141	0.8399:0.1601:0.0:0.0	rs3795958;rs52806794;rs61481502;rs3795958	357	Q96MC2	CC164_HUMAN	E	357	ENSP00000288710:K357E	ENSP00000288710:K357E	K	+	1	0	CCDC164	26520634	1.000000	0.71417	0.711000	0.30485	0.997000	0.91878	3.392000	0.52537	0.943000	0.37553	0.528000	0.53228	AAG	A|0.858;G|0.142	0.142	strong		0.408	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
PARP9	83666	hgsc.bcm.edu	37	3	122259640	122259640	+	Missense_Mutation	SNP	T	T	C	rs28365795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:122259640T>C	ENST00000360356.2	-	8	1776	c.1549A>G	c.(1549-1551)Atc>Gtc	p.I517V	PARP9_ENST00000492382.1_Missense_Mutation_p.I62V|PARP9_ENST00000477522.2_Missense_Mutation_p.I482V|PARP9_ENST00000462315.1_Missense_Mutation_p.I482V|PARP9_ENST00000471785.1_Missense_Mutation_p.I482V	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	517			I -> V (in dbSNP:rs28365795). {ECO:0000269|PubMed:15489334}.		cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		ATCAGATTGATGGCAGGAGAT	0.448													T|||	640	0.127796	0.0938	0.111	5008	,	,		18669	0.1101		0.1541	False		,,,				2504	0.1769				p.I517V		Atlas-SNP	.											.	PARP9	72	.	0			c.A1549G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	515,3891	235.2+/-247.8	29,457,1717	126.0	126.0	126.0		1549,1444,1444,1444,1444,1549	2.7	0.1	3	dbSNP_125	126	1351,7249	264.2+/-285.4	120,1111,3069	yes	missense,missense,missense,missense,missense,missense	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	29,29,29,29,29,29	149,1568,4786	CC,CT,TT		15.7093,11.6886,14.3472	benign,benign,benign,benign,benign,benign	517/855,482/820,482/820,482/820,482/711,517/855	122259640	1866,11140	2203	4300	6503	SO:0001583	missense	83666	exon8			GATTGATGGCAGG	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.1549A>G	3.37:g.122259640T>C	ENSP00000353512:p.Ile517Val	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	251	159	0.633466	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	254	0.1163003663003663	51	0.10365853658536585	49	0.13535911602209943	51	0.08916083916083917	103	0.1358839050131926	T	5.844	0.339849	0.11069	0.116886	0.157093	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T;T	0.17054	3.33;2.79;3.18;3.18;2.3	5.07	2.68	0.31781	.	0.119302	0.38164	N	0.001786	T	0.00073	0.0002	M	0.65975	2.015	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.27264	0.156;0.007;0.173;0.059	B;B;B;B	0.24848	0.043;0.008;0.056;0.043	T	0.11203	-1.0597	9	0.49607	T	0.09	.	4.3067	0.10951	0.1743:0.0929:0.0:0.7328	rs28365795;rs28365795	482;517;62;482	E9PFM7;Q8IXQ6;G5E9U8;Q8IXQ6-2	.;PARP9_HUMAN;.;.	V	517;62;482;482;440;482	ENSP00000353512:I517V;ENSP00000417664:I62V;ENSP00000419506:I482V;ENSP00000419001:I482V;ENSP00000418894:I482V	ENSP00000353512:I517V	I	-	1	0	PARP9	123742330	0.598000	0.26882	0.051000	0.19133	0.335000	0.28730	0.977000	0.29475	0.403000	0.25479	0.528000	0.53228	ATC	T|0.867;C|0.133	0.133	strong		0.448	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
SLC28A1	9154	hgsc.bcm.edu	37	15	85476441	85476441	+	Silent	SNP	G	G	A	rs2305367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:85476441G>A	ENST00000286749.3	+	12	1239	c.1149G>A	c.(1147-1149)aaG>aaA	p.K383K	SLC28A1_ENST00000537624.1_Silent_p.K383K|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000394573.1_Silent_p.K383K|SLC28A1_ENST00000537216.1_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	84	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	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		
FAM35A	54537	hgsc.bcm.edu	37	10	88911830	88911830	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88911830C>A	ENST00000298784.1	+	3	833	c.719C>A	c.(718-720)aCa>aAa	p.T240K	FAM35A_ENST00000298786.4_Missense_Mutation_p.T240K|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	240								p.T240K(2)		endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						TCAACTGATACAGAATTTCTC	0.388																																					p.T240K	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											FAM35A,NS,carcinoma,0,3	FAM35A	48	3	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C719A						scavenged	.						30.0	30.0	30.0					10																	88911830		2203	4295	6498	SO:0001583	missense	54537	exon3			CTGATACAGAATT	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.719C>A	10.37:g.88911830C>A	ENSP00000298784:p.Thr240Lys	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	101	3	0.029703	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	c	16.25	3.071539	0.55646	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.27104	1.7;1.69;1.69	4.09	3.09	0.35607	.	0.289768	0.25801	N	0.028214	T	0.45716	0.1356	.	.	.	0.34044	D	0.655393	D	0.63046	0.992	D	0.65573	0.936	T	0.61700	-0.7009	9	0.59425	D	0.04	-9.6069	12.3445	0.55114	0.0:0.9021:0.0:0.0979	.	240	Q86V20	FA35A_HUMAN	K	240	ENSP00000298786:T240K;ENSP00000298784:T240K;ENSP00000351064:T240K	ENSP00000298784:T240K	T	+	2	0	FAM35A	88901810	1.000000	0.71417	0.665000	0.29768	0.884000	0.51177	2.667000	0.46808	2.134000	0.65973	0.537000	0.68136	ACA	.	.	weak		0.388	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
ZFP41	286128	hgsc.bcm.edu	37	8	144332082	144332082	+	Silent	SNP	T	T	C	rs11136275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144332082T>C	ENST00000330701.4	+	2	438	c.69T>C	c.(67-69)agT>agC	p.S23S	ZFP41_ENST00000520584.1_Silent_p.S23S|ZFP41_ENST00000522452.1_Silent_p.S23S	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	23					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)			TGCAGAAGAGTGCGCTCAGAG	0.602													C|||	3086	0.616214	0.5522	0.6585	5008	,	,		17593	0.744		0.5159	False		,,,				2504	0.6442				p.S23S		Atlas-SNP	.											.	ZFP41	25	.	0			c.T69C						PASS	.	C		2377,2027	552.0+/-378.4	635,1107,460	37.0	43.0	41.0		69	1.8	0.0	8	dbSNP_120	41	4463,4137	559.6+/-387.4	1178,2107,1015	no	coding-synonymous	ZFP41	NM_173832.3		1813,3214,1475	CC,CT,TT		48.1047,46.0263,47.4008		23/199	144332082	6840,6164	2202	4300	6502	SO:0001819	synonymous_variant	286128	exon2			GAAGAGTGCGCTC		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"""Zinc fingers, C2H2-type"""	26786	protein-coding gene	gene with protein product			"""zinc finger protein 41 homolog (mouse)"""			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.69T>C	8.37:g.144332082T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_173832	D3DWJ5	Silent	SNP	ENST00000330701.4	37	CCDS6397.1																																																																																			T|0.448;C|0.552	0.552	strong		0.602	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832	
PCNT	5116	hgsc.bcm.edu	37	21	47811272	47811272	+	Silent	SNP	C	C	T	rs3737438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47811272C>T	ENST00000359568.5	+	21	4304	c.4197C>T	c.(4195-4197)gaC>gaT	p.D1399D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1399					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)					CAGCCACGGACGCCGAGGCCA	0.701													C|||	1510	0.301518	0.2073	0.2262	5008	,	,		16283	0.4008		0.3907	False		,,,				2504	0.2883				p.D1399D		Atlas-SNP	.											PCNT,NS,carcinoma,0,1	PCNT	283	1	0			c.C4197T						PASS	.	C		798,3288		84,630,1329	6.0	7.0	6.0		4197	-9.4	0.0	21	dbSNP_107	6	2727,5429		466,1795,1817	no	coding-synonymous	PCNT	NM_006031.5		550,2425,3146	TT,TC,CC		33.4355,19.5301,28.7943		1399/3337	47811272	3525,8717	2043	4078	6121	SO:0001819	synonymous_variant	5116	exon21			CACGGACGCCGAG	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.4197C>T	21.37:g.47811272C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.650;T|0.350	0.350	strong		0.701	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
VCAN	1462	hgsc.bcm.edu	37	5	82817843	82817843	+	Missense_Mutation	SNP	C	C	G	rs374590975		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:82817843C>G	ENST00000265077.3	+	7	4283	c.3718C>G	c.(3718-3720)Cct>Gct	p.P1240A	VCAN_ENST00000342785.4_Missense_Mutation_p.P1240A|VCAN_ENST00000512590.2_Missense_Mutation_p.P1192A|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1240	GAG-alpha (glucosaminoglycan attachment domain).				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)	CGACAGGGAACCTGGTGAAGA	0.443																																					p.P1240A		Atlas-SNP	.											.	VCAN	498	.	0			c.C3718G						PASS	.	C	ALA/PRO,ALA/PRO,,	0,4406		0,0,2203	134.0	129.0	131.0		3718,3718,,	2.5	0.0	5		131	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron	VCAN	NM_001164098.1,NM_004385.4,NM_001126336.2,NM_001164097.1	27,27,,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,	1240/1643,1240/3397,,	82817843	1,13005	2203	4300	6503	SO:0001583	missense	1462	exon7			AGGGAACCTGGTG	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.3718C>G	5.37:g.82817843C>G	ENSP00000265077:p.Pro1240Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348713	0.24426	0.0	1.16E-4	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.87571	-2.2;-2.24;-2.27	5.39	2.49	0.30216	.	0.322422	0.27155	N	0.020667	D	0.86661	0.5986	M	0.68952	2.095	0.24807	N	0.992661	P;D	0.54397	0.944;0.966	P;P	0.50617	0.646;0.583	T	0.77571	-0.2538	10	0.40728	T	0.16	.	6.7264	0.23359	0.1164:0.5654:0.2497:0.0685	.	1240;1240	P13611-3;P13611	.;CSPG2_HUMAN	A	1240;1240;1192	ENSP00000265077:P1240A;ENSP00000342768:P1240A;ENSP00000425959:P1192A	ENSP00000265077:P1240A	P	+	1	0	VCAN	82853599	0.818000	0.29161	0.046000	0.18839	0.310000	0.27922	1.228000	0.32588	0.195000	0.20347	0.650000	0.86243	CCT	.	.	weak		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
MRPL54	116541	hgsc.bcm.edu	37	19	3767265	3767265	+	Silent	SNP	C	C	T	rs7239	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3767265C>T	ENST00000330133.4	+	3	328	c.291C>T	c.(289-291)ttC>ttT	p.F97F		NM_172251.2	NP_758455.1	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54	97						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5		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)		TCAGGCTGTTCGAGATGAACT	0.682													C|||	3044	0.607827	0.4236	0.621	5008	,	,		14851	0.8026		0.5775	False		,,,				2504	0.6779				p.F97F		Atlas-SNP	.											.	MRPL54	9	.	0			c.C291T						PASS	.	C		2079,2327	565.0+/-381.6	478,1123,602	40.0	43.0	42.0		291	3.0	1.0	19	dbSNP_52	42	5016,3584	623.4+/-397.5	1486,2044,770	yes	coding-synonymous	MRPL54	NM_172251.2		1964,3167,1372	TT,TC,CC		41.6744,47.1857,45.4483		97/139	3767265	7095,5911	2203	4300	6503	SO:0001819	synonymous_variant	116541	exon3			GCTGTTCGAGATG		CCDS12111.1	19p13.3	2012-11-14			ENSG00000183617	ENSG00000183617		"""Mitochondrial ribosomal proteins / large subunits"""	16685	protein-coding gene	gene with protein product		611858				11551941	Standard	NM_172251		Approved		uc002lyq.4	Q6P161	OTTHUMG00000180873	ENST00000330133.4:c.291C>T	19.37:g.3767265C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_172251		Silent	SNP	ENST00000330133.4	37	CCDS12111.1																																																																																			C|0.442;T|0.558	0.558	strong		0.682	MRPL54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453443.1	NM_172251	
SALL4	57167	hgsc.bcm.edu	37	20	50407162	50407162	+	Silent	SNP	T	T	C	rs6021437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50407162T>C	ENST00000217086.4	-	2	1971	c.1860A>G	c.(1858-1860)acA>acG	p.T620T	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	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	168	0	0		WXS	Illumina HiSeq	Phase_I	171	84	0.491228	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		
CEACAM20	125931	hgsc.bcm.edu	37	19	45024581	45024581	+	RNA	SNP	C	C	G	rs12982449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45024581C>G	ENST00000454753.1	-	0	1235							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)				CATAGGGCCCCGTGTCATTCC	0.627													c|||	1870	0.373403	0.1392	0.4265	5008	,	,		19458	0.2698		0.6392	False		,,,				2504	0.4857				p.T319T		Atlas-SNP	.											.	CEACAM20	31	.	0			c.G957C						PASS	.		,,,	884,3018		114,656,1181	58.0	57.0	57.0		957,957,957,957	-7.5	0.0	19	dbSNP_121	57	5113,3187		1597,1919,634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	,,,	1711,2575,1815	GG,GC,CC		38.3976,22.655,49.1477	,,,	319/597,319/492,319/504,319/585	45024581	5997,6205	1951	4150	6101			125931	exon5			GGGCCCCGTGTCA	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.45024581C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001102600		Silent	SNP	ENST00000454753.1	37																																																																																				C|0.617;G|0.383	0.383	strong		0.627	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
CEP290	80184	hgsc.bcm.edu	37	12	88472996	88472996	+	Missense_Mutation	SNP	C	C	T	rs61941020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:88472996C>T	ENST00000552810.1	-	39	5580	c.5237G>A	c.(5236-5238)cGg>cAg	p.R1746Q	CEP290_ENST00000309041.7_Missense_Mutation_p.R1748Q|CEP290_ENST00000397838.3_Missense_Mutation_p.R806Q|CEP290_ENST00000547691.2_Missense_Mutation_p.R806Q	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1746					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						TAAAAGTGCCCGACTAAGTGC	0.313													C|||	57	0.0113818	0.0008	0.0072	5008	,	,		13924	0.005		0.004	False		,,,				2504	0.0429				p.R1746Q		Atlas-SNP	.											.	CEP290	195	.	0			c.G5237A						PASS	.	C	GLN/ARG	7,3589		0,7,1791	60.0	50.0	53.0		5237	4.3	1.0	12	dbSNP_129	53	79,8059		0,79,3990	yes	missense	CEP290	NM_025114.3	43	0,86,5781	TT,TC,CC		0.9708,0.1947,0.7329	possibly-damaging	1746/2480	88472996	86,11648	1798	4069	5867	SO:0001583	missense	80184	exon39			AGTGCCCGACTAA	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.5237G>A	12.37:g.88472996C>T	ENSP00000448012:p.Arg1746Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	3	0.00395778364116095	C	16.75	3.208964	0.58343	0.001947	0.009708	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;T;T;D	0.91577	-2.87;0.0;0.0;-2.87	5.19	4.28	0.50868	.	0.056184	0.64402	D	0.000002	T	0.62245	0.2412	N	0.03608	-0.345	0.34762	D	0.732881	P	0.34743	0.466	B	0.23716	0.048	T	0.71411	-0.4601	10	0.09084	T	0.74	.	5.1781	0.15146	0.0:0.7111:0.0:0.2889	rs61941020	1746	O15078	CE290_HUMAN	Q	806;1746;1748;806	ENSP00000446905:R806Q;ENSP00000448012:R1746Q;ENSP00000308021:R1748Q;ENSP00000380938:R806Q	ENSP00000308021:R1748Q	R	-	2	0	CEP290	86997127	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.734000	0.47368	2.590000	0.87494	0.655000	0.94253	CGG	C|0.996;T|0.004	0.004	strong		0.313	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
OR2G2	81470	hgsc.bcm.edu	37	1	247752367	247752367	+	Missense_Mutation	SNP	A	A	G	rs869111	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247752367A>G	ENST00000320065.1	+	1	706	c.706A>G	c.(706-708)Agg>Ggg	p.R236G	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	236			R -> G (in dbSNP:rs869111).			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)			GTCAGCTACCAGGAGACAGAA	0.483													G|||	1947	0.388778	0.3116	0.3444	5008	,	,		19344	0.4444		0.5159	False		,,,				2504	0.3364				p.R236G		Atlas-SNP	.											.	OR2G2	88	.	0			c.A706G						PASS	.	G	GLY/ARG	1377,3029	690.5+/-405.3	220,937,1046	146.0	134.0	138.0		706	4.3	0.0	1	dbSNP_86	138	4290,4310	577.6+/-390.6	1074,2142,1084	yes	missense	OR2G2	NM_001001915.1	125	1294,3079,2130	GG,GA,AA		49.8837,31.2528,43.5722	benign	236/318	247752367	5667,7339	2203	4300	6503	SO:0001583	missense	81470	exon1			GCTACCAGGAGAC	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.706A>G	1.37:g.247752367A>G	ENSP00000326349:p.Arg236Gly	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	199	115	0.577889	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	928	0.4249084249084249	145	0.29471544715447157	143	0.39502762430939226	252	0.4405594405594406	388	0.5118733509234829	G	0.006	-2.051580	0.00394	0.312528	0.498837	ENSG00000177489	ENST00000320065	T	0.00013	9.24	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36972	N	0.002316	T	0.00012	0.0000	N	0.00012	-2.96	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.02654	T	1	.	10.1869	0.43002	0.0989:0.0:0.9011:0.0	rs869111;rs17318855;rs52811386;rs58487812;rs869111	236	Q8NGZ5	OR2G2_HUMAN	G	236	ENSP00000326349:R236G	ENSP00000326349:R236G	R	+	1	2	OR2G2	245818990	0.290000	0.24343	0.038000	0.18304	0.008000	0.06430	0.583000	0.23849	1.023000	0.39654	-0.186000	0.12905	AGG	A|0.573;G|0.426	0.426	strong		0.483	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
ABCA1	19	hgsc.bcm.edu	37	9	107562804	107562804	+	Missense_Mutation	SNP	T	T	C	rs2230808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:107562804T>C	ENST00000374736.3	-	35	5154	c.4760A>G	c.(4759-4761)aAa>aGa	p.K1587R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1587			K -> R (associated with HDL cholesterol; dbSNP:rs2230808). {ECO:0000269|PubMed:10092505, ECO:0000269|PubMed:10431238, ECO:0000269|PubMed:10884428, ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11352567, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867, ECO:0000269|Ref.2}.		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)	GACATTATTTTTGGTGTCCAG	0.398													T|||	2696	0.538339	0.1324	0.7478	5008	,	,		20994	0.5883		0.7922	False		,,,				2504	0.6258				p.K1587R		Atlas-SNP	.											.	ABCA1	244	.	0			c.A4760G	GRCh37	CM042912	ABCA1	M	rs2230808	PASS	.	T	ARG/LYS	1069,3337	388.6+/-327.0	141,787,1275	186.0	157.0	167.0		4760	5.9	1.0	9	dbSNP_98	167	6540,2060	719.3+/-406.3	2486,1568,246	yes	missense	ABCA1	NM_005502.3	26	2627,2355,1521	CC,CT,TT		23.9535,24.2624,41.4962	benign	1587/2262	107562804	7609,5397	2203	4300	6503	SO:0001583	missense	19	exon35			TTATTTTTGGTGT	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.4760A>G	9.37:g.107562804T>C	ENSP00000363868:p.Lys1587Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	1288	0.5897435897435898	85	0.17276422764227642	256	0.7071823204419889	349	0.6101398601398601	598	0.7889182058047494	T	10.84	1.465085	0.26335	0.242624	0.760465	ENSG00000165029	ENST00000374736	D	0.87256	-2.23	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11870	0.19	0.09310	P	1.0	B	0.16603	0.018	B	0.21360	0.034	T	0.35699	-0.9778	9	0.02654	T	1	.	16.3798	0.83452	0.0:0.0:0.0:1.0	rs2230808;rs2234886;rs57688810;rs2230808	1587	O95477	ABCA1_HUMAN	R	1587	ENSP00000363868:K1587R	ENSP00000363868:K1587R	K	-	2	0	ABCA1	106602625	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.978000	0.70501	2.271000	0.75665	0.533000	0.62120	AAA	T|0.422;C|0.578	0.578	strong		0.398	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183108	11183108	+	Missense_Mutation	SNP	G	G	C	rs12318612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11183108G>C	ENST00000390675.2	-	1	898	c.827C>G	c.(826-828)cCa>cGa	p.P276R	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_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	276	0	0		WXS	Illumina HiSeq	Phase_I	266	253	0.951128	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	
LRRC66	339977	hgsc.bcm.edu	37	4	52862020	52862020	+	Missense_Mutation	SNP	C	C	G	rs202189181		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:52862020C>G	ENST00000343457.3	-	4	1174	c.1168G>C	c.(1168-1170)Gcc>Ccc	p.A390P		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	390						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						AGGCTGAAGGCGACAAGGAAT	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		18727	0.0		0.0	False		,,,				2504	0.001				p.A390P		Atlas-SNP	.											.	LRRC66	128	.	0			c.G1168C						PASS	.	C	PRO/ALA	1,3953		0,1,1976	53.0	54.0	54.0		1168	4.7	1.0	4		54	4,8318		0,4,4157	yes	missense	LRRC66	NM_001024611.1	27	0,5,6133	GG,GC,CC		0.0481,0.0253,0.0407	probably-damaging	390/881	52862020	5,12271	1977	4161	6138	SO:0001583	missense	339977	exon4			TGAAGGCGACAAG	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.1168G>C	4.37:g.52862020C>G	ENSP00000341944:p.Ala390Pro	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	128	69	0.539062	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	37	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812710	0.50527	2.53E-4	4.81E-4	ENSG00000188993	ENST00000343457	T	0.49432	0.78	4.67	4.67	0.58626	.	0.000000	0.45867	D	0.000335	T	0.65533	0.2700	M	0.63843	1.955	0.40966	D	0.98466	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.3724	14.6507	0.68794	0.0:1.0:0.0:0.0	.	390	Q68CR7	LRC66_HUMAN	P	390	ENSP00000341944:A390P	ENSP00000341944:A390P	A	-	1	0	LRRC66	52556777	0.999000	0.42202	0.997000	0.53966	0.011000	0.07611	4.870000	0.63035	2.306000	0.77630	0.467000	0.42956	GCC	.	.	weak		0.557	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611	
A4GNT	51146	hgsc.bcm.edu	37	3	137843106	137843106	+	Silent	SNP	T	T	C	rs2170309	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137843106T>C	ENST00000236709.3	-	3	1224	c.1023A>G	c.(1021-1023)taA>taG	p.*341*		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	0					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						AGTGTTAGCTTTATTTGTTAC	0.517													C|||	3276	0.654153	0.6384	0.7233	5008	,	,		19524	0.6389		0.672	False		,,,				2504	0.6237				p.X341X		Atlas-SNP	.											.	A4GNT	42	.	0			c.A1023G						PASS	.	C		2836,1570	489.0+/-361.4	916,1004,283	82.0	93.0	89.0		1023	3.7	0.0	3	dbSNP_96	89	5757,2843	446.6+/-361.3	1918,1921,461	no	coding-synonymous	A4GNT	NM_016161.2		2834,2925,744	CC,CT,TT		33.0581,35.6332,33.9305		341/341	137843106	8593,4413	2203	4300	6503	SO:0001819	synonymous_variant	51146	exon3			TTAGCTTTATTTG	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.1023A>G	3.37:g.137843106T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_016161	Q0VDK1|Q0VDK2	Silent	SNP	ENST00000236709.3	37	CCDS3097.1																																																																																			T|0.339;C|0.661	0.661	strong		0.517	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	
UNC5B	219699	hgsc.bcm.edu	37	10	73046617	73046617	+	Missense_Mutation	SNP	A	A	G	rs34957097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:73046617A>G	ENST00000335350.6	+	5	1140	c.724A>G	c.(724-726)Atc>Gtc	p.I242V	UNC5B_ENST00000373192.4_Missense_Mutation_p.I242V	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	242	Ig-like C2-type.		I -> V (in dbSNP:rs34957097).		anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						TGCCACCGTCATCGTCTACGG	0.652													A|||	292	0.0583067	0.003	0.1023	5008	,	,		20355	0.0675		0.0497	False		,,,				2504	0.1012				p.I242V		Atlas-SNP	.											.	UNC5B	123	.	0			c.A724G						PASS	.	A	VAL/ILE	44,4362	46.7+/-81.2	0,44,2159	127.0	122.0	124.0		724	4.2	0.4	10	dbSNP_126	124	414,8186	129.5+/-187.6	11,392,3897	yes	missense	UNC5B	NM_170744.4	29	11,436,6056	GG,GA,AA		4.814,0.9986,3.5215	possibly-damaging	242/946	73046617	458,12548	2203	4300	6503	SO:0001583	missense	219699	exon5			ACCGTCATCGTCT	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.724A>G	10.37:g.73046617A>G	ENSP00000334329:p.Ile242Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	102	0.046703296703296704	3	0.006097560975609756	27	0.07458563535911603	34	0.05944055944055944	38	0.05013192612137203	A	7.950	0.744610	0.15710	0.009986	0.04814	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.66815	-0.23;-0.23	5.34	4.21	0.49690	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.212178	0.49305	D	0.000155	T	0.07369	0.0186	L	0.31157	0.91	0.53688	D	0.999974	B;B	0.18863	0.025;0.031	B;B	0.24974	0.034;0.057	T	0.07888	-1.0749	10	0.24483	T	0.36	-8.4774	10.562	0.45150	0.9246:0.0:0.0754:0.0	rs34957097;rs61851302	242;242	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	V	242	ENSP00000334329:I242V;ENSP00000362288:I242V	ENSP00000334329:I242V	I	+	1	0	UNC5B	72716623	1.000000	0.71417	0.393000	0.26258	0.067000	0.16453	4.540000	0.60664	2.027000	0.59764	0.459000	0.35465	ATC	A|0.963;G|0.037	0.037	strong		0.652	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
UROS	7390	hgsc.bcm.edu	37	10	127484721	127484721	+	Missense_Mutation	SNP	A	A	G	rs17173752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127484721A>G	ENST00000368797.4	-	8	736	c.512T>C	c.(511-513)gTt>gCt	p.V171A	UROS_ENST00000368786.1_Missense_Mutation_p.V171A|UROS_ENST00000462490.1_5'UTR	NM_000375.2	NP_000366.1	P10746	HEM4_HUMAN	uroporphyrinogen III synthase	171			V -> G (in dbSNP:rs17173752).		cellular response to amine stimulus (GO:0071418)|cellular response to arsenic-containing substance (GO:0071243)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to antibiotic (GO:0046677)|small molecule metabolic process (GO:0044281)|uroporphyrinogen III biosynthetic process (GO:0006780)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|uroporphyrinogen-III synthase activity (GO:0004852)			endometrium(2)|large_intestine(2)|lung(2)|skin(1)	7		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)				TGGGTGTGCAACTGTCTGATA	0.557																																					p.V171A		Atlas-SNP	.											.	UROS	20	.	0			c.T512C						PASS	.						298.0	255.0	269.0					10																	127484721		2203	4300	6503	SO:0001583	missense	7390	exon8			TGTGCAACTGTCT	J03824	CCDS7648.1	10q25.2-q26.3	2008-07-31	2008-07-31		ENSG00000188690	ENSG00000188690	4.2.1.75		12592	protein-coding gene	gene with protein product	"""congenital erythropoietic porphyria"""	606938				2037278	Standard	NM_000375		Approved		uc001lix.4	P10746	OTTHUMG00000019236	ENST00000368797.4:c.512T>C	10.37:g.127484721A>G	ENSP00000357787:p.Val171Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_000375	B2RC13|D3DRF7|Q9H2T1	Missense_Mutation	SNP	ENST00000368797.4	37	CCDS7648.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608054	0.00842	.	.	ENSG00000188690	ENST00000368797;ENST00000368786;ENST00000420761	D;D;D	0.93604	-3.25;-3.25;-3.25	4.98	2.59	0.31030	Tetrapyrrole biosynthesis, uroporphyrinogen III synthase (2);	0.587899	0.17904	N	0.158084	T	0.78039	0.4221	N	0.02391	-0.57	0.58432	P	1.0000000000287557E-6	B;B	0.09022	0.002;0.002	B;B	0.16722	0.005;0.016	T	0.70163	-0.4947	9	0.08599	T	0.76	-0.1402	5.5774	0.17231	0.7614:0.0:0.2386:0.0	.	171;143	P10746;E9PG85	HEM4_HUMAN;.	A	171;171;143	ENSP00000357787:V171A;ENSP00000357775:V171A;ENSP00000414833:V143A	ENSP00000357775:V171A	V	-	2	0	UROS	127474711	0.005000	0.15991	0.006000	0.13384	0.004000	0.04260	1.536000	0.36072	0.703000	0.31848	-0.417000	0.06048	GTT	A|0.994;C|0.006	.	alt		0.557	UROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050929.1	NM_000375	
TMEM132A	54972	hgsc.bcm.edu	37	11	60701176	60701176	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60701176G>A	ENST00000453848.2	+	8	1677	c.1519G>A	c.(1519-1521)Gag>Aag	p.E507K	TMEM132A_ENST00000005286.4_Missense_Mutation_p.E508K			Q24JP5	T132A_HUMAN	transmembrane protein 132A	507						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CACCACCCTCGAGCAGGTCCG	0.701																																					p.E508K		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G1522A						PASS	.						13.0	12.0	12.0					11																	60701176		2189	4283	6472	SO:0001583	missense	54972	exon8			ACCCTCGAGCAGG	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1519G>A	11.37:g.60701176G>A	ENSP00000405823:p.Glu507Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.013820|4.013820	0.75161|0.75161	.|.	.|.	ENSG00000006118|ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286|ENST00000536409	T;T|.	0.13538|.	2.58;2.58|.	4.25|4.25	4.25|4.25	0.50352|0.50352	.|.	0.338551|.	0.26387|.	N|.	0.024675|.	T|T	0.61553|0.61553	0.2356|0.2356	L|L	0.47716|0.47716	1.5|1.5	0.34210|0.34210	D|D	0.674176|0.674176	D;D;D|.	0.62365|.	0.989;0.991;0.991|.	P;P;P|.	0.54270|.	0.743;0.677;0.747|.	T|T	0.69416|0.69416	-0.5151|-0.5151	10|5	0.87932|.	D|.	0|.	.|.	15.3168|15.3168	0.74085|0.74085	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	258;507;508|.	Q24JP5-4;Q24JP5;Q24JP5-2|.	.;T132A_HUMAN;.|.	K|Q	258;507;508|98	ENSP00000405823:E507K;ENSP00000005286:E508K|.	ENSP00000005286:E508K|.	E|R	+|+	1|2	0|0	TMEM132A|TMEM132A	60457752|60457752	0.987000|0.987000	0.35691|0.35691	0.975000|0.975000	0.42487|0.42487	0.817000|0.817000	0.46193|0.46193	1.938000|1.938000	0.40203|0.40203	2.285000|2.285000	0.76669|0.76669	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	none		0.701	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
STEAP2	261729	hgsc.bcm.edu	37	7	89856644	89856644	+	Silent	SNP	C	C	T	rs2016903	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:89856644C>T	ENST00000287908.3	+	3	1245	c.852C>T	c.(850-852)taC>taT	p.Y284Y	STEAP2_ENST00000394621.2_Silent_p.Y284Y|STEAP2_ENST00000394622.2_Silent_p.Y284Y|STEAP2_ENST00000394626.1_Silent_p.Y284Y|STEAP2_ENST00000394632.1_Silent_p.Y284Y|STEAP2_ENST00000394629.2_Silent_p.Y284Y|STEAP2_ENST00000402625.2_Silent_p.Y284Y	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	284	Ferric oxidoreductase.				copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					AACTTTATTACGGCACCAAGT	0.408													C|||	392	0.0782748	0.0136	0.0821	5008	,	,		18256	0.0149		0.2097	False		,,,				2504	0.093				p.Y284Y		Atlas-SNP	.											STEAP2_ENST00000394626,NS,adenoma,0,2	STEAP2	78	2	0			c.C852T						PASS	.	C	,,	251,4155	144.6+/-179.5	12,227,1964	87.0	85.0	86.0		852,852,852	-5.2	1.0	7	dbSNP_92	86	1939,6661	340.8+/-323.8	220,1499,2581	no	coding-synonymous,coding-synonymous,coding-synonymous	STEAP2	NM_001040665.1,NM_001040666.1,NM_152999.3	,,	232,1726,4545	TT,TC,CC		22.5465,5.6968,16.8384	,,	284/491,284/455,284/491	89856644	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	261729	exon4			TTATTACGGCACC	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"""prostate cancer associated protein 1"", ""six transmembrane epithelial antigen of the prostate 2"""	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.852C>T	7.37:g.89856644C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Silent	SNP	ENST00000287908.3	37	CCDS5615.1																																																																																			C|0.869;T|0.131	0.131	strong		0.408	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999	
WDR66	144406	hgsc.bcm.edu	37	12	122361711	122361711	+	Missense_Mutation	SNP	C	C	T	rs34703321	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122361711C>T	ENST00000288912.4	+	3	1416	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W	WDR66_ENST00000397454.2_Missense_Mutation_p.R188W	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	188							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)		GAAAACCGACCGGATGCCCCA	0.478													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16696	0.0		0.007	False		,,,				2504	0.002				p.R188W	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C562T						PASS	.	C	TRP/ARG,TRP/ARG	8,3728		0,8,1860	104.0	100.0	101.0		562,562	2.5	0.0	12	dbSNP_126	101	68,8122		1,66,4028	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	101,101	1,74,5888	TT,TC,CC		0.8303,0.2141,0.6373	benign,benign	188/942,188/1150	122361711	76,11850	1868	4095	5963	SO:0001583	missense	144406	exon3			ACCGACCGGATGC	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.562C>T	12.37:g.122361711C>T	ENSP00000288912:p.Arg188Trp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	6.949	0.544851	0.13312	0.002141	0.008303	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.17854	2.25;2.25	4.43	2.53	0.30540	.	3.743330	0.00887	N	0.002196	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.31110	-0.9955	10	0.51188	T	0.08	.	9.2319	0.37441	0.0:0.7611:0.1476:0.0914	rs34703321	188	Q8TBY9	WDR66_HUMAN	W	188	ENSP00000288912:R188W;ENSP00000380595:R188W	ENSP00000288912:R188W	R	+	1	2	WDR66	120846094	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.848000	0.27710	0.188000	0.20168	-1.641000	0.00772	CGG	C|0.995;T|0.005	0.005	strong		0.478	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
AKAP11	11215	hgsc.bcm.edu	37	13	42882620	42882620	+	Silent	SNP	C	C	T	rs17521586	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42882620C>T	ENST00000025301.2	+	9	5323	c.5148C>T	c.(5146-5148)acC>acT	p.T1716T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1716	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTCAGTCAACCGAGTCTGTCA	0.363													C|||	572	0.114217	0.0424	0.1297	5008	,	,		16301	0.123		0.1282	False		,,,				2504	0.1769				p.T1716T		Atlas-SNP	.											.	AKAP11	146	.	0			c.C5148T						PASS	.	C		282,4124	157.0+/-190.0	14,254,1935	102.0	97.0	99.0		5148	-0.9	0.1	13	dbSNP_123	99	1322,7278	259.9+/-283.0	94,1134,3072	no	coding-synonymous	AKAP11	NM_016248.3		108,1388,5007	TT,TC,CC		15.3721,6.4004,12.3328		1716/1902	42882620	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon9			GTCAACCGAGTCT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.5148C>T	13.37:g.42882620C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			C|0.882;T|0.118	0.118	strong		0.363	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
CR1	1378	hgsc.bcm.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	T	C	rs61822976		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:207787796T>C	ENST00000367049.4	+	40	6623	c.6623T>C	c.(6622-6624)aTg>aCg	p.M2208T	CR1_ENST00000400960.2_Missense_Mutation_p.M1758T|CR1_ENST00000367051.1_Missense_Mutation_p.M1758T|CR1_ENST00000367052.1_Missense_Mutation_p.M1758T|CR1_ENST00000367053.1_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						PASS	.						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	160	0	0		WXS	Illumina HiSeq	Phase_I	196	12	0.0612245	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	
ESPNL	339768	hgsc.bcm.edu	37	2	239038912	239038912	+	Silent	SNP	T	T	C	rs57813708	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239038912T>C	ENST00000343063.3	+	9	1820	c.1557T>C	c.(1555-1557)ctT>ctC	p.L519L	ESPNL_ENST00000409169.1_Silent_p.L475L|ESPNL_ENST00000409506.1_Silent_p.L151L|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	519										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)		ACCTGCAGCTTCGGCGCCGCT	0.632													T|||	1243	0.248203	0.3215	0.2709	5008	,	,		17111	0.1835		0.2386	False		,,,				2504	0.2096				p.L519L		Atlas-SNP	.											.	ESPNL	63	.	0			c.T1557C						PASS	.	T		1358,3038		206,946,1046	24.0	24.0	24.0		1557	0.8	1.0	2	dbSNP_129	24	1944,6650		230,1484,2583	yes	coding-synonymous	ESPNL	NM_194312.2		436,2430,3629	CC,CT,TT		22.6204,30.8917,25.4196		519/1006	239038912	3302,9688	2198	4297	6495	SO:0001819	synonymous_variant	339768	exon9			GCAGCTTCGGCGC	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.1557T>C	2.37:g.239038912T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.748;C|0.252	0.252	strong		0.632	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
LDB3	11155	hgsc.bcm.edu	37	10	88446985	88446985	+	Silent	SNP	T	T	C	rs76615432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88446985T>C	ENST00000372066.3	+	5	583	c.504T>C	c.(502-504)gaT>gaC	p.D168D	LDB3_ENST00000458213.2_Silent_p.D168D|LDB3_ENST00000429277.2_Silent_p.D283D|LDB3_ENST00000372056.4_Silent_p.D283D|LDB3_ENST00000310944.6_Intron|LDB3_ENST00000542786.1_3'UTR|LDB3_ENST00000361373.4_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000263066.6_Silent_p.D168D	NM_001080116.1	NP_001073585.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CCATCATGGATGCCATCGCTG	0.622													C|||	284	0.0567093	0.1498	0.0245	5008	,	,		20082	0.005		0.0288	False		,,,				2504	0.0358				p.D283D		Atlas-SNP	.											.	LDB3	164	.	0			c.T849C						PASS	.	C	,,,,,	593,3763		39,515,1624	101.0	117.0	112.0		504,,504,849,849,	-1.1	1.0	10	dbSNP_132	112	347,8177		11,325,3926	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	LDB3	NM_001080114.1,NM_001080115.1,NM_001080116.1,NM_001171610.1,NM_001171611.1,NM_007078.2	,,,,,	50,840,5550	CC,CT,TT		4.0709,13.6134,7.2981	,,,,,	168/618,,168/284,283/733,283/399,	88446985	940,11940	2178	4262	6440	SO:0001819	synonymous_variant	11155	exon6			CATGGATGCCATC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000372066.3:c.504T>C	10.37:g.88446985T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_001171610		Silent	SNP	ENST00000372066.3	37	CCDS41545.1																																																																																			T|0.954;C|0.046	0.046	strong		0.622	LDB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049161.1		
SRSF9	8683	hgsc.bcm.edu	37	12	120907271	120907271	+	Silent	SNP	G	G	T	rs11548262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:120907271G>T	ENST00000229390.3	-	1	325	c.142C>A	c.(142-144)Cgg>Agg	p.R48R	DYNLL1_ENST00000548342.1_5'Flank|DYNLL1_ENST00000392509.2_5'Flank	NM_003769.2	NP_003760.1	Q13242	SRSF9_HUMAN	serine/arginine-rich splicing factor 9	48	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	9						AGGCCGTGCCGGTTCTTGAGC	0.682													G|||	370	0.0738818	0.0272	0.0879	5008	,	,		6308	0.0794		0.1074	False		,,,				2504	0.0869				p.R48R		Atlas-SNP	.											SRSF9,colon,carcinoma,0,1	SRSF9	14	1	0			c.C142A						PASS	.	G		135,4271	95.7+/-134.4	2,131,2070	56.0	57.0	56.0		142	4.5	1.0	12	dbSNP_120	56	918,7682	201.7+/-245.1	40,838,3422	no	coding-synonymous	SRSF9	NM_003769.2		42,969,5492	TT,TG,GG		10.6744,3.064,8.0963		48/222	120907271	1053,11953	2203	4300	6503	SO:0001819	synonymous_variant	8683	exon1			CGTGCCGGTTCTT	U30825	CCDS9199.1	12q24.31	2013-02-12	2010-06-22	2010-06-22	ENSG00000111786	ENSG00000111786		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10791	protein-coding gene	gene with protein product	"""SR splicing factor 9"""	601943	"""splicing factor, arginine/serine-rich 9"""	SFRS9		7556075, 20516191	Standard	NM_003769		Approved	SRp30c	uc001tyi.3	Q13242	OTTHUMG00000047790	ENST00000229390.3:c.142C>A	12.37:g.120907271G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_003769	Q52LD1	Silent	SNP	ENST00000229390.3	37	CCDS9199.1	195	0.08928571428571429	29	0.05894308943089431	34	0.09392265193370165	44	0.07692307692307693	88	0.11609498680738786	G	12.78	2.041780	0.35989	0.03064	0.106744	ENSG00000111786	ENST00000550458	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	T	0.01189	0.0039	.	.	.	0.09310	P	0.999999999999944	.	.	.	.	.	.	T	0.20638	-1.0269	3	.	.	.	.	11.9964	0.53206	0.0:0.0:0.8261:0.1739	rs11548262	.	.	.	Q	35	.	.	P	-	2	0	SRSF9	119391654	0.731000	0.28111	1.000000	0.80357	0.996000	0.88848	0.492000	0.22435	2.362000	0.80069	0.499000	0.49734	CCG	G|0.918;T|0.082	0.082	strong		0.682	SRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108983.2	NM_003769	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869769	36869769	+	Missense_Mutation	SNP	C	C	T	rs41282824	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36869769C>T	ENST00000279024.4	-	3	1035	c.764G>A	c.(763-765)cGg>cAg	p.R255Q		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	255										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CTCCCCACACCGGGCTTGCTC	0.577													C|||	161	0.0321486	0.0741	0.0231	5008	,	,		19097	0.002		0.0209	False		,,,				2504	0.0245				p.R255Q		Atlas-SNP	.											KIAA1755,colon,carcinoma,0,1	KIAA1755	145	1	0			c.G764A						scavenged	.	C	GLN/ARG	329,4077	173.0+/-202.9	13,303,1887	137.0	121.0	126.0		764	5.3	0.3	20	dbSNP_127	126	216,8384	90.4+/-152.6	4,208,4088	yes	missense	KIAA1755	NM_001029864.1	43	17,511,5975	TT,TC,CC		2.5116,7.4671,4.1904	possibly-damaging	255/1201	36869769	545,12461	2203	4300	6503	SO:0001583	missense	85449	exon3			CCACACCGGGCTT	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.764G>A	20.37:g.36869769C>T	ENSP00000279024:p.Arg255Gln	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	143	74	0.517483	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	62	0.028388278388278388	34	0.06910569105691057	13	0.03591160220994475	0	0.0	15	0.01978891820580475	C	7.853	0.724435	0.15439	0.074671	0.025116	ENSG00000149633	ENST00000279024	T	0.05786	3.39	5.31	5.31	0.75309	.	0.347836	0.24952	N	0.034290	T	0.00845	0.0028	L	0.50333	1.59	0.09310	N	0.999999	D	0.71674	0.998	P	0.50860	0.652	T	0.15150	-1.0447	10	0.25106	T	0.35	.	16.293	0.82759	0.0:1.0:0.0:0.0	rs41282824;rs61735726	255	Q5JYT7	K1755_HUMAN	Q	255	ENSP00000279024:R255Q	ENSP00000279024:R255Q	R	-	2	0	KIAA1755	36303183	0.000000	0.05858	0.251000	0.24312	0.112000	0.19704	0.255000	0.18333	2.764000	0.94973	0.655000	0.94253	CGG	C|0.961;T|0.039	0.039	strong		0.577	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PI4KA	5297	hgsc.bcm.edu	37	22	21064203	21064203	+	Missense_Mutation	SNP	G	G	A	rs535848772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	532	4	0.0075188		WXS	Illumina HiSeq	Phase_I	600	10	0.0166667	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	
ZNF12	7559	hgsc.bcm.edu	37	7	6732315	6732315	+	Missense_Mutation	SNP	A	A	C	rs61227179	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6732315A>C	ENST00000405858.1	-	5	799	c.258T>G	c.(256-258)gaT>gaG	p.D86E	ZNF12_ENST00000342651.5_Missense_Mutation_p.D86E|AC073343.13_ENST00000366167.2_RNA|AC073343.2_ENST00000577401.1_RNA|ZNF12_ENST00000404360.1_Missense_Mutation_p.D50E	NM_006956.2|NM_016265.3	NP_008887.2|NP_057349.2	P17014	ZNF12_HUMAN	zinc finger protein 12	86				D -> E (in Ref. 7; AAI54415). {ECO:0000305}.	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)		CTATTAGGTCATCAGTTTGCC	0.343													A|||	330	0.0658946	0.1884	0.0331	5008	,	,		19152	0.001		0.0348	False		,,,				2504	0.0225				p.D86E		Atlas-SNP	.											.	ZNF12	53	.	0			c.T258G						PASS	.	A	GLU/ASP,GLU/ASP	685,2947		62,561,1193	104.0	106.0	105.0		258,258	1.8	0.0	7	dbSNP_129	105	391,7781		8,375,3703	yes	missense,missense	ZNF12	NM_006956.2,NM_016265.3	45,45	70,936,4896	CC,CA,AA		4.7846,18.8601,9.1156	benign,benign	86/660,86/698	6732315	1076,10728	1816	4086	5902	SO:0001583	missense	7559	exon5			TAGGTCATCAGTT	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.258T>G	7.37:g.6732315A>C	ENSP00000385939:p.Asp86Glu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	211	139	0.658768	NM_016265	A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	Missense_Mutation	SNP	ENST00000405858.1	37	CCDS47538.1	135	0.061813186813186816	93	0.18902439024390244	11	0.03038674033149171	0	0.0	31	0.040897097625329816	A	7.256	0.604266	0.14002	0.188601	0.047846	ENSG00000164631	ENST00000404360;ENST00000405858;ENST00000342651;ENST00000399476;ENST00000330442	T;T;T	0.06068	3.35;3.4;3.48	4.7	1.77	0.24775	.	0.570877	0.14701	N	0.303545	T	0.00012	0.0000	N	0.17872	0.535	0.80722	P	0.0	B;B	0.20261	0.025;0.043	B;B	0.23852	0.024;0.049	T	0.44574	-0.9319	9	0.07325	T	0.83	.	2.9065	0.05722	0.6449:0.0:0.1559:0.1992	rs61227179;rs61731530	86;86	P17014;P17014-5	ZNF12_HUMAN;.	E	50;86;86;144;50	ENSP00000384405:D50E;ENSP00000385939:D86E;ENSP00000344745:D86E	ENSP00000331039:D50E	D	-	3	2	ZNF12	6698840	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.737000	0.26144	0.221000	0.20879	0.528000	0.53228	GAT	A|0.942;C|0.058	0.058	strong		0.343	ZNF12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324373.2	NM_016265	
OR51B6	390058	hgsc.bcm.edu	37	11	5373111	5373111	+	Missense_Mutation	SNP	G	G	A	rs7479477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373111G>A	ENST00000380219.1	+	1	374	c.374G>A	c.(373-375)cGc>cAc	p.R125H	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	125			R -> H (in dbSNP:rs7479477).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	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)		ATTACCATCCGCAGCCCCTTA	0.468													G|||	1188	0.23722	0.3389	0.2363	5008	,	,		23005	0.0863		0.2644	False		,,,				2504	0.228				p.R125H		Atlas-SNP	.											.	OR51B6	53	.	0			c.G374A						PASS	.	G	HIS/ARG	1273,3129	430.1+/-342.5	189,895,1117	126.0	116.0	119.0		374	1.1	0.0	11	dbSNP_116	119	2202,6392	370.3+/-335.8	307,1588,2402	yes	missense	OR51B6	NM_001004750.1	29	496,2483,3519	AA,AG,GG		25.6225,28.9187,26.739	benign	125/313	5373111	3475,9521	2201	4297	6498	SO:0001583	missense	390058	exon1			CCATCCGCAGCCC		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.374G>A	11.37:g.5373111G>A	ENSP00000369568:p.Arg125His	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	173	61	0.352601	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	475	0.2174908424908425	161	0.32723577235772355	92	0.2541436464088398	30	0.05244755244755245	192	0.2532981530343008	G	3.536	-0.094754	0.07053	0.289187	0.256225	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.19806	2.12	5.01	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	0.488989	0.19156	N	0.121339	T	0.00012	0.0000	L	0.49455	1.56	0.09310	N	0.999999	B	0.12630	0.006	B	0.11329	0.006	T	0.44726	-0.9309	10	0.49607	T	0.09	.	9.4751	0.38867	0.2976:0.0:0.7024:0.0	rs7479477;rs52815192;rs7479477	125	Q9H340	O51B6_HUMAN	H	124;125	ENSP00000369568:R125H	ENSP00000369568:R125H	R	+	2	0	OR51B6	5329687	0.000000	0.05858	0.044000	0.18714	0.012000	0.07955	0.546000	0.23284	0.050000	0.15949	-1.505000	0.00955	CGC	G|0.768;A|0.232	0.232	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
NOBOX	135935	hgsc.bcm.edu	37	7	144107279	144107279	+	Silent	SNP	A	A	G	rs1208179	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:144107279A>G	ENST00000467773.1	-	1	41	c.42T>C	c.(40-42)ggT>ggC	p.G14G	NOBOX_ENST00000483238.1_Silent_p.G14G	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	14					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|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)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					TGTCCCAGGTACCCTCCAGGT	0.502													A|||	526	0.105032	0.0431	0.0965	5008	,	,		20108	0.0238		0.1461	False		,,,				2504	0.2362				p.G14G		Atlas-SNP	.											NOBOX_ENST00000467773,NS,carcinoma,0,4	NOBOX	130	4	0			c.T42C						scavenged	.	A		234,3704		6,222,1741	105.0	106.0	106.0		42	-7.0	0.0	7	dbSNP_87	106	1321,6997		103,1115,2941	no	coding-synonymous	NOBOX	NM_001080413.3		109,1337,4682	GG,GA,AA		15.8812,5.9421,12.6877		14/692	144107279	1555,10701	1969	4159	6128	SO:0001819	synonymous_variant	135935	exon1			CCAGGTACCCTCC			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.42T>C	7.37:g.144107279A>G		Somatic	207	2	0.00966184		WXS	Illumina HiSeq	Phase_I	194	93	0.479381	NM_001080413	A6NCD3|A8MZN5	Silent	SNP	ENST00000467773.1	37																																																																																				A|0.900;G|0.100	0.100	strong		0.502	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
TMBIM4	51643	hgsc.bcm.edu	37	12	66546100	66546100	+	Missense_Mutation	SNP	A	A	G	rs8793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:66546100A>G	ENST00000358230.3	-	3	383	c.263T>C	c.(262-264)aTt>aCt	p.I88T	TMBIM4_ENST00000286424.7_Missense_Mutation_p.I135T|TMBIM4_ENST00000542724.1_Missense_Mutation_p.I57T|TMBIM4_ENST00000539652.1_Missense_Mutation_p.I88T|TMBIM4_ENST00000556010.1_Missense_Mutation_p.I88T|TMBIM4_ENST00000398033.4_Missense_Mutation_p.I88T|TMBIM4_ENST00000544599.1_5'UTR	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	88			I -> T (in dbSNP:rs8793). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:10931946, ECO:0000269|PubMed:16303743}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		TCTGTTTAAAATCAACGCAAA	0.338													G|||	2356	0.470447	0.2496	0.245	5008	,	,		13287	0.8839		0.4175	False		,,,				2504	0.5573				p.I88T		Atlas-SNP	.											.	TMBIM4	47	.	0			c.T263C						PASS	.	G	THR/ILE	1064,2606		153,758,924	93.0	91.0	91.0		263	2.6	0.9	12	dbSNP_52	91	3453,4711		736,1981,1365	yes	missense	TMBIM4	NM_016056.2	89	889,2739,2289	GG,GA,AA		42.2954,28.9918,38.1697	benign	88/239	66546100	4517,7317	1835	4082	5917	SO:0001583	missense	51643	exon3			TTTAAAATCAACG	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.263T>C	12.37:g.66546100A>G	ENSP00000350965:p.Ile88Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	37	CCDS41805.1	1029	0.47115384615384615	119	0.241869918699187	99	0.27348066298342544	503	0.8793706293706294	308	0.40633245382585753	G	4.389	0.071874	0.08436	0.289918	0.422954	ENSG00000155957	ENST00000556010;ENST00000358230;ENST00000426857;ENST00000286424;ENST00000398033;ENST00000539043;ENST00000539427;ENST00000542724	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.87	2.64	0.31445	.	0.218305	0.47852	N	0.000212	T	0.00012	0.0000	N	0.02345	-0.59	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.0;0.001;0.0;0.003;0.002	T	0.26744	-1.0094	8	.	.	.	-3.3271	8.1268	0.31003	0.2159:0.0:0.6664:0.1177	rs8793;rs17180104;rs58374222;rs8793	88;135;88;57;88	E7EWY5;G3XAA5;E7EQ00;G3V1M2;Q9HC24	.;.;.;.;TMBI4_HUMAN	T	88;88;88;135;88;88;134;57	ENSP00000451688:I88T;ENSP00000350965:I88T;ENSP00000286424:I135T;ENSP00000381114:I88T;ENSP00000441291:I57T	.	I	-	2	0	TMBIM4	64832367	0.986000	0.35501	0.900000	0.35374	0.336000	0.28762	1.350000	0.34010	0.413000	0.25759	-0.983000	0.02560	ATT	G|0.478;N|0.000	0.478	strong		0.338	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056	
SHF	90525	hgsc.bcm.edu	37	15	45491136	45491136	+	Missense_Mutation	SNP	C	C	G	rs62026667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45491136C>G	ENST00000290894.8	-	2	631	c.137G>C	c.(136-138)tGg>tCg	p.W46S	CTD-2651B20.6_ENST00000563103.1_RNA|CTD-2651B20.7_ENST00000568314.1_RNA|RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000318390.6_Missense_Mutation_p.W103S	NM_138356.2	NP_612365			Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CGTGAGCATCCAGGAATGGGG	0.607											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	198	0.0395367	0.003	0.062	5008	,	,		17412	0.001		0.1143	False		,,,				2504	0.0358				p.W46S		Atlas-SNP	.											.	SHF	27	.	0			c.G137C						PASS	.	C	SER/TRP	82,3874		2,78,1898	52.0	56.0	55.0		137	0.3	0.0	15	dbSNP_129	55	851,7485		44,763,3361	yes	missense	SHF	NM_138356.2	177	46,841,5259	GG,GC,CC		10.2087,2.0728,7.5903	benign	46/424	45491136	933,11359	1978	4168	6146	SO:0001583	missense	90525	exon2			AGCATCCAGGAAT	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.137G>C	15.37:g.45491136C>G	ENSP00000290894:p.Trp46Ser	Somatic	76	0	0	932	WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_138356		Missense_Mutation	SNP	ENST00000290894.8	37	CCDS10120.2	107	0.04899267399267399	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	83	0.10949868073878628	C	14.15	2.450179	0.43531	0.020728	0.102087	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390	T;T	0.43294	1.47;0.95	3.44	0.306	0.15806	.	29.593600	0.00166	N	0.000000	T	0.00496	0.0016	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.04593	-1.0940	9	0.20046	T	0.44	0.1759	2.0018	0.03469	0.2051:0.4781:0.1996:0.1172	rs62026667	46	Q7M4L6	SHF_HUMAN	S	46;46;103	ENSP00000290894:W46S;ENSP00000315978:W103S	ENSP00000290894:W46S	W	-	2	0	SHF	43278428	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.056000	0.11787	0.084000	0.17077	0.655000	0.94253	TGG	C|0.938;G|0.062	0.062	strong		0.607	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356	
AGT	183	hgsc.bcm.edu	37	1	230845794	230845794	+	Missense_Mutation	SNP	A	A	G	rs699	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:230845794A>G	ENST00000366667.4	-	2	1017	c.803T>C	c.(802-804)aTg>aCg	p.M268T	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	268			M -> I (in dbSNP:rs11568053).|M -> T (associated with essential hypertension and pre-eclampsia; dbSNP:rs699). {ECO:0000269|PubMed:1394429, ECO:0000269|PubMed:8513325}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACTGGCTCCCATCAGGGAGCA	0.547													G|||	3531	0.705072	0.9032	0.6354	5008	,	,		18819	0.8532		0.4115	False		,,,				2504	0.636				p.M268T		Atlas-SNP	.											AGT,rectum,carcinoma,0,2	AGT	62	2	0			c.T803C	GRCh37	CM920010	AGT	M	rs699	PASS	.	G	THR/MET	3643,763	308.8+/-290.8	1504,635,64	82.0	91.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	803	-0.4	0.0	1	dbSNP_36	88	3662,4938	620.8+/-397.1	801,2060,1439	yes	missense	AGT	NM_000029.3	81	2305,2695,1503	GG,GA,AA		42.5814,17.3173,43.8336	benign	268/486	230845794	7305,5701	2203	4300	6503	SO:0001583	missense	183	exon2			GCTCCCATCAGGG	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.803T>C	1.37:g.230845794A>G	ENSP00000355627:p.Met268Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	73	0.973333	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	1446	0.6620879120879121	427	0.8678861788617886	230	0.6353591160220995	479	0.8374125874125874	310	0.40897097625329815	G	0.001	-2.932260	0.00053	0.826827	0.425814	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.86694	-2.16	5.1	-0.372	0.12520	Serpin domain (3);	0.941754	0.08896	N	0.877893	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	0.32481	-0.9905	9	0.10636	T	0.68	.	5.2545	0.15540	0.2662:0.0:0.5073:0.2265	rs699;rs4714;rs3182295;rs17856353;rs61617185;rs699	268;268;268	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	T	268;186	ENSP00000355627:M268T	ENSP00000355627:M268T	M	-	2	0	AGT	228912417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.431000	0.21444	-0.242000	0.09667	-0.733000	0.03571	ATG	T|0.033;G|0.557	0.557	strong		0.547	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
WWC2	80014	hgsc.bcm.edu	37	4	184203886	184203886	+	Missense_Mutation	SNP	G	G	C	rs3814422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184203886G>C	ENST00000403733.3	+	18	2909	c.2710G>C	c.(2710-2712)Gat>Cat	p.D904H	WWC2_ENST00000513834.1_Missense_Mutation_p.D855H|WWC2_ENST00000508747.1_Missense_Mutation_p.D32H|WWC2_ENST00000504005.1_Missense_Mutation_p.D586H|WWC2_ENST00000448232.2_Missense_Mutation_p.D928H	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	904			D -> H (in dbSNP:rs3814422). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		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)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		AGAGGCCTCTGATGAAATTGT	0.428													G|||	1271	0.253794	0.1959	0.4063	5008	,	,		21674	0.2391		0.2634	False		,,,				2504	0.229				p.D904H		Atlas-SNP	.											WWC2,colon,carcinoma,0,1	WWC2	78	1	0			c.G2710C						PASS	.	G	HIS/ASP	956,3442		106,744,1349	49.0	46.0	47.0		2710	2.6	0.0	4	dbSNP_107	47	2477,6121		377,1723,2199	yes	missense	WWC2	NM_024949.5	81	483,2467,3548	CC,CG,GG		28.809,21.7372,26.4158	probably-damaging	904/1193	184203886	3433,9563	2199	4299	6498	SO:0001583	missense	80014	exon18			GCCTCTGATGAAA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2710G>C	4.37:g.184203886G>C	ENSP00000384222:p.Asp904His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	538	0.24633699633699635	96	0.1951219512195122	129	0.356353591160221	130	0.22727272727272727	183	0.24142480211081793	G	13.46	2.244444	0.39697	0.217372	0.28809	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.26373	3.46;3.46;3.26;3.3;1.74	5.27	2.62	0.31277	.	0.627510	0.16122	N	0.228617	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;B;D;P	0.53151	0.773;0.429;0.958;0.915	P;B;P;P	0.51170	0.487;0.372;0.661;0.621	T	0.42207	-0.9465	9	0.46703	T	0.11	-2.9709	10.708	0.45966	0.2825:0.0:0.7175:0.0	rs3814422;rs17855701;rs52831700;rs3814422	928;904;32;855	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	H	904;855;928;586;32	ENSP00000384222:D904H;ENSP00000425054:D855H;ENSP00000398577:D928H;ENSP00000427569:D586H;ENSP00000420835:D32H	ENSP00000384222:D904H	D	+	1	0	WWC2	184440880	0.002000	0.14202	0.000000	0.03702	0.697000	0.40408	0.703000	0.25646	0.105000	0.17753	-0.797000	0.03246	GAT	G|0.747;C|0.253	0.253	strong		0.428	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
SMC1A	8243	hgsc.bcm.edu	37	X	53407996	53407996	+	Silent	SNP	G	G	A	rs142611198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:53407996G>A	ENST00000322213.4	-	23	3577	c.3450C>T	c.(3448-3450)gcC>gcT	p.A1150A	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1150	Ala/Asp-rich (DA-box).				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CGAAGAAGGGGGCTGGCTTGT	0.617													G|||	2	0.000529801	0.0	0.0014	3775	,	,		10861	0.0		0.001	False		,,,				2504	0.0				p.A1150A		Atlas-SNP	.											.	SMC1A	112	.	0			c.C3450T						PASS	.	G		0,3835		0,0,0,1632,571	67.0	58.0	61.0		3450	3.5	1.0	X	dbSNP_134	61	10,6718		0,8,2,2420,1870	no	coding-synonymous	SMC1A	NM_006306.2		0,8,2,4052,2441	AA,AG,A,GG,G		0.1486,0.0,0.0947		1150/1234	53407996	10,10553	2203	4300	6503	SO:0001819	synonymous_variant	8243	exon23			GAAGGGGGCTGGC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3450C>T	X.37:g.53407996G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	106	103	0.971698	NM_006306	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	37	CCDS14352.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
HLA-B	3106	hgsc.bcm.edu	37	6	31324921	31324921	+	Silent	SNP	C	C	T	rs1050459	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324921C>T	ENST00000412585.2	-	1	43	c.15G>A	c.(13-15)gcG>gcA	p.A5A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	5					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						CGGTTCGGGGCGCCATGACCA	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	796	0.158946	0.1513	0.1153	5008	,	,		9261	0.1895		0.1799	False		,,,				2504	0.1472				p.A5A		Atlas-SNP	.											.	HLA-B	54	.	0			c.G15A						PASS	.	C		512,3686		51,410,1638	14.0	12.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	15	-4.8	0.0	6	dbSNP_86	13	948,7200		67,814,3193	no	coding-synonymous	HLA-B	NM_005514.6		118,1224,4831	TT,TC,CC		11.6348,12.1963,11.8257		5/363	31324921	1460,10886	2099	4074	6173	SO:0001819	synonymous_variant	3106	exon1	Familial Cancer Database	;Lichen Sclerosis, Familial	TCGGGGCGCCATG	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.15G>A	6.37:g.31324921C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.873;T|0.127	0.127	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
BAG3	9531	hgsc.bcm.edu	37	10	121429633	121429633	+	Missense_Mutation	SNP	T	T	C	rs2234962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:121429633T>C	ENST00000369085.3	+	2	757	c.451T>C	c.(451-453)Tgt>Cgt	p.C151R		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	151	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.		C -> R (in dbSNP:rs2234962). {ECO:0000269|PubMed:10597216, ECO:0000269|PubMed:21459883}.		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)		AGATAAACAGTGTGGACAGGT	0.667													T|||	483	0.0964457	0.0106	0.1037	5008	,	,		16366	0.002		0.2187	False		,,,				2504	0.1789				p.C151R		Atlas-SNP	.											.	BAG3	42	.	0			c.T451C						PASS	.	T	ARG/CYS	182,4218		1,180,2019	37.0	42.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	451	0.1	1.0	10	dbSNP_98	40	1782,6814		189,1404,2705	yes	missense	BAG3	NM_004281.3	180	190,1584,4724	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	20.7306,4.1364,15.1123	possibly-damaging	151/576	121429633	1964,11032	2200	4298	6498	SO:0001583	missense	9531	exon2			AAACAGTGTGGAC	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.451T>C	10.37:g.121429633T>C	ENSP00000358081:p.Cys151Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	217	0.09935897435897435	3	0.006097560975609756	47	0.1298342541436464	2	0.0034965034965034965	165	0.21767810026385223	T	17.09	3.300901	0.60195	0.041364	0.207306	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.79554	-1.02;-1.28	5.28	0.0636	0.14349	.	0.695305	0.15601	N	0.253939	T	0.00073	0.0002	N	0.24115	0.695	0.09310	P	0.999999761886	P	0.39216	0.664	B	0.40038	0.317	T	0.03945	-1.0990	9	0.16420	T	0.52	-0.1774	5.4126	0.16356	0.3916:0.0709:0.0:0.5374	rs2234962;rs60180987;rs2234962	151	O95817	BAG3_HUMAN	R	151;93	ENSP00000358081:C151R;ENSP00000410036:C93R	ENSP00000358081:C151R	C	+	1	0	BAG3	121419623	1.000000	0.71417	0.975000	0.42487	0.879000	0.50718	0.566000	0.23593	-0.242000	0.09667	-0.496000	0.04628	TGT	T|0.867;C|0.133	0.133	strong		0.667	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
FOXN2	3344	hgsc.bcm.edu	37	2	48602252	48602252	+	Silent	SNP	C	C	T	rs17855177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48602252C>T	ENST00000340553.3	+	7	1227	c.966C>T	c.(964-966)tcC>tcT	p.S322S		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	322					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			GCGTGTCTTCCCTGTCTTCTG	0.448													C|||	1280	0.255591	0.1218	0.2104	5008	,	,		22555	0.4603		0.3101	False		,,,				2504	0.2014				p.S322S		Atlas-SNP	.											.	FOXN2	39	.	0			c.C966T						PASS	.	C		698,3708	291.3+/-281.4	59,580,1564	135.0	111.0	119.0		966	-0.5	1.0	2	dbSNP_123	119	2775,5825	440.8+/-359.6	432,1911,1957	no	coding-synonymous	FOXN2	NM_002158.3		491,2491,3521	TT,TC,CC		32.2674,15.842,26.7031		322/432	48602252	3473,9533	2203	4300	6503	SO:0001819	synonymous_variant	3344	exon7			GTCTTCCCTGTCT		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"""Forkhead boxes"""	5281	protein-coding gene	gene with protein product		143089	"""human T-cell leukemia virus enhancer factor"""	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.966C>T	2.37:g.48602252C>T		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_002158	Q15769|Q6P4Q2	Silent	SNP	ENST00000340553.3	37	CCDS1838.1																																																																																			C|0.730;T|0.270	0.270	strong		0.448	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158	
WBP2NL	164684	hgsc.bcm.edu	37	22	42423110	42423110	+	Missense_Mutation	SNP	G	G	C	rs2301521	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42423110G>C	ENST00000328823.9	+	6	886	c.855G>C	c.(853-855)caG>caC	p.Q285H	WBP2NL_ENST00000543212.1_Missense_Mutation_p.Q211H	NM_152613.2	NP_689826.2	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	285			Q -> H (in dbSNP:rs2301521). {ECO:0000269|PubMed:15489334}.		egg activation (GO:0007343)|male pronucleus assembly (GO:0035039)|meiotic nuclear division (GO:0007126)	perinuclear theca (GO:0033011)	WW domain binding (GO:0050699)			breast(2)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)	14						CCAGGCCTCAGGAATCTACAG	0.557													c|||	3895	0.777756	0.9455	0.7046	5008	,	,		18318	0.8542		0.671	False		,,,				2504	0.6339				p.Q285H		Atlas-SNP	.											.	WBP2NL	24	.	0			c.G855C						PASS	.	T	HIS/GLN	3964,442	211.2+/-231.4	1785,394,24	74.0	84.0	81.0		855	-7.8	0.0	22	dbSNP_100	81	5768,2832	446.7+/-361.3	1951,1866,483	yes	missense	WBP2NL	NM_152613.2	24	3736,2260,507	CC,CG,GG		32.9302,10.0318,25.173	benign	285/310	42423110	9732,3274	2203	4300	6503	SO:0001583	missense	164684	exon6			GCCTCAGGAATCT	BC022546	CCDS14029.1	22q13.2	2007-07-18			ENSG00000183066	ENSG00000183066			28389	protein-coding gene	gene with protein product	"""postacrosomal sheath WW domain-binding protein"""	610981				17289678	Standard	NM_152613		Approved	FLJ26145, MGC26816, PAWP	uc003bbt.3	Q6ICG8	OTTHUMG00000151270	ENST00000328823.9:c.855G>C	22.37:g.42423110G>C	ENSP00000332983:p.Gln285His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	66	0.970588	NM_152613	A3KFF7|A8MSG5|B3KXX4|Q8TBF0|Q8TBF3	Missense_Mutation	SNP	ENST00000328823.9	37	CCDS14029.1	1708	0.782051282051282	460	0.9349593495934959	258	0.712707182320442	480	0.8391608391608392	510	0.6728232189973615	c	0.012	-1.653181	0.00785	0.899682	0.670698	ENSG00000183066	ENST00000328823;ENST00000543212	T;T	0.22743	2.22;1.94	3.89	-7.78	0.01223	.	.	.	.	.	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	0.14090	-1.0485	8	0.12766	T	0.61	.	0.3602	0.00363	0.3232:0.1524:0.1625:0.3618	rs2301521;rs17466551;rs17845706;rs17858650;rs52806929;rs2301521	285	Q6ICG8	WBP2L_HUMAN	H	285;211	ENSP00000332983:Q285H;ENSP00000442447:Q211H	ENSP00000332983:Q285H	Q	+	3	2	WBP2NL	40753056	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.008000	0.00649	-4.641000	0.00038	-4.874000	0.00002	CAG	G|0.245;C|0.755	0.755	strong		0.557	WBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322037.1	NM_152613	
RREB1	6239	hgsc.bcm.edu	37	6	7229346	7229346	+	Silent	SNP	T	T	C	rs2714315	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7229346T>C	ENST00000349384.6	+	10	1328	c.1014T>C	c.(1012-1014)caT>caC	p.H338H	RREB1_ENST00000379938.2_Silent_p.H338H|RREB1_ENST00000379933.3_Silent_p.H338H|RREB1_ENST00000334984.6_Silent_p.H338H	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	338					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)				AGCAGACCCATGTGGCGGCAG	0.627													C|||	2044	0.408147	0.792	0.2147	5008	,	,		16187	0.2718		0.3419	False		,,,				2504	0.2352				p.H338H		Atlas-SNP	.											.	RREB1	242	.	0			c.T1014C						PASS	.	C	,,,	3059,1347	448.5+/-348.7	1056,947,200	44.0	40.0	41.0		1014,1014,1014,1014	-0.2	0.2	6	dbSNP_100	41	2631,5969	685.0+/-404.0	408,1815,2077	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	1464,2762,2277	CC,CT,TT		30.593,30.5719,43.749	,,,	338/1688,338/1743,338/1477,338/1688	7229346	5690,7316	2203	4300	6503	SO:0001819	synonymous_variant	6239	exon10			GACCCATGTGGCG	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.1014T>C	6.37:g.7229346T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			T|0.555;C|0.445	0.445	strong		0.627	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
CARD11	84433	hgsc.bcm.edu	37	7	2957005	2957005	+	Silent	SNP	T	T	C	rs3735124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:2957005T>C	ENST00000396946.4	-	20	3025	c.2622A>G	c.(2620-2622)ccA>ccG	p.P874P		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	874					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)		GCGCTTCTTCTGGCTGCAGGG	0.567			Mis		DLBCL								C|||	2319	0.463059	0.5787	0.4207	5008	,	,		14294	0.6101		0.2087	False		,,,				2504	0.4468				p.P874P		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A2622G						PASS	.	C		2343,2063	562.8+/-381.0	613,1117,473	37.0	49.0	45.0		2622	-10.0	0.1	7	dbSNP_107	45	1779,6819	731.4+/-406.8	165,1449,2685	no	coding-synonymous	CARD11	NM_032415.4		778,2566,3158	CC,CT,TT		20.6909,46.8225,31.6979		874/1155	2957005	4122,8882	2203	4299	6502	SO:0001819	synonymous_variant	84433	exon20			TTCTTCTGGCTGC	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.2622A>G	7.37:g.2957005T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	49	9	0.183673	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			T|0.633;C|0.367	0.367	strong		0.567	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
ADRB2	154	hgsc.bcm.edu	37	5	148206440	148206440	+	Missense_Mutation	SNP	G	G	A	rs1042713	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148206440G>A	ENST00000305988.4	+	1	285	c.46G>A	c.(46-48)Gga>Aga	p.G16R		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	16			G -> R (common polymorphism; dbSNP:rs1042713). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3025863, ECO:0000269|PubMed:3033609, ECO:0000269|PubMed:3034889, ECO:0000269|PubMed:7706471, ECO:0000269|PubMed:7915137, ECO:0000269|PubMed:8383511, ECO:0000269|Ref.8}.		activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	GGCACCCAATGGAAGCCATGC	0.672													G|||	2382	0.475639	0.5204	0.4568	5008	,	,		16385	0.5486		0.3857	False		,,,				2504	0.4458				p.G16R		Atlas-SNP	.											.	ADRB2	42	.	0			c.G46A	GRCh37	CM950016	ADRB2	M	rs1042713	PASS	.	G	ARG/GLY	2147,2259	581.2+/-385.3	538,1071,594	113.0	110.0	111.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	46	3.7	0.3	5	dbSNP_86	111	3249,5351	488.1+/-372.3	619,2011,1670	yes	missense	ADRB2	NM_000024.5	125	1157,3082,2264	AA,AG,GG		37.7791,48.729,41.4885	benign	16/414	148206440	5396,7610	2203	4300	6503	SO:0001583	missense	154	exon1			CCCAATGGAAGCC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.46G>A	5.37:g.148206440G>A	ENSP00000305372:p.Gly16Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Missense_Mutation	SNP	ENST00000305988.4	37	CCDS4292.1	1027	0.47023809523809523	259	0.5264227642276422	171	0.4723756906077348	307	0.5367132867132867	290	0.38258575197889183	G	7.133	0.580326	0.13686	0.48729	0.377791	ENSG00000169252	ENST00000305988	T	0.65732	-0.17	4.67	3.73	0.42828	.	0.865291	0.09840	N	0.748967	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.20261	0.043	B	0.20955	0.032	T	0.46373	-0.9196	9	0.19147	T	0.46	.	8.2137	0.31499	0.0839:0.0:0.7586:0.1575	rs1042713;rs3182174;rs3729940;rs17287432;rs17334179;rs17334242;rs17721693;rs17839749;rs17846639;rs17859732;rs52812686;rs56964295;rs1042713	16	P07550	ADRB2_HUMAN	R	16	ENSP00000305372:G16R	ENSP00000305372:G16R	G	+	1	0	ADRB2	148186633	0.003000	0.15002	0.258000	0.24420	0.308000	0.27856	1.131000	0.31406	2.583000	0.87209	0.655000	0.94253	GGA	G|0.576;A|0.424	0.424	strong		0.672	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
C15orf39	56905	hgsc.bcm.edu	37	15	75498744	75498744	+	Missense_Mutation	SNP	G	G	C	rs1873379	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75498744G>C	ENST00000360639.2	+	2	675	c.355G>C	c.(355-357)Gct>Cct	p.A119P	C15orf39_ENST00000394987.4_Missense_Mutation_p.A119P|C15orf39_ENST00000567617.1_Missense_Mutation_p.A119P			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	119			A -> P (in dbSNP:rs1873379). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CAGTCCCCAGGCTCACTCCTA	0.602													G|||	490	0.0978435	0.0197	0.1916	5008	,	,		18326	0.0298		0.2465	False		,,,				2504	0.0542				p.A119P		Atlas-SNP	.											C15orf39,NS,carcinoma,0,1	C15orf39	64	1	0			c.G355C						PASS	.	G	PRO/ALA	240,4154	138.8+/-174.5	7,226,1964	45.0	43.0	44.0		355	-1.0	0.1	15	dbSNP_92	44	2351,6239	390.2+/-343.2	309,1733,2253	yes	missense	C15orf39	NM_015492.4	27	316,1959,4217	CC,CG,GG		27.369,5.462,19.9553	benign	119/1048	75498744	2591,10393	2197	4295	6492	SO:0001583	missense	56905	exon2			CCCCAGGCTCACT	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.355G>C	15.37:g.75498744G>C	ENSP00000353854:p.Ala119Pro	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	298	0.13644688644688643	15	0.03048780487804878	79	0.21823204419889503	15	0.026223776223776224	189	0.24934036939313983	G	9.878	1.200885	0.22121	0.05462	0.27369	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.69806	-0.43;-0.43	5.13	-1.0	0.10196	.	1.904580	0.02757	N	0.118116	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.10753	-1.0616	9	0.54805	T	0.06	-0.2632	2.7776	0.05352	0.0895:0.3361:0.2799:0.2945	rs1873379;rs1873379	119	Q6ZRI6	CO039_HUMAN	P	119	ENSP00000353854:A119P;ENSP00000378438:A119P	ENSP00000353854:A119P	A	+	1	0	C15orf39	73285797	0.004000	0.15560	0.110000	0.21437	0.497000	0.33675	0.038000	0.13862	-0.145000	0.11294	0.561000	0.74099	GCT	G|0.828;C|0.172	0.172	strong		0.602	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
SYNE2	23224	hgsc.bcm.edu	37	14	64408852	64408852	+	Silent	SNP	G	G	C	rs33976862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64408852G>C	ENST00000344113.4	+	6	611	c.399G>C	c.(397-399)ctG>ctC	p.L133L	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000341472.5_Silent_p.L133L|SYNE2_ENST00000554584.1_Silent_p.L133L|SYNE2_ENST00000356081.3_Silent_p.L133L|SYNE2_ENST00000358025.3_Silent_p.L133L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	133	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.L133L(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CAATTATCCTGCACTTTCATG	0.313													G|||	546	0.109026	0.2542	0.1138	5008	,	,		18493	0.0466		0.0467	False		,,,				2504	0.0378				p.L133L		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	stomach(1)	c.G399C						PASS	.	G	,	742,2888		80,582,1153	75.0	68.0	70.0		399,399	5.0	1.0	14	dbSNP_126	70	588,7584		25,538,3523	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	105,1120,4676	CC,CG,GG		7.1953,20.4408,11.2693	,	133/6886,133/6908	64408852	1330,10472	1815	4086	5901	SO:0001819	synonymous_variant	23224	exon6			TATCCTGCACTTT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.399G>C	14.37:g.64408852G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			G|0.904;C|0.096	0.096	strong		0.313	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
TOP2B	7155	hgsc.bcm.edu	37	3	25639849	25639849	+	Silent	SNP	A	A	G	rs11548723	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:25639849A>G	ENST00000264331.4	-	36	4829	c.4830T>C	c.(4828-4830)ttT>ttC	p.F1610F	TOP2B_ENST00000435706.2_Silent_p.F1605F|TOP2B_ENST00000542520.1_Silent_p.F462F|TOP2B_ENST00000540199.1_Silent_p.F462F	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1610					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	CAGACTCTGCAAAATATTTTA	0.408													A|||	66	0.0131789	0.0015	0.036	5008	,	,		17937	0.0		0.0378	False		,,,				2504	0.001				p.F1605F		Atlas-SNP	.											.	TOP2B	98	.	0			c.T4815C						PASS	.	A		32,3680		0,32,1824	150.0	146.0	147.0		4815	4.6	1.0	3	dbSNP_120	147	381,7821		9,363,3729	no	coding-synonymous	TOP2B	NM_001068.2		9,395,5553	GG,GA,AA		4.6452,0.8621,3.4665		1605/1622	25639849	413,11501	1856	4101	5957	SO:0001819	synonymous_variant	7155	exon36			CTCTGCAAAATAT	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.4830T>C	3.37:g.25639849A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	134	84	0.626866	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	37																																																																																				A|0.977;G|0.023	0.023	strong		0.408	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
KCNK18	338567	hgsc.bcm.edu	37	10	118957027	118957027	+	Missense_Mutation	SNP	A	A	G	rs67346047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	69	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	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	
QRFPR	84109	hgsc.bcm.edu	37	4	122301622	122301622	+	Missense_Mutation	SNP	A	A	C	rs17438900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:122301622A>C	ENST00000394427.2	-	1	592	c.181T>G	c.(181-183)Ttt>Gtt	p.F61V	QRFPR_ENST00000334383.5_Missense_Mutation_p.F61V	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	61			F -> V (in dbSNP:rs17438900).		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)|neuropeptide Y receptor activity (GO:0004983)	p.F61V(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCATTGCCAAAGAGCGCCAGG	0.627													A|||	507	0.101238	0.0189	0.1484	5008	,	,		15024	0.0704		0.2266	False		,,,				2504	0.0818				p.F61V		Atlas-SNP	.											QRFPR,NS,carcinoma,0,1	QRFPR	65	1	1	Substitution - Missense(1)	prostate(1)	c.T181G						PASS	.	A	VAL/PHE	248,4158	142.3+/-177.5	9,230,1964	73.0	62.0	65.0		181	3.9	1.0	4	dbSNP_123	65	1997,6603	349.2+/-327.3	234,1529,2537	yes	missense	QRFPR	NM_198179.2	50	243,1759,4501	CC,CA,AA		23.2209,5.6287,17.2613	benign	61/432	122301622	2245,10761	2203	4300	6503	SO:0001583	missense	84109	exon1			TGCCAAAGAGCGC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.181T>G	4.37:g.122301622A>C	ENSP00000377948:p.Phe61Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	161	84	0.521739	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	279	0.12774725274725274	10	0.02032520325203252	50	0.13812154696132597	46	0.08041958041958042	173	0.22823218997361477	A	5.780	0.328349	0.10956	0.056287	0.232209	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.35421	1.31;1.31	5.18	3.92	0.45320	.	0.213542	0.49305	D	0.000148	T	0.00012	0.0000	N	0.20986	0.625	0.22787	P	0.99873549	B;B;B	0.13145	0.001;0.003;0.007	B;B;B	0.12837	0.001;0.003;0.008	T	0.12142	-1.0559	9	0.02654	T	1	.	11.4128	0.49935	0.8489:0.1511:0.0:0.0	rs17438900;rs52798239;rs17438900	61;61;61	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	V	61	ENSP00000377948:F61V;ENSP00000335610:F61V	ENSP00000335610:F61V	F	-	1	0	QRFPR	122521072	0.982000	0.34865	0.999000	0.59377	0.993000	0.82548	2.020000	0.41010	1.930000	0.55929	0.383000	0.25322	TTT	A|0.852;C|0.147	0.147	strong		0.627	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
CHD2	1106	hgsc.bcm.edu	37	15	93557954	93557954	+	Missense_Mutation	SNP	G	G	C	rs56227200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:93557954G>C	ENST00000394196.4	+	37	5789	c.4721G>C	c.(4720-4722)gGg>gCg	p.G1574A	CHD2_ENST00000557381.1_Missense_Mutation_p.G1574A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1574			G -> A (in dbSNP:rs56227200).		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)			GACGTGACTGGGGGTAAGAAA	0.483													G|||	53	0.0105831	0.0015	0.0173	5008	,	,		16711	0.0		0.0378	False		,,,				2504	0.001				p.G1574A		Atlas-SNP	.											.	CHD2	280	.	0			c.G4721C						PASS	.	G	ALA/GLY	22,4372	28.1+/-56.4	0,22,2175	96.0	101.0	99.0		4721	5.8	1.0	15	dbSNP_129	99	246,8350	97.2+/-158.9	1,244,4053	yes	missense	CHD2	NM_001271.3	60	1,266,6228	CC,CG,GG		2.8618,0.5007,2.0631	benign	1574/1829	93557954	268,12722	2197	4298	6495	SO:0001583	missense	1106	exon37			TGACTGGGGGTAA	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.4721G>C	15.37:g.93557954G>C	ENSP00000377747:p.Gly1574Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	38	0.0173992673992674	0	0.0	8	0.022099447513812154	0	0.0	30	0.0395778364116095	G	4.134	0.023158	0.08006	0.005007	0.028618	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000557759	D;D;T	0.89343	-2.5;-2.49;0.98	5.76	5.76	0.90799	.	0.239796	0.21044	U	0.081118	T	0.51958	0.1705	N	0.19112	0.55	0.80722	D	1	B;B	0.26147	0.088;0.143	B;B	0.28465	0.025;0.09	T	0.66960	-0.5791	10	0.06236	T	0.91	-18.5026	13.4137	0.60956	0.0745:0.0:0.9255:0.0	rs56227200;rs61735574	1574;1574	O14647;O14647-2	CHD2_HUMAN;.	A	1574;1574;99	ENSP00000377747:G1574A;ENSP00000451366:G1574A;ENSP00000451539:G99A	ENSP00000377747:G1574A	G	+	2	0	CHD2	91358958	1.000000	0.71417	0.994000	0.49952	0.542000	0.35054	6.743000	0.74848	2.730000	0.93505	0.591000	0.81541	GGG	G|0.981;C|0.019	0.019	strong		0.483	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136291361	136291361	+	Silent	SNP	C	C	T	rs34054981	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136291361C>T	ENST00000371929.3	+	6	1026	c.582C>T	c.(580-582)ggC>ggT	p.G194G	ADAMTS13_ENST00000356589.2_Silent_p.G194G|ADAMTS13_ENST00000371911.3_Silent_p.G194G|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000536611.1_5'Flank|ADAMTS13_ENST00000371916.1_Silent_p.G194G|ADAMTS13_ENST00000355699.2_Silent_p.G194G	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	194	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)		AGGTGCGGGGCGTCACCCAGC	0.627													C|||	139	0.0277556	0.0053	0.036	5008	,	,		18895	0.001		0.0805	False		,,,				2504	0.0256				p.G194G		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C582T						PASS	.	C	,,	74,4332	65.8+/-103.3	1,72,2130	73.0	65.0	68.0		582,582,582	-4.6	0.9	9	dbSNP_126	68	734,7866	177.5+/-227.1	35,664,3601	yes	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	36,736,5731	TT,TC,CC		8.5349,1.6795,6.2125	,,	194/1428,194/1341,194/1372	136291361	808,12198	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon6			GCGGGGCGTCACC	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.582C>T	9.37:g.136291361C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			C|0.942;T|0.058	0.058	strong		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
CMYA5	202333	hgsc.bcm.edu	37	5	79028472	79028472	+	Missense_Mutation	SNP	C	C	T	rs4704585	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79028472C>T	ENST00000446378.2	+	2	3915	c.3884C>T	c.(3883-3885)gCt>gTt	p.A1295V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1295			A -> V (in dbSNP:rs4704585). {ECO:0000269|PubMed:17974005}.		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)		GGACCTGAGGCTTTATCAGCA	0.383													T|||	2781	0.555312	0.7837	0.4107	5008	,	,		22030	0.6448		0.3907	False		,,,				2504	0.4264				p.A1295V		Atlas-SNP	.											.	CMYA5	643	.	0			c.C3884T						PASS	.	T	VAL/ALA	2684,1056		989,706,175	51.0	51.0	51.0		3884	-0.0	0.1	5	dbSNP_111	51	3168,5036		634,1900,1568	yes	missense	CMYA5	NM_153610.3	64	1623,2606,1743	TT,TC,CC		38.6153,28.2353,48.9953	benign	1295/4070	79028472	5852,6092	1870	4102	5972	SO:0001583	missense	202333	exon2			CTGAGGCTTTATC	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.3884C>T	5.37:g.79028472C>T	ENSP00000394770:p.Ala1295Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	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	1232	0.5641025641025641	398	0.8089430894308943	151	0.4171270718232044	386	0.6748251748251748	297	0.391820580474934	T	0.003	-2.452451	0.00175	0.717647	0.386153	ENSG00000164309	ENST00000446378	T	0.02472	4.28	5.28	-0.023	0.13945	.	0.780759	0.11178	N	0.591268	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.17048	-1.0382	9	0.02654	T	1	.	4.9625	0.14074	0.0:0.227:0.274:0.499	rs4704585;rs52819464;rs58871960;rs4704585	1295	Q8N3K9	CMYA5_HUMAN	V	1295	ENSP00000394770:A1295V	ENSP00000394770:A1295V	A	+	2	0	CMYA5	79064228	0.002000	0.14202	0.079000	0.20413	0.028000	0.11728	0.131000	0.15870	-0.390000	0.07774	-1.126000	0.01995	GCT	C|0.428;T|0.572	0.572	strong		0.383	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ZDBF2	57683	hgsc.bcm.edu	37	2	207174559	207174559	+	Silent	SNP	A	A	G	rs13408088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207174559A>G	ENST00000374423.3	+	5	5693	c.5307A>G	c.(5305-5307)aaA>aaG	p.K1769K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1769							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CTGTTAAGAAAAGACACCCTT	0.413													A|||	157	0.0313498	0.1051	0.0159	5008	,	,		20253	0.0		0.006	False		,,,				2504	0.001				p.K1769K		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A5307G						PASS	.	A		352,3382		17,318,1532	55.0	56.0	56.0		5307	2.6	0.0	2	dbSNP_121	56	71,8127		0,71,4028	no	coding-synonymous	ZDBF2	NM_020923.1		17,389,5560	GG,GA,AA		0.8661,9.4269,3.5451		1769/2355	207174559	423,11509	1867	4099	5966	SO:0001819	synonymous_variant	57683	exon5			TAAGAAAAGACAC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5307A>G	2.37:g.207174559A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			A|0.970;G|0.030	0.030	strong		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	88	2	0.0227273		WXS	Illumina HiSeq	Phase_I	118	5	0.0423729	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	
GPR144	347088	hgsc.bcm.edu	37	9	127216378	127216378	+	Splice_Site	SNP	T	T	C	rs118108631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127216378T>C	ENST00000334810.1	+	5	1078		c.e5+2					Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144						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)			central_nervous_system(1)|endometrium(3)	4						ACCGGACAGGTGCGCCCTGGC	0.647													T|||	19	0.00379393	0.0008	0.0058	5008	,	,		13610	0.0		0.0109	False		,,,				2504	0.0031				.		Atlas-SNP	.											GPR144,NS,carcinoma,0,1	GPR144	33	1	0			c.1078+2T>C						scavenged	.	T		2,1382		0,2,690	15.0	20.0	18.0			4.3	1.0	9	dbSNP_132	18	42,3138		0,42,1548	yes	splice-5	GPR144	NM_001161808.1		0,44,2238	CC,CT,TT		1.3208,0.1445,0.9641			127216378	44,4520	692	1590	2282	SO:0001630	splice_region_variant	347088	exon5			GACAGGTGCGCCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1078+2T>C	9.37:g.127216378T>C		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_001161808	Q86SL4|Q8NH12	Splice_Site	SNP	ENST00000334810.1	37	CCDS48016.1	14	0.00641025641025641	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	16.08	3.022012	0.54576	0.001445	0.013208	ENSG00000180264	ENST00000334810	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1411	0.42736	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR144	126256199	0.995000	0.38212	0.966000	0.40874	0.606000	0.37113	0.972000	0.29409	1.707000	0.51288	0.379000	0.24179	.	T|0.993;C|0.007	0.007	strong		0.647	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	Intron
NUP205	23165	hgsc.bcm.edu	37	7	135333172	135333172	+	Silent	SNP	C	C	T	rs61740269	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135333172C>T	ENST00000285968.6	+	43	5933	c.5907C>T	c.(5905-5907)aaC>aaT	p.N1969N		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1969					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						ATGCAATCAACGCTTTTGGAG	0.338													C|||	271	0.0541134	0.0401	0.0504	5008	,	,		16726	0.0546		0.0497	False		,,,				2504	0.0798				p.N1969N		Atlas-SNP	.											.	NUP205	198	.	0			c.C5907T						PASS	.	C		174,4232	114.2+/-152.2	2,170,2031	87.0	86.0	86.0		5907	-8.0	0.0	7	dbSNP_129	86	385,8215	124.3+/-183.0	6,373,3921	no	coding-synonymous	NUP205	NM_015135.2		8,543,5952	TT,TC,CC		4.4767,3.9492,4.298		1969/2013	135333172	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon43			AATCAACGCTTTT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5907C>T	7.37:g.135333172C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	43	32	0.744186	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			C|0.954;T|0.046	0.046	strong		0.338	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
DLG5	9231	hgsc.bcm.edu	37	10	79584178	79584178	+	Silent	SNP	G	G	C	rs1248629	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:79584178G>C	ENST00000372391.2	-	14	2351	c.2346C>G	c.(2344-2346)cgC>cgG	p.R782R	DLG5_ENST00000459739.1_5'Flank|DLG5_ENST00000372388.2_Silent_p.R782R	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	782	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			CCTGGCAGCTGCGCAGCAGAG	0.582													C|||	3727	0.744209	0.8737	0.7795	5008	,	,		21623	0.7282		0.6491	False		,,,				2504	0.6585				p.R782R		Atlas-SNP	.											.	DLG5	154	.	0			c.C2346G						PASS	.	C		3698,708	295.6+/-283.7	1559,580,64	86.0	65.0	72.0		2346	-3.3	0.9	10	dbSNP_87	72	5618,2982	461.0+/-365.3	1842,1934,524	no	coding-synonymous	DLG5	NM_004747.3		3401,2514,588	CC,CG,GG		34.6744,16.069,28.3715		782/1920	79584178	9316,3690	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon14			GCAGCTGCGCAGC	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.2346C>G	10.37:g.79584178G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.288;C|0.712	0.712	strong		0.582	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
B4GALNT1	2583	hgsc.bcm.edu	37	12	58024278	58024278	+	Missense_Mutation	SNP	C	C	G	rs810205	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:58024278C>G	ENST00000341156.4	-	5	1098	c.514G>C	c.(514-516)Ggt>Cgt	p.G172R	B4GALNT1_ENST00000552350.1_Missense_Mutation_p.G172R|B4GALNT1_ENST00000550943.1_5'Flank|B4GALNT1_ENST00000449184.3_Missense_Mutation_p.G172R|B4GALNT1_ENST00000418555.2_Missense_Mutation_p.G117R|B4GALNT1_ENST00000550764.1_Missense_Mutation_p.G172R	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	172			G -> R (in dbSNP:rs810205).		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			ACCTCCTGACCAGAAGCTGCC	0.532													C|||	103	0.0205671	0.0469	0.0072	5008	,	,		20485	0.0		0.0189	False		,,,				2504	0.0174				p.X172Q		Atlas-SNP	.											.	B4GALNT1	53	.	0			c.T514C						PASS	.	C	ARG/GLY	219,4187		10,199,1994	108.0	86.0	93.0		514	4.5	0.2	12	dbSNP_86	93	155,8445		0,155,4145	yes	missense	B4GALNT1	NM_001478.3	125	10,354,6139	GG,GC,CC		1.8023,4.9705,2.8756	benign	172/534	58024278	374,12632	2203	4300	6503	SO:0001583	missense	2583	exon5			CCTGACCAGAAGC	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	4117	protein-coding gene	gene with protein product	"""GD2 synthase, GM2 synthase"""	601873	"""UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)"", ""UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1"", ""spastic paraplegia 26"""	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.514G>C	12.37:g.58024278C>G	ENSP00000341562:p.Gly172Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001478	B4DE26|Q8N636	Missense_Mutation	SNP	ENST00000341156.4	37	CCDS8950.1	38	0.0173992673992674	19	0.03861788617886179	3	0.008287292817679558	0	0.0	16	0.021108179419525065	.	9.260	1.042939	0.19748	0.049705	0.018023	ENSG00000135454	ENST00000341156;ENST00000418555;ENST00000550764;ENST00000552350;ENST00000548888	T;T;T;T;T	0.30182	2.31;2.33;1.54;1.54;1.59	4.53	4.53	0.55603	.	1.092340	0.06878	N	0.801975	T	0.05227	0.0139	N	0.25647	0.755	0.09310	N	1	P;B;D;B	0.53745	0.513;0.037;0.962;0.0	B;B;P;B	0.46718	0.238;0.016;0.525;0.001	T	0.04178	-1.0971	10	0.17832	T	0.49	-9.4325	12.9331	0.58299	0.0:1.0:0.0:0.0	rs810205;rs810205	172;117;172;172	B4DSP5;B4DE26;Q8N636;Q00973	.;.;.;B4GN1_HUMAN	R	172;117;172;172;172	ENSP00000341562:G172R;ENSP00000401601:G117R;ENSP00000450303:G172R;ENSP00000448500:G172R;ENSP00000447945:G172R	ENSP00000341562:G172R	G	-	1	0	B4GALNT1	56310545	0.003000	0.15002	0.200000	0.23457	0.577000	0.36160	0.518000	0.22847	2.519000	0.84933	0.205000	0.17691	GGT	C|0.966;G|0.034	0.034	strong		0.532	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478	
RAD18	56852	hgsc.bcm.edu	37	3	8955389	8955389	+	Missense_Mutation	SNP	C	C	T	rs373572	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:8955389C>T	ENST00000264926.2	-	8	1021	c.905G>A	c.(904-906)cGa>cAa	p.R302Q		NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	302			R -> Q (in dbSNP:rs373572). {ECO:0000269|PubMed:10884424, ECO:0000269|PubMed:10908344, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		TTCGATTTCTCGAACTATTTC	0.299								Rad6 pathway					T|||	3243	0.647564	0.6543	0.7118	5008	,	,		18337	0.3591		0.7624	False		,,,				2504	0.772				p.R302Q		Atlas-SNP	.											.	RAD18	52	.	0			c.G905A						PASS	.	T	GLN/ARG	2931,1473	465.7+/-354.3	976,979,247	74.0	70.0	71.0		905	4.5	1.0	3	dbSNP_80	71	6219,2369	383.4+/-340.7	2265,1689,340	yes	missense	RAD18	NM_020165.3	43	3241,2668,587	TT,TC,CC		27.585,33.4469,29.572	benign	302/496	8955389	9150,3842	2202	4294	6496	SO:0001583	missense	56852	exon8			ATTTCTCGAACTA		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"""RING-type (C3HC4) zinc fingers"""	18278	protein-coding gene	gene with protein product		605256	"""RAD18 homolog (S. cerevisiae)"""			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.905G>A	3.37:g.8955389C>T	ENSP00000264926:p.Arg302Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	212	209	0.985849	NM_020165	Q58F55|Q9NRT6	Missense_Mutation	SNP	ENST00000264926.2	37	CCDS2571.1	1380	0.6318681318681318	330	0.6707317073170732	244	0.6740331491712708	227	0.3968531468531469	579	0.7638522427440633	T	7.019	0.558314	0.13436	0.665531	0.72415	ENSG00000070950	ENST00000264926	T	0.24538	1.85	4.47	4.47	0.54385	.	0.113232	0.64402	N	0.000016	T	0.00012	0.0000	N	0.00146	-1.995	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.33085	-0.9882	9	0.08599	T	0.76	-20.1883	7.0217	0.24918	0.0:0.1038:0.0:0.8962	rs373572;rs17856044;rs52822231;rs59941373;rs373572	302	Q9NS91	RAD18_HUMAN	Q	302	ENSP00000264926:R302Q	ENSP00000264926:R302Q	R	-	2	0	RAD18	8930389	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	2.422000	0.44696	0.849000	0.35215	-0.381000	0.06696	CGA	T|0.661;G|0.003	0.661	strong		0.299	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165	
SEC61A2	55176	hgsc.bcm.edu	37	10	12191933	12191933	+	Silent	SNP	C	C	T	rs10466280	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12191933C>T	ENST00000298428.9	+	6	524	c.435C>T	c.(433-435)gcC>gcT	p.A145A	SEC61A2_ENST00000379020.4_Silent_p.A145A|SEC61A2_ENST00000379033.3_Silent_p.A123A|SEC61A2_ENST00000379051.1_Silent_p.A145A|SEC61A2_ENST00000304267.8_Silent_p.A145A|SEC61A2_ENST00000495368.1_3'UTR|SEC61A2_ENST00000379017.3_Silent_p.A145A	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	145					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)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				AAATGGGTGCCGGAATCTGTC	0.418													C|||	2125	0.424321	0.41	0.4986	5008	,	,		19774	0.5258		0.4056	False		,,,				2504	0.3057				p.A145A		Atlas-SNP	.											.	SEC61A2	48	.	0			c.C435T						PASS	.	C	,,	1844,2562	538.7+/-375.1	401,1042,760	142.0	137.0	139.0		435,369,435	-3.7	0.9	10	dbSNP_119	139	3583,5017	519.1+/-379.4	736,2111,1453	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	1137,3153,2213	TT,TC,CC		41.6628,41.852,41.7269	,,	145/438,123/455,145/477	12191933	5427,7579	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon6			GGGTGCCGGAATC	AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.435C>T	10.37:g.12191933C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1	963	0.4409340659340659	184	0.37398373983739835	165	0.4558011049723757	295	0.5157342657342657	319	0.420844327176781	C	5.271	0.235421	0.10023	0.41852	0.416628	ENSG00000065665	ENST00000418772;ENST00000419021	.	.	.	5.07	-3.7	0.04437	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44636	-0.9315	3	.	.	.	-10.1484	6.6785	0.23108	0.1062:0.2462:0.0:0.6476	rs10466280;rs17558441;rs17845804;rs17858766;rs61561401;rs10466280	.	.	.	W	91;27	.	.	R	+	1	2	SEC61A2	12231939	0.942000	0.31987	0.874000	0.34290	0.562000	0.35680	-0.009000	0.12765	-1.051000	0.03226	-1.402000	0.01139	CGG	C|0.580;T|0.420	0.420	strong		0.418	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
HOGA1	112817	hgsc.bcm.edu	37	10	99371344	99371344	+	Silent	SNP	C	C	A	rs12261752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99371344C>A	ENST00000370646.4	+	7	1273	c.912C>A	c.(910-912)gcC>gcA	p.A304A	HOGA1_ENST00000370647.4_Silent_p.A141A|PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	304					4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						CCTGCCGCGCCCCCTTGCAGG	0.627													C|||	1590	0.317492	0.3177	0.2363	5008	,	,		17499	0.3492		0.2545	False		,,,				2504	0.407				p.A304A		Atlas-SNP	.											HOGA1,colon,carcinoma,+2,1	HOGA1	25	1	0			c.C912A						PASS	.	C	,	1348,3058	446.9+/-348.2	195,958,1050	41.0	44.0	43.0		423,912	4.1	0.9	10	dbSNP_120	43	2573,6027	414.9+/-351.6	392,1789,2119	no	coding-synonymous,coding-synonymous	HOGA1	NM_001134670.1,NM_138413.3	,	587,2747,3169	AA,AC,CC		29.9186,30.5946,30.1476	,	141/165,304/328	99371344	3921,9085	2203	4300	6503	SO:0001819	synonymous_variant	112817	exon7			CCGCGCCCCCTTG	BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935			25155	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 2 (E. coli)"", ""N-acetylneuraminate pyruvate lyase 2 (putative)"""	613597	"""chromosome 10 open reading frame 65"", ""dihydrodipicolinate synthase-like, mitochondrial"""	C10orf65, DHDPSL		20797690	Standard	NM_001134670		Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.912C>A	10.37:g.99371344C>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_138413	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	Silent	SNP	ENST00000370646.4	37	CCDS7467.1																																																																																			C|0.700;A|0.300	0.300	strong		0.627	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049726.1	NM_138413	
MYRIP	25924	hgsc.bcm.edu	37	3	40275461	40275461	+	Missense_Mutation	SNP	C	C	T	rs34800524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:40275461C>T	ENST00000302541.6	+	12	2359	c.2017C>T	c.(2017-2019)Cct>Tct	p.P673S	MYRIP_ENST00000396217.3_Missense_Mutation_p.P584S|MYRIP_ENST00000539167.1_Missense_Mutation_p.P486S|MYRIP_ENST00000425621.1_Intron|MYRIP_ENST00000444716.1_Missense_Mutation_p.P673S|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	673	Actin-binding.		P -> S (in dbSNP:rs34800524).		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)		CCCACAAGTCCCTCCTGACAG	0.517													C|||	339	0.0676917	0.112	0.0389	5008	,	,		20457	0.0526		0.0477	False		,,,				2504	0.0644				p.P673S		Atlas-SNP	.											.	MYRIP	98	.	0			c.C2017T						PASS	.	C	SER/PRO	382,4024	193.0+/-218.2	13,356,1834	76.0	70.0	72.0		2017	1.9	0.0	3	dbSNP_126	72	406,8194	129.2+/-187.3	10,386,3904	yes	missense	MYRIP	NM_015460.2	74	23,742,5738	TT,TC,CC		4.7209,8.67,6.0587	benign	673/860	40275461	788,12218	2203	4300	6503	SO:0001583	missense	25924	exon12			CAAGTCCCTCCTG	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.2017C>T	3.37:g.40275461C>T	ENSP00000301972:p.Pro673Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	105	0.04807692307692308	44	0.08943089430894309	12	0.03314917127071823	18	0.03146853146853147	31	0.040897097625329816	C	1.911	-0.450711	0.04572	0.0867	0.047209	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000396217;ENST00000539167	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	5.79	1.91	0.25777	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.327406	0.33610	N	0.004735	T	0.00328	0.0010	N	0.15975	0.35	0.09310	N	1	B;B	0.22800	0.007;0.075	B;B	0.22601	0.005;0.04	T	0.28713	-1.0035	9	.	.	.	.	1.1181	0.01718	0.1591:0.4287:0.1544:0.2578	rs34800524	584;673	Q32M42;Q8NFW9	.;MYRIP_HUMAN	S	673;673;584;486	ENSP00000398665:P673S;ENSP00000301972:P673S;ENSP00000379519:P584S;ENSP00000438297:P486S	.	P	+	1	0	MYRIP	40250465	0.000000	0.05858	0.002000	0.10522	0.960000	0.62799	0.021000	0.13489	0.330000	0.23485	0.655000	0.94253	CCT	C|0.942;T|0.058	0.058	strong		0.517	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
TAS2R38	5726	hgsc.bcm.edu	37	7	141673345	141673345	+	Missense_Mutation	SNP	C	C	G	rs713598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141673345C>G	ENST00000547270.1	-	1	228	c.145G>C	c.(145-147)Gca>Cca	p.A49P		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	49			A -> P (in dbSNP:rs713598). {ECO:0000269|PubMed:12595690}.		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)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					TTGCTCAGTGCCTGCCTCTTC	0.488													G|||	2528	0.504792	0.475	0.6585	5008	,	,		22514	0.6756		0.4225	False		,,,				2504	0.3446				p.A49P		Atlas-SNP	.											.	TAS2R38	51	.	0			c.G145C	GRCh37	CM031368	TAS2R38	M	rs713598	PASS	.	G	PRO/ALA	2070,2336	607.5+/-391.0	475,1120,608	99.0	93.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	145	5.1	0.6	7	dbSNP_86	95	3530,5070	631.3+/-398.5	706,2118,1476	yes	missense	TAS2R38	NM_176817.4	27	1181,3238,2084	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	41.0465,46.9814,43.0571	benign	49/334	141673345	5600,7406	2203	4300	6503	SO:0001583	missense	5726	exon1			TCAGTGCCTGCCT	AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	9584	protein-coding gene	gene with protein product		607751	"""phenylthiocarbamide tasting"""	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.145G>C	7.37:g.141673345C>G	ENSP00000448219:p.Ala49Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_176817	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Missense_Mutation	SNP	ENST00000547270.1	37	CCDS34765.1	1158	0.5302197802197802	250	0.508130081300813	220	0.6077348066298343	369	0.6451048951048951	319	0.420844327176781	G	0.978	-0.697866	0.03279	0.469814	0.410465	ENSG00000257138	ENST00000547270	T	0.00768	5.72	5.1	5.1	0.69264	.	0.248924	0.33127	N	0.005260	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.02437	-1.1159	9	0.23302	T	0.38	.	11.663	0.51358	0.0:0.1782:0.8218:0.0	rs713598;rs17634738;rs52812444;rs713598	49	P59533	T2R38_HUMAN	P	49	ENSP00000448219:A49P	ENSP00000331291:A49P	A	-	1	0	TAS2R38	141319814	0.887000	0.30362	0.557000	0.28306	0.232000	0.25224	2.468000	0.45102	1.402000	0.46780	-0.120000	0.15030	GCA	C|0.528;G|0.472	0.472	strong		0.488	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350810.2	NM_176817	
OR52B6	340980	hgsc.bcm.edu	37	11	5602928	5602928	+	Silent	SNP	G	G	C	rs10838375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602928G>C	ENST00000345043.2	+	1	822	c.822G>C	c.(820-822)gcG>gcC	p.A274A	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	274						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)		ATGTCCCTGCGCTTTTTTCTG	0.517													C|||	3585	0.715855	0.7383	0.67	5008	,	,		21833	0.9792		0.4761	False		,,,				2504	0.6933				p.A274A		Atlas-SNP	.											.	OR52B6	37	.	0			c.G822C						PASS	.	C		2778,1154		973,832,161	266.0	272.0	270.0		822	0.3	0.6	11	dbSNP_120	270	3939,4379		931,2077,1151	yes	coding-synonymous	OR52B6	NM_001005162.2		1904,2909,1312	CC,CG,GG		47.3551,29.3489,45.1673		274/336	5602928	6717,5533	1966	4159	6125	SO:0001819	synonymous_variant	340980	exon1			CCCTGCGCTTTTT	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.822G>C	11.37:g.5602928G>C		Somatic	213	2	0.00938967		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001005162	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																			A|0.000;C|0.633;G|0.366	0.633	strong		0.517	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
KRT76	51350	hgsc.bcm.edu	37	12	53167395	53167395	+	Missense_Mutation	SNP	C	C	T	rs11170271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53167395C>T	ENST00000332411.2	-	3	900	c.847G>A	c.(847-849)Gca>Aca	p.A283T		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	283	Coil 1B.|Rod.		A -> T (in dbSNP:rs11170271).		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)	p.A283T(1)		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						TCATTCTCTGCGGCAGTGCGT	0.493													C|||	821	0.163938	0.028	0.2795	5008	,	,		19874	0.1587		0.2644	False		,,,				2504	0.1677				p.A283T		Atlas-SNP	.											KRT76,NS,carcinoma,0,1	KRT76	72	1	1	Substitution - Missense(1)	stomach(1)	c.G847A						PASS	.	C	THR/ALA	241,4165	141.9+/-177.2	6,229,1968	147.0	119.0	128.0		847	4.5	0.8	12	dbSNP_120	128	2340,6260	391.6+/-343.7	311,1718,2271	yes	missense	KRT76	NM_015848.4	58	317,1947,4239	TT,TC,CC		27.2093,5.4698,19.8447	possibly-damaging	283/639	53167395	2581,10425	2203	4300	6503	SO:0001583	missense	51350	exon3			TCTCTGCGGCAGT	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.847G>A	12.37:g.53167395C>T	ENSP00000330101:p.Ala283Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	389	0.17811355311355312	21	0.042682926829268296	90	0.24861878453038674	86	0.15034965034965034	192	0.2532981530343008	C	15.41	2.826063	0.50739	0.054698	0.272093	ENSG00000185069	ENST00000332411	D	0.88586	-2.4	4.48	4.48	0.54585	Filament (1);	0.000000	0.44097	D	0.000486	T	0.00144	0.0004	M	0.75150	2.29	0.58432	P	5.999999999950489E-6	D	0.89917	1.0	D	0.76071	0.987	T	0.00000	-1.3632	9	0.87932	D	0	.	18.0452	0.89330	0.0:1.0:0.0:0.0	rs11170271;rs52799703;rs56756879;rs11170271	283	Q01546	K22O_HUMAN	T	283	ENSP00000330101:A283T	ENSP00000330101:A283T	A	-	1	0	KRT76	51453662	0.000000	0.05858	0.805000	0.32314	0.361000	0.29550	0.820000	0.27323	2.423000	0.82170	0.557000	0.71058	GCA	C|0.817;T|0.183	0.183	strong		0.493	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
FAM160A2	84067	hgsc.bcm.edu	37	11	6238960	6238960	+	Missense_Mutation	SNP	C	C	A	rs3750943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6238960C>A	ENST00000449352.2	-	9	2119	c.1856G>T	c.(1855-1857)cGg>cTg	p.R619L	FAM160A2_ENST00000529360.1_5'Flank|FAM160A2_ENST00000265978.4_Missense_Mutation_p.R633L|FAM160A2_ENST00000524416.1_Missense_Mutation_p.R619L			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	619			R -> L (in dbSNP:rs3750943).		early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						acccccagcccgccccctcct	0.652													A|||	654	0.130591	0.059	0.0778	5008	,	,		8807	0.2431		0.1461	False		,,,				2504	0.1329				p.R633L		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G1898T						PASS	.	A	LEU/ARG,LEU/ARG	318,4002		17,284,1859	9.0	10.0	10.0		1856,1898	4.0	0.9	11	dbSNP_107	10	1364,7104		122,1120,2992	no	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	102,102	139,1404,4851	AA,AC,CC		16.1077,7.3611,13.153	benign,benign	619/973,633/987	6238960	1682,11106	2160	4234	6394	SO:0001583	missense	84067	exon9			CCAGCCCGCCCCC		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1856G>T	11.37:g.6238960C>A	ENSP00000416918:p.Arg619Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	320	0.14652014652014653	37	0.07520325203252033	36	0.09944751381215469	125	0.21853146853146854	122	0.16094986807387862	A	1.787	-0.480378	0.04383	0.073611	0.161077	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.46819	0.86;0.86;0.86	5.16	3.97	0.46021	.	0.645966	0.14866	N	0.293783	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.24764	-1.0151	9	0.09084	T	0.74	-18.0925	5.0671	0.14587	0.6113:0.1554:0.0:0.2333	rs3750943	619;619;633	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	L	619;544;633;619	ENSP00000416918:R619L;ENSP00000265978:R633L;ENSP00000431773:R619L	ENSP00000265978:R633L	R	-	2	0	FAM160A2	6195536	0.534000	0.26362	0.881000	0.34555	0.135000	0.20990	1.447000	0.35101	0.994000	0.38892	-0.363000	0.07495	CGG	C|0.853;A|0.147	0.147	strong		0.652	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
PROS1	5627	hgsc.bcm.edu	37	3	93593119	93593119	+	Silent	SNP	T	T	C	rs6123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:93593119T>C	ENST00000394236.3	-	15	2317	c.2001A>G	c.(1999-2001)ccA>ccG	p.P667P	PROS1_ENST00000407433.1_Silent_p.P536P	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	667			P -> L (in THPH5). {ECO:0000269|PubMed:10790208, ECO:0000269|PubMed:15238143}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	TCCAAACTGATGGACATGAGT	0.333													T|||	1929	0.385184	0.115	0.4769	5008	,	,		17748	0.5675		0.3946	False		,,,				2504	0.4877				p.P667P		Atlas-SNP	.											.	PROS1	126	.	0			c.A2001G	GRCh37	CM994426	PROS1	M	rs6123	PASS	.	T		683,3723	287.2+/-279.2	64,555,1584	97.0	91.0	93.0		2001	0.9	0.9	3	dbSNP_52	93	3494,5106	510.0+/-377.4	711,2072,1517	no	coding-synonymous	PROS1	NM_000313.3		775,2627,3101	CC,CT,TT		40.6279,15.5016,32.1159		667/677	93593119	4177,8829	2203	4300	6503	SO:0001819	synonymous_variant	5627	exon15			AACTGATGGACAT		CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.2001A>G	3.37:g.93593119T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	360	119	0.330556	NM_000313	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Silent	SNP	ENST00000394236.3	37	CCDS2923.1																																																																																			T|0.649;C|0.351	0.351	strong		0.333	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313	
SVIL	6840	hgsc.bcm.edu	37	10	29812602	29812602	+	Silent	SNP	G	G	T	rs7070678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29812602G>T	ENST00000355867.4	-	15	3693	c.2941C>A	c.(2941-2943)Cga>Aga	p.R981R	SVIL_ENST00000535393.1_5'Flank|SVIL_ENST00000375398.2_Silent_p.R981R|SVIL_ENST00000375400.3_Silent_p.R555R	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						PASS	.	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	114	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	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		
PSD4	23550	hgsc.bcm.edu	37	2	113953346	113953346	+	Splice_Site	SNP	G	G	A	rs370284646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113953346G>A	ENST00000245796.6	+	11	2419	c.2224G>A	c.(2224-2226)Gtg>Atg	p.V742M	PSD4_ENST00000441564.3_Splice_Site_p.V714M	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	742					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						CGAGTGGGCCGTGTGAGTGAG	0.592																																					p.V742M		Atlas-SNP	.											.	PSD4	74	.	0			c.G2224A						PASS	.	G	MET/VAL	0,4406		0,0,2203	152.0	141.0	145.0		2224	-0.4	0.1	2		145	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice	PSD4	NM_012455.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	742/1057	113953346	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	23550	exon11			TGGGCCGTGTGAG	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.2225+1G>A	2.37:g.113953346G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	57	11	0.192982	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627464	0.28978	0.0	1.16E-4	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.30182	1.54;1.54	5.65	-0.402	0.12404	SEC7-like, alpha orthogonal bundle (1);SEC7-like (1);	0.449069	0.25267	N	0.031905	T	0.23210	0.0561	L	0.45581	1.43	0.80722	D	1	B;B;B	0.24882	0.113;0.027;0.016	B;B;B	0.22880	0.042;0.015;0.007	T	0.05007	-1.0912	10	0.39692	T	0.17	.	9.3598	0.38188	0.57:0.0:0.43:0.0	.	400;714;742	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	M	742;714	ENSP00000245796:V742M;ENSP00000413997:V714M	ENSP00000245796:V742M	V	+	1	0	PSD4	113669817	0.000000	0.05858	0.084000	0.20598	0.906000	0.53458	-0.730000	0.04915	-0.136000	0.11475	-0.140000	0.14226	GTG	.	.	weak		0.592	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	Missense_Mutation
SALL3	27164	hgsc.bcm.edu	37	18	76753768	76753768	+	Missense_Mutation	SNP	C	C	G	rs2447437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:76753768C>G	ENST00000537592.2	+	2	1777	c.1777C>G	c.(1777-1779)Ctc>Gtc	p.L593V	SALL3_ENST00000575389.2_Missense_Mutation_p.L593V|SALL3_ENST00000536229.3_Missense_Mutation_p.L460V	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	593			L -> V (in dbSNP:rs2447437). {ECO:0000269|Ref.1}.		forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|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.L593V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGGGCCGCCCCTCACTAAAGC	0.731													C|||	3973	0.793331	0.5825	0.8444	5008	,	,		9900	0.9226		0.8648	False		,,,				2504	0.8354				p.L593V		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	1	Substitution - Missense(1)	prostate(1)	c.C1777G						PASS	.	C	VAL/LEU	2422,1000		875,672,164	3.0	4.0	4.0		1777	5.2	0.2	18	dbSNP_100	4	6372,926		2808,756,85	yes	missense	SALL3	NM_171999.2	32	3683,1428,249	GG,GC,CC		12.6884,29.2227,17.9664	benign	593/1301	76753768	8794,1926	1711	3649	5360	SO:0001583	missense	27164	exon2			CCGCCCCTCACTA	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1777C>G	18.37:g.76753768C>G	ENSP00000441823:p.Leu593Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	1724	0.7893772893772893	287	0.5833333333333334	299	0.8259668508287292	511	0.8933566433566433	627	0.8271767810026385	C	0.073	-1.197989	0.01594	0.707773	0.873116	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.08984	3.03	5.2	5.2	0.72013	.	0.464067	0.17974	N	0.155779	T	0.00012	0.0000	L	0.35288	1.05	0.80722	P	0.0	B;B	0.15473	0.013;0.006	B;B	0.18561	0.022;0.002	T	0.36237	-0.9756	9	0.14656	T	0.56	-21.7235	10.231	0.43256	0.2471:0.6277:0.1252:0.0	rs2447437	325;593	F5GXY4;Q9BXA9	.;SALL3_HUMAN	V	593;593;325	ENSP00000441823:L593V	ENSP00000299466:L593V	L	+	1	0	SALL3	74854756	0.002000	0.14202	0.157000	0.22605	0.006000	0.05464	0.292000	0.19011	2.584000	0.87258	0.563000	0.77884	CTC	C|0.211;G|0.789	0.789	strong		0.731	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
MARCH7	64844	hgsc.bcm.edu	37	2	160604812	160604812	+	Silent	SNP	C	C	T	rs1427329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160604812C>T	ENST00000259050.4	+	5	1133	c.1011C>T	c.(1009-1011)ccC>ccT	p.P337P	MARCH7_ENST00000409175.1_Silent_p.P337P|MARCH7_ENST00000539065.1_Silent_p.P281P|MARCH7_ENST00000409591.1_Silent_p.P299P	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	337	Ser-rich.				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						CTGAAGTTCCCGATAATAGGG	0.413													C|||	1768	0.353035	0.3669	0.196	5008	,	,		19291	0.3373		0.3509	False		,,,				2504	0.4642				p.P337P		Atlas-SNP	.											MARCH7,NS,haematopoietic_neoplasm,+2,1	MARCH7	48	1	0			c.C1011T						PASS	.	C		1552,2854	455.3+/-351.0	270,1012,921	53.0	57.0	56.0		1011	-6.8	0.0	2	dbSNP_88	56	3073,5527	463.2+/-365.9	537,1999,1764	no	coding-synonymous	MARCH7	NM_022826.2		807,3011,2685	TT,TC,CC		35.7326,35.2247,35.5605		337/705	160604812	4625,8381	2203	4300	6503	SO:0001819	synonymous_variant	64844	exon5			AGTTCCCGATAAT	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.1011C>T	2.37:g.160604812C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Silent	SNP	ENST00000259050.4	37	CCDS2210.1																																																																																			C|0.649;T|0.351	0.351	strong		0.413	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
ABCB11	8647	hgsc.bcm.edu	37	2	169789016	169789016	+	Silent	SNP	T	T	C	rs497692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:169789016T>C	ENST00000263817.6	-	24	3208	c.3084A>G	c.(3082-3084)gcA>gcG	p.A1028A		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1028	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.A1028A(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CAAGAGCTGTTGCACTCAGTA	0.493													C|||	2488	0.496805	0.2254	0.5086	5008	,	,		19594	0.6409		0.5318	False		,,,				2504	0.6708				p.A1028A		Atlas-SNP	.											ABCB11,colon,carcinoma,-1,2	ABCB11	136	2	1	Substitution - coding silent(1)	stomach(1)	c.A3084G						PASS	.	C		1076,2938		160,756,1091	84.0	81.0	82.0		3084	-10.8	0.0	2	dbSNP_83	82	4552,3814		1240,2072,871	yes	coding-synonymous	ABCB11	NM_003742.2		1400,2828,1962	CC,CT,TT		45.5893,26.8062,45.4604		1028/1322	169789016	5628,6752	2007	4183	6190	SO:0001819	synonymous_variant	8647	exon24			AGCTGTTGCACTC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3084A>G	2.37:g.169789016T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			T|0.519;C|0.481	0.481	strong		0.493	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459520	24459520	+	Silent	SNP	T	T	C	rs45583341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24459520T>C	ENST00000335125.6	+	2	384	c.258T>C	c.(256-258)acT>acC	p.T86T	DHRS4L2_ENST00000382755.4_Silent_p.T84T|DHRS4L2_ENST00000545240.1_Silent_p.T86T|DHRS4L2_ENST00000558753.1_Silent_p.T86T|DHRS4L2_ENST00000543805.1_5'UTR|DHRS4L2_ENST00000537912.1_Silent_p.T86T|DHRS4L2_ENST00000397071.1_Silent_p.T86T|DHRS4L2_ENST00000534993.1_5'UTR	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	84						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		TGACGGGCACTGTGTGCCATG	0.677													N|||	815	0.16274	0.0968	0.1499	5008	,	,		14725	0.2262		0.1223	False		,,,				2504	0.2372				p.T86T		Atlas-SNP	.											DHRS4L2,colon,carcinoma,0,1	DHRS4L2	29	1	0			c.T258C						PASS	.	C	,,,	340,4060	773.1+/-413.9	24,292,1884	37.0	40.0	39.0		174,,,258	0.2	1.0	14	dbSNP_127	39	850,7746	759.3+/-407.5	63,724,3511	no	coding-synonymous,utr-5,utr-5,coding-synonymous	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	87,1016,5395	CC,CT,TT		9.8883,7.7273,9.1567	,,,	58/171,,,86/233	24459520	1190,11806	2200	4298	6498	SO:0001819	synonymous_variant	317749	exon2			GGGCACTGTGTGC		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.258T>C	14.37:g.24459520T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_198083	Q3YLD4	Silent	SNP	ENST00000335125.6	37	CCDS9606.2																																																																																			T|0.868;C|0.132	0.132	strong		0.677	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
ZNF410	57862	hgsc.bcm.edu	37	14	74388908	74388908	+	Splice_Site	SNP	T	T	C	rs1127392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74388908T>C	ENST00000555044.1	+	10	1463	c.1269T>C	c.(1267-1269)gaT>gaC	p.D423D	RP5-1021I20.5_ENST00000555916.1_RNA|ZNF410_ENST00000334521.4_Splice_Site_p.D370D|ZNF410_ENST00000442160.3_Splice_Site_p.D440D|RP5-1021I20.4_ENST00000556551.2_3'UTR|ZNF410_ENST00000540593.1_Splice_Site_p.D350D|RP5-1021I20.5_ENST00000554009.1_RNA|ZNF410_ENST00000324593.6_Intron	NM_001242928.1|NM_021188.2	NP_001229857.1|NP_067011.1	Q86VK4	ZN410_HUMAN	zinc finger protein 410	423					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(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.00369)		GAGTTGATGATGGTAAGACTT	0.438													T|||	1142	0.228035	0.1626	0.3357	5008	,	,		16968	0.0476		0.4105	False		,,,				2504	0.2382				p.D440D		Atlas-SNP	.											.	ZNF410	25	.	0			c.T1320C						PASS	.	T	,,,,	854,3552	332.8+/-302.6	84,686,1433	60.0	52.0	55.0		1320,,1050,681,1269	3.8	1.0	14	dbSNP_86	55	3570,5030	517.6+/-379.1	735,2100,1465	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF410	NM_001242924.1,NM_001242926.1,NM_001242927.1,NM_001242928.1,NM_021188.2	,,,,	819,2786,2898	CC,CT,TT		41.5116,19.3827,34.0151	,,,,	440/517,,350/406,227/313,423/479	74388908	4424,8582	2203	4300	6503	SO:0001630	splice_region_variant	57862	exon11			TGATGATGGTAAG	U90919	CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1	14q24.3	2013-01-08				ENSG00000119725		"""Zinc fingers, C2H2-type"""	20144	protein-coding gene	gene with protein product						12370286	Standard	NM_001242924		Approved	APA1, APA-1	uc010arz.2	Q86VK4		ENST00000555044.1:c.1270+1T>C	14.37:g.74388908T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001242924	B4DDV5|B4DR78|O00153|Q9BQ19	Silent	SNP	ENST00000555044.1	37	CCDS9821.1	557	0.25503663003663	74	0.15040650406504066	129	0.356353591160221	35	0.06118881118881119	319	0.420844327176781	T	11.90	1.776962	0.31411	0.193827	0.415116	ENSG00000119725	ENST00000557214	.	.	.	5.0	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999702	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7001	0.17877	0.1499:0.0:0.2294:0.6207	rs1127392;rs1804842;rs3177095;rs3183290;rs11540491;rs17182692;rs17423892;rs3177095	.	.	.	R	84	.	.	X	+	1	0	ZNF410	73458661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.363000	0.44178	2.222000	0.72286	0.477000	0.44152	TGA	A|0.000;C|0.298;T|0.702	0.298	strong		0.438	ZNF410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412597.1	NM_021188	Silent
DNAH2	146754	hgsc.bcm.edu	37	17	7664239	7664239	+	Silent	SNP	C	C	T	rs12185237	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7664239C>T	ENST00000572933.1	+	18	4427	c.2967C>T	c.(2965-2967)gcC>gcT	p.A989A	DNAH2_ENST00000389173.2_Silent_p.A989A			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	989	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)				CTTTTGTTGCCGACATTGCCC	0.552													C|||	105	0.0209665	0.0038	0.0245	5008	,	,		19400	0.0		0.0368	False		,,,				2504	0.047				p.A989A		Atlas-SNP	.											.	DNAH2	498	.	0			c.C2967T						PASS	.	C		37,4369	41.6+/-74.8	0,37,2166	159.0	130.0	140.0		2967	-10.4	0.7	17	dbSNP_120	140	410,8190	129.2+/-187.3	10,390,3900	no	coding-synonymous	DNAH2	NM_020877.2		10,427,6066	TT,TC,CC		4.7674,0.8398,3.4369		989/4428	7664239	447,12559	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon17			TGTTGCCGACATT	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.2967C>T	17.37:g.7664239C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	149	58	0.389262	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			C|0.971;T|0.029	0.029	strong		0.552	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
RNF32	140545	hgsc.bcm.edu	37	7	156469123	156469123	+	Missense_Mutation	SNP	G	G	A	rs2302148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:156469123G>A	ENST00000405335.1	+	10	1272	c.863G>A	c.(862-864)cGg>cAg	p.R288Q	RNF32_ENST00000317955.5_Missense_Mutation_p.R288Q|RNF32_ENST00000311822.8_3'UTR|RNF32_ENST00000392743.2_Missense_Mutation_p.R288Q|RNF32_ENST00000343665.4_Missense_Mutation_p.R264Q|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000432459.2_Missense_Mutation_p.R288Q			Q9H0A6	RNF32_HUMAN	ring finger protein 32	288			R -> Q (in dbSNP:rs2302148).			aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GCTCTGCGCCGGGAGACCCAC	0.627													G|||	370	0.0738818	0.1309	0.0303	5008	,	,		13676	0.1101		0.0457	False		,,,				2504	0.0194				p.R288Q		Atlas-SNP	.											.	RNF32	77	.	0			c.G863A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	447,3959	208.5+/-229.5	26,395,1782	37.0	37.0	37.0		863,863,863	2.6	0.0	7	dbSNP_100	37	262,8338	97.0+/-158.7	3,256,4041	yes	missense,missense,missense	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	43,43,43	29,651,5823	AA,AG,GG		3.0465,10.1453,5.4513	possibly-damaging,possibly-damaging,possibly-damaging	288/363,288/363,288/363	156469123	709,12297	2203	4300	6503	SO:0001583	missense	140545	exon9			TGCGCCGGGAGAC		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.863G>A	7.37:g.156469123G>A	ENSP00000385285:p.Arg288Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Missense_Mutation	SNP	ENST00000405335.1	37	CCDS5944.1	162	0.07417582417582418	47	0.09552845528455285	14	0.03867403314917127	68	0.11888111888111888	33	0.04353562005277045	G	11.68	1.711970	0.30322	0.101453	0.030465	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000392743;ENST00000343665	T;T;T;T;T	0.25250	2.14;2.14;2.14;2.14;1.81	4.71	2.62	0.31277	Zinc finger, RING/FYVE/PHD-type (1);	0.244989	0.41294	N	0.000908	T	0.00178	0.0005	L	0.28054	0.825	0.80722	D	1	B	0.29037	0.231	B	0.14023	0.01	T	0.42531	-0.9446	10	0.21014	T	0.42	-4.1649	5.8249	0.18548	0.7701:0.0:0.2299:0.0	rs2302148;rs58946744	288	Q9H0A6	RNF32_HUMAN	Q	288;288;288;288;264	ENSP00000405588:R288Q;ENSP00000315950:R288Q;ENSP00000385285:R288Q;ENSP00000376499:R288Q;ENSP00000341185:R264Q	ENSP00000315950:R288Q	R	+	2	0	RNF32	156161884	1.000000	0.71417	0.023000	0.16930	0.051000	0.14879	2.315000	0.43752	0.319000	0.23209	0.563000	0.77884	CGG	G|0.941;A|0.059	0.059	strong		0.627	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
IL18	3606	hgsc.bcm.edu	37	11	112020916	112020916	+	Silent	SNP	T	T	G	rs549908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:112020916T>G	ENST00000280357.7	-	4	324	c.105A>C	c.(103-105)tcA>tcC	p.S35S	IL18_ENST00000533858.1_5'UTR|IL18_ENST00000524595.1_Silent_p.S31S|SDHD_ENST00000532699.1_Intron|IL18_ENST00000528832.1_Silent_p.S35S	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	35					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-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;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		CAAAGTAATCTGATTCCAGGT	0.274													T|||	1101	0.219848	0.1846	0.3357	5008	,	,		17668	0.1181		0.3082	False		,,,				2504	0.1994				p.S35S		Atlas-SNP	.											.	IL18	10	.	0			c.A105C	GRCh37	CM056601	IL18	M	rs549908	PASS	.	T		727,2843		73,581,1131	70.0	65.0	66.0		105	2.5	1.0	11	dbSNP_83	66	2455,5663		377,1701,1981	no	coding-synonymous	IL18	NM_001562.3		450,2282,3112	GG,GT,TT		30.2414,20.3641,27.2245		35/194	112020916	3182,8506	1785	4059	5844	SO:0001819	synonymous_variant	3606	exon4			GTAATCTGATTCC	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"""Interleukins and interleukin receptors"""	5986	protein-coding gene	gene with protein product	"""interferon-gamma-inducing factor"""	600953	"""interleukin 18 (interferon-gamma-inducing factor)"""			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.105A>C	11.37:g.112020916T>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001562	O75599|Q6FGY3|Q6WWJ7	Silent	SNP	ENST00000280357.7	37	CCDS44731.1																																																																																			T|0.780;G|0.220	0.220	strong		0.274	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562	
NUP107	57122	hgsc.bcm.edu	37	12	69113184	69113184	+	Silent	SNP	C	C	T	rs35209116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:69113184C>T	ENST00000229179.4	+	13	1479	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	NUP107_ENST00000539906.1_Silent_p.L354L|NUP107_ENST00000378905.2_Silent_p.L232L	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	383					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)			AGGCTGGAAACTGTACCATGA	0.413													C|||	22	0.00439297	0.0	0.0072	5008	,	,		18922	0.0		0.007	False		,,,				2504	0.0102				p.L383L		Atlas-SNP	.											.	NUP107	88	.	0			c.C1147T						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	122.0	112.0	115.0		1147	1.2	0.0	12	dbSNP_126	115	47,8553	32.8+/-85.7	1,45,4254	no	coding-synonymous	NUP107	NM_020401.2		1,52,6450	TT,TC,CC		0.5465,0.1589,0.4152		383/926	69113184	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon13			TGGAAACTGTACC	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.1147C>T	12.37:g.69113184C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			C|0.996;T|0.004	0.004	strong		0.413	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
COMP	1311	hgsc.bcm.edu	37	19	18897440	18897440	+	Missense_Mutation	SNP	T	T	C	rs397515510|rs61739916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18897440T>C	ENST00000222271.2	-	11	1200	c.1156A>G	c.(1156-1158)Aac>Gac	p.N386D	COMP_ENST00000542601.2_Missense_Mutation_p.N353D|COMP_ENST00000425807.1_Missense_Mutation_p.N333D	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	386					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CTAGGGCAGTTGTCGGCCTGG	0.572													T|||	105	0.0209665	0.0	0.0259	5008	,	,		14861	0.0		0.0487	False		,,,				2504	0.0389				p.N386D		Atlas-SNP	.											.	COMP	62	.	0			c.A1156G						PASS	.	T	ASP/ASN	60,4346	57.4+/-93.9	0,60,2143	132.0	97.0	109.0		1156	3.3	1.0	19	dbSNP_129	109	407,8193	128.3+/-186.6	10,387,3903	yes	missense	COMP	NM_000095.2	23	10,447,6046	CC,CT,TT		4.7326,1.3618,3.5907	probably-damaging	386/758	18897440	467,12539	2203	4300	6503	SO:0001583	missense	1311	exon11			GGCAGTTGTCGGC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1156A>G	19.37:g.18897440T>C	ENSP00000222271:p.Asn386Asp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	37	CCDS12385.1	42	0.019230769230769232	0	0.0	7	0.019337016574585635	0	0.0	35	0.04617414248021108	T	18.69	3.678556	0.68042	0.013618	0.047326	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.99409	-5.85;-5.85;-5.85	3.35	3.35	0.38373	.	0.000000	0.85682	U	0.000000	D	0.97848	0.9293	H	0.96889	3.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.86530	0.1821	10	0.72032	D	0.01	-40.6123	10.7166	0.46015	0.0:0.0:0.0:1.0	.	333;386	B4DKJ3;P49747	.;COMP_HUMAN	D	353;386;333;373	ENSP00000439156:N353D;ENSP00000222271:N386D;ENSP00000403792:N333D	ENSP00000222271:N386D	N	-	1	0	COMP	18758440	1.000000	0.71417	0.994000	0.49952	0.388000	0.30384	7.702000	0.84576	1.409000	0.46915	0.260000	0.18958	AAC	T|0.969;C|0.031	0.031	strong		0.572	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
TYR	7299	hgsc.bcm.edu	37	11	88911575	88911575	+	Missense_Mutation	SNP	C	C	T	rs145513733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:88911575C>T	ENST00000263321.5	+	1	956	c.454C>T	c.(454-456)Ccc>Tcc	p.P152S	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	152			P -> S (in OCA1B). {ECO:0000269|PubMed:8128955}.		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)	CTATGTCATCCCCATAGGGAC	0.403																																					p.P152S		Atlas-SNP	.											.	TYR	130	.	0			c.C454T	GRCh37	CM941344	TYR	M	rs145513733	PASS	.	C	SER/PRO	0,4402		0,0,2201	152.0	144.0	147.0		454	5.0	1.0	11	dbSNP_134	147	3,8595	3.0+/-9.4	0,3,4296	yes	missense	TYR	NM_000372.4	74	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	152/530	88911575	3,12997	2201	4299	6500	SO:0001583	missense	7299	exon1			GTCATCCCCATAG	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.454C>T	11.37:g.88911575C>T	ENSP00000263321:p.Pro152Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485562	0.63962	0.0	3.49E-4	ENSG00000077498	ENST00000263321	D	0.83591	-1.74	5.97	5.01	0.66863	Uncharacterised domain, di-copper centre (2);	0.157178	0.56097	D	0.000032	T	0.80042	0.4551	L	0.41573	1.285	0.36372	D	0.861346	P	0.45078	0.85	P	0.46208	0.507	T	0.81814	-0.0760	9	.	.	.	.	14.0119	0.64503	0.0:0.6866:0.3134:0.0	.	152	P14679	TYRO_HUMAN	S	152	ENSP00000263321:P152S	.	P	+	1	0	TYR	88551223	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.338000	0.59316	2.828000	0.97474	0.655000	0.94253	CCC	C|0.999;T|0.001	0.001	strong		0.403	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
BTBD16	118663	hgsc.bcm.edu	37	10	124096014	124096014	+	Missense_Mutation	SNP	A	A	G	rs150944464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:124096014A>G	ENST00000260723.4	+	15	1520	c.1269A>G	c.(1267-1269)atA>atG	p.I423M	BTBD16_ENST00000368994.2_Missense_Mutation_p.I424M|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	423										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TGCAGAGAATAAAGCACACAG	0.542													A|||	25	0.00499201	0.0	0.0043	5008	,	,		18397	0.0		0.0209	False		,,,				2504	0.001				p.I423M		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1269G						PASS	.	A	MET/ILE	13,4393	21.2+/-45.6	0,13,2190	52.0	45.0	47.0		1269	-8.5	0.0	10	dbSNP_134	47	129,8471	58.7+/-120.3	0,129,4171	yes	missense	BTBD16	NM_144587.2	10	0,142,6361	GG,GA,AA		1.5,0.2951,1.0918	benign	423/507	124096014	142,12864	2203	4300	6503	SO:0001583	missense	118663	exon15			GAGAATAAAGCAC	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1269A>G	10.37:g.124096014A>G	ENSP00000260723:p.Ile423Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	17	0.269841	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	A	15.45	2.838596	0.51057	0.002951	0.015	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.22134	1.97;1.97	5.68	-8.52	0.00920	.	0.900138	0.09479	N	0.796551	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	P;P	0.37207	0.587;0.587	B;B	0.32465	0.146;0.146	T	0.17107	-1.0380	10	0.44086	T	0.13	-1.7584	9.6517	0.39902	0.1783:0.3913:0.4304:0.0	.	424;423	Q32M84-2;Q32M84	.;BTBDG_HUMAN	M	423;424	ENSP00000260723:I423M;ENSP00000357990:I424M	ENSP00000260723:I423M	I	+	3	3	BTBD16	124086004	0.338000	0.24775	0.016000	0.15963	0.381000	0.30169	-0.278000	0.08490	-1.358000	0.02177	-0.290000	0.09829	ATA	A|0.990;G|0.010	0.010	strong		0.542	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
PTX4	390667	hgsc.bcm.edu	37	16	1537956	1537956	+	Missense_Mutation	SNP	C	C	G	rs144904207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1537956C>G	ENST00000447419.2	-	2	182	c.157G>C	c.(157-159)Gag>Cag	p.E53Q	PTX4_ENST00000293922.1_Missense_Mutation_p.E48Q|PTX4_ENST00000440447.2_Missense_Mutation_p.E53Q			Q96A99	PTX4_HUMAN	pentraxin 4, long	53						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						CAGGTCACCTCCTGGAATCTC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		16358	0.0		0.003	False		,,,				2504	0.0				p.E48Q		Atlas-SNP	.											.	PTX4	46	.	0			c.G142C						PASS	.	C	GLN/GLU	0,4236		0,0,2118	81.0	81.0	81.0		142	4.7	0.1	16	dbSNP_134	81	10,8270		0,10,4130	yes	missense	PTX4	NM_001013658.1	29	0,10,6248	GG,GC,CC		0.1208,0.0,0.0799	benign	48/474	1537956	10,12506	2118	4140	6258	SO:0001583	missense	390667	exon2			TCACCTCCTGGAA		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.157G>C	16.37:g.1537956C>G	ENSP00000445277:p.Glu53Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		.	.	.	.	.	.	.	.	.	.	C	6.632	0.485074	0.12641	0.0	0.001208	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06768	3.39;3.26	5.68	4.71	0.59529	.	0.500926	0.20061	N	0.100088	T	0.07728	0.0194	L	0.34521	1.04	0.20196	N	0.999925	B	0.30033	0.266	B	0.30401	0.115	T	0.31475	-0.9942	10	0.23302	T	0.38	.	12.3329	0.55049	0.0:0.8226:0.1774:0.0	.	48	Q96A99-2	.	Q	53;48	ENSP00000445277:E53Q;ENSP00000293922:E48Q	ENSP00000293922:E48Q	E	-	1	0	PTX4	1477957	1.000000	0.71417	0.060000	0.19600	0.002000	0.02628	2.545000	0.45769	1.368000	0.46115	0.563000	0.77884	GAG	C|0.998;G|0.002	0.002	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
RRN3	54700	hgsc.bcm.edu	37	16	15188018	15188018	+	Missense_Mutation	SNP	C	C	T	rs141593500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15188018C>T	ENST00000198767.6	-	1	156	c.73G>A	c.(73-75)Ggc>Agc	p.G25S	RRN3_ENST00000429751.2_Missense_Mutation_p.G25S|RP11-72I8.1_ENST00000569858.1_RNA|RRN3_ENST00000563559.1_Missense_Mutation_p.G25S|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000564131.1_Missense_Mutation_p.G25S|RRN3_ENST00000327307.7_5'Flank	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	25					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						CTCGACGCGCCCAGCTTCTTA	0.617													.|||	5	0.000998403	0.0	0.0	5008	,	,		9426	0.0		0.0	False		,,,				2504	0.0051				p.G25S		Atlas-SNP	.											.	RRN3	36	.	0			c.G73A						PASS	.	C	SER/GLY	0,4394		0,0,2197	26.0	23.0	24.0		73	1.1	0.0	16	dbSNP_134	24	4,8596		0,4,4296	yes	missense	RRN3	NM_018427.3	56	0,4,6493	TT,TC,CC		0.0465,0.0,0.0308	benign	25/652	15188018	4,12990	2197	4300	6497	SO:0001583	missense	54700	exon1			ACGCGCCCAGCTT	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.73G>A	16.37:g.15188018C>T	ENSP00000198767:p.Gly25Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	12.30	1.897935	0.33535	0.0	4.65E-4	ENSG00000085721	ENST00000198767;ENST00000429751	T;T	0.44881	1.0;0.91	3.13	1.07	0.20283	.	.	.	.	.	T	0.17195	0.0413	N	0.08118	0	0.26447	N	0.975673	B;B;B	0.13145	0.0;0.007;0.001	B;B;B	0.12156	0.003;0.007;0.003	T	0.30327	-0.9982	9	0.07813	T	0.8	.	4.8484	0.13524	0.0:0.6849:0.0:0.3151	.	25;25;25	F5H148;Q3MHU9;Q9NYV6	.;.;RRN3_HUMAN	S	25	ENSP00000198767:G25S;ENSP00000402027:G25S	ENSP00000198767:G25S	G	-	1	0	RRN3	15095519	0.000000	0.05858	0.029000	0.17559	0.160000	0.22226	-0.057000	0.11768	0.155000	0.19261	0.305000	0.20034	GGC	C|1.000;T|0.000	0.000	weak		0.617	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
FAT2	2196	hgsc.bcm.edu	37	5	150905485	150905485	+	Silent	SNP	C	C	T	rs36092108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150905485C>T	ENST00000261800.5	-	17	10362	c.10350G>A	c.(10348-10350)ctG>ctA	p.L3450L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3450	Cadherin 31. {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)			CTGGGTCACTCAGGATCAGCT	0.567													C|||	480	0.0958466	0.0038	0.0173	5008	,	,		20940	0.1756		0.0338	False		,,,				2504	0.2577				p.L3450L		Atlas-SNP	.											.	FAT2	465	.	0			c.G10350A						PASS	.	C		72,4334	64.1+/-101.4	1,70,2132	46.0	44.0	45.0		10350	3.3	1.0	5	dbSNP_126	45	414,8186	128.8+/-187.0	12,390,3898	no	coding-synonymous	FAT2	NM_001447.2		13,460,6030	TT,TC,CC		4.814,1.6341,3.7367		3450/4350	150905485	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			GTCACTCAGGATC	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.10350G>A	5.37:g.150905485C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	134	0.06135531135531135	2	0.0040650406504065045	11	0.03038674033149171	96	0.16783216783216784	25	0.032981530343007916	C	9.730	1.161976	0.21538	0.016341	0.04814	ENSG00000086570	ENST00000520200	.	.	.	5.2	3.32	0.38043	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06570	-1.0819	3	.	.	.	.	10.5378	0.45016	0.1415:0.5853:0.2732:0.0	rs36092108	.	.	.	K	309	.	.	E	-	1	0	FAT2	150885678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.390000	0.44416	0.630000	0.30394	0.544000	0.68410	GAG	C|0.954;T|0.046	0.046	strong		0.567	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
OBSCN	84033	hgsc.bcm.edu	37	1	228476420	228476420	+	Silent	SNP	C	C	T	rs56367754		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228476420C>T	ENST00000422127.1	+	38	10214	c.10170C>T	c.(10168-10170)ccC>ccT	p.P3390P	OBSCN_ENST00000359599.6_Silent_p.P2237P|OBSCN_ENST00000570156.2_Silent_p.P3819P|OBSCN_ENST00000284548.11_Silent_p.P3390P|OBSCN_ENST00000366707.4_Silent_p.P509P|OBSCN_ENST00000366709.4_Silent_p.P509P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3390	Ig-like 34.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGCGGCCCCCGTGGAGTGGA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		21068	0.0		0.001	False		,,,				2504	0.0				p.P3819P		Atlas-SNP	.											OBSCN_ENST00000570156,colon,carcinoma,+1,4	OBSCN	2142	4	0			c.C11457T						PASS	.	C	,	2,4160		0,2,2079	88.0	98.0	95.0		10170,10170	-9.9	0.0	1	dbSNP_129	95	33,8355		0,33,4161	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,35,6240	TT,TC,CC		0.3934,0.0481,0.2789	,	3390/7969,3390/6621	228476420	35,12515	2081	4194	6275	SO:0001819	synonymous_variant	84033	exon43			GGCCCCCGTGGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10170C>T	1.37:g.228476420C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.995;T|0.005	0.005	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC16	94025	hgsc.bcm.edu	37	19	9024994	9024994	+	Missense_Mutation	SNP	C	C	T	rs67631215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9024994C>T	ENST00000397910.4	-	16	37071	c.36868G>A	c.(36868-36870)Gag>Aag	p.E12290K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12292	SEA 2. {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)		p.E12290K(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						CCATCTTTCTCGGGCCTGGGG	0.547													C|||	1523	0.304113	0.2201	0.2939	5008	,	,		18746	0.2421		0.4026	False		,,,				2504	0.3875				p.E12290K		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,1	MUC16	4315	1	1	Substitution - Missense(1)	stomach(1)	c.G36868A						PASS	.	C	LYS/GLU	916,2792		124,668,1062	57.0	54.0	55.0		36868	1.5	0.0	19	dbSNP_130	55	3105,5093		572,1961,1566	yes	missense	MUC16	NM_024690.2	56	696,2629,2628	TT,TC,CC		37.8751,24.7033,33.7729	benign	12290/14508	9024994	4021,7885	1854	4099	5953	SO:0001583	missense	94025	exon16			CTTTCTCGGGCCT	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.36868G>A	19.37:g.9024994C>T	ENSP00000381008:p.Glu12290Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	682	0.31227106227106227	103	0.20934959349593496	119	0.3287292817679558	153	0.2674825174825175	307	0.4050131926121372	c	10.19	1.282635	0.23392	0.247033	0.378751	ENSG00000181143	ENST00000397910	T	0.43688	0.94	2.57	1.51	0.23008	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	.	.	.	B	0.14012	0.009	B	0.15484	0.013	T	0.37291	-0.9712	8	0.87932	D	0	.	5.6295	0.17501	0.0:0.8391:0.0:0.1609	.	12290	B5ME49	.	K	12290	ENSP00000381008:E12290K	ENSP00000381008:E12290K	E	-	1	0	MUC16	8885994	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.021000	0.12504	0.643000	0.30638	-1.098000	0.02139	GAG	C|0.686;T|0.314	0.314	strong		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ABCC6	368	hgsc.bcm.edu	37	16	16291971	16291971	+	Silent	SNP	C	C	T	rs9940825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:16291971C>T	ENST00000205557.7	-	10	1274	c.1245G>A	c.(1243-1245)gtG>gtA	p.V415V	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	415	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	GCTGCACGTCCACGGACACCA	0.612													C|||	1163	0.232228	0.2466	0.3084	5008	,	,		12667	0.0972		0.3191	False		,,,				2504	0.2086				p.V415V		Atlas-SNP	.											.	ABCC6	110	.	0			c.G1245A						PASS	.	C		1085,3309	379.7+/-323.4	129,827,1241	69.0	48.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1245	3.4	1.0	16	dbSNP_119	56	2891,5707	437.9+/-358.8	486,1919,1894	no	coding-synonymous	ABCC6	NM_001171.5		615,2746,3135	TT,TC,CC		33.6241,24.6928,30.6034		415/1504	16291971	3976,9016	2197	4299	6496	SO:0001819	synonymous_variant	368	exon10			CACGTCCACGGAC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1245G>A	16.37:g.16291971C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	61	0.554545	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	37	CCDS10568.1																																																																																			C|0.732;T|0.268	0.268	strong		0.612	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
SGTA	6449	hgsc.bcm.edu	37	19	2767192	2767192	+	Silent	SNP	G	G	T	rs1128925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2767192G>T	ENST00000221566.2	-	4	395	c.234C>A	c.(232-234)ccC>ccA	p.P78P		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	78					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		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)		GGGTTCGCGCGGGGCTCCTCA	0.672													G|||	1415	0.282548	0.177	0.2277	5008	,	,		15276	0.5169		0.2107	False		,,,				2504	0.2965				p.P78P		Atlas-SNP	.											.	SGTA	19	.	0			c.C234A						PASS	.	G		772,3624	293.0+/-282.3	58,656,1484	61.0	54.0	56.0		234	-7.1	0.0	19	dbSNP_86	56	1855,6745	304.1+/-306.8	206,1443,2651	no	coding-synonymous	SGTA	NM_003021.3		264,2099,4135	TT,TG,GG		21.5698,17.5614,20.2139		78/314	2767192	2627,10369	2198	4300	6498	SO:0001819	synonymous_variant	6449	exon4			TCGCGCGGGGCTC	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.234C>A	19.37:g.2767192G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	76	22	0.289474	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Silent	SNP	ENST00000221566.2	37	CCDS12094.1																																																																																			G|0.780;T|0.220	0.220	strong		0.672	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021	
COBL	23242	hgsc.bcm.edu	37	7	51093049	51093049	+	Silent	SNP	C	C	T	rs1129262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:51093049C>T	ENST00000265136.7	-	12	3690	c.3525G>A	c.(3523-3525)gaG>gaA	p.E1175E	COBL_ENST00000395542.2_Silent_p.E1257E|RP4-724E13.2_ENST00000582616.1_RNA	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1175					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TCTGGAGCTCCTCAGAAGCAG	0.527													C|||	15	0.00299521	0.0045	0.0043	5008	,	,		12853	0.0		0.005	False		,,,				2504	0.001				p.E1175E	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											COBL,NS,haematopoietic_neoplasm,0,1	COBL	167	1	0			c.G3525A						PASS	.	C		14,4390		0,14,2188	35.0	37.0	36.0		3525	1.3	1.0	7	dbSNP_86	36	88,8508		0,88,4210	no	coding-synonymous	COBL	NM_015198.3		0,102,6398	TT,TC,CC		1.0237,0.3179,0.7846		1175/1262	51093049	102,12898	2202	4298	6500	SO:0001819	synonymous_variant	23242	exon12			GAGCTCCTCAGAA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3525G>A	7.37:g.51093049C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	138	31	0.224638	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
HERC2	8924	hgsc.bcm.edu	37	15	28419746	28419746	+	Silent	SNP	G	G	A	rs139335991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28419746G>A	ENST00000261609.7	-	65	9960	c.9852C>T	c.(9850-9852)aaC>aaT	p.N3284N		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)		GGCCGTGGTCGTTGTCACCCC	0.458																																					p.N3284N		Atlas-SNP	.											.	HERC2	501	.	0			c.C9852T						PASS	.						56.0	39.0	45.0					15																	28419746		2202	4279	6481	SO:0001819	synonymous_variant	8924	exon65			GTGGTCGTTGTCA	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.9852C>T	15.37:g.28419746G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	284	32	0.112676	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.942;A|0.058	0.058	strong		0.458	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
EXOSC10	5394	hgsc.bcm.edu	37	1	11137661	11137661	+	Silent	SNP	A	A	G	rs2273339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11137661A>G	ENST00000376936.4	-	15	1846	c.1797T>C	c.(1795-1797)gcT>gcC	p.A599A	EXOSC10_ENST00000304457.7_Silent_p.A599A|EXOSC10_ENST00000544779.1_Silent_p.A599A	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	599					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A599A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		ACTCTACCTCAGCACTGGGCA	0.542													G|||	603	0.120407	0.1664	0.0764	5008	,	,		17823	0.1577		0.0258	False		,,,				2504	0.1483				p.A599A	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											EXOSC10,NS,carcinoma,0,1	EXOSC10	59	1	1	Substitution - coding silent(1)	stomach(1)	c.T1797C						PASS	.	G	,	606,3800	770.2+/-413.7	43,520,1640	80.0	75.0	77.0		1797,1797	-9.7	0.0	1	dbSNP_100	77	201,8399	810.5+/-407.1	5,191,4104	no	coding-synonymous,coding-synonymous	EXOSC10	NM_001001998.1,NM_002685.2	,	48,711,5744	GG,GA,AA		2.3372,13.754,6.2048	,	599/886,599/861	11137661	807,12199	2203	4300	6503	SO:0001819	synonymous_variant	5394	exon15			TACCTCAGCACTG	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.1797T>C	1.37:g.11137661A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	37	CCDS30584.1																																																																																			A|0.930;G|0.070	0.070	strong		0.542	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
DENND1A	57706	hgsc.bcm.edu	37	9	126219706	126219706	+	Silent	SNP	A	A	G	rs3829851	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:126219706A>G	ENST00000373624.2	-	15	1308	c.1107T>C	c.(1105-1107)gaT>gaC	p.D369D	DENND1A_ENST00000394219.3_Silent_p.D337D|DENND1A_ENST00000373618.1_Silent_p.D337D|DENND1A_ENST00000373620.3_Silent_p.D369D|DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000394215.2_Silent_p.D339D|DENND1A_ENST00000542603.1_Silent_p.D111D	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	369	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)	p.D369D(1)		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						CTAATCGACCATCAATAAACT	0.428													A|||	278	0.0555112	0.0598	0.0288	5008	,	,		19199	0.0754		0.0467	False		,,,				2504	0.0573				p.D369D		Atlas-SNP	.											DENND1A,NS,carcinoma,0,1	DENND1A	112	1	1	Substitution - coding silent(1)	stomach(1)	c.T1107C						PASS	.	A	,	219,4187	131.8+/-168.3	6,207,1990	99.0	96.0	97.0		1107,1107	5.5	1.0	9	dbSNP_107	97	473,8127	139.8+/-196.4	8,457,3835	no	coding-synonymous,coding-synonymous	DENND1A	NM_020946.1,NM_024820.2	,	14,664,5825	GG,GA,AA		5.5,4.9705,5.3206	,	369/1010,369/560	126219706	692,12314	2203	4300	6503	SO:0001819	synonymous_variant	57706	exon15			TCGACCATCAATA	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.1107T>C	9.37:g.126219706A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																			A|0.943;G|0.057	0.057	strong		0.428	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887429	9887429	+	Missense_Mutation	SNP	C	C	T	rs2240908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:9887429C>T	ENST00000306084.6	+	2	1152	c.953C>T	c.(952-954)cCa>cTa	p.P318L	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Missense_Mutation_p.P251L	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	318	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CCCAAGTCCCCAGAAGAAGCC	0.592													C|||	1240	0.247604	0.3434	0.1787	5008	,	,		20626	0.1488		0.2952	False		,,,				2504	0.2198				p.P318L		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C953T						PASS	.	C	LEU/PRO,LEU/PRO	857,3543		164,529,1507	114.0	113.0	113.0		752,953	1.7	0.0	18	dbSNP_98	113	1675,6925		248,1179,2873	no	missense,missense	TXNDC2	NM_032243.5,NM_001098529.1	98,98	412,1708,4380	TT,TC,CC		19.4767,19.4773,19.4769	benign,benign	251/487,318/554	9887429	2532,10468	2200	4300	6500	SO:0001583	missense	84203	exon2			AGTCCCCAGAAGA	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.953C>T	18.37:g.9887429C>T	ENSP00000304908:p.Pro318Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	202	0.0924908424908425	52	0.10569105691056911	35	0.09668508287292818	44	0.07692307692307693	71	0.09366754617414248	-	9.978	1.227431	0.22542	0.194773	0.194767	ENSG00000168454	ENST00000357775;ENST00000306084	T;T	0.16597	2.33;2.33	4.51	1.67	0.24075	.	1.719520	0.03612	N	0.235008	T	0.00039	0.0001	L	0.31926	0.97	0.80722	P	0.0	B	0.10296	0.003	B	0.15052	0.012	T	0.35351	-0.9792	8	.	.	.	4.9001	8.3773	0.32451	0.0:0.7317:0.0:0.2683	.	318	Q86VQ3	TXND2_HUMAN	L	251;318	ENSP00000350419:P251L;ENSP00000304908:P318L	.	P	+	2	0	TXNDC2	9877429	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.321000	0.08018	0.245000	0.21373	0.644000	0.83932	CCA	C|0.809;T|0.191	0.191	strong		0.592	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
ADCY2	108	hgsc.bcm.edu	37	5	7743787	7743787	+	Silent	SNP	C	C	T	rs62342477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:7743787C>T	ENST00000338316.4	+	15	1967	c.1878C>T	c.(1876-1878)tcC>tcT	p.S626S	ADCY2_ENST00000537121.1_Silent_p.S446S|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	626					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						GTAGAACGTCCGTCCTGGGCA	0.493													C|||	1621	0.323682	0.2973	0.3199	5008	,	,		17509	0.0585		0.5755	False		,,,				2504	0.3763				p.S626S		Atlas-SNP	.											ADCY2,bladder,carcinoma,+1,1	ADCY2	337	1	0			c.C1878T						PASS	.	C		1501,2905	478.8+/-358.3	266,969,968	351.0	315.0	327.0		1878	0.2	0.0	5	dbSNP_129	327	4983,3617	626.0+/-397.8	1462,2059,779	yes	coding-synonymous	ADCY2	NM_020546.2		1728,3028,1747	TT,TC,CC		42.0581,34.0672,49.8539		626/1092	7743787	6484,6522	2203	4300	6503	SO:0001819	synonymous_variant	108	exon15			AACGTCCGTCCTG	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.1878C>T	5.37:g.7743787C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			C|0.541;T|0.459	0.459	strong		0.493	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
FCAMR	83953	hgsc.bcm.edu	37	1	207140440	207140440	+	Silent	SNP	C	C	T	rs11119933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:207140440C>T	ENST00000324852.4	-	3	600	c.126G>A	c.(124-126)gcG>gcA	p.A42A	FCAMR_ENST00000450945.2_Silent_p.A42A|FCAMR_ENST00000400962.3_Silent_p.A42A	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	341					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A42A(1)		endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TTTTCCATCCCGCCCTCCTGC	0.522													C|||	1185	0.236621	0.3797	0.1715	5008	,	,		19779	0.3165		0.165	False		,,,				2504	0.0808				p.A42A	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											FCAMR,NS,carcinoma,0,1	FCAMR	125	1	1	Substitution - coding silent(1)	stomach(1)	c.G126A						PASS	.	C	,,	1024,2112		155,714,699	67.0	60.0	62.0		126,126,126	-1.1	0.0	1	dbSNP_120	62	1345,5819		134,1077,2371	no	coding-synonymous,coding-synonymous,coding-synonymous	FCAMR	NM_001122979.2,NM_001170631.1,NM_032029.4	,,	289,1791,3070	TT,TC,CC		18.7744,32.6531,23.0	,,	42/266,42/578,42/266	207140440	2369,7931	1568	3582	5150	SO:0001819	synonymous_variant	83953	exon3			CCATCCCGCCCTC	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.126G>A	1.37:g.207140440C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Silent	SNP	ENST00000324852.4	37	CCDS53468.1																																																																																			C|0.778;T|0.222	0.222	strong		0.522	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
C12orf5	57103	hgsc.bcm.edu	37	12	4459032	4459032	+	Silent	SNP	G	G	A	rs7309402	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:4459032G>A	ENST00000179259.4	+	4	307	c.240G>A	c.(238-240)acG>acA	p.T80T	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	80					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)			AAGATATGACGGTAAAGTATG	0.353													G|||	1369	0.273363	0.3109	0.2435	5008	,	,		19888	0.5109		0.0984	False		,,,				2504	0.1789				p.T80T	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											.	C12orf5	28	.	0			c.G240A						PASS	.	G		1288,3118	438.8+/-345.5	192,904,1107	98.0	101.0	100.0		240	-1.0	0.9	12	dbSNP_116	100	651,7949	166.2+/-218.2	27,597,3676	no	coding-synonymous	C12orf5	NM_020375.2		219,1501,4783	AA,AG,GG		7.5698,29.2329,14.9085		80/271	4459032	1939,11067	2203	4300	6503	SO:0001819	synonymous_variant	57103	exon4			TATGACGGTAAAG	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.240G>A	12.37:g.4459032G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_020375	B2R840	Silent	SNP	ENST00000179259.4	37	CCDS8525.1																																																																																			G|0.742;A|0.258	0.258	strong		0.353	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375	
HAS3	3038	hgsc.bcm.edu	37	16	69143481	69143481	+	Silent	SNP	T	T	G	rs2232227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:69143481T>G	ENST00000306560.1	+	2	339	c.183T>G	c.(181-183)ctT>ctG	p.L61L	HAS3_ENST00000219322.3_Silent_p.L61L|HAS3_ENST00000569188.1_Silent_p.L61L	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	61					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		TTCAGAGCCTTTTTGCCTTCC	0.647													G|||	463	0.0924521	0.1475	0.0562	5008	,	,		20799	0.0466		0.0616	False		,,,				2504	0.1227				p.L61L		Atlas-SNP	.											.	HAS3	61	.	0			c.T183G						PASS	.	G	,,	628,3768	767.3+/-413.5	52,524,1622	84.0	73.0	77.0		183,183,183	0.8	1.0	16	dbSNP_98	77	614,7986	791.6+/-407.5	22,570,3708	no	coding-synonymous,coding-synonymous,coding-synonymous	HAS3	NM_001199280.1,NM_005329.2,NM_138612.2	,,	74,1094,5330	GG,GT,TT		7.1395,14.2857,9.5568	,,	61/554,61/554,61/282	69143481	1242,11754	2198	4300	6498	SO:0001819	synonymous_variant	3038	exon2			GAGCCTTTTTGCC	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.183T>G	16.37:g.69143481T>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_138612	A8K5T5|Q8WTZ0|Q9NYP0	Silent	SNP	ENST00000306560.1	37	CCDS10871.1																																																																																			T|0.913;G|0.087	0.087	strong		0.647	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612	
KRT3	3850	hgsc.bcm.edu	37	12	53185492	53185492	+	Missense_Mutation	SNP	C	C	T	rs61929765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53185492C>T	ENST00000417996.2	-	6	1371	c.1297G>A	c.(1297-1299)Gag>Aag	p.E433K	KRT3_ENST00000309505.3_Missense_Mutation_p.E433K	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	433	Coil 2.|Rod.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						TTGACACCCTCGATCTCTGCC	0.567													C|||	448	0.0894569	0.0121	0.1599	5008	,	,		20247	0.0804		0.1302	False		,,,				2504	0.1115				p.E433K		Atlas-SNP	.											.	KRT3	65	.	0			c.G1297A						PASS	.	C	LYS/GLU	99,4305	77.8+/-116.1	1,97,2104	109.0	110.0	110.0		1297	4.0	0.5	12	dbSNP_129	110	1099,7501	225.5+/-261.6	66,967,3267	yes	missense	KRT3	NM_057088.2	56	67,1064,5371	TT,TC,CC		12.7791,2.248,9.2125	probably-damaging	433/629	53185492	1198,11806	2202	4300	6502	SO:0001583	missense	3850	exon6			CACCCTCGATCTC		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1297G>A	12.37:g.53185492C>T	ENSP00000413479:p.Glu433Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	162	64	0.395062	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	189	0.08653846153846154	5	0.01016260162601626	41	0.1132596685082873	50	0.08741258741258741	93	0.12269129287598944	C	18.58	3.655627	0.67586	0.02248	0.127791	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.89415	-2.51;-2.51	4.02	4.02	0.46733	Filament (1);	0.000000	0.45867	D	0.000334	T	0.26011	0.0634	H	0.94345	3.525	0.21220	P	0.999755015	D	0.76494	0.999	D	0.63283	0.913	T	0.62996	-0.6735	9	0.72032	D	0.01	.	16.702	0.85351	0.0:1.0:0.0:0.0	rs61929765	433	P12035	K2C3_HUMAN	K	433	ENSP00000413479:E433K;ENSP00000312206:E433K	ENSP00000312206:E433K	E	-	1	0	KRT3	51471759	1.000000	0.71417	0.501000	0.27601	0.098000	0.18820	4.733000	0.62036	2.247000	0.74100	0.462000	0.41574	GAG	C|0.907;T|0.093	0.093	strong		0.567	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
HID1	283987	hgsc.bcm.edu	37	17	72949167	72949167	+	Silent	SNP	T	T	C	rs2307011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72949167T>C	ENST00000425042.2	-	16	2063	c.1986A>G	c.(1984-1986)gcA>gcG	p.A662A		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	662					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)											GCTCCCTCCATGCCTGGCTGG	0.697													C|||	1136	0.226837	0.3071	0.1023	5008	,	,		14259	0.505		0.0189	False		,,,				2504	0.1339				p.A662A		Atlas-SNP	.											.	.	.	.	0			c.A1986G						PASS	.	C		1095,3311		140,815,1248	19.0	17.0	18.0		1986	-10.2	0.0	17	dbSNP_100	18	210,8384		6,198,4093	no	coding-synonymous	C17orf28	NM_030630.2		146,1013,5341	CC,CT,TT		2.4436,24.8525,10.0385		662/789	72949167	1305,11695	2203	4297	6500	SO:0001819	synonymous_variant	283987	exon16			CCTCCATGCCTGG		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.1986A>G	17.37:g.72949167T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																			T|0.841;C|0.159	0.159	strong		0.697	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
KCNA7	3743	hgsc.bcm.edu	37	19	49573438	49573438	+	Missense_Mutation	SNP	A	A	G	rs1017219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	55	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	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	
C12orf43	64897	hgsc.bcm.edu	37	12	121442241	121442241	+	Silent	SNP	C	C	T	rs73214128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121442241C>T	ENST00000288757.3	-	6	526	c.504G>A	c.(502-504)gcG>gcA	p.A168A	C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000366211.2_Silent_p.A127A|C12orf43_ENST00000537817.1_Silent_p.A169A|C12orf43_ENST00000539736.1_Silent_p.A158A|C12orf43_ENST00000445832.3_Silent_p.A138A	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	168										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGATGTCGGACGCCGACACAG	0.582													.|||	200	0.0399361	0.0045	0.0461	5008	,	,		16552	0.0079		0.0616	False		,,,				2504	0.0941				p.A168A		Atlas-SNP	.											.	C12orf43	30	.	0			c.G504A						PASS	.	C		54,4352	52.9+/-88.7	2,50,2151	87.0	102.0	97.0		504	-4.5	0.0	12	dbSNP_130	97	481,8119	139.5+/-196.2	15,451,3834	no	coding-synonymous	C12orf43	NM_022895.1		17,501,5985	TT,TC,CC		5.593,1.2256,4.1135		168/263	121442241	535,12471	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon6			GTCGGACGCCGAC	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.504G>A	12.37:g.121442241C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	75	0.034340659340659344	5	0.01016260162601626	19	0.052486187845303865	2	0.0034965034965034965	49	0.06464379947229551	C	1.352	-0.591095	0.03799	0.012256	0.05593	ENSG00000157895	ENST00000546272	.	.	.	5.73	-4.49	0.03504	.	.	.	.	.	T	0.01627	0.0052	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22977	-1.0201	4	.	.	.	-6.4613	0.8027	0.01078	0.3201:0.2727:0.2234:0.1838	.	.	.	.	H	122	.	.	R	-	2	0	C12orf43	119926624	0.001000	0.12720	0.012000	0.15200	0.137000	0.21094	-0.285000	0.08410	-0.458000	0.07023	-0.302000	0.09304	CGT	C|0.960;T|0.040	0.040	strong		0.582	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
C16orf59	80178	hgsc.bcm.edu	37	16	2511114	2511114	+	Missense_Mutation	SNP	G	G	A	rs199831316	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2511114G>A	ENST00000361837.4	+	4	559	c.494G>A	c.(493-495)cGt>cAt	p.R165H	C16orf59_ENST00000483320.1_5'UTR|C16orf59_ENST00000563531.1_Missense_Mutation_p.R165H|C16orf59_ENST00000569496.1_Missense_Mutation_p.R165H|RP11-715J22.4_ENST00000566085.1_lincRNA	NM_025108.2	NP_079384.2	Q7L2K0	CP059_HUMAN	chromosome 16 open reading frame 59	165										lung(1)|skin(1)|urinary_tract(1)	3		Ovarian(90;0.17)				GATGGGACCCGTGTTGGGATG	0.687													G|||	11	0.00219649	0.0	0.0058	5008	,	,		15343	0.002		0.004	False		,,,				2504	0.001				p.R165H		Atlas-SNP	.											.	C16orf59	13	.	0			c.G494A						PASS	.	G	HIS/ARG	4,3846		0,4,1921	19.0	23.0	22.0		494	-2.8	0.0	16		22	58,8188		1,56,4066	no	missense	C16orf59	NM_025108.2	29	1,60,5987	AA,AG,GG		0.7034,0.1039,0.5126	benign	165/434	2511114	62,12034	1925	4123	6048	SO:0001583	missense	80178	exon4			GGACCCGTGTTGG	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.494G>A	16.37:g.2511114G>A	ENSP00000355022:p.Arg165His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_025108	B4DXD7|Q96H61|Q9H872	Missense_Mutation	SNP	ENST00000361837.4	37	CCDS10468.2	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	3	0.00395778364116095	G	10.94	1.493102	0.26774	0.001039	0.007034	ENSG00000162062	ENST00000361837	T	0.41400	1.0	3.54	-2.78	0.05859	.	2.952440	0.01641	N	0.024034	T	0.13798	0.0334	N	0.03608	-0.345	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.10177	-1.0641	10	0.29301	T	0.29	5.5872	5.0734	0.14618	0.5967:0.1863:0.217:0.0	.	165	Q7L2K0	CP059_HUMAN	H	165	ENSP00000355022:R165H	ENSP00000355022:R165H	R	+	2	0	C16orf59	2451115	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.824000	0.01708	-0.494000	0.06669	-0.140000	0.14226	CGT	G|0.997;A|0.003	0.003	strong		0.687	C16orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250802.3	NM_025108	
GBP1	2633	hgsc.bcm.edu	37	1	89521841	89521841	+	Missense_Mutation	SNP	G	G	C	rs1048443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:89521841G>C	ENST00000370473.4	-	8	1445	c.1226C>G	c.(1225-1227)gCt>gGt	p.A409G	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	409			A -> G (in dbSNP:rs1048443). {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)		CTGAAGTAAAGCTGAGCAACG	0.408													.|||	1782	0.355831	0.5749	0.3055	5008	,	,		19712	0.2014		0.3022	False		,,,				2504	0.3098				p.A409G		Atlas-SNP	.											.	GBP1	68	.	0			c.C1226G						PASS	.	C	GLY/ALA	2295,2111	574.2+/-383.7	613,1069,521	111.0	116.0	115.0		1226	-0.7	0.7	1	dbSNP_86	115	2537,6057	691.3+/-404.5	340,1857,2100	no	missense	GBP1	NM_002053.2	60	953,2926,2621	CC,CG,GG		29.5206,47.9119,37.1692	benign	409/593	89521841	4832,8168	2203	4297	6500	SO:0001583	missense	2633	exon8			AGTAAAGCTGAGC	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.1226C>G	1.37:g.89521841G>C	ENSP00000359504:p.Ala409Gly	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	293	131	0.447099	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	731	0.3347069597069597	275	0.5589430894308943	118	0.3259668508287293	111	0.19405594405594406	227	0.2994722955145119	C	11.02	1.516417	0.27123	0.520881	0.295206	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.02369	4.32	4.8	-0.712	0.11226	Guanylate-binding protein, C-terminal (3);	0.499201	0.21562	N	0.072552	T	0.03564	0.0102	M	0.90542	3.125	0.80722	P	0.0	P	0.46621	0.881	P	0.51516	0.672	T	0.05273	-1.0895	9	0.54805	T	0.06	.	3.0636	0.06207	0.0831:0.248:0.2348:0.4342	rs1048443;rs2230335;rs3188450;rs17849643;rs58851967;rs1048443	409	P32455	GBP1_HUMAN	G	409;372	ENSP00000359504:A409G	ENSP00000359504:A409G	A	-	2	0	GBP1	89294429	0.000000	0.05858	0.718000	0.30602	0.002000	0.02628	-0.072000	0.11486	-0.180000	0.10637	-1.308000	0.01314	GCT	G|0.208;C|0.792	0.792	strong		0.408	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
FRY	10129	hgsc.bcm.edu	37	13	32785086	32785086	+	Silent	SNP	G	G	A	rs798981	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	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	
LRPAP1	4043	hgsc.bcm.edu	37	4	3516560	3516560	+	Silent	SNP	G	G	A	rs11549512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3516560G>A	ENST00000500728.2	-	7	1076	c.930C>T	c.(928-930)agC>agT	p.S310S	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	310	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGTCGCCCACGCTCTCTGCGT	0.637													.|||	95	0.0189696	0.0023	0.0519	5008	,	,		17011	0.001		0.0497	False		,,,				2504	0.0051				p.S310S		Atlas-SNP	.											.	LRPAP1	29	.	0			c.C930T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	127.0	104.0	112.0		930	0.3	0.3	4	dbSNP_120	112	401,8199	127.7+/-186.0	7,387,3906	no	coding-synonymous	LRPAP1	NM_002337.3		7,426,6070	AA,AG,GG		4.6628,0.8852,3.3831		310/358	3516560	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	4043	exon7			GCCCACGCTCTCT		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.930C>T	4.37:g.3516560G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			G|0.971;A|0.029	0.029	strong		0.637	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
A2ML1	144568	hgsc.bcm.edu	37	12	8975901	8975901	+	Silent	SNP	C	C	T	rs17792974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:8975901C>T	ENST00000299698.7	+	2	366	c.186C>T	c.(184-186)acC>acT	p.T62T	A2ML1-AS2_ENST00000394240.3_RNA|A2ML1-AS1_ENST00000537288.1_RNA	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AGGACAAGACCCAGAAGTTGC	0.478													C|||	652	0.130192	0.0484	0.0504	5008	,	,		-128	0.1964		0.0567	False		,,,				2504	0.3047				p.T62T		Atlas-SNP	.											.	A2ML1	199	.	0			c.C186T						PASS	.	C		163,3677		2,159,1759	104.0	103.0	104.0		186	-0.9	1.0	12	dbSNP_123	104	387,7855		7,373,3741	no	coding-synonymous	A2ML1	NM_144670.3		9,532,5500	TT,TC,CC		4.6955,4.2448,4.5522		62/1455	8975901	550,11532	1920	4121	6041	SO:0001819	synonymous_variant	144568	exon2			CAAGACCCAGAAG	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.186C>T	12.37:g.8975901C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			C|0.909;T|0.091	0.091	strong		0.478	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
FITM2	128486	hgsc.bcm.edu	37	20	42939693	42939693	+	Missense_Mutation	SNP	C	C	T	rs148377517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42939693C>T	ENST00000396825.3	-	1	116	c.96G>A	c.(94-96)atG>atA	p.M32I		NM_001080472.1	NP_001073941.1	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	32					cellular triglyceride homeostasis (GO:0035356)|cytoskeleton organization (GO:0007010)|lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of cell morphogenesis (GO:0022604)|regulation of triglyceride biosynthetic process (GO:0010866)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)				endometrium(2)|lung(2)|skin(2)	6						AGCCCGCCAGCATGGAGGCCA	0.687											OREG0025965	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	28	0.00559105	0.0	0.0115	5008	,	,		15729	0.0		0.0169	False		,,,				2504	0.0031				p.M32I		Atlas-SNP	.											.	FITM2	15	.	0			c.G96A						PASS	.	C	ILE/MET	5,4383		0,5,2189	44.0	36.0	39.0		96	5.2	1.0	20	dbSNP_134	39	154,8426		1,152,4137	yes	missense	FITM2	NM_001080472.1	10	1,157,6326	TT,TC,CC		1.7949,0.1139,1.2261	benign	32/263	42939693	159,12809	2194	4290	6484	SO:0001583	missense	128486	exon1			CGCCAGCATGGAG	BC029662	CCDS33473.1	20q13.12	2009-04-29	2009-04-29	2009-04-29	ENSG00000197296	ENSG00000197296			16135	protein-coding gene	gene with protein product	"""fat inducing transcript 2"""	612029	"""chromosome 20 open reading frame 142"""	C20orf142		18160536	Standard	NM_001080472		Approved	dJ881L22.2, FIT2	uc002xlr.1	Q8N6M3	OTTHUMG00000032522	ENST00000396825.3:c.96G>A	20.37:g.42939693C>T	ENSP00000380037:p.Met32Ile	Somatic	114	0	0	912	WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_001080472	A1L492|B9EGQ4|Q5TE59|Q9H3Y1	Missense_Mutation	SNP	ENST00000396825.3	37	CCDS33473.1	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	C	13.84	2.357072	0.41801	0.001139	0.017949	ENSG00000197296	ENST00000396825	.	.	.	5.21	5.21	0.72293	.	0.262126	0.46145	D	0.000301	T	0.18676	0.0448	N	0.19112	0.55	0.34363	D	0.691172	B	0.24768	0.111	B	0.16289	0.015	T	0.34403	-0.9830	9	0.23302	T	0.38	.	9.0605	0.36431	0.0:0.758:0.161:0.081	.	32	Q8N6M3	FITM2_HUMAN	I	32	.	ENSP00000380037:M32I	M	-	3	0	FITM2	42373107	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	1.025000	0.30090	2.430000	0.82344	0.484000	0.47621	ATG	C|0.991;T|0.009	0.009	strong		0.687	FITM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079342.2	XM_371399	
RICTOR	253260	hgsc.bcm.edu	37	5	38955796	38955796	+	Missense_Mutation	SNP	G	G	A	rs2043112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	100	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	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	
PSCA	8000	hgsc.bcm.edu	37	8	143763547	143763547	+	Silent	SNP	C	C	A	rs1045531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143763547C>A	ENST00000301258.4	+	3	425	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	123						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CCGGCCAGCTCTAGGCTCTGG	0.706													A|||	2013	0.401957	0.354	0.5072	5008	,	,		13713	0.3423		0.4473	False		,,,				2504	0.407				p.L114L		Atlas-SNP	.											.	PSCA	9	.	0			c.C342A						PASS	.	A		1450,2534		293,864,835	13.0	15.0	14.0		342	1.4	0.3	8	dbSNP_86	14	3740,4612		857,2026,1293	no	coding-synonymous	PSCA	NM_005672.4		1150,2890,2128	AA,AC,CC		44.7797,36.3956,42.072		114/115	143763547	5190,7146	1992	4176	6168	SO:0001819	synonymous_variant	8000	exon3			CCAGCTCTAGGCT	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.342C>A	8.37:g.143763547C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	37	CCDS47925.2																																																																																			C|0.584;A|0.416	0.416	strong		0.706	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
HS3ST1	9957	hgsc.bcm.edu	37	4	11401087	11401087	+	Silent	SNP	A	A	G	rs1047389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	96	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	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	
UGT2B28	54490	hgsc.bcm.edu	37	4	70160338	70160338	+	Silent	SNP	G	G	C	rs72552703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:70160338G>C	ENST00000335568.5	+	6	1403	c.1401G>C	c.(1399-1401)gtG>gtC	p.V467V	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	467					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						TTGAATTTGTGATGTGCCACA	0.443													N|||	1214	0.242412	0.2632	0.2161	5008	,	,		12627	0.2034		0.2813	False		,,,				2504	0.2331				p.V467V		Atlas-SNP	.											.	UGT2B28	101	.	0			c.G1401C						PASS	.	C	,	830,3228		274,282,1473	72.0	81.0	78.0		,1401	0.7	1.0	4	dbSNP_130	78	1619,6833		436,747,3043	no	utr-3,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	710,1029,4516	CC,CG,GG		19.1552,20.4534,19.5763	,	,467/530	70160338	2449,10061	2029	4226	6255	SO:0001819	synonymous_variant	54490	exon6			ATTTGTGATGTGC	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.1401G>C	4.37:g.70160338G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	25	0.333333	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			G|0.792;C|0.208	0.208	strong		0.443	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
KNDC1	85442	hgsc.bcm.edu	37	10	134997480	134997480	+	Silent	SNP	C	C	T	rs57510763	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:134997480C>T	ENST00000304613.3	+	5	633	c.612C>T	c.(610-612)ttC>ttT	p.F204F	KNDC1_ENST00000368571.2_Silent_p.F139F|KNDC1_ENST00000368572.2_Silent_p.F204F			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	204	KIND 1. {ECO:0000255|PROSITE- ProRule:PRU00709}.				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)		TCGAGTCCTTCGGAGCGCTGC	0.577													c|||	2101	0.419529	0.118	0.3876	5008	,	,		20472	0.5843		0.4384	False		,,,				2504	0.6605				p.F204F		Atlas-SNP	.											.	KNDC1	155	.	0			c.C612T						PASS	.			737,3669	300.4+/-286.3	62,613,1528	156.0	130.0	139.0		612	-1.1	1.0	10	dbSNP_129	139	4027,4573	555.7+/-386.7	951,2125,1224	no	coding-synonymous	KNDC1	NM_152643.6		1013,2738,2752	TT,TC,CC		46.8256,16.7272,36.6292		204/1750	134997480	4764,8242	2203	4300	6503	SO:0001819	synonymous_variant	85442	exon5			GTCCTTCGGAGCG	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.612C>T	10.37:g.134997480C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																			C|0.611;T|0.389	0.389	strong		0.577	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43685357	43685357	+	Missense_Mutation	SNP	C	C	A	rs372133350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	58	0	0		WXS	Illumina HiSeq	Phase_I	87	18	0.206897	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		
C3orf30	152405	hgsc.bcm.edu	37	3	118866376	118866376	+	Missense_Mutation	SNP	C	C	T	rs56317615	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	106	0	0		WXS	Illumina HiSeq	Phase_I	159	104	0.654088	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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607291	84607291	+	Missense_Mutation	SNP	T	T	G	rs201182137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84607291T>G	ENST00000344803.2	+	4	1953	c.1906T>G	c.(1906-1908)Ttg>Gtg	p.L636V		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	636					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCAGGAAAGTTTGTGGGGCTT	0.478													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19868	0.0		0.001	False		,,,				2504	0.001				p.L636V		Atlas-SNP	.											FAM75D4,NS,carcinoma,0,2	.	.	2	0			c.T1906G						scavenged	.	G	VAL/LEU	0,3730		0,0,1865	101.0	98.0	99.0		1906	-3.7	0.0	9		99	1,8223		0,1,4111	no	missense	FAM75D1	NM_001001670.2	32	0,1,5976	GG,GT,TT		0.0122,0.0,0.0084	benign	636/1577	84607291	1,11953	1865	4112	5977	SO:0001583	missense	389763	exon4			GAAAGTTTGTGGG		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.1906T>G	9.37:g.84607291T>G	ENSP00000341988:p.Leu636Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	4	0.0366972	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	4.363	0.066840	0.08388	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05786	3.39	3.83	-3.67	0.04476	.	1.454400	0.04584	N	0.395509	T	0.02970	0.0088	N	0.11023	0.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.43261	-0.9402	10	0.16420	T	0.52	0.4754	3.7406	0.08528	0.108:0.096:0.4463:0.3497	.	636	Q6ZQQ2	F75D1_HUMAN	V	636	ENSP00000341988:L636V	ENSP00000341988:L636V	L	+	1	2	FAM75D1	83797111	0.011000	0.17503	0.002000	0.10522	0.000000	0.00434	-0.756000	0.04777	-1.293000	0.02362	-0.729000	0.03580	TTG	.	.	weak		0.478	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
ADAD2	161931	hgsc.bcm.edu	37	16	84229580	84229580	+	Silent	SNP	C	C	T	rs2303239	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84229580C>T	ENST00000315906.5	+	7	1264	c.1212C>T	c.(1210-1212)gcC>gcT	p.A404A	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.A486A	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	404	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CACGCTGGGCCGTGCTGGGGC	0.677													C|||	1453	0.290136	0.1793	0.4352	5008	,	,		15982	0.2421		0.325	False		,,,				2504	0.3507				p.A486A		Atlas-SNP	.											.	ADAD2	46	.	0			c.C1458T						PASS	.	C	,	928,3466		111,706,1380	20.0	24.0	23.0		1212,1458	-11.0	0.0	16	dbSNP_100	23	2702,5880		455,1792,2044	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	566,2498,3424	TT,TC,CC		31.4845,21.1197,27.9747	,	404/584,486/666	84229580	3630,9346	2197	4291	6488	SO:0001819	synonymous_variant	161931	exon8			CTGGGCCGTGCTG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1212C>T	16.37:g.84229580C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			C|0.720;T|0.280	0.280	strong		0.677	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
PRKCZ	5590	hgsc.bcm.edu	37	1	1987993	1987993	+	IGR	SNP	T	T	C	rs12184	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1987993T>C								RP11-547D24.3 (6484 upstream) : PRKCZ (16907 downstream)																							AGTGCAGGGATGAAGGCCTCA	0.627													C|||	3355	0.669928	0.8873	0.402	5008	,	,		14345	0.9454		0.3429	False		,,,				2504	0.6186				p.D88D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.T264C						PASS	.	C		3609,797	317.4+/-295.1	1478,653,72	74.0	65.0	68.0		264	-3.4	0.6	1	dbSNP_52	68	2955,5645	667.1+/-402.4	516,1923,1861	no	coding-synonymous	PRKCZ	NM_002744.4		1994,2576,1933	CC,CT,TT		34.3605,18.089,49.531		88/593	1987993	6564,6442	2203	4300	6503	SO:0001628	intergenic_variant	5590	exon3			CAGGGATGAAGGC																													1.37:g.1987993T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	173	87	0.50289	NM_002744		Silent	SNP		37																																																																																				T|0.462;C|0.538	0.538	strong	0	0.627								
ABCA1	19	hgsc.bcm.edu	37	9	107602678	107602678	+	Silent	SNP	G	G	A	rs2274873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:107602678G>A	ENST00000374736.3	-	9	1330	c.936C>T	c.(934-936)ccC>ccT	p.P312P		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	312					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)	CCCCTCCCTCGGGATGCCCGC	0.527													G|||	411	0.0820687	0.1006	0.0461	5008	,	,		19356	0.0665		0.0964	False		,,,				2504	0.0838				p.P312P		Atlas-SNP	.											.	ABCA1	244	.	0			c.C936T						PASS	.	G		425,3981	206.8+/-228.3	19,387,1797	99.0	76.0	84.0		936	-3.0	1.0	9	dbSNP_100	84	862,7738	195.5+/-240.7	49,764,3487	no	coding-synonymous	ABCA1	NM_005502.3		68,1151,5284	AA,AG,GG		10.0233,9.6459,9.8954		312/2262	107602678	1287,11719	2203	4300	6503	SO:0001819	synonymous_variant	19	exon9			TCCCTCGGGATGC	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.936C>T	9.37:g.107602678G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	166	80	0.481928	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			G|0.901;A|0.099	0.099	strong		0.527	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
FAM92B	339145	hgsc.bcm.edu	37	16	85141661	85141661	+	Silent	SNP	G	G	A	rs17200833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:85141661G>A	ENST00000539556.1	-	3	455	c.300C>T	c.(298-300)taC>taT	p.Y100Y		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	100										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						TCTGTGCCCCGTAGAGCTTCA	0.652													G|||	352	0.0702875	0.0174	0.0836	5008	,	,		15220	0.002		0.1461	False		,,,				2504	0.1247				p.Y100Y		Atlas-SNP	.											.	FAM92B	29	.	0			c.C300T						PASS	.	G		193,4203	123.7+/-161.0	5,183,2010	98.0	95.0	96.0		300	-6.9	0.1	16	dbSNP_123	96	1384,7216	268.2+/-287.7	95,1194,3011	no	coding-synonymous	FAM92B	NM_198491.1		100,1377,5021	AA,AG,GG		16.093,4.3904,12.1345		100/305	85141661	1577,11419	2198	4300	6498	SO:0001819	synonymous_variant	339145	exon3			TGCCCCGTAGAGC		CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.300C>T	16.37:g.85141661G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_198491		Silent	SNP	ENST00000539556.1	37	CCDS32500.1																																																																																			G|0.904;A|0.096	0.096	strong		0.652	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491	
ZNF519	162655	hgsc.bcm.edu	37	18	14105016	14105016	+	Missense_Mutation	SNP	C	C	A	rs61609068	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:14105016C>A	ENST00000590202.1	-	3	1675	c.1523G>T	c.(1522-1524)aGa>aTa	p.R508I	ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	508					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						AGTATGAATTCTCTGATGTTG	0.383													C|||	1463	0.292133	0.112	0.2622	5008	,	,		20730	0.6597		0.1958	False		,,,				2504	0.2771				p.R508I		Atlas-SNP	.											.	ZNF519	53	.	0			c.G1523T						PASS	.	C	ILE/ARG	573,3833	251.5+/-258.2	39,495,1669	80.0	84.0	83.0		1523	0.6	0.8	18	dbSNP_129	83	1882,6718	333.6+/-320.6	211,1460,2629	no	missense	ZNF519	NM_145287.3	97	250,1955,4298	AA,AC,CC		21.8837,13.005,18.8759	probably-damaging	508/541	14105016	2455,10551	2203	4300	6503	SO:0001583	missense	162655	exon3			TGAATTCTCTGAT	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.1523G>T	18.37:g.14105016C>A	ENSP00000464872:p.Arg508Ile	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	670	0.3067765567765568	55	0.11178861788617886	86	0.23756906077348067	382	0.6678321678321678	147	0.19393139841688653	C	5.798	0.331605	0.10956	0.13005	0.218837	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.77313	2.365	0.28266	P	0.9246309	P	0.45396	0.857	B	0.39419	0.299	T	0.45101	-0.9284	7	0.33141	T	0.24	.	7.2226	0.25997	0.0:0.9999:0.0:1.0E-4	rs61609068;rs61730994	508	Q8TB69	ZN519_HUMAN	I	508	.	ENSP00000307908:R508I	R	-	2	0	ZNF519	14095016	0.000000	0.05858	0.791000	0.31998	0.513000	0.34164	0.368000	0.20399	0.661000	0.30985	0.089000	0.15464	AGA	C|0.781;A|0.219	0.219	strong		0.383	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
PTCH2	8643	hgsc.bcm.edu	37	1	45307694	45307694	+	Silent	SNP	C	C	T	rs45573433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45307694C>T	ENST00000372192.3	-	2	220	c.90G>A	c.(88-90)ctG>ctA	p.L30L	PTCH2_ENST00000447098.2_Silent_p.L30L	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	30					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)	p.L30L(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GTGGAGCCTTCAGGCTCCCAG	0.537									Basal Cell Nevus syndrome				C|||	28	0.00559105	0.0008	0.0058	5008	,	,		19978	0.0		0.0219	False		,,,				2504	0.001				p.L30L		Atlas-SNP	.											PTCH2,mouth,carcinoma,0,1	PTCH2	96	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G90A						PASS	.	C	,	12,4394	20.2+/-43.8	0,12,2191	78.0	82.0	80.0		90,90	1.7	1.0	1	dbSNP_127	80	102,8498	56.0+/-117.1	1,100,4199	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	1,112,6390	TT,TC,CC		1.186,0.2724,0.8765	,	30/1147,30/1204	45307694	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon2	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AGCCTTCAGGCTC	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.90G>A	1.37:g.45307694C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			C|0.992;T|0.008	0.008	strong		0.537	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
SIM1	6492	hgsc.bcm.edu	37	6	100868779	100868779	+	Missense_Mutation	SNP	G	G	T	rs3734354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:100868779G>T	ENST00000369208.3	-	10	1836	c.1054C>A	c.(1054-1056)Cca>Aca	p.P352T	SIM1_ENST00000262901.4_Missense_Mutation_p.P352T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	352	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		P -> T (in dbSNP:rs3734354).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P352T(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GAGAAGGCTGGTTTGGAGGCT	0.537													G|||	892	0.178115	0.0038	0.2089	5008	,	,		14363	0.4067		0.1471	False		,,,				2504	0.1881				p.P352T		Atlas-SNP	.											SIM1,NS,carcinoma,+2,2	SIM1	173	2	1	Substitution - Missense(1)	stomach(1)	c.C1054A						PASS	.	G	THR/PRO	138,4268	95.7+/-134.4	2,134,2067	109.0	98.0	102.0		1054	5.8	1.0	6	dbSNP_107	102	1171,7429	237.9+/-269.6	62,1047,3191	yes	missense	SIM1	NM_005068.2	38	64,1181,5258	TT,TG,GG		13.6163,3.1321,10.0646	possibly-damaging	352/767	100868779	1309,11697	2203	4300	6503	SO:0001583	missense	6492	exon9			AGGCTGGTTTGGA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1054C>A	6.37:g.100868779G>T	ENSP00000358210:p.Pro352Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	430	0.19688644688644688	5	0.01016260162601626	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	17.17	3.320485	0.60634	0.031321	0.136163	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.03772	3.81;3.81	5.8	5.8	0.92144	Single-minded, C-terminal (1);	0.208574	0.48767	D	0.000176	T	0.03827	0.0108	L	0.50333	1.59	0.09310	P	0.99999845931	B	0.21147	0.052	B	0.17098	0.017	T	0.35525	-0.9785	9	0.42905	T	0.14	.	20.0567	0.97653	0.0:0.0:1.0:0.0	rs3734354;rs52789631;rs56928625;rs3734354	352	P81133	SIM1_HUMAN	T	352	ENSP00000358210:P352T;ENSP00000262901:P352T	ENSP00000262901:P352T	P	-	1	0	SIM1	100975500	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.059000	0.71133	2.752000	0.94435	0.650000	0.86243	CCA	T|0.145;G|0.854;A|0.000	0.145	strong		0.537	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
ZNF512B	57473	hgsc.bcm.edu	37	20	62595169	62595169	+	Silent	SNP	A	A	G	rs817325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62595169A>G	ENST00000450537.1	-	9	1638	c.1578T>C	c.(1576-1578)ctT>ctC	p.L526L	ZNF512B_ENST00000369888.1_Silent_p.L526L|ZNF512B_ENST00000217130.3_Silent_p.L526L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	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)			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)					TGTGCTTCTTAAGCCCCACGA	0.652													G|||	2466	0.492412	0.7549	0.4294	5008	,	,		17627	0.0546		0.5696	False		,,,				2504	0.5542				p.L526L		Atlas-SNP	.											.	ZNF512B	72	.	0			c.T1578C						PASS	.	G		3231,1175	411.1+/-335.6	1200,831,172	88.0	88.0	88.0		1578	-0.2	1.0	20	dbSNP_86	88	4905,3695	524.6+/-380.6	1406,2093,801	no	coding-synonymous	ZNF512B	NM_020713.1		2606,2924,973	GG,GA,AA		42.9651,26.6682,37.4443		526/893	62595169	8136,4870	2203	4300	6503	SO:0001819	synonymous_variant	57473	exon9			CTTCTTAAGCCCC	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.1578T>C	20.37:g.62595169A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			A|0.423;G|0.577	0.577	strong		0.652	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
HLA-B	3106	hgsc.bcm.edu	37	6	31324064	31324064	+	Missense_Mutation	SNP	T	T	A	rs41541519|rs281864629	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324064T>A	ENST00000412585.2	-	3	527	c.499A>T	c.(499-501)Acc>Tcc	p.T167S		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	167	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						TTGCGCTGGGTGATCTGAGCC	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				T|||	342	0.0682907	0.0749	0.0576	5008	,	,		12488	0.12		0.0577	False		,,,				2504	0.0245				p.T167S		Atlas-SNP	.											.	HLA-B	54	.	0			c.A499T						PASS	.	T	SER/THR	229,4057		0,229,1914	29.0	20.0	23.0		499	-0.9	0.0	6	dbSNP_134	23	417,8017		3,411,3803	no	missense	HLA-B	NM_005514.6	58	3,640,5717	AA,AT,TT		4.9443,5.343,5.0786		167/363	31324064	646,12074	2143	4217	6360	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GCTGGGTGATCTG	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.499A>T	6.37:g.31324064T>A	ENSP00000399168:p.Thr167Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	209	60	0.287081	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	169	0.07738095238095238	36	0.07317073170731707	19	0.052486187845303865	71	0.12412587412587413	43	0.05672823218997362	N	5.999	0.368207	0.11352	0.05343	0.049443	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00940	5.52;5.52	3.18	-0.943	0.10395	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.380494	0.18332	U	0.144459	T	0.00580	0.0019	M	0.85859	2.78	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.003	T	0.34304	-0.9834	9	0.72032	D	0.01	.	4.6914	0.12783	0.2903:0.0971:0.0:0.6126	rs41541519	167;167	P30480;P01889	1B42_HUMAN;1B07_HUMAN	S	167;46;46;178	ENSP00000399168:T167S;ENSP00000405931:T178S	ENSP00000399168:T167S	T	-	1	0	HLA-B	31432043	0.900000	0.30661	0.000000	0.03702	0.000000	0.00434	1.078000	0.30754	-0.714000	0.04975	-2.763000	0.00121	ACC	T|0.939;A|0.061	0.061	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
RB1CC1	9821	hgsc.bcm.edu	37	8	53537316	53537316	+	Silent	SNP	A	A	G	rs1129660	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Silent_p.L1553L	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	138	0	0		WXS	Illumina HiSeq	Phase_I	150	57	0.38	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	
CYP2A6	1548	hgsc.bcm.edu	37	19	41352807	41352807	+	Silent	SNP	A	A	G	rs55805386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41352807A>G	ENST00000301141.5	-	5	824	c.804T>C	c.(802-804)atT>atC	p.I268I	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	268					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|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)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GAAAGGAGTCAATGAAGTCCC	0.582																																					p.I268I		Atlas-SNP	.											.	CYP2A6	69	.	0			c.T804C						PASS	.						119.0	96.0	104.0					19																	41352807		2203	4300	6503	SO:0001819	synonymous_variant	1548	exon5			GGAGTCAATGAAG	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.804T>C	19.37:g.41352807A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	255	32	0.12549	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Silent	SNP	ENST00000301141.5	37	CCDS12568.1																																																																																			A|0.947;G|0.053	0.053	strong		0.582	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
ZDHHC11	79844	hgsc.bcm.edu	37	5	833915	833915	+	Missense_Mutation	SNP	G	G	T	rs605088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:833915G>T	ENST00000283441.8	-	7	1291	c.908C>A	c.(907-909)gCt>gAt	p.A303D	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.A303D|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	303						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.A303D(10)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CAGGGCGCCAGCTCCTTGCTG	0.438																																					p.A303D		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,0,10	ZDHHC11	97	10	10	Substitution - Missense(10)	prostate(8)|liver(2)	c.C908A						scavenged	.						8.0	8.0	8.0					5																	833915		2154	4191	6345	SO:0001583	missense	79844	exon7			GCGCCAGCTCCTT	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.908C>A	5.37:g.833915G>T	ENSP00000283441:p.Ala303Asp	Somatic	294	127	0.431973		WXS	Illumina HiSeq	Phase_I	216	80	0.37037	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	515	0.2358058608058608	134	0.27235772357723576	83	0.2292817679558011	145	0.2534965034965035	153	0.20184696569920843	t	0.056	-1.237364	0.01493	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.32023	1.47;1.47	1.32	-2.64	0.06114	.	159.412000	0.01375	U	0.012736	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	0.24333	-1.0163	9	0.30854	T	0.27	.	0.5085	0.00591	0.2028:0.3259:0.2042:0.267	rs605088;rs4045358;rs59272565	303	Q9H8X9	ZDH11_HUMAN	D	303	ENSP00000397719:A303D;ENSP00000283441:A303D	ENSP00000283441:A303D	A	-	2	0	ZDHHC11	886915	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.877000	0.00717	-2.317000	0.00644	-1.448000	0.01049	GCT	G|0.500;T|0.500	0.500	strong		0.438	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
AK4	205	hgsc.bcm.edu	37	1	65690461	65690461	+	Silent	SNP	G	G	A	rs4915685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:65690461G>A	ENST00000327299.7	+	4	670	c.465G>A	c.(463-465)ccG>ccA	p.P155P	AK4_ENST00000470888.2_3'UTR|AK4_ENST00000395334.2_Silent_p.P155P|AK4_ENST00000546702.1_Silent_p.P103P|AK4_ENST00000545314.1_Silent_p.P155P	NM_013410.3	NP_037542.1			adenylate kinase 4											breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						CTGGTGAACCGTTAGTCCAGC	0.413													A|||	1853	0.370008	0.3298	0.3314	5008	,	,		20813	0.6726		0.1769	False		,,,				2504	0.3384				p.P155P		Atlas-SNP	.											.	AK4	22	.	0			c.G465A						PASS	.	A	,,	1379,3027	689.8+/-405.2	220,939,1044	134.0	130.0	131.0		465,465,465	-9.7	0.0	1	dbSNP_111	131	1801,6799	732.9+/-406.9	187,1427,2686	no	coding-synonymous,coding-synonymous,coding-synonymous	AK4	NM_001005353.2,NM_013410.3,NM_203464.2	,,	407,2366,3730	AA,AG,GG		20.9419,31.2982,24.4503	,,	155/224,155/224,155/224	65690461	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	205	exon5			TGAACCGTTAGTC	AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"""Adenylate kinases"""	363	protein-coding gene	gene with protein product		103030	"""adenylate kinase 3"", ""adenylate kinase 3-like 1"""	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.465G>A	1.37:g.65690461G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_203464		Silent	SNP	ENST00000327299.7	37	CCDS629.1																																																																																			G|0.726;A|0.274	0.274	strong		0.413	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_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						PASS	.	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	108	0	0		WXS	Illumina HiSeq	Phase_I	63	20	0.31746	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	
KIAA1522	57648	hgsc.bcm.edu	37	1	33231403	33231403	+	Silent	SNP	G	G	T	rs6702519	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:33231403G>T	ENST00000373480.1	+	1	136	c.33G>T	c.(31-33)gcG>gcT	p.A11A	KIAA1522_ENST00000401073.2_Intron|KIAA1522_ENST00000373481.3_Intron|KIAA1522_ENST00000294521.3_Silent_p.A11A	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	11										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)				GCCTCCCGGCGCTCCTAGGGC	0.637													G|||	708	0.141374	0.0113	0.1023	5008	,	,		13017	0.2262		0.1849	False		,,,				2504	0.2127				p.A11A		Atlas-SNP	.											KIAA1522_ENST00000373480,rectum,carcinoma,0,1	KIAA1522	68	1	0			c.G33T						PASS	.																																			SO:0001819	synonymous_variant	57648	exon1			CCCGGCGCTCCTA	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.33G>T	1.37:g.33231403G>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_001198972	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	37	CCDS55588.1																																																																																			G|0.855;T|0.145	0.145	strong		0.637	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
CHD9	80205	hgsc.bcm.edu	37	16	53326860	53326860	+	Silent	SNP	G	G	A	rs2287078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53326860G>A	ENST00000398510.3	+	28	5493	c.5406G>A	c.(5404-5406)caG>caA	p.Q1802Q	CHD9_ENST00000566029.1_Silent_p.Q1802Q|CHD9_ENST00000447540.1_Silent_p.Q1802Q|CHD9_ENST00000564845.1_Silent_p.Q1802Q			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1802					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q1802Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GACAAATTCAGCAGATACAAC	0.428													A|||	1497	0.298922	0.3729	0.1902	5008	,	,		16272	0.247		0.2962	False		,,,				2504	0.3323				p.Q1802Q		Atlas-SNP	.											CHD9,NS,carcinoma,0,1	CHD9	203	1	1	Substitution - coding silent(1)	stomach(1)	c.G5406A						PASS	.	A		1258,2540		201,856,842	106.0	98.0	100.0		5406	1.1	1.0	16	dbSNP_100	100	2575,5677		402,1771,1953	no	coding-synonymous	CHD9	NM_025134.4		603,2627,2795	AA,AG,GG		31.2046,33.1227,31.8091		1802/2882	53326860	3833,8217	1899	4126	6025	SO:0001819	synonymous_variant	80205	exon29			AATTCAGCAGATA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.5406G>A	16.37:g.53326860G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	128	54	0.421875	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																				G|0.692;A|0.308	0.308	strong		0.428	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
GABRR2	2570	hgsc.bcm.edu	37	6	89967498	89967498	+	Missense_Mutation	SNP	G	G	A	rs282129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:89967498G>A	ENST00000402938.3	-	9	1422	c.1289C>T	c.(1288-1290)aCg>aTg	p.T430M	GABRR2_ENST00000602399.1_Missense_Mutation_p.T455M	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	430					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	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)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	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)	ACGAAAACCCGTCTGGCCCTT	0.458													g|||	1263	0.252196	0.4561	0.1657	5008	,	,		19676	0.1389		0.2525	False		,,,				2504	0.1544				p.T430M		Atlas-SNP	.											.	GABRR2	41	.	0			c.C1289T						PASS	.	G	MET/THR	1877,2529	541.3+/-375.7	413,1051,739	93.0	82.0	86.0		1364	3.5	0.9	6	dbSNP_79	86	2397,6203	398.9+/-346.3	336,1725,2239	yes	missense	GABRR2	NM_002043.2	81	749,2776,2978	AA,AG,GG		27.8721,42.601,32.8618	benign	455/491	89967498	4274,8732	2203	4300	6503	SO:0001583	missense	2570	exon9			AAACCCGTCTGGC		CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4091	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 2"""	137162	"""gamma-aminobutyric acid (GABA) receptor, rho 2"""			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.1289C>T	6.37:g.89967498G>A	ENSP00000386029:p.Thr430Met	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	194	101	0.520619	NM_002043	A2BDE4|Q9H153	Missense_Mutation	SNP	ENST00000402938.3	37	CCDS5020.3	586	0.2683150183150183	231	0.4695121951219512	68	0.1878453038674033	88	0.15384615384615385	199	0.262532981530343	g	10.33	1.320004	0.23994	0.42601	0.278721	ENSG00000111886	ENST00000402938	.	.	.	5.92	3.47	0.39725	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.704828	0.15948	N	0.236871	T	0.03915	0.0110	N	0.00648	-1.295	0.53005	P	4.0000000000040004E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40194	-0.9576	7	.	.	.	.	8.9229	0.35623	0.8082:0.1265:0.0653:0.0	rs282129;rs52805113;rs56794643;rs282129	455	P28476	GBRR2_HUMAN	M	455	.	.	T	-	2	0	GABRR2	90024217	0.159000	0.22864	0.902000	0.35471	0.775000	0.43874	2.846000	0.48262	0.459000	0.27016	-0.295000	0.09555	ACG	G|0.693;T|0.005	.	strong		0.458	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3		
TRAPPC12	51112	hgsc.bcm.edu	37	2	3392295	3392295	+	Missense_Mutation	SNP	A	A	G	rs11686212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:3392295A>G	ENST00000324266.5	+	2	1096	c.901A>G	c.(901-903)Agc>Ggc	p.S301G	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.S301G	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	301			S -> G (in dbSNP:rs11686212). {ECO:0000269|Ref.2}.		vesicle-mediated transport (GO:0016192)												CCTGAGCATGAGCGAGATGGA	0.706													A|||	2343	0.467851	0.4175	0.3141	5008	,	,		12932	0.6081		0.4006	False		,,,				2504	0.5695				p.S301G		Atlas-SNP	.											TTC15,NS,carcinoma,0,2	.	.	2	0			c.A901G						PASS	.	A	GLY/SER	1819,2587		370,1079,754	37.0	32.0	33.0		901	5.1	1.0	2	dbSNP_120	33	3217,5383		614,1989,1697	yes	missense	TTC15	NM_016030.5	56	984,3068,2451	GG,GA,AA		37.407,41.2846,38.7206	probably-damaging	301/736	3392295	5036,7970	2203	4300	6503	SO:0001583	missense	51112	exon2			AGCATGAGCGAGA	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.901A>G	2.37:g.3392295A>G	ENSP00000324318:p.Ser301Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	90	29	0.322222	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	967	0.44276556776556775	199	0.40447154471544716	125	0.3453038674033149	348	0.6083916083916084	295	0.3891820580474934	A	28.1	4.889728	0.91889	0.412846	0.37407	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.59772	0.24;0.24	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.999999833179	D;D;D	0.71674	0.996;0.993;0.998	P;P;D	0.70487	0.787;0.777;0.969	T	0.52726	-0.8537	9	0.66056	D	0.02	.	14.4554	0.67413	1.0:0.0:0.0:0.0	rs11686212	284;301;301	E7ENL7;Q8WVT3;Q53S18	.;TPC12_HUMAN;.	G	301;284;301	ENSP00000371544:S301G;ENSP00000324318:S301G	ENSP00000303612:S284G	S	+	1	0	TTC15	3371302	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	8.568000	0.90741	2.248000	0.74166	0.459000	0.35465	AGC	A|0.595;G|0.405	0.405	strong		0.706	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
LTF	4057	hgsc.bcm.edu	37	3	46480958	46480958	+	Missense_Mutation	SNP	C	C	G	rs2073495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46480958C>G	ENST00000231751.4	-	15	2032	c.1737G>C	c.(1735-1737)gaG>gaC	p.E579D	LTF_ENST00000417439.1_Missense_Mutation_p.E577D|LTF_ENST00000493056.1_5'UTR|LTF_ENST00000426532.2_Missense_Mutation_p.E535D	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	579	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.		E -> D (in dbSNP:rs2073495). {ECO:0000269|PubMed:11702692, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:22900286, ECO:0000269|Ref.24, ECO:0000269|Ref.9}.		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)		TAGCCCATGCCTCATTGTTAT	0.542													C|||	1388	0.277157	0.059	0.3501	5008	,	,		21415	0.3661		0.3221	False		,,,				2504	0.3824				p.E579D		Atlas-SNP	.											LTF,NS,carcinoma,0,1	LTF	98	1	0			c.G1737C	GRCh37	CM051945	LTF	M	rs2073495	PASS	.	C	ASP/GLU,ASP/GLU	441,3965	212.5+/-232.4	17,407,1779	84.0	75.0	78.0		1605,1737	-10.3	0.0	3	dbSNP_96	78	2912,5688	454.0+/-363.4	513,1886,1901	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	45,45	530,2293,3680	GG,GC,CC		33.8605,10.0091,25.7804	benign,benign	535/667,579/711	46480958	3353,9653	2203	4300	6503	SO:0001583	missense	4057	exon15			CCATGCCTCATTG		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.1737G>C	3.37:g.46480958C>G	ENSP00000231751:p.Glu579Asp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	610	0.2793040293040293	33	0.06707317073170732	134	0.3701657458563536	206	0.36013986013986016	237	0.31266490765171506	C	6.870	0.529868	0.13127	0.100091	0.338605	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496	T;T;T;T	0.07216	3.21;3.21;3.21;3.21	5.16	-10.3	0.00346	.	0.579288	0.18664	N	0.134621	T	0.00012	0.0000	L	0.31120	0.905	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.003;0.005	T	0.34925	-0.9809	9	0.23302	T	0.38	.	5.8011	0.18414	0.0769:0.453:0.2327:0.2375	rs55765065	577;566;579	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	D	579;535;577;566	ENSP00000231751:E579D;ENSP00000405719:E535D;ENSP00000405546:E577D;ENSP00000397427:E566D	ENSP00000231751:E579D	E	-	3	2	LTF	46455962	0.000000	0.05858	0.000000	0.03702	0.223000	0.24884	-4.284000	0.00260	-3.002000	0.00275	-0.984000	0.02558	GAG	C|0.739;G|0.261	0.261	strong		0.542	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
PRKD3	23683	hgsc.bcm.edu	37	2	37518045	37518045	+	Silent	SNP	G	G	C	rs10177176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	113	62	0.548673	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	
ALOX12	239	hgsc.bcm.edu	37	17	6909838	6909838	+	Silent	SNP	A	A	G	rs2307214	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6909838A>G	ENST00000251535.6	+	11	1505	c.1452A>G	c.(1450-1452)caA>caG	p.Q484Q	AC027763.2_ENST00000399540.2_Intron|RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000573939.1_Intron	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	484	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|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 endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						TCTTCTACCAAAGGGATGACA	0.592													A|||	452	0.0902556	0.0061	0.3228	5008	,	,		15811	0.1161		0.0726	False		,,,				2504	0.0307				p.Q484Q		Atlas-SNP	.											.	ALOX12	49	.	0			c.A1452G						PASS	.	A		78,4328	68.7+/-106.4	1,76,2126	81.0	78.0	79.0		1452	-3.3	0.0	17	dbSNP_100	79	584,8016	156.0+/-209.9	15,554,3731	no	coding-synonymous	ALOX12	NM_000697.2		16,630,5857	GG,GA,AA		6.7907,1.7703,5.09		484/664	6909838	662,12344	2203	4300	6503	SO:0001819	synonymous_variant	239	exon11			CTACCAAAGGGAT	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1452A>G	17.37:g.6909838A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_000697	O95569|Q6ISF8|Q9UQM4	Silent	SNP	ENST00000251535.6	37	CCDS11084.1																																																																																			A|0.931;G|0.069	0.069	strong		0.592	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
MUC2	4583	hgsc.bcm.edu	37	11	1093272	1093272	+	Silent	SNP	A	A	C	rs56230143		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1093272A>C	ENST00000441003.2	+	30	5118	c.5091A>C	c.(5089-5091)acA>acC	p.T1697T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1664T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1664T(2)|p.T1697T(2)		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)	agaccccaacatcgacaccca	0.637																																					p.T1697T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	4	Substitution - coding silent(4)	kidney(2)|endometrium(2)	c.A5091C						scavenged	.						128.0	167.0	153.0					11																	1093272		1845	3351	5196	SO:0001819	synonymous_variant	4583	exon30			CCCAACATCGACA	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.5091A>C	11.37:g.1093272A>C		Somatic	22	7	0.318182		WXS	Illumina HiSeq	Phase_I	24	4	0.166667	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ANO8	57719	hgsc.bcm.edu	37	19	17435887	17435887	+	Silent	SNP	C	C	T	rs56286266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17435887C>T	ENST00000159087.4	-	17	3128	c.2970G>A	c.(2968-2970)tcG>tcA	p.S990S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	990					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)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						TGGCCCCTGACGAGAGGAATT	0.672													C|||	1233	0.246206	0.1293	0.2406	5008	,	,		15681	0.1429		0.34	False		,,,				2504	0.4182				p.S990S		Atlas-SNP	.											.	ANO8	67	.	0			c.G2970A						PASS	.	C		778,3628	302.7+/-287.5	73,632,1498	80.0	88.0	85.0		2970	-7.7	0.0	19	dbSNP_129	85	2754,5846	415.2+/-351.7	466,1822,2012	no	coding-synonymous	ANO8	NM_020959.2		539,2454,3510	TT,TC,CC		32.0233,17.6577,27.1567		990/1233	17435887	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	57719	exon17			CCCTGACGAGAGG	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.2970G>A	19.37:g.17435887C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	37	CCDS32949.1																																																																																			C|0.746;T|0.254	0.254	strong		0.672	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
GPR116	221395	hgsc.bcm.edu	37	6	46846043	46846043	+	Missense_Mutation	SNP	T	T	A	rs41273668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46846043T>A	ENST00000283296.7	-	10	1424	c.1136A>T	c.(1135-1137)aAg>aTg	p.K379M	GPR116_ENST00000362015.4_Missense_Mutation_p.K379M|GPR116_ENST00000456426.2_Intron|GPR116_ENST00000265417.7_Missense_Mutation_p.K379M	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	379	Ig-like 2.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GCACATCACCTTCATTTCTTC	0.348													T|||	36	0.0071885	0.0015	0.0173	5008	,	,		21041	0.0		0.0149	False		,,,				2504	0.0072				p.K379M	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.A1136T						PASS	.	T	MET/LYS,MET/LYS	39,4367	43.8+/-77.6	1,37,2165	155.0	140.0	145.0		1136,1136	3.4	0.3	6	dbSNP_127	145	277,8323	104.6+/-165.6	5,267,4028	yes	missense,missense	GPR116	NM_001098518.1,NM_015234.4	95,95	6,304,6193	AA,AT,TT		3.2209,0.8852,2.4296	probably-damaging,probably-damaging	379/1347,379/1347	46846043	316,12690	2203	4300	6503	SO:0001583	missense	221395	exon10			ATCACCTTCATTT	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1136A>T	6.37:g.46846043T>A	ENSP00000283296:p.Lys379Met	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	217	114	0.525346	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	21	0.009615384615384616	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	13.85	2.358887	0.41801	0.008852	0.032209	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000265417	T;T;T	0.27720	1.65;2.03;1.65	5.8	3.37	0.38596	Immunoglobulin-like (1);	0.265874	0.32430	N	0.006104	T	0.24084	0.0583	M	0.62723	1.935	0.50813	D	0.999898	D;D;D	0.59357	0.985;0.985;0.985	P;P;P	0.52710	0.707;0.707;0.707	T	0.06716	-1.0811	10	0.72032	D	0.01	-7.7173	4.8444	0.13507	0.1643:0.0869:0.0:0.7488	rs41273668	379;379;379	E9PBS6;A8K0D8;Q8IZF2	.;.;GP116_HUMAN	M	379	ENSP00000283296:K379M;ENSP00000354563:K379M;ENSP00000265417:K379M	ENSP00000265417:K379M	K	-	2	0	GPR116	46954002	0.025000	0.19082	0.341000	0.25589	0.222000	0.24845	0.489000	0.22387	0.443000	0.26582	0.528000	0.53228	AAG	T|0.980;A|0.020	0.020	strong		0.348	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
ALG1	56052	hgsc.bcm.edu	37	16	5123201	5123201	+	Missense_Mutation	SNP	A	A	C	rs113219939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5123201A>C	ENST00000262374.5	+	3	365	c.334A>C	c.(334-336)Atg>Ctg	p.M112L	ALG1_ENST00000588623.1_Start_Codon_SNP_p.M1L|ALG1_ENST00000544428.1_Start_Codon_SNP_p.M1L	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	112					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)				ACTTCAGGCTATGTACTTGCT	0.512													A|||	66	0.0131789	0.0492	0.0014	5008	,	,		19810	0.0		0.0	False		,,,				2504	0.0				p.M112L		Atlas-SNP	.											.	ALG1	35	.	0			c.A334C						PASS	.	A	LEU/MET	169,4225	112.5+/-150.6	4,161,2032	251.0	230.0	237.0		334	-2.3	0.0	16	dbSNP_132	237	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	15	4,162,6331	CC,CA,AA		0.0116,3.8462,1.3083	benign	112/465	5123201	170,12824	2197	4300	6497	SO:0001583	missense	56052	exon3			CAGGCTATGTACT	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.334A>C	16.37:g.5123201A>C	ENSP00000262374:p.Met112Leu	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	220	96	0.436364	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	A	0.289	-0.981205	0.02197	0.038462	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.80994	-1.44;-0.88	4.82	-2.31	0.06765	.	0.580414	0.18457	N	0.140653	T	0.08626	0.0214	N	0.00221	-1.82	0.45046	D	0.99806	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44236	-0.9341	10	0.02654	T	1	-10.1101	0.992	0.01459	0.1831:0.3173:0.2475:0.2521	.	1;112	B4DP08;Q9BT22	.;ALG1_HUMAN	L	112;1	ENSP00000262374:M112L;ENSP00000440019:M1L	ENSP00000262374:M112L	M	+	1	0	ALG1	5063202	0.004000	0.15560	0.022000	0.16811	0.284000	0.27059	-0.033000	0.12246	-0.059000	0.13154	-0.337000	0.08149	ATG	A|0.984;C|0.016	0.016	strong		0.512	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
ABCC6	368	hgsc.bcm.edu	37	16	16291983	16291983	+	Silent	SNP	A	A	G	rs9930886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:16291983A>G	ENST00000205557.7	-	10	1262	c.1233T>C	c.(1231-1233)aaT>aaC	p.N411N	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	411	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		N -> K (in PXE; autosomal dominant; dbSNP:rs9930886). {ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:15459974}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CGGACACCAGATTGACCACAT	0.627													G|||	1416	0.282748	0.2526	0.3127	5008	,	,		12770	0.3214		0.326	False		,,,				2504	0.2178				p.N411N		Atlas-SNP	.											.	ABCC6	110	.	0			c.T1233C	GRCh37	CM014481	ABCC6	M	rs9930886	PASS	.	G		1119,3275	700.3+/-406.6	134,851,1212	63.0	44.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1233	2.3	1.0	16	dbSNP_119	51	2952,5648	649.3+/-400.6	502,1948,1850	no	coding-synonymous	ABCC6	NM_001171.5		636,2799,3062	GG,GA,AA		34.3256,25.4665,31.3298		411/1504	16291983	4071,8923	2197	4300	6497	SO:0001819	synonymous_variant	368	exon10			CACCAGATTGACC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1233T>C	16.37:g.16291983A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	37	CCDS10568.1																																																																																			A|0.707;G|0.293	0.293	strong		0.627	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
CHD9	80205	hgsc.bcm.edu	37	16	53358439	53358439	+	Missense_Mutation	SNP	A	A	G	rs3743771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53358439A>G	ENST00000398510.3	+	38	8413	c.8326A>G	c.(8326-8328)Aca>Gca	p.T2776A	CHD9_ENST00000566029.1_Missense_Mutation_p.T2760A|CHD9_ENST00000447540.1_Missense_Mutation_p.T2761A|CHD9_ENST00000564845.1_Missense_Mutation_p.T2760A			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2776				T -> A (in Ref. 1; AAQ24287 and 6; BAA20767). {ECO:0000305}.	cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TTCTCCTTCCACATCCTCTAC	0.428													A|||	1055	0.210663	0.1309	0.1571	5008	,	,		19386	0.2341		0.2704	False		,,,				2504	0.271				p.T2760A		Atlas-SNP	.											CHD9,NS,carcinoma,0,1	CHD9	203	1	0			c.A8278G						PASS	.	A	ALA/THR	581,3251		39,503,1374	50.0	49.0	49.0		8278	3.2	0.8	16	dbSNP_107	49	2358,5918		327,1704,2107	yes	missense	CHD9	NM_025134.4	58	366,2207,3481	GG,GA,AA		28.492,15.1618,24.2732	benign	2760/2882	53358439	2939,9169	1916	4138	6054	SO:0001583	missense	80205	exon39			CCTTCCACATCCT	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8326A>G	16.37:g.53358439A>G	ENSP00000381522:p.Thr2776Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		494	0.2261904761904762	79	0.16056910569105692	70	0.19337016574585636	136	0.23776223776223776	209	0.2757255936675462	A	1.152	-0.646382	0.03531	0.151618	0.28492	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.85484	-1.99	5.47	3.22	0.36961	.	0.110120	0.40064	N	0.001198	T	0.00012	0.0000	L	0.34521	1.04	0.24658	P	0.99348232	B;B;B;B	0.11235	0.001;0.004;0.002;0.004	B;B;B;B	0.13407	0.003;0.009;0.004;0.009	T	0.04178	-1.0971	9	0.05436	T	0.98	-7.4837	9.8557	0.41084	0.8604:0.0:0.1396:0.0	rs3743771;rs17395331;rs52814680;rs56719806;rs3743771	842;2761;2776;2760	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	A	2761;2760;842	ENSP00000396345:T2761A	ENSP00000381522:T2760A	T	+	1	0	CHD9	51915940	0.970000	0.33590	0.847000	0.33407	0.734000	0.41952	2.344000	0.44010	0.457000	0.26962	0.533000	0.62120	ACA	A|0.774;G|0.225	0.225	strong		0.428	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
PIBF1	10464	hgsc.bcm.edu	37	13	73369642	73369642	+	Missense_Mutation	SNP	A	A	G	rs1372000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:73369642A>G	ENST00000326291.6	+	4	837	c.499A>G	c.(499-501)Att>Gtt	p.I167V		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	167			I -> V (in dbSNP:rs1372000).			centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		AGAGCAATATATTAAATTAAA	0.328													A|||	1677	0.334864	0.5802	0.183	5008	,	,		15815	0.3075		0.2237	False		,,,				2504	0.2536				p.I167V		Atlas-SNP	.											.	PIBF1	65	.	0			c.A499G						PASS	.	A	VAL/ILE	2327,2079	598.1+/-389.0	604,1119,480	68.0	72.0	71.0		499	-1.8	0.2	13	dbSNP_88	71	1981,6619	344.5+/-325.3	243,1495,2562	yes	missense	PIBF1	NM_006346.2	29	847,2614,3042	GG,GA,AA		23.0349,47.1857,33.1232	benign	167/758	73369642	4308,8698	2203	4300	6503	SO:0001583	missense	10464	exon4			CAATATATTAAAT	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"""progesterone-induced blocking factor 1"""	607532	"""chromosome 13 open reading frame 24"""	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.499A>G	13.37:g.73369642A>G	ENSP00000317144:p.Ile167Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	69	0.683168	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	37	CCDS31991.1	688	0.315018315018315	271	0.5508130081300813	71	0.19613259668508287	192	0.3356643356643357	154	0.20316622691292877	A	0.345	-0.947992	0.02304	0.528143	0.230349	ENSG00000083535	ENST00000326291;ENST00000538949	T	0.06142	3.34	5.71	-1.77	0.07982	.	0.834519	0.11625	N	0.545419	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	0.23404	-1.0189	9	0.31617	T	0.26	1.2122	6.2837	0.21021	0.3386:0.2597:0.4017:0.0	rs1372000;rs52797084;rs59823248;rs1372000	167	Q8WXW3	PIBF1_HUMAN	V	167	ENSP00000317144:I167V	ENSP00000317144:I167V	I	+	1	0	PIBF1	72267643	0.087000	0.21565	0.215000	0.23724	0.263000	0.26337	-0.107000	0.10873	-0.257000	0.09459	-0.313000	0.08912	ATT	G|0.329;N|0.000	0.329	strong		0.328	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	
FHAD1	114827	hgsc.bcm.edu	37	1	15687059	15687059	+	Missense_Mutation	SNP	A	A	G	rs4661330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15687059A>G	ENST00000375998.4	+	20	2756	c.2756A>G	c.(2755-2757)gAa>gGa	p.E919G	FHAD1_ENST00000314740.8_Missense_Mutation_p.E172G|FHAD1_ENST00000417793.1_Missense_Mutation_p.E883G|FHAD1_ENST00000375999.3_Missense_Mutation_p.E919G|FHAD1_ENST00000471347.1_3'UTR|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	81	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	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	
PPP1R18	170954	hgsc.bcm.edu	37	6	30647035	30647035	+	Missense_Mutation	SNP	G	G	T	rs115169407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30647035G>T	ENST00000274853.3	-	2	3619	c.1743C>A	c.(1741-1743)gaC>gaA	p.D581E	PPP1R18_ENST00000399199.3_Missense_Mutation_p.D581E|PPP1R18_ENST00000488324.1_5'UTR	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	581						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCTCTTCGTCGTCGGGTTGGG	0.667													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		11756	0.0		0.005	False		,,,				2504	0.0				p.D581E		Atlas-SNP	.											KIAA1949,NS,carcinoma,0,1	.	.	1	0			c.C1743A						PASS	.	G	GLU/ASP,GLU/ASP	3,2425		0,3,1211	42.0	46.0	45.0		1743,1743	0.7	1.0	6	dbSNP_132	45	26,4986		0,26,2480	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	45,45	0,29,3691	TT,TG,GG		0.5188,0.1236,0.3898	benign,benign	581/614,581/614	30647035	29,7411	1214	2506	3720	SO:0001583	missense	170954	exon3			TTCGTCGTCGGGT	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1743C>A	6.37:g.30647035G>T	ENSP00000274853:p.Asp581Glu	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	15.40	2.822116	0.50739	0.001236	0.005188	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.25579	1.79;1.79	5.08	0.679	0.17975	.	0.378241	0.23744	N	0.044992	T	0.04998	0.0134	N	0.17474	0.49	0.23076	N	0.998333	P	0.48407	0.91	P	0.45660	0.489	T	0.18366	-1.0339	10	0.34782	T	0.22	-7.4927	0.6512	0.00827	0.3521:0.1647:0.3139:0.1693	.	581	Q6NYC8	PPR18_HUMAN	E	581	ENSP00000274853:D581E;ENSP00000382150:D581E	ENSP00000274853:D581E	D	-	3	2	KIAA1949	30755014	0.253000	0.23982	0.953000	0.39169	0.881000	0.50899	-0.738000	0.04871	0.560000	0.29169	0.650000	0.86243	GAC	G|0.997;T|0.003	0.003	strong		0.667	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
SCRN2	90507	hgsc.bcm.edu	37	17	45917703	45917703	+	Silent	SNP	C	C	T	rs11652952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	97	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	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	
ZNF696	79943	hgsc.bcm.edu	37	8	144378184	144378184	+	Silent	SNP	C	C	G	rs2235115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	31	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	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	
LPA	4018	hgsc.bcm.edu	37	6	161006077	161006077	+	Splice_Site	SNP	C	C	T	rs41272114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:161006077C>T	ENST00000316300.5	-	26	4334		c.e26+1		LPA_ENST00000447678.1_Splice_Site			P08519	APOA_HUMAN	lipoprotein, Lp(a)						blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GATAGACATACGCATTTGGAT	0.428													C|||	117	0.0233626	0.0023	0.0778	5008	,	,		20107	0.0		0.0308	False		,,,				2504	0.0297				.		Atlas-SNP	.											LPA,colon,carcinoma,-1,1	LPA	237	1	0			c.4289+1G>A	GRCh37	CS992248	LPA	S	rs41272114	scavenged	.	C		31,4205		0,31,2087	184.0	179.0	181.0			2.6	1.0	6	dbSNP_127	181	295,8241		8,279,3981	yes	splice-5	LPA	NM_005577.2		8,310,6068	TT,TC,CC		3.456,0.7318,2.5525			161006077	326,12446	2118	4268	6386	SO:0001630	splice_region_variant	4018	exon28			GACATACGCATTT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4289+1G>A	6.37:g.161006077C>T		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_005577	Q5VTD7|Q9UD88	Splice_Site	SNP	ENST00000316300.5	37	CCDS43523.1	40	0.018315018315018316	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	21	0.027704485488126648	C	6.212	0.407180	0.11754	0.007318	0.03456	ENSG00000198670	ENST00000316300;ENST00000447678	.	.	.	2.56	2.56	0.30785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6141	0.33820	0.0:1.0:0.0:0.0	rs41272114	.	.	.	.	-1	.	.	.	-	.	.	LPA	160926067	1.000000	0.71417	0.971000	0.41717	0.044000	0.14063	2.676000	0.46883	1.415000	0.47037	0.436000	0.28706	.	C|0.977;T|0.023	0.023	strong		0.428	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	Intron
SYNE2	23224	hgsc.bcm.edu	37	14	64637147	64637147	+	Silent	SNP	C	C	A	rs7161192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64637147C>A	ENST00000344113.4	+	94	17414	c.17202C>A	c.(17200-17202)ctC>ctA	p.L5734L	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L2368L|SYNE2_ENST00000357395.3_Silent_p.L2119L|SYNE2_ENST00000394768.2_Silent_p.L2119L|SYNE2_ENST00000554584.1_Intron|SYNE2_ENST00000358025.3_Silent_p.L5734L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5734					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTTCAGCCTCTACCAAACCA	0.498													C|||	1832	0.365815	0.3464	0.3055	5008	,	,		20635	0.5526		0.335	False		,,,				2504	0.274				p.L5734L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C17202A						PASS	.	C	,	1625,2781	499.1+/-364.3	318,989,896	77.0	54.0	62.0		17202,17202	3.6	0.7	14	dbSNP_116	62	2795,5805	440.8+/-359.6	455,1885,1960	yes	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	773,2874,2856	AA,AC,CC		32.5,36.8815,33.9843	,	5734/6886,5734/6908	64637147	4420,8586	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon94			CAGCCTCTACCAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17202C>A	14.37:g.64637147C>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.628;A|0.372	0.372	strong		0.498	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
COBLL1	22837	hgsc.bcm.edu	37	2	165551201	165551201	+	Missense_Mutation	SNP	T	T	C	rs7607980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165551201T>C	ENST00000392717.2	-	13	2933	c.2929A>G	c.(2929-2931)Aat>Gat	p.N977D	COBLL1_ENST00000194871.6_Missense_Mutation_p.N1006D|COBLL1_ENST00000409184.3_Missense_Mutation_p.N939D|COBLL1_ENST00000342193.4_Missense_Mutation_p.N939D|COBLL1_ENST00000375458.2_Missense_Mutation_p.N901D			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	977						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GCCTCTTTATTTGTCAGTTCT	0.463													T|||	538	0.107428	0.1861	0.0821	5008	,	,		17891	0.001		0.1541	False		,,,				2504	0.0808				p.N939D		Atlas-SNP	.											.	COBLL1	122	.	0			c.A2815G						PASS	.	T	ASP/ASN	687,3719	285.5+/-278.2	58,571,1574	51.0	52.0	52.0		2815	-2.7	0.0	2	dbSNP_116	52	1074,7526	222.6+/-259.6	72,930,3298	yes	missense	COBLL1	NM_014900.3	23	130,1501,4872	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	12.4884,15.5924,13.5399	benign	939/1167	165551201	1761,11245	2203	4300	6503	SO:0001583	missense	22837	exon12			CTTTATTTGTCAG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2929A>G	2.37:g.165551201T>C	ENSP00000376478:p.Asn977Asp	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		249	0.11401098901098901	102	0.2073170731707317	34	0.09392265193370165	0	0.0	113	0.14907651715039577	T	5.776	0.327468	0.10956	0.155924	0.124884	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.49	-2.65	0.06095	.	0.747690	0.12754	N	0.441935	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P;P	0.43352	0.704;0.804	B;B	0.39840	0.165;0.311	T	0.26018	-1.0115	8	0.12766	T	0.61	0.0091	6.0314	0.19683	0.097:0.0642:0.4336:0.4052	rs7607980;rs52821863;rs59793124;rs7607980	977;939	Q53SF7;Q53SF7-2	COBL1_HUMAN;.	D	901;939;939;977;1006	.	ENSP00000194871:N1006D	N	-	1	0	COBLL1	165259447	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.534000	0.23098	-0.224000	0.09928	0.533000	0.62120	AAT	T|0.872;C|0.128	0.128	strong		0.463	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
DZIP1L	199221	hgsc.bcm.edu	37	3	137786442	137786442	+	Missense_Mutation	SNP	T	T	C	rs442800	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137786442T>C	ENST00000327532.2	-	14	2295	c.1933A>G	c.(1933-1935)Aag>Gag	p.K645E	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	645			K -> E (in dbSNP:rs442800).		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CAGTCATCCTTGGGCCGGGGC	0.627													C|||	2770	0.553115	0.2579	0.6902	5008	,	,		16083	0.6141		0.6928	False		,,,				2504	0.6483				p.K645E		Atlas-SNP	.											.	DZIP1L	88	.	0			c.A1933G						PASS	.	C	GLU/LYS	1583,2823	667.4+/-401.8	276,1031,896	56.0	55.0	56.0		1933	1.6	0.0	3	dbSNP_80	56	6134,2466	406.3+/-348.8	2184,1766,350	yes	missense	DZIP1L	NM_173543.2	56	2460,2797,1246	CC,CT,TT		28.6744,35.9283,40.6658	benign	645/768	137786442	7717,5289	2203	4300	6503	SO:0001583	missense	199221	exon14			CATCCTTGGGCCG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1933A>G	3.37:g.137786442T>C	ENSP00000332148:p.Lys645Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1269|1269	0.5810439560439561|0.5810439560439561	152|152	0.3089430894308943|0.3089430894308943	236|236	0.6519337016574586|0.6519337016574586	361|361	0.6311188811188811|0.6311188811188811	520|520	0.6860158311345647|0.6860158311345647	C|C	0.246|0.246	-1.010063|-1.010063	0.02095|0.02095	0.359283|0.359283	0.713256|0.713256	ENSG00000158163|ENSG00000158163	ENST00000327532|ENST00000486487	T|.	0.42513|.	0.97|.	4.45|4.45	1.64|1.64	0.23874|0.23874	.|.	1.038400|.	0.07592|.	N|.	0.922141|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00823|0.00823	-1.155|-1.155	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.30707|0.30707	-0.9969|-0.9969	9|4	0.21014|.	T|.	0.42|.	-4.5815|-4.5815	5.7096|5.7096	0.17927|0.17927	0.0:0.5007:0.3216:0.1777|0.0:0.5007:0.3216:0.1777	rs442800;rs52799594;rs57276654;rs442800|rs442800;rs52799594;rs57276654;rs442800	645|.	Q8IYY4|.	DZI1L_HUMAN|.	E|R	645|14	ENSP00000332148:K645E|.	ENSP00000332148:K645E|.	K|Q	-|-	1|2	0|0	DZIP1L|DZIP1L	139269132|139269132	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.239000|-0.239000	0.08965|0.08965	-0.081000|-0.081000	0.12662|0.12662	-0.215000|-0.215000	0.12644|0.12644	AAG|CAA	C|0.571;N|0.001	0.571	strong		0.627	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
UEVLD	55293	hgsc.bcm.edu	37	11	18555949	18555949	+	Silent	SNP	T	T	C	rs55999230	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18555949T>C	ENST00000396197.3	-	11	1204	c.1176A>G	c.(1174-1176)ctA>ctG	p.L392L	UEVLD_ENST00000320750.6_Intron|UEVLD_ENST00000535484.1_Intron|UEVLD_ENST00000379387.4_Silent_p.L370L|UEVLD_ENST00000543987.1_Intron|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000540666.1_5'UTR	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CAGCTACTGATAGTCCAACAG	0.348													T|||	1262	0.251997	0.0469	0.2363	5008	,	,		17841	0.4415		0.1958	False		,,,				2504	0.4029				p.L392L		Atlas-SNP	.											.	UEVLD	58	.	0			c.A1176G						PASS	.	T	,	256,3444		7,242,1601	116.0	106.0	109.0		1176,	-3.1	1.0	11	dbSNP_129	109	1273,6923		117,1039,2942	no	coding-synonymous,intron	UEVLD	NM_001040697.1,NM_018314.3	,	124,1281,4543	CC,CT,TT		15.532,6.9189,12.8531	,	392/472,	18555949	1529,10367	1850	4098	5948	SO:0001819	synonymous_variant	55293	exon11			TACTGATAGTCCA	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1176A>G	11.37:g.18555949T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_001040697		Silent	SNP	ENST00000396197.3	37	CCDS41624.1																																																																																			T|0.793;C|0.207	0.207	strong		0.348	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
FLG	2312	hgsc.bcm.edu	37	1	152276149	152276149	+	Missense_Mutation	SNP	C	C	T	rs77422831	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276149C>T	ENST00000368799.1	-	3	11248	c.11213G>A	c.(11212-11214)cGc>cAc	p.R3738H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3738	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)			CTGCTCGTGGCGGGATCCTTG	0.607									Ichthyosis				C|||	1437	0.286941	0.0113	0.3919	5008	,	,		20123	0.5804		0.1421	False		,,,				2504	0.4315				p.R3738H		Atlas-SNP	.											.	FLG	900	.	0			c.G11213A						PASS	.	C	HIS/ARG	163,4243	109.1+/-147.4	2,159,2042	235.0	236.0	236.0		11213	-2.2	0.0	1	dbSNP_131	236	1240,7360	249.0+/-276.5	97,1046,3157	no	missense	FLG	NM_002016.1	29	99,1205,5199	TT,TC,CC		14.4186,3.6995,10.7873	possibly-damaging	3738/4062	152276149	1403,11603	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCGTGGCGGGATC	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.11213G>A	1.37:g.152276149C>T	ENSP00000357789:p.Arg3738His	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	221	134	0.606335	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	568	0.2600732600732601	10	0.02032520325203252	117	0.32320441988950277	330	0.5769230769230769	111	0.14643799472295516	C	11.18	1.563264	0.27915	0.036995	0.144186	ENSG00000143631	ENST00000368799	T	0.01705	4.68	3.5	-2.2	0.06994	.	.	.	.	.	T	0.00210	0.0006	N	0.02751	-0.505	0.80722	P	0.0	P	0.41475	0.751	B	0.25987	0.065	T	0.42068	-0.9473	8	0.30854	T	0.27	.	4.1707	0.10327	0.0:0.343:0.2091:0.448	rs3126080	3738	P20930	FILA_HUMAN	H	3738	ENSP00000357789:R3738H	ENSP00000357789:R3738H	R	-	2	0	FLG	150542773	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.253000	0.01184	-0.570000	0.06022	-0.267000	0.10333	CGC	C|0.841;T|0.159	0.159	strong		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
RYR1	6261	hgsc.bcm.edu	37	19	38956803	38956803	+	Silent	SNP	G	G	A	rs2228069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	0	0		WXS	Illumina HiSeq	Phase_I	71	69	0.971831	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		
PEBP4	157310	hgsc.bcm.edu	37	8	22675196	22675196	+	Missense_Mutation	SNP	T	T	C	rs34057411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22675196T>C	ENST00000256404.6	-	4	402	c.311A>G	c.(310-312)gAa>gGa	p.E104G	PEBP4_ENST00000521284.1_5'UTR	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	104						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)		CTGTCTGGGTTCTGCTCTGCT	0.488													T|||	112	0.0223642	0.0227	0.0086	5008	,	,		21138	0.0		0.0338	False		,,,				2504	0.0429				p.E104G		Atlas-SNP	.											.	PEBP4	23	.	0			c.A311G						PASS	.	T	GLY/GLU	71,3845		1,69,1888	125.0	126.0	126.0		311	0.0	0.0	8	dbSNP_126	126	256,8068		0,256,3906	yes	missense	PEBP4	NM_144962.2	98	1,325,5794	CC,CT,TT		3.0754,1.8131,2.6716	benign	104/228	22675196	327,11913	1958	4162	6120	SO:0001583	missense	157310	exon4			CTGGGTTCTGCTC	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.311A>G	8.37:g.22675196T>C	ENSP00000256404:p.Glu104Gly	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	205	101	0.492683	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	39	0.017857142857142856	11	0.022357723577235773	3	0.008287292817679558	0	0.0	25	0.032981530343007916	T	12.17	1.856285	0.32791	0.018131	0.030754	ENSG00000134020	ENST00000256404	T	0.42513	0.97	5.09	0.0128	0.14093	Phosphatidylethanolamine-binding, conserved site (1);	1.451270	0.04472	N	0.376265	T	0.11410	0.0278	N	0.25286	0.73	0.09310	N	1	B	0.20780	0.048	B	0.22386	0.039	T	0.24476	-1.0159	10	0.54805	T	0.06	0.0532	5.4725	0.16678	0.2316:0.0:0.1919:0.5766	rs34057411	104	Q96S96	PEBP4_HUMAN	G	104	ENSP00000256404:E104G	ENSP00000256404:E104G	E	-	2	0	PEBP4	22731141	0.010000	0.17322	0.000000	0.03702	0.023000	0.10783	1.880000	0.39628	0.071000	0.16664	0.533000	0.62120	GAA	T|0.978;C|0.022	0.022	strong		0.488	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
TMEM68	137695	hgsc.bcm.edu	37	8	56675384	56675384	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:56675384C>T	ENST00000434581.2	-	3	334	c.135G>A	c.(133-135)ttG>ttA	p.L45L	TMEM68_ENST00000521229.1_Silent_p.L45L|TMEM68_ENST00000519784.1_Intron|TMEM68_ENST00000334667.2_Silent_p.L45L|TMEM68_ENST00000522576.1_Silent_p.L45L|TMEM68_ENST00000523073.1_Intron			Q96MH6	TMM68_HUMAN	transmembrane protein 68	45						integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6			Epithelial(17;0.000361)|all cancers(17;0.00326)			TAAAAACCCACAAGAGATAGT	0.333																																					p.L45L		Atlas-SNP	.											TMEM68,NS,carcinoma,+2,1	TMEM68	25	1	0			c.G135A						scavenged	.						70.0	69.0	69.0					8																	56675384		2203	4300	6503	SO:0001819	synonymous_variant	137695	exon3			AACCCACAAGAGA	AK056932	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	8q12.1	2011-12-12			ENSG00000167904	ENSG00000167904			26510	protein-coding gene	gene with protein product						12477932	Standard	XM_005251150		Approved	FLJ32370	uc003xsh.1	Q96MH6	OTTHUMG00000164293	ENST00000434581.2:c.135G>A	8.37:g.56675384C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_152417	Q658X6|Q8WUD2	Silent	SNP	ENST00000434581.2	37																																																																																				.	.	none		0.333	TMEM68-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378137.1	NM_152417	
VGLL2	245806	hgsc.bcm.edu	37	6	117591755	117591755	+	Silent	SNP	T	T	C	rs13194610	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	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	
OR10R2	343406	hgsc.bcm.edu	37	1	158450314	158450314	+	Missense_Mutation	SNP	A	A	G	rs6679056	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158450314A>G	ENST00000368152.1	+	1	647	c.647A>G	c.(646-648)gAa>gGa	p.E216G	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	216			E -> G (in dbSNP:rs6679056).			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(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					GATGTTAACGAATTTGTGATA	0.403													A|||	2486	0.496406	0.4781	0.4424	5008	,	,		23048	0.5675		0.5577	False		,,,				2504	0.4233				p.E216G		Atlas-SNP	.											OR10R2,colon,carcinoma,+1,1	OR10R2	81	1	0			c.A647G						PASS	.	A	GLY/GLU	2124,2282	577.1+/-384.4	498,1128,577	158.0	147.0	151.0		647	4.4	0.1	1	dbSNP_116	151	4582,4018	596.6+/-393.6	1248,2086,966	yes	missense	OR10R2	NM_001004472.1	98	1746,3214,1543	GG,GA,AA		46.7209,48.207,48.4392	probably-damaging	216/336	158450314	6706,6300	2203	4300	6503	SO:0001583	missense	343406	exon1			TTAACGAATTTGT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.647A>G	1.37:g.158450314A>G	ENSP00000357134:p.Glu216Gly	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	246	86	0.349593	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	1191	0.5453296703296703	246	0.5	162	0.44751381215469616	349	0.6101398601398601	434	0.5725593667546174	a	10.57	1.387362	0.25031	0.48207	0.532791	ENSG00000198965	ENST00000368152	T	0.00258	8.41	4.37	4.37	0.52481	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	M	0.73962	2.25	0.58432	P	4.000000000004E-6	B	0.20052	0.041	B	0.25405	0.06	T	0.23261	-1.0193	8	0.56958	D	0.05	.	8.3167	0.32104	0.8235:0.0:0.0:0.1765	rs6679056;rs17629469;rs61345997;rs6679056	216	Q8NGX6	O10R2_HUMAN	G	216	ENSP00000357134:E216G	ENSP00000357134:E216G	E	+	2	0	OR10R2	156716938	0.008000	0.16893	0.124000	0.21820	0.888000	0.51559	1.838000	0.39211	1.801000	0.52704	0.533000	0.62120	GAA	A|0.467;G|0.533	0.533	strong		0.403	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
ZNF695	57116	hgsc.bcm.edu	37	1	247151557	247151557	+	Splice_Site	SNP	A	A	G	rs2642992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247151557A>G	ENST00000339986.7	-	4	407	c.260T>C	c.(259-261)gTt>gCt	p.V87A	ZNF695_ENST00000498046.2_5'UTR|ZNF695_ENST00000487338.2_Splice_Site_p.V87A	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	87	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> A (in dbSNP:rs2642992). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.V87A(1)		endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AGAAGACAAAACTGGAAAAAA	0.328													G|||	3133	0.625599	0.2882	0.7392	5008	,	,		19389	0.9712		0.6412	False		,,,				2504	0.6288				p.V87A		Atlas-SNP	.											ZNF695,NS,carcinoma,0,1	ZNF695	55	1	1	Substitution - Missense(1)	prostate(1)	c.T260C						PASS	.	G	ALA/VAL,ALA/VAL	1212,2428		209,794,817	45.0	43.0	43.0		260,260	0.5	0.0	1	dbSNP_100	43	5264,2898		1711,1842,528	yes	missense-near-splice,missense-near-splice	ZNF695	NM_001204221.1,NM_020394.4	64,64	1920,2636,1345	GG,GA,AA		35.506,33.2967,45.1279	benign,benign	87/173,87/516	247151557	6476,5326	1820	4081	5901	SO:0001630	splice_region_variant	57116	exon4			GACAAAACTGGAA		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.260-1T>C	1.37:g.247151557A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	1436	0.6575091575091575	139	0.28252032520325204	256	0.7071823204419889	559	0.9772727272727273	482	0.6358839050131926	G	0.415	-0.911175	0.02434	0.332967	0.64494	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.06449	5.77;3.3	0.459	0.459	0.16678	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	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	0.13072	-1.0523	8	0.08599	T	0.76	.	3.8938	0.09130	0.5822:0.0:0.4178:0.0	rs2642992;rs17236521;rs52826933;rs2642992	87;75;87	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	A	87	ENSP00000429736:V87A;ENSP00000341236:V87A	ENSP00000428213:V75A	V	-	2	0	ZNF695	245218180	0.004000	0.15560	0.033000	0.17914	0.356000	0.29392	0.072000	0.14617	-0.405000	0.07599	-1.063000	0.02288	GTT	A|0.368;G|0.632	0.632	strong		0.328	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195505774	195505774	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195505774G>T	ENST00000463781.3	-	2	13136	c.12677C>A	c.(12676-12678)cCt>cAt	p.P4226H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4226H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	983					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4226H(1)		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)		GCTGGTGACAGGAAGAGGGGT	0.587																																					p.P4226H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C12677A						scavenged	.						35.0	35.0	35.0					3																	195505774		2091	4190	6281	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.12677C>A	3.37:g.195505774G>T	ENSP00000417498:p.Pro4226His	Somatic	96	3	0.03125		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	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	10.38	1.335266	0.24253	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.43294	1.33;0.95	1.57	1.57	0.23409	.	.	.	.	.	T	0.40448	0.1117	N	0.14661	0.345	0.26065	N	0.981307	D	0.89917	1.0	D	0.72982	0.979	T	0.18840	-1.0324	8	.	.	.	.	6.711	0.23276	0.0:0.0:1.0:0.0	.	4098	E7ESK3	.	H	4226	ENSP00000417498:P4226H;ENSP00000420243:P4226H	.	P	-	2	0	MUC4	196990553	0.000000	0.05858	0.040000	0.18447	0.017000	0.09413	-0.298000	0.08265	1.213000	0.43380	0.484000	0.47621	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR1D5	8386	hgsc.bcm.edu	37	17	2966191	2966191	+	Silent	SNP	G	G	A	rs2676566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2966191G>A	ENST00000575751.1	-	1	710	c.711C>T	c.(709-711)acC>acT	p.T237T		NM_014566.1	NP_055381.1	P58170	OR1D5_HUMAN	olfactory receptor, family 1, subfamily D, member 5	237					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|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(1)|lung(10)	11						AGGTAGAGAAGGTTTTGTATT	0.498													g|||	1361	0.271765	0.3843	0.2968	5008	,	,		28808	0.0228		0.333	False		,,,				2504	0.2955				p.T237T		Atlas-SNP	.											.	OR1D5	33	.	0			c.C711T						PASS	.						79.0	93.0	88.0					17																	2966191		2188	4296	6484	SO:0001819	synonymous_variant	8386	exon1			AGAGAAGGTTTTG	AF087923	CCDS58499.1	17p13.3	2012-10-09			ENSG00000262628	ENSG00000262628		"""GPCR / Class A : Olfactory receptors"""	8186	protein-coding gene	gene with protein product						10673334	Standard	NM_014566		Approved	OR17-31	uc021tns.1	P58170	OTTHUMG00000177676	ENST00000575751.1:c.711C>T	17.37:g.2966191G>A		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	421	129	0.306413	NM_014566	Q96RA6	Silent	SNP	ENST00000575751.1	37	CCDS58499.1																																																																																			G|0.625;A|0.375	0.375	strong		0.498	OR1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438410.2	NM_014566	
CALD1	800	hgsc.bcm.edu	37	7	134618710	134618710	+	Missense_Mutation	SNP	A	A	G	rs6973420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:134618710A>G	ENST00000361675.2	+	5	1419	c.1190A>G	c.(1189-1191)cAt>cGt	p.H397R	CALD1_ENST00000393118.2_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000422748.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000543443.1_Intron			Q05682	CALD1_HUMAN	caldesmon 1	397			H -> R (in dbSNP:rs6973420). {ECO:0000269|PubMed:1555769}.		cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GAGAAAAAACATGCCATGCAA	0.428													G|||	2546	0.508387	0.4357	0.366	5008	,	,		21799	0.8581		0.4821	False		,,,				2504	0.3742				p.H397R		Atlas-SNP	.											.	CALD1	150	.	0			c.A1190G						PASS	.	G	,,,,ARG/HIS	1958,2448	620.6+/-393.6	451,1056,696	113.0	122.0	119.0		,,,,1190	-4.5	0.0	7	dbSNP_116	119	3900,4700	605.5+/-395.0	906,2088,1306	yes	intron,intron,intron,intron,missense	CALD1	NM_004342.6,NM_033139.3,NM_033140.3,NM_033157.3,NM_033138.3	,,,,29	1357,3144,2002	GG,GA,AA		45.3488,44.4394,45.0408	,,,,benign	,,,,397/794	134618710	5858,7148	2203	4300	6503	SO:0001583	missense	800	exon5			AAAAACATGCCAT	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1190A>G	7.37:g.134618710A>G	ENSP00000354826:p.His397Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	160	92	0.575	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	1206	0.5521978021978022	210	0.4268292682926829	139	0.3839779005524862	490	0.8566433566433567	367	0.4841688654353562	G	0.040	-1.287969	0.01387	0.444394	0.453488	ENSG00000122786	ENST00000361675	T	0.28069	1.63	4.15	-4.5	0.03493	.	2.361110	0.01783	N	0.031867	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	0.25882	-1.0119	8	.	.	.	12.5912	6.3213	0.21219	0.3306:0.2473:0.4222:0.0	rs6973420;rs17803435;rs59805101;rs6973420	397	Q05682	CALD1_HUMAN	R	397	ENSP00000354826:H397R	.	H	+	2	0	CALD1	134269250	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.464000	0.02359	-1.211000	0.02624	-2.371000	0.00235	CAT	A|0.502;G|0.496	0.496	strong		0.428	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
KIF7	374654	hgsc.bcm.edu	37	15	90196008	90196008	+	Missense_Mutation	SNP	C	C	T	rs8179065	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90196008C>T	ENST00000394412.3	-	2	230	c.154G>A	c.(154-156)Gac>Aac	p.D52N		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	52	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		D -> N (in dbSNP:rs8179065).		ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			AAGTGTCGGTCACGGCCCAGA	0.672													C|||	1214	0.242412	0.0507	0.2651	5008	,	,		17437	0.4117		0.2614	False		,,,				2504	0.2914				p.D52N		Atlas-SNP	.											.	KIF7	130	.	0			c.G154A						PASS	.						46.0	53.0	51.0					15																	90196008		689	1590	2279	SO:0001583	missense	374654	exon2			GTCGGTCACGGCC	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.154G>A	15.37:g.90196008C>T	ENSP00000377934:p.Asp52Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	516	0.23626373626373626	30	0.06097560975609756	85	0.23480662983425415	205	0.3583916083916084	196	0.25857519788918204	C	13.49	2.253446	0.39797	.	.	ENSG00000166813	ENST00000394412	T	0.74947	-0.89	4.66	2.35	0.29111	Kinesin, motor domain (4);	.	.	.	.	T	0.00012	0.0000	L	0.28344	0.845	0.29058	P	0.884112	B	0.15719	0.014	B	0.16289	0.015	T	0.14643	-1.0465	8	0.62326	D	0.03	.	4.3016	0.10927	0.0:0.4722:0.1771:0.3507	rs8179065	52	Q2M1P5	KIF7_HUMAN	N	52	ENSP00000377934:D52N	ENSP00000377934:D52N	D	-	1	0	KIF7	87997012	0.117000	0.22190	0.763000	0.31416	0.798000	0.45092	0.710000	0.25748	0.942000	0.37525	0.655000	0.94253	GAC	C|0.763;T|0.237	0.237	strong		0.672	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
ABCA4	24	hgsc.bcm.edu	37	1	94544234	94544234	+	Missense_Mutation	SNP	T	T	C	rs3112831	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	144	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	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	
ZNF285	26974	hgsc.bcm.edu	37	19	44890817	44890817	+	Silent	SNP	G	G	A	rs73039937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44890817G>A	ENST00000330997.4	-	4	1654	c.1590C>T	c.(1588-1590)caC>caT	p.H530H	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Silent_p.H530H|ZNF285_ENST00000591679.1_Silent_p.H537H	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GGACTCTGAGGTGAACATTAA	0.423													A|||	349	0.0696885	0.1853	0.0418	5008	,	,		22692	0.005		0.0338	False		,,,				2504	0.0368				p.H530H		Atlas-SNP	.											.	ZNF285	86	.	0			c.C1590T						PASS	.	A		723,3683	756.2+/-412.6	58,607,1538	100.0	100.0	100.0		1590	1.4	0.5	19	dbSNP_130	100	377,8223	801.9+/-407.4	12,353,3935	no	coding-synonymous	ZNF285	NM_152354.3		70,960,5473	AA,AG,GG		4.3837,16.4094,8.4576		530/591	44890817	1100,11906	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			TCTGAGGTGAACA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1590C>T	19.37:g.44890817G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			G|0.932;A|0.068	0.068	strong		0.423	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
EPB41L3	23136	hgsc.bcm.edu	37	18	5478295	5478295	+	Missense_Mutation	SNP	C	C	A	rs117900256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:5478295C>A	ENST00000341928.2	-	3	666	c.326G>T	c.(325-327)aGc>aTc	p.S109I	EPB41L3_ENST00000342933.3_Missense_Mutation_p.S109I|EPB41L3_ENST00000400111.3_Missense_Mutation_p.S109I|EPB41L3_ENST00000540638.2_Missense_Mutation_p.S109I|EPB41L3_ENST00000544123.1_Missense_Mutation_p.S109I|RP11-286N3.1_ENST00000577527.1_RNA	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	109					apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GCACTGCATGCTTTTAGGCTT	0.383													C|||	61	0.0121805	0.003	0.0101	5008	,	,		17612	0.0		0.0119	False		,,,				2504	0.0389				p.S109I		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G326T						PASS	.	C	ILE/SER	12,4394	20.2+/-43.8	0,12,2191	180.0	162.0	168.0		326	4.3	1.0	18	dbSNP_132	168	107,8493	57.5+/-118.9	0,107,4193	yes	missense	EPB41L3	NM_012307.2	142	0,119,6384	AA,AC,CC		1.2442,0.2724,0.915	benign	109/1088	5478295	119,12887	2203	4300	6503	SO:0001583	missense	23136	exon3			TGCATGCTTTTAG	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.326G>T	18.37:g.5478295C>A	ENSP00000343158:p.Ser109Ile	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	310	175	0.564516	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	18	0.008241758241758242	3	0.006097560975609756	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	13.03	2.115698	0.37339	0.002724	0.012442	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	T;D;T;D	0.83075	-1.46;-1.64;-1.46;-1.68	5.16	4.27	0.50696	Band 4.1 domain (1);	0.241444	0.40385	N	0.001115	T	0.74268	0.3694	L	0.51422	1.61	0.80722	D	1	D;B;P;B	0.56746	0.977;0.002;0.858;0.002	P;B;B;B	0.47470	0.548;0.003;0.255;0.004	T	0.76814	-0.2820	10	0.42905	T	0.14	.	8.9723	0.35915	0.0:0.7703:0.0:0.2297	.	109;109;109;109	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	I	109;109;109;109;190	ENSP00000343158:S109I;ENSP00000441174:S109I;ENSP00000341138:S109I;ENSP00000382981:S109I	ENSP00000343158:S109I	S	-	2	0	EPB41L3	5468295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.834000	0.27518	2.378000	0.81104	0.579000	0.79373	AGC	C|0.990;A|0.010	0.010	strong		0.383	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
TRGC1	6966	hgsc.bcm.edu	37	7	38305083	38305083	+	RNA	SNP	G	G	A	rs2007081	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:38305083G>A	ENST00000443402.2	-	0	196					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)											TGTATGTGTCGTTAGTCTTCA	0.398													g|||	631	0.125998	0.0454	0.0965	5008	,	,		17925	0.1736		0.1243	False		,,,				2504	0.2086				p.N4N		Atlas-SNP	.											.	.	.	.	0			c.C12T						PASS	.	G	,	198,3470		15,168,1651	180.0	177.0	178.0		,12	-8.9	0.0	7	dbSNP_92	178	1032,7148		76,880,3134	no	utr-3,coding-synonymous	TARP	NM_001003799.1,NM_001003806.1	,	91,1048,4785	AA,AG,GG		12.6161,5.398,10.3815	,	,4/112	38305083	1230,10618	1834	4090	5924			0	exon2			TGTGTCGTTAGTC	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.38305083G>A		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	520	417	0.801923	NM_001003806		Silent	SNP	ENST00000443402.2	37																																																																																				.	.	weak		0.398	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336	
ERCC4	2072	hgsc.bcm.edu	37	16	14014055	14014055	+	Silent	SNP	C	C	T	rs3136042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:14014055C>T	ENST00000311895.7	+	1	42	c.33C>T	c.(31-33)gcC>gcT	p.A11A	ERCC4_ENST00000575156.1_Silent_p.A11A	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	11	Helicase-like.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						GACGGATTGCCATGGCGCCGC	0.672			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	29	0.00579073	0.0023	0.0144	5008	,	,		16787	0.0		0.0149	False		,,,				2504	0.001				p.A11A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""		E	.	ERCC4	100	.	0			c.C33T						PASS	.	C		29,4361		0,29,2166	36.0	39.0	38.0		33	-7.8	0.0	16	dbSNP_103	38	191,8403		4,183,4110	no	coding-synonymous	ERCC4	NM_005236.2		4,212,6276	TT,TC,CC		2.2225,0.6606,1.6944		11/917	14014055	220,12764	2195	4297	6492	SO:0001819	synonymous_variant	2072	exon1	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GATTGCCATGGCG	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"""xeroderma pigmentosum, complementation group F"""	133520	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.33C>T	16.37:g.14014055C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																			C|0.986;T|0.014	0.014	strong		0.672	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
PITX1	5307	hgsc.bcm.edu	37	5	134364518	134364518	+	Missense_Mutation	SNP	C	C	G	rs479632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:134364518C>G	ENST00000265340.7	-	3	1312	c.896G>C	c.(895-897)gGc>gCc	p.G299A	PITX1_ENST00000506438.1_Missense_Mutation_p.G299A	NM_002653.4	NP_002644.4	P78337	PITX1_HUMAN	paired-like homeodomain 1	299			G -> A (in dbSNP:rs479632). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15372022, ECO:0000269|PubMed:15489334}.		anatomical structure morphogenesis (GO:0009653)|branchiomeric skeletal muscle development (GO:0014707)|cartilage development (GO:0051216)|embryonic hindlimb morphogenesis (GO:0035116)|myoblast fate commitment (GO:0048625)|pituitary gland development (GO:0021983)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|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 positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)			central_nervous_system(1)|cervix(3)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)		GCCCTGCAGGCCGCCGTAGCC	0.721													C|||	1602	0.319888	0.1339	0.3271	5008	,	,		9300	0.4762		0.2704	False		,,,				2504	0.456				p.G299A		Atlas-SNP	.											.	PITX1	31	.	0			c.G896C						PASS	.	C	ALA/GLY	685,3721		52,581,1570	24.0	25.0	25.0		896	4.3	1.0	5	dbSNP_83	25	2132,6468		259,1614,2427	yes	missense	PITX1	NM_002653.4	60	311,2195,3997	GG,GC,CC		24.7907,15.547,21.6592	benign	299/315	134364518	2817,10189	2203	4300	6503	SO:0001583	missense	5307	exon3			TGCAGGCCGCCGT	AF009648	CCDS4182.1	5q31.1	2011-06-20	2007-07-12		ENSG00000069011	ENSG00000069011		"""Homeoboxes / PRD class"""	9004	protein-coding gene	gene with protein product		602149	"""paired-like homeodomain transcription factor 1"""	BFT		9337397, 9070926	Standard	NM_002653		Approved	PTX1, POTX	uc010jea.3	P78337	OTTHUMG00000149983	ENST00000265340.7:c.896G>C	5.37:g.134364518C>G	ENSP00000265340:p.Gly299Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_002653	A8K3M0|D3DQB0|O14677|O60425|Q9BTI5	Missense_Mutation	SNP	ENST00000265340.7	37	CCDS4182.1	695	0.3182234432234432	89	0.18089430894308944	110	0.30386740331491713	280	0.48951048951048953	216	0.2849604221635884	C	10.90	1.482622	0.26598	0.15547	0.247907	ENSG00000069011	ENST00000265340;ENST00000506438	D;D	0.88975	-2.45;-2.45	4.32	4.32	0.51571	.	0.269095	0.40818	N	0.001017	T	0.00012	0.0000	N	0.03154	-0.405	0.20307	P	0.9999179817	B	0.26363	0.147	B	0.25405	0.06	T	0.14896	-1.0456	9	0.10377	T	0.69	.	15.7942	0.78398	0.0:1.0:0.0:0.0	rs479632;rs17856095;rs479632	299	P78337	PITX1_HUMAN	A	299	ENSP00000265340:G299A;ENSP00000427542:G299A	ENSP00000265340:G299A	G	-	2	0	PITX1	134392417	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.423000	0.80229	1.954000	0.56735	0.462000	0.41574	GGC	C|0.748;G|0.252	0.252	strong		0.721	PITX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251195.3		
MUC16	94025	hgsc.bcm.edu	37	19	9072742	9072742	+	Missense_Mutation	SNP	T	T	C	rs2591590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9072742T>C	ENST00000397910.4	-	3	14907	c.14704A>G	c.(14704-14706)Atc>Gtc	p.I4902V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4904	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.I4902V(2)|p.I535V(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						TCCTGGGAGATGCTGGTCTCC	0.488													T|||	1054	0.210463	0.0628	0.2046	5008	,	,		23106	0.249		0.3101	False		,,,				2504	0.272				p.I4902V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,6	MUC16	4315	6	3	Substitution - Missense(3)	stomach(3)	c.A14704G						PASS	.	T	VAL/ILE	426,3770		24,378,1696	232.0	219.0	223.0		14704	2.2	0.0	19	dbSNP_100	223	2412,6032		344,1724,2154	yes	missense	MUC16	NM_024690.2	29	368,2102,3850	CC,CT,TT		28.5647,10.1525,22.4525	benign	4902/14508	9072742	2838,9802	2098	4222	6320	SO:0001583	missense	94025	exon3			GGGAGATGCTGGT	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.14704A>G	19.37:g.9072742T>C	ENSP00000381008:p.Ile4902Val	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	375	168	0.448	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	488	0.22344322344322345	47	0.09552845528455285	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	t	10.67	1.416022	0.25552	0.101525	0.285647	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.18	2.18	0.27775	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.22983	0.078	B	0.31946	0.138	T	0.47355	-0.9124	8	0.87932	D	0	.	6.3469	0.21355	0.0:0.0:0.0:1.0	rs2591590;rs52802082;rs58556174;rs2591590	4902	B5ME49	.	V	4902	ENSP00000381008:I4902V	ENSP00000381008:I4902V	I	-	1	0	MUC16	8933742	0.000000	0.05858	0.017000	0.16124	0.787000	0.44495	0.373000	0.20484	1.268000	0.44264	0.248000	0.18094	ATC	T|0.787;C|0.213	0.213	strong		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DCAF12	25853	hgsc.bcm.edu	37	9	34107504	34107504	+	Silent	SNP	C	C	T	rs1378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34107504C>T	ENST00000361264.4	-	3	734	c.393G>A	c.(391-393)cgG>cgA	p.R131R	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	131			R -> Q (in dbSNP:rs11557154). {ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						CTCCAGGCTCCCGGTCTTTCA	0.483													C|||	278	0.0555112	0.0038	0.0706	5008	,	,		19303	0.0079		0.1511	False		,,,				2504	0.0654				p.R131R		Atlas-SNP	.											DCAF12,colon,carcinoma,0,1	DCAF12	37	1	0			c.G393A						PASS	.	C		102,4304	81.4+/-119.9	3,96,2104	105.0	101.0	102.0		393	-2.9	0.8	9	dbSNP_36	102	1011,7589	217.1+/-255.9	49,913,3338	no	coding-synonymous	DCAF12	NM_015397.3		52,1009,5442	TT,TC,CC		11.7558,2.315,8.5576		131/454	34107504	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	25853	exon3			AGGCTCCCGGTCT	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	19911	protein-coding gene	gene with protein product	"""cancer/testis antigen 102"""		"""KIAA1892"", ""WD repeat domain 40A"""	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.393G>A	9.37:g.34107504C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Silent	SNP	ENST00000361264.4	37	CCDS6549.1																																																																																			C|0.923;T|0.077	0.077	strong		0.483	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397	
WTAP	9589	hgsc.bcm.edu	37	6	160169258	160169258	+	Silent	SNP	G	G	T	rs7766006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160169258G>T	ENST00000358372.4	+	6	2066	c.309G>T	c.(307-309)ccG>ccT	p.P103P	WTAP_ENST00000337387.4_Silent_p.P103P|SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	103					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		TCCAGCAGCCGAGCGTTGCCC	0.423													G|||	1304	0.260383	0.1747	0.2161	5008	,	,		20479	0.4256		0.2097	False		,,,				2504	0.2894				p.P103P		Atlas-SNP	.											WTAP,NS,carcinoma,+2,1	WTAP	44	1	0			c.G309T						PASS	.	G	,,	843,3563	333.3+/-302.9	92,659,1452	63.0	63.0	63.0		309,309,309	2.3	1.0	6	dbSNP_116	63	1498,7102	284.0+/-296.4	138,1222,2940	no	coding-synonymous,coding-synonymous,coding-synonymous	WTAP	NM_004906.3,NM_152857.1,NM_152858.1	,,	230,1881,4392	TT,TG,GG		17.4186,19.133,17.9994	,,	103/397,103/152,103/152	160169258	2341,10665	2203	4300	6503	SO:0001819	synonymous_variant	9589	exon6			GCAGCCGAGCGTT	AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.309G>T	6.37:g.160169258G>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	247	224	0.906883	NM_001270533	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Silent	SNP	ENST00000358372.4	37	CCDS5266.1																																																																																			G|0.800;T|0.200	0.200	strong		0.423	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857	
OSBPL8	114882	hgsc.bcm.edu	37	12	76844711	76844711	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:76844711C>T	ENST00000261183.3	-	4	616	c.137G>A	c.(136-138)cGc>cAc	p.R46H	OSBPL8_ENST00000393250.4_Missense_Mutation_p.R4H|OSBPL8_ENST00000393249.2_Missense_Mutation_p.R4H	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	46					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TTTTCCTTGGCGCTGACTCAT	0.443																																					p.R46H		Atlas-SNP	.											.	OSBPL8	86	.	0			c.G137A						PASS	.						160.0	139.0	146.0					12																	76844711		2203	4300	6503	SO:0001583	missense	114882	exon4			CCTTGGCGCTGAC	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.137G>A	12.37:g.76844711C>T	ENSP00000261183:p.Arg46His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	5	0.0423729	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Missense_Mutation	SNP	ENST00000261183.3	37	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943872	0.73672	.	.	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250;ENST00000438913;ENST00000547540;ENST00000548341;ENST00000553139;ENST00000549570;ENST00000551927;ENST00000547544	T;T;T;T;T;T	0.53423	1.34;2.64;1.34;2.64;2.64;0.62	5.66	5.66	0.87406	.	0.368655	0.29752	N	0.011290	T	0.37320	0.0999	N	0.19112	0.55	0.42098	D	0.991322	D	0.61080	0.989	B	0.42087	0.375	T	0.26573	-1.0099	10	0.42905	T	0.14	-3.9225	18.3033	0.90171	0.0:1.0:0.0:0.0	.	46	Q9BZF1	OSBL8_HUMAN	H	4;46;31;4;46;46;33;4;4;46;43	ENSP00000376939:R4H;ENSP00000261183:R46H;ENSP00000376940:R4H;ENSP00000450238:R46H;ENSP00000446886:R33H;ENSP00000449618:R4H	ENSP00000261183:R46H	R	-	2	0	OSBPL8	75368842	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.348000	0.52209	2.669000	0.90835	0.655000	0.94253	CGC	.	.	none		0.443	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657798	46657798	+	Silent	SNP	A	A	G	rs6007748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46657798A>G	ENST00000253255.5	-	1	1421	c.1422T>C	c.(1420-1422)gaT>gaC	p.D474D		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	474	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AAGAAAATCTATCAGAGACAA	0.393													A|||	1198	0.239217	0.6558	0.1326	5008	,	,		18300	0.001		0.16	False		,,,				2504	0.0787				p.D474D		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T1422C						PASS	.	A		2538,1868	631.6+/-395.7	719,1100,384	98.0	103.0	101.0		1422	-7.0	0.0	22	dbSNP_114	101	1255,7345	250.8+/-277.5	87,1081,3132	no	coding-synonymous	PKDREJ	NM_006071.1		806,2181,3516	GG,GA,AA		14.593,42.3967,29.1635		474/2254	46657798	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AAATCTATCAGAG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1422T>C	22.37:g.46657798A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.737;G|0.263	0.263	strong		0.393	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
SBNO2	22904	hgsc.bcm.edu	37	19	1119963	1119963	+	Silent	SNP	A	A	G	rs2074921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1119963A>G	ENST00000361757.3	-	12	1446	c.1209T>C	c.(1207-1209)gcT>gcC	p.A403A	SBNO2_ENST00000587024.1_Silent_p.A403A|SBNO2_ENST00000438103.2_Silent_p.A346A	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	403					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)		GGTCTAGCACAGCCTTGCCCA	0.627													G|||	2205	0.440296	0.5	0.6037	5008	,	,		18548	0.2371		0.4642	False		,,,				2504	0.4284				p.A403A		Atlas-SNP	.											.	SBNO2	112	.	0			c.T1209C						PASS	.	G	,	1862,2130		461,940,595	49.0	53.0	52.0		1038,1209	-7.8	0.7	19	dbSNP_96	52	3411,4615		785,1841,1387	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	1246,2781,1982	GG,GA,AA		42.4994,46.6433,43.8759	,	346/1310,403/1367	1119963	5273,6745	1996	4013	6009	SO:0001819	synonymous_variant	22904	exon12			TAGCACAGCCTTG	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.1209T>C	19.37:g.1119963A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			A|0.566;C|0.000;G|0.433;T|0.000	0.433	strong		0.627	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
PCTP	58488	hgsc.bcm.edu	37	17	53851237	53851237	+	Silent	SNP	C	C	T	rs34608946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:53851237C>T	ENST00000268896.5	+	4	617	c.492C>T	c.(490-492)gaC>gaT	p.D164D	PCTP_ENST00000325214.6_Silent_p.D92D|PCTP_ENST00000573500.1_Silent_p.D164D|PCTP_ENST00000576221.1_3'UTR|PCTP_ENST00000576183.1_Silent_p.D164D	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	164	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			TCGAGAGTGACGGCAAGAAGG	0.622													C|||	25	0.00499201	0.0	0.0101	5008	,	,		21559	0.003		0.0129	False		,,,				2504	0.002				p.D164D		Atlas-SNP	.											.	PCTP	17	.	0			c.C492T						PASS	.	C	,	15,4391	24.3+/-50.5	0,15,2188	62.0	50.0	54.0		276,492	-2.2	0.9	17	dbSNP_126	54	125,8475	62.8+/-124.8	2,121,4177	no	coding-synonymous,coding-synonymous	PCTP	NM_001102402.2,NM_021213.3	,	2,136,6365	TT,TC,CC		1.4535,0.3404,1.0764	,	92/143,164/215	53851237	140,12866	2203	4300	6503	SO:0001819	synonymous_variant	58488	exon4			GAGTGACGGCAAG	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.492C>T	17.37:g.53851237C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Silent	SNP	ENST00000268896.5	37	CCDS11588.1																																																																																			C|0.990;T|0.010	0.010	strong		0.622	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
CCDC61	729440	hgsc.bcm.edu	37	19	46518682	46518682	+	Missense_Mutation	SNP	G	G	A	rs7271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46518682G>A	ENST00000595358.1	+	7	891	c.842G>A	c.(841-843)aGg>aAg	p.R281K	CCDC61_ENST00000536603.1_Intron|CCDC61_ENST00000594087.1_Intron|CCDC61_ENST00000263284.2_Missense_Mutation_p.R338K	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	281						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTGTACAAGAGGGGGTGAGAG	0.731													G|||	577	0.115216	0.0545	0.0663	5008	,	,		6255	0.1081		0.1392	False		,,,				2504	0.2147				p.R281K		Atlas-SNP	.											.	CCDC61	32	.	0			c.G842A						PASS	.						13.0	15.0	14.0					19																	46518682		1883	3970	5853	SO:0001583	missense	729440	exon7			ACAAGAGGGGGTG		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.842G>A	19.37:g.46518682G>A	ENSP00000471454:p.Arg281Lys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	221	0.10119047619047619	24	0.04878048780487805	28	0.07734806629834254	71	0.12412587412587413	98	0.12928759894459102	G	8.736	0.917912	0.17982	.	.	ENSG00000104983	ENST00000263284	.	.	.	3.86	1.66	0.24008	.	0.491827	0.21716	N	0.070186	T	0.00384	0.0012	L	0.54323	1.7	0.22446	P	0.999091975	B	0.31817	0.341	B	0.25140	0.058	T	0.06356	-1.0831	8	0.59425	D	0.04	-6.385	6.3339	0.21285	0.2413:0.0:0.7587:0.0	rs7271;rs17294786;rs17353314	281	Q9Y6R9	CCD61_HUMAN	K	338	.	ENSP00000263284:R338K	R	+	2	0	CCDC61	51210522	0.017000	0.18338	0.052000	0.19188	0.089000	0.18198	0.580000	0.23803	0.700000	0.31782	-1.267000	0.01435	AGG	G|0.900;A|0.100	0.100	strong		0.731	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
OBSCN	84033	hgsc.bcm.edu	37	1	228401329	228401329	+	Silent	SNP	C	C	T	rs185717159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228401329C>T	ENST00000422127.1	+	3	1220	c.1176C>T	c.(1174-1176)cgC>cgT	p.R392R	C1orf145_ENST00000295012.5_Silent_p.L11L|OBSCN_ENST00000570156.2_Silent_p.R392R|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.R392R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	392	Ig-like 4.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGACCGTGCGCAATGTCTCGG	0.706													C|||	17	0.00339457	0.0	0.0029	5008	,	,		6657	0.0		0.0139	False		,,,				2504	0.001				p.R392R		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1176T						PASS	.	C	,	1,4053		0,1,2026	12.0	14.0	13.0		1176,1176	1.1	0.1	1		13	61,8229		0,61,4084	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,62,6110	TT,TC,CC		0.7358,0.0247,0.5023	,	392/7969,392/6621	228401329	62,12282	2027	4145	6172	SO:0001819	synonymous_variant	84033	exon3			CGTGCGCAATGTC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.1176C>T	1.37:g.228401329C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.994;T|0.006	0.006	strong		0.706	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FKTN	2218	hgsc.bcm.edu	37	9	108366734	108366734	+	Missense_Mutation	SNP	G	G	A	rs34787999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:108366734G>A	ENST00000223528.2	+	5	732	c.608G>A	c.(607-609)cGa>cAa	p.R203Q	FKTN_ENST00000602661.1_Missense_Mutation_p.R203Q|FKTN_ENST00000448551.2_Missense_Mutation_p.R203Q|FKTN_ENST00000540160.1_Missense_Mutation_p.R203Q|FKTN_ENST00000357998.5_Missense_Mutation_p.R203Q	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	203			R -> Q (in dbSNP:rs34787999). {ECO:0000269|PubMed:9690476}.		muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						GTTCCCTTCCGAAAGTTACAG	0.433													G|||	792	0.158147	0.1339	0.2205	5008	,	,		16548	0.0913		0.2724	False		,,,				2504	0.0982				p.R203Q		Atlas-SNP	.											.	FKTN	47	.	0			c.G608A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	698,3708	291.5+/-281.6	57,584,1562	78.0	76.0	77.0		608,608,608	5.4	1.0	9	dbSNP_126	77	2743,5857	435.7+/-358.1	394,1955,1951	yes	missense,missense,missense	FKTN	NM_001079802.1,NM_001198963.1,NM_006731.2	43,43,43	451,2539,3513	AA,AG,GG		31.8953,15.842,26.457	benign,benign,benign	203/462,203/431,203/462	108366734	3441,9565	2203	4300	6503	SO:0001583	missense	2218	exon5			CCTTCCGAAAGTT		CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"""Fukuyama type congenital muscular dystrophy (fukutin)"""	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.608G>A	9.37:g.108366734G>A	ENSP00000223528:p.Arg203Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	37	CCDS6766.1	426	0.19505494505494506	63	0.12804878048780488	87	0.24033149171270718	57	0.09965034965034965	219	0.28891820580474936	G	17.31	3.356859	0.61293	0.15842	0.318953	ENSG00000106692	ENST00000223528;ENST00000540160;ENST00000357998;ENST00000374705	D;D;D;D	0.90844	-2.41;-1.61;-2.74;-1.63	5.36	5.36	0.76844	.	0.279452	0.35407	N	0.003239	T	0.00012	0.0000	M	0.67953	2.075	0.28330	P	0.9218189999999999	P;B;B	0.51653	0.947;0.332;0.074	B;B;B	0.35182	0.197;0.013;0.013	T	0.00953	-1.1502	9	0.40728	T	0.16	-14.7124	11.5448	0.50688	0.081:0.0:0.919:0.0	rs34787999;rs52801818;rs57126925;rs62575143	203;203;203	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	Q	203;203;203;180	ENSP00000223528:R203Q;ENSP00000439423:R203Q;ENSP00000350687:R203Q;ENSP00000363837:R180Q	ENSP00000223528:R203Q	R	+	2	0	FKTN	107406555	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.399000	0.59703	2.496000	0.84212	0.563000	0.77884	CGA	G|0.755;A|0.245	0.245	strong		0.433	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045362	76045362	+	Missense_Mutation	SNP	T	T	C	rs2287015	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0	1165	WXS	Illumina HiSeq	Phase_I	65	25	0.384615	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	
MMAB	326625	hgsc.bcm.edu	37	12	110011230	110011230	+	Missense_Mutation	SNP	C	C	T	rs10774775|rs36013132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:110011230C>T	ENST00000545712.2	-	1	449	c.56G>A	c.(55-57)cGc>cAc	p.R19H	MVK_ENST00000535044.1_3'UTR|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000539575.1_5'Flank|MVK_ENST00000541384.1_5'Flank|MVK_ENST00000539696.1_5'Flank|MVK_ENST00000228510.3_5'Flank|MMAB_ENST00000540016.1_Missense_Mutation_p.R19H|MVK_ENST00000392727.3_5'Flank	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	19			R -> H (in dbSNP:rs10774775).|R -> Q (in dbSNP:rs36013132). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAAGCACCCGCGCAGGCCAAG	0.716													C|||	1427	0.284944	0.438	0.2939	5008	,	,		12948	0.1607		0.2853	False		,,,				2504	0.1994				p.R19H		Atlas-SNP	.											.	MMAB	16	.	0			c.G56A						PASS	.	C	HIS/ARG	1710,2678		354,1002,838	15.0	17.0	16.0		56	3.9	0.9	12	dbSNP_120	16	2293,6297		369,1555,2371	no	missense	MMAB	NM_052845.3	29	723,2557,3209	TT,TC,CC		26.6938,38.9699,30.8445	probably-damaging	19/251	110011230	4003,8975	2194	4295	6489	SO:0001583	missense	326625	exon1			CACCCGCGCAGGC	AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"""ATP:cob(I)alamin adenosyltransferase"", ""cilia and flagella associated protein 23"""	607568	"""methylmalonic aciduria (cobalamin deficiency) type B"""			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.56G>A	12.37:g.110011230C>T	ENSP00000445920:p.Arg19His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_052845	C5HU05|Q9BSH0	Missense_Mutation	SNP	ENST00000545712.2	37	CCDS9131.1	634	0.2902930402930403	223	0.4532520325203252	112	0.30939226519337015	83	0.1451048951048951	216	0.2849604221635884	C	13.88	2.368378	0.42003	0.389699	0.266938	ENSG00000139428	ENST00000545712;ENST00000542390	D	0.83755	-1.76	4.79	3.89	0.44902	.	0.375104	0.24940	N	0.034391	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999808155	D	0.61080	0.989	P	0.47744	0.556	T	0.29458	-1.0011	8	.	.	.	-18.7787	11.184	0.48644	0.0:0.8144:0.1856:0.0	rs10774775	19	Q96EY8	MMAB_HUMAN	H	19	ENSP00000445920:R19H	.	R	-	2	0	MMAB	108495613	0.712000	0.27916	0.852000	0.33557	0.108000	0.19459	1.236000	0.32683	1.351000	0.45789	0.591000	0.81541	CGC	C|0.693;T|0.307	0.307	strong		0.716	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2		
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:100047812G>A	ENST00000265512.7	-	8	1125	c.1051C>T	c.(1051-1053)Ctg>Ttg	p.L351L	RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Silent_p.L370L|ADH4_ENST00000505590.1_Silent_p.L370L|ADH4_ENST00000423445.1_Silent_p.L370L	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	351					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)	p.L351L(2)		NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TGGGTCACCAGTGCATCCAGA	0.363													A|||	587	0.117212	0.0696	0.1729	5008	,	,		15373	0.0		0.2773	False		,,,				2504	0.0982				p.L351L		Atlas-SNP	.											ADH4,NS,carcinoma,0,1	ADH4	35	1	2	Substitution - coding silent(2)	prostate(2)	c.C1051T						PASS	.	A		484,3922	781.9+/-414.5	21,442,1740	142.0	138.0	139.0		1051	-3.5	0.0	4	dbSNP_86	139	2481,6119	696.0+/-404.8	343,1795,2162	no	coding-synonymous	ADH4	NM_000670.3		364,2237,3902	AA,AG,GG		28.8488,10.985,22.7972		351/381	100047812	2965,10041	2203	4300	6503	SO:0001819	synonymous_variant	127	exon8			TCACCAGTGCATC	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.1051C>T	4.37:g.100047812G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	37	CCDS34032.1																																																																																			G|0.824;A|0.176	0.176	strong		0.363	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
PTPRS	5802	hgsc.bcm.edu	37	19	5212380	5212380	+	Silent	SNP	C	C	T	rs1064300	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5212380C>T	ENST00000587303.1	-	30	4836	c.4737G>A	c.(4735-4737)ccG>ccA	p.P1579P	PTPRS_ENST00000372412.4_Silent_p.P1580P|PTPRS_ENST00000262963.6_Silent_p.P1559P|PTPRS_ENST00000353284.2_Silent_p.P1132P|PTPRS_ENST00000357368.4_Silent_p.P1579P|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000592099.1_Silent_p.P1132P|PTPRS_ENST00000588012.1_Silent_p.P1541P|PTPRS_ENST00000348075.2_Silent_p.P1541P			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1579	Tyrosine-protein phosphatase 1. {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)			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)	CGGCATCTGGCGGGTTGCAGG	0.672													C|||	1590	0.317492	0.4372	0.415	5008	,	,		16131	0.0556		0.3469	False		,,,				2504	0.3262				p.P1579P		Atlas-SNP	.											.	PTPRS	169	.	0			c.G4737A						PASS	.	C	,,,	1662,2738		324,1014,862	61.0	44.0	50.0		4737,3396,4623,3408	-1.2	1.0	19	dbSNP_86	50	2824,5774		484,1856,1959	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	808,2870,2821	TT,TC,CC		32.8448,37.7727,34.513	,,,	1579/1949,1132/1502,1541/1911,1136/1506	5212380	4486,8512	2200	4299	6499	SO:0001819	synonymous_variant	5802	exon31			ATCTGGCGGGTTG	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.4737G>A	19.37:g.5212380C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			C|0.669;T|0.331	0.331	strong		0.672	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
PYCR2	29920	hgsc.bcm.edu	37	1	226108200	226108200	+	Silent	SNP	C	C	T	rs73131849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:226108200C>T	ENST00000343818.6	-	7	1066	c.918G>A	c.(916-918)ggG>ggA	p.G306G	PYCR2_ENST00000478402.1_5'UTR|RP4-559A3.7_ENST00000432920.2_Intron	NM_013328.2	NP_037460.2	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member 2	306					L-proline biosynthetic process (GO:0055129)	cytoplasm (GO:0005737)	pyrroline-5-carboxylate reductase activity (GO:0004735)			kidney(1)|lung(3)	4	Breast(184;0.197)				L-Proline(DB00172)	TGAGGAGCTTCCCTGGGCTGG	0.577													C|||	864	0.172524	0.3048	0.2378	5008	,	,		12278	0.0833		0.16	False		,,,				2504	0.0521				p.G306G		Atlas-SNP	.											.	PYCR2	13	.	0			c.G918A						PASS	.	C		1271,3135	434.3+/-343.9	173,925,1105	80.0	85.0	83.0		918	-0.2	0.9	1	dbSNP_130	83	1299,7301	256.3+/-280.9	100,1099,3101	no	coding-synonymous	PYCR2	NM_013328.2		273,2024,4206	TT,TC,CC		15.1047,28.847,19.7601		306/321	226108200	2570,10436	2203	4300	6503	SO:0001819	synonymous_variant	29920	exon7			GAGCTTCCCTGGG	AF151351	CCDS31043.1, CCDS73039.1	1q42.13	2008-02-05			ENSG00000143811	ENSG00000143811			30262	protein-coding gene	gene with protein product						12477932	Standard	NM_013328		Approved	P5CR2	uc001hpq.4	Q96C36	OTTHUMG00000037506	ENST00000343818.6:c.918G>A	1.37:g.226108200C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	47	0.61039	NM_013328	A8K798|Q7Z515|Q9Y5J4	Silent	SNP	ENST00000343818.6	37	CCDS31043.1																																																																																			C|0.808;T|0.192	0.192	strong		0.577	PYCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091314.1	NM_013328	
GOLGB1	2804	hgsc.bcm.edu	37	3	121415720	121415720	+	Missense_Mutation	SNP	T	T	C	rs3732410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121415720T>C	ENST00000340645.5	-	13	3760	c.3635A>G	c.(3634-3636)tAt>tGt	p.Y1212C	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Y1217C	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1212			Y -> C (in dbSNP:rs3732410). {ECO:0000269|PubMed:18487259}.		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)		CAAGCGATTATAGTCATCTTT	0.428													T|||	1101	0.219848	0.0522	0.1585	5008	,	,		22709	0.4841		0.2505	False		,,,				2504	0.1861				p.Y1217C		Atlas-SNP	.											GOLGB1,NS,carcinoma,0,1	GOLGB1	319	1	0			c.A3650G						PASS	.	T	CYS/TYR	327,4079	171.9+/-202.1	11,305,1887	221.0	217.0	219.0		3635	4.6	0.9	3	dbSNP_107	219	2113,6487	365.1+/-333.8	277,1559,2464	yes	missense	GOLGB1	NM_004487.3	194	288,1864,4351	CC,CT,TT		24.5698,7.4217,18.7606	probably-damaging	1212/3260	121415720	2440,10566	2203	4300	6503	SO:0001583	missense	2804	exon13			CGATTATAGTCAT	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.3635A>G	3.37:g.121415720T>C	ENSP00000341848:p.Tyr1212Cys	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	420	155	0.369048	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	563	0.25778388278388276	33	0.06707317073170732	70	0.19337016574585636	267	0.46678321678321677	193	0.2546174142480211	T	10.43	1.349415	0.24426	0.074217	0.245698	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.32515	2.09;2.09;1.45	5.81	4.59	0.56863	.	0.000000	0.56097	D	0.000036	T	0.00012	0.0000	L	0.32530	0.975	0.29624	P	0.845993	D;P;P;D	0.76494	0.999;0.936;0.936;0.999	D;P;P;D	0.70487	0.912;0.609;0.609;0.969	T	0.49113	-0.8973	9	0.39692	T	0.17	.	10.852	0.46775	0.0:0.0:0.1579:0.8421	rs3732410;rs52794344;rs61628092;rs3732410	1137;1176;1217;1212	F1T0J2;E7EU81;E7EP74;Q14789	.;.;.;GOGB1_HUMAN	C	1212;1217;1176	ENSP00000341848:Y1212C;ENSP00000377275:Y1217C;ENSP00000418231:Y1176C	ENSP00000341848:Y1212C	Y	-	2	0	GOLGB1	122898410	1.000000	0.71417	0.911000	0.35937	0.780000	0.44128	1.966000	0.40481	2.210000	0.71456	0.533000	0.62120	TAT	T|0.787;C|0.213	0.213	strong		0.428	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
CDH20	28316	hgsc.bcm.edu	37	18	59195229	59195229	+	Silent	SNP	C	C	T	rs34784622	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:59195229C>T	ENST00000262717.4	+	7	1445	c.1047C>T	c.(1045-1047)taC>taT	p.Y349Y	CDH20_ENST00000536675.2_Silent_p.Y349Y|CDH20_ENST00000538374.1_Silent_p.Y349Y			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	349	Cadherin 3. {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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				AGAAAAGCTACACCTTAAAGG	0.443													C|||	38	0.00758786	0.003	0.0159	5008	,	,		19991	0.0		0.0199	False		,,,				2504	0.0031				p.Y349Y		Atlas-SNP	.											.	CDH20	117	.	0			c.C1047T						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	79.0	74.0	76.0		1047	1.1	1.0	18	dbSNP_126	76	181,8419	82.9+/-145.4	1,179,4120	no	coding-synonymous	CDH20	NM_031891.2		1,203,6299	TT,TC,CC		2.1047,0.5447,1.5762		349/802	59195229	205,12801	2203	4300	6503	SO:0001819	synonymous_variant	28316	exon6			AAGCTACACCTTA	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1047C>T	18.37:g.59195229C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	130	53	0.407692	NM_031891	Q495S3	Silent	SNP	ENST00000262717.4	37	CCDS11977.1																																																																																			C|0.987;T|0.013	0.013	strong		0.443	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48608598	48608598	+	Missense_Mutation	SNP	C	C	G	rs2307279	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48608598C>G	ENST00000599921.1	-	3	469	c.112G>C	c.(112-114)Gct>Cct	p.A38P	PLA2G4C_ENST00000354276.3_Missense_Mutation_p.A38P|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.A38P|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.A48P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	38	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		A -> P (in dbSNP:rs2307279). {ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|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)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		ACCTCATCAGCCTCAATCCTT	0.557													C|||	1291	0.257788	0.5779	0.098	5008	,	,		14764	0.2698		0.0497	False		,,,				2504	0.1401				p.A48P		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.G142C						PASS	.	C	PRO/ALA,PRO/ALA,PRO/ALA	2130,2276	577.8+/-384.5	534,1062,607	105.0	112.0	110.0		142,112,112	0.3	0.0	19	dbSNP_100	110	382,8218	123.9+/-182.7	9,364,3927	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	27,27,27	543,1426,4534	GG,GC,CC		4.4419,48.3432,19.3142	probably-damaging,probably-damaging,probably-damaging	48/552,38/528,38/542	48608598	2512,10494	2203	4300	6503	SO:0001583	missense	8605	exon3			CATCAGCCTCAAT	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.112G>C	19.37:g.48608598C>G	ENSP00000469473:p.Ala38Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	533	0.24404761904761904	293	0.5955284552845529	42	0.11602209944751381	159	0.27797202797202797	39	0.051451187335092345	C	9.081	0.999212	0.19121	0.483432	0.044419	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.04502	3.61;3.61	2.72	0.3	0.15776	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.925114	0.08988	N	0.864910	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	P;B;P	0.41159	0.74;0.086;0.584	B;B;B	0.39904	0.313;0.03;0.182	T	0.13899	-1.0492	9	0.31617	T	0.26	-2.4264	3.7445	0.08542	0.0:0.5823:0.2581:0.1596	rs2307279;rs3760816;rs52828945;rs2307279	48;38;38	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	P	38	ENSP00000346228:A38P;ENSP00000400036:A38P	ENSP00000346228:A38P	A	-	1	0	PLA2G4C	53300410	0.004000	0.15560	0.000000	0.03702	0.082000	0.17680	1.035000	0.30216	0.026000	0.15269	0.205000	0.17691	GCT	C|0.781;G|0.219	0.219	strong		0.557	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
OR52B6	340980	hgsc.bcm.edu	37	11	5602790	5602790	+	Silent	SNP	A	A	G	rs2163946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602790A>G	ENST00000345043.2	+	1	684	c.684A>G	c.(682-684)ctA>ctG	p.L228L	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	228						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)		CCACAGGCCTAGACATCATGC	0.502													G|||	3590	0.716853	0.7413	0.67	5008	,	,		22811	0.9802		0.4761	False		,,,				2504	0.6933				p.L228L		Atlas-SNP	.											.	OR52B6	37	.	0			c.A684G						PASS	.	G		3022,1242		1079,864,189	189.0	200.0	196.0		684	0.1	0.1	11	dbSNP_96	196	3997,4459		943,2111,1174	no	coding-synonymous	OR52B6	NM_001005162.2		2022,2975,1363	GG,GA,AA		47.2682,29.1276,44.8192		228/336	5602790	7019,5701	2132	4228	6360	SO:0001819	synonymous_variant	340980	exon1			AGGCCTAGACATC	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.684A>G	11.37:g.5602790A>G		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_001005162	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																			A|0.342;G|0.658	0.658	strong		0.502	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
DRD2	1813	hgsc.bcm.edu	37	11	113287694	113287694	+	Silent	SNP	C	C	T	rs1800499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:113287694C>T	ENST00000362072.3	-	4	767	c.423G>A	c.(421-423)ctG>ctA	p.L141L	DRD2_ENST00000538967.1_Silent_p.L141L|DRD2_ENST00000544518.1_Silent_p.L140L|DRD2_ENST00000535984.1_Intron|DRD2_ENST00000542968.1_Silent_p.L141L|DRD2_ENST00000355319.2_Silent_p.L141L|DRD2_ENST00000346454.3_Silent_p.L141L	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	141					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)	GCGTATTGTACAGCATGGGCA	0.607													C|||	81	0.0161741	0.0045	0.0058	5008	,	,		21318	0.0		0.0338	False		,,,				2504	0.0378				p.L141L		Atlas-SNP	.											DRD2,NS,carcinoma,-2,1	DRD2	98	1	0			c.G423A						PASS	.	C	,	38,4364	40.8+/-73.8	1,36,2164	120.0	94.0	103.0		423,423	1.4	1.0	11	dbSNP_89	103	337,8255	115.9+/-175.7	12,313,3971	no	coding-synonymous,coding-synonymous	DRD2	NM_000795.3,NM_016574.3	,	13,349,6135	TT,TC,CC		3.9223,0.8632,2.8859	,	141/444,141/415	113287694	375,12619	2201	4296	6497	SO:0001819	synonymous_variant	1813	exon4			ATTGTACAGCATG	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.423G>A	11.37:g.113287694C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_016574	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	37	CCDS8361.1																																																																																			C|0.977;T|0.023	0.023	strong		0.607	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795	
VWA2	340706	hgsc.bcm.edu	37	10	116008497	116008497	+	Missense_Mutation	SNP	G	G	A	rs9664945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:116008497G>A	ENST00000392982.3	+	2	275	c.25G>A	c.(25-27)Gcc>Acc	p.A9T	VWA2_ENST00000603594.1_Missense_Mutation_p.A9T			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	9			A -> T (in dbSNP:rs9664945). {ECO:0000269|PubMed:14506275, ECO:0000269|PubMed:14702039}.		calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GTTGCTGGAAGCCGTCTGTGT	0.468													A|||	1018	0.203275	0.3396	0.2176	5008	,	,		19544	0.0605		0.2515	False		,,,				2504	0.1063				p.A9T		Atlas-SNP	.											.	VWA2	64	.	0			c.G25A						PASS	.	A	THR/ALA	1361,3045	691.9+/-405.5	202,957,1044	271.0	231.0	245.0		25	3.1	0.3	10	dbSNP_119	245	2043,6557	720.2+/-406.3	251,1541,2508	yes	missense	VWA2	NM_198496.1	58	453,2498,3552	AA,AG,GG		23.7558,30.8897,26.1725	benign	9/726	116008497	3404,9602	2203	4300	6503	SO:0001583	missense	340706	exon2			CTGGAAGCCGTCT	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.25G>A	10.37:g.116008497G>A	ENSP00000376708:p.Ala9Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		444	0.2032967032967033	138	0.2804878048780488	88	0.2430939226519337	35	0.06118881118881119	183	0.24142480211081793	A	3.769	-0.047993	0.07407	0.308897	0.237558	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.69306	-0.39	4.98	3.07	0.35406	.	0.802559	0.11330	N	0.575165	T	0.00012	0.0000	L	0.46157	1.445	0.58432	P	5.999999999950489E-6	B;B	0.06786	0.001;0.001	B;B	0.10450	0.002;0.005	T	0.16541	-1.0399	9	0.15066	T	0.55	.	7.1349	0.25523	0.178:0.0:0.6789:0.1431	rs9664945;rs52800746;rs59454685;rs9664945	9;9	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	T	9	ENSP00000376708:A9T	ENSP00000298715:A9T	A	+	1	0	VWA2	115998487	0.252000	0.23972	0.350000	0.25708	0.270000	0.26580	0.762000	0.26503	0.600000	0.29862	-1.014000	0.02459	GCC	G|0.764;A|0.236	0.236	strong		0.468	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
DPPA4	55211	hgsc.bcm.edu	37	3	109049384	109049384	+	Silent	SNP	T	T	C	rs13059848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:109049384T>C	ENST00000335658.6	-	5	720	c.666A>G	c.(664-666)ccA>ccG	p.P222P	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	222					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						AGGCCTCTTGTGGAGATTCCA	0.478													T|||	339	0.0676917	0.0106	0.0836	5008	,	,		16038	0.003		0.1481	False		,,,				2504	0.1176				p.P222P		Atlas-SNP	.											.	DPPA4	56	.	0			c.A666G						PASS	.	T		191,4215	118.4+/-156.1	2,187,2014	48.0	51.0	50.0		666	-5.4	0.0	3	dbSNP_121	50	1574,7026	283.3+/-296.1	142,1290,2868	no	coding-synonymous	DPPA4	NM_018189.3		144,1477,4882	CC,CT,TT		18.3023,4.335,13.5707		222/305	109049384	1765,11241	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon5			CTCTTGTGGAGAT	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.666A>G	3.37:g.109049384T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			T|0.879;C|0.121	0.121	strong		0.478	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
RFC5	5985	hgsc.bcm.edu	37	12	118465820	118465820	+	Silent	SNP	T	T	C	rs5745873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:118465820T>C	ENST00000454402.2	+	9	974	c.856T>C	c.(856-858)Ttg>Ctg	p.L286L	RFC5_ENST00000543153.1_3'UTR|RFC5_ENST00000392542.2_Silent_p.L265L|RFC5_ENST00000229043.3_Silent_p.L201L	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	39	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	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	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523943	42523943	+	Missense_Mutation	SNP	A	A	G	rs16947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42523943A>G	ENST00000360608.5	-	6	1000	c.886T>C	c.(886-888)Tgc>Cgc	p.C296R	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.C296R|CYP2D6_ENST00000359033.4_Missense_Mutation_p.C245R	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	296			R -> C (in allele CYP2D6*2, allele CYP2D6*12, allele CYP2D6*14, allele CYP2D6*17, allele CYP2D6*45A, allele CYP2D6*45B and allele CYP2D6*46; dbSNP:rs16947). {ECO:0000269|PubMed:10591208, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15768052}.		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)	p.C245R(1)|p.C296R(1)		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)	ACCACTATGCACAGGTTCTCA	0.607													G|||	3209	0.640775	0.4463	0.6729	5008	,	,		21695	0.8601		0.6571	False		,,,				2504	0.638				p.C296R		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	2	Substitution - Missense(2)	prostate(2)	c.T886C	GRCh37	CM930187	CYP2D6	M	rs16947	PASS	.	G	ARG/CYS,ARG/CYS	2137,2255		577,983,636	98.0	85.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	886,733	-0.2	0.0	22	dbSNP_60	89	5650,2946		1936,1778,584	yes	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	180,180	2513,2761,1220	GG,GA,AA		34.2718,48.6566,40.0447	benign,benign	296/498,245/447	42523943	7787,5201	2196	4298	6494	SO:0001583	missense	1565	exon6			CTATGCACAGGTT	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.886T>C	22.37:g.42523943A>G	ENSP00000353820:p.Cys296Arg	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	1436	0.6575091575091575	203	0.41260162601626016	248	0.6850828729281768	485	0.8479020979020979	500	0.6596306068601583	G	0.545	-0.851746	0.02651	0.486566	0.657282	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.65178	-0.14;-0.14;-0.14	4.45	-0.156	0.13391	.	0.830949	0.11049	N	0.605212	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.35076	-0.9803	7	.	.	.	.	9.5064	0.39048	0.4973:0.0:0.5027:0.0	rs16947;rs57836231	245;296	Q6NXU8;Q6NWU0	.;.	R	296;296;242;245;245	ENSP00000353820:C296R;ENSP00000374620:C296R;ENSP00000351927:C245R	.	C	-	1	0	CYP2D6	40853887	0.000000	0.05858	0.019000	0.16419	0.041000	0.13682	-1.200000	0.03029	-0.119000	0.11830	-0.227000	0.12334	TGC	A|0.378;G|0.622	0.622	strong		0.607	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
KANK1	23189	hgsc.bcm.edu	37	9	732536	732536	+	Missense_Mutation	SNP	T	T	C	rs34832656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:732536T>C	ENST00000382303.1	+	10	3816	c.3164T>C	c.(3163-3165)aTt>aCt	p.I1055T	KANK1_ENST00000382293.3_Missense_Mutation_p.I897T|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.I1055T	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1055			I -> T (in dbSNP:rs34832656).		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GCAGTTAATATTGAAGGTTTG	0.478													T|||	631	0.125998	0.1929	0.2075	5008	,	,		19155	0.004		0.174	False		,,,				2504	0.0542				p.I1055T		Atlas-SNP	.											.	KANK1	231	.	0			c.T3164C						PASS	.	T	THR/ILE,THR/ILE	821,3585	328.0+/-300.3	84,653,1466	191.0	169.0	176.0		3164,2690	0.2	0.1	9	dbSNP_126	176	1521,7079	285.4+/-297.1	151,1219,2930	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	89,89	235,1872,4396	CC,CT,TT		17.686,18.6337,18.0071	benign,benign	1055/1353,897/1195	732536	2342,10664	2203	4300	6503	SO:0001583	missense	23189	exon10			TTAATATTGAAGG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3164T>C	9.37:g.732536T>C	ENSP00000371740:p.Ile1055Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	283	0.1295787545787546	83	0.16869918699186992	76	0.20994475138121546	2	0.0034965034965034965	122	0.16094986807387862	T	0.359	-0.940718	0.02322	0.186337	0.17686	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293;ENST00000382289	T;T;T	0.44881	0.91;0.91;0.91	5.62	0.228	0.15364	.	1.292170	0.05556	N	0.568328	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.15930	0.004;0.015	B;B	0.17433	0.018;0.014	T	0.18587	-1.0332	9	0.12103	T	0.63	0.1227	0.3629	0.00367	0.3558:0.1491:0.2364:0.2587	rs34832656	78;1055	F5H7I5;Q14678	.;KANK1_HUMAN	T	1055;78;1055;897;10	ENSP00000371740:I1055T;ENSP00000371734:I1055T;ENSP00000371730:I897T	ENSP00000371726:I10T	I	+	2	0	KANK1	722536	0.000000	0.05858	0.097000	0.21041	0.994000	0.84299	0.214000	0.17541	0.080000	0.16959	-0.259000	0.10710	ATT	T|0.838;C|0.162	0.162	strong		0.478	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
EXOC4	60412	hgsc.bcm.edu	37	7	133580447	133580447	+	Silent	SNP	G	G	A	rs2042456	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:133580447G>A	ENST00000253861.4	+	12	1859	c.1830G>A	c.(1828-1830)gtG>gtA	p.V610V	EXOC4_ENST00000539845.1_Silent_p.V509V|EXOC4_ENST00000545148.1_Silent_p.V220V|EXOC4_ENST00000460346.1_3'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	610					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)				TGGTGTGCGTGAAGCTCCAGG	0.473													G|||	2695	0.538139	0.7262	0.3184	5008	,	,		23292	0.4613		0.4165	False		,,,				2504	0.6442				p.V610V		Atlas-SNP	.											.	EXOC4	118	.	0			c.G1830A						PASS	.	G		2866,1540	671.9+/-402.5	933,1000,270	172.0	142.0	153.0		1830	4.4	1.0	7	dbSNP_94	153	3403,5197	503.5+/-375.9	687,2029,1584	no	coding-synonymous	EXOC4	NM_021807.3		1620,3029,1854	AA,AG,GG		39.5698,34.9523,48.2008		610/975	133580447	6269,6737	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon12			GTGCGTGAAGCTC	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.1830G>A	7.37:g.133580447G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			G|0.501;A|0.499	0.499	strong		0.473	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
USP25	29761	hgsc.bcm.edu	37	21	17203785	17203785	+	Silent	SNP	A	A	T	rs2297248	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:17203785A>T	ENST00000285679.6	+	16	2199	c.1830A>T	c.(1828-1830)gcA>gcT	p.A610A	USP25_ENST00000285681.2_Silent_p.A610A|USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Silent_p.A610A	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	610	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		ACTACTGGGCATATATTTTTG	0.393													A|||	981	0.195887	0.413	0.121	5008	,	,		19491	0.1915		0.0537	False		,,,				2504	0.1063				p.A610A		Atlas-SNP	.											.	USP25	156	.	0			c.A1830T						PASS	.	A		1461,2945	470.4+/-355.7	268,925,1010	150.0	148.0	149.0		1830	-9.7	0.8	21	dbSNP_100	149	431,8169	132.8+/-190.4	10,411,3879	no	coding-synonymous	USP25	NM_013396.3		278,1336,4889	TT,TA,AA		5.0116,33.1593,14.5471		610/1056	17203785	1892,11114	2203	4300	6503	SO:0001819	synonymous_variant	29761	exon16			CTGGGCATATATT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.1830A>T	21.37:g.17203785A>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	247	135	0.546559	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1	417	0.19093406593406592	225	0.4573170731707317	36	0.09944751381215469	118	0.2062937062937063	38	0.05013192612137203	A	11.00	1.509046	0.27036	0.331593	0.050116	ENSG00000155313	ENST00000453553	.	.	.	4.87	-9.73	0.00512	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43360	-0.9396	3	.	.	.	-15.2678	0.4793	0.00545	0.2014:0.194:0.2235:0.3811	rs2297248;rs2297248	.	.	.	L	139	.	.	H	+	2	0	USP25	16125656	0.008000	0.16893	0.848000	0.33437	0.965000	0.64279	-0.943000	0.03917	-1.637000	0.01531	-1.004000	0.02495	CAT	A|0.826;T|0.174	0.174	strong		0.393	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
PSMB7	5695	hgsc.bcm.edu	37	9	127177161	127177161	+	Missense_Mutation	SNP	A	A	G	rs4574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127177161A>G	ENST00000259457.3	-	2	129	c.116T>C	c.(115-117)gTc>gCc	p.V39A	PSMB7_ENST00000498485.1_5'UTR|PSMB7_ENST00000536392.1_Missense_Mutation_p.V39A	NM_002799.3	NP_002790.1	Q99436	PSB7_HUMAN	proteasome (prosome, macropain) subunit, beta type, 7	39			V -> A (in dbSNP:rs4574). {ECO:0000269|PubMed:15489334}.		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)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)	5						AGTTTTCCGGACCTTTGGAAG	0.507													G|||	2078	0.414936	0.6067	0.3804	5008	,	,		17625	0.2262		0.3956	False		,,,				2504	0.3947				p.V39A		Atlas-SNP	.											.	PSMB7	11	.	0			c.T116C						PASS	.	G	ALA/VAL	2673,1733	516.8+/-369.3	795,1083,325	82.0	77.0	79.0		116	6.2	1.0	9	dbSNP_52	79	3739,4861	617.1+/-396.6	807,2125,1368	yes	missense	PSMB7	NM_002799.2	64	1602,3208,1693	GG,GA,AA		43.4767,39.3327,49.3003	benign	39/278	127177161	6412,6594	2203	4300	6503	SO:0001583	missense	5695	exon2			TTCCGGACCTTTG	AJ420455	CCDS6855.1	9q34.11-q34.12	2008-02-05			ENSG00000136930	ENSG00000136930		"""Proteasome (prosome, macropain) subunits"""	9544	protein-coding gene	gene with protein product		604030				8811196	Standard	NM_002799		Approved	Z	uc004boj.4	Q99436	OTTHUMG00000021042	ENST00000259457.3:c.116T>C	9.37:g.127177161A>G	ENSP00000259457:p.Val39Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_002799	B4E0P1|Q5TBG6|Q96AG8|Q9BWA7	Missense_Mutation	SNP	ENST00000259457.3	37	CCDS6855.1	869	0.39789377289377287	289	0.5873983739837398	145	0.4005524861878453	134	0.23426573426573427	301	0.3970976253298153	G	10.66	1.412608	0.25465	0.606673	0.434767	ENSG00000136930	ENST00000259457;ENST00000536392;ENST00000441097	T;T;T	0.28069	1.63;1.63;1.63	6.17	6.17	0.99709	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00053	-2.385	0.48975	P	2.6199999999998447E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44174	-0.9345	9	0.02654	T	1	-0.4428	14.6008	0.68441	0.0699:0.0:0.9301:0.0	rs4574;rs1054103;rs3194638;rs7871785;rs17224581;rs17856007;rs52823974;rs60950928;rs4574	39;39	B4E0P1;Q99436	.;PSB7_HUMAN	A	39	ENSP00000259457:V39A;ENSP00000440247:V39A;ENSP00000393157:V39A	ENSP00000259457:V39A	V	-	2	0	PSMB7	126216982	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	6.279000	0.72620	1.644000	0.50603	-0.119000	0.15052	GTC	A|0.553;G|0.447	0.447	strong		0.507	PSMB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055525.1	NM_002799	
ERICH6B	220081	hgsc.bcm.edu	37	13	46124380	46124380	+	Silent	SNP	C	C	T	rs149506203	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:46124380C>T	ENST00000298738.2	-	12	1643	c.1479G>A	c.(1477-1479)ggG>ggA	p.G493G	RNA5SP27_ENST00000363839.1_RNA|FAM194B_ENST00000504261.1_5'UTR	NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		493										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						TCTGGCCTGTCCCATCAGGAA	0.413													C|||	50	0.00998403	0.0	0.0115	5008	,	,		20839	0.0		0.0139	False		,,,				2504	0.0286				p.G493G		Atlas-SNP	.											.	FAM194B	42	.	0			c.G1479A						PASS	.	C		4,1380		0,4,688	161.0	143.0	148.0		1479	-1.8	1.0	13	dbSNP_134	148	64,3118		0,64,1527	no	coding-synonymous	FAM194B	NM_182542.2		0,68,2215	TT,TC,CC		2.0113,0.289,1.4893		493/697	46124380	68,4498	692	1591	2283	SO:0001819	synonymous_variant	220081	exon12			GCCTGTCCCATCA																												ENST00000298738.2:c.1479G>A	13.37:g.46124380C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	39	0.639344	NM_182542	Q96MB5	Silent	SNP	ENST00000298738.2	37	CCDS45045.1																																																																																			C|0.987;T|0.013	0.013	strong		0.413	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
CSRNP1	64651	hgsc.bcm.edu	37	3	39186728	39186728	+	Silent	SNP	C	C	T	rs784517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:39186728C>T	ENST00000273153.5	-	3	402	c.225G>A	c.(223-225)cgG>cgA	p.R75R	CSRNP1_ENST00000514182.1_Silent_p.R75R	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	75					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						CCCGGCGAGCCCGCTTCAGGA	0.587													C|||	2311	0.461462	0.1188	0.5908	5008	,	,		15602	0.5615		0.5845	False		,,,				2504	0.6033				p.R75R		Atlas-SNP	.											.	CSRNP1	59	.	0			c.G225A						PASS	.	C		873,3533	331.8+/-302.1	88,697,1418	45.0	46.0	45.0		225	3.1	0.9	3	dbSNP_86	45	4858,3742	604.8+/-394.9	1374,2110,816	no	coding-synonymous	CSRNP1	NM_033027.3		1462,2807,2234	TT,TC,CC		43.5116,19.8139,44.0643		75/590	39186728	5731,7275	2203	4300	6503	SO:0001819	synonymous_variant	64651	exon3			GCGAGCCCGCTTC	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.225G>A	3.37:g.39186728C>T		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_033027	Q69YY5	Silent	SNP	ENST00000273153.5	37	CCDS2682.1																																																																																			T|0.456;G|0.000;C|0.544	0.456	strong		0.587	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
GTSE1	51512	hgsc.bcm.edu	37	22	46719100	46719100	+	Missense_Mutation	SNP	C	C	G	rs6008684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46719100C>G	ENST00000454366.1	+	8	1658	c.1446C>G	c.(1444-1446)gaC>gaG	p.D482E		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	463					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		ACTCCCCGGACAGCTCAACAC	0.557													C|||	573	0.114417	0.2791	0.0692	5008	,	,		20772	0.001		0.1223	False		,,,				2504	0.0327				p.D482E	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1446G						PASS	.	C	GLU/ASP	1138,3268	405.8+/-333.6	152,834,1217	158.0	146.0	150.0		1446	-4.4	0.0	22	dbSNP_114	150	953,7647	208.4+/-249.9	55,843,3402	yes	missense	GTSE1	NM_016426.6	45	207,1677,4619	GG,GC,CC		11.0814,25.8284,16.0772	possibly-damaging	482/740	46719100	2091,10915	2203	4300	6503	SO:0001583	missense	51512	exon8			CCCGGACAGCTCA	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1446C>G	22.37:g.46719100C>G	ENSP00000415430:p.Asp482Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	263	0.12042124542124542	135	0.27439024390243905	32	0.08839779005524862	0	0.0	96	0.1266490765171504	C	4.984	0.182775	0.09495	0.258284	0.110814	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.06142	3.34	3.31	-4.36	0.03645	.	1.514080	0.03735	N	0.254078	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B;B	0.25609	0.007;0.13	B;B	0.22880	0.028;0.042	T	0.42832	-0.9428	9	0.49607	T	0.09	0.0	3.1854	0.06599	0.2794:0.2923:0.0:0.4283	rs6008684;rs6008684	463;442	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	E	482;442	ENSP00000415430:D482E	ENSP00000354634:D442E	D	+	3	2	GTSE1	45097764	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.322000	0.08007	-0.816000	0.04340	0.313000	0.20887	GAC	C|0.856;G|0.144	0.144	strong		0.557	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
MYO10	4651	hgsc.bcm.edu	37	5	16676247	16676247	+	Missense_Mutation	SNP	G	G	A	rs61744227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16676247G>A	ENST00000513610.1	-	34	5013	c.4559C>T	c.(4558-4560)tCg>tTg	p.S1520L	MYO10_ENST00000427430.2_Missense_Mutation_p.S877L|MYO10_ENST00000274203.9_Missense_Mutation_p.S877L|MYO10_ENST00000505695.1_Missense_Mutation_p.S859L|MYO10_ENST00000515803.1_Missense_Mutation_p.S859L	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1520					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CACCACATCCGAGTTCAGGCA	0.428													G|||	19	0.00379393	0.0	0.0029	5008	,	,		17461	0.0		0.0109	False		,,,				2504	0.0061				p.S1520L		Atlas-SNP	.											.	MYO10	198	.	0			c.C4559T						PASS	.	G	LEU/SER	7,3821		0,7,1907	119.0	127.0	125.0		4559	3.3	0.0	5	dbSNP_129	125	84,8158		2,80,4039	yes	missense	MYO10	NM_012334.2	145	2,87,5946	AA,AG,GG		1.0192,0.1829,0.7539	benign	1520/2059	16676247	91,11979	1914	4121	6035	SO:0001583	missense	4651	exon34			ACATCCGAGTTCA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4559C>T	5.37:g.16676247G>A	ENSP00000421280:p.Ser1520Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	G	10.94	1.493361	0.26774	0.001829	0.010192	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.31	3.27	0.37495	.	.	.	.	.	T	0.18425	0.0442	N	0.17674	0.51	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.17289	-1.0374	9	0.27785	T	0.31	.	6.3605	0.21425	0.1845:0.1421:0.6734:0.0	.	399;1160;1520	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	L	1520;859;877;859;877	ENSP00000421280:S1520L;ENSP00000425051:S859L;ENSP00000274203:S877L;ENSP00000421170:S859L;ENSP00000391106:S877L	ENSP00000274203:S877L	S	-	2	0	MYO10	16729247	0.013000	0.17824	0.008000	0.14137	0.950000	0.60333	1.891000	0.39738	0.554000	0.29061	0.563000	0.77884	TCG	G|0.994;A|0.006	0.006	strong		0.428	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74921072G>C	ENST00000569840.2	+	9	1624	c.1050G>C	c.(1048-1050)cgG>cgC	p.R350R	MGAT5B_ENST00000301618.4_Silent_p.R350R|MGAT5B_ENST00000428789.2_Silent_p.R361R	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	350					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CGCCAGGCCGGGGAAGCTGCC	0.612													G|||	1087	0.217053	0.1884	0.1988	5008	,	,		10952	0.1677		0.2157	False		,,,				2504	0.3211				p.R361R		Atlas-SNP	.											MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	0			c.G1083C						PASS	.	G	,,	857,3549	333.9+/-303.2	85,687,1431	83.0	87.0	86.0		1050,1050,1083	2.1	1.0	17	dbSNP_108	86	2021,6579	352.0+/-328.5	231,1559,2510	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	316,2246,3941	CC,CG,GG		23.5,19.4507,22.1282	,,	350/793,350/791,361/802	74921072	2878,10128	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon8			AGGCCGGGGAAGC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1050G>C	17.37:g.74921072G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			G|0.785;C|0.215	0.215	strong		0.612	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
ATP12A	479	hgsc.bcm.edu	37	13	25265103	25265103	+	Intron	SNP	A	A	G	rs7981616	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25265103A>G	ENST00000381946.3	+	8	966				ATP12A_ENST00000218548.6_Splice_Site_p.A267A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide						ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GGAATAAAGCATCTACTTCCC	0.572													a|||	1479	0.295327	0.1747	0.3617	5008	,	,		20322	0.4762		0.1899	False		,,,				2504	0.3333				p.A267A	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A801G						PASS	.	A	,	775,3631	311.9+/-292.3	68,639,1496	122.0	117.0	119.0		801,	-1.8	0.0	13	dbSNP_116	119	1883,6717	335.3+/-321.3	225,1433,2642	yes	coding-synonymous-near-splice,intron	ATP12A	NM_001185085.1,NM_001676.5	,	293,2072,4138	GG,GA,AA		21.8953,17.5897,20.4367	,	267/1046,	25265103	2658,10348	2203	4300	6503	SO:0001627	intron_variant	479	exon8			TAAAGCATCTACT	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.800-17A>G	13.37:g.25265103A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			A|0.726;G|0.273	0.273	strong		0.572	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056590	7056590	+	Missense_Mutation	SNP	C	C	T	rs201052967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7056590C>T	ENST00000333843.4	-	2	404	c.370G>A	c.(370-372)Ggt>Agt	p.G124S		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					central_nervous_system(1)|lung(5)|stomach(1)	7						AGAGATTCACCGGCCGTCCCC	0.642																																					p.G124S		Atlas-SNP	.											MBD3L3,NS,haematopoietic_neoplasm,0,1	MBD3L3	12	1	0			c.G370A						scavenged	.						37.0	47.0	44.0					19																	7056590		692	1591	2283	SO:0001583	missense	653657	exon2			ATTCACCGGCCGT		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.370G>A	19.37:g.7056590C>T	ENSP00000333183:p.Gly124Ser	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	282	51	0.180851	NM_001164425		Missense_Mutation	SNP	ENST00000333843.4	37	CCDS45944.1	.	.	.	.	.	.	.	.	.	.	.	6.048	0.377169	0.11466	.	.	ENSG00000182315	ENST00000333843	.	.	.	0.742	0.742	0.18341	.	.	.	.	.	T	0.39937	0.1097	L	0.54323	1.7	0.80722	P	0.0	.	.	.	.	.	.	T	0.42155	-0.9468	5	0.13853	T	0.58	-14.6112	4.8637	0.13598	0.0:1.0:0.0:0.0	.	.	.	.	S	124	.	ENSP00000333183:G124S	G	-	1	0	MBD3L3	7007590	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.055000	0.14229	0.683000	0.31428	0.392000	0.25879	GGT	.	.	weak		0.642	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
HLA-C	3107	hgsc.bcm.edu	37	6	31237858	31237858	+	Silent	SNP	T	T	C	rs281860578|rs34794906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31237858T>C	ENST00000376228.5	-	5	914	c.900A>G	c.(898-900)ccA>ccG	p.P300P	HLA-C_ENST00000383329.3_Silent_p.P300P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	300	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						GCTGGGAAGATGGCTCTGGGA	0.592													t|||	2055	0.410343	0.4463	0.4438	5008	,	,		15975	0.5665		0.337	False		,,,				2504	0.2526				p.P300P		Atlas-SNP	.											.	HLA-C	92	.	0			c.A900G						PASS	.	C		1466,2932		353,760,1086	42.0	43.0	43.0		900	-5.3	0.0	6	dbSNP_126	43	2113,6485		349,1415,2535	no	coding-synonymous	HLA-C	NM_002117.5		702,2175,3621	CC,CT,TT		24.5755,33.3333,27.5392		300/367	31237858	3579,9417	2199	4299	6498	SO:0001819	synonymous_variant	3107	exon5			GGAAGATGGCTCT	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.900A>G	6.37:g.31237858T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			T|0.659;C|0.341	0.341	strong		0.592	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
POTEC	388468	hgsc.bcm.edu	37	18	14535001	14535001	+	Silent	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:14535001G>C	ENST00000358970.5	-	4	815	c.816C>G	c.(814-816)ggC>ggG	p.G272G	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	272										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GTGGTGTGAGGCCACACTGTA	0.313																																					p.G272G		Atlas-SNP	.											POTEC,NS,carcinoma,0,2	POTEC	129	2	0			c.C816G						scavenged	.						7.0	6.0	6.0					18																	14535001		666	1525	2191	SO:0001819	synonymous_variant	388468	exon4			TGTGAGGCCACAC	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.816C>G	18.37:g.14535001G>C		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	411	59	0.143552	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	weak		0.313	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
ST7	7982	hgsc.bcm.edu	37	7	116849886	116849886	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116849886C>T	ENST00000393446.2	+	12	1534	c.1231C>T	c.(1231-1233)Ctg>Ttg	p.L411L	ST7_ENST00000393443.1_Silent_p.L361L|ST7_ENST00000393447.4_Silent_p.L391L|ST7_ENST00000393449.1_Silent_p.L434L|ST7_ENST00000393451.3_Silent_p.L411L|ST7_ENST00000432298.1_Silent_p.L388L|ST7_ENST00000323984.3_Silent_p.L434L|ST7_ENST00000265437.5_Silent_p.L434L|ST7_ENST00000393444.3_Silent_p.L368L|ST7_ENST00000422922.1_Silent_p.L365L			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AGAACATATCCTGAAGAGAGG	0.388																																					p.L434L		Atlas-SNP	.											ST7,bladder,carcinoma,-2,1	ST7	64	1	0			c.C1300T						scavenged	.						99.0	87.0	91.0					7																	116849886		2203	4300	6503	SO:0001819	synonymous_variant	7982	exon13			CATATCCTGAAGA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.1231C>T	7.37:g.116849886C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	2	0.0266667	NM_021908	A8K137|B4DRQ2	Silent	SNP	ENST00000393446.2	37																																																																																				.	.	none		0.388	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908	
ZSWIM8	23053	hgsc.bcm.edu	37	10	75558867	75558867	+	Silent	SNP	G	G	A	rs2271271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:75558867G>A	ENST00000605216.1	+	21	4486	c.4269G>A	c.(4267-4269)ctG>ctA	p.L1423L	ZSWIM8_ENST00000603114.1_Silent_p.L1390L|ZSWIM8_ENST00000604524.1_Intron|ZSWIM8-AS1_ENST00000456638.2_RNA|RP11-574K11.31_ENST00000603027.1_Intron|ZSWIM8_ENST00000604729.1_Silent_p.L1428L|ZSWIM8_ENST00000398706.2_Silent_p.L1428L	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1423							zinc ion binding (GO:0008270)	p.L1428L(1)									GGTTCTGGCTGTATGAGCAAA	0.587													A|||	2443	0.487819	0.4887	0.4755	5008	,	,		19612	0.2351		0.7575	False		,,,				2504	0.4785				p.L1428L		Atlas-SNP	.											KIAA0913_ENST00000398706,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G4284A						PASS	.	A	,,	2251,1787		629,993,397	70.0	77.0	75.0		4269,4269,4284	-7.4	0.8	10	dbSNP_100	75	6280,2072		2374,1532,270	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	3003,2525,667	AA,AG,GG		24.8084,44.2546,31.1461	,,	1423/1838,1423/1893,1428/1843	75558867	8531,3859	2019	4176	6195	SO:0001819	synonymous_variant	23053	exon21			CTGGCTGTATGAG	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.4269G>A	10.37:g.75558867G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		1133|1133	0.5187728937728938|0.5187728937728938	242|242	0.491869918699187|0.491869918699187	199|199	0.5497237569060773|0.5497237569060773	134|134	0.23426573426573427|0.23426573426573427	558|558	0.7361477572559367|0.7361477572559367	A|A	6.766|6.766	0.510148|0.510148	0.12883|0.12883	0.557454|0.557454	0.751916|0.751916	ENSG00000214655|ENSG00000214655	ENST00000412198|ENST00000433366	.|.	.|.	.|.	5.59|5.59	-7.37|-7.37	0.01412|0.01412	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999095434|0.9999999999095434	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.26087|0.26087	-1.0113|-1.0113	3|3	.|.	.|.	.|.	-3.31|-3.31	7.2207|7.2207	0.25985|0.25985	0.1379:0.0839:0.5369:0.2413|0.1379:0.0839:0.5369:0.2413	rs2271271;rs58670385;rs2271271|rs2271271;rs58670385;rs2271271	.|.	.|.	.|.	Y|I	698|1139	.|.	.|.	C|V	+|+	2|1	0|0	KIAA0913|KIAA0913	75228873|75228873	0.217000|0.217000	0.23597|0.23597	0.814000|0.814000	0.32528|0.32528	0.981000|0.981000	0.71138|0.71138	-0.488000|-0.488000	0.06497|0.06497	-1.254000|-1.254000	0.02485|0.02485	-0.982000|-0.982000	0.02568|0.02568	TGT|GTA	G|0.465;A|0.535	0.535	strong		0.587	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
TMEM176B	28959	hgsc.bcm.edu	37	7	150491084	150491084	+	Missense_Mutation	SNP	T	T	G	rs3173833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150491084T>G	ENST00000447204.2	-	3	652	c.280A>C	c.(280-282)Agt>Cgt	p.S94R	TMEM176B_ENST00000326442.5_Missense_Mutation_p.S94R|TMEM176B_ENST00000450753.2_Intron|TMEM176B_ENST00000434545.1_Missense_Mutation_p.S94R|TMEM176B_ENST00000429904.2_Missense_Mutation_p.S94R|TMEM176B_ENST00000492607.1_Missense_Mutation_p.S94R	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	94			S -> R (in dbSNP:rs3173833). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9922225, ECO:0000269|Ref.2}.		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.S94R(1)		cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTGAGGCACTCAGCACAGTC	0.567													G|||	2725	0.544129	0.5045	0.4597	5008	,	,		17925	0.6111		0.5825	False		,,,				2504	0.5491				p.S94R		Atlas-SNP	.											TMEM176B,colon,carcinoma,0,2	TMEM176B	36	2	1	Substitution - Missense(1)	lung(1)	c.A280C						PASS	.	G	ARG/SER,ARG/SER,,ARG/SER	2240,2166	582.0+/-385.5	560,1120,523	220.0	191.0	201.0		280,280,,280	-0.5	0.4	7	dbSNP_105	201	4975,3625	522.3+/-380.1	1444,2087,769	yes	missense,missense,intron,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	110,110,,110	2004,3207,1292	GG,GT,TT		42.1512,49.1602,44.5256	benign,benign,,benign	94/271,94/271,,94/271	150491084	7215,5791	2203	4300	6503	SO:0001583	missense	28959	exon3			AGGCACTCAGCAC	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.280A>C	7.37:g.150491084T>G	ENSP00000410269:p.Ser94Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	1207	0.5526556776556777	243	0.49390243902439024	169	0.46685082872928174	373	0.6520979020979021	422	0.5567282321899736	g	0.561	-0.845274	0.02671	0.508398	0.578488	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000528038	T;T;T;T;T	0.02197	4.4;4.4;4.4;4.4;4.4	4.93	-0.527	0.11909	.	1.179070	0.06200	N	0.683094	T	0.00012	0.0000	N	0.00459	-1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13282	-1.0515	9	0.19590	T	0.45	-2.429	3.2027	0.06655	0.3704:0.0:0.3311:0.2985	rs3173833;rs11546673;rs17845015;rs17857781;rs17858296;rs52803574;rs59354064;rs3173833	94	Q3YBM2	T176B_HUMAN	R	94	ENSP00000419258:S94R;ENSP00000318409:S94R;ENSP00000410269:S94R;ENSP00000413531:S94R;ENSP00000397810:S94R	ENSP00000318409:S94R	S	-	1	0	TMEM176B	150122017	0.001000	0.12720	0.361000	0.25849	0.070000	0.16714	-0.697000	0.05098	-0.080000	0.12685	-0.245000	0.11935	AGT	T|0.444;G|0.556	0.556	strong		0.567	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
GPR52	9293	hgsc.bcm.edu	37	1	174417941	174417941	+	Missense_Mutation	SNP	G	G	A	rs200286780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:174417941G>A	ENST00000367685.2	+	1	730	c.692G>A	c.(691-693)cGt>cAt	p.R231H	RABGAP1L_ENST00000251507.4_Intron|RABGAP1L_ENST00000357444.6_Intron|RABGAP1L_ENST00000367689.3_Intron	NM_005684.4	NP_005675.3	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	231					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(3)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|prostate(1)|skin(2)	20						AAAATTTGCCGTCAGCACACC	0.463													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19971	0.0		0.0	False		,,,				2504	0.0				p.R231H	Ovarian(92;924 1390 1930 16467 40583)	Atlas-SNP	.											.	GPR52	40	.	0			c.G692A						PASS	.	G	HIS/ARG,	4,4402	8.1+/-20.4	0,4,2199	196.0	181.0	186.0		692,	6.2	1.0	1		186	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron	GPR52,RABGAP1L	NM_005684.4,NM_014857.4	29,	0,6,6497	AA,AG,GG		0.0233,0.0908,0.0461	probably-damaging,	231/362,	174417941	6,13000	2203	4300	6503	SO:0001583	missense	9293	exon1			TTTGCCGTCAGCA	AF096784	CCDS30941.1	1q24	2012-08-21			ENSG00000203737	ENSG00000203737		"""GPCR / Class A : Orphans"""	4508	protein-coding gene	gene with protein product		604106				9931487	Standard	NM_005684		Approved		uc001gka.1	Q9Y2T5	OTTHUMG00000034901	ENST00000367685.2:c.692G>A	1.37:g.174417941G>A	ENSP00000356658:p.Arg231His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_005684	O75654|Q4VBL6|Q6ISM0	Missense_Mutation	SNP	ENST00000367685.2	37	CCDS30941.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793374	0.70452	9.08E-4	2.33E-4	ENSG00000203737	ENST00000367685	T	0.42513	0.97	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.089581	0.47093	D	0.000250	T	0.55433	0.1920	L	0.54908	1.71	0.37430	D	0.913987	D	0.65815	0.995	P	0.52793	0.709	T	0.58352	-0.7651	10	0.66056	D	0.02	-9.9631	20.8598	0.99761	0.0:0.0:1.0:0.0	.	231	Q9Y2T5	GPR52_HUMAN	H	231	ENSP00000356658:R231H	ENSP00000356658:R231H	R	+	2	0	GPR52	172684564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.126000	0.77201	2.937000	0.99478	0.650000	0.86243	CGT	.	.	weak		0.463	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684	
DNAH2	146754	hgsc.bcm.edu	37	17	7701922	7701922	+	Silent	SNP	G	G	A	rs146210717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7701922G>A	ENST00000572933.1	+	55	9905	c.8445G>A	c.(8443-8445)acG>acA	p.T2815T	DNAH2_ENST00000389173.2_Silent_p.T2815T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2815	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(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)				TCAAGACCACGTCCTTCATTT	0.547													G|||	4	0.000798722	0.0	0.0	5008	,	,		18237	0.0		0.004	False		,,,				2504	0.0				p.T2815T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G8445A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	111.0	102.0	105.0		8445	-9.6	0.9	17	dbSNP_134	105	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous	DNAH2	NM_020877.2		0,26,6477	AA,AG,GG		0.2791,0.0454,0.1999		2815/4428	7701922	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon54			GACCACGTCCTTC	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.8445G>A	17.37:g.7701922G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.999;A|0.001	0.001	strong		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
SLC36A3	285641	hgsc.bcm.edu	37	5	150664183	150664183	+	Silent	SNP	G	G	C	rs17111902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150664183G>C	ENST00000335230.3	-	7	1209	c.798C>G	c.(796-798)ggC>ggG	p.G266G	SLC36A3_ENST00000377713.3_Silent_p.G307G	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	266						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)			CCATACCGACGCCTTCAAATG	0.458													G|||	500	0.0998403	0.295	0.0403	5008	,	,		20976	0.0		0.0408	False		,,,				2504	0.0419				p.G307G		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C921G						PASS	.	G	,	1178,3228	413.7+/-336.6	151,876,1176	107.0	97.0	101.0		921,798	-6.7	0.0	5	dbSNP_123	101	379,8221	123.8+/-182.6	4,371,3925	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	155,1247,5101	CC,CG,GG		4.407,26.7363,11.9714	,	307/512,266/471	150664183	1557,11449	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon8			ACCGACGCCTTCA	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.798C>G	5.37:g.150664183G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			G|0.895;C|0.105	0.105	strong		0.458	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
SERINC2	347735	hgsc.bcm.edu	37	1	31896608	31896608	+	Silent	SNP	C	C	T	rs78029434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:31896608C>T	ENST00000373709.3	+	2	258	c.108C>T	c.(106-108)acC>acT	p.T36T	SERINC2_ENST00000373710.1_Silent_p.T45T|SERINC2_ENST00000536384.1_Silent_p.T40T|SERINC2_ENST00000536859.1_Silent_p.T40T|SERINC2_ENST00000491976.1_3'UTR	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	36					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		GCAACTCCACCGTGAGCCGCC	0.642													C|||	76	0.0151757	0.0	0.0086	5008	,	,		16664	0.002		0.0338	False		,,,				2504	0.0348				p.T45T		Atlas-SNP	.											.	SERINC2	44	.	0			c.C135T						PASS	.	C	,,,,	23,4383	31.7+/-61.6	0,23,2180	62.0	64.0	63.0		120,135,,120,108	-2.2	0.8	1	dbSNP_131	63	280,8318	105.0+/-166.0	4,272,4023	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous,coding-synonymous	SERINC2	NM_001199037.1,NM_001199038.1,NM_001199039.1,NM_018565.3,NM_178865.4	,,,,	4,295,6203	TT,TC,CC		3.2566,0.522,2.3301	,,,,	40/460,45/465,,40/460,36/456	31896608	303,12701	2203	4299	6502	SO:0001819	synonymous_variant	347735	exon3			CTCCACCGTGAGC	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"""tumor differentially expressed 2-like"""	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.108C>T	1.37:g.31896608C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_001199038	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Silent	SNP	ENST00000373709.3	37	CCDS30662.1																																																																																			C|0.980;T|0.020	0.020	strong		0.642	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565	
ADAMTSL2	9719	hgsc.bcm.edu	37	9	136412296	136412296	+	Silent	SNP	C	C	T	rs2073877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136412296C>T	ENST00000354484.4	+	9	1457	c.900C>T	c.(898-900)atC>atT	p.I300I	ADAMTSL2_ENST00000393060.1_Silent_p.I300I|ADAMTSL2_ENST00000393061.3_Silent_p.I409I	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	300					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		TCGAGTACATCGTGGCACAGG	0.607													C|||	480	0.0958466	0.0129	0.0951	5008	,	,		17249	0.1419		0.1521	False		,,,				2504	0.1033				p.I300I		Atlas-SNP	.											.	ADAMTSL2	40	.	0			c.C900T						PASS	.	C	,	170,4236	113.3+/-151.4	4,162,2037	150.0	143.0	145.0		900,900	-6.0	0.9	9	dbSNP_96	145	1105,7495	229.7+/-264.3	79,947,3274	no	coding-synonymous,coding-synonymous	ADAMTSL2	NM_001145320.1,NM_014694.3	,	83,1109,5311	TT,TC,CC		12.8488,3.8584,9.8032	,	300/952,300/952	136412296	1275,11731	2203	4300	6503	SO:0001819	synonymous_variant	9719	exon9			GTACATCGTGGCA	AB011177	CCDS6976.1	9q34.3	2005-01-12			ENSG00000197859	ENSG00000197859			14631	protein-coding gene	gene with protein product		612277				9628581, 14667842	Standard	NM_014694		Approved	KIAA0605	uc004cei.3	Q86TH1	OTTHUMG00000131706	ENST00000354484.4:c.900C>T	9.37:g.136412296C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_014694	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	37	CCDS6976.1																																																																																			C|0.895;T|0.105	0.105	strong		0.607	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694	
NRAP	4892	hgsc.bcm.edu	37	10	115422474	115422474	+	Silent	SNP	A	A	G	rs3127122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115422474A>G	ENST00000359988.3	-	3	463	c.219T>C	c.(217-219)aaT>aaC	p.N73N	NRAP_ENST00000360478.3_Silent_p.N73N|NRAP_ENST00000369360.3_Silent_p.N73N|NRAP_ENST00000369358.4_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	66	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	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	
NLRP14	338323	hgsc.bcm.edu	37	11	7059981	7059981	+	Missense_Mutation	SNP	G	G	A	rs61063081	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7059981G>A	ENST00000299481.4	+	2	510	c.164G>A	c.(163-165)cGg>cAg	p.R55Q		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	55	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		R -> E (requires 2 nucleotide substitutions). {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)		AAGGCCAGGCGGGAGGACCTG	0.443													G|||	482	0.096246	0.0666	0.1297	5008	,	,		18849	0.0179		0.2147	False		,,,				2504	0.0716				p.R55Q		Atlas-SNP	.											.	NLRP14	187	.	0			c.G164A						PASS	.	G	GLN/ARG	370,4032	182.9+/-210.6	13,344,1844	58.0	63.0	61.0		164	2.2	0.0	11	dbSNP_129	61	1840,6752	325.0+/-316.7	200,1440,2656	yes	missense	NLRP14	NM_176822.3	43	213,1784,4500	AA,AG,GG		21.4153,8.4053,17.0078	probably-damaging	55/1094	7059981	2210,10784	2201	4296	6497	SO:0001583	missense	338323	exon2			CCAGGCGGGAGGA	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.164G>A	11.37:g.7059981G>A	ENSP00000299481:p.Arg55Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	247	0.1130952380952381	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	162	0.21372031662269128	G	14.50	2.554234	0.45487	0.084053	0.214153	ENSG00000158077	ENST00000299481	T	0.53857	0.6	4.22	2.23	0.28157	Pyrin (2);DEATH-like (2);	0.529188	0.15927	N	0.237859	T	0.00109	0.0003	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	P	0.62089	0.898	T	0.17289	-1.0374	9	0.19147	T	0.46	.	10.4223	0.44356	0.0:0.3865:0.6135:0.0	rs61063081;rs61879042	55	Q86W24	NAL14_HUMAN	Q	55	ENSP00000299481:R55Q	ENSP00000299481:R55Q	R	+	2	0	NLRP14	7016557	0.001000	0.12720	0.000000	0.03702	0.948000	0.59901	0.751000	0.26348	0.659000	0.30945	0.655000	0.94253	CGG	G|0.835;A|0.165	0.165	strong		0.443	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
KRT37	8688	hgsc.bcm.edu	37	17	39579059	39579059	+	Nonsense_Mutation	SNP	G	G	A	rs78158550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39579059G>A	ENST00000225550.3	-	3	702	c.703C>T	c.(703-705)Cag>Tag	p.Q235*	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	235	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				AGGGAGAGCTGCTCCTCCTTC	0.692													G|||	862	0.172125	0.034	0.1268	5008	,	,		17559	0.3214		0.1759	False		,,,				2504	0.2331				p.Q235X		Atlas-SNP	.											.	KRT37	61	.	0			c.C703T						PASS	.						53.0	45.0	48.0					17																	39579059		2203	4298	6501	SO:0001587	stop_gained	8688	exon3			AGAGCTGCTCCTC	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.703C>T	17.37:g.39579059G>A	ENSP00000225550:p.Gln235*	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_003770		Nonsense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	381	0.17445054945054944	21	0.042682926829268296	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	25.9	4.682848	0.88542	.	.	ENSG00000108417	ENST00000225550	.	.	.	4.86	3.87	0.44632	.	0.713944	0.11971	N	0.511799	.	.	.	.	.	.	0.09310	P	0.9999999999999974	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.7517	0.62912	0.0:0.0:0.8457:0.1543	.	.	.	.	X	235	.	ENSP00000225550:Q235X	Q	-	1	0	KRT37	36832585	0.982000	0.34865	0.981000	0.43875	0.878000	0.50629	3.380000	0.52448	1.016000	0.39470	0.655000	0.94253	CAG	G|0.847;A|0.153	0.153	strong		0.692	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
FBXO17	115290	hgsc.bcm.edu	37	19	39433299	39433299	+	Silent	SNP	A	A	G	rs8113389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39433299A>G	ENST00000292852.4	-	6	1127	c.786T>C	c.(784-786)taT>taC	p.Y262Y	FBXO17_ENST00000595329.1_Silent_p.Y262Y|SARS2_ENST00000448145.2_Intron|CTC-360G5.8_ENST00000599996.1_Intron	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	262	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)	p.Y271Y(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CAAGGGCGCCATAGTGCCCCA	0.582													G|||	4193	0.83726	0.9228	0.8314	5008	,	,		17929	0.9782		0.671	False		,,,				2504	0.7515				p.Y271Y		Atlas-SNP	.											FBXO17,NS,carcinoma,0,1	FBXO17	42	1	1	Substitution - coding silent(1)	prostate(1)	c.T813C						PASS	.	G	,	3870,536	242.5+/-252.5	1698,474,31	113.0	100.0	104.0		786,813	-9.5	0.0	19	dbSNP_116	104	5351,3249	488.2+/-372.3	1650,2051,599	no	coding-synonymous,coding-synonymous	FBXO17	NM_024907.5,NM_148169.1	,	3348,2525,630	GG,GA,AA		37.7791,12.1652,29.102	,	262/279,271/288	39433299	9221,3785	2203	4300	6503	SO:0001819	synonymous_variant	115290	exon6			GGCGCCATAGTGC	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"""F-boxes /  ""other"""""	18754	protein-coding gene	gene with protein product	"""F-box only protein 26"""	609094	"""F-box only protein 17"""	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.786T>C	19.37:g.39433299A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_148169	Q96LQ4	Silent	SNP	ENST00000292852.4	37	CCDS12526.1																																																																																			A|0.241;G|0.759	0.759	strong		0.582	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907	
ENKD1	84080	hgsc.bcm.edu	37	16	67697922	67697922	+	Missense_Mutation	SNP	C	C	T	rs143645135	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:67697922C>T	ENST00000243878.4	-	4	818	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	C16orf86_ENST00000403458.4_5'Flank|ENKD1_ENST00000602644.1_Missense_Mutation_p.R166Q|ENKD1_ENST00000602409.1_Intron	NM_032140.1	NP_115516.1	Q9H0I2	ENKD1_HUMAN	enkurin domain containing 1	166						cytoplasmic microtubule (GO:0005881)|microtubule cytoskeleton (GO:0015630)											GGAGTGCGCCCGCAGGAAGTG	0.667													c|||	39	0.00778754	0.0023	0.0159	5008	,	,		16164	0.0		0.0229	False		,,,				2504	0.002				p.R166Q		Atlas-SNP	.											.	.	.	.	0			c.G497A						PASS	.		GLN/ARG	28,4350		0,28,2161	23.0	24.0	24.0		497	3.6	1.0	16	dbSNP_134	24	221,8361		1,219,4071	yes	missense	C16orf48	NM_032140.1	43	1,247,6232	TT,TC,CC		2.5752,0.6396,1.9213	probably-damaging	166/347	67697922	249,12711	2189	4291	6480	SO:0001583	missense	84080	exon4			TGCGCCCGCAGGA	BC008284	CCDS10844.1	16q22.1	2012-10-09	2012-10-09	2012-10-09	ENSG00000124074	ENSG00000124074			25246	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 48"""	C16orf48		11230166	Standard	NM_032140		Approved	DKFZP434A1319	uc002etw.1	Q9H0I2	OTTHUMG00000137550	ENST00000243878.4:c.497G>A	16.37:g.67697922C>T	ENSP00000243878:p.Arg166Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_032140	Q6UWD7	Missense_Mutation	SNP	ENST00000243878.4	37	CCDS10844.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	c	15.33	2.802673	0.50315	0.006396	0.025752	ENSG00000124074	ENST00000243878	.	.	.	4.54	3.58	0.41010	.	0.126742	0.53938	D	0.000051	T	0.45418	0.1341	M	0.68952	2.095	0.36328	D	0.858656	D;D	0.89917	0.979;1.0	B;D	0.81914	0.328;0.995	T	0.65298	-0.6202	9	0.39692	T	0.17	-9.5053	7.5019	0.27522	0.0:0.7984:0.0:0.2016	.	166;48	Q9H0I2;Q9H0I2-2	CP048_HUMAN;.	Q	166	.	ENSP00000243878:R166Q	R	-	2	0	C16orf48	66255423	0.428000	0.25522	0.999000	0.59377	0.390000	0.30446	1.170000	0.31883	1.040000	0.40099	0.556000	0.70494	CGG	C|0.984;T|0.016	0.016	strong		0.667	ENKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268884.1	NM_032140	
IL12RB2	3595	hgsc.bcm.edu	37	1	67852335	67852335	+	Silent	SNP	G	G	A	rs2228420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000541374.1_Silent_p.T643T|IL12RB2_ENST00000371000.1_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	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	157	157	1	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	
USP35	57558	hgsc.bcm.edu	37	11	77920930	77920930	+	Missense_Mutation	SNP	A	A	G	rs2511188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77920930A>G	ENST00000529308.1	+	10	2290	c.2029A>G	c.(2029-2031)Ata>Gta	p.I677V	USP35_ENST00000530267.1_Missense_Mutation_p.I245V|USP35_ENST00000526425.1_Missense_Mutation_p.I408V|USP35_ENST00000441408.2_Missense_Mutation_p.I263V|USP35_ENST00000530535.1_3'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	677	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)			GGAGGAAAGGATAgagaggga	0.572													G|||	1753	0.35004	0.4425	0.3501	5008	,	,		17920	0.4087		0.2356	False		,,,				2504	0.2822				p.I677V		Atlas-SNP	.											.	USP35	179	.	0			c.A2029G						PASS	.	G	VAL/ILE	1585,2413		324,937,738	57.0	75.0	69.0		2029	4.2	0.0	11	dbSNP_100	69	1661,6659		177,1307,2676	yes	missense	USP35	NM_020798.2	29	501,2244,3414	GG,GA,AA		19.9639,39.6448,26.3517	benign	677/1019	77920930	3246,9072	1999	4160	6159	SO:0001583	missense	57558	exon10			GAAAGGATAGAGA	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.2029A>G	11.37:g.77920930A>G	ENSP00000431876:p.Ile677Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	734	0.3360805860805861	210	0.4268292682926829	112	0.30939226519337015	232	0.40559440559440557	180	0.23746701846965698	G	1.578	-0.532275	0.04112	0.396448	0.199639	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.06371	3.33;3.47;3.47;3.31	5.18	4.24	0.50183	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.086910	0.02959	N	0.142834	T	0.00012	0.0000	N	0.05351	-0.065	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46775	-0.9167	9	0.13470	T	0.59	-0.7345	7.0124	0.24869	0.0915:0.1736:0.7349:0.0	rs2511188;rs3740675;rs52810330;rs59657177;rs2511188	677;263	Q9P2H5;E7EWV7	UBP35_HUMAN;.	V	245;677;263;408	ENSP00000435468:I245V;ENSP00000431876:I677V;ENSP00000400825:I263V;ENSP00000434942:I408V	ENSP00000400825:I263V	I	+	1	0	USP35	77598578	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.431000	0.21444	0.737000	0.32582	-0.119000	0.15052	ATA	A|0.644;G|0.356	0.356	strong		0.572	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
CCNY	219771	hgsc.bcm.edu	37	10	35772402	35772402	+	Silent	SNP	G	G	A	rs3802509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:35772402G>A	ENST00000374704.4	+	2	405	c.225G>A	c.(223-225)acG>acA	p.T75T	CCNY_ENST00000265375.9_Silent_p.T21T|CCNY_ENST00000492478.1_3'UTR|CCNY_ENST00000374706.1_Silent_p.T21T|CCNY_ENST00000339497.5_Intron	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	75					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						AATCTCAGACGGACGGTAGGT	0.343													A|||	2289	0.457069	0.6536	0.4539	5008	,	,		17108	0.4266		0.3241	False		,,,				2504	0.362				p.T75T		Atlas-SNP	.											CCNY,rectum,carcinoma,+1,1	CCNY	22	1	0			c.G225A						PASS	.	A	,	2720,1686	511.6+/-367.8	849,1022,332	86.0	82.0	83.0		225,63	-11.7	0.0	10	dbSNP_107	83	2772,5828	678.6+/-403.5	433,1906,1961	no	coding-synonymous,coding-synonymous	CCNY	NM_145012.4,NM_181698.2	,	1282,2928,2293	AA,AG,GG		32.2326,38.266,42.2267	,	75/342,21/288	35772402	5492,7514	2203	4300	6503	SO:0001819	synonymous_variant	219771	exon2			TCAGACGGACGGT	AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100			23354	protein-coding gene	gene with protein product		612786	"""chromosome 10 open reading frame 9"""	C10orf9		20441050	Standard	XM_005252388		Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.225G>A	10.37:g.35772402G>A		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	254	114	0.448819	NM_145012	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	Silent	SNP	ENST00000374704.4	37	CCDS7189.1																																																																																			G|0.564;A|0.436	0.436	strong		0.343	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047568.2	NM_181698	
HCN2	610	hgsc.bcm.edu	37	19	613307	613307	+	Silent	SNP	C	C	T	rs2301778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:613307C>T	ENST00000251287.2	+	6	1697	c.1644C>T	c.(1642-1644)gcC>gcT	p.A548A	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	548					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		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)		TCGCCAACGCCGACCCCAACT	0.627													c|||	1428	0.285144	0.2837	0.1859	5008	,	,		11918	0.2659		0.3241	False		,,,				2504	0.3374				p.A548A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C1644T						PASS	.	T		1182,3224		148,886,1169	60.0	50.0	53.0		1644	-7.9	0.0	19	dbSNP_100	53	2551,6047		378,1795,2126	no	coding-synonymous	HCN2	NM_001194.3		526,2681,3295	TT,TC,CC		29.6697,26.8271,28.7066		548/890	613307	3733,9271	2203	4299	6502	SO:0001819	synonymous_variant	610	exon6			CAACGCCGACCCC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1644C>T	19.37:g.613307C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.712;T|0.288	0.288	strong		0.627	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
ZNF345	25850	hgsc.bcm.edu	37	19	37368887	37368887	+	Silent	SNP	T	T	A	rs4806370	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37368887T>A	ENST00000529555.1	+	2	1943	c.1155T>A	c.(1153-1155)ctT>ctA	p.L385L	ZNF345_ENST00000420450.1_Silent_p.L385L|ZNF345_ENST00000589046.1_Silent_p.L385L|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	385					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	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(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GCTCAAAACTTATCCAACACC	0.423													T|||	97	0.019369	0.0015	0.0403	5008	,	,		21000	0.0		0.0606	False		,,,				2504	0.0061				p.L385L		Atlas-SNP	.											.	ZNF345	68	.	0			c.T1155A						PASS	.	T	,,,,	49,4357	50.2+/-85.5	0,49,2154	88.0	82.0	84.0		1155,1155,1155,1155,1155	1.8	1.0	19	dbSNP_111	84	516,8084	146.5+/-202.0	13,490,3797	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF345	NM_001242472.1,NM_001242474.1,NM_001242475.1,NM_001242476.1,NM_003419.4	,,,,	13,539,5951	AA,AT,TT		6.0,1.1121,4.3441	,,,,	385/489,385/489,385/489,385/489,385/489	37368887	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	25850	exon4			AAAACTTATCCAA	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1155T>A	19.37:g.37368887T>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001242476		Silent	SNP	ENST00000529555.1	37	CCDS12497.1																																																																																			T|0.961;A|0.039	0.039	strong		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
BCR	613	hgsc.bcm.edu	37	22	23615946	23615946	+	Silent	SNP	G	G	A	rs34646520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23615946G>A	ENST00000305877.8	+	8	2851	c.2100G>A	c.(2098-2100)acG>acA	p.T700T	BCR_ENST00000359540.3_Silent_p.T700T	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	700					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)	AGTCCATGACGGTGAAGAAGG	0.632			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""								G|||	80	0.0159744	0.0287	0.0086	5008	,	,		21593	0.0		0.0298	False		,,,				2504	0.0061				p.T700T		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	BCR,NS,carcinoma,+1,1	BCR	74	1	0			c.G2100A						scavenged	.	G	,	129,4277	94.4+/-133.1	4,121,2078	91.0	81.0	84.0		2100,2100	-9.3	0.2	22	dbSNP_126	84	212,8388	91.1+/-153.3	4,204,4092	no	coding-synonymous,coding-synonymous	BCR	NM_004327.3,NM_021574.2	,	8,325,6170	AA,AG,GG		2.4651,2.9278,2.6219	,	700/1272,700/1228	23615946	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	613	exon8			CATGACGGTGAAG		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.2100G>A	22.37:g.23615946G>A		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			G|0.978;A|0.022	0.022	strong		0.632	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
MYOF	26509	hgsc.bcm.edu	37	10	95168634	95168634	+	Silent	SNP	A	A	G	rs2296142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:95168634A>G	ENST00000359263.4	-	7	638	c.639T>C	c.(637-639)ggT>ggC	p.G213G	MYOF_ENST00000358334.5_Silent_p.G213G|MYOF_ENST00000371502.4_Silent_p.G213G|MYOF_ENST00000371489.1_Silent_p.G213G|MYOF_ENST00000371501.4_Silent_p.G213G	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	213	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Necessary for interaction with EHD2.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTATGTTGTTACCACTTAACT	0.507													g|||	1049	0.209465	0.059	0.1499	5008	,	,		22153	0.6677		0.0318	False		,,,				2504	0.1656				p.G213G		Atlas-SNP	.											.	MYOF	177	.	0			c.T639C						PASS	.	G	,	249,3717		3,243,1737	148.0	134.0	138.0		639,639	1.3	1.0	10	dbSNP_100	138	275,8055		4,267,3894	no	coding-synonymous,coding-synonymous	MYOF	NM_013451.3,NM_133337.2	,	7,510,5631	GG,GA,AA		3.3013,6.2784,4.2615	,	213/2062,213/2049	95168634	524,11772	1983	4165	6148	SO:0001819	synonymous_variant	26509	exon7			GTTGTTACCACTT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.639T>C	10.37:g.95168634A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_133337	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																			A|0.857;G|0.143	0.143	strong		0.507	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
MYOM3	127294	hgsc.bcm.edu	37	1	24394811	24394811	+	Missense_Mutation	SNP	A	A	G	rs12145360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24394811A>G	ENST00000374434.3	-	26	3359	c.3197T>C	c.(3196-3198)aTc>aCc	p.I1066T	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000329601.7_Missense_Mutation_p.I1066T|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000338909.5_5'Flank|MYOM3_ENST00000330966.7_Missense_Mutation_p.I1067T	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1066			I -> T (in dbSNP:rs12145360).			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)		GTTCTGGATGATCACTTCCAC	0.478													A|||	982	0.196086	0.2262	0.1427	5008	,	,		16302	0.1964		0.1372	False		,,,				2504	0.2536				p.I1066T		Atlas-SNP	.											.	MYOM3	131	.	0			c.T3197C						PASS	.	A	THR/ILE	715,3291		61,593,1349	284.0	282.0	282.0		3197	4.7	1.0	1	dbSNP_120	282	1118,7206		69,980,3113	yes	missense	MYOM3	NM_152372.3	89	130,1573,4462	GG,GA,AA		13.431,17.8482,14.8662	benign	1066/1438	24394811	1833,10497	2003	4162	6165	SO:0001583	missense	127294	exon26			TGGATGATCACTT	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.3197T>C	1.37:g.24394811A>G	ENSP00000363557:p.Ile1066Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	352	0.16117216117216118	90	0.18292682926829268	52	0.143646408839779	109	0.19055944055944055	101	0.13324538258575197	A	12.56	1.975219	0.34848	0.178482	0.13431	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.04317	3.65;3.65;3.65	4.69	4.69	0.59074	Immunoglobulin-like fold (1);	0.245363	0.35936	N	0.002893	T	0.00012	0.0000	L	0.31578	0.945	0.27553	P	0.9504333	B;B	0.16166	0.004;0.016	B;B	0.17979	0.02;0.008	T	0.47446	-0.9117	9	0.19590	T	0.45	.	9.5611	0.39369	0.9152:0.0:0.0848:0.0	rs12145360;rs52790715;rs12145360	1066;1066	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	T	1066;1067;1066	ENSP00000363557:I1066T;ENSP00000332670:I1067T;ENSP00000328415:I1066T	ENSP00000328415:I1066T	I	-	2	0	MYOM3	24267398	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.548000	0.60718	1.887000	0.54652	0.379000	0.24179	ATC	A|0.836;G|0.164	0.164	strong		0.478	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
ABHD8	79575	hgsc.bcm.edu	37	19	17412399	17412399	+	Silent	SNP	G	G	A	rs11086067	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17412399G>A	ENST00000247706.3	-	2	266	c.27C>T	c.(25-27)atC>atT	p.I9I	MRPL34_ENST00000594999.1_5'Flank|MRPL34_ENST00000595444.1_Intron|MRPL34_ENST00000600434.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	9							hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						GGCAACAGAAGATACCGTCGG	0.637													G|||	1195	0.238618	0.1309	0.2277	5008	,	,		15449	0.1319		0.329	False		,,,				2504	0.409				p.I9I	Ovarian(156;1368 2543 15275 41187)	Atlas-SNP	.											.	ABHD8	26	.	0			c.C27T						PASS	.	G		712,3626		64,584,1521	25.0	27.0	26.0		27	4.0	1.0	19	dbSNP_120	26	2408,5992		361,1686,2153	no	coding-synonymous	ABHD8	NM_024527.4		425,2270,3674	AA,AG,GG		28.6667,16.4131,24.4936		9/440	17412399	3120,9618	2169	4200	6369	SO:0001819	synonymous_variant	79575	exon2			ACAGAAGATACCG	AK021805	CCDS12355.1	19p13.12	2010-12-09			ENSG00000127220	ENSG00000127220		"""Abhydrolase domain containing"""	23759	protein-coding gene	gene with protein product						12477932	Standard	NM_024527		Approved	FLJ11743, MGC14280, MGC2512	uc002ngb.4	Q96I13		ENST00000247706.3:c.27C>T	19.37:g.17412399G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_024527	Q9HAE9	Silent	SNP	ENST00000247706.3	37	CCDS12355.1																																																																																			G|0.778;A|0.222	0.222	strong		0.637	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	NM_024527	
OR5H14	403273	hgsc.bcm.edu	37	3	97868656	97868656	+	Missense_Mutation	SNP	C	C	T	rs146577101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:97868656C>T	ENST00000437310.1	+	1	487	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	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)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ACTGTGCATCCGGCTATTAAT	0.388																																					p.R143W		Atlas-SNP	.											.	OR5H14	56	.	0			c.C427T						PASS	.	C	TRP/ARG	107,4297		0,107,2095	118.0	120.0	119.0		427	-0.7	0.0	3	dbSNP_134	119	163,8435		0,163,4136	no	missense	OR5H14	NM_001005514.1	101	0,270,6231	TT,TC,CC		1.8958,2.4296,2.0766	benign	143/311	97868656	270,12732	2202	4299	6501	SO:0001583	missense	403273	exon1			TGCATCCGGCTAT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.427C>T	3.37:g.97868656C>T	ENSP00000401706:p.Arg143Trp	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	529	72	0.136106	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	5.787	0.329517	0.10956	0.024296	0.018958	ENSG00000236032	ENST00000437310	T	0.00130	8.69	2.49	-0.723	0.11181	GPCR, rhodopsin-like superfamily (1);	1.524830	0.04305	N	0.347965	T	0.00073	0.0002	L	0.39467	1.215	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.23190	-1.0195	10	0.34782	T	0.22	.	3.4429	0.07470	0.0:0.3739:0.2056:0.4205	.	143	A6NHG9	O5H14_HUMAN	W	143	ENSP00000401706:R143W	ENSP00000401706:R143W	R	+	1	2	OR5H14	99351346	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.390000	0.00487	-0.356000	0.08187	0.195000	0.17529	CGG	C|0.936;T|0.064	0.064	strong		0.388	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
LRRK2	120892	hgsc.bcm.edu	37	12	40758652	40758652	+	Missense_Mutation	SNP	T	T	C	rs3761863	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:40758652T>C	ENST00000298910.7	+	49	7248	c.7190T>C	c.(7189-7191)aTg>aCg	p.M2397T		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2397			M -> T (in dbSNP:rs3761863). {ECO:0000269|PubMed:16157901, ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:22415848}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGGGAGGTAATGGTAAAAGAA	0.313											OREG0003828	type=REGULATORY REGION|Gene=LRRK2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2763	0.551717	0.4917	0.5288	5008	,	,		17212	0.4603		0.67	False		,,,				2504	0.6217				p.M2397T		Atlas-SNP	.											.	LRRK2	763	.	0			c.T7190C						PASS	.	C	THR/MET	2328,2076	565.4+/-381.7	620,1088,494	59.0	59.0	59.0		7190	3.0	0.0	12	dbSNP_107	59	5634,2966	456.7+/-364.1	1835,1964,501	yes	missense	LRRK2	NM_198578.3	81	2455,3052,995	CC,CT,TT		34.4884,47.139,38.7727	benign	2397/2528	40758652	7962,5042	2202	4300	6502	SO:0001583	missense	120892	exon49			AGGTAATGGTAAA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.7190T>C	12.37:g.40758652T>C	ENSP00000298910:p.Met2397Thr	Somatic	41	0	0	895	WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	1200	0.5494505494505495	227	0.4613821138211382	200	0.5524861878453039	254	0.44405594405594406	519	0.6846965699208444	C	0.003	-2.416372	0.00188	0.52861	0.655116	ENSG00000188906	ENST00000298910	T	0.70986	-0.53	5.42	3.03	0.35002	WD40 repeat-like-containing domain (1);	0.488362	0.23914	N	0.043310	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45833	-0.9234	9	0.20519	T	0.43	.	10.427	0.44385	0.0:0.2005:0.0:0.7995	rs3761863;rs17444209;rs17520641;rs52804951;rs57437154;rs3761863	2397	Q5S007	LRRK2_HUMAN	T	2397	ENSP00000298910:M2397T	ENSP00000298910:M2397T	M	+	2	0	LRRK2	39044919	0.003000	0.15002	0.005000	0.12908	0.154000	0.21943	0.377000	0.20552	0.378000	0.24764	-1.160000	0.01791	ATG	T|0.417;C|0.583	0.583	strong		0.313	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
FLNB	2317	hgsc.bcm.edu	37	3	58081888	58081888	+	Silent	SNP	T	T	C	rs1522384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000429972.2_Silent_p.S309S|FLNB_ENST00000493452.1_Silent_p.S140S|FLNB_ENST00000419752.2_Silent_p.S140S|FLNB_ENST00000358537.3_Silent_p.S309S|FLNB_ENST00000357272.4_Silent_p.S309S|FLNB_ENST00000348383.5_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	59	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	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	
PIK3R3	8503	hgsc.bcm.edu	37	1	46521517	46521517	+	Silent	SNP	G	G	A	rs785468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46521517G>A	ENST00000262741.5	-	7	1580	c.891C>T	c.(889-891)agC>agT	p.S297S	PIK3R3_ENST00000420542.1_Silent_p.S297S|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000540385.1_Silent_p.S343S|PIK3R3_ENST00000340332.6_Intron|PIK3R3_ENST00000354242.4_Intron|PIK3R3_ENST00000423209.1_Intron|PIK3R3_ENST00000372006.1_Silent_p.S297S	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	297					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CAGGTTTGATGCTATTCATTT	0.438													A|||	3195	0.637979	0.5893	0.6254	5008	,	,		15100	0.6885		0.7336	False		,,,				2504	0.5624				p.S297S		Atlas-SNP	.											.	PIK3R3	41	.	0			c.C891T						PASS	.	A	,	2648,1758	522.2+/-370.7	802,1044,357	218.0	199.0	206.0		891,891	0.7	1.0	1	dbSNP_86	206	6086,2514	411.6+/-350.5	2163,1760,377	no	coding-synonymous,coding-synonymous	PIK3R3	NM_001114172.1,NM_003629.3	,	2965,2804,734	AA,AG,GG		29.2326,39.9001,32.8464	,	297/462,297/462	46521517	8734,4272	2203	4300	6503	SO:0001819	synonymous_variant	8503	exon8			TTTGATGCTATTC	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"""SH2 domain containing"""	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.891C>T	1.37:g.46521517G>A		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_001114172	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Silent	SNP	ENST00000262741.5	37	CCDS529.1																																																																																			G|0.336;A|0.664	0.664	strong		0.438	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	
TMEM63A	9725	hgsc.bcm.edu	37	1	226034909	226034909	+	Silent	SNP	G	G	A	rs41441645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:226034909G>A	ENST00000366835.3	-	24	2526	c.2256C>T	c.(2254-2256)taC>taT	p.Y752Y	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	752					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)					TCCGAGGCACGTAGGGCTGTC	0.592													G|||	113	0.0225639	0.003	0.0029	5008	,	,		20337	0.0863		0.0119	False		,,,				2504	0.0082				p.Y752Y		Atlas-SNP	.											TMEM63A,colon,carcinoma,-2,1	TMEM63A	75	1	0			c.C2256T						PASS	.	G		41,4361	42.3+/-75.8	0,41,2160	69.0	59.0	62.0		2256	-8.2	0.7	1	dbSNP_127	62	138,8458	63.9+/-126.0	1,136,4161	no	coding-synonymous	TMEM63A	NM_014698.2		1,177,6321	AA,AG,GG		1.6054,0.9314,1.3771		752/808	226034909	179,12819	2201	4298	6499	SO:0001819	synonymous_variant	9725	exon24			AGGCACGTAGGGC		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.2256C>T	1.37:g.226034909G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.983;A|0.017	0.017	strong		0.592	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
VEGFA	7422	hgsc.bcm.edu	37	6	43738977	43738977	+	5'UTR	SNP	C	C	T	rs25648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43738977C>T	ENST00000523873.1	+	0	32				RP1-261G23.7_ENST00000607600.1_RNA|VEGFA_ENST00000230480.6_5'Flank|VEGFA_ENST00000417285.2_Silent_p.S178S|VEGFA_ENST00000372077.4_5'UTR|VEGFA_ENST00000520948.1_5'UTR|VEGFA_ENST00000523950.1_5'UTR|VEGFA_ENST00000518689.1_5'Flank|VEGFA_ENST00000372055.4_Silent_p.S178S|VEGFA_ENST00000457104.2_5'Flank|VEGFA_ENST00000518824.1_5'Flank|VEGFA_ENST00000482630.2_Silent_p.S178S|VEGFA_ENST00000372067.3_Silent_p.S178S|VEGFA_ENST00000523125.1_5'Flank|VEGFA_ENST00000324450.6_Silent_p.S178S|VEGFA_ENST00000425836.2_Silent_p.S178S|VEGFA_ENST00000372064.4_Silent_p.S178S|VEGFA_ENST00000413642.3_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	32	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	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	
WDR63	126820	hgsc.bcm.edu	37	1	85589842	85589842	+	Missense_Mutation	SNP	A	A	G	rs17121745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85589842A>G	ENST00000294664.6	+	19	2200	c.2020A>G	c.(2020-2022)Act>Gct	p.T674A	WDR63_ENST00000370596.1_Missense_Mutation_p.T635A|WDR63_ENST00000326813.8_Missense_Mutation_p.T635A	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	674			T -> A (in dbSNP:rs17121745).							NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TCACGACGGAACTGTCCACAC	0.448													A|||	264	0.0527157	0.0023	0.0418	5008	,	,		22605	0.1438		0.0686	False		,,,				2504	0.0184				p.T674A		Atlas-SNP	.											.	WDR63	91	.	0			c.A2020G						PASS	.	A	ALA/THR	46,4360	48.9+/-83.8	0,46,2157	329.0	260.0	283.0		2020	0.4	0.0	1	dbSNP_123	283	570,8030	154.3+/-208.6	16,538,3746	yes	missense	WDR63	NM_145172.3	58	16,584,5903	GG,GA,AA		6.6279,1.044,4.7363	benign	674/892	85589842	616,12390	2203	4300	6503	SO:0001583	missense	126820	exon19			GACGGAACTGTCC		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2020A>G	1.37:g.85589842A>G	ENSP00000294664:p.Thr674Ala	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	211	99	0.469194	NM_145172	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	CCDS702.1	136	0.06227106227106227	1	0.0020325203252032522	16	0.04419889502762431	64	0.11188811188811189	55	0.07255936675461741	A	0.003	-2.525689	0.00147	0.01044	0.066279	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664	T;T;T	0.61980	0.06;0.06;0.06	5.35	0.436	0.16549	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.689205	0.15504	N	0.258915	T	0.05823	0.0152	N	0.00237	-1.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41215	-0.9521	10	0.16420	T	0.52	-1.2742	2.8913	0.05677	0.1884:0.2413:0.4476:0.1226	rs17121745;rs52832290;rs57964656;rs17121745	635;674	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	A	635;635;674	ENSP00000359628:T635A;ENSP00000317463:T635A;ENSP00000294664:T674A	ENSP00000294664:T674A	T	+	1	0	WDR63	85362430	0.000000	0.05858	0.049000	0.19019	0.014000	0.08584	-0.124000	0.10595	0.262000	0.21774	-0.462000	0.05337	ACT	A|0.944;G|0.056	0.056	strong		0.448	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	
OR52I2	143502	hgsc.bcm.edu	37	11	4608393	4608393	+	Silent	SNP	A	A	G	rs56002758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4608393A>G	ENST00000312614.4	+	1	373	c.351A>G	c.(349-351)tcA>tcG	p.S117S		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	117						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(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTTCTGCTCAGGAGACAGCT	0.512													A|||	138	0.0275559	0.0915	0.0029	5008	,	,		24334	0.0109		0.0	False		,,,				2504	0.0041				p.S117S		Atlas-SNP	.											OR52I2,NS,carcinoma,0,1	OR52I2	50	1	0			c.A351G						scavenged	.						202.0	191.0	195.0					11																	4608393		2201	4298	6499	SO:0001819	synonymous_variant	143502	exon1			CTGCTCAGGAGAC	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.351A>G	11.37:g.4608393A>G		Somatic	295	11	0.0372881		WXS	Illumina HiSeq	Phase_I	272	23	0.0845588	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Silent	SNP	ENST00000312614.4	37	CCDS31355.1																																																																																			A|0.972;G|0.028	0.028	strong		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625715	74625715	+	Silent	SNP	T	T	C	rs8081258	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	247	0	0		WXS	Illumina HiSeq	Phase_I	247	117	0.473684	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	
PGR	5241	hgsc.bcm.edu	37	11	100998623	100998623	+	Silent	SNP	G	G	A	rs1379130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:100998623G>A	ENST00000325455.5	-	1	2632	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	PGR_ENST00000263463.5_Silent_p.G393G|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	393	Modulating, Pro-Rich.				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)	AGGCCTCCGCGCCTTCCTCCT	0.697													G|||	720	0.14377	0.034	0.2406	5008	,	,		10133	0.006		0.3211	False		,,,				2504	0.183				p.G393G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C1179T						PASS	.	G	,	359,3637		37,285,1676	8.0	11.0	10.0		1179,687	1.5	1.0	11	dbSNP_88	10	2558,5530		453,1652,1939	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	490,1937,3615	AA,AG,GG		31.6271,8.984,24.1394	,	393/934,229/770	100998623	2917,9167	1998	4044	6042	SO:0001819	synonymous_variant	5241	exon1			CTCCGCGCCTTCC	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.1179C>T	11.37:g.100998623G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.842;A|0.158	0.158	strong		0.697	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
ST6GAL2	84620	hgsc.bcm.edu	37	2	107450589	107450589	+	Silent	SNP	C	C	T	rs3796111	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:107450589C>T	ENST00000409382.3	-	3	1567	c.957G>A	c.(955-957)gcG>gcA	p.A319A	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Silent_p.A319A|ST6GAL2_ENST00000409087.3_Silent_p.A319A	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	319					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						ATCTCAAAACCGCATCATGAG	0.368													T|||	1859	0.371206	0.4138	0.2983	5008	,	,		18189	0.5694		0.1759	False		,,,				2504	0.362				p.A319A		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.G957A						PASS	.	T	,,	1677,2729	655.6+/-399.9	309,1059,835	154.0	151.0	152.0		957,957,957	-0.6	1.0	2	dbSNP_107	152	1378,7222	754.8+/-407.5	89,1200,3011	no	coding-synonymous,coding-synonymous,coding-synonymous	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	,,	398,2259,3846	TT,TC,CC		16.0233,38.0617,23.4892	,,	319/530,319/467,319/530	107450589	3055,9951	2203	4300	6503	SO:0001819	synonymous_variant	84620	exon3			CAAAACCGCATCA	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.957G>A	2.37:g.107450589C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1																																																																																			C|0.716;T|0.284	0.284	strong		0.368	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
IGFN1	91156	hgsc.bcm.edu	37	1	201195119	201195119	+	Missense_Mutation	SNP	C	C	T	rs3738270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201195119C>T	ENST00000335211.4	+	22	10784	c.10654C>T	c.(10654-10656)Cac>Tac	p.H3552Y	IGFN1_ENST00000295591.8_3'UTR|RP11-567E21.3_ENST00000453155.1_RNA	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1095						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						CGACCGCATCCACACCAACCG	0.657													C|||	2843	0.567692	0.1989	0.5893	5008	,	,		17777	0.8313		0.7038	False		,,,				2504	0.6391				p.H3552Y		Atlas-SNP	.											IGFN1_ENST00000335211,caecum,carcinoma,0,6	IGFN1	220	6	0			c.C10654T						PASS	.	C	TYR/HIS	1280,3126	433.7+/-343.7	181,918,1104	87.0	67.0	74.0		10654	3.1	1.0	1	dbSNP_107	74	5752,2848	672.2+/-402.9	1914,1924,462	yes	missense	IGFN1	NM_001164586.1	83	2095,2842,1566	TT,TC,CC		33.1163,29.0513,45.9326	benign	3552/3709	201195119	7032,5974	2203	4300	6503	SO:0001583	missense	91156	exon22			CGCATCCACACCA	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.10654C>T	1.37:g.201195119C>T	ENSP00000334714:p.His3552Tyr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	59	0.62766	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	1336|1336	0.6117216117216118|0.6117216117216118	107|107	0.21747967479674796|0.21747967479674796	220|220	0.6077348066298343|0.6077348066298343	472|472	0.8251748251748252|0.8251748251748252	537|537	0.7084432717678101|0.7084432717678101	C|C	0.236|0.236	-1.017435|-1.017435	0.02078|0.02078	0.290513|0.290513	0.668837|0.668837	ENSG00000163395|ENSG00000163395	ENST00000335211|ENST00000412892	T|.	0.57436|.	0.4|.	5.0|5.0	3.09|3.09	0.35607|0.35607	.|.	0.331149|.	0.33199|.	N|.	0.005165|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	P|P	0.9999999999098946|0.9999999999098946	B|.	0.22851|.	0.076|.	B|.	0.30029|.	0.11|.	T|T	0.18650|0.18650	-1.0330|-1.0330	9|4	0.42905|.	T|.	0.14|.	.|.	6.5506|6.5506	0.22431|0.22431	0.0:0.6864:0.0:0.3136|0.0:0.6864:0.0:0.3136	rs3738270;rs17424416;rs52823855;rs61528795;rs3738270|rs3738270;rs17424416;rs52823855;rs61528795;rs3738270	3552|.	F8WAI1|.	.|.	Y|L	3552|969	ENSP00000334714:H3552Y|.	ENSP00000334714:H3552Y|.	H|P	+|+	1|2	0|0	IGFN1|IGFN1	199461742|199461742	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.516000|0.516000	0.34256|0.34256	2.889000|2.889000	0.48601|0.48601	1.344000|1.344000	0.45657|0.45657	-0.258000|-0.258000	0.10820|0.10820	CAC|CCA	C|0.435;T|0.565	0.565	strong		0.657	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
THADA	63892	hgsc.bcm.edu	37	2	43732823	43732823	+	Missense_Mutation	SNP	T	T	C	rs7578597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43732823T>C	ENST00000405006.4	-	24	3910	c.3559A>G	c.(3559-3561)Aca>Gca	p.T1187A	THADA_ENST00000405975.2_Missense_Mutation_p.T1187A|THADA_ENST00000415080.2_Missense_Mutation_p.T897A|THADA_ENST00000330266.7_Missense_Mutation_p.T897A	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1187			T -> A (in dbSNP:rs7578597).							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)				TCTTTCATTGTTATTTTCAAC	0.383													T|||	687	0.137181	0.3094	0.0749	5008	,	,		18321	0.006		0.0905	False		,,,				2504	0.1319				p.T1187A		Atlas-SNP	.											.	THADA	131	.	0			c.A3559G						PASS	.	T	ALA/THR,ALA/THR	968,2752		116,736,1008	100.0	99.0	99.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3559,3559	5.5	1.0	2	dbSNP_116	99	897,7277		52,793,3242	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	58,58	168,1529,4250	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	10.9738,26.0215,15.6802	possibly-damaging,possibly-damaging	1187/1954,1187/1954	43732823	1865,10029	1860	4087	5947	SO:0001583	missense	63892	exon24			TCATTGTTATTTT	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.3559A>G	2.37:g.43732823T>C	ENSP00000385995:p.Thr1187Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	149	59	0.395973	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	262	0.11996336996336997	165	0.3353658536585366	26	0.0718232044198895	5	0.008741258741258742	66	0.0870712401055409	T	16.35	3.099337	0.56183	0.260215	0.109738	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.54	5.54	0.83059	Domain of unknown function DUF2428, death-receptor-like (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35249	1.045	0.22378	P	0.999152804	P;D;B;B	0.89917	0.514;1.0;0.426;0.17	B;D;B;B	0.87578	0.187;0.998;0.151;0.077	T	0.31138	-0.9954	9	0.46703	T	0.11	.	14.7954	0.69873	0.0:0.0:0.0:1.0	rs7578597;rs52815224;rs59135183;rs7578597	897;1188;897;1187	Q6YHU6-2;B6ZDQ0;C9JJB1;Q6YHU6	.;.;.;THADA_HUMAN	A	897;1187;1188;897;1187	ENSP00000331105:T897A;ENSP00000386088:T1187A;ENSP00000416048:T897A;ENSP00000385995:T1187A	ENSP00000331105:T897A	T	-	1	0	THADA	43586327	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	4.611000	0.61162	2.323000	0.78572	0.528000	0.53228	ACA	T|0.871;C|0.129	0.129	strong		0.383	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
USP10	9100	hgsc.bcm.edu	37	16	84778762	84778762	+	Silent	SNP	C	C	T	rs4553618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84778762C>T	ENST00000219473.7	+	4	788	c.675C>T	c.(673-675)gaC>gaT	p.D225D	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.D229D	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	225					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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						TTGTGCCTGACAGTCCTTTCC	0.597													C|||	1160	0.231629	0.0507	0.3934	5008	,	,		17012	0.4018		0.2107	False		,,,				2504	0.2076				p.D229D		Atlas-SNP	.											.	USP10	51	.	0			c.C687T						PASS	.	C		313,3549		5,303,1623	20.0	20.0	20.0		675	-9.7	0.0	16	dbSNP_111	20	1784,6442		201,1382,2530	no	coding-synonymous	USP10	NM_005153.2		206,1685,4153	TT,TC,CC		21.6873,8.1046,17.3478		225/799	84778762	2097,9991	1931	4113	6044	SO:0001819	synonymous_variant	9100	exon5			GCCTGACAGTCCT	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.675C>T	16.37:g.84778762C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			C|0.779;T|0.221	0.221	strong		0.597	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144941419	144941419	+	Silent	SNP	C	C	T	rs12681478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144941419C>T	ENST00000525985.1	-	2	6074	c.6003G>A	c.(6001-6003)gcG>gcA	p.A2001A				P58107	EPIPL_HUMAN	epiplakin 1	2001						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)			TCAGTGCCTCCGCCTTCTCGA	0.642													C|||	1066	0.212859	0.0113	0.33	5008	,	,		18060	0.1399		0.3708	False		,,,				2504	0.3149				p.A2001A		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.G6003A						scavenged	.	C		369,3945		22,325,1810	35.0	39.0	37.0		6003	-3.7	0.0	8	dbSNP_120	37	3411,5111		676,2059,1526	no	coding-synonymous	EPPK1	NM_031308.1		698,2384,3336	TT,TC,CC		40.0258,8.5535,29.4484		2001/2420	144941419	3780,9056	2157	4261	6418	SO:0001819	synonymous_variant	83481	exon1			TGCCTCCGCCTTC	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.6003G>A	8.37:g.144941419C>T		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.740;T|0.260	0.260	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
UBD	10537	hgsc.bcm.edu	37	6	29523952	29523952	+	Missense_Mutation	SNP	A	A	G	rs2076485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29523952A>G	ENST00000377050.4	-	2	426	c.203T>C	c.(202-204)aTt>aCt	p.I68T	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	68	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.		I -> T (in dbSNP:rs2076485).		aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTCTTTGTCAATGCCATAAGA	0.507													A|||	909	0.18151	0.0295	0.2089	5008	,	,		21002	0.1756		0.2495	False		,,,				2504	0.3037				p.I68T		Atlas-SNP	.											UBD,caecum,carcinoma,0,1	UBD	13	1	0			c.T203C						PASS	.	A	THR/ILE	205,2817		5,195,1311	63.0	63.0	63.0		203	3.0	1.0	6	dbSNP_96	63	1423,3995		187,1049,1473	yes	missense	UBD	NM_006398.3	89	192,1244,2784	GG,GA,AA		26.2643,6.7836,19.2891	probably-damaging	68/166	29523952	1628,6812	1511	2709	4220	SO:0001583	missense	10537	exon2			TTGTCAATGCCAT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.203T>C	6.37:g.29523952A>G	ENSP00000366249:p.Ile68Thr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	136	84	0.617647	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	37	CCDS4662.1	381	0.17445054945054944	16	0.032520325203252036	69	0.19060773480662985	99	0.17307692307692307	197	0.2598944591029024	A	16.06	3.016838	0.54576	0.067836	0.262643	ENSG00000213886	ENST00000377050	T	0.80566	-1.39	5.38	3.0	0.34707	Ubiquitin supergroup (1);Ubiquitin (2);	0.797152	0.10010	N	0.727390	D	0.86590	0.5969	M	0.90705	3.14	0.23795	P	0.99682049	D	0.89917	1.0	D	0.77557	0.99	T	0.79225	-0.1891	9	0.87932	D	0	-28.5473	7.0335	0.24980	0.8189:0.0:0.1811:0.0	rs2076485;rs17177888;rs17431005;rs2076485	68	O15205	UBD_HUMAN	T	68	ENSP00000366249:I68T	ENSP00000366249:I68T	I	-	2	0	UBD	29631931	0.627000	0.27129	0.991000	0.47740	0.853000	0.48598	1.033000	0.30191	0.352000	0.24053	-0.321000	0.08615	ATT	G|0.183;N|0.000	0.183	strong		0.507	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
COLEC11	78989	hgsc.bcm.edu	37	2	3673648	3673648	+	Intron	SNP	G	G	A	rs10170348	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:3673648G>A	ENST00000349077.4	+	4	305				COLEC11_ENST00000487365.1_Intron|COLEC11_ENST00000402922.1_Intron|COLEC11_ENST00000403096.3_Intron|COLEC11_ENST00000402794.1_Intron|COLEC11_ENST00000418971.2_Intron|COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000404205.1_Intron|COLEC11_ENST00000236693.7_Silent_p.K53K	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11						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)		CCAAAAGGAAGTGCACCTCGT	0.453													G|||	597	0.119209	0.0129	0.0735	5008	,	,		21665	0.3115		0.1571	False		,,,				2504	0.0583				p.K53K		Atlas-SNP	.											.	COLEC11	93	.	0			c.G159A						PASS	.	G	,	164,4242	108.6+/-147.0	6,152,2045	193.0	189.0	191.0		,159	-2.2	0.0	2	dbSNP_119	191	1240,7360	249.2+/-276.5	95,1050,3155	no	intron,coding-synonymous	COLEC11	NM_024027.3,NM_199235.1	,	101,1202,5200	AA,AG,GG		14.4186,3.7222,10.795	,	,53/269	3673648	1404,11602	2203	4300	6503	SO:0001627	intron_variant	78989	exon4			AAGGAAGTGCACC	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.203-11475G>A	2.37:g.3673648G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_199235	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			G|0.878;A|0.122	0.122	strong		0.453	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
PDIA3	2923	hgsc.bcm.edu	37	15	44038850	44038850	+	Missense_Mutation	SNP	G	G	T	rs61734331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44038850G>T	ENST00000300289.5	+	1	261	c.113G>T	c.(112-114)cGc>cTc	p.R38L	PDIA3_ENST00000538521.1_5'UTR|CATSPER2P1_ENST00000381680.2_RNA|PDIA3_ENST00000469684.1_3'UTR	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	38	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		TTCGAGAGTCGCATCTCCGAC	0.682													G|||	8	0.00159744	0.0	0.0	5008	,	,		12466	0.001		0.003	False		,,,				2504	0.0041				p.R38L		Atlas-SNP	.											.	PDIA3	40	.	0			c.G113T						PASS	.	G	LEU/ARG	0,4334		0,0,2167	33.0	33.0	33.0		113	4.5	1.0	15	dbSNP_129	33	3,8511		0,3,4254	yes	missense	PDIA3	NM_005313.4	102	0,3,6421	TT,TG,GG		0.0352,0.0,0.0233	benign	38/506	44038850	3,12845	2167	4257	6424	SO:0001583	missense	2923	exon1			AGAGTCGCATCTC		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"""Protein disulfide isomerases"""	4606	protein-coding gene	gene with protein product		602046	"""glucose regulated protein, 58kDa"", ""protein disulfide isomerase-associated 3"""	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.113G>T	15.37:g.44038850G>T	ENSP00000300289:p.Arg38Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Missense_Mutation	SNP	ENST00000300289.5	37	CCDS10101.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	12.28	1.890128	0.33348	0.0	3.52E-4	ENSG00000167004	ENST00000300289	T	0.34667	1.35	5.46	4.53	0.55603	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.293323	0.39834	N	0.001245	T	0.18173	0.0436	N	0.03324	-0.35	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.03773	-1.1005	10	0.27082	T	0.32	.	14.1256	0.65217	0.0:0.1506:0.8494:0.0	rs61734331	38	P30101	PDIA3_HUMAN	L	38	ENSP00000300289:R38L	ENSP00000300289:R38L	R	+	2	0	PDIA3	41826142	1.000000	0.71417	0.997000	0.53966	0.228000	0.25075	2.749000	0.47492	1.273000	0.44346	0.313000	0.20887	CGC	G|0.999;T|0.001	0.001	strong		0.682	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313	
ZNF311	282890	hgsc.bcm.edu	37	6	28964086	28964086	+	Silent	SNP	G	G	A	rs61751894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:28964086G>A	ENST00000377179.3	-	7	1205	c.693C>T	c.(691-693)aaC>aaT	p.N231N	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	231					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)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						TATGTTTTGAGTTTGGATTCA	0.388													G|||	417	0.0832668	0.0575	0.1023	5008	,	,		20289	0.0972		0.0895	False		,,,				2504	0.0838				p.N231N		Atlas-SNP	.											.	ZNF311	59	.	0			c.C693T						PASS	.	G		150,2870		2,146,1362	119.0	142.0	134.0		693	1.2	0.0	6	dbSNP_129	134	504,4914		26,452,2231	no	coding-synonymous	ZNF311	NM_001010877.2		28,598,3593	AA,AG,GG		9.3023,4.9669,7.7507		231/667	28964086	654,7784	1510	2709	4219	SO:0001819	synonymous_variant	282890	exon7			TTTTGAGTTTGGA	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.693C>T	6.37:g.28964086G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001010877	A2BFK5|B0S7Y4|Q92971	Silent	SNP	ENST00000377179.3	37	CCDS34357.1																																																																																			G|0.919;A|0.081	0.081	strong		0.388	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
ESR1	2099	hgsc.bcm.edu	37	6	152420095	152420095	+	Silent	SNP	G	G	A	rs2228480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152420095G>A	ENST00000206249.3	+	8	2144	c.1782G>A	c.(1780-1782)acG>acA	p.T594T	ESR1_ENST00000443427.1_Silent_p.T594T|ESR1_ENST00000338799.5_Silent_p.T594T|ESR1_ENST00000440973.1_Silent_p.T594T|ESR1_ENST00000406599.1_Silent_p.T333T|ESR1_ENST00000427531.2_Intron|ESR1_ENST00000456483.2_Silent_p.T482T	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	594	Interaction with AKAP13.|Self-association.|Transactivation AF-2.				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)	TCCCTGCCACGGTCTGAGAGC	0.532													A|||	945	0.188698	0.1452	0.2378	5008	,	,		20228	0.2014		0.175	False		,,,				2504	0.2137				p.T594T		Atlas-SNP	.											.	ESR1	94	.	0			c.G1782A	GRCh37	CM056948	ESR1	M	rs2228480	PASS	.	A	,,,	691,3715	760.6+/-413.0	45,601,1557	47.0	44.0	45.0		1782,1782,1782,1782	-10.3	0.0	6	dbSNP_98	45	1546,7054	745.0+/-407.3	129,1288,2883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	174,1889,4440	AA,AG,GG		17.9767,15.6832,17.1998	,,,	594/596,594/596,594/596,594/596	152420095	2237,10769	2203	4300	6503	SO:0001819	synonymous_variant	2099	exon8			TGCCACGGTCTGA	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.1782G>A	6.37:g.152420095G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			G|0.822;A|0.178	0.178	strong		0.532	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
RP1	6101	hgsc.bcm.edu	37	8	55540141	55540141	+	Silent	SNP	C	C	T	rs114557304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55540141C>T	ENST00000220676.1	+	4	3847	c.3699C>T	c.(3697-3699)tcC>tcT	p.S1233S		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1233					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAGGAATCTCCTCTTTGGATG	0.443													C|||	117	0.0233626	0.0635	0.0231	5008	,	,		23602	0.001		0.0099	False		,,,				2504	0.0061				p.S1233S	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C3699T						PASS	.	C		286,4120	160.0+/-192.4	9,268,1926	128.0	124.0	125.0		3699	-1.2	0.0	8	dbSNP_132	125	141,8459	70.0+/-132.6	0,141,4159	no	coding-synonymous	RP1	NM_006269.1		9,409,6085	TT,TC,CC		1.6395,6.4911,3.2831		1233/2157	55540141	427,12579	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			AATCTCCTCTTTG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3699C>T	8.37:g.55540141C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	175	91	0.52	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			C|0.970;T|0.030	0.030	strong		0.443	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
RIPK3	11035	hgsc.bcm.edu	37	14	24805463	24805463	+	Missense_Mutation	SNP	G	G	T	rs3212254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24805463G>T	ENST00000216274.5	-	10	1693	c.1475C>A	c.(1474-1476)cCa>cAa	p.P492Q	RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000554068.2_5'Flank|ADCY4_ENST00000310677.4_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000418030.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	492			P -> Q (in dbSNP:rs3212254). {ECO:0000269|PubMed:17344846}.		activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		ACCTACTGGTGGGGGGTGCTG	0.547													G|||	602	0.120208	0.239	0.036	5008	,	,		15712	0.1339		0.0537	False		,,,				2504	0.0736				p.P492Q	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C1475A						PASS	.	G	GLN/PRO	886,3520	343.1+/-307.5	92,702,1409	74.0	77.0	76.0		1475	1.9	0.0	14	dbSNP_105	76	486,8114	141.1+/-197.5	13,460,3827	yes	missense	RIPK3	NM_006871.3	76	105,1162,5236	TT,TG,GG		5.6512,20.1089,10.549	benign	492/519	24805463	1372,11634	2203	4300	6503	SO:0001583	missense	11035	exon10			ACTGGTGGGGGGT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1475C>A	14.37:g.24805463G>T	ENSP00000216274:p.Pro492Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	37	CCDS9628.1	233	0.10668498168498168	108	0.21951219512195122	15	0.04143646408839779	67	0.11713286713286714	43	0.05672823218997362	G	7.107	0.575327	0.13623	0.201089	0.056512	ENSG00000129465	ENST00000216274	T	0.77620	-1.11	2.77	1.86	0.25419	.	0.903075	0.09280	N	0.823841	T	0.00109	0.0003	N	0.12182	0.205	0.80722	P	0.0	D	0.76494	0.999	D	0.65010	0.931	T	0.12116	-1.0560	9	0.52906	T	0.07	-0.7917	7.7066	0.28653	0.0:0.2611:0.7389:0.0	rs3212254;rs3212254	492	Q9Y572	RIPK3_HUMAN	Q	492	ENSP00000216274:P492Q	ENSP00000216274:P492Q	P	-	2	0	RIPK3	23875303	0.009000	0.17119	0.002000	0.10522	0.078000	0.17371	1.803000	0.38863	0.719000	0.32188	-0.304000	0.09214	CCA	G|0.896;T|0.104	0.104	strong		0.547	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
ZNF91	7644	hgsc.bcm.edu	37	19	23545447	23545447	+	Missense_Mutation	SNP	A	A	G	rs296091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23545447A>G	ENST00000300619.7	-	4	539	c.334T>C	c.(334-336)Tat>Cat	p.Y112H	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.Y80H	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	112			Y -> H (in dbSNP:rs296091).		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)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CATTTTTCATATTTTCTCAGT	0.323													A|||	863	0.172324	0.1884	0.0418	5008	,	,		14667	0.3472		0.0636	False		,,,				2504	0.1748				p.Y112H		Atlas-SNP	.											.	ZNF91	349	.	0			c.T334C						PASS	.	A	HIS/TYR	668,3428		47,574,1427	51.0	52.0	51.0		334	0.1	0.2	19	dbSNP_79	51	447,8011		9,429,3791	yes	missense	ZNF91	NM_003430.2	83	56,1003,5218	GG,GA,AA		5.2849,16.3086,8.8816	probably-damaging	112/1192	23545447	1115,11439	2048	4229	6277	SO:0001583	missense	7644	exon4			TTTCATATTTTCT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.334T>C	19.37:g.23545447A>G	ENSP00000300619:p.Tyr112His	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	374	0.17124542124542125	101	0.20528455284552846	16	0.04419889502762431	203	0.3548951048951049	54	0.0712401055408971	A	1.145	-0.648423	0.03506	0.163086	0.052849	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05382	3.45;3.45	0.131	0.131	0.14755	.	.	.	.	.	T	0.00012	0.0000	L	0.46947	1.48	0.80722	P	0.0	B;P	0.34615	0.291;0.459	B;B	0.34301	0.17;0.179	T	0.47355	-0.9124	7	0.18710	T	0.47	.	.	.	.	rs296091;rs3826669;rs52806469;rs296091	80;112	Q05481-2;Q05481	.;ZNF91_HUMAN	H	112;80	ENSP00000300619:Y112H;ENSP00000380272:Y80H	ENSP00000300619:Y112H	Y	-	1	0	ZNF91	23337287	0.000000	0.05858	0.236000	0.24074	0.720000	0.41350	-0.641000	0.05434	0.148000	0.19059	0.147000	0.16070	TAT	A|0.841;G|0.159	0.159	strong		0.323	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
NLRP4	147945	hgsc.bcm.edu	37	19	56369215	56369215	+	Silent	SNP	C	C	T	rs395503|rs199476224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56369215C>T	ENST00000301295.6	+	3	878	c.456C>T	c.(454-456)atC>atT	p.I152I	NLRP4_ENST00000587891.1_Silent_p.I77I|NLRP4_ENST00000346986.5_Silent_p.I152I	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	152	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)		GTACAGTGATCATTCAAGGAC	0.473													C|||	2584	0.515974	0.447	0.464	5008	,	,		20382	0.6657		0.3827	False		,,,				2504	0.6288				p.I152I		Atlas-SNP	.											.	NLRP4	331	.	0			c.C456T						PASS	.	C		1905,2501	546.1+/-377.0	413,1079,711	135.0	121.0	126.0		456	3.0	0.1	19	dbSNP_80	126	3180,5420	481.5+/-370.7	598,1984,1718	no	coding-synonymous	NLRP4	NM_134444.4		1011,3063,2429	TT,TC,CC		36.9767,43.2365,39.0973		152/995	56369215	5085,7921	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			AGTGATCATTCAA	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.456C>T	19.37:g.56369215C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.574;T|0.426	0.426	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
WNT9B	7484	hgsc.bcm.edu	37	17	44950122	44950122	+	Missense_Mutation	SNP	T	T	C	rs4968281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:44950122T>C	ENST00000290015.2	+	2	370	c.317T>C	c.(316-318)aTg>aCg	p.M106T	WNT9B_ENST00000393461.2_Missense_Mutation_p.M106T	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	106			M -> T (in dbSNP:rs4968281). {ECO:0000269|PubMed:11604992}.		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)			GAGGGCAGGATGGGCCTGCTC	0.657													C|||	3541	0.707069	0.9387	0.6354	5008	,	,		11999	0.4643		0.7465	False		,,,				2504	0.6544				p.M106T		Atlas-SNP	.											.	WNT9B	37	.	0			c.T317C						PASS	.	C	THR/MET	3968,416		1798,372,22	15.0	18.0	17.0		317	-0.0	0.2	17	dbSNP_111	17	6275,2283		2319,1637,323	yes	missense	WNT9B	NM_003396.1	81	4117,2009,345	CC,CT,TT		26.6768,9.4891,20.8546	benign	106/358	44950122	10243,2699	2192	4279	6471	SO:0001583	missense	7484	exon2			GCAGGATGGGCCT	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.317T>C	17.37:g.44950122T>C	ENSP00000290015:p.Met106Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	1509	0.6909340659340659	448	0.9105691056910569	237	0.6546961325966851	276	0.4825174825174825	548	0.7229551451187335	C	0.010	-1.754299	0.00663	0.905109	0.733232	ENSG00000158955	ENST00000393461;ENST00000290015	T;T	0.74737	-0.87;-0.87	4.49	-0.0339	0.13898	.	0.972799	0.08470	N	0.941186	T	0.00012	0.0000	N	0.02391	-0.57	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31392	-0.9945	8	.	.	.	.	2.2191	0.03968	0.1163:0.4099:0.2644:0.2095	rs4968281;rs17846667;rs17859764;rs61635510;rs4968281	106;106	E7EPC3;O14905	.;WNT9B_HUMAN	T	106	ENSP00000377105:M106T;ENSP00000290015:M106T	.	M	+	2	0	WNT9B	42305121	0.449000	0.25689	0.235000	0.24058	0.346000	0.29079	0.967000	0.29344	-0.234000	0.09782	-1.694000	0.00725	ATG	T|0.264;C|0.736	0.736	strong		0.657	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
ANKMY2	57037	hgsc.bcm.edu	37	7	16666741	16666741	+	Silent	SNP	T	T	G	rs11532682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:16666741T>G	ENST00000306999.2	-	3	438	c.195A>C	c.(193-195)ctA>ctC	p.L65L	ANKMY2_ENST00000421746.1_5'UTR	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	65						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CATGTCGCAGTAGTAATTTGC	0.348													T|||	701	0.139976	0.093	0.2075	5008	,	,		16241	0.1438		0.2187	False		,,,				2504	0.0706				p.L65L		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A195C						PASS	.	T		417,3989	205.2+/-227.1	14,389,1800	96.0	83.0	88.0		195	-11.5	0.0	7	dbSNP_120	88	1840,6760	329.0+/-318.6	201,1438,2661	no	coding-synonymous	ANKMY2	NM_020319.2		215,1827,4461	GG,GT,TT		21.3953,9.4644,17.3535		65/442	16666741	2257,10749	2203	4300	6503	SO:0001819	synonymous_variant	57037	exon3			TCGCAGTAGTAAT	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.195A>C	7.37:g.16666741T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																			T|0.823;G|0.177	0.177	strong		0.348	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
POLR2D	5433	hgsc.bcm.edu	37	2	128608184	128608184	+	Silent	SNP	C	C	T	rs11556864	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128608184C>T	ENST00000272645.4	-	3	386	c.330G>A	c.(328-330)gaG>gaA	p.E110E	POLR2D_ENST00000409698.1_Silent_p.E72E|POLR2D_ENST00000409955.1_Intron|POLR2D_ENST00000487079.1_Intron	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	197	0	0		WXS	Illumina HiSeq	Phase_I	208	93	0.447115	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	
IGSF9B	22997	hgsc.bcm.edu	37	11	133788992	133788992	+	Missense_Mutation	SNP	T	T	C	rs12800905	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:133788992T>C	ENST00000321016.8	-	19	4222	c.3992A>G	c.(3991-3993)cAg>cGg	p.Q1331R	IGSF9B_ENST00000533871.2_Intron			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1331	Pro-rich.			Q -> R (in Ref. 2; BAA82982). {ECO:0000305}.	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)		TCTGTCTCTCTGCAGCTTCCT	0.632													T|||	2080	0.415335	0.6218	0.3876	5008	,	,		7224	0.253		0.3738	False		,,,				2504	0.3661				p.Q1331R		Atlas-SNP	.											.	IGSF9B	290	.	0			c.A3992G						PASS	.	T	ARG/GLN	2088,1612		633,822,395	23.0	25.0	25.0		3992	4.6	1.0	11	dbSNP_121	25	3113,5071		611,1891,1590	yes	missense	IGSF9B	NM_014987.1	43	1244,2713,1985	CC,CT,TT		38.0376,43.5676,43.7647	benign	1331/1350	133788992	5201,6683	1850	4092	5942	SO:0001583	missense	22997	exon19			TCTCTCTGCAGCT	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.3992A>G	11.37:g.133788992T>C	ENSP00000317980:p.Gln1331Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		902	0.413003663003663	307	0.6239837398373984	146	0.40331491712707185	163	0.28496503496503495	286	0.37730870712401055	T	5.915	0.352945	0.11182	0.564324	0.380376	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.62941	0.33;-0.01	4.63	4.63	0.57726	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.45946	P	0.0012219999999999454	B	0.18310	0.027	B	0.20767	0.031	T	0.38286	-0.9668	8	0.02654	T	1	.	8.8556	0.35225	0.0:0.0:0.2505:0.7495	rs12800905;rs56884318	1331	Q9UPX0	TUTLB_HUMAN	R	1331;1173	ENSP00000317980:Q1331R;ENSP00000436552:Q1173R	ENSP00000317980:Q1331R	Q	-	2	0	IGSF9B	133294202	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	3.272000	0.51616	1.929000	0.55896	0.379000	0.24179	CAG	T|0.585;C|0.415	0.415	strong		0.632	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421054	29421054	+	Missense_Mutation	SNP	C	C	T	rs2306933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:29421054C>T	ENST00000261275.4	-	8	940	c.941G>A	c.(940-942)gGt>gAt	p.G314D		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	314	Pro-rich.		G -> D (in dbSNP:rs2306933).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						CACCTGCTGACCTATACTTGT	0.552													T|||	677	0.135184	0.1263	0.1138	5008	,	,		16994	0.2093		0.0706	False		,,,				2504	0.1524				p.G314D		Atlas-SNP	.											.	FAM189A1	20	.	0			c.G941A						PASS	.	T	ASP/GLY	160,1224		10,140,542	53.0	54.0	54.0		941	2.7	0.0	15	dbSNP_100	54	230,2952		11,208,1372	yes	missense	FAM189A1	NM_015307.1	94	21,348,1914	TT,TC,CC		7.2282,11.5607,8.5414	benign	314/540	29421054	390,4176	692	1591	2283	SO:0001583	missense	23359	exon8			TGCTGACCTATAC		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.941G>A	15.37:g.29421054C>T	ENSP00000261275:p.Gly314Asp	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	260	0.11904761904761904	56	0.11382113821138211	35	0.09668508287292818	121	0.21153846153846154	48	0.0633245382585752	T	0.011	-1.701260	0.00725	0.115607	0.072282	ENSG00000104059	ENST00000261275	T	0.02737	4.18	5.07	2.73	0.32206	.	0.239743	0.41001	N	0.000968	T	0.00012	0.0000	N	0.00159	-1.955	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42582	-0.9443	9	0.02654	T	1	-16.8578	7.6984	0.28608	0.0:0.2482:0.0:0.7518	rs2306933;rs59289923;rs2306933	314	O60320	F1891_HUMAN	D	314	ENSP00000261275:G314D	ENSP00000261275:G314D	G	-	2	0	FAM189A1	27208346	0.944000	0.32072	0.004000	0.12327	0.014000	0.08584	1.419000	0.34793	0.048000	0.15891	-0.254000	0.11334	GGT	C|0.877;T|0.123	0.123	strong		0.552	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
PYGL	5836	hgsc.bcm.edu	37	14	51410969	51410969	+	Silent	SNP	G	G	A	rs77316189	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:51410969G>A	ENST00000216392.7	-	1	485	c.153C>T	c.(151-153)gaC>gaT	p.D51D	PYGL_ENST00000532462.1_Silent_p.D51D|PYGL_ENST00000544180.2_Silent_p.D51D	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	51					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)	CGAAGTAGTAGTCGCGGGTGG	0.642													G|||	290	0.0579073	0.1566	0.0231	5008	,	,		13995	0.001		0.0338	False		,,,				2504	0.0327				p.D51D		Atlas-SNP	.											PYGL,NS,carcinoma,0,1	PYGL	77	1	0			c.C153T						PASS	.	G	,	677,3729	284.9+/-277.9	49,579,1575	72.0	55.0	60.0		153,153	2.5	1.0	14	dbSNP_131	60	310,8290	111.2+/-171.5	4,302,3994	no	coding-synonymous,coding-synonymous	PYGL	NM_001163940.1,NM_002863.4	,	53,881,5569	AA,AG,GG		3.6047,15.3654,7.5888	,	51/814,51/848	51410969	987,12019	2203	4300	6503	SO:0001819	synonymous_variant	5836	exon1			GTAGTAGTCGCGG		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.153C>T	14.37:g.51410969G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Silent	SNP	ENST00000216392.7	37	CCDS32080.1																																																																																			G|0.933;A|0.067	0.067	strong		0.642	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329676	8329676	+	Missense_Mutation	SNP	C	C	T	rs10743252	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	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	
RRP12	23223	hgsc.bcm.edu	37	10	99150237	99150237	+	Silent	SNP	G	G	A	rs41300219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000414986.1_Silent_p.P171P|RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000315563.6_Intron	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	232						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GAAGGGTCACGGGGTAGCCCC	0.612													G|||	201	0.0401358	0.0598	0.0533	5008	,	,		19526	0.0		0.0716	False		,,,				2504	0.0133				p.P232P		Atlas-SNP	.											.	RRP12	97	.	0			c.C696T						PASS	.	G	,	254,4152	148.0+/-182.4	9,236,1958	58.0	56.0	57.0		513,696	-11.0	0.0	10	dbSNP_127	57	501,8099	144.5+/-200.4	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,703,5774	AA,AG,GG		5.8256,5.7649,5.805	,	171/1237,232/1298	99150237	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon6			GGTCACGGGGTAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.696C>T	10.37:g.99150237G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.949;A|0.051	0.051	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
BTN1A1	696	hgsc.bcm.edu	37	6	26505403	26505403	+	Silent	SNP	C	C	A	rs3736782	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26505403C>A	ENST00000244513.6	+	3	744	c.678C>A	c.(676-678)ggC>ggA	p.G226G		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	226	Ig-like V-type 2.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TCCTTCTTGGCCAGGAGAAGA	0.468													C|||	2843	0.567692	0.5121	0.5879	5008	,	,		19737	0.745		0.4423	False		,,,				2504	0.5746				p.G226G		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C678A						PASS	.	C		2288,2118	600.5+/-389.5	588,1112,503	89.0	92.0	91.0		678	3.6	1.0	6	dbSNP_107	91	4045,4555	557.2+/-387.0	984,2077,1239	no	coding-synonymous	BTN1A1	NM_001732.2		1572,3189,1742	AA,AC,CC		47.0349,48.0708,48.6929		226/527	26505403	6333,6673	2203	4300	6503	SO:0001819	synonymous_variant	696	exon3			TCTTGGCCAGGAG	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.678C>A	6.37:g.26505403C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Silent	SNP	ENST00000244513.6	37	CCDS4614.1																																																																																			C|0.487;A|0.513	0.513	strong		0.468	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
SCGB1D2	10647	hgsc.bcm.edu	37	11	62010863	62010863	+	Missense_Mutation	SNP	C	C	T	rs2232950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	158	0	0		WXS	Illumina HiSeq	Phase_I	160	76	0.475	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	
SH3BP1	23616	hgsc.bcm.edu	37	22	38046695	38046695	+	Missense_Mutation	SNP	C	C	A	rs12170939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38046695C>A	ENST00000357436.4	+	16	1874	c.1561C>A	c.(1561-1563)Ccg>Acg	p.P521T	SH3BP1_ENST00000599616.1_Missense_Mutation_p.P457T|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	521					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)					agctccagctccggccccagc	0.657													C|||	664	0.132588	0.0756	0.2824	5008	,	,		14412	0.0635		0.1849	False		,,,				2504	0.1207				p.P521T		Atlas-SNP	.											.	SH3BP1	41	.	0			c.C1561A						PASS	.	C	THR/PRO	349,4055		16,317,1869	26.0	30.0	29.0		1561	0.3	0.0	22	dbSNP_120	29	1331,7267		102,1127,3070	yes	missense	SH3BP1	NM_018957.3	38	118,1444,4939	AA,AC,CC		15.4803,7.9246,12.9211	benign	521/702	38046695	1680,11322	2202	4299	6501	SO:0001583	missense	23616	exon16			CCAGCTCCGGCCC		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.1561C>A	22.37:g.38046695C>A	ENSP00000350018:p.Pro521Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	37	CCDS13952.2	304	0.1391941391941392	41	0.08333333333333333	98	0.27071823204419887	27	0.0472027972027972	138	0.1820580474934037	C	2.918	-0.223802	0.06061	0.079246	0.154803	ENSG00000100092	ENST00000357436;ENST00000397014	T	0.17854	2.25	0.312	0.312	0.15837	.	0.804139	0.10756	N	0.637701	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P;B;B	0.48350	0.063;0.909;0.022;0.063	B;P;B;B	0.50440	0.012;0.641;0.003;0.012	T	0.39143	-0.9628	8	0.13853	T	0.58	.	.	.	.	rs12170939	435;457;521;435	E7EUD3;Q6ZT62;Q9Y3L3;Q6ZTJ5	.;.;3BP1_HUMAN;.	T	521;435	ENSP00000350018:P521T	ENSP00000350018:P521T	P	+	1	0	SH3BP1	36376641	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-0.295000	0.08298	0.420000	0.25954	0.089000	0.15464	CCG	C|0.871;A|0.129	0.129	strong		0.657	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
OVGP1	5016	hgsc.bcm.edu	37	1	111957570	111957570	+	Missense_Mutation	SNP	G	G	C	rs376377993|rs45455292	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	119	0	0		WXS	Illumina HiSeq	Phase_I	102	30	0.294118	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	
REXO4	57109	hgsc.bcm.edu	37	9	136279935	136279935	+	Missense_Mutation	SNP	C	C	T	rs6597630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136279935C>T	ENST00000371942.3	-	2	621	c.422G>A	c.(421-423)aGg>aAg	p.R141K	REXO4_ENST00000371935.2_Missense_Mutation_p.G82R|ADAMTS13_ENST00000485925.1_Intron|REXO4_ENST00000478037.1_5'UTR	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	141			R -> K (in dbSNP:rs6597630).		regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		TACTGGCGCCCTCCTGTCCAT	0.542													T|||	449	0.0896565	0.2126	0.0519	5008	,	,		18683	0.0198		0.0855	False		,,,				2504	0.0266				p.R141K		Atlas-SNP	.											.	REXO4	27	.	0			c.G422A						PASS	.	T	LYS/ARG	824,3582	748.0+/-411.9	84,656,1463	147.0	118.0	128.0		422	-3.9	0.0	9	dbSNP_116	128	743,7857	785.5+/-407.6	37,669,3594	yes	missense	REXO4	NM_020385.2	26	121,1325,5057	TT,TC,CC		8.6395,18.7018,12.0483	benign	141/423	136279935	1567,11439	2203	4300	6503	SO:0001583	missense	57109	exon2			GGCGCCCTCCTGT	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.422G>A	9.37:g.136279935C>T	ENSP00000361010:p.Arg141Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	37	CCDS6969.1	198|198	0.09065934065934066|0.09065934065934066	98|98	0.1991869918699187|0.1991869918699187	21|21	0.058011049723756904|0.058011049723756904	12|12	0.02097902097902098|0.02097902097902098	67|67	0.08839050131926121|0.08839050131926121	T|T	1.245|1.245	-0.620319|-0.620319	0.03636|0.03636	0.187018|0.187018	0.086395|0.086395	ENSG00000148300|ENSG00000148300	ENST00000371935;ENST00000454825|ENST00000453165;ENST00000371942;ENST00000445916	.|T;T;T	.|0.19105	.|2.43;2.44;2.17	4.45|4.45	-3.93|-3.93	0.04143|0.04143	.|.	.|18.384800	.|0.00481	.|N	.|0.000133	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00179|0.00179	-1.91|-1.91	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.35525|0.35525	-0.9785|-0.9785	7|9	0.87932|0.02654	D|T	0|1	.|.	7.2986|7.2986	0.26408|0.26408	0.0:0.2359:0.483:0.2811|0.0:0.2359:0.483:0.2811	rs6597630|rs6597630	82|141	Q9GZR2-2|Q9GZR2	.|REXO4_HUMAN	R|K	82|126;141;48	.|ENSP00000403272:R126K;ENSP00000361010:R141K;ENSP00000391534:R48K	ENSP00000361003:G82R|ENSP00000361010:R141K	G|R	-|-	1|2	0|0	REXO4|REXO4	135269756|135269756	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.094000|-0.094000	0.11094|0.11094	-1.093000|-1.093000	0.03058|0.03058	-0.361000|-0.361000	0.07541|0.07541	GGG|AGG	C|0.889;T|0.111	0.111	strong		0.542	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
ITGAX	3687	hgsc.bcm.edu	37	16	31371674	31371674	+	Missense_Mutation	SNP	G	G	A	rs2230428	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	132	0	0		WXS	Illumina HiSeq	Phase_I	177	83	0.468927	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	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124229429	124229429	+	Splice_Site	SNP	T	T	C	rs7135542	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124229429T>C	ENST00000330342.3	+	13	1763	c.1515T>C	c.(1513-1515)aaT>aaC	p.N505N		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	505					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|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)	p.N505N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TTTGTTACAGTGACAGCGTCG	0.517													C|||	4004	0.799521	0.8759	0.7867	5008	,	,		22659	0.9504		0.6292	False		,,,				2504	0.7249				p.N505N		Atlas-SNP	.											ATP6V0A2,NS,carcinoma,0,1	ATP6V0A2	68	1	1	Substitution - coding silent(1)	prostate(1)	c.T1515C						PASS	.	C		3614,792	320.2+/-296.5	1489,636,78	160.0	137.0	145.0		1515	-5.4	0.7	12	dbSNP_116	145	5430,3170	481.6+/-370.7	1735,1960,605	yes	coding-synonymous-near-splice	ATP6V0A2	NM_012463.3		3224,2596,683	CC,CT,TT		36.8605,17.9755,30.4629		505/857	124229429	9044,3962	2203	4300	6503	SO:0001630	splice_region_variant	23545	exon13			TTACAGTGACAGC	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.1515-1T>C	12.37:g.124229429T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	120	0.983607	NM_012463	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																			T|0.266;C|0.734	0.734	strong		0.517	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	Silent
CNRIP1	25927	hgsc.bcm.edu	37	2	68546449	68546449	+	Silent	SNP	G	G	A	rs13025842	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68546449G>A	ENST00000263655.3	-	1	689	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CNRIP1_ENST00000409862.1_Silent_p.D28D|CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409559.3_Silent_p.D28D	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	28										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						AGCGCTGCCCGTCCACCTTGT	0.632													G|||	1044	0.208466	0.1589	0.3026	5008	,	,		15369	0.0794		0.331	False		,,,				2504	0.2157				p.D28D		Atlas-SNP	.											.	CNRIP1	45	.	0			c.C84T						PASS	.	G	,	718,3632		64,590,1521	47.0	36.0	40.0		84,84	2.9	1.0	2	dbSNP_121	40	2642,5878		429,1784,2047	no	coding-synonymous,coding-synonymous	CNRIP1	NM_001111101.1,NM_015463.2	,	493,2374,3568	AA,AG,GG		31.0094,16.5057,26.1072	,	28/129,28/165	68546449	3360,9510	2175	4260	6435	SO:0001819	synonymous_variant	25927	exon1			CTGCCCGTCCACC	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 32"""	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.84C>T	2.37:g.68546449G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Silent	SNP	ENST00000263655.3	37	CCDS1886.1																																																																																			G|0.780;A|0.220	0.220	strong		0.632	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463	
TOP1MT	116447	hgsc.bcm.edu	37	8	144392368	144392368	+	Missense_Mutation	SNP	G	G	A	rs2293925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144392368G>A	ENST00000329245.4	-	13	1607	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	TOP1MT_ENST00000519148.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000523676.1_Missense_Mutation_p.R427W|TOP1MT_ENST00000521193.1_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	27	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	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	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27788021	27788021	+	Silent	SNP	G	G	A	rs2075378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:27788021G>A	ENST00000318304.8	+	4	526	c.243G>A	c.(241-243)acG>acA	p.T81T	PPFIBP1_ENST00000535047.1_Silent_p.T81T|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000542629.1_Silent_p.T81T|PPFIBP1_ENST00000545334.1_Silent_p.T81T|PPFIBP1_ENST00000228425.6_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	93	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	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	
C12orf54	121273	hgsc.bcm.edu	37	12	48884610	48884610	+	Missense_Mutation	SNP	C	C	T	rs61940778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	83	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	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	
BTN1A1	696	hgsc.bcm.edu	37	6	26505362	26505362	+	Missense_Mutation	SNP	G	G	A	rs3736781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26505362G>A	ENST00000244513.6	+	3	703	c.637G>A	c.(637-639)Gcg>Acg	p.A213T		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	213	Ig-like V-type 2.		A -> T (in dbSNP:rs3736781). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8611614, ECO:0000269|Ref.3}.			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						AGACACTTCTGCGAAAAATGT	0.453													G|||	2846	0.568291	0.5129	0.5879	5008	,	,		19887	0.746		0.4423	False		,,,				2504	0.5757				p.A213T		Atlas-SNP	.											.	BTN1A1	68	.	0			c.G637A						PASS	.	G	THR/ALA	2288,2118	600.7+/-389.6	588,1112,503	106.0	108.0	108.0		637	-10.5	0.0	6	dbSNP_107	108	4044,4556	557.3+/-387.0	984,2076,1240	yes	missense	BTN1A1	NM_001732.2	58	1572,3188,1743	AA,AG,GG		47.0233,48.0708,48.6852	benign	213/527	26505362	6332,6674	2203	4300	6503	SO:0001583	missense	696	exon3			ACTTCTGCGAAAA	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.637G>A	6.37:g.26505362G>A	ENSP00000244513:p.Ala213Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	1195	0.5471611721611722	229	0.4654471544715447	206	0.569060773480663	413	0.722027972027972	347	0.4577836411609499	G	10.72	1.428849	0.25726	0.519292	0.470233	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.75938	-0.98	5.63	-10.5	0.00291	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.626750	0.03193	N	0.173551	T	0.26231	0.0640	N	0.05351	-0.065	0.80722	P	0.0	B	0.12013	0.005	B	0.20577	0.03	T	0.08207	-1.0733	9	0.19147	T	0.46	.	9.9966	0.41902	0.1031:0.5725:0.3244:0.0	rs3736781;rs52816922;rs57753800;rs3736781	213	Q13410	BT1A1_HUMAN	T	213	ENSP00000244513:A213T	ENSP00000244513:A213T	A	+	1	0	BTN1A1	26613341	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.603000	0.02077	-1.142000	0.02869	-0.345000	0.07892	GCG	G|0.485;A|0.515	0.515	strong		0.453	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
SEMA6D	80031	hgsc.bcm.edu	37	15	48058071	48058071	+	Missense_Mutation	SNP	G	G	A	rs532598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:48058071G>A	ENST00000316364.5	+	14	1872	c.1433G>A	c.(1432-1434)aGt>aAt	p.S478N	SEMA6D_ENST00000358066.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000354744.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000558014.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000389432.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000536845.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000537942.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S478N|SEMA6D_ENST00000558816.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000355997.3_Missense_Mutation_p.S478N	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	478	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		S -> N (in dbSNP:rs532598).		axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AATAGGTGCAGTGCTGAGAAT	0.408													g|||	2332	0.465655	0.5817	0.3617	5008	,	,		20797	0.6032		0.3509	False		,,,				2504	0.3589				p.S478N		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G1433A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	2581,1815	637.1+/-396.7	752,1077,369	155.0	133.0	140.0		1433,1433,1433,1433,1433,1433	-1.9	0.8	15	dbSNP_83	140	2874,5720	451.8+/-362.8	490,1894,1913	yes	missense,missense,missense,missense,missense,missense	SEMA6D	NM_001198999.1,NM_020858.1,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	46,46,46,46,46,46	1242,2971,2282	AA,AG,GG		33.4419,41.2875,41.9938	benign,benign,benign,benign,benign,benign	478/1012,478/1012,478/999,478/1018,478/1074,478/598	48058071	5455,7535	2198	4297	6495	SO:0001583	missense	80031	exon14			GGTGCAGTGCTGA	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1433G>A	15.37:g.48058071G>A	ENSP00000324857:p.Ser478Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	1019	0.4665750915750916	270	0.5487804878048781	122	0.3370165745856354	361	0.6311188811188811	266	0.35092348284960423	g	7.087	0.571452	0.13623	0.587125	0.334419	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997	T;T;T;T;T;T;T;T;T	0.18338	2.27;2.28;2.28;2.26;2.26;2.27;2.27;2.28;2.22	5.68	-1.93	0.07594	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (3);	0.589000	0.18988	N	0.125674	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	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;0.0;0.001;0.0	T	0.35126	-0.9801	9	0.22109	T	0.4	.	7.2106	0.25931	0.5129:0.1163:0.3707:0.0	rs532598;rs52797909;rs56494183;rs57496672;rs532598	478;478;478;478;478	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	N	478	ENSP00000442040:S478N;ENSP00000446152:S478N;ENSP00000324857:S478N;ENSP00000374084:S478N;ENSP00000374083:S478N;ENSP00000346786:S478N;ENSP00000350770:S478N;ENSP00000374079:S478N;ENSP00000348276:S478N	ENSP00000324857:S478N	S	+	2	0	SEMA6D	45845363	0.967000	0.33354	0.756000	0.31282	0.895000	0.52256	0.315000	0.19451	-0.278000	0.09180	-1.154000	0.01816	AGT	G|0.549;N|0.000	.	strong		0.408	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
PI3	5266	hgsc.bcm.edu	37	20	43803606	43803606	+	Missense_Mutation	SNP	G	G	A	rs41282752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:43803606G>A	ENST00000243924.3	+	1	90	c.43G>A	c.(43-45)Gct>Act	p.A15T		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	15					copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GTTCCTCATCGCTGGGACGCT	0.572													G|||	56	0.0111821	0.0015	0.0144	5008	,	,		18483	0.0		0.0348	False		,,,				2504	0.0092				p.A15T		Atlas-SNP	.											.	PI3	21	.	0			c.G43A						PASS	.	G	THR/ALA	30,4376	36.0+/-67.5	0,30,2173	181.0	137.0	152.0		43	1.9	0.0	20	dbSNP_127	152	348,8252	117.4+/-177.0	7,334,3959	yes	missense	PI3	NM_002638.3	58	7,364,6132	AA,AG,GG		4.0465,0.6809,2.9064	benign	15/118	43803606	378,12628	2203	4300	6503	SO:0001583	missense	5266	exon1			CTCATCGCTGGGA	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"""WAP four-disulfide core domain containing"""	8947	protein-coding gene	gene with protein product	"""skin-derived antileukoproteinase"", ""trappin-2"""	182257	"""protease inhibitor 3, skin-derived (SKALP)"""			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.43G>A	20.37:g.43803606G>A	ENSP00000243924:p.Ala15Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_002638	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	36	0.016483516483516484	0	0.0	7	0.019337016574585635	0	0.0	29	0.03825857519788918	G	10.12	1.261995	0.23051	0.006809	0.040465	ENSG00000124102	ENST00000243924	T	0.23348	1.91	3.9	1.85	0.25348	.	0.708561	0.11636	N	0.544326	T	0.03220	0.0094	L	0.36672	1.1	0.09310	N	1	P	0.34826	0.471	B	0.21151	0.033	T	0.13926	-1.0491	10	0.27785	T	0.31	.	6.7736	0.23607	0.1923:0.5998:0.2079:0.0	rs41282752;rs61729432	15	P19957	ELAF_HUMAN	T	15	ENSP00000243924:A15T	ENSP00000243924:A15T	A	+	1	0	PI3	43237020	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.130000	0.10498	0.352000	0.24053	-0.311000	0.09066	GCT	G|0.973;A|0.027	0.027	strong		0.572	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638	
JRK	8629	hgsc.bcm.edu	37	8	143740311	143740311	+	RNA	SNP	A	A	C	rs117839538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143740311A>C	ENST00000507178.2	-	0	7499							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				GGAATTGCCAACTCCTCTGGT	0.527													A|||	103	0.0205671	0.0045	0.0173	5008	,	,		18792	0.0298		0.0437	False		,,,				2504	0.0112				p.L543V		Atlas-SNP	.											.	.	.	.	0			c.T1627G						PASS	.	A	VAL/LEU,	42,4004		0,42,1981	69.0	70.0	70.0		1629,	-1.7	0.0	8	dbSNP_132	70	420,7948		8,404,3772	yes	missense,utr-3	JRK	NM_001077527.1,NM_003724.2	32,	8,446,5753	CC,CA,AA		5.0191,1.0381,3.7216	possibly-damaging,	543/557,	143740311	462,11952	2023	4184	6207			8629	exon4			TTGCCAACTCCTC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143740311A>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001077527	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				A|0.969;C|0.031	0.031	strong		0.527	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
RYR1	6261	hgsc.bcm.edu	37	19	38935280	38935280	+	Silent	SNP	A	A	G	rs2229139	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:38935280A>G	ENST00000359596.3	+	7	594	c.594A>G	c.(592-594)ctA>ctG	p.L198L	RYR1_ENST00000360985.3_Silent_p.L198L|RYR1_ENST00000355481.4_Silent_p.L198L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	198	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				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)	TGCAGACACTATGGAACATGA	0.602													G|||	2721	0.543331	0.475	0.6571	5008	,	,		15820	0.6121		0.6471	False		,,,				2504	0.3773				p.L198L		Atlas-SNP	.											.	RYR1	708	.	0			c.A594G						PASS	.	G	,	2310,2096	571.5+/-383.1	591,1128,484	49.0	42.0	44.0		594,594	-2.5	1.0	19	dbSNP_98	44	5533,3067	468.5+/-367.3	1790,1953,557	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	2381,3081,1041	GG,GA,AA		35.6628,47.5715,39.6971	,	198/5039,198/5034	38935280	7843,5163	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon7			GACACTATGGAAC	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.594A>G	19.37:g.38935280A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.408;G|0.592	0.592	strong		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
KRT40	125115	hgsc.bcm.edu	37	17	39139370	39139370	+	Missense_Mutation	SNP	G	G	A	rs9908304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	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	
DCAF11	80344	hgsc.bcm.edu	37	14	24587667	24587667	+	Silent	SNP	C	C	T	rs17101367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24587667C>T	ENST00000446197.3	+	7	1375	c.648C>T	c.(646-648)gaC>gaT	p.D216D	RP11-468E2.6_ENST00000558325.1_5'Flank|DCAF11_ENST00000396941.4_Silent_p.D190D|DCAF11_ENST00000559115.1_Silent_p.D216D|DCAF11_ENST00000396936.1_Silent_p.D116D|DCAF11_ENST00000560171.1_3'UTR	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	216					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											AGGCCCGCGACGTAGGCTGGA	0.507													t|||	1664	0.332268	0.3094	0.4107	5008	,	,		22213	0.3889		0.2167	False		,,,				2504	0.3681				p.D216D		Atlas-SNP	.											.	.	.	.	0			c.C648T						PASS	.	T	,,	1225,3181	706.2+/-407.3	168,889,1146	126.0	116.0	120.0		648,648,570	2.9	1.0	14	dbSNP_123	120	1547,7053	746.7+/-407.3	140,1267,2893	no	coding-synonymous,coding-synonymous,coding-synonymous	DCAF11	NM_001163484.1,NM_025230.4,NM_181357.2	,,	308,2156,4039	TT,TC,CC		17.9884,27.803,21.3132	,,	216/547,216/547,190/521	24587667	2772,10234	2203	4300	6503	SO:0001819	synonymous_variant	80344	exon7			CCGCGACGTAGGC	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20258	protein-coding gene	gene with protein product		613317	"""WD repeat domain 23"""	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.648C>T	14.37:g.24587667C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Silent	SNP	ENST00000446197.3	37	CCDS9610.1																																																																																			C|0.753;N|0.000	.	strong		0.507	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		
NRAP	4892	hgsc.bcm.edu	37	10	115381747	115381747	+	Missense_Mutation	SNP	G	G	A	rs868738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115381747G>A	ENST00000359988.3	-	24	2894	c.2650C>T	c.(2650-2652)Cgc>Tgc	p.R884C	NRAP_ENST00000360478.3_Missense_Mutation_p.R849C|NRAP_ENST00000369360.3_Missense_Mutation_p.R857C|NRAP_ENST00000369358.4_Missense_Mutation_p.R892C	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	161	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	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	
MAN2C1	4123	hgsc.bcm.edu	37	15	75650836	75650836	+	Silent	SNP	G	G	A	rs1128933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75650836G>A	ENST00000267978.5	-	20	2416	c.2370C>T	c.(2368-2370)gaC>gaT	p.D790D	MAN2C1_ENST00000569482.1_Silent_p.D790D|MAN2C1_ENST00000563622.1_Silent_p.D691D|RP11-817O13.6_ENST00000563660.1_lincRNA|MAN2C1_ENST00000565683.1_Silent_p.D807D	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	790					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						GGCAGCCAACGTCCAGCACAA	0.662													G|||	1835	0.366414	0.0393	0.4337	5008	,	,		19719	0.4782		0.4662	False		,,,				2504	0.5429				p.D807D		Atlas-SNP	.											.	MAN2C1	76	.	0			c.C2421T						PASS	.	G		497,3897	222.3+/-239.2	35,427,1735	48.0	50.0	49.0		2370	-7.0	0.0	15	dbSNP_86	49	4037,4551	541.1+/-383.9	937,2163,1194	no	coding-synonymous	MAN2C1	NM_006715.2		972,2590,2929	AA,AG,GG		47.0075,11.3109,34.9253		790/1041	75650836	4534,8448	2197	4294	6491	SO:0001819	synonymous_variant	4123	exon20			GCCAACGTCCAGC	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.2370C>T	15.37:g.75650836G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Silent	SNP	ENST00000267978.5	37	CCDS32298.1																																																																																			G|0.651;A|0.349	0.349	strong		0.662	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39915637	39915637	+	Silent	SNP	G	G	A	rs31727	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39915637G>A	ENST00000409794.3	+	19	4714	c.3864G>A	c.(3862-3864)caG>caA	p.Q1288Q	PLEKHG2_ENST00000409797.2_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Silent_p.Q1259Q	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1288					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)			ATATCAGCCAGAGCCTGGCTC	0.697													G|||	2989	0.596845	0.6762	0.5086	5008	,	,		13379	0.5962		0.5358	False		,,,				2504	0.6155				p.Q1288Q		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G3864A						PASS	.	G		2901,1505		958,985,260	35.0	39.0	38.0		3864	4.1	1.0	19	dbSNP_76	38	4356,4242		1135,2086,1078	no	coding-synonymous	PLEKHG2	NM_022835.2		2093,3071,1338	AA,AG,GG		49.3371,34.158,44.1941		1288/1387	39915637	7257,5747	2203	4299	6502	SO:0001819	synonymous_variant	64857	exon19			CAGCCAGAGCCTG	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.3864G>A	19.37:g.39915637G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	1221	0.5590659340659341	320	0.6504065040650406	185	0.511049723756906	314	0.548951048951049	402	0.5303430079155673	G	9.065	0.995379	0.19043	0.65842	0.506629	ENSG00000090924	ENST00000205135	.	.	.	5.14	4.1	0.47936	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999787	.	.	.	.	.	.	T	0.45542	-0.9254	3	.	.	.	.	9.7782	0.40632	0.0962:0.0:0.9038:0.0	rs31727;rs520911;rs17851041;rs17858333;rs61179908;rs31727	.	.	.	K	1156	.	.	R	+	2	0	PLEKHG2	44607477	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.675000	0.46875	1.175000	0.42826	0.561000	0.74099	AGA	G|0.437;A|0.563	0.563	strong		0.697	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
RAPH1	65059	hgsc.bcm.edu	37	2	204306093	204306093	+	Missense_Mutation	SNP	G	G	A	rs541342499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204306093G>A	ENST00000319170.5	-	14	2119	c.1820C>T	c.(1819-1821)cCc>cTc	p.P607L	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Missense_Mutation_p.P659L	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	607					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGATAAAGGGGGCACAAGTGA	0.517																																					p.P607L		Atlas-SNP	.											.	RAPH1	118	.	0			c.C1820T						PASS	.						32.0	35.0	34.0					2																	204306093		1757	3443	5200	SO:0001583	missense	65059	exon14			AAAGGGGGCACAA	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.1820C>T	2.37:g.204306093G>A	ENSP00000316543:p.Pro607Leu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	92	61	0.663043	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	g	11.68	1.710804	0.30322	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.75154	-0.91;-0.91	3.02	3.02	0.34903	.	1.838130	0.03300	U	0.188852	T	0.63546	0.2520	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.25187	-1.0139	10	0.34782	T	0.22	-8.7148	13.4277	0.61035	0.0:0.0:1.0:0.0	.	607	Q70E73	RAPH1_HUMAN	L	607;659	ENSP00000316543:P607L;ENSP00000363617:P659L	ENSP00000316543:P607L	P	-	2	0	RAPH1	204014338	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.020000	0.57189	2.008000	0.58898	0.479000	0.44913	CCC	.	.	none		0.517	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
FAT4	79633	hgsc.bcm.edu	37	4	126372742	126372742	+	Missense_Mutation	SNP	G	G	A	rs1567047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:126372742G>A	ENST00000394329.3	+	9	10584	c.10571G>A	c.(10570-10572)gGc>gAc	p.G3524D	FAT4_ENST00000335110.5_Missense_Mutation_p.G1822D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3524	Cadherin 34. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> D (in dbSNP:rs1567047).		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						AAACGGCCAGGCACTTTGGTG	0.478													G|||	1155	0.230631	0.0242	0.2522	5008	,	,		18233	0.3909		0.2952	False		,,,				2504	0.2628				p.G3524D		Atlas-SNP	.											.	FAT4	1752	.	0			c.G10571A						PASS	.	G	ASP/GLY	292,4114	157.8+/-190.6	10,272,1921	121.0	118.0	119.0		10571	5.8	0.9	4	dbSNP_88	119	2578,6022	417.3+/-352.4	400,1778,2122	yes	missense	FAT4	NM_024582.4	94	410,2050,4043	AA,AG,GG		29.9767,6.6273,22.0667	probably-damaging	3524/4982	126372742	2870,10136	2203	4300	6503	SO:0001583	missense	79633	exon9			GGCCAGGCACTTT	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.10571G>A	4.37:g.126372742G>A	ENSP00000377862:p.Gly3524Asp	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	565	0.2586996336996337	15	0.03048780487804878	107	0.2955801104972376	225	0.39335664335664333	218	0.287598944591029	G	23.6	4.435957	0.83885	0.066273	0.299767	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.54071	0.59;0.59	5.77	5.77	0.91146	Cadherin (3);Cadherin-like (1);	0.000000	0.33670	U	0.004671	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.9999999999954321	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.05801	-1.0863	9	0.66056	D	0.02	.	19.9983	0.97395	0.0:0.0:1.0:0.0	rs1567047;rs52797800;rs60153785;rs1567047	1822;3524;3524	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	3524;1822	ENSP00000377862:G3524D;ENSP00000335169:G1822D	ENSP00000335169:G1822D	G	+	2	0	FAT4	126592192	1.000000	0.71417	0.935000	0.37517	0.783000	0.44284	9.666000	0.98612	2.724000	0.93272	0.561000	0.74099	GGC	G|0.769;A|0.231	0.231	strong		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
MAP9	79884	hgsc.bcm.edu	37	4	156276289	156276289	+	Silent	SNP	C	C	T	rs2341894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156276289C>T	ENST00000311277.4	-	10	1577	c.1314G>A	c.(1312-1314)gtG>gtA	p.V438V	AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000594666.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000593387.2_RNA|MAP9_ENST00000515654.1_Silent_p.V414V|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000596754.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000594492.1_RNA|AC097467.2_ENST00000601977.1_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	135	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	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	
SCTR	6344	hgsc.bcm.edu	37	2	120194682	120194682	+	IGR	SNP	A	A	C	rs200510439		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:120194682A>C	ENST00000019103.5	-	0	1865				TMEM37_ENST00000306406.4_Missense_Mutation_p.H80P|TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Missense_Mutation_p.H92P	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	GGCCAGGCCCATGTGCCCGGG	0.667													A|||	1	0.000199681	0.0	0.0	5008	,	,		14518	0.0		0.001	False		,,,				2504	0.0				p.H80P		Atlas-SNP	.											.	TMEM37	40	.	0			c.A239C						PASS	.	A	PRO/HIS	0,4406		0,0,2203	51.0	54.0	53.0		239	-1.9	0.0	2		53	5,8595	4.3+/-15.6	0,5,4295	no	missense	TMEM37	NM_183240.2	77	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	benign	80/191	120194682	5,13001	2203	4300	6503	SO:0001628	intergenic_variant	140738	exon2			AGGCCCATGTGCC		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194682A>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	A	7.689	0.690644	0.15039	0.0	5.81E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	-1.88	0.07713	.	1.326400	0.04832	N	0.438832	T	0.37571	0.1008	L	0.44542	1.39	0.09310	N	1	B	0.32620	0.378	B	0.34931	0.192	T	0.39522	-0.9610	9	0.35671	T	0.21	0.0526	11.2183	0.48840	0.5495:0.0:0.4505:0.0	.	80	Q8WXS4	CCGL_HUMAN	P	92;80	.	ENSP00000303148:H80P	H	+	2	0	TMEM37	119911152	0.000000	0.05858	0.001000	0.08648	0.381000	0.30169	0.049000	0.14099	-0.500000	0.06614	0.459000	0.35465	CAT	.	.	weak		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
HDAC7	51564	hgsc.bcm.edu	37	12	48177906	48177906	+	Silent	SNP	C	C	T	rs7306788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:48177906C>T	ENST00000427332.2	-	25	2925	c.2769G>A	c.(2767-2769)gtG>gtA	p.V923V	AC004466.1_ENST00000599515.1_5'Flank|HDAC7_ENST00000080059.7_Silent_p.V962V|HDAC7_ENST00000552960.1_Silent_p.V945V|HDAC7_ENST00000380610.4_Silent_p.*1015*|HDAC7_ENST00000354334.3_Silent_p.V925V			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	923	Interaction with SIN3A. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|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 kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		CCAGTGCGGTCACTGCCTCCA	0.627													C|||	358	0.0714856	0.0197	0.0951	5008	,	,		17928	0.002		0.1769	False		,,,				2504	0.0879				p.V962V		Atlas-SNP	.											.	HDAC7	71	.	0			c.G2886A						PASS	.	C	,	184,4222	118.4+/-156.1	4,176,2023	55.0	51.0	52.0		2775,2886	2.4	1.0	12	dbSNP_116	52	1624,6976	299.5+/-304.5	130,1364,2806	no	coding-synonymous,coding-synonymous	HDAC7	NM_001098416.2,NM_015401.3	,	134,1540,4829	TT,TC,CC		18.8837,4.1761,13.9013	,	925/955,962/992	48177906	1808,11198	2203	4300	6503	SO:0001819	synonymous_variant	51564	exon25			TGCGGTCACTGCC	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.2769G>A	12.37:g.48177906C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Silent	SNP	ENST00000427332.2	37																																																																																				C|0.879;G|0.000;T|0.121	0.121	strong		0.627	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
CPNE6	9362	hgsc.bcm.edu	37	14	24545366	24545366	+	Silent	SNP	T	T	C	rs2070342	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24545366T>C	ENST00000397016.2	+	12	1244	c.933T>C	c.(931-933)atT>atC	p.I311I	CPNE6_ENST00000216775.2_Silent_p.I311I|CPNE6_ENST00000537691.1_Silent_p.I366I	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	311	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)		AGGTGGCCATTGACTTCACCG	0.622													C|||	2492	0.497604	0.5968	0.4337	5008	,	,		16063	0.4861		0.3579	False		,,,				2504	0.5644				p.I311I		Atlas-SNP	.											.	CPNE6	40	.	0			c.T933C						PASS	.	C		2454,1952	549.0+/-377.7	693,1068,442	47.0	45.0	46.0		933	-4.6	0.8	14	dbSNP_96	46	2986,5614	663.0+/-402.0	509,1968,1823	no	coding-synonymous	CPNE6	NM_006032.2		1202,3036,2265	CC,CT,TT		34.7209,44.3032,41.8268		311/558	24545366	5440,7566	2203	4300	6503	SO:0001819	synonymous_variant	9362	exon11			GGCCATTGACTTC	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.933T>C	14.37:g.24545366T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			T|0.579;C|0.421	0.421	strong		0.622	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
CD6	923	hgsc.bcm.edu	37	11	60776306	60776306	+	Missense_Mutation	SNP	C	C	T	rs386754116|rs2074225	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60776306C>T	ENST00000313421.7	+	4	956	c.770C>T	c.(769-771)gCg>gTg	p.A257V	CD6_ENST00000344028.5_Missense_Mutation_p.A257V|CD6_ENST00000352009.5_Missense_Mutation_p.A257V|CD6_ENST00000545105.1_Intron|CD6_ENST00000346437.4_Missense_Mutation_p.A257V|CD6_ENST00000452451.2_Missense_Mutation_p.A257V	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	257	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		A -> V (in dbSNP:rs2074225). {ECO:0000269|PubMed:17371992, ECO:0000269|PubMed:1919444, ECO:0000269|PubMed:9013954}.		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GACGCGGGCGCGGTGTGCTCA	0.657													T|||	2686	0.536342	0.6702	0.4438	5008	,	,		15796	0.4067		0.6243	False		,,,				2504	0.4642				p.A257V	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,NS,carcinoma,-1,2	CD6	122	2	0			c.C770T						PASS	.	T	VAL/ALA	2410,1978		825,760,609	14.0	14.0	14.0		770	3.3	0.0	11	dbSNP_96	14	4699,3875		1512,1675,1100	no	missense	CD6	NM_006725.3	64	2337,2435,1709	TT,TC,CC		45.1948,45.0775,45.1551	benign	257/669	60776306	7109,5853	2194	4287	6481	SO:0001583	missense	923	exon4			CGGGCGCGGTGTG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.770C>T	11.37:g.60776306C>T	ENSP00000323280:p.Ala257Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	1187|1187	0.5434981684981685|0.5434981684981685	312|312	0.6341463414634146|0.6341463414634146	183|183	0.505524861878453|0.505524861878453	236|236	0.4125874125874126|0.4125874125874126	456|456	0.6015831134564644|0.6015831134564644	T|T	0.455|0.455	-0.892056|-0.892056	0.02491|0.02491	0.549225|0.549225	0.548052|0.548052	ENSG00000013725|ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009|ENST00000538611	T;T;T;T;T;T;T|.	0.18338|.	2.22;2.22;2.22;2.22;2.22;2.22;2.22|.	4.42|4.42	3.3|3.3	0.37823|0.37823	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);|.	0.121248|.	0.29846|.	N|.	0.011057|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00040|0.00040	-2.495|-2.495	0.52099|0.52099	P|P	5.8000000000002494E-5|5.8000000000002494E-5	B;B;B;B;B|.	0.09022|.	0.002;0.001;0.001;0.0;0.0|.	B;B;B;B;B|.	0.06405|.	0.002;0.001;0.001;0.0;0.001|.	T|T	0.41627|0.41627	-0.9498|-0.9498	9|4	0.02654|.	T|.	1|.	.|.	8.4555|8.4555	0.32897|0.32897	0.0:0.1619:0.0:0.8381|0.0:0.1619:0.0:0.8381	rs2074225;rs59498421;rs2074225|rs2074225;rs59498421;rs2074225	257;257;257;257;257|.	E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7|.	.;.;.;CD6_HUMAN;.|.	V|W	257|101	ENSP00000344108:A257V;ENSP00000345566:A257V;ENSP00000323280:A257V;ENSP00000440055:A257V;ENSP00000410638:A257V;ENSP00000390676:A257V;ENSP00000340628:A257V|.	ENSP00000323280:A257V|.	A|R	+|+	2|1	0|2	CD6|CD6	60532882|60532882	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.028000|0.028000	0.11728|0.11728	4.111000|4.111000	0.57838|0.57838	0.258000|0.258000	0.21686|0.21686	-0.254000|-0.254000	0.11334|0.11334	GCG|CGG	C|0.409;T|0.591	0.591	strong		0.657	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
C20orf194	25943	hgsc.bcm.edu	37	20	3285140	3285140	+	Missense_Mutation	SNP	T	T	C	rs2422864	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3285140T>C	ENST00000252032.9	-	21	1796	c.1729A>G	c.(1729-1731)Aga>Gga	p.R577G	C20orf194_ENST00000453730.2_Missense_Mutation_p.R315G|C20orf194_ENST00000498079.1_5'UTR	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	577			R -> G (in dbSNP:rs2422864). {ECO:0000269|PubMed:17974005}.							NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						ATGATACTTCTATGACGACAG	0.453													C|||	4676	0.933706	0.9478	0.9294	5008	,	,		21008	1.0		0.8579	False		,,,				2504	0.9274				p.R577G		Atlas-SNP	.											.	C20orf194	83	.	0			c.A1729G						PASS	.	C	GLY/ARG	3624,194		1720,184,5	112.0	103.0	106.0		1729	5.7	1.0	20	dbSNP_100	106	6982,1276		2944,1094,91	yes	missense	C20orf194	NM_001009984.1	125	4664,1278,96	CC,CT,TT		15.4517,5.0812,12.1729	benign	577/1178	3285140	10606,1470	1909	4129	6038	SO:0001583	missense	25943	exon21			TACTTCTATGACG	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.1729A>G	20.37:g.3285140T>C	ENSP00000252032:p.Arg577Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	2012	0.9212454212454212	463	0.9410569105691057	332	0.9171270718232044	572	1.0	645	0.8509234828496042	C	6.887	0.533036	0.13188	0.949188	0.845483	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.19250	2.81;2.16	5.66	5.66	0.87406	.	0.056274	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00092	-2.175	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40327	-0.9569	9	0.02654	T	1	.	12.0952	0.53750	0.0:0.9192:0.0:0.0808	rs2422864;rs17698838;rs60330897;rs2422864	577	Q5TEA3	CT194_HUMAN	G	577;315	ENSP00000252032:R577G;ENSP00000407229:R315G	ENSP00000252032:R577G	R	-	1	2	C20orf194	3233140	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.056000	0.49923	1.393000	0.46605	-0.320000	0.08662	AGA	T|0.098;C|0.902	0.902	strong		0.453	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
DZIP1L	199221	hgsc.bcm.edu	37	3	137807259	137807259	+	Missense_Mutation	SNP	G	G	A	rs2724693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137807259G>A	ENST00000327532.2	-	6	1323	c.961C>T	c.(961-963)Cgg>Tgg	p.R321W	DZIP1L_ENST00000488595.1_5'UTR|DZIP1L_ENST00000469243.1_Missense_Mutation_p.R321W	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	321			R -> W (in dbSNP:rs2724693). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TGAAGCTCCCGTGCCTGCCGA	0.547													G|||	2689	0.536941	0.1884	0.6859	5008	,	,		17069	0.6131		0.6869	False		,,,				2504	0.6697				p.R321W		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C961T						PASS	.	G	TRP/ARG,TRP/ARG	1291,3115	437.2+/-344.9	180,931,1092	65.0	54.0	58.0		961,961	3.3	0.1	3	dbSNP_100	58	6110,2490	694.8+/-404.8	2164,1782,354	yes	missense,missense	DZIP1L	NM_001170538.1,NM_173543.2	101,101	2344,2713,1446	AA,AG,GG		28.9535,29.301,43.0955	probably-damaging,probably-damaging	321/540,321/768	137807259	7401,5605	2203	4300	6503	SO:0001583	missense	199221	exon7			GCTCCCGTGCCTG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.961C>T	3.37:g.137807259G>A	ENSP00000332148:p.Arg321Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1229	0.5627289377289377	118	0.23983739837398374	234	0.6464088397790055	360	0.6293706293706294	517	0.6820580474934037	G	12.10	1.835476	0.32421	0.29301	0.710465	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.47869	0.83;0.83	5.33	3.29	0.37713	.	0.680747	0.12775	N	0.440182	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D;D	0.65815	0.995;0.995	P;B	0.46975	0.533;0.446	T	0.17561	-1.0365	9	0.66056	D	0.02	-5.9845	6.8846	0.24193	0.0:0.1434:0.5549:0.3017	rs2724693;rs13060733;rs16847842;rs52833476;rs59499377;rs2724693	321;321	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	W	321	ENSP00000332148:R321W;ENSP00000419486:R321W	ENSP00000332148:R321W	R	-	1	2	DZIP1L	139289949	0.574000	0.26684	0.113000	0.21522	0.002000	0.02628	0.994000	0.29693	1.206000	0.43276	0.655000	0.94253	CGG	G|0.448;A|0.552	0.552	strong		0.547	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
ARHGAP17	55114	hgsc.bcm.edu	37	16	24955183	24955183	+	Splice_Site	SNP	T	T	C	rs17624477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24955183T>C	ENST00000289968.6	-	15	1311	c.1242A>G	c.(1240-1242)ggA>ggG	p.G414G	ARHGAP17_ENST00000303665.5_Splice_Site_p.G414G|ARHGAP17_ENST00000441763.2_3'UTR	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	414	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		CAGCAAGTGTTCTGCAAAGCA	0.408													T|||	199	0.0397364	0.0015	0.0836	5008	,	,		18381	0.0208		0.0934	False		,,,				2504	0.0245				p.G414G		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.A1242G						PASS	.	T	,	44,4350	41.6+/-74.8	0,44,2153	82.0	72.0	75.0		1242,1242	0.9	1.0	16	dbSNP_123	75	610,7990	147.1+/-202.6	18,574,3708	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ARHGAP17	NM_001006634.1,NM_018054.4	,	18,618,5861	CC,CT,TT		7.093,1.0014,5.0331	,	414/882,414/804	24955183	654,12340	2197	4300	6497	SO:0001630	splice_region_variant	55114	exon15			AAGTGTTCTGCAA	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.1242-1A>G	16.37:g.24955183T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	37	CCDS32409.1																																																																																			T|0.946;C|0.054	0.054	strong		0.408	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	Silent
FSTL5	56884	hgsc.bcm.edu	37	4	163032498	163032498	+	Missense_Mutation	SNP	C	C	G	rs140747357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:163032498C>G	ENST00000306100.5	-	2	487	c.51G>C	c.(49-51)gaG>gaC	p.E17D	FSTL5_ENST00000427802.2_Missense_Mutation_p.E17D|FSTL5_ENST00000379164.4_Missense_Mutation_p.E17D|FSTL5_ENST00000536695.1_Missense_Mutation_p.E17D	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	17						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)		TTCCTTCCGACTCCAGAAAAA	0.398													C|||	4	0.000798722	0.0	0.0	5008	,	,		14268	0.0		0.004	False		,,,				2504	0.0				p.E17D		Atlas-SNP	.											.	FSTL5	207	.	0			c.G51C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	131.0	125.0	127.0		51,51,51	-2.3	0.5	4	dbSNP_134	127	45,8555	29.0+/-79.6	0,45,4255	yes	missense,missense,missense	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	45,45,45	0,52,6451	GG,GC,CC		0.5233,0.1589,0.3998	benign,benign,benign	17/847,17/838,17/848	163032498	52,12954	2203	4300	6503	SO:0001583	missense	56884	exon2			TTCCGACTCCAGA	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.51G>C	4.37:g.163032498C>G	ENSP00000305334:p.Glu17Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001128428	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.069	-0.413600	0.04799	0.001589	0.005233	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72725	-0.66;-0.65;-0.68;-0.65	5.51	-2.26	0.06867	.	0.753644	0.12056	N	0.503598	T	0.32556	0.0833	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.14671	-1.0464	10	0.17832	T	0.49	.	4.3997	0.11381	0.2402:0.3205:0.0:0.4394	.	17;17;17	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	D	17	ENSP00000305334:E17D;ENSP00000368462:E17D;ENSP00000389270:E17D;ENSP00000440409:E17D	ENSP00000305334:E17D	E	-	3	2	FSTL5	163251948	0.865000	0.29922	0.477000	0.27303	0.010000	0.07245	-0.188000	0.09642	-0.753000	0.04721	-1.975000	0.00460	GAG	C|0.996;G|0.004	0.004	strong		0.398	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
GZMB	3002	hgsc.bcm.edu	37	14	25101589	25101589	+	Missense_Mutation	SNP	G	G	C	rs11539752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:25101589G>C	ENST00000216341.4	-	3	386	c.280C>G	c.(280-282)Ccc>Gcc	p.P94A	RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000526004.1_Intron|GZMB_ENST00000415355.3_Missense_Mutation_p.P82A|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Missense_Mutation_p.P128A			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	94	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		P -> A (in dbSNP:rs11539752). {ECO:0000269|PubMed:2332171, ECO:0000269|PubMed:3258865}.		apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.P94A(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		TGGGGGATGGGTCTTTTCACA	0.512													g|||	1512	0.301917	0.3759	0.2118	5008	,	,		17810	0.2867		0.2475	False		,,,				2504	0.3374				p.P94A		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - Missense(1)	stomach(1)	c.C280G	GRCh37	CM033776	GZMB	M	rs11539752	PASS	.						128.0	144.0	138.0					14																	25101589		2203	4300	6503	SO:0001583	missense	3002	exon3			GGATGGGTCTTTT	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.280C>G	14.37:g.25101589G>C	ENSP00000216341:p.Pro94Ala	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	164	155	0.945122	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	608	0.2783882783882784	195	0.39634146341463417	83	0.2292817679558011	138	0.24125874125874125	192	0.2532981530343008	g	0.017	-1.508410	0.00984	.	.	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542	D;D;D	0.87491	-2.26;-2.26;-2.26	5.4	-0.755	0.11061	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.747530	0.03630	N	0.237718	T	0.00012	0.0000	N	0.00317	-1.655	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26360	-1.0105	9	0.02654	T	1	.	1.3803	0.02229	0.138:0.3597:0.2697:0.2327	rs11539752	82;94	Q6XGZ4;P10144	.;GRAB_HUMAN	A	82;94;128	ENSP00000387385:P82A;ENSP00000216341:P94A;ENSP00000371982:P128A	ENSP00000216341:P94A	P	-	1	0	GZMB	24171429	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.100000	0.03339	-0.316000	0.08690	-0.745000	0.03516	CCC	G|0.724;C|0.276	0.276	strong		0.512	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
HLA-A	3105	hgsc.bcm.edu	37	6	29910752	29910752	+	Missense_Mutation	SNP	G	G	C	rs1136683	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910752G>C	ENST00000396634.1	+	4	633	c.292G>C	c.(292-294)Gac>Cac	p.D98H	HLA-A_ENST00000376806.5_Missense_Mutation_p.D98H|HLA-A_ENST00000376809.5_Missense_Mutation_p.D98H|HLA-A_ENST00000376802.2_Missense_Mutation_p.D98H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	98	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTCACAGACTGACCGAGTGGA	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1142	0.228035	0.1778	0.3012	5008	,	,		10698	0.2966		0.3141	False		,,,				2504	0.0849				p.D98H		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.G292C						PASS	.	T	HIS/ASP	760,3636		79,602,1517	68.0	73.0	71.0		292	-7.2	0.0	6	dbSNP_131	71	2250,6334		356,1538,2398	no	missense	HLA-A	NM_002116.7	81	435,2140,3915	CC,CG,GG		26.2116,17.2884,23.1895	possibly-damaging	98/366	29910752	3010,9970	2198	4292	6490	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CAGACTGACCGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.292G>C	6.37:g.29910752G>C	ENSP00000379873:p.Asp98His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	191	38	0.198953	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	607	0.27793040293040294	92	0.18699186991869918	90	0.24861878453038674	170	0.2972027972027972	255	0.33641160949868076	.	0.246	-1.009865	0.02095	0.172884	0.262116	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.46;9.46;9.46;9.46	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	8.950690	0.01007	U	0.003778	T	0.00039	0.0001	L	0.37507	1.11	0.80722	P	0.0	B;B;B;P;B	0.44241	0.003;0.004;0.009;0.829;0.009	B;B;B;D;B	0.69824	0.016;0.136;0.17;0.966;0.17	T	0.51204	-0.8735	9	0.22706	T	0.39	.	1.9089	0.03283	0.1091:0.1996:0.2109:0.4803	rs1136683;rs2231000;rs3173423;rs12721692;rs16867781;rs16896598;rs28749147;rs41554813	98;98;98;98;98	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	H	98	ENSP00000379873:D98H;ENSP00000366002:D98H;ENSP00000366005:D98H;ENSP00000365998:D98H	ENSP00000348012:D98H	D	+	1	0	HLA-A	30018731	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.437000	0.02419	-1.229000	0.02564	-0.349000	0.07799	GAC	C|0.195;G|0.805	0.195	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13936385	13936385	+	Missense_Mutation	SNP	C	C	T	rs62620757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13936385C>T	ENST00000254323.2	+	11	2075	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.T463M	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	629				T -> M (in Ref. 1; BAB15742). {ECO:0000305}.			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)			TGGCTGCACACGGTACTGGGC	0.637													C|||	594	0.11861	0.1634	0.085	5008	,	,		15642	0.122		0.0805	False		,,,				2504	0.1176				p.T629M		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.C1886T						PASS	.	C	MET/THR	634,3772	271.0+/-269.9	48,538,1617	86.0	88.0	87.0		1886	4.0	0.4	19	dbSNP_129	87	628,7972	162.0+/-214.8	19,590,3691	yes	missense	ZSWIM4	NM_023072.2	81	67,1128,5308	TT,TC,CC		7.3023,14.3895,9.7032	probably-damaging	629/990	13936385	1262,11744	2203	4300	6503	SO:0001583	missense	65249	exon11			TGCACACGGTACT	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.1886C>T	19.37:g.13936385C>T	ENSP00000254323:p.Thr629Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	255	0.11675824175824176	82	0.16666666666666666	38	0.10497237569060773	70	0.12237762237762238	65	0.08575197889182058	C	12.12	1.841425	0.32513	0.143895	0.073023	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.47869	0.83;0.83	3.99	3.99	0.46301	.	1.016850	0.07928	N	0.977092	T	0.00210	0.0006	L	0.60455	1.87	0.44254	P	0.0028920000000000057	B;B	0.25667	0.004;0.131	B;B	0.29440	0.002;0.102	T	0.09335	-1.0679	9	0.54805	T	0.06	-29.1387	13.598	0.62002	0.0:1.0:0.0:0.0	rs62620757	463;629	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	M	629;463	ENSP00000254323:T629M;ENSP00000405278:T463M	ENSP00000254323:T629M	T	+	2	0	ZSWIM4	13797385	0.960000	0.32886	0.429000	0.26710	0.596000	0.36781	2.353000	0.44089	2.059000	0.61396	0.591000	0.81541	ACG	C|0.892;T|0.108	0.108	strong		0.637	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
DHDDS	79947	hgsc.bcm.edu	37	1	26786627	26786627	+	Missense_Mutation	SNP	G	G	A	rs3816539	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:26786627G>A	ENST00000236342.7	+	8	850	c.757G>A	c.(757-759)Gtg>Atg	p.V253M	DHDDS_ENST00000526219.1_Missense_Mutation_p.V214M|RP3-476K8.3_ENST00000423060.1_RNA|DHDDS_ENST00000360009.2_Missense_Mutation_p.V253M|DHDDS_ENST00000525682.2_Missense_Mutation_p.V219M			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	108	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	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	
TAF5L	27097	hgsc.bcm.edu	37	1	229730452	229730452	+	Silent	SNP	G	G	A	rs2295625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229730452G>A	ENST00000366676.1	-	4	1361	c.1362C>T	c.(1360-1362)agC>agT	p.S454S	TAF5L_ENST00000258281.2_Silent_p.S454S			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	454					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CCTGCTGAGCGCTCCACAGCC	0.572													G|||	1520	0.303514	0.0938	0.2666	5008	,	,		20263	0.3254		0.4612	False		,,,				2504	0.4284				p.S454S		Atlas-SNP	.											.	TAF5L	76	.	0			c.C1362T						PASS	.	G		649,3757	274.6+/-272.0	44,561,1598	82.0	86.0	85.0		1362	-5.3	0.0	1	dbSNP_100	85	3987,4613	548.2+/-385.3	931,2125,1244	no	coding-synonymous	TAF5L	NM_014409.3		975,2686,2842	AA,AG,GG		46.3605,14.7299,35.6451		454/590	229730452	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	27097	exon5			CTGAGCGCTCCAC	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"""WD repeat domain containing"""	17304	protein-coding gene	gene with protein product	"""PCAF associated factor 65 beta"""		"""TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.1362C>T	1.37:g.229730452G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_014409	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			G|0.674;A|0.326	0.326	strong		0.572	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	
MAP2K3	5606	hgsc.bcm.edu	37	17	21203907	21203907	+	Silent	SNP	T	T	C	rs73311539	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:21203907T>C	ENST00000342679.4	+	4	465	c.216T>C	c.(214-216)cgT>cgC	p.R72R	MAP2K3_ENST00000316920.6_Silent_p.R43R|MAP2K3_ENST00000361818.5_Silent_p.R43R	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|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)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R76R(2)|p.R43R(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		AACTGGGCCGTGGAGCCTATG	0.607																																					p.R72R		Atlas-SNP	.											MAP2K3_ENST00000316920,NS,carcinoma,0,4	MAP2K3	135	4	3	Substitution - coding silent(3)	prostate(2)|haematopoietic_and_lymphoid_tissue(1)	c.T216C						PASS	.						59.0	54.0	55.0					17																	21203907		2203	4300	6503	SO:0001819	synonymous_variant	5606	exon4			GGGCCGTGGAGCC	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.216T>C	17.37:g.21203907T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																			T|0.741;C|0.259	0.259	strong		0.607	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
PFN4	375189	hgsc.bcm.edu	37	2	24342532	24342532	+	Silent	SNP	G	G	A	rs1134516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:24342532G>A	ENST00000313213.4	-	4	647	c.276C>T	c.(274-276)gtC>gtT	p.V92V	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	92					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGTCTTCACGACAACCACAC	0.463													g|||	643	0.128395	0.1278	0.0793	5008	,	,		18773	0.0456		0.1561	False		,,,				2504	0.2209				p.V92V		Atlas-SNP	.											.	PFN4	16	.	0			c.C276T						PASS	.	A		556,3850	248.7+/-256.4	26,504,1673	110.0	101.0	104.0		276	-5.6	0.1	2	dbSNP_86	104	1382,7218	267.9+/-287.5	110,1162,3028	no	coding-synonymous	PFN4	NM_199346.1		136,1666,4701	AA,AG,GG		16.0698,12.6192,14.9008		92/130	24342532	1938,11068	2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			CTTCACGACAACC	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.276C>T	2.37:g.24342532G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	37	CCDS1709.1																																																																																			G|0.866;A|0.134	0.134	strong		0.463	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
HLA-A	3105	hgsc.bcm.edu	37	6	29912042	29912042	+	Missense_Mutation	SNP	G	G	A	rs150028516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29912042G>A	ENST00000396634.1	+	6	1104	c.763G>A	c.(763-765)Gtg>Atg	p.V255M	HLA-A_ENST00000376806.5_Missense_Mutation_p.V255M|HLA-A_ENST00000376809.5_Missense_Mutation_p.V255M|HLA-A_ENST00000376802.2_Missense_Mutation_p.V255M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	255	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.V255M(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CACGGAGCTCGTGGAGACCAG	0.637									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	860	0.171725	0.1051	0.2262	5008	,	,		17643	0.2242		0.2127	False		,,,				2504	0.1268				p.V255M		Atlas-SNP	.											HLA-A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HLA-A	89	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.G763A						scavenged	.						32.0	38.0	36.0					6																	29912042		1509	2697	4206	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGCTCGTGGAGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.763G>A	6.37:g.29912042G>A	ENSP00000379873:p.Val255Met	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	109	20	0.183486	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.542	1.113576	0.20795	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.02890	4.12;4.12;4.12;4.12	3.69	0.88	0.19161	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	1.039740	0.07764	U	0.950678	T	0.07143	0.0181	M	0.87682	2.9	0.21527	N	0.999656	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.983;1.0;0.999;1.0;0.999;1.0;1.0	T	0.15578	-1.0432	10	0.72032	D	0.01	.	5.5915	0.17303	0.3615:0.0:0.6385:0.0	.	134;255;255;255;255;255;255	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	M	255;255;43;255;255	ENSP00000379873:V255M;ENSP00000366002:V255M;ENSP00000366005:V255M;ENSP00000365998:V255M	ENSP00000365998:V255M	V	+	1	0	HLA-A	30020021	0.125000	0.22332	0.677000	0.29947	0.503000	0.33858	0.399000	0.20916	0.365000	0.24400	-0.674000	0.03794	GTG	A|1.000;|0.000	1.000	weak		0.637	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
C5orf60	285679	hgsc.bcm.edu	37	5	179069468	179069468	+	Missense_Mutation	SNP	A	A	G	rs62405726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	41	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	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	
INCENP	3619	hgsc.bcm.edu	37	11	61913196	61913196	+	Missense_Mutation	SNP	G	G	T	rs7129085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:61913196G>T	ENST00000394818.3	+	14	2134	c.1932G>T	c.(1930-1932)gaG>gaT	p.E644D	INCENP_ENST00000278849.4_Missense_Mutation_p.E640D	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	644			E -> D (in dbSNP:rs7129085). {ECO:0000269|PubMed:11453556, ECO:0000269|PubMed:15316025, ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGGAAGAGGAGGCACGTAGGC	0.657													G|||	1472	0.29393	0.1974	0.3444	5008	,	,		17951	0.12		0.6252	False		,,,				2504	0.227				p.E644D		Atlas-SNP	.											.	INCENP	122	.	0			c.G1932T						PASS	.	G	ASP/GLU,ASP/GLU	1143,3235		175,793,1221	76.0	48.0	57.0		1932,1920	0.4	1.0	11	dbSNP_116	57	5307,3249		1692,1923,663	yes	missense,missense	INCENP	NM_001040694.1,NM_020238.2	45,45	1867,2716,1884	TT,TG,GG		37.9734,26.1078,49.8686	probably-damaging,probably-damaging	644/919,640/915	61913196	6450,6484	2189	4278	6467	SO:0001583	missense	3619	exon14			AGAGGAGGCACGT	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1932G>T	11.37:g.61913196G>T	ENSP00000378295:p.Glu644Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	770	0.3525641025641026	116	0.23577235772357724	136	0.3756906077348066	48	0.08391608391608392	470	0.6200527704485488	G	13.95	2.390187	0.42410	0.261078	0.620266	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.19394	2.15;2.17	5.43	0.398	0.16319	.	0.000000	0.56097	D	0.000035	T	0.00012	0.0000	L	0.52011	1.625	0.30946	P	0.725236	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.991	T	0.44159	-0.9346	9	0.49607	T	0.09	.	8.8745	0.35337	0.3967:0.0:0.6033:0.0	rs7129085;rs59143588;rs7129085	640;644	Q9NQS7-2;Q9NQS7	.;INCE_HUMAN	D	644;640	ENSP00000378295:E644D;ENSP00000278849:E640D	ENSP00000278849:E640D	E	+	3	2	INCENP	61669772	1.000000	0.71417	0.965000	0.40720	0.739000	0.42172	1.144000	0.31565	0.281000	0.22233	0.561000	0.74099	GAG	G|0.625;T|0.375	0.375	strong		0.657	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
TRIM10	10107	hgsc.bcm.edu	37	6	30121525	30121525	+	3'UTR	SNP	G	G	A	rs12210298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30121525G>A	ENST00000449742.2	-	0	1742				TRIM10_ENST00000376704.3_Silent_p.D376D	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10						erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						AGCAGCCTGAGTCCCCAGGTA	0.547													G|||	76	0.0151757	0.003	0.013	5008	,	,		17602	0.002		0.0527	False		,,,				2504	0.0082				p.D376D		Atlas-SNP	.											.	TRIM10	65	.	0			c.C1128T						PASS	.	G	,	22,3000		0,22,1489	69.0	57.0	61.0		,1128	0.8	0.0	6	dbSNP_120	61	237,5181		6,225,2478	no	utr-3,coding-synonymous	TRIM10	NM_006778.3,NM_052828.2	,	6,247,3967	AA,AG,GG		4.3743,0.728,3.0687	,	,376/396	30121525	259,8181	1511	2709	4220	SO:0001624	3_prime_UTR_variant	10107	exon8			GCCTGAGTCCCCA	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.*221C>T	6.37:g.30121525G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_052828	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	37	CCDS34375.1																																																																																			G|0.970;A|0.030	0.030	strong		0.547	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
GALK1	2584	hgsc.bcm.edu	37	17	73751175	73751175	+	Intron	SNP	C	C	T	rs140501692		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73751175C>T	ENST00000225614.2	-	8	1301				ITGB4_ENST00000449880.2_Missense_Mutation_p.P1463L|ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000339591.3_Missense_Mutation_p.P1463L|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000200181.3_Intron			P51570	GALK1_HUMAN	galactokinase 1						carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGCAGGCTTCCGCTGTCCTGG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17871	0.001		0.0	False		,,,				2504	0.0				p.P1463L		Atlas-SNP	.											ITGB4_ENST00000339591,colon,carcinoma,+1,1	ITGB4	165	1	0			c.C4388T						PASS	.	C	,LEU/PRO,	0,4406		0,0,2203	47.0	49.0	48.0		,4388,	5.3	1.0	17	dbSNP_134	48	5,8589		0,5,4292	yes	intron,missense,intron	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,98,	0,5,6495	TT,TC,CC		0.0582,0.0,0.0385	,,	,1463/1806,	73751175	5,12995	2203	4297	6500	SO:0001627	intron_variant	3691	exon33			GGCTTCCGCTGTC		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000225614.2:c.1176+2939G>A	17.37:g.73751175C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_001005619	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000225614.2	37	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025433	0.54683	0.0	5.82E-4	ENSG00000132470	ENST00000339591;ENST00000449880	T;T	0.73152	-0.72;-0.72	5.26	5.26	0.73747	.	.	.	.	.	T	0.58323	0.2114	.	.	.	0.80722	D	1	B	0.20459	0.045	B	0.13407	0.009	T	0.53920	-0.8370	8	0.30078	T	0.28	.	11.5095	0.50486	0.0:0.9144:0.0:0.0856	.	1463	P16144-3	.	L	1463	ENSP00000344079:P1463L;ENSP00000400217:P1463L	ENSP00000344079:P1463L	P	+	2	0	ITGB4	71262770	0.989000	0.36119	1.000000	0.80357	0.996000	0.88848	1.319000	0.33655	2.455000	0.83008	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	weak		0.622	GALK1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448427.1		
MUC16	94025	hgsc.bcm.edu	37	19	9077264	9077264	+	Silent	SNP	T	T	G	rs1862461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9077264T>G	ENST00000397910.4	-	3	10385	c.10182A>C	c.(10180-10182)gtA>gtC	p.V3394V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3395	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.V3394V(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						CTGTGGTGCTTACCCATGTCT	0.438													G|||	1250	0.249601	0.202	0.2133	5008	,	,		21618	0.251		0.3121	False		,,,				2504	0.274				p.V3394V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.A10182C						PASS	.	G		852,3122		101,650,1236	265.0	251.0	256.0		10182	2.0	0.1	19	dbSNP_92	256	2409,5935		349,1711,2112	no	coding-synonymous	MUC16	NM_024690.2		450,2361,3348	GG,GT,TT		28.871,21.4394,26.4735		3394/14508	9077264	3261,9057	1987	4172	6159	SO:0001819	synonymous_variant	94025	exon3			GGTGCTTACCCAT	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.10182A>C	19.37:g.9077264T>G		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	225	118	0.524444	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.748;G|0.252	0.252	strong		0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CHST15	51363	hgsc.bcm.edu	37	10	125798111	125798111	+	Silent	SNP	T	T	C	rs28375663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:125798111T>C	ENST00000346248.5	-	5	1752	c.1110A>G	c.(1108-1110)ccA>ccG	p.P370P	CHST15_ENST00000435907.1_Silent_p.P370P|CHST15_ENST00000421115.1_Silent_p.P370P	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	370					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TCAGAAACGGTGGCTCGCCAT	0.532													T|||	594	0.11861	0.1891	0.1585	5008	,	,		16463	0.0089		0.164	False		,,,				2504	0.0613				p.P370P		Atlas-SNP	.											CHST15_ENST00000421115,NS,carcinoma,0,2	CHST15	134	2	0			c.A1110G						PASS	.	T	,	754,3652	310.0+/-291.3	62,630,1511	124.0	97.0	106.0		1110,1110	-10.2	0.3	10	dbSNP_125	106	1402,7198	270.8+/-289.2	120,1162,3018	no	coding-synonymous,coding-synonymous	CHST15	NM_014863.2,NM_015892.3	,	182,1792,4529	CC,CT,TT		16.3023,17.113,16.577	,	370/507,370/562	125798111	2156,10850	2203	4300	6503	SO:0001819	synonymous_variant	51363	exon5			AAACGGTGGCTCG	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1110A>G	10.37:g.125798111T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_014863	O60338|O60474|Q86VM4	Silent	SNP	ENST00000346248.5	37	CCDS7638.1																																																																																			T|0.852;C|0.148	0.148	strong		0.532	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892	
BMPER	168667	hgsc.bcm.edu	37	7	34091570	34091570	+	Silent	SNP	T	T	G	rs117988035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:34091570T>G	ENST00000297161.2	+	9	1148	c.774T>G	c.(772-774)gcT>gcG	p.A258A	BMPER_ENST00000494786.1_3'UTR|BMPER_ENST00000426693.1_Silent_p.A258A	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	258	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						ACTGCACAGCTTGTACCTGCA	0.478													T|||	36	0.0071885	0.0	0.0173	5008	,	,		22541	0.0		0.0149	False		,,,				2504	0.0092				p.A258A		Atlas-SNP	.											.	BMPER	131	.	0			c.T774G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	168.0	147.0	154.0		774	-10.2	0.0	7	dbSNP_132	154	103,8497	57.2+/-118.5	0,103,4197	no	coding-synonymous	BMPER	NM_133468.3		0,112,6391	GG,GT,TT		1.1977,0.2043,0.8611		258/686	34091570	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon9			CACAGCTTGTACC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.774T>G	7.37:g.34091570T>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	156	43	0.275641	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			T|0.990;G|0.010	0.010	strong		0.478	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
MUC16	94025	hgsc.bcm.edu	37	19	9049726	9049726	+	Silent	SNP	G	G	A	rs11670328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9049726G>A	ENST00000397910.4	-	5	32108	c.31905C>T	c.(31903-31905)gaC>gaT	p.D10635D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10637	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						CTGAGCTGACGTCTGCCCCAT	0.473													G|||	1247	0.249002	0.1558	0.2233	5008	,	,		20530	0.2351		0.337	False		,,,				2504	0.317				p.D10635D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C31905T						PASS	.			701,3289		66,569,1360	119.0	109.0	112.0		31905	-2.0	0.0	19	dbSNP_120	112	2693,5643		421,1851,1896	no	coding-synonymous	MUC16	NM_024690.2		487,2420,3256	AA,AG,GG		32.3057,17.5689,27.5353		10635/14508	9049726	3394,8932	1995	4168	6163	SO:0001819	synonymous_variant	94025	exon5			GCTGACGTCTGCC	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.31905C>T	19.37:g.9049726G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	170	85	0.5	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.737;A|0.263	0.263	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ACAD11	84129	hgsc.bcm.edu	37	3	132361596	132361596	+	Silent	SNP	G	G	A	rs9877018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132361596G>A	ENST00000264990.6	-	3	1271	c.300C>T	c.(298-300)ccC>ccT	p.P100P	ACAD11_ENST00000489991.1_Intron|ACAD11_ENST00000481970.2_Silent_p.P100P|ACAD11_ENST00000545291.1_5'UTR|ACAD11_ENST00000355458.3_Silent_p.P100P	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	100					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						GCTTGGGAACGGGGAATCCAA	0.323													G|||	177	0.0353435	0.0151	0.0533	5008	,	,		15422	0.0129		0.0656	False		,,,				2504	0.0419				p.P100P		Atlas-SNP	.											ACAD11,NS,carcinoma,-2,2	ACAD11	78	2	0			c.C300T						scavenged	.	G		91,4315	75.7+/-113.9	0,91,2112	91.0	95.0	94.0		300	-7.4	0.9	3	dbSNP_119	94	601,7999	158.6+/-212.1	17,567,3716	no	coding-synonymous	ACAD11	NM_032169.4		17,658,5828	AA,AG,GG		6.9884,2.0654,5.3206		100/781	132361596	692,12314	2203	4300	6503	SO:0001819	synonymous_variant	84129	exon3			GGGAACGGGGAAT	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.300C>T	3.37:g.132361596G>A		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	228	83	0.364035	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Silent	SNP	ENST00000264990.6	37	CCDS3074.1																																																																																			G|0.953;A|0.047	0.047	strong		0.323	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	
ZNF846	162993	hgsc.bcm.edu	37	19	9868404	9868404	+	Missense_Mutation	SNP	C	C	T	rs10414485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9868404C>T	ENST00000397902.2	-	6	1762	c.1349G>A	c.(1348-1350)tGt>tAt	p.C450Y	ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000586293.1_3'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	450			C -> Y (in dbSNP:rs10414485).		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(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						CTTACATTCACAGGCCTTTTC	0.428													N|||	1379	0.275359	0.4728	0.3804	5008	,	,		21932	0.0714		0.2127	False		,,,				2504	0.2086				p.C450Y		Atlas-SNP	.											.	ZNF846	61	.	0			c.G1349A						PASS	.	T	TYR/CYS	1577,2711		336,905,903	84.0	96.0	92.0		1349	-0.4	0.0	19	dbSNP_119	92	1694,6864		171,1352,2756	yes	missense	ZNF846	NM_001077624.1	194	507,2257,3659	TT,TC,CC		19.7943,36.7771,25.4632	benign	450/534	9868404	3271,9575	2144	4279	6423	SO:0001583	missense	162993	exon6			CATTCACAGGCCT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1349G>A	19.37:g.9868404C>T	ENSP00000380999:p.Cys450Tyr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	40	0.347826	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	546	0.25	231	0.4695121951219512	122	0.3370165745856354	31	0.05419580419580419	162	0.21372031662269128	.	0.003	-2.444505	0.00178	0.367771	0.197943	ENSG00000196605	ENST00000397902	T	0.12039	2.72	2.04	-0.357	0.12579	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00068	-2.285	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38499	-0.9658	7	.	.	.	.	3.3875	0.07277	0.5722:0.1347:0.0:0.2931	rs10414485;rs52801835;rs59999512;rs10414485	450	Q147U1	ZN846_HUMAN	Y	450	ENSP00000380999:C450Y	.	C	-	2	0	ZNF846	9729404	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.861000	0.04268	-0.578000	0.05959	-0.369000	0.07265	TGT	C|0.749;T|0.251	0.251	strong		0.428	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
COMMD10	51397	hgsc.bcm.edu	37	5	115428334	115428334	+	Silent	SNP	G	G	T	rs1129494	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:115428334G>T	ENST00000274458.4	+	4	398	c.336G>T	c.(334-336)acG>acT	p.T112T	COMMD10_ENST00000515539.1_Silent_p.T98T	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	112								p.T112T(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(2)	9		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		TTGTCAATACGTGGTCTTCTA	0.383													G|||	2213	0.441893	0.1725	0.5346	5008	,	,		18192	0.3849		0.66	False		,,,				2504	0.5746				p.T112T		Atlas-SNP	.											COMMD10,NS,carcinoma,0,1	COMMD10	18	1	1	Substitution - coding silent(1)	stomach(1)	c.G336T						PASS	.	G		1126,3278	399.7+/-331.3	152,822,1228	99.0	90.0	93.0		336	-4.6	0.1	5	dbSNP_86	93	5535,3065	660.6+/-401.8	1784,1967,549	no	coding-synonymous	COMMD10	NM_016144.2		1936,2789,1777	TT,TG,GG		35.6395,25.5677,48.7773		112/203	115428334	6661,6343	2202	4300	6502	SO:0001819	synonymous_variant	51397	exon4			CAATACGTGGTCT	AY542165	CCDS34215.1	5q23.1	2008-02-05				ENSG00000145781			30201	protein-coding gene	gene with protein product						15799966	Standard	NM_016144		Approved	PTD002	uc003krt.1	Q9Y6G5		ENST00000274458.4:c.336G>T	5.37:g.115428334G>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_016144	D3DT07|Q9P077	Silent	SNP	ENST00000274458.4	37	CCDS34215.1																																																																																			G|0.536;T|0.464	0.464	strong		0.383	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371033.1	NM_016144	
RARS2	57038	hgsc.bcm.edu	37	6	88239365	88239365	+	Splice_Site	SNP	C	C	T	rs145297855		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88239365C>T	ENST00000369536.5	-	10	818	c.773G>A	c.(772-774)cGt>cAt	p.R258H		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	258					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)		TACTCCCAGACGCTAAAAGAG	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		18689	0.0		0.001	False		,,,				2504	0.0				p.R258H		Atlas-SNP	.											RARS2,NS,carcinoma,0,2	RARS2	61	2	0			c.G773A						scavenged	.	C	HIS/ARG	1,4397	2.1+/-5.4	0,1,2198	45.0	48.0	47.0		773	5.5	1.0	6	dbSNP_134	47	4,8582	3.7+/-12.6	0,4,4289	no	missense-near-splice	RARS2	NM_020320.3	29	0,5,6487	TT,TC,CC		0.0466,0.0227,0.0385	probably-damaging	258/579	88239365	5,12979	2199	4293	6492	SO:0001630	splice_region_variant	57038	exon10			CCCAGACGCTAAA	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.772-1G>A	6.37:g.88239365C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	142	3	0.0211268	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608465	0.87258	2.27E-4	4.66E-4	ENSG00000146282	ENST00000369536	T	0.64618	-0.11	5.51	5.51	0.81932	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.85626	0.5740	H	0.97390	3.995	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.90047	0.4146	10	0.62326	D	0.03	.	19.0049	0.92846	0.0:1.0:0.0:0.0	.	258	Q5T160	SYRM_HUMAN	H	258	ENSP00000358549:R258H	ENSP00000358549:R258H	R	-	2	0	RARS2	88296084	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.618000	0.67722	2.582000	0.87167	0.655000	0.94253	CGT	A|0.000;C|1.000;T|0.000	0.000	strong		0.358	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	Missense_Mutation
SMCR8	140775	hgsc.bcm.edu	37	17	18219835	18219835	+	Silent	SNP	T	T	C	rs3829956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18219835T>C	ENST00000406438.3	+	1	1212	c.732T>C	c.(730-732)atT>atC	p.I244I	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	244						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						AGTCCATCATTGAACATCAAG	0.488													T|||	1076	0.214856	0.1452	0.2421	5008	,	,		22242	0.3185		0.2435	False		,,,				2504	0.1534				p.I244I		Atlas-SNP	.											.	SMCR8	62	.	0			c.T732C						PASS	.	T		684,3722	288.4+/-279.8	65,554,1584	69.0	56.0	60.0		732	-0.1	1.0	17	dbSNP_107	60	2196,6404	371.9+/-336.4	284,1628,2388	no	coding-synonymous	SMCR8	NM_144775.2		349,2182,3972	CC,CT,TT		25.5349,15.5243,22.1436		244/938	18219835	2880,10126	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CATCATTGAACAT	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.732T>C	17.37:g.18219835T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			T|0.772;C|0.228	0.228	strong		0.488	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
NRP1	8829	hgsc.bcm.edu	37	10	33559711	33559711	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:33559711C>A	ENST00000265371.4	-	4	847	c.322G>T	c.(322-324)Gcc>Tcc	p.A108S	NRP1_ENST00000395995.1_Missense_Mutation_p.A108S|NRP1_ENST00000374875.1_Intron|NRP1_ENST00000374822.4_Missense_Mutation_p.A108S|NRP1_ENST00000374867.2_Missense_Mutation_p.A108S|NRP1_ENST00000374816.3_Missense_Mutation_p.A108S|NRP1_ENST00000374821.5_Missense_Mutation_p.A108S|NRP1_ENST00000374823.5_Missense_Mutation_p.A108S|NRP1_ENST00000432372.2_Missense_Mutation_p.A108S			O14786	NRP1_HUMAN	neuropilin 1	108	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|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 peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.A108T(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	GGAGGAGGGGCTATCTTTCCA	0.383																																					p.A108S	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1_ENST00000374823,NS,carcinoma,0,3	NRP1	126	3	1	Substitution - Missense(1)	kidney(1)	c.G322T						scavenged	.						87.0	89.0	89.0					10																	33559711		2203	4300	6503	SO:0001583	missense	8829	exon3			GAGGGGCTATCTT	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.322G>T	10.37:g.33559711C>A	ENSP00000265371:p.Ala108Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	187	2	0.0106952	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	37	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092145	0.76756	.	.	ENSG00000099250	ENST00000265371;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816	T;T;T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24;2.24;2.24	5.71	5.71	0.89125	CUB (5);	0.047005	0.85682	D	0.000000	T	0.32941	0.0846	N	0.25825	0.765	0.80722	D	1	D;D;D;P;D;D;D;D	0.76494	0.999;0.999;0.999;0.784;0.994;0.996;0.999;0.999	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.924;0.952;0.981;0.999;0.999	T	0.06391	-1.0829	10	0.87932	D	0	-26.8958	19.8625	0.96789	0.0:1.0:0.0:0.0	.	108;108;108;108;108;108;108;108	A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;E9PEP6	.;.;.;.;.;.;NRP1_HUMAN;.	S	108	ENSP00000265371:A108S;ENSP00000364001:A108S;ENSP00000379317:A108S;ENSP00000363955:A108S;ENSP00000363954:A108S;ENSP00000363956:A108S;ENSP00000363949:A108S	ENSP00000265371:A108S	A	-	1	0	NRP1	33599717	1.000000	0.71417	0.951000	0.38953	0.845000	0.48019	5.912000	0.69948	2.689000	0.91719	0.655000	0.94253	GCC	.	.	none		0.383	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
MYBL2	4605	hgsc.bcm.edu	37	20	42320881	42320881	+	Silent	SNP	C	C	T	rs2229036	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42320881C>T	ENST00000217026.4	+	6	712	c.585C>T	c.(583-585)gaC>gaT	p.D195D	MYBL2_ENST00000396863.4_Silent_p.D171D	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	195					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			AGTCCAAAGACTGCAAGCCCC	0.577													C|||	253	0.0505192	0.0295	0.0375	5008	,	,		18114	0.0754		0.0447	False		,,,				2504	0.0685				p.D195D		Atlas-SNP	.											.	MYBL2	82	.	0			c.C585T						PASS	.	C		132,4274	95.7+/-134.4	6,120,2077	89.0	85.0	86.0		585	4.1	1.0	20	dbSNP_126	86	395,8205	126.3+/-184.8	9,377,3914	no	coding-synonymous	MYBL2	NM_002466.2		15,497,5991	TT,TC,CC		4.593,2.9959,4.052		195/701	42320881	527,12479	2203	4300	6503	SO:0001819	synonymous_variant	4605	exon6			CAAAGACTGCAAG		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.585C>T	20.37:g.42320881C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	37	CCDS13322.1																																																																																			C|0.953;T|0.047	0.047	strong		0.577	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
HIVEP1	3096	hgsc.bcm.edu	37	6	12125772	12125772	+	Missense_Mutation	SNP	A	A	G	rs1126472	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:12125772A>G	ENST00000379388.2	+	4	6076	c.5744A>G	c.(5743-5745)cAg>cGg	p.Q1915R	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1915			Q -> R (in dbSNP:rs1126472). {ECO:0000269|PubMed:2106471}.		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)				CAAAGTCAACAGCCAGTCACT	0.403													G|||	852	0.170128	0.2352	0.1282	5008	,	,		19758	0.131		0.1362	False		,,,				2504	0.1871				p.Q1915R		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A5744G						PASS	.	G	ARG/GLN	789,3057		89,611,1223	78.0	76.0	76.0		5744	-6.6	0.0	6	dbSNP_86	76	823,7403		40,743,3330	yes	missense	HIVEP1	NM_002114.2	43	129,1354,4553	GG,GA,AA		10.0049,20.5148,13.3532	benign	1915/2719	12125772	1612,10460	1923	4113	6036	SO:0001583	missense	3096	exon4			GTCAACAGCCAGT	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.5744A>G	6.37:g.12125772A>G	ENSP00000368698:p.Gln1915Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	326	0.14926739926739926	115	0.23373983739837398	53	0.1464088397790055	63	0.11013986013986014	95	0.12532981530343007	G	0.005	-2.198926	0.00299	0.205148	0.100049	ENSG00000095951	ENST00000379388	T	0.08807	3.05	4.39	-6.62	0.01813	.	.	.	.	.	T	0.00724	0.0024	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.14023	0.01	T	0.48080	-0.9066	7	.	.	.	-0.0166	1.2719	0.02022	0.3723:0.1291:0.1058:0.3928	rs1126472;rs3734272;rs16872291;rs59768221;rs1126472	1915	P15822	ZEP1_HUMAN	R	1915	ENSP00000368698:Q1915R	.	Q	+	2	0	HIVEP1	12233758	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.171000	0.00573	-1.569000	0.01668	-2.706000	0.00135	CAG	A|0.845;G|0.155	0.155	strong		0.403	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
OR2K2	26248	hgsc.bcm.edu	37	9	114089882	114089882	+	Missense_Mutation	SNP	C	C	T	rs61748723	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:114089882C>T	ENST00000374428.1	-	1	918	c.919G>A	c.(919-921)Gga>Aga	p.G307R	OR2K2_ENST00000302681.1_Missense_Mutation_p.G278R			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	307						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)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						GTAAGCACTCCGTAAAGCAAC	0.383													C|||	434	0.0866613	0.0015	0.085	5008	,	,		22377	0.1855		0.0755	False		,,,				2504	0.1125				p.G278R		Atlas-SNP	.											OR2K2_ENST00000374428,NS,malignant_melanoma,+1,2	OR2K2	77	2	0			c.G832A						PASS	.	C	ARG/GLY	75,4331	65.8+/-103.3	1,73,2129	130.0	124.0	126.0		832	4.6	1.0	9	dbSNP_129	126	529,8071	147.9+/-203.2	20,489,3791	yes	missense	OR2K2	NM_205859.1	125	21,562,5920	TT,TC,CC		6.1512,1.7022,4.644	benign	278/317	114089882	604,12402	2203	4300	6503	SO:0001583	missense	26248	exon1			GCACTCCGTAAAG	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"""GPCR / Class A : Olfactory receptors"""	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.919G>A	9.37:g.114089882C>T	ENSP00000363550:p.Gly307Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		210	0.09615384615384616	2	0.0040650406504065045	41	0.1132596685082873	111	0.19405594405594406	56	0.07387862796833773	C	12.29	1.892187	0.33442	0.017022	0.061512	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.00084	8.75;8.75	4.55	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	U	0.001169	T	0.00012	0.0000	M	0.81942	2.565	0.35792	P	0.17751899999999998	P	0.41450	0.75	B	0.32149	0.141	T	0.17379	-1.0371	9	0.59425	D	0.04	.	8.7289	0.34487	0.0:0.8983:0.0:0.1017	.	307	Q8NGT1	OR2K2_HUMAN	R	278;307	ENSP00000305055:G278R;ENSP00000363550:G307R	ENSP00000305055:G278R	G	-	1	0	OR2K2	113129703	0.019000	0.18553	1.000000	0.80357	0.895000	0.52256	0.534000	0.23098	2.531000	0.85337	0.591000	0.81541	GGA	C|0.939;T|0.061	0.061	strong		0.383	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
ATP11A	23250	hgsc.bcm.edu	37	13	113479820	113479820	+	Missense_Mutation	SNP	A	A	G	rs368865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:113479820A>G	ENST00000487903.1	+	11	1037	c.949A>G	c.(949-951)Atg>Gtg	p.M317V	ATP11A_ENST00000283558.8_Missense_Mutation_p.M317V|ATP11A_ENST00000375645.3_Missense_Mutation_p.M317V|ATP11A_ENST00000375630.2_Missense_Mutation_p.M317V			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	317			M -> V (in dbSNP:rs368865). {ECO:0000269|PubMed:10470851}.		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)	p.M317V(1)		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)				GCTGAAATACATGTGGCAGAG	0.458													G|||	4218	0.842252	0.9894	0.8473	5008	,	,		23175	0.8661		0.7445	False		,,,				2504	0.7157				p.M317V		Atlas-SNP	.											ATP11A,NS,carcinoma,0,1	ATP11A	225	1	1	Substitution - Missense(1)	stomach(1)	c.A949G						PASS	.	G	VAL/MET,VAL/MET	4163,243	142.3+/-177.5	1970,223,10	124.0	106.0	112.0		949,949	5.1	1.0	13	dbSNP_80	112	6223,2377	397.0+/-345.6	2237,1749,314	yes	missense,missense	ATP11A	NM_015205.2,NM_032189.3	21,21	4207,1972,324	GG,GA,AA		27.6395,5.5152,20.1445	benign,benign	317/1135,317/1192	113479820	10386,2620	2203	4300	6503	SO:0001583	missense	23250	exon11			AAATACATGTGGC	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.949A>G	13.37:g.113479820A>G	ENSP00000420387:p.Met317Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	187	76	0.406417	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	1848	0.8461538461538461	486	0.9878048780487805	305	0.8425414364640884	493	0.8618881118881119	564	0.7440633245382586	G	1.065	-0.671815	0.03403	0.944848	0.723605	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43	5.14	5.14	0.70334	ATPase, P-type, ATPase-associated domain (1);	0.242574	0.41194	N	0.000921	T	0.00012	0.0000	N	0.00096	-2.155	0.53688	P	2.8999999999945736E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42498	-0.9448	9	0.10636	T	0.68	.	10.1209	0.42621	0.1524:0.0:0.8476:0.0	rs368865;rs59209406;rs368865	317;317;317	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	V	317	ENSP00000420387:M317V;ENSP00000364781:M317V;ENSP00000364796:M317V;ENSP00000283558:M317V	ENSP00000283558:M317V	M	+	1	0	ATP11A	112527821	0.994000	0.37717	0.993000	0.49108	0.657000	0.38888	3.156000	0.50708	1.176000	0.42840	-0.282000	0.10007	ATG	A|0.187;G|0.813	0.813	strong		0.458	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
ODAM	54959	hgsc.bcm.edu	37	4	71068489	71068489	+	Missense_Mutation	SNP	T	T	C	rs3196714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71068489T>C	ENST00000396094.2	+	9	713	c.665T>C	c.(664-666)aTa>aCa	p.I222T		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	222			I -> T (in dbSNP:rs3196714). {ECO:0000269|PubMed:14702039}.		biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						GGAGAAGAGATACCATATTTA	0.388													T|||	1421	0.283746	0.1596	0.2017	5008	,	,		15660	0.3006		0.2753	False		,,,				2504	0.501				p.I222T		Atlas-SNP	.											.	ODAM	38	.	0			c.T665C						PASS	.	T	THR/ILE	851,3555	332.3+/-302.4	86,679,1438	67.0	63.0	64.0		665	0.7	0.0	4	dbSNP_105	64	2459,6135	403.7+/-347.9	352,1755,2190	yes	missense	ODAM	NM_017855.3	89	438,2434,3628	CC,CT,TT		28.613,19.3146,25.4615	benign	222/280	71068489	3310,9690	2203	4297	6500	SO:0001583	missense	54959	exon9			AAGAGATACCATA	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.665T>C	4.37:g.71068489T>C	ENSP00000379401:p.Ile222Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	194	83	0.427835	NM_017855	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	37	CCDS3536.2	543	0.24862637362637363	87	0.17682926829268292	80	0.22099447513812154	171	0.29895104895104896	205	0.2704485488126649	T	5.932	0.355955	0.11239	0.193146	0.28613	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.50548	0.74;0.74	4.85	0.676	0.17958	.	1.354960	0.04719	N	0.418965	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.13145	0.007	B	0.10450	0.005	T	0.24190	-1.0167	9	0.16896	T	0.51	-0.0118	7.0742	0.25195	0.0:0.2961:0.0:0.7039	rs3196714;rs17419342;rs17653374;rs52834624;rs3196714	222	A1E959	ODAM_HUMAN	T	222;208;159	ENSP00000379401:I222T;ENSP00000426106:I159T	ENSP00000379401:I222T	I	+	2	0	ODAM	71103078	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.329000	0.19698	0.042000	0.15717	-0.254000	0.11334	ATA	C|0.258;N|0.001	0.258	strong		0.388	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855	
ACKR3	57007	hgsc.bcm.edu	37	2	237489904	237489904	+	Silent	SNP	C	C	T	rs1045879	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:237489904C>T	ENST00000272928.3	+	2	1106	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	266					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										TGTCTGCTGGCTGCCCTACCA	0.607													c|||	1739	0.347244	0.7398	0.2176	5008	,	,		22079	0.0486		0.2485	False		,,,				2504	0.318				p.L266L		Atlas-SNP	.											CXCR7_ENST00000272928,lower_third,carcinoma,-1,1	CXCR7	72	1	0			c.C796T						PASS	.	T		2915,1491	677.9+/-403.5	987,941,275	161.0	136.0	145.0		796	4.9	1.0	2	dbSNP_86	145	2289,6311	385.5+/-341.5	323,1643,2334	no	coding-synonymous	CXCR7	NM_020311.2		1310,2584,2609	TT,TC,CC		26.6163,33.8402,40.0123		266/363	237489904	5204,7802	2203	4300	6503	SO:0001819	synonymous_variant	57007	exon2			TGCTGGCTGCCCT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.796C>T	2.37:g.237489904C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	37	CCDS2516.1																																																																																			C|0.632;T|0.368	0.368	strong		0.607	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
KRT39	390792	hgsc.bcm.edu	37	17	39114962	39114962	+	Missense_Mutation	SNP	C	C	T	rs7213256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39114962C>T	ENST00000355612.2	-	7	1402	c.1367G>A	c.(1366-1368)cGg>cAg	p.R456Q	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	456	Tail.		R -> Q (in dbSNP:rs7213256). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15617563}.			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)				AACCAGTATCCGGGACAGGGG	0.522													C|||	1248	0.249201	0.5408	0.1902	5008	,	,		18783	0.0327		0.161	False		,,,				2504	0.2106				p.R456Q		Atlas-SNP	.											KRT39,colon,carcinoma,0,1	KRT39	53	1	0			c.G1367A						PASS	.	C	GLN/ARG	2085,2321	571.7+/-383.1	488,1109,606	112.0	104.0	107.0		1367	1.0	0.1	17	dbSNP_116	107	1364,7228	265.0+/-285.9	110,1144,3042	yes	missense	KRT39	NM_213656.3	43	598,2253,3648	TT,TC,CC		15.8752,47.3218,26.5349	probably-damaging	456/492	39114962	3449,9549	2203	4296	6499	SO:0001583	missense	390792	exon7			AGTATCCGGGACA	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.1367G>A	17.37:g.39114962C>T	ENSP00000347823:p.Arg456Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	37	CCDS11382.1	469	0.21474358974358973	260	0.5284552845528455	65	0.17955801104972377	23	0.04020979020979021	121	0.15963060686015831	C	16.04	3.008632	0.54361	0.473218	0.158752	ENSG00000196859	ENST00000355612	D	0.82081	-1.57	5.54	1.04	0.20106	.	0.000000	0.36167	N	0.002746	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B	0.28880	0.226	B	0.14578	0.011	T	0.44892	-0.9298	9	0.16896	T	0.51	.	5.8871	0.18888	0.0:0.5356:0.2959:0.1685	rs7213256	456	Q6A163	K1C39_HUMAN	Q	456	ENSP00000347823:R456Q	ENSP00000347823:R456Q	R	-	2	0	KRT39	36368488	0.946000	0.32159	0.066000	0.19879	0.914000	0.54420	0.213000	0.17521	0.280000	0.22209	0.655000	0.94253	CGG	C|0.741;T|0.259	0.259	strong		0.522	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
ITPR3	3710	hgsc.bcm.edu	37	6	33643558	33643558	+	Silent	SNP	G	G	A	rs2229637	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	113	0	0		WXS	Illumina HiSeq	Phase_I	116	44	0.37931	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	
MUC16	94025	hgsc.bcm.edu	37	19	9076858	9076858	+	Missense_Mutation	SNP	C	C	T	rs2547074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076858C>T	ENST00000397910.4	-	3	10791	c.10588G>A	c.(10588-10590)Gta>Ata	p.V3530I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3531	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						GCTGTGGTTACGTCCAGGATG	0.517													C|||	1244	0.248403	0.2005	0.2118	5008	,	,		23229	0.25		0.3121	False		,,,				2504	0.272				p.V3530I		Atlas-SNP	.											.	MUC16	4315	.	0			c.G10588A						PASS	.	C	ILE/VAL	914,3354		107,700,1327	249.0	237.0	241.0		10588	-2.8	0.0	19	dbSNP_100	241	2444,6004		351,1742,2131	yes	missense	MUC16	NM_024690.2	29	458,2442,3458	TT,TC,CC		28.9299,21.4152,26.4077	benign	3530/14508	9076858	3358,9358	2134	4224	6358	SO:0001583	missense	94025	exon3			TGGTTACGTCCAG	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.10588G>A	19.37:g.9076858C>T	ENSP00000381008:p.Val3530Ile	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	299	145	0.48495	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	c	4.266	0.048546	0.08243	0.214152	0.289299	ENSG00000181143	ENST00000397910	T	0.02421	4.3	1.76	-2.83	0.05769	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.27932	0.194	B	0.20577	0.03	T	0.47573	-0.9107	8	0.87932	D	0	.	2.7925	0.05392	0.0:0.3474:0.248:0.4046	rs2547074;rs17516104;rs2547074	3530	B5ME49	.	I	3530	ENSP00000381008:V3530I	ENSP00000381008:V3530I	V	-	1	0	MUC16	8937858	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.014000	0.12656	-0.634000	0.05538	0.313000	0.20887	GTA	C|0.749;T|0.251	0.251	strong		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SLIT3	6586	hgsc.bcm.edu	37	5	168175324	168175324	+	Silent	SNP	G	G	T	rs17634681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:168175324G>T	ENST00000519560.1	-	20	2672	c.2253C>A	c.(2251-2253)ccC>ccA	p.P751P	SLIT3_ENST00000332966.8_Silent_p.P751P|SLIT3_ENST00000404867.3_Silent_p.P751P	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	751	LRRNT 4.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCACATCCTTGGGCATGCCTC	0.617													G|||	124	0.0247604	0.0038	0.0403	5008	,	,		18810	0.001		0.0706	False		,,,				2504	0.0194				p.P751P	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C2253A						PASS	.			62,4344	58.7+/-95.3	0,62,2141	109.0	110.0	110.0		2253	4.4	1.0	5	dbSNP_123	110	602,7998	156.6+/-210.4	19,564,3717	no	coding-synonymous	SLIT3	NM_003062.2		19,626,5858	TT,TG,GG		7.0,1.4072,5.1053		751/1524	168175324	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon20			ATCCTTGGGCATG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2253C>A	5.37:g.168175324G>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.957;T|0.043	0.043	strong		0.617	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
PRPF40B	25766	hgsc.bcm.edu	37	12	50037071	50037071	+	Silent	SNP	G	G	A	rs115544158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:50037071G>A	ENST00000380281.1	+	22	2272	c.2208G>A	c.(2206-2208)cgG>cgA	p.R736R	FMNL3_ENST00000335154.5_3'UTR|PRPF40B_ENST00000548825.2_Silent_p.R757R|PRPF40B_ENST00000261897.1_Silent_p.R723R			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	736					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						GGAGGAGGCGGAACCCCTCAG	0.612													G|||	42	0.00838658	0.0008	0.0317	5008	,	,		17721	0.0		0.0189	False		,,,				2504	0.0				p.R757R		Atlas-SNP	.											PRPF40B,colon,carcinoma,+2,1	PRPF40B	83	1	0			c.G2271A						PASS	.	G	,,,	17,4389	24.3+/-50.5	0,17,2186	71.0	76.0	75.0		2208,2169,,	3.4	1.0	12	dbSNP_132	75	150,8450	72.9+/-135.5	1,148,4151	no	coding-synonymous,coding-synonymous,utr-3,utr-3	PRPF40B,FMNL3	NM_001031698.1,NM_012272.1,NM_175736.4,NM_198900.2	,,,	1,165,6337	AA,AG,GG		1.7442,0.3858,1.284	,,,	736/872,723/859,,	50037071	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	25766	exon23			GAGGCGGAACCCC	AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"""Huntingtin interacting protein C"""		"""PRP40 pre-mRNA processing factor 40 homolog B (yeast)"""			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.2208G>A	12.37:g.50037071G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Silent	SNP	ENST00000380281.1	37																																																																																				G|0.987;A|0.013	0.013	strong		0.612	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272	
DNAH5	1767	hgsc.bcm.edu	37	5	13913885	13913885	+	Silent	SNP	A	A	G	rs3213936	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13913885A>G	ENST00000265104.4	-	11	1607	c.1503T>C	c.(1501-1503)atT>atC	p.I501I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	501	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)					CCAGCCCTTCAATTGTGGAAT	0.343									Kartagener syndrome				G|||	2648	0.528754	0.5666	0.4496	5008	,	,		17549	0.8492		0.3797	False		,,,				2504	0.3569				p.I501I		Atlas-SNP	.											.	DNAH5	868	.	0			c.T1503C						PASS	.	G		2330,2076	569.4+/-382.6	601,1128,474	121.0	124.0	123.0		1503	-6.6	0.1	5	dbSNP_106	123	3258,5342	648.2+/-400.5	628,2002,1670	no	coding-synonymous	DNAH5	NM_001369.2		1229,3130,2144	GG,GA,AA		37.8837,47.1176,42.9648		501/4625	13913885	5588,7418	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCCTTCAATTGTG	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.1503T>C	5.37:g.13913885A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.439;G|0.561	0.561	strong		0.343	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
RPP38	10557	hgsc.bcm.edu	37	10	15146061	15146061	+	Missense_Mutation	SNP	C	C	G	rs34040166	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:15146061C>G	ENST00000378197.4	+	3	1262	c.748C>G	c.(748-750)Cgg>Ggg	p.R250G	RPP38_ENST00000378202.5_Missense_Mutation_p.R250G|NMT2_ENST00000466201.1_Intron|RPP38_ENST00000451677.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	250			R -> G (in dbSNP:rs34040166).		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)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						TGCTGACGGTCGGCAGGCTTC	0.393													C|||	226	0.0451278	0.0401	0.0245	5008	,	,		18266	0.0625		0.0467	False		,,,				2504	0.047				p.R250G	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.C748G						PASS	.	C	GLY/ARG,GLY/ARG,GLY/ARG	208,4194	110.4+/-148.6	2,204,1995	55.0	60.0	58.0		748,748,748	3.6	0.0	10	dbSNP_126	58	535,8063	145.9+/-201.5	24,487,3788	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	125,125,125	26,691,5783	GG,GC,CC		6.2224,4.7251,5.7154	benign,benign,benign	250/284,250/284,250/284	15146061	743,12257	2201	4299	6500	SO:0001583	missense	10557	exon2			GACGGTCGGCAGG	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.748C>G	10.37:g.15146061C>G	ENSP00000367439:p.Arg250Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	103	0.04716117216117216	23	0.046747967479674794	11	0.03038674033149171	32	0.055944055944055944	37	0.048812664907651716	C	0.018	-1.473220	0.01044	0.047251	0.062224	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.09630	2.96;2.96;2.96	5.71	3.63	0.41609	.	1.581750	0.03610	N	0.234684	T	0.00608	0.0020	N	0.02539	-0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	10	0.21540	T	0.41	-2.3688	9.7877	0.40686	0.3529:0.5237:0.1235:0.0	rs34040166	250	P78345	RPP38_HUMAN	G	250	ENSP00000367445:R250G;ENSP00000367444:R250G;ENSP00000367439:R250G	ENSP00000367439:R250G	R	+	1	2	RPP38	15186067	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	0.406000	0.21032	0.542000	0.28846	0.467000	0.42956	CGG	C|0.945;G|0.055	0.055	strong		0.393	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
BRCA2	675	hgsc.bcm.edu	37	13	32906729	32906729	+	Missense_Mutation	SNP	A	A	C	rs144848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:32906729A>C	ENST00000380152.3	+	10	1347	c.1114A>C	c.(1114-1116)Aat>Cat	p.N372H	BRCA2_ENST00000544455.1_Missense_Mutation_p.N372H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	372			H -> N (common polymorphism; associated with an increased risk of breast cancer and with an effect on prenatal viability with increased fitness of males and decreased fitness of females; dbSNP:rs144848). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:10978364, ECO:0000269|PubMed:11062481, ECO:0000269|PubMed:12552570, ECO:0000269|PubMed:15057823, ECO:0000269|PubMed:15172753, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:8665505, 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)	p.N372H(1)		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)		AAATGTAGCAAATCAGAAGCC	0.373			"""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|||	1249	0.249401	0.084	0.2997	5008	,	,		17972	0.2847		0.2952	False		,,,				2504	0.3538				p.N372H	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_ENST00000544455,NS,carcinoma,0,1	BRCA2	812	1	1	Substitution - Missense(1)	stomach(1)	c.A1114C	GRCh37	CM002750	BRCA2	M	rs144848	PASS	.	A	HIS/ASN	558,3770		42,474,1648	167.0	186.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1114	0.4	0.0	13	dbSNP_83	180	2449,6117		345,1759,2179	yes	missense	BRCA2	NM_000059.3	68	387,2233,3827	CC,CA,AA		28.5898,12.8928,23.3209	benign	372/3419	32906729	3007,9887	2164	4283	6447	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)	GTAGCAAATCAGA	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.1114A>C	13.37:g.32906729A>C	ENSP00000369497:p.Asn372His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	525	0.2403846153846154	48	0.0975609756097561	113	0.31215469613259667	146	0.25524475524475526	218	0.287598944591029	A	6.228	0.410176	0.11812	0.128928	0.285898	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00717	5.79;5.79	5.6	0.396	0.16309	.	1.242150	0.05390	N	0.538920	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41448	-0.9508	6	0.46703	T	0.11	.	5.256	0.15548	0.4454:0.162:0.3926:0.0	rs144848;rs703222;rs766172;rs17593227;rs52835869;rs60042381;rs144848	.	.	.	H	372;372;370	ENSP00000369497:N372H;ENSP00000439902:N372H	ENSP00000369497:N372H	N	+	1	0	BRCA2	31804729	0.001000	0.12720	0.000000	0.03702	0.316000	0.28119	0.757000	0.26433	-0.147000	0.11254	-0.250000	0.11733	AAT	T|0.005;G|0.003	.	strong		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
ANK3	288	hgsc.bcm.edu	37	10	62038544	62038544	+	Silent	SNP	A	A	G	rs1031688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:62038544A>G	ENST00000280772.2	-	4	593	c.402T>C	c.(400-402)aaT>aaC	p.N134N	ANK3_ENST00000503366.1_Silent_p.N117N|ANK3_ENST00000373827.2_Silent_p.N128N	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	134					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)			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						GAGATTGTGCATTGACATTGG	0.423													A|||	120	0.0239617	0.0257	0.0187	5008	,	,		18222	0.001		0.0348	False		,,,				2504	0.0378				p.N134N		Atlas-SNP	.											.	ANK3	703	.	0			c.T402C						PASS	.	A	,,	85,4321	72.5+/-110.5	0,85,2118	265.0	221.0	236.0		384,351,402	0.6	1.0	10	dbSNP_86	236	257,8343	100.6+/-161.9	6,245,4049	no	coding-synonymous,coding-synonymous,coding-synonymous	ANK3	NM_001204403.1,NM_001204404.1,NM_020987.3	,,	6,330,6167	GG,GA,AA		2.9884,1.9292,2.6296	,,	128/1862,117/1869,134/4378	62038544	342,12664	2203	4300	6503	SO:0001819	synonymous_variant	288	exon4			TTGTGCATTGACA	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.402T>C	10.37:g.62038544A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.975;G|0.025	0.025	strong		0.423	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
TMEM222	84065	hgsc.bcm.edu	37	1	27660731	27660731	+	Silent	SNP	G	G	C	rs6663062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27660731G>C	ENST00000374076.4	+	5	536	c.498G>C	c.(496-498)gtG>gtC	p.V166V	TMEM222_ENST00000608611.1_Silent_p.V133V	NM_032125.2	NP_115501.2	Q9H0R3	TM222_HUMAN	transmembrane protein 222	166						integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						GGAATATGGTGACGCTCTGCT	0.582													G|||	162	0.0323482	0.0386	0.0259	5008	,	,		23077	0.001		0.0507	False		,,,				2504	0.0419				p.V166V		Atlas-SNP	.											.	TMEM222	16	.	0			c.G498C						PASS	.	G		165,4241	109.5+/-147.8	1,163,2039	224.0	189.0	201.0		498	3.2	1.0	1	dbSNP_116	201	288,8312	107.8+/-168.5	5,278,4017	no	coding-synonymous	TMEM222	NM_032125.2		6,441,6056	CC,CG,GG		3.3488,3.7449,3.483		166/209	27660731	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	84065	exon5			TATGGTGACGCTC	AL136683	CCDS297.2	1p36.11	2008-07-07	2008-07-07	2008-07-07	ENSG00000186501	ENSG00000186501			25363	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 160"""	C1orf160		11230166	Standard	NM_032125		Approved	DKFZP564D0478	uc001bnr.4	Q9H0R3	OTTHUMG00000004410	ENST00000374076.4:c.498G>C	1.37:g.27660731G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_032125	D3DPL6|Q53HD8|Q5FVE9	Silent	SNP	ENST00000374076.4	37	CCDS297.2	63	0.028846153846153848	18	0.036585365853658534	9	0.024861878453038673	1	0.0017482517482517483	35	0.04617414248021108	G	9.718	1.158967	0.21454	0.037449	0.033488	ENSG00000186501	ENST00000464813	.	.	.	5.09	3.23	0.37069	.	.	.	.	.	T	0.16642	0.0400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11767	-1.0574	4	.	.	.	-30.776	6.0198	0.19623	0.2303:0.2043:0.5653:0.0	rs6663062;rs6663062	.	.	.	H	139	.	.	D	+	1	0	TMEM222	27533318	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.287000	0.33284	0.739000	0.32628	0.655000	0.94253	GAC	G|0.969;C|0.031	0.031	strong		0.582	TMEM222-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012809.2	NM_032125	
ARPP21	10777	hgsc.bcm.edu	37	3	35778773	35778773	+	Silent	SNP	A	A	G	rs2278757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:35778773A>G	ENST00000187397.4	+	16	2019	c.1563A>G	c.(1561-1563)ccA>ccG	p.P521P	ARPP21_ENST00000337271.5_Silent_p.P467P|ARPP21_ENST00000417925.1_Silent_p.P487P|ARPP21_ENST00000444190.1_Silent_p.P467P|ARPP21_ENST00000458225.1_Silent_p.P487P	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	521	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						AACAGCAGCCACCACAGCAGC	0.637													G|||	2044	0.408147	0.5825	0.4035	5008	,	,		13700	0.1468		0.4732	False		,,,				2504	0.3783				p.P521P		Atlas-SNP	.											.	ARPP21	153	.	0			c.A1563G						PASS	.	G		2479,1923		711,1057,433	36.0	42.0	40.0		1563	-2.0	0.0	3	dbSNP_100	40	4104,4488		995,2114,1187	no	coding-synonymous	ARPP21	NM_016300.4		1706,3171,1620	GG,GA,AA		47.7654,43.6847,49.3382		521/813	35778773	6583,6411	2201	4296	6497	SO:0001819	synonymous_variant	10777	exon16			GCAGCCACCACAG	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1563A>G	3.37:g.35778773A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	58	0.95082	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Silent	SNP	ENST00000187397.4	37	CCDS2661.1																																																																																			A|0.525;G|0.475	0.475	strong		0.637	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399	
OR6P1	128366	hgsc.bcm.edu	37	1	158533140	158533140	+	Silent	SNP	A	A	G	rs12080815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158533140A>G	ENST00000334632.1	-	1	254	c.255T>C	c.(253-255)ttT>ttC	p.F85F		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	85						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(4)|lung(1)	6						CCTGGGTAAGAAAGGCTGCCA	0.483													A|||	2524	0.503994	0.5794	0.4135	5008	,	,		21013	0.5863		0.4732	False		,,,				2504	0.4131				p.F85F		Atlas-SNP	.											OR6P1,NS,carcinoma,0,1	OR6P1	47	1	0			c.T255C						PASS	.	A		785,599		208,369,115	63.0	54.0	57.0		255	1.4	0.9	1	dbSNP_120	57	1454,1728		346,762,483	no	coding-synonymous	OR6P1	NM_001160325.1		554,1131,598	GG,GA,AA		45.6945,43.2803,49.0364		85/318	158533140	2239,2327	692	1591	2283	SO:0001819	synonymous_variant	128366	exon1			GGTAAGAAAGGCT	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.255T>C	1.37:g.158533140A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	22	0.34375	NM_001160325	Q6IFR9	Silent	SNP	ENST00000334632.1	37	CCDS53391.1																																																																																			A|0.465;G|0.535	0.535	strong		0.483	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:117086378C>A	ENST00000368557.4	-	2	359	c.213G>T	c.(211-213)caG>caT	p.Q71H		NM_001085480.2	NP_001078949.1	Q5T6X4	F162B_HUMAN	family with sequence similarity 162, member B	71			Q -> H (in dbSNP:rs654128).			integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)	6						TCTTGTCGAACTGCGAAGGCC	0.617													C|||	429	0.0856629	0.0787	0.1182	5008	,	,		15996	0.0655		0.1491	False		,,,				2504	0.0276				p.Q71H		Atlas-SNP	.											.	FAM162B	19	.	0			c.G213T						PASS	.	C	HIS/GLN	407,3927		21,365,1781	54.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/pubmed?term	213	-7.3	0.3	6	dbSNP_83	59	1354,7202		116,1122,3040	yes	missense	FAM162B	NM_001085480.2	24	137,1487,4821	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	15.8252,9.3909,13.6618	possibly-damaging	71/163	117086378	1761,11129	2167	4278	6445	SO:0001583	missense	221303	exon2			GTCGAACTGCGAA	BC038997	CCDS43497.1	6q22.31	2014-01-28	2008-06-05	2008-06-05	ENSG00000183807	ENSG00000183807			21549	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 189"""	C6orf189			Standard	NM_001085480		Approved	bA86F4.2	uc003pxi.2	Q5T6X4	OTTHUMG00000015446	ENST00000368557.4:c.213G>T	6.37:g.117086378C>A	ENSP00000357545:p.Gln71His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_001085480	Q8IXW8	Missense_Mutation	SNP	ENST00000368557.4	37	CCDS43497.1	215	0.09844322344322344	37	0.07520325203252033	46	0.1270718232044199	26	0.045454545454545456	106	0.13984168865435356	C	10.99	1.505972	0.26949	0.093909	0.158252	ENSG00000183807	ENST00000368557	T	0.31769	1.48	3.65	-7.29	0.01451	.	0.412070	0.26397	N	0.024604	T	0.15955	0.0384	L	0.41236	1.265	0.52501	P	4.700000000001925E-5	D	0.55385	0.971	P	0.54372	0.75	T	0.14671	-1.0464	9	0.46703	T	0.11	-4.7106	11.3138	0.49379	0.0:0.6433:0.1333:0.2234	rs654128;rs3737130;rs17264045;rs60583751;rs654128	71	Q5T6X4	F162B_HUMAN	H	71	ENSP00000357545:Q71H	ENSP00000357545:Q71H	Q	-	3	2	FAM162B	117193071	0.004000	0.15560	0.346000	0.25655	0.172000	0.22775	-2.282000	0.01156	-1.544000	0.01721	-1.069000	0.02264	CAG	C|0.895;A|0.105	0.105	strong		0.617	FAM162B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041965.1	XM_927381	
MYH7	4625	hgsc.bcm.edu	37	14	23884930	23884930	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23884930G>A	ENST00000355349.3	-	35	5227	c.5065C>T	c.(5065-5067)Cgt>Tgt	p.R1689C	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1689					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|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)	p.R1689C(2)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ACCACGGCACGCAACTCCTCC	0.627																																					p.R1689C		Atlas-SNP	.											MYH7,caecum,carcinoma,0,3	MYH7	349	3	2	Substitution - Missense(2)	large_intestine(2)	c.C5065T						scavenged	.						75.0	66.0	69.0					14																	23884930		2203	4300	6503	SO:0001583	missense	4625	exon35			CGGCACGCAACTC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5065C>T	14.37:g.23884930G>A	ENSP00000347507:p.Arg1689Cys	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909553	0.72868	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.83250	-1.7	5.31	4.4	0.53042	Myosin tail (1);	.	.	.	.	D	0.94019	0.8084	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95988	0.8983	9	0.87932	D	0	.	15.3427	0.74311	0.0:0.0:0.8594:0.1406	.	1689	P12883	MYH7_HUMAN	C	1689;1694	ENSP00000347507:R1689C	ENSP00000347507:R1689C	R	-	1	0	MYH7	22954770	0.998000	0.40836	0.998000	0.56505	0.992000	0.81027	2.975000	0.49281	1.435000	0.47434	0.561000	0.74099	CGT	.	.	none		0.627	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
MRPL34	64981	hgsc.bcm.edu	37	19	17417080	17417080	+	Silent	SNP	C	C	T	rs11548548	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17417080C>T	ENST00000252602.1	+	2	396	c.171C>T	c.(169-171)aaC>aaT	p.N57N	ABHD8_ENST00000247706.3_5'Flank|MRPL34_ENST00000594999.1_Silent_p.N57N|MRPL34_ENST00000602206.1_Missense_Mutation_p.T24I|MRPL34_ENST00000595444.1_Silent_p.N149N|MRPL34_ENST00000600434.1_Silent_p.N57N	NM_023937.3	NP_076426.1	Q9BQ48	RM34_HUMAN	mitochondrial ribosomal protein L34	57					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(1)	2						AGCCGAGCAACATCAAACGCA	0.692													C|||	232	0.0463259	0.0454	0.0519	5008	,	,		14993	0.001		0.1044	False		,,,				2504	0.0307				p.N57N		Atlas-SNP	.											.	MRPL34	5	.	0			c.C171T						PASS	.	C		190,4172		4,182,1995	9.0	13.0	12.0		171	2.5	1.0	19	dbSNP_120	12	859,7663		38,783,3440	no	coding-synonymous	MRPL34	NM_023937.3		42,965,5435	TT,TC,CC		10.0798,4.3558,8.1419		57/93	17417080	1049,11835	2181	4261	6442	SO:0001819	synonymous_variant	64981	exon2			GAGCAACATCAAA	AB049652	CCDS12356.1	19p13.1	2012-09-13						"""Mitochondrial ribosomal proteins / large subunits"""	14488	protein-coding gene	gene with protein product		611840				11543634	Standard	NM_023937		Approved	L34mt, MGC2633, MGC24974	uc002ngc.1	Q9BQ48		ENST00000252602.1:c.171C>T	19.37:g.17417080C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_023937		Silent	SNP	ENST00000252602.1	37	CCDS12356.1																																																																																			C|0.936;T|0.064	0.064	strong		0.692	MRPL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463516.1	NM_023937	
SYNGR1	9145	hgsc.bcm.edu	37	22	39777880	39777880	+	Silent	SNP	C	C	T	rs74681509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39777880C>T	ENST00000328933.5	+	4	678	c.663C>T	c.(661-663)ttC>ttT	p.F221F		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	221					protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					CCAACACCTTCGACACCGAGC	0.701													C|||	2	0.000399361	0.0	0.0	5008	,	,		13145	0.001		0.0	False		,,,				2504	0.001				p.F221F		Atlas-SNP	.											SYNGR1,colon,carcinoma,0,1	SYNGR1	19	1	0			c.C663T						PASS	.	C		1,4405		0,1,2202	25.0	26.0	25.0		663	-6.1	0.3	22	dbSNP_131	25	0,8594		0,0,4297	no	coding-synonymous	SYNGR1	NM_004711.4		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		221/234	39777880	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	9145	exon4			CACCTTCGACACC	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.663C>T	22.37:g.39777880C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Silent	SNP	ENST00000328933.5	37	CCDS13989.1																																																																																			C|1.000;T|0.000	0.000	strong		0.701	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711	
KLHL30	377007	hgsc.bcm.edu	37	2	239059686	239059686	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239059686G>A	ENST00000409223.1	+	8	1824	c.1717G>A	c.(1717-1719)Ggc>Agc	p.G573S	KLHL30_ENST00000305959.4_Missense_Mutation_p.G555S			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	573										lung(4)	4		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)		CCAGCCCTCCGGCCCCACCCA	0.687																																					p.G573S		Atlas-SNP	.											KLHL30_ENST00000409223,caecum,carcinoma,0,2	KLHL30	79	2	0			c.G1717A						scavenged	.						7.0	9.0	9.0					2																	239059686		1843	4067	5910	SO:0001583	missense	377007	exon8			CCCTCCGGCCCCA		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1717G>A	2.37:g.239059686G>A	ENSP00000386389:p.Gly573Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	2	0.0152672	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	A	2.171	-0.389811	0.04932	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.72167	-0.62;-0.63	4.47	-8.95	0.00765	.	2.069400	0.02014	N	0.047227	T	0.45776	0.1359	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.49093	-0.8975	10	0.05525	T	0.97	.	9.225	0.37400	0.0884:0.3292:0.5003:0.082	.	573	Q0D2K2	KLH30_HUMAN	S	573;555	ENSP00000386389:G573S;ENSP00000302386:G555S	ENSP00000302386:G555S	G	+	1	0	KLHL30	238724425	0.023000	0.18921	0.000000	0.03702	0.001000	0.01503	0.657000	0.24963	-4.084000	0.00075	-4.023000	0.00013	GGC	.	.	none		0.687	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
FAM135B	51059	hgsc.bcm.edu	37	8	139149406	139149406	+	Silent	SNP	G	G	A	rs6577876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:139149406G>A	ENST00000395297.1	-	19	4169	c.3999C>T	c.(3997-3999)ctC>ctT	p.L1333L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1333										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)			GTCTGTCTTTGAGGGCAGTTT	0.408										HNSCC(54;0.14)			G|||	984	0.196486	0.3101	0.2017	5008	,	,		18941	0.0139		0.2575	False		,,,				2504	0.1646				p.L1333L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C3999T						PASS	.	G		1137,2587		177,783,902	153.0	151.0	152.0		3999	-0.4	0.9	8	dbSNP_116	152	2241,5981		295,1651,2165	no	coding-synonymous	FAM135B	NM_015912.3		472,2434,3067	AA,AG,GG		27.2561,30.5317,28.2772		1333/1407	139149406	3378,8568	1862	4111	5973	SO:0001819	synonymous_variant	51059	exon19			GTCTTTGAGGGCA	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.3999C>T	8.37:g.139149406G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			G|0.777;A|0.223	0.223	strong		0.408	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
RAB5A	5868	hgsc.bcm.edu	37	3	20017628	20017628	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:20017628C>T	ENST00000273047.4	+	4	941	c.405C>T	c.(403-405)gcC>gcT	p.A135A	RAB5A_ENST00000422242.1_Silent_p.A121A	NM_004162.4	NP_004153.2	P20339	RAB5A_HUMAN	RAB5A, member RAS oncogene family	135					blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|nervous system development (GO:0007399)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of endosome size (GO:0051036)|regulation of filopodium assembly (GO:0051489)|regulation of synaptic vesicle exocytosis (GO:2000300)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytoplasmic side of early endosome membrane (GO:0098559)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|somatodendritic compartment (GO:0036477)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(1)|urinary_tract(1)	2						GAAACAAGGCCGACCTAGCAA	0.363																																					p.A135A		Atlas-SNP	.											RAB5A,caecum,carcinoma,+1,1	RAB5A	19	1	0			c.C405T						scavenged	.						67.0	63.0	64.0					3																	20017628		2203	4300	6503	SO:0001819	synonymous_variant	5868	exon4			CAAGGCCGACCTA		CCDS2633.1	3p24-p22	2008-07-18			ENSG00000144566	ENSG00000144566		"""RAB, member RAS oncogene"""	9783	protein-coding gene	gene with protein product	"""RAS-associated protein RAB5A"""	179512		RAB5		1999336	Standard	NM_004162		Approved		uc003cbn.3	P20339	OTTHUMG00000129889	ENST00000273047.4:c.405C>T	3.37:g.20017628C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	259	4	0.015444	NM_004162	B4DJA5|Q6FI44	Silent	SNP	ENST00000273047.4	37	CCDS2633.1																																																																																			.	.	none		0.363	RAB5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252137.2	NM_004162	
SCN10A	6336	hgsc.bcm.edu	37	3	38763863	38763863	+	Silent	SNP	G	G	C	rs6771157	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38763863G>C	ENST00000449082.2	-	19	3392	c.3393C>G	c.(3391-3393)acC>acG	p.T1131T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1131					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)			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)	ATGGACTCTTGGTGGTATCCA	0.547													G|||	1100	0.219649	0.121	0.121	5008	,	,		20313	0.376		0.2465	False		,,,				2504	0.2342				p.T1131T		Atlas-SNP	.											.	SCN10A	359	.	0			c.C3393G						PASS	.	G		626,3780	269.5+/-269.1	47,532,1624	166.0	143.0	151.0		3393	-1.6	0.0	3	dbSNP_116	151	2238,6362	379.8+/-339.4	288,1662,2350	no	coding-synonymous	SCN10A	NM_006514.2		335,2194,3974	CC,CG,GG		26.0233,14.2079,22.0206		1131/1957	38763863	2864,10142	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon19			ACTCTTGGTGGTA	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.3393C>G	3.37:g.38763863G>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.767;C|0.233	0.233	strong		0.547	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
SPEG	10290	hgsc.bcm.edu	37	2	220315970	220315970	+	Silent	SNP	G	G	A	rs10932806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220315970G>A	ENST00000312358.7	+	5	2358	c.2226G>A	c.(2224-2226)aaG>aaA	p.K742K	SPEG_ENST00000396695.2_5'UTR|SPEG_ENST00000396698.1_Silent_p.K638K|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	742	Ig-like 2.				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)		TGCTGCTCAAGTGTATCATCA	0.622													G|||	2165	0.432308	0.1392	0.4914	5008	,	,		16324	0.6716		0.5119	False		,,,				2504	0.4581				p.K742K		Atlas-SNP	.											.	SPEG	272	.	0			c.G2226A						PASS	.	G		781,3281		94,593,1344	61.0	64.0	63.0		2226	4.2	1.0	2	dbSNP_120	63	4290,4032		1099,2092,970	no	coding-synonymous	SPEG	NM_005876.4		1193,2685,2314	AA,AG,GG		48.4499,19.227,40.948		742/3268	220315970	5071,7313	2031	4161	6192	SO:0001819	synonymous_variant	10290	exon5			GCTCAAGTGTATC	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.2226G>A	2.37:g.220315970G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.544;A|0.456	0.456	strong		0.622	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
JRK	8629	hgsc.bcm.edu	37	8	143745981	143745981	+	RNA	SNP	G	G	A	rs35419434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143745981G>A	ENST00000507178.2	-	0	1829							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tccgcaaagcgcaggactgcg	0.677													g|||	103	0.0205671	0.003	0.0173	5008	,	,		17582	0.0298		0.0437	False		,,,				2504	0.0133				p.R499C		Atlas-SNP	.											.	.	.	.	0			c.C1495T						PASS	.	A	CYS/ARG,CYS/ARG	39,4219		0,39,2090	13.0	17.0	15.0		1497,1497	-4.2	0.0	8	dbSNP_126	15	424,8064		6,412,3826	no	missense,missense	JRK	NM_001077527.1,NM_003724.2	180,180	6,451,5916	AA,AG,GG		4.9953,0.9159,3.6325	possibly-damaging,possibly-damaging	499/557,499/569	143745981	463,12283	2129	4244	6373			8629	exon3			CAAAGCGCAGGAC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143745981G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				G|0.971;A|0.029	0.029	strong		0.677	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
CCDC153	283152	hgsc.bcm.edu	37	11	119063908	119063908	+	Missense_Mutation	SNP	C	C	T	rs2301574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	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	
ZNF19	7567	hgsc.bcm.edu	37	16	71509588	71509588	+	Silent	SNP	G	G	A	rs2288487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:71509588G>A	ENST00000288177.5	-	6	1117	c.862C>T	c.(862-864)Cta>Tta	p.L288L	ZNF19_ENST00000565100.2_Silent_p.L218L|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000565637.1_Silent_p.L246L|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	61	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	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	
ALX4	60529	hgsc.bcm.edu	37	11	44286566	44286566	+	Silent	SNP	G	G	A	rs3802805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	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		
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:61415492A>G	ENST00000398571.2	-	80	10462	c.10386T>C	c.(10384-10386)gcT>gcC	p.A3462A	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3462					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATTCTTCCTCAGCTAGGGTAG	0.453													A|||	2062	0.411741	0.4781	0.4164	5008	,	,		21759	0.3929		0.4901	False		,,,				2504	0.2577				p.A3462A		Atlas-SNP	.											.	USP34	334	.	0			c.T10386C						PASS	.	A		1798,1958		455,888,535	85.0	79.0	80.0		10386	-0.6	1.0	2	dbSNP_52	80	4028,4222		984,2060,1081	no	coding-synonymous	USP34	NM_014709.3		1439,2948,1616	GG,GA,AA		48.8242,47.8701,48.5257		3462/3547	61415492	5826,6180	1878	4125	6003	SO:0001819	synonymous_variant	9736	exon80			TTCCTCAGCTAGG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.10386T>C	2.37:g.61415492A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	1003	0.4592490842490842	240	0.4878048780487805	165	0.4558011049723757	217	0.3793706293706294	381	0.5026385224274407	.	4.254	0.046111	0.08243	0.478701	0.488242	ENSG00000115464	ENST00000411912	.	.	.	5.52	-0.572	0.11745	.	.	.	.	.	.	.	.	.	.	.	0.18873	P	0.999985041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.133	0.06430	0.3824:0.1165:0.3872:0.1138	rs14170;rs3205597;rs3814034;rs11548862;rs17540386;rs17846593;rs17859675;rs61060947	.	.	.	R	1139	.	.	X	-	1	0	USP34	61268996	0.078000	0.21339	0.957000	0.39632	0.987000	0.75469	-0.555000	0.05999	0.049000	0.15920	0.482000	0.46254	TGA	A|0.525;G|0.475	0.475	strong		0.453	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
S100A5	6276	hgsc.bcm.edu	37	1	153509892	153509892	+	Silent	SNP	A	A	G	rs2248745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:153509892A>G	ENST00000368718.1	-	4	440	c.159T>C	c.(157-159)gaT>gaC	p.D53D	S100A6_ENST00000368719.4_5'Flank|BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000496817.1_5'Flank|S100A5_ENST00000359215.1_Silent_p.D71D|S100A5_ENST00000368717.2_Silent_p.D53D|S100A6_ENST00000368720.2_5'Flank	NM_002962.1	NP_002953.2	P33763	S10A5_HUMAN	S100 calcium binding protein A5	53	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					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)			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)			TCATCAAGTCATCGATGCTGC	0.562													A|||	575	0.114816	0.1967	0.1066	5008	,	,		20539	0.0724		0.0905	False		,,,				2504	0.0787				p.D53D		Atlas-SNP	.											S100A5,NS,carcinoma,-2,1	S100A5	10	1	0			c.T159C						PASS	.	A		854,3552	335.2+/-303.8	82,690,1431	246.0	204.0	218.0		159	-5.2	0.1	1	dbSNP_100	218	826,7774	190.7+/-237.1	43,740,3517	no	coding-synonymous	S100A5	NM_002962.1		125,1430,4948	GG,GA,AA		9.6047,19.3827,12.9171		53/93	153509892	1680,11326	2203	4300	6503	SO:0001819	synonymous_variant	6276	exon4			CAAGTCATCGATG	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.159T>C	1.37:g.153509892A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	151	56	0.370861	NM_002962	Q52LE7|Q5RHS3	Silent	SNP	ENST00000368718.1	37	CCDS1041.2																																																																																			A|0.877;G|0.123	0.123	strong		0.562	S100A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037719.1	NM_002962	
APLF	200558	hgsc.bcm.edu	37	2	68794483	68794483	+	Missense_Mutation	SNP	C	C	A	rs36021078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68794483C>A	ENST00000303795.4	+	9	1468	c.1297C>A	c.(1297-1299)Cag>Aag	p.Q433K	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	433					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						GAAGAATCCCCAGCACAAGAT	0.318													C|||	134	0.0267572	0.003	0.0144	5008	,	,		15806	0.0317		0.0408	False		,,,				2504	0.0481				p.Q433K		Atlas-SNP	.											APLF,NS,carcinoma,-1,1	APLF	69	1	0			c.C1297A						PASS	.	C	LYS/GLN	25,4381	27.2+/-55.0	0,25,2178	63.0	63.0	63.0		1297	5.0	1.0	2	dbSNP_126	63	319,8277	107.2+/-168.0	8,303,3987	yes	missense	APLF	NM_173545.2	53	8,328,6165	AA,AC,CC		3.711,0.5674,2.6457	probably-damaging	433/512	68794483	344,12658	2203	4298	6501	SO:0001583	missense	200558	exon9			AATCCCCAGCACA	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.1297C>A	2.37:g.68794483C>A	ENSP00000307004:p.Gln433Lys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	193	96	0.497409	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	54	0.024725274725274724	2	0.0040650406504065045	5	0.013812154696132596	18	0.03146853146853147	29	0.03825857519788918	C	22.1	4.241121	0.79912	0.005674	0.03711	ENSG00000169621	ENST00000303795	T	0.26660	1.72	4.99	4.99	0.66335	Zinc finger, C2H2, APLF-like (1);	0.067342	0.64402	D	0.000005	T	0.17195	0.0413	M	0.64170	1.965	0.38110	D	0.937548	D	0.69078	0.997	D	0.83275	0.996	T	0.18903	-1.0322	10	0.62326	D	0.03	.	13.9502	0.64111	0.0:1.0:0.0:0.0	rs36021078	433	Q8IW19	APLF_HUMAN	K	433	ENSP00000307004:Q433K	ENSP00000307004:Q433K	Q	+	1	0	APLF	68647987	0.997000	0.39634	0.998000	0.56505	0.948000	0.59901	3.381000	0.52455	2.739000	0.93911	0.585000	0.79938	CAG	C|0.973;A|0.027	0.027	strong		0.318	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
KIF20B	9585	hgsc.bcm.edu	37	10	91498254	91498254	+	Missense_Mutation	SNP	A	A	G	rs1886997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91498254A>G	ENST00000371728.3	+	20	3721	c.3656A>G	c.(3655-3657)aAt>aGt	p.N1219S	KIF20B_ENST00000394289.2_Missense_Mutation_p.N1219S|KIF20B_ENST00000416354.1_Missense_Mutation_p.N1249S|KIF20B_ENST00000260753.4_Missense_Mutation_p.N1179S|KIF20B_ENST00000478929.1_3'UTR	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	98	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	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	
POTEH	23784	hgsc.bcm.edu	37	22	16287538	16287538	+	Silent	SNP	G	G	A	rs200179046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:16287538G>A	ENST00000343518.6	-	1	399	c.348C>T	c.(346-348)aaC>aaT	p.N116N		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	116										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						AAGTGCCCACGTTGCTCTTGC	0.602													G|||	29	0.00579073	0.0113	0.0	5008	,	,		24150	0.001		0.002	False		,,,				2504	0.0112				p.N116N		Atlas-SNP	.											POTEH,colon,carcinoma,0,1	POTEH	114	1	0			c.C348T						scavenged	.						95.0	108.0	103.0					22																	16287538		2058	3900	5958	SO:0001819	synonymous_variant	23784	exon1			GCCCACGTTGCTC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	133	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 7"""	608913	"""actin, beta-like 1"", ""ANKRD26-like family C, member 3"""	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.348C>T	22.37:g.16287538G>A		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	270	22	0.0814815	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Silent	SNP	ENST00000343518.6	37	CCDS46658.1																																																																																			A|0.008;C|0.006;G|0.986	0.008	strong		0.602	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213	
EPHB1	2047	hgsc.bcm.edu	37	3	134898742	134898742	+	Silent	SNP	C	C	T	rs1042787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	186	0	0		WXS	Illumina HiSeq	Phase_I	191	55	0.287958	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	
CEP170B	283638	hgsc.bcm.edu	37	14	105352651	105352651	+	Missense_Mutation	SNP	C	C	T	rs62641737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105352651C>T	ENST00000414716.3	+	12	2303	c.2075C>T	c.(2074-2076)tCc>tTc	p.S692F	CEP170B_ENST00000418279.1_Missense_Mutation_p.S622F|CEP170B_ENST00000556508.1_Missense_Mutation_p.S622F|CEP170B_ENST00000453495.1_Missense_Mutation_p.S693F	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	692						cytoplasm (GO:0005737)|microtubule (GO:0005874)											CCGGAGGGGTCCCTGCCTGTG	0.706													C|||	57	0.0113818	0.003	0.0231	5008	,	,		12933	0.0		0.0328	False		,,,				2504	0.0041				p.S692F		Atlas-SNP	.											.	.	.	.	0			c.C2075T						PASS	.	C	PHE/SER,PHE/SER	28,3862		0,28,1917	5.0	8.0	7.0		2075,1865	3.4	0.5	14	dbSNP_129	7	308,7816		5,298,3759	yes	missense,missense	KIAA0284	NM_001112726.2,NM_015005.2	155,155	5,326,5676	TT,TC,CC		3.7912,0.7198,2.7967	benign,benign	692/1555,622/1520	105352651	336,11678	1945	4062	6007	SO:0001583	missense	283638	exon12			AGGGGTCCCTGCC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.2075C>T	14.37:g.105352651C>T	ENSP00000404151:p.Ser692Phe	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	37	CCDS45175.1	31	0.014194139194139194	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	22	0.029023746701846966	C	9.229	1.035426	0.19590	0.007198	0.037912	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	4.31	3.42	0.39159	.	1.355880	0.04923	N	0.455350	T	0.06645	0.0170	L	0.27053	0.805	0.09310	N	1	P;B;P	0.46706	0.883;0.207;0.73	P;B;B	0.45946	0.498;0.048;0.234	T	0.18272	-1.0342	10	0.72032	D	0.01	-2.6107	8.584	0.33646	0.0:0.8239:0.0:0.1761	rs62641737	692;692;622	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	F	622;692;693;622	ENSP00000451249:S622F;ENSP00000404151:S692F;ENSP00000407238:S693F;ENSP00000415006:S622F	ENSP00000404151:S692F	S	+	2	0	KIAA0284	104423696	0.001000	0.12720	0.490000	0.27465	0.381000	0.30169	1.224000	0.32539	1.039000	0.40074	0.561000	0.74099	TCC	C|0.985;T|0.015	0.015	strong		0.706	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
NCOA4	8031	hgsc.bcm.edu	37	10	51568378	51568378	+	Intron	SNP	T	T	G	rs10761581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:51568378T>G	ENST00000374087.4	+	1	70				NCOA4_ENST00000438493.1_Missense_Mutation_p.F8V|NCOA4_ENST00000498586.1_Intron|NCOA4_ENST00000414907.2_Intron|NCOA4_ENST00000430396.2_Intron|NCOA4_ENST00000452682.1_Missense_Mutation_p.F8V	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	117	0	0		WXS	Illumina HiSeq	Phase_I	99	96	0.969697	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	
NADK	65220	hgsc.bcm.edu	37	1	1684472	1684472	+	Silent	SNP	C	C	T	rs7407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1684472C>T	ENST00000341426.5	-	12	1433	c.1212G>A	c.(1210-1212)ccG>ccA	p.P404P	NADK_ENST00000378625.1_Silent_p.P549P|NADK_ENST00000342348.5_Silent_p.P372P|NADK_ENST00000341991.3_Silent_p.P404P|NADK_ENST00000344463.4_Silent_p.P549P	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	404					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TGGAGGGGAGCGGGTAGCATG	0.637													C|||	1701	0.339657	0.0552	0.5634	5008	,	,		15082	0.3452		0.505	False		,,,				2504	0.3896				p.P549P		Atlas-SNP	.											NADK,NS,carcinoma,-2,1	NADK	79	1	0			c.G1647A						scavenged	.	C	,,,	549,3849	232.6+/-246.1	43,463,1693	44.0	29.0	34.0		1212,1647,1116,1212	-6.1	0.7	1	dbSNP_52	34	4405,4193	553.0+/-386.2	1171,2063,1065	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NADK	NM_001198993.1,NM_001198994.1,NM_001198995.1,NM_023018.4	,,,	1214,2526,2758	TT,TC,CC		48.7672,12.4829,38.1194	,,,	404/447,549/592,372/415,404/447	1684472	4954,8042	2199	4299	6498	SO:0001819	synonymous_variant	65220	exon14			GGGGAGCGGGTAG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.1212G>A	1.37:g.1684472C>T		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	194	84	0.43299	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	37	CCDS30565.1																																																																																			C|0.648;T|0.352	0.352	strong		0.637	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
MST1L	11223	hgsc.bcm.edu	37	1	17083837	17083837	+	RNA	SNP	T	T	C	rs7798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17083837T>C	ENST00000455405.2	-	0	751							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CTAATTCCTTTCAGGACCCAG	0.572													.|||	796	0.158946	0.3442	0.147	5008	,	,		39830	0.0139		0.1183	False		,,,				2504	0.1084				p.K654E		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.A1960G						scavenged	.																																					11223	exon15			TTCCTTTCAGGAC	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.17083837T>C		Somatic	203	9	0.044335		WXS	Illumina HiSeq	Phase_I	244	16	0.0655738	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	4.613	0.113916	0.08831	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.354697	0.20253	N	0.096033	T	0.15478	0.0373	.	.	.	.	.	.	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31752	-0.9932	6	0.07030	T	0.85	.	4.4522	0.11626	0.0:0.6658:0.0:0.3342	rs7798;rs1065517;rs3206536;rs4661972;rs9329464;rs11545932;rs17349417;rs7798	654;680	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	E	654;680	.	ENSP00000439273:K654E	K	-	1	0	MST1P9	16956424	1.000000	0.71417	0.916000	0.36221	0.000000	0.00434	2.244000	0.43124	-0.406000	0.07588	0.000000	0.15137	AAA	T|0.943;C|0.057	0.057	strong		0.572	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
STOX2	56977	hgsc.bcm.edu	37	4	184930646	184930646	+	Missense_Mutation	SNP	G	G	A	rs61730738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184930646G>A	ENST00000308497.4	+	3	2090	c.655G>A	c.(655-657)Gcc>Acc	p.A219T	STOX2_ENST00000438269.1_Missense_Mutation_p.A219T	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	219					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AAGGAAGTCTGCCAAGGACTG	0.517													G|||	90	0.0179712	0.003	0.0735	5008	,	,		18821	0.0		0.0318	False		,,,				2504	0.0031				p.A219T		Atlas-SNP	.											.	STOX2	142	.	0			c.G655A						PASS	.	G	THR/ALA	23,4109		0,23,2043	54.0	58.0	57.0		655	4.4	0.8	4	dbSNP_129	57	296,8118		3,290,3914	yes	missense	STOX2	NM_020225.1	58	3,313,5957	AA,AG,GG		3.5179,0.5566,2.5426	benign	219/927	184930646	319,12227	2066	4207	6273	SO:0001583	missense	56977	exon3			AAGTCTGCCAAGG	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.655G>A	4.37:g.184930646G>A	ENSP00000311257:p.Ala219Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	37	CCDS47167.1	36	0.016483516483516484	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	24	0.0316622691292876	G	8.893	0.954441	0.18431	0.005566	0.035179	ENSG00000173320	ENST00000308497;ENST00000438269	T;T	0.76839	-0.04;-1.05	6.08	4.37	0.52481	.	0.119634	0.56097	D	0.000029	T	0.19248	0.0462	N	0.03608	-0.345	0.41073	D	0.985467	P	0.43094	0.799	B	0.37047	0.24	T	0.25950	-1.0117	10	0.21014	T	0.42	-13.8149	8.3537	0.32318	0.1344:0.1276:0.738:0.0	rs61730738	219	Q9P2F5	STOX2_HUMAN	T	219	ENSP00000311257:A219T;ENSP00000390127:A219T	ENSP00000311257:A219T	A	+	1	0	STOX2	185167640	0.959000	0.32827	0.750000	0.31169	0.511000	0.34104	1.695000	0.37763	0.914000	0.36822	0.655000	0.94253	GCC	G|0.982;A|0.018	0.018	strong		0.517	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
CASZ1	54897	hgsc.bcm.edu	37	1	10713765	10713765	+	Silent	SNP	T	T	C	rs284294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10713765T>C	ENST00000377022.3	-	11	2666	c.2349A>G	c.(2347-2349)tcA>tcG	p.S783S	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.S783S	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	783					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)		CCAGGGGGATTGAGCCAGGCA	0.711													C|||	2730	0.545128	0.7194	0.4539	5008	,	,		16126	0.3095		0.5646	False		,,,				2504	0.5971				p.S783S		Atlas-SNP	.											CASZ1,colon,carcinoma,0,1	CASZ1	150	1	0			c.A2349G						PASS	.	C	,	2890,1470		976,938,266	25.0	33.0	30.0		2349,2349	3.0	0.9	1	dbSNP_79	30	4701,3873		1298,2105,884	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	2274,3043,1150	CC,CT,TT		45.1714,33.7156,41.3097	,	783/1760,783/1167	10713765	7591,5343	2180	4287	6467	SO:0001819	synonymous_variant	54897	exon11			GGGGATTGAGCCA	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.2349A>G	1.37:g.10713765T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			T|0.453;C|0.547	0.547	strong		0.711	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
FBLN2	2199	hgsc.bcm.edu	37	3	13679335	13679335	+	Silent	SNP	C	C	T	rs1061376	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13679335C>T	ENST00000295760.7	+	17	3540	c.3471C>T	c.(3469-3471)gaC>gaT	p.D1157D	FBLN2_ENST00000492059.1_Silent_p.D1204D|FBLN2_ENST00000535798.1_Silent_p.D1183D|FBLN2_ENST00000404922.3_Silent_p.D1204D	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	1157	Domain III.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			TTGCCCTGGACGTGGAGATGA	0.632													C|||	2478	0.494808	0.6876	0.3761	5008	,	,		18377	0.6399		0.3241	False		,,,				2504	0.3446				p.D1204D		Atlas-SNP	.											.	FBLN2	137	.	0			c.C3612T						PASS	.	C	,,	2345,1769		693,959,405	97.0	108.0	105.0		3612,3612,3471	-1.8	1.0	3	dbSNP_86	105	2510,5894		385,1740,2077	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	1078,2699,2482	TT,TC,CC		29.8667,42.9995,38.7842	,,	1204/1232,1204/1232,1157/1185	13679335	4855,7663	2057	4202	6259	SO:0001819	synonymous_variant	2199	exon18			CCTGGACGTGGAG	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.3471C>T	3.37:g.13679335C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			C|0.518;N|0.000	.	strong		0.632	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
KLHL17	339451	hgsc.bcm.edu	37	1	900505	900505	+	Silent	SNP	G	G	C	rs28705211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:900505G>C	ENST00000338591.3	+	12	1970	c.1863G>C	c.(1861-1863)gtG>gtC	p.V621V	PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank|PLEKHN1_ENST00000379410.3_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	621	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	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;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTGTGGCGGTGCTGGAGCTGC	0.642													G|||	845	0.16873	0.0174	0.2017	5008	,	,		10946	0.0913		0.2903	False		,,,				2504	0.3047				p.V621V		Atlas-SNP	.											KLHL17,NS,carcinoma,0,1	KLHL17	31	1	0			c.G1863C						PASS	.						107.0	82.0	90.0					1																	900505		2198	4298	6496	SO:0001819	synonymous_variant	339451	exon12			GGCGGTGCTGGAG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1863G>C	1.37:g.900505G>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_198317	Q5SV94	Silent	SNP	ENST00000338591.3	37	CCDS30550.1																																																																																			G|0.802;C|0.198	0.198	strong		0.642	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
GRM7	2917	hgsc.bcm.edu	37	3	7620789	7620789	+	Silent	SNP	T	T	C	rs1485175	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:7620789T>C	ENST00000357716.4	+	8	2470	c.2196T>C	c.(2194-2196)taT>taC	p.Y732Y	GRM7_ENST00000389336.4_Silent_p.Y732Y|GRM7_ENST00000402647.2_Silent_p.Y732Y|GRM7_ENST00000486284.1_Silent_p.Y732Y|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000403881.1_Silent_p.Y732Y	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	732					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TCATAGACTATGATGAACACA	0.423													T|||	2632	0.525559	0.5703	0.5144	5008	,	,		18820	0.4355		0.5835	False		,,,				2504	0.5061				p.Y732Y		Atlas-SNP	.											.	GRM7	223	.	0			c.T2196C						PASS	.	T	,	2528,1878	631.3+/-395.6	723,1082,398	132.0	114.0	120.0		2196,2196	-0.1	1.0	3	dbSNP_88	120	4815,3785	614.9+/-396.3	1334,2147,819	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	2057,3229,1217	CC,CT,TT		44.0116,42.6237,43.5414	,	732/916,732/923	7620789	7343,5663	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			AGACTATGATGAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2196T>C	3.37:g.7620789T>C		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	273	273	1	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			T|0.451;C|0.549	0.549	strong		0.423	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
PIGL	9487	hgsc.bcm.edu	37	17	16203290	16203290	+	Missense_Mutation	SNP	C	C	A	rs115958467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:16203290C>A	ENST00000225609.5	+	3	441	c.424C>A	c.(424-426)Ctg>Atg	p.L142M	PIGL_ENST00000498772.2_Missense_Mutation_p.L142M|PIGL_ENST00000581006.1_Missense_Mutation_p.L142M|PIGL_ENST00000395844.4_Missense_Mutation_p.L142M	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	142					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)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		TGGCATCAATCTGGTAAGGGG	0.522													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20273	0.0		0.005	False		,,,				2504	0.0				p.L142M		Atlas-SNP	.											.	PIGL	16	.	0			c.C424A						PASS	.	C	MET/LEU	10,4396	16.8+/-37.8	0,10,2193	133.0	115.0	121.0		424	1.3	1.0	17	dbSNP_132	121	61,8539	38.3+/-94.2	1,59,4240	yes	missense	PIGL	NM_004278.3	15	1,69,6433	AA,AC,CC		0.7093,0.227,0.5459	probably-damaging	142/253	16203290	71,12935	2203	4300	6503	SO:0001583	missense	9487	exon3			ATCAATCTGGTAA	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"""Phosphatidylinositol glycan anchor biosynthesis"""	8966	protein-coding gene	gene with protein product	"""N-acetylglucosaminylphosphatidylinositol deacetylase"""	605947	"""phosphatidylinositol glycan, class L"""			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.424C>A	17.37:g.16203290C>A	ENSP00000225609:p.Leu142Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	37	CCDS11176.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	12.67	2.008068	0.35415	0.00227	0.007093	ENSG00000108474	ENST00000225609;ENST00000395844	T;T	0.78707	-1.2;-1.2	4.47	1.28	0.21552	Putative deacetylase LmbE-like domain (2);	0.000000	0.64402	D	0.000001	T	0.73426	0.3585	M	0.66378	2.025	0.35873	D	0.828373	D;D	0.56968	0.978;0.978	P;P	0.54499	0.754;0.754	T	0.77930	-0.2403	10	0.54805	T	0.06	-14.4259	6.9712	0.24650	0.0:0.7108:0.0:0.2892	.	142;142	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	M	142	ENSP00000225609:L142M;ENSP00000379185:L142M	ENSP00000225609:L142M	L	+	1	2	PIGL	16144015	0.733000	0.28132	0.962000	0.40283	0.273000	0.26683	0.159000	0.16442	0.221000	0.20879	0.460000	0.39030	CTG	C|0.996;A|0.004	0.004	strong		0.522	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1		
BCL7A	605	hgsc.bcm.edu	37	12	122468687	122468687	+	Splice_Site	SNP	C	C	T	rs2272132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122468687C>T	ENST00000261822.4	+	2	380	c.174C>T	c.(172-174)gaC>gaT	p.D58D	BCL7A_ENST00000538010.1_Splice_Site_p.D58D	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	58					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		AGGTTGATGACGTGAGTATGG	0.592			T	MYC	BNHL								C|||	173	0.0345447	0.0045	0.0375	5008	,	,		19084	0.0476		0.0487	False		,,,				2504	0.045				p.D58D	GBM(17;197 467 16477 23242 44349)	Atlas-SNP	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	BCL7A	31	.	0			c.C174T						PASS	.	C	,	55,4351	54.9+/-90.9	2,51,2150	141.0	109.0	120.0		174,174	-5.3	0.8	12	dbSNP_100	120	392,8208	126.3+/-184.8	15,362,3923	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	BCL7A	NM_001024808.1,NM_020993.3	,	17,413,6073	TT,TC,CC		4.5581,1.2483,3.4369	,	58/211,58/232	122468687	447,12559	2203	4300	6503	SO:0001630	splice_region_variant	605	exon2			TGATGACGTGAGT	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.174+1C>T	12.37:g.122468687C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Silent	SNP	ENST00000261822.4	37	CCDS53841.1																																																																																			C|0.964;T|0.036	0.036	strong		0.592	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		Silent
WSCD1	23302	hgsc.bcm.edu	37	17	6012955	6012955	+	Nonsense_Mutation	SNP	G	G	A	rs267604993		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6012955G>A	ENST00000574946.1	+	6	1268	c.878G>A	c.(877-879)tGg>tAg	p.W293*	WSCD1_ENST00000317744.5_Nonsense_Mutation_p.W293*|WSCD1_ENST00000573634.1_Nonsense_Mutation_p.W177*|WSCD1_ENST00000574232.1_Nonsense_Mutation_p.W293*|WSCD1_ENST00000539421.1_Nonsense_Mutation_p.W293*			Q658N2	WSCD1_HUMAN	WSC domain containing 1	293	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					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						CTCAGGGGCTGGGAATGCTAC	0.572																																					p.W293X		Atlas-SNP	.											.	WSCD1	84	.	0			c.G878A						PASS	.						241.0	225.0	231.0					17																	6012955		2203	4300	6503	SO:0001587	stop_gained	23302	exon6			GGGGCTGGGAATG		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.878G>A	17.37:g.6012955G>A	ENSP00000460825:p.Trp293*	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	19	0.301587	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Nonsense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	G	37	6.412301	0.97546	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	.	.	.	5.91	3.83	0.44106	.	0.417502	0.27122	N	0.020825	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-23.0413	13.247	0.60028	0.0:0.4832:0.5167:0.0	.	.	.	.	X	293	.	ENSP00000323087:W293X	W	+	2	0	WSCD1	5953679	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.973000	0.29422	1.464000	0.47987	0.650000	0.86243	TGG	.	.	none		0.572	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
HMHA1	23526	hgsc.bcm.edu	37	19	1085966	1085966	+	Silent	SNP	A	A	G	rs3761028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1085966A>G	ENST00000313093.2	+	23	3603	c.3372A>G	c.(3370-3372)acA>acG	p.T1124T	HMHA1_ENST00000543365.1_Silent_p.T1007T|HMHA1_ENST00000590577.1_Silent_p.T759T|HMHA1_ENST00000590214.1_Silent_p.T1151T|HMHA1_ENST00000591169.1_3'UTR|HMHA1_ENST00000539243.2_Silent_p.T1140T|HMHA1_ENST00000586866.1_Silent_p.T1128T|HMHA1_ENST00000536472.1_Silent_p.T992T|POLR2E_ENST00000585838.1_5'Flank	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	97	0	0		WXS	Illumina HiSeq	Phase_I	101	98	0.970297	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		
MAGEC1	9947	hgsc.bcm.edu	37	X	140995315	140995315	+	Missense_Mutation	SNP	C	C	T	rs56256227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:140995315C>T	ENST00000285879.4	+	4	2411	c.2125C>T	c.(2125-2127)Cat>Tat	p.H709Y	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	709			H -> Y (in dbSNP:rs56256227).							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)					GTCTTCTCTCCATTTTCCTCA	0.557										HNSCC(15;0.026)			C|||	311	0.0823841	0.056	0.0562	3775	,	,		13461	0.0327		0.0626	False		,,,				2504	0.1043				p.H709Y		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C2125T						PASS	.	C	TYR/HIS	263,3572		7,203,46,1422,525	71.0	75.0	74.0		2125	-1.9	0.0	X	dbSNP_129	74	663,6065		28,433,174,1967,1698	yes	missense	MAGEC1	NM_005462.4	83	35,636,220,3389,2223	TT,TC,T,CC,C		9.8543,6.8579,8.7664	benign	709/1143	140995315	926,9637	2203	4300	6503	SO:0001583	missense	9947	exon4			TCTCTCCATTTTC	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.2125C>T	X.37:g.140995315C>T	ENSP00000285879:p.His709Tyr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	121	0.07293550331525014	27	0.056962025316455694	12	0.03508771929824561	9	0.01601423487544484	33	0.045454545454545456	c	4.028	0.002776	0.07866	0.068579	0.098543	ENSG00000155495	ENST00000285879	T	0.02737	4.18	0.96	-1.92	0.07618	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45629	-0.9248	8	0.87932	D	0	.	5.0203	0.14358	0.0:0.5102:0.0:0.4898	rs56256227	709	O60732	MAGC1_HUMAN	Y	709	ENSP00000285879:H709Y	ENSP00000285879:H709Y	H	+	1	0	MAGEC1	140822981	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.621000	0.02044	-1.095000	0.03050	-1.093000	0.02169	CAT	C|0.922;T|0.078	0.078	strong		0.557	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
ZNF880	400713	hgsc.bcm.edu	37	19	52887282	52887282	+	Missense_Mutation	SNP	A	A	G	rs324125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	123	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	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	
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1092890C>T	ENST00000441003.2	+	30	4736	c.4709C>T	c.(4708-4710)aCc>aTc	p.T1570I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1571I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCACGGTGaccccaacccca	0.637																																					p.T1570I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	0			c.C4709T						scavenged	.						119.0	156.0	143.0					11																	1092890		1961	3652	5613	SO:0001583	missense	4583	exon30			CGGTGACCCCAAC	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.4709C>T	11.37:g.1092890C>T	ENSP00000415183:p.Thr1570Ile	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	5	0.121951	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.561	-0.536608	0.04082	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.42;3.24	1.3	-2.33	0.06724	.	0.589600	0.12692	U	0.447130	T	0.07548	0.0190	.	.	.	0.09310	N	1	P	0.34699	0.464	B	0.21546	0.035	T	0.24799	-1.0150	9	0.38643	T	0.18	.	4.395	0.11358	0.3284:0.4793:0.1923:0.0	.	1570	E7EUV1	.	I	1570;1571	ENSP00000415183:T1570I;ENSP00000351956:T1571I	ENSP00000351956:T1571I	T	+	2	0	MUC2	1082890	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	0.404000	0.20999	-0.107000	0.12088	0.064000	0.15345	ACC	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
C9orf24	84688	hgsc.bcm.edu	37	9	34379692	34379692	+	Silent	SNP	C	C	T	rs3737242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34379692C>T	ENST00000297623.2	-	6	939	c.741G>A	c.(739-741)gtG>gtA	p.V247V	KIAA1161_ENST00000297625.7_5'Flank|C9orf24_ENST00000379127.1_Missense_Mutation_p.C114Y|C9orf24_ENST00000481295.1_5'UTR|C9orf24_ENST00000379124.1_Missense_Mutation_p.C114Y|C9orf24_ENST00000379126.3_Missense_Mutation_p.C61Y|C9orf24_ENST00000379133.3_Silent_p.V112V	NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	247					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)		TGTAACAGCACACTGCATTCC	0.567											OREG0019150	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	709	0.141573	0.0408	0.1657	5008	,	,		17564	0.0942		0.2087	False		,,,				2504	0.2403				p.C114Y		Atlas-SNP	.											.	C9orf24	15	.	0			c.G341A						PASS	.	C	,,TYR/CYS	316,4090	166.5+/-197.7	12,292,1899	126.0	113.0	118.0		741,336,182	3.8	1.0	9	dbSNP_107	118	1739,6861	316.6+/-312.8	187,1365,2748	yes	coding-synonymous,coding-synonymous,missense	C9orf24	NM_032596.3,NM_147168.1,NM_147169.1	,,194	199,1657,4647	TT,TC,CC		20.2209,7.172,15.8004	,,	247/263,112/128,61/112	34379692	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	84688	exon4			ACAGCACACTGCA	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.741G>A	9.37:g.34379692C>T		Somatic	109	0	0	847	WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001252195	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Missense_Mutation	SNP	ENST00000297623.2	37	CCDS6554.1	302	0.1382783882783883	16	0.032520325203252036	63	0.17403314917127072	61	0.10664335664335664	162	0.21372031662269128	C	20.2	3.942210	0.73672	0.07172	0.202209	ENSG00000164972	ENST00000379126;ENST00000379127;ENST00000379112;ENST00000379124	T;T	0.52295	0.67;0.67	4.73	3.82	0.43975	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.28668	P	0.9057922	B	0.13594	0.008	B	0.17433	0.018	T	0.05818	-1.0862	7	0.22706	T	0.39	-5.1863	10.4135	0.44307	0.0:0.904:0.0:0.096	rs3737242;rs52833185;rs60665408;rs3737242	61	Q8NCR6-3	.	Y	61;114;44;114	ENSP00000368422:C114Y;ENSP00000368419:C114Y	ENSP00000368407:C44Y	C	-	2	0	C9orf24	34369692	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.351000	0.44071	2.627000	0.88993	0.561000	0.74099	TGT	C|0.860;T|0.140	0.140	strong		0.567	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
TICAM1	148022	hgsc.bcm.edu	37	19	4818378	4818378	+	Silent	SNP	T	T	C	rs7255265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4818378T>C	ENST00000248244.5	-	2	241	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	4					apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GTGATGGGCCTGTGCAGGCCA	0.622													c|||	3634	0.725639	0.9735	0.6671	5008	,	,		18753	0.5893		0.6233	False		,,,				2504	0.6779				p.T4T		Atlas-SNP	.											.	TICAM1	69	.	0			c.A12G						PASS	.	G		4051,347		1875,301,23	25.0	24.0	24.0		12	-8.1	0.0	19	dbSNP_116	24	5444,3138		1728,1988,575	no	coding-synonymous	TICAM1	NM_182919.2		3603,2289,598	CC,CT,TT		36.5649,7.8899,26.849		4/713	4818378	9495,3485	2199	4291	6490	SO:0001819	synonymous_variant	148022	exon2			TGGGCCTGTGCAG	AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.12A>G	19.37:g.4818378T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	Silent	SNP	ENST00000248244.5	37	CCDS12136.1																																																																																			T|0.268;C|0.732	0.732	strong		0.622	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261	
SAFB2	9667	hgsc.bcm.edu	37	19	5590291	5590291	+	Silent	SNP	G	G	T	rs117896034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5590291G>T	ENST00000252542.4	-	18	2787	c.2523C>A	c.(2521-2523)ccC>ccA	p.P841P		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	841	Gly-rich.|Interacts with SAFB1.				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)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CCACTAACCTGGGGGGAGGGG	0.677													G|||	44	0.00878594	0.0	0.0144	5008	,	,		15349	0.0089		0.0199	False		,,,				2504	0.0051				p.P841P	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C2523A						PASS	.	G		8,4326		0,8,2159	7.0	10.0	9.0		2523	3.3	1.0	19	dbSNP_132	9	122,8386		1,120,4133	no	coding-synonymous	SAFB2	NM_014649.2		1,128,6292	TT,TG,GG		1.4339,0.1846,1.0123		841/954	5590291	130,12712	2167	4254	6421	SO:0001819	synonymous_variant	9667	exon18			TAACCTGGGGGGA	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2523C>A	19.37:g.5590291G>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_014649	B4DKG3|Q8TB13	Silent	SNP	ENST00000252542.4	37	CCDS32879.1																																																																																			G|0.984;T|0.016	0.016	strong		0.677	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
DRC1	92749	hgsc.bcm.edu	37	2	26679362	26679362	+	Missense_Mutation	SNP	G	G	A	rs35313480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	138	0	0		WXS	Illumina HiSeq	Phase_I	176	74	0.420455	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	
SGCD	6444	hgsc.bcm.edu	37	5	155771579	155771579	+	Silent	SNP	T	T	C	rs1801193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:155771579T>C	ENST00000435422.3	+	2	568	c.81T>C	c.(79-81)taT>taC	p.Y27Y	SGCD_ENST00000447401.1_Silent_p.Y28Y|SGCD_ENST00000337851.4_Silent_p.Y28Y|SGCD_ENST00000517913.1_Silent_p.Y28Y	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	27					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGGGATTTATGGCTGGCGGA	0.493													C|||	2431	0.485423	0.2436	0.464	5008	,	,		16931	0.7937		0.4473	False		,,,				2504	0.5491				p.Y28Y		Atlas-SNP	.											.	SGCD	52	.	0			c.T84C						PASS	.	C	,,	1034,2886		143,748,1069	110.0	118.0	116.0		84,81,84	-2.0	1.0	5	dbSNP_89	116	3575,4709		751,2073,1318	no	coding-synonymous,coding-synonymous,coding-synonymous	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	,,	894,2821,2387	CC,CT,TT		43.1555,26.3776,37.7663	,,	28/291,27/290,28/257	155771579	4609,7595	1960	4142	6102	SO:0001819	synonymous_variant	6444	exon3			GATTTATGGCTGG	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.81T>C	5.37:g.155771579T>C		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	212	98	0.462264	NM_000337	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			T|0.516;C|0.484	0.484	strong		0.493	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
ZZEF1	23140	hgsc.bcm.edu	37	17	3999199	3999199	+	Silent	SNP	C	C	T	rs12947597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3999199C>T	ENST00000381638.2	-	11	1963	c.1839G>A	c.(1837-1839)gcG>gcA	p.A613A	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	613							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						AGTGTTCTTCCGCACAAAATT	0.403													c|||	773	0.154353	0.1339	0.1427	5008	,	,		18187	0.1835		0.171	False		,,,				2504	0.1431				p.A613A		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G1839A						PASS	.	C		635,3771	272.2+/-270.6	44,547,1612	78.0	77.0	77.0		1839	1.3	1.0	17	dbSNP_121	77	1448,7152	277.9+/-293.1	116,1216,2968	no	coding-synonymous	ZZEF1	NM_015113.3		160,1763,4580	TT,TC,CC		16.8372,14.4122,16.0157		613/2962	3999199	2083,10923	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon11			TTCTTCCGCACAA	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.1839G>A	17.37:g.3999199C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			C|0.834;T|0.166	0.166	strong		0.403	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
MAML2	84441	hgsc.bcm.edu	37	11	95825401	95825401	+	Silent	SNP	C	C	T	rs564983573	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:95825401C>T	ENST00000524717.1	-	2	3078	c.1794G>A	c.(1792-1794)caG>caA	p.Q598Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	598					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)	p.Q598Q(1)	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)				gctgctgctgctgctgctgct	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid								C|||	13	0.00259585	0.0008	0.0	5008	,	,		15311	0.0		0.004	False		,,,				2504	0.0082				p.Q598Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,2	MAML2	94	2	1	Substitution - coding silent(1)	endometrium(1)	c.G1794A						scavenged	.						23.0	30.0	28.0					11																	95825401		2070	4064	6134	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	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.1794G>A	11.37:g.95825401C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	88	29	0.329545	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	none		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
PACS2	23241	hgsc.bcm.edu	37	14	105858022	105858022	+	Missense_Mutation	SNP	C	C	T	rs147461490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105858022C>T	ENST00000325438.8	+	21	2633	c.2129C>T	c.(2128-2130)cCg>cTg	p.P710L	PACS2_ENST00000430725.2_Missense_Mutation_p.P635L|PACS2_ENST00000447393.1_Missense_Mutation_p.P714L|PACS2_ENST00000547217.1_Missense_Mutation_p.P680L|PACS2_ENST00000551743.1_Missense_Mutation_p.P224L|PACS2_ENST00000551801.1_5'UTR|PACS2_ENST00000458164.2_Missense_Mutation_p.P725L			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	710					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		TCCACCCCGCCGTCCGCATCT	0.716													C|||	84	0.0167732	0.0008	0.0447	5008	,	,		13167	0.0		0.0388	False		,,,				2504	0.0133				p.P725L		Atlas-SNP	.											PACS2,caecum,carcinoma,-1,4	PACS2	75	4	0			c.C2174T						PASS	.	C	LEU/PRO,LEU/PRO	55,4331		0,55,2138	20.0	21.0	21.0		2141,2129	3.1	0.8	14	dbSNP_134	21	439,8153		10,419,3867	no	missense,missense	PACS2	NM_001100913.2,NM_015197.3	98,98	10,474,6005	TT,TC,CC		5.1094,1.254,3.8064	possibly-damaging,possibly-damaging	714/894,710/890	105858022	494,12484	2193	4296	6489	SO:0001583	missense	23241	exon22			CCCCGCCGTCCGC	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"""phosphofurin acidic cluster sorting protein 1-like"""	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.2129C>T	14.37:g.105858022C>T	ENSP00000321834:p.Pro710Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	37	CCDS32168.1	49	0.022435897435897436	3	0.006097560975609756	19	0.052486187845303865	0	0.0	27	0.03562005277044855	C	15.13	2.741116	0.49151	0.01254	0.051094	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217;ENST00000551743	T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61	4.97	3.08	0.35506	.	0.126903	0.53938	D	0.000048	T	0.18593	0.0446	L	0.47190	1.495	0.80722	D	1	D;D;B;D	0.89917	0.958;0.989;0.144;1.0	B;P;B;D	0.91635	0.36;0.512;0.028;0.999	T	0.20840	-1.0263	10	0.54805	T	0.06	-13.6782	9.0338	0.36275	0.0:0.7676:0.1489:0.0836	.	714;725;710;711	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	L	635;710;725;714;680;224	ENSP00000393524:P635L;ENSP00000321834:P710L;ENSP00000399732:P725L;ENSP00000393559:P714L;ENSP00000449525:P680L;ENSP00000449254:P224L	ENSP00000321834:P710L	P	+	2	0	PACS2	104929067	1.000000	0.71417	0.751000	0.31187	0.292000	0.27327	5.588000	0.67517	0.459000	0.27016	0.462000	0.41574	CCG	C|0.965;T|0.035	0.035	strong		0.716	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
SPEG	10290	hgsc.bcm.edu	37	2	220354365	220354365	+	Silent	SNP	C	C	T	rs56132883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220354365C>T	ENST00000312358.7	+	36	8757	c.8625C>T	c.(8623-8625)ttC>ttT	p.F2875F	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2875	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)		CCAAGCCTTTCGTCCTTGACA	0.607													C|||	1435	0.286542	0.2905	0.2723	5008	,	,		10793	0.1468		0.2734	False		,,,				2504	0.4489				p.F2875F		Atlas-SNP	.											.	SPEG	272	.	0			c.C8625T						PASS	.	C		1047,2959		145,757,1101	133.0	142.0	139.0		8625	-3.5	0.4	2	dbSNP_129	139	2113,6187		273,1567,2310	no	coding-synonymous	SPEG	NM_005876.4		418,2324,3411	TT,TC,CC		25.4578,26.1358,25.6785		2875/3268	220354365	3160,9146	2003	4150	6153	SO:0001819	synonymous_variant	10290	exon36			GCCTTTCGTCCTT	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.8625C>T	2.37:g.220354365C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			C|0.748;T|0.252	0.252	strong		0.607	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50987287	50987287	+	Missense_Mutation	SNP	A	A	G	rs5770886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50987287A>G	ENST00000395676.2	+	1	826	c.692A>G	c.(691-693)cAg>cGg	p.Q231R	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	231										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)		GCCTTTGCCCAGCAGCACGGA	0.736													A|||	2108	0.420927	0.5749	0.4424	5008	,	,		11029	0.4157		0.171	False		,,,				2504	0.4601				p.Q231R		Atlas-SNP	.											KLHDC7B_ENST00000395676,NS,carcinoma,0,2	KLHDC7B	39	2	0			c.A692G						scavenged	.	A	ARG/GLN	1604,2170		328,948,611	5.0	4.0	4.0		692	2.5	1.0	22	dbSNP_114	4	1120,6254		94,932,2661	no	missense	KLHDC7B	NM_138433.3	43	422,1880,3272	GG,GA,AA		15.1885,42.5013,24.4349	benign	231/595	50987287	2724,8424	1887	3687	5574	SO:0001583	missense	113730	exon1			TTGCCCAGCAGCA	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.692A>G	22.37:g.50987287A>G	ENSP00000379034:p.Gln231Arg	Somatic	6	2	0.333333		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_138433		Missense_Mutation	SNP	ENST00000395676.2	37	CCDS14097.2	767	0.35119047619047616	264	0.5365853658536586	134	0.3701657458563536	232	0.40559440559440557	137	0.18073878627968337	A	13.36	2.214665	0.39102	0.425013	0.151885	ENSG00000130487	ENST00000395676	D	0.83837	-1.77	4.58	2.45	0.29901	.	0.580298	0.12868	N	0.432556	T	0.00012	0.0000	M	0.63428	1.95	0.40591	P	0.018514999999999948	B	0.25955	0.138	B	0.26770	0.073	T	0.38520	-0.9657	9	0.48119	T	0.1	.	6.9952	0.24779	0.8043:0.0:0.1957:0.0	rs5770886;rs5770886	231	Q96G42	KLD7B_HUMAN	R	231	ENSP00000379034:Q231R	ENSP00000379034:Q231R	Q	+	2	0	KLHDC7B	49334153	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	5.219000	0.65262	0.624000	0.30286	-0.899000	0.02877	CAG	A|0.627;G|0.373	0.373	strong		0.736	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
NMUR2	56923	hgsc.bcm.edu	37	5	151784183	151784183	+	Silent	SNP	G	G	A	rs3749787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:151784183G>A	ENST00000255262.3	-	1	657	c.492C>T	c.(490-492)ctC>ctT	p.L164L	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	164					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CGAGGATCCTGAGGGCCCGGC	0.637													G|||	1155	0.230631	0.2466	0.2421	5008	,	,		17302	0.2956		0.1948	False		,,,				2504	0.1708				p.L164L		Atlas-SNP	.											NMUR2,NS,carcinoma,-2,1	NMUR2	111	1	0			c.C492T						PASS	.	G		1114,3292	396.0+/-329.9	131,852,1220	47.0	55.0	52.0		492	3.5	0.5	5	dbSNP_107	52	1764,6836	315.8+/-312.4	169,1426,2705	no	coding-synonymous	NMUR2	NM_020167.4		300,2278,3925	AA,AG,GG		20.5116,25.2837,22.1282		164/416	151784183	2878,10128	2203	4300	6503	SO:0001819	synonymous_variant	56923	exon1			GATCCTGAGGGCC	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.492C>T	5.37:g.151784183G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Silent	SNP	ENST00000255262.3	37	CCDS4321.1																																																																																			G|0.781;A|0.219	0.219	strong		0.637	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
DNA2	1763	hgsc.bcm.edu	37	10	70227964	70227964	+	Silent	SNP	C	C	T	rs10998205	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70227964C>T	ENST00000358410.3	-	3	407	c.357G>A	c.(355-357)ctG>ctA	p.L119L	DNA2_ENST00000399179.2_Silent_p.L119L|DNA2_ENST00000399180.2_Silent_p.L205L	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	96	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	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		
TTN	7273	hgsc.bcm.edu	37	2	179611847	179611847	+	Intron	SNP	T	T	G	rs141105907|rs397517814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611847T>G	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.R5094R|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTGGAGTATCTCTCCAGAGTC	0.537													T|||	5	0.000998403	0.0	0.0029	5008	,	,		15680	0.0		0.003	False		,,,				2504	0.0				p.R5094R		Atlas-SNP	.											.	TTN	18412	.	0			c.A15280C						PASS	.	T	,,,,	0,4406		0,0,2203	62.0	74.0	70.0		,,15280,,	4.4	1.0	2	dbSNP_134	70	2,8596		0,2,4297	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,2,6500	GG,GT,TT		0.0233,0.0,0.0154	,,,,	,,5094/5605,,	179611847	2,13002	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGTATCTCTCCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5199A>C	2.37:g.179611847T>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	35	0.236486	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.998;G|0.002	0.002	strong		0.537	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
BTN1A1	696	hgsc.bcm.edu	37	6	26509330	26509330	+	Missense_Mutation	SNP	C	C	G	rs9393728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26509330C>G	ENST00000244513.6	+	7	1575	c.1509C>G	c.(1507-1509)gaC>gaG	p.D503E		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	503			D -> E (in dbSNP:rs9393728). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8611614, ECO:0000269|Ref.3}.			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TGGGGGAGGACTCTGCCCCTA	0.527													C|||	2849	0.56889	0.5159	0.5879	5008	,	,		3909	0.746		0.4423	False		,,,				2504	0.5746				p.D503E		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C1509G						PASS	.	C	GLU/ASP	2297,2109	597.9+/-389.0	593,1111,499	96.0	100.0	98.0		1509	-1.9	0.0	6	dbSNP_119	98	4047,4553	555.1+/-386.6	986,2075,1239	yes	missense	BTN1A1	NM_001732.2	45	1579,3186,1738	GG,GC,CC		47.0581,47.8665,48.7775	benign	503/527	26509330	6344,6662	2203	4300	6503	SO:0001583	missense	696	exon7			GGAGGACTCTGCC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1509C>G	6.37:g.26509330C>G	ENSP00000244513:p.Asp503Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	1125	0.5151098901098901	203	0.41260162601626016	199	0.5497237569060773	394	0.6888111888111889	329	0.4340369393139842	C	0.514	-0.865325	0.02590	0.521335	0.470581	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.34472	1.36	5.05	-1.89	0.07689	.	0.635484	0.14826	N	0.296156	T	0.03827	0.0108	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.36187	-0.9758	9	0.02654	T	1	.	4.4229	0.11490	0.2574:0.418:0.0:0.3246	rs9393728	503	Q13410	BT1A1_HUMAN	E	503;471	ENSP00000244513:D503E	ENSP00000244513:D503E	D	+	3	2	BTN1A1	26617309	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-1.754000	0.01816	-0.191000	0.10448	0.563000	0.77884	GAC	C|0.505;G|0.495	0.495	strong		0.527	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
SVIL	6840	hgsc.bcm.edu	37	10	29843833	29843833	+	Silent	SNP	C	C	T	rs1547169	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29843833C>T	ENST00000355867.4	-	5	791	c.39G>A	c.(37-39)ggG>ggA	p.G13G	SVIL_ENST00000375398.2_Silent_p.G13G|SVIL_ENST00000375400.3_Silent_p.G13G	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	13	Interaction with MYLK. {ECO:0000250}.				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)				CATTTTCAATCCCTTCCAGGC	0.502													C|||	1289	0.257388	0.2352	0.245	5008	,	,		16868	0.3552		0.2386	False		,,,				2504	0.2147				p.G13G		Atlas-SNP	.											.	SVIL	226	.	0			c.G39A						PASS	.	C	,	1161,3245	408.6+/-334.7	153,855,1195	77.0	74.0	75.0		39,39	-7.4	0.3	10	dbSNP_88	75	2236,6364	379.1+/-339.1	291,1654,2355	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	444,2509,3550	TT,TC,CC		26.0,26.3504,26.1187	,	13/1789,13/2215	29843833	3397,9609	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon7			TTCAATCCCTTCC	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.39G>A	10.37:g.29843833C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			C|0.740;T|0.260	0.260	strong		0.502	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1817855	1817855	+	Silent	SNP	C	C	T	rs118038816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1817855C>T	ENST00000250894.4	+	28	3613	c.3456C>T	c.(3454-3456)gtC>gtT	p.V1152V	MAPK8IP3_ENST00000356010.5_Silent_p.V1146V	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	1152					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						CCCTGCTTGTCGCGGGCAGCC	0.667													C|||	46	0.0091853	0.0189	0.0014	5008	,	,		18035	0.0		0.005	False		,,,				2504	0.0153				p.V1152V		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C3456T						PASS	.	C	,	63,4141		0,63,2039	61.0	73.0	69.0		3438,3456	-5.8	0.1	16	dbSNP_132	69	31,8405		0,31,4187	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	0,94,6226	TT,TC,CC		0.3675,1.4986,0.7437	,	1146/1331,1152/1337	1817855	94,12546	2102	4218	6320	SO:0001819	synonymous_variant	23162	exon28			GCTTGTCGCGGGC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.3456C>T	16.37:g.1817855C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			C|0.995;T|0.005	0.005	strong		0.667	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181015	19181015	+	Missense_Mutation	SNP	G	G	C	rs34447754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19181015G>C	ENST00000375371.3	-	3	970	c.949C>G	c.(949-951)Cgc>Ggc	p.R317G	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	317			R -> G (in dbSNP:rs34447754). {ECO:0000269|PubMed:11917125}.		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CCCAAGTGGCGCAGCTCCGTG	0.662													G|||	1193	0.238219	0.2602	0.2507	5008	,	,		19800	0.1032		0.3191	False		,,,				2504	0.2556				p.R317G		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C949G						PASS	.	G	GLY/ARG	1096,3310	394.9+/-329.4	130,836,1237	56.0	55.0	55.0		949	2.8	0.2	1	dbSNP_126	55	2795,5803	441.0+/-359.7	443,1909,1947	yes	missense	TAS1R2	NM_152232.2	125	573,2745,3184	CC,CG,GG		32.5076,24.8752,29.9216	benign	317/840	19181015	3891,9113	2203	4299	6502	SO:0001583	missense	80834	exon3			AGTGGCGCAGCTC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.949C>G	1.37:g.19181015G>C	ENSP00000364520:p.Arg317Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	525	0.2403846153846154	124	0.25203252032520324	104	0.287292817679558	54	0.0944055944055944	243	0.32058047493403696	G	3.588	-0.084220	0.07097	0.248752	0.325076	ENSG00000179002	ENST00000375371	D	0.83419	-1.72	4.8	2.84	0.33178	Extracellular ligand-binding receptor (1);	1.158180	0.06535	N	0.742189	T	0.00012	0.0000	L	0.39245	1.2	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.04165	-1.0972	9	0.12103	T	0.63	.	10.6868	0.45848	0.0:0.0:0.4503:0.5497	rs34447754	317	Q8TE23	TS1R2_HUMAN	G	317	ENSP00000364520:R317G	ENSP00000364520:R317G	R	-	1	0	TAS1R2	19053602	0.249000	0.23941	0.156000	0.22583	0.115000	0.19883	0.582000	0.23834	0.556000	0.29098	0.561000	0.74099	CGC	G|0.720;C|0.280	0.280	strong		0.662	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249152	71249152	+	Silent	SNP	C	C	T	rs112809261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	75	16	0.213333	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	
OBSL1	23363	hgsc.bcm.edu	37	2	220427347	220427347	+	Silent	SNP	G	G	T	rs10804275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220427347G>T	ENST00000404537.1	-	8	2786	c.2730C>A	c.(2728-2730)gcC>gcA	p.A910A	RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000289656.3_Silent_p.A497A|OBSL1_ENST00000603926.1_Silent_p.A910A|OBSL1_ENST00000373873.4_Silent_p.A910A|OBSL1_ENST00000265318.4_Silent_p.A910A|OBSL1_ENST00000373876.1_Silent_p.A910A	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	910	Ig-like 7.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CCAGGCGCACGGCTGCCACAT	0.672													G|||	850	0.169728	0.0983	0.2608	5008	,	,		17634	0.2123		0.2406	False		,,,				2504	0.0849				p.A910A		Atlas-SNP	.											.	OBSL1	120	.	0			c.C2730A						PASS	.	G	,,	601,3791		49,503,1644	29.0	35.0	33.0		2730,2730,2730	-4.7	0.6	2	dbSNP_120	33	2123,6451		272,1579,2436	no	coding-synonymous,coding-synonymous,coding-synonymous	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	,,	321,2082,4080	TT,TG,GG		24.7609,13.684,21.0088	,,	910/1026,910/1544,910/1897	220427347	2724,10242	2196	4287	6483	SO:0001819	synonymous_variant	23363	exon8			GCGCACGGCTGCC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2730C>A	2.37:g.220427347G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			C|0.000;G|0.794;T|0.206	0.206	strong		0.672	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
GRPR	2925	hgsc.bcm.edu	37	X	16168677	16168677	+	Silent	SNP	T	T	C	rs4986946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:16168677T>C	ENST00000380289.2	+	2	1061	c.663T>C	c.(661-663)atT>atC	p.I221I	RP11-431J24.2_ENST00000435789.1_RNA|RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000454712.2_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	90	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	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	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551958	32551958	+	Missense_Mutation	SNP	C	C	T	rs1064592|rs568948309|rs200320734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32551958C>T	ENST00000360004.5	-	2	403	c.298G>A	c.(298-300)Gcg>Acg	p.A100T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	100	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						GCGGCCCGCGCCTGCTCCAGG	0.682										Multiple Myeloma(14;0.17)																											p.A100T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G298A						PASS	.	C	THR/ALA	846,3170		215,416,1377	26.0	28.0	27.0		298	-7.0	0.0	6	dbSNP_86	27	2648,5580		781,1086,2247	no	missense	HLA-DRB1	NM_002124.3	58	996,1502,3624	TT,TC,CC		32.1828,21.0657,28.5364		100/267	32551958	3494,8750	2008	4114	6122	SO:0001583	missense	3123	exon2			CCCGCGCCTGCTC	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.298G>A	6.37:g.32551958C>T	ENSP00000353099:p.Ala100Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	34	31	0.911765	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.62	1.993888	0.35131	0.210657	0.321828	ENSG00000196126	ENST00000360004	T	0.00321	8.11	3.52	-7.04	0.01578	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);	7.036940	0.00166	N	0.000001	T	0.00039	0.0001	L	0.33245	0.995	0.80722	P	0.0	B	0.17852	0.024	B	0.25140	0.058	T	0.26744	-1.0094	9	0.56958	D	0.05	.	5.9518	0.19250	0.0:0.3325:0.1332:0.5343	rs1064592;rs1064593;rs3208227;rs3208228;rs9269943;rs16822852;rs17879929	100	P01911	2B1F_HUMAN	T	100	ENSP00000353099:A100T	ENSP00000353099:A100T	A	-	1	0	HLA-DRB1	32659936	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.035000	0.00084	-1.314000	0.02300	-0.517000	0.04412	GCG	T|0.683;C|0.317	0.683	strong		0.682	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204396830	204396830	+	Silent	SNP	G	G	A	rs17334387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204396830G>A	ENST00000367187.3	-	32	5089	c.4533C>T	c.(4531-4533)tcC>tcT	p.S1511S	PIK3C2B_ENST00000424712.2_Silent_p.S1483S|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1511					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|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)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGTAGGAGATGGACAGCTTCA	0.488													G|||	688	0.13738	0.2776	0.1023	5008	,	,		19457	0.0774		0.1113	False		,,,				2504	0.0613				p.S1511S		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4533T						PASS	.	G		1131,3275	405.1+/-333.4	142,847,1214	197.0	189.0	191.0		4533	2.2	1.0	1	dbSNP_123	191	741,7859	178.0+/-227.5	28,685,3587	no	coding-synonymous	PIK3C2B	NM_002646.3		170,1532,4801	AA,AG,GG		8.6163,25.6695,14.3934		1511/1635	204396830	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon32			GGAGATGGACAGC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4533C>T	1.37:g.204396830G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	37	0.366337	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.857;A|0.143	0.143	strong		0.488	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
GTF3C4	9329	hgsc.bcm.edu	37	9	135554566	135554566	+	Silent	SNP	G	G	A	rs371169	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135554566G>A	ENST00000372146.4	+	2	2124	c.1560G>A	c.(1558-1560)gaG>gaA	p.E520E	GTF3C4_ENST00000483873.2_3'UTR	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	520					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)	p.E520E(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		CCTTTGAAGAGGCAGCTGCTC	0.423													G|||	2568	0.51278	0.6498	0.4971	5008	,	,		19032	0.5714		0.4036	False		,,,				2504	0.3906				p.E520E	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											GTF3C4,colon,carcinoma,0,1	GTF3C4	53	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1560A						PASS	.	G		2680,1726	621.6+/-393.8	821,1038,344	75.0	84.0	81.0		1560	4.7	1.0	9	dbSNP_80	81	3325,5275	480.4+/-370.4	636,2053,1611	no	coding-synonymous	GTF3C4	NM_012204.2		1457,3091,1955	AA,AG,GG		38.6628,39.1739,46.171		520/823	135554566	6005,7001	2203	4300	6503	SO:0001819	synonymous_variant	9329	exon2			TGAAGAGGCAGCT	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""General transcription factors"""	4667	protein-coding gene	gene with protein product		604892	"""general transcription factor IIIC, polypeptide 4 (90kD)"""			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.1560G>A	9.37:g.135554566G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	173	63	0.364162	NM_012204	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																			G|0.531;A|0.469	0.469	strong		0.423	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1		
TRIM26	7726	hgsc.bcm.edu	37	6	30154049	30154049	+	Silent	SNP	G	G	A	rs16897204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30154049G>A	ENST00000454678.2	-	10	1660	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TRIM26_ENST00000437089.1_Silent_p.D408D|TRIM26_ENST00000453195.1_Silent_p.D408D	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	408	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						TTTCCCAGTCGTCATATCCAT	0.567													G|||	95	0.0189696	0.003	0.0216	5008	,	,		19480	0.002		0.0656	False		,,,				2504	0.0082				p.D408D		Atlas-SNP	.											.	TRIM26	74	.	0			c.C1224T						PASS	.	G	,	24,2996		0,24,1486	138.0	76.0	98.0		1224,1224	-10.1	0.0	6	dbSNP_123	98	278,5140		7,264,2438	yes	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	7,288,3924	AA,AG,GG		5.131,0.7947,3.579	,	408/540,408/540	30154049	302,8136	1510	2709	4219	SO:0001819	synonymous_variant	7726	exon9			CCAGTCGTCATAT	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.1224C>T	6.37:g.30154049G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			G|0.968;A|0.032	0.032	strong		0.567	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
HLA-C	3107	hgsc.bcm.edu	37	6	31238009	31238009	+	Silent	SNP	T	T	C	rs1131014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238009T>C	ENST00000376228.5	-	4	887	c.873A>G	c.(871-873)caA>caG	p.Q291Q	HLA-C_ENST00000383329.3_Silent_p.Q291Q	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						TGAGGGGCTCTTGCAGCCCCT	0.592													C|||	2561	0.511382	0.6172	0.549	5008	,	,		13431	0.5744		0.4404	False		,,,				2504	0.3497				p.Q291Q		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	0			c.A873G						scavenged	.						23.0	30.0	28.0					6																	31238009		2121	4194	6315	SO:0001819	synonymous_variant	3107	exon4			GGGCTCTTGCAGC	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.873A>G	6.37:g.31238009T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	36	35	0.972222	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	872	0.3992673992673993	230	0.46747967479674796	148	0.4088397790055249	255	0.4458041958041958	239	0.3153034300791557	.	0.019	-1.465537	0.01053	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.67	-5.33	0.02713	.	.	.	.	.	T	0.06005	0.0156	.	.	.	0.53005	P	3.799999999998249E-5	.	.	.	.	.	.	T	0.24154	-1.0168	3	.	.	.	.	2.6503	0.04996	0.1827:0.239:0.4507:0.1277	rs41551714	.	.	.	R	255	.	.	K	-	2	0	HLA-C	31345988	0.000000	0.05858	0.108000	0.21378	0.013000	0.08279	-3.876000	0.00344	-1.974000	0.00998	-0.711000	0.03637	AAG	T|0.651;C|0.349	0.349	strong		0.592	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
DNHD1	144132	hgsc.bcm.edu	37	11	6532519	6532519	+	Missense_Mutation	SNP	C	C	T	rs4758423	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6532519C>T	ENST00000527990.2	+	5	1252	c.1252C>T	c.(1252-1254)Cac>Tac	p.H418Y	DNHD1_ENST00000254579.6_Missense_Mutation_p.H418Y|DNHD1_ENST00000354685.3_Missense_Mutation_p.H418Y			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	418			H -> Y (in dbSNP:rs4758423).		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)		GCAGGAGCTACACTCTGTGTC	0.547													C|||	1104	0.220447	0.1377	0.3199	5008	,	,		19977	0.128		0.3549	False		,,,				2504	0.2188				p.H418Y		Atlas-SNP	.											DNHD1,NS,adenoma,0,2	DNHD1	198	2	0			c.C1252T						PASS	.	C	TYR/HIS,TYR/HIS	734,3668	300.1+/-286.2	59,616,1526	118.0	102.0	108.0		1252,1252	4.4	0.4	11	dbSNP_111	108	2831,5761	447.9+/-361.7	464,1903,1929	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	83,83	523,2519,3455	TT,TC,CC		32.9493,16.6742,27.4357	possibly-damaging,possibly-damaging	418/4754,418/598	6532519	3565,9429	2201	4296	6497	SO:0001583	missense	144132	exon6			GAGCTACACTCTG	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.1252C>T	11.37:g.6532519C>T	ENSP00000436180:p.His418Tyr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	533	0.24404761904761904	66	0.13414634146341464	120	0.3314917127071823	86	0.15034965034965034	261	0.34432717678100266	C	10.10	1.257615	0.22965	0.166742	0.329493	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.26957	1.7;2.7;1.7	5.32	4.41	0.53225	.	1.602800	0.03315	N	0.190977	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P;B	0.44521	0.837;0.168	B;B	0.34991	0.193;0.086	T	0.32640	-0.9899	9	0.31617	T	0.26	.	8.1675	0.31235	0.0:0.8193:0.0:0.1807	rs4758423;rs17244249;rs61213507;rs4758423	418;418	Q96M86;Q96M86-4	DNHD1_HUMAN;.	Y	418	ENSP00000254579:H418Y;ENSP00000346716:H418Y;ENSP00000436180:H418Y	ENSP00000254579:H418Y	H	+	1	0	DNHD1	6489095	0.000000	0.05858	0.406000	0.26421	0.327000	0.28475	0.136000	0.15974	1.372000	0.46190	0.655000	0.94253	CAC	C|0.748;T|0.252	0.252	strong		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
TMEM52B	120939	hgsc.bcm.edu	37	12	10339178	10339178	+	Silent	SNP	C	C	T	rs4764308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10339178C>T	ENST00000381923.2	+	5	701	c.297C>T	c.(295-297)agC>agT	p.S99S	TMEM52B_ENST00000298530.3_Silent_p.S79S|TMEM52B_ENST00000536952.1_Silent_p.S99S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	99						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTCTCCAGAGCACTATCACAT	0.507													C|||	67	0.0133786	0.0023	0.013	5008	,	,		14362	0.0		0.0477	False		,,,				2504	0.0072				p.S79S		Atlas-SNP	.											.	.	.	.	0			c.C237T						PASS	.	C		44,4362	47.5+/-82.1	1,42,2160	82.0	76.0	78.0		237	2.4	0.9	12	dbSNP_111	78	392,8208	125.8+/-184.4	15,362,3923	no	coding-synonymous	C12orf59	NM_153022.2		16,404,6083	TT,TC,CC		4.5581,0.9986,3.3523		79/164	10339178	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	120939	exon3			CCAGAGCACTATC	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.297C>T	12.37:g.10339178C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_153022	Q96NA7	Silent	SNP	ENST00000381923.2	37																																																																																				C|0.970;T|0.030	0.030	strong		0.507	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
KRT6C	286887	hgsc.bcm.edu	37	12	52865900	52865900	+	Silent	SNP	C	C	T	rs117030701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52865900C>T	ENST00000252250.6	-	2	752	c.705G>A	c.(703-705)ctG>ctA	p.L235L		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	235	Coil 1B.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		GCTCCGAGTCCAGGCGGCCCC	0.567													C|||	161	0.0321486	0.0023	0.0663	5008	,	,		17313	0.001		0.1054	False		,,,				2504	0.0051				p.L235L		Atlas-SNP	.											.	KRT6C	55	.	0			c.G705A						PASS	.	C		80,4326	68.1+/-105.8	1,78,2124	139.0	99.0	112.0		705	2.9	1.0	12	dbSNP_132	112	792,7808	185.0+/-232.9	42,708,3550	no	coding-synonymous	KRT6C	NM_173086.4		43,786,5674	TT,TC,CC		9.2093,1.8157,6.7046		235/565	52865900	872,12134	2203	4300	6503	SO:0001819	synonymous_variant	286887	exon2			CGAGTCCAGGCGG	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.705G>A	12.37:g.52865900C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	244	125	0.512295	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			C|0.940;T|0.060	0.060	strong		0.567	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343233	94343233	+	Silent	SNP	T	T	C	rs3789457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:94343233T>C	ENST00000436063.2	-	2	315	c.258A>G	c.(256-258)gaA>gaG	p.E86E	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CCTCAGAGGTTTCTCCATCCG	0.448													C|||	3802	0.759185	0.8094	0.8069	5008	,	,		20028	0.7857		0.662	False		,,,				2504	0.7301				p.E86E		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.A258G						PASS	.	C		3026,806		1184,658,74	110.0	105.0	106.0		258	-0.2	0.1	1	dbSNP_107	106	5732,2506		2002,1728,389	no	coding-synonymous	DNTTIP2	NM_014597.4		3186,2386,463	CC,CT,TT		30.42,21.0334,27.4399		86/757	94343233	8758,3312	1916	4119	6035	SO:0001819	synonymous_variant	30836	exon2			AGAGGTTTCTCCA	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.258A>G	1.37:g.94343233T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	49	0.392	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																			T|0.239;C|0.761	0.761	strong		0.448	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
SLC23A2	9962	hgsc.bcm.edu	37	20	4855309	4855309	+	Silent	SNP	G	G	A	rs41282100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Silent_p.Y172Y	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	286					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATTTCTGGCGTATTGAGAAA	0.368													A|||	32	0.00638978	0.0129	0.0101	5008	,	,		20889	0.0		0.008	False		,,,				2504	0.0				p.Y286Y		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C858T						PASS	.	A	,	55,4351	821.2+/-416.4	0,55,2148	119.0	122.0	121.0		858,858	3.7	1.0	20	dbSNP_127	121	107,8493	814.5+/-407.0	1,105,4194	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1,160,6342	AA,AG,GG		1.2442,1.2483,1.2456	,	286/651,286/651	4855309	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon10			TCTGGCGTATTGA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.858C>T	20.37:g.4855309G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	11	0.005036630036630037	3	0.006097560975609756	5	0.013812154696132596	0	0.0	3	0.00395778364116095	A	0.141	-1.102585	0.01828	0.012483	0.012442	ENSG00000089057	ENST00000423430	.	.	.	5.9	3.67	0.42095	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44772	-0.9306	4	.	.	.	-10.7793	8.3011	0.32014	0.7051:0.0:0.2949:0.0	rs41282100	.	.	.	C	43	.	.	R	-	1	0	SLC23A2	4803309	1.000000	0.71417	0.982000	0.44146	0.006000	0.05464	2.001000	0.40825	0.161000	0.19458	-0.982000	0.02568	CGC	G|0.990;A|0.010	0.010	strong		0.368	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
ZNF705A	440077	hgsc.bcm.edu	37	12	8329833	8329833	+	Missense_Mutation	SNP	G	G	A	rs11043758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:8329833G>A	ENST00000359286.4	+	5	646	c.557G>A	c.(556-558)cGc>cAc	p.R186H	FAM66C_ENST00000454799.2_RNA|FAM66C_ENST00000544214.1_RNA|FAM66C_ENST00000456135.2_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	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	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	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166912062	166912062	+	Silent	SNP	C	C	T	rs2230732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:166912062C>T	ENST00000265678.4	-	8	904	c.681G>A	c.(679-681)gcG>gcA	p.A227A	RPS6KA2_ENST00000481261.2_Silent_p.A138A|RPS6KA2_ENST00000405189.3_Silent_p.A138A|RPS6KA2_ENST00000503859.1_Silent_p.A235A|RPS6KA2_ENST00000366863.2_Silent_p.A73A|RPS6KA2_ENST00000510118.1_Silent_p.A252A	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	227	Protein kinase 1. {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)		CCACCTCGGGCGCCATGTACT	0.602													C|||	1029	0.205471	0.5356	0.1744	5008	,	,		21865	0.0179		0.0746	False		,,,				2504	0.1094				p.A235A		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.G705A						PASS	.	C	,	2040,2366	565.7+/-381.7	464,1112,627	179.0	116.0	137.0		705,681	-7.4	1.0	6	dbSNP_98	137	735,7865	178.0+/-227.5	42,651,3607	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	506,1763,4234	TT,TC,CC		8.5465,46.3005,21.3363	,	235/742,227/734	166912062	2775,10231	2203	4300	6503	SO:0001819	synonymous_variant	6196	exon9			CTCGGGCGCCATG	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.681G>A	6.37:g.166912062C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			C|0.805;T|0.194	0.194	strong		0.602	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
SLITRK6	84189	hgsc.bcm.edu	37	13	86370422	86370422	+	Silent	SNP	G	G	A	rs35342386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:86370422G>A	ENST00000400286.2	-	2	820	c.222C>T	c.(220-222)aaC>aaT	p.N74N		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	74					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		TCGTCAAGCCGTTATTTAATA	0.368													A|||	67	0.0133786	0.0318	0.0202	5008	,	,		20982	0.0		0.0099	False		,,,				2504	0.001				p.N74N		Atlas-SNP	.											.	SLITRK6	150	.	0			c.C222T						PASS	.	A		128,3710		2,124,1793	169.0	161.0	164.0		222	3.8	1.0	13	dbSNP_126	164	144,8096		1,142,3977	no	coding-synonymous	SLITRK6	NM_032229.2		3,266,5770	AA,AG,GG		1.7476,3.3351,2.252		74/842	86370422	272,11806	1919	4120	6039	SO:0001819	synonymous_variant	84189	exon2			CAAGCCGTTATTT	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.222C>T	13.37:g.86370422G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Silent	SNP	ENST00000400286.2	37	CCDS41903.1																																																																																			G|0.983;A|0.017	0.017	strong		0.368	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
UPF2	26019	hgsc.bcm.edu	37	10	12071397	12071397	+	Silent	SNP	G	G	A	rs11257490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12071397G>A	ENST00000356352.2	-	2	965	c.492C>T	c.(490-492)ctC>ctT	p.L164L	UPF2_ENST00000397053.2_Silent_p.L164L|UPF2_ENST00000357604.5_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	113	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	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		
C11orf21	29125	hgsc.bcm.edu	37	11	2323089	2323089	+	5'UTR	SNP	C	C	T	rs188839109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2323089C>T	ENST00000381153.3	-	0	201				C11orf21_ENST00000470369.1_5'UTR|TSPAN32_ENST00000182290.4_5'Flank|TSPAN32_ENST00000451520.2_5'Flank|TSPAN32_ENST00000381121.3_5'Flank			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21							cytoplasm (GO:0005737)											AGAACGAGGCCATGTCTTCCT	0.652											OREG0003773	type=REGULATORY REGION|Gene=TSPAN32|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	28	0.00559105	0.0008	0.0101	5008	,	,		16840	0.0		0.0159	False		,,,				2504	0.0041				p.M1I		Atlas-SNP	.											.	C11orf21	11	.	0			c.G3A						PASS	.	C	ILE/MET	3,1381		0,3,689	62.0	64.0	64.0		3	1.4	0.0	11		64	43,3139		1,41,1549	yes	missense	C11orf21	NM_001142946.1	10	1,44,2238	TT,TC,CC		1.3514,0.2168,1.0074	benign	1/179	2323089	46,4520	692	1591	2283	SO:0001623	5_prime_UTR_variant	29125	exon1			CGAGGCCATGTCT	AB029488	CCDS44518.1	11p15.5	2012-08-09			ENSG00000110665	ENSG00000110665			13231	protein-coding gene	gene with protein product		611033				11054561	Standard	NM_001142946		Approved		uc009ydj.2	Q9P2W6	OTTHUMG00000009759	ENST00000381153.3:c.-51G>A	11.37:g.2323089C>T		Somatic	48	0	0	602	WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_001142946		Missense_Mutation	SNP	ENST00000381153.3	37		15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	C	5.850	0.341111	0.11069	0.002168	0.013514	ENSG00000110665	ENST00000456145	.	.	.	1.41	1.41	0.22369	.	.	.	.	.	T	0.27798	0.0684	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	7	0.87932	D	0	.	6.4156	0.21715	0.0:1.0:0.0:0.0	.	1	E9PAM5	.	I	1	.	ENSP00000406541:M1I	M	-	3	0	C11orf21	2279665	0.000000	0.05858	0.008000	0.14137	0.013000	0.08279	-0.053000	0.11846	1.158000	0.42547	0.388000	0.25769	ATG	C|0.993;T|0.007	0.007	strong		0.652	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259997	71259997	+	Missense_Mutation	SNP	G	G	T	rs61746411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:71259997G>T	ENST00000528743.2	+	1	532	c.294G>T	c.(292-294)caG>caT	p.Q98H		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	98	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CCTGCTGCCAGTGCAGCTGCT	0.622													N|||	108	0.0215655	0.003	0.0259	5008	,	,		19915	0.0		0.0676	False		,,,				2504	0.0184				p.Q98H		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.G294T						PASS	.	G	HIS/GLN	65,4335		0,65,2135	109.0	123.0	118.0		294	2.3	1.0	11	dbSNP_129	118	620,7966		22,576,3695	no	missense	KRTAP5-9	NM_005553.3	24	22,641,5830	TT,TG,GG		7.2211,1.4773,5.2749	possibly-damaging	98/170	71259997	685,12301	2200	4293	6493	SO:0001583	missense	3846	exon1			CTGCCAGTGCAGC	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.294G>T	11.37:g.71259997G>T	ENSP00000431443:p.Gln98His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	75	0.034340659340659344	3	0.006097560975609756	13	0.03591160220994475	0	0.0	59	0.07783641160949868	N	7.751	0.703418	0.15172	0.014773	0.072211	ENSG00000254997	ENST00000528743	T	0.03717	3.83	2.26	2.26	0.28386	.	.	.	.	.	T	0.00552	0.0018	M	0.88181	2.935	0.23036	N	0.998392	P	0.50272	0.933	P	0.50082	0.63	T	0.10177	-1.0641	9	0.48119	T	0.1	.	6.6302	0.22853	0.0:0.0:0.7164:0.2836	rs61746411	98	P26371	KRA59_HUMAN	H	98	ENSP00000431443:Q98H	ENSP00000431443:Q98H	Q	+	3	2	KRTAP5-9	70937645	0.001000	0.12720	0.998000	0.56505	0.722000	0.41435	0.113000	0.15499	1.189000	0.43028	0.442000	0.29010	CAG	G|0.959;T|0.041	0.041	strong		0.622	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
BANP	54971	hgsc.bcm.edu	37	16	88017809	88017809	+	Silent	SNP	C	C	T	rs3815820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88017809C>T	ENST00000393207.1	+	4	503	c.282C>T	c.(280-282)gtC>gtT	p.V94V	BANP_ENST00000393208.2_Silent_p.V102V|BANP_ENST00000355022.4_Silent_p.V102V|BANP_ENST00000355163.5_Silent_p.V108V|BANP_ENST00000479780.2_Silent_p.V102V|BANP_ENST00000286122.7_Silent_p.V94V|BANP_ENST00000538234.1_Silent_p.V102V	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	94					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CCATCCAGGTCCCCATGGTGG	0.562													T|||	2941	0.58726	0.7496	0.7017	5008	,	,		19107	0.5218		0.6133	False		,,,				2504	0.3272				p.V108V		Atlas-SNP	.											.	BANP	67	.	0			c.C324T						PASS	.						18.0	17.0	17.0					16																	88017809		2197	4299	6496	SO:0001819	synonymous_variant	54971	exon4			CCAGGTCCCCATG	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.282C>T	16.37:g.88017809C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_001173540	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.376;T|0.624	0.624	strong		0.562	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
FAT1	2195	hgsc.bcm.edu	37	4	187549428	187549428	+	Missense_Mutation	SNP	C	C	T	rs2304867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187549428C>T	ENST00000441802.2	-	9	4899	c.4690G>A	c.(4690-4692)Gct>Act	p.A1564T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1564	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in dbSNP:rs2304867).		actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAGGAGGAAGCGGTGAACCAC	0.502										HNSCC(5;0.00058)			C|||	346	0.0690895	0.003	0.1499	5008	,	,		18441	0.1825		0.0338	False		,,,				2504	0.0204				p.A1564T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,colon,carcinoma,0,2	FAT1	500	2	0			c.G4690A						PASS	.	C	THR/ALA	41,4153		0,41,2056	51.0	54.0	53.0		4690	3.1	1.0	4	dbSNP_100	53	255,8217		4,247,3985	yes	missense	FAT1	NM_005245.3	58	4,288,6041	TT,TC,CC		3.0099,0.9776,2.337	benign	1564/4589	187549428	296,12370	2097	4236	6333	SO:0001583	missense	2195	exon9			AGGAAGCGGTGAA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4690G>A	4.37:g.187549428C>T	ENSP00000406229:p.Ala1564Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	191	0.08745421245421245	3	0.006097560975609756	40	0.11049723756906077	117	0.20454545454545456	31	0.040897097625329816	C	14.75	2.629927	0.46944	0.009776	0.030099	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01821	4.62	5.49	3.09	0.35607	Cadherin (2);Cadherin-like (1);	0.170756	0.64402	D	0.000004	T	0.00012	0.0000	L	0.31371	0.925	0.32901	P	0.48679300000000003	B	0.26547	0.152	B	0.18561	0.022	T	0.50558	-0.8814	9	0.22109	T	0.4	.	7.3645	0.26766	0.1287:0.0695:0.0:0.8018	rs2304867;rs17692527;rs52820211;rs61327668;rs2304867	1564	Q14517	FAT1_HUMAN	T	1564;1563	ENSP00000406229:A1564T	ENSP00000260147:A1563T	A	-	1	0	FAT1	187786422	0.993000	0.37304	0.998000	0.56505	0.760000	0.43138	2.569000	0.45973	0.530000	0.28619	-1.093000	0.02169	GCT	C|0.922;T|0.078	0.078	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
IL18	3606	hgsc.bcm.edu	37	11	112014328	112014328	+	Silent	SNP	G	G	A	rs5744290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:112014328G>A	ENST00000280357.7	-	6	792	c.573C>T	c.(571-573)aaC>aaT	p.N191N	IL18_ENST00000533858.1_5'Flank|IL18_ENST00000524595.1_Silent_p.N187N|SDHD_ENST00000532699.1_Intron|IL18_ENST00000528832.1_Silent_p.N191N	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	191				N -> S (in Ref. 3; AAC27787). {ECO:0000305}.	angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-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;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		GCTAGTCTTCGTTTTGAACAG	0.448													g|||	21	0.00419329	0.0008	0.0058	5008	,	,		16933	0.001		0.0119	False		,,,				2504	0.0031				p.N191N		Atlas-SNP	.											.	IL18	10	.	0			c.C573T						PASS	.	A		12,3632		0,12,1810	42.0	38.0	39.0		573	-3.0	0.0	11	dbSNP_114	39	173,7981		2,169,3906	no	coding-synonymous	IL18	NM_001562.3		2,181,5716	AA,AG,GG		2.1217,0.3293,1.5681		191/194	112014328	185,11613	1822	4077	5899	SO:0001819	synonymous_variant	3606	exon6			GTCTTCGTTTTGA	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"""Interleukins and interleukin receptors"""	5986	protein-coding gene	gene with protein product	"""interferon-gamma-inducing factor"""	600953	"""interleukin 18 (interferon-gamma-inducing factor)"""			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.573C>T	11.37:g.112014328G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001562	O75599|Q6FGY3|Q6WWJ7	Silent	SNP	ENST00000280357.7	37	CCDS44731.1																																																																																			G|0.993;A|0.007	0.007	strong		0.448	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802768	31802768	+	Missense_Mutation	SNP	G	G	A	rs2226548	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:31802768G>A	ENST00000334068.2	+	1	197	c.175G>A	c.(175-177)Gcc>Acc	p.A59T		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	59	4 X 10 AA approximate repeats.		A -> T (in dbSNP:rs2226548). {ECO:0000269|PubMed:15489334}.			intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CTGGGAGCCCGCCAGCTGCCA	0.622													-|||	2760	0.551118	0.6452	0.6427	5008	,	,		17651	0.2758		0.5736	False		,,,				2504	0.6196				p.A59T	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.G175A						PASS	.	A	THR/ALA	2801,1605		880,1041,282	59.0	59.0	59.0		175	-2.5	0.0	21	dbSNP_96	59	5047,3553		1483,2081,736	yes	missense	KRTAP13-4	NM_181600.1	58	2363,3122,1018	AA,AG,GG		41.314,36.4276,39.6586	benign	59/161	31802768	7848,5158	2203	4300	6503	SO:0001583	missense	284827	exon1			GAGCCCGCCAGCT	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"""Keratin associated proteins"""	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.175G>A	21.37:g.31802768G>A	ENSP00000334834:p.Ala59Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	1146	0.5247252747252747	325	0.6605691056910569	234	0.6464088397790055	167	0.291958041958042	420	0.554089709762533	-	0.010	-1.772617	0.00640	0.635724	0.58686	ENSG00000186971	ENST00000334068	T	0.02498	4.27	4.95	-2.5	0.06384	.	1.375280	0.05046	N	0.477219	T	0.00012	0.0000	N	0.00056	-2.365	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47736	-0.9094	9	0.02654	T	1	.	0.6398	0.00809	0.4482:0.1285:0.1727:0.2506	rs2226548	59	Q3LI77	KR134_HUMAN	T	59	ENSP00000334834:A59T	ENSP00000334834:A59T	A	+	1	0	KRTAP13-4	30724639	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.656000	0.05342	-0.445000	0.07159	-0.988000	0.02552	GCC	G|0.411;A|0.589	0.589	strong		0.622	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
SDCBP2	27111	hgsc.bcm.edu	37	20	1301053	1301053	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1301053G>A	ENST00000360779.3	-	2	181	c.8C>T	c.(7-9)tCc>tTc	p.S3F	SDCBP2_ENST00000339987.3_Missense_Mutation_p.S3F|SDCBP2_ENST00000381812.1_Missense_Mutation_p.S3F	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	3					intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						TGGGTACAGGGATGACATGGC	0.552																																					p.S3F		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C8T						PASS	.						142.0	138.0	139.0					20																	1301053		1976	4166	6142	SO:0001583	missense	27111	exon2			TACAGGGATGACA	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.8C>T	20.37:g.1301053G>A	ENSP00000354013:p.Ser3Phe	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	22	0.247191	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434411	0.25813	.	.	ENSG00000125775	ENST00000381812;ENST00000360779;ENST00000339987	T;T;T	0.44881	0.91;0.91;0.91	4.83	0.43	0.16515	.	1.007080	0.07972	N	0.984107	T	0.54711	0.1875	L	0.55481	1.735	0.23204	N	0.998129	P;D	0.67145	0.911;0.996	B;D	0.63033	0.382;0.91	T	0.47156	-0.9139	10	0.87932	D	0	-5.793	9.2402	0.37491	0.3788:0.0:0.6212:0.0	.	3;3	B4DKI5;Q9H190	.;SDCB2_HUMAN	F	3	ENSP00000371233:S3F;ENSP00000354013:S3F;ENSP00000342935:S3F	ENSP00000342935:S3F	S	-	2	0	SDCBP2	1249053	0.635000	0.27199	0.232000	0.24009	0.011000	0.07611	3.304000	0.51866	0.243000	0.21327	-0.258000	0.10820	TCC	.	.	none		0.552	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
WDR36	134430	hgsc.bcm.edu	37	5	110456263	110456263	+	Silent	SNP	C	C	G	rs17624563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:110456263C>G	ENST00000513710.2	+	18	2146	c.2142C>G	c.(2140-2142)gtC>gtG	p.V714V	WDR36_ENST00000506538.2_Silent_p.V714V			Q8NI36	WDR36_HUMAN	WD repeat domain 36	714					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTTCAATAGTCATGCTTCCTG	0.333													C|||	658	0.13139	0.1452	0.0533	5008	,	,		16656	0.0685		0.1103	False		,,,				2504	0.2546				p.V714V		Atlas-SNP	.											.	WDR36	111	.	0			c.C2142G						PASS	.	C		524,3880	239.0+/-250.2	36,452,1714	146.0	143.0	144.0		2142	-0.1	1.0	5	dbSNP_123	144	800,7800	186.0+/-233.6	39,722,3539	no	coding-synonymous	WDR36	NM_139281.2		75,1174,5253	GG,GC,CC		9.3023,11.8983,10.1815		714/952	110456263	1324,11680	2202	4300	6502	SO:0001819	synonymous_variant	134430	exon18			AATAGTCATGCTT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.2142C>G	5.37:g.110456263C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																			C|0.897;G|0.103	0.103	strong		0.333	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
LYZL6	57151	hgsc.bcm.edu	37	17	34264862	34264862	+	Silent	SNP	T	T	C	rs1052266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:34264862T>C	ENST00000585556.1	-	3	532	c.198A>G	c.(196-198)gcA>gcG	p.A66A	LYZL6_ENST00000394523.3_Silent_p.A66A|LYZL6_ENST00000492340.2_5'UTR|LYZL6_ENST00000293274.4_Silent_p.A66A			O75951	LYZL6_HUMAN	lysozyme-like 6	66					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGCTTCCATCTGCATTTTCAT	0.443													T|||	435	0.086861	0.0053	0.1513	5008	,	,		23468	0.1637		0.0875	False		,,,				2504	0.0716				p.A66A		Atlas-SNP	.											.	LYZL6	18	.	0			c.A198G						PASS	.	T	,	87,4319	73.1+/-111.1	0,87,2116	101.0	100.0	100.0		198,198	1.5	0.0	17	dbSNP_86	100	745,7855	179.3+/-228.5	36,673,3591	no	coding-synonymous,coding-synonymous	LYZL6	NM_001199951.1,NM_020426.2	,	36,760,5707	CC,CT,TT		8.6628,1.9746,6.397	,	66/149,66/149	34264862	832,12174	2203	4300	6503	SO:0001819	synonymous_variant	57151	exon2			TCCATCTGCATTT	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.198A>G	17.37:g.34264862T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	73	0.561538	NM_020426	Q6UW30	Silent	SNP	ENST00000585556.1	37	CCDS11302.1																																																																																			T|0.923;C|0.077	0.077	strong		0.443	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426	
BZRAP1	9256	hgsc.bcm.edu	37	17	56383744	56383744	+	Missense_Mutation	SNP	T	T	C	rs11079346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56383744T>C	ENST00000343736.4	-	26	5346	c.5183A>G	c.(5182-5184)cAc>cGc	p.H1728R	BZRAP1_ENST00000355701.3_Missense_Mutation_p.H1728R|BZRAP1_ENST00000268893.6_Missense_Mutation_p.H1668R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1728			H -> R (in dbSNP:rs11079346). {ECO:0000269|PubMed:9734811}.			cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCCAGTTGTGTGGGCTGTGGA	0.597													C|||	1454	0.290335	0.3533	0.2709	5008	,	,		15017	0.249		0.3161	False		,,,				2504	0.2352				p.H1728R		Atlas-SNP	.											.	BZRAP1	287	.	0			c.A5183G						PASS	.	C	ARG/HIS,ARG/HIS	1477,2895		256,965,965	59.0	53.0	55.0		5183,5003	-6.6	0.0	17	dbSNP_120	55	2345,6149		352,1641,2254	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	29,29	608,2606,3219	CC,CT,TT		27.6077,33.7832,29.7062	benign,benign	1728/1858,1668/1798	56383744	3822,9044	2186	4247	6433	SO:0001583	missense	9256	exon26			GTTGTGTGGGCTG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.5183A>G	17.37:g.56383744T>C	ENSP00000345824:p.His1728Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	650	0.2976190476190476	168	0.34146341463414637	110	0.30386740331491713	142	0.24825174825174826	230	0.3034300791556728	C	2.707	-0.269685	0.05716	0.337832	0.276077	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.03831	3.8;3.79;3.8	5.71	-6.59	0.01830	.	0.398534	0.28026	N	0.016885	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.0	T	0.43782	-0.9370	9	0.12766	T	0.61	.	11.3801	0.49752	0.0:0.3607:0.084:0.5552	rs11079346;rs61579152;rs11079346	1719;1668;1728	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	R	1728;1728;1668	ENSP00000347929:H1728R;ENSP00000345824:H1728R;ENSP00000268893:H1668R	ENSP00000268893:H1668R	H	-	2	0	BZRAP1	53738743	0.014000	0.17966	0.002000	0.10522	0.144000	0.21451	-0.628000	0.05515	-1.538000	0.01734	-0.735000	0.03563	CAC	T|0.694;C|0.306	0.306	strong		0.597	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
USP4	7375	hgsc.bcm.edu	37	3	49362369	49362369	+	Silent	SNP	C	C	T	rs56038006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000351842.4_Silent_p.K197K|USP4_ENST00000416417.1_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	194	0	0		WXS	Illumina HiSeq	Phase_I	250	134	0.536	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	
MYO19	80179	hgsc.bcm.edu	37	17	34854121	34854121	+	Missense_Mutation	SNP	C	C	T	rs139565052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:34854121C>T	ENST00000431794.3	-	25	3268	c.2746G>A	c.(2746-2748)Gcg>Acg	p.A916T	ZNHIT3_ENST00000588253.1_3'UTR|ZNHIT3_ENST00000590858.1_3'UTR|MYO19_ENST00000268852.9_Missense_Mutation_p.A716T	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	916	Mitochondrial targeting.					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)		TGAGGCAGCGCTCGGATGGAC	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17680	0.0		0.002	False		,,,				2504	0.0				p.A916T		Atlas-SNP	.											.	MYO19	130	.	0			c.G2746A						PASS	.	C	THR/ALA,THR/ALA	1,4313		0,1,2156	74.0	76.0	75.0		2746,2146	5.9	1.0	17	dbSNP_134	75	18,8512		0,18,4247	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	58,58	0,19,6403	TT,TC,CC		0.211,0.0232,0.1479	probably-damaging,probably-damaging	916/971,716/771	34854121	19,12825	2157	4265	6422	SO:0001583	missense	80179	exon26			GCAGCGCTCGGAT	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.2746G>A	17.37:g.34854121C>T	ENSP00000409936:p.Ala916Thr	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	27.1	4.800048	0.90538	2.32E-4	0.00211	ENSG00000141140	ENST00000415126;ENST00000431794;ENST00000268852	T;T	0.74002	-0.8;-0.8	5.91	5.91	0.95273	.	0.000000	0.42294	D	0.000730	D	0.85353	0.5677	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.85959	0.1469	10	0.87932	D	0	.	17.0716	0.86576	0.0:1.0:0.0:0.0	.	916;716	Q96H55;Q96H55-4	MYO19_HUMAN;.	T	374;916;716	ENSP00000409936:A916T;ENSP00000268852:A716T	ENSP00000268852:A716T	A	-	1	0	MYO19	31928234	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	4.579000	0.60936	2.821000	0.97095	0.485000	0.47835	GCG	C|0.999;T|0.001	0.001	strong		0.572	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
IFNAR2	3455	hgsc.bcm.edu	37	21	34614255	34614255	+	Missense_Mutation	SNP	T	T	G	rs1051393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34614255T>G	ENST00000342136.4	+	2	354	c.28T>G	c.(28-30)Ttc>Gtc	p.F10V	IFNAR2_ENST00000342101.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000404220.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000382264.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000382241.3_Missense_Mutation_p.F10V|IFNAR2_ENST00000420068.1_3'UTR|IFNAR2_ENST00000413881.1_Intron			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	10			F -> V (in dbSNP:rs1051393). {ECO:0000269|PubMed:16757563, ECO:0000269|PubMed:7759950, ECO:0000269|PubMed:8181059, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|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)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	TGCCTTCATCTTCAGATCACT	0.393													G|||	1962	0.391773	0.171	0.4481	5008	,	,		20781	0.5754		0.333	False		,,,				2504	0.5215				p.F10V		Atlas-SNP	.											.	IFNAR2	44	.	0			c.T28G	GRCh37	CM057711	IFNAR2	M	rs1051393	PASS	.	G	VAL/PHE,VAL/PHE,VAL/PHE	828,3578	747.1+/-411.8	86,656,1461	191.0	170.0	177.0		28,28,28	-7.2	0.0	21	dbSNP_86	177	2726,5874	681.0+/-403.7	408,1910,1982	yes	missense,missense,missense	IFNAR2	NM_000874.3,NM_207584.1,NM_207585.1	50,50,50	494,2566,3443	GG,GT,TT		31.6977,18.7926,27.3258	benign,benign,benign	10/332,10/332,10/516	34614255	3554,9452	2203	4300	6503	SO:0001583	missense	3455	exon2			TTCATCTTCAGAT		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"""Interferons"""	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.28T>G	21.37:g.34614255T>G	ENSP00000343957:p.Phe10Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_207585	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Missense_Mutation	SNP	ENST00000342136.4	37	CCDS13621.1	835	0.3823260073260073	82	0.16666666666666666	158	0.43646408839779005	342	0.5979020979020979	253	0.3337730870712401	G	5.665	0.307370	0.10733	0.187926	0.316977	ENSG00000159110	ENST00000382264;ENST00000404220;ENST00000382241;ENST00000342136;ENST00000342101;ENST00000447980	T;T;T;T;T;T	0.26810	2.14;2.14;2.19;2.19;2.18;1.71	4.51	-7.2	0.01495	.	1.247330	0.05490	N	0.556450	T	0.00012	0.0000	N	0.00707	-1.245	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	0.38436	-0.9661	9	0.02654	T	1	.	6.9718	0.24652	0.2442:0.0:0.513:0.2429	rs1051393;rs2229208;rs3191789;rs4986955;rs7279064;rs17413985;rs17856075;rs17860177;rs52819787;rs7279064	10;10;10	P48551-3;P48551;P48551-2	.;INAR2_HUMAN;.	V	10;10;10;10;10;34	ENSP00000371699:F10V;ENSP00000384309:F10V;ENSP00000371676:F10V;ENSP00000343957:F10V;ENSP00000343289:F10V;ENSP00000402311:F34V	ENSP00000343289:F10V	F	+	1	0	IFNAR2	33536125	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.080000	0.01368	-1.939000	0.01044	-1.389000	0.01157	TTC	A|0.000;G|0.315;T|0.685	0.315	strong		0.393	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1		
DBR1	51163	hgsc.bcm.edu	37	3	137880743	137880743	+	Silent	SNP	G	G	A	rs376362448|rs2622736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137880743G>A	ENST00000260803.4	-	8	1776	c.1623C>T	c.(1621-1623)gaC>gaT	p.D541D	DBR1_ENST00000505015.2_Silent_p.D307D	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	541					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						AAGCTGCATCGTCATCATCAT	0.393													A|||	2921	0.583267	0.4584	0.7017	5008	,	,		23029	0.5526		0.6809	False		,,,				2504	0.5992				p.D541D		Atlas-SNP	.											.	DBR1	45	.	0			c.C1623T						PASS	.	A		2159,2247	593.8+/-388.1	525,1109,569	206.0	180.0	189.0		1623	-6.2	0.0	3	dbSNP_100	189	5918,2682	430.1+/-356.4	2027,1864,409	no	coding-synonymous	DBR1	NM_016216.3		2552,2973,978	AA,AG,GG		31.186,49.0014,37.8979		541/545	137880743	8077,4929	2203	4300	6503	SO:0001819	synonymous_variant	51163	exon8			TGCATCGTCATCA	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"""debranching enzyme (S. Cerevisiae) homolog 1"", ""debranching enzyme homolog 1 (S. cerevisiae)"""			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.1623C>T	3.37:g.137880743G>A		Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	347	346	0.997118	NM_016216	Q96GH0|Q9NXQ6	Silent	SNP	ENST00000260803.4	37	CCDS33863.1																																																																																			G|0.392;A|0.608	0.608	strong		0.393	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1		
ZNF112	7771	hgsc.bcm.edu	37	19	44832693	44832693	+	Silent	SNP	T	T	C	rs61733037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44832693T>C	ENST00000337401.4	-	5	1723	c.1635A>G	c.(1633-1635)agA>agG	p.R545R	ZNF112_ENST00000354340.4_Silent_p.R539R|ZNF112_ENST00000536500.1_Silent_p.R562R	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	545					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CTGTGTGGACTCTCTGATGAA	0.418													T|||	368	0.0734824	0.1467	0.0216	5008	,	,		22299	0.002		0.0706	False		,,,				2504	0.0879				p.R545R		Atlas-SNP	.											ZFP112_ENST00000337401,colon,carcinoma,-2,2	ZFP112	219	2	0			c.A1635G						PASS	.	T	,	552,3854	250.0+/-257.2	36,480,1687	133.0	136.0	135.0		1635,1617	-0.2	1.0	19	dbSNP_129	135	426,8174	132.2+/-189.8	12,402,3886	no	coding-synonymous,coding-synonymous	ZFP112	NM_001083335.1,NM_013380.3	,	48,882,5573	CC,CT,TT		4.9535,12.5284,7.5196	,	545/914,539/908	44832693	978,12028	2203	4300	6503	SO:0001819	synonymous_variant	7771	exon5			GTGGACTCTCTGA	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"""Zinc fingers, C2H2-type"""	12892	protein-coding gene	gene with protein product		603994	"""zinc finger protein 112 homolog (mouse)"", ""zinc finger protein 228"""	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1635A>G	19.37:g.44832693T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001083335	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																			T|0.931;C|0.069	0.069	strong		0.418	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
PPM1F	9647	hgsc.bcm.edu	37	22	22287862	22287862	+	Silent	SNP	G	G	A	rs2027789	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:22287862G>A	ENST00000263212.5	-	5	753	c.648C>T	c.(646-648)aaC>aaT	p.N216N	PPM1F_ENST00000407142.1_Silent_p.N48N|PPM1F_ENST00000397495.4_Silent_p.N216N|PPM1F_ENST00000538191.1_Silent_p.N112N	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	216					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GGCGGGCAGCGTTGGTGTGCA	0.632													G|||	1237	0.247005	0.2874	0.2939	5008	,	,		17553	0.0863		0.4006	False		,,,				2504	0.1667				p.N216N		Atlas-SNP	.											.	PPM1F	34	.	0			c.C648T						PASS	.	G		1232,3174	425.1+/-340.7	161,910,1132	69.0	59.0	63.0		648	-8.1	0.0	22	dbSNP_94	63	3386,5214	501.0+/-375.3	671,2044,1585	no	coding-synonymous	PPM1F	NM_014634.3		832,2954,2717	AA,AG,GG		39.3721,27.9619,35.5067		216/455	22287862	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	9647	exon5			GGCAGCGTTGGTG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.648C>T	22.37:g.22287862G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Silent	SNP	ENST00000263212.5	37	CCDS13796.1																																																																																			G|0.665;A|0.335	0.335	strong		0.632	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
SH3RF1	57630	hgsc.bcm.edu	37	4	170077789	170077789	+	Silent	SNP	A	A	G	rs10518039	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:170077789A>G	ENST00000284637.9	-	3	776	c.435T>C	c.(433-435)taT>taC	p.Y145Y	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	145	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.Y145Y(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		CTTTTCCTTCATAGTTGTATA	0.353													G|||	1357	0.270966	0.3979	0.2017	5008	,	,		19172	0.0942		0.3131	False		,,,				2504	0.2873				p.Y145Y		Atlas-SNP	.											SH3RF1,NS,carcinoma,0,1	SH3RF1	60	1	1	Substitution - coding silent(1)	stomach(1)	c.T435C						PASS	.	G		1769,2637	645.1+/-398.1	353,1063,787	117.0	122.0	120.0		435	-1.8	1.0	4	dbSNP_119	120	2624,5976	687.5+/-404.2	396,1832,2072	no	coding-synonymous	SH3RF1	NM_020870.3		749,2895,2859	GG,GA,AA		30.5116,40.1498,33.7767		145/889	170077789	4393,8613	2203	4300	6503	SO:0001819	synonymous_variant	57630	exon3			TCCTTCATAGTTG	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"""RING-type (C3HC4) zinc fingers"""	17650	protein-coding gene	gene with protein product	"""plenty of SH3 domains"""		"""SH3 multiple domains 2"""	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.435T>C	4.37:g.170077789A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	37	CCDS34099.1																																																																																			A|0.681;G|0.319	0.319	strong		0.353	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	
FCGBP	8857	hgsc.bcm.edu	37	19	40368619	40368619	+	Silent	SNP	G	G	A	rs150027077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40368619G>A	ENST00000221347.6	-	28	12736	c.12729C>T	c.(12727-12729)ggC>ggT	p.G4243G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4243	VWFD 10. {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)			GCCAGCTGCCGCCCCAGATGG	0.647																																					p.G4243G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.C12729T						scavenged	.						12.0	15.0	14.0					19																	40368619		2182	4225	6407	SO:0001819	synonymous_variant	8857	exon28			GCTGCCGCCCCAG	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.12729C>T	19.37:g.40368619G>A		Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	326	41	0.125767	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.932;A|0.068	0.068	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SCARA5	286133	hgsc.bcm.edu	37	8	27737180	27737180	+	Silent	SNP	G	G	A	rs6983356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:27737180G>A	ENST00000354914.3	-	8	1742	c.1257C>T	c.(1255-1257)gaC>gaT	p.D419D	SCARA5_ENST00000380385.2_Silent_p.D194D	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	419	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)		CCCAGCCGTCGTCACACACGG	0.657													G|||	657	0.13119	0.3313	0.0562	5008	,	,		17161	0.0		0.0805	False		,,,				2504	0.1012				p.D419D		Atlas-SNP	.											.	SCARA5	53	.	0			c.C1257T						PASS	.	G		1216,3190	425.7+/-340.9	164,888,1151	124.0	99.0	107.0		1257	-4.4	0.9	8	dbSNP_116	107	822,7778	189.4+/-236.2	36,750,3514	no	coding-synonymous	SCARA5	NM_173833.5		200,1638,4665	AA,AG,GG		9.5581,27.5987,15.6697		419/496	27737180	2038,10968	2203	4300	6503	SO:0001819	synonymous_variant	286133	exon8			GCCGTCGTCACAC	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.1257C>T	8.37:g.27737180G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Silent	SNP	ENST00000354914.3	37	CCDS6064.1																																																																																			G|0.852;A|0.148	0.148	strong		0.657	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
SEMA3G	56920	hgsc.bcm.edu	37	3	52476899	52476899	+	Missense_Mutation	SNP	G	G	A	rs138988057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52476899G>A	ENST00000231721.2	-	2	139	c.140C>T	c.(139-141)gCc>gTc	p.A47V		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	47	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)		CAGAAAGATGGCAGAGCGGTT	0.617													G|||	10	0.00199681	0.0	0.0	5008	,	,		19476	0.0		0.0099	False		,,,				2504	0.0				p.A47V		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C140T						PASS	.	G	VAL/ALA	0,4404		0,0,2202	54.0	55.0	54.0		140	4.1	1.0	3	dbSNP_134	54	23,8575		0,23,4276	yes	missense	SEMA3G	NM_020163.1	64	0,23,6478	AA,AG,GG		0.2675,0.0,0.1769	benign	47/783	52476899	23,12979	2202	4299	6501	SO:0001583	missense	56920	exon2			AAGATGGCAGAGC		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.140C>T	3.37:g.52476899G>A	ENSP00000231721:p.Ala47Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	94	57	0.606383	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	7.761	0.705426	0.15172	0.0	0.002675	ENSG00000010319	ENST00000231721;ENST00000475739	T;T	0.20069	2.1;2.1	4.93	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.142087	0.47852	D	0.000201	T	0.06371	0.0164	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.30475	-0.9977	10	0.13853	T	0.58	.	5.736	0.18067	0.2264:0.0:0.7736:0.0	.	47	Q9NS98	SEM3G_HUMAN	V	47;65	ENSP00000231721:A47V;ENSP00000419181:A65V	ENSP00000231721:A47V	A	-	2	0	SEMA3G	52451939	0.000000	0.05858	0.962000	0.40283	0.733000	0.41908	0.733000	0.26087	2.302000	0.77476	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.617	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
ATP9A	10079	hgsc.bcm.edu	37	20	50287736	50287736	+	Silent	SNP	C	C	T	rs2255341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50287736C>T	ENST00000338821.5	-	12	1362	c.1098G>A	c.(1096-1098)tcG>tcA	p.S366S	ATP9A_ENST00000402822.1_Silent_p.S245S|ATP9A_ENST00000311637.5_Silent_p.S230S	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	82	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	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	
SULT1C3	442038	hgsc.bcm.edu	37	2	108875198	108875198	+	Missense_Mutation	SNP	G	G	A	rs2219078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:108875198G>A	ENST00000329106.2	+	5	535	c.535G>A	c.(535-537)Ggg>Agg	p.G179R	SULT1C3_ENST00000376700.1_Missense_Mutation_p.G179R	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3	179			G -> R (in dbSNP:rs2219078).		sulfur compound metabolic process (GO:0006790)	cytoplasm (GO:0005737)	alcohol sulfotransferase activity (GO:0004027)|aryl sulfotransferase activity (GO:0004062)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						AGTTGTTGGCGGGTCCTGGTT	0.448													.|||	1752	0.34984	0.3064	0.3876	5008	,	,		17900	0.6766		0.1918	False		,,,				2504	0.2076				p.G179R		Atlas-SNP	.											.	SULT1C3	53	.	0			c.G535A						PASS	.	G	ARG/GLY	1295,3111	438.0+/-345.2	206,883,1114	122.0	131.0	128.0		535	2.2	0.4	2	dbSNP_96	128	1660,6940	307.2+/-308.3	155,1350,2795	yes	missense	SULT1C3	NM_001008743.1	125	361,2233,3909	AA,AG,GG		19.3023,29.3917,22.7203	probably-damaging	179/305	108875198	2955,10051	2203	4300	6503	SO:0001583	missense	442038	exon5			GTTGGCGGGTCCT	BC146362	CCDS33267.1	2q12.3	2007-07-26			ENSG00000196228	ENSG00000196228		"""Sulfotransferases, cytosolic"""	33543	protein-coding gene	gene with protein product						14676822, 17425406	Standard	NM_001008743		Approved		uc010ywo.2	Q6IMI6	OTTHUMG00000153227	ENST00000329106.2:c.535G>A	2.37:g.108875198G>A	ENSP00000333310:p.Gly179Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_001008743	Q6IMI5	Missense_Mutation	SNP	ENST00000329106.2	37	CCDS33267.1	862	0.3946886446886447	148	0.3008130081300813	135	0.3729281767955801	418	0.7307692307692307	161	0.21240105540897097	G	13.17	2.156047	0.38021	0.293917	0.193023	ENSG00000196228	ENST00000329106;ENST00000376700	D;D	0.87256	-2.23;-2.23	3.1	2.21	0.28008	Sulfotransferase domain (1);	0.114376	0.38837	N	0.001551	T	0.00012	0.0000	H	0.97516	4.02	0.20489	P	0.999898434	D	0.89917	1.0	D	0.97110	1.0	T	0.48547	-0.9026	9	0.87932	D	0	.	9.2077	0.37300	0.1101:0.0:0.8899:0.0	rs2219078;rs57930263;rs2219078	179	Q6IMI6	ST1C3_HUMAN	R	179	ENSP00000333310:G179R;ENSP00000365890:G179R	ENSP00000333310:G179R	G	+	1	0	SULT1C3	108241630	1.000000	0.71417	0.438000	0.26821	0.132000	0.20833	5.240000	0.65378	0.617000	0.30160	0.609000	0.83330	GGG	G|0.694;A|0.306	0.306	strong		0.448	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743	
RASA4	10156	hgsc.bcm.edu	37	7	102246311	102246311	+	Missense_Mutation	SNP	T	T	C	rs11547189		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102246311T>C	ENST00000262940.7	-	5	489	c.422A>G	c.(421-423)gAg>gGg	p.E141G	AC105052.1_ENST00000411396.1_RNA|RP11-514P8.6_ENST00000519541.1_3'UTR|RASA4_ENST00000461209.1_Missense_Mutation_p.E69G|RASA4_ENST00000449970.2_Missense_Mutation_p.E141G|RASA4_ENST00000462172.1_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	100	2	0.02		WXS	Illumina HiSeq	Phase_I	248	47	0.189516	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	
POLA1	5422	hgsc.bcm.edu	37	X	25014016	25014016	+	Silent	SNP	C	C	T	rs11573531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:25014016C>T	ENST00000379059.3	+	37	4353	c.4338C>T	c.(4336-4338)taC>taT	p.Y1446Y	POLA1_ENST00000379068.3_Silent_p.Y1452Y	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1446					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|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)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GAAGTGGCTACTCCGAAGTGA	0.443													C|||	8	0.00211921	0.0	0.0014	3775	,	,		12343	0.0		0.007	False		,,,				2504	0.0				p.Y1446Y		Atlas-SNP	.											.	POLA1	117	.	0			c.C4338T						PASS	.	C		9,3824		0,7,2,1624,569	73.0	60.0	64.0		4338	3.3	1.0	X	dbSNP_120	64	101,6627		0,79,22,2349,1850	no	coding-synonymous	POLA1	NM_016937.3		0,86,24,3973,2419	TT,TC,T,CC,C		1.5012,0.2348,1.0416		1446/1463	25014016	110,10451	2202	4300	6502	SO:0001819	synonymous_variant	5422	exon37			TGGCTACTCCGAA		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.4338C>T	X.37:g.25014016C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_016937	Q86UQ7	Silent	SNP	ENST00000379059.3	37	CCDS14214.1																																																																																			C|0.990;T|0.010	0.010	strong		0.443	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
TMEM245	23731	hgsc.bcm.edu	37	9	111881856	111881856	+	Missense_Mutation	SNP	T	T	C	rs1051474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111881856T>C	ENST00000374586.3	-	1	369	c.338A>G	c.(337-339)cAc>cGc	p.H113R		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	113						integral component of membrane (GO:0016021)											GTGCGCGCGGTGCAGGCGCTG	0.726													T|||	986	0.196885	0.0174	0.3256	5008	,	,		10110	0.2937		0.2793	False		,,,				2504	0.1636				p.H113R		Atlas-SNP	.											.	.	.	.	0			c.A338G						PASS	.	T	ARG/HIS	133,3651		2,129,1761	4.0	8.0	7.0		338	2.6	1.0	9	dbSNP_86	7	1618,6032		132,1354,2339	no	missense	C9orf5	NM_032012.3	29	134,1483,4100	CC,CT,TT		21.1503,3.5148,15.314	benign	113/880	111881856	1751,9683	1892	3825	5717	SO:0001583	missense	23731	exon1			GCGCGGTGCAGGC	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.338A>G	9.37:g.111881856T>C	ENSP00000363714:p.His113Arg	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Missense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	502	0.22985347985347984	16	0.032520325203252036	101	0.27900552486187846	175	0.30594405594405594	210	0.2770448548812665	T	3.632	-0.075434	0.07184	0.035148	0.211503	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	T	0.20881	2.04	4.9	2.58	0.30949	.	0.127703	0.53938	N	0.000041	T	0.00012	0.0000	N	0.04508	-0.205	0.28353	P	0.9208218	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.46247	-0.9205	9	0.33141	T	0.24	-7.6069	7.8579	0.29493	0.0:0.2415:0.0:0.7585	rs1051474;rs3174326;rs1051474	113;113	Q9H330-2;Q9H330	.;CI005_HUMAN	R	113	ENSP00000363714:H113R	ENSP00000223608:H113R	H	-	2	0	C9orf5	110921677	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.881000	0.39638	0.724000	0.32296	0.533000	0.62120	CAC	T|0.646;C|0.354	0.354	strong		0.726	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
PTX4	390667	hgsc.bcm.edu	37	16	1536499	1536499	+	Missense_Mutation	SNP	G	G	T	rs2745097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1536499G>T	ENST00000447419.2	-	3	903	c.878C>A	c.(877-879)gCc>gAc	p.A293D	PTX4_ENST00000293922.1_Missense_Mutation_p.A288D|PTX4_ENST00000440447.2_Missense_Mutation_p.P145T			Q96A99	PTX4_HUMAN	pentraxin 4, long	293	Pentaxin.					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						GGCTCGCAGGGCAGTGACGAA	0.642													G|||	1399	0.279353	0.5983	0.1744	5008	,	,		17855	0.0665		0.2296	False		,,,				2504	0.1933				p.A288D		Atlas-SNP	.											.	PTX4	46	.	0			c.C863A						PASS	.	G	ASP/ALA	2329,2069	598.7+/-389.1	611,1107,481	62.0	66.0	64.0		863	3.6	0.2	16	dbSNP_100	64	1830,6770	327.1+/-317.7	191,1448,2661	yes	missense	PTX4	NM_001013658.1	126	802,2555,3142	TT,TG,GG		21.2791,47.0441,31.9972	benign	288/474	1536499	4159,8839	2199	4300	6499	SO:0001583	missense	390667	exon3			CGCAGGGCAGTGA		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.878C>A	16.37:g.1536499G>T	ENSP00000445277:p.Ala293Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		570	0.260989010989011	283	0.5752032520325203	67	0.1850828729281768	33	0.057692307692307696	187	0.24670184696569922	G	9.665	1.145245	0.21288	0.529559	0.212791	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06528	3.29;3.29	5.58	3.6	0.41247	.	0.615939	0.16451	N	0.213852	T	0.00012	0.0000	N	0.03029	-0.43	0.44834	P	0.0021569999999999645	B	0.15473	0.013	B	0.15484	0.013	T	0.18840	-1.0324	9	0.45353	T	0.12	.	14.376	0.66879	0.0:0.7622:0.2378:0.0	rs2745097;rs2745097	288	Q96A99-2	.	D	293;288	ENSP00000445277:A293D;ENSP00000293922:A288D	ENSP00000293922:A288D	A	-	2	0	PTX4	1476500	0.001000	0.12720	0.244000	0.24202	0.012000	0.07955	1.124000	0.31320	0.703000	0.31848	0.655000	0.94253	GCC	G|0.692;T|0.308	0.308	strong		0.642	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
RNF8	9025	hgsc.bcm.edu	37	6	37349033	37349033	+	Silent	SNP	G	G	A	rs2284922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:37349033G>A	ENST00000373479.4	+	7	1537	c.1344G>A	c.(1342-1344)acG>acA	p.T448T	RNF8_ENST00000469731.1_Intron	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	448					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						AGTCCAAAACGTACTCTTTGG	0.413													A|||	2806	0.560304	0.5582	0.549	5008	,	,		22516	0.7361		0.3588	False		,,,				2504	0.5971				p.T448T		Atlas-SNP	.											RNF8,NS,carcinoma,+1,1	RNF8	78	1	0			c.G1344A						PASS	.	A	,	2285,2121	577.4+/-384.4	573,1139,491	145.0	126.0	132.0		1344,	-3.5	0.3	6	dbSNP_100	132	2973,5627	666.1+/-402.3	544,1885,1871	no	coding-synonymous,intron	RNF8	NM_003958.3,NM_183078.2	,	1117,3024,2362	AA,AG,GG		34.5698,48.1389,40.4275	,	448/486,	37349033	5258,7748	2203	4300	6503	SO:0001819	synonymous_variant	9025	exon7			CAAAACGTACTCT	AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"""RING-type (C3HC4) zinc fingers"""	10071	protein-coding gene	gene with protein product		611685	"""ring finger protein (C3HC4 type) 8"", ""ring finger protein 8"""			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1344G>A	6.37:g.37349033G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	53	0.414062	NM_003958	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Silent	SNP	ENST00000373479.4	37	CCDS4834.1																																																																																			G|0.535;A|0.465	0.465	strong		0.413	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2		
KRT40	125115	hgsc.bcm.edu	37	17	39135084	39135084	+	Missense_Mutation	SNP	A	A	G	rs8064733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	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	
GRIN3A	116443	hgsc.bcm.edu	37	9	104357062	104357062	+	Intron	SNP	C	C	T	rs151333989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104357062C>T	ENST00000361820.3	-	7	3367				PPP3R2_ENST00000374806.1_Missense_Mutation_p.E51K	NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A						calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TGGCGCAGCTCCGGCAGGGAC	0.537													C|||	9	0.00179712	0.0	0.0043	5008	,	,		16522	0.0		0.002	False		,,,				2504	0.0041				p.E51K		Atlas-SNP	.											.	PPP3R2	38	.	0			c.G151A						PASS	.	C	,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	65.0	65.0	65.0		,151	0.9	0.0	9	dbSNP_134	65	45,8555	30.7+/-82.3	0,45,4255	yes	intron,missense	PPP3R2,GRIN3A	NM_133445.2,NM_147180.2	,56	0,48,6455	TT,TC,CC		0.5233,0.0681,0.3691	,benign	,51/174	104357062	48,12958	2203	4300	6503	SO:0001627	intron_variant	5535	exon1			GCAGCTCCGGCAG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2767-15420G>A	9.37:g.104357062C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_147180	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	11.39	1.623600	0.28889	6.81E-4	0.005233	ENSG00000188386	ENST00000374806;ENST00000541976	T	0.69040	-0.37	3.94	0.879	0.19155	EF-hand-like domain (1);	0.454821	0.16664	N	0.204653	T	0.55878	0.1948	L	0.54965	1.715	0.31019	N	0.718406	B	0.25235	0.121	B	0.33339	0.162	T	0.65117	-0.6246	10	0.72032	D	0.01	-8.8891	13.0633	0.59020	0.0:0.5326:0.4674:0.0	.	48	Q96LZ3	CANB2_HUMAN	K	51	ENSP00000363939:E51K	ENSP00000363939:E51K	E	-	1	0	PPP3R2	103396883	0.698000	0.27777	0.001000	0.08648	0.037000	0.13140	1.393000	0.34497	0.192000	0.20272	0.563000	0.77884	GAG	C|0.998;T|0.002	0.002	strong		0.537	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
HELZ2	85441	hgsc.bcm.edu	37	20	62196182	62196182	+	Silent	SNP	G	G	C	rs3810488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	63	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	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	
TOR1B	27348	hgsc.bcm.edu	37	9	132569553	132569553	+	Silent	SNP	C	C	T	rs36036025|rs1043178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:132569553C>T	ENST00000259339.2	+	3	612	c.552C>T	c.(550-552)ccC>ccT	p.P184P		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	184					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				AATTGCACCCCGGGATCATTG	0.493													C|||	838	0.167332	0.0537	0.2839	5008	,	,		18896	0.0288		0.3161	False		,,,				2504	0.228				p.P184P		Atlas-SNP	.											.	TOR1B	20	.	0			c.C552T						PASS	.	C		373,4033	189.9+/-215.9	12,349,1842	191.0	179.0	183.0		552	-9.2	0.2	9	dbSNP_86	183	2872,5728	450.9+/-362.5	486,1900,1914	no	coding-synonymous	TOR1B	NM_014506.1		498,2249,3756	TT,TC,CC		33.3953,8.4657,24.95		184/337	132569553	3245,9761	2203	4300	6503	SO:0001819	synonymous_variant	27348	exon3			GCACCCCGGGATC	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.552C>T	9.37:g.132569553C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	169	73	0.431953	NM_014506		Silent	SNP	ENST00000259339.2	37	CCDS6929.1																																																																																			C|0.794;N|0.000	.	strong		0.493	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084787	31084787	+	Intron	SNP	A	A	G	rs707913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31084787A>G	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.F202S|PSORS1C1_ENST00000467107.1_3'UTR	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	68	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	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	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35944609	35944609	+	Missense_Mutation	SNP	T	T	C	rs34372241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35944609T>C	ENST00000325722.3	-	4	1105	c.871A>G	c.(871-873)Acc>Gcc	p.T291A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	291						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCCTGGGGGGTAGGGGTAGCA	0.488													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17721	0.0		0.0089	False		,,,				2504	0.0				p.T291A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.A871G						PASS	.	T	ALA/THR	9,4397	15.5+/-35.6	0,9,2194	80.0	85.0	84.0		871	-1.9	0.0	1	dbSNP_126	84	86,8514	49.4+/-109.1	1,84,4215	yes	missense	KIAA0319L	NM_024874.4	58	1,93,6409	CC,CT,TT		1.0,0.2043,0.7304	benign	291/1050	35944609	95,12911	2203	4300	6503	SO:0001583	missense	79932	exon4			GGGGGGTAGGGGT	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.871A>G	1.37:g.35944609T>C	ENSP00000318406:p.Thr291Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	3.559|3.559	-0.090063|-0.090063	0.07053|0.07053	0.002043|0.002043	0.01|0.01	ENSG00000142687|ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258|ENST00000431916	T;T;T;T|.	0.34667|.	3.24;3.24;2.68;1.35|.	5.65|5.65	-1.92|-1.92	0.07618|0.07618	Fibronectin, type III (1);|.	0.784679|.	0.11712|.	N|.	0.536788|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.09022|.	0.002;0.0;0.0|.	B;B;B|.	0.11329|.	0.006;0.0;0.001|.	T|T	0.27365|0.27365	-1.0076|-1.0076	10|5	0.45353|.	T|.	0.12|.	-3.0E-4|-3.0E-4	10.2654|10.2654	0.43452|0.43452	0.0:0.5192:0.0:0.4807|0.0:0.5192:0.0:0.4807	rs34372241|rs34372241	291;291;291|.	B4DYG9;B1AN14;Q8IZA0|.	.;.;K319L_HUMAN|.	A|C	291|154	ENSP00000318406:T291A;ENSP00000395883:T291A;ENSP00000407576:T291A;ENSP00000362355:T291A|.	ENSP00000318406:T291A|.	T|Y	-|-	1|2	0|0	KIAA0319L|KIAA0319L	35717196|35717196	0.012000|0.012000	0.17670|0.17670	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	0.013000|0.013000	0.13310|0.13310	-0.368000|-0.368000	0.08040|0.08040	-0.297000|-0.297000	0.09499|0.09499	ACC|TAC	T|0.994;C|0.006	0.006	strong		0.488	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
OVGP1	5016	hgsc.bcm.edu	37	1	111957693	111957693	+	Missense_Mutation	SNP	A	A	G	rs2485319	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111957693A>G	ENST00000369732.3	-	11	1485	c.1430T>C	c.(1429-1431)aTg>aCg	p.M477T		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	477			M -> T (in dbSNP:rs2485319). {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)		AGTCATGGTCATTGCCCCAGT	0.522													g|||	3164	0.631789	0.7572	0.3573	5008	,	,		19965	0.7718		0.4364	False		,,,				2504	0.7137				p.M477T		Atlas-SNP	.											.	OVGP1	177	.	0			c.T1430C						PASS	.	G	THR/MET	3118,1288	438.2+/-345.2	1098,922,183	124.0	104.0	111.0		1430	-1.1	0.0	1	dbSNP_100	111	3799,4801	613.6+/-396.1	838,2123,1339	yes	missense	OVGP1	NM_002557.3	81	1936,3045,1522	GG,GA,AA		44.1744,29.2329,46.8169	benign	477/679	111957693	6917,6089	2203	4300	6503	SO:0001583	missense	5016	exon11			ATGGTCATTGCCC	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.1430T>C	1.37:g.111957693A>G	ENSP00000358747:p.Met477Thr	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	224	120	0.535714	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	1264	0.5787545787545788	361	0.733739837398374	138	0.3812154696132597	440	0.7692307692307693	325	0.4287598944591029	g	0.042	-1.281576	0.01398	0.707671	0.441744	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03982	3.74	3.58	-1.06	0.10002	.	3.712600	0.01003	N	0.003714	T	0.00552	0.0018	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	0.43491	-0.9388	9	0.09590	T	0.72	0.0079	4.4317	0.11531	0.2936:0.0:0.3433:0.3631	rs2485319;rs3767606;rs17528138;rs61105440;rs2485319	477;541	Q12889;Q59HH5	OVGP1_HUMAN;.	T	477;541;285	ENSP00000358747:M477T	ENSP00000358743:M541T	M	-	2	0	OVGP1	111759216	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	-0.339000	0.07832	-0.608000	0.05731	-1.636000	0.00776	ATG	A|0.440;G|0.560	0.560	strong		0.522	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
MYH14	79784	hgsc.bcm.edu	37	19	50720940	50720940	+	Silent	SNP	T	T	C	rs34796700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50720940T>C	ENST00000596571.1	+	2	474	c.474T>C	c.(472-474)atT>atC	p.I158I	MYH14_ENST00000262269.8_Silent_p.I158I|MYH14_ENST00000425460.1_Silent_p.I158I|MYH14_ENST00000440075.2_Silent_p.I158I|MYH14_ENST00000598205.1_Silent_p.I158I|MYH14_ENST00000601313.1_Silent_p.I158I|MYH14_ENST00000376970.2_Silent_p.I158I			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	158	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CAGAAGCCATTGTGGAGATGT	0.602													T|||	69	0.013778	0.0023	0.0303	5008	,	,		18858	0.0		0.0358	False		,,,				2504	0.0092				p.I158I		Atlas-SNP	.											.	MYH14	261	.	0			c.T474C						PASS	.	T	,,	35,4323		1,33,2145	94.0	103.0	100.0		474,474,474	-9.3	0.7	19	dbSNP_126	100	353,8207		7,339,3934	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	8,372,6079	CC,CT,TT		4.1238,0.8031,3.0036	,,	158/2004,158/2037,158/1996	50720940	388,12530	2179	4280	6459	SO:0001819	synonymous_variant	79784	exon3			AGCCATTGTGGAG	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.474T>C	19.37:g.50720940T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			T|0.980;C|0.020	0.020	strong		0.602	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
CDC5L	988	hgsc.bcm.edu	37	6	44413463	44413463	+	Silent	SNP	T	T	A	rs2273666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	117	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	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		
CDON	50937	hgsc.bcm.edu	37	11	125891269	125891269	+	Missense_Mutation	SNP	C	C	T	rs3740912	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125891269C>T	ENST00000392693.3	-	3	350	c.223G>A	c.(223-225)Gtt>Att	p.V75I	CDON_ENST00000263577.7_Missense_Mutation_p.V75I	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	75	Ig-like C2-type 1.			V -> I (in Ref. 1; AAC34901 and 3; AAH98583). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V75I(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TGAATCTTAACATGTTCCAGG	0.458													T|||	2866	0.572284	0.8563	0.5173	5008	,	,		18993	0.3452		0.5308	False		,,,				2504	0.5041				p.V75I		Atlas-SNP	.											CDON,NS,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	stomach(1)	c.G223A						PASS	.	T	ILE/VAL	3530,872	338.9+/-305.5	1413,704,84	106.0	101.0	103.0		223	1.8	0.0	11	dbSNP_107	103	4857,3741	532.6+/-382.2	1391,2075,833	yes	missense	CDON	NM_016952.4	29	2804,2779,917	TT,TC,CC		43.5101,19.8092,35.4846	benign	75/1265	125891269	8387,4613	2201	4299	6500	SO:0001583	missense	50937	exon3			TCTTAACATGTTC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.223G>A	11.37:g.125891269C>T	ENSP00000376458:p.Val75Ile	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	1194|1194	0.5467032967032966|0.5467032967032966	397|397	0.806910569105691|0.806910569105691	201|201	0.5552486187845304|0.5552486187845304	189|189	0.3304195804195804|0.3304195804195804	407|407	0.5369393139841688|0.5369393139841688	T|T	0.008|0.008	-1.905451|-1.905451	0.00512|0.00512	0.801908|0.801908	0.564899|0.564899	ENSG00000064309|ENSG00000064309	ENST00000534661|ENST00000392693;ENST00000263577;ENST00000531586;ENST00000527967;ENST00000534818	.|T;T;T;T;T	.|0.39406	.|1.08;1.08;1.08;1.08;1.08	5.4|5.4	1.84|1.84	0.25277|0.25277	.|Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.618492	.|0.14418	.|N	.|0.320824	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16166|0.16166	0.38|0.38	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.06786	.|0.0;0.001;0.001	.|B;B;B	.|0.15052	.|0.003;0.012;0.007	T|T	0.39663|0.39663	-0.9603|-0.9603	4|9	.|0.06236	.|T	.|0.91	-7.9123|-7.9123	4.7519|4.7519	0.13064|0.13064	0.0:0.4272:0.1826:0.3902|0.0:0.4272:0.1826:0.3902	rs3740912;rs17527371;rs60942054;rs3740912|rs3740912;rs17527371;rs60942054;rs3740912	.|75;75;75	.|E9PRD8;Q4KMG0;Q4KMG0-2	.|.;CDON_HUMAN;.	Y|I	50|75	.|ENSP00000376458:V75I;ENSP00000263577:V75I;ENSP00000434212:V75I;ENSP00000436940:V75I;ENSP00000437176:V75I	.|ENSP00000263577:V75I	C|V	-|-	2|1	0|0	CDON|CDON	125396479|125396479	0.977000|0.977000	0.34250|0.34250	0.006000|0.006000	0.13384|0.13384	0.019000|0.019000	0.09904|0.09904	1.485000|1.485000	0.35519|0.35519	0.052000|0.052000	0.16007|0.16007	-1.755000|-1.755000	0.00674|0.00674	TGT|GTT	C|0.401;T|0.599	0.599	strong		0.458	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
KRT32	3882	hgsc.bcm.edu	37	17	39619219	39619219	+	Silent	SNP	G	G	A	rs2857257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39619219G>A	ENST00000225899.3	-	6	1183	c.1080C>T	c.(1078-1080)aaC>aaT	p.N360N		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	360	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GGGCCTCAACGTTGGTGATCA	0.632													G|||	3081	0.615216	0.6309	0.5706	5008	,	,		17780	0.6815		0.673	False		,,,				2504	0.498				p.N360N		Atlas-SNP	.											KRT32,colon,carcinoma,0,1	KRT32	57	1	0			c.C1080T						PASS	.	G		2756,1650	659.1+/-400.5	860,1036,307	79.0	77.0	78.0		1080	-2.8	0.2	17	dbSNP_100	78	5518,3082	658.6+/-401.6	1775,1968,557	no	coding-synonymous	KRT32	NM_002278.3		2635,3004,864	AA,AG,GG		35.8372,37.4489,36.3832		360/449	39619219	8274,4732	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon6			CTCAACGTTGGTG	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.1080C>T	17.37:g.39619219G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			G|0.352;A|0.648	0.648	strong		0.632	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
SVOPL	136306	hgsc.bcm.edu	37	7	138363767	138363767	+	Silent	SNP	A	A	G	rs10250576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:138363767A>G	ENST00000419765.3	-	1	57	c.24T>C	c.(22-24)ccT>ccC	p.P8P	SVOPL_ENST00000421622.1_Silent_p.P8P	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	8						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						GGATCGTGACAGGCTCTGTTG	0.493													G|||	3027	0.604433	0.9228	0.4481	5008	,	,		18186	0.627		0.4036	False		,,,				2504	0.4683				p.P8P		Atlas-SNP	.											.	SVOPL	111	.	0			c.T24C						PASS	.	G		1158,226		486,186,20	100.0	96.0	97.0		24	-9.8	0.0	7	dbSNP_119	97	1289,1893		261,767,563	no	coding-synonymous	SVOPL	NM_001139456.1		747,953,583	GG,GA,AA		40.5091,16.3295,46.4082		8/493	138363767	2447,2119	692	1591	2283	SO:0001819	synonymous_variant	136306	exon1			CGTGACAGGCTCT	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.24T>C	7.37:g.138363767A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_001139456		Silent	SNP	ENST00000419765.3	37	CCDS47721.1																																																																																			A|0.433;G|0.567	0.567	strong		0.493	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
RIN3	79890	hgsc.bcm.edu	37	14	93118669	93118669	+	Silent	SNP	G	G	A	rs3742716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:93118669G>A	ENST00000216487.7	+	6	1434	c.1275G>A	c.(1273-1275)acG>acA	p.T425T	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	425	Pro-rich.		T -> I (in dbSNP:rs3742717).|T -> M (in dbSNP:rs3742717). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CTGAGGACACGCCCCGGGAGA	0.652													g|||	1194	0.238419	0.0295	0.2594	5008	,	,		13370	0.4494		0.2883	False		,,,				2504	0.2372				p.T425T		Atlas-SNP	.											RIN3,rectum,carcinoma,0,1	RIN3	81	1	0			c.G1275A						PASS	.	A		330,4076	173.0+/-202.9	18,294,1891	56.0	64.0	62.0		1275	0.9	0.0	14	dbSNP_107	62	2738,5862	433.0+/-357.3	433,1872,1995	no	coding-synonymous	RIN3	NM_024832.3		451,2166,3886	AA,AG,GG		31.8372,7.4898,23.5891		425/986	93118669	3068,9938	2203	4300	6503	SO:0001819	synonymous_variant	79890	exon6			GGACACGCCCCGG	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1275G>A	14.37:g.93118669G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	77	30	0.38961	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			G|0.748;A|0.252	0.252	strong		0.652	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
SCN7A	6332	hgsc.bcm.edu	37	2	167262939	167262939	+	Silent	SNP	A	A	G	rs33953730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	293	0	0		WXS	Illumina HiSeq	Phase_I	266	261	0.981203	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		
C12orf42	374470	hgsc.bcm.edu	37	12	103872172	103872172	+	Missense_Mutation	SNP	T	T	G	rs10778257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:103872172T>G	ENST00000378113.2	-	2	258	c.33A>C	c.(31-33)gaA>gaC	p.E11D	C12orf42_ENST00000315192.8_Missense_Mutation_p.E11D|C12orf42_ENST00000548048.1_5'UTR|C12orf42_ENST00000548789.1_5'UTR|C12orf42_ENST00000548883.1_Missense_Mutation_p.E11D	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	11			E -> D (in dbSNP:rs10778257). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						AGAATTCTTCTTCCCTTTGTT	0.333																																					p.E11D		Atlas-SNP	.											.	C12orf42	50	.	0			c.A33C						PASS	.	T	ASP/GLU,ASP/GLU	1318,2396		228,862,767	144.0	130.0	135.0		33,33	-0.6	0.0	12	dbSNP_120	135	5577,2601		1918,1741,430	yes	missense,missense	C12orf42	NM_001099336.1,NM_198521.2	45,45	2146,2603,1197	GG,GT,TT		31.8048,35.4873,42.0198	probably-damaging,probably-damaging	11/361,11/361	103872172	6895,4997	1857	4089	5946	SO:0001583	missense	374470	exon2			TTCTTCTTCCCTT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.33A>C	12.37:g.103872172T>G	ENSP00000367353:p.Glu11Asp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	37	CCDS44963.1	1188	0.5439560439560439	138	0.2804878048780488	255	0.7044198895027625	297	0.5192307692307693	498	0.6569920844327177	T	12.42	1.931885	0.34096	0.354873	0.681952	ENSG00000179088	ENST00000315192;ENST00000548883;ENST00000378113;ENST00000552578	T;T;T;T	0.53640	0.61;1.27;1.27;1.25	3.44	-0.6	0.11642	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.28552	0.215	B	0.26693	0.072	T	0.34004	-0.9846	8	0.39692	T	0.17	-8.3748	2.6914	0.05122	0.1934:0.2294:0.0:0.5773	rs10778257;rs52838147;rs57730714;rs10778257	11	Q96LP6	CL042_HUMAN	D	11	ENSP00000324984:E11D;ENSP00000447908:E11D;ENSP00000367353:E11D;ENSP00000447795:E11D	ENSP00000324984:E11D	E	-	3	2	C12orf42	102396302	0.004000	0.15560	0.002000	0.10522	0.013000	0.08279	0.051000	0.14141	-0.099000	0.12263	0.459000	0.35465	GAA	T|0.451;G|0.549	0.549	strong		0.333	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521	
VPS18	57617	hgsc.bcm.edu	37	15	41192540	41192540	+	Silent	SNP	C	C	T	rs79536497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41192540C>T	ENST00000220509.5	+	4	1863	c.1524C>T	c.(1522-1524)ggC>ggT	p.G508G	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	508					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTCTGCAGGGCGACCCAGAGG	0.612													C|||	7	0.00139776	0.0008	0.0	5008	,	,		17114	0.0		0.006	False		,,,				2504	0.0				p.G508G		Atlas-SNP	.											.	VPS18	67	.	0			c.C1524T						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	76.0	86.0	82.0		1524	-5.3	0.7	15	dbSNP_131	82	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous	VPS18	NM_020857.2		0,70,6433	TT,TC,CC		0.7558,0.1135,0.5382		508/974	41192540	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	57617	exon4			GCAGGGCGACCCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.1524C>T	15.37:g.41192540C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_020857	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	37	CCDS10069.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
KRT37	8688	hgsc.bcm.edu	37	17	39579112	39579112	+	Missense_Mutation	SNP	G	G	A	rs16966811	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39579112G>A	ENST00000225550.3	-	3	649	c.650C>T	c.(649-651)gCg>gTg	p.A217V	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	217	Coil 1B.|Rod.		A -> V (in dbSNP:rs16966811).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GGCCAGGGTCGCGTCATCCAG	0.657													G|||	868	0.173323	0.0378	0.1268	5008	,	,		18610	0.3224		0.1759	False		,,,				2504	0.2331				p.A217V		Atlas-SNP	.											.	KRT37	61	.	0			c.C650T						PASS	.	G	VAL/ALA	255,4151		9,237,1957	78.0	68.0	71.0		650	1.4	0.7	17	dbSNP_123	71	1522,7078		120,1282,2898	yes	missense	KRT37	NM_003770.4	64	129,1519,4855	AA,AG,GG		17.6977,5.7876,13.6629	benign	217/450	39579112	1777,11229	2203	4300	6503	SO:0001583	missense	8688	exon3			AGGGTCGCGTCAT	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.650C>T	17.37:g.39579112G>A	ENSP00000225550:p.Ala217Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	384	0.17582417582417584	24	0.04878048780487805	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	10.94	1.492672	0.26774	0.057876	0.176977	ENSG00000108417	ENST00000225550	D	0.90004	-2.6	4.86	1.39	0.22231	Filament (1);	1.577570	0.04549	N	0.389541	T	0.00012	0.0000	L	0.37507	1.11	0.58432	P	1.999999999946489E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.12293	-1.0553	9	0.72032	D	0.01	.	8.1678	0.31237	0.7857:0.0:0.2143:0.0	rs16966811;rs16966811	217	O76014	KRT37_HUMAN	V	217	ENSP00000225550:A217V	ENSP00000225550:A217V	A	-	2	0	KRT37	36832638	0.041000	0.20044	0.743000	0.31040	0.247000	0.25773	2.537000	0.45702	0.233000	0.21120	-0.136000	0.14681	GCG	G|0.849;A|0.151	0.151	strong		0.657	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
TRDN	10345	hgsc.bcm.edu	37	6	123696766	123696766	+	Missense_Mutation	SNP	G	G	T	rs17737379	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:123696766G>T	ENST00000398178.3	-	19	1278	c.1257C>A	c.(1255-1257)gaC>gaA	p.D419E	TRDN_ENST00000334268.4_Missense_Mutation_p.D419E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	419			D -> E (in dbSNP:rs17737379).		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)		TTACTTGTTTGTCACTTGGAA	0.289													T|||	738	0.147364	0.3116	0.1196	5008	,	,		15478	0.0665		0.1312	False		,,,				2504	0.045				p.D420E		Atlas-SNP	.											.	TRDN	88	.	0			c.C1260A						PASS	.	T	GLU/ASP	908,2626		105,698,964	59.0	60.0	60.0		1257	4.1	1.0	6	dbSNP_123	60	949,7037		66,817,3110	yes	missense	TRDN	NM_006073.2	45	171,1515,4074	TT,TG,GG		11.8833,25.6933,16.1198	benign	419/730	123696766	1857,9663	1767	3993	5760	SO:0001583	missense	10345	exon19			TTGTTTGTCACTT	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.1257C>A	6.37:g.123696766G>T	ENSP00000381240:p.Asp419Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	342	0.1565934065934066	157	0.31910569105691056	54	0.14917127071823205	27	0.0472027972027972	104	0.13720316622691292	T	0.981	-0.696976	0.03279	0.256933	0.118833	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.13657	2.58;2.57	5.31	4.14	0.48551	.	0.652897	0.14317	N	0.327315	T	0.01092	0.0036	N	0.01576	-0.805	0.09310	P	0.999999999874142	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47699	-0.9097	9	0.02654	T	1	-5.4775	9.685	0.40094	0.0:0.0:0.341:0.659	rs17737379;rs52828160;rs59471828;rs17737379	419;420;419	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	E	419;421;419	ENSP00000381240:D419E;ENSP00000333984:D419E	ENSP00000333984:D419E	D	-	3	2	TRDN	123738465	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	0.544000	0.23253	0.452000	0.26830	-1.170000	0.01741	GAC	G|0.834;N|0.000	.	strong		0.289	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	25	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	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		
BRD9	65980	hgsc.bcm.edu	37	5	870619	870619	+	Silent	SNP	A	A	G	rs1051630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:870619A>G	ENST00000467963.1	-	14	1660	c.1494T>C	c.(1492-1494)gtT>gtC	p.V498V	BRD9_ENST00000483173.1_Silent_p.V445V|BRD9_ENST00000323510.4_Silent_p.V402V|BRD9_ENST00000388890.4_Silent_p.V382V	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	498					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			TATCCACAGAAACGTCGGGAT	0.517													G|||	557	0.111222	0.3328	0.0504	5008	,	,		20083	0.005		0.0417	False		,,,				2504	0.0358				p.V498V		Atlas-SNP	.											.	BRD9	113	.	0			c.T1494C						PASS	.	G	,	1399,3007	688.4+/-405.0	217,965,1021	147.0	128.0	134.0		1335,1494	3.5	0.9	5	dbSNP_86	134	484,8116	797.8+/-407.4	20,444,3836	no	coding-synonymous,coding-synonymous	BRD9	NM_001009877.2,NM_023924.4	,	237,1409,4857	GG,GA,AA		5.6279,31.7522,14.4779	,	445/545,498/598	870619	1883,11123	2203	4300	6503	SO:0001819	synonymous_variant	65980	exon14			CACAGAAACGTCG	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1494T>C	5.37:g.870619A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Silent	SNP	ENST00000467963.1	37	CCDS34127.2																																																																																			A|0.865;G|0.135	0.135	strong		0.517	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924	
PCDHA6	56142	hgsc.bcm.edu	37	5	140209185	140209185	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140209185G>A	ENST00000529310.1	+	1	1623	c.1509G>A	c.(1507-1509)gcG>gcA	p.A503A	PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Silent_p.A503A	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	503	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(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)			GCGAGCGCGCGTTGTCGAGCT	0.672																																					p.A503A		Atlas-SNP	.											PCDHA6_ENST00000529310,caecum,carcinoma,0,2	PCDHA6	442	2	0			c.G1509A						scavenged	.						53.0	59.0	57.0					5																	140209185		2203	4299	6502	SO:0001819	synonymous_variant	56142	exon1			GCGCGCGTTGTCG	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.1509G>A	5.37:g.140209185G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	130	2	0.0153846	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			.	.	none		0.672	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
NEK2	4751	hgsc.bcm.edu	37	1	211840498	211840498	+	Missense_Mutation	SNP	T	T	C	rs2230489	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:211840498T>C	ENST00000366999.4	-	7	1199	c.1061A>G	c.(1060-1062)aAc>aGc	p.N354S	NEK2_ENST00000540251.1_Missense_Mutation_p.N311S|NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000366998.3_Missense_Mutation_p.N354S	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	354	Interaction with PCNT.|Necessary for interaction with MAD1L1.|Required for microtubule binding and for localization to the centrosomes.		N -> S (in dbSNP:rs2230489). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.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)		CAAGCTGTAGTTCTTCAACAG	0.413													T|||	863	0.172324	0.1778	0.2061	5008	,	,		17236	0.2242		0.1282	False		,,,				2504	0.1329				p.N354S		Atlas-SNP	.											.	NEK2	49	.	0			c.A1061G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	718,3688	297.0+/-284.5	69,580,1554	128.0	128.0	128.0		1061,1061,1061	4.9	1.0	1	dbSNP_98	128	1131,7469	233.5+/-266.7	81,969,3250	yes	missense,missense,missense	NEK2	NM_001204182.1,NM_001204183.1,NM_002497.3	46,46,46	150,1549,4804	CC,CT,TT		13.1512,16.296,14.2165	benign,benign,benign	354/389,354/385,354/446	211840498	1849,11157	2203	4300	6503	SO:0001583	missense	4751	exon7			CTGTAGTTCTTCA	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.1061A>G	1.37:g.211840498T>C	ENSP00000355966:p.Asn354Ser	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	194	89	0.458763	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	380	0.17399267399267399	84	0.17073170731707318	61	0.1685082872928177	135	0.23601398601398602	100	0.13192612137203166	T	12.22	1.874092	0.33069	0.16296	0.131512	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.36520	1.25;1.25;1.25	4.89	4.89	0.63831	.	0.199697	0.52532	D	0.000068	T	0.00012	0.0000	L	0.45581	1.43	0.24716	P	0.99317538	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.002	T	0.19647	-1.0299	9	0.20519	T	0.43	.	9.1214	0.36788	0.0:0.0829:0.0:0.9171	rs2230489;rs2289726;rs10429965;rs52795825;rs58622133;rs10429965	354;354;354	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	S	354;311;354	ENSP00000355966:N354S;ENSP00000440237:N311S;ENSP00000355965:N354S	ENSP00000355965:N354S	N	-	2	0	NEK2	209907121	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.120000	0.31271	1.964000	0.57103	0.528000	0.53228	AAC	T|0.684;G|0.030	.	strong		0.413	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
POTEG	404785	hgsc.bcm.edu	37	14	19553680	19553680	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:19553680C>T	ENST00000409832.3	+	1	316	c.264C>T	c.(262-264)gaC>gaT	p.D88D		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	88										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						ACCACGACGACTCTGCTATGA	0.617																																					p.D88D		Atlas-SNP	.											POTEG,bladder,carcinoma,0,1	POTEG	118	1	0			c.C264T						scavenged	.						67.0	87.0	80.0					14																	19553680		1966	4009	5975	SO:0001819	synonymous_variant	404785	exon1			CGACGACTCTGCT		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.264C>T	14.37:g.19553680C>T		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	407	9	0.022113	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																			.	.	weak		0.617	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
TEKT4	150483	hgsc.bcm.edu	37	2	95537572	95537572	+	Missense_Mutation	SNP	C	C	T	rs4854235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:95537572C>T	ENST00000295201.4	+	1	385	c.248C>T	c.(247-249)aCg>aTg	p.T83M	TEKT4_ENST00000427593.2_Missense_Mutation_p.T83M|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	83			T -> M (in dbSNP:rs4854235).		cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCGCAGCGCACGCAGCAAGAC	0.701													.|||	1952	0.389776	0.5083	0.4063	5008	,	,		16701	0.4831		0.2744	False		,,,				2504	0.2403				p.T83M		Atlas-SNP	.											.	TEKT4	72	.	0			c.C248T						PASS	.	C	MET/THR	2061,2321		492,1077,622	16.0	17.0	16.0		248	2.0	0.7	2	dbSNP_111	16	2526,6032		388,1750,2141	yes	missense	TEKT4	NM_144705.2	81	880,2827,2763	TT,TC,CC		29.5162,47.0333,35.4482	possibly-damaging	83/436	95537572	4587,8353	2191	4279	6470	SO:0001583	missense	150483	exon1			AGCGCACGCAGCA	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.248C>T	2.37:g.95537572C>T	ENSP00000295201:p.Thr83Met	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	830	0.38003663003663	243	0.49390243902439024	133	0.3674033149171271	263	0.4597902097902098	191	0.2519788918205805	.	12.95	2.091221	0.36855	0.470333	0.295162	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.02709	4.19;4.19	1.97	1.97	0.26223	.	0.240312	0.41396	D	0.000888	T	0.00012	0.0000	L	0.56769	1.78	0.27389	P	0.955185	D	0.55800	0.973	P	0.47251	0.542	T	0.45396	-0.9264	9	0.44086	T	0.13	-15.3745	9.5816	0.39490	0.0:1.0:0.0:0.0	rs4854235;rs56557828;rs4854235	83	Q8WW24	TEKT4_HUMAN	M	83	ENSP00000295201:T83M;ENSP00000407596:T83M	ENSP00000295201:T83M	T	+	2	0	TEKT4	94901299	0.774000	0.28592	0.671000	0.29857	0.454000	0.32378	3.622000	0.54217	1.094000	0.41399	0.558000	0.71614	ACG	C|0.646;T|0.354	0.354	strong		0.701	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
RDH8	50700	hgsc.bcm.edu	37	19	10132318	10132318	+	Missense_Mutation	SNP	T	T	C	rs45503592	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10132318T>C	ENST00000171214.1	+	6	1078	c.829T>C	c.(829-831)Tat>Cat	p.Y277H	RDH8_ENST00000591589.1_Missense_Mutation_p.Y297H	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	277					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)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGGCAGCCTGTATGTGCGAAC	0.637													T|||	22	0.00439297	0.0015	0.0058	5008	,	,		18548	0.0		0.0139	False		,,,				2504	0.002				p.Y297H		Atlas-SNP	.											.	RDH8	51	.	0			c.T889C						PASS	.	T	HIS/TYR	11,4395	17.9+/-39.9	0,11,2192	113.0	107.0	109.0		829	3.4	0.7	19	dbSNP_127	109	111,8489	59.5+/-121.1	1,109,4190	yes	missense	RDH8	NM_015725.2	83	1,120,6382	CC,CT,TT		1.2907,0.2497,0.938	possibly-damaging	277/312	10132318	122,12884	2203	4300	6503	SO:0001583	missense	50700	exon6			AGCCTGTATGTGC	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.829T>C	19.37:g.10132318T>C	ENSP00000171214:p.Tyr277His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	14.74	2.624219	0.46840	0.002497	0.012907	ENSG00000080511	ENST00000171214	D	0.82619	-1.63	4.41	3.39	0.38822	.	0.140657	0.49305	D	0.000154	T	0.75177	0.3814	M	0.73217	2.22	0.35526	D	0.80184	P	0.51240	0.943	P	0.46718	0.525	T	0.78534	-0.2167	10	0.16896	T	0.51	.	7.3638	0.26762	0.0:0.1066:0.0:0.8934	rs45503592	277	Q9NYR8	RDH8_HUMAN	H	277	ENSP00000171214:Y277H	ENSP00000171214:Y277H	Y	+	1	0	RDH8	9993318	1.000000	0.71417	0.654000	0.29608	0.185000	0.23345	3.477000	0.53151	1.629000	0.50426	0.247000	0.18012	TAT	T|0.990;C|0.010	0.010	strong		0.637	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
STIL	6491	hgsc.bcm.edu	37	1	47726087	47726087	+	Missense_Mutation	SNP	T	T	C	rs13376679	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:47726087T>C	ENST00000360380.3	-	17	3314	c.2951A>G	c.(2950-2952)cAt>cGt	p.H984R	STIL_ENST00000243182.6_Missense_Mutation_p.H984R|STIL_ENST00000396221.2_Missense_Mutation_p.H967R|STIL_ENST00000371877.3_Missense_Mutation_p.H985R|STIL_ENST00000337817.5_Missense_Mutation_p.H984R	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	984			H -> R (in dbSNP:rs13376679). {ECO:0000269|PubMed:17974005}.		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)				TCTTGAATGATGTGTTTTTTT	0.388													T|||	893	0.178315	0.1831	0.2161	5008	,	,		14920	0.0298		0.2893	False		,,,				2504	0.184				p.H985R		Atlas-SNP	.											.	STIL	91	.	0			c.A2954G						PASS	.	T	ARG/HIS,ARG/HIS	966,3440	363.4+/-316.5	110,746,1347	238.0	229.0	232.0		2954,2951	0.3	0.0	1	dbSNP_121	232	2710,5890	434.0+/-357.6	429,1852,2019	yes	missense,missense	STIL	NM_001048166.1,NM_003035.2	29,29	539,2598,3366	CC,CT,TT		31.5116,21.9246,28.2639	benign,benign	985/1289,984/1288	47726087	3676,9330	2203	4300	6503	SO:0001583	missense	6491	exon16			GAATGATGTGTTT	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.2951A>G	1.37:g.47726087T>C	ENSP00000353544:p.His984Arg	Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	289	146	0.50519	NM_001048166	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	409	0.18727106227106227	84	0.17073170731707318	79	0.21823204419889503	14	0.024475524475524476	232	0.30606860158311344	T	0.435	-0.901436	0.02453	0.219246	0.315116	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182	T;T;T;T;T	0.17054	2.31;2.31;2.31;2.3;2.31	5.93	0.313	0.15842	.	1.532230	0.03091	N	0.159754	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.43228	-0.9404	9	0.22109	T	0.4	-0.0533	8.2989	0.32001	0.0:0.1432:0.2785:0.5783	rs13376679;rs59925302;rs13376679	967;985;984	E9PSF2;Q15468-2;Q15468	.;.;STIL_HUMAN	R	984;984;985;967;984	ENSP00000353544:H984R;ENSP00000337367:H984R;ENSP00000360944:H985R;ENSP00000379523:H967R;ENSP00000243182:H984R	ENSP00000243182:H984R	H	-	2	0	STIL	47498674	0.001000	0.12720	0.002000	0.10522	0.066000	0.16364	0.041000	0.13927	0.118000	0.18165	0.533000	0.62120	CAT	T|0.764;C|0.236	0.236	strong		0.388	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035	
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000397073.2_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	Somatic	685	0	0		WXS	Illumina HiSeq	Phase_I	751	38	0.0505992	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
TLN1	7094	hgsc.bcm.edu	37	9	35705759	35705759	+	Silent	SNP	G	G	A	rs11541908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35705759G>A	ENST00000314888.9	-	42	5954	c.5601C>T	c.(5599-5601)acC>acT	p.T1867T	TLN1_ENST00000540444.1_Silent_p.T1801T|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1867	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCTCCTGAACGGTCACTGCAA	0.522													G|||	847	0.169129	0.0197	0.2305	5008	,	,		21120	0.253		0.2515	False		,,,				2504	0.1564				p.T1867T		Atlas-SNP	.											.	TLN1	185	.	0			c.C5601T						PASS	.	G		265,4141	150.3+/-184.3	14,237,1952	105.0	104.0	104.0		5601	-4.3	1.0	9	dbSNP_120	104	2295,6305	386.7+/-342.0	293,1709,2298	no	coding-synonymous	TLN1	NM_006289.3		307,1946,4250	AA,AG,GG		26.686,6.0145,19.6832		1867/2542	35705759	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon42			CTGAACGGTCACT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5601C>T	9.37:g.35705759G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.806;A|0.194	0.194	strong		0.522	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
XYLT2	64132	hgsc.bcm.edu	37	17	48432324	48432324	+	Missense_Mutation	SNP	G	G	C	rs12451299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48432324G>C	ENST00000017003.2	+	4	963	c.914G>C	c.(913-915)aGg>aCg	p.R305T	XYLT2_ENST00000507602.1_Missense_Mutation_p.R305T	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	305			R -> T (in dbSNP:rs12451299). {ECO:0000269|PubMed:11099377, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16571645}.		chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					AGCCTCCTGAGGATGTACCTG	0.637													g|||	658	0.13139	0.0408	0.2795	5008	,	,		19087	0.0784		0.2127	False		,,,				2504	0.1196				p.R305T		Atlas-SNP	.											XYLT2,NS,carcinoma,+1,1	XYLT2	51	1	0			c.G914C						PASS	.		THR/ARG	328,4078	174.1+/-203.8	19,290,1894	73.0	72.0	72.0		914	3.6	1.0	17	dbSNP_120	72	1917,6683	339.5+/-323.2	210,1497,2593	yes	missense	XYLT2	NM_022167.2	71	229,1787,4487	CC,CG,GG		22.2907,7.4444,17.2613	benign	305/866	48432324	2245,10761	2203	4300	6503	SO:0001583	missense	64132	exon4			TCCTGAGGATGTA	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.914G>C	17.37:g.48432324G>C	ENSP00000017003:p.Arg305Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	310	0.14194139194139194	19	0.03861788617886179	90	0.24861878453038674	43	0.07517482517482517	158	0.20844327176781002	g	2.759	-0.258362	0.05791	0.074444	0.222907	ENSG00000015532	ENST00000017003;ENST00000507602	T;T	0.11385	2.78;2.78	4.61	3.57	0.40892	.	0.179563	0.47093	D	0.000258	T	0.00012	0.0000	N	0.01109	-1.01	0.39741	P	0.02824899999999997	B	0.06786	0.001	B	0.11329	0.006	T	0.48559	-0.9025	9	0.07175	T	0.84	-16.396	3.2345	0.06760	0.1848:0.2897:0.5255:0.0	rs12451299	305	Q9H1B5	XYLT2_HUMAN	T	305	ENSP00000017003:R305T;ENSP00000426501:R305T	ENSP00000017003:R305T	R	+	2	0	XYLT2	45787323	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.212000	0.42835	2.399000	0.81585	0.306000	0.20318	AGG	G|0.835;C|0.165	0.165	strong		0.637	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
ARVCF	421	hgsc.bcm.edu	37	22	19968971	19968971	+	Missense_Mutation	SNP	G	G	A	rs2073748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19968971G>A	ENST00000263207.3	-	5	950	c.659C>T	c.(658-660)cCa>cTa	p.P220L	ARVCF_ENST00000406259.1_Missense_Mutation_p.P220L|ARVCF_ENST00000406522.1_Missense_Mutation_p.P157L|ARVCF_ENST00000401994.1_Missense_Mutation_p.P157L|ARVCF_ENST00000344269.3_Missense_Mutation_p.P157L|ARVCF_ENST00000487793.1_5'UTR	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	220			P -> L (in dbSNP:rs2073748).		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)					ACCAGGGCCTGGGCCAAGGGG	0.736													G|||	1803	0.360024	0.3858	0.3501	5008	,	,		14736	0.2302		0.3439	False		,,,				2504	0.4826				p.P220L		Atlas-SNP	.											.	ARVCF	54	.	0			c.C659T						PASS	.	G	LEU/PRO	1437,2667		325,787,940	4.0	6.0	5.0		659	1.3	0.3	22	dbSNP_96	5	2767,5341		604,1559,1891	yes	missense	ARVCF	NM_001670.2	98	929,2346,2831	AA,AG,GG		34.1268,35.0146,34.4252	possibly-damaging	220/963	19968971	4204,8008	2052	4054	6106	SO:0001583	missense	421	exon5			GGGCCTGGGCCAA		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.659C>T	22.37:g.19968971G>A	ENSP00000263207:p.Pro220Leu	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	710	0.3250915750915751	185	0.37601626016260165	124	0.3425414364640884	132	0.23076923076923078	269	0.3548812664907652	G	5.855	0.341913	0.11069	0.350146	0.341268	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	4.71	1.26	0.21427	.	0.259697	0.36591	N	0.002506	T	0.00012	0.0000	N	0.22421	0.69	0.41181	P	0.01376299999999997	B	0.02656	0.0	B	0.04013	0.001	T	0.46693	-0.9173	8	.	.	.	-2.486	1.505	0.02484	0.1767:0.1188:0.4279:0.2766	rs2073748;rs2073748	220	O00192	ARVC_HUMAN	L	220;157;157;157;220	ENSP00000263207:P220L;ENSP00000342042:P157L;ENSP00000384341:P157L;ENSP00000384732:P157L;ENSP00000385444:P220L	.	P	-	2	0	ARVCF	18348971	0.023000	0.18921	0.293000	0.24932	0.524000	0.34500	0.843000	0.27640	0.719000	0.32188	-0.140000	0.14226	CCA	G|0.654;T|0.005	.	strong		0.736	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
MAP3K1	4214	hgsc.bcm.edu	37	5	56177743	56177743	+	Missense_Mutation	SNP	G	G	A	rs832582	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:56177743G>A	ENST00000399503.3	+	14	2716	c.2716G>A	c.(2716-2718)Gtc>Atc	p.V906I		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	906			V -> I (in dbSNP:rs832582).		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)		TGAGTGCACAGTCCATTTAGA	0.458													A|||	3547	0.708267	0.7126	0.6527	5008	,	,		21250	0.5704		0.8062	False		,,,				2504	0.7832				p.V906I		Atlas-SNP	.											.	MAP3K1	355	.	0			c.G2716A						PASS	.	A	ILE/VAL	2819,963		1045,729,117	68.0	63.0	65.0		2716	3.6	0.0	5	dbSNP_86	65	6785,1461		2793,1199,131	yes	missense	MAP3K1	NM_005921.1	29	3838,1928,248	AA,AG,GG		17.7177,25.4627,20.153	benign	906/1513	56177743	9604,2424	1891	4123	6014	SO:0001583	missense	4214	exon14			TGCACAGTCCATT	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.2716G>A	5.37:g.56177743G>A	ENSP00000382423:p.Val906Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	1524	0.6978021978021978	364	0.7398373983739838	247	0.6823204419889503	304	0.5314685314685315	609	0.8034300791556728	A	0.006	-2.035567	0.00406	0.745373	0.822823	ENSG00000095015	ENST00000399503	T	0.29655	1.56	5.41	3.58	0.41010	.	0.660702	0.15127	N	0.279052	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26950	-1.0088	9	0.08179	T	0.78	.	12.2359	0.54516	0.2091:0.0:0.7909:0.0	rs832582;rs889306;rs52797878;rs59004603;rs832582	906	Q13233	M3K1_HUMAN	I	906	ENSP00000382423:V906I	ENSP00000382423:V906I	V	+	1	0	MAP3K1	56213500	0.972000	0.33761	0.042000	0.18584	0.036000	0.12997	0.964000	0.29306	0.764000	0.33197	-0.977000	0.02584	GTC	G|0.285;A|0.715	0.715	strong		0.458	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
ROS1	6098	hgsc.bcm.edu	37	6	117724379	117724379	+	Missense_Mutation	SNP	C	C	T	rs2243380	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:117724379C>T	ENST00000368508.3	-	6	698	c.500G>A	c.(499-501)cGa>cAa	p.R167Q	ROS1_ENST00000368507.3_Missense_Mutation_p.R176Q|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	167	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q (in dbSNP:rs2243380). {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)		CCAAACCACTCGGAAAATGTA	0.493			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								C|||	251	0.0501198	0.0038	0.0865	5008	,	,		17090	0.0407		0.0934	False		,,,				2504	0.0521				p.R167Q		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.G500A						PASS	.	C	GLN/ARG	79,4327	68.1+/-105.8	1,77,2125	89.0	83.0	85.0		500	4.4	1.0	6	dbSNP_98	85	789,7811	185.2+/-233.0	39,711,3550	yes	missense	ROS1	NM_002944.2	43	40,788,5675	TT,TC,CC		9.1744,1.793,6.6738	possibly-damaging	167/2348	117724379	868,12138	2203	4300	6503	SO:0001583	missense	6098	exon6			ACCACTCGGAAAA	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.500G>A	6.37:g.117724379C>T	ENSP00000357494:p.Arg167Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	134	0.06135531135531135	4	0.008130081300813009	31	0.0856353591160221	23	0.04020979020979021	76	0.10026385224274406	C	19.72	3.880534	0.72294	0.01793	0.091744	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.59772	0.24;0.24	5.35	4.44	0.53790	.	0.000000	0.53938	D	0.000055	T	0.37919	0.1021	M	0.69823	2.125	0.09310	P	0.9999999999999803	P	0.48294	0.908	B	0.36335	0.222	T	0.53294	-0.8459	9	0.54805	T	0.06	.	9.6529	0.39908	0.0:0.7755:0.1433:0.0812	rs2243380;rs52809211;rs60405196;rs2243380	167	P08922	ROS1_HUMAN	Q	167;176	ENSP00000357494:R167Q;ENSP00000357493:R176Q	ENSP00000357493:R176Q	R	-	2	0	ROS1	117831072	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.643000	0.46604	2.687000	0.91594	0.655000	0.94253	CGA	C|0.939;T|0.061	0.061	strong		0.493	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
KIF14	9928	hgsc.bcm.edu	37	1	200558420	200558420	+	Silent	SNP	C	C	T	rs77213709	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:200558420C>T	ENST00000367350.4	-	18	3477	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1013	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GCTGCTTTGCCTTTTCTAATT	0.303													C|||	30	0.00599042	0.0	0.0	5008	,	,		19286	0.0		0.007	False		,,,				2504	0.0235				p.K1013K		Atlas-SNP	.											.	KIF14	156	.	0			c.G3039A						PASS	.	C		3,4401	6.2+/-15.9	0,3,2199	158.0	146.0	150.0		3039	3.1	0.3	1	dbSNP_132	150	33,8567	22.2+/-67.0	0,33,4267	no	coding-synonymous	KIF14	NM_014875.2		0,36,6466	TT,TC,CC		0.3837,0.0681,0.2768		1013/1649	200558420	36,12968	2202	4300	6502	SO:0001819	synonymous_variant	9928	exon18			CTTTGCCTTTTCT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3039G>A	1.37:g.200558420C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	303	175	0.577558	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																			C|0.996;T|0.004	0.004	strong		0.303	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
APOBEC3G	60489	hgsc.bcm.edu	37	22	39477123	39477123	+	Silent	SNP	T	T	C	rs5757465	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39477123T>C	ENST00000407997.3	+	3	714	c.357T>C	c.(355-357)ttT>ttC	p.F119F	APOBEC3G_ENST00000461827.1_3'UTR|APOBEC3G_ENST00000452957.2_Silent_p.F119F	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	119					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F119F(1)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TGACCATCTTTGTTGCCCGCC	0.557													T|||	1425	0.284545	0.0287	0.3977	5008	,	,		16691	0.2242		0.4473	False		,,,				2504	0.4448				p.F119F		Atlas-SNP	.											APOBEC3G_ENST00000407997,NS,carcinoma,0,1	APOBEC3G	69	1	1	Substitution - coding silent(1)	stomach(1)	c.T357C						PASS	.	T		391,4015		18,355,1830	102.0	90.0	94.0		357	-4.9	0.0	22	dbSNP_114	94	3739,4861		831,2077,1392	no	coding-synonymous	APOBEC3G	NM_021822.3		849,2432,3222	CC,CT,TT		43.4767,8.8743,31.7546		119/385	39477123	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	60489	exon3			CATCTTTGTTGCC	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.357T>C	22.37:g.39477123T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	37	CCDS13984.1																																																																																			T|0.692;C|0.308	0.308	strong		0.557	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
VPS13C	54832	hgsc.bcm.edu	37	15	62259637	62259637	+	Missense_Mutation	SNP	C	C	T	rs3784634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:62259637C>T	ENST00000261517.5	-	29	2994	c.2921G>A	c.(2920-2922)aGg>aAg	p.R974K	VPS13C_ENST00000249837.3_Missense_Mutation_p.R931K|VPS13C_ENST00000395898.3_Missense_Mutation_p.R931K|VPS13C_ENST00000395896.4_Missense_Mutation_p.R974K	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AAGGGGCTTCCTTTTGGATCC	0.269													T|||	3783	0.755391	0.9228	0.6052	5008	,	,		15751	0.8542		0.5636	False		,,,				2504	0.7311				p.R974K		Atlas-SNP	.											.	VPS13C	506	.	0			c.G2921A						PASS	.	T	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	3738,664		1600,538,63	53.0	61.0	58.0		2921,2792,2792,2921	1.6	1.0	15	dbSNP_107	58	4936,3652		1449,2038,807	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	26,26,26,26	3049,2576,870	TT,TC,CC		42.5245,15.0841,33.2256	benign,benign,benign,benign	974/3629,931/3711,931/3586,974/3754	62259637	8674,4316	2201	4294	6495	SO:0001583	missense	54832	exon29			GGCTTCCTTTTGG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.2921G>A	15.37:g.62259637C>T	ENSP00000261517:p.Arg974Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	1568	0.717948717948718	449	0.9126016260162602	212	0.585635359116022	489	0.8548951048951049	418	0.5514511873350924	T	1.921	-0.448323	0.04572	0.849159	0.574755	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.16597	2.33;2.33;2.33	5.2	1.62	0.23740	.	0.398165	0.27451	N	0.019320	T	0.00012	0.0000	N	0.00436	-1.5	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	0.33828	-0.9853	9	0.02654	T	1	.	9.7549	0.40498	0.0:0.2833:0.0:0.7167	rs3784634;rs17271277;rs52818014;rs57842846;rs3784634	931;974;931;974	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	K	931;974;974;974	ENSP00000249837:R931K;ENSP00000261517:R974K;ENSP00000379233:R974K	ENSP00000249837:R931K	R	-	2	0	VPS13C	60046929	0.997000	0.39634	0.995000	0.50966	0.699000	0.40488	1.921000	0.40035	0.084000	0.17077	-1.390000	0.01156	AGG	C|0.293;T|0.707	0.707	strong		0.269	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ITPR2	3709	hgsc.bcm.edu	37	12	26733062	26733062	+	Silent	SNP	T	T	C	rs2230375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:26733062T>C	ENST00000381340.3	-	33	4823	c.4407A>G	c.(4405-4407)aaA>aaG	p.K1469K		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1469					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGCATGTTTCCTGTCTG	0.358													T|||	1001	0.19988	0.0885	0.2305	5008	,	,		18889	0.0764		0.3559	False		,,,				2504	0.2955				p.K1469K		Atlas-SNP	.											.	ITPR2	270	.	0			c.A4407G						PASS	.	T		466,3188		29,408,1390	164.0	146.0	151.0		4407	-8.6	0.4	12	dbSNP_98	151	2793,5383		484,1825,1779	no	coding-synonymous	ITPR2	NM_002223.2		513,2233,3169	CC,CT,TT		34.161,12.7531,27.5486		1469/2702	26733062	3259,8571	1827	4088	5915	SO:0001819	synonymous_variant	3709	exon33			TGCATGTTTCCTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4407A>G	12.37:g.26733062T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.774;C|0.226	0.226	strong		0.358	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ST5	6764	hgsc.bcm.edu	37	11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	rs113126215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8724191A>G	ENST00000534127.1	-	17	3033	c.2648T>C	c.(2647-2649)gTg>gCg	p.V883A	ST5_ENST00000530991.1_Missense_Mutation_p.V355A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|ST5_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|ST5_ENST00000534278.1_Missense_Mutation_p.V74A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	883	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GAGCTGGCGCACACTGAGGCA	0.582													a|||	8	0.00159744	0.0008	0.0014	5008	,	,		19188	0.0		0.005	False		,,,				2504	0.001				p.V883A		Atlas-SNP	.											.	ST5	85	.	0			c.T2648C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	9,4393	15.5+/-35.6	0,9,2192	86.0	79.0	81.0		2648,1388,2648	4.7	1.0	11	dbSNP_132	81	48,8544	31.2+/-83.2	0,48,4248	yes	missense,missense,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	64,64,64	0,57,6440	GG,GA,AA		0.5587,0.2045,0.4387	benign,benign,benign	883/1138,463/718,883/1138	8724191	57,12937	2201	4296	6497	SO:0001583	missense	6764	exon17			TGGCGCACACTGA	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2648T>C	11.37:g.8724191A>G	ENSP00000433528:p.Val883Ala	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	a	16.30	3.083512	0.55861	0.002045	0.005587	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438;ENST00000533081	T;T;T;T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71	4.72	4.72	0.59763	DENN (3);	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.78801	2.425	0.53005	D	0.999961	B;B;B	0.28026	0.023;0.012;0.198	B;B;B	0.38755	0.202;0.038;0.281	T	0.05699	-1.0869	10	0.87932	D	0	-10.884	14.2346	0.65916	1.0:0.0:0.0:0.0	.	396;463;883	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	A	463;883;883;355;883;396;74;463;73	ENSP00000435097:V463A;ENSP00000433528:V883A;ENSP00000319678:V883A;ENSP00000432887:V355A;ENSP00000350294:V883A;ENSP00000436808:V396A;ENSP00000433349:V74A;ENSP00000436802:V463A;ENSP00000436067:V73A	ENSP00000319678:V883A	V	-	2	0	ST5	8680767	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	7.573000	0.82421	1.760000	0.52011	0.398000	0.26397	GTG	A|0.996;G|0.004	0.004	strong		0.582	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
PRG3	10394	hgsc.bcm.edu	37	11	57146202	57146202	+	Silent	SNP	G	G	A	rs1940145	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57146202G>A	ENST00000287143.2	-	4	568	c.459C>T	c.(457-459)agC>agT	p.S153S		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						GGTTGACTGTGCTAGTGCAGC	0.493													G|||	94	0.01877	0.0023	0.0288	5008	,	,		19071	0.0		0.0497	False		,,,				2504	0.0215				p.S153S	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.C459T						PASS	.	G		44,4358	46.7+/-81.2	1,42,2158	262.0	248.0	253.0		459	-10.5	0.0	11	dbSNP_92	253	434,8158	133.3+/-190.8	7,420,3869	no	coding-synonymous	PRG3	NM_006093.3		8,462,6027	AA,AG,GG		5.0512,0.9995,3.6786		153/226	57146202	478,12516	2201	4296	6497	SO:0001819	synonymous_variant	10394	exon4			GACTGTGCTAGTG	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.459C>T	11.37:g.57146202G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_006093	Q5VX23|Q9NXE2	Silent	SNP	ENST00000287143.2	37	CCDS7954.1																																																																																			G|0.966;A|0.034	0.034	strong		0.493	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
RTP1	132112	hgsc.bcm.edu	37	3	186917751	186917751	+	Missense_Mutation	SNP	C	C	G	rs6764714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186917751C>G	ENST00000312295.4	+	2	715	c.685C>G	c.(685-687)Cag>Gag	p.Q229E	RP11-208N14.4_ENST00000356133.3_RNA	NM_153708.2	NP_714919.2	P59025	RTP1_HUMAN	receptor (chemosensory) transporter protein 1	229			Q -> E (in dbSNP:rs6764714).		protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			breast(2)|endometrium(4)|large_intestine(5)|lung(6)|ovary(3)|skin(2)	22	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GTCGCAGGACCAGACGGGCTC	0.622													G|||	2141	0.427516	0.3971	0.4683	5008	,	,		15902	0.2837		0.5437	False		,,,				2504	0.4683				p.Q229E		Atlas-SNP	.											.	RTP1	51	.	0			c.C685G						PASS	.	G	GLU/GLN	1779,2627	642.1+/-397.6	373,1033,797	65.0	61.0	62.0		685	5.7	0.3	3	dbSNP_116	62	4504,4096	560.7+/-387.6	1199,2106,995	yes	missense	RTP1	NM_153708.2	29	1572,3139,1792	GG,GC,CC		47.6279,40.3768,48.3085	benign	229/264	186917751	6283,6723	2203	4300	6503	SO:0001583	missense	132112	exon2			CAGGACCAGACGG	BC034744	CCDS3287.2	3q27.3	2014-02-20	2006-11-21		ENSG00000175077	ENSG00000175077		"""Receptor transporter proteins"""	28580	protein-coding gene	gene with protein product	"""receptor transporting protein 1"", ""zinc finger, 3CxxC-type 1"""	609137	"""receptor transporter protein 1"""			16271481, 15550249, 16720576	Standard	NM_153708		Approved	MGC35450, Z3CXXC1	uc003frg.3	P59025	OTTHUMG00000149886	ENST00000312295.4:c.685C>G	3.37:g.186917751C>G	ENSP00000311712:p.Gln229Glu	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	258	127	0.492248	NM_153708		Missense_Mutation	SNP	ENST00000312295.4	37	CCDS3287.2	930	0.4258241758241758	201	0.40853658536585363	173	0.47790055248618785	148	0.25874125874125875	408	0.5382585751978892	G	7.016	0.557770	0.13436	0.403768	0.523721	ENSG00000175077	ENST00000312295	T	0.28255	1.62	5.74	5.74	0.90152	.	0.244180	0.35262	N	0.003335	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	0.36065	-0.9763	9	0.02654	T	1	.	12.9927	0.58630	0.0:0.162:0.838:0.0	rs6764714;rs17721141;rs6764714	229	P59025	RTP1_HUMAN	E	229	ENSP00000311712:Q229E	ENSP00000311712:Q229E	Q	+	1	0	RTP1	188400445	0.883000	0.30277	0.270000	0.24601	0.222000	0.24845	1.717000	0.37991	1.456000	0.47831	-0.120000	0.15030	CAG	C|0.544;G|0.456	0.456	strong		0.622	RTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313731.2	NM_153708	
GDF5	8200	hgsc.bcm.edu	37	20	34022196	34022196	+	Silent	SNP	C	C	T	rs224330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34022196C>T	ENST00000374372.1	-	4	1520	c.1017G>A	c.(1015-1017)aaG>aaA	p.K339K	GDF5_ENST00000374369.3_Silent_p.K339K|GDF5OS_ENST00000374375.1_Silent_p.A80A			P43026	GDF5_HUMAN	growth differentiation factor 5	339					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			GGAACAGGGCCTTCTCGTGGA	0.647													C|||	817	0.163139	0.2284	0.0533	5008	,	,		15038	0.1865		0.0577	False		,,,				2504	0.2372				p.K339K		Atlas-SNP	.											.	GDF5	66	.	0			c.G1017A						PASS	.	C		867,3539		96,675,1432	39.0	40.0	40.0		1017	1.7	1.0	20	dbSNP_79	40	472,8120		17,438,3841	no	coding-synonymous	GDF5	NM_000557.2		113,1113,5273	TT,TC,CC		5.4935,19.6777,10.3016		339/502	34022196	1339,11659	2203	4296	6499	SO:0001819	synonymous_variant	8200	exon2			CAGGGCCTTCTCG	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.1017G>A	20.37:g.34022196C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_000557	E1P5Q2|Q96SB1	Silent	SNP	ENST00000374372.1	37	CCDS13254.1																																																																																			C|0.877;T|0.123	0.123	strong		0.647	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
CLSTN2	64084	hgsc.bcm.edu	37	3	140282861	140282861	+	Silent	SNP	C	C	T	rs10804675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:140282861C>T	ENST00000458420.3	+	16	2731	c.2541C>T	c.(2539-2541)gtC>gtT	p.V847V		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	847				V -> D (in Ref. 6; AAI03507). {ECO:0000305}.	homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TTGTGTTTGTCGTGGCCATGG	0.547										HNSCC(16;0.037)			C|||	1870	0.373403	0.1982	0.5101	5008	,	,		20261	0.1032		0.6769	False		,,,				2504	0.4796				p.V847V	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.C2541T						PASS	.	C		1221,3185	423.2+/-340.0	177,867,1159	267.0	223.0	238.0		2541	-11.2	0.1	3	dbSNP_120	238	6115,2485	695.3+/-404.8	2168,1779,353	no	coding-synonymous	CLSTN2	NM_022131.2		2345,2646,1512	TT,TC,CC		28.8953,27.7122,43.5953		847/956	140282861	7336,5670	2203	4300	6503	SO:0001819	synonymous_variant	64084	exon16			GTTTGTCGTGGCC	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.2541C>T	3.37:g.140282861C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	176	118	0.670455	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																			C|0.523;T|0.477	0.477	strong		0.547	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
ARAP1	116985	hgsc.bcm.edu	37	11	72421569	72421569	+	Missense_Mutation	SNP	C	C	T	rs369752678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:72421569C>T	ENST00000393609.3	-	10	1479	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	ARAP1_ENST00000455638.2_Missense_Mutation_p.R426Q|ARAP1_ENST00000426523.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000334211.8_Missense_Mutation_p.R181Q|ARAP1_ENST00000429686.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000393605.3_Missense_Mutation_p.R186Q|ARAP1_ENST00000359373.5_Missense_Mutation_p.R426Q	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	426					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GCTAGAGAGCCGGGCCCGGGC	0.632													C|||	2	0.000399361	0.0015	0.0	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.R426Q	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.G1277A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4400		0,0,2200	34.0	36.0	35.0		1277,542,542	1.5	0.0	11		35	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	43,43,43	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	426/1451,181/1134,181/1206	72421569	1,12985	2200	4293	6493	SO:0001583	missense	116985	exon10			GAGAGCCGGGCCC	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.1277G>A	11.37:g.72421569C>T	ENSP00000377233:p.Arg426Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	2.665	-0.278826	0.05642	0.0	1.16E-4	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.06371	3.34;3.34;3.33;3.38;3.36;3.37;3.31	5.55	1.46	0.22682	.	0.843042	0.10345	N	0.685879	T	0.04543	0.0124	L	0.36672	1.1	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	0.06405	0.001;0.0;0.001;0.0;0.002	T	0.49113	-0.8973	10	0.08381	T	0.77	.	4.7688	0.13146	0.0:0.5092:0.148:0.3428	.	181;181;426;426;186	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	Q	426;426;186;181;426;181;181;215	ENSP00000352332:R426Q;ENSP00000390461:R426Q;ENSP00000377230:R186Q;ENSP00000335506:R181Q;ENSP00000377233:R426Q;ENSP00000392264:R181Q;ENSP00000403127:R181Q	ENSP00000335506:R181Q	R	-	2	0	ARAP1	72099217	0.000000	0.05858	0.013000	0.15412	0.255000	0.26057	0.317000	0.19487	0.014000	0.14944	0.655000	0.94253	CGG	.	.	weak		0.632	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
KIF2C	11004	hgsc.bcm.edu	37	1	45226084	45226084	+	Silent	SNP	G	G	A	rs1140279	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45226084G>A	ENST00000372224.4	+	15	1613	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	RP11-269F19.2_ENST00000428791.1_RNA|RP11-269F19.2_ENST00000440985.1_RNA|KIF2C_ENST00000372222.3_Silent_p.A387A|KIF2C_ENST00000372217.1_Silent_p.A446A|KIF2C_ENST00000372218.4_Silent_p.A459A	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	500	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|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)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					AGCGAGGCGCGGACACTTCCA	0.567													G|||	955	0.190695	0.1362	0.2464	5008	,	,		20856	0.2857		0.1382	False		,,,				2504	0.181				p.A500A		Atlas-SNP	.											KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	0			c.G1500A						PASS	.	G		637,3769	273.4+/-271.3	49,539,1615	47.0	46.0	46.0		1500	-10.8	0.4	1	dbSNP_86	46	1450,7150	276.8+/-292.5	129,1192,2979	no	coding-synonymous	KIF2C	NM_006845.3		178,1731,4594	AA,AG,GG		16.8605,14.4576,16.0464		500/726	45226084	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	11004	exon15			AGGCGCGGACACT	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1500G>A	1.37:g.45226084G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Silent	SNP	ENST00000372224.4	37	CCDS512.1																																																																																			G|0.834;A|0.166	0.166	strong		0.567	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
FMN1	342184	hgsc.bcm.edu	37	15	33359950	33359950	+	Intron	SNP	C	C	G	rs141655944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:33359950C>G	ENST00000559047.1	-	3	2043				FMN1_ENST00000561249.1_Intron|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.E46Q|FMN1_ENST00000334528.9_Missense_Mutation_p.E46Q			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)		TTCACAGATTCTAATTTACTC	0.443													C|||	17	0.00339457	0.0	0.0014	5008	,	,		21879	0.0		0.0149	False		,,,				2504	0.001				p.E46Q		Atlas-SNP	.											.	FMN1	174	.	0			c.G136C						PASS	.	C	GLN/GLU	12,3768		0,12,1878	71.0	68.0	69.0		136	4.9	1.0	15	dbSNP_134	69	111,8147		2,107,4020	yes	missense	FMN1	NM_001103184.2	29	2,119,5898	GG,GC,CC		1.3442,0.3175,1.0218	probably-damaging	46/1197	33359950	123,11915	1890	4129	6019	SO:0001627	intron_variant	342184	exon1			CAGATTCTAATTT	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.2044-2675G>C	15.37:g.33359950C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	C	11.34	1.608899	0.28623	0.003175	0.013442	ENSG00000248905	ENST00000334528	T	0.52983	0.64	4.92	4.92	0.64577	.	.	.	.	.	T	0.50616	0.1626	.	.	.	.	.	.	D;D	0.67145	0.996;0.989	P;P	0.59357	0.856;0.714	T	0.66333	-0.5950	7	0.66056	D	0.02	.	18.2894	0.90124	0.0:1.0:0.0:0.0	.	46;46	Q68DA7-3;Q68DA7-5	.;.	Q	46	ENSP00000333950:E46Q	ENSP00000333950:E46Q	E	-	1	0	FMN1	31147242	0.996000	0.38824	0.977000	0.42913	0.071000	0.16799	5.064000	0.64338	2.556000	0.86216	0.655000	0.94253	GAA	C|0.993;G|0.007	0.007	strong		0.443	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
IL36A	27179	hgsc.bcm.edu	37	2	113763575	113763575	+	Missense_Mutation	SNP	A	A	G	rs895497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113763575A>G	ENST00000259211.6	+	2	446	c.35A>G	c.(34-36)cAg>cGg	p.Q12R		NM_014440.1	NP_055255.1	Q9UHA7	IL36A_HUMAN	interleukin 36, alpha	12			Q -> R (in dbSNP:rs895497). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			large_intestine(1)|lung(3)|ovary(2)|skin(1)|stomach(2)	9						ACACCTCAGCAGGGGAGCATT	0.463													G|||	4210	0.840655	0.764	0.8156	5008	,	,		21196	0.9901		0.7247	False		,,,				2504	0.9274				p.Q12R		Atlas-SNP	.											IL36A,NS,carcinoma,0,2	IL36A	17	2	0			c.A35G						PASS	.	G	ARG/GLN	2945,875		1148,649,113	104.0	106.0	105.0		35	-7.6	0.0	2	dbSNP_86	105	5799,2441		2040,1719,361	yes	missense	IL36A	NM_014440.1	43	3188,2368,474	GG,GA,AA		29.6238,22.9058,27.4959	benign	12/159	113763575	8744,3316	1910	4120	6030	SO:0001583	missense	27179	exon2			CTCAGCAGGGGAG	AF201831	CCDS42734.1	2q12-q14.1	2011-07-14	2011-06-06	2011-06-06	ENSG00000136694	ENSG00000136694		"""Interleukins and interleukin receptors"""	15562	protein-coding gene	gene with protein product		605509	"""interleukin 1 family, member 6 (epsilon)"""	IL1F6		10625660	Standard	XM_005263639		Approved	FIL1, FIL1E, IL-1F6, IL1(EPSILON), MGC129553, MGC129552	uc010yxr.2	Q9UHA7	OTTHUMG00000153320	ENST00000259211.6:c.35A>G	2.37:g.113763575A>G	ENSP00000259211:p.Gln12Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_014440	B2RAD9|Q53SR7|Q5BLR4|Q7RTZ8	Missense_Mutation	SNP	ENST00000259211.6	37	CCDS42734.1	1794	0.8214285714285714	382	0.7764227642276422	287	0.7928176795580111	570	0.9965034965034965	555	0.7321899736147758	G	6.833	0.522839	0.13066	0.770942	0.703762	ENSG00000136694	ENST00000259211	T	0.17213	2.29	4.9	-7.62	0.01294	.	4.855280	0.00751	N	0.001070	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	0.31779	-0.9931	9	0.15952	T	0.53	-29.7709	0.7536	0.00994	0.417:0.1454:0.2213:0.2163	rs895497;rs52799607;rs56872263;rs895497	12	Q9UHA7	IL36A_HUMAN	R	12	ENSP00000259211:Q12R	ENSP00000259211:Q12R	Q	+	2	0	IL36A	113480046	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.459000	0.01000	-2.239000	0.00711	-4.544000	0.00004	CAG	A|0.212;G|0.788	0.788	strong		0.463	IL36A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330711.1	NM_014440	
OR7A17	26333	hgsc.bcm.edu	37	19	14991439	14991439	+	Silent	SNP	T	T	G	rs34590588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14991439T>G	ENST00000327462.2	-	1	825	c.729A>C	c.(727-729)tcA>tcC	p.S243S		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	243						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)					CTGAGAGGTGTGATGCACAGG	0.478													.|||	270	0.0539137	0.1354	0.0461	5008	,	,		17091	0.0159		0.0139	False		,,,				2504	0.0297				p.S243S		Atlas-SNP	.											.	OR7A17	37	.	0			c.A729C						PASS	.	C		500,3906		31,438,1734	112.0	97.0	102.0		729	1.2	0.7	19	dbSNP_126	102	256,8344		3,250,4047	no	coding-synonymous	OR7A17	NM_030901.1		34,688,5781	GG,GT,TT		2.9767,11.3482,5.8127		243/310	14991439	756,12250	2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			GAGGTGTGATGCA	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.729A>C	19.37:g.14991439T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			T|0.950;G|0.050	0.050	strong		0.478	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
KRT71	112802	hgsc.bcm.edu	37	12	52946498	52946498	+	Missense_Mutation	SNP	C	C	T	rs665470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	150	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	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	
PLB1	151056	hgsc.bcm.edu	37	2	28854958	28854958	+	Missense_Mutation	SNP	C	C	T	rs2199619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:28854958C>T	ENST00000327757.5	+	55	3997	c.3953C>T	c.(3952-3954)gCg>gTg	p.A1318V	PLB1_ENST00000422425.2_Missense_Mutation_p.A1307V|PLB1_ENST00000541605.1_Missense_Mutation_p.A283V|AC074011.2_ENST00000431376.1_RNA	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1318	4 X 308-326 AA approximate repeats.		A -> V (in dbSNP:rs2199619).		glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GAGGACTTTGCGGTTGTGGTG	0.547													C|||	1269	0.253395	0.1921	0.1844	5008	,	,		18352	0.3204		0.2823	False		,,,				2504	0.2863				p.A1318V		Atlas-SNP	.											.	PLB1	255	.	0			c.C3953T						PASS	.	C	VAL/ALA,VAL/ALA	966,3440	366.4+/-317.8	101,764,1338	151.0	120.0	130.0		3920,3953	4.5	0.0	2	dbSNP_96	130	2291,6309	385.9+/-341.7	312,1667,2321	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	64,64	413,2431,3659	TT,TC,CC		26.6395,21.9246,25.0423	probably-damaging,probably-damaging	1307/1448,1318/1459	28854958	3257,9749	2203	4300	6503	SO:0001583	missense	151056	exon55			ACTTTGCGGTTGT		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3953C>T	2.37:g.28854958C>T	ENSP00000330442:p.Ala1318Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	568|568	0.2600732600732601|0.2600732600732601	110|110	0.22357723577235772|0.22357723577235772	69|69	0.19060773480662985|0.19060773480662985	165|165	0.28846153846153844|0.28846153846153844	224|224	0.2955145118733509|0.2955145118733509	C|C	17.28|17.28	3.349364|3.349364	0.61183|0.61183	0.219246|0.219246	0.266395|0.266395	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605|ENST00000404858	T;T;T|.	0.33654|.	1.4;1.4;1.4|.	5.37|5.37	4.49|4.49	0.54785|0.54785	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.	0.507528|.	0.19024|.	N|.	0.124729|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.67569|0.67569	2.06|2.06	0.80722|0.80722	P|P	0.0|0.0	D;D|.	0.63880|.	0.993;0.985|.	P;P|.	0.55011|.	0.655;0.766|.	T|T	0.14035|0.14035	-1.0487|-1.0487	9|4	0.46703|.	T|.	0.11|.	-3.2628|-3.2628	9.8924|9.8924	0.41298|0.41298	0.0:0.906:0.0:0.094|0.0:0.906:0.0:0.094	rs2199619;rs57133235;rs2199619|rs2199619;rs57133235;rs2199619	1307;1318|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	V|W	1318;1307;283|1306	ENSP00000330442:A1318V;ENSP00000416440:A1307V;ENSP00000437426:A283V|.	ENSP00000330442:A1318V|.	A|R	+|+	2|1	0|2	PLB1|PLB1	28708462|28708462	0.011000|0.011000	0.17503|0.17503	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	2.540000|2.540000	0.45727|0.45727	1.290000|1.290000	0.44636|0.44636	0.655000|0.655000	0.94253|0.94253	GCG|CGG	C|0.742;A|0.002	.	strong		0.547	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
ANK3	288	hgsc.bcm.edu	37	10	61831290	61831290	+	Missense_Mutation	SNP	T	T	C	rs28932171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61831290T>C	ENST00000280772.2	-	37	9540	c.9349A>G	c.(9349-9351)Atc>Gtc	p.I3117V	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3117			I -> V (in dbSNP:rs28932171).		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)			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						TGACTTATGATTTTTTTTACA	0.403													T|||	158	0.0315495	0.0053	0.049	5008	,	,		19965	0.0		0.1044	False		,,,				2504	0.0123				p.I3117V		Atlas-SNP	.											.	ANK3	703	.	0			c.A9349G						PASS	.	T	,,,VAL/ILE	85,4321	69.8+/-107.6	4,77,2122	144.0	152.0	150.0		,,,9349	5.2	1.0	10	dbSNP_125	150	942,7658	202.4+/-245.7	59,824,3417	yes	intron,intron,intron,missense	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,29	63,901,5539	CC,CT,TT		10.9535,1.9292,7.8964	,,,possibly-damaging	,,,3117/4378	61831290	1027,11979	2203	4300	6503	SO:0001583	missense	288	exon37			TTATGATTTTTTT	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.9349A>G	10.37:g.61831290T>C	ENSP00000280772:p.Ile3117Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	105	0.04807692307692308	3	0.006097560975609756	22	0.06077348066298342	0	0.0	80	0.10554089709762533	T	4.914	0.169753	0.09339	0.019292	0.109535	ENSG00000151150	ENST00000280772	T	0.64991	-0.13	5.23	5.23	0.72850	.	0.000000	0.42821	D	0.000651	T	0.01029	0.0034	N	0.12887	0.27	0.80722	D	1	B	0.14012	0.009	B	0.10450	0.005	T	0.01249	-1.1406	10	0.24483	T	0.36	.	15.1124	0.72368	0.0:0.0:0.0:1.0	rs28932171;rs28932171	3117	Q12955	ANK3_HUMAN	V	3117	ENSP00000280772:I3117V	ENSP00000280772:I3117V	I	-	1	0	ANK3	61501296	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	4.220000	0.58567	1.983000	0.57843	0.260000	0.18958	ATC	T|0.936;C|0.064	0.064	strong		0.403	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
LZTR1	8216	hgsc.bcm.edu	37	22	21347142	21347142	+	Silent	SNP	C	C	T	rs145833752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21347142C>T	ENST00000215739.8	+	11	1568	c.1209C>T	c.(1207-1209)ttC>ttT	p.F403F	LZTR1_ENST00000389355.3_Silent_p.F384F|LZTR1_ENST00000479606.1_3'UTR	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	403					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)			TGTACATCTTCGGGGGCACGG	0.652													C|||	24	0.00479233	0.0023	0.0029	5008	,	,		19667	0.001		0.0109	False		,,,				2504	0.0072				p.F403F		Atlas-SNP	.											.	LZTR1	99	.	0			c.C1209T						PASS	.	C		7,4393	12.9+/-30.5	0,7,2193	55.0	45.0	48.0		1209	-5.1	1.0	22	dbSNP_134	48	78,8522	43.6+/-101.6	0,78,4222	no	coding-synonymous	LZTR1	NM_006767.3		0,85,6415	TT,TC,CC		0.907,0.1591,0.6538		403/841	21347142	85,12915	2200	4300	6500	SO:0001819	synonymous_variant	8216	exon11			CATCTTCGGGGGC	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.1209C>T	22.37:g.21347142C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			C|0.994;T|0.006	0.006	strong		0.652	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10575824	10575824	+	Silent	SNP	C	C	A	rs1970817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	73	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	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	
OBFC1	79991	hgsc.bcm.edu	37	10	105657363	105657363	+	Silent	SNP	C	C	G	rs11191853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:105657363C>G	ENST00000224950.3	-	7	863	c.696G>C	c.(694-696)gtG>gtC	p.V232V	OBFC1_ENST00000369764.1_Silent_p.V232V|OBFC1_ENST00000466828.1_5'UTR	NM_024928.4	NP_079204.2	Q9H668	STN1_HUMAN	oligonucleotide/oligosaccharide-binding fold containing 1	232	Winged helix-turn-helix (wHTH) 1.				positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromosome, telomeric region (GO:0000784)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)|single-stranded telomeric DNA binding (GO:0043047)			large_intestine(3)|lung(7)|ovary(1)|pancreas(2)	13		Colorectal(252;0.178)		Epithelial(162;3.39e-10)|all cancers(201;1.32e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0151)		GCAAAGACTCCACCATTTCCA	0.527													C|||	942	0.188099	0.2035	0.2046	5008	,	,		19002	0.1577		0.2545	False		,,,				2504	0.1186				p.V232V		Atlas-SNP	.											.	OBFC1	33	.	0			c.G696C						PASS	.	C		957,3449	362.1+/-316.0	115,727,1361	131.0	108.0	116.0		696	5.4	0.5	10	dbSNP_120	116	2007,6593	351.9+/-328.4	205,1597,2498	no	coding-synonymous	OBFC1	NM_024928.4		320,2324,3859	GG,GC,CC		23.3372,21.7204,22.7895		232/369	105657363	2964,10042	2203	4300	6503	SO:0001819	synonymous_variant	79991	exon7			AGACTCCACCATT	BC017400	CCDS7552.1	10q25.1	2011-06-14				ENSG00000107960			26200	protein-coding gene	gene with protein product		613128				12477932	Standard	NM_024928		Approved	FLJ22559, bA541N10.2	uc001kxm.3	Q9H668		ENST00000224950.3:c.696G>C	10.37:g.105657363C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	35	0.393258	NM_024928	D3DR99|Q5TCZ0	Silent	SNP	ENST00000224950.3	37	CCDS7552.1																																																																																			C|0.780;G|0.220	0.220	strong		0.527	OBFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050174.1	NM_024928	
F5	2153	hgsc.bcm.edu	37	1	169511734	169511734	+	Missense_Mutation	SNP	T	T	C	rs4525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169511734T>C	ENST00000367797.3	-	13	2795	c.2594A>G	c.(2593-2595)cAt>cGt	p.H865R	F5_ENST00000367796.3_Missense_Mutation_p.H870R	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	865	B.		H -> R (in dbSNP:rs4525). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	GGGTCCCTTATGCTTAGCATG	0.448													T|||	1316	0.26278	0.1679	0.3948	5008	,	,		21442	0.248		0.2535	False		,,,				2504	0.3221				p.H865R		Atlas-SNP	.											F5,NS,carcinoma,-1,1	F5	301	1	0			c.A2594G						PASS	.	T	ARG/HIS	814,3592	321.5+/-297.2	68,678,1457	193.0	179.0	184.0		2594	-1.1	0.0	1	dbSNP_52	184	2356,6244	393.9+/-344.5	300,1756,2244	yes	missense	F5	NM_000130.4	29	368,2434,3701	CC,CT,TT		27.3953,18.4748,24.3734	benign	865/2225	169511734	3170,9836	2203	4300	6503	SO:0001583	missense	2153	exon13			CCCTTATGCTTAG	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.2594A>G	1.37:g.169511734T>C	ENSP00000356771:p.His865Arg	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	284	170	0.598592	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	T	5.461	0.270076	0.10349	0.184748	0.273953	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.19806	2.12;2.12	5.72	-1.12	0.09808	.	1.326480	0.04974	N	0.464508	T	0.05181	0.0138	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37314	-0.9711	9	0.22109	T	0.4	-5.295	5.176	0.15135	0.0:0.2234:0.2754:0.5013	rs4525;rs3186700;rs52799245;rs57691265;rs4525	865	P12259	FA5_HUMAN	R	865;870	ENSP00000356771:H865R;ENSP00000356770:H870R	ENSP00000356770:H870R	H	-	2	0	F5	167778358	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.167000	0.09940	-0.449000	0.07117	-0.351000	0.07748	CAT	T|0.758;C|0.242	0.242	strong		0.448	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
LRWD1	222229	hgsc.bcm.edu	37	7	102112914	102112914	+	Silent	SNP	C	C	T	rs184787600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102112914C>T	ENST00000292616.5	+	13	1700	c.1548C>T	c.(1546-1548)agC>agT	p.S516S	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	516					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						CCAAGGGGAGCGGCCTGGGCA	0.682													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		14662	0.0		0.008	False		,,,				2504	0.0051				p.S516S		Atlas-SNP	.											LRWD1,colon,carcinoma,0,1	LRWD1	41	1	0			c.C1548T						PASS	.	C		10,4230		0,10,2110	11.0	12.0	12.0		1548	-4.2	0.0	7		12	86,8236		0,86,4075	no	coding-synonymous	LRWD1	NM_152892.1		0,96,6185	TT,TC,CC		1.0334,0.2358,0.7642		516/648	102112914	96,12466	2120	4161	6281	SO:0001819	synonymous_variant	222229	exon13			GGGGAGCGGCCTG	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.1548C>T	7.37:g.102112914C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	C	5.586	0.292913	0.10567	0.002358	0.010334	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-4.25	0.03766	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34254	-0.9836	4	.	.	.	-19.7101	8.7692	0.34722	0.0949:0.4915:0.0:0.4135	.	.	.	.	V	127;102	.	.	A	+	2	0	LRWD1	101899919	0.000000	0.05858	0.001000	0.08648	0.712000	0.41017	-1.540000	0.02200	-0.725000	0.04901	0.655000	0.94253	GCG	C|0.995;T|0.005	0.005	strong		0.682	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs61746100|rs806607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:65427040T>C	ENST00000343002.2	+	13	2959	c.2295T>C	c.(2293-2295)taT>taC	p.Y765Y	HEPH_ENST00000519389.1_Silent_p.Y819Y|HEPH_ENST00000336279.5_Silent_p.Y498Y|HEPH_ENST00000441993.2_Silent_p.Y768Y|HEPH_ENST00000374727.3_Silent_p.Y768Y|HEPH_ENST00000419594.1_Silent_p.Y576Y			Q9BQS7	HEPH_HUMAN	hephaestin	765	Plastocyanin-like 5.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						CCTCTAGTTATGGTTACATTT	0.448													C|||	1320	0.349669	0.7141	0.1988	3775	,	,		9954	0.001		0.171	False		,,,				2504	0.0665				p.Y819Y		Atlas-SNP	.											.	HEPH	224	.	0			c.T2457C						PASS	.	C	,,	3276,559		1190,402,494,40,77	114.0	98.0	103.0		2304,1494,2457	3.6	1.0	X	dbSNP_86	103	1509,5219		122,788,477,1518,1395	no	coding-synonymous,coding-synonymous,coding-synonymous	HEPH	NM_001130860.2,NM_014799.2,NM_138737.3	,,	1312,1190,971,1558,1472	CC,CT,C,TT,T		22.4287,14.5763,45.2996	,,	768/1161,498/892,819/1213	65427040	4785,5778	2203	4300	6503	SO:0001819	synonymous_variant	9843	exon14			TAGTTATGGTTAC	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.2295T>C	X.37:g.65427040T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	37																																																																																				0|0.020;C|0.435	0.435	strong		0.448	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	
PGAM5	192111	hgsc.bcm.edu	37	12	133294333	133294333	+	Silent	SNP	C	C	T	rs61978651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133294333C>T	ENST00000498926.2	+	4	592	c.534C>T	c.(532-534)ggC>ggT	p.G178G	PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000454808.2_Silent_p.G29G|PGAM5_ENST00000543955.1_Silent_p.G29G|PGAM5_ENST00000317555.2_Silent_p.G178G	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	178					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		TGCGGGAAGGCGCCCCCATCG	0.667													C|||	273	0.0545128	0.0015	0.0461	5008	,	,		11840	0.1081		0.0855	False		,,,				2504	0.045				p.G178G		Atlas-SNP	.											PGAM5,NS,carcinoma,+1,1	PGAM5	18	1	0			c.C534T						PASS	.	C	,,	57,4269		0,57,2106	20.0	26.0	24.0		534,534,534	-5.2	1.0	12	dbSNP_129	24	669,7871		29,611,3630	no	coding-synonymous,coding-synonymous,coding-synonymous	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	,,	29,668,5736	TT,TC,CC		7.8337,1.3176,5.6428	,,	178/290,178/289,178/256	133294333	726,12140	2163	4270	6433	SO:0001819	synonymous_variant	192111	exon4			GGAAGGCGCCCCC	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.534C>T	12.37:g.133294333C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_138575	A9LN06|C9IZY7|Q96JB0	Silent	SNP	ENST00000498926.2	37	CCDS53845.1																																																																																			C|0.942;T|0.058	0.058	strong		0.667	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575	
HORMAD1	84072	hgsc.bcm.edu	37	1	150679033	150679033	+	Missense_Mutation	SNP	G	G	A	rs1336900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150679033G>A	ENST00000361824.2	-	10	905	c.800C>T	c.(799-801)aCa>aTa	p.T267I	HORMAD1_ENST00000368993.2_Missense_Mutation_p.T267I|HORMAD1_ENST00000368995.4_Missense_Mutation_p.T187I|HORMAD1_ENST00000322343.7_Missense_Mutation_p.T260I	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	267			T -> I (in dbSNP:rs1336900). {ECO:0000269|PubMed:15489334}.		blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|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;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			ACTTACACTTGTATAATGCTC	0.289													G|||	1931	0.385583	0.2269	0.4467	5008	,	,		18017	0.3571		0.4095	False		,,,				2504	0.5613				p.T267I		Atlas-SNP	.											.	HORMAD1	59	.	0			c.C800T						PASS	.	G	ILE/THR,ILE/THR	1157,3249	406.6+/-333.9	156,845,1202	131.0	125.0	127.0		779,800	-1.2	0.0	1	dbSNP_88	127	3356,5242	496.4+/-374.3	655,2046,1598	yes	missense,missense	HORMAD1	NM_001199829.1,NM_032132.4	89,89	811,2891,2800	AA,AG,GG		39.0323,26.2596,34.7047	benign,benign	260/388,267/395	150679033	4513,8491	2203	4299	6502	SO:0001583	missense	84072	exon10			ACACTTGTATAAT	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"""cancer/testis antigen 46"""	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.800C>T	1.37:g.150679033G>A	ENSP00000355167:p.Thr267Ile	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_032132	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Missense_Mutation	SNP	ENST00000361824.2	37	CCDS967.1	796	0.36446886446886445	124	0.25203252032520324	162	0.44751381215469616	202	0.3531468531468531	308	0.40633245382585753	G	1.299	-0.605312	0.03717	0.262596	0.390323	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824	T;T;T;T	0.42900	0.96;1.53;1.53;1.54	5.19	-1.24	0.09435	.	0.527882	0.19357	N	0.116243	T	0.03871	0.0109	N	0.02916	-0.46	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.33954	-0.9848	9	0.17369	T	0.5	-4.4113	2.2235	0.03978	0.4694:0.1209:0.2923:0.1174	rs1336900;rs17600196;rs52823371;rs59645580;rs1336900	187;260;267	Q86X24-4;Q86X24-2;Q86X24	.;.;HORM1_HUMAN	I	187;267;196;187;260;267	ENSP00000357991:T187I;ENSP00000357989:T267I;ENSP00000326489:T260I;ENSP00000355167:T267I	ENSP00000326489:T260I	T	-	2	0	HORMAD1	148945657	0.039000	0.19947	0.037000	0.18230	0.469000	0.32828	0.546000	0.23284	-0.101000	0.12219	-1.363000	0.01210	ACA	G|0.641;A|0.359	0.359	strong		0.289	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33877570	33877570	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:33877570G>A	ENST00000307296.3	+	8	1246	c.869G>A	c.(868-870)cGc>cAc	p.R290H	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.R295H			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	290	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				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)	p.R290L(1)		central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						GTGGCATCTCGCTATGATGAA	0.358																																					p.R295H		Atlas-SNP	.											PDCD6IP,NS,carcinoma,0,1	PDCD6IP	62	1	1	Substitution - Missense(1)	lung(1)	c.G884A						scavenged	.						117.0	120.0	119.0					3																	33877570		2203	4300	6503	SO:0001583	missense	10015	exon8			CATCTCGCTATGA	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.869G>A	3.37:g.33877570G>A	ENSP00000307387:p.Arg290His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339566	0.95783	.	.	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.18174	2.23;2.23	5.18	5.18	0.71444	BRO1 domain (3);	0.052437	0.64402	D	0.000001	T	0.40347	0.1113	M	0.74258	2.255	0.80722	D	1	D;D;D	0.69078	0.966;0.997;0.994	B;P;P	0.62491	0.335;0.893;0.903	T	0.12243	-1.0555	10	0.29301	T	0.29	-3.8982	18.691	0.91582	0.0:0.0:1.0:0.0	.	71;295;290	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	H	290;295	ENSP00000307387:R290H;ENSP00000411825:R295H	ENSP00000307387:R290H	R	+	2	0	PDCD6IP	33852574	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.852000	0.99516	2.407000	0.81776	0.650000	0.86243	CGC	.	.	none		0.358	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
PDZRN3	23024	hgsc.bcm.edu	37	3	73433494	73433494	+	Silent	SNP	T	T	C	rs13091636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:73433494T>C	ENST00000263666.4	-	10	2337	c.2223A>G	c.(2221-2223)tcA>tcG	p.S741S	PDZRN3_ENST00000462146.2_Silent_p.S398S|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000466780.1_Silent_p.S398S|PDZRN3_ENST00000479530.1_Silent_p.S458S|PDZRN3_ENST00000535920.1_Silent_p.S463S	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	741					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CGGTGATATCTGAGAGCTCGT	0.612													T|||	1794	0.358227	0.1331	0.428	5008	,	,		17770	0.5357		0.4702	False		,,,				2504	0.3149				p.S741S		Atlas-SNP	.											.	PDZRN3	196	.	0			c.A2223G						PASS	.	T		796,3610	319.3+/-296.1	79,638,1486	50.0	45.0	47.0		2223	-4.7	0.9	3	dbSNP_121	47	3931,4669	547.3+/-385.1	898,2135,1267	no	coding-synonymous	PDZRN3	NM_015009.1		977,2773,2753	CC,CT,TT		45.7093,18.0663,36.3448		741/1067	73433494	4727,8279	2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			GATATCTGAGAGC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2223A>G	3.37:g.73433494T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			A|0.000;C|0.372;T|0.627	0.372	strong		0.612	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
MLPH	79083	hgsc.bcm.edu	37	2	238434245	238434245	+	Splice_Site	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238434245C>G	ENST00000264605.3	+	7	971	c.677C>G	c.(676-678)tCc>tGc	p.S226C	MLPH_ENST00000445024.2_Splice_Site_p.S226C|MLPH_ENST00000410032.1_Intron|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000338530.4_Splice_Site_p.S226C|MLPH_ENST00000409373.1_Splice_Site_p.S186C	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	226					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		TGTGCTTAGTCCCTCACAGAT	0.607																																					p.S226C		Atlas-SNP	.											.	MLPH	41	.	0			c.C677G						PASS	.						42.0	44.0	44.0					2																	238434245		2203	4300	6503	SO:0001630	splice_region_variant	79083	exon7			CTTAGTCCCTCAC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.676-1C>G	2.37:g.238434245C>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.10|10.10	1.256882|1.256882	0.22965|0.22965	.|.	.|.	ENSG00000115648|ENSG00000115648	ENST00000437893|ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T|T;T;T;T	0.30182|0.29655	1.54|1.92;1.91;1.78;1.56	3.35|3.35	1.51|1.51	0.23008|0.23008	.|.	.|2.607010	.|0.01744	.|N	.|0.029577	T|T	0.39655|0.39655	0.1086|0.1086	L|L	0.40543|0.40543	1.245|1.245	0.35469|0.35469	D|D	0.797185|0.797185	.|B;D;B;D;B;B	.|0.71674	.|0.017;0.998;0.085;0.986;0.137;0.021	.|B;P;B;P;B;B	.|0.56216	.|0.017;0.747;0.071;0.794;0.149;0.023	T|T	0.32640|0.32640	-0.9899|-0.9899	7|10	0.87932|0.54805	D|T	0|0.06	-6.1716|-6.1716	4.7792|4.7792	0.13194|0.13194	0.0:0.6545:0.2219:0.1236|0.0:0.6545:0.2219:0.1236	.|.	.|226;110;226;186;226;226	.|B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36	.|.;.;.;.;.;MELPH_HUMAN	A|C	33|226;226;226;186	ENSP00000412438:P33A|ENSP00000264605:S226C;ENSP00000414849:S226C;ENSP00000341845:S226C;ENSP00000386780:S186C	ENSP00000412438:P33A|ENSP00000264605:S226C	P|S	+|+	1|2	0|0	MLPH|MLPH	238098984|238098984	0.730000|0.730000	0.28100|0.28100	0.950000|0.950000	0.38849|0.38849	0.777000|0.777000	0.43975|0.43975	-0.133000|-0.133000	0.10451|0.10451	0.424000|0.424000	0.26061|0.26061	0.563000|0.563000	0.77884|0.77884	CCC|TCC	.	.	none		0.607	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	Missense_Mutation
CCDC180	100499483	hgsc.bcm.edu	37	9	100105782	100105782	+	Missense_Mutation	SNP	C	C	G	rs2061634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100105782C>G	ENST00000357054.1	+	33	3919	c.2984C>G	c.(2983-2985)tCc>tGc	p.S995C	CCDC180_ENST00000411667.2_Missense_Mutation_p.S853C|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.S856C|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.S856C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	995			S -> C (in dbSNP:rs2061634).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AACGACACTTCCAGTGCCAAG	0.383													C|||	1394	0.278355	0.41	0.304	5008	,	,		19363	0.1835		0.1998	False		,,,				2504	0.2607				p.S856C		Atlas-SNP	.											.	.	.	.	0			c.C2567G						PASS	.	C	CYS/SER	1846,2560	537.6+/-374.8	400,1046,757	100.0	94.0	96.0		2567	1.9	0.0	9	dbSNP_94	96	2349,6251	392.1+/-343.9	320,1709,2271	yes	missense	C9orf174	NM_020893.2	112	720,2755,3028	GG,GC,CC		27.314,41.8974,32.2543	benign	856/1702	100105782	4195,8811	2203	4300	6503	SO:0001583	missense	0	exon19			ACACTTCCAGTGC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2984C>G	9.37:g.100105782C>G	ENSP00000349562:p.Ser995Cys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		542	0.24816849816849818	207	0.42073170731707316	88	0.2430939226519337	106	0.1853146853146853	141	0.18601583113456466	C	15.07	2.723583	0.48728	0.418974	0.27314	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.13307	2.9;2.9;2.6;2.9	5.39	1.93	0.25924	.	1.074820	0.07175	N	0.853079	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.17038	0.02;0.012;0.02	B;B;B	0.17098	0.017;0.01;0.017	T	0.47761	-0.9092	9	0.52906	T	0.07	-0.9304	4.218	0.10544	0.0:0.5169:0.2133:0.2698	rs2061634;rs2061634	879;995;995	Q86Y65;B7ZMG3;Q9P1Z9	.;.;CI174_HUMAN	C	995;856;853;879;856	ENSP00000349562:S995C;ENSP00000364348:S856C;ENSP00000414000:S853C;ENSP00000434727:S856C	ENSP00000349562:S995C	S	+	2	0	C9orf174	99145603	0.001000	0.12720	0.002000	0.10522	0.059000	0.15707	0.649000	0.24843	0.490000	0.27771	0.655000	0.94253	TCC	C|0.698;G|0.302	0.302	strong		0.383	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
CUL9	23113	hgsc.bcm.edu	37	6	43184132	43184132	+	Missense_Mutation	SNP	A	A	C	rs2273709	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43184132A>C	ENST00000252050.4	+	31	6257	c.6173A>C	c.(6172-6174)cAc>cCc	p.H2058P	CUL9_ENST00000372647.2_Missense_Mutation_p.H2030P|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Missense_Mutation_p.H1948P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2058			H -> P (in dbSNP:rs2273709).	HQ -> PL (in Ref. 3; CAH18696). {ECO:0000305}.	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						CTGTGCGTACACCAGGCTCAG	0.632													C|||	2000	0.399361	0.7254	0.2233	5008	,	,		17713	0.4226		0.174	False		,,,				2504	0.2914				p.H2058P		Atlas-SNP	.											CUL9,colon,carcinoma,0,1	CUL9	248	1	0			c.A6173C						PASS	.	C	PRO/HIS	2916,1490	473.1+/-356.6	970,976,257	70.0	66.0	67.0		6173	5.7	1.0	6	dbSNP_100	67	1803,6797	731.6+/-406.8	179,1445,2676	yes	missense	CUL9	NM_015089.2	77	1149,2421,2933	CC,CA,AA		20.9651,33.8175,36.2833	benign	2058/2518	43184132	4719,8287	2203	4300	6503	SO:0001583	missense	23113	exon31			GCGTACACCAGGC	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.6173A>C	6.37:g.43184132A>C	ENSP00000252050:p.His2058Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	809	0.37042124542124544	355	0.7215447154471545	84	0.23204419889502761	232	0.40559440559440557	138	0.1820580474934037	C	0.015	-1.547485	0.00926	0.661825	0.209651	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.03663	3.85;3.85;3.85	5.7	5.7	0.88788	.	0.058585	0.64402	N	0.000002	T	0.00328	0.0010	N	0.00289	-1.7	0.52099	P	5.299999999996974E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44452	-0.9327	9	0.02654	T	1	-18.3709	10.902	0.47058	0.2694:0.6127:0.1179:0.0	rs2273709;rs61442708;rs2273709	1948;2030;2058	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	P	2058;1948;2030	ENSP00000252050:H2058P;ENSP00000346490:H1948P;ENSP00000361730:H2030P	ENSP00000252050:H2058P	H	+	2	0	CUL9	43292110	0.995000	0.38212	0.998000	0.56505	0.076000	0.17211	2.797000	0.47877	1.430000	0.47334	-0.121000	0.15023	CAC	A|0.629;C|0.371	0.371	strong		0.632	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
SURF2	6835	hgsc.bcm.edu	37	9	136228006	136228006	+	Silent	SNP	G	G	A	rs34939258	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136228006G>A	ENST00000371964.4	+	6	803	c.762G>A	c.(760-762)caG>caA	p.Q254Q	SURF4_ENST00000467910.1_5'Flank	NM_017503.3	NP_059973.4	Q15527	SURF2_HUMAN	surfeit 2	254						nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)		CCTGTAAACAGCCAGGTTAAT	0.458													G|||	157	0.0313498	0.0038	0.0389	5008	,	,		20944	0.0198		0.0815	False		,,,				2504	0.0235				p.Q254Q		Atlas-SNP	.											.	SURF2	9	.	0			c.G762A						PASS	.	G		75,4331	67.0+/-104.6	1,73,2129	135.0	136.0	136.0		762	1.2	0.0	9	dbSNP_126	136	725,7875	176.6+/-226.4	35,655,3610	no	coding-synonymous	SURF2	NM_017503.3		36,728,5739	AA,AG,GG		8.4302,1.7022,6.151		254/257	136228006	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	6835	exon6			TAAACAGCCAGGT		CCDS6967.1	9q33-q34	2008-07-21			ENSG00000148291	ENSG00000148291			11475	protein-coding gene	gene with protein product	"""surfeit locus protein 2"""	185630					Standard	NM_017503		Approved		uc004cdi.2	Q15527	OTTHUMG00000020867	ENST00000371964.4:c.762G>A	9.37:g.136228006G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_017503	Q6IBP9|Q96CD1	Silent	SNP	ENST00000371964.4	37	CCDS6967.1																																																																																			G|0.940;A|0.060	0.060	strong		0.458	SURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054883.1	NM_017503	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41610024	41610024	+	Silent	SNP	G	G	A	rs139451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:41610024G>A	ENST00000216237.5	+	3	548	c.390G>A	c.(388-390)agG>agA	p.R130R	RP4-756G23.5_ENST00000441316.1_RNA|L3MBTL2_ENST00000489136.1_3'UTR|RP4-756G23.5_ENST00000451176.1_RNA	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	130					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCTTGGCTAGGTTACAGGTGA	0.527													A|||	1823	0.364018	0.5749	0.3357	5008	,	,		18957	0.1885		0.3638	False		,,,				2504	0.2802				p.R130R		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.G390A						PASS	.	A		2451,1955	552.3+/-378.5	691,1069,443	96.0	92.0	93.0		390	0.9	0.6	22	dbSNP_78	93	3277,5323	647.6+/-400.4	659,1959,1682	no	coding-synonymous	L3MBTL2	NM_031488.4		1350,3028,2125	AA,AG,GG		38.1047,44.3713,44.0412		130/706	41610024	5728,7278	2203	4300	6503	SO:0001819	synonymous_variant	83746	exon3			GGCTAGGTTACAG	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.390G>A	22.37:g.41610024G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Silent	SNP	ENST00000216237.5	37	CCDS14011.1																																																																																			G|0.598;A|0.402	0.402	strong		0.527	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
ITIH4	3700	hgsc.bcm.edu	37	3	52861211	52861211	+	Missense_Mutation	SNP	A	A	T	rs13072536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52861211A>T	ENST00000266041.4	-	3	350	c.254T>A	c.(253-255)aTc>aAc	p.I85N	ITIH4_ENST00000485816.1_Missense_Mutation_p.I85N|ITIH4_ENST00000406595.1_Missense_Mutation_p.I85N|ITIH4_ENST00000346281.5_Missense_Mutation_p.I85N|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000434759.3_5'UTR|RP5-966M1.6_ENST00000513520.1_5'Flank|ITIH4-AS1_ENST00000478366.1_RNA	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	96	0	0		WXS	Illumina HiSeq	Phase_I	141	79	0.560284	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	
SPEN	23013	hgsc.bcm.edu	37	1	16265904	16265904	+	Silent	SNP	T	T	A	rs41269155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16265904T>A	ENST00000375759.3	+	15	11181	c.10977T>A	c.(10975-10977)atT>atA	p.I3659I		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3659	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				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)		ACCTCATGATTGTCATTGCCT	0.552													T|||	224	0.0447284	0.0613	0.0375	5008	,	,		17655	0.0079		0.0616	False		,,,				2504	0.0481				p.I3659I		Atlas-SNP	.											.	SPEN	374	.	0			c.T10977A						PASS	.	T		314,4092	168.7+/-199.5	14,286,1903	208.0	197.0	200.0		10977	0.8	1.0	1	dbSNP_127	200	678,7922	169.9+/-221.1	33,612,3655	no	coding-synonymous	SPEN	NM_015001.2		47,898,5558	AA,AT,TT		7.8837,7.1266,7.6272		3659/3665	16265904	992,12014	2203	4300	6503	SO:0001819	synonymous_variant	23013	exon15			CATGATTGTCATT		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.10977T>A	1.37:g.16265904T>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																			T|0.932;A|0.068	0.068	strong		0.552	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
NKAIN4	128414	hgsc.bcm.edu	37	20	61879009	61879009	+	Missense_Mutation	SNP	G	G	T	rs2236194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61879009G>T	ENST00000370316.3	-	4	481	c.392C>A	c.(391-393)gCc>gAc	p.A131D	NKAIN4_ENST00000466885.1_5'UTR|NKAIN4_ENST00000370307.2_Missense_Mutation_p.A69D|NKAIN4_ENST00000370313.1_Missense_Mutation_p.A69D	NM_152864.3	NP_690603.3	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4	131			A -> D (in dbSNP:rs2236194).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|lung(1)|ovary(1)	4	all_cancers(38;2.72e-09)					TGACACCAGGGCCTGGCCATG	0.687													G|||	1007	0.201078	0.1271	0.1643	5008	,	,		15597	0.3413		0.1759	False		,,,				2504	0.2086				p.A131D		Atlas-SNP	.											NKAIN4,NS,carcinoma,0,1	NKAIN4	23	1	0			c.C392A						scavenged	.	G	ASP/ALA	528,3306		37,454,1426	15.0	15.0	15.0		392	3.5	0.9	20	dbSNP_98	15	1019,6147		63,893,2627	yes	missense	NKAIN4	NM_152864.3	126	100,1347,4053	TT,TG,GG		14.2199,13.7715,14.0636	benign	131/209	61879009	1547,9453	1917	3583	5500	SO:0001583	missense	128414	exon4			ACCAGGGCCTGGC	BC041812	CCDS13514.1	20q13.33	2007-10-04	2007-10-04	2007-10-04	ENSG00000101198	ENSG00000101198		"""Na+/K+ transporting ATPase interacting"""	16191	protein-coding gene	gene with protein product		612873	"""chromosome 20 open reading frame 58"""	C20orf58		17606467	Standard	NM_152864		Approved	bA261N11.2, FAM77A	uc002yek.3	Q8IVV8	OTTHUMG00000032959	ENST00000370316.3:c.392C>A	20.37:g.61879009G>T	ENSP00000359340:p.Ala131Asp	Somatic	192	2	0.0104167		WXS	Illumina HiSeq	Phase_I	179	71	0.396648	NM_152864	Q4VXQ6|Q9BQU8|Q9BQU9	Missense_Mutation	SNP	ENST00000370316.3	37	CCDS13514.1	440	0.20146520146520147	69	0.1402439024390244	60	0.16574585635359115	184	0.32167832167832167	127	0.16754617414248021	G	10.49	1.365976	0.24684	0.137715	0.142199	ENSG00000101198	ENST00000370313;ENST00000370316;ENST00000370307;ENST00000370317	T;T;T;T	0.14022	2.54;2.54;2.54;2.54	3.48	3.48	0.39840	.	0.140296	0.49305	U	0.000143	T	0.00012	0.0000	L	0.47716	1.5	0.28771	P	0.9003507	D;D	0.60575	0.988;0.978	P;P	0.57846	0.828;0.828	T	0.48547	-0.9026	9	0.22706	T	0.39	-15.0334	10.0854	0.42415	0.0:0.0:0.7988:0.2012	rs2236194;rs2236194	69;131	A6NNM2;Q8IVV8	.;NKAI4_HUMAN	D	69;131;69;61	ENSP00000359336:A69D;ENSP00000359340:A131D;ENSP00000359330:A69D;ENSP00000359341:A61D	ENSP00000359330:A69D	A	-	2	0	NKAIN4	61349454	1.000000	0.71417	0.867000	0.34043	0.328000	0.28507	5.746000	0.68681	1.465000	0.48006	0.313000	0.20887	GCC	G|0.819;T|0.181	0.181	strong		0.687	NKAIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080117.3	NM_152864	
ITPKC	80271	hgsc.bcm.edu	37	19	41235167	41235167	+	Missense_Mutation	SNP	G	G	A	rs112628847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41235167G>A	ENST00000263370.2	+	3	1349	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H		NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	439					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGTGAGCAGCGCAGCCTGGAG	0.532													G|||	72	0.014377	0.0023	0.0144	5008	,	,		14148	0.0		0.0537	False		,,,				2504	0.0051				p.R439H		Atlas-SNP	.											.	ITPKC	36	.	0			c.G1316A						PASS	.	G	HIS/ARG	44,4362	47.5+/-82.1	0,44,2159	70.0	61.0	64.0		1316	2.2	1.0	19	dbSNP_132	64	505,8095	144.8+/-200.6	15,475,3810	yes	missense	ITPKC	NM_025194.2	29	15,519,5969	AA,AG,GG		5.8721,0.9986,4.2211	benign	439/684	41235167	549,12457	2203	4300	6503	SO:0001583	missense	80271	exon3			AGCAGCGCAGCCT	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"""inositol 1,4,5-trisphosphate 3-kinase C"""			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.1316G>A	19.37:g.41235167G>A	ENSP00000263370:p.Arg439His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_025194	Q9UE25|Q9Y475	Missense_Mutation	SNP	ENST00000263370.2	37	CCDS12563.1	46	0.021062271062271064	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	42	0.055408970976253295	G	12.47	1.948867	0.34377	0.009986	0.058721	ENSG00000086544	ENST00000263370	T	0.14266	2.52	5.49	2.23	0.28157	.	0.236396	0.44688	N	0.000430	T	0.00998	0.0033	L	0.58101	1.795	0.46131	D	0.998883	P	0.35908	0.527	B	0.21546	0.035	T	0.19095	-1.0316	10	0.51188	T	0.08	-14.7372	6.6184	0.22790	0.4071:0.0:0.5929:0.0	.	439	Q96DU7	IP3KC_HUMAN	H	439	ENSP00000263370:R439H	ENSP00000263370:R439H	R	+	2	0	ITPKC	45927007	0.003000	0.15002	1.000000	0.80357	0.998000	0.95712	0.076000	0.14712	0.819000	0.34492	0.561000	0.74099	CGC	G|0.967;A|0.033	0.033	strong		0.532	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
TNS4	84951	hgsc.bcm.edu	37	17	38640744	38640744	+	Missense_Mutation	SNP	C	C	T	rs2290207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38640744C>T	ENST00000254051.6	-	6	1651	c.1493G>A	c.(1492-1494)aGt>aAt	p.S498N		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	498	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		S -> N (in dbSNP:rs2290207). {ECO:0000269|PubMed:12154022, ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			ACCTGGTCGACTCTGAGCAGA	0.597													T|||	1386	0.276757	0.1248	0.2954	5008	,	,		19494	0.3562		0.2594	False		,,,				2504	0.4049				p.S498N		Atlas-SNP	.											.	TNS4	72	.	0			c.G1493A						PASS	.	T	ASN/SER	731,3675	757.5+/-412.7	68,595,1540	71.0	60.0	64.0		1493	0.6	0.1	17	dbSNP_100	64	2111,6489	716.5+/-406.1	257,1597,2446	yes	missense	TNS4	NM_032865.5	46	325,2192,3986	TT,TC,CC		24.5465,16.591,21.8515	benign	498/716	38640744	2842,10164	2203	4300	6503	SO:0001583	missense	84951	exon6			GGTCGACTCTGAG	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1493G>A	17.37:g.38640744C>T	ENSP00000254051:p.Ser498Asn	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Missense_Mutation	SNP	ENST00000254051.6	37	CCDS11368.1	556	0.25457875457875456	60	0.12195121951219512	99	0.27348066298342544	201	0.3513986013986014	196	0.25857519788918204	T	1.181	-0.638024	0.03557	0.16591	0.245465	ENSG00000131746	ENST00000377816;ENST00000254051	T	0.19105	2.17	5.6	0.651	0.17817	SH2 motif (4);	0.738911	0.12343	N	0.477279	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.48801	-0.9003	9	0.11485	T	0.65	-11.1851	6.0639	0.19852	0.0:0.4904:0.2062:0.3034	rs2290207;rs57765426;rs2290207	498	Q8IZW8	TENS4_HUMAN	N	498	ENSP00000254051:S498N	ENSP00000254051:S498N	S	-	2	0	TNS4	35894270	0.982000	0.34865	0.073000	0.20177	0.023000	0.10783	0.553000	0.23391	-0.112000	0.11979	-0.361000	0.07541	AGT	C|0.761;T|0.239	0.239	strong		0.597	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045963	76045963	+	Silent	SNP	C	C	G	rs2287017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	0	0		WXS	Illumina HiSeq	Phase_I	61	43	0.704918	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	
ECM2	1842	hgsc.bcm.edu	37	9	95284873	95284873	+	Silent	SNP	A	A	G	rs9299405	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:95284873A>G	ENST00000344604.5	-	2	425	c.276T>C	c.(274-276)agT>agC	p.S92S	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.S92S|ECM2_ENST00000375540.1_Silent_p.S92S	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	92					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.S92S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ACACATTATAACTTGATTCTA	0.408													A|||	1680	0.335463	0.7564	0.2435	5008	,	,		15137	0.0903		0.2932	False		,,,				2504	0.1278				p.S92S		Atlas-SNP	.											ECM2,NS,carcinoma,0,1	ECM2	147	1	1	Substitution - coding silent(1)	stomach(1)	c.T276C						PASS	.	A	,,,	2912,1492	653.6+/-399.6	966,980,256	56.0	59.0	58.0		,276,276,276	0.7	1.0	9	dbSNP_119	58	2498,6102	406.7+/-348.9	372,1754,2174	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	1338,2734,2430	GG,GA,AA		29.0465,33.8783,41.6026	,,,	,92/678,92/644,92/700	95284873	5410,7594	2202	4300	6502	SO:0001819	synonymous_variant	1842	exon2			ATTATAACTTGAT	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.276T>C	9.37:g.95284873A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			A|0.691;G|0.309	0.309	strong		0.408	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
CPN1	1369	hgsc.bcm.edu	37	10	101823428	101823428	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101823428C>T	ENST00000370418.3	-	5	1065	c.814G>A	c.(814-816)Gga>Aga	p.G272R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	272	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		AAGTAATCTCCGCAGTTCCAA	0.502																																					p.G272R		Atlas-SNP	.											.	CPN1	62	.	0			c.G814A						PASS	.						120.0	109.0	113.0					10																	101823428		2203	4300	6503	SO:0001583	missense	1369	exon5			AATCTCCGCAGTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.814G>A	10.37:g.101823428C>T	ENSP00000359446:p.Gly272Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143860	0.77888	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.32023	2.15;1.47	5.61	4.7	0.59300	Peptidase M14, carboxypeptidase A (2);	0.098868	0.64402	D	0.000001	T	0.46249	0.1383	L	0.48174	1.505	0.58432	D	0.999995	D	0.71674	0.998	D	0.64144	0.922	T	0.33240	-0.9876	10	0.36615	T	0.2	-13.7978	15.9713	0.80024	0.1358:0.8642:0.0:0.0	.	272	P15169	CBPN_HUMAN	R	272;69	ENSP00000359446:G272R;ENSP00000410895:G69R	ENSP00000359446:G272R	G	-	1	0	CPN1	101813418	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.341000	0.79300	1.355000	0.45865	0.555000	0.69702	GGA	.	.	none		0.502	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
WBP2NL	164684	hgsc.bcm.edu	37	22	42416056	42416056	+	Missense_Mutation	SNP	A	A	G	rs133335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42416056A>G	ENST00000328823.9	+	4	393	c.362A>G	c.(361-363)gAt>gGt	p.D121G	WBP2NL_ENST00000543212.1_Missense_Mutation_p.D47G	NM_152613.2	NP_689826.2	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	121			D -> G (in dbSNP:rs133335). {ECO:0000269|PubMed:15489334}.		egg activation (GO:0007343)|male pronucleus assembly (GO:0035039)|meiotic nuclear division (GO:0007126)	perinuclear theca (GO:0033011)	WW domain binding (GO:0050699)			breast(2)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)	14						AGAAATGGAGATGCCATTGAA	0.428													G|||	2735	0.546126	0.4697	0.3631	5008	,	,		19560	0.8641		0.4791	False		,,,				2504	0.5204				p.D121G		Atlas-SNP	.											.	WBP2NL	24	.	0			c.A362G						PASS	.	G	GLY/ASP	2118,2288	600.3+/-389.5	515,1088,600	139.0	141.0	140.0		362	5.2	1.0	22	dbSNP_78	140	3992,4608	600.1+/-394.2	944,2104,1252	yes	missense	WBP2NL	NM_152613.2	94	1459,3192,1852	GG,GA,AA		46.4186,48.0708,46.9783	benign	121/310	42416056	6110,6896	2203	4300	6503	SO:0001583	missense	164684	exon4			ATGGAGATGCCAT	BC022546	CCDS14029.1	22q13.2	2007-07-18			ENSG00000183066	ENSG00000183066			28389	protein-coding gene	gene with protein product	"""postacrosomal sheath WW domain-binding protein"""	610981				17289678	Standard	NM_152613		Approved	FLJ26145, MGC26816, PAWP	uc003bbt.3	Q6ICG8	OTTHUMG00000151270	ENST00000328823.9:c.362A>G	22.37:g.42416056A>G	ENSP00000332983:p.Asp121Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_152613	A3KFF7|A8MSG5|B3KXX4|Q8TBF0|Q8TBF3	Missense_Mutation	SNP	ENST00000328823.9	37	CCDS14029.1	1219	0.5581501831501832	240	0.4878048780487805	128	0.35359116022099446	487	0.8513986013986014	364	0.48021108179419525	G	0.762	-0.769100	0.02974	0.480708	0.464186	ENSG00000183066	ENST00000328823;ENST00000543212	T;T	0.03441	3.93;3.93	5.23	5.23	0.72850	WW-domain-binding protein (1);	0.000000	0.46442	N	0.000295	T	0.00012	0.0000	N	0.00039	-2.505	0.45502	P	0.0015340000000000353	B	0.02656	0.0	B	0.01281	0.0	T	0.29701	-1.0003	9	0.02654	T	1	-5.2897	13.0995	0.59212	0.0782:0.0:0.9218:0.0	rs133335;rs17856677;rs17856678;rs52820053;rs58275644;rs133335	121	Q6ICG8	WBP2L_HUMAN	G	121;47	ENSP00000332983:D121G;ENSP00000442447:D47G	ENSP00000332983:D121G	D	+	2	0	WBP2NL	40746002	1.000000	0.71417	1.000000	0.80357	0.086000	0.17979	5.333000	0.65917	1.454000	0.47793	-0.119000	0.15052	GAT	A|0.488;G|0.512	0.512	strong		0.428	WBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322037.1	NM_152613	
UNC80	285175	hgsc.bcm.edu	37	2	210705348	210705348	+	Silent	SNP	C	C	G	rs10178675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:210705348C>G	ENST00000439458.1	+	20	3419	c.3339C>G	c.(3337-3339)ctC>ctG	p.L1113L	UNC80_ENST00000272845.6_Silent_p.L1108L	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1113					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TGGACCGACTCTCTTTCATCA	0.458													C|||	971	0.19389	0.3714	0.1095	5008	,	,		17314	0.0079		0.1223	False		,,,				2504	0.2791				p.L1113L		Atlas-SNP	.											.	UNC80	280	.	0			c.C3339G						PASS	.	C	,	435,949		71,293,328	137.0	116.0	123.0		3339,3324	2.0	1.0	2	dbSNP_119	123	378,2804		23,332,1236	no	coding-synonymous,coding-synonymous	UNC80	NM_032504.1,NM_182587.3	,	94,625,1564	GG,GC,CC		11.8793,31.4306,17.8055	,	1113/3259,1108/3235	210705348	813,3753	692	1591	2283	SO:0001819	synonymous_variant	285175	exon20			CCGACTCTCTTTC	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.3339C>G	2.37:g.210705348C>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	37	CCDS46504.1																																																																																			C|0.831;G|0.169	0.169	strong		0.458	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
ANGEL1	23357	hgsc.bcm.edu	37	14	77275630	77275630	+	Missense_Mutation	SNP	C	C	A	rs34270005	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77275630C>A	ENST00000251089.2	-	2	533	c.421G>T	c.(421-423)Ggg>Tgg	p.G141W	ANGEL1_ENST00000554941.1_5'UTR	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	141			G -> W (in dbSNP:rs34270005).							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCCTCCACCCCCTCCACCTCC	0.637													C|||	234	0.0467252	0.0809	0.0403	5008	,	,		18327	0.0		0.0577	False		,,,				2504	0.0419				p.G141W		Atlas-SNP	.											ANGEL1,NS,carcinoma,0,1	ANGEL1	63	1	0			c.G421T						PASS	.	C	TRP/GLY	335,4071	170.1+/-200.6	14,307,1882	32.0	35.0	34.0		421	4.7	0.1	14	dbSNP_126	34	431,8169	131.8+/-189.6	15,401,3884	yes	missense	ANGEL1	NM_015305.3	184	29,708,5766	AA,AC,CC		5.0116,7.6033,5.8896	probably-damaging	141/671	77275630	766,12240	2203	4300	6503	SO:0001583	missense	23357	exon2			CCACCCCCTCCAC	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.421G>T	14.37:g.77275630C>A	ENSP00000251089:p.Gly141Trp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_015305	B4DWL7|O94859|Q8NCS9	Missense_Mutation	SNP	ENST00000251089.2	37	CCDS9852.1	95	0.043498168498168496	36	0.07317073170731707	13	0.03591160220994475	0	0.0	46	0.06068601583113457	C	6.819	0.520194	0.13005	0.076033	0.050116	ENSG00000013523	ENST00000251089	T	0.24538	1.85	5.6	4.7	0.59300	.	.	.	.	.	T	0.01387	0.0045	N	0.08118	0	0.20307	N	0.999912	D;D	0.76494	0.999;0.998	D;D	0.74674	0.984;0.965	T	0.04153	-1.0973	9	0.72032	D	0.01	.	6.3431	0.21335	0.0:0.6977:0.1842:0.118	rs34270005	141;141	B4DVG4;Q9UNK9	.;ANGE1_HUMAN	W	141	ENSP00000251089:G141W	ENSP00000251089:G141W	G	-	1	0	ANGEL1	76345383	0.903000	0.30736	0.066000	0.19879	0.088000	0.18126	3.226000	0.51254	1.353000	0.45828	-0.176000	0.13171	GGG	C|0.945;A|0.055	0.055	strong		0.637	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305	
PEAR1	375033	hgsc.bcm.edu	37	1	156878737	156878737	+	Silent	SNP	T	T	C	rs6671392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156878737T>C	ENST00000338302.3	+	12	1545	c.1320T>C	c.(1318-1320)ccT>ccC	p.P440P	PEAR1_ENST00000292357.7_Silent_p.P440P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	440					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TTTGTCCTCCTGACACCTACG	0.592													C|||	1119	0.223442	0.2617	0.1585	5008	,	,		18742	0.3145		0.1243	False		,,,				2504	0.226				p.P440P		Atlas-SNP	.											.	PEAR1	118	.	0			c.T1320C						PASS	.	C		1112,3294	718.6+/-408.9	150,812,1241	109.0	86.0	94.0		1320	-9.7	0.1	1	dbSNP_116	94	1087,7513	769.1+/-407.6	75,937,3288	no	coding-synonymous	PEAR1	NM_001080471.1		225,1749,4529	CC,CT,TT		12.6395,25.2383,16.9076		440/1038	156878737	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon11			TCCTCCTGACACC	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1320T>C	1.37:g.156878737T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			T|0.809;C|0.191	0.191	strong		0.592	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
CHAF1B	8208	hgsc.bcm.edu	37	21	37759957	37759957	+	Missense_Mutation	SNP	C	C	T	rs62229404	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	236	114	0.483051	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	
SEC31B	25956	hgsc.bcm.edu	37	10	102265183	102265183	+	Missense_Mutation	SNP	G	G	A	rs2295772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102265183G>A	ENST00000370345.3	-	10	1211	c.1114C>T	c.(1114-1116)Cca>Tca	p.P372S	SEC31B_ENST00000451524.1_Missense_Mutation_p.P372S	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	372			P -> S (in dbSNP:rs2295772).		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGTATCAGTGGTGCTTGTGCC	0.512													A|||	927	0.185104	0.1997	0.1844	5008	,	,		20023	0.1319		0.1909	False		,,,				2504	0.2147				p.P372S		Atlas-SNP	.											.	SEC31B	84	.	0			c.C1114T						PASS	.	A	SER/PRO	858,3548	744.3+/-411.5	86,686,1431	182.0	190.0	187.0		1114	3.5	0.4	10	dbSNP_100	187	1893,6707	728.3+/-406.7	216,1461,2623	yes	missense	SEC31B	NM_015490.3	74	302,2147,4054	AA,AG,GG		22.0116,19.4734,21.1518	benign	372/1180	102265183	2751,10255	2203	4300	6503	SO:0001583	missense	25956	exon10			TCAGTGGTGCTTG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1114C>T	10.37:g.102265183G>A	ENSP00000359370:p.Pro372Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	395	0.18086080586080586	71	0.1443089430894309	71	0.19613259668508287	94	0.16433566433566432	159	0.20976253298153033	A	4.865	0.160694	0.09287	0.194734	0.220116	ENSG00000075826	ENST00000370345;ENST00000451524	T;T	0.58358	0.74;0.34	5.82	3.47	0.39725	.	0.219047	0.46758	N	0.000273	T	0.00012	0.0000	N	0.00729	-1.24	0.09310	P	0.999999999998951	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21724	-1.0237	9	0.02654	T	1	-0.5132	1.7084	0.02887	0.3605:0.1058:0.093:0.4407	rs2295772;rs17672591;rs52801527;rs59297200;rs2295772	371;372	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	S	372	ENSP00000359370:P372S;ENSP00000391178:P372S	ENSP00000359370:P372S	P	-	1	0	SEC31B	102255173	1.000000	0.71417	0.368000	0.25939	0.978000	0.69477	2.770000	0.47662	0.123000	0.18342	-0.361000	0.07541	CCA	G|0.808;A|0.192	0.192	strong		0.512	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
CRELD2	79174	hgsc.bcm.edu	37	22	50315382	50315382	+	Missense_Mutation	SNP	C	C	G	rs74510325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50315382C>G	ENST00000328268.4	+	5	639	c.565C>G	c.(565-567)Cgg>Ggg	p.R189G	CRELD2_ENST00000403427.3_Missense_Mutation_p.R189G|CRELD2_ENST00000404488.3_Missense_Mutation_p.R189G|CRELD2_ENST00000407217.3_Missense_Mutation_p.R189G|CRELD2_ENST00000444954.1_3'UTR	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	189						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		CAGCTCGCTCCGGAACGAGAC	0.672													C|||	43	0.00858626	0.0015	0.0115	5008	,	,		18650	0.0		0.0288	False		,,,				2504	0.0041				p.R189G		Atlas-SNP	.											.	CRELD2	57	.	0			c.C565G						PASS	.	C	GLY/ARG,GLY/ARG	40,4366	43.1+/-76.7	0,40,2163	81.0	82.0	82.0		565,565	-1.7	0.4	22	dbSNP_132	82	341,8259	116.3+/-176.0	8,325,3967	yes	missense,missense	CRELD2	NM_001135101.1,NM_024324.3	125,125	8,365,6130	GG,GC,CC		3.9651,0.9079,2.9294	probably-damaging,probably-damaging	189/403,189/354	50315382	381,12625	2203	4300	6503	SO:0001583	missense	79174	exon5			TCGCTCCGGAACG	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.565C>G	22.37:g.50315382C>G	ENSP00000332223:p.Arg189Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	CCDS14082.1	25	0.011446886446886446	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	12.01	1.808463	0.31961	0.009079	0.039651	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	T;T;T;T;T	0.58358	2.46;0.51;0.38;0.56;0.34	4.12	-1.66	0.08265	EGF-like, laminin (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	N	0.20483	0.58	0.37318	D	0.90941	D;D;D;P;D;D	0.71674	0.997;0.998;0.997;0.91;0.99;0.98	D;D;D;P;P;P	0.69307	0.915;0.963;0.915;0.492;0.825;0.857	T	0.47522	-0.9111	10	0.59425	D	0.04	.	14.2293	0.65879	0.302:0.698:0.0:0.0	.	189;189;189;189;189;189	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	G	189	ENSP00000387769:R189G;ENSP00000383938:R189G;ENSP00000332223:R189G;ENSP00000386034:R189G;ENSP00000384111:R189G	ENSP00000332223:R189G	R	+	1	2	CRELD2	48701386	0.963000	0.33076	0.423000	0.26634	0.819000	0.46315	0.917000	0.28665	-0.606000	0.05746	-0.274000	0.10170	CGG	C|0.978;G|0.022	0.022	strong		0.672	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
FARP1	10160	hgsc.bcm.edu	37	13	98896776	98896776	+	Intron	SNP	C	C	T	rs7318267	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:98896776C>T	ENST00000319562.6	+	2	436				FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Missense_Mutation_p.T68I|FARP1_ENST00000376586.2_Intron	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						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)			CTCAAAGCCACCGGCTCCTCC	0.468													C|||	1888	0.376997	0.1891	0.3804	5008	,	,		18609	0.6171		0.3787	False		,,,				2504	0.3793				p.T68I		Atlas-SNP	.											.	FARP1	207	.	0			c.C203T						PASS	.	C	ILE/THR,	994,3412	371.0+/-319.8	114,766,1323	70.0	64.0	66.0		203,	-0.9	0.0	13	dbSNP_116	66	3401,5199	501.8+/-375.5	673,2055,1572	yes	missense,intron	FARP1	NM_001001715.2,NM_005766.2	89,	787,2821,2895	TT,TC,CC		39.5465,22.5601,33.7921	,	68/130,	98896776	4395,8611	2203	4300	6503	SO:0001627	intron_variant	10160	exon3			AAGCCACCGGCTC	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.171+31109C>T	13.37:g.98896776C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_001001715	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	878	0.40201465201465203	94	0.1910569105691057	132	0.36464088397790057	359	0.6276223776223776	293	0.3865435356200528	C	9.722	1.160042	0.21454	0.225601	0.395465	ENSG00000152767	ENST00000376581	T	0.52754	0.65	3.05	-0.857	0.10693	.	.	.	.	.	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	0.42172	-0.9467	8	0.87932	D	0	.	0.5672	0.00689	0.1982:0.3656:0.1938:0.2423	rs7318267;rs17453789;rs59141390;rs7318267	68	Q5JVI9	.	I	68	ENSP00000365765:T68I	ENSP00000365765:T68I	T	+	2	0	FARP1	97694777	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.015000	0.13355	-0.241000	0.09681	-0.282000	0.10007	ACC	C|0.627;T|0.373	0.373	strong		0.468	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
HLA-C	3107	hgsc.bcm.edu	37	6	31239010	31239010	+	Silent	SNP	G	G	A	rs1050371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31239010G>A	ENST00000376228.5	-	3	473	c.459C>T	c.(457-459)gaC>gaT	p.D153D	HLA-C_ENST00000383329.3_Silent_p.D153D	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	153	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						AGGAGCGCAGGTCCTCGTTCA	0.692																																					p.D153D		Atlas-SNP	.											.	HLA-C	92	.	0			c.C459T						PASS	.						37.0	28.0	31.0					6																	31239010		2184	4246	6430	SO:0001819	synonymous_variant	3107	exon3			GCGCAGGTCCTCG	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.459C>T	6.37:g.31239010G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	79	23	0.291139	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	555	0.2541208791208791	123	0.25	95	0.26243093922651933	172	0.3006993006993007	165	0.21767810026385223	.	9.953	1.220699	0.22457	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	2.81	0.32909	.	.	.	.	.	T	0.27524	0.0676	.	.	.	0.09310	P	0.9999999999897135	.	.	.	.	.	.	T	0.08554	-1.0716	3	.	.	.	.	7.8755	0.29590	0.0:0.2576:0.7424:0.0	rs1050371;rs2308581;rs3177878;rs3190666	.	.	.	S	153	.	.	P	-	1	0	HLA-C	31346989	0.026000	0.19158	1.000000	0.80357	0.103000	0.19146	0.681000	0.25320	1.886000	0.54624	0.305000	0.20034	CCT	G|0.930;A|0.070	0.070	strong		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PERP	64065	hgsc.bcm.edu	37	6	138413333	138413333	+	Missense_Mutation	SNP	G	G	C	rs648802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:138413333G>C	ENST00000421351.3	-	3	598	c.428C>G	c.(427-429)cCt>cGt	p.P143R		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	143			P -> R (in dbSNP:rs648802). {ECO:0000269|PubMed:12752121, ECO:0000269|PubMed:16303743}.		activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		AGTGACAGCAGGGTTGGCATG	0.507													G|||	3161	0.63119	0.5507	0.5274	5008	,	,		19485	0.7222		0.5775	False		,,,				2504	0.7751				p.P143R		Atlas-SNP	.											.	PERP	15	.	0			c.C428G						PASS	.	G	ARG/PRO	2339,2067	606.9+/-390.8	626,1087,490	94.0	90.0	91.0		428	-2.6	0.0	6	dbSNP_83	91	4745,3855	609.1+/-395.5	1309,2127,864	yes	missense	PERP	NM_022121.4	103	1935,3214,1354	CC,CG,GG		44.8256,46.9133,45.5328	possibly-damaging	143/194	138413333	7084,5922	2203	4300	6503	SO:0001583	missense	64065	exon3			ACAGCAGGGTTGG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.428C>G	6.37:g.138413333G>C	ENSP00000397157:p.Pro143Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Missense_Mutation	SNP	ENST00000421351.3	37	CCDS5188.1	1262	0.5778388278388278	254	0.516260162601626	195	0.5386740331491713	384	0.6713286713286714	429	0.5659630606860159	G	5.215	0.225135	0.09916	0.530867	0.551744	ENSG00000112378	ENST00000421351;ENST00000265603	D	0.88975	-2.45	5.1	-2.56	0.06268	.	1.226220	0.05769	N	0.606299	T	0.56140	0.1965	N	0.22421	0.69	0.80722	P	0.0	B	0.20550	0.046	B	0.22601	0.04	T	0.48790	-0.9004	9	0.11182	T	0.66	0.2946	2.0754	0.03623	0.3902:0.122:0.3634:0.1244	rs648802;rs17090835;rs52818511;rs60547415;rs648802	143	Q96FX8	PERP_HUMAN	R	143;125	ENSP00000397157:P143R	ENSP00000265603:P125R	P	-	2	0	PERP	138455026	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.125000	0.10579	-0.508000	0.06540	0.561000	0.74099	CCT	G|0.435;C|0.565	0.565	strong		0.507	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
PRR5	55615	hgsc.bcm.edu	37	22	45128232	45128232	+	Silent	SNP	T	T	C	rs8141631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45128232T>C	ENST00000336985.6	+	6	793	c.516T>C	c.(514-516)cgT>cgC	p.R172R	PRR5_ENST00000477331.1_3'UTR|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.R172R|PRR5_ENST00000403581.1_Silent_p.R195R|PRR5-ARHGAP8_ENST00000361473.5_Intron|PRR5_ENST00000006251.7_Silent_p.R163R|ARHGAP8_ENST00000517296.3_Silent_p.R172R|ARHGAP8_ENST00000389773.5_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	172					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CCCATGCCCGTGTGCCCCCTG	0.667													C|||	1910	0.38139	0.6271	0.3012	5008	,	,		19009	0.3889		0.2247	False		,,,				2504	0.2597				p.R195R		Atlas-SNP	.											PRR5_ENST00000432186,caecum,carcinoma,+2,3	PRR5	75	3	0			c.T585C						scavenged	.	C	,,,,,,	2467,1935	518.1+/-369.6	695,1077,429	36.0	35.0	35.0		489,231,231,585,489,516,	-8.4	0.8	22	dbSNP_116	35	1850,6742	701.9+/-405.2	195,1460,2641	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	PRR5,PRR5-ARHGAP8	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3,NM_181333.3,NM_181334.4	,,,,,,	890,2537,3070	CC,CT,TT		21.5317,43.9573,33.223	,,,,,,	163/380,77/294,77/294,195/412,163/380,172/389,	45128232	4317,8677	2201	4296	6497	SO:0001819	synonymous_variant	55615	exon8			TGCCCGTGTGCCC	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.516T>C	22.37:g.45128232T>C		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000336985.6	37	CCDS14058.1	764	0.3498168498168498	292	0.5934959349593496	106	0.292817679558011	212	0.3706293706293706	154	0.20316622691292877	C	9.896	1.205467	0.22205	0.560427	0.215317	ENSG00000186654	ENST00000455389	.	.	.	5.17	-8.44	0.00950	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996719	.	.	.	.	.	.	T	0.41998	-0.9477	3	.	.	.	.	4.2231	0.10567	0.0896:0.1526:0.2356:0.5222	rs8141631;rs57695052	.	.	.	A	132	.	.	V	+	2	0	PRR5	43506896	0.001000	0.12720	0.766000	0.31476	0.726000	0.41606	-1.994000	0.01474	-1.442000	0.01955	-0.726000	0.03593	GTG	T|0.655;C|0.345	0.345	strong		0.667	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528	
FSCN1	6624	hgsc.bcm.edu	37	7	5643145	5643145	+	Silent	SNP	T	T	C	rs1640233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0		WXS	Illumina HiSeq	Phase_I	129	85	0.658915	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	
RSL1D1	26156	hgsc.bcm.edu	37	16	11935639	11935639	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11935639C>A	ENST00000571133.1	-	7	840	c.768G>T	c.(766-768)gaG>gaT	p.E256D	RSL1D1_ENST00000542106.1_Missense_Mutation_p.E36D	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	256					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						CAGCCGATTTCTCAGTTTTCA	0.358																																					p.E256D		Atlas-SNP	.											.	RSL1D1	40	.	0			c.G768T						PASS	.						71.0	72.0	72.0					16																	11935639		2197	4300	6497	SO:0001583	missense	26156	exon7			CGATTTCTCAGTT	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.768G>T	16.37:g.11935639C>A	ENSP00000460871:p.Glu256Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615664	0.28801	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T	0.42513	0.97	4.91	2.53	0.30540	Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.556020	0.17525	N	0.171095	T	0.50718	0.1632	M	0.72479	2.2	0.19300	N	0.999975	D;P	0.55800	0.973;0.952	P;P	0.58928	0.848;0.785	T	0.35699	-0.9778	10	0.21014	T	0.42	-11.795	5.6426	0.17572	0.3284:0.5515:0.0:0.12	.	256;256	Q32Q62;O76021	.;RL1D1_HUMAN	D	255;256;36	ENSP00000347897:E255D	ENSP00000347897:E255D	E	-	3	2	RSL1D1	11843140	0.118000	0.22208	0.556000	0.28293	0.161000	0.22273	-0.318000	0.08050	0.599000	0.29845	-2.175000	0.00321	GAG	.	.	none		0.358	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
CLSTN1	22883	hgsc.bcm.edu	37	1	9811541	9811541	+	Silent	SNP	A	A	G	rs11674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9811541A>G	ENST00000377298.4	-	5	1431	c.639T>C	c.(637-639)gtT>gtC	p.V213V	CLSTN1_ENST00000377288.3_Silent_p.V213V|CLSTN1_ENST00000361311.4_Silent_p.V203V	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CATCTTTGTCAACAGTAAAGG	0.522													G|||	1550	0.309505	0.6089	0.2219	5008	,	,		19507	0.1855		0.0775	False		,,,				2504	0.3333				p.V213V		Atlas-SNP	.											.	CLSTN1	88	.	0			c.T639C						PASS	.	G	,	2304,2102	573.6+/-383.6	595,1114,494	84.0	81.0	82.0		639,609	-11.2	0.0	1	dbSNP_52	82	725,7875	786.9+/-407.6	41,643,3616	no	coding-synonymous,coding-synonymous	CLSTN1	NM_001009566.1,NM_014944.3	,	636,1757,4110	GG,GA,AA		8.4302,47.7077,23.2893	,	213/982,203/972	9811541	3029,9977	2203	4300	6503	SO:0001819	synonymous_variant	22883	exon5			TTTGTCAACAGTA	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.639T>C	1.37:g.9811541A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Silent	SNP	ENST00000377298.4	37	CCDS30580.1																																																																																			A|0.749;G|0.251	0.251	strong		0.522	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
TBRG4	9238	hgsc.bcm.edu	37	7	45148773	45148773	+	Missense_Mutation	SNP	C	C	A	rs2304694	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45148773C>A	ENST00000258770.3	-	2	185	c.64G>T	c.(64-66)Gcc>Tcc	p.A22S	TBRG4_ENST00000471142.1_5'UTR|TBRG4_ENST00000395655.4_Missense_Mutation_p.A22S|TBRG4_ENST00000494076.1_Missense_Mutation_p.A22S|TBRG4_ENST00000361278.3_Missense_Mutation_p.A22S	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	22			A -> S (in dbSNP:rs2304694). {ECO:0000269|PubMed:17974005}.		cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.A22S(1)		cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						GGAGCCATGGCAGGGGCCTGA	0.577													C|||	632	0.126198	0.0068	0.2205	5008	,	,		18016	0.1766		0.162	False		,,,				2504	0.1319				p.A33S		Atlas-SNP	.											TBRG4,NS,carcinoma,0,1	TBRG4	52	1	1	Substitution - Missense(1)	stomach(1)	c.G97T						PASS	.	C	SER/ALA,SER/ALA,SER/ALA	161,4245	107.8+/-146.2	5,151,2047	63.0	59.0	61.0		64,64,64	2.6	0.1	7	dbSNP_100	61	1447,7153	274.1+/-291.0	127,1193,2980	yes	missense,missense,missense	TBRG4	NM_004749.2,NM_030900.2,NM_199122.1	99,99,99	132,1344,5027	AA,AC,CC		16.8256,3.6541,12.3635	benign,benign,benign	22/632,22/522,22/522	45148773	1608,11398	2203	4300	6503	SO:0001583	missense	9238	exon2			CCATGGCAGGGGC	AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"""FAST kinase domains 4"", ""cell cycle progression 2 protein"""	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.64G>T	7.37:g.45148773C>A	ENSP00000258770:p.Ala22Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	122	44	0.360656	NM_001261834	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Missense_Mutation	SNP	ENST00000258770.3	37	CCDS5501.1	306	0.1401098901098901	4	0.008130081300813009	69	0.19060773480662985	103	0.18006993006993008	130	0.17150395778364116	C	13.36	2.212885	0.39102	0.036541	0.168256	ENSG00000136270	ENST00000258770;ENST00000361278;ENST00000395655;ENST00000494076;ENST00000478532;ENST00000475893;ENST00000482285;ENST00000495078	T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.64	2.59	0.31030	.	0.671364	0.13840	N	0.359114	T	0.00073	0.0002	M	0.69823	2.125	0.80722	P	0.0	B;B;B	0.30686	0.088;0.29;0.088	B;B;B	0.33196	0.051;0.159;0.031	T	0.10965	-1.0607	9	0.08179	T	0.78	.	7.3904	0.26907	0.1194:0.6718:0.1314:0.0774	rs2304694;rs11541072;rs17550469;rs58693180;rs2304694	33;22;22	B4DU42;Q969Z0-2;Q969Z0	.;.;TBRG4_HUMAN	S	22	ENSP00000258770:A22S;ENSP00000354992:A22S;ENSP00000379016:A22S;ENSP00000420597:A22S;ENSP00000418631:A22S;ENSP00000417324:A22S;ENSP00000417967:A22S;ENSP00000417071:A22S	ENSP00000258770:A22S	A	-	1	0	TBRG4	45115298	0.000000	0.05858	0.135000	0.22099	0.647000	0.38526	-0.097000	0.11042	0.699000	0.31761	0.655000	0.94253	GCC	C|0.875;A|0.125	0.125	strong		0.577	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900	
RNF126	55658	hgsc.bcm.edu	37	19	652238	652238	+	Silent	SNP	A	A	G	rs11554788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:652238A>G	ENST00000292363.5	-	3	348	c.193T>C	c.(193-195)Ttg>Ctg	p.L65L		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)		CTCACCTCCAACGGTGGCCGG	0.687													A|||	1387	0.276957	0.3911	0.3084	5008	,	,		12265	0.0893		0.3817	False		,,,				2504	0.1861				p.L65L		Atlas-SNP	.											.	RNF126	15	.	0			c.T193C						PASS	.	A		1614,2756		325,964,896	46.0	42.0	43.0		193	2.2	0.1	19	dbSNP_120	43	3238,5312		630,1978,1667	no	coding-synonymous	RNF126	NM_194460.2		955,2942,2563	GG,GA,AA		37.8713,36.9336,37.5542		65/312	652238	4852,8068	2185	4275	6460	SO:0001819	synonymous_variant	55658	exon3			CCTCCAACGGTGG	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.193T>C	19.37:g.652238A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_194460		Silent	SNP	ENST00000292363.5	37	CCDS12039.1																																																																																			A|0.667;G|0.333	0.333	strong		0.687	RNF126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452104.2	NM_017876	
EFCAB12	90288	hgsc.bcm.edu	37	3	129137188	129137188	+	Missense_Mutation	SNP	C	C	T	rs62266958	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:129137188C>T	ENST00000505956.1	-	3	752	c.590G>A	c.(589-591)cGc>cAc	p.R197H	EFCAB12_ENST00000326085.3_Missense_Mutation_p.R197H	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	197	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CTTGATCTTGCGGCTATGCAG	0.602													C|||	110	0.0219649	0.003	0.0389	5008	,	,		15664	0.0		0.0676	False		,,,				2504	0.0112				p.R197H		Atlas-SNP	.											.	.	.	.	0			c.G590A						PASS	.	C	HIS/ARG	57,3801		1,55,1873	57.0	52.0	54.0		590	-3.3	0.0	3	dbSNP_129	54	522,7740		17,488,3626	yes	missense	C3orf25	NM_207307.1	29	18,543,5499	TT,TC,CC		6.3181,1.4774,4.7772	probably-damaging	197/573	129137188	579,11541	1929	4131	6060	SO:0001583	missense	90288	exon3			ATCTTGCGGCTAT	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.590G>A	3.37:g.129137188C>T	ENSP00000420854:p.Arg197His	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	76	0.0347985347985348	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	58	0.07651715039577836	C	4.105	0.017548	0.07959	0.014774	0.063181	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.42900	0.96;0.96;0.96	4.73	-3.31	0.04988	EF-hand-like domain (1);	0.433971	0.21885	N	0.067674	T	0.00936	0.0031	N	0.19112	0.55	0.09310	N	1	P	0.41624	0.757	B	0.31686	0.134	T	0.10870	-1.0611	10	0.38643	T	0.18	-13.6049	11.0011	0.47607	0.0:0.2885:0.0:0.7115	rs62266958	197	Q6NXP0	CC025_HUMAN	H	197;197;47	ENSP00000420854:R197H;ENSP00000324241:R197H;ENSP00000421462:R47H	ENSP00000324241:R197H	R	-	2	0	C3orf25	130619878	0.008000	0.16893	0.026000	0.17262	0.053000	0.15095	-1.603000	0.02077	-0.590000	0.05866	0.561000	0.74099	CGC	C|0.960;T|0.040	0.040	strong		0.602	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892159	62892159	+	Missense_Mutation	SNP	G	G	T	rs17857225		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62892159G>T	ENST00000584306.1	-	3	1747	c.1217C>A	c.(1216-1218)gCt>gAt	p.A406D	RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000339474.5_Intron|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.A406D|RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	406						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ACTGGGTGAAGCTAAATGATG	0.537																																					p.A406D		Atlas-SNP	.											LRRC37A3,NS,carcinoma,0,1	LRRC37A3	75	1	0			c.C1217A						scavenged	.						1.0	1.0	1.0					17																	62892159		292	887	1179	SO:0001583	missense	374819	exon3			GGTGAAGCTAAAT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1217C>A	17.37:g.62892159G>T	ENSP00000464535:p.Ala406Asp	Somatic	417	1	0.00239808		WXS	Illumina HiSeq	Phase_I	286	66	0.230769	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.581395	0.00129	.	.	ENSG00000176809	ENST00000319651	T	0.59772	0.24	2.63	-5.25	0.02781	.	.	.	.	.	T	0.16342	0.0393	N	0.00483	-1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11108	-1.0601	9	0.11794	T	0.64	.	2.8545	0.05568	0.2063:0.2804:0.3945:0.1188	.	406	O60309	L37A3_HUMAN	D	406	ENSP00000325713:A406D	ENSP00000325713:A406D	A	-	2	0	LRRC37A3	60322621	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.921000	0.01569	-5.806000	0.00009	-2.171000	0.00323	GCT	.	.	weak		0.537	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32729618	32729618	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32729618G>A	ENST00000437316.2	-	2	246	c.183C>T	c.(181-183)aaC>aaT	p.N61N	HLA-DQB2_ENST00000435145.2_Silent_p.N61N|HLA-DQB2_ENST00000411527.1_Silent_p.N61N			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	65	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|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)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACTCCTCGCGGTTATAGATGT	0.577																																					p.N61N		Atlas-SNP	.											.	HLA-DQB2	22	.	0			c.C183T						PASS	.																																			SO:0001819	synonymous_variant	3120	exon2			CTCGCGGTTATAG	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.183C>T	6.37:g.32729618G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Silent	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	G	7.517	0.655922	0.14580	.	.	ENSG00000232629	ENST00000427449	.	.	.	3.48	2.59	0.31030	.	.	.	.	.	T	0.45196	0.1330	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41413	-0.9510	4	.	.	.	.	8.4756	0.33012	0.125:0.0:0.875:0.0	.	.	.	.	I	60	.	.	T	-	2	0	HLA-DQB2	32837596	0.991000	0.36638	0.792000	0.32020	0.021000	0.10359	2.255000	0.43222	1.937000	0.56155	0.491000	0.48974	ACC	.	.	none		0.577	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
PNMAL1	55228	hgsc.bcm.edu	37	19	46974003	46974003	+	Missense_Mutation	SNP	C	C	T	rs7248888	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46974003C>T	ENST00000313683.10	-	2	595	c.290G>A	c.(289-291)tGt>tAt	p.C97Y	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Missense_Mutation_p.C97Y	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	97			C -> Y (in dbSNP:rs7248888).							cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		agggtctctacagaccactct	0.542													C|||	337	0.0672923	0.1649	0.0418	5008	,	,		19029	0.0129		0.0586	False		,,,				2504	0.0184				p.C97Y		Atlas-SNP	.											.	PNMAL1	87	.	0			c.G290A						PASS	.	C	TYR/CYS,TYR/CYS	597,3809	262.8+/-265.1	33,531,1639	49.0	46.0	47.0		290,290	2.4	1.0	19	dbSNP_116	47	503,8097	144.2+/-200.1	7,489,3804	yes	missense,missense	PNMAL1	NM_001103149.1,NM_018215.3	194,194	40,1020,5443	TT,TC,CC		5.8488,13.5497,8.4576	benign,benign	97/379,97/440	46974003	1100,11906	2203	4300	6503	SO:0001583	missense	55228	exon2			TCTCTACAGACCA	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.290G>A	19.37:g.46974003C>T	ENSP00000318131:p.Cys97Tyr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Missense_Mutation	SNP	ENST00000313683.10	37	CCDS33059.1	138	0.06318681318681318	81	0.16463414634146342	12	0.03314917127071823	7	0.012237762237762238	38	0.05013192612137203	C	7.921	0.738653	0.15642	0.135497	0.058488	ENSG00000182013	ENST00000438932;ENST00000313683;ENST00000417103	T;T	0.10099	2.91;2.91	3.46	2.39	0.29439	.	0.187510	0.26474	N	0.024161	T	0.00039	0.0001	L	0.36672	1.1	0.31986	P	0.605256	B;B	0.32800	0.385;0.063	B;B	0.30251	0.113;0.04	T	0.40021	-0.9585	9	0.13470	T	0.59	-17.1361	7.161	0.25664	0.0:0.8754:0.0:0.1246	rs7248888;rs52809978;rs7248888	97;97	Q86V59-2;Q86V59	.;PNML1_HUMAN	Y	97	ENSP00000410273:C97Y;ENSP00000318131:C97Y	ENSP00000318131:C97Y	C	-	2	0	PNMAL1	51665843	0.005000	0.15991	0.991000	0.47740	0.979000	0.70002	0.623000	0.24447	1.011000	0.39340	0.655000	0.94253	TGT	C|0.924;T|0.076	0.076	strong		0.542	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
FETUB	26998	hgsc.bcm.edu	37	3	186370350	186370350	+	Missense_Mutation	SNP	A	A	G	rs7999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186370350A>G	ENST00000265029.3	+	7	1180	c.1079A>G	c.(1078-1080)aAa>aGa	p.K360R	RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000382136.3_Missense_Mutation_p.K323R|FETUB_ENST00000382134.3_Missense_Mutation_p.K295R|FETUB_ENST00000450521.1_Missense_Mutation_p.K360R|FETUB_ENST00000539949.1_Missense_Mutation_p.K212R|RP11-134F2.2_ENST00000428501.1_RNA	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	360			K -> R (in dbSNP:rs7999).		binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		CCTTTCCCCAAAGAAAAAGCA	0.552													A|||	367	0.0732827	0.1165	0.0576	5008	,	,		19426	0.0903		0.0427	False		,,,				2504	0.0399				p.K360R		Atlas-SNP	.											.	FETUB	53	.	0			c.A1079G						PASS	.	A	ARG/LYS	426,3980	200.8+/-224.0	23,380,1800	54.0	59.0	57.0		1079	-2.6	0.0	3	dbSNP_52	57	397,8203	125.0+/-183.6	8,381,3911	yes	missense	FETUB	NM_014375.2	26	31,761,5711	GG,GA,AA		4.6163,9.6686,6.3278	benign	360/383	186370350	823,12183	2203	4300	6503	SO:0001583	missense	26998	exon7			TCCCCAAAGAAAA	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.1079A>G	3.37:g.186370350A>G	ENSP00000265029:p.Lys360Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	37	CCDS3279.1	162	0.07417582417582418	68	0.13821138211382114	25	0.06906077348066299	42	0.07342657342657342	27	0.03562005277044855	A	4.489	0.090600	0.08632	0.096686	0.046163	ENSG00000090512	ENST00000450521;ENST00000539949;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	3.97	-2.58	0.06228	.	2.018410	0.02384	N	0.079042	T	0.00300	0.0009	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.12156	0.007;0.007;0.007	T	0.03807	-1.1002	9	0.19590	T	0.45	1.1389	6.2991	0.21103	0.473:0.1467:0.3803:0.0	rs7999;rs1131362;rs3191246;rs7999	323;295;360	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	R	360;212;360;295;323	ENSP00000404288:K360R;ENSP00000443704:K212R;ENSP00000265029:K360R;ENSP00000371569:K295R;ENSP00000371571:K323R	ENSP00000265029:K360R	K	+	2	0	FETUB	187853044	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.269000	0.08596	-0.862000	0.04089	-2.200000	0.00306	AAA	A|0.929;G|0.071	0.071	strong		0.552	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375	
F5	2153	hgsc.bcm.edu	37	1	169511403	169511403	+	Silent	SNP	G	G	A	rs41272457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169511403G>A	ENST00000367797.3	-	13	3126	c.2925C>T	c.(2923-2925)ccC>ccT	p.P975P	F5_ENST00000367796.3_Silent_p.P980P	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	975	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)	AGGCATTCTGGGGGCTGATCA	0.468													G|||	26	0.00519169	0.0008	0.0115	5008	,	,		19616	0.0		0.0169	False		,,,				2504	0.0				p.P975P		Atlas-SNP	.											F5,NS,carcinoma,-2,1	F5	301	1	0			c.C2925T						scavenged	.	G		15,4391	22.3+/-47.3	0,15,2188	106.0	110.0	109.0		2925	0.7	0.1	1	dbSNP_127	109	195,8405	86.3+/-148.7	2,191,4107	no	coding-synonymous	F5	NM_000130.4		2,206,6295	AA,AG,GG		2.2674,0.3404,1.6146		975/2225	169511403	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			ATTCTGGGGGCTG	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.2925C>T	1.37:g.169511403G>A		Somatic	93	2	0.0215054		WXS	Illumina HiSeq	Phase_I	111	74	0.666667	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.986;A|0.014	0.014	strong		0.468	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
HTT	3064	hgsc.bcm.edu	37	4	3148653	3148653	+	Missense_Mutation	SNP	T	T	G	rs1143646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3148653T>G	ENST00000355072.5	+	25	3418	c.3273T>G	c.(3271-3273)atT>atG	p.I1091M		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1091			I -> M (in dbSNP:rs1143646).		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)		ATGCTTTGATTTTGGCCGGAA	0.502													T|||	112	0.0223642	0.0023	0.0231	5008	,	,		19236	0.0		0.0487	False		,,,				2504	0.045				p.I1091M		Atlas-SNP	.											.	HTT	221	.	0			c.T3273G						PASS	.	T	MET/ILE	35,3891		0,35,1928	351.0	350.0	351.0		3273	-4.2	0.0	4	dbSNP_86	351	403,7927		11,381,3773	yes	missense	HTT	NM_002111.6	10	11,416,5701	GG,GT,TT		4.8379,0.8915,3.5738	benign	1091/3143	3148653	438,11818	1963	4165	6128	SO:0001583	missense	3064	exon25			TTTGATTTTGGCC	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.3273T>G	4.37:g.3148653T>G	ENSP00000347184:p.Ile1091Met	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	50	0.022893772893772892	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	41	0.05408970976253298	T	13.78	2.338654	0.41398	0.008915	0.048379	ENSG00000197386	ENST00000355072	T	0.64803	-0.12	4.68	-4.18	0.03846	Armadillo-type fold (1);	0.398024	0.28057	N	0.016777	T	0.08223	0.0205	L	0.40543	1.245	0.25629	N	0.986323	P	0.35208	0.49	B	0.32624	0.149	T	0.07947	-1.0746	10	0.33940	T	0.23	.	2.2434	0.04025	0.2123:0.3798:0.1117:0.2962	rs1143646;rs3025846;rs17362442;rs17781557;rs17781557	1091	P42858	HD_HUMAN	M	1091	ENSP00000347184:I1091M	ENSP00000347184:I1091M	I	+	3	3	HTT	3118451	0.381000	0.25140	0.023000	0.16930	0.993000	0.82548	-0.425000	0.07017	-0.600000	0.05790	0.460000	0.39030	ATT	T|0.968;G|0.032	0.032	strong		0.502	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
CCL27	10850	hgsc.bcm.edu	37	9	34661994	34661994	+	Missense_Mutation	SNP	G	G	A	rs11575584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34661994G>A	ENST00000259631.4	-	3	344	c.286C>T	c.(286-288)Ctc>Ttc	p.L96F	CCL27_ENST00000557161.1_5'UTR|RP11-195F19.30_ENST00000564224.1_RNA	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	96			L -> F (in dbSNP:rs11575584).		cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			kidney(1)|large_intestine(3)|ovary(1)	5	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GTCCCATGGAGCTTTCTCTCT	0.502													G|||	207	0.0413339	0.003	0.0418	5008	,	,		19142	0.0159		0.0755	False		,,,				2504	0.0838				p.L96F		Atlas-SNP	.											CCL27,lymph_node,lymphoid_neoplasm,0,1	CCL27	6	1	0			c.C286T						PASS	.	G	PHE/LEU	75,4331	68.1+/-105.8	1,73,2129	108.0	116.0	113.0		286	-4.7	0.0	9	dbSNP_120	113	526,8074	147.6+/-202.9	17,492,3791	yes	missense	CCL27	NM_006664.2	22	18,565,5920	AA,AG,GG		6.1163,1.7022,4.6209	probably-damaging	96/113	34661994	601,12405	2203	4300	6503	SO:0001583	missense	10850	exon3			CATGGAGCTTTCT	AJ243542	CCDS6569.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000213927	ENSG00000213927		"""Chemokine ligands"", ""Endogenous ligands"""	10626	protein-coding gene	gene with protein product	"""CC chemokine ILC"", ""IL-11 Ralpha-locus chemokine"", ""cutaneous T-cell attracting chemokine"""	604833	"""small inducible cytokine subfamily A (Cys-Cys), member 27"""	SCYA27		10556532, 10588729	Standard	NM_006664		Approved	ALP, ILC, CTACK, skinkine, ESkine, PESKY, CTAK	uc003zvm.1	Q9Y4X3	OTTHUMG00000019834	ENST00000259631.4:c.286C>T	9.37:g.34661994G>A	ENSP00000259631:p.Leu96Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_006664		Missense_Mutation	SNP	ENST00000259631.4	37	CCDS6569.1	84	0.038461538461538464	2	0.0040650406504065045	15	0.04143646408839779	8	0.013986013986013986	59	0.07783641160949868	G	8.367	0.834384	0.16820	0.017022	0.061163	ENSG00000213927	ENST00000259631	T	0.32023	1.47	4.99	-4.65	0.03339	Chemokine interleukin-8-like domain (1);	1.572910	0.03568	N	0.228121	T	0.00906	0.0030	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17592	-1.0364	10	0.48119	T	0.1	-0.009	2.4773	0.04579	0.4822:0.1255:0.2646:0.1277	rs11575584;rs52820755;rs58368429;rs11575584	96	Q9Y4X3	CCL27_HUMAN	F	96	ENSP00000259631:L96F	ENSP00000259631:L96F	L	-	1	0	CCL27	34651994	0.000000	0.05858	0.000000	0.03702	0.465000	0.32709	-0.881000	0.04179	-0.691000	0.05135	0.655000	0.94253	CTC	G|0.957;A|0.043	0.043	strong		0.502	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664	
FCGBP	8857	hgsc.bcm.edu	37	19	40408821	40408821	+	Missense_Mutation	SNP	C	C	G	rs11083543	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40408821C>G	ENST00000221347.6	-	8	4025	c.4018G>C	c.(4018-4020)Gtg>Ctg	p.V1340L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1340	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> L (in dbSNP:rs11083543).			extracellular vesicular exosome (GO:0070062)		p.V1340L(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)			GCCAGCACCACGGGCAGCTTC	0.577													C|||	1291	0.257788	0.121	0.4092	5008	,	,		19419	0.2173		0.3608	False		,,,				2504	0.271				p.V1340L		Atlas-SNP	.											FCGBP,caecum,carcinoma,0,2	FCGBP	416	2	1	Substitution - Missense(1)	ovary(1)	c.G4018C						PASS	.	C	LEU/VAL	611,3795		45,521,1637	23.0	20.0	21.0		4018	-0.1	0.0	19	dbSNP_120	21	2976,5622		523,1930,1846	yes	missense	FCGBP	NM_003890.2	32	568,2451,3483	GG,GC,CC		34.6127,13.8675,27.5838	probably-damaging	1340/5406	40408821	3587,9417	2203	4299	6502	SO:0001583	missense	8857	exon8			GCACCACGGGCAG	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.4018G>C	19.37:g.40408821C>G	ENSP00000221347:p.Val1340Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	624	0.2857142857142857	76	0.15447154471544716	148	0.4088397790055249	125	0.21853146853146854	275	0.3627968337730871	C	12.27	1.888760	0.33348	0.138675	0.346127	ENSG00000090920	ENST00000221347	T	0.58797	0.31	4.95	-0.14	0.13456	von Willebrand factor, type D domain (3);	0.451564	0.18780	N	0.131345	T	0.00012	0.0000	N	0.25031	0.7	0.80722	P	0.0	B	0.25235	0.121	B	0.21151	0.033	T	0.40232	-0.9574	9	0.11485	T	0.65	.	2.6779	0.05085	0.1375:0.4356:0.268:0.1589	rs11083543;rs11083543	1340	Q9Y6R7	FCGBP_HUMAN	L	1340	ENSP00000221347:V1340L	ENSP00000221347:V1340L	V	-	1	0	FCGBP	45100661	0.000000	0.05858	0.015000	0.15790	0.023000	0.10783	-0.881000	0.04179	0.120000	0.18254	-0.182000	0.12963	GTG	.	.	weak		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
F5	2153	hgsc.bcm.edu	37	1	169510380	169510380	+	Silent	SNP	G	G	A	rs9287090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169510380G>A	ENST00000367797.3	-	13	4149	c.3948C>T	c.(3946-3948)ctC>ctT	p.L1316L	F5_ENST00000367796.3_Silent_p.L1321L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1316	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)	GCATCTGACCGAGGGCTGGGG	0.498													G|||	1320	0.263578	0.1717	0.3948	5008	,	,		22137	0.248		0.2535	False		,,,				2504	0.3211				p.L1316L		Atlas-SNP	.											.	F5	301	.	0			c.C3948T						PASS	.	G		821,3585	323.2+/-298.0	72,677,1454	249.0	273.0	265.0		3948	-4.7	0.0	1	dbSNP_119	265	2356,6244	393.5+/-344.4	300,1756,2244	no	coding-synonymous	F5	NM_000130.4		372,2433,3698	AA,AG,GG		27.3953,18.6337,24.4272		1316/2225	169510380	3177,9829	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			CTGACCGAGGGCT	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.3948C>T	1.37:g.169510380G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	341	207	0.607038	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.758;A|0.242	0.242	strong		0.498	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
MUC4	4585	hgsc.bcm.edu	37	3	195508133	195508133	+	Missense_Mutation	SNP	G	G	A	rs202065387		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195508133G>A	ENST00000463781.3	-	2	10777	c.10318C>T	c.(10318-10320)Cct>Tct	p.P3440S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3440S	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)	p.P3440S(2)		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)		ACAGGAACAGGGGTGGCGTGA	0.592																																					p.P3440S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - Missense(2)	endometrium(2)	c.C10318T						scavenged	.						30.0	24.0	26.0					3																	195508133		685	1583	2268	SO:0001583	missense	4585	exon2			GAACAGGGGTGGC	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.10318C>T	3.37:g.195508133G>A	ENSP00000417498:p.Pro3440Ser	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	131	5	0.0381679	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	3.286	-0.146045	0.06627	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.58;1.55	.	.	.	.	.	.	.	.	T	0.22003	0.0530	N	0.14661	0.345	0.09310	N	1	P	0.48350	0.909	P	0.50440	0.641	T	0.15809	-1.0424	6	.	.	.	.	.	.	.	.	3312	E7ESK3	.	S	3440	ENSP00000417498:P3440S;ENSP00000420243:P3440S	.	P	-	1	0	MUC4	196992912	0.016000	0.18221	0.006000	0.13384	0.005000	0.04900	-0.684000	0.05173	0.088000	0.17205	0.089000	0.15464	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMIGD2	126259	hgsc.bcm.edu	37	19	4292597	4292597	+	Silent	SNP	C	C	T	rs888932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4292597C>T	ENST00000301272.2	-	5	893	c.848G>A	c.(847-849)tGa>tAa	p.*283*	TMIGD2_ENST00000600349.1_Silent_p.*111*|TMIGD2_ENST00000595645.1_Silent_p.*279*|TMIGD2_ENST00000600114.1_Silent_p.*163*	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	0					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGATCTCTCACTCCTCTCC	0.617													T|||	2306	0.460463	0.7905	0.3818	5008	,	,		14645	0.3552		0.2803	False		,,,				2504	0.364				p.X283X		Atlas-SNP	.											.	TMIGD2	38	.	0			c.G848A						PASS	.	T	,	3084,1322	444.7+/-347.4	1086,912,205	94.0	106.0	102.0		836,848	-3.6	0.0	19	dbSNP_86	102	2376,6224	700.7+/-405.2	370,1636,2294	no	coding-synonymous,coding-synonymous	TMIGD2	NM_001169126.1,NM_144615.2	,	1456,2548,2499	TT,TC,CC		27.6279,30.0045,41.9806	,	279/279,283/283	4292597	5460,7546	2203	4300	6503	SO:0001819	synonymous_variant	126259	exon5			ATCTCTCACTCCT	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.848G>A	19.37:g.4292597C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_144615	Q6UW59	Silent	SNP	ENST00000301272.2	37	CCDS12126.1																																																																																			C|0.569;T|0.431	0.431	strong		0.617	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
TAS2R46	259292	hgsc.bcm.edu	37	12	11214360	11214360	+	Silent	SNP	C	C	T	rs73260771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11214360C>T	ENST00000533467.1	-	1	533	c.534G>A	c.(532-534)acG>acA	p.T178T	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	178					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)		GGATGGTTACCGTTGTATTTG	0.373													.|||	621	0.124002	0.1029	0.2248	5008	,	,		21835	0.0		0.2773	False		,,,				2504	0.0511				p.T178T		Atlas-SNP	.											.	TAS2R46	43	.	0			c.G534A						PASS	.	C		593,3809	239.9+/-250.9	50,493,1658	174.0	177.0	176.0		534	-5.1	0.0	12	dbSNP_130	176	2238,6358	370.8+/-336.0	307,1624,2367	no	coding-synonymous	TAS2R46	NM_176887.2		357,2117,4025	TT,TC,CC		26.0354,13.4711,21.7803		178/310	11214360	2831,10167	2201	4298	6499	SO:0001819	synonymous_variant	259292	exon1			GGTTACCGTTGTA	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.534G>A	12.37:g.11214360C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	132	0.90411	NM_176887	P59548|Q645X6	Silent	SNP	ENST00000533467.1	37	CCDS53748.1																																																																																			C|0.833;T|0.167	0.167	strong		0.373	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
DZIP1	22873	hgsc.bcm.edu	37	13	96293631	96293631	+	Missense_Mutation	SNP	G	G	A	rs9561921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96293631G>A	ENST00000376829.2	-	5	1366	c.515C>T	c.(514-516)aCg>aTg	p.T172M	DZIP1_ENST00000361396.2_Missense_Mutation_p.T172M|DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000347108.3_Missense_Mutation_p.T172M|DZIP1_ENST00000361156.3_Missense_Mutation_p.T172M	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	172			T -> M (in dbSNP:rs9561921).		cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TTCCTTGAGCGTCTTGATCTC	0.602													G|||	493	0.0984425	0.112	0.0922	5008	,	,		16754	0.1716		0.0656	False		,,,				2504	0.0429				p.T172M		Atlas-SNP	.											.	DZIP1	195	.	0			c.C515T						PASS	.	G	MET/THR,MET/THR	475,3931	223.9+/-240.3	30,415,1758	112.0	71.0	85.0		515,515	3.5	0.1	13	dbSNP_119	85	758,7842	181.3+/-230.0	34,690,3576	yes	missense,missense	DZIP1	NM_014934.3,NM_198968.2	81,81	64,1105,5334	AA,AG,GG		8.814,10.7808,9.4802	benign,benign	172/849,172/868	96293631	1233,11773	2203	4300	6503	SO:0001583	missense	22873	exon5			TTGAGCGTCTTGA	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.515C>T	13.37:g.96293631G>A	ENSP00000366025:p.Thr172Met	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	174	73	0.41954	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	265	0.12133699633699634	68	0.13821138211382114	43	0.11878453038674033	102	0.17832167832167833	52	0.06860158311345646	G	1.494	-0.553964	0.03996	0.107808	0.08814	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.68	3.49	0.39957	.	1.685550	0.02965	N	0.143627	T	0.00039	0.0001	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.09840	-1.0656	9	0.39692	T	0.17	-7.0E-4	4.2879	0.10863	0.5511:0.1859:0.263:0.0	rs9561921;rs57792076;rs9561921	172;172	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	M	172	ENSP00000257312:T172M;ENSP00000355018:T172M;ENSP00000355175:T172M;ENSP00000366025:T172M	ENSP00000257312:T172M	T	-	2	0	DZIP1	95091632	0.000000	0.05858	0.139000	0.22197	0.002000	0.02628	0.646000	0.24797	0.661000	0.30985	-0.238000	0.12139	ACG	G|0.895;A|0.105	0.105	strong		0.602	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
ZNF440	126070	hgsc.bcm.edu	37	19	11942362	11942362	+	Missense_Mutation	SNP	A	A	G	rs427880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	213	0	0		WXS	Illumina HiSeq	Phase_I	202	99	0.490099	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	
LSS	4047	hgsc.bcm.edu	37	21	47635627	47635627	+	Silent	SNP	C	C	G	rs9980968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47635627C>G	ENST00000397728.3	-	8	942	c.864G>C	c.(862-864)ccG>ccC	p.P288P	LSS_ENST00000356396.4_Silent_p.P288P|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000457828.2_Silent_p.P208P|LSS_ENST00000522411.1_Silent_p.P277P	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	288					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GCCAGCTGTGCGGCGTGTACA	0.657													C|||	1808	0.361022	0.4675	0.2781	5008	,	,		13305	0.127		0.4235	False		,,,				2504	0.453				p.P288P	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G864C						PASS	.	C	,,,	1929,2477	524.1+/-371.2	429,1071,703	31.0	35.0	34.0		864,831,624,864	-10.4	0.3	21	dbSNP_119	34	3403,5197	478.6+/-369.9	680,2043,1577	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	1109,3114,2280	GG,GC,CC		39.5698,43.7812,40.9965	,,,	288/733,277/722,208/653,288/733	47635627	5332,7674	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon8			GCTGTGCGGCGTG	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.864G>C	21.37:g.47635627C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																			C|0.618;G|0.382	0.382	strong		0.657	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178540975	178540975	+	Missense_Mutation	SNP	G	G	A	rs1054480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178540975G>A	ENST00000251582.7	-	22	3630	c.3529C>T	c.(3529-3531)Ccc>Tcc	p.P1177S		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1177			P -> S (in dbSNP:rs1054480).		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)		ATTAGGTTGGGTGGCTGGACT	0.498													G|||	1321	0.263778	0.0401	0.3833	5008	,	,		18793	0.3105		0.2952	False		,,,				2504	0.4008				p.P1177S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C3529T						PASS	.	G	SER/PRO	357,4049	183.6+/-211.2	14,329,1860	219.0	212.0	215.0		3529	5.1	1.0	5	dbSNP_86	215	2527,6073	414.0+/-351.3	386,1755,2159	yes	missense	ADAMTS2	NM_014244.4	74	400,2084,4019	AA,AG,GG		29.3837,8.1026,22.1744	possibly-damaging	1177/1212	178540975	2884,10122	2203	4300	6503	SO:0001583	missense	9509	exon22			GGTTGGGTGGCTG	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.3529C>T	5.37:g.178540975G>A	ENSP00000251582:p.Pro1177Ser	Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	279	269	0.964158	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	551	0.2522893772893773	26	0.052845528455284556	123	0.3397790055248619	176	0.3076923076923077	226	0.29815303430079154	G	10.57	1.386031	0.25031	0.081026	0.293837	ENSG00000087116	ENST00000251582	T	0.58210	0.35	5.05	5.05	0.67936	.	0.126916	0.34676	N	0.003764	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	P	0.38922	0.651	B	0.27887	0.084	T	0.37753	-0.9692	9	0.14252	T	0.57	.	17.3941	0.87440	0.0:0.0:1.0:0.0	rs1054480;rs3195011;rs17603677;rs52799825;rs58744885;rs1054480	1177	O95450	ATS2_HUMAN	S	1177	ENSP00000251582:P1177S	ENSP00000251582:P1177S	P	-	1	0	ADAMTS2	178473581	1.000000	0.71417	0.973000	0.42090	0.192000	0.23643	3.893000	0.56243	2.308000	0.77769	0.561000	0.74099	CCC	G|0.764;N|0.000	.	strong		0.498	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
MICAL3	57553	hgsc.bcm.edu	37	22	18301693	18301693	+	Missense_Mutation	SNP	T	T	C	rs8135914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	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		
NUP205	23165	hgsc.bcm.edu	37	7	135292080	135292080	+	Silent	SNP	G	G	A	rs61734146	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135292080G>A	ENST00000285968.6	+	22	3182	c.3156G>A	c.(3154-3156)gcG>gcA	p.A1052A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1052					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GCCCAGTGGCGGTGCGAGAAT	0.493													A|||	178	0.0355431	0.0356	0.049	5008	,	,		17392	0.003		0.0457	False		,,,				2504	0.0491				p.A1052A		Atlas-SNP	.											.	NUP205	198	.	0			c.G3156A						PASS	.	A		150,4256	812.9+/-416.1	2,146,2055	87.0	84.0	85.0		3156	-10.3	0.0	7	dbSNP_129	85	341,8259	804.3+/-407.3	4,333,3963	no	coding-synonymous	NUP205	NM_015135.2		6,479,6018	AA,AG,GG		3.9651,3.4044,3.7752		1052/2013	135292080	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon22			AGTGGCGGTGCGA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.3156G>A	7.37:g.135292080G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			G|0.962;A|0.038	0.038	strong		0.493	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
PRTG	283659	hgsc.bcm.edu	37	15	56032872	56032872	+	Silent	SNP	G	G	A	rs77118243	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:56032872G>A	ENST00000561292.1	-	2	263	c.105C>T	c.(103-105)tgC>tgT	p.C35C	PRTG_ENST00000389286.4_Silent_p.C35C					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)		GTTCGCTAAAGCACCACACTC	0.403													G|||	80	0.0159744	0.0023	0.0288	5008	,	,		17906	0.0		0.0467	False		,,,				2504	0.0102				p.C35C		Atlas-SNP	.											.	PRTG	110	.	0			c.C105T						PASS	.	G		46,3614		0,46,1784	50.0	47.0	48.0		105	3.9	1.0	15	dbSNP_132	48	448,7728		16,416,3656	no	coding-synonymous	PRTG	NM_173814.4		16,462,5440	AA,AG,GG		5.4795,1.2568,4.1737		35/1151	56032872	494,11342	1830	4088	5918	SO:0001819	synonymous_variant	283659	exon2			GCTAAAGCACCAC	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		ENST00000561292.1:c.105C>T	15.37:g.56032872G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_173814		Silent	SNP	ENST00000561292.1	37																																																																																				G|0.965;A|0.035	0.035	strong		0.403	PRTG-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000419360.1	NM_173814	
NASP	4678	hgsc.bcm.edu	37	1	46078854	46078854	+	Silent	SNP	A	A	G	rs2230658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46078854A>G	ENST00000350030.3	+	7	1527	c.1440A>G	c.(1438-1440)tcA>tcG	p.S480S	NASP_ENST00000351223.3_Silent_p.S141S|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000372052.4_Silent_p.S114S|NASP_ENST00000537798.1_Silent_p.S416S|NASP_ENST00000402363.3_Silent_p.S482S	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	480	Glu-rich (acidic).|Histone-binding.				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)					CTGAAGGCTCAGAAGAGGATG	0.368													A|||	3401	0.679113	0.733	0.6527	5008	,	,		22765	0.6577		0.7177	False		,,,				2504	0.6074				p.S480S		Atlas-SNP	.											.	NASP	77	.	0			c.A1440G						PASS	.	A	,,	3306,1100	715.4+/-408.5	1247,812,144	76.0	77.0	77.0		1248,1440,423	3.2	1.0	1	dbSNP_98	77	6062,2538	689.6+/-404.4	2149,1764,387	no	coding-synonymous,coding-synonymous,coding-synonymous	NASP	NM_001195193.1,NM_002482.3,NM_152298.3	,,	3396,2576,531	GG,GA,AA		29.5116,24.966,27.9717	,,	416/725,480/789,141/450	46078854	9368,3638	2203	4300	6503	SO:0001819	synonymous_variant	4678	exon7			AGGCTCAGAAGAG	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.1440A>G	1.37:g.46078854A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	37	CCDS524.1	1511	0.6918498168498168	359	0.7296747967479674	248	0.6850828729281768	365	0.6381118881118881	539	0.7110817941952506	A	9.010	0.982274	0.18889	0.75034	0.704884	ENSG00000132780	ENST00000531612	.	.	.	5.57	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999996	.	.	.	.	.	.	T	0.37911	-0.9685	3	.	.	.	-6.4668	6.8154	0.23826	0.6832:0.1241:0.0:0.1927	rs2230658;rs3014250;rs17401812;rs17849727;rs59926663;rs2230658	.	.	.	R	5	.	.	Q	+	2	0	NASP	45851441	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	1.628000	0.37060	2.248000	0.74166	0.533000	0.62120	CAG	A|0.297;G|0.703	0.703	strong		0.368	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
OR5R1	219479	hgsc.bcm.edu	37	11	56185159	56185159	+	Missense_Mutation	SNP	A	A	G	rs7930678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56185159A>G	ENST00000312253.1	-	1	549	c.550T>C	c.(550-552)Ttc>Ctc	p.F184L		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	184			F -> L (in dbSNP:rs7930678).			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)					AGAGCTAAGAAGGGGAGGTCA	0.448													G|||	1414	0.282348	0.5378	0.1916	5008	,	,		22594	0.1369		0.2664	False		,,,				2504	0.1677				p.F184L		Atlas-SNP	.											.	OR5R1	83	.	0			c.T550C						PASS	.	G	LEU/PHE	2202,2200	587.9+/-386.8	568,1066,567	97.0	88.0	91.0		550	2.7	0.1	11	dbSNP_116	91	2395,6195	698.9+/-405.0	320,1755,2220	yes	missense	OR5R1	NM_001004744.1	22	888,2821,2787	GG,GA,AA		27.8813,49.9773,35.3833	benign	184/325	56185159	4597,8395	2201	4295	6496	SO:0001583	missense	219479	exon1			CTAAGAAGGGGAG	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.550T>C	11.37:g.56185159A>G	ENSP00000308595:p.Phe184Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	608	0.2783882783882784	249	0.5060975609756098	63	0.17403314917127072	88	0.15384615384615385	208	0.27440633245382584	G	0.744	-0.775389	0.02951	0.500227	0.278813	ENSG00000174942	ENST00000312253	T	0.00022	9.01	5.72	2.66	0.31614	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00013	-2.93	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48958	-0.8988	8	0.02654	T	1	-5.8891	3.8239	0.08846	0.1973:0.1109:0.578:0.1138	rs7930678;rs52817684;rs59315437;rs7930678	184	Q8NH85	OR5R1_HUMAN	L	184	ENSP00000308595:F184L	ENSP00000308595:F184L	F	-	1	0	OR5R1	55941735	0.000000	0.05858	0.062000	0.19696	0.746000	0.42486	-0.573000	0.05874	0.360000	0.24265	-0.200000	0.12747	TTC	A|0.675;G|0.324	0.324	strong		0.448	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
RAB3C	115827	hgsc.bcm.edu	37	5	58120940	58120940	+	Silent	SNP	C	C	T	rs373970752		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:58120940C>T	ENST00000282878.4	+	4	616	c.447C>T	c.(445-447)gaC>gaT	p.D149D		NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	149					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		ACATGGAAGACGAGCGGGTCA	0.368																																					p.D149D		Atlas-SNP	.											RAB3C,NS,carcinoma,0,1	RAB3C	47	1	0			c.C447T						scavenged	.	C		0,4406		0,0,2203	106.0	96.0	99.0		447	-5.2	1.0	5		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RAB3C	NM_138453.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		149/228	58120940	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	115827	exon4			GGAAGACGAGCGG	AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"""RAB, member RAS oncogene"""	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.447C>T	5.37:g.58120940C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	195	2	0.0102564	NM_138453		Silent	SNP	ENST00000282878.4	37	CCDS3976.1																																																																																			.	.	weak		0.368	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453	
C21orf2	755	hgsc.bcm.edu	37	21	45750145	45750145	+	Missense_Mutation	SNP	T	T	C	rs11552066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45750145T>C	ENST00000339818.4	-	7	914	c.707A>G	c.(706-708)cAg>cGg	p.Q236R	C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000397956.3_Missense_Mutation_p.Q355R|C21orf2_ENST00000325223.7_Missense_Mutation_p.Q235R|AP001062.7_ENST00000448927.1_RNA|AP001062.8_ENST00000422357.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	236					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		CACAGTCTGCTGCACGGCCTC	0.701													T|||	432	0.086262	0.0348	0.1657	5008	,	,		15202	0.0298		0.1213	False		,,,				2504	0.1217				p.Q355R		Atlas-SNP	.											.	C21orf2	10	.	0			c.A1064G						PASS	.	T	ARG/GLN	192,4168		2,188,1990	13.0	13.0	13.0		707	2.8	0.1	21	dbSNP_120	13	939,7611		53,833,3389	no	missense	C21orf2	NM_004928.2	43	55,1021,5379	CC,CT,TT		10.9825,4.4037,8.7607	possibly-damaging	236/257	45750145	1131,11779	2180	4275	6455	SO:0001583	missense	755	exon7			GTCTGCTGCACGG	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.707A>G	21.37:g.45750145T>C	ENSP00000344566:p.Gln236Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001271441	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	167	0.07646520146520147	25	0.0508130081300813	41	0.1132596685082873	10	0.017482517482517484	91	0.12005277044854881	T	9.745	1.165795	0.21538	0.044037	0.109825	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.40756	1.56;1.02;1.57	5.13	2.77	0.32553	.	0.575196	0.19755	N	0.106812	T	0.00412	0.0013	L	0.50333	1.59	0.44000	P	0.003299000000000052	B;B;B;B	0.16166	0.004;0.016;0.003;0.01	B;B;B;B	0.11329	0.004;0.005;0.002;0.006	T	0.20273	-1.0280	9	0.02654	T	1	-17.6614	7.3568	0.26723	0.0:0.1776:0.0:0.8224	rs11552066	235;355;236;195	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	R	236;355;235	ENSP00000344566:Q236R;ENSP00000381047:Q355R;ENSP00000317302:Q235R	ENSP00000317302:Q235R	Q	-	2	0	C21orf2	44574573	0.999000	0.42202	0.107000	0.21349	0.065000	0.16274	2.749000	0.47492	0.299000	0.22661	-0.256000	0.11100	CAG	T|0.913;C|0.087	0.087	strong		0.701	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
WNK1	65125	hgsc.bcm.edu	37	12	998378	998378	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:998378T>A	ENST00000315939.6	+	21	6080	c.5437T>A	c.(5437-5439)Tct>Act	p.S1813T	WNK1_ENST00000535572.1_Missense_Mutation_p.S1566T|WNK1_ENST00000537687.1_Missense_Mutation_p.S2073T|WNK1_ENST00000340908.4_Missense_Mutation_p.S1406T|WNK1_ENST00000530271.2_Missense_Mutation_p.S2311T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1813					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)			CACAGTGACTTCTGCGGTTGG	0.363																																					p.S2073T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T6217A						PASS	.						166.0	161.0	163.0					12																	998378		2203	4300	6503	SO:0001583	missense	65125	exon21			GTGACTTCTGCGG	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.5437T>A	12.37:g.998378T>A	ENSP00000313059:p.Ser1813Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.778019	0.31502	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.77	2.15	0.27550	.	0.284463	0.31092	N	0.008273	T	0.29783	0.0744	L	0.40543	1.245	0.25832	N	0.984158	B;B;B	0.13594	0.003;0.003;0.008	B;B;B	0.13407	0.006;0.009;0.004	T	0.23940	-1.0174	10	0.66056	D	0.02	-5.5426	5.5835	0.17262	0.128:0.1412:0.0:0.7307	.	1566;1566;1813	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1566;1813;2073;986;2311;1406	ENSP00000441972:S1566T;ENSP00000313059:S1813T;ENSP00000444465:S2073T;ENSP00000433548:S2311T;ENSP00000341292:S1406T	ENSP00000252477:S986T	S	+	1	0	WNK1	868639	0.866000	0.29940	0.306000	0.25113	0.265000	0.26407	1.118000	0.31246	0.528000	0.28580	-0.336000	0.08194	TCT	.	.	none		0.363	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
CSMD1	64478	hgsc.bcm.edu	37	8	3224561	3224561	+	Silent	SNP	T	T	C	rs4875703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:3224561T>C	ENST00000520002.1	-	21	3666	c.3111A>G	c.(3109-3111)acA>acG	p.T1037T	CSMD1_ENST00000602557.1_Silent_p.T1037T|CSMD1_ENST00000602723.1_Silent_p.T1037T|CSMD1_ENST00000537824.1_Silent_p.T1036T|CSMD1_ENST00000539096.1_Silent_p.T1036T|CSMD1_ENST00000542608.1_Silent_p.T1036T|CSMD1_ENST00000400186.3_Silent_p.T1037T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1037	CUB 6. {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)		TACCTGAAAATGTGATATTGA	0.438													C|||	1428	0.285144	0.326	0.3775	5008	,	,		19000	0.3284		0.2505	False		,,,				2504	0.1554				p.T1036T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A3108G						PASS	.	C		1128,2830		161,806,1012	54.0	59.0	58.0		3108	-10.2	0.0	8	dbSNP_111	58	1976,6340		226,1524,2408	no	coding-synonymous	CSMD1	NM_033225.5		387,2330,3420	CC,CT,TT		23.7614,28.4992,25.2892		1036/3565	3224561	3104,9170	1979	4158	6137	SO:0001819	synonymous_variant	64478	exon20			TGAAAATGTGATA			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.3111A>G	8.37:g.3224561T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		685	0.31364468864468864	170	0.34552845528455284	118	0.3259668508287293	211	0.3688811188811189	186	0.24538258575197888	C	0.133	-1.111616	0.01813	0.284992	0.237614	ENSG00000183117	ENST00000335551	.	.	.	5.09	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999945	.	.	.	.	.	.	T	0.35549	-0.9784	3	.	.	.	.	11.8873	0.52610	0.0:0.2765:0.4646:0.259	rs4875703;rs57705395;rs4875703	.	.	.	V	517	.	.	I	-	1	0	CSMD1	3211968	0.002000	0.14202	0.025000	0.17156	0.066000	0.16364	-1.405000	0.02492	-5.492000	0.00013	-2.764000	0.00121	ATT	T|0.701;C|0.299	0.299	strong		0.438	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
ARSA	410	hgsc.bcm.edu	37	22	51065361	51065361	+	Missense_Mutation	SNP	C	C	A	rs6151415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:51065361C>A	ENST00000547307.1	-	3	984	c.579G>T	c.(577-579)tgG>tgT	p.W193C	ARSA_ENST00000216124.5_Missense_Mutation_p.W195C|ARSA_ENST00000356098.5_Missense_Mutation_p.W195C|ARSA_ENST00000547805.1_Missense_Mutation_p.W193C|ARSA_ENST00000395619.3_Missense_Mutation_p.W195C|ARSA_ENST00000395621.3_Missense_Mutation_p.W195C|ARSA_ENST00000453344.2_Missense_Mutation_p.W109C			P15289	ARSA_HUMAN	arylsulfatase A	193			W -> C (in dbSNP:rs6151415). {ECO:0000269|PubMed:10477432, ECO:0000269|PubMed:11456299, ECO:0000269|PubMed:15326627, ECO:0000269|PubMed:1670590, ECO:0000269|PubMed:9888390, ECO:0000269|Ref.6}.		autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|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)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|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)	Micafungin(DB01141)|Suramin(DB04786)	GTCCGGGCAGCCAGGGGGGCT	0.677													C|||	95	0.0189696	0.003	0.0231	5008	,	,		15319	0.0		0.0626	False		,,,				2504	0.0123				p.W195C		Atlas-SNP	.											.	ARSA	19	.	0			c.G585T	GRCh37	CM990179	ARSA	M	rs6151415	PASS	.	C	CYS/TRP,CYS/TRP,CYS/TRP,CYS/TRP,CYS/TRP	75,4327		1,73,2127	45.0	56.0	52.0		585,585,585,585,327	3.3	1.0	22	dbSNP_114	52	663,7933		35,593,3670	yes	missense,missense,missense,missense,missense	ARSA	NM_000487.5,NM_001085425.2,NM_001085426.2,NM_001085427.2,NM_001085428.2	215,215,215,215,215	36,666,5797	AA,AC,CC		7.7129,1.7038,5.6778	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/510,195/510,195/510,195/510,109/424	51065361	738,12260	2201	4298	6499	SO:0001583	missense	410	exon4			GGGCAGCCAGGGG	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"""Arylsulfatase family"""	713	protein-coding gene	gene with protein product	"""metachromatic leucodystrophy"""	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.579G>T	22.37:g.51065361C>A	ENSP00000448440:p.Trp193Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	56	0.622222	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		51	0.023351648351648352	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	39	0.051451187335092345	C	15.47	2.843658	0.51164	0.017038	0.077129	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64	5.51	3.27	0.37495	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.349478	0.31484	N	0.007569	T	0.45816	0.1361	N	0.08118	0	0.50039	D	0.999842	D	0.64830	0.994	P	0.59288	0.855	T	0.75861	-0.3168	10	0.59425	D	0.04	.	7.969	0.30117	0.3227:0.5209:0.1564:0.0	rs6151415;rs6151415	193	P15289	ARSA_HUMAN	C	195;195;193;193;195;109;195	ENSP00000348406:W195C;ENSP00000216124:W195C;ENSP00000448440:W193C;ENSP00000448932:W193C;ENSP00000378983:W195C;ENSP00000412542:W109C;ENSP00000378981:W195C	ENSP00000216124:W195C	W	-	3	0	ARSA	49412227	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	0.854000	0.27791	1.318000	0.45170	-0.251000	0.11542	TGG	C|0.958;A|0.042	0.042	strong		0.677	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
DSG1	1828	hgsc.bcm.edu	37	18	28934274	28934274	+	Silent	SNP	C	C	T	rs146192657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:28934274C>T	ENST00000257192.4	+	15	2327	c.2115C>T	c.(2113-2115)taC>taT	p.Y705Y	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG1_ENST00000462981.2_Silent_p.Y64Y|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	705					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.Y705*(2)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CATATGCTTACGCAGATGAAG	0.373													T|||	15	0.00299521	0.0008	0.0072	5008	,	,		17640	0.0		0.0089	False		,,,				2504	0.0				p.Y705Y		Atlas-SNP	.											.	DSG1	176	.	2	Substitution - Nonsense(2)	lung(2)	c.C2115T						PASS	.	T		7,4399	825.6+/-416.5	0,7,2196	91.0	90.0	90.0		2115	3.6	1.0	18	dbSNP_134	90	77,8523	815.9+/-406.9	0,77,4223	no	coding-synonymous	DSG1	NM_001942.2		0,84,6419	TT,TC,CC		0.8953,0.1589,0.6459		705/1050	28934274	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon15			TGCTTACGCAGAT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.2115C>T	18.37:g.28934274C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	135	87	0.644444	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.994;T|0.006	0.006	strong		0.373	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
SLC25A45	283130	hgsc.bcm.edu	37	11	65144331	65144331	+	Missense_Mutation	SNP	C	C	T	rs371949191		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65144331C>T	ENST00000527174.1	-	5	611	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	SLC25A45_ENST00000377152.2_Missense_Mutation_p.E82K|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000360662.3_Missense_Mutation_p.E162K|SLC25A45_ENST00000294187.6_Missense_Mutation_p.E144K|SLC25A45_ENST00000526432.1_Missense_Mutation_p.E124K|SLC25A45_ENST00000398802.1_Missense_Mutation_p.E186K|SLC25A45_ENST00000534028.1_Missense_Mutation_p.E162K|SLC25A45_ENST00000417511.2_Missense_Mutation_p.E144K			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	186					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						CAGAGCCCTTCATAGGTGATG	0.627																																					p.E186K		Atlas-SNP	.											.	SLC25A45	23	.	0			c.G556A						PASS	.	C	LYS/GLU,LYS/GLU	0,4070		0,0,2035	138.0	145.0	143.0		556,430	4.3	0.2	11		143	1,8389		0,1,4194	no	missense,missense	SLC25A45	NM_182556.2,NM_001077241.1	56,56	0,1,6229	TT,TC,CC		0.0119,0.0,0.0080	benign,benign	186/289,144/247	65144331	1,12459	2035	4195	6230	SO:0001583	missense	283130	exon6			GCCCTTCATAGGT	BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.556G>A	11.37:g.65144331C>T	ENSP00000435489:p.Glu186Lys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	211	89	0.421801	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983275	0.53827	0.0	1.19E-4	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	D;D;D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	5.23	4.26	0.50523	Mitochondrial carrier domain (2);	0.116851	0.53938	D	0.000048	D	0.89336	0.6686	M	0.86343	2.81	0.39497	D	0.968142	D;B;B	0.54964	0.969;0.203;0.242	P;B;B	0.58077	0.832;0.099;0.159	D	0.88486	0.3072	10	0.27785	T	0.31	-0.3137	13.3171	0.60413	0.0:0.8399:0.1601:0.0	.	124;162;186	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	K	186;162;186;162;82;144;144;124	ENSP00000435489:E186K;ENSP00000431769:E162K;ENSP00000381782:E186K;ENSP00000353879:E162K;ENSP00000366357:E82K;ENSP00000294187:E144K;ENSP00000407530:E144K;ENSP00000435547:E124K	ENSP00000294187:E144K	E	-	1	0	SLC25A45	64900907	0.000000	0.05858	0.240000	0.24138	0.281000	0.26958	0.738000	0.26158	2.617000	0.88574	0.561000	0.74099	GAA	.	.	weak		0.627	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556	
KLHL6	89857	hgsc.bcm.edu	37	3	183226114	183226114	+	Silent	SNP	G	G	T	rs73188786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183226114G>T	ENST00000341319.3	-	3	677	c.642C>A	c.(640-642)ccC>ccA	p.P214P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	214	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			gagtgtccacgggcaggtcaa	0.502													G|||	313	0.0625	0.0083	0.0576	5008	,	,		21109	0.0069		0.1143	False		,,,				2504	0.1431				p.P214P		Atlas-SNP	.											.	KLHL6	100	.	0			c.C642A						PASS	.	G		102,4304	80.4+/-118.8	0,102,2101	77.0	68.0	71.0		642	-11.7	0.0	3	dbSNP_130	71	1047,7553	220.1+/-257.9	69,909,3322	no	coding-synonymous	KLHL6	NM_130446.2		69,1011,5423	TT,TG,GG		12.1744,2.315,8.8344		214/622	183226114	1149,11857	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon3			GTCCACGGGCAGG	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.642C>A	3.37:g.183226114G>T		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			G|0.917;T|0.083	0.083	strong		0.502	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
APCDD1L	164284	hgsc.bcm.edu	37	20	57045667	57045667	+	Silent	SNP	T	T	C	rs1980576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:57045667T>C	ENST00000371149.3	-	2	416	c.186A>G	c.(184-186)acA>acG	p.T62T	APCDD1L_ENST00000439429.1_Silent_p.T73T	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	62						integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			AGTCTTACCCTGTGGAGATCC	0.567													C|||	2303	0.459864	0.6157	0.4265	5008	,	,		17671	0.3978		0.3688	False		,,,				2504	0.4305				p.T62T		Atlas-SNP	.											.	APCDD1L	48	.	0			c.A186G						PASS	.	C		2475,1931		711,1053,439	57.0	45.0	49.0		186	-4.1	1.0	20	dbSNP_92	49	3123,5475		553,2017,1729	no	coding-synonymous	APCDD1L	NM_153360.1		1264,3070,2168	CC,CT,TT		36.3224,43.8266,43.0483		62/502	57045667	5598,7406	2203	4299	6502	SO:0001819	synonymous_variant	164284	exon2			TTACCCTGTGGAG	AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.186A>G	20.37:g.57045667T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_153360		Silent	SNP	ENST00000371149.3	37	CCDS13467.1																																																																																			T|0.564;C|0.436	0.436	strong		0.567	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
ARSB	411	hgsc.bcm.edu	37	5	78135241	78135241	+	Missense_Mutation	SNP	C	C	T	rs25414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:78135241C>T	ENST00000264914.4	-	6	1687	c.1151G>A	c.(1150-1152)aGc>aAc	p.S384N	ARSB_ENST00000396151.3_Missense_Mutation_p.S384N|ARSB_ENST00000565165.1_Missense_Mutation_p.S384N	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	384			S -> N (in MPS6; dbSNP:rs25414). {ECO:0000269|PubMed:14974081}.		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)		GGGGGATGGGCTTCCTTCACT	0.383													C|||	98	0.0195687	0.0038	0.0216	5008	,	,		19269	0.001		0.0408	False		,,,				2504	0.0368				p.S384N	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G1151A	GRCh37	CM003999	ARSB	M	rs25414	PASS	.	C	ASN/SER,ASN/SER	55,4351	54.9+/-90.9	0,55,2148	121.0	121.0	121.0		1151,1151	4.0	1.0	5	dbSNP_71	121	539,8061	149.8+/-204.8	21,497,3782	yes	missense,missense	ARSB	NM_000046.3,NM_198709.2	46,46	21,552,5930	TT,TC,CC		6.2674,1.2483,4.5671	benign,benign	384/534,384/414	78135241	594,12412	2203	4300	6503	SO:0001583	missense	411	exon7			GATGGGCTTCCTT	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.1151G>A	5.37:g.78135241C>T	ENSP00000264914:p.Ser384Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_198709	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	47	0.02152014652014652	4	0.008130081300813009	11	0.03038674033149171	1	0.0017482517482517483	31	0.040897097625329816	C	10.20	1.285339	0.23478	0.012483	0.062674	ENSG00000113273	ENST00000264914;ENST00000396151	D;D	0.96459	-4.02;-4.02	5.78	3.98	0.46160	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.286415	0.44483	D	0.000457	T	0.62527	0.2435	N	0.21508	0.67	0.24754	N	0.992965	B;B	0.23540	0.087;0.007	B;B	0.21917	0.037;0.015	T	0.67341	-0.5695	10	0.16896	T	0.51	.	11.3121	0.49370	0.0:0.8645:0.0:0.1355	rs25414;rs52806985;rs25414	384;384	Q8N322;P15848	.;ARSB_HUMAN	N	384	ENSP00000264914:S384N;ENSP00000379455:S384N	ENSP00000264914:S384N	S	-	2	0	ARSB	78170997	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	0.477000	0.22196	0.767000	0.33267	0.561000	0.74099	AGC	C|0.963;T|0.037	0.037	strong		0.383	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
SLC39A12	221074	hgsc.bcm.edu	37	10	18254595	18254595	+	Missense_Mutation	SNP	C	C	T	rs62619938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:18254595C>T	ENST00000377369.2	+	4	1000	c.727C>T	c.(727-729)Cgt>Tgt	p.R243C	SLC39A12_ENST00000539911.1_Missense_Mutation_p.R109C|SLC39A12_ENST00000377374.4_Missense_Mutation_p.R243C|SLC39A12_ENST00000377371.3_Missense_Mutation_p.R243C	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	243					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TTCCTTGAATCGTACGAATAC	0.418													C|||	130	0.0259585	0.0068	0.0403	5008	,	,		18927	0.0		0.0875	False		,,,				2504	0.0051				p.R243C		Atlas-SNP	.											SLC39A12,NS,carcinoma,-1,1	SLC39A12	181	1	0			c.C727T						PASS	.	C	CYS/ARG,CYS/ARG	50,4356	50.2+/-85.5	2,46,2155	53.0	52.0	52.0		727,727	3.5	0.6	10	dbSNP_129	52	582,8018	155.5+/-209.5	20,542,3738	yes	missense,missense	SLC39A12	NM_001145195.1,NM_152725.3	180,180	22,588,5893	TT,TC,CC		6.7674,1.1348,4.8593	possibly-damaging,possibly-damaging	243/692,243/655	18254595	632,12374	2203	4300	6503	SO:0001583	missense	221074	exon4			TTGAATCGTACGA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.727C>T	10.37:g.18254595C>T	ENSP00000366586:p.Arg243Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	37	CCDS44362.1	83	0.038003663003663	5	0.01016260162601626	18	0.049723756906077346	0	0.0	60	0.079155672823219	C	6.711	0.499822	0.12762	0.011348	0.067674	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.62364	0.15;0.03;0.15;0.04	5.81	3.49	0.39957	.	0.362650	0.35838	N	0.002960	T	0.05502	0.0145	L	0.53249	1.67	0.42390	D	0.992526	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.14578	0.011;0.003;0.002	T	0.09530	-1.0670	10	0.56958	D	0.05	-1.9829	8.7303	0.34494	0.7981:0.1345:0.0674:0.0	rs62619938	243;243;243	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	C	243;243;243;109;163	ENSP00000366586:R243C;ENSP00000366591:R243C;ENSP00000366588:R243C;ENSP00000440445:R109C	ENSP00000366586:R243C	R	+	1	0	SLC39A12	18294601	1.000000	0.71417	0.560000	0.28344	0.007000	0.05969	2.918000	0.48829	0.476000	0.27440	-0.262000	0.10625	CGT	C|0.956;T|0.044	0.044	strong		0.418	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
CAPN1	823	hgsc.bcm.edu	37	11	64981472	64981472	+	IGR	SNP	G	G	C	rs239258	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64981472G>C	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.T43T(2)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		AGAACTTCACGGCCGCTGTCC	0.687													G|||	1736	0.346645	0.233	0.2939	5008	,	,		12972	0.3929		0.4553	False		,,,				2504	0.3783				p.T43T		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,6	SLC22A20	36	6	2	Substitution - coding silent(2)	prostate(2)	c.G129C						PASS	.	G		845,3041		105,635,1203	10.0	15.0	13.0		129	-4.7	0.8	11	dbSNP_79	13	3702,4532		877,1948,1292	no	coding-synonymous	SLC22A20	NM_001004326.4		982,2583,2495	CC,CG,GG		44.9599,21.7447,37.5165		43/350	64981472	4547,7573	1943	4117	6060	SO:0001628	intergenic_variant	440044	exon1			CTTCACGGCCGCT	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981472G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_001004326	Q2TTR0|Q6DHV4	Silent	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.614;C|0.386	0.386	strong		0.687	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
PMS2	5395	hgsc.bcm.edu	37	7	6026942	6026942	+	Missense_Mutation	SNP	G	G	T	rs1805323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6026942G>T	ENST00000265849.7	-	11	1559	c.1454C>A	c.(1453-1455)aCg>aAg	p.T485K	PMS2_ENST00000441476.2_Missense_Mutation_p.T379K|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.T485K	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	485			T -> K (in dbSNP:rs1805323). {ECO:0000269|PubMed:10480359}.		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)	p.T485K(1)		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)		CGCTCTGTCCGTAGGGTCACT	0.592			"""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|||	561	0.112021	0.0098	0.0173	5008	,	,		16417	0.3373		0.0457	False		,,,				2504	0.1534				p.T485K		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	PMS2,NS,carcinoma,+1,2	PMS2	88	2	1	Substitution - Missense(1)	stomach(1)	c.C1454A						scavenged	.	G	LYS/THR	86,4320	72.0+/-110.0	1,84,2118	88.0	88.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1454	-10.2	0.0	7	dbSNP_98	88	350,8250	118.8+/-178.2	7,336,3957	no	missense	PMS2	NM_000535.5	78	8,420,6075	TT,TG,GG		4.0698,1.9519,3.3523	benign	485/863	6026942	436,12570	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	CTGTCCGTAGGGT		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.1454C>A	7.37:g.6026942G>T	ENSP00000265849:p.Thr485Lys	Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	247	0.1130952380952381	4	0.008130081300813009	4	0.011049723756906077	203	0.3548951048951049	36	0.047493403693931395	g	2.010	-0.427336	0.04701	0.019519	0.040698	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.85339	1.13;1.13;-1.97	5.1	-10.2	0.00374	.	5.407520	0.00166	N	0.000000	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	0.04013	0.001;0.001;0.001	T	0.21177	-1.0253	9	0.05833	T	0.94	0.8267	4.7783	0.13190	0.4093:0.4036:0.1016:0.0855	rs1805323;rs2266664	485;485;379	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	K	485;438;379;485	ENSP00000265849:T485K;ENSP00000392843:T379K;ENSP00000384308:T485K	ENSP00000265849:T485K	T	-	2	0	PMS2	5993468	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.027000	0.13621	-1.911000	0.01082	-0.355000	0.07637	ACG	G|0.944;T|0.056	0.056	strong		0.592	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
DPPA3	359787	hgsc.bcm.edu	37	12	7864199	7864199	+	Silent	SNP	C	C	T	rs61753205	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7864199C>T	ENST00000345088.2	+	1	150	c.33C>T	c.(31-33)atC>atT	p.I11I		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	11					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CAACCTACATCCCAGGGTCTC	0.493													C|||	15	0.00299521	0.0008	0.0058	5008	,	,		-128	0.0		0.0099	False		,,,				2504	0.0				p.I11I		Atlas-SNP	.											.	DPPA3	26	.	0			c.C33T						PASS	.	C		10,4396	15.5+/-35.6	0,10,2193	74.0	63.0	66.0		33	1.9	0.0	12	dbSNP_129	66	103,8497	55.2+/-116.2	2,99,4199	no	coding-synonymous	DPPA3	NM_199286.2		2,109,6392	TT,TC,CC		1.1977,0.227,0.8688		11/160	7864199	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	359787	exon1			CTACATCCCAGGG	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.33C>T	12.37:g.7864199C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_199286	Q0P5U3|Q6JZS6	Silent	SNP	ENST00000345088.2	37	CCDS8582.1																																																																																			C|0.993;T|0.007	0.007	strong		0.493	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286	
ATXN1	6310	hgsc.bcm.edu	37	6	16327921	16327921	+	Missense_Mutation	SNP	C	C	A	rs201030692		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:16327921C>A	ENST00000244769.4	-	8	1557	c.621G>T	c.(619-621)caG>caT	p.Q207H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q207H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	207	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.Q207H(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgatgctgctgctgctgct	0.662																																					p.Q207H		Atlas-SNP	.											ATXN1,NS,carcinoma,0,1	ATXN1	117	1	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.G621T						scavenged	.						5.0	8.0	7.0					6																	16327921		1605	3502	5107	SO:0001583	missense	6310	exon7			ATGCTGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.621G>T	6.37:g.16327921C>A	ENSP00000244769:p.Gln207His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	38	3	0.0789474	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	c	0.699	-0.791581	0.02884	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56275	0.47;0.47	0.0465	-0.093	0.13652	.	.	.	.	.	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	D	0.54964	0.969	B	0.38106	0.265	T	0.21042	-1.0257	8	0.35671	T	0.21	.	.	.	.	.	207	P54253	ATX1_HUMAN	H	207	ENSP00000244769:Q207H;ENSP00000416360:Q207H	ENSP00000244769:Q207H	Q	-	3	2	ATXN1	16435900	0.128000	0.22383	0.017000	0.16124	0.068000	0.16541	-0.076000	0.11412	-1.412000	0.02030	-1.404000	0.01136	CAG	.	.	weak		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
TAF1C	9013	hgsc.bcm.edu	37	16	84215390	84215390	+	Silent	SNP	T	T	C	rs2230127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84215390T>C	ENST00000567759.1	-	8	1178	c.996A>G	c.(994-996)gcA>gcG	p.A332A	TAF1C_ENST00000378541.4_Silent_p.A332A|TAF1C_ENST00000570117.1_5'UTR|TAF1C_ENST00000566732.1_Silent_p.A306A|TAF1C_ENST00000541676.1_Silent_p.A239A|TAF1C_ENST00000341690.6_Silent_p.A239A	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	332					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)	p.A332A(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						CCACCTGCATTGCCTGCAGAA	0.632													T|||	1663	0.332069	0.2413	0.4337	5008	,	,		17008	0.377		0.3638	False		,,,				2504	0.3037				p.A332A		Atlas-SNP	.											TAF1C,NS,carcinoma,0,1	TAF1C	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A996G						PASS	.	T	,	1173,3227	411.1+/-335.6	156,861,1183	64.0	63.0	63.0		996,717	3.6	1.0	16	dbSNP_98	63	3323,5277	492.3+/-373.3	672,1979,1649	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	828,2840,2832	CC,CT,TT		38.6395,26.6591,34.5846	,	332/870,239/776	84215390	4496,8504	2200	4300	6500	SO:0001819	synonymous_variant	9013	exon8			CTGCATTGCCTGC	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.996A>G	16.37:g.84215390T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			T|0.654;C|0.346	0.346	strong		0.632	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
SLFN14	342618	hgsc.bcm.edu	37	17	33884804	33884804	+	Missense_Mutation	SNP	T	T	C	rs10512472	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33884804T>C	ENST00000415846.3	-	1	313	c.278A>G	c.(277-279)cAg>cGg	p.Q93R		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	93			Q -> R (in dbSNP:rs10512472).				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						AAGGTATTTCTGTGAACCTGA	0.433													T|||	1178	0.235224	0.2284	0.2522	5008	,	,		20357	0.3056		0.172	False		,,,				2504	0.2249				p.Q93R		Atlas-SNP	.											.	SLFN14	43	.	0			c.A278G						PASS	.	T	ARG/GLN	288,1096		36,216,440	88.0	71.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	278	4.3	1.0	17	dbSNP_119	76	549,2633		44,461,1086	yes	missense	SLFN14	NM_001129820.1	43	80,677,1526	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	17.2533,20.8092,18.3311	possibly-damaging	93/913	33884804	837,3729	692	1591	2283	SO:0001583	missense	342618	exon1			TATTTCTGTGAAC		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.278A>G	17.37:g.33884804T>C	ENSP00000391101:p.Gln93Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	505	0.23122710622710624	111	0.22560975609756098	95	0.26243093922651933	179	0.3129370629370629	120	0.158311345646438	T	14.25	2.478941	0.44044	0.208092	0.172533	ENSG00000236320	ENST00000415846	T	0.01998	4.51	4.28	4.28	0.50868	.	.	.	.	.	T	0.00012	0.0000	L	0.45422	1.42	0.47621	P	5.209999999999937E-4	P	0.43094	0.799	B	0.34722	0.188	T	0.52646	-0.8548	8	0.62326	D	0.03	-3.1007	9.9792	0.41802	0.0:0.0:0.0:1.0	rs10512472;rs61277257;rs10512472	93	P0C7P3	SLN14_HUMAN	R	93	ENSP00000391101:Q93R	ENSP00000391101:Q93R	Q	-	2	0	SLFN14	30908917	0.985000	0.35326	1.000000	0.80357	0.998000	0.95712	1.662000	0.37418	1.908000	0.55244	0.533000	0.62120	CAG	T|0.743;C|0.257	0.257	strong		0.433	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
OSBPL5	114879	hgsc.bcm.edu	37	11	3111866	3111866	+	Missense_Mutation	SNP	C	C	T	rs2277301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:3111866C>T	ENST00000263650.7	-	20	2479	c.2320G>A	c.(2320-2322)Gcc>Acc	p.A774T	OSBPL5_ENST00000389989.3_Missense_Mutation_p.A706T|OSBPL5_ENST00000478260.1_Missense_Mutation_p.A228T|OSBPL5_ENST00000525498.1_Missense_Mutation_p.A685T|OSBPL5_ENST00000542243.1_Missense_Mutation_p.A405T|OSBPL5_ENST00000348039.5_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	142	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	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		
PIK3R5	23533	hgsc.bcm.edu	37	17	8814719	8814719	+	Silent	SNP	G	G	A	rs56121082	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8814719G>A	ENST00000447110.1	-	2	217	c.93C>T	c.(91-93)acC>acT	p.T31T	PIK3R5_ENST00000581552.1_Silent_p.T31T|PIK3R5_ENST00000584803.1_Silent_p.T31T	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	31	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						CTGACCAGGAGGTGGAGCGGC	0.662													G|||	109	0.0217652	0.0	0.0331	5008	,	,		18301	0.0		0.0606	False		,,,				2504	0.0256				p.T31T	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C93T						PASS	.	G	,	44,4356		0,44,2156	51.0	48.0	49.0		93,93	-3.8	0.2	17	dbSNP_129	49	504,8080		11,482,3799	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	11,526,5955	AA,AG,GG		5.8714,1.0,4.2206	,	31/881,31/881	8814719	548,12436	2200	4292	6492	SO:0001819	synonymous_variant	23533	exon2			CCAGGAGGTGGAG	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.93C>T	17.37:g.8814719G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.960;A|0.040	0.040	strong		0.662	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
CSMD3	114788	hgsc.bcm.edu	37	8	113349030	113349030	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:113349030C>A	ENST00000297405.5	-	44	7114	c.6870G>T	c.(6868-6870)atG>atT	p.M2290I	CSMD3_ENST00000455883.2_Missense_Mutation_p.M2186I|CSMD3_ENST00000352409.3_Missense_Mutation_p.M2220I|CSMD3_ENST00000343508.3_Missense_Mutation_p.M2250I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2290	CUB 13. {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						TGGTGCCATTCATTGCAGTTA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.M2290I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6870T						PASS	.						79.0	73.0	75.0					8																	113349030		2203	4300	6503	SO:0001583	missense	114788	exon44			GCCATTCATTGCA	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.6870G>T	8.37:g.113349030C>A	ENSP00000297405:p.Met2290Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	60	10	0.166667	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.177692	0.38413	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26	5.64	5.64	0.86602	CUB (5);	0.057323	0.64402	D	0.000003	T	0.25121	0.0610	L	0.39326	1.205	0.45097	D	0.998113	B;B;P	0.37688	0.171;0.257;0.605	B;B;P	0.46076	0.193;0.216;0.503	T	0.00417	-1.1752	10	0.30078	T	0.28	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2186;2290;2250	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2250;2290;1560;2186;2220	ENSP00000345799:M2250I;ENSP00000297405:M2290I;ENSP00000341558:M1560I;ENSP00000412263:M2186I;ENSP00000343124:M2220I	ENSP00000297405:M2290I	M	-	3	0	CSMD3	113418206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.429000	0.44758	2.937000	0.99478	0.650000	0.86243	ATG	.	.	none		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5190182	5190182	+	Silent	SNP	C	C	T	rs34105281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:5190182C>T	ENST00000274181.7	+	7	1284	c.1146C>T	c.(1144-1146)caC>caT	p.H382H	ADAMTS16_ENST00000511368.1_Silent_p.H382H	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	382	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						GTCATGACCACGCCATCTTAC	0.522													C|||	95	0.0189696	0.003	0.0072	5008	,	,		18691	0.0		0.0239	False		,,,				2504	0.0634				p.H382H		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C1146T						PASS	.	C		18,4116		0,18,2049	164.0	161.0	162.0		1146	-4.8	0.9	5	dbSNP_126	162	241,8167		5,231,3968	no	coding-synonymous	ADAMTS16	NM_139056.2		5,249,6017	TT,TC,CC		2.8663,0.4354,2.0651		382/1225	5190182	259,12283	2067	4204	6271	SO:0001819	synonymous_variant	170690	exon7			TGACCACGCCATC	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.1146C>T	5.37:g.5190182C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			C|0.982;T|0.018	0.018	strong		0.522	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
DDX58	23586	hgsc.bcm.edu	37	9	32457189	32457189	+	Silent	SNP	T	T	C	rs10970987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32457189T>C	ENST00000379883.2	-	18	2866	c.2709A>G	c.(2707-2709)acA>acG	p.T903T	DDX58_ENST00000542096.1_Silent_p.T832T|DDX58_ENST00000379868.1_Silent_p.T700T|DDX58_ENST00000379882.1_Silent_p.T858T	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	903	Interaction with ZC3HAV1.|Repressor domain.				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 defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TCGAGTACAGTGTCTGAACTC	0.403													T|||	201	0.0401358	0.0061	0.121	5008	,	,		16645	0.0		0.0686	False		,,,				2504	0.0409				p.T903T		Atlas-SNP	.											.	DDX58	82	.	0			c.A2709G						PASS	.	T		75,4331	64.7+/-102.0	0,75,2128	103.0	96.0	98.0		2709	-8.2	0.0	9	dbSNP_120	98	746,7854	179.9+/-228.9	37,672,3591	no	coding-synonymous	DDX58	NM_014314.3		37,747,5719	CC,CT,TT		8.6744,1.7022,6.3125		903/926	32457189	821,12185	2203	4300	6503	SO:0001819	synonymous_variant	23586	exon18			GTACAGTGTCTGA	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2709A>G	9.37:g.32457189T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	37	CCDS6526.1																																																																																			T|0.947;C|0.053	0.053	strong		0.403	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
HLA-B	3106	hgsc.bcm.edu	37	6	31324128	31324128	+	Silent	SNP	C	C	T	rs1050642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324128C>T	ENST00000412585.2	-	3	463	c.435G>A	c.(433-435)aaG>aaA	p.K145K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	145	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						CGATGTAATCCTTGCCGTCGT	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.K145K		Atlas-SNP	.											.	HLA-B	54	.	0			c.G435A						PASS	.	C		141,4101		2,137,1982	30.0	23.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	435	-6.4	0.0	6	dbSNP_86	25	392,7990		0,392,3799	no	coding-synonymous	HLA-B	NM_005514.6		2,529,5781	TT,TC,CC		4.6767,3.3239,4.2221		145/363	31324128	533,12091	2121	4191	6312	SO:0001819	synonymous_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GTAATCCTTGCCG	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.435G>A	6.37:g.31324128C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	138	38	0.275362	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.945;T|0.055	0.055	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SLC2A13	114134	hgsc.bcm.edu	37	12	40499347	40499347	+	Silent	SNP	G	G	A	rs7305377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	45	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	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		
KRT75	9119	hgsc.bcm.edu	37	12	52827818	52827818	+	Missense_Mutation	SNP	T	T	C	rs298109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52827818T>C	ENST00000252245.5	-	1	491	c.271A>G	c.(271-273)Agg>Ggg	p.R91G		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	91	Gly-rich.|Head.		R -> G (in dbSNP:rs298109). {ECO:0000269|PubMed:10692104, ECO:0000269|PubMed:9856802}.		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		ACTCCAAACCTGTTGCTGGCC	0.617													C|||	3069	0.612819	0.643	0.6888	5008	,	,		15093	0.6825		0.6133	False		,,,				2504	0.4458				p.R91G		Atlas-SNP	.											.	KRT75	75	.	0			c.A271G						PASS	.	C	GLY/ARG	2729,1677	508.9+/-367.1	844,1041,318	92.0	98.0	96.0		271	3.8	0.1	12	dbSNP_79	96	5141,3459	508.4+/-377.0	1530,2081,689	yes	missense	KRT75	NM_004693.2	125	2374,3122,1007	CC,CT,TT		40.2209,38.0617,39.4895	benign	91/552	52827818	7870,5136	2203	4300	6503	SO:0001583	missense	9119	exon1			CAAACCTGTTGCT	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.271A>G	12.37:g.52827818T>C	ENSP00000252245:p.Arg91Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	1466	0.6712454212454212	327	0.6646341463414634	246	0.6795580110497238	435	0.7604895104895105	458	0.604221635883905	C	0.007	-1.979022	0.00448	0.619383	0.597791	ENSG00000170454	ENST00000252245	T	0.74947	-0.89	5.61	3.77	0.43336	.	0.110915	0.39615	N	0.001302	T	0.00012	0.0000	N	0.00392	-1.555	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47315	-0.9127	9	0.02654	T	1	.	11.6068	0.51037	0.0:0.8035:0.0:0.1965	rs298109;rs729385;rs17716701;rs60475909;rs298109	91	O95678	K2C75_HUMAN	G	91	ENSP00000252245:R91G	ENSP00000252245:R91G	R	-	1	2	KRT75	51114085	0.002000	0.14202	0.116000	0.21606	0.059000	0.15707	0.973000	0.29422	0.313000	0.23062	-0.213000	0.12676	AGG	T|0.365;G|0.002	.	strong		0.617	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
RIMBP2	23504	hgsc.bcm.edu	37	12	130941150	130941150	+	Silent	SNP	G	G	C	rs2277361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:130941150G>C	ENST00000261655.4	-	4	361	c.198C>G	c.(196-198)ggC>ggG	p.G66G	RIMBP2_ENST00000535703.1_5'UTR|RIMBP2_ENST00000536002.1_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	40	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	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	
FAT1	2195	hgsc.bcm.edu	37	4	187629896	187629896	+	Silent	SNP	G	G	A	rs11722204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187629896G>A	ENST00000441802.2	-	2	1295	c.1086C>T	c.(1084-1086)gcC>gcT	p.A362A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	362					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A362A(3)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TGACTGGCCCGGCTTTGAACT	0.448										HNSCC(5;0.00058)			G|||	76	0.0151757	0.0	0.0216	5008	,	,		20402	0.0		0.0537	False		,,,				2504	0.0072				p.A362A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	3	Substitution - coding silent(3)	prostate(3)	c.C1086T						PASS	.	G		38,3692		0,38,1827	114.0	108.0	110.0		1086	-10.6	0.4	4	dbSNP_120	110	542,7672		14,514,3579	no	coding-synonymous	FAT1	NM_005245.3		14,552,5406	AA,AG,GG		6.5985,1.0188,4.856		362/4589	187629896	580,11364	1865	4107	5972	SO:0001819	synonymous_variant	2195	exon2			TGGCCCGGCTTTG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1086C>T	4.37:g.187629896G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.969;A|0.031	0.031	strong		0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21742598	21742598	+	Missense_Mutation	SNP	G	G	A	rs468931		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21742598G>A	ENST00000434111.1	+	1	4936	c.4451G>A	c.(4450-4452)aGg>aAg	p.R1484K	RN7SKP63_ENST00000363187.1_RNA|SCARNA18_ENST00000516505.1_RNA|SCARNA17_ENST00000516211.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	1484	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.																TTCCAGAAAAGGCAGTTGCTA	0.567																																					p.R1484K		Atlas-SNP	.											RIMBP3B,NS,carcinoma,0,3	RIMBP3C	6	3	0			c.G4451A						scavenged	.						1.0	1.0	1.0					22																	21742598		15	32	47	SO:0001583	missense	150221	exon1			AGAAAAGGCAGTT		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.4451G>A	22.37:g.21742598G>A	ENSP00000407925:p.Arg1484Lys	Somatic	646	3	0.00464396		WXS	Illumina HiSeq	Phase_I	652	336	0.515337	NM_001128633		Missense_Mutation	SNP	ENST00000434111.1	37	CCDS46668.1	.	.	.	.	.	.	.	.	.	.	G	6.731	0.503660	0.12822	.	.	ENSG00000196934	ENST00000434111;ENST00000357029	T	0.28895	1.59	3.01	3.01	0.34805	Src homology-3 domain (2);	0.065884	0.64402	D	0.000011	T	0.17619	0.0423	N	0.14661	0.345	0.43412	P	0.00444599999999995	B	0.14438	0.01	B	0.15484	0.013	T	0.14448	-1.0472	9	0.59425	D	0.04	-15.075	9.6938	0.40145	0.0:0.0:1.0:0.0	.	1390	A6NNM3	RIM3B_HUMAN	K	1484;1390	ENSP00000407925:R1484K	ENSP00000349531:R1390K	R	+	2	0	RIMBP3B	20072598	1.000000	0.71417	0.995000	0.50966	0.065000	0.16274	6.798000	0.75155	1.708000	0.51301	0.454000	0.30748	AGG	G|0.250;A|0.750	0.750	weak		0.567	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
FBLN2	2199	hgsc.bcm.edu	37	3	13679203	13679203	+	Silent	SNP	G	G	A	rs1061375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13679203G>A	ENST00000295760.7	+	17	3408	c.3339G>A	c.(3337-3339)acG>acA	p.T1113T	FBLN2_ENST00000492059.1_Silent_p.T1160T|FBLN2_ENST00000535798.1_Silent_p.T1139T|FBLN2_ENST00000404922.3_Silent_p.T1160T	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	1113	Domain III.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			CAGCCTTCACGGGGGACACCA	0.627													G|||	2583	0.515775	0.764	0.3876	5008	,	,		20113	0.6369		0.3231	False		,,,				2504	0.3446				p.T1160T		Atlas-SNP	.											.	FBLN2	137	.	0			c.G3480A						PASS	.	G	,,	2780,1502		926,928,287	44.0	49.0	48.0		3480,3480,3339	-6.8	0.7	3	dbSNP_86	48	2542,5918		391,1760,2079	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	1317,2688,2366	AA,AG,GG		30.0473,35.0771,41.7674	,,	1160/1232,1160/1232,1113/1185	13679203	5322,7420	2141	4230	6371	SO:0001819	synonymous_variant	2199	exon18			CTTCACGGGGGAC	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.3339G>A	3.37:g.13679203G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	204	123	0.602941	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			G|0.494;A|0.506	0.506	strong		0.627	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
CC2D2A	57545	hgsc.bcm.edu	37	4	15569018	15569018	+	Silent	SNP	G	G	A	rs73125627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15569018G>A	ENST00000503292.1	+	26	3381	c.3201G>A	c.(3199-3201)tcG>tcA	p.S1067S	CC2D2A_ENST00000424120.1_Silent_p.S1067S|CC2D2A_ENST00000413206.1_Silent_p.S1067S|CC2D2A_ENST00000389652.5_Silent_p.S1018S	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	325	0	0		WXS	Illumina HiSeq	Phase_I	338	161	0.476331	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	
NLRP5	126206	hgsc.bcm.edu	37	19	56539240	56539240	+	Silent	SNP	C	C	T	rs397977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56539240C>T	ENST00000390649.3	+	7	1641	c.1641C>T	c.(1639-1641)gaC>gaT	p.D547D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	547	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.D547D(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGTGTTTGACGGTGACGACC	0.547													C|||	1740	0.347444	0.1316	0.4366	5008	,	,		18759	0.3571		0.4235	False		,,,				2504	0.4877				p.D547D		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.C1641T						PASS	.	C		816,3442		98,620,1411	59.0	62.0	61.0		1641	-4.4	0.0	19	dbSNP_80	61	3833,4665		889,2055,1305	no	coding-synonymous	NLRP5	NM_153447.4		987,2675,2716	TT,TC,CC		45.1047,19.1639,36.4456		547/1201	56539240	4649,8107	2129	4249	6378	SO:0001819	synonymous_variant	126206	exon7			GTTTGACGGTGAC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1641C>T	19.37:g.56539240C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			C|0.671;N|0.000	.	strong		0.547	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
OBSCN	84033	hgsc.bcm.edu	37	1	228554725	228554725	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228554725T>G	ENST00000422127.1	+	86	19521	c.19477T>G	c.(19477-19479)Ttg>Gtg	p.L6493V	OBSCN_ENST00000570156.2_Missense_Mutation_p.L7450V|OBSCN_ENST00000366707.4_Missense_Mutation_p.L4127V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6493	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AAACAAGATCTTGTGCGCTGC	0.607																																					p.L7450V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T22348G						PASS	.						47.0	50.0	49.0					1																	228554725		2026	4164	6190	SO:0001583	missense	84033	exon97			AAGATCTTGTGCG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.19477T>G	1.37:g.228554725T>G	ENSP00000409493:p.Leu6493Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.92|10.92	1.486513|1.486513	0.26686|0.26686	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66099	.|-0.19;-0.19	4.69|4.69	1.05|1.05	0.20165|0.20165	.|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|T	0.36026|0.36026	0.0952|0.0952	N|N	0.13043|0.13043	0.29|0.29	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.18871	.|0.023	T|T	0.17167|0.17167	-1.0378|-1.0378	5|9	.|0.20046	.|T	.|0.44	.|.	1.1263|1.1263	0.01736|0.01736	0.1407:0.236:0.146:0.4773|0.1407:0.236:0.146:0.4773	.|.	.|6493	.|Q5VST9	.|OBSCN_HUMAN	R|V	1109|6493;4127	.|ENSP00000409493:L6493V;ENSP00000355668:L4127V	.|ENSP00000355668:L4127V	L|L	+|+	2|1	0|2	OBSCN|OBSCN	226621348|226621348	0.003000|0.003000	0.15002|0.15002	0.016000|0.016000	0.15963|0.15963	0.385000|0.385000	0.30292|0.30292	0.243000|0.243000	0.18106|0.18106	0.018000|0.018000	0.15052|0.15052	0.402000|0.402000	0.26972|0.26972	CTT|TTG	.	.	none		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
PLEK	5341	hgsc.bcm.edu	37	2	68607947	68607947	+	Missense_Mutation	SNP	G	G	T	rs3816281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68607947G>T	ENST00000234313.7	+	3	470	c.291G>T	c.(289-291)aaG>aaT	p.K97N		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	97	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.		K -> N (in dbSNP:rs3816281). {ECO:0000269|PubMed:2768345, ECO:0000269|PubMed:2897630}.		actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		GGGATATCAAGAAGGCCATTA	0.468													G|||	2139	0.427117	0.2958	0.415	5008	,	,		22034	0.6885		0.2704	False		,,,				2504	0.5051				p.K97N		Atlas-SNP	.											.	PLEK	64	.	0			c.G291T						PASS	.	G	ASN/LYS	1270,3136	432.8+/-343.4	193,884,1126	135.0	132.0	133.0		291	4.0	1.0	2	dbSNP_107	133	2211,6389	376.3+/-338.1	294,1623,2383	yes	missense	PLEK	NM_002664.2	94	487,2507,3509	TT,TG,GG		25.7093,28.8243,26.7646	probably-damaging	97/351	68607947	3481,9525	2203	4300	6503	SO:0001583	missense	5341	exon3			TATCAAGAAGGCC	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.291G>T	2.37:g.68607947G>T	ENSP00000234313:p.Lys97Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	873	0.39972527472527475	132	0.2682926829268293	148	0.4088397790055249	382	0.6678321678321678	211	0.2783641160949868	G	17.20	3.328837	0.60743	0.288243	0.257093	ENSG00000115956	ENST00000234313	T	0.11930	2.73	5.8	4.0	0.46444	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.044743	0.85682	D	0.000000	T	0.00012	0.0000	N	0.20357	0.565	0.09310	P	0.99999762462	D;D	0.76494	0.999;0.997	D;D	0.66847	0.947;0.935	T	0.01982	-1.1235	9	0.19147	T	0.46	.	9.8947	0.41311	0.2667:0.0:0.7332:0.0	rs3816281;rs52809606;rs59032714;rs3816281	115;97	Q59GZ2;P08567	.;PLEK_HUMAN	N	97	ENSP00000234313:K97N	ENSP00000234313:K97N	K	+	3	2	PLEK	68461451	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.172000	0.42463	1.469000	0.48083	0.655000	0.94253	AAG	G|0.661;N|0.000	.	strong		0.468	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
ABL1	25	hgsc.bcm.edu	37	9	133755528	133755528	+	Silent	SNP	A	A	G	rs2227985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133755528A>G	ENST00000318560.5	+	9	1878	c.1497A>G	c.(1495-1497)gaA>gaG	p.E499E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	499					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)	TGTTCCAGGAATCCAGTATCT	0.542			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								A|||	429	0.0856629	0.2057	0.0836	5008	,	,		18557	0.001		0.0696	False		,,,				2504	0.0286				p.E518E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A1554G						PASS	.	A	,	757,3649	309.7+/-291.2	52,653,1498	106.0	106.0	106.0		1497,1554	-2.8	1.0	9	dbSNP_98	106	641,7959	164.3+/-216.7	27,587,3686	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	79,1240,5184	GG,GA,AA		7.4535,17.1811,10.7489	,	499/1131,518/1150	133755528	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	25	exon9			CCAGGAATCCAGT	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.1497A>G	9.37:g.133755528A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.898;G|0.102	0.102	strong		0.542	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
TREM1	54210	hgsc.bcm.edu	37	6	41250466	41250466	+	Missense_Mutation	SNP	T	T	A	rs2234237	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:41250466T>A	ENST00000244709.4	-	2	136	c.73A>T	c.(73-75)Act>Tct	p.T25S	TREM1_ENST00000589614.1_Missense_Mutation_p.T25S|TREM1_ENST00000591620.1_Missense_Mutation_p.T25S|TREM1_ENST00000334475.6_Missense_Mutation_p.T25S	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	25			T -> S (in dbSNP:rs2234237). {ECO:0000269|Ref.7}.		blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					TTTTCCTCAGTTAATTTAGTT	0.453													T|||	821	0.163938	0.1467	0.1268	5008	,	,		19561	0.3165		0.1054	False		,,,				2504	0.1166				p.T25S		Atlas-SNP	.											.	TREM1	38	.	0			c.A73T						PASS	.	T	SER/THR,SER/THR,SER/THR	549,3857	231.4+/-245.2	32,485,1686	93.0	101.0	98.0		73,73,73	-7.6	0.0	6	dbSNP_98	98	809,7791	187.4+/-234.7	38,733,3529	yes	missense,missense,missense	TREM1	NM_001242589.1,NM_001242590.1,NM_018643.3	58,58,58	70,1218,5215	AA,AT,TT		9.407,12.4603,10.4413	benign,benign,benign	25/226,25/151,25/235	41250466	1358,11648	2203	4300	6503	SO:0001583	missense	54210	exon2			CCTCAGTTAATTT	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.73A>T	6.37:g.41250466T>A	ENSP00000244709:p.Thr25Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	157	90	0.573248	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	37	CCDS4854.1	375	0.1717032967032967	76	0.15447154471544716	41	0.1132596685082873	187	0.3269230769230769	71	0.09366754617414248	T	0.003	-2.472380	0.00167	0.124603	0.09407	ENSG00000124731	ENST00000244709;ENST00000334475	T;T	0.11495	3.15;2.77	3.81	-7.63	0.01290	.	7.407340	0.00166	N	0.000001	T	0.00906	0.0030	N	0.22421	0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21724	-1.0237	9	0.07813	T	0.8	16.5111	2.0976	0.03672	0.4434:0.2584:0.1481:0.1501	rs2234237;rs2234237	25;25	Q9NP99-2;Q9NP99	.;TREM1_HUMAN	S	25	ENSP00000244709:T25S;ENSP00000334284:T25S	ENSP00000244709:T25S	T	-	1	0	TREM1	41358444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.456000	0.00121	-6.077000	0.00006	-2.334000	0.00248	ACT	T|0.853;N|0.000	.	strong		0.453	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643	
SPINK5	11005	hgsc.bcm.edu	37	5	147510866	147510866	+	Silent	SNP	T	T	C	rs2400478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:147510866T>C	ENST00000256084.7	+	31	3051	c.3009T>C	c.(3007-3009)ggT>ggC	p.G1003G	SPINK5_ENST00000359874.3_Silent_p.G1033G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	1003	Kazal-like 15. {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.G1033G(1)|p.G1003G(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)			CCAGGATAGGTTATCTTTGTC	0.423													T|||	2550	0.509185	0.3903	0.6398	5008	,	,		17662	0.4821		0.5924	False		,,,				2504	0.5194				p.G1033G		Atlas-SNP	.											SPINK5_ENST00000359874,NS,carcinoma,0,2	SPINK5	245	2	2	Substitution - coding silent(2)	stomach(2)	c.T3099C						PASS	.	T	,	1696,2170		364,968,601	258.0	242.0	247.0		3099,3009	-0.5	1.0	5	dbSNP_100	247	5109,3171		1554,2001,585	no	coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_006846.3	,	1918,2969,1186	CC,CT,TT		38.2971,43.8696,43.9733	,	1033/1095,1003/1065	147510866	6805,5341	1933	4140	6073	SO:0001819	synonymous_variant	11005	exon32			GATAGGTTATCTT	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.3009T>C	5.37:g.147510866T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			T|0.486;C|0.514	0.514	strong		0.423	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
DNAJB13	374407	hgsc.bcm.edu	37	11	73670645	73670645	+	Silent	SNP	T	T	C	rs653263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73670645T>C	ENST00000339764.1	+	3	1030	c.279T>C	c.(277-279)caT>caC	p.H93H		NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	93					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					ACGTCTTCCATGGCAAACCTG	0.507													t|||	3010	0.601038	0.8971	0.5663	5008	,	,		15368	0.4534		0.4751	False		,,,				2504	0.5072				p.H93H		Atlas-SNP	.											.	DNAJB13	28	.	0			c.T279C						PASS	.			3532,868	744.3+/-411.5	1428,676,96	113.0	97.0	102.0		279	-8.4	0.2	11	dbSNP_83	102	3949,4637	549.7+/-385.6	918,2113,1262	no	coding-synonymous	DNAJB13	NM_153614.2		2346,2789,1358	CC,CT,TT		45.9935,19.7273,42.3918		93/317	73670645	7481,5505	2200	4293	6493	SO:0001819	synonymous_variant	374407	exon3			CTTCCATGGCAAA	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.279T>C	11.37:g.73670645T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_153614	B3LEP4|Q8IZW5	Silent	SNP	ENST00000339764.1	37	CCDS8227.1																																																																																			T|0.418;C|0.582	0.582	strong		0.507	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
EPHA8	2046	hgsc.bcm.edu	37	1	22919904	22919904	+	Silent	SNP	C	C	T	rs209696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22919904C>T	ENST00000166244.3	+	6	1473	c.1401C>T	c.(1399-1401)aaC>aaT	p.N467N		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	467	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGCAGCCGAACGGCATCATCC	0.672													C|||	1684	0.336262	0.3918	0.353	5008	,	,		15063	0.1726		0.2664	False		,,,				2504	0.4898				p.N467N		Atlas-SNP	.											.	EPHA8	221	.	0			c.C1401T						PASS	.	C		1655,2741		329,997,872	22.0	21.0	21.0		1401	-3.7	1.0	1	dbSNP_79	21	2104,6486		271,1562,2462	no	coding-synonymous	EPHA8	NM_020526.3		600,2559,3334	TT,TC,CC		24.4936,37.6479,28.9466		467/1006	22919904	3759,9227	2198	4295	6493	SO:0001819	synonymous_variant	2046	exon6			GCCGAACGGCATC	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.1401C>T	1.37:g.22919904C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	52	0.38806	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			C|0.706;T|0.294	0.294	strong		0.672	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
TMEM206	55248	hgsc.bcm.edu	37	1	212558679	212558679	+	Silent	SNP	C	C	T	rs11556401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:212558679C>T	ENST00000261455.4	-	4	569	c.432G>A	c.(430-432)ccG>ccA	p.P144P	TMEM206_ENST00000471937.1_5'UTR|TMEM206_ENST00000535273.1_Silent_p.P205P	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	144						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TCATGTCACCCGGCTGGCCAG	0.572													c|||	34	0.00678914	0.0008	0.013	5008	,	,		20368	0.0		0.0199	False		,,,				2504	0.0041				p.P205P		Atlas-SNP	.											TMEM206,NS,carcinoma,-2,2	TMEM206	41	2	0			c.G615A						PASS	.	T	,	7,4399	15.5+/-35.6	0,7,2196	132.0	124.0	126.0		615,432	-10.9	0.0	1	dbSNP_120	126	184,8416	82.0+/-144.6	5,174,4121	no	coding-synonymous,coding-synonymous	TMEM206	NM_001198862.1,NM_018252.2	,	5,181,6317	TT,TC,CC		2.1395,0.1589,1.4686	,	205/412,144/351	212558679	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	55248	exon5			GTCACCCGGCTGG	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 75"""	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.432G>A	1.37:g.212558679C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	149	80	0.536913	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Silent	SNP	ENST00000261455.4	37	CCDS1504.1																																																																																			C|0.987;T|0.013	0.013	strong		0.572	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252	
MCTP2	55784	hgsc.bcm.edu	37	15	94884108	94884108	+	Silent	SNP	G	G	C	rs8025851	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:94884108G>C	ENST00000357742.4	+	6	924	c.924G>C	c.(922-924)gtG>gtC	p.V308V	MCTP2_ENST00000543482.1_Silent_p.V308V|MCTP2_ENST00000451018.3_Silent_p.V308V|MCTP2_ENST00000331706.4_5'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	308					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.V308V(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GAGTGATCGTGTTAAATTTGA	0.363													C|||	2410	0.48123	0.587	0.5418	5008	,	,		18919	0.3383		0.5099	False		,,,				2504	0.4131				p.V308V		Atlas-SNP	.											MCTP2,NS,carcinoma,0,2	MCTP2	122	2	1	Substitution - coding silent(1)	stomach(1)	c.G924C						scavenged	.	C	,	2483,1911	544.8+/-376.6	705,1073,419	93.0	91.0	92.0		924,924	-6.0	0.6	15	dbSNP_116	92	3895,4701	605.3+/-394.9	902,2091,1305	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	1607,3164,1724	CC,CG,GG		45.3118,43.4911,49.0993	,	308/824,308/879	94884108	6378,6612	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon6			GATCGTGTTAAAT	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.924G>C	15.37:g.94884108G>C		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.505;C|0.495	0.495	strong		0.363	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
SPNS1	83985	hgsc.bcm.edu	37	16	28995145	28995145	+	Silent	SNP	C	C	T	rs4788114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:28995145C>T	ENST00000311008.11	+	11	1736	c.1359C>T	c.(1357-1359)ttC>ttT	p.F453F	LAT_ENST00000395461.3_5'Flank|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000454369.2_5'Flank|SPNS1_ENST00000334536.8_Silent_p.F401F|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000352260.7_Silent_p.F379F|SPNS1_ENST00000565975.1_Silent_p.F498F|SPNS1_ENST00000323081.8_Silent_p.F380F|LAT_ENST00000360872.5_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	453					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CCCCCTCCTTCTTGTCCGAGT	0.637													C|||	272	0.0543131	0.0053	0.2363	5008	,	,		18278	0.0		0.0765	False		,,,				2504	0.0245				p.F453F		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1359T						PASS	.	C	,,,,	89,4305	73.1+/-111.1	0,89,2108	61.0	66.0	64.0		1359,1137,1140,1203,1359	4.6	1.0	16	dbSNP_111	64	643,7957	157.5+/-211.1	31,581,3688	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	31,670,5796	TT,TC,CC		7.4767,2.0255,5.6334	,,,,	453/529,379/455,380/456,401/477,453/529	28995145	732,12262	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			CTCCTTCTTGTCC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1359C>T	16.37:g.28995145C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.943;T|0.057	0.057	strong		0.637	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
ACTL7B	10880	hgsc.bcm.edu	37	9	111617341	111617341	+	Silent	SNP	A	A	G	rs3750467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	79	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	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	
KAZALD1	81621	hgsc.bcm.edu	37	10	102824292	102824292	+	Missense_Mutation	SNP	G	G	A	rs11190812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102824292G>A	ENST00000370200.5	+	4	1033	c.707G>A	c.(706-708)gGc>gAc	p.G236D		NM_030929.4	NP_112191.2	Q96I82	KAZD1_HUMAN	Kazal-type serine peptidase inhibitor domain 1	236	Ig-like C2-type.		G -> D (in dbSNP:rs11190812).		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)		GAGGTGACTGGCTGGCTGCAG	0.627													G|||	106	0.0211661	0.003	0.0562	5008	,	,		19684	0.001		0.0388	False		,,,				2504	0.0235				p.G236D		Atlas-SNP	.											.	KAZALD1	14	.	0			c.G707A						PASS	.	G	ASP/GLY	29,4377	36.0+/-67.5	0,29,2174	58.0	53.0	55.0		707	5.6	1.0	10	dbSNP_120	55	373,8227	122.7+/-181.7	10,353,3937	yes	missense	KAZALD1	NM_030929.4	94	10,382,6111	AA,AG,GG		4.3372,0.6582,3.0909	probably-damaging	236/305	102824292	402,12604	2203	4300	6503	SO:0001583	missense	81621	exon4			TGACTGGCTGGCT	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.707G>A	10.37:g.102824292G>A	ENSP00000359219:p.Gly236Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_030929	D3DR74|Q6ZMB1|Q9BQ73	Missense_Mutation	SNP	ENST00000370200.5	37	CCDS7509.1	53	0.024267399267399268	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	30	0.0395778364116095	G	32	5.112586	0.94339	0.006582	0.043372	ENSG00000107821	ENST00000370200	T	0.66638	-0.22	5.63	5.63	0.86233	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.180792	0.64402	D	0.000013	T	0.36386	0.0965	M	0.76574	2.34	0.80722	D	1	D	0.61697	0.99	P	0.58130	0.833	T	0.67288	-0.5708	10	0.62326	D	0.03	-11.0466	19.6913	0.96002	0.0:0.0:1.0:0.0	rs11190812;rs60320550;rs11190812	236	Q96I82	KAZD1_HUMAN	D	236	ENSP00000359219:G236D	ENSP00000359219:G236D	G	+	2	0	KAZALD1	102814282	1.000000	0.71417	0.973000	0.42090	0.996000	0.88848	4.070000	0.57548	2.654000	0.90174	0.561000	0.74099	GGC	G|0.974;A|0.026	0.026	strong		0.627	KAZALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049891.2	NM_030929	
SLC4A11	83959	hgsc.bcm.edu	37	20	3218563	3218563	+	5'Flank	SNP	T	T	C	rs79057061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3218563T>C	ENST00000380056.3	-	0	0				SLC4A11_ENST00000380059.3_Missense_Mutation_p.R50G|SLC4A11_ENST00000539553.2_Intron	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)			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						CAGGTTTTCCTGAGAAAACCC	0.642													T|||	321	0.0640974	0.1195	0.0648	5008	,	,		16349	0.001		0.1044	False		,,,				2504	0.0123				p.R50G	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											SLC4A11_ENST00000380059,NS,carcinoma,0,1	SLC4A11	188	1	0			c.A148G						PASS	.																																			SO:0001631	upstream_gene_variant	83959	exon1			TTTTCCTGAGAAA	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.3218563T>C	Exception_encountered	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	139	0.06364468864468864	47	0.09552845528455285	25	0.06906077348066299	0	0.0	67	0.08839050131926121	T	6.325	0.428152	0.11987	.	.	ENSG00000088836	ENST00000380059	D	0.81908	-1.55	3.26	0.569	0.17340	.	.	.	.	.	T	0.03263	0.0095	N	0.08118	0	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.14282	-1.0478	8	0.22706	T	0.39	.	3.4068	0.07344	0.2334:0.0:0.2404:0.5262	.	50	B4DKC8	.	G	50	ENSP00000369399:R50G	ENSP00000369399:R50G	R	-	1	2	SLC4A11	3166563	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	0.121000	0.15667	0.414000	0.25790	0.402000	0.26972	AGG	T|0.935;C|0.065	0.065	strong		0.642	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
INVS	27130	hgsc.bcm.edu	37	9	103054951	103054951	+	Silent	SNP	T	T	C	rs2787374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:103054951T>C	ENST00000262457.2	+	14	2597	c.2412T>C	c.(2410-2412)tcT>tcC	p.S804S	INVS_ENST00000262456.2_Intron|INVS_ENST00000541287.1_Silent_p.S708S	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	804					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				GAAGGTGCTCTCCGGCTGGTT	0.607													C|||	2040	0.407348	0.615	0.3516	5008	,	,		18587	0.1577		0.5726	False		,,,				2504	0.2536				p.S804S		Atlas-SNP	.											.	INVS	81	.	0			c.T2412C						PASS	.	C	,	2579,1827	532.6+/-373.5	753,1073,377	56.0	57.0	57.0		2412,	4.6	1.0	9	dbSNP_100	57	4885,3715	528.5+/-381.4	1380,2125,795	no	coding-synonymous,intron	INVS	NM_014425.2,NM_183245.1	,	2133,3198,1172	CC,CT,TT		43.1977,41.4662,42.6111	,	804/1066,	103054951	7464,5542	2203	4300	6503	SO:0001819	synonymous_variant	27130	exon14			GTGCTCTCCGGCT	AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"""Ankyrin repeat domain containing"""	17870	protein-coding gene	gene with protein product	"""nephrocystin 2"""	243305	"""nephronophthisis 2 (infantile)"""	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.2412T>C	9.37:g.103054951T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Silent	SNP	ENST00000262457.2	37	CCDS6746.1																																																																																			T|0.489;C|0.511	0.511	strong		0.607	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425	
DEDD2	162989	hgsc.bcm.edu	37	19	42703833	42703833	+	Silent	SNP	A	A	G	rs2303652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:42703833A>G	ENST00000595337.1	-	5	825	c.738T>C	c.(736-738)tcT>tcC	p.S246S	DEDD2_ENST00000593804.1_5'UTR|DEDD2_ENST00000336034.4_Silent_p.S241S|DEDD2_ENST00000596251.1_Silent_p.S246S	NM_001270614.1	NP_001257543.1	Q8WXF8	DEDD2_HUMAN	death effector domain containing 2	246					apoptotic nuclear changes (GO:0030262)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|RNA processing (GO:0006396)|rRNA catabolic process (GO:0016075)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(2)	5		Prostate(69;0.0704)				CACAAACCACAGAGCCCAGGT	0.677													G|||	647	0.129193	0.1581	0.1138	5008	,	,		16242	0.0873		0.0934	False		,,,				2504	0.181				p.S246S		Atlas-SNP	.											.	DEDD2	16	.	0			c.T738C						PASS	.	G		720,3686	749.0+/-412.0	60,600,1543	45.0	41.0	42.0		738	-7.1	0.8	19	dbSNP_100	42	888,7712	772.5+/-407.7	49,790,3461	no	coding-synonymous	DEDD2	NM_133328.2		109,1390,5004	GG,GA,AA		10.3256,16.3414,12.3635		246/327	42703833	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	162989	exon5			AACCACAGAGCCC	AY125488	CCDS12597.1, CCDS59391.1	19q13.31	2008-02-05				ENSG00000160570			24450	protein-coding gene	gene with protein product						11965497, 12235123	Standard	NM_133328		Approved	FLAME-3	uc031rkv.1	Q8WXF8		ENST00000595337.1:c.738T>C	19.37:g.42703833A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_133328	Q8NBR2|Q8NES1|Q8TAA8|Q96D35	Silent	SNP	ENST00000595337.1	37	CCDS12597.1																																																																																			A|0.871;G|0.129	0.129	strong		0.677	DEDD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463508.1	NM_133328	
DAK	26007	hgsc.bcm.edu	37	11	61111346	61111346	+	Missense_Mutation	SNP	C	C	G	rs35723406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:61111346C>G	ENST00000394900.3	+	12	1230	c.1001C>G	c.(1000-1002)gCa>gGa	p.A334G		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	334	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.		A -> G (in dbSNP:rs35723406).		carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						ACCACTGCAGCAGCCTGGCCT	0.617													C|||	194	0.038738	0.0038	0.0648	5008	,	,		19467	0.001		0.1213	False		,,,				2504	0.0215				p.A334G		Atlas-SNP	.											.	DAK	52	.	0			c.C1001G						PASS	.	C	GLY/ALA	109,4297	83.4+/-121.9	1,107,2095	84.0	92.0	89.0		1001	-0.7	0.0	11	dbSNP_126	89	1029,7569	218.7+/-257.0	61,907,3331	yes	missense	DAK	NM_015533.3	60	62,1014,5426	GG,GC,CC		11.9679,2.4739,8.7512	benign	334/576	61111346	1138,11866	2203	4299	6502	SO:0001583	missense	26007	exon12			CTGCAGCAGCCTG		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"""dihydroxyacetone kinase 2 homolog (yeast)"""				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1001C>G	11.37:g.61111346C>G	ENSP00000378360:p.Ala334Gly	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	37	CCDS8003.1	106	0.048534798534798536	2	0.0040650406504065045	24	0.06629834254143646	1	0.0017482517482517483	79	0.10422163588390501	C	12.44	1.938144	0.34189	0.024739	0.119679	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.30448	1.53;1.53	5.84	-0.714	0.11219	Dak kinase (2);	0.692145	0.14877	N	0.293164	T	0.00328	0.0010	L	0.43152	1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.002;0.005	T	0.07309	-1.0779	9	0.66056	D	0.02	3.3223	8.2482	0.31702	0.099:0.5216:0.0:0.3794	rs35723406	334;334	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	G	334;333	ENSP00000378360:A334G;ENSP00000432539:A333G	ENSP00000378360:A334G	A	+	2	0	DAK	60867922	0.000000	0.05858	0.044000	0.18714	0.914000	0.54420	0.683000	0.25349	-0.346000	0.08312	-0.797000	0.03246	GCA	C|0.923;G|0.077	0.077	strong		0.617	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533	
CLEC12A	160364	hgsc.bcm.edu	37	12	10131939	10131939	+	Silent	SNP	C	C	T	rs536947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10131939C>T	ENST00000304361.4	+	3	377	c.195C>T	c.(193-195)caC>caT	p.H65H	CLEC12A_ENST00000355690.4_Silent_p.H75H|CLEC12A_ENST00000350667.4_Silent_p.H32H|CLEC12A_ENST00000434319.2_Silent_p.H65H	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A	65						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						GTGGAGTTCACGTAACTTTGA	0.308													C|||	968	0.193291	0.0998	0.1167	5008	,	,		18574	0.2222		0.1829	False		,,,				2504	0.3548				p.H75H	Melanoma(197;1487 2125 16611 22221 34855)	Atlas-SNP	.											.	CLEC12A	65	.	0			c.C225T						PASS	.	C	,,	402,4000		21,360,1820	26.0	24.0	25.0		225,195,96	-5.6	0.0	12	dbSNP_83	25	1411,7187		119,1173,3007	no	coding-synonymous,coding-synonymous,coding-synonymous	CLEC12A	NM_001207010.1,NM_138337.5,NM_201623.3	,,	140,1533,4827	TT,TC,CC		16.4108,9.1322,13.9462	,,	75/276,65/266,32/233	10131939	1813,11187	2201	4299	6500	SO:0001819	synonymous_variant	160364	exon4			AGTTCACGTAACT	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.195C>T	12.37:g.10131939C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_001207010	B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Silent	SNP	ENST00000304361.4	37	CCDS8608.1																																																																																			C|0.806;A|0.000	.	strong		0.308	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337	
PRKRA	8575	hgsc.bcm.edu	37	2	179300979	179300979	+	Missense_Mutation	SNP	A	A	T	rs77419724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179300979A>T	ENST00000325748.4	-	7	877	c.677T>A	c.(676-678)aTc>aAc	p.I226N	AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000432031.2_Missense_Mutation_p.I215N|PRKRA_ENST00000438687.3_Missense_Mutation_p.I113N|AC009948.5_ENST00000436616.2_RNA|PRKRA_ENST00000487082.1_Missense_Mutation_p.I201N	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	226	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.I226N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CAGTAAGTTGATCTTTTCACC	0.353																																					p.I226N	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,NS,carcinoma,0,1	PRKRA	56	1	1	Substitution - Missense(1)	pancreas(1)	c.T677A						PASS	.	A	ASN/ILE,ASN/ILE,ASN/ILE	226,4180		0,226,1977	157.0	179.0	172.0		644,602,677	5.9	1.0	2	dbSNP_132	172	835,7765		0,835,3465	yes	missense,missense,missense	PRKRA	NM_001139517.1,NM_001139518.1,NM_003690.4	149,149,149	0,1061,5442	TT,TA,AA		9.7093,5.1294,8.1578	probably-damaging,probably-damaging,probably-damaging	215/303,201/289,226/314	179300979	1061,11945	2203	4300	6503	SO:0001583	missense	8575	exon7			AAGTTGATCTTTT	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.677T>A	2.37:g.179300979A>T	ENSP00000318176:p.Ile226Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	29	0.325843	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	256	0.11721611721611722	26	0.052845528455284556	59	0.16298342541436464	51	0.08916083916083917	120	0.158311345646438	A	25.3	4.621990	0.87460	0.051294	0.097093	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	T;T;T;T	0.79247	-1.18;-1.25;-1.11;-1.17	5.92	5.92	0.95590	.	0.196115	0.42053	N	0.000775	T	0.01421	0.0046	L	0.50333	1.59	0.42971	D	0.994437	D;B	0.67145	0.996;0.138	D;B	0.64595	0.927;0.037	T	0.23797	-1.0178	10	0.72032	D	0.01	.	13.9014	0.63806	1.0:0.0:0.0:0.0	.	226;215	O75569;O75569-2	PRKRA_HUMAN;.	N	226;113;201;215	ENSP00000318176:I226N;ENSP00000398980:I113N;ENSP00000430604:I201N;ENSP00000393883:I215N	ENSP00000318176:I226N	I	-	2	0	PRKRA	179009225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.644000	0.83416	2.277000	0.76020	0.528000	0.53228	ATC	A|0.879;T|0.121	0.121	strong		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
FAM198A	729085	hgsc.bcm.edu	37	3	43097710	43097710	+	Silent	SNP	A	A	G	rs664628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:43097710A>G	ENST00000430121.2	+	5	1655	c.1560A>G	c.(1558-1560)ctA>ctG	p.L520L		NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	520						extracellular region (GO:0005576)				endometrium(1)	1						CAGGGTGTCTACAGAACATGC	0.567													A|||	1950	0.389377	0.2685	0.5058	5008	,	,		19848	0.5823		0.3887	False		,,,				2504	0.272				p.L520L		Atlas-SNP	.											.	FAM198A	23	.	0			c.A1560G						PASS	.	A		400,984		56,288,348	43.0	42.0	42.0		1560	-3.7	0.0	3	dbSNP_83	42	1211,1971		234,743,614	no	coding-synonymous	FAM198A	NM_001129908.2		290,1031,962	GG,GA,AA		38.0578,28.9017,35.2825		520/576	43097710	1611,2955	692	1591	2283	SO:0001819	synonymous_variant	729085	exon5			GTGTCTACAGAAC	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.1560A>G	3.37:g.43097710A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			A|0.589;G|0.411	0.411	strong		0.567	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
OVGP1	5016	hgsc.bcm.edu	37	1	111966291	111966291	+	Silent	SNP	C	C	T	rs954739	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111966291C>T	ENST00000369732.3	-	5	412	c.357G>A	c.(355-357)aaG>aaA	p.K119K	OVGP1_ENST00000540696.1_Silent_p.K59K|OVGP1_ENST00000481495.1_5'Flank	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	125	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	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	
SOCS4	122809	hgsc.bcm.edu	37	14	55510110	55510110	+	Silent	SNP	G	G	A	rs17128136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:55510110G>A	ENST00000395472.2	+	2	683	c.351G>A	c.(349-351)ccG>ccA	p.P117P	SOCS4_ENST00000555846.1_Silent_p.P117P|SOCS4_ENST00000339298.2_Silent_p.P117P	NM_080867.2|NM_199421.1	NP_543143.1|NP_955453.1	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	117					intracellular signal transduction (GO:0035556)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)					central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	14						CAGGGCTTCCGTCTAAAAGGA	0.408													g|||	164	0.0327476	0.0045	0.0375	5008	,	,		21115	0.0		0.0954	False		,,,				2504	0.0368				p.P117P		Atlas-SNP	.											.	SOCS4	34	.	0			c.G351A						PASS	.	A	,	60,4346	54.2+/-90.2	0,60,2143	70.0	73.0	72.0		351,351	-6.7	0.8	14	dbSNP_123	72	677,7921	167.8+/-219.5	19,639,3641	no	coding-synonymous,coding-synonymous	SOCS4	NM_080867.2,NM_199421.1	,	19,699,5784	AA,AG,GG		7.8739,1.3618,5.6675	,	117/441,117/441	55510110	737,12267	2203	4299	6502	SO:0001819	synonymous_variant	122809	exon2			GCTTCCGTCTAAA	AF424815	CCDS9722.1	14q22.1	2013-02-14	2004-02-25	2004-02-27	ENSG00000180008	ENSG00000180008		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19392	protein-coding gene	gene with protein product			"""suppressor of cytokine signaling 7"""	SOCS7		12076535, 10500304	Standard	NM_080867		Approved		uc001xbp.3	Q8WXH5	OTTHUMG00000140311	ENST00000395472.2:c.351G>A	14.37:g.55510110G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	38	0.644068	NM_080867		Silent	SNP	ENST00000395472.2	37	CCDS9722.1																																																																																			G|0.944;A|0.056	0.056	strong		0.408	SOCS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276910.1		
PDGFRB	5159	hgsc.bcm.edu	37	5	149497228	149497228	+	Silent	SNP	G	G	A	rs2228440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:149497228G>A	ENST00000261799.4	-	22	3559	c.3090C>T	c.(3088-3090)ccC>ccT	p.P1030P		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	1030					adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|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 chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|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)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCAACCTCGGGTTTGGGGT	0.612			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								G|||	310	0.061901	0.0794	0.0735	5008	,	,		16115	0.0		0.1103	False		,,,				2504	0.044				p.P1030P		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.C3090T						PASS	.	G		367,4039	186.7+/-213.5	12,343,1848	73.0	72.0	73.0		3090	-6.3	0.5	5	dbSNP_98	73	934,7666	206.2+/-248.4	49,836,3415	no	coding-synonymous	PDGFRB	NM_002609.3		61,1179,5263	AA,AG,GG		10.8605,8.3296,10.0031		1030/1107	149497228	1301,11705	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon22			AACCTCGGGTTTG	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.3090C>T	5.37:g.149497228G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			G|0.910;A|0.091	0.091	strong		0.612	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
KMT2B	9757	hgsc.bcm.edu	37	19	36223699	36223699	+	Silent	SNP	G	G	T	rs375564425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36223699G>T	ENST00000222270.7	+	28	6249	c.6249G>T	c.(6247-6249)acG>acT	p.T2083T	KMT2B_ENST00000420124.1_Silent_p.T2083T|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2083					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCCAGGGCACGCCTCCTTCGG	0.687													T|||	2	0.000399361	0.0008	0.0	5008	,	,		12848	0.0		0.001	False		,,,				2504	0.0				p.T2083T		Atlas-SNP	.											.	MLL4	229	.	0			c.G6249T						PASS	.	T		1,3869		0,1,1934	11.0	13.0	12.0		6249	0.5	1.0	19		12	18,8212		0,18,4097	no	coding-synonymous	MLL4	NM_014727.1		0,19,6031	TT,TG,GG		0.2187,0.0258,0.157		2083/2716	36223699	19,12081	1935	4115	6050	SO:0001819	synonymous_variant	8085	exon28			GGGCACGCCTCCT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6249G>T	19.37:g.36223699G>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			.	.	weak		0.687	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
SLC6A19	340024	hgsc.bcm.edu	37	5	1213668	1213668	+	Missense_Mutation	SNP	G	G	A	rs7732589	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:1213668G>A	ENST00000304460.10	+	5	810	c.754G>A	c.(754-756)Gtc>Atc	p.V252I		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	252			V -> I (in dbSNP:rs7732589). {ECO:0000269|PubMed:15286788}.		amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CAATGGCATCGTCTTCCTCTT	0.662													g|||	974	0.194489	0.3238	0.1383	5008	,	,		12069	0.1825		0.1292	False		,,,				2504	0.1391				p.V252I		Atlas-SNP	.											.	SLC6A19	99	.	0			c.G754A						PASS	.		ILE/VAL	1314,3092	440.6+/-346.1	190,934,1079	109.0	71.0	84.0		754	3.0	0.3	5	dbSNP_116	84	1241,7357	247.9+/-275.8	111,1019,3169	yes	missense	SLC6A19	NM_001003841.2	29	301,1953,4248	AA,AG,GG		14.4336,29.823,19.6478	benign	252/635	1213668	2555,10449	2203	4299	6502	SO:0001583	missense	340024	exon5			GGCATCGTCTTCC	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"""Solute carriers"""	27960	protein-coding gene	gene with protein product	"""Hartnup disease"""	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.754G>A	5.37:g.1213668G>A	ENSP00000305302:p.Val252Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	37	CCDS34130.1	415	0.190018315018315	154	0.3130081300813008	54	0.14917127071823205	101	0.17657342657342656	106	0.13984168865435356	g	8.416	0.845390	0.16963	0.29823	0.144336	ENSG00000174358	ENST00000304460	T	0.74209	-0.82	4.87	3.03	0.35002	.	0.340398	0.32093	N	0.006587	T	0.00012	0.0000	N	0.04043	-0.29	0.43971	P	0.0033450000000000424	B	0.06786	0.001	B	0.06405	0.002	T	0.13818	-1.0495	9	0.17369	T	0.5	.	8.3185	0.32115	0.0807:0.0:0.7661:0.1532	rs7732589;rs60779552;rs7732589	252	Q695T7	S6A19_HUMAN	I	252	ENSP00000305302:V252I	ENSP00000305302:V252I	V	+	1	0	SLC6A19	1266668	0.996000	0.38824	0.300000	0.25030	0.795000	0.44927	2.685000	0.46959	0.453000	0.26858	0.466000	0.42574	GTC	G|0.808;A|0.192	0.192	strong		0.662	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120	
CBFA2T3	863	hgsc.bcm.edu	37	16	88951466	88951466	+	Missense_Mutation	SNP	G	G	A	rs143614023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88951466G>A	ENST00000268679.4	-	7	1501	c.1105C>T	c.(1105-1107)Cat>Tat	p.H369Y	CBFA2T3_ENST00000436887.2_Missense_Mutation_p.H331Y|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.H293Y|RP11-830F9.5_ENST00000569249.1_RNA|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000565053.1_RNA|RP11-830F9.5_ENST00000562574.1_RNA|CBFA2T3_ENST00000327483.5_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000562405.1_RNA	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	369	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AGCGGCCGATGGCGCTCTCGT	0.682			T	RUNX1	AML																																p.H369Y		Atlas-SNP	.		Dom	yes		16	16q24	863	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"""		L	.	CBFA2T3	47	.	0			c.C1105T						PASS	.	G	TYR/HIS,TYR/HIS	0,4376		0,0,2188	50.0	47.0	48.0		1105,847	4.3	1.0	16	dbSNP_134	48	5,8579	4.3+/-15.6	0,5,4287	yes	missense,missense	CBFA2T3	NM_005187.5,NM_175931.2	83,83	0,5,6475	AA,AG,GG		0.0582,0.0,0.0386	benign,benign	369/654,283/568	88951466	5,12955	2188	4292	6480	SO:0001583	missense	863	exon7			GCCGATGGCGCTC	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"""Zinc fingers, MYND-type"", ""A-kinase anchor proteins"""	1537	protein-coding gene	gene with protein product	"""myeloid translocation gene 8 and 16b"""	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.1105C>T	16.37:g.88951466G>A	ENSP00000268679:p.His369Tyr	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627420	0.46944	0.0	5.82E-4	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.48201	1.41;0.82;0.85;1.41;1.41	4.32	4.32	0.51571	.	0.293527	0.31335	N	0.007833	T	0.52354	0.1729	M	0.61703	1.905	0.58432	D	0.999993	P;P;B;B	0.49185	0.92;0.586;0.186;0.134	P;B;B;B	0.46419	0.516;0.125;0.141;0.183	T	0.55903	-0.8067	10	0.39692	T	0.17	-1.3703	16.93	0.86188	0.0:0.0:1.0:0.0	.	331;369;369;283	E7EU24;B2RBQ7;O75081;O75081-2	.;.;MTG16_HUMAN;.	Y	283;369;331;293;283	ENSP00000332122:H283Y;ENSP00000268679:H369Y;ENSP00000395739:H331Y;ENSP00000401254:H293Y;ENSP00000353449:H283Y	ENSP00000268679:H369Y	H	-	1	0	CBFA2T3	87478967	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	7.062000	0.76706	2.386000	0.81285	0.561000	0.74099	CAT	G|1.000;A|0.000	0.000	strong		0.682	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187	
MRPL39	54148	hgsc.bcm.edu	37	21	26965148	26965148	+	Silent	SNP	G	G	A	rs1135638	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:26965148G>A	ENST00000352957.4	-	8	938	c.897C>T	c.(895-897)ggC>ggT	p.G299G	MRPL39_ENST00000307301.7_Silent_p.G299G	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	299						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						GTAAAGACACGCCCTGGAATC	0.393													A|||	3668	0.732428	0.7284	0.8199	5008	,	,		16394	0.7153		0.8121	False		,,,				2504	0.6115				p.G299G		Atlas-SNP	.											.	MRPL39	61	.	0			c.C897T						PASS	.	A	,	3307,1099	395.6+/-329.7	1229,849,125	79.0	73.0	75.0		897,897	3.0	1.0	21	dbSNP_86	75	7111,1489	283.7+/-296.3	2954,1203,143	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4183,2052,268	AA,AG,GG		17.314,24.9433,19.8985	,	299/339,299/354	26965148	10418,2588	2203	4300	6503	SO:0001819	synonymous_variant	54148	exon8			AGACACGCCCTGG	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.897C>T	21.37:g.26965148G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			G|0.221;A|0.779	0.779	strong		0.393	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
PRPF8	10594	hgsc.bcm.edu	37	17	1565211	1565211	+	Silent	SNP	T	T	C	rs118000367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1565211T>C	ENST00000572621.1	-	24	4276	c.4011A>G	c.(4009-4011)caA>caG	p.Q1337Q	PRPF8_ENST00000304992.6_Silent_p.Q1337Q			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1337	Linker.				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)		TGAGGTCGGATTGGGGGATGA	0.498													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		20374	0.0		0.0249	False		,,,				2504	0.002				p.Q1337Q		Atlas-SNP	.											.	PRPF8	169	.	0			c.A4011G						PASS	.	T		29,4377	35.2+/-66.4	0,29,2174	91.0	79.0	83.0		4011	3.5	1.0	17	dbSNP_132	83	227,8373	93.8+/-155.7	3,221,4076	no	coding-synonymous	PRPF8	NM_006445.3		3,250,6250	CC,CT,TT		2.6395,0.6582,1.9683		1337/2336	1565211	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon25			GTCGGATTGGGGG	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.4011A>G	17.37:g.1565211T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			T|0.983;C|0.017	0.017	strong		0.498	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
ELP5	23587	hgsc.bcm.edu	37	17	7155861	7155861	+	Missense_Mutation	SNP	G	G	A	rs2521988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7155861G>A	ENST00000396628.2	+	1	257	c.40G>A	c.(40-42)Gag>Aag	p.E14K	CTDNEP1_ENST00000574322.1_5'Flank|CTDNEP1_ENST00000318988.6_5'Flank|ELP5_ENST00000574993.1_Missense_Mutation_p.E14K|ELP5_ENST00000574255.1_Missense_Mutation_p.E14K|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000354429.2_Missense_Mutation_p.E14K|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000396627.2_Missense_Mutation_p.E14K|ELP5_ENST00000356683.2_Missense_Mutation_p.E14K|ELP5_ENST00000573657.1_Missense_Mutation_p.E14K|CTDNEP1_ENST00000572043.1_5'Flank	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	14			E -> K (in dbSNP:rs2521988). {ECO:0000269|Ref.2}.		chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GACCGGACGCGAGTTGGAGAT	0.692													G|||	403	0.0804712	0.0068	0.049	5008	,	,		15804	0.0367		0.1421	False		,,,				2504	0.184				p.E14K		Atlas-SNP	.											.	.	.	.	0			c.G40A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	121,4285	90.2+/-128.9	3,115,2085	58.0	51.0	53.0		40,40,40,40	-6.9	0.0	17	dbSNP_100	53	1183,7417	238.2+/-269.8	77,1029,3194	yes	missense,missense,missense,missense	C17orf81	NM_015362.3,NM_203413.1,NM_203414.1,NM_203415.1	56,56,56,56	80,1144,5279	AA,AG,GG		13.7558,2.7463,10.0261	benign,benign,benign,benign	14/317,14/280,14/317,14/317	7155861	1304,11702	2203	4300	6503	SO:0001583	missense	23587	exon1			GGACGCGAGTTGG	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.40G>A	17.37:g.7155861G>A	ENSP00000379869:p.Glu14Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_203414	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	37	CCDS11094.1	161	0.07371794871794872	3	0.006097560975609756	17	0.04696132596685083	25	0.043706293706293704	116	0.15303430079155672	G	0.121	-1.125829	0.01770	0.027463	0.137558	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.49;1.49;1.49;0.83	3.48	-6.95	0.01628	.	4.253690	0.00357	N	0.000026	T	0.00144	0.0004	N	0.19112	0.55	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	0.04178	-1.0971	9	0.30854	T	0.27	40.3597	1.568	0.02608	0.3587:0.327:0.1448:0.1695	rs2521988	14;14;14;14	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	K	14	ENSP00000346412:E14K;ENSP00000379869:E14K;ENSP00000379868:E14K;ENSP00000349111:E14K	ENSP00000346412:E14K	E	+	1	0	C17orf81	7096585	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.798000	0.00363	-5.095000	0.00022	-1.040000	0.02373	GAG	G|0.906;A|0.094	0.094	strong		0.692	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560845	160560845	+	Missense_Mutation	SNP	A	A	G	rs628031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160560845A>G	ENST00000366963.4	+	7	1369	c.1222A>G	c.(1222-1224)Atg>Gtg	p.M408V	SLC22A1_ENST00000324965.4_Missense_Mutation_p.M408V|SLC22A1_ENST00000457470.2_Missense_Mutation_p.M408V	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	408			M -> V (no changes in the MPP uptake. No changes in the MPP uptake; when associated with F-14. No changes in the MPP uptake; when associated with F-85. No changes in the MPP uptake; when associated with L-189. No changes in the MPP uptake; when associated with His-342. No changes in the MPP uptake; when associated with M-420 del. No changes in the MPP uptake; when associated with I- 440. No changes in the MPP uptake; when associated with I-461. No changes in the MPP uptake; when associated with M-488. Reduction of the MPP uptake; when associated with C-61. No MPP uptake; when associated with V-220. Reduction of the MPP uptake; when associated with L-341. No MPP uptake; when associated with S- 401. No MPP uptake; when associated with R-465; dbSNP:rs628031). {ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15499200}.		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)	CCCCATGGCCATGTCAAATTT	0.527													G|||	3444	0.6877	0.7307	0.7839	5008	,	,		14343	0.7411		0.5865	False		,,,				2504	0.6104				p.M408V		Atlas-SNP	.											.	SLC22A1	69	.	0			c.A1222G						PASS	.	G	VAL/MET,VAL/MET	3200,1206	418.9+/-338.5	1173,854,176	67.0	67.0	67.0		1222,1222	-9.1	0.0	6	dbSNP_83	67	5093,3507	511.4+/-377.7	1516,2061,723	yes	missense,missense	SLC22A1	NM_003057.2,NM_153187.1	21,21	2689,2915,899	GG,GA,AA		40.7791,27.3718,36.2371	benign,benign	408/555,408/507	160560845	8293,4713	2203	4300	6503	SO:0001583	missense	6580	exon7			ATGGCCATGTCAA	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.1222A>G	6.37:g.160560845A>G	ENSP00000355930:p.Met408Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	15	0.267857	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	1524	0.6978021978021978	368	0.7479674796747967	279	0.7707182320441989	435	0.7604895104895105	442	0.58311345646438	G	0.022	-1.406937	0.01155	0.726282	0.592209	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.73047	-0.71;0.48;0.48	5.08	-9.1	0.00714	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.244500	0.05468	N	0.552535	T	0.06917	0.0176	N	0.00569	-1.365	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.04165	-1.0972	9	0.07175	T	0.84	.	1.367	0.02203	0.3768:0.2354:0.2283:0.1594	rs628031;rs1086277;rs17202481;rs60990824;rs628031	408;408	O15245-2;O15245	.;S22A1_HUMAN	V	408	ENSP00000355930:M408V;ENSP00000318103:M408V;ENSP00000409557:M408V	ENSP00000318103:M408V	M	+	1	0	SLC22A1	160480835	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.590000	0.00899	-2.233000	0.00716	-0.994000	0.02522	ATG	A|0.330;G|0.669	0.669	strong		0.527	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
CHRNA7	1139	hgsc.bcm.edu	37	15	32322929	32322929	+	Intron	SNP	G	G	A	rs2292571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:32322929G>A	ENST00000306901.3	+	1	152				CHRNA7_ENST00000454250.3_Silent_p.A44A|CHRNA7_ENST00000455693.2_Intron	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)						activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-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)	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)	TGCGCCCCGCGCCTGGGCCAG	0.776													G|||	457	0.091254	0.0106	0.0793	5008	,	,		6499	0.1607		0.0954	False		,,,				2504	0.1329				p.A44A	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											.	CHRNA7	57	.	0			c.G132A						PASS	.																																			SO:0001627	intron_variant	1139	exon1			CCCCGCGCCTGGG	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.55+77G>A	15.37:g.32322929G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	37	CCDS10027.1																																																																																			G|0.920;A|0.080	0.080	strong		0.776	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
CCDC74B	91409	hgsc.bcm.edu	37	2	130897218	130897218	+	Silent	SNP	T	T	C	rs13006246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:130897218T>C	ENST00000310463.6	-	8	1190	c.1053A>G	c.(1051-1053)gcA>gcG	p.A351A	CCDC74B_ENST00000409943.3_Silent_p.A285A|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000392984.3_Silent_p.A453A	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	351										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					TCTGCTTCAGTGCGGGCAGGA	0.632													.|||	549	0.109625	0.025	0.1873	5008	,	,		16457	0.0288		0.2863	False		,,,				2504	0.0706				p.A351A		Atlas-SNP	.											.	CCDC74B	27	.	0			c.A1053G						PASS	.	T		293,4109		9,275,1917	40.0	36.0	37.0		1053	-9.4	0.0	2	dbSNP_121	37	2250,6348		287,1676,2336	no	coding-synonymous	CCDC74B	NM_207310.1		296,1951,4253	CC,CT,TT		26.1689,6.6561,19.5615		351/381	130897218	2543,10457	2201	4299	6500	SO:0001819	synonymous_variant	91409	exon8			CTTCAGTGCGGGC		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.1053A>G	2.37:g.130897218T>C		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	204	93	0.455882	NM_207310	Q6NW18	Silent	SNP	ENST00000310463.6	37	CCDS2155.1	305	0.13965201465201466	16	0.032520325203252036	80	0.22099447513812154	21	0.03671328671328671	188	0.24802110817941952	.	0.207	-1.039639	0.02013	0.066561	0.261689	ENSG00000152076	ENST00000409488	.	.	.	4.68	-9.37	0.00626	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999467645	.	.	.	.	.	.	T	0.16837	-1.0389	4	0.87932	D	0	.	2.0144	0.03495	0.1495:0.3335:0.2059:0.3111	rs13006246	.	.	.	R	245	.	ENSP00000386250:H245R	H	-	2	0	CCDC74B	130613688	0.408000	0.25360	0.005000	0.12908	0.007000	0.05969	-1.147000	0.03188	-3.106000	0.00243	-2.385000	0.00230	CAC	T|0.826;C|0.174	0.174	strong		0.632	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
ATAD3C	219293	hgsc.bcm.edu	37	1	1390875	1390875	+	Silent	SNP	C	C	T	rs1781147	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1390875C>T	ENST00000378785.2	+	5	1409	c.414C>T	c.(412-414)gaC>gaT	p.D138D		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	138							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)		GACCCCAGGACGTGCTGGAGG	0.677													c|||	2129	0.42512	0.528	0.4323	5008	,	,		12946	0.499		0.1879	False		,,,				2504	0.4489				p.D138D		Atlas-SNP	.											ATAD3C,NS,carcinoma,+2,1	ATAD3C	23	1	0			c.C414T						PASS	.	C		656,728		164,328,200	61.0	62.0	62.0		414	-1.4	0.2	1	dbSNP_89	62	617,2565		72,473,1046	no	coding-synonymous	ATAD3C	NM_001039211.2		236,801,1246	TT,TC,CC		19.3903,47.3988,27.88		138/412	1390875	1273,3293	692	1591	2283	SO:0001819	synonymous_variant	219293	exon5			CCAGGACGTGCTG	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.414C>T	1.37:g.1390875C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	105	40	0.380952	NM_001039211	Q8N1Z5	Silent	SNP	ENST00000378785.2	37	CCDS44039.1																																																																																			C|0.608;T|0.392	0.392	strong		0.677	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
DNAH10	196385	hgsc.bcm.edu	37	12	124267703	124267703	+	Silent	SNP	T	T	C	rs11057355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124267703T>C	ENST00000409039.3	+	7	733	c.708T>C	c.(706-708)tcT>tcC	p.S236S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	236	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAGAGGTGTCTGACCTGGCAG	0.458													C|||	4013	0.801318	0.8321	0.7262	5008	,	,		18806	0.996		0.6451	False		,,,				2504	0.773				p.S236S		Atlas-SNP	.											.	DNAH10	888	.	0			c.T708C						PASS	.	C		3472,934	355.4+/-313.0	1352,768,83	109.0	105.0	106.0		708	-12.0	0.0	12	dbSNP_120	106	5200,3400	502.5+/-375.7	1594,2012,694	no	coding-synonymous	DNAH10	NM_207437.3		2946,2780,777	CC,CT,TT		39.5349,21.1984,33.3231		236/4472	124267703	8672,4334	2203	4300	6503	SO:0001819	synonymous_variant	196385	exon7			GGTGTCTGACCTG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.708T>C	12.37:g.124267703T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			T|0.292;C|0.708	0.708	strong		0.458	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
OR56B4	196335	hgsc.bcm.edu	37	11	6129837	6129837	+	Missense_Mutation	SNP	C	C	T	rs1462983	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6129837C>T	ENST00000316529.3	+	1	924	c.829C>T	c.(829-831)Cct>Tct	p.P277S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	277			P -> S (in dbSNP:rs1462983).			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(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCCCTTATTCCTGTGTTCCT	0.507													.|||	2524	0.503994	0.1029	0.6023	5008	,	,		20307	0.8839		0.4463	False		,,,				2504	0.6442				p.P277S		Atlas-SNP	.											.	OR56B4	50	.	0			c.C829T						PASS	.	C	SER/PRO	756,3646	308.0+/-290.3	70,616,1515	111.0	113.0	112.0		829	4.0	0.2	11	dbSNP_88	112	3891,4701	546.1+/-384.9	911,2069,1316	yes	missense	OR56B4	NM_001005181.1	74	981,2685,2831	TT,TC,CC		45.2863,17.174,35.7627	probably-damaging	277/320	6129837	4647,8347	2201	4296	6497	SO:0001583	missense	196335	exon1			CTTATTCCTGTGT	AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"""GPCR / Class A : Olfactory receptors"""	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.829C>T	11.37:g.6129837C>T	ENSP00000321196:p.Pro277Ser	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_001005181	Q6IFD7	Missense_Mutation	SNP	ENST00000316529.3	37	CCDS31406.1	1080	0.4945054945054945	59	0.11991869918699187	193	0.5331491712707183	493	0.8618881118881119	335	0.4419525065963061	C	9.190	1.025691	0.19512	0.17174	0.452863	ENSG00000180919	ENST00000316529	T	0.00048	8.82	4.01	4.01	0.46588	.	0.000000	0.36703	U	0.002457	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	D	0.76494	0.999	D	0.76071	0.987	T	0.04708	-1.0932	9	0.72032	D	0.01	.	13.6372	0.62229	0.0:0.8434:0.1566:0.0	rs1462983;rs52812111;rs58438951;rs1462983	277	Q8NH76	O56B4_HUMAN	S	277	ENSP00000321196:P277S	ENSP00000321196:P277S	P	+	1	0	OR56B4	6086413	0.000000	0.05858	0.201000	0.23476	0.133000	0.20885	1.001000	0.29783	2.220000	0.72140	0.549000	0.68633	CCT	C|0.575;T|0.425	0.425	strong		0.507	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181	
ANKRD65	441869	hgsc.bcm.edu	37	1	1354515	1354515	+	Missense_Mutation	SNP	C	C	G	rs534554090|rs904589	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1354515C>G	ENST00000537107.1	-	4	1302	c.1165G>C	c.(1165-1167)Gag>Cag	p.E389Q	RP4-758J18.7_ENST00000428932.1_RNA|ANKRD65_ENST00000454272.1_5'UTR|ANKRD65_ENST00000520296.1_3'UTR|ANKRD65_ENST00000427211.1_3'UTR	NM_001145210.2	NP_001138682.1	E5RJM6	ANR65_HUMAN	ankyrin repeat domain 65	389										breast(1)	1						CACTCCTTCTCCCCCCCTCCA	0.687													G|||	1617	0.322883	0.8222	0.1945	5008	,	,		16520	0.1131		0.0964	False		,,,				2504	0.1881				p.E389Q		Atlas-SNP	.											.	ANKRD65	4	.	0			c.G1165C						PASS	.						2.0	3.0	3.0					1																	1354515		507	1316	1823	SO:0001583	missense	441869	exon4			CCTTCTCCCCCCC		CCDS55558.1, CCDS57962.1, CCDS57963.1	1p36.33	2013-01-10			ENSG00000235098	ENSG00000235098		"""Ankyrin repeat domain containing"""	42950	protein-coding gene	gene with protein product							Standard	NM_001243535		Approved		uc010nyo.2	E5RJM6	OTTHUMG00000002911	ENST00000537107.1:c.1165G>C	1.37:g.1354515C>G	ENSP00000445688:p.Glu389Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	165	87	0.527273	NM_001145210	J3KR93	Missense_Mutation	SNP	ENST00000537107.1	37	CCDS55558.1	622	0.2847985347985348	404	0.8211382113821138	79	0.21823204419889503	67	0.11713286713286714	72	0.09498680738786279	G	0.243	-1.012516	0.02095	.	.	ENSG00000235098	ENST00000537107	T	0.68624	-0.34	1.28	0.254	0.15557	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38520	-0.9657	8	0.10902	T	0.67	.	6.8436	0.23977	0.0:0.5817:0.4183:0.0	rs904589;rs3766168	389	E5RJM6	ANR65_HUMAN	Q	389	ENSP00000445688:E389Q	ENSP00000445688:E389Q	E	-	1	0	RP4-758J18.6	1344378	0.004000	0.15560	0.001000	0.08648	0.007000	0.05969	-0.137000	0.10389	-0.272000	0.09259	-0.497000	0.04613	GAG	C|0.714;G|0.286	0.286	strong		0.687	ANKRD65-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DTX2	113878	hgsc.bcm.edu	37	7	76111994	76111994	+	Silent	SNP	C	C	G	rs1638075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76111994C>G	ENST00000324432.5	+	5	948	c.438C>G	c.(436-438)gcC>gcG	p.A146A	DTX2_ENST00000446600.1_Silent_p.A55A|DTX2_ENST00000430490.2_Silent_p.A146A|DTX2_ENST00000307569.8_Silent_p.A146A|DTX2_ENST00000446820.2_Silent_p.A146A|DTX2_ENST00000413936.2_Silent_p.A146A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	146	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.				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.A146A(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TGGACTTGGCCCCCCTGGGGT	0.622													.|||	629	0.125599	0.0537	0.1369	5008	,	,		16537	0.0516		0.2276	False		,,,				2504	0.1861				p.A146A		Atlas-SNP	.											DTX2,NS,carcinoma,0,1	DTX2	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C438G						PASS	.	C	,,,	400,4006		21,358,1824	50.0	42.0	44.0		438,438,438,438	-10.8	0.0	7	dbSNP_89	44	2054,6542		249,1556,2493	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	270,1914,4317	GG,GC,CC		23.8948,9.0785,18.874	,,,	146/623,146/623,146/576,146/623	76111994	2454,10548	2203	4298	6501	SO:0001819	synonymous_variant	113878	exon2			CTTGGCCCCCCTG		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.438C>G	7.37:g.76111994C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			.	.	weak		0.622	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
VN1R4	317703	hgsc.bcm.edu	37	19	53770746	53770746	+	Missense_Mutation	SNP	C	C	A	rs140031028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.						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	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	124	22	0.177419	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	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209738	84209738	+	Missense_Mutation	SNP	T	T	C	rs2288020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84209738T>C	ENST00000378553.5	+	11	2022	c.1898T>C	c.(1897-1899)tTg>tCg	p.L633S	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	633			L -> S (in dbSNP:rs2288020). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)	p.L633S(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AAGAGGGACTTGGAAATCCGA	0.517													T|||	1339	0.267372	0.0613	0.4049	5008	,	,		17263	0.376		0.3439	False		,,,				2504	0.2577				p.L633S		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,2	DNAAF1	81	2	1	Substitution - Missense(1)	stomach(1)	c.T1898C						PASS	.	T	SER/LEU	489,3911	223.9+/-240.3	32,425,1743	37.0	39.0	38.0		1898	-3.4	0.0	16	dbSNP_100	38	3054,5546	464.9+/-366.4	558,1938,1804	yes	missense	DNAAF1	NM_178452.4	145	590,2363,3547	CC,CT,TT		35.5116,11.1136,27.2538	benign	633/726	84209738	3543,9457	2200	4300	6500	SO:0001583	missense	123872	exon11			GGGACTTGGAAAT	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.1898T>C	16.37:g.84209738T>C	ENSP00000367815:p.Leu633Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	660	0.3021978021978022	36	0.07317073170731707	124	0.3425414364640884	238	0.4160839160839161	262	0.34564643799472294	T	2.115	-0.402769	0.04865	0.111136	0.355116	ENSG00000154099	ENST00000378553	T	0.32023	1.47	4.79	-3.4	0.04853	.	1.974810	0.02961	N	0.143145	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.32101	0.356;0.102	B;B	0.29598	0.104;0.034	T	0.35599	-0.9782	9	0.20519	T	0.43	-0.7212	6.0115	0.19578	0.1502:0.4791:0.0:0.3708	rs2288020;rs17728304;rs17845736;rs17858686;rs58400300;rs2288020	397;633	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	S	633	ENSP00000367815:L633S	ENSP00000367815:L633S	L	+	2	0	DNAAF1	82767239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.092000	0.00608	-0.980000	0.03524	-0.400000	0.06385	TTG	C|0.283;N|0.000	0.283	strong		0.517	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570852	113570852	+	Silent	SNP	C	C	T	rs3802854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:113570852C>T	ENST00000299882.5	-	2	190	c.42G>A	c.(40-42)caG>caA	p.Q14Q	TMPRSS5_ENST00000540540.1_Intron|TMPRSS5_ENST00000545579.1_5'UTR|TMPRSS5_ENST00000536856.1_Intron|TMPRSS5_ENST00000538955.1_Intron|TMPRSS5_ENST00000544634.1_Silent_p.Q14Q|TMPRSS5_ENST00000544476.1_Intron	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	14					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		CCTCTGCATACTGGGCCTCCA	0.592													c|||	1071	0.213858	0.1135	0.1873	5008	,	,		17684	0.2619		0.2485	False		,,,				2504	0.2832				p.Q14Q		Atlas-SNP	.											.	TMPRSS5	69	.	0			c.G42A						PASS	.			536,3272		34,468,1402	30.0	33.0	32.0		42	2.9	0.1	11	dbSNP_107	32	1874,6354		203,1468,2443	no	coding-synonymous	TMPRSS5	NM_030770.2		237,1936,3845	TT,TC,CC		22.7759,14.0756,20.0233		14/458	113570852	2410,9626	1904	4114	6018	SO:0001819	synonymous_variant	80975	exon2			TGCATACTGGGCC	AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682		"""Serine peptidases / Transmembrane"""	14908	protein-coding gene	gene with protein product	"""spinesin"""	606751					Standard	NM_030770		Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000299882.5:c.42G>A	11.37:g.113570852C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_030770		Silent	SNP	ENST00000299882.5	37	CCDS44735.1																																																																																			C|0.764;T|0.236	0.236	strong		0.592	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
WBSCR17	64409	hgsc.bcm.edu	37	7	70800578	70800578	+	Missense_Mutation	SNP	G	G	T	rs145721199	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:70800578G>T	ENST00000333538.5	+	2	915	c.281G>T	c.(280-282)cGg>cTg	p.R94L	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	94					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TATGGTGGGCGGGGTAAAGGG	0.453																																					p.R94L		Atlas-SNP	.											WBSCR17,mouth,carcinoma,+1,1	WBSCR17	208	1	0			c.G281T						scavenged	.						32.0	38.0	36.0					7																	70800578		2203	4300	6503	SO:0001583	missense	64409	exon2			GTGGGCGGGGTAA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.281G>T	7.37:g.70800578G>T	ENSP00000329654:p.Arg94Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	2	0.0540541	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	9.064	0.995119	0.19043	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.52983	0.64;1.93	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	N	0.02539	-0.55	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.13150	-1.0520	10	0.10902	T	0.67	.	17.1948	0.86890	0.0:0.0:1.0:0.0	.	94	Q6IS24	GLTL3_HUMAN	L	94;72	ENSP00000329654:R94L;ENSP00000392019:R72L	ENSP00000329654:R94L	R	+	2	0	WBSCR17	70438514	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.307000	0.78920	2.530000	0.85305	0.491000	0.48974	CGG	G|0.999;A|0.001	.	alt		0.453	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
PTPN3	5774	hgsc.bcm.edu	37	9	112219474	112219474	+	Missense_Mutation	SNP	C	C	G	rs3793524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	105	0	0		WXS	Illumina HiSeq	Phase_I	104	100	0.961538	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		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242102	81242102	+	RNA	SNP	G	G	A	rs6420424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	47	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	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		
DNTTIP2	30836	hgsc.bcm.edu	37	1	94342564	94342564	+	Missense_Mutation	SNP	C	C	A	rs3747965	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:94342564C>A	ENST00000436063.2	-	2	984	c.927G>T	c.(925-927)gaG>gaT	p.E309D	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	309			E -> D (in dbSNP:rs3747965). {ECO:0000269|PubMed:12786946, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTCTTTCCCCTCATCTGTTA	0.378													C|||	1727	0.344848	0.0817	0.33	5008	,	,		19818	0.5565		0.325	False		,,,				2504	0.5133				p.E309D		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.G927T						PASS	.	C	ASP/GLU	505,3149		34,437,1356	65.0	54.0	58.0		927	0.4	0.0	1	dbSNP_107	58	2741,5429		446,1849,1790	yes	missense	DNTTIP2	NM_014597.4	45	480,2286,3146	AA,AC,CC		33.5496,13.8205,27.4526	possibly-damaging	309/757	94342564	3246,8578	1827	4085	5912	SO:0001583	missense	30836	exon2			TTTCCCCTCATCT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.927G>T	1.37:g.94342564C>A	ENSP00000411010:p.Glu309Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	741	0.3392857142857143	44	0.08943089430894309	124	0.3425414364640884	325	0.5681818181818182	248	0.32717678100263853	C	7.180	0.589308	0.13812	0.138205	0.335496	ENSG00000067334	ENST00000436063	T	0.22134	1.97	4.83	0.373	0.16178	.	1.095520	0.06942	N	0.813102	T	0.07324	0.0185	L	0.56769	1.78	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.35943	-0.9768	9	0.38643	T	0.18	.	4.5422	0.12064	0.2991:0.529:0.0:0.1719	rs3747965;rs17846411;rs17859454;rs52797280;rs59636660;rs3747965	309	Q5QJE6	TDIF2_HUMAN	D	309	ENSP00000411010:E309D	ENSP00000352137:E309D	E	-	3	2	DNTTIP2	94115152	0.000000	0.05858	0.001000	0.08648	0.292000	0.27327	-1.753000	0.01818	-0.083000	0.12618	-0.345000	0.07892	GAG	C|0.661;A|0.339	0.339	strong		0.378	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
CLRN3	119467	hgsc.bcm.edu	37	10	129690826	129690826	+	Missense_Mutation	SNP	A	A	T	rs35070529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:129690826A>T	ENST00000368671.3	-	1	385	c.223T>A	c.(223-225)Ttt>Att	p.F75I		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	75			F -> I (in dbSNP:rs35070529).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TTACCTGCAAACTTTTTCTTT	0.338													A|||	183	0.0365415	0.0106	0.062	5008	,	,		18810	0.0		0.1083	False		,,,				2504	0.0174				p.F75I		Atlas-SNP	.											.	CLRN3	27	.	0			c.T223A						PASS	.	A	ILE/PHE	78,4328	68.1+/-105.8	0,78,2125	72.0	69.0	70.0		223	5.5	0.9	10	dbSNP_126	70	791,7809	185.6+/-233.3	42,707,3551	yes	missense	CLRN3	NM_152311.3	21	42,785,5676	TT,TA,AA		9.1977,1.7703,6.6815	probably-damaging	75/227	129690826	869,12137	2203	4300	6503	SO:0001583	missense	119467	exon1			CTGCAAACTTTTT	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.223T>A	10.37:g.129690826A>T	ENSP00000357660:p.Phe75Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	110	0.05036630036630037	8	0.016260162601626018	23	0.06353591160220995	0	0.0	79	0.10422163588390501	A	16.40	3.113079	0.56398	0.017703	0.091977	ENSG00000180745	ENST00000368671	T	0.77750	-1.12	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.18425	0.0442	M	0.75777	2.31	0.09310	P	0.99999088844	D	0.89917	1.0	D	0.91635	0.999	T	0.64287	-0.6443	9	0.27082	T	0.32	.	13.273	0.60172	1.0:0.0:0.0:0.0	rs35070529	75	Q8NCR9	CLRN3_HUMAN	I	75	ENSP00000357660:F75I	ENSP00000357660:F75I	F	-	1	0	CLRN3	129580816	0.998000	0.40836	0.934000	0.37439	0.116000	0.19942	4.942000	0.63547	2.323000	0.78572	0.533000	0.62120	TTT	A|0.944;T|0.056	0.056	strong		0.338	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
PCDHB12	56124	hgsc.bcm.edu	37	5	140589738	140589738	+	Missense_Mutation	SNP	C	C	T	rs2910327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	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	
COL5A3	50509	hgsc.bcm.edu	37	19	10079093	10079093	+	Missense_Mutation	SNP	C	C	T	rs3815746	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10079093C>T	ENST00000264828.3	-	59	4367	c.4282G>A	c.(4282-4284)Gtg>Atg	p.V1428M		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1428	Triple-helical region.		V -> M (in dbSNP:rs3815746).		axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GGTCCCTGCACGCCTGGCAAC	0.587													C|||	900	0.179712	0.1838	0.1383	5008	,	,		16730	0.2222		0.2048	False		,,,				2504	0.1339				p.V1428M		Atlas-SNP	.											.	COL5A3	243	.	0			c.G4282A						PASS	.	C	MET/VAL	840,3566	331.5+/-302.0	80,680,1443	109.0	124.0	119.0		4282	1.7	1.0	19	dbSNP_107	119	1917,6683	336.3+/-321.8	206,1505,2589	yes	missense	COL5A3	NM_015719.3	21	286,2185,4032	TT,TC,CC		22.2907,19.0649,21.1979	benign	1428/1746	10079093	2757,10249	2203	4300	6503	SO:0001583	missense	50509	exon59			CCTGCACGCCTGG	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.4282G>A	19.37:g.10079093C>T	ENSP00000264828:p.Val1428Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	462	0.21153846153846154	102	0.2073170731707317	57	0.1574585635359116	143	0.25	160	0.21108179419525067	C	5.488	0.275036	0.10403	0.190649	0.222907	ENSG00000080573	ENST00000264828	D	0.93604	-3.25	3.92	1.72	0.24424	.	0.205140	0.33401	N	0.004946	T	0.00073	0.0002	N	0.16368	0.405	0.44117	P	0.0031079999999999997	B	0.15930	0.015	B	0.09377	0.004	T	0.10800	-1.0614	9	0.33141	T	0.24	.	6.1598	0.20358	0.0:0.6715:0.0:0.3285	rs3815746;rs57414063;rs3815746	1428	P25940	CO5A3_HUMAN	M	1428	ENSP00000264828:V1428M	ENSP00000264828:V1428M	V	-	1	0	COL5A3	9940093	0.000000	0.05858	0.994000	0.49952	0.020000	0.10135	-0.266000	0.08631	0.861000	0.35504	-0.216000	0.12614	GTG	C|0.783;T|0.216	0.216	strong		0.587	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
AMBN	258	hgsc.bcm.edu	37	4	71472426	71472426	+	Silent	SNP	A	A	G	rs7680880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71472426A>G	ENST00000322937.6	+	13	1426	c.1323A>G	c.(1321-1323)gcA>gcG	p.A441A	AMBN_ENST00000449493.2_Silent_p.A426A	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	441					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)			TGCATGACGCATGGCATTTCC	0.488													a|||	1381	0.275759	0.6793	0.1297	5008	,	,		19196	0.1468		0.0825	False		,,,				2504	0.1656				p.A441A		Atlas-SNP	.											.	AMBN	73	.	0			c.A1323G						PASS	.	A		2426,1946		682,1062,442	45.0	51.0	49.0		1323	-9.0	0.0	4	dbSNP_116	49	612,7966		15,582,3692	no	coding-synonymous	AMBN	NM_016519.5		697,1644,4134	GG,GA,AA		7.1345,44.5105,23.4595		441/448	71472426	3038,9912	2186	4289	6475	SO:0001819	synonymous_variant	258	exon13			TGACGCATGGCAT	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.1323A>G	4.37:g.71472426A>G		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	194	112	0.57732	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																			A|0.762;G|0.238	0.238	strong		0.488	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
DSG1	1828	hgsc.bcm.edu	37	18	28913599	28913599	+	Silent	SNP	C	C	T	rs12967407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:28913599C>T	ENST00000257192.4	+	7	944	c.732C>T	c.(730-732)ggC>ggT	p.G244G		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	244	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			ACCGAGATGGCGGGGCAGATG	0.423													C|||	1641	0.327676	0.292	0.2882	5008	,	,		18910	0.0665		0.501	False		,,,				2504	0.4949				p.G244G		Atlas-SNP	.											DSG1,colon,carcinoma,+2,1	DSG1	176	1	0			c.C732T	GRCh37	CM014354	DSG1	M	rs12967407	scavenged	.	C		1396,3010	460.0+/-352.4	216,964,1023	141.0	127.0	132.0		732	-11.6	0.2	18	dbSNP_121	132	4281,4319	575.4+/-390.2	1043,2195,1062	no	coding-synonymous	DSG1	NM_001942.2		1259,3159,2085	TT,TC,CC		49.7791,31.6841,43.6491		244/1050	28913599	5677,7329	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon7			AGATGGCGGGGCA	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.732C>T	18.37:g.28913599C>T		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	140	58	0.414286	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.616;T|0.384	0.384	strong		0.423	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
FOXI1	2299	hgsc.bcm.edu	37	5	169533240	169533240	+	Silent	SNP	G	G	A	rs2277944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169533240G>A	ENST00000306268.6	+	1	340	c.279G>A	c.(277-279)agG>agA	p.R93R	FOXI1_ENST00000449804.2_Silent_p.R93R			Q12951	FOXI1_HUMAN	forkhead box I1	93	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGTGCAGAGGCCGCTGCTGC	0.697									Pendred syndrome				G|||	1813	0.362021	0.5923	0.1888	5008	,	,		11776	0.4821		0.1521	False		,,,				2504	0.2658				p.R93R		Atlas-SNP	.											.	FOXI1	70	.	0			c.G279A						PASS	.	G	,	2227,2139		571,1085,527	9.0	8.0	8.0		279,279	2.4	1.0	5	dbSNP_100	8	1309,7201		143,1023,3089	no	coding-synonymous,coding-synonymous	FOXI1	NM_012188.4,NM_144769.2	,	714,2108,3616	AA,AG,GG		15.3819,48.9922,27.4619	,	93/379,93/284	169533240	3536,9340	2183	4255	6438	SO:0001819	synonymous_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	GCAGAGGCCGCTG	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"""Forkhead boxes"""	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.279G>A	5.37:g.169533240G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	37	CCDS4372.1																																																																																			G|0.676;A|0.324	0.324	strong		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188	
PIEZO1	9780	hgsc.bcm.edu	37	16	88787673	88787673	+	Missense_Mutation	SNP	G	G	A	rs35159887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88787673G>A	ENST00000301015.9	-	39	5815	c.5569C>T	c.(5569-5571)Ccc>Tcc	p.P1857S	PIEZO1_ENST00000327397.7_5'Flank|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1857					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						TCCACTTGGGGTTCTGGGGTC	0.652													G|||	832	0.166134	0.0144	0.1787	5008	,	,		17762	0.0764		0.3072	False		,,,				2504	0.3098				p.P1857S		Atlas-SNP	.											PIEZO1,NS,carcinoma,0,1	PIEZO1	79	1	0			c.C5569T						PASS	.	G	SER/PRO	84,1300		3,78,611	58.0	57.0	57.0		5569	-0.4	0.0	16	dbSNP_126	57	1069,2109		167,735,687	yes	missense	PIEZO1	NM_001142864.2	74	170,813,1298	AA,AG,GG		33.6375,6.0694,25.274	benign	1857/2522	88787673	1153,3409	692	1589	2281	SO:0001583	missense	9780	exon39			CTTGGGGTTCTGG	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.5569C>T	16.37:g.88787673G>A	ENSP00000301015:p.Pro1857Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	359|359	0.16437728937728938|0.16437728937728938	13|13	0.026422764227642278|0.026422764227642278	81|81	0.22375690607734808|0.22375690607734808	39|39	0.06818181818181818|0.06818181818181818	226|226	0.29815303430079154|0.29815303430079154	G|G	6.191|6.191	0.403423|0.403423	0.11754|0.11754	0.060694|0.060694	0.336375|0.336375	ENSG00000103335|ENSG00000103335	ENST00000301015|ENST00000451779	T|.	0.71579|.	-0.58|.	4.48|4.48	-0.409|-0.409	0.12378|0.12378	.|.	1.563880|.	0.04107|.	N|.	0.313931|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.42965|0.42965	-0.9420|-0.9420	9|4	0.08837|.	T|.	0.75|.	-3.4232|-3.4232	7.7829|7.7829	0.29074|0.29074	0.1446:0.3574:0.498:0.0|0.1446:0.3574:0.498:0.0	rs35159887|rs35159887	1857|.	Q92508|.	PIEZ1_HUMAN|.	S|I	1857|1802	ENSP00000301015:P1857S|.	ENSP00000301015:P1857S|.	P|T	-|-	1|2	0|0	FAM38A|FAM38A	87315174|87315174	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.292000|0.292000	0.27327|0.27327	-0.123000|-0.123000	0.10611|0.10611	0.077000|0.077000	0.16863|0.16863	0.448000|0.448000	0.29417|0.29417	CCC|ACC	G|0.825;A|0.175	0.175	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
KNDC1	85442	hgsc.bcm.edu	37	10	135012162	135012162	+	Missense_Mutation	SNP	T	T	C	rs2998139	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:135012162T>C	ENST00000304613.3	+	14	2171	c.2150T>C	c.(2149-2151)cTg>cCg	p.L717P	KNDC1_ENST00000368571.2_Missense_Mutation_p.L652P|KNDC1_ENST00000368572.2_Missense_Mutation_p.L717P			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	717			L -> P (in dbSNP:rs2998139). {ECO:0000269|Ref.1}.		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)		AAGCTCTCCCTGGAGGCCCAC	0.706													C|||	2794	0.557907	0.5182	0.4914	5008	,	,		12230	0.6121		0.5308	False		,,,				2504	0.6309				p.L717P		Atlas-SNP	.											KNDC1,NS,carcinoma,0,1	KNDC1	155	1	0			c.T2150C						PASS	.		PRO/LEU	2365,1941		685,995,473	7.0	10.0	9.0		2150	2.8	0.0	10	dbSNP_101	9	4790,3688		1424,1942,873	no	missense	KNDC1	NM_152643.6	98	2109,2937,1346	CC,CT,TT		43.5008,45.0766,44.0316	benign	717/1750	135012162	7155,5629	2153	4239	6392	SO:0001583	missense	85442	exon14			TCTCCCTGGAGGC	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.2150T>C	10.37:g.135012162T>C	ENSP00000304437:p.Leu717Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	1195	0.5471611721611722	233	0.4735772357723577	184	0.5082872928176796	364	0.6363636363636364	414	0.5461741424802111	C	7.498	0.652101	0.14580	0.549234	0.564992	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.15834	2.83;2.83;2.39	2.82	2.82	0.32997	.	1.232730	0.06215	N	0.685777	T	0.00012	0.0000	N	0.00729	-1.24	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	0.38929	-0.9638	9	0.30854	T	0.27	5.8541	6.0141	0.19592	0.0:0.8532:0.0:0.1468	rs2998139;rs59625486;rs2998139	717;652;717	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	P	717;717;652	ENSP00000304437:L717P;ENSP00000357561:L717P;ENSP00000357560:L652P	ENSP00000304437:L717P	L	+	2	0	KNDC1	134862152	0.004000	0.15560	0.001000	0.08648	0.000000	0.00434	1.349000	0.33998	0.768000	0.33290	-0.674000	0.03794	CTG	T|0.452;C|0.548	0.548	strong		0.706	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
ZNF772	400720	hgsc.bcm.edu	37	19	57984918	57984918	+	Silent	SNP	A	A	G	rs2074058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57984918A>G	ENST00000343280.4	-	5	1454	c.1194T>C	c.(1192-1194)agT>agC	p.S398S	ZNF772_ENST00000601768.1_Intron|ZNF772_ENST00000425074.3_3'UTR|ZNF772_ENST00000427512.2_Silent_p.S286S|ZNF772_ENST00000356584.3_Silent_p.S357S|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000600175.1_Intron|AC004076.9_ENST00000596831.1_Intron	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	37	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	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	
CFAP46	54777	hgsc.bcm.edu	37	10	134736052	134736052	+	Missense_Mutation	SNP	G	G	T	rs4880287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	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		
SELP	6403	hgsc.bcm.edu	37	1	169565346	169565346	+	Missense_Mutation	SNP	C	C	A	rs6133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169565346C>A	ENST00000263686.6	-	12	1955	c.1918G>T	c.(1918-1920)Gtg>Ttg	p.V640L	SELP_ENST00000367794.2_Missense_Mutation_p.V578L|SELP_ENST00000367788.2_Missense_Mutation_p.V578L|SELP_ENST00000367793.2_Missense_Mutation_p.V578L|SELP_ENST00000367786.2_Missense_Mutation_p.V578L|SELP_ENST00000367791.2_Missense_Mutation_p.V454L|SELP_ENST00000367792.2_Missense_Mutation_p.V456L|SELP_ENST00000458599.2_Missense_Mutation_p.V456L	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	640	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.		L -> V (associated with susceptibility to ischemic stroke; dbSNP:rs6133). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:16710414, ECO:0000269|PubMed:9668170, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		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)	GGACATTGCACCCCTGGAGTA	0.468													C|||	1097	0.21905	0.6589	0.1268	5008	,	,		21961	0.002		0.1193	False		,,,				2504	0.0164				p.V640L		Atlas-SNP	.											.	SELP	132	.	0			c.G1918T	GRCh37	CM035894	SELP	M	rs6133	PASS	.	C	LEU/VAL	2425,1981	619.8+/-393.4	681,1063,459	190.0	192.0	191.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1918	3.2	0.0	1	dbSNP_52	191	1003,7597	214.8+/-254.3	45,913,3342	yes	missense	SELP	NM_003005.3	32	726,1976,3801	AA,AC,CC		11.6628,44.9614,26.3571	benign	640/831	169565346	3428,9578	2203	4300	6503	SO:0001583	missense	6403	exon12			ATTGCACCCCTGG	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.1918G>T	1.37:g.169565346C>A	ENSP00000263686:p.Val640Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	202	82	0.405941	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	437|437	0.2000915750915751|0.2000915750915751	300|300	0.6097560975609756|0.6097560975609756	56|56	0.15469613259668508|0.15469613259668508	2|2	0.0034965034965034965|0.0034965034965034965	79|79	0.10422163588390501|0.10422163588390501	C|C	9.698|9.698	1.153716|1.153716	0.21371|0.21371	0.550386|0.550386	0.116628|0.116628	ENSG00000174175|ENSG00000174175	ENST00000446728|ENST00000367795;ENST00000367790;ENST00000426706;ENST00000367789;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367792;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599	.|T;T;T;T;T;T;T	.|0.27256	.|2.2;2.02;1.77;1.68;1.88;2.02;1.77	4.22|4.22	3.22|3.22	0.36961|0.36961	.|.	.|0.615146	.|0.14437	.|N	.|0.319613	T|T	0.05914|0.05914	0.0154|0.0154	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.16166	.|0.005;0.016	.|B;B	.|0.19946	.|0.012;0.027	T|T	0.25676|0.25676	-1.0125|-1.0125	4|8	0.13853|0.33141	T|T	0.58|0.24	-7.6326|-7.6326	4.4232|4.4232	0.11490|0.11490	0.0:0.7617:0.0:0.2383|0.0:0.7617:0.0:0.2383	rs6133;rs52815631;rs58648729;rs6133|rs6133;rs52815631;rs58648729;rs6133	.|640;640	.|Q6NUL9;G3V1U2	.|.;.	V|L	455|454;640;639;456;640;640;578;578;456;454;578;578;563	.|ENSP00000263686:V640L;ENSP00000356767:V578L;ENSP00000356768:V578L;ENSP00000356766:V456L;ENSP00000356765:V454L;ENSP00000356762:V578L;ENSP00000356760:V578L	ENSP00000388683:G455V|ENSP00000263686:V640L	G|V	-|-	2|1	0|0	SELP|SELP	167831970|167831970	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.014000|0.014000	0.08584|0.08584	0.427000|0.427000	0.21379|0.21379	1.016000|1.016000	0.39470|0.39470	0.563000|0.563000	0.77884|0.77884	GGT|GTG	C|0.768;A|0.232	0.232	strong		0.468	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
CR2	1380	hgsc.bcm.edu	37	1	207646923	207646923	+	Intron	SNP	G	G	A	rs17616	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	190	0	0		WXS	Illumina HiSeq	Phase_I	210	94	0.447619	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	
NPEPPS	9520	hgsc.bcm.edu	37	17	45669878	45669878	+	Silent	SNP	T	T	C	rs148379754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45669878T>C	ENST00000322157.4	+	12	1630	c.1393T>C	c.(1393-1395)Tta>Cta	p.L465L	NPEPPS_ENST00000530173.1_Silent_p.L461L|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Silent_p.L385L	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	465					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GAACATGTATTTAACCAAGTT	0.338													T|||	108	0.0215655	0.0015	0.0576	5008	,	,		17526	0.0		0.0537	False		,,,				2504	0.0123				p.L465L		Atlas-SNP	.											.	NPEPPS	59	.	0			c.T1393C						PASS	.	T		50,3554		0,50,1752	23.0	20.0	21.0		1393	4.5	1.0	17	dbSNP_134	21	496,7628		12,472,3578	no	coding-synonymous	NPEPPS	NM_006310.3		12,522,5330	CC,CT,TT		6.1054,1.3873,4.6555		465/920	45669878	546,11182	1802	4062	5864	SO:0001819	synonymous_variant	9520	exon12			ATGTATTTAACCA	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1393T>C	17.37:g.45669878T>C		Somatic	356	1	0.00280899		WXS	Illumina HiSeq	Phase_I	420	203	0.483333	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	37	CCDS45721.1																																																																																			T|0.963;C|0.037	0.037	strong		0.338	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
RBM33	155435	hgsc.bcm.edu	37	7	155531080	155531080	+	Missense_Mutation	SNP	A	A	G	rs3735576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:155531080A>G	ENST00000401878.3	+	11	1918	c.1720A>G	c.(1720-1722)Aca>Gca	p.T574A		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	574	Pro-rich.		T -> A (in dbSNP:rs3735576).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		GCCCACACACACACAGCCCAA	0.517													G|||	1830	0.365415	0.7239	0.281	5008	,	,		16725	0.3135		0.1869	False		,,,				2504	0.1779				p.T574A		Atlas-SNP	.											.	RBM33	157	.	0			c.A1720G						PASS	.	G	ALA/THR	2440,1538		766,908,315	41.0	47.0	45.0		1720	2.9	0.5	7	dbSNP_107	45	1637,6699		186,1265,2717	yes	missense	RBM33	NM_053043.2	58	952,2173,3032	GG,GA,AA		19.6377,38.6626,33.1087	benign	574/1171	155531080	4077,8237	1989	4168	6157	SO:0001583	missense	155435	exon11			ACACACACACAGC	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1720A>G	7.37:g.155531080A>G	ENSP00000384160:p.Thr574Ala	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	ENST00000401878.3	37	CCDS5941.2	788	0.3608058608058608	344	0.6991869918699187	106	0.292817679558011	196	0.34265734265734266	142	0.18733509234828497	G	0.637	-0.814922	0.02776	0.613374	0.196377	ENSG00000184863	ENST00000401878	T	0.41065	1.01	5.04	2.89	0.33648	.	0.473568	0.15017	N	0.285215	T	0.00012	0.0000	N	0.20685	0.6	0.22591	P	0.99895561	B	0.02656	0.0	B	0.04013	0.001	T	0.44452	-0.9327	9	0.02654	T	1	.	7.3237	0.26542	0.5619:0.0:0.4381:0.0	rs3735576;rs10332471;rs10440916;rs60191321;rs3735576	574	Q96EV2	RBM33_HUMAN	A	574	ENSP00000384160:T574A	ENSP00000384160:T574A	T	+	1	0	RBM33	155223841	0.194000	0.23325	0.531000	0.27976	0.611000	0.37282	1.813000	0.38962	0.503000	0.28060	-0.213000	0.12676	ACA	A|0.633;G|0.367	0.367	strong		0.517	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
MUC16	94025	hgsc.bcm.edu	37	19	9065632	9065632	+	Missense_Mutation	SNP	T	T	C	rs1867691	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9065632T>C	ENST00000397910.4	-	3	22017	c.21814A>G	c.(21814-21816)Att>Gtt	p.I7272V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7274	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						GTAGCACCAATGGACACTTCA	0.488													t|||	1081	0.215855	0.0802	0.2061	5008	,	,		21790	0.249		0.3111	False		,,,				2504	0.274				p.I7272V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A21814G						PASS	.	T	VAL/ILE	473,3545		28,417,1564	141.0	134.0	136.0		21814	-2.7	0.0	19	dbSNP_92	136	2385,5961		340,1705,2128	yes	missense	MUC16	NM_024690.2	29	368,2122,3692	CC,CT,TT		28.5766,11.772,23.1155	benign	7272/14508	9065632	2858,9506	2009	4173	6182	SO:0001583	missense	94025	exon3			CACCAATGGACAC	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.21814A>G	19.37:g.9065632T>C	ENSP00000381008:p.Ile7272Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	494	0.2261904761904762	53	0.10772357723577236	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	t	2.759	-0.258393	0.05791	0.11772	0.285766	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.82	-2.74	0.05932	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	.	.	.	B	0.06786	0.001	B	0.09377	0.004	T	0.47724	-0.9095	8	0.87932	D	0	.	0.9168	0.01306	0.1569:0.2308:0.1592:0.4531	rs1867691;rs2547061;rs17515635;rs59475496;rs1867691	7272	B5ME49	.	V	7272	ENSP00000381008:I7272V	ENSP00000381008:I7272V	I	-	1	0	MUC16	8926632	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.502000	0.06390	-1.196000	0.02676	-1.120000	0.02017	ATT	T|0.778;C|0.222	0.222	strong		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRT14	3861	hgsc.bcm.edu	37	17	39738752	39738752	+	Missense_Mutation	SNP	C	C	T	rs11551760	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39738752C>T	ENST00000167586.6	-	8	1440	c.1354G>A	c.(1354-1356)Gtc>Atc	p.V452I		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	452	Interaction with Type I keratins and keratin filaments.|Tail.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				ACATCCATGACCTTGGTGCGG	0.607													.|||	37	0.00738818	0.0	0.0173	5008	,	,		20119	0.0		0.0229	False		,,,				2504	0.002				p.V452I		Atlas-SNP	.											KRT14,caecum,carcinoma,+1,1	KRT14	65	1	0			c.G1354A						PASS	.	C	ILE/VAL	25,4375		0,25,2175	63.0	46.0	52.0		1354	5.4	1.0	17	dbSNP_120	52	190,8404		3,184,4110	yes	missense	KRT14	NM_000526.4	29	3,209,6285	TT,TC,CC		2.2108,0.5682,1.6546	possibly-damaging	452/473	39738752	215,12779	2200	4297	6497	SO:0001583	missense	3861	exon8			CCATGACCTTGGT	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.1354G>A	17.37:g.39738752C>T	ENSP00000167586:p.Val452Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	26	0.011904761904761904	0	0.0	10	0.027624309392265192	0	0.0	16	0.021108179419525065	C	18.40	3.616454	0.66672	0.005682	0.022108	ENSG00000186847	ENST00000167586	D	0.83992	-1.79	5.38	5.38	0.77491	.	0.000000	0.45606	D	0.000359	T	0.59169	0.2174	L	0.60845	1.875	0.34009	D	0.651217	B	0.24426	0.103	B	0.22753	0.041	T	0.76152	-0.3064	10	0.48119	T	0.1	.	10.5187	0.44905	0.0:0.9113:0.0:0.0887	rs11551760	452	P02533	K1C14_HUMAN	I	452	ENSP00000167586:V452I	ENSP00000167586:V452I	V	-	1	0	KRT14	36992278	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.591000	0.36665	2.689000	0.91719	0.655000	0.94253	GTC	C|0.985;T|0.015	0.015	strong		0.607	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
OR2J3	442186	hgsc.bcm.edu	37	6	29080004	29080004	+	Missense_Mutation	SNP	A	A	G	rs28757581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29080004A>G	ENST00000377169.1	+	1	337	c.337A>G	c.(337-339)Aca>Gca	p.T113A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	113			T -> A (in allele 6M1-3*02; decreased response to C3HEX; dbSNP:rs28757581). {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						ACTGGGAACCACAGAGTGTGT	0.498													A|||	961	0.191893	0.3812	0.1499	5008	,	,		22982	0.1101		0.1193	False		,,,				2504	0.1247				p.T113A		Atlas-SNP	.											OR2J3,NS,carcinoma,0,1	OR2J3	53	1	0			c.A337G						scavenged	.	A	ALA/THR	809,1911		118,573,669	297.0	340.0	325.0		337	2.8	1.0	6	dbSNP_125	325	569,4693		36,497,2098	no	missense	OR2J3	NM_001005216.2	58	154,1070,2767	GG,GA,AA		10.8134,29.7426,17.2638	benign	113/312	29080004	1378,6604	1360	2631	3991	SO:0001583	missense	442186	exon1			GGAACCACAGAGT		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.337A>G	6.37:g.29080004A>G	ENSP00000366374:p.Thr113Ala	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	242	110	0.454545	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	407	0.18635531135531136	203	0.41260162601626016	48	0.13259668508287292	67	0.11713286713286714	89	0.11741424802110818	A	5.246	0.230828	0.09969	0.297426	0.108134	ENSG00000204701	ENST00000377169	T	0.01685	4.69	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	L	0.45422	1.42	0.80722	P	0.0	B	0.11235	0.004	B	0.15052	0.012	T	0.39742	-0.9599	8	0.52906	T	0.07	.	7.2096	0.25927	0.8801:0.0:0.1199:0.0	rs28757581	113	O76001	OR2J3_HUMAN	A	113	ENSP00000366374:T113A	ENSP00000366374:T113A	T	+	1	0	OR2J3	29187983	0.000000	0.05858	0.988000	0.46212	0.407000	0.30961	0.679000	0.25291	1.268000	0.44264	0.358000	0.22013	ACA	A|0.839;G|0.161	0.161	strong		0.498	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
UMPS	7372	hgsc.bcm.edu	37	3	124456742	124456742	+	Missense_Mutation	SNP	G	G	C	rs1801019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124456742G>C	ENST00000232607.2	+	3	744	c.638G>C	c.(637-639)gGt>gCt	p.G213A	UMPS_ENST00000536109.1_Missense_Mutation_p.G121A|UMPS_ENST00000498715.1_3'UTR|UMPS_ENST00000538242.1_Missense_Mutation_p.G35A|UMPS_ENST00000413078.2_Missense_Mutation_p.G35A	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	213	OPRTase.		G -> A (in dbSNP:rs1801019). {ECO:0000269|PubMed:9042911, ECO:0000269|Ref.8}.		'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	AATCATAATGGTTCTCCCCTT	0.488													G|||	931	0.185903	0.152	0.2622	5008	,	,		20706	0.1677		0.1491	False		,,,				2504	0.2342				p.G213A		Atlas-SNP	.											.	UMPS	43	.	0			c.G638C						PASS	.	G	ALA/GLY	681,3725	287.2+/-279.2	57,567,1579	83.0	79.0	81.0		638	3.0	0.0	3	dbSNP_89	81	1470,7130	280.1+/-294.3	122,1226,2952	yes	missense	UMPS	NM_000373.3	60	179,1793,4531	CC,CG,GG		17.093,15.4562,16.5385	benign	213/481	124456742	2151,10855	2203	4300	6503	SO:0001583	missense	7372	exon3			ATAATGGTTCTCC		CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"""orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"""	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.638G>C	3.37:g.124456742G>C	ENSP00000232607:p.Gly213Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_000373	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	Missense_Mutation	SNP	ENST00000232607.2	37	CCDS3029.1	372	0.17032967032967034	73	0.1483739837398374	87	0.24033149171270718	106	0.1853146853146853	106	0.13984168865435356	G	3.378	-0.126888	0.06795	0.154562	0.17093	ENSG00000114491	ENST00000232607;ENST00000536109;ENST00000538242;ENST00000413078	T;T;T;T	0.69561	-0.01;-0.41;0.59;0.57	5.65	2.95	0.34219	.	0.206122	0.51477	D	0.000084	T	0.00039	0.0001	L	0.53561	1.675	0.24864	P	0.99232114	P;B	0.48407	0.91;0.0	B;B	0.42462	0.388;0.001	T	0.18147	-1.0346	9	0.08837	T	0.75	-3.2823	9.6638	0.39972	0.2127:0.0:0.7873:0.0	rs1801019;rs3172286;rs3772805;rs17843818;rs52826107;rs58177968;rs1801019	35;213	B5LY72;P11172	.;UMPS_HUMAN	A	213;121;35;35	ENSP00000232607:G213A;ENSP00000443577:G121A;ENSP00000444988:G35A;ENSP00000397965:G35A	ENSP00000232607:G213A	G	+	2	0	UMPS	125939432	0.999000	0.42202	0.001000	0.08648	0.003000	0.03518	3.284000	0.51708	0.503000	0.28060	-0.136000	0.14681	GGT	G|0.832;C|0.168	0.168	strong		0.488	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33576803	33576803	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:33576803C>T	ENST00000504830.1	-	19	3663	c.3328G>A	c.(3328-3330)Gat>Aat	p.D1110N	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.D1025N|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1110	Spacer 2.				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						GGACCAGTATCTGAACTGGAA	0.507										HNSCC(64;0.19)																											p.D1110N		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G3328A						PASS	.						95.0	89.0	91.0					5																	33576803		2203	4300	6503	SO:0001583	missense	81792	exon19			CAGTATCTGAACT	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.3328G>A	5.37:g.33576803C>T	ENSP00000422554:p.Asp1110Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	c	8.033	0.762246	0.15914	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59772	0.25;0.24	5.22	4.33	0.51752	.	1.532230	0.03305	N	0.189648	T	0.45637	0.1352	L	0.27053	0.805	0.21675	N	0.999593	B;B	0.34015	0.435;0.201	B;B	0.30572	0.117;0.055	T	0.35351	-0.9792	10	0.21014	T	0.42	.	8.6051	0.33769	0.0:0.7653:0.1545:0.0802	.	1025;1110	P58397-3;P58397	.;ATS12_HUMAN	N	1110;1025	ENSP00000422554:D1110N;ENSP00000344847:D1025N	ENSP00000344847:D1025N	D	-	1	0	ADAMTS12	33612560	0.000000	0.05858	0.170000	0.22879	0.143000	0.21401	-0.091000	0.11146	1.391000	0.46566	0.651000	0.88453	GAT	.	.	none		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
CTBS	1486	hgsc.bcm.edu	37	1	85029077	85029077	+	Missense_Mutation	SNP	C	C	T	rs15911|rs35270754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85029077C>T	ENST00000370630.5	-	6	868	c.820G>A	c.(820-822)Gtc>Atc	p.V274I	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	274			V -> I (in dbSNP:rs15911).		chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		CGGAAAGGGACTTTTGCAATG	0.373													C|||	742	0.148163	0.1082	0.1254	5008	,	,		12711	0.0298		0.2038	False		,,,				2504	0.2832				p.V274I		Atlas-SNP	.											.	CTBS	24	.	0			c.G820A						PASS	.	C	ILE/VAL	564,3840		42,480,1680	43.0	48.0	46.0		820	2.6	1.0	1	dbSNP_52	46	1870,6728		217,1436,2646	yes	missense	CTBS	NM_004388.2	29	259,1916,4326	TT,TC,CC		21.7492,12.8065,18.7202	possibly-damaging	274/386	85029077	2434,10568	2202	4299	6501	SO:0001583	missense	1486	exon6			AAGGGACTTTTGC	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.820G>A	1.37:g.85029077C>T	ENSP00000359664:p.Val274Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	287	0.13141025641025642	50	0.1016260162601626	57	0.1574585635359116	21	0.03671328671328671	159	0.20976253298153033	C	17.50	3.403971	0.62288	0.128065	0.217492	ENSG00000117151	ENST00000370630	T	0.07216	3.21	5.5	2.56	0.30785	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.175582	0.49305	D	0.000141	T	0.05227	0.0139	M	0.85197	2.74	0.25967	P	0.9825421	P	0.35192	0.489	B	0.37731	0.257	T	0.16217	-1.0410	9	0.32370	T	0.25	-1.2041	5.7446	0.18112	0.2649:0.549:0.1192:0.067	rs15911;rs3177079;rs17297378;rs17359075;rs17374997;rs52800947;rs57212367;rs15911	274	Q01459	DIAC_HUMAN	I	274	ENSP00000359664:V274I	ENSP00000359659:V183I	V	-	1	0	CTBS	84801665	0.989000	0.36119	0.991000	0.47740	0.909000	0.53808	0.705000	0.25675	0.271000	0.22005	0.650000	0.86243	GTC	C|0.831;T|0.169	0.169	strong		0.373	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
HPS1	3257	hgsc.bcm.edu	37	10	100185638	100185638	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100185638T>C	ENST00000325103.6	-	12	1325	c.1092A>G	c.(1090-1092)ctA>ctG	p.L364L	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Silent_p.L364L	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	364					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGTGGGGCACTAGGGGGCAGT	0.612									Hermansky-Pudlak syndrome		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L364L		Atlas-SNP	.											.	HPS1	65	.	0			c.A1092G						PASS	.						105.0	108.0	107.0					10																	100185638		2203	4300	6503	SO:0001819	synonymous_variant	3257	exon12	Familial Cancer Database	HPS, HPS1-8	GGGCACTAGGGGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1092A>G	10.37:g.100185638T>C		Somatic	112	0	0	1349	WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																			.	.	none		0.612	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
ROS1	6098	hgsc.bcm.edu	37	6	117631431	117631431	+	Silent	SNP	T	T	G	rs552183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:117631431T>G	ENST00000368508.3	-	40	6445	c.6247A>C	c.(6247-6249)Aga>Cga	p.R2083R	ROS1_ENST00000368507.3_Silent_p.R2077R	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2083	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		AGGCAATTTCTAGCTGCCAGA	0.363			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	596	0.11901	0.1331	0.1052	5008	,	,		14018	0.119		0.1451	False		,,,				2504	0.0828				p.R2083R		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.A6247C						PASS	.	G		619,3787		34,551,1618	71.0	72.0	72.0		6247	4.7	1.0	6	dbSNP_83	72	1148,7452		72,1004,3224	no	coding-synonymous	ROS1	NM_002944.2		106,1555,4842	GG,GT,TT		13.3488,14.049,13.586		2083/2348	117631431	1767,11239	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon40			AATTTCTAGCTGC	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.6247A>C	6.37:g.117631431T>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			T|0.864;G|0.136	0.136	strong		0.363	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
ATXN7	6314	hgsc.bcm.edu	37	3	63982082	63982082	+	Missense_Mutation	SNP	G	G	A	rs3774729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:63982082G>A	ENST00000295900.6	+	12	3134	c.2584G>A	c.(2584-2586)Gtg>Atg	p.V862M	ATXN7_ENST00000398590.3_Missense_Mutation_p.V862M|ATXN7_ENST00000484332.1_Missense_Mutation_p.V717M|ATXN7_ENST00000487717.1_Missense_Mutation_p.V862M|ATXN7_ENST00000538065.1_Missense_Mutation_p.V862M	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	862			V -> M (in dbSNP:rs3774729). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9425224}.		cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		AGTGCCAGCCGTGAACAATGT	0.507													A|||	2192	0.4377	0.6354	0.3429	5008	,	,		18405	0.4603		0.334	False		,,,				2504	0.3211				p.V862M		Atlas-SNP	.											ATXN7_ENST00000398590,rectum,carcinoma,0,2	ATXN7	126	2	0			c.G2584A						scavenged	.	A	MET/VAL,MET/VAL,MET/VAL	2374,1882		676,1022,430	65.0	69.0	68.0		2584,2149,2584	-1.6	1.0	3	dbSNP_107	68	2612,5894		406,1800,2047	yes	missense,missense,missense	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	21,21,21	1082,2822,2477	AA,AG,GG		30.7077,44.2199,39.0691	benign,benign,benign	862/893,717/748,862/946	63982082	4986,7776	2128	4253	6381	SO:0001583	missense	6314	exon12			CCAGCCGTGAACA	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2584G>A	3.37:g.63982082G>A	ENSP00000295900:p.Val862Met	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	284	106	0.373239	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	954	0.4368131868131868	288	0.5853658536585366	128	0.35359116022099446	284	0.4965034965034965	254	0.33509234828496043	A	1.225	-0.625811	0.03610	0.557801	0.307077	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332;ENST00000522345	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.07	-1.61	0.08399	.	0.335977	0.36893	N	0.002341	T	0.00012	0.0000	N	0.04746	-0.17	0.46798	P	7.989999999999942E-4	B;B;B	0.18461	0.006;0.028;0.005	B;B;B	0.08055	0.003;0.003;0.001	T	0.41342	-0.9514	9	0.02654	T	1	0.1485	9.2895	0.37778	0.2927:0.1299:0.5775:0.0	rs3774729;rs57082092;rs3774729	717;862;862	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	M	862;862;862;862;717;33	ENSP00000381590:V862M;ENSP00000295900:V862M;ENSP00000420234:V862M;ENSP00000439585:V862M;ENSP00000428277:V717M;ENSP00000428067:V33M	ENSP00000295900:V862M	V	+	1	0	ATXN7	63957122	0.000000	0.05858	0.983000	0.44433	0.990000	0.78478	-0.265000	0.08644	-0.467000	0.06932	-0.260000	0.10688	GTG	G|0.550;A|0.450	0.450	strong		0.507	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
MYO5A	4644	hgsc.bcm.edu	37	15	52664408	52664408	+	Silent	SNP	G	G	A	rs11637651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52664408G>A	ENST00000399231.3	-	21	2973	c.2730C>T	c.(2728-2730)atC>atT	p.I910I	MYO5A_ENST00000358212.6_Silent_p.I910I|MYO5A_ENST00000399233.2_Silent_p.I910I|MYO5A_ENST00000553916.1_Silent_p.I910I|MYO5A_ENST00000356338.6_Silent_p.I910I	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	910	IQ 6. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		AGCGAGCCTCGATTTTGAGCT	0.522													G|||	301	0.0601038	0.0182	0.036	5008	,	,		15879	0.0804		0.0706	False		,,,				2504	0.1022				p.I910I		Atlas-SNP	.											.	MYO5A	145	.	0			c.C2730T						PASS	.	G	,	115,3875		1,113,1881	69.0	66.0	67.0		2730,2730	-3.4	1.0	15	dbSNP_120	67	521,7835		12,497,3669	no	coding-synonymous,coding-synonymous	MYO5A	NM_000259.3,NM_001142495.1	,	13,610,5550	AA,AG,GG		6.235,2.8822,5.1515	,	910/1856,910/1829	52664408	636,11710	1995	4178	6173	SO:0001819	synonymous_variant	4644	exon21			AGCCTCGATTTTG		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.2730C>T	15.37:g.52664408G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			G|0.944;A|0.056	0.056	strong		0.522	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
HAUS6	54801	hgsc.bcm.edu	37	9	19058743	19058743	+	Missense_Mutation	SNP	G	G	C	rs10511670	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19058743G>C	ENST00000380502.3	-	16	2489	c.2022C>G	c.(2020-2022)caC>caG	p.H674Q	HAUS6_ENST00000380496.1_Missense_Mutation_p.H538Q	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	674			H -> Q (in dbSNP:rs10511670). {ECO:0000269|PubMed:14702039}.		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)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GTTCATCTATGTGACTGGTCA	0.378													G|||	387	0.0772764	0.0666	0.0476	5008	,	,		20189	0.13		0.0855	False		,,,				2504	0.0501				p.H674Q		Atlas-SNP	.											.	HAUS6	66	.	0			c.C2022G						PASS	.	G	GLN/HIS	290,4116	160.3+/-192.7	12,266,1925	120.0	119.0	119.0		2022	-4.4	0.0	9	dbSNP_119	119	777,7823	184.5+/-232.4	46,685,3569	yes	missense	HAUS6	NM_017645.3	24	58,951,5494	CC,CG,GG		9.0349,6.5819,8.2039	benign	674/956	19058743	1067,11939	2203	4300	6503	SO:0001583	missense	54801	exon16			ATCTATGTGACTG	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.2022C>G	9.37:g.19058743G>C	ENSP00000369871:p.His674Gln	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	270	115	0.425926	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	181	0.08287545787545787	23	0.046747967479674794	17	0.04696132596685083	71	0.12412587412587413	70	0.09234828496042216	G	1.349	-0.591964	0.03799	0.065819	0.090349	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.23552	1.91;1.9	5.06	-4.36	0.03645	.	1.075000	0.07015	N	0.825785	T	0.00210	0.0006	L	0.42245	1.32	0.09310	N	1	B;B;B	0.13594	0.008;0.003;0.008	B;B;B	0.13407	0.009;0.009;0.009	T	0.33059	-0.9883	10	0.13470	T	0.59	13.9473	3.0345	0.06117	0.4343:0.3174:0.146:0.1023	rs10511670;rs10511670	639;538;674	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	Q	674;538	ENSP00000369871:H674Q;ENSP00000369865:H538Q	ENSP00000369865:H538Q	H	-	3	2	HAUS6	19048743	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-0.161000	0.10026	-0.856000	0.04120	0.467000	0.42956	CAC	G|1.000;|0.000	.	weak		0.378	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
CHD3	1107	hgsc.bcm.edu	37	17	7796805	7796805	+	Silent	SNP	C	C	G	rs199898244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7796805C>G	ENST00000330494.7	+	5	861	c.711C>G	c.(709-711)tcC>tcG	p.S237S	CHD3_ENST00000358181.4_Silent_p.S237S|CHD3_ENST00000380358.4_Silent_p.S296S	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	237					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TAGCACCCTCCGGACCCCCCG	0.647													C|||	7	0.00139776	0.0	0.0058	5008	,	,		7723	0.0		0.003	False		,,,				2504	0.0				p.S296S		Atlas-SNP	.											.	CHD3	169	.	0			c.C888G						PASS	.	C	,,	1,4397		0,1,2198	16.0	17.0	17.0		888,711,711	-6.8	0.9	17		17	21,8559		0,21,4269	yes	coding-synonymous,coding-synonymous,coding-synonymous	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,,	0,22,6467	GG,GC,CC		0.2448,0.0227,0.1695	,,	296/2060,237/2001,237/1967	7796805	22,12956	2199	4290	6489	SO:0001819	synonymous_variant	1107	exon5			ACCCTCCGGACCC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.711C>G	17.37:g.7796805C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	37	CCDS32554.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	5.459	0.269736	0.10349	2.27E-4	0.002448	ENSG00000170004	ENST00000452447	.	.	.	4.82	-6.78	0.01721	.	.	.	.	.	T	0.45377	0.1339	.	.	.	0.46901	D	0.999246	.	.	.	.	.	.	T	0.49725	-0.8909	4	.	.	.	-19.0971	6.1106	0.20097	0.195:0.3477:0.0:0.4573	.	.	.	.	G	112	.	.	R	+	1	2	CHD3	7737530	0.596000	0.26866	0.933000	0.37362	0.882000	0.50991	-0.099000	0.11007	-0.867000	0.04063	-1.391000	0.01154	CGG	C|0.999;G|0.001	0.001	strong		0.647	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
LAMP5	24141	hgsc.bcm.edu	37	20	9496716	9496716	+	Missense_Mutation	SNP	C	C	G	rs2232264	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:9496716C>G	ENST00000246070.2	+	3	799	c.307C>G	c.(307-309)Cag>Gag	p.Q103E	RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Intron	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						scavenged	.	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	111	2	0.018018		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	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	
LSP1	4046	hgsc.bcm.edu	37	11	1902768	1902768	+	Missense_Mutation	SNP	G	G	A	rs621679	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1902768G>A	ENST00000311604.3	+	3	473	c.298G>A	c.(298-300)Gcc>Acc	p.A100T	LSP1_ENST00000405957.2_Missense_Mutation_p.A38T|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Missense_Mutation_p.A228T|LSP1_ENST00000406638.2_Missense_Mutation_p.A38T	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	100			A -> T (in dbSNP:rs621679). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.	Missing (in Ref. 3; AAB29545). {ECO:0000305}.	cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		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;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GGCGCAGGGCGCCTTGGACAG	0.706													g|||	1988	0.396965	0.2595	0.5418	5008	,	,		14019	0.5863		0.3867	False		,,,				2504	0.2955				p.A228T		Atlas-SNP	.											.	LSP1	59	.	0			c.G682A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1155,3175		182,791,1192	15.0	16.0	16.0		112,112,112,298	-6.0	0.0	11	dbSNP_83	16	3046,5380		606,1834,1773	no	missense,missense,missense,missense	LSP1	NM_001013253.1,NM_001013254.1,NM_001013255.1,NM_002339.2	58,58,58,58	788,2625,2965	AA,AG,GG		36.15,26.6744,32.9335	benign,benign,benign,benign	38/278,38/278,38/278,100/340	1902768	4201,8555	2165	4213	6378	SO:0001583	missense	4046	exon4			CAGGGCGCCTTGG	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.298G>A	11.37:g.1902768G>A	ENSP00000308383:p.Ala100Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	913	0.41804029304029305	134	0.27235772357723576	168	0.46408839779005523	327	0.5716783216783217	284	0.37467018469656993	.	0.009	-1.859750	0.00552	0.266744	0.3615	ENSG00000130592	ENST00000311604;ENST00000421485;ENST00000446808;ENST00000381775;ENST00000405957;ENST00000451814;ENST00000457279;ENST00000429923;ENST00000406638;ENST00000418975;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T;T;T;T;T;T	0.49139	2.0;1.49;1.54;1.93;1.99;1.48;1.98;1.55;1.99;0.79;1.99;1.99	2.98	-5.97	0.02227	.	1.832530	0.03432	N	0.207919	T	0.00012	0.0000	N	0.01493	-0.835	0.80722	P	0.0	B;B	0.24920	0.114;0.01	B;B	0.13407	0.009;0.002	T	0.10660	-1.0620	9	0.02654	T	1	-1.6885	1.6488	0.02767	0.385:0.1022:0.3106:0.2021	rs621679;rs3188464;rs16927670;rs17855362;rs57739592	228;100	E9PFP3;P33241	.;LSP1_HUMAN	T	100;38;38;228;38;38;91;83;38;118;38;38	ENSP00000308383:A100T;ENSP00000411191:A38T;ENSP00000402543:A38T;ENSP00000371194:A228T;ENSP00000383932:A38T;ENSP00000414106:A38T;ENSP00000400346:A91T;ENSP00000400999:A83T;ENSP00000384022:A38T;ENSP00000403460:A118T;ENSP00000416363:A38T;ENSP00000412405:A38T	ENSP00000308383:A100T	A	+	1	0	LSP1	1859344	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.012000	0.01451	-4.340000	0.00055	-1.783000	0.00646	GCC	G|0.638;A|0.362	0.362	strong		0.706	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
COL25A1	84570	hgsc.bcm.edu	37	4	109863370	109863370	+	Missense_Mutation	SNP	C	C	T	rs17531474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	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	
ABCB5	340273	hgsc.bcm.edu	37	7	20762646	20762646	+	Missense_Mutation	SNP	G	G	T	rs62453384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	116	27	0.232759	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	
CNTRL	11064	hgsc.bcm.edu	37	9	123929770	123929770	+	Silent	SNP	C	C	T	rs61745682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:123929770C>T	ENST00000373855.1	+	37	5919	c.5659C>T	c.(5659-5661)Ctg>Ttg	p.L1887L	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Silent_p.L1887L|CNTRL_ENST00000373850.1_Silent_p.L1335L			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	138	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	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	
DPYD	1806	hgsc.bcm.edu	37	1	97981395	97981395	+	Missense_Mutation	SNP	T	T	C	rs1801159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:97981395T>C	ENST00000370192.3	-	13	1727	c.1627A>G	c.(1627-1629)Ata>Gta	p.I543V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	543			I -> V (in allele DPYD*5; dbSNP:rs1801159). {ECO:0000269|PubMed:15489334}.		beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AAAGGATTTATAAACTTCAAT	0.448													T|||	926	0.184904	0.1536	0.2666	5008	,	,		14548	0.2659		0.1879	False		,,,				2504	0.0828				p.I543V		Atlas-SNP	.											.	DPYD	219	.	0			c.A1627G	GRCh37	CM033371	DPYD	M	rs1801159	PASS	.	T	VAL/ILE	684,3722	287.8+/-279.5	56,572,1575	80.0	75.0	77.0		1627	-3.1	0.0	1	dbSNP_89	77	1704,6896	311.6+/-310.4	192,1320,2788	yes	missense	DPYD	NM_000110.3	29	248,1892,4363	CC,CT,TT		19.814,15.5243,18.3608	benign	543/1026	97981395	2388,10618	2203	4300	6503	SO:0001583	missense	1806	exon13			GATTTATAAACTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1627A>G	1.37:g.97981395T>C	ENSP00000359211:p.Ile543Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	447	0.20467032967032966	100	0.2032520325203252	69	0.19060773480662985	148	0.25874125874125875	130	0.17150395778364116	T	12.85	2.060151	0.36373	0.155243	0.19814	ENSG00000188641	ENST00000370192	T	0.74002	-0.8	5.05	-3.13	0.05266	Aldolase-type TIM barrel (1);	0.378314	0.31612	N	0.007342	T	0.22044	0.0531	N	0.11427	0.14	0.09310	P	0.99999788442	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.02654	T	1	0.1698	9.7016	0.40189	0.0:0.1666:0.6128:0.2206	rs1801159;rs17116825;rs58945530;rs1801159	543	Q12882	DPYD_HUMAN	V	543	ENSP00000359211:I543V	ENSP00000359211:I543V	I	-	1	0	DPYD	97753983	0.993000	0.37304	0.026000	0.17262	0.842000	0.47809	1.371000	0.34250	-0.215000	0.10063	0.477000	0.44152	ATA	T|0.802;C|0.198	0.198	strong		0.448	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
HIF3A	64344	hgsc.bcm.edu	37	19	46823751	46823751	+	Silent	SNP	C	C	T	rs3764610	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000300862.3_Silent_p.H357H|HIF3A_ENST00000339613.2_Silent_p.H303H|HIF3A_ENST00000472815.1_Silent_p.H290H|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000600383.1_Silent_p.H290H|HIF3A_ENST00000420102.2_Silent_p.H308H	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	39	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	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		
NRROS	375387	hgsc.bcm.edu	37	3	196388023	196388023	+	Silent	SNP	C	C	G	rs62636585	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196388023C>G	ENST00000328557.4	+	3	1712	c.1509C>G	c.(1507-1509)ctC>ctG	p.L503L		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	503					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)											ATGGGAGCCTCGCCCCACTCC	0.587													C|||	27	0.00539137	0.0015	0.0115	5008	,	,		17690	0.0		0.0159	False		,,,				2504	0.001				p.L503L		Atlas-SNP	.											.	LRRC33	91	.	0			c.C1509G						PASS	.	C		26,4380	32.6+/-62.9	0,26,2177	82.0	80.0	81.0		1509	-9.3	0.0	3	dbSNP_129	81	190,8410	84.2+/-146.7	1,188,4111	no	coding-synonymous	LRRC33	NM_198565.1		1,214,6288	GG,GC,CC		2.2093,0.5901,1.6608		503/693	196388023	216,12790	2203	4300	6503	SO:0001819	synonymous_variant	375387	exon3			GAGCCTCGCCCCA	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.1509C>G	3.37:g.196388023C>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	167	109	0.652695	NM_198565		Silent	SNP	ENST00000328557.4	37	CCDS3319.1																																																																																			C|0.984;G|0.016	0.016	strong		0.587	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565	
ZNF512B	57473	hgsc.bcm.edu	37	20	62595547	62595547	+	Missense_Mutation	SNP	C	C	T	rs6062599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	23	0.433962	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	
MROH2B	133558	hgsc.bcm.edu	37	5	41069852	41069852	+	Missense_Mutation	SNP	T	T	C	rs13174484	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:41069852T>C	ENST00000399564.4	-	2	481	c.31A>G	c.(31-33)Atg>Gtg	p.M11V		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	11			M -> V (in dbSNP:rs13174484). {ECO:0000269|PubMed:15489334}.														TCCCCAAACATCTCTAAAACG	0.323													T|||	1184	0.236422	0.2307	0.219	5008	,	,		19034	0.1429		0.3728	False		,,,				2504	0.2127				p.M11V		Atlas-SNP	.											.	.	.	.	0			c.A31G						PASS	.	T	VAL/MET	935,2721		115,705,1008	59.0	57.0	57.0		31	0.5	0.1	5	dbSNP_121	57	3015,5143		590,1835,1654	yes	missense	HEATR7B2	NM_173489.4	21	705,2540,2662	CC,CT,TT		36.9576,25.5744,33.4349	benign	11/1586	41069852	3950,7864	1828	4079	5907	SO:0001583	missense	133558	exon2			CAAACATCTCTAA		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.31A>G	5.37:g.41069852T>C	ENSP00000382476:p.Met11Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	134	53	0.395522	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	578	0.26465201465201466	114	0.23170731707317074	91	0.2513812154696133	79	0.1381118881118881	294	0.38786279683377306	T	6.078	0.382630	0.11524	0.255744	0.369576	ENSG00000171495	ENST00000399564	T	0.01084	5.36	6.16	0.491	0.16867	.	0.844718	0.10419	N	0.676930	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	0.23726	-1.0180	9	0.13853	T	0.58	.	2.0595	0.03589	0.1507:0.0892:0.3126:0.4475	rs13174484;rs52831286;rs58493754;rs13174484	11	Q7Z745	HTRB2_HUMAN	V	11	ENSP00000382476:M11V	ENSP00000382476:M11V	M	-	1	0	HEATR7B2	41105609	0.108000	0.22018	0.092000	0.20876	0.745000	0.42441	0.854000	0.27791	0.139000	0.18822	-0.417000	0.06048	ATG	T|0.743;C|0.257	0.257	strong		0.323	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
GCA	25801	hgsc.bcm.edu	37	2	163208893	163208893	+	Missense_Mutation	SNP	T	T	G	rs17783344	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:163208893T>G	ENST00000437150.2	+	3	399	c.238T>G	c.(238-240)Tct>Gct	p.S80A	GCA_ENST00000429691.2_Missense_Mutation_p.S61A|GCA_ENST00000473240.1_3'UTR|GCA_ENST00000233612.4_Missense_Mutation_p.S61A	NM_012198.3	NP_036330.1	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	80	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		S -> A (in dbSNP:rs17783344). {ECO:0000269|Ref.3}.		membrane fusion (GO:0061025)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	9						TTTGACACAGTCTGGAATTAA	0.303													T|||	261	0.0521166	0.0068	0.0749	5008	,	,		17087	0.003		0.1571	False		,,,				2504	0.0399				p.S80A		Atlas-SNP	.											.	GCA	15	.	0			c.T238G						PASS	.	T	ALA/SER	140,4266	98.9+/-137.6	3,134,2066	176.0	176.0	176.0		238	5.2	1.0	2	dbSNP_123	176	1247,7353	249.9+/-277.0	87,1073,3140	yes	missense	GCA	NM_012198.3	99	90,1207,5206	GG,GT,TT		14.5,3.1775,10.6643	benign	80/218	163208893	1387,11619	2203	4300	6503	SO:0001583	missense	25801	exon3			ACACAGTCTGGAA	M81637	CCDS2218.1	2q24.2	2013-01-10	2001-11-28		ENSG00000115271	ENSG00000115271		"""EF-hand domain containing"""	15990	protein-coding gene	gene with protein product		607030	"""grancalcin, EF-hand calcium-binding protein"""			1737748, 1530588, 12804766	Standard	NM_012198		Approved	GCL	uc002ucg.3	P28676	OTTHUMG00000132057	ENST00000437150.2:c.238T>G	2.37:g.163208893T>G	ENSP00000394842:p.Ser80Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_012198	B2R5X3|Q53TB5|Q59EP3	Missense_Mutation	SNP	ENST00000437150.2	37	CCDS2218.1	149	0.06822344322344322	1	0.0020325203252032522	33	0.09116022099447514	1	0.0017482517482517483	114	0.1503957783641161	T	11.80	1.746380	0.30955	0.031775	0.145	ENSG00000115271	ENST00000446271;ENST00000429691;ENST00000437150;ENST00000453113;ENST00000233612	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	5.19	5.19	0.71726	EF-hand-like domain (1);	0.286388	0.21989	U	0.066197	T	0.00754	0.0025	L	0.44542	1.39	0.25090	P	0.99086955	B	0.06786	0.001	B	0.11329	0.006	T	0.31613	-0.9937	9	0.21014	T	0.42	.	10.2648	0.43449	0.0:0.0:0.1659:0.834	rs17783344;rs59762430;rs17783344	80	P28676	GRAN_HUMAN	A	106;61;80;61;61	ENSP00000393218:S106A;ENSP00000412899:S61A;ENSP00000394842:S80A;ENSP00000403805:S61A;ENSP00000233612:S61A	ENSP00000233612:S61A	S	+	1	0	GCA	162917139	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	1.858000	0.39408	1.951000	0.56629	0.528000	0.53228	TCT	T|0.908;G|0.092	0.092	strong		0.303	GCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255080.3	NM_012198	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	2	0.030303		WXS	Illumina HiSeq	Phase_I	52	5	0.0961538	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		
SPAG16	79582	hgsc.bcm.edu	37	2	214727221	214727221	+	Missense_Mutation	SNP	A	A	C	rs2042791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	97	2	0.0206186		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	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	
MORC1	27136	hgsc.bcm.edu	37	3	108754214	108754214	+	Missense_Mutation	SNP	T	T	C	rs3762697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	82	0	0		WXS	Illumina HiSeq	Phase_I	123	42	0.341463	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		
ASIC2	40	hgsc.bcm.edu	37	17	32483270	32483270	+	Silent	SNP	C	C	G	rs2228989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:32483270C>G	ENST00000359872.6	-	1	1043	c.282G>C	c.(280-282)ctG>ctC	p.L94L		NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	94					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GGAAGCCATTCAGGTTACAGA	0.577													G|||	1163	0.232228	0.0439	0.3573	5008	,	,		19977	0.3532		0.2008	False		,,,				2504	0.3057				p.L94L		Atlas-SNP	.											.	.	.	.	0			c.G282C						PASS	.	G		279,4085		6,267,1909	75.0	83.0	80.0		282	2.9	1.0	17	dbSNP_98	80	1632,6926		151,1330,2798	no	coding-synonymous	ACCN1	NM_001094.4		157,1597,4707	GG,GC,CC		19.0699,6.3932,14.7887		94/513	32483270	1911,11011	2182	4279	6461	SO:0001819	synonymous_variant	40	exon1			GCCATTCAGGTTA	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.282G>C	17.37:g.32483270C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001094	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																			C|0.782;G|0.218	0.218	strong		0.577	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
FMN2	56776	hgsc.bcm.edu	37	1	240371075	240371075	+	Missense_Mutation	SNP	C	C	T	rs71646825		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	0	0		WXS	Illumina HiSeq	Phase_I	73	12	0.164384	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	
CUL2	8453	hgsc.bcm.edu	37	10	35302705	35302705	+	Silent	SNP	C	C	T	rs12830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:35302705C>T	ENST00000374748.1	-	20	2224	c.1911G>A	c.(1909-1911)tcG>tcA	p.S637S	CUL2_ENST00000374746.1_Silent_p.S637S|CUL2_ENST00000374749.3_Silent_p.S637S|CUL2_ENST00000602371.1_Silent_p.S580S|CUL2_ENST00000537177.1_Silent_p.S656S|CUL2_ENST00000374742.1_Silent_p.S637S|CUL2_ENST00000374751.3_Silent_p.S637S			Q13617	CUL2_HUMAN	cullin 2	637					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TTAATGAAAACGAAGATTCTG	0.264													C|||	1421	0.283746	0.1483	0.3314	5008	,	,		15043	0.3125		0.3598	False		,,,				2504	0.3252				p.S656S		Atlas-SNP	.											CUL2,colon,carcinoma,-1,1	CUL2	63	1	0			c.G1968A						scavenged	.	C	,,,	739,3659	282.5+/-276.6	72,595,1532	104.0	88.0	94.0		1911,1968,1950,1911	0.6	1.0	10	dbSNP_52	94	2928,5654	423.6+/-354.4	495,1938,1858	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUL2	NM_001198777.1,NM_001198778.1,NM_001198779.1,NM_003591.3	,,,	567,2533,3390	TT,TC,CC		34.1179,16.8031,28.2512	,,,	637/746,656/765,650/759,637/746	35302705	3667,9313	2199	4291	6490	SO:0001819	synonymous_variant	8453	exon19			TGAAAACGAAGAT	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1911G>A	10.37:g.35302705C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	13	5	0.384615	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Silent	SNP	ENST00000374748.1	37	CCDS7179.1																																																																																			T|0.272;G|0.012	0.272	strong		0.264	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591	
CXorf65	158830	hgsc.bcm.edu	37	X	70324157	70324157	+	Silent	SNP	C	C	T	rs1130009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:70324157C>T	ENST00000374251.5	-	5	465	c.417G>A	c.(415-417)gcG>gcA	p.A139A		NM_001025265.2	NP_001020436.1	A6NEN9	CX065_HUMAN	chromosome X open reading frame 65	139										breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)	10						CCGGGACACTCGCAGGGGGTT	0.507													C|||	422	0.111788	0.0197	0.1326	3775	,	,		13137	0.001		0.2555	False		,,,				2504	0.047				p.A139A		Atlas-SNP	.											.	CXorf65	23	.	0			c.G417A						PASS	.	C		243,3592		11,187,34,1434,537	82.0	64.0	70.0		417	2.1	0.0	X	dbSNP_86	70	2153,4575		236,1079,602,1113,1270	no	coding-synonymous	CXorf65	NM_001025265.2		247,1266,636,2547,1807	TT,TC,T,CC,C		32.0006,6.3364,22.6829		139/184	70324157	2396,8167	2203	4300	6503	SO:0001819	synonymous_variant	158830	exon5			GACACTCGCAGGG	BC144434	CCDS35324.1	Xq13.1	2009-03-06			ENSG00000204165	ENSG00000204165			33713	protein-coding gene	gene with protein product							Standard	NM_001025265		Approved		uc011mpo.2	A6NEN9	OTTHUMG00000021785	ENST00000374251.5:c.417G>A	X.37:g.70324157C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001025265		Silent	SNP	ENST00000374251.5	37	CCDS35324.1																																																																																			0|0.002;T|0.182	0.182	strong		0.507	CXorf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057089.2	NM_001025265	
CNOT1	23019	hgsc.bcm.edu	37	16	58616984	58616984	+	Silent	SNP	T	T	C	rs17854029	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:58616984T>C	ENST00000317147.5	-	9	1241	c.909A>G	c.(907-909)ggA>ggG	p.G303G	CNOT1_ENST00000569240.1_Silent_p.G303G|CNOT1_ENST00000441024.2_Silent_p.G303G	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	303					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|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 stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CATCTGTTAATCCTGAATGAG	0.393													T|||	1012	0.202077	0.1218	0.268	5008	,	,		19053	0.0288		0.4264	False		,,,				2504	0.2117				p.G303G		Atlas-SNP	.											CNOT1_ENST00000441024,NS,carcinoma,0,2	CNOT1	359	2	0			c.A909G						PASS	.	T	,	824,3572	326.7+/-299.7	79,666,1453	104.0	91.0	95.0		909,909	1.3	1.0	16	dbSNP_123	95	3863,4737	542.3+/-384.2	880,2103,1317	no	coding-synonymous,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	959,2769,2770	CC,CT,TT		44.9186,18.7443,36.0649	,	303/2377,303/1552	58616984	4687,8309	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon9			TGTTAATCCTGAA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.909A>G	16.37:g.58616984T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	159	74	0.465409	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			T|0.709;C|0.291	0.291	strong		0.393	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
HSD17B1	3292	hgsc.bcm.edu	37	17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	rs147402365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	RP11-400F19.6_ENST00000590513.1_RNA|RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	238			A -> V. {ECO:0000269|PubMed:8389226}.		bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	GAGGAGGTGGCGGAGGTGAGC	0.687													C|||	14	0.00279553	0.0008	0.0	5008	,	,		12600	0.0		0.0129	False		,,,				2504	0.0				p.A238V		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C713T						PASS	.	C	VAL/ALA	9,4395	15.5+/-35.6	0,9,2193	39.0	31.0	34.0		713	-0.4	0.0	17	dbSNP_134	34	70,8530	42.2+/-99.7	0,70,4230	yes	missense	HSD17B1	NM_000413.2	64	0,79,6423	TT,TC,CC		0.814,0.2044,0.6075	benign	238/329	40706596	79,12925	2202	4300	6502	SO:0001583	missense	3292	exon5			AGGTGGCGGAGGT		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5210	protein-coding gene	gene with protein product	"""Estradiol 17-beta-dehydrogenase-1"", ""short chain dehydrogenase/reductase family 28CE, member 1"""	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.713C>T	17.37:g.40706596C>T	ENSP00000466799:p.Ala238Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	43	28	0.651163	NM_000413	B3KXS1|Q2M2L8	Missense_Mutation	SNP	ENST00000585807.1	37	CCDS11428.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.655	0.899159	0.17686	0.002044	0.00814	ENSG00000108786	ENST00000225929	.	.	.	4.16	-0.383	0.12477	NAD(P)-binding domain (1);	1.163550	0.06218	N	0.686122	T	0.07503	0.0189	N	0.04636	-0.2	0.09310	N	1	B;P	0.41102	0.002;0.738	B;B	0.28553	0.002;0.091	T	0.15065	-1.0450	9	0.30854	T	0.27	.	6.1916	0.20528	0.0:0.5144:0.0:0.4856	.	269;238	B3RFR9;P14061	.;DHB1_HUMAN	V	238	.	ENSP00000225929:A238V	A	+	2	0	HSD17B1	37960122	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.067000	0.14510	0.095000	0.17434	-0.658000	0.03865	GCG	C|0.996;T|0.004	0.004	strong		0.687	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413	
TEX2	55852	hgsc.bcm.edu	37	17	62270941	62270941	+	Silent	SNP	C	C	T	rs34343500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62270941C>T	ENST00000583097.1	-	4	2326	c.2154G>A	c.(2152-2154)tcG>tcA	p.S718S	TEX2_ENST00000584379.1_Silent_p.S718S|TEX2_ENST00000258991.3_Silent_p.S718S			Q8IWB9	TEX2_HUMAN	testis expressed 2	718					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		CAGAGACACCCGATGACTTCT	0.413													C|||	537	0.107228	0.2443	0.0663	5008	,	,		21779	0.0129		0.0895	False		,,,				2504	0.0665				p.S718S		Atlas-SNP	.											.	TEX2	89	.	0			c.G2154A						PASS	.	C		948,3458	358.6+/-314.5	106,736,1361	154.0	153.0	153.0		2154	1.1	1.0	17	dbSNP_126	153	881,7719	198.0+/-242.5	44,793,3463	no	coding-synonymous	TEX2	NM_018469.3		150,1529,4824	TT,TC,CC		10.2442,21.5161,14.0627		718/1135	62270941	1829,11177	2203	4300	6503	SO:0001819	synonymous_variant	55852	exon4			GACACCCGATGAC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"""transmembrane protein 96"""		"""testis expressed sequence 2"""			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.2154G>A	17.37:g.62270941C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	37																																																																																				C|0.874;T|0.126	0.126	strong		0.413	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469	
PRODH2	58510	hgsc.bcm.edu	37	19	36298022	36298022	+	Splice_Site	SNP	T	T	C	rs73594420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36298022T>C	ENST00000301175.3	-	6	844	c.827A>G	c.(826-828)aAc>aGc	p.N276S		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	276					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GACCTGGAGGTTCTAGGGGGC	0.532													C|||	537	0.107228	0.3517	0.0346	5008	,	,		16769	0.0387		0.008	False		,,,				2504	0.001				p.N276S		Atlas-SNP	.											PRODH2,NS,carcinoma,0,1	PRODH2	68	1	0			c.A827G						PASS	.	C	SER/ASN	1113,3119		132,849,1135	24.0	28.0	27.0		827	-5.0	0.0	19	dbSNP_130	27	27,8263		0,27,4118	yes	missense-near-splice	PRODH2	NM_021232.1	46	132,876,5253	CC,CT,TT		0.3257,26.2996,9.104	benign	276/537	36298022	1140,11382	2116	4145	6261	SO:0001630	splice_region_variant	58510	exon6			TGGAGGTTCTAGG	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.826-1A>G	19.37:g.36298022T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	203	0.09294871794871795	173	0.3516260162601626	13	0.03591160220994475	13	0.022727272727272728	4	0.005277044854881266	C	0.021	-1.423479	0.01126	0.262996	0.003257	ENSG00000250799	ENST00000301175	T	0.31769	1.48	5.11	-5.04	0.02964	Proline dehydrogenase (1);	.	.	.	.	T	0.00012	0.0000	N	0.11313	0.125	0.48511	P	3.330000000000277E-4	B	0.10296	0.003	B	0.10450	0.005	T	0.44205	-0.9343	8	0.09590	T	0.72	.	15.4242	0.75038	0.0:0.5657:0.0:0.4343	.	276	Q9UF12	PROD2_HUMAN	S	276	ENSP00000301175:N276S	ENSP00000301175:N276S	N	-	2	0	PRODH2	40989862	0.350000	0.24878	0.006000	0.13384	0.128000	0.20619	-0.419000	0.07071	-1.895000	0.01104	-2.040000	0.00418	AAC	T|0.889;C|0.111	0.111	strong		0.532	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	Missense_Mutation
C16orf71	146562	hgsc.bcm.edu	37	16	4797457	4797457	+	Missense_Mutation	SNP	C	C	T	rs17853375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4797457C>T	ENST00000299320.5	+	9	1872	c.1394C>T	c.(1393-1395)cCt>cTt	p.P465L	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.P482L	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	465			P -> L (in dbSNP:rs17853375). {ECO:0000269|PubMed:15489334}.							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCTCAGGCCCCTGAAGACACA	0.647													C|||	2143	0.427915	0.0582	0.5086	5008	,	,		17368	0.6528		0.5994	False		,,,				2504	0.4622				p.P465L		Atlas-SNP	.											.	C16orf71	46	.	0			c.C1394T						PASS	.	C	LEU/PRO	621,3769		53,515,1627	30.0	35.0	33.0		1394	0.6	0.0	16	dbSNP_123	33	5119,3475		1552,2015,730	yes	missense	C16orf71	NM_139170.2	98	1605,2530,2357	TT,TC,CC		40.4352,14.1458,44.2083	probably-damaging	465/521	4797457	5740,7244	2195	4297	6492	SO:0001583	missense	146562	exon9			AGGCCCCTGAAGA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1394C>T	16.37:g.4797457C>T	ENSP00000299320:p.Pro465Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	1068	0.489010989010989	36	0.07317073170731707	187	0.5165745856353591	393	0.6870629370629371	452	0.5963060686015831	C	12.94	2.087887	0.36855	0.141458	0.595648	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.33654	1.4	4.89	0.549	0.17213	.	1.628840	0.03628	N	0.237451	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.14805	0.011	B	0.11329	0.006	T	0.48328	-0.9045	9	0.51188	T	0.08	0.0573	4.3323	0.11069	0.3111:0.5144:0.0:0.1745	rs17853375	465	Q8IYS4	CP071_HUMAN	L	465;220	ENSP00000299320:P465L	ENSP00000299320:P465L	P	+	2	0	C16orf71	4737458	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.107000	0.10873	-0.045000	0.13468	-0.521000	0.04368	CCT	C|0.555;G|0.000;T|0.445	0.445	strong		0.647	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
C14orf37	145407	hgsc.bcm.edu	37	14	58605790	58605790	+	Missense_Mutation	SNP	G	G	A	rs3829765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:58605790G>A	ENST00000267485.7	-	2	481	c.287C>T	c.(286-288)aCc>aTc	p.T96I	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	96			T -> I (in dbSNP:rs3829765).			integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TCCAGGCTGGGTTTCTTTGTT	0.483													G|||	1709	0.341254	0.2239	0.3415	5008	,	,		20976	0.2857		0.5129	False		,,,				2504	0.3804				p.T96I		Atlas-SNP	.											.	C14orf37	87	.	0			c.C287T						PASS	.	G	ILE/THR	1177,3229	414.6+/-336.9	174,829,1200	110.0	110.0	110.0		287	4.9	0.1	14	dbSNP_107	110	4640,3960	602.5+/-394.5	1260,2120,920	yes	missense	C14orf37	NM_001001872.2	89	1434,2949,2120	AA,AG,GG		46.0465,26.7136,44.7255	possibly-damaging	96/775	58605790	5817,7189	2203	4300	6503	SO:0001583	missense	145407	exon2			GGCTGGGTTTCTT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.287C>T	14.37:g.58605790G>A	ENSP00000267485:p.Thr96Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	156	88	0.564103	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	810	0.3708791208791209	117	0.23780487804878048	145	0.4005524861878453	172	0.3006993006993007	376	0.49604221635883905	G	16.97	3.269065	0.59540	0.267136	0.539535	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.22134	1.97	5.82	4.91	0.64330	.	0.612367	0.16344	N	0.218553	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;P;P	0.51351	0.944;0.904;0.904	P;P;P	0.52957	0.714;0.494;0.494	T	0.46748	-0.9169	9	0.66056	D	0.02	-0.7524	8.0769	0.30722	0.0847:0.168:0.7474:0.0	rs3829765;rs17254347;rs52807111;rs59160487;rs3829765	96;96;96	Q86TY3-2;A8K990;Q86TY3	.;.;CN037_HUMAN	I	96;134	ENSP00000267485:T96I	ENSP00000267485:T96I	T	-	2	0	C14orf37	57675543	0.002000	0.14202	0.065000	0.19835	0.051000	0.14879	0.605000	0.24179	1.417000	0.47077	0.655000	0.94253	ACC	G|0.593;A|0.407	0.407	strong		0.483	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
PRB3	5544	hgsc.bcm.edu	37	12	11420941	11420941	+	Missense_Mutation	SNP	G	G	T	rs61737269	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11420941G>T	ENST00000279573.7	-	3	377	c.242C>A	c.(241-243)cCa>cAa	p.P81Q	PRB3_ENST00000538488.1_Missense_Mutation_p.P81Q|PRB3_ENST00000381842.3_Missense_Mutation_p.P81Q|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	81	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			P -> Q (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			TTGTGGGGGTGGTCCTTCTGG	0.622													G|||	104	0.0207668	0.0038	0.0389	5008	,	,		13092	0.0		0.0666	False		,,,				2504	0.0051				p.P81Q		Atlas-SNP	.											PRB3_ENST00000538488,NS,carcinoma,0,2	PRB3	84	2	0			c.C242A						PASS	.	T	GLN/PRO	24,4296		1,22,2137	147.0	178.0	168.0		242	0.0	0.0	12	dbSNP_129	168	245,8299		9,227,4036	no	missense	PRB3	NM_006249.4	76	10,249,6173	TT,TG,GG		2.8675,0.5556,2.0911	probably-damaging	81/310	11420941	269,12595	2160	4272	6432	SO:0001583	missense	5544	exon3			GGGGGTGGTCCTT			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.242C>A	12.37:g.11420941G>T	ENSP00000279573:p.Pro81Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		79	0.036172161172161175	9	0.018292682926829267	16	0.04419889502762431	10	0.017482517482517484	44	0.05804749340369393	.	0.921	-0.715860	0.03206	0.005556	0.028675	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.04156	3.69;3.69	0.948	0.01	0.14081	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.20307	N	0.999916	D	0.89917	1.0	D	0.78314	0.991	T	0.32929	-0.9888	8	0.19590	T	0.45	.	4.2052	0.10485	0.0:0.0:0.6008:0.3992	.	81	Q04118	PRB3_HUMAN	Q	81	ENSP00000371264:P81Q;ENSP00000442626:P81Q	ENSP00000279573:P81Q	P	-	2	0	PRB3	11312208	0.374000	0.25081	0.021000	0.16686	0.012000	0.07955	0.340000	0.19892	-0.003000	0.14444	-1.048000	0.02349	CCA	G|0.961;T|0.039	0.039	strong		0.622	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152279729C>T	ENST00000368799.1	-	3	7668	c.7633G>A	c.(7633-7635)Gga>Aga	p.G2545R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2545	Ser-rich.		G -> R (in dbSNP:rs3126072).		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)			TGCGAGTGTCCAGAGCTGTCG	0.577									Ichthyosis				T|||	2378	0.47484	0.5658	0.451	5008	,	,		19229	0.6548		0.173	False		,,,				2504	0.4939				p.G2545R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.G7633A						PASS	.	T	ARG/GLY	2198,2202	581.0+/-385.3	593,1012,595	204.0	228.0	220.0		7633	0.8	0.0	1	dbSNP_103	220	1457,7143	750.7+/-407.4	126,1205,2969	no	missense	FLG	NM_002016.1	125	719,2217,3564	TT,TC,CC		16.9419,49.9545,28.1154	benign	2545/4062	152279729	3655,9345	2200	4300	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTGTCCAGAGCT	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.7633G>A	1.37:g.152279729C>T	ENSP00000357789:p.Gly2545Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	225	153	0.68	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	882	0.40384615384615385	256	0.5203252032520326	135	0.3729281767955801	358	0.6258741258741258	133	0.17546174142480211	T	2.868	-0.234541	0.05983	0.499545	0.169419	ENSG00000143631	ENST00000368799	T	0.01705	4.68	1.97	0.755	0.18415	.	.	.	.	.	T	0.00144	0.0004	N	0.00265	-1.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12656	-1.0539	8	0.14252	T	0.57	.	4.4439	0.11588	0.0:0.4317:0.0:0.5682	.	2545	P20930	FILA_HUMAN	R	2545	ENSP00000357789:G2545R	ENSP00000357789:G2545R	G	-	1	0	FLG	150546353	0.408000	0.25360	0.001000	0.08648	0.010000	0.07245	-0.243000	0.08915	-0.360000	0.08138	-0.848000	0.03037	GGA	C|0.682;T|0.318	0.318	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139442	178139442	+	Silent	SNP	T	T	G	rs1132338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178139442T>G	ENST00000335815.2	-	5	1634	c.1437A>C	c.(1435-1437)tcA>tcC	p.S479S		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	479					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|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.S479S(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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;0.185)		GAATGAGAGCTGAACTCTGTC	0.393													t|||	1429	0.285343	0.1694	0.2522	5008	,	,		20228	0.3343		0.2813	False		,,,				2504	0.4192				p.S479S		Atlas-SNP	.											ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.A1437C						scavenged	.	G		870,3536	333.1+/-302.8	94,682,1427	122.0	115.0	118.0		1437	0.9	1.0	5	dbSNP_86	118	2291,6309	377.8+/-338.7	324,1643,2333	no	coding-synonymous	ZNF354A	NM_005649.2		418,2325,3760	GG,GT,TT		26.6395,19.7458,24.3042		479/606	178139442	3161,9845	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			GAGAGCTGAACTC	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1437A>C	5.37:g.178139442T>G		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			.	.	weak		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
FAM221B	392307	hgsc.bcm.edu	37	9	35826058	35826058	+	Missense_Mutation	SNP	T	T	C	rs13294256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35826058T>C	ENST00000423537.2	-	2	370	c.101A>G	c.(100-102)cAt>cGt	p.H34R	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	34			H -> R (in dbSNP:rs13294256). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(4)	7						TTCAGAGATATGGTTCTCCTG	0.517											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	1148	0.229233	0.208	0.1988	5008	,	,		20257	0.375		0.1998	False		,,,				2504	0.1595				p.H34R		Atlas-SNP	.											.	FAM221B	38	.	0			c.A101G						PASS	.		ARG/HIS	731,3079		78,575,1252	75.0	76.0	76.0		101	-4.1	0.0	9	dbSNP_121	76	1570,6650		146,1278,2686	yes	missense	C9orf128	NM_001012446.2	29	224,1853,3938	CC,CT,TT		19.0998,19.1864,19.1272	benign	34/403	35826058	2301,9729	1905	4110	6015	SO:0001583	missense	392307	exon2			GAGATATGGTTCT	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.101A>G	9.37:g.35826058T>C	ENSP00000415299:p.His34Arg	Somatic	76	0	0	858	WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001012446	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	551	0.2522893772893773	105	0.21341463414634146	82	0.2265193370165746	220	0.38461538461538464	144	0.18997361477572558	t	5.958	0.360791	0.11296	0.191864	0.190998	ENSG00000204930	ENST00000423537;ENST00000377984;ENST00000472182	T;T;T	0.29397	2.6;2.33;1.57	3.8	-4.13	0.03904	.	1.108070	0.06941	N	0.812752	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	0.42732	-0.9434	9	0.08381	T	0.77	-20.1312	1.2171	0.01916	0.2466:0.1181:0.1707:0.4646	rs13294256;rs59381554	34	A6H8Z2	CI128_HUMAN	R	34	ENSP00000415299:H34R;ENSP00000367222:H34R;ENSP00000420279:H34R	ENSP00000367222:H34R	H	-	2	0	C9orf128	35816058	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	-3.012000	0.00647	-1.431000	0.01982	-2.108000	0.00357	CAT	T|0.764;C|0.236	0.236	strong		0.517	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446	
DST	667	hgsc.bcm.edu	37	6	56437729	56437729	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:56437729C>T	ENST00000361203.3	-	48	12744	c.12737G>A	c.(12736-12738)cGg>cAg	p.R4246Q	DST_ENST00000244364.6_Missense_Mutation_p.R1834Q|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.R2160Q|DST_ENST00000370788.2_Missense_Mutation_p.R2160Q|DST_ENST00000446842.2_Missense_Mutation_p.R3922Q|DST_ENST00000370769.4_Missense_Mutation_p.R4248Q|DST_ENST00000370754.5_Missense_Mutation_p.R4426Q			Q03001	DYST_HUMAN	dystonin	4246					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)			TTCTGAAAACCGAGCAGACAA	0.388																																					p.R1834Q		Atlas-SNP	.											DST_ENST00000370769,NS,carcinoma,0,2	DST	1427	2	0			c.G5501A						scavenged	.						109.0	95.0	99.0					6																	56437729		1858	4116	5974	SO:0001583	missense	667	exon33			GAAAACCGAGCAG	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	ENST00000361203.3:c.12737G>A	6.37:g.56437729C>T	ENSP00000354508:p.Arg4246Gln	Somatic	334	2	0.00598802		WXS	Illumina HiSeq	Phase_I	314	4	0.0127389	NM_015548	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	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	20.5	4.000733	0.74818	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.78	5.78	0.91487	.	0.000000	0.45606	D	0.000355	T	0.51635	0.1686	M	0.63428	1.95	0.31913	N	0.614395	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.997;0.995	D;D;D;P;P	0.81914	0.984;0.987;0.995;0.67;0.79	T	0.32798	-0.9893	9	0.34782	T	0.22	.	20.0175	0.97485	0.0:1.0:0.0:0.0	.	2160;4248;4426;4246;1834	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	Q	1834;4426;4248;2160;3922;2160;4246	ENSP00000244364:R1834Q;ENSP00000359790:R4426Q;ENSP00000359805:R4248Q;ENSP00000400883:R2160Q;ENSP00000393645:R3922Q;ENSP00000359824:R2160Q;ENSP00000354508:R4246Q	ENSP00000244364:R1834Q	R	-	2	0	DST	56545688	1.000000	0.71417	0.908000	0.35775	0.904000	0.53231	5.518000	0.67068	2.730000	0.93505	0.650000	0.86243	CGG	.	.	none		0.388	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
SLC22A12	116085	hgsc.bcm.edu	37	11	64359286	64359286	+	Silent	SNP	C	C	T	rs3825016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64359286C>T	ENST00000377574.1	+	1	1005	c.258C>T	c.(256-258)caC>caT	p.H86H	SLC22A12_ENST00000377567.2_Silent_p.H86H|SLC22A12_ENST00000336464.7_Silent_p.H86H|SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377572.1_Silent_p.H86H	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	86					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	AGAGGCCCCACCAGTGCCGCC	0.672													C|||	1939	0.387181	0.1014	0.4323	5008	,	,		12614	0.2192		0.7058	False		,,,				2504	0.5869				p.H86H		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C258T	GRCh37	CM063146	SLC22A12	M	rs3825016	PASS	.	C	,	909,3489		99,711,1389	24.0	28.0	27.0		258,	1.3	0.0	11	dbSNP_107	27	6085,2509		2167,1751,379	no	coding-synonymous,utr-5	SLC22A12	NM_144585.2,NM_153378.1	,	2266,2462,1768	TT,TC,CC		29.1948,20.6685,46.1669	,	86/554,	64359286	6994,5998	2199	4297	6496	SO:0001819	synonymous_variant	116085	exon1			GCCCCACCAGTGC	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"""Solute carriers"""	17989	protein-coding gene	gene with protein product		607096	"""solute carrier family 22 (organic anion/cation transporter), member 12"""			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.258C>T	11.37:g.64359286C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	37	CCDS8075.1																																																																																			C|0.512;T|0.488	0.488	strong		0.672	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
SLCO5A1	81796	hgsc.bcm.edu	37	8	70588878	70588878	+	Silent	SNP	T	T	C	rs10448034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:70588878T>C	ENST00000260126.4	-	9	2761	c.2055A>G	c.(2053-2055)gcA>gcG	p.A685A	SLCO5A1_ENST00000524945.1_Intron|SLCO5A1_ENST00000530307.1_Silent_p.A630A	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	685						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			GCATTCCCAGTGCAAAAGGTC	0.418													C|||	520	0.103834	0.1551	0.1009	5008	,	,		19120	0.005		0.161	False		,,,				2504	0.0798				p.A685A		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.A2055G						PASS	.	C	,,	589,3817	771.7+/-413.8	28,533,1642	157.0	133.0	141.0		,1890,2055	-12.3	0.0	8	dbSNP_119	141	1407,7193	753.5+/-407.4	114,1179,3007	yes	intron,coding-synonymous,coding-synonymous	SLCO5A1	NM_001146008.1,NM_001146009.1,NM_030958.2	,,	142,1712,4649	CC,CT,TT		16.3605,13.3681,15.3468	,,	,630/794,685/849	70588878	1996,11010	2203	4300	6503	SO:0001819	synonymous_variant	81796	exon9			TCCCAGTGCAAAA	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"""Solute carriers"""	19046	protein-coding gene	gene with protein product		613543	"""solute carrier family 21 (organic anion transporter), member 15"""	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.2055A>G	8.37:g.70588878T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Silent	SNP	ENST00000260126.4	37	CCDS6205.1																																																																																			T|0.864;C|0.136	0.136	strong		0.418	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958	
KRT75	9119	hgsc.bcm.edu	37	12	52825363	52825363	+	Silent	SNP	G	G	A	rs1798640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52825363G>A	ENST00000252245.5	-	4	1054	c.834C>T	c.(832-834)ccC>ccT	p.P278P		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	278	Coil 1B.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGATCTCCTCGGGCAGAGATT	0.498													G|||	3070	0.613019	0.6422	0.6888	5008	,	,		19946	0.6825		0.6143	False		,,,				2504	0.4468				p.P278P		Atlas-SNP	.											.	KRT75	75	.	0			c.C834T						PASS	.	G		2729,1677	656.1+/-400.0	843,1043,317	178.0	153.0	162.0		834	-12.1	0.0	12	dbSNP_89	162	5143,3457	636.0+/-399.0	1531,2081,688	no	coding-synonymous	KRT75	NM_004693.2		2374,3124,1005	AA,AG,GG		40.1977,38.0617,39.4741		278/552	52825363	7872,5134	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon4			CTCCTCGGGCAGA	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.834C>T	12.37:g.52825363G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			G|0.370;A|0.630	0.630	strong		0.498	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
TMEM186	25880	hgsc.bcm.edu	37	16	8890322	8890322	+	Silent	SNP	G	G	A	rs74689268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:8890322G>A	ENST00000333050.6	-	2	162	c.129C>T	c.(127-129)atC>atT	p.I43I	PMM2_ENST00000566983.1_Intron|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000539622.1_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000569958.1_5'Flank|PMM2_ENST00000268261.4_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	43						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						TCTCCTTCGAGATGGGTGAAC	0.532													G|||	21	0.00419329	0.0008	0.0043	5008	,	,		22464	0.0		0.0129	False		,,,				2504	0.0041				p.I43I		Atlas-SNP	.											.	TMEM186	21	.	0			c.C129T						PASS	.	G		20,4374	27.2+/-55.0	0,20,2177	122.0	127.0	125.0		129	1.6	0.0	16	dbSNP_132	125	190,8410	84.8+/-147.2	1,188,4111	no	coding-synonymous	TMEM186	NM_015421.3		1,208,6288	AA,AG,GG		2.2093,0.4552,1.6161		43/214	8890322	210,12784	2197	4300	6497	SO:0001819	synonymous_variant	25880	exon2			CTTCGAGATGGGT	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 51"""	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.129C>T	16.37:g.8890322G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_015421	B2RAY0|Q9Y4T4	Silent	SNP	ENST00000333050.6	37	CCDS10535.1																																																																																			G|0.986;A|0.014	0.014	strong		0.532	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421	
UGT1A3	54659	hgsc.bcm.edu	37	2	234637803	234637803	+	Missense_Mutation	SNP	T	T	C	rs3821242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234637803T>C	ENST00000482026.1	+	1	50	c.31T>C	c.(31-33)Tgg>Cgg	p.W11R	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.W11R|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	11			W -> R (in dbSNP:rs3821242). {ECO:0000269|PubMed:19204906}.		cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	TCCCCTGCCGTGGCTGGCCAC	0.587											OREG0003835	type=REGULATORY REGION|Gene=UGT1A3|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2679	0.534944	0.6974	0.5101	5008	,	,		18298	0.3552		0.4145	False		,,,				2504	0.6421				p.W11R		Atlas-SNP	.											UGT1A3,colon,carcinoma,0,1	UGT1A3	91	1	0			c.T31C	GRCh37	CM042128	UGT1A3	M	rs3821242	PASS	.	C	,,,,,,ARG/TRP,,	2766,1638	618.1+/-393.1	890,986,326	55.0	56.0	56.0		,,,,,,31,,	-6.8	0.0	2	dbSNP_107	56	3816,4782	506.5+/-376.6	833,2150,1316	no	intron,intron,intron,intron,intron,intron,missense,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,101,,	1723,3136,1642	CC,CT,TT		44.3824,37.1935,49.377	,,,,,,,,	,,,,,,11/535,,	234637803	6582,6420	2202	4299	6501	SO:0001583	missense	54659	exon1			CTGCCGTGGCTGG	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.31T>C	2.37:g.234637803T>C	ENSP00000418532:p.Trp11Arg	Somatic	156	0	0	2375	WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	37	CCDS2509.1	963	0.4409340659340659	323	0.6565040650406504	169	0.46685082872928174	172	0.3006993006993007	299	0.3944591029023747	t	5.567	0.289422	0.10567	0.628065	0.443824	ENSG00000243135	ENST00000482026	T	0.59083	0.29	3.52	-6.75	0.01738	.	.	.	.	.	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	0.40794	-0.9544	8	0.33141	T	0.24	.	1.1348	0.01752	0.2222:0.2725:0.1161:0.3893	rs3821242;rs17869158;rs57799629	11;11	Q5DT01;P35503	.;UD13_HUMAN	R	11	ENSP00000418532:W11R	ENSP00000418532:W11R	W	+	1	0	UGT1A3	234302542	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.001000	0.00652	-2.064000	0.00888	-2.727000	0.00130	TGG	T|0.511;C|0.489	0.489	strong		0.587	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
TAS2R13	50838	hgsc.bcm.edu	37	12	11061122	11061122	+	Missense_Mutation	SNP	T	T	C	rs1015443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11061122T>C	ENST00000390677.2	-	1	1039	c.776A>G	c.(775-777)aAc>aGc	p.N259S	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	259			N -> S (in dbSNP:rs1015443). {ECO:0000269|PubMed:15489334}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						GATCACTGTGTTCTGATACAG	0.388													T|||	2606	0.520367	0.1528	0.5908	5008	,	,		18568	0.7242		0.6243	False		,,,				2504	0.6503				p.N259S		Atlas-SNP	.											.	TAS2R13	29	.	0			c.A776G						PASS	.	T	SER/ASN	967,3439	363.9+/-316.7	114,739,1350	91.0	83.0	86.0		776	0.2	0.0	12	dbSNP_86	86	5005,3595	625.9+/-397.8	1470,2065,765	yes	missense	TAS2R13	NM_023920.2	46	1584,2804,2115	CC,CT,TT		41.8023,21.9473,45.9173	benign	259/304	11061122	5972,7034	2203	4300	6503	SO:0001583	missense	50838	exon1			ACTGTGTTCTGAT	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.776A>G	12.37:g.11061122T>C	ENSP00000375095:p.Asn259Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_023920	Q4G0I5|Q502V8|Q645X2	Missense_Mutation	SNP	ENST00000390677.2	37	CCDS8635.1	1180	0.5402930402930403	81	0.16463414634146342	221	0.6104972375690608	409	0.715034965034965	469	0.6187335092348285	T	4.365	0.067332	0.08388	0.219473	0.581977	ENSG00000212128	ENST00000390677	T	0.00760	5.73	2.71	0.219	0.15274	.	0.840598	0.09541	N	0.788221	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.19935	0.04	B	0.31390	0.129	T	0.00842	-1.1544	9	0.25751	T	0.34	.	4.853	0.13545	0.0:0.2661:0.0:0.7339	rs1015443;rs17743263;rs52835765;rs59560426;rs1015443	259	Q9NYV9	T2R13_HUMAN	S	259	ENSP00000375095:N259S	ENSP00000375095:N259S	N	-	2	0	TAS2R13	10952389	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-1.097000	0.03349	-0.077000	0.12752	0.377000	0.23210	AAC	T|0.499;C|0.501	0.501	strong		0.388	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607492	84607492	+	Missense_Mutation	SNP	C	C	T	rs190878253		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84607492C>T	ENST00000344803.2	+	4	2154	c.2107C>T	c.(2107-2109)Ccc>Tcc	p.P703S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	703					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATGGGGCCTGCCCCGCAGAAT	0.473																																					p.P703S		Atlas-SNP	.											.	.	.	.	0			c.C2107T						PASS	.						59.0	57.0	58.0					9																	84607492		1839	4077	5916	SO:0001583	missense	389763	exon4			GGCCTGCCCCGCA		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.2107C>T	9.37:g.84607492C>T	ENSP00000341988:p.Pro703Ser	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	272	62	0.227941	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.61	2.587655	0.46110	.	.	ENSG00000214929	ENST00000344803	T	0.24151	1.87	3.51	2.51	0.30379	.	0.258257	0.27946	N	0.017208	T	0.48624	0.1510	M	0.85462	2.755	0.19945	N	0.999942	D	0.64830	0.994	D	0.71184	0.972	T	0.22173	-1.0224	10	0.66056	D	0.02	-8.1379	8.1735	0.31268	0.0:0.7513:0.2486:0.0	.	703	Q6ZQQ2	F75D1_HUMAN	S	703	ENSP00000341988:P703S	ENSP00000341988:P703S	P	+	1	0	FAM75D1	83797312	0.161000	0.22892	0.349000	0.25694	0.013000	0.08279	1.044000	0.30329	1.978000	0.57642	0.561000	0.74099	CCC	C|0.999;T|0.001	0.001	strong		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
CBL	867	hgsc.bcm.edu	37	11	119168130	119168130	+	Silent	SNP	G	G	C	rs143840974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119168130G>C	ENST00000264033.4	+	14	2566	c.2190G>C	c.(2188-2190)acG>acC	p.T730T		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	730	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T730T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		ATAGCTGTACGTATGAAGCAA	0.393			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	2	0.000399361	0.0	0.0	5008	,	,		20497	0.0		0.002	False		,,,				2504	0.0				p.T730T		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	CBL,NS,haematopoietic_neoplasm,0,1	CBL	408	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2190C						PASS	.	G		2,4396	4.2+/-10.8	0,2,2197	117.0	106.0	110.0		2190	-10.6	0.2	11	dbSNP_134	110	28,8562	19.8+/-62.0	0,28,4267	no	coding-synonymous	CBL	NM_005188.2		0,30,6464	CC,CG,GG		0.326,0.0455,0.231		730/907	119168130	30,12958	2199	4295	6494	SO:0001819	synonymous_variant	867	exon14	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	CTGTACGTATGAA	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2190G>C	11.37:g.119168130G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			G|0.997;C|0.003	0.003	strong		0.393	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351500	134351500	+	Silent	SNP	C	C	T	rs113338693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134351500C>T	ENST00000357304.4	+	15	4039	c.3984C>T	c.(3982-3984)ccC>ccT	p.P1328P	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1328							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						TGTGGGGACCCGAGGAGGAGC	0.682											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	243	0.0485224	0.0091	0.1383	5008	,	,		14582	0.0546		0.0577	False		,,,				2504	0.0225				p.P1328P		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C3984T						PASS	.	C		73,3701		1,71,1815	27.0	34.0	32.0		3984	-11.3	0.0	9	dbSNP_132	32	372,7844		12,348,3748	no	coding-synonymous	PRRC2B	NM_013318.3		13,419,5563	TT,TC,CC		4.5278,1.9343,3.7114		1328/2230	134351500	445,11545	1887	4108	5995	SO:0001819	synonymous_variant	84726	exon15			GGGACCCGAGGAG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3984C>T	9.37:g.134351500C>T		Somatic	17	0	0	1610	WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	123	0.05631868131868132	6	0.012195121951219513	40	0.11049723756906077	34	0.05944055944055944	43	0.05672823218997362	C	2.521	-0.310833	0.05458	0.019343	0.045278	ENSG00000130723	ENST00000451855	.	.	.	5.66	-11.3	0.00108	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.364	0.04314	0.1886:0.254:0.0846:0.4729	.	.	.	.	X	62	.	.	R	+	1	2	PRRC2B	133341321	0.000000	0.05858	0.009000	0.14445	0.639000	0.38242	-5.361000	0.00128	-3.751000	0.00111	-0.857000	0.03018	CGA	C|0.943;T|0.057	0.057	strong		0.682	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TSPO	706	hgsc.bcm.edu	37	22	43558972	43558972	+	Silent	SNP	G	G	A	rs41371752|rs6972	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000583777.1_Missense_Mutation_p.R58H|TSPO_ENST00000337554.3_Missense_Mutation_p.R162H			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	81	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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	
PTPN21	11099	hgsc.bcm.edu	37	14	88935925	88935925	+	Silent	SNP	A	A	G	rs2297129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	141	0	0		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	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		
ANKRD18A	253650	hgsc.bcm.edu	37	9	38577092	38577092	+	Missense_Mutation	SNP	C	C	G	rs2993206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:38577092C>G	ENST00000399703.5	-	14	3073	c.2699G>C	c.(2698-2700)gGa>gCa	p.G900A	ANKRD18A_ENST00000357072.5_5'UTR|ANKRD18A_ENST00000313339.3_Missense_Mutation_p.G21A|ANKRD18A_ENST00000566717.2_Missense_Mutation_p.G38A|ANKRD18A_ENST00000607974.1_Missense_Mutation_p.G21A	NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	900				G -> A (in Ref. 1; BAC23111 and 4; AAI52435). {ECO:0000305}.						NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TTTCACTGCTCCTGCAAAGGC	0.313													.|||	285	0.0569089	0.1422	0.0403	5008	,	,		16716	0.0		0.0139	False		,,,				2504	0.0562				p.G900A		Atlas-SNP	.											.	ANKRD18A	49	.	0			c.G2699C						PASS	.						32.0	27.0	28.0					9																	38577092		692	1583	2275	SO:0001583	missense	253650	exon14			ACTGCTCCTGCAA	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.2699G>C	9.37:g.38577092C>G	ENSP00000382610:p.Gly900Ala	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	115	41	0.356522	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	80	0.03663003663003663	51	0.10365853658536585	18	0.049723756906077346	0	0.0	11	0.014511873350923483	c	0.001	-3.004484	0.00044	.	.	ENSG00000180071	ENST00000313339;ENST00000357072;ENST00000399703	T;T	0.27256	1.68;1.68	1.53	-3.06	0.05379	.	.	.	.	.	T	0.00241	0.0007	N	0.04768	-0.165	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.12156	0.007;0.0	T	0.22034	-1.0228	9	0.20046	T	0.44	.	0.2367	0.00187	0.3844:0.1539:0.2038:0.2579	rs2993206;rs2993206	21;900	Q6QA70;Q8IVF6	.;AN18A_HUMAN	A	21;21;900	ENSP00000326555:G21A;ENSP00000382610:G900A	ENSP00000326555:G21A	G	-	2	0	ANKRD18A	38567092	0.010000	0.17322	0.000000	0.03702	0.000000	0.00434	-0.055000	0.11807	-2.538000	0.00487	-3.716000	0.00023	GGA	C|0.968;G|0.032	0.032	strong		0.313	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
CACHD1	57685	hgsc.bcm.edu	37	1	65098309	65098309	+	Silent	SNP	G	G	A	rs61731122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:65098309G>A	ENST00000371073.2	+	6	672	c.672G>A	c.(670-672)ccG>ccA	p.P224P	CACHD1_ENST00000495994.1_Intron|CACHD1_ENST00000290039.5_Silent_p.P173P			Q5VU97	CAHD1_HUMAN	cache domain containing 1	224					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						CAGTCCGGCCGCAGTCAAAGC	0.537													G|||	45	0.00898562	0.0008	0.0072	5008	,	,		20119	0.0		0.0368	False		,,,				2504	0.002				p.P173P		Atlas-SNP	.											.	CACHD1	125	.	0			c.G519A						PASS	.	G		31,4049		0,31,2009	102.0	104.0	103.0		519	-11.3	0.4	1	dbSNP_129	103	269,8111		7,255,3928	no	coding-synonymous	CACHD1	NM_020925.2		7,286,5937	AA,AG,GG		3.21,0.7598,2.4077		173/1224	65098309	300,12160	2040	4190	6230	SO:0001819	synonymous_variant	57685	exon6			CCGGCCGCAGTCA	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.672G>A	1.37:g.65098309G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																				G|0.983;A|0.017	0.017	strong		0.537	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
NLRP4	147945	hgsc.bcm.edu	37	19	56390237	56390237	+	Missense_Mutation	SNP	A	A	T	rs302453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	172	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	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	
RASA3	22821	hgsc.bcm.edu	37	13	114780764	114780764	+	Silent	SNP	A	A	G	rs2274717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:114780764A>G	ENST00000334062.7	-	14	1447	c.1326T>C	c.(1324-1326)acT>acC	p.T442T	RASA3_ENST00000389544.4_Silent_p.T410T	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	442	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|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)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CCCCAGACTCAGTGATGGCGT	0.642													N|||	3635	0.725839	0.9183	0.6585	5008	,	,		16916	0.6558		0.6461	False		,,,				2504	0.6677				p.T442T		Atlas-SNP	.											.	RASA3	83	.	0			c.T1326C						PASS	.	G		3787,619	267.1+/-267.6	1636,515,52	120.0	103.0	109.0		1326	-1.8	0.1	13	dbSNP_100	109	5445,3155	478.5+/-369.9	1715,2015,570	no	coding-synonymous	RASA3	NM_007368.2		3351,2530,622	GG,GA,AA		36.686,14.049,29.0174		442/835	114780764	9232,3774	2203	4300	6503	SO:0001819	synonymous_variant	22821	exon14			AGACTCAGTGATG		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1326T>C	13.37:g.114780764A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	37	CCDS32016.1																																																																																			A|0.286;G|0.714	0.714	strong		0.642	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
CARD16	114769	hgsc.bcm.edu	37	11	104912221	104912221	+	Missense_Mutation	SNP	T	T	A	rs542571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:104912221T>A	ENST00000375706.2	-	3	517	c.500A>T	c.(499-501)aAc>aTc	p.N167I	CASP1_ENST00000593315.1_Intron|CASP1_ENST00000598974.1_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000415981.2_Intron	NM_001017534.1	NP_001017534.1	Q5EG05	CAR16_HUMAN	caspase recruitment domain family, member 16	167			N -> I (in dbSNP:rs542571).		regulation of apoptotic process (GO:0042981)		cysteine-type endopeptidase inhibitor activity (GO:0004869)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	11						CAGAAGTATGTTCCTCCAGAA	0.368													.|||	1095	0.21865	0.4244	0.2939	5008	,	,		20036	0.0069		0.1799	False		,,,				2504	0.1452				p.N167I		Atlas-SNP	.											.	CARD16	29	.	0			c.A500T						PASS	.	A	,ILE/ASN	1699,2705		340,1019,843	81.0	83.0	82.0		,500	0.2	0.0	11	dbSNP_83	82	1428,7170		130,1168,3001	yes	utr-3,missense	CARD16	NM_052889.2,NM_001017534.1	,149	470,2187,3844	AA,AT,TT		16.6085,38.5786,24.0501	,benign	,167/198	104912221	3127,9875	2202	4299	6501	SO:0001583	missense	114769	exon3			AGTATGTTCCTCC		CCDS31661.1, CCDS41705.1	11q23	2008-09-15				ENSG00000204397			33701	protein-coding gene	gene with protein product		615680				11432859, 11536016	Standard	NM_052889		Approved	COP1, COP, PSEUDO-ICE		Q5EG05		ENST00000375706.2:c.500A>T	11.37:g.104912221T>A	ENSP00000364858:p.Asn167Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	47	0.734375	NM_001017534	Q96RJ9	Missense_Mutation	SNP	ENST00000375706.2	37	CCDS31661.1	433	0.19826007326007325	205	0.4166666666666667	100	0.27624309392265195	2	0.0034965034965034965	126	0.1662269129287599	.	0.003	-2.417365	0.00188	0.385786	0.166085	ENSG00000204397	ENST00000375706	T	0.19394	2.15	1.36	0.171	0.15026	.	0.975408	0.08410	N	0.949995	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	0.45160	-0.9280	9	0.07482	T	0.82	.	1.5094	0.02493	0.4768:0.0:0.2154:0.3078	rs542571;rs542571	167	Q5EG05	CAR16_HUMAN	I	167	ENSP00000364858:N167I	ENSP00000364858:N167I	N	-	2	0	CARD16	104417431	0.001000	0.12720	0.003000	0.11579	0.021000	0.10359	-0.047000	0.11963	-0.424000	0.07382	-0.827000	0.03088	AAC	T|0.776;A|0.224	0.224	strong		0.368	CARD16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388147.1		
PAPSS1	9061	hgsc.bcm.edu	37	4	108575955	108575955	+	Missense_Mutation	SNP	G	G	A	rs35176475	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	158	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	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		
TCEA3	6920	hgsc.bcm.edu	37	1	23743859	23743859	+	Missense_Mutation	SNP	T	T	C	rs192746462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23743859T>C	ENST00000450454.2	-	4	369	c.263A>G	c.(262-264)gAa>gGa	p.E88G	TCEA3_ENST00000461794.1_Missense_Mutation_p.E51G|TCEA3_ENST00000374601.3_Missense_Mutation_p.E88G	NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	88					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)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ctctcctttttctcctTTTGG	0.493													T|||	9	0.00179712	0.0	0.0043	5008	,	,		19825	0.0		0.004	False		,,,				2504	0.002				p.E88G		Atlas-SNP	.											.	TCEA3	20	.	0			c.A263G						PASS	.	T	GLY/GLU	2,3698		0,2,1848	92.0	90.0	90.0		263	5.0	1.0	1		90	43,8161		0,43,4059	yes	missense	TCEA3	NM_003196.1	98	0,45,5907	CC,CT,TT		0.5241,0.0541,0.378	possibly-damaging	88/349	23743859	45,11859	1850	4102	5952	SO:0001583	missense	6920	exon4			CCTTTTTCTCCTT	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.263A>G	1.37:g.23743859T>C	ENSP00000406293:p.Glu88Gly	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_003196	A8K2K7|Q5DR83	Missense_Mutation	SNP	ENST00000450454.2	37	CCDS44086.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	13.93	2.384002	0.42308	5.41E-4	0.005241	ENSG00000204219	ENST00000450454;ENST00000374601	.	.	.	5.02	5.02	0.67125	Transcription factor IIS, N-terminal (2);	0.911073	0.09406	N	0.806532	T	0.24661	0.0598	N	0.24115	0.695	0.24955	N	0.991769	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09143	-1.0688	9	0.48119	T	0.1	-12.8917	11.3324	0.49484	0.0:0.0:0.0:1.0	.	88;88	A8K2K7;O75764	.;TCEA3_HUMAN	G	88	.	ENSP00000363729:E88G	E	-	2	0	TCEA3	23616446	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.690000	0.37711	2.244000	0.73946	0.533000	0.62120	GAA	T|0.998;C|0.002	0.002	strong		0.493	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	
SPSB4	92369	hgsc.bcm.edu	37	3	140785175	140785175	+	Silent	SNP	C	C	A	rs890529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:140785175C>A	ENST00000310546.2	+	2	973	c.229C>A	c.(229-231)Cgg>Agg	p.R77R		NM_080862.1	NP_543138.1	Q96A44	SPSB4_HUMAN	splA/ryanodine receptor domain and SOCS box containing 4	77	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	4						CACCTTCCACCGGCACCCCGT	0.736													C|||	2150	0.429313	0.7148	0.3602	5008	,	,		12691	0.3571		0.2455	False		,,,				2504	0.3558				p.R77R		Atlas-SNP	.											.	SPSB4	19	.	0			c.C229A						PASS	.	C		2664,1616		874,916,350	14.0	12.0	12.0		229	3.4	1.0	3	dbSNP_86	12	1857,6623		273,1311,2656	yes	coding-synonymous	SPSB4	NM_080862.1		1147,2227,3006	AA,AC,CC		21.8986,37.757,35.431		77/274	140785175	4521,8239	2140	4240	6380	SO:0001819	synonymous_variant	92369	exon2			TTCCACCGGCACC		CCDS3115.1	3q23	2008-02-05			ENSG00000175093	ENSG00000175093			30630	protein-coding gene	gene with protein product		611660				12076535	Standard	NM_080862		Approved	SSB-4	uc003ett.3	Q96A44	OTTHUMG00000160223	ENST00000310546.2:c.229C>A	3.37:g.140785175C>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_080862		Silent	SNP	ENST00000310546.2	37	CCDS3115.1																																																																																			C|0.613;A|0.387	0.387	strong		0.736	SPSB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359727.1	NM_080862	
CAMK2D	817	hgsc.bcm.edu	37	4	114429407	114429407	+	Intron	SNP	C	C	T	rs11098193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:114429407C>T	ENST00000342666.5	-	13	984				CAMK2D_ENST00000505990.1_Intron|CAMK2D_ENST00000514328.1_Intron|CAMK2D_ENST00000379773.2_Intron|CAMK2D_ENST00000429180.1_Intron|CAMK2D_ENST00000454265.2_Silent_p.S334S|CAMK2D_ENST00000394522.3_Intron|CAMK2D_ENST00000508738.1_Silent_p.S334S|CAMK2D_ENST00000296402.5_Intron|CAMK2D_ENST00000394524.3_Intron|CAMK2D_ENST00000394526.2_Silent_p.S334S|CAMK2D_ENST00000511664.1_Intron|CAMK2D_ENST00000515496.1_Silent_p.S334S|CAMK2D_ENST00000418639.2_Intron			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta						calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|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 cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		TCTGAACACTCGAACTGGACT	0.353													C|||	646	0.128994	0.0348	0.1556	5008	,	,		17779	0.0883		0.2714	False		,,,				2504	0.1329				p.S334S		Atlas-SNP	.											.	CAMK2D	55	.	0			c.G1002A						PASS	.	C	,,,,,	214,2888		10,194,1347	52.0	44.0	46.0		,,,,,1002	5.6	1.0	4	dbSNP_120	46	1597,5443		188,1221,2111	no	intron,intron,intron,intron,intron,coding-synonymous	CAMK2D	NM_001221.3,NM_172114.1,NM_172115.2,NM_172127.2,NM_172128.2,NM_172129.1	,,,,,	198,1415,3458	TT,TC,CC		22.6847,6.8988,17.8564	,,,,,	,,,,,334/490	114429407	1811,8331	1551	3520	5071	SO:0001627	intron_variant	817	exon14			AACACTCGAACTG	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.984+1386G>A	4.37:g.114429407C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_172129	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1																																																																																			C|0.853;T|0.147	0.147	strong		0.353	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
CUL3	8452	hgsc.bcm.edu	37	2	225346646	225346646	+	Silent	SNP	T	T	C	rs2070127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:225346646T>C	ENST00000264414.4	-	14	2330	c.1992A>G	c.(1990-1992)caA>caG	p.Q664Q	CUL3_ENST00000344951.4_Silent_p.Q598Q|CUL3_ENST00000409777.1_Silent_p.Q640Q|CUL3_ENST00000409096.1_Silent_p.Q640Q	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	664					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGGATGTGAATTGATCATTAA	0.318													T|||	1165	0.232628	0.2534	0.2262	5008	,	,		15330	0.2401		0.1312	False		,,,				2504	0.3057				p.Q670Q		Atlas-SNP	.											.	CUL3	96	.	0			c.A2010G						PASS	.	T		1119,3287	398.5+/-330.9	163,793,1247	124.0	122.0	123.0		1992	2.1	1.0	2	dbSNP_96	123	1149,7451	236.0+/-268.3	86,977,3237	no	coding-synonymous	CUL3	NM_003590.3		249,1770,4484	CC,CT,TT		13.3605,25.3972,17.4381		664/769	225346646	2268,10738	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon14			TGTGAATTGATCA	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1992A>G	2.37:g.225346646T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	37	CCDS2462.1																																																																																			T|0.816;C|0.184	0.184	strong		0.318	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
PUS3	83480	hgsc.bcm.edu	37	11	125766044	125766044	+	Missense_Mutation	SNP	C	C	A	rs549990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125766044C>A	ENST00000530811.1	-	1	181	c.136G>T	c.(136-138)Gca>Tca	p.A46S	HYLS1_ENST00000425380.2_Intron|PUS3_ENST00000227474.3_Missense_Mutation_p.A46S|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	46			A -> S (in dbSNP:rs549990). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.A46S(1)		NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	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;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		CCAGCTCCTGCTGAATTTTCT	0.448													A|||	3192	0.63738	0.6074	0.6023	5008	,	,		20694	0.6964		0.673	False		,,,				2504	0.6053				p.A46S		Atlas-SNP	.											PUS3,NS,carcinoma,0,1	PUS3	33	1	1	Substitution - Missense(1)	prostate(1)	c.G136T						PASS	.	A	,SER/ALA,	2755,1647	504.7+/-365.9	846,1063,292	225.0	224.0	224.0		,136,	3.9	0.6	11	dbSNP_83	224	5857,2741	436.6+/-358.4	2003,1851,445	yes	intron,missense,intron	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	,99,	2849,2914,737	AA,AC,CC		31.8795,37.4148,33.7538	,benign,	,46/482,	125766044	8612,4388	2201	4299	6500	SO:0001583	missense	83480	exon2			CTCCTGCTGAATT	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.136G>T	11.37:g.125766044C>A	ENSP00000432386:p.Ala46Ser	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	291	156	0.536082	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	1434	0.6565934065934066	301	0.6117886178861789	225	0.6215469613259669	402	0.7027972027972028	506	0.6675461741424802	A	0.006	-2.066169	0.00382	0.625852	0.681205	ENSG00000110060	ENST00000227474;ENST00000530811;ENST00000534158;ENST00000529801	T;T;T;T	0.55234	1.49;1.49;0.53;1.55	5.11	3.91	0.45181	.	0.627475	0.15533	N	0.257382	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	0.43540	-0.9385	9	0.07175	T	0.84	-0.1633	2.1408	0.03775	0.5881:0.1507:0.116:0.1452	rs549990;rs1285175;rs1285316;rs1285709;rs17856119;rs52794946;rs61539703;rs549990	46	Q9BZE2	PUS3_HUMAN	S	46	ENSP00000227474:A46S;ENSP00000432386:A46S;ENSP00000432272:A46S;ENSP00000437077:A46S	ENSP00000227474:A46S	A	-	1	0	PUS3	125271254	0.000000	0.05858	0.629000	0.29254	0.303000	0.27691	0.706000	0.25690	1.082000	0.41137	-0.310000	0.09108	GCA	C|0.337;A|0.663	0.663	strong		0.448	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68130065	68130065	+	Missense_Mutation	SNP	T	T	C	rs200528352		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:68130065T>C	ENST00000262215.3	-	32	4954	c.4565A>G	c.(4564-4566)aAa>aGa	p.K1522R	ARFGEF1_ENST00000518230.1_Missense_Mutation_p.K360R|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.K976R	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1522					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GTTGCAAGTTTTATCCCAGAT	0.343																																					p.K1522R		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.A4565G						PASS	.						105.0	104.0	104.0					8																	68130065		2203	4300	6503	SO:0001583	missense	10565	exon32			CAAGTTTTATCCC	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4565A>G	8.37:g.68130065T>C	ENSP00000262215:p.Lys1522Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.339243	0.60963	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.48522	0.81;0.81;0.81	5.48	5.48	0.80851	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41558	0.1164	L	0.40543	1.245	0.58432	D	0.999994	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.18561	0.022;0.003;0.003	T	0.19712	-1.0297	10	0.35671	T	0.21	.	15.8539	0.78960	0.0:0.0:0.0:1.0	.	1522;1000;976	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	R	976;1522;360	ENSP00000428429:K976R;ENSP00000262215:K1522R;ENSP00000430891:K360R	ENSP00000262215:K1522R	K	-	2	0	ARFGEF1	68292619	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.153000	0.71819	2.199000	0.70637	0.533000	0.62120	AAA	.	.	weak		0.343	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230399	23230399	+	Missense_Mutation	SNP	G	G	C	rs531309531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230399G>C	ENST00000526893.1	+	1	440	c.166G>C	c.(166-168)Gtt>Ctt	p.V56L	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.V56L|IGLL5_ENST00000531372.1_Missense_Mutation_p.V56L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	56						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGGAGCCTCAGTTGGAAGCAG	0.667													G|||	2	0.000399361	0.0008	0.0	5008	,	,		10555	0.0		0.001	False		,,,				2504	0.0				p.V56L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G166C						PASS	.																																			SO:0001583	missense	100423062	exon1			GCCTCAGTTGGAA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.166G>C	22.37:g.23230399G>C	ENSP00000431254:p.Val56Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	35	0.324074	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.282876	0.23392	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00573	6.48;6.48	3.92	-7.84	0.01196	.	.	.	.	.	T	0.00412	0.0013	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47058	-0.9146	9	0.87932	D	0	.	3.3385	0.07110	0.5698:0.1407:0.1627:0.1268	.	56	B9A064	IGLL5_HUMAN	L	56	ENSP00000436353:V56L;ENSP00000431254:V56L	ENSP00000431254:V56L	V	+	1	0	IGLL5	21560399	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.883000	0.04170	-1.783000	0.01274	-0.152000	0.13540	GTT	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
CABS1	85438	hgsc.bcm.edu	37	4	71201943	71201943	+	Silent	SNP	A	A	G	rs13039	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	95	55	0.578947	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	
VWA3A	146177	hgsc.bcm.edu	37	16	22144318	22144318	+	Missense_Mutation	SNP	C	C	T	rs1105929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:22144318C>T	ENST00000389398.5	+	20	2066	c.1970C>T	c.(1969-1971)aCa>aTa	p.T657I	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	657	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> I (in dbSNP:rs1105929). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		ATGGACACCACACCCCCTGCC	0.627													c|||	3000	0.599042	0.8177	0.353	5008	,	,		17039	0.7788		0.2734	False		,,,				2504	0.6278				p.T657I		Atlas-SNP	.											.	VWA3A	115	.	0			c.C1970T						PASS	.	T	ILE/THR	2900,1284		1007,886,199	45.0	50.0	48.0		1970	-5.8	0.0	16	dbSNP_86	48	2277,6105		321,1635,2235	yes	missense	VWA3A	NM_173615.3	89	1328,2521,2434	TT,TC,CC		27.1654,30.6883,41.1985	benign	657/1185	22144318	5177,7389	2092	4191	6283	SO:0001583	missense	146177	exon20			ACACCACACCCCC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.1970C>T	16.37:g.22144318C>T	ENSP00000374049:p.Thr657Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	1120	0.5128205128205128	370	0.7520325203252033	119	0.3287292817679558	422	0.7377622377622378	209	0.2757255936675462	c	0.412	-0.912760	0.02415	0.693117	0.271654	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.23348	1.91	5.49	-5.8	0.02347	.	1.126930	0.06439	N	0.725536	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.002	T	0.31888	-0.9927	9	0.15499	T	0.54	.	12.3394	0.55085	0.0:0.1593:0.1052:0.7355	rs1105929;rs4261529;rs52803518;rs59925558;rs1105929	657;281	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	I	657;280	ENSP00000374049:T657I	ENSP00000299840:T280I	T	+	2	0	VWA3A	22051819	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	-2.116000	0.01327	-1.309000	0.02315	-0.753000	0.03488	ACA	C|0.477;T|0.523	0.523	strong		0.627	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
EVC	2121	hgsc.bcm.edu	37	4	5749904	5749904	+	Silent	SNP	T	T	C	rs4688963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	81	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	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		
C1orf87	127795	hgsc.bcm.edu	37	1	60506762	60506762	+	Silent	SNP	G	G	A	rs74843231	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:60506762G>A	ENST00000371201.3	-	4	491	c.384C>T	c.(382-384)acC>acT	p.T128T	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	128							calcium ion binding (GO:0005509)	p.T128T(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ACTGGTCTCCGGTTGGTACAG	0.507													G|||	267	0.0533147	0.0234	0.072	5008	,	,		20972	0.0645		0.0755	False		,,,				2504	0.046				p.T128T	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											C1orf87,NS,carcinoma,0,1	C1orf87	55	1	1	Substitution - coding silent(1)	stomach(1)	c.C384T						PASS	.	G		133,4273	95.3+/-134.0	1,131,2071	115.0	97.0	103.0		384	-1.9	0.9	1	dbSNP_131	103	643,7957	164.1+/-216.5	26,591,3683	no	coding-synonymous	C1orf87	NM_152377.2		27,722,5754	AA,AG,GG		7.4767,3.0186,5.9665		128/547	60506762	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	127795	exon4			GTCTCCGGTTGGT	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.384C>T	1.37:g.60506762G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	37	CCDS614.1																																																																																			G|0.938;A|0.062	0.062	strong		0.507	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2421857	2421857	+	Silent	SNP	C	C	T	rs72971482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2421857C>T	ENST00000332578.3	+	13	2058	c.2058C>T	c.(2056-2058)gaC>gaT	p.D686D		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	686	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		TCTAGGGTGACTCTGGGGGCC	0.627													C|||	10	0.00199681	0.0	0.0014	5008	,	,		15313	0.0		0.008	False		,,,				2504	0.001				p.D686D		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C2058T						PASS	.	C		14,4390	20.2+/-43.8	0,14,2188	43.0	50.0	48.0		2058	-0.4	1.0	19	dbSNP_130	48	102,8496	52.3+/-112.8	1,100,4198	no	coding-synonymous	TMPRSS9	NM_182973.1		1,114,6386	TT,TC,CC		1.1863,0.3179,0.8922		686/1060	2421857	116,12886	2202	4299	6501	SO:0001819	synonymous_variant	360200	exon13			GGGTGACTCTGGG	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.2058C>T	19.37:g.2421857C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.993;T|0.007	0.007	strong		0.627	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
RFPL4A	342931	hgsc.bcm.edu	37	19	56274453	56274453	+	Missense_Mutation	SNP	G	G	A	rs75239380	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56274453G>A	ENST00000434937.2	+	3	947	c.776G>A	c.(775-777)gGa>gAa	p.G259E		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	259	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.G259E(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						CATAAACGTGGAAGTCAAGAT	0.438																																					p.G259E		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.G776A						scavenged	.						18.0	22.0	21.0					19																	56274453		691	1590	2281	SO:0001583	missense	342931	exon3			AACGTGGAAGTCA		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.776G>A	19.37:g.56274453G>A	ENSP00000392936:p.Gly259Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	151	16	0.10596	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.580299	0.00879	.	.	ENSG00000223638	ENST00000434937	T	0.62498	0.02	2.78	-5.56	0.02529	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.24928	0.0605	N	0.01751	-0.74	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.10776	-1.0615	8	0.25751	T	0.34	-12.9296	1.2915	0.02061	0.279:0.1414:0.3715:0.2082	.	259	A6NLU0	RFPLA_HUMAN	E	259	ENSP00000392936:G259E	ENSP00000392936:G259E	G	+	2	0	RFPL4A	60966265	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.179000	0.03090	-1.696000	0.01421	-1.408000	0.01128	GGA	G|0.760;A|0.240	0.240	strong		0.438	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
BAIAP3	8938	hgsc.bcm.edu	37	16	1397815	1397815	+	Silent	SNP	C	C	T	rs1132358	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1397815C>T	ENST00000324385.5	+	31	3281	c.3123C>T	c.(3121-3123)gaC>gaT	p.D1041D	BAIAP3_ENST00000562208.1_Silent_p.D983D|BAIAP3_ENST00000397489.1_Silent_p.D1023D|BAIAP3_ENST00000397488.2_Silent_p.D1023D|BAIAP3_ENST00000421665.2_Silent_p.D970D|BAIAP3_ENST00000426824.3_Silent_p.D1006D|BAIAP3_ENST00000568887.1_Silent_p.D978D	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	13	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	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		
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				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)	ATTTTGTGCACGGATGGATAA	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110.0	123.0	118.0		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		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.489C>T	9.37:g.5050706C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
GPR55	9290	hgsc.bcm.edu	37	2	231775297	231775297	+	Silent	SNP	T	T	G	rs1992186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231775297T>G	ENST00000392040.1	-	2	573	c.381A>C	c.(379-381)ctA>ctC	p.L127L	GPR55_ENST00000392039.2_Silent_p.L127L|AC012507.4_ENST00000454890.1_RNA	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	54	27	0.5	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	
FMN2	56776	hgsc.bcm.edu	37	1	240256668	240256668	+	Missense_Mutation	SNP	A	A	C	rs146681532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:240256668A>C	ENST00000319653.9	+	1	1489	c.1259A>C	c.(1258-1260)aAg>aCg	p.K420T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	420					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)			TGCTACATCAAGACCACCACC	0.677													A|||	7	0.00139776	0.0	0.0029	5008	,	,		11822	0.0		0.003	False		,,,				2504	0.002				p.K420T		Atlas-SNP	.											.	FMN2	451	.	0			c.A1259C						PASS	.	A	THR/LYS	4,4402	8.1+/-20.4	0,4,2199	48.0	56.0	54.0		1259	3.0	1.0	1	dbSNP_134	54	55,8545	33.8+/-87.4	0,55,4245	yes	missense	FMN2	NM_020066.4	78	0,59,6444	CC,CA,AA		0.6395,0.0908,0.4536	probably-damaging	420/1723	240256668	59,12947	2203	4300	6503	SO:0001583	missense	56776	exon1			ACATCAAGACCAC	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.1259A>C	1.37:g.240256668A>C	ENSP00000318884:p.Lys420Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.29	1.892175	0.33442	9.08E-4	0.006395	ENSG00000155816	ENST00000319653	D	0.83591	-1.74	4.15	3.02	0.34903	.	0.084158	0.49305	D	0.000158	T	0.74846	0.3770	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	P	0.53266	0.722	T	0.77611	-0.2523	10	0.87932	D	0	.	9.2617	0.37616	0.9135:0.0:0.0865:0.0	.	420	Q9NZ56	FMN2_HUMAN	T	420	ENSP00000318884:K420T	ENSP00000318884:K420T	K	+	2	0	FMN2	238323291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.340000	0.72973	0.647000	0.30713	0.379000	0.24179	AAG	A|0.997;C|0.003	0.003	strong		0.677	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
HINFP	25988	hgsc.bcm.edu	37	11	119005132	119005132	+	Missense_Mutation	SNP	C	C	T	rs100803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119005132C>T	ENST00000350777.2	+	10	1541	c.1478C>T	c.(1477-1479)gCc>gTc	p.A493V		NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	493	Interaction with NPAT.		A -> V (in dbSNP:rs100803). {ECO:0000269|PubMed:15489334}.		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|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)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCTCCCCCAGCCCCTGAGCCA	0.562											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2012	0.401757	0.1687	0.2839	5008	,	,		19450	0.7183		0.4433	False		,,,				2504	0.4315				p.A493V		Atlas-SNP	.											.	HINFP	50	.	0			c.C1478T						PASS	.	C	VAL/ALA,VAL/ALA	843,3557	330.4+/-301.5	75,693,1432	43.0	48.0	46.0		1478,1478	-0.7	0.0	11	dbSNP_83	46	3610,4980	518.7+/-379.3	790,2030,1475	yes	missense,missense	HINFP	NM_015517.4,NM_198971.2	64,64	865,2723,2907	TT,TC,CC		42.0256,19.1591,34.2802	benign,benign	493/518,493/518	119005132	4453,8537	2200	4295	6495	SO:0001583	missense	25988	exon11			CCCCAGCCCCTGA	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1478C>T	11.37:g.119005132C>T	ENSP00000318085:p.Ala493Val	Somatic	55	0	0	1492	WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	966	0.4423076923076923	90	0.18292682926829268	120	0.3314917127071823	422	0.7377622377622378	334	0.44063324538258575	C	5.618	0.298738	0.10622	0.191591	0.420256	ENSG00000172273	ENST00000350777	T	0.10099	2.91	4.9	-0.697	0.11284	.	1.282940	0.05442	N	0.547761	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.23833	-1.0177	9	0.36615	T	0.2	-0.0432	2.4679	0.04557	0.1403:0.4289:0.2726:0.1583	rs100803;rs753835;rs3741335;rs3889924;rs17844880;rs17856531;rs17857597;rs17857666;rs17858206;rs61095432	493	Q9BQA5	HINFP_HUMAN	V	493	ENSP00000318085:A493V	ENSP00000318085:A493V	A	+	2	0	HINFP	118510342	0.002000	0.14202	0.000000	0.03702	0.091000	0.18340	-0.098000	0.11024	-0.001000	0.14495	-0.136000	0.14681	GCC	C|0.611;T|0.389	0.389	strong		0.562	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517	
PTPN3	5774	hgsc.bcm.edu	37	9	112172674	112172674	+	Silent	SNP	C	C	T	rs17803052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:112172674C>T	ENST00000374541.2	-	15	1439	c.1335G>A	c.(1333-1335)ccG>ccA	p.P445P	PTPN3_ENST00000394827.3_5'UTR|PTPN3_ENST00000446349.1_Silent_p.P269P|PTPN3_ENST00000412145.1_Silent_p.P314P|PTPN3_ENST00000262539.3_Silent_p.P291P	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	445					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						AGCTTTGTGCCGGATTGTTCT	0.468													C|||	257	0.0513179	0.0015	0.0519	5008	,	,		20000	0.0595		0.0736	False		,,,				2504	0.0869				p.P445P		Atlas-SNP	.											.	PTPN3	106	.	0			c.G1335A						PASS	.	C	,,,,,	51,4353	48.2+/-83.0	0,51,2151	85.0	92.0	90.0		1200,942,807,474,339,1335	2.0	1.0	9	dbSNP_123	90	607,7993	156.4+/-210.3	26,555,3719	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	,,,,,	26,606,5870	TT,TC,CC		7.0581,1.158,5.06	,,,,,	400/869,314/783,269/738,158/627,113/582,445/914	112172674	658,12346	2202	4300	6502	SO:0001819	synonymous_variant	5774	exon15			TTGTGCCGGATTG		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.1335G>A	9.37:g.112172674C>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	300	126	0.42	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			C|0.946;T|0.054	0.054	strong		0.468	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
CCDC152	100129792	hgsc.bcm.edu	37	5	42759295	42759295	+	Silent	SNP	C	C	T	rs200364347	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:42759295C>T	ENST00000361970.5	+	2	159	c.72C>T	c.(70-72)ttC>ttT	p.F24F	CCDC152_ENST00000388827.4_Silent_p.F24F	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152	24										endometrium(1)	1						TAAATGACTTCTCACAGATAG	0.343													C|||	6	0.00119808	0.0	0.0014	5008	,	,		17411	0.0		0.002	False		,,,				2504	0.0031				p.F24F		Atlas-SNP	.											CCDC152,NS,carcinoma,0,1	CCDC152	10	1	0			c.C72T						PASS	.						94.0	83.0	86.0					5																	42759295		692	1590	2282	SO:0001819	synonymous_variant	100129792	exon2			TGACTTCTCACAG		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141	ENST00000361970.5:c.72C>T	5.37:g.42759295C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_001134848	B3KXI4|B4E0P7|Q5BLP6	Silent	SNP	ENST00000361970.5	37	CCDS47203.1																																																																																			C|0.995;T|0.005	0.005	strong		0.343	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367497.1	XM_001717416	
GEM	2669	hgsc.bcm.edu	37	8	95272605	95272605	+	Missense_Mutation	SNP	G	G	C	rs2170363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:95272605G>C	ENST00000297596.2	-	2	391	c.127C>G	c.(127-129)Cgc>Ggc	p.R43G	GEM_ENST00000396194.2_Missense_Mutation_p.R43G	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	43			R -> G (in dbSNP:rs2170363).		cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			TGGCGGTTGCGGTGGCTGTAC	0.607													G|||	565	0.112819	0.0923	0.0576	5008	,	,		15583	0.1438		0.1183	False		,,,				2504	0.1421				p.R43G	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											GEM,colon,carcinoma,+1,1	GEM	40	1	0			c.C127G						PASS	.	G	GLY/ARG,GLY/ARG	463,3943		57,349,1797	76.0	74.0	75.0		127,127	5.3	0.0	8	dbSNP_96	75	1222,7378		104,1014,3182	yes	missense,missense	GEM	NM_005261.3,NM_181702.2	125,125	161,1363,4979	CC,CG,GG		14.2093,10.5084,12.9556	benign,benign	43/297,43/297	95272605	1685,11321	2203	4300	6503	SO:0001583	missense	2669	exon2			GGTTGCGGTGGCT		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"""kinase-inducible Ras-like protein"""	600164	"""GTP-binding protein overexpressed in skeletal muscle"""			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.127C>G	8.37:g.95272605G>C	ENSP00000297596:p.Arg43Gly	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_181702	B2RA31	Missense_Mutation	SNP	ENST00000297596.2	37	CCDS6261.1	.	.	.	.	.	.	.	.	.	.	G	4.826	0.153596	0.09185	0.105084	0.142093	ENSG00000164949	ENST00000396194;ENST00000297596;ENST00000523433	T;T;T	0.64618	-0.11;-0.11;1.51	5.28	5.28	0.74379	.	0.771703	0.12758	N	0.441589	T	0.00637	0.0021	L	0.44542	1.39	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.21793	-1.0235	9	0.17369	T	0.5	.	18.9302	0.92561	0.0:0.0:1.0:0.0	rs2170363;rs3735859;rs3943139;rs17847125;rs52798968;rs2170363	43	P55040	GEM_HUMAN	G	43	ENSP00000379497:R43G;ENSP00000297596:R43G;ENSP00000428258:R43G	ENSP00000297596:R43G	R	-	1	0	GEM	95341781	0.995000	0.38212	0.013000	0.15412	0.059000	0.15707	7.430000	0.80321	2.469000	0.83416	0.655000	0.94253	CGC	A|0.009;C|0.090;G|0.902;N|0.000	0.090	strong		0.607	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702	
PPAT	5471	hgsc.bcm.edu	37	4	57273840	57273840	+	Silent	SNP	C	C	G	rs11538098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57273840C>G	ENST00000264220.2	-	2	308	c.171G>C	c.(169-171)tcG>tcC	p.S57S	AC068620.1_ENST00000598320.1_5'Flank|PPAT_ENST00000507648.1_5'UTR	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	95	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	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	
GLRA4	441509	hgsc.bcm.edu	37	X	102978806	102978806	+	Silent	SNP	G	G	C	rs5945807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	206	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	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	
PRDM5	11107	hgsc.bcm.edu	37	4	121719544	121719544	+	Missense_Mutation	SNP	A	A	T	rs140634372	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:121719544A>T	ENST00000264808.3	-	10	1306	c.1066T>A	c.(1066-1068)Tct>Act	p.S356T	PRDM5_ENST00000428209.2_Missense_Mutation_p.S325T|PRDM5_ENST00000515109.1_Missense_Mutation_p.S325T	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	356					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.S356P(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						CTCTTGAAAGACTTATTACAA	0.348													A|||	77	0.0153754	0.0015	0.0216	5008	,	,		13046	0.001		0.0288	False		,,,				2504	0.0307				p.S356T		Atlas-SNP	.											PRDM5,NS,carcinoma,0,1	PRDM5	76	1	1	Substitution - Missense(1)	prostate(1)	c.T1066A						PASS	.	A	THR/SER	24,4382	29.9+/-59.1	0,24,2179	68.0	69.0	68.0		1066	4.4	0.9	4	dbSNP_134	68	212,8388	89.7+/-151.9	4,204,4092	yes	missense	PRDM5	NM_018699.2	58	4,228,6271	TT,TA,AA		2.4651,0.5447,1.8145	benign	356/631	121719544	236,12770	2203	4300	6503	SO:0001583	missense	11107	exon10			TGAAAGACTTATT	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.1066T>A	4.37:g.121719544A>T	ENSP00000264808:p.Ser356Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	105	39	0.371429	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	A	12.61	1.990850	0.35131	0.005447	0.024651	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.35973	1.28;1.28;1.28	5.63	4.43	0.53597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.219938	0.47852	D	0.000202	T	0.10637	0.0260	L	0.35644	1.08	0.80722	D	1	P;B;P	0.43938	0.822;0.173;0.722	B;B;B	0.39379	0.298;0.061;0.205	T	0.00870	-1.1533	10	0.30078	T	0.28	-27.0974	12.2566	0.54627	0.8725:0.0:0.0:0.1275	.	325;325;356	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	T	356;325;325	ENSP00000264808:S356T;ENSP00000422309:S325T;ENSP00000404832:S325T	ENSP00000264808:S356T	S	-	1	0	PRDM5	121938994	1.000000	0.71417	0.873000	0.34254	0.960000	0.62799	6.925000	0.75829	1.032000	0.39892	0.533000	0.62120	TCT	A|0.982;T|0.018	0.018	strong		0.348	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
WDR90	197335	hgsc.bcm.edu	37	16	708275	708275	+	Missense_Mutation	SNP	C	C	A	rs45613635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:708275C>A	ENST00000293879.4	+	22	2697	c.2697C>A	c.(2695-2697)caC>caA	p.H899Q	WDR90_ENST00000549091.1_Missense_Mutation_p.H899Q|LA16c-349E10.1_ENST00000573609.1_RNA			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	97	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	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	
CDC37L1	55664	hgsc.bcm.edu	37	9	4685008	4685008	+	Silent	SNP	C	C	T	rs2295967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:4685008C>T	ENST00000381854.3	+	2	466	c.264C>T	c.(262-264)tcC>tcT	p.S88S	CDC37L1_ENST00000381858.1_Silent_p.S88S|CDC37L1_ENST00000479095.1_3'UTR	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	129	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	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	
MST1L	11223	hgsc.bcm.edu	37	1	17084510	17084510	+	RNA	SNP	G	G	A	rs11260921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17084510G>A	ENST00000455405.2	-	0	379							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.L525L(2)|p.L530L(2)									ACCCGCTGTAGGCCTGGCTCT	0.577																																					p.L530L		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,14	.	.	14	4	Substitution - coding silent(4)	endometrium(2)|kidney(2)	c.C1588T						PASS	.																																					11223	exon12			GCTGTAGGCCTGG	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.17084510G>A		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	385	42	0.109091	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				G|0.981;A|0.019	0.019	strong		0.577	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SLC27A1	376497	hgsc.bcm.edu	37	19	17608183	17608183	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17608183G>A	ENST00000252595.7	+	7	1213	c.1116G>A	c.(1114-1116)gaG>gaA	p.E372E	CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000598424.1_Silent_p.E193E|SLC27A1_ENST00000442725.1_Silent_p.E372E	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	372	Sufficient for oligomerization. {ECO:0000250}.				adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.E372D(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CCATCTGGGAGGAGTTCACGG	0.667																																					p.E372E		Atlas-SNP	.											SLC27A1,NS,carcinoma,0,1	SLC27A1	97	1	1	Substitution - Missense(1)	lung(1)	c.G1116A						scavenged	.						55.0	47.0	50.0					19																	17608183		2203	4300	6503	SO:0001819	synonymous_variant	376497	exon7			CTGGGAGGAGTTC	BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1116G>A	19.37:g.17608183G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	169	4	0.0236686	NM_198580	A6NIH2|B7Z662	Silent	SNP	ENST00000252595.7	37	CCDS32953.1																																																																																			.	.	none		0.667	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580	
WDR66	144406	hgsc.bcm.edu	37	12	122386948	122386948	+	Missense_Mutation	SNP	G	G	A	rs78910014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122386948G>A	ENST00000288912.4	+	8	2104	c.1250G>A	c.(1249-1251)cGg>cAg	p.R417Q	WDR66_ENST00000397454.2_Missense_Mutation_p.R417Q	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	417							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)		AGTAAAACACGGGCAATATAT	0.274													G|||	181	0.0361422	0.0098	0.0375	5008	,	,		12978	0.0496		0.0457	False		,,,				2504	0.047				p.R417Q	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	WDR66	143	1	0			c.G1250A						PASS	.	G	GLN/ARG,GLN/ARG	43,3583		2,39,1772	75.0	76.0	76.0		1250,1250	-0.9	0.0	12	dbSNP_131	76	361,7741		14,333,3704	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	43,43	16,372,5476	AA,AG,GG		4.4557,1.1859,3.4447	benign,benign	417/942,417/1150	122386948	404,11324	1813	4051	5864	SO:0001583	missense	144406	exon8			AAACACGGGCAAT	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.1250G>A	12.37:g.122386948G>A	ENSP00000288912:p.Arg417Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	78	0.03571428571428571	12	0.024390243902439025	15	0.04143646408839779	20	0.03496503496503497	31	0.040897097625329816	G	7.855	0.724754	0.15439	0.011859	0.044557	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.05258	3.48;3.47	5.69	-0.905	0.10527	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.302125	0.37669	N	0.002000	T	0.00356	0.0011	N	0.00446	-1.495	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45614	-0.9249	10	0.02654	T	1	.	10.3649	0.44017	0.6673:0.0:0.3327:0.0	.	417	Q8TBY9	WDR66_HUMAN	Q	417	ENSP00000288912:R417Q;ENSP00000380595:R417Q	ENSP00000288912:R417Q	R	+	2	0	WDR66	120871331	0.002000	0.14202	0.011000	0.14972	0.818000	0.46254	0.622000	0.24433	-0.100000	0.12241	-0.247000	0.11927	CGG	G|0.956;A|0.044	0.044	strong		0.274	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
SLC35G3	146861	hgsc.bcm.edu	37	17	33520965	33520965	+	Missense_Mutation	SNP	G	G	A	rs8079507	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33520965G>A	ENST00000297307.5	-	1	447	c.362C>T	c.(361-363)gCg>gTg	p.A121V	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	121	EamA 1.					integral component of membrane (GO:0016021)		p.A121V(1)									CACCTGAACCGCACTGTAGGC	0.607													G|||	594	0.11861	0.1959	0.0418	5008	,	,		17830	0.2073		0.0119	False		,,,				2504	0.0869				p.A121V		Atlas-SNP	.											AMAC1,NS,carcinoma,0,2	.	.	2	1	Substitution - Missense(1)	stomach(1)	c.C362T						PASS	.	G	VAL/ALA	724,3682	299.8+/-286.0	63,598,1542	120.0	122.0	121.0		362		0.2	17	dbSNP_116	121	70,8530	41.2+/-98.3	0,70,4230	no	missense	SLC35G3	NM_152462.2	64	63,668,5772	AA,AG,GG		0.814,16.4321,6.1049	probably-damaging	121/339	33520965	794,12212	2203	4300	6503	SO:0001583	missense	146861	exon1			TGAACCGCACTGT	AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"""Solute carriers"""	26848	protein-coding gene	gene with protein product			"""transmembrane protein 21A"", ""acyl-malonyl condensing enzyme 1"""	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.362C>T	17.37:g.33520965G>A	ENSP00000297307:p.Ala121Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_152462	B9EGE9	Missense_Mutation	SNP	ENST00000297307.5	37	CCDS11293.1	240	0.10989010989010989	90	0.18292682926829268	18	0.049723756906077346	125	0.21853146853146854	7	0.009234828496042216	G	15.07	2.724801	0.48833	0.164321	0.00814	ENSG00000164729	ENST00000297307	T	0.77098	-1.07	.	.	.	.	0.000000	0.47455	D	0.000229	T	0.00109	0.0003	L	0.27053	0.805	0.30380	P	0.782045	D	0.67145	0.996	P	0.60117	0.869	T	0.17258	-1.0375	8	0.72032	D	0.01	-7.9038	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	rs8079507;rs60406165	121	Q8N808	S35G3_HUMAN	V	121	ENSP00000297307:A121V	ENSP00000297307:A121V	A	-	2	0	SLC35G3	30545078	1.000000	0.71417	0.225000	0.23894	0.226000	0.24999	2.771000	0.47670	0.064000	0.16427	0.064000	0.15345	GCG	G|0.925;A|0.075	0.075	strong		0.607	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462	
MTUS1	57509	hgsc.bcm.edu	37	8	17612694	17612694	+	Missense_Mutation	SNP	C	C	G	rs73206291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17612694C>G	ENST00000262102.6	-	2	847	c.623G>C	c.(622-624)tGg>tCg	p.W208S	MTUS1_ENST00000381862.3_Missense_Mutation_p.W208S|MTUS1_ENST00000381869.3_Missense_Mutation_p.W208S|MTUS1_ENST00000519263.1_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	86	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	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	
SEMA4B	10509	hgsc.bcm.edu	37	15	90768320	90768320	+	Silent	SNP	C	C	T	rs11073918	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90768320C>T	ENST00000411539.2	+	10	1575	c.1315C>T	c.(1315-1317)Ctg>Ttg	p.L439L	SEMA4B_ENST00000379122.3_Silent_p.L434L|SEMA4B_ENST00000332496.6_Silent_p.L439L	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	434	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CCGCATGCTGCTGCTGCAGCC	0.617													C|||	1308	0.261182	0.0802	0.317	5008	,	,		20606	0.37		0.2584	False		,,,				2504	0.3569				p.L439L		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C1315T						PASS	.	C	,	503,3789		38,427,1681	52.0	61.0	58.0		1315,1315	4.2	0.9	15	dbSNP_120	58	1954,6536		227,1500,2518	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	265,1927,4199	TT,TC,CC		23.0153,11.7195,19.2223	,	439/838,439/838	90768320	2457,10325	2146	4245	6391	SO:0001819	synonymous_variant	10509	exon11			ATGCTGCTGCTGC	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.1315C>T	15.37:g.90768320C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			C|0.755;T|0.245	0.245	strong		0.617	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
SRMS	6725	hgsc.bcm.edu	37	20	62173817	62173817	+	Missense_Mutation	SNP	C	C	T	rs34969822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62173817C>T	ENST00000217188.1	-	4	803	c.763G>A	c.(763-765)Gtg>Atg	p.V255M		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> M (in dbSNP:rs34969822).		peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			TTGATCGCCACGGGCAGGGAG	0.662													C|||	211	0.0421326	0.1135	0.0216	5008	,	,		15413	0.0079		0.0348	False		,,,				2504	0.0031				p.V255M		Atlas-SNP	.											.	SRMS	48	.	0			c.G763A						PASS	.	C	MET/VAL	295,4107	158.5+/-191.2	8,279,1914	61.0	51.0	54.0		763	3.8	0.2	20	dbSNP_126	54	268,8322	101.4+/-162.7	4,260,4031	yes	missense	SRMS	NM_080823.2	21	12,539,5945	TT,TC,CC		3.1199,6.7015,4.3334	probably-damaging	255/489	62173817	563,12429	2201	4295	6496	SO:0001583	missense	6725	exon4			TCGCCACGGGCAG		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.763G>A	20.37:g.62173817C>T	ENSP00000217188:p.Val255Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	173	100	0.578035	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	85	0.03891941391941392	40	0.08130081300813008	8	0.022099447513812154	7	0.012237762237762238	30	0.0395778364116095	C	18.55	3.647768	0.67358	0.067015	0.031199	ENSG00000125508	ENST00000217188	D	0.89939	-2.59	4.76	3.82	0.43975	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000108	T	0.67887	0.2941	H	0.96333	3.805	0.36941	D	0.892401	D	0.89917	1.0	D	0.97110	1.0	T	0.82255	-0.0548	10	0.87932	D	0	.	12.3331	0.55051	0.0:0.9165:0.0:0.0835	rs34969822	255	Q9H3Y6	SRMS_HUMAN	M	255	ENSP00000217188:V255M	ENSP00000217188:V255M	V	-	1	0	SRMS	61644261	1.000000	0.71417	0.165000	0.22776	0.836000	0.47400	3.834000	0.55798	1.004000	0.39156	0.561000	0.74099	GTG	C|0.957;T|0.043	0.043	strong		0.662	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2306053	2306053	+	Missense_Mutation	SNP	A	A	G	rs661301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2306053A>G	ENST00000290974.2	-	8	2353	c.2014T>C	c.(2014-2016)Tcg>Ccg	p.S672P	RP11-478C1.7_ENST00000510632.1_RNA|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.S602P|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.S642P	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	672			S -> P (in dbSNP:rs661301). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						TCGTGAGCCGAGGGGCTCCCA	0.667													A|||	3625	0.723842	0.6536	0.7608	5008	,	,		15450	0.6806		0.833	False		,,,				2504	0.7249				p.S672P		Atlas-SNP	.											ZFYVE28,NS,carcinoma,+1,2	ZFYVE28	79	2	0			c.T2014C						scavenged	.	A	PRO/SER,PRO/SER,PRO/SER	3044,1358		1060,924,217	39.0	45.0	43.0		1924,1804,2014	-6.3	0.0	4	dbSNP_83	43	7130,1462		2971,1188,137	yes	missense,missense,missense	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	74,74,74	4031,2112,354	GG,GA,AA		17.0158,30.8496,21.7023	benign,benign,benign	642/858,602/818,672/888	2306053	10174,2820	2201	4296	6497	SO:0001583	missense	57732	exon8			GAGCCGAGGGGCT	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.2014T>C	4.37:g.2306053A>G	ENSP00000290974:p.Ser672Pro	Somatic	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	37	CCDS33942.1	1627	0.74496336996337	330	0.6707317073170732	284	0.7845303867403315	394	0.6888111888111889	619	0.816622691292876	A	8.438	0.850079	0.17034	0.691504	0.829842	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.58797	0.31;0.32;0.32	3.14	-6.27	0.02026	.	3.264500	0.00799	N	0.001410	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	0.27739	-1.0065	9	0.23302	T	0.38	.	2.167	0.03840	0.1753:0.1447:0.4204:0.2596	rs661301;rs59420090;rs661301	642;672	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	P	672;642;602	ENSP00000290974:S672P;ENSP00000425706:S642P;ENSP00000426299:S602P	ENSP00000290974:S672P	S	-	1	0	ZFYVE28	2275851	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-1.570000	0.02140	-2.013000	0.00949	0.254000	0.18369	TCG	A|0.238;G|0.762	0.762	strong		0.667	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
ZNF695	57116	hgsc.bcm.edu	37	1	247150740	247150740	+	Silent	SNP	T	T	C	rs3749427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247150740T>C	ENST00000339986.7	-	4	1224	c.1077A>G	c.(1075-1077)aaA>aaG	p.K359K	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	359					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GGTTAAAGGCTTTTCCACATT	0.388													T|||	2949	0.588858	0.1634	0.719	5008	,	,		21192	0.9722		0.6362	False		,,,				2504	0.6278				p.K359K		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1077G						PASS	.	T	,	1061,3229		153,755,1237	48.0	51.0	50.0		,1077	-0.8	0.1	1	dbSNP_107	50	5503,3045		1796,1911,567	no	intron,coding-synonymous	ZNF695	NM_001204221.1,NM_020394.4	,	1949,2666,1804	CC,CT,TT		35.6224,24.7319,48.8705	,	,359/516	247150740	6564,6274	2145	4274	6419	SO:0001819	synonymous_variant	57116	exon4			AAAGGCTTTTCCA		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1077A>G	1.37:g.247150740T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Silent	SNP	ENST00000339986.7	37	CCDS44344.1																																																																																			T|0.388;C|0.612	0.612	strong		0.388	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
CYP2D6	1565	hgsc.bcm.edu	37	22	42522613	42522613	+	Missense_Mutation	SNP	G	G	C	rs1135840	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42522613G>C	ENST00000360608.5	-	9	1571	c.1457C>G	c.(1456-1458)aCc>aGc	p.T486S	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.T486S|CYP2D6_ENST00000359033.4_Missense_Mutation_p.T435S	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	486			S -> T (in allele CYP2D6*2, allele CYP2D6*10, allele CYP2D6*12, allele CYP2D6*14, allele CYP2D6*17, allele CYP2D6*45A, allele CYP2D6*45B and allele CYP2D6*46; impaired metabolism of sparteine; dbSNP:rs1135840). {ECO:0000269|PubMed:10591208, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15768052, 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)	GGGGGATGGGGTCACCAGGAA	0.577													G|||	2009	0.401158	0.3238	0.5245	5008	,	,		18454	0.2956		0.4543	False		,,,				2504	0.4724				p.T486S		Atlas-SNP	.											CYP2D6_ENST00000360608,brain,glioma,0,2	CYP2D6	104	2	0			c.C1457G	GRCh37	CM931123	CYP2D6	M	rs1135840	PASS	.	G	SER/THR,SER/THR	1594,2790	468.1+/-355.0	356,882,954	34.0	31.0	32.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1457,1304	-2.7	0.0	22	dbSNP_86	32	3706,4890	501.7+/-375.5	881,1944,1473	yes	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	58,58	1237,2826,2427	CC,CG,GG		43.1131,36.3595,40.832	benign,benign	486/498,435/447	42522613	5300,7680	2192	4298	6490	SO:0001583	missense	1565	exon9			GATGGGGTCACCA	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.1457C>G	22.37:g.42522613G>C	ENSP00000353820:p.Thr486Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	60	0.560748	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	877	0.4015567765567766	156	0.3170731707317073	188	0.5193370165745856	190	0.3321678321678322	343	0.4525065963060686	G	3.127	-0.179188	0.06380	0.363595	0.431131	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.68765	-0.35;-0.35;5.1	4.85	-2.65	0.06095	.	1.222600	0.05550	N	0.567358	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.17038	0.02;0.02;0.02	B;B;B	0.18871	0.023;0.023;0.023	T	0.32798	-0.9893	8	0.08381	T	0.77	.	5.2556	0.15546	0.4162:0.2592:0.3246:0.0	rs1135840;rs57862116	486;435;486	C1ID54;Q6NXU8;Q6NWU0	.;.;.	S	486;486;432;435;435	ENSP00000353820:T486S;ENSP00000374620:T486S;ENSP00000351927:T435S	ENSP00000351927:T435S	T	-	2	0	CYP2D6	40852557	0.080000	0.21391	0.001000	0.08648	0.004000	0.04260	0.361000	0.20267	-0.465000	0.06953	-0.315000	0.08773	ACC	G|0.600;C|0.400	0.400	strong		0.577	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
EID2	163126	hgsc.bcm.edu	37	19	40030654	40030654	+	Silent	SNP	G	G	C	rs76765165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40030654G>C	ENST00000390658.2	-	1	216	c.66C>G	c.(64-66)gtC>gtG	p.V22V		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)			CCGCCTGCGGGACGTCTCTGT	0.731													.|||	1153	0.230232	0.1853	0.2507	5008	,	,		9909	0.2937		0.2614	False		,,,				2504	0.1789				p.V22V		Atlas-SNP	.											EID2,NS,carcinoma,0,1	EID2	14	1	0			c.C66G						scavenged	.						19.0	22.0	21.0					19																	40030654		1398	2975	4373	SO:0001819	synonymous_variant	163126	exon1			CTGCGGGACGTCT	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.66C>G	19.37:g.40030654G>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_153232		Silent	SNP	ENST00000390658.2	37	CCDS12540.2																																																																																			G|0.786;C|0.214	0.214	strong		0.731	EID2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157251.1	NM_153232	
CRYM	1428	hgsc.bcm.edu	37	16	21272591	21272591	+	Silent	SNP	G	G	C	rs14122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21272591G>C	ENST00000219599.3	-	9	1129	c.864C>G	c.(862-864)acC>acG	p.T288T	CRYM_ENST00000396023.2_Silent_p.T288T|CRYM_ENST00000543948.1_Silent_p.T288T|CRYM_ENST00000415987.2_Silent_p.T246T	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	288					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)		ACTTGAACACGGTGGTCTTCT	0.512													C|||	2517	0.502596	0.826	0.4179	5008	,	,		18706	0.2966		0.4016	False		,,,				2504	0.4417				p.T288T		Atlas-SNP	.											.	CRYM	13	.	0			c.C864G						PASS	.	C	,	3338,1060	386.1+/-326.0	1261,816,122	166.0	136.0	146.0		738,864	-10.6	0.1	16	dbSNP_52	146	3570,5030	628.8+/-398.2	752,2066,1482	no	coding-synonymous,coding-synonymous	CRYM	NM_001014444.2,NM_001888.3	,	2013,2882,1604	CC,CG,GG		41.5116,24.1019,46.8534	,	246/273,288/315	21272591	6908,6090	2199	4300	6499	SO:0001819	synonymous_variant	1428	exon9			GAACACGGTGGTC		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.864C>G	16.37:g.21272591G>C		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	146	89	0.609589	NM_001888	D5MNX0|Q5HYB7	Silent	SNP	ENST00000219599.3	37	CCDS10597.1																																																																																			G|0.488;C|0.512	0.512	strong		0.512	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1		
HELZ2	85441	hgsc.bcm.edu	37	20	62193445	62193445	+	Missense_Mutation	SNP	G	G	A	rs3810481	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	82	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	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	
ADCK2	90956	hgsc.bcm.edu	37	7	140394587	140394587	+	Missense_Mutation	SNP	C	C	T	rs1046515	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140394587C>T	ENST00000072869.4	+	8	2043	c.1865C>T	c.(1864-1866)cCa>cTa	p.P622L	NDUFB2_ENST00000471136.1_5'Flank|NDUFB2_ENST00000472695.1_5'Flank|NDUFB2_ENST00000476279.1_5'Flank|NDUFB2_ENST00000482954.1_Intron|NDUFB2-AS1_ENST00000465466.1_RNA|NDUFB2_ENST00000247866.4_5'Flank|NDUFB2_ENST00000465506.1_5'Flank|NDUFB2_ENST00000476470.1_5'Flank|NDUFB2_ENST00000460088.1_5'Flank|NDUFB2_ENST00000204307.5_5'Flank|ADCK2_ENST00000476491.1_Intron|NDUFB2_ENST00000461457.1_5'Flank	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	622			P -> L (in dbSNP:rs1046515). {ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					CTCACGGGCCCAGTGTGCCCC	0.617													C|||	750	0.14976	0.1929	0.1628	5008	,	,		17638	0.1002		0.0775	False		,,,				2504	0.2076				p.P622L		Atlas-SNP	.											.	ADCK2	37	.	0			c.C1865T						PASS	.	C	LEU/PRO	766,3640	310.2+/-291.5	61,644,1498	73.0	68.0	69.0		1865	2.8	0.2	7	dbSNP_86	69	637,7963	164.1+/-216.5	25,587,3688	yes	missense	ADCK2	NM_052853.3	98	86,1231,5186	TT,TC,CC		7.407,17.3854,10.7873	benign	622/627	140394587	1403,11603	2203	4300	6503	SO:0001583	missense	90956	exon8			CGGGCCCAGTGTG	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.1865C>T	7.37:g.140394587C>T	ENSP00000072869:p.Pro622Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	37	CCDS5861.1	253	0.11584249084249085	95	0.19308943089430894	44	0.12154696132596685	50	0.08741258741258741	64	0.08443271767810026	C	11.63	1.696930	0.30142	0.173854	0.07407	ENSG00000133597	ENST00000072869;ENST00000473512	T;T	0.16597	3.16;2.33	4.66	2.8	0.32819	.	0.413038	0.25786	N	0.028318	T	0.00012	0.0000	N	0.16478	0.41	0.47621	P	5.260000000000264E-4	B	0.12630	0.006	B	0.06405	0.002	T	0.34104	-0.9842	9	0.38643	T	0.18	-1.9639	10.237	0.43288	0.0:0.8391:0.0:0.1609	rs1046515;rs3173555;rs58335969;rs1046515	622	Q7Z695	ADCK2_HUMAN	L	622;219	ENSP00000072869:P622L;ENSP00000420288:P219L	ENSP00000072869:P622L	P	+	2	0	ADCK2	140041056	0.002000	0.14202	0.205000	0.23548	0.091000	0.18340	0.604000	0.24164	0.371000	0.24564	0.561000	0.74099	CCA	C|0.890;T|0.110	0.110	strong		0.617	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
SDK2	54549	hgsc.bcm.edu	37	17	71398170	71398170	+	Silent	SNP	G	G	C	rs9302962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:71398170G>C	ENST00000392650.3	-	19	2595	c.2595C>G	c.(2593-2595)acC>acG	p.T865T	SDK2_ENST00000388726.3_Silent_p.T865T	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	865	Fibronectin type-III 3. {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						TGAAGTACTCGGTGAACTTCT	0.627													G|||	1913	0.381989	0.6793	0.2622	5008	,	,		17594	0.2133		0.3817	False		,,,				2504	0.2393				p.T865T		Atlas-SNP	.											SDK2,NS,carcinoma,0,2	SDK2	219	2	0			c.C2595G						scavenged	.	G		2813,1593	663.7+/-401.3	917,979,307	90.0	66.0	74.0		2595	-10.2	0.4	17	dbSNP_119	74	3391,5209	500.1+/-375.1	660,2071,1569	no	coding-synonymous	SDK2	NM_001144952.1		1577,3050,1876	CC,CG,GG		39.4302,36.1552,47.7011		865/2173	71398170	6204,6802	2203	4300	6503	SO:0001819	synonymous_variant	54549	exon19			GTACTCGGTGAAC	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.2595C>G	17.37:g.71398170G>C		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																			G|0.547;C|0.453	0.453	strong		0.627	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
CLCA2	9635	hgsc.bcm.edu	37	1	86913265	86913265	+	Silent	SNP	C	C	T	rs2275001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:86913265C>T	ENST00000370565.4	+	11	1950	c.1788C>T	c.(1786-1788)cgC>cgT	p.R596R		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	596					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TGACCTCTCGCGCCTCCAACT	0.493													C|||	1275	0.254593	0.0908	0.2032	5008	,	,		17596	0.3889		0.2634	False		,,,				2504	0.365				p.R596R	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1788T						PASS	.	C		581,3825	256.7+/-261.4	40,501,1662	132.0	129.0	130.0		1788	-11.2	0.0	1	dbSNP_100	130	2352,6248	393.4+/-344.3	306,1740,2254	no	coding-synonymous	CLCA2	NM_006536.5		346,2241,3916	TT,TC,CC		27.3488,13.1866,22.5511		596/944	86913265	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon11			CTCTCGCGCCTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1788C>T	1.37:g.86913265C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	56	0.57732	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			C|0.765;T|0.235	0.235	strong		0.493	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
C7orf62	219557	hgsc.bcm.edu	37	7	88423881	88423881	+	Missense_Mutation	SNP	T	T	C	rs2293583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:88423881T>C	ENST00000297203.2	-	2	561	c.376A>G	c.(376-378)Att>Gtt	p.I126V	ZNF804B_ENST00000333190.4_Intron	NM_152706.3	NP_689919.1	Q8TBZ9	CG062_HUMAN	chromosome 7 open reading frame 62	126			I -> V (in dbSNP:rs2293583).							NS(1)|breast(1)|endometrium(3)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	30						ATTTGTTGAATAAAAAATACT	0.348													T|||	609	0.121605	0.1051	0.062	5008	,	,		21075	0.124		0.0875	False		,,,				2504	0.2188				p.I126V		Atlas-SNP	.											.	C7orf62	63	.	0			c.A376G						PASS	.	T	VAL/ILE,	488,3918	225.9+/-241.6	22,444,1737	49.0	51.0	50.0		376,	1.1	0.0	7	dbSNP_100	50	691,7909	171.4+/-222.4	35,621,3644	yes	missense,intron	C7orf62,ZNF804B	NM_152706.2,NM_181646.2	29,	57,1065,5381	CC,CT,TT		8.0349,11.0758,9.065	benign,	126/254,	88423881	1179,11827	2203	4300	6503	SO:0001583	missense	219557	exon2			GTTGAATAAAAAA	BC028365	CCDS34678.1	7q21.13	2013-10-11			ENSG00000164645	ENSG00000164645			22402	protein-coding gene	gene with protein product						12690205	Standard	NM_152706		Approved	MGC26647	uc003ujv.3	Q8TBZ9	OTTHUMG00000153859	ENST00000297203.2:c.376A>G	7.37:g.88423881T>C	ENSP00000297203:p.Ile126Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_152706		Missense_Mutation	SNP	ENST00000297203.2	37	CCDS34678.1	210	0.09615384615384616	51	0.10365853658536585	31	0.0856353591160221	65	0.11363636363636363	63	0.08311345646437995	T	0.804	-0.754563	0.03041	0.110758	0.080349	ENSG00000164645	ENST00000297203	T	0.15256	2.44	6.06	1.07	0.20283	.	0.617976	0.17229	N	0.182026	T	0.00241	0.0007	L	0.48362	1.52	0.80722	P	0.0	B	0.17268	0.021	B	0.15484	0.013	T	0.20706	-1.0267	9	0.25751	T	0.34	-18.19	5.3759	0.16164	0.0:0.1703:0.3664:0.4632	rs2293583;rs2293583	126	Q8TBZ9	CG062_HUMAN	V	126	ENSP00000297203:I126V	ENSP00000297203:I126V	I	-	1	0	C7orf62	88261817	0.003000	0.15002	0.009000	0.14445	0.042000	0.13812	-0.033000	0.12246	0.164000	0.19529	-0.263000	0.10527	ATT	T|0.902;C|0.098	0.098	strong		0.348	C7orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332714.1	NM_152706	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657913	46657913	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46657913C>T	ENST00000253255.5	-	1	1306	c.1307G>A	c.(1306-1308)cGg>cAg	p.R436Q		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	436	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AGAGTCCTTCCGAATCACCAT	0.488																																					p.R436Q		Atlas-SNP	.											PKDREJ,NS,carcinoma,-1,2	PKDREJ	195	2	0			c.G1307A						scavenged	.						111.0	105.0	107.0					22																	46657913		2203	4300	6503	SO:0001583	missense	10343	exon1			TCCTTCCGAATCA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1307G>A	22.37:g.46657913C>T	ENSP00000253255:p.Arg436Gln	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	159	3	0.0188679	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	C	2.422	-0.332883	0.05314	.	.	ENSG00000130943	ENST00000253255	T	0.69435	-0.4	5.18	-0.961	0.10337	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.142330	0.06544	N	0.743741	T	0.29491	0.0735	N	0.00960	-1.095	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.25882	-1.0119	10	0.05833	T	0.94	-1.1304	5.9626	0.19308	0.0:0.2966:0.1273:0.5761	.	436	Q9NTG1	PKDRE_HUMAN	Q	436	ENSP00000253255:R436Q	ENSP00000253255:R436Q	R	-	2	0	PKDREJ	45036577	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	-0.275000	0.08525	-0.479000	0.06813	-1.004000	0.02495	CGG	.	.	none		0.488	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
HFM1	164045	hgsc.bcm.edu	37	1	91851193	91851193	+	Silent	SNP	G	G	A	rs12144808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:91851193G>A	ENST00000370425.3	-	5	791	c.693C>T	c.(691-693)atC>atT	p.I231I	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Intron	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	231					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGCCTTCTCCGATTTCAGAAG	0.338													G|||	390	0.0778754	0.1528	0.0504	5008	,	,		17586	0.001		0.0924	False		,,,				2504	0.0603				p.I231I		Atlas-SNP	.											.	HFM1	188	.	0			c.C693T						PASS	.	G		621,3785	268.9+/-268.7	48,525,1630	80.0	76.0	77.0		693	0.9	0.1	1	dbSNP_120	77	817,7783	190.3+/-236.8	47,723,3530	no	coding-synonymous	HFM1	NM_001017975.3		95,1248,5160	AA,AG,GG		9.5,14.0944,11.0564		231/1436	91851193	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	164045	exon5			TTCTCCGATTTCA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.693C>T	1.37:g.91851193G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2																																																																																			G|0.898;A|0.102	0.102	strong		0.338	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
PRODH2	58510	hgsc.bcm.edu	37	19	36303664	36303664	+	Missense_Mutation	SNP	G	G	C	rs3848666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36303664G>C	ENST00000301175.3	-	2	289	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	91			P -> R (in dbSNP:rs3848666).		proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCCCCTGGAGGGGGGACCAGC	0.637													g|||	272	0.0543131	0.0061	0.0965	5008	,	,		18695	0.0		0.1561	False		,,,				2504	0.0409				p.P91R		Atlas-SNP	.											.	PRODH2	68	.	0			c.C272G						PASS	.	A	ARG/PRO	147,4259	99.4+/-138.0	3,141,2059	42.0	42.0	42.0		272	0.6	0.0	19	dbSNP_108	42	1425,7175	267.9+/-287.5	126,1173,3001	yes	missense	PRODH2	NM_021232.1	103	129,1314,5060	CC,CG,GG		16.5698,3.3364,12.0867	benign	91/537	36303664	1572,11434	2203	4300	6503	SO:0001583	missense	58510	exon2			CTGGAGGGGGGAC	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.272C>G	19.37:g.36303664G>C	ENSP00000301175:p.Pro91Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	166	0.076007326007326	5	0.01016260162601626	45	0.12430939226519337	0	0.0	116	0.15303430079155672	g	6.252	0.414685	0.11870	0.033364	0.165698	ENSG00000250799	ENST00000301175	T	0.23754	1.89	5.19	0.647	0.17796	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.58432	P	1.999999999946489E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.31110	-0.9955	8	0.35671	T	0.21	.	6.956	0.24572	0.2961:0.1194:0.5845:0.0	rs3848666;rs52793092;rs3848666	91	Q9UF12	PROD2_HUMAN	R	91	ENSP00000301175:P91R	ENSP00000301175:P91R	P	-	2	0	PRODH2	40995504	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.765000	0.26546	0.103000	0.17682	-2.308000	0.00257	CCC	G|0.901;C|0.099	0.099	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390155	208390155	+	Silent	SNP	C	C	T	rs4844657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:208390155C>T	ENST00000367033.3	-	2	1870	c.1113G>A	c.(1111-1113)ctG>ctA	p.L371L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	371	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)		AGCAGGACTGCAGGCGCTCCT	0.612													C|||	639	0.127596	0.0461	0.2046	5008	,	,		22102	0.1429		0.2078	False		,,,				2504	0.0849				p.L371L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G1113A						PASS	.	C		258,4148	146.5+/-181.1	8,242,1953	70.0	67.0	68.0		1113	0.8	1.0	1	dbSNP_111	68	1646,6954	303.7+/-306.6	167,1312,2821	no	coding-synonymous	PLXNA2	NM_025179.3		175,1554,4774	TT,TC,CC		19.1395,5.8557,14.6394		371/1895	208390155	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			GGACTGCAGGCGC	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.1113G>A	1.37:g.208390155C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			C|0.856;T|0.144	0.144	strong		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
GPR98	84059	hgsc.bcm.edu	37	5	90079820	90079820	+	Silent	SNP	A	A	G	rs17554631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:90079820A>G	ENST00000405460.2	+	67	13695	c.13599A>G	c.(13597-13599)acA>acG	p.T4533T	GPR98_ENST00000425867.2_Silent_p.T194T	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4533	Calx-beta 31. {ECO:0000305|PubMed:11606593}.				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)		CCAATTCCACAATGATTTTAT	0.378													A|||	462	0.0922524	0.0113	0.1369	5008	,	,		18897	0.005		0.2465	False		,,,				2504	0.1012				p.T4533T		Atlas-SNP	.											.	GPR98	605	.	0			c.A13599G						PASS	.	A		154,3544		3,148,1698	37.0	37.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	13599	-1.3	0.9	5	dbSNP_123	37	1807,6369		185,1437,2466	no	coding-synonymous	GPR98	NM_032119.3		188,1585,4164	GG,GA,AA		22.1013,4.1644,16.5151		4533/6307	90079820	1961,9913	1849	4088	5937	SO:0001819	synonymous_variant	84059	exon67			TTCCACAATGATT	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.13599A>G	5.37:g.90079820A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			A|0.881;G|0.119	0.119	strong		0.378	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
LDHA	3939	hgsc.bcm.edu	37	11	18427072	18427072	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18427072A>G	ENST00000422447.3	+	7	1060	c.787A>G	c.(787-789)Ata>Gta	p.I263V	LDHA_ENST00000542179.1_Missense_Mutation_p.I263V|LDHA_ENST00000396222.2_Intron|LDHA_ENST00000379412.5_Missense_Mutation_p.I263V|LDHA_ENST00000227157.4_Intron|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000430553.2_Missense_Mutation_p.I205V|LDHA_ENST00000540430.1_Missense_Mutation_p.I292V	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	263					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						GGCAGAGAGTATAATGAAGAA	0.423																																					p.I292V		Atlas-SNP	.											.	LDHA	118	.	0			c.A874G						PASS	.						111.0	113.0	112.0					11																	18427072		2199	4293	6492	SO:0001583	missense	3939	exon7			GAGAGTATAATGA	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.787A>G	11.37:g.18427072A>G	ENSP00000395337:p.Ile263Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502896	0.44558	.	.	ENSG00000134333	ENST00000422447;ENST00000430553;ENST00000541620;ENST00000445376;ENST00000540430;ENST00000379412;ENST00000542179	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.12	5.12	0.69794	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.103731	0.64402	D	0.000003	T	0.66197	0.2765	L	0.55834	1.745	0.80722	D	1	B;B;B;B	0.16166	0.016;0.001;0.001;0.013	B;B;B;B	0.30251	0.113;0.025;0.026;0.056	T	0.65886	-0.6059	10	0.62326	D	0.03	-3.2056	15.205	0.73173	1.0:0.0:0.0:0.0	.	292;205;236;263	B7Z5E3;B4DKQ2;B4DJI1;P00338	.;.;.;LDHA_HUMAN	V	263;205;235;236;292;263;263	ENSP00000395337:I263V;ENSP00000406172:I205V;ENSP00000445175:I292V;ENSP00000368722:I263V;ENSP00000445331:I263V	ENSP00000368722:I263V	I	+	1	0	LDHA	18383648	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	4.095000	0.57728	2.056000	0.61249	0.374000	0.22700	ATA	.	.	none		0.423	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566	
PIGX	54965	hgsc.bcm.edu	37	3	196460680	196460680	+	Silent	SNP	C	C	T	rs34830136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196460680C>T	ENST00000314118.4	+	6	843	c.561C>T	c.(559-561)acC>acT	p.T187T	PIGX_ENST00000541663.1_Silent_p.T138T	NM_017861.3	NP_060331.3	Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class X	228					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)				endometrium(1)|large_intestine(5)|lung(4)|stomach(1)	11	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00322)		CTGTACATACCTCTCTAGTAT	0.388													C|||	652	0.130192	0.1241	0.1599	5008	,	,		19508	0.001		0.2286	False		,,,				2504	0.1493				p.T246T		Atlas-SNP	.											.	PIGX	16	.	0			c.C738T						PASS	.	C	,	712,3694	297.6+/-284.8	57,598,1548	219.0	185.0	196.0		738,684	5.0	1.0	3	dbSNP_126	196	1927,6673	340.9+/-323.8	179,1569,2552	no	coding-synonymous,coding-synonymous	PIGX	NM_001166304.1,NM_017861.3	,	236,2167,4100	TT,TC,CC		22.407,16.1598,20.2906	,	246/277,228/259	196460680	2639,10367	2203	4300	6503	SO:0001819	synonymous_variant	54965	exon7			ACATACCTCTCTA	AK000529	CCDS3320.1, CCDS3320.2, CCDS54701.1	3q29	2013-02-26	2006-06-28		ENSG00000163964	ENSG00000163964		"""Phosphatidylinositol glycan anchor biosynthesis"""	26046	protein-coding gene	gene with protein product		610276	"""phosphatidylinositol glycan, class X"""			15635094	Standard	NM_017861		Approved	FLJ20522	uc010iaj.3	Q8TBF5	OTTHUMG00000155535	ENST00000314118.4:c.561C>T	3.37:g.196460680C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	173	99	0.572254	NM_001166304	Q9NWZ2	Silent	SNP	ENST00000314118.4	37																																																																																				C|0.811;T|0.189	0.189	strong		0.388	PIGX-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017861	
SLC4A2	6522	hgsc.bcm.edu	37	7	150761680	150761680	+	Silent	SNP	C	C	A	rs1050702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150761680C>A	ENST00000485713.1	+	4	1325	c.285C>A	c.(283-285)cgC>cgA	p.R95R	SLC4A2_ENST00000461735.1_Silent_p.R81R|SLC4A2_ENST00000413384.2_Silent_p.R95R|SLC4A2_ENST00000310317.5_Intron|SLC4A2_ENST00000392826.2_Silent_p.R86R	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	95	Pro-rich.				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)		ATGCACGCCGCCGCAAGACAC	0.682													C|||	891	0.177915	0.0825	0.1311	5008	,	,		11083	0.2312		0.1809	False		,,,				2504	0.2822				p.R95R		Atlas-SNP	.											SLC4A2,NS,carcinoma,+1,1	SLC4A2	98	1	0			c.C285A						PASS	.	C	,,,	426,3978	197.1+/-221.3	24,378,1800	58.0	67.0	64.0		285,258,243,285	2.9	1.0	7	dbSNP_86	64	1769,6825	304.2+/-306.8	174,1421,2702	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	198,1799,4502	AA,AC,CC		20.5841,9.673,16.8872	,,,	95/1242,86/1233,81/1228,95/1242	150761680	2195,10803	2202	4297	6499	SO:0001819	synonymous_variant	6522	exon4			ACGCCGCCGCAAG		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.285C>A	7.37:g.150761680C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			C|0.839;A|0.161	0.161	strong		0.682	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
MMP10	4319	hgsc.bcm.edu	37	11	102650424	102650424	+	Missense_Mutation	SNP	C	C	T	rs486055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:102650424C>T	ENST00000279441.4	-	2	194	c.158G>A	c.(157-159)aGa>aAa	p.R53K		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	53			R -> K (in dbSNP:rs486055). {ECO:0000269|Ref.4, 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)	ACTGTCCTTTCTTCTAAACTG	0.378													C|||	227	0.0453275	0.0045	0.0663	5008	,	,		19174	0.001		0.1382	False		,,,				2504	0.0358				p.R53K		Atlas-SNP	.											.	MMP10	44	.	0			c.G158A						PASS	.	C	LYS/ARG	120,4286	87.8+/-126.4	2,116,2085	85.0	77.0	80.0		158	4.2	1.0	11	dbSNP_83	80	1343,7255	262.4+/-284.4	108,1127,3064	yes	missense	MMP10	NM_002425.2	26	110,1243,5149	TT,TC,CC		15.6199,2.7236,11.2504	benign	53/477	102650424	1463,11541	2203	4299	6502	SO:0001583	missense	4319	exon2			TCCTTTCTTCTAA	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.158G>A	11.37:g.102650424C>T	ENSP00000279441:p.Arg53Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	138	0.06318681318681318	2	0.0040650406504065045	29	0.08011049723756906	0	0.0	107	0.14116094986807387	c	4.269	0.048987	0.08243	0.027236	0.156199	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.32753	1.44;1.44	4.25	4.25	0.50352	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.121332	0.37178	N	0.002214	T	0.00039	0.0001	N	0.13168	0.305	0.09310	N	1	B	0.19073	0.033	B	0.22152	0.038	T	0.34004	-0.9846	10	0.02654	T	1	.	8.6471	0.34011	0.0:0.7624:0.153:0.0845	rs486055;rs17359452;rs17860947;rs60436444;rs486055	53	P09238	MMP10_HUMAN	K	53	ENSP00000279441:R53K;ENSP00000441485:R53K	ENSP00000279441:R53K	R	-	2	0	MMP10	102155634	0.000000	0.05858	0.977000	0.42913	0.046000	0.14306	0.542000	0.23222	2.365000	0.80145	0.591000	0.81541	AGA	C|0.916;T|0.084	0.084	strong		0.378	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
CCDC168	643677	hgsc.bcm.edu	37	13	103388370	103388370	+	Missense_Mutation	SNP	C	C	T	rs9518825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:103388370C>T	ENST00000322527.2	-	1	789	c.790G>A	c.(790-792)Ggt>Agt	p.G264S		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	264			G -> S (in dbSNP:rs9518825).					p.G264S(2)									AGTATTCTACCTTCCCTGCCT	0.398													C|||	1172	0.234026	0.2769	0.1931	5008	,	,		22757	0.4097		0.1123	False		,,,				2504	0.1493				p.G4893S		Atlas-SNP	.											Q8N800_HUMAN,NS,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	kidney(2)	c.G14677A						scavenged	.	C	SER/GLY	398,986		59,280,353	217.0	183.0	193.0		14677	2.3	0.0	13	dbSNP_119	193	404,2778		24,356,1211	yes	missense	CCDC168	NM_001146197.1	56	83,636,1564	TT,TC,CC		12.6964,28.7572,17.5646	probably-damaging	4893/7082	103388370	802,3764	692	1591	2283	SO:0001583	missense	643677	exon4			TTCTACCTTCCCT		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.790G>A	13.37:g.103388370C>T	ENSP00000320232:p.Gly264Ser	Somatic	140	3	0.0214286		WXS	Illumina HiSeq	Phase_I	168	88	0.52381	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		537	0.24587912087912087	127	0.258130081300813	73	0.20165745856353592	251	0.4388111888111888	86	0.11345646437994723	C	16.33	3.091642	0.55968	0.287572	0.126964	ENSG00000175820	ENST00000322527	T	0.05199	3.48	3.25	2.35	0.29111	.	0.246855	0.21252	N	0.077635	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.71674	0.998	D	0.67725	0.953	T	0.06232	-1.0838	9	0.05620	T	0.96	.	7.5159	0.27600	0.2562:0.7438:0.0:0.0	rs9518825;rs17635161;rs52793883;rs61475030;rs9518825	264	Q8NDH2	CC168_HUMAN	S	264	ENSP00000320232:G264S	ENSP00000320232:G264S	G	-	1	0	CCDC168	102186371	0.000000	0.05858	0.006000	0.13384	0.433000	0.31745	-0.484000	0.06528	0.882000	0.36016	0.404000	0.27445	GGT	C|0.737;T|0.263	0.263	strong		0.398	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5239921	5239921	+	Silent	SNP	C	C	T	rs11742341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:5239921C>T	ENST00000274181.7	+	16	2544	c.2406C>T	c.(2404-2406)acC>acT	p.T802T		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	802	Spacer.				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						GGCACTGGACCGTGGACTGGC	0.527													C|||	574	0.114617	0.0061	0.111	5008	,	,		17373	0.0764		0.1928	False		,,,				2504	0.2229				p.T802T		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2406T						PASS	.	C		126,3638		1,124,1757	106.0	101.0	103.0		2406	-11.1	0.3	5	dbSNP_120	103	1609,6609		163,1283,2663	no	coding-synonymous	ADAMTS16	NM_139056.2		164,1407,4420	TT,TC,CC		19.579,3.3475,14.4801		802/1225	5239921	1735,10247	1882	4109	5991	SO:0001819	synonymous_variant	170690	exon16			CTGGACCGTGGAC	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.2406C>T	5.37:g.5239921C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			C|0.865;T|0.135	0.135	strong		0.527	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
SLC36A3	285641	hgsc.bcm.edu	37	5	150663655	150663655	+	Silent	SNP	C	C	T	rs17660011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150663655C>T	ENST00000335230.3	-	8	1335	c.924G>A	c.(922-924)aaG>aaA	p.K308K	SLC36A3_ENST00000377713.3_Silent_p.K349K	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	308						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)			CTGACCCAAACTTCATGTAGC	0.498													C|||	99	0.0197684	0.003	0.0202	5008	,	,		21814	0.0		0.0398	False		,,,				2504	0.0419				p.K349K		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G1047A						PASS	.	C	,	63,4343	58.1+/-94.6	1,61,2141	185.0	164.0	171.0		1047,924	2.4	1.0	5	dbSNP_123	171	372,8228	123.1+/-182.0	4,364,3932	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	5,425,6073	TT,TC,CC		4.3256,1.4299,3.3446	,	349/512,308/471	150663655	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon9			CCCAAACTTCATG	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.924G>A	5.37:g.150663655C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	87	53	0.609195	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			C|0.976;T|0.024	0.024	strong		0.498	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
USP35	57558	hgsc.bcm.edu	37	11	77920863	77920863	+	Silent	SNP	C	C	A	rs2512527	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000526425.1_Silent_p.P385P|USP35_ENST00000441408.2_Silent_p.P240P|USP35_ENST00000530535.1_3'UTR	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	93	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	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	
MUC16	94025	hgsc.bcm.edu	37	19	9077436	9077436	+	Missense_Mutation	SNP	G	G	A	rs1862462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9077436G>A	ENST00000397910.4	-	3	10213	c.10010C>T	c.(10009-10011)tCa>tTa	p.S3337L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3338	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						AGTTGTCTTTGAAACCAGTTC	0.502													G|||	1243	0.248203	0.1997	0.2118	5008	,	,		21495	0.249		0.3121	False		,,,				2504	0.273				p.S3337L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C10010T						PASS	.	G	LEU/SER	834,3080		98,638,1221	144.0	134.0	137.0		10010	-0.1	0.0	19	dbSNP_92	137	2394,5932		347,1700,2116	yes	missense	MUC16	NM_024690.2	145	445,2338,3337	AA,AG,GG		28.7533,21.3081,26.3725	benign	3337/14508	9077436	3228,9012	1957	4163	6120	SO:0001583	missense	94025	exon3			GTCTTTGAAACCA	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.10010C>T	19.37:g.9077436G>A	ENSP00000381008:p.Ser3337Leu	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	193	87	0.450777	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	552	0.25274725274725274	108	0.21951219512195122	88	0.2430939226519337	124	0.21678321678321677	232	0.30606860158311344	g	3.953	-0.011966	0.07727	0.213081	0.287533	ENSG00000181143	ENST00000397910	T	0.02656	4.21	2.13	-0.123	0.13527	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.06405	0.002	T	0.47459	-0.9116	8	0.87932	D	0	.	4.6935	0.12791	0.3344:0.0:0.6656:0.0	rs1862462;rs17516250;rs56508237;rs58424799;rs1862462	3337	B5ME49	.	L	3337	ENSP00000381008:S3337L	ENSP00000381008:S3337L	S	-	2	0	MUC16	8938436	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.053000	0.11846	0.035000	0.15519	-1.054000	0.02325	TCA	G|0.749;A|0.251	0.251	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713821	32713821	+	Silent	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32713821C>A	ENST00000374940.3	+	3	687	c.585C>A	c.(583-585)ggC>ggA	p.G195G		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	195	Alpha-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)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	AGCACTGGGGCCTGGACGAGC	0.493																																					p.G195G		Atlas-SNP	.											HLA-DQA2,NS,carcinoma,+2,1	HLA-DQA2	27	1	0			c.C585A						scavenged	.						170.0	197.0	188.0					6																	32713821		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			CTGGGGCCTGGAC		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.585C>A	6.37:g.32713821C>A		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	408	19	0.0465686	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|0.778;A|0.222	0.222	strong		0.493	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
RCC2	55920	hgsc.bcm.edu	37	1	17739586	17739586	+	Silent	SNP	G	G	A	rs942457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17739586G>A	ENST00000375436.4	-	10	1483	c.1296C>T	c.(1294-1296)atC>atT	p.I432I	RCC2_ENST00000375433.3_Silent_p.I432I|AC004824.1_ENST00000583469.1_RNA	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	432					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)			breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|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;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		CCAGGCTCCGGATTCTCCAGC	0.582													G|||	1657	0.330871	0.3661	0.3689	5008	,	,		17975	0.1647		0.3688	False		,,,				2504	0.3885				p.I432I		Atlas-SNP	.											.	RCC2	46	.	0			c.C1296T						PASS	.	G	,	1710,2696	512.6+/-368.1	351,1008,844	43.0	41.0	42.0		1296,1296	4.3	1.0	1	dbSNP_86	42	3022,5578	464.2+/-366.2	549,1924,1827	no	coding-synonymous,coding-synonymous	RCC2	NM_001136204.2,NM_018715.3	,	900,2932,2671	AA,AG,GG		35.1395,38.8107,36.3832	,	432/523,432/523	17739586	4732,8274	2203	4300	6503	SO:0001819	synonymous_variant	55920	exon9			GCTCCGGATTCTC		CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.1296C>T	1.37:g.17739586G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001136204	Q8IVL9|Q9BSN6|Q9NPV8	Silent	SNP	ENST00000375436.4	37	CCDS181.1																																																																																			G|0.657;A|0.343	0.343	strong		0.582	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007144.1	NM_018715	
INPP4A	3631	hgsc.bcm.edu	37	2	99179971	99179971	+	Silent	SNP	C	C	G	rs61748143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:99179971C>G	ENST00000523221.1	+	17	1914	c.1914C>G	c.(1912-1914)acC>acG	p.T638T	INPP4A_ENST00000409540.3_Silent_p.T599T|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000074304.5_Silent_p.T638T|INPP4A_ENST00000409016.4_Silent_p.T599T|INPP4A_ENST00000545415.1_Silent_p.T599T|INPP4A_ENST00000409851.3_Silent_p.T633T			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	638					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						CCACTCTCACCGACTGCGTGG	0.552													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18327	0.0		0.0119	False		,,,				2504	0.0051				p.T638T		Atlas-SNP	.											INPP4A_ENST00000409540,caecum,carcinoma,+2,3	INPP4A	205	3	0			c.C1914G						PASS	.	C	,,,	5,4177		0,5,2086	36.0	41.0	39.0		1914,1899,1797,1797	-10.9	0.0	2	dbSNP_129	39	104,8340		1,102,4119	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	1,107,6205	GG,GC,CC		1.2316,0.1196,0.8633	,,,	638/978,633/973,599/955,599/939	99179971	109,12517	2091	4222	6313	SO:0001819	synonymous_variant	3631	exon19			TCTCACCGACTGC	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1914C>G	2.37:g.99179971C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.994;G|0.006	0.006	strong		0.552	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		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)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19.0	24.0	22.0		3184	2.8	1.0	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	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.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
MYO1H	283446	hgsc.bcm.edu	37	12	109853349	109853349	+	Silent	SNP	A	A	G	rs73194218	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109853349A>G	ENST00000431443.2	+	14	1503	c.1503A>G	c.(1501-1503)ccA>ccG	p.P501P	MYO1H_ENST00000310903.5_Silent_p.P491P	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	501	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TGGCTGGTCCAAAGGGCCGAA	0.522													A|||	138	0.0275559	0.0023	0.049	5008	,	,		17594	0.0		0.0785	False		,,,				2504	0.0225				p.P491P		Atlas-SNP	.											.	MYO1H	98	.	0			c.A1473G						PASS	.	A		51,3821		0,51,1885	47.0	48.0	48.0		1473	-11.0	0.0	12	dbSNP_130	48	551,7759		19,513,3623	no	coding-synonymous	MYO1H	NM_001101421.3		19,564,5508	GG,GA,AA		6.6306,1.3171,4.9417		491/1023	109853349	602,11580	1936	4155	6091	SO:0001819	synonymous_variant	283446	exon14			TGGTCCAAAGGGC		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1503A>G	12.37:g.109853349A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				A|0.958;G|0.042	0.042	strong		0.522	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
ANKRD2	26287	hgsc.bcm.edu	37	10	99332488	99332488	+	Silent	SNP	A	A	C	rs12221474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99332488A>C	ENST00000307518.5	+	1	291	c.24A>C	c.(22-24)gcA>gcC	p.A8A	ANKRD2_ENST00000455090.1_5'Flank|ANKRD2_ENST00000370655.1_5'UTR|ANKRD2_ENST00000298808.5_Silent_p.A8A			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	8	May mediate interaction with PML, p53/TP53 and YBX1.				muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		CCAGCTGGGCAGGGGTGGGTG	0.677											OREG0020418	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1770	0.353435	0.2557	0.2666	5008	,	,		16027	0.5288		0.2724	False		,,,				2504	0.4499				p.A8A		Atlas-SNP	.											.	ANKRD2	27	.	0			c.A24C						PASS	.	A	,	1027,3379		125,777,1301	25.0	23.0	24.0		24,24	2.8	0.6	10	dbSNP_120	24	2202,6394		276,1650,2372	no	coding-synonymous,coding-synonymous	ANKRD2	NM_001129981.1,NM_020349.2	,	401,2427,3673	CC,CA,AA		25.6166,23.3091,24.8346	,	8/328,8/361	99332488	3229,9773	2203	4298	6501	SO:0001819	synonymous_variant	26287	exon1			CTGGGCAGGGGTG	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"""Ankyrin repeat domain containing"""	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.24A>C	10.37:g.99332488A>C		Somatic	134	0	0	1342	WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_001129981	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Silent	SNP	ENST00000307518.5	37	CCDS7466.1																																																																																			A|0.721;C|0.279	0.279	strong		0.677	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SELP	6403	hgsc.bcm.edu	37	1	169566313	169566313	+	Missense_Mutation	SNP	C	C	T	rs6127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169566313C>T	ENST00000263686.6	-	11	1844	c.1807G>A	c.(1807-1809)Gac>Aac	p.D603N	SELP_ENST00000367794.2_Missense_Mutation_p.D541N|SELP_ENST00000367788.2_Missense_Mutation_p.D541N|SELP_ENST00000367793.2_Missense_Mutation_p.D541N|SELP_ENST00000367786.2_Missense_Mutation_p.D541N|SELP_ENST00000367791.2_Intron|SELP_ENST00000367792.2_Intron|SELP_ENST00000458599.2_Intron	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	603	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.		D -> N (in dbSNP:rs6127). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2466574, ECO:0000269|PubMed:9668170, ECO:0000269|Ref.2}.		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)	AAGCCGTTGTCACAAGAGAAA	0.488													T|||	3760	0.750799	0.8729	0.7003	5008	,	,		16183	0.9573		0.5905	False		,,,				2504	0.5736				p.D603N		Atlas-SNP	.											.	SELP	132	.	0			c.G1807A						PASS	.	T	ASN/ASP	3593,813	322.1+/-297.4	1483,627,93	70.0	73.0	72.0		1807	-1.8	0.0	1	dbSNP_52	72	4802,3798	537.9+/-383.3	1332,2138,830	yes	missense	SELP	NM_003005.3	23	2815,2765,923	TT,TC,CC		44.1628,18.4521,35.4529	benign	603/831	169566313	8395,4611	2203	4300	6503	SO:0001583	missense	6403	exon11			CGTTGTCACAAGA	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.1807G>A	1.37:g.169566313C>T	ENSP00000263686:p.Asp603Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	176	175	0.994318	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	1642	0.7518315018315018	411	0.8353658536585366	254	0.7016574585635359	545	0.9527972027972028	432	0.5699208443271768	T	0.033	-1.325092	0.01309	0.815479	0.558372	ENSG00000174175	ENST00000367790;ENST00000426706;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367788;ENST00000367786;ENST00000458599	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.13	-1.76	0.08006	Complement control module (2);Sushi/SCR/CCP (3);	0.773311	0.11700	N	0.538069	T	0.09730	0.0239	N	0.03016	-0.435	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.18871	-1.0323	9	0.07325	T	0.83	-2.9349	5.7018	0.17887	0.1435:0.4348:0.0:0.4217	rs6127;rs6127	603;603	P16109;G3V1U2	LYAM3_HUMAN;.	N	603;602;603;603;541;541;541;541;526	ENSP00000263686:D603N;ENSP00000356767:D541N;ENSP00000356768:D541N;ENSP00000356762:D541N;ENSP00000356760:D541N	ENSP00000263686:D603N	D	-	1	0	SELP	167832937	0.000000	0.05858	0.010000	0.14722	0.320000	0.28249	-0.666000	0.05280	-0.262000	0.09392	-0.269000	0.10298	GAC	C|0.306;T|0.694	0.694	strong		0.488	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
DCHS1	8642	hgsc.bcm.edu	37	11	6648424	6648424	+	Missense_Mutation	SNP	G	G	A	rs4758443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6648424G>A	ENST00000299441.3	-	14	6257	c.5846C>T	c.(5845-5847)aCg>aTg	p.T1949M		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1949	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs4758443).		branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCGCGCACCGTGATGGTGAC	0.612													G|||	1490	0.297524	0.1233	0.3372	5008	,	,		18735	0.4236		0.3728	False		,,,				2504	0.2975				p.T1949M		Atlas-SNP	.											DCHS1,colon,carcinoma,0,1	DCHS1	277	1	0			c.C5846T						PASS	.	G	MET/THR	758,3644	302.4+/-287.4	78,602,1521	88.0	73.0	78.0		5846	2.3	0.4	11	dbSNP_111	78	3160,5432	468.9+/-367.4	568,2024,1704	yes	missense	DCHS1	NM_003737.2	81	646,2626,3225	AA,AG,GG		36.7784,17.2194,30.1524	benign	1949/3299	6648424	3918,9076	2201	4296	6497	SO:0001583	missense	8642	exon14			CGCACCGTGATGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5846C>T	11.37:g.6648424G>A	ENSP00000299441:p.Thr1949Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	728	0.3333333333333333	61	0.12398373983739837	124	0.3425414364640884	254	0.44405594405594406	289	0.3812664907651715	G	0.539	-0.854540	0.02630	0.172194	0.367784	ENSG00000166341	ENST00000299441	T	0.01838	4.61	5.18	2.32	0.28847	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.48286	D	0.000181	T	0.00012	0.0000	M	0.75447	2.3	0.53005	P	3.6999999999953737E-5	B	0.17667	0.023	B	0.14023	0.01	T	0.41875	-0.9484	9	0.41790	T	0.15	.	5.9633	0.19310	0.2566:0.0:0.6189:0.1246	rs4758443;rs52796770;rs61481044;rs4758443	1949	Q96JQ0	PCD16_HUMAN	M	1949	ENSP00000299441:T1949M	ENSP00000299441:T1949M	T	-	2	0	DCHS1	6605000	0.423000	0.25482	0.399000	0.26333	0.063000	0.16089	0.935000	0.28924	0.359000	0.24239	-1.450000	0.01041	ACG	G|0.687;A|0.313	0.313	strong		0.612	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
USP35	57558	hgsc.bcm.edu	37	11	77909014	77909014	+	Missense_Mutation	SNP	G	G	A	rs2510044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77909014G>A	ENST00000529308.1	+	3	967	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_5'Flank|USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530535.1_Intron	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	72	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	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	
YWHAB	7529	hgsc.bcm.edu	37	20	43530234	43530234	+	Silent	SNP	A	A	C	rs4931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:43530234A>C	ENST00000372839.3	+	3	334	c.60A>C	c.(58-60)cgA>cgC	p.R20R	YWHAB_ENST00000479421.1_3'UTR|YWHAB_ENST00000353703.4_Silent_p.R20R	NM_003404.3	NP_003395.1	P31946	1433B_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta	20					activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cytoplasmic sequestering of protein (GO:0051220)|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)|hippo signaling (GO:0035329)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|MAPK cascade (GO:0000165)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of catalytic activity (GO:0043085)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein heterooligomerization (GO:0051291)|protein targeting (GO:0006605)|Ras protein signal transduction (GO:0007265)|RNA metabolic process (GO:0016070)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(1)	12		Myeloproliferative disorder(115;0.0122)				AGGCTGAGCGATATGATGATA	0.463													C|||	1505	0.300519	0.5514	0.1916	5008	,	,		19591	0.1409		0.2903	False		,,,				2504	0.2137				p.R20R		Atlas-SNP	.											.	YWHAB	24	.	0			c.A60C						PASS	.	C	,	2198,2208	582.3+/-385.5	563,1072,568	69.0	68.0	68.0		60,60	3.7	1.0	20	dbSNP_52	68	2573,6027	679.4+/-403.5	410,1753,2137	no	coding-synonymous,coding-synonymous	YWHAB	NM_003404.3,NM_139323.2	,	973,2825,2705	CC,CA,AA		29.9186,49.8865,36.6831	,	20/247,20/247	43530234	4771,8235	2203	4300	6503	SO:0001819	synonymous_variant	7529	exon3			TGAGCGATATGAT	X57346	CCDS13339.1	20q13.1	2013-12-03	2013-12-03		ENSG00000166913	ENSG00000166913			12849	protein-coding gene	gene with protein product	"""14-3-3 beta"", ""14-3-3 alpha"""	601289	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, alpha polypeptide"", ""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide"""	YWHAA		8617504, 7890696	Standard	NM_003404		Approved		uc002xmu.3	P31946	OTTHUMG00000032549	ENST00000372839.3:c.60A>C	20.37:g.43530234A>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	47	0.401709	NM_003404	A8K9K2|E1P616	Silent	SNP	ENST00000372839.3	37	CCDS13339.1																																																																																			A|0.659;C|0.340;G|0.000;T|0.000	0.340	strong		0.463	YWHAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079386.3	NM_003404	
SLC25A46	91137	hgsc.bcm.edu	37	5	110074967	110074967	+	Silent	SNP	C	C	T	rs145421520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:110074967C>T	ENST00000355943.3	+	1	273	c.147C>T	c.(145-147)atC>atT	p.I49I	SLC25A46_ENST00000504098.1_5'Flank|SLC25A46_ENST00000513807.1_Intron|SLC25A46_ENST00000447245.2_Silent_p.I49I|SLC25A46_ENST00000509442.2_Intron	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	49					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)		CCCCAGATATCCCCGGCAGCC	0.692													C|||	82	0.0163738	0.0212	0.0202	5008	,	,		12986	0.0079		0.0288	False		,,,				2504	0.0031				p.I49I		Atlas-SNP	.											.	SLC25A46	33	.	0			c.C147T						PASS	.	C		82,4276		0,82,2097	13.0	15.0	14.0		147	2.4	1.0	5	dbSNP_134	14	121,8419		1,119,4150	no	coding-synonymous	SLC25A46	NM_138773.1		1,201,6247	TT,TC,CC		1.4169,1.8816,1.5739		49/419	110074967	203,12695	2179	4270	6449	SO:0001819	synonymous_variant	91137	exon1			AGATATCCCCGGC	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.147C>T	5.37:g.110074967C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_138773	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Silent	SNP	ENST00000355943.3	37	CCDS4100.1																																																																																			C|0.982;T|0.018	0.018	strong		0.692	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773	
TNIP1	10318	hgsc.bcm.edu	37	5	150425467	150425467	+	Silent	SNP	G	G	A	rs2233299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000522226.1_Silent_p.G297G|TNIP1_ENST00000523200.1_Silent_p.G297G|TNIP1_ENST00000518977.1_Silent_p.G297G|TNIP1_ENST00000524280.1_Silent_p.G297G|TNIP1_ENST00000520931.1_Silent_p.G244G|TNIP1_ENST00000521591.1_Silent_p.G297G|TNIP1_ENST00000315050.7_Silent_p.G297G|TNIP1_ENST00000521423.1_Intron	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	54	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	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	
FBLN5	10516	hgsc.bcm.edu	37	14	92347680	92347680	+	Silent	SNP	A	A	G	rs2430347	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:92347680A>G	ENST00000342058.4	-	9	1538	c.945T>C	c.(943-945)atT>atC	p.I315I	FBLN5_ENST00000556154.1_Silent_p.I320I|FBLN5_ENST00000267620.10_Silent_p.I356I	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	315	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				GGATGGGGTCAATGCATTTGA	0.532													G|||	3931	0.784944	0.7708	0.8415	5008	,	,		20322	0.8323		0.7525	False		,,,				2504	0.7485				p.I315I		Atlas-SNP	.											.	FBLN5	60	.	0			c.T945C						PASS	.	G		3469,937	356.1+/-313.4	1364,741,98	101.0	83.0	89.0		945	-11.0	0.1	14	dbSNP_100	89	6374,2226	378.4+/-338.9	2367,1640,293	no	coding-synonymous	FBLN5	NM_006329.3		3731,2381,391	GG,GA,AA		25.8837,21.2665,24.3195		315/449	92347680	9843,3163	2203	4300	6503	SO:0001819	synonymous_variant	10516	exon9			GGGGTCAATGCAT	AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"""Fibulins"""	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.945T>C	14.37:g.92347680A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_006329	O75966|Q6IAL4|Q6UWA3	Silent	SNP	ENST00000342058.4	37	CCDS9898.1																																																																																			A|0.229;G|0.771	0.771	strong		0.532	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39387558	39387558	+	Silent	SNP	C	C	T	rs1065184	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39387558C>T	ENST00000333467.3	+	6	990	c.945C>T	c.(943-945)taC>taT	p.Y315Y	APOBEC3B_ENST00000402182.3_Silent_p.Y315Y|APOBEC3B-AS1_ENST00000513758.2_RNA|APOBEC3B_ENST00000407298.3_Silent_p.Y290Y	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	315					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)					TCTATGATTACGACCCCCTAT	0.582																																					p.Y315Y		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C945T						PASS	.	C		2368,2032		490,1388,322	108.0	102.0	104.0		945	-3.4	0.0	22	dbSNP_86	104	3902,4662		697,2508,1077	no	coding-synonymous	APOBEC3B	NM_004900.3		1187,3896,1399	TT,TC,CC		45.5628,46.1818,48.3647		315/383	39387558	6270,6694	2200	4282	6482	SO:0001819	synonymous_variant	9582	exon6			TGATTACGACCCC	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.945C>T	22.37:g.39387558C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	102	69	0.676471	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.333;T|0.667	0.667	strong		0.582	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1988167	1988167	+	Silent	SNP	T	T	C	rs7966806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000585732.1_Silent_p.S418S|CACNA2D4_ENST00000585708.1_Silent_p.S469S|CACNA2D4_ENST00000587995.1_Silent_p.S533S|CACNA2D4_ENST00000588077.1_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	31	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	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		
TMEM156	80008	hgsc.bcm.edu	37	4	38987965	38987965	+	Missense_Mutation	SNP	C	C	T	rs75988651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:38987965C>T	ENST00000381938.3	-	5	921	c.814G>A	c.(814-816)Gtt>Att	p.V272I		NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	272						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CCTGAAAGAACCTGCACATTC	0.398													C|||	76	0.0151757	0.0045	0.0216	5008	,	,		19678	0.0		0.0477	False		,,,				2504	0.0072				p.V272I		Atlas-SNP	.											.	TMEM156	31	.	0			c.G814A						PASS	.	C	ILE/VAL	35,4371	40.0+/-72.8	1,33,2169	122.0	109.0	113.0		814	5.1	0.6	4	dbSNP_131	113	449,8151	135.7+/-192.9	10,429,3861	yes	missense	TMEM156	NM_024943.1	29	11,462,6030	TT,TC,CC		5.2209,0.7944,3.7214	possibly-damaging	272/297	38987965	484,12522	2203	4300	6503	SO:0001583	missense	80008	exon5			AAAGAACCTGCAC	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.814G>A	4.37:g.38987965C>T	ENSP00000371364:p.Val272Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	49	0.022435897435897436	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	37	0.048812664907651716	C	16.23	3.065636	0.55539	0.007944	0.052209	ENSG00000121895	ENST00000381938	T	0.27104	1.69	5.08	5.08	0.68730	.	0.222920	0.31554	N	0.007453	T	0.10252	0.0251	L	0.58101	1.795	0.43381	D	0.995483	D	0.71674	0.998	D	0.66084	0.941	T	0.00166	-1.1966	10	0.30078	T	0.28	-7.5312	14.1658	0.65475	0.0:1.0:0.0:0.0	.	272	Q8N614	TM156_HUMAN	I	272	ENSP00000371364:V272I	ENSP00000371364:V272I	V	-	1	0	TMEM156	38664360	0.894000	0.30519	0.551000	0.28230	0.005000	0.04900	3.303000	0.51858	2.804000	0.96469	0.462000	0.41574	GTT	C|0.965;T|0.035	0.035	strong		0.398	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	
XRCC1	7515	hgsc.bcm.edu	37	19	44057227	44057227	+	Silent	SNP	T	T	C	rs915927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44057227T>C	ENST00000262887.5	-	7	1165	c.618A>G	c.(616-618)ccA>ccG	p.P206P	XRCC1_ENST00000543982.1_Silent_p.P175P|L34079.3_ENST00000597119.1_RNA			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	206					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)				TAGGTCCTGCTGGGTCGCTGG	0.552								Other BER factors					C|||	1609	0.321286	0.4047	0.255	5008	,	,		17750	0.1161		0.4175	False		,,,				2504	0.3681				p.P206P		Atlas-SNP	.											.	XRCC1	47	.	0			c.A618G						PASS	.	C		1779,2623		364,1051,786	54.0	50.0	51.0		618	-7.8	0.2	19	dbSNP_86	51	3686,4914		800,2086,1414	no	coding-synonymous	XRCC1	NM_006297.2		1164,3137,2200	CC,CT,TT		42.8605,40.4134,42.032		206/634	44057227	5465,7537	2201	4300	6501	SO:0001819	synonymous_variant	7515	exon7			TCCTGCTGGGTCG	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.618A>G	19.37:g.44057227T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	25	11	0.44	NM_006297	Q6IBS4|Q9HCB1	Silent	SNP	ENST00000262887.5	37	CCDS12624.1																																																																																			T|0.645;G|0.000;C|0.355;A|0.000	0.355	strong		0.552	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232596728	232596728	+	Silent	SNP	G	G	A	rs74807360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:232596728G>A	ENST00000366630.1	-	9	3358	c.3000C>T	c.(2998-3000)gcC>gcT	p.A1000A	SIPA1L2_ENST00000262861.4_Silent_p.A1000A|SIPA1L2_ENST00000308942.4_Silent_p.A74A			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1000	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)				GGGTCAGAGTGGCCACGGCTA	0.572													G|||	137	0.0273562	0.0023	0.0519	5008	,	,		19230	0.001		0.0785	False		,,,				2504	0.0184				p.A1000A		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C3000T						PASS	.	G		55,4351	49.6+/-84.7	0,55,2148	45.0	49.0	47.0		3000	4.7	1.0	1	dbSNP_132	47	610,7990	153.4+/-207.8	21,568,3711	no	coding-synonymous	SIPA1L2	NM_020808.3		21,623,5859	AA,AG,GG		7.093,1.2483,5.113		1000/1723	232596728	665,12341	2203	4300	6503	SO:0001819	synonymous_variant	57568	exon8			CAGAGTGGCCACG	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.3000C>T	1.37:g.232596728G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.947;A|0.053	0.053	strong		0.572	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
RNF19A	25897	hgsc.bcm.edu	37	8	101299859	101299859	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:101299859G>A	ENST00000519449.1	-	3	860	c.544C>T	c.(544-546)Cgg>Tgg	p.R182W	RNF19A_ENST00000341084.2_Missense_Mutation_p.R182W	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	182					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			GGATTAAACCGTTCAGTACAT	0.373																																					p.R182W		Atlas-SNP	.											RNF19A,NS,carcinoma,+2,1	RNF19A	67	1	0			c.C544T						scavenged	.						123.0	127.0	126.0					8																	101299859		2203	4300	6503	SO:0001583	missense	25897	exon3			TAAACCGTTCAGT	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"""RING-type (C3HC4) zinc fingers"""	13432	protein-coding gene	gene with protein product		607119	"""ring finger protein 19"", ""ring finger protein 19A"", ""ring finger protein 19A, E3 ubiquitin protein ligase"""	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.544C>T	8.37:g.101299859G>A	ENSP00000428968:p.Arg182Trp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	138	2	0.0144928	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165417	0.78339	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.84070	-1.8;-1.8	5.57	5.57	0.84162	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89743	0.6803	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.88618	0.3161	10	0.38643	T	0.18	.	14.8593	0.70366	0.0:0.0:0.8558:0.1442	.	182	Q9NV58	RN19A_HUMAN	W	182	ENSP00000428968:R182W;ENSP00000342667:R182W	ENSP00000342667:R182W	R	-	1	2	RNF19A	101369035	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.638000	0.67861	2.606000	0.88127	0.650000	0.86243	CGG	.	.	none		0.373	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435	
PHIP	55023	hgsc.bcm.edu	37	6	79657391	79657391	+	Silent	SNP	G	G	A	rs1984195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:79657391G>A	ENST00000275034.4	-	36	4322	c.4155C>T	c.(4153-4155)gtC>gtT	p.V1385V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1385	Bromo 2. {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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AAATAAGTCTGACATCTTTAC	0.338													G|||	2545	0.508187	0.3018	0.4611	5008	,	,		17684	0.6835		0.4791	False		,,,				2504	0.6697				p.V1385V		Atlas-SNP	.											.	PHIP	177	.	0			c.C4155T						PASS	.	G		1368,3038	454.0+/-350.5	210,948,1045	145.0	137.0	140.0		4155	4.4	1.0	6	dbSNP_92	140	4234,4366	571.4+/-389.5	1037,2160,1103	no	coding-synonymous	PHIP	NM_017934.5		1247,3108,2148	AA,AG,GG		49.2326,31.0486,43.0724		1385/1822	79657391	5602,7404	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon36			AAGTCTGACATCT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4155C>T	6.37:g.79657391G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			G|0.542;A|0.458	0.458	strong		0.338	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
EFCAB11	90141	hgsc.bcm.edu	37	14	90398907	90398907	+	Silent	SNP	G	G	A	rs8778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:90398907G>A	ENST00000316738.7	-	4	310	c.282C>T	c.(280-282)aaC>aaT	p.N94N	EFCAB11_ENST00000556005.1_Silent_p.N70N|EFCAB11_ENST00000267544.9_Silent_p.N31N|EFCAB11_ENST00000555872.1_Silent_p.N70N|EFCAB11_ENST00000556609.1_Silent_p.N46N|EFCAB11_ENST00000550103.2_5'UTR|RP11-33N16.3_ENST00000555070.1_RNA|EFCAB11_ENST00000538485.2_Silent_p.N94N	NM_001284267.1|NM_145231.3	NP_001271196.1|NP_660274.1	Q9BUY7	EFC11_HUMAN	EF-hand calcium binding domain 11	94	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			large_intestine(1)|lung(1)	2						GTCTTACTTCGTTCCGATATC	0.333													A|||	1277	0.254992	0.2844	0.2594	5008	,	,		16591	0.255		0.1044	False		,,,				2504	0.3671				p.N94N		Atlas-SNP	.											.	EFCAB11	12	.	0			c.C282T						PASS	.	A		1198,3208	709.3+/-407.7	145,908,1150	132.0	127.0	128.0		282	2.9	1.0	14	dbSNP_52	128	1001,7599	773.5+/-407.7	58,885,3357	no	coding-synonymous	EFCAB11	NM_145231.2		203,1793,4507	AA,AG,GG		11.6395,27.1902,16.9076		94/164	90398907	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	90141	exon4			TACTTCGTTCCGA	AK094740	CCDS9887.1, CCDS61522.1, CCDS61523.1, CCDS61524.1, CCDS61525.1	14q32.11	2013-01-10	2011-01-31	2011-01-31	ENSG00000140025	ENSG00000140025		"""EF-hand domain containing"""	20357	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 143"""	C14orf143			Standard	NM_145231		Approved		uc001xxt.3	Q9BUY7	OTTHUMG00000148671	ENST00000316738.7:c.282C>T	14.37:g.90398907G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_145231	B3KT10|B7Z5G9|G3V5G1|Q86T09|Q86TV7|Q8NDQ1	Silent	SNP	ENST00000316738.7	37	CCDS9887.1																																																																																			G|0.806;A|0.194	0.194	strong		0.333	EFCAB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309022.2	NM_145231	
CPZ	8532	hgsc.bcm.edu	37	4	8594616	8594616	+	Missense_Mutation	SNP	G	G	C	rs79736750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:8594616G>C	ENST00000360986.4	+	1	230	c.56G>C	c.(55-57)cGg>cCg	p.R19P	CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000315782.6_Missense_Mutation_p.R19P|CPZ_ENST00000506287.1_3'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	19					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						GCCGCTGCCCGGCCGGGGTGC	0.716													G|||	487	0.0972444	0.0227	0.0807	5008	,	,		9050	0.0476		0.162	False		,,,				2504	0.1943				p.R19P		Atlas-SNP	.											.	CPZ	95	.	0			c.G56C						PASS	.	G	PRO/ARG,,PRO/ARG	147,3233		8,131,1551	2.0	3.0	3.0		56,,56	0.8	0.0	4	dbSNP_131	3	1040,6070		84,872,2599	no	missense,utr-5,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	103,,103	92,1003,4150	CC,CG,GG		14.6273,4.3491,11.3155	possibly-damaging,,possibly-damaging	19/653,,19/642	8594616	1187,9303	1690	3555	5245	SO:0001583	missense	8532	exon1			CTGCCCGGCCGGG	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.56G>C	4.37:g.8594616G>C	ENSP00000354255:p.Arg19Pro	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	30	11	0.366667	NM_003652	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	196	0.08974358974358974	20	0.04065040650406504	32	0.08839779005524862	21	0.03671328671328671	123	0.16226912928759896	G	9.624	1.134623	0.21123	0.043491	0.146273	ENSG00000109625	ENST00000360986;ENST00000315782	T;T	0.58210	0.68;0.35	1.74	0.828	0.18841	.	14.553000	0.00559	N	0.000270	T	0.00300	0.0009	N	0.19112	0.55	0.58432	P	2.9999999999752447E-6	D;P	0.64830	0.994;0.931	D;B	0.65233	0.933;0.084	T	0.08827	-1.0703	9	0.34782	T	0.22	.	4.5504	0.12108	0.2087:0.0:0.7913:0.0	.	19;19	Q66K79-2;Q66K79	.;CBPZ_HUMAN	P	19	ENSP00000354255:R19P;ENSP00000315074:R19P	ENSP00000315074:R19P	R	+	2	0	CPZ	8645516	0.015000	0.18098	0.001000	0.08648	0.102000	0.19082	0.349000	0.20055	0.272000	0.22027	0.298000	0.19748	CGG	G|0.910;C|0.090	0.090	strong		0.716	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
CEP128	145508	hgsc.bcm.edu	37	14	81244337	81244337	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:81244337C>T	ENST00000555265.1	-	16	2640	c.2265G>A	c.(2263-2265)gaG>gaA	p.E755E	CEP128_ENST00000281129.3_Silent_p.E755E			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	755						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				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						ATTTCAACTTCTCCAGCTGAC	0.373																																					p.E755E		Atlas-SNP	.											CEP128,NS,carcinoma,-2,1	CEP128	146	1	0			c.G2265A						scavenged	.						109.0	109.0	109.0					14																	81244337		2203	4300	6503	SO:0001819	synonymous_variant	145508	exon15			CAACTTCTCCAGC	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.2265G>A	14.37:g.81244337C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_152446	B9EK52|Q86X97|Q96ML4	Silent	SNP	ENST00000555265.1	37	CCDS32130.1																																																																																			.	.	none		0.373	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
PDIA2	64714	hgsc.bcm.edu	37	16	336660	336660	+	Silent	SNP	G	G	A	rs11647490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:336660G>A	ENST00000219406.6	+	9	1365	c.1347G>A	c.(1345-1347)acG>acA	p.T449T	PDIA2_ENST00000404312.1_Silent_p.T446T	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	449	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)				TGGATGCCACGGCCAACGAGC	0.612													g|||	2954	0.589856	0.3185	0.6859	5008	,	,		16810	0.8085		0.5835	False		,,,				2504	0.6697				p.T449T		Atlas-SNP	.											PDIA2,NS,carcinoma,0,1	PDIA2	51	1	0			c.G1347A						PASS	.			1662,2658		336,990,834	45.0	47.0	47.0		1347	-9.2	0.8	16	dbSNP_120	47	4841,3643		1394,2053,795	no	coding-synonymous	PDIA2	NM_006849.2		1730,3043,1629	AA,AG,GG		42.9397,38.4722,49.2112		449/526	336660	6503,6301	2160	4242	6402	SO:0001819	synonymous_variant	64714	exon9			TGCCACGGCCAAC	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.1347G>A	16.37:g.336660G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	63	61	0.968254	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1																																																																																			G|0.400;A|0.600	0.600	strong		0.612	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
NID2	22795	hgsc.bcm.edu	37	14	52509063	52509063	+	Missense_Mutation	SNP	G	G	A	rs17831525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52509063G>A	ENST00000216286.5	-	7	1584	c.1585C>T	c.(1585-1587)Cct>Tct	p.P529S	NID2_ENST00000541773.1_Missense_Mutation_p.P476S	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	529	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.		P -> S (in dbSNP:rs17831525).		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)					ACTCGGTGAGGTGCCCCTAAA	0.512													g|||	53	0.0105831	0.0008	0.0173	5008	,	,		21125	0.0		0.0398	False		,,,				2504	0.0				p.P529S		Atlas-SNP	.											.	NID2	201	.	0			c.C1585T						PASS	.	G	SER/PRO	34,4372	38.4+/-70.7	0,34,2169	104.0	105.0	105.0		1585	6.2	1.0	14	dbSNP_123	105	269,8331	103.1+/-164.3	7,255,4038	yes	missense	NID2	NM_007361.3	74	7,289,6207	AA,AG,GG		3.1279,0.7717,2.3297	probably-damaging	529/1376	52509063	303,12703	2203	4300	6503	SO:0001583	missense	22795	exon7			GGTGAGGTGCCCC	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.1585C>T	14.37:g.52509063G>A	ENSP00000216286:p.Pro529Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	28	0.036939313984168866	G	19.57	3.851885	0.71719	0.007717	0.031279	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.53640	0.61;0.61	6.16	6.16	0.99307	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.147145	0.64402	D	0.000007	T	0.37945	0.1022	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	P;D;D	0.69479	0.893;0.964;0.934	T	0.60424	-0.7266	10	0.72032	D	0.01	.	16.2426	0.82423	0.0:0.1689:0.8311:0.0	rs17831525;rs52794399;rs17831525	476;531;529	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	S	529;476;531	ENSP00000216286:P529S;ENSP00000443730:P476S	ENSP00000216286:P529S	P	-	1	0	NID2	51578813	1.000000	0.71417	0.970000	0.41538	0.553000	0.35397	5.969000	0.70422	2.937000	0.99478	0.650000	0.86243	CCT	G|0.978;A|0.022	0.022	strong		0.512	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
TBK1	29110	hgsc.bcm.edu	37	12	64875787	64875787	+	Silent	SNP	T	T	A	rs7486100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:64875787T>A	ENST00000331710.5	+	8	1317	c.978T>A	c.(976-978)atT>atA	p.I326I		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	326	Ubiquitin-like.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		AGATTTATATTCATAGCTATA	0.303													T|||	1769	0.353235	0.1649	0.4798	5008	,	,		15961	0.3046		0.5388	False		,,,				2504	0.3773				p.I326I		Atlas-SNP	.											.	TBK1	149	.	0			c.T978A						PASS	.	T		925,3481	350.0+/-310.6	100,725,1378	67.0	63.0	64.0		978	4.0	1.0	12	dbSNP_116	64	4794,3806	607.5+/-395.3	1329,2136,835	no	coding-synonymous	TBK1	NM_013254.3		1429,2861,2213	AA,AT,TT		44.2558,20.9941,43.972		326/730	64875787	5719,7287	2203	4300	6503	SO:0001819	synonymous_variant	29110	exon8			TTATATTCATAGC	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.978T>A	12.37:g.64875787T>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Silent	SNP	ENST00000331710.5	37	CCDS8968.1																																																																																			T|0.570;A|0.430	0.430	strong		0.303	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254	
NUP210	23225	hgsc.bcm.edu	37	3	13364876	13364876	+	Silent	SNP	G	G	T	rs514084	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13364876G>T	ENST00000254508.5	-	34	4783	c.4701C>A	c.(4699-4701)acC>acA	p.T1567T		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1567					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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CCTGGAAGCTGGTCTGGATGG	0.582													G|||	2793	0.557708	0.3744	0.6124	5008	,	,		18380	0.6974		0.5129	False		,,,				2504	0.6687				p.T1567T		Atlas-SNP	.											.	NUP210	182	.	0			c.C4701A						PASS	.	G		1773,2633	523.9+/-371.2	345,1083,775	122.0	121.0	121.0		4701	2.4	0.0	3	dbSNP_83	121	4191,4409	569.1+/-389.1	1030,2131,1139	no	coding-synonymous	NUP210	NM_024923.2		1375,3214,1914	TT,TG,GG		48.7326,40.2406,45.8558		1567/1888	13364876	5964,7042	2203	4300	6503	SO:0001819	synonymous_variant	23225	exon34			GAAGCTGGTCTGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4701C>A	3.37:g.13364876G>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			G|0.517;T|0.483	0.483	strong		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
TOPORS	10210	hgsc.bcm.edu	37	9	32542793	32542793	+	Missense_Mutation	SNP	G	G	T	rs79708790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32542793G>T	ENST00000360538.2	-	3	1846	c.1730C>A	c.(1729-1731)tCt>tAt	p.S577Y	TOPORS_ENST00000379858.1_Missense_Mutation_p.S512Y	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	577	Interaction with SUMO1.|Interaction with TOP1.|Interaction with p53/TP53.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TCCTCTTACAGATGAGTTCAG	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		22549	0.0		0.001	False		,,,				2504	0.0				p.S577Y		Atlas-SNP	.											.	TOPORS	127	.	0			c.C1730A						PASS	.	G	TYR/SER,TYR/SER	0,4406		0,0,2203	176.0	175.0	175.0		1535,1730	5.7	0.8	9	dbSNP_131	175	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	144,144	0,30,6473	TT,TG,GG		0.3488,0.0,0.2307	possibly-damaging,possibly-damaging	512/981,577/1046	32542793	30,12976	2203	4300	6503	SO:0001583	missense	10210	exon3			CTTACAGATGAGT	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1730C>A	9.37:g.32542793G>T	ENSP00000353735:p.Ser577Tyr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	168	77	0.458333	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	4.776	0.144262	0.09134	0.0	0.003488	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.17528	2.3;2.27	5.65	5.65	0.86999	.	0.000000	0.39615	N	0.001311	T	0.18718	0.0449	N	0.24115	0.695	0.40496	D	0.980597	P	0.48407	0.91	P	0.45946	0.498	T	0.01212	-1.1417	10	0.72032	D	0.01	-10.5062	18.4994	0.90876	0.0:0.0:1.0:0.0	.	577	Q9NS56	TOPRS_HUMAN	Y	577;512	ENSP00000353735:S577Y;ENSP00000369187:S512Y	ENSP00000353735:S577Y	S	-	2	0	TOPORS	32532793	1.000000	0.71417	0.754000	0.31244	0.181000	0.23173	6.680000	0.74518	2.655000	0.90218	0.557000	0.71058	TCT	G|0.998;T|0.002	0.002	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55281315	55281315	+	Intron	SNP	G	G	T	rs2304224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55281315G>T	ENST00000538269.1	+	1	61				KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Intron|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.V5F|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.V5F|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GTCGCTCTTGGTCGTCAGCAT	0.602											OREG0003674	type=REGULATORY REGION|Gene=KIR2DL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	.|||	785	0.156749	0.0855	0.134	5008	,	,		16808	0.127		0.3062	False		,,,				2504	0.1462				p.V5F		Atlas-SNP	.											KIR2DL1,NS,carcinoma,0,1	KIR2DL1	46	1	0			c.G13T						PASS	.	G	PHE/VAL	457,3855		75,307,1774	114.0	99.0	104.0		13	-1.0	0.0	19	dbSNP_100	104	2620,5770		659,1302,2234	no	missense	KIR2DL1	NM_014218.2	50	734,1609,4008	TT,TG,GG		31.2277,10.5983,24.2245		5/349	55281315	3077,9625	2156	4195	6351	SO:0001627	intron_variant	3802	exon1			CTCTTGGTCGTCA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.34+45280G>T	19.37:g.55281315G>T		Somatic	72	0	0	1006	WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_014218	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37		405	0.18543956043956045	39	0.07926829268292683	59	0.16298342541436464	67	0.11713286713286714	240	0.316622691292876	G	9.149	1.015848	0.19355	0.105983	0.312277	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.00498	6.97;7.03	0.514	-1.03	0.10102	.	.	.	.	.	T	0.00012	0.0000	L	0.56340	1.77	0.48632	P	3.130000000000077E-4	B;P	0.41546	0.001;0.754	B;P	0.49192	0.003;0.602	T	0.44952	-0.9294	7	0.62326	D	0.03	.	.	.	.	rs2304224;rs17699016	5;5	Q6IST4;Q6H2H3	.;.	F	5	ENSP00000336769:V5F;ENSP00000291633:V5F	ENSP00000291633:V5F	V	+	1	0	KIR2DL1	59973127	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-1.332000	0.02670	-1.276000	0.02414	-0.779000	0.03376	GTC	G|0.886;T|0.114	0.114	strong		0.602	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
FAT4	79633	hgsc.bcm.edu	37	4	126336703	126336703	+	Silent	SNP	T	T	C	rs17009618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:126336703T>C	ENST00000394329.3	+	5	6598	c.6585T>C	c.(6583-6585)aaT>aaC	p.N2195N	FAT4_ENST00000335110.5_Silent_p.N493N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2195	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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						GCATTGTTAATGGTAATACCA	0.413													T|||	1025	0.204673	0.1452	0.2738	5008	,	,		20411	0.2262		0.1461	False		,,,				2504	0.274				p.N2195N		Atlas-SNP	.											FAT4_ENST00000394329,colon,carcinoma,0,2	FAT4	1752	2	0			c.T6585C						PASS	.	T		576,3830	257.7+/-262.0	37,502,1664	166.0	150.0	156.0		6585	-5.6	0.0	4	dbSNP_123	156	1154,7446	236.9+/-269.0	82,990,3228	no	coding-synonymous	FAT4	NM_024582.4		119,1492,4892	CC,CT,TT		13.4186,13.0731,13.3016		2195/4982	126336703	1730,11276	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon5			TGTTAATGGTAAT	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.6585T>C	4.37:g.126336703T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			T|0.848;C|0.152	0.152	strong		0.413	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
SART1	9092	hgsc.bcm.edu	37	11	65733393	65733393	+	Silent	SNP	C	C	T	rs688862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	70	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	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		
TPTE2	93492	hgsc.bcm.edu	37	13	20006620	20006620	+	Silent	SNP	C	C	T	rs147012324	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:20006620C>T	ENST00000400230.2	-	16	1259	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	TPTE2_ENST00000382978.1_Silent_p.S365S|TPTE2_ENST00000382977.4_Silent_p.S405S|TPTE2_ENST00000457266.2_Silent_p.S294S|TPTE2_ENST00000255310.6_Silent_p.S328S|TPTE2_ENST00000382975.4_Silent_p.S365S|TPTE2_ENST00000400103.2_Silent_p.S294S|TPTE2_ENST00000390680.2_Silent_p.S328S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	405	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S405S(2)|p.S328S(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TACCACGAATCGAATAAATAA	0.388																																					p.S405S		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,6	TPTE2	225	6	4	Substitution - coding silent(4)	prostate(2)|lung(2)	c.G1215A						scavenged	.						32.0	29.0	30.0					13																	20006620		2203	4297	6500	SO:0001819	synonymous_variant	93492	exon17			ACGAATCGAATAA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1215G>A	13.37:g.20006620C>T		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	163	37	0.226994	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	37	CCDS45014.1																																																																																			.	.	weak		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
IL1RL2	8808	hgsc.bcm.edu	37	2	102842467	102842467	+	Silent	SNP	T	T	C	rs2302620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:102842467T>C	ENST00000264257.2	+	9	1227	c.1101T>C	c.(1099-1101)taT>taC	p.Y367Y	IL1RL2_ENST00000441515.2_Silent_p.Y249Y|IL1RL2_ENST00000539491.1_Silent_p.Y367Y|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	367					cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TTCTTTGGTATCGAAGTGCCT	0.393													T|||	936	0.186901	0.2118	0.3804	5008	,	,		14695	0.2004		0.1213	False		,,,				2504	0.0695				p.Y367Y		Atlas-SNP	.											.	IL1RL2	118	.	0			c.T1101C						PASS	.	T		796,3610	321.3+/-297.0	65,666,1472	153.0	130.0	137.0		1101	2.0	0.9	2	dbSNP_100	137	977,7623	211.4+/-252.0	55,867,3378	yes	coding-synonymous	IL1RL2	NM_003854.2		120,1533,4850	CC,CT,TT		11.3605,18.0663,13.6322		367/576	102842467	1773,11233	2203	4300	6503	SO:0001819	synonymous_variant	8808	exon9			TTGGTATCGAAGT	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1101T>C	2.37:g.102842467T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Silent	SNP	ENST00000264257.2	37	CCDS2056.1																																																																																			T|0.845;C|0.155	0.155	strong		0.393	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
MUC2	4583	hgsc.bcm.edu	37	11	1093452	1093452	+	Silent	SNP	G	G	A	rs34136803		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1093452G>A	ENST00000441003.2	+	30	5298	c.5271G>A	c.(5269-5271)ccG>ccA	p.P1757P	MUC2_ENST00000333592.6_Silent_p.P45P|MUC2_ENST00000359061.5_Silent_p.P1724P|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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.P1724P(1)|p.P1757P(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)	ccccaaccccgacacccaccg	0.617																																					p.P1757P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - coding silent(2)	prostate(2)	c.G5271A						scavenged	.						107.0	134.0	125.0					11																	1093452		2040	4045	6085	SO:0001819	synonymous_variant	4583	exon30			AACCCCGACACCC	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.5271G>A	11.37:g.1093452G>A		Somatic	49	6	0.122449		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				A|1.000;|0.000	1.000	weak		0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF264	9422	hgsc.bcm.edu	37	19	57723013	57723013	+	Missense_Mutation	SNP	G	G	A	rs917340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57723013G>A	ENST00000263095.6	+	4	962	c.548G>A	c.(547-549)cGt>cAt	p.R183H	ZNF264_ENST00000536056.1_Missense_Mutation_p.R183H	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	183			R -> H (in dbSNP:rs917340).		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(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		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;0.0135)		GATAGAGTCCGTAGCCATAAC	0.433													.|||	3111	0.621206	0.8427	0.6369	5008	,	,		22916	0.3125		0.6481	False		,,,				2504	0.6012				p.R183H		Atlas-SNP	.											.	ZNF264	65	.	0			c.G548A						PASS	.	A	HIS/ARG	3599,807	750.0+/-412.1	1474,651,78	92.0	83.0	86.0		548	-0.8	0.0	19	dbSNP_86	86	5198,3402	639.8+/-399.5	1571,2056,673	yes	missense	ZNF264	NM_003417.4	29	3045,2707,751	AA,AG,GG		39.5581,18.3159,32.362	benign	183/628	57723013	8797,4209	2203	4300	6503	SO:0001583	missense	9422	exon4			GAGTCCGTAGCCA	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"""Zinc fingers, C2H2-type"", ""-"""	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.548G>A	19.37:g.57723013G>A	ENSP00000263095:p.Arg183His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_003417	A8K8Y9|Q9P1V0	Missense_Mutation	SNP	ENST00000263095.6	37	CCDS33127.1	1306	0.597985347985348	412	0.8373983739837398	232	0.6408839779005525	172	0.3006993006993007	490	0.6464379947229552	g	0.008	-1.921084	0.00498	0.816841	0.604419	ENSG00000083844	ENST00000263095;ENST00000536056	T;T	0.19938	2.11;2.11	1.79	-0.786	0.10946	.	.	.	.	.	T	0.00012	0.0000	N	0.00496	-1.435	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13926	-1.0491	8	0.29301	T	0.29	.	2.5508	0.04748	0.3096:0.0:0.2868:0.4036	rs917340;rs60825977;rs917340	183	O43296	ZN264_HUMAN	H	183	ENSP00000263095:R183H;ENSP00000440376:R183H	ENSP00000263095:R183H	R	+	2	0	ZNF264	62414825	0.002000	0.14202	0.000000	0.03702	0.010000	0.07245	-0.941000	0.03925	-0.873000	0.04032	-0.381000	0.06696	CGT	G|0.358;A|0.642	0.642	strong		0.433	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1		
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497962	32497962	+	Missense_Mutation	SNP	T	T	C	rs701884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32497962T>C	ENST00000374975.3	-	1	102	c.40A>G	c.(40-42)Aag>Gag	p.K14E		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						ACTGTCAGCTTTGCCATGTAG	0.582																																					p.K14E		Atlas-SNP	.											HLA-DRB5,colon,carcinoma,0,2	HLA-DRB5	31	2	0			c.A40G						scavenged	.	C	GLU/LYS	2826,1506		1186,454,526	54.0	60.0	58.0		40	2.7	0.0	6	dbSNP_86	58	5826,2702		2594,638,1032	yes	missense	HLA-DRB5	NM_002125.3	56	3780,1092,1558	CC,CT,TT		31.6839,34.7645,32.7216	benign	14/267	32497962	8652,4208	2166	4264	6430	SO:0001583	missense	3127	exon1			TCAGCTTTGCCAT		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.40A>G	6.37:g.32497962T>C	ENSP00000364114:p.Lys14Glu	Somatic	113	12	0.106195		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	11.88	1.769769	0.31320	0.652355	0.683161	ENSG00000198502	ENST00000374975	T	0.00262	8.4	4.54	2.72	0.32119	MHC classes I/II-like antigen recognition protein (1);	0.968061	0.08500	N	0.936540	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	0.25606	-1.0127	9	0.87932	D	0	.	5.2092	0.15307	0.0:0.6396:0.1692:0.1913	rs701884;rs2308660;rs3176031;rs12722419;rs16870206;rs17204723;rs59934457	14	Q30154	DRB5_HUMAN	E	14	ENSP00000364114:K14E	ENSP00000364114:K14E	K	-	1	0	HLA-DRB5	32605940	0.030000	0.19436	0.007000	0.13788	0.000000	0.00434	0.270000	0.18607	0.564000	0.29238	-1.815000	0.00603	AAG	G|0.542;C|0.051;A|0.407	0.051	strong		0.582	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
GREB1	9687	hgsc.bcm.edu	37	2	11750985	11750985	+	Silent	SNP	C	C	T	rs374277928		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11750985C>T	ENST00000381486.2	+	18	3138	c.2838C>T	c.(2836-2838)caC>caT	p.H946H	GREB1_ENST00000234142.5_Silent_p.H946H|GREB1_ENST00000396123.1_5'Flank	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	946						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCTGCGGCCACGGGCTCATGG	0.687																																					p.H946H	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C2838T						PASS	.	C		0,4120		0,0,2060	29.0	33.0	32.0		2838	4.2	1.0	2		32	1,8383		0,1,4191	no	coding-synonymous	GREB1	NM_014668.3		0,1,6251	TT,TC,CC		0.0119,0.0,0.0080		946/1950	11750985	1,12503	2060	4192	6252	SO:0001819	synonymous_variant	9687	exon18			CGGCCACGGGCTC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2838C>T	2.37:g.11750985C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																			.	.	weak		0.687	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
C6orf1	221491	hgsc.bcm.edu	37	6	34214525	34214525	+	Silent	SNP	G	G	A	rs141610597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:34214525G>A	ENST00000476320.1	-	5	928	c.246C>T	c.(244-246)ccC>ccT	p.P82P	C6orf1_ENST00000413013.2_Silent_p.P62P|C6orf1_ENST00000468145.1_Silent_p.P82P|C6orf1_ENST00000481533.1_Silent_p.P82P|C6orf1_ENST00000335352.3_Silent_p.P62P|C6orf1_ENST00000394990.4_Silent_p.P82P	NM_001008703.1	NP_001008703.1	Q86T20	CF001_HUMAN	chromosome 6 open reading frame 1	82						extracellular region (GO:0005576)				endometrium(1)|prostate(1)	2		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)		GCAGATGGCAGGGCCCCAGGC	0.647											OREG0017364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	8	0.00159744	0.0008	0.0014	5008	,	,		18697	0.0		0.005	False		,,,				2504	0.001				p.P82P		Atlas-SNP	.											.	C6orf1	6	.	0			c.C246T						PASS	.	-	,,	5,4401	9.9+/-24.2	0,5,2198	44.0	41.0	42.0		246,246,246	0.4	0.3	6	dbSNP_134	42	73,8527	40.8+/-97.7	0,73,4227	no	coding-synonymous,coding-synonymous,coding-synonymous	C6orf1	NM_001008703.1,NM_001008704.1,NM_178508.3	,,	0,78,6425	AA,AG,GG		0.8488,0.1135,0.5997	,,	82/160,82/160,82/160	34214525	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	221491	exon5			ATGGCAGGGCCCC	AY062936	CCDS4790.1, CCDS75433.1	6p21.3	2011-12-12			ENSG00000186577	ENSG00000186577			1340	protein-coding gene	gene with protein product		611419				10036196	Standard	NM_178508		Approved	LBH, MGC57858	uc003ojh.3	Q86T20	OTTHUMG00000159754	ENST00000476320.1:c.246C>T	6.37:g.34214525G>A		Somatic	74	0	0	846	WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_001008704	A8K299	Silent	SNP	ENST00000476320.1	37	CCDS4790.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	C6orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357175.1	NM_178508	
ABCC8	6833	hgsc.bcm.edu	37	11	17452492	17452492	+	Silent	SNP	G	G	A	rs1799857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17452492G>A	ENST00000389817.3	-	12	1754	c.1686C>T	c.(1684-1686)caC>caT	p.H562H	ABCC8_ENST00000528202.1_5'UTR|ABCC8_ENST00000302539.4_Silent_p.H562H			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	562	ABC transmembrane type-1 1. {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)	AGAAGCTGACGTGGCCCACGA	0.597													A|||	2153	0.429912	0.4841	0.3516	5008	,	,		20682	0.3125		0.4404	False		,,,				2504	0.5225				p.H562H		Atlas-SNP	.											.	ABCC8	170	.	0			c.C1686T						PASS	.	A		2081,2319	603.7+/-390.2	497,1087,616	70.0	65.0	66.0		1686	-6.9	0.6	11	dbSNP_89	66	3876,4710	606.5+/-395.1	850,2176,1267	no	coding-synonymous	ABCC8	NM_000352.3		1347,3263,1883	AA,AG,GG		45.1433,47.2955,45.8725		562/1582	17452492	5957,7029	2200	4293	6493	SO:0001819	synonymous_variant	6833	exon12			GCTGACGTGGCCC	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.1686C>T	11.37:g.17452492G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1																																																																																			G|0.566;A|0.434	0.434	strong		0.597	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
LVRN	206338	hgsc.bcm.edu	37	5	115298977	115298977	+	Silent	SNP	C	C	T	rs1445708	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:115298977C>T	ENST00000357872.4	+	1	787	c.663C>T	c.(661-663)ttC>ttT	p.F221F	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		221						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGGGACTCTTCCTCAACGTCT	0.667													C|||	1949	0.389177	0.2708	0.4265	5008	,	,		12229	0.4246		0.3917	False		,,,				2504	0.4836				p.F221F		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.C663T						PASS	.	C		1134,3256		174,786,1235	18.0	21.0	20.0		663	3.7	1.0	5	dbSNP_88	20	3333,5213		723,1887,1663	no	coding-synonymous	AQPEP	NM_173800.4		897,2673,2898	TT,TC,CC		39.0007,25.8314,34.5315		221/991	115298977	4467,8469	2195	4273	6468	SO:0001819	synonymous_variant	0	exon1			ACTCTTCCTCAAC																												ENST00000357872.4:c.663C>T	5.37:g.115298977C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			C|0.644;T|0.356	0.356	strong		0.667	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44143153	44143153	+	Missense_Mutation	SNP	C	C	T	rs36086089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:44143153C>T	ENST00000398722.4	-	11	1638	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	LOXHD1_ENST00000441551.2_Missense_Mutation_p.V825M|LOXHD1_ENST00000536736.1_Missense_Mutation_p.V825M			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	547	PLAT 5. {ECO:0000255|PROSITE- ProRule:PRU00152}.		V -> M (in dbSNP:rs36086089).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GCGCCACCCACATCTCCTGTC	0.468													C|||	417	0.0832668	0.1377	0.0519	5008	,	,		19876	0.001		0.0855	False		,,,				2504	0.1145				p.V825M		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G2473A						PASS	.	C	MET/VAL	194,1190		14,166,512	47.0	42.0	44.0		2473	4.1	0.8	18	dbSNP_126	44	276,2906		10,256,1325	yes	missense	LOXHD1	NM_144612.6	21	24,422,1837	TT,TC,CC		8.6738,14.0173,10.2935	benign	825/2212	44143153	470,4096	692	1591	2283	SO:0001583	missense	125336	exon18			CACCCACATCTCC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1639G>A	18.37:g.44143153C>T	ENSP00000381707:p.Val547Met	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		159|159	0.07280219780219781|0.07280219780219781	71|71	0.1443089430894309|0.1443089430894309	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	69|69	0.09102902374670185|0.09102902374670185	C|C	11.71|11.71	1.721028|1.721028	0.30503|0.30503	0.140173|0.140173	0.086738|0.086738	ENSG00000167210|ENSG00000167210	ENST00000441551|ENST00000398722;ENST00000536736;ENST00000335730	.|T;T	.|0.64085	.|-0.08;-0.08	5.05|5.05	4.05|4.05	0.47172|0.47172	.|.	.|0.252404	.|0.41001	.|D	.|0.000970	T|T	0.00412|0.00412	0.0013|0.0013	L|L	0.28556|0.28556	0.865|0.865	0.09310|0.09310	P|P	1.0|1.0	.|B;B	.|0.32753	.|0.194;0.383	.|B;B	.|0.27608	.|0.056;0.081	T|T	0.14282|0.14282	-1.0478|-1.0478	4|9	.|0.45353	.|T	.|0.12	.|.	10.07|10.07	0.42328|0.42328	0.0:0.8682:0.0:0.1318|0.0:0.8682:0.0:0.1318	rs36086089;rs58426200|rs36086089;rs58426200	.|825;547	.|F5GZB4;Q8IVV2-2	.|.;.	Y|M	805|547;825;547	.|ENSP00000381707:V547M;ENSP00000444586:V825M	.|ENSP00000338222:V547M	C|V	-|-	2|1	0|0	LOXHD1|LOXHD1	42397151|42397151	0.198000|0.198000	0.23374|0.23374	0.755000|0.755000	0.31263|0.31263	0.949000|0.949000	0.60115|0.60115	0.749000|0.749000	0.26320|0.26320	2.351000|2.351000	0.79841|0.79841	0.484000|0.484000	0.47621|0.47621	TGT|GTG	C|0.919;T|0.081	0.081	strong		0.468	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
DENND2A	27147	hgsc.bcm.edu	37	7	140244560	140244560	+	Missense_Mutation	SNP	C	C	T	rs2293177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140244560C>T	ENST00000275884.6	-	13	2602	c.2185G>A	c.(2185-2187)Gaa>Aaa	p.E729K	DENND2A_ENST00000496613.1_Missense_Mutation_p.E729K|DENND2A_ENST00000492720.1_Missense_Mutation_p.E729K|DENND2A_ENST00000537639.1_Missense_Mutation_p.E729K			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	729	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.		E -> K (in dbSNP:rs2293177).		positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					CGGCACAGTTCGATCACCTGC	0.642													C|||	1298	0.259185	0.2776	0.2723	5008	,	,		13210	0.1389		0.3191	False		,,,				2504	0.2873				p.E729K		Atlas-SNP	.											.	DENND2A	132	.	0			c.G2185A						PASS	.	C	LYS/GLU	1190,3148		184,822,1163	14.0	19.0	17.0		2185	4.2	0.9	7	dbSNP_100	17	2612,5954		416,1780,2087	yes	missense	DENND2A	NM_015689.3	56	600,2602,3250	TT,TC,CC		30.4926,27.432,29.4637	benign	729/1010	140244560	3802,9102	2169	4283	6452	SO:0001583	missense	27147	exon12			ACAGTTCGATCAC	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2185G>A	7.37:g.140244560C>T	ENSP00000275884:p.Glu729Lys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	CCDS43659.1	512	0.23443223443223443	112	0.22764227642276422	92	0.2541436464088398	71	0.12412587412587413	237	0.31266490765171506	C	22.6	4.306822	0.81247	0.27432	0.304926	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000469373;ENST00000492720	T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77	5.1	4.22	0.49857	DENN (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.74881	2.28	0.09310	P	0.99999483753	B;B	0.24092	0.097;0.068	B;B	0.35312	0.025;0.2	T	0.40590	-0.9555	9	0.39692	T	0.17	-17.0605	14.0959	0.65021	0.0:0.9275:0.0:0.0725	rs2293177;rs9655589;rs10378074;rs17695200;rs57420875;rs2293177	729;729	Q9ULE3-2;Q9ULE3	.;DEN2A_HUMAN	K	729;729;729;76;729	ENSP00000275884:E729K;ENSP00000442245:E729K;ENSP00000419654:E729K;ENSP00000420145:E76K;ENSP00000419464:E729K	ENSP00000275884:E729K	E	-	1	0	DENND2A	139891029	1.000000	0.71417	0.943000	0.38184	0.994000	0.84299	4.769000	0.62300	1.383000	0.46405	0.650000	0.86243	GAA	C|0.758;T|0.242	0.242	strong		0.642	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
SLC14A2	8170	hgsc.bcm.edu	37	18	43204739	43204739	+	Missense_Mutation	SNP	C	C	T	rs34461862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43204739C>T	ENST00000255226.6	+	2	926	c.110C>T	c.(109-111)aCt>aTt	p.T37I	SLC14A2_ENST00000586448.1_Missense_Mutation_p.T37I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	37			T -> I (in dbSNP:rs34461862).		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						TCCCCGGATACTCACCCAGCT	0.582													C|||	72	0.014377	0.0015	0.0346	5008	,	,		19755	0.0		0.0417	False		,,,				2504	0.0041				p.T37I		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C110T						PASS	.	C	ILE/THR,ILE/THR	26,4380	31.7+/-61.6	0,26,2177	82.0	78.0	80.0		110,110	4.5	1.0	18	dbSNP_126	80	383,8217	124.3+/-183.0	9,365,3926	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	89,89	9,391,6103	TT,TC,CC		4.4535,0.5901,3.1447	benign,benign	37/921,37/921	43204739	409,12597	2203	4300	6503	SO:0001583	missense	8170	exon3			CGGATACTCACCC	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.110C>T	18.37:g.43204739C>T	ENSP00000255226:p.Thr37Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.62	1.992557	0.35131	0.005901	0.044535	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.57752	1.09;0.38	5.38	4.47	0.54385	.	0.382979	0.24666	N	0.036585	T	0.27697	0.0681	L	0.54323	1.7	0.32498	N	0.539278	D;D	0.65815	0.995;0.969	P;P	0.56278	0.795;0.585	T	0.58381	-0.7646	10	0.45353	T	0.12	-9.3842	12.1733	0.54172	0.0:0.829:0.171:0.0	rs34461862	37;37	Q15849;E7EPU1	UT2_HUMAN;.	I	37	ENSP00000255226:T37I;ENSP00000320689:T37I	ENSP00000255226:T37I	T	+	2	0	SLC14A2	41458737	0.988000	0.35896	0.998000	0.56505	0.260000	0.26232	1.538000	0.36094	2.517000	0.84864	0.462000	0.41574	ACT	C|0.973;T|0.027	0.027	strong		0.582	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
SFXN5	94097	hgsc.bcm.edu	37	2	73226090	73226090	+	Silent	SNP	G	G	A	rs12233055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73226090G>A	ENST00000272433.2	-	9	652	c.522C>T	c.(520-522)gcC>gcT	p.A174A	SFXN5_ENST00000410065.1_Silent_p.A174A|SFXN5_ENST00000474528.1_5'UTR	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	174					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						CAATGGAGACGGCGCTGATGA	0.592													g|||	1689	0.33726	0.4259	0.2795	5008	,	,		20111	0.4931		0.2197	False		,,,				2504	0.2188				p.A174A		Atlas-SNP	.											SFXN5,NS,carcinoma,-2,1	SFXN5	31	1	0			c.C522T						PASS	.	A		1841,2565	532.6+/-373.5	402,1037,764	112.0	101.0	105.0		522	-12.1	0.3	2	dbSNP_120	105	1897,6703	334.0+/-320.8	200,1497,2603	no	coding-synonymous	SFXN5	NM_144579.2		602,2534,3367	AA,AG,GG		22.0581,41.7839,28.7406		174/341	73226090	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	94097	exon9			GGAGACGGCGCTG	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"""Sideroflexins"""	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.522C>T	2.37:g.73226090G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_144579	A8K116|Q494Y3|Q53T29	Silent	SNP	ENST00000272433.2	37	CCDS1922.1	772	0.3534798534798535	219	0.4451219512195122	100	0.27624309392265195	280	0.48951048951048953	173	0.22823218997361477	g	8.569	0.879549	0.17467	0.417839	0.220581	ENSG00000144040	ENST00000411783	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999129714	.	.	.	.	.	.	T	0.10776	-1.0615	3	.	.	.	-7.2324	12.5892	0.56434	0.7043:0.1036:0.1921:0.0	rs12233055;rs12233055	.	.	.	C	164	.	.	R	-	1	0	SFXN5	73079598	0.011000	0.17503	0.287000	0.24848	0.837000	0.47467	-1.585000	0.02112	-2.225000	0.00724	-2.203000	0.00303	CGT	G|0.682;A|0.318	0.318	strong		0.592	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579	
USP10	9100	hgsc.bcm.edu	37	16	84792371	84792371	+	Silent	SNP	C	C	G	rs71386866	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84792371C>G	ENST00000219473.7	+	5	1355	c.1242C>G	c.(1240-1242)ccC>ccG	p.P414P	USP10_ENST00000570191.1_Silent_p.P418P	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	414					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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						CGTTGCAACCCCGTGGGCTGA	0.473													C|||	121	0.0241613	0.0023	0.0403	5008	,	,		22224	0.0		0.0577	False		,,,				2504	0.0327				p.P418P		Atlas-SNP	.											.	USP10	51	.	0			c.C1254G						PASS	.	C		54,3846		0,54,1896	167.0	160.0	162.0		1242	-2.2	1.0	16	dbSNP_130	162	553,7721		21,511,3605	no	coding-synonymous	USP10	NM_005153.2		21,565,5501	GG,GC,CC		6.6836,1.3846,4.986		414/799	84792371	607,11567	1950	4137	6087	SO:0001819	synonymous_variant	9100	exon6			GCAACCCCGTGGG	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.1242C>G	16.37:g.84792371C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			C|0.964;G|0.036	0.036	strong		0.473	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
HIPK2	28996	hgsc.bcm.edu	37	7	139415943	139415943	+	Silent	SNP	G	G	A	rs4074826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:139415943G>A	ENST00000406875.3	-	2	985	c.891C>T	c.(889-891)ccC>ccT	p.P297P	HIPK2_ENST00000342645.6_Silent_p.P297P|HIPK2_ENST00000428878.2_Silent_p.P297P	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	297	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)					TGTATTTGAGGGGCAAGGGGC	0.483													G|||	597	0.119209	0.1051	0.1729	5008	,	,		23447	0.1081		0.164	False		,,,				2504	0.0654				p.P297P		Atlas-SNP	.											.	HIPK2	192	.	0			c.C891T						PASS	.	G	,	394,2742		24,346,1198	148.0	134.0	138.0		891,891	4.4	1.0	7	dbSNP_108	138	1164,6000		80,1004,2498	no	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2.dup,NM_022740.4.dup	,	104,1350,3696	AA,AG,GG		16.2479,12.5638,15.1262	,	297/368,297/368	139415943	1558,8742	1568	3582	5150	SO:0001819	synonymous_variant	28996	exon2			TTTGAGGGGCAAG	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.891C>T	7.37:g.139415943G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	195	98	0.502564	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				G|0.847;A|0.153	0.153	strong		0.483	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
GZF1	64412	hgsc.bcm.edu	37	20	23350790	23350790	+	Silent	SNP	C	C	T	rs10485644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23350790C>T	ENST00000338121.5	+	6	1925	c.1848C>T	c.(1846-1848)aaC>aaT	p.N616N	GZF1_ENST00000377051.2_Silent_p.N616N|GZF1_ENST00000544236.1_Silent_p.N140N|GZF1_ENST00000542987.1_Silent_p.N125N			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	616					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	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)|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 negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					CGCCCAAGAACGATGACGGAC	0.418													C|||	498	0.0994409	0.2269	0.0303	5008	,	,		23169	0.0794		0.0547	False		,,,				2504	0.0429				p.N616N		Atlas-SNP	.											.	GZF1	61	.	0			c.C1848T						PASS	.	C		885,3521	344.4+/-308.1	92,701,1410	88.0	78.0	81.0		1848	-0.4	0.9	20	dbSNP_119	81	427,8173	132.6+/-190.3	10,407,3883	no	coding-synonymous	GZF1	NM_022482.3		102,1108,5293	TT,TC,CC		4.9651,20.0862,10.0877		616/712	23350790	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	64412	exon5			CAAGAACGATGAC	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1848C>T	20.37:g.23350790C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	37	CCDS13151.1																																																																																			C|0.893;T|0.107	0.107	strong		0.418	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
HOXD12	3238	hgsc.bcm.edu	37	2	176965086	176965086	+	Missense_Mutation	SNP	G	G	A	rs35817516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	167	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	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	
ABCC12	94160	hgsc.bcm.edu	37	16	48164777	48164777	+	Silent	SNP	T	T	C	rs12149826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:48164777T>C	ENST00000311303.3	-	8	1503	c.1158A>G	c.(1156-1158)gtA>gtG	p.V386V	ABCC12_ENST00000416054.1_Silent_p.V386V|ABCC12_ENST00000448542.1_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	68	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	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	
ATP10D	57205	hgsc.bcm.edu	37	4	47578971	47578971	+	Missense_Mutation	SNP	G	G	A	rs16851681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:47578971G>A	ENST00000273859.3	+	19	3817	c.3548G>A	c.(3547-3549)aGa>aAa	p.R1183K		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1183			R -> K (in dbSNP:rs16851681).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|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(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						GAACTTTACAGAAGTGGTCAG	0.428													A|||	1412	0.281949	0.3707	0.3487	5008	,	,		20469	0.2004		0.2575	False		,,,				2504	0.2239				p.R1183K		Atlas-SNP	.											.	ATP10D	168	.	0			c.G3548A						PASS	.	A	LYS/ARG	1516,2890	674.8+/-403.0	244,1028,931	95.0	88.0	90.0		3548	-6.0	0.0	4	dbSNP_123	90	2003,6597	722.2+/-406.4	232,1539,2529	yes	missense	ATP10D	NM_020453.3	26	476,2567,3460	AA,AG,GG		23.2907,34.4076,27.0567	benign	1183/1427	47578971	3519,9487	2203	4300	6503	SO:0001583	missense	57205	exon19			TTTACAGAAGTGG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.3548G>A	4.37:g.47578971G>A	ENSP00000273859:p.Arg1183Lys	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	211	210	0.995261	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	657	0.3008241758241758	198	0.4024390243902439	134	0.3701657458563536	123	0.21503496503496503	202	0.26649076517150394	A	0.090	-1.169224	0.01660	0.344076	0.232907	ENSG00000145246	ENST00000273859	T	0.75154	-0.91	5.21	-5.96	0.02234	.	0.669752	0.15504	N	0.258904	T	0.00012	0.0000	N	0.05441	-0.05	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13229	-1.0517	9	0.02654	T	1	-2.1125	2.5327	0.04707	0.2771:0.1853:0.3696:0.168	rs16851681;rs52806274;rs61423063;rs16851681	1183	Q9P241	AT10D_HUMAN	K	1183	ENSP00000273859:R1183K	ENSP00000273859:R1183K	R	+	2	0	ATP10D	47273728	0.000000	0.05858	0.029000	0.17559	0.460000	0.32559	-0.312000	0.08113	-1.293000	0.02362	-1.322000	0.01289	AGA	G|0.728;A|0.272	0.272	strong		0.428	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
HMMR	3161	hgsc.bcm.edu	37	5	162902516	162902516	+	Missense_Mutation	SNP	T	T	C	rs299290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:162902516T>C	ENST00000358715.3	+	11	1139	c.1103T>C	c.(1102-1104)gTt>gCt	p.V368A	HMMR_ENST00000393915.4_Missense_Mutation_p.V369A|HMMR_ENST00000353866.3_Missense_Mutation_p.V353A|HMMR_ENST00000432118.2_Missense_Mutation_p.V282A			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	368			V -> A (in dbSNP:rs299290). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)	p.V368A(1)		cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	GAGGAAATGGTTAAAGAGAAG	0.368													T|||	1566	0.3127	0.2935	0.2608	5008	,	,		14152	0.4841		0.2604	False		,,,				2504	0.2526				p.V369A		Atlas-SNP	.											HMMR,NS,carcinoma,0,1	HMMR	64	1	1	Substitution - Missense(1)	stomach(1)	c.T1106C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	1323,3083	441.8+/-346.5	176,971,1056	78.0	81.0	80.0		1106,845,1103,1058	-3.3	0.0	5	dbSNP_79	80	2105,6495	361.6+/-332.4	269,1567,2464	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	64,64,64,64	445,2538,3520	CC,CT,TT		24.4767,30.0272,26.3571	benign,benign,benign,benign	369/726,282/639,368/725,353/710	162902516	3428,9578	2203	4300	6503	SO:0001583	missense	3161	exon11			AAATGGTTAAAGA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1103T>C	5.37:g.162902516T>C	ENSP00000351554:p.Val368Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	705	0.3228021978021978	128	0.2601626016260163	103	0.2845303867403315	269	0.47027972027972026	205	0.2704485488126649	T	1.315	-0.601048	0.03744	0.300272	0.244767	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.06849	3.25;3.25;3.25;3.25;3.25	5.67	-3.29	0.05017	.	0.911338	0.09637	N	0.775460	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.20671	0.047;0.004;0.047;0.047	B;B;B;B	0.21360	0.034;0.006;0.021;0.021	T	0.43782	-0.9370	9	0.08837	T	0.75	0.4166	4.2691	0.10778	0.3275:0.3024:0.0:0.3701	rs299290;rs3172949;rs61170357;rs299290	282;369;353;368	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	A	254;353;369;345;282;368	ENSP00000400527:V254A;ENSP00000185942:V353A;ENSP00000377492:V369A;ENSP00000402673:V282A;ENSP00000351554:V368A	ENSP00000185942:V353A	V	+	2	0	HMMR	162835094	0.661000	0.27430	0.001000	0.08648	0.365000	0.29674	0.122000	0.15687	-0.460000	0.07003	-0.481000	0.04817	GTT	C|0.290;N|0.000	0.290	strong		0.368	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
ZNF492	57615	hgsc.bcm.edu	37	19	22847072	22847072	+	Missense_Mutation	SNP	G	G	C	rs146300593	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22847072G>C	ENST00000456783.2	+	4	845	c.601G>C	c.(601-603)Gag>Cag	p.E201Q	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	201					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.E201Q(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				CAAATGCGAAGAGTGTGGAAA	0.388													N|||	1057	0.211062	0.3994	0.1326	5008	,	,		16714	0.1736		0.1362	False		,,,				2504	0.1278				p.E201Q		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G601C						scavenged	.						12.0	16.0	15.0					19																	22847072		1865	4135	6000	SO:0001583	missense	57615	exon4			TGCGAAGAGTGTG	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.601G>C	19.37:g.22847072G>C	ENSP00000413660:p.Glu201Gln	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	197	67	0.340102	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	373	0.1707875457875458	149	0.30284552845528456	48	0.13259668508287292	92	0.16083916083916083	84	0.11081794195250659	.	6.551	0.469928	0.12461	.	.	ENSG00000229676	ENST00000456783	T	0.36157	1.27	1.3	-0.404	0.12396	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	0.28900	0.227	B	0.27796	0.083	T	0.40757	-0.9546	8	0.51188	T	0.08	.	6.7259	0.23357	0.0:0.2945:0.7055:0.0	.	201	Q9P255	ZN492_HUMAN	Q	201	ENSP00000413660:E201Q	ENSP00000413660:E201Q	E	+	1	0	ZNF492	22638912	0.002000	0.14202	0.003000	0.11579	0.015000	0.08874	0.167000	0.16602	0.492000	0.27815	0.274000	0.19336	GAG	G|0.500;C|0.500	0.500	strong		0.388	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
FOLH1	2346	hgsc.bcm.edu	37	11	49208267	49208267	+	Missense_Mutation	SNP	G	G	A	rs75940285	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49208267G>A	ENST00000256999.2	-	5	828	c.568C>T	c.(568-570)Cgg>Tgg	p.R190W	FOLH1_ENST00000340334.7_Missense_Mutation_p.R175W|FOLH1_ENST00000533034.1_Missense_Mutation_p.R175W|FOLH1_ENST00000343844.4_De_novo_Start_InFrame|FOLH1_ENST00000356696.3_Missense_Mutation_p.R190W	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	190					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R190W(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TTCATGTCCCGTTCCAATTTA	0.348																																					p.R190W		Atlas-SNP	.											FOLH1,NS,carcinoma,+1,2	FOLH1	141	2	1	Substitution - Missense(1)	NS(1)	c.C568T						PASS	.						80.0	84.0	82.0					11																	49208267		2201	4296	6497	SO:0001583	missense	2346	exon5			TGTCCCGTTCCAA	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.568C>T	11.37:g.49208267G>A	ENSP00000256999:p.Arg190Trp	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	336	60	0.178571	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889502	0.52014	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	3.05	0.979	0.19745	Protease-associated domain, PA (1);	0.000000	0.48286	D	0.000192	T	0.59985	0.2234	M	0.82056	2.57	0.80722	D	1	D;D;D;P	0.76494	0.999;0.998;0.987;0.941	D;P;P;B	0.70016	0.967;0.821;0.742;0.422	T	0.60250	-0.7300	10	0.87932	D	0	.	8.9034	0.35507	0.0:0.0:0.3751:0.6249	.	175;175;190;190	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	W	190;190;175;175;190	ENSP00000256999:R190W;ENSP00000349129:R190W;ENSP00000344131:R175W;ENSP00000431463:R175W	ENSP00000256999:R190W	R	-	1	2	FOLH1	49164843	0.953000	0.32496	0.991000	0.47740	0.964000	0.63967	1.623000	0.37008	0.120000	0.18254	0.430000	0.28490	CGG	G|0.877;A|0.123	0.123	strong		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
TRIM49	57093	hgsc.bcm.edu	37	11	89531540	89531540	+	Missense_Mutation	SNP	C	C	T	rs12417980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89531540C>T	ENST00000329758.1	-	8	1445	c.1117G>A	c.(1117-1119)Gga>Aga	p.G373R	TRIM49_ENST00000532501.2_Missense_Mutation_p.G296R	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	373	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> R (in dbSNP:rs12417980).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.G373R(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CCCGCCTTTCCATCTATCTTC	0.428													c|||	1372	0.273962	0.087	0.33	5008	,	,		18725	0.3958		0.3827	False		,,,				2504	0.2495				p.G373R		Atlas-SNP	.											TRIM49,NS,carcinoma,0,1	TRIM49	45	1	1	Substitution - Missense(1)	stomach(1)	c.G1117A						scavenged	.	C	ARG/GLY	710,3652		161,388,1632	76.0	83.0	81.0		1117	-1.8	0.0	11	dbSNP_120	81	3282,5312		714,1854,1729	no	missense	TRIM49	NM_020358.2	125	875,2242,3361	TT,TC,CC		38.1894,16.2769,30.812	possibly-damaging	373/453	89531540	3992,8964	2181	4297	6478	SO:0001583	missense	57093	exon8			CCTTTCCATCTAT	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13431	protein-coding gene	gene with protein product		606124	"""ring finger protein 18"", ""tripartite motif-containing 49"""	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.1117G>A	11.37:g.89531540C>T	ENSP00000327604:p.Gly373Arg	Somatic	162	2	0.0123457		WXS	Illumina HiSeq	Phase_I	289	84	0.290657	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000329758.1	37	CCDS8287.1	625	0.28617216117216115	46	0.09349593495934959	100	0.27624309392265195	222	0.3881118881118881	257	0.3390501319261214	C	8.805	0.933832	0.18206	0.162769	0.381894	ENSG00000168930	ENST00000329758;ENST00000532501	T	0.67865	-0.29	1.04	-1.8	0.07907	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.00012	0.0000	N	0.17248	0.465	0.80722	P	0.0	P	0.44380	0.834	P	0.52598	0.703	T	0.15065	-1.0450	7	.	.	.	.	1.806	0.03081	0.318:0.4353:0.0:0.2467	rs12417980	373	P0CI25	TRI49_HUMAN	R	373;296	ENSP00000327604:G373R	.	G	-	1	0	TRIM49	89171188	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.015000	0.12634	-0.534000	0.06315	0.194000	0.17425	GGA	C|0.707;T|0.293	0.293	strong		0.428	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358	
ZZEF1	23140	hgsc.bcm.edu	37	17	3977532	3977532	+	Silent	SNP	G	G	A	rs34760976	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3977532G>A	ENST00000381638.2	-	24	3721	c.3597C>T	c.(3595-3597)gcC>gcT	p.A1199A	ZZEF1_ENST00000574474.1_5'Flank	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1199							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						CCCAAGACACGGCAACATCGG	0.587													G|||	487	0.0972444	0.0371	0.0793	5008	,	,		20215	0.1071		0.1193	False		,,,				2504	0.1585				p.A1199A		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C3597T						PASS	.	G		194,4212	121.7+/-159.2	0,194,2009	187.0	177.0	181.0		3597	-11.7	0.1	17	dbSNP_126	181	1171,7429	239.3+/-270.5	75,1021,3204	no	coding-synonymous	ZZEF1	NM_015113.3		75,1215,5213	AA,AG,GG		13.6163,4.4031,10.4952		1199/2962	3977532	1365,11641	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon24			AGACACGGCAACA	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.3597C>T	17.37:g.3977532G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			G|0.893;A|0.107	0.107	strong		0.587	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350374	65350374	+	Silent	SNP	A	A	G	rs36303	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:65350374A>G	ENST00000284037.5	+	21	3617	c.3228A>G	c.(3226-3228)cgA>cgG	p.R1076R	ERBB2IP_ENST00000380943.2_Silent_p.R1076R|ERBB2IP_ENST00000508515.1_Silent_p.R1076R|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380935.1_Silent_p.R1076R|ERBB2IP_ENST00000506030.1_Silent_p.R1076R|ERBB2IP_ENST00000511297.1_Silent_p.R1072R|ERBB2IP_ENST00000380936.1_Silent_p.R1076R|ERBB2IP_ENST00000380939.2_Silent_p.R1076R|ERBB2IP_ENST00000380938.2_Silent_p.R1076R	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1076					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)		CAATCCAGCGACAAAGTAGTG	0.473													A|||	1050	0.209665	0.09	0.2968	5008	,	,		19190	0.4623		0.1203	False		,,,				2504	0.1411				p.R1076R		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A3228G						PASS	.	A	,	418,3988	205.2+/-227.1	11,396,1796	128.0	123.0	125.0		3228,3228	0.3	1.0	5	dbSNP_76	125	1191,7409	241.0+/-271.5	84,1023,3193	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	95,1419,4989	GG,GA,AA		13.8488,9.4871,12.3712	,	1076/1303,1076/1372	65350374	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	55914	exon21			CCAGCGACAAAGT		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.3228A>G	5.37:g.65350374A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.830;G|0.170	0.170	strong		0.473	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
CCDC154	645811	hgsc.bcm.edu	37	16	1484455	1484455	+	Missense_Mutation	SNP	T	T	C	rs61743495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1484455T>C	ENST00000389176.3	-	17	2145	c.1979A>G	c.(1978-1980)cAg>cGg	p.Q660R	CCDC154_ENST00000409671.1_Missense_Mutation_p.Q508R	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	660						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CACCTGCTCCTGGCTGTGGGG	0.587													T|||	363	0.072484	0.149	0.0562	5008	,	,		11748	0.0119		0.0388	False		,,,				2504	0.0777				p.Q653R		Atlas-SNP	.											.	CCDC154	27	.	0			c.A1958G						PASS	.	T	ARG/GLN	172,1212		11,150,531	82.0	78.0	79.0		1958	-7.3	0.0	16	dbSNP_129	79	129,3053		2,125,1464	yes	missense	CCDC154	NM_001143980.1	43	13,275,1995	CC,CT,TT		4.0541,12.4277,6.5922	benign	653/668	1484455	301,4265	692	1591	2283	SO:0001583	missense	645811	exon17			TGCTCCTGGCTGT			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.1979A>G	16.37:g.1484455T>C	ENSP00000373828:p.Gln660Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		124	0.056776556776556776	69	0.1402439024390244	21	0.058011049723756904	7	0.012237762237762238	27	0.03562005277044855	T	2.573	-0.299171	0.05532	0.124277	0.040541	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	3.68	-7.35	0.01422	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14062	-1.0486	8	0.05721	T	0.95	.	3.1587	0.06512	0.1626:0.4405:0.1035:0.2933	.	660	A6NI56	CC154_HUMAN	R	508;660	.	ENSP00000373828:Q660R	Q	-	2	0	CCDC154	1424456	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-4.550000	0.00217	-1.927000	0.01060	-0.736000	0.03550	CAG	T|0.943;C|0.057	0.057	strong		0.587	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
ITGAE	3682	hgsc.bcm.edu	37	17	3635740	3635740	+	Missense_Mutation	SNP	C	C	G	rs3744679	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3635740C>G	ENST00000263087.4	-	22	2774	c.2676G>C	c.(2674-2676)caG>caC	p.Q892H	CTD-3195I5.4_ENST00000575043.1_RNA|ITGAE_ENST00000571185.1_5'UTR	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	892			Q -> H (in dbSNP:rs3744679).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)	p.Q892H(1)		NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GGTCATCACACTGAATGTTTG	0.468													C|||	403	0.0804712	0.1044	0.219	5008	,	,		21355	0.0347		0.0497	False		,,,				2504	0.0286				p.Q892H	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											ITGAE,NS,carcinoma,0,1	ITGAE	96	1	1	Substitution - Missense(1)	stomach(1)	c.G2676C						PASS	.	C	HIS/GLN	424,3982	208.5+/-229.5	18,388,1797	145.0	121.0	129.0		2676	5.1	1.0	17	dbSNP_107	129	452,8148	137.1+/-194.1	10,432,3858	yes	missense	ITGAE	NM_002208.4	24	28,820,5655	GG,GC,CC		5.2558,9.6232,6.7354	probably-damaging	892/1180	3635740	876,12130	2203	4300	6503	SO:0001583	missense	3682	exon22			ATCACACTGAATG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.2676G>C	17.37:g.3635740C>G	ENSP00000263087:p.Gln892His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	170	0.07783882783882784	53	0.10772357723577236	54	0.14917127071823205	26	0.045454545454545456	37	0.048812664907651716	C	16.82	3.227509	0.58668	0.096232	0.052558	ENSG00000083457	ENST00000263087	T	0.46451	0.87	5.12	5.12	0.69794	Integrin alpha-2 (1);	.	.	.	.	T	0.00468	0.0015	M	0.67953	2.075	0.34345	P	0.31084	D	0.61080	0.989	D	0.63113	0.911	T	0.05131	-1.0904	8	0.49607	T	0.09	.	12.0951	0.53750	0.0:0.8272:0.1728:0.0	rs3744679;rs3744679	892	P38570	ITAE_HUMAN	H	892	ENSP00000263087:Q892H	ENSP00000263087:Q892H	Q	-	3	2	ITGAE	3582489	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	0.766000	0.26560	2.847000	0.97988	0.597000	0.82753	CAG	C|0.920;G|0.080	0.080	strong		0.468	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
OR52N2	390077	hgsc.bcm.edu	37	11	5841701	5841701	+	Missense_Mutation	SNP	G	G	A	rs73394370	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5841701G>A	ENST00000317037.2	+	1	158	c.136G>A	c.(136-138)Ggg>Agg	p.G46R	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	46						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)		GGGGAACTGTGGGCTCATCTG	0.537													G|||	204	0.0407348	0.0749	0.0259	5008	,	,		20244	0.001		0.0467	False		,,,				2504	0.0399				p.G46R		Atlas-SNP	.											.	OR52N2	58	.	0			c.G136A						PASS	.	G	ARG/GLY	338,4064	178.0+/-206.8	9,320,1872	135.0	115.0	122.0		136	5.9	1.0	11	dbSNP_130	122	576,8016	154.8+/-208.9	16,544,3736	yes	missense	OR52N2	NM_001005174.1	125	25,864,5608	AA,AG,GG		6.7039,7.6783,7.034	probably-damaging	46/322	5841701	914,12080	2201	4296	6497	SO:0001583	missense	390077	exon1			AACTGTGGGCTCA	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.136G>A	11.37:g.5841701G>A	ENSP00000322801:p.Gly46Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	82	0.037545787545787544	37	0.07520325203252033	12	0.03314917127071823	0	0.0	33	0.04353562005277045	G	12.92	2.083840	0.36758	0.076783	0.067039	ENSG00000180988	ENST00000317037	T	0.19394	2.15	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000012	T	0.03477	0.0100	M	0.83774	2.66	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.15752	-1.0426	10	0.49607	T	0.09	.	8.7296	0.34491	0.0789:0.1531:0.768:0.0	.	46	Q8NGI0	O52N2_HUMAN	R	46	ENSP00000322801:G46R	ENSP00000322801:G46R	G	+	1	0	OR52N2	5798277	0.000000	0.05858	0.953000	0.39169	0.489000	0.33432	-0.155000	0.10115	2.801000	0.96364	0.655000	0.94253	GGG	G|0.939;A|0.061	0.061	strong		0.537	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
FOXN1	8456	hgsc.bcm.edu	37	17	26857788	26857788	+	Silent	SNP	T	T	C	rs12449554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26857788T>C	ENST00000226247.2	+	5	881	c.852T>C	c.(850-852)ctT>ctC	p.L284L	FOXN1_ENST00000579795.1_Silent_p.L284L	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	284					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)	p.L284L(1)		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)					TCATGGCCCTTAAGAACAGTA	0.537													T|||	626	0.125	0.0537	0.2305	5008	,	,		15495	0.2163		0.1213	False		,,,				2504	0.0562				p.L284L		Atlas-SNP	.											FOXN1,NS,carcinoma,0,1	FOXN1	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T852C						PASS	.	T		235,4171	137.7+/-173.5	5,225,1973	101.0	99.0	100.0		852	-2.7	1.0	17	dbSNP_120	100	652,7948	165.8+/-217.9	24,604,3672	no	coding-synonymous	FOXN1	NM_003593.2		29,829,5645	CC,CT,TT		7.5814,5.3336,6.8199		284/649	26857788	887,12119	2203	4300	6503	SO:0001819	synonymous_variant	8456	exon5			GGCCCTTAAGAAC	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.852T>C	17.37:g.26857788T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_003593	B2R9Q7|O15352	Silent	SNP	ENST00000226247.2	37	CCDS11232.1																																																																																			T|0.896;C|0.104	0.104	strong		0.537	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
HECW1	23072	hgsc.bcm.edu	37	7	43484310	43484310	+	Silent	SNP	T	T	C	rs73098706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	87	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	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	
GPR125	166647	hgsc.bcm.edu	37	4	22390167	22390167	+	Missense_Mutation	SNP	C	C	T	rs9002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:22390167C>T	ENST00000334304.5	-	19	3396	c.3127G>A	c.(3127-3129)Gtg>Atg	p.V1043M	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1043			V -> M (in dbSNP:rs9002).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.V1043M(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				TGGTGGACCACGAAGAACGCA	0.478													T|||	1344	0.268371	0.2995	0.232	5008	,	,		18502	0.2272		0.2008	False		,,,				2504	0.364				p.V1043M		Atlas-SNP	.											GPR125,NS,carcinoma,0,1	GPR125	118	1	1	Substitution - Missense(1)	stomach(1)	c.G3127A						PASS	.	T	MET/VAL	1359,3047	691.9+/-405.5	221,917,1065	103.0	92.0	96.0		3127	-3.9	0.0	4	dbSNP_52	96	1693,6907	738.9+/-407.1	172,1349,2779	yes	missense	GPR125	NM_145290.2	21	393,2266,3844	TT,TC,CC		19.686,30.8443,23.4661	benign	1043/1322	22390167	3052,9954	2203	4300	6503	SO:0001583	missense	166647	exon19			GGACCACGAAGAA	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.3127G>A	4.37:g.22390167C>T	ENSP00000334952:p.Val1043Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	494	0.2261904761904762	150	0.3048780487804878	71	0.19613259668508287	134	0.23426573426573427	139	0.18337730870712401	T	0.920	-0.716300	0.03206	0.308443	0.19686	ENSG00000152990	ENST00000334304	T	0.51071	0.72	5.94	-3.93	0.04143	GPCR, family 2-like (1);	0.427481	0.30269	N	0.010005	T	0.00012	0.0000	L	0.29908	0.895	0.20074	P	0.9999318739	B;B	0.19331	0.013;0.035	B;B	0.17979	0.02;0.015	T	0.28586	-1.0039	9	0.33940	T	0.23	.	1.6018	0.02675	0.1861:0.3412:0.1891:0.2836	rs9002;rs3186408;rs13135922;rs52796127;rs61303351;rs9002	900;1043	Q8IWK6-3;Q8IWK6	.;GP125_HUMAN	M	1043	ENSP00000334952:V1043M	ENSP00000334952:V1043M	V	-	1	0	GPR125	21999265	0.006000	0.16342	0.004000	0.12327	0.080000	0.17528	-0.160000	0.10041	-1.393000	0.02079	-3.357000	0.00042	GTG	C|0.755;T|0.245	0.245	strong		0.478	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610495	32610495	+	Missense_Mutation	SNP	A	A	G	rs9272793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32610495A>G	ENST00000343139.5	+	4	824	c.722A>G	c.(721-723)cAa>cGa	p.Q241R	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.Q241R|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.Q241R	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	240					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TTCATCATCCAAGGCCTGCGT	0.547													.|||	2751	0.549321	0.4992	0.696	5008	,	,		13770	0.5407		0.5944	False		,,,				2504	0.4755				p.Q241R		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A722G						PASS	.	G	ARG/GLN	1158,1860		424,310,775	135.0	107.0	117.0		722	-8.2	0.0	6	dbSNP_118	117	2423,2987		942,539,1224	no	missense	HLA-DQA1	NM_002122.3	43	1366,849,1999	GG,GA,AA		44.7874,38.3698,42.4893	benign	241/256	32610495	3581,4847	1509	2705	4214	SO:0001583	missense	3117	exon4			TCATCCAAGGCCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.722A>G	6.37:g.32610495A>G	ENSP00000339398:p.Gln241Arg	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.039841	0.00039	0.383698	0.447874	ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000374949	T;T;T	0.01613	4.73;4.73;4.73	4.08	-8.17	0.01057	.	0.660550	0.13443	N	0.387519	T	0.00210	0.0006	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.39440	-0.9614	9	0.07813	T	0.8	.	18.1457	0.89653	0.3989:0.0:0.6011:0.0	rs9272793;rs12722096;rs17840134;rs34081406	241	G4XQK2	.	R	241	ENSP00000339398:Q241R;ENSP00000378767:Q241R;ENSP00000364087:Q241R	ENSP00000339398:Q241R	Q	+	2	0	HLA-DQA1	32718473	0.403000	0.25319	0.001000	0.08648	0.037000	0.13140	-0.307000	0.08167	-3.647000	0.00127	-2.677000	0.00143	CAA	A|0.444;G|0.556	0.556	strong		0.547	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65351074	65351074	+	Silent	SNP	G	G	A	rs10896018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65351074G>A	ENST00000309295.4	+	9	3196	c.2931G>A	c.(2929-2931)gcG>gcA	p.A977A		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	977						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						CCCAGGAAGCGGAGGCTGGGG	0.577													G|||	1391	0.277756	0.0658	0.4524	5008	,	,		15972	0.4504		0.2654	False		,,,				2504	0.2751				p.A977A		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G2931A						PASS	.	G		362,3338		27,308,1515	15.0	16.0	16.0		2931	1.6	1.0	11	dbSNP_120	16	2334,5852		344,1646,2103	no	coding-synonymous	EHBP1L1	NM_001099409.1		371,1954,3618	AA,AG,GG		28.5121,9.7838,22.6821		977/1524	65351074	2696,9190	1850	4093	5943	SO:0001819	synonymous_variant	254102	exon9			GGAAGCGGAGGCT	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.2931G>A	11.37:g.65351074G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1	645	0.29532967032967034	36	0.07317073170731707	152	0.4198895027624309	256	0.44755244755244755	201	0.26517150395778366	G	4.671	0.124677	0.08931	0.097838	0.285121	ENSG00000173442	ENST00000533465	.	.	.	5.41	1.59	0.23543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.6000000000016E-5	.	.	.	.	.	.	T	0.47861	-0.9084	3	.	.	.	.	6.7906	0.23697	0.4492:0.465:0.0858:0.0	rs10896018;rs10896018	.	.	.	R	27	.	.	G	+	1	0	EHBP1L1	65107650	0.002000	0.14202	0.994000	0.49952	0.571000	0.35966	0.223000	0.17719	0.017000	0.15025	-0.436000	0.05848	GGA	G|0.705;A|0.295	0.295	strong		0.577	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
SLC26A8	116369	hgsc.bcm.edu	37	6	35967772	35967772	+	Missense_Mutation	SNP	T	T	C	rs17713154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	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		
HAND1	9421	hgsc.bcm.edu	37	5	153857101	153857101	+	Silent	SNP	A	A	C	rs34402828	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	119	0	0		WXS	Illumina HiSeq	Phase_I	138	80	0.57971	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	
LMO7	4008	hgsc.bcm.edu	37	13	76409436	76409436	+	Silent	SNP	A	A	G	rs2273997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:76409436A>G	ENST00000321797.8	+	16	3316	c.2595A>G	c.(2593-2595)ctA>ctG	p.L865L	LMO7_ENST00000465261.2_Silent_p.L865L|LMO7_ENST00000526202.1_Silent_p.L742L|LMO7_ENST00000357063.3_Silent_p.L1150L|LMO7_ENST00000341547.4_Silent_p.L816L|LMO7_ENST00000377534.3_Silent_p.L1150L			Q8WWI1	LMO7_HUMAN	LIM domain 7	1150					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.L1150L(1)|p.L816L(1)		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)		CTTCAAATCTATCTGTAACAA	0.378													A|||	1133	0.226238	0.1082	0.2349	5008	,	,		16249	0.0655		0.3598	False		,,,				2504	0.408				p.L865L		Atlas-SNP	.											LMO7_ENST00000465261,NS,carcinoma,0,3	LMO7	334	3	2	Substitution - coding silent(2)	prostate(2)	c.A2595G						PASS	.	A	,	577,3827	254.9+/-260.3	50,477,1675	90.0	91.0	91.0		2448,2595	-9.3	0.0	13	dbSNP_100	91	3120,5480	474.7+/-368.9	561,1998,1741	no	coding-synonymous,coding-synonymous	LMO7	NM_005358.5,NM_015842.2	,	611,2475,3416	GG,GA,AA		36.2791,13.1017,28.4297	,	816/1350,865/1386	76409436	3697,9307	2202	4300	6502	SO:0001819	synonymous_variant	4008	exon15			AAATCTATCTGTA	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	ENST00000321797.8:c.2595A>G	13.37:g.76409436A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000321797.8	37		454|454	0.2078754578754579|0.2078754578754579	62|62	0.12601626016260162|0.12601626016260162	91|91	0.2513812154696133|0.2513812154696133	41|41	0.07167832167832168|0.07167832167832168	260|260	0.34300791556728233|0.34300791556728233	A|A	0.352|0.352	-0.944115|-0.944115	0.02322|0.02322	0.131017|0.131017	0.362791|0.362791	ENSG00000136153|ENSG00000136153	ENST00000447038;ENST00000525914|ENST00000524651;ENST00000525107	.|.	.|.	.|.	5.78|5.78	-9.28|-9.28	0.00656|0.00656	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.19575|0.19575	P|P	0.9999632735|0.9999632735	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35375|0.35375	-0.9791|-0.9791	3|3	.|.	.|.	.|.	-5.6978|-5.6978	4.2042|4.2042	0.10481|0.10481	0.2426:0.1679:0.4326:0.1569|0.2426:0.1679:0.4326:0.1569	rs2273997;rs17713708|rs2273997;rs17713708	.|.	.|.	.|.	V|C	774;53|197;104	.|.	.|.	I|Y	+|+	1|2	0|0	LMO7|LMO7	75307437|75307437	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.118000|0.118000	0.20060|0.20060	-1.837000|-1.837000	0.01689|0.01689	-1.404000|-1.404000	0.02050|0.02050	-1.039000|-1.039000	0.02377|0.02377	ATC|TAT	G|0.263;N|0.000	0.263	strong		0.378	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
MCM3AP	8888	hgsc.bcm.edu	37	21	47664746	47664746	+	Silent	SNP	C	C	A	rs17183255	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47664746C>A	ENST00000397708.1	-	24	5267	c.5013G>T	c.(5011-5013)ccG>ccT	p.P1671P	MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP_ENST00000291688.1_Silent_p.P1671P|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1671	Acetyltransferase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GGTCCATCTGCGGAAGCTGGA	0.637																																					p.P1671P		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G5013T						PASS	.						34.0	35.0	35.0					21																	47664746		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon23			CATCTGCGGAAGC	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.5013G>T	21.37:g.47664746C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			C|0.997;T|0.003	.	alt		0.637	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
CDH15	1013	hgsc.bcm.edu	37	16	89256695	89256695	+	Silent	SNP	G	G	A	rs72819366	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89256695G>A	ENST00000289746.2	+	8	1088	c.1023G>A	c.(1021-1023)tcG>tcA	p.S341S		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	341	Cadherin 3. {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)		TCAAAGTGTCGGTGCAGAATG	0.647													g|||	879	0.175519	0.0499	0.0937	5008	,	,		15936	0.3512		0.1899	False		,,,				2504	0.2076				p.S341S		Atlas-SNP	.											.	CDH15	54	.	0			c.G1023A						PASS	.	A		314,4078	162.2+/-194.2	14,286,1896	34.0	31.0	32.0		1023	-8.7	0.0	16	dbSNP_130	32	1676,6922	298.7+/-304.1	179,1318,2802	no	coding-synonymous	CDH15	NM_004933.2		193,1604,4698	AA,AG,GG		19.4929,7.1494,15.3195		341/815	89256695	1990,11000	2196	4299	6495	SO:0001819	synonymous_variant	1013	exon8			AGTGTCGGTGCAG	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.1023G>A	16.37:g.89256695G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			G|0.840;A|0.160	0.160	strong		0.647	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
AKAP11	11215	hgsc.bcm.edu	37	13	42872719	42872719	+	Silent	SNP	A	A	G	rs2273952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42872719A>G	ENST00000025301.2	+	7	577	c.402A>G	c.(400-402)ccA>ccG	p.P134P		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	134					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CTACATCACCAAGACTTAGGA	0.343													A|||	570	0.113818	0.0416	0.1297	5008	,	,		20034	0.123		0.1272	False		,,,				2504	0.1769				p.P134P		Atlas-SNP	.											.	AKAP11	146	.	0			c.A402G						PASS	.	A		281,4125	156.6+/-189.7	13,255,1935	128.0	121.0	124.0		402	4.9	1.0	13	dbSNP_100	124	1321,7277	259.7+/-282.8	94,1133,3072	no	coding-synonymous	AKAP11	NM_016248.3		107,1388,5007	GG,GA,AA		15.364,6.3777,12.3193		134/1902	42872719	1602,11402	2203	4299	6502	SO:0001819	synonymous_variant	11215	exon7			ATCACCAAGACTT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.402A>G	13.37:g.42872719A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	59	0.59596	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			A|0.882;G|0.118	0.118	strong		0.343	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58565233	58565233	+	Silent	SNP	G	G	A	rs73071865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58565233G>A	ENST00000282326.1	+	6	1288	c.1041G>A	c.(1039-1041)ccG>ccA	p.P347P		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	347					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)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TGGAGCCACCGAGGAAGAAAG	0.667													g|||	134	0.0267572	0.003	0.1009	5008	,	,		16480	0.0		0.0517	False		,,,				2504	0.0082				p.P347P		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G1041A						PASS	.	G		39,4367	43.1+/-76.7	0,39,2164	43.0	42.0	42.0		1041	-2.8	0.0	19	dbSNP_130	42	441,8159	133.9+/-191.4	11,419,3870	no	coding-synonymous	ZSCAN1	NM_182572.3		11,458,6034	AA,AG,GG		5.1279,0.8852,3.6906		347/409	58565233	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	284312	exon6			GCCACCGAGGAAG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.1041G>A	19.37:g.58565233G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_182572	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	37	CCDS12969.1																																																																																			G|0.963;A|0.037	0.037	strong		0.667	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
VNN1	8876	hgsc.bcm.edu	37	6	133013544	133013544	+	Missense_Mutation	SNP	T	T	C	rs45562238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:133013544T>C	ENST00000367928.4	-	5	1019	c.1006A>G	c.(1006-1008)Act>Gct	p.T336A		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	336			T -> A (in dbSNP:rs45562238). {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)		AAAAAGACAGTGCCTTTAAAT	0.423													T|||	56	0.0111821	0.0008	0.013	5008	,	,		18365	0.001		0.0447	False		,,,				2504	0.0				p.T336A		Atlas-SNP	.											.	VNN1	69	.	0			c.A1006G						PASS	.	T	ALA/THR	30,4376	33.5+/-64.1	0,30,2173	84.0	82.0	82.0		1006	-2.1	0.0	6	dbSNP_127	82	313,8287	111.0+/-171.3	10,293,3997	yes	missense	VNN1	NM_004666.2	58	10,323,6170	CC,CT,TT		3.6395,0.6809,2.6372	benign	336/514	133013544	343,12663	2203	4300	6503	SO:0001583	missense	8876	exon5			AGACAGTGCCTTT	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.1006A>G	6.37:g.133013544T>C	ENSP00000356905:p.Thr336Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	42	0.019230769230769232	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	35	0.04617414248021108	T	0.008	-1.877009	0.00537	0.006809	0.036395	ENSG00000112299	ENST00000367928	D	0.86865	-2.18	5.85	-2.06	0.07298	.	1.477880	0.03583	N	0.230396	T	0.49864	0.1582	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.47182	-0.9137	10	0.08381	T	0.77	-26.282	0.6355	0.00801	0.2625:0.1359:0.2607:0.3409	rs45562238	336	O95497	VNN1_HUMAN	A	336	ENSP00000356905:T336A	ENSP00000356905:T336A	T	-	1	0	VNN1	133055237	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.107000	0.03316	-0.141000	0.11374	-0.371000	0.07208	ACT	T|0.976;C|0.024	0.024	strong		0.423	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
UBQLN1	29979	hgsc.bcm.edu	37	9	86278817	86278817	+	Silent	SNP	C	C	A	rs7866234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:86278817C>A	ENST00000376395.4	-	10	2113	c.1590G>T	c.(1588-1590)ctG>ctT	p.L530L	UBQLN1_ENST00000257468.7_Silent_p.L502L	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	530					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CAAGAGCCTGCAGCATCTGCT	0.413													C|||	1927	0.384784	0.2005	0.4164	5008	,	,		17810	0.8075		0.2217	False		,,,				2504	0.3436				p.L530L	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.G1590T						PASS	.	C	,	895,3511	347.5+/-309.5	92,711,1400	157.0	143.0	148.0		1590,1506	-0.4	1.0	9	dbSNP_116	148	2031,6569	354.0+/-329.3	225,1581,2494	no	coding-synonymous,coding-synonymous	UBQLN1	NM_013438.4,NM_053067.2	,	317,2292,3894	AA,AC,CC		23.6163,20.3132,22.4973	,	530/590,502/562	86278817	2926,10080	2203	4300	6503	SO:0001819	synonymous_variant	29979	exon10			AGCCTGCAGCATC	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1590G>T	9.37:g.86278817C>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1	878	0.40201465201465203	105	0.21341463414634146	143	0.39502762430939226	454	0.7937062937062938	176	0.23218997361477572	C	5.480	0.273549	0.10403	0.203132	0.236163	ENSG00000135018	ENST00000526134	.	.	.	5.74	-0.392	0.12442	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.29181	-1.0020	3	.	.	.	.	12.9536	0.58415	0.0:0.7091:0.0:0.2909	rs7866234;rs60840479;rs7866234	.	.	.	F	137	.	.	C	-	2	0	UBQLN1	85468637	0.959000	0.32827	0.985000	0.45067	0.631000	0.37964	0.036000	0.13819	-0.369000	0.08028	-1.708000	0.00717	TGC	C|0.700;A|0.300	0.300	strong		0.413	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
MYLK4	340156	hgsc.bcm.edu	37	6	2749381	2749381	+	Missense_Mutation	SNP	C	C	T	rs2296356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	123	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	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	
LIG4	3981	hgsc.bcm.edu	37	13	108863609	108863609	+	Missense_Mutation	SNP	G	G	A	rs1805389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:108863609G>A	ENST00000356922.4	-	2	280	c.8C>T	c.(7-9)gCc>gTc	p.A3V	LIG4_ENST00000442234.1_Missense_Mutation_p.A3V|LIG4_ENST00000405925.1_Missense_Mutation_p.A3V	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	3			A -> V (associated with resistance to multiple myeloma; dbSNP:rs1805389). {ECO:0000269|PubMed:12471202}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|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)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					AGTTTGTGAGGCAGCCATCAA	0.328								Non-homologous end-joining					G|||	271	0.0541134	0.0015	0.0793	5008	,	,		17139	0.1002		0.0586	False		,,,				2504	0.0552				p.A3V		Atlas-SNP	.											.	LIG4	91	.	0			c.C8T	GRCh37	CM023642	LIG4	M	rs1805389	PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	53,4315		0,53,2131	27.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8,8,8	5.8	1.0	13	dbSNP_92	27	429,7989		10,409,3790	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	64,64,64	10,462,5921	AA,AG,GG		5.0962,1.2134,3.7697	benign,benign,benign	3/912,3/912,3/912	108863609	482,12304	2184	4209	6393	SO:0001583	missense	3981	exon3			TGTGAGGCAGCCA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.8C>T	13.37:g.108863609G>A	ENSP00000349393:p.Ala3Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	124	0.056776556776556776	4	0.008130081300813009	21	0.058011049723756904	54	0.0944055944055944	45	0.059366754617414245	G	15.10	2.732522	0.48939	0.012134	0.050962	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.61980	0.06;0.06;0.06	5.82	5.82	0.92795	DNA ligase, ATP-dependent, N-terminal (1);	0.448521	0.24037	N	0.042138	T	0.02267	0.0070	N	0.08118	0	0.38382	P	0.054835999999999996	B	0.32573	0.376	B	0.28465	0.09	T	0.29458	-1.0011	9	0.59425	D	0.04	.	19.0813	0.93182	0.0:0.0:1.0:0.0	rs1805389;rs1805389	3	P49917	DNLI4_HUMAN	V	3	ENSP00000385955:A3V;ENSP00000402030:A3V;ENSP00000349393:A3V	ENSP00000349393:A3V	A	-	2	0	LIG4	107661610	0.991000	0.36638	0.997000	0.53966	0.436000	0.31835	4.221000	0.58574	2.761000	0.94854	0.643000	0.83706	GCC	G|0.955;A|0.045	0.045	strong		0.328	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
SORCS1	114815	hgsc.bcm.edu	37	10	108339209	108339209	+	Missense_Mutation	SNP	T	T	C	rs187136160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108339209T>C	ENST00000263054.6	-	25	3296	c.3289A>G	c.(3289-3291)Acc>Gcc	p.T1097A	SORCS1_ENST00000344440.6_Missense_Mutation_p.T1097A|SORCS1_ENST00000369698.1_Missense_Mutation_p.T632A	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1097					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CCACTGTGGGTTGGAGTGAGG	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		16881	0.0		0.002	False		,,,				2504	0.0				p.T1097A		Atlas-SNP	.											SORCS1_ENST00000344440,NS,carcinoma,+2,4	SORCS1	534	4	0			c.A3289G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	94.0	74.0	81.0		3289,3289,3289,3289,3289,3289	3.6	0.9	10		81	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	58,58,58,58,58,58	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1097/1199,1097/1180,1097/1131,1097/1160,1097/1180,1097/1169	108339209	3,13003	2203	4300	6503	SO:0001583	missense	114815	exon25			TGTGGGTTGGAGT	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3289A>G	10.37:g.108339209T>C	ENSP00000263054:p.Thr1097Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.840	1.190688	0.21954	0.0	3.49E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.20881	2.04;2.57;2.6	5.92	3.59	0.41128	.	0.242564	0.40222	N	0.001147	T	0.09291	0.0229	N	0.08118	0	0.32196	N	0.578402	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;0.002;0.001;0.001;0.001	T	0.22661	-1.0210	9	.	.	.	-10.911	7.9891	0.30229	0.0:0.232:0.0:0.768	.	1097;1097;1097;1097;1097	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	A	632;1097;1097	ENSP00000358712:T632A;ENSP00000263054:T1097A;ENSP00000345964:T1097A	.	T	-	1	0	SORCS1	108329199	0.989000	0.36119	0.910000	0.35882	0.943000	0.58893	2.132000	0.42083	0.495000	0.27882	-0.385000	0.06624	ACC	T|0.999;C|0.001	0.001	strong		0.527	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
APOB	338	hgsc.bcm.edu	37	2	21225281	21225281	+	Missense_Mutation	SNP	C	C	T	rs1042034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21225281C>T	ENST00000233242.1	-	29	13140	c.13013G>A	c.(13012-13014)aGt>aAt	p.S4338N	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4338			S -> N (in dbSNP:rs1042034). {ECO:0000269|PubMed:1979313, ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2883086, ECO:0000269|PubMed:2932736, ECO:0000269|PubMed:2994225, ECO:0000269|PubMed:3030729, ECO:0000269|PubMed:3464946, ECO:0000269|PubMed:3652907, ECO:0000269|PubMed:3759943, ECO:0000269|PubMed:3763409, ECO:0000269|Ref.6}.		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)					GATATAATCACTGAAGATTGT	0.279													T|||	3153	0.629593	0.8759	0.7493	5008	,	,		19325	0.2798		0.7823	False		,,,				2504	0.4151				p.S4338N		Atlas-SNP	.											.	APOB	761	.	0			c.G13013A						PASS	.	T	ASN/SER	3708,690	257.0+/-261.6	1562,584,53	28.0	31.0	30.0	http://www.ncbi.nlm.nih.gov/pubmed?term	13013	1.6	0.0	2	dbSNP_86	30	6721,1869	317.6+/-313.3	2655,1411,229	yes	missense	APOB	NM_000384.2	46	4217,1995,282	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	21.7579,15.6889,19.7028	benign	4338/4564	21225281	10429,2559	2199	4295	6494	SO:0001583	missense	338	exon29			TAATCACTGAAGA	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.13013G>A	2.37:g.21225281C>T	ENSP00000233242:p.Ser4338Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	1446	0.6620879120879121	415	0.8434959349593496	283	0.7817679558011049	166	0.2902097902097902	582	0.7678100263852242	T	0.140	-1.103068	0.01828	0.843111	0.782421	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.36520	1.25	5.41	1.61	0.23674	.	1.173870	0.06125	N	0.669497	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36480	-0.9746	9	0.02654	T	1	.	5.789	0.18349	0.0:0.269:0.1281:0.6029	rs1042034;rs3181514;rs17041706;rs17240958;rs52829794;rs60186088;rs1042034	4338	P04114	APOB_HUMAN	N	4338	ENSP00000233242:S4338N	ENSP00000233242:S4338N	S	-	2	0	APOB	21078786	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.640000	0.24705	-0.124000	0.11724	-0.516000	0.04426	AGT	C|0.265;T|0.735	0.735	strong		0.279	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
TRMT2A	27037	hgsc.bcm.edu	37	22	20103264	20103264	+	Silent	SNP	C	C	T	rs9605068|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103264C>T	ENST00000252136.7	-	3	1027	c.639G>A	c.(637-639)ctG>ctA	p.L213L	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000404751.3_Silent_p.L213L|RANBP1_ENST00000430524.1_5'Flank|RANBP1_ENST00000331821.3_5'Flank|TRMT2A_ENST00000439169.2_Silent_p.L213L|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Silent_p.L213L	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	213					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						TCTGCTCGAGCAGCCAGGGCA	0.637													C|||	59	0.0117812	0.0023	0.013	5008	,	,		18163	0.0		0.0378	False		,,,				2504	0.0092				p.L213L		Atlas-SNP	.											.	TRMT2A	34	.	0			c.G639A						PASS	.	C	,	27,4377	33.5+/-64.1	1,25,2176	45.0	42.0	43.0		639,639	1.8	0.7	22	dbSNP_119	43	327,8273	114.0+/-174.0	12,303,3985	no	coding-synonymous,coding-synonymous	TRMT2A	NM_022727.4,NM_182984.3	,	13,328,6161	TT,TC,CC		3.8023,0.6131,2.7222	,	213/626,213/626	20103264	354,12650	2202	4300	6502	SO:0001819	synonymous_variant	27037	exon3			CTCGAGCAGCCAG	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.639G>A	22.37:g.20103264C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	203	98	0.482759	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Silent	SNP	ENST00000252136.7	37	CCDS13774.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
DBR1	51163	hgsc.bcm.edu	37	3	137881265	137881265	+	Silent	SNP	T	T	A	rs3732839	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137881265T>A	ENST00000260803.4	-	8	1254	c.1101A>T	c.(1099-1101)acA>acT	p.T367T	DBR1_ENST00000505015.2_Silent_p.T133T	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	367					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						AAAATTCAGTTGTCTGAGGAT	0.413													A|||	3472	0.693291	0.8124	0.7435	5008	,	,		20129	0.5526		0.6849	False		,,,				2504	0.6503				p.T367T		Atlas-SNP	.											.	DBR1	45	.	0			c.A1101T						PASS	.	A		3514,892	343.6+/-307.7	1403,708,92	110.0	103.0	105.0		1101	-8.9	0.5	3	dbSNP_107	105	5934,2666	428.2+/-355.8	2038,1858,404	no	coding-synonymous	DBR1	NM_016216.3		3441,2566,496	AA,AT,TT		31.0,20.2451,27.3566		367/545	137881265	9448,3558	2203	4300	6503	SO:0001819	synonymous_variant	51163	exon8			TTCAGTTGTCTGA	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"""debranching enzyme (S. Cerevisiae) homolog 1"", ""debranching enzyme homolog 1 (S. cerevisiae)"""			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.1101A>T	3.37:g.137881265T>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	246	246	1	NM_016216	Q96GH0|Q9NXQ6	Silent	SNP	ENST00000260803.4	37	CCDS33863.1																																																																																			T|0.292;A|0.708	0.708	strong		0.413	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1		
MROH9	80133	hgsc.bcm.edu	37	1	170927615	170927615	+	Missense_Mutation	SNP	A	A	G	rs17563089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:170927615A>G	ENST00000367758.3	+	4	185	c.86A>G	c.(85-87)aAc>aGc	p.N29S	MROH9_ENST00000367759.4_Missense_Mutation_p.N29S	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	29			N -> S (in dbSNP:rs17563089).														CATAAAGTTAACAGCCTATTG	0.353													G|||	274	0.0547125	0.0204	0.0937	5008	,	,		15781	0.0		0.1163	False		,,,				2504	0.0665				p.N29S		Atlas-SNP	.											.	.	.	.	0			c.A86G						PASS	.	G	SER/ASN,SER/ASN	128,3538		2,124,1707	123.0	118.0	119.0		86,86	0.6	0.0	1	dbSNP_123	119	855,7321		46,763,3279	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	46,46	48,887,4986	GG,GA,AA		10.4574,3.4915,8.301	benign,benign	29/862,29/574	170927615	983,10859	1833	4088	5921	SO:0001583	missense	80133	exon4			AAGTTAACAGCCT	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.86A>G	1.37:g.170927615A>G	ENSP00000356732:p.Asn29Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	238	135	0.567227	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	137	0.06272893772893773	12	0.024390243902439025	37	0.10220994475138122	0	0.0	88	0.11609498680738786	G	0.208	-1.038608	0.02013	0.034915	0.104574	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.14516	4.12;2.5	4.94	0.597	0.17504	.	1.603560	0.03542	N	0.224062	T	0.01730	0.0055	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	0.39742	-0.9599	9	0.10902	T	0.67	0.5413	7.9489	0.30003	0.3205:0.3165:0.363:0.0	rs17563089;rs52838266;rs61047203;rs17563089	29;29	F5GWX6;Q5TGP6	.;CA129_HUMAN	S	29	ENSP00000356733:N29S;ENSP00000356732:N29S	ENSP00000356732:N29S	N	+	2	0	C1orf129	169194239	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.115000	0.15540	-0.198000	0.10333	-2.081000	0.00379	AAC	A|0.938;G|0.062	0.062	strong		0.353	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
ALK	238	hgsc.bcm.edu	37	2	29416366	29416366	+	Missense_Mutation	SNP	G	G	C	rs1881421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29416366G>C	ENST00000389048.3	-	29	5493	c.4587C>G	c.(4585-4587)gaC>gaG	p.D1529E	ALK_ENST00000431873.1_Missense_Mutation_p.D359E	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1529			D -> E (in dbSNP:rs1881421). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9053841, ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GGTTACCCCTGTCGTGTGGCT	0.547			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	2869	0.572883	0.643	0.5706	5008	,	,		17724	0.7292		0.3837	False		,,,				2504	0.5133				p.D1529E		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C4587G						PASS	.	C	GLU/ASP	2681,1725	517.7+/-369.5	834,1013,356	180.0	196.0	191.0		4587	-3.4	0.0	2	dbSNP_92	191	2957,5643	667.4+/-402.5	508,1941,1851	yes	missense	ALK	NM_004304.4	45	1342,2954,2207	CC,CG,GG		34.3837,39.1512,43.3492	benign	1529/1621	29416366	5638,7368	2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ACCCCTGTCGTGT	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4587C>G	2.37:g.29416366G>C	ENSP00000373700:p.Asp1529Glu	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	269	127	0.472119	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	1235	0.5654761904761905	327	0.6646341463414634	191	0.5276243093922652	415	0.7255244755244755	302	0.39841688654353563	C	2.203	-0.382484	0.04966	0.608488	0.343837	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.26957	1.7;1.7	5.11	-3.42	0.04825	.	0.428474	0.19238	N	0.119246	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	0.31861	-0.9928	9	0.02654	T	1	.	11.8015	0.52130	0.0:0.2641:0.5636:0.1723	rs1881421;rs3738872;rs17007643;rs52821197;rs60882094;rs1881421	1529	Q9UM73	ALK_HUMAN	E	1529;359	ENSP00000373700:D1529E;ENSP00000414027:D359E	ENSP00000373700:D1529E	D	-	3	2	ALK	29269870	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.022000	0.12480	-1.464000	0.01902	-0.357000	0.07601	GAC	G|0.518;C|0.482	0.482	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
C19orf57	79173	hgsc.bcm.edu	37	19	14000170	14000170	+	Missense_Mutation	SNP	T	T	C	rs3803892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14000170T>C	ENST00000586783.1	-	5	1498	c.1499A>G	c.(1498-1500)cAg>cGg	p.Q500R	C19orf57_ENST00000346736.2_Missense_Mutation_p.Q500R|C19orf57_ENST00000454313.1_Missense_Mutation_p.Q500R|C19orf57_ENST00000591586.1_Intron			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	82	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	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	
METTL3	56339	hgsc.bcm.edu	37	14	21967916	21967916	+	Silent	SNP	A	A	G	rs1139130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:21967916A>G	ENST00000298717.4	-	7	1486	c.1335T>C	c.(1333-1335)aaT>aaC	p.N445N		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	445					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		ACCCCCAGAGATTTAGACATT	0.388													G|||	2564	0.511981	0.5749	0.6282	5008	,	,		19002	0.3542		0.5	False		,,,				2504	0.5194				p.N445N		Atlas-SNP	.											.	METTL3	48	.	0			c.T1335C						PASS	.	G		2340,2066	570.8+/-382.9	614,1112,477	162.0	150.0	154.0		1335	1.0	1.0	14	dbSNP_86	154	4327,4273	575.6+/-390.3	1130,2067,1103	no	coding-synonymous	METTL3	NM_019852.3		1744,3179,1580	GG,GA,AA		49.686,46.8906,48.739		445/581	21967916	6667,6339	2203	4300	6503	SO:0001819	synonymous_variant	56339	exon7			CCAGAGATTTAGA	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1335T>C	14.37:g.21967916A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_019852	O14736|Q86V05|Q9HB32	Silent	SNP	ENST00000298717.4	37	CCDS32044.1																																																																																			A|0.488;G|0.512	0.512	strong		0.388	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
OR52B6	340980	hgsc.bcm.edu	37	11	5602275	5602275	+	Missense_Mutation	SNP	A	A	G	rs1077126	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602275A>G	ENST00000345043.2	+	1	169	c.169A>G	c.(169-171)Act>Gct	p.T57A	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	57			T -> A (in dbSNP:rs1077126).			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)		CATGTACATCACTGCCCTGGA	0.517													G|||	2866	0.572284	0.6362	0.5692	5008	,	,		22571	0.7669		0.331	False		,,,				2504	0.5358				p.T57A		Atlas-SNP	.											.	OR52B6	37	.	0			c.A169G						PASS	.	G	ALA/THR	2410,1890		676,1058,416	137.0	134.0	135.0		169	3.2	0.0	11	dbSNP_86	135	2665,5879		430,1805,2037	yes	missense	OR52B6	NM_001005162.2	58	1106,2863,2453	GG,GA,AA		31.1915,43.9535,39.5126	benign	57/336	5602275	5075,7769	2150	4272	6422	SO:0001583	missense	340980	exon1			TACATCACTGCCC	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.169A>G	11.37:g.5602275A>G	ENSP00000341581:p.Thr57Ala	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	165	162	0.981818	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	1194	0.5467032967032966	309	0.6280487804878049	191	0.5276243093922652	437	0.763986013986014	257	0.3390501319261214	G	0.219	-1.029841	0.02045	0.560465	0.311915	ENSG00000187747	ENST00000345043	T	0.00424	7.45	5.15	3.24	0.37175	.	0.000000	0.39146	N	0.001448	T	0.00012	0.0000	N	0.16567	0.415	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.04065	-1.0980	9	0.28530	T	0.3	.	9.2843	0.37746	0.2456:0.0:0.7544:0.0	rs1077126;rs16933198;rs17341305;rs52803016;rs58461358;rs1077126	57	Q8NGF0	O52B6_HUMAN	A	57	ENSP00000341581:T57A	ENSP00000341581:T57A	T	+	1	0	OR52B6	5558851	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.981000	0.03766	0.774000	0.33427	-0.748000	0.03510	ACT	A|0.482;G|0.518	0.518	strong		0.517	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
TTC16	158248	hgsc.bcm.edu	37	9	130489743	130489743	+	Splice_Site	SNP	A	A	G	rs13298768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:130489743A>G	ENST00000373289.3	+	12	1843	c.1763A>G	c.(1762-1764)gAg>gGg	p.E588G	PTRH1_ENST00000429848.1_5'Flank|TTC16_ENST00000489226.1_3'UTR|PTRH1_ENST00000419060.1_5'Flank	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	588			E -> G (in dbSNP:rs13298768). {ECO:0000269|PubMed:15489334}.							central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						gagaaaaaagaggTAAGTGGA	0.607													A|||	1698	0.339058	0.2171	0.4625	5008	,	,		19083	0.245		0.499	False		,,,				2504	0.3487				p.E588G		Atlas-SNP	.											.	TTC16	55	.	0			c.A1763G						PASS	.	A	GLY/GLU	1125,3207		186,753,1227	7.0	8.0	7.0		1763	1.7	0.5	9	dbSNP_121	7	3722,4792		873,1976,1408	yes	missense-near-splice	TTC16	NM_144965.1	98	1059,2729,2635	GG,GA,AA		43.7162,25.9695,37.7316	benign	588/874	130489743	4847,7999	2166	4257	6423	SO:0001630	splice_region_variant	158248	exon12			AAAAAGAGGTAAG	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1764+1A>G	9.37:g.130489743A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	838	0.3836996336996337	132	0.2682926829268293	173	0.47790055248618785	151	0.263986013986014	382	0.503957783641161	A	10.94	1.491729	0.26774	0.259695	0.437162	ENSG00000167094	ENST00000373289;ENST00000373288	T	0.17213	2.29	4.07	1.73	0.24493	.	1.745110	0.02966	N	0.143856	T	0.00012	0.0000	N	0.24115	0.695	0.19575	P	0.9999695627	B;P	0.35077	0.006;0.483	B;B	0.24974	0.003;0.057	T	0.45891	-0.9230	9	0.62326	D	0.03	-2.2453	5.5863	0.17277	0.776:0.0:0.224:0.0	rs13298768;rs17856925;rs57133291;rs13298768	575;588	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	588;366	ENSP00000362386:E588G	ENSP00000362385:E366G	E	+	2	0	TTC16	129529564	0.972000	0.33761	0.476000	0.27291	0.034000	0.12701	2.120000	0.41968	0.372000	0.24591	0.459000	0.35465	GAG	A|0.638;G|0.362	0.362	strong		0.607	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	Missense_Mutation
UBASH3A	53347	hgsc.bcm.edu	37	21	43854985	43854985	+	Silent	SNP	A	A	C	rs17114925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43854985A>C	ENST00000319294.6	+	10	1345	c.1314A>C	c.(1312-1314)ccA>ccC	p.P438P	UBASH3A_ENST00000398367.1_Silent_p.P400P|UBASH3A_ENST00000291535.6_Silent_p.P400P	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	438	Phosphatase-like.				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						GCAGTCTGCCAAGACGGAGTC	0.438													C|||	1253	0.2502	0.4864	0.2017	5008	,	,		23312	0.2073		0.1262	False		,,,				2504	0.137				p.P438P		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A1314C						PASS	.	C	,	1918,2488	624.6+/-394.4	424,1070,709	109.0	104.0	105.0		1200,1314	2.7	0.5	21	dbSNP_123	105	1259,7341	761.0+/-407.6	105,1049,3146	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	529,2119,3855	CC,CA,AA		14.6395,43.5315,24.4272	,	400/624,438/662	43854985	3177,9829	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon10			TCTGCCAAGACGG	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.1314A>C	21.37:g.43854985A>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			A|0.750;C|0.250	0.250	strong		0.438	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542574	133542574	+	Missense_Mutation	SNP	C	C	T	rs61995744	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:133542574C>T	ENST00000409261.1	-	14	2183	c.1810G>A	c.(1810-1812)Gtg>Atg	p.V604M	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.V604M|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_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	84	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	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	
PLIN1	5346	hgsc.bcm.edu	37	15	90210257	90210257	+	Silent	SNP	G	G	A	rs2304796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	143	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	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	
PIGN	23556	hgsc.bcm.edu	37	18	59774037	59774037	+	Silent	SNP	C	C	T	rs9319997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	121	121	1	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	
OVGP1	5016	hgsc.bcm.edu	37	1	111957097	111957097	+	Missense_Mutation	SNP	C	C	G	rs7825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111957097C>G	ENST00000369732.3	-	11	2081	c.2026G>C	c.(2026-2028)Gaa>Caa	p.E676Q		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	676			E -> Q (in dbSNP:rs7825). {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)		TAGGCTTCTTCATCCACAGCA	0.463													G|||	3117	0.622404	0.7315	0.353	5008	,	,		17926	0.7589		0.4364	False		,,,				2504	0.7168				p.E676Q		Atlas-SNP	.											.	OVGP1	177	.	0			c.G2026C						PASS	.	G	GLN/GLU	3025,1379	445.5+/-347.7	1031,963,208	66.0	72.0	70.0		2026	0.2	0.0	1	dbSNP_52	70	3798,4802	607.5+/-395.3	841,2116,1343	yes	missense	OVGP1	NM_002557.3	29	1872,3079,1551	GG,GC,CC		44.1628,31.3124,47.5315	benign	676/679	111957097	6823,6181	2202	4300	6502	SO:0001583	missense	5016	exon11			CTTCTTCATCCAC	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.2026G>C	1.37:g.111957097C>G	ENSP00000358747:p.Glu676Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	1243	0.5691391941391941	348	0.7073170731707317	137	0.3784530386740331	433	0.756993006993007	325	0.4287598944591029	G	0.012	-1.686550	0.00738	0.686876	0.441628	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.05319	3.46	4.26	0.154	0.14901	.	31.936600	0.00166	N	0.000001	T	0.00524	0.0017	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	0.35549	-0.9784	9	0.02654	T	1	16.4499	2.7748	0.05344	0.0874:0.2937:0.3172:0.3017	rs7825;rs3181832;rs3754039;rs11564874;rs17528028;rs52804140;rs7825	676;740	Q12889;Q59HH5	OVGP1_HUMAN;.	Q	676;740;484	ENSP00000358747:E676Q	ENSP00000358743:E740Q	E	-	1	0	OVGP1	111758620	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	0.052000	0.14163	-0.136000	0.11475	-1.890000	0.00535	GAA	C|0.415;G|0.585	0.585	strong		0.463	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
TTC5	91875	hgsc.bcm.edu	37	14	20757804	20757804	+	Silent	SNP	C	C	A	rs3737220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20757804C>A	ENST00000258821.3	-	10	1361	c.1305G>T	c.(1303-1305)tcG>tcT	p.S435S	TTC5_ENST00000556592.1_5'Flank	NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	435					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		ACTGTGGTCGCGATGCCACTG	0.562													C|||	583	0.116414	0.0333	0.0821	5008	,	,		19180	0.0972		0.1918	False		,,,				2504	0.1953				p.S435S		Atlas-SNP	.											TTC5,NS,carcinoma,-1,3	TTC5	34	3	0			c.G1305T						PASS	.	C		233,4173	140.4+/-175.9	4,225,1974	88.0	66.0	74.0		1305	-11.0	0.0	14	dbSNP_107	74	1724,6876	313.7+/-311.4	176,1372,2752	no	coding-synonymous	TTC5	NM_138376.2		180,1597,4726	AA,AC,CC		20.0465,5.2882,15.0469		435/441	20757804	1957,11049	2203	4300	6503	SO:0001819	synonymous_variant	91875	exon10			TGGTCGCGATGCC	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"""Tetratricopeptide (TTC) repeat domain containing"""	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.1305G>T	14.37:g.20757804C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_138376	A8MQ18|Q96HF9	Silent	SNP	ENST00000258821.3	37	CCDS9546.1	240	0.10989010989010989	15	0.03048780487804878	34	0.09392265193370165	50	0.08741258741258741	141	0.18601583113456466	C	0.191	-1.053540	0.01965	0.052882	0.200465	ENSG00000136319	ENST00000423949	.	.	.	5.48	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.32804	P	0.499533	.	.	.	.	.	.	T	0.03017	-1.1082	3	.	.	.	.	3.4477	0.07486	0.3023:0.3955:0.2168:0.0855	rs3737220;rs3737220	.	.	.	S	380	.	.	A	-	1	0	TTC5	19827644	0.000000	0.05858	0.003000	0.11579	0.150000	0.21749	-5.813000	0.00097	-3.884000	0.00095	-1.283000	0.01379	GCG	C|0.873;A|0.127	0.127	strong		0.562	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
CCDC39	339829	hgsc.bcm.edu	37	3	180334623	180334623	+	Silent	SNP	C	C	T	rs7612917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:180334623C>T	ENST00000442201.2	-	17	2516	c.2397G>A	c.(2395-2397)gtG>gtA	p.V799V	TTC14_ENST00000382584.4_Intron|CCDC39_ENST00000273654.4_3'UTR	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	799					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|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)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTGTTTGGTCACTCTTTCTA	0.308													C|||	658	0.13139	0.1536	0.2061	5008	,	,		15917	0.002		0.2147	False		,,,				2504	0.0961				p.V799V		Atlas-SNP	.											CCDC39_ENST00000442201,NS,carcinoma,-2,1	CCDC39	242	1	0			c.G2397A						PASS	.	C		549,3081		37,475,1303	171.0	152.0	158.0		2397	-0.5	1.0	3	dbSNP_116	158	1589,6541		141,1307,2617	no	coding-synonymous	CCDC39	NM_181426.1		178,1782,3920	TT,TC,CC		19.5449,15.124,18.1803		799/942	180334623	2138,9622	1815	4065	5880	SO:0001819	synonymous_variant	339829	exon17			TTTGGTCACTCTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.2397G>A	3.37:g.180334623C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	86	51	0.593023	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	37	CCDS46964.1																																																																																			C|0.838;T|0.162	0.162	strong		0.308	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
ZNF471	57573	hgsc.bcm.edu	37	19	57036678	57036678	+	Silent	SNP	G	G	A	rs3752177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57036678G>A	ENST00000308031.5	+	5	1375	c.1242G>A	c.(1240-1242)tcG>tcA	p.S414S	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	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	53	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	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	
AKAP3	10566	hgsc.bcm.edu	37	12	4737042	4737042	+	Silent	SNP	G	G	A	rs7972737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:4737042G>A	ENST00000545990.2	-	5	1550	c.1026C>T	c.(1024-1026)caC>caT	p.H342H	AKAP3_ENST00000228850.1_Silent_p.H342H|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	342					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						CTGTGACGCTGTGGAGATTCC	0.488													G|||	1425	0.284545	0.0371	0.4625	5008	,	,		23282	0.2073		0.5258	False		,,,				2504	0.3241				p.H342H		Atlas-SNP	.											AKAP3_ENST00000545990,colon,carcinoma,0,2	AKAP3	212	2	0			c.C1026T						PASS	.	G		482,3924	224.3+/-240.5	40,402,1761	157.0	149.0	152.0		1026	3.8	1.0	12	dbSNP_116	152	4404,4196	585.5+/-391.9	1154,2096,1050	no	coding-synonymous	AKAP3	NM_006422.2		1194,2498,2811	AA,AG,GG		48.7907,10.9396,37.5673		342/854	4737042	4886,8120	2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			GACGCTGTGGAGA	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.1026C>T	12.37:g.4737042G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																			G|0.653;A|0.347	0.347	strong		0.488	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
SSX1	6756	hgsc.bcm.edu	37	X	48125798	48125798	+	Silent	SNP	T	T	C	rs5952493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:48125798T>C	ENST00000376919.3	+	7	679	c.543T>C	c.(541-543)agT>agC	p.S181S		NM_001278691.1|NM_005635.2	NP_001265620.1|NP_005626.1	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	181					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						AAGAGATCAGTGACCCTGAGG	0.498			T	SS18	synovial sarcoma								-|||	1835	0.486093	0.3245	0.3761	3775	,	,		15488	0.4127		0.3767	False		,,,				2504	0.3579				p.S181S	Esophageal Squamous(175;994 1982 2214 6527 18857)	Atlas-SNP	.		Dom	yes		X	Xp11.23-p11.22	6756	"""synovial sarcoma, X breakpoint 1"""		M	.	SSX1	27	.	0			c.T543C						PASS	.	C		1225,1401		256,543,170,316,226	318.0	295.0	304.0		543	-1.4	0.1	X	dbSNP_114	304	2064,2272		371,829,493,428,587	no	coding-synonymous	SSX1	NM_005635.2		627,1372,663,744,813	CC,CT,C,TT,T		47.6015,46.6489,47.2422		181/189	48125798	3289,3673	1511	2708	4219	SO:0001819	synonymous_variant	6756	exon7			GATCAGTGACCCT	BC001003	CCDS14290.1	Xp11.23	2009-03-12			ENSG00000126752	ENSG00000126752			11335	protein-coding gene	gene with protein product	"""cancer/testis antigen family 5, member 1"""	312820				7655467	Standard	NM_005635		Approved	CT5.1	uc004djb.1	Q16384	OTTHUMG00000021488	ENST00000376919.3:c.543T>C	X.37:g.48125798T>C		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	309	309	1	NM_005635	A3KN76|Q08AJ2|Q5JQ64	Silent	SNP	ENST00000376919.3	37	CCDS14290.1																																																																																			.	.	weak		0.498	SSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056485.1	NM_005635	
FLG	2312	hgsc.bcm.edu	37	1	152278856	152278856	+	Missense_Mutation	SNP	T	T	G	rs11582087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152278856T>G	ENST00000368799.1	-	3	8541	c.8506A>C	c.(8506-8508)Agt>Cgt	p.S2836R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2836	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)			CTGCTTGCACTTCTGGATCCT	0.562									Ichthyosis																												p.S2836R		Atlas-SNP	.											.	FLG	900	.	0			c.A8506C						PASS	.	T	ARG/SER	136,4198		0,136,2031	264.0	395.0	351.0		8506	-0.9	0.0	1	dbSNP_120	351	951,7643		0,951,3346	no	missense	FLG	NM_002016.1	110	0,1087,5377	GG,GT,TT		11.0659,3.138,8.4081	possibly-damaging	2836/4062	152278856	1087,11841	2167	4297	6464	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCACTTCTGGA	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.8506A>C	1.37:g.152278856T>G	ENSP00000357789:p.Ser2836Arg	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	505	118	0.233663	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	419	0.19184981684981686	8	0.016260162601626018	92	0.2541436464088398	232	0.40559440559440557	87	0.11477572559366754	T	8.326	0.825345	0.16749	0.03138	0.110659	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.03745	3.82	1.87	-0.845	0.10737	.	.	.	.	.	T	0.01092	0.0036	M	0.76838	2.35	0.09310	N	1	P	0.42993	0.797	B	0.28305	0.088	T	0.45614	-0.9249	9	0.28530	T	0.3	-0.3021	2.3761	0.04342	0.0:0.1966:0.3031:0.5003	.	2836	P20930	FILA_HUMAN	R	2836;98	ENSP00000357789:S2836R	ENSP00000357786:S98R	S	-	1	0	FLG	150545480	.	.	0.000000	0.03702	0.028000	0.11728	.	.	-0.204000	0.10235	0.254000	0.18369	AGT	T|0.892;G|0.108	0.108	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TNNT3	7140	hgsc.bcm.edu	37	11	1959707	1959707	+	Silent	SNP	C	C	T	rs4727	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1959707C>T	ENST00000397301.1	+	17	803	c.795C>T	c.(793-795)ggC>ggT	p.G265G	TNNT3_ENST00000278317.6_Silent_p.G254G|TNNT3_ENST00000381589.3_Silent_p.G252G|TNNT3_ENST00000446240.1_Silent_p.G235G|TNNT3_ENST00000381561.4_Silent_p.G257G|TNNT3_ENST00000381548.3_Silent_p.G256G|TNNT3_ENST00000381549.3_Silent_p.G246G|TNNT3_ENST00000381579.3_Silent_p.G246G|TNNT3_ENST00000360603.3_Silent_p.G248G|TNNT3_ENST00000397304.2_Silent_p.G235G|TNNT3_ENST00000381558.1_Silent_p.G246G			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	265					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		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;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		GCAAAGTCGGCGGGCGCTGGA	0.652													C|||	686	0.136981	0.0212	0.0937	5008	,	,		16576	0.3214		0.1819	False		,,,				2504	0.0879				p.G254G		Atlas-SNP	.											TNNT3_ENST00000381589,NS,carcinoma,+2,2	TNNT3	68	2	0			c.C762T						PASS	.	C	,,,	160,4244		2,156,2044	45.0	56.0	52.0		738,756,738,762	-4.5	0.9	11	dbSNP_52	52	1328,7268		108,1112,3078	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNNT3	NM_001042780.2,NM_001042781.2,NM_001042782.2,NM_006757.3	,,,	110,1268,5122	TT,TC,CC		15.449,3.6331,11.4462	,,,	246/251,252/257,246/251,254/259	1959707	1488,11512	2202	4298	6500	SO:0001819	synonymous_variant	7140	exon16			AGTCGGCGGGCGC	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"""troponin-T3, skeletal, fast"""	600692	"""troponin T3, skeletal, fast"""			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	ENST00000397301.1:c.795C>T	11.37:g.1959707C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Silent	SNP	ENST00000397301.1	37																																																																																				C|0.866;T|0.134	0.134	strong		0.652	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757	
DMPK	1760	hgsc.bcm.edu	37	19	46275976	46275976	+	Missense_Mutation	SNP	G	G	C	rs527221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46275976G>C	ENST00000291270.4	-	10	1392	c.1267C>G	c.(1267-1269)Ctg>Gtg	p.L423V	DMPK_ENST00000595361.1_5'Flank|AC074212.6_ENST00000590076.1_RNA|AC074212.6_ENST00000586498.1_RNA|DMPK_ENST00000458663.2_Missense_Mutation_p.L418V|DMPK_ENST00000447742.2_Missense_Mutation_p.L418V|DMPK_ENST00000600757.1_Missense_Mutation_p.L428V|DMPK_ENST00000354227.5_Missense_Mutation_p.L418V|AC074212.6_ENST00000591530.1_RNA|AC074212.5_ENST00000592217.2_RNA|DMPK_ENST00000343373.4_Missense_Mutation_p.L433V|AC074212.6_ENST00000586251.1_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						PASS	.	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	53	0	0		WXS	Illumina HiSeq	Phase_I	52	38	0.730769	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	
CHTF18	63922	hgsc.bcm.edu	37	16	842450	842450	+	Silent	SNP	C	C	T	rs2277897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:842450C>T	ENST00000262315.9	+	11	1401	c.1338C>T	c.(1336-1338)aaC>aaT	p.N446N	CHTF18_ENST00000455171.2_Silent_p.N474N|CHTF18_ENST00000317063.6_Silent_p.N641N	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	446					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)				CCGCCATCAACGTCCTCCTGA	0.726													c|||	710	0.141773	0.0424	0.1167	5008	,	,		13067	0.2401		0.1501	False		,,,				2504	0.184				p.N446N		Atlas-SNP	.											.	CHTF18	52	.	0			c.C1338T						PASS	.			204,3830		10,184,1823	8.0	11.0	10.0		1338	-5.0	0.6	16	dbSNP_100	10	1283,6921		107,1069,2926	no	coding-synonymous	CHTF18	NM_022092.2		117,1253,4749	TT,TC,CC		15.6387,5.057,12.1507		446/976	842450	1487,10751	2017	4102	6119	SO:0001819	synonymous_variant	63922	exon11			CATCAACGTCCTC	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.1338C>T	16.37:g.842450C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1																																																																																			C|0.852;T|0.148	0.148	strong		0.726	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
ZFPM1	161882	hgsc.bcm.edu	37	16	88552370	88552370	+	Missense_Mutation	SNP	A	A	G	rs3751673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88552370A>G	ENST00000319555.3	+	2	386	c.64A>G	c.(64-66)Aga>Gga	p.R22G	ZFPM1_ENST00000569086.1_3'UTR	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	22				R -> G (in Ref. 1; AAN45858). {ECO:0000305}.	atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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 negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		CATGGAGGCCAGAGAGGAGGT	0.647													a|||	2673	0.533746	0.7405	0.5634	5008	,	,		16316	0.4891		0.3588	False		,,,				2504	0.4591				p.R22G	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											.	ZFPM1	32	.	0			c.A64G						PASS	.	G	GLY/ARG	3033,1359	441.4+/-346.4	1048,937,211	66.0	65.0	65.0		64	-5.4	0.0	16	dbSNP_107	65	3225,5375	647.2+/-400.4	605,2015,1680	yes	missense	ZFPM1	NM_153813.2	125	1653,2952,1891	GG,GA,AA		37.5,30.9426,48.1681	benign	22/1007	88552370	6258,6734	2196	4300	6496	SO:0001583	missense	161882	exon2			GAGGCCAGAGAGG	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.64A>G	16.37:g.88552370A>G	ENSP00000326630:p.Arg22Gly	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_153813		Missense_Mutation	SNP	ENST00000319555.3	37	CCDS32502.1	1131	0.5178571428571429	378	0.7682926829268293	194	0.5359116022099447	297	0.5192307692307693	262	0.34564643799472294	G	2.861	-0.236090	0.05944	0.690574	0.375	ENSG00000179588	ENST00000319555	T	0.06449	3.3	3.77	-5.43	0.02632	.	4.679000	0.02024	N	0.048037	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38735	-0.9647	9	0.02654	T	1	1.7923	4.7628	0.13116	0.4218:0.0:0.3529:0.2252	rs3751673;rs59029382;rs3751673	22	Q8IX07	FOG1_HUMAN	G	22	ENSP00000326630:R22G	ENSP00000326630:R22G	R	+	1	2	ZFPM1	87079871	0.000000	0.05858	0.002000	0.10522	0.206000	0.24218	-1.363000	0.02592	-1.708000	0.01401	-1.945000	0.00491	AGA	A|0.492;G|0.508	0.508	strong		0.647	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
RPP21	79897	hgsc.bcm.edu	37	6	30313268	30313268	+	Splice_Site	SNP	G	G	A	rs11967|rs17354619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30313268G>A	ENST00000442966.2	+	3	172	c.159G>A	c.(157-159)cgG>cgA	p.R53R	RPP21_ENST00000436442.2_Splice_Site_p.R53R|TRIM39-RPP21_ENST00000513556.1_Splice_Site_p.R314R|RPP21_ENST00000433076.2_Silent_p.R61R|RPP21_ENST00000466327.1_3'UTR|RPP21_ENST00000428040.2_Splice_Site_p.R76R			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	53					response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						CCGCCCCCAGGGATCCCTCGG	0.711													G|||	774	0.154553	0.0265	0.1974	5008	,	,		8049	0.2431		0.2624	False		,,,				2504	0.0951				p.R402R		Atlas-SNP	.											.	.	.	.	0			c.G1206A						PASS	.	G	,,,	178,2840		7,164,1338	23.0	17.0	19.0		1206,183,159,159	3.8	1.0	6	dbSNP_52	19	1335,4073		174,987,1543	yes	coding-synonymous-near-splice,coding-synonymous,coding-synonymous-near-splice,coding-synonymous-near-splice	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	,,,	181,1151,2881	AA,AG,GG		24.6857,5.8979,17.9563	,,,	402/504,61/163,53/145,53/155	30313268	1513,6913	1509	2704	4213	SO:0001630	splice_region_variant	202658	exon8			CCCCAGGGATCCC	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"""chromosome 6 open reading frame 135"", ""ribonuclease P 21kDa subunit"""	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.159-1G>A	6.37:g.30313268G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Silent	SNP	ENST00000442966.2	37	CCDS4679.1																																																																																			G|0.836;C|0.000;A|0.164	0.164	strong		0.711	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	Silent
NCAPH	23397	hgsc.bcm.edu	37	2	97020049	97020049	+	Silent	SNP	T	T	C	rs3731935	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:97020049T>C	ENST00000240423.4	+	9	1174	c.1131T>C	c.(1129-1131)gaT>gaC	p.D377D	NCAPH_ENST00000427946.1_Silent_p.D241D|NCAPH_ENST00000455200.1_Silent_p.D366D	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	377					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.D377D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				ATGCCAACGATGAACCTGACC	0.532													T|||	1398	0.279153	0.0416	0.2334	5008	,	,		14804	0.2232		0.2763	False		,,,				2504	0.6933				p.D377D		Atlas-SNP	.											NCAPH,NS,carcinoma,+2,2	NCAPH	67	2	1	Substitution - coding silent(1)	stomach(1)	c.T1131C						PASS	.	T		351,4055	181.5+/-209.5	10,331,1862	149.0	144.0	145.0		1131	1.9	0.6	2	dbSNP_107	145	2470,6130	406.5+/-348.9	363,1744,2193	no	coding-synonymous	NCAPH	NM_015341.3		373,2075,4055	CC,CT,TT		28.7209,7.9664,21.69		377/742	97020049	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	23397	exon9			CAACGATGAACCT	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.1131T>C	2.37:g.97020049T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_015341	B4E189|Q8TB87	Silent	SNP	ENST00000240423.4	37	CCDS2021.1																																																																																			T|0.781;C|0.219	0.219	strong		0.532	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341	
KRT19	3880	hgsc.bcm.edu	37	17	39681475	39681475	+	Silent	SNP	A	A	G	rs4601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39681475A>G	ENST00000361566.3	-	2	531	c.471T>C	c.(469-471)aaT>aaC	p.N157N	KRT15_ENST00000254043.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	157	Coil 1B.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				CCAGACGGGCATTGTCGATCT	0.562													A|||	3665	0.731829	0.5908	0.7853	5008	,	,		16837	0.9137		0.6471	False		,,,				2504	0.7843				p.N157N		Atlas-SNP	.											.	KRT19	41	.	0			c.T471C						PASS	.	A		2586,1820	638.0+/-396.9	759,1068,376	135.0	128.0	131.0		471	0.0	1.0	17	dbSNP_52	131	5479,3121	657.4+/-401.5	1746,1987,567	no	coding-synonymous	KRT19	NM_002276.4		2505,3055,943	GG,GA,AA		36.2907,41.3073,37.9902		157/401	39681475	8065,4941	2203	4300	6503	SO:0001819	synonymous_variant	3880	exon2			ACGGGCATTGTCG		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.471T>C	17.37:g.39681475A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Silent	SNP	ENST00000361566.3	37	CCDS11399.1																																																																																			A|0.357;G|0.643	0.643	strong		0.562	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276	
DMD	1756	hgsc.bcm.edu	37	X	32503194	32503194	+	Missense_Mutation	SNP	T	T	C	rs228406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:32503194T>C	ENST00000357033.4	-	21	2851	c.2645A>G	c.(2644-2646)gAt>gGt	p.D882G	DMD_ENST00000378677.2_Missense_Mutation_p.D878G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	882			D -> G (in dbSNP:rs228406). {ECO:0000269|PubMed:2668885, ECO:0000269|PubMed:3282674, ECO:0000269|PubMed:3428261}.		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGGTTGAAGATCTGATAGCCG	0.383													C|||	2825	0.748344	0.4834	0.5893	3775	,	,		14500	0.6607		0.5219	False		,,,				2504	0.5992				p.D882G		Atlas-SNP	.											.	DMD	2127	.	0			c.A2645G						PASS	.	C	GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP	2407,1426		650,750,357,231,214	131.0	117.0	122.0		2621,2645,2276,2633,2276	3.1	1.0	X	dbSNP_79	122	4460,2268		1075,1058,1252,295,620	yes	missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	94,94,94,94,94	1725,1808,1609,526,834	CC,CT,C,TT,T		33.7099,37.2032,34.9777	benign,benign,benign,benign,benign	874/3678,882/3686,759/3563,878/3682,759/3563	32503194	6867,3694	2202	4300	6502	SO:0001583	missense	1756	exon21			TGAAGATCTGATA	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2645A>G	X.37:g.32503194T>C	ENSP00000354923:p.Asp882Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	1211	0.729957805907173	167	0.48546511627906974	136	0.6071428571428571	252	0.7455621301775148	283	0.5380228136882129	C	3.351	-0.132443	0.06753	0.627968	0.662901	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.50813	0.73;0.73	4.84	3.07	0.35406	.	0.414645	0.17155	N	0.184893	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999741131	B;B;B	0.11235	0.0;0.004;0.0	B;B;B	0.15484	0.0;0.013;0.0	T	0.35748	-0.9776	9	0.13470	T	0.59	.	5.7099	0.17929	0.0731:0.2485:0.5474:0.131	rs228406;rs56488430;rs58656805;rs228406	874;882;878	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	G	874;878;882;882;759	ENSP00000367948:D878G;ENSP00000354923:D882G	ENSP00000354923:D882G	D	-	2	0	DMD	32413115	0.953000	0.32496	0.992000	0.48379	0.462000	0.32619	0.899000	0.28417	0.088000	0.17205	-0.995000	0.02519	GAT	0|0.010;C|0.678	0.678	strong		0.383	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
EHD2	30846	hgsc.bcm.edu	37	19	48244569	48244569	+	Silent	SNP	G	G	A	rs3745758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48244569G>A	ENST00000263277.3	+	6	1763	c.1512G>A	c.(1510-1512)gaG>gaA	p.E504E	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.E368E	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	504	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				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)		TGGATGATGAGGAGTTCGCGC	0.672													G|||	2265	0.452276	0.1309	0.4885	5008	,	,		16609	0.5536		0.5497	False		,,,				2504	0.6564				p.E504E		Atlas-SNP	.											.	EHD2	59	.	0			c.G1512A						PASS	.	G		927,3479	344.1+/-307.9	111,705,1387	43.0	36.0	38.0		1512	3.9	1.0	19	dbSNP_107	38	4924,3676	607.3+/-395.2	1389,2146,765	no	coding-synonymous	EHD2	NM_014601.3		1500,2851,2152	AA,AG,GG		42.7442,21.0395,44.9869		504/544	48244569	5851,7155	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			TGATGAGGAGTTC	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.1512G>A	19.37:g.48244569G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			G|0.559;A|0.441	0.441	strong		0.672	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
TRIP6	7205	hgsc.bcm.edu	37	7	100466441	100466441	+	Missense_Mutation	SNP	G	G	A	rs2075756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100466441G>A	ENST00000200457.4	+	4	1048	c.688G>A	c.(688-690)Gtc>Atc	p.V230I		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	230			V -> I (in dbSNP:rs2075756). {ECO:0000269|PubMed:15489334}.		focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGCTGCTGGGGTCTCTGGCCC	0.652													G|||	1360	0.271565	0.0575	0.4553	5008	,	,		13728	0.4464		0.2644	False		,,,				2504	0.2577				p.V230I		Atlas-SNP	.											.	TRIP6	45	.	0			c.G688A						PASS	.	G	ILE/VAL	414,3298		26,362,1468	16.0	20.0	19.0		688	5.1	0.2	7	dbSNP_96	19	2193,5959		328,1537,2211	yes	missense	TRIP6	NM_003302.2	29	354,1899,3679	AA,AG,GG		26.9014,11.153,21.974	benign	230/477	100466441	2607,9257	1856	4076	5932	SO:0001583	missense	7205	exon4			GCTGGGGTCTCTG	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.688G>A	7.37:g.100466441G>A	ENSP00000200457:p.Val230Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	615	0.2815934065934066	29	0.05894308943089431	142	0.39226519337016574	256	0.44755244755244755	188	0.24802110817941952	G	16.62	3.175315	0.57692	0.11153	0.269014	ENSG00000087077	ENST00000200457	T	0.59638	0.25	5.09	5.09	0.68999	.	1.627630	0.03005	N	0.148728	T	0.00012	0.0000	L	0.36672	1.1	0.47584	P	5.309999999999482E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17471	-1.0368	9	0.35671	T	0.21	.	13.9605	0.64175	0.0:0.0:1.0:0.0	rs2075756;rs11539291;rs17844960;rs17857700;rs59470193;rs2075756	230	Q15654	TRIP6_HUMAN	I	230	ENSP00000200457:V230I	ENSP00000200457:V230I	V	+	1	0	TRIP6	100304377	0.105000	0.21958	0.188000	0.23233	0.787000	0.44495	0.540000	0.23191	2.341000	0.79615	0.561000	0.74099	GTC	G|0.746;A|0.254	0.254	strong		0.652	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
OR51B5	282763	hgsc.bcm.edu	37	11	5364476	5364476	+	Silent	SNP	C	C	T	rs61738485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43.0	42.0	42.0		279	-8.9	0.0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
ACSF2	80221	hgsc.bcm.edu	37	17	48549791	48549791	+	Silent	SNP	C	C	G	rs17850845|rs2305998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48549791C>G	ENST00000300441.4	+	12	1430	c.1326C>G	c.(1324-1326)gcC>gcG	p.A442A	ACSF2_ENST00000502667.1_Silent_p.A429A|ACSF2_ENST00000541920.1_Silent_p.A282A|ACSF2_ENST00000504392.1_Silent_p.A399A|ACSF2_ENST00000427954.2_Silent_p.A467A|ACSF2_ENST00000506085.1_Intron	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	442					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TGTCCCAGGCCCGGATCATGA	0.617													C|||	930	0.185703	0.0855	0.2493	5008	,	,		19289	0.1409		0.2992	False		,,,				2504	0.2055				p.A442A		Atlas-SNP	.											.	ACSF2	46	.	0			c.C1326G						PASS	.	C		568,3838	252.4+/-258.8	37,494,1672	47.0	45.0	46.0		1326	3.1	1.0	17	dbSNP_100	46	2609,5991	421.0+/-353.6	395,1819,2086	no	coding-synonymous	ACSF2	NM_025149.4		432,2313,3758	GG,GC,CC		30.3372,12.8915,24.4272		442/616	48549791	3177,9829	2203	4300	6503	SO:0001819	synonymous_variant	80221	exon12			CCAGGCCCGGATC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1326C>G	17.37:g.48549791C>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Silent	SNP	ENST00000300441.4	37	CCDS11567.1																																																																																			C|0.772;G|0.228	0.228	strong		0.617	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
FARP1	10160	hgsc.bcm.edu	37	13	99064244	99064244	+	Silent	SNP	T	T	C	rs11556829	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:99064244T>C	ENST00000319562.6	+	16	2047	c.1782T>C	c.(1780-1782)ttT>ttC	p.F594F	FARP1_ENST00000595437.1_Silent_p.F594F|FARP1_ENST00000376586.2_Silent_p.F594F	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	594	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)			TGCACAAATTTCATACTAATT	0.443													T|||	145	0.0289537	0.0038	0.0259	5008	,	,		21149	0.001		0.0785	False		,,,				2504	0.0429				p.F594F		Atlas-SNP	.											.	FARP1	207	.	0			c.T1782C						PASS	.	T		87,4319	73.6+/-111.7	1,85,2117	154.0	152.0	153.0		1782	-0.6	1.0	13	dbSNP_120	153	666,7934	168.4+/-220.0	29,608,3663	no	coding-synonymous	FARP1	NM_005766.2		30,693,5780	CC,CT,TT		7.7442,1.9746,5.7896		594/1046	99064244	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	10160	exon16			CAAATTTCATACT	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.1782T>C	13.37:g.99064244T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	102	39	0.382353	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1	81	0.03708791208791209	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	68	0.08970976253298153	T	10.73	1.433796	0.25813	0.019746	0.077442	ENSG00000152767	ENST00000457029	.	.	.	5.91	-0.59	0.11679	.	0.000000	0.85682	D	0.000000	T	0.07548	0.0190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45644	-0.9247	6	0.87932	D	0	.	10.5059	0.44834	0.0:0.4534:0.0:0.5466	rs11556829	.	.	.	S	123	.	ENSP00000406623:F123S	F	+	2	0	FARP1	97862245	0.987000	0.35691	0.991000	0.47740	0.992000	0.81027	0.186000	0.16978	-0.299000	0.08909	0.533000	0.62120	TTC	T|0.949;C|0.051	0.051	strong		0.443	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497943	32497943	+	Missense_Mutation	SNP	A	A	G	rs17211043	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32497943A>G	ENST00000374975.3	-	1	121	c.59T>C	c.(58-60)aTg>aCg	p.M20T		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						GCTCAGCACCATCAGTGTCAC	0.562																																					p.M20T		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.T59C						PASS	.	A	THR/MET	988,3418		20,948,1235	87.0	91.0	89.0		59	2.1	0.0	6	dbSNP_123	89	2883,5717		116,2651,1533	yes	missense	HLA-DRB5	NM_002125.3	81	136,3599,2768	GG,GA,AA		33.5233,22.424,29.7632	benign	20/267	32497943	3871,9135	2203	4300	6503	SO:0001583	missense	3127	exon1			AGCACCATCAGTG		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.59T>C	6.37:g.32497943A>G	ENSP00000364114:p.Met20Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	635	0.2907509157509158	87	0.17682926829268292	126	0.34806629834254144	173	0.30244755244755245	249	0.32849604221635886	.	10.44	1.351576	0.24512	0.22424	0.335233	ENSG00000198502	ENST00000374975	T	0.00253	8.43	4.54	2.12	0.27331	MHC classes I/II-like antigen recognition protein (1);	1.776370	0.02816	N	0.124960	T	0.00073	0.0002	L	0.45137	1.4	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43909	-0.9362	9	0.59425	D	0.04	.	5.8435	0.18647	0.7842:0.0:0.2158:0.0	rs17211043	20	Q30154	DRB5_HUMAN	T	20	ENSP00000364114:M20T	ENSP00000364114:M20T	M	-	2	0	HLA-DRB5	32605921	0.027000	0.19231	0.005000	0.12908	0.208000	0.24298	2.358000	0.44134	0.278000	0.22164	0.397000	0.26171	ATG	A|0.707;G|0.293	0.293	strong		0.562	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967981	49967981	+	Silent	SNP	T	T	G	rs11558188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49967981T>G	ENST00000293350.4	+	12	1693	c.1530T>G	c.(1528-1530)gtT>gtG	p.V510V	ALDH16A1_ENST00000540132.1_Silent_p.V347V|CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000455361.2_Silent_p.V459V|ALDH16A1_ENST00000433981.2_Silent_p.V345V	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	510						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GCCTCGCTGTTCCCTCAACCC	0.612													T|||	1051	0.209864	0.3396	0.2277	5008	,	,		14798	0.005		0.335	False		,,,				2504	0.1043				p.V510V		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.T1530G						PASS	.	T	,	1368,3038	451.4+/-349.7	214,940,1049	126.0	132.0	130.0		1377,1530	-9.3	0.0	19	dbSNP_120	130	3014,5586	465.2+/-366.4	527,1960,1813	yes	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	741,2900,2862	GG,GT,TT		35.0465,31.0486,33.6921	,	459/752,510/803	49967981	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CGCTGTTCCCTCA	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1530T>G	19.37:g.49967981T>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			T|0.692;G|0.308	0.308	strong		0.612	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
ZNF106	64397	hgsc.bcm.edu	37	15	42720288	42720288	+	Silent	SNP	G	G	C	rs11544099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42720288G>C	ENST00000263805.4	-	12	5183	c.4857C>G	c.(4855-4857)ctC>ctG	p.L1619L	RNU6-188P_ENST00000364207.1_RNA|ZNF106_ENST00000565611.1_Silent_p.L804L|ZNF106_ENST00000565380.1_Silent_p.L847L	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1619					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TGTGGAGGCAGAGGACCCGGT	0.498													G|||	261	0.0521166	0.0431	0.0735	5008	,	,		19492	0.006		0.1173	False		,,,				2504	0.0297				p.L1619L		Atlas-SNP	.											ZFP106,NS,carcinoma,0,1	ZFP106	117	1	0			c.C4857G						PASS	.	G		258,4148	147.6+/-182.1	4,250,1949	133.0	106.0	115.0		4857	3.4	1.0	15	dbSNP_120	115	1188,7410	242.4+/-272.4	85,1018,3196	no	coding-synonymous	ZFP106	NM_022473.1		89,1268,5145	CC,CG,GG		13.8172,5.8557,11.1197		1619/1884	42720288	1446,11558	2203	4299	6502	SO:0001819	synonymous_variant	64397	exon12			GAGGCAGAGGACC	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.4857C>G	15.37:g.42720288G>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			G|0.904;C|0.096	0.096	strong		0.498	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SLC1A5	6510	hgsc.bcm.edu	37	19	47280587	47280587	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47280587G>A	ENST00000542575.2	-	6	1762	c.1134C>T	c.(1132-1134)atC>atT	p.I378I	SLC1A5_ENST00000594991.1_Silent_p.I202I|SLC1A5_ENST00000434726.2_Silent_p.I176I|SLC1A5_ENST00000412532.2_Silent_p.I150I	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	378					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	CGATGGGCAGGATGAAACGGC	0.607																																					p.I378I		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1134T						PASS	.						67.0	56.0	60.0					19																	47280587		2203	4300	6503	SO:0001819	synonymous_variant	6510	exon6			GGGCAGGATGAAA	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1134C>T	19.37:g.47280587G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			.	.	none		0.607	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
MACROD1	28992	hgsc.bcm.edu	37	11	63884561	63884561	+	Intron	SNP	G	G	A	rs34856996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:63884561G>A	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Silent_p.K274K|RP11-21A7A.3_ENST00000543817.1_RNA	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						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						ACCTGCAGAAGCTCTACCTGC	0.617													G|||	98	0.0195687	0.0023	0.0288	5008	,	,		19308	0.0		0.0626	False		,,,				2504	0.0123				p.K274K		Atlas-SNP	.											.	FLRT1	46	.	0			c.G822A						PASS	.	G	,	67,4329		1,65,2132	45.0	29.0	35.0		822,	2.2	1.0	11	dbSNP_126	35	535,8049		17,501,3774	yes	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	18,566,5906	AA,AG,GG		6.2325,1.5241,4.6379	,	274/675,	63884561	602,12378	2198	4292	6490	SO:0001627	intron_variant	23769	exon2			GCAGAAGCTCTAC	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.517+34149C>T	11.37:g.63884561G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	153	89	0.581699	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			G|0.964;A|0.036	0.036	strong		0.617	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
HLA-C	3107	hgsc.bcm.edu	37	6	31239585	31239585	+	Missense_Mutation	SNP	C	C	T	rs1050437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	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	
EIF2B3	8891	hgsc.bcm.edu	37	1	45444038	45444038	+	Silent	SNP	G	G	A	rs11556200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45444038G>A	ENST00000360403.2	-	3	369	c.243C>T	c.(241-243)gaC>gaT	p.D81D	EIF2B3_ENST00000372183.3_Silent_p.D81D|EIF2B3_ENST00000480675.1_5'UTR	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	81					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|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)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					CCATGTCAGCGTCATCAGGAA	0.363													A|||	1485	0.296526	0.4032	0.4265	5008	,	,		17307	0.2758		0.1998	False		,,,				2504	0.181				p.D81D	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.C243T						PASS	.	A	,	1705,2701	653.0+/-399.5	345,1015,843	215.0	210.0	211.0		243,243	-4.9	0.8	1	dbSNP_120	211	1990,6610	723.2+/-406.4	234,1522,2544	no	coding-synonymous,coding-synonymous	EIF2B3	NM_001166588.1,NM_020365.3	,	579,2537,3387	AA,AG,GG		23.1395,38.6972,28.41	,	81/413,81/453	45444038	3695,9311	2203	4300	6503	SO:0001819	synonymous_variant	8891	exon3			GTCAGCGTCATCA	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"""eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"""			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.243C>T	1.37:g.45444038G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Silent	SNP	ENST00000360403.2	37	CCDS517.1																																																																																			G|0.714;A|0.286	0.286	strong		0.363	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365	
XDH	7498	hgsc.bcm.edu	37	2	31560572	31560572	+	Missense_Mutation	SNP	G	G	A	rs45564939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:31560572G>A	ENST00000379416.3	-	35	3934	c.3886C>T	c.(3886-3888)Cgg>Tgg	p.R1296W		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	1296			R -> W (in dbSNP:rs45564939). {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)	CTGTCTAGCCGGAAGAGTTCC	0.572													G|||	34	0.00678914	0.0023	0.0101	5008	,	,		21336	0.0		0.0189	False		,,,				2504	0.0051				p.R1296W	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C3886T						PASS	.	G	TRP/ARG	13,4393	20.2+/-43.8	0,13,2190	118.0	104.0	109.0		3886	5.9	1.0	2	dbSNP_127	109	158,8442	75.1+/-137.7	0,158,4142	yes	missense	XDH	NM_000379.3	101	0,171,6332	AA,AG,GG		1.8372,0.2951,1.3148	probably-damaging	1296/1334	31560572	171,12835	2203	4300	6503	SO:0001583	missense	7498	exon35			CTAGCCGGAAGAG	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.3886C>T	2.37:g.31560572G>A	ENSP00000368727:p.Arg1296Trp	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	218	112	0.513761	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	18	0.008241758241758242	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	14	0.018469656992084433	G	21.2	4.108097	0.77096	0.002951	0.018372	ENSG00000158125	ENST00000379416	T	0.68624	-0.34	5.89	5.89	0.94794	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (2);	0.664346	0.14708	N	0.303151	T	0.66317	0.2777	M	0.88181	2.935	0.47949	D	0.99955	D	0.64830	0.994	P	0.52758	0.708	T	0.77397	-0.2603	10	0.72032	D	0.01	.	10.0984	0.42488	0.0:0.1271:0.6854:0.1875	rs45564939	1296	P47989	XDH_HUMAN	W	1296	ENSP00000368727:R1296W	ENSP00000368727:R1296W	R	-	1	2	XDH	31414076	0.996000	0.38824	0.977000	0.42913	0.957000	0.61999	2.494000	0.45329	2.793000	0.96121	0.655000	0.94253	CGG	G|0.989;A|0.011	0.011	strong		0.572	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
DNAH7	56171	hgsc.bcm.edu	37	2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	rs72917299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	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						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181.0	174.0	176.0		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	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.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
OR51A7	119687	hgsc.bcm.edu	37	11	4929061	4929061	+	Silent	SNP	C	C	G	rs10500627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4929061C>G	ENST00000359350.4	+	1	462	c.462C>G	c.(460-462)ctC>ctG	p.L154L	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	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L154L(1)		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)		GGAGCATTCTCTTAGTGATTC	0.388													C|||	891	0.177915	0.0613	0.1527	5008	,	,		23387	0.5437		0.0845	False		,,,				2504	0.0726				p.L154L		Atlas-SNP	.											OR51A7,colon,carcinoma,+2,2	OR51A7	86	2	1	Substitution - coding silent(1)	stomach(1)	c.C462G						PASS	.	C		335,4067	178.0+/-206.8	13,309,1879	99.0	98.0	98.0		462	-3.6	0.0	11	dbSNP_119	98	669,7927	169.0+/-220.4	25,619,3654	no	coding-synonymous	OR51A7	NM_001004749.1		38,928,5533	GG,GC,CC		7.7827,7.6102,7.7243		154/313	4929061	1004,11994	2201	4298	6499	SO:0001819	synonymous_variant	119687	exon1			CATTCTCTTAGTG	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.462C>G	11.37:g.4929061C>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001004749	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																			C|0.879;G|0.121	0.121	strong		0.388	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
USP45	85015	hgsc.bcm.edu	37	6	99893938	99893938	+	Silent	SNP	T	T	C	rs4504482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:99893938T>C	ENST00000327681.6	-	14	2242	c.1710A>G	c.(1708-1710)ggA>ggG	p.G570G	USP45_ENST00000500704.2_Silent_p.G570G|USP45_ENST00000539675.1_Intron|USP45_ENST00000392738.2_Silent_p.G250G|USP45_ENST00000369233.2_Silent_p.G522G	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	38	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	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	
SPTLC3	55304	hgsc.bcm.edu	37	20	13053018	13053018	+	Missense_Mutation	SNP	T	T	G	rs243887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:13053018T>G	ENST00000399002.2	+	3	692	c.418T>G	c.(418-420)Ttg>Gtg	p.L140V	SPTLC3_ENST00000378194.4_Missense_Mutation_p.L140V	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	140			L -> V (in dbSNP:rs243887). {ECO:0000269|PubMed:15489334}.		small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						TCTGTTTGATTTGATGGAGAG	0.433													G|||	3686	0.736022	0.9682	0.7349	5008	,	,		18800	0.6052		0.7565	False		,,,				2504	0.5368				p.L140V		Atlas-SNP	.											.	SPTLC3	78	.	0			c.T418G						PASS	.	G	VAL/LEU	3414,250		1590,234,8	206.0	212.0	210.0		418	-6.3	0.0	20	dbSNP_79	210	6000,2172		2213,1574,299	yes	missense	SPTLC3	NM_018327.2	32	3803,1808,307	GG,GT,TT		26.5786,6.8231,20.463	benign	140/553	13053018	9414,2422	1832	4086	5918	SO:0001583	missense	55304	exon3			TTTGATTTGATGG	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.418T>G	20.37:g.13053018T>G	ENSP00000381968:p.Leu140Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	1647	0.7541208791208791	483	0.9817073170731707	278	0.7679558011049724	316	0.5524475524475524	570	0.7519788918205804	G	5.154	0.213945	0.09810	0.931769	0.734214	ENSG00000172296	ENST00000399002;ENST00000378194;ENST00000450297	T;T;T	0.68765	-0.35;-0.35;-0.35	5.48	-6.28	0.02020	Pyridoxal phosphate-dependent transferase, major domain (1);	0.575158	0.17871	N	0.159173	T	0.00012	0.0000	N	0.13327	0.33	0.47659	P	5.199999999999649E-4	B	0.11235	0.004	B	0.15052	0.012	T	0.36480	-0.9746	9	0.10636	T	0.68	-0.0436	1.1148	0.01712	0.4391:0.1439:0.1798:0.2372	rs243887;rs17173261;rs17262985;rs58540638;rs243887	140	Q9NUV7	SPTC3_HUMAN	V	140;140;113	ENSP00000381968:L140V;ENSP00000367436:L140V;ENSP00000409125:L113V	ENSP00000367436:L140V	L	+	1	2	SPTLC3	13001018	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.808000	0.04515	-1.590000	0.01623	-0.729000	0.03580	TTG	T|0.243;G|0.747	0.747	strong		0.433	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
CELA3A	10136	hgsc.bcm.edu	37	1	22336308	22336308	+	Silent	SNP	G	G	A	rs12908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	223	91	0.408072	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	
HRSP12	10247	hgsc.bcm.edu	37	8	99115082	99115082	+	Silent	SNP	C	C	T	rs11537947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:99115082C>T	ENST00000254878.3	-	6	546	c.402G>A	c.(400-402)acG>acA	p.T134T		NM_005836.2	NP_005827.1	P52758	UK114_HUMAN	heat-responsive protein 12	134					regulation of translational termination (GO:0006449)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deaminase activity (GO:0019239)|endonuclease activity (GO:0004519)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	6	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			ATAGTGATGCCGTTGTCAGTG	0.348													T|||	308	0.0615016	0.0877	0.0648	5008	,	,		19758	0.001		0.1034	False		,,,				2504	0.0429				p.T134T		Atlas-SNP	.											.	HRSP12	13	.	0			c.G402A						PASS	.	T		329,4077	796.4+/-415.4	11,307,1885	140.0	136.0	138.0		402	-0.2	0.0	8	dbSNP_120	138	687,7913	788.5+/-407.6	25,637,3638	no	coding-synonymous	HRSP12	NM_005836.2		36,944,5523	TT,TC,CC		7.9884,7.4671,7.8118		134/138	99115082	1016,11990	2203	4300	6503	SO:0001819	synonymous_variant	10247	exon6			TGATGCCGTTGTC	BC008418	CCDS6276.1	8q22	2014-05-09			ENSG00000132541	ENSG00000132541			16897	protein-coding gene	gene with protein product	"""translational inhibitor p14.5"""	602487				8973653, 9405234, 20817725	Standard	NM_005836		Approved	UK114, P14.5, PSP	uc003yii.1	P52758	OTTHUMG00000164670	ENST00000254878.3:c.402G>A	8.37:g.99115082C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_005836	Q6FHU9|Q6IBG0	Silent	SNP	ENST00000254878.3	37	CCDS6276.1	127|127	0.05815018315018315|0.05815018315018315	29|29	0.05894308943089431|0.05894308943089431	25|25	0.06906077348066299|0.06906077348066299	0|0	0.0|0.0	73|73	0.09630606860158311|0.09630606860158311	T|T	5.053|5.053	0.195374|0.195374	0.09599|0.09599	0.074671|0.074671	0.079884|0.079884	ENSG00000132541|ENSG00000132541	ENST00000520507|ENST00000521560	.|.	.|.	.|.	5.49|5.49	-0.158|-0.158	0.13383|0.13383	.|.	.|.	.|.	.|.	.|.	T|T	0.00524|0.00524	0.0017|0.0017	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18147|0.18147	-1.0346|-1.0346	3|3	.|.	.|.	.|.	.|.	1.1412|1.1412	0.01766|0.01766	0.1291:0.2341:0.2659:0.3709|0.1291:0.2341:0.2659:0.3709	rs11537947;rs11537947|rs11537947;rs11537947	.|.	.|.	.|.	S|Q	145|124	.|.	.|.	G|R	-|-	1|2	0|0	HRSP12|HRSP12	99184258|99184258	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.154000|0.154000	0.21943|0.21943	-0.269000|-0.269000	0.08596|0.08596	-0.121000|-0.121000	0.11787|0.11787	-0.254000|-0.254000	0.11334|0.11334	GGC|CGG	C|0.923;T|0.077	0.077	strong		0.348	HRSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379687.1	NM_005836	
MTMR4	9110	hgsc.bcm.edu	37	17	56584508	56584508	+	Missense_Mutation	SNP	T	T	C	rs2302190	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56584508T>C	ENST00000323456.5	-	9	962	c.838A>G	c.(838-840)Agc>Ggc	p.S280G	MTMR4_ENST00000579925.1_Missense_Mutation_p.S280G	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	280	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.		S -> G (in dbSNP:rs2302190). {ECO:0000269|PubMed:15489334}.		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)					CACGCCTCGCTGGTATCATTA	0.602													T|||	1643	0.328075	0.4652	0.1398	5008	,	,		19038	0.3214		0.2187	False		,,,				2504	0.3957				p.S280G		Atlas-SNP	.											.	MTMR4	91	.	0			c.A838G						PASS	.	T	GLY/SER	1840,2566	531.5+/-373.2	401,1038,764	64.0	66.0	65.0		838	4.1	0.9	17	dbSNP_100	65	1750,6850	314.5+/-311.8	190,1370,2740	yes	missense	MTMR4	NM_004687.4	56	591,2408,3504	CC,CT,TT		20.3488,41.7612,27.6026	benign	280/1196	56584508	3590,9416	2203	4300	6503	SO:0001583	missense	9110	exon9			CCTCGCTGGTATC	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.838A>G	17.37:g.56584508T>C	ENSP00000325285:p.Ser280Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	602	0.27564102564102566	215	0.4369918699186992	58	0.16022099447513813	166	0.2902097902097902	163	0.21503957783641162	T	7.155	0.584622	0.13749	0.417612	0.203488	ENSG00000108389	ENST00000323456	D	0.93604	-3.25	5.19	4.09	0.47781	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.185631	0.64402	D	0.000017	T	0.00012	0.0000	N	0.08118	0	0.44956	P	0.0020259999999999723	B	0.02656	0.0	B	0.10450	0.005	T	0.12167	-1.0558	9	0.11794	T	0.64	.	10.7076	0.45965	0.0:0.0762:0.0:0.9238	rs2302190;rs17853448;rs52820040;rs56508278;rs58284955;rs2302190	280	Q9NYA4	MTMR4_HUMAN	G	280	ENSP00000325285:S280G	ENSP00000325285:S280G	S	-	1	0	MTMR4	53939507	0.990000	0.36364	0.863000	0.33907	0.996000	0.88848	1.581000	0.36558	0.914000	0.36822	0.524000	0.50904	AGC	T|0.709;C|0.291	0.291	strong		0.602	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
LPPR5	163404	hgsc.bcm.edu	37	1	99418647	99418647	+	Silent	SNP	G	G	C	rs309087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:99418647G>C	ENST00000263177.4	-	3	821	c.600C>G	c.(598-600)gtC>gtG	p.V200V	LPPR5_ENST00000370188.3_Silent_p.V200V	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		200						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										TAGCTGCATAGACACTGAGAG	0.393													G|||	1117	0.223043	0.2738	0.1571	5008	,	,		17020	0.2351		0.1789	False		,,,				2504	0.2342				p.V200V		Atlas-SNP	.											.	.	.	.	0			c.C600G						PASS	.	G	,	1181,3225	415.0+/-337.0	163,855,1185	116.0	106.0	109.0		600,600	2.1	1.0	1	dbSNP_79	109	1501,7099	285.4+/-297.1	118,1265,2917	no	coding-synonymous,coding-synonymous	LPPR5	NM_001010861.2,NM_001037317.1	,	281,2120,4102	CC,CG,GG		17.4535,26.8044,20.6213	,	200/317,200/322	99418647	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGCATAGACACTG																												ENST00000263177.4:c.600C>G	1.37:g.99418647G>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Silent	SNP	ENST00000263177.4	37	CCDS30778.1																																																																																			G|0.786;C|0.214	0.214	strong		0.393	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1		
ZNF595	152687	hgsc.bcm.edu	37	4	59350	59350	+	Missense_Mutation	SNP	A	A	G	rs6834707	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:59350A>G	ENST00000509152.2	+	2	216	c.31A>G	c.(31-33)Ata>Gta	p.I11V	ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_Missense_Mutation_p.I11V			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	11	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(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GGATGTGGCCATAGAATTCTC	0.428																																					p.I11V		Atlas-SNP	.											.	.	.	.	0			c.A31G						PASS	.	A	VAL/ILE	117,4289	69.2+/-107.0	0,117,2086	360.0	388.0	379.0		31	0.1	0.7	4	dbSNP_116	379	165,8435	62.8+/-124.8	0,165,4135	no	missense	ZNF595	NM_182524.2	29	0,282,6221	GG,GA,AA		1.9186,2.6555,2.1682	benign	11/649	59350	282,12724	2203	4300	6503	SO:0001583	missense	255403	exon2			GTGGCCATAGAAT	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.31A>G	4.37:g.59350A>G	ENSP00000434858:p.Ile11Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	160	17	0.10625	NM_001039127		Missense_Mutation	SNP	ENST00000509152.2	37		.	.	.	.	.	.	.	.	.	.	A	11.22	1.574255	0.28092	0.026555	0.019186	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.00824	5.65;5.65	1.26	0.0585	0.14328	Krueppel-associated box (8);	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	N	0.999993	B;B	0.28026	0.198;0.046	B;B	0.30316	0.114;0.017	T	0.48479	-0.9032	8	0.33940	T	0.23	.	3.5569	0.07867	0.4697:0.0:0.5303:0.0	rs6834707;rs6834707	11;11	Q8IYB9;Q3SXZ3	ZN595_HUMAN;ZN718_HUMAN	V	11	ENSP00000434858:I11V;ENSP00000437878:I11V	ENSP00000434858:I11V	I	+	1	0	ZNF595	49350	0.068000	0.21057	0.711000	0.30485	0.284000	0.27059	0.134000	0.15932	0.549000	0.28973	0.397000	0.26171	ATA	A|0.997;G|0.003	0.003	strong		0.428	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524	
TMC8	147138	hgsc.bcm.edu	37	17	76130575	76130575	+	Missense_Mutation	SNP	A	A	T	rs7208422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76130575A>T	ENST00000318430.5	+	8	1291	c.917A>T	c.(916-918)aAc>aTc	p.N306I	TMC8_ENST00000589691.1_Missense_Mutation_p.N83I|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	306			N -> I (in dbSNP:rs7208422). {ECO:0000269|Ref.3}.		ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			AACGTACTCAACGGGCTCCTG	0.612													T|||	2766	0.552316	0.7126	0.5879	5008	,	,		17585	0.4236		0.4901	False		,,,				2504	0.5072				p.N306I		Atlas-SNP	.											TMC8,NS,carcinoma,-1,1	TMC8	44	1	0			c.A917T						PASS	.	T	ILE/ASN	3021,1385	449.2+/-349.0	1044,933,226	51.0	56.0	54.0		917	4.7	0.7	17	dbSNP_116	54	4209,4391	578.9+/-390.8	1055,2099,1146	yes	missense	TMC8	NM_152468.4	149	2099,3032,1372	TT,TA,AA		48.9419,31.4344,44.4103	benign	306/727	76130575	7230,5776	2203	4300	6503	SO:0001583	missense	147138	exon8			TACTCAACGGGCT	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.917A>T	17.37:g.76130575A>T	ENSP00000325561:p.Asn306Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Missense_Mutation	SNP	ENST00000318430.5	37	CCDS32749.1	1186	0.543040293040293	339	0.6890243902439024	211	0.5828729281767956	264	0.46153846153846156	372	0.49076517150395776	T	0.194	-1.051025	0.01981	0.685656	0.489419	ENSG00000167895	ENST00000318430	T	0.59502	0.26	4.71	4.71	0.59529	.	0.193322	0.44483	N	0.000458	T	0.00012	0.0000	N	0.00119	-2.075	0.53005	P	3.2000000000032E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43180	-0.9407	9	0.14656	T	0.56	-11.1433	9.0321	0.36264	0.1652:0.0:0.0:0.8348	rs7208422;rs7208422	306;306	A5D8Y4;Q8IU68	.;TMC8_HUMAN	I	306	ENSP00000325561:N306I	ENSP00000325561:N306I	N	+	2	0	TMC8	73642170	0.917000	0.31117	0.724000	0.30704	0.095000	0.18619	1.351000	0.34022	0.657000	0.30906	-0.364000	0.07487	AAC	A|0.444;T|0.556	0.556	strong		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
RPP21	79897	hgsc.bcm.edu	37	6	30313340	30313340	+	Missense_Mutation	SNP	G	G	C	rs6986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30313340G>C	ENST00000442966.2	+	3	244	c.231G>C	c.(229-231)caG>caC	p.Q77H	RPP21_ENST00000436442.2_Missense_Mutation_p.Q77H|TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.Q338H|RPP21_ENST00000433076.2_Missense_Mutation_p.Q85H|RPP21_ENST00000466327.1_3'UTR|RPP21_ENST00000428040.2_Missense_Mutation_p.Q100H			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	77			Q -> H (in dbSNP:rs6986). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						CCTGCACCCAGCGCCAGAGAC	0.697													G|||	1302	0.259984	0.2905	0.1816	5008	,	,		7455	0.1667		0.2545	False		,,,				2504	0.3763				p.Q426H		Atlas-SNP	.											.	.	.	.	0			c.G1278C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	952,2048		158,636,706	14.0	9.0	11.0		1278,255,231,231	4.7	1.0	6	dbSNP_52	11	1197,4197		151,895,1651	yes	missense,missense,missense,missense	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	24,24,24,24	309,1531,2357	CC,CG,GG		22.1913,31.7333,25.6016	,,,	426/504,85/163,77/145,77/155	30313340	2149,6245	1500	2697	4197	SO:0001583	missense	202658	exon8			CACCCAGCGCCAG	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"""chromosome 6 open reading frame 135"", ""ribonuclease P 21kDa subunit"""	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.231G>C	6.37:g.30313340G>C	ENSP00000403833:p.Gln77His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	15	0.272727	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Missense_Mutation	SNP	ENST00000442966.2	37	CCDS4679.1	489	0.2239010989010989	134	0.27235772357723576	69	0.19060773480662985	93	0.16258741258741258	193	0.2546174142480211	G	16.57	3.159557	0.57368	0.317333	0.221913	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040;ENST00000436442	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.53	4.66	0.58398	.	0.397524	0.25564	N	0.029811	T	0.36771	0.0979	N	0.25890	0.77	0.31574	P	0.655968	D;B;B;B	0.69078	0.997;0.106;0.245;0.004	D;B;B;B	0.71870	0.975;0.019;0.048;0.004	T	0.46707	-0.9172	9	0.87932	D	0	-5.2369	10.8448	0.46737	0.0876:0.0:0.9124:0.0	rs6986;rs1137108;rs2516690;rs3179290;rs3200884;rs11557496;rs17341450;rs17353244;rs17362218;rs6986	340;77;77;100	F5H2V3;Q9H633-3;Q9H633;Q9H633-2	.;.;RPP21_HUMAN;.	H	340;338;85;77;100;77	ENSP00000424048:Q338H;ENSP00000409799:Q85H;ENSP00000403833:Q77H;ENSP00000394320:Q100H;ENSP00000397778:Q77H	ENSP00000394320:Q100H	Q	+	3	2	RPP21;TRIM39-RPP21;TRIM39	30421319	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.966000	0.56795	1.466000	0.48025	0.650000	0.86243	CAG	G|0.754;C|0.246	0.246	strong		0.697	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
CCDC129	223075	hgsc.bcm.edu	37	7	31611758	31611758	+	Silent	SNP	G	G	T	rs67930674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:31611758G>T	ENST00000407970.3	+	6	389	c.351G>T	c.(349-351)ggG>ggT	p.G117G	CCDC129_ENST00000319386.3_Silent_p.G117G|CCDC129_ENST00000451887.2_Silent_p.G143G|CCDC129_ENST00000409210.1_Silent_p.G25G|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	117										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TATCCAGAGGGACCAGTTTCA	0.403													G|||	2209	0.441094	0.5378	0.5101	5008	,	,		19577	0.3383		0.4036	False		,,,				2504	0.4059				p.G143G		Atlas-SNP	.											.	CCDC129	127	.	0			c.G429T						PASS	.	G		2273,2133	592.7+/-387.9	582,1109,512	122.0	106.0	111.0		351	2.8	1.0	7	dbSNP_130	111	3598,5002	515.5+/-378.6	751,2096,1453	no	coding-synonymous	CCDC129	NM_194300.2		1333,3205,1965	TT,TG,GG		41.8372,48.4113,45.1407		117/1045	31611758	5871,7135	2203	4300	6503	SO:0001819	synonymous_variant	223075	exon6			CAGAGGGACCAGT	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.351G>T	7.37:g.31611758G>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	171	57	0.333333	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			G|0.555;T|0.445	0.445	strong		0.403	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
AKAP6	9472	hgsc.bcm.edu	37	14	33293122	33293122	+	Missense_Mutation	SNP	A	A	G	rs1051695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	42	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	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	
MAN2B1	4125	hgsc.bcm.edu	37	19	12772165	12772165	+	Missense_Mutation	SNP	G	G	A	rs1054487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12772165G>A	ENST00000456935.2	-	7	975	c.935C>T	c.(934-936)aCt>aTt	p.T312I	MAN2B1_ENST00000495617.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.T312I	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	157	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	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		
CYP4F2	8529	hgsc.bcm.edu	37	19	16001215	16001215	+	Missense_Mutation	SNP	C	C	A	rs3093153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:16001215C>A	ENST00000221700.6	-	6	649	c.554G>T	c.(553-555)gGt>gTt	p.G185V	CYP4F2_ENST00000011989.7_Missense_Mutation_p.G36V	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ACAGGCACTACCCTCTGAGGC	0.542													.|||	150	0.0299521	0.0378	0.0389	5008	,	,		19645	0.0		0.0696	False		,,,				2504	0.0031				p.G185V		Atlas-SNP	.											.	CYP4F2	97	.	0			c.G554T						PASS	.	C	VAL/GLY	131,4275	95.7+/-134.4	2,127,2074	92.0	87.0	88.0		554	3.1	0.0	19	dbSNP_103	88	511,8089	145.6+/-201.3	11,489,3800	no	missense	CYP4F2	NM_001082.3	109	13,616,5874	AA,AC,CC		5.9419,2.9732,4.9362	possibly-damaging	185/521	16001215	642,12364	2203	4300	6503	SO:0001583	missense	8529	exon6			GCACTACCCTCTG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.554G>T	19.37:g.16001215C>A	ENSP00000221700:p.Gly185Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	86	0.039377289377289376	13	0.026422764227642278	16	0.04419889502762431	0	0.0	57	0.07519788918205805	c	14.11	2.437343	0.43224	0.029732	0.059419	ENSG00000186115	ENST00000221700;ENST00000392846;ENST00000011989	T;T	0.74002	-0.8;1.06	3.07	3.07	0.35406	.	0.082265	0.47455	U	0.000235	T	0.26919	0.0659	M	0.80183	2.485	0.47407	D	0.999416	P;P	0.48911	0.915;0.917	P;P	0.62649	0.883;0.905	T	0.65187	-0.6229	10	0.72032	D	0.01	.	9.7294	0.40352	0.0:1.0:0.0:0.0	rs3093153;rs17750271;rs52798286;rs56751925;rs3093153	36;185	B4DV75;P78329	.;CP4F2_HUMAN	V	185;36;36	ENSP00000221700:G185V;ENSP00000011989:G36V	ENSP00000011989:G36V	G	-	2	0	CYP4F2	15862215	0.675000	0.27558	0.015000	0.15790	0.004000	0.04260	2.436000	0.44819	1.696000	0.51158	0.195000	0.17529	GGT	C|0.957;A|0.043	0.043	strong		0.542	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
DPYD	1806	hgsc.bcm.edu	37	1	98165091	98165091	+	Missense_Mutation	SNP	T	T	C	rs2297595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:98165091T>C	ENST00000370192.3	-	6	596	c.496A>G	c.(496-498)Atg>Gtg	p.M166V	DPYD_ENST00000474241.1_5'UTR|DPYD_ENST00000423006.2_3'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	166			M -> V (in dbSNP:rs2297595).		beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	GGGATACTCATTGCTTTGAAT	0.388													T|||	283	0.0565096	0.031	0.0634	5008	,	,		18189	0.0179		0.1193	False		,,,				2504	0.0613				p.M166V		Atlas-SNP	.											DPYD,NS,carcinoma,+1,3	DPYD	219	3	0			c.A496G	GRCh37	CM003589	DPYD	M	rs2297595	PASS	.	T	VAL/MET	180,4226	117.5+/-155.4	7,166,2030	123.0	125.0	124.0		496	5.3	1.0	1	dbSNP_100	124	852,7748	194.4+/-239.8	44,764,3492	yes	missense	DPYD	NM_000110.3	21	51,930,5522	CC,CT,TT		9.907,4.0853,7.9348	probably-damaging	166/1026	98165091	1032,11974	2203	4300	6503	SO:0001583	missense	1806	exon6			TACTCATTGCTTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.496A>G	1.37:g.98165091T>C	ENSP00000359211:p.Met166Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	130	53	0.407692	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	145	0.06639194139194139	24	0.04878048780487805	28	0.07734806629834254	2	0.0034965034965034965	91	0.12005277044854881	T	18.97	3.736404	0.69189	0.040853	0.09907	ENSG00000188641	ENST00000370192	T	0.71579	-0.58	5.26	5.26	0.73747	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	M	0.85299	2.745	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	D	0.85494	0.1187	9	0.56958	D	0.05	-23.1633	15.1667	0.72833	0.0:0.0:0.0:1.0	rs2297595;rs52827192;rs61243782;rs2297595	166	Q12882	DPYD_HUMAN	V	166	ENSP00000359211:M166V	ENSP00000359211:M166V	M	-	1	0	DPYD	97937679	1.000000	0.71417	0.999000	0.59377	0.862000	0.49288	7.664000	0.83830	2.002000	0.58637	0.477000	0.44152	ATG	T|0.934;C|0.066	0.066	strong		0.388	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
ZNF217	7764	hgsc.bcm.edu	37	20	52192637	52192637	+	Missense_Mutation	SNP	T	T	C	rs34323943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:52192637T>C	ENST00000371471.2	-	4	3091	c.2666A>G	c.(2665-2667)gAc>gGc	p.D889G	ZNF217_ENST00000302342.3_Missense_Mutation_p.D889G|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	889			D -> G (in dbSNP:rs34323943).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CCACGGGCTGTCGTTCTTGGC	0.527													T|||	435	0.086861	0.0023	0.0951	5008	,	,		18538	0.0833		0.1203	False		,,,				2504	0.1646				p.D889G		Atlas-SNP	.											.	ZNF217	227	.	0			c.A2666G						PASS	.	T	GLY/ASP	103,4303	80.4+/-118.8	1,101,2101	74.0	70.0	71.0		2666	3.9	0.0	20	dbSNP_126	71	1043,7557	218.1+/-256.6	58,927,3315	yes	missense	ZNF217	NM_006526.2	94	59,1028,5416	CC,CT,TT		12.1279,2.3377,8.8113	benign	889/1049	52192637	1146,11860	2203	4300	6503	SO:0001583	missense	7764	exon3			GGGCTGTCGTTCT	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2666A>G	20.37:g.52192637T>C	ENSP00000360526:p.Asp889Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	161	0.07371794871794872	5	0.01016260162601626	39	0.10773480662983426	33	0.057692307692307696	84	0.11081794195250659	T	8.423	0.846730	0.16963	0.023377	0.121279	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.08102	3.13;3.13	5.06	3.94	0.45596	.	1.338930	0.04449	N	0.372289	T	0.00178	0.0005	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.39014	-0.9634	10	0.66056	D	0.02	-17.0378	11.513	0.50504	0.0:0.0:0.4757:0.5243	rs34323943	889	O75362	ZN217_HUMAN	G	889;889;49	ENSP00000360526:D889G;ENSP00000304308:D889G	ENSP00000304308:D889G	D	-	2	0	ZNF217	51626044	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.316000	0.33620	0.741000	0.32674	0.528000	0.53228	GAC	T|0.918;C|0.082;A|0.000	0.082	strong		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
RP1L1	94137	hgsc.bcm.edu	37	8	10467637	10467637	+	Missense_Mutation	SNP	T	T	C	rs386722179|rs4240659|rs369606728		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10467637T>C	ENST00000382483.3	-	4	4194	c.3971A>G	c.(3970-3972)gAa>gGa	p.E1324G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1340	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		E -> G (in allele RP1L1-3; dbSNP:rs4240659).		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)		tgttttagtttcctctaactg	0.463																																					p.E1324G		Atlas-SNP	.											.	RP1L1	453	.	0			c.A3971G						PASS	.						134.0	131.0	132.0					8																	10467637		1936	4126	6062	SO:0001583	missense	94137	exon4			TTAGTTTCCTCTA	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.3971A>G	8.37:g.10467637T>C	ENSP00000371923:p.Glu1324Gly	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	18	0.206897	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	6.544	0.468724	0.12461	.	.	ENSG00000183638	ENST00000382483	T	0.09817	2.94	1.91	-1.85	0.07784	.	.	.	.	.	T	0.04815	0.0130	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39800	-0.9596	8	0.29301	T	0.29	-1.4809	7.7672	0.28986	0.0:0.1404:0.0:0.8596	rs4240659	1324	A6NKC6	.	G	1324	ENSP00000371923:E1324G	ENSP00000371923:E1324G	E	-	2	0	RP1L1	10505047	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.133000	0.31430	-0.966000	0.03587	-1.983000	0.00453	GAA	T|1.000;|0.000	.	strong		0.463	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KLHL35	283212	hgsc.bcm.edu	37	11	75134832	75134832	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:75134832G>T	ENST00000539798.1	-	5	1466	c.1467C>A	c.(1465-1467)gaC>gaA	p.D489E	KLHL35_ENST00000376292.4_Missense_Mutation_p.D269E	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	489										lung(2)|stomach(1)	3						CATAGATGGTGTCCTCAAGGG	0.597																																					p.D489E	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.C1467A						PASS	.						99.0	109.0	105.0					11																	75134832		2031	4177	6208	SO:0001583	missense	283212	exon5			GATGGTGTCCTCA		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"""Kelch-like"", ""BTB/POZ domain containing"""	26597	protein-coding gene	gene with protein product			"""kelch-like 35 (Drosophila)"""				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1467C>A	11.37:g.75134832G>T	ENSP00000438526:p.Asp489Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	4	0.0493827	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	37	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	G	10.26	1.300475	0.23650	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.68903	-0.36;-0.36	5.12	3.23	0.37069	Kelch-type beta propeller (1);	0.216802	0.37304	N	0.002158	T	0.52075	0.1712	L	0.35793	1.09	0.24569	N	0.993936	B	0.19200	0.034	B	0.23150	0.044	T	0.49244	-0.8960	10	0.66056	D	0.02	.	4.9596	0.14059	0.1754:0.0:0.658:0.1666	.	269	Q6PF15	KLH35_HUMAN	E	269;489	ENSP00000365469:D269E;ENSP00000438526:D489E	ENSP00000365469:D269E	D	-	3	2	KLHL35	74812480	1.000000	0.71417	0.986000	0.45419	0.202000	0.24057	0.617000	0.24359	0.726000	0.32339	0.650000	0.86243	GAC	.	.	none		0.597	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583	
SGK223	157285	hgsc.bcm.edu	37	8	8234526	8234526	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:8234526T>A	ENST00000520004.1	-	3	1657	c.1393A>T	c.(1393-1395)Act>Tct	p.T465S	SGK223_ENST00000330777.4_Missense_Mutation_p.T465S			Q86YV5	SG223_HUMAN		467							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACCTGGGGAGTTGGGTCTGGG	0.637																																					p.T465S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.A1393T						PASS	.						43.0	50.0	48.0					8																	8234526		2092	4227	6319	SO:0001583	missense	0	exon2			GGGGAGTTGGGTC																												ENST00000520004.1:c.1393A>T	8.37:g.8234526T>A	ENSP00000428054:p.Thr465Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	30	0.32967	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707584	0.30322	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.58940	0.3;0.3	5.02	1.03	0.20045	.	2.041710	0.02601	N	0.101061	T	0.43612	0.1255	N	0.19112	0.55	0.09310	N	1	B	0.14012	0.009	B	0.16289	0.015	T	0.25152	-1.0140	10	0.34782	T	0.22	.	7.1243	0.25463	0.0:0.4468:0.0:0.5532	.	465	Q86YV5	SG223_HUMAN	S	465	ENSP00000330930:T465S;ENSP00000428054:T465S	ENSP00000330930:T465S	T	-	1	0	AC068353.1	8271936	0.000000	0.05858	0.000000	0.03702	0.894000	0.52154	-0.045000	0.12003	0.249000	0.21456	-0.177000	0.13119	ACT	.	.	none		0.637	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SORBS2	8470	hgsc.bcm.edu	37	4	186544435	186544435	+	Silent	SNP	C	C	T	rs28528960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186544435C>T	ENST00000284776.7	-	13	2645	c.2136G>A	c.(2134-2136)tcG>tcA	p.S712S	SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000431808.1_Silent_p.S712S|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000355634.5_Silent_p.S812S|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000418609.1_Silent_p.S616S	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	712					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TCTTAGGAGCCGAATTTTTTT	0.443													T|||	582	0.116214	0.298	0.0836	5008	,	,		17781	0.003		0.0954	False		,,,				2504	0.0317				p.S812S	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2,colon,carcinoma,-1,1	SORBS2	300	1	0			c.G2436A						scavenged	.	T	,,,,,,,	1281,3125	699.3+/-406.5	191,899,1113	126.0	139.0	134.0		,,,,1848,,,2136	-11.8	0.0	4	dbSNP_125	134	691,7909	787.1+/-407.6	31,629,3640	no	intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	222,1528,4753	TT,TC,CC		8.0349,29.074,15.1622	,,,,,,,	,,,,616/1005,,,712/1101	186544435	1972,11034	2203	4300	6503	SO:0001819	synonymous_variant	8470	exon16			AGGAGCCGAATTT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2136G>A	4.37:g.186544435C>T		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																			C|0.865;T|0.135	0.135	strong		0.443	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
SLIT1	6585	hgsc.bcm.edu	37	10	98803252	98803252	+	Silent	SNP	G	G	A	rs35388136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:98803252G>A	ENST00000266058.4	-	19	2117	c.1872C>T	c.(1870-1872)cgC>cgT	p.R624R	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Silent_p.R624R	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	624					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGCAGCTGATGCGGTTGTTCC	0.647													G|||	234	0.0467252	0.0106	0.0634	5008	,	,		16252	0.0		0.1262	False		,,,				2504	0.0501				p.R624R		Atlas-SNP	.											.	SLIT1	154	.	0			c.C1872T						PASS	.	G		109,4297	84.4+/-122.9	1,107,2095	147.0	141.0	143.0		1872	-0.6	1.0	10	dbSNP_126	143	1182,7418	240.4+/-271.1	71,1040,3189	no	coding-synonymous	SLIT1	NM_003061.2		72,1147,5284	AA,AG,GG		13.7442,2.4739,9.9262		624/1535	98803252	1291,11715	2203	4300	6503	SO:0001819	synonymous_variant	6585	exon19			GCTGATGCGGTTG	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1872C>T	10.37:g.98803252G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																			G|0.920;A|0.080	0.080	strong		0.647	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:107459974C>T	ENST00000409382.3	-	2	1070	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.G154R|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						scavenged	.	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	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	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	
OR9K2	441639	hgsc.bcm.edu	37	12	55523833	55523833	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523833T>C	ENST00000305377.5	+	1	369	c.281T>C	c.(280-282)aTt>aCt	p.I94T		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	94						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(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CTCTCCTTCATTGATCTTTTC	0.423																																					p.I94T		Atlas-SNP	.											.	OR9K2	63	.	0			c.T281C						PASS	.						181.0	179.0	180.0					12																	55523833		2203	4300	6503	SO:0001583	missense	441639	exon1			CCTTCATTGATCT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.281T>C	12.37:g.55523833T>C	ENSP00000307598:p.Ile94Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071507	0.36566	.	.	ENSG00000170605	ENST00000305377	T	0.03181	4.02	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.256644	0.27384	N	0.019611	T	0.07234	0.0183	L	0.37561	1.115	0.09310	N	1	P	0.49358	0.923	P	0.49597	0.616	T	0.09885	-1.0654	10	0.72032	D	0.01	-15.6178	14.8097	0.69985	0.0:0.0:0.0:1.0	.	94	Q8NGE7	OR9K2_HUMAN	T	94	ENSP00000307598:I94T	ENSP00000307598:I94T	I	+	2	0	OR9K2	53810100	0.007000	0.16637	0.673000	0.29887	0.816000	0.46133	1.733000	0.38156	2.223000	0.72356	0.528000	0.53228	ATT	.	.	none		0.423	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
PSAPL1	768239	hgsc.bcm.edu	37	4	7436073	7436073	+	Silent	SNP	C	C	T	rs61740031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7436073C>T	ENST00000319098.4	-	1	627	c.534G>A	c.(532-534)gcG>gcA	p.A178A	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	178					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CTCCTTCAGGCGCCTGGCGGG	0.627													C|||	637	0.127196	0.0976	0.1369	5008	,	,		17302	0.0764		0.1948	False		,,,				2504	0.1431				p.A178A		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G534A						PASS	.	C	,	464,3454		22,420,1517	12.0	14.0	13.0		534,	-3.3	0.0	4	dbSNP_129	13	1608,6656		161,1286,2685	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	183,1706,4202	TT,TC,CC		19.4579,11.8428,17.0087	,	178/522,	7436073	2072,10110	1959	4132	6091	SO:0001819	synonymous_variant	768239	exon1			TTCAGGCGCCTGG	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.534G>A	4.37:g.7436073C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			C|0.870;T|0.130	0.130	strong		0.627	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
PIDD1	55367	hgsc.bcm.edu	37	11	801092	801092	+	Silent	SNP	G	G	A	rs11539604	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:801092G>A	ENST00000347755.5	-	10	1800	c.1659C>T	c.(1657-1659)caC>caT	p.H553H	PIDD_ENST00000411829.2_Silent_p.H553H|PIDD_ENST00000534649.1_5'Flank	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					AGTACAACAGGTGCAGGCGGG	0.662													G|||	143	0.0285543	0.0053	0.0533	5008	,	,		15051	0.0		0.0865	False		,,,				2504	0.0123				p.H553H		Atlas-SNP	.											.	PIDD	76	.	0			c.C1659T						PASS	.	G	,	47,4317		1,45,2136	29.0	23.0	25.0		1659,1659	1.5	1.0	11	dbSNP_120	25	612,7964		19,574,3695	no	coding-synonymous,coding-synonymous	PIDD	NM_145886.3,NM_145887.3	,	20,619,5831	AA,AG,GG		7.1362,1.077,5.0927	,	553/911,553/894	801092	659,12281	2182	4288	6470	SO:0001819	synonymous_variant	55367	exon10			CAACAGGTGCAGG																												ENST00000347755.5:c.1659C>T	11.37:g.801092G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_145887		Silent	SNP	ENST00000347755.5	37	CCDS7716.1																																																																																			G|0.959;A|0.041	0.041	strong		0.662	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1		
FAM214A	56204	hgsc.bcm.edu	37	15	52903772	52903772	+	Splice_Site	SNP	T	T	C	rs8036680	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52903772T>C	ENST00000261844.7	-	4	556	c.404A>G	c.(403-405)cAg>cGg	p.Q135R	FAM214A_ENST00000546305.2_Splice_Site_p.Q142R	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	135			Q -> R (in dbSNP:rs8036680).														AACAACTTACTGTCGAGGAAC	0.353													T|||	391	0.0780751	0.1377	0.0706	5008	,	,		20253	0.001		0.0865	False		,,,				2504	0.0736				p.Q135R		Atlas-SNP	.											.	.	.	.	0			c.A404G						PASS	.	T	ARG/GLN	465,3227		23,419,1404	81.0	77.0	78.0		404	6.2	1.0	15	dbSNP_116	78	804,7392		58,688,3352	yes	missense-near-splice	KIAA1370	NM_019600.2	43	81,1107,4756	CC,CT,TT		9.8097,12.5948,10.6746	probably-damaging	135/1077	52903772	1269,10619	1846	4098	5944	SO:0001630	splice_region_variant	56204	exon4			ACTTACTGTCGAG	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.404+1A>G	15.37:g.52903772T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	163	0.07463369963369963	63	0.12804878048780488	33	0.09116022099447514	0	0.0	67	0.08839050131926121	T	28.9	4.958215	0.92726	0.125948	0.098097	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.33438	1.41;1.42	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.38531	1.155	0.09310	P	1.0	D;D	0.76494	0.999;0.998	D;D	0.81914	0.995;0.99	T	0.00268	-1.1862	8	.	.	.	-10.6085	16.8061	0.85666	0.0:0.0:0.0:1.0	rs8036680;rs52827404;rs58457000;rs8036680	142;135	F5H8G0;Q32MH5	.;K1370_HUMAN	R	135;135;134;142	ENSP00000261844:Q135R;ENSP00000443598:Q142R	.	Q	-	2	0	KIAA1370	50691064	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.981000	0.70524	2.367000	0.80283	0.528000	0.53228	CAG	T|0.902;C|0.098	0.098	strong		0.353	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	Missense_Mutation
KLHL14	57565	hgsc.bcm.edu	37	18	30350165	30350165	+	Silent	SNP	G	G	A	rs61737324	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:30350165G>A	ENST00000359358.4	-	2	828	c.390C>T	c.(388-390)tgC>tgT	p.C130C	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Silent_p.C130C	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	130	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						CGATGGACGAGCAGCCCTGCA	0.672													G|||	287	0.0573083	0.1188	0.0418	5008	,	,		16238	0.0079		0.0447	False		,,,				2504	0.0491				p.C130C		Atlas-SNP	.											.	KLHL14	92	.	0			c.C390T						PASS	.	G		531,3875	239.6+/-250.7	34,463,1706	87.0	91.0	90.0		390	1.3	1.0	18	dbSNP_129	90	426,8174	131.3+/-189.1	11,404,3885	no	coding-synonymous	KLHL14	NM_020805.1		45,867,5591	AA,AG,GG		4.9535,12.0517,7.3581		130/629	30350165	957,12049	2203	4300	6503	SO:0001819	synonymous_variant	57565	exon2			GGACGAGCAGCCC	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.390C>T	18.37:g.30350165G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	172	117	0.680233	NM_020805	A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	37	CCDS32813.1																																																																																			G|0.934;A|0.066	0.066	strong		0.672	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
CORIN	10699	hgsc.bcm.edu	37	4	47682174	47682174	+	Silent	SNP	A	A	G	rs10517195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:47682174A>G	ENST00000273857.4	-	8	1115	c.1116T>C	c.(1114-1116)tcT>tcC	p.S372S	CORIN_ENST00000508498.1_Silent_p.S233S|CORIN_ENST00000502252.1_Silent_p.S305S|CORIN_ENST00000505909.1_Intron|CORIN_ENST00000504584.1_Intron	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	372	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGACCTCGTCAGACTTATCCA	0.507													G|||	1858	0.371006	0.2549	0.5173	5008	,	,		22550	0.1319		0.5785	False		,,,				2504	0.4571				p.S372S		Atlas-SNP	.											.	CORIN	154	.	0			c.T1116C						PASS	.	G		1327,3079	695.5+/-405.9	215,897,1091	136.0	99.0	111.0		1116	-11.3	0.1	4	dbSNP_119	111	5103,3497	512.6+/-378.0	1527,2049,724	yes	coding-synonymous	CORIN	NM_006587.2		1742,2946,1815	GG,GA,AA		40.6628,30.118,49.4387		372/1043	47682174	6430,6576	2203	4300	6503	SO:0001819	synonymous_variant	10699	exon8			CTCGTCAGACTTA	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.1116T>C	4.37:g.47682174A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Silent	SNP	ENST00000273857.4	37	CCDS3477.1																																																																																			A|0.562;G|0.438	0.438	strong		0.507	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
GRM7	2917	hgsc.bcm.edu	37	3	7620828	7620828	+	Silent	SNP	G	G	A	rs1485174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:7620828G>A	ENST00000357716.4	+	8	2509	c.2235G>A	c.(2233-2235)ggG>ggA	p.G745G	GRM7_ENST00000389336.4_Silent_p.G745G|GRM7_ENST00000402647.2_Silent_p.G745G|GRM7_ENST00000486284.1_Silent_p.G745G|GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000403881.1_Silent_p.G745G	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	745			G -> E (in dbSNP:rs1485174).		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AAGCCAGAGGGGTTCTCAAGT	0.443													G|||	855	0.170727	0.0552	0.2565	5008	,	,		19555	0.1399		0.2932	False		,,,				2504	0.1718				p.G745G		Atlas-SNP	.											.	GRM7	223	.	0			c.G2235A						PASS	.	G	,	372,4034	187.4+/-214.1	16,340,1847	131.0	116.0	121.0		2235,2235	-11.7	0.4	3	dbSNP_88	121	2388,6212	398.3+/-346.1	338,1712,2250	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	354,2052,4097	AA,AG,GG		27.7674,8.443,21.221	,	745/916,745/923	7620828	2760,10246	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			CAGAGGGGTTCTC	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2235G>A	3.37:g.7620828G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	231	136	0.588745	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			G|0.803;A|0.197	0.197	strong		0.443	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
ASB15	142685	hgsc.bcm.edu	37	7	123264804	123264804	+	Silent	SNP	C	C	T	rs11769381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:123264804C>T	ENST00000451558.1	+	10	1154	c.633C>T	c.(631-633)gtC>gtT	p.V211V	RP11-390E23.3_ENST00000440504.1_RNA|RP11-390E23.3_ENST00000451016.1_RNA|ASB15_ENST00000540573.1_Silent_p.V211V|RP11-390E23.3_ENST00000418409.1_RNA|ASB15_ENST00000451215.1_Silent_p.V211V|RP11-390E23.3_ENST00000422401.1_RNA|ASB15_ENST00000434204.1_Silent_p.V211V|RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000275699.3_Silent_p.V211V			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	141	0	0	1525	WXS	Illumina HiSeq	Phase_I	130	70	0.538462	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		
SEC31B	25956	hgsc.bcm.edu	37	10	102247526	102247526	+	Silent	SNP	G	G	C	rs2298074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102247526G>C	ENST00000370345.3	-	26	3484	c.3387C>G	c.(3385-3387)ctC>ctG	p.L1129L		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1129					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CAACCTCATGGAGCCCAGCCA	0.597													G|||	713	0.142372	0.0401	0.1772	5008	,	,		20066	0.129		0.1998	False		,,,				2504	0.2106				p.L1129L		Atlas-SNP	.											.	SEC31B	84	.	0			c.C3387G						PASS	.	G		263,4143	148.8+/-183.1	11,241,1951	39.0	38.0	39.0		3387	0.7	0.8	10	dbSNP_100	39	1940,6660	332.8+/-320.3	222,1496,2582	no	coding-synonymous	SEC31B	NM_015490.3		233,1737,4533	CC,CG,GG		22.5581,5.9691,16.9383		1129/1180	102247526	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon26			CTCATGGAGCCCA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3387C>G	10.37:g.102247526G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			G|0.833;C|0.167	0.167	strong		0.597	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118363642	118363642	+	Silent	SNP	T	T	C	rs3010501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118363642T>C	ENST00000528052.1	+	11	1235	c.1164T>C	c.(1162-1164)agT>agC	p.S388S	PNLIPRP1_ENST00000534537.1_Silent_p.S388S|PNLIPRP1_ENST00000358834.4_Silent_p.S388S			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	388	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		ACCAGTACAGTATCTTCAGGT	0.383													-|||	3537	0.70627	0.5363	0.7637	5008	,	,		17649	0.8988		0.6918	False		,,,				2504	0.7117				p.S388S		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.T1164C						PASS	.			2498,1908		714,1070,419	132.0	118.0	123.0		1164	-9.6	0.0	10	dbSNP_101	123	6130,2470		2180,1770,350	no	coding-synonymous	PNLIPRP1	NM_006229.2		2894,2840,769	CC,CT,TT		28.7209,43.3046,33.6614		388/468	118363642	8628,4378	2203	4300	6503	SO:0001819	synonymous_variant	5407	exon11			GTACAGTATCTTC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1164T>C	10.37:g.118363642T>C		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Silent	SNP	ENST00000528052.1	37	CCDS7595.1																																																																																			T|0.317;C|0.683	0.683	strong		0.383	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41383137C>T	ENST00000301146.4	-	7	1660	c.1119G>A	c.(1117-1119)agG>agA	p.R373R	CYP2A7_ENST00000291764.3_Silent_p.R322R|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	373						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTTTAACCCTGCGGGCCA	0.542													.|||	59	0.0117812	0.0	0.0144	5008	,	,		18858	0.002		0.0457	False		,,,				2504	0.001				p.R373R		Atlas-SNP	.											CYP2A7,NS,carcinoma,-1,1	CYP2A7	71	1	0			c.G1119A						PASS	.	C	,	23,4383	28.1+/-56.4	0,23,2180	103.0	91.0	95.0		1119,966	-1.3	0.0	19	dbSNP_134	95	283,8315	98.8+/-160.4	14,255,4030	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	14,278,6210	TT,TC,CC		3.2915,0.522,2.3531	,	373/495,322/444	41383137	306,12698	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			TTTAACCCTGCGG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1119G>A	19.37:g.41383137C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			C|0.978;T|0.022	0.022	strong		0.542	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
ZNF214	7761	hgsc.bcm.edu	37	11	7022038	7022038	+	Silent	SNP	A	A	G	rs12575236	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7022038A>G	ENST00000278314.4	-	3	1191	c.876T>C	c.(874-876)ttT>ttC	p.F292F	ZNF214_ENST00000531083.1_5'Flank|ZNF214_ENST00000536068.1_Silent_p.F292F	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	66	0	0		WXS	Illumina HiSeq	Phase_I	50	32	0.64	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		
PTPRQ	374462	hgsc.bcm.edu	37	12	81028838	81028838	+	Silent	SNP	C	C	T	rs61729309	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:81028838C>T	ENST00000266688.5	+	40	5889	c.5889C>T	c.(5887-5889)gaC>gaT	p.D1963D				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	2009					regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)	p.D1963D(1)		breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						AACTGAAGGACGAGAGATTAA	0.493													C|||	416	0.0830671	0.0847	0.1196	5008	,	,		16199	0.126		0.0338	False		,,,				2504	0.0613				p.D1795D		Atlas-SNP	.											PTPRQ,NS,carcinoma,0,1	PTPRQ	119	1	1	Substitution - coding silent(1)	stomach(1)	c.C5385T						PASS	.	C		99,1285		2,95,595	86.0	70.0	75.0		5447	-3.4	1.0	12	dbSNP_129	75	130,3052		5,120,1466	no	coding-synonymous	PTPRQ	NM_001145026.1		7,215,2061	TT,TC,CC		4.0855,7.1532,5.0153		1967/2300	81028838	229,4337	692	1591	2283	SO:0001819	synonymous_variant	374462	exon32			GAAGGACGAGAGA	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.5889C>T	12.37:g.81028838C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_001145026		Silent	SNP	ENST00000266688.5	37		215	0.09844322344322344	50	0.1016260162601626	45	0.12430939226519337	91	0.1590909090909091	29	0.03825857519788918	C	8.739	0.918572	0.17982	0.071532	0.040855	ENSG00000139304	ENST00000532722;ENST00000547881	.	.	.	5.39	-3.41	0.04839	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33675	-0.9859	3	.	.	.	.	13.4616	0.61231	0.0:0.2508:0.0:0.7492	rs61729309	.	.	.	M	1664;62	.	.	T	+	2	0	PTPRQ	79552969	0.360000	0.24964	0.984000	0.44739	0.988000	0.76386	-0.713000	0.05007	-0.466000	0.06943	-0.119000	0.15052	ACG	C|0.903;T|0.097	0.097	strong		0.493	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
GCN1L1	10985	hgsc.bcm.edu	37	12	120593190	120593190	+	Missense_Mutation	SNP	G	G	A	rs183298599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:120593190G>A	ENST00000300648.6	-	30	3497	c.3485C>T	c.(3484-3486)tCc>tTc	p.S1162F	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1162					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AATCAGCAAGGAGCAGAGGTC	0.607													G|||	3	0.000599042	0.0	0.0	5008	,	,		19268	0.0		0.003	False		,,,				2504	0.0				p.S1162F		Atlas-SNP	.											GCN1L1,NS,lymphoid_neoplasm,0,1	GCN1L1	207	1	0			c.C3485T						PASS	.	G	PHE/SER	0,4058		0,0,2029	69.0	74.0	72.0		3485	4.7	1.0	12		72	9,8377		0,9,4184	yes	missense	GCN1L1	NM_006836.1	155	0,9,6213	AA,AG,GG		0.1073,0.0,0.0723	possibly-damaging	1162/2672	120593190	9,12435	2029	4193	6222	SO:0001583	missense	10985	exon30			AGCAAGGAGCAGA	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3485C>T	12.37:g.120593190G>A	ENSP00000300648:p.Ser1162Phe	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	24.2	4.503043	0.85176	0.0	0.001073	ENSG00000089154	ENST00000300648	T	0.38560	1.13	5.56	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.111386	0.64402	N	0.000005	T	0.44222	0.1283	M	0.63843	1.955	0.80722	D	1	D	0.54397	0.966	B	0.43536	0.423	T	0.50127	-0.8864	10	0.59425	D	0.04	.	14.1912	0.65639	0.0713:0.0:0.9287:0.0	.	1162	Q92616	GCN1L_HUMAN	F	1162	ENSP00000300648:S1162F	ENSP00000300648:S1162F	S	-	2	0	GCN1L1	119077573	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.119000	0.71590	1.358000	0.45922	0.655000	0.94253	TCC	G|0.998;A|0.002	0.002	strong		0.607	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
PARP4	143	hgsc.bcm.edu	37	13	25000617	25000617	+	Missense_Mutation	SNP	C	C	G	rs7571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25000617C>G	ENST00000381989.3	-	33	5071	c.4966G>C	c.(4966-4968)Gct>Cct	p.A1656P		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1656	Interaction with the major vault protein.			A -> P (in Ref. 1; AAD47250, 2; AAC62491 and 3; BAA11494). {ECO:0000305}.	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)	p.A1656P(1)		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)		GAAATAGAAGCGTCATCCATT	0.343													g|||	2103	0.419928	0.6233	0.3559	5008	,	,		18196	0.3671		0.4105	False		,,,				2504	0.2546				p.A1656P		Atlas-SNP	.											PARP4,NS,carcinoma,0,1	PARP4	142	1	1	Substitution - Missense(1)	stomach(1)	c.G4966C						PASS	.	G	PRO/ALA	2507,1899	541.0+/-375.7	709,1089,405	79.0	80.0	79.0		4966	-4.3	0.0	13	dbSNP_52	79	3207,5393	651.2+/-400.8	594,2019,1687	yes	missense	PARP4	NM_006437.3	27	1303,3108,2092	GG,GC,CC		37.2907,43.1003,43.9336	probably-damaging	1656/1725	25000617	5714,7292	2203	4300	6503	SO:0001583	missense	143	exon33			TAGAAGCGTCATC	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.4966G>C	13.37:g.25000617C>G	ENSP00000371419:p.Ala1656Pro	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	276	274	0.992754	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	926	0.423992673992674	300	0.6097560975609756	126	0.34806629834254144	185	0.32342657342657344	315	0.4155672823218997	g	6.453	0.451821	0.12283	0.568997	0.372907	ENSG00000102699	ENST00000381989	D	0.88509	-2.39	4.09	-4.32	0.03688	.	0.441750	0.17430	N	0.174485	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.40572	-0.9556	9	0.27082	T	0.32	.	3.8199	0.08832	0.1321:0.2003:0.5103:0.1573	rs7571;rs1130967;rs3190437;rs4987096;rs52806064;rs7571	1656	Q9UKK3	PARP4_HUMAN	P	1656	ENSP00000371419:A1656P	ENSP00000371419:A1656P	A	-	1	0	PARP4	23898617	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.291000	0.01147	-0.515000	0.06479	-0.371000	0.07208	GCT	C|0.568;G|0.432	0.432	strong		0.343	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
FAT1	2195	hgsc.bcm.edu	37	4	187534375	187534375	+	Silent	SNP	A	A	G	rs2249917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187534375A>G	ENST00000441802.2	-	13	9560	c.9351T>C	c.(9349-9351)gaT>gaC	p.D3117D		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3117	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TATCGTTCACATCTTCTAGCG	0.527										HNSCC(5;0.00058)			G|||	2093	0.417931	0.5446	0.4683	5008	,	,		18291	0.2808		0.4702	False		,,,				2504	0.2986				p.D3117D	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T9351C						PASS	.	G		2142,1938		580,982,478	98.0	105.0	102.0		9351	-7.3	0.7	4	dbSNP_100	102	3759,4629		846,2067,1281	no	coding-synonymous	FAT1	NM_005245.3		1426,3049,1759	GG,GA,AA		44.814,47.5,47.3292		3117/4589	187534375	5901,6567	2040	4194	6234	SO:0001819	synonymous_variant	2195	exon13			GTTCACATCTTCT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.9351T>C	4.37:g.187534375A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.006;G|0.430	0.430	strong		0.527	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
KIAA0368	23392	hgsc.bcm.edu	37	9	114184259	114184259	+	Missense_Mutation	SNP	G	G	C	rs16916091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:114184259G>C	ENST00000338205.5	-	14	1616	c.1397C>G	c.(1396-1398)aCt>aGt	p.T466S	KIAA0368_ENST00000259335.4_Missense_Mutation_p.T644S			Q5VYK3	ECM29_HUMAN	KIAA0368	472					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CCCTTCCAAAGTACTATACGC	0.438													G|||	145	0.0289537	0.0015	0.0317	5008	,	,		19196	0.0645		0.0308	False		,,,				2504	0.0256				p.T644S		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C1931G						PASS	.	G	SER/THR	38,3748		0,38,1855	80.0	74.0	76.0		1931	5.6	1.0	9	dbSNP_123	76	328,7910		8,312,3799	yes	missense	KIAA0368	NM_001080398.1	58	8,350,5654	CC,CG,GG		3.9815,1.0037,3.0439	benign	644/2018	114184259	366,11658	1893	4119	6012	SO:0001583	missense	23392	exon16			TCCAAAGTACTAT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1397C>G	9.37:g.114184259G>C	ENSP00000339889:p.Thr466Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		76	0.0347985347985348	1	0.0020325203252032522	16	0.04419889502762431	38	0.06643356643356643	21	0.027704485488126648	G	5.779	0.328033	0.10956	0.010037	0.039815	ENSG00000136813	ENST00000338205;ENST00000259335	T	0.40225	1.04	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.229173	0.42821	N	0.000653	T	0.01222	0.0040	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13656	-1.0501	10	0.09590	T	0.72	.	9.6994	0.40178	0.0:0.1225:0.6308:0.2466	rs16916091;rs52797847;rs16916091	472	Q5VYK3	ECM29_HUMAN	S	466;644	ENSP00000259335:T644S	ENSP00000259335:T644S	T	-	2	0	KIAA0368	113224080	1.000000	0.71417	0.986000	0.45419	0.931000	0.56810	2.773000	0.47686	2.776000	0.95493	0.655000	0.94253	ACT	G|0.946;C|0.054	0.054	strong		0.438	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
ARFGAP2	84364	hgsc.bcm.edu	37	11	47188411	47188411	+	Missense_Mutation	SNP	C	C	T	rs3740691	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47188411C>T	ENST00000524782.1	-	13	1460	c.1232G>A	c.(1231-1233)aGc>aAc	p.S411N	ARFGAP2_ENST00000395449.3_5'UTR|RP11-390K5.6_ENST00000524412.1_RNA|ARFGAP2_ENST00000426335.2_Missense_Mutation_p.S275N|ARFGAP2_ENST00000319543.6_Missense_Mutation_p.S142N|ARFGAP2_ENST00000419701.2_Missense_Mutation_p.S304N	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	411	Required for interaction with coatomer.		S -> N (in dbSNP:rs3740691). {ECO:0000269|PubMed:12880961}.		protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TGAGCTCCGGCTCTCCACTTC	0.562													C|||	1946	0.388578	0.6853	0.2435	5008	,	,		22014	0.124		0.335	False		,,,				2504	0.4182				p.S411N		Atlas-SNP	.											.	ARFGAP2	43	.	0			c.G1232A						PASS	.	C	ASN/SER,ASN/SER	2697,1705	651.6+/-399.3	837,1023,341	121.0	125.0	123.0		1148,1232	3.8	0.9	11	dbSNP_107	123	2729,5869	435.0+/-357.9	432,1865,2002	no	missense,missense	ARFGAP2	NM_001242832.1,NM_032389.4	46,46	1269,2888,2343	TT,TC,CC		31.7399,38.7324,41.7385	benign,benign	383/494,411/522	47188411	5426,7574	2201	4299	6500	SO:0001583	missense	84364	exon13			CTCCGGCTCTCCA	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"""ADP-ribosylation factor GTPase activating proteins"""	13504	protein-coding gene	gene with protein product		606908	"""zinc finger protein 289, ID1 regulated"""	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.1232G>A	11.37:g.47188411C>T	ENSP00000434442:p.Ser411Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_032389	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Missense_Mutation	SNP	ENST00000524782.1	37	CCDS7926.1	747	0.34203296703296704	319	0.6483739837398373	94	0.2596685082872928	81	0.14160839160839161	253	0.3337730870712401	C	11.84	1.757403	0.31137	0.612676	0.317399	ENSG00000149182	ENST00000426335;ENST00000524782;ENST00000319543;ENST00000419701;ENST00000526342	T;T;T;T;T	0.18016	3.37;3.5;3.1;3.22;2.24	5.67	3.76	0.43208	.	0.420602	0.32106	N	0.006579	T	0.00012	0.0000	L	0.28192	0.835	0.39789	P	0.027595000000000036	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.28744	-1.0034	9	0.25751	T	0.34	-1.2283	6.6827	0.23129	0.1396:0.6627:0.1237:0.074	rs3740691;rs57763298;rs3740691	304;275;411	B4DX29;G5E9L0;Q8N6H7	.;.;ARFG2_HUMAN	N	275;411;142;304;118	ENSP00000400226:S275N;ENSP00000434442:S411N;ENSP00000327309:S142N;ENSP00000389264:S304N;ENSP00000437305:S118N	ENSP00000327309:S142N	S	-	2	0	ARFGAP2	47144987	0.994000	0.37717	0.864000	0.33941	0.722000	0.41435	0.616000	0.24344	0.703000	0.31848	0.655000	0.94253	AGC	C|0.607;T|0.393	0.393	strong		0.562	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389	
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32834095	32834095	+	Silent	SNP	T	T	C	rs2289037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:32834095T>C	ENST00000420878.3	-	5	1259	c.804A>G	c.(802-804)acA>acG	p.T268T	ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000261333.6_Intron|ZSCAN30_ENST00000333206.5_Silent_p.T268T	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	268					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)			large_intestine(5)|lung(3)|urinary_tract(1)	9						CACTGTGTTCTGTGGGGATTC	0.428													T|||	361	0.0720847	0.0	0.098	5008	,	,		21520	0.2252		0.0258	False		,,,				2504	0.0409				p.T268T		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.A804G						PASS	.	T	,,	25,3111		0,25,1543	209.0	183.0	191.0		804,804,	-3.3	0.0	18	dbSNP_100	191	179,6985		4,171,3407	no	coding-synonymous,coding-synonymous,intron	ZNF397,ZSCAN30	NM_001112734.2,NM_001166012.1,NM_032347.2	,,	4,196,4950	CC,CT,TT		2.4986,0.7972,1.9806	,,	268/495,268/495,	32834095	204,10096	1568	3582	5150	SO:0001819	synonymous_variant	100101467	exon5			GTGTTCTGTGGGG	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.804A>G	18.37:g.32834095T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	184	112	0.608696	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Silent	SNP	ENST00000420878.3	37	CCDS42427.1																																																																																			T|0.931;C|0.069	0.069	strong		0.428	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
FAM187B	148109	hgsc.bcm.edu	37	19	35718938	35718938	+	Missense_Mutation	SNP	C	C	T	rs564117	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35718938C>T	ENST00000324675.3	-	1	694	c.646G>A	c.(646-648)Gtc>Atc	p.V216I		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	216			V -> I (in dbSNP:rs564117).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TCAAAAATGACGTAATCCACC	0.542													C|||	863	0.172324	0.2716	0.1354	5008	,	,		20025	0.0188		0.2008	False		,,,				2504	0.1933				p.V216I		Atlas-SNP	.											FAM187B,caecum,carcinoma,0,1	FAM187B	28	1	0			c.G646A						PASS	.	C	ILE/VAL	1161,3245	409.3+/-334.9	164,833,1206	99.0	82.0	88.0		646	-10.0	0.0	19	dbSNP_83	88	1679,6921	306.9+/-308.1	165,1349,2786	yes	missense	FAM187B	NM_152481.1	29	329,2182,3992	TT,TC,CC		19.5233,26.3504,21.8361	benign	216/370	35718938	2840,10166	2203	4300	6503	SO:0001583	missense	148109	exon1			AAATGACGTAATC	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.646G>A	19.37:g.35718938C>T	ENSP00000323355:p.Val216Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	156	64	0.410256	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	332	0.152014652014652	123	0.25	62	0.1712707182320442	3	0.005244755244755245	144	0.18997361477572558	C	6.670	0.492149	0.12702	0.263504	0.195233	ENSG00000177558	ENST00000324675	T	0.22945	1.93	5.01	-10.0	0.00425	.	1.372100	0.05061	N	0.479938	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.24368	0.102	B	0.17979	0.02	T	0.22208	-1.0223	9	0.06099	T	0.92	-9.6868	4.7828	0.13210	0.1076:0.2031:0.106:0.5833	rs564117;rs52835776;rs56745910;rs564117	216	Q17R55	F187B_HUMAN	I	216	ENSP00000323355:V216I	ENSP00000323355:V216I	V	-	1	0	FAM187B	40410778	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.444000	0.01012	-1.365000	0.02158	-0.150000	0.13652	GTC	C|0.811;T|0.189	0.189	strong		0.542	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993264	140993264	+	Missense_Mutation	SNP	G	G	A	rs176036	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:140993264G>A	ENST00000285879.4	+	4	360	c.74G>A	c.(73-75)tGt>tAt	p.C25Y	MAGEC1_ENST00000406005.2_5'UTR	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	25			C -> Y (in dbSNP:rs176036). {ECO:0000269|PubMed:9485030}.							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)					CCTCAGAGTTGTCCTGAGGGG	0.562										HNSCC(15;0.026)			G|||	490	0.129801	0.1225	0.1182	3775	,	,		13207	0.0466		0.164	False		,,,				2504	0.0348				p.C25Y		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G74A						PASS	.	G	TYR/CYS	612,3223		43,438,88,1151,483	71.0	70.0	71.0		74	-0.3	0.0	X	dbSNP_79	71	1399,5329		100,803,396,1525,1476	yes	missense	MAGEC1	NM_005462.4	194	143,1241,484,2676,1959	AA,AG,A,GG,G		20.7937,15.9583,19.0382	possibly-damaging	25/1143	140993264	2011,8552	2203	4300	6503	SO:0001583	missense	9947	exon4			AGAGTTGTCCTGA	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.74G>A	X.37:g.140993264G>A	ENSP00000285879:p.Cys25Tyr	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	25	0.925926	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	255	0.15370705244122965	39	0.08441558441558442	30	0.09090909090909091	16	0.029411764705882353	85	0.12536873156342182	g	4.683	0.126992	0.08931	0.159583	0.207937	ENSG00000155495	ENST00000285879;ENST00000370511;ENST00000370510	T;T	0.12569	4.02;2.67	0.149	-0.298	0.12814	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.2000000000032E-5	P	0.42993	0.797	B	0.42343	0.384	T	0.37150	-0.9718	7	0.41790	T	0.15	.	.	.	.	rs176036;rs389145	25	O60732	MAGC1_HUMAN	Y	25;25;24	ENSP00000285879:C25Y;ENSP00000359542:C25Y	ENSP00000285879:C25Y	C	+	2	0	MAGEC1	140820930	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-2.582000	0.00905	-1.172000	0.02762	-1.175000	0.01729	TGT	G|0.829;A|0.171	0.171	strong		0.562	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145039594	145039594	+	Missense_Mutation	SNP	T	T	C	rs111958438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145039594T>C	ENST00000493130.2	-	1	177	c.16A>G	c.(16-18)Acg>Gcg	p.T6A	PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T6A|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.T6A|PDE4DIP_ENST00000369348.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					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)		ACCTACCTCGTCCAGGTCTGC	0.617			T	PDGFRB	MPD																																p.T6A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000313382,caecum,carcinoma,0,1	PDE4DIP	817	1	0			c.A16G						scavenged	.						79.0	80.0	80.0					1																	145039594		876	1991	2867	SO:0001583	missense	9659	exon1			ACCTCGTCCAGGT	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	ENST00000493130.2:c.16A>G	1.37:g.145039594T>C	ENSP00000432251:p.Thr6Ala	Somatic	111	2	0.018018		WXS	Illumina HiSeq	Phase_I	126	10	0.0793651	NM_001198832	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	ENST00000493130.2	37		.	.	.	.	.	.	.	.	.	.	T	11.17	1.560174	0.27827	.	.	ENSG00000178104	ENST00000313382;ENST00000532801;ENST00000530078;ENST00000493130;ENST00000478649	T;T	0.46063	4.7;0.88	4.4	2.11	0.27256	.	.	.	.	.	T	0.08179	0.0204	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.10847	-1.0612	9	0.42905	T	0.14	.	4.7526	0.13068	0.0:0.3309:0.0:0.6691	.	6;6	Q5VU43-3;E9PQH9	.;.	A	6	ENSP00000327209:T6A;ENSP00000436751:T6A	ENSP00000327209:T6A	T	-	1	0	PDE4DIP	143750951	0.974000	0.33945	0.944000	0.38274	0.633000	0.38033	0.722000	0.25925	0.262000	0.21774	0.454000	0.30748	ACG	T|0.995;C|0.005	0.005	strong		0.617	PDE4DIP-027	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000099618.2	NM_022359	
THBS2	7058	hgsc.bcm.edu	37	6	169621536	169621536	+	Silent	SNP	A	A	G	rs1132742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:169621536A>G	ENST00000366787.3	-	21	3609	c.3360T>C	c.(3358-3360)acT>acC	p.T1120T	THBS2_ENST00000488355.1_5'UTR|XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1120	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.T1120T(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		TGATGTAGCCAGTCTTGGGCC	0.522													G|||	1331	0.265775	0.3684	0.2421	5008	,	,		17798	0.2361		0.2078	False		,,,				2504	0.2342				p.T1120T	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	1	Substitution - coding silent(1)	stomach(1)	c.T3360C						PASS	.	G		1413,2993	686.4+/-404.7	227,959,1017	159.0	138.0	145.0		3360	-9.9	0.0	6	dbSNP_86	145	1758,6842	735.4+/-406.9	177,1404,2719	no	coding-synonymous	THBS2	NM_003247.2		404,2363,3736	GG,GA,AA		20.4419,32.0699,24.3811		1120/1173	169621536	3171,9835	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon21			GTAGCCAGTCTTG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3360T>C	6.37:g.169621536A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.242;N|0.001	0.242	strong		0.522	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167189607A>C	ENST00000476257.1	-	3	314	c.16T>G	c.(16-18)Ttg>Gtg	p.L6V	SERPINI2_ENST00000465031.1_5'UTR|SERPINI2_ENST00000461846.1_Missense_Mutation_p.L6V|SERPINI2_ENST00000264677.4_Missense_Mutation_p.L6V|SERPINI2_ENST00000471111.1_Missense_Mutation_p.L6V			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	6			L -> V (in dbSNP:rs17246389).		cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						AGACTCCACAAGAAGATTGTG	0.338													A|||	840	0.167732	0.056	0.134	5008	,	,		16707	0.0972		0.2624	False		,,,				2504	0.318				p.L16V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.T46G	GRCh37	CM067714	SERPINI2	M	rs17246389	PASS	.	A	VAL/LEU	391,4015	191.2+/-216.9	14,363,1826	108.0	120.0	116.0		16	-1.4	0.0	3	dbSNP_123	116	2220,6378	375.5+/-337.8	304,1612,2383	yes	missense	SERPINI2	NM_006217.3	32	318,1975,4209	CC,CA,AA		25.82,8.8743,20.0784	possibly-damaging	6/406	167189607	2611,10393	2203	4299	6502	SO:0001583	missense	5276	exon3			TCCACAAGAAGAT	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.16T>G	3.37:g.167189607A>C	ENSP00000420621:p.Leu6Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	338	0.15476190476190477	31	0.06300813008130081	56	0.15469613259668508	52	0.09090909090909091	199	0.262532981530343	A	10.34	1.322455	0.23994	0.088743	0.2582	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	T;T;T;T;T;T	0.81247	-0.94;-0.94;-0.94;-0.94;-0.94;-1.47	5.41	-1.41	0.08941	Serpin domain (1);	0.649667	0.14912	N	0.291166	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P	0.37781	0.608;0.608	B;B	0.32090	0.14;0.14	T	0.01972	-1.1237	9	0.72032	D	0.01	.	9.7473	0.40455	0.5821:0.0:0.4179:0.0	rs17246389;rs52822774;rs59746421;rs17246389	6;6	B4DDY9;O75830	.;SPI2_HUMAN	V	6	ENSP00000420621:L6V;ENSP00000417692:L6V;ENSP00000264677:L6V;ENSP00000419407:L6V;ENSP00000417752:L6V;ENSP00000419255:L6V	ENSP00000264677:L6V	L	-	1	2	SERPINI2	168672301	0.030000	0.19436	0.010000	0.14722	0.015000	0.08874	0.115000	0.15540	-0.484000	0.06763	-0.417000	0.06048	TTG	A|0.830;C|0.170	0.170	strong		0.338	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
IGFN1	91156	hgsc.bcm.edu	37	1	201184878	201184878	+	Missense_Mutation	SNP	C	C	A	rs61743921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201184878C>A	ENST00000335211.4	+	15	9337	c.9207C>A	c.(9205-9207)agC>agA	p.S3069R	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_Missense_Mutation_p.S229R	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	612						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						GCCTCCCCAGCGCAGGCAGGA	0.657													C|||	110	0.0219649	0.0076	0.0447	5008	,	,		18927	0.0		0.0517	False		,,,				2504	0.0174				p.S3069R		Atlas-SNP	.											.	IGFN1	220	.	0			c.C9207A						PASS	.	C	ARG/SER	84,4322	69.8+/-107.6	0,84,2119	33.0	31.0	32.0		9207	-0.5	0.1	1	dbSNP_129	32	589,8011	152.8+/-207.3	17,555,3728	yes	missense	IGFN1	NM_001164586.1	110	17,639,5847	AA,AC,CC		6.8488,1.9065,5.1745	benign	3069/3709	201184878	673,12333	2203	4300	6503	SO:0001583	missense	91156	exon15			CCCCAGCGCAGGC	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.9207C>A	1.37:g.201184878C>A	ENSP00000334714:p.Ser3069Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	99	33	0.333333	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	66|66	0.03021978021978022|0.03021978021978022	11|11	0.022357723577235773|0.022357723577235773	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	37|37	0.048812664907651716|0.048812664907651716	C|C	13.68|13.68	2.308775|2.308775	0.40895|0.40895	0.019065|0.019065	0.068488|0.068488	ENSG00000163395|ENSG00000163395	ENST00000412892|ENST00000335211;ENST00000295591	.|T;T	.|0.43294	.|0.95;0.95	4.83|4.83	-0.489|-0.489	0.12052|0.12052	.|.	.|0.316472	.|0.32357	.|N	.|0.006220	T|T	0.06142|0.06142	0.0159|0.0159	L|L	0.61387|0.61387	1.9|1.9	0.09310|0.09310	N|N	0.999994|0.999994	.|P	.|0.40619	.|0.724	.|P	.|0.51974	.|0.686	T|T	0.10451|0.10451	-1.0629|-1.0629	5|9	.|.	.|.	.|.	.|.	10.6295|10.6295	0.45527|0.45527	0.0:0.4955:0.0:0.5045|0.0:0.4955:0.0:0.5045	rs61743921|rs61743921	.|3069	.|F8WAI1	.|.	S|R	487|3069;229	.|ENSP00000334714:S3069R;ENSP00000295591:S229R	.|.	R|S	+|+	1|3	0|2	IGFN1|IGFN1	199451501|199451501	0.000000|0.000000	0.05858|0.05858	0.089000|0.089000	0.20774|0.20774	0.004000|0.004000	0.04260|0.04260	-1.017000|-1.017000	0.03630|0.03630	-0.108000|-0.108000	0.12066|0.12066	-0.997000|-0.997000	0.02515|0.02515	CGC|AGC	C|0.957;A|0.043	0.043	strong		0.657	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
ENOSF1	55556	hgsc.bcm.edu	37	18	691266	691266	+	Missense_Mutation	SNP	A	A	G	rs2612086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:691266A>G	ENST00000251101.7	-	6	522	c.434T>C	c.(433-435)aTg>aCg	p.M145T	ENOSF1_ENST00000539164.1_3'UTR|ENOSF1_ENST00000383578.3_Missense_Mutation_p.M63T|ENOSF1_ENST00000580982.1_Intron|ENOSF1_ENST00000340116.7_Missense_Mutation_p.M166T	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	145			M -> T (in dbSNP:rs2612086). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8493092, ECO:0000269|PubMed:8764108, ECO:0000269|Ref.5}.		cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						GGATACCAGCATCCTGGGATC	0.428													G|||	1280	0.255591	0.2927	0.3516	5008	,	,		19176	0.0942		0.3469	False		,,,				2504	0.2096				p.M166T		Atlas-SNP	.											.	ENOSF1	44	.	0			c.T497C						PASS	.	G	THR/MET,THR/MET,THR/MET	1346,3060	689.8+/-405.2	214,918,1071	63.0	60.0	61.0		188,434,497	-1.3	0.1	18	dbSNP_100	61	3088,5512	656.7+/-401.4	547,1994,1759	yes	missense,missense,missense	ENOSF1	NM_001126123.3,NM_017512.5,NM_202758.3	81,81,81	761,2912,2830	GG,GA,AA		35.907,30.5493,34.092	benign,benign,benign	63/362,145/444,166/451	691266	4434,8572	2203	4300	6503	SO:0001583	missense	55556	exon6			ACCAGCATCCTGG	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.434T>C	18.37:g.691266A>G	ENSP00000251101:p.Met145Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	170	119	0.7	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	37	CCDS11822.1	573	0.2623626373626374	150	0.3048780487804878	122	0.3370165745856354	47	0.08216783216783216	254	0.33509234828496043	G	8.524	0.869414	0.17322	0.305493	0.35907	ENSG00000132199	ENST00000383578;ENST00000251101;ENST00000340116	T;T;T	0.28069	1.63;2.03;2.04	5.37	-1.31	0.09230	.	0.326617	0.37012	N	0.002281	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.999999425105	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	0.46105	-0.9215	9	0.44086	T	0.13	.	4.7042	0.12841	0.3927:0.0:0.2228:0.3845	rs2612086;rs11555884;rs60754709;rs2612086	166;190;145;63	A6NMP3;Q6ZS08;Q7L5Y1;Q7L5Y1-2	.;.;ENOF1_HUMAN;.	T	63;145;166	ENSP00000373072:M63T;ENSP00000251101:M145T;ENSP00000345974:M166T	ENSP00000251101:M145T	M	-	2	0	ENOSF1	681266	0.336000	0.24757	0.055000	0.19348	0.852000	0.48524	-0.106000	0.10890	-0.377000	0.07930	-0.724000	0.03597	ATG	T|0.005;G|0.301	0.301	strong		0.428	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
SSTR3	6753	hgsc.bcm.edu	37	22	37603021	37603021	+	Silent	SNP	G	G	A	rs2071710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	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		
COL21A1	81578	hgsc.bcm.edu	37	6	55925801	55925801	+	Missense_Mutation	SNP	G	G	T	rs9464337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:55925801G>T	ENST00000244728.5	-	26	2637	c.2240C>A	c.(2239-2241)gCc>gAc	p.A747D	COL21A1_ENST00000370819.1_Missense_Mutation_p.A744D|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370808.2_Missense_Mutation_p.A147D|COL21A1_ENST00000535941.1_Missense_Mutation_p.A747D	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	747	Collagen-like 5.		A -> D (in dbSNP:rs9464337).		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				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)			TGATCCAATGGCACCTCGGAC	0.483													G|||	209	0.0417332	0.0794	0.0173	5008	,	,		16689	0.0397		0.006	False		,,,				2504	0.047				p.A747D		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2240A						PASS	.	G	ASP/ALA	284,3426		12,260,1583	58.0	56.0	57.0		2240	3.9	0.5	6	dbSNP_119	57	54,8128		1,52,4038	yes	missense	COL21A1	NM_030820.3	126	13,312,5621	TT,TG,GG		0.66,7.655,2.8422	benign	747/958	55925801	338,11554	1855	4091	5946	SO:0001583	missense	81578	exon26			CCAATGGCACCTC	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.2240C>A	6.37:g.55925801G>T	ENSP00000244728:p.Ala747Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	72	0.03296703296703297	45	0.09146341463414634	8	0.022099447513812154	17	0.02972027972027972	2	0.002638522427440633	G	3.291	-0.144886	0.06627	0.07655	0.0066	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;T	0.94376	-3.41;-3.41;-3.41;-1.07	4.77	3.9	0.45041	.	0.411176	0.21246	N	0.077734	T	0.68072	0.2961	N	0.12182	0.205	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.10450	0.002;0.003;0.005;0.003	T	0.58405	-0.7642	10	0.13108	T	0.6	.	3.8636	0.09007	0.2009:0.0:0.5938:0.2053	rs9464337;rs52804762;rs9464337	147;747;747;104	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	D	747;744;747;744;147	ENSP00000244728:A747D;ENSP00000359855:A744D;ENSP00000444384:A747D;ENSP00000359844:A147D	ENSP00000244728:A747D	A	-	2	0	COL21A1	56033760	0.847000	0.29606	0.523000	0.27875	0.413000	0.31143	2.015000	0.40961	1.132000	0.42129	-0.268000	0.10319	GCC	G|0.960;T|0.040	0.040	strong		0.483	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
MGA	23269	hgsc.bcm.edu	37	15	42026764	42026764	+	Silent	SNP	C	C	T	rs1918314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42026764C>T	ENST00000570161.1	+	11	3888	c.3888C>T	c.(3886-3888)gaC>gaT	p.D1296D	MGA_ENST00000566586.1_Silent_p.D1296D|MGA_ENST00000389936.4_Silent_p.D1296D|MGA_ENST00000545763.1_Silent_p.D1296D|MGA_ENST00000219905.7_Silent_p.D1296D			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCACCTGTGACTTGGAGGATG	0.328													C|||	3747	0.748203	0.5386	0.8242	5008	,	,		18640	0.8919		0.8161	False		,,,				2504	0.7597				p.D1296D		Atlas-SNP	.											.	MGA	264	.	0			c.C3888T						PASS	.	C	,	2071,1573		582,907,333	58.0	52.0	54.0		3888,3888	0.9	0.8	15	dbSNP_92	54	6615,1549		2689,1237,156	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	3271,2144,489	TT,TC,CC		18.9735,43.1668,26.4397	,	1296/2857,1296/3066	42026764	8686,3122	1822	4082	5904	SO:0001819	synonymous_variant	23269	exon12			CTGTGACTTGGAG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3888C>T	15.37:g.42026764C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			C|0.228;T|0.772	0.772	strong		0.328	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
SULT1C4	27233	hgsc.bcm.edu	37	2	108994808	108994808	+	Missense_Mutation	SNP	C	C	G	rs1402467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:108994808C>G	ENST00000272452.2	+	1	341	c.15C>G	c.(13-15)gaC>gaG	p.D5E	SULT1C4_ENST00000409309.3_Missense_Mutation_p.D5E	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	5			D -> E (in dbSNP:rs1402467). {ECO:0000269|PubMed:9852044, ECO:0000269|Ref.4}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CCTTACACGACATGGAGGATT	0.443													G|||	2092	0.417732	0.8752	0.1801	5008	,	,		22504	0.1081		0.2634	False		,,,				2504	0.4458				p.D5E		Atlas-SNP	.											.	SULT1C4	41	.	0			c.C15G						PASS	.	G	GLU/ASP	3378,1028	377.1+/-322.3	1306,766,131	162.0	169.0	167.0		15	-1.8	0.0	2	dbSNP_88	167	2118,6482	716.6+/-406.1	254,1610,2436	yes	missense	SULT1C4	NM_006588.2	45	1560,2376,2567	GG,GC,CC		24.6279,23.3318,42.2574	benign	5/303	108994808	5496,7510	2203	4300	6503	SO:0001583	missense	27233	exon1			ACACGACATGGAG	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"""Sulfotransferases, cytosolic"""	11457	protein-coding gene	gene with protein product		608357	"""sulfotransferase family, cytosolic, 1C, member 2"""	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.15C>G	2.37:g.108994808C>G	ENSP00000272452:p.Asp5Glu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_006588	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	37	CCDS2077.1	776	0.3553113553113553	444	0.9024390243902439	70	0.19337016574585636	62	0.10839160839160839	200	0.2638522427440633	G	1.450	-0.565305	0.03939	0.766682	0.246279	ENSG00000198075	ENST00000272452;ENST00000409309	T;T	0.01745	5.01;4.66	4.88	-1.75	0.08031	.	7739.210000	0.00166	N	0.000000	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	0.26950	-1.0088	9	0.02654	T	1	.	6.7063	0.23252	0.4812:0.3766:0.1422:0.0	rs1402467;rs52816974;rs61392346;rs1402467	5;5;5	Q08AS5;O75897;Q6PD90	.;ST1C4_HUMAN;.	E	5	ENSP00000272452:D5E;ENSP00000387225:D5E	ENSP00000272452:D5E	D	+	3	2	SULT1C4	108361240	0.281000	0.24258	0.007000	0.13788	0.136000	0.21042	-0.691000	0.05133	-0.973000	0.03555	-0.167000	0.13348	GAC	C|0.602;G|0.398	0.398	strong		0.443	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588	
ZNF557	79230	hgsc.bcm.edu	37	19	7083629	7083629	+	Silent	SNP	A	A	G	rs966591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	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	
PCDH12	51294	hgsc.bcm.edu	37	5	141335284	141335284	+	Silent	SNP	G	G	A	rs164074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141335284G>A	ENST00000231484.3	-	1	3343	c.2133C>T	c.(2131-2133)gcC>gcT	p.A711A	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	711	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATGCTCAAGGCCCCAGGCT	0.582													G|||	2990	0.597045	0.323	0.6599	5008	,	,		19776	0.8581		0.5497	False		,,,				2504	0.7025				p.A711A		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2133T						PASS	.	G		1631,2775	495.0+/-363.1	302,1027,874	53.0	44.0	47.0		2133	1.6	0.2	5	dbSNP_79	47	4553,4047	585.2+/-391.8	1225,2103,972	no	coding-synonymous	PCDH12	NM_016580.2		1527,3130,1846	AA,AG,GG		47.0581,37.0177,47.5473		711/1185	141335284	6184,6822	2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			GCTCAAGGCCCCA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2133C>T	5.37:g.141335284G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																			G|0.476;A|0.524	0.524	strong		0.582	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
SPINT3	10816	hgsc.bcm.edu	37	20	44141331	44141331	+	Missense_Mutation	SNP	A	A	G	rs6032259	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44141331A>G	ENST00000217428.6	-	2	245	c.230T>C	c.(229-231)tTg>tCg	p.L77S		NM_006652.1	NP_006643.1	P49223	SPIT3_HUMAN	serine peptidase inhibitor, Kunitz type, 3	77	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		L -> S (in dbSNP:rs6032259).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)	1						TTCTTTCCTCAAAAAGTTGTT	0.443													G|||	2303	0.459864	0.5545	0.4481	5008	,	,		21673	0.3264		0.5109	False		,,,				2504	0.4254				p.L77S		Atlas-SNP	.											.	SPINT3	12	.	0			c.T230C						PASS	.						105.0	91.0	95.0					20																	44141331		692	1591	2283	SO:0001583	missense	10816	exon2			TTCCTCAAAAAGT	X77166	CCDS46608.1	20q12-q13.2	2012-08-20	2005-08-17		ENSG00000101446	ENSG00000101446			11248	protein-coding gene	gene with protein product		613941	"""serine protease inhibitor, Kunitz type, 3"""			21988899	Standard	NM_006652		Approved	HKIB9	uc010ghg.1	P49223	OTTHUMG00000032585	ENST00000217428.6:c.230T>C	20.37:g.44141331A>G	ENSP00000217428:p.Leu77Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	34	0.369565	NM_006652	A6NCQ6|Q6UDR8|Q96KK2	Missense_Mutation	SNP	ENST00000217428.6	37	CCDS46608.1	967	0.44276556776556775	249	0.5060975609756098	168	0.46408839779005523	165	0.28846153846153844	385	0.5079155672823219	G	0.018	-1.474504	0.01044	.	.	ENSG00000101446	ENST00000217428	T	0.56444	0.46	3.25	-6.5	0.01884	Proteinase inhibitor I2, Kunitz metazoa (6);Proteinase inhibitor I2, Kunitz, conserved site (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.15141	0.012	B	0.18263	0.021	T	0.29243	-1.0018	7	0.21014	T	0.42	.	1.4375	0.02346	0.2518:0.0918:0.2376:0.4187	rs6032259;rs7274991;rs52805157;rs59517836;rs6032259	77	P49223	SPIT3_HUMAN	S	77	ENSP00000217428:L77S	ENSP00000217428:L77S	L	-	2	0	SPINT3	43574745	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.126000	0.03254	-3.407000	0.00169	-1.690000	0.00728	TTG	A|0.558;G|0.442	0.442	strong		0.443	SPINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079464.5	NM_006652	
COL6A2	1292	hgsc.bcm.edu	37	21	47545768	47545768	+	Missense_Mutation	SNP	G	G	A	rs1042917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47545768G>A	ENST00000300527.4	+	26	2143	c.2039G>A	c.(2038-2040)cGt>cAt	p.R680H	COL6A2_ENST00000409416.1_Missense_Mutation_p.R680H|COL6A2_ENST00000397763.1_Missense_Mutation_p.R680H|COL6A2_ENST00000310645.5_Missense_Mutation_p.R680H|COL6A2_ENST00000357838.4_Missense_Mutation_p.R680H	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	680	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> H (in dbSNP:rs1042917). {ECO:0000269|PubMed:15563506, ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:1690728, ECO:0000269|PubMed:17886299, ECO:0000269|Ref.1}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GACGACGAACGTATCGACTCC	0.632													G|||	1973	0.39397	0.208	0.6398	5008	,	,		15125	0.4306		0.5099	False		,,,				2504	0.3139				p.R680H		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2039A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	1061,3345	385.6+/-325.8	148,765,1290	69.0	58.0	62.0		2039,2039,2039	4.4	1.0	21	dbSNP_86	62	4310,4290	576.3+/-390.4	1050,2210,1040	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	29,29,29	1198,2975,2330	AA,AG,GG		49.8837,24.0808,41.2963	probably-damaging,probably-damaging,probably-damaging	680/1020,680/919,680/829	47545768	5371,7635	2203	4300	6503	SO:0001583	missense	1292	exon26			ACGAACGTATCGA	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2039G>A	21.37:g.47545768G>A	ENSP00000300527:p.Arg680His	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	966	0.4423076923076923	111	0.22560975609756098	223	0.6160220994475138	233	0.40734265734265734	399	0.5263852242744064	G	14.70	2.613296	0.46631	0.240808	0.501163	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	4.4	4.4	0.53042	von Willebrand factor, type A (3);	0.119103	0.56097	D	0.000030	T	0.00012	0.0000	L	0.44542	1.39	0.20196	P	0.9999286073	D;D;D	0.89917	1.0;0.999;0.998	D;P;P	0.74023	0.982;0.871;0.784	T	0.52675	-0.8544	9	0.49607	T	0.09	-16.3153	16.9942	0.86362	0.0:0.0:1.0:0.0	rs1042917;rs3171502;rs17272877;rs59723476;rs1042917	680;680;680	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	H	680;680;680;680;680;237	ENSP00000300527:R680H;ENSP00000350497:R680H;ENSP00000312529:R680H;ENSP00000387115:R680H;ENSP00000380870:R680H;ENSP00000395751:R237H	ENSP00000300527:R680H	R	+	2	0	COL6A2	46370196	1.000000	0.71417	0.998000	0.56505	0.638000	0.38207	4.764000	0.62264	1.998000	0.58463	0.491000	0.48974	CGT	G|0.585;A|0.415	0.415	strong		0.632	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
LSS	4047	hgsc.bcm.edu	37	21	47642626	47642626	+	Missense_Mutation	SNP	G	G	A	rs139003098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47642626G>A	ENST00000397728.3	-	4	424	c.346C>T	c.(346-348)Cgc>Tgc	p.R116C	LSS_ENST00000356396.4_Missense_Mutation_p.R116C|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000457828.2_Missense_Mutation_p.R36C|LSS_ENST00000522411.1_Missense_Mutation_p.R116C|AP001469.5_ENST00000418029.1_RNA	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	116					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					AGAGGGATGCGTGCCACGTGG	0.617													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20008	0.0		0.002	False		,,,				2504	0.001				p.R116C	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C346T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	115.0	91.0	99.0		346,346,106,346	0.2	0.0	21	dbSNP_134	99	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	180,180,180,180	0,21,6482	AA,AG,GG		0.186,0.1135,0.1615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	116/733,116/722,36/653,116/733	47642626	21,12985	2203	4300	6503	SO:0001583	missense	4047	exon4			GGATGCGTGCCAC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.346C>T	21.37:g.47642626G>A	ENSP00000380837:p.Arg116Cys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.36	2.214719	0.39102	0.001135	0.00186	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.17	0.224	0.15297	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	1.046430	0.07412	N	0.892629	T	0.35799	0.0944	L	0.34521	1.04	0.09310	N	1	D;D	0.60160	0.987;0.978	B;B	0.41412	0.356;0.194	T	0.47560	-0.9108	10	0.87932	D	0	.	14.9473	0.71042	0.0:0.0:0.3631:0.6369	.	116;116	E9PEI9;P48449	.;ERG7_HUMAN	C	116;36;116;116;117	ENSP00000348762:R116C;ENSP00000409191:R36C;ENSP00000380837:R116C;ENSP00000429133:R116C;ENSP00000391368:R117C	ENSP00000348762:R116C	R	-	1	0	LSS	46467054	0.001000	0.12720	0.000000	0.03702	0.690000	0.40134	0.702000	0.25631	0.228000	0.21019	0.609000	0.83330	CGC	G|0.998;A|0.002	0.002	strong		0.617	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
IMPG1	3617	hgsc.bcm.edu	37	6	76660551	76660551	+	Missense_Mutation	SNP	G	G	C	rs3734311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:76660551G>C	ENST00000369950.3	-	13	1741	c.1552C>G	c.(1552-1554)Cac>Gac	p.H518D	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TCATCTAGGTGTCTGACCATA	0.483													C|||	2679	0.534944	0.5628	0.5677	5008	,	,		21059	0.6607		0.4066	False		,,,				2504	0.4765				p.H518D	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1552G						PASS	.	C	ASP/HIS	2293,2113	576.7+/-384.3	587,1119,497	98.0	83.0	88.0		1552	1.5	0.0	6	dbSNP_107	88	3486,5114	635.3+/-399.0	693,2100,1507	yes	missense	IMPG1	NM_001563.2	81	1280,3219,2004	CC,CG,GG		40.5349,47.9573,44.4333	benign	518/798	76660551	5779,7227	2203	4300	6503	SO:0001583	missense	3617	exon13			CTAGGTGTCTGAC	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1552C>G	6.37:g.76660551G>C	ENSP00000358966:p.His518Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	1186	0.543040293040293	294	0.5975609756097561	194	0.5359116022099447	373	0.6520979020979021	325	0.4287598944591029	C	0.608	-0.826040	0.02734	0.520427	0.405349	ENSG00000112706	ENST00000369950	T	0.17854	2.25	5.53	1.48	0.22813	.	0.296955	0.28748	N	0.014261	T	0.00724	0.0024	N	0.00308	-1.67	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.42413	-0.9453	9	0.05833	T	0.94	.	5.5603	0.17140	0.236:0.358:0.3431:0.0629	rs3734311;rs52797778;rs3734311	518	Q17R60	IMPG1_HUMAN	D	518	ENSP00000358966:H518D	ENSP00000358966:H518D	H	-	1	0	IMPG1	76717271	0.002000	0.14202	0.032000	0.17829	0.193000	0.23685	0.545000	0.23268	-0.246000	0.09611	-0.225000	0.12378	CAC	G|0.518;C|0.482	0.482	strong		0.483	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
FBXO5	26271	hgsc.bcm.edu	37	6	153296541	153296541	+	Missense_Mutation	SNP	G	G	C	rs2073260	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:153296541G>C	ENST00000229758.3	-	2	377	c.319C>G	c.(319-321)Caa>Gaa	p.Q107E	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Missense_Mutation_p.Q61E	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	107			Q -> E (in dbSNP:rs2073260). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		GTTTCAAGTTGTACAATCCTA	0.408													C|||	3870	0.772764	0.9841	0.7363	5008	,	,		20979	0.5982		0.6799	False		,,,				2504	0.7883				p.Q107E	NSCLC(121;372 1757 17721 17977 29669)	Atlas-SNP	.											.	FBXO5	40	.	0			c.C319G						PASS	.	C	GLU/GLN,GLU/GLN	4085,321	169.4+/-200.1	1900,285,18	166.0	162.0	163.0		181,319	4.5	0.4	6	dbSNP_96	163	5793,2807	444.4+/-360.7	1934,1925,441	yes	missense,missense	FBXO5	NM_001142522.1,NM_012177.3	29,29	3834,2210,459	CC,CG,GG		32.6395,7.2855,24.0504	benign,benign	61/402,107/448	153296541	9878,3128	2203	4300	6503	SO:0001583	missense	26271	exon2			CAAGTTGTACAAT	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.319C>G	6.37:g.153296541G>C	ENSP00000229758:p.Gln107Glu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Missense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	1601	0.733058608058608	479	0.9735772357723578	273	0.7541436464088398	335	0.5856643356643356	514	0.6781002638522428	C	0.012	-1.650753	0.00785	0.927145	0.673605	ENSG00000112029	ENST00000229758;ENST00000367241	T;T	0.26373	1.76;1.74	5.4	4.54	0.55810	.	0.480315	0.22481	N	0.059484	T	0.01222	0.0040	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45948	-0.9226	9	0.02654	T	1	-9.4165	6.968	0.24632	0.0:0.5852:0.2708:0.144	rs2073260;rs17317934;rs17845592;rs17858497;rs56479982;rs57128510;rs2073260	107	Q9UKT4	FBX5_HUMAN	E	107;61	ENSP00000229758:Q107E;ENSP00000356210:Q61E	ENSP00000229758:Q107E	Q	-	1	0	FBXO5	153338234	0.059000	0.20769	0.442000	0.26870	0.598000	0.36846	0.756000	0.26419	0.675000	0.31264	-0.120000	0.15030	CAA	G|0.245;C|0.755	0.755	strong		0.408	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
CCDC180	100499483	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100105735T>C	ENST00000357054.1	+	33	3872	c.2937T>C	c.(2935-2937)tgT>tgC	p.C979C	CCDC180_ENST00000411667.2_Silent_p.C837C|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Silent_p.C840C|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Silent_p.C840C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	979						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AAGAGCATTGTAGGAAGTCCC	0.423													C|||	2973	0.59365	0.7458	0.6628	5008	,	,		17941	0.5843		0.3936	False		,,,				2504	0.5542				p.C840C		Atlas-SNP	.											.	.	.	.	0			c.T2520C						PASS	.	C		3195,1211	420.2+/-338.9	1154,887,162	123.0	113.0	116.0		2520	2.3	0.0	9	dbSNP_92	116	3980,4620	600.2+/-394.2	912,2156,1232	no	coding-synonymous	C9orf174	NM_020893.2		2066,3043,1394	CC,CT,TT		46.2791,27.4852,44.8332		840/1702	100105735	7175,5831	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19			GCATTGTAGGAAG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2937T>C	9.37:g.100105735T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				T|0.445;C|0.555	0.555	strong		0.423	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
CHIA	27159	hgsc.bcm.edu	37	1	111857208	111857208	+	Missense_Mutation	SNP	G	G	A	rs3818822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111857208G>A	ENST00000369740.1	+	5	407	c.304G>A	c.(304-306)Ggg>Agg	p.G102R	CHIA_ENST00000353665.6_5'UTR|CHIA_ENST00000343320.6_Missense_Mutation_p.G102R|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000483391.1_5'UTR|CHIA_ENST00000430615.1_5'UTR	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	102			G -> R (in dbSNP:rs3818822). {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)		CTGGAACTTCGGGACTGCCCC	0.453													G|||	649	0.129593	0.1936	0.0807	5008	,	,		16492	0.0933		0.0984	False		,,,				2504	0.1472				p.G102R		Atlas-SNP	.											.	CHIA	115	.	0			c.G304A						PASS	.	G	,ARG/GLY	610,3136		42,526,1305	110.0	107.0	108.0		,304	4.6	1.0	1	dbSNP_107	108	880,7322		46,788,3267	yes	utr-5,missense	CHIA	NM_021797.2,NM_201653.2	,125	88,1314,4572	AA,AG,GG		10.7291,16.284,12.4707	,probably-damaging	,102/477	111857208	1490,10458	1873	4101	5974	SO:0001583	missense	27159	exon5			AACTTCGGGACTG	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.304G>A	1.37:g.111857208G>A	ENSP00000358755:p.Gly102Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	230	0.10531135531135531	83	0.16869918699186992	34	0.09392265193370165	51	0.08916083916083917	62	0.08179419525065963	G	19.93	3.918008	0.73098	0.16284	0.107291	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320	T;T;T	0.05855	3.38;3.38;3.38	4.56	4.56	0.56223	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.080948	0.47455	N	0.000223	T	0.28499	0.0705	H	0.95816	3.725	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.49293	-0.8955	9	0.87932	D	0	1.0E-4	15.1925	0.73057	0.0:0.0:1.0:0.0	rs3818822;rs52810904;rs60274821;rs3818822	102	Q9BZP6	CHIA_HUMAN	R	46;102;102	ENSP00000387671:G46R;ENSP00000358755:G102R;ENSP00000341828:G102R	ENSP00000341828:G102R	G	+	1	0	CHIA	111658731	1.000000	0.71417	1.000000	0.80357	0.563000	0.35712	8.823000	0.92018	2.233000	0.73108	0.462000	0.41574	GGG	G|0.888;A|0.112	0.112	strong		0.453	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ANGPT2	285	hgsc.bcm.edu	37	8	6371291	6371291	+	Silent	SNP	A	A	G	rs2916747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:6371291A>G	ENST00000325203.5	-	7	1581	c.1107T>C	c.(1105-1107)taT>taC	p.Y369Y	MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000523120.1_Silent_p.Y368Y|ANGPT2_ENST00000415216.1_Silent_p.Y368Y|ANGPT2_ENST00000338312.6_Silent_p.Y317Y			O15123	ANGP2_HUMAN	angiopoietin 2	369	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		TTTTAAGCACATAGCGTTGCT	0.373													A|||	878	0.175319	0.354	0.0793	5008	,	,		17950	0.1637		0.0417	False		,,,				2504	0.1513				p.Y369Y		Atlas-SNP	.											.	ANGPT2	126	.	0			c.T1107C						PASS	.	A	,,,	1401,3005	459.4+/-352.3	219,963,1021	104.0	104.0	104.0		1104,951,1107,	-7.4	0.0	8	dbSNP_101	104	347,8253	117.0+/-176.6	8,331,3961	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	227,1294,4982	GG,GA,AA		4.0349,31.7975,13.44	,,,	368/496,317/445,369/497,	6371291	1748,11258	2203	4300	6503	SO:0001819	synonymous_variant	285	exon7			AAGCACATAGCGT	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.1107T>C	8.37:g.6371291A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			A|0.859;G|0.141	0.141	strong		0.373	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
KAT6A	7994	hgsc.bcm.edu	37	8	41798417	41798417	+	Silent	SNP	C	C	T	rs3824275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:41798417C>T	ENST00000396930.3	-	16	3525	c.2982G>A	c.(2980-2982)ccG>ccA	p.P994P	KAT6A_ENST00000406337.1_Silent_p.P994P|KAT6A_ENST00000265713.2_Silent_p.P994P	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	994	Poly-Glu.				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)										GAGGGCTTTCCGGCTCCTCCT	0.562													C|||	821	0.163938	0.0998	0.1859	5008	,	,		17882	0.2341		0.0716	False		,,,				2504	0.2577				p.P994P		Atlas-SNP	.											MYST3,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	.	.	1	0			c.G2982A						PASS	.						143.0	145.0	144.0					8																	41798417		2203	4300	6503	SO:0001819	synonymous_variant	7994	exon16			GCTTTCCGGCTCC	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.2982G>A	8.37:g.41798417C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			C|0.863;T|0.137	0.137	strong		0.562	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
MARCH1	55016	hgsc.bcm.edu	37	4	165118652	165118652	+	Intron	SNP	C	C	T	rs2288675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:165118652C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						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)			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)				CCCTGAGACTCTTAGTTCAAG	0.403													C|||	1463	0.292133	0.1067	0.3112	5008	,	,		18350	0.2163		0.4732	False		,,,				2504	0.4213				p.R71K		Atlas-SNP	.											.	ANP32C	59	.	0			c.G212A						PASS	.	C	,LYS/ARG	714,3692	295.3+/-283.6	68,578,1557	120.0	121.0	121.0		,212	0.5	0.7	4	dbSNP_100	121	4249,4351	572.9+/-389.8	1049,2151,1100	yes	intron,missense	ANP32C,MARCH1	NM_001166373.1,NM_012403.1	,26	1117,2729,2657	TT,TC,CC		49.407,16.2052,38.1593	,benign	,71/235	165118652	4963,8043	2203	4300	6503	SO:0001627	intron_variant	23520	exon1			GAGACTCTTAGTT	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.113-85838G>A	4.37:g.165118652C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	165	83	0.50303	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			C|0.676;T|0.324	0.324	strong		0.403	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
OR8H3	390152	hgsc.bcm.edu	37	11	55890732	55890732	+	Missense_Mutation	SNP	G	G	A	rs11606538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55890732G>A	ENST00000313472.3	+	1	884	c.884G>A	c.(883-885)aGa>aAa	p.R295K		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	295			R -> K (in dbSNP:rs11606538).			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)					CTTAGAAACAGAGAAGTGAAA	0.368													A|||	354	0.0706869	0.0234	0.0562	5008	,	,		17825	0.0873		0.0954	False		,,,				2504	0.1022				p.R295K		Atlas-SNP	.											.	OR8H3	92	.	0			c.G884A						PASS	.	A	LYS/ARG	130,4272		2,126,2073	96.0	100.0	99.0		884	3.6	1.0	11	dbSNP_120	99	653,7935		45,563,3686	no	missense	OR8H3	NM_001005201.1	26	47,689,5759	AA,AG,GG		7.6036,2.9532,6.0277	benign	295/313	55890732	783,12207	2201	4294	6495	SO:0001583	missense	390152	exon1			GAAACAGAGAAGT	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.884G>A	11.37:g.55890732G>A	ENSP00000323928:p.Arg295Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	132	0.06043956043956044	4	0.008130081300813009	19	0.052486187845303865	52	0.09090909090909091	57	0.07519788918205805	A	0.279	-0.987851	0.02162	0.029532	0.076036	ENSG00000181761	ENST00000313472	T	0.32515	1.45	3.62	3.62	0.41486	.	0.000000	0.56097	N	0.000025	T	0.00271	0.0008	N	0.00303	-1.675	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29731	-1.0002	9	0.02654	T	1	.	8.2249	0.31562	0.8212:0.0:0.1788:0.0	rs11606538	295	Q8N146	OR8H3_HUMAN	K	295	ENSP00000323928:R295K	ENSP00000323928:R295K	R	+	2	0	OR8H3	55647308	0.004000	0.15560	0.990000	0.47175	0.596000	0.36781	0.668000	0.25127	0.399000	0.25367	-1.467000	0.01014	AGA	G|0.924;A|0.076	0.076	strong		0.368	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
DNAH17	8632	hgsc.bcm.edu	37	17	76533456	76533456	+	Silent	SNP	G	G	A	rs61741432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76533456G>A	ENST00000585328.1	-	19	2899	c.2775C>T	c.(2773-2775)atC>atT	p.I925I	DNAH17_ENST00000389840.5_Silent_p.I928I	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	928	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)			CCAGGCCCTCGATCAGTGCCA	0.607													G|||	82	0.0163738	0.0333	0.0072	5008	,	,		16281	0.002		0.0229	False		,,,				2504	0.0082				p.I928I		Atlas-SNP	.											.	DNAH17	347	.	0			c.C2784T						PASS	.	G		128,3950		1,126,1912	57.0	65.0	62.0		2784	-1.2	0.9	17	dbSNP_129	62	144,8190		1,142,4024	no	coding-synonymous	DNAH17	NM_173628.3		2,268,5936	AA,AG,GG		1.7279,3.1388,2.1914		928/4463	76533456	272,12140	2039	4167	6206	SO:0001819	synonymous_variant	8632	exon19			GCCCTCGATCAGT	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.2775C>T	17.37:g.76533456G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.987;A|0.013	0.013	strong		0.607	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
ZNF581	51545	hgsc.bcm.edu	37	19	56156447	56156447	+	Silent	SNP	A	A	G	rs11084406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56156447A>G	ENST00000587252.1	+	2	783	c.510A>G	c.(508-510)gaA>gaG	p.E170E	ZNF581_ENST00000588537.1_Silent_p.E170E|CCDC106_ENST00000308964.3_5'Flank|ZNF581_ENST00000270451.5_Silent_p.E170E			Q9P0T4	ZN581_HUMAN	zinc finger protein 581	170					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(1)|lung(1)|ovary(1)	3		Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		ACTCTGGGGAACGCCCGTTTC	0.687													A|||	280	0.0559105	0.0174	0.0778	5008	,	,		16394	0.0069		0.1093	False		,,,				2504	0.0879				p.E170E		Atlas-SNP	.											.	ZNF581	13	.	0			c.A510G						PASS	.	A		158,4248	101.2+/-139.8	1,156,2046	54.0	58.0	57.0		510	1.8	0.8	19	dbSNP_120	57	1231,7369	232.8+/-266.3	94,1043,3163	no	coding-synonymous	ZNF581	NM_016535.3		95,1199,5209	GG,GA,AA		14.314,3.586,10.6797		170/198	56156447	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	51545	exon2			TGGGGAACGCCCG	AK026203	CCDS12932.1	19q13.42	2013-09-20			ENSG00000171425	ENSG00000171425		"""Zinc fingers, C2H2-type"""	25017	protein-coding gene	gene with protein product						11042152	Standard	NM_016535		Approved	HSPC189, FLJ22550	uc002qlq.3	Q9P0T4	OTTHUMG00000180869	ENST00000587252.1:c.510A>G	19.37:g.56156447A>G		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_016535	B2RDM6	Silent	SNP	ENST00000587252.1	37	CCDS12932.1																																																																																			A|0.916;G|0.084	0.084	strong		0.687	ZNF581-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453430.1	NM_016535	
PGS1	9489	hgsc.bcm.edu	37	17	76421443	76421443	+	IGR	SNP	G	G	A	rs1134541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76421443G>A	ENST00000262764.6	+	0	2201				AC061992.1_ENST00000600087.1_5'Flank|DNAH17_ENST00000585328.1_Silent_p.Y4370Y|DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.Y4398Y	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TGAAGAGTCCGTACACGTAGG	0.532													G|||	536	0.107029	0.1997	0.072	5008	,	,		20979	0.0288		0.0905	False		,,,				2504	0.1043				p.Y4375Y	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.C13125T						PASS	.	G		726,3680	301.3+/-286.8	57,612,1534	101.0	101.0	101.0		13125	0.4	1.0	17	dbSNP_86	101	800,7800	187.3+/-234.6	47,706,3547	no	coding-synonymous	DNAH17	NM_173628.3		104,1318,5081	AA,AG,GG		9.3023,16.4775,11.733		4375/4463	76421443	1526,11480	2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			GAGTCCGTACACG		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76421443G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			G|0.885;A|0.115	0.115	strong		0.532	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
FAM135A	57579	hgsc.bcm.edu	37	6	71269459	71269459	+	Silent	SNP	C	C	T	rs16869371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000457062.2_Silent_p.P1248P|FAM135A_ENST00000370479.3_Silent_p.P1248P|FAM135A_ENST00000505769.1_Silent_p.P1041P	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	61	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	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	
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000457780.2_Silent_p.F193F	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72.0	61.0	65.0		579	-5.2	1.0	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.579C>T	22.37:g.50217387G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
CRB2	286204	hgsc.bcm.edu	37	9	126129904	126129904	+	Silent	SNP	C	C	T	rs10818812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:126129904C>T	ENST00000373631.3	+	6	994	c.993C>T	c.(991-993)aaC>aaT	p.N331N	CRB2_ENST00000359999.3_Silent_p.N331N|CRB2_ENST00000373629.2_5'Flank	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	331	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CATGCCTCAACGGAGGCCACT	0.652													C|||	1422	0.283946	0.087	0.3228	5008	,	,		8749	0.38		0.3767	False		,,,				2504	0.3282				p.N331N		Atlas-SNP	.											.	CRB2	86	.	0			c.C993T						PASS	.	C		497,3885		30,437,1724	45.0	36.0	39.0		993	-4.8	0.0	9	dbSNP_120	39	3194,5378		614,1966,1706	no	coding-synonymous	CRB2	NM_173689.5		644,2403,3430	TT,TC,CC		37.2608,11.3419,28.4931		331/1286	126129904	3691,9263	2191	4286	6477	SO:0001819	synonymous_variant	286204	exon6			CCTCAACGGAGGC	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.993C>T	9.37:g.126129904C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.729;T|0.271	0.271	strong		0.652	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
THADA	63892	hgsc.bcm.edu	37	2	43797619	43797619	+	Missense_Mutation	SNP	C	C	T	rs17031056	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43797619C>T	ENST00000405006.4	-	14	2446	c.2095G>A	c.(2095-2097)Gta>Ata	p.V699I	THADA_ENST00000402360.2_Missense_Mutation_p.V699I|THADA_ENST00000404790.1_Missense_Mutation_p.V699I|THADA_ENST00000403856.1_Missense_Mutation_p.V699I|THADA_ENST00000415080.2_Missense_Mutation_p.V409I|THADA_ENST00000405975.2_Missense_Mutation_p.V699I|THADA_ENST00000330266.7_Missense_Mutation_p.V409I	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	699			V -> I (in dbSNP:rs17031056). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039}.							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)				TTATAAAGTACCTGAGAACTT	0.383													C|||	1096	0.21885	0.149	0.147	5008	,	,		16229	0.253		0.2286	False		,,,				2504	0.319				p.V699I		Atlas-SNP	.											.	THADA	131	.	0			c.G2095A						PASS	.	C	ILE/VAL,ILE/VAL	579,3081		47,485,1298	124.0	117.0	119.0		2095,2095	4.5	1.0	2	dbSNP_123	119	1661,6525		168,1325,2600	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	29,29	215,1810,3898	TT,TC,CC		20.2907,15.8197,18.9093	benign,benign	699/1954,699/1954	43797619	2240,9606	1830	4093	5923	SO:0001583	missense	63892	exon14			AAAGTACCTGAGA	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.2095G>A	2.37:g.43797619C>T	ENSP00000385995:p.Val699Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	86	0.589041	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	463	0.211996336996337	76	0.15447154471544716	60	0.16574585635359115	157	0.2744755244755245	170	0.22427440633245382	C	16.35	3.097924	0.56075	0.158197	0.202907	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360;ENST00000404790;ENST00000403856	T;T;T;T;T;T;T	0.63913	1.51;1.51;2.69;1.51;-0.07;-0.07;1.45	5.41	4.53	0.55603	Armadillo-type fold (1);	0.224028	0.38058	N	0.001824	T	0.00012	0.0000	L	0.57536	1.79	0.35896	P	0.169952	P;P;B;B;P	0.47762	0.9;0.493;0.045;0.124;0.682	B;B;B;B;B	0.43082	0.407;0.178;0.047;0.035;0.197	T	0.17137	-1.0379	9	0.10111	T	0.7	.	14.1442	0.65339	0.0:0.9279:0.0:0.0721	rs17031056;rs52816054;rs56795971;rs17031056	699;699;699;409;699	B5MC89;Q8IY32;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	I	409;699;700;409;699;699;699;699	ENSP00000331105:V409I;ENSP00000386088:V699I;ENSP00000416048:V409I;ENSP00000385995:V699I;ENSP00000385441:V699I;ENSP00000384266:V699I;ENSP00000385469:V699I	ENSP00000331105:V409I	V	-	1	0	THADA	43651123	0.998000	0.40836	1.000000	0.80357	0.970000	0.65996	2.527000	0.45615	1.287000	0.44583	0.591000	0.81541	GTA	C|0.781;N|0.000;T|0.219	0.219	strong		0.383	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
SYDE2	84144	hgsc.bcm.edu	37	1	85655916	85655916	+	Missense_Mutation	SNP	G	G	A	rs56191061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85655916G>A	ENST00000341460.5	-	2	1314	c.1265C>T	c.(1264-1266)tCa>tTa	p.S422L		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	422					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)		AGAGCACAGTGAGTCTTCAGT	0.488													G|||	286	0.0571086	0.0023	0.0418	5008	,	,		18962	0.1756		0.0577	False		,,,				2504	0.0194				p.S422L		Atlas-SNP	.											SYDE2,NS,carcinoma,-1,1	SYDE2	135	1	0			c.C1265T						PASS	.	G	LEU/SER	41,4011		0,41,1985	168.0	158.0	161.0		1265	-5.3	0.0	1	dbSNP_129	161	493,7889		15,463,3713	yes	missense	SYDE2	NM_032184.1	145	15,504,5698	AA,AG,GG		5.8817,1.0118,4.2947	benign	422/1195	85655916	534,11900	2026	4191	6217	SO:0001583	missense	84144	exon2			CACAGTGAGTCTT	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.1265C>T	1.37:g.85655916G>A	ENSP00000340594:p.Ser422Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	140	0.0641025641025641	1	0.0020325203252032522	16	0.04419889502762431	77	0.1346153846153846	46	0.06068601583113457	G	0.004	-2.308492	0.00237	0.010118	0.058817	ENSG00000097096	ENST00000341460	T	0.05925	3.37	5.96	-5.28	0.02755	.	3.104450	0.00982	N	0.003387	T	0.01061	0.0035	N	0.05383	-0.06	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42103	-0.9471	9	0.38643	T	0.18	.	10.5938	0.45325	0.4792:0.0929:0.428:0.0	rs56191061;rs57930414;rs61748708	422;422	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	L	422	ENSP00000340594:S422L	ENSP00000340594:S422L	S	-	2	0	SYDE2	85428504	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.097000	0.15168	-1.386000	0.02098	-2.078000	0.00380	TCA	G|0.937;A|0.063	0.063	strong		0.488	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32128611A>G	ENST00000344936.2	-	8	1559	c.1325T>C	c.(1324-1326)tTt>tCt	p.F442S	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000375250.5_Intron|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.F442S	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	442			F -> S (in dbSNP:rs2808096).		morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				ATTTTCAGGAAAGCAGGGTTT	0.343													A|||	1161	0.231829	0.0545	0.2954	5008	,	,		13632	0.4127		0.2048	False		,,,				2504	0.2679				p.F442S		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.T1325C						PASS	.	A	SER/PHE	371,4035	186.4+/-213.3	16,339,1848	109.0	110.0	110.0		1325	3.2	1.0	10	dbSNP_100	110	1824,6776	326.4+/-317.4	190,1444,2666	yes	missense	ARHGAP12	NM_018287.5	155	206,1783,4514	GG,GA,AA		21.2093,8.4203,16.8768	benign	442/847	32128611	2195,10811	2203	4300	6503	SO:0001583	missense	94134	exon8			TCAGGAAAGCAGG	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1325T>C	10.37:g.32128611A>G	ENSP00000345808:p.Phe442Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_001270695	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	A	11.71	1.718440	0.30503	0.084203	0.212093	ENSG00000165322	ENST00000311380;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.51	3.15	0.36227	.	0.228703	0.38548	N	0.001653	T	0.00012	0.0000	N	0.08118	0	0.36264	P	0.145235	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.48091	-0.9065	9	0.20046	T	0.44	.	6.4215	0.21746	0.7804:0.0:0.0739:0.1457	rs2808096;rs17582209;rs52793660;rs2808096	442;442;395	Q504X1;Q8IWW6;Q8IWW6-3	.;RHG12_HUMAN;.	S	395;442;442;395	ENSP00000310984:F395S;ENSP00000345808:F442S;ENSP00000379448:F442S;ENSP00000364394:F395S	ENSP00000310984:F395S	F	-	2	0	ARHGAP12	32168617	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.817000	0.39002	0.443000	0.26582	0.533000	0.62120	TTT	G|0.199;N|0.000	0.199	strong		0.343	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
ADAMTS4	9507	hgsc.bcm.edu	37	1	161163037	161163037	+	Missense_Mutation	SNP	T	T	C	rs4233367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161163037T>C	ENST00000367996.5	-	7	2305	c.1877A>G	c.(1876-1878)cAg>cGg	p.Q626R	ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	626	Cys-rich.		Q -> R (in dbSNP:rs4233367). {ECO:0000269|PubMed:10356395, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9734811}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GCCCAGTGCCTGGGCCTGGCA	0.637													C|||	3540	0.706869	0.5893	0.7089	5008	,	,		16806	0.8859		0.6093	False		,,,				2504	0.7802				p.Q626R		Atlas-SNP	.											ADAMTS4_ENST00000367996,NS,carcinoma,0,2	ADAMTS4	171	2	0			c.A1877G						scavenged	.	C	ARG/GLN	2678,1728	515.0+/-368.8	802,1074,327	38.0	37.0	37.0		1877	1.9	1.0	1	dbSNP_111	37	5162,3438	500.0+/-375.1	1528,2106,666	yes	missense	ADAMTS4	NM_005099.4	43	2330,3180,993	CC,CT,TT		39.9767,39.2192,39.7201	benign	626/838	161163037	7840,5166	2203	4300	6503	SO:0001583	missense	9507	exon7			AGTGCCTGGGCCT	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.1877A>G	1.37:g.161163037T>C	ENSP00000356975:p.Gln626Arg	Somatic	32	2	0.0625		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	1514	0.6932234432234432	291	0.5914634146341463	241	0.6657458563535912	524	0.916083916083916	458	0.604221635883905	C	3.766	-0.048557	0.07407	0.607808	0.600233	ENSG00000158859	ENST00000367996	T	0.03553	3.89	4.81	1.94	0.25998	.	0.334200	0.24267	N	0.040032	T	0.00241	0.0007	N	0.00223	-1.815	0.09310	P	0.99999999320295	B	0.02656	0.0	B	0.01281	0.0	T	0.39333	-0.9619	9	0.02654	T	1	.	8.5312	0.33335	0.0:0.5923:0.0:0.4077	rs4233367;rs52809265;rs59726055;rs4233367	626	O75173	ATS4_HUMAN	R	626	ENSP00000356975:Q626R	ENSP00000356975:Q626R	Q	-	2	0	ADAMTS4	159429661	0.000000	0.05858	0.990000	0.47175	0.933000	0.57130	0.127000	0.15790	0.011000	0.14865	-0.226000	0.12346	CAG	T|0.348;C|0.652	0.652	strong		0.637	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
INPP1	3628	hgsc.bcm.edu	37	2	191231503	191231503	+	Silent	SNP	G	G	A	rs4940|rs10931450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:191231503G>A	ENST00000322522.4	+	4	804	c.348G>A	c.(346-348)gtG>gtA	p.V116V	INPP1_ENST00000541441.1_Silent_p.V116V|INPP1_ENST00000392329.2_Silent_p.V116V	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	116					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			GTAACAAGGTGGCATCTGAAG	0.463													G|||	1385	0.276558	0.2201	0.2233	5008	,	,		19977	0.4623		0.2316	False		,,,				2504	0.2454				p.V116V	Melanoma(130;184 1743 2185 19805 38428)	Atlas-SNP	.											.	INPP1	29	.	0			c.G348A						PASS	.	G	,	968,3438	367.1+/-318.1	110,748,1345	175.0	167.0	169.0		348,348	0.9	0.1	2	dbSNP_120	169	2050,6550	354.6+/-329.6	236,1578,2486	no	coding-synonymous,coding-synonymous	INPP1	NM_001128928.1,NM_002194.3	,	346,2326,3831	AA,AG,GG		23.8372,21.97,23.2047	,	116/400,116/400	191231503	3018,9988	2203	4300	6503	SO:0001819	synonymous_variant	3628	exon4			CAAGGTGGCATCT		CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.348G>A	2.37:g.191231503G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_002194		Silent	SNP	ENST00000322522.4	37	CCDS2305.1																																																																																			G|0.733;A|0.267	0.267	strong		0.463	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2		
ABCD2	225	hgsc.bcm.edu	37	12	40010863	40010863	+	Silent	SNP	C	C	T	rs61736446	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:40010863C>T	ENST00000308666.3	-	2	1182	c.1047G>A	c.(1045-1047)aaG>aaA	p.K349K		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	349	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						TCCAAACATACTTCATCAGGA	0.373													C|||	88	0.0175719	0.0	0.0202	5008	,	,		16594	0.0		0.0477	False		,,,				2504	0.0266				p.K349K		Atlas-SNP	.											.	ABCD2	127	.	0			c.G1047A						PASS	.	C		42,4364	46.0+/-80.4	0,42,2161	171.0	146.0	155.0		1047	4.1	1.0	12	dbSNP_129	155	430,8170	132.8+/-190.4	14,402,3884	no	coding-synonymous	ABCD2	NM_005164.3		14,444,6045	TT,TC,CC		5.0,0.9532,3.6291		349/741	40010863	472,12534	2203	4300	6503	SO:0001819	synonymous_variant	225	exon2			AACATACTTCATC	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"""ATP binding cassette transporters / subfamily D"""	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1047G>A	12.37:g.40010863C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_005164	B2RAM3|Q13210|Q2M3H9	Silent	SNP	ENST00000308666.3	37	CCDS8734.1																																																																																			C|0.968;T|0.032	0.032	strong		0.373	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	
CEP70	80321	hgsc.bcm.edu	37	3	138289163	138289163	+	Silent	SNP	T	T	C	rs1673608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:138289163T>C	ENST00000264982.3	-	6	728	c.462A>G	c.(460-462)ttA>ttG	p.L154L	CEP70_ENST00000481834.1_Silent_p.L154L|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000484888.1_Silent_p.L154L|CEP70_ENST00000464035.1_Silent_p.L154L|CEP70_ENST00000542237.1_Silent_p.L134L|CEP70_ENST00000489254.1_Intron	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	203	0	0		WXS	Illumina HiSeq	Phase_I	227	132	0.581498	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	
RPS16	6217	hgsc.bcm.edu	37	19	39926521	39926521	+	Silent	SNP	G	G	A	rs17626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39926521G>A	ENST00000251453.3	-	1	67	c.15C>T	c.(13-15)ggC>ggT	p.G5G	RPS16_ENST00000339471.4_Silent_p.G5G|RPS16_ENST00000601655.1_Silent_p.G5G|RPS16_ENST00000599539.1_Silent_p.G5G	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	5					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)			ACTGCAGCGGGCCCTTGGACG	0.667													G|||	2562	0.511581	0.7126	0.3804	5008	,	,		14063	0.5506		0.3827	False		,,,				2504	0.4254				p.G5G		Atlas-SNP	.											.	RPS16	12	.	0			c.C15T						PASS	.	G		2832,1572	661.6+/-400.9	909,1014,279	45.0	45.0	45.0		15	-12.1	0.3	19	dbSNP_63	45	2926,5674	451.6+/-362.7	492,1942,1866	no	coding-synonymous	RPS16	NM_001020.4		1401,2956,2145	AA,AG,GG		34.0233,35.6948,44.2787		5/147	39926521	5758,7246	2202	4300	6502	SO:0001819	synonymous_variant	6217	exon1			CAGCGGGCCCTTG	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.15C>T	19.37:g.39926521G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_001020	B2RDD5|P17008	Silent	SNP	ENST00000251453.3	37	CCDS12535.1																																																																																			G|0.546;A|0.454	0.454	strong		0.667	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487170	32487170	+	Missense_Mutation	SNP	G	G	A	rs1136633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32487170G>A	ENST00000374975.3	-	3	691	c.629C>T	c.(628-630)aCg>aTg	p.T210M		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						GAGAGGGCTCGTCACGCTTGG	0.488													A|||	1326	0.264776	0.1876	0.3184	5008	,	,		12433	0.2956		0.2604	False		,,,				2504	0.3037				p.T210M		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,+1,1	HLA-DRB5	31	1	0			c.C629T						scavenged	.	A	MET/THR	491,3289		88,315,1487	73.0	83.0	80.0		629	-8.7	0.0	6	dbSNP_86	80	1057,6447		111,835,2806	no	missense	HLA-DRB5	NM_002125.3	81	199,1150,4293	AA,AG,GG		14.0858,12.9894,13.7185	benign	210/267	32487170	1548,9736	1890	3752	5642	SO:0001583	missense	3127	exon3			GGGCTCGTCACGC		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.629C>T	6.37:g.32487170G>A	ENSP00000364114:p.Thr210Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	7	0.0486111	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	1.089	-0.664536	0.03428	0.129894	0.140858	ENSG00000198502	ENST00000374975	T	0.03124	4.04	4.36	-8.71	0.00848	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.255310	0.05108	N	0.488406	T	0.01254	0.0041	M	0.79011	2.435	0.80722	P	0.0	B;B	0.20459	0.045;0.007	B;B	0.13407	0.009;0.003	T	0.44421	-0.9329	9	0.42905	T	0.14	.	1.1219	0.01726	0.2262:0.1878:0.1331:0.4529	.	137;210	Q29973;Q30154	.;DRB5_HUMAN	M	210	ENSP00000364114:T210M	ENSP00000364114:T210M	T	-	2	0	HLA-DRB5	32595148	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.520000	0.00951	-1.663000	0.01481	-0.992000	0.02543	ACG	G|0.440;A|0.560	0.560	strong		0.488	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
NUDT18	79873	hgsc.bcm.edu	37	8	21965113	21965113	+	Missense_Mutation	SNP	T	T	C	rs3739435	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:21965113T>C	ENST00000309188.6	-	5	788	c.670A>G	c.(670-672)Atg>Gtg	p.M224V	NUDT18_ENST00000522405.1_Missense_Mutation_p.M147V|NUDT18_ENST00000521807.2_3'UTR	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	224				M -> V (in Ref. 1; BAB15376/BAC85853). {ECO:0000305}.	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)		CTCTGCTCCATAGGGTCGAGG	0.617													T|||	2775	0.554113	0.525	0.6614	5008	,	,		18738	0.619		0.4563	False		,,,				2504	0.5511				p.M224V		Atlas-SNP	.											.	NUDT18	13	.	0			c.A670G						PASS	.	T	VAL/MET	2182,2088		560,1062,513	60.0	67.0	65.0		672	-2.2	0.0	8	dbSNP_107	65	3870,4608		898,2074,1267	no	missense	NUDT18	NM_024815.3	21	1458,3136,1780	CC,CT,TT		45.6476,48.8993,47.4741	benign	224/324	21965113	6052,6696	2135	4239	6374	SO:0001583	missense	79873	exon5			GCTCCATAGGGTC		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.670A>G	8.37:g.21965113T>C	ENSP00000307852:p.Met224Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_024815	Q8IZ75|Q9H687	Missense_Mutation	SNP	ENST00000309188.6	37		1179|1179	0.5398351648351648|0.5398351648351648	245|245	0.49796747967479676|0.49796747967479676	223|223	0.6160220994475138|0.6160220994475138	345|345	0.6031468531468531|0.6031468531468531	366|366	0.48284960422163586|0.48284960422163586	T|T	1.637|1.637	-0.517536|-0.517536	0.04171|0.04171	0.511007|0.511007	0.456476|0.456476	ENSG00000173566|ENSG00000173566	ENST00000522405;ENST00000309188|ENST00000522379	.|.	.|.	.|.	5.38|5.38	-2.23|-2.23	0.06930|0.06930	.|.	0.810801|.	0.11595|.	N|.	0.548297|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43540|0.43540	-0.9385|-0.9385	5|3	0.24483|.	T|.	0.36|.	-5.4957|-5.4957	4.9963|4.9963	0.14242|0.14242	0.2473:0.2275:0.0:0.5252|0.2473:0.2275:0.0:0.5252	rs3739435;rs52804017;rs60999375;rs3739435|rs3739435;rs52804017;rs60999375;rs3739435	.|.	.|.	.|.	V|C	147;224|259	.|.	ENSP00000307852:M224V|.	M|Y	-|-	1|2	0|0	NUDT18|NUDT18	22021058|22021058	0.000000|0.000000	0.05858|0.05858	0.033000|0.033000	0.17914|0.17914	0.244000|0.244000	0.25665|0.25665	-0.416000|-0.416000	0.07097|0.07097	-0.488000|-0.488000	0.06726|0.06726	-2.215000|-2.215000	0.00298|0.00298	ATG|TAT	T|0.476;C|0.524	0.524	strong		0.617	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815	
ST7L	54879	hgsc.bcm.edu	37	1	113098534	113098534	+	Missense_Mutation	SNP	C	C	T	rs6658555	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:113098534C>T	ENST00000358039.4	-	12	1656	c.1352G>A	c.(1351-1353)cGa>cAa	p.R451Q	ST7L_ENST00000538187.1_Missense_Mutation_p.R395Q|ST7L_ENST00000360743.4_Missense_Mutation_p.R451Q|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369668.2_Missense_Mutation_p.R451Q|ST7L_ENST00000544629.1_Missense_Mutation_p.R386Q|ST7L_ENST00000343210.7_Missense_Mutation_p.R451Q|ST7L_ENST00000369666.1_Missense_Mutation_p.R434Q|ST7L_ENST00000543570.1_Intron|ST7L_ENST00000369669.1_Missense_Mutation_p.R268Q|ST7L_ENST00000490067.1_Missense_Mutation_p.R434Q	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	451			R -> Q (in dbSNP:rs6658555). {ECO:0000269|PubMed:14702039}.		negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)		p.R451Q(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		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)		ACCTTCTATTCGTTTCCAGTG	0.363													C|||	625	0.1248	0.093	0.1196	5008	,	,		18068	0.0893		0.2406	False		,,,				2504	0.089				p.R451Q		Atlas-SNP	.											ST7L,NS,carcinoma,0,1	ST7L	31	1	1	Substitution - Missense(1)	stomach(1)	c.G1352A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	520,3886	238.0+/-249.6	31,458,1714	135.0	127.0	130.0		1352,1301,1352,1352	5.6	1.0	1	dbSNP_116	130	2139,6461	366.0+/-334.1	278,1583,2439	yes	missense,missense,missense,missense	ST7L	NM_017744.4,NM_138727.3,NM_138728.2,NM_138729.3	43,43,43,43	309,2041,4153	TT,TC,CC		24.8721,11.8021,20.4444	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	451/576,434/559,451/545,451/556	113098534	2659,10347	2203	4300	6503	SO:0001583	missense	54879	exon12			TCTATTCGTTTCC	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1352G>A	1.37:g.113098534C>T	ENSP00000350734:p.Arg451Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	348|348	0.15934065934065933|0.15934065934065933	55|55	0.11178861788617886|0.11178861788617886	56|56	0.15469613259668508|0.15469613259668508	39|39	0.06818181818181818|0.06818181818181818	198|198	0.2612137203166227|0.2612137203166227	C|C	32|32	5.171196|5.171196	0.94807|0.94807	0.118021|0.118021	0.248721|0.248721	ENSG00000007341|ENSG00000007341	ENST00000418497|ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187	.|T;T;T;T;T;T;T;T;T	.|0.20738	.|2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35480|0.35480	0.0933|0.0933	L|L	0.56280|0.56280	1.765|1.765	0.09310|0.09310	P|P	1.0|1.0	.|P;D;P;D;P;P;D;P	.|0.89917	.|0.837;1.0;0.884;0.969;0.946;0.857;0.985;0.883	.|B;D;B;P;B;P;P;P	.|0.87578	.|0.142;0.998;0.271;0.493;0.342;0.532;0.63;0.663	T|T	0.01739|0.01739	-1.1284|-1.1284	4|9	.|0.42905	.|T	.|0.14	-6.2202|-6.2202	19.1881|19.1881	0.93653|0.93653	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs6658555;rs52816791;rs57329181;rs6658555|rs6658555;rs52816791;rs57329181;rs6658555	.|395;386;386;451;434;434;451;451	.|B7Z7D4;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.|.;.;.;.;.;.;.;ST7L_HUMAN	K|Q	226|451;451;232;386;268;434;451;451;434;395	.|ENSP00000350734:R451Q;ENSP00000353972:R451Q;ENSP00000445499:R386Q;ENSP00000358683:R268Q;ENSP00000417140:R434Q;ENSP00000358682:R451Q;ENSP00000345312:R451Q;ENSP00000358680:R434Q;ENSP00000444021:R395Q	.|ENSP00000345312:R451Q	E|R	-|-	1|2	0|0	ST7L|ST7L	112900057|112900057	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.968000|0.968000	0.65278|0.65278	6.086000|6.086000	0.71352|0.71352	2.625000|2.625000	0.88918|0.88918	0.585000|0.585000	0.79938|0.79938	GAA|CGA	C|0.817;T|0.183	0.183	strong		0.363	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
ERO1LB	56605	hgsc.bcm.edu	37	1	236413230	236413230	+	Missense_Mutation	SNP	T	T	A	rs2477599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236413230T>A	ENST00000354619.5	-	5	587	c.386A>T	c.(385-387)gAt>gTt	p.D129V	ERO1LB_ENST00000327333.8_Missense_Mutation_p.D129V	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	129			D -> V (in dbSNP:rs2477599). {ECO:0000269|PubMed:15489334}.		4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TTGCTCACAATCTTCTAATTC	0.279													T|||	1680	0.335463	0.1354	0.3646	5008	,	,		15154	0.1329		0.6014	False		,,,				2504	0.5204				p.D129V		Atlas-SNP	.											.	ERO1LB	48	.	0			c.A386T						PASS	.	T	VAL/ASP	858,3546	337.6+/-304.9	86,686,1430	146.0	130.0	136.0		386	4.7	0.8	1	dbSNP_100	136	5117,3469	632.1+/-398.6	1514,2089,690	yes	missense	ERO1LB	NM_019891.3	152	1600,2775,2120	AA,AT,TT		40.403,19.4823,45.9969	benign	129/468	236413230	5975,7015	2202	4293	6495	SO:0001583	missense	56605	exon5			TCACAATCTTCTA	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.386A>T	1.37:g.236413230T>A	ENSP00000346635:p.Asp129Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	22	0.297297	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	754	0.34523809523809523	75	0.1524390243902439	131	0.36187845303867405	75	0.13111888111888112	473	0.6240105540897097	T	16.85	3.236060	0.58886	0.194823	0.59597	ENSG00000086619	ENST00000354619;ENST00000327333;ENST00000366589	D;T;D	0.82255	-1.59;0.88;-1.59	5.85	4.72	0.59763	.	0.217492	0.49916	D	0.000135	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999810693	P;B	0.49185	0.92;0.1	P;B	0.45712	0.491;0.042	T	0.49844	-0.8896	9	0.56958	D	0.05	-17.6697	11.2036	0.48756	0.0:0.0:0.2933:0.7067	rs2477599;rs17853094;rs17854313;rs2477599	129;129	B4DF57;Q86YB8	.;ERO1B_HUMAN	V	129;129;10	ENSP00000346635:D129V;ENSP00000377574:D129V;ENSP00000355548:D10V	ENSP00000377574:D129V	D	-	2	0	ERO1LB	234479853	1.000000	0.71417	0.809000	0.32408	0.980000	0.70556	4.282000	0.58971	1.025000	0.39708	-0.475000	0.04921	GAT	T|0.570;A|0.430	0.430	strong		0.279	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
FAM109B	150368	hgsc.bcm.edu	37	22	42473603	42473603	+	Silent	SNP	C	C	T	rs133383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42473603C>T	ENST00000321753.3	+	3	493	c.306C>T	c.(304-306)gcC>gcT	p.A102A	SMDT1_ENST00000331479.3_5'Flank|snoU13_ENST00000458891.1_RNA	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	102	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						ACCTGCTGGCCGCAGAAGGGC	0.657													C|||	1640	0.327476	0.053	0.4971	5008	,	,		17222	0.2917		0.4592	False		,,,				2504	0.4796				p.A102A		Atlas-SNP	.											.	FAM109B	22	.	0			c.C306T						PASS	.	C		523,3883	238.4+/-249.8	37,449,1717	60.0	65.0	63.0		306	-10.1	0.0	22	dbSNP_78	63	3786,4814	532.8+/-382.3	847,2092,1361	yes	coding-synonymous	FAM109B	NM_001002034.2		884,2541,3078	TT,TC,CC		44.0233,11.8702,33.1309		102/260	42473603	4309,8697	2203	4300	6503	SO:0001819	synonymous_variant	150368	exon3			GCTGGCCGCAGAA	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.306C>T	22.37:g.42473603C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001002034	Q3SXQ3|Q8N6L9	Silent	SNP	ENST00000321753.3	37	CCDS33655.1																																																																																			C|0.682;T|0.318	0.318	strong		0.657	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
EFS	10278	hgsc.bcm.edu	37	14	23829164	23829164	+	Missense_Mutation	SNP	G	G	A	rs2231805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23829164G>A	ENST00000216733.3	-	4	1130	c.523C>T	c.(523-525)Cgg>Tgg	p.R175W	EFS_ENST00000351354.3_Missense_Mutation_p.R82W|EFS_ENST00000429593.2_Missense_Mutation_p.R82W|RP11-124D2.3_ENST00000554010.1_RNA	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	175	Pro-rich.				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)		GGGGCAACCCGGGTCAGAGGG	0.647													G|||	614	0.122604	0.3011	0.0749	5008	,	,		13281	0.0		0.0954	False		,,,				2504	0.0695				p.R175W		Atlas-SNP	.											EFS,NS,carcinoma,0,2	EFS	37	2	0			c.C523T						PASS	.	G	TRP/ARG,TRP/ARG	921,3263		82,757,1253	35.0	44.0	41.0		523,244	-2.8	0.0	14	dbSNP_98	41	928,7176		57,814,3181	yes	missense,missense	EFS	NM_005864.2,NM_032459.1	101,101	139,1571,4434	AA,AG,GG		11.4511,22.0124,15.0472	probably-damaging,probably-damaging	175/562,82/469	23829164	1849,10439	2092	4052	6144	SO:0001583	missense	10278	exon4			CAACCCGGGTCAG	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.523C>T	14.37:g.23829164G>A	ENSP00000216733:p.Arg175Trp	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	267	0.12225274725274725	158	0.32113821138211385	35	0.09668508287292818	0	0.0	74	0.09762532981530343	G	4.309	0.056599	0.08291	0.220124	0.114511	ENSG00000100842	ENST00000216733;ENST00000351354;ENST00000429593	T;T;T	0.58210	0.35;0.85;0.72	4.92	-2.79	0.05841	.	4.233020	0.00357	N	0.000021	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.13594	0.001;0.008;0.002	B;B;B	0.08055	0.0;0.003;0.0	T	0.23762	-1.0179	9	0.51188	T	0.08	4.9719	6.4106	0.21688	0.4459:0.1204:0.4337:0.0	rs2231805;rs60687060	82;82;175	B4DJ56;O43281-2;O43281	.;.;EFS_HUMAN	W	175;82;82	ENSP00000216733:R175W;ENSP00000340607:R82W;ENSP00000416684:R82W	ENSP00000216733:R175W	R	-	1	2	EFS	22899004	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.237000	0.08990	-0.859000	0.04105	-1.218000	0.01608	CGG	G|0.872;A|0.128	0.128	strong		0.647	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
PANX1	24145	hgsc.bcm.edu	37	11	93913036	93913036	+	Missense_Mutation	SNP	A	A	G	rs12793348	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:93913036A>G	ENST00000227638.3	+	4	1199	c.814A>G	c.(814-816)Atc>Gtc	p.I272V	PANX1_ENST00000436171.2_Missense_Mutation_p.I272V	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	272			I -> V (in dbSNP:rs12793348).		calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	TGCCGTGGGCATCTTCCAGTT	0.502													A|||	704	0.140575	0.143	0.0793	5008	,	,		19100	0.2609		0.0915	False		,,,				2504	0.1074				p.I272V		Atlas-SNP	.											.	PANX1	38	.	0			c.A814G						PASS	.	A	VAL/ILE	646,3756	277.2+/-273.6	37,572,1592	315.0	271.0	286.0		814	-3.2	0.8	11	dbSNP_121	286	663,7933	167.3+/-219.0	31,601,3666	yes	missense	PANX1	NM_015368.3	29	68,1173,5258	GG,GA,AA		7.7129,14.6751,10.0708	benign	272/427	93913036	1309,11689	2201	4298	6499	SO:0001583	missense	24145	exon4			GTGGGCATCTTCC	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.814A>G	11.37:g.93913036A>G	ENSP00000227638:p.Ile272Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	286	0.13095238095238096	51	0.10365853658536585	28	0.07734806629834254	140	0.24475524475524477	67	0.08839050131926121	A	0.022	-1.408327	0.01155	0.146751	0.077129	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.14391	2.53;2.51	5.95	-3.19	0.05171	.	0.490245	0.24592	N	0.037204	T	0.00012	0.0000	N	0.04959	-0.14	0.41476	P	0.01186100000000001	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.41088	-0.9528	9	0.02654	T	1	-15.4374	16.4637	0.84072	0.3411:0.0:0.6589:0.0	rs12793348;rs52804213;rs60205083;rs12793348	272;272	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	V	272	ENSP00000227638:I272V;ENSP00000411461:I272V	ENSP00000227638:I272V	I	+	1	0	PANX1	93552684	0.025000	0.19082	0.817000	0.32601	0.270000	0.26580	0.248000	0.18198	-0.976000	0.03542	-1.139000	0.01908	ATC	A|0.883;G|0.117	0.117	strong		0.502	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
STK39	27347	hgsc.bcm.edu	37	2	168931636	168931636	+	Missense_Mutation	SNP	C	C	T	rs56031549	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	163	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	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	
OR5H15	403274	hgsc.bcm.edu	37	3	97887970	97887970	+	Missense_Mutation	SNP	C	C	T	rs72933946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	400	7	0.0175	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		
TOX3	27324	hgsc.bcm.edu	37	16	52478206	52478206	+	Silent	SNP	C	C	T	rs3743796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:52478206C>T	ENST00000219746.9	-	6	1253	c.969G>A	c.(967-969)agG>agA	p.R323R	TOX3_ENST00000407228.3_Silent_p.R318R	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	323					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)	p.R323R(1)		NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CGAGGCTGGCCCTGTATGCCG	0.468													C|||	506	0.101038	0.0522	0.0749	5008	,	,		15347	0.1488		0.0984	False		,,,				2504	0.1391				p.R323R		Atlas-SNP	.											TOX3_ENST00000407228,caecum,carcinoma,-1,3	TOX3	121	3	1	Substitution - coding silent(1)	stomach(1)	c.G969A						PASS	.	C	,	206,3442		5,196,1623	46.0	45.0	45.0		969,954	3.0	1.0	16	dbSNP_107	45	614,7562		26,562,3500	no	coding-synonymous,coding-synonymous	TOX3	NM_001080430.2,NM_001146188.1	,	31,758,5123	TT,TC,CC		7.5098,5.6469,6.935	,	323/577,318/572	52478206	820,11004	1824	4088	5912	SO:0001819	synonymous_variant	27324	exon6			GCTGGCCCTGTAT	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.969G>A	16.37:g.52478206C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001080430	B4DRD0|B5MCW4	Silent	SNP	ENST00000219746.9	37	CCDS54009.1																																																																																			C|0.891;T|0.109	0.109	strong		0.468	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
ERC1	23085	hgsc.bcm.edu	37	12	1137145	1137145	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:1137145C>T	ENST00000397203.2	+	2	482	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C	ERC1_ENST00000589028.1_Missense_Mutation_p.R26C|ERC1_ENST00000543086.3_Missense_Mutation_p.R26C|ERC1_ENST00000355446.5_Missense_Mutation_p.R26C|ERC1_ENST00000546231.2_Missense_Mutation_p.R26C|ERC1_ENST00000360905.4_Missense_Mutation_p.R26C			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	26					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			CAGGCTTCCACGTTCCCCTCG	0.572																																					p.R26C		Atlas-SNP	.											.	ERC1	95	.	0			c.C76T						PASS	.						96.0	95.0	95.0					12																	1137145		2203	4300	6503	SO:0001583	missense	23085	exon2			CTTCCACGTTCCC	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"""RAB6 interacting protein 2"""	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.76C>T	12.37:g.1137145C>T	ENSP00000380386:p.Arg26Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678245	0.68042	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394	D;D;D;D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.91267	0.7247	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.952	D	0.92057	0.5653	10	0.87932	D	0	-10.8759	15.2513	0.73549	0.141:0.859:0.0:0.0	.	26;26;26	Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;RB6I2_HUMAN	C	26	ENSP00000340054:R26C;ENSP00000380386:R26C;ENSP00000438546:R26C;ENSP00000445336:R26C;ENSP00000442976:R26C;ENSP00000442739:R26C;ENSP00000347621:R26C;ENSP00000354158:R26C;ENSP00000410064:R26C	ENSP00000299183:R26C	R	+	1	0	ERC1	1007406	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	4.827000	0.62723	2.644000	0.89710	0.655000	0.94253	CGT	.	.	none		0.572	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064	
COL18A1	80781	hgsc.bcm.edu	37	21	46899872	46899872	+	Silent	SNP	C	C	A	rs1131102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46899872C>A	ENST00000359759.4	+	9	2571	c.2550C>A	c.(2548-2550)ggC>ggA	p.G850G	COL18A1_ENST00000400337.2_Silent_p.G435G|COL18A1_ENST00000355480.5_Silent_p.G615G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	850	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)		GTCCCAAGGGCGACAAGGTGA	0.662													C|||	703	0.140375	0.2247	0.0706	5008	,	,		17006	0.1081		0.0696	False		,,,				2504	0.182				p.G615G		Atlas-SNP	.											COL18A1_ENST00000359759,NS,carcinoma,+1,2	COL18A1	129	2	0			c.C1845A						PASS	.	C	,	868,3160		100,668,1246	68.0	83.0	78.0		1845,1305	-8.0	0.7	21	dbSNP_86	78	544,7794		18,508,3643	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	118,1176,4889	AA,AC,CC		6.5243,21.5492,11.4184	,	615/1520,435/1340	46899872	1412,10954	2014	4169	6183	SO:0001819	synonymous_variant	80781	exon9			CAAGGGCGACAAG		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.2550C>A	21.37:g.46899872C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.896;A|0.104	0.104	strong		0.662	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
SOX21	11166	hgsc.bcm.edu	37	13	95364046	95364046	+	Silent	SNP	C	C	G	rs1060474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:95364046C>G	ENST00000376945.2	-	1	343	c.258G>C	c.(256-258)ctG>ctC	p.L86L	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	86					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					CCTTCTTGAGCAGCGTCTTGG	0.692													c|||	1905	0.380391	0.267	0.428	5008	,	,		8078	0.4692		0.4692	False		,,,				2504	0.317				p.L86L		Atlas-SNP	.											.	SOX21	21	.	0			c.G258C						PASS	.	C		1334,3072	442.5+/-346.7	205,924,1074	67.0	60.0	62.0		258	3.0	1.0	13	dbSNP_86	62	3639,4961	522.1+/-380.0	760,2119,1421	no	coding-synonymous	SOX21	NM_007084.2		965,3043,2495	GG,GC,CC		42.314,30.2769,38.2362		86/277	95364046	4973,8033	2203	4300	6503	SO:0001819	synonymous_variant	11166	exon1			CTTGAGCAGCGTC	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"""SRY (sex determining region Y)-boxes"""	11197	protein-coding gene	gene with protein product	"""SRY-box 21"""	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.258G>C	13.37:g.95364046C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	37	CCDS9473.1																																																																																			C|0.605;G|0.395	0.395	strong		0.692	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084	
ECM2	1842	hgsc.bcm.edu	37	9	95274338	95274338	+	Silent	SNP	A	A	G	rs2296667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:95274338A>G	ENST00000344604.5	-	5	1274	c.1125T>C	c.(1123-1125)agT>agC	p.S375S	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.S353S	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	375					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						TATTATTTTTACTCAGATCAA	0.393													G|||	2040	0.407348	0.7844	0.2896	5008	,	,		21588	0.1528		0.3618	False		,,,				2504	0.2904				p.S375S		Atlas-SNP	.											.	ECM2	147	.	0			c.T1125C						PASS	.	G	,,,	3063,1343	447.1+/-348.2	1065,933,205	179.0	163.0	168.0		,1059,1059,1125	4.8	1.0	9	dbSNP_100	168	3283,5317	646.7+/-400.3	631,2021,1648	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	1696,2954,1853	GG,GA,AA		38.1744,30.4812,48.7929	,,,	,353/678,353/644,375/700	95274338	6346,6660	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon5			ATTTTTACTCAGA	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.1125T>C	9.37:g.95274338A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	189	90	0.47619	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			A|0.543;G|0.457	0.457	strong		0.393	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
HELQ	113510	hgsc.bcm.edu	37	4	84374480	84374480	+	Missense_Mutation	SNP	C	C	T	rs1494961	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:84374480C>T	ENST00000295488.3	-	2	1078	c.916G>A	c.(916-918)Gtt>Att	p.V306I	MRPS18C_ENST00000507349.1_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000440639.2_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.V306I|MRPS18C_ENST00000295491.4_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	306				V -> I (in Ref. 1; AAL85274, 2; BAC87559 and 4; AAH95473). {ECO:0000305}.	double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						GATGACTCAACTGTTTTCTTA	0.373								Other identified genes with known or suspected DNA repair function					T|||	3328	0.664537	0.826	0.6441	5008	,	,		19522	0.6776		0.4901	False		,,,				2504	0.6268				p.V306I		Atlas-SNP	.											.	HELQ	95	.	0			c.G916A						PASS	.	T	ILE/VAL	3420,986	366.8+/-318.0	1321,778,104	98.0	102.0	101.0	http://www.ncbi.nlm.nih.gov/pubmed?term	916	2.3	0.9	4	dbSNP_88	101	4311,4289	576.2+/-390.4	1082,2147,1071	yes	missense	HELQ	NM_133636.2	29	2403,2925,1175	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	49.8721,22.3786,40.5582	benign	306/1102	84374480	7731,5275	2203	4300	6503	SO:0001583	missense	113510	exon2			ACTCAACTGTTTT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.916G>A	4.37:g.84374480C>T	ENSP00000295488:p.Val306Ile	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	1367	0.6259157509157509	401	0.8150406504065041	220	0.6077348066298343	371	0.6486013986013986	375	0.4947229551451187	T	4.651	0.120977	0.08881	0.776214	0.501279	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.57595	0.39;1.35	5.92	2.29	0.28610	.	0.284381	0.36234	N	0.002702	T	0.00012	0.0000	N	0.00801	-1.175	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	0.26326	-1.0106	9	0.25751	T	0.34	-5.3209	5.8264	0.18556	0.0:0.1996:0.2338:0.5666	rs1494961;rs3733332;rs17354958;rs59130103;rs1494961	306;306;269;306	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	I	306	ENSP00000295488:V306I;ENSP00000424539:V306I	ENSP00000295488:V306I	V	-	1	0	HELQ	84593504	1.000000	0.71417	0.944000	0.38274	0.925000	0.55904	2.390000	0.44416	0.166000	0.19597	-0.254000	0.11334	GTT	C|0.384;N|0.000	.	strong		0.373	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
SCN5A	6331	hgsc.bcm.edu	37	3	38645420	38645420	+	Missense_Mutation	SNP	T	T	C	rs1805124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38645420T>C	ENST00000333535.4	-	12	1822	c.1673A>G	c.(1672-1674)cAc>cGc	p.H558R	SCN5A_ENST00000414099.2_Missense_Mutation_p.H558R|SCN5A_ENST00000449557.2_Missense_Mutation_p.H558R|SCN5A_ENST00000443581.1_Missense_Mutation_p.H558R|SCN5A_ENST00000425664.1_Missense_Mutation_p.H558R|SCN5A_ENST00000450102.2_Missense_Mutation_p.H558R|SCN5A_ENST00000451551.2_Missense_Mutation_p.H558R|SCN5A_ENST00000413689.1_Missense_Mutation_p.H558R|SCN5A_ENST00000423572.2_Missense_Mutation_p.H558R|SCN5A_ENST00000455624.2_Missense_Mutation_p.H558R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	558			H -> R (channels properties are similar to wild-type; the double mutant Arg-558/ Ile-512 channel shows that Arg-558 eliminates the negative shift induced by Ile-512 but only partially restores the kinetic abnormalities; can modulate the gating defects caused by Ala-2006 and other mutations; dbSNP:rs1805124). {ECO:0000269|PubMed:11997281, ECO:0000269|PubMed:12051963, ECO:0000269|PubMed:12454206, ECO:0000269|PubMed:12569159, ECO:0000269|PubMed:14500339, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18368697, ECO:0000269|PubMed:18378609}.		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGTGATGTGTGGTGGCTCTC	0.627													C|||	1154	0.230431	0.3094	0.2277	5008	,	,		17254	0.1012		0.2167	False		,,,				2504	0.273				p.H558R		Atlas-SNP	.											SCN5A_ENST00000413689,colon,carcinoma,0,3	SCN5A	634	3	0			c.A1673G	GRCh37	CM031355	SCN5A	M	rs1805124	PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	1151,3037		156,839,1099	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1673,1673,1673,1673,1673,1673	2.4	1.0	3	dbSNP_89	52	1957,6475		248,1461,2507	yes	missense,missense,missense,missense,missense,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	29,29,29,29,29,29	404,2300,3606	CC,CT,TT		23.2092,27.4833,24.6276	benign,benign,benign,benign,benign,benign	558/2016,558/2017,558/1999,558/1984,558/1963,558/2017	38645420	3108,9512	2094	4216	6310	SO:0001583	missense	6331	exon12			GATGTGTGGTGGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1673A>G	3.37:g.38645420T>C	ENSP00000328968:p.His558Arg	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	174	97	0.557471	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	450	0.20604395604395603	147	0.29878048780487804	75	0.20718232044198895	63	0.11013986013986014	165	0.21767810026385223	C	0.349	-0.945829	0.02304	0.274833	0.232092	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.94613	-3.39;-3.41;-3.41;-3.46;-3.41;-3.39;-3.42;-3.47;-3.46;-3.46	4.27	2.44	0.29823	Domain of unknown function DUF3451 (1);	0.329193	0.30602	N	0.009278	T	0.00012	0.0000	N	0.00114	-2.085	0.44771	P	0.0022280000000000078	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	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.45702	-0.9243	9	0.02654	T	1	.	15.5745	0.76365	0.0:0.9158:0.0:0.0842	rs1805124;rs58801095;rs1805124	558;558;558;558;558;558;558	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	R	558	ENSP00000398962:H558R;ENSP00000398266:H558R;ENSP00000410257:H558R;ENSP00000388797:H558R;ENSP00000397915:H558R;ENSP00000416634:H558R;ENSP00000328968:H558R;ENSP00000399524:H558R;ENSP00000403355:H558R;ENSP00000413996:H558R	ENSP00000328968:H558R	H	-	2	0	SCN5A	38620424	0.998000	0.40836	0.992000	0.48379	0.570000	0.35934	1.656000	0.37355	0.109000	0.17891	-2.400000	0.00224	CAC	T|0.790;C|0.210	0.210	strong		0.627	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
KLHL6	89857	hgsc.bcm.edu	37	3	183273248	183273248	+	Missense_Mutation	SNP	A	A	G	rs148924291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183273248A>G	ENST00000341319.3	-	1	229	c.194T>C	c.(193-195)cTg>cCg	p.L65P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	65					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.L65P(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			TTCCATTCGCAGGGTTTCCAG	0.498													A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16106	0.0		0.0	False		,,,				2504	0.0				p.L65P		Atlas-SNP	.											KLHL6,NS,lymphoid_neoplasm,-1,2	KLHL6	100	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T194C						scavenged	.	A	PRO/LEU	0,4406		0,0,2203	140.0	139.0	139.0		194	5.6	0.9	3	dbSNP_134	139	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLHL6	NM_130446.2	98	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	65/622	183273248	1,13005	2203	4300	6503	SO:0001583	missense	89857	exon1			ATTCGCAGGGTTT	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.194T>C	3.37:g.183273248A>G	ENSP00000341342:p.Leu65Pro	Somatic	190	2	0.0105263		WXS	Illumina HiSeq	Phase_I	228	96	0.421053	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	A	17.61	3.433538	0.62955	0.0	1.16E-4	ENSG00000172578	ENST00000341319	T	0.75154	-0.91	5.56	5.56	0.83823	BTB/POZ (1);BTB/POZ fold (2);	0.066358	0.64402	D	0.000007	D	0.90487	0.7020	H	0.96142	3.775	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.93464	0.6813	10	0.87932	D	0	.	15.7124	0.77641	1.0:0.0:0.0:0.0	.	65	Q8WZ60	KLHL6_HUMAN	P	65	ENSP00000341342:L65P	ENSP00000341342:L65P	L	-	2	0	KLHL6	184755942	1.000000	0.71417	0.941000	0.38009	0.438000	0.31896	7.483000	0.81158	2.108000	0.64289	0.533000	0.62120	CTG	A|1.000;G|0.000	0.000	weak		0.498	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
YTHDC2	64848	hgsc.bcm.edu	37	5	112899702	112899702	+	Silent	SNP	A	A	G	rs6886628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	167	0	0		WXS	Illumina HiSeq	Phase_I	170	81	0.476471	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	
ZNF80	7634	hgsc.bcm.edu	37	3	113955187	113955187	+	Nonsense_Mutation	SNP	A	A	C	rs3732781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0		WXS	Illumina HiSeq	Phase_I	108	24	0.222222	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	
FBXO5	26271	hgsc.bcm.edu	37	6	153296370	153296370	+	Missense_Mutation	SNP	G	G	A	rs7763565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:153296370G>A	ENST00000229758.3	-	2	548	c.490C>T	c.(490-492)Ctc>Ttc	p.L164F	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Missense_Mutation_p.L118F	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	164	Interaction with EVI5.		L -> F (in dbSNP:rs7763565).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		TCCTCCAGGAGGCTACCTTCT	0.423													G|||	478	0.0954473	0.1551	0.1988	5008	,	,		17886	0.0198		0.0517	False		,,,				2504	0.0644				p.L164F	NSCLC(121;372 1757 17721 17977 29669)	Atlas-SNP	.											.	FBXO5	40	.	0			c.C490T						PASS	.	G	PHE/LEU,PHE/LEU	611,3795	265.9+/-266.9	40,531,1632	123.0	126.0	125.0		352,490	0.9	0.1	6	dbSNP_116	125	549,8051	150.4+/-205.3	18,513,3769	yes	missense,missense	FBXO5	NM_001142522.1,NM_012177.3	22,22	58,1044,5401	AA,AG,GG		6.3837,13.8675,8.919	probably-damaging,probably-damaging	118/402,164/448	153296370	1160,11846	2203	4300	6503	SO:0001583	missense	26271	exon2			CCAGGAGGCTACC	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.490C>T	6.37:g.153296370G>A	ENSP00000229758:p.Leu164Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Missense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	187	0.08562271062271062	67	0.13617886178861788	62	0.1712707182320442	16	0.027972027972027972	42	0.055408970976253295	G	14.99	2.700064	0.48307	0.138675	0.063837	ENSG00000112029	ENST00000229758;ENST00000367241	T;T	0.47528	0.84;0.84	5.92	0.943	0.19531	.	0.649006	0.15030	N	0.284489	T	0.33381	0.0861	M	0.61703	1.905	0.80722	P	0.0	D	0.56521	0.976	P	0.52267	0.694	T	0.10520	-1.0626	9	0.48119	T	0.1	-5.5095	4.4233	0.11492	0.3194:0.0:0.3789:0.3017	rs7763565;rs52802786;rs60639869;rs7763565	164	Q9UKT4	FBX5_HUMAN	F	164;118	ENSP00000229758:L164F;ENSP00000356210:L118F	ENSP00000229758:L164F	L	-	1	0	FBXO5	153338063	0.000000	0.05858	0.097000	0.21041	0.992000	0.81027	0.319000	0.19522	0.417000	0.25871	0.655000	0.94253	CTC	G|0.911;A|0.089	0.089	strong		0.423	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
PARP9	83666	hgsc.bcm.edu	37	3	122277268	122277268	+	Missense_Mutation	SNP	G	G	A	rs34006803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:122277268G>A	ENST00000360356.2	-	3	289	c.62C>T	c.(61-63)tCg>tTg	p.S21L	PARP9_ENST00000492382.1_Intron|PARP9_ENST00000477522.2_Intron|PARP9_ENST00000462315.1_Intron|PARP9_ENST00000471785.1_Intron	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	21			S -> L (in dbSNP:rs34006803).		cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		GAGTGAGAGCGAGGTAATCCT	0.443													G|||	380	0.0758786	0.0053	0.0951	5008	,	,		19559	0.0367		0.1213	False		,,,				2504	0.1513				p.S21L		Atlas-SNP	.											.	PARP9	72	.	0			c.C62T						PASS	.	G	LEU/SER,,,,,LEU/SER	107,4299	83.9+/-122.4	0,107,2096	130.0	124.0	126.0		62,,,,,62	1.7	0.0	3	dbSNP_126	126	1048,7552	222.2+/-259.3	77,894,3329	yes	missense,intron,intron,intron,intron,missense	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	145,,,,,145	77,1001,5425	AA,AG,GG		12.186,2.4285,8.8805	possibly-damaging,,,,,possibly-damaging	21/855,,,,,21/855	122277268	1155,11851	2203	4300	6503	SO:0001583	missense	83666	exon3			GAGAGCGAGGTAA	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.62C>T	3.37:g.122277268G>A	ENSP00000353512:p.Ser21Leu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	51	0.64557	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	146	0.06684981684981685	4	0.008130081300813009	42	0.11602209944751381	21	0.03671328671328671	79	0.10422163588390501	G	8.104	0.777244	0.16120	0.024285	0.12186	ENSG00000138496	ENST00000360356	T	0.08546	3.08	4.56	1.71	0.24356	.	0.789321	0.10808	N	0.631916	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.21688	0.059	B	0.15484	0.013	T	0.45279	-0.9272	10	0.87932	D	0	.	6.561	0.22485	0.0961:0.3538:0.5502:0.0	rs34006803	21	Q8IXQ6	PARP9_HUMAN	L	21	ENSP00000353512:S21L	ENSP00000353512:S21L	S	-	2	0	PARP9	123759958	0.171000	0.23029	0.001000	0.08648	0.153000	0.21895	0.441000	0.21611	0.394000	0.25230	-0.300000	0.09419	TCG	G|0.914;A|0.086	0.086	strong		0.443	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
DHX33	56919	hgsc.bcm.edu	37	17	5366947	5366947	+	Missense_Mutation	SNP	G	G	A	rs8069315	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:5366947G>A	ENST00000225296.3	-	2	552	c.352C>T	c.(352-354)Cgc>Tgc	p.R118C	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	118	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		R -> C (in dbSNP:rs8069315).		positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						ATGCCCTGGCGGCTGATCCCT	0.512													G|||	542	0.108227	0.233	0.0677	5008	,	,		18270	0.0228		0.1233	False		,,,				2504	0.0409				p.R118C		Atlas-SNP	.											.	DHX33	41	.	0			c.C352T						PASS	.	G	,CYS/ARG	904,3502	348.7+/-310.1	100,704,1399	79.0	72.0	74.0		,352	5.0	1.0	17	dbSNP_116	74	982,7618	212.2+/-252.6	57,868,3375	yes	intron,missense	DHX33	NM_001199699.1,NM_020162.3	,180	157,1572,4774	AA,AG,GG		11.4186,20.5175,14.501	,probably-damaging	,118/708	5366947	1886,11120	2203	4300	6503	SO:0001583	missense	56919	exon2			CCTGGCGGCTGAT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.352C>T	17.37:g.5366947G>A	ENSP00000225296:p.Arg118Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	248	0.11355311355311355	109	0.22154471544715448	31	0.0856353591160221	12	0.02097902097902098	96	0.1266490765171504	G	27.4	4.825669	0.90955	0.205175	0.114186	ENSG00000005100	ENST00000225296	T	0.07800	3.16	5.04	5.04	0.67666	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.81614	2.55	0.09310	P	1.0	B	0.25850	0.136	B	0.20955	0.032	T	0.15292	-1.0442	9	0.72032	D	0.01	.	17.3684	0.87369	0.0:0.0:1.0:0.0	rs8069315;rs52830117;rs57788243;rs8069315	118	Q9H6R0	DHX33_HUMAN	C	118	ENSP00000225296:R118C	ENSP00000225296:R118C	R	-	1	0	DHX33	5307671	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	4.532000	0.60608	2.340000	0.79590	0.563000	0.77884	CGC	G|0.856;A|0.144	0.144	strong		0.512	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
STARD3	10948	hgsc.bcm.edu	37	17	37817254	37817254	+	Missense_Mutation	SNP	G	G	A	rs34408242		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:37817254G>A	ENST00000336308.5	+	13	1273	c.1055G>A	c.(1054-1056)cGc>cAc	p.R352H	STARD3_ENST00000394250.4_Missense_Mutation_p.R334H|STARD3_ENST00000544210.2_Missense_Mutation_p.R352H|STARD3_ENST00000580611.1_Missense_Mutation_p.R326H	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	352	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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)			AATGTCCGGCGCATTGAGCGG	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18489	0.0		0.0	False		,,,				2504	0.0				p.R352H		Atlas-SNP	.											.	STARD3	33	.	0			c.G1055A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	74.0	66.0	68.0		1055,1001,1055	4.0	0.8	17	dbSNP_126	68	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	29,29,29	0,18,6485	AA,AG,GG		0.186,0.0454,0.1384	probably-damaging,probably-damaging,probably-damaging	352/446,334/428,352/446	37817254	18,12988	2203	4300	6503	SO:0001583	missense	10948	exon13			TCCGGCGCATTGA		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.1055G>A	17.37:g.37817254G>A	ENSP00000337446:p.Arg352His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Missense_Mutation	SNP	ENST00000336308.5	37	CCDS11341.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	22.3	4.270034	0.80469	4.54E-4	0.00186	ENSG00000131748	ENST00000336308;ENST00000544210;ENST00000394250	T;T;T	0.77877	-1.13;-1.13;-1.13	5.02	4.03	0.46877	Lipid-binding START (3);START-like domain (1);	0.191292	0.46758	D	0.000272	T	0.80639	0.4661	L	0.29908	0.895	0.80722	D	1	D;D;P;D;D	0.89917	0.998;1.0;0.913;0.998;0.989	P;D;P;P;P	0.91635	0.815;0.999;0.511;0.831;0.685	T	0.77869	-0.2427	10	0.27785	T	0.31	.	14.652	0.68805	0.0:0.0:0.8531:0.1469	rs34408242	352;117;352;334;352	F5H0G2;Q59EN9;B4DUY1;A8MXA4;Q14849	.;.;.;.;STAR3_HUMAN	H	352;352;334	ENSP00000337446:R352H;ENSP00000439869:R352H;ENSP00000377794:R334H	ENSP00000337446:R352H	R	+	2	0	STARD3	35070780	1.000000	0.71417	0.821000	0.32701	0.998000	0.95712	7.207000	0.77899	1.094000	0.41399	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.607	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		
MORC1	27136	hgsc.bcm.edu	37	3	108723983	108723983	+	Missense_Mutation	SNP	C	C	T	rs35421732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:108723983C>T	ENST00000483760.1	-	18	1927	c.1884G>A	c.(1882-1884)atG>atA	p.M628I	MORC1_ENST00000232603.5_Missense_Mutation_p.M649I					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						GTTGAGAGTTCATTTTCTCCT	0.363													C|||	67	0.0133786	0.0	0.0231	5008	,	,		16137	0.0		0.0497	False		,,,				2504	0.001				p.M649I		Atlas-SNP	.											.	MORC1	211	.	0			c.G1947A						PASS	.	C	ILE/MET	42,4362	43.1+/-76.7	0,42,2160	102.0	105.0	104.0		1947	-2.0	0.0	3	dbSNP_126	104	401,8199	128.2+/-186.4	14,373,3913	yes	missense	MORC1	NM_014429.3	10	14,415,6073	TT,TC,CC		4.6628,0.9537,3.4066	benign	649/985	108723983	443,12561	2202	4300	6502	SO:0001583	missense	27136	exon19			AGAGTTCATTTTC	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.1884G>A	3.37:g.108723983C>T	ENSP00000417282:p.Met628Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	18	0.227848	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		49	0.022435897435897436	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	37	0.048812664907651716	C	4.574	0.106543	0.08780	0.009537	0.046628	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05382	3.5;3.45	4.11	-1.98	0.07480	.	3.152720	0.00941	N	0.002824	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.39251	-0.9623	10	0.31617	T	0.26	5.4385	4.2307	0.10601	0.1623:0.3617:0.0:0.476	rs35421732	628;649	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	649;628	ENSP00000232603:M649I;ENSP00000417282:M628I	ENSP00000232603:M649I	M	-	3	0	MORC1	110206673	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.154000	0.10130	-0.447000	0.07138	0.557000	0.71058	ATG	C|0.965;T|0.035	0.035	strong		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75981765	75981765	+	Missense_Mutation	SNP	G	G	T	rs149356457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75981765G>T	ENST00000308508.5	-	3	1733	c.1641C>A	c.(1639-1641)aaC>aaA	p.N547K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	547	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						CATTGACAGGGTTGACCTGGA	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20725	0.0		0.001	False		,,,				2504	0.0041				p.N547K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C1641A						PASS	.	G	LYS/ASN	1,4393		0,1,2196	35.0	31.0	32.0		1641	3.2	0.1	15	dbSNP_134	32	13,8563		0,13,4275	no	missense	CSPG4	NM_001897.4	94	0,14,6471	TT,TG,GG		0.1516,0.0228,0.1079	benign	547/2323	75981765	14,12956	2197	4288	6485	SO:0001583	missense	1464	exon3			GACAGGGTTGACC	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.1641C>A	15.37:g.75981765G>T	ENSP00000312506:p.Asn547Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.454	-0.325794	0.05350	2.28E-4	0.001516	ENSG00000173546	ENST00000308508	T	0.45668	0.89	5.21	3.23	0.37069	.	0.608532	0.16274	N	0.221645	T	0.29288	0.0729	L	0.60455	1.87	0.41510	D	0.988332	B	0.32302	0.363	B	0.26969	0.075	T	0.08785	-1.0705	10	0.06236	T	0.91	.	5.9733	0.19365	0.1589:0.0:0.6881:0.153	.	547	Q6UVK1	CSPG4_HUMAN	K	547	ENSP00000312506:N547K	ENSP00000312506:N547K	N	-	3	2	CSPG4	73768820	0.381000	0.25140	0.100000	0.21137	0.055000	0.15305	0.522000	0.22909	0.507000	0.28148	0.555000	0.69702	AAC	G|0.998;T|0.002	0.002	strong		0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
RAB17	64284	hgsc.bcm.edu	37	2	238494681	238494681	+	Silent	SNP	G	G	A	rs34052613	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238494681G>A	ENST00000264601.3	-	2	746	c.117C>T	c.(115-117)taC>taT	p.Y39Y	RAB17_ENST00000538644.1_De_novo_Start_InFrame|RAB17_ENST00000409822.1_Intron|RAB17_ENST00000416106.1_5'UTR|RAB17_ENST00000409576.1_Intron	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	39					cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		CGTTCTTCACGTACCGAAGAG	0.607													G|||	414	0.0826677	0.1172	0.0677	5008	,	,		18531	0.0159		0.0994	False		,,,				2504	0.0982				p.Y39Y	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.C117T						PASS	.	G		500,3906	231.4+/-245.2	41,418,1744	98.0	86.0	90.0		117	-2.1	0.8	2	dbSNP_126	90	1055,7545	222.6+/-259.6	61,933,3306	no	coding-synonymous	RAB17	NM_022449.3		102,1351,5050	AA,AG,GG		12.2674,11.3482,11.956		39/213	238494681	1555,11451	2203	4300	6503	SO:0001819	synonymous_variant	64284	exon2			CTTCACGTACCGA	AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"""RAB, member RAS oncogene"""	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.117C>T	2.37:g.238494681G>A		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Silent	SNP	ENST00000264601.3	37	CCDS2520.1																																																																																			G|0.890;A|0.110	0.110	strong		0.607	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2		
CCT6B	10693	hgsc.bcm.edu	37	17	33288363	33288363	+	Missense_Mutation	SNP	C	C	T	rs9635769	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33288363C>T	ENST00000314144.5	-	1	165	c.50G>A	c.(49-51)cGg>cAg	p.R17Q	CCT6B_ENST00000436961.3_Missense_Mutation_p.R17Q|CCT6B_ENST00000421975.3_Missense_Mutation_p.R17Q|ZNF830_ENST00000361952.3_5'Flank	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	38	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	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	
TFAP2C	7022	hgsc.bcm.edu	37	20	55209257	55209257	+	Silent	SNP	T	T	C	rs35023929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	63	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	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	
MAP9	79884	hgsc.bcm.edu	37	4	156289900	156289900	+	Silent	SNP	C	C	T	rs3733390	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156289900C>T	ENST00000311277.4	-	5	809	c.546G>A	c.(544-546)ttG>ttA	p.L182L	AC097467.2_ENST00000597831.1_RNA|MAP9_ENST00000515654.1_Silent_p.L182L|MAP9_ENST00000379248.2_Silent_p.L109L|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000596165.1_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	415	1	0.00240964		WXS	Illumina HiSeq	Phase_I	353	171	0.484419	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	
GPC6	10082	hgsc.bcm.edu	37	13	95034749	95034749	+	Missense_Mutation	SNP	G	G	A	rs1535692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:95034749G>A	ENST00000377047.4	+	7	1849	c.1234G>A	c.(1234-1236)Gtg>Atg	p.V412M		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	412			V -> M (in dbSNP:rs1535692). {ECO:0000269|PubMed:14702039}.		carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GGACGAGAGCGTGACAGCGGG	0.527													G|||	856	0.170927	0.0598	0.2695	5008	,	,		21317	0.2093		0.1918	False		,,,				2504	0.1902				p.V412M		Atlas-SNP	.											GPC6,NS,carcinoma,0,1	GPC6	102	1	0			c.G1234A						PASS	.	G	MET/VAL	353,4053	182.6+/-210.3	20,313,1870	152.0	136.0	141.0		1234	4.0	0.8	13	dbSNP_88	141	1637,6963	303.0+/-306.2	166,1305,2829	yes	missense	GPC6	NM_005708.3	21	186,1618,4699	AA,AG,GG		19.0349,8.0118,15.3006	benign	412/556	95034749	1990,11016	2203	4300	6503	SO:0001583	missense	10082	exon7			GAGAGCGTGACAG	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1234G>A	13.37:g.95034749G>A	ENSP00000366246:p.Val412Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	406	0.1858974358974359	32	0.06504065040650407	90	0.24861878453038674	136	0.23776223776223776	148	0.19525065963060687	G	2.075	-0.412013	0.04799	0.080118	0.190349	ENSG00000183098	ENST00000377047	T	0.50001	0.76	5.74	3.97	0.46021	.	0.284066	0.33916	N	0.004424	T	0.00012	0.0000	N	0.02802	-0.49	0.34299	P	0.31582299999999996	B	0.24823	0.112	B	0.25884	0.064	T	0.23404	-1.0189	9	0.10636	T	0.68	.	10.4396	0.44457	0.1561:0.0:0.8439:0.0	rs1535692;rs17791864;rs52821250;rs57981092;rs1535692	412	Q9Y625	GPC6_HUMAN	M	412	ENSP00000366246:V412M	ENSP00000366246:V412M	V	+	1	0	GPC6	93832750	1.000000	0.71417	0.821000	0.32701	0.597000	0.36814	5.119000	0.64679	0.734000	0.32515	-0.133000	0.14855	GTG	G|0.835;A|0.165	0.165	strong		0.527	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
CRLF3	51379	hgsc.bcm.edu	37	17	29111368	29111368	+	Missense_Mutation	SNP	A	A	G	rs11867457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:29111368A>G	ENST00000324238.6	-	8	1290	c.1166T>C	c.(1165-1167)cTa>cCa	p.L389P	CRLF3_ENST00000577725.1_5'Flank|CRLF3_ENST00000544695.1_Missense_Mutation_p.L273P|CTD-2349P21.10_ENST00000585212.1_RNA	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	389			L -> P (in dbSNP:rs11867457).		G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GGTGGTTCCTAGAGTCACGGC	0.393													A|||	672	0.134185	0.2027	0.0893	5008	,	,		20220	0.119		0.167	False		,,,				2504	0.0552				p.L389P	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.T1166C						PASS	.	A	PRO/LEU	942,3464	356.9+/-313.7	107,728,1368	82.0	78.0	79.0		1166	5.2	1.0	17	dbSNP_120	79	1510,7090	285.2+/-297.1	132,1246,2922	yes	missense	CRLF3	NM_015986.3	98	239,1974,4290	GG,GA,AA		17.5581,21.3799,18.8528	possibly-damaging	389/443	29111368	2452,10554	2203	4300	6503	SO:0001583	missense	51379	exon8			GTTCCTAGAGTCA	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.1166T>C	17.37:g.29111368A>G	ENSP00000318804:p.Leu389Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	37	CCDS32607.1	347	0.15888278388278387	116	0.23577235772357724	35	0.09668508287292818	63	0.11013986013986014	133	0.17546174142480211	A	14.55	2.567474	0.45694	0.213799	0.175581	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.64438	-0.1;-0.1	5.17	5.17	0.71159	.	0.143297	0.48767	D	0.000180	T	0.00039	0.0001	L	0.46157	1.445	0.09310	P	0.999999943019	D	0.57571	0.98	P	0.56700	0.804	T	0.09228	-1.0684	9	0.54805	T	0.06	-11.9363	9.7774	0.40628	0.9218:0.0:0.0782:0.0	rs11867457;rs52820860;rs11867457	389	Q8IUI8	CRLF3_HUMAN	P	389;273	ENSP00000318804:L389P;ENSP00000444188:L273P	ENSP00000318804:L389P	L	-	2	0	CRLF3	26135494	1.000000	0.71417	0.998000	0.56505	0.312000	0.27988	7.107000	0.77047	2.069000	0.61940	0.460000	0.39030	CTA	A|0.829;G|0.171	0.171	strong		0.393	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1		
SBNO2	22904	hgsc.bcm.edu	37	19	1119019	1119019	+	Silent	SNP	C	C	T	rs2074920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	23	0	0		WXS	Illumina HiSeq	Phase_I	17	16	0.941176	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	
CTSH	1512	hgsc.bcm.edu	37	15	79224732	79224732	+	Silent	SNP	G	G	A	rs149231812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79224732G>A	ENST00000220166.5	-	6	583	c.474C>T	c.(472-474)acC>acT	p.T158T	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	158					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						GCATCTTTCCGGTTGCGATGG	0.622																																					p.T158T		Atlas-SNP	.											.	CTSH	23	.	0			c.C474T						PASS	.	G		0,4392		0,0,2196	73.0	72.0	73.0		474	-9.4	0.0	15	dbSNP_134	73	7,8579	5.0+/-18.6	0,7,4286	no	coding-synonymous	CTSH	NM_004390.3		0,7,6482	AA,AG,GG		0.0815,0.0,0.0539		158/336	79224732	7,12971	2196	4293	6489	SO:0001819	synonymous_variant	1512	exon6			CTTTCCGGTTGCG	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.474C>T	15.37:g.79224732G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Silent	SNP	ENST00000220166.5	37	CCDS10308.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
YTHDC2	64848	hgsc.bcm.edu	37	5	112899573	112899573	+	Silent	SNP	T	T	C	rs6867579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112899573T>C	ENST00000161863.4	+	20	2673	c.2460T>C	c.(2458-2460)gaT>gaC	p.D820D		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	820					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)		ATGCAATGGATACATGGGAAG	0.368													T|||	469	0.0936502	0.025	0.0908	5008	,	,		16509	0.0794		0.1759	False		,,,				2504	0.1186				p.D820D		Atlas-SNP	.											YTHDC2,NS,carcinoma,+1,1	YTHDC2	118	1	0			c.T2460C						PASS	.	T		217,4187	131.4+/-167.9	4,209,1989	160.0	146.0	151.0		2460	1.3	1.0	5	dbSNP_116	151	1476,7124	282.1+/-295.4	136,1204,2960	no	coding-synonymous	YTHDC2	NM_022828.3		140,1413,4949	CC,CT,TT		17.1628,4.9273,13.0191		820/1431	112899573	1693,11311	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon20			AATGGATACATGG	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.2460T>C	5.37:g.112899573T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			T|0.881;C|0.119	0.119	strong		0.368	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
C20orf196	149840	hgsc.bcm.edu	37	20	5753579	5753579	+	Missense_Mutation	SNP	C	C	T	rs237422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:5753579C>T	ENST00000303142.6	+	2	155	c.68C>T	c.(67-69)gCg>gTg	p.A23V	C20orf196_ENST00000378979.4_Missense_Mutation_p.A23V	NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	23			A -> V (in dbSNP:rs237422).					p.A23V(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						CTGCCATCAGCGTGTGACATA	0.493													C|||	1172	0.234026	0.2958	0.2507	5008	,	,		16552	0.1518		0.2604	False		,,,				2504	0.1963				p.A23V		Atlas-SNP	.											C20orf196,NS,carcinoma,-1,2	C20orf196	17	2	1	Substitution - Missense(1)	stomach(1)	c.C68T						PASS	.	C	VAL/ALA	1180,3226	417.4+/-337.9	163,854,1186	133.0	125.0	128.0		68	1.7	0.0	20	dbSNP_79	128	2370,6230	395.9+/-345.2	355,1660,2285	yes	missense	C20orf196	NM_152504.2	64	518,2514,3471	TT,TC,CC		27.5581,26.7817,27.2951	benign	23/206	5753579	3550,9456	2203	4300	6503	SO:0001583	missense	149840	exon2			CATCAGCGTGTGA	AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984			26318	protein-coding gene	gene with protein product						12477932	Standard	NM_152504		Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.68C>T	20.37:g.5753579C>T	ENSP00000305875:p.Ala23Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_152504	A8K9J3|Q5TGA9|Q96LU1	Missense_Mutation	SNP	ENST00000303142.6	37	CCDS13091.1	545	0.24954212454212454	156	0.3170731707317073	106	0.292817679558011	89	0.1555944055944056	194	0.2559366754617414	C	0.006	-2.095195	0.00364	0.267817	0.275581	ENSG00000171984	ENST00000378979;ENST00000303142;ENST00000378971;ENST00000445603;ENST00000442185;ENST00000541651	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.81	1.73	0.24493	.	0.922436	0.09160	N	0.840298	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.41627	-0.9498	9	0.05620	T	0.96	-13.5873	10.1005	0.42502	0.0:0.6975:0.0:0.3025	rs237422;rs527738;rs52800907;rs59006821;rs237422	23	Q8IYI0	CT196_HUMAN	V	23;23;23;23;70;70	ENSP00000368263:A23V;ENSP00000305875:A23V;ENSP00000399331:A23V;ENSP00000410534:A70V	ENSP00000305875:A23V	A	+	2	0	C20orf196	5701579	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.551000	0.23361	-0.095000	0.12351	-1.761000	0.00669	GCG	T|0.257;G|0.002	0.257	strong		0.493	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077882.2	NM_152504	
KIF17	57576	hgsc.bcm.edu	37	1	21012575	21012575	+	Silent	SNP	G	G	A	rs479323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:21012575G>A	ENST00000247986.2	-	9	2293	c.1983C>T	c.(1981-1983)ccC>ccT	p.P661P	KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000375044.1_Silent_p.P561P|KIF17_ENST00000400463.3_Silent_p.P661P			Q9P2E2	KIF17_HUMAN	kinesin family member 17	661					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CCTCGGCTTCGGGCCTGGCAT	0.632													G|||	1046	0.208866	0.5794	0.0937	5008	,	,		16132	0.0357		0.0706	False		,,,				2504	0.1104				p.P661P		Atlas-SNP	.											.	KIF17	130	.	0			c.C1983T						PASS	.	G	,	1947,2415		426,1095,660	29.0	29.0	29.0		1983,1983	-7.3	0.0	1	dbSNP_83	29	487,8055		13,461,3797	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	439,1556,4457	AA,AG,GG		5.7012,44.6355,18.8624	,	661/1029,661/1030	21012575	2434,10470	2181	4271	6452	SO:0001819	synonymous_variant	57576	exon9			GGCTTCGGGCCTG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1983C>T	1.37:g.21012575G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	34	0.361702	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|0.793;A|0.207	0.207	strong		0.632	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
MAEA	10296	hgsc.bcm.edu	37	4	1305802	1305802	+	Silent	SNP	C	C	T	rs34402978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:1305802C>T	ENST00000303400.4	+	2	168	c.105C>T	c.(103-105)gcC>gcT	p.A35A	MAEA_ENST00000505839.1_5'UTR|MAEA_ENST00000505177.2_Silent_p.A35A|MAEA_ENST00000264750.6_Silent_p.A35A|MAEA_ENST00000510794.1_Silent_p.A34A|MAEA_ENST00000514708.1_Silent_p.A35A|MAEA_ENST00000452175.2_Silent_p.A24A	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	35	Extracellular and involved in cell to cell contact.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	GCTTTCGCGCCGCTCAGAAGA	0.642													C|||	67	0.0133786	0.0008	0.0159	5008	,	,		18940	0.001		0.0388	False		,,,				2504	0.0153				p.A35A		Atlas-SNP	.											.	MAEA	39	.	0			c.C105T						PASS	.	C	,	34,4372	39.2+/-71.8	0,34,2169	72.0	57.0	62.0		105,105	-4.3	0.9	4	dbSNP_126	62	415,8185	129.2+/-187.3	11,393,3896	yes	coding-synonymous,coding-synonymous	MAEA	NM_001017405.1,NM_005882.3	,	11,427,6065	TT,TC,CC		4.8256,0.7717,3.4523	,	35/397,35/356	1305802	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	10296	exon2			TCGCGCCGCTCAG	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"""GID complex subunit 9, FYV10 homolog (S. cerevisiae)"""	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.105C>T	4.37:g.1305802C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	210	108	0.514286	NM_005882	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Silent	SNP	ENST00000303400.4	37	CCDS33936.1																																																																																			C|0.972;T|0.028	0.028	strong		0.642	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882	
SLC22A1	6580	hgsc.bcm.edu	37	6	160543123	160543123	+	Silent	SNP	T	T	C	rs1867351	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160543123T>C	ENST00000366963.4	+	1	303	c.156T>C	c.(154-156)agT>agC	p.S52S	SLC22A1_ENST00000324965.4_Silent_p.S52S|SLC22A1_ENST00000457470.2_Silent_p.S52S	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	52					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)	ACTGCCAGAGTCCTGGGGTGG	0.637													C|||	1408	0.28115	0.326	0.2882	5008	,	,		18882	0.3909		0.1849	False		,,,				2504	0.2014				p.S52S		Atlas-SNP	.											.	SLC22A1	69	.	0			c.T156C						PASS	.	C	,	1305,3101	697.3+/-406.2	202,901,1100	80.0	88.0	86.0		156,156	2.6	0.9	6	dbSNP_92	86	1742,6858	734.5+/-406.9	173,1396,2731	no	coding-synonymous,coding-synonymous	SLC22A1	NM_003057.2,NM_153187.1	,	375,2297,3831	CC,CT,TT		20.2558,29.6187,23.4276	,	52/555,52/507	160543123	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	6580	exon1			CCAGAGTCCTGGG	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.156T>C	6.37:g.160543123T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Silent	SNP	ENST00000366963.4	37	CCDS5274.1																																																																																			T|0.754;C|0.246	0.246	strong		0.637	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71365676	71365676	+	Silent	SNP	G	G	A	rs357756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71365676G>A	ENST00000244230.2	+	5	1507	c.1155G>A	c.(1153-1155)caG>caA	p.Q385Q	MPHOSPH10_ENST00000498451.2_Silent_p.Q385Q	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	385					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						AGCCGTGGCAGCTTCAGGGGG	0.413													G|||	1532	0.305911	0.261	0.3934	5008	,	,		14422	0.2639		0.2942	False		,,,				2504	0.3599				p.Q385Q		Atlas-SNP	.											MPHOSPH10,rectum,carcinoma,0,1	MPHOSPH10	81	1	0			c.G1155A						PASS	.	G		1101,3305	393.3+/-328.8	137,827,1239	35.0	38.0	37.0		1155	-0.1	1.0	2	dbSNP_79	37	2544,6056	411.3+/-350.5	395,1754,2151	no	coding-synonymous	MPHOSPH10	NM_005791.2		532,2581,3390	AA,AG,GG		29.5814,24.9887,28.0255		385/682	71365676	3645,9361	2203	4300	6503	SO:0001819	synonymous_variant	10199	exon5			GTGGCAGCTTCAG	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1155G>A	2.37:g.71365676G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_005791	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																			G|0.712;A|0.288	0.288	strong		0.413	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
IGFALS	3483	hgsc.bcm.edu	37	16	1841033	1841033	+	Silent	SNP	G	G	A	rs17559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	9	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	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		
DDX11	1663	hgsc.bcm.edu	37	12	31255405	31255405	+	Silent	SNP	C	C	T	rs77340729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:31255405C>T	ENST00000407793.2	+	23	2567	c.2316C>T	c.(2314-2316)ctC>ctT	p.L772L	DDX11_ENST00000545668.1_Silent_p.L772L|DDX11_ENST00000228264.6_Silent_p.L746L|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Silent_p.L772L|DDX11_ENST00000350437.4_Silent_p.L722L	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	772					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)					CCCTGCTCCTCTCTGTGGTTG	0.567										Multiple Myeloma(12;0.14)			C|||	397	0.0792732	0.1029	0.0245	5008	,	,		17510	0.1508		0.0239	False		,,,				2504	0.0695				p.L772L		Atlas-SNP	.											.	DDX11	188	.	0			c.C2316T						PASS	.	C	,,	376,4030	186.0+/-213.0	15,346,1842	70.0	76.0	74.0		2166,2316,2316	0.4	1.0	12	dbSNP_131	74	252,8348	96.6+/-158.3	3,246,4051	no	coding-synonymous,coding-synonymous,coding-synonymous	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	,,	18,592,5893	TT,TC,CC		2.9302,8.5338,4.8285	,,	722/857,772/907,772/971	31255405	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	1663	exon23			GCTCCTCTCTGTG	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.2316C>T	12.37:g.31255405C>T		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	272	128	0.470588	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1	156	0.07142857142857142	53	0.10772357723577236	7	0.019337016574585635	78	0.13636363636363635	18	0.023746701846965697	C	4.645	0.119826	0.08881	0.085338	0.029302	ENSG00000013573	ENST00000539702	.	.	.	3.55	0.419	0.16438	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.09310	P	0.9999999999996162	.	.	.	.	.	.	T	0.12656	-1.0539	3	.	.	.	.	7.0871	0.25264	0.0:0.5712:0.3264:0.1024	.	.	.	.	F	38	.	.	S	+	2	0	DDX11	31146672	0.995000	0.38212	0.996000	0.52242	0.246000	0.25737	0.292000	0.19011	0.185000	0.20105	-0.241000	0.12123	TCT	C|0.951;T|0.049	0.049	strong		0.567	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
ALG1	56052	hgsc.bcm.edu	37	16	5132636	5132636	+	Silent	SNP	C	C	T	rs1047732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5132636C>T	ENST00000262374.5	+	11	1180	c.1149C>T	c.(1147-1149)ttC>ttT	p.F383F	ALG1_ENST00000588623.1_Silent_p.F272F|ALG1_ENST00000544428.1_Silent_p.F272F	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	383					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)				TGGACATGTTCGGGTGCTGTT	0.592													C|||	2603	0.519768	0.3903	0.415	5008	,	,		20459	0.629		0.495	False		,,,				2504	0.682				p.F383F		Atlas-SNP	.											.	ALG1	35	.	0			c.C1149T						PASS	.	C		1679,2475		348,983,746	87.0	66.0	73.0		1149	-3.4	1.0	16	dbSNP_86	73	3990,3934		1038,1914,1010	no	coding-synonymous	ALG1	NM_019109.4		1386,2897,1756	TT,TC,CC		49.6466,40.4189,46.9366		383/465	5132636	5669,6409	2077	3962	6039	SO:0001819	synonymous_variant	56052	exon11			CATGTTCGGGTGC	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.1149C>T	16.37:g.5132636C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Silent	SNP	ENST00000262374.5	37	CCDS10528.1																																																																																			C|0.536;T|0.464	0.464	strong		0.592	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
FAM153B	202134	hgsc.bcm.edu	37	5	175528584	175528584	+	Splice_Site	SNP	C	C	T	rs200684937		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:175528584C>T	ENST00000253490.4	+	12	721	c.664C>T	c.(664-666)Ctt>Ttt	p.L222F	FAM153B_ENST00000515817.1_Splice_Site_p.L145F|FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000510151.1_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	338	1	0.00295858		WXS	Illumina HiSeq	Phase_I	263	10	0.0380228	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
USP32	84669	hgsc.bcm.edu	37	17	58288421	58288421	+	Missense_Mutation	SNP	C	C	T	rs146577219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	445	1	0.00224719		WXS	Illumina HiSeq	Phase_I	452	74	0.163717	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	
MAD1L1	8379	hgsc.bcm.edu	37	7	1976457	1976457	+	Missense_Mutation	SNP	C	C	T	rs1801368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1976457C>T	ENST00000406869.1	-	17	2230	c.1673G>A	c.(1672-1674)cGc>cAc	p.R558H	MAD1L1_ENST00000402746.1_Missense_Mutation_p.R466H|MAD1L1_ENST00000399654.2_Missense_Mutation_p.R558H|MAD1L1_ENST00000265854.7_Missense_Mutation_p.R558H			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	558			R -> H (in a cancer cell line; dbSNP:rs1801368). {ECO:0000269|PubMed:10366450, ECO:0000269|PubMed:10597320, ECO:0000269|PubMed:11423979}.		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GTGGTCCTCGCGCAGGCGCTG	0.667													C|||	1526	0.304712	0.0295	0.4366	5008	,	,		17568	0.4454		0.3877	False		,,,				2504	0.3528				p.R558H		Atlas-SNP	.											.	MAD1L1	81	.	0			c.G1673A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	398,3902		30,338,1782	21.0	27.0	25.0		1673,1673,1673	0.0	0.0	7	dbSNP_89	25	3114,5360		559,1996,1682	yes	missense,missense,missense	MAD1L1	NM_001013836.1,NM_001013837.1,NM_003550.2	29,29,29	589,2334,3464	TT,TC,CC		36.7477,9.2558,27.4933	benign,benign,benign	558/719,558/719,558/719	1976457	3512,9262	2150	4237	6387	SO:0001583	missense	8379	exon17			TCCTCGCGCAGGC	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1673G>A	7.37:g.1976457C>T	ENSP00000385334:p.Arg558His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	78	29	0.371795	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	712	0.326007326007326	17	0.034552845528455285	157	0.43370165745856354	251	0.4388111888111888	287	0.3786279683377309	C	10.34	1.322527	0.23994	0.092558	0.367477	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000437877	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	4.77	-0.00151	0.14034	.	0.592432	0.18541	N	0.138191	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.06405	0.002;0.001;0.001	T	0.47661	-0.9100	9	0.45353	T	0.12	-4.9239	8.2117	0.31488	0.0:0.5493:0.0:0.4507	rs1801368;rs2280551;rs11557346;rs61400777	557;466;558	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	H	466;558;558;109;558;109;14	ENSP00000384155:R466H;ENSP00000382562:R558H;ENSP00000385334:R558H;ENSP00000265854:R558H;ENSP00000394886:R109H;ENSP00000394069:R14H	ENSP00000265854:R558H	R	-	2	0	MAD1L1	1942983	0.000000	0.05858	0.002000	0.10522	0.579000	0.36224	-0.301000	0.08232	0.085000	0.17107	0.555000	0.69702	CGC	T|0.328;G|0.000;C|0.671	0.328	strong		0.667	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
HDAC7	51564	hgsc.bcm.edu	37	12	48190044	48190044	+	Silent	SNP	C	C	T	rs11831883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:48190044C>T	ENST00000427332.2	-	8	780	c.624G>A	c.(622-624)ggG>ggA	p.G208G	HDAC7_ENST00000080059.7_Silent_p.G247G|HDAC7_ENST00000552960.1_Silent_p.G230G|HDAC7_ENST00000380610.4_Silent_p.G264G|HDAC7_ENST00000354334.3_Silent_p.G247G			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	208	Transcription repression 1. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|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 kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		GGGAGCTGCACCCTGATGCGG	0.647													C|||	853	0.170327	0.202	0.1643	5008	,	,		16277	0.0159		0.2753	False		,,,				2504	0.183				p.G247G		Atlas-SNP	.											.	HDAC7	71	.	0			c.G741A						PASS	.	C	,	963,3443	351.1+/-311.1	102,759,1342	43.0	46.0	45.0		741,741	-0.3	1.0	12	dbSNP_120	45	2632,5968	416.1+/-352.0	389,1854,2057	no	coding-synonymous,coding-synonymous	HDAC7	NM_001098416.2,NM_015401.3	,	491,2613,3399	TT,TC,CC		30.6047,21.8566,27.6411	,	247/955,247/992	48190044	3595,9411	2203	4300	6503	SO:0001819	synonymous_variant	51564	exon8			GCTGCACCCTGAT	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.624G>A	12.37:g.48190044C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Silent	SNP	ENST00000427332.2	37																																																																																				C|0.776;T|0.224	0.224	strong		0.647	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
BUB1B	701	hgsc.bcm.edu	37	15	40462780	40462780	+	Silent	SNP	G	G	A	rs1801389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40462780G>A	ENST00000287598.6	+	4	477	c.282G>A	c.(280-282)aaG>aaA	p.K94K	BUB1B_ENST00000412359.3_Silent_p.K108K|BUB1B_ENST00000560120.1_3'UTR	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	94	BUB1 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00822}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|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)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		AAGGTGGGAAGGAGAGTAATA	0.358			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	438	0.0874601	0.1422	0.0879	5008	,	,		18598	0.003		0.1342	False		,,,				2504	0.0521				p.K94K		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G282A						PASS	.	G		603,3803	265.0+/-266.4	40,523,1640	113.0	107.0	109.0		282	1.3	1.0	15	dbSNP_89	109	1266,7334	252.2+/-278.4	83,1100,3117	no	coding-synonymous	BUB1B	NM_001211.5		123,1623,4757	AA,AG,GG		14.7209,13.6859,14.3703		94/1051	40462780	1869,11137	2203	4300	6503	SO:0001819	synonymous_variant	701	exon4	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	TGGGAAGGAGAGT	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.282G>A	15.37:g.40462780G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.879;A|0.121	0.121	strong		0.358	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
DSP	1832	hgsc.bcm.edu	37	6	7585670	7585670	+	Silent	SNP	C	C	A	rs11558731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7585670C>A	ENST00000379802.3	+	24	8516	c.8175C>A	c.(8173-8175)cgC>cgA	p.R2725R	DSP_ENST00000418664.2_Silent_p.R2126R	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2725	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				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)		CTGGCCAGCGCTTCCTGGAGT	0.542													C|||	120	0.0239617	0.0023	0.0447	5008	,	,		17024	0.0		0.0706	False		,,,				2504	0.0153				p.R2725R		Atlas-SNP	.											.	DSP	306	.	0			c.C8175A						PASS	.	C	,	55,4351	56.2+/-92.4	0,55,2148	97.0	102.0	100.0		6378,8175	3.8	1.0	6	dbSNP_120	100	544,8056	149.8+/-204.8	17,510,3773	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	17,565,5921	AA,AC,CC		6.3256,1.2483,4.6056	,	2126/2273,2725/2872	7585670	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			CCAGCGCTTCCTG	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.8175C>A	6.37:g.7585670C>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			A|0.045;C|0.955;G|0.000	0.045	strong		0.542	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
CD99	4267	hgsc.bcm.edu	37	X	2644302	2644302	+	Splice_Site	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:2644302C>T	ENST00000381192.3	+	8	545	c.363C>T	c.(361-363)gcC>gcT	p.A121A	CD99_ENST00000381187.3_Splice_Site_p.A105A|CD99_ENST00000482405.2_3'UTR|CD99_ENST00000381184.1_Splice_Site_p.A121A	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule	121					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11						CTCCTGCAGCCGACGCCCCAG	0.597													.|||	594	0.11861	0.0741	0.2075	5008	,	,		18276	0.0804		0.1362	False		,,,				2504	0.137				p.A121A		Atlas-SNP	.											.	CD99	12	.	0			c.C363T						PASS	.	C	,	405,4001		22,361,1820	72.0	72.0	72.0		315,363	-5.0	0.0	X	dbSNP_134	72	1289,7303		91,1107,3098	no	coding-synonymous-near-splice,coding-synonymous-near-splice	CD99	NM_001122898.1,NM_002414.3	,	113,1468,4918	TT,TC,CC		15.0023,9.192,13.0328	,	105/170,121/186	2644302	1694,11304	2203	4296	6499	SO:0001630	splice_region_variant	4267	exon8			TGCAGCCGACGCC	M16279	CCDS14119.1, CCDS48071.1, CCDS75947.1	Xp22.32 and Yp11.3	2012-10-02	2006-03-28	2003-02-14	ENSG00000002586	ENSG00000002586		"""Pseudoautosomal regions / PAR1"", ""CD molecules"""	7082	protein-coding gene	gene with protein product		313470, 450000	"""antigen identified by monoclonal antibodies 12E7, F21 and O13"", ""CD99 antigen"""	MIC2			Standard	NM_001122898		Approved		uc004cqm.3	P14209	OTTHUMG00000021073	ENST00000381192.3:c.362-1C>T	X.37:g.2644302C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	75	52	0.693333	NM_002414	A6NIW1|O00518|Q6ICV7	Silent	SNP	ENST00000381192.3	37	CCDS14119.1																																																																																			.	.	weak		0.597	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	NM_001122898	Silent
CPNE4	131034	hgsc.bcm.edu	37	3	131624120	131624120	+	Silent	SNP	C	C	G	rs3749263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:131624120C>G	ENST00000512055.1	-	6	2294	c.168G>C	c.(166-168)ggG>ggC	p.G56G	CPNE4_ENST00000511604.1_Silent_p.G56G|CPNE4_ENST00000512332.1_Silent_p.G74G|CPNE4_ENST00000429747.1_Silent_p.G56G|CPNE4_ENST00000502818.1_Silent_p.G74G			Q96A23	CPNE4_HUMAN	copine IV	56	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CAAACCACTGCCCATGAGACT	0.453													C|||	878	0.175319	0.3147	0.0879	5008	,	,		19673	0.1508		0.1103	False		,,,				2504	0.1411				p.G56G		Atlas-SNP	.											.	CPNE4	112	.	0			c.G168C						PASS	.	C		1294,3112	438.2+/-345.2	190,914,1099	133.0	124.0	127.0		168	1.8	1.0	3	dbSNP_107	127	882,7718	198.6+/-242.9	53,776,3471	no	coding-synonymous	CPNE4	NM_130808.1		243,1690,4570	GG,GC,CC		10.2558,29.369,16.7307		56/558	131624120	2176,10830	2203	4300	6503	SO:0001819	synonymous_variant	131034	exon2			CCACTGCCCATGA	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.168G>C	3.37:g.131624120C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	152	89	0.585526	NM_130808	D3DNC5|Q8TEX1	Silent	SNP	ENST00000512055.1	37	CCDS3072.1																																																																																			C|0.834;G|0.166	0.166	strong		0.453	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
SPEF2	79925	hgsc.bcm.edu	37	5	35695844	35695844	+	Silent	SNP	T	T	C	rs78576797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:35695844T>C	ENST00000356031.3	+	14	2137	c.1983T>C	c.(1981-1983)aaT>aaC	p.N661N	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Silent_p.N656N|SPEF2_ENST00000440995.2_Silent_p.N656N	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	661					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)			TAGGTGCTAATGCTGATAAAA	0.323													T|||	104	0.0207668	0.0159	0.0159	5008	,	,		19276	0.002		0.0229	False		,,,				2504	0.0481				p.N661N		Atlas-SNP	.											.	SPEF2	324	.	0			c.T1983C						PASS	.	T		68,3614		1,66,1774	124.0	113.0	116.0		1983	-2.6	0.0	5	dbSNP_132	116	202,7978		3,196,3891	no	coding-synonymous	SPEF2	NM_024867.3		4,262,5665	CC,CT,TT		2.4694,1.8468,2.2762		661/1823	35695844	270,11592	1841	4090	5931	SO:0001819	synonymous_variant	79925	exon14			TGCTAATGCTGAT	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.1983T>C	5.37:g.35695844T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	37	CCDS43309.1																																																																																			T|0.979;C|0.021	0.021	strong		0.323	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
CSMD3	114788	hgsc.bcm.edu	37	8	113237134	113237134	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:113237134C>T	ENST00000297405.5	-	71	11234	c.10990G>A	c.(10990-10992)Gga>Aga	p.G3664R	CSMD3_ENST00000455883.2_Missense_Mutation_p.G3495R|CSMD3_ENST00000352409.3_Missense_Mutation_p.G3594R|CSMD3_ENST00000343508.3_Missense_Mutation_p.G3624R	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3664						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						ACTGAACATCCTGTATACTGT	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G3664R		Atlas-SNP	.											CSMD3_ENST00000343508,right_upper_lobe,carcinoma,0,2	CSMD3	2325	2	0			c.G10990A						scavenged	.						319.0	290.0	300.0					8																	113237134		2203	4300	6503	SO:0001583	missense	114788	exon71			AACATCCTGTATA	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.10990G>A	8.37:g.113237134C>T	ENSP00000297405:p.Gly3664Arg	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	229	3	0.0131004	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262704	0.80358	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.36520	1.59;1.58;1.66;1.25;1.63	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000001	T	0.63343	0.2503	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.964	T	0.65886	-0.6059	10	0.72032	D	0.01	.	19.4694	0.94956	0.0:1.0:0.0:0.0	.	3495;3664;3624	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	R	3624;3664;2934;3495;3594	ENSP00000345799:G3624R;ENSP00000297405:G3664R;ENSP00000341558:G2934R;ENSP00000412263:G3495R;ENSP00000343124:G3594R	ENSP00000297405:G3664R	G	-	1	0	CSMD3	113306310	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.701000	0.84566	2.587000	0.87381	0.591000	0.81541	GGA	.	.	none		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
MKNK2	2872	hgsc.bcm.edu	37	19	2041146	2041146	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2041146C>T	ENST00000591601.1	-	11	1038	c.1003G>A	c.(1003-1005)Gcc>Acc	p.A335T	MKNK2_ENST00000591142.1_Missense_Mutation_p.A79T|MKNK2_ENST00000541165.1_Missense_Mutation_p.A204T|MKNK2_ENST00000591588.1_Missense_Mutation_p.A79T|MKNK2_ENST00000588014.1_Missense_Mutation_p.A79T|MKNK2_ENST00000250896.3_Missense_Mutation_p.A335T|MKNK2_ENST00000309340.7_Missense_Mutation_p.A335T			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	335	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|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)		GAGATGTGGGCCCAGTCCTTG	0.607																																					p.A335T		Atlas-SNP	.											MKNK2_ENST00000250896,NS,carcinoma,+2,2	MKNK2	56	2	0			c.G1003A						scavenged	.						200.0	151.0	168.0					19																	2041146		2203	4300	6503	SO:0001583	missense	2872	exon12			TGTGGGCCCAGTC	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.1003G>A	19.37:g.2041146C>T	ENSP00000467811:p.Ala335Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	178	4	0.0224719	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319608	0.41096	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.64991	-0.13;-0.13;-0.13	3.84	1.57	0.23409	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.180634	0.48286	D	0.000198	T	0.45597	0.1350	L	0.27975	0.815	0.58432	D	0.999997	B;B;B;B	0.22604	0.041;0.007;0.072;0.022	B;B;B;B	0.25405	0.035;0.056;0.06;0.056	T	0.18808	-1.0325	10	0.24483	T	0.36	-10.355	10.9315	0.47220	0.3527:0.6473:0.0:0.0	.	140;335;335;237	Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28	.;MKNK2_HUMAN;.;.	T	335;335;204;275	ENSP00000309485:A335T;ENSP00000250896:A335T;ENSP00000438904:A204T	ENSP00000250896:A335T	A	-	1	0	MKNK2	1992146	1.000000	0.71417	1.000000	0.80357	0.603000	0.37013	2.882000	0.48546	0.246000	0.21394	-0.324000	0.08512	GCC	.	.	none		0.607	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	
IFNL2	282616	hgsc.bcm.edu	37	19	39760191	39760191	+	Missense_Mutation	SNP	A	A	G	rs8103362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39760191A>G	ENST00000331982.5	+	4	389	c.334A>G	c.(334-336)Acc>Gcc	p.T112A		NM_172138.1	NP_742150.1	Q8IZJ0	IFNL2_HUMAN	interferon, lambda 2	112			T -> A (in dbSNP:rs8103362).		defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|mucosal immune response (GO:0002385)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											TCTGGAGGCCACCGCTGACAC	0.642													G|||	1176	0.234824	0.3169	0.2262	5008	,	,		15712	0.0327		0.2256	False		,,,				2504	0.3476				p.T112A		Atlas-SNP	.											.	.	.	.	0			c.A334G						PASS	.	G	ALA/THR	1447,2959	680.2+/-403.8	237,973,993	52.0	58.0	56.0		334	-6.2	0.0	19	dbSNP_116	56	1774,6826	733.4+/-406.9	198,1378,2724	no	missense	IL28A	NM_172138.1	58	435,2351,3717	GG,GA,AA		20.6279,32.8416,24.7655	benign	112/201	39760191	3221,9785	2203	4300	6503	SO:0001583	missense	282616	exon4			GAGGCCACCGCTG	AY129148	CCDS42567.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000183709	ENSG00000183709		"""Interferons"""	18364	protein-coding gene	gene with protein product		607401	"""interleukin 28A"", ""interleukin 28A (interferon, lambda 2)"""	IL28A			Standard	NM_172138		Approved	IL-28A	uc002oku.1	Q8IZJ0		ENST00000331982.5:c.334A>G	19.37:g.39760191A>G	ENSP00000333639:p.Thr112Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_172138	Q45KQ8|Q6VN55|Q8IWL7	Missense_Mutation	SNP	ENST00000331982.5	37	CCDS42567.1	422	0.19322344322344323	141	0.2865853658536585	95	0.26243093922651933	21	0.03671328671328671	165	0.21767810026385223	G	2.131	-0.399201	0.04865	0.328416	0.206279	ENSG00000183709	ENST00000331982	T	0.28069	1.63	3.09	-6.19	0.02078	.	1.433330	0.04280	N	0.343644	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31696	-0.9934	9	0.10377	T	0.69	-0.043	5.726	0.18013	0.5911:0.0:0.1584:0.2504	rs8103362;rs60021767	112	Q8IZJ0	IL28A_HUMAN	A	112	ENSP00000333639:T112A	ENSP00000333639:T112A	T	+	1	0	IL28A	44452031	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.615000	0.00414	-2.156000	0.00790	-0.528000	0.04320	ACC	A|0.795;G|0.205	0.205	strong		0.642	IFNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463833.1	NM_172138	
PSG4	5672	hgsc.bcm.edu	37	19	43699417	43699417	+	Missense_Mutation	SNP	A	A	G	rs3859474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43699417A>G	ENST00000405312.3	-	4	955	c.718T>C	c.(718-720)Tcc>Ccc	p.S240P	PSG4_ENST00000433626.2_Missense_Mutation_p.S147P|PSG4_ENST00000244295.9_Intron	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	240	Ig-like C2-type 2.		S -> P (in dbSNP:rs3859474).		female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				TAGGGCTTGGACAGCTTTGCT	0.448													G|||	3385	0.675919	0.7806	0.5029	5008	,	,		21072	0.9196		0.3748	False		,,,				2504	0.7157				p.G240R		Atlas-SNP	.											.	PSG4	129	.	0			c.G718C						PASS	.	G	PRO/SER,	3115,1289		1142,831,229	226.0	249.0	241.0		718,	0.7	0.0	19	dbSNP_108	241	2884,5706		613,1658,2024	no	missense,intron	PSG4	NM_002780.3,NM_213633.1	74,	1755,2489,2253	GG,GA,AA		33.5739,29.2688,46.1675	,	240/420,	43699417	5999,6995	2202	4295	6497	SO:0001583	missense	5672	exon4			GCTTGGACAGCTT		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.718T>C	19.37:g.43699417A>G	ENSP00000384770:p.Ser240Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	113	44	0.389381	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	1388	0.6355311355311355	400	0.8130081300813008	174	0.48066298342541436	536	0.9370629370629371	278	0.36675461741424803	g	1.545	-0.540857	0.04053	0.707312	0.335739	ENSG00000243137	ENST00000405312;ENST00000433626	T;T	0.56444	0.46;1.62	1.79	0.708	0.18144	Immunoglobulin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00885	-1.115	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20306	-1.0279	8	0.17832	T	0.49	.	3.9233	0.09253	0.44:0.0:0.56:0.0	rs3859474;rs11544957;rs17855784;rs52830368;rs3859474	147;240	E7EX79;Q00888	.;PSG4_HUMAN	P	240;147	ENSP00000384770:S240P;ENSP00000387864:S147P	ENSP00000384770:S240P	S	-	1	0	PSG4	48391257	0.001000	0.12720	0.006000	0.13384	0.002000	0.02628	-0.163000	0.09997	0.114000	0.18032	-0.273000	0.10243	TCC	A|0.397;G|0.603	0.603	strong		0.448	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
MORC3	23515	hgsc.bcm.edu	37	21	37710067	37710067	+	Missense_Mutation	SNP	G	G	A	rs370616843		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:37710067G>A	ENST00000400485.1	+	4	359	c.283G>A	c.(283-285)Gtc>Atc	p.V95I	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	95					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						GAATGGTCATGTCCCAGTTGG	0.348																																					p.V95I		Atlas-SNP	.											.	MORC3	78	.	0			c.G283A						PASS	.	G	ILE/VAL	0,3660		0,0,1830	90.0	79.0	82.0		283	4.3	1.0	21		82	1,8161		0,1,4080	no	missense	MORC3	NM_015358.2	29	0,1,5910	AA,AG,GG		0.0123,0.0,0.0085	possibly-damaging	95/940	37710067	1,11821	1830	4081	5911	SO:0001583	missense	23515	exon4			GGTCATGTCCCAG	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.283G>A	21.37:g.37710067G>A	ENSP00000383333:p.Val95Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908699	0.72868	0.0	1.23E-4	ENSG00000159256	ENST00000400485	D	0.94862	-3.54	5.21	4.33	0.51752	ATPase-like, ATP-binding domain (2);	0.187242	0.45361	D	0.000366	D	0.91533	0.7326	L	0.31664	0.95	0.47698	D	0.999497	B	0.34241	0.444	B	0.42062	0.374	D	0.88791	0.3278	10	0.24483	T	0.36	-11.2373	14.267	0.66126	0.0727:0.0:0.9273:0.0	.	95	Q14149	MORC3_HUMAN	I	95	ENSP00000383333:V95I	ENSP00000383333:V95I	V	+	1	0	MORC3	36631937	1.000000	0.71417	0.998000	0.56505	0.863000	0.49368	6.480000	0.73604	1.323000	0.45263	0.591000	0.81541	GTC	.	.	weak		0.348	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
DRD2	1813	hgsc.bcm.edu	37	11	113283459	113283459	+	Silent	SNP	G	G	A	rs6277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:113283459G>A	ENST00000362072.3	-	7	1301	c.957C>T	c.(955-957)ccC>ccT	p.P319P	DRD2_ENST00000538967.1_Silent_p.P321P|DRD2_ENST00000544518.1_Silent_p.P318P|RP11-159N11.3_ENST00000546284.1_RNA|DRD2_ENST00000535984.1_5'Flank|DRD2_ENST00000542968.1_Silent_p.P319P|DRD2_ENST00000355319.2_Silent_p.P321P|DRD2_ENST00000346454.3_Silent_p.P290P	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	319	Interaction with PPP1R9B. {ECO:0000250}.				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)	CGGGGCTGTCGGGAGTGCTGT	0.617													G|||	1222	0.24401	0.0552	0.3256	5008	,	,		14821	0.0625		0.5437	False		,,,				2504	0.32				p.P319P		Atlas-SNP	.											.	DRD2	98	.	0			c.C957T	GRCh37	CM030215	DRD2	M	rs6277	PASS	.	G	,	628,3774	272.8+/-271.0	49,530,1622	116.0	98.0	104.0		957,870	-9.2	0.0	11	dbSNP_52	104	4685,3907	604.2+/-394.8	1292,2101,903	no	coding-synonymous,coding-synonymous	DRD2	NM_000795.3,NM_016574.3	,	1341,2631,2525	AA,AG,GG		45.4725,14.2662,40.8881	,	319/444,290/415	113283459	5313,7681	2201	4296	6497	SO:0001819	synonymous_variant	1813	exon7			GCTGTCGGGAGTG	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.957C>T	11.37:g.113283459G>A		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	214	207	0.96729	NM_000795	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	37	CCDS8361.1																																																																																			G|0.641;A|0.359	0.359	strong		0.617	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795	
GCAT	23464	hgsc.bcm.edu	37	22	38211287	38211287	+	Splice_Site	SNP	G	G	A	rs200392738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38211287G>A	ENST00000248924.6	+	5	787	c.731G>A	c.(730-732)cGg>cAg	p.R244Q	GCAT_ENST00000323205.6_Splice_Site_p.R270Q	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	244					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	CCCACAGGACGGTGGGACCAT	0.622													G|||	2	0.000399361	0.0	0.0	5008	,	,		18933	0.002		0.0	False		,,,				2504	0.0				p.R270Q		Atlas-SNP	.											.	GCAT	27	.	0			c.G809A						PASS	.	G	GLN/ARG,GLN/ARG	0,4404		0,0,2202	30.0	27.0	28.0		809,731	2.5	1.0	22		28	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	GCAT	NM_001171690.1,NM_014291.3	43,43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	270/446,244/420	38211287	1,13003	2202	4300	6502	SO:0001630	splice_region_variant	23464	exon5			CAGGACGGTGGGA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.731+1G>A	22.37:g.38211287G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	62	0.681319	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.426184	0.83667	0.0	1.16E-4	ENSG00000100116	ENST00000323205;ENST00000248924	D;D	0.90504	-2.68;-2.68	4.68	2.53	0.30540	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.109395	0.64402	D	0.000014	D	0.95831	0.8643	M	0.91038	3.17	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.75020	0.985;0.922	D	0.96264	0.9193	10	0.87932	D	0	-6.0188	14.7411	0.69455	0.0:0.2752:0.7248:0.0	.	270;244	E2QC23;O75600	.;KBL_HUMAN	Q	270;244	ENSP00000371110:R270Q;ENSP00000248924:R244Q	ENSP00000248924:R244Q	R	+	2	0	GCAT	36541233	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.642000	0.74329	0.563000	0.29222	-0.305000	0.09177	CGG	.	.	weak		0.622	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	Missense_Mutation
AIF1	199	hgsc.bcm.edu	37	6	31583931	31583931	+	Intron	SNP	C	C	T	rs2269475	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31583931C>T	ENST00000376059.3	+	4	342				AIF1_ENST00000376049.4_Intron	NM_001623.3	NP_001614.3	P55008	AIF1_HUMAN	allograft inflammatory factor 1						actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cellular response to interferon-gamma (GO:0071346)|inflammatory response (GO:0006954)|microglial cell activation (GO:0001774)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell proliferation (GO:0048662)|phagocytosis, engulfment (GO:0006911)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|Rac protein signal transduction (GO:0016601)|ruffle assembly (GO:0097178)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|ruffle membrane (GO:0032587)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)|ovary(1)	3						TGGTGAGAAACGGGTGATTTG	0.532													C|||	653	0.130391	0.0968	0.1888	5008	,	,		19558	0.128		0.16	False		,,,				2504	0.1063				p.R15W	Ovarian(23;358 734 36938 38933 52312)	Atlas-SNP	.											.	AIF1	13	.	0			c.C43T	GRCh37	CM077912	AIF1	M	rs2269475	PASS	.	C	,TRP/ARG,	315,2703		18,279,1212	158.0	151.0	154.0		,43,	-2.0	0.8	6	dbSNP_100	154	716,4700		51,614,2043	yes	intron,missense,intron	AIF1	NM_001623.3,NM_004847.3,NM_032955.1	,101,	69,893,3255	TT,TC,CC		13.2201,10.4374,12.2243	,,	,15/133,	31583931	1031,7403	1509	2708	4217	SO:0001627	intron_variant	199	exon3			GAGAAACGGGTGA	U19713	CCDS4706.1, CCDS34398.1	6p21.3	2013-01-10			ENSG00000204472	ENSG00000204472		"""EF-hand domain containing"""	352	protein-coding gene	gene with protein product	"""interferon gamma responsive transcript"", ""ionized calcium-binding adapter molecule 1"""	601833				8912632	Standard	NM_032955		Approved	IRT-1, AIF-1, Em:AF129756.17, IBA1	uc003nuy.3	P55008	OTTHUMG00000031246	ENST00000376059.3:c.196+9C>T	6.37:g.31583931C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	177	84	0.474576	NM_004847	A8K406|O43904|Q9UIV4|Q9UKS9	Missense_Mutation	SNP	ENST00000376059.3	37	CCDS4706.1																																																																																			C|0.862;T|0.138	0.138	strong		0.532	AIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076512.3		
MGMT	4255	hgsc.bcm.edu	37	10	131506192	131506192	+	Silent	SNP	C	C	T	rs1803965	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:131506192C>T	ENST00000306010.7	+	3	284	c.252C>T	c.(250-252)ctC>ctT	p.L84L	MGMT_ENST00000462672.1_3'UTR	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	53			L -> F (in dbSNP:rs12917).		cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	CTGCGGTTCTCGGAGGTCCGG	0.607								Direct reversal of damage					C|||	737	0.147165	0.18	0.1988	5008	,	,		16957	0.1032		0.1153	False		,,,				2504	0.1442				p.L84L		Atlas-SNP	.											.	MGMT	32	.	0			c.C252T						PASS	.	C		762,3644	310.0+/-291.3	61,640,1502	67.0	71.0	70.0		252	2.8	0.0	10	dbSNP_89	70	990,7610	214.8+/-254.3	63,864,3373	no	coding-synonymous	MGMT	NM_002412.3		124,1504,4875	TT,TC,CC		11.5116,17.2946,13.4707		84/239	131506192	1752,11254	2203	4300	6503	SO:0001819	synonymous_variant	4255	exon3			GGTTCTCGGAGGT	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.252C>T	10.37:g.131506192C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_002412	Q5VY78	Silent	SNP	ENST00000306010.7	37	CCDS7660.2																																																																																			A|0.000;C|0.859;T|0.140	0.140	strong		0.607	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
MST1L	11223	hgsc.bcm.edu	37	1	17084581	17084581	+	RNA	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17084581T>C	ENST00000455405.2	-	0	308							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GAGAGGCATATGGCTGGGAGA	0.562																																					p.H506R		Atlas-SNP	.											.	.	.	.	0			c.A1517G						PASS	.																																					11223	exon12			GGCATATGGCTGG	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.17084581T>C		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	317	42	0.132492	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	2.857	-0.237075	0.05944	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41396	D	0.000892	T	0.26629	0.0651	.	.	.	.	.	.	B;B	0.15141	0.012;0.001	B;B	0.13407	0.009;0.002	T	0.10660	-1.0620	6	0.24483	T	0.36	.	4.4758	0.11739	0.0:8.0E-4:0.0:0.9992	.	506;532	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	R	501;506;532	.	ENSP00000439273:H506R	H	-	2	0	MST1P9	16957168	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	4.034000	0.57289	0.000000	0.14550	0.000000	0.15137	CAT	.	.	none		0.562	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
JDP2	122953	hgsc.bcm.edu	37	14	75904660	75904660	+	Missense_Mutation	SNP	A	A	G	rs3625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:75904660A>G	ENST00000435893.2	+	2	310	c.37A>G	c.(37-39)Aca>Gca	p.T13A	JDP2_ENST00000559773.1_3'UTR|JDP2_ENST00000267569.5_Missense_Mutation_p.T24A|JDP2_ENST00000419727.2_Missense_Mutation_p.T13A|JDP2_ENST00000437176.1_Missense_Mutation_p.T13A	NM_001135047.1|NM_130469.3	NP_001128519.1|NP_569736.1	Q8WYK2	JDP2_HUMAN	Jun dimerization protein 2	13			T -> A (in dbSNP:rs3625).		negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone deacetylation (GO:0031065)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.0296)	Pseudoephedrine(DB00852)	TTCGGTGACCACAGGCTCCCT	0.652													G|||	3037	0.60643	0.7859	0.4409	5008	,	,		17763	0.6567		0.5239	False		,,,				2504	0.5143				p.T24A		Atlas-SNP	.											.	JDP2	8	.	0			c.A70G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR	3272,1132	389.8+/-327.4	1195,882,125	28.0	32.0	30.0		37,70,37,37	4.7	0.5	14	dbSNP_36	30	4544,4054	546.7+/-385.0	1195,2154,950	yes	missense,missense,missense,missense	JDP2	NM_130469.3,NM_001135049.1,NM_001135048.1,NM_001135047.1	58,58,58,58	2390,3036,1075	GG,GA,AA		47.1505,25.7039,39.8862	benign,benign,benign,benign	13/164,24/175,13/164,13/164	75904660	7816,5186	2202	4299	6501	SO:0001583	missense	122953	exon2			GTGACCACAGGCT	AF111167	CCDS9842.1, CCDS45139.1	14q24.2	2013-01-10		2008-04-10				"""basic leucine zipper proteins"""	17546	protein-coding gene	gene with protein product	"""progesterone receptor co-activator"""	608657				12052888, 9154808, 17545590	Standard	NM_130469		Approved	JUNDM2	uc001xrq.3	Q8WYK2		ENST00000435893.2:c.37A>G	14.37:g.75904660A>G	ENSP00000399587:p.Thr13Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_001135049	J3KN58|O95430|Q9UIE4	Missense_Mutation	SNP	ENST00000435893.2	37	CCDS9842.1	1371	0.6277472527472527	402	0.8170731707317073	185	0.511049723756906	387	0.6765734265734266	397	0.5237467018469657	G	1.845	-0.466478	0.04476	0.742961	0.528495	ENSG00000140044	ENST00000419727;ENST00000437176;ENST00000435893;ENST00000267569	T;T;T;T	0.53640	0.7;0.7;0.7;0.61	5.61	4.72	0.59763	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01168	-0.975	0.52501	P	4.999999999999449E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41770	-0.9490	9	0.02654	T	1	-14.5269	10.7179	0.46023	0.147:0.0:0.853:0.0	rs3625;rs17783072;rs59990027;rs3625	13	Q8WYK2	JDP2_HUMAN	A	13;13;13;24	ENSP00000415558:T13A;ENSP00000409787:T13A;ENSP00000399587:T13A;ENSP00000267569:T24A	ENSP00000267569:T24A	T	+	1	0	JDP2	74974413	1.000000	0.71417	0.525000	0.27900	0.229000	0.25112	7.140000	0.77322	0.749000	0.32854	-0.215000	0.12644	ACA	A|0.386;G|0.614	0.614	strong		0.652	JDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415505.1	NM_130469	
FBN3	84467	hgsc.bcm.edu	37	19	8159362	8159362	+	Missense_Mutation	SNP	G	G	T	rs7245429	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8159362G>T	ENST00000600128.1	-	47	6287	c.5873C>A	c.(5872-5874)cCt>cAt	p.P1958H	FBN3_ENST00000601739.1_Missense_Mutation_p.P1958H|FBN3_ENST00000270509.2_Missense_Mutation_p.P1958H			Q75N90	FBN3_HUMAN	fibrillin 3	1958	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		P -> H (in dbSNP:rs7245429).			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						CTGGAAGCCAGGGGGACAGAT	0.587													G|||	2433	0.485823	0.2209	0.5403	5008	,	,		20228	0.7331		0.4006	False		,,,				2504	0.638				p.P1958H		Atlas-SNP	.											.	FBN3	300	.	0			c.C5873A						PASS	.	G	HIS/PRO	1034,3372	379.7+/-323.4	134,766,1303	77.0	58.0	64.0		5873	1.4	0.6	19	dbSNP_116	64	3332,5268	494.1+/-373.7	654,2024,1622	yes	missense	FBN3	NM_032447.3	77	788,2790,2925	TT,TG,GG		38.7442,23.468,33.5691	probably-damaging	1958/2810	8159362	4366,8640	2203	4300	6503	SO:0001583	missense	84467	exon46			AAGCCAGGGGGAC		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.5873C>A	19.37:g.8159362G>T	ENSP00000470498:p.Pro1958His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	1031|1031	0.47206959706959706|0.47206959706959706	114|114	0.23170731707317074|0.23170731707317074	190|190	0.5248618784530387|0.5248618784530387	422|422	0.7377622377622378|0.7377622377622378	305|305	0.4023746701846966|0.4023746701846966	G|G	18.00|18.00	3.525861|3.525861	0.64860|0.64860	0.23468|0.23468	0.387442|0.387442	ENSG00000142449|ENSG00000142449	ENST00000341066|ENST00000270509	.|D	.|0.92199	.|-2.99	4.69|4.69	1.38|1.38	0.22167|0.22167	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|0.061519	.|0.64402	.|U	.|0.000003	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.55213|0.55213	1.73|1.73	0.19945|0.19945	P|P	0.9999416979|0.9999416979	.|D	.|0.53151	.|0.958	.|P	.|0.50440	.|0.641	T|T	0.49725|0.49725	-0.8909|-0.8909	5|9	0.34782|0.66056	T|D	0.22|0.02	.|.	9.8691|9.8691	0.41164|0.41164	0.2158:0.0:0.7842:0.0|0.2158:0.0:0.7842:0.0	rs7245429;rs17395421;rs52835316;rs60633933;rs7245429|rs7245429;rs17395421;rs52835316;rs60633933;rs7245429	.|1958	.|Q75N90	.|FBN3_HUMAN	M|H	78|1958	.|ENSP00000270509:P1958H	ENSP00000341317:L78M|ENSP00000270509:P1958H	L|P	-|-	1|2	2|0	FBN3|FBN3	8065362|8065362	1.000000|1.000000	0.71417|0.71417	0.566000|0.566000	0.28421|0.28421	0.913000|0.913000	0.54294|0.54294	5.137000|5.137000	0.64789|0.64789	0.085000|0.085000	0.17107|0.17107	-0.355000|-0.355000	0.07637|0.07637	CTG|CCT	G|0.603;T|0.397	0.397	strong		0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
AFMID	125061	hgsc.bcm.edu	37	17	76198587	76198587	+	Silent	SNP	A	A	G	rs72897838	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76198587A>G	ENST00000327898.5	+	3	171	c.162A>G	c.(160-162)acA>acG	p.T54T	AFMID_ENST00000409257.5_Silent_p.T54T|AFMID_ENST00000588800.1_Intron|AFMID_ENST00000591952.1_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	36	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	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	
SLC43A3	29015	hgsc.bcm.edu	37	11	57177593	57177593	+	Splice_Site	SNP	A	A	G	rs62640922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57177593A>G	ENST00000395123.2	-	12	1366	c.1062T>C	c.(1060-1062)ggT>ggC	p.G354G	SLC43A3_ENST00000529554.1_Splice_Site_p.G354G|SLC43A3_ENST00000352187.1_Splice_Site_p.G354G|SLC43A3_ENST00000395124.1_Splice_Site_p.G354G|SLC43A3_ENST00000533524.1_Splice_Site_p.G367G|RP11-872D17.8_ENST00000529411.1_5'Flank	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	354					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						AAGTGGAGGAACCTGGGCGAA	0.597													A|||	76	0.0151757	0.0023	0.0187	5008	,	,		18859	0.0		0.0348	False		,,,				2504	0.0256				p.G354G		Atlas-SNP	.											.	SLC43A3	54	.	0			c.T1062C						PASS	.	A	,,	35,4365		0,35,2165	48.0	37.0	40.0		1062,1062,1062	-3.3	0.0	11	dbSNP_129	40	358,8232		4,350,3941	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SLC43A3	NM_014096.2,NM_017611.2,NM_199329.1	,,	4,385,6106	GG,GA,AA		4.1676,0.7955,3.0254	,,	354/492,354/492,354/492	57177593	393,12597	2200	4295	6495	SO:0001630	splice_region_variant	29015	exon12			GGAGGAACCTGGG	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"""Solute carriers"""	17466	protein-coding gene	gene with protein product	"""likely ortholog of mouse embryonic epithelial gene 1"""					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.1061-1T>C	11.37:g.57177593A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_017611	B4DNR8|E7EQD2|Q9NSS4	Silent	SNP	ENST00000395123.2	37	CCDS7956.1																																																																																			A|0.975;G|0.025	0.025	strong		0.597	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611	Silent
KIAA1211	57482	hgsc.bcm.edu	37	4	57180616	57180616	+	Silent	SNP	G	G	C	rs11723379	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57180616G>C	ENST00000504228.1	+	6	1053	c.948G>C	c.(946-948)gcG>gcC	p.A316A	KIAA1211_ENST00000264229.6_Silent_p.A316A|KIAA1211_ENST00000541073.1_Silent_p.A309A			Q6ZU35	K1211_HUMAN	KIAA1211	316	Glu-rich.									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)					GCCTGGAGGCGGAGGAGGAGC	0.741													C|||	1512	0.301917	0.3926	0.2853	5008	,	,		13558	0.0694		0.4095	False		,,,				2504	0.32				p.A316A		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	0			c.G948C						PASS	.	C		1210,2614		228,754,930	5.0	7.0	6.0		948	-10.4	0.0	4	dbSNP_120	6	2621,5055		547,1527,1764	no	coding-synonymous	KIAA1211	NM_020722.1		775,2281,2694	CC,CG,GG		34.1454,31.6423,33.313		316/1234	57180616	3831,7669	1912	3838	5750	SO:0001819	synonymous_variant	57482	exon8			GGAGGCGGAGGAG	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.948G>C	4.37:g.57180616G>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.702;C|0.298	0.298	strong		0.741	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
Unknown	0	hgsc.bcm.edu	37	1	16134072	16134072	+	IGR	SNP	C	C	T	rs61744357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16134072C>T								FBLIM1 (20983 upstream) : RP11-169K16.9 (26487 downstream)																							TCCACTAATtcctcctcttcc	0.507													C|||	732	0.146166	0.3638	0.0965	5008	,	,		17878	0.0099		0.0994	False		,,,				2504	0.0757				p.E25K		Atlas-SNP	.											.	.	.	.	0			c.G73A						PASS	.	C	LYS/GLU	1490,2916	478.8+/-358.3	268,954,981	112.0	108.0	109.0		73	1.9	1.0	1	dbSNP_129	109	1036,7564	220.1+/-257.9	64,908,3328	yes	missense	UQCRHL	NM_001089591.1	56	332,1862,4309	TT,TC,CC		12.0465,33.8175,19.4218	probably-damaging	25/92	16134072	2526,10480	2203	4300	6503	SO:0001628	intergenic_variant	0	exon1			CTAATTCCTCCTC																													1.37:g.16134072C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001089591		Missense_Mutation	SNP		37																																																																																				C|0.854;T|0.146	0.146	strong	0	0.507								
ROBO4	54538	hgsc.bcm.edu	37	11	124767125	124767125	+	Silent	SNP	G	G	A	rs73016370	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124767125G>A	ENST00000306534.3	-	2	588	c.103C>T	c.(103-105)Cta>Tta	p.L35L	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Intron	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	46	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	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	
CCDC17	149483	hgsc.bcm.edu	37	1	46086077	46086077	+	Missense_Mutation	SNP	C	C	T	rs3014246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46086077C>T	ENST00000528266.1	-	13	1886	c.1739G>A	c.(1738-1740)aGc>aAc	p.S580N	CCDC17_ENST00000343901.2_Missense_Mutation_p.S548N|CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000421127.2_Missense_Mutation_p.S571N|CCDC17_ENST00000445048.2_Missense_Mutation_p.S68N			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	580			S -> N (in dbSNP:rs3014246). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					GGTGAGGAAGCTGGCTTCCAG	0.522													T|||	3438	0.686502	0.7292	0.6542	5008	,	,		22464	0.6925		0.7207	False		,,,				2504	0.6104				p.S580N		Atlas-SNP	.											.	CCDC17	54	.	0			c.G1739A						PASS	.	T	ASN/SER,ASN/SER	3277,1127	390.3+/-327.6	1223,831,148	26.0	27.0	26.0		1712,1739	-0.8	0.0	1	dbSNP_101	26	6083,2517	392.7+/-344.1	2165,1753,382	yes	missense,missense	CCDC17	NM_001190182.1,NM_001114938.2	46,46	3388,2584,530	TT,TC,CC		29.2674,25.5904,28.0221	benign,benign	571/614,580/623	46086077	9360,3644	2202	4300	6502	SO:0001583	missense	149483	exon13			AGGAAGCTGGCTT		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1739G>A	1.37:g.46086077C>T	ENSP00000432172:p.Ser580Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	1542	0.7060439560439561	358	0.7276422764227642	249	0.6878453038674033	394	0.6888111888111889	541	0.7137203166226913	T	0.533	-0.856824	0.02630	0.744096	0.707326	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266;ENST00000445048	T;T;T;T	0.53640	2.25;2.25;2.25;0.61	4.86	-0.827	0.10802	.	.	.	.	.	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.46762	-0.9168	8	0.07990	T	0.79	.	6.0695	0.19881	0.0:0.4992:0.1427:0.3581	rs3014246;rs3818786;rs59744193	580;571;68	Q96LX7;Q96LX7-5;Q96LX7-3	CCD17_HUMAN;.;.	N	571;548;580;68	ENSP00000389415:S571N;ENSP00000341451:S548N;ENSP00000432172:S580N;ENSP00000411335:S68N	ENSP00000341451:S548N	S	-	2	0	CCDC17	45858664	0.005000	0.15991	0.012000	0.15200	0.006000	0.05464	-0.302000	0.08221	-0.505000	0.06568	-0.254000	0.11334	AGC	C|0.286;T|0.714	0.714	strong		0.522	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
PIWIL1	9271	hgsc.bcm.edu	37	12	130841638	130841638	+	Missense_Mutation	SNP	G	G	A	rs1106042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	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		
ZNF790	388536	hgsc.bcm.edu	37	19	37310344	37310344	+	Missense_Mutation	SNP	T	T	C	rs3745775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37310344T>C	ENST00000356725.4	-	5	1022	c.902A>G	c.(901-903)cAg>cGg	p.Q301R	CTD-2162K18.5_ENST00000587278.1_RNA|CTD-2162K18.5_ENST00000588906.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	301			Q -> R (in dbSNP:rs3745775). {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)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATGAATTCTCTGATGTCGAGT	0.383													T|||	1455	0.290535	0.2988	0.2161	5008	,	,		19923	0.2232		0.2922	False		,,,				2504	0.3998				p.Q301R		Atlas-SNP	.											.	ZNF790	89	.	0			c.A902G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1261,3145	425.7+/-340.9	183,895,1125	55.0	57.0	56.0		902,902,902,902	2.1	0.2	19	dbSNP_107	56	2337,6263	385.3+/-341.4	335,1667,2298	no	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	43,43,43,43	518,2562,3423	CC,CT,TT		27.1744,28.6201,27.6642	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	301/637,301/637,301/637,301/637	37310344	3598,9408	2203	4300	6503	SO:0001583	missense	388536	exon5			ATTCTCTGATGTC	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"""Zinc fingers, C2H2-type"", ""-"""	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.902A>G	19.37:g.37310344T>C	ENSP00000349161:p.Gln301Arg	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	569	0.26053113553113555	152	0.3089430894308943	89	0.24585635359116023	121	0.21153846153846154	207	0.27308707124010556	T	13.67	2.307549	0.40795	0.286201	0.271744	ENSG00000197863	ENST00000356725	T	0.17691	2.26	3.14	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12831	0.26	0.58432	P	1.0000000000287557E-6	B	0.23185	0.081	B	0.18263	0.021	T	0.44907	-0.9297	8	0.52906	T	0.07	.	7.2311	0.26043	0.0:0.1139:0.0:0.8861	rs3745775;rs17846550;rs17859625;rs52814390;rs3745775	301	Q6PG37	ZN790_HUMAN	R	301	ENSP00000349161:Q301R	ENSP00000349161:Q301R	Q	-	2	0	ZNF790	42002184	0.002000	0.14202	0.207000	0.23584	0.976000	0.68499	0.644000	0.24766	0.425000	0.26087	0.402000	0.26972	CAG	T|0.723;C|0.277	0.277	strong		0.383	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894	
KIF2C	11004	hgsc.bcm.edu	37	1	45224998	45224998	+	Missense_Mutation	SNP	A	A	C	rs4342887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45224998A>C	ENST00000372224.4	+	14	1458	c.1345A>C	c.(1345-1347)Atc>Ctc	p.I449L	RP11-269F19.2_ENST00000428791.1_RNA|RP11-269F19.2_ENST00000440985.1_RNA|KIF2C_ENST00000372222.3_Missense_Mutation_p.I336L|KIF2C_ENST00000372217.1_Missense_Mutation_p.I395L|KIF2C_ENST00000372218.4_Missense_Mutation_p.I408L	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	449	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		I -> L (in dbSNP:rs4342887). {ECO:0000269|PubMed:12383881, ECO:0000269|PubMed:9434124, ECO:0000269|Ref.5}.		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)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|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)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					CATCAAGATGATCGACATGGG	0.547													A|||	1017	0.203075	0.1808	0.2507	5008	,	,		21901	0.2857		0.1382	False		,,,				2504	0.181				p.I449L		Atlas-SNP	.											.	KIF2C	68	.	0			c.A1345C						PASS	.	A	LEU/ILE	841,3565	332.0+/-302.3	82,677,1444	111.0	89.0	97.0		1345	4.7	1.0	1	dbSNP_111	97	1449,7151	276.9+/-292.6	128,1193,2979	yes	missense	KIF2C	NM_006845.3	5	210,1870,4423	CC,CA,AA		16.8488,19.0876,17.6073	benign	449/726	45224998	2290,10716	2203	4300	6503	SO:0001583	missense	11004	exon14			AAGATGATCGACA	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.1345A>C	1.37:g.45224998A>C	ENSP00000361298:p.Ile449Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	122	46	0.377049	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	426	0.19505494505494506	92	0.18699186991869918	73	0.20165745856353592	151	0.263986013986014	110	0.14511873350923482	A	18.34	3.603032	0.66445	0.190876	0.168488	ENSG00000142945	ENST00000372224;ENST00000372218;ENST00000372222;ENST00000372217	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.87	4.72	0.59763	Kinesin, motor domain (4);	0.179339	0.49916	N	0.000140	T	0.00012	0.0000	N	0.13352	0.335	0.09310	P	0.999999790191	B;B;B	0.21520	0.002;0.019;0.057	B;B;B	0.37015	0.155;0.044;0.239	T	0.15809	-1.0424	9	0.66056	D	0.02	.	13.045	0.58920	0.8655:0.1345:0.0:0.0	rs4342887;rs59548070;rs4342887	408;395;449	B7Z6Q6;Q99661-2;Q99661	.;.;KIF2C_HUMAN	L	449;408;336;395	ENSP00000361298:I449L;ENSP00000361292:I408L;ENSP00000361296:I336L;ENSP00000361291:I395L	ENSP00000361291:I395L	I	+	1	0	KIF2C	44997585	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	5.178000	0.65037	1.017000	0.39495	0.533000	0.62120	ATC	A|0.816;C|0.184	0.184	strong		0.547	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
CKAP2L	150468	hgsc.bcm.edu	37	2	113520129	113520129	+	Missense_Mutation	SNP	G	G	A	rs36093393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113520129G>A	ENST00000302450.6	-	2	133	c.55C>T	c.(55-57)Ctt>Ttt	p.L19F	CKAP2L_ENST00000541405.1_5'UTR|CKAP2L_ENST00000481732.1_5'UTR	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	19			L -> F (in dbSNP:rs36093393).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TACTCCTGAAGCTTTCTCTGC	0.398													G|||	165	0.0329473	0.0053	0.062	5008	,	,		19482	0.0		0.0825	False		,,,				2504	0.0327				p.L19F		Atlas-SNP	.											.	CKAP2L	54	.	0			c.C55T						PASS	.	G	PHE/LEU	75,4331	65.3+/-102.7	0,75,2128	165.0	137.0	147.0		55	5.2	1.0	2	dbSNP_126	147	738,7862	179.2+/-228.4	36,666,3598	yes	missense	CKAP2L	NM_152515.3	22	36,741,5726	AA,AG,GG		8.5814,1.7022,6.251	probably-damaging	19/746	113520129	813,12193	2203	4300	6503	SO:0001583	missense	150468	exon2			CCTGAAGCTTTCT	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.55C>T	2.37:g.113520129G>A	ENSP00000305204:p.Leu19Phe	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	89	0.04075091575091575	4	0.008130081300813009	27	0.07458563535911603	0	0.0	58	0.07651715039577836	G	21.4	4.139749	0.77775	0.017022	0.085814	ENSG00000169607	ENST00000302450	T	0.20200	2.09	5.16	5.16	0.70880	.	0.000000	0.46442	D	0.000291	T	0.02267	0.0070	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00111	-1.2045	10	0.87932	D	0	-4.5155	14.0027	0.64444	0.0:0.0:1.0:0.0	rs36093393	19	Q8IYA6	CKP2L_HUMAN	F	19	ENSP00000305204:L19F	ENSP00000305204:L19F	L	-	1	0	CKAP2L	113236600	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	4.879000	0.63100	2.692000	0.91855	0.561000	0.74099	CTT	G|0.946;A|0.054	0.054	strong		0.398	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
PRKCG	5582	hgsc.bcm.edu	37	19	54394965	54394965	+	Silent	SNP	T	T	C	rs3745406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54394965T>C	ENST00000263431.3	+	6	849	c.567T>C	c.(565-567)aaT>aaC	p.N189N	PRKCG_ENST00000542049.1_Silent_p.N76N|PRKCG_ENST00000536044.1_Silent_p.N189N|PRKCG_ENST00000540413.1_Silent_p.N189N	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	189	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.N189N(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TGGACCCCAATGGTCTCTCTG	0.552													T|||	1650	0.329473	0.1702	0.415	5008	,	,		15447	0.2946		0.4195	False		,,,				2504	0.4274				p.N189N		Atlas-SNP	.											PRKCG_ENST00000540413,NS,carcinoma,0,1	PRKCG	246	1	1	Substitution - coding silent(1)	stomach(1)	c.T567C						PASS	.	T		982,3424	369.8+/-319.3	112,758,1333	146.0	134.0	139.0		567	-1.7	1.0	19	dbSNP_107	139	3519,5081	513.4+/-378.2	707,2105,1488	no	coding-synonymous	PRKCG	NM_002739.3		819,2863,2821	CC,CT,TT		40.9186,22.2878,34.6071		189/698	54394965	4501,8505	2203	4300	6503	SO:0001819	synonymous_variant	5582	exon6			CCCCAATGGTCTC	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.567T>C	19.37:g.54394965T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	37	CCDS12867.1																																																																																			T|0.673;C|0.327	0.327	strong		0.552	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
FGD6	55785	hgsc.bcm.edu	37	12	95604290	95604290	+	Missense_Mutation	SNP	T	T	C	rs10507047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:95604290T>C	ENST00000343958.4	-	2	993	c.770A>G	c.(769-771)cAg>cGg	p.Q257R	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.Q257R|FGD6_ENST00000546711.1_Missense_Mutation_p.Q257R	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	257			Q -> R (in dbSNP:rs10507047).		actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|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.Q257R(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						ACTGTCATCCTGGCAAGTTTC	0.393													T|||	644	0.128594	0.0983	0.1571	5008	,	,		20012	0.2331		0.0775	False		,,,				2504	0.0941				p.Q257R		Atlas-SNP	.											FGD6,NS,carcinoma,0,2	FGD6	127	2	1	Substitution - Missense(1)	prostate(1)	c.A770G						PASS	.	T	ARG/GLN	422,3984	204.8+/-226.9	19,384,1800	73.0	73.0	73.0		770	4.8	0.2	12	dbSNP_119	73	836,7764	190.4+/-236.9	45,746,3509	yes	missense	FGD6	NM_018351.3	43	64,1130,5309	CC,CT,TT		9.7209,9.5778,9.6725	possibly-damaging	257/1431	95604290	1258,11748	2203	4300	6503	SO:0001583	missense	55785	exon2			TCATCCTGGCAAG	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.770A>G	12.37:g.95604290T>C	ENSP00000344446:p.Gln257Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	307	0.14056776556776557	51	0.10365853658536585	58	0.16022099447513813	139	0.243006993006993	59	0.07783641160949868	T	5.000	0.185724	0.09495	0.095778	0.097209	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.71222	-0.45;-0.55;-0.5	5.99	4.85	0.62838	.	0.000000	0.46442	D	0.000293	T	0.00039	0.0001	M	0.62723	1.935	0.80722	P	0.0	P	0.35077	0.483	B	0.27887	0.084	T	0.07888	-1.0749	9	0.49607	T	0.09	-6.0663	7.7203	0.28729	0.0:0.0732:0.1495:0.7773	rs10507047;rs52818706;rs61586134;rs10507047	257	Q6ZV73	FGD6_HUMAN	R	257	ENSP00000344446:Q257R;ENSP00000450342:Q257R;ENSP00000449005:Q257R	ENSP00000344446:Q257R	Q	-	2	0	FGD6	94128421	0.311000	0.24536	0.174000	0.22961	0.090000	0.18270	1.955000	0.40372	1.093000	0.41377	0.533000	0.62120	CAG	T|0.842;C|0.158	0.158	strong		0.393	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
OR2A14	135941	hgsc.bcm.edu	37	7	143826697	143826697	+	Missense_Mutation	SNP	C	C	G	rs2961161	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	220	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	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		
KIAA1217	56243	hgsc.bcm.edu	37	10	24832885	24832885	+	Silent	SNP	C	C	T	rs3748218	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24832885C>T	ENST00000376454.3	+	19	4716	c.4686C>T	c.(4684-4686)acC>acT	p.T1562T	KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Silent_p.T1245T|KIAA1217_ENST00000458595.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1562					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AGGACGCGACCGATGACCAGT	0.483													C|||	1397	0.278954	0.3343	0.2233	5008	,	,		19554	0.3988		0.1521	False		,,,				2504	0.2505				p.T1562T		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C4686T						PASS	.	C	,,	1394,3012	455.5+/-351.0	230,934,1039	90.0	97.0	95.0		,,4686	-10.9	0.0	10	dbSNP_107	95	1245,7355	246.5+/-274.9	85,1075,3140	no	intron,intron,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	315,2009,4179	TT,TC,CC		14.4767,31.6387,20.2906	,,	,,1562/1944	24832885	2639,10367	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			CGCGACCGATGAC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4686C>T	10.37:g.24832885C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			C|0.774;T|0.226	0.226	strong		0.483	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
ZNF273	10793	hgsc.bcm.edu	37	7	64388472	64388472	+	Missense_Mutation	SNP	C	C	A	rs62455581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:64388472C>A	ENST00000476120.1	+	4	837	c.766C>A	c.(766-768)Cat>Aat	p.H256N	ZNF273_ENST00000319636.5_Missense_Mutation_p.H191N|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	256					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(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TAAGATAATTCATCCTGAAGT	0.333													C|||	211	0.0421326	0.0015	0.0331	5008	,	,		18522	0.128		0.0388	False		,,,				2504	0.0184				p.H256N	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.C766A						PASS	.	C	ASN/HIS	53,4353		0,53,2150	48.0	53.0	51.0		766	1.2	0.0	7	dbSNP_129	51	399,8197		13,373,3912	no	missense	ZNF273	NM_021148.2	68	13,426,6062	AA,AC,CC		4.6417,1.2029,3.4764	benign	256/570	64388472	452,12550	2203	4298	6501	SO:0001583	missense	10793	exon4			ATAATTCATCCTG	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"""Zinc fingers, C2H2-type"", ""-"""	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.766C>A	7.37:g.64388472C>A	ENSP00000418719:p.His256Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	114	0.0521978021978022	1	0.0020325203252032522	8	0.022099447513812154	72	0.1258741258741259	33	0.04353562005277045	.	14.01	2.407294	0.42715	0.012029	0.046417	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.67345	-0.26;-0.26	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02342	0.0072	H	0.95611	3.695	0.29812	P	0.831521	B	0.18610	0.029	B	0.31812	0.136	T	0.56294	-0.8003	8	0.66056	D	0.02	.	7.3527	0.26700	0.0:1.0:0.0:0.0	rs62455581	256	Q14593	ZN273_HUMAN	N	256;191	ENSP00000418719:H256N;ENSP00000324518:H191N	ENSP00000324518:H191N	H	+	1	0	ZNF273	64025907	0.953000	0.32496	0.014000	0.15608	0.013000	0.08279	2.831000	0.48144	0.202000	0.20498	0.205000	0.17691	CAT	C|0.962;A|0.038	0.038	strong		0.333	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
ZNF275	10838	hgsc.bcm.edu	37	X	152613112	152613112	+	Silent	SNP	C	C	T	rs7066295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:152613112C>T	ENST00000421401.3	+	4	1146	c.969C>T	c.(967-969)tgC>tgT	p.C323C	ZNF275_ENST00000370251.3_Splice_Site_p.C323C|ZNF275_ENST00000370249.2_Silent_p.C270C|ZNF275_ENST00000440091.1_Silent_p.C353C			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	323					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(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTACGCCTGCGGCCAGTGCG	0.682													C|||	2726	0.722119	0.6604	0.5692	3775	,	,		12575	0.5992		0.3827	False		,,,				2504	0.4796				p.C323C		Atlas-SNP	.											.	ZNF275	44	.	0			c.C969T						PASS	.	C		3033,788		1033,516,451,78,116	15.0	17.0	16.0		969	-1.7	0.0	X	dbSNP_116	16	3384,3332		617,1232,918,578,944	no	coding-synonymous-near-splice	ZNF275	NM_001080485.3		1650,1748,1369,656,1060	TT,TC,T,CC,C		49.6129,20.6229,39.1003		323/330	152613112	6417,4120	2194	4289	6483	SO:0001819	synonymous_variant	10838	exon4			CGCCTGCGGCCAG	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.969C>T	X.37:g.152613112C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001080485	A6NE92	Silent	SNP	ENST00000421401.3	37																																																																																				C|0.293;T|0.707	0.707	strong		0.682	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
MACROD1	28992	hgsc.bcm.edu	37	11	63767186	63767186	+	Silent	SNP	A	A	G	rs709594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	22	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	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	
CAPN1	823	hgsc.bcm.edu	37	11	64981871	64981871	+	IGR	SNP	G	G	C	rs61742578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64981871G>C	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		TGCTGGTGGGGGCTGCCGTGT	0.642													G|||	145	0.0289537	0.0401	0.0303	5008	,	,		14853	0.0		0.0487	False		,,,				2504	0.0225				p.G152G		Atlas-SNP	.											.	SLC22A20	36	.	0			c.G456C						PASS	.	G		133,3887		2,129,1879	26.0	30.0	29.0		456	-5.4	0.9	11	dbSNP_129	29	425,7911		12,401,3755	no	coding-synonymous	SLC22A20	NM_001004326.4		14,530,5634	CC,CG,GG		5.0984,3.3085,4.516		152/350	64981871	558,11798	2010	4168	6178	SO:0001628	intergenic_variant	440044	exon2			GGTGGGGGCTGCC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981871G>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_001004326	Q2TTR0|Q6DHV4	Silent	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.967;C|0.033	0.033	strong		0.642	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
RREB1	6239	hgsc.bcm.edu	37	6	7247344	7247344	+	Missense_Mutation	SNP	C	C	A	rs35742417	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7247344C>A	ENST00000349384.6	+	11	4810	c.4496C>A	c.(4495-4497)tCc>tAc	p.S1499Y	RREB1_ENST00000379938.2_Missense_Mutation_p.S1554Y|RREB1_ENST00000379933.3_Missense_Mutation_p.S1499Y|RREB1_ENST00000334984.6_Intron	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1499			S -> Y (in dbSNP:rs35742417).		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)	p.S1499Y(1)		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)				AAGACAGACTCCCCCAAAAGC	0.617													C|||	638	0.127396	0.239	0.0908	5008	,	,		17771	0.0357		0.161	False		,,,				2504	0.0624				p.S1554Y		Atlas-SNP	.											RREB1,NS,carcinoma,0,1	RREB1	242	1	1	Substitution - Missense(1)	stomach(1)	c.C4661A						scavenged	.	C	TYR/SER,TYR/SER,,TYR/SER	897,3509	329.3+/-301.0	101,695,1407	74.0	71.0	72.0		4496,4661,,4496	3.4	1.0	6	dbSNP_126	72	1381,7219	251.8+/-278.1	104,1173,3023	yes	missense,missense,intron,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	144,144,,144	205,1868,4430	AA,AC,CC		16.0581,20.3586,17.515	benign,benign,,benign	1499/1688,1554/1743,,1499/1688	7247344	2278,10728	2203	4300	6503	SO:0001583	missense	6239	exon12			CAGACTCCCCCAA	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.4496C>A	6.37:g.7247344C>A	ENSP00000305560:p.Ser1499Tyr	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	297	0.13598901098901098	105	0.21341463414634146	35	0.09668508287292818	25	0.043706293706293704	132	0.1741424802110818	C	11.75	1.731099	0.30684	0.203586	0.160581	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.08193	3.12;3.12;3.12	5.24	3.42	0.39159	.	0.762218	0.11459	N	0.561966	T	0.02727	0.0082	L	0.40543	1.245	0.44798	P	0.0021999999999999797	B;P	0.36315	0.07;0.547	B;B	0.37888	0.123;0.26	T	0.44528	-0.9322	9	0.41790	T	0.15	-28.114	4.3196	0.11011	0.1154:0.4061:0.3851:0.0934	rs35742417;rs61234629	1499;1554	Q92766;Q92766-2	RREB1_HUMAN;.	Y	1499;1554;1499	ENSP00000369265:S1499Y;ENSP00000369270:S1554Y;ENSP00000305560:S1499Y	ENSP00000305560:S1499Y	S	+	2	0	RREB1	7192343	0.999000	0.42202	0.963000	0.40424	0.943000	0.58893	2.107000	0.41844	1.215000	0.43411	-0.254000	0.11334	TCC	C|0.843;A|0.157	0.157	strong		0.617	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
SLC26A8	116369	hgsc.bcm.edu	37	6	35923246	35923246	+	Missense_Mutation	SNP	T	T	C	rs2295852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:35923246T>C	ENST00000490799.1	-	17	2268	c.1915A>G	c.(1915-1917)Att>Gtt	p.I639V	SLC26A8_ENST00000355574.2_Missense_Mutation_p.I639V|SLC26A8_ENST00000394602.2_Missense_Mutation_p.I534V	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						ATCAGGTTAATGGAGGATGCT	0.463													N|||	2041	0.407548	0.6967	0.2867	5008	,	,		21471	0.2758		0.3529	False		,,,				2504	0.2945				p.I639V		Atlas-SNP	.											SLC26A8,rectum,carcinoma,0,1	SLC26A8	95	1	0			c.A1915G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE	2807,1599	496.2+/-363.5	886,1035,282	198.0	191.0	193.0		1915,1915,1600	-5.0	0.0	6	dbSNP_100	193	3003,5597	664.5+/-402.2	551,1901,1848	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	29,29,29	1437,2936,2130	CC,CT,TT		34.9186,36.2914,44.6717	benign,benign,benign	639/971,639/971,534/866	35923246	5810,7196	2203	4300	6503	SO:0001583	missense	116369	exon17			GGTTAATGGAGGA	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.1915A>G	6.37:g.35923246T>C	ENSP00000417638:p.Ile639Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	835	0.3823260073260073	322	0.6544715447154471	106	0.292817679558011	152	0.26573426573426573	255	0.33641160949868076	C	3.950	-0.012529	0.07727	0.637086	0.349186	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	D;D;D	0.94862	-3.16;-3.54;-3.16	5.01	-4.99	0.03010	Sulphate transporter/antisigma-factor antagonist STAS (3);	1.172630	0.06260	N	0.693768	T	0.72581	0.3478	L	0.31752	0.955	0.80722	P	0.0	B;B;B	0.15141	0.0;0.012;0.0	B;B;B	0.14023	0.001;0.01;0.001	T	0.67166	-0.5739	9	0.11485	T	0.65	.	2.4043	0.04409	0.1092:0.3104:0.1431:0.4373	rs2295852;rs17706470;rs52831325;rs58070509;rs2295852	639;534;221	Q96RN1;Q96RN1-2;Q96RN1-3	S26A8_HUMAN;.;.	V	639;534;639	ENSP00000417638:I639V;ENSP00000378100:I534V;ENSP00000347778:I639V	ENSP00000347778:I639V	I	-	1	0	SLC26A8	36031224	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.320000	0.02700	-1.280000	0.02402	-2.418000	0.00219	ATT	T|0.572;C|0.428	0.428	strong		0.463	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
SPIB	6689	hgsc.bcm.edu	37	19	50926265	50926265	+	Missense_Mutation	SNP	G	G	C	rs113934432|rs11546996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50926265G>C	ENST00000595883.1	+	4	335	c.310G>C	c.(310-312)Gca>Cca	p.A104P	SPIB_ENST00000597855.1_Missense_Mutation_p.A104P|SPIB_ENST00000270632.7_Missense_Mutation_p.A104P|CTD-2545M3.6_ENST00000599632.1_Missense_Mutation_p.C238S|SPIB_ENST00000596074.1_Intron|SPIB_ENST00000439922.2_Intron	NM_001243999.1|NM_001244000.1|NM_003121.4	NP_001230928.1|NP_001230929.1|NP_003112.2	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	104			A -> P (in dbSNP:rs11546996). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)	14		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		TGGCCTCCCTGCATACCCCAC	0.642													G|||	2349	0.46905	0.2534	0.6268	5008	,	,		13228	0.2143		0.7704	False		,,,				2504	0.6012				p.A104P		Atlas-SNP	.											.	SPIB	23	.	0			c.G310C						PASS	.	G	PRO/ALA	1316,3070		281,754,1158	24.0	26.0	25.0		310	-2.1	0.0	19	dbSNP_120	25	5995,2561		2441,1113,724	yes	missense	SPIB	NM_003121.4	27	2722,1867,1882	CC,CG,GG		29.9322,30.0046,43.5095	possibly-damaging	104/263	50926265	7311,5631	2193	4278	6471	SO:0001583	missense	6689	exon4			CTCCCTGCATACC		CCDS33080.1, CCDS58674.1, CCDS59412.1	19q13.3-q13.4	2008-07-22				ENSG00000269404			11242	protein-coding gene	gene with protein product		606802				1406622	Standard	NM_003121		Approved	SPI-B	uc002psd.3	Q01892		ENST00000595883.1:c.310G>C	19.37:g.50926265G>C	ENSP00000471921:p.Ala104Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_001243999	A8K9C9|B4DUG6|Q15359	Missense_Mutation	SNP	ENST00000595883.1	37	CCDS33080.1	1076	0.4926739926739927	145	0.29471544715447157	218	0.6022099447513812	117	0.20454545454545456	596	0.7862796833773087	.	0.626	-0.819108	0.02776	0.300046	0.700678	ENSG00000142539	ENST00000270632	T	0.48201	0.82	5.11	-2.12	0.07165	.	0.621973	0.13854	N	0.358127	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.18166	0.026;0.004	B;B	0.16289	0.015;0.002	T	0.34054	-0.9844	9	0.15952	T	0.53	-0.1057	4.825	0.13412	0.4217:0.1557:0.4225:0.0	rs11546996	104;104	Q01892-2;Q01892	.;SPIB_HUMAN	P	104	ENSP00000270632:A104P	ENSP00000270632:A104P	A	+	1	0	SPIB	55618077	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.775000	0.26689	0.029000	0.15352	0.561000	0.74099	GCA	G|0.413;C|0.587	0.587	strong		0.642	SPIB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464744.1	NM_003121	
DNHD1	144132	hgsc.bcm.edu	37	11	6579354	6579354	+	Silent	SNP	G	G	C	rs16915382	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6579354G>C	ENST00000527990.2	+	23	8829	c.8829G>C	c.(8827-8829)ctG>ctC	p.L2943L	DNHD1_ENST00000254579.6_Silent_p.L2943L			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2943					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)		CAGTGGCTCTGTTGGTACCCA	0.547													G|||	1144	0.228435	0.5545	0.1599	5008	,	,		18259	0.0159		0.0994	False		,,,				2504	0.1881				p.L2943L		Atlas-SNP	.											.	DNHD1	198	.	0			c.G8829C						PASS	.	G		719,665		187,345,160	76.0	66.0	69.0		8829	-0.0	0.1	11	dbSNP_123	69	420,2762		30,360,1201	no	coding-synonymous	DNHD1	NM_144666.2		217,705,1361	CC,CG,GG		13.1992,48.0491,24.9452		2943/4754	6579354	1139,3427	692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			GGCTCTGTTGGTA	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.8829G>C	11.37:g.6579354G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.805;C|0.195	0.195	strong		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
STIL	6491	hgsc.bcm.edu	37	1	47767914	47767914	+	Missense_Mutation	SNP	G	G	A	rs3125630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:47767914G>A	ENST00000360380.3	-	5	620	c.257C>T	c.(256-258)gCa>gTa	p.A86V	STIL_ENST00000243182.6_Missense_Mutation_p.A86V|STIL_ENST00000396221.2_Missense_Mutation_p.A86V|STIL_ENST00000371877.3_Missense_Mutation_p.A86V|STIL_ENST00000337817.5_Missense_Mutation_p.A86V	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	86			A -> V (in dbSNP:rs3125630). {ECO:0000269|PubMed:12438740, ECO:0000269|PubMed:17974005}.		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)				ACCTTCGTCTGCTGTCAGAGA	0.453													A|||	3037	0.60643	0.8805	0.5937	5008	,	,		18335	0.5675		0.4553	False		,,,				2504	0.4407				p.A86V		Atlas-SNP	.											.	STIL	91	.	0			c.C257T						PASS	.	A	VAL/ALA,VAL/ALA	3612,794	316.6+/-294.7	1481,650,72	98.0	103.0	101.0		257,257	5.4	1.0	1	dbSNP_103	101	4102,4498	591.2+/-392.8	975,2152,1173	yes	missense,missense	STIL	NM_001048166.1,NM_003035.2	64,64	2456,2802,1245	AA,AG,GG		47.6977,18.0209,40.6889	benign,benign	86/1289,86/1288	47767914	7714,5292	2203	4300	6503	SO:0001583	missense	6491	exon4			TCGTCTGCTGTCA	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.257C>T	1.37:g.47767914G>A	ENSP00000353544:p.Ala86Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_003035	Q5T0C5|Q68CN9	Missense_Mutation	SNP	ENST00000360380.3	37	CCDS548.1	1325	0.6066849816849816	423	0.8597560975609756	205	0.5662983425414365	338	0.5909090909090909	359	0.4736147757255937	A	3.420	-0.118387	0.06838	0.819791	0.476977	ENSG00000123473	ENST00000360380;ENST00000337817;ENST00000371877;ENST00000396221;ENST00000243182;ENST00000447475;ENST00000413565	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.42	5.42	0.78866	.	0.062472	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00069	-2.28	0.53005	P	3.399999999997849E-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	0.38351	-0.9665	9	0.02654	T	1	-4.2025	10.1156	0.42589	0.9237:0.0:0.0763:0.0	rs3125630;rs17418655;rs52792735;rs57179878;rs3125630	86;86;86;86	E9PSF2;Q5T0C7;Q15468-2;Q15468	.;.;.;STIL_HUMAN	V	86;86;86;86;86;86;90	ENSP00000353544:A86V;ENSP00000337367:A86V;ENSP00000360944:A86V;ENSP00000379523:A86V;ENSP00000243182:A86V;ENSP00000411664:A86V;ENSP00000412019:A90V	ENSP00000243182:A86V	A	-	2	0	STIL	47540501	1.000000	0.71417	1.000000	0.80357	0.258000	0.26162	5.182000	0.65059	0.891000	0.36235	-0.556000	0.04195	GCA	G|0.398;A|0.602	0.602	strong		0.453	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035	
KCNK10	54207	hgsc.bcm.edu	37	14	88652389	88652389	+	Silent	SNP	C	C	T	rs3742692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88652389C>T	ENST00000340700.5	-	7	1558	c.1107G>A	c.(1105-1107)gcG>gcA	p.A369A	KCNK10_ENST00000319231.5_Silent_p.A374A|KCNK10_ENST00000312350.5_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	56	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	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	
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	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	
GIMAP8	155038	hgsc.bcm.edu	37	7	150171710	150171710	+	Silent	SNP	T	T	C	rs60114833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	49	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	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	
CARD6	84674	hgsc.bcm.edu	37	5	40841741	40841741	+	Missense_Mutation	SNP	C	C	T	rs10512747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:40841741C>T	ENST00000254691.5	+	1	456	c.257C>T	c.(256-258)tCa>tTa	p.S86L	CARD6_ENST00000381677.3_Missense_Mutation_p.S86L	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	86	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		S -> L (in dbSNP:rs10512747). {ECO:0000269|Ref.1}.		apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TTTCCACAGTCAGCTGCCATT	0.413													C|||	241	0.048123	0.0068	0.0605	5008	,	,		17389	0.005		0.1272	False		,,,				2504	0.0583				p.S86L		Atlas-SNP	.											.	CARD6	141	.	0			c.C257T						PASS	.	C	LEU/SER	108,4298	80.4+/-118.8	2,104,2097	100.0	105.0	103.0		257	4.0	0.8	5	dbSNP_119	103	1036,7564	218.0+/-256.5	53,930,3317	yes	missense	CARD6	NM_032587.3	145	55,1034,5414	TT,TC,CC		12.0465,2.4512,8.7959	probably-damaging	86/1038	40841741	1144,11862	2203	4300	6503	SO:0001583	missense	84674	exon1			CACAGTCAGCTGC	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.257C>T	5.37:g.40841741C>T	ENSP00000254691:p.Ser86Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	127	0.05815018315018315	3	0.006097560975609756	24	0.06629834254143646	1	0.0017482517482517483	99	0.13060686015831136	C	19.51	3.840641	0.71488	0.024512	0.120465	ENSG00000132357	ENST00000254691;ENST00000381677;ENST00000444789;ENST00000509771	T;T	0.11604	2.76;2.76	4.88	4.01	0.46588	DEATH-like (2);Caspase Recruitment (2);	0.404992	0.18636	N	0.135436	T	0.00241	0.0007	M	0.62723	1.935	0.36453	P	0.133811	D	0.61080	0.989	P	0.58780	0.845	T	0.04991	-1.0913	9	0.87932	D	0	-2.8394	8.5439	0.33410	0.0:0.8962:0.0:0.1038	rs10512747;rs17240044;rs52789341;rs60928010;rs10512747	86	Q9BX69	CARD6_HUMAN	L	86	ENSP00000254691:S86L;ENSP00000371093:S86L	ENSP00000254691:S86L	S	+	2	0	CARD6	40877498	0.026000	0.19158	0.805000	0.32314	0.858000	0.48976	0.479000	0.22228	1.275000	0.44379	0.563000	0.77884	TCA	C|0.922;T|0.078	0.078	strong		0.413	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
ASXL2	55252	hgsc.bcm.edu	37	2	25991713	25991713	+	Missense_Mutation	SNP	T	T	G	rs190136878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25991713T>G	ENST00000435504.4	-	7	822	c.529A>C	c.(529-531)Aag>Cag	p.K177Q	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000336112.4_Missense_Mutation_p.K149Q|ASXL2_ENST00000404843.1_5'UTR|ASXL2_ENST00000497092.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	177	Ser-rich.				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)					tgctgctgcttcttctgctgt	0.393													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		14558	0.0		0.0	False		,,,				2504	0.001				p.K177Q		Atlas-SNP	.											.	ASXL2	217	.	0			c.A529C						PASS	.	T	GLN/LYS	2,4014		0,2,2006	141.0	143.0	142.0		529	6.0	1.0	2		142	11,8399		0,11,4194	yes	missense	ASXL2	NM_018263.4	53	0,13,6200	GG,GT,TT		0.1308,0.0498,0.1046	probably-damaging	177/1436	25991713	13,12413	2008	4205	6213	SO:0001583	missense	55252	exon6			GCTGCTTCTTCTG			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.529A>C	2.37:g.25991713T>G	ENSP00000391447:p.Lys177Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	18.47	3.630847	0.67015	4.98E-4	0.001308	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.19669	2.13;2.13	6.03	6.03	0.97812	.	0.168425	0.53938	D	0.000053	T	0.19604	0.0471	N	0.02011	-0.69	0.35856	D	0.827145	D	0.89917	1.0	D	0.63488	0.915	T	0.50947	-0.8767	10	0.87932	D	0	-15.1812	12.95	0.58394	0.0:0.0:0.0:1.0	.	177	Q76L83	ASXL2_HUMAN	Q	177;149	ENSP00000391447:K177Q;ENSP00000337250:K149Q	ENSP00000337250:K149Q	K	-	1	0	ASXL2	25845217	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.963000	0.49184	2.308000	0.77769	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.393	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
CNNM1	26507	hgsc.bcm.edu	37	10	101090246	101090246	+	Missense_Mutation	SNP	G	G	A	rs144944413	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101090246G>A	ENST00000356713.4	+	1	1391	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	CNNM1_ENST00000370528.3_Missense_Mutation_p.A297T|CNNM1_ENST00000370534.4_Missense_Mutation_p.A3T|CNNM1_ENST00000446890.1_Missense_Mutation_p.A297T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	368	DUF21.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		TCTGATGGCAGCCGCCTTCCC	0.657													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15163	0.0		0.002	False		,,,				2504	0.0				p.A368T		Atlas-SNP	.											.	CNNM1	101	.	0			c.G1102A						PASS	.	G	THR/ALA	2,4362		0,2,2180	8.0	9.0	8.0		1102	4.7	1.0	10	dbSNP_134	8	7,8501		0,7,4247	yes	missense	CNNM1	NM_020348.2	58	0,9,6427	AA,AG,GG		0.0823,0.0458,0.0699	benign	368/952	101090246	9,12863	2182	4254	6436	SO:0001583	missense	26507	exon1			ATGGCAGCCGCCT	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1102G>A	10.37:g.101090246G>A	ENSP00000349147:p.Ala368Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	36	0.654545	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	14.74	2.624272	0.46840	4.58E-4	8.23E-4	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534	D;D;D;T	0.88431	-2.38;-2.38;-2.38;-0.66	4.67	4.67	0.58626	Domain of unknown function DUF21 (1);	0.155169	0.45361	D	0.000368	T	0.78033	0.4220	N	0.19112	0.55	0.36254	D	0.854107	P;B;B;B	0.35033	0.481;0.209;0.133;0.268	B;B;B;B	0.34536	0.164;0.185;0.045;0.143	D	0.85941	0.1458	10	0.72032	D	0.01	-5.7061	17.3611	0.87350	0.0:0.0:1.0:0.0	.	3;368;3;368	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	T	368;297;297;3	ENSP00000349147:A368T;ENSP00000406492:A297T;ENSP00000359559:A297T;ENSP00000359565:A3T	ENSP00000349147:A368T	A	+	1	0	CNNM1	101080236	0.002000	0.14202	1.000000	0.80357	0.908000	0.53690	0.819000	0.27308	2.425000	0.82216	0.462000	0.41574	GCC	G|0.999;A|0.001	0.001	strong		0.657	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
PCNT	5116	hgsc.bcm.edu	37	21	47848466	47848466	+	Missense_Mutation	SNP	C	C	T	rs12481791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47848466C>T	ENST00000359568.5	+	35	7759	c.7652C>T	c.(7651-7653)gCg>gTg	p.A2551V	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2551					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)					AGCGCAGAGGCGCGCGGGAGC	0.692													C|||	31	0.0061901	0.0008	0.0115	5008	,	,		16456	0.0		0.0169	False		,,,				2504	0.0051				p.A2551V		Atlas-SNP	.											.	PCNT	283	.	0			c.C7652T						PASS	.	C	VAL/ALA	16,4372		0,16,2178	14.0	15.0	15.0		7652	3.5	1.0	21	dbSNP_120	15	139,8433		1,137,4148	yes	missense	PCNT	NM_006031.5	64	1,153,6326	TT,TC,CC		1.6216,0.3646,1.196	possibly-damaging	2551/3337	47848466	155,12805	2194	4286	6480	SO:0001583	missense	5116	exon35			CAGAGGCGCGCGG	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.7652C>T	21.37:g.47848466C>T	ENSP00000352572:p.Ala2551Val	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	20	0.009157509157509158	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	14	0.018469656992084433	C	13.20	2.166118	0.38217	0.003646	0.016216	ENSG00000160299	ENST00000359568	T	0.01821	4.62	4.51	3.53	0.40419	.	0.272836	0.19735	N	0.107243	T	0.02342	0.0072	L	0.56769	1.78	0.30737	N	0.74663	D;B	0.76494	0.999;0.256	P;B	0.60345	0.873;0.24	T	0.06267	-1.0836	10	0.34782	T	0.22	.	9.8669	0.41150	0.3675:0.6325:0.0:0.0	rs12481791	2433;2551	O95613-2;O95613	.;PCNT_HUMAN	V	2551	ENSP00000352572:A2551V	ENSP00000352572:A2551V	A	+	2	0	PCNT	46672894	1.000000	0.71417	0.993000	0.49108	0.023000	0.10783	4.473000	0.60196	2.440000	0.82611	0.563000	0.77884	GCG	C|0.988;T|0.012	0.012	strong		0.692	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:87229739C>T	ENST00000297524.3	-	3	1242	c.1139G>A	c.(1138-1140)aGg>aAg	p.R380K	SLC7A13_ENST00000520624.1_5'Flank|SLC7A13_ENST00000419776.2_Missense_Mutation_p.R371K	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	380			R -> K (in dbSNP:rs4419794).			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						GTATCTCCGCCTTAGTATTCC	0.299													C|||	973	0.194289	0.0401	0.1945	5008	,	,		17064	0.3383		0.1372	False		,,,				2504	0.3129				p.R380K		Atlas-SNP	.											SLC7A13,NS,carcinoma,+1,1	SLC7A13	97	1	0			c.G1139A						PASS	.	C	LYS/ARG	248,4140		9,230,1955	29.0	34.0	32.0		1139	-0.8	0.0	8	dbSNP_111	32	1088,7496		80,928,3284	yes	missense	SLC7A13	NM_138817.2	26	89,1158,5239	TT,TC,CC		12.6747,5.6518,10.2991	benign	380/471	87229739	1336,11636	2194	4292	6486	SO:0001583	missense	157724	exon3			CTCCGCCTTAGTA	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.1139G>A	8.37:g.87229739C>T	ENSP00000297524:p.Arg380Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	368	0.1684981684981685	18	0.036585365853658534	56	0.15469613259668508	193	0.3374125874125874	101	0.13324538258575197	C	0.005	-2.129682	0.00338	0.056518	0.126747	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.88818	-2.43;-2.43	5.03	-0.761	0.11038	.	0.592368	0.15885	N	0.239861	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.01281	0.0;0.0	T	0.38478	-0.9659	9	0.27082	T	0.32	.	3.1871	0.06604	0.246:0.2762:0.0:0.4778	rs4419794;rs60737499;rs4419794	371;380	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	K	380;371	ENSP00000297524:R380K;ENSP00000410982:R371K	ENSP00000297524:R380K	R	-	2	0	SLC7A13	87298855	0.931000	0.31567	0.005000	0.12908	0.003000	0.03518	0.841000	0.27613	0.109000	0.17891	-1.124000	0.02001	AGG	C|0.856;T|0.144	0.144	strong		0.299	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
SH3RF2	153769	hgsc.bcm.edu	37	5	145442133	145442133	+	Missense_Mutation	SNP	G	G	A	rs11435	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:145442133G>A	ENST00000511217.1	+	9	2111	c.2059G>A	c.(2059-2061)Gtc>Atc	p.V687I	SH3RF2_ENST00000359120.4_Missense_Mutation_p.V687I|SH3RF2_ENST00000511705.1_3'UTR			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	687			V -> I (in dbSNP:rs11435). {ECO:0000269|PubMed:14702039}.		negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGATGACCGTCCTATTTGC	0.607													G|||	871	0.173922	0.0106	0.2233	5008	,	,		17455	0.3036		0.1342	False		,,,				2504	0.2669				p.V687I		Atlas-SNP	.											.	SH3RF2	58	.	0			c.G2059A						PASS	.	G	ILE/VAL	125,4281	91.6+/-130.3	1,123,2079	70.0	66.0	67.0		2059	-11.0	0.2	5	dbSNP_52	67	1259,7341	250.8+/-277.5	89,1081,3130	yes	missense	SH3RF2	NM_152550.3	29	90,1204,5209	AA,AG,GG		14.6395,2.837,10.6412	benign	687/730	145442133	1384,11622	2203	4300	6503	SO:0001583	missense	153769	exon10			ATGACCGTCCTAT	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.2059G>A	5.37:g.145442133G>A	ENSP00000424497:p.Val687Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	CCDS4280.1	345	0.15796703296703296	10	0.02032520325203252	68	0.1878453038674033	158	0.2762237762237762	109	0.1437994722955145	G	1.821	-0.472314	0.04445	0.02837	0.146395	ENSG00000156463	ENST00000359120;ENST00000511217;ENST00000513503	T;T	0.16897	2.31;2.31	5.5	-11.0	0.00169	.	1.098730	0.06975	N	0.818854	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	0.42799	-0.9430	9	0.10377	T	0.69	-3.4037	9.6766	0.40045	0.1565:0.0:0.5959:0.2476	rs11435;rs3172985;rs52836280;rs61334088;rs11435	178;687	Q8TEC5-2;Q8TEC5	.;SH3R2_HUMAN	I	687;687;86	ENSP00000352028:V687I;ENSP00000424497:V687I	ENSP00000352028:V687I	V	+	1	0	SH3RF2	145422326	0.000000	0.05858	0.182000	0.23118	0.636000	0.38137	-1.931000	0.01556	-1.851000	0.01168	-0.678000	0.03780	GTC	G|0.867;A|0.133	0.133	strong		0.607	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
TMEM63B	55362	hgsc.bcm.edu	37	6	44117619	44117619	+	Silent	SNP	C	C	T	rs75310630		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44117619C>T	ENST00000259746.9	+	16	1620	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	TMEM63B_ENST00000323267.6_Silent_p.F479F			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	479					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	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;0.0215)			CCCAGTTCTTCCCCACCCTGC	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		19084	0.0		0.001	False		,,,				2504	0.0				p.F479F		Atlas-SNP	.											.	TMEM63B	77	.	0			c.C1437T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	206.0	141.0	163.0		1437	4.5	1.0	6	dbSNP_133	163	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	TMEM63B	NM_018426.1		0,15,6488	TT,TC,CC		0.1628,0.0227,0.1153		479/833	44117619	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon16			GTTCTTCCCCACC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1437C>T	6.37:g.44117619C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.77	1.443996	0.25987	2.27E-4	0.001628	ENSG00000137216	ENST00000371893	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53099	-0.8486	4	.	.	.	.	12.2754	0.54733	0.0:0.9139:0.0:0.0861	.	.	.	.	F	408	.	.	S	+	2	0	TMEM63B	44225597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.121000	0.50438	2.488000	0.83962	0.549000	0.68633	TCC	C|0.999;T|0.001	0.001	strong		0.622	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
C19orf35	374872	hgsc.bcm.edu	37	19	2280885	2280885	+	Missense_Mutation	SNP	G	G	A	rs55662626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2280885G>A	ENST00000342063.3	-	2	139	c.46C>T	c.(46-48)Ccc>Tcc	p.P16S		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	16										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				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)		GACCAGGTGGGGTTGTCGGGC	0.687													g|||	999	0.199481	0.1445	0.2767	5008	,	,		11315	0.3284		0.0497	False		,,,				2504	0.2403				p.P16S		Atlas-SNP	.											C19orf35,colon,carcinoma,0,1	C19orf35	18	1	0			c.C46T						PASS	.	G	SER/PRO	649,3755		47,555,1600	23.0	25.0	25.0		46	1.7	0.0	19	dbSNP_129	25	474,8124		17,440,3842	yes	missense	C19orf35	NM_198532.2	74	64,995,5442	AA,AG,GG		5.5129,14.7366,8.6371	probably-damaging	16/474	2280885	1123,11879	2202	4299	6501	SO:0001583	missense	374872	exon2			AGGTGGGGTTGTC	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.46C>T	19.37:g.2280885G>A	ENSP00000345102:p.Pro16Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	222	102	0.459459	NM_198532		Missense_Mutation	SNP	ENST00000342063.3	37	CCDS12087.1	378	0.17307692307692307	72	0.14634146341463414	76	0.20994475138121546	191	0.3339160839160839	39	0.051451187335092345	g	8.261	0.811282	0.16537	0.147366	0.055129	ENSG00000188305	ENST00000342063	T	0.17054	2.3	2.84	1.72	0.24424	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.50528	0.936	P	0.45276	0.475	T	0.47315	-0.9127	8	0.34782	T	0.22	.	9.2613	0.37614	0.0:0.2244:0.7756:0.0	rs55662626;rs61737273	16	Q6ZS72	CS035_HUMAN	S	16	ENSP00000345102:P16S	ENSP00000345102:P16S	P	-	1	0	C19orf35	2231885	0.000000	0.05858	0.001000	0.08648	0.051000	0.14879	0.375000	0.20518	0.481000	0.27557	0.556000	0.70494	CCC	G|0.880;A|0.120	0.120	strong		0.687	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	NM_198532	
DEC1	50514	hgsc.bcm.edu	37	9	118163563	118163563	+	Missense_Mutation	SNP	C	C	T	rs2269700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:118163563C>T	ENST00000374016.1	+	7	698	c.179C>T	c.(178-180)gCc>gTc	p.A60V		NM_017418.2	NP_059114.1	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1	60			A -> V (in dbSNP:rs2269700).		negative regulation of cell proliferation (GO:0008285)					kidney(1)|large_intestine(1)|ovary(1)	3						GTATCTCTTGCCAGGCCCAAG	0.408													T|||	3817	0.762181	0.9115	0.6009	5008	,	,		21050	0.8492		0.6451	False		,,,				2504	0.7055				p.A60V		Atlas-SNP	.											.	DEC1	8	.	0			c.C179T						PASS	.	T	VAL/ALA	3858,548	246.5+/-255.1	1697,464,42	127.0	125.0	126.0		179	-1.6	0.0	9	dbSNP_100	126	5294,3306	494.6+/-373.8	1665,1964,671	yes	missense	DEC1	NM_017418.2	64	3362,2428,713	TT,TC,CC		38.4419,12.4376,29.6325	benign	60/71	118163563	9152,3854	2203	4300	6503	SO:0001583	missense	50514	exon7			CTCTTGCCAGGCC	AB022761	CCDS6812.1	9q32	2008-02-05			ENSG00000173077	ENSG00000173077			23658	protein-coding gene	gene with protein product		604767				8603412, 10612805	Standard	NM_017418		Approved	CTS9	uc004bjk.1	Q9P2X7	OTTHUMG00000020549	ENST00000374016.1:c.179C>T	9.37:g.118163563C>T	ENSP00000363128:p.Ala60Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_017418		Missense_Mutation	SNP	ENST00000374016.1	37	CCDS6812.1	1626	0.7445054945054945	432	0.8780487804878049	221	0.6104972375690608	474	0.8286713286713286	499	0.658311345646438	T	6.767	0.510439	0.12883	0.875624	0.615581	ENSG00000173077	ENST00000374016	T	0.57273	0.41	3.85	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28427	-1.0044	7	0.87932	D	0	.	0.09	0.00039	0.3142:0.1933:0.1617:0.3309	rs2269700;rs17292199;rs52803110;rs61681994;rs2269700	60	Q9P2X7	DEC1_HUMAN	V	60	ENSP00000363128:A60V	ENSP00000363128:A60V	A	+	2	0	DEC1	117203384	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.236000	0.17967	-0.628000	0.05582	-0.254000	0.11334	GCC	C|0.265;A|0.006	.	strong		0.408	DEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053791.1	NM_017418	
SEMA4B	10509	hgsc.bcm.edu	37	15	90764219	90764219	+	Missense_Mutation	SNP	G	G	A	rs4932305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90764219G>A	ENST00000411539.2	+	5	749	c.489G>A	c.(487-489)atG>atA	p.M163I	SEMA4B_ENST00000379122.3_Missense_Mutation_p.M158I|SEMA4B_ENST00000332496.6_Missense_Mutation_p.M163I	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	158	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			TGCAGAACATGGAGAACTTCA	0.582													G|||	1387	0.276957	0.0613	0.2291	5008	,	,		21391	0.6081		0.1491	False		,,,				2504	0.3926				p.M163I		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G489A						PASS	.	G	ILE/MET,ILE/MET	352,3776		20,312,1732	50.0	51.0	51.0		489,489	2.5	0.2	15	dbSNP_111	51	1175,7251		90,995,3128	yes	missense,missense	SEMA4B	NM_020210.3,NM_198925.2	10,10	110,1307,4860	AA,AG,GG		13.9449,8.5271,12.1635	benign,benign	163/838,163/838	90764219	1527,11027	2064	4213	6277	SO:0001583	missense	10509	exon6			GAACATGGAGAAC	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.489G>A	15.37:g.90764219G>A	ENSP00000394720:p.Met163Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Missense_Mutation	SNP	ENST00000411539.2	37	CCDS45347.1	546	0.25	31	0.06300813008130081	56	0.15469613259668508	348	0.6083916083916084	111	0.14643799472295516	G	16.69	3.192268	0.58017	0.085271	0.139449	ENSG00000185033	ENST00000332496;ENST00000379122;ENST00000411539	T;T;T	0.09445	2.98;2.98;2.98	5.58	2.5	0.30297	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.935120	0.09097	N	0.849095	T	0.00012	0.0000	N	0.01686	-0.76	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33803	-0.9854	9	0.18710	T	0.47	.	3.6283	0.08121	0.1476:0.1317:0.586:0.1348	rs4932305;rs52807404;rs58528304;rs4932305	163;158	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	I	163;158;163	ENSP00000332204:M163I;ENSP00000368417:M158I;ENSP00000394720:M163I	ENSP00000332204:M163I	M	+	3	0	SEMA4B	88565223	0.000000	0.05858	0.245000	0.24217	0.330000	0.28571	0.077000	0.14738	0.809000	0.34255	0.655000	0.94253	ATG	G|0.755;A|0.245	0.245	strong		0.582	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
PDHX	8050	hgsc.bcm.edu	37	11	34969112	34969112	+	Missense_Mutation	SNP	A	A	G	rs11539202	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:34969112A>G	ENST00000227868.4	+	3	385	c.301A>G	c.(301-303)Acc>Gcc	p.T101A	PDHX_ENST00000430469.2_Missense_Mutation_p.T101A|PDHX_ENST00000448838.3_Missense_Mutation_p.T86A			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	101	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.		T -> A (in dbSNP:rs11539202).		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)			AGCTGTGGTTACCTTAGATGC	0.353													A|||	545	0.108826	0.0257	0.1527	5008	,	,		15764	0.0		0.3191	False		,,,				2504	0.0859				p.T101A		Atlas-SNP	.											.	PDHX	40	.	0			c.A301G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	381,4023	191.9+/-217.4	10,361,1831	200.0	186.0	191.0		256,301,301	4.9	1.0	11	dbSNP_120	191	2764,5832	440.6+/-359.6	429,1906,1963	yes	missense,missense,missense	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	58,58,58	439,2267,3794	GG,GA,AA		32.1545,8.6512,24.1923	possibly-damaging,possibly-damaging,possibly-damaging	86/487,101/275,101/502	34969112	3145,9855	2202	4298	6500	SO:0001583	missense	8050	exon3			GTGGTTACCTTAG	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	ENST00000227868.4:c.301A>G	11.37:g.34969112A>G	ENSP00000227868:p.Thr101Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	328	0.15018315018315018	17	0.034552845528455285	58	0.16022099447513813	0	0.0	253	0.3337730870712401	A	16.82	3.228063	0.58777	0.086512	0.321545	ENSG00000110435	ENST00000533550;ENST00000448838;ENST00000227868;ENST00000430469;ENST00000533262	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	6.06	4.93	0.64822	Single hybrid motif (1);Biotin/lipoyl attachment (2);	0.151252	0.64402	D	0.000017	T	0.00012	0.0000	N	0.04994	-0.135	0.29635	P	0.845129	D;P;B	0.76494	0.999;0.843;0.246	D;B;B	0.83275	0.996;0.336;0.241	T	0.47169	-0.9138	9	0.26408	T	0.33	-21.7084	11.872	0.52525	0.8689:0.0:0.0:0.131	rs11539202;rs52812226;rs60066295;rs11539202	101;86;101	E9PBP7;E9PB14;O00330	.;.;ODPX_HUMAN	A	41;86;101;101;74	ENSP00000431281:T41A;ENSP00000389404:T86A;ENSP00000227868:T101A;ENSP00000415695:T101A;ENSP00000432277:T74A	ENSP00000227868:T101A	T	+	1	0	PDHX	34925688	1.000000	0.71417	0.998000	0.56505	0.747000	0.42532	8.129000	0.89597	1.091000	0.41335	0.528000	0.53228	ACC	A|0.800;G|0.200	0.200	strong		0.353	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
GSTM3	2947	hgsc.bcm.edu	37	1	110279701	110279701	+	Missense_Mutation	SNP	C	C	T	rs7483	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:110279701C>T	ENST00000540225.1	-	9	980	c.670G>A	c.(670-672)Gta>Ata	p.V224I	GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000256594.3_Missense_Mutation_p.V224I|GSTM3_ENST00000361066.2_Missense_Mutation_p.V224I|RP4-735C1.4_ENST00000431955.1_RNA			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	140	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	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	
TIRAP	114609	hgsc.bcm.edu	37	11	126162468	126162468	+	Missense_Mutation	SNP	G	G	A	rs3802813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126162468G>A	ENST00000392680.2	+	5	569	c.164G>A	c.(163-165)aGc>aAc	p.S55N	TIRAP_ENST00000392678.3_Missense_Mutation_p.S55N|RP11-712L6.7_ENST00000533378.1_RNA|RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392679.1_Missense_Mutation_p.S55N	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	83	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	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	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299809	145299809	+	Missense_Mutation	SNP	G	G	A	rs61814630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145299809G>A	ENST00000369338.1	+	2	235	c.45G>A	c.(43-45)atG>atA	p.M15I	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.M286I|NBPF10_ENST00000369339.3_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	286						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.M15I(1)|p.M286I(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGGCAGAGATGAACATTCTAG	0.502													.|||	179	0.0357428	0.0015	0.0231	5008	,	,		41767	0.0635		0.0487	False		,,,				2504	0.0491				p.M286I		Atlas-SNP	.											NBPF10_ENST00000369338,extremity,malignant_melanoma,0,3	NBPF10	221	3	2	Substitution - Missense(2)	skin(2)	c.G858A						scavenged	.																																			SO:0001583	missense	100132406	exon6			AGAGATGAACATT	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.45G>A	1.37:g.145299809G>A	ENSP00000358344:p.Met15Ile	Somatic	28	1	0.0357143		WXS	Illumina HiSeq	Phase_I	49	8	0.163265	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	10.66	1.411877	0.25465	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.02863	4.13;4.13	1.05	-0.082	0.13700	.	.	.	.	.	T	0.01092	0.0036	L	0.49350	1.555	0.09310	N	1	B	0.14805	0.011	B	0.23018	0.043	T	0.44544	-0.9321	9	0.56958	D	0.05	.	4.7437	0.13028	0.0:0.404:0.596:0.0	rs61814630	15	Q86T75-2	.	I	211;15;15;286	ENSP00000358344:M15I;ENSP00000345684:M286I	ENSP00000345684:M286I	M	+	3	0	NBPF10	144011166	0.000000	0.05858	0.003000	0.11579	0.029000	0.11900	-1.452000	0.02385	-0.014000	0.14175	0.281000	0.19383	ATG	.	.	weak		0.502	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
FLG	2312	hgsc.bcm.edu	37	1	152277345	152277345	+	Silent	SNP	C	C	T	rs2065956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152277345C>T	ENST00000368799.1	-	3	10052	c.10017G>A	c.(10015-10017)caG>caA	p.Q3339Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3339	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)			TATCACTGGCCTGACTACCAC	0.572									Ichthyosis				C|||	1440	0.28754	0.0113	0.3905	5008	,	,		19931	0.5823		0.1421	False		,,,				2504	0.4335				p.Q3339Q		Atlas-SNP	.											.	FLG	900	.	0			c.G10017A						PASS	.	C		161,4245	107.8+/-146.2	2,157,2044	382.0	376.0	378.0		10017	0.7	0.0	1	dbSNP_94	378	1244,7356	248.6+/-276.2	102,1040,3158	no	coding-synonymous	FLG	NM_002016.1		104,1197,5202	TT,TC,CC		14.4651,3.6541,10.8027		3339/4062	152277345	1405,11601	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGGCCTGACTA	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.10017G>A	1.37:g.152277345C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	153	93	0.607843	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			C|0.843;T|0.157	0.157	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
DYDC2	84332	hgsc.bcm.edu	37	10	82122793	82122793	+	Silent	SNP	G	G	A	rs1538818	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:82122793G>A	ENST00000372199.1	+	5	832	c.234G>A	c.(232-234)gaG>gaA	p.E78E	DYDC2_ENST00000444807.2_Silent_p.E78E|DYDC2_ENST00000372198.1_Silent_p.E92E|DYDC2_ENST00000256039.2_Silent_p.E78E|DYDC2_ENST00000372197.1_Silent_p.E78E			Q96IM9	DYDC2_HUMAN	DPY30 domain containing 2	78										breast(1)|large_intestine(3)|lung(6)|skin(1)	11			Colorectal(32;0.229)			AACAGGAAGAGTATCAGATTC	0.468													G|||	573	0.114417	0.0204	0.1671	5008	,	,		18874	0.0288		0.1103	False		,,,				2504	0.2965				p.E92E		Atlas-SNP	.											.	DYDC2	18	.	0			c.G276A						PASS	.	G		203,4203	125.3+/-162.5	8,187,2008	115.0	105.0	108.0		234	2.2	0.0	10	dbSNP_88	108	1019,7581	219.5+/-257.5	46,927,3327	no	coding-synonymous	DYDC2	NM_032372.4		54,1114,5335	AA,AG,GG		11.8488,4.6074,9.3957		78/178	82122793	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	84332	exon3			GGAAGAGTATCAG	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.234G>A	10.37:g.82122793G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001270042	D3DWD6|Q5QP07|Q5QP11	Silent	SNP	ENST00000372199.1	37	CCDS7367.1																																																																																			G|0.915;A|0.085	0.085	strong		0.468	DYDC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049063.1	NM_032372	
LY6G6F	259215	hgsc.bcm.edu	37	6	31675765	31675765	+	Missense_Mutation	SNP	G	G	A	rs2242653	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31675765G>A	ENST00000375832.4	+	3	522	c.500G>A	c.(499-501)aGg>aAg	p.R167K	LY6G6F_ENST00000556581.1_Missense_Mutation_p.R167K|XXbac-BPG32J3.20_ENST00000461287.1_Intron|MEGT1_ENST00000503322.1_Missense_Mutation_p.R167K	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	167			R -> K (in dbSNP:rs2242653).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GGTCCCGTGAGGGGCCGTGTT	0.622													G|||	735	0.146765	0.0915	0.1945	5008	,	,		16938	0.1379		0.1859	False		,,,				2504	0.1564				p.R167K		Atlas-SNP	.											.	LY6G6F	23	.	0			c.G500A						PASS	.	G	LYS/ARG	303,2719		12,279,1220	99.0	99.0	99.0		500	0.9	1.0	6	dbSNP_98	99	823,4595		65,693,1951	yes	missense	LY6G6F	NM_001003693.1	26	77,972,3171	AA,AG,GG		15.1901,10.0265,13.3412	benign	167/298	31675765	1126,7314	1511	2709	4220	SO:0001583	missense	259215	exon3			CCGTGAGGGGCCG		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.500G>A	6.37:g.31675765G>A	ENSP00000364992:p.Arg167Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	371	0.16987179487179488	41	0.08333333333333333	67	0.1850828729281768	107	0.18706293706293706	156	0.20580474934036938	G	3.011	-0.203892	0.06180	0.100265	0.151901	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.17213	2.57;2.29;2.57	5.3	0.874	0.19124	.	0.372460	0.26432	N	0.024409	T	0.02156	0.0067	N	0.12569	0.235	0.53688	P	2.4000000000024002E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.47898	-0.9081	9	0.12430	T	0.62	-9.4381	8.385	0.32494	0.4256:0.0:0.5744:0.0	rs2242653;rs52821566;rs60939183;rs2242653	167;167	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	K	167	ENSP00000452432:R167K;ENSP00000364992:R167K;ENSP00000421232:R167K	ENSP00000364992:R167K	R	+	2	0	XXbac-BPG32J3.19;LY6G6F	31783744	0.707000	0.27866	0.953000	0.39169	0.623000	0.37688	-0.750000	0.04808	0.000000	0.14550	-1.094000	0.02160	AGG	G|0.859;A|0.141	0.141	strong		0.622	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
AQP12A	375318	hgsc.bcm.edu	37	2	241631413	241631413	+	Missense_Mutation	SNP	T	T	G	rs71428454	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241631413T>G	ENST00000337801.4	+	1	152	c.83T>G	c.(82-84)cTg>cGg	p.L28R	AC011298.2_ENST00000407635.2_lincRNA|AQP12A_ENST00000429564.1_Missense_Mutation_p.L28R	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	28						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)		TCCAAGGCCCTGCTCCCAGTG	0.692													t|||	1001	0.19988	0.1989	0.3242	5008	,	,		17103	0.0357		0.3519	False		,,,				2504	0.1258				p.L28R		Atlas-SNP	.											AQP12A,caecum,carcinoma,0,1	AQP12A	32	1	0			c.T83G						PASS	.						40.0	47.0	45.0					2																	241631413		2180	4285	6465	SO:0001583	missense	375318	exon1			AGGCCCTGCTCCC	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.83T>G	2.37:g.241631413T>G	ENSP00000337144:p.Leu28Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_198998		Missense_Mutation	SNP	ENST00000337801.4	37		457|457	0.20924908424908426|0.20924908424908426	95|95	0.19308943089430894|0.19308943089430894	110|110	0.30386740331491713|0.30386740331491713	18|18	0.03146853146853147|0.03146853146853147	234|234	0.3087071240105541|0.3087071240105541	.|.	3.061|3.061	-0.193201|-0.193201	0.06259|0.06259	.|.	.|.	ENSG00000184945|ENSG00000184945	ENST00000420599|ENST00000337801;ENST00000429564	.|T;T	.|0.11385	.|2.78;2.78	2.43|2.43	2.43|2.43	0.29744|0.29744	.|.	.|0.166965	.|0.42682	.|D	.|0.000664	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62723|0.62723	1.935|1.935	0.25432|0.25432	P|P	0.9881739|0.9881739	.|D	.|0.67145	.|0.996	.|P	.|0.57548	.|0.823	T|T	0.38457|0.38457	-0.9660|-0.9660	5|9	0.87932|0.66056	D|D	0|0.02	-20.1652|-20.1652	8.4076|8.4076	0.32625|0.32625	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|28	.|Q8IXF9	.|AQ12A_HUMAN	G|R	1|28	.|ENSP00000337144:L28R;ENSP00000405899:L28R	ENSP00000399666:C1G|ENSP00000337144:L28R	C|L	+|+	1|2	0|0	AQP12A|AQP12A	241280086|241280086	0.134000|0.134000	0.22483|0.22483	0.878000|0.878000	0.34440|0.34440	0.334000|0.334000	0.28698|0.28698	1.538000|1.538000	0.36094|0.36094	1.134000|1.134000	0.42165|0.42165	0.156000|0.156000	0.16432|0.16432	TGC|CTG	T|0.790;G|0.210	0.210	strong		0.692	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
USP35	57558	hgsc.bcm.edu	37	11	77920563	77920563	+	Silent	SNP	G	G	T	rs2510045	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000526425.1_Silent_p.P285P|USP35_ENST00000441408.2_Silent_p.P140P|USP35_ENST00000530535.1_3'UTR	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	86	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	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	
OTUD4	54726	hgsc.bcm.edu	37	4	146062585	146062585	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:146062585G>A	ENST00000447906.2	-	19	2216	c.2029C>T	c.(2029-2031)Cga>Tga	p.R677*	OTUD4_ENST00000454497.2_Nonsense_Mutation_p.R612*|OTUD4_ENST00000455611.2_5'UTR			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	677					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					ACAATGGCTCGATCTCCCTTT	0.453																																					p.R612X		Atlas-SNP	.											OTUD4,NS,carcinoma,+1,1	OTUD4	120	1	0			c.C1834T						scavenged	.						73.0	72.0	72.0					4																	146062585		2203	4300	6503	SO:0001587	stop_gained	54726	exon19			TGGCTCGATCTCC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2029C>T	4.37:g.146062585G>A	ENSP00000395487:p.Arg677*	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	173	3	0.017341	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Nonsense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	G	38	7.016813	0.98006	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	.	.	.	6.17	3.44	0.39384	.	0.090350	0.45361	D	0.000380	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.625	16.0009	0.80292	0.0:0.0:0.4126:0.5874	.	.	.	.	X	612;677	.	ENSP00000395487:R677X	R	-	1	2	OTUD4	146282035	0.997000	0.39634	0.999000	0.59377	0.836000	0.47400	1.095000	0.30964	0.429000	0.26202	-0.182000	0.12963	CGA	.	.	none		0.453	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	46000398	46000398	+	Missense_Mutation	SNP	C	C	T	rs2020221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	87	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	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		
HERC2	8924	hgsc.bcm.edu	37	15	28419619	28419619	+	Missense_Mutation	SNP	C	C	T	rs141441362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28419619C>T	ENST00000261609.7	-	65	10087	c.9979G>A	c.(9979-9981)Gtg>Atg	p.V3327M		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)		GCCACATCCACAGTTGTCCAC	0.547																																					p.V3327M		Atlas-SNP	.											.	HERC2	501	.	0			c.G9979A						PASS	.						54.0	37.0	43.0					15																	28419619		2203	4300	6503	SO:0001583	missense	8924	exon65			CATCCACAGTTGT	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.9979G>A	15.37:g.28419619C>T	ENSP00000261609:p.Val3327Met	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	254	43	0.169291	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	127	0.05815018315018315	30	0.06097560975609756	24	0.06629834254143646	0	0.0	73	0.09630606860158311	C	10.06	1.246296	0.22796	.	.	ENSG00000128731	ENST00000261609	T	0.39787	1.06	5.72	4.81	0.61882	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (1);	0.063541	0.64402	D	0.000009	T	0.01156	0.0038	L	0.59436	1.845	0.54753	D	0.999986	B	0.15719	0.014	B	0.15052	0.012	T	0.01294	-1.1393	10	0.30078	T	0.28	.	11.8976	0.52665	0.0:0.8593:0.0:0.1407	.	3327	O95714	HERC2_HUMAN	M	3327	ENSP00000261609:V3327M	ENSP00000261609:V3327M	V	-	1	0	HERC2	26093214	1.000000	0.71417	0.016000	0.15963	0.067000	0.16453	4.974000	0.63771	1.420000	0.47138	0.591000	0.81541	GTG	C|0.947;T|0.053	0.053	strong		0.547	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
KLF17	128209	hgsc.bcm.edu	37	1	44595426	44595426	+	Silent	SNP	G	G	A	rs2429050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44595426G>A	ENST00000372299.3	+	2	541	c.483G>A	c.(481-483)tcG>tcA	p.S161S	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	161					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)					TGCCAGTCTCGGCTTCCACTG	0.577													G|||	1378	0.27516	0.0915	0.2579	5008	,	,		17305	0.4236		0.3966	False		,,,				2504	0.2577				p.S161S		Atlas-SNP	.											.	KLF17	92	.	0			c.G483A						PASS	.	G		638,3768	270.1+/-269.4	49,540,1614	34.0	38.0	36.0		483	-2.0	0.0	1	dbSNP_100	36	3202,5396	475.0+/-369.0	589,2024,1686	no	coding-synonymous	KLF17	NM_173484.3		638,2564,3300	AA,AG,GG		37.2412,14.4803,29.5294		161/390	44595426	3840,9164	2203	4299	6502	SO:0001819	synonymous_variant	128209	exon2			AGTCTCGGCTTCC	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.483G>A	1.37:g.44595426G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_173484	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	37	CCDS508.1																																																																																			G|0.699;A|0.301	0.301	strong		0.577	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
ANKRD33	341405	hgsc.bcm.edu	37	12	52284500	52284500	+	Missense_Mutation	SNP	A	A	G	rs34494292	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52284500A>G	ENST00000340970.4	+	5	766	c.395A>G	c.(394-396)cAg>cGg	p.Q132R	ANKRD33_ENST00000301190.6_Missense_Mutation_p.Q257R|ANKRD33_ENST00000538991.1_Missense_Mutation_p.Q63R|ANKRD33_ENST00000547119.1_3'UTR			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	132			Q -> R (in dbSNP:rs34494292). {ECO:0000269|PubMed:14702039}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		CAGCTTAGCCAGCACTACAAG	0.672													A|||	746	0.148962	0.0318	0.134	5008	,	,		13096	0.2063		0.1918	False		,,,				2504	0.2147				p.Q257R		Atlas-SNP	.											.	ANKRD33	33	.	0			c.A770G						PASS	.	A	ARG/GLN,ARG/GLN	278,4128	142.7+/-177.9	6,266,1931	24.0	26.0	25.0		395,770	-0.6	0.2	12	dbSNP_126	25	1751,6849	290.5+/-299.9	193,1365,2742	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	43,43	199,1631,4673	GG,GA,AA		20.3605,6.3096,15.6005	possibly-damaging,possibly-damaging	132/273,257/453	52284500	2029,10977	2203	4300	6503	SO:0001583	missense	341405	exon5			TTAGCCAGCACTA		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.395A>G	12.37:g.52284500A>G	ENSP00000344690:p.Gln132Arg	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	340	0.15567765567765568	23	0.046747967479674794	50	0.13812154696132597	126	0.2202797202797203	141	0.18601583113456466	A	11.27	1.588295	0.28357	0.063096	0.203605	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.22539	2.09;1.95;2.4	4.7	-0.552	0.11818	.	0.858027	0.10348	N	0.685403	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;P;B	0.38370	0.146;0.628;0.003	B;B;B	0.28465	0.024;0.09;0.003	T	0.35968	-0.9767	9	0.15066	T	0.55	-3.0E-4	3.2663	0.06867	0.529:0.0:0.1748:0.2962	rs34494292	132;63;257	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	R	257;63;132	ENSP00000301190:Q257R;ENSP00000443722:Q63R;ENSP00000344690:Q132R	ENSP00000301190:Q257R	Q	+	2	0	ANKRD33	50570767	0.000000	0.05858	0.201000	0.23476	0.720000	0.41350	0.671000	0.25172	0.026000	0.15269	0.459000	0.35465	CAG	A|0.845;G|0.155	0.155	strong		0.672	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
SPINK5	11005	hgsc.bcm.edu	37	5	147505116	147505116	+	Intron	SNP	G	G	A	rs3764930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:147505116G>A	ENST00000256084.7	+	29	2781				SPINK5_ENST00000359874.3_Silent_p.A923A	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5						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)			AGAATGAAGCGGAGGATGCAA	0.463													G|||	2270	0.453275	0.1876	0.6225	5008	,	,		19509	0.4821		0.5915	False		,,,				2504	0.5204				p.A923A		Atlas-SNP	.											.	SPINK5	245	.	0			c.G2769A						PASS	.	G	,	824,2312		112,600,856	73.0	64.0	67.0		2769,	-6.9	0.0	5	dbSNP_107	67	4393,2771		1319,1755,508	no	coding-synonymous,intron	SPINK5	NM_001127698.1,NM_006846.3	,	1431,2355,1364	AA,AG,GG		38.6795,26.2755,49.3495	,	923/1095,	147505116	5217,5083	1568	3582	5150	SO:0001627	intron_variant	11005	exon29			TGAAGCGGAGGAT	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.2740-170G>A	5.37:g.147505116G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	191	189	0.989529	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			G|0.545;A|0.455	0.455	strong		0.463	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
STRN3	29966	hgsc.bcm.edu	37	14	31425437	31425437	+	Silent	SNP	T	T	C	rs12886419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31425437T>C	ENST00000357479.5	-	2	490	c.294A>G	c.(292-294)gcA>gcG	p.A98A	STRN3_ENST00000355683.5_Silent_p.A98A	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	98					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)			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)		CTTGTAGAAATGCAATCCGGG	0.328													T|||	859	0.171526	0.2526	0.17	5008	,	,		19408	0.003		0.2704	False		,,,				2504	0.135				p.A98A		Atlas-SNP	.											.	STRN3	117	.	0			c.A294G						PASS	.	T	,	1093,3313	395.4+/-329.6	135,823,1245	125.0	113.0	117.0		294,294	2.8	1.0	14	dbSNP_121	117	2247,6351	379.4+/-339.3	260,1727,2312	no	coding-synonymous,coding-synonymous	STRN3	NM_001083893.1,NM_014574.3	,	395,2550,3557	CC,CT,TT		26.134,24.8071,25.6844	,	98/798,98/714	31425437	3340,9664	2203	4299	6502	SO:0001819	synonymous_variant	29966	exon2			TAGAAATGCAATC		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.294A>G	14.37:g.31425437T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Silent	SNP	ENST00000357479.5	37	CCDS41938.1																																																																																			T|0.773;C|0.227	0.227	strong		0.328	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
PDE11A	50940	hgsc.bcm.edu	37	2	178565913	178565913	+	Missense_Mutation	SNP	T	T	C	rs17400325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:178565913T>C	ENST00000286063.6	-	14	2497	c.2180A>G	c.(2179-2181)tAt>tGt	p.Y727C	AC012499.1_ENST00000412133.1_RNA|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000389683.3_Missense_Mutation_p.Y283C|PDE11A_ENST00000449286.2_Missense_Mutation_p.Y369C|PDE11A_ENST00000409504.1_Missense_Mutation_p.Y369C|PDE11A_ENST00000358450.4_Missense_Mutation_p.Y477C|AC012499.1_ENST00000450227.1_RNA	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	727	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	AGAGGTTCCATAGAGTTGGGC	0.532									Primary Pigmented Nodular Adrenocortical Disease, Familial				T|||	111	0.0221645	0.003	0.0375	5008	,	,		18572	0.0		0.0676	False		,,,				2504	0.0133				p.Y727C		Atlas-SNP	.											.	PDE11A	283	.	0			c.A2180G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	29,4377	35.2+/-66.4	0,29,2174	124.0	103.0	110.0		848,1430,1106,2180	5.7	1.0	2	dbSNP_123	110	347,8253	117.2+/-176.8	13,321,3966	yes	missense,missense,missense,missense	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	194,194,194,194	13,350,6140	CC,CT,TT		4.0349,0.6582,2.891	probably-damaging,probably-damaging,probably-damaging,probably-damaging	283/490,477/684,369/576,727/934	178565913	376,12630	2203	4300	6503	SO:0001583	missense	50940	exon14	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	GTTCCATAGAGTT	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2180A>G	2.37:g.178565913T>C	ENSP00000286063:p.Tyr727Cys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	58	0.417266	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	68|68	0.031135531135531136|0.031135531135531136	2|2	0.0040650406504065045|0.0040650406504065045	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	48|48	0.0633245382585752|0.0633245382585752	T|T	21.6|21.6	4.173676|4.173676	0.78452|0.78452	0.006582|0.006582	0.040349|0.040349	ENSG00000128655|ENSG00000128655	ENST00000433879|ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286	.|D;D;D;D;D	.|0.87887	.|-2.31;-2.31;-2.31;-2.31;-2.31	5.7|5.7	5.7|5.7	0.88788|0.88788	.|Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78362|0.78362	0.4271|0.4271	H|H	0.95187|0.95187	3.635|3.635	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.81914	.|0.961;0.995	D|D	0.85446|0.85446	0.1158|0.1158	5|10	.|0.87932	.|D	.|0	.|.	15.9755|15.9755	0.80060|0.80060	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs17400325;rs52828785;rs17400325|rs17400325;rs52828785;rs17400325	.|477;727	.|Q9HCR9-2;Q9HCR9	.|.;PDE11_HUMAN	V|C	335|727;477;369;283;369	.|ENSP00000286063:Y727C;ENSP00000351232:Y477C;ENSP00000386539:Y369C;ENSP00000374333:Y283C;ENSP00000390599:Y369C	.|ENSP00000286063:Y727C	M|Y	-|-	1|2	0|0	PDE11A|PDE11A	178274159|178274159	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.824000|0.824000	0.46624|0.46624	7.646000|7.646000	0.83445|0.83445	2.165000|2.165000	0.68154|0.68154	0.454000|0.454000	0.30748|0.30748	ATG|TAT	T|0.971;C|0.029	0.029	strong		0.532	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
MGA	23269	hgsc.bcm.edu	37	15	42032383	42032383	+	Missense_Mutation	SNP	C	C	G	rs17677991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42032383C>G	ENST00000570161.1	+	13	4567	c.4567C>G	c.(4567-4569)Cca>Gca	p.P1523A	MGA_ENST00000566586.1_Missense_Mutation_p.P1523A|MGA_ENST00000389936.4_Missense_Mutation_p.P1523A|MGA_ENST00000545763.1_Missense_Mutation_p.P1523A|MGA_ENST00000219905.7_Missense_Mutation_p.P1523A			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGCGTTTGTCCCAGCAAAACG	0.488													C|||	1509	0.301318	0.2141	0.4597	5008	,	,		17579	0.1875		0.3797	False		,,,				2504	0.3436				p.P1523A		Atlas-SNP	.											.	MGA	264	.	0			c.C4567G						PASS	.	C	ALA/PRO,ALA/PRO	871,2961		109,653,1154	55.0	53.0	54.0		4567,4567	4.2	1.0	15	dbSNP_123	54	2850,5406		486,1878,1764	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	27,27	595,2531,2918	GG,GC,CC		34.5203,22.7296,30.7826	probably-damaging,probably-damaging	1523/2857,1523/3066	42032383	3721,8367	1916	4128	6044	SO:0001583	missense	23269	exon14			TTTGTCCCAGCAA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.4567C>G	15.37:g.42032383C>G	ENSP00000457035:p.Pro1523Ala	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	661	0.30265567765567764	110	0.22357723577235772	161	0.4447513812154696	98	0.17132867132867133	292	0.38522427440633245	C	11.03	1.520149	0.27211	0.227296	0.345203	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.94828	-2.08;-2.09;-3.53	6.08	4.22	0.49857	.	0.216114	0.32459	N	0.006068	T	0.00012	0.0000	N	0.19112	0.55	0.33472	P	0.41374200000000005	P;P;B	0.51147	0.657;0.942;0.189	B;P;B	0.48304	0.138;0.573;0.058	T	0.01276	-1.1398	9	0.66056	D	0.02	.	8.768	0.34715	0.0:0.722:0.0:0.278	rs17677991;rs57914890;rs17677991	139;1523;1523	B4DVS1;F5H7K2;E7ENI0	.;.;.	A	1523	ENSP00000219905:P1523A;ENSP00000374586:P1523A;ENSP00000442467:P1523A	ENSP00000219905:P1523A	P	+	1	0	MGA	39819675	1.000000	0.71417	0.990000	0.47175	0.940000	0.58332	1.448000	0.35112	0.919000	0.36945	-0.218000	0.12543	CCA	C|0.698;G|0.302	0.302	strong		0.488	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
BRF1	2972	hgsc.bcm.edu	37	14	105707747	105707747	+	Silent	SNP	C	C	T	rs144658695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105707747C>T	ENST00000546474.1	-	6	15508	c.549G>A	c.(547-549)ccG>ccA	p.P183P	BRF1_ENST00000327359.3_Silent_p.P68P|BRF1_ENST00000440513.3_Silent_p.P68P|BRF1_ENST00000392557.4_De_novo_Start_OutOfFrame|BRF1_ENST00000551787.1_De_novo_Start_OutOfFrame|BRF1_ENST00000379932.4_De_novo_Start_OutOfFrame|BRF1_ENST00000446501.2_Intron|BRF1_ENST00000379937.2_Silent_p.P156P	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	183					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		TATACAGGCACGGGTCTGCGG	0.627													C|||	13	0.00259585	0.0015	0.0	5008	,	,		18733	0.0		0.006	False		,,,				2504	0.0051				p.P183P		Atlas-SNP	.											.	BRF1	102	.	0			c.G549A						PASS	.	C	,,,,,	2,4396	6.2+/-15.9	0,2,2197	82.0	67.0	72.0		204,204,468,,549,	-9.0	0.8	14	dbSNP_134	72	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,utr-5	BRF1	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001242789.1,NM_001519.3,NM_145685.2	,,,,,	0,43,6456	TT,TC,CC		0.4767,0.0455,0.3308	,,,,,	68/585,68/563,156/651,,183/678,	105707747	43,12955	2199	4300	6499	SO:0001819	synonymous_variant	2972	exon6			CAGGCACGGGTCT	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.549G>A	14.37:g.105707747C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	3.854	-0.031251	0.07543	4.55E-4	0.004767	ENSG00000185024	ENST00000546417	.	.	.	4.51	-9.01	0.00744	.	.	.	.	.	T	0.27967	0.0689	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41324	-0.9515	4	.	.	.	.	3.9767	0.09478	0.0832:0.3485:0.3231:0.2452	.	.	.	.	M	37	.	.	V	-	1	0	BRF1	104778792	0.000000	0.05858	0.826000	0.32828	0.338000	0.28826	-4.034000	0.00309	-1.654000	0.01499	-0.191000	0.12829	GTG	C|0.997;T|0.003	0.003	strong		0.627	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
HECW1	23072	hgsc.bcm.edu	37	7	43540887	43540887	+	Silent	SNP	A	A	C	rs17339479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:43540887A>C	ENST00000395891.2	+	21	4202	c.3597A>C	c.(3595-3597)cgA>cgC	p.R1199R	HECW1_ENST00000453890.1_Silent_p.R1165R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1199					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1199R(2)|p.R1178R(1)		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						TCTCTCCCCGATGTTCACCCT	0.473													C|||	583	0.116414	0.0696	0.1499	5008	,	,		16872	0.0079		0.2068	False		,,,				2504	0.1748				p.R1199R		Atlas-SNP	.											HECW1_ENST00000395891,caecum,adenoma,+1,3	HECW1	540	3	3	Substitution - coding silent(3)	prostate(3)	c.A3597C						PASS	.	C		295,3569		6,283,1643	84.0	80.0	81.0		3597	1.7	1.0	7	dbSNP_123	81	1675,6575		184,1307,2634	no	coding-synonymous	HECW1	NM_015052.3		190,1590,4277	CC,CA,AA		20.303,7.6346,16.2622		1199/1607	43540887	1970,10144	1932	4125	6057	SO:0001819	synonymous_variant	23072	exon21			TCCCCGATGTTCA	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.3597A>C	7.37:g.43540887A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.838;C|0.162	0.162	strong		0.473	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
AK5	26289	hgsc.bcm.edu	37	1	77759578	77759578	+	Silent	SNP	A	A	G	rs2815311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:77759578A>G	ENST00000354567.2	+	3	611	c.348A>G	c.(346-348)gcA>gcG	p.A116A	AK5_ENST00000317704.4_3'UTR|AK5_ENST00000344720.5_Silent_p.A90A	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	116					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						CTGAGACTGCAGAGTTGATTG	0.428													A|||	576	0.115016	0.0613	0.1023	5008	,	,		14067	0.1359		0.2038	False		,,,				2504	0.0838				p.A116A		Atlas-SNP	.											.	AK5	86	.	0			c.A348G						PASS	.	A	,	333,4073	173.7+/-203.5	12,309,1882	69.0	70.0	69.0		270,348	-7.4	1.0	1	dbSNP_100	69	1806,6794	325.1+/-316.8	178,1450,2672	no	coding-synonymous,coding-synonymous	AK5	NM_012093.3,NM_174858.2	,	190,1759,4554	GG,GA,AA		21.0,7.5579,16.4463	,	90/537,116/563	77759578	2139,10867	2203	4300	6503	SO:0001819	synonymous_variant	26289	exon3			GACTGCAGAGTTG	AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"""Adenylate kinases"""	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.348A>G	1.37:g.77759578A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_174858	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Silent	SNP	ENST00000354567.2	37	CCDS675.1																																																																																			A|0.843;G|0.157	0.157	strong		0.428	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858	
TSACC	128229	hgsc.bcm.edu	37	1	156314497	156314497	+	Missense_Mutation	SNP	C	C	T	rs41265043	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000368253.2_Missense_Mutation_p.S54L|TSACC_ENST00000368251.1_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	33	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	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	
RCBTB1	55213	hgsc.bcm.edu	37	13	50134099	50134099	+	Silent	SNP	T	T	C	rs17073145	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50134099T>C	ENST00000378302.2	-	5	659	c.399A>G	c.(397-399)gtA>gtG	p.V133V	RCBTB1_ENST00000258646.3_Silent_p.V133V|RCBTB1_ENST00000546015.1_Silent_p.V133V	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	133					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		AGCCACAAGCTACTTCCACCA	0.438													C|||	1563	0.312101	0.5	0.1311	5008	,	,		19167	0.2788		0.167	False		,,,				2504	0.3701				p.V133V		Atlas-SNP	.											.	RCBTB1	34	.	0			c.A399G						PASS	.	C		1981,2425	617.7+/-393.0	440,1101,662	190.0	185.0	187.0		399	0.8	1.0	13	dbSNP_123	187	1257,7343	761.4+/-407.6	80,1097,3123	no	coding-synonymous	RCBTB1	NM_018191.3		520,2198,3785	CC,CT,TT		14.6163,44.9614,24.8962		133/532	50134099	3238,9768	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon5			ACAAGCTACTTCC	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.399A>G	13.37:g.50134099T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			T|0.733;C|0.267	0.267	strong		0.438	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
CEP131	22994	hgsc.bcm.edu	37	17	79182778	79182778	+	Silent	SNP	T	T	C	rs62075318	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79182778T>C	ENST00000269392.4	-	3	469	c.222A>G	c.(220-222)agA>agG	p.R74R	AZI1_ENST00000374782.3_Silent_p.R74R|AZI1_ENST00000450824.2_Silent_p.R74R|AZI1_ENST00000575907.1_Silent_p.R74R	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		74					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)			TGTTGGATCTTCTAAGGTTGT	0.592													T|||	2096	0.41853	0.0227	0.6095	5008	,	,		18179	0.626		0.4443	False		,,,				2504	0.5777				p.R74R		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,0,4	AZI1	145	4	0			c.A222G						PASS	.	T	,	442,3964	208.8+/-229.8	26,390,1787	79.0	78.0	78.0		222,222	-9.5	0.0	17	dbSNP_129	78	4061,4539	553.6+/-386.3	971,2119,1210	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	997,2509,2997	CC,CT,TT		47.2209,10.0318,34.6225	,	74/1045,74/1081	79182778	4503,8503	2203	4300	6503	SO:0001819	synonymous_variant	22994	exon3			GGATCTTCTAAGG																												ENST00000269392.4:c.222A>G	17.37:g.79182778T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				T|0.621;C|0.379	0.379	strong		0.592	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
TAS1R3	83756	hgsc.bcm.edu	37	1	1268159	1268159	+	Silent	SNP	C	C	T	rs3813210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1268159C>T	ENST00000339381.5	+	3	1280	c.1248C>T	c.(1246-1248)ccC>ccT	p.P416P		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	416					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		CAGGCTGCCCCGCGCAGGACC	0.652													c|||	704	0.140575	0.3185	0.1052	5008	,	,		17974	0.0794		0.0487	False		,,,				2504	0.0828				p.P416P		Atlas-SNP	.											.	TAS1R3	39	.	0			c.C1248T						PASS	.	C		1174,3222		153,868,1177	23.0	25.0	24.0		1248	-3.8	0.0	1	dbSNP_107	24	342,8252		12,318,3967	no	coding-synonymous	TAS1R3	NM_152228.1		165,1186,5144	TT,TC,CC		3.9795,26.7061,11.6705		416/853	1268159	1516,11474	2198	4297	6495	SO:0001819	synonymous_variant	83756	exon3			CTGCCCCGCGCAG	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1248C>T	1.37:g.1268159C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_152228	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																			C|0.874;T|0.126	0.126	strong		0.652	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
USH2A	7399	hgsc.bcm.edu	37	1	215848062	215848062	+	Silent	SNP	C	C	T	rs2009923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:215848062C>T	ENST00000307340.3	-	63	13577	c.13191G>A	c.(13189-13191)gaG>gaA	p.E4397E	USH2A_ENST00000366943.2_Silent_p.E4397E	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4397	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|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)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAGCAAGGGACTCTTTATTAT	0.473										HNSCC(13;0.011)			C|||	1019	0.203474	0.0348	0.1844	5008	,	,		18977	0.3522		0.1859	False		,,,				2504	0.3098				p.E4397E		Atlas-SNP	.											.	USH2A	1168	.	0			c.G13191A						PASS	.	C		274,4132	153.7+/-187.2	7,260,1936	61.0	64.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	13191	2.9	0.3	1	dbSNP_92	63	1605,6995	298.9+/-304.1	152,1301,2847	no	coding-synonymous	USH2A	NM_206933.2		159,1561,4783	TT,TC,CC		18.6628,6.2188,14.4472		4397/5203	215848062	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			AAGGGACTCTTTA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.13191G>A	1.37:g.215848062C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.826;A|0.003	.	strong		0.473	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
FREM1	158326	hgsc.bcm.edu	37	9	14770658	14770658	+	Silent	SNP	G	G	T	rs17219005	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:14770658G>T	ENST00000380880.3	-	26	5787	c.5004C>A	c.(5002-5004)atC>atA	p.I1668I	FREM1_ENST00000380894.1_Silent_p.I204I|FREM1_ENST00000422223.2_Silent_p.I1668I|FREM1_ENST00000380881.4_Silent_p.I1669I|FREM1_ENST00000486223.1_5'UTR			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	112	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	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	
DNAJB13	374407	hgsc.bcm.edu	37	11	73681090	73681090	+	Silent	SNP	C	C	T	rs2306819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73681090C>T	ENST00000339764.1	+	8	1633	c.882C>T	c.(880-882)ttC>ttT	p.F294F	DNAJB13_ENST00000543947.1_Silent_p.F119F|DNAJB13_ENST00000537753.1_Silent_p.F119F|RP11-167N4.2_ENST00000537019.1_RNA	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	294					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					TCATCTTCTTCGACATCCAGT	0.562													c|||	1263	0.252196	0.2095	0.3847	5008	,	,		18781	0.1637		0.3161	False		,,,				2504	0.2413				p.F294F		Atlas-SNP	.											.	DNAJB13	28	.	0			c.C882T						PASS	.	C		959,3441	362.9+/-316.3	97,765,1338	151.0	132.0	138.0		882	-6.4	0.9	11	dbSNP_100	138	2677,5909	429.8+/-356.3	392,1893,2008	no	coding-synonymous	DNAJB13	NM_153614.2		489,2658,3346	TT,TC,CC		31.1787,21.7955,27.9994		294/317	73681090	3636,9350	2200	4293	6493	SO:0001819	synonymous_variant	374407	exon8			CTTCTTCGACATC	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.882C>T	11.37:g.73681090C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_153614	B3LEP4|Q8IZW5	Silent	SNP	ENST00000339764.1	37	CCDS8227.1	579	0.2651098901098901	107	0.21747967479674796	130	0.35911602209944754	94	0.16433566433566432	248	0.32717678100263853	C	12.58	1.979869	0.34942	0.217955	0.311787	ENSG00000187726	ENST00000542350	.	.	.	5.54	-6.43	0.01926	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999713483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2747	0.43504	0.0:0.2988:0.094:0.6072	rs2306819;rs57057868;rs2306819	.	.	.	X	195	.	.	R	+	1	2	DNAJB13	73358738	0.032000	0.19561	0.862000	0.33874	0.988000	0.76386	-0.949000	0.03893	-1.213000	0.02617	-0.365000	0.07479	CGA	C|0.731;T|0.269	0.269	strong		0.562	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
FILIP1L	11259	hgsc.bcm.edu	37	3	99567247	99567247	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:99567247T>C	ENST00000354552.3	-	5	3743	c.3273A>G	c.(3271-3273)cgA>cgG	p.R1091R	CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000383694.2_Silent_p.R851R|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000331335.5_Silent_p.R1091R|FILIP1L_ENST00000471562.1_Silent_p.R851R|FILIP1L_ENST00000476723.1_Intron|FILIP1L_ENST00000487087.1_Silent_p.R667R	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	1091						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						AGCCTTGAGTTCGGTTATCCT	0.463																																					p.R1091R		Atlas-SNP	.											FILIP1L_ENST00000354552,NS,lymphoid_neoplasm,-2,2	FILIP1L	154	2	0			c.A3273G						scavenged	.						282.0	283.0	283.0					3																	99567247		2025	4184	6209	SO:0001819	synonymous_variant	11259	exon5			TTGAGTTCGGTTA		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.3273A>G	3.37:g.99567247T>C		Somatic	397	0	0		WXS	Illumina HiSeq	Phase_I	491	5	0.0101833	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Silent	SNP	ENST00000354552.3	37	CCDS43117.1																																																																																			.	.	none		0.463	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
ADRB2	154	hgsc.bcm.edu	37	5	148206473	148206473	+	Missense_Mutation	SNP	G	G	C	rs35892629|rs1042714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148206473G>C	ENST00000305988.4	+	1	318	c.79G>C	c.(79-81)Gaa>Caa	p.E27Q		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	27			E -> Q (in dbSNP:rs1042714). {ECO:0000269|PubMed:11246467, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2823249, ECO:0000269|PubMed:3025863, ECO:0000269|PubMed:3026848, ECO:0000269|PubMed:3033609, ECO:0000269|PubMed:3034889, ECO:0000269|PubMed:7915137, ECO:0000269|PubMed:8383511, ECO:0000269|Ref.10, ECO:0000269|Ref.11, ECO:0000269|Ref.12, ECO:0000269|Ref.8}.		activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	CGTCACGCAGGAAAGGGACGA	0.622													G|||	3985	0.795727	0.8638	0.7579	5008	,	,		17308	0.9266		0.5905	False		,,,				2504	0.8067				p.E27Q		Atlas-SNP	.											.	ADRB2	42	.	0			c.G79C	GRCh37	CM970061	ADRB2	M	rs1042714	PASS	.	G	GLN/GLU	3597,809	750.4+/-412.1	1474,649,80	159.0	148.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	79	4.0	0.5	5	dbSNP_86	152	4987,3613	626.2+/-397.8	1445,2097,758	yes	missense	ADRB2	NM_000024.5	29	2919,2746,838	CC,CG,GG		42.0116,18.3613,33.9997	benign	27/414	148206473	8584,4422	2203	4300	6503	SO:0001583	missense	154	exon1			ACGCAGGAAAGGG	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.79G>C	5.37:g.148206473G>C	ENSP00000305372:p.Glu27Gln	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Missense_Mutation	SNP	ENST00000305988.4	37	CCDS4292.1	1663	0.7614468864468864	414	0.8414634146341463	266	0.7348066298342542	532	0.9300699300699301	451	0.5949868073878628	G	2.677	-0.276314	0.05679	0.816387	0.579884	ENSG00000169252	ENST00000305988	T	0.37584	1.19	4.94	4.04	0.47022	.	0.565059	0.18728	N	0.132808	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14012	0.009	B	0.13407	0.009	T	0.25710	-1.0124	9	0.19590	T	0.45	.	11.1901	0.48679	0.0:0.1855:0.8145:0.0	rs1042714;rs3182175;rs3729941;rs17287411;rs17287474;rs17334200;rs17640526;rs17845338;rs17858183;rs17859733;rs52793394;rs60374884;rs1042714	27	P07550	ADRB2_HUMAN	Q	27	ENSP00000305372:E27Q	ENSP00000305372:E27Q	E	+	1	0	ADRB2	148186666	1.000000	0.71417	0.549000	0.28204	0.529000	0.34654	1.400000	0.34577	1.387000	0.46486	0.655000	0.94253	GAA	G|0.327;C|0.673	0.673	strong		0.622	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	94	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	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	
CCSER2	54462	hgsc.bcm.edu	37	10	86273249	86273249	+	Missense_Mutation	SNP	T	T	C	rs11557865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:86273249T>C	ENST00000224756.8	+	11	2640	c.2455T>C	c.(2455-2457)Tca>Cca	p.S819P	CCSER2_ENST00000372088.2_Silent_p.D790D|CCSER2_ENST00000543283.1_Missense_Mutation_p.S246P|CCSER2_ENST00000494144.1_3'UTR	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	819			S -> P (in dbSNP:rs11557865).		microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											GACCCACAGATCACACCCAGG	0.468													C|||	1084	0.216454	0.152	0.3631	5008	,	,		16776	0.2302		0.1948	False		,,,				2504	0.2076				p.S819P		Atlas-SNP	.											.	CCSER2	7	.	0			c.T2455C						PASS	.	C	PRO/SER	728,3678	758.9+/-412.8	63,602,1538	158.0	136.0	143.0		2455	6.0	1.0	10	dbSNP_120	143	1718,6882	737.3+/-407.0	174,1370,2756	yes	missense	FAM190B	NM_018999.2	74	237,1972,4294	CC,CT,TT		19.9767,16.5229,18.8067		819/835	86273249	2446,10560	2203	4300	6503	SO:0001583	missense	54462	exon11			CACAGATCACACC		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.2455T>C	10.37:g.86273249T>C	ENSP00000224756:p.Ser819Pro	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	37	CCDS31235.1	502	0.22985347985347984	81	0.16463414634146342	119	0.3287292817679558	144	0.2517482517482518	158	0.20844327176781002	C	1.035	-0.680603	0.03353	0.165229	0.199767	ENSG00000107771	ENST00000224756;ENST00000543283	T;T	0.15834	2.74;2.39	6.03	6.03	0.97812	.	0.137938	0.47455	N	0.000228	T	0.00012	0.0000	N	0.00436	-1.5	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	9	0.02654	T	1	2.2294	9.5382	0.39235	0.0:0.8425:0.0:0.1575	rs11557865;rs52810183;rs59787665;rs11557865	819	Q9H7U1	F190B_HUMAN	P	819;246	ENSP00000224756:S819P;ENSP00000439944:S246P	ENSP00000224756:S819P	S	+	1	0	FAM190B	86263229	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	2.860000	0.48372	1.579000	0.49836	-0.226000	0.12346	TCA	T|0.798;C|0.202	0.202	strong		0.468	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999	
HPS1	3257	hgsc.bcm.edu	37	10	100179851	100179851	+	Missense_Mutation	SNP	T	T	C	rs2296436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100179851T>C	ENST00000325103.6	-	18	2041	c.1808A>G	c.(1807-1809)cAg>cGg	p.Q603R	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Missense_Mutation_p.Q603R	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	603			Q -> R (in dbSNP:rs2296436).		blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		ATCCCCCTCCTGGAACAGCAG	0.587									Hermansky-Pudlak syndrome				T|||	618	0.123403	0.171	0.1196	5008	,	,		20716	0.1538		0.1103	False		,,,				2504	0.044				p.Q603R		Atlas-SNP	.											.	HPS1	65	.	0			c.A1808G						PASS	.	T	ARG/GLN	614,3792	266.5+/-267.3	38,538,1627	218.0	182.0	194.0		1808	3.4	1.0	10	dbSNP_100	194	728,7872	176.9+/-226.6	33,662,3605	yes	missense	HPS1	NM_000195.3	43	71,1200,5232	CC,CT,TT		8.4651,13.9355,10.3183	benign	603/701	100179851	1342,11664	2203	4300	6503	SO:0001583	missense	3257	exon18	Familial Cancer Database	HPS, HPS1-8	CCCTCCTGGAACA	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1808A>G	10.37:g.100179851T>C	ENSP00000326649:p.Gln603Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	55	0.572917	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	37	CCDS7475.1	300	0.13736263736263737	97	0.19715447154471544	39	0.10773480662983426	78	0.13636363636363635	86	0.11345646437994723	T	4.144	0.025165	0.08054	0.139355	0.084651	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891	T;T	0.40476	1.03;1.03	5.45	3.43	0.39272	.	0.252706	0.41294	N	0.000906	T	0.00012	0.0000	N	0.02315	-0.6	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.003;0.004	T	0.27872	-1.0061	9	0.02654	T	1	.	6.2945	0.21079	0.0:0.5165:0.0:0.4835	rs2296436;rs52796369;rs60019970;rs2296436	570;603;604	Q92902-2;Q8WXE5;D3DR62	.;.;.	R	603;603;570	ENSP00000326649:Q603R;ENSP00000355310:Q603R	ENSP00000326649:Q603R	Q	-	2	0	HPS1	100169841	0.913000	0.31002	0.983000	0.44433	0.911000	0.54048	1.305000	0.33493	0.498000	0.27948	0.459000	0.35465	CAG	.	.	none		0.587	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
SLC36A3	285641	hgsc.bcm.edu	37	5	150667016	150667016	+	Missense_Mutation	SNP	T	T	C	rs978012	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	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	
TMEM9	252839	hgsc.bcm.edu	37	1	201112981	201112981	+	Silent	SNP	A	A	G	rs8158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201112981A>G	ENST00000367330.1	-	4	882	c.366T>C	c.(364-366)taT>taC	p.Y122Y	TMEM9_ENST00000367334.5_Silent_p.Y122Y|TMEM9_ENST00000367332.1_Silent_p.Y125Y|TMEM9_ENST00000472411.1_5'UTR|TMEM9_ENST00000367333.2_Silent_p.Y122Y|TMEM9_ENST00000485839.2_Silent_p.Y122Y			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	122					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)		p.Y122Y(1)		liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				GTTGCTCAGTATATGCATCCG	0.567													G|||	3471	0.693091	0.6362	0.7133	5008	,	,		21567	0.626		0.7644	False		,,,				2504	0.7515				p.Y122Y		Atlas-SNP	.											TMEM9,NS,carcinoma,0,1	TMEM9	12	1	1	Substitution - coding silent(1)	stomach(1)	c.T366C						PASS	.	G		2910,1496	477.9+/-358.1	966,978,259	124.0	111.0	115.0		366	3.2	0.9	1	dbSNP_52	115	6611,1989	350.2+/-327.8	2532,1547,221	no	coding-synonymous	TMEM9	NM_016456.3		3498,2525,480	GG,GA,AA		23.1279,33.9537,26.7953		122/184	201112981	9521,3485	2203	4300	6503	SO:0001819	synonymous_variant	252839	exon5			CTCAGTATATGCA		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.366T>C	1.37:g.201112981A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_016456	B1ALM6|Q96NQ9|Q9BQF5	Silent	SNP	ENST00000367330.1	37	CCDS1408.1																																																																																			A|0.282;G|0.718	0.718	strong		0.567	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456	
CMYA5	202333	hgsc.bcm.edu	37	5	79031558	79031558	+	Missense_Mutation	SNP	G	G	A	rs62621912	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79031558G>A	ENST00000446378.2	+	2	7001	c.6970G>A	c.(6970-6972)Ggt>Agt	p.G2324S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2324					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)		TTCACTAATCGGTGAGAAATT	0.378													G|||	835	0.166733	0.0696	0.2003	5008	,	,		18940	0.2639		0.1451	False		,,,				2504	0.1963				p.G2324S		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6970A						PASS	.	G	SER/GLY	292,3394		11,270,1562	71.0	68.0	69.0		6970	-1.7	0.0	5	dbSNP_129	69	1160,7012		95,970,3021	yes	missense	CMYA5	NM_153610.3	56	106,1240,4583	AA,AG,GG		14.1948,7.9219,12.2449	probably-damaging	2324/4070	79031558	1452,10406	1843	4086	5929	SO:0001583	missense	202333	exon2			CTAATCGGTGAGA	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.6970G>A	5.37:g.79031558G>A	ENSP00000394770:p.Gly2324Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	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	358	0.16391941391941392	36	0.07317073170731707	70	0.19337016574585636	141	0.2465034965034965	111	0.14643799472295516	G	11.17	1.559197	0.27827	0.079219	0.141948	ENSG00000164309	ENST00000446378	T	0.21734	1.99	5.65	-1.67	0.08238	.	0.967888	0.08507	N	0.935481	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.25312	0.123	B	0.16289	0.015	T	0.40534	-0.9558	9	0.21540	T	0.41	.	0.4092	0.00438	0.311:0.1292:0.2954:0.2644	rs62621912	2324	Q8N3K9	CMYA5_HUMAN	S	2324	ENSP00000394770:G2324S	ENSP00000394770:G2324S	G	+	1	0	CMYA5	79067314	0.000000	0.05858	0.000000	0.03702	0.458000	0.32498	-0.308000	0.08156	-0.312000	0.08741	0.655000	0.94253	GGT	A|0.166;C|0.000;G|0.834	0.166	strong		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
RGS12	6002	hgsc.bcm.edu	37	4	3318726	3318726	+	Missense_Mutation	SNP	A	A	T	rs16844152	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3318726A>T	ENST00000344733.5	+	2	1733	c.829A>T	c.(829-831)Atg>Ttg	p.M277L	RGS12_ENST00000382788.3_Missense_Mutation_p.M277L|RGS12_ENST00000336727.3_Missense_Mutation_p.M277L|RGS12_ENST00000543385.1_Missense_Mutation_p.M277L	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	277	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.		M -> L (in dbSNP:rs16844152).		positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CATGAAGATCATGCACGACTG	0.647													A|||	221	0.0441294	0.0371	0.0231	5008	,	,		18329	0.0218		0.0477	False		,,,				2504	0.0879				p.M277L		Atlas-SNP	.											.	RGS12	128	.	0			c.A829T						PASS	.	A	LEU/MET,LEU/MET	129,4277	92.5+/-131.2	0,129,2074	38.0	38.0	38.0		829,829	-4.5	0.8	4	dbSNP_123	38	393,8207	125.0+/-183.6	10,373,3917	yes	missense,missense	RGS12	NM_002926.3,NM_198229.2	15,15	10,502,5991	TT,TA,AA		4.5698,2.9278,4.0135	benign,benign	277/1377,277/1448	3318726	522,12484	2203	4300	6503	SO:0001583	missense	6002	exon2			AAGATCATGCACG	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.829A>T	4.37:g.3318726A>T	ENSP00000339381:p.Met277Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	76	0.0347985347985348	21	0.042682926829268296	5	0.013812154696132596	10	0.017482517482517484	40	0.052770448548812667	A	9.960	1.222583	0.22457	0.029278	0.045698	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.95	-4.53	0.03462	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.246278	0.45606	N	0.000349	T	0.00967	0.0032	L	0.31752	0.955	0.80722	D	1	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.16289	0.015;0.004;0.01	T	0.43556	-0.9384	10	0.12766	T	0.61	-11.3624	8.9568	0.35823	0.35:0.5694:0.0806:0.0	rs16844152;rs56640892;rs16844152	277;277;277	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	L	277	ENSP00000440566:M277L;ENSP00000339381:M277L;ENSP00000338509:M277L;ENSP00000372238:M277L	ENSP00000338509:M277L	M	+	1	0	RGS12	3288524	0.999000	0.42202	0.834000	0.33040	0.797000	0.45037	2.511000	0.45476	-1.062000	0.03181	-0.415000	0.06103	ATG	A|0.961;T|0.039	0.039	strong		0.647	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
ATXN1	6310	hgsc.bcm.edu	37	6	16328068	16328068	+	Silent	SNP	T	T	C	rs2072736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:16328068T>C	ENST00000244769.4	-	8	1410	c.474A>G	c.(472-474)gcA>gcG	p.A158A	ATXN1_ENST00000436367.1_Silent_p.A158A	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	158					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCGAGGCCACTGCACTGGTGA	0.627													C|||	1093	0.218251	0.2882	0.1801	5008	,	,		14127	0.374		0.0447	False		,,,				2504	0.1687				p.A158A		Atlas-SNP	.											ATXN1,middle_lobe,carcinoma,-1,1	ATXN1	117	1	0			c.A474G						PASS	.	C	,	989,3403		107,775,1314	55.0	62.0	59.0		474,474	-5.0	0.8	6	dbSNP_96	59	383,8201		7,369,3916	no	coding-synonymous,coding-synonymous	ATXN1	NM_000332.3,NM_001128164.1	,	114,1144,5230	CC,CT,TT		4.4618,22.5182,10.5734	,	158/816,158/816	16328068	1372,11604	2196	4292	6488	SO:0001819	synonymous_variant	6310	exon7			GGCCACTGCACTG	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.474A>G	6.37:g.16328068T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Silent	SNP	ENST00000244769.4	37	CCDS34342.1																																																																																			T|0.864;C|0.136	0.136	strong		0.627	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
DMXL2	23312	hgsc.bcm.edu	37	15	51791559	51791559	+	Missense_Mutation	SNP	A	A	G	rs12102203	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51791559A>G	ENST00000251076.5	-	18	4149	c.3862T>C	c.(3862-3864)Tct>Cct	p.S1288P	DMXL2_ENST00000449909.3_Intron|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.S1288P	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1288			S -> P (in dbSNP:rs12102203). {ECO:0000269|PubMed:10048485, ECO:0000269|PubMed:15489334}.			cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.S1288P(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCTGCATTAGAACTATCAGCT	0.398													G|||	2190	0.4373	0.3941	0.4914	5008	,	,		24831	0.4087		0.5149	False		,,,				2504	0.407				p.S1288P		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	1	1	Substitution - Missense(1)	stomach(1)	c.T3862C						PASS	.	G	PRO/SER,,PRO/SER	1902,2486	616.4+/-392.8	414,1074,706	166.0	164.0	165.0		3862,,3862	1.7	0.7	15	dbSNP_120	165	4332,4254	570.7+/-389.4	1106,2120,1067	yes	missense,intron,missense	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	74,,74	1520,3194,1773	GG,GA,AA		49.5458,43.3455,48.0499	benign,,benign	1288/3038,,1288/3037	51791559	6234,6740	2194	4293	6487	SO:0001583	missense	23312	exon18			CATTAGAACTATC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.3862T>C	15.37:g.51791559A>G	ENSP00000251076:p.Ser1288Pro	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	1039	0.4757326007326007	210	0.4268292682926829	174	0.48066298342541436	260	0.45454545454545453	395	0.521108179419525	G	0.413	-0.912045	0.02415	0.433455	0.504542	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.21932	1.98;1.98	5.66	1.7	0.24286	.	0.673581	0.16046	N	0.232187	T	0.00012	0.0000	L	0.27053	0.805	0.54753	P	1.0999999999983245E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44128	-0.9348	9	0.35671	T	0.21	.	9.3262	0.37995	0.5114:0.0:0.4885:0.0	rs12102203;rs17609478;rs52792675;rs56869598;rs12102203	1288;1288	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	P	1288	ENSP00000251076:S1288P;ENSP00000441858:S1288P	ENSP00000251076:S1288P	S	-	1	0	DMXL2	49578851	0.605000	0.26941	0.679000	0.29978	0.067000	0.16453	0.251000	0.18257	0.088000	0.17205	-0.186000	0.12905	TCT	A|0.527;G|0.472	0.472	strong		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
OR52I1	390037	hgsc.bcm.edu	37	11	4616119	4616119	+	Missense_Mutation	SNP	T	T	C	rs61997192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4616119T>C	ENST00000530443.2	+	1	851	c.851T>C	c.(850-852)cTg>cCg	p.L284P	OR52I1_ENST00000450052.2_Missense_Mutation_p.L308P	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	284						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(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTAGCTGACCTGTACGTGATC	0.488													T|||	95	0.0189696	0.0015	0.0418	5008	,	,		18899	0.0		0.0517	False		,,,				2504	0.0123				p.L284P		Atlas-SNP	.											.	OR52I1	29	.	0			c.T851C						PASS	.	T	PRO/LEU	54,4348	51.6+/-87.1	2,50,2149	147.0	140.0	142.0		851	5.0	0.7	11	dbSNP_129	142	516,8080	146.9+/-202.4	20,476,3802	no	missense	OR52I1	NM_001005169.1	98	22,526,5951	CC,CT,TT		6.0028,1.2267,4.3853	probably-damaging	284/325	4616119	570,12428	2201	4298	6499	SO:0001583	missense	390037	exon1			CTGACCTGTACGT	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.851T>C	11.37:g.4616119T>C	ENSP00000436453:p.Leu284Pro	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	172	74	0.430233	NM_001005169	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	64	0.029304029304029304	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	39	0.051451187335092345	T	11.31	1.601680	0.28534	0.012267	0.060028	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.73681	-0.77;-0.77	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.422957	0.17347	N	0.177532	T	0.54351	0.1853	M	0.91612	3.225	0.35959	D	0.834439	D	0.89917	1.0	D	0.77004	0.989	T	0.81837	-0.0749	9	0.87932	D	0	-11.1723	12.8837	0.58032	0.0:0.0:0.0:1.0	rs61997192	284	Q8NGK6	O52I1_HUMAN	P	308;284	ENSP00000409094:L308P;ENSP00000436453:L284P	ENSP00000409094:L308P	L	+	2	0	OR52I1	4572695	0.039000	0.19947	0.663000	0.29738	0.012000	0.07955	2.055000	0.41345	2.212000	0.71576	0.454000	0.30748	CTG	T|0.967;C|0.033	0.033	strong		0.488	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632744	32632744	+	Silent	SNP	C	C	T	rs1049082	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632744C>T	ENST00000399084.1	-	3	388	c.210G>A	c.(208-210)gcG>gcA	p.A70A	HLA-DQB1_ENST00000434651.2_Silent_p.A70A|HLA-DQB1_ENST00000374943.4_Silent_p.A70A|HLA-DQB1_ENST00000399079.3_Silent_p.A70A|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	70	Beta-1.		A -> T (in allele DQB1*03:20; dbSNP:rs45519640).|A -> V (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*06:01, allele DQB1*06:28 and allele DQB1*06:35; dbSNP:rs1063318).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TGTCGAAGCGCGCGTACTCCT	0.607									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1874	0.374201	0.2806	0.4827	5008	,	,		6825	0.4365		0.3897	False		,,,				2504	0.3436				p.A70A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G210A						PASS	.	C		1037,3243		221,595,1324	37.0	37.0	37.0		210	3.1	0.9	6	dbSNP_86	37	3122,5344		846,1430,1957	no	coding-synonymous	HLA-DQB1	NM_002123.4		1067,2025,3281	TT,TC,CC		36.8769,24.229,32.6298		70/262	32632744	4159,8587	2140	4233	6373	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GAAGCGCGCGTAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.210G>A	6.37:g.32632744C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	35	32	0.914286	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			C|0.668;T|0.332	0.332	strong		0.607	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
CEACAM20	125931	hgsc.bcm.edu	37	19	45016116	45016116	+	RNA	SNP	A	A	G	rs8100718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	123	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	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	
ERCC2	2068	hgsc.bcm.edu	37	19	45867259	45867259	+	Missense_Mutation	SNP	C	C	T	rs1799793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45867259C>T	ENST00000391945.4	-	10	1011	c.934G>A	c.(934-936)Gac>Aac	p.D312N	ERCC2_ENST00000391944.3_Missense_Mutation_p.D234N|ERCC2_ENST00000221481.6_3'UTR|ERCC2_ENST00000485403.2_Missense_Mutation_p.D288N|ERCC2_ENST00000391940.4_Missense_Mutation_p.D288N	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	312			D -> N (in dbSNP:rs1799793). {ECO:0000269|PubMed:11245433, ECO:0000269|PubMed:11470747, ECO:0000269|PubMed:11709541, ECO:0000269|Ref.3}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|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 initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGCACTTCGTCGGGCAGCACG	0.746			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	974	0.194489	0.0734	0.1988	5008	,	,		10423	0.0496		0.3588	False		,,,				2504	0.3354				p.D312N		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.G934A	GRCh37	CM015299	ERCC2	M	rs1799793	PASS	.	C	ASN/ASP,ASN/ASP	387,3577		30,327,1625	5.0	8.0	7.0		934,862	5.2	0.5	19	dbSNP_89	7	2507,5397		444,1619,1889	no	missense,missense	ERCC2	NM_000400.3,NM_001130867.1	23,23	474,1946,3514	TT,TC,CC		31.7181,9.7629,24.3849	benign,benign	312/761,288/406	45867259	2894,8974	1982	3952	5934	SO:0001583	missense	2068	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTTCGTCGGGCAG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.934G>A	19.37:g.45867259C>T	ENSP00000375809:p.Asp312Asn	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	423	0.1936813186813187	34	0.06910569105691057	70	0.19337016574585636	38	0.06643356643356643	281	0.370712401055409	C	20.0	3.930510	0.73327	0.097629	0.317181	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940	T;T;T	0.64438	-0.1;-0.1;-0.1	5.15	5.15	0.70609	Domain of unknown function DUF1227 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.46947	1.48	0.09310	P	1.0	B;P;B	0.34639	0.065;0.461;0.053	B;B;B	0.35353	0.059;0.201;0.051	T	0.28267	-1.0049	9	0.33940	T	0.23	-30.0006	16.1268	0.81402	0.0:1.0:0.0:0.0	rs1799793;rs3916814;rs58989209;rs1799793	234;288;312	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	N	262;288;312;234;288	ENSP00000375809:D312N;ENSP00000375808:D234N;ENSP00000375804:D288N	ENSP00000375804:D288N	D	-	1	0	ERCC2	50559099	1.000000	0.71417	0.523000	0.27875	0.865000	0.49528	7.192000	0.77771	2.388000	0.81334	0.561000	0.74099	GAC	C|0.804;T|0.196	0.196	strong		0.746	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
TEX14	56155	hgsc.bcm.edu	37	17	56636908	56636908	+	Silent	SNP	T	T	C	rs9903050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56636908T>C	ENST00000240361.8	-	31	4396	c.4311A>G	c.(4309-4311)aaA>aaG	p.K1437K	TEX14_ENST00000584699.1_5'UTR|TEX14_ENST00000349033.5_Silent_p.K1391K|TEX14_ENST00000389934.3_Silent_p.K1431K|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA			Q8IWB6	TEX14_HUMAN	testis expressed 14	1437					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTTTTGATCTTTGATATTTG	0.363													T|||	1385	0.276558	0.3359	0.1182	5008	,	,		19276	0.3036		0.1978	False		,,,				2504	0.362				p.K1437K		Atlas-SNP	.											.	TEX14	343	.	0			c.A4311G						PASS	.	T	,,	1296,3110	431.4+/-342.9	182,932,1089	201.0	195.0	197.0		4311,4173,4293	-0.6	0.9	17	dbSNP_119	197	1587,7013	283.9+/-296.4	161,1265,2874	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	343,2197,3963	CC,CT,TT		18.4535,29.4144,22.1667	,,	1437/1498,1391/1452,1431/1492	56636908	2883,10123	2203	4300	6503	SO:0001819	synonymous_variant	56155	exon31			TTGATCTTTGATA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.4311A>G	17.37:g.56636908T>C		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	441	207	0.469388	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																			T|0.759;C|0.241	0.241	strong		0.363	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
FAM8A1	51439	hgsc.bcm.edu	37	6	17601213	17601213	+	Silent	SNP	C	C	T	rs61736671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17601213C>T	ENST00000259963.3	+	1	628	c.573C>T	c.(571-573)gcC>gcT	p.A191A		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	191						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			GGACAGCTGCCGGCATCAGCA	0.741													C|||	49	0.00978435	0.0038	0.0173	5008	,	,		12226	0.0		0.0189	False		,,,				2504	0.0133				p.A191A		Atlas-SNP	.											.	FAM8A1	26	.	0			c.C573T						PASS	.	C		20,3506		0,20,1743	4.0	5.0	5.0		573	-8.8	0.0	6	dbSNP_129	5	182,6986		1,180,3403	no	coding-synonymous	FAM8A1	NM_016255.2		1,200,5146	TT,TC,CC		2.5391,0.5672,1.8889		191/414	17601213	202,10492	1763	3584	5347	SO:0001819	synonymous_variant	51439	exon1			AGCTGCCGGCATC	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.573C>T	6.37:g.17601213C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_016255	B2R725	Silent	SNP	ENST00000259963.3	37	CCDS4540.1																																																																																			C|0.991;T|0.009	0.009	strong		0.741	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1		
CPAMD8	27151	hgsc.bcm.edu	37	19	17108094	17108094	+	Missense_Mutation	SNP	C	C	T	rs143454938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	162	55	0.339506	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	
BDP1	55814	hgsc.bcm.edu	37	5	70798541	70798541	+	Missense_Mutation	SNP	A	A	G	rs36009281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	107	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	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	
ABCB11	8647	hgsc.bcm.edu	37	2	169830328	169830328	+	Missense_Mutation	SNP	A	A	G	rs2287622	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:169830328A>G	ENST00000263817.6	-	13	1455	c.1331T>C	c.(1330-1332)gTc>gCc	p.V444A		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	444	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		V -> A (more frequent in patients with drug-induced cholestasis than healthy controls; associated with lower hepatic expression; does not affect transport capacity for taurocholate; dbSNP:rs2287622). {ECO:0000269|PubMed:11829140, ECO:0000269|PubMed:15077010, ECO:0000269|PubMed:16763017, ECO:0000269|PubMed:16799996, ECO:0000269|PubMed:17264802, ECO:0000269|Ref.2}.|V -> D (in dbSNP:rs2287622).|V -> G (in dbSNP:rs2287622).		bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TGGTTTAATGACCATGTTGAG	0.438													A|||	2948	0.588658	0.5537	0.4524	5008	,	,		19286	0.6984		0.6044	False		,,,				2504	0.6033				p.V444A		Atlas-SNP	.											.	ABCB11	136	.	0			c.T1331C	GRCh37	CM071525	ABCB11	M	rs2287622	PASS	.	A	ALA/VAL	2194,1552		652,890,331	134.0	127.0	129.0		1331	4.6	1.0	2	dbSNP_100	129	4941,3289		1500,1941,674	yes	missense	ABCB11	NM_003742.2	64	2152,2831,1005	GG,GA,AA		39.9635,41.4309,40.4225	benign	444/1322	169830328	7135,4841	1873	4115	5988	SO:0001583	missense	8647	exon13			TTAATGACCATGT	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.1331T>C	2.37:g.169830328A>G	ENSP00000263817:p.Val444Ala	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	1297	0.5938644688644689	266	0.540650406504065	182	0.5027624309392266	398	0.6958041958041958	451	0.5949868073878628	A	12.71	2.019565	0.35606	0.585691	0.600365	ENSG00000073734	ENST00000263817	D	0.93307	-3.2	5.78	4.62	0.57501	ABC transporter-like (1);	0.518639	0.22383	N	0.060788	T	0.00012	0.0000	N	0.02765	-0.5	0.28281	P	0.9239859	B	0.06786	0.001	B	0.08055	0.003	T	0.49224	-0.8962	9	0.25751	T	0.34	.	11.852	0.52417	0.9315:0.0:0.0685:0.0	rs2287622;rs52815003;rs60464808;rs2287622	444	O95342	ABCBB_HUMAN	A	444	ENSP00000263817:V444A	ENSP00000263817:V444A	V	-	2	0	ABCB11	169538574	0.929000	0.31497	1.000000	0.80357	0.924000	0.55760	2.033000	0.41136	1.114000	0.41781	0.533000	0.62120	GTC	T|0.006;G|0.594;C|0.006;A|0.395	0.594	strong		0.438	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
USP16	10600	hgsc.bcm.edu	37	21	30408670	30408670	+	Missense_Mutation	SNP	A	A	T	rs2274802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:30408670A>T	ENST00000334352.4	+	6	654	c.423A>T	c.(421-423)caA>caT	p.Q141H	USP16_ENST00000399976.2_Missense_Mutation_p.Q141H|USP16_ENST00000399975.3_Missense_Mutation_p.Q141H|USP16_ENST00000535828.1_Intron	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						TCAGAAAACAAGCCAGCATTA	0.353													A|||	891	0.177915	0.0885	0.17	5008	,	,		19840	0.1131		0.2783	False		,,,				2504	0.2679				p.Q141H	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.A423T						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN	508,3898	235.5+/-248.0	31,446,1726	144.0	137.0	139.0		423,423,423	2.0	1.0	21	dbSNP_100	139	2121,6479	367.5+/-334.7	264,1593,2443	yes	missense,missense,missense	USP16	NM_001001992.1,NM_001032410.1,NM_006447.2	24,24,24	295,2039,4169	TT,TA,AA		24.6628,11.5297,20.2137	possibly-damaging,possibly-damaging,possibly-damaging	141/823,141/824,141/824	30408670	2629,10377	2203	4300	6503	SO:0001583	missense	10600	exon5			AAAACAAGCCAGC	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"""Ubiquitin-specific peptidases"""	12614	protein-coding gene	gene with protein product		604735	"""ubiquitin specific protease 16"""			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.423A>T	21.37:g.30408670A>T	ENSP00000334808:p.Gln141His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_006447		Missense_Mutation	SNP	ENST00000334352.4	37	CCDS13583.1	375	0.1717032967032967	43	0.08739837398373984	66	0.18232044198895028	61	0.10664335664335664	205	0.2704485488126649	A	8.584	0.883010	0.17467	0.115297	0.246628	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352	T;T;T	0.06294	3.32;3.35;3.35	5.85	2.02	0.26589	Zinc finger, RING/FYVE/PHD-type (1);	0.104153	0.64402	D	0.000002	T	0.00012	0.0000	N	0.11201	0.11	0.09310	P	0.9999999999999911	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.77004	0.961;0.989;0.961	T	0.20240	-1.0281	9	0.06494	T	0.89	.	6.7394	0.23426	0.7366:0.1286:0.1349:0.0	rs2274802;rs17852823;rs52826900;rs2274802	127;141;141	Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;UBP16_HUMAN	H	141	ENSP00000382857:Q141H;ENSP00000382858:Q141H;ENSP00000334808:Q141H	ENSP00000334808:Q141H	Q	+	3	2	USP16	29330541	1.000000	0.71417	0.969000	0.41365	0.293000	0.27360	3.760000	0.55235	0.478000	0.27488	0.533000	0.62120	CAA	A|0.804;T|0.196	0.196	strong		0.353	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1		
ZFP28	140612	hgsc.bcm.edu	37	19	57065189	57065189	+	Silent	SNP	T	T	C	rs145011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57065189T>C	ENST00000301318.3	+	8	1106	c.1035T>C	c.(1033-1035)ttT>ttC	p.F345F	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	345					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.F345F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		ACTATGTGTTTGGAAGGAAGC	0.388													T|||	1160	0.231629	0.0545	0.304	5008	,	,		18113	0.3294		0.2396	False		,,,				2504	0.3108				p.F345F	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,1	ZFP28	99	1	1	Substitution - coding silent(1)	stomach(1)	c.T1035C						PASS	.	T		322,4084	170.5+/-200.9	9,304,1890	84.0	77.0	80.0		1035	3.7	1.0	19	dbSNP_80	80	2173,6427	372.1+/-336.5	298,1577,2425	no	coding-synonymous	ZFP28	NM_020828.1		307,1881,4315	CC,CT,TT		25.2674,7.3082,19.1835		345/869	57065189	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	140612	exon8			TGTGTTTGGAAGG		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1035T>C	19.37:g.57065189T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Silent	SNP	ENST00000301318.3	37	CCDS12946.1																																																																																			T|0.798;C|0.202	0.202	strong		0.388	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
OR9G1	390174	hgsc.bcm.edu	37	11	56468638	56468638	+	Missense_Mutation	SNP	G	G	T	rs7121276	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56468638G>T	ENST00000312153.1	+	1	775	c.775G>T	c.(775-777)Gct>Tct	p.A259S		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	259			A -> S (in dbSNP:rs7121276).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTACATCTACGCTCTCCCCAG	0.448													G|||	548	0.109425	0.2209	0.098	5008	,	,		20049	0.0129		0.1402	False		,,,				2504	0.0348				p.A259S		Atlas-SNP	.											.	.	.	.	0			c.G775T						PASS	.	G	SER/ALA	883,3519		0,883,1318	222.0	232.0	229.0		775	-9.2	0.0	11	dbSNP_116	229	1097,7495		0,1097,3199	yes	missense	OR9G1	NM_001005213.1	99	0,1980,4517	TT,TG,GG		12.7677,20.0591,15.2378	benign	259/306	56468638	1980,11014	2201	4296	6497	SO:0001583	missense	504191	exon1			ATCTACGCTCTCC	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.775G>T	11.37:g.56468638G>T	ENSP00000309012:p.Ala259Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	126	53	0.420635	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	230	0.10531135531135531	94	0.1910569105691057	28	0.07734806629834254	6	0.01048951048951049	102	0.1345646437994723	G	0.277	-0.988898	0.02162	0.200591	0.127677	ENSG00000174914	ENST00000312153	T	0.37411	1.2	4.62	-9.23	0.00672	GPCR, rhodopsin-like superfamily (1);	1.012140	0.07923	N	0.976244	T	0.00012	0.0000	N	0.13327	0.33	0.09310	N	1	B	0.09022	0.002	B	0.17722	0.019	T	0.25117	-1.0141	10	0.49607	T	0.09	-0.9312	2.053	0.03574	0.2562:0.123:0.4045:0.2162	rs7121276;rs52837721;rs59679378;rs7121276	259	Q8NH87	OR9G1_HUMAN	S	259	ENSP00000309012:A259S	ENSP00000309012:A259S	A	+	1	0	OR9G1	56225214	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-3.055000	0.00626	-2.019000	0.00942	-1.120000	0.02017	GCT	G|0.877;T|0.123	0.123	strong		0.448	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
CAPN2	824	hgsc.bcm.edu	37	1	223954080	223954080	+	Missense_Mutation	SNP	A	A	C	rs17599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223954080A>C	ENST00000295006.5	+	16	2011	c.1702A>C	c.(1702-1704)Aag>Cag	p.K568Q	CAPN2_ENST00000433674.2_Missense_Mutation_p.K490Q|CAPN2_ENST00000474026.1_3'UTR	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	568	Domain IV.		K -> Q (in dbSNP:rs17599). {ECO:0000269|Ref.4}.		blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.K568Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CCAAGATATCAAGTCAGATGG	0.403													A|||	1038	0.207268	0.0983	0.2493	5008	,	,		22375	0.2698		0.2425	False		,,,				2504	0.2239				p.K568Q		Atlas-SNP	.											CAPN2,NS,carcinoma,0,1	CAPN2	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1702C						PASS	.	A	GLN/LYS,GLN/LYS	554,3852	249.3+/-256.8	38,478,1687	142.0	126.0	132.0		1468,1702	5.5	1.0	1	dbSNP_63	132	2104,6496	362.6+/-332.8	269,1566,2465	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	53,53	307,2044,4152	CC,CA,AA		24.4651,12.5738,20.4367	probably-damaging,probably-damaging	490/623,568/701	223954080	2658,10348	2203	4300	6503	SO:0001583	missense	824	exon16			GATATCAAGTCAG	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1702A>C	1.37:g.223954080A>C	ENSP00000295006:p.Lys568Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	466	0.21336996336996336	51	0.10365853658536585	91	0.2513812154696133	132	0.23076923076923078	192	0.2532981530343008	A	16.47	3.132564	0.56828	0.125738	0.244651	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.32988	1.43;1.43	5.47	5.47	0.80525	EF-hand-like domain (1);	0.154834	0.56097	D	0.000021	T	0.00012	0.0000	M	0.77712	2.385	0.09310	P	0.999999146384	B;B;B	0.17465	0.007;0.022;0.007	B;B;B	0.27796	0.032;0.083;0.02	T	0.07424	-1.0773	9	0.59425	D	0.04	.	15.5473	0.76112	1.0:0.0:0.0:0.0	rs17599;rs1130849;rs3190187;rs3738372;rs11547592;rs17318843;rs17398495;rs52809008;rs59544343;rs3738372	490;151;568	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	Q	490;568;597	ENSP00000413158:K490Q;ENSP00000295006:K568Q	ENSP00000295006:K568Q	K	+	1	0	CAPN2	222020703	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.158000	0.77470	2.069000	0.61940	0.459000	0.35465	AAG	A|0.649;C|0.175;G|0.031;T|0.145	0.175	strong		0.403	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
FAM71E2	284418	hgsc.bcm.edu	37	19	55870835	55870835	+	Silent	SNP	A	A	C	rs113307911	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55870835A>C	ENST00000424985.3	-	9	1594	c.1401T>G	c.(1399-1401)gcT>gcG	p.A467A	CTD-2105E13.6_ENST00000591954.3_Missense_Mutation_p.L17R	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	467	Ala-rich.|Pro-rich.									NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						TCTGGGATGGAGCAGGTACGG	0.667													a|||	169	0.033746	0.0045	0.0793	5008	,	,		9699	0.0		0.0835	False		,,,				2504	0.0245				p.A467A		Atlas-SNP	.											.	FAM71E2	41	.	0			c.T1401G						PASS	.						4.0	9.0	7.0					19																	55870835		649	1515	2164	SO:0001819	synonymous_variant	284418	exon9			GGATGGAGCAGGT	AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.1401T>G	19.37:g.55870835A>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001145402	Q8ND99	Silent	SNP	ENST00000424985.3	37																																																																																				A|0.953;C|0.047	0.047	strong		0.667	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
CHTF18	63922	hgsc.bcm.edu	37	16	847743	847743	+	Missense_Mutation	SNP	C	C	T	rs2294451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:847743C>T	ENST00000262315.9	+	21	2846	c.2783C>T	c.(2782-2784)cCg>cTg	p.P928L	CHTF18_ENST00000455171.2_Missense_Mutation_p.P956L|CHTF18_ENST00000317063.6_Missense_Mutation_p.P1137L	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	928			P -> L (in dbSNP:rs2294451). {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)				ACAGCAGTCCCGAGTGCAGGT	0.627													C|||	760	0.151757	0.0144	0.147	5008	,	,		6422	0.245		0.1958	False		,,,				2504	0.1994				p.P928L		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2783T						PASS	.	C	LEU/PRO	141,3727		3,135,1796	65.0	64.0	64.0		2783	0.3	0.0	16	dbSNP_100	64	1720,6532		172,1376,2578	yes	missense	CHTF18	NM_022092.2	98	175,1511,4374	TT,TC,CC		20.8434,3.6453,15.3548	benign	928/976	847743	1861,10259	1934	4126	6060	SO:0001583	missense	63922	exon21			CAGTCCCGAGTGC	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.2783C>T	16.37:g.847743C>T	ENSP00000262315:p.Pro928Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	370	0.16941391941391942	13	0.026422764227642278	58	0.16022099447513813	148	0.25874125874125875	151	0.19920844327176782	C	9.164	1.019354	0.19355	0.036453	0.208434	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.11930	2.73;2.78;2.78	4.85	0.291	0.15732	.	0.475979	0.23072	N	0.052255	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.06405	0.002;0.002	T	0.42816	-0.9429	9	0.36615	T	0.2	-11.8552	8.2344	0.31616	0.0:0.7785:0.1205:0.101	rs2294451;rs3197376;rs17856179;rs52802857;rs58362911;rs2294451	956;928	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	L	1137;956;928	ENSP00000313029:P1137L;ENSP00000406252:P956L;ENSP00000262315:P928L	ENSP00000262315:P928L	P	+	2	0	CHTF18	787744	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.115000	0.01328	-0.182000	0.10602	-0.218000	0.12543	CCG	C|0.833;T|0.167	0.167	strong		0.627	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
MUC16	94025	hgsc.bcm.edu	37	19	9076950	9076950	+	Missense_Mutation	SNP	C	C	A	rs2547076	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076950C>A	ENST00000397910.4	-	3	10699	c.10496G>T	c.(10495-10497)aGg>aTg	p.R3499M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3500	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						TACATTGGCCCTCAGAGTCTC	0.502													A|||	1243	0.248203	0.2005	0.2118	5008	,	,		24394	0.249		0.3121	False		,,,				2504	0.272				p.R3499M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G10496T						PASS	.	A	MET/ARG	886,3278		102,682,1298	127.0	121.0	123.0		10496	0.5	0.0	19	dbSNP_100	123	2432,6002		352,1728,2137	yes	missense	MUC16	NM_024690.2	91	454,2410,3435	AA,AC,CC		28.8357,21.2776,26.3375	benign	3499/14508	9076950	3318,9280	2082	4217	6299	SO:0001583	missense	94025	exon3			TTGGCCCTCAGAG	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.10496G>T	19.37:g.9076950C>A	ENSP00000381008:p.Arg3499Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	a	2.270	-0.367308	0.05069	0.212776	0.288357	ENSG00000181143	ENST00000397910	T	0.02974	4.09	1.51	0.457	0.16661	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.48692	-0.9013	8	0.87932	D	0	.	2.3614	0.04308	0.4966:0.3054:0.198:0.0	rs2547076;rs17418490;rs57816798;rs2547076	3499	B5ME49	.	M	3499	ENSP00000381008:R3499M	ENSP00000381008:R3499M	R	-	2	0	MUC16	8937950	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-0.617000	0.05584	-0.277000	0.09193	-1.032000	0.02404	AGG	C|0.750;A|0.250	0.250	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
L1TD1	54596	hgsc.bcm.edu	37	1	62675673	62675673	+	Missense_Mutation	SNP	G	G	T	rs532563709|rs386631745|rs200789118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62675673G>T	ENST00000498273.1	+	4	1522	c.1227G>T	c.(1225-1227)gaG>gaT	p.E409D	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	409	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						aggaggaagagccctcagggc	0.557													G|||	160	0.0319489	0.0658	0.0231	5008	,	,		15817	0.001		0.0417	False		,,,				2504	0.0143				p.E409D		Atlas-SNP	.											.	L1TD1	114	.	0			c.G1227T						PASS	.						34.0	38.0	36.0					1																	62675673		2200	4298	6498	SO:0001583	missense	54596	exon5			GGAAGAGCCCTCA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1227G>T	1.37:g.62675673G>T	ENSP00000419901:p.Glu409Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	69	23	0.333333	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.695799	0.30052	.	.	ENSG00000240563	ENST00000498273	T	0.18810	2.19	3.26	-1.27	0.09347	.	.	.	.	.	T	0.08088	0.0202	N	0.12182	0.205	0.09310	N	1	B	0.17852	0.024	B	0.15870	0.014	T	0.39099	-0.9630	9	0.13108	T	0.6	.	2.2943	0.04146	0.1154:0.3623:0.3374:0.1849	.	409	Q5T7N2	LITD1_HUMAN	D	409	ENSP00000419901:E409D	ENSP00000419901:E409D	E	+	3	2	L1TD1	62448261	0.001000	0.12720	0.000000	0.03702	0.109000	0.19521	-0.211000	0.09332	-0.223000	0.09943	0.448000	0.29417	GAG	.	.	weak		0.557	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
CDCA2	157313	hgsc.bcm.edu	37	8	25364960	25364960	+	Silent	SNP	A	A	G	rs6990278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:25364960A>G	ENST00000330560.3	+	15	3255	c.2778A>G	c.(2776-2778)acA>acG	p.T926T	CDCA2_ENST00000521098.2_3'UTR|CDCA2_ENST00000380665.3_Silent_p.T911T	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	38	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	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	
PDCD1	5133	hgsc.bcm.edu	37	2	242793273	242793273	+	Silent	SNP	A	A	G	rs2227981	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242793273A>G	ENST00000334409.5	-	5	873	c.804T>C	c.(802-804)gcT>gcC	p.A268A		NM_005018.2	NP_005009.2	Q15116	PDCD1_HUMAN	programmed cell death 1	268					apoptotic process (GO:0006915)|humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			endometrium(1)|lung(2)|ovary(1)|prostate(3)|skin(1)	8		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;0.0219)		GAGGGCCGTCAGCTGAGCCCC	0.662													G|||	3245	0.647963	0.5499	0.6282	5008	,	,		16254	0.7321		0.5984	False		,,,				2504	0.7587				p.A268A		Atlas-SNP	.											.	PDCD1	31	.	0			c.T804C						PASS	.	G		2611,1795	498.3+/-364.1	764,1083,356	27.0	30.0	29.0		804	-6.3	0.0	2	dbSNP_98	29	5014,3584	492.9+/-373.4	1454,2106,739	no	coding-synonymous	PDCD1	NM_005018.2		2218,3189,1095	GG,GA,AA		41.6841,40.7399,41.3642		268/289	242793273	7625,5379	2203	4299	6502	SO:0001819	synonymous_variant	5133	exon5			GCCGTCAGCTGAG	AY206416	CCDS33428.1	2q37.3	2014-01-29			ENSG00000188389	ENSG00000188389		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	8760	protein-coding gene	gene with protein product		600244	"""systemic lupus erythematosus susceptibility 2"""	SLEB2		7851902, 12402038	Standard	NM_005018		Approved	CD279, PD1, hSLE1	uc002wcq.4	Q15116	OTTHUMG00000151342	ENST00000334409.5:c.804T>C	2.37:g.242793273A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_005018	O00517|Q8IX89	Silent	SNP	ENST00000334409.5	37	CCDS33428.1																																																																																			A|0.409;G|0.591	0.591	strong		0.662	PDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322313.1	NM_005018	
PCDH9	5101	hgsc.bcm.edu	37	13	67800935	67800935	+	Silent	SNP	G	G	A	rs9571740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:67800935G>A	ENST00000377865.2	-	1	1772	c.1638C>T	c.(1636-1638)gaC>gaT	p.D546D	PCDH9_ENST00000328454.5_Silent_p.D546D|PCDH9_ENST00000544246.1_Silent_p.D546D|PCDH9_ENST00000456367.1_Silent_p.D546D|PCDH9_ENST00000377861.3_Silent_p.D546D			Q9HC56	PCDH9_HUMAN	protocadherin 9	546	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GGGTCCCATTGTCCCTGGCAG	0.428													G|||	2137	0.426717	0.2163	0.4697	5008	,	,		18272	0.5536		0.5298	False		,,,				2504	0.4438				p.D546D		Atlas-SNP	.											.	PCDH9	252	.	0			c.C1638T						PASS	.	G	,	1150,3256	406.4+/-333.9	138,874,1191	84.0	87.0	86.0		1638,1638	5.8	1.0	13	dbSNP_119	86	4705,3895	603.7+/-394.7	1291,2123,886	no	coding-synonymous,coding-synonymous	PCDH9	NM_020403.4,NM_203487.2	,	1429,2997,2077	AA,AG,GG		45.2907,26.1008,45.0177	,	546/1204,546/1238	67800935	5855,7151	2203	4300	6503	SO:0001819	synonymous_variant	5101	exon2			CCCATTGTCCCTG	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1638C>T	13.37:g.67800935G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																			G|0.559;A|0.441	0.441	strong		0.428	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37578579	37578579	+	Silent	SNP	C	C	T	rs229519	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37578579C>T	ENST00000337843.2	-	3	561	c.486G>A	c.(484-486)acG>acA	p.T162T	C1QTNF6_ENST00000255836.6_Silent_p.T38T|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000397110.2_Silent_p.T162T	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						PASS	.	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	46	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	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	
STK36	27148	hgsc.bcm.edu	37	2	219553423	219553423	+	Missense_Mutation	SNP	C	C	G	rs45586733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:219553423C>G	ENST00000295709.3	+	12	1663	c.1384C>G	c.(1384-1386)Ctg>Gtg	p.L462V	STK36_ENST00000392106.2_Missense_Mutation_p.L462V|STK36_ENST00000440309.1_Missense_Mutation_p.L462V|STK36_ENST00000392105.3_Missense_Mutation_p.L462V	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CACCCAGATCCTGAAAGGCAT	0.498													C|||	22	0.00439297	0.0	0.0101	5008	,	,		22309	0.0		0.0149	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	STK36	111	.	0			c.C1384G						PASS	.	C	VAL/LEU	17,4389	25.3+/-52.1	0,17,2186	223.0	210.0	215.0		1384	4.5	1.0	2	dbSNP_127	215	124,8476	66.0+/-128.3	0,124,4176	yes	missense	STK36	NM_015690.4	32	0,141,6362	GG,GC,CC		1.4419,0.3858,1.0841	probably-damaging	462/1316	219553423	141,12865	2203	4300	6503	SO:0001583	missense	27148	exon12			CAGATCCTGAAAG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1384C>G	2.37:g.219553423C>G	ENSP00000295709:p.Leu462Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	17.41	3.382206	0.61845	0.003858	0.014419	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.78126	-1.15;-1.15;-1.11;-1.15	5.38	4.51	0.55191	.	0.000000	0.34110	N	0.004245	T	0.73976	0.3656	L	0.27053	0.805	0.42723	D	0.993681	D;D	0.71674	0.998;0.997	D;D	0.68765	0.96;0.913	T	0.80125	-0.1513	10	0.72032	D	0.01	-8.883	12.2295	0.54480	0.0:0.9212:0.0:0.0788	rs45586733	462;462	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	V	462	ENSP00000295709:L462V;ENSP00000375955:L462V;ENSP00000375954:L462V;ENSP00000394095:L462V	ENSP00000295709:L462V	L	+	1	2	STK36	219261667	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.753000	0.38359	1.505000	0.48720	-0.140000	0.14226	CTG	C|0.990;G|0.010	0.010	strong		0.498	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
RPL36	25873	hgsc.bcm.edu	37	19	5692192	5692192	+	IGR	SNP	C	C	T	rs1062373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5692192C>T	ENST00000577222.1	+	0	874				LONP1_ENST00000585374.1_Missense_Mutation_p.V797I|LONP1_ENST00000593119.1_Missense_Mutation_p.V847I|LONP1_ENST00000540670.2_Missense_Mutation_p.V715I|LONP1_ENST00000590729.1_Missense_Mutation_p.V781I|LONP1_ENST00000360614.3_Missense_Mutation_p.V911I			Q9Y3U8	RL36_HUMAN	ribosomal protein L36						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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|upper_aerodigestive_tract(1)	2						GCTGGCAGGACGATGCACGTC	0.632													C|||	73	0.0145767	0.0	0.0187	5008	,	,		17051	0.0228		0.0288	False		,,,				2504	0.0082				p.I911I		Atlas-SNP	.											.	LONP1	66	.	0			c.A2731A						PASS	.	C	ILE/VAL	18,4388	26.2+/-53.5	0,18,2185	147.0	123.0	131.0		2731	-3.6	0.0	19	dbSNP_86	131	235,8365	95.2+/-157.0	3,229,4068	yes	missense	LONP1	NM_004793.2	29	3,247,6253	TT,TC,CC		2.7326,0.4085,1.9453	benign	911/960	5692192	253,12753	2203	4300	6503	SO:0001628	intergenic_variant	9361	exon18			GCAGGACGATGCA		CCDS12147.1	19p13.2	2011-04-06				ENSG00000130255		"""L ribosomal proteins"""	13631	protein-coding gene	gene with protein product							Standard	NM_033643		Approved	DKFZp566B023, L36	uc002mcv.3	Q9Y3U8			19.37:g.5692192C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_004793	B2R4Y1|D6W634|Q6FIG1|Q9UQF6	Silent	SNP	ENST00000577222.1	37	CCDS12147.1	59	0.027014652014652016	4	0.008130081300813009	8	0.022099447513812154	21	0.03671328671328671	26	0.03430079155672823	C	4.630	0.117037	0.08881	0.004085	0.027326	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.24151	1.87;1.87	4.43	-3.62	0.04543	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	0.174472	0.47852	N	0.000210	T	0.00936	0.0031	N	0.00419	-1.52	0.26329	N	0.977544	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.34750	-0.9816	10	0.02654	T	1	-24.9714	10.5044	0.44826	0.0:0.2087:0.0:0.7913	rs1062373;rs1062373	847;911	Q8N8K8;P36776	.;LONM_HUMAN	I	911;875;715	ENSP00000353826:V911I;ENSP00000441523:V715I	ENSP00000351177:V875I	V	-	1	0	LONP1	5643192	0.360000	0.24964	0.018000	0.16275	0.675000	0.39556	0.517000	0.22832	-0.442000	0.07190	0.456000	0.33151	GTC	C|0.980;T|0.020	0.020	strong		0.632	RPL36-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442561.1	NM_015414	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363043	42363043	+	Missense_Mutation	SNP	T	T	G	rs74678783	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363043T>G	ENST00000290472.3	-	18	2009	c.1915A>C	c.(1915-1917)Aag>Cag	p.K639Q		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	639	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CGGGGCTCCTTGGGGGTCAGC	0.632													G|||	222	0.0443291	0.0144	0.0749	5008	,	,		17980	0.0		0.1083	False		,,,				2504	0.0429				p.K639Q		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.A1915C						PASS	.	G	GLN/LYS	142,4264		1,140,2062	61.0	65.0	64.0		1915	3.0	0.9	15	dbSNP_131	64	853,7745		43,767,3489	yes	missense	PLA2G4D	NM_178034.3	53	44,907,5551	GG,GT,TT		9.9209,3.2229,7.6515	benign	639/819	42363043	995,12009	2203	4299	6502	SO:0001583	missense	283748	exon18			GCTCCTTGGGGGT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1915A>C	15.37:g.42363043T>G	ENSP00000290472:p.Lys639Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	128	0.05860805860805861	10	0.02032520325203252	31	0.0856353591160221	0	0.0	87	0.11477572559366754	G	0.496	-0.873328	0.02570	0.032229	0.099209	ENSG00000159337	ENST00000290472	T	0.10288	2.89	4.85	2.95	0.34219	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.129710	0.06570	N	0.748353	T	0.00073	0.0002	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	9	0.11485	T	0.65	-3.982	2.0561	0.03582	0.2199:0.1405:0.4948:0.1447	.	639	Q86XP0	PA24D_HUMAN	Q	639	ENSP00000290472:K639Q	ENSP00000290472:K639Q	K	-	1	0	PLA2G4D	40150335	0.000000	0.05858	0.864000	0.33941	0.260000	0.26232	0.081000	0.14823	0.253000	0.21552	-0.143000	0.13931	AAG	T|0.928;G|0.072	0.072	strong		0.632	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
FAM154A	158297	hgsc.bcm.edu	37	9	18950932	18950932	+	Silent	SNP	C	C	T	rs149656581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:18950932C>T	ENST00000380534.4	-	2	321	c.42G>A	c.(40-42)cgG>cgA	p.R14R	FAM154A_ENST00000542071.1_5'UTR|FAM154A_ENST00000583128.1_5'UTR|FAM154A_ENST00000380530.1_Silent_p.R14R	NM_153707.2	NP_714918.2	Q8IYX7	F154A_HUMAN	family with sequence similarity 154, member A	14										breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|skin(1)	26				GBM - Glioblastoma multiforme(50;6.53e-16)		GACAGTGATGCCGCCTATAAA	0.408													C|||	4	0.000798722	0.0	0.0	5008	,	,		19884	0.0		0.004	False		,,,				2504	0.0				p.R14R		Atlas-SNP	.											.	FAM154A	61	.	0			c.G42A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	120.0	115.0	117.0		42	-0.3	1.0	9	dbSNP_134	117	31,8569	21.0+/-64.5	1,29,4270	no	coding-synonymous	FAM154A	NM_153707.2		1,33,6469	TT,TC,CC		0.3605,0.0908,0.2691		14/475	18950932	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	158297	exon2			GTGATGCCGCCTA	BC033489	CCDS6487.1, CCDS75819.1, CCDS75820.1	9p22.1	2012-03-23	2008-02-21	2008-02-21	ENSG00000155875	ENSG00000155875			28566	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 138"""	C9orf138		12477932	Standard	NM_153707		Approved	MGC35182	uc003zni.2	Q8IYX7	OTTHUMG00000019609	ENST00000380534.4:c.42G>A	9.37:g.18950932C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_153707	Q5VY58	Silent	SNP	ENST00000380534.4	37	CCDS6487.1																																																																																			C|0.997;T|0.003	0.003	strong		0.408	FAM154A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051811.1	NM_153707	
MUC4	4585	hgsc.bcm.edu	37	3	195509941	195509941	+	Missense_Mutation	SNP	A	A	C	rs199849290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195509941A>C	ENST00000463781.3	-	2	8969	c.8510T>G	c.(8509-8511)aTc>aGc	p.I2837S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I2837S	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)	p.I2837S(1)		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)		TGAGGAAGGGATGGTGACAGG	0.592													.|||	318	0.0634984	0.0045	0.0432	5008	,	,		7808	0.0417		0.1521	False		,,,				2504	0.089				p.I2837S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.T8510G						scavenged	.	T	,,SER/ILE	2,1378		0,2,688	109.0	67.0	80.0		,,8510		0.0	3		80	27,3107		0,27,1540	no	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,142	0,29,2228	CC,CA,AA		0.8615,0.1449,0.6424	,,benign	,,2837/5413	195509941	29,4485	690	1567	2257	SO:0001583	missense	4585	exon2			GAAGGGATGGTGA	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.8510T>G	3.37:g.195509941A>C	ENSP00000417498:p.Ile2837Ser	Somatic	135	2	0.0148148		WXS	Illumina HiSeq	Phase_I	146	13	0.0890411	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	.	.	.	.	.	.	.	.	.	.	N	7.247	0.602483	0.13939	0.001449	0.008615	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.6	.	.	.	.	.	.	.	.	T	0.08133	0.0203	N	0.08118	0	0.21290	N	0.99974	B	0.30727	0.292	B	0.21708	0.036	T	0.26503	-1.0101	7	.	.	.	.	5.3345	0.15949	0.9999:0.0:1.0E-4:0.0	.	2709	E7ESK3	.	S	2837	ENSP00000417498:I2837S;ENSP00000420243:I2837S	.	I	-	2	0	MUC4	196994720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.560000	0.00113	-0.000000	0.14550	0.000000	0.15137	ATC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM115A	9747	hgsc.bcm.edu	37	7	143573195	143573195	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143573195C>T	ENST00000479870.1	-	2	715	c.507G>A	c.(505-507)acG>acA	p.T169T	FAM115A_ENST00000392900.3_Intron|FAM115A_ENST00000355951.2_Silent_p.T169T	NM_001206938.1|NM_001206941.1|NM_014719.2	NP_001193867.1|NP_001193870.1|NP_055534	Q9Y4C2	F115A_HUMAN	family with sequence similarity 115, member A	169										NS(1)|endometrium(1)|lung(5)	7	Melanoma(164;0.0903)					TCCCAGGGAACGTGAACAGAA	0.507																																					p.T169T		Atlas-SNP	.											FAM115A,NS,carcinoma,-1,1	FAM115A	26	1	0			c.G507A						scavenged	.						66.0	57.0	60.0					7																	143573195		2203	4300	6503	SO:0001819	synonymous_variant	9747	exon2			AGGGAACGTGAAC	AB018281	CCDS5886.1, CCDS56514.1	7q35	2011-05-03	2006-03-23	2006-03-23	ENSG00000198420	ENSG00000198420			22201	protein-coding gene	gene with protein product						9872452	Standard	NM_014719		Approved	KIAA0738	uc003wdo.2	Q9Y4C2	OTTHUMG00000157773	ENST00000479870.1:c.507G>A	7.37:g.143573195C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	76	2	0.0263158	NM_001206938	A8K6E0|Q75KM8|Q75KM9|Q7L665|Q9BW63	Silent	SNP	ENST00000479870.1	37	CCDS5886.1																																																																																			.	.	none		0.507	FAM115A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349583.1	NM_014719	
TBX15	6913	hgsc.bcm.edu	37	1	119469188	119469188	+	Missense_Mutation	SNP	G	G	T	rs10494217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:119469188G>T	ENST00000369429.3	-	3	475	c.466C>A	c.(466-468)Cat>Aat	p.H156N	TBX15_ENST00000207157.3_Missense_Mutation_p.H50N			Q96SF7	TBX15_HUMAN	T-box 15	156			H -> N (in dbSNP:rs10494217).		embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	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)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		TACTGCTGATGTGGATCTAGG	0.428													G|||	423	0.0844649	0.0076	0.1023	5008	,	,		19815	0.0655		0.165	False		,,,				2504	0.1125				p.H50N		Atlas-SNP	.											.	TBX15	95	.	0			c.C148A						PASS	.	G	ASN/HIS	151,4255	103.0+/-141.5	4,143,2056	170.0	140.0	150.0		148	6.1	1.0	1	dbSNP_119	150	1560,7040	291.7+/-300.5	146,1268,2886	yes	missense	TBX15	NM_152380.2	68	150,1411,4942	TT,TG,GG		18.1395,3.4271,13.1555	benign	50/497	119469188	1711,11295	2203	4300	6503	SO:0001583	missense	6913	exon3			GCTGATGTGGATC	AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.466C>A	1.37:g.119469188G>T	ENSP00000358437:p.His156Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_152380	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		213	0.09752747252747253	4	0.008130081300813009	37	0.10220994475138122	43	0.07517482517482517	129	0.17018469656992086	G	15.39	2.819013	0.50633	0.034271	0.181395	ENSG00000092607	ENST00000207157;ENST00000369429	D;D	0.86956	-2.19;-2.19	6.06	6.06	0.98353	p53-like transcription factor, DNA-binding (1);	0.044485	0.85682	D	0.000000	T	0.77922	0.4203	N	0.11845	0.185	0.09310	P	0.9999999999531072	B	0.25105	0.118	B	0.39339	0.297	T	0.74074	-0.3782	9	0.34782	T	0.22	.	20.2501	0.98402	0.0:0.0:1.0:0.0	rs10494217;rs17185917;rs52794873;rs59613865;rs10494217	156	Q96SF7	TBX15_HUMAN	N	50;156	ENSP00000207157:H50N;ENSP00000358437:H156N	ENSP00000207157:H50N	H	-	1	0	TBX15	119270711	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.017000	0.88712	2.880000	0.98712	0.650000	0.86243	CAT	G|0.891;T|0.109	0.109	strong		0.428	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37480797	37480797	+	Silent	SNP	C	C	T	rs2111833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37480797C>T	ENST00000346753.3	-	9	1199	c.1083G>A	c.(1081-1083)tcG>tcA	p.S361S	RP5-1170K4.7_ENST00000414203.2_RNA|TMPRSS6_ENST00000381792.2_Silent_p.S352S|TMPRSS6_ENST00000442782.2_Silent_p.S361S|TMPRSS6_ENST00000406856.1_Silent_p.S352S|TMPRSS6_ENST00000406725.1_Silent_p.S352S	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	361	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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						GGGTTTGGGGCGAGTAGTAGC	0.652													C|||	1567	0.312899	0.3797	0.1988	5008	,	,		18698	0.3046		0.3877	False		,,,				2504	0.2352				p.S361S		Atlas-SNP	.											TMPRSS6_ENST00000442782,NS,carcinoma,-1,2	TMPRSS6	99	2	0			c.G1083A						PASS	.	C		1646,2752		331,984,884	87.0	73.0	78.0		1083	-9.1	0.9	22	dbSNP_96	78	2875,5703		527,1821,1941	no	coding-synonymous	TMPRSS6	NM_153609.2		858,2805,2825	TT,TC,CC		33.516,37.4261,34.8412		361/812	37480797	4521,8455	2199	4289	6488	SO:0001819	synonymous_variant	164656	exon9			TTGGGGCGAGTAG	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.1083G>A	22.37:g.37480797C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			C|0.669;T|0.331	0.331	strong		0.652	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
FOXD4	2298	hgsc.bcm.edu	37	9	117934	117934	+	Silent	SNP	C	C	G	rs62533589	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:117934C>G	ENST00000382500.2	-	1	483	c.186G>C	c.(184-186)ggG>ggC	p.G62G		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	62					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)		GAAGCGCAACCCCGCCCCACC	0.701																																					p.G62G		Atlas-SNP	.											.	FOXD4	75	.	0			c.G186C						PASS	.	C		215,4175		4,207,1984	24.0	38.0	33.0		186	-3.9	0.0	9	dbSNP_129	33	1060,7508		43,974,3267	no	coding-synonymous	FOXD4	NM_207305.3		47,1181,5251	GG,GC,CC		12.3716,4.8975,9.8395		62/440	117934	1275,11683	2195	4284	6479	SO:0001819	synonymous_variant	2298	exon1			CGCAACCCCGCCC	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.186G>C	9.37:g.117934C>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	58	0.367089	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			C|0.901;G|0.099	0.099	strong		0.701	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
PPAPDC1A	196051	hgsc.bcm.edu	37	10	122348969	122348969	+	Silent	SNP	C	C	T	rs1047369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:122348969C>T	ENST00000398250.1	+	7	1123	c.771C>T	c.(769-771)agC>agT	p.S257S	PPAPDC1A_ENST00000398248.1_3'UTR|PPAPDC1A_ENST00000439221.1_Silent_p.S194S|PPAPDC1A_ENST00000369073.3_Silent_p.S247S	NM_001030059.1	NP_001025230.1	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain containing 1A	257					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)		CAGCTGACAGCGCACCCAGCT	0.587													C|||	841	0.167931	0.1498	0.1614	5008	,	,		17117	0.0685		0.2117	False		,,,				2504	0.2546				p.S257S		Atlas-SNP	.											.	PPAPDC1A	48	.	0			c.C771T						PASS	.	C		615,3545		45,525,1510	60.0	67.0	65.0		771	1.2	0.9	10	dbSNP_86	65	1987,6425		234,1519,2453	no	coding-synonymous	PPAPDC1A	NM_001030059.1		279,2044,3963	TT,TC,CC		23.621,14.7837,20.6968		257/272	122348969	2602,9970	2080	4206	6286	SO:0001819	synonymous_variant	196051	exon7			TGACAGCGCACCC	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.771C>T	10.37:g.122348969C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001030059	A2RU82|Q08EQ2|Q0IIP2|Q495B4|Q5VZY1	Silent	SNP	ENST00000398250.1	37	CCDS41573.1																																																																																			C|0.840;T|0.160	0.160	strong		0.587	PPAPDC1A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_113641	
NRXN2	9379	hgsc.bcm.edu	37	11	64418900	64418900	+	Silent	SNP	G	G	A	rs526338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64418900G>A	ENST00000377551.1	-	13	2956	c.2745C>T	c.(2743-2745)atC>atT	p.I915I	NRXN2_ENST00000265459.6_Silent_p.I915I|NRXN2_ENST00000409571.1_Silent_p.I908I|NRXN2_ENST00000377559.3_Silent_p.I875I|AP001092.4_ENST00000433606.1_RNA			Q9P2S2	NRX2A_HUMAN	neurexin 2	915					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GATCGGCCACGATGGCACGCA	0.572											OREG0021057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1912	0.381789	0.0635	0.415	5008	,	,		19799	0.2212		0.7137	False		,,,				2504	0.6125				p.I915I		Atlas-SNP	.											.	NRXN2	247	.	0			c.C2745T						PASS	.	G	,	727,3675	299.8+/-286.0	64,599,1538	125.0	80.0	95.0		2745,2625	-1.4	1.0	11	dbSNP_83	95	6085,2509	693.2+/-404.6	2169,1747,381	no	coding-synonymous,coding-synonymous	NRXN2	NM_015080.3,NM_138732.2	,	2233,2346,1919	AA,AG,GG		29.1948,16.5152,47.5839	,	915/1713,875/1643	64418900	6812,6184	2201	4297	6498	SO:0001819	synonymous_variant	9379	exon14			GGCCACGATGGCA		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.2745C>T	11.37:g.64418900G>A		Somatic	108	1	0.00925926	1076	WXS	Illumina HiSeq	Phase_I	124	124	1	NM_015080	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	37	CCDS8077.1																																																																																			G|0.542;A|0.458	0.458	strong		0.572	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557504	32557504	+	Missense_Mutation	SNP	G	G	A	rs17879020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32557504G>A	ENST00000360004.5	-	1	121	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	6					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						CCTCCAGGGAGCTTCAGACAC	0.582										Multiple Myeloma(14;0.17)																											p.L6F		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C16T						PASS	.						77.0	91.0	86.0					6																	32557504		1511	2709	4220	SO:0001583	missense	3123	exon1			CAGGGAGCTTCAG	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.16C>T	6.37:g.32557504G>A	ENSP00000353099:p.Leu6Phe	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	153	41	0.267974	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	4.787	0.146342	0.09134	.	.	ENSG00000196126	ENST00000360004	T	0.00281	8.32	4.51	-6.2	0.02072	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.35542	1.07	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.34453	-0.9828	9	0.07030	T	0.85	.	0.7046	0.00913	0.3901:0.1208:0.2505:0.2385	rs17879020;rs34518239	6	P01911	2B1F_HUMAN	F	6	ENSP00000353099:L6F	ENSP00000353099:L6F	L	-	1	0	HLA-DRB1	32665482	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.135000	0.10420	-0.923000	0.03785	-1.250000	0.01514	CTC	G|0.978;A|0.022	0.022	strong		0.582	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SETDB2	83852	hgsc.bcm.edu	37	13	50050620	50050620	+	Missense_Mutation	SNP	A	A	G	rs7998427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50050620A>G	ENST00000317257.8	+	7	1175	c.350A>G	c.(349-351)gAa>gGa	p.E117G	SETDB2_ENST00000354234.4_Missense_Mutation_p.E105G|SETDB2_ENST00000258672.5_Missense_Mutation_p.E105G	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	117			E -> G (in dbSNP:rs7998427). {ECO:0000269|PubMed:11306461, ECO:0000269|PubMed:12754510}.		chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		AGAACAACAGAAAATAAGGAA	0.279													A|||	3642	0.727236	0.7874	0.7507	5008	,	,		18147	0.8046		0.673	False		,,,				2504	0.6053				p.E117G		Atlas-SNP	.											.	SETDB2	48	.	0			c.A350G	GRCh37	CM067715	SETDB2	M	rs7998427	PASS	.	A	GLY/GLU,GLY/GLU	3419,977		1350,719,129	43.0	49.0	47.0		314,350	3.5	0.4	13	dbSNP_116	47	5910,2688		2057,1796,446	yes	missense,missense	SETDB2	NM_001160308.1,NM_031915.2	98,98	3407,2515,575	GG,GA,AA		31.2631,22.2247,28.2053	benign,benign	105/708,117/720	50050620	9329,3665	2198	4299	6497	SO:0001583	missense	83852	exon7			CAACAGAAAATAA	AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"""Chromatin-modifying enzymes / K-methyltransferases"""	20263	protein-coding gene	gene with protein product		607865	"""chromosome 13 open reading frame 4"""	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.350A>G	13.37:g.50050620A>G	ENSP00000326477:p.Glu117Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_031915	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Missense_Mutation	SNP	ENST00000317257.8	37	CCDS9417.1	1629	0.7458791208791209	377	0.766260162601626	272	0.7513812154696132	464	0.8111888111888111	516	0.6807387862796834	A	2.062	-0.415170	0.04766	0.777753	0.687369	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	D;D;T	0.86865	-2.17;-2.18;1.14	5.96	3.52	0.40303	.	1.193590	0.05468	N	0.552626	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.999999999946489E-6	B;B;B	0.15473	0.0;0.013;0.008	B;B;B	0.17722	0.002;0.019;0.008	T	0.44772	-0.9306	9	0.17369	T	0.5	.	8.5912	0.33688	0.8466:0.0:0.1534:0.0	rs7998427;rs17846399;rs17859441;rs52791138;rs59813340;rs7998427	117;105;117	Q96T68-3;Q96T68-2;Q96T68	.;.;SETB2_HUMAN	G	105;117;105	ENSP00000346175:E105G;ENSP00000326477:E117G;ENSP00000258672:E105G	ENSP00000258672:E105G	E	+	2	0	SETDB2	48948621	0.914000	0.31030	0.414000	0.26521	0.065000	0.16274	3.304000	0.51866	0.499000	0.27970	0.533000	0.62120	GAA	A|0.271;G|0.728	0.728	strong		0.279	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915	
CFAP61	26074	hgsc.bcm.edu	37	20	20079360	20079360	+	Missense_Mutation	SNP	A	A	G	rs6075614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:20079360A>G	ENST00000245957.5	+	8	837	c.761A>G	c.(760-762)cAt>cGt	p.H254R	C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_Missense_Mutation_p.H254R|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Missense_Mutation_p.H254R	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		254			H -> R (in dbSNP:rs6075614).							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)		CAACTGCTGCATGAGTGCTTT	0.453													A|||	314	0.0626997	0.0053	0.0648	5008	,	,		18770	0.001		0.1302	False		,,,				2504	0.1329				p.H254R		Atlas-SNP	.											.	C20orf26	188	.	0			c.A761G						PASS	.	A	ARG/HIS,ARG/HIS	143,4263	100.3+/-138.9	5,133,2065	200.0	168.0	179.0		761,761	5.4	0.2	20	dbSNP_114	179	1256,7344	251.8+/-278.1	92,1072,3136	yes	missense,missense	C20orf26	NM_001167816.1,NM_015585.3	29,29	97,1205,5201	GG,GA,AA		14.6047,3.2456,10.7566	benign,benign	254/471,254/1238	20079360	1399,11607	2203	4300	6503	SO:0001583	missense	26074	exon8			TGCTGCATGAGTG																												ENST00000245957.5:c.761A>G	20.37:g.20079360A>G	ENSP00000245957:p.His254Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	199	116	0.582915	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	132	0.06043956043956044	3	0.006097560975609756	25	0.06906077348066299	1	0.0017482517482517483	103	0.1358839050131926	A	3.326	-0.137624	0.06711	0.032456	0.146047	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767;ENST00000472660;ENST00000442372;ENST00000377297	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	5.44	5.44	0.79542	.	0.531595	0.18883	N	0.128539	T	0.00178	0.0005	N	0.21448	0.665	0.09310	P	0.9999999999999901	D;B;B;B	0.63880	0.993;0.003;0.056;0.089	P;B;B;B	0.57057	0.812;0.009;0.031;0.035	T	0.02004	-1.1231	9	0.07482	T	0.82	.	11.4723	0.50278	0.9271:0.0:0.0729:0.0	rs6075614;rs17306632;rs52815119;rs61592058;rs6075614	254;254;208;254	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	R	208;254;254;254;254;254;150;13;46	ENSP00000345553:H208R;ENSP00000245957:H254R;ENSP00000366521:H254R;ENSP00000414537:H254R;ENSP00000420498:H150R;ENSP00000397311:H13R	ENSP00000245957:H254R	H	+	2	0	C20orf26	20027360	0.994000	0.37717	0.227000	0.23927	0.124000	0.20399	5.249000	0.65427	2.066000	0.61787	0.533000	0.62120	CAT	A|0.909;G|0.091	0.091	strong		0.453	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
DOCK6	57572	hgsc.bcm.edu	37	19	11332570	11332570	+	Silent	SNP	T	T	A	rs3810307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11332570T>A	ENST00000294618.7	-	28	3518	c.3507A>T	c.(3505-3507)ctA>ctT	p.L1169L	DOCK6_ENST00000319867.7_Silent_p.L508L	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1169					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						GTGCAATCGATAGCAGTGGCA	0.602													t|||	1570	0.313498	0.5582	0.2579	5008	,	,		22542	0.2986		0.1431	False		,,,				2504	0.2127				p.L1169L		Atlas-SNP	.											.	DOCK6	104	.	0			c.A3507T						PASS	.	A		2025,2151		492,1041,555	95.0	105.0	102.0		3507	-0.2	0.4	19	dbSNP_107	102	1579,6867		156,1267,2800	no	coding-synonymous	DOCK6	NM_020812.2		648,2308,3355	AA,AT,TT		18.6952,48.4914,28.5533		1169/2048	11332570	3604,9018	2088	4223	6311	SO:0001819	synonymous_variant	57572	exon28			AATCGATAGCAGT		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.3507A>T	19.37:g.11332570T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			T|0.723;A|0.277	0.277	strong		0.602	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156351699G>A	ENST00000368249.1	+	6	981	c.943G>A	c.(943-945)Ggg>Agg	p.G315R	RHBG_ENST00000368246.2_Missense_Mutation_p.G315R|RHBG_ENST00000451864.2_Intron|RHBG_ENST00000537040.1_Missense_Mutation_p.G153R|RHBG_ENST00000255013.3_Missense_Mutation_p.G246R|RHBG_ENST00000400992.2_Missense_Mutation_p.G283R	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	185	0	0		WXS	Illumina HiSeq	Phase_I	290	288	0.993103	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	
NAT2	10	hgsc.bcm.edu	37	8	18257994	18257994	+	Silent	SNP	C	C	T	rs1799929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:18257994C>T	ENST00000286479.3	+	2	588	c.481C>T	c.(481-483)Ctg>Ttg	p.L161L	NAT2_ENST00000520116.1_Silent_p.L31L	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	161					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	AATCTGGTACCTGGACCAAAT	0.413									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				C|||	1342	0.267971	0.2375	0.3444	5008	,	,		17491	0.0367		0.4354	False		,,,				2504	0.3211				p.L161L		Atlas-SNP	.											.	NAT2	34	.	0			c.C481T						PASS	.	C		1118,3288	384.9+/-325.5	142,834,1227	58.0	61.0	60.0		481	1.9	1.0	8	dbSNP_89	60	3707,4893	526.9+/-381.1	779,2149,1372	yes	coding-synonymous	NAT2	NM_000015.2		921,2983,2599	TT,TC,CC		43.1047,25.3745,37.0983		161/291	18257994	4825,8181	2203	4300	6503	SO:0001819	synonymous_variant	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TGGTACCTGGACC	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.481C>T	8.37:g.18257994C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Silent	SNP	ENST00000286479.3	37	CCDS6008.1																																																																																			C|0.677;T|0.323	0.323	strong		0.413	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037560	33037560	+	Silent	SNP	G	G	A	rs1042176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33037560G>A	ENST00000419277.1	-	3	333	c.204C>T	c.(202-204)gaC>gaT	p.D68D	HLA-DPA1_ENST00000428995.1_Silent_p.D68D|HLA-DPA1_ENST00000463066.1_5'UTR	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	112	0	0		WXS	Illumina HiSeq	Phase_I	130	48	0.369231	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	
GPAM	57678	hgsc.bcm.edu	37	10	113935379	113935379	+	Missense_Mutation	SNP	T	T	C	rs10787428	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:113935379T>C	ENST00000348367.4	-	6	589	c.392A>G	c.(391-393)gAa>gGa	p.E131G	GPAM_ENST00000423155.1_Missense_Mutation_p.E131G|GPAM_ENST00000369425.1_Missense_Mutation_p.E131G			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	131			E -> G (in dbSNP:rs10787428).		acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		CAGCACATTTTCAGTCACATT	0.502													T|||	2778	0.554712	0.528	0.4582	5008	,	,		20154	0.6042		0.5437	False		,,,				2504	0.6196				p.E131G	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A392G	GRCh37	CM067418	GPAM	M	rs10787428	PASS	.	T	GLY/GLU	2220,2186	591.0+/-387.5	554,1112,537	184.0	157.0	166.0		392	5.1	0.7	10	dbSNP_120	166	5054,3546	630.8+/-398.4	1504,2046,750	yes	missense	GPAM	NM_020918.4	98	2058,3158,1287	CC,CT,TT		41.2326,49.6142,44.072	benign	131/829	113935379	7274,5732	2203	4300	6503	SO:0001583	missense	57678	exon6			ACATTTTCAGTCA	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.392A>G	10.37:g.113935379T>C	ENSP00000265276:p.Glu131Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	1198	0.5485347985347986	278	0.5650406504065041	170	0.4696132596685083	338	0.5909090909090909	412	0.5435356200527705	T	18.26	3.584072	0.65992	0.503858	0.587674	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.70869	-0.52;-0.52;-0.51	5.11	5.11	0.69529	.	0.118515	0.56097	D	0.000025	T	0.00012	0.0000	M	0.62723	1.935	0.18873	P	0.9999885123	P;B	0.34562	0.457;0.247	B;B	0.27608	0.081;0.057	T	0.48547	-0.9026	9	0.44086	T	0.13	-12.3902	13.5006	0.61452	0.0:0.0:0.0:1.0	rs10787428;rs52812454;rs59176203;rs10787428	131;131	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	G	131	ENSP00000265276:E131G;ENSP00000409242:E131G;ENSP00000358433:E131G	ENSP00000265276:E131G	E	-	2	0	GPAM	113925369	1.000000	0.71417	0.729000	0.30791	0.982000	0.71751	7.129000	0.77225	1.929000	0.55896	0.528000	0.53228	GAA	C|0.558;N|0.000	0.558	strong		0.502	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
MUC16	94025	hgsc.bcm.edu	37	19	9065203	9065203	+	Missense_Mutation	SNP	T	T	C	rs62118307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9065203T>C	ENST00000397910.4	-	3	22446	c.22243A>G	c.(22243-22245)Agc>Ggc	p.S7415G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7417	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						GAGGAGTGGCTACTTGCTGGT	0.502													N|||	836	0.166933	0.1626	0.183	5008	,	,		22270	0.2679		0.0855	False		,,,				2504	0.1411				p.S7415G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A22243G						PASS	.	T	GLY/SER	601,3449		46,509,1470	86.0	84.0	85.0		22243	-2.8	0.0	19	dbSNP_129	85	645,7713		25,595,3559	yes	missense	MUC16	NM_024690.2	56	71,1104,5029	CC,CT,TT		7.7172,14.8395,10.0419	possibly-damaging	7415/14508	9065203	1246,11162	2025	4179	6204	SO:0001583	missense	94025	exon3			AGTGGCTACTTGC	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.22243A>G	19.37:g.9065203T>C	ENSP00000381008:p.Ser7415Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	367	0.16804029304029305	72	0.14634146341463414	57	0.1574585635359116	169	0.29545454545454547	69	0.09102902374670185	N	4.596	0.110781	0.08780	0.148395	0.077172	ENSG00000181143	ENST00000397910	T	0.22945	1.93	2.66	-2.82	0.05787	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	.	.	.	B	0.12013	0.005	B	0.08055	0.003	T	0.42172	-0.9467	8	0.87932	D	0	.	3.8873	0.09103	0.0:0.2601:0.3916:0.3483	rs62118307	7415	B5ME49	.	G	7415	ENSP00000381008:S7415G	ENSP00000381008:S7415G	S	-	1	0	MUC16	8926203	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.098000	0.03346	-0.825000	0.04290	-0.385000	0.06624	AGC	T|0.848;C|0.152	0.152	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781614	88781614	+	IGR	SNP	G	G	C	rs1058158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88781614G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.R414R|CTU2_ENST00000453996.2_Silent_p.R501R|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000567949.1_Silent_p.R572R|CTU2_ENST00000312060.5_Missense_Mutation_p.G482R	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						AGGAGATCCGGGACTGTCTGA	0.662													G|||	967	0.193091	0.1021	0.1844	5008	,	,		13563	0.0913		0.3082	False		,,,				2504	0.3088				p.G482R		Atlas-SNP	.											.	CTU2	66	.	0			c.G1444C						PASS	.	G	,ARG/GLY	584,3800	254.0+/-259.7	35,514,1643	89.0	80.0	83.0		1503,1444	2.1	0.9	16	dbSNP_86	83	2639,5949	423.7+/-354.4	407,1825,2062	yes	coding-synonymous,missense	CTU2	NM_001012759.1,NM_001012762.1	,125	442,2339,3705	CC,CG,GG		30.7289,13.3212,24.8458	,	501/516,482/486	88781614	3223,9749	2192	4294	6486	SO:0001628	intergenic_variant	348180	exon14			GATCCGGGACTGT	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		16.37:g.88781614G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_001012762	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	396	0.1813186813186813	53	0.10772357723577236	78	0.2154696132596685	48	0.08391608391608392	217	0.2862796833773087	G	7.321	0.616970	0.14129	0.133212	0.307289	ENSG00000174177	ENST00000312060	T	0.13901	2.55	5.19	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	B	0.31413	0.322	B	0.31812	0.136	T	0.49679	-0.8914	7	0.19147	T	0.46	.	9.0299	0.36252	0.2539:0.0:0.7461:0.0	rs1058158;rs3169255;rs17846640;rs17859735;rs56871681	482	Q2VPK5-5	.	R	482	ENSP00000308617:G482R	ENSP00000308617:G482R	G	+	1	0	CTU2	87309115	0.126000	0.22350	0.870000	0.34147	0.009000	0.06853	0.362000	0.20284	0.699000	0.31761	-0.258000	0.10820	GGA	C|0.228;G|0.772;T|0.000	0.228	strong		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
RRP36	88745	hgsc.bcm.edu	37	6	42992808	42992808	+	Silent	SNP	T	T	C	rs3749904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:42992808T>C	ENST00000244496.5	+	2	226	c.216T>C	c.(214-216)aaT>aaC	p.N72N		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	72					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						TAGCTGGAAATAGTCCTAAGA	0.453													C|||	1724	0.344249	0.7133	0.2421	5008	,	,		22411	0.2123		0.1223	False		,,,				2504	0.2822				p.N72N		Atlas-SNP	.											.	RRP36	20	.	0			c.T216C						PASS	.	C		2782,1624	499.5+/-364.4	882,1018,303	135.0	118.0	124.0		216	2.0	0.0	6	dbSNP_107	124	1118,7482	767.9+/-407.6	65,988,3247	no	coding-synonymous	RRP36	NM_033112.2		947,2006,3550	CC,CT,TT		13.0,36.8588,29.9862		72/260	42992808	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	88745	exon2			TGGAAATAGTCCT	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.216T>C	6.37:g.42992808T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_033112	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	37	CCDS34453.1																																																																																			T|0.691;C|0.309	0.309	strong		0.453	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
BRSK2	9024	hgsc.bcm.edu	37	11	1477642	1477642	+	Missense_Mutation	SNP	G	G	C	rs33996815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1477642G>C	ENST00000528841.1	+	17	2117	c.1733G>C	c.(1732-1734)gGg>gCg	p.G578A	BRSK2_ENST00000308219.9_Missense_Mutation_p.G578A|BRSK2_ENST00000528710.1_Missense_Mutation_p.G518A|BRSK2_ENST00000382179.1_Missense_Mutation_p.G624A|BRSK2_ENST00000308230.5_Missense_Mutation_p.G600A|BRSK2_ENST00000544817.1_Missense_Mutation_p.G273A|BRSK2_ENST00000526678.1_Missense_Mutation_p.G600A|BRSK2_ENST00000531197.1_Missense_Mutation_p.G578A			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	578					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)		AAGGCCACGGGGGGGCCAGCC	0.622													g|||	13	0.00259585	0.0008	0.0029	5008	,	,		16317	0.0		0.0089	False		,,,				2504	0.001				p.G624A		Atlas-SNP	.											.	BRSK2	97	.	0			c.G1871C						PASS	.	G	ALA/GLY	8,4046		0,8,2019	21.0	27.0	25.0		1733	3.7	0.9	11	dbSNP_126	25	81,8259		0,81,4089	yes	missense	BRSK2	NM_003957.2	60	0,89,6108	CC,CG,GG		0.9712,0.1973,0.7181	benign	578/669	1477642	89,12305	2027	4170	6197	SO:0001583	missense	9024	exon17			CCACGGGGGGGCC	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.1733G>C	11.37:g.1477642G>C	ENSP00000432000:p.Gly578Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	12.23	1.876787	0.33162	0.001973	0.009712	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179;ENST00000544817	T;T;T;T;T;T;T;T	0.73789	-0.76;-0.78;-0.76;-0.77;-0.76;-0.59;-0.62;0.8	3.67	3.67	0.42095	.	0.212851	0.38436	U	0.001699	T	0.56321	0.1977	L	0.28014	0.82	0.42212	D	0.99181	B;B;B;B;B	0.14805	0.01;0.007;0.004;0.011;0.009	B;B;B;B;B	0.26770	0.073;0.013;0.046;0.011;0.035	T	0.59537	-0.7436	10	0.33141	T	0.24	.	15.5722	0.76349	0.0:0.0:1.0:0.0	rs33996815	600;624;578;578;578	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	A	578;578;600;578;600;518;624;273	ENSP00000310697:G578A;ENSP00000431152:G578A;ENSP00000310805:G600A;ENSP00000432000:G578A;ENSP00000433370:G600A;ENSP00000433235:G518A;ENSP00000371614:G624A;ENSP00000445168:G273A	ENSP00000310697:G578A	G	+	2	0	BRSK2	1434218	1.000000	0.71417	0.918000	0.36340	0.363000	0.29612	5.585000	0.67497	1.877000	0.54381	0.457000	0.33378	GGG	G|0.997;C|0.003	0.003	strong		0.622	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
SZT2	23334	hgsc.bcm.edu	37	1	43909129	43909129	+	Missense_Mutation	SNP	C	C	T	rs372395617		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:43909129C>T	ENST00000562955.1	+	60	8435	c.8435C>T	c.(8434-8436)tCt>tTt	p.S2812F	SZT2_ENST00000372442.1_Missense_Mutation_p.S1970F	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2869					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						CCAGAGACCTCTGGACCCCCT	0.617																																					p.S2812F		Atlas-SNP	.											SZT2_ENST00000562955,NS,carcinoma,-1,3	SZT2	383	3	0			c.C8435T						PASS	.	C	PHE/SER	0,4406		0,0,2203	35.0	37.0	36.0		8435	2.3	0.8	1		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	SZT2	NM_015284.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	2812/3376	43909129	1,13005	2203	4300	6503	SO:0001583	missense	23334	exon60			AGACCTCTGGACC	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.8435C>T	1.37:g.43909129C>T	ENSP00000457168:p.Ser2812Phe	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	9.750	1.167172	0.21621	0.0	1.16E-4	ENSG00000198198	ENST00000372442	.	.	.	5.4	2.26	0.28386	.	0.695263	0.14386	N	0.322843	T	0.25269	0.0614	N	0.08118	0	0.09310	N	1	B	0.31351	0.32	B	0.38056	0.264	T	0.24154	-1.0168	9	0.11485	T	0.65	.	12.9384	0.58329	0.0:0.52:0.48:0.0	.	2812	Q5T011-5	.	F	1970	.	ENSP00000361519:S1970F	S	+	2	0	SZT2	43681716	0.011000	0.17503	0.770000	0.31555	0.933000	0.57130	0.549000	0.23329	0.604000	0.29930	0.655000	0.94253	TCT	.	.	none		0.617	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
ACACB	32	hgsc.bcm.edu	37	12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	rs60293430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109665242G>A	ENST00000338432.7	+	28	4068	c.3949G>A	c.(3949-3951)Ggc>Agc	p.G1317S	ACACB_ENST00000377854.5_Missense_Mutation_p.G1247S|ACACB_ENST00000377848.3_Missense_Mutation_p.G1317S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1317					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)	GCTCCCGGACGGCACCTGCGT	0.577													G|||	259	0.0517173	0.1074	0.0548	5008	,	,		17197	0.002		0.0586	False		,,,				2504	0.0184				p.G1317S		Atlas-SNP	.											.	ACACB	330	.	0			c.G3949A						PASS	.	G	SER/GLY	456,3950	214.8+/-234.0	23,410,1770	53.0	45.0	47.0		3949	5.4	1.0	12	dbSNP_129	47	522,8078	144.3+/-200.2	19,484,3797	yes	missense	ACACB	NM_001093.3	56	42,894,5567	AA,AG,GG		6.0698,10.3495,7.5196	benign	1317/2459	109665242	978,12028	2203	4300	6503	SO:0001583	missense	32	exon27			CCGGACGGCACCT	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.3949G>A	12.37:g.109665242G>A	ENSP00000341044:p.Gly1317Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	22	0.06077348066298342	0	0.0	38	0.05013192612137203	G	16.13	3.034855	0.54896	0.103495	0.060698	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.38	5.38	0.77491	Acetyl-CoA carboxylase, central domain (1);	0.053759	0.85682	D	0.000000	T	0.02342	0.0072	L	0.55213	1.73	0.09310	P	1.0	D	0.65815	0.995	P	0.62813	0.907	T	0.04128	-1.0975	9	0.17832	T	0.49	.	14.364	0.66792	0.0:0.0:0.852:0.148	rs60293430;rs61752506	1317	O00763	ACACB_HUMAN	S	1317;1317;1247;548	ENSP00000341044:G1317S;ENSP00000367079:G1317S;ENSP00000367085:G1247S	ENSP00000341044:G1317S	G	+	1	0	ACACB	108149625	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	4.727000	0.61993	2.679000	0.91253	0.655000	0.94253	GGC	G|0.932;A|0.068	0.068	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
DHRS4	10901	hgsc.bcm.edu	37	14	24424420	24424420	+	Splice_Site	SNP	C	C	T	rs537144117	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24424420C>T	ENST00000313250.5	+	2	508	c.305C>T	c.(304-306)aCg>aTg	p.T102M	DHRS4_ENST00000543741.2_Splice_Site_p.T102M|DHRS4_ENST00000397075.3_Splice_Site_p.T102M|DHRS4_ENST00000559632.1_Splice_Site_p.T102M|DHRS4_ENST00000382761.3_Splice_Site_p.T84M|DHRS4_ENST00000421831.1_Splice_Site_p.T84M|DHRS4_ENST00000558263.1_Splice_Site_p.T102M|DHRS4_ENST00000558581.1_Splice_Site_p.T102M|DHRS4_ENST00000397074.3_Splice_Site_p.T102M|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_Splice_Site_p.T84M|DHRS4_ENST00000397073.2_Splice_Site_p.T84M	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	102				T -> M (in Ref. 1; AAD02292). {ECO:0000305}.	alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)	p.T102M(4)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGTGGCCACGGTGAGCTGC	0.652													.|||	14	0.00279553	0.0008	0.0	5008	,	,		13962	0.003		0.004	False		,,,				2504	0.0061				p.T102M		Atlas-SNP	.											DHRS4,NS,carcinoma,0,5	DHRS4	22	5	4	Substitution - Missense(4)	central_nervous_system(2)|lung(1)|kidney(1)	c.C305T						scavenged	.																																			SO:0001630	splice_region_variant	10901	exon2			TGGCCACGGTGAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.306+1C>T	14.37:g.24424420C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	131	15	0.114504	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	.	8.197	0.797295	0.16327	.	.	ENSG00000157326	ENST00000313250;ENST00000421831;ENST00000397073;ENST00000308178;ENST00000382761;ENST00000397075;ENST00000397074;ENST00000543741	T;T;D;D;D;D;D;D	0.88201	0.93;0.93;-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	3.78	0.837	0.18896	NAD(P)-binding domain (1);	0.264094	0.42294	N	0.000732	D	0.83839	0.5341	M	0.77712	2.385	0.36055	D	0.841007	P;B;B;B;B;B	0.45011	0.848;0.001;0.002;0.065;0.05;0.035	B;B;B;B;B;B	0.34180	0.177;0.002;0.001;0.016;0.064;0.044	T	0.80294	-0.1443	10	0.37606	T	0.19	.	7.6245	0.28204	0.0:0.6987:0.0:0.3013	.	102;102;102;102;102;102	Q9BTZ2-5;F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2-4;Q9BTZ2	.;.;.;.;.;DHRS4_HUMAN	M	102;84;84;84;84;102;102;102	ENSP00000326219:T102M;ENSP00000404147:T84M;ENSP00000380263:T84M;ENSP00000311993:T84M;ENSP00000372209:T84M;ENSP00000380265:T102M;ENSP00000380264:T102M;ENSP00000440508:T102M	ENSP00000311993:T84M	T	+	2	0	DHRS4	23494260	0.410000	0.25376	0.968000	0.41197	0.539000	0.34962	-0.130000	0.10498	-0.015000	0.14150	0.479000	0.44913	ACG	.	.	none		0.652	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		Missense_Mutation
ARHGEF3	50650	hgsc.bcm.edu	37	3	56766435	56766435	+	Silent	SNP	C	C	G	rs3732511	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56766435C>G	ENST00000296315.3	-	9	1227	c.1059G>C	c.(1057-1059)ctG>ctC	p.L353L	ARHGEF3_ENST00000495373.1_Silent_p.L353L|ARHGEF3_ENST00000497267.1_Silent_p.L324L|ARHGEF3_ENST00000338458.4_Silent_p.L385L|ARHGEF3_ENST00000496106.1_Silent_p.L359L|ARHGEF3_ENST00000413728.2_Silent_p.L359L	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	353	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CTTCTTGGAACAGGAAAACAT	0.458													C|||	1285	0.256589	0.239	0.1023	5008	,	,		20815	0.3442		0.1372	False		,,,				2504	0.4223				p.L385L		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.G1155C						PASS	.	C	,,	1020,3386	378.0+/-322.7	99,822,1282	102.0	104.0	103.0		1155,1077,1059	3.0	1.0	3	dbSNP_107	103	992,7608	212.8+/-253.0	65,862,3373	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	164,1684,4655	GG,GC,CC		11.5349,23.1502,15.4698	,,	385/559,359/533,353/527	56766435	2012,10994	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon12			TTGGAACAGGAAA	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.1059G>C	3.37:g.56766435C>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	32	0.380952	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			C|0.827;G|0.173	0.173	strong		0.458	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
TBATA	219793	hgsc.bcm.edu	37	10	72536936	72536936	+	Silent	SNP	A	A	G	rs2254433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:72536936A>G	ENST00000299290.1	-	7	1052	c.663T>C	c.(661-663)gcT>gcC	p.A221A	TBATA_ENST00000456372.2_Silent_p.A221A	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	221					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											GAAGGAGGAAAGCCTGGACTC	0.617													G|||	1185	0.236621	0.3268	0.1571	5008	,	,		17113	0.1091		0.2863	False		,,,				2504	0.2515				p.A221A		Atlas-SNP	.											C10orf27,NS,carcinoma,-2,1	.	.	1	0			c.T663C						PASS	.	G		1542,2864	671.3+/-402.5	266,1010,927	58.0	59.0	59.0		663	0.6	0.0	10	dbSNP_100	59	2545,6055	690.8+/-404.5	374,1797,2129	no	coding-synonymous	C10orf27	NM_152710.2		640,2807,3056	GG,GA,AA		29.593,34.9977,31.424		221/352	72536936	4087,8919	2203	4300	6503	SO:0001819	synonymous_variant	219793	exon7			GAGGAAAGCCTGG	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"""chromosome 10 open reading frame 27"""	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.663T>C	10.37:g.72536936A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Silent	SNP	ENST00000299290.1	37	CCDS7308.1																																																																																			A|0.710;G|0.290	0.290	strong		0.617	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710	
MTMR7	9108	hgsc.bcm.edu	37	8	17198953	17198953	+	Silent	SNP	T	T	C	rs4921756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17198953T>C	ENST00000180173.5	-	6	685	c.651A>G	c.(649-651)ctA>ctG	p.L217L	MTMR7_ENST00000521857.1_Silent_p.L217L|MTMR7_ENST00000523571.1_5'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	217	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				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)		GCTCGTCCTCTAGGCACCGGG	0.577													T|||	223	0.0445288	0.0076	0.0634	5008	,	,		19385	0.002		0.1491	False		,,,				2504	0.0174				p.L217L		Atlas-SNP	.											.	MTMR7	75	.	0			c.A651G						PASS	.	T		132,4274	94.8+/-133.5	3,126,2074	115.0	78.0	91.0		651	1.1	1.0	8	dbSNP_111	91	1227,7373	246.4+/-274.8	84,1059,3157	no	coding-synonymous	MTMR7	NM_004686.4		87,1185,5231	CC,CT,TT		14.2674,2.9959,10.449		217/661	17198953	1359,11647	2203	4300	6503	SO:0001819	synonymous_variant	9108	exon6			GTCCTCTAGGCAC	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.651A>G	8.37:g.17198953T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_004686	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	37	CCDS34851.1																																																																																			T|0.909;C|0.091	0.091	strong		0.577	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
SLC18A1	6570	hgsc.bcm.edu	37	8	20038466	20038466	+	Missense_Mutation	SNP	T	T	G	rs2270641	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:20038466T>G	ENST00000276373.5	-	2	276	c.10A>C	c.(10-12)Acc>Ccc	p.T4P	SLC18A1_ENST00000440926.1_Missense_Mutation_p.T4P|SLC18A1_ENST00000381608.4_Missense_Mutation_p.T4P|SLC18A1_ENST00000265808.7_Missense_Mutation_p.T4P|SLC18A1_ENST00000437980.1_Missense_Mutation_p.T4P|SLC18A1_ENST00000519026.1_Missense_Mutation_p.T4P	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	4			T -> P (in dbSNP:rs2270641). {ECO:0000269|PubMed:15489334}.		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)	p.T4P(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TCCAGAATGGTCCGGAGCATG	0.607													T|||	1233	0.246206	0.1029	0.3012	5008	,	,		13281	0.248		0.3638	False		,,,				2504	0.2781				p.T4P		Atlas-SNP	.											SLC18A1,NS,lymphoid_neoplasm,0,1	SLC18A1	68	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A10C	GRCh37	CM057213	SLC18A1	M	rs2270641	scavenged	.	T	PRO/THR,PRO/THR,PRO/THR,PRO/THR	686,3714		57,572,1571	49.0	40.0	43.0		10,10,10,10	0.6	0.0	8	dbSNP_100	43	3086,5506		573,1940,1783	yes	missense,missense,missense,missense	SLC18A1	NM_001135691.2,NM_001142324.1,NM_001142325.1,NM_003053.3	38,38,38,38	630,2512,3354	GG,GT,TT		35.9171,15.5909,29.0333	benign,benign,benign,benign	4/526,4/494,4/473,4/526	20038466	3772,9220	2200	4296	6496	SO:0001583	missense	6570	exon3			GAATGGTCCGGAG		CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"""Solute carriers"""	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.10A>C	8.37:g.20038466T>G	ENSP00000276373:p.Thr4Pro	Somatic	31	1	0.0322581		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	596	0.27289377289377287	63	0.12804878048780488	112	0.30939226519337015	152	0.26573426573426573	269	0.3548812664907652	T	7.431	0.638805	0.14386	0.155909	0.359171	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608;ENST00000522513	T;T;T;T;T;T;T	0.04454	3.93;3.93;3.93;3.89;3.93;3.89;3.62	5.71	0.564	0.17302	.	1.085600	0.06916	N	0.808479	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.27068	0.001;0.167;0.0	B;B;B	0.20384	0.001;0.029;0.0	T	0.47886	-0.9082	9	0.30078	T	0.28	0.6653	8.8235	0.35041	0.0:0.3955:0.0:0.6045	rs2270641;rs17222099;rs17490072;rs17856183;rs56575139;rs2270641	4;4;4	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	P	4	ENSP00000265808:T4P;ENSP00000276373:T4P;ENSP00000387549:T4P;ENSP00000413361:T4P;ENSP00000429664:T4P;ENSP00000371021:T4P;ENSP00000428999:T4P	ENSP00000265808:T4P	T	-	1	0	SLC18A1	20082746	0.000000	0.05858	0.002000	0.10522	0.100000	0.18952	-0.897000	0.04110	-0.183000	0.10585	0.533000	0.62120	ACC	A|0.013;C|0.004	.	strong		0.607	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
MMP14	4323	hgsc.bcm.edu	37	14	23312594	23312594	+	Missense_Mutation	SNP	G	G	A	rs1042704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23312594G>A	ENST00000311852.6	+	5	1078	c.817G>A	c.(817-819)Gat>Aat	p.D273N	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	273			D -> N (in dbSNP:rs1042704). {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)	TGTGCTGCCCGATGATGACCG	0.597													G|||	550	0.109824	0.0091	0.1311	5008	,	,		17770	0.0258		0.1988	False		,,,				2504	0.226				p.D273N		Atlas-SNP	.											.	MMP14	40	.	0			c.G817A						PASS	.	G	ASN/ASP	197,4209	122.5+/-159.9	2,193,2008	106.0	108.0	107.0		817	5.6	1.0	14	dbSNP_86	107	1747,6853	317.6+/-313.3	167,1413,2720	yes	missense	MMP14	NM_004995.2	23	169,1606,4728	AA,AG,GG		20.314,4.4712,14.9469	benign	273/583	23312594	1944,11062	2203	4300	6503	SO:0001583	missense	4323	exon5			CTGCCCGATGATG		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.817G>A	14.37:g.23312594G>A	ENSP00000308208:p.Asp273Asn	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	37	CCDS9577.1	231	0.10576923076923077	8	0.016260162601626018	53	0.1464088397790055	13	0.022727272727272728	157	0.20712401055408972	G	9.413	1.081018	0.20309	0.044712	0.20314	ENSG00000157227	ENST00000311852	T	0.20598	2.06	5.6	5.6	0.85130	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.143577	0.64402	D	0.000009	T	0.00012	0.0000	L	0.35414	1.06	0.18873	P	0.9999895192	B	0.12013	0.005	B	0.09377	0.004	T	0.29579	-1.0007	9	0.32370	T	0.25	.	18.3853	0.90464	0.0:0.0:1.0:0.0	rs1042704;rs3182168;rs17881628;rs52820031;rs60437546;rs1042704	273	P50281	MMP14_HUMAN	N	273	ENSP00000308208:D273N	ENSP00000308208:D273N	D	+	1	0	MMP14	22382434	1.000000	0.71417	0.979000	0.43373	0.140000	0.21249	4.763000	0.62257	2.644000	0.89710	0.563000	0.77884	GAT	G|0.873;A|0.127	0.127	strong		0.597	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
OR10A2	341276	hgsc.bcm.edu	37	11	6891704	6891704	+	Missense_Mutation	SNP	T	T	C	rs10839632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6891704T>C	ENST00000307322.4	+	1	781	c.719T>C	c.(718-720)aTa>aCa	p.I240T		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	240			I -> T (in dbSNP:rs10839632).			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)		CTTTTCTATATATCATTAAGC	0.428													-|||	1557	0.310903	0.205	0.2882	5008	,	,		23908	0.4067		0.325	False		,,,				2504	0.3569				p.I240T		Atlas-SNP	.											.	OR10A2	55	.	0			c.T719C						PASS	.	T	THR/ILE	1041,3361	382.8+/-324.6	133,775,1293	217.0	196.0	203.0		719	1.6	1.0	11	dbSNP_120	203	2448,6144	403.4+/-347.8	363,1722,2211	yes	missense	OR10A2	NM_001004460.1	89	496,2497,3504	CC,CT,TT		28.4916,23.6483,26.8509	benign	240/304	6891704	3489,9505	2201	4296	6497	SO:0001583	missense	341276	exon1			TCTATATATCATT	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.719T>C	11.37:g.6891704T>C	ENSP00000303862:p.Ile240Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	653	0.298992673992674	95	0.19308943089430894	102	0.281767955801105	206	0.36013986013986016	250	0.32981530343007914	t	3.738	-0.054205	0.07362	0.236483	0.284916	ENSG00000170790	ENST00000307322	T	0.37915	1.17	4.18	1.6	0.23607	GPCR, rhodopsin-like superfamily (1);	0.240340	0.28606	N	0.014748	T	0.00012	0.0000	N	0.04373	-0.215	0.54753	P	2.0000000000020002E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.42327	-0.9458	9	0.87932	D	0	.	9.3933	0.38386	0.0:0.0:0.3374:0.6626	rs10839632;rs52827835;rs58894419;rs10839632	240	Q9H208	O10A2_HUMAN	T	240	ENSP00000303862:I240T	ENSP00000303862:I240T	I	+	2	0	OR10A2	6848280	0.000000	0.05858	0.986000	0.45419	0.121000	0.20230	0.050000	0.14120	0.754000	0.32968	-0.323000	0.08544	ATA	T|0.723;C|0.277	0.277	strong		0.428	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
NME4	4833	hgsc.bcm.edu	37	16	450309	450309	+	Silent	SNP	C	C	T	rs5841	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:450309C>T	ENST00000219479.2	+	5	545	c.531C>T	c.(529-531)gaC>gaT	p.D177D	DECR2_ENST00000397710.1_5'Flank|DECR2_ENST00000219481.5_5'Flank|NME4_ENST00000382940.4_Silent_p.D185D|DECR2_ENST00000424398.2_5'Flank|NME4_ENST00000397722.1_Silent_p.D107D|NME4_ENST00000450036.1_Silent_p.D107D	NM_005009.2	NP_005000.1	O00746	NDKM_HUMAN	NME/NM23 nucleoside diphosphate kinase 4	177					CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|lung(1)|stomach(1)|urinary_tract(1)	4		Hepatocellular(16;0.00015)				GCTGGGCAGACGGGGGCCAGC	0.647													C|||	2074	0.414137	0.472	0.4164	5008	,	,		18357	0.3423		0.3638	False		,,,				2504	0.4601				p.D177D		Atlas-SNP	.											.	NME4	9	.	0			c.C531T						PASS	.	C		2071,2333	554.2+/-379.0	485,1101,616	49.0	53.0	51.0		531	-6.9	0.0	16	dbSNP_52	51	3349,5245	491.7+/-373.2	633,2083,1581	no	coding-synonymous	NME4	NM_005009.2		1118,3184,2197	TT,TC,CC		38.969,47.0254,41.6987		177/188	450309	5420,7578	2202	4297	6499	SO:0001819	synonymous_variant	4833	exon5			GGCAGACGGGGGC	Y07604	CCDS10408.1, CCDS66886.1, CCDS73797.1	16p13.3	2013-04-29	2012-05-18		ENSG00000103202	ENSG00000103202			7852	protein-coding gene	gene with protein product		601818	"""non-metastatic cells 4, protein expressed in"""			9099850, 19852809	Standard	NM_005009		Approved	nm23-H4, NM23H4, NDPKD	uc002cgz.3	O00746	OTTHUMG00000047995	ENST00000219479.2:c.531C>T	16.37:g.450309C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_005009	A2IDD0|Q5U0M9	Silent	SNP	ENST00000219479.2	37	CCDS10408.1																																																																																			C|0.595;T|0.405	0.405	strong		0.647	NME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109256.2	NM_005009	
PGLYRP3	114771	hgsc.bcm.edu	37	1	153279696	153279696	+	Missense_Mutation	SNP	C	C	T	rs55991125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:153279696C>T	ENST00000290722.1	-	2	155	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	35			A -> T (in dbSNP:rs55991125).		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCCTGCAGGCGAGCGGTCTT	0.627													C|||	93	0.0185703	0.0045	0.0303	5008	,	,		18833	0.0		0.0398	False		,,,				2504	0.0266				p.A35T		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.G103A						PASS	.	C	THR/ALA	47,4359	46.0+/-80.4	1,45,2157	45.0	42.0	43.0		103	1.9	0.3	1	dbSNP_129	43	503,8097	136.4+/-193.5	7,489,3804	yes	missense	PGLYRP3	NM_052891.1	58	8,534,5961	TT,TC,CC		5.8488,1.0667,4.2288	benign	35/342	153279696	550,12456	2203	4300	6503	SO:0001583	missense	114771	exon2			TGCAGGCGAGCGG	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.103G>A	1.37:g.153279696C>T	ENSP00000290722:p.Ala35Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	33	0.354839	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	38	0.0173992673992674	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	25	0.032981530343007916	C	4.156	0.027487	0.08054	0.010667	0.058488	ENSG00000159527	ENST00000290722	T	0.29142	1.58	4.21	1.87	0.25490	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (3);	0.308555	0.23642	N	0.046009	T	0.02929	0.0087	N	0.05078	-0.115	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43343	-0.9397	10	0.11794	T	0.64	2.1343	3.2751	0.06896	0.2022:0.1146:0.0:0.6832	rs55991125	35	Q96LB9	PGRP3_HUMAN	T	35	ENSP00000290722:A35T	ENSP00000290722:A35T	A	-	1	0	PGLYRP3	151546320	0.000000	0.05858	0.339000	0.25562	0.000000	0.00434	-0.174000	0.09839	0.269000	0.21961	-1.106000	0.02097	GCC	C|0.967;T|0.033	0.033	strong		0.627	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	
CPA6	57094	hgsc.bcm.edu	37	8	68396915	68396915	+	Splice_Site	SNP	T	T	C	rs17343819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:68396915T>C	ENST00000297770.4	-	7	961	c.746A>G	c.(745-747)aAt>aGt	p.N249S	CPA6_ENST00000297769.4_Splice_Site_p.N101S|CPA6_ENST00000518549.1_Splice_Site_p.N249S	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	249			N -> S (in dbSNP:rs17343819).			proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			GTGACTTACATTGGTCCAACT	0.383													T|||	396	0.0790735	0.0575	0.121	5008	,	,		17805	0.0		0.166	False		,,,				2504	0.0706				p.N249S		Atlas-SNP	.											CPA6,colon,carcinoma,-1,1	CPA6	69	1	0			c.A746G						scavenged	.	T	SER/ASN	276,4130	153.7+/-187.2	8,260,1935	106.0	94.0	98.0		746	4.1	1.0	8	dbSNP_123	98	1338,7262	262.0+/-284.2	115,1108,3077	yes	missense-near-splice	CPA6	NM_020361.4	46	123,1368,5012	CC,CT,TT		15.5581,6.2642,12.4097	benign	249/438	68396915	1614,11392	2203	4300	6503	SO:0001630	splice_region_variant	57094	exon7			CTTACATTGGTCC	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.747+1A>G	8.37:g.68396915T>C		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	186	0.08516483516483517	24	0.04878048780487805	48	0.13259668508287292	0	0.0	114	0.1503957783641161	T	8.362	0.833381	0.16820	0.062642	0.155581	ENSG00000165078	ENST00000297769;ENST00000297770;ENST00000518549	T;T;T	0.10099	2.91;2.91;2.91	5.25	4.09	0.47781	Peptidase M14, carboxypeptidase A (2);	0.431443	0.27650	N	0.018439	T	0.00039	0.0001	N	0.05280	-0.08	0.43531	P	0.004184999999999994	B;B;B	0.11235	0.002;0.004;0.001	B;B;B	0.11329	0.005;0.006;0.004	T	0.41466	-0.9507	9	0.17369	T	0.5	.	8.4804	0.33038	0.0:0.0902:0.0:0.9098	rs17343819;rs17343819	249;101;249	Q8N4T0-2;Q8N4T0-3;Q8N4T0	.;.;CBPA6_HUMAN	S	101;249;249	ENSP00000297769:N101S;ENSP00000297770:N249S;ENSP00000431112:N249S	ENSP00000297769:N101S	N	-	2	0	CPA6	68559469	0.999000	0.42202	0.999000	0.59377	0.956000	0.61745	0.915000	0.28638	2.096000	0.63516	0.523000	0.50628	AAT	T|0.893;C|0.107	0.107	strong		0.383	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361	Missense_Mutation
AASDHPPT	60496	hgsc.bcm.edu	37	11	105962172	105962172	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:105962172G>A	ENST00000278618.4	+	4	883	c.661G>A	c.(661-663)Gat>Aat	p.D221N	RP11-677I18.3_ENST00000532422.1_RNA	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	221					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)		TTTATTCCTGGATGGAGAGGA	0.323																																					p.D221N		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.G661A						PASS	.						72.0	79.0	77.0					11																	105962172		2200	4299	6499	SO:0001583	missense	60496	exon4			TTCCTGGATGGAG	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.661G>A	11.37:g.105962172G>A	ENSP00000278618:p.Asp221Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	29	0.318681	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447623	0.84101	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.77	5.77	0.91146	4&apos (2);-phosphopantetheinyl transferase (2);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	L	0.33753	1.03	0.58432	D	0.999998	P	0.51057	0.941	P	0.44647	0.456	T	0.49969	-0.8882	9	0.33141	T	0.24	.	19.981	0.97324	0.0:0.0:1.0:0.0	.	221	Q9NRN7	ADPPT_HUMAN	N	156;156;221	.	ENSP00000278618:D221N	D	+	1	0	AASDHPPT	105467382	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	8.453000	0.90349	2.729000	0.93468	0.585000	0.79938	GAT	.	.	none		0.323	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423	
ABCC10	89845	hgsc.bcm.edu	37	6	43400050	43400050	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43400050C>T	ENST00000372530.4	+	3	547	c.332C>T	c.(331-333)gCc>gTc	p.A111V	ABCC10_ENST00000244533.3_Missense_Mutation_p.A68V|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	111					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GCAGCTGTGGCCTGGATCAGC	0.647																																					p.A111V		Atlas-SNP	.											.	ABCC10	118	.	0			c.C332T						PASS	.						61.0	61.0	61.0					6																	43400050		2203	4300	6503	SO:0001583	missense	89845	exon3			CTGTGGCCTGGAT	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.332C>T	6.37:g.43400050C>T	ENSP00000361608:p.Ala111Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767863	0.69878	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.41065	1.01;1.01	5.94	5.94	0.96194	.	0.106734	0.64402	D	0.000004	T	0.37758	0.1015	L	0.32530	0.975	0.52099	D	0.999942	D;P	0.55385	0.971;0.952	P;P	0.50825	0.651;0.449	T	0.13361	-1.0512	10	0.56958	D	0.05	-20.1624	20.3633	0.98874	0.0:1.0:0.0:0.0	.	68;111	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	111;68	ENSP00000361608:A111V;ENSP00000244533:A68V	ENSP00000244533:A68V	A	+	2	0	ABCC10	43508028	1.000000	0.71417	1.000000	0.80357	0.054000	0.15201	7.418000	0.80167	2.826000	0.97356	0.561000	0.74099	GCC	.	.	none		0.647	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
PKHD1	5314	hgsc.bcm.edu	37	6	51917968	51917968	+	Silent	SNP	T	T	G	rs4715271	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:51917968T>G	ENST00000371117.3	-	21	2321	c.2046A>C	c.(2044-2046)ccA>ccC	p.P682P	PKHD1_ENST00000340994.4_Silent_p.P682P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	682					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)					GAACCAGCACTGGGGAGTTTG	0.527													T|||	294	0.0587061	0.0242	0.0749	5008	,	,		19890	0.0407		0.1113	False		,,,				2504	0.0583				p.P682P		Atlas-SNP	.											PKHD1_ENST00000340994,NS,malignant_melanoma,-1,4	PKHD1	927	4	0			c.A2046C						PASS	.	T	,	168,4238	110.8+/-149.0	5,158,2040	71.0	73.0	72.0		2046,2046	-11.3	0.0	6	dbSNP_111	72	952,7648	207.9+/-249.5	60,832,3408	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	65,990,5448	GG,GT,TT		11.0698,3.813,8.6114	,	682/4075,682/3397	51917968	1120,11886	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGCACTGGGGAG	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.2046A>C	6.37:g.51917968T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.921;G|0.079	0.079	strong		0.527	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
CNOT6L	246175	hgsc.bcm.edu	37	4	78697538	78697538	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78697538C>T	ENST00000504123.1	-	2	144	c.14G>A	c.(13-15)gGg>gAg	p.G5E	CNOT6L_ENST00000264903.4_Missense_Mutation_p.G5E|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	5	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						CTTTGGCATCCCTATTAGTCT	0.358																																					p.G5E		Atlas-SNP	.											.	CNOT6L	57	.	0			c.G14A						PASS	.						60.0	53.0	55.0					4																	78697538		1804	4080	5884	SO:0001583	missense	246175	exon2			GGCATCCCTATTA	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.14G>A	4.37:g.78697538C>T	ENSP00000424896:p.Gly5Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	37		.	.	.	.	.	.	.	.	.	.	C	19.78	3.890592	0.72524	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000515441	T;T;T;T	0.35605	1.3;1.3;1.67;1.98	5.72	5.72	0.89469	.	0.000000	0.44285	D	0.000480	T	0.39860	0.1094	L	0.29908	0.895	0.58432	D	0.999993	D;P	0.58268	0.982;0.866	P;P	0.51550	0.622;0.673	T	0.22347	-1.0219	10	0.72032	D	0.01	-2.6931	16.1856	0.81948	0.1336:0.8664:0.0:0.0	.	5;5	B4E2S0;Q96LI5	.;CNO6L_HUMAN	E	5;5;12;5	ENSP00000424896:G5E;ENSP00000264903:G5E;ENSP00000425571:G12E;ENSP00000426269:G5E	ENSP00000264903:G5E	G	-	2	0	CNOT6L	78916562	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.037000	0.70956	2.695000	0.91970	0.557000	0.71058	GGG	.	.	none		0.358	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
ANO3	63982	hgsc.bcm.edu	37	11	26656563	26656563	+	Silent	SNP	C	C	T	rs7946841	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:26656563C>T	ENST00000256737.3	+	20	2841	c.1989C>T	c.(1987-1989)ttC>ttT	p.F663F	ANO3_ENST00000537978.1_Silent_p.F647F|ANO3_ENST00000531568.1_Silent_p.F517F|ANO3_ENST00000525139.1_Silent_p.F647F	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	663					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						CTTACAGATTCGTAGGCCACC	0.433													C|||	1709	0.341254	0.2277	0.2507	5008	,	,		18554	0.3552		0.4165	False		,,,				2504	0.4673				p.F663F		Atlas-SNP	.											.	ANO3	145	.	0			c.C1989T						PASS	.	C		1032,3374	381.8+/-324.2	112,808,1283	134.0	121.0	125.0		1989	1.3	1.0	11	dbSNP_116	125	3589,5009	519.7+/-379.5	735,2119,1445	no	coding-synonymous	ANO3	NM_031418.2		847,2927,2728	TT,TC,CC		41.7423,23.4226,35.5352		663/982	26656563	4621,8383	2203	4299	6502	SO:0001819	synonymous_variant	63982	exon20			CAGATTCGTAGGC	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1989C>T	11.37:g.26656563C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			C|0.652;T|0.348	0.348	strong		0.433	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
TBC1D10A	83874	hgsc.bcm.edu	37	22	30689998	30689998	+	Silent	SNP	G	G	A	rs11089442	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:30689998G>A	ENST00000215790.7	-	7	971	c.807C>T	c.(805-807)ctC>ctT	p.L269L	TBC1D10A_ENST00000403362.1_Silent_p.L181L|RP1-130H16.18_ENST00000447976.1_Silent_p.L143L|TBC1D10A_ENST00000403477.3_Silent_p.L276L	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	269	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CTGTCATATAGAGGAGCGGGT	0.582													G|||	988	0.197284	0.0182	0.2421	5008	,	,		20240	0.3046		0.1561	False		,,,				2504	0.3395				p.L276L		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.C828T						PASS	.	G	,	184,4222	118.8+/-156.5	4,176,2023	157.0	143.0	147.0		828,807	-0.2	1.0	22	dbSNP_120	147	1308,7292	258.4+/-282.1	111,1086,3103	no	coding-synonymous,coding-synonymous	TBC1D10A	NM_001204240.1,NM_031937.2	,	115,1262,5126	AA,AG,GG		15.2093,4.1761,11.4716	,	276/516,269/509	30689998	1492,11514	2203	4300	6503	SO:0001819	synonymous_variant	83874	exon7			CATATAGAGGAGC	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.807C>T	22.37:g.30689998G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	191	92	0.481675	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Silent	SNP	ENST00000215790.7	37	CCDS13874.1																																																																																			G|0.855;A|0.145	0.145	strong		0.582	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
TAF1C	9013	hgsc.bcm.edu	37	16	84213434	84213434	+	Missense_Mutation	SNP	A	A	T	rs2230129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84213434A>T	ENST00000567759.1	-	14	1905	c.1723T>A	c.(1723-1725)Ttg>Atg	p.L575M	TAF1C_ENST00000378541.4_Missense_Mutation_p.L575M|TAF1C_ENST00000570117.1_Missense_Mutation_p.L243M|TAF1C_ENST00000566732.1_Missense_Mutation_p.L549M|TAF1C_ENST00000541676.1_Missense_Mutation_p.L482M|TAF1C_ENST00000341690.6_Missense_Mutation_p.L481M	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	575			L -> M (in dbSNP:rs2230129). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, 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						GCTGAGGGCAAGGGCGGGACG	0.677													A|||	1604	0.320288	0.1626	0.4481	5008	,	,		16102	0.375		0.3936	False		,,,				2504	0.3108				p.L575M		Atlas-SNP	.											.	TAF1C	60	.	0			c.T1723A						PASS	.	A	MET/LEU,MET/LEU	693,3309		90,513,1398	9.0	11.0	10.0		1723,1441	1.2	0.0	16	dbSNP_98	10	2966,4846		667,1632,1607	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	15,15	757,2145,3005	TT,TA,AA		37.9672,17.3163,30.9717	possibly-damaging,possibly-damaging	575/870,481/776	84213434	3659,8155	2001	3906	5907	SO:0001583	missense	9013	exon14			AGGGCAAGGGCGG	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.1723T>A	16.37:g.84213434A>T	ENSP00000455265:p.Leu575Met	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	769	0.35210622710622713	94	0.1910569105691057	144	0.39779005524861877	237	0.4143356643356643	294	0.38786279683377306	A	13.25	2.181226	0.38511	0.173163	0.379672	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.04275	3.75;3.66;3.66	4.48	1.24	0.21308	.	0.935040	0.08398	U	0.951847	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;D;P;P	0.55605	0.899;0.972;0.899;0.899	P;P;P;P	0.52217	0.466;0.693;0.466;0.466	T	0.48559	-0.9025	9	0.29301	T	0.29	.	4.1716	0.10332	0.2289:0.1919:0.5792:0.0	rs2230129;rs2278041;rs4150171;rs17856788;rs2230129	549;98;575;481	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	M	575;482;481;98	ENSP00000367802:L575M;ENSP00000437900:L482M;ENSP00000345305:L481M	ENSP00000345305:L481M	L	-	1	2	TAF1C	82770935	0.000000	0.05858	0.001000	0.08648	0.214000	0.24535	-1.933000	0.01553	-0.011000	0.14247	0.260000	0.18958	TTG	A|0.640;T|0.360	0.360	strong		0.677	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121513570	121513570	+	Missense_Mutation	SNP	G	G	T	rs11980387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:121513570G>T	ENST00000393386.2	+	1	428	c.17G>T	c.(16-18)cGt>cTt	p.R6L	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.R6L	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	6			R -> L (in dbSNP:rs11980387).		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						ATCCTAAAGCGTTTCCTCGCT	0.592													G|||	160	0.0319489	0.0817	0.0086	5008	,	,		12992	0.001		0.0139	False		,,,				2504	0.0317				p.R6L		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G17T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG	313,4093	168.0+/-198.9	15,283,1905	104.0	98.0	100.0		17,17,17	3.3	1.0	7	dbSNP_120	100	151,8449	72.6+/-135.2	4,143,4153	yes	missense,missense,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	102,102,102	19,426,6058	TT,TG,GG		1.7558,7.1039,3.5676	benign,benign,benign	6/1456,6/1449,6/2316	121513570	464,12542	2203	4300	6503	SO:0001583	missense	5803	exon1			TAAAGCGTTTCCT	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.17G>T	7.37:g.121513570G>T	ENSP00000377047:p.Arg6Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	57	0.0260989010989011	45	0.09146341463414634	3	0.008287292817679558	1	0.0017482517482517483	8	0.010554089709762533	G	10.49	1.365765	0.24684	0.071039	0.017558	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.41065	1.05;1.01	4.27	3.31	0.37934	.	0.283886	0.24748	N	0.035926	T	0.00875	0.0029	N	0.14661	0.345	0.21604	N	0.999623	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.03840	-1.0999	10	0.49607	T	0.09	.	9.8317	0.40946	0.0:0.0:0.796:0.204	rs11980387;rs52832686;rs11980387	6;6	C9JFM0;P23471	.;PTPRZ_HUMAN	L	6	ENSP00000377047:R6L;ENSP00000410000:R6L	ENSP00000377047:R6L	R	+	2	0	PTPRZ1	121300806	1.000000	0.71417	0.969000	0.41365	0.072000	0.16883	1.373000	0.34272	2.031000	0.59945	0.561000	0.74099	CGT	G|0.968;T|0.032	0.032	strong		0.592	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
HLA-A	3105	hgsc.bcm.edu	37	6	29911296	29911296	+	Missense_Mutation	SNP	G	G	A	rs41559916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29911296G>A	ENST00000396634.1	+	5	936	c.595G>A	c.(595-597)Ggg>Agg	p.G199R	HLA-A_ENST00000376806.5_Missense_Mutation_p.G199R|HLA-A_ENST00000376809.5_Missense_Mutation_p.G199R|HLA-A_ENST00000376802.2_Missense_Mutation_p.G199R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	199	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCTGGAGAACGGGAAGGAGAC	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.G199R		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.G595A						PASS	.						48.0	43.0	45.0					6																	29911296		1510	2704	4214	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGAACGGGAAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.595G>A	6.37:g.29911296G>A	ENSP00000379873:p.Gly199Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	125	22	0.176	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	310	0.14194139194139194	89	0.18089430894308944	51	0.1408839779005525	52	0.09090909090909091	118	0.15567282321899736	.	13.19	2.162852	0.38217	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.01068	5.38;5.38;5.38;5.38	3.54	3.54	0.40534	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.000000	0.38605	U	0.001626	T	0.06325	0.0163	H	0.95328	3.655	0.34266	P	0.31949700000000003	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	1.0;1.0;1.0;0.998;1.0;1.0;1.0	T	0.01805	-1.1270	9	0.72032	D	0.01	.	13.0189	0.58775	0.0:0.0:1.0:0.0	rs41559916	78;199;199;199;199;199;199	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	R	199	ENSP00000379873:G199R;ENSP00000366002:G199R;ENSP00000366005:G199R;ENSP00000365998:G199R	ENSP00000365998:G199R	G	+	1	0	HLA-A	30019275	1.000000	0.71417	0.505000	0.27651	0.339000	0.28857	4.611000	0.61162	1.987000	0.57996	0.485000	0.47835	GGG	A|0.146;G|0.854	0.146	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507116	24507116	+	RNA	SNP	G	G	A	rs55933233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24507116G>A	ENST00000558293.1	+	0	176					NR_102693.1																						GACTGGGAGCGGCTGGTGGCC	0.622													G|||	52	0.0103834	0.0015	0.013	5008	,	,		16889	0.0		0.0338	False		,,,				2504	0.0072				p.R98Q		Atlas-SNP	.											.	.	.	.	0			c.G293A						PASS	.	G	GLN/ARG	28,4376		0,28,2174	22.0	25.0	24.0		293	-0.9	0.8	14	dbSNP_129	24	279,8319		1,277,4021	yes	missense	DHRS4L1	NM_001082488.1	43	1,305,6195	AA,AG,GG		3.2449,0.6358,2.3612	benign	98/282	24507116	307,12695	2202	4299	6501			728635	exon2			GGGAGCGGCTGGT																													14.37:g.24507116G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	158	63	0.398734	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	37		31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	-	10.46	1.356327	0.24598	0.006358	0.032449	ENSG00000225766	ENST00000397065	.	.	.	3.32	-0.931	0.10438	NAD(P)-binding domain (1);	.	.	.	.	T	0.12987	0.0315	L	0.41124	1.26	.	.	.	B	0.20671	0.047	B	0.17979	0.02	T	0.27123	-1.0083	7	0.20519	T	0.43	.	7.5359	0.27710	0.4719:0.0:0.5281:0.0	rs55933233;rs62000816	98	P0CG22	DR4L1_HUMAN	Q	98	.	ENSP00000380255:R98Q	R	+	2	0	AL136295.1	23576956	0.631000	0.27164	0.809000	0.32408	0.513000	0.34164	0.415000	0.21181	-0.070000	0.12908	0.400000	0.26472	CGG	G|0.983;A|0.017	0.017	strong		0.622	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689232	41689232	+	Missense_Mutation	SNP	C	C	T	rs1899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41689232C>T	ENST00000260361.4	-	2	407	c.26G>A	c.(25-27)cGt>cAt	p.R9H		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	9			R -> H (in dbSNP:rs1899). {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)		ATAAGTACCACGCAGCAATTT	0.408													C|||	763	0.152356	0.1392	0.1744	5008	,	,		17465	0.0079		0.2724	False		,,,				2504	0.18				p.R9H		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G26A						PASS	.	C	HIS/ARG	721,3681		61,599,1541	33.0	34.0	33.0		26	-4.7	0.0	15	dbSNP_36	33	2232,6364		279,1674,2345	yes	missense	NDUFAF1	NM_016013.2	29	340,2273,3886	TT,TC,CC		25.9656,16.3789,22.7189	benign	9/328	41689232	2953,10045	2201	4298	6499	SO:0001583	missense	51103	exon2			GTACCACGCAGCA	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.26G>A	15.37:g.41689232C>T	ENSP00000260361:p.Arg9His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	346	0.15842490842490842	69	0.1402439024390244	73	0.20165745856353592	3	0.005244755244755245	201	0.26517150395778366	C	6.822	0.520728	0.13005	0.163789	0.259656	ENSG00000137806	ENST00000260361	T	0.59502	0.26	4.7	-4.67	0.03319	.	1.281150	0.04961	N	0.462130	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.21452	0.056	B	0.14578	0.011	T	0.08534	-1.0717	9	0.28530	T	0.3	-5.8832	1.2213	0.01924	0.1242:0.221:0.257:0.3977	rs1899;rs3193542;rs59161962;rs1899	9	Q9Y375	CIA30_HUMAN	H	9	ENSP00000260361:R9H	ENSP00000260361:R9H	R	-	2	0	NDUFAF1	39476524	0.000000	0.05858	0.001000	0.08648	0.051000	0.14879	-0.810000	0.04505	-0.867000	0.04063	-0.458000	0.05436	CGT	C|0.825;T|0.175	0.175	strong		0.408	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116220	31116220	+	Silent	SNP	G	G	A	rs130070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31116220G>A	ENST00000376266.5	-	10	1397	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	CCHCR1_ENST00000396268.3_Silent_p.A514A|CCHCR1_ENST00000396263.2_Silent_p.A425A|CCHCR1_ENST00000451521.2_Silent_p.A478A|CCHCR1_ENST00000480060.1_5'Flank	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	425					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						GCTGCTCCTCGGCTGAGGCTG	0.627													G|||	572	0.114217	0.1528	0.1254	5008	,	,		17316	0.0625		0.167	False		,,,				2504	0.0532				p.A514A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C1542T						PASS	.		,,	449,2571		33,383,1094	105.0	105.0	105.0		1434,1542,1275	-10.5	0.0	6	dbSNP_78	105	807,4609		68,671,1969	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	101,1054,3063	AA,AG,GG		14.9003,14.8675,14.8886	,,	478/836,514/872,425/783	31116220	1256,7180	1510	2708	4218	SO:0001819	synonymous_variant	54535	exon10			CTCCTCGGCTGAG	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.1275C>T	6.37:g.31116220G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			G|0.871;A|0.129	0.129	strong		0.627	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
LRWD1	222229	hgsc.bcm.edu	37	7	102105566	102105566	+	Silent	SNP	G	G	A	rs79978502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102105566G>A	ENST00000292616.5	+	1	191	c.39G>A	c.(37-39)ggG>ggA	p.G13G	ALKBH4_ENST00000292566.3_5'Flank|MIR5090_ENST00000582533.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	13					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						TGCAGCGCGGGCGCCCCAAGA	0.746													G|||	181	0.0361422	0.0446	0.0418	5008	,	,		12157	0.0		0.0716	False		,,,				2504	0.0215				p.G13G		Atlas-SNP	.											.	LRWD1	41	.	0			c.G39A						PASS	.	G		125,3713		0,125,1794	3.0	5.0	5.0		39	0.2	1.0	7	dbSNP_131	5	470,7478		12,446,3516	no	coding-synonymous	LRWD1	NM_152892.1		12,571,5310	AA,AG,GG		5.9134,3.2569,5.0484		13/648	102105566	595,11191	1919	3974	5893	SO:0001819	synonymous_variant	222229	exon1			GCGCGGGCGCCCC	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.39G>A	7.37:g.102105566G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			A|0.043;C|0.000;G|0.957	0.043	strong		0.746	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
GJA9	81025	hgsc.bcm.edu	37	1	39340607	39340607	+	Silent	SNP	A	A	G	rs16825625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:39340607A>G	ENST00000360786.3	-	1	1416	c.1164T>C	c.(1162-1164)cgT>cgC	p.R388R	GJA9_ENST00000454994.2_Silent_p.R388R|MYCBP_ENST00000397572.2_5'Flank|RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000443161.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA|MYCBP_ENST00000489803.1_5'UTR|GJA9_ENST00000357771.3_Silent_p.R388R			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	388					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)			CTGGAATAGAACGGTGACCTC	0.423													A|||	270	0.0539137	0.0182	0.0504	5008	,	,		21207	0.0823		0.0706	False		,,,				2504	0.0583				p.R388R		Atlas-SNP	.											GJA9,NS,carcinoma,-1,1	GJA9	55	1	0			c.T1164C						scavenged	.	A		173,4233	115.0+/-153.0	5,163,2035	184.0	172.0	176.0		1164	-1.2	0.0	1	dbSNP_123	176	870,7730	197.9+/-242.4	60,750,3490	no	coding-synonymous	GJA9	NM_030772.4		65,913,5525	GG,GA,AA		10.1163,3.9265,8.0194		388/516	39340607	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			AATAGAACGGTGA	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.1164T>C	1.37:g.39340607A>G		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			A|0.929;G|0.071	0.071	strong		0.423	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247769752A>G	ENST00000320002.2	+	1	897	c.865A>G	c.(865-867)Atc>Gtc	p.I289V	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	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(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)			AAATCCTATCATCTATACTTT	0.418													A|||	1693	0.338059	0.2307	0.3127	5008	,	,		19391	0.4325		0.4394	False		,,,				2504	0.2996				p.I289V		Atlas-SNP	.											.	OR2G3	108	.	0			c.A865G						PASS	.	A	VAL/ILE	1057,3349	385.1+/-325.6	140,777,1286	85.0	82.0	83.0		865	3.7	0.5	1	dbSNP_129	83	3646,4954	524.7+/-380.6	790,2066,1444	yes	missense	OR2G3	NM_001001914.1	29	930,2843,2730	GG,GA,AA		42.3953,23.99,36.1602	probably-damaging	289/310	247769752	4703,8303	2203	4300	6503	SO:0001583	missense	81469	exon1			CCTATCATCTATA	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.865A>G	1.37:g.247769752A>G	ENSP00000326301:p.Ile289Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	814	0.3727106227106227	104	0.21138211382113822	134	0.3701657458563536	247	0.4318181818181818	329	0.4340369393139842	A	14.76	2.630914	0.46944	0.2399	0.423953	ENSG00000177476	ENST00000320002	T	0.52057	0.68	3.65	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37178	U	0.002213	T	0.00012	0.0000	M	0.86651	2.83	0.49130	P	2.4500000000005073E-4	D	0.63046	0.992	D	0.80764	0.994	T	0.37731	-0.9693	9	0.66056	D	0.02	.	10.5906	0.45308	1.0:0.0:0.0:0.0	rs61730407	289	Q8NGZ4	OR2G3_HUMAN	V	289	ENSP00000326301:I289V	ENSP00000326301:I289V	I	+	1	0	OR2G3	245836375	0.445000	0.25657	0.531000	0.27976	0.988000	0.76386	0.983000	0.29552	1.648000	0.50643	0.403000	0.27427	ATC	A|0.629;G|0.371	0.371	strong		0.418	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
SDK1	221935	hgsc.bcm.edu	37	7	4026944	4026944	+	Silent	SNP	C	C	G	rs7785899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4026944C>G	ENST00000404826.2	+	14	2260	c.2121C>G	c.(2119-2121)ctC>ctG	p.L707L	SDK1_ENST00000389531.3_Silent_p.L707L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	707	Fibronectin type-III 1. {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)		TCGTGGAGCTCTCTGAAAACA	0.458													G|||	2114	0.422125	0.7451	0.3718	5008	,	,		20231	0.1647		0.2942	False		,,,				2504	0.4182				p.L707L		Atlas-SNP	.											.	SDK1	361	.	0			c.C2121G						PASS	.	G		3069,1337	446.7+/-348.1	1081,907,215	130.0	132.0	131.0		2121	1.2	0.9	7	dbSNP_116	131	2946,5654	668.5+/-402.6	533,1880,1887	no	coding-synonymous	SDK1	NM_152744.3		1614,2787,2102	GG,GC,CC		34.2558,30.345,46.2479		707/2214	4026944	6015,6991	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon14			GGAGCTCTCTGAA	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.2121C>G	7.37:g.4026944C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.566;G|0.434	0.434	strong		0.458	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
SLC18B1	116843	hgsc.bcm.edu	37	6	133118214	133118214	+	Silent	SNP	C	C	T	rs34688576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:133118214C>T	ENST00000275227.4	-	2	186	c.90G>A	c.(88-90)tcG>tcA	p.S30S	SLC18B1_ENST00000460518.1_5'UTR|SLC18B1_ENST00000367918.1_Silent_p.S30S|SLC18B1_ENST00000538764.1_5'UTR	NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	30			S -> P (in dbSNP:rs41286192).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)											CCTGTTCTCTCGAAAGCCACC	0.448													C|||	487	0.0972444	0.2012	0.0389	5008	,	,		15038	0.0268		0.0577	False		,,,				2504	0.1115				p.S30S		Atlas-SNP	.											C6orf192,NS,malignant_melanoma,-1,2	.	.	2	0			c.G90A						PASS	.	C		814,3592	325.0+/-298.9	76,662,1465	99.0	100.0	100.0		90	-10.6	0.1	6	dbSNP_126	100	398,8202	126.8+/-185.2	9,380,3911	no	coding-synonymous	C6orf192	NM_052831.2		85,1042,5376	TT,TC,CC		4.6279,18.4748,9.3188		30/457	133118214	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	116843	exon2			TTCTCTCGAAAGC	AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	Standard	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.90G>A	6.37:g.133118214C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_052831	A8K1K3|B3KW77|Q6ISF2	Silent	SNP	ENST00000275227.4	37	CCDS5163.1																																																																																			C|0.907;T|0.093	0.093	strong		0.448	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1	NM_052831	
RCBTB1	55213	hgsc.bcm.edu	37	13	50123649	50123649	+	Silent	SNP	G	G	A	rs3751383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50123649G>A	ENST00000378302.2	-	9	1250	c.990C>T	c.(988-990)gaC>gaT	p.D330D	RCBTB1_ENST00000258646.3_Silent_p.D330D|RCBTB1_ENST00000546015.1_Silent_p.D330D	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	330					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		CAAACACGTCGTCGGTGCAGG	0.632													G|||	1527	0.304912	0.4977	0.1311	5008	,	,		15892	0.2788		0.167	False		,,,				2504	0.3364				p.D330D		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C990T						PASS	.	G		1965,2441	554.6+/-379.1	432,1101,670	90.0	67.0	75.0		990	-0.8	1.0	13	dbSNP_107	75	1264,7336	250.4+/-277.3	81,1102,3117	no	coding-synonymous	RCBTB1	NM_018191.3		513,2203,3787	AA,AG,GG		14.6977,44.5983,24.827		330/532	50123649	3229,9777	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon9			CACGTCGTCGGTG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.990C>T	13.37:g.50123649G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			G|0.732;A|0.268	0.268	strong		0.632	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
STKLD1	169436	hgsc.bcm.edu	37	9	136268912	136268912	+	Silent	SNP	A	A	G	rs28510482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136268912A>G	ENST00000371957.3	+	15	1670	c.1563A>G	c.(1561-1563)gcA>gcG	p.A521A	C9orf96_ENST00000371955.1_Silent_p.A54A	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		521							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)		GGGAAATGGCAGAAGCCAGCT	0.652													G|||	823	0.164337	0.2073	0.1715	5008	,	,		16710	0.0516		0.165	False		,,,				2504	0.2168				p.A521A		Atlas-SNP	.											.	C9orf96	77	.	0			c.A1563G						PASS	.	G		864,3542	741.0+/-411.2	92,680,1431	41.0	41.0	41.0		1563	-9.2	0.0	9	dbSNP_125	41	1517,7083	744.8+/-407.2	146,1225,2929	no	coding-synonymous	C9orf96	NM_153710.3		238,1905,4360	GG,GA,AA		17.6395,19.6096,18.3069		521/681	136268912	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	169436	exon15			AATGGCAGAAGCC																												ENST00000371957.3:c.1563A>G	9.37:g.136268912A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			A|0.830;G|0.170	0.170	strong		0.652	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
CCZ1B	221960	hgsc.bcm.edu	37	7	6859402	6859402	+	Silent	SNP	G	G	A	rs200223833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6859402G>A	ENST00000316731.8	-	7	1265	c.693C>T	c.(691-693)ctC>ctT	p.L231L	CCZ1B_ENST00000538180.1_Silent_p.L88L	NM_198097.3	NP_932765.1	P86790	CCZ1B_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog B (S. cerevisiae)	231						lysosome (GO:0005764)|membrane (GO:0016020)											CCTACCAGATGAGCTGATCGT	0.358																																					p.L231L		Atlas-SNP	.											C7orf28B,NS,carcinoma,0,2	.	.	2	0			c.C693T						scavenged	.						12.0	11.0	11.0					7																	6859402		1992	4118	6110	SO:0001819	synonymous_variant	221960	exon7			CCAGATGAGCTGA	BC010130	CCDS5354.1	7p22.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000146574	ENSG00000146574			21717	protein-coding gene	gene with protein product	"""similar to CGI-43 protein"""		"""chromosome 7 open reading frame 28B"""	C7orf28B		12477932	Standard	NM_198097		Approved	DKFZP586I1023, H_NH0577018.2, MGC19819	uc003sqx.2	P86790	OTTHUMG00000152441	ENST00000316731.8:c.693C>T	7.37:g.6859402G>A		Somatic	503	0	0		WXS	Illumina HiSeq	Phase_I	877	293	0.334094	NM_198097	A2RU45|O95766|Q9UG65|Q9Y359	Silent	SNP	ENST00000316731.8	37	CCDS5354.1																																																																																			G|0.921;A|0.079	0.079	strong		0.358	CCZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246858.1	NM_198097	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464046	39464046	+	Missense_Mutation	SNP	G	G	C	rs2074286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39464046G>C	ENST00000391352.1	-	1	1459	c.1460C>G	c.(1459-1461)gCt>gGt	p.A487G		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	487						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CTGGCAGGGAGCCTCTTCTGA	0.562													C|||	1607	0.320887	0.4834	0.1974	5008	,	,		18491	0.371		0.2634	False		,,,				2504	0.1963				p.A487G		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C1460G						PASS	.																																			SO:0001583	missense	100505753	exon1			CAGGGAGCCTCTT	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.1460C>G	17.37:g.39464046G>C	ENSP00000375147:p.Ala487Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	717	0.3282967032967033	229	0.4654471544715447	79	0.21823204419889503	206	0.36013986013986016	203	0.2678100263852243	C	3.360	-0.130781	0.06753	.	.	ENSG00000212657	ENST00000391352	T	0.00745	5.75	4.97	0.351	0.16042	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.00795	-1.1563	6	0.30078	T	0.28	.	7.3651	0.26768	0.0:0.3403:0.4902:0.1695	rs2074286;rs2074286	.	.	.	G	487	ENSP00000375147:A487G	ENSP00000375147:A487G	A	-	2	0	KRTAP16-1	36717572	0.003000	0.15002	0.001000	0.08648	0.830000	0.47004	-0.813000	0.04491	-0.255000	0.09486	-0.216000	0.12614	GCT	G|0.675;C|0.325	0.325	strong		0.562	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
ZNF19	7567	hgsc.bcm.edu	37	16	71509634	71509634	+	Silent	SNP	G	G	C	rs2288488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:71509634G>C	ENST00000288177.5	-	6	1071	c.816C>G	c.(814-816)ccC>ccG	p.P272P	ZNF19_ENST00000565100.2_Silent_p.P202P|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000565637.1_Silent_p.P230P|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	51	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	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	
MTRR	4552	hgsc.bcm.edu	37	5	7897319	7897319	+	Silent	SNP	G	G	A	rs1802059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:7897319G>A	ENST00000264668.2	+	14	2022	c.1992G>A	c.(1990-1992)gcG>gcA	p.A664A	MTRR_ENST00000440940.2_Silent_p.A637A	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	664					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)	AGCAGGTGGCGAGAATCCTCC	0.512													G|||	1334	0.266374	0.2557	0.2133	5008	,	,		16470	0.13		0.336	False		,,,				2504	0.3875				p.A664A		Atlas-SNP	.											MTRR,NS,carcinoma,+1,1	MTRR	74	1	0			c.G1992A						PASS	.	G	,	1122,3284	402.4+/-332.3	145,832,1226	109.0	105.0	106.0		1911,1992	-10.8	0.0	5	dbSNP_89	106	3087,5513	472.7+/-368.4	578,1931,1791	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	723,2763,3017	AA,AG,GG		35.8953,25.4653,32.362	,	637/699,664/726	7897319	4209,8797	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon14			GGTGGCGAGAATC	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.1992G>A	5.37:g.7897319G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			G|0.703;A|0.297	0.297	strong		0.512	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
SLC36A2	153201	hgsc.bcm.edu	37	5	150696447	150696447	+	Silent	SNP	C	C	T	rs369907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150696447C>T	ENST00000335244.4	-	10	1512	c.1383G>A	c.(1381-1383)caG>caA	p.Q461Q	SLC36A2_ENST00000450886.1_Silent_p.Q185Q	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	461					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)	CGTCCAGGGCCTGGTAGGTCC	0.587													C|||	3373	0.673522	0.5862	0.683	5008	,	,		14122	0.8482		0.5348	False		,,,				2504	0.7474				p.Q461Q		Atlas-SNP	.											.	SLC36A2	71	.	0			c.G1383A						PASS	.	C		2613,1793	642.1+/-397.6	771,1071,361	71.0	71.0	71.0		1383	4.0	1.0	5	dbSNP_80	71	4538,4062	594.4+/-393.3	1186,2166,948	no	coding-synonymous	SLC36A2	NM_181776.2		1957,3237,1309	TT,TC,CC		47.2326,40.6945,45.0177		461/484	150696447	7151,5855	2203	4300	6503	SO:0001819	synonymous_variant	153201	exon10			CAGGGCCTGGTAG	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.1383G>A	5.37:g.150696447C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			C|0.415;T|0.585	0.585	strong		0.587	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
GRAMD1C	54762	hgsc.bcm.edu	37	3	113634682	113634682	+	Missense_Mutation	SNP	A	A	C	rs78547874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:113634682A>C	ENST00000358160.4	+	10	1579	c.1087A>C	c.(1087-1089)Ata>Cta	p.I363L	GRAMD1C_ENST00000452134.2_Missense_Mutation_p.I92L|GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000440446.2_Missense_Mutation_p.I158L|GRAMD1C_ENST00000472026.1_Missense_Mutation_p.I196L	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	363						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						TAGAAATATAATAGGTTAGTC	0.318													A|||	16	0.00319489	0.0008	0.0029	5008	,	,		17339	0.001		0.008	False		,,,				2504	0.0041				p.I363L		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.A1087C						PASS	.	A	LEU/ILE,LEU/ILE	11,4393	16.8+/-37.8	0,11,2191	76.0	76.0	76.0		472,1087	3.3	1.0	3	dbSNP_132	76	77,8515	44.0+/-102.2	1,75,4220	yes	missense,missense	GRAMD1C	NM_001172105.1,NM_017577.4	5,5	1,86,6411	CC,CA,AA		0.8962,0.2498,0.6771	benign,benign	158/458,363/663	113634682	88,12908	2202	4296	6498	SO:0001583	missense	54762	exon10			AATATAATAGGTT		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.1087A>C	3.37:g.113634682A>C	ENSP00000350881:p.Ile363Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	47	0.373016	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Missense_Mutation	SNP	ENST00000358160.4	37	CCDS33826.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	6	0.0079155672823219	A	11.58	1.682193	0.29872	0.002498	0.008962	ENSG00000178075	ENST00000358160;ENST00000452134;ENST00000472026;ENST00000462838;ENST00000440446	T;T;T;T	0.42131	1.59;0.98;1.0;1.0	5.98	3.3	0.37823	.	0.479810	0.25517	N	0.030128	T	0.19287	0.0463	L	0.32530	0.975	0.27980	N	0.936074	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.002	T	0.18241	-1.0343	10	0.17832	T	0.49	.	5.6635	0.17682	0.7409:0.0:0.0781:0.181	.	196;363	E9PHT3;Q8IYS0	.;GRM1C_HUMAN	L	363;92;196;158;158	ENSP00000350881:I363L;ENSP00000399844:I92L;ENSP00000419132:I196L;ENSP00000408135:I158L	ENSP00000350881:I363L	I	+	1	0	GRAMD1C	115117372	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.491000	0.35583	0.371000	0.24564	0.533000	0.62120	ATA	A|0.995;C|0.005	0.005	strong		0.318	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577	
AASDH	132949	hgsc.bcm.edu	37	4	57215677	57215677	+	Missense_Mutation	SNP	G	G	A	rs3796544	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57215677G>A	ENST00000205214.6	-	11	2420	c.2240C>T	c.(2239-2241)gCg>gTg	p.A747V	AASDH_ENST00000434343.2_Missense_Mutation_p.A262V|AASDH_ENST00000451613.1_Missense_Mutation_p.A747V|AASDH_ENST00000602986.1_Missense_Mutation_p.A594V|AASDH_ENST00000513376.1_Missense_Mutation_p.A647V|AASDH_ENST00000502617.1_Missense_Mutation_p.A747V	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	747			A -> V (in dbSNP:rs3796544). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.A747V(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)				AGTCCCTATCGCAGGTTTCCC	0.418													G|||	1392	0.277955	0.2829	0.2939	5008	,	,		19646	0.0724		0.4155	False		,,,				2504	0.3303				p.A747V		Atlas-SNP	.											AASDH,NS,carcinoma,0,3	AASDH	101	3	1	Substitution - Missense(1)	prostate(1)	c.C2240T						PASS	.	G	VAL/ALA	1285,3121	437.2+/-344.9	170,945,1088	123.0	119.0	121.0		2240	-10.5	0.0	4	dbSNP_107	121	3665,4935	526.7+/-381.0	760,2145,1395	yes	missense	AASDH	NM_181806.2	64	930,3090,2483	AA,AG,GG		42.6163,29.1648,38.0594	benign	747/1099	57215677	4950,8056	2203	4300	6503	SO:0001583	missense	132949	exon11			CCTATCGCAGGTT	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.2240C>T	4.37:g.57215677G>A	ENSP00000205214:p.Ala747Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	608	0.2783882783882784	139	0.28252032520325204	112	0.30939226519337015	36	0.06293706293706294	321	0.4234828496042216	G	0.022	-1.407769	0.01155	0.291648	0.426163	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.63255	-0.03;0.1;2.3;0.51;0.52	5.26	-10.5	0.00291	Quinonprotein alcohol dehydrogenase-like (1);	1.244260	0.05327	N	0.527586	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B;B;B	0.10296	0.003;0.001;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.0	T	0.13072	-1.0523	9	0.14656	T	0.56	0.0183	1.9415	0.03348	0.2842:0.2376:0.3226:0.1556	rs3796544;rs17490588;rs52809767;rs59885880;rs3796544	594;747;747;747	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	V	747;647;262;747;594;747	ENSP00000205214:A747V;ENSP00000423760:A647V;ENSP00000392158:A262V;ENSP00000409656:A747V;ENSP00000421171:A747V	ENSP00000205214:A747V	A	-	2	0	AASDH	56910434	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.527000	0.06200	-2.299000	0.00659	-2.178000	0.00318	GCG	G|0.679;A|0.321	0.321	strong		0.418	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
ATP2B2	491	hgsc.bcm.edu	37	3	10443827	10443827	+	Silent	SNP	G	G	C	rs13084776	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10443827G>C	ENST00000352432.4	-	3	672	c.603C>G	c.(601-603)gtC>gtG	p.V201V	ATP2B2_ENST00000383800.4_Silent_p.V201V|ATP2B2_ENST00000397077.1_Silent_p.V201V|ATP2B2_ENST00000360273.2_Silent_p.V201V|ATP2B2_ENST00000343816.4_Silent_p.V201V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	201					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CAGGGATCTGGACCACCTGGC	0.572													G|||	848	0.169329	0.1233	0.3256	5008	,	,		19126	0.0099		0.2097	False		,,,				2504	0.2434				p.V201V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.C603G						PASS	.	G	,	582,3824	257.4+/-261.8	31,520,1652	132.0	144.0	140.0		603,603	1.4	1.0	3	dbSNP_121	140	1848,6752	329.6+/-318.8	203,1442,2655	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	234,1962,4307	CC,CG,GG		21.4884,13.2093,18.6837	,	201/1244,201/1199	10443827	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	491	exon4			GATCTGGACCACC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.603C>G	3.37:g.10443827G>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001683	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			G|0.823;C|0.177	0.177	strong		0.572	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
PKDREJ	10343	hgsc.bcm.edu	37	22	46655948	46655948	+	Missense_Mutation	SNP	T	T	C	rs6008384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46655948T>C	ENST00000253255.5	-	1	3271	c.3272A>G	c.(3271-3273)aAt>aGt	p.N1091S		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1091			N -> S (in dbSNP:rs6008384).		acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TAGCTTGTCATTGAGCTTCAT	0.483													T|||	1229	0.245407	0.6785	0.134	5008	,	,		23472	0.001		0.16	False		,,,				2504	0.0787				p.N1091S		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A3272G						PASS	.	T	SER/ASN	2656,1750	645.8+/-398.3	795,1066,342	77.0	70.0	72.0		3272	-8.3	0.0	22	dbSNP_114	72	1259,7341	251.5+/-278.0	88,1083,3129	yes	missense	PKDREJ	NM_006071.1	46	883,2149,3471	CC,CT,TT		14.6395,39.7186,30.1015	benign	1091/2254	46655948	3915,9091	2203	4300	6503	SO:0001583	missense	10343	exon1			TTGTCATTGAGCT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.3272A>G	22.37:g.46655948T>C	ENSP00000253255:p.Asn1091Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	477	0.2184065934065934	309	0.6280487804878049	55	0.15193370165745856	0	0.0	113	0.14907651715039577	T	0.065	-1.215526	0.01542	0.602814	0.146395	ENSG00000130943	ENST00000253255	T	0.35421	1.31	5.2	-8.26	0.01021	.	0.805875	0.11434	N	0.564463	T	0.00012	0.0000	N	0.01219	-0.95	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.31724	-0.9933	9	0.06494	T	0.89	-3.5036	8.6733	0.34163	0.0:0.3609:0.4339:0.2053	rs6008384;rs7287374;rs60191122;rs6008384	1091	Q9NTG1	PKDRE_HUMAN	S	1091	ENSP00000253255:N1091S	ENSP00000253255:N1091S	N	-	2	0	PKDREJ	45034612	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.624000	0.00876	-1.777000	0.01283	-0.624000	0.04008	AAT	T|0.721;C|0.279	0.279	strong		0.483	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435486	7435486	+	Missense_Mutation	SNP	G	G	T	rs61738677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7435486G>T	ENST00000319098.4	-	1	1214	c.1121C>A	c.(1120-1122)gCa>gAa	p.A374E	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	374					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						ATCATGGACTGCCCGGGCCCG	0.622													G|||	384	0.0766773	0.0129	0.1037	5008	,	,		20007	0.0734		0.1342	False		,,,				2504	0.0879				p.A374E		Atlas-SNP	.											.	PSAPL1	51	.	0			c.C1121A						PASS	.	G	GLU/ALA,	112,4106		1,110,1998	77.0	82.0	80.0		1121,	-0.5	0.0	4	dbSNP_129	80	1157,7275		76,1005,3135	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	107,	77,1115,5133	TT,TG,GG		13.7215,2.6553,10.0316	benign,	374/522,	7435486	1269,11381	2109	4216	6325	SO:0001583	missense	768239	exon1			TGGACTGCCCGGG	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.1121C>A	4.37:g.7435486G>T	ENSP00000317445:p.Ala374Glu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	183	0.08379120879120878	8	0.016260162601626018	44	0.12154696132596685	33	0.057692307692307696	98	0.12928759894459102	G	8.527	0.870137	0.17322	0.026553	0.137215	ENSG00000178597	ENST00000319098	T	0.67171	-0.25	3.8	-0.503	0.12000	.	0.966691	0.08446	N	0.944753	T	0.00300	0.0009	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06338	-1.0832	9	0.09338	T	0.73	-5.5767	5.0721	0.14611	0.1119:0.0:0.3044:0.5836	rs61738677	374	Q6NUJ1	SAPL1_HUMAN	E	374	ENSP00000317445:A374E	ENSP00000317445:A374E	A	-	2	0	PSAPL1	7486387	0.021000	0.18746	0.001000	0.08648	0.002000	0.02628	0.718000	0.25866	-0.011000	0.14247	-0.397000	0.06425	GCA	G|0.900;T|0.100	0.100	strong		0.622	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
SERPINI2	5276	hgsc.bcm.edu	37	3	167159968	167159968	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167159968T>C	ENST00000476257.1	-	10	1445	c.1147A>G	c.(1147-1149)Att>Gtt	p.I383V	SERPINI2_ENST00000461846.1_Missense_Mutation_p.I383V|SERPINI2_ENST00000264677.4_Missense_Mutation_p.I383V|SERPINI2_ENST00000471111.1_Missense_Mutation_p.I383V			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	383					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						ATAAACAGAATTGATTCTAGG	0.308																																					p.I393V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A1177G						PASS	.						88.0	80.0	83.0					3																	167159968		2203	4299	6502	SO:0001583	missense	5276	exon10			ACAGAATTGATTC	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.1147A>G	3.37:g.167159968T>C	ENSP00000420621:p.Ile383Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.149400	0.37923	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111	D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98	6.17	5.0	0.66597	Serpin domain (3);	0.102768	0.64402	D	0.000004	D	0.83496	0.5267	L	0.60845	1.875	0.80722	D	1	P;P	0.45634	0.863;0.863	P;P	0.45538	0.484;0.484	T	0.81402	-0.0949	10	0.39692	T	0.17	.	9.7406	0.40416	0.1538:0.0:0.0:0.8462	.	383;383	B4DDY9;O75830	.;SPI2_HUMAN	V	383	ENSP00000420621:I383V;ENSP00000417692:I383V;ENSP00000264677:I383V;ENSP00000419407:I383V	ENSP00000264677:I383V	I	-	1	0	SERPINI2	168642662	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.916000	0.39986	1.120000	0.41904	0.533000	0.62120	ATT	.	.	none		0.308	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
SLC26A8	116369	hgsc.bcm.edu	37	6	35960390	35960390	+	Missense_Mutation	SNP	C	C	T	rs17707331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:35960390C>T	ENST00000490799.1	-	6	1042	c.689G>A	c.(688-690)aGt>aAt	p.S230N	SLC26A8_ENST00000355574.2_Missense_Mutation_p.S230N|SLC26A8_ENST00000394602.2_Intron	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						CAGGTAAGCACTCATTGCAGA	0.478													C|||	448	0.0894569	0.0325	0.1383	5008	,	,		20612	0.0506		0.1402	False		,,,				2504	0.1196				p.S230N		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G689A						PASS	.	C	ASN/SER,ASN/SER,	188,4218	118.8+/-156.5	3,182,2018	133.0	125.0	128.0		689,689,	3.3	0.7	6	dbSNP_123	128	1143,7457	234.3+/-267.3	89,965,3246	yes	missense,missense,intron	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	46,46,	92,1147,5264	TT,TC,CC		13.2907,4.2669,10.2337	benign,benign,	230/971,230/971,	35960390	1331,11675	2203	4300	6503	SO:0001583	missense	116369	exon6			TAAGCACTCATTG	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.689G>A	6.37:g.35960390C>T	ENSP00000417638:p.Ser230Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	221	0.10119047619047619	22	0.044715447154471545	60	0.16574585635359115	34	0.05944055944055944	105	0.13852242744063326	C	0.032	-1.328172	0.01309	0.042669	0.132907	ENSG00000112053	ENST00000490799;ENST00000355574	D;D	0.93859	-3.3;-3.3	5.26	3.26	0.37387	Sulphate transporter (1);	0.337905	0.28790	N	0.014127	T	0.75635	0.3876	L	0.28054	0.825	0.38754	P	0.04583300000000001	B	0.18863	0.031	B	0.19946	0.027	T	0.61083	-0.7134	9	0.28530	T	0.3	.	4.1904	0.10417	0.0:0.4915:0.0:0.5085	rs17707331;rs52836854;rs17707331	230	Q96RN1	S26A8_HUMAN	N	230	ENSP00000417638:S230N;ENSP00000347778:S230N	ENSP00000347778:S230N	S	-	2	0	SLC26A8	36068368	0.310000	0.24527	0.680000	0.29994	0.068000	0.16541	-0.214000	0.09292	0.501000	0.28013	0.655000	0.94253	AGT	C|0.898;N|0.000	.	strong		0.478	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
CYP2B6	1555	hgsc.bcm.edu	37	19	41522715	41522715	+	Missense_Mutation	SNP	C	C	T	rs3211371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41522715C>T	ENST00000324071.4	+	9	1466	c.1459C>T	c.(1459-1461)Cgc>Tgc	p.R487C	CYP2B6_ENST00000593831.1_Missense_Mutation_p.R251C|CYP2B6_ENST00000330446.5_Missense_Mutation_p.R287C	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	487			R -> C (in allele CYP2B6*5 and allele CYP2B6*7; dbSNP:rs3211371). {ECO:0000269|PubMed:11470993, ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:14551287, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.4}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|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, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	ATACCAGATCCGCTTCCTGCC	0.597													C|||	268	0.0535144	0.0113	0.072	5008	,	,		14174	0.003		0.1123	False		,,,				2504	0.089				p.R487C		Atlas-SNP	.											CYP2B6,NS,carcinoma,-1,1	CYP2B6	79	1	0			c.C1459T	GRCh37	CM016107	CYP2B6	M	rs3211371	PASS	.	C	CYS/ARG	135,4271	93.0+/-131.7	2,131,2070	44.0	36.0	39.0		1459	-6.0	0.0	19	dbSNP_105	39	1047,7553	210.5+/-251.4	75,897,3328	no	missense	CYP2B6	NM_000767.4	180	77,1028,5398	TT,TC,CC		12.1744,3.064,9.0881	benign	487/492	41522715	1182,11824	2203	4300	6503	SO:0001583	missense	1555	exon9			CAGATCCGCTTCC	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.1459C>T	19.37:g.41522715C>T	ENSP00000324648:p.Arg487Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	110	0.05036630036630037	5	0.01016260162601626	27	0.07458563535911603	1	0.0017482517482517483	77	0.10158311345646438	C	4.132	0.022744	0.08006	0.03064	0.121744	ENSG00000197408	ENST00000324071;ENST00000330446	T;T	0.67171	-0.25;-0.25	4.52	-6.04	0.02178	.	1.083070	0.07081	N	0.837138	T	0.00328	0.0010	N	0.00859	-1.14	0.09310	N	1	B;B	0.18013	0.008;0.025	B;B	0.14023	0.001;0.01	T	0.05920	-1.0856	10	0.02654	T	1	.	4.282	0.10838	0.3927:0.2232:0.0:0.3841	rs3211371;rs12721654	287;487	B4DWP3;P20813	.;CP2B6_HUMAN	C	487;287	ENSP00000324648:R487C;ENSP00000330650:R287C	ENSP00000324648:R487C	R	+	1	0	CYP2B6	46214555	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.681000	0.05191	-0.883000	0.03982	-0.384000	0.06662	CGC	C|0.933;T|0.067	0.067	strong		0.597	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
IGDCC4	57722	hgsc.bcm.edu	37	15	65688088	65688088	+	Splice_Site	SNP	C	C	A	rs201037111		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65688088C>A	ENST00000352385.2	-	7	1620	c.1411G>T	c.(1411-1413)Ggc>Tgc	p.G471C		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	471	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GCCGACGTACCCCGTGCCTTC	0.662																																					p.G471C		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G1411T						PASS	.	C	CYS/GLY	1,4241		0,1,2120	7.0	7.0	7.0		1411	4.4	1.0	15		7	2,8360		0,2,4179	yes	missense-near-splice	IGDCC4	NM_020962.1	159	0,3,6299	AA,AC,CC		0.0239,0.0236,0.0238	probably-damaging	471/1251	65688088	3,12601	2121	4181	6302	SO:0001630	splice_region_variant	57722	exon7			ACGTACCCCGTGC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.1411+1G>T	15.37:g.65688088C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319127	0.60524	2.36E-4	2.39E-4	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.59638	0.25	4.45	4.45	0.53987	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055509	0.64402	D	0.000001	T	0.62636	0.2444	M	0.73217	2.22	0.80722	D	1	P	0.48764	0.915	P	0.45343	0.477	T	0.67499	-0.5655	9	.	.	.	-21.5089	17.4669	0.87635	0.0:1.0:0.0:0.0	.	471	Q8TDY8	IGDC4_HUMAN	C	471;200	ENSP00000319623:G471C	.	G	-	1	0	IGDCC4	63475141	1.000000	0.71417	0.981000	0.43875	0.079000	0.17450	6.706000	0.74649	2.187000	0.69744	0.462000	0.41574	GGC	.	.	weak		0.662	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	Missense_Mutation
EPX	8288	hgsc.bcm.edu	37	17	56270442	56270442	+	Missense_Mutation	SNP	A	A	G	rs11079339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56270442A>G	ENST00000225371.5	+	2	230	c.120A>G	c.(118-120)atA>atG	p.I40M		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	40			I -> M (in dbSNP:rs11079339). {ECO:0000269|Ref.2}.		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)	GAGACTGCATAGCAGAGGCCA	0.612													A|||	611	0.122005	0.1233	0.1412	5008	,	,		19426	0.0992		0.1531	False		,,,				2504	0.0982				p.I40M		Atlas-SNP	.											.	EPX	95	.	0			c.A120G						PASS	.	A	MET/ILE	623,3783	271.6+/-270.3	38,547,1618	118.0	118.0	118.0		120	-6.1	0.2	17	dbSNP_120	118	1212,7388	244.6+/-273.7	97,1018,3185	yes	missense	EPX	NM_000502.4	10	135,1565,4803	GG,GA,AA		14.093,14.1398,14.1089	benign	40/716	56270442	1835,11171	2203	4300	6503	SO:0001583	missense	8288	exon2			CTGCATAGCAGAG	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.120A>G	17.37:g.56270442A>G	ENSP00000225371:p.Ile40Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	270	0.12362637362637363	58	0.11788617886178862	44	0.12154696132596685	46	0.08041958041958042	122	0.16094986807387862	A	14.04	2.415976	0.42817	0.141398	0.14093	ENSG00000121053	ENST00000225371	T	0.72167	-0.63	5.13	-6.08	0.02151	.	0.590152	0.18122	N	0.151005	T	0.00210	0.0006	N	0.20445	0.575	0.48901	P	2.769999999999717E-4	B	0.12630	0.006	B	0.06405	0.002	T	0.02232	-1.1191	9	0.26408	T	0.33	-3.6705	4.1458	0.10215	0.1691:0.5197:0.1921:0.1191	rs11079339;rs56469108;rs60296065;rs11079339	40	P11678	PERE_HUMAN	M	40	ENSP00000225371:I40M	ENSP00000225371:I40M	I	+	3	3	EPX	53625441	0.000000	0.05858	0.194000	0.23346	0.907000	0.53573	-0.651000	0.05372	-0.983000	0.03511	0.444000	0.29173	ATA	A|0.876;G|0.124	0.124	strong		0.612	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
SEMA3C	10512	hgsc.bcm.edu	37	7	80387766	80387766	+	Silent	SNP	C	C	T	rs1058425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:80387766C>T	ENST00000265361.3	-	15	2085	c.1524G>A	c.(1522-1524)caG>caA	p.Q508Q	SEMA3C_ENST00000419255.2_Silent_p.Q508Q|SEMA3C_ENST00000544525.1_Silent_p.Q526Q	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	508	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GCAGAGATACCTGGGAAACCC	0.483													T|||	2064	0.412141	0.6498	0.3285	5008	,	,		17783	0.4286		0.1928	False		,,,				2504	0.3589				p.Q508Q		Atlas-SNP	.											.	SEMA3C	106	.	0			c.G1524A						PASS	.	T		2650,1756	523.0+/-370.9	789,1072,342	103.0	106.0	105.0		1524	4.1	1.0	7	dbSNP_86	105	1672,6928	739.4+/-407.1	173,1326,2801	no	coding-synonymous	SEMA3C	NM_006379.3		962,2398,3143	TT,TC,CC		19.4419,39.8547,33.2308		508/752	80387766	4322,8684	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon15			AGATACCTGGGAA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1524G>A	7.37:g.80387766C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			C|0.633;T|0.367	0.367	strong		0.483	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629889	32629889	+	Silent	SNP	G	G	A	rs1049087|rs386699585	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629889G>A	ENST00000399082.3	-	2	290	c.246C>T	c.(244-246)gcC>gcT	p.A82A	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.A172A|HLA-DQB1_ENST00000374943.4_Silent_p.A172A|HLA-DQB1_ENST00000399079.3_Silent_p.A172A|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Silent_p.A172A			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	172	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACACAACGCCGGCTGTCTCCT	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	2257	0.450679	0.3185	0.5317	5008	,	,		15556	0.4931		0.4215	False		,,,				2504	0.5583				p.A172A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,colon,carcinoma,-1,1	HLA-DQB1	15	1	0			c.C516T						PASS	.	G		1448,2936		285,878,1029	46.0	48.0	48.0		516	-9.0	0.0	6	dbSNP_86	48	3438,5154		752,1934,1610	no	coding-synonymous	HLA-DQB1	NM_002123.4		1037,2812,2639	AA,AG,GG		40.014,33.0292,37.6541		172/262	32629889	4886,8090	2192	4296	6488	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AACGCCGGCTGTC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.246C>T	6.37:g.32629889G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	44	14	0.318182	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				G|0.576;A|0.424	0.424	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
MYO1C	4641	hgsc.bcm.edu	37	17	1370542	1370542	+	Silent	SNP	C	C	A	rs2302458	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1370542C>A	ENST00000575158.1	-	31	3230	c.3054G>T	c.(3052-3054)ctG>ctT	p.L1018L	MYO1C_ENST00000438665.2_Silent_p.L1034L|MYO1C_ENST00000359786.5_Silent_p.L1053L|MYO1C_ENST00000361007.2_Silent_p.L1018L|MYO1C_ENST00000545534.2_Silent_p.L1029L			Q12965	MYO1E_HUMAN	myosin IC	0					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)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCACCACAGCCAGGTGCCCGT	0.642													C|||	463	0.0924521	0.1112	0.0735	5008	,	,		14864	0.0903		0.0924	False		,,,				2504	0.0828				p.L1053L		Atlas-SNP	.											.	MYO1C	57	.	0			c.G3159T						PASS	.	C	,,	517,3889	223.3+/-239.8	31,455,1717	61.0	47.0	52.0		3159,3102,3054	3.3	1.0	17	dbSNP_100	52	862,7738	186.4+/-233.9	42,778,3480	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	73,1233,5197	AA,AC,CC		10.0233,11.734,10.6028	,,	1053/1064,1034/1045,1018/1029	1370542	1379,11627	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon31			CACAGCCAGGTGC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.3054G>T	17.37:g.1370542C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			C|0.904;A|0.096	0.096	strong		0.642	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110397780	110397780	+	Missense_Mutation	SNP	A	A	G	rs62508075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:110397780A>G	ENST00000378402.5	+	6	594	c.490A>G	c.(490-492)Atc>Gtc	p.I164V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	164	IPT/TIG 2.				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)			ACTAATAACAATCCAAGGCAG	0.323										HNSCC(38;0.096)			A|||	65	0.0129792	0.0038	0.0202	5008	,	,		15871	0.0		0.0378	False		,,,				2504	0.0082				p.I164V		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A490G						PASS	.	A	VAL/ILE	44,3558		1,42,1758	58.0	56.0	57.0		490	5.6	1.0	8	dbSNP_129	57	389,7739		13,363,3688	yes	missense	PKHD1L1	NM_177531.4	29	14,405,5446	GG,GA,AA		4.7859,1.2215,3.6914	benign	164/4244	110397780	433,11297	1801	4064	5865	SO:0001583	missense	93035	exon6			ATAACAATCCAAG	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.490A>G	8.37:g.110397780A>G	ENSP00000367655:p.Ile164Val	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	43	0.019688644688644688	4	0.008130081300813009	8	0.022099447513812154	0	0.0	31	0.040897097625329816	A	9.419	1.082586	0.20309	0.012215	0.047859	ENSG00000205038	ENST00000378402	T	0.64260	-0.09	5.58	5.58	0.84498	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.234810	0.37906	N	0.001891	T	0.16471	0.0396	N	0.20483	0.58	0.27144	N	0.961579	D	0.53462	0.96	P	0.50570	0.644	T	0.19844	-1.0293	10	0.22706	T	0.39	.	13.699	0.62597	1.0:0.0:0.0:0.0	rs62508075	164	Q86WI1	PKHL1_HUMAN	V	164	ENSP00000367655:I164V	ENSP00000367655:I164V	I	+	1	0	PKHD1L1	110466956	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.483000	0.45233	2.129000	0.65627	0.454000	0.30748	ATC	A|0.975;G|0.025	0.025	strong		0.323	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Splice_Site	SNP	T	T	A	rs61731219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000358212.6_Splice_Site_p.R1320S|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S|MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000356338.6_Intron	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92.0	85.0	87.0		3960,	5.9	1.0	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3960-1A>T	15.37:g.52635394T>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation
UGT1A6	54578	hgsc.bcm.edu	37	2	234601669	234601669	+	Missense_Mutation	SNP	T	T	G	rs6759892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234601669T>G	ENST00000305139.6	+	1	158	c.19T>G	c.(19-21)Tca>Gca	p.S7A	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	7			S -> A (in allele UGT1A6*2, allele UGT1A6*3 and allele UGT1A6*4; dbSNP:rs6759892). {ECO:0000269|PubMed:15284531}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CCTCCTTCGCTCATTTCAGAG	0.478													G|||	1814	0.36222	0.3767	0.3444	5008	,	,		17751	0.2242		0.3827	False		,,,				2504	0.4765				p.S7A		Atlas-SNP	.											.	UGT1A6	63	.	0			c.T19G	GRCh37	CM057769	UGT1A6	M	rs6759892	PASS	.	G	ALA/SER,,,,,	1700,2706		341,1018,844	45.0	49.0	48.0		19,,,,,	-0.7	0.0	2	dbSNP_116	48	3557,5043		749,2059,1492	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	99,,,,,	1090,3077,2336	GG,GT,TT		41.3605,38.5837,40.4198	,,,,,	7/533,,,,,	234601669	5257,7749	2203	4300	6503	SO:0001583	missense	54578	exon1			CTTCGCTCATTTC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.19T>G	2.37:g.234601669T>G	ENSP00000303174:p.Ser7Ala	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	204	103	0.504902	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	751	0.34386446886446886	189	0.38414634146341464	135	0.3729281767955801	136	0.23776223776223776	291	0.3839050131926121	G	0.023	-1.395150	0.01175	0.385837	0.413605	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.58506	1.61;0.33	4.58	-0.718	0.11205	.	.	.	.	.	T	0.00012	0.0000	N	0.01473	-0.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32903	-0.9889	8	0.02654	T	1	.	0.7682	0.01019	0.2218:0.1509:0.3261:0.3012	rs6759892;rs17670302;rs60624335;rs6759892	7;7	B8K289;P19224	.;UD16_HUMAN	A	7	ENSP00000389637:S7A;ENSP00000303174:S7A	ENSP00000303174:S7A	S	+	1	0	UGT1A6	234266408	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.178000	0.09782	-0.187000	0.10516	-0.729000	0.03580	TCA	G|0.364;N|0.000	0.364	strong		0.478	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
LNP1	348801	hgsc.bcm.edu	37	3	100170598	100170598	+	Silent	SNP	C	C	T	rs78633312|rs386663873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100170598C>T	ENST00000383693.3	+	3	1472	c.192C>T	c.(190-192)tgC>tgT	p.C64C	LNP1_ENST00000489752.1_Silent_p.C77C	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	64										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						CATCTGACTGCCATCCTAGAA	0.443																																					p.C64C		Atlas-SNP	.											.	LNP1	26	.	0			c.C192T						PASS	.						78.0	71.0	73.0					3																	100170598		1873	4103	5976	SO:0001819	synonymous_variant	348801	exon3			TGACTGCCATCCT		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.192C>T	3.37:g.100170598C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	146	15	0.10274	NM_001085451	B7ZLT3	Silent	SNP	ENST00000383693.3	37	CCDS43120.1																																																																																			C|0.817;T|0.183	0.183	strong		0.443	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
TMEM30A	55754	hgsc.bcm.edu	37	6	75994151	75994151	+	Silent	SNP	A	A	G	rs240374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:75994151A>G	ENST00000230461.6	-	1	533	c.204T>C	c.(202-204)atT>atC	p.I68I	TMEM30A_ENST00000475111.2_Silent_p.I68I|RP1-234P15.4_ENST00000607221.1_lincRNA	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	68					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AGGTGACAAAAATGCCAATGC	0.582													G|||	749	0.149561	0.3502	0.0937	5008	,	,		16318	0.1062		0.0835	False		,,,				2504	0.0307				p.I68I		Atlas-SNP	.											.	TMEM30A	40	.	0			c.T204C						PASS	.	G	,	1503,2903	674.8+/-403.0	255,993,955	77.0	65.0	69.0		204,204	2.1	1.0	6	dbSNP_79	69	760,7840	785.0+/-407.6	32,696,3572	no	coding-synonymous,coding-synonymous	TMEM30A	NM_001143958.1,NM_018247.3	,	287,1689,4527	GG,GA,AA		8.8372,34.1126,17.3997	,	68/326,68/362	75994151	2263,10743	2203	4300	6503	SO:0001819	synonymous_variant	55754	exon1			GACAAAAATGCCA	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.204T>C	6.37:g.75994151A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	NM_001143958	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Silent	SNP	ENST00000230461.6	37	CCDS4983.1																																																																																			A|0.828;G|0.172	0.172	strong		0.582	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
CASR	846	hgsc.bcm.edu	37	3	122003757	122003757	+	Missense_Mutation	SNP	G	G	T	rs1801725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:122003757G>T	ENST00000490131.1	+	7	3328	c.2956G>T	c.(2956-2958)Gcc>Tcc	p.A986S	AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000296154.5_Missense_Mutation_p.A986S|CASR_ENST00000498619.1_Missense_Mutation_p.A996S	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	197	0	0		WXS	Illumina HiSeq	Phase_I	267	145	0.543071	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	
FAM166B	730112	hgsc.bcm.edu	37	9	35562549	35562549	+	Silent	SNP	G	G	A	rs755774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	38	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	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	
PBX4	80714	hgsc.bcm.edu	37	19	19680276	19680276	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19680276G>A	ENST00000251203.9	-	5	1036	c.750C>T	c.(748-750)ggC>ggT	p.G250G		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	250					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						TGGTGAGGCCGCCCTTCCTGG	0.567																																					p.G250G		Atlas-SNP	.											.	PBX4	34	.	0			c.C750T						PASS	.						187.0	159.0	168.0					19																	19680276		2203	4300	6503	SO:0001819	synonymous_variant	80714	exon5			GAGGCCGCCCTTC	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"""Homeoboxes / TALE class"""	13403	protein-coding gene	gene with protein product		608127	"""pre-B-cell leukemia transcription factor 4"""				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.750C>T	19.37:g.19680276G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_025245	A5D8Y0|B3KUK9	Silent	SNP	ENST00000251203.9	37	CCDS12406.1																																																																																			.	.	none		0.567	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6		
INHA	3623	hgsc.bcm.edu	37	2	220439678	220439678	+	Silent	SNP	C	C	T	rs12720063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	74	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	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		
ZGRF1	55345	hgsc.bcm.edu	37	4	113553098	113553098	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:113553098G>A	ENST00000505019.1	-	3	215	c.90C>T	c.(88-90)caC>caT	p.H30H	C4orf21_ENST00000309071.5_Silent_p.H30H|C4orf21_ENST00000445203.2_5'UTR	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		30						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TGTTTCCTAAGTGAGTGATCT	0.323																																					p.H30H		Atlas-SNP	.											.	C4orf21	223	.	0			c.C90T						PASS	.						103.0	94.0	97.0					4																	113553098		2202	4298	6500	SO:0001819	synonymous_variant	55345	exon3			TCCTAAGTGAGTG																												ENST00000505019.1:c.90C>T	4.37:g.113553098G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	37																																																																																				.	.	none		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
OR52E6	390078	hgsc.bcm.edu	37	11	5863113	5863113	+	Silent	SNP	G	G	A	rs10742810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5863113G>A	ENST00000329322.5	-	1	14	c.15C>T	c.(13-15)aaC>aaT	p.N5N	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Silent_p.N9N	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	5						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(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACTGGGTGTCGTTAGCTATAG	0.408													A|||	1924	0.384185	0.379	0.3184	5008	,	,		20800	0.4593		0.3728	False		,,,				2504	0.3722				p.N5N		Atlas-SNP	.											OR52E6,NS,carcinoma,0,1	OR52E6	70	1	0			c.C15T						PASS	.	A		1565,2771		287,991,890	66.0	63.0	64.0		15	-0.6	0.0	11	dbSNP_120	64	2999,5575		538,1923,1826	no	coding-synonymous	OR52E6	NM_001005167.1		825,2914,2716	AA,AG,GG		34.9778,36.0932,35.3524		5/314	5863113	4564,8346	2168	4287	6455	SO:0001819	synonymous_variant	390078	exon1			GGTGTCGTTAGCT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.15C>T	11.37:g.5863113G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001005167	Q6IFF8	Silent	SNP	ENST00000329322.5	37	CCDS53597.1																																																																																			G|0.605;A|0.395	0.395	strong		0.408	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
OR4S2	219431	hgsc.bcm.edu	37	11	55418693	55418693	+	Missense_Mutation	SNP	T	T	C	rs11230541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55418693T>C	ENST00000312422.2	+	1	314	c.314T>C	c.(313-315)tTt>tCt	p.F105S		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	105						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)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				GTACATTTCTTTGGTTGCACT	0.433													t|||	1689	0.33726	0.2716	0.3112	5008	,	,		16389	0.4623		0.1799	False		,,,				2504	0.4775				p.F105S		Atlas-SNP	.											.	OR4S2	89	.	0			c.T314C						PASS	.	T	SER/PHE	1179,3191		269,641,1275	217.0	182.0	194.0		314	5.4	1.0	11	dbSNP_120	194	1209,6869		310,589,3140	yes	missense	OR4S2	NM_001004059.2	155	579,1230,4415	CC,CT,TT		14.9666,26.9794,19.1838	probably-damaging	105/312	55418693	2388,10060	2185	4039	6224	SO:0001583	missense	219431	exon1			ATTTCTTTGGTTG	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"""GPCR / Class A : Olfactory receptors"""	15183	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily S, member 2 pseudogene"""	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.314T>C	11.37:g.55418693T>C	ENSP00000310337:p.Phe105Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	267	137	0.513109	NM_001004059	Q6IF72	Missense_Mutation	SNP	ENST00000312422.2	37	CCDS31505.1	518	0.23717948717948717	134	0.27235772357723576	81	0.22375690607734808	213	0.3723776223776224	90	0.11873350923482849	T	21.5	4.163497	0.78226	0.269794	0.149666	ENSG00000174982	ENST00000312422	T	0.01388	4.95	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.00012	0.0000	M	0.73962	2.25	0.26673	P	0.9716803	D	0.53462	0.96	P	0.51945	0.685	T	0.54906	-0.8223	9	0.72032	D	0.01	.	14.1779	0.65555	0.0:0.0:0.0:1.0	rs11230541	105	Q8NH73	OR4S2_HUMAN	S	105	ENSP00000310337:F105S	ENSP00000310337:F105S	F	+	2	0	OR4S2	55175269	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	0.727000	0.25999	2.031000	0.59945	0.448000	0.29417	TTT	T|0.764;C|0.236	0.236	strong		0.433	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459493	24459493	+	Silent	SNP	G	G	A	rs60865462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24459493G>A	ENST00000335125.6	+	2	357	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4L2_ENST00000382755.4_Silent_p.Q75Q|DHRS4L2_ENST00000545240.1_Silent_p.Q77Q|DHRS4L2_ENST00000558753.1_Silent_p.Q77Q|DHRS4L2_ENST00000543805.1_5'UTR|DHRS4L2_ENST00000537912.1_Silent_p.Q77Q|DHRS4L2_ENST00000397071.1_Silent_p.Q77Q|DHRS4L2_ENST00000534993.1_5'UTR	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	75						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)	p.Q77Q(1)		breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		CCACGCTGCAGGGGGAGGGGC	0.692													g|||	757	0.151158	0.093	0.1354	5008	,	,		15450	0.2252		0.0885	False		,,,				2504	0.229				p.Q77Q		Atlas-SNP	.											DHRS4L2,NS,carcinoma,0,1	DHRS4L2	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G231A						PASS	.	G	,,,	319,4085	126.1+/-163.2	22,275,1905	36.0	39.0	38.0		147,,,231	0.6	0.0	14	dbSNP_129	38	653,7945	137.9+/-194.8	40,573,3686	no	coding-synonymous,utr-5,utr-5,coding-synonymous	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	62,848,5591	AA,AG,GG		7.5948,7.2434,7.4758	,,,	49/171,,,77/233	24459493	972,12030	2202	4299	6501	SO:0001819	synonymous_variant	317749	exon2			GCTGCAGGGGGAG		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.231G>A	14.37:g.24459493G>A		Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	125	88	0.704	NM_198083	Q3YLD4	Silent	SNP	ENST00000335125.6	37	CCDS9606.2																																																																																			G|0.911;A|0.089	0.089	strong		0.692	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
CLCNKA	1187	hgsc.bcm.edu	37	1	16354394	16354394	+	Missense_Mutation	SNP	C	C	T	rs200268763	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16354394C>T	ENST00000331433.4	+	9	879	c.860C>T	c.(859-861)gCg>gTg	p.A287V	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.A287V|CLCNKA_ENST00000439316.2_Missense_Mutation_p.A244V|CLCNKA_ENST00000420078.1_Missense_Mutation_p.A287V			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	287			A -> V (in dbSNP:rs34188929).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TTTTTTGTGGCGCTGGGGTGA	0.612													C|||	87	0.0173722	0.0363	0.0029	5008	,	,		18143	0.0347		0.0	False		,,,				2504	0.002				p.A287V		Atlas-SNP	.											CLCNKA,NS,carcinoma,+1,1	CLCNKA	56	1	0			c.C860T						scavenged	.						63.0	57.0	59.0					1																	16354394		2202	4277	6479	SO:0001583	missense	1187	exon9			TTGTGGCGCTGGG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.860C>T	1.37:g.16354394C>T	ENSP00000332771:p.Ala287Val	Somatic	506	77	0.152174		WXS	Illumina HiSeq	Phase_I	563	110	0.195382	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	85	0.03891941391941392	21	0.042682926829268296	1	0.0027624309392265192	32	0.055944055944055944	31	0.040897097625329816	C	0.012	-1.662340	0.00772	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17	3.3	-2.47	0.06442	Chloride channel, core (2);	0.863417	0.10401	N	0.679201	T	0.41050	0.1142	N	0.16166	0.38	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.004	T	0.58381	-0.7646	10	0.07030	T	0.85	.	9.3698	0.38248	0.0:0.1918:0.0:0.8082	.	244;287;287	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	V	287;287;244;287	ENSP00000364844:A287V;ENSP00000410353:A287V;ENSP00000414445:A244V;ENSP00000332771:A287V	ENSP00000332771:A287V	A	+	2	0	CLCNKA	16226981	0.000000	0.05858	0.054000	0.19295	0.085000	0.17905	0.478000	0.22212	-0.479000	0.06813	-0.657000	0.03884	GCG	C|0.240;T|0.760	0.760	strong		0.612	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
DNAH12	201625	hgsc.bcm.edu	37	3	57414071	57414071	+	Missense_Mutation	SNP	G	G	A	rs4681982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:57414071G>A	ENST00000351747.2	-	35	5468	c.5288C>T	c.(5287-5289)aCa>aTa	p.T1763I		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1763			T -> I (in dbSNP:rs4681982).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						CTCACTAAATGTACATTGAGT	0.259													A|||	2957	0.590455	0.8336	0.5533	5008	,	,		17500	0.4216		0.4563	False		,,,				2504	0.6002				p.T1763I		Atlas-SNP	.											DNAH12,NS,carcinoma,0,1	DNAH12	182	1	0			c.C5288T						PASS	.						10.0	10.0	10.0					3																	57414071		689	1564	2253	SO:0001583	missense	201625	exon35			CTAAATGTACATT	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5288C>T	3.37:g.57414071G>A	ENSP00000295937:p.Thr1763Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		1160	0.5311355311355311	390	0.7926829268292683	199	0.5497237569060773	241	0.42132867132867136	330	0.43535620052770446	A	4.196	0.034973	0.08101	.	.	ENSG00000174844	ENST00000351747	T	0.20598	2.06	1.04	-0.547	0.11836	.	.	.	.	.	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11792	-1.0573	8	0.48119	T	0.1	.	4.7927	0.13257	0.4541:0.0:0.5459:0.0	rs4681982;rs17736539;rs57979239	1763	Q6ZR08	DYH12_HUMAN	I	1763	ENSP00000295937:T1763I	ENSP00000295937:T1763I	T	-	2	0	DNAH12	57389111	0.097000	0.21791	0.003000	0.11579	0.015000	0.08874	-0.100000	0.10990	-0.772000	0.04602	-0.351000	0.07748	ACA	G|0.472;A|0.528	0.528	strong		0.259	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
RGL1	23179	hgsc.bcm.edu	37	1	183876182	183876182	+	Silent	SNP	C	C	T	rs11591089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:183876182C>T	ENST00000360851.3	+	14	1687	c.1509C>T	c.(1507-1509)gaC>gaT	p.D503D	RGL1_ENST00000304685.4_Silent_p.D538D|RGL1_ENST00000539189.1_Silent_p.D474D|RGL1_ENST00000536277.1_Silent_p.D501D			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	503					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.D538D(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CAGCTGCTGACGCCAGCACCA	0.532													C|||	1087	0.217053	0.2201	0.2853	5008	,	,		18342	0.0754		0.3012	False		,,,				2504	0.2239				p.D538D		Atlas-SNP	.											RGL1,NS,carcinoma,0,1	RGL1	91	1	1	Substitution - coding silent(1)	stomach(1)	c.C1614T						PASS	.	C		1083,3323	386.5+/-326.1	138,807,1258	51.0	47.0	49.0		1614	-10.1	0.0	1	dbSNP_120	49	2562,6038	406.4+/-348.8	407,1748,2145	no	coding-synonymous	RGL1	NM_015149.3		545,2555,3403	TT,TC,CC		29.7907,24.5801,28.0255		538/804	183876182	3645,9361	2203	4300	6503	SO:0001819	synonymous_variant	23179	exon15			TGCTGACGCCAGC	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1509C>T	1.37:g.183876182C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Silent	SNP	ENST00000360851.3	37																																																																																				C|0.745;T|0.255	0.255	strong		0.532	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	
RCBTB1	55213	hgsc.bcm.edu	37	13	50141362	50141362	+	Silent	SNP	G	G	A	rs9562900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50141362G>A	ENST00000378302.2	-	3	314	c.54C>T	c.(52-54)atC>atT	p.I18I	RCBTB1_ENST00000258646.3_Silent_p.I18I|RCBTB1_ENST00000546015.1_Silent_p.I18I	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	18					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GAATAGACGCGATCTCTTGAG	0.488													G|||	1538	0.307109	0.4955	0.1311	5008	,	,		18156	0.2788		0.167	False		,,,				2504	0.3507				p.I18I		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C54T						PASS	.	G		1979,2427	557.0+/-379.6	437,1105,661	124.0	112.0	116.0		54	-5.0	0.0	13	dbSNP_119	116	1257,7343	249.6+/-276.8	80,1097,3123	no	coding-synonymous	RCBTB1	NM_018191.3		517,2202,3784	AA,AG,GG		14.6163,44.916,24.8808		18/532	50141362	3236,9770	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon3			AGACGCGATCTCT	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.54C>T	13.37:g.50141362G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			G|0.732;A|0.268	0.268	strong		0.488	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
POC5	134359	hgsc.bcm.edu	37	5	74998489	74998489	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:74998489A>G	ENST00000428202.2	-	5	643	c.454T>C	c.(454-456)Tct>Cct	p.S152P	POC5_ENST00000514838.2_Missense_Mutation_p.S124P|POC5_ENST00000510798.1_Missense_Mutation_p.S35P|POC5_ENST00000380475.2_Missense_Mutation_p.S35P|POC5_ENST00000446329.2_Missense_Mutation_p.S127P|POC5_ENST00000504862.1_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	152					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTTTCATCAGAAACAAGAAAA	0.378																																					p.S152P		Atlas-SNP	.											.	POC5	82	.	0			c.T454C						PASS	.						89.0	84.0	86.0					5																	74998489		1888	4109	5997	SO:0001583	missense	134359	exon5			CATCAGAAACAAG	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.454T>C	5.37:g.74998489A>G	ENSP00000410216:p.Ser152Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	99	4	0.040404	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.046958	0.36085	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329;ENST00000503835;ENST00000502826	T;T;T;T;T	0.48836	1.84;1.42;0.8;0.8;1.84	5.78	4.51	0.55191	.	0.325126	0.38492	N	0.001678	T	0.51907	0.1702	L	0.47716	1.5	0.32491	N	0.54012	D;B;B	0.76494	0.999;0.148;0.281	D;B;B	0.64776	0.929;0.07;0.122	T	0.58457	-0.7633	10	0.26408	T	0.33	-9.7843	5.43	0.16448	0.7038:0.0:0.144:0.1522	.	35;152;127	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	P	152;124;35;35;127;35;35	ENSP00000410216:S152P;ENSP00000420971:S124P;ENSP00000369842:S35P;ENSP00000426796:S35P;ENSP00000399481:S127P	ENSP00000369842:S35P	S	-	1	0	POC5	75034245	1.000000	0.71417	0.975000	0.42487	0.928000	0.56348	0.951000	0.29135	2.205000	0.71048	0.533000	0.62120	TCT	.	.	none		0.378	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363433	42363433	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363433T>A	ENST00000290472.3	-	17	1858	c.1764A>T	c.(1762-1764)gcA>gcT	p.A588A		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	588	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		AGCCTTTAAATGCCTGGGCCA	0.642																																					p.A588A		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.A1764T						PASS	.						28.0	32.0	30.0					15																	42363433		2202	4297	6499	SO:0001819	synonymous_variant	283748	exon17			TTTAAATGCCTGG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1764A>T	15.37:g.42363433T>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	NM_178034	Q8N176	Silent	SNP	ENST00000290472.3	37	CCDS32203.1																																																																																			.	.	none		0.642	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
MYH10	4628	hgsc.bcm.edu	37	17	8413247	8413247	+	Silent	SNP	G	G	A	rs139264814		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8413247G>A	ENST00000269243.4	-	23	3018	c.2880C>T	c.(2878-2880)gaC>gaT	p.D960D	MYH10_ENST00000360416.3_Silent_p.D991D|MYH10_ENST00000379980.4_Silent_p.D976D|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000396239.1_Silent_p.D981D	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	960					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTTCCTCCTCGTCTAGCTGTT	0.493																																					p.D991D		Atlas-SNP	.											.	MYH10	148	.	0			c.C2973T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88.0	81.0	83.0		2880	-8.3	0.7	17	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	MYH10	NM_005964.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		960/1977	8413247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon25			CTCCTCGTCTAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2880C>T	17.37:g.8413247G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	13	0.22807	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			G|1.000;A|0.000	0.000	weak		0.493	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
OXLD1	339229	hgsc.bcm.edu	37	17	79632327	79632327	+	Silent	SNP	C	C	T	rs137928765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79632327C>T	ENST00000374741.3	-	2	358	c.348G>A	c.(346-348)gaG>gaA	p.E116E	OXLD1_ENST00000571503.1_3'UTR|PDE6G_ENST00000571224.1_5'Flank|OXLD1_ENST00000573786.1_5'UTR|PDE6G_ENST00000574777.1_5'Flank|CCDC137_ENST00000329214.8_5'Flank	NM_001039842.1	NP_001034931.1	Q5BKU9	OXLD1_HUMAN	oxidoreductase-like domain containing 1	116						mitochondrion (GO:0005739)											CCAGGGCCCGCTCCCCACCGT	0.657																																					p.E116E		Atlas-SNP	.											.	.	.	.	0			c.G348A						PASS	.	C		0,4406		0,0,2203	40.0	39.0	39.0		348	2.7	1.0	17	dbSNP_134	39	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	C17orf90	NM_001039842.1		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		116/148	79632327	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	339229	exon2			GGCCCGCTCCCCA		CCDS32766.1	17q25.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000204237	ENSG00000204237			27901	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 90"""	C17orf90			Standard	NM_001039842		Approved	MGC104712	uc002kba.3	Q5BKU9	OTTHUMG00000178063	ENST00000374741.3:c.348G>A	17.37:g.79632327C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_001039842	A6ND24	Silent	SNP	ENST00000374741.3	37	CCDS32766.1																																																																																			C|1.000;T|0.000	0.000	strong		0.657	OXLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440380.1	NM_001039842	
MED12L	116931	hgsc.bcm.edu	37	3	151112568	151112568	+	Silent	SNP	G	G	A	rs3732768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:151112568G>A	ENST00000474524.1	+	37	5666	c.5628G>A	c.(5626-5628)tcG>tcA	p.S1876S	MED12L_ENST00000273432.4_Silent_p.S1736S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1876						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAATCACATCGCAGCAGCAGT	0.547													G|||	1497	0.298922	0.3707	0.2233	5008	,	,		16917	0.2778		0.2028	False		,,,				2504	0.3763				p.S1876S		Atlas-SNP	.											MED12L,NS,carcinoma,+1,2	MED12L	271	2	0			c.G5628A						PASS	.	G		1547,2859	487.8+/-361.0	282,983,938	90.0	90.0	90.0		5628	-11.8	0.0	3	dbSNP_107	90	1835,6765	327.5+/-317.9	210,1415,2675	no	coding-synonymous	MED12L	NM_053002.4		492,2398,3613	AA,AG,GG		21.3372,35.1112,26.0034		1876/2146	151112568	3382,9624	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon37			CACATCGCAGCAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5628G>A	3.37:g.151112568G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.724;A|0.276	0.276	strong		0.547	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
CROCC	9696	hgsc.bcm.edu	37	1	17273396	17273396	+	Silent	SNP	A	A	G	rs7537468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17273396A>G	ENST00000375541.5	+	17	2493	c.2424A>G	c.(2422-2424)ctA>ctG	p.L808L	CROCC_ENST00000467938.1_3'UTR	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)		AGGGCTCCCTACGAGTGGCGG	0.692																																					p.L808L		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.A2424G						scavenged	.	A		216,4104		1,214,1945	14.0	13.0	13.0		2424	1.4	0.8	1	dbSNP_116	13	1332,7146		2,1328,2909	no	coding-synonymous	CROCC	NM_014675.3		3,1542,4854	GG,GA,AA		15.7113,5.0,12.0956		808/2018	17273396	1548,11250	2160	4239	6399	SO:0001819	synonymous_variant	9696	exon17			CTCCCTACGAGTG	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.2424A>G	1.37:g.17273396A>G		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	114	29	0.254386	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			A|0.845;G|0.155	0.155	strong		0.692	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
KRT32	3882	hgsc.bcm.edu	37	17	39619094	39619094	+	Missense_Mutation	SNP	T	T	C	rs2604955|rs386797091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39619094T>C	ENST00000225899.3	-	6	1308	c.1205A>G	c.(1204-1206)aAc>aGc	p.N402S		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	402	Coil 2.|Rod.		N -> S (in dbSNP:rs2604955). {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)				GCAGTCCTCGTTCTCCAGCAG	0.622													C|||	3081	0.615216	0.6309	0.5706	5008	,	,		17040	0.6815		0.673	False		,,,				2504	0.498				p.N402S		Atlas-SNP	.											.	KRT32	57	.	0			c.A1205G						PASS	.	C	SER/ASN	2726,1680		860,1006,337	60.0	62.0	61.0		1205	5.1	1.0	17	dbSNP_100	61	5448,3152		1775,1898,627	no	missense	KRT32	NM_002278.3	46	2635,2904,964	CC,CT,TT		36.6512,38.1298,37.1521	benign	402/449	39619094	8174,4832	2203	4300	6503	SO:0001583	missense	3882	exon6			TCCTCGTTCTCCA	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.1205A>G	17.37:g.39619094T>C	ENSP00000225899:p.Asn402Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	1202	0.5503663003663004	245	0.49796747967479676	171	0.4723756906077348	357	0.6241258741258742	429	0.5659630606860159	C	3.542	-0.093527	0.07053	0.618702	0.633488	ENSG00000108759	ENST00000225899	D	0.87571	-2.27	5.07	5.07	0.68467	Filament (1);	0.000000	0.46758	N	0.000273	T	0.00012	0.0000	N	0.00746	-1.225	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.36601	-0.9741	9	0.02654	T	1	.	13.1569	0.59522	0.0:0.9225:0.0:0.0775	rs2604955;rs60774372	402	Q14532	K1H2_HUMAN	S	402	ENSP00000225899:N402S	ENSP00000225899:N402S	N	-	2	0	KRT32	36872620	0.980000	0.34600	1.000000	0.80357	0.831000	0.47069	1.910000	0.39927	1.263000	0.44181	-0.215000	0.12644	AAC	T|0.383;C|0.617	0.617	strong		0.622	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
RRP12	23223	hgsc.bcm.edu	37	10	99130282	99130282	+	Silent	SNP	T	T	G	rs11189170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99130282T>G	ENST00000370992.4	-	23	2730	c.2619A>C	c.(2617-2619)gcA>gcC	p.A873A	RRP12_ENST00000414986.1_Silent_p.A812A|RRP12_ENST00000536831.1_Silent_p.A591A|RRP12_ENST00000315563.6_Silent_p.A773A|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	873						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CGTTCTTCCGTGCGCCCACCG	0.607													T|||	201	0.0401358	0.059	0.0548	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0133				p.A873A		Atlas-SNP	.											RRP12,NS,carcinoma,-2,1	RRP12	97	1	0			c.A2619C						scavenged	.	T	,	254,4152	147.3+/-181.8	9,236,1958	118.0	90.0	99.0		2436,2619	-9.4	0.4	10	dbSNP_120	99	503,8097	144.7+/-200.5	17,469,3814	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,705,5772	GG,GT,TT		5.8488,5.7649,5.8204	,	812/1237,873/1298	99130282	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon23			CTTCCGTGCGCCC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.2619A>C	10.37:g.99130282T>G		Somatic	105	3	0.0285714		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			T|0.952;G|0.048	0.048	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
IGFL3	388555	hgsc.bcm.edu	37	19	46627294	46627294	+	Missense_Mutation	SNP	G	G	A	rs147128538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46627294G>A	ENST00000341415.2	-	3	223	c.199C>T	c.(199-201)Cgc>Tgc	p.R67C	AC007193.6_ENST00000597989.1_lincRNA	NM_207393.1	NP_997276.1	Q6UXB1	IGFL3_HUMAN	IGF-like family member 3	67						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(5)	7		Ovarian(192;0.0175)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00473)|GBM - Glioblastoma multiforme(486;0.0149)|Epithelial(262;0.239)		CCACAGCGGCGGGTCTCCTTT	0.547													G|||	8	0.00159744	0.0008	0.0	5008	,	,		16916	0.0		0.007	False		,,,				2504	0.0				p.R67C		Atlas-SNP	.											.	IGFL3	17	.	0			c.C199T						PASS	.	G	CYS/ARG	0,4372		0,0,2186	74.0	93.0	87.0		199	0.5	0.0	19	dbSNP_134	87	13,8587	9.1+/-34.3	0,13,4287	yes	missense	IGFL3	NM_207393.1	180	0,13,6473	AA,AG,GG		0.1512,0.0,0.1002	probably-damaging	67/126	46627294	13,12959	2186	4300	6486	SO:0001583	missense	388555	exon3			AGCGGCGGGTCTC	AY358434	CCDS33058.1	19q13.32	2006-07-14				ENSG00000188624			32930	protein-coding gene	gene with protein product		610546				14702039	Standard	NM_207393		Approved	UNQ483	uc002pea.1	Q6UXB1		ENST00000341415.2:c.199C>T	19.37:g.46627294G>A	ENSP00000344860:p.Arg67Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_207393		Missense_Mutation	SNP	ENST00000341415.2	37	CCDS33058.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	G	10.39	1.337672	0.24253	0.0	0.001512	ENSG00000188624	ENST00000341415	T	0.27557	1.66	1.65	0.462	0.16695	.	.	.	.	.	T	0.20007	0.0481	L	0.52573	1.65	0.09310	N	1	P	0.52463	0.953	P	0.44561	0.453	T	0.13575	-1.0504	9	0.87932	D	0	-33.7815	4.7804	0.13199	0.0:0.0:0.611:0.389	.	67	Q6UXB1	IGFL3_HUMAN	C	67	ENSP00000344860:R67C	ENSP00000344860:R67C	R	-	1	0	IGFL3	51319134	0.002000	0.14202	0.001000	0.08648	0.014000	0.08584	0.237000	0.17985	0.178000	0.19917	0.411000	0.27672	CGC	G|0.998;A|0.002	0.002	strong		0.547	IGFL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421323.1	NM_207393	
GRPR	2925	hgsc.bcm.edu	37	X	16168467	16168467	+	Silent	SNP	T	T	C	rs4986945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:16168467T>C	ENST00000380289.2	+	2	851	c.453T>C	c.(451-453)tcT>tcC	p.S151S	RP11-431J24.2_ENST00000435789.1_RNA|RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000454712.2_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	65	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	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	
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000342989.5_Missense_Mutation_p.A325T|BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59.0	63.0	62.0		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
TERF2IP	54386	hgsc.bcm.edu	37	16	75690279	75690279	+	Missense_Mutation	SNP	A	A	G	rs4888444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:75690279A>G	ENST00000300086.4	+	3	1067	c.970A>G	c.(970-972)Aag>Gag	p.K324E		NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	324			K -> E (in dbSNP:rs4888444).		negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						GTTAATGGAGAAGTTTAACTT	0.453													A|||	115	0.0229633	0.0015	0.0288	5008	,	,		21100	0.001		0.0398	False		,,,				2504	0.0532				p.K324E		Atlas-SNP	.											.	TERF2IP	17	.	0			c.A970G						PASS	.	A	GLU/LYS	39,4357	45.3+/-79.5	1,37,2160	133.0	132.0	132.0		970	4.6	1.0	16	dbSNP_111	132	399,8201	127.2+/-185.5	11,377,3912	yes	missense	TERF2IP	NM_018975.3	56	12,414,6072	GG,GA,AA		4.6395,0.8872,3.3703	benign	324/400	75690279	438,12558	2198	4300	6498	SO:0001583	missense	54386	exon3			ATGGAGAAGTTTA	AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.970A>G	16.37:g.75690279A>G	ENSP00000300086:p.Lys324Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_018975	B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	Missense_Mutation	SNP	ENST00000300086.4	37	CCDS32491.1	45	0.020604395604395604	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	30	0.0395778364116095	A	5.039	0.192905	0.09599	0.008872	0.046395	ENSG00000166848	ENST00000300086	T	0.38887	1.11	5.75	4.63	0.57726	.	0.099700	0.64402	D	0.000003	T	0.01976	0.0062	N	0.02247	-0.625	0.34478	D	0.70354	B	0.13594	0.008	B	0.10450	0.005	T	0.20706	-1.0267	10	0.02654	T	1	-24.6925	6.2929	0.21069	0.7932:0.0:0.2068:0.0	rs4888444;rs52798012;rs59055041;rs4888444	324	Q9NYB0	TE2IP_HUMAN	E	324	ENSP00000300086:K324E	ENSP00000300086:K324E	K	+	1	0	TERF2IP	74247780	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.219000	0.42899	2.183000	0.69458	0.482000	0.46254	AAG	A|0.969;G|0.031	0.031	strong		0.453	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975	
ENTHD2	146705	hgsc.bcm.edu	37	17	79202956	79202956	+	Silent	SNP	T	T	C	rs2048057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79202956T>C	ENST00000300714.3	-	12	1407	c.1350A>G	c.(1348-1350)ccA>ccG	p.P450P	AC027601.1_ENST00000569559.1_RNA|ENTHD2_ENST00000374769.2_Silent_p.P366P|AC027601.1_ENST00000575922.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	450						cytoplasmic vesicle (GO:0031410)											CCGTGCCCCCTGGGATCCGTT	0.692													T|||	2308	0.460863	0.0703	0.6282	5008	,	,		11278	0.6756		0.4682	False		,,,				2504	0.6411				p.P450P		Atlas-SNP	.											C17orf56,colon,carcinoma,0,1	.	.	1	0			c.A1350G						scavenged	.	T		605,3801	246.2+/-254.9	51,503,1649	31.0	30.0	30.0		1350	-6.9	0.0	17	dbSNP_94	30	4124,4476	528.6+/-381.4	1006,2112,1182	no	coding-synonymous	C17orf56	NM_144679.2		1057,2615,2831	CC,CT,TT		47.9535,13.7313,36.3601		450/526	79202956	4729,8277	2203	4300	6503	SO:0001819	synonymous_variant	146705	exon12			GCCCCCTGGGATC	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 56"""	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.1350A>G	17.37:g.79202956T>C		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_144679	Q6ZQU0|Q6ZSQ9	Silent	SNP	ENST00000300714.3	37	CCDS11779.1																																																																																			A|0.000;C|0.395;T|0.605	0.395	strong		0.692	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
SLC5A4	6527	hgsc.bcm.edu	37	22	32647802	32647802	+	Silent	SNP	C	C	T	rs144495809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32647802C>T	ENST00000266086.4	-	3	278	c.267G>A	c.(265-267)ggG>ggA	p.G89G	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	89					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						CTGCTCCTGTCCCAGCCAGCC	0.478													c|||	11	0.00219649	0.0008	0.0072	5008	,	,		17002	0.004		0.001	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.											.	SLC5A4	82	.	0			c.G267A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	96.0	95.0	95.0		267	-2.2	0.4	22	dbSNP_134	95	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	SLC5A4	NM_014227.2		0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537		89/660	32647802	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	6527	exon3			TCCTGTCCCAGCC	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.267G>A	22.37:g.32647802C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_014227	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
MMEL1	79258	hgsc.bcm.edu	37	1	2535613	2535613	+	Silent	SNP	C	C	A	rs4648562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:2535613C>A	ENST00000378412.3	-	10	1085	c.924G>T	c.(922-924)gtG>gtT	p.V308V	MMEL1_ENST00000502556.1_Intron|MMEL1_ENST00000288709.6_Silent_p.V299V			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	308						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)		CCAGCTCCAGCACCTGCACCA	0.677													C|||	2484	0.496006	0.6112	0.4481	5008	,	,		12736	0.5288		0.3121	False		,,,				2504	0.5297				p.V308V		Atlas-SNP	.											.	MMEL1	64	.	0			c.G924T						PASS	.	C		2518,1888		728,1062,413	36.0	36.0	36.0		924	3.5	1.0	1	dbSNP_111	36	2731,5867		435,1861,2003	no	coding-synonymous	MMEL1	NM_033467.3		1163,2923,2416	AA,AC,CC		31.7632,42.8507,40.3645		308/780	2535613	5249,7755	2203	4299	6502	SO:0001819	synonymous_variant	79258	exon10			CTCCAGCACCTGC	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.924G>T	1.37:g.2535613C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2	947	0.4336080586080586	289	0.5873983739837398	150	0.4143646408839779	271	0.4737762237762238	237	0.31266490765171506	C	0.350	-0.945647	0.02304	0.571493	0.317632	ENSG00000142606	ENST00000378411	.	.	.	4.43	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.4639	0.04548	0.1496:0.533:0.1454:0.1719	rs4648562	.	.	.	.	-1	.	.	.	-	.	.	MMEL1	2525473	0.994000	0.37717	0.999000	0.59377	0.089000	0.18198	0.369000	0.20416	0.930000	0.37217	-0.687000	0.03738	.	C|0.594;A|0.406	0.406	strong		0.677	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
DEFA5	1670	hgsc.bcm.edu	37	8	6914169	6914169	+	Silent	SNP	G	G	A	rs147432781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:6914169G>A	ENST00000330590.2	-	1	87	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_021010.1	NP_066290.1	Q01523	DEF5_HUMAN	defensin, alpha 5, Paneth cell-specific	17					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)				NS(1)|lung(4)|skin(1)|stomach(1)	7				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		ACTCAGCCTGGGCCTGCAGGG	0.582													.|||	10	0.00199681	0.0	0.0	5008	,	,		18658	0.0		0.008	False		,,,				2504	0.002				p.A17A		Atlas-SNP	.											.	DEFA5	17	.	0			c.C51T						PASS	.	G		13,4393		0,13,2190	109.0	99.0	102.0		51	0.8	0.1	8	dbSNP_134	102	108,8492		0,108,4192	no	coding-synonymous	DEFA5	NM_021010.1		0,121,6382	AA,AG,GG		1.2558,0.2951,0.9303		17/95	6914169	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	1670	exon1			AGCCTGGGCCTGC	BC069690	CCDS5963.1	8p23.1	2007-02-20			ENSG00000164816	ENSG00000164816		"""Defensins, alpha"""	2764	protein-coding gene	gene with protein product		600472		DEF5		1429669	Standard	NM_021010		Approved	HD-5	uc003wra.1	Q01523	OTTHUMG00000090383	ENST00000330590.2:c.51C>T	8.37:g.6914169G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_021010	A0JDY6|Q3KNV2	Silent	SNP	ENST00000330590.2	37	CCDS5963.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DEFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206755.1	NM_021010	
PLD2	5338	hgsc.bcm.edu	37	17	4718776	4718776	+	Silent	SNP	G	G	A	rs1132448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4718776G>A	ENST00000263088.6	+	13	1310	c.1179G>A	c.(1177-1179)gaG>gaA	p.E393E	PLD2_ENST00000572940.1_Silent_p.E393E	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	393					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)	ACCAGGAGGAGGGTGTCCGTG	0.542											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3131	0.6252	0.388	0.7435	5008	,	,		21414	0.6349		0.7028	False		,,,				2504	0.772				p.E393E		Atlas-SNP	.											.	PLD2	138	.	0			c.G1179A						PASS	.	G		1962,2444	553.3+/-378.7	429,1104,670	311.0	277.0	289.0		1179	2.5	1.0	17	dbSNP_86	289	6193,2407	699.9+/-405.1	2251,1691,358	no	coding-synonymous	PLD2	NM_002663.4		2680,2795,1028	AA,AG,GG		27.9884,44.5302,37.2982		393/934	4718776	8155,4851	2203	4300	6503	SO:0001819	synonymous_variant	5338	exon13			GGAGGAGGGTGTC	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.1179G>A	17.37:g.4718776G>A		Somatic	120	0	0	621	WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			G|0.370;A|0.630	0.630	strong		0.542	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
EME1	146956	hgsc.bcm.edu	37	17	48456193	48456193	+	Missense_Mutation	SNP	T	T	C	rs12450550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48456193T>C	ENST00000338165.4	+	5	1131	c.1049T>C	c.(1048-1050)aTc>aCc	p.I350T	EME1_ENST00000511648.2_Missense_Mutation_p.I350T|EME1_ENST00000393271.2_Missense_Mutation_p.I350T	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	350			I -> T (in dbSNP:rs12450550).		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)	p.I350T(1)		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)			GTAACTGACATCACAGCAAAG	0.473								Direct reversal of damage;Homologous recombination					T|||	714	0.142572	0.0416	0.2911	5008	,	,		21774	0.0804		0.2445	False		,,,				2504	0.1329				p.I350T		Atlas-SNP	.											EME1,NS,carcinoma,0,1	EME1	39	1	1	Substitution - Missense(1)	stomach(1)	c.T1049C						PASS	.	T	THR/ILE,THR/ILE	357,4049	183.6+/-211.2	21,315,1867	87.0	89.0	88.0		1049,1049	2.1	0.0	17	dbSNP_120	88	2244,6356	380.3+/-339.6	297,1650,2353	yes	missense,missense	EME1	NM_001166131.1,NM_152463.2	89,89	318,1965,4220	CC,CT,TT		26.093,8.1026,19.9985	benign,benign	350/584,350/571	48456193	2601,10405	2203	4300	6503	SO:0001583	missense	146956	exon5			CTGACATCACAGC	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.1049T>C	17.37:g.48456193T>C	ENSP00000339897:p.Ile350Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	340	0.15567765567765568	19	0.03861788617886179	94	0.2596685082872928	44	0.07692307692307693	183	0.24142480211081793	T	13.58	2.279564	0.40294	0.081026	0.26093	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.23754	1.89;1.89;1.89	5.58	2.1	0.27182	ERCC4 domain (2);	1.100420	0.06824	N	0.792688	T	0.00012	0.0000	M	0.65498	2.005	0.53005	P	3.2000000000032E-5	P;P	0.43352	0.804;0.695	B;B	0.40066	0.292;0.318	T	0.22347	-1.0219	9	0.59425	D	0.04	-21.7026	8.9778	0.35946	0.0:0.2212:0.0:0.7788	rs12450550;rs17714916;rs52794199;rs56987872;rs12450550	350;350	Q96AY2-2;Q96AY2	.;EME1_HUMAN	T	350	ENSP00000339897:I350T;ENSP00000376952:I350T;ENSP00000421700:I350T	ENSP00000339897:I350T	I	+	2	0	EME1	45811192	0.076000	0.21285	0.023000	0.16930	0.240000	0.25518	1.796000	0.38794	0.468000	0.27243	-0.451000	0.05528	ATC	C|0.175;N|0.000	0.175	strong		0.473	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
ATP6V1G3	127124	hgsc.bcm.edu	37	1	198505830	198505830	+	Intron	SNP	C	C	T	rs3736930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:198505830C>T	ENST00000367382.1	-	1	167				ATP6V1G3_ENST00000281087.2_Intron|ATP6V1G3_ENST00000489986.1_Intron|ATP6V1G3_ENST00000309309.7_Missense_Mutation_p.R36Q|ATP6V1G3_ENST00000367381.1_Intron			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3						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)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	7						CCAGTCTCTTCGTTTTAGGAA	0.343													C|||	137	0.0273562	0.0008	0.0058	5008	,	,		17088	0.0933		0.0308	False		,,,				2504	0.0072				p.R36Q		Atlas-SNP	.											.	ATP6V1G3	26	.	0			c.G107A						PASS	.	C	,GLN/ARG	28,4378	35.2+/-66.4	0,28,2175	154.0	172.0	166.0		,107	-2.7	0.0	1	dbSNP_107	166	260,8336	101.0+/-162.3	5,250,4043	yes	intron,missense	ATP6V1G3	NM_133262.2,NM_133326.1	,43	5,278,6218	TT,TC,CC		3.0247,0.6355,2.215	,	,36/60	198505830	288,12714	2203	4298	6501	SO:0001627	intron_variant	127124	exon3			TCTCTTCGTTTTA	AY039760	CCDS1395.1, CCDS1396.1	1q32.2	2010-04-21	2006-01-13		ENSG00000151418	ENSG00000151418		"""ATPases / V-type"""	18265	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 13kD, V1 subunit G isoform 3"", ""ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3"""			9442887	Standard	NM_133262		Approved	ATP6G3, Vma10	uc001gup.3	Q96LB4	OTTHUMG00000035661	ENST00000367382.1:c.82+3868G>A	1.37:g.198505830C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	376	130	0.345745	NM_133326	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	91	0.041666666666666664	1	0.0020325203252032522	1	0.0027624309392265192	61	0.10664335664335664	28	0.036939313984168866	C	5.081	0.200592	0.09652	0.006355	0.030247	ENSG00000151418	ENST00000309309	.	.	.	2.88	-2.69	0.06022	.	.	.	.	.	T	0.00468	0.0015	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.17930	-1.0353	6	0.87932	D	0	.	1.7252	0.02920	0.1591:0.4582:0.1569:0.2258	rs3736930;rs52818788;rs3736930	36	Q96LB4-3	.	Q	36	.	ENSP00000309574:R36Q	R	-	2	0	ATP6V1G3	196772453	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.890000	0.04140	-0.649000	0.05430	-0.752000	0.03492	CGA	C|0.970;T|0.030	0.030	strong		0.343	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326	
SLC3A1	6519	hgsc.bcm.edu	37	2	44547574	44547574	+	Missense_Mutation	SNP	G	G	A	rs698761	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:44547574G>A	ENST00000260649.6	+	10	1930	c.1854G>A	c.(1852-1854)atG>atA	p.M618I	PREPL_ENST00000409957.1_3'UTR|SLC3A1_ENST00000409740.3_Missense_Mutation_p.M249I|PREPL_ENST00000409411.1_3'UTR|PREPL_ENST00000409936.1_3'UTR|SLC3A1_ENST00000409380.1_Missense_Mutation_p.M340I|PREPL_ENST00000541738.1_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	109	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	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	
PI4KA	5297	hgsc.bcm.edu	37	22	21064270	21064270	+	Silent	SNP	C	C	T	rs151214632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21064270C>T	ENST00000572273.1	-	53	6155	c.5925G>A	c.(5923-5925)gcG>gcA	p.A1975A	PI4KA_ENST00000255882.6_Silent_p.A2033A|PI4KA_ENST00000414196.3_Silent_p.A785A			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1975	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)			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)			GGGAGACGACCGCGTCCATGT	0.617													N|||	1	0.000199681	0.0	0.0	5008	,	,		20530	0.0		0.001	False		,,,				2504	0.0				p.A2033A	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G6099A						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	113.0	89.0	97.0		2355,5925	-10.5	0.2	22	dbSNP_134	97	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous,coding-synonymous	PI4KA	NM_002650.2,NM_058004.3	,	0,29,6474	TT,TC,CC		0.3023,0.0681,0.223	,	785/855,1975/2045	21064270	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5297	exon53			GACGACCGCGTCC	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.5925G>A	22.37:g.21064270C>T		Somatic	429	0	0		WXS	Illumina HiSeq	Phase_I	465	234	0.503226	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				C|0.998;T|0.002	0.002	strong		0.617	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
MUC4	4585	hgsc.bcm.edu	37	3	195511102	195511102	+	Missense_Mutation	SNP	G	G	A	rs200212097		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195511102G>A	ENST00000463781.3	-	2	7808	c.7349C>T	c.(7348-7350)cCt>cTt	p.P2450L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2450L	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)		GCTGGTGACAGGAAGAGGGGT	0.582																																					p.P2450L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C7349T						PASS	.						40.0	38.0	38.0					3																	195511102		675	1586	2261	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.7349C>T	3.37:g.195511102G>A	ENSP00000417498:p.Pro2450Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	288	18	0.0625	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	6.334	0.429752	0.11987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35236	1.42;1.32	1.04	-2.07	0.07276	.	.	.	.	.	T	0.17109	0.0411	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.23511	-1.0186	8	.	.	.	.	2.913	0.05743	0.2179:0.0:0.5196:0.2625	.	2450	E7ESK3	.	L	2450	ENSP00000417498:P2450L;ENSP00000420243:P2450L	.	P	-	2	0	MUC4	196995497	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.435000	0.07264	0.000000	0.15137	CCT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70968505	70968505	+	Missense_Mutation	SNP	C	C	T	rs28932172	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70968505C>T	ENST00000359655.4	+	15	2135	c.2075C>T	c.(2074-2076)cCa>cTa	p.P692L		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	692	Interaction with LAMTOR5, important for protein stability.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GAGGGCTTTCCATCAGGGAGC	0.458													C|||	34	0.00678914	0.003	0.0086	5008	,	,		19200	0.0		0.0239	False		,,,				2504	0.0				p.P692L		Atlas-SNP	.											SUPV3L1,NS,carcinoma,-1,1	SUPV3L1	61	1	0			c.C2075T						PASS	.	C	LEU/PRO	11,4395	16.8+/-37.8	0,11,2192	83.0	83.0	83.0		2075	3.7	0.0	10	dbSNP_125	83	137,8463	69.0+/-131.5	3,131,4166	yes	missense	SUPV3L1	NM_003171.3	98	3,142,6358	TT,TC,CC		1.593,0.2497,1.1379	benign	692/787	70968505	148,12858	2203	4300	6503	SO:0001583	missense	6832	exon15			GCTTTCCATCAGG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.2075C>T	10.37:g.70968505C>T	ENSP00000352678:p.Pro692Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	37	CCDS7287.1	21	0.009615384615384616	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	16	0.021108179419525065	C	7.671	0.687072	0.14973	0.002497	0.01593	ENSG00000156502	ENST00000359655	T	0.30182	1.54	5.58	3.72	0.42706	.	1.305070	0.04657	N	0.408209	T	0.12860	0.0312	N	0.22421	0.69	0.20764	N	0.999851	B	0.10296	0.003	B	0.06405	0.002	T	0.20773	-1.0265	10	0.36615	T	0.2	-8.7476	9.4973	0.38995	0.0:0.7771:0.1435:0.0793	rs28932172	692	Q8IYB8	SUV3_HUMAN	L	692	ENSP00000352678:P692L	ENSP00000352678:P692L	P	+	2	0	SUPV3L1	70638511	0.001000	0.12720	0.001000	0.08648	0.007000	0.05969	1.033000	0.30191	0.716000	0.32124	0.650000	0.86243	CCA	T|0.011;C|0.989	0.011	strong		0.458	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
TTLL12	23170	hgsc.bcm.edu	37	22	43579083	43579083	+	Missense_Mutation	SNP	G	G	A	rs138951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43579083G>A	ENST00000216129.6	-	2	313	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	84			R -> W (in dbSNP:rs138951).		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)				CGCACCTCCCGGGCTGCCTCG	0.637													G|||	183	0.0365415	0.0038	0.0389	5008	,	,		19228	0.001		0.1302	False		,,,				2504	0.0194				p.R84W		Atlas-SNP	.											.	TTLL12	50	.	0			c.C250T						PASS	.	G	TRP/ARG	103,4303	80.4+/-118.8	0,103,2100	145.0	142.0	143.0		250	-0.8	0.0	22	dbSNP_78	143	988,7612	213.5+/-253.4	57,874,3369	no	missense	TTLL12	NM_015140.3	101	57,977,5469	AA,AG,GG		11.4884,2.3377,8.3884	probably-damaging	84/645	43579083	1091,11915	2203	4300	6503	SO:0001583	missense	23170	exon2			CCTCCCGGGCTGC	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.250C>T	22.37:g.43579083G>A	ENSP00000216129:p.Arg84Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	122	0.055860805860805864	6	0.012195121951219513	17	0.04696132596685083	3	0.005244755244755245	96	0.1266490765171504	G	9.569	1.120483	0.20877	0.023377	0.114884	ENSG00000100304	ENST00000216129;ENST00000357017;ENST00000423379	T	0.07800	3.16	5.08	-0.805	0.10879	.	1.539810	0.03716	N	0.251140	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D;P	0.60160	0.987;0.951	B;B	0.42653	0.394;0.394	T	0.15037	-1.0451	9	0.72032	D	0.01	-31.435	2.5325	0.04706	0.144:0.2853:0.3873:0.1834	rs138951;rs52835787;rs138951	84;84	B1AH89;Q14166	.;TTL12_HUMAN	W	84	ENSP00000216129:R84W	ENSP00000216129:R84W	R	-	1	2	TTLL12	41909027	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.346000	0.19997	-0.339000	0.08401	-0.140000	0.14226	CGG	G|0.927;A|0.073	0.073	strong		0.637	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
GLDC	2731	hgsc.bcm.edu	37	9	6610326	6610326	+	Silent	SNP	C	C	T	rs35374927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:6610326C>T	ENST00000321612.6	-	4	651	c.501G>A	c.(499-501)gaG>gaA	p.E167E		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	167					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)	CCTGAGACACCTCAGGCTGGT	0.498													C|||	962	0.192093	0.1437	0.1902	5008	,	,		18973	0.0863		0.2753	False		,,,				2504	0.2822				p.E167E		Atlas-SNP	.											.	GLDC	118	.	0			c.G501A						PASS	.	C		640,3766	276.3+/-273.0	44,552,1607	63.0	52.0	56.0		501	1.5	1.0	9	dbSNP_126	56	2432,6168	402.3+/-347.4	351,1730,2219	no	coding-synonymous	GLDC	NM_000170.2		395,2282,3826	TT,TC,CC		28.2791,14.5256,23.6199		167/1021	6610326	3072,9934	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon4			AGACACCTCAGGC	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.501G>A	9.37:g.6610326C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	53	0.398496	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			C|0.773;T|0.227	0.227	strong		0.498	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
COL18A1	80781	hgsc.bcm.edu	37	21	46910210	46910210	+	Missense_Mutation	SNP	G	G	A	rs62000962	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46910210G>A	ENST00000359759.4	+	19	3247	c.3226G>A	c.(3226-3228)Gtc>Atc	p.V1076I	COL18A1_ENST00000400337.2_Missense_Mutation_p.V661I|COL18A1_ENST00000355480.5_Missense_Mutation_p.V841I			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1076	Triple-helical region 4 (COL4).		V -> I (in dbSNP:rs62000962). {ECO:0000269|PubMed:11606364, ECO:0000269|PubMed:14614989, ECO:0000269|PubMed:14695535, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9503365}.		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)		AGCAGATGGAGTCCCCGGGTT	0.677													G|||	579	0.115615	0.1483	0.0821	5008	,	,		9232	0.0129		0.1322	False		,,,				2504	0.184				p.V841I		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2521A						PASS	.	G	ILE/VAL,ILE/VAL	564,3226		42,480,1373	17.0	21.0	20.0		2521,1981	-2.5	0.0	21	dbSNP_129	20	918,7298		47,824,3237	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	29,29	89,1304,4610	AA,AG,GG		11.1733,14.8813,12.3438	possibly-damaging,possibly-damaging	841/1520,661/1340	46910210	1482,10524	1895	4108	6003	SO:0001583	missense	80781	exon19			GATGGAGTCCCCG		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.3226G>A	21.37:g.46910210G>A	ENSP00000352798:p.Val1076Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		220	0.10073260073260074	80	0.16260162601626016	32	0.08839779005524862	5	0.008741258741258742	103	0.1358839050131926	G	2.001	-0.429456	0.04701	0.148813	0.111733	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	D;D;D;D	0.93426	-3.2;-3.2;-3.2;-3.22	3.37	-2.52	0.06346	.	1.629170	0.03721	U	0.251925	T	0.01320	0.0043	N	0.03177	-0.4	0.80722	P	0.0	B;B;B	0.20780	0.048;0.016;0.016	B;B;B	0.19391	0.025;0.01;0.01	T	0.52366	-0.8585	9	0.16420	T	0.52	.	9.8421	0.41004	0.0934:0.5729:0.3337:0.0	rs62000962	1076;841;661	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	I	661;661;841;1076;1076;8	ENSP00000383191:V661I;ENSP00000347665:V841I;ENSP00000352798:V1076I;ENSP00000339118:V8I	ENSP00000339118:V8I	V	+	1	0	COL18A1	45734638	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.168000	0.09925	-0.562000	0.06086	0.460000	0.39030	GTC	G|0.896;A|0.104	0.104	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
RRP36	88745	hgsc.bcm.edu	37	6	42995211	42995211	+	Silent	SNP	A	A	G	rs1138141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	114	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	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	
RHPN2	85415	hgsc.bcm.edu	37	19	33499071	33499071	+	Silent	SNP	G	G	A	rs10410414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:33499071G>A	ENST00000254260.3	-	7	644	c.609C>T	c.(607-609)acC>acT	p.T203T	RHPN2_ENST00000400226.4_Silent_p.T52T	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	203	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				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)					CCGGAACCCCGGTGAGAGAGT	0.473													G|||	1090	0.217652	0.2345	0.1744	5008	,	,		16699	0.1796		0.1988	False		,,,				2504	0.2843				p.T203T		Atlas-SNP	.											.	RHPN2	107	.	0			c.C609T						PASS	.	G		913,3493		96,721,1386	26.0	28.0	27.0		609	-6.8	0.8	19	dbSNP_119	27	1480,7120		129,1222,2949	no	coding-synonymous	RHPN2	NM_033103.4		225,1943,4335	AA,AG,GG		17.2093,20.7217,18.3992		203/687	33499071	2393,10613	2203	4300	6503	SO:0001819	synonymous_variant	85415	exon7			AACCCCGGTGAGA	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.609C>T	19.37:g.33499071G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Silent	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																			G|0.809;A|0.191	0.191	strong		0.473	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
SGK223	157285	hgsc.bcm.edu	37	8	8176221	8176221	+	Missense_Mutation	SNP	C	C	T	rs13269488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:8176221C>T	ENST00000520004.1	-	6	3928	c.3664G>A	c.(3664-3666)Ggc>Agc	p.G1222S	SGK223_ENST00000330777.4_Missense_Mutation_p.G1222S			Q86YV5	SG223_HUMAN		1226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TTTGGGGTGCCGCCCGGCTTC	0.657													C|||	2413	0.481829	0.4085	0.5058	5008	,	,		9810	0.5665		0.5229	False		,,,				2504	0.4346				p.G1222S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3664A						PASS	.	C	SER/GLY	1665,2079		378,909,585	26.0	29.0	28.0		3664	0.7	0.1	8	dbSNP_121	28	4397,3789		1188,2021,884	yes	missense	SGK223	NM_001080826.1	56	1566,2930,1469	TT,TC,CC		46.2863,44.4712,49.1869	probably-damaging	1222/1403	8176221	6062,5868	1872	4093	5965	SO:0001583	missense	0	exon5			GGGTGCCGCCCGG																												ENST00000520004.1:c.3664G>A	8.37:g.8176221C>T	ENSP00000428054:p.Gly1222Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	1130	0.5173992673992674	210	0.4268292682926829	167	0.4613259668508287	356	0.6223776223776224	397	0.5237467018469657	C	6.482	0.457070	0.12283	0.444712	0.537137	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.64085	-0.08;-0.08	4.95	0.737	0.18314	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.515636	0.22128	N	0.064233	T	0.00012	0.0000	L	0.37697	1.125	0.58432	P	6.999999999979245E-6	D	0.71674	0.998	P	0.62740	0.906	T	0.46789	-0.9166	9	0.36615	T	0.2	.	3.5532	0.07854	0.1775:0.3829:0.0:0.4396	rs13269488	1222	Q86YV5	SG223_HUMAN	S	1222	ENSP00000330930:G1222S;ENSP00000428054:G1222S	ENSP00000330930:G1222S	G	-	1	0	AC068353.1	8213631	0.000000	0.05858	0.137000	0.22149	0.060000	0.15804	-0.622000	0.05553	0.252000	0.21531	0.467000	0.42956	GGC	C|0.478;T|0.522	0.522	strong		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
RRS1	23212	hgsc.bcm.edu	37	8	67342077	67342077	+	Silent	SNP	G	G	A	rs3739337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:67342077G>A	ENST00000320270.2	+	1	815	c.711G>A	c.(709-711)gaG>gaA	p.E237E	ADHFE1_ENST00000415254.1_5'Flank|ADHFE1_ENST00000396623.3_5'Flank|ADHFE1_ENST00000379385.4_5'Flank|RP11-346I3.4_ENST00000499642.1_lincRNA	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	237					hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GCTTTCAGGAGCGCCTCCCCA	0.627													G|||	614	0.122604	0.1377	0.219	5008	,	,		15552	0.1538		0.0398	False		,,,				2504	0.0869				p.E237E		Atlas-SNP	.											.	RRS1	13	.	0			c.G711A						PASS	.	G		557,3829		35,487,1671	18.0	23.0	21.0		711	4.0	1.0	8	dbSNP_107	21	270,8312		3,264,4024	no	coding-synonymous	RRS1	NM_015169.3		38,751,5695	AA,AG,GG		3.1461,12.6995,6.3772		237/366	67342077	827,12141	2193	4291	6484	SO:0001819	synonymous_variant	23212	exon1			TCAGGAGCGCCTC	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.711G>A	8.37:g.67342077G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_015169	Q9BUX8	Silent	SNP	ENST00000320270.2	37	CCDS6189.1																																																																																			G|0.918;A|0.082	0.082	strong		0.627	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169	
DLL3	10683	hgsc.bcm.edu	37	19	39996027	39996027	+	Silent	SNP	C	C	T	rs2304214	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39996027C>T	ENST00000205143.4	+	6	1036	c.1029C>T	c.(1027-1029)ccC>ccT	p.P343P	DLL3_ENST00000356433.5_Silent_p.P343P	NM_016941.3	NP_058637.1	Q9NYJ7	DLL3_HUMAN	delta-like 3 (Drosophila)	343	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				compartment pattern specification (GO:0007386)|negative regulation of neurogenesis (GO:0050768)|Notch signaling pathway (GO:0007219)|paraxial mesoderm development (GO:0048339)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)	integral component of membrane (GO:0016021)	Notch binding (GO:0005112)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)	19	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;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ACTGCCCACCCGGTTTCCAAG	0.637													C|||	1212	0.242013	0.1377	0.2608	5008	,	,		16444	0.1468		0.3429	False		,,,				2504	0.364				p.P343P		Atlas-SNP	.											.	DLL3	47	.	0			c.C1029T						PASS	.	C	,	805,3601	323.4+/-298.1	69,667,1467	105.0	101.0	103.0		1029,1029	-6.6	0.7	19	dbSNP_100	103	2863,5737	448.8+/-361.9	478,1907,1915	no	coding-synonymous,coding-synonymous	DLL3	NM_016941.3,NM_203486.2	,	547,2574,3382	TT,TC,CC		33.2907,18.2705,28.2024	,	343/619,343/588	39996027	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	10683	exon6			CCCACCCGGTTTC	AF241373	CCDS12537.1, CCDS12538.1	19q13.2	2008-05-14	2001-12-03			ENSG00000090932			2909	protein-coding gene	gene with protein product		602768	"""delta (Drosophila)-like 3"""			10364530, 10742114	Standard	NM_203486		Approved	SCDO1	uc002olx.2	Q9NYJ7		ENST00000205143.4:c.1029C>T	19.37:g.39996027C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	78	75	0.961538	NM_016941	E9PFG2|Q8NBS4	Silent	SNP	ENST00000205143.4	37	CCDS12538.1																																																																																			C|0.741;T|0.259	0.259	strong		0.637	DLL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464958.1		
CBWD6	644019	hgsc.bcm.edu	37	9	69256833	69256833	+	Missense_Mutation	SNP	A	A	G	rs113407575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:69256833A>G	ENST00000377457.5	-	3	403	c.298T>C	c.(298-300)Tgg>Cgg	p.W100R	CBWD6_ENST00000382399.4_Missense_Mutation_p.W100R|CBWD6_ENST00000377441.1_Missense_Mutation_p.W100R|CBWD6_ENST00000377449.1_Missense_Mutation_p.W64R	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	100							ATP binding (GO:0005524)			lung(4)	4						AGTTCCAGCCACTCTTCATAG	0.378													.|||	617	0.123203	0.1362	0.0965	5008	,	,		17436	0.2083		0.0825	False		,,,				2504	0.0787				p.W100R		Atlas-SNP	.											.	CBWD6	19	.	0			c.T298C						PASS	.	A	ARG/TRP	558,3828		74,410,1709	80.0	89.0	86.0		298	2.5	1.0	9	dbSNP_132	86	666,7870		51,564,3653	no	missense	CBWD6	NM_001085457.1	101	125,974,5362	GG,GA,AA		7.8022,12.7223,9.4722	possibly-damaging	100/396	69256833	1224,11698	2193	4268	6461	SO:0001583	missense	644019	exon3			CCAGCCACTCTTC		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.298T>C	9.37:g.69256833A>G	ENSP00000366677:p.Trp100Arg	Somatic	946	0	0		WXS	Illumina HiSeq	Phase_I	2154	403	0.187094	NM_001085457		Missense_Mutation	SNP	ENST00000377457.5	37	CCDS43827.1	256	0.11721611721611722	66	0.13414634146341464	41	0.1132596685082873	93	0.16258741258741258	56	0.07387862796833773	.	14.82	2.650268	0.47362	0.127223	0.078022	ENSG00000204790	ENST00000377457;ENST00000377450;ENST00000377449;ENST00000382399;ENST00000377445;ENST00000536466;ENST00000377441	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	2.53	2.53	0.30540	Cobalamin (vitamin B12) biosynthesis CobW-like (1);	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	M	0.90650	3.135	0.09310	P	0.9999959727	D	0.89917	1.0	D	0.97110	1.0	T	0.33497	-0.9866	9	0.72032	D	0.01	-15.4598	8.5798	0.33621	1.0:0.0:0.0:0.0	.	100	Q4V339	CBWD6_HUMAN	R	100;100;64;100;100;100;100	ENSP00000366677:W100R;ENSP00000366668:W64R;ENSP00000371836:W100R;ENSP00000366660:W100R	ENSP00000366660:W100R	W	-	1	0	CBWD6	68546653	1.000000	0.71417	0.998000	0.56505	0.713000	0.41058	8.056000	0.89455	1.168000	0.42723	0.155000	0.16302	TGG	A|0.897;G|0.103	0.103	strong		0.378	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656607	46656607	+	Silent	SNP	G	G	A	rs8143066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46656607G>A	ENST00000253255.5	-	1	2612	c.2613C>T	c.(2611-2613)atC>atT	p.I871I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	871	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AGAGCTGGTTGATACCCCACT	0.413													A|||	1229	0.245407	0.6785	0.134	5008	,	,		20155	0.001		0.16	False		,,,				2504	0.0787				p.I871I		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C2613T						PASS	.	A		2654,1752	520.9+/-370.4	793,1068,342	70.0	70.0	70.0		2613	-1.7	0.0	22	dbSNP_116	70	1260,7340	760.1+/-407.6	88,1084,3128	no	coding-synonymous	PKDREJ	NM_006071.1		881,2152,3470	AA,AG,GG		14.6512,39.764,30.0938		871/2254	46656607	3914,9092	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			CTGGTTGATACCC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2613C>T	22.37:g.46656607G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.722;A|0.278	0.278	strong		0.413	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CLDN14	23562	hgsc.bcm.edu	37	21	37833307	37833307	+	Silent	SNP	C	C	T	rs219780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:37833307C>T	ENST00000399137.1	-	3	1553	c.687G>A	c.(685-687)acG>acA	p.T229T	CLDN14_ENST00000399135.1_Silent_p.T229T|AP000695.4_ENST00000428667.1_RNA|AP000695.6_ENST00000429588.1_RNA|CLDN14_ENST00000399136.1_Silent_p.T229T|CLDN14_ENST00000399139.1_Silent_p.T229T|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000342108.2_Silent_p.T229T	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	152	0	0		WXS	Illumina HiSeq	Phase_I	190	103	0.542105	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	
SELL	6402	hgsc.bcm.edu	37	1	169673838	169673838	+	Missense_Mutation	SNP	G	G	A	rs2229569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169673838G>A	ENST00000236147.4	-	5	836	c.676C>T	c.(676-678)Cct>Tct	p.P226S	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	213	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					TTTCCCAAAGGGTGAGTACAG	0.478													G|||	1222	0.24401	0.27	0.2752	5008	,	,		19408	0.254		0.175	False		,,,				2504	0.2474				p.P226S		Atlas-SNP	.											.	SELL	43	.	0			c.C676T						PASS	.	G	SER/PRO	809,2909		85,639,1135	47.0	47.0	47.0		676	5.3	0.9	1	dbSNP_98	47	1076,7044		73,930,3057	yes	missense	SELL	NM_000655.4	74	158,1569,4192	AA,AG,GG		13.2512,21.759,15.9233	probably-damaging	226/386	169673838	1885,9953	1859	4060	5919	SO:0001583	missense	6402	exon5			CCAAAGGGTGAGT	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"""CD molecules"""	10720	protein-coding gene	gene with protein product		153240	"""lymphocyte adhesion molecule 1"""	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.676C>T	1.37:g.169673838G>A	ENSP00000236147:p.Pro226Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_000655	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	523	0.23946886446886448	139	0.28252032520325204	91	0.2513812154696133	163	0.28496503496503495	130	0.17150395778364116	G	18.76	3.692950	0.68271	0.21759	0.132512	ENSG00000188404	ENST00000236147	T	0.48201	0.82	5.31	5.31	0.75309	Complement control module (2);Sushi/SCR/CCP (3);	0.117810	0.38326	N	0.001734	T	0.56717	0.2004	M	0.63843	1.955	0.23533	P	0.99747012	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.61033	-0.7144	9	0.56958	D	0.05	-9.9883	12.5565	0.56257	0.0:0.1674:0.8325:0.0	rs2229569;rs4987310;rs52812496;rs58249723;rs4987310	226;213	Q8WW79;P14151	.;LYAM1_HUMAN	S	226	ENSP00000236147:P226S	ENSP00000236147:P226S	P	-	1	0	SELL	167940462	0.994000	0.37717	0.872000	0.34217	0.870000	0.49936	2.131000	0.42074	2.631000	0.89168	0.655000	0.94253	CCT	G|0.766;A|0.234	0.234	strong		0.478	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655	
TM2D3	80213	hgsc.bcm.edu	37	15	102192540	102192540	+	Silent	SNP	T	T	G	rs675436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:102192540T>G	ENST00000333202.3	-	1	30	c.25A>C	c.(25-27)Agg>Cgg	p.R9R	TM2D3_ENST00000428002.2_Silent_p.R9R|TM2D3_ENST00000559107.1_Silent_p.R9R|TM2D3_ENST00000347970.3_Silent_p.R9R|TARSL2_ENST00000559492.1_5'Flank|TM2D3_ENST00000561373.1_5'Flank	NM_078474.2	NP_510883.2	Q9BRN9	TM2D3_HUMAN	TM2 domain containing 3	9						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(6)|ovary(1)	10	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)			CGGAGGCCCCTCAGCGGGAGC	0.721													G|||	1297	0.258986	0.2428	0.2507	5008	,	,		12715	0.0456		0.4443	False		,,,				2504	0.316				p.R9R		Atlas-SNP	.											.	TM2D3	18	.	0			c.A25C						PASS	.	G	,	1285,3077		192,901,1088	21.0	23.0	23.0		25,25	-2.0	0.0	15	dbSNP_83	23	3824,4730		867,2090,1320	no	coding-synonymous,coding-synonymous	TM2D3	NM_025141.3,NM_078474.2	,	1059,2991,2408	GG,GT,TT		44.7042,29.459,39.5556	,	9/222,9/248	102192540	5109,7807	2181	4277	6458	SO:0001819	synonymous_variant	80213	exon1			GGCCCCTCAGCGG	AK094955	CCDS10392.1, CCDS10393.1	15q26.3	2014-02-12			ENSG00000184277	ENSG00000184277			24128	protein-coding gene	gene with protein product		610014				11278849	Standard	XM_005254980		Approved	BLP2, FLJ22604	uc002bxi.3	Q9BRN9	OTTHUMG00000149872	ENST00000333202.3:c.25A>C	15.37:g.102192540T>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_025141	B2RDK9|Q9H046|Q9H651	Silent	SNP	ENST00000333202.3	37	CCDS10393.1																																																																																			T|0.666;G|0.334	0.334	strong		0.721	TM2D3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313623.1	NM_078474	
ZNF285	26974	hgsc.bcm.edu	37	19	44892266	44892266	+	Splice_Site	SNP	T	T	C	rs200167944		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44892266T>C	ENST00000330997.4	-	4	207		c.e4-2		CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Splice_Site|ZNF285_ENST00000591679.1_Splice_Site	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TCCCGTCTCCTAGGAGAAGAA	0.413																																					.		Atlas-SNP	.											ZNF285,colon,carcinoma,0,1	ZNF285	86	1	0			c.143-2A>G						scavenged	.						50.0	54.0	53.0					19																	44892266		2173	4283	6456	SO:0001630	splice_region_variant	26974	exon5			GTCTCCTAGGAGA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.143-2A>G	19.37:g.44892266T>C		Somatic	87	3	0.0344828		WXS	Illumina HiSeq	Phase_I	119	4	0.0336134	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Splice_Site	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	9.943	1.218077	0.22373	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	.	.	.	3.86	3.86	0.44501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3975	0.38412	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF285	49584106	0.507000	0.26146	0.215000	0.23724	0.122000	0.20287	3.134000	0.50538	1.528000	0.49103	0.373000	0.22412	.	.	.	weak		0.413	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	Intron
MT-ND6	4541	hgsc.bcm.edu	37	M	14470	14470	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrM:14470T>A	ENST00000361681.2	-	1	203	c.204A>T	c.(202-204)ggA>ggT	p.G68G	MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	68					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						GCTGTAGTATATCCAAAGACA	0.438																																					p.G68G		Atlas-SNP	.											.	.	.	.	0			c.A204T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGTATATCCAAAG			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.204A>T	M.37:g.14470T>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.438	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
VPS53	55275	hgsc.bcm.edu	37	17	465775	465775	+	Silent	SNP	G	G	A	rs2075443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:465775G>A	ENST00000571805.1	-	14	1660	c.1524C>T	c.(1522-1524)taC>taT	p.Y508Y	VPS53_ENST00000574029.1_Intron|VPS53_ENST00000446250.2_Silent_p.Y310Y|VPS53_ENST00000401468.3_Silent_p.Y231Y|VPS53_ENST00000291074.5_Silent_p.Y479Y|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000437048.2_Silent_p.Y508Y			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	201	0	0		WXS	Illumina HiSeq	Phase_I	261	101	0.386973	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	
SLC5A10	125206	hgsc.bcm.edu	37	17	18880268	18880268	+	Silent	SNP	C	C	A	rs2472715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18880268C>A	ENST00000395645.3	+	9	966	c.948C>A	c.(946-948)atC>atA	p.I316I	FAM83G_ENST00000345041.4_Intron|SLC5A10_ENST00000317977.6_Silent_p.I233I|FAM83G_ENST00000388995.6_Intron|FAM83G_ENST00000585154.2_Intron|SLC5A10_ENST00000395642.1_Silent_p.I233I|SLC5A10_ENST00000417251.2_Silent_p.I316I|SLC5A10_ENST00000395647.2_Silent_p.I316I|SLC5A10_ENST00000395643.2_Silent_p.I289I	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	72	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	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	
SELL	6402	hgsc.bcm.edu	37	1	169677709	169677709	+	Silent	SNP	A	A	G	rs1051091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169677709A>G	ENST00000236147.4	-	3	520	c.360T>C	c.(358-360)ctT>ctC	p.L120L	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	107	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					CTTCTTCAGTAAGAGATTTGT	0.463													G|||	1503	0.30012	0.2965	0.3401	5008	,	,		19771	0.2679		0.2724	False		,,,				2504	0.3384				p.L120L		Atlas-SNP	.											.	SELL	43	.	0			c.T360C						PASS	.	G		1070,2948		137,796,1076	89.0	87.0	88.0		360	2.7	0.9	1	dbSNP_86	88	2025,6351		226,1573,2389	no	coding-synonymous	SELL	NM_000655.4		363,2369,3465	GG,GA,AA		24.1762,26.6302,24.9718		120/386	169677709	3095,9299	2009	4188	6197	SO:0001819	synonymous_variant	6402	exon3			TTCAGTAAGAGAT	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"""CD molecules"""	10720	protein-coding gene	gene with protein product		153240	"""lymphocyte adhesion molecule 1"""	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.360T>C	1.37:g.169677709A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_000655	B2R6Q8|P15023|Q9UJ43	Silent	SNP	ENST00000236147.4	37	CCDS53427.1																																																																																			G|0.290;N|0.000	0.290	strong		0.463	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655	
TMEM171	134285	hgsc.bcm.edu	37	5	72419617	72419617	+	Missense_Mutation	SNP	C	C	A	rs636926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:72419617C>A	ENST00000454765.2	+	2	890	c.417C>A	c.(415-417)aaC>aaA	p.N139K	TMEM171_ENST00000287773.5_Missense_Mutation_p.N139K			Q8WVE6	TM171_HUMAN	transmembrane protein 171	139			N -> K (in dbSNP:rs636926). {ECO:0000269|PubMed:12044878}.			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)		GTGGCTCCAACTGGGCGCAGG	0.572													C|||	2245	0.448283	0.5696	0.3285	5008	,	,		17783	0.5942		0.2654	False		,,,				2504	0.407				p.N139K	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.C417A						PASS	.	C	LYS/ASN,LYS/ASN	2335,2071	606.2+/-390.7	611,1113,479	122.0	124.0	123.0		417,417	1.2	0.8	5	dbSNP_83	123	2128,6472	365.5+/-333.9	283,1562,2455	yes	missense,missense	TMEM171	NM_001161342.1,NM_173490.6	94,94	894,2675,2934	AA,AC,CC		24.7442,47.0041,34.3149	benign,benign	139/324,139/325	72419617	4463,8543	2203	4300	6503	SO:0001583	missense	134285	exon2			CTCCAACTGGGCG	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.417C>A	5.37:g.72419617C>A	ENSP00000415030:p.Asn139Lys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	920	0.42124542124542125	269	0.5467479674796748	127	0.35082872928176795	328	0.5734265734265734	196	0.25857519788918204	C	6.847	0.525579	0.13066	0.529959	0.247442	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.21932	1.98;1.98	5.35	1.2	0.21068	.	0.509796	0.19767	N	0.106533	T	0.00012	0.0000	N	0.08118	0	0.49483	P	2.0600000000003948E-4	B;B	0.17038	0.02;0.02	B;B	0.18871	0.023;0.023	T	0.40590	-0.9555	9	0.36615	T	0.2	-7.0417	2.9391	0.05824	0.1693:0.4878:0.1912:0.1516	rs636926;rs60384768;rs636926	139;139	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	K	139	ENSP00000415030:N139K;ENSP00000287773:N139K	ENSP00000287773:N139K	N	+	3	2	TMEM171	72455373	0.064000	0.20934	0.796000	0.32109	0.013000	0.08279	0.304000	0.19228	0.626000	0.30322	-0.379000	0.06801	AAC	C|0.610;A|0.390	0.390	strong		0.572	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
COL25A1	84570	hgsc.bcm.edu	37	4	109841743	109841743	+	Silent	SNP	C	C	T	rs17596705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:109841743C>T	ENST00000399132.1	-	12	1256	c.726G>A	c.(724-726)ccG>ccA	p.P242P	COL25A1_ENST00000399127.1_Silent_p.P238P|COL25A1_ENST00000399126.1_Silent_p.P242P	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)		CCTTTTGTCCCGGAGGCCCTA	0.363													C|||	614	0.122604	0.1868	0.1671	5008	,	,		16387	0.003		0.2107	False		,,,				2504	0.0368				p.P242P		Atlas-SNP	.											.	COL25A1	178	.	0			c.G726A						PASS	.	C	,	643,3031		49,545,1243	157.0	140.0	145.0		726,726	-2.3	1.0	4	dbSNP_123	145	1834,6344		204,1426,2459	no	coding-synonymous,coding-synonymous	COL25A1	NM_032518.2,NM_198721.1	,	253,1971,3702	TT,TC,CC		22.426,17.5014,20.8994	,	242/643,242/655	109841743	2477,9375	1837	4089	5926	SO:0001819	synonymous_variant	84570	exon11			TTGTCCCGGAGGC	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.726G>A	4.37:g.109841743C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_198721		Silent	SNP	ENST00000399132.1	37	CCDS43258.1																																																																																			C|0.843;T|0.157	0.157	strong		0.363	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518	
SBNO2	22904	hgsc.bcm.edu	37	19	1113701	1113701	+	Missense_Mutation	SNP	G	G	A	rs2302110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	76	0	0		WXS	Illumina HiSeq	Phase_I	117	114	0.974359	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	
IKBKAP	8518	hgsc.bcm.edu	37	9	111659439	111659439	+	Missense_Mutation	SNP	T	T	C	rs2230794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	148	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	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		
ZNF638	27332	hgsc.bcm.edu	37	2	71658541	71658541	+	Missense_Mutation	SNP	C	C	T	rs11542286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71658541C>T	ENST00000409544.1	+	26	6365	c.5735C>T	c.(5734-5736)gCg>gTg	p.A1912V	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000409407.1_Missense_Mutation_p.A852V|ZNF638_ENST00000264447.4_Missense_Mutation_p.A1912V	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1912			A -> V (in dbSNP:rs11542286). {ECO:0000269|PubMed:11149944}.		regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAATCAGTGGCGTCTGATGTC	0.433													C|||	582	0.116214	0.1278	0.0576	5008	,	,		16949	0.1647		0.0795	False		,,,				2504	0.1299				p.A1912V		Atlas-SNP	.											ZNF638,NS,carcinoma,-1,1	ZNF638	179	1	0			c.C5735T						PASS	.	C	VAL/ALA,VAL/ALA	584,3822	258.3+/-262.4	38,508,1657	50.0	49.0	49.0		5735,5735	1.9	0.0	2	dbSNP_120	49	785,7815	185.5+/-233.2	41,703,3556	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	64,64	79,1211,5213	TT,TC,CC		9.1279,13.2547,10.5259	benign,benign	1912/1979,1912/1979	71658541	1369,11637	2203	4300	6503	SO:0001583	missense	27332	exon26			CAGTGGCGTCTGA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5735C>T	2.37:g.71658541C>T	ENSP00000386433:p.Ala1912Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	182	87	0.478022	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	221	0.10119047619047619	53	0.10772357723577236	28	0.07734806629834254	77	0.1346153846153846	63	0.08311345646437995	C	11.38	1.621672	0.28889	0.132547	0.091279	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.32023	1.47;1.47;1.87	4.75	1.86	0.25419	.	1.713730	0.03115	N	0.163046	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	B;B	0.16396	0.017;0.002	B;B	0.08055	0.003;0.001	T	0.14008	-1.0488	9	0.28530	T	0.3	2.4669	4.3683	0.11235	0.2015:0.5979:0.0:0.2006	rs11542286;rs13383900;rs52791043;rs60248575;rs13383900	1912;1912	Q14966-3;Q14966	.;ZN638_HUMAN	V	1912;1912;852	ENSP00000264447:A1912V;ENSP00000386433:A1912V;ENSP00000386813:A852V	ENSP00000264447:A1912V	A	+	2	0	ZNF638	71512049	0.521000	0.26258	0.006000	0.13384	0.983000	0.72400	1.016000	0.29976	0.263000	0.21812	0.478000	0.44815	GCG	T|0.085;G|0.166	0.085	strong		0.433	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
ZNF589	51385	hgsc.bcm.edu	37	3	48282695	48282695	+	Missense_Mutation	SNP	A	A	G	rs9847953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48282695A>G	ENST00000354698.3	+	1	106	c.34A>G	c.(34-36)Act>Gct	p.T12A	ZNF589_ENST00000412564.1_Missense_Mutation_p.T12A|ZNF589_ENST00000427617.2_Missense_Mutation_p.T12A|ZNF589_ENST00000440261.2_Missense_Mutation_p.T12A	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	12			T -> A (in dbSNP:rs9847953). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACTGGGCTGGACTGCGGAAGG	0.682													G|||	1179	0.235423	0.264	0.2161	5008	,	,		13191	0.121		0.2913	False		,,,				2504	0.271				p.T12A	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											ZNF589,NS,carcinoma,0,2	ZNF589	20	2	0			c.A34G						PASS	.	G	ALA/THR	1069,2907		162,745,1081	24.0	29.0	27.0		34	-2.0	0.0	3	dbSNP_119	27	2570,5764		419,1732,2016	yes	missense	ZNF589	NM_016089.2	58	581,2477,3097	GG,GA,AA		30.8375,26.8863,29.5613	benign	12/365	48282695	3639,8671	1988	4167	6155	SO:0001583	missense	51385	exon1			GGCTGGACTGCGG	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"""Zinc fingers, C2H2-type"", ""-"""	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	ENST00000354698.3:c.34A>G	3.37:g.48282695A>G	ENSP00000346729:p.Thr12Ala	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	166	93	0.560241	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	37	CCDS43085.1	489	0.2239010989010989	123	0.25	86	0.23756906077348067	64	0.11188811188811189	216	0.2849604221635884	G	6.344	0.431497	0.12045	0.268863	0.308375	ENSG00000164048	ENST00000354698;ENST00000427617;ENST00000412564;ENST00000440261	T;T;T;T	0.05717	3.4;4.81;4.75;4.98	1.32	-1.99	0.07457	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.0	T	0.42632	-0.9440	8	0.07175	T	0.84	.	3.5587	0.07874	0.5199:0.2168:0.2633:0.0	rs9847953;rs9847953	12;12	B4DQF9;Q86UQ0	.;ZN589_HUMAN	A	12	ENSP00000346729:T12A;ENSP00000392719:T12A;ENSP00000404398:T12A;ENSP00000408719:T12A	ENSP00000346729:T12A	T	+	1	0	ZNF589	48257699	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.672000	0.05244	-1.395000	0.02074	-0.471000	0.05019	ACT	A|0.753;G|0.247	0.247	strong		0.682	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089	
ZNF492	57615	hgsc.bcm.edu	37	19	22846867	22846867	+	Silent	SNP	G	G	A	rs74406853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22846867G>A	ENST00000456783.2	+	4	640	c.396G>A	c.(394-396)acG>acA	p.T132T	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	132					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(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ACAGACATACGATAAGACATA	0.313													N|||	190	0.0379393	0.0295	0.0187	5008	,	,		15276	0.0813		0.0398	False		,,,				2504	0.0164				p.T132T		Atlas-SNP	.											.	ZNF492	129	.	0			c.G396A						PASS	.	G		80,4134		0,80,2027	35.0	37.0	36.0		396	0.3	0.0	19	dbSNP_131	36	249,8261		3,243,4009	no	coding-synonymous	ZNF492	NM_020855.2		3,323,6036	AA,AG,GG		2.926,1.8984,2.5857		132/532	22846867	329,12395	2107	4255	6362	SO:0001819	synonymous_variant	57615	exon4			ACATACGATAAGA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.396G>A	19.37:g.22846867G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	145	81	0.558621	NM_020855	Q08EI7|Q08EI8	Silent	SNP	ENST00000456783.2	37	CCDS46032.1																																																																																			G|0.955;A|0.045	0.045	strong		0.313	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
FHIT	2272	hgsc.bcm.edu	37	3	59908126	59908126	+	Silent	SNP	A	A	G	rs1385816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:59908126A>G	ENST00000468189.1	-	8	664	c.294T>C	c.(292-294)caT>caC	p.H98H	FHIT_ENST00000341848.4_Silent_p.H98H|FHIT_ENST00000492590.1_Silent_p.H98H|FHIT_ENST00000466788.1_5'UTR|FHIT_ENST00000476844.1_Silent_p.H98H			P49789	FHIT_HUMAN	fragile histidine triad	98	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				DNA replication (GO:0006260)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide metabolic process (GO:0009117)|purine nucleotide metabolic process (GO:0006163)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|catalytic activity (GO:0003824)|hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|ubiquitin protein ligase binding (GO:0031625)	p.H98H(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)	12		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		TGGGAAGAACATGGACGTGAA	0.428			T	HMGA2	pleomorphic salivary gland adenoma				Renal Cell Cancer associated with constitutional translocation of chromosome 3				A|||	1126	0.22484	0.0719	0.3429	5008	,	,		20133	0.3333		0.2028	False		,,,				2504	0.2587				p.H98H		Atlas-SNP	.		Dom	yes		3	3p14.2	2272	fragile histidine triad gene		E	FHIT,NS,carcinoma,0,1	FHIT	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T294C						PASS	.	A	,	394,4012	196.4+/-220.7	15,364,1824	136.0	119.0	124.0		294,294	3.5	1.0	3	dbSNP_88	124	1779,6821	321.1+/-314.9	170,1439,2691	no	coding-synonymous,coding-synonymous	FHIT	NM_001166243.1,NM_002012.2	,	185,1803,4515	GG,GA,AA		20.686,8.9424,16.7077	,	98/148,98/148	59908126	2173,10833	2203	4300	6503	SO:0001819	synonymous_variant	2272	exon8	Familial Cancer Database		AAGAACATGGACG	BC032336	CCDS2894.1	3p14.2	2012-02-27	2012-02-27		ENSG00000189283	ENSG00000189283			3701	protein-coding gene	gene with protein product		601153	"""fragile histidine triad gene"""			8598045, 9671749	Standard	NM_002012		Approved	FRA3B, AP3Aase	uc003dky.3	P49789	OTTHUMG00000158591	ENST00000468189.1:c.294T>C	3.37:g.59908126A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	33	0.647059	NM_002012	A2IAS9|A2IAT0|A2IAT6|A8K1A9|Q45QG9|Q6IU12	Silent	SNP	ENST00000468189.1	37	CCDS2894.1																																																																																			A|0.816;G|0.184	0.184	strong		0.428	FHIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351648.1	NM_002012	
WISP3	8838	hgsc.bcm.edu	37	6	112382313	112382313	+	Missense_Mutation	SNP	G	G	T	rs1230345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:112382313G>T	ENST00000368666.2	+	2	454	c.168G>T	c.(166-168)caG>caT	p.Q56H	WISP3_ENST00000409166.1_5'Flank|WISP3_ENST00000604763.1_Missense_Mutation_p.Q56H|WISP3_ENST00000368663.3_Missense_Mutation_p.Q34H|WISP3_ENST00000361714.1_Missense_Mutation_p.Q74H|WISP3_ENST00000230529.5_Missense_Mutation_p.Q56H	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	56	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.		Q -> H (common polymorphism; dbSNP:rs1230345). {ECO:0000269|PubMed:10471507}.		cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		AATGCCCTCAGCAGAAGCCCC	0.532													T|||	1497	0.298922	0.4705	0.2392	5008	,	,		19236	0.3313		0.2465	False		,,,				2504	0.1299				p.Q74H		Atlas-SNP	.											.	WISP3	33	.	0			c.G222T						PASS	.	T	HIS/GLN,HIS/GLN	1991,2415	616.9+/-392.9	462,1067,674	135.0	124.0	128.0		168,222	-7.2	0.0	6	dbSNP_87	128	2381,6219	701.1+/-405.2	311,1759,2230	yes	missense,missense	WISP3	NM_003880.3,NM_198239.1	24,24	773,2826,2904	TT,TG,GG		27.686,45.1884,33.6153	benign,benign	56/355,74/373	112382313	4372,8634	2203	4300	6503	SO:0001583	missense	8838	exon2			CCCTCAGCAGAAG	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.168G>T	6.37:g.112382313G>T	ENSP00000357655:p.Gln56His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Missense_Mutation	SNP	ENST00000368666.2	37	CCDS5098.1	656	0.30036630036630035	220	0.44715447154471544	88	0.2430939226519337	172	0.3006993006993007	176	0.23218997361477572	T	0.324	-0.960165	0.02267	0.451884	0.27686	ENSG00000112761	ENST00000368666;ENST00000230529;ENST00000361714;ENST00000541400;ENST00000368663	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	3.77	-7.25	0.01470	Insulin-like growth factor-binding protein, IGFBP (3);	1.850360	0.02256	N	0.067100	T	0.10423	0.0255	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	0.05649	-1.0872	9	0.44086	T	0.13	5.8147	3.0603	0.06197	0.1172:0.3374:0.3572:0.1882	rs1230345;rs1709860;rs52826752;rs61572383;rs1230345	74;56	O95389-2;O95389	.;WISP3_HUMAN	H	56;56;74;56;34	ENSP00000357655:Q56H;ENSP00000230529:Q56H;ENSP00000354734:Q74H;ENSP00000357652:Q34H	ENSP00000230529:Q56H	Q	+	3	2	WISP3	112489006	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.729000	0.04920	-1.590000	0.01623	-0.362000	0.07510	CAG	G|0.673;T|0.321	0.321	strong		0.532	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880	
CRMP1	1400	hgsc.bcm.edu	37	4	5838513	5838513	+	Silent	SNP	C	C	G	rs12331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:5838513C>G	ENST00000397890.2	-	10	1303	c.1089G>C	c.(1087-1089)acG>acC	p.T363T	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Silent_p.T361T|CRMP1_ENST00000324989.7_Silent_p.T477T	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	363				Missing (in Ref. 7; AAK55500). {ECO:0000305}.	axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CCCAGACGACCGTCATCCGCT	0.582													G|||	2948	0.588658	0.9198	0.4035	5008	,	,		21340	0.6002		0.4066	False		,,,				2504	0.4479				p.T477T		Atlas-SNP	.											CRMP1,NS,carcinoma,0,1	CRMP1	118	1	0			c.G1431C						PASS	.	G	,	3722,684	291.8+/-281.7	1583,556,64	140.0	116.0	124.0		1431,1089	-5.5	0.7	4	dbSNP_52	124	3836,4764	611.6+/-395.8	853,2130,1317	no	coding-synonymous,coding-synonymous	CRMP1	NM_001014809.1,NM_001313.3	,	2436,2686,1381	GG,GC,CC		44.6047,15.5243,41.8884	,	477/687,363/573	5838513	7558,5448	2203	4300	6503	SO:0001819	synonymous_variant	1400	exon10			GACGACCGTCATC	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1089G>C	4.37:g.5838513C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			G|0.588;C|0.412	0.588	strong		0.582	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
ABCA2	20	hgsc.bcm.edu	37	9	139916879	139916879	+	Missense_Mutation	SNP	C	C	T	rs34039859	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139916879C>T	ENST00000371605.3	-	5	635	c.488G>A	c.(487-489)cGt>cAt	p.R163H	ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000341511.6_Missense_Mutation_p.R164H|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	121	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	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	
SMTNL2	342527	hgsc.bcm.edu	37	17	4498611	4498611	+	Silent	SNP	G	G	A	rs12103697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4498611G>A	ENST00000389313.4	+	5	1045	c.978G>A	c.(976-978)acG>acA	p.T326T	SMTNL2_ENST00000338859.4_Silent_p.T182T	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	326										breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		AGCAGGAAACGGCGGCCGGCA	0.682													G|||	829	0.165535	0.0703	0.1657	5008	,	,		16274	0.0992		0.3022	False		,,,				2504	0.2219				p.T326T		Atlas-SNP	.											.	SMTNL2	57	.	0			c.G978A						PASS	.	G	,	457,3949		24,409,1770	23.0	29.0	27.0		978,546	-7.2	0.0	17	dbSNP_120	27	2415,6179		341,1733,2223	no	coding-synonymous,coding-synonymous	SMTNL2	NM_001114974.1,NM_198501.2	,	365,2142,3993	AA,AG,GG		28.101,10.3722,22.0923	,	326/462,182/318	4498611	2872,10128	2203	4297	6500	SO:0001819	synonymous_variant	342527	exon5			GGAAACGGCGGCC	AK124452	CCDS11048.1, CCDS45583.1	17p13.2	2006-04-26			ENSG00000188176	ENSG00000188176			24764	protein-coding gene	gene with protein product							Standard	NM_001114974		Approved	FLJ42461	uc002fyf.1	Q2TAL5	OTTHUMG00000132938	ENST00000389313.4:c.978G>A	17.37:g.4498611G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_001114974	Q6ZVK6	Silent	SNP	ENST00000389313.4	37	CCDS45583.1																																																																																			G|0.812;A|0.188	0.188	strong		0.682	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421014	29421014	+	Silent	SNP	G	G	C	rs2306934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:29421014G>C	ENST00000261275.4	-	8	980	c.981C>G	c.(979-981)acC>acG	p.T327T		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	327	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						AGCCAGCACTGGTGTTTGGGT	0.537													G|||	690	0.13778	0.1271	0.1196	5008	,	,		18171	0.2103		0.0805	False		,,,				2504	0.1493				p.T327T		Atlas-SNP	.											.	FAM189A1	20	.	0			c.C981G						PASS	.	G		160,1224		9,142,541	60.0	62.0	61.0		981	1.8	0.0	15	dbSNP_100	61	249,2933		12,225,1354	no	coding-synonymous	FAM189A1	NM_015307.1		21,367,1895	CC,CG,GG		7.8253,11.5607,8.9575		327/540	29421014	409,4157	692	1591	2283	SO:0001819	synonymous_variant	23359	exon8			AGCACTGGTGTTT		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.981C>G	15.37:g.29421014G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			G|0.869;C|0.131	0.131	strong		0.537	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
TRIP13	9319	hgsc.bcm.edu	37	5	914664	914664	+	Silent	SNP	T	T	C	rs35725571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:914664T>C	ENST00000166345.3	+	11	1461	c.1105T>C	c.(1105-1107)Ttg>Ctg	p.L369L		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	369					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CGTGTCAAAATTGAGCCTTCT	0.413													T|||	97	0.019369	0.0023	0.0202	5008	,	,		21239	0.005		0.0388	False		,,,				2504	0.0368				p.L369L		Atlas-SNP	.											.	TRIP13	41	.	0			c.T1105C						PASS	.	T		43,4363		0,43,2160	181.0	186.0	185.0		1105	-5.6	0.0	5	dbSNP_126	185	431,8169		20,391,3889	no	coding-synonymous	TRIP13	NM_004237.3		20,434,6049	CC,CT,TT		5.0116,0.9759,3.6445		369/433	914664	474,12532	2203	4300	6503	SO:0001819	synonymous_variant	9319	exon11			TCAAAATTGAGCC	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"""ATPases / AAA-type"""	12307	protein-coding gene	gene with protein product	"""thyroid receptor interacting protein 13"""	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.1105T>C	5.37:g.914664T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	37	CCDS3858.1																																																																																			T|0.968;C|0.032;A|0.000	0.032	strong		0.413	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237	
OR5L2	26338	hgsc.bcm.edu	37	11	55595324	55595324	+	Silent	SNP	C	C	T	rs7102663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55595324C>T	ENST00000378397.1	+	1	630	c.630C>T	c.(628-630)acC>acT	p.T210T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	210						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				AGAGTGTTACCATCATGATCA	0.493										HNSCC(27;0.073)			N|||	551	0.110024	0.2617	0.0865	5008	,	,		20329	0.0		0.1302	False		,,,				2504	0.0143				p.T210T		Atlas-SNP	.											.	OR5L2	135	.	0			c.C630T						PASS	.	C		1135,3265		168,799,1233	242.0	199.0	214.0		630	-0.6	0.2	11	dbSNP_116	214	1200,7388		89,1022,3183	no	coding-synonymous	OR5L2	NM_001004739.1		257,1821,4416	TT,TC,CC		13.973,25.7955,17.9781		210/312	55595324	2335,10653	2200	4294	6494	SO:0001819	synonymous_variant	26338	exon1			TGTTACCATCATG	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.630C>T	11.37:g.55595324C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			C|0.840;T|0.160	0.160	strong		0.493	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
SCN10A	6336	hgsc.bcm.edu	37	3	38798171	38798171	+	Silent	SNP	C	C	T	rs62244070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38798171C>T	ENST00000449082.2	-	9	1283	c.1284G>A	c.(1282-1284)gaG>gaA	p.E428E		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	428					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)			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)	AAACCTCCTGCTCCTTCCGGA	0.498													C|||	1039	0.207468	0.0794	0.1052	5008	,	,		19656	0.372		0.2485	False		,,,				2504	0.2413				p.E428E		Atlas-SNP	.											.	SCN10A	359	.	0			c.G1284A						PASS	.	C		474,3932	222.3+/-239.2	25,424,1754	126.0	124.0	124.0		1284	0.0	1.0	3	dbSNP_129	124	2158,6442	370.4+/-335.9	271,1616,2413	no	coding-synonymous	SCN10A	NM_006514.2		296,2040,4167	TT,TC,CC		25.093,10.7581,20.2368		428/1957	38798171	2632,10374	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon9			CTCCTGCTCCTTC	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.1284G>A	3.37:g.38798171C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.785;T|0.215	0.215	strong		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
MUC4	4585	hgsc.bcm.edu	37	3	195510030	195510030	+	Silent	SNP	C	C	G	rs374297426	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195510030C>G	ENST00000463781.3	-	2	8880	c.8421G>C	c.(8419-8421)tcG>tcC	p.S2807S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2807S	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)	p.S2807S(1)		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)		TGGACACTGACGAAGCGTCGG	0.582													.|||	29	0.00579073	0.0174	0.0014	5008	,	,		6131	0.002		0.001	False		,,,				2504	0.002				p.S2807S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.G8421C						scavenged	.						75.0	46.0	55.0					3																	195510030		683	1492	2175	SO:0001819	synonymous_variant	4585	exon2			CACTGACGAAGCG	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.8421G>C	3.37:g.195510030C>G		Somatic	111	8	0.0720721		WXS	Illumina HiSeq	Phase_I	83	12	0.144578	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NACAD	23148	hgsc.bcm.edu	37	7	45122324	45122324	+	Missense_Mutation	SNP	C	C	A	rs3735493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45122324C>A	ENST00000490531.2	-	2	3474	c.3455G>T	c.(3454-3456)tGc>tTc	p.C1152F		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1152			C -> F (in dbSNP:rs3735493).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGACTCTGGGCAGGAGTCCAG	0.662													C|||	553	0.110423	0.0166	0.1657	5008	,	,		15349	0.121		0.174	False		,,,				2504	0.1217				p.C1152F		Atlas-SNP	.											.	NACAD	44	.	0			c.G3455T						PASS	.						19.0	28.0	25.0					7																	45122324		692	1590	2282	SO:0001583	missense	23148	exon2			TCTGGGCAGGAGT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3455G>T	7.37:g.45122324C>A	ENSP00000420477:p.Cys1152Phe	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	92	22	0.23913	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	262	0.11996336996336997	8	0.016260162601626018	64	0.17679558011049723	59	0.10314685314685315	131	0.17282321899736147	c	14.82	2.649534	0.47362	.	.	ENSG00000136274	ENST00000490531	T	0.12984	2.63	3.08	2.16	0.27623	.	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.80722	P	0.0	D	0.65815	0.995	P	0.57911	0.829	T	0.24333	-1.0163	8	0.42905	T	0.14	-2.9206	9.0995	0.36660	0.0:0.557:0.443:0.0	rs3735493;rs10377947;rs3735493	1152	O15069	NACAD_HUMAN	F	1152	ENSP00000420477:C1152F	ENSP00000420477:C1152F	C	-	2	0	NACAD	45088849	0.000000	0.05858	0.319000	0.25293	0.438000	0.31896	-0.135000	0.10420	0.576000	0.29452	0.290000	0.19541	TGC	C|0.891;A|0.109	0.109	strong		0.662	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ALMS1	7840	hgsc.bcm.edu	37	2	73829362	73829362	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73829362G>A	ENST00000264448.6	+	20	12273	c.12162G>A	c.(12160-12162)cgG>cgA	p.R4054R	ALMS1_ENST00000409009.1_Silent_p.R4012R|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4054	ALMS motif.				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						CTGGGGAGCGGATAAAGCGCC	0.483																																					p.R4054R		Atlas-SNP	.											ALMS1,rectum,carcinoma,+2,1	ALMS1	384	1	0			c.G12162A						PASS	.						50.0	54.0	52.0					2																	73829362		2203	4300	6503	SO:0001819	synonymous_variant	7840	exon20			GGAGCGGATAAAG	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.12162G>A	2.37:g.73829362G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	200	103	0.515	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.483	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ATP10D	57205	hgsc.bcm.edu	37	4	47593283	47593283	+	Missense_Mutation	SNP	G	G	C	rs4145944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:47593283G>C	ENST00000273859.3	+	23	4435	c.4166G>C	c.(4165-4167)aGt>aCt	p.S1389T		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1389			S -> T (in dbSNP:rs4145944). {ECO:0000269|PubMed:10819331}.		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|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(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						AAGTCAGCAAGTTCCTGTGCT	0.448													C|||	1888	0.376997	0.6899	0.4006	5008	,	,		19538	0.123		0.3638	False		,,,				2504	0.2127				p.S1389T		Atlas-SNP	.											.	ATP10D	168	.	0			c.G4166C						PASS	.	C	THR/SER	2708,1698	514.9+/-368.7	840,1028,335	148.0	146.0	147.0		4166	3.6	0.0	4	dbSNP_110	147	3009,5591	664.9+/-402.2	556,1897,1847	yes	missense	ATP10D	NM_020453.3	58	1396,2925,2182	CC,CG,GG		34.9884,38.5384,43.9566	benign	1389/1427	47593283	5717,7289	2203	4300	6503	SO:0001583	missense	57205	exon23			CAGCAAGTTCCTG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.4166G>C	4.37:g.47593283G>C	ENSP00000273859:p.Ser1389Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	888	0.4065934065934066	353	0.717479674796748	159	0.43922651933701656	87	0.1520979020979021	289	0.3812664907651715	C	0.369	-0.935039	0.02340	0.614616	0.349884	ENSG00000145246	ENST00000273859	T	0.37752	1.18	4.45	3.59	0.41128	.	1.477610	0.03813	N	0.266213	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	0.40098	-0.9581	9	0.10902	T	0.67	-0.0353	6.374	0.21497	0.0:0.7135:0.1846:0.1019	rs4145944;rs56510786;rs4145944	1389	Q9P241	AT10D_HUMAN	T	1389	ENSP00000273859:S1389T	ENSP00000273859:S1389T	S	+	2	0	ATP10D	47288040	0.001000	0.12720	0.002000	0.10522	0.255000	0.26057	0.929000	0.28844	0.480000	0.27534	-0.499000	0.04595	AGT	G|0.592;C|0.408	0.408	strong		0.448	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
CNGB3	54714	hgsc.bcm.edu	37	8	87660100	87660100	+	Missense_Mutation	SNP	T	T	C	rs13265557	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	137	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	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	
C6orf136	221545	hgsc.bcm.edu	37	6	30615284	30615284	+	Intron	SNP	G	G	A	rs116816200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30615284G>A	ENST00000376473.5	+	1	231				C6orf136_ENST00000528347.2_5'Flank|C6orf136_ENST00000493705.1_Intron|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000376471.4_Intron|C6orf136_ENST00000293604.6_Silent_p.T92T	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136							mitochondrion (GO:0005739)				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCGCAAGGACGTCGGTCCTCC	0.731													G|||	39	0.00778754	0.0015	0.0173	5008	,	,		11518	0.0		0.0239	False		,,,				2504	0.001				p.T92T		Atlas-SNP	.											.	C6orf136	31	.	0			c.G276A						PASS	.						3.0	5.0	4.0					6																	30615284		633	1490	2123	SO:0001627	intron_variant	221545	exon1			AAGGACGTCGGTC	BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.72+204G>A	6.37:g.30615284G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001161376	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Silent	SNP	ENST00000376473.5	37	CCDS43443.1																																																																																			G|0.986;A|0.014	0.014	strong		0.731	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029	
PTPRT	11122	hgsc.bcm.edu	37	20	41306600	41306600	+	Silent	SNP	A	A	G	rs2425516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:41306600A>G	ENST00000373187.1	-	7	1058	c.1059T>C	c.(1057-1059)gaT>gaC	p.D353D	PTPRT_ENST00000373193.3_Silent_p.D353D|PTPRT_ENST00000373190.1_Silent_p.D353D|PTPRT_ENST00000373184.1_Silent_p.D353D|PTPRT_ENST00000356100.2_Silent_p.D353D|PTPRT_ENST00000373198.4_Silent_p.D353D|PTPRT_ENST00000373201.1_Silent_p.D353D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	353	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CATACTCAACATCGGGGTCCA	0.582													a|||	1927	0.384784	0.4599	0.4337	5008	,	,		16295	0.3462		0.3529	False		,,,				2504	0.3211				p.D353D		Atlas-SNP	.											.	PTPRT	372	.	0			c.T1059C						PASS	.	G	,	1763,2207		402,959,624	128.0	131.0	130.0		1059,1059	-2.8	0.7	20	dbSNP_100	130	2932,5414		527,1878,1768	no	coding-synonymous,coding-synonymous	PTPRT	NM_007050.5,NM_133170.3	,	929,2837,2392	GG,GA,AA		35.1306,44.4081,38.1211	,	353/1442,353/1461	41306600	4695,7621	1985	4173	6158	SO:0001819	synonymous_variant	11122	exon7			CTCAACATCGGGG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1059T>C	20.37:g.41306600A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			A|0.612;G|0.388	0.388	strong		0.582	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:216258213A>G	ENST00000307340.3	-	25	5380	c.4994T>C	c.(4993-4995)aTc>aCc	p.I1665T	RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.I1665T|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1665	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		I -> T (in dbSNP:rs56222536). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|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)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCTTTTTGGATTATCTCTGC	0.328										HNSCC(13;0.011)			A|||	314	0.0626997	0.003	0.0937	5008	,	,		16915	0.0248		0.163	False		,,,				2504	0.0573				p.I1665T		Atlas-SNP	.											.	USH2A	1168	.	0			c.T4994C						PASS	.	A	THR/ILE	124,4278	88.2+/-126.9	2,120,2079	62.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4994	2.6	0.3	1	dbSNP_129	64	1354,7246	258.8+/-282.3	113,1128,3059	yes	missense	USH2A	NM_206933.2	89	115,1248,5138	GG,GA,AA		15.7442,2.8169,11.3675	benign	1665/5203	216258213	1478,11524	2201	4300	6501	SO:0001583	missense	7399	exon25			TTTTGGATTATCT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4994T>C	1.37:g.216258213A>G	ENSP00000305941:p.Ile1665Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	176	0.08058608058608059	2	0.0040650406504065045	40	0.11049723756906077	13	0.022727272727272728	121	0.15963060686015831	A	10.62	1.400689	0.25291	0.028169	0.157442	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.79247	-1.25;-1.25	4.93	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.479810	0.17138	N	0.185577	T	0.00552	0.0018	L	0.56769	1.78	0.47511	P	5.549999999999722E-4	B	0.13145	0.007	B	0.12837	0.008	T	0.14337	-1.0476	9	0.31617	T	0.26	.	4.44	0.11570	0.7008:0.0:0.1555:0.1437	rs56222536	1665	O75445	USH2A_HUMAN	T	1665	ENSP00000305941:I1665T;ENSP00000355910:I1665T	ENSP00000305941:I1665T	I	-	2	0	USH2A	214324836	0.854000	0.29725	0.299000	0.25016	0.951000	0.60555	0.932000	0.28884	0.261000	0.21753	-0.262000	0.10625	ATC	A|0.892;G|0.108	0.108	strong		0.328	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SEPT4	5414	hgsc.bcm.edu	37	17	56598991	56598991	+	Missense_Mutation	SNP	T	T	A	rs17741424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56598991T>A	ENST00000317268.3	-	8	1108	c.932A>T	c.(931-933)gAg>gTg	p.E311V	SEPT4_ENST00000583114.1_Missense_Mutation_p.E164V|SEPT4_ENST00000579371.1_Missense_Mutation_p.E212V|SEPT4_ENST00000412945.3_Missense_Mutation_p.E303V|SEPT4_ENST00000457347.2_Missense_Mutation_p.E326V|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000317256.6_Missense_Mutation_p.E292V|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000580844.1_Missense_Mutation_p.E212V|SEPT4_ENST00000580809.1_3'UTR|SEPT4_ENST00000393086.1_Missense_Mutation_p.E292V	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	311	Septin-type G.		E -> V (in dbSNP:rs17741424).		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)					TCCAAAATGCTCAATCTCCTC	0.522													T|||	218	0.0435304	0.0045	0.0533	5008	,	,		19419	0.0		0.1243	False		,,,				2504	0.0511				p.E326V		Atlas-SNP	.											SEPT4,lymph_node,lymphoid_neoplasm,0,1	SEPT4	48	1	0			c.A977T						PASS	.	T	VAL/GLU,VAL/GLU,,VAL/GLU	101,4305	80.4+/-118.8	1,99,2103	123.0	118.0	120.0		908,932,,875	5.6	1.0	17	dbSNP_123	120	1037,7563	220.1+/-257.9	69,899,3332	yes	missense,missense,utr-3,missense	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	121,121,,121	70,998,5435	AA,AT,TT		12.0581,2.2923,8.7498	possibly-damaging,possibly-damaging,,possibly-damaging	303/471,311/479,,292/460	56598991	1138,11868	2203	4300	6503	SO:0001583	missense	5414	exon9			AAATGCTCAATCT	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.932A>T	17.37:g.56598991T>A	ENSP00000321674:p.Glu311Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	112	0.05128205128205128	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	86	0.11345646437994723	T	8.736	0.917894	0.17982	0.022923	0.120581	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.59	5.59	0.84812	.	0.112753	0.64402	D	0.000011	T	0.00724	0.0024	L	0.41079	1.255	0.09310	P	0.999999833909	P;P;B;P;P	0.48089	0.726;0.905;0.422;0.833;0.768	P;P;P;P;P	0.54140	0.499;0.605;0.499;0.68;0.743	T	0.05616	-1.0874	9	0.62326	D	0.03	.	13.7051	0.62633	0.0:0.0:0.0:1.0	rs17741424;rs52801197;rs17741424	303;326;292;164;311	O43236-3;O43236-4;O43236-2;O43236-5;O43236	.;.;.;.;SEPT4_HUMAN	V	303;325;292;311;292	ENSP00000414779:E303V;ENSP00000321071:E292V;ENSP00000321674:E311V;ENSP00000376801:E292V	ENSP00000321071:E292V	E	-	2	0	SEPT4	53953990	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	5.151000	0.64875	2.116000	0.64780	0.455000	0.32223	GAG	T|0.923;A|0.077	0.077	strong		0.522	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
XDH	7498	hgsc.bcm.edu	37	2	31593230	31593230	+	Silent	SNP	C	C	T	rs557103794		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:31593230C>T	ENST00000379416.3	-	18	2019	c.1971G>A	c.(1969-1971)gcG>gcA	p.A657A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	657					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)	p.A657A(1)		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)	CCTTATCCTTCGCAAAGACTG	0.358																																					p.A657A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											XDH,colon,carcinoma,0,1	XDH	191	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1971A						scavenged	.						84.0	83.0	83.0					2																	31593230		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon18			ATCCTTCGCAAAG	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.1971G>A	2.37:g.31593230C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	3	0.047619	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.358	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64607670	64607670	+	Missense_Mutation	SNP	G	G	A	rs34454471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64607670G>A	ENST00000342711.5	-	5	502	c.503C>T	c.(502-504)cCg>cTg	p.P168L		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CAGCTCGGGCGGGAGACGGTC	0.642													G|||	22	0.00439297	0.0008	0.0014	5008	,	,		17162	0.0		0.0169	False		,,,				2504	0.0031				p.P168L		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C503T						PASS	.	G	LEU/PRO	9,4393	14.3+/-33.2	0,9,2192	66.0	58.0	61.0		503	5.3	0.3	11	dbSNP_126	61	97,8495	52.7+/-113.3	1,95,4200	yes	missense	CDC42BPG	NM_017525.2	98	1,104,6392	AA,AG,GG		1.129,0.2045,0.8158	probably-damaging	168/1552	64607670	106,12888	2201	4296	6497	SO:0001583	missense	55561	exon5			TCGGGCGGGAGAC	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.503C>T	11.37:g.64607670G>A	ENSP00000345133:p.Pro168Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	37	CCDS31601.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	26.7	4.764874	0.90020	0.002045	0.01129	ENSG00000171219	ENST00000342711	T	0.27104	1.69	5.27	5.27	0.74061	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	0.56097	D	0.000037	T	0.37376	0.1001	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51060	-0.8753	10	0.87932	D	0	.	16.7448	0.85469	0.0:0.0:1.0:0.0	rs34454471	168	Q6DT37	MRCKG_HUMAN	L	168	ENSP00000345133:P168L	ENSP00000345133:P168L	P	-	2	0	CDC42BPG	64364246	1.000000	0.71417	0.307000	0.25127	0.819000	0.46315	9.691000	0.98679	2.621000	0.88768	0.655000	0.94253	CCG	G|0.992;A|0.008	0.008	strong		0.642	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
EDNRA	1909	hgsc.bcm.edu	37	4	148461037	148461037	+	Silent	SNP	T	T	C	rs5333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:148461037T>C	ENST00000324300.5	+	6	1484	c.969T>C	c.(967-969)caT>caC	p.H323H	EDNRA_ENST00000511804.1_Silent_p.H98H|EDNRA_ENST00000358556.4_Silent_p.H214H|EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_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	180	0	0		WXS	Illumina HiSeq	Phase_I	166	77	0.463855	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		
HLA-B	3106	hgsc.bcm.edu	37	6	31324925	31324925	+	Missense_Mutation	SNP	A	A	G	rs1050458	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324925A>G	ENST00000412585.2	-	1	39	c.11T>C	c.(10-12)aTg>aCg	p.M4T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	4			M -> T (in dbSNP:rs1050458).		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						TCGGGGCGCCATGACCAGCAT	0.662									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	3968	0.792332	0.7958	0.7277	5008	,	,		9371	0.8452		0.7177	False		,,,				2504	0.8558				p.M4T		Atlas-SNP	.											.	HLA-B	54	.	0			c.T11C						PASS	.						14.0	12.0	13.0					6																	31324925		2097	4079	6176	SO:0001583	missense	3106	exon1	Familial Cancer Database	;Lichen Sclerosis, Familial	GGCGCCATGACCA	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.11T>C	6.37:g.31324925A>G	ENSP00000399168:p.Met4Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1605	0.7348901098901099	363	0.7378048780487805	248	0.6850828729281768	480	0.8391608391608392	514	0.6781002638522428	N	2.606	-0.291885	0.05568	.	.	ENSG00000234745	ENST00000412585	T	0.00634	6.07	3.34	-0.676	0.11361	.	3.232980	0.02078	U	0.052113	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44065	-0.9352	8	0.33940	T	0.23	.	3.3491	0.07146	0.5554:0.2072:0.2374:0.0	rs1050458;rs2308331;rs3175988;rs9266205	4	P01889	1B07_HUMAN	T	4	ENSP00000399168:M4T	ENSP00000399168:M4T	M	-	2	0	HLA-B	31432904	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.137000	0.03219	-0.217000	0.10033	-1.590000	0.00845	ATG	G|0.684;C|0.000;A|0.315	0.684	strong		0.662	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
CLEC4F	165530	hgsc.bcm.edu	37	2	71036482	71036482	+	Missense_Mutation	SNP	T	T	C	rs2287101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71036482T>C	ENST00000272367.2	-	7	1767	c.1691A>G	c.(1690-1692)aAg>aGg	p.K564R	CLEC4F_ENST00000426626.1_Intron	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	564	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> R (in dbSNP:rs2287101). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						AATAATATACTTTCTGAGTGG	0.527													C|||	915	0.182708	0.3601	0.085	5008	,	,		21488	0.2391		0.0577	False		,,,				2504	0.0828				p.K564R	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.A1691G						PASS	.	C	ARG/LYS	1282,3124	699.9+/-406.5	184,914,1105	66.0	65.0	65.0		1691	0.9	0.0	2	dbSNP_100	65	361,8239	803.2+/-407.3	12,337,3951	yes	missense	CLEC4F	NM_173535.2	26	196,1251,5056	CC,CT,TT		4.1977,29.0967,12.6326	benign	564/590	71036482	1643,11363	2203	4300	6503	SO:0001583	missense	165530	exon7			ATATACTTTCTGA	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1691A>G	2.37:g.71036482T>C	ENSP00000272367:p.Lys564Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	412	0.18864468864468864	193	0.39227642276422764	42	0.11602209944751381	127	0.22202797202797203	50	0.06596306068601583	C	0.009	-1.832717	0.00579	0.290967	0.041977	ENSG00000152672	ENST00000272367	T	0.01705	4.68	2.49	0.876	0.19138	C-type lectin (2);	.	.	.	.	T	0.00012	0.0000	N	0.00392	-1.555	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21143	-1.0254	8	0.25751	T	0.34	.	4.9349	0.13935	0.0:0.5549:0.0:0.4451	rs2287101;rs57410762;rs2287101	564	Q8N1N0	CLC4F_HUMAN	R	564	ENSP00000272367:K564R	ENSP00000272367:K564R	K	-	2	0	CLEC4F	70889990	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.471000	0.06631	-0.054000	0.13266	-0.684000	0.03749	AAG	T|0.833;C|0.167	0.167	strong		0.527	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
PTPRU	10076	hgsc.bcm.edu	37	1	29631909	29631909	+	Missense_Mutation	SNP	A	A	G	rs2235937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000460170.2_Missense_Mutation_p.N930S|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000323874.8_Missense_Mutation_p.N930S|PTPRU_ENST00000373779.3_Missense_Mutation_p.N930S	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	61	28	0.459016	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		
TRPM5	29850	hgsc.bcm.edu	37	11	2432964	2432964	+	Silent	SNP	T	T	C	rs2074234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2432964T>C	ENST00000155858.6	-	17	2516	c.2508A>G	c.(2506-2508)acA>acG	p.T836T	TRPM5_ENST00000528453.1_Silent_p.T836T|TRPM5_ENST00000533060.1_Silent_p.T836T|TRPM5_ENST00000452833.1_Silent_p.T838T	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGGCGAGGACTGTGCGGCCAG	0.632													T|||	1658	0.33107	0.2027	0.366	5008	,	,		16312	0.4643		0.3509	False		,,,				2504	0.3221				p.T836T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.A2508G						PASS	.	T		1061,3343	380.6+/-323.8	126,809,1267	59.0	57.0	58.0		2508	-8.6	0.0	11	dbSNP_96	58	3014,5584	461.1+/-365.4	542,1930,1827	no	coding-synonymous	TRPM5	NM_014555.3		668,2739,3094	CC,CT,TT		35.0547,24.0917,31.3413		836/1166	2432964	4075,8927	2202	4299	6501	SO:0001819	synonymous_variant	29850	exon17			GAGGACTGTGCGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2508A>G	11.37:g.2432964T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_014555		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			C|0.328;N|0.001;T|0.671	0.328	strong		0.632	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
DDX46	9879	hgsc.bcm.edu	37	5	134126198	134126198	+	Silent	SNP	T	T	C	rs34125601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:134126198T>C	ENST00000354283.4	+	13	1717	c.1582T>C	c.(1582-1584)Tta>Cta	p.L528L	DDX46_ENST00000452510.2_Silent_p.L528L|DDX46_ENST00000509178.1_3'UTR			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	528	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATATGTTGTTTTAGATGAAGC	0.303													T|||	21	0.00419329	0.0015	0.0115	5008	,	,		18851	0.0		0.0109	False		,,,				2504	0.0				p.L528L	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.T1582C						PASS	.	T		19,4387	25.3+/-52.1	0,19,2184	92.0	91.0	91.0		1582	3.6	1.0	5	dbSNP_126	91	133,8465	66.3+/-128.7	3,127,4169	no	coding-synonymous	DDX46	NM_014829.2		3,146,6353	CC,CT,TT		1.5469,0.4312,1.1689		528/1032	134126198	152,12852	2203	4299	6502	SO:0001819	synonymous_variant	9879	exon13			GTTGTTTTAGATG		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"""DEAD-boxes"""	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1582T>C	5.37:g.134126198T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	37	CCDS34240.1																																																																																			T|0.989;C|0.011	0.011	strong		0.303	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829	
DNAJC16	23341	hgsc.bcm.edu	37	1	15892415	15892415	+	Splice_Site	SNP	A	A	C	rs2236215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15892415A>C	ENST00000375847.3	+	12	1764	c.1600A>C	c.(1600-1602)Agg>Cgg	p.R534R	DNAJC16_ENST00000375838.1_Splice_Site_p.R534R|DNAJC16_ENST00000375849.1_Splice_Site_p.R534R|DNAJC16_ENST00000483270.1_3'UTR|RP4-680D5.8_ENST00000606186.1_RNA	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	534					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TGGTTTTAGGAGGGAAATGAT	0.408													C|||	1443	0.288139	0.6082	0.219	5008	,	,		17020	0.0565		0.2326	False		,,,				2504	0.2004				p.R534R		Atlas-SNP	.											.	DNAJC16	59	.	0			c.A1600C						PASS	.	C		2537,1869	540.2+/-375.5	739,1059,405	276.0	305.0	295.0		1600	5.0	1.0	1	dbSNP_98	295	2129,6471	715.6+/-406.1	253,1623,2424	yes	coding-synonymous-near-splice	DNAJC16	NM_015291.2		992,2682,2829	CC,CA,AA		24.7558,42.4194,35.8757		534/783	15892415	4666,8340	2203	4300	6503	SO:0001630	splice_region_variant	23341	exon12			TTTAGGAGGGAAA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"""Heat shock proteins / DNAJ (HSP40)"""	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1599-1A>C	1.37:g.15892415A>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_015291	Q68D57|Q86X32|Q8N5P4	Silent	SNP	ENST00000375847.3	37	CCDS30606.1																																																																																			A|0.668;C|0.332	0.332	strong		0.408	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291	Silent
DYRK2	8445	hgsc.bcm.edu	37	12	68052178	68052178	+	Silent	SNP	G	G	T	rs3741644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:68052178G>T	ENST00000344096.3	+	3	1904	c.1491G>T	c.(1489-1491)ggG>ggT	p.G497G	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.G424G	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	497	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		GAGAGTGGGGGAACGCGCTGA	0.582													G|||	2559	0.510982	0.3192	0.6037	5008	,	,		18694	0.6052		0.5726	False		,,,				2504	0.544				p.G497G		Atlas-SNP	.											.	DYRK2	63	.	0			c.G1491T						PASS	.	G	,	1563,2843	488.1+/-361.1	271,1021,911	59.0	62.0	61.0		1272,1491	1.0	1.0	12	dbSNP_107	61	5031,3569	624.6+/-397.6	1493,2045,762	no	coding-synonymous,coding-synonymous	DYRK2	NM_003583.3,NM_006482.2	,	1764,3066,1673	TT,TG,GG		41.5,35.4744,49.3003	,	424/529,497/602	68052178	6594,6412	2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			GTGGGGGAACGCG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1491G>T	12.37:g.68052178G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																			C|0.000;G|0.472;T|0.528	0.528	strong		0.582	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
HECW1	23072	hgsc.bcm.edu	37	7	43483981	43483981	+	Missense_Mutation	SNP	G	G	C	rs61756574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:43483981G>C	ENST00000395891.2	+	11	1815	c.1210G>C	c.(1210-1212)Ggt>Cgt	p.G404R	HECW1_ENST00000453890.1_Missense_Mutation_p.G404R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	404				G -> R (in Ref. 1; BAA20780, 4; AAI51228 and 5; BAB13352). {ECO:0000305}.	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						TGTCCCCGATGGTCCAGGGAA	0.602													G|||	467	0.0932508	0.0091	0.1081	5008	,	,		20248	0.0089		0.1909	False		,,,				2504	0.183				p.G404R		Atlas-SNP	.											HECW1_ENST00000395891,NS,carcinoma,-2,2	HECW1	540	2	0			c.G1210C						PASS	.	G	ARG/GLY	136,4040		1,134,1953	43.0	47.0	46.0		1210	-3.7	0.0	7	dbSNP_129	46	1641,6813		161,1319,2747	yes	missense	HECW1	NM_015052.3	125	162,1453,4700	CC,CG,GG		19.4109,3.2567,14.0697	benign	404/1607	43483981	1777,10853	2088	4227	6315	SO:0001583	missense	23072	exon11			CCCGATGGTCCAG	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.1210G>C	7.37:g.43483981G>C	ENSP00000379228:p.Gly404Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	210	0.09615384615384616	6	0.012195121951219513	50	0.13812154696132597	5	0.008741258741258742	149	0.19656992084432717	G	12.52	1.963650	0.34659	0.032567	0.194109	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.30448	1.55;1.53	5.4	-3.65	0.04502	.	4.093410	0.00575	N	0.000304	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.23735	0.09;0.09	B;B	0.20384	0.021;0.029	T	0.13548	-1.0505	9	0.39692	T	0.17	.	4.0835	0.09937	0.4797:0.1008:0.3227:0.0968	rs61756574	404;404	B4DH42;Q76N89	.;HECW1_HUMAN	R	404	ENSP00000379228:G404R;ENSP00000407774:G404R	ENSP00000265522:G404R	G	+	1	0	HECW1	43450506	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.043000	0.12043	-1.119000	0.02958	0.655000	0.94253	GGT	G|0.872;C|0.128	0.128	strong		0.602	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
HECTD1	25831	hgsc.bcm.edu	37	14	31647439	31647439	+	Silent	SNP	T	T	C	rs33983486	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31647439T>C	ENST00000399332.1	-	3	650	c.162A>G	c.(160-162)ttA>ttG	p.L54L	HECTD1_ENST00000553700.1_Silent_p.L54L	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	54					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AAAGGGCTGGTAAGAAAGTGC	0.353													T|||	248	0.0495208	0.0061	0.0591	5008	,	,		16287	0.0		0.1372	False		,,,				2504	0.0624				p.L54L		Atlas-SNP	.											.	HECTD1	159	.	0			c.A162G						PASS	.	T		91,3615		2,87,1764	66.0	61.0	63.0		162	2.6	1.0	14	dbSNP_126	63	1010,7168		50,910,3129	no	coding-synonymous	HECTD1	NM_015382.2		52,997,4893	CC,CT,TT		12.3502,2.4555,9.2646		54/2611	31647439	1101,10783	1853	4089	5942	SO:0001819	synonymous_variant	25831	exon3			GGCTGGTAAGAAA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.162A>G	14.37:g.31647439T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			T|0.918;C|0.082	0.082	strong		0.353	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
KRTAP9-3	83900	hgsc.bcm.edu	37	17	39388811	39388811	+	Missense_Mutation	SNP	C	C	A	rs112082369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39388811C>A	ENST00000411528.2	+	1	97	c.58C>A	c.(58-60)Cag>Aag	p.Q20K		NM_031962.2	NP_114168.1	Q9BYQ3	KRA93_HUMAN	keratin associated protein 9-3	20	16 X 5 AA repeats of C-C-[RQVSHE]-[SPTN]- [TASPI].					keratin filament (GO:0045095)				breast(1)|endometrium(3)|lung(2)|ovary(1)|prostate(1)	8		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CACCTGCTGGCAGCCCACCAC	0.602													.|||	979	0.195487	0.1505	0.1354	5008	,	,		17008	0.3194		0.1918	False		,,,				2504	0.1748				p.Q20K		Atlas-SNP	.											.	KRTAP9-3	11	.	0			c.C58A						PASS	.	C	LYS/GLN	756,3454		177,402,1526	71.0	79.0	76.0		58	-2.4	0.0	17	dbSNP_132	76	1565,7035		136,1293,2871	no	missense	KRTAP9-3	NM_031962.2	53	313,1695,4397	AA,AC,CC		18.1977,17.9572,18.1187		20/160	39388811	2321,10489	2105	4300	6405	SO:0001583	missense	83900	exon1			TGCTGGCAGCCCA	AJ406947	CCDS11385.1	17q21.2	2013-06-25			ENSG00000204873	ENSG00000204873		"""Keratin associated proteins"""	16927	protein-coding gene	gene with protein product						11279113	Standard	NM_031962		Approved	KAP9.3	uc021txg.1	Q9BYQ3	OTTHUMG00000133427	ENST00000411528.2:c.58C>A	17.37:g.39388811C>A	ENSP00000392189:p.Gln20Lys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_031962		Missense_Mutation	SNP	ENST00000411528.2	37	CCDS11385.1	375	0.1717032967032967	65	0.13211382113821138	46	0.1270718232044199	154	0.2692307692307692	110	0.14511873350923482	.	0.003	-2.481142	0.00165	0.179572	0.181977	ENSG00000204873	ENST00000411528	T	0.01455	4.87	1.22	-2.44	0.06502	.	.	.	.	.	T	0.00012	0.0000	L	0.43598	1.365	0.80722	P	0.0	.	.	.	.	.	.	T	0.42120	-0.9470	6	0.19147	T	0.46	.	5.0219	0.14365	0.2322:0.5773:0.0:0.1905	.	.	.	.	K	20	ENSP00000392189:Q20K	ENSP00000392189:Q20K	Q	+	1	0	KRTAP9-3	36642337	0.784000	0.28713	0.047000	0.18901	0.087000	0.18053	-0.050000	0.11904	-2.202000	0.00745	-1.432000	0.01085	CAG	C|0.828;A|0.172	0.172	strong		0.602	KRTAP9-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257290.1		
KIAA1671	85379	hgsc.bcm.edu	37	22	25586744	25586744	+	Silent	SNP	T	T	G	rs2330986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:25586744T>G	ENST00000406486.4	+	13	5805	c.5418T>G	c.(5416-5418)gtT>gtG	p.V1806V	KIAA1671_ENST00000358431.3_Silent_p.V1806V|KIAA1671_ENST00000401395.1_Silent_p.V313V			Q9BY89	K1671_HUMAN	KIAA1671	1806										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						AGAACCAAGTTTGACCAGGTA	0.527													T|||	192	0.0383387	0.0023	0.0403	5008	,	,		17474	0.0		0.0736	False		,,,				2504	0.089				p.V1806V		Atlas-SNP	.											.	KIAA1671	28	.	0			c.T5418G						PASS	.	T		25,1359		0,25,667	114.0	96.0	101.0		5418	-0.9	1.0	22	dbSNP_100	101	304,2878		18,268,1305	no	coding-synonymous	KIAA1671	NM_001145206.1		18,293,1972	GG,GT,TT		9.5537,1.8064,7.2054		1806/1807	25586744	329,4237	692	1591	2283	SO:0001819	synonymous_variant	85379	exon10			CCAAGTTTGACCA		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.5418T>G	22.37:g.25586744T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			T|0.952;G|0.048	0.048	strong		0.527	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
CCP110	9738	hgsc.bcm.edu	37	16	19548030	19548030	+	Missense_Mutation	SNP	T	T	A	rs11645625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19548030T>A	ENST00000381396.5	+	4	1286	c.1039T>A	c.(1039-1041)Ttt>Att	p.F347I	CCP110_ENST00000396208.2_Missense_Mutation_p.F347I|CCP110_ENST00000396212.2_Missense_Mutation_p.F347I	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	347			F -> I (in dbSNP:rs11645625). {ECO:0000269|PubMed:9455477}.		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						TATTCCCACTTTTGTTACCGA	0.383													T|||	68	0.0135783	0.0008	0.0259	5008	,	,		21203	0.001		0.0457	False		,,,				2504	0.002				p.F347I		Atlas-SNP	.											.	CCP110	57	.	0			c.T1039A						PASS	.	T	ILE/PHE,ILE/PHE	28,4366	34.3+/-65.2	0,28,2169	44.0	43.0	43.0		1039,1039	5.0	1.0	16	dbSNP_120	43	372,8228	119.9+/-179.2	10,352,3938	yes	missense,missense	CCP110	NM_001199022.1,NM_014711.4	21,21	10,380,6107	AA,AT,TT		4.3256,0.6372,3.0783	benign,benign	347/1013,347/992	19548030	400,12594	2197	4300	6497	SO:0001583	missense	9738	exon4			CCCACTTTTGTTA	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.1039T>A	16.37:g.19548030T>A	ENSP00000370803:p.Phe347Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	T	12.20	1.867965	0.32977	0.006372	0.043256	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.16743	2.32;2.32;2.32	6.07	4.98	0.66077	.	0.460249	0.25258	N	0.031970	T	0.02688	0.0081	L	0.44542	1.39	0.24544	N	0.994054	B;B	0.14438	0.01;0.01	B;B	0.13407	0.009;0.009	T	0.24870	-1.0148	10	0.35671	T	0.21	-15.0891	3.2466	0.06799	0.1357:0.0775:0.1413:0.6455	rs11645625;rs52811325;rs11645625	347;347	O43303;O43303-2	CP110_HUMAN;.	I	347	ENSP00000379515:F347I;ENSP00000370803:F347I;ENSP00000379511:F347I	ENSP00000370803:F347I	F	+	1	0	CCP110	19455531	0.964000	0.33143	0.997000	0.53966	0.995000	0.86356	1.608000	0.36847	1.126000	0.42016	0.533000	0.62120	TTT	T|0.974;A|0.026	0.026	strong		0.383	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
ABCC8	6833	hgsc.bcm.edu	37	11	17414570	17414570	+	Missense_Mutation	SNP	C	C	T	rs8192690	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17414570C>T	ENST00000389817.3	-	39	4782	c.4714G>A	c.(4714-4716)Gtc>Atc	p.V1572I	ABCC8_ENST00000302539.4_Missense_Mutation_p.V1573I			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1572	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		V -> I (in dbSNP:rs8192690). {ECO:0000269|PubMed:10447255, ECO:0000269|PubMed:16429405, ECO:0000269|PubMed:8923011}.		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)	GAGGCGAAGACGCTGTCCTTC	0.587													C|||	156	0.0311502	0.0272	0.0331	5008	,	,		15940	0.001		0.0527	False		,,,				2504	0.044				p.V1572I		Atlas-SNP	.											.	ABCC8	170	.	0			c.G4714A						PASS	.	C	ILE/VAL	154,4246	105.6+/-144.1	3,148,2049	118.0	97.0	104.0		4714	1.3	0.9	11	dbSNP_117	104	566,8020	153.1+/-207.6	23,520,3750	yes	missense	ABCC8	NM_000352.3	29	26,668,5799	TT,TC,CC		6.5921,3.5,5.5444	benign	1572/1582	17414570	720,12266	2200	4293	6493	SO:0001583	missense	6833	exon39			CGAAGACGCTGTC	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.4714G>A	11.37:g.17414570C>T	ENSP00000374467:p.Val1572Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	69	0.03159340659340659	14	0.028455284552845527	14	0.03867403314917127	1	0.0017482517482517483	40	0.052770448548812667	C	6.000	0.368388	0.11352	0.035	0.065921	ENSG00000006071	ENST00000389817;ENST00000302539	D;D	0.90385	-2.66;-2.66	5.2	1.28	0.21552	ABC transporter-like (1);	0.211847	0.39985	N	0.001201	T	0.24624	0.0597	N	0.16743	0.435	0.47374	D	0.999403	B	0.12013	0.005	B	0.06405	0.002	T	0.50162	-0.8860	10	0.06891	T	0.86	.	8.3464	0.32275	0.0:0.6252:0.0:0.3748	rs8192690;rs56698850;rs8192690	1572	Q09428	ABCC8_HUMAN	I	1572;1573	ENSP00000374467:V1572I;ENSP00000303960:V1573I	ENSP00000303960:V1573I	V	-	1	0	ABCC8	17371146	0.101000	0.21875	0.865000	0.33974	0.959000	0.62525	0.663000	0.25053	0.227000	0.20999	-0.258000	0.10820	GTC	C|0.947;T|0.053	0.053	strong		0.587	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
CDRT15	146822	hgsc.bcm.edu	37	17	14140081	14140081	+	Nonsense_Mutation	SNP	G	G	A	rs11651890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:14140081G>A	ENST00000420162.2	-	1	85	c.70C>T	c.(70-72)Cga>Tga	p.R24*	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)		CGGCATCGTCGGAAAAGGCTC	0.582																																					p.R24X		Atlas-SNP	.											.	CDRT15	20	.	0			c.C70T						PASS	.						52.0	49.0	50.0					17																	14140081		2203	4298	6501	SO:0001587	stop_gained	146822	exon1			ATCGTCGGAAAAG	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.70C>T	17.37:g.14140081G>A	ENSP00000402355:p.Arg24*	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	18	0.105263	NM_001007530	B2RUU5	Nonsense_Mutation	SNP	ENST00000420162.2	37	CCDS32569.1	214	0.09798534798534798	26	0.052845528455284556	34	0.09392265193370165	76	0.13286713286713286	78	0.10290237467018469	G	10.90	1.482013	0.26598	.	.	ENSG00000223510	ENST00000420162	.	.	.	0.675	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	rs11651890	.	.	.	X	24	.	ENSP00000402355:R24X	R	-	1	2	CDRT15	14080806	0.951000	0.32395	0.000000	0.03702	0.003000	0.03518	0.838000	0.27572	-1.643000	0.01519	-1.082000	0.02213	CGA	G|0.908;A|0.092	0.092	strong		0.582	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
GDPD4	220032	hgsc.bcm.edu	37	11	76944178	76944178	+	Silent	SNP	G	G	A	rs17751194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76944178G>A	ENST00000376217.2	-	13	1531	c.1281C>T	c.(1279-1281)acC>acT	p.T427T	GDPD4_ENST00000315938.4_Silent_p.T427T			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	427	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						GCTCATTGACGGTGTATACGT	0.443													G|||	30	0.00599042	0.0	0.0058	5008	,	,		20824	0.0		0.0179	False		,,,				2504	0.0082				p.T427T		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1281T						PASS	.	G		15,4385	22.3+/-47.3	1,13,2186	176.0	154.0	162.0		1281	-5.5	0.0	11	dbSNP_123	162	136,8448	68.4+/-130.8	2,132,4158	no	coding-synonymous	GDPD4	NM_182833.1		3,145,6344	AA,AG,GG		1.5843,0.3409,1.163		427/521	76944178	151,12833	2200	4292	6492	SO:0001819	synonymous_variant	220032	exon13			ATTGACGGTGTAT	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.1281C>T	11.37:g.76944178G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_182833	Q7Z5B0	Silent	SNP	ENST00000376217.2	37																																																																																				G|0.988;A|0.012	0.012	strong		0.443	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
RABL6	55684	hgsc.bcm.edu	37	9	139732462	139732462	+	Silent	SNP	C	C	T	rs2811740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139732462C>T	ENST00000311502.7	+	10	1511	c.1275C>T	c.(1273-1275)agC>agT	p.S425S	RABL6_ENST00000432842.2_Silent_p.S387S|RABL6_ENST00000371663.4_Silent_p.S426S|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371675.3_Silent_p.S310S			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	425					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										AGCAGGACAGCGACAGGTGAG	0.677													C|||	515	0.102835	0.0091	0.2176	5008	,	,		15137	0.0119		0.2097	False		,,,				2504	0.1319				p.S426S		Atlas-SNP	.											C9orf86_ENST00000371663,NS,carcinoma,0,2	.	.	2	0			c.C1278T						PASS	.	C	,	125,3785		2,121,1832	14.0	15.0	14.0		1278,1275	-5.6	0.9	9	dbSNP_100	14	1552,6656		155,1242,2707	no	coding-synonymous,coding-synonymous	C9orf86	NM_001173988.1,NM_024718.4	,	157,1363,4539	TT,TC,CC		18.9084,3.1969,13.8389	,	426/731,425/730	139732462	1677,10441	1955	4104	6059	SO:0001819	synonymous_variant	55684	exon10			GGACAGCGACAGG	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1275C>T	9.37:g.139732462C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Silent	SNP	ENST00000311502.7	37	CCDS48058.1																																																																																			C|0.891;T|0.109	0.109	strong		0.677	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
TMEM63B	55362	hgsc.bcm.edu	37	6	44119604	44119604	+	Silent	SNP	C	C	T	rs139920210		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44119604C>T	ENST00000259746.9	+	19	1878	c.1695C>T	c.(1693-1695)aaC>aaT	p.N565N	TMEM63B_ENST00000323267.6_Silent_p.N565N			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	565					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	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;0.0215)			TGCCCGACAACGGCGCCTTCT	0.632											OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		16614	0.0		0.001	False		,,,				2504	0.0				p.N565N		Atlas-SNP	.											.	TMEM63B	77	.	0			c.C1695T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	134.0	104.0	115.0		1695	4.2	1.0	6	dbSNP_134	115	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TMEM63B	NM_018426.1		0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076		565/833	44119604	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon19			CGACAACGGCGCC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1695C>T	6.37:g.44119604C>T		Somatic	130	0	0	921	WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.87	1.472484	0.26423	2.27E-4	0.001512	ENSG00000137216	ENST00000371893	.	.	.	5.01	4.15	0.48705	.	.	.	.	.	T	0.42245	0.1194	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42599	-0.9442	4	.	.	.	.	6.4801	0.22057	0.0:0.7235:0.0:0.2765	.	.	.	.	M	494	.	.	T	+	2	0	TMEM63B	44227582	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	0.365000	0.20348	1.349000	0.45751	0.460000	0.39030	ACG	C|0.999;T|0.001	0.001	strong		0.632	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
MUC16	94025	hgsc.bcm.edu	37	19	9076929	9076929	+	Missense_Mutation	SNP	T	T	G	rs2547075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076929T>G	ENST00000397910.4	-	3	10720	c.10517A>C	c.(10516-10518)aAa>aCa	p.K3506T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3507	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						AATGTCACTTTTCACTGCACT	0.512													G|||	1243	0.248203	0.2005	0.2118	5008	,	,		24537	0.249		0.3121	False		,,,				2504	0.272				p.K3506T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A10517C						PASS	.	G	THR/LYS	895,3329		104,687,1321	147.0	140.0	142.0		10517	0.6	0.0	19	dbSNP_100	142	2436,6014		352,1732,2141	yes	missense	MUC16	NM_024690.2	78	456,2419,3462	GG,GT,TT		28.8284,21.1884,26.2822	benign	3506/14508	9076929	3331,9343	2112	4225	6337	SO:0001583	missense	94025	exon3			TCACTTTTCACTG	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.10517A>C	19.37:g.9076929T>G	ENSP00000381008:p.Lys3506Thr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	192	91	0.473958	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	g	3.061	-0.193142	0.06259	0.211884	0.288284	ENSG00000181143	ENST00000397910	T	0.02763	4.17	1.66	0.596	0.17496	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.49011	-0.8983	8	0.87932	D	0	.	2.3389	0.04254	0.1874:0.0:0.5152:0.2974	rs2547075;rs17516118;rs60765070	3506	B5ME49	.	T	3506	ENSP00000381008:K3506T	ENSP00000381008:K3506T	K	-	2	0	MUC16	8937929	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.092000	0.11129	-0.065000	0.13021	-0.750000	0.03501	AAA	T|0.743;G|0.257	0.257	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124210782	124210782	+	Silent	SNP	T	T	C	rs1399961	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124210782T>C	ENST00000330342.3	+	5	719	c.471T>C	c.(469-471)agT>agC	p.S157S		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	157					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		CCTTAGAGAGTGATTCTTTGT	0.418													C|||	3755	0.7498	0.7027	0.7709	5008	,	,		20389	0.9474		0.6233	False		,,,				2504	0.7249				p.S157S		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.T471C						PASS	.	C		2984,1422	464.5+/-353.9	1027,930,246	106.0	106.0	106.0		471	-11.8	0.0	12	dbSNP_88	106	5338,3262	490.3+/-372.8	1674,1990,636	no	coding-synonymous	ATP6V0A2	NM_012463.3		2701,2920,882	CC,CT,TT		37.9302,32.2742,36.0141		157/857	124210782	8322,4684	2203	4300	6503	SO:0001819	synonymous_variant	23545	exon5			AGAGAGTGATTCT	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.471T>C	12.37:g.124210782T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_012463	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																			T|0.317;C|0.683	0.683	strong		0.418	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
HLA-B	3106	hgsc.bcm.edu	37	6	31324666	31324666	+	Missense_Mutation	SNP	A	A	C	rs713031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324666A>C	ENST00000412585.2	-	2	170	c.142T>G	c.(142-144)Tca>Gca	p.S48A		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				.|||	2486	0.496406	0.4871	0.4597	5008	,	,		9910	0.5724		0.3728	False		,,,				2504	0.5838				p.S48A		Atlas-SNP	.											.	HLA-B	54	.	0			c.T142G						PASS	.	A	ALA/SER	1957,2285		653,651,817	28.0	22.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	142	-6.4	0.0	6	dbSNP_86	24	3187,5047		1002,1183,1932	no	missense	HLA-B	NM_005514.6	99	1655,1834,2749	CC,CA,AA		38.7054,46.1339,41.2312		48/363	31324666	5144,7332	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>G	6.37:g.31324666A>C	ENSP00000399168:p.Ser48Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	33	30	0.909091	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1316	0.6025641025641025	265	0.5386178861788617	205	0.5662983425414365	439	0.7674825174825175	407	0.5369393139841688	N	0.012	-1.682920	0.00745	0.461339	0.387054	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00007	9.65;9.65	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	U	0.141997	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12156	0.003;0.002;0.007	T	0.24657	-1.0154	8	0.02654	T	1	.	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;.	A	48;59	ENSP00000399168:S48A;ENSP00000405931:S59A	ENSP00000399168:S48A	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	0.549	strong		0.692	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ATXN7L3B	552889	hgsc.bcm.edu	37	12	74932159	74932159	+	Silent	SNP	G	G	C	rs590352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:74932159G>C	ENST00000519948.2	+	1	609	c.267G>C	c.(265-267)ctG>ctC	p.L89L	RP11-56G10.2_ENST00000550926.1_RNA	NM_001136262.1	NP_001129734.1	Q96GX2	A7L3B_HUMAN	ataxin 7-like 3B	89																	ATCAGCAGCTGCAGCGCTCAC	0.542													G|||	3352	0.669329	0.2383	0.7824	5008	,	,		15790	0.9058		0.7793	False		,,,				2504	0.8149				p.L89L		Atlas-SNP	.											.	ATXN7L3B	1	.	0			c.G267C						PASS	.	G		430,954		74,282,336	24.0	24.0	24.0		267	4.1	1.0	12	dbSNP_83	24	2402,780		901,600,90	no	coding-synonymous	ATXN7L3B	NM_001136262.1		975,882,426	CC,CG,GG		24.5129,31.0694,37.9763		89/98	74932159	2832,1734	692	1591	2283	SO:0001819	synonymous_variant	552889	exon1			GCAGCTGCAGCGC		CCDS53815.1	12q21	2013-02-15			ENSG00000253719	ENSG00000253719			37931	protein-coding gene	gene with protein product		615579					Standard	NM_001136262		Approved		uc001sxd.4	Q96GX2	OTTHUMG00000163936	ENST00000519948.2:c.267G>C	12.37:g.74932159G>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001136262		Silent	SNP	ENST00000519948.2	37	CCDS53815.1																																																																																			G|0.316;C|0.684	0.684	strong		0.542	ATXN7L3B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376473.1	NM_001136262	
POTEF	728378	hgsc.bcm.edu	37	2	130832598	130832598	+	Missense_Mutation	SNP	C	C	T	rs3948036		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:130832598C>T	ENST00000409914.2	-	17	2846	c.2447G>A	c.(2446-2448)cGc>cAc	p.R816H	POTEF_ENST00000357462.5_Missense_Mutation_p.R816H	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	816	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.R816H(1)		breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CATCTTCTCGCGGTTGGCCTT	0.592																																					p.R816H		Atlas-SNP	.											POTEF,trunk,malignant_melanoma,0,3	POTEF	140	3	1	Substitution - Missense(1)	skin(1)	c.G2447A						scavenged	.						118.0	129.0	125.0					2																	130832598		2203	4300	6503	SO:0001583	missense	728378	exon17			TTCTCGCGGTTGG	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.2447G>A	2.37:g.130832598C>T	ENSP00000386786:p.Arg816His	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	233	14	0.0600858	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	16.87	3.242651	0.58995	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.97066	-4.23;-4.23	.	.	.	Actin/actin-like conserved site (1);	.	.	.	.	D	0.98817	0.9601	H	0.99299	4.505	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.96667	0.9493	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	rs3948036	816	A5A3E0	POTEF_HUMAN	H	816	ENSP00000350052:R816H;ENSP00000386786:R816H	ENSP00000350052:R816H	R	-	2	0	POTEF	130549068	1.000000	0.71417	0.246000	0.24233	0.249000	0.25844	5.228000	0.65310	0.119000	0.18210	0.121000	0.15741	CGC	.	.	weak		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
CECR6	27439	hgsc.bcm.edu	37	22	17600977	17600977	+	Silent	SNP	G	G	A	rs5994165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:17600977G>A	ENST00000331437.3	-	1	1166	c.1041C>T	c.(1039-1041)ttC>ttT	p.F347F	CECR6_ENST00000399875.1_5'UTR|AC006946.15_ENST00000441544.1_5'Flank	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	347										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		CCGTGGTGCCGAAGGGCGCGC	0.667													g|||	2388	0.476837	0.4856	0.5101	5008	,	,		12678	0.495		0.3847	False		,,,				2504	0.5174				p.F347F		Atlas-SNP	.											.	CECR6	11	.	0			c.C1041T						PASS	.		,	2078,2324		511,1056,634	57.0	44.0	49.0		,1041	-2.8	1.0	22	dbSNP_114	49	3195,5397		588,2019,1689	no	utr-5,coding-synonymous	CECR6	NM_001163079.1,NM_031890.3	,	1099,3075,2323	AA,AG,GG		37.1858,47.2058,40.5803	,	,347/579	17600977	5273,7721	2201	4296	6497	SO:0001819	synonymous_variant	27439	exon1			GGTGCCGAAGGGC	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1041C>T	22.37:g.17600977G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_031890	A8MYY1	Silent	SNP	ENST00000331437.3	37	CCDS13740.1																																																																																			G|0.559;A|0.441	0.441	strong		0.667	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863092	30863092	+	Silent	SNP	C	C	T	rs12467646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:30863092C>T	ENST00000309052.4	+	7	1061	c.852C>T	c.(850-852)caC>caT	p.H284H	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000540623.1_Silent_p.H246H|LCLAT1_ENST00000379509.3_Silent_p.H246H	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	284					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCCACTTTCACGTCCACCGGT	0.512													C|||	842	0.168131	0.0923	0.2205	5008	,	,		18550	0.2222		0.1173	False		,,,				2504	0.2301				p.H284H		Atlas-SNP	.											.	LCLAT1	51	.	0			c.C852T						PASS	.	C	,	375,4031	190.9+/-216.7	20,335,1848	100.0	96.0	97.0		738,852	0.4	1.0	2	dbSNP_120	97	1150,7450	236.8+/-268.9	94,962,3244	no	coding-synonymous,coding-synonymous	LCLAT1	NM_001002257.1,NM_182551.3	,	114,1297,5092	TT,TC,CC		13.3721,8.5111,11.7254	,	246/377,284/415	30863092	1525,11481	2203	4300	6503	SO:0001819	synonymous_variant	253558	exon7			CTTTCACGTCCAC	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.852C>T	2.37:g.30863092C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_182551	A6H8Z7|Q8N1Q7	Silent	SNP	ENST00000309052.4	37	CCDS1772.1																																																																																			C|0.872;T|0.128	0.128	strong		0.512	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	
ANK1	286	hgsc.bcm.edu	37	8	41563685	41563685	+	Silent	SNP	G	G	A	rs1137177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:41563685G>A	ENST00000347528.4	-	18	2156	c.2073C>T	c.(2071-2073)ggC>ggT	p.G691G	ANK1_ENST00000396945.1_Silent_p.G691G|ANK1_ENST00000352337.4_Silent_p.G691G|ANK1_ENST00000396942.1_Silent_p.G691G|ANK1_ENST00000265709.8_Silent_p.G724G|ANK1_ENST00000289734.7_Silent_p.G691G|ANK1_ENST00000379758.2_Silent_p.G691G	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	691	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCACCATGACGCCGTGTTTGA	0.542													G|||	906	0.180911	0.0159	0.2954	5008	,	,		17858	0.0794		0.2823	False		,,,				2504	0.3231				p.G724G		Atlas-SNP	.											.	ANK1	497	.	0			c.C2172T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	82.0	73.0	76.0		2073,2172,2073,2073,2073	-10.6	0.0	8	dbSNP_86	76	2304,6296	387.5+/-342.2	320,1664,2316	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	327,1900,4276	AA,AG,GG		26.7907,5.6741,19.6371	,,,,	691/1881,724/1898,691/1857,691/1882,691/1720	41563685	2554,10452	2203	4300	6503	SO:0001819	synonymous_variant	286	exon18			CATGACGCCGTGT	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2073C>T	8.37:g.41563685G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	369	0.16895604395604397	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	221	0.29155672823219	G	0.494	-0.874159	0.02550	0.056741	0.267907	ENSG00000029534	ENST00000520299	.	.	.	5.32	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999952	.	.	.	.	.	.	T	0.17228	-1.0376	3	.	.	.	.	1.3955	0.02260	0.2645:0.2406:0.3132:0.1818	rs1137177;rs2304878;rs3200981;rs17424473;rs17602822;rs1137177	.	.	.	C	5	.	.	R	-	1	0	ANK1	41682842	0.002000	0.14202	0.002000	0.10522	0.035000	0.12851	-1.576000	0.02129	-3.094000	0.00246	-1.075000	0.02238	CGT	G|0.832;N|0.000	.	strong		0.542	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:27374180T>C	ENST00000395762.2	+	11	1766	c.1507T>C	c.(1507-1509)Tcc>Ccc	p.S503P	IL4R_ENST00000380922.3_Missense_Mutation_p.S488P|IL4R_ENST00000170630.2_Missense_Mutation_p.S503P|IL4R_ENST00000543915.2_Missense_Mutation_p.S503P	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	503	Required for IRS1 activation and IL4- induced cell growth.		S -> P (lowered total IgE concentration; dbSNP:rs1805015). {ECO:0000269|PubMed:10233717, ECO:0000269|PubMed:11285129, 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						CTTCAGCAACTCCCTGAGCCA	0.622													T|||	1010	0.201677	0.4251	0.1614	5008	,	,		19105	0.0843		0.1521	False		,,,				2504	0.1002				p.S503P		Atlas-SNP	.											IL4R,colon,carcinoma,0,1	IL4R	70	1	0			c.T1507C	GRCh37	CM993667	IL4R	M	rs1805015	PASS	.	T	PRO/SER	1595,2799	491.1+/-362.0	292,1011,894	78.0	83.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1507	1.6	0.0	16	dbSNP_89	81	1391,7209	265.3+/-286.1	110,1171,3019	yes	missense	IL4R	NM_000418.2	74	402,2182,3913	CC,CT,TT		16.1744,36.2995,22.9798	possibly-damaging	503/826	27374180	2986,10008	2197	4300	6497	SO:0001583	missense	3566	exon11			AGCAACTCCCTGA	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.1507T>C	16.37:g.27374180T>C	ENSP00000379111:p.Ser503Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	458	0.2097069597069597	227	0.4613821138211382	62	0.1712707182320442	43	0.07517482517482517	126	0.1662269129287599	T	12.87	2.068150	0.36470	0.362995	0.161744	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	4.99	1.57	0.23409	.	10.161500	0.00166	N	0.000000	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;P;P	0.36144	0.539;0.539;0.539	B;B;B	0.31016	0.123;0.123;0.123	T	0.45056	-0.9287	9	0.33141	T	0.24	.	6.2127	0.20638	0.0:0.2856:0.0:0.7143	rs1805015;rs17513769;rs60163518;rs1805015	488;503;503	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	P	503;503;488;503	ENSP00000379111:S503P;ENSP00000441667:S503P;ENSP00000370309:S488P;ENSP00000170630:S503P	ENSP00000170630:S503P	S	+	1	0	IL4R	27281681	0.000000	0.05858	0.001000	0.08648	0.081000	0.17604	0.118000	0.15605	0.762000	0.33152	0.459000	0.35465	TCC	T|0.773;C|0.227	0.227	strong		0.622	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
GLYATL3	389396	hgsc.bcm.edu	37	6	49479750	49479750	+	Missense_Mutation	SNP	T	T	C	rs13193063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:49479750T>C	ENST00000371197.4	+	2	160	c.47T>C	c.(46-48)aTg>aCg	p.M16T		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	16						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.M16T(1)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						CTGGAGAAAATGTTGAAGAGT	0.318													T|||	912	0.182109	0.0537	0.1931	5008	,	,		11526	0.2044		0.333	False		,,,				2504	0.1697				p.M16T		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,1	GLYATL3	19	1	1	Substitution - Missense(1)	kidney(1)	c.T47C						PASS	.						237.0	204.0	214.0					6																	49479750		692	1591	2283	SO:0001583	missense	389396	exon2			AGAAAATGTTGAA		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.47T>C	6.37:g.49479750T>C	ENSP00000360240:p.Met16Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	438	0.20054945054945056	29	0.05894308943089431	73	0.20165745856353592	94	0.16433566433566432	242	0.31926121372031663	T	11.00	1.509980	0.27036	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.13538	2.58;2.58	5.8	5.8	0.92144	Glycine N-acyltransferase, N-terminal (1);	0.349316	0.32970	N	0.005433	T	0.06142	0.0159	L	0.48986	1.54	0.36788	P	0.11531100000000005	B	0.31459	0.324	B	0.31390	0.129	T	0.25467	-1.0131	9	0.19590	T	0.45	-1.7855	12.5278	0.56096	0.0:0.0:0.0:1.0	rs13193063;rs17663633;rs13193063	16	Q5SZD4	GLYL3_HUMAN	T	16	ENSP00000360240:M16T;ENSP00000440029:M16T	ENSP00000360240:M16T	M	+	2	0	GLYATL3	49587709	0.923000	0.31300	0.746000	0.31095	0.992000	0.81027	1.779000	0.38624	2.215000	0.71742	0.472000	0.43445	ATG	C|0.179;N|0.000	0.179	strong		0.318	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
ADAM12	8038	hgsc.bcm.edu	37	10	127753388	127753388	+	Silent	SNP	C	C	T	rs2279091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127753388C>T	ENST00000368679.4	-	14	1914	c.1605G>A	c.(1603-1605)acG>acA	p.T535T	ADAM12_ENST00000368676.4_Silent_p.T535T|ADAM12_ENST00000467145.1_5'UTR	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	535	Cys-rich.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GTCCCCAGAGCGTGACACACT	0.607													C|||	378	0.0754792	0.0651	0.072	5008	,	,		18889	0.0595		0.1243	False		,,,				2504	0.0583				p.T535T		Atlas-SNP	.											.	ADAM12	388	.	0			c.G1605A						PASS	.	C	,	302,4104		6,290,1907	84.0	59.0	67.0		1605,1605	-10.2	0.1	10	dbSNP_100	67	988,7610		62,864,3373	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	68,1154,5280	TT,TC,CC		11.491,6.8543,9.92	,	535/910,535/739	127753388	1290,11714	2203	4299	6502	SO:0001819	synonymous_variant	8038	exon14			CCAGAGCGTGACA	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1605G>A	10.37:g.127753388C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			C|0.908;T|0.092	0.092	strong		0.607	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
STRADB	55437	hgsc.bcm.edu	37	2	202337730	202337730	+	Silent	SNP	A	A	G	rs1019299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:202337730A>G	ENST00000194530.3	+	5	611	c.246A>G	c.(244-246)acA>acG	p.T82T	STRADB_ENST00000392249.2_Silent_p.T82T	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	82	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						ATACTCCCACAGGAACACTGG	0.358													G|||	3557	0.710264	0.6732	0.5893	5008	,	,		14490	0.7421		0.66	False		,,,				2504	0.865				p.T82T		Atlas-SNP	.											.	STRADB	33	.	0			c.A246G						PASS	.	G	,	2916,1490	476.3+/-357.6	966,984,253	120.0	118.0	119.0		246,246	1.1	1.0	2	dbSNP_86	119	5792,2808	442.6+/-360.1	1937,1918,445	no	coding-synonymous,coding-synonymous	STRADB	NM_001206864.1,NM_018571.5	,	2903,2902,698	GG,GA,AA		32.6512,33.8175,33.0463	,	82/378,82/419	202337730	8708,4298	2203	4300	6503	SO:0001819	synonymous_variant	55437	exon5			TCCCACAGGAACA	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"""	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.246A>G	2.37:g.202337730A>G		Somatic	450	1	0.00222222		WXS	Illumina HiSeq	Phase_I	405	404	0.997531	NM_001206864	Q5BKY7|Q9P1L0	Silent	SNP	ENST00000194530.3	37	CCDS2348.1																																																																																			A|0.352;G|0.648	0.648	strong		0.358	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571	
FOXM1	2305	hgsc.bcm.edu	37	12	2973547	2973547	+	Missense_Mutation	SNP	G	G	T	rs28990715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:2973547G>T	ENST00000359843.3	-	8	1273	c.1205C>A	c.(1204-1206)gCg>gAg	p.A402E	FOXM1_ENST00000342628.2_Missense_Mutation_p.A402E|FOXM1_ENST00000537018.1_5'Flank|FOXM1_ENST00000361953.3_Missense_Mutation_p.A387E	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	402			A -> E (in dbSNP:rs28990715). {ECO:0000269|Ref.3}.		cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|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 double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GAGGGAAGCCGCCAGGGGCAA	0.587													G|||	31	0.0061901	0.0	0.0159	5008	,	,		15345	0.0		0.0179	False		,,,				2504	0.002				p.A402E		Atlas-SNP	.											.	FOXM1	62	.	0			c.C1205A						PASS	.	G	GLU/ALA,GLU/ALA,GLU/ALA	15,4391	23.3+/-48.9	0,15,2188	84.0	94.0	91.0		1205,1205,1160	4.1	1.0	12	dbSNP_125	91	178,8422	81.2+/-143.8	2,174,4124	yes	missense,missense,missense	FOXM1	NM_021953.3,NM_202002.2,NM_202003.2	107,107,107	2,189,6312	TT,TG,GG		2.0698,0.3404,1.4839	probably-damaging,probably-damaging,probably-damaging	402/764,402/802,387/749	2973547	193,12813	2203	4300	6503	SO:0001583	missense	2305	exon8			GAAGCCGCCAGGG	Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1205C>A	12.37:g.2973547G>T	ENSP00000352901:p.Ala402Glu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_021953	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Missense_Mutation	SNP	ENST00000359843.3	37	CCDS8515.1	24	0.01098901098901099	0	0.0	9	0.024861878453038673	0	0.0	15	0.01978891820580475	G	20.8	4.050029	0.75846	0.003404	0.020698	ENSG00000111206	ENST00000342628;ENST00000361953;ENST00000359843	D;D;D	0.92911	-3.06;-3.13;-3.05	5.09	4.14	0.48551	.	0.115779	0.64402	D	0.000013	D	0.86314	0.5903	N	0.24115	0.695	0.36602	D	0.874713	P;P;P;P;D	0.71674	0.8;0.881;0.873;0.881;0.998	B;B;P;B;D	0.74348	0.428;0.428;0.631;0.428;0.983	D	0.90538	0.4500	10	0.87932	D	0	.	11.5949	0.50968	0.0:0.0:0.6933:0.3067	rs28990715;rs28990715	386;402;387;402;402	A8K591;Q53Y49;Q08050-2;Q08050;Q08050-3	.;.;.;FOXM1_HUMAN;.	E	402;387;402	ENSP00000342307:A402E;ENSP00000354492:A387E;ENSP00000352901:A402E	ENSP00000342307:A402E	A	-	2	0	FOXM1	2843808	1.000000	0.71417	0.970000	0.41538	0.701000	0.40568	4.003000	0.57061	2.367000	0.80283	0.561000	0.74099	GCG	G|0.985;T|0.015	0.015	strong		0.587	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953	
ZNF77	58492	hgsc.bcm.edu	37	19	2934249	2934249	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2934249T>C	ENST00000314531.4	-	4	968	c.876A>G	c.(874-876)ggA>ggG	p.G292G		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	292					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)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGTTTCTCTCCAGTGTGTG	0.458																																					p.G292G		Atlas-SNP	.											.	ZNF77	47	.	0			c.A876G						PASS	.						167.0	152.0	157.0					19																	2934249		2203	4300	6503	SO:0001819	synonymous_variant	58492	exon4			TTTCTCTCCAGTG	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"""Zinc fingers, C2H2-type"", ""-"""	13150	protein-coding gene	gene with protein product		194551	"""zinc finger protein 77 (pT1)"""			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.876A>G	19.37:g.2934249T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	39	0.39	NM_021217	Q86XJ3|Q9NPP0	Silent	SNP	ENST00000314531.4	37	CCDS12099.1																																																																																			.	.	none		0.458	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217	
PRICKLE2	166336	hgsc.bcm.edu	37	3	64142859	64142859	+	Silent	SNP	C	C	T	rs17720698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:64142859C>T	ENST00000295902.6	-	5	1164	c.579G>A	c.(577-579)ccG>ccA	p.P193P	PRICKLE2_ENST00000564377.1_Silent_p.P249P	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	193	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.|LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		CAGCACAGCGCGGCTTCAGGC	0.522													C|||	926	0.184904	0.295	0.1282	5008	,	,		19988	0.0119		0.2525	False		,,,				2504	0.1851				p.P193P		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.G579A						PASS	.	C		1177,3229	412.2+/-336.0	149,879,1175	68.0	63.0	65.0		579	-11.6	0.2	3	dbSNP_123	65	1973,6627	345.6+/-325.8	222,1529,2549	no	coding-synonymous	PRICKLE2	NM_198859.3		371,2408,3724	TT,TC,CC		22.9419,26.7136,24.2196		193/845	64142859	3150,9856	2203	4300	6503	SO:0001819	synonymous_variant	166336	exon5			ACAGCGCGGCTTC	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"""prickle-like 2 (Drosophila)"""			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.579G>A	3.37:g.64142859C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	284	278	0.978873	NM_198859	Q0VF44	Silent	SNP	ENST00000295902.6	37	CCDS2902.1																																																																																			C|0.776;T|0.224	0.224	strong		0.522	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859	
LTBP3	4054	hgsc.bcm.edu	37	11	65319751	65319751	+	Missense_Mutation	SNP	G	G	A	rs11545200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65319751G>A	ENST00000301873.5	-	7	1581	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V	LTBP3_ENST00000322147.4_Missense_Mutation_p.A438V|LTBP3_ENST00000536982.1_Missense_Mutation_p.A64V	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	438	TB 2.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CTGACACCGCGCGCCCCAGGC	0.637											OREG0021081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	315	0.0628994	0.0144	0.0447	5008	,	,		17993	0.0327		0.0696	False		,,,				2504	0.1656				p.A438V		Atlas-SNP	.											.	LTBP3	55	.	0			c.C1313T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	92,4310	76.2+/-114.5	1,90,2110	73.0	77.0	76.0		1313,962,1313	4.0	0.2	11	dbSNP_120	76	619,7975	161.9+/-214.7	26,567,3704	yes	missense,missense,missense	LTBP3	NM_001130144.2,NM_001164266.1,NM_021070.4	64,64,64	27,657,5814	AA,AG,GG		7.2027,2.09,5.4709	possibly-damaging,possibly-damaging,possibly-damaging	438/1304,321/1140,438/1257	65319751	711,12285	2201	4297	6498	SO:0001583	missense	4054	exon7			CACCGCGCGCCCC	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"""Latent transforming growth factor, beta binding proteins"""	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1313C>T	11.37:g.65319751G>A	ENSP00000301873:p.Ala438Val	Somatic	60	0	0	1083	WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	37	CCDS44647.1	101	0.04624542124542125	8	0.016260162601626018	17	0.04696132596685083	24	0.04195804195804196	52	0.06860158311345646	G	18.97	3.735612	0.69189	0.0209	0.072027	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000536982;ENST00000530866;ENST00000530426	D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02	3.99	3.99	0.46301	Matrix fibril-associated (3);TGF-beta binding (1);	0.364335	0.28214	N	0.016174	T	0.47948	0.1473	N	0.14661	0.345	0.80722	P	0.0	D;D;D;D;D	0.69078	0.992;0.995;0.983;0.996;0.997	P;P;P;P;P	0.54312	0.732;0.748;0.532;0.732;0.692	T	0.78612	-0.2136	9	0.40728	T	0.16	.	13.6128	0.62091	0.0:0.0:1.0:0.0	rs11545200	349;64;321;438;438	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2	.;.;.;LTBP3_HUMAN;.	V	438;438;64;349;118	ENSP00000326647:A438V;ENSP00000301873:A438V;ENSP00000441912:A64V;ENSP00000435276:A349V;ENSP00000432476:A118V	ENSP00000301873:A438V	A	-	2	0	LTBP3	65076327	0.007000	0.16637	0.213000	0.23690	0.986000	0.74619	1.747000	0.38298	2.064000	0.61679	0.407000	0.27541	GCG	G|0.945;A|0.055	0.055	strong		0.637	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070	
COL11A2	1302	hgsc.bcm.edu	37	6	33133555	33133555	+	Silent	SNP	C	C	T	rs114580597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33133555C>T	ENST00000374708.4	-	61	4521	c.4263G>A	c.(4261-4263)caG>caA	p.Q1421Q	COL11A2_ENST00000341947.2_Silent_p.Q1507Q|COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000374714.1_Silent_p.Q1481Q|COL11A2_ENST00000357486.1_Silent_p.Q1486Q|COL11A2_ENST00000395197.1_Silent_p.Q1447Q|COL11A2_ENST00000374713.1_Silent_p.Q1460Q|COL11A2_ENST00000374712.1_Silent_p.Q1426Q|COL11A2_ENST00000361917.1_Silent_p.Q1400Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1507	Triple-helical region.				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						TCTTGGGCATCTGAATGGGCA	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		18621	0.0		0.003	False		,,,				2504	0.001				p.Q1507Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G4521A						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	59.0	60.0	60.0		4200,4521,4263	3.8	1.0	6	dbSNP_132	60	33,8567	19.8+/-62.0	0,33,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	0,37,6466	TT,TC,CC		0.3837,0.0908,0.2845	,,	1400/1630,1507/1737,1421/1651	33133555	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1302	exon63			GGGCATCTGAATG	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	ENST00000374708.4:c.4263G>A	6.37:g.33133555C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
COL19A1	1310	hgsc.bcm.edu	37	6	70733547	70733547	+	Missense_Mutation	SNP	C	C	G	rs2273426	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:70733547C>G	ENST00000322773.4	+	12	1157	c.1055C>G	c.(1054-1056)gCt>gGt	p.A352G		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	352	Collagen-like 2.		A -> G (in dbSNP:rs2273426).		cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GGAGATCCAGCTCTGGCTGGC	0.308													G|||	1416	0.282748	0.5522	0.1744	5008	,	,		18317	0.2986		0.1123	False		,,,				2504	0.1544				p.A352G		Atlas-SNP	.											.	COL19A1	232	.	0			c.C1055G						PASS	.	G	GLY/ALA	2030,2376	610.5+/-391.6	482,1066,655	90.0	88.0	89.0		1055	5.5	1.0	6	dbSNP_100	89	922,7678	777.1+/-407.7	50,822,3428	yes	missense	COL19A1	NM_001858.4	60	532,1888,4083	GG,GC,CC		10.7209,46.0735,22.6972	benign	352/1143	70733547	2952,10054	2203	4300	6503	SO:0001583	missense	1310	exon12			ATCCAGCTCTGGC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1055C>G	6.37:g.70733547C>G	ENSP00000316030:p.Ala352Gly	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	565	0.2586996336996337	241	0.4898373983739837	62	0.1712707182320442	175	0.30594405594405594	87	0.11477572559366754	G	14.10	2.434956	0.43224	0.460735	0.107209	ENSG00000082293	ENST00000322773	T	0.71934	-0.61	5.5	5.5	0.81552	.	0.068567	0.64402	N	0.000018	T	0.08133	0.0203	N	0.00012	-2.965	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	9	0.02654	T	1	.	15.6391	0.76981	0.0:0.1376:0.8624:0.0	rs2273426;rs61647969;rs2273426	352	Q14993	COJA1_HUMAN	G	352	ENSP00000316030:A352G	ENSP00000316030:A352G	A	+	2	0	COL19A1	70790268	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.235000	0.58666	1.342000	0.45619	-0.120000	0.15030	GCT	C|0.761;G|0.239	0.239	strong		0.308	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
PAPLN	89932	hgsc.bcm.edu	37	14	73727509	73727509	+	Missense_Mutation	SNP	T	T	G	rs177389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73727509T>G	ENST00000554301.1	+	16	2241	c.2078T>G	c.(2077-2079)aTg>aGg	p.M693R	PAPLN_ENST00000427855.1_Missense_Mutation_p.M693R|PAPLN_ENST00000555445.1_Missense_Mutation_p.M693R|PAPLN_ENST00000381166.3_Missense_Mutation_p.M693R|PAPLN_ENST00000340738.5_Missense_Mutation_p.M666R			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	693				M -> R (in Ref. 2; BAG57757, 5; CAD97826 and 6; BAC85123). {ECO:0000305}.		basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		ACCGGGGGCATGCCCAGGTCA	0.647													G|||	3286	0.65615	0.7481	0.6801	5008	,	,		15634	0.7103		0.4841	False		,,,				2504	0.636				p.M666R		Atlas-SNP	.											.	PAPLN	180	.	0			c.T1997G						PASS	.	G	ARG/MET	3585,821		1484,617,102	44.0	42.0	43.0		1997	3.7	0.0	14	dbSNP_79	43	4465,4135		1180,2105,1015	yes	missense	PAPLN	NM_173462.3	91	2664,2722,1117	GG,GT,TT		48.0814,18.6337,38.1055	benign	666/1252	73727509	8050,4956	2203	4300	6503	SO:0001583	missense	89932	exon16			GGGGCATGCCCAG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2078T>G	14.37:g.73727509T>G	ENSP00000451803:p.Met693Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		1453	0.6652930402930403	421	0.8556910569105691	245	0.6767955801104972	405	0.708041958041958	382	0.503957783641161	G	0.498	-0.872174	0.02570	0.813663	0.519186	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.62105	0.05;0.05;0.36;0.05;0.21	4.57	3.65	0.41850	.	.	.	.	.	T	0.00012	0.0000	N	0.00146	-1.995	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	0.36335	-0.9752	8	0.13470	T	0.59	.	9.7617	0.40537	0.0:0.0:0.6233:0.3767	rs177389;rs1735108	693;693;666	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	R	666;693;693;693;693	ENSP00000345395:M666R;ENSP00000403403:M693R;ENSP00000370558:M693R;ENSP00000451803:M693R;ENSP00000451729:M693R	ENSP00000216658:M693R	M	+	2	0	PAPLN	72797262	0.342000	0.24809	0.029000	0.17559	0.255000	0.26057	1.696000	0.37773	0.630000	0.30394	-0.217000	0.12591	ATG	C|0.003;G|0.633;T|0.364	0.633	strong		0.647	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
TTLL12	23170	hgsc.bcm.edu	37	22	43576880	43576880	+	Silent	SNP	C	C	A	rs11090144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43576880C>A	ENST00000216129.6	-	3	477	c.414G>T	c.(412-414)gtG>gtT	p.V138V		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	138					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)				GCAGCCCGGGCACCTGCTGCA	0.662													C|||	241	0.048123	0.0522	0.0692	5008	,	,		17744	0.001		0.0905	False		,,,				2504	0.0327				p.V138V		Atlas-SNP	.											.	TTLL12	50	.	0			c.G414T						PASS	.	C		319,4087	166.2+/-197.5	12,295,1896	57.0	50.0	52.0		414	-0.4	1.0	22	dbSNP_120	52	913,7687	201.0+/-244.6	52,809,3439	no	coding-synonymous	TTLL12	NM_015140.3		64,1104,5335	AA,AC,CC		10.6163,7.2401,9.4726		138/645	43576880	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	23170	exon3			CCCGGGCACCTGC	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.414G>T	22.37:g.43576880C>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_015140	Q20WK5|Q9UGU3	Silent	SNP	ENST00000216129.6	37	CCDS14047.1																																																																																			C|0.917;A|0.083	0.083	strong		0.662	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
OR2G2	81470	hgsc.bcm.edu	37	1	247751731	247751731	+	Missense_Mutation	SNP	C	C	G	rs12737801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247751731C>G	ENST00000320065.1	+	1	70	c.70C>G	c.(70-72)Cct>Gct	p.P24A	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	24			P -> A (in dbSNP:rs12737801).			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)			TTCTGATTATCCTCAGTTACA	0.413													C|||	382	0.076278	0.0673	0.0865	5008	,	,		20844	0.005		0.1223	False		,,,				2504	0.1074				p.P24A		Atlas-SNP	.											.	OR2G2	88	.	0			c.C70G						PASS	.	C	ALA/PRO	347,4059	179.0+/-207.6	16,315,1872	195.0	187.0	190.0		70	2.8	0.7	1	dbSNP_121	190	1214,7386	246.1+/-274.7	86,1042,3172	yes	missense	OR2G2	NM_001001915.1	27	102,1357,5044	GG,GC,CC		14.1163,7.8756,12.0022	probably-damaging	24/318	247751731	1561,11445	2203	4300	6503	SO:0001583	missense	81470	exon1			GATTATCCTCAGT	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.70C>G	1.37:g.247751731C>G	ENSP00000326349:p.Pro24Ala	Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	269	132	0.490706	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	170	0.07783882783882784	32	0.06504065040650407	38	0.10497237569060773	2	0.0034965034965034965	98	0.12928759894459102	C	14.94	2.686342	0.47991	0.078756	0.141163	ENSG00000177489	ENST00000320065	T	0.00428	7.44	3.79	2.81	0.32909	.	0.000000	0.33235	U	0.005126	T	0.00012	0.0000	M	0.86420	2.815	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.33471	-0.9867	9	0.72032	D	0.01	.	5.2644	0.15591	0.0:0.6714:0.2115:0.1171	rs12737801;rs52798143;rs12737801	24	Q8NGZ5	OR2G2_HUMAN	A	24	ENSP00000326349:P24A	ENSP00000326349:P24A	P	+	1	0	OR2G2	245818354	0.000000	0.05858	0.686000	0.30086	0.928000	0.56348	0.253000	0.18296	1.925000	0.55765	0.591000	0.81541	CCT	C|0.897;G|0.103	0.103	strong		0.413	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
TIMP2	7077	hgsc.bcm.edu	37	17	76867017	76867017	+	Silent	SNP	C	C	T	rs2277698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76867017C>T	ENST00000262768.7	-	3	601	c.303G>A	c.(301-303)tcG>tcA	p.S101S	TIMP2_ENST00000536189.2_Silent_p.S24S|TIMP2_ENST00000585421.1_Silent_p.S24S|TIMP2_ENST00000586057.1_Silent_p.S24S	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	101	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.			S -> E (in Ref. 6; AA sequence and 7; AA sequence). {ECO:0000305}.	aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			CAACGTCCAGCGAGACCCCAC	0.547													C|||	846	0.16893	0.1006	0.1196	5008	,	,		17527	0.2639		0.1252	False		,,,				2504	0.2434				p.S101S		Atlas-SNP	.											.	TIMP2	27	.	0			c.G303A	GRCh37	CM991178	TIMP2	M	rs2277698	PASS	.	C		420,3986	206.2+/-227.9	25,370,1808	114.0	106.0	109.0		303	-1.7	1.0	17	dbSNP_100	109	1034,7566	220.5+/-258.2	56,922,3322	no	coding-synonymous	TIMP2	NM_003255.4		81,1292,5130	TT,TC,CC		12.0233,9.5325,11.1795		101/221	76867017	1454,11552	2203	4300	6503	SO:0001819	synonymous_variant	7077	exon3			GTCCAGCGAGACC		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"""tissue inhibitor of metalloproteinase 2"""			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.303G>A	17.37:g.76867017C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_003255	Q16121|Q93006|Q9UDF7	Silent	SNP	ENST00000262768.7	37	CCDS11758.1																																																																																			C|0.868;T|0.132	0.132	strong		0.547	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255	
HLA-A	3105	hgsc.bcm.edu	37	6	29910604	29910604	+	Silent	SNP	C	C	A	rs12721675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910604C>A	ENST00000396634.1	+	4	485	c.144C>A	c.(142-144)gcC>gcA	p.A48A	HLA-A_ENST00000376806.5_Silent_p.A48A|HLA-A_ENST00000376809.5_Silent_p.A48A|HLA-A_ENST00000376802.2_Silent_p.A48A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCTTCATCGCCGTGGGCTACG	0.701									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	1915	0.382388	0.4425	0.4597	5008	,	,		15112	0.3899		0.3807	False		,,,				2504	0.2403				p.A48A		Atlas-SNP	.											HLA-A,NS,carcinoma,0,4	HLA-A	89	4	0			c.C144A						PASS	.						33.0	29.0	30.0					6																	29910604		2201	4298	6499	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CATCGCCGTGGGC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.144C>A	6.37:g.29910604C>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	142	50	0.352113	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.361;C|0.639	0.361	strong		0.701	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ABCC6	368	hgsc.bcm.edu	37	16	16259742	16259742	+	Missense_Mutation	SNP	C	C	T	rs373863345		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:16259742C>T	ENST00000205557.7	-	23	3073	c.3044G>A	c.(3043-3045)cGg>cAg	p.R1015Q		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1015	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCTGGATGCCCGGGCCCCACC	0.617																																					p.R1015Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3044A						PASS	.	C	GLN/ARG	0,4394		0,0,2197	36.0	37.0	36.0		3044	2.1	1.0	16		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCC6	NM_001171.5	43	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1015/1504	16259742	1,12993	2197	4300	6497	SO:0001583	missense	368	exon23			GATGCCCGGGCCC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3044G>A	16.37:g.16259742C>T	ENSP00000205557:p.Arg1015Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751682	0.31046	0.0	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91351	-2.83	5.52	2.07	0.26955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.724655	0.11525	U	0.555272	T	0.80768	0.4686	L	0.31476	0.935	0.09310	N	0.999997	B	0.30211	0.273	B	0.19946	0.027	T	0.66736	-0.5848	10	0.26408	T	0.33	.	4.8069	0.13325	0.2447:0.4906:0.0:0.2647	.	1015	O95255	MRP6_HUMAN	Q	1015;20	ENSP00000205557:R1015Q	ENSP00000205557:R1015Q	R	-	2	0	ABCC6	16167243	0.036000	0.19791	0.983000	0.44433	0.808000	0.45660	1.233000	0.32648	0.701000	0.31803	0.561000	0.74099	CGG	.	.	weak		0.617	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
MORF4L1	10933	hgsc.bcm.edu	37	15	79185898	79185898	+	Silent	SNP	C	C	A	rs1435163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79185898C>A	ENST00000331268.5	+	10	879	c.675C>A	c.(673-675)gcC>gcA	p.A225A	MORF4L1_ENST00000558746.1_Silent_p.A159A|MORF4L1_ENST00000558502.1_Silent_p.A98A|MORF4L1_ENST00000559345.1_Silent_p.A98A|MORF4L1_ENST00000561171.1_Intron|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	177	0	0		WXS	Illumina HiSeq	Phase_I	165	67	0.406061	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	
GART	2618	hgsc.bcm.edu	37	21	34897113	34897113	+	Missense_Mutation	SNP	C	C	T	rs8788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34897113C>T	ENST00000381831.3	-	11	1524	c.1261G>A	c.(1261-1263)Gtc>Atc	p.V421I	GART_ENST00000543717.1_5'Flank|GART_ENST00000381815.4_Missense_Mutation_p.V421I|GART_ENST00000381839.3_Missense_Mutation_p.V421I|GART_ENST00000361093.5_Missense_Mutation_p.V421I	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	421			V -> I (in dbSNP:rs8788). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9224613}.		'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)	CGAAAGCCGACGTCTTTCCTA	0.463													T|||	4378	0.874201	0.9191	0.8703	5008	,	,		16595	0.9831		0.7753	False		,,,				2504	0.8057				p.V421I		Atlas-SNP	.											.	GART	81	.	0			c.G1261A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	3973,433	210.5+/-231.0	1788,397,18	114.0	109.0	110.0		1261,1261,1261,1261	6.0	1.0	21	dbSNP_52	110	6541,2059	357.5+/-330.8	2489,1563,248	yes	missense,missense,missense,missense	GART	NM_000819.4,NM_001136005.1,NM_001136006.1,NM_175085.2	29,29,29,29	4277,1960,266	TT,TC,CC		23.9419,9.8275,19.1604	benign,benign,benign,benign	421/1011,421/1011,421/1011,421/434	34897113	10514,2492	2203	4300	6503	SO:0001583	missense	2618	exon11			AGCCGACGTCTTT	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.1261G>A	21.37:g.34897113C>T	ENSP00000371253:p.Val421Ile	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	37	CCDS13627.1	1904	0.8717948717948718	444	0.9024390243902439	314	0.8674033149171271	564	0.986013986013986	582	0.7678100263852242	T	3.979	-0.006732	0.07773	0.901725	0.760581	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093	T;T;T;T	0.19532	2.14;2.14;2.14;2.14	6.03	6.03	0.97812	Rudiment single hybrid motif (1);Phosphoribosylglycinamide synthetase, C-domain (2);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00002	-3.51	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41805	-0.9488	9	0.02654	T	1	-17.8274	12.349	0.55136	0.0:0.0655:0.0:0.9345	rs8788;rs1051054;rs2230038;rs3171430;rs9984077;rs17173504;rs52815665;rs60421747;rs9984077	421	P22102	PUR2_HUMAN	I	421	ENSP00000371236:V421I;ENSP00000371253:V421I;ENSP00000371261:V421I;ENSP00000354388:V421I	ENSP00000354388:V421I	V	-	1	0	GART	33818983	1.000000	0.71417	0.991000	0.47740	0.182000	0.23217	5.789000	0.69029	1.107000	0.41642	-0.381000	0.06696	GTC	T|0.663;G|0.024;C|0.147;A|0.166	0.663	strong		0.463	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819	
USP36	57602	hgsc.bcm.edu	37	17	76817090	76817090	+	Missense_Mutation	SNP	C	C	T	rs3744793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76817090C>T	ENST00000542802.3	-	8	1254	c.811G>A	c.(811-813)Gtc>Atc	p.V271I	USP36_ENST00000449938.2_5'UTR|USP36_ENST00000588467.1_5'Flank|USP36_ENST00000312010.6_Missense_Mutation_p.V271I			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	271	USP.		V -> I (in dbSNP:rs3744793). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			TCCAGCGCGACGTCCAAGTAG	0.587													C|||	1796	0.358626	0.1104	0.3876	5008	,	,		14949	0.504		0.4115	False		,,,				2504	0.4693				p.V271I		Atlas-SNP	.											.	USP36	243	.	0			c.G811A						PASS	.	C	ILE/VAL	715,3691	288.1+/-279.7	65,585,1553	72.0	52.0	59.0		811	-1.4	0.3	17	dbSNP_107	59	3677,4923	502.5+/-375.7	800,2077,1423	yes	missense	USP36	NM_025090.3	29	865,2662,2976	TT,TC,CC		42.7558,16.2279,33.769	benign	271/1124	76817090	4392,8614	2203	4300	6503	SO:0001583	missense	57602	exon8			GCGCGACGTCCAA	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.811G>A	17.37:g.76817090C>T	ENSP00000441214:p.Val271Ile	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	37	CCDS32755.1	793	0.3630952380952381	51	0.10365853658536585	127	0.35082872928176795	294	0.513986013986014	321	0.4234828496042216	C	3.607	-0.080424	0.07141	0.162279	0.427558	ENSG00000055483	ENST00000312010;ENST00000542802;ENST00000432878	T;T	0.04706	3.57;3.57	5.13	-1.35	0.09114	.	0.233624	0.42821	N	0.000652	T	0.00012	0.0000	N	0.01146	-0.985	0.09310	P	1.0	B	0.14438	0.01	B	0.17979	0.02	T	0.39881	-0.9592	9	0.02654	T	1	-2.8851	12.0683	0.53601	0.0:0.7153:0.0:0.2847	rs3744793;rs60261013;rs3744793	271	Q9P275-2	.	I	271	ENSP00000310590:V271I;ENSP00000441214:V271I	ENSP00000310590:V271I	V	-	1	0	USP36	74328685	0.982000	0.34865	0.327000	0.25402	0.920000	0.55202	0.167000	0.16602	-0.216000	0.10048	-0.290000	0.09829	GTC	C|0.659;T|0.341	0.341	strong		0.587	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
SOS1	6654	hgsc.bcm.edu	37	2	39241107	39241107	+	Missense_Mutation	SNP	G	G	A	rs56219475	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:39241107G>A	ENST00000426016.1	-	13	2050	c.1964C>T	c.(1963-1965)cCa>cTa	p.P655L	SOS1_ENST00000395038.2_Missense_Mutation_p.P655L|SOS1_ENST00000402219.2_Missense_Mutation_p.P655L			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	655	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.		P -> L (in dbSNP:rs56219475). {ECO:0000269|PubMed:17143282, ECO:0000269|PubMed:17143285, ECO:0000269|PubMed:19953625, ECO:0000269|PubMed:21387466}.		apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|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)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AGCTTCTGTTGGCTCAGGCTC	0.353									Noonan syndrome				G|||	16	0.00319489	0.0015	0.0029	5008	,	,		14941	0.0		0.0119	False		,,,				2504	0.0				p.P655L		Atlas-SNP	.											.	SOS1	134	.	0			c.C1964T	GRCh37	CM070277	SOS1	M	rs56219475	PASS	.	G	LEU/PRO	9,4397	15.5+/-35.6	0,9,2194	65.0	65.0	65.0		1964	5.8	1.0	2	dbSNP_129	65	84,8516	48.9+/-108.6	0,84,4216	yes	missense	SOS1	NM_005633.3	98	0,93,6410	AA,AG,GG		0.9767,0.2043,0.7151	benign	655/1334	39241107	93,12913	2203	4300	6503	SO:0001583	missense	6654	exon12	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TCTGTTGGCTCAG	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1964C>T	2.37:g.39241107G>A	ENSP00000387784:p.Pro655Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.30	1.598667	0.28445	0.002043	0.009767	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.47528	0.84;0.84;0.84	5.82	5.82	0.92795	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.053759	0.85682	D	0.000000	T	0.27933	0.0688	N	0.13235	0.315	0.80722	D	1	B	0.22211	0.066	B	0.25987	0.065	T	0.09574	-1.0668	10	0.19590	T	0.45	.	20.088	0.97803	0.0:0.0:1.0:0.0	rs56219475;rs61754252	655	Q07889	SOS1_HUMAN	L	655;655;387;655;655	ENSP00000387784:P655L;ENSP00000384675:P655L;ENSP00000378479:P655L	ENSP00000263879:P655L	P	-	2	0	SOS1	39094611	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.483000	0.66838	2.739000	0.93911	0.655000	0.94253	CCA	G|0.991;A|0.009	0.009	strong		0.353	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
ITGAL	3683	hgsc.bcm.edu	37	16	30518041	30518041	+	Missense_Mutation	SNP	G	G	C	rs2230433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30518041G>C	ENST00000356798.6	+	21	2552	c.2372G>C	c.(2371-2373)aGa>aCa	p.R791T	ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Missense_Mutation_p.R707T|MIR4518_ENST00000580665.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	791			R -> T (in dbSNP:rs2230433). {ECO:0000269|Ref.2}.		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.R791T(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)	CACAGATCCAGAGCCCTGCGT	0.532													g|||	1823	0.364018	0.4206	0.1888	5008	,	,		14147	0.1339		0.3012	False		,,,				2504	0.7137				p.R791T	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											ITGAL,NS,carcinoma,0,1	ITGAL	149	1	1	Substitution - Missense(1)	stomach(1)	c.G2372C						PASS	.		THR/ARG,THR/ARG	1827,2567	535.3+/-374.2	382,1063,752	236.0	242.0	240.0		2120,2372	-10.4	0.0	16	dbSNP_98	240	2498,6102	410.2+/-350.1	347,1804,2149	yes	missense,missense	ITGAL	NM_001114380.1,NM_002209.2	71,71	729,2867,2901	CC,CG,GG		29.0465,41.5794,33.2846	benign,benign	707/1087,791/1171	30518041	4325,8669	2197	4300	6497	SO:0001583	missense	3683	exon21			GATCCAGAGCCCT		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.2372G>C	16.37:g.30518041G>C	ENSP00000349252:p.Arg791Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	546	0.25	200	0.4065040650406504	74	0.20441988950276244	53	0.09265734265734266	219	0.28891820580474936	g	17.12	3.307785	0.60305	0.415794	0.290465	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.42513	0.97;0.97	5.22	-10.4	0.00318	Integrin alpha-2 (1);	1.402230	0.04360	N	0.357340	T	0.00012	0.0000	L	0.40543	1.245	0.53688	P	2.8000000000028002E-5	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.19712	-1.0297	9	0.29301	T	0.29	.	6.1617	0.20368	0.2875:0.5122:0.1116:0.0887	rs2230433;rs3087440;rs17839546;rs59554592;rs2230433	707;791	Q96HB1;P20701	.;ITAL_HUMAN	T	791;707	ENSP00000349252:R791T;ENSP00000350886:R707T	ENSP00000349252:R791T	R	+	2	0	ITGAL	30425542	0.000000	0.05858	0.001000	0.08648	0.849000	0.48306	-1.370000	0.02575	-1.940000	0.01043	0.450000	0.29827	AGA	G|0.694;C|0.306	0.306	strong		0.532	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
OR52B6	340980	hgsc.bcm.edu	37	11	5602679	5602679	+	Silent	SNP	T	T	C	rs892336	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602679T>C	ENST00000345043.2	+	1	573	c.573T>C	c.(571-573)aaT>aaC	p.N191N	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	191						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)		GCCAGATCAATATCATTGCAC	0.478													C|||	3588	0.716454	0.7413	0.67	5008	,	,		26074	0.9792		0.4761	False		,,,				2504	0.6922				p.N191N		Atlas-SNP	.											.	OR52B6	37	.	0			c.T573C						PASS	.	C		3073,1297		1092,889,204	202.0	205.0	204.0		573	1.8	0.1	11	dbSNP_86	204	4030,4532		949,2132,1200	no	coding-synonymous	OR52B6	NM_001005162.2		2041,3021,1404	CC,CT,TT		47.0684,29.6796,45.0742		191/336	5602679	7103,5829	2185	4281	6466	SO:0001819	synonymous_variant	340980	exon1			GATCAATATCATT	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.573T>C	11.37:g.5602679T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001005162	Q6IFI7	Silent	SNP	ENST00000345043.2	37	CCDS41611.1																																																																																			T|0.342;C|0.658	0.658	strong		0.478	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
MRPL11	65003	hgsc.bcm.edu	37	11	66206169	66206169	+	Silent	SNP	C	C	T	rs11110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:66206169C>T	ENST00000310999.7	-	1	150	c.57G>A	c.(55-57)gtG>gtA	p.V19V	MRPL11_ENST00000524576.1_Intron|MRPL11_ENST00000329819.4_Silent_p.V19V|MRPL11_ENST00000430466.2_Intron	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	19					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						TCGCCCGGATCACACCGCCGA	0.721													C|||	1158	0.23123	0.2254	0.2003	5008	,	,		14099	0.2798		0.3002	False		,,,				2504	0.1401				p.V19V		Atlas-SNP	.											.	MRPL11	25	.	0			c.G57A						PASS	.	C	,,	870,3286		105,660,1313	9.0	12.0	11.0		57,,57	1.6	1.0	11	dbSNP_52	11	2320,6066		337,1646,2210	no	coding-synonymous,intron,coding-synonymous	MRPL11	NM_016050.3,NM_170738.2,NM_170739.2	,,	442,2306,3523	TT,TC,CC		27.6652,20.9336,25.4345	,,	19/193,,19/182	66206169	3190,9352	2078	4193	6271	SO:0001819	synonymous_variant	65003	exon1			CCGGATCACACCG	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"""Mitochondrial ribosomal proteins / large subunits"""	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.57G>A	11.37:g.66206169C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_170739	A6NLT0|A8K219|Q32P46|Q96Q73	Silent	SNP	ENST00000310999.7	37	CCDS8139.1																																																																																			C|0.735;T|0.265	0.265	strong		0.721	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900341	4900341	+	Silent	SNP	G	G	A	rs17135247	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4900341G>A	ENST00000404991.1	-	1	1284	c.1098C>T	c.(1096-1098)agC>agT	p.S366S	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	366					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		TTTGAAAGAAGCTTGGAGCTT	0.418													G|||	1179	0.235423	0.0325	0.2622	5008	,	,		20833	0.3105		0.2515	False		,,,				2504	0.3967				p.S367S		Atlas-SNP	.											PAPOLB_ENST00000404991,NS,carcinoma,-1,2	PAPOLB	93	2	0			c.C1101T						PASS	.	G	,	281,4119	146.5+/-181.1	9,263,1928	128.0	130.0	129.0		,1101	4.5	1.0	7	dbSNP_123	129	2363,6237	387.8+/-342.3	330,1703,2267	no	intron,coding-synonymous	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,	339,1966,4195	AA,AG,GG		27.4767,6.3864,20.3385	,	,367/638	4900341	2644,10356	2200	4300	6500	SO:0001819	synonymous_variant	56903	exon1			AAAGAAGCTTGGA	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1098C>T	7.37:g.4900341G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	260	78	0.3	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																				G|0.777;A|0.223	0.223	strong		0.418	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
SVIL	6840	hgsc.bcm.edu	37	10	29822159	29822159	+	Silent	SNP	T	T	C	rs7076239	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29822159T>C	ENST00000355867.4	-	8	1889	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	SVIL_ENST00000375398.2_Silent_p.L379L|SVIL_ENST00000375400.3_Intron	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	172	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	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		
IL4R	3566	hgsc.bcm.edu	37	16	27373915	27373915	+	Silent	SNP	G	G	T	rs2234898	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000170630.2_Silent_p.L414L|IL4R_ENST00000543915.2_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						PASS	.	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	57	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	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		
ZNF160	90338	hgsc.bcm.edu	37	19	53572494	53572494	+	Silent	SNP	G	G	T	rs11665677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53572494G>T	ENST00000429604.1	-	7	1708	c.1293C>A	c.(1291-1293)ggC>ggA	p.G431G	ZNF160_ENST00000418871.1_Silent_p.G431G|ZNF160_ENST00000599056.1_Silent_p.G431G|ZNF160_ENST00000601421.1_Silent_p.G395G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	431					hemopoiesis (GO:0030097)|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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TAAAGACTTTGCCACATTCAT	0.428													g|||	1378	0.27516	0.4629	0.2795	5008	,	,		21830	0.0714		0.3022	False		,,,				2504	0.2004				p.G431G		Atlas-SNP	.											ZNF160,NS,carcinoma,-1,1	ZNF160	75	1	0			c.C1293A						scavenged	.	A	,,	1816,2590	530.8+/-373.0	369,1078,756	130.0	131.0	131.0		1293,1293,1293	-4.3	0.0	19	dbSNP_120	131	2678,5922	429.5+/-356.2	418,1842,2040	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF160	NM_001102603.1,NM_033288.3,NM_198893.2	,,	787,2920,2796	TT,TG,GG		31.1395,41.2165,34.5533	,,	431/819,431/819,431/819	53572494	4494,8512	2203	4300	6503	SO:0001819	synonymous_variant	90338	exon7			GACTTTGCCACAT	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1293C>A	19.37:g.53572494G>T		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	37	CCDS12859.1																																																																																			G|0.683;T|0.317	0.317	strong		0.428	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
HNF1A	6927	hgsc.bcm.edu	37	12	121416622	121416622	+	Silent	SNP	C	C	G	rs1169289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A-AS1_ENST00000537361.1_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A_ENST00000541395.1_Silent_p.L17L			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				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)	p.?(1)		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)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						scavenged	.	C		1508,2894		278,952,971	24.0	29.0	27.0		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	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.51C>G	12.37:g.121416622C>G		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
TOPBP1	11073	hgsc.bcm.edu	37	3	133329943	133329943	+	Silent	SNP	G	G	A	rs1444601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133329943G>A	ENST00000260810.5	-	25	4209	c.4078C>T	c.(4078-4080)Ctg>Ttg	p.L1360L		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1360					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						ATTCCAGTCAGAACATCAAGT	0.418								Other conserved DNA damage response genes					A|||	3416	0.682109	0.7829	0.634	5008	,	,		17725	0.626		0.7465	False		,,,				2504	0.5716				p.L1360L	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.C4078T						PASS	.	A		2917,841		1131,655,93	195.0	182.0	186.0		4078	0.4	1.0	3	dbSNP_88	186	6028,2192		2227,1574,309	no	coding-synonymous	TOPBP1	NM_007027.3		3358,2229,402	AA,AG,GG		26.6667,22.3789,25.3214		1360/1523	133329943	8945,3033	1879	4110	5989	SO:0001819	synonymous_variant	11073	exon25			CAGTCAGAACATC	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4078C>T	3.37:g.133329943G>A		Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	267	265	0.992509	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			G|0.298;A|0.702	0.702	strong		0.418	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24423007G>A	ENST00000313250.5	+	1	213	c.10G>A	c.(10-12)Gcg>Acg	p.A4T	DHRS4_ENST00000543741.2_Missense_Mutation_p.A4T|DHRS4_ENST00000397075.3_Missense_Mutation_p.A4T|DHRS4_ENST00000559632.1_Missense_Mutation_p.A4T|DHRS4_ENST00000382761.3_5'UTR|DHRS4_ENST00000421831.1_5'UTR|DHRS4_ENST00000558263.1_Missense_Mutation_p.A4T|DHRS4_ENST00000558581.1_Missense_Mutation_p.A4T|DHRS4_ENST00000397074.3_Missense_Mutation_p.A4T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_5'UTR|DHRS4_ENST00000397073.2_5'UTR	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	4					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CATGCACAAGGCGGGGCTGCT	0.662													.|||	988	0.197284	0.6135	0.1023	5008	,	,		16663	0.0099		0.0517	False		,,,				2504	0.045				p.A4T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G10A						PASS	.	A	THR/ALA	2359,2047		647,1065,491	49.0	54.0	52.0		10	1.8	0.0	14	dbSNP_123	52	456,8144		13,430,3857	yes	missense	DHRS4	NM_021004.2	58	660,1495,4348	AA,AG,GG		5.3023,46.4594,21.6439	benign	4/279	24423007	2815,10191	2203	4300	6503	SO:0001583	missense	10901	exon1			CACAAGGCGGGGC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.10G>A	14.37:g.24423007G>A	ENSP00000326219:p.Ala4Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	393	0.17994505494505494	312	0.6341463414634146	36	0.09944751381215469	8	0.013986013986013986	37	0.048812664907651716	.	10.41	1.343665	0.24339	0.535406	0.053023	ENSG00000157326	ENST00000313250;ENST00000397075;ENST00000397074;ENST00000543741	D;T;T;T	0.84298	-1.83;1.85;0.42;1.63	2.71	1.81	0.25067	.	0.882556	0.09474	N	0.797291	T	0.00012	0.0000	L	0.60455	1.87	0.48571	P	3.300000000000525E-4	B;B;B;B;B;B	0.16603	0.011;0.001;0.0;0.018;0.003;0.001	B;B;B;B;B;B	0.17722	0.009;0.003;0.002;0.019;0.003;0.002	T	0.44390	-0.9331	9	0.42905	T	0.14	.	5.8712	0.18805	0.149:0.0:0.851:0.0	rs17099455;rs52815329;rs17099455	4;4;4;4;4;4	Q9BTZ2-5;F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2-4;Q9BTZ2	.;.;.;.;.;DHRS4_HUMAN	T	4	ENSP00000326219:A4T;ENSP00000380265:A4T;ENSP00000380264:A4T;ENSP00000440508:A4T	ENSP00000326219:A4T	A	+	1	0	DHRS4	23492847	0.004000	0.15560	0.001000	0.08648	0.005000	0.04900	1.198000	0.32223	0.744000	0.32741	-0.346000	0.07831	GCG	G|0.795;A|0.205	0.205	strong		0.662	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
ATF7IP	55729	hgsc.bcm.edu	37	12	14577892	14577892	+	Missense_Mutation	SNP	A	A	T	rs2231909	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:14577892A>T	ENST00000540793.1	+	1	1198	c.1043A>T	c.(1042-1044)aAt>aTt	p.N348I	ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000536444.1_Missense_Mutation_p.N348I|ATF7IP_ENST00000261168.4_Missense_Mutation_p.N348I|ATF7IP_ENST00000544627.1_Missense_Mutation_p.N356I|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	54	0	0		WXS	Illumina HiSeq	Phase_I	59	22	0.372881	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	
KMT2D	8085	hgsc.bcm.edu	37	12	49445028	49445028	+	Missense_Mutation	SNP	G	G	A	rs75226229	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49445028G>A	ENST00000301067.7	-	10	2437	c.2438C>T	c.(2437-2439)cCg>cTg	p.P813L		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	813	Pro-rich.		P -> L (in dbSNP:rs75226229). {ECO:0000269|PubMed:21280141}.	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)										AGACAGGTGCGGCTCCTCAGT	0.647													G|||	80	0.0159744	0.0023	0.0274	5008	,	,		15268	0.0		0.0487	False		,,,				2504	0.0092				p.P813L		Atlas-SNP	.											.	MLL2	1173	.	0			c.C2438T						PASS	.	G	LEU/PRO	45,3979		0,45,1967	36.0	40.0	38.0		2438	-1.4	0.0	12	dbSNP_132	38	424,7814		15,394,3710	yes	missense	MLL2	NM_003482.3	98	15,439,5677	AA,AG,GG		5.1469,1.1183,3.8248	probably-damaging	813/5538	49445028	469,11793	2012	4119	6131	SO:0001583	missense	8085	exon10			AGGTGCGGCTCCT	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.2438C>T	12.37:g.49445028G>A	ENSP00000301067:p.Pro813Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	56	0.02564102564102564	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	43	0.05672823218997362	G	5.855	0.341913	0.11069	0.011183	0.051469	ENSG00000167548	ENST00000301067	T	0.33216	1.42	3.68	-1.4	0.08968	.	.	.	.	.	T	0.01189	0.0039	N	0.02539	-0.55	0.21386	N	0.999707	B	0.02656	0.0	B	0.01281	0.0	T	0.22730	-1.0208	9	0.87932	D	0	.	8.578	0.33609	0.6006:0.0:0.3994:0.0	.	813	O14686	MLL2_HUMAN	L	813	ENSP00000301067:P813L	ENSP00000301067:P813L	P	-	2	0	MLL2	47731295	0.000000	0.05858	0.028000	0.17463	0.009000	0.06853	-0.587000	0.05780	-0.301000	0.08882	-0.972000	0.02603	CCG	G|0.971;A|0.029	0.029	strong		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ITGA7	3679	hgsc.bcm.edu	37	12	56082025	56082025	+	Silent	SNP	G	G	C	rs17117883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56082025G>C	ENST00000555728.1	-	24	3178	c.3150C>G	c.(3148-3150)tcC>tcG	p.S1050S	ITGA7_ENST00000347027.6_Silent_p.S1000S|ITGA7_ENST00000257879.6_Silent_p.S1006S|ITGA7_ENST00000257880.7_Silent_p.S1050S|ITGA7_ENST00000452168.2_Silent_p.S913S|ITGA7_ENST00000394230.2_Silent_p.S1010S|ITGA7_ENST00000394229.2_Silent_p.S1006S|ITGA7_ENST00000553804.1_Silent_p.S1010S			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	183	0	0		WXS	Illumina HiSeq	Phase_I	166	79	0.475904	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	
C2orf40	84417	hgsc.bcm.edu	37	2	106690493	106690493	+	Silent	SNP	C	C	T	rs41280609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:106690493C>T	ENST00000238044.3	+	3	388	c.279C>T	c.(277-279)gaC>gaT	p.D93D	C2orf40_ENST00000409944.1_Silent_p.D57D|C2orf40_ENST00000489174.1_3'UTR	NM_032411.2	NP_115787.1	Q9H1Z8	AUGN_HUMAN	chromosome 2 open reading frame 40	93					cellular senescence (GO:0090398)|cyclin catabolic process (GO:0008054)|G1 to G0 transition (GO:0070314)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				lung(7)|urinary_tract(1)	8						TGGGCTTTGACGAAGCGGTAG	0.612													.|||	122	0.024361	0.0015	0.0634	5008	,	,		17838	0.001		0.0388	False		,,,				2504	0.0368				p.D93D		Atlas-SNP	.											.	C2orf40	16	.	0			c.C279T						PASS	.	C		57,4349	55.5+/-91.7	0,57,2146	62.0	64.0	64.0		279	-3.0	0.7	2	dbSNP_127	64	511,8089	144.0+/-200.0	10,491,3799	no	coding-synonymous	C2orf40	NM_032411.2		10,548,5945	TT,TC,CC		5.9419,1.2937,4.3672		93/149	106690493	568,12438	2203	4300	6503	SO:0001819	synonymous_variant	84417	exon3			CTTTGACGAAGCG	BC021742	CCDS2072.1	2q12.2	2014-01-28			ENSG00000119147	ENSG00000119147			24642	protein-coding gene	gene with protein product	"""esophageal cancer related gene 4 protein"""	611752				12800218	Standard	NM_032411		Approved	ECRG4, augurin	uc010fjf.3	Q9H1Z8	OTTHUMG00000130921	ENST00000238044.3:c.279C>T	2.37:g.106690493C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_032411	D3DVK2	Silent	SNP	ENST00000238044.3	37	CCDS2072.1																																																																																			C|0.961;T|0.039	0.039	strong		0.612	C2orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253515.2	NM_032411	
HLA-C	3107	hgsc.bcm.edu	37	6	31239430	31239430	+	Missense_Mutation	SNP	C	C	T	rs41543814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	136	5	0.0367647		WXS	Illumina HiSeq	Phase_I	209	207	0.990431	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	
EFCAB6	64800	hgsc.bcm.edu	37	22	43936219	43936219	+	Missense_Mutation	SNP	C	C	T	rs61995890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43936219C>T	ENST00000262726.7	-	28	3920	c.3667G>A	c.(3667-3669)Gag>Aag	p.E1223K	EFCAB6_ENST00000396231.2_Missense_Mutation_p.E1071K|EFCAB6_ENST00000461800.1_5'UTR	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1223	EF-hand 14. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)				ACTGGCATCTCGTTCCAGAGT	0.567													C|||	493	0.0984425	0.0847	0.1066	5008	,	,		17636	0.0288		0.172	False		,,,				2504	0.1074				p.E1223K		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G3667A						PASS	.	C	LYS/GLU,LYS/GLU	456,3950	218.1+/-236.3	22,412,1769	74.0	60.0	65.0		3667,3211	2.0	0.7	22	dbSNP_129	65	1444,7156	277.5+/-292.9	110,1224,2966	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	56,56	132,1636,4735	TT,TC,CC		16.7907,10.3495,14.6086	benign,benign	1223/1502,1071/1350	43936219	1900,11106	2203	4300	6503	SO:0001583	missense	64800	exon28			GCATCTCGTTCCA	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.3667G>A	22.37:g.43936219C>T	ENSP00000262726:p.Glu1223Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	255	0.11675824175824176	57	0.11585365853658537	44	0.12154696132596685	19	0.033216783216783216	135	0.17810026385224276	C	11.66	1.704657	0.30232	0.103495	0.167907	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.80123	-1.34;-1.34	5.49	2.02	0.26589	EF-hand calcium-binding domain-containing protein 6 (1);EF-hand-like domain (1);	0.360922	0.26112	N	0.026268	T	0.00300	0.0009	L	0.43701	1.375	0.26526	P	0.9743357	B	0.19583	0.037	B	0.20955	0.032	T	0.05517	-1.0880	9	0.25751	T	0.34	-29.1738	5.0927	0.14718	0.0:0.4816:0.3178:0.2005	.	1223	Q5THR3	EFCB6_HUMAN	K	1071;1223	ENSP00000379533:E1071K;ENSP00000262726:E1223K	ENSP00000262726:E1223K	E	-	1	0	EFCAB6	42267552	0.269000	0.24143	0.687000	0.30102	0.981000	0.71138	0.472000	0.22116	0.787000	0.33731	0.650000	0.86243	GAG	C|0.860;T|0.140	0.140	strong		0.567	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161161284	161161284	+	Missense_Mutation	SNP	G	G	C	rs41270041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161161284G>C	ENST00000367996.5	-	9	2586	c.2158C>G	c.(2158-2160)Cct>Gct	p.P720A	ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	720	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CGGTGGCCAGGGTTTCCCTGC	0.582													G|||	499	0.0996406	0.1157	0.0677	5008	,	,		20568	0.0665		0.0726	False		,,,				2504	0.1626				p.P720A		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.C2158G						PASS	.	G	ALA/PRO	535,3871	244.7+/-253.9	37,461,1705	65.0	68.0	67.0		2158	0.3	0.0	1	dbSNP_127	67	696,7904	172.0+/-222.8	30,636,3634	yes	missense	ADAMTS4	NM_005099.4	27	67,1097,5339	CC,CG,GG		8.093,12.1425,9.4649	benign	720/838	161161284	1231,11775	2203	4300	6503	SO:0001583	missense	9507	exon9			GGCCAGGGTTTCC	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.2158C>G	1.37:g.161161284G>C	ENSP00000356975:p.Pro720Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	162	0.07417582417582418	49	0.09959349593495935	22	0.06077348066298342	35	0.06118881118881119	56	0.07387862796833773	G	2.807	-0.247892	0.05867	0.121425	0.08093	ENSG00000158859	ENST00000367996	T	0.48836	0.8	4.39	0.261	0.15592	ADAM-TS Spacer 1 (1);	0.307814	0.27782	N	0.017880	T	0.10937	0.0267	N	0.24115	0.695	0.49051	P	2.590000000000092E-4	B	0.06786	0.001	B	0.14023	0.01	T	0.07751	-1.0756	9	0.54805	T	0.06	.	1.5245	0.02523	0.274:0.1456:0.4318:0.1486	rs41270041;rs60958497;rs61737001	720	O75173	ATS4_HUMAN	A	720	ENSP00000356975:P720A	ENSP00000356975:P720A	P	-	1	0	ADAMTS4	159427908	0.000000	0.05858	0.007000	0.13788	0.218000	0.24690	0.003000	0.13083	0.182000	0.20032	0.561000	0.74099	CCT	G|0.910;C|0.090	0.090	strong		0.582	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
DLL3	10683	hgsc.bcm.edu	37	19	39994711	39994711	+	Splice_Site	SNP	T	T	C	rs1110627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39994711T>C	ENST00000205143.4	+	5	660	c.653T>C	c.(652-654)cTg>cCg	p.L218P	DLL3_ENST00000356433.5_Splice_Site_p.L218P	NM_016941.3	NP_058637.1	Q9NYJ7	DLL3_HUMAN	delta-like 3 (Drosophila)	218	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		L -> P (in dbSNP:rs1110627). {ECO:0000269|PubMed:16303743, ECO:0000269|PubMed:18485326}.		compartment pattern specification (GO:0007386)|negative regulation of neurogenesis (GO:0050768)|Notch signaling pathway (GO:0007219)|paraxial mesoderm development (GO:0048339)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)	integral component of membrane (GO:0016021)	Notch binding (GO:0005112)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)	19	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;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCCCCCATAGTGGTGTGCCGA	0.617													C|||	3155	0.629992	0.7511	0.5231	5008	,	,		19573	0.6111		0.5596	False		,,,				2504	0.6339				p.L218P		Atlas-SNP	.											.	DLL3	47	.	0			c.T653C						PASS	.	C	PRO/LEU,PRO/LEU	3172,1234	423.6+/-340.2	1145,882,176	71.0	64.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	653,653	0.8	0.0	19	dbSNP_86	67	4503,4097	561.6+/-387.8	1203,2097,1000	yes	missense-near-splice,missense-near-splice	DLL3	NM_016941.3,NM_203486.2	98,98	2348,2979,1176	CC,CT,TT		47.6395,28.0073,40.9888	benign,benign	218/619,218/588	39994711	7675,5331	2203	4300	6503	SO:0001630	splice_region_variant	10683	exon5			CCATAGTGGTGTG	AF241373	CCDS12537.1, CCDS12538.1	19q13.2	2008-05-14	2001-12-03			ENSG00000090932			2909	protein-coding gene	gene with protein product		602768	"""delta (Drosophila)-like 3"""			10364530, 10742114	Standard	NM_203486		Approved	SCDO1	uc002olx.2	Q9NYJ7		ENST00000205143.4:c.653-1T>C	19.37:g.39994711T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_016941	E9PFG2|Q8NBS4	Missense_Mutation	SNP	ENST00000205143.4	37	CCDS12538.1	1298	0.5943223443223443	368	0.7479674796747967	192	0.5303867403314917	313	0.5472027972027972	425	0.5606860158311345	C	1.326	-0.597997	0.03771	0.719927	0.523605	ENSG00000090932	ENST00000356433;ENST00000205143	D;D	0.89123	-2.41;-2.47	4.87	0.831	0.18860	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	1.742270	0.03180	N	0.171947	T	0.00012	0.0000	N	0.00050	-2.41	0.32789	P	0.501413	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37314	-0.9711	8	.	.	.	.	8.0038	0.30313	0.0:0.5714:0.0:0.4286	rs1110627;rs52827355;rs56660933;rs1110627	218;218	Q9NYJ7;E9PFG2	DLL3_HUMAN;.	P	218	ENSP00000348810:L218P;ENSP00000205143:L218P	.	L	+	2	0	DLL3	44686551	0.932000	0.31603	0.001000	0.08648	0.009000	0.06853	1.879000	0.39618	0.021000	0.15133	-0.215000	0.12644	CTG	T|0.400;C|0.600	0.600	strong		0.617	DLL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464958.1		Missense_Mutation
TFRC	7037	hgsc.bcm.edu	37	3	195800811	195800811	+	Missense_Mutation	SNP	C	C	T	rs3817672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195800811C>T	ENST00000360110.4	-	4	593	c.424G>A	c.(424-426)Ggc>Agc	p.G142S	TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Missense_Mutation_p.G142S|TFRC_ENST00000535031.1_Intron|RNU7-18P_ENST00000516365.1_RNA|TFRC_ENST00000420415.1_Missense_Mutation_p.G61S	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	142			G -> S (rare polymorphism; dbSNP:rs3817672). {ECO:0000269|PubMed:11702220, ECO:0000269|PubMed:6090955, ECO:0000269|PubMed:6094009}.		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)	TTGATGGTGCCGGTGAAGTCT	0.502			T	BCL6	NHL						OREG0016005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1534	0.30631	0.1641	0.3617	5008	,	,		18870	0.1518		0.5427	False		,,,				2504	0.3753				p.G142S		Atlas-SNP	.		Dom	yes		3	3q29	7037	"""transferrin receptor (p90, CD71)"""		L	.	TFRC	54	.	0			c.G424A	GRCh37	CM991171	TFRC	M	rs3817672	PASS	.	C	SER/GLY,SER/GLY	1004,3402	373.7+/-320.9	112,780,1311	76.0	69.0	72.0		424,424	1.5	0.0	3	dbSNP_107	72	4692,3908	605.0+/-394.9	1281,2130,889	yes	missense,missense	TFRC	NM_001128148.1,NM_003234.2	56,56	1393,2910,2200	TT,TC,CC		45.4419,22.7871,43.7952	benign,benign	142/761,142/761	195800811	5696,7310	2203	4300	6503	SO:0001583	missense	7037	exon4			TGGTGCCGGTGAA	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.424G>A	3.37:g.195800811C>T	ENSP00000353224:p.Gly142Ser	Somatic	71	0	0	2078	WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	37	CCDS3312.1	718	0.32875457875457875	83	0.16869918699186992	138	0.3812154696132597	83	0.1451048951048951	414	0.5461741424802111	c	7.704	0.693807	0.15039	0.227871	0.545581	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396	T;T;T	0.38240	1.15;1.15;1.15	5.2	1.51	0.23008	.	1.393470	0.03757	N	0.257483	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43196	-0.9406	9	0.12103	T	0.63	0.58	6.9135	0.24347	0.0:0.2856:0.0:0.7144	rs3817672;rs17196183;rs52799905;rs61158992;rs3817672	142	P02786	TFR1_HUMAN	S	142;61;142	ENSP00000353224:G142S;ENSP00000390133:G61S;ENSP00000376197:G142S	ENSP00000353224:G142S	G	-	1	0	TFRC	197285208	0.000000	0.05858	0.001000	0.08648	0.080000	0.17528	-0.262000	0.08682	0.076000	0.16826	-0.374000	0.07098	GGC	C|0.624;T|0.376	0.376	strong		0.502	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1		
MASP2	10747	hgsc.bcm.edu	37	1	11097867	11097867	+	Splice_Site	SNP	C	C	T	rs12142107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11097867C>T	ENST00000400897.3	-	7	906	c.891G>A	c.(889-891)gcG>gcA	p.A297A		NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	297					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		GGCAAGGCTGCGCTGCGCAGA	0.478											OREG0013096	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	658	0.13139	0.2519	0.0778	5008	,	,		18493	0.1121		0.0219	False		,,,				2504	0.1391				p.A297A	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.G891A						PASS	.	C		905,3501	348.2+/-309.8	95,715,1393	100.0	96.0	98.0		891	-6.5	0.0	1	dbSNP_120	98	181,8419	82.0+/-144.6	2,177,4121	yes	coding-synonymous-near-splice	MASP2	NM_006610.3		97,892,5514	TT,TC,CC		2.1047,20.5402,8.35		297/687	11097867	1086,11920	2203	4300	6503	SO:0001630	splice_region_variant	10747	exon7			AGGCTGCGCTGCG	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.890-1G>A	1.37:g.11097867C>T		Somatic	33	0	0	669	WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Silent	SNP	ENST00000400897.3	37	CCDS123.1																																																																																			C|0.914;T|0.086	0.086	strong		0.478	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	Silent
SEC14L5	9717	hgsc.bcm.edu	37	16	5064917	5064917	+	Silent	SNP	C	C	T	rs2012649	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5064917C>T	ENST00000251170.7	+	16	2217	c.2037C>T	c.(2035-2037)gcC>gcT	p.A679A	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	679	Ser-rich.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						TCAGCGCCGCCACCTCGTCCT	0.662													C|||	767	0.153155	0.0371	0.3833	5008	,	,		17274	0.0645		0.2624	False		,,,				2504	0.1258				p.A679A		Atlas-SNP	.											.	SEC14L5	79	.	0			c.C2037T						PASS	.	C		330,3988		6,318,1835	46.0	53.0	51.0		2037	3.7	0.9	16	dbSNP_92	51	2149,6389		264,1621,2384	no	coding-synonymous	SEC14L5	NM_014692.1		270,1939,4219	TT,TC,CC		25.1698,7.6424,19.2828		679/697	5064917	2479,10377	2159	4269	6428	SO:0001819	synonymous_variant	9717	exon16			CGCCGCCACCTCG	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.2037C>T	16.37:g.5064917C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.846;T|0.154	0.154	strong		0.662	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
KIAA1586	57691	hgsc.bcm.edu	37	6	56918933	56918933	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:56918933A>G	ENST00000370733.4	+	4	1843	c.1636A>G	c.(1636-1638)Aga>Gga	p.R546G	KIAA1586_ENST00000545356.1_Missense_Mutation_p.R519G	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	546							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ATTACAGTCAAGATCAACTAA	0.299																																					p.R546G		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A1636G						PASS	.						30.0	31.0	31.0					6																	56918933		2174	4281	6455	SO:0001583	missense	57691	exon4			CAGTCAAGATCAA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.1636A>G	6.37:g.56918933A>G	ENSP00000359768:p.Arg546Gly	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	10.50	1.368490	0.24771	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.21191	2.02;2.02	3.84	2.66	0.31614	Ribonuclease H-like (1);	.	.	.	.	T	0.03305	0.0096	N	0.08118	0	0.23107	N	0.998283	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.40831	-0.9542	9	0.62326	D	0.03	-3.9313	5.9809	0.19407	0.8787:0.0:0.1213:0.0	.	519;546	F5H2N6;Q9HCI6	.;K1586_HUMAN	G	546;519	ENSP00000359768:R546G;ENSP00000445507:R519G	ENSP00000359768:R546G	R	+	1	2	KIAA1586	57026892	0.999000	0.42202	0.959000	0.39883	0.992000	0.81027	1.557000	0.36299	0.637000	0.30526	-0.263000	0.10527	AGA	.	.	none		0.299	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
PDYN	5173	hgsc.bcm.edu	37	20	1961134	1961134	+	Silent	SNP	A	A	G	rs6045819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1961134A>G	ENST00000217305.2	-	4	825	c.600T>C	c.(598-600)caT>caC	p.H200H	PDYN_ENST00000539905.1_Silent_p.H200H|PDYN_ENST00000540134.1_Silent_p.H200H|RP4-684O24.5_ENST00000446562.1_RNA	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	200					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACAGGTCCTCATGGCCCATGC	0.597													a|||	652	0.130192	0.32	0.1037	5008	,	,		17033	0.0		0.1103	False		,,,				2504	0.047				p.H200H		Atlas-SNP	.											.	PDYN	74	.	0			c.T600C						PASS	.	A	,,,,	1203,3203	420.4+/-339.0	165,873,1165	102.0	112.0	108.0		600,600,600,600,600	-7.3	0.7	20	dbSNP_114	108	1047,7553	220.9+/-258.5	54,939,3307	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDYN	NM_001190892.1,NM_001190898.2,NM_001190899.2,NM_001190900.1,NM_024411.4	,,,,	219,1812,4472	GG,GA,AA		12.1744,27.3037,17.2997	,,,,	200/255,200/255,200/255,200/255,200/255	1961134	2250,10756	2203	4300	6503	SO:0001819	synonymous_variant	5173	exon4			GTCCTCATGGCCC		CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"""Endogenous ligands"""	8820	protein-coding gene	gene with protein product	"""preproenkephalin B"", ""rimorphin"", ""beta-neoendorphin"", ""dynorphin"", ""leu-enkephalin"", ""leumorphin"", ""neoendorphin-dynorphin-enkephalin prepropeptide"""	131340	"""spinocerebellar ataxia 23"""	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.600T>C	20.37:g.1961134A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_001190898	A8K0Q3	Silent	SNP	ENST00000217305.2	37	CCDS13023.1																																																																																			A|0.834;G|0.166	0.166	strong		0.597	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2		
ATP13A5	344905	hgsc.bcm.edu	37	3	193039597	193039597	+	Silent	SNP	G	G	A	rs61753889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:193039597G>A	ENST00000342358.4	-	16	1905	c.1788C>T	c.(1786-1788)tgC>tgT	p.C596C		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	596						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)		ATGGAAACTGGCACAAGGTGA	0.483													G|||	336	0.0670927	0.0946	0.0634	5008	,	,		18426	0.0		0.0616	False		,,,				2504	0.1074				p.C596C		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C1788T						PASS	.	G		398,4008	199.1+/-222.7	14,370,1819	92.0	88.0	89.0		1788	-0.2	0.7	3	dbSNP_129	89	485,8115	142.2+/-198.4	20,445,3835	no	coding-synonymous	ATP13A5	NM_198505.2		34,815,5654	AA,AG,GG		5.6395,9.0331,6.7892		596/1219	193039597	883,12123	2203	4300	6503	SO:0001819	synonymous_variant	344905	exon16			AAACTGGCACAAG	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.1788C>T	3.37:g.193039597G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_198505	Q6UWS4|Q6ZWL0	Silent	SNP	ENST00000342358.4	37	CCDS33914.1																																																																																			G|0.933;A|0.067	0.067	strong		0.483	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
PTPRF	5792	hgsc.bcm.edu	37	1	44035352	44035352	+	Silent	SNP	C	C	T	rs1065771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44035352C>T	ENST00000359947.4	+	6	811	c.471C>T	c.(469-471)gcC>gcT	p.A157A	PTPRF_ENST00000372414.3_Silent_p.A157A|PTPRF_ENST00000372413.3_Silent_p.A157A|PTPRF_ENST00000438120.1_Silent_p.A157A	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	157	Ig-like C2-type 2.				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)				TGCTATGTGCCGCAGGCGGAA	0.592													C|||	1112	0.222045	0.0356	0.2363	5008	,	,		20025	0.2917		0.3101	False		,,,				2504	0.3016				p.A157A		Atlas-SNP	.											.	PTPRF	172	.	0			c.C471T						PASS	.	C	,	369,4037	188.5+/-214.9	17,335,1851	94.0	92.0	92.0		471,471	-1.0	1.0	1	dbSNP_86	92	2666,5934	429.0+/-356.1	427,1812,2061	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	444,2147,3912	TT,TC,CC		31.0,8.3749,23.3354	,	157/1908,157/1899	44035352	3035,9971	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon6			ATGTGCCGCAGGC	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.471C>T	1.37:g.44035352C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	80	47	0.5875	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2																																																																																			C|0.774;T|0.226	0.226	strong		0.592	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
MRC1	4360	hgsc.bcm.edu	37	10	17891705	17891705	+	Missense_Mutation	SNP	A	A	G	rs1926736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:17891705A>G	ENST00000331429.2	+	7	1289	c.1186A>G	c.(1186-1188)Agt>Ggt	p.S396G	MRC1L1_ENST00000457317.1_Missense_Mutation_p.S396G																breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GAAGGAAGGCAGTGACCTCGC	0.453													G|||	3115	0.622005	0.9002	0.4193	5008	,	,		10035	0.5833		0.5348	False		,,,				2504	0.5194				p.S396G		Atlas-SNP	.											.	MRC1	13	.	0			c.A1186G						PASS	.	G		3535,779		1611,313,233	152.0	181.0	171.0			3.7	1.0	10	dbSNP_92	171	4317,3961		1531,1255,1353	yes	intergenic				3142,1568,1586	GG,GA,AA		47.8497,18.0575,37.6429			17891705	7852,4740	2157	4139	6296	SO:0001583	missense	4360	exon7			GAAGGCAGTGACC																												ENST00000331429.2:c.1186A>G	10.37:g.17891705A>G	ENSP00000332124:p.Ser396Gly	Somatic	397	1	0.00251889		WXS	Illumina HiSeq	Phase_I	343	341	0.994169	NM_002438		Missense_Mutation	SNP	ENST00000331429.2	37		1273	0.5828754578754579	425	0.8638211382113821	173	0.47790055248618785	287	0.5017482517482518	388	0.5118733509234829	G	0.018	-1.471947	0.01044	0.819425	0.521503	ENSG00000183748	ENST00000331429;ENST00000457317	T;T	0.16743	2.32;2.32	3.74	3.74	0.42951	.	0.000000	0.56097	N	0.000031	T	0.00012	0.0000	.	.	.	0.09310	P	0.999993	.	.	.	.	.	.	T	0.32929	-0.9888	6	0.02654	T	1	-10.1753	10.1029	0.42515	0.0957:0.0:0.9043:0.0	rs1926736;rs7077734;rs1926736	.	.	.	G	396	ENSP00000332124:S396G;ENSP00000391843:S396G	ENSP00000332124:S396G	S	+	1	0	AL928580.1	17931711	1.000000	0.71417	0.961000	0.40146	0.006000	0.05464	6.527000	0.73803	0.922000	0.37019	-0.360000	0.07572	AGT	.	.	weak		0.453	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1		
RASAL2	9462	hgsc.bcm.edu	37	1	178442222	178442222	+	Missense_Mutation	SNP	G	G	A	rs371002131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:178442222G>A	ENST00000462775.1	+	16	3393	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	RASAL2_ENST00000367649.3_Missense_Mutation_p.V1231M|RASAL2_ENST00000448150.3_Missense_Mutation_p.V1220M	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	1090					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)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						AAAACGGATCGTGTCCCTGGA	0.522													G|||	2	0.000399361	0.0	0.0	5008	,	,		21631	0.0		0.0	False		,,,				2504	0.002				p.V1231M		Atlas-SNP	.											.	RASAL2	334	.	0			c.G3691A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	148.0	129.0	136.0		3268,3691	1.7	1.0	1		136	0,8600		0,0,4300	no	missense,missense	RASAL2	NM_004841.3,NM_170692.2	21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	1090/1140,1231/1281	178442222	1,13005	2203	4300	6503	SO:0001583	missense	9462	exon18			CGGATCGTGTCCC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.3268G>A	1.37:g.178442222G>A	ENSP00000420558:p.Val1090Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	168	105	0.625	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.86|12.86	2.064109|2.064109	0.36373|0.36373	2.27E-4|2.27E-4	0.0|0.0	ENSG00000075391|ENSG00000075391	ENST00000367647|ENST00000448150;ENST00000367649;ENST00000462775	.|T;T;T	.|0.12569	.|2.67;2.67;2.67	5.79|5.79	1.68|1.68	0.24146|0.24146	.|.	.|0.649779	.|0.15466	.|N	.|0.260880	T|T	0.05364|0.05364	0.0142|0.0142	N|N	0.08118|0.08118	0|0	0.32851|0.32851	D|D	0.506687|0.506687	.|P;P	.|0.46952	.|0.842;0.887	.|B;B	.|0.39379	.|0.298;0.157	T|T	0.31420|0.31420	-0.9944|-0.9944	6|10	0.87932|0.59425	D|D	0|0.04	.|.	1.8144|1.8144	0.03097|0.03097	0.2871:0.1267:0.4559:0.1303|0.2871:0.1267:0.4559:0.1303	.|.	.|1090;1231	.|Q9UJF2;F8W755	.|NGAP_HUMAN;.	H|M	43|1220;1231;1090	.|ENSP00000407768:V1220M;ENSP00000356621:V1231M;ENSP00000420558:V1090M	ENSP00000356619:R43H|ENSP00000356621:V1231M	R|V	+|+	2|1	0|0	RASAL2|RASAL2	176708845|176708845	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.793000|0.793000	0.26944|0.26944	0.382000|0.382000	0.24878|0.24878	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.	none		0.522	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	
OR52E6	390078	hgsc.bcm.edu	37	11	5862532	5862532	+	Missense_Mutation	SNP	A	A	C	rs10742809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5862532A>C	ENST00000329322.5	-	1	595	c.596T>G	c.(595-597)aTg>aGg	p.M199R	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.M203R	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	199			M -> R (in dbSNP:rs10742809).			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(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAGACCAAACATAATGTTGAC	0.473													A|||	1644	0.328275	0.2224	0.304	5008	,	,		21378	0.4593		0.3439	False		,,,				2504	0.3374				p.M199R		Atlas-SNP	.											.	OR52E6	70	.	0			c.T596G						PASS	.	A	ARG/MET	1031,3371	373.4+/-320.8	122,787,1292	87.0	84.0	85.0		596	3.5	0.0	11	dbSNP_120	85	2800,5792	441.4+/-359.8	448,1904,1944	yes	missense	OR52E6	NM_001005167.1	91	570,2691,3236	CC,CA,AA		32.5885,23.4212,29.4828	benign	199/314	5862532	3831,9163	2201	4296	6497	SO:0001583	missense	390078	exon1			CCAAACATAATGT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.596T>G	11.37:g.5862532A>C	ENSP00000328878:p.Met199Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	751	0.34386446886446886	102	0.2073170731707317	115	0.31767955801104975	264	0.46153846153846156	270	0.3562005277044855	A	8.103	0.777055	0.16120	0.234212	0.325885	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00084	8.75;8.75	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	1.217830	0.05771	N	0.606787	T	0.00012	0.0000	N	0.16201	0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.10450	0.005	T	0.13335	-1.0513	9	0.48119	T	0.1	.	10.9113	0.47110	1.0:0.0:0.0:0.0	rs10742809;rs61269500;rs10742809	199	Q96RD3	O52E6_HUMAN	R	199;203	ENSP00000328878:M199R;ENSP00000369279:M203R	ENSP00000328878:M199R	M	-	2	0	OR52E6	5819108	0.000000	0.05858	0.003000	0.11579	0.564000	0.35744	0.650000	0.24858	1.430000	0.47334	0.450000	0.29827	ATG	A|0.670;C|0.330	0.330	strong		0.473	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
FLG	2312	hgsc.bcm.edu	37	1	152276377	152276377	+	Missense_Mutation	SNP	C	C	G	rs139284720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276377C>G	ENST00000368799.1	-	3	11020	c.10985G>C	c.(10984-10986)aGt>aCt	p.S3662T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3662	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.S3662T(2)		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)			ACTGGCCTGACTACCACTGGA	0.587									Ichthyosis																												p.S3662T		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,2	FLG	900	2	2	Substitution - Missense(2)	skin(2)	c.G10985C						scavenged	.						34.0	36.0	35.0					1																	152276377		2199	4266	6465	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCCTGACTACCAC	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.10985G>C	1.37:g.152276377C>G	ENSP00000357789:p.Ser3662Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	166	44	0.26506	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330609	0.24167	.	.	ENSG00000143631	ENST00000368799	T	0.20598	2.06	4.62	-2.36	0.06663	.	.	.	.	.	T	0.14874	0.0359	M	0.69823	2.125	0.09310	N	1	P	0.40211	0.707	P	0.54889	0.763	T	0.26883	-1.0090	9	0.25751	T	0.34	.	3.5688	0.07909	0.4266:0.3171:0.0:0.2564	.	3662	P20930	FILA_HUMAN	T	3662	ENSP00000357789:S3662T	ENSP00000357789:S3662T	S	-	2	0	FLG	150543001	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.742000	0.04850	-0.547000	0.06207	-0.240000	0.12126	AGT	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC4	4585	hgsc.bcm.edu	37	3	195508249	195508249	+	Missense_Mutation	SNP	A	A	G	rs201846606		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195508249A>G	ENST00000463781.3	-	2	10661	c.10202T>C	c.(10201-10203)gTa>gCa	p.V3401A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3401A	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)	p.V3401A(3)		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)		ACCTGTGGATACTGAGGAAGT	0.577																																					p.V3401A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,7	MUC4	1505	7	3	Substitution - Missense(3)	stomach(2)|kidney(1)	c.T10202C						scavenged	.						33.0	25.0	27.0					3																	195508249		685	1579	2264	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	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.10202T>C	3.37:g.195508249A>G	ENSP00000417498:p.Val3401Ala	Somatic	88	9	0.102273		WXS	Illumina HiSeq	Phase_I	152	21	0.138158	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	.	.	.	.	.	.	.	.	.	.	a	0.030	-1.338402	0.01287	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.54;1.48	0.743	-1.49	0.08718	.	.	.	.	.	T	0.07908	0.0198	N	0.02539	-0.55	0.09310	N	1	B	0.33494	0.414	B	0.19946	0.027	T	0.18366	-1.0339	8	.	.	.	.	2.8398	0.05525	0.2532:0.0:0.4936:0.2531	.	3273	E7ESK3	.	A	3401	ENSP00000417498:V3401A;ENSP00000420243:V3401A	.	V	-	2	0	MUC4	196993028	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-0.712000	0.05013	-1.995000	0.00971	-2.001000	0.00444	GTA	A|0.500;G|0.500	0.500	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SVIL	6840	hgsc.bcm.edu	37	10	29840038	29840038	+	Silent	SNP	A	A	G	rs3740003	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29840038A>G	ENST00000355867.4	-	6	1067	c.315T>C	c.(313-315)atT>atC	p.I105I	SVIL_ENST00000375398.2_Silent_p.I105I|SVIL_ENST00000375400.3_Silent_p.I105I	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	105	Interaction with MYLK. {ECO:0000250}.				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)	p.I105I(1)		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)				TGTACCTTGCAATTCTTTCGG	0.527													G|||	1625	0.324481	0.4228	0.2666	5008	,	,		19588	0.3472		0.2416	False		,,,				2504	0.2945				p.I105I		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.T315C						scavenged	.	G	,	1833,2573	636.9+/-396.7	375,1083,745	184.0	156.0	165.0		315,315	-1.8	0.0	10	dbSNP_107	165	2271,6329	707.6+/-405.6	294,1683,2323	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	669,2766,3068	GG,GA,AA		26.407,41.6024,31.5547	,	105/1789,105/2215	29840038	4104,8902	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			CCTTGCAATTCTT	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.315T>C	10.37:g.29840038A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	139	54	0.388489	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.678;G|0.322	0.322	strong		0.527	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
KIAA1279	26128	hgsc.bcm.edu	37	10	70748784	70748784	+	Missense_Mutation	SNP	G	G	A	rs2255607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	28	0	0		WXS	Illumina HiSeq	Phase_I	28	20	0.714286	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	
C2orf70	339778	hgsc.bcm.edu	37	2	26798893	26798893	+	Missense_Mutation	SNP	A	A	T	rs13002673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26798893A>T	ENST00000329615.3	+	2	229	c.198A>T	c.(196-198)caA>caT	p.Q66H	C2orf70_ENST00000409392.1_Missense_Mutation_p.R54W	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	66			Q -> H (in dbSNP:rs13002673).			nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						CCTTCAGCCAAGGCGGCCATT	0.627													A|||	1675	0.334465	0.0953	0.2262	5008	,	,		18527	0.623		0.336	False		,,,				2504	0.4356				p.Q66H		Atlas-SNP	.											.	C2orf70	26	.	0			c.A198T						PASS	.	A	HIS/GLN	537,3657		41,455,1601	118.0	129.0	125.0		198	-1.1	0.0	2	dbSNP_121	125	2502,5954		350,1802,2076	yes	missense	C2orf70	NM_001105519.1	24	391,2257,3677	TT,TA,AA		29.5885,12.804,24.0237	benign	66/202	26798893	3039,9611	2097	4228	6325	SO:0001583	missense	339778	exon2			CAGCCAAGGCGGC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"""hypothetical protein LOC339778"""						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.198A>T	2.37:g.26798893A>T	ENSP00000332875:p.Gln66His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	24	0.363636	NM_001105519		Missense_Mutation	SNP	ENST00000329615.3	37	CCDS42661.1	721|721	0.3301282051282051|0.3301282051282051	52|52	0.10569105691056911|0.10569105691056911	74|74	0.20441988950276244|0.20441988950276244	341|341	0.5961538461538461|0.5961538461538461	254|254	0.33509234828496043|0.33509234828496043	A|A	6.171|6.171	0.399809|0.399809	0.11696|0.11696	0.12804|0.12804	0.295885|0.295885	ENSG00000173557|ENSG00000173557	ENST00000329615|ENST00000409392	T|.	0.49139|.	0.79|.	4.43|4.43	-1.1|-1.1	0.09872|0.09872	.|.	1.741470|.	0.03300|.	N|.	0.188809|.	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|.	0.40731|.	0.728|.	B|.	0.36092|.	0.217|.	T|T	0.40136|0.40136	-0.9579|-0.9579	9|5	0.59425|0.87932	D|D	0.04|0	1.3311|1.3311	4.1823|4.1823	0.10381|0.10381	0.3399:0.3594:0.3007:0.0|0.3399:0.3594:0.3007:0.0	rs13002673;rs60890621;rs13002673|rs13002673;rs60890621;rs13002673	66|.	A6NJV1|.	CB070_HUMAN|.	H|W	66|54	ENSP00000332875:Q66H|.	ENSP00000332875:Q66H|ENSP00000386615:R54W	Q|R	+|+	3|1	2|2	C2orf70|C2orf70	26652397|26652397	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.252000|0.252000	0.25951|0.25951	-1.156000|-1.156000	0.03160|0.03160	-0.206000|-0.206000	0.10203|0.10203	0.379000|0.379000	0.24179|0.24179	CAA|AGG	A|0.675;T|0.325	0.325	strong		0.627	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519	
C15orf56	644809	hgsc.bcm.edu	37	15	40544493	40544493	+	Missense_Mutation	SNP	A	A	G	rs55799438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40544493A>G	ENST00000319503.3	-	2	500	c.479T>C	c.(478-480)aTc>aCc	p.I160T	PAK6_ENST00000260404.4_Intron|C15orf56_ENST00000559727.1_3'UTR|PAK6_ENST00000441369.1_Intron|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000560346.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000453867.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	160			I -> T (in dbSNP:rs55799438).							lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CGCTCAGCTGATTCTCCAGGT	0.726													G|||	793	0.158347	0.0499	0.1988	5008	,	,		11580	0.0873		0.3072	False		,,,				2504	0.1963				p.I160T		Atlas-SNP	.											.	C15orf56	3	.	0			c.T479C						PASS	.	G	,,,THR/ILE	337,3755		19,299,1728	6.0	7.0	7.0		,,,479	-4.1	0.0	15	dbSNP_129	7	2297,5829		358,1581,2124	yes	intron,intron,intron,missense	PAK6,C15orf56	NM_001128628.1,NM_001128629.1,NM_020168.4,NM_001039905.1	,,,89	377,1880,3852	GG,GA,AA		28.2673,8.2356,21.5584	,,,benign	,,,160/162	40544493	2634,9584	2046	4063	6109	SO:0001583	missense	644809	exon2			CAGCTGATTCTCC		CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.479T>C	15.37:g.40544493A>G	ENSP00000315794:p.Ile160Thr	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001039905		Missense_Mutation	SNP	ENST00000319503.3	37	CCDS32197.1	384	0.17582417582417584	30	0.06097560975609756	84	0.23204419889502761	40	0.06993006993006994	230	0.3034300791556728	G	6.507	0.461713	0.12342	0.082356	0.282673	ENSG00000176753	ENST00000319503	T	0.29917	1.55	3.57	-4.1	0.03940	.	.	.	.	.	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	0.40776	-0.9545	8	0.87932	D	0	.	3.4486	0.07490	0.401:0.0:0.1961:0.4028	rs55799438	160	Q8N910	CO056_HUMAN	T	160	ENSP00000315794:I160T	ENSP00000315794:I160T	I	-	2	0	C15orf56	38331785	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.657000	0.05335	-1.570000	0.01665	-1.212000	0.01626	ATC	A|0.824;G|0.176	0.176	strong		0.726	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905	
TMEM190	147744	hgsc.bcm.edu	37	19	55889451	55889451	+	Silent	SNP	G	G	A	rs77912983	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	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	
MROH2B	133558	hgsc.bcm.edu	37	5	41033163	41033163	+	Missense_Mutation	SNP	T	T	C	rs10067611	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:41033163T>C	ENST00000399564.4	-	23	2791	c.2341A>G	c.(2341-2343)Atg>Gtg	p.M781V	MROH2B_ENST00000506092.2_Missense_Mutation_p.M336V	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	781			M -> V (in dbSNP:rs10067611).														CCAATCAGCATCTCCTTGTAG	0.443													T|||	154	0.0307508	0.0303	0.0115	5008	,	,		21483	0.0536		0.0368	False		,,,				2504	0.0153				p.M781V		Atlas-SNP	.											.	.	.	.	0			c.A2341G						PASS	.	T	VAL/MET	131,3905		4,123,1891	122.0	113.0	116.0		2341	-0.3	0.1	5	dbSNP_119	116	246,8104		4,238,3933	yes	missense	HEATR7B2	NM_173489.4	21	8,361,5824	CC,CT,TT		2.9461,3.2458,3.0438	benign	781/1586	41033163	377,12009	2018	4175	6193	SO:0001583	missense	133558	exon23			TCAGCATCTCCTT		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.2341A>G	5.37:g.41033163T>C	ENSP00000382476:p.Met781Val	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	289	120	0.415225	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	81	0.03708791208791209	19	0.03861788617886179	5	0.013812154696132596	31	0.05419580419580419	26	0.03430079155672823	T	0.028	-1.353425	0.01256	0.032458	0.029461	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.05199	3.48;3.48	5.55	-0.28	0.12886	Armadillo-type fold (1);	1.162530	0.06333	N	0.706578	T	0.00384	0.0012	N	0.02011	-0.69	0.19300	N	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.44922	-0.9296	10	0.30854	T	0.27	.	0.1565	0.00098	0.3332:0.2446:0.1654:0.2568	rs10067611;rs52811327;rs60860203;rs10067611	781	Q7Z745	HTRB2_HUMAN	V	336;486;781	ENSP00000441504:M336V;ENSP00000382476:M781V	ENSP00000296803:M486V	M	-	1	0	HEATR7B2	41068920	0.851000	0.29673	0.131000	0.22000	0.099000	0.18886	0.119000	0.15626	-0.087000	0.12528	-0.333000	0.08304	ATG	T|0.963;C|0.037	0.037	strong		0.443	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
CCDC141	285025	hgsc.bcm.edu	37	2	179732845	179732845	+	Missense_Mutation	SNP	G	G	A	rs12988301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	98	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	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	
CTSB	1508	hgsc.bcm.edu	37	8	11706581	11706581	+	Silent	SNP	T	T	G	rs13332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11706581T>G	ENST00000353047.6	-	5	673	c.420A>C	c.(418-420)acA>acC	p.T140T	CTSB_ENST00000434271.1_Silent_p.T140T|CTSB_ENST00000533455.1_Silent_p.T140T|CTSB_ENST00000415599.2_Intron|CTSB_ENST00000534510.1_Silent_p.T140T|CTSB_ENST00000530640.2_Silent_p.T140T|CTSB_ENST00000531089.1_Silent_p.T140T|CTSB_ENST00000453527.2_Silent_p.T140T|CTSB_ENST00000345125.3_Silent_p.T140T|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000525076.1_5'UTR	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	140					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.T140T(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		TGCCACAGCATGTGAGCAGGT	0.632													G|||	2854	0.569888	0.6051	0.5389	5008	,	,		18558	0.5119		0.6163	False		,,,				2504	0.5562				p.T140T		Atlas-SNP	.											CTSB,NS,lymphoid_neoplasm,0,1	CTSB	24	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A420C						PASS	.	G	,,,,	3095,1311		1109,877,217	51.0	40.0	44.0		420,420,420,420,420	3.6	1.0	8	dbSNP_52	44	5359,3241		1675,2009,616	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CTSB	NM_001908.3,NM_147780.2,NM_147781.2,NM_147782.2,NM_147783.2	,,,,	2784,2886,833	GG,GT,TT		37.686,29.7549,34.9992	,,,,	140/340,140/340,140/340,140/340,140/340	11706581	8454,4552	2203	4300	6503	SO:0001819	synonymous_variant	1508	exon7			ACAGCATGTGAGC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.420A>C	8.37:g.11706581T>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Silent	SNP	ENST00000353047.6	37	CCDS5986.1																																																																																			T|0.358;G|0.637;C|0.006	0.637	strong		0.632	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68337948	68337948	+	Missense_Mutation	SNP	T	T	C	rs11548855	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:68337948T>C	ENST00000263997.6	-	3	677	c.659A>G	c.(658-660)tAc>tGc	p.Y220C		NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	220			Y -> C (in dbSNP:rs11548855).		hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		TTCTTGGCTGTAGGGCTGCAC	0.522													T|||	89	0.0177716	0.0023	0.0274	5008	,	,		18947	0.001		0.0567	False		,,,				2504	0.0092				p.Y220C		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.A659G						PASS	.	T	CYS/TYR	58,4338	55.5+/-91.7	0,58,2140	105.0	93.0	97.0		659	4.7	0.7	16	dbSNP_120	97	566,8034	153.6+/-207.9	16,534,3750	yes	missense	SLC7A6OS	NM_032178.2	194	16,592,5890	CC,CT,TT		6.5814,1.3194,4.8015	probably-damaging	220/310	68337948	624,12372	2198	4300	6498	SO:0001583	missense	84138	exon3			TGGCTGTAGGGCT		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.659A>G	16.37:g.68337948T>C	ENSP00000263997:p.Tyr220Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	184	97	0.527174	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	37	CCDS10865.1	60	0.027472527472527472	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	45	0.059366754617414245	T	19.49	3.837918	0.71373	0.013194	0.065814	ENSG00000103061	ENST00000263997	T	0.20463	2.07	5.79	4.68	0.58851	.	0.111684	0.64402	D	0.000006	T	0.03739	0.0106	L	0.58354	1.805	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.00069	-1.2138	10	0.46703	T	0.11	-15.2116	10.5	0.44800	0.1453:0.0:0.0:0.8547	rs11548855;rs11548855	220	Q96CW6	S7A6O_HUMAN	C	220	ENSP00000263997:Y220C	ENSP00000263997:Y220C	Y	-	2	0	SLC7A6OS	66895449	1.000000	0.71417	0.681000	0.30009	0.955000	0.61496	5.530000	0.67141	0.999000	0.39023	0.454000	0.30748	TAC	T|0.956;C|0.044	0.044	strong		0.522	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
PPFIA1	8500	hgsc.bcm.edu	37	11	70185325	70185325	+	Silent	SNP	C	C	T	rs1061328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70185325C>T	ENST00000253925.7	+	14	1835	c.1620C>T	c.(1618-1620)gaC>gaT	p.D540D	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Silent_p.D540D	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	540					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CCATGGCAGACGGCCACACAG	0.517													C|||	1074	0.214457	0.5219	0.2262	5008	,	,		16990	0.0407		0.1233	False		,,,				2504	0.0634				p.D540D		Atlas-SNP	.											.	PPFIA1	114	.	0			c.C1620T						PASS	.	C	,	2054,2346	559.2+/-380.2	481,1092,627	54.0	57.0	56.0		1620,1620	-3.0	0.0	11	dbSNP_86	56	1045,7543	220.2+/-258.0	66,913,3315	no	coding-synonymous,coding-synonymous	PPFIA1	NM_003626.2,NM_177423.1	,	547,2005,3942	TT,TC,CC		12.1681,46.6818,23.8605	,	540/1203,540/1186	70185325	3099,9889	2200	4294	6494	SO:0001819	synonymous_variant	8500	exon14			GGCAGACGGCCAC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.1620C>T	11.37:g.70185325C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	152	85	0.559211	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Silent	SNP	ENST00000253925.7	37	CCDS31627.1	418	0.19139194139194138	230	0.46747967479674796	69	0.19060773480662985	27	0.0472027972027972	92	0.12137203166226913	C	10.25	1.297429	0.23650	0.466818	0.121681	ENSG00000131626	ENST00000530798	.	.	.	5.13	-2.95	0.05564	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19945	P	0.9999429774	.	.	.	.	.	.	T	0.47886	-0.9082	3	.	.	.	.	6.9386	0.24481	0.0:0.4076:0.1164:0.4759	rs1061328;rs3202388;rs17846080;rs17859080;rs57951249;rs1061328	.	.	.	W	92	.	.	R	+	1	2	PPFIA1	69862973	0.657000	0.27393	0.040000	0.18447	0.017000	0.09413	-0.118000	0.10692	-0.263000	0.09378	-0.258000	0.10820	CGG	C|0.776;T|0.224	0.224	strong		0.517	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
GAB4	128954	hgsc.bcm.edu	37	22	17446157	17446157	+	Splice_Site	SNP	G	G	T	rs1541529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:17446157G>T	ENST00000400588.1	-	7	1397	c.1290C>A	c.(1288-1290)gcC>gcA	p.A430A	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	430										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GTGTTGGGTTGGCTGGAGCAG	0.557													T|||	163	0.0325479	0.0008	0.0317	5008	,	,		18394	0.0069		0.0686	False		,,,				2504	0.0654				p.A430A		Atlas-SNP	.											.	GAB4	95	.	0			c.C1290A						PASS	.	T		75,4029		0,75,1977	151.0	160.0	157.0		1290	0.8	0.9	22	dbSNP_88	157	592,7856		17,558,3649	yes	coding-synonymous-near-splice	GAB4	NM_001037814.1		17,633,5626	TT,TG,GG		7.0076,1.8275,5.3139		430/575	17446157	667,11885	2052	4224	6276	SO:0001630	splice_region_variant	128954	exon7			TGGGTTGGCTGGA	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1289-1C>A	22.37:g.17446157G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.960;T|0.040	0.040	strong		0.557	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Silent
ZBTB14	7541	hgsc.bcm.edu	37	18	5292030	5292030	+	Silent	SNP	A	A	G	rs620652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:5292030A>G	ENST00000357006.4	-	4	515	c.177T>C	c.(175-177)acT>acC	p.T59T	ZBTB14_ENST00000400143.3_Silent_p.T59T	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	59	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|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)|transcription regulatory region DNA binding (GO:0044212)										TTTTAAAGTAAGTGCTGCAGG	0.378													G|||	4224	0.84345	0.9251	0.8401	5008	,	,		16642	0.8254		0.8032	False		,,,				2504	0.7955				p.T59T		Atlas-SNP	.											.	.	.	.	0			c.T177C						PASS	.	G	,	4074,332	175.1+/-204.6	1886,302,15	89.0	89.0	89.0		177,177	5.3	1.0	18	dbSNP_83	89	7123,1477	280.9+/-294.7	2963,1197,140	no	coding-synonymous,coding-synonymous	ZFP161	NM_001143823.2,NM_003409.4	,	4849,1499,155	GG,GA,AA		17.1744,7.5352,13.909	,	59/450,59/450	5292030	11197,1809	2203	4300	6503	SO:0001819	synonymous_variant	7541	exon4			AAAGTAAGTGCTG	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12860	protein-coding gene	gene with protein product		602126	"""zinc finger protein 161 homolog (mouse)"", ""zinc finger protein 161"", ""ZFP161 zinc finger protein"""	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.177T>C	18.37:g.5292030A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001243702	O00403|Q2TB80	Silent	SNP	ENST00000357006.4	37	CCDS11837.1																																																																																			A|0.148;G|0.852	0.852	strong		0.378	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409	
JAK2	3717	hgsc.bcm.edu	37	9	5081780	5081780	+	Silent	SNP	G	G	A	rs2230724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5081780G>A	ENST00000381652.3	+	19	2984	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000539801.1_Silent_p.L830L|JAK2_ENST00000544510.1_Silent_p.L681L	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	830					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)	TAGGTGCCCTGGGGTTTTCTG	0.348		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				A|||	3089	0.616813	0.9312	0.5879	5008	,	,		17517	0.4395		0.5239	False		,,,				2504	0.4908				p.L830L		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2490A						PASS	.	A		3825,581	258.0+/-262.2	1671,483,49	109.0	110.0	110.0		2490	-3.0	0.1	9	dbSNP_98	110	4294,4306	577.7+/-390.6	1073,2148,1079	no	coding-synonymous	JAK2	NM_004972.3		2744,2631,1128	AA,AG,GG		49.9302,13.1866,37.575		830/1133	5081780	8119,4887	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon19	Familial Cancer Database		TGCCCTGGGGTTT		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.2490G>A	9.37:g.5081780G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			G|0.386;A|0.614	0.614	strong		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4510723	4510723	+	Silent	SNP	G	G	A	rs78776990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4510723G>A	ENST00000301286.3	-	3	3206	c.3207C>T	c.(3205-3207)agC>agT	p.S1069S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1069						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						CCTCTTGGGGGCTCAGGGCAG	0.647													g|||	567	0.113219	0.0416	0.0865	5008	,	,		15958	0.0972		0.1372	False		,,,				2504	0.2209				p.S1069S		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.C3207T						PASS	.			234,3900		2,230,1835	30.0	35.0	34.0		3207	-2.5	0.0	19	dbSNP_131	34	1014,7384		64,886,3249	no	coding-synonymous	PLIN4	NM_001080400.1		66,1116,5084	AA,AG,GG		12.0743,5.6604,9.9585		1069/1358	4510723	1248,11284	2067	4199	6266	SO:0001819	synonymous_variant	729359	exon3			TTGGGGGCTCAGG	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.3207C>T	19.37:g.4510723G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.105;C|0.000;G|0.894	0.105	strong		0.647	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
MTRF1L	54516	hgsc.bcm.edu	37	6	153315695	153315695	+	Missense_Mutation	SNP	C	C	T	rs3192723	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:153315695C>T	ENST00000367233.5	-	4	639	c.640G>A	c.(640-642)Gtc>Atc	p.V214I	MTRF1L_ENST00000367230.1_Missense_Mutation_p.V178I|MTRF1L_ENST00000367231.5_Missense_Mutation_p.V214I|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	214			V -> I (in dbSNP:rs3192723).			mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		CTAGTATGGACGCGGCCTTGC	0.507													C|||	1186	0.236821	0.2663	0.3026	5008	,	,		15054	0.1498		0.162	False		,,,				2504	0.317				p.V214I		Atlas-SNP	.											.	MTRF1L	21	.	0			c.G640A						PASS	.	C	ILE/VAL,ILE/VAL	1094,3312	393.1+/-328.7	134,826,1243	185.0	161.0	169.0		640,640	-0.0	1.0	6	dbSNP_105	169	1540,7060	290.1+/-299.6	149,1242,2909	no	missense,missense	MTRF1L	NM_001114184.1,NM_019041.5	29,29	283,2068,4152	TT,TC,CC		17.907,24.8298,20.2522	benign,benign	214/272,214/381	153315695	2634,10372	2203	4300	6503	SO:0001583	missense	54516	exon4			TATGGACGCGGCC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.640G>A	6.37:g.153315695C>T	ENSP00000356202:p.Val214Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	37	CCDS5243.1	444	0.2032967032967033	138	0.2804878048780488	108	0.2983425414364641	76	0.13286713286713286	122	0.16094986807387862	C	4.256	0.046602	0.08243	0.248298	0.17907	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771;ENST00000448966	T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85	5.18	-0.0148	0.13979	.	0.373796	0.34291	N	0.004098	T	0.00784	0.0026	N	0.02169	-0.655	0.46113	P	0.0011250000000000426	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.47420	-0.9119	9	0.02654	T	1	-2.1994	9.1054	0.36694	0.0:0.285:0.0:0.715	rs3192723;rs3799134;rs6942312;rs52828127;rs3192723	214;178;214	Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;RF1ML_HUMAN	I	214;214;178;65;78	ENSP00000356202:V214I;ENSP00000356200:V214I;ENSP00000356199:V178I;ENSP00000414383:V65I;ENSP00000415113:V78I	ENSP00000356199:V178I	V	-	1	0	MTRF1L	153357388	1.000000	0.71417	0.979000	0.43373	0.903000	0.53119	1.945000	0.40273	-0.140000	0.11394	-0.324000	0.08512	GTC	C|0.800;T|0.200	0.200	strong		0.507	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
SLC6A20	54716	hgsc.bcm.edu	37	3	45837886	45837886	+	Missense_Mutation	SNP	G	G	C	rs2271615	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:45837886G>C	ENST00000358525.4	-	1	141	c.26C>G	c.(25-27)gCc>gGc	p.A9G	SLC6A20_ENST00000456124.2_Missense_Mutation_p.A9G|SLC6A20_ENST00000353278.4_Missense_Mutation_p.A9G	NM_020208.3	NP_064593.1	Q9NP91	S6A20_HUMAN	solute carrier family 6 (proline IMINO transporter), member 20	9			A -> G (in dbSNP:rs2271615).		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|glycine transport (GO:0015816)|ion transport (GO:0006811)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|large_intestine(6)|ovary(2)|skin(2)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.01)|KIRC - Kidney renal clear cell carcinoma(197;0.0225)|Kidney(197;0.0267)		TAGCGAGTTGGCCCACAGCGG	0.706													G|||	443	0.0884585	0.0106	0.1124	5008	,	,		11404	0.0833		0.1581	False		,,,				2504	0.1104				p.A9G		Atlas-SNP	.											.	SLC6A20	96	.	0			c.C26G						PASS	.	G	GLY/ALA,GLY/ALA	132,4274	87.3+/-125.9	1,130,2072	57.0	44.0	48.0		26,26	1.2	1.0	3	dbSNP_100	48	1319,7281	240.3+/-271.1	106,1107,3087	yes	missense,missense	SLC6A20	NM_020208.3,NM_022405.3	60,60	107,1237,5159	CC,CG,GG		15.3372,2.9959,11.1564	benign,benign	9/593,9/556	45837886	1451,11555	2203	4300	6503	SO:0001583	missense	54716	exon1			GAGTTGGCCCACA	AF075260	CCDS2730.1, CCDS43077.1	3p21.6	2013-05-22			ENSG00000163817	ENSG00000163817		"""Solute carriers"""	30927	protein-coding gene	gene with protein product		605616				9932288, 11352561	Standard	NM_022405		Approved	XT3, Xtrp3	uc011bai.2	Q9NP91	OTTHUMG00000133446	ENST00000358525.4:c.26C>G	3.37:g.45837886G>C	ENSP00000346298:p.Ala9Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_022405	A1A4F2|O75590|Q8TF10|Q9NPQ2|Q9NQ77	Missense_Mutation	SNP	ENST00000358525.4	37	CCDS43077.1	216	0.0989010989010989	8	0.016260162601626018	43	0.11878453038674033	48	0.08391608391608392	117	0.15435356200527706	G	10.29	1.310229	0.23821	0.029959	0.153372	ENSG00000163817	ENST00000353278;ENST00000358525;ENST00000456124;ENST00000413781	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	4.33	1.2	0.21068	.	1.071760	0.07206	N	0.858378	T	0.00300	0.0009	N	0.02830	-0.485	0.54753	P	1.4999999999987246E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04165	-1.0972	9	0.26408	T	0.33	.	7.051	0.25073	0.0:0.1419:0.4269:0.4313	rs2271615;rs2271615	9;9	Q9NP91-2;Q9NP91	.;S6A20_HUMAN	G	9	ENSP00000296133:A9G;ENSP00000346298:A9G;ENSP00000404310:A9G;ENSP00000395506:A9G	ENSP00000296133:A9G	A	-	2	0	SLC6A20	45812890	0.994000	0.37717	0.996000	0.52242	0.063000	0.16089	0.771000	0.26633	0.363000	0.24346	0.313000	0.20887	GCC	G|0.891;C|0.109	0.109	strong		0.706	SLC6A20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257318.3	NM_020208	
XRN1	54464	hgsc.bcm.edu	37	3	142145605	142145605	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:142145605A>G	ENST00000264951.4	-	3	504	c.387T>C	c.(385-387)gaT>gaC	p.D129D	XRN1_ENST00000392981.2_Silent_p.D129D|XRN1_ENST00000544157.1_Intron|XRN1_ENST00000463916.1_Silent_p.D129D	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	129					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.D129E(1)		NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TACAGTTGGAATCAAATCTGG	0.328																																					p.D129D		Atlas-SNP	.											XRN1,colon,carcinoma,0,1	XRN1	138	1	1	Substitution - Missense(1)	large_intestine(1)	c.T387C						scavenged	.						168.0	164.0	165.0					3																	142145605		2203	4300	6503	SO:0001819	synonymous_variant	54464	exon3			GTTGGAATCAAAT	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.387T>C	3.37:g.142145605A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	127	3	0.023622	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			.	.	none		0.328	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
LRRC6	23639	hgsc.bcm.edu	37	8	133637659	133637659	+	Missense_Mutation	SNP	G	G	A	rs2293979	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:133637659G>A	ENST00000519595.1	-	6	793	c.695C>T	c.(694-696)aCa>aTa	p.T232I	LRRC6_ENST00000520446.1_5'UTR|LRRC6_ENST00000250173.1_Missense_Mutation_p.T232I|LRRC6_ENST00000518642.1_Missense_Mutation_p.T232I			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	232			T -> I (in dbSNP:rs2293979). {ECO:0000269|Ref.1}.		cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			GTGTTCCTCTGTGTCTGGTGC	0.378													A|||	2435	0.486222	0.8956	0.3199	5008	,	,		18056	0.2827		0.3777	False		,,,				2504	0.3722				p.T232I		Atlas-SNP	.											.	LRRC6	58	.	0			c.C695T						PASS	.	A	ILE/THR	3606,800	317.7+/-295.3	1479,648,76	182.0	180.0	181.0		695	-9.6	0.0	8	dbSNP_100	181	3654,4946	623.5+/-397.5	777,2100,1423	yes	missense	LRRC6	NM_012472.3	89	2256,2748,1499	AA,AG,GG		42.4884,18.1571,44.1796	benign	232/467	133637659	7260,5746	2203	4300	6503	SO:0001583	missense	23639	exon6			TCCTCTGTGTCTG	U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"""leucine rich testes protein"""	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.695C>T	8.37:g.133637659G>A	ENSP00000429791:p.Thr232Ile	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	NM_012472	Q13648|Q4G183	Missense_Mutation	SNP	ENST00000519595.1	37		1002	0.45879120879120877	428	0.8699186991869918	133	0.3674033149171271	141	0.2465034965034965	300	0.39577836411609496	A	6.833	0.522900	0.13066	0.818429	0.424884	ENSG00000129295	ENST00000519595;ENST00000518642;ENST00000250173;ENST00000395414	T;T;T	0.53640	0.76;0.61;0.76	5.07	-9.57	0.00562	.	1.367430	0.04086	N	0.310545	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	0.29852	-0.9998	9	0.33940	T	0.23	0.3719	2.7647	0.05317	0.2794:0.1688:0.3852:0.1666	rs2293979;rs17605638;rs52821378;rs59765270;rs2293979	232	Q86X45	LRRC6_HUMAN	I	232	ENSP00000429791:T232I;ENSP00000428610:T232I;ENSP00000250173:T232I	ENSP00000250173:T232I	T	-	2	0	LRRC6	133706841	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.791000	0.00767	-2.791000	0.00356	-3.279000	0.00047	ACA	G|0.487;A|0.513	0.513	strong		0.378	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472	
CTBS	1486	hgsc.bcm.edu	37	1	85040069	85040069	+	Silent	SNP	G	G	A	rs2911592	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85040069G>A	ENST00000370630.5	-	1	78	c.30C>T	c.(28-30)cgC>cgT	p.R10R	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	10					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		TAGAGACGAGGCGCCAGCGTC	0.756													G|||	1363	0.272165	0.2496	0.2421	5008	,	,		8547	0.2312		0.2455	False		,,,				2504	0.3937				p.R10R		Atlas-SNP	.											.	CTBS	24	.	0			c.C30T						PASS	.	G		612,2646		64,484,1081	3.0	3.0	3.0		30	2.5	0.1	1	dbSNP_101	3	1349,5697		164,1021,2338	no	coding-synonymous	CTBS	NM_004388.2		228,1505,3419	AA,AG,GG		19.1456,18.7845,19.0314		10/386	85040069	1961,8343	1629	3523	5152	SO:0001819	synonymous_variant	1486	exon1			GACGAGGCGCCAG	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.30C>T	1.37:g.85040069G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_004388	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																			G|0.761;A|0.239	0.239	strong		0.756	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
PSD3	23362	hgsc.bcm.edu	37	8	18656820	18656820	+	Silent	SNP	G	G	A	rs150513733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:18656820G>A	ENST00000327040.8	-	8	2169	c.2067C>T	c.(2065-2067)acC>acT	p.T689T	PSD3_ENST00000286485.8_Silent_p.T155T|PSD3_ENST00000440756.2_Silent_p.T689T|PSD3_ENST00000523619.1_Silent_p.T624T	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	689	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CATGTAGATCGGTATTAAGAA	0.383													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18427	0.0		0.005	False		,,,				2504	0.001				p.T689T		Atlas-SNP	.											PSD3_ENST00000440756,NS,carcinoma,0,2	PSD3	142	2	0			c.C2067T						PASS	.	G	,	8,4398	14.3+/-33.2	0,8,2195	132.0	120.0	124.0		2067,465	-11.3	0.0	8	dbSNP_134	124	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous,coding-synonymous	PSD3	NM_015310.3,NM_206909.2	,	0,66,6437	AA,AG,GG		0.6744,0.1816,0.5075	,	689/1048,155/514	18656820	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	23362	exon8			TAGATCGGTATTA	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.2067C>T	8.37:g.18656820G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	37	CCDS43720.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.740	-0.053826	0.07362	0.001816	0.006744	ENSG00000156011	ENST00000520858	.	.	.	5.64	-11.3	0.00108	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.1748	0.00117	0.3233:0.166:0.2228:0.2878	.	.	.	.	X	122	.	.	R	-	1	2	PSD3	18701100	0.000000	0.05858	0.022000	0.16811	0.736000	0.42039	-4.268000	0.00263	-4.720000	0.00035	-2.703000	0.00135	CGA	G|0.997;A|0.003	0.003	strong		0.383	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
PIK3R3	8503	hgsc.bcm.edu	37	1	46521559	46521559	+	Missense_Mutation	SNP	A	A	T	rs785467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46521559A>T	ENST00000262741.5	-	7	1538	c.849T>A	c.(847-849)aaT>aaA	p.N283K	PIK3R3_ENST00000420542.1_Missense_Mutation_p.N283K|PIK3R3_ENST00000488808.1_5'UTR|PIK3R3_ENST00000540385.1_Missense_Mutation_p.N329K|PIK3R3_ENST00000340332.6_Intron|PIK3R3_ENST00000354242.4_Intron|PIK3R3_ENST00000423209.1_Intron|PIK3R3_ENST00000372006.1_Missense_Mutation_p.N283K	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	283			N -> K (in dbSNP:rs785467). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9524259, ECO:0000269|Ref.2, ECO:0000269|Ref.5}.		insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	CCAAAGCTTGATTCTTCAAAT	0.358													T|||	3416	0.682109	0.7474	0.6412	5008	,	,		17376	0.6885		0.7346	False		,,,				2504	0.5624				p.N283K		Atlas-SNP	.											.	PIK3R3	41	.	0			c.T849A						PASS	.	T	LYS/ASN,LYS/ASN	3252,1154	408.2+/-334.5	1200,852,151	154.0	146.0	149.0		849,849	4.0	1.0	1	dbSNP_86	149	6090,2510	410.1+/-350.0	2167,1756,377	yes	missense,missense	PIK3R3	NM_001114172.1,NM_003629.3	94,94	3367,2608,528	TT,TA,AA		29.186,26.1916,28.1716	benign,benign	283/462,283/462	46521559	9342,3664	2203	4300	6503	SO:0001583	missense	8503	exon8			AGCTTGATTCTTC	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"""SH2 domain containing"""	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.849T>A	1.37:g.46521559A>T	ENSP00000262741:p.Asn283Lys	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_001114172	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	37	CCDS529.1	1549	0.7092490842490843	362	0.7357723577235772	246	0.6795580110497238	390	0.6818181818181818	551	0.7269129287598944	T	3.697	-0.062398	0.07273	0.738084	0.70814	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000540385	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.1	3.95	0.45737	.	0.091297	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00358	-1.6	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.39663	-0.9603	9	0.02654	T	1	.	6.2461	0.20818	0.1281:0.1277:0.0:0.7442	rs785467;rs2230662;rs17411824;rs52814039;rs59392092;rs785467	329;316;283	F6TDL0;Q7Z3W2;Q92569	.;.;P55G_HUMAN	K	283;283;283;329	ENSP00000361075:N283K;ENSP00000262741:N283K;ENSP00000412546:N283K;ENSP00000439913:N329K	ENSP00000262741:N283K	N	-	3	2	PIK3R3	46294146	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.159000	0.31749	0.898000	0.36418	-0.265000	0.10407	AAT	A|0.291;T|0.709	0.709	strong		0.358	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802331	24802331	+	Silent	SNP	C	C	T	rs72770409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24802331C>T	ENST00000395799.3	+	6	2497	c.2368C>T	c.(2368-2370)Ctg>Ttg	p.L790L	TNRC6A_ENST00000315183.7_Silent_p.L790L	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	790	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				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)		CAAACCTGCTCTGAGGTGGGG	0.498													C|||	93	0.0185703	0.0015	0.0288	5008	,	,		17897	0.0		0.0547	False		,,,				2504	0.0164				p.L790L		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2368T						PASS	.	C		36,4348		0,36,2156	35.0	37.0	36.0		2368	1.1	1.0	16	dbSNP_130	36	481,8113		14,453,3830	no	coding-synonymous	TNRC6A	NM_014494.2		14,489,5986	TT,TC,CC		5.5969,0.8212,3.9837		790/1963	24802331	517,12461	2192	4297	6489	SO:0001819	synonymous_variant	27327	exon6			CCTGCTCTGAGGT	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.2368C>T	16.37:g.24802331C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.966;T|0.034	0.034	strong		0.498	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
OR7D4	125958	hgsc.bcm.edu	37	19	9325116	9325116	+	Missense_Mutation	SNP	G	G	A	rs5020278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9325116G>A	ENST00000308682.2	-	1	426	c.398C>T	c.(397-399)aCg>aTg	p.T133M		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	133			T -> M (impaired response to androstenone and androstadienone; when associated with W-88; dbSNP:rs5020278). {ECO:0000269|PubMed:17873857}.			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(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						CATGATGACCGTGTAGTGCAG	0.488													G|||	739	0.147564	0.0567	0.1066	5008	,	,		20522	0.2153		0.2018	False		,,,				2504	0.1738				p.T133M		Atlas-SNP	.											.	OR7D4	66	.	0			c.C398T						PASS	.	G	MET/THR	350,4056	181.9+/-209.8	7,336,1860	86.0	81.0	83.0		398	-4.5	0.0	19	dbSNP_113	83	1573,7027	292.3+/-300.8	138,1297,2865	yes	missense	OR7D4	NM_001005191.2	81	145,1633,4725	AA,AG,GG		18.2907,7.9437,14.7855	benign	133/313	9325116	1923,11083	2203	4300	6503	SO:0001583	missense	125958	exon1			ATGACCGTGTAGT		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.398C>T	19.37:g.9325116G>A	ENSP00000310488:p.Thr133Met	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	37	CCDS32901.1	341	0.15613553113553114	22	0.044715447154471545	38	0.10497237569060773	129	0.22552447552447552	152	0.20052770448548812	G	1.270	-0.613412	0.03690	0.079437	0.182907	ENSG00000174667	ENST00000308682	T	0.20200	2.09	4.0	-4.5	0.03493	GPCR, rhodopsin-like superfamily (1);	0.998718	0.08103	N	0.997365	T	0.00012	0.0000	L	0.60067	1.865	0.80722	P	0.0	B	0.29909	0.261	B	0.17098	0.017	T	0.33574	-0.9863	9	0.21014	T	0.42	.	7.1843	0.25791	0.5595:0.1222:0.3183:0.0	rs5020278	133	Q8NG98	OR7D4_HUMAN	M	133	ENSP00000310488:T133M	ENSP00000310488:T133M	T	-	2	0	OR7D4	9186116	0.000000	0.05858	0.000000	0.03702	0.352000	0.29268	-4.418000	0.00237	-0.901000	0.03891	-0.436000	0.05848	ACG	G|0.845;A|0.155	0.155	strong		0.488	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
STOX2	56977	hgsc.bcm.edu	37	4	184932088	184932088	+	Silent	SNP	C	C	T	rs61730747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184932088C>T	ENST00000308497.4	+	3	3532	c.2097C>T	c.(2095-2097)agC>agT	p.S699S	STOX2_ENST00000438269.1_Silent_p.S699S	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	699					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AGATATTTAGCAAAGACACAC	0.542													C|||	204	0.0407348	0.0809	0.0865	5008	,	,		19935	0.0		0.0318	False		,,,				2504	0.0051				p.S699S		Atlas-SNP	.											STOX2_ENST00000308497,colon,carcinoma,+1,1	STOX2	142	1	0			c.C2097T						PASS	.	C		316,3714		19,278,1718	34.0	39.0	37.0		2097	5.2	1.0	4	dbSNP_129	37	296,8054		3,290,3882	no	coding-synonymous	STOX2	NM_020225.1		22,568,5600	TT,TC,CC		3.5449,7.8412,4.9435		699/927	184932088	612,11768	2015	4175	6190	SO:0001819	synonymous_variant	56977	exon3			ATTTAGCAAAGAC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.2097C>T	4.37:g.184932088C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	220	113	0.513636	NM_020225	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																			C|0.967;T|0.033	0.033	strong		0.542	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
TBCD	6904	hgsc.bcm.edu	37	17	80710097	80710097	+	Missense_Mutation	SNP	G	G	T	rs11550062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80710097G>T	ENST00000355528.4	+	1	158	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	TBCD_ENST00000397466.2_5'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.G10C	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	10					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ACCGGCCGCGGGCGGCCCCGA	0.741													G|||	564	0.11262	0.0045	0.0692	5008	,	,		8990	0.0685		0.1342	False		,,,				2504	0.3129				p.G10C		Atlas-SNP	.											TBCD_ENST00000355528,rectum,carcinoma,-2,1	TBCD	94	1	0			c.G28T						PASS	.	G	CYS/GLY	61,2941		0,61,1440	3.0	4.0	4.0		28	1.0	0.0	17	dbSNP_120	4	657,5909		15,627,2641	no	missense	TBCD	NM_005993.4	159	15,688,4081	TT,TG,GG		10.0061,2.032,7.5042	probably-damaging	10/1193	80710097	718,8850	1501	3283	4784	SO:0001583	missense	6904	exon1			GCCGCGGGCGGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.28G>T	17.37:g.80710097G>T	ENSP00000347719:p.Gly10Cys	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	179	0.08195970695970696	10	0.02032520325203252	29	0.08011049723756906	39	0.06818181818181818	101	0.13324538258575197	G	16.63	3.175996	0.57692	0.02032	0.100061	ENSG00000141556	ENST00000355528;ENST00000269368;ENST00000536182	T	0.18960	2.18	2.39	0.978	0.19740	.	.	.	.	.	T	0.00178	0.0005	N	0.22421	0.69	0.27423	P	0.9542346	D;D;D	0.65815	0.986;0.995;0.982	P;P;P	0.52909	0.52;0.713;0.54	T	0.17623	-1.0363	7	.	.	.	.	6.572	0.22543	0.2283:0.0:0.7717:0.0	rs11550062	10;10;10	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	C	10	ENSP00000347719:G10C	.	G	+	1	0	TBCD	78303386	0.004000	0.15560	0.001000	0.08648	0.006000	0.05464	0.507000	0.22675	0.309000	0.22966	0.456000	0.33151	GGC	G|0.918;T|0.082	0.082	strong		0.741	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
ZNF469	84627	hgsc.bcm.edu	37	16	88502208	88502208	+	Missense_Mutation	SNP	A	A	T	rs3812954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88502208A>T	ENST00000437464.1	+	2	8246	c.8246A>T	c.(8245-8247)gAc>gTc	p.D2749V	ZNF469_ENST00000565624.1_Missense_Mutation_p.D2777V	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2749			D -> V (in dbSNP:rs3812954).		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(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CCTGCGGAGGACAGCAGCAGG	0.652													A|||	218	0.0435304	0.0068	0.0432	5008	,	,		16230	0.0427		0.0984	False		,,,				2504	0.0378				p.D2749V		Atlas-SNP	.											.	ZNF469	121	.	0			c.A8246T						PASS	.	A	VAL/ASP	16,1368		1,14,677	45.0	62.0	57.0		8246	2.2	0.0	16	dbSNP_107	57	239,2943		7,225,1359	yes	missense	ZNF469	NM_001127464.1	152	8,239,2036	TT,TA,AA		7.511,1.1561,5.5848	possibly-damaging	2749/3926	88502208	255,4311	692	1591	2283	SO:0001583	missense	84627	exon2			CGGAGGACAGCAG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8246A>T	16.37:g.88502208A>T	ENSP00000402343:p.Asp2749Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	123	0.05631868131868132	6	0.012195121951219513	23	0.06353591160220995	27	0.0472027972027972	67	0.08839050131926121	A	11.24	1.580640	0.28180	0.011561	0.07511	ENSG00000225614	ENST00000437464	T	0.07567	3.18	4.56	2.24	0.28232	.	.	.	.	.	T	0.00210	0.0006	N	0.19112	0.55	0.80722	P	0.0	P	0.46512	0.879	B	0.37943	0.261	T	0.38887	-0.9640	8	0.62326	D	0.03	.	5.1164	0.14836	0.544:0.3576:0.0984:0.0	rs3812954	2749	Q96JG9	ZN469_HUMAN	V	2749	ENSP00000402343:D2749V	ENSP00000402343:D2749V	D	+	2	0	ZNF469	87029709	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.155000	0.10115	0.136000	0.18733	0.459000	0.35465	GAC	A|0.944;T|0.056	0.056	strong		0.652	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ERBB4	2066	hgsc.bcm.edu	37	2	212587119	212587119	+	Splice_Site	SNP	T	T	C	rs77309171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:212587119T>C	ENST00000342788.4	-	7	1192	c.882A>G	c.(880-882)ccA>ccG	p.P294P	ERBB4_ENST00000484474.1_5'Flank|ERBB4_ENST00000436443.1_Splice_Site_p.P294P|ERBB4_ENST00000402597.1_Splice_Site_p.P294P	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	294	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|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)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GTTACTTACGTGGACATTTCT	0.313										TSP Lung(8;0.080)			T|||	10	0.00199681	0.0	0.0029	5008	,	,		16437	0.0		0.005	False		,,,				2504	0.0031				p.P294P		Atlas-SNP	.											.	ERBB4	480	.	0			c.A882G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	146.0	133.0	138.0		882,882	1.9	1.0	2	dbSNP_131	138	46,8554	30.1+/-81.4	0,46,4254	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ERBB4	NM_001042599.1,NM_005235.2	,	0,47,6456	CC,CT,TT		0.5349,0.0227,0.3614	,	294/1293,294/1309	212587119	47,12959	2203	4300	6503	SO:0001630	splice_region_variant	2066	exon7			CTTACGTGGACAT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.883+1A>G	2.37:g.212587119T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	109	61	0.559633	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	12.44	1.939839	0.34189	2.27E-4	0.005349	ENSG00000178568	ENST00000260943	.	.	.	5.67	1.89	0.25635	.	.	.	.	.	T	0.43765	0.1262	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29119	-1.0022	4	.	.	.	.	4.9983	0.14251	0.2313:0.1302:0.0:0.6385	.	.	.	.	R	294	.	.	H	-	2	0	ERBB4	212295364	0.999000	0.42202	1.000000	0.80357	0.976000	0.68499	0.474000	0.22148	0.078000	0.16900	-0.344000	0.07964	CAC	T|0.997;C|0.003	0.003	strong		0.313	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	Silent
CHAD	1101	hgsc.bcm.edu	37	17	48545596	48545596	+	Silent	SNP	G	G	A	rs34864120	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48545596G>A	ENST00000508540.1	-	1	731	c.579C>T	c.(577-579)gaC>gaT	p.D193D	ACSF2_ENST00000502667.1_Intron|CHAD_ENST00000258969.4_Silent_p.D193D|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	193					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGTTCTCCACGTCGTCCAGGG	0.647													G|||	945	0.188698	0.0946	0.2536	5008	,	,		19319	0.1419		0.2992	False		,,,				2504	0.2045				p.D193D		Atlas-SNP	.											.	CHAD	36	.	0			c.C579T						PASS	.	G	,	606,3800	264.7+/-266.2	39,528,1636	80.0	87.0	85.0		579,	-8.9	0.4	17	dbSNP_126	85	2611,5989	423.0+/-354.2	397,1817,2086	no	coding-synonymous,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	,	436,2345,3722	AA,AG,GG		30.3605,13.754,24.7347	,	193/360,	48545596	3217,9789	2203	4300	6503	SO:0001819	synonymous_variant	1101	exon1			CTCCACGTCGTCC	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.579C>T	17.37:g.48545596G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			G|0.767;A|0.233	0.233	strong		0.647	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
CPNE1	8904	hgsc.bcm.edu	37	20	34218673	34218673	+	Missense_Mutation	SNP	G	G	C	rs12481228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34218673G>C	ENST00000317619.3	-	14	1434	c.1040C>G	c.(1039-1041)cCt>cGt	p.P347R	CPNE1_ENST00000397445.1_Missense_Mutation_p.P347R|CPNE1_ENST00000397442.1_Missense_Mutation_p.P347R|CPNE1_ENST00000397443.1_Missense_Mutation_p.P347R|CPNE1_ENST00000352393.4_Missense_Mutation_p.P347R|CPNE1_ENST00000317677.5_Missense_Mutation_p.P352R|CPNE1_ENST00000397446.1_Missense_Mutation_p.P347R			Q99829	CPNE1_HUMAN	copine I	347	VWFA.		P -> R (in dbSNP:rs12481228).		lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CTGCCAGTCAGGGGGAACCTG	0.527													G|||	519	0.103634	0.0749	0.1225	5008	,	,		21085	0.0833		0.1004	False		,,,				2504	0.1534				p.P352R		Atlas-SNP	.											.	CPNE1	44	.	0			c.C1055G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO	384,4022	191.6+/-217.2	10,364,1829	83.0	90.0	88.0		1040,1055,1040,1040,1040,1040	5.3	1.0	20	dbSNP_120	88	915,7685	202.1+/-245.5	49,817,3434	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	103,103,103,103,103,103	59,1181,5263	CC,CG,GG		10.6395,8.7154,9.9877	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	347/537,352/543,347/538,347/538,347/538,347/538	34218673	1299,11707	2203	4300	6503	SO:0001583	missense	8904	exon12			CAGTCAGGGGGAA	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1040C>G	20.37:g.34218673G>C	ENSP00000326126:p.Pro347Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	189	0.08653846153846154	30	0.06097560975609756	47	0.1298342541436464	39	0.06818181818181818	73	0.09630606860158311	G	26.7	4.759408	0.89932	0.087154	0.106395	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570	T;T;T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0	5.32	5.32	0.75619	von Willebrand factor, type A (1);Copine (1);	0.067489	0.64402	U	0.000011	T	0.00524	0.0017	M	0.81614	2.55	0.09310	P	0.99999988961	P;P;B;P	0.41848	0.763;0.763;0.12;0.528	P;P;B;B	0.51016	0.656;0.656;0.179;0.294	T	0.00052	-1.2190	9	0.66056	D	0.02	-15.5548	18.7852	0.91952	0.0:0.0:1.0:0.0	rs34351453	352;347;347;327	B0QZ18;A6PVH9;Q99829;Q59EI4	.;.;CPNE1_HUMAN;.	R	347;352;347;347;347;347;347;347;323	ENSP00000336945:P347R;ENSP00000317257:P352R;ENSP00000326126:P347R;ENSP00000380588:P347R;ENSP00000380587:P347R;ENSP00000380585:P347R;ENSP00000380584:P347R;ENSP00000415597:P347R;ENSP00000390626:P323R	ENSP00000326126:P347R	P	-	2	0	CPNE1	33682087	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.577000	0.98196	2.767000	0.95098	0.655000	0.94253	CCT	G|0.904;C|0.096	0.096	strong		0.527	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
GRIN2A	2903	hgsc.bcm.edu	37	16	9916204	9916204	+	Silent	SNP	C	C	G	rs9806806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:9916204C>G	ENST00000396573.2	-	11	2394	c.2085G>C	c.(2083-2085)cgG>cgC	p.R695R	GRIN2A_ENST00000404927.2_Silent_p.R695R|GRIN2A_ENST00000330684.3_Silent_p.R695R|GRIN2A_ENST00000562109.1_Silent_p.R695R|GRIN2A_ENST00000535259.1_Silent_p.R538R|GRIN2A_ENST00000396575.2_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	234	0	0		WXS	Illumina HiSeq	Phase_I	240	98	0.408333	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		
FRMD6	122786	hgsc.bcm.edu	37	14	52156575	52156575	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52156575T>C	ENST00000344768.5	+	2	217	c.21T>C	c.(19-21)caT>caC	p.H7H	RNA5SP385_ENST00000515947.1_RNA|FRMD6_ENST00000356218.4_Silent_p.H7H|FRMD6_ENST00000395718.2_Silent_p.H7H			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	7					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					TGAATTTTCATAACAACAGAG	0.458																																					p.H7H		Atlas-SNP	.											FRMD6,NS,carcinoma,0,1	FRMD6	100	1	0			c.T21C						scavenged	.						103.0	84.0	90.0					14																	52156575		2203	4300	6503	SO:0001819	synonymous_variant	122786	exon2			TTTTCATAACAAC	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"""expanded homolog"""	614555	"""chromosome 14 open reading frame 31"""	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.21T>C	14.37:g.52156575T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	180	9	0.05	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			.	.	none		0.458	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12248942	12248942	+	Silent	SNP	A	A	G	rs945439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12248942A>G	ENST00000376259.3	+	2	257	c.168A>G	c.(166-168)aaA>aaG	p.K56K	TNFRSF1B_ENST00000492361.1_Intron|TNFRSF1B_ENST00000536782.1_Silent_p.K56K|MIR4632_ENST00000584158.1_RNA	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	56					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	GCTGCAGCAAATGCTCGCCGG	0.632													G|||	998	0.199281	0.2012	0.134	5008	,	,		18420	0.1548		0.2147	False		,,,				2504	0.273				p.K56K		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.A168G						PASS	.	G		976,3430	729.2+/-410.0	109,758,1336	38.0	41.0	40.0		168	2.5	0.0	1	dbSNP_86	40	2082,6518	714.2+/-406.0	274,1534,2492	no	coding-synonymous	TNFRSF1B	NM_001066.2		383,2292,3828	GG,GA,AA		24.2093,22.1516,23.5122		56/462	12248942	3058,9948	2203	4300	6503	SO:0001819	synonymous_variant	7133	exon2			CAGCAAATGCTCG	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.168A>G	1.37:g.12248942A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Silent	SNP	ENST00000376259.3	37	CCDS145.1																																																																																			A|0.787;G|0.213	0.213	strong		0.632	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
GTSE1	51512	hgsc.bcm.edu	37	22	46709881	46709881	+	Missense_Mutation	SNP	G	G	A	rs6008622	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46709881G>A	ENST00000454366.1	+	6	1234	c.1022G>A	c.(1021-1023)aGt>aAt	p.S341N		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	322					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GGGGCATCCAGTGCGTGCACA	0.622											OREG0026653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	644	0.128594	0.3192	0.0836	5008	,	,		18464	0.001		0.1223	False		,,,				2504	0.0409				p.S341N	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.G1022A						PASS	.	G	ASN/SER	1317,3089	442.5+/-346.7	207,903,1093	81.0	80.0	80.0		1022	0.4	0.0	22	dbSNP_114	80	922,7678	204.5+/-247.2	49,824,3427	yes	missense	GTSE1	NM_016426.6	46	256,1727,4520	AA,AG,GG		10.7209,29.8911,17.2151	benign	341/740	46709881	2239,10767	2203	4300	6503	SO:0001583	missense	51512	exon6			CATCCAGTGCGTG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1022G>A	22.37:g.46709881G>A	ENSP00000415430:p.Ser341Asn	Somatic	32	0	0	941	WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	280	0.1282051282051282	151	0.30691056910569103	35	0.09668508287292818	0	0.0	94	0.12401055408970976	G	7.393	0.631216	0.14322	0.298911	0.107209	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.14144	2.53	3.78	0.429	0.16506	.	0.740024	0.12537	N	0.460234	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.18013	0.025	B	0.20955	0.032	T	0.46247	-0.9205	9	0.36615	T	0.2	-1.1845	5.9398	0.19186	0.1067:0.3771:0.5162:0.0	rs6008622;rs7284449;rs52831485;rs59709957;rs6008622	322	Q9NYZ3	GTSE1_HUMAN	N	341;301	ENSP00000415430:S341N	ENSP00000354634:S301N	S	+	2	0	GTSE1	45088545	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.164000	0.16542	0.186000	0.20125	-0.175000	0.13238	AGT	G|0.845;A|0.155	0.155	strong		0.622	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs60268710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1267562C>T	ENST00000529681.1	+	31	9510	c.9452C>T	c.(9451-9453)aCg>aTg	p.T3151M	MUC5B_ENST00000447027.1_Missense_Mutation_p.T3154M|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3151	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|TGPTA -> LPHG (in Ref. 4; CAA96577). {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)		ACTGGCCCCACGGCCACCCCG	0.677													c|||	1706	0.340655	0.2133	0.33	5008	,	,		17737	0.6012		0.2883	False		,,,				2504	0.3057				p.T3151M		Atlas-SNP	.											MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	0			c.C9452T						PASS	.	C	MET/THR	782,3294		71,640,1327	53.0	69.0	63.0		9452	-3.5	0.0	11	dbSNP_129	63	2471,5819		394,1683,2068	no	missense	MUC5B	NM_002458.2	81	465,2323,3395	TT,TC,CC		29.807,19.1855,26.306	possibly-damaging	3151/5763	1267562	3253,9113	2038	4145	6183	SO:0001583	missense	727897	exon31			GCCCCACGGCCAC	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.9452C>T	11.37:g.1267562C>T	ENSP00000436812:p.Thr3151Met	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	769	0.35210622710622713	111	0.22560975609756098	107	0.2955801104972376	346	0.6048951048951049	205	0.2704485488126649	c	2.006	-0.428266	0.04701	0.191855	0.29807	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20332	2.08;2.26	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.44260	0.707;0.83	B;B	0.28139	0.029;0.086	T	0.35699	-0.9778	8	0.87932	D	0	.	5.8817	0.18858	0.0:0.1548:0.426:0.4192	rs60268710	3734;3154	A7Y9J9;E9PBJ0	.;.	M	3151;3154;3123;3111	ENSP00000436812:T3151M;ENSP00000415793:T3154M	ENSP00000343037:T3123M	T	+	2	0	MUC5B	1224138	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.828000	0.01702	-1.881000	0.01123	-0.708000	0.03648	ACG	C|0.929;T|0.071	0.071	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
HLA-C	3107	hgsc.bcm.edu	37	6	31238886	31238886	+	Missense_Mutation	SNP	A	A	G	rs77935220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238886A>G	ENST00000376228.5	-	3	597	c.583T>C	c.(583-585)Tac>Cac	p.Y195H	HLA-C_ENST00000383329.3_Missense_Mutation_p.Y195H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	195	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						TTCTCCAGGTATCTGCGGAGC	0.672																																					p.Y195H		Atlas-SNP	.											.	HLA-C	92	.	0			c.T583C						PASS	.						52.0	42.0	45.0					6																	31238886		2202	4298	6500	SO:0001583	missense	3107	exon3			CCAGGTATCTGCG	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.583T>C	6.37:g.31238886A>G	ENSP00000365402:p.Tyr195His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	97	22	0.226804	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	94|94	0.04304029304029304|0.04304029304029304	16|16	0.032520325203252036|0.032520325203252036	35|35	0.09668508287292818|0.09668508287292818	17|17	0.02972027972027972|0.02972027972027972	26|26	0.03430079155672823|0.03430079155672823	.|.	9.585|9.585	1.124510|1.124510	0.20959|0.20959	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.01203	.|5.18;5.18	2.71|2.71	-1.2|-1.2	0.09554|0.09554	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.416377	.|0.17377	.|N	.|0.176439	T|T	0.00552|0.00552	0.0018|0.0018	L|L	0.55990|0.55990	1.75|1.75	0.22811|0.22811	N|N	0.998706|0.998706	.|B;B;B;B	.|0.20550	.|0.046;0.006;0.006;0.01	.|B;B;B;B	.|0.31495	.|0.131;0.036;0.059;0.105	T|T	0.41215|0.41215	-0.9521|-0.9521	5|10	.|0.48119	.|T	.|0.1	.|.	6.6487|6.6487	0.22949|0.22949	0.6285:0.0:0.3715:0.0|0.6285:0.0:0.3715:0.0	.|.	.|195;195;195;195	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	T|H	194|195;195;195;232	.|ENSP00000365402:Y195H;ENSP00000372819:Y195H	.|ENSP00000365402:Y195H	I|Y	-|-	2|1	0|0	HLA-C|HLA-C	31346865|31346865	0.004000|0.004000	0.15560|0.15560	0.410000|0.410000	0.26471|0.26471	0.044000|0.044000	0.14063|0.14063	-0.338000|-0.338000	0.07842|0.07842	-0.240000|-0.240000	0.09696|0.09696	0.254000|0.254000	0.18369|0.18369	ATA|TAC	A|0.956;G|0.044	0.044	strong		0.672	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
TDRD7	23424	hgsc.bcm.edu	37	9	100194406	100194406	+	Missense_Mutation	SNP	T	T	C	rs2045732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100194406T>C	ENST00000355295.4	+	4	744	c.449T>C	c.(448-450)gTt>gCt	p.V150A	TDRD7_ENST00000422139.2_Missense_Mutation_p.V76A	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	150			V -> A (in dbSNP:rs2045732). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)	p.V150A(1)		endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				GGAAACTCTGTTGGAGTTAAG	0.413													C|||	2728	0.544728	0.6127	0.598	5008	,	,		21263	0.5784		0.5129	False		,,,				2504	0.4131				p.V150A		Atlas-SNP	.											TDRD7,NS,carcinoma,0,1	TDRD7	78	1	1	Substitution - Missense(1)	stomach(1)	c.T449C						PASS	.	C	ALA/VAL	2664,1742	519.0+/-369.9	797,1070,336	157.0	158.0	158.0		449	1.0	0.0	9	dbSNP_94	158	4088,4512	592.6+/-393.0	978,2132,1190	yes	missense	TDRD7	NM_014290.2	64	1775,3202,1526	CC,CT,TT		47.5349,39.537,48.0855	benign	150/1099	100194406	6752,6254	2203	4300	6503	SO:0001583	missense	23424	exon4			ACTCTGTTGGAGT	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"""Tudor domain containing"""	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.449T>C	9.37:g.100194406T>C	ENSP00000347444:p.Val150Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Missense_Mutation	SNP	ENST00000355295.4	37	CCDS6725.1	1239	0.5673076923076923	308	0.6260162601626016	214	0.5911602209944752	327	0.5716783216783217	390	0.5145118733509235	C	0.056	-1.236835	0.01493	0.60463	0.475349	ENSG00000196116	ENST00000355295;ENST00000422139	T;T	0.12255	2.7;2.7	4.98	0.998	0.19857	.	1.655750	0.02869	N	0.131355	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.14438	0.01	B	0.06405	0.002	T	0.40776	-0.9545	9	0.13470	T	0.59	-0.3418	5.7697	0.18247	0.2585:0.0841:0.0:0.6574	rs2045732;rs17332669;rs52796736;rs57645526;rs2045732	150	Q8NHU6	TDRD7_HUMAN	A	150;76	ENSP00000347444:V150A;ENSP00000413608:V76A	ENSP00000347444:V150A	V	+	2	0	TDRD7	99234227	0.031000	0.19500	0.012000	0.15200	0.004000	0.04260	-0.001000	0.12947	0.092000	0.17331	-1.333000	0.01266	GTT	T|0.469;C|0.531	0.531	strong		0.413	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290	
USP47	55031	hgsc.bcm.edu	37	11	11977573	11977573	+	Silent	SNP	T	T	C	rs2307073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:11977573T>C	ENST00000399455.2	+	29	4099	c.3979T>C	c.(3979-3981)Ttg>Ctg	p.L1327L	USP47_ENST00000305481.6_3'UTR|USP47_ENST00000539466.1_Silent_p.L109L|USP47_ENST00000339865.5_Silent_p.L1239L|USP47_ENST00000527733.1_Silent_p.L1307L	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1327					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)		ATTAATGGAATTGACAGATGA	0.363													T|||	572	0.114217	0.0136	0.0922	5008	,	,		19590	0.1806		0.1958	False		,,,				2504	0.1135				p.L1239L		Atlas-SNP	.											.	USP47	91	.	0			c.T3715C						PASS	.	T		113,3545		1,111,1717	94.0	94.0	94.0		3715	4.1	1.0	11	dbSNP_100	94	1363,6791		119,1125,2833	no	coding-synonymous	USP47	NM_017944.3		120,1236,4550	CC,CT,TT		16.7157,3.0891,12.4958		1239/1288	11977573	1476,10336	1829	4077	5906	SO:0001819	synonymous_variant	55031	exon27			ATGGAATTGACAG	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.3979T>C	11.37:g.11977573T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	37																																																																																				T|0.852;C|0.148	0.148	strong		0.363	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
SERPINB7	8710	hgsc.bcm.edu	37	18	61471529	61471529	+	Missense_Mutation	SNP	C	C	T	rs61735186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:61471529C>T	ENST00000398019.2	+	8	1128	c.803C>T	c.(802-804)aCc>aTc	p.T268I	SERPINB7_ENST00000336429.2_Missense_Mutation_p.T268I|SERPINB7_ENST00000546027.1_Missense_Mutation_p.T268I|SERPINB7_ENST00000540675.1_Missense_Mutation_p.T251I	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	28	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	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	
NME7	29922	hgsc.bcm.edu	37	1	169293721	169293721	+	Silent	SNP	G	G	A	rs1140523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169293721G>A	ENST00000367811.3	-	2	277	c.21C>T	c.(19-21)ttC>ttT	p.F7F	NME7_ENST00000472647.1_Intron|NME7_ENST00000469474.1_5'Flank|RP4-800F24.1_ENST00000432081.1_RNA	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	7	DM10. {ECO:0000255|PROSITE- ProRule:PRU00665}.				brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					CAATGAAAACGAATCTTTCAC	0.348													G|||	1137	0.227037	0.1732	0.389	5008	,	,		17160	0.0238		0.4394	False		,,,				2504	0.1759				p.F7F		Atlas-SNP	.											.	NME7	34	.	0			c.C21T						PASS	.	G	,	999,3407	373.4+/-320.8	115,769,1319	86.0	81.0	83.0		21,	-1.0	0.5	1	dbSNP_116	83	3677,4923	525.5+/-380.8	784,2109,1407	no	coding-synonymous,intron	NME7	NM_013330.3,NM_197972.1	,	899,2878,2726	AA,AG,GG		42.7558,22.6736,35.9526	,	7/377,	169293721	4676,8330	2203	4300	6503	SO:0001819	synonymous_variant	29922	exon2			GAAAACGAATCTT	AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 67"""	613465	"""non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"""			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.21C>T	1.37:g.169293721G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_013330	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Silent	SNP	ENST00000367811.3	37	CCDS1277.1																																																																																			G|0.693;A|0.307	0.307	strong		0.348	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330	
CCDC178	374864	hgsc.bcm.edu	37	18	30969567	30969567	+	Missense_Mutation	SNP	G	G	T	rs76952832	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:30969567G>T	ENST00000383096.3	-	5	327	c.145C>A	c.(145-147)Cta>Ata	p.L49I	CCDC178_ENST00000583930.1_Missense_Mutation_p.L49I|CCDC178_ENST00000406524.2_Missense_Mutation_p.L49I|CCDC178_ENST00000402325.1_Missense_Mutation_p.L49I|CCDC178_ENST00000300227.8_Missense_Mutation_p.L49I|CCDC178_ENST00000579947.1_Missense_Mutation_p.L49I|CCDC178_ENST00000579916.1_Missense_Mutation_p.L49I|CCDC178_ENST00000403303.1_Missense_Mutation_p.L49I			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	49				L -> I (in Ref. 1; BAC86407). {ECO:0000305}.													GCTCCATATAGAACCAAACTT	0.294													G|||	56	0.0111821	0.0008	0.0187	5008	,	,		12641	0.0		0.0268	False		,,,				2504	0.0153				p.L49I		Atlas-SNP	.											.	.	.	.	0			c.C145A						PASS	.	G	ILE/LEU,ILE/LEU	24,4382	29.9+/-59.1	0,24,2179	77.0	79.0	79.0		145,145	-5.7	0.0	18	dbSNP_131	79	203,8385	86.9+/-149.2	5,193,4096	yes	missense,missense	C18orf34	NM_001105528.1,NM_198995.2	5,5	5,217,6275	TT,TG,GG		2.3638,0.5447,1.747	possibly-damaging,possibly-damaging	49/868,49/830	30969567	227,12767	2203	4294	6497	SO:0001583	missense	374864	exon4			CATATAGAACCAA	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.145C>A	18.37:g.30969567G>T	ENSP00000372576:p.Leu49Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	247	129	0.522267	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	31	0.014194139194139194	0	0.0	10	0.027624309392265192	0	0.0	21	0.027704485488126648	G	3.717	-0.058393	0.07317	0.005447	0.023638	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.46451	2.46;2.46;2.46;2.45;2.46;0.87	3.4	-5.74	0.02391	.	.	.	.	.	T	0.09379	0.0231	L	0.43152	1.355	0.09310	N	1	P;B;P;P;P	0.38677	0.642;0.386;0.642;0.642;0.642	B;B;B;B;B	0.35353	0.201;0.125;0.201;0.201;0.201	T	0.06180	-1.0841	9	0.21540	T	0.41	5.3447	6.1537	0.20326	0.5274:0.2709:0.2017:0.0	.	49;49;49;49;49	F8W7A7;A1L4G8;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	I	49	ENSP00000385591:L49I;ENSP00000372576:L49I;ENSP00000300227:L49I;ENSP00000385867:L49I;ENSP00000385234:L49I;ENSP00000382130:L49I	ENSP00000300227:L49I	L	-	1	2	C18orf34	29223565	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.483000	0.06536	-1.558000	0.01690	-0.918000	0.02743	CTA	G|0.982;T|0.018	0.018	strong		0.294	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
LGI2	55203	hgsc.bcm.edu	37	4	25014048	25014048	+	Silent	SNP	G	G	A	rs34079294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:25014048G>A	ENST00000382114.4	-	7	914	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	243						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CGATGGCCACGTACACATCGT	0.468													G|||	12	0.00239617	0.0	0.0043	5008	,	,		21248	0.0		0.0089	False		,,,				2504	0.0				p.Y243Y		Atlas-SNP	.											.	LGI2	62	.	0			c.C729T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	145.0	122.0	130.0		729	1.0	1.0	4	dbSNP_126	130	60,8540	37.8+/-93.5	0,60,4240	no	coding-synonymous	LGI2	NM_018176.3		0,65,6438	AA,AG,GG		0.6977,0.1135,0.4998		243/546	25014048	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55203	exon7			GGCCACGTACACA	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.729C>T	4.37:g.25014048G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	151	67	0.443709	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																			G|0.995;A|0.005	0.005	strong		0.468	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
NOLC1	9221	hgsc.bcm.edu	37	10	103912218	103912218	+	Silent	SNP	C	C	A	rs117993238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:103912218C>A	ENST00000605788.1	+	1	286	c.51C>A	c.(49-51)ctC>ctA	p.L17L	NOLC1_ENST00000603742.1_De_novo_Start_OutOfFrame|NOLC1_ENST00000488254.2_Silent_p.L17L|NOLC1_ENST00000405356.1_Silent_p.L17L	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	17	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		TGTATCCCCTCGTGCTCGGCT	0.637													C|||	4	0.000798722	0.0	0.0014	5008	,	,		18450	0.0		0.003	False		,,,				2504	0.0				p.L17L		Atlas-SNP	.											.	NOLC1	61	.	0			c.C51A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	81.0	77.0	78.0		51	-4.4	1.0	10	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	NOLC1	NM_004741.3		0,12,6491	AA,AC,CC		0.1279,0.0227,0.0923		17/700	103912218	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon1			TCCCCTCGTGCTC	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.51C>A	10.37:g.103912218C>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			C|0.999;A|0.001	0.001	strong		0.637	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
GPR50	9248	hgsc.bcm.edu	37	X	150349533	150349533	+	Missense_Mutation	SNP	G	G	A	rs62620754		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150349533G>A	ENST00000218316.3	+	2	1547	c.1478G>A	c.(1477-1479)aGt>aAt	p.S493N	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	493	Pro-rich.				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)					TCTGCCTTCAGTGCTGCCACC	0.582													G|||	351	0.0929801	0.1142	0.0476	3775	,	,		13457	0.0556		0.0666	False		,,,				2504	0.045				p.S493N		Atlas-SNP	.											.	GPR50	195	.	0			c.G1478A						PASS	.	G	ASN/SER	490,3157		20,361,89,1157,482	111.0	124.0	120.0		1478	3.5	0.0	X	dbSNP_129	120	558,6036		16,366,160,2006,1658	yes	missense	GPR50	NM_004224.3	46	36,727,249,3163,2140	AA,AG,A,GG,G		8.4622,13.4357,10.2334	possibly-damaging	493/618	150349533	1048,9193	2109	4206	6315	SO:0001583	missense	9248	exon2			CCTTCAGTGCTGC	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.1478G>A	X.37:g.150349533G>A	ENSP00000218316:p.Ser493Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	160	0.09644364074743822	35	0.078125	14	0.03932584269662921	24	0.043795620437956206	32	0.044444444444444446	G	14.27	2.485956	0.44147	0.134357	0.084622	ENSG00000102195	ENST00000218316	T	0.72942	-0.7	3.47	3.47	0.39725	.	0.000000	0.40469	N	0.001084	T	0.00815	0.0027	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.21905	0.062	B	0.19391	0.025	T	0.39187	-0.9626	9	0.87932	D	0	-8.5366	12.092	0.53733	0.0:0.0:1.0:0.0	rs62620754	493	Q13585	MTR1L_HUMAN	N	493	ENSP00000218316:S493N	ENSP00000218316:S493N	S	+	2	0	GPR50	150100191	0.004000	0.15560	0.038000	0.18304	0.546000	0.35178	1.144000	0.31565	1.996000	0.58369	0.529000	0.55759	AGT	G|0.903;A|0.097	0.097	strong		0.582	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
ACAP1	9744	hgsc.bcm.edu	37	17	7246851	7246851	+	Silent	SNP	C	C	T	rs3809828	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7246851C>T	ENST00000158762.3	+	6	704	c.498C>T	c.(496-498)taC>taT	p.Y166Y	ACAP1_ENST00000573893.1_3'UTR	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	166	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GAGCTGGGTACCGGGGACGGG	0.657													C|||	267	0.0533147	0.0023	0.0231	5008	,	,		14038	0.127		0.0656	False		,,,				2504	0.0552				p.Y166Y		Atlas-SNP	.											.	ACAP1	66	.	0			c.C498T						PASS	.	C		50,4356	49.6+/-84.7	0,50,2153	44.0	52.0	50.0		498	5.1	1.0	17	dbSNP_107	50	506,8094	141.9+/-198.1	15,476,3809	no	coding-synonymous	ACAP1	NM_014716.3		15,526,5962	TT,TC,CC		5.8837,1.1348,4.275		166/741	7246851	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	9744	exon6			TGGGTACCGGGGA	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.498C>T	17.37:g.7246851C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																			C|0.944;T|0.056	0.056	strong		0.657	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
SHD	56961	hgsc.bcm.edu	37	19	4280207	4280207	+	Silent	SNP	G	G	C	rs56261530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4280207G>C	ENST00000543264.2	+	1	1610	c.147G>C	c.(145-147)gcG>gcC	p.A49A	SHD_ENST00000599689.1_Silent_p.A49A	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	49										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGAGGACGCGGAGAGCCGCT	0.672													G|||	171	0.0341454	0.0015	0.0389	5008	,	,		13047	0.0		0.0875	False		,,,				2504	0.0552				p.A49A		Atlas-SNP	.											SHD,colon,NS,+2,1	SHD	33	1	0			c.G147C						PASS	.	G		54,4352		0,54,2149	21.0	26.0	25.0		147	-9.2	0.0	19	dbSNP_129	25	711,7887		26,659,3614	no	coding-synonymous	SHD	NM_020209.3		26,713,5763	CC,CG,GG		8.2694,1.2256,5.8828		49/341	4280207	765,12239	2203	4299	6502	SO:0001819	synonymous_variant	56961	exon1			GGACGCGGAGAGC	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.147G>C	19.37:g.4280207G>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_020209	Q96NC2	Silent	SNP	ENST00000543264.2	37	CCDS12125.1																																																																																			G|0.945;C|0.055	0.055	strong		0.672	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
CLCNKB	1188	hgsc.bcm.edu	37	1	16378000	16378000	+	Missense_Mutation	SNP	A	A	G	rs6650119|rs386628877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16378000A>G	ENST00000375679.4	+	13	1366	c.1255A>G	c.(1255-1257)Atc>Gtc	p.I419V	CLCNKB_ENST00000375667.3_Missense_Mutation_p.I250V	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	419			I -> V (in dbSNP:rs6650119).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCACCACCATCCCCATGCC	0.597													a|||	492	0.0982428	0.2148	0.0677	5008	,	,		18974	0.0099		0.0984	False		,,,				2504	0.0532				p.I419V		Atlas-SNP	.											.	CLCNKB	50	.	0			c.A1255G						PASS	.	G	VAL/ILE,VAL/ILE	868,3538		106,656,1441	210.0	199.0	203.0		1255,748	2.0	1.0	1	dbSNP_116	203	831,7769		55,721,3524	no	missense,missense	CLCNKB	NM_000085.3,NM_001165945.1	29,29	161,1377,4965	GG,GA,AA		9.6628,19.7004,13.0632	benign,benign	419/688,250/519	16378000	1699,11307	2203	4300	6503	SO:0001583	missense	1188	exon13			ACCACCATCCCCA	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1255A>G	1.37:g.16378000A>G	ENSP00000364831:p.Ile419Val	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	226	98	0.433628	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	37	CCDS168.1	149	0.06822344322344322	67	0.13617886178861788	23	0.06353591160220995	3	0.005244755244755245	56	0.07387862796833773	N	8.795	0.931437	0.18131	0.197004	0.096628	ENSG00000184908	ENST00000375679;ENST00000331579;ENST00000375667	D;D	0.94280	-3.39;-3.39	4.38	1.96	0.26148	Chloride channel, core (2);	0.357814	0.28989	N	0.013487	T	0.00666	0.0022	L	0.53729	1.69	0.50467	P	1.2299999999998423E-4	B;B	0.17852	0.024;0.005	B;B	0.28011	0.085;0.05	T	0.48269	-0.9050	9	0.52906	T	0.07	.	6.0253	0.19652	0.6018:0.3101:0.0881:0.0	rs6650119	250;419	Q5T5Q7;P51801	.;CLCKB_HUMAN	V	419;291;250	ENSP00000364831:I419V;ENSP00000364819:I250V	ENSP00000332055:I291V	I	+	1	0	CLCNKB	16250587	0.213000	0.23551	0.959000	0.39883	0.664000	0.39144	0.968000	0.29357	0.089000	0.17243	-0.377000	0.06932	ATC	A|0.886;G|0.114	0.114	strong		0.597	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
MUC4	4585	hgsc.bcm.edu	37	3	195509212	195509212	+	Missense_Mutation	SNP	G	G	A	rs200749420		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195509212G>A	ENST00000463781.3	-	2	9698	c.9239C>T	c.(9238-9240)tCa>tTa	p.S3080L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3080L	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)		TGTGGATGCTGAGGAAGTGTC	0.597																																					p.S3080L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9239T						PASS	.						12.0	10.0	10.0					3																	195509212		659	1537	2196	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	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.9239C>T	3.37:g.195509212G>A	ENSP00000417498:p.Ser3080Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	31	0.256198	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	7.190	0.591379	0.13812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.43	.	.	.	.	.	.	.	.	T	0.19087	0.0458	N	0.19112	0.55	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.24799	-1.0150	6	.	.	.	.	5.4195	0.16392	0.0:0.0:1.0:0.0	.	2952	E7ESK3	.	L	3080	ENSP00000417498:S3080L;ENSP00000420243:S3080L	.	S	-	2	0	MUC4	196993991	0.013000	0.17824	0.004000	0.12327	0.000000	0.00434	1.082000	0.30803	0.497000	0.27926	0.000000	0.15137	TCA	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IFIT1	3434	hgsc.bcm.edu	37	10	91162677	91162677	+	Silent	SNP	C	C	T	rs303210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	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	
HAUS6	54801	hgsc.bcm.edu	37	9	19058821	19058821	+	Silent	SNP	A	A	G	rs10511671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19058821A>G	ENST00000380502.3	-	16	2411	c.1944T>C	c.(1942-1944)ttT>ttC	p.F648F	HAUS6_ENST00000380496.1_Silent_p.F512F	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	648					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)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAGACTGGCCAAAATCTGATA	0.398													A|||	389	0.0776757	0.0673	0.0476	5008	,	,		19442	0.13		0.0865	False		,,,				2504	0.0501				p.F648F		Atlas-SNP	.											.	HAUS6	66	.	0			c.T1944C						PASS	.	A		289,4117	159.2+/-191.8	11,267,1925	96.0	92.0	93.0		1944	2.6	0.0	9	dbSNP_119	93	777,7823	184.0+/-232.1	46,685,3569	no	coding-synonymous	HAUS6	NM_017645.3		57,952,5494	GG,GA,AA		9.0349,6.5592,8.1962		648/956	19058821	1066,11940	2203	4300	6503	SO:0001819	synonymous_variant	54801	exon16			CTGGCCAAAATCT	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1944T>C	9.37:g.19058821A>G		Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	268	124	0.462687	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			A|0.910;G|0.090	0.090	strong		0.398	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
TMEM171	134285	hgsc.bcm.edu	37	5	72419456	72419456	+	Missense_Mutation	SNP	C	C	G	rs637450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:72419456C>G	ENST00000454765.2	+	2	729	c.256C>G	c.(256-258)Cgt>Ggt	p.R86G	TMEM171_ENST00000287773.5_Missense_Mutation_p.R86G			Q8WVE6	TM171_HUMAN	transmembrane protein 171	86			R -> G (in dbSNP:rs637450). {ECO:0000269|PubMed:12044878}.			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)		ACTTCAGCTCCGTGCAGGGCT	0.632													C|||	2195	0.438299	0.5325	0.3285	5008	,	,		15716	0.5933		0.2654	False		,,,				2504	0.407				p.R86G	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.C256G						PASS	.	C	GLY/ARG,GLY/ARG	2186,2220	586.0+/-386.4	539,1108,556	53.0	55.0	55.0		256,256	-0.8	0.0	5	dbSNP_83	55	2125,6475	364.1+/-333.4	284,1557,2459	yes	missense,missense	TMEM171	NM_001161342.1,NM_173490.6	125,125	823,2665,3015	GG,GC,CC		24.7093,49.6142,33.1462	benign,benign	86/324,86/325	72419456	4311,8695	2203	4300	6503	SO:0001583	missense	134285	exon2			CAGCTCCGTGCAG	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.256C>G	5.37:g.72419456C>G	ENSP00000415030:p.Arg86Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	901	0.4125457875457875	250	0.508130081300813	127	0.35082872928176795	328	0.5734265734265734	196	0.25857519788918204	C	8.646	0.897133	0.17686	0.496142	0.247093	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.24908	1.83;1.83	5.2	-0.798	0.10905	.	0.836303	0.10116	N	0.714050	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P;P	0.34662	0.462;0.462	B;B	0.32724	0.151;0.151	T	0.44528	-0.9322	9	0.51188	T	0.08	-0.0497	8.079	0.30733	0.4258:0.428:0.0:0.1461	rs637450;rs58426328;rs637450	86;86	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	G	86	ENSP00000415030:R86G;ENSP00000287773:R86G	ENSP00000287773:R86G	R	+	1	0	TMEM171	72455212	0.000000	0.05858	0.000000	0.03702	0.430000	0.31655	0.482000	0.22276	-0.053000	0.13289	0.462000	0.41574	CGT	C|0.639;G|0.361	0.361	strong		0.632	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
SAFB	6294	hgsc.bcm.edu	37	19	5654449	5654449	+	Silent	SNP	G	G	A	rs1129046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5654449G>A	ENST00000292123.5	+	13	1844	c.1737G>A	c.(1735-1737)acG>acA	p.T579T	SAFB_ENST00000592224.1_Silent_p.T579T|SAFB_ENST00000454510.1_Silent_p.T510T|SAFB_ENST00000588852.1_Silent_p.T579T|SAFB_ENST00000433404.1_Silent_p.T409T|SAFB_ENST00000538656.1_Silent_p.T422T	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	579	Interaction with POLR2A.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GTGTAAAAACGTCCGGGTCCA	0.423													A|||	292	0.0583067	0.1634	0.0288	5008	,	,		17061	0.0228		0.0249	False		,,,				2504	0.0082				p.T579T	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.G1737A						PASS	.	A	,,,	621,3785	767.5+/-413.5	33,555,1615	140.0	150.0	146.0		1737,1737,1530,1737	-10.7	0.0	19	dbSNP_86	146	194,8406	810.5+/-407.1	3,188,4109	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SAFB	NM_001201338.1,NM_001201339.1,NM_001201340.1,NM_002967.3	,,,	36,743,5724	AA,AG,GG		2.2558,14.0944,6.2663	,,,	579/918,579/917,510/849,579/916	5654449	815,12191	2203	4300	6503	SO:0001819	synonymous_variant	6294	exon13			AAAAACGTCCGGG	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1737G>A	19.37:g.5654449G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	37	CCDS12142.1																																																																																			G|0.783;T|0.012	.	strong		0.423	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
SEC14L3	266629	hgsc.bcm.edu	37	22	30864610	30864610	+	Missense_Mutation	SNP	A	A	G	rs4820853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:30864610A>G	ENST00000215812.4	-	5	398	c.308T>C	c.(307-309)aTt>aCt	p.I103T	SEC14L3_ENST00000540910.1_Missense_Mutation_p.I26T|SEC14L3_ENST00000402286.1_Missense_Mutation_p.I26T|SEC14L3_ENST00000415957.2_Missense_Mutation_p.I44T|SEC14L3_ENST00000403066.1_Missense_Mutation_p.I44T|SEC14L3_ENST00000539629.1_Missense_Mutation_p.I44T|SEC14L3_ENST00000401751.1_Missense_Mutation_p.I44T	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	103	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		I -> T (in dbSNP:rs4820853). {ECO:0000269|PubMed:15489334}.			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)	AAGTGGCCCAATGATGTCATA	0.547													A|||	2271	0.453474	0.4486	0.3501	5008	,	,		18827	0.4663		0.338	False		,,,				2504	0.6391				p.I103T	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											SEC14L3,NS,malignant_melanoma,-1,1	SEC14L3	46	1	0			c.T308C						PASS	.	A	THR/ILE	1798,2608	529.5+/-372.7	375,1048,780	189.0	151.0	164.0		308	4.6	1.0	22	dbSNP_111	164	2877,5723	451.1+/-362.6	470,1937,1893	yes	missense	SEC14L3	NM_174975.4	89	845,2985,2673	GG,GA,AA		33.4535,40.808,35.9449	benign	103/401	30864610	4675,8331	2203	4300	6503	SO:0001583	missense	266629	exon5			GGCCCAATGATGT	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.308T>C	22.37:g.30864610A>G	ENSP00000215812:p.Ile103Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	904	0.4139194139194139	243	0.49390243902439024	149	0.4116022099447514	256	0.44755244755244755	256	0.33773087071240104	A	15.93	2.979447	0.53827	0.40808	0.334535	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99;-0.99;-0.99	4.55	4.55	0.56014	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.175010	0.49305	D	0.000146	T	0.00012	0.0000	L	0.42581	1.335	0.09310	P	1.0	B;B	0.15930	0.015;0.001	B;B	0.32211	0.142;0.061	T	0.43556	-0.9384	9	0.48119	T	0.1	-8.023	13.8493	0.63487	1.0:0.0:0.0:0.0	rs4820853;rs52825334;rs58974618;rs4820853	26;103	E9PE57;Q9UDX4	.;S14L3_HUMAN	T	44;44;103;26;44;44;26	ENSP00000385941:I44T;ENSP00000401864:I44T;ENSP00000215812:I103T;ENSP00000385004:I26T;ENSP00000383896:I44T;ENSP00000444691:I44T;ENSP00000439752:I26T	ENSP00000215812:I103T	I	-	2	0	SEC14L3	29194610	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	7.394000	0.79862	1.810000	0.52873	0.519000	0.50382	ATT	A|0.608;G|0.392	0.392	strong		0.547	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
AKR1C1	1645	hgsc.bcm.edu	37	10	5011027	5011027	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5011027G>A	ENST00000380872.4	+	5	653	c.461G>A	c.(460-462)tGt>tAt	p.C154Y	AKR1C1_ENST00000434459.2_Missense_Mutation_p.C154Y|AKR1C1_ENST00000380859.1_Missense_Mutation_p.C156Y|AKR1C1_ENST00000477661.1_3'UTR	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	154					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|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)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	GTGGAGAAGTGTAAAGATGCA	0.473																																					p.C154Y	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.G461A						PASS	.						131.0	115.0	121.0					10																	5011027		2203	4300	6503	SO:0001583	missense	1645	exon5			AGAAGTGTAAAGA	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"""Aldo-keto reductases"""	384	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"""	600449	"""aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"""	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.461G>A	10.37:g.5011027G>A	ENSP00000370254:p.Cys154Tyr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	34	0.25	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	37	CCDS7061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.273|4.273	0.049878|0.049878	0.08243|0.08243	.|.	.|.	ENSG00000187134|ENSG00000187134	ENST00000434459;ENST00000380872;ENST00000380859|ENST00000442997	T;T;T|.	0.23552|.	1.9;1.9;1.9|.	2.1|2.1	2.1|2.1	0.27182|0.27182	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);|.	0.170003|.	0.42053|.	D|.	0.000762|.	T|T	0.41488|0.41488	0.1161|0.1161	L|L	0.46670|0.46670	1.46|1.46	0.28041|0.28041	N|N	0.933763|0.933763	D|.	0.62365|.	0.991|.	D|.	0.67103|.	0.949|.	T|T	0.31138|0.31138	-0.9954|-0.9954	10|5	0.87932|.	D|.	0|.	.|.	10.2386|10.2386	0.43299|0.43299	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	154|.	Q04828|.	AK1C1_HUMAN|.	Y|I	154;154;156|121	ENSP00000412248:C154Y;ENSP00000370254:C154Y;ENSP00000370240:C156Y|.	ENSP00000370240:C156Y|.	C|V	+|+	2|1	0|0	AKR1C1|AKR1C1	5001027|5001027	1.000000|1.000000	0.71417|0.71417	0.820000|0.820000	0.32676|0.32676	0.054000|0.054000	0.15201|0.15201	3.786000|3.786000	0.55431|0.55431	1.475000|1.475000	0.48197|0.48197	0.305000|0.305000	0.20034|0.20034	TGT|GTA	.	.	none		0.473	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353	
SVIL	6840	hgsc.bcm.edu	37	10	29747221	29747221	+	Silent	SNP	G	G	A	rs41299212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29747221G>A	ENST00000355867.4	-	38	7352	c.6600C>T	c.(6598-6600)ccC>ccT	p.P2200P	PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000535393.1_Silent_p.P1114P|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|SVIL_ENST00000375398.2_Silent_p.P2200P|PTCHD3P1_ENST00000445521.1_RNA|SVIL_ENST00000375400.3_Silent_p.P1774P	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2200	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.				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)				GCTTCCAGGCGGGCAGGGCGT	0.587													G|||	253	0.0505192	0.0371	0.0533	5008	,	,		16594	0.001		0.1362	False		,,,				2504	0.0297				p.P2200P		Atlas-SNP	.											.	SVIL	226	.	0			c.C6600T						PASS	.	G	,	222,4184	132.9+/-169.3	0,222,1981	120.0	105.0	110.0		5322,6600	-5.1	0.5	10	dbSNP_127	110	1132,7468	233.9+/-267.0	81,970,3249	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	81,1192,5230	AA,AG,GG		13.1628,5.0386,10.4106	,	1774/1789,2200/2215	29747221	1354,11652	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon38			CCAGGCGGGCAGG	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.6600C>T	10.37:g.29747221G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.910;A|0.090	0.090	strong		0.587	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ZNF205	7755	hgsc.bcm.edu	37	16	3170188	3170188	+	Silent	SNP	C	C	T	rs12032	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:3170188C>T	ENST00000382192.3	+	7	1732	c.1527C>T	c.(1525-1527)tgC>tgT	p.C509C	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Silent_p.C509C|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	509					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						GCCCGTTGTGCGGCAAGAGCT	0.706													C|||	1924	0.384185	0.2859	0.4496	5008	,	,		14798	0.4365		0.4076	False		,,,				2504	0.3926				p.C509C		Atlas-SNP	.											.	ZNF205	42	.	0			c.C1527T						PASS	.	C	,	1268,3126	424.7+/-340.5	167,934,1096	42.0	40.0	41.0		1527,1527	-2.4	0.9	16	dbSNP_52	41	3344,5252	484.9+/-371.5	672,2000,1626	no	coding-synonymous,coding-synonymous	ZNF205	NM_001042428.1,NM_003456.2	,	839,2934,2722	TT,TC,CC		38.9018,28.8575,35.5042	,	509/555,509/555	3170188	4612,8378	2197	4298	6495	SO:0001819	synonymous_variant	7755	exon7			GTTGTGCGGCAAG	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.1527C>T	16.37:g.3170188C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_003456	A8MZK0|D3DUB4|Q9BU95	Silent	SNP	ENST00000382192.3	37	CCDS10494.2																																																																																			C|0.639;T|0.361	0.361	strong		0.706	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
PDPR	55066	hgsc.bcm.edu	37	16	70170222	70170222	+	Missense_Mutation	SNP	G	G	T	rs59034887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70170222G>T	ENST00000288050.4	+	10	2080	c.1123G>T	c.(1123-1125)Gtg>Ttg	p.V375L	PDPR_ENST00000398122.3_Missense_Mutation_p.V275L|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000568530.1_Missense_Mutation_p.V375L	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	375					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)	p.V375L(1)		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)		GTCTCCTGCAGTGCAGGGCTA	0.512																																					p.V375L		Atlas-SNP	.											PDPR,NS,carcinoma,0,1	PDPR	66	1	1	Substitution - Missense(1)	stomach(1)	c.G1123T						PASS	.	G	LEU/VAL	599,3339		0,599,1370	76.0	78.0	77.0		1123	4.4	0.0	16	dbSNP_129	77	1136,7204		0,1136,3034	no	missense	PDPR	NM_017990.3	32	0,1735,4404	TT,TG,GG		13.6211,15.2108,14.131	benign	375/880	70170222	1735,10543	1969	4170	6139	SO:0001583	missense	55066	exon10			CCTGCAGTGCAGG		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.1123G>T	16.37:g.70170222G>T	ENSP00000288050:p.Val375Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	153	29	0.189542	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	298	0.13644688644688643	88	0.17886178861788618	45	0.12430939226519337	50	0.08741258741258741	115	0.1517150395778364	G	12.75	2.030632	0.35797	0.152108	0.136211	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.85258	-1.96;-1.96	4.42	4.42	0.53409	FAD dependent oxidoreductase (1);	0.130868	0.51477	D	0.000085	T	0.00328	0.0010	N	0.16066	0.365	0.80722	D	1	B;B	0.11235	0.004;0.001	B;B	0.16289	0.01;0.015	T	0.03695	-1.1012	10	0.07644	T	0.81	.	11.9828	0.53129	0.0:0.1751:0.8249:0.0	rs59034887	103;375	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	L	375;275;103	ENSP00000288050:V375L;ENSP00000381190:V275L	ENSP00000205055:V103L	V	+	1	0	PDPR	68727723	1.000000	0.71417	0.039000	0.18376	0.977000	0.68977	7.777000	0.85628	1.985000	0.57927	0.455000	0.32223	GTG	G|0.870;T|0.130	0.130	strong		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
VCX	26609	hgsc.bcm.edu	37	X	7812052	7812052	+	Missense_Mutation	SNP	G	G	A	rs79139778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:7812052G>A	ENST00000381059.3	+	3	835	c.616G>A	c.(616-618)Gtg>Atg	p.V206M	VCX_ENST00000341408.4_Missense_Mutation_p.V186M	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	206	Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				ACTACCGAGTGTGTAGACGGC	0.577																																					p.V206M		Atlas-SNP	.											.	VCX	28	.	0			c.G616A						PASS	.	G	MET/VAL	468,3051		22,343,81,1145,418	112.0	107.0	108.0		616		0.0	X	dbSNP_131	108	847,5320		79,442,247,1754,1370	no	missense	VCX	NM_013452.2	21	101,785,328,2899,1788	AA,AG,A,GG,G		13.7344,13.2992,13.5763	probably-damaging	206/207	7812052	1315,8371	2009	3892	5901	SO:0001583	missense	26609	exon3			CCGAGTGTGTAGA	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"""variable charge, X chromosome"""			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.616G>A	X.37:g.7812052G>A	ENSP00000370447:p.Val206Met	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	325	281	0.864615	NM_013452	A0JNS5|Q4V774|Q9P0H3	Missense_Mutation	SNP	ENST00000381059.3	37	CCDS14128.1	.	.	.	.	.	.	.	.	.	.	g	9.482	1.098464	0.20552	0.132992	0.137344	ENSG00000182583	ENST00000381059;ENST00000341408	T;T	0.23950	1.88;1.95	.	.	.	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.53688	P	2.599999999997049E-5	D	0.58268	0.982	P	0.53549	0.729	T	0.18903	-1.0322	6	0.72032	D	0.01	.	.	.	.	.	206	Q9H320	VCX1_HUMAN	M	206;186	ENSP00000370447:V206M;ENSP00000344144:V186M	ENSP00000344144:V186M	V	+	1	0	VCX	7772052	0.928000	0.31464	0.011000	0.14972	0.011000	0.07611	1.998000	0.40796	0.113000	0.18004	0.115000	0.15696	GTG	G|0.862;A|0.138	0.138	strong		0.577	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452	
IRAK2	3656	hgsc.bcm.edu	37	3	10251340	10251340	+	Silent	SNP	C	C	G	rs464286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	47	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	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		
TEKT4	150483	hgsc.bcm.edu	37	2	95542364	95542364	+	Silent	SNP	G	G	A	rs113812263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:95542364G>A	ENST00000295201.4	+	6	1295	c.1158G>A	c.(1156-1158)gcG>gcA	p.A386A	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	386					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						TTCTAGAAGCGGAGCAGTCCC	0.597																																					p.A386A		Atlas-SNP	.											TEKT4,caecum,carcinoma,0,3	TEKT4	72	3	0			c.G1158A						scavenged	.						63.0	50.0	54.0					2																	95542364		2203	4300	6503	SO:0001819	synonymous_variant	150483	exon6			AGAAGCGGAGCAG	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1158G>A	2.37:g.95542364G>A		Somatic	39	1	0.025641		WXS	Illumina HiSeq	Phase_I	38	3	0.0789474	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			G|0.972;A|0.028	0.028	strong		0.597	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
UGT1A6	54578	hgsc.bcm.edu	37	2	234602202	234602202	+	Missense_Mutation	SNP	A	A	C	rs1105879	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234602202A>C	ENST00000305139.6	+	1	691	c.552A>C	c.(550-552)agA>agC	p.R184S	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	184			R -> S (in allele UGT1A6*2 and allele UGT1A6*4; dbSNP:rs1105879). {ECO:0000269|PubMed:15284531, ECO:0000269|PubMed:19204906, ECO:0000269|PubMed:9429234, ECO:0000269|Ref.4}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CATTCAGCAGAAGCCCAGACC	0.502													A|||	1626	0.324681	0.3018	0.3012	5008	,	,		19814	0.2242		0.333	False		,,,				2504	0.4673				p.R184S		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A552C	GRCh37	CM057768	UGT1A6	M	rs1105879	PASS	.	A	SER/ARG,,,,,	1345,3061	450.0+/-349.2	223,899,1081	157.0	148.0	151.0		552,,,,,	-3.3	0.0	2	dbSNP_86	151	3076,5524	471.0+/-368.0	563,1950,1787	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	110,,,,,	786,2849,2868	CC,CA,AA		35.7674,30.5266,33.992	,,,,,	184/533,,,,,	234602202	4421,8585	2203	4300	6503	SO:0001583	missense	54578	exon1			CAGCAGAAGCCCA	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.552A>C	2.37:g.234602202A>C	ENSP00000303174:p.Arg184Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	154	59	0.383117	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	662	0.3031135531135531	157	0.31910569105691056	116	0.32044198895027626	136	0.23776223776223776	253	0.3337730870712401	A	11.30	1.597632	0.28445	0.305266	0.357674	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.59502	0.26;3.34	5.31	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	L	0.45137	1.4	0.45899	P	0.0012510000000000021	B	0.19706	0.038	B	0.29524	0.103	T	0.40590	-0.9555	8	0.46703	T	0.11	.	9.9644	0.41715	0.1906:0.1494:0.66:0.0	rs1105879;rs4365457;rs17684024;rs61226878;rs1105879	184	P19224	UD16_HUMAN	S	184	ENSP00000389637:R184S;ENSP00000303174:R184S	ENSP00000303174:R184S	R	+	3	2	UGT1A6	234266941	0.000000	0.05858	0.000000	0.03702	0.434000	0.31775	-0.753000	0.04792	-0.435000	0.07264	0.533000	0.62120	AGA	A|0.682;C|0.318	0.318	strong		0.502	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
CD247	919	hgsc.bcm.edu	37	1	167407839	167407839	+	Missense_Mutation	SNP	G	G	A	rs148513413		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:167407839G>A	ENST00000362089.5	-	4	340	c.268C>T	c.(268-270)Cgt>Tgt	p.R90C	CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_Missense_Mutation_p.R90C			P20963	CD3Z_HUMAN	CD247 molecule	90					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.R90C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	TCCCGGCCACGTCTCTTGTCC	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		17232	0.001		0.0	False		,,,				2504	0.0				p.R90C	Ovarian(192;1815 2869 36877 43334)	Atlas-SNP	.											CD247,NS,carcinoma,+1,2	CD247	25	2	1	Substitution - Missense(1)	large_intestine(1)	c.C268T						PASS	.						151.0	141.0	145.0					1																	167407839		2203	4300	6503	SO:0001583	missense	919	exon4			GGCCACGTCTCTT	BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"""CD molecules"""	1677	protein-coding gene	gene with protein product		186780	"""CD3z antigen, zeta polypeptide (TiT3 complex)"", ""CD247 antigen"""	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.268C>T	1.37:g.167407839G>A	ENSP00000354782:p.Arg90Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_198053	B1AK49|Q5VX13|Q8TAX4	Missense_Mutation	SNP	ENST00000362089.5	37	CCDS1261.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.10	3.026161	0.54683	.	.	ENSG00000198821	ENST00000392122;ENST00000362089	.	.	.	4.52	2.45	0.29901	.	0.137776	0.28718	U	0.014364	T	0.54224	0.1845	M	0.64997	1.995	0.35719	D	0.816966	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.74023	0.982;0.855;0.72	T	0.58978	-0.7540	8	0.72032	D	0.01	.	8.5233	0.33289	0.0:0.1632:0.6634:0.1734	.	90;90;90	Q6KAV0;P20963-3;P20963	.;.;CD3Z_HUMAN	C	90	.	ENSP00000354782:R90C	R	-	1	0	CD247	165674463	0.000000	0.05858	0.115000	0.21578	0.951000	0.60555	0.149000	0.16243	1.096000	0.41439	0.563000	0.77884	CGT	G|1.000;A|0.000	0.000	strong		0.552	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053	
SBF1	6305	hgsc.bcm.edu	37	22	50895020	50895020	+	Silent	SNP	C	C	T	rs5771001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50895020C>T	ENST00000390679.3	-	29	4093	c.3909G>A	c.(3907-3909)gcG>gcA	p.A1303A	SBF1_ENST00000380817.3_Silent_p.A1329A|SBF1_ENST00000476293.1_5'UTR|SBF1_ENST00000348911.6_Silent_p.A1304A			O95248	MTMR5_HUMAN	SET binding factor 1	1303	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		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;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGGGCCAGCGCGTCTCTGC	0.677													C|||	1549	0.309305	0.0832	0.3718	5008	,	,		9483	0.7133		0.2256	False		,,,				2504	0.2403				p.A1329A		Atlas-SNP	.											.	SBF1	211	.	0			c.G3987A						PASS	.	C		369,3573		21,327,1623	7.0	9.0	9.0		3987	0.8	0.0	22	dbSNP_114	9	1571,6675		160,1251,2712	no	coding-synonymous	SBF1	NM_002972.2		181,1578,4335	TT,TC,CC		19.0517,9.3607,15.9173		1329/1894	50895020	1940,10248	1971	4123	6094	SO:0001819	synonymous_variant	6305	exon30			GGCCAGCGCGTCT	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.3909G>A	22.37:g.50895020C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				C|0.661;T|0.339	0.339	strong		0.677	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_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	112	0	0		WXS	Illumina HiSeq	Phase_I	66	20	0.30303	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	
MMP9	4318	hgsc.bcm.edu	37	20	44643111	44643111	+	Missense_Mutation	SNP	G	G	A	rs17577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44643111G>A	ENST00000372330.3	+	12	2022	c.2003G>A	c.(2002-2004)cGa>cAa	p.R668Q	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	668			R -> Q (in dbSNP:rs17577). {ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	TTCCAGTACCGAGGTGAGGGC	0.582											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	956	0.190895	0.1634	0.0836	5008	,	,		16389	0.1637		0.175	False		,,,				2504	0.3487				p.R668Q		Atlas-SNP	.											.	MMP9	84	.	0			c.G2003A	GRCh37	CM061854	MMP9	M	rs17577	PASS	.	G	GLN/ARG	614,3240		49,516,1362	24.0	20.0	21.0		2003	-9.3	0.3	20	dbSNP_63	21	860,6502		48,764,2869	yes	missense	MMP9	NM_004994.2	43	97,1280,4231	AA,AG,GG		11.6816,15.9315,13.1419	benign	668/708	44643111	1474,9742	1927	3681	5608	SO:0001583	missense	4318	exon12			AGTACCGAGGTGA		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.2003G>A	20.37:g.44643111G>A	ENSP00000361405:p.Arg668Gln	Somatic	48	0	0	925	WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	357	0.16346153846153846	85	0.17276422764227642	37	0.10220994475138122	101	0.17657342657342656	134	0.17678100263852242	G	6.232	0.410858	0.11812	0.159315	0.116816	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.02812	4.15	5.11	-9.33	0.00639	Hemopexin/matrixin (2);	0.852608	0.10295	N	0.691883	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.14438	0.01	B	0.04013	0.001	T	0.43376	-0.9395	9	0.07030	T	0.85	.	17.5333	0.87820	0.8078:0.0:0.1922:0.0	rs17577;rs2274756;rs3197194;rs11556879;rs17376226;rs17402681;rs52794457;rs58178187;rs2274756	668	P14780	MMP9_HUMAN	Q	668;238	ENSP00000361405:R668Q	ENSP00000361405:R668Q	R	+	2	0	MMP9	44076518	0.953000	0.32496	0.251000	0.24312	0.684000	0.39900	0.147000	0.16202	-2.524000	0.00495	-2.010000	0.00438	CGA	A|0.167;C|0.000;G|0.833	0.167	strong		0.582	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
MME	4311	hgsc.bcm.edu	37	3	154859862	154859862	+	Missense_Mutation	SNP	A	A	G	rs138218277		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:154859862A>G	ENST00000460393.1	+	11	1160	c.1040A>G	c.(1039-1041)tAt>tGt	p.Y347C	MME_ENST00000493237.1_Missense_Mutation_p.Y347C|MME_ENST00000492661.1_Missense_Mutation_p.Y347C|MME_ENST00000462745.1_Missense_Mutation_p.Y347C|MME_ENST00000360490.2_Missense_Mutation_p.Y347C	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	347					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	GTGGTTGTTTATGCTCCAGAA	0.368													A|||	1	0.000199681	0.0	0.0014	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.Y347C		Atlas-SNP	.											.	MME	133	.	0			c.A1040G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	140.0	142.0	142.0		1040,1040,1040,1040	6.0	1.0	3	dbSNP_134	142	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense,missense	MME	NM_000902.3,NM_007287.2,NM_007288.2,NM_007289.2	194,194,194,194	0,8,6495	GG,GA,AA		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	347/751,347/751,347/751,347/751	154859862	8,12998	2203	4300	6503	SO:0001583	missense	4311	exon11			TTGTTTATGCTCC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1040A>G	3.37:g.154859862A>G	ENSP00000418525:p.Tyr347Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	151	97	0.642384	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.227122	0.58668	4.54E-4	6.98E-4	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	6.02	6.02	0.97574	Peptidase M13 (1);	0.189758	0.47852	D	0.000203	T	0.80824	0.4697	M	0.85197	2.74	0.58432	D	0.999999	P	0.47350	0.894	P	0.47891	0.56	D	0.83807	0.0239	10	0.66056	D	0.02	-17.4255	11.5514	0.50723	0.931:0.0:0.069:0.0	.	347	P08473	NEP_HUMAN	C	347	ENSP00000420389:Y347C;ENSP00000418525:Y347C;ENSP00000419653:Y347C;ENSP00000417079:Y347C;ENSP00000353679:Y347C	ENSP00000353679:Y347C	Y	+	2	0	MME	156342556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.179000	0.71974	2.306000	0.77630	0.482000	0.46254	TAT	A|0.999;G|0.001	0.001	strong		0.368	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
CASP1	834	hgsc.bcm.edu	37	11	104905047	104905047	+	Silent	SNP	G	G	A	rs539595	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:104905047G>A	ENST00000533400.1	-	2	197	c.162C>T	c.(160-162)acC>acT	p.T54T	CASP1_ENST00000593315.1_Silent_p.T54T|CASP1_ENST00000446369.1_Intron|CASP1_ENST00000527979.1_Silent_p.T38T|CASP1_ENST00000598974.1_Silent_p.T54T|CASP1_ENST00000525825.1_Silent_p.T54T|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000526568.1_Intron|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000393136.4_Silent_p.T54T|CASP1_ENST00000436863.3_Silent_p.T54T|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000528974.1_Silent_p.T15T	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	54	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TCAAAGCTCGGGTCTTATCCA	0.433													.|||	715	0.142772	0.1846	0.2594	5008	,	,		22798	0.006		0.1759	False		,,,				2504	0.1104				p.T54T	NSCLC(41;1246 1743 4934)	Atlas-SNP	.											.	CASP1	53	.	0			c.C162T						PASS	.	A	,,,,	816,3588		75,666,1461	218.0	207.0	211.0		162,162,,,	1.5	1.0	11	dbSNP_83	211	1408,7184		127,1154,3015	no	coding-synonymous,coding-synonymous,intron,intron,intron	CASP1	NM_001223.3,NM_033292.2,NM_033293.2,NM_033294.2,NM_033295.2	,,,,	202,1820,4476	AA,AG,GG		16.3873,18.5286,17.113	,,,,	54/384,54/405,,,	104905047	2224,10772	2202	4296	6498	SO:0001819	synonymous_variant	834	exon2			AGCTCGGGTCTTA	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.162C>T	11.37:g.104905047G>A		Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	312	139	0.445513	NM_001257119	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																			G|0.719;A|0.281	0.281	strong		0.433	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292	
HACE1	57531	hgsc.bcm.edu	37	6	105198267	105198267	+	Silent	SNP	A	A	G	rs7752614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:105198267A>G	ENST00000262903.4	-	20	2568	c.2292T>C	c.(2290-2292)ttT>ttC	p.F764F	HACE1_ENST00000369125.2_Silent_p.F549F|HACE1_ENST00000517995.1_5'UTR	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	764	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TGAACATATGAAAGCCCTGTA	0.383													A|||	871	0.173922	0.3699	0.1398	5008	,	,		15848	0.003		0.1481	False		,,,				2504	0.136				p.F764F		Atlas-SNP	.											HACE1,NS,adenoma,0,1	HACE1	96	1	0			c.T2292C						PASS	.	A		1549,2857	484.8+/-360.1	263,1023,917	111.0	105.0	107.0		2292	2.5	1.0	6	dbSNP_116	107	1403,7197	268.5+/-287.9	114,1175,3011	no	coding-synonymous	HACE1	NM_020771.3		377,2198,3928	GG,GA,AA		16.314,35.1566,22.6972		764/910	105198267	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	57531	exon20			CATATGAAAGCCC	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.2292T>C	6.37:g.105198267A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Silent	SNP	ENST00000262903.4	37	CCDS5050.1																																																																																			A|0.805;G|0.195	0.195	strong		0.383	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
USP10	9100	hgsc.bcm.edu	37	16	84796603	84796603	+	Silent	SNP	A	A	G	rs12932018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84796603A>G	ENST00000219473.7	+	9	1676	c.1563A>G	c.(1561-1563)caA>caG	p.Q521Q	USP10_ENST00000570191.1_Silent_p.Q525Q	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	521	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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AGGGTCGACAAGAAGATGCTG	0.413													A|||	1315	0.26258	0.053	0.428	5008	,	,		19120	0.4087		0.2525	False		,,,				2504	0.2883				p.Q525Q		Atlas-SNP	.											.	USP10	51	.	0			c.A1575G						PASS	.	A		339,3455		5,329,1563	149.0	135.0	140.0		1563	-5.3	0.9	16	dbSNP_121	140	2207,6047		302,1603,2222	no	coding-synonymous	USP10	NM_005153.2		307,1932,3785	GG,GA,AA		26.7386,8.9352,21.1321		521/799	84796603	2546,9502	1897	4127	6024	SO:0001819	synonymous_variant	9100	exon10			TCGACAAGAAGAT	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.1563A>G	16.37:g.84796603A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			A|0.752;G|0.248	0.248	strong		0.413	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461017	141461017	+	Silent	SNP	G	G	A	rs61740786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461017G>A	ENST00000438773.2	-	2	589	c.456C>T	c.(454-456)atC>atT	p.I152I	TRAPPC9_ENST00000389327.3_Silent_p.I152I|TRAPPC9_ENST00000389328.4_Silent_p.I250I	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	152					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						ACAGTGACTCGATGAAGTCCT	0.572													G|||	26	0.00519169	0.0015	0.0101	5008	,	,		19773	0.0		0.0169	False		,,,				2504	0.0				p.I250I		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C750T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	66.0	56.0	59.0		456,750	-2.4	1.0	8	dbSNP_129	59	130,8470	66.3+/-128.7	1,128,4171	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,142,6360	AA,AG,GG		1.5116,0.3177,1.1072	,	152/1149,250/1247	141461017	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			TGACTCGATGAAG	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.456C>T	8.37:g.141461017G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	8.082	0.772536	0.16051	0.003177	0.015116	ENSG00000167632	ENST00000520857	.	.	.	5.61	-2.44	0.06502	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0785	0.36536	0.538:0.1001:0.3619:0.0	.	.	.	.	X	5	.	.	R	-	1	2	TRAPPC9	141530199	0.083000	0.21467	0.973000	0.42090	0.755000	0.42902	-0.396000	0.07278	-0.397000	0.07691	-0.812000	0.03155	CGA	G|0.989;A|0.011	0.011	strong		0.572	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
PPARG	5468	hgsc.bcm.edu	37	3	12475557	12475557	+	Silent	SNP	C	C	T	rs3856806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:12475557C>T	ENST00000287820.6	+	7	1552	c.1431C>T	c.(1429-1431)caC>caT	p.H477H	PPARG_ENST00000397000.1_3'UTR|PPARG_ENST00000397015.2_Silent_p.H449H|PPARG_ENST00000397010.2_Silent_p.H449H|PPARG_ENST00000397026.2_Silent_p.H455H|PPARG_ENST00000539812.1_3'UTR|PPARG_ENST00000309576.6_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	146	0	0		WXS	Illumina HiSeq	Phase_I	166	95	0.572289	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	
DCLRE1B	64858	hgsc.bcm.edu	37	1	114448389	114448389	+	Missense_Mutation	SNP	C	C	T	rs11552449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:114448389C>T	ENST00000369563.3	+	1	627	c.181C>T	c.(181-183)Cac>Tac	p.H61Y	DCLRE1B_ENST00000466480.1_3'UTR|AP4B1_ENST00000369566.3_5'Flank|AP4B1_ENST00000369567.1_5'Flank|AP4B1_ENST00000369569.1_5'Flank|AP4B1_ENST00000256658.4_5'Flank	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	61			H -> Y (in dbSNP:rs11552449). {ECO:0000269|Ref.2}.		cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		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)		CTTGCATCGTCACCTACAGGT	0.592								Other identified genes with known or suspected DNA repair function			OREG0004772	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	C|||	1213	0.242212	0.0151	0.3833	5008	,	,		16208	0.5873		0.1909	False		,,,				2504	0.1462				p.H61Y		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.C181T						PASS	.	C	TYR/HIS	185,4221	116.7+/-154.6	9,167,2027	45.0	42.0	43.0		181	3.6	0.3	1	dbSNP_120	43	1495,7105	282.5+/-295.6	130,1235,2935	yes	missense	DCLRE1B	NM_022836.3	83	139,1402,4962	TT,TC,CC		17.3837,4.1988,12.9171	benign	61/533	114448389	1680,11326	2203	4300	6503	SO:0001583	missense	64858	exon1			CATCGTCACCTAC	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.181C>T	1.37:g.114448389C>T	ENSP00000358576:p.His61Tyr	Somatic	54	0	0	1458	WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_022836	Q9H9E5	Missense_Mutation	SNP	ENST00000369563.3	37	CCDS866.1	604	0.2765567765567766	14	0.028455284552845527	111	0.30662983425414364	334	0.583916083916084	145	0.19129287598944592	C	11.60	1.687518	0.29962	0.041988	0.173837	ENSG00000118655	ENST00000369563	T	0.76186	-1.0	5.56	3.57	0.40892	Beta-lactamase-like (1);	0.798476	0.12346	N	0.477046	T	0.34279	0.0892	N	0.14661	0.345	0.80722	P	0.0	B	0.25850	0.136	B	0.35182	0.197	T	0.09487	-1.0672	9	0.02654	T	1	-4.4801	8.133	0.31037	0.3264:0.5989:0.0:0.0747	rs11552449;rs12022378;rs52822912;rs12022378	61	Q9H816	DCR1B_HUMAN	Y	61	ENSP00000358576:H61Y	ENSP00000358576:H61Y	H	+	1	0	DCLRE1B	114249912	0.995000	0.38212	0.269000	0.24586	0.677000	0.39632	3.647000	0.54403	1.337000	0.45525	0.561000	0.74099	CAC	C|0.806;G|0.000;T|0.194	0.194	strong		0.592	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836	
SDHA	6389	hgsc.bcm.edu	37	5	223646	223646	+	Missense_Mutation	SNP	A	A	T	rs34635677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:223646A>T	ENST00000264932.6	+	2	228	c.113A>T	c.(112-114)gAt>gTt	p.D38V	SDHA_ENST00000504309.1_Missense_Mutation_p.D38V|SDHA_ENST00000510361.1_Missense_Mutation_p.D38V	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	38			D -> V (in dbSNP:rs34635677). {ECO:0000269|PubMed:14702039}.		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)	TTCACTGTTGATGGGAACAAG	0.428									Familial Paragangliomas				A|||	93	0.0185703	0.0	0.0159	5008	,	,		19506	0.0		0.0318	False		,,,				2504	0.0511				p.D38V		Atlas-SNP	.											.	SDHA	80	.	0			c.A113T						PASS	.	A	VAL/ASP	35,4371	40.0+/-72.8	0,35,2168	108.0	104.0	105.0		113	1.6	0.0	5	dbSNP_126	105	392,8208	126.7+/-185.1	8,376,3916	yes	missense	SDHA	NM_004168.2	152	8,411,6084	TT,TA,AA		4.5581,0.7944,3.2831	benign	38/665	223646	427,12579	2203	4300	6503	SO:0001583	missense	6389	exon2	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	CTGTTGATGGGAA	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.113A>T	5.37:g.223646A>T	ENSP00000264932:p.Asp38Val	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	357	167	0.467787	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	A	10.49	1.366118	0.24684	0.007944	0.045581	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.71934	-0.6;0.25;-0.61	5.81	1.56	0.23342	.	0.349316	0.26734	U	0.022772	T	0.16385	0.0394	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.07139	-1.0788	10	0.14252	T	0.57	.	8.3967	0.32561	0.7045:0.0:0.2955:0.0	rs34635677	38;38;38;44	E9PBJ5;D6RFM5;P31040;Q59GW8	.;.;DHSA_HUMAN;.	V	38	ENSP00000264932:D38V;ENSP00000426514:D38V;ENSP00000427703:D38V	ENSP00000264932:D38V	D	+	2	0	SDHA	276646	0.961000	0.32948	0.009000	0.14445	0.801000	0.45260	2.727000	0.47311	0.319000	0.23209	0.455000	0.32223	GAT	A|0.968;T|0.032	0.032	strong		0.428	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
NGFR	4804	hgsc.bcm.edu	37	17	47579567	47579567	+	Splice_Site	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:47579567G>A	ENST00000172229.3	+	2	333		c.e2+1		NGFR_ENST00000504201.1_Splice_Site	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor						apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGCCTGGACAGTGAGTAGAGG	0.637																																					.		Atlas-SNP	.											.	NGFR	46	.	0			c.208+1G>A						PASS	.						47.0	42.0	44.0					17																	47579567		2203	4300	6503	SO:0001630	splice_region_variant	4804	exon2			TGGACAGTGAGTA	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.208+1G>A	17.37:g.47579567G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	35	9	0.257143	NM_002507	B2R961|B4E096	Splice_Site	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132712	0.77662	.	.	ENSG00000064300	ENST00000172229	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8004	0.88585	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NGFR	44934566	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	9.150000	0.94667	2.513000	0.84729	0.561000	0.74099	.	.	.	none		0.637	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		Intron
SLC29A4	222962	hgsc.bcm.edu	37	7	5338714	5338714	+	Silent	SNP	T	T	C	rs6950111	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5338714T>C	ENST00000396872.3	+	8	1139	c.978T>C	c.(976-978)gaT>gaC	p.D326D	SLC29A4_ENST00000406453.3_Silent_p.D312D|SLC29A4_ENST00000297195.4_Silent_p.D326D			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	326					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)	TGCGCTTTGATGTGCCGCGGC	0.716													C|||	1447	0.288938	0.5151	0.2795	5008	,	,		13632	0.12		0.3052	False		,,,				2504	0.1472				p.D326D		Atlas-SNP	.											.	SLC29A4	52	.	0			c.T978C						PASS	.	C	,	1951,2423		439,1073,675	12.0	17.0	15.0		978,978	-5.9	0.0	7	dbSNP_116	15	2915,5669		503,1909,1880	no	coding-synonymous,coding-synonymous	SLC29A4	NM_001040661.1,NM_153247.2	,	942,2982,2555	CC,CT,TT		33.9585,44.6045,37.5521	,	326/531,326/531	5338714	4866,8092	2187	4292	6479	SO:0001819	synonymous_variant	222962	exon8			CTTTGATGTGCCG	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.978T>C	7.37:g.5338714T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	CCDS5340.1																																																																																			T|0.699;C|0.301	0.301	strong		0.716	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247	
CD80	941	hgsc.bcm.edu	37	3	119263680	119263680	+	Silent	SNP	C	C	T	rs2228017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:119263680C>T	ENST00000264246.3	-	3	497	c.135G>A	c.(133-135)gtG>gtA	p.V45V	CD80_ENST00000383668.3_Silent_p.V45V|CD80_ENST00000383669.3_Silent_p.V45V|CD80_ENST00000478182.1_Silent_p.V45V	NM_005191.3	NP_005182.1	P33681	CD80_HUMAN	CD80 molecule	45	Ig-like V-type.				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)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of signal transduction (GO:0009967)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	12					Abatacept(DB01281)|Belatacept(DB06681)	ACAGCGTTGCCACTTCTTTCA	0.428													C|||	1107	0.221046	0.1679	0.2147	5008	,	,		20312	0.2669		0.2624	False		,,,				2504	0.2076				p.V45V	Melanoma(132;135 1764 1806 5833 14593)	Atlas-SNP	.											.	CD80	35	.	0			c.G135A						PASS	.	C		816,3590	325.9+/-299.3	64,688,1451	118.0	103.0	108.0		135	-0.8	0.0	3	dbSNP_98	108	2141,6459	367.8+/-334.9	256,1629,2415	no	coding-synonymous	CD80	NM_005191.3		320,2317,3866	TT,TC,CC		24.8953,18.5202,22.7357		45/289	119263680	2957,10049	2203	4300	6503	SO:0001819	synonymous_variant	941	exon3			CGTTGCCACTTCT		CCDS2989.1	3q13.3-q21	2013-01-11	2006-03-31		ENSG00000121594	ENSG00000121594		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1700	protein-coding gene	gene with protein product	"""B-lymphocyte activation antigen B7"""	112203	"""CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)"", ""CD80 molecule """	CD28LG, CD28LG1		1370389	Standard	NM_005191		Approved	B7.1, B7-1	uc003ecq.3	P33681	OTTHUMG00000159419	ENST00000264246.3:c.135G>A	3.37:g.119263680C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	305	172	0.563934	NM_005191	Q5DTA9|Q5DTB0	Silent	SNP	ENST00000264246.3	37	CCDS2989.1																																																																																			C|0.766;T|0.234	0.234	strong		0.428	CD80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355196.1	NM_005191	
AADAC	13	hgsc.bcm.edu	37	3	151531989	151531989	+	Silent	SNP	C	C	A	rs35544417	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:151531989C>A	ENST00000232892.7	+	1	165	c.39C>A	c.(37-39)atC>atA	p.I13I	AADAC_ENST00000488869.1_Silent_p.I13I|RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	13					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TTGTGGGGATCCTCATAGCAT	0.418													C|||	56	0.0111821	0.0008	0.062	5008	,	,		18856	0.0		0.008	False		,,,				2504	0.0041				p.I13I	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											AADAC,NS,carcinoma,+2,1	AADAC	49	1	0			c.C39A						PASS	.	C		17,4389	24.3+/-50.5	0,17,2186	141.0	138.0	139.0		39	1.9	0.0	3	dbSNP_126	139	128,8472	66.0+/-128.3	2,124,4174	no	coding-synonymous	AADAC	NM_001086.2		2,141,6360	AA,AC,CC		1.4884,0.3858,1.1149		13/400	151531989	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	13	exon1			GGGGATCCTCATA	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"""arylacetamide deacetylase (esterase)"""			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.39C>A	3.37:g.151531989C>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	184	65	0.353261	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	37	CCDS33877.1																																																																																			C|0.988;A|0.012	0.012	strong		0.418	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086	
PRR21	643905	hgsc.bcm.edu	37	2	240982271	240982271	+	Silent	SNP	G	G	A	rs76841013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240982271G>A	ENST00000408934.1	-	1	128	c.129C>T	c.(127-129)caC>caT	p.H43H		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	43	Pro-rich.							p.H43H(4)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGCCGTGGATGAAGG	0.577													N|||	1226	0.244808	0.1838	0.2061	5008	,	,		19244	0.4167		0.2555	False		,,,				2504	0.1667				p.H43H		Atlas-SNP	.											PRR21,NS,lymphoid_neoplasm,0,4	PRR21	53	4	4	Substitution - coding silent(4)	haematopoietic_and_lymphoid_tissue(4)	c.C129T						PASS	.						110.0	98.0	102.0					2																	240982271		2203	4300	6503	SO:0001819	synonymous_variant	643905	exon1			AGAGCCGTGGATG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.129C>T	2.37:g.240982271G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	65	14	0.215385	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			G|0.755;A|0.245	0.245	strong		0.577	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
MICAL3	57553	hgsc.bcm.edu	37	22	18300240	18300240	+	Silent	SNP	T	T	C	rs5992854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:18300240T>C	ENST00000441493.2	-	26	5539	c.5187A>G	c.(5185-5187)ctA>ctG	p.L1729L	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1729					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)		CGGCTTCTTCTAGGAGGTTGG	0.592													C|||	1934	0.386182	0.6876	0.2651	5008	,	,		13557	0.1726		0.3897	False		,,,				2504	0.2812				p.L1729L		Atlas-SNP	.											.	MICAL3	53	.	0			c.A5187G						PASS	.	C		2404,1312		766,872,220	28.0	31.0	30.0		5187	-2.6	0.0	22	dbSNP_114	30	3278,4894		664,1950,1472	no	coding-synonymous	MICAL3	NM_015241.2		1430,2822,1692	CC,CT,TT		40.1126,35.3068,47.7961		1729/2003	18300240	5682,6206	1858	4086	5944	SO:0001819	synonymous_variant	57553	exon26			TTCTTCTAGGAGG	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.5187A>G	22.37:g.18300240T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	169	82	0.485207	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	841	0.3850732600732601	342	0.6951219512195121	106	0.292817679558011	103	0.18006993006993008	290	0.38258575197889183	C	0.013	-1.642718	0.00792	0.646932	0.401126	ENSG00000093100	ENST00000252134	.	.	.	4.65	-2.63	0.06133	.	.	.	.	.	.	.	.	.	.	.	0.24623	P	0.99366634	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7809	0.23646	0.0:0.4922:0.1112:0.3966	rs5992854;rs58221441;rs5992854	.	.	.	W	711	.	.	X	-	2	0	XXbac-B461K10.4	16680240	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-1.496000	0.02291	-0.962000	0.03604	-2.031000	0.00424	TAG	T|0.599;C|0.401	0.401	strong		0.592	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
NTRK3	4916	hgsc.bcm.edu	37	15	88576185	88576185	+	Silent	SNP	G	G	C	rs2229910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:88576185G>C	ENST00000360948.2	-	13	1649	c.1488C>G	c.(1486-1488)gcC>gcG	p.A496A	NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000317501.3_Silent_p.A496A|NTRK3_ENST00000542733.2_Silent_p.A398A|NTRK3_ENST00000557856.1_Silent_p.A488A|NTRK3_ENST00000394480.2_Silent_p.A496A|NTRK3_ENST00000357724.2_Silent_p.A488A|NTRK3_ENST00000355254.2_Silent_p.A496A|NTRK3_ENST00000558676.1_Silent_p.A488A|NTRK3_ENST00000540489.2_Silent_p.A496A	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						PASS	.	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	61	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	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			
ZNF623	9831	hgsc.bcm.edu	37	8	144732319	144732319	+	Missense_Mutation	SNP	A	A	G	rs141901810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144732319A>G	ENST00000501748.2	+	1	366	c.277A>G	c.(277-279)Aca>Gca	p.T93A	ZNF623_ENST00000458270.2_Missense_Mutation_p.T53A|ZNF623_ENST00000526926.1_Missense_Mutation_p.T53A	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	93					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(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GACAGGAGAGACAGCTCAAGT	0.522													A|||	8	0.00159744	0.0008	0.0029	5008	,	,		19162	0.0		0.002	False		,,,				2504	0.0031				p.T93A		Atlas-SNP	.											.	ZNF623	63	.	0			c.A277G						PASS	.	A	ALA/THR,ALA/THR	2,4404	4.2+/-10.8	0,2,2201	85.0	86.0	85.0		157,277	-1.3	0.4	8	dbSNP_134	85	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense	ZNF623	NM_001082480.1,NM_014789.3	58,58	0,26,6477	GG,GA,AA		0.2791,0.0454,0.1999	benign,benign	53/497,93/537	144732319	26,12980	2203	4300	6503	SO:0001583	missense	9831	exon1			GGAGAGACAGCTC	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.277A>G	8.37:g.144732319A>G	ENSP00000445979:p.Thr93Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_014789	A4FU80|B4DGP3|E7ENV5	Missense_Mutation	SNP	ENST00000501748.2	37	CCDS34957.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	A	11.29	1.594716	0.28445	4.54E-4	0.002791	ENSG00000183309	ENST00000526926;ENST00000328466;ENST00000458270;ENST00000532796;ENST00000501748	T;T;T	0.14893	2.47;2.47;2.47	4.35	-1.26	0.09376	.	.	.	.	.	T	0.13030	0.0316	L	0.42245	1.32	0.24401	N	0.994708	B	0.02656	0.0	B	0.04013	0.001	T	0.30504	-0.9976	9	0.87932	D	0	-0.5094	5.2459	0.15496	0.6286:0.1525:0.2189:0.0	.	93	O75123	ZN623_HUMAN	A	53;53;53;93;93	ENSP00000435232:T53A;ENSP00000411139:T53A;ENSP00000445979:T93A	ENSP00000330358:T53A	T	+	1	0	ZNF623	144803462	0.168000	0.22989	0.351000	0.25721	0.463000	0.32649	1.634000	0.37123	-0.285000	0.09089	0.533000	0.62120	ACA	A|0.998;G|0.002	0.002	strong		0.522	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
NFKBIL1	4795	hgsc.bcm.edu	37	6	31525448	31525448	+	Silent	SNP	C	C	T	rs2230365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	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	
FLG	2312	hgsc.bcm.edu	37	1	152277396	152277396	+	Silent	SNP	T	T	C	rs6681433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152277396T>C	ENST00000368799.1	-	3	10001	c.9966A>G	c.(9964-9966)caA>caG	p.Q3322Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3322	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)			CAGATGAAGCTTGTCCACGCG	0.547									Ichthyosis				T|||	1708	0.341054	0.115	0.4193	5008	,	,		20684	0.6062		0.171	False		,,,				2504	0.4928				p.Q3322Q		Atlas-SNP	.											.	FLG	900	.	0			c.A9966G						PASS	.	T		582,3824	260.1+/-263.5	40,502,1661	416.0	405.0	409.0		9966	-6.5	0.0	1	dbSNP_116	409	1447,7153	276.8+/-292.5	129,1189,2982	no	coding-synonymous	FLG	NM_002016.1		169,1691,4643	CC,CT,TT		16.8256,13.2093,15.6005		3322/4062	152277396	2029,10977	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGAAGCTTGTCCA	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.9966A>G	1.37:g.152277396T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	180	108	0.6	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.794;C|0.206	0.206	strong		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PRR21	643905	hgsc.bcm.edu	37	2	240981487	240981487	+	Missense_Mutation	SNP	A	A	G	rs60617721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240981487A>G	ENST00000408934.1	-	1	912	c.913T>C	c.(913-915)Tgc>Cgc	p.C305R		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	305	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGGCATGGACGAAGG	0.632													a|||	2078	0.414936	0.4455	0.3775	5008	,	,		16158	0.5744		0.332	False		,,,				2504	0.3211				p.C305R		Atlas-SNP	.											PRR21,rectum,carcinoma,0,2	PRR21	53	2	0			c.T913C						scavenged	.						25.0	21.0	23.0					2																	240981487		1766	3570	5336	SO:0001583	missense	643905	exon1			AGAGGCATGGACG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.913T>C	2.37:g.240981487A>G	ENSP00000386166:p.Cys305Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.707321	0.00096	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	0.623	-1.25	0.09405	.	.	.	.	.	T	0.04452	0.0122	N	0.08118	0	0.80722	P	0.0	B	0.19073	0.033	B	0.08055	0.003	T	0.43360	-0.9396	8	0.08381	T	0.77	.	2.6586	0.05019	0.2679:0.4862:0.0:0.2459	rs60617721;rs62184584	305	Q8WXC7	PRR21_HUMAN	R	305	ENSP00000386166:C305R;ENSP00000418240:C305R	ENSP00000386166:C305R	C	-	1	0	PRR21	240630160	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.193000	0.01244	-1.350000	0.02199	-1.198000	0.01671	TGC	A|0.695;G|0.305	0.305	strong		0.632	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
NR2C2	7182	hgsc.bcm.edu	37	3	15080696	15080696	+	Silent	SNP	G	G	A	rs2230444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:15080696G>A	ENST00000425241.1	+	13	1940	c.1578G>A	c.(1576-1578)caG>caA	p.Q526Q	NR2C2_ENST00000406272.2_Silent_p.Q526Q|NR2C2_ENST00000478572.1_3'UTR|NR2C2_ENST00000323373.6_Silent_p.Q545Q|NR2C2_ENST00000393102.3_Silent_p.Q526Q			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	526	Ligand-binding. {ECO:0000250}.				cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGGAGTTGCAGGACTATGTTC	0.502													G|||	252	0.0503195	0.0688	0.049	5008	,	,		17070	0.0		0.0885	False		,,,				2504	0.0389				p.Q545Q		Atlas-SNP	.											.	NR2C2	44	.	0			c.G1635A						PASS	.	G		258,4148	147.6+/-182.1	3,252,1948	96.0	86.0	90.0		1635	3.0	1.0	3	dbSNP_98	90	866,7734	196.9+/-241.7	48,770,3482	no	coding-synonymous	NR2C2	NM_003298.3		51,1022,5430	AA,AG,GG		10.0698,5.8557,8.6422		545/616	15080696	1124,11882	2203	4300	6503	SO:0001819	synonymous_variant	7182	exon14			GTTGCAGGACTAT	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"""Nuclear hormone receptors"""	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.1578G>A	3.37:g.15080696G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	120	31	0.258333	NM_003298	A8K3H5|B6ZGT8|P55092	Silent	SNP	ENST00000425241.1	37																																																																																				A|0.082;C|0.000;G|0.917	0.082	strong		0.502	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298	
ZNF846	162993	hgsc.bcm.edu	37	19	9868278	9868278	+	Missense_Mutation	SNP	T	T	C	rs10420364	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9868278T>C	ENST00000397902.2	-	6	1888	c.1475A>G	c.(1474-1476)tAc>tGc	p.Y492C	ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000586293.1_3'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	492			Y -> C (in dbSNP:rs10420364).		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(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AACGTTAAGGTATGTGGAATA	0.403													N|||	1378	0.27516	0.472	0.3804	5008	,	,		22298	0.0714		0.2127	False		,,,				2504	0.2086				p.Y492C		Atlas-SNP	.											.	ZNF846	61	.	0			c.A1475G						PASS	.	C	CYS/TYR	1561,2749		326,909,920	117.0	127.0	123.0		1475	-1.6	0.0	19	dbSNP_119	123	1693,6869		167,1359,2755	yes	missense	ZNF846	NM_001077624.1	194	493,2268,3675	CC,CT,TT		19.7734,36.2181,25.2797	benign	492/534	9868278	3254,9618	2155	4281	6436	SO:0001583	missense	162993	exon6			TTAAGGTATGTGG	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1475A>G	19.37:g.9868278T>C	ENSP00000380999:p.Tyr492Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	546	0.25	231	0.4695121951219512	122	0.3370165745856354	31	0.05419580419580419	162	0.21372031662269128	.	3.453	-0.111549	0.06881	0.362181	0.197734	ENSG00000196605	ENST00000397902	T	0.07908	3.15	1.91	-1.57	0.08506	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43310	-0.9399	8	0.35671	T	0.21	.	7.8475	0.29435	0.0:0.29:0.0:0.71	rs10420364;rs10420364	492	Q147U1	ZN846_HUMAN	C	492	ENSP00000380999:Y492C	ENSP00000380999:Y492C	Y	-	2	0	ZNF846	9729278	0.000000	0.05858	0.000000	0.03702	0.206000	0.24218	-0.908000	0.04063	-0.743000	0.04784	-0.366000	0.07423	TAC	T|0.774;C|0.226	0.226	strong		0.403	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
TPST2	8459	hgsc.bcm.edu	37	22	26937087	26937087	+	Silent	SNP	C	C	A	rs5761587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26937087C>A	ENST00000338754.4	-	3	780	c.510G>T	c.(508-510)tcG>tcT	p.S170S	TPST2_ENST00000398110.2_Silent_p.S170S|TPST2_ENST00000403880.1_Silent_p.S170S	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	170					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						GGAACAGGCGCGACAGGTAGA	0.617													C|||	198	0.0395367	0.0121	0.0403	5008	,	,		19873	0.0169		0.0885	False		,,,				2504	0.0491				p.S170S		Atlas-SNP	.											.	TPST2	23	.	0			c.G510T						PASS	.	C	,	124,4282	92.5+/-131.2	0,124,2079	96.0	74.0	81.0		510,510	-2.7	1.0	22	dbSNP_114	81	828,7772	191.7+/-237.8	41,746,3513	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	41,870,5592	AA,AC,CC		9.6279,2.8143,7.3197	,	170/378,170/378	26937087	952,12054	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGCGCGACAGG	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.510G>T	22.37:g.26937087C>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			C|0.935;A|0.065	0.065	strong		0.617	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
ZNF285	26974	hgsc.bcm.edu	37	19	44891405	44891405	+	Silent	SNP	A	A	G	rs151111866	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44891405A>G	ENST00000330997.4	-	4	1066	c.1002T>C	c.(1000-1002)caT>caC	p.H334H	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Silent_p.H334H|ZNF285_ENST00000591679.1_Silent_p.H341H	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	334					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GGACTCGATGATGGTTGTGAA	0.478													A|||	76	0.0151757	0.0	0.0144	5008	,	,		21126	0.001		0.0408	False		,,,				2504	0.0245				p.H334H		Atlas-SNP	.											.	ZNF285	86	.	0			c.T1002C						PASS	.	A		22,4384	29.0+/-57.7	0,22,2181	97.0	97.0	97.0		1002	2.2	0.0	19	dbSNP_134	97	291,8309	107.6+/-168.3	3,285,4012	no	coding-synonymous	ZNF285	NM_152354.3		3,307,6193	GG,GA,AA		3.3837,0.4993,2.4066		334/591	44891405	313,12693	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			TCGATGATGGTTG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1002T>C	19.37:g.44891405A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			A|0.977;G|0.023	0.023	strong		0.478	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
TTN	7273	hgsc.bcm.edu	37	2	179495650	179495650	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179495650G>A	ENST00000591111.1	-	188	39336	c.39112C>T	c.(39112-39114)Cga>Tga	p.R13038*	TTN_ENST00000589042.1_Nonsense_Mutation_p.R14679*|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.R12111*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.R5806*|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R5739*|TTN_ENST00000460472.2_Nonsense_Mutation_p.R5614*|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13038					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)			TGCAGGGGTCGCACCAGTTTA	0.483																																					p.R14679X		Atlas-SNP	.											TTN_ENST00000359218,colon,carcinoma,0,5	TTN	18412	5	0			c.C44035T						scavenged	.						84.0	82.0	83.0					2																	179495650		1935	4132	6067	SO:0001587	stop_gained	7273	exon238			GGGGTCGCACCAG	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.39112C>T	2.37:g.179495650G>A	ENSP00000465570:p.Arg13038*	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	2	0.0253165	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	58	30.919340	0.99978	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	12111;5614;5806;5739;5614	.	ENSP00000340554:R5806X	R	-	1	2	TTN	179203895	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.803000	0.85983	2.941000	0.99782	0.655000	0.94253	CGA	.	.	none		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FAM171B	165215	hgsc.bcm.edu	37	2	187605000	187605000	+	Missense_Mutation	SNP	G	G	A	rs73979354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:187605000G>A	ENST00000304698.5	+	2	487	c.284G>A	c.(283-285)cGt>cAt	p.R95H		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	95						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						ATCATCAGTCGTCAGTACCTG	0.403													G|||	72	0.014377	0.0393	0.0115	5008	,	,		19566	0.0		0.008	False		,,,				2504	0.0041				p.R95H		Atlas-SNP	.											.	FAM171B	146	.	0			c.G284A						PASS	.	G	HIS/ARG	156,4250	105.6+/-144.1	2,152,2049	106.0	91.0	96.0		284	5.3	1.0	2	dbSNP_130	96	40,8560	26.8+/-75.7	0,40,4260	yes	missense	FAM171B	NM_177454.3	29	2,192,6309	AA,AG,GG		0.4651,3.5406,1.507	benign	95/827	187605000	196,12810	2203	4300	6503	SO:0001583	missense	165215	exon2			TCAGTCGTCAGTA	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.284G>A	2.37:g.187605000G>A	ENSP00000304108:p.Arg95His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	30	0.013736263736263736	18	0.036585365853658534	6	0.016574585635359115	0	0.0	6	0.0079155672823219	G	9.869	1.198429	0.22037	0.035406	0.004651	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.31769	1.48	6.16	5.26	0.73747	.	0.252210	0.41938	N	0.000786	T	0.03053	0.0090	N	0.08118	0	0.34129	D	0.665083	B;B	0.19583	0.037;0.037	B;B	0.12837	0.008;0.008	T	0.17623	-1.0363	10	0.22706	T	0.39	-4.6378	7.6817	0.28518	0.227:0.0:0.773:0.0	.	95;96	Q6P995;A8K122	F171B_HUMAN;.	H	95	ENSP00000304108:R95H	ENSP00000272804:R95H	R	+	2	0	FAM171B	187313245	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	2.871000	0.48459	1.557000	0.49525	0.650000	0.86243	CGT	G|0.987;A|0.013	0.013	strong		0.403	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
ASB17	127247	hgsc.bcm.edu	37	1	76397972	76397972	+	Missense_Mutation	SNP	C	C	T	rs3795251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:76397972C>T	ENST00000284142.6	-	1	144	c.5G>A	c.(4-6)aGt>aAt	p.S2N		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	2			S -> N (in dbSNP:rs3795251).		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						AGTAGATTTACTCATTGTTAC	0.353													C|||	1986	0.396565	0.1884	0.2983	5008	,	,		19811	0.7073		0.3221	False		,,,				2504	0.5041				p.S2N		Atlas-SNP	.											.	ASB17	53	.	0			c.G5A						PASS	.	C	ASN/SER	873,3519		86,701,1409	42.0	45.0	44.0		5	3.1	1.0	1	dbSNP_107	44	3022,5566		543,1936,1815	yes	missense	ASB17	NM_080868.2	46	629,2637,3224	TT,TC,CC		35.1886,19.877,30.0077	benign	2/296	76397972	3895,9085	2196	4294	6490	SO:0001583	missense	127247	exon1			GATTTACTCATTG	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.5G>A	1.37:g.76397972C>T	ENSP00000284142:p.Ser2Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	37	CCDS671.1	832	0.38095238095238093	95	0.19308943089430894	117	0.32320441988950277	367	0.6416083916083916	253	0.3337730870712401	C	7.663	0.685413	0.14973	0.19877	0.351886	ENSG00000154007	ENST00000284142	T	0.35605	1.3	5.98	3.13	0.36017	.	0.251428	0.35207	N	0.003379	T	0.07503	0.0189	N	0.12182	0.205	0.41782	P	0.010174000000000016	B	0.09022	0.002	B	0.06405	0.002	T	0.18209	-1.0344	9	0.34782	T	0.22	.	8.1764	0.31285	0.0:0.756:0.0:0.244	rs3795251;rs17596467;rs52792838;rs57374823;rs3795251	2	Q8WXJ9	ASB17_HUMAN	N	2	ENSP00000284142:S2N	ENSP00000284142:S2N	S	-	2	0	ASB17	76170560	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	1.304000	0.33482	0.434000	0.26340	-0.793000	0.03317	AGT	C|0.652;T|0.348	0.348	strong		0.353	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
ITGB6	3694	hgsc.bcm.edu	37	2	161029218	161029218	+	Silent	SNP	G	G	A	rs2305818	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:161029218G>A	ENST00000283249.2	-	6	1020	c.783C>T	c.(781-783)gaC>gaT	p.D261D	ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000428609.2_Silent_p.D219D|ITGB6_ENST00000409872.1_Silent_p.D261D|ITGB6_ENST00000409967.2_Silent_p.D261D	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	261	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						GGTGGAGGGAGTCATTCCGCC	0.453													G|||	1144	0.228435	0.0325	0.2594	5008	,	,		17071	0.3323		0.4225	False		,,,				2504	0.1646				p.D261D		Atlas-SNP	.											.	ITGB6	68	.	0			c.C783T						PASS	.	G		413,3993	200.8+/-224.0	14,385,1804	127.0	121.0	123.0		783	-5.1	0.8	2	dbSNP_100	123	3499,5101	512.2+/-377.9	740,2019,1541	no	coding-synonymous	ITGB6	NM_000888.3		754,2404,3345	AA,AG,GG		40.686,9.3736,30.0784		261/789	161029218	3912,9094	2203	4300	6503	SO:0001819	synonymous_variant	3694	exon6			GAGGGAGTCATTC		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.783C>T	2.37:g.161029218G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Silent	SNP	ENST00000283249.2	37	CCDS2212.1																																																																																			G|0.727;A|0.273	0.273	strong		0.453	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
FOLH1	2346	hgsc.bcm.edu	37	11	49196490	49196490	+	Silent	SNP	T	T	C	rs202716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49196490T>C	ENST00000256999.2	-	9	1319	c.1059A>G	c.(1057-1059)acA>acG	p.T353T	FOLH1_ENST00000340334.7_Silent_p.T338T|FOLH1_ENST00000533034.1_Silent_p.T338T|FOLH1_ENST00000525629.1_5'UTR|FOLH1_ENST00000343844.4_Silent_p.T45T|FOLH1_ENST00000356696.3_Silent_p.T353T	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	353	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGTAAATTCTTGTCACTTCAT	0.338													C|||	2095	0.418331	0.6483	0.3156	5008	,	,		17405	0.3175		0.2744	False		,,,				2504	0.4325				p.T353T		Atlas-SNP	.											.	FOLH1	141	.	0			c.A1059G						PASS	.						90.0	110.0	103.0					11																	49196490		2201	4297	6498	SO:0001819	synonymous_variant	2346	exon9			AATTCTTGTCACT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.1059A>G	11.37:g.49196490T>C		Somatic	346	1	0.00289017		WXS	Illumina HiSeq	Phase_I	307	103	0.335505	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																			C|1.000;|0.000	1.000	weak		0.338	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
TGM1	7051	hgsc.bcm.edu	37	14	24728294	24728294	+	Silent	SNP	G	G	T	rs1126432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24728294G>T	ENST00000206765.6	-	7	1269	c.1146C>A	c.(1144-1146)ggC>ggA	p.G382G	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	382			G -> R (in ARCI1).		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	TGGTGGTCACGCCAGCAAAGA	0.632													G|||	778	0.155351	0.1815	0.1657	5008	,	,		18927	0.0853		0.2028	False		,,,				2504	0.136				p.G382G		Atlas-SNP	.											.	TGM1	73	.	0			c.C1146A						PASS	.	G		774,3632	314.1+/-293.5	74,626,1503	80.0	62.0	68.0		1146	-2.0	1.0	14	dbSNP_86	68	1680,6920	308.5+/-308.9	153,1374,2773	no	coding-synonymous	TGM1	NM_000359.2		227,2000,4276	TT,TG,GG		19.5349,17.567,18.8682		382/818	24728294	2454,10552	2203	4300	6503	SO:0001819	synonymous_variant	7051	exon7			GGTCACGCCAGCA	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.1146C>A	14.37:g.24728294G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_000359	B4DWR7|Q197M4	Silent	SNP	ENST00000206765.6	37	CCDS9622.1																																																																																			G|0.828;T|0.172	0.172	strong		0.632	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359	
FAM187B	148109	hgsc.bcm.edu	37	19	35719020	35719020	+	Nonsense_Mutation	SNP	C	C	T	rs541169	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35719020C>T	ENST00000324675.3	-	1	612	c.564G>A	c.(562-564)tgG>tgA	p.W188*		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	188						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						AGCGGCTAGACCACACCAGCA	0.572													C|||	1594	0.318291	0.3124	0.3487	5008	,	,		17240	0.1746		0.3221	False		,,,				2504	0.4489				p.W188X		Atlas-SNP	.											.	FAM187B	28	.	0			c.G564A						PASS	.	C	stop/TRP	1409,2997	460.0+/-352.4	232,945,1026	66.0	60.0	62.0		564	1.2	0.0	19	dbSNP_83	62	2823,5777	444.3+/-360.6	452,1919,1929	yes	stop-gained	FAM187B	NM_152481.1		684,2864,2955	TT,TC,CC		32.8256,31.9791,32.5388		188/370	35719020	4232,8774	2203	4300	6503	SO:0001587	stop_gained	148109	exon1			GCTAGACCACACC	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.564G>A	19.37:g.35719020C>T	ENSP00000323355:p.Trp188*	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_152481	Q8N7G6	Nonsense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	606	0.2774725274725275	146	0.2967479674796748	132	0.36464088397790057	90	0.15734265734265734	238	0.31398416886543534	C	17.24	3.338827	0.60963	0.319791	0.328256	ENSG00000177558	ENST00000324675	.	.	.	4.65	1.22	0.21188	.	1.033650	0.07717	N	0.942959	.	.	.	.	.	.	0.09310	P	0.9999999999887824	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-1.6996	3.618	0.08085	0.1706:0.5689:0.1652:0.0953	rs541169;rs3746246;rs17614052;rs60899247;rs541169	.	.	.	X	188	.	ENSP00000323355:W188X	W	-	3	0	FAM187B	40410860	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.391000	0.20784	0.236000	0.21180	0.655000	0.94253	TGG	C|0.697;T|0.303	0.303	strong		0.572	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
ARAP3	64411	hgsc.bcm.edu	37	5	141041735	141041735	+	Missense_Mutation	SNP	G	G	A	rs536504402		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141041735G>A	ENST00000239440.4	-	20	2953	c.2888C>T	c.(2887-2889)tCg>tTg	p.S963L	ARAP3_ENST00000513878.1_Missense_Mutation_p.S625L|ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000508305.1_Intron	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	963	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GAGCTTCACCGACCGGGCATC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17730	0.0		0.0	False		,,,				2504	0.0				p.S963L		Atlas-SNP	.											.	ARAP3	139	.	0			c.C2888T						PASS	.						116.0	114.0	115.0					5																	141041735		2203	4300	6503	SO:0001583	missense	64411	exon20			TTCACCGACCGGG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.2888C>T	5.37:g.141041735G>A	ENSP00000239440:p.Ser963Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	129	31	0.24031	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	32	5.167079	0.94768	.	.	ENSG00000120318	ENST00000239440;ENST00000513878	T;T	0.10477	2.87;2.87	5.27	5.27	0.74061	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.129855	0.45606	D	0.000345	T	0.18341	0.0440	L	0.33624	1.015	0.44155	D	0.996956	D;D	0.76494	0.995;0.999	P;P	0.61132	0.884;0.833	T	0.00202	-1.1925	10	0.49607	T	0.09	.	11.6675	0.51383	0.0:0.0:0.7116:0.2884	.	625;963	B4DIT1;Q8WWN8	.;ARAP3_HUMAN	L	963;625	ENSP00000239440:S963L;ENSP00000421468:S625L	ENSP00000239440:S963L	S	-	2	0	ARAP3	141021919	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	6.365000	0.73090	2.741000	0.93983	0.650000	0.86243	TCG	.	.	none		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
SPTB	6710	hgsc.bcm.edu	37	14	65253749	65253749	+	Silent	SNP	C	C	T	rs72724498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:65253749C>T	ENST00000389721.5	-	15	2966	c.2934G>A	c.(2932-2934)gaG>gaA	p.E978E	SPTB_ENST00000542895.1_Silent_p.E978E|SPTB_ENST00000389720.3_Silent_p.E978E|SPTB_ENST00000556626.1_Silent_p.E978E|SPTB_ENST00000389722.3_Silent_p.E978E	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	978					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)		CTTTTGTGGACTCCACTACCT	0.612													c|||	31	0.0061901	0.0023	0.0115	5008	,	,		18897	0.0		0.0199	False		,,,				2504	0.0				p.E978E		Atlas-SNP	.											.	SPTB	378	.	0			c.G2934A						PASS	.		,	19,4387	26.2+/-53.5	0,19,2184	84.0	79.0	81.0		2934,2934	5.1	1.0	14	dbSNP_130	81	194,8406	85.8+/-148.2	0,194,4106	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	0,213,6290	TT,TC,CC		2.2558,0.4312,1.6377	,	978/2138,978/2329	65253749	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon15			TGTGGACTCCACT		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.2934G>A	14.37:g.65253749C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
MUC16	94025	hgsc.bcm.edu	37	19	9048342	9048342	+	Missense_Mutation	SNP	C	C	T	rs10854118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9048342C>T	ENST00000397910.4	-	5	33492	c.33289G>A	c.(33289-33291)Gtg>Atg	p.V11097M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11099	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.V11097M(1)|p.V6730M(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						GGGGTCACCACTCCTGATACC	0.512													C|||	2196	0.438498	0.4062	0.4092	5008	,	,		23561	0.497		0.4245	False		,,,				2504	0.4571				p.V11097M		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - Missense(2)	stomach(2)	c.G33289A						PASS	.		MET/VAL	1540,2296		332,876,710	77.0	69.0	71.0		33289	-0.5	0.0	19	dbSNP_120	71	3319,4959		658,2003,1478	yes	missense	MUC16	NM_024690.2	21	990,2879,2188	TT,TC,CC		40.0942,40.146,40.1106	benign	11097/14508	9048342	4859,7255	1918	4139	6057	SO:0001583	missense	94025	exon5			TCACCACTCCTGA	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.33289G>A	19.37:g.9048342C>T	ENSP00000381008:p.Val11097Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	938	0.42948717948717946	183	0.3719512195121951	150	0.4143646408839779	283	0.49475524475524474	322	0.42480211081794195	c	4.287	0.052413	0.08291	0.40146	0.400942	ENSG00000181143	ENST00000397910	T	0.02837	4.14	2.96	-0.543	0.11851	.	.	.	.	.	T	0.00012	0.0000	L	0.35414	1.06	.	.	.	B	0.12630	0.006	B	0.13407	0.009	T	0.40270	-0.9572	8	0.87932	D	0	.	2.2098	0.03945	0.2278:0.2815:0.0:0.4908	rs10854118;rs10854118	11097	B5ME49	.	M	11097	ENSP00000381008:V11097M	ENSP00000381008:V11097M	V	-	1	0	MUC16	8909342	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.431000	0.00123	-0.200000	0.10300	-0.447000	0.05616	GTG	C|0.570;T|0.430	0.430	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZDBF2	57683	hgsc.bcm.edu	37	2	207170242	207170242	+	Silent	SNP	T	T	C	rs112075178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170242T>C	ENST00000374423.3	+	5	1376	c.990T>C	c.(988-990)caT>caC	p.H330H		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	330							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CAAAGAACCATGAGGAATTCT	0.358													T|||	116	0.0231629	0.0741	0.0159	5008	,	,		19800	0.0		0.006	False		,,,				2504	0.001				p.H330H		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T990C						PASS	.	T		248,3394		8,232,1581	47.0	46.0	46.0		990	-1.2	0.0	2	dbSNP_132	46	70,8096		0,70,4013	no	coding-synonymous	ZDBF2	NM_020923.1		8,302,5594	CC,CT,TT		0.8572,6.8094,2.6931		330/2355	207170242	318,11490	1821	4083	5904	SO:0001819	synonymous_variant	57683	exon5			GAACCATGAGGAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.990T>C	2.37:g.207170242T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.358	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
PREX1	57580	hgsc.bcm.edu	37	20	47253043	47253043	+	Silent	SNP	G	G	A	rs11553083	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	42	0	0		WXS	Illumina HiSeq	Phase_I	95	92	0.968421	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	
STAB2	55576	hgsc.bcm.edu	37	12	104086631	104086631	+	Silent	SNP	C	C	T	rs703651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104086631C>T	ENST00000388887.2	+	31	3543	c.3339C>T	c.(3337-3339)aaC>aaT	p.N1113N		NM_017564.9	NP_060034.9			stabilin 2									p.N1113N(1)		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						ATGGGGACAACGCAGCCACAA	0.448													C|||	2343	0.467851	0.4463	0.4092	5008	,	,		18770	0.5585		0.4632	False		,,,				2504	0.4499				p.N1113N		Atlas-SNP	.											STAB2,rectum,carcinoma,0,2	STAB2	370	2	1	Substitution - coding silent(1)	stomach(1)	c.C3339T						PASS	.	C		1941,2465	550.9+/-378.2	420,1101,682	164.0	139.0	147.0		3339	-9.7	0.0	12	dbSNP_86	147	3825,4775	536.4+/-383.0	839,2147,1314	no	coding-synonymous	STAB2	NM_017564.9		1259,3248,1996	TT,TC,CC		44.4767,44.0536,44.3334		1113/2552	104086631	5766,7240	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon31			GGACAACGCAGCC	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.3339C>T	12.37:g.104086631C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.546;T|0.453	0.453	strong		0.448	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
MERTK	10461	hgsc.bcm.edu	37	2	112751928	112751928	+	Missense_Mutation	SNP	G	G	A	rs386649210|rs7604639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	155	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	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		
MYBPC3	4607	hgsc.bcm.edu	37	11	47371598	47371598	+	Missense_Mutation	SNP	C	C	T	rs3729986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47371598C>T	ENST00000545968.1	-	4	526	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	MYBPC3_ENST00000399249.2_Missense_Mutation_p.V158M|MYBPC3_ENST00000256993.4_Missense_Mutation_p.V158M	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	158	Ig-like C2-type 1.		V -> M (in dbSNP:rs3729986). {ECO:0000269|PubMed:15519027, ECO:0000269|PubMed:18403758, ECO:0000269|Ref.4}.		cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		GGCCGCATCACGAAGAGGCCA	0.607													C|||	165	0.0329473	0.003	0.0418	5008	,	,		16449	0.0		0.1064	False		,,,				2504	0.0256				p.V158M		Atlas-SNP	.											.	MYBPC3	102	.	0			c.G472A						PASS	.	C	MET/VAL	69,3977		1,67,1955	46.0	54.0	52.0		472	1.5	1.0	11	dbSNP_107	52	718,7594		24,670,3462	yes	missense	MYBPC3	NM_000256.3	21	25,737,5417	TT,TC,CC		8.6381,1.7054,6.3683	possibly-damaging	158/1275	47371598	787,11571	2023	4156	6179	SO:0001583	missense	4607	exon4			GCATCACGAAGAG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.472G>A	11.37:g.47371598C>T	ENSP00000442795:p.Val158Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	101	0.04624542124542125	4	0.008130081300813009	15	0.04143646408839779	0	0.0	82	0.10817941952506596	C	12.45	1.940633	0.34283	0.017054	0.086381	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.71341	-0.56;-0.56;-0.56	3.49	1.52	0.23074	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03783	0.0107	L	0.58101	1.795	0.29523	N	0.853368	P	0.43750	0.816	P	0.44447	0.45	T	0.21930	-1.0231	9	0.87932	D	0	.	13.4269	0.61030	0.0:0.4198:0.5802:0.0	rs3729986;rs3729986	158	Q14896	MYPC3_HUMAN	M	158	ENSP00000442795:V158M;ENSP00000382193:V158M;ENSP00000256993:V158M	ENSP00000256993:V158M	V	-	1	0	MYBPC3	47328174	0.991000	0.36638	0.995000	0.50966	0.379000	0.30106	0.745000	0.26259	0.277000	0.22141	-0.502000	0.04539	GTG	C|0.956;T|0.044	0.044	strong		0.607	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
UGT1A6	54578	hgsc.bcm.edu	37	2	234602191	234602191	+	Missense_Mutation	SNP	A	A	G	rs2070959	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234602191A>G	ENST00000305139.6	+	1	680	c.541A>G	c.(541-543)Aca>Gca	p.T181A	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	181			T -> A (in allele UGT1A6*2; dbSNP:rs2070959). {ECO:0000269|PubMed:15284531, ECO:0000269|PubMed:19204906, ECO:0000269|PubMed:9429234, ECO:0000269|Ref.4}.		cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CCTGGAGCATACATTCAGCAG	0.512													A|||	1390	0.277556	0.239	0.2233	5008	,	,		19575	0.1964		0.3101	False		,,,				2504	0.4182				p.T181A		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A541G	GRCh37	CM057770|CP995124	UGT1A6	M|X	rs2070959	PASS	.	A	ALA/THR,,,,,	1110,3296	400.1+/-331.5	155,800,1248	158.0	148.0	152.0		541,,,,,	-9.4	0.0	2	dbSNP_96	152	2852,5748	448.5+/-361.8	480,1892,1928	yes	missense,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	58,,,,,	635,2692,3176	GG,GA,AA		33.1628,25.1929,30.4629	,,,,,	181/533,,,,,	234602191	3962,9044	2203	4300	6503	SO:0001583	missense	54578	exon1			GAGCATACATTCA	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.541A>G	2.37:g.234602191A>G	ENSP00000303174:p.Thr181Ala	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	135	51	0.377778	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	581	0.266025641025641	118	0.23983739837398374	96	0.26519337016574585	130	0.22727272727272727	237	0.31266490765171506	A	0.018	-1.475651	0.01035	0.251929	0.331628	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.59224	0.28;0.28	5.31	-9.43	0.00607	.	.	.	.	.	T	0.00012	0.0000	N	0.05259	-0.085	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22695	-1.0209	8	0.12766	T	0.61	.	11.5483	0.50706	0.6559:0.0:0.2517:0.0924	rs2070959;rs3903007;rs17683988;rs61246460;rs2070959	181	P19224	UD16_HUMAN	A	181	ENSP00000389637:T181A;ENSP00000303174:T181A	ENSP00000303174:T181A	T	+	1	0	UGT1A6	234266930	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.930000	0.03972	-1.892000	0.01108	-0.959000	0.02639	ACA	A|0.710;G|0.290	0.290	strong		0.512	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
PERP	64065	hgsc.bcm.edu	37	6	138428379	138428379	+	Silent	SNP	G	G	A	rs145663845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:138428379G>A	ENST00000421351.3	-	1	269	c.99C>T	c.(97-99)cgC>cgT	p.R33R		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	33					activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		GCAACCAGCCGCGGCCGGCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		11494	0.0		0.0089	False		,,,				2504	0.0102				p.R33R		Atlas-SNP	.											.	PERP	15	.	0			c.C99T						PASS	.	G		12,4260		0,12,2124	31.0	39.0	36.0		99	-0.4	1.0	6	dbSNP_134	36	95,8285		0,95,4095	no	coding-synonymous	PERP	NM_022121.4		0,107,6219	AA,AG,GG		1.1337,0.2809,0.8457		33/194	138428379	107,12545	2136	4190	6326	SO:0001819	synonymous_variant	64065	exon1			CCAGCCGCGGCCG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.99C>T	6.37:g.138428379G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Silent	SNP	ENST00000421351.3	37	CCDS5188.1																																																																																			G|0.993;A|0.007	0.007	strong		0.682	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
ZNF260	339324	hgsc.bcm.edu	37	19	37004938	37004938	+	Silent	SNP	T	T	C	rs2967505	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37004938T>C	ENST00000523638.1	-	3	2324	c.1203A>G	c.(1201-1203)tcA>tcG	p.S401S	ZNF260_ENST00000592282.1_Silent_p.S401S|ZNF260_ENST00000588993.1_Silent_p.S401S|ZNF260_ENST00000593142.1_Silent_p.S401S	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	401					multicellular organismal development (GO:0007275)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					TAATGTGATGTGACTTTTGGC	0.378													T|||	1728	0.345048	0.4153	0.2478	5008	,	,		20286	0.245		0.3479	False		,,,				2504	0.4192				p.S401S		Atlas-SNP	.											.	ZNF260	34	.	0			c.A1203G						PASS	.	T	,,,	1831,2575	532.8+/-373.5	364,1103,736	85.0	82.0	83.0		1203,1203,1203,1203	1.7	1.0	19	dbSNP_101	83	2926,5674	456.4+/-364.1	518,1890,1892	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF260	NM_001012756.2,NM_001166036.1,NM_001166037.1,NM_001166038.1	,,,	882,2993,2628	CC,CT,TT		34.0233,41.557,36.5754	,,,	401/413,401/413,401/413,401/413	37004938	4757,8249	2203	4300	6503	SO:0001819	synonymous_variant	339324	exon3			GTGATGTGACTTT	AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"""Zinc fingers, C2H2-type"""	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.1203A>G	19.37:g.37004938T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001166038	Q0VF43	Silent	SNP	ENST00000523638.1	37	CCDS33003.1																																																																																			T|0.648;C|0.352	0.352	strong		0.378	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756	
LATS2	26524	hgsc.bcm.edu	37	13	21563311	21563311	+	Missense_Mutation	SNP	G	G	A	rs77919685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21563311G>A	ENST00000382592.4	-	4	1013	c.608C>T	c.(607-609)gCg>gTg	p.A203V	LATS2_ENST00000542899.1_Missense_Mutation_p.A203V|LATS2_ENST00000472754.1_5'UTR	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)		CTCCTCCAGCGCCGTGGGGCC	0.692													G|||	103	0.0205671	0.0	0.0216	5008	,	,		14848	0.0248		0.0249	False		,,,				2504	0.0389				p.A203V		Atlas-SNP	.											.	LATS2	176	.	0			c.C608T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	50.0	45.0	46.0		608	3.0	0.0	13	dbSNP_131	46	149,8449	71.0+/-133.6	4,141,4154	yes	missense	LATS2	NM_014572.2	64	4,160,6338	AA,AG,GG		1.733,0.4312,1.2919	benign	203/1089	21563311	168,12836	2203	4299	6502	SO:0001583	missense	26524	exon4			TCCAGCGCCGTGG	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.608C>T	13.37:g.21563311G>A	ENSP00000372035:p.Ala203Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	43	0.019688644688644688	0	0.0	6	0.016574585635359115	18	0.03146853146853147	19	0.025065963060686015	G	7.001	0.554851	0.13436	0.004312	0.01733	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.26957	1.7;1.7	5.05	3.04	0.35103	.	1.593970	0.03426	N	0.207082	T	0.03739	0.0106	N	0.02011	-0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16928	-1.0386	10	0.52906	T	0.07	.	5.4494	0.16554	0.7351:0.0:0.2649:0.0	.	203	Q9NRM7	LATS2_HUMAN	V	203	ENSP00000372035:A203V;ENSP00000441817:A203V	ENSP00000372035:A203V	A	-	2	0	LATS2	20461311	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.484000	0.35508	0.425000	0.26087	0.485000	0.47835	GCG	G|0.986;A|0.014	0.014	strong		0.692	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
MUC16	94025	hgsc.bcm.edu	37	19	9011412	9011412	+	Missense_Mutation	SNP	C	C	T	rs114676657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9011412C>T	ENST00000397910.4	-	36	39024	c.38821G>A	c.(38821-38823)Gag>Aag	p.E12941K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12943	SEA 6. {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						TACAGCTGCTCTCTGTTGAGT	0.572													N|||	66	0.0131789	0.0121	0.0101	5008	,	,		17786	0.0		0.0288	False		,,,				2504	0.0143				p.E12941K		Atlas-SNP	.											.	MUC16	4315	.	0			c.G38821A						PASS	.	C	LYS/GLU	40,3884		1,38,1923	195.0	173.0	180.0		38821	2.8	0.0	19	dbSNP_132	180	221,8077		6,209,3934	no	missense	MUC16	NM_024690.2	56	7,247,5857	TT,TC,CC		2.6633,1.0194,2.1355	probably-damaging	12941/14508	9011412	261,11961	1962	4149	6111	SO:0001583	missense	94025	exon36			GCTGCTCTCTGTT	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.38821G>A	19.37:g.9011412C>T	ENSP00000381008:p.Glu12941Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	160	88	0.55	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	24	0.01098901098901099	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	.	12.85	2.061979	0.36373	0.010194	0.026633	ENSG00000181143	ENST00000397910;ENST00000441155	T	0.63255	-0.03	2.76	2.76	0.32466	.	.	.	.	.	T	0.54854	0.1884	M	0.79258	2.445	.	.	.	D	0.71674	0.998	D	0.80764	0.994	T	0.76903	-0.2787	8	0.87932	D	0	-19.752	9.6026	0.39615	0.0:1.0:0.0:0.0	.	12941	B5ME49	.	K	12941;94	ENSP00000381008:E12941K	ENSP00000381008:E12941K	E	-	1	0	MUC16	8872412	0.001000	0.12720	0.025000	0.17156	0.022000	0.10575	0.101000	0.15251	1.474000	0.48178	0.305000	0.20034	GAG	C|0.986;T|0.014	0.014	strong		0.572	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF526	116115	hgsc.bcm.edu	37	19	42729106	42729106	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:42729106C>T	ENST00000301215.3	+	3	776	c.551C>T	c.(550-552)cCt>cTt	p.P184L		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	184					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.P184L(1)		autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				ACACCACTGCCTCCACCTTCT	0.612																																					p.P184L		Atlas-SNP	.											ZNF526,face,carcinoma,0,1	ZNF526	51	1	1	Substitution - Missense(1)	skin(1)	c.C551T						scavenged	.						122.0	113.0	116.0					19																	42729106		2203	4300	6503	SO:0001583	missense	116115	exon3			CACTGCCTCCACC	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"""Zinc fingers, C2H2-type"""	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.551C>T	19.37:g.42729106C>T	ENSP00000301215:p.Pro184Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	37	CCDS12598.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.621903	0.28889	.	.	ENSG00000167625	ENST00000301215	T	0.08984	3.03	3.91	2.88	0.33553	.	0.810560	0.10396	N	0.679849	T	0.07638	0.0192	L	0.44542	1.39	0.30629	N	0.757666	B	0.25904	0.137	B	0.18561	0.022	T	0.14980	-1.0453	9	.	.	.	.	7.4356	0.27154	0.0:0.8822:0.0:0.1178	.	184	Q8TF50	ZN526_HUMAN	L	184	ENSP00000301215:P184L	.	P	+	2	0	ZNF526	47420946	0.000000	0.05858	0.022000	0.16811	0.668000	0.39293	0.195000	0.17155	1.229000	0.43630	0.563000	0.77884	CCT	.	.	none		0.612	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401	
CASP10	843	hgsc.bcm.edu	37	2	202082459	202082459	+	Intron	SNP	T	T	A	rs13006529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:202082459T>A	ENST00000272879.5	+	9	1599				CASP10_ENST00000286186.6_Missense_Mutation_p.L522I|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000313728.7_Missense_Mutation_p.L455I|CASP10_ENST00000448480.1_Intron|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000346817.5_Missense_Mutation_p.L479I	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	142	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	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	
LMAN1	3998	hgsc.bcm.edu	37	18	57026361	57026361	+	Missense_Mutation	SNP	A	A	G	rs33926449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:57026361A>G	ENST00000251047.5	-	1	833	c.116T>C	c.(115-117)gTc>gCc	p.V39A	RP11-27G24.1_ENST00000591331.1_lincRNA	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	39			V -> A (in dbSNP:rs33926449). {ECO:0000269|PubMed:10090935}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TGGCAACGCGACCGCGGGGTC	0.677													G|||	378	0.0754792	0.143	0.0764	5008	,	,		13902	0.0		0.0964	False		,,,				2504	0.0399				p.V39A		Atlas-SNP	.											.	LMAN1	57	.	0			c.T116C						PASS	.	G	ALA/VAL	567,3839	766.3+/-413.4	41,485,1677	63.0	69.0	67.0		116	-5.1	0.0	18	dbSNP_126	67	744,7854	781.7+/-407.6	36,672,3591	yes	missense	LMAN1	NM_005570.3	64	77,1157,5268	GG,GA,AA		8.6532,12.8688,10.0815	benign	39/511	57026361	1311,11693	2203	4299	6502	SO:0001583	missense	3998	exon1			AACGCGACCGCGG	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.116T>C	18.37:g.57026361A>G	ENSP00000251047:p.Val39Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	148	87	0.587838	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	165	0.07554945054945054	68	0.13821138211382114	32	0.08839779005524862	0	0.0	65	0.08575197889182058	G	0.010	-1.772631	0.00640	0.128688	0.086532	ENSG00000074695	ENST00000251047	T	0.52754	0.65	3.83	-5.14	0.02875	.	0.486353	0.15095	N	0.280828	T	0.00144	0.0004	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	0.21449	-1.0245	9	0.07325	T	0.83	-1.5572	9.5938	0.39563	0.2303:0.5434:0.2262:0.0	rs33926449	39;39	B4DVV0;P49257	.;LMAN1_HUMAN	A	39	ENSP00000251047:V39A	ENSP00000251047:V39A	V	-	2	0	LMAN1	55177341	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.169000	0.09911	-1.538000	0.01734	-0.974000	0.02594	GTC	A|0.903;G|0.097	0.097	strong		0.677	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570	
CYP2D6	1565	hgsc.bcm.edu	37	22	42524924	42524924	+	Silent	SNP	A	A	G	rs111606937		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42524924A>G	ENST00000360608.5	-	4	642	c.528T>C	c.(526-528)ggT>ggC	p.G176G	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Silent_p.G176G|CYP2D6_ENST00000359033.4_Silent_p.G125G	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	176					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)	p.G176G(2)|p.G125G(2)		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)	TGTCCAAGAGACCGTTGGGGC	0.667																																					p.G176G		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,4	CYP2D6	104	4	4	Substitution - coding silent(4)	prostate(4)	c.T528C						scavenged	.						16.0	15.0	16.0					22																	42524924		2178	4269	6447	SO:0001819	synonymous_variant	1565	exon4			CAAGAGACCGTTG	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.528T>C	22.37:g.42524924A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	195	33	0.169231	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	N	6.286	0.420922	0.11928	.	.	ENSG00000100197	ENST00000413640	.	.	.	3.52	-7.03	0.01584	.	.	.	.	.	T	0.35941	0.0949	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.49523	-0.8931	5	0.72032	D	0.01	.	7.5516	0.27800	0.394:0.4262:0.1798:0.0	.	.	.	.	A	124	.	ENSP00000414432:V124A	V	-	2	0	CYP2D6	40854868	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.972000	0.03802	-2.634000	0.00433	-0.684000	0.03749	GTC	A|0.500;G|0.500	0.500	weak		0.667	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
C3orf70	285382	hgsc.bcm.edu	37	3	184801094	184801094	+	Missense_Mutation	SNP	G	G	A	rs61740263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184801094G>A	ENST00000335012.2	-	2	644	c.454C>T	c.(454-456)Cca>Tca	p.P152S		NM_001025266.1	NP_001020437.1	A6NLC5	CC070_HUMAN	chromosome 3 open reading frame 70	152										breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|urinary_tract(1)	13						TGGGAATGTGGTGCCGGCTGC	0.433													G|||	317	0.0632987	0.0522	0.0634	5008	,	,		20870	0.0526		0.0865	False		,,,				2504	0.0654				p.P152S		Atlas-SNP	.											.	C3orf70	29	.	0			c.C454T						PASS	.	G	SER/PRO	279,4127	155.2+/-188.4	12,255,1936	97.0	93.0	95.0		454	4.0	0.0	3	dbSNP_129	95	756,7844	181.9+/-230.5	45,666,3589	yes	missense	C3orf70	NM_001025266.1	74	57,921,5525	AA,AG,GG		8.7907,6.3323,7.9579	benign	152/251	184801094	1035,11971	2203	4300	6503	SO:0001583	missense	285382	exon2			AATGTGGTGCCGG		CCDS33900.1	3q27	2008-08-08			ENSG00000187068	ENSG00000187068			33731	protein-coding gene	gene with protein product							Standard	NM_001025266		Approved		uc003fpd.3	A6NLC5	OTTHUMG00000156696	ENST00000335012.2:c.454C>T	3.37:g.184801094G>A	ENSP00000334974:p.Pro152Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	193	111	0.57513	NM_001025266	B2RNY2|B9EH83	Missense_Mutation	SNP	ENST00000335012.2	37	CCDS33900.1	134	0.06135531135531135	14	0.028455284552845527	24	0.06629834254143646	22	0.038461538461538464	74	0.09762532981530343	G	7.567	0.665885	0.14710	0.063323	0.087907	ENSG00000187068	ENST00000335012	.	.	.	5.04	4.04	0.47022	.	0.165966	0.53938	D	0.000048	T	0.00666	0.0022	N	0.14661	0.345	0.53688	P	2.4000000000024002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.03473	-1.1033	8	0.29301	T	0.29	.	6.6067	0.22729	0.1293:0.2547:0.6159:0.0	rs61740263	152	A6NLC5	CC070_HUMAN	S	152	.	ENSP00000334974:P152S	P	-	1	0	C3orf70	186283788	0.925000	0.31364	0.037000	0.18230	0.574000	0.36063	1.956000	0.40382	2.339000	0.79563	0.655000	0.94253	CCA	G|0.925;A|0.075	0.075	strong		0.433	C3orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345323.1	NM_001025266	
PLG	5340	hgsc.bcm.edu	37	6	161173946	161173946	+	Silent	SNP	T	T	G	rs11060	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:161173946T>G	ENST00000308192.9	+	19	2349	c.2286T>G	c.(2284-2286)ggT>ggG	p.G762G		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	762	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	ACAGTGGAGGTCCTCTGGTTT	0.468													T|||	3411	0.68111	0.5348	0.7075	5008	,	,		18500	0.9782		0.5249	False		,,,				2504	0.7147				p.G762G		Atlas-SNP	.											.	PLG	150	.	0			c.T2286G						PASS	.						97.0	91.0	93.0					6																	161173946		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon19			TGGAGGTCCTCTG	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.2286T>G	6.37:g.161173946T>G		Somatic	395	1	0.00253165		WXS	Illumina HiSeq	Phase_I	350	349	0.997143	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.358;G|0.642	0.642	strong		0.468	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
HEATR5B	54497	hgsc.bcm.edu	37	2	37230734	37230734	+	Silent	SNP	C	C	T	rs17497654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:37230734C>T	ENST00000233099.5	-	31	5096	c.5001G>A	c.(4999-5001)caG>caA	p.Q1667Q	HEATR5B_ENST00000354531.2_Silent_p.Q1667Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1667						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)				CTCTTACTATCTGTTGTACAA	0.378													C|||	652	0.130192	0.2345	0.1326	5008	,	,		15144	0.0238		0.1461	False		,,,				2504	0.0808				p.Q1667Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G5001A						PASS	.	C		921,3485	353.6+/-312.2	97,727,1379	84.0	84.0	84.0		5001	4.6	1.0	2	dbSNP_123	84	1401,7199	271.2+/-289.4	120,1161,3019	no	coding-synonymous	HEATR5B	NM_019024.1		217,1888,4398	TT,TC,CC		16.2907,20.9033,17.8533		1667/2072	37230734	2322,10684	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon31			TACTATCTGTTGT	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.5001G>A	2.37:g.37230734C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			C|0.834;T|0.166	0.166	strong		0.378	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222641	140222641	+	Missense_Mutation	SNP	A	A	G	rs6580012	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140222641A>G	ENST00000531613.1	+	1	1735	c.1735A>G	c.(1735-1737)Aag>Gag	p.K579E	PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.K579E	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	579			K -> E (in dbSNP:rs6580012).		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(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)			CGCAGCGAGCAAGCTGGTGCC	0.677													.|||	2882	0.575479	0.7345	0.562	5008	,	,		14758	0.5268		0.4911	False		,,,				2504	0.5072				p.K579E		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,4	PCDHA8	366	4	0			c.A1735G						PASS	.	G	,,,,,,,GLU/LYS,,,GLU/LYS	3133,1257		1169,795,231	52.0	57.0	55.0		,,,,,,,1735,,,1735	0.4	0.0	5	dbSNP_116	55	4023,4497		1149,1725,1386	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	,,,,,,,56,,,56	2318,2520,1617	GG,GA,AA		47.2183,28.6333,44.5701	,,,,,,,,,,	,,,,,,,579/951,,,579/815	140222641	7156,5754	2195	4260	6455	SO:0001583	missense	56140	exon1			GCGAGCAAGCTGG	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.1735A>G	5.37:g.140222641A>G	ENSP00000434655:p.Lys579Glu	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	1207	0.5526556776556777	350	0.7113821138211383	184	0.5082872928176796	302	0.527972027972028	371	0.4894459102902375	G	1.084	-0.665977	0.03428	0.713667	0.472183	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.19806	2.12;2.12	3.49	0.381	0.16228	Cadherin-like (1);	0.000000	0.36932	N	0.002335	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	0.34750	-0.9816	9	0.02654	T	1	.	6.1288	0.20194	0.2432:0.4246:0.3322:0.0	rs6580012;rs17844319	579;579	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	E	579	ENSP00000434655:K579E;ENSP00000367363:K579E	ENSP00000367363:K579E	K	+	1	0	PCDHA8	140202825	0.192000	0.23301	0.000000	0.03702	0.029000	0.11900	1.550000	0.36223	-0.581000	0.05937	-0.665000	0.03846	AAG	A|0.480;G|0.520	0.520	strong		0.677	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
DLG5	9231	hgsc.bcm.edu	37	10	79579222	79579222	+	Splice_Site	SNP	G	G	A	rs1248634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:79579222G>A	ENST00000372391.2	-	17	3533	c.3528C>T	c.(3526-3528)ggC>ggT	p.G1176G	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Splice_Site_p.G836G	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1176					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GGGGAACAGTGCCTAGAAATG	0.607													G|||	1279	0.255391	0.0908	0.4625	5008	,	,		16812	0.2917		0.2753	False		,,,				2504	0.273				p.G1176G		Atlas-SNP	.											.	DLG5	154	.	0			c.C3528T						PASS	.	G		572,3834	252.1+/-258.6	46,480,1677	43.0	45.0	44.0		3528	2.5	1.0	10	dbSNP_87	44	2379,6221	395.4+/-345.0	322,1735,2243	yes	coding-synonymous-near-splice	DLG5	NM_004747.3		368,2215,3920	AA,AG,GG		27.6628,12.9823,22.6895		1176/1920	79579222	2951,10055	2203	4300	6503	SO:0001630	splice_region_variant	9231	exon17			AACAGTGCCTAGA	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.3527-1C>T	10.37:g.79579222G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	14	0.583333	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.756;T|0.003	.	strong		0.607	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		Silent
SLC7A2	6542	hgsc.bcm.edu	37	8	17396380	17396380	+	Intron	SNP	G	G	A	rs13259948	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17396380G>A	ENST00000494857.1	+	3	196				SLC7A2_ENST00000398090.3_Missense_Mutation_p.R16Q|SLC7A2_ENST00000470360.1_Missense_Mutation_p.R16Q|SLC7A2_ENST00000004531.10_Missense_Mutation_p.R16Q|SLC7A2_ENST00000522656.1_Intron	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CTAATTTGTCGAGGGTTTATT	0.418													g|||	298	0.0595048	0.0098	0.0937	5008	,	,		17361	0.0		0.1869	False		,,,				2504	0.0327				p.R16Q		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G47A						PASS	.	A	,GLN/ARG,GLN/ARG	134,3584		3,128,1728	109.0	99.0	102.0		,47,47	0.6	0.0	8	dbSNP_121	102	1578,6608		168,1242,2683	yes	intron,missense,missense	SLC7A2	NM_001008539.3,NM_003046.5,NM_001164771.1	,43,43	171,1370,4411	AA,AG,GG		19.2768,3.6041,14.3817	,benign,benign	,16/698,16/699	17396380	1712,10192	1859	4093	5952	SO:0001627	intron_variant	6542	exon1			TTTGTCGAGGGTT	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.-22-4447G>A	8.37:g.17396380G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	42	0.608696	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	175	0.08012820512820513	5	0.01016260162601626	39	0.10773480662983426	0	0.0	131	0.17282321899736147	g	11.79	1.743855	0.30865	0.036041	0.192768	ENSG00000003989	ENST00000470360;ENST00000004531;ENST00000398090	D;D;D	0.88818	-2.43;-2.29;-2.43	3.34	0.559	0.17272	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	7	0.87932	D	0	.	5.4713	0.16672	0.3777:0.0:0.6223:0.0	rs13259948;rs17504833;rs56458067;rs13259948	16;16	P52569-3;P52569-2	.;.	Q	16	ENSP00000419873:R16Q;ENSP00000004531:R16Q;ENSP00000381164:R16Q	ENSP00000004531:R16Q	R	+	2	0	SLC7A2	17440759	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.782000	0.26788	0.106000	0.17784	-0.355000	0.07637	CGA	G|0.897;A|0.103	0.103	strong		0.418	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
SDR42E1	93517	hgsc.bcm.edu	37	16	82033612	82033612	+	Missense_Mutation	SNP	T	T	C	rs16956174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:82033612T>C	ENST00000328945.5	-	3	413	c.286A>G	c.(286-288)Aaa>Gaa	p.K96E	SDR42E1_ENST00000534209.1_5'UTR	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	96			K -> E (in dbSNP:rs16956174).		steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						TTGACTTCTTTGATCAGGTTT	0.488													C|||	1141	0.227835	0.7088	0.0677	5008	,	,		21252	0.0536		0.0179	False		,,,				2504	0.0869				p.K96E		Atlas-SNP	.											.	SDR42E1	26	.	0			c.A286G						PASS	.	C	GLU/LYS	2302,1742		650,1002,370	157.0	158.0	158.0		286	1.8	0.0	16	dbSNP_123	158	151,8207		0,151,4028	yes	missense	SDR42E1	NM_145168.2	56	650,1153,4398	CC,CT,TT		1.8067,43.0762,19.7791	benign	96/394	82033612	2453,9949	2022	4179	6201	SO:0001583	missense	93517	exon3			CTTCTTTGATCAG	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.286A>G	16.37:g.82033612T>C	ENSP00000332407:p.Lys96Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_145168	B2RDS1|Q9P0D1	Missense_Mutation	SNP	ENST00000328945.5	37	CCDS42205.1	376	0.17216117216117216	326	0.6626016260162602	23	0.06353591160220995	17	0.02972027972027972	10	0.013192612137203167	C	0.013	-1.634753	0.00806	0.569238	0.018067	ENSG00000184860	ENST00000328945;ENST00000532128	D;D	0.87809	-2.3;-2.3	6.03	1.82	0.25136	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.139530	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00116	-2.08	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.44452	-0.9327	9	0.02654	T	1	-4.4625	7.1368	0.25533	0.0:0.5818:0.2278:0.1904	rs16956174;rs56515135;rs60686248;rs16956174	96	Q8WUS8	D42E1_HUMAN	E	96;93	ENSP00000332407:K96E;ENSP00000434529:K93E	ENSP00000332407:K96E	K	-	1	0	SDR42E1	80591113	0.984000	0.35163	0.008000	0.14137	0.025000	0.11179	2.684000	0.46951	-0.070000	0.12908	-0.812000	0.03155	AAA	T|0.823;C|0.177	0.177	strong		0.488	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168	
KRT15	3866	hgsc.bcm.edu	37	17	39674641	39674641	+	Missense_Mutation	SNP	T	T	C	rs1050784	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39674641T>C	ENST00000254043.3	-	1	4024	c.439A>G	c.(439-441)Acc>Gcc	p.T147A	KRT15_ENST00000393974.3_Silent_p.Q9Q|KRT15_ENST00000393981.3_Silent_p.Q9Q|KRT15_ENST00000393976.2_Missense_Mutation_p.T147A	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	147	Linker 1.|Rod.		T -> A (in dbSNP:rs1050784). {ECO:0000269|PubMed:2452170, ECO:0000269|PubMed:2468493}.		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				TCTGGGCTGGTTGGGGTCTGC	0.577													T|||	3670	0.732827	0.593	0.7867	5008	,	,		15760	0.9147		0.6481	False		,,,				2504	0.7832				p.T147A		Atlas-SNP	.											.	KRT15	60	.	0			c.A439G						PASS	.	T	ALA/THR	2583,1823	637.5+/-396.8	756,1071,376	176.0	171.0	173.0		439	-3.0	0.0	17	dbSNP_86	173	5485,3115	658.1+/-401.5	1751,1983,566	yes	missense	KRT15	NM_002275.3	58	2507,3054,942	CC,CT,TT		36.2209,41.3754,37.9671	benign	147/457	39674641	8068,4938	2203	4300	6503	SO:0001583	missense	3866	exon1			GGCTGGTTGGGGT		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.439A>G	17.37:g.39674641T>C	ENSP00000254043:p.Thr147Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	55	0.433071	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	CCDS11398.1	1567	0.7174908424908425	288	0.5853658536585366	268	0.7403314917127072	531	0.9283216783216783	480	0.633245382585752	T	0.021	-1.421478	0.01126	0.586246	0.637791	ENSG00000171346	ENST00000254043;ENST00000393976	D;D	0.94687	-3.49;-3.49	5.31	-3.05	0.05396	Filament (1);	0.782790	0.11059	N	0.604104	T	0.00012	0.0000	L	0.28115	0.83	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.11329	0.006	T	0.31308	-0.9948	9	0.16420	T	0.52	.	5.6988	0.17871	0.2465:0.4527:0.0:0.3008	rs1050784;rs3191133;rs3744785;rs52811723;rs58144290;rs1050784	147	P19012	K1C15_HUMAN	A	147	ENSP00000254043:T147A;ENSP00000377546:T147A	ENSP00000254043:T147A	T	-	1	0	KRT15	36928167	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-0.885000	0.04161	-0.744000	0.04778	0.459000	0.35465	ACC	T|0.341;C|0.659	0.659	strong		0.577	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	
C12orf54	121273	hgsc.bcm.edu	37	12	48888594	48888594	+	Missense_Mutation	SNP	C	C	T	rs11458	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	76	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	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	
DMXL2	23312	hgsc.bcm.edu	37	15	51783820	51783820	+	Silent	SNP	T	T	C	rs10851500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51783820T>C	ENST00000251076.5	-	20	5195	c.4908A>G	c.(4906-4908)ggA>ggG	p.G1636G	DMXL2_ENST00000449909.3_Silent_p.G1000G|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Silent_p.G1636G	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1636						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.G1636G(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TCACCCACCATCCTATGCCCA	0.398													C|||	2229	0.445088	0.4259	0.4942	5008	,	,		17100	0.4038		0.5169	False		,,,				2504	0.4049				p.G1636G		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	1	1	Substitution - coding silent(1)	stomach(1)	c.A4908G						PASS	.	C	,,	2013,2377	612.4+/-392.0	466,1081,648	119.0	121.0	120.0		4908,3000,4908	-8.5	0.1	15	dbSNP_120	120	4339,4247	572.8+/-389.8	1107,2125,1061	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1573,3206,1709	CC,CT,TT		49.4642,45.8542,48.9519	,,	1636/3038,1000/2401,1636/3037	51783820	6352,6624	2195	4293	6488	SO:0001819	synonymous_variant	23312	exon20			CCACCATCCTATG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.4908A>G	15.37:g.51783820T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			T|0.514;C|0.486	0.486	strong		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
CLCNKA	1187	hgsc.bcm.edu	37	1	16357147	16357147	+	Missense_Mutation	SNP	C	C	T	rs12140223	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16357147C>T	ENST00000331433.4	+	15	1619	c.1600C>T	c.(1600-1602)Cgg>Tgg	p.R534W	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R534W|CLCNKA_ENST00000439316.2_Missense_Mutation_p.R491W|CLCNKA_ENST00000420078.1_Missense_Mutation_p.R534W			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	534			R -> W (in dbSNP:rs12140223).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	ATACCTGCCACGGATTCTGGG	0.607													C|||	268	0.0535144	0.0802	0.0447	5008	,	,		20348	0.006		0.0775	False		,,,				2504	0.0481				p.R534W		Atlas-SNP	.											.	CLCNKA	56	.	0			c.C1600T						PASS	.	C	TRP/ARG,TRP/ARG	378,4026	186.7+/-213.5	10,358,1834	42.0	37.0	39.0		1600,1600	-2.6	0.2	1	dbSNP_120	39	805,7791	182.3+/-230.8	35,735,3528	no	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	101,101	45,1093,5362	TT,TC,CC		9.3648,8.5831,9.1	benign,benign	534/687,534/688	16357147	1183,11817	2202	4298	6500	SO:0001583	missense	1187	exon15			CTGCCACGGATTC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1600C>T	1.37:g.16357147C>T	ENSP00000332771:p.Arg534Trp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	116	0.05311355311355311	38	0.07723577235772358	18	0.049723756906077346	4	0.006993006993006993	56	0.07387862796833773	C	4.728	0.135402	0.09032	0.085831	0.093648	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	3.89	-2.57	0.06248	Chloride channel, core (2);	0.563319	0.19723	N	0.107547	T	0.11580	0.0282	N	0.03948	-0.315	0.09310	N	1	B;B;B;B	0.18741	0.03;0.001;0.001;0.001	B;B;B;B	0.19666	0.026;0.001;0.001;0.001	T	0.53500	-0.8430	10	0.38643	T	0.18	.	5.0883	0.14694	0.3097:0.4793:0.0:0.211	rs12140223	270;491;534;534	B4DE56;E7EPH6;Q5T5Q4;P51800	.;.;.;CLCKA_HUMAN	W	534;534;491;534	ENSP00000364844:R534W;ENSP00000410353:R534W;ENSP00000414445:R491W;ENSP00000332771:R534W	ENSP00000332771:R534W	R	+	1	2	CLCNKA	16229734	0.000000	0.05858	0.250000	0.24296	0.109000	0.19521	-1.349000	0.02627	-0.379000	0.07906	0.313000	0.20887	CGG	.	.	weak		0.607	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
COBL	23242	hgsc.bcm.edu	37	7	51096974	51096974	+	Missense_Mutation	SNP	C	C	T	rs2240090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:51096974C>T	ENST00000265136.7	-	10	1984	c.1819G>A	c.(1819-1821)Gtc>Atc	p.V607I	COBL_ENST00000395542.2_Missense_Mutation_p.V689I	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	607			V -> I (in dbSNP:rs2240090). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CCTTTTCCGACGTCATGGGAA	0.542													T|||	3046	0.608227	0.6649	0.5937	5008	,	,		20187	0.4643		0.6938	False		,,,				2504	0.6022				p.V607I	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.G1819A						PASS	.	T	ILE/VAL	3043,1363	451.4+/-349.7	1044,955,204	83.0	76.0	78.0		1819	-11.6	0.0	7	dbSNP_98	78	5790,2810	444.6+/-360.7	1948,1894,458	yes	missense	COBL	NM_015198.3	29	2992,2849,662	TT,TC,CC		32.6744,30.9351,32.0852	benign	607/1262	51096974	8833,4173	2203	4300	6503	SO:0001583	missense	23242	exon10			TTCCGACGTCATG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1819G>A	7.37:g.51096974C>T	ENSP00000265136:p.Val607Ile	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	235	159	0.676596	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	1310|1310	0.5998168498168498|0.5998168498168498	320|320	0.6504065040650406|0.6504065040650406	219|219	0.6049723756906077|0.6049723756906077	253|253	0.4423076923076923|0.4423076923076923	518|518	0.683377308707124|0.683377308707124	T|T	0.536|0.536	-0.855524|-0.855524	0.02630|0.02630	0.690649|0.690649	0.673256|0.673256	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	.|T;T;T;T	.|0.22743	.|1.94;1.94;1.94;1.94	5.82|5.82	-11.6|-11.6	0.00059|0.00059	.|.	.|6.244210	.|0.00166	.|N	.|0.000002	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00926|0.00926	-1.1|-1.1	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;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	0.48547|0.48547	-0.9026|-0.9026	4|9	.|0.20519	.|T	.|0.43	.|.	6.3893|6.3893	0.21577|0.21577	0.1827:0.4105:0.3186:0.0882|0.1827:0.4105:0.3186:0.0882	rs2240090;rs10384224;rs17845884;rs17858859;rs60777538;rs2240090|rs2240090;rs10384224;rs17845884;rs17858859;rs60777538;rs2240090	.|607;664;607;689;149	.|O75128-3;O75128-7;O75128;O75128-2;O75128-6	.|.;.;COBL_HUMAN;.;.	H|I	582|607;499;492;689;105	.|ENSP00000265136:V607I;ENSP00000401204:V499I;ENSP00000413498:V492I;ENSP00000378912:V689I	.|ENSP00000265136:V607I	R|V	-|-	2|1	0|0	COBL|COBL	51064468|51064468	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-4.240000|-4.240000	0.00268|0.00268	-8.048000|-8.048000	0.00000|0.00000	-3.861000|-3.861000	0.00018|0.00018	CGT|GTC	C|0.360;T|0.640	0.640	strong		0.542	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
ZNF276	92822	hgsc.bcm.edu	37	16	89789898	89789898	+	Missense_Mutation	SNP	T	T	C	rs6500437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89789898T>C	ENST00000443381.2	+	4	884	c.787T>C	c.(787-789)Tgg>Cgg	p.W263R	ZNF276_ENST00000568064.1_Silent_p.H181H|ZNF276_ENST00000446326.2_Silent_p.H59H|VPS9D1_ENST00000389386.3_5'Flank|ZNF276_ENST00000289816.5_Missense_Mutation_p.W188R	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	263			W -> R (in dbSNP:rs6500437). {ECO:0000269|PubMed:14605947, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CAAGTGGCCATGGGACAAAGA	0.657													T|||	2722	0.54353	0.5809	0.5562	5008	,	,		18600	0.7282		0.3101	False		,,,				2504	0.5337				p.W263R		Atlas-SNP	.											ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	0			c.T787C						PASS	.	T	ARG/TRP,ARG/TRP	2271,2125	566.4+/-381.9	579,1113,506	39.0	34.0	36.0		787,562	3.1	1.0	16	dbSNP_116	36	2516,6074	387.0+/-342.0	381,1754,2160	yes	missense,missense	ZNF276	NM_001113525.1,NM_152287.3	101,101	960,2867,2666	CC,CT,TT		29.2899,48.3394,36.8628	benign,benign	263/615,188/540	89789898	4787,8199	2198	4295	6493	SO:0001583	missense	92822	exon4			TGGCCATGGGACA	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.787T>C	16.37:g.89789898T>C	ENSP00000415836:p.Trp263Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	37	CCDS45554.1	1147	0.5251831501831502	283	0.5752032520325203	177	0.4889502762430939	450	0.7867132867132867	237	0.31266490765171506	T	14.51	2.558270	0.45590	0.516606	0.292899	ENSG00000158805	ENST00000289816;ENST00000443381	T;T	0.05447	3.44;3.48	5.42	3.13	0.36017	.	0.297893	0.33591	N	0.004757	T	0.00012	0.0000	L	0.45581	1.43	0.09310	P	1.0	B;B	0.16166	0.005;0.016	B;B	0.12837	0.008;0.008	T	0.31024	-0.9958	9	0.07644	T	0.81	-19.3524	6.2916	0.21063	0.1425:0.077:0.0:0.7805	rs6500437;rs58773785;rs6500437	101;263	B4DIT3;Q8N554	.;ZN276_HUMAN	R	188;263	ENSP00000289816:W188R;ENSP00000415836:W263R	ENSP00000289816:W188R	W	+	1	0	ZNF276	88317399	0.916000	0.31088	0.961000	0.40146	0.673000	0.39480	1.332000	0.33805	0.861000	0.35504	0.459000	0.35465	TGG	T|0.562;C|0.438	0.438	strong		0.657	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
FAM151B	167555	hgsc.bcm.edu	37	5	79797690	79797690	+	Nonsense_Mutation	SNP	G	G	A	rs149355931		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79797690G>A	ENST00000282226.4	+	2	260	c.105G>A	c.(103-105)tgG>tgA	p.W35*	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	35										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		AGATCACCTGGTATCATGCAG	0.358													G|||	1	0.000199681	0.0	0.0014	5008	,	,		11791	0.0		0.0	False		,,,				2504	0.0				p.W35X		Atlas-SNP	.											.	FAM151B	25	.	0			c.G105A						PASS	.	G	stop/TRP	0,4406		0,0,2203	165.0	166.0	166.0		105	5.9	1.0	5	dbSNP_134	166	5,8595	4.3+/-15.6	0,5,4295	yes	stop-gained	FAM151B	NM_205548.2		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		35/277	79797690	5,13001	2203	4300	6503	SO:0001587	stop_gained	167555	exon2			CACCTGGTATCAT		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.105G>A	5.37:g.79797690G>A	ENSP00000282226:p.Trp35*	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	208	99	0.475962	NM_205548	A2RRE4	Nonsense_Mutation	SNP	ENST00000282226.4	37	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	G	37	6.368955	0.97511	0.0	5.81E-4	ENSG00000152380	ENST00000282226	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2276	19.0783	0.93171	0.0:0.0:1.0:0.0	.	.	.	.	X	35	.	ENSP00000282226:W35X	W	+	3	0	FAM151B	79833446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.660000	0.68018	2.803000	0.96430	0.591000	0.81541	TGG	G|1.000;A|0.000	0.000	strong		0.358	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548	
BANP	54971	hgsc.bcm.edu	37	16	88061150	88061150	+	Silent	SNP	C	C	T	rs74740586	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88061150C>T	ENST00000393207.1	+	8	1154	c.933C>T	c.(931-933)atC>atT	p.I311I	BANP_ENST00000393208.2_Silent_p.I280I|BANP_ENST00000355022.4_Silent_p.I280I|BANP_ENST00000355163.5_Silent_p.I286I|BANP_ENST00000479780.2_Silent_p.I280I|BANP_ENST00000286122.7_Silent_p.I311I|BANP_ENST00000538234.1_Silent_p.I319I	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	311	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.|Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		AGCAGAGCATCGACTCCAAGT	0.587													c|||	1877	0.3748	0.3601	0.4496	5008	,	,		16720	0.5476		0.2674	False		,,,				2504	0.274				p.I319I		Atlas-SNP	.											.	BANP	67	.	0			c.C957T						PASS	.	C	,,,,,,	1486,2910	473.0+/-356.5	269,948,981	77.0	83.0	81.0		957,858,840,957,933,840,840	-9.5	0.5	16	dbSNP_131	81	2097,6503	362.1+/-332.6	268,1561,2471	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	537,2509,3452	TT,TC,CC		24.3837,33.8035,27.57	,,,,,,	319/506,286/498,280/467,319/509,311/520,280/470,280/492	88061150	3583,9413	2198	4300	6498	SO:0001819	synonymous_variant	54971	exon8			GAGCATCGACTCC	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.933C>T	16.37:g.88061150C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	203	97	0.477833	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.682;T|0.318	0.318	strong		0.587	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
NPTX1	4884	hgsc.bcm.edu	37	17	78444679	78444679	+	Silent	SNP	T	T	C	rs28364735	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	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		
OVCH2	341277	hgsc.bcm.edu	37	11	7727886	7727886	+	lincRNA	SNP	C	C	T	rs7927138	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7727886C>T	ENST00000527565.1	-	0	542				OVCH2_ENST00000454689.1_RNA|OVCH2_ENST00000534193.2_RNA|RP11-35J10.4_ENST00000527443.1_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	65	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	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		
MCM9	254394	hgsc.bcm.edu	37	6	119136759	119136759	+	Missense_Mutation	SNP	A	A	C	rs65685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:119136759A>C	ENST00000316316.6	-	13	2946	c.2660T>G	c.(2659-2661)aTg>aGg	p.M887R		NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	887					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)		TGAGTCCAGCATTCTGTCTGG	0.532													A|||	454	0.090655	0.034	0.1037	5008	,	,		19843	0.0605		0.1262	False		,,,				2504	0.1524				p.M887R		Atlas-SNP	.											.	MCM9	73	.	0			c.T2660G						PASS	.																																			SO:0001583	missense	254394	exon12			TCCAGCATTCTGT	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.2660T>G	6.37:g.119136759A>C	ENSP00000314505:p.Met887Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	192	0.08791208791208792	20	0.04065040650406504	43	0.11878453038674033	34	0.05944055944055944	95	0.12532981530343007	A	6.329	0.428846	0.11987	.	.	ENSG00000111877	ENST00000316316;ENST00000243218	T	0.03301	3.98	6.03	-12.1	0.00011	.	.	.	.	.	T	0.00241	0.0007	N	0.01352	-0.895	0.80722	P	0.0	.	.	.	.	.	.	T	0.49615	-0.8921	6	0.13470	T	0.59	.	0.0368	0.00007	0.2851:0.2236:0.2089:0.2823	rs65685;rs3751443;rs17235356;rs60968013;rs65685	.	.	.	R	887;506	ENSP00000314505:M887R	ENSP00000243218:M506R	M	-	2	0	MCM9	119243462	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.254000	0.02874	-2.074000	0.00877	-0.177000	0.13119	ATG	A|0.878;C|0.085	0.085	strong		0.532	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
MEGF11	84465	hgsc.bcm.edu	37	15	66206303	66206303	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:66206303T>C	ENST00000409699.2	-	20	2654	c.2482A>G	c.(2482-2484)Atg>Gtg	p.M828V	MEGF11_ENST00000288745.3_Missense_Mutation_p.M753V|MEGF11_ENST00000422354.1_Missense_Mutation_p.M828V|MEGF11_ENST00000478721.1_5'UTR|MEGF11_ENST00000395614.1_Start_Codon_SNP_p.M1V|MEGF11_ENST00000395625.2_Missense_Mutation_p.M753V|MEGF11_ENST00000360698.4_3'UTR			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	828					homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						TCCTCCATCATGAGGGCAGCT	0.607																																					p.M828V		Atlas-SNP	.											.	MEGF11	70	.	0			c.A2482G						PASS	.						39.0	37.0	38.0					15																	66206303		2201	4299	6500	SO:0001583	missense	84465	exon20			CCATCATGAGGGC	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.2482A>G	15.37:g.66206303T>C	ENSP00000386908:p.Met828Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	T	18.50	3.636511	0.67130	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000395614	T;T;T;T;T	0.34472	2.4;2.4;2.4;2.4;1.36	4.65	4.65	0.58169	.	0.000000	0.51477	U	0.000100	T	0.16342	0.0393	N	0.04508	-0.205	0.80722	D	1	B;B	0.25441	0.092;0.126	B;B	0.25987	0.065;0.039	T	0.10042	-1.0647	10	0.02654	T	1	.	14.2339	0.65911	0.0:0.0:0.0:1.0	.	828;753	A6BM72;A6BM72-2	MEG11_HUMAN;.	V	828;753;828;753;1	ENSP00000386908:M828V;ENSP00000288745:M753V;ENSP00000414475:M828V;ENSP00000378987:M753V;ENSP00000378976:M1V	ENSP00000288745:M753V	M	-	1	0	MEGF11	63993357	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.659000	0.61504	1.948000	0.56530	0.454000	0.30748	ATG	.	.	none		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
CSF3	1440	hgsc.bcm.edu	37	17	38173143	38173143	+	Silent	SNP	G	G	A	rs25645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38173143G>A	ENST00000225474.2	+	5	586	c.555G>A	c.(553-555)ctG>ctA	p.L185L	CSF3_ENST00000331769.2_Silent_p.L178L|CSF3_ENST00000577675.1_Silent_p.L142L|CSF3_ENST00000394149.3_Silent_p.L182L|RP11-387H17.6_ENST00000583462.1_lincRNA|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	41	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	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	
ZNF512B	57473	hgsc.bcm.edu	37	20	62595990	62595990	+	Missense_Mutation	SNP	T	T	C	rs817326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	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	
MYH15	22989	hgsc.bcm.edu	37	3	108147728	108147728	+	Splice_Site	SNP	T	T	C	rs3900940	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:108147728T>C	ENST00000273353.3	-	28	3429	c.3373A>G	c.(3373-3375)Act>Gct	p.T1125A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1125			T -> A (in dbSNP:rs3900940).			cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTTATTTGAGTCTGTAGCAAG	0.388													T|||	846	0.16893	0.1241	0.2032	5008	,	,		18526	0.0119		0.3131	False		,,,				2504	0.2188				p.T1125A		Atlas-SNP	.											.	MYH15	223	.	0			c.A3373G	GRCh37	CM074941	MYH15	M	rs3900940	PASS	.	T	ALA/THR	524,3160		31,462,1349	76.0	71.0	73.0		3373	-1.7	0.0	3	dbSNP_108	73	2352,5806		337,1678,2064	yes	missense-near-splice	MYH15	NM_014981.1	58	368,2140,3413	CC,CT,TT		28.8306,14.2237,24.2864	benign	1125/1947	108147728	2876,8966	1842	4079	5921	SO:0001630	splice_region_variant	22989	exon28			TTTGAGTCTGTAG	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3373-1A>G	3.37:g.108147728T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	402	0.18406593406593408	62	0.12601626016260162	93	0.2569060773480663	0	0.0	247	0.3258575197889182	T	0.022	-1.409432	0.01155	0.142237	0.288306	ENSG00000144821	ENST00000273353	T	0.74947	-0.89	5.63	-1.67	0.08238	Myosin tail (1);	.	.	.	.	T	0.00012	0.0000	N	0.00890	-1.11	0.31558	P	0.657914	B	0.06786	0.001	B	0.13407	0.009	T	0.12319	-1.0552	8	0.02654	T	1	.	5.5574	0.17123	0.1708:0.5263:0.0:0.3029	rs3900940;rs17610187;rs52830059;rs57572156;rs3900940	1125	Q9Y2K3	MYH15_HUMAN	A	1125	ENSP00000273353:T1125A	ENSP00000273353:T1125A	T	-	1	0	MYH15	109630418	1.000000	0.71417	0.010000	0.14722	0.083000	0.17756	1.227000	0.32576	-0.097000	0.12307	0.528000	0.53228	ACT	T|0.802;C|0.198	0.198	strong		0.388	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation
VPS9D1	9605	hgsc.bcm.edu	37	16	89777761	89777761	+	Silent	SNP	C	C	T	rs12920315	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89777761C>T	ENST00000389386.3	-	9	931	c.807G>A	c.(805-807)gtG>gtA	p.V269V	VPS9D1_ENST00000565452.1_5'UTR|VPS9D1_ENST00000561976.1_Silent_p.V199V|VPS9D1-AS1_ENST00000562866.1_RNA	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	269					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCAGGCTGGTCACGAGTGACA	0.667													c|||	2815	0.562101	0.4546	0.5951	5008	,	,		12592	0.4623		0.5527	False		,,,				2504	0.7965				p.V269V		Atlas-SNP	.											C16orf7,NS,carcinoma,0,1	.	.	1	0			c.G807A						PASS	.			2075,1981		537,1001,490	62.0	77.0	73.0		807	1.8	1.0	16	dbSNP_121	73	4573,3759		1274,2025,867	no	coding-synonymous	C16orf7	NM_004913.2		1811,3026,1357	TT,TC,CC		45.1152,48.8412,46.3352		269/632	89777761	6648,5740	2028	4166	6194	SO:0001819	synonymous_variant	9605	exon9			GCTGGTCACGAGT	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.807G>A	16.37:g.89777761C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			A|0.000;C|0.471;G|0.000;T|0.529	0.529	strong		0.667	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
CNNM3	26505	hgsc.bcm.edu	37	2	97493877	97493877	+	Silent	SNP	T	T	C	rs1320149	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:97493877T>C	ENST00000305510.3	+	5	1759	c.1731T>C	c.(1729-1731)ttT>ttC	p.F577F	CNNM3_ENST00000377060.3_Silent_p.F529F|ANKRD23_ENST00000476975.1_Intron	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	577					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						GTCTGAAGTTTGAGAATGGGG	0.582													C|||	1592	0.317891	0.857	0.1311	5008	,	,		22096	0.1885		0.0954	False		,,,				2504	0.0838				p.F577F		Atlas-SNP	.											.	CNNM3	33	.	0			c.T1731C						PASS	.	C	,	3170,1236	426.8+/-341.3	1140,890,173	129.0	134.0	132.0		1731,1587	-1.1	1.0	2	dbSNP_88	132	727,7873	786.3+/-407.6	40,647,3613	no	coding-synonymous,coding-synonymous	CNNM3	NM_017623.4,NM_199078.2	,	1180,1537,3786	CC,CT,TT		8.4535,28.0527,29.9631	,	577/708,529/660	97493877	3897,9109	2203	4300	6503	SO:0001819	synonymous_variant	26505	exon5			GAAGTTTGAGAAT	AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"""cyclin M3"""	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.1731T>C	2.37:g.97493877T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_017623	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Silent	SNP	ENST00000305510.3	37	CCDS2025.1																																																																																			T|0.721;G|0.000	.	strong		0.582	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458476	39458476	+	Missense_Mutation	SNP	A	A	T	rs1001191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39458476A>T	ENST00000391353.1	-	1	627	c.628T>A	c.(628-630)Tgc>Agc	p.C210S		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	210	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											AAAATATAGCAGATGGGTTGA	0.483													A|||	1159	0.23143	0.2821	0.1484	5008	,	,		23289	0.3204		0.1879	False		,,,				2504	0.1748				p.C210S		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.T628A						PASS	.																																			SO:0001583	missense	100533177	exon1			TATAGCAGATGGG		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.628T>A	17.37:g.39458476A>T	ENSP00000375148:p.Cys210Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		495	0.22664835164835165	124	0.25203252032520324	57	0.1574585635359116	175	0.30594405594405594	139	0.18337730870712401	A	12.00	1.805895	0.31961	.	.	ENSG00000212658	ENST00000391353	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.10941	-1.0608	4	0.42905	T	0.14	.	12.4283	0.55559	1.0:0.0:0.0:0.0	rs1001191;rs1001191	.	.	.	S	210	.	ENSP00000375148:C210S	C	-	1	0	KRTAP29-1	36712002	1.000000	0.71417	0.911000	0.35937	0.092000	0.18411	2.951000	0.49089	1.979000	0.57680	0.374000	0.22700	TGC	A|0.766;T|0.234	0.234	strong		0.483	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
CPT2	1376	hgsc.bcm.edu	37	1	53679229	53679229	+	Missense_Mutation	SNP	A	A	G	rs1799822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:53679229A>G	ENST00000371486.3	+	5	2454	c.1939A>G	c.(1939-1941)Atg>Gtg	p.M647V	RP5-1024G6.2_ENST00000452466.1_RNA|C1orf123_ENST00000470385.1_5'Flank	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	647			M -> V (common polymorphism; confirmed at protein level; dbSNP:rs1799822). {ECO:0000269|PubMed:14605500, ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:18306170, ECO:0000269|PubMed:9600456, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CTTAGAAGACATGTTTGATGC	0.483													A|||	503	0.100439	0.0227	0.1542	5008	,	,		20518	0.0853		0.2068	False		,,,				2504	0.0736				p.M647V		Atlas-SNP	.											.	CPT2	34	.	0			c.A1939G						PASS	.	A	VAL/MET	240,4166	140.8+/-176.2	7,226,1970	88.0	80.0	83.0		1939	5.9	1.0	1	dbSNP_89	83	1937,6663	341.9+/-324.3	208,1521,2571	yes	missense	CPT2	NM_000098.2	21	215,1747,4541	GG,GA,AA		22.5233,5.4471,16.7384	benign	647/659	53679229	2177,10829	2203	4300	6503	SO:0001583	missense	1376	exon5			GAAGACATGTTTG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1939A>G	1.37:g.53679229A>G	ENSP00000360541:p.Met647Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	280	0.1282051282051282	14	0.028455284552845527	68	0.1878453038674033	54	0.0944055944055944	144	0.18997361477572558	A	17.02	3.280726	0.59758	0.054471	0.225233	ENSG00000157184	ENST00000371486	D	0.90133	-2.62	5.9	5.9	0.94986	.	0.189419	0.56097	D	0.000031	T	0.00178	0.0005	L	0.31752	0.955	0.23371	P	0.99781582	B	0.09022	0.002	B	0.13407	0.009	T	0.11665	-1.0578	9	0.44086	T	0.13	-32.7754	16.3322	0.83039	1.0:0.0:0.0:0.0	rs1799822;rs17377870;rs17848486;rs17849929;rs17857680;rs52797123;rs1799822	647	P23786	CPT2_HUMAN	V	647	ENSP00000360541:M647V	ENSP00000360541:M647V	M	+	1	0	CPT2	53451817	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.445000	0.80570	2.251000	0.74343	0.528000	0.53228	ATG	A|0.854;G|0.146	0.146	strong		0.483	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
ZNF625	90589	hgsc.bcm.edu	37	19	12256912	12256912	+	Missense_Mutation	SNP	C	C	T	rs7258368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12256912C>T	ENST00000355738.1	-	4	470	c.121G>A	c.(121-123)Gtg>Atg	p.V41M	ZNF625_ENST00000542938.1_Missense_Mutation_p.V41M|ZNF625_ENST00000439556.2_Missense_Mutation_p.V107M|CTC-359D24.3_ENST00000472362.1_RNA|ZNF625_ENST00000455799.1_3'UTR|ZNF625-ZNF20_ENST00000430024.1_Intron			Q96I27	ZN625_HUMAN	zinc finger protein 625	41			V -> M (in dbSNP:rs7258368).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						GCATGACCCACGCTGACTTCT	0.433													C|||	986	0.196885	0.3011	0.1311	5008	,	,		17942	0.2133		0.1282	False		,,,				2504	0.1564				p.V107M		Atlas-SNP	.											ZNF625,NS,carcinoma,+2,2	ZNF625	37	2	0			c.G319A						PASS	.	C	MET/VAL	1231,3175	423.8+/-340.2	175,881,1147	86.0	80.0	82.0		319	-1.7	0.0	19	dbSNP_116	82	925,7675	204.2+/-247.0	48,829,3423	yes	missense	ZNF625	NM_145233.3	21	223,1710,4570	TT,TC,CC		10.7558,27.9392,16.577	benign	107/373	12256912	2156,10850	2203	4300	6503	SO:0001583	missense	90589	exon4			GACCCACGCTGAC	BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"""Zinc fingers, C2H2-type"", ""-"""	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.121G>A	19.37:g.12256912C>T	ENSP00000347977:p.Val41Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_145233	A4FU45|I3L0E9	Missense_Mutation	SNP	ENST00000355738.1	37		424	0.19413919413919414	136	0.2764227642276423	45	0.12430939226519337	145	0.2534965034965035	98	0.12928759894459102	C	0.003	-2.466354	0.00169	0.279392	0.107558	ENSG00000257591	ENST00000542938;ENST00000355738;ENST00000439556	T;T;T	0.15603	2.41;2.41;2.41	0.856	-1.71	0.08133	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.25272	0.122;0.002	B;B	0.10450	0.005;0.002	T	0.43475	-0.9389	8	0.39692	T	0.17	.	2.8518	0.05560	0.4053:0.3678:0.0:0.2269	rs7258368;rs52800829;rs7258368	41;41	A8K8U0;Q96I27	.;ZN625_HUMAN	M	41;41;107	ENSP00000438436:V41M;ENSP00000347977:V41M;ENSP00000394380:V107M	ENSP00000347977:V41M	V	-	1	0	AC022415.5	12117912	0.000000	0.05858	0.000000	0.03702	0.309000	0.27889	-1.382000	0.02546	-1.747000	0.01333	-0.752000	0.03492	GTG	C|0.818;T|0.182	0.182	strong		0.433	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233	
FPR1	2357	hgsc.bcm.edu	37	19	52249702	52249702	+	Silent	SNP	G	G	T	rs2070746	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52249702G>T	ENST00000595042.1	-	3	687	c.546C>A	c.(544-546)ccC>ccA	p.P182P	FPR1_ENST00000304748.4_Silent_p.P182P	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	182					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)	CGTTGGTCCAGGGCGAAAAGT	0.517													G|||	1758	0.351038	0.3215	0.4164	5008	,	,		21166	0.4484		0.2763	False		,,,				2504	0.3211				p.P182P		Atlas-SNP	.											.	FPR1	64	.	0			c.C546A						PASS	.	G	,	1314,3092		198,918,1087	103.0	97.0	99.0		546,546	2.6	0.7	19	dbSNP_96	99	2446,6154		332,1782,2186	no	coding-synonymous,coding-synonymous	FPR1	NM_001193306.1,NM_002029.3	,	530,2700,3273	TT,TG,GG		28.4419,29.823,28.9097	,	182/351,182/351	52249702	3760,9246	2203	4300	6503	SO:0001819	synonymous_variant	2357	exon3			GGTCCAGGGCGAA	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.546C>A	19.37:g.52249702G>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Silent	SNP	ENST00000595042.1	37	CCDS12839.1																																																																																			G|0.682;T|0.318	0.318	strong		0.517	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
PLD2	5338	hgsc.bcm.edu	37	17	4720469	4720469	+	Missense_Mutation	SNP	C	C	T	rs1052748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	157	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	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	
LRMP	4033	hgsc.bcm.edu	37	12	25243115	25243115	+	Missense_Mutation	SNP	G	G	C	rs1908946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:25243115G>C	ENST00000354454.3	+	13	1419	c.590G>C	c.(589-591)tGt>tCt	p.C197S	LRMP_ENST00000547044.1_Missense_Mutation_p.C197S|LRMP_ENST00000548766.1_Missense_Mutation_p.C197S	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	253			L -> V (in dbSNP:rs7969931). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8021504}.		immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					ATCACTAACTGTTTAAAACTA	0.418													G|||	2501	0.499401	0.1657	0.5231	5008	,	,		20220	0.8095		0.5189	False		,,,				2504	0.5941				p.C197S		Atlas-SNP	.											.	LRMP	51	.	0			c.G590C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS	1012,3394	361.9+/-315.9	120,772,1311	79.0	79.0	79.0		590,590,590	5.8	1.0	12	dbSNP_92	79	4574,4026	593.4+/-393.1	1204,2166,930	yes	missense,missense,missense	LRMP	NM_001204126.1,NM_001204127.1,NM_006152.3	112,112,112	1324,2938,2241	CC,CG,GG		46.814,22.9687,42.9494	probably-damaging,probably-damaging,probably-damaging	197/500,197/500,197/500	25243115	5586,7420	2203	4300	6503	SO:0001583	missense	4033	exon12			CTAACTGTTTAAA		CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.590G>C	12.37:g.25243115G>C	ENSP00000346442:p.Cys197Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_001204126	A0AVM2|B4E077|Q8N301	Missense_Mutation	SNP	ENST00000354454.3	37	CCDS8701.1	1153|1153	0.5279304029304029|0.5279304029304029	104|104	0.21138211382113822|0.21138211382113822	202|202	0.5580110497237569|0.5580110497237569	444|444	0.7762237762237763|0.7762237762237763	403|403	0.5316622691292876|0.5316622691292876	G|G	27.5|27.5	4.832726|4.832726	0.91036|0.91036	0.229687|0.229687	0.53186|0.53186	ENSG00000118308|ENSG00000118308	ENST00000354454;ENST00000536173;ENST00000548766;ENST00000547044|ENST00000555885	T;T;T;T|.	0.15834|.	2.39;2.39;2.39;2.39|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.105878|.	0.64402|.	D|.	0.000003|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72894|0.72894	2.215|2.215	0.09310|0.09310	P|P	0.9999999089398|0.9999999089398	P|.	0.51240|.	0.943|.	P|.	0.51582|.	0.674|.	T|T	0.45673|0.45673	-0.9245|-0.9245	9|4	0.52906|.	T|.	0.07|.	-13.6954|-13.6954	17.4676|17.4676	0.87638|0.87638	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs1908946;rs17327056;rs52802443;rs1908946|rs1908946;rs17327056;rs52802443;rs1908946	253|.	Q12912|.	LRMP_HUMAN|.	S|L	197;144;197;197|48	ENSP00000346442:C197S;ENSP00000444056:C144S;ENSP00000446496:C197S;ENSP00000450246:C197S|.	ENSP00000346442:C197S|.	C|V	+|+	2|1	0|0	LRMP|LRMP	25134382|25134382	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.996000|0.996000	0.88848|0.88848	5.897000|5.897000	0.69831|0.69831	2.732000|2.732000	0.93576|0.93576	0.655000|0.655000	0.94253|0.94253	TGT|GTT	G|0.535;C|0.465	0.465	strong		0.418	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152	
CCDC3	83643	hgsc.bcm.edu	37	10	12940631	12940631	+	Missense_Mutation	SNP	C	C	T	rs145872952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12940631C>T	ENST00000378825.3	-	3	724	c.598G>A	c.(598-600)Gtc>Atc	p.V200I	CCDC3_ENST00000378839.1_Missense_Mutation_p.V75I	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	200						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			AGTTTCTTGACGTGGTCCTCC	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.V200I		Atlas-SNP	.											.	CCDC3	27	.	0			c.G598A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	72.0	62.0	65.0		598	5.4	1.0	10	dbSNP_134	65	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCDC3	NM_031455.3	29	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	benign	200/271	12940631	4,13002	2203	4300	6503	SO:0001583	missense	83643	exon3			TCTTGACGTGGTC	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.598G>A	10.37:g.12940631C>T	ENSP00000368102:p.Val200Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.455433	0.84209	0.0	4.65E-4	ENSG00000151468	ENST00000378839;ENST00000378825	T	0.17691	2.26	5.42	5.42	0.78866	.	0.330512	0.26106	N	0.026308	T	0.18257	0.0438	M	0.64997	1.995	0.40106	D	0.976437	P	0.44946	0.846	B	0.30251	0.113	T	0.10245	-1.0638	10	0.56958	D	0.05	-25.0542	18.1996	0.89833	0.0:1.0:0.0:0.0	.	200	Q9BQI4	CCDC3_HUMAN	I	75;200	ENSP00000368116:V75I	ENSP00000368102:V200I	V	-	1	0	CCDC3	12980637	0.999000	0.42202	0.998000	0.56505	0.880000	0.50808	4.526000	0.60566	2.550000	0.86006	0.561000	0.74099	GTC	C|1.000;T|0.000	0.000	strong		0.602	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629847	32629847	+	Silent	SNP	A	A	G	rs1049133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629847A>G	ENST00000399082.3	-	2	332	c.288T>C	c.(286-288)acT>acC	p.T96T	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.T186T|HLA-DQB1_ENST00000374943.4_Silent_p.T186T|HLA-DQB1_ENST00000399079.3_Silent_p.T186T|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Silent_p.T186T			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	186	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GGATCTGGAAAGTCCAGTCAC	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	4163	0.83127	0.7375	0.8703	5008	,	,		16941	0.9087		0.7903	False		,,,				2504	0.8926				p.T186T	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T558C						PASS	.	G		3135,1267		1155,825,221	54.0	58.0	57.0		558	2.7	1.0	6	dbSNP_86	57	6471,2129		2505,1461,334	no	coding-synonymous	HLA-DQB1	NM_002123.4		3660,2286,555	GG,GA,AA		24.7558,28.7824,26.1191		186/262	32629847	9606,3396	2201	4300	6501	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CTGGAAAGTCCAG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.288T>C	6.37:g.32629847A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				A|0.213;G|0.787	0.787	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
LRRN2	10446	hgsc.bcm.edu	37	1	204587569	204587569	+	Missense_Mutation	SNP	G	G	C	rs3747631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204587569G>C	ENST00000367175.1	-	1	3764	c.1552C>G	c.(1552-1554)Ctc>Gtc	p.L518V	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367177.3_Missense_Mutation_p.L518V|LRRN2_ENST00000367176.3_Missense_Mutation_p.L518V|LRRN2_ENST00000496057.1_5'Flank			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	64	0	0		WXS	Illumina HiSeq	Phase_I	115	33	0.286957	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	
DNAH17	8632	hgsc.bcm.edu	37	17	76503593	76503593	+	Missense_Mutation	SNP	T	T	C	rs9896398	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76503593T>C	ENST00000585328.1	-	28	4646	c.4522A>G	c.(4522-4524)Acc>Gcc	p.T1508A	DNAH17_ENST00000389840.5_Missense_Mutation_p.T1507A	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1507	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)	p.T1508A(1)		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)			GGGAGCTGGGTGCGGATGTCT	0.592													C|||	2897	0.578474	0.7375	0.4452	5008	,	,		19160	0.4653		0.5984	False		,,,				2504	0.5542				p.T1511A		Atlas-SNP	.											DNAH17,NS,carcinoma,0,1	DNAH17	347	1	1	Substitution - Missense(1)	stomach(1)	c.A4531G						PASS	.	C	ALA/THR	3068,1102		1140,788,157	45.0	51.0	49.0		4531	1.6	0.3	17	dbSNP_119	49	5214,3280		1611,1992,644	yes	missense	DNAH17	NM_173628.3	58	2751,2780,801	CC,CT,TT		38.6155,26.4269,34.602	benign	1511/4463	76503593	8282,4382	2085	4247	6332	SO:0001583	missense	8632	exon28			GCTGGGTGCGGAT	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.4522A>G	17.37:g.76503593T>C	ENSP00000465516:p.Thr1508Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		1287	0.5892857142857143	373	0.758130081300813	180	0.4972375690607735	269	0.47027972027972026	465	0.6134564643799473	C	0.367	-0.936325	0.02340	0.735731	0.613845	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.60299	0.2	4.97	1.63	0.23807	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.00788	-1.185	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37934	-0.9684	8	0.07813	T	0.8	.	3.1544	0.06499	0.297:0.3484:0.0:0.3547	rs9896398;rs57733591;rs9896398	1507	Q9UFH2	DYH17_HUMAN	A	1508;1507	ENSP00000374490:T1507A	ENSP00000300671:T1508A	T	-	1	0	DNAH17	74015188	0.000000	0.05858	0.273000	0.24645	0.918000	0.54935	0.112000	0.15479	0.123000	0.18342	-0.213000	0.12676	ACC	T|0.403;C|0.597	0.597	strong		0.592	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
SFT2D1	113402	hgsc.bcm.edu	37	6	166736362	166736362	+	Silent	SNP	C	C	T	rs7088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:166736362C>T	ENST00000361731.3	-	7	532	c.423G>A	c.(421-423)tcG>tcA	p.S141S	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 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)		ATGGGATGTACGACAGGCTAT	0.318													C|||	2365	0.472244	0.3283	0.4784	5008	,	,		16981	0.6161		0.3996	False		,,,				2504	0.589				p.S141S		Atlas-SNP	.											.	SFT2D1	12	.	0			c.G423A						PASS	.	C		1417,2989	463.6+/-353.6	233,951,1019	128.0	122.0	124.0		423	-9.9	0.9	6	dbSNP_52	124	3415,5185	504.6+/-376.2	705,2005,1590	no	coding-synonymous	SFT2D1	NM_145169.1		938,2956,2609	TT,TC,CC		39.7093,32.1607,37.1521		141/160	166736362	4832,8174	2203	4300	6503	SO:0001819	synonymous_variant	113402	exon7			GATGTACGACAGG	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.423G>A	6.37:g.166736362C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_145169		Silent	SNP	ENST00000361731.3	37	CCDS5292.1																																																																																			T|0.319;G|0.105;C|0.484;A|0.092	0.319	strong		0.318	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169	
LNP1	348801	hgsc.bcm.edu	37	3	100170628	100170628	+	Silent	SNP	A	A	G	rs9844083	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:100170628A>G	ENST00000383693.3	+	3	1502	c.222A>G	c.(220-222)caA>caG	p.Q74Q	LNP1_ENST00000489752.1_Silent_p.Q87Q	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	74										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						ATGAGGACCAAGAATTTCGAT	0.423																																					p.Q74Q		Atlas-SNP	.											.	LNP1	26	.	0			c.A222G						PASS	.						100.0	91.0	94.0					3																	100170628		1872	4101	5973	SO:0001819	synonymous_variant	348801	exon3			GGACCAAGAATTT		CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.222A>G	3.37:g.100170628A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	122	33	0.270492	NM_001085451	B7ZLT3	Silent	SNP	ENST00000383693.3	37	CCDS43120.1																																																																																			A|0.500;G|0.500	0.500	strong		0.423	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1		
APBA3	9546	hgsc.bcm.edu	37	19	3752515	3752515	+	Silent	SNP	G	G	A	rs61735536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	12	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	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		
ODF2L	57489	hgsc.bcm.edu	37	1	86852621	86852621	+	Silent	SNP	A	A	G	rs2390096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:86852621A>G	ENST00000359242.3	-	2	371	c.90T>C	c.(88-90)tgT>tgC	p.C30C	ODF2L_ENST00000394731.1_5'UTR|ODF2L_ENST00000317336.7_Silent_p.C30C|ODF2L_ENST00000486215.1_Silent_p.C30C|ODF2L_ENST00000370567.1_Silent_p.C30C|ODF2L_ENST00000370566.3_Silent_p.C30C|ODF2L_ENST00000478286.2_Silent_p.C30C|ODF2L_ENST00000294678.2_Silent_p.C30C	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	30						centrosome (GO:0005813)		p.C30C(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTTCACTGGTACACCGTGGTA	0.338													A|||	1576	0.314696	0.2352	0.2637	5008	,	,		12595	0.4167		0.3181	False		,,,				2504	0.3497				p.C30C		Atlas-SNP	.											ODF2L,NS,carcinoma,0,1	ODF2L	53	1	1	Substitution - coding silent(1)	stomach(1)	c.T90C						PASS	.	A	,,,	1182,3224	414.8+/-337.0	171,840,1192	118.0	127.0	124.0		90,90,90,90	1.5	0.0	1	dbSNP_100	124	2923,5677	455.7+/-363.9	464,1995,1841	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	635,2835,3033	GG,GA,AA		33.9884,26.8271,31.5624	,,,	30/637,30/621,30/592,30/621	86852621	4105,8901	2203	4300	6503	SO:0001819	synonymous_variant	57489	exon2			ACTGGTACACCGT		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.90T>C	1.37:g.86852621A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2																																																																																			A|0.692;G|0.308	0.308	strong		0.338	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
NUP54	53371	hgsc.bcm.edu	37	4	77055474	77055474	+	Silent	SNP	A	A	G	rs11097244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77055474A>G	ENST00000264883.3	-	5	704	c.564T>C	c.(562-564)gaT>gaC	p.D188D	NUP54_ENST00000458189.2_Silent_p.D8D|NUP54_ENST00000342467.6_Silent_p.D8D|NUP54_ENST00000514987.1_Silent_p.D140D|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	188	9 X 2 AA repeats of F-G.				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 targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						CCACTAGCCCATCTTCATCTT	0.343													A|||	777	0.155152	0.0567	0.1297	5008	,	,		16365	0.3512		0.1312	False		,,,				2504	0.1288				p.D188D		Atlas-SNP	.											NUP54,colon,carcinoma,-2,1	NUP54	48	1	0			c.T564C						PASS	.	A		308,4098	165.8+/-197.2	15,278,1910	69.0	60.0	63.0		564	4.7	1.0	4	dbSNP_120	63	1300,7300	256.2+/-280.8	101,1098,3101	no	coding-synonymous	NUP54	NM_017426.2		116,1376,5011	GG,GA,AA		15.1163,6.9905,12.3635		188/508	77055474	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon5			TAGCCCATCTTCA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.564T>C	4.37:g.77055474A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.343	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
SPATA4	132851	hgsc.bcm.edu	37	4	177113956	177113956	+	Silent	SNP	A	A	G	rs2291244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:177113956A>G	ENST00000280191.2	-	4	618	c.510T>C	c.(508-510)taT>taC	p.Y170Y	SPATA4_ENST00000515234.1_5'UTR	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	170						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)		TCTGGTAGCTATAGTCCGTGA	0.338													A|||	1133	0.226238	0.1573	0.1614	5008	,	,		18209	0.381		0.1769	False		,,,				2504	0.2566				p.Y170Y		Atlas-SNP	.											.	SPATA4	44	.	0			c.T510C						PASS	.	A		727,3679	299.6+/-285.9	67,593,1543	61.0	61.0	61.0		510	-7.6	0.4	4	dbSNP_100	61	1497,7103	282.9+/-295.8	138,1221,2941	no	coding-synonymous	SPATA4	NM_144644.2		205,1814,4484	GG,GA,AA		17.407,16.5002,17.0998		170/306	177113956	2224,10782	2203	4300	6503	SO:0001819	synonymous_variant	132851	exon4			GTAGCTATAGTCC	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.510T>C	4.37:g.177113956A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_144644	Q8NCS5|Q8WW15	Silent	SNP	ENST00000280191.2	37	CCDS3826.1																																																																																			A|0.801;G|0.199	0.199	strong		0.338	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
ARVCF	421	hgsc.bcm.edu	37	22	19969075	19969075	+	Silent	SNP	A	A	G	rs2073747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19969075A>G	ENST00000263207.3	-	5	846	c.555T>C	c.(553-555)agT>agC	p.S185S	ARVCF_ENST00000406259.1_Silent_p.S185S|ARVCF_ENST00000406522.1_Silent_p.S122S|ARVCF_ENST00000401994.1_Silent_p.S122S|ARVCF_ENST00000344269.3_Silent_p.S122S|ARVCF_ENST00000487793.1_5'UTR	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	185					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)					AGCCACCCCCACTGCTGAGGT	0.697													G|||	3613	0.721446	0.8026	0.6455	5008	,	,		15005	0.6081		0.7674	False		,,,				2504	0.7352				p.S185S		Atlas-SNP	.											.	ARVCF	54	.	0			c.T555C						PASS	.	G		3306,698		1375,556,71	10.0	14.0	13.0		555	-6.7	0.5	22	dbSNP_96	13	6367,1601		2551,1265,168	no	coding-synonymous	ARVCF	NM_001670.2		3926,1821,239	GG,GA,AA		20.0929,17.4326,19.2031		185/963	19969075	9673,2299	2002	3984	5986	SO:0001819	synonymous_variant	421	exon5			ACCCCCACTGCTG		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.555T>C	22.37:g.19969075A>G		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			T|0.002;G|0.709	0.709	strong		0.697	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
MMP27	64066	hgsc.bcm.edu	37	11	102567522	102567522	+	Silent	SNP	G	G	A	rs201248506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:102567522G>A	ENST00000260229.4	-	5	755	c.664C>T	c.(664-666)Ctg>Ttg	p.L222L		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	222					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)	GAGAGCCCCAGTGCATGACCA	0.423													G|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.L222L		Atlas-SNP	.											.	MMP27	84	.	0			c.C664T						PASS	.	G		0,4406		0,0,2203	81.0	69.0	73.0		664	3.9	0.9	11		73	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	MMP27	NM_022122.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		222/514	102567522	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon5			GCCCCAGTGCATG	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.664C>T	11.37:g.102567522G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			G|0.999;A|0.001	0.001	strong		0.423	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
PPARG	5468	hgsc.bcm.edu	37	3	12393125	12393125	+	Missense_Mutation	SNP	C	C	G	rs1801282	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:12393125C>G	ENST00000287820.6	+	1	155	c.34C>G	c.(34-36)Cca>Gca	p.P12A	PPARG_ENST00000397000.1_Intron|PPARG_ENST00000397015.2_Intron|PPARG_ENST00000397010.2_Intron|PPARG_ENST00000397026.2_Intron|PPARG_ENST00000539812.1_Intron|PPARG_ENST00000309576.6_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	89	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	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	
SETBP1	26040	hgsc.bcm.edu	37	18	42456653	42456653	+	Intron	SNP	G	G	A	rs663651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:42456653G>A	ENST00000282030.5	+	3	836				SETBP1_ENST00000426838.4_Missense_Mutation_p.A222T	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1							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)		CCCATTCCCCGCAAAACCCGG	0.522									Schinzel-Giedion syndrome				A|||	2469	0.493011	0.5076	0.4524	5008	,	,		18355	0.4762		0.5616	False		,,,				2504	0.4489				p.A222T		Atlas-SNP	.											.	SETBP1	577	.	0			c.G664A						PASS	.						92.0	88.0	89.0					18																	42456653		692	1591	2283	SO:0001627	intron_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	TTCCCCGCAAAAC	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.540+7405G>A	18.37:g.42456653G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	160	93	0.58125	NM_001130110	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	1152	0.5274725274725275	264	0.5365853658536586	170	0.4696132596685083	287	0.5017482517482518	431	0.5686015831134564	A	1.344	-0.593310	0.03771	.	.	ENSG00000152217	ENST00000426838	.	.	.	3.41	-0.915	0.10494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	6	0.46703	T	0.11	.	0.4254	0.00463	0.4119:0.1847:0.2238:0.1797	rs663651;rs1276248;rs1317106;rs60104088	222	Q9Y6X0-2	.	T	222	.	ENSP00000390687:A222T	A	+	1	0	SETBP1	40710651	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.969000	0.03813	-0.462000	0.06984	-0.254000	0.11334	GCA	G|0.471;A|0.529	0.529	strong		0.522	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
HCST	10870	hgsc.bcm.edu	37	19	36394678	36394678	+	Silent	SNP	T	T	C	rs8106495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36394678T>C	ENST00000246551.4	+	3	228	c.114T>C	c.(112-114)tcT>tcC	p.S38S	NFKBID_ENST00000606253.1_5'Flank|NFKBID_ENST00000352614.2_5'Flank|HCST_ENST00000437550.2_Silent_p.S38S			Q9UBK5	HCST_HUMAN	hematopoietic cell signal transducer	38					positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of immune response (GO:0050776)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase binding (GO:0043548)|receptor binding (GO:0005102)			lung(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCCAGGCTCTTGTTCCGGAT	0.662													C|||	468	0.0934505	0.2186	0.0331	5008	,	,		15383	0.1002		0.0089	False		,,,				2504	0.047				p.S38S		Atlas-SNP	.											.	HCST	10	.	0			c.T114C						PASS	.	C	,	879,3527	731.4+/-410.3	95,689,1419	42.0	36.0	38.0		114,114	3.4	1.0	19	dbSNP_116	38	120,8480	804.1+/-407.3	1,118,4181	yes	coding-synonymous,coding-synonymous	HCST	NM_001007469.1,NM_014266.3	,	96,807,5600	CC,CT,TT		1.3953,19.9501,7.6811	,	38/93,38/94	36394678	999,12007	2203	4300	6503	SO:0001819	synonymous_variant	10870	exon3			AGGCTCTTGTTCC	AF072844	CCDS32998.1, CCDS46057.1	19q13.1	2009-05-07	2003-10-14	2003-10-15	ENSG00000126264	ENSG00000126264			16977	protein-coding gene	gene with protein product	"""DNAX-activation protein 10"", ""kinase assoc pro of ~10kDa"""	604089	"""phosphoinositide-3-kinase adaptor protein"""	PIK3AP		10426994	Standard	NM_014266		Approved	DAP10, DKFZP586C1522, KAP10	uc002ocl.1	Q9UBK5	OTTHUMG00000048132	ENST00000246551.4:c.114T>C	19.37:g.36394678T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_001007469	Q9UBS1|Q9Y3Y0	Silent	SNP	ENST00000246551.4	37	CCDS32998.1																																																																																			T|0.912;C|0.088	0.088	strong		0.662	HCST-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109520.3	NM_014266	
CNOT3	4849	hgsc.bcm.edu	37	19	54656709	54656709	+	Silent	SNP	A	A	T	rs77902046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54656709A>T	ENST00000406403.1	+	15	3613	c.2010A>T	c.(2008-2010)acA>acT	p.T670T	CNOT3_ENST00000358389.3_Silent_p.T489T|CNOT3_ENST00000496327.1_3'UTR|CNOT3_ENST00000221232.5_Silent_p.T670T			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	670	Repressor domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGACCGAGACACTCTTCTTCA	0.687													A|||	193	0.0385383	0.0008	0.0288	5008	,	,		11766	0.0903		0.0268	False		,,,				2504	0.0552				p.T670T		Atlas-SNP	.											.	CNOT3	133	.	0			c.A2010T						PASS	.	A		14,4392	22.3+/-47.3	0,14,2189	128.0	128.0	128.0		2010	-1.9	1.0	19	dbSNP_131	128	237,8363	95.9+/-157.7	5,227,4068	no	coding-synonymous	CNOT3	NM_014516.3		5,241,6257	TT,TA,AA		2.7558,0.3177,1.9299		670/754	54656709	251,12755	2203	4300	6503	SO:0001819	synonymous_variant	4849	exon16			CGAGACACTCTTC	AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"""NOT3 (negative regulator of transcription 3, yeast) homolog"""	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.2010A>T	19.37:g.54656709A>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	145	60	0.413793	NM_014516	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	37	CCDS12880.1	106	0.048534798534798536	1	0.0020325203252032522	10	0.027624309392265192	71	0.12412587412587413	24	0.0316622691292876	A	10.23	1.291776	0.23564	0.003177	0.027558	ENSG00000088038	ENST00000457463	T	0.56776	0.44	3.08	-1.88	0.07713	.	0.000000	0.85682	D	0.000000	T	0.00695	0.0023	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.08166	-1.0735	6	0.59425	D	0.04	-9.6472	2.4993	0.04630	0.1732:0.4153:0.2717:0.1399	.	.	.	.	S	202	ENSP00000401703:T202S	ENSP00000401703:T202S	T	+	1	0	CNOT3	59348521	0.019000	0.18553	0.996000	0.52242	0.979000	0.70002	-1.599000	0.02085	-0.264000	0.09365	-0.379000	0.06801	ACT	A|0.973;T|0.027	0.027	strong		0.687	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516	
BRSK1	84446	hgsc.bcm.edu	37	19	55815159	55815159	+	Silent	SNP	C	C	A	rs17851415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55815159C>A	ENST00000309383.1	+	12	1528	c.1251C>A	c.(1249-1251)acC>acA	p.T417T	BRSK1_ENST00000326848.7_Silent_p.T112T|BRSK1_ENST00000590333.1_Silent_p.T433T	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	417					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CTGTACCCACCCGACGGGCCT	0.637													C|||	420	0.0838658	0.1452	0.0576	5008	,	,		15128	0.0883		0.0268	False		,,,				2504	0.0736				p.T417T		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1251A						PASS	.	C		529,3877		37,455,1711	39.0	45.0	43.0		1251	-1.2	1.0	19	dbSNP_123	43	311,8289		8,295,3997	no	coding-synonymous	BRSK1	NM_032430.1		45,750,5708	AA,AC,CC		3.6163,12.0064,6.4586		417/779	55815159	840,12166	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			ACCCACCCGACGG	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1251C>A	19.37:g.55815159C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.936;A|0.064	0.064	strong		0.637	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
ARSH	347527	hgsc.bcm.edu	37	X	2928170	2928170	+	Silent	SNP	C	C	T	rs77183343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	81	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	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	
DLX2	1746	hgsc.bcm.edu	37	2	172966250	172966250	+	Silent	SNP	T	T	C	rs2228184	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:172966250T>C	ENST00000234198.4	-	2	886	c.525A>G	c.(523-525)caA>caG	p.Q175Q	AC104801.1_ENST00000448117.1_lincRNA|DLX2_ENST00000466293.2_Silent_p.Q175Q	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	175					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			AGGCCAAGTATTGAGTCTTTT	0.637													T|||	1797	0.358826	0.1021	0.3098	5008	,	,		12417	0.6587		0.3907	False		,,,				2504	0.3988				p.Q175Q	GBM(188;775 2993 11256 23072)	Atlas-SNP	.											.	DLX2	29	.	0			c.A525G						PASS	.	T		682,3724	269.5+/-269.1	55,572,1576	27.0	28.0	27.0		525	-9.4	0.5	2	dbSNP_98	27	3404,5196	469.8+/-367.7	676,2052,1572	no	coding-synonymous	DLX2	NM_004405.3		731,2624,3148	CC,CT,TT		39.5814,15.4789,31.4163		175/329	172966250	4086,8920	2203	4300	6503	SO:0001819	synonymous_variant	1746	exon2			CAAGTATTGAGTC	U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.525A>G	2.37:g.172966250T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_004405	B4DMK4|B7ZA14	Silent	SNP	ENST00000234198.4	37	CCDS2248.1																																																																																			T|0.667;C|0.333	0.333	strong		0.637	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3		
UCP3	7352	hgsc.bcm.edu	37	11	73715542	73715542	+	Silent	SNP	G	G	A	rs2075577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73715542G>A	ENST00000314032.4	-	5	1182	c.630C>T	c.(628-630)taC>taT	p.Y210Y	UCP3_ENST00000348534.4_Intron|UCP3_ENST00000545271.1_5'Flank|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	117	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	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	
SLITRK6	84189	hgsc.bcm.edu	37	13	86370317	86370317	+	Silent	SNP	A	A	G	rs35119660	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:86370317A>G	ENST00000400286.2	-	2	925	c.327T>C	c.(325-327)aaT>aaC	p.N109N		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	109					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GGCCAAGGCCATTAAATGCAC	0.373													A|||	66	0.0131789	0.0318	0.0187	5008	,	,		19985	0.0		0.0099	False		,,,				2504	0.001				p.N109N		Atlas-SNP	.											SLITRK6,colon,carcinoma,-2,1	SLITRK6	150	1	0			c.T327C						PASS	.	A		126,3572		2,122,1725	139.0	129.0	132.0		327	3.8	1.0	13	dbSNP_126	132	144,8028		1,142,3943	no	coding-synonymous	SLITRK6	NM_032229.2		3,264,5668	GG,GA,AA		1.7621,3.4072,2.2746		109/842	86370317	270,11600	1849	4086	5935	SO:0001819	synonymous_variant	84189	exon2			AAGGCCATTAAAT	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.327T>C	13.37:g.86370317A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Silent	SNP	ENST00000400286.2	37	CCDS41903.1																																																																																			A|0.983;G|0.017	0.017	strong		0.373	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
MYRIP	25924	hgsc.bcm.edu	37	3	40231383	40231383	+	Missense_Mutation	SNP	C	C	T	rs55785561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:40231383C>T	ENST00000302541.6	+	10	1436	c.1094C>T	c.(1093-1095)cCc>cTc	p.P365L	MYRIP_ENST00000396217.3_Missense_Mutation_p.P276L|MYRIP_ENST00000539167.1_Missense_Mutation_p.P178L|MYRIP_ENST00000425621.1_Missense_Mutation_p.P365L|MYRIP_ENST00000444716.1_Missense_Mutation_p.P365L|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	365	Myosin-binding.		P -> L (in dbSNP:rs55785561).		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)		GCTCCACCCCCCACCCGACTA	0.622													C|||	480	0.0958466	0.031	0.0591	5008	,	,		15830	0.1994		0.0606	False		,,,				2504	0.1391				p.P365L		Atlas-SNP	.											.	MYRIP	98	.	0			c.C1094T						PASS	.	C	LEU/PRO	164,4242	109.9+/-148.2	2,160,2041	63.0	64.0	64.0		1094	3.0	0.1	3	dbSNP_129	64	596,8004	158.3+/-211.8	22,552,3726	yes	missense	MYRIP	NM_015460.2	98	24,712,5767	TT,TC,CC		6.9302,3.7222,5.8435	benign	365/860	40231383	760,12246	2203	4300	6503	SO:0001583	missense	25924	exon10			CACCCCCCACCCG	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.1094C>T	3.37:g.40231383C>T	ENSP00000301972:p.Pro365Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	192	0.08791208791208792	18	0.036585365853658534	22	0.06077348066298342	109	0.19055944055944055	43	0.05672823218997362	C	12.67	2.006561	0.35415	0.037222	0.069302	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84	5.94	3.0	0.34707	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.340989	0.31859	N	0.006960	T	0.00039	0.0001	L	0.43152	1.355	0.20975	P	0.999818001	P;P;P	0.51147	0.918;0.493;0.942	P;B;P	0.54856	0.762;0.372;0.76	T	0.06844	-1.0804	8	.	.	.	.	5.7865	0.18336	0.1456:0.6448:0.1284:0.0813	rs55785561	276;365;365	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	L	365;365;365;276;178	ENSP00000398665:P365L;ENSP00000301972:P365L;ENSP00000389323:P365L;ENSP00000379519:P276L;ENSP00000438297:P178L	.	P	+	2	0	MYRIP	40206387	0.715000	0.27946	0.105000	0.21289	0.008000	0.06430	1.341000	0.33907	1.528000	0.49103	-0.140000	0.14226	CCC	C|0.931;T|0.069	0.069	strong		0.622	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
DIS3	22894	hgsc.bcm.edu	37	13	73349359	73349359	+	Missense_Mutation	SNP	G	G	C	rs7332388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:73349359G>C	ENST00000377767.4	-	6	1077	c.977C>G	c.(976-978)aCa>aGa	p.T326R	DIS3_ENST00000545453.1_Missense_Mutation_p.T164R|DIS3_ENST00000377780.4_Missense_Mutation_p.T296R	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	205	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	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	
GPR155	151556	hgsc.bcm.edu	37	2	175300997	175300997	+	Silent	SNP	G	G	A	rs6757461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:175300997G>A	ENST00000392552.2	-	16	2698	c.2460C>T	c.(2458-2460)aaC>aaT	p.N820N	GPR155_ENST00000295500.4_Silent_p.N820N|GPR155_ENST00000392551.2_Silent_p.N820N|GPR155_ENST00000459996.1_5'Flank	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	127	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	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	
FAM161B	145483	hgsc.bcm.edu	37	14	74404756	74404756	+	Missense_Mutation	SNP	T	T	C	rs28927675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74404756T>C	ENST00000534936.1	-	6	1565	c.1460A>G	c.(1459-1461)aAa>aGa	p.K487R	FAM161B_ENST00000286544.3_Missense_Mutation_p.K550R|RP5-1021I20.5_ENST00000555916.1_RNA			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	487			K -> R (in dbSNP:rs28927675). {ECO:0000269|PubMed:14702039}.							breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						AGACTTCTTTTTGTGTATCTC	0.418													T|||	2040	0.407348	0.2179	0.4251	5008	,	,		20524	0.4583		0.4831	False		,,,				2504	0.5204				p.K550R		Atlas-SNP	.											.	FAM161B	67	.	0			c.A1649G						PASS	.	T	ARG/LYS	1015,3391	375.9+/-321.8	123,769,1311	171.0	166.0	168.0		1649	4.3	1.0	14	dbSNP_125	168	4054,4546	559.0+/-387.3	954,2146,1200	yes	missense	FAM161B	NM_152445.2	26	1077,2915,2511	CC,CT,TT		47.1395,23.0368,38.9743	possibly-damaging	550/711	74404756	5069,7937	2203	4300	6503	SO:0001583	missense	145483	exon6			TTCTTTTTGTGTA	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.1460A>G	14.37:g.74404756T>C	ENSP00000445326:p.Lys487Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	198	81	0.409091	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	37		933	0.4271978021978022	109	0.22154471544715448	163	0.45027624309392267	294	0.513986013986014	367	0.4841688654353562	T	11.84	1.759817	0.31137	0.230368	0.471395	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.23950	1.88;1.88	5.46	4.31	0.51392	.	0.340178	0.28268	N	0.015973	T	0.00012	0.0000	L	0.41573	1.285	0.29487	P	0.855927	P	0.41978	0.767	B	0.38683	0.279	T	0.48151	-0.9060	9	0.22109	T	0.4	-20.2077	9.6153	0.39687	0.0:0.1298:0.0:0.8702	rs28927675	487	Q96MY7	F161B_HUMAN	R	550;487	ENSP00000286544:K550R;ENSP00000445326:K487R	ENSP00000286544:K550R	K	-	2	0	FAM161B	73474509	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	1.109000	0.31135	2.291000	0.77112	0.533000	0.62120	AAA	T|0.585;C|0.415	0.415	strong		0.418	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
TP53BP2	7159	hgsc.bcm.edu	37	1	223985963	223985963	+	Missense_Mutation	SNP	C	C	G	rs61824007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223985963C>G	ENST00000343537.7	-	12	2193	c.1902G>C	c.(1900-1902)caG>caC	p.Q634H	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_Intron|TP53BP2_ENST00000391878.2_Missense_Mutation_p.Q505H	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	628					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)		TCAACGCGCTCTGCACAGCCT	0.473													C|||	18	0.00359425	0.0	0.0072	5008	,	,		20516	0.0		0.0129	False		,,,				2504	0.0				p.Q634H		Atlas-SNP	.											.	TP53BP2	144	.	0			c.G1902C						PASS	.	C	HIS/GLN,HIS/GLN	13,4393	20.2+/-43.8	0,13,2190	129.0	127.0	128.0		1902,1515	5.0	1.0	1	dbSNP_129	128	117,8483	61.7+/-123.6	0,117,4183	yes	missense,missense	TP53BP2	NM_001031685.2,NM_005426.2	24,24	0,130,6373	GG,GC,CC		1.3605,0.2951,0.9995	probably-damaging,probably-damaging	634/1135,505/1006	223985963	130,12876	2203	4300	6503	SO:0001583	missense	7159	exon12			CGCGCTCTGCACA	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.1902G>C	1.37:g.223985963C>G	ENSP00000341957:p.Gln634His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	13.03	2.114524	0.37339	0.002951	0.013605	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.48836	0.8;0.97	5.88	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.41961	1.31	0.80722	D	1	D;B	0.71674	0.998;0.23	D;B	0.79784	0.993;0.106	T	0.48163	-0.9059	10	0.22706	T	0.39	.	10.2673	0.43462	0.0:0.7947:0.0:0.2053	rs61824007	634;628	B4DG66;Q13625	.;ASPP2_HUMAN	H	505;634	ENSP00000375750:Q505H;ENSP00000341957:Q634H	ENSP00000341957:Q634H	Q	-	3	2	TP53BP2	222052586	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	2.476000	0.45171	1.496000	0.48567	-0.140000	0.14226	CAG	C|0.990;G|0.010	0.010	strong		0.473	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
DNAH17	8632	hgsc.bcm.edu	37	17	76525759	76525759	+	Missense_Mutation	SNP	G	G	C	rs61741523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76525759G>C	ENST00000585328.1	-	22	3417	c.3293C>G	c.(3292-3294)gCc>gGc	p.A1098G	DNAH17_ENST00000389840.5_Missense_Mutation_p.A1101G	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1101	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)			TTTCATGAAGGCTTCCAGGTC	0.597													G|||	633	0.126398	0.0159	0.1916	5008	,	,		20528	0.1081		0.173	False		,,,				2504	0.2004				p.A1101G		Atlas-SNP	.											.	DNAH17	347	.	0			c.C3302G						PASS	.	G	GLY/ALA	164,3728		5,154,1787	78.0	79.0	78.0		3302	1.4	0.6	17	dbSNP_129	78	1576,6692		168,1240,2726	yes	missense	DNAH17	NM_173628.3	60	173,1394,4513	CC,CG,GG		19.0614,4.2138,14.3092		1101/4463	76525759	1740,10420	1946	4134	6080	SO:0001583	missense	8632	exon22			ATGAAGGCTTCCA	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.3293C>G	17.37:g.76525759G>C	ENSP00000465516:p.Ala1098Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		288	0.13186813186813187	14	0.028455284552845527	75	0.20718232044198895	63	0.11013986013986014	136	0.17941952506596306	G	0.799	-0.756235	0.03019	0.042138	0.190614	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.24538	1.85	4.85	1.44	0.22558	.	.	.	.	.	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	.	.	.	.	.	.	T	0.41431	-0.9509	6	0.25751	T	0.34	.	9.5025	0.39026	0.0:0.1283:0.3819:0.4898	rs61741523	.	.	.	G	1098;1101	ENSP00000374490:A1101G	ENSP00000300671:A1098G	A	-	2	0	DNAH17	74037354	0.000000	0.05858	0.590000	0.28732	0.086000	0.17979	-0.369000	0.07533	0.404000	0.25506	-0.310000	0.09108	GCC	G|0.839;C|0.161	0.161	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
SPTA1	6708	hgsc.bcm.edu	37	1	158607935	158607935	+	Missense_Mutation	SNP	T	T	G	rs857725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0		WXS	Illumina HiSeq	Phase_I	94	32	0.340426	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	
SERPINA9	327657	hgsc.bcm.edu	37	14	94935901	94935901	+	Missense_Mutation	SNP	G	G	C	rs12879019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:94935901G>C	ENST00000380365.3	-	2	355	c.277C>G	c.(277-279)Cag>Gag	p.Q93E	SERPINA9_ENST00000298845.7_Intron|SERPINA9_ENST00000448305.2_Missense_Mutation_p.Q13E|SERPINA9_ENST00000337425.5_Missense_Mutation_p.Q111E|SERPINA9_ENST00000546329.1_Missense_Mutation_p.Q75E|SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000539349.1_5'Flank			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	93				Q -> E (in Ref. 4; BAG62686). {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)		TGGAGAATCTGGGTCTTGGTG	0.577													G|||	893	0.178315	0.0106	0.1787	5008	,	,		18172	0.3472		0.2356	False		,,,				2504	0.1718				p.Q111E		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C331G						PASS	.	G	,GLU/GLN	184,4086		4,176,1955	77.0	83.0	81.0		,331	4.1	1.0	14	dbSNP_121	81	1745,6787		192,1361,2713	yes	intron,missense	SERPINA9	NM_001042518.1,NM_175739.3	,29	196,1537,4668	CC,CG,GG		20.4524,4.3091,15.068	,benign	,111/436	94935901	1929,10873	2135	4266	6401	SO:0001583	missense	327657	exon2			GAATCTGGGTCTT	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.277C>G	14.37:g.94935901G>C	ENSP00000369723:p.Gln93Glu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		446	0.2042124542124542	7	0.014227642276422764	71	0.19613259668508287	192	0.3356643356643357	176	0.23218997361477572	G	10.76	1.441231	0.25900	0.043091	0.204524	ENSG00000170054	ENST00000448305;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37	4.12	4.12	0.48240	Serpin domain (3);	0.110623	0.39341	U	0.001386	T	0.00012	0.0000	L	0.53780	1.695	0.29507	P	0.854496	P;P;P;P	0.48230	0.907;0.837;0.907;0.805	P;P;P;P	0.53593	0.664;0.669;0.517;0.73	T	0.51795	-0.8660	9	0.02654	T	1	.	13.3858	0.60795	0.0:0.1591:0.8409:0.0	rs12879019;rs17825566;rs52793329;rs12879019	75;93;13;111	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7	.;SPA9_HUMAN;.;.	E	13;111;93;75	ENSP00000414092:Q13E;ENSP00000337133:Q111E;ENSP00000369723:Q93E;ENSP00000445476:Q75E	ENSP00000337133:Q111E	Q	-	1	0	SERPINA9	94005654	1.000000	0.71417	0.991000	0.47740	0.803000	0.45373	4.681000	0.61663	2.014000	0.59158	0.462000	0.41574	CAG	G|0.779;C|0.221	0.221	strong		0.577	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
HLA-C	3107	hgsc.bcm.edu	37	6	31239621	31239621	+	Missense_Mutation	SNP	T	T	A	rs1071650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31239621T>A	ENST00000376228.5	-	2	112	c.98A>T	c.(97-99)gAc>gTc	p.D33V	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	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						CACGGCGGTGTCGAAATACCT	0.726													t|||	342	0.0682907	0.0053	0.098	5008	,	,		11351	0.1895		0.0368	False		,,,				2504	0.0399				p.D33V		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,-1,2	HLA-C	92	2	0			c.A98T						scavenged	.						17.0	17.0	17.0					6																	31239621		1474	2673	4147	SO:0001583	missense	3107	exon2			GCGGTGTCGAAAT	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.98A>T	6.37:g.31239621T>A	ENSP00000365402:p.Asp33Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	t	9.181	1.023660	0.19433	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00008	9.56;9.56	2.16	-4.05	0.03998	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	10.311600	0.00879	U	0.002109	T	0.00073	0.0002	M	0.79926	2.475	0.09310	N	1	P;B;B;P	0.37708	0.606;0.175;0.175;0.468	P;P;B;P	0.52454	0.59;0.59;0.426;0.699	T	0.17289	-1.0374	10	0.87932	D	0	.	3.4331	0.07436	0.2114:0.443:0.0:0.3456	rs1071650;rs1071739;rs1131149;rs1131150;rs2234796;rs3177896;rs3190763;rs3190765;rs3190810;rs3190811;rs3200098;rs3206397;rs11547355;rs17362036;rs17366179;rs3190764	33;33;33;33	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	V	33;33;33;70	ENSP00000365402:D33V;ENSP00000372819:D33V	ENSP00000365402:D33V	D	-	2	0	HLA-C	31347600	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.960000	0.00673	-1.035000	0.03291	-0.756000	0.03474	GAC	T|0.936;G|0.058;A|0.007	0.007	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
COL18A1	80781	hgsc.bcm.edu	37	21	46899857	46899857	+	Silent	SNP	C	C	T	rs1131101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46899857C>T	ENST00000359759.4	+	9	2556	c.2535C>T	c.(2533-2535)gaC>gaT	p.D845D	COL18A1_ENST00000400337.2_Silent_p.D430D|COL18A1_ENST00000355480.5_Silent_p.D610D			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	845	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)		CTCCAGGGGACGTAGGTCCCA	0.692													C|||	788	0.157348	0.2874	0.0735	5008	,	,		16974	0.1081		0.0696	False		,,,				2504	0.182				p.D610D		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1830T						PASS	.	C	,	1059,2917		135,789,1064	61.0	73.0	69.0		1830,1290	-1.8	0.6	21	dbSNP_86	69	547,7773		18,511,3631	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	153,1300,4695	TT,TC,CC		6.5745,26.6348,13.0612	,	610/1520,430/1340	46899857	1606,10690	1988	4160	6148	SO:0001819	synonymous_variant	80781	exon9			AGGGGACGTAGGT		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.2535C>T	21.37:g.46899857C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.888;T|0.112	0.112	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
FAM208A	23272	hgsc.bcm.edu	37	3	56716922	56716922	+	Missense_Mutation	SNP	T	T	G	rs958755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56716922T>G	ENST00000493960.2	-	1	123	c.113A>C	c.(112-114)cAa>cCa	p.Q38P	FAM208A_ENST00000355628.5_Missense_Mutation_p.Q38P	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	38			Q -> P (in dbSNP:rs958755).				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						GCCATTTTGTTGGGAGGACTC	0.697													G|||	3928	0.784345	0.9259	0.7147	5008	,	,		12874	0.9514		0.4592	False		,,,				2504	0.8047				p.Q38P		Atlas-SNP	.											.	FAM208A	113	.	0			c.A113C						PASS	.	G	PRO/GLN	1142,218		491,160,29	5.0	6.0	6.0		113	3.5	1.0	3	dbSNP_86	6	1433,1719		368,697,511	yes	missense	FAM208A	NM_001112736.1	76	859,857,540	GG,GT,TT		45.4632,16.0294,42.93	benign	38/1513	56716922	2575,1937	680	1576	2256	SO:0001583	missense	23272	exon1			TTTTGTTGGGAGG	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.113A>C	3.37:g.56716922T>G	ENSP00000417509:p.Gln38Pro	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	1567	0.7174908424908425	450	0.9146341463414634	243	0.6712707182320442	538	0.9405594405594405	336	0.44327176781002636	G	10.72	1.430635	0.25726	0.839706	0.454632	ENSG00000163946	ENST00000493960;ENST00000355628	T;T	0.09723	2.95;2.96	4.37	3.47	0.39725	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52501	P	4.4000000000044004E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14896	-1.0456	8	0.25106	T	0.35	.	6.8312	0.23911	0.0931:0.0:0.7325:0.1745	rs958755;rs52796415;rs57994579;rs958755	38;38	Q9UK61-3;Q9UK61-4	.;.	P	38	ENSP00000417509:Q38P;ENSP00000347845:Q38P	ENSP00000347845:Q38P	Q	-	2	0	C3orf63	56691962	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	1.260000	0.32968	0.571000	0.29365	-0.285000	0.09966	CAA	T|0.246;G|0.754	0.754	strong		0.697	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
ZNF439	90594	hgsc.bcm.edu	37	19	11979164	11979164	+	Missense_Mutation	SNP	T	T	C	rs10500209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11979164T>C	ENST00000304030.2	+	3	1480	c.1280T>C	c.(1279-1281)tTg>tCg	p.L427S	ZNF439_ENST00000455282.1_Missense_Mutation_p.L291S|ZNF439_ENST00000592534.1_Intron	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	45	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	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		
C9orf84	158401	hgsc.bcm.edu	37	9	114484837	114484837	+	Silent	SNP	G	G	T	rs62569959	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:114484837G>T	ENST00000318737.4	-	13	1919	c.1791C>A	c.(1789-1791)ctC>ctA	p.L597L	C9orf84_ENST00000394779.3_Silent_p.L558L|C9orf84_ENST00000394777.4_Silent_p.L558L|C9orf84_ENST00000374287.3_Silent_p.L597L	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	47	24	0.510638	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	
UNC5C	8633	hgsc.bcm.edu	37	4	96140151	96140151	+	Silent	SNP	C	C	T	rs61741188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:96140151C>T	ENST00000453304.1	-	9	1962	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	UNC5C_ENST00000506749.1_Silent_p.S557S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	538	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)		GACCTCCCAGCGAGTTGAAGC	0.443													C|||	151	0.0301518	0.0318	0.0202	5008	,	,		20428	0.0		0.0219	False		,,,				2504	0.0746				p.S538S		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1614A						PASS	.	C		134,4272	98.5+/-137.1	0,134,2069	108.0	86.0	94.0		1614	-1.9	0.9	4	dbSNP_129	94	231,8369	94.0+/-155.9	3,225,4072	no	coding-synonymous	UNC5C	NM_003728.3		3,359,6141	TT,TC,CC		2.686,3.0413,2.8064		538/932	96140151	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon9			TCCCAGCGAGTTG	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.1614G>A	4.37:g.96140151C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.977;T|0.023	0.023	strong		0.443	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
MYH14	79784	hgsc.bcm.edu	37	19	50771609	50771609	+	Silent	SNP	G	G	A	rs3745504	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50771609G>A	ENST00000596571.1	+	21	2895	c.2895G>A	c.(2893-2895)ctG>ctA	p.L965L	MYH14_ENST00000376970.2_Silent_p.L998L|MYH14_ENST00000425460.1_Silent_p.L973L|MYH14_ENST00000601313.1_Silent_p.L1006L|MYH14_ENST00000598205.1_Silent_p.L973L|MYH14_ENST00000440075.2_Silent_p.L1006L|MYH14_ENST00000262269.8_Silent_p.L1006L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	965					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)		AGAAGAGGCTGCAGCAGCACA	0.607													G|||	2426	0.484425	0.4221	0.6873	5008	,	,		15070	0.3829		0.5905	False		,,,				2504	0.4202				p.L1006L		Atlas-SNP	.											.	MYH14	261	.	0			c.G3018A						PASS	.	G	,,	1972,2276		477,1018,629	32.0	43.0	40.0		2919,3018,2895	3.9	1.0	19	dbSNP_107	40	4782,3680		1368,2046,817	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	1845,3064,1446	AA,AG,GG		43.4885,46.4218,46.8607	,,	973/2004,1006/2037,965/1996	50771609	6754,5956	2124	4231	6355	SO:0001819	synonymous_variant	79784	exon24			GAGGCTGCAGCAG	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.2895G>A	19.37:g.50771609G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			G|0.514;A|0.486	0.486	strong		0.607	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
F11	2160	hgsc.bcm.edu	37	4	187205301	187205301	+	Silent	SNP	T	T	C	rs5970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187205301T>C	ENST00000403665.2	+	11	1543	c.1191T>C	c.(1189-1191)ggT>ggC	p.G397G	F11-AS1_ENST00000505103.1_RNA|F11_ENST00000264692.4_Silent_p.G345G	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	397	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	CTGTTCGTGGTGAGTGGCCGT	0.527													T|||	848	0.169329	0.2587	0.1369	5008	,	,		17990	0.0387		0.166	False		,,,				2504	0.2096				p.G397G		Atlas-SNP	.											.	F11	65	.	0			c.T1191C						PASS	.	T		947,3459	358.9+/-314.6	108,731,1364	145.0	130.0	135.0		1191	-9.9	0.0	4	dbSNP_52	135	1224,7376	245.8+/-274.5	91,1042,3167	no	coding-synonymous	F11	NM_000128.3		199,1773,4531	CC,CT,TT		14.2326,21.4934,16.6923		397/626	187205301	2171,10835	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon11			TCGTGGTGAGTGG	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.1191T>C	4.37:g.187205301T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1																																																																																			T|0.839;C|0.161	0.161	strong		0.527	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
HNRNPLL	92906	hgsc.bcm.edu	37	2	38829682	38829682	+	Silent	SNP	C	C	T	rs13028141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:38829682C>T	ENST00000449105.3	-	1	426	c.87G>A	c.(85-87)gaG>gaA	p.E29E	HNRNPLL_ENST00000498516.1_5'UTR|AC011247.3_ENST00000457097.1_RNA|HNRNPLL_ENST00000378915.3_Silent_p.E29E|HNRNPLL_ENST00000409636.1_Silent_p.E24E|HNRNPLL_ENST00000358367.4_Silent_p.E29E|HNRNPLL_ENST00000608859.1_Silent_p.E29E|HNRNPLL_ENST00000410076.1_Silent_p.E24E|HNRNPLL_ENST00000409328.1_Silent_p.E29E			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	29					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										CGATCTCCCCCTCCTCGGTCT	0.716													C|||	8	0.00159744	0.0	0.0	5008	,	,		11134	0.0		0.008	False		,,,				2504	0.0				p.E29E		Atlas-SNP	.											.	HNRPLL	19	.	0			c.G87A						PASS	.	C	,	3,4307		0,3,2152	27.0	21.0	23.0		72,87	1.1	1.0	2	dbSNP_121	23	29,8449		0,29,4210	no	coding-synonymous,coding-synonymous	HNRPLL	NM_001142650.1,NM_138394.3	,	0,32,6362	TT,TC,CC		0.3421,0.0696,0.2502	,	24/538,29/543	38829682	32,12756	2155	4239	6394	SO:0001819	synonymous_variant	92906	exon1			CTCCCCCTCCTCG	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"""RNA binding motif (RRM) containing"""	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.87G>A	2.37:g.38829682C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Silent	SNP	ENST00000449105.3	37																																																																																				C|0.997;T|0.003	0.003	strong		0.716	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394	
WDR92	116143	hgsc.bcm.edu	37	2	68361859	68361859	+	Missense_Mutation	SNP	C	C	T	rs138784630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68361859C>T	ENST00000295121.6	-	7	957	c.841G>A	c.(841-843)Gcc>Acc	p.A281T	WDR92_ENST00000409164.1_Missense_Mutation_p.A281T|RP11-474G23.1_ENST00000406334.3_3'UTR|WDR92_ENST00000492039.2_5'UTR|WDR92_ENST00000406245.2_Missense_Mutation_p.A180T	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	281					apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)			endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						AGGCCGCCGGCGCCTCCAGCT	0.488													C|||	36	0.0071885	0.0008	0.0058	5008	,	,		14412	0.0		0.0169	False		,,,				2504	0.0143				p.A281T		Atlas-SNP	.											WDR92,colon,carcinoma,+2,1	WDR92	21	1	0			c.G841A						PASS	.	C	THR/ALA	17,4389	24.3+/-50.5	0,17,2186	48.0	52.0	51.0		841	4.5	1.0	2	dbSNP_134	51	139,8461	68.7+/-131.2	1,137,4162	yes	missense	WDR92	NM_138458.2	58	1,154,6348	TT,TC,CC		1.6163,0.3858,1.1994	benign	281/358	68361859	156,12850	2203	4300	6503	SO:0001583	missense	116143	exon7			CGCCGGCGCCTCC	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"""WD repeat domain containing"""	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.841G>A	2.37:g.68361859C>T	ENSP00000295121:p.Ala281Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_001256476	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	37	CCDS1884.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	12.41	1.928147	0.34002	0.003858	0.016163	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	T;T;T	0.65178	1.6;1.6;-0.14	5.35	4.48	0.54585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.169183	0.35903	N	0.002917	T	0.26629	0.0651	N	0.16743	0.435	0.80722	D	1	B	0.13145	0.007	B	0.04013	0.001	T	0.14337	-1.0476	10	0.30078	T	0.28	.	9.299	0.37833	0.1426:0.7827:0.0:0.0747	.	281	Q96MX6	WDR92_HUMAN	T	281;180;281	ENSP00000295121:A281T;ENSP00000384518:A180T;ENSP00000386746:A281T	ENSP00000295121:A281T	A	-	1	0	WDR92	68215363	0.941000	0.31946	0.988000	0.46212	0.994000	0.84299	2.043000	0.41231	1.393000	0.46605	0.655000	0.94253	GCC	C|0.989;T|0.011	0.011	strong		0.488	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458	
HLA-A	3105	hgsc.bcm.edu	37	6	29910730	29910730	+	Missense_Mutation	SNP	T	T	A	rs199474436|rs281864737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910730T>A	ENST00000396634.1	+	4	611	c.270T>A	c.(268-270)aaT>aaA	p.N90K	HLA-A_ENST00000376806.5_Missense_Mutation_p.N90K|HLA-A_ENST00000376809.5_Missense_Mutation_p.N90K|HLA-A_ENST00000376802.2_Missense_Mutation_p.N90K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	90	Alpha-1.		N -> K (in allele A*31:02).		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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGACACGGAATGTGAAGGCCC	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1976	0.394569	0.3003	0.5086	5008	,	,		10700	0.4891		0.4215	False		,,,				2504	0.316				p.N90K		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.T270A						scavenged	.						80.0	84.0	82.0					6																	29910730		2199	4290	6489	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACGGAATGTGAAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.270T>A	6.37:g.29910730T>A	ENSP00000379873:p.Asn90Lys	Somatic	146	3	0.0205479		WXS	Illumina HiSeq	Phase_I	202	43	0.212871	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	837	0.38324175824175827	122	0.24796747967479674	151	0.4171270718232044	275	0.4807692307692308	289	0.3812664907651715	.	8.031	0.761803	0.15914	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.48;9.48;9.48;9.48	3.48	-6.97	0.01616	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	7739.210000	0.00166	N	0.000013	T	0.00012	0.0000	N	0.25031	0.7	0.80722	P	0.0	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.0	B;B;B;B;B	0.17722	0.006;0.011;0.006;0.019;0.006	T	0.22243	-1.0222	9	0.02654	T	1	.	3.5967	0.08009	0.5715:0.2096:0.122:0.0969	rs1059460;rs2230995;rs3173426;rs16868229;rs41558518	90;90;90;90;90	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	90	ENSP00000379873:N90K;ENSP00000366002:N90K;ENSP00000366005:N90K;ENSP00000365998:N90K	ENSP00000348012:N90K	N	+	3	2	HLA-A	30018709	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.261000	0.00536	-1.477000	0.01872	-2.887000	0.00096	AAT	A|0.321;T|0.679	0.321	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
AJAP1	55966	hgsc.bcm.edu	37	1	4772053	4772053	+	Silent	SNP	T	T	C	rs1061968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:4772053T>C	ENST00000378191.4	+	2	504	c.123T>C	c.(121-123)tgT>tgC	p.C41C	AJAP1_ENST00000466761.1_3'UTR|AJAP1_ENST00000378190.3_Silent_p.C41C	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	41					cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		TGCCCGCCTGTGAGGCCCTGG	0.716													C|||	2638	0.526757	0.5212	0.5014	5008	,	,		10861	0.6567		0.3668	False		,,,				2504	0.5828				p.C41C		Atlas-SNP	.											AJAP1,NS,carcinoma,0,1	AJAP1	68	1	0			c.T123C						PASS	.	C	,	2212,2168		585,1042,563	54.0	74.0	67.0		123,123	-0.2	0.8	1	dbSNP_86	67	3110,5456		593,1924,1766	no	coding-synonymous,coding-synonymous	AJAP1	NM_001042478.1,NM_018836.3	,	1178,2966,2329	CC,CT,TT		36.3063,49.4977,41.1092	,	41/412,41/412	4772053	5322,7624	2190	4283	6473	SO:0001819	synonymous_variant	55966	exon2			CGCCTGTGAGGCC	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"""transmembrane protein SHREW1"""	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.123T>C	1.37:g.4772053T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_018836	Q9Y229	Silent	SNP	ENST00000378191.4	37	CCDS54.1																																																																																			T|0.549;C|0.451	0.451	strong		0.716	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836	
FSCB	84075	hgsc.bcm.edu	37	14	44975510	44975510	+	Silent	SNP	C	C	T	rs372153461|rs3809430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:44975510C>T	ENST00000340446.4	-	1	972	c.681G>A	c.(679-681)ccG>ccA	p.P227P	RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	227						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CTAAAAGTACCGGGGGACCTT	0.403													C|||	1625	0.324481	0.2284	0.33	5008	,	,		18394	0.3859		0.3479	False		,,,				2504	0.363				p.P227P		Atlas-SNP	.											.	FSCB	173	.	0			c.G681A						PASS	.	C		1065,3341	384.9+/-325.5	131,803,1269	96.0	99.0	98.0		681	-8.2	0.0	14	dbSNP_107	98	3204,5396	484.5+/-371.4	627,1950,1723	no	coding-synonymous	FSCB	NM_032135.3		758,2753,2992	TT,TC,CC		37.2558,24.1716,32.8233		227/826	44975510	4269,8737	2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			AAGTACCGGGGGA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.681G>A	14.37:g.44975510C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			C|0.674;T|0.326	0.326	strong		0.403	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
ILK	3611	hgsc.bcm.edu	37	11	6631016	6631016	+	Silent	SNP	C	C	T	rs2292195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6631016C>T	ENST00000396751.2	+	9	1374	c.918C>T	c.(916-918)gcC>gcT	p.A306A	ILK_ENST00000537806.1_Silent_p.A172A|ILK_ENST00000526711.1_3'UTR|TAF10_ENST00000531760.1_5'Flank|RP11-732A19.2_ENST00000527398.1_RNA|ILK_ENST00000528995.1_Silent_p.A245A|ILK_ENST00000420936.2_Silent_p.A306A|ILK_ENST00000299421.4_Silent_p.A306A	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	306	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)		GGGGCATGGCCTTCCTACACA	0.547													C|||	802	0.160144	0.1256	0.2219	5008	,	,		21063	0.0833		0.2575	False		,,,				2504	0.1421				p.A306A		Atlas-SNP	.											.	ILK	41	.	0			c.C918T						PASS	.	C	,,	680,3722	286.6+/-278.8	52,576,1573	136.0	120.0	126.0		918,918,918	0.7	1.0	11	dbSNP_100	126	2274,6318	384.7+/-341.2	310,1654,2332	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	362,2230,3905	TT,TC,CC		26.4665,15.4475,22.7336	,,	306/453,306/453,306/453	6631016	2954,10040	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon10			CATGGCCTTCCTA	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.918C>T	11.37:g.6631016C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			C|0.793;T|0.207	0.207	strong		0.547	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
MYOM1	8736	hgsc.bcm.edu	37	18	3215030	3215030	+	Silent	SNP	C	C	A	rs9964300	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:3215030C>A	ENST00000356443.4	-	2	525	c.192G>T	c.(190-192)gcG>gcT	p.A64A	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000261606.7_Silent_p.A64A|MYOM1_ENST00000400569.3_Silent_p.A64A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	64					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						AGGAGGCGGACGCCCGACGGA	0.687													C|||	366	0.0730831	0.1505	0.0994	5008	,	,		14216	0.0119		0.0547	False		,,,				2504	0.0317				p.A64A		Atlas-SNP	.											.	MYOM1	192	.	0			c.G192T						PASS	.	C	,	473,3599		31,411,1594	28.0	33.0	31.0		192,192	-4.2	0.0	18	dbSNP_119	31	474,7914		11,452,3731	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	42,863,5325	AA,AC,CC		5.6509,11.6159,7.6003	,	64/1686,64/1590	3215030	947,11513	2036	4194	6230	SO:0001819	synonymous_variant	8736	exon2			GGCGGACGCCCGA	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.192G>T	18.37:g.3215030C>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.932;A|0.068	0.068	strong		0.687	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
GIF	2694	hgsc.bcm.edu	37	11	59611362	59611362	+	Silent	SNP	G	G	A	rs35792306	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:59611362G>A	ENST00000257248.2	-	2	293	c.246C>T	c.(244-246)agC>agT	p.S82S	GIF_ENST00000541311.1_Silent_p.S57S	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	82					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)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	CGTTGTTGTCGCTGGACATGA	0.547													G|||	269	0.0537141	0.003	0.0259	5008	,	,		19218	0.0952		0.0785	False		,,,				2504	0.0736				p.S82S	NSCLC(53;1139 1245 16872 38474 42853)	Atlas-SNP	.											.	GIF	43	.	0			c.C246T						PASS	.	G		84,4318	72.0+/-110.0	1,82,2118	100.0	87.0	91.0		246	-0.0	0.8	11	dbSNP_126	91	680,7910	169.7+/-221.0	24,632,3639	no	coding-synonymous	GIF	NM_005142.2		25,714,5757	AA,AG,GG		7.9162,1.9082,5.8805		82/418	59611362	764,12228	2201	4295	6496	SO:0001819	synonymous_variant	2694	exon2			GTTGTCGCTGGAC	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.246C>T	11.37:g.59611362G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_005142	B2RAN8|B4DVZ1	Silent	SNP	ENST00000257248.2	37	CCDS7977.1																																																																																			G|0.937;A|0.063	0.063	strong		0.547	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18504916	18504916	+	Silent	SNP	T	T	A	rs2277160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:18504916T>A	ENST00000380548.4	+	2	492	c.153T>A	c.(151-153)ggT>ggA	p.G51G	ADAMTSL1_ENST00000431052.2_Silent_p.G51G|ADAMTSL1_ENST00000380570.4_Silent_p.G51G|ADAMTSL1_ENST00000276935.6_Silent_p.G51G|ADAMTSL1_ENST00000327883.7_Silent_p.G51G|ADAMTSL1_ENST00000380566.4_Silent_p.G51G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	51	TSP type-1 1. {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)		CCTGCGGGGGTGGGGCCTCCT	0.627													A|||	2859	0.570887	0.6725	0.5418	5008	,	,		16226	0.4444		0.5755	False		,,,				2504	0.5798				p.G51G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.T153A						PASS	.	A	,	2876,1530	481.9+/-359.3	952,972,279	41.0	44.0	43.0		153,153	0.1	0.7	9	dbSNP_100	43	4844,3756	530.6+/-381.8	1368,2108,824	no	coding-synonymous,coding-synonymous	ADAMTSL1	NM_001040272.5,NM_052866.4	,	2320,3080,1103	AA,AT,TT		43.6744,34.7254,40.6428	,	51/1763,51/526	18504916	7720,5286	2203	4300	6503	SO:0001819	synonymous_variant	92949	exon2			CGGGGGTGGGGCC	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.153T>A	9.37:g.18504916T>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			T|0.415;A|0.585	0.585	strong		0.627	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
DAW1	164781	hgsc.bcm.edu	37	2	228758580	228758580	+	Silent	SNP	G	G	C	rs16824157	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:228758580G>C	ENST00000309931.2	+	5	470	c.387G>C	c.(385-387)acG>acC	p.T129T	DAW1_ENST00000373666.2_Silent_p.T129T|DAW1_ENST00000472604.1_3'UTR|DAW1_ENST00000545118.1_Silent_p.T114T	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	129			T -> M (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cilium (GO:0005929)											AGCTGAACACGCTGGAGGGCC	0.448													C|||	349	0.0696885	0.0817	0.0447	5008	,	,		19046	0.0734		0.0686	False		,,,				2504	0.0685				p.T129T		Atlas-SNP	.											WDR69,colon,carcinoma,+1,2	.	.	2	0			c.G387C						PASS	.	C		327,4079	796.0+/-415.3	20,287,1896	110.0	99.0	103.0		387	-5.5	0.9	2	dbSNP_123	103	553,8047	793.9+/-407.5	23,507,3770	no	coding-synonymous	WDR69	NM_178821.1		43,794,5666	CC,CG,GG		6.4302,7.4217,6.7661		129/416	228758580	880,12126	2203	4300	6503	SO:0001819	synonymous_variant	164781	exon5			GAACACGCTGGAG		CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"""WD repeat domain containing"""	26383	protein-coding gene	gene with protein product	"""outer row dynein assembly 16 homolog (Chlamydomonas)"""		"""WD repeat domain 69"""	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.387G>C	2.37:g.228758580G>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_178821	Q6ZRY1|Q8N776	Silent	SNP	ENST00000309931.2	37	CCDS2470.1																																																																																			G|0.928;C|0.072	0.072	strong		0.448	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821	
CA10	56934	hgsc.bcm.edu	37	17	49713300	49713300	+	Silent	SNP	G	G	A	rs11870209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:49713300G>A	ENST00000285273.4	-	8	1816	c.705C>T	c.(703-705)taC>taT	p.Y235Y	CA10_ENST00000571918.1_5'UTR|CA10_ENST00000442502.2_Silent_p.Y235Y|CA10_ENST00000570565.1_Silent_p.Y160Y|CA10_ENST00000451037.2_Silent_p.Y235Y|CA10_ENST00000340813.6_Silent_p.Y241Y	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	235					brain development (GO:0007420)			p.Y235Y(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TCGACCCATCGTAAGTGATGA	0.403													G|||	1823	0.364018	0.2481	0.4496	5008	,	,		18533	0.3442		0.4911	False		,,,				2504	0.3497				p.Y235Y		Atlas-SNP	.											CA10,NS,carcinoma,0,2	CA10	84	2	1	Substitution - coding silent(1)	stomach(1)	c.C705T						PASS	.	G	,,	1231,3175	428.7+/-342.0	182,867,1154	116.0	106.0	109.0		705,705,705	-9.6	0.5	17	dbSNP_120	109	4165,4435	568.5+/-389.0	1014,2137,1149	no	coding-synonymous,coding-synonymous,coding-synonymous	CA10	NM_001082533.1,NM_001082534.1,NM_020178.4	,,	1196,3004,2303	AA,AG,GG		48.4302,27.9392,41.4885	,,	235/329,235/329,235/329	49713300	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	56934	exon8			CCCATCGTAAGTG	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.705C>T	17.37:g.49713300G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001082534	B2R7J0|B4DGL6	Silent	SNP	ENST00000285273.4	37	CCDS32684.1																																																																																			G|0.606;A|0.394	0.394	strong		0.403	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178	
AP4M1	9179	hgsc.bcm.edu	37	7	99704104	99704104	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99704104G>A	ENST00000359593.4	+	14	1262	c.1104G>A	c.(1102-1104)gtG>gtA	p.V368V	AP4M1_ENST00000421755.1_Silent_p.V368V|AP4M1_ENST00000422582.1_Silent_p.V240V|AP4M1_ENST00000429084.1_Silent_p.V375V	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	368	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGCCTCGGGTGCAAGGAGGCT	0.632																																					p.V368V	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.G1104A						PASS	.						42.0	45.0	44.0					7																	99704104		2203	4300	6503	SO:0001819	synonymous_variant	9179	exon14			TCGGGTGCAAGGA	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.1104G>A	7.37:g.99704104G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Silent	SNP	ENST00000359593.4	37	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	G	9.825	1.186877	0.21870	.	.	ENSG00000221838	ENST00000445295	.	.	.	4.81	-3.93	0.04143	.	.	.	.	.	T	0.36248	0.0960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33343	-0.9872	4	.	.	.	-22.5569	0.9269	0.01327	0.4879:0.1198:0.1523:0.2401	.	.	.	.	Y	94	.	.	C	+	2	0	AP4M1	99542040	0.957000	0.32711	0.976000	0.42696	0.997000	0.91878	0.023000	0.13533	-0.749000	0.04747	0.561000	0.74099	TGC	.	.	none		0.632	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
ITGB4	3691	hgsc.bcm.edu	37	17	73732428	73732428	+	Silent	SNP	G	G	A	rs2290460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73732428G>A	ENST00000200181.3	+	15	2008	c.1821G>A	c.(1819-1821)tcG>tcA	p.S607S	ITGB4_ENST00000449880.2_Silent_p.S607S|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000579662.1_Silent_p.S607S|ITGB4_ENST00000339591.3_Silent_p.S607S|ITGB4_ENST00000450894.3_Silent_p.S607S	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	607	Cysteine-rich tandem repeats.				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)			ACCAGCAGTCGCTCTACACGG	0.637													G|||	733	0.146366	0.084	0.1758	5008	,	,		20530	0.2788		0.0099	False		,,,				2504	0.2137				p.S607S		Atlas-SNP	.											.	ITGB4	165	.	0			c.G1821A						PASS	.	G	,,	347,4059	181.2+/-209.3	13,321,1869	81.0	83.0	82.0		1821,1821,1821	-9.2	0.9	17	dbSNP_100	82	120,8480	63.1+/-125.2	2,116,4182	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	15,437,6051	AA,AG,GG		1.3953,7.8756,3.5907	,,	607/1823,607/1806,607/1753	73732428	467,12539	2203	4300	6503	SO:0001819	synonymous_variant	3691	exon15			GCAGTCGCTCTAC		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.1821G>A	17.37:g.73732428G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			G|0.932;A|0.068	0.068	strong		0.637	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
PYROXD2	84795	hgsc.bcm.edu	37	10	100148176	100148176	+	Missense_Mutation	SNP	A	A	G	rs2147896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100148176A>G	ENST00000370575.4	-	13	1430	c.1382T>C	c.(1381-1383)aTg>aCg	p.M461T	PYROXD2_ENST00000483923.1_Intron	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	461			M -> T (in dbSNP:rs2147896). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CGTATAGGGCATGTACTGAGT	0.607													G|||	3003	0.599641	0.8752	0.5418	5008	,	,		19828	0.5833		0.3479	False		,,,				2504	0.544				p.M461T		Atlas-SNP	.											.	PYROXD2	43	.	0			c.T1382C						PASS	.	G	THR/MET	3380,1026	379.2+/-323.2	1312,756,135	70.0	58.0	62.0		1382	4.9	1.0	10	dbSNP_96	62	3079,5521	659.9+/-401.7	579,1921,1800	yes	missense	PYROXD2	NM_032709.2	81	1891,2677,1935	GG,GA,AA		35.8023,23.2864,49.6617	benign	461/582	100148176	6459,6547	2203	4300	6503	SO:0001583	missense	84795	exon13			TAGGGCATGTACT	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1382T>C	10.37:g.100148176A>G	ENSP00000359607:p.Met461Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Missense_Mutation	SNP	ENST00000370575.4	37	CCDS7474.1	1215	0.5563186813186813	430	0.8739837398373984	183	0.505524861878453	335	0.5856643356643356	267	0.35224274406332456	G	0.834	-0.744101	0.03088	0.767136	0.358023	ENSG00000119943	ENST00000370575	T	0.20463	2.07	4.92	4.92	0.64577	.	0.047135	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00069	-2.28	0.47341	P	6.070000000000242E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.37957	-0.9683	9	0.02654	T	1	-40.2811	13.1208	0.59325	0.0789:0.0:0.9211:0.0	rs2147896;rs17856169;rs52809965;rs59725796;rs2147896	461	Q8N2H3	PYRD2_HUMAN	T	461	ENSP00000359607:M461T	ENSP00000359607:M461T	M	-	2	0	PYROXD2	100138166	1.000000	0.71417	0.998000	0.56505	0.284000	0.27059	6.425000	0.73370	1.095000	0.41419	-0.642000	0.03964	ATG	T|0.003;G|0.526	0.526	strong		0.607	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	
SI	6476	hgsc.bcm.edu	37	3	164764719	164764719	+	Silent	SNP	C	C	A	rs9838509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	169	0	0		WXS	Illumina HiSeq	Phase_I	219	141	0.643836	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	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629955	32629955	+	Silent	SNP	C	C	T	rs1063321	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629955C>T	ENST00000399082.3	-	2	224	c.180G>A	c.(178-180)tcG>tcA	p.S60S	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.S150S|HLA-DQB1_ENST00000374943.4_Silent_p.S150S|HLA-DQB1_ENST00000399079.3_Silent_p.S150S|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Silent_p.S150S			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	150	Beta-1.		T -> S (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04 and allele DQB1*02:05; dbSNP:rs9274405).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	AATCTGTCACCGAGCAGACCA	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				c|||	1961	0.391573	0.3147	0.5447	5008	,	,		12272	0.4712		0.3867	False		,,,				2504	0.3098				p.S150S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G450A						PASS	.						27.0	25.0	26.0					6																	32629955		1960	4141	6101	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TGTCACCGAGCAG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.180G>A	6.37:g.32629955C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				C|0.370;T|0.630	0.630	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
PTPN21	11099	hgsc.bcm.edu	37	14	88946622	88946622	+	Missense_Mutation	SNP	G	G	A	rs2401751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88946622G>A	ENST00000556564.1	-	13	1437	c.1153C>T	c.(1153-1155)Ctc>Ttc	p.L385F	PTPN21_ENST00000328736.3_Missense_Mutation_p.L385F	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	385			L -> F (in dbSNP:rs2401751). {ECO:0000269|PubMed:7519780}.		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						CGACCGTTGAGGTCAATCTGG	0.478													G|||	1785	0.35643	0.3835	0.2651	5008	,	,		18536	0.38		0.2962	False		,,,				2504	0.4223				p.L385F		Atlas-SNP	.											.	PTPN21	113	.	0			c.C1153T						PASS	.	G	PHE/LEU	1636,2770	502.5+/-365.3	299,1038,866	87.0	76.0	79.0		1153	1.0	0.0	14	dbSNP_100	79	2931,5669	457.5+/-364.3	489,1953,1858	yes	missense	PTPN21	NM_007039.3	22	788,2991,2724	AA,AG,GG		34.0814,37.1312,35.1146	benign	385/1175	88946622	4567,8439	2203	4300	6503	SO:0001583	missense	11099	exon13			CGTTGAGGTCAAT	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.1153C>T	14.37:g.88946622G>A	ENSP00000452414:p.Leu385Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	735	0.33653846153846156	198	0.4024390243902439	99	0.27348066298342544	205	0.3583916083916084	233	0.3073878627968338	G	8.490	0.861786	0.17178	0.371312	0.340814	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.73681	-0.77;-0.77	5.5	0.973	0.19710	.	0.264843	0.38778	N	0.001564	T	0.00012	0.0000	L	0.27053	0.805	0.49130	P	2.4400000000002198E-4	B	0.29188	0.236	B	0.20577	0.03	T	0.33189	-0.9878	9	0.23891	T	0.37	.	3.566	0.07900	0.4895:0.2061:0.3044:0.0	rs2401751;rs3742685;rs17203670;rs52826621;rs58090049;rs2401751	385	Q16825	PTN21_HUMAN	F	385	ENSP00000330276:L385F;ENSP00000452414:L385F	ENSP00000330276:L385F	L	-	1	0	PTPN21	88016375	1.000000	0.71417	0.008000	0.14137	0.488000	0.33401	4.629000	0.61290	0.284000	0.22305	-1.077000	0.02231	CTC	G|0.651;N|0.000	.	strong		0.478	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190649	209190649	+	Silent	SNP	A	A	G	rs999891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209190649A>G	ENST00000264380.4	+	20	3272	c.3114A>G	c.(3112-3114)cgA>cgG	p.R1038R		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1038					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						AAGATAAACGAAAGACTTATT	0.413													A|||	496	0.0990415	0.1513	0.1081	5008	,	,		20915	0.0089		0.1282	False		,,,				2504	0.0849				p.R1038R		Atlas-SNP	.											PIKFYVE,colon,carcinoma,+1,1	PIKFYVE	223	1	0			c.A3114G						PASS	.	A		626,3780	265.6+/-266.7	39,548,1616	95.0	99.0	98.0		3114	-10.8	0.6	2	dbSNP_86	98	1205,7395	243.3+/-273.0	76,1053,3171	no	coding-synonymous	PIKFYVE	NM_015040.3		115,1601,4787	GG,GA,AA		14.0116,14.2079,14.0781		1038/2099	209190649	1831,11175	2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			TAAACGAAAGACT	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.3114A>G	2.37:g.209190649A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			A|0.882;G|0.118	0.118	strong		0.413	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
MAN2A1	4124	hgsc.bcm.edu	37	5	109110537	109110537	+	Silent	SNP	T	T	A	rs6894260	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:109110537T>A	ENST00000261483.4	+	8	2297	c.1245T>A	c.(1243-1245)cgT>cgA	p.R415R		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	415					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)		AGCTTTTTCGTACCAAAGTTC	0.363													T|||	1683	0.336062	0.5552	0.3314	5008	,	,		14466	0.2609		0.3489	False		,,,				2504	0.1074				p.R415R		Atlas-SNP	.											MAN2A1,extremity,malignant_melanoma,+2,1	MAN2A1	136	1	0			c.T1245A						PASS	.	T		2462,1942	621.9+/-393.8	701,1060,441	77.0	76.0	76.0		1245	-3.9	0.5	5	dbSNP_116	76	2914,5686	454.3+/-363.5	522,1870,1908	no	coding-synonymous	MAN2A1	NM_002372.2		1223,2930,2349	AA,AT,TT		33.8837,44.0963,41.3411		415/1145	109110537	5376,7628	2202	4300	6502	SO:0001819	synonymous_variant	4124	exon8			TTTTCGTACCAAA		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.1245T>A	5.37:g.109110537T>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	61	59	0.967213	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			A|0.390;N|0.000	0.390	strong		0.363	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
ZNF729	100287226	hgsc.bcm.edu	37	19	22498943	22498943	+	Silent	SNP	T	T	C	rs8104705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22498943T>C	ENST00000601693.1	+	4	2842	c.2724T>C	c.(2722-2724)tgT>tgC	p.C908C	ZNF729_ENST00000357491.6_Intron			A6NN14	ZN729_HUMAN	zinc finger protein 729	908					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(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						AGAAACCCTGTAAATGTGAAG	0.353													C|||	3279	0.654752	0.6846	0.5403	5008	,	,		20307	0.6815		0.5477	False		,,,				2504	0.7781				p.C908C		Atlas-SNP	.											.	ZNF729	78	.	0			c.T2724C						PASS	.																																			SO:0001819	synonymous_variant	100287226	exon4			ACCCTGTAAATGT		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.2724T>C	19.37:g.22498943T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001242680	M0QY45	Silent	SNP	ENST00000601693.1	37	CCDS59368.1																																																																																			T|0.467;C|0.533	0.533	strong		0.353	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
PFAS	5198	hgsc.bcm.edu	37	17	8172506	8172506	+	Missense_Mutation	SNP	T	T	G	rs62637606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8172506T>G	ENST00000314666.6	+	28	4074	c.3941T>G	c.(3940-3942)tTt>tGt	p.F1314C	PFAS_ENST00000545834.1_Missense_Mutation_p.F890C	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1314					'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)	CCCCCTCCATTTGATACTCTG	0.637													T|||	130	0.0259585	0.0023	0.0591	5008	,	,		14648	0.0		0.0467	False		,,,				2504	0.0399				p.F1314C		Atlas-SNP	.											.	PFAS	91	.	0			c.T3941G						PASS	.	T	CYS/PHE	60,4346	57.4+/-93.9	1,58,2144	45.0	45.0	45.0		3941	5.5	1.0	17	dbSNP_129	45	549,8051	150.1+/-205.1	19,511,3770	yes	missense	PFAS	NM_012393.2	205	20,569,5914	GG,GT,TT		6.3837,1.3618,4.6825	benign	1314/1339	8172506	609,12397	2203	4300	6503	SO:0001583	missense	5198	exon28			CTCCATTTGATAC	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.3941T>G	17.37:g.8172506T>G	ENSP00000313490:p.Phe1314Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	69	0.03159340659340659	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	36	0.047493403693931395	T	14.30	2.494705	0.44352	0.013618	0.063837	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.30981	1.51;2.25	5.46	5.46	0.80206	Glutamine amidotransferase type 1 (1);	0.179053	0.46145	D	0.000302	T	0.01287	0.0042	L	0.55017	1.72	0.38160	D	0.939011	B	0.28998	0.23	B	0.32211	0.142	T	0.02698	-1.1122	10	0.87932	D	0	-5.1281	13.4903	0.61390	0.0:0.0:0.0:1.0	rs62637606	1314	O15067	PUR4_HUMAN	C	890;1314;723	ENSP00000441706:F890C;ENSP00000313490:F1314C	ENSP00000313490:F1314C	F	+	2	0	PFAS	8113231	0.941000	0.31946	0.969000	0.41365	0.996000	0.88848	1.167000	0.31847	2.057000	0.61298	0.533000	0.62120	TTT	T|0.957;G|0.043	0.043	strong		0.637	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
OR2H2	7932	hgsc.bcm.edu	37	6	29555778	29555778	+	Silent	SNP	A	A	G	rs2235698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29555778A>G	ENST00000383640.2	+	1	96	c.57A>G	c.(55-57)ccA>ccG	p.P19P	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	19					defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	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)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						CTGAACACCCAGGGCTGGAAA	0.557													A|||	1347	0.26897	0.1573	0.2997	5008	,	,		19973	0.3393		0.2555	False		,,,				2504	0.3395				p.P19P		Atlas-SNP	.											OR2H2,NS,carcinoma,+1,1	OR2H2	29	1	0			c.A57G						PASS	.	A		622,2400		74,474,963	173.0	178.0	176.0		57	-1.5	0.1	6	dbSNP_98	176	1286,4132		168,950,1591	no	coding-synonymous	OR2H2	NM_007160.3		242,1424,2554	GG,GA,AA		23.7357,20.5824,22.6066		19/313	29555778	1908,6532	1511	2709	4220	SO:0001819	synonymous_variant	7932	exon1			ACACCCAGGGCTG		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"""GPCR / Class A : Olfactory receptors"""	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.57A>G	6.37:g.29555778A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Silent	SNP	ENST00000383640.2	37	CCDS34365.1																																																																																			A|0.764;G|0.236	0.236	strong		0.557	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2		
BZRAP1	9256	hgsc.bcm.edu	37	17	56388238	56388238	+	Missense_Mutation	SNP	C	C	G	rs2680704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56388238C>G	ENST00000343736.4	-	19	3581	c.3418G>C	c.(3418-3420)Gca>Cca	p.A1140P	BZRAP1_ENST00000355701.3_Missense_Mutation_p.A1140P|BZRAP1_ENST00000268893.6_Missense_Mutation_p.A1080P			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1140	Pro-rich.		A -> P (in dbSNP:rs2680704). {ECO:0000269|PubMed:9734811}.			cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GACCCTTTTGCCATCTCTCTG	0.657													G|||	1310	0.261581	0.2375	0.2637	5008	,	,		17851	0.2391		0.331	False		,,,				2504	0.2444				p.A1140P		Atlas-SNP	.											BZRAP1_ENST00000355701,NS,carcinoma,0,4	BZRAP1	287	4	0			c.G3418C						PASS	.	G	PRO/ALA,PRO/ALA	1005,3355		114,777,1289	14.0	15.0	15.0		3418,3238	-1.0	0.0	17	dbSNP_100	15	2456,6040		397,1662,2189	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	27,27	511,2439,3478	GG,GC,CC		28.9077,23.0505,26.9213	benign,benign	1140/1858,1080/1798	56388238	3461,9395	2180	4248	6428	SO:0001583	missense	9256	exon19			CTTTTGCCATCTC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.3418G>C	17.37:g.56388238C>G	ENSP00000345824:p.Ala1140Pro	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	590	0.27014652014652013	107	0.21747967479674796	107	0.2955801104972376	135	0.23601398601398602	241	0.3179419525065963	G	7.172	0.587841	0.13812	0.230505	0.289077	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04406	3.64;3.64;3.63	5.8	-1.05	0.10036	.	1.823320	0.02195	N	0.061728	T	0.00012	0.0000	N	0.02011	-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	0.47947	-0.9077	9	0.20519	T	0.43	.	6.008	0.19557	0.2611:0.3743:0.3647:0.0	rs2680704;rs3744100;rs2680704	1140;1080;1140	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	P	1140;1140;1080	ENSP00000347929:A1140P;ENSP00000345824:A1140P;ENSP00000268893:A1080P	ENSP00000268893:A1080P	A	-	1	0	BZRAP1	53743237	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-0.383000	0.07398	-0.170000	0.10816	-0.215000	0.12644	GCA	C|0.730;G|0.270	0.270	strong		0.657	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
USP47	55031	hgsc.bcm.edu	37	11	11976628	11976628	+	Silent	SNP	G	G	A	rs7933089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:11976628G>A	ENST00000399455.2	+	28	3990	c.3870G>A	c.(3868-3870)caG>caA	p.Q1290Q	USP47_ENST00000305481.6_3'UTR|USP47_ENST00000539466.1_Silent_p.Q72Q|USP47_ENST00000339865.5_Silent_p.Q1202Q|USP47_ENST00000527733.1_Silent_p.Q1270Q	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1290					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)		ATATTCATCAGGATTTAGACT	0.353													A|||	3577	0.714257	0.8654	0.8429	5008	,	,		16544	0.4861		0.6879	False		,,,				2504	0.681				p.Q1202Q		Atlas-SNP	.											.	USP47	91	.	0			c.G3606A						PASS	.	A		3137,531		1352,433,49	167.0	152.0	157.0		3606	1.9	1.0	11	dbSNP_116	157	5475,2705		1839,1797,454	no	coding-synonymous	USP47	NM_017944.3		3191,2230,503	AA,AG,GG		33.0685,14.4766,27.3126		1202/1288	11976628	8612,3236	1834	4090	5924	SO:0001819	synonymous_variant	55031	exon26			TCATCAGGATTTA	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.3870G>A	11.37:g.11976628G>A		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	37																																																																																				G|0.303;A|0.697	0.697	strong		0.353	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609126	32609126	+	Missense_Mutation	SNP	T	T	C	rs1071630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609126T>C	ENST00000343139.5	+	2	224	c.122T>C	c.(121-123)tTt>tCt	p.F41S	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.F41S|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.F41S	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	41	Alpha-1.		S -> F (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06 and allele DQA1*01:07; dbSNP:rs1071630).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TTGTACCAGTTTTACGGTCCC	0.512													.|||	2770	0.553115	0.5076	0.6974	5008	,	,		15988	0.5446		0.5964	False		,,,				2504	0.4765				p.F41S		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.T122C						PASS	.	C	SER/PHE	1711,2695		607,497,1099	140.0	117.0	125.0		122	3.0	0.5	6	dbSNP_86	125	3781,4795		1499,783,2006	yes	missense	HLA-DQA1	NM_002122.3	155	2106,1280,3105	CC,CT,TT		44.0882,38.8334,42.3047	benign	41/256	32609126	5492,7490	2203	4288	6491	SO:0001583	missense	3117	exon2			ACCAGTTTTACGG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.122T>C	6.37:g.32609126T>C	ENSP00000339398:p.Phe41Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	1236|1236	0.5659340659340659|0.5659340659340659	233|233	0.4735772357723577|0.4735772357723577	247|247	0.6823204419889503|0.6823204419889503	318|318	0.5559440559440559|0.5559440559440559	438|438	0.5778364116094987|0.5778364116094987	.|.	0.529|0.529	-0.858787|-0.858787	0.02610|0.02610	0.388334|0.388334	0.440882|0.440882	ENSG00000196735|ENSG00000196735	ENST00000486548|ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	.|T;T;T;T	.|0.01113	.|5.32;5.32;5.32;5.32	3.84|3.84	2.95|2.95	0.34219|0.34219	.|.	0.176324|0.176324	0.27302|0.27302	U|N	0.019987|0.019987	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.00008|0.00008	-3.11|-3.11	0.42258|0.42258	P|P	0.008000000000000007|0.008000000000000007	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.10450	.|0.005;0.0	T|T	0.11397|0.11397	-1.0589|-1.0589	6|9	0.87932|0.02654	D|T	0|1	.|.	6.6795|6.6795	0.23113|0.23113	0.1754:0.7258:0.0:0.0988|0.1754:0.7258:0.0:0.0988	rs1071630;rs3187990;rs3205983;rs3208178;rs9272690;rs12722047;rs17415861|rs1071630;rs3187990;rs3205983;rs3208178;rs9272690;rs12722047;rs17415861	.|47;41	.|Q59F33;G4XQK2	.|.;.	L|S	14|41	.|ENSP00000339398:F41S;ENSP00000378767:F41S;ENSP00000437302:F41S;ENSP00000364087:F41S	ENSP00000437183:F14L|ENSP00000339398:F41S	F|F	+|+	1|2	0|0	HLA-DQA1|HLA-DQA1	32717104|32717104	0.113000|0.113000	0.22115|0.22115	0.496000|0.496000	0.27539|0.27539	0.021000|0.021000	0.10359|0.10359	0.696000|0.696000	0.25541|0.25541	0.401000|0.401000	0.25424|0.25424	-0.355000|-0.355000	0.07637|0.07637	TTT|TTT	T|0.423;C|0.577	0.577	strong		0.512	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
CEP57	9702	hgsc.bcm.edu	37	11	95555133	95555133	+	Silent	SNP	A	A	G	rs61903295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:95555133A>G	ENST00000325542.5	+	7	1036	c.798A>G	c.(796-798)ccA>ccG	p.P266P	CEP57_ENST00000325486.5_Silent_p.P266P|CEP57_ENST00000537677.1_Silent_p.P239P|CEP57_ENST00000538658.1_Silent_p.P266P|CEP57_ENST00000541150.1_Silent_p.P257P	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	266					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)				AGTCAAAACCACCAGAAAAGG	0.373									Mosaic Variegated Aneuploidy Syndrome				A|||	80	0.0159744	0.0045	0.0274	5008	,	,		19580	0.0		0.0477	False		,,,				2504	0.0072				p.P266P		Atlas-SNP	.											.	CEP57	40	.	0			c.A798G						PASS	.	A		35,4367	36.8+/-68.6	1,33,2167	46.0	45.0	45.0		798	3.7	1.0	11	dbSNP_129	45	355,8241	118.5+/-177.9	7,341,3950	no	coding-synonymous	CEP57	NM_014679.4		8,374,6117	GG,GA,AA		4.1298,0.7951,3.0005		266/501	95555133	390,12608	2201	4298	6499	SO:0001819	synonymous_variant	9702	exon7	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AAAACCACCAGAA	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.798A>G	11.37:g.95555133A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_001243777	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Silent	SNP	ENST00000325542.5	37	CCDS8304.1	59	0.027014652014652016	4	0.008130081300813009	13	0.03591160220994475	0	0.0	42	0.055408970976253295	A	10.31	1.315409	0.23908	0.007951	0.041298	ENSG00000166037	ENST00000535224	.	.	.	6.06	3.69	0.42338	.	.	.	.	.	T	0.07908	0.0198	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11275	-1.0594	4	.	.	.	-1.7025	2.2798	0.04112	0.5658:0.0:0.1533:0.2809	rs61903295	.	.	.	A	82	.	.	T	+	1	0	CEP57	95194781	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.235000	0.32671	1.069000	0.40788	0.528000	0.53228	ACC	A|0.971;G|0.029	0.029	strong		0.373	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
WDR18	57418	hgsc.bcm.edu	37	19	984554	984554	+	Silent	SNP	C	C	G	rs4806884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:984554C>G	ENST00000251289.5	+	1	224	c.201C>G	c.(199-201)ctC>ctG	p.L67L	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.L67L	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	28	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	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		
KRT6A	3853	hgsc.bcm.edu	37	12	52884735	52884735	+	Silent	SNP	A	A	G	rs12578949	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52884735A>G	ENST00000330722.6	-	4	887	c.819T>C	c.(817-819)gaT>gaC	p.D273D		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	273	Coil 1B.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGCATCCACATCCTGGGGAA	0.507													N|||	1602	0.319888	0.4463	0.4179	5008	,	,		20585	0.2034		0.2555	False		,,,				2504	0.2658				p.D273D		Atlas-SNP	.											.	KRT6A	89	.	0			c.T819C						PASS	.	G		1761,2645		352,1057,794	65.0	62.0	63.0		819	-5.0	0.7	12	dbSNP_120	63	1937,6657		219,1499,2579	no	coding-synonymous	KRT6A	NM_005554.3		571,2556,3373	GG,GA,AA		22.539,39.9682,28.4462		273/565	52884735	3698,9302	2203	4297	6500	SO:0001819	synonymous_variant	3853	exon4			ATCCACATCCTGG	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.819T>C	12.37:g.52884735A>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	167	91	0.54491	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			A|0.703;G|0.297	0.297	strong		0.507	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
TENM2	57451	hgsc.bcm.edu	37	5	167645888	167645888	+	Silent	SNP	T	T	C	rs1363560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:167645888T>C	ENST00000518659.1	+	23	5031	c.4992T>C	c.(4990-4992)aaT>aaC	p.N1664N	TENM2_ENST00000545108.1_Silent_p.N1663N|TENM2_ENST00000519204.1_Silent_p.N1543N|TENM2_ENST00000403607.2_Silent_p.N1488N|TENM2_ENST00000520394.1_Silent_p.N1425N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1664					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)										TGGGCACCAATGGAGGCCTCA	0.557													.|||	2052	0.409744	0.6422	0.2205	5008	,	,		20614	0.5942		0.2207	False		,,,				2504	0.2342				p.N1655N		Atlas-SNP	.											.	.	.	.	0			c.T4965C						PASS	.	T		2411,1783		709,993,395	147.0	153.0	151.0		4965	-9.2	0.0	5	dbSNP_88	151	1905,6525		229,1447,2539	no	coding-synonymous	ODZ2	NM_001122679.1		938,2440,2934	CC,CT,TT		22.5979,42.5131,34.1888		1655/2766	167645888	4316,8308	2097	4215	6312	SO:0001819	synonymous_variant	57451	exon23			CACCAATGGAGGC	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.4992T>C	5.37:g.167645888T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				T|0.589;C|0.411	0.411	strong		0.557	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
CD302	9936	hgsc.bcm.edu	37	2	160639970	160639970	+	Silent	SNP	T	T	C	rs2114626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160639970T>C	ENST00000259053.4	-	2	121	c.78A>G	c.(76-78)tcA>tcG	p.S26S	LY75-CD302_ENST00000505052.1_Silent_p.S1611S|CD302_ENST00000480212.1_5'UTR|LY75_ENST00000554112.1_Silent_p.S1667S|CD302_ENST00000429078.2_Silent_p.S26S|LY75_ENST00000553424.1_Silent_p.S1611S|LY75-CD302_ENST00000504764.1_Silent_p.S1667S	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	26					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						TCCAAGTAGATGAAGGACAGT	0.328													T|||	1764	0.352236	0.3669	0.1945	5008	,	,		19446	0.3373		0.3479	False		,,,				2504	0.4642				p.S1667S		Atlas-SNP	.											.	.	.	.	0			c.A5001G						PASS	.	T	,,,,	1556,2850	487.8+/-361.0	269,1018,916	110.0	108.0	109.0		5001,4833,78,,78	-5.9	0.5	2	dbSNP_96	109	3024,5576	466.1+/-366.7	526,1972,1802	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	CD302,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_001198763.1,NM_001198764.1,NM_014880.4	,,,,	795,2990,2718	CC,CT,TT		35.1628,35.3155,35.2145	,,,,	1667/1874,1611/1818,26/175,,26/233	160639970	4580,8426	2203	4300	6503	SO:0001819	synonymous_variant	100526664	exon35			AGTAGATGAAGGA	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"""CD molecules"", ""C-type lectin domain containing"""	30843	protein-coding gene	gene with protein product	"""C-type lectin domain family 13, member A"""	612246	"""CD302 antigen"""			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.78A>G	2.37:g.160639970T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001198759	A8K5G4|B4E2T9|Q15009	Silent	SNP	ENST00000259053.4	37	CCDS33308.1																																																																																			T|0.650;C|0.350	0.350	strong		0.328	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880	
ACKR2	1238	hgsc.bcm.edu	37	3	42907112	42907112	+	Missense_Mutation	SNP	A	A	C	rs2228468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:42907112A>C	ENST00000422265.1	+	3	1293	c.1118A>C	c.(1117-1119)tAc>tCc	p.Y373S	ACKR2_ENST00000442925.1_Missense_Mutation_p.Y373S|KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|ACKR2_ENST00000273145.2_Missense_Mutation_p.Y373S|CYP8B1_ENST00000437102.1_Intron	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						scavenged	.	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	143	2	0.013986		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	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	
SORCS1	114815	hgsc.bcm.edu	37	10	108432670	108432670	+	Missense_Mutation	SNP	G	G	A	rs143914023		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108432670G>A	ENST00000263054.6	-	15	2021	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W	SORCS1_ENST00000344440.6_Missense_Mutation_p.R672W|SORCS1_ENST00000369698.1_Missense_Mutation_p.R207W	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	672					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TCGGCACACCGTCTATCAAAA	0.488																																					p.R672W		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2014T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	84.0	70.0	75.0		2014,2014,2014,2014,2014,2014	-0.1	0.8	10	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	101,101,101,101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	672/1199,672/1180,672/1131,672/1160,672/1180,672/1169	108432670	1,13005	2203	4300	6503	SO:0001583	missense	114815	exon15			CACACCGTCTATC	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2014C>T	10.37:g.108432670G>A	ENSP00000263054:p.Arg672Trp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681592	0.68042	0.0	1.16E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.29917	1.55;1.55;1.55	5.47	-0.143	0.13444	VPS10 (1);	0.132411	0.49305	N	0.000151	T	0.47691	0.1459	M	0.67953	2.075	0.40136	D	0.976777	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.75484	0.968;0.978;0.986;0.968;0.986	T	0.42137	-0.9469	9	.	.	.	-6.2946	11.4184	0.49967	0.064:0.0:0.2926:0.6433	.	672;672;672;672;672	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	W	207;672;672	ENSP00000358712:R207W;ENSP00000263054:R672W;ENSP00000345964:R672W	.	R	-	1	2	SORCS1	108422660	0.134000	0.22483	0.849000	0.33467	0.991000	0.79684	0.199000	0.17237	-0.009000	0.14296	0.563000	0.77884	CGG	G|1.000;A|0.000	0.000	weak		0.488	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
SAMD15	161394	hgsc.bcm.edu	37	14	77843814	77843814	+	Missense_Mutation	SNP	T	T	C	rs11844594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77843814T>C	ENST00000216471.4	+	1	339	c.53T>C	c.(52-54)cTg>cCg	p.L18P	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	18			L -> P (in dbSNP:rs11844594).					p.L18P(1)		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						GATGGAGAGCTGGAGCCTGAG	0.537													C|||	2570	0.513179	0.888	0.4841	5008	,	,		18514	0.0893		0.497	False		,,,				2504	0.4806				p.L18P		Atlas-SNP	.											SAMD15,NS,carcinoma,0,1	SAMD15	60	1	1	Substitution - Missense(1)	stomach(1)	c.T53C						scavenged	.	C	PRO/LEU	3625,781	312.7+/-292.7	1498,629,76	59.0	69.0	65.0		53	-1.7	0.0	14	dbSNP_120	65	4030,4570	597.8+/-393.8	957,2116,1227	yes	missense	SAMD15	NM_001010860.1	98	2455,2745,1303	CC,CT,TT		46.8605,17.7258,41.1425	benign	18/675	77843814	7655,5351	2203	4300	6503	SO:0001583	missense	161394	exon1			GAGAGCTGGAGCC	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.53T>C	14.37:g.77843814T>C	ENSP00000216471:p.Leu18Pro	Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	1052	0.4816849816849817	436	0.8861788617886179	197	0.5441988950276243	44	0.07692307692307693	375	0.4947229551451187	C	9.626	1.135248	0.21123	0.822742	0.468605	ENSG00000100583	ENST00000216471	T	0.37235	1.21	5.2	-1.74	0.08056	.	0.969853	0.08350	N	0.959327	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	0.21449	-1.0245	9	0.26408	T	0.33	16.0091	5.4263	0.16427	0.0:0.2387:0.2757:0.4856	rs11844594;rs58457097;rs11844594	18	Q9P1V8	SAM15_HUMAN	P	18	ENSP00000216471:L18P	ENSP00000216471:L18P	L	+	2	0	SAMD15	76913567	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.605000	0.05661	-1.173000	0.02758	-0.215000	0.12644	CTG	T|0.457;C|0.543	0.543	strong		0.537	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
ENTPD4	9583	hgsc.bcm.edu	37	8	23294761	23294761	+	Missense_Mutation	SNP	T	T	C	rs2272641	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:23294761T>C	ENST00000358689.4	-	10	1295	c.1060A>G	c.(1060-1062)Aaa>Gaa	p.K354E	ENTPD4_ENST00000356206.6_Missense_Mutation_p.K346E|ENTPD4_ENST00000521321.1_5'Flank|ENTPD4_ENST00000417069.2_Missense_Mutation_p.K346E	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	354			K -> E (in dbSNP:rs2272641).		UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		CCAGTCTGTTTACCCAGGAGC	0.448													T|||	780	0.155751	0.1558	0.2147	5008	,	,		19915	0.2708		0.0596	False		,,,				2504	0.0941				p.K354E		Atlas-SNP	.											.	ENTPD4	56	.	0			c.A1060G						PASS	.	T	GLU/LYS,GLU/LYS	635,3771	270.7+/-269.8	41,553,1609	74.0	63.0	67.0		1036,1060	4.4	1.0	8	dbSNP_100	67	487,8113	140.8+/-197.2	9,469,3822	yes	missense,missense	ENTPD4	NM_001128930.2,NM_004901.4	56,56	50,1022,5431	CC,CT,TT		5.6628,14.4122,8.6268	benign,benign	346/609,354/617	23294761	1122,11884	2203	4300	6503	SO:0001583	missense	9583	exon10			TCTGTTTACCCAG	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"""lysosomal apyrase-like 1"""	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1060A>G	8.37:g.23294761T>C	ENSP00000351520:p.Lys354Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	386	0.17673992673992675	96	0.1951219512195122	78	0.2154696132596685	169	0.29545454545454547	43	0.05672823218997362	T	11.90	1.777817	0.31502	0.144122	0.056628	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.14766	2.48;2.5;2.49	5.57	4.39	0.52855	.	0.188777	0.56097	D	0.000029	T	0.00012	0.0000	N	0.20483	0.58	0.27727	P	0.9449281	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.13407	0.007;0.001;0.009	T	0.41805	-0.9488	9	0.07325	T	0.83	-10.1231	11.6906	0.51514	0.0:0.0:0.1485:0.8515	rs2272641;rs58788167;rs2272641	346;346;354	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	E	346;354;346	ENSP00000348536:K346E;ENSP00000351520:K354E;ENSP00000408573:K346E	ENSP00000348536:K346E	K	-	1	0	ENTPD4	23350706	0.993000	0.37304	0.995000	0.50966	0.834000	0.47266	1.617000	0.36943	0.923000	0.37045	0.260000	0.18958	AAA	T|0.868;G|0.001	.	strong		0.448	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
CELF5	60680	hgsc.bcm.edu	37	19	3281298	3281298	+	Silent	SNP	G	G	A	rs36030381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3281298G>A	ENST00000292672.2	+	6	742	c.705G>A	c.(703-705)ccG>ccA	p.P235P	CELF5_ENST00000541430.2_Silent_p.P235P	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	235					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						TCCTGACGCCGTCCCTCACAT	0.652													G|||	403	0.0804712	0.0295	0.072	5008	,	,		18514	0.0218		0.1044	False		,,,				2504	0.1912				p.P235P		Atlas-SNP	.											.	CELF5	32	.	0			c.G705A						PASS	.	G	,	140,4266	98.9+/-137.6	2,136,2065	101.0	89.0	93.0		705,705	-7.2	0.9	19	dbSNP_126	93	1018,7582	217.0+/-255.8	55,908,3337	no	coding-synonymous,coding-synonymous	CELF5	NM_001172673.1,NM_021938.3	,	57,1044,5402	AA,AG,GG		11.8372,3.1775,8.9036	,	235/410,235/486	3281298	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	60680	exon6			GACGCCGTCCCTC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.705G>A	19.37:g.3281298G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	17	0.62963	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Silent	SNP	ENST00000292672.2	37	CCDS12106.1																																																																																			G|0.917;A|0.083	0.083	strong		0.652	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
ANKLE1	126549	hgsc.bcm.edu	37	19	17394124	17394124	+	Missense_Mutation	SNP	T	T	G	rs2363956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17394124T>G	ENST00000394458.3	+	5	827	c.551T>G	c.(550-552)tTg>tGg	p.L184W	ANKLE1_ENST00000598347.1_Missense_Mutation_p.L184W|ANKLE1_ENST00000433424.2_Missense_Mutation_p.L238W|ANKLE1_ENST00000594072.1_Missense_Mutation_p.L173W|ANKLE1_ENST00000404085.1_Missense_Mutation_p.L206W	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	184			L -> W (in dbSNP:rs2363956). {ECO:0000269|Ref.1}.							large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GACATTGGCTTGGAGGCTGAC	0.602													T|||	2307	0.460663	0.5045	0.3905	5008	,	,		18682	0.3115		0.5726	False		,,,				2504	0.4898				p.L184W		Atlas-SNP	.											.	ANKLE1	27	.	0			c.T551G						PASS	.	T	TRP/LEU	2204,2200		565,1074,563	70.0	77.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	551	2.3	0.0	19	dbSNP_100	75	4461,4139		1169,2123,1008	yes	missense	ANKLE1	NM_152363.4	61	1734,3197,1571	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	48.1279,49.9546,48.7465	probably-damaging	184/616	17394124	6665,6339	2202	4300	6502	SO:0001583	missense	126549	exon5			TTGGCTTGGAGGC	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.551T>G	19.37:g.17394124T>G	ENSP00000377971:p.Leu184Trp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	22	0.34375	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	983	0.4500915750915751	235	0.47764227642276424	158	0.43646408839779005	160	0.27972027972027974	430	0.5672823218997362	T	15.91	2.973793	0.53720	0.500454	0.518721	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.74526	-0.74;-0.85;-0.83	3.28	2.26	0.28386	.	2.608830	0.02141	U	0.057120	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B;D;D	0.89917	0.246;1.0;0.999	B;D;D	0.87578	0.066;0.998;0.997	T	0.44345	-0.9334	9	0.34782	T	0.22	-8.2236	4.588	0.12291	0.0:0.1487:0.0:0.8513	rs2363956;rs57542473;rs2363956	184;170;184	E7ETZ9;Q8NAG6-1;Q8NAG6	.;.;ANKL1_HUMAN	W	184;238;206;173;184	ENSP00000384753:L184W;ENSP00000394460:L238W;ENSP00000384008:L206W	ENSP00000377971:L173W	L	+	2	0	ANKLE1	17255124	0.000000	0.05858	0.032000	0.17829	0.220000	0.24768	0.409000	0.21082	1.505000	0.48720	0.260000	0.18958	TTG	T|0.509;G|0.491	0.491	strong		0.602	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
EMR1	2015	hgsc.bcm.edu	37	19	6913811	6913811	+	Missense_Mutation	SNP	A	A	G	rs457857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6913811A>G	ENST00000312053.4	+	11	1307	c.1270A>G	c.(1270-1272)Atc>Gtc	p.I424V	EMR1_ENST00000381407.5_Missense_Mutation_p.I283V|EMR1_ENST00000450315.3_Missense_Mutation_p.I247V|EMR1_ENST00000250572.8_Missense_Mutation_p.I424V|EMR1_ENST00000381404.4_Missense_Mutation_p.I372V	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	424	Ser/Thr-rich.		I -> V (in dbSNP:rs457857). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7601460, ECO:0000269|Ref.2}.	I -> A (in Ref. 4; BAH12475). {ECO:0000305}.	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)					CTCAGCAAATATCACTCCGGC	0.483													G|||	3539	0.706669	0.5681	0.7695	5008	,	,		18988	0.7679		0.7445	False		,,,				2504	0.7474				p.I424V		Atlas-SNP	.											.	EMR1	153	.	0			c.A1270G						PASS	.	G	VAL/ILE	2651,1755	523.1+/-371.0	788,1075,340	152.0	139.0	143.0		1270	-1.9	0.0	19	dbSNP_80	143	6549,2051	355.9+/-330.1	2477,1595,228	yes	missense	EMR1	NM_001974.3	29	3265,2670,568	GG,GA,AA		23.8488,39.832,29.2634	benign	424/887	6913811	9200,3806	2203	4300	6503	SO:0001583	missense	2015	exon11			GCAAATATCACTC	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.1270A>G	19.37:g.6913811A>G	ENSP00000311545:p.Ile424Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	1614	0.739010989010989	279	0.5670731707317073	290	0.8011049723756906	462	0.8076923076923077	583	0.7691292875989446	G	1.983	-0.433599	0.04669	0.60168	0.761512	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.77620	-1.07;-1.1;-1.11;0.08;0.4	4.95	-1.87	0.07737	.	.	.	.	.	T	0.00012	0.0000	N	0.00237	-1.79	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	0.38628	-0.9652	8	0.26408	T	0.33	.	5.3598	0.16081	0.5674:0.1652:0.2675:0.0	rs457857;rs2228538;rs52805199;rs60962111;rs457857	247;283;424;372;424	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	V	424;424;372;424;283;247	ENSP00000311545:I424V;ENSP00000370811:I372V;ENSP00000250572:I424V;ENSP00000370814:I283V;ENSP00000405974:I247V	ENSP00000250572:I424V	I	+	1	0	EMR1	6864811	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.408000	0.02485	-0.359000	0.08150	-0.215000	0.12644	ATC	A|0.286;G|0.714	0.714	strong		0.483	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
TTYH1	57348	hgsc.bcm.edu	37	19	54946784	54946784	+	Silent	SNP	A	A	G	rs3745420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54946784A>G	ENST00000376530.3	+	11	1291	c.1188A>G	c.(1186-1188)ctA>ctG	p.L396L	AC008746.3_ENST00000457113.1_RNA|TTYH1_ENST00000391739.3_Missense_Mutation_p.T427A|CTD-2587H19.3_ENST00000597355.1_lincRNA|TTYH1_ENST00000301194.4_Silent_p.L396L|TTYH1_ENST00000489425.1_3'UTR|TTYH1_ENST00000376531.3_Silent_p.L396L|CTD-2587H19.2_ENST00000596631.1_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						scavenged	.	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	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	146	73	0.5	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		
ACAP1	9744	hgsc.bcm.edu	37	17	7245371	7245371	+	Silent	SNP	A	A	G	rs4796407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7245371A>G	ENST00000158762.3	+	3	422	c.216A>G	c.(214-216)ccA>ccG	p.P72P		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	72	BAR.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						TGGGTCCACCAGAGCCCATGA	0.632													A|||	1577	0.314896	0.3669	0.451	5008	,	,		20495	0.0486		0.4076	False		,,,				2504	0.3272				p.P72P		Atlas-SNP	.											.	ACAP1	66	.	0			c.A216G						PASS	.	A		1671,2735	508.1+/-366.9	305,1061,837	87.0	87.0	87.0		216	0.9	1.0	17	dbSNP_111	87	3622,4978	519.9+/-379.6	767,2088,1445	no	coding-synonymous	ACAP1	NM_014716.3		1072,3149,2282	GG,GA,AA		42.1163,37.9256,40.6966		72/741	7245371	5293,7713	2203	4300	6503	SO:0001819	synonymous_variant	9744	exon3			TCCACCAGAGCCC	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.216A>G	17.37:g.7245371A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	37	CCDS11101.1																																																																																			A|0.642;G|0.358	0.358	strong		0.632	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
NUP205	23165	hgsc.bcm.edu	37	7	135304215	135304215	+	Silent	SNP	C	C	T	rs11550518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135304215C>T	ENST00000285968.6	+	29	4034	c.4008C>T	c.(4006-4008)gcC>gcT	p.A1336A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1336					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTGTGGTCGCCGGGGCAGTGT	0.483													C|||	178	0.0355431	0.0356	0.049	5008	,	,		17803	0.003		0.0457	False		,,,				2504	0.0491				p.A1336A		Atlas-SNP	.											.	NUP205	198	.	0			c.C4008T						PASS	.	C		155,4251	105.2+/-143.6	2,151,2050	109.0	110.0	109.0		4008	-10.2	0.1	7	dbSNP_120	109	366,8234	121.0+/-180.1	7,352,3941	no	coding-synonymous	NUP205	NM_015135.2		9,503,5991	TT,TC,CC		4.2558,3.5179,4.0058		1336/2013	135304215	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon29			GGTCGCCGGGGCA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.4008C>T	7.37:g.135304215C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			C|0.960;T|0.040	0.040	strong		0.483	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
TSC1	7248	hgsc.bcm.edu	37	9	135771682	135771682	+	Silent	SNP	C	C	T	rs140352085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135771682C>T	ENST00000298552.3	-	23	3656	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P	TSC1_ENST00000545250.1_Silent_p.P1094P|TSC1_ENST00000440111.2_Silent_p.P1145P	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1145					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CAACACTGTCCGGGGTCGGGG	0.498			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	4	0.000798722	0.0	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.002				p.P1145P		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.G3435A						PASS	.	C	,,	0,4406		0,0,2203	177.0	153.0	161.0		3435,3432,3282	-5.2	0.0	9	dbSNP_134	161	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	,,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,,	1145/1165,1144/1164,1094/1114	135771682	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACTGTCCGGGGTC	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3435G>A	9.37:g.135771682C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	152	63	0.414474	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			C|1.000;T|0.000	0.000	strong		0.498	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
FLG	2312	hgsc.bcm.edu	37	1	152282311	152282311	+	Missense_Mutation	SNP	C	C	T	rs12407807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152282311C>T	ENST00000368799.1	-	3	5086	c.5051G>A	c.(5050-5052)cGc>cAc	p.R1684H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1684	Ser-rich.		R -> H (in dbSNP:rs12407807).		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)			CTGCTGGTGGCGGGATCCATG	0.562									Ichthyosis				C|||	1486	0.296725	0.0461	0.3905	5008	,	,		20240	0.5843		0.1421	False		,,,				2504	0.4315				p.R1684H		Atlas-SNP	.											.	FLG	900	.	0			c.G5051A						PASS	.	C	HIS/ARG	303,4103	164.4+/-196.0	5,293,1905	303.0	304.0	304.0		5051	-5.0	0.0	1	dbSNP_120	304	1241,7359	249.0+/-276.5	97,1047,3156	no	missense	FLG	NM_002016.1	29	102,1340,5061	TT,TC,CC		14.4302,6.877,11.8714	probably-damaging	1684/4062	152282311	1544,11462	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGGCGGGATC	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.5051G>A	1.37:g.152282311C>T	ENSP00000357789:p.Arg1684His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	175	108	0.617143	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	596	0.27289377289377287	32	0.06504065040650407	118	0.3259668508287293	335	0.5856643356643356	111	0.14643799472295516	C	11.22	1.575161	0.28092	0.06877	0.144302	ENSG00000143631	ENST00000368799	T	0.04015	3.73	2.9	-5.01	0.02991	.	.	.	.	.	T	0.01976	0.0062	N	0.12746	0.255	0.80722	P	0.0	D	0.76494	0.999	D	0.71656	0.974	T	0.23476	-1.0187	8	0.28530	T	0.3	.	5.6496	0.17608	0.0:0.5734:0.1604:0.2663	rs12407807;rs59897311	1684	P20930	FILA_HUMAN	H	1684	ENSP00000357789:R1684H	ENSP00000357789:R1684H	R	-	2	0	FLG	150548935	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.483000	0.00980	-0.996000	0.03455	0.306000	0.20318	CGC	C|0.829;T|0.171	0.171	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
IQCF1	132141	hgsc.bcm.edu	37	3	51930850	51930850	+	Missense_Mutation	SNP	T	T	C	rs57859638	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:51930850T>C	ENST00000310914.5	-	3	231	c.169A>G	c.(169-171)Aaa>Gaa	p.K57E		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	57										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGTCATACTTTTTCTGATTTC	0.488													T|||	494	0.0986422	0.0772	0.1441	5008	,	,		15992	0.0169		0.1899	False		,,,				2504	0.0859				p.K57E		Atlas-SNP	.											IQCF1,tonsil,carcinoma,0,1	IQCF1	26	1	0			c.A169G						PASS	.	T	GLU/LYS	440,3966	211.8+/-231.9	25,390,1788	168.0	155.0	160.0		169	-5.5	0.0	3	dbSNP_129	160	1647,6953	304.8+/-307.1	158,1331,2811	yes	missense	IQCF1	NM_152397.2	56	183,1721,4599	CC,CT,TT		19.1512,9.9864,16.0464	benign	57/206	51930850	2087,10919	2203	4300	6503	SO:0001583	missense	132141	exon3			ATACTTTTTCTGA	BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.169A>G	3.37:g.51930850T>C	ENSP00000307958:p.Lys57Glu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	169	91	0.538462	NM_152397	Q8N711	Missense_Mutation	SNP	ENST00000310914.5	37	CCDS2836.1	258	0.11813186813186813	54	0.10975609756097561	50	0.13812154696132597	6	0.01048951048951049	148	0.19525065963060687	T	7.233	0.599696	0.13939	0.099864	0.191512	ENSG00000173389	ENST00000535733;ENST00000310914	T	0.30182	1.54	3.15	-5.5	0.02576	.	2.522450	0.01453	N	0.015570	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	0.18493	-1.0335	9	0.07644	T	0.81	-12.336	6.6923	0.23179	0.0:0.1824:0.1462:0.6715	rs57859638	57	Q8N6M8	IQCF1_HUMAN	E	57	ENSP00000307958:K57E	ENSP00000307958:K57E	K	-	1	0	IQCF1	51905890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.751000	0.01821	-1.368000	0.02149	0.448000	0.29417	AAA	T|0.851;C|0.149	0.149	strong		0.488	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397	
IFT80	57560	hgsc.bcm.edu	37	3	159997061	159997061	+	Missense_Mutation	SNP	T	T	A	rs6778728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:159997061T>A	ENST00000326448.7	-	16	2188	c.1756A>T	c.(1756-1758)Aca>Tca	p.T586S	IFT80_ENST00000496589.1_Missense_Mutation_p.T449S|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.T757S|IFT80_ENST00000483465.1_Missense_Mutation_p.T449S	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	586			T -> S (in dbSNP:rs6778728). {ECO:0000269|PubMed:17974005}.		bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGATATGGTGTTATGCTGATG	0.358													A|||	1309	0.261382	0.5598	0.1859	5008	,	,		17580	0.0685		0.2356	False		,,,				2504	0.137				p.T586S		Atlas-SNP	.											.	IFT80	68	.	0			c.A1756T						PASS	.	A	SER/THR,SER/THR,SER/THR	2086,2320	605.2+/-390.5	478,1130,595	96.0	96.0	96.0		1345,1345,1756	2.5	1.0	3	dbSNP_116	96	2165,6435	712.7+/-405.9	270,1625,2405	yes	missense,missense,missense	IFT80	NM_001190241.1,NM_001190242.1,NM_020800.2	58,58,58	748,2755,3000	AA,AT,TT		25.1744,47.3445,32.6849	benign,benign,benign	449/641,449/641,586/778	159997061	4251,8755	2203	4300	6503	SO:0001583	missense	57560	exon16			ATGGTGTTATGCT	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29262	protein-coding gene	gene with protein product		611177	"""WD repeat domain 56"", ""intraflagellar transport 80 homolog (Chlamydomonas)"""	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1756A>T	3.37:g.159997061T>A	ENSP00000312778:p.Thr586Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	211	109	0.516588	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	560	0.2564102564102564	271	0.5508130081300813	77	0.212707182320442	34	0.05944055944055944	178	0.23482849604221637	A	5.706	0.314848	0.10789	0.473445	0.251744	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.69806	0.38;-0.43;-0.43	6.16	2.54	0.30619	.	0.117523	0.36703	N	0.002458	T	0.00012	0.0000	N	0.00205	-1.85	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45571	-0.9252	9	0.02654	T	1	-25.5461	5.8425	0.18641	0.7021:0.0:0.185:0.1129	rs6778728;rs52833709;rs6778728	586	Q9P2H3	IFT80_HUMAN	S	586;449;449	ENSP00000312778:T586S;ENSP00000418196:T449S;ENSP00000420646:T449S	ENSP00000312778:T586S	T	-	1	0	IFT80	161479755	0.998000	0.40836	0.978000	0.43139	0.955000	0.61496	2.644000	0.46613	-0.015000	0.14150	-0.265000	0.10407	ACA	T|0.699;A|0.301	0.301	strong		0.358	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800	
SLFN5	162394	hgsc.bcm.edu	37	17	33592621	33592621	+	Missense_Mutation	SNP	C	C	T	rs2291189	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33592621C>T	ENST00000299977.4	+	5	2538	c.2390C>T	c.(2389-2391)gCa>gTa	p.A797V	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	797			A -> V (in dbSNP:rs2291189).		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)		TTCACCAAAGCAAGTGAAGTG	0.413													C|||	793	0.158347	0.1551	0.1571	5008	,	,		22462	0.2331		0.0417	False		,,,				2504	0.2065				p.A797V		Atlas-SNP	.											.	SLFN5	92	.	0			c.C2390T						PASS	.	C	VAL/ALA	590,3816	258.9+/-262.7	46,498,1659	112.0	106.0	108.0		2390	-0.1	0.0	17	dbSNP_100	108	464,8136	137.0+/-194.0	13,438,3849	yes	missense	SLFN5	NM_144975.3	64	59,936,5508	TT,TC,CC		5.3953,13.3908,8.104	benign	797/892	33592621	1054,11952	2203	4300	6503	SO:0001583	missense	162394	exon5			CCAAAGCAAGTGA	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.2390C>T	17.37:g.33592621C>T	ENSP00000299977:p.Ala797Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	318	0.14560439560439561	92	0.18699186991869918	48	0.13259668508287292	145	0.2534965034965035	33	0.04353562005277045	c	8.641	0.896020	0.17686	0.133908	0.053953	ENSG00000166750	ENST00000299977	D	0.82255	-1.59	3.28	-0.128	0.13506	.	1.037170	0.07731	N	0.945277	T	0.00039	0.0001	L	0.38531	1.155	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.02214	-1.1194	9	0.27082	T	0.32	.	2.6153	0.04902	0.2287:0.5033:0.0:0.268	rs2291189;rs52833734;rs2291189	797	Q08AF3	SLFN5_HUMAN	V	797	ENSP00000299977:A797V	ENSP00000299977:A797V	A	+	2	0	SLFN5	30616734	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-1.037000	0.03557	0.165000	0.19558	0.655000	0.94253	GCA	C|0.883;T|0.117	0.117	strong		0.413	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
OR4S1	256148	hgsc.bcm.edu	37	11	48328644	48328644	+	Silent	SNP	C	C	T	rs753095	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:48328644C>T	ENST00000319988.1	+	1	870	c.870C>T	c.(868-870)aaC>aaT	p.N290N		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, 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(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						TAAGGAACAACGATGTGAAAA	0.458													T|||	2160	0.43131	0.5113	0.2911	5008	,	,		20978	0.4544		0.3042	False		,,,				2504	0.5297				p.N290N		Atlas-SNP	.											.	OR4S1	52	.	0			c.C870T						PASS	.	T		2148,2254	594.7+/-388.3	516,1116,569	91.0	83.0	86.0		870	-3.7	0.0	11	dbSNP_86	86	2567,6029	691.3+/-404.5	373,1821,2104	no	coding-synonymous	OR4S1	NM_001004725.1		889,2937,2673	TT,TC,CC		29.8627,48.796,36.2748		290/310	48328644	4715,8283	2201	4298	6499	SO:0001819	synonymous_variant	256148	exon1			GAACAACGATGTG	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"""GPCR / Class A : Olfactory receptors"""	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.870C>T	11.37:g.48328644C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_001004725	Q6IFB4	Silent	SNP	ENST00000319988.1	37	CCDS31488.1																																																																																			C|0.618;T|0.382	0.382	strong		0.458	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725	
HADHA	3030	hgsc.bcm.edu	37	2	26455127	26455127	+	Silent	SNP	G	G	A	rs11552518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26455127G>A	ENST00000380649.3	-	6	603	c.474C>T	c.(472-474)taC>taT	p.Y158Y	HADHA_ENST00000461025.1_5'UTR|HADHA_ENST00000457468.2_Silent_p.Y71Y	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	158					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCTATTCTGTATTGGCATG	0.398													G|||	713	0.142372	0.0219	0.1571	5008	,	,		16530	0.1458		0.2087	False		,,,				2504	0.2229				p.Y158Y		Atlas-SNP	.											.	HADHA	87	.	0			c.C474T						PASS	.	G		237,4169	138.8+/-174.5	8,221,1974	99.0	92.0	94.0		474	4.8	1.0	2	dbSNP_120	94	1862,6738	332.1+/-320.0	205,1452,2643	no	coding-synonymous	HADHA	NM_000182.4		213,1673,4617	AA,AG,GG		21.6512,5.379,16.1387		158/764	26455127	2099,10907	2203	4300	6503	SO:0001819	synonymous_variant	3030	exon6			TATTCTGTATTGG	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.474C>T	2.37:g.26455127G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	37	CCDS1721.1																																																																																			G|0.834;C|0.000;A|0.165	0.165	strong		0.398	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
PFKP	5214	hgsc.bcm.edu	37	10	3155698	3155698	+	Silent	SNP	C	C	T	rs4881086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:3155698C>T	ENST00000381125.4	+	13	1435	c.1359C>T	c.(1357-1359)ttC>ttT	p.F453F	PFKP_ENST00000381075.2_Silent_p.F445F	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	453	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)		TTGACGGCTTCGCCAAGGGCC	0.672													C|||	1340	0.267572	0.3215	0.3127	5008	,	,		17197	0.1349		0.2485	False		,,,				2504	0.319				p.F453F		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,0,2	PFKP	182	2	0			c.C1359T						PASS	.	C	,	1255,3151	419.1+/-338.5	210,835,1158	39.0	36.0	37.0		1335,1359	-10.3	0.0	10	dbSNP_111	37	2232,6368	367.3+/-334.7	277,1678,2345	yes	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	487,2513,3503	TT,TC,CC		25.9535,28.4839,26.8107	,	445/777,453/785	3155698	3487,9519	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon13			CGGCTTCGCCAAG	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.1359C>T	10.37:g.3155698C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	562	0.2573260073260073	164	0.3333333333333333	123	0.3397790055248619	85	0.1486013986013986	190	0.25065963060686014	C	0.187	-1.056887	0.01965	0.284839	0.259535	ENSG00000067057	ENST00000413079	.	.	.	5.16	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999564984	.	.	.	.	.	.	T	0.07986	-1.0744	3	.	.	.	.	12.2192	0.54425	0.0:0.2036:0.2044:0.5919	rs4881086;rs11542773;rs17285564;rs60582502;rs4881086	.	.	.	C	17	.	.	R	+	1	0	PFKP	3145698	0.000000	0.05858	0.004000	0.12327	0.016000	0.09150	-3.262000	0.00535	-3.323000	0.00187	-1.844000	0.00574	CGC	C|0.734;T|0.266	0.266	strong		0.672	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
FASN	2194	hgsc.bcm.edu	37	17	80044214	80044214	+	Silent	SNP	G	G	A	rs530379505		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80044214G>A	ENST00000306749.2	-	22	3866	c.3648C>T	c.(3646-3648)agC>agT	p.S1216S		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1216					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)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CCAGGAGGCCGCTGAGCAGAG	0.672																																					p.S1216S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3648T						PASS	.						26.0	23.0	24.0					17																	80044214		2184	4293	6477	SO:0001819	synonymous_variant	2194	exon22			GAGGCCGCTGAGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3648C>T	17.37:g.80044214G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	4	0.0506329	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			.	.	none		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
KLHL12	59349	hgsc.bcm.edu	37	1	202863792	202863792	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202863792G>A	ENST00000367261.3	-	9	1439	c.1221C>T	c.(1219-1221)agC>agT	p.S407S	KLHL12_ENST00000435533.3_Silent_p.S445S|KLHL12_ENST00000367259.1_Silent_p.S140S	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	407	Interaction with DVL3.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTCCCAGCATGCTCCACTGGT	0.517																																					p.S407S		Atlas-SNP	.											.	KLHL12	50	.	0			c.C1221T						PASS	.						153.0	147.0	149.0					1																	202863792		2203	4300	6503	SO:0001819	synonymous_variant	59349	exon9			CAGCATGCTCCAC	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.1221C>T	1.37:g.202863792G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	192	71	0.369792	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			.	.	none		0.517	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	
RAC1	5879	hgsc.bcm.edu	37	7	6441971	6441971	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6441971C>T	ENST00000348035.4	+	6	686	c.473C>T	c.(472-474)tCg>tTg	p.S158L	RAC1_ENST00000356142.4_Missense_Mutation_p.S177L|RAC1_ENST00000488373.1_3'UTR	NM_006908.4	NP_008839.2	P63000	RAC1_HUMAN	ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)	158					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|anatomical structure arrangement (GO:0048532)|anatomical structure morphogenesis (GO:0009653)|apoptotic signaling pathway (GO:0097190)|auditory receptor cell morphogenesis (GO:0002093)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell adhesion (GO:0007155)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|cerebral cortex radially oriented cell migration (GO:0021799)|cochlea morphogenesis (GO:0090103)|dendrite morphogenesis (GO:0048813)|dopaminergic neuron differentiation (GO:0071542)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|engulfment of apoptotic cell (GO:0043652)|epithelial cell morphogenesis (GO:0003382)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor signaling pathway (GO:0007186)|hyperosmotic response (GO:0006972)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|mast cell chemotaxis (GO:0002551)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of receptor-mediated endocytosis (GO:0048261)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA replication (GO:0045740)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein localization to plasma membrane (GO:0072659)|regulation of cell migration (GO:0030334)|regulation of defense response to virus by virus (GO:0050690)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|response to wounding (GO:0009611)|ruffle assembly (GO:0097178)|ruffle organization (GO:0031529)|semaphorin-plexin signaling pathway (GO:0071526)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell costimulation (GO:0031295)|viral process (GO:0016032)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GDP-dissociation inhibitor binding (GO:0051022)|thioesterase binding (GO:0031996)			cervix(1)|endometrium(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Dextromethorphan(DB00514)	CTGGAGTGCTCGGCGCTCACA	0.572																																					p.S177L		Atlas-SNP	.											RAC1_ENST00000356142,NS,carcinoma,-1,2	RAC1	101	2	0			c.C530T						scavenged	.						136.0	111.0	120.0					7																	6441971		2203	4300	6503	SO:0001583	missense	5879	exon7			AGTGCTCGGCGCT	AJ132695	CCDS5348.1, CCDS5349.1	7p22	2014-01-30			ENSG00000136238	ENSG00000136238		"""Endogenous ligands"""	9801	protein-coding gene	gene with protein product		602048				2674130, 10597294	Standard	NM_006908		Approved	TC-25, p21-Rac1, Rac-1	uc003spw.3	P63000	OTTHUMG00000023540	ENST00000348035.4:c.473C>T	7.37:g.6441971C>T	ENSP00000258737:p.Ser158Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	131	2	0.0152672	NM_018890	O95501|P15154|Q3Y4D3|Q5JAA8|Q9BTB4	Missense_Mutation	SNP	ENST00000348035.4	37	CCDS5348.1	.	.	.	.	.	.	.	.	.	.	.	37	6.204951	0.97376	.	.	ENSG00000136238	ENST00000348035;ENST00000356142	D;D	0.86627	-2.15;-2.15	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	D	0.97142	0.9066	H	0.99830	4.82	0.80722	D	1	P;D	0.59357	0.951;0.985	P;D	0.67382	0.781;0.951	D	0.98111	1.0420	10	0.87932	D	0	.	20.731	0.99711	0.0:1.0:0.0:0.0	.	158;177	P63000;A4D2P0	RAC1_HUMAN;.	L	158;177	ENSP00000258737:S158L;ENSP00000348461:S177L	ENSP00000258737:S158L	S	+	2	0	RAC1	6408496	1.000000	0.71417	0.972000	0.41901	0.924000	0.55760	7.715000	0.84713	2.907000	0.99374	0.609000	0.83330	TCG	.	.	none		0.572	RAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242868.2	NM_018890	
CUL9	23113	hgsc.bcm.edu	37	6	43155718	43155718	+	Missense_Mutation	SNP	G	G	A	rs145911635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43155718G>A	ENST00000252050.4	+	7	1933	c.1849G>A	c.(1849-1851)Gag>Aag	p.E617K	CUL9_ENST00000372647.2_Missense_Mutation_p.E617K|CUL9_ENST00000354495.3_Missense_Mutation_p.E507K	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	617					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						AGCAAAGGCCGAGGCCCCTAA	0.557													G|||	11	0.00219649	0.0	0.0043	5008	,	,		16267	0.0		0.007	False		,,,				2504	0.001				p.E617K		Atlas-SNP	.											.	CUL9	248	.	0			c.G1849A						PASS	.	G	LYS/GLU	9,4397	16.8+/-37.8	0,9,2194	63.0	61.0	62.0		1849	2.9	0.2	6	dbSNP_134	62	77,8523	44.0+/-102.2	0,77,4223	yes	missense	CUL9	NM_015089.2	56	0,86,6417	AA,AG,GG		0.8953,0.2043,0.6612	benign	617/2518	43155718	86,12920	2203	4300	6503	SO:0001583	missense	23113	exon7			AAGGCCGAGGCCC	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.1849G>A	6.37:g.43155718G>A	ENSP00000252050:p.Glu617Lys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	11.61	1.691091	0.30052	0.002043	0.008953	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.73258	-0.73;-0.7;-0.63	4.72	2.9	0.33743	.	1.879480	0.02107	N	0.054435	T	0.39937	0.1097	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.30909	-0.9962	10	0.87932	D	0	-5.0552	5.3876	0.16226	0.1878:0.1703:0.6419:0.0	.	617;617;617	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	K	617;507;617	ENSP00000252050:E617K;ENSP00000346490:E507K;ENSP00000361730:E617K	ENSP00000252050:E617K	E	+	1	0	CUL9	43263696	0.020000	0.18652	0.189000	0.23252	0.870000	0.49936	1.715000	0.37971	0.658000	0.30925	0.467000	0.42956	GAG	G|0.995;A|0.005	0.005	strong		0.557	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
TAS2R4	50832	hgsc.bcm.edu	37	7	141478308	141478308	+	Missense_Mutation	SNP	T	T	C	rs2233998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141478308T>C	ENST00000247881.2	+	1	67	c.20T>C	c.(19-21)tTc>tCc	p.F7S	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	7			F -> S (in dbSNP:rs2233998).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		TTATTCTATTTCTCTGCTATT	0.358													T|||	2156	0.430511	0.1725	0.5245	5008	,	,		20668	0.6667		0.4662	False		,,,				2504	0.4325				p.F7S		Atlas-SNP	.											.	TAS2R4	25	.	0			c.T20C						PASS	.	T	SER/PHE	996,3410	371.0+/-319.8	121,754,1328	72.0	70.0	71.0		20	1.6	0.0	7	dbSNP_98	71	4228,4372	569.0+/-389.1	1033,2162,1105	yes	missense	TAS2R4	NM_016944.1	155	1154,2916,2433	CC,CT,TT		49.1628,22.6055,40.1661	benign	7/300	141478308	5224,7782	2203	4300	6503	SO:0001583	missense	50832	exon1			TCTATTTCTCTGC	AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.20T>C	7.37:g.141478308T>C	ENSP00000247881:p.Phe7Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	1023	0.4684065934065934	99	0.20121951219512196	191	0.5276243093922652	385	0.6730769230769231	348	0.45910290237467016	T	3.837	-0.034653	0.07543	0.226055	0.491628	ENSG00000127364	ENST00000247881	T	0.00691	5.84	5.38	1.63	0.23807	.	1.653120	0.03116	N	0.163157	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.14559	-1.0468	9	0.25751	T	0.34	.	8.4546	0.32890	0.0:0.2331:0.0:0.7669	rs2233998;rs3807567;rs52795179;rs2233998	7	Q9NYW5	TA2R4_HUMAN	S	7	ENSP00000247881:F7S	ENSP00000247881:F7S	F	+	2	0	TAS2R4	141124777	0.003000	0.15002	0.000000	0.03702	0.009000	0.06853	1.441000	0.35035	0.123000	0.18342	-0.263000	0.10527	TTC	T|0.571;C|0.429	0.429	strong		0.358	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238126	31238126	+	Silent	SNP	G	G	A	rs2308618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238126G>A	ENST00000376228.5	-	4	770	c.756C>T	c.(754-756)acC>acT	p.T252T	HLA-C_ENST00000383329.3_Silent_p.T252T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	252	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						CCACAAGCTCGGTGTCCTGGG	0.617																																					p.T252T		Atlas-SNP	.											.	HLA-C	92	.	0			c.C756T						PASS	.	G		253,4153		17,219,1967	49.0	42.0	45.0		756	-2.7	0.0	6	dbSNP_126	45	740,7856		50,640,3608	no	coding-synonymous	HLA-C	NM_002117.5		67,859,5575	AA,AG,GG		8.6087,5.7422,7.6373		252/367	31238126	993,12009	2203	4298	6501	SO:0001819	synonymous_variant	3107	exon4			AAGCTCGGTGTCC	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.756C>T	6.37:g.31238126G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			G|0.908;A|0.092	0.092	strong		0.617	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
NACAD	23148	hgsc.bcm.edu	37	7	45122723	45122723	+	Missense_Mutation	SNP	G	G	A	rs61740895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45122723G>A	ENST00000490531.2	-	2	3075	c.3056C>T	c.(3055-3057)gCg>gTg	p.A1019V		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1019					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGTGGAATCCGCATCTTCCTG	0.622													G|||	1204	0.240415	0.0272	0.3833	5008	,	,		21118	0.2877		0.332	False		,,,				2504	0.2843				p.A1019V		Atlas-SNP	.											.	NACAD	44	.	0			c.C3056T						PASS	.	G	VAL/ALA	114,1270		8,98,586	19.0	18.0	19.0		3056	2.0	0.0	7	dbSNP_129	19	1117,2065		187,743,661	yes	missense	NACAD	NM_001146334.1	64	195,841,1247	AA,AG,GG		35.1037,8.237,26.9601	benign	1019/1563	45122723	1231,3335	692	1591	2283	SO:0001583	missense	23148	exon2			GAATCCGCATCTT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3056C>T	7.37:g.45122723G>A	ENSP00000420477:p.Ala1019Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	127	33	0.259843	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	551	0.2522893772893773	13	0.026422764227642278	134	0.3701657458563536	150	0.26223776223776224	254	0.33509234828496043	G	7.346	0.621835	0.14193	0.08237	0.351037	ENSG00000136274	ENST00000490531	T	0.11385	2.78	3.79	1.97	0.26223	.	2.516370	0.03046	U	0.153903	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.41998	-0.9477	9	0.02654	T	1	0.6018	3.6281	0.08121	0.2167:0.0:0.5896:0.1937	.	1019	O15069	NACAD_HUMAN	V	1019	ENSP00000420477:A1019V	ENSP00000420477:A1019V	A	-	2	0	NACAD	45089248	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.103000	0.10940	0.395000	0.25257	-0.480000	0.04831	GCG	G|0.739;A|0.261	0.261	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
PRRG2	5639	hgsc.bcm.edu	37	19	50086806	50086806	+	Silent	SNP	C	C	T	rs3745474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50086806C>T	ENST00000246794.5	+	3	262	c.93C>T	c.(91-93)ttC>ttT	p.F31F	NOSIP_ENST00000339093.3_5'Flank|PRRG2_ENST00000596700.1_Intron|NOSIP_ENST00000596358.1_5'Flank	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	31						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		CAGAAGTCTTCCTGGGTCCCC	0.587													C|||	1502	0.29992	0.4849	0.2622	5008	,	,		16279	0.1875		0.173	False		,,,				2504	0.3231				p.F31F		Atlas-SNP	.											PRRG2,NS,carcinoma,0,1	PRRG2	13	1	0			c.C93T						PASS	.	C		1862,2544		403,1056,744	77.0	90.0	86.0		93	3.8	1.0	19	dbSNP_107	86	1575,7025		128,1319,2853	no	coding-synonymous	PRRG2	NM_000951.2		531,2375,3597	TT,TC,CC		18.314,42.2606,26.4263		31/203	50086806	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	5639	exon3			AGTCTTCCTGGGT		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.93C>T	19.37:g.50086806C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_000951	Q6IBF8	Silent	SNP	ENST00000246794.5	37	CCDS12773.1																																																																																			C|0.741;T|0.259	0.259	strong		0.587	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	A	G	rs34988193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65235776A>G	ENST00000380230.3	+	11	1092	c.1063A>G	c.(1063-1065)Aag>Gag	p.K355E	ANKDD1A_ENST00000395723.1_Missense_Mutation_p.K264E|ANKDD1A_ENST00000395720.1_Missense_Mutation_p.K355E|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.K355E	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	116	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	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	
RANBP9	10048	hgsc.bcm.edu	37	6	13711279	13711279	+	Silent	SNP	A	A	G	rs6905991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	69	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	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		
TBC1D32	221322	hgsc.bcm.edu	37	6	121629167	121629167	+	Silent	SNP	G	G	A	rs9398629	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	194	0	0		WXS	Illumina HiSeq	Phase_I	158	71	0.449367	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	
PRR15	222171	hgsc.bcm.edu	37	7	29606316	29606316	+	Missense_Mutation	SNP	C	C	A	rs112093295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:29606316C>A	ENST00000319694.2	+	2	1083	c.371C>A	c.(370-372)cCc>cAc	p.P124H		NM_175887.2	NP_787083.1	Q8IV56	PRR15_HUMAN	proline rich 15	124					multicellular organismal development (GO:0007275)					endometrium(1)|lung(1)|skin(1)	3						CCTGGTGACCCCCACGAGGAC	0.657													C|||	270	0.0539137	0.003	0.0476	5008	,	,		11674	0.002		0.0815	False		,,,				2504	0.1524				p.P124H		Atlas-SNP	.											PRR15,NS,carcinoma,0,3	PRR15	6	3	0			c.C371A						PASS	.	C	HIS/PRO	47,4289		0,47,2121	6.0	7.0	7.0		371	4.5	0.0	7	dbSNP_132	7	584,7910		14,556,3677	yes	missense	PRR15	NM_175887.2	77	14,603,5798	AA,AC,CC		6.8754,1.0839,4.9182	probably-damaging	124/130	29606316	631,12199	2168	4247	6415	SO:0001583	missense	222171	exon2			GTGACCCCCACGA	BC029131	CCDS5421.1	7p15.1	2006-08-21			ENSG00000176532	ENSG00000176532			22310	protein-coding gene	gene with protein product						12477932	Standard	NM_175887		Approved		uc003tac.1	Q8IV56	OTTHUMG00000128555	ENST00000319694.2:c.371C>A	7.37:g.29606316C>A	ENSP00000317836:p.Pro124His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	101	30	0.29703	NM_175887		Missense_Mutation	SNP	ENST00000319694.2	37	CCDS5421.1	79	0.036172161172161175	2	0.0040650406504065045	16	0.04419889502762431	1	0.0017482517482517483	60	0.079155672823219	C	19.68	3.872544	0.72180	0.010839	0.068754	ENSG00000176532	ENST00000319694	T	0.51817	0.69	5.43	4.54	0.55810	.	0.553031	0.18142	N	0.150373	T	0.06600	0.0169	L	0.60455	1.87	0.22389	N	0.999143	D	0.65815	0.995	P	0.60415	0.874	T	0.02437	-1.1159	10	0.44086	T	0.13	-2.6431	10.0131	0.41999	0.0:0.9066:0.0:0.0934	.	124	Q8IV56	PRR15_HUMAN	H	124	ENSP00000317836:P124H	ENSP00000317836:P124H	P	+	2	0	PRR15	29572841	0.783000	0.28701	0.036000	0.18154	0.299000	0.27559	3.047000	0.49854	1.292000	0.44672	0.491000	0.48974	CCC	A|0.036;C|0.963;G|0.000	0.036	strong		0.657	PRR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250402.2	NM_175887	
GPR116	221395	hgsc.bcm.edu	37	6	46846060	46846060	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46846060C>T	ENST00000283296.7	-	10	1407	c.1119G>A	c.(1117-1119)ttG>ttA	p.L373L	GPR116_ENST00000362015.4_Silent_p.L373L|GPR116_ENST00000456426.2_Intron|GPR116_ENST00000265417.7_Silent_p.L373L	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	373	Ig-like 2.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CTTCATTTGCCAAAATTTGGA	0.358																																					p.L373L	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G1119A						PASS	.						138.0	123.0	128.0					6																	46846060		2202	4300	6502	SO:0001819	synonymous_variant	221395	exon10			ATTTGCCAAAATT	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1119G>A	6.37:g.46846060C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	208	54	0.259615	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			.	.	none		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
SLC24A4	123041	hgsc.bcm.edu	37	14	92922900	92922900	+	Silent	SNP	G	G	A	rs77671856	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:92922900G>A	ENST00000532405.1	+	12	1429	c.1203G>A	c.(1201-1203)ccG>ccA	p.P401P	SLC24A4_ENST00000298877.1_Silent_p.P384P|SLC24A4_ENST00000351924.5_Silent_p.P365P|SLC24A4_ENST00000531433.1_Silent_p.P382P|SLC24A4_ENST00000556739.1_3'UTR|SLC24A4_ENST00000393265.2_Silent_p.P337P			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	401	Poly-Pro.				amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		AGCCACCACCGCCAGAGCCAG	0.622											OREG0022876	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	858	0.171326	0.1596	0.2392	5008	,	,		16905	0.0724		0.2445	False		,,,				2504	0.1656				p.P401P	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											SLC24A4,colon,carcinoma,0,1	SLC24A4	112	1	0			c.G1203A						PASS	.	G	,,	737,3659		68,601,1529	30.0	36.0	34.0		1203,1146,1011	1.1	0.2	14	dbSNP_131	34	2181,6399		274,1633,2383	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC24A4	NM_153646.3,NM_153647.3,NM_153648.3	,,	342,2234,3912	AA,AG,GG		25.4196,16.7652,22.4877	,,	401/623,382/604,337/559	92922900	2918,10058	2198	4290	6488	SO:0001819	synonymous_variant	123041	exon12			ACCACCGCCAGAG	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"""Solute carriers"""	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1203G>A	14.37:g.92922900G>A		Somatic	33	0	0	1293	WXS	Illumina HiSeq	Phase_I	38	35	0.921053	NM_153646	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Silent	SNP	ENST00000532405.1	37	CCDS9903.2	389	0.17811355311355312	71	0.1443089430894309	93	0.2569060773480663	42	0.07342657342657342	183	0.24142480211081793	G	0.084	-1.179173	0.01633	0.167652	0.254196	ENSG00000140090	ENST00000525557	.	.	.	4.15	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.23762	-1.0179	3	.	.	.	.	6.9551	0.24565	0.1773:0.4239:0.3988:0.0	.	.	.	.	T	267	.	.	A	+	1	0	SLC24A4	91992653	0.000000	0.05858	0.203000	0.23512	0.007000	0.05969	-0.606000	0.05654	0.388000	0.25054	-0.384000	0.06662	GCC	G|0.792;A|0.208	0.208	strong		0.622	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646	
GPR108	56927	hgsc.bcm.edu	37	19	6737516	6737516	+	Silent	SNP	C	C	T	rs11539591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6737516C>T	ENST00000264080.7	-	1	98	c.72G>A	c.(70-72)gtG>gtA	p.V24V	TRIP10_ENST00000313285.8_5'Flank|TRIP10_ENST00000596758.1_5'Flank|GPR108_ENST00000430424.4_5'Flank|TRIP10_ENST00000313244.9_5'Flank|TRIP10_ENST00000600428.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	24						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						CCAGCAGCAGCACCAGAAGTA	0.726													C|||	466	0.0930511	0.0408	0.2291	5008	,	,		11089	0.002		0.172	False		,,,				2504	0.0798				p.V24V		Atlas-SNP	.											.	GPR108	35	.	0			c.G72A						PASS	.	C		159,3439		5,149,1645	4.0	8.0	7.0		72	3.0	0.8	19	dbSNP_120	7	1213,6641		77,1059,2791	no	coding-synonymous	GPR108	NM_001080452.1		82,1208,4436	TT,TC,CC		15.4444,4.4191,11.9804		24/544	6737516	1372,10080	1799	3927	5726	SO:0001819	synonymous_variant	56927	exon1			CAGCAGCACCAGA		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"""GPCR / Unclassified : 7TM orphan receptors"""	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.72G>A	19.37:g.6737516C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_001080452	B9EJD7	Silent	SNP	ENST00000264080.7	37	CCDS42479.1	217	0.09935897435897435	27	0.054878048780487805	71	0.19613259668508287	1	0.0017482517482517483	118	0.15567282321899736	C	8.583	0.882728	0.17467	0.044191	0.154444	ENSG00000125734	ENST00000549846	.	.	.	4.1	3.04	0.35103	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999994513	.	.	.	.	.	.	T	0.07309	-1.0779	3	.	.	.	-19.2802	9.5993	0.39593	0.0:0.786:0.214:0.0	rs11539591	.	.	.	T	24	.	.	A	-	1	0	GPR108	6688516	0.212000	0.23540	0.829000	0.32907	0.497000	0.33675	0.038000	0.13862	0.919000	0.36945	0.555000	0.69702	GCT	C|0.900;T|0.100	0.100	strong		0.726	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		
CA9	768	hgsc.bcm.edu	37	9	35674053	35674053	+	Missense_Mutation	SNP	G	G	A	rs2071676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35674053G>A	ENST00000378357.4	+	1	201	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	33			V -> M (in dbSNP:rs2071676). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8084592}.		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)	GCTGCTTCTGGTGCCTGTCCA	0.657													G|||	1619	0.323283	0.0764	0.4078	5008	,	,		17771	0.4444		0.3569	False		,,,				2504	0.4376				p.V33M		Atlas-SNP	.											.	CA9	48	.	0			c.G97A						PASS	.	G	MET/VAL	507,3899	236.1+/-248.4	28,451,1724	62.0	56.0	58.0		97	3.1	1.0	9	dbSNP_96	58	2993,5607	462.1+/-365.6	527,1939,1834	yes	missense	CA9	NM_001216.2	21	555,2390,3558	AA,AG,GG		34.8023,11.507,26.9107	possibly-damaging	33/460	35674053	3500,9506	2203	4300	6503	SO:0001583	missense	768	exon1			CTTCTGGTGCCTG	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.97G>A	9.37:g.35674053G>A	ENSP00000367608:p.Val33Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	37	CCDS6585.1	705	0.3228021978021978	54	0.10975609756097561	133	0.3674033149171271	264	0.46153846153846156	254	0.33509234828496043	G	11.61	1.688594	0.29962	0.11507	0.348023	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.72505	-0.66	5.01	3.11	0.35812	.	1.392810	0.04640	N	0.405154	T	0.00012	0.0000	L	0.34521	1.04	0.39357	P	0.034143000000000034	P;P	0.43701	0.815;0.718	P;B	0.46389	0.515;0.316	T	0.22836	-1.0205	9	0.87932	D	0	.	8.0091	0.30342	0.0:0.1758:0.6418:0.1824	rs2071676;rs17855453;rs2071676	33;33	F5H404;Q16790	.;CAH9_HUMAN	M	33	ENSP00000367608:V33M	ENSP00000367608:V33M	V	+	1	0	CA9	35664053	0.004000	0.15560	0.989000	0.46669	0.478000	0.33099	0.359000	0.20233	0.654000	0.30846	0.655000	0.94253	GTG	G|0.707;A|0.293	0.293	strong		0.657	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
SIGLEC8	27181	hgsc.bcm.edu	37	19	51961519	51961519	+	Silent	SNP	C	C	A	rs140904107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51961519C>A	ENST00000321424.3	-	1	189	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SIGLEC8_ENST00000430817.1_Silent_p.L41L|SIGLEC8_ENST00000340550.5_Silent_p.L41L|SIGLEC8_ENST00000597352.1_5'Flank	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	41	Ig-like V-type.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			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)		CATGGACACACAGGCCCTCCT	0.597																																					p.L41L		Atlas-SNP	.											SIGLEC8,NS,carcinoma,-2,1	SIGLEC8	130	1	0			c.G123T						PASS	.	C		2,4404		0,2,2201	141.0	124.0	130.0		123	-0.2	0.8	19	dbSNP_134	130	6,8594		0,6,4294	no	coding-synonymous	SIGLEC8	NM_014442.2		0,8,6495	AA,AC,CC		0.0698,0.0454,0.0615		41/500	51961519	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	27181	exon1			GACACACAGGCCC	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.123G>T	19.37:g.51961519C>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																			C|0.999;A|0.001	0.001	strong		0.597	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
FGFR4	2264	hgsc.bcm.edu	37	5	176517797	176517797	+	Missense_Mutation	SNP	C	C	T	rs376618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176517797C>T	ENST00000292408.4	+	4	652	c.407C>T	c.(406-408)cCc>cTc	p.P136L	FGFR4_ENST00000292410.3_Missense_Mutation_p.P136L|FGFR4_ENST00000393637.1_Missense_Mutation_p.P136L|FGFR4_ENST00000502906.1_Missense_Mutation_p.P136L|FGFR4_ENST00000393648.2_Missense_Mutation_p.P136L	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	136			P -> L (in dbSNP:rs376618). {ECO:0000269|PubMed:10631118, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.10, ECO:0000269|Ref.7, 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)	CATAGGGACCCCTCGAATAGG	0.562										TSP Lung(9;0.080)			C|||	4043	0.807308	0.6301	0.8271	5008	,	,		19623	1.0		0.7396	False		,,,				2504	0.9039				p.P136L		Atlas-SNP	.											.	FGFR4	174	.	0			c.C407T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	2911,1495	677.1+/-403.3	952,1007,244	113.0	104.0	107.0		407,407,407	2.8	0.0	5	dbSNP_80	107	6467,2133	714.9+/-406.0	2424,1619,257	yes	missense,missense,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	98,98,98	3376,2626,501	TT,TC,CC		24.8023,33.931,27.8948	benign,benign,benign	136/803,136/763,136/803	176517797	9378,3628	2203	4300	6503	SO:0001583	missense	2264	exon3			GGGACCCCTCGAA	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.407C>T	5.37:g.176517797C>T	ENSP00000292408:p.Pro136Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	1779|1779	0.8145604395604396|0.8145604395604396	350|350	0.7113821138211383|0.7113821138211383	294|294	0.8121546961325967|0.8121546961325967	572|572	1.0|1.0	563|563	0.7427440633245382|0.7427440633245382	C|C	2.403|2.403	-0.337075|-0.337075	0.05278|0.05278	0.66069|0.66069	0.751977|0.751977	ENSG00000160867|ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637|ENST00000377207	T;T;T;T;T;T|.	0.79352|.	-1.26;-1.01;-1.21;-1.26;-1.24;-1.24|.	5.01|5.01	2.85|2.85	0.33270|0.33270	.|.	2.189500|2.189500	0.02831|0.02831	U|N	0.126819|0.126819	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;B;B|.	0.06786|.	0.0;0.001;0.0;0.0;0.0|.	B;B;B;B;B|.	0.06405|.	0.001;0.002;0.001;0.0;0.0|.	T|T	0.39781|0.39781	-0.9597|-0.9597	9|6	0.26408|0.15066	T|T	0.33|0.55	.|.	9.6489|9.6489	0.39886|0.39886	0.0:0.803:0.0:0.197|0.0:0.803:0.0:0.197	rs376618;rs1057632;rs61561915;rs376618|rs376618;rs1057632;rs61561915;rs376618	136;136;136;136;136|.	B5A965;B4DVP5;P22455-2;E7EWF4;P22455|.	.;.;.;.;FGFR4_HUMAN|.	L|S	136|211	ENSP00000292408:P136L;ENSP00000424905:P136L;ENSP00000377259:P136L;ENSP00000424960:P136L;ENSP00000292410:P136L;ENSP00000377254:P136L|.	ENSP00000292408:P136L|ENSP00000366412:P211S	P|P	+|+	2|1	0|0	FGFR4|FGFR4	176450403|176450403	0.094000|0.094000	0.21725|0.21725	0.018000|0.018000	0.16275|0.16275	0.107000|0.107000	0.19398|0.19398	1.658000|1.658000	0.37376|0.37376	1.120000|1.120000	0.41904|0.41904	0.313000|0.313000	0.20887|0.20887	CCC|CCT	C|0.247;T|0.753	0.753	strong		0.562	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
ANKRD18A	253650	hgsc.bcm.edu	37	9	38577101	38577101	+	Missense_Mutation	SNP	G	G	A	rs2996335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:38577101G>A	ENST00000399703.5	-	14	3064	c.2690C>T	c.(2689-2691)gCc>gTc	p.A897V	ANKRD18A_ENST00000357072.5_5'UTR|ANKRD18A_ENST00000313339.3_Missense_Mutation_p.A18V|ANKRD18A_ENST00000566717.2_Missense_Mutation_p.A35V|ANKRD18A_ENST00000607974.1_Missense_Mutation_p.A18V	NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	897				A -> V (in Ref. 1; BAC23111 and 4; AAI52435). {ECO:0000305}.						NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TCCTGCAAAGGCTTCCTTAAA	0.313													.|||	287	0.0573083	0.1437	0.0403	5008	,	,		16714	0.0		0.0139	False		,,,				2504	0.0562				p.A897V		Atlas-SNP	.											.	ANKRD18A	49	.	0			c.C2690T						PASS	.						30.0	25.0	27.0					9																	38577101		692	1582	2274	SO:0001583	missense	253650	exon14			GCAAAGGCTTCCT	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.2690C>T	9.37:g.38577101G>A	ENSP00000382610:p.Ala897Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	116	39	0.336207	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	84	0.038461538461538464	51	0.10365853658536585	20	0.055248618784530384	0	0.0	13	0.017150395778364115	G	9.530	1.110677	0.20714	.	.	ENSG00000180071	ENST00000313339;ENST00000357072;ENST00000399703	T;T	0.30448	1.53;1.53	1.53	0.336	0.15958	.	.	.	.	.	T	0.01592	0.0051	M	0.72479	2.2	0.09310	N	1	D;P	0.69078	0.997;0.794	D;P	0.77004	0.989;0.676	T	0.01508	-1.1337	9	0.45353	T	0.12	.	3.2241	0.06726	0.742:0.0:0.258:0.0	rs2996335;rs2996335	18;897	Q6QA70;Q8IVF6	.;AN18A_HUMAN	V	18;18;897	ENSP00000326555:A18V;ENSP00000382610:A897V	ENSP00000326555:A18V	A	-	2	0	ANKRD18A	38567101	0.961000	0.32948	0.004000	0.12327	0.001000	0.01503	1.577000	0.36515	0.086000	0.17137	-0.498000	0.04607	GCC	G|0.966;A|0.034	0.034	strong		0.313	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
GRID2IP	392862	hgsc.bcm.edu	37	7	6550540	6550540	+	Splice_Site	SNP	G	G	A	rs61732373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6550540G>A	ENST00000457091.2	-	9	1553	c.1554C>T	c.(1552-1554)tgC>tgT	p.C518C	GRID2IP_ENST00000452113.1_Splice_Site_p.C327C|GRID2IP_ENST00000435185.1_Splice_Site_p.C334C	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	518					long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						CAGCCTTACCGCAGCTGAGGC	0.672													G|||	43	0.00858626	0.0015	0.0014	5008	,	,		16778	0.003		0.0219	False		,,,				2504	0.0153				p.C518C		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C1554T						PASS	.	G		14,1370		0,14,678	32.0	33.0	33.0		1554	-4.4	0.5	7	dbSNP_129	33	111,3071		1,109,1481	yes	coding-synonymous-near-splice	GRID2IP	NM_001145118.1		1,123,2159	AA,AG,GG		3.4884,1.0116,2.7376		518/1212	6550540	125,4441	692	1591	2283	SO:0001630	splice_region_variant	392862	exon9			CTTACCGCAGCTG		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.1555+1C>T	7.37:g.6550540G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	142	94	0.661972	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			G|0.984;A|0.016	0.016	strong		0.672	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	Silent
CHFR	55743	hgsc.bcm.edu	37	12	133435716	133435716	+	Silent	SNP	T	T	G	rs35011845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133435716T>G	ENST00000432561.2	-	8	958	c.885A>C	c.(883-885)ccA>ccC	p.P295P	CHFR_ENST00000537522.1_5'Flank|CHFR_ENST00000315585.7_Silent_p.P254P|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000266880.7_Silent_p.P295P|CHFR_ENST00000450056.2_Silent_p.P283P|CHFR_ENST00000443047.2_Silent_p.P203P			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	295					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		CCATCTTGTCTGGCTTCCCAG	0.592													T|||	712	0.142173	0.0106	0.1585	5008	,	,		18006	0.1726		0.2793	False		,,,				2504	0.136				p.P295P		Atlas-SNP	.											.	CHFR	83	.	0			c.A885C						PASS	.	T	,,,,	223,4183	137.3+/-173.1	9,205,1989	216.0	124.0	155.0		885,885,849,609,762	-11.0	0.1	12	dbSNP_126	155	2569,6031	417.4+/-352.4	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GT,TT		29.8721,5.0613,21.467	,,,,	295/665,295/664,283/653,203/573,254/624	133435716	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon8			CTTGTCTGGCTTC	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.885A>C	12.37:g.133435716T>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			T|0.796;G|0.204	0.204	strong		0.592	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
MYRF	745	hgsc.bcm.edu	37	11	61551356	61551356	+	Silent	SNP	T	T	C	rs174535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:61551356T>C	ENST00000278836.5	+	24	3249	c.3153T>C	c.(3151-3153)agT>agC	p.S1051S	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Silent_p.S1011S|MYRF_ENST00000389602.4_Silent_p.S437S	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	1051					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCCCTGTCAGTAGTGGCACCC	0.637													C|||	1703	0.340056	0.1467	0.6037	5008	,	,		18016	0.5694		0.3549	False		,,,				2504	0.1626				p.S1051S		Atlas-SNP	.											C11orf9,colon,carcinoma,0,1	.	.	1	0			c.T3153C						scavenged	.	C	,	894,3510	726.5+/-409.7	107,680,1415	53.0	39.0	44.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3153,3033	1.3	0.9	11	dbSNP_79	44	2860,5738	657.4+/-401.5	498,1864,1937	no	coding-synonymous,coding-synonymous	C11orf9	NM_001127392.1,NM_013279.2	,	605,2544,3352	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	33.2635,20.2997,28.8725	,	1051/1152,1011/1112	61551356	3754,9248	2202	4299	6501	SO:0001819	synonymous_variant	745	exon24			TGTCAGTAGTGGC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.3153T>C	11.37:g.61551356T>C		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_001127392	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																			T|0.705;C|0.295	0.295	strong		0.637	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
PRR32	100130613	hgsc.bcm.edu	37	X	125955428	125955428	+	Silent	SNP	G	G	A	rs2269777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:125955428G>A	ENST00000371125.3	+	2	887	c.807G>A	c.(805-807)ccG>ccA	p.P269P		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		269	Pro-rich.																CTCCTCCTCCGATATTTGGTC	0.483													G|||	1178	0.312053	0.0386	0.2363	3775	,	,		14648	0.3601		0.3827	False		,,,				2504	0.2198				p.P269P		Atlas-SNP	.											.	.	.	.	0			c.G807A						PASS	.	G		121,1088		6,85,24,426,151	356.0	235.0	272.0		807	-7.9	0.0	X	dbSNP_100	272	1227,1164		216,397,398,187,393	no	coding-synonymous	CXorf64	NM_001122716.1		222,482,422,613,544	AA,AG,A,GG,G		48.6826,10.0083,37.4444		269/299	125955428	1348,2252	692	1591	2283	SO:0001819	synonymous_variant	100130613	exon2			TCCTCCGATATTT																												ENST00000371125.3:c.807G>A	X.37:g.125955428G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001122716		Silent	SNP	ENST00000371125.3	37	CCDS48163.1																																																																																			G|0.667;0|0.006	.	strong		0.483	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
MFF	56947	hgsc.bcm.edu	37	2	228194480	228194480	+	Missense_Mutation	SNP	A	A	T	rs3211097|rs386655869	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:228194480A>T	ENST00000353339.3	+	3	460	c.19A>T	c.(19-21)Agt>Tgt	p.S7C	MFF_ENST00000524634.1_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000409616.1_5'UTR|MFF_ENST00000409565.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7C|MFF_ENST00000349901.7_Intron|MFF_ENST00000476924.1_Intron	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						AGGAACAAGCAGTGACACATC	0.368													A|||	1349	0.269369	0.0961	0.245	5008	,	,		17571	0.2431		0.3678	False		,,,				2504	0.4468				p.S7C		Atlas-SNP	.											.	MFF	48	.	0			c.A19T						PASS	.	A	CYS/SER	521,3885		30,461,1712	125.0	117.0	120.0		19	4.8	1.0	2	dbSNP_105	120	3003,5597		552,1899,1849	yes	missense	MFF	NM_020194.4	112	582,2360,3561	TT,TA,AA		34.9186,11.8248,27.0952	probably-damaging	7/343	228194480	3524,9482	2203	4300	6503	SO:0001583	missense	56947	exon3			ACAAGCAGTGACA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.19A>T	2.37:g.228194480A>T	ENSP00000302037:p.Ser7Cys	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	147	59	0.401361	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	429	0.19642857142857142	32	0.06504065040650407	88	0.2430939226519337	107	0.18706293706293706	202	0.26649076517150394	A	14.82	2.649436	0.47362	0.118248	0.349186	ENSG00000168958	ENST00000353339;ENST00000436237;ENST00000443428;ENST00000392059	T;T;T;T	0.61859	1.33;0.07;1.32;1.33	5.97	4.8	0.61643	.	0.300115	0.29253	N	0.012695	T	0.00012	0.0000	N	0.22421	0.69	0.36388	P	0.13765799999999995	B	0.02656	0.0	B	0.04013	0.001	T	0.32824	-0.9892	8	.	.	.	-1.6615	10.3927	0.44181	0.8539:0.0:0.0:0.1461	rs3211097;rs10166885;rs17414924;rs3211097	7	Q9GZY8	MFF_HUMAN	C	7	ENSP00000302037:S7C;ENSP00000411386:S7C;ENSP00000391829:S7C;ENSP00000375912:S7C	.	S	+	1	0	MFF	227902724	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.440000	0.52886	1.049000	0.40321	0.528000	0.53228	AGT	A|0.744;T|0.256	0.256	strong		0.368	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
MAF1	84232	hgsc.bcm.edu	37	8	145161823	145161823	+	Missense_Mutation	SNP	G	G	A	rs11546144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145161823G>A	ENST00000322428.5	+	7	1110	c.706G>A	c.(706-708)Ggg>Agg	p.G236R	MAF1_ENST00000534585.1_Missense_Mutation_p.G266R|SHARPIN_ENST00000533948.1_5'Flank|MAF1_ENST00000532522.1_Missense_Mutation_p.G236R|SHARPIN_ENST00000398712.2_5'Flank|KIAA1875_ENST00000323662.8_5'Flank	NM_032272.4	NP_115648.2	Q9H063	MAF1_HUMAN	MAF1 homolog (S. cerevisiae)	236			G -> R (in dbSNP:rs11546144). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	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)			central_nervous_system(1)|lung(8)|urinary_tract(1)	10	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;3.1e-42)|Epithelial(56;1.23e-40)|all cancers(56;4.84e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AAGCAGAAGCGGGGGCAGTGG	0.642													G|||	4429	0.884385	0.6876	0.9366	5008	,	,		16457	0.999		0.9105	False		,,,				2504	0.9683				p.G236R		Atlas-SNP	.											.	MAF1	16	.	0			c.G706A						PASS	.	G	ARG/GLY	3163,1231		1141,881,175	40.0	46.0	44.0		706	0.4	0.1	8	dbSNP_120	44	7891,701		3626,639,31	yes	missense	MAF1	NM_032272.4	125	4767,1520,206	AA,AG,GG		8.1588,28.0155,14.8776	benign	236/257	145161823	11054,1932	2197	4296	6493	SO:0001583	missense	84232	exon7			AGAAGCGGGGGCA		CCDS6416.1	8q24.3	2012-10-29			ENSG00000179632	ENSG00000179632			24966	protein-coding gene	gene with protein product		610210				11230166, 11438659	Standard	NM_032272		Approved	DKFZp586G1123	uc003zbc.1	Q9H063	OTTHUMG00000165244	ENST00000322428.5:c.706G>A	8.37:g.145161823G>A	ENSP00000318604:p.Gly236Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_032272	D3DWL4	Missense_Mutation	SNP	ENST00000322428.5	37	CCDS6416.1	1938	0.8873626373626373	339	0.6890243902439024	337	0.930939226519337	571	0.9982517482517482	691	0.9116094986807388	G	4.978	0.181685	0.09495	0.719845	0.918412	ENSG00000179632	ENST00000322428;ENST00000534585;ENST00000532522;ENST00000534811	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	4.8	0.43	0.16515	.	0.543925	0.15793	N	0.244347	T	0.00012	0.0000	N	0.14661	0.345	0.53005	P	3.500000000000725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.34079	-0.9843	9	0.10111	T	0.7	-0.2861	6.7493	0.23477	0.6533:0.0:0.3467:0.0	rs11546144;rs17851097;rs17851671;rs17852937;rs58268825;rs11546144	236	Q9H063	MAF1_HUMAN	R	236;266;236;54	ENSP00000318604:G236R;ENSP00000433979:G266R;ENSP00000436720:G236R;ENSP00000436639:G54R	ENSP00000318604:G236R	G	+	1	0	MAF1	145233811	0.223000	0.23663	0.066000	0.19879	0.053000	0.15095	1.526000	0.35964	-0.072000	0.12864	-0.136000	0.14681	GGG	G|0.144;A|0.856	0.856	strong		0.642	MAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382910.1	NM_032272	
LRRTM1	347730	hgsc.bcm.edu	37	2	80530819	80530819	+	Silent	SNP	C	C	A	rs186584392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:80530819C>A	ENST00000295057.3	-	2	782	c.126G>T	c.(124-126)ctG>ctT	p.L42L	CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Silent_p.L42L|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000541047.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	42	LRRNT.				exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CGCACCGGCACAGCTGCGGGC	0.692										HNSCC(69;0.2)			C|||	56	0.0111821	0.0	0.0115	5008	,	,		11537	0.002		0.0298	False		,,,				2504	0.0164				p.L42L		Atlas-SNP	.											LRRTM1_ENST00000295057,NS,carcinoma,0,2	LRRTM1	251	2	0			c.G126T						PASS	.	C	,,	16,4180		0,16,2082	13.0	17.0	16.0		,,126	2.7	1.0	2		16	151,8177		0,151,4013	no	intron,intron,coding-synonymous	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,	0,167,6095	AA,AC,CC		1.8132,0.3813,1.3334	,,	,,42/523	80530819	167,12357	2098	4164	6262	SO:0001819	synonymous_variant	347730	exon2			CCGGCACAGCTGC	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.126G>T	2.37:g.80530819C>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																			C|0.983;A|0.017	0.017	strong		0.692	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
APLP1	333	hgsc.bcm.edu	37	19	36370011	36370011	+	Silent	SNP	G	G	A	rs2227909	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36370011G>A	ENST00000221891.4	+	16	1941	c.1749G>A	c.(1747-1749)gtG>gtA	p.V583V	APLP1_ENST00000537454.2_Silent_p.V543V|APLP1_ENST00000586861.1_Silent_p.V576V|RN7SL402P_ENST00000465059.1_RNA	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	582					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTGAGGCTGTGTCGGGTCTGC	0.637													G|||	577	0.115216	0.3003	0.0403	5008	,	,		17147	0.0823		0.0249	False		,,,				2504	0.045				p.V583V		Atlas-SNP	.											.	APLP1	77	.	0			c.G1749A						PASS	.	G	,	1211,3195	421.3+/-339.3	163,885,1155	47.0	48.0	47.0		1749,1746	5.2	1.0	19	dbSNP_98	47	306,8294	109.6+/-170.1	2,302,3996	no	coding-synonymous,coding-synonymous	APLP1	NM_001024807.1,NM_005166.3	,	165,1187,5151	AA,AG,GG		3.5581,27.4852,11.6638	,	583/652,582/651	36370011	1517,11489	2203	4300	6503	SO:0001819	synonymous_variant	333	exon16			GGCTGTGTCGGGT	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"""amyloid-like protein 1"", ""amyloid precursor-like protein 1"""	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1749G>A	19.37:g.36370011G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001024807	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																			G|0.886;A|0.114	0.114	strong		0.637	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
LAMA1	284217	hgsc.bcm.edu	37	18	7034508	7034508	+	Missense_Mutation	SNP	T	T	G	rs566655	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:7034508T>G	ENST00000389658.3	-	14	2114	c.2021A>C	c.(2020-2022)aAc>aCc	p.N674T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	674	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.		N -> T (in dbSNP:rs566655). {ECO:0000269|PubMed:1714537, ECO:0000269|PubMed:2049067}.		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)				AGAATTGTAGTTGGCTCTGAT	0.378													T|||	752	0.15016	0.1467	0.1974	5008	,	,		17017	0.1042		0.2247	False		,,,				2504	0.092				p.N674T		Atlas-SNP	.											.	LAMA1	458	.	0			c.A2021C						PASS	.	T	THR/ASN	724,3682	298.4+/-285.3	65,594,1544	115.0	111.0	113.0		2021	4.8	1.0	18	dbSNP_83	113	1987,6613	347.4+/-326.6	242,1503,2555	yes	missense	LAMA1	NM_005559.3	65	307,2097,4099	GG,GT,TT		23.1047,16.4321,20.8442	benign	674/3076	7034508	2711,10295	2203	4300	6503	SO:0001583	missense	284217	exon14			TTGTAGTTGGCTC	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.2021A>C	18.37:g.7034508T>G	ENSP00000374309:p.Asn674Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	382	0.1749084249084249	70	0.14227642276422764	65	0.17955801104972377	72	0.1258741258741259	175	0.23087071240105542	T	4.754	0.140128	0.09083	0.164321	0.231047	ENSG00000101680	ENST00000389658	T	0.29917	1.55	5.9	4.75	0.60458	Laminin B type IV (2);Laminin B, subgroup (1);	0.170205	0.51477	D	0.000090	T	0.00012	0.0000	N	0.05050	-0.12	0.32727	P	0.509567	P	0.41475	0.751	B	0.44315	0.446	T	0.13575	-1.0504	9	0.02654	T	1	.	9.7988	0.40751	0.0:0.1374:0.0:0.8626	rs566655;rs17442820;rs52791113;rs59387906;rs566655	674	P25391	LAMA1_HUMAN	T	674	ENSP00000374309:N674T	ENSP00000374309:N674T	N	-	2	0	LAMA1	7024508	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.256000	0.18351	1.067000	0.40740	0.533000	0.62120	AAC	T|0.807;G|0.193	0.193	strong		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
GPR98	84059	hgsc.bcm.edu	37	5	90079811	90079811	+	Silent	SNP	C	C	T	rs41311745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:90079811C>T	ENST00000405460.2	+	67	13686	c.13590C>T	c.(13588-13590)ccC>ccT	p.P4530P	GPR98_ENST00000425867.2_Silent_p.P191P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4530	Calx-beta 31. {ECO:0000305|PubMed:11606593}.				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)		TTGCTAATCCCAATTCCACAA	0.398													C|||	28	0.00559105	0.0008	0.0043	5008	,	,		18649	0.0		0.0219	False		,,,				2504	0.002				p.P4530P		Atlas-SNP	.											.	GPR98	605	.	0			c.C13590T						PASS	.	C		21,3687		0,21,1833	41.0	41.0	41.0		13590	2.7	1.0	5	dbSNP_127	41	157,8011		2,153,3929	no	coding-synonymous	GPR98	NM_032119.3		2,174,5762	TT,TC,CC		1.9221,0.5663,1.4988		4530/6307	90079811	178,11698	1854	4084	5938	SO:0001819	synonymous_variant	84059	exon67			TAATCCCAATTCC	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.13590C>T	5.37:g.90079811C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			A|0.001;C|0.992;T|0.006	0.006	strong		0.398	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
OR5B2	390190	hgsc.bcm.edu	37	11	58190112	58190112	+	Missense_Mutation	SNP	A	A	G	rs10466659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:58190112A>G	ENST00000302581.2	-	1	674	c.623T>C	c.(622-624)gTt>gCt	p.V208A		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	208			V -> A (in dbSNP:rs10466659).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V208A(1)		NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AACTAGAAGAACAAAAAAGAT	0.383													G|||	1120	0.223642	0.2708	0.2032	5008	,	,		22875	0.1448		0.2097	False		,,,				2504	0.2699				p.V208A		Atlas-SNP	.											OR5B2,NS,carcinoma,0,1	OR5B2	75	1	1	Substitution - Missense(1)	stomach(1)	c.T623C						scavenged	.	G	ALA/VAL	1033,3369	726.5+/-409.7	104,825,1272	61.0	60.0	61.0		623	3.7	0.8	11	dbSNP_119	61	1854,6736	729.5+/-406.7	200,1454,2641	yes	missense	OR5B2	NM_001005566.2	64	304,2279,3913	GG,GA,AA		21.5832,23.4666,22.2214	benign	208/310	58190112	2887,10105	2201	4295	6496	SO:0001583	missense	390190	exon1			AGAAGAACAAAAA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.623T>C	11.37:g.58190112A>G	ENSP00000303076:p.Val208Ala	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	476	0.21794871794871795	159	0.3231707317073171	60	0.16574585635359115	95	0.1660839160839161	162	0.21372031662269128	G	0.003	-2.458902	0.00173	0.234666	0.215832	ENSG00000172365	ENST00000302581	T	0.37235	1.21	3.73	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35291	N	0.003307	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39313	-0.9620	9	0.07813	T	0.8	-5.0223	7.397	0.26942	0.1004:0.1696:0.73:0.0	rs10466659;rs17565464;rs10466659	208	Q96R09	OR5B2_HUMAN	A	208	ENSP00000303076:V208A	ENSP00000303076:V208A	V	-	2	0	OR5B2	57946688	0.013000	0.17824	0.831000	0.32960	0.037000	0.13140	1.975000	0.40569	0.932000	0.37266	-0.197000	0.12766	GTT	A|0.781;G|0.219	0.219	strong		0.383	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74205878C>T	ENST00000286523.5	-	2	1616	c.834G>A	c.(832-834)ccG>ccA	p.P278P	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Silent_p.P278P	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	95	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	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	
SLC5A1	6523	hgsc.bcm.edu	37	22	32487744	32487744	+	Silent	SNP	C	C	T	rs17683448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32487744C>T	ENST00000266088.4	+	11	1525	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	SLC5A1_ENST00000543737.1_Silent_p.A298A	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	425					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TCATGATTGCCGGAAGGTAAA	0.532													C|||	111	0.0221645	0.003	0.0259	5008	,	,		12307	0.0		0.0606	False		,,,				2504	0.0286				p.A425A		Atlas-SNP	.											.	SLC5A1	80	.	0			c.C1275T	GRCh37	CI962348	SLC5A1	I	rs17683448	PASS	.	C		61,4345	58.1+/-94.6	0,61,2142	88.0	73.0	78.0		1275	-4.7	0.8	22	dbSNP_123	78	602,7998	157.9+/-211.5	20,562,3718	no	coding-synonymous	SLC5A1	NM_000343.3		20,623,5860	TT,TC,CC		7.0,1.3845,5.0976		425/665	32487744	663,12343	2203	4300	6503	SO:0001819	synonymous_variant	6523	exon11			GATTGCCGGAAGG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1275C>T	22.37:g.32487744C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Silent	SNP	ENST00000266088.4	37	CCDS13902.1																																																																																			C|0.955;T|0.045	0.045	strong		0.532	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
LRP1B	53353	hgsc.bcm.edu	37	2	141751592	141751592	+	Silent	SNP	G	G	A	rs13007735	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:141751592G>A	ENST00000389484.3	-	16	3587	c.2616C>T	c.(2614-2616)gaC>gaT	p.D872D	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	872	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)		CATCGCTTCCGTCTAGGCAGT	0.433										TSP Lung(27;0.18)			G|||	2552	0.509585	0.6059	0.3847	5008	,	,		17244	0.6141		0.3748	False		,,,				2504	0.499				p.D872D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,lymphoid_neoplasm,-2,1	LRP1B	1315	1	0			c.C2616T						PASS	.	G		2406,2000	615.0+/-392.5	650,1106,447	129.0	122.0	125.0		2616	-5.2	0.7	2	dbSNP_121	125	2780,5820	440.7+/-359.6	451,1878,1971	no	coding-synonymous	LRP1B	NM_018557.2		1101,2984,2418	AA,AG,GG		32.3256,45.3926,39.8739		872/4600	141751592	5186,7820	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon16			GCTTCCGTCTAGG	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.2616C>T	2.37:g.141751592G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.558;A|0.442	0.442	strong		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721036	135721036	+	Silent	SNP	C	C	T	rs34629706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:135721036C>T	ENST00000264977.3	+	2	1313	c.696C>T	c.(694-696)tgC>tgT	p.C232C	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	232					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						TAAAGATGTGCTTGGACATCT	0.328													C|||	177	0.0353435	0.0023	0.0216	5008	,	,		19948	0.001		0.0954	False		,,,				2504	0.0634				p.C232C		Atlas-SNP	.											PPP2R3A,colon,carcinoma,+1,1	PPP2R3A	114	1	0			c.C696T						PASS	.	C	,	62,4318		0,62,2128	42.0	46.0	45.0		,696	3.4	1.0	3	dbSNP_126	45	643,7951		18,607,3672	no	intron,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4	,	18,669,5800	TT,TC,CC		7.482,1.4155,5.4339	,	,232/1151	135721036	705,12269	2190	4297	6487	SO:0001819	synonymous_variant	5523	exon2			GATGTGCTTGGAC	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.696C>T	3.37:g.135721036C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			C|0.945;T|0.055	0.055	strong		0.328	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
MUC4	4585	hgsc.bcm.edu	37	3	195474159	195474159	+	Missense_Mutation	SNP	G	G	A	rs62284986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195474159G>A	ENST00000346145.4	-	24	3458	c.3419C>T	c.(3418-3420)gCc>gTc	p.A1140V	MUC4_ENST00000463781.3_Missense_Mutation_p.A5376V|MUC4_ENST00000349607.4_Missense_Mutation_p.A1089V|MUC4_ENST00000475231.1_Missense_Mutation_p.A5324V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2133					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)		GCCGCCCAGGGCCCCAAAGAA	0.617													.|||	616	0.123003	0.1165	0.0994	5008	,	,		27753	0.0466		0.1938	False		,,,				2504	0.1544				p.A5376V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C16127T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	465,3941	214.5+/-233.7	11,443,1749	73.0	72.0	72.0		3419,16127,3266	4.3	0.1	3	dbSNP_129	72	1654,6946	300.6+/-305.0	144,1366,2790	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	64,64,64	155,1809,4539	AA,AG,GG		19.2326,10.5538,16.2925	probably-damaging,probably-damaging,probably-damaging	1140/1177,5376/5413,1089/1126	195474159	2119,10887	2203	4300	6503	SO:0001583	missense	4585	exon25			CCCAGGGCCCCAA	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	ENST00000346145.4:c.3419C>T	3.37:g.195474159G>A	ENSP00000304207:p.Ala1140Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	263	53	0.201521	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	ENST00000346145.4	37	CCDS3310.1	279	0.12774725274725274	53	0.10772357723577236	38	0.10497237569060773	36	0.06293706293706294	152	0.20052770448548812	g	14.14	2.445671	0.43429	0.105538	0.192326	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.51071	0.72;1.07;1.15;1.13	5.14	4.26	0.50523	.	0.574939	0.15528	N	0.257648	T	0.00073	0.0002	M	0.69823	2.125	0.80722	P	0.0	D;B;B;B;B;B	0.58268	0.982;0.068;0.068;0.041;0.041;0.068	P;B;B;B;B;B	0.48627	0.584;0.058;0.058;0.026;0.026;0.058	T	0.07868	-1.0750	9	0.72032	D	0.01	-16.8905	9.2366	0.37470	0.0999:0.0:0.9001:0.0	rs62284986	5248;1089;1140;5376;5324;2081	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	V	1089;1140;5376;5324;1876	ENSP00000338109:A1089V;ENSP00000304207:A1140V;ENSP00000417498:A5376V;ENSP00000420243:A5324V	ENSP00000304207:A1140V	A	-	2	0	MUC4	196959830	0.942000	0.31987	0.141000	0.22245	0.580000	0.36256	4.549000	0.60726	1.171000	0.42768	0.543000	0.68304	GCC	G|0.849;A|0.151	0.151	strong		0.617	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
OR2C3	81472	hgsc.bcm.edu	37	1	247694949	247694949	+	Missense_Mutation	SNP	G	G	C	rs6702693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247694949G>C	ENST00000366487.3	-	2	1226	c.865C>G	c.(865-867)Ctt>Gtt	p.L289V	GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366490.3_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	289			L -> V (in dbSNP:rs6702693).			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(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-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)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			GTGTAAATAAGTGGGTTCAGC	0.532													G|||	712	0.142173	0.1029	0.098	5008	,	,		21698	0.1042		0.173	False		,,,				2504	0.2342				p.L289V		Atlas-SNP	.											.	OR2C3	92	.	0			c.C865G						PASS	.	G	VAL/LEU	485,3921	226.5+/-242.0	30,425,1748	95.0	83.0	87.0		865	0.8	0.0	1	dbSNP_116	87	1362,7238	266.0+/-286.5	99,1164,3037	yes	missense	OR2C3	NM_198074.4	32	129,1589,4785	CC,CG,GG		15.8372,11.0077,14.2011	possibly-damaging	289/321	247694949	1847,11159	2203	4300	6503	SO:0001583	missense	81472	exon2			AAATAAGTGGGTT	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"""GPCR / Class A : Olfactory receptors"""	15005	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily C, member 4"""	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.865C>G	1.37:g.247694949G>C	ENSP00000355443:p.Leu289Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	37	CCDS1634.2	277	0.12683150183150182	52	0.10569105691056911	40	0.11049723756906077	52	0.09090909090909091	133	0.17546174142480211	G	6.291	0.421715	0.11928	0.110077	0.158372	ENSG00000196242	ENST00000366487	T	0.39592	1.07	3.91	0.788	0.18601	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31392	U	0.007725	T	0.00039	0.0001	N	0.21097	0.63	0.80722	P	0.0	B	0.16603	0.018	B	0.19666	0.026	T	0.09079	-1.0691	9	0.59425	D	0.04	.	5.0558	0.14531	0.2966:0.0:0.558:0.1455	rs6702693	289	Q8N628	OR2C3_HUMAN	V	289	ENSP00000355443:L289V	ENSP00000355443:L289V	L	-	1	0	OR2C3	245761572	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-2.875000	0.00718	-0.174000	0.10743	-0.797000	0.03246	CTT	G|0.854;C|0.146	0.146	strong		0.532	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
KMT2C	58508	hgsc.bcm.edu	37	7	151962134	151962134	+	Nonsense_Mutation	SNP	G	G	T	rs146238849		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151962134G>T	ENST00000262189.6	-	8	1391	c.1173C>A	c.(1171-1173)tgC>tgA	p.C391*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.C391*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	391					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)	p.C391*(2)									TGCAGTTCTGGCACACTTTGC	0.408																																					p.C391X		Atlas-SNP	.											MLL3_ENST00000355193,NS,malignant_melanoma,0,2	MLL3	1564	2	2	Substitution - Nonsense(2)	NS(2)	c.C1173A						scavenged	.						230.0	213.0	219.0					7																	151962134		2203	4297	6500	SO:0001587	stop_gained	58508	exon8			GTTCTGGCACACT	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.1173C>A	7.37:g.151962134G>T	ENSP00000262189:p.Cys391*	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	185	24	0.12973	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	39	7.887843	0.98545	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	4.53	3.62	0.41486	.	0.000000	0.45867	U	0.000330	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2395	0.54534	0.0835:0.0:0.9165:0.0	.	.	.	.	X	391	.	ENSP00000262189:C391X	C	-	3	2	MLL3	151593067	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.718000	0.74713	2.206000	0.71126	0.460000	0.39030	TGC	.	.	weak		0.408	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ITGB5	3693	hgsc.bcm.edu	37	3	124515509	124515509	+	Silent	SNP	G	G	A	rs2291088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124515509G>A	ENST00000296181.4	-	10	1715	c.1419C>T	c.(1417-1419)agC>agT	p.S473S		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	473	Cysteine-rich tandem repeats.				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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TGCACCTGGCGCTGTTGGGTT	0.667													G|||	817	0.163139	0.118	0.2565	5008	,	,		18336	0.1657		0.1521	False		,,,				2504	0.1667				p.S473S		Atlas-SNP	.											.	ITGB5	66	.	0			c.C1419T						PASS	.	G		543,3863	239.6+/-250.7	41,461,1701	31.0	32.0	32.0		1419	1.3	0.1	3	dbSNP_100	32	1387,7213	261.4+/-283.8	108,1171,3021	no	coding-synonymous	ITGB5	NM_002213.3		149,1632,4722	AA,AG,GG		16.1279,12.3241,14.8393		473/800	124515509	1930,11076	2203	4300	6503	SO:0001819	synonymous_variant	3693	exon10			CCTGGCGCTGTTG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1419C>T	3.37:g.124515509G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	37	CCDS3030.1	359|359	0.16437728937728938|0.16437728937728938	59|59	0.11991869918699187|0.11991869918699187	84|84	0.23204419889502761|0.23204419889502761	107|107	0.18706293706293706|0.18706293706293706	109|109	0.1437994722955145|0.1437994722955145	G|G	0.422|0.422	-0.907623|-0.907623	0.02434|0.02434	0.123241|0.123241	0.161279|0.161279	ENSG00000082781|ENSG00000082781	ENST00000481591|ENST00000496703	.|.	.|.	.|.	5.26|5.26	1.33|1.33	0.21861|0.21861	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10245|0.10245	-1.0638|-1.0638	3|3	.|.	.|.	.|.	.|.	9.2896|9.2896	0.37778|0.37778	0.2929:0.0:0.7071:0.0|0.2929:0.0:0.7071:0.0	rs2291088;rs3197039;rs17850112;rs2291088|rs2291088;rs3197039;rs17850112;rs2291088	.|.	.|.	.|.	V|C	163|240	.|.	.|.	A|R	-|-	2|1	0|0	ITGB5|ITGB5	125998199|125998199	0.995000|0.995000	0.38212|0.38212	0.118000|0.118000	0.21660|0.21660	0.019000|0.019000	0.09904|0.09904	2.252000|2.252000	0.43196|0.43196	0.054000|0.054000	0.16065|0.16065	0.563000|0.563000	0.77884|0.77884	GCG|CGC	G|0.851;A|0.149	0.149	strong		0.667	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
SLC6A2	6530	hgsc.bcm.edu	37	16	55690874	55690874	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:55690874G>A	ENST00000379906.2	+	1	523	c.268G>A	c.(268-270)Ggc>Agc	p.G90S	SLC6A2_ENST00000219833.8_Missense_Mutation_p.G90S|SLC6A2_ENST00000568943.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000414754.3_Missense_Mutation_p.G90S|SLC6A2_ENST00000566163.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000561820.1_Missense_Mutation_p.G90S	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	90					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTACAAGAACGGCGGCGGTGA	0.622																																					p.G90S		Atlas-SNP	.											SLC6A2_ENST00000219833,colon,carcinoma,0,2	SLC6A2	189	2	0			c.G268A						PASS	.						69.0	74.0	72.0					16																	55690874		2198	4300	6498	SO:0001583	missense	6530	exon2			AAGAACGGCGGCG		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.268G>A	16.37:g.55690874G>A	ENSP00000369237:p.Gly90Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879435	0.72294	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	D;D;D	0.87491	-2.26;-2.26;-2.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.96775	0.8947	H	0.99169	4.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98465	1.0598	10	0.87932	D	0	.	19.2658	0.93984	0.0:0.0:1.0:0.0	.	90;90	Q96KH8;P23975	.;SC6A2_HUMAN	S	90	ENSP00000394956:G90S;ENSP00000369237:G90S;ENSP00000219833:G90S	ENSP00000219833:G90S	G	+	1	0	SLC6A2	54248375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.728000	0.98792	2.620000	0.88729	0.563000	0.77884	GGC	.	.	none		0.622	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
PTPN2	5771	hgsc.bcm.edu	37	18	12814237	12814237	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:12814237C>T	ENST00000309660.5	-	7	916	c.823G>A	c.(823-825)Gga>Aga	p.G275R	PTPN2_ENST00000353319.4_Missense_Mutation_p.G275R|PTPN2_ENST00000591115.1_Missense_Mutation_p.G298R|PTPN2_ENST00000327283.3_Missense_Mutation_p.G275R|PTPN2_ENST00000591497.1_Missense_Mutation_p.G246R	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	275	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				CATTTTGCTCCTTCTATTATA	0.318																																					p.G298R		Atlas-SNP	.											PTPN2,bladder,carcinoma,+1,1	PTPN2	37	1	0			c.G892A						scavenged	.						97.0	92.0	93.0					18																	12814237		2202	4300	6502	SO:0001583	missense	5771	exon8			TTGCTCCTTCTAT	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.823G>A	18.37:g.12814237C>T	ENSP00000311857:p.Gly275Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	2	0.0186916	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.736965	0.89482	.	.	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	T;T;T	0.04317	3.69;3.71;3.65	5.86	5.86	0.93980	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.244648	0.28683	N	0.014496	T	0.21347	0.0514	M	0.88181	2.935	0.80722	D	1	P;P;P;B;P	0.46020	0.871;0.868;0.512;0.398;0.792	P;P;B;B;B	0.50049	0.629;0.628;0.334;0.22;0.424	T	0.00728	-1.1591	10	0.87932	D	0	.	20.1931	0.98233	0.0:1.0:0.0:0.0	.	275;275;252;275;275	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	R	275;275;252;275	ENSP00000320298:G275R;ENSP00000320546:G275R;ENSP00000311857:G275R	ENSP00000311857:G275R	G	-	1	0	PTPN2	12804237	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.771000	0.95319	0.563000	0.77884	GGA	.	.	none		0.318	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423	
MIER2	54531	hgsc.bcm.edu	37	19	307345	307345	+	Missense_Mutation	SNP	G	G	A	rs34129568	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:307345G>A	ENST00000264819.4	-	13	1400	c.1390C>T	c.(1390-1392)Cca>Tca	p.P464S	CTD-3113P16.5_ENST00000591533.1_RNA	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	464			P -> S (in dbSNP:rs34129568).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)		CTGGCGTCTGGCTCCGGAGCA	0.677													G|||	27	0.00539137	0.0008	0.0144	5008	,	,		15015	0.0		0.0159	False		,,,				2504	0.0				p.P464S		Atlas-SNP	.											.	MIER2	51	.	0			c.C1390T						PASS	.	G	SER/PRO	17,4383		0,17,2183	17.0	18.0	18.0		1390	0.5	0.0	19	dbSNP_126	18	172,8424		5,162,4131	yes	missense	MIER2	NM_017550.1	74	5,179,6314	AA,AG,GG		2.0009,0.3864,1.4543	possibly-damaging	464/546	307345	189,12807	2200	4298	6498	SO:0001583	missense	54531	exon13			CGTCTGGCTCCGG	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"""KIAA1193"""	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.1390C>T	19.37:g.307345G>A	ENSP00000264819:p.Pro464Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	127	48	0.377953	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	23	0.010531135531135532	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	14	0.018469656992084433	G	8.445	0.851638	0.17034	0.003864	0.020009	ENSG00000105556	ENST00000264819	T	0.20332	2.08	4.02	0.505	0.16953	.	0.708385	0.12017	N	0.507328	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	P	0.43094	0.799	B	0.30401	0.115	T	0.23154	-1.0196	10	0.38643	T	0.18	-2.3485	9.1802	0.37136	0.0846:0.2782:0.6371:0.0	rs34129568	464	Q8N344	MIER2_HUMAN	S	464	ENSP00000264819:P464S	ENSP00000264819:P464S	P	-	1	0	MIER2	258345	0.941000	0.31946	0.000000	0.03702	0.003000	0.03518	1.174000	0.31932	-0.122000	0.11766	-0.795000	0.03280	CCA	G|0.988;A|0.012	0.012	strong		0.677	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
GPR113	165082	hgsc.bcm.edu	37	2	26533898	26533898	+	Missense_Mutation	SNP	C	C	T	rs72811754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26533898C>T	ENST00000311519.1	-	11	2697	c.2698G>A	c.(2698-2700)Gtc>Atc	p.V900I	GPR113_ENST00000333478.6_Missense_Mutation_p.V701I|GPR113_ENST00000541401.1_Missense_Mutation_p.V503I|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Missense_Mutation_p.V831I	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	900					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)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGGGTGACACCTGCCAAC	0.612													C|||	9	0.00179712	0.0	0.0	5008	,	,		17885	0.0		0.006	False		,,,				2504	0.0031				p.V900I		Atlas-SNP	.											.	GPR113	134	.	0			c.G2698A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	38.0	36.0	36.0		2698,2491,2101	0.9	0.0	2	dbSNP_130	36	36,8564	23.4+/-69.3	0,36,4264	yes	missense,missense,missense	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	29,29,29	0,39,6464	TT,TC,CC		0.4186,0.0681,0.2999	benign,benign,benign	900/1080,831/998,701/874	26533898	39,12967	2203	4300	6503	SO:0001583	missense	165082	exon11			GGGTGACACCTGC	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.2698G>A	2.37:g.26533898C>T	ENSP00000307831:p.Val900Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	0.726	-0.781775	0.02929	6.81E-4	0.004186	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.78	0.853	0.19001	GPCR, family 2-like (1);	.	.	.	.	T	0.13628	0.0330	N	0.17631	0.505	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.18871	0.023;0.013;0.023;0.008	T	0.31447	-0.9943	9	0.11485	T	0.65	-4.2378	6.3783	0.21519	0.0:0.5889:0.1217:0.2894	.	831;701;900;503	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	I	503;701;831;900	ENSP00000445729:V503I;ENSP00000327396:V701I;ENSP00000388537:V831I;ENSP00000307831:V900I	ENSP00000307831:V900I	V	-	1	0	GPR113	26387402	0.000000	0.05858	0.000000	0.03702	0.992000	0.81027	0.166000	0.16583	0.093000	0.17368	0.650000	0.86243	GTC	C|0.998;T|0.002	0.002	strong		0.612	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
KIF19	124602	hgsc.bcm.edu	37	17	72346918	72346918	+	Silent	SNP	C	C	T	rs73995260	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72346918C>T	ENST00000389916.4	+	12	1599	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	AC103809.2_ENST00000599136.1_Silent_p.S131S	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	487					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						ACGCTAAGGACGACAGCGAGA	0.642													c|||	364	0.0726837	0.1952	0.0447	5008	,	,		17763	0.001		0.0586	False		,,,				2504	0.0153				p.D487D		Atlas-SNP	.											.	KIF19	102	.	0			c.C1461T						PASS	.			807,3599	320.4+/-296.6	83,641,1479	124.0	112.0	116.0		1461	-10.7	0.0	17	dbSNP_130	116	444,8156	134.9+/-192.2	15,414,3871	no	coding-synonymous	KIF19	NM_153209.3		98,1055,5350	TT,TC,CC		5.1628,18.3159,9.6186		487/999	72346918	1251,11755	2203	4300	6503	SO:0001819	synonymous_variant	124602	exon12			TAAGGACGACAGC	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.1461C>T	17.37:g.72346918C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.906;T|0.094	0.094	strong		0.642	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
PEAR1	375033	hgsc.bcm.edu	37	1	156882996	156882996	+	Silent	SNP	G	G	C	rs822441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156882996G>C	ENST00000338302.3	+	20	2658	c.2433G>C	c.(2431-2433)ccG>ccC	p.P811P	PEAR1_ENST00000292357.7_Silent_p.P811P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	811	Pro-rich.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATGTCCCTCCGAGCTACAGTC	0.597													G|||	1599	0.319289	0.5477	0.147	5008	,	,		18610	0.3323		0.159	False		,,,				2504	0.2843				p.P811P		Atlas-SNP	.											PEAR1,NS,carcinoma,+2,1	PEAR1	118	1	0			c.G2433C						scavenged	.	G		2121,2285	577.1+/-384.4	487,1147,569	124.0	117.0	120.0		2433	-10.6	0.0	1	dbSNP_86	120	1372,7228	267.2+/-287.2	116,1140,3044	no	coding-synonymous	PEAR1	NM_001080471.1		603,2287,3613	CC,CG,GG		15.9535,48.1389,26.8568		811/1038	156882996	3493,9513	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon19			CCCTCCGAGCTAC	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2433G>C	1.37:g.156882996G>C		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	111	27	0.243243	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			G|0.714;C|0.285	0.285	strong		0.597	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
NTNG2	84628	hgsc.bcm.edu	37	9	135073877	135073877	+	Silent	SNP	C	C	T	rs3824574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135073877C>T	ENST00000393229.3	+	3	1514	c.738C>T	c.(736-738)ttC>ttT	p.F246F	NTNG2_ENST00000360670.3_Silent_p.F246F|NTNG2_ENST00000372179.3_Silent_p.F246F|NTNG2_ENST00000393228.4_Silent_p.F246F	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	246	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		TCAAGGAGTTCTTCACCCTCA	0.647													C|||	1454	0.290335	0.1936	0.2493	5008	,	,		18045	0.378		0.3211	False		,,,				2504	0.3282				p.F246F		Atlas-SNP	.											NTNG2,NS,carcinoma,0,1	NTNG2	66	1	0			c.C738T						PASS	.	C		847,3559		86,675,1442	49.0	53.0	52.0		738	2.1	1.0	9	dbSNP_107	52	2736,5860		441,1854,2003	no	coding-synonymous	NTNG2	NM_032536.2		527,2529,3445	TT,TC,CC		31.8288,19.2238,27.5573		246/531	135073877	3583,9419	2203	4298	6501	SO:0001819	synonymous_variant	84628	exon3			GGAGTTCTTCACC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.738C>T	9.37:g.135073877C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																			C|0.711;T|0.289	0.289	strong		0.647	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
FAM78B	149297	hgsc.bcm.edu	37	1	166039898	166039898	+	Silent	SNP	C	C	G	rs41269662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:166039898C>G	ENST00000338353.3	-	3	955	c.366G>C	c.(364-366)gtG>gtC	p.V122V	FAM78B_ENST00000354422.3_Silent_p.V122V			Q5VT40	FA78B_HUMAN	family with sequence similarity 78, member B	122										central_nervous_system(1)|endometrium(5)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					CAACCAGGGTCACAGTTTCTG	0.542													C|||	1120	0.223642	0.211	0.3156	5008	,	,		19058	0.256		0.1501	False		,,,				2504	0.2178				p.V122V		Atlas-SNP	.											.	FAM78B	51	.	0			c.G366C						PASS	.	C		895,3511	347.2+/-309.4	91,713,1399	139.0	128.0	132.0		366	4.6	1.0	1	dbSNP_127	132	1132,7468	233.9+/-267.0	76,980,3244	no	coding-synonymous	FAM78B	NM_001017961.3		167,1693,4643	GG,GC,CC		13.1628,20.3132,15.5851		122/262	166039898	2027,10979	2203	4300	6503	SO:0001819	synonymous_variant	149297	exon2			CAGGGTCACAGTT	AL626787	CCDS30931.1	1q24.1	2008-02-05			ENSG00000188859	ENSG00000188859			13495	protein-coding gene	gene with protein product							Standard	NM_001017961		Approved		uc021pee.1	Q5VT40	OTTHUMG00000034705	ENST00000338353.3:c.366G>C	1.37:g.166039898C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_001017961	B7Z693	Silent	SNP	ENST00000338353.3	37	CCDS30931.1																																																																																			C|0.820;G|0.180	0.180	strong		0.542	FAM78B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343108.1	NM_001017961	
ZP3	7784	hgsc.bcm.edu	37	7	76069629	76069629	+	Silent	SNP	G	G	A	rs73363163		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76069629G>A	ENST00000394857.3	+	6	952	c.894G>A	c.(892-894)aaG>aaA	p.K298K	ZP3_ENST00000336517.4_Silent_p.K247K|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Silent_p.K122K	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	298	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						AACTCAACAAGGCCTGTTCCT	0.522																																					p.K298K		Atlas-SNP	.											.	ZP3	32	.	0			c.G894A						PASS	.	A	,	291,4111		0,291,1910	89.0	82.0	84.0		894,741	-0.7	1.0	7	dbSNP_131	84	1567,7031		10,1547,2742	no	coding-synonymous,coding-synonymous	ZP3	NM_001110354.1,NM_007155.5	,	10,1838,4652	AA,AG,GG		18.2252,6.6106,14.2923	,	298/425,247/374	76069629	1858,11142	2201	4299	6500	SO:0001819	synonymous_variant	7784	exon6			CAACAAGGCCTGT	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.894G>A	7.37:g.76069629G>A		Somatic	702	0	0		WXS	Illumina HiSeq	Phase_I	867	273	0.314879	NM_001110354	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1	399	0.18269230769230768	83	0.16869918699186992	65	0.17955801104972377	89	0.1555944055944056	162	0.21372031662269128	A	1.322	-0.599172	0.03744	0.066106	0.182252	ENSG00000188372	ENST00000394860	.	.	.	4.33	-0.658	0.11428	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01021	-1.1478	4	.	.	.	-23.2076	10.8429	0.46726	0.3399:0.0:0.6601:0.0	.	.	.	.	K	120	.	.	R	+	2	0	ZP3	75907565	1.000000	0.71417	0.968000	0.41197	0.203000	0.24098	0.911000	0.28584	-0.255000	0.09486	-0.361000	0.07541	AGG	.	.	weak		0.522	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
CCDC122	160857	hgsc.bcm.edu	37	13	44411432	44411432	+	Missense_Mutation	SNP	A	A	G	rs9567280	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:44411432A>G	ENST00000444614.3	-	7	1064	c.806T>C	c.(805-807)aTt>aCt	p.I269T		NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	269			I -> T (in dbSNP:rs9567280).							endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		TTGCATTCCAATGCATTTTCT	0.378													A|||	310	0.061901	0.0023	0.0447	5008	,	,		19468	0.1111		0.0577	False		,,,				2504	0.1084				p.I269T		Atlas-SNP	.											.	CCDC122	21	.	0			c.T806C						PASS	.	A	THR/ILE	25,3705		0,25,1840	155.0	137.0	143.0		806	5.3	0.2	13	dbSNP_119	143	388,7788		11,366,3711	yes	missense	CCDC122	NM_144974.3	89	11,391,5551	GG,GA,AA		4.7456,0.6702,3.4688	benign	269/274	44411432	413,11493	1865	4088	5953	SO:0001583	missense	160857	exon7			ATTCCAATGCATT	AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.806T>C	13.37:g.44411432A>G	ENSP00000407763:p.Ile269Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	185	99	0.535135	NM_144974	B2RP70|B7ZMI9|Q96MV0	Missense_Mutation	SNP	ENST00000444614.3	37	CCDS9390.2	130	0.05952380952380952	2	0.0040650406504065045	15	0.04143646408839779	64	0.11188811188811189	49	0.06464379947229551	A	15.73	2.919662	0.52653	0.006702	0.047456	ENSG00000151773	ENST00000444614	T	0.45276	0.9	5.35	5.35	0.76521	.	.	.	.	.	T	0.01124	0.0037	L	0.56769	1.78	0.09310	P	0.9999999808811	P	0.44429	0.835	P	0.44990	0.466	T	0.28267	-1.0049	8	0.72032	D	0.01	.	13.0079	0.58717	1.0:0.0:0.0:0.0	rs9567280	269	Q5T0U0	CC122_HUMAN	T	269	ENSP00000407763:I269T	ENSP00000407763:I269T	I	-	2	0	CCDC122	43309432	0.912000	0.30974	0.249000	0.24280	0.407000	0.30961	4.507000	0.60434	2.143000	0.66587	0.477000	0.44152	ATT	A|0.943;G|0.057	0.057	strong		0.378	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974	
TM7SF2	7108	hgsc.bcm.edu	37	11	64882789	64882789	+	Missense_Mutation	SNP	C	C	T	rs1129195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64882789C>T	ENST00000279263.7	+	8	1058	c.896C>T	c.(895-897)aCt>aTt	p.T299I	AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000345348.5_Intron|TM7SF2_ENST00000540748.1_Missense_Mutation_p.T183I	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	299			T -> I (in dbSNP:rs1129195). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9615229, ECO:0000269|PubMed:9878250}.		cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCACCAGCTACTGGTTACTAC	0.552													T|||	1829	0.365216	0.3268	0.5821	5008	,	,		20623	0.2728		0.4463	False		,,,				2504	0.2751				p.T299I		Atlas-SNP	.											.	TM7SF2	30	.	0			c.C896T						PASS	.	T	ILE/THR	1277,2639		223,831,904	130.0	136.0	134.0		896	2.7	0.0	11	dbSNP_86	134	3656,4642		801,2054,1294	yes	missense	TM7SF2	NM_003273.2	89	1024,2885,2198	TT,TC,CC		44.0588,32.6098,40.3881	benign	299/419	64882789	4933,7281	1958	4149	6107	SO:0001583	missense	7108	exon8			CAGCTACTGGTTA	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"""delta(14)-sterol reductase"""	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.896C>T	11.37:g.64882789C>T	ENSP00000279263:p.Thr299Ile	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	37	CCDS41669.1	834	0.38186813186813184	162	0.32926829268292684	202	0.5580110497237569	140	0.24475524475524477	330	0.43535620052770446	T	1.563	-0.536194	0.04082	0.326098	0.440588	ENSG00000149809	ENST00000526809;ENST00000279263;ENST00000534371;ENST00000540748;ENST00000525385;ENST00000531321;ENST00000527968	D;D;D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44	4.99	2.68	0.31781	.	0.722338	0.13496	N	0.383630	T	0.00012	0.0000	N	0.01019	-1.045	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38178	-0.9673	9	0.11485	T	0.65	-14.2266	7.7879	0.29103	0.0:0.2521:0.0:0.7479	rs1129195;rs2075758;rs3186811;rs17742646;rs17845357;rs17858207;rs60275679;rs1129195	183;299	F5GYV3;O76062	.;ERG24_HUMAN	I	181;299;231;183;270;205;131	ENSP00000432171:T181I;ENSP00000279263:T299I;ENSP00000432187:T231I;ENSP00000441215:T183I;ENSP00000433325:T270I;ENSP00000431300:T205I;ENSP00000431685:T131I	ENSP00000279263:T299I	T	+	2	0	TM7SF2	64639365	0.138000	0.22547	0.034000	0.17996	0.739000	0.42172	2.583000	0.46094	0.076000	0.16826	-0.361000	0.07541	ACT	C|0.636;T|0.364	0.364	strong		0.552	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
ZBTB40	9923	hgsc.bcm.edu	37	1	22852880	22852880	+	Missense_Mutation	SNP	G	G	C	rs45502998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22852880G>C	ENST00000375647.4	+	18	3918	c.3711G>C	c.(3709-3711)gaG>gaC	p.E1237D	ZBTB40_ENST00000374651.4_Missense_Mutation_p.E1125D|ZBTB40_ENST00000404138.1_Missense_Mutation_p.E1237D	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1237					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|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(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		TCTGTGGTGAGGCCAAATGAG	0.597													G|||	132	0.0263578	0.0015	0.0187	5008	,	,		20073	0.0		0.0368	False		,,,				2504	0.0818				p.E1237D		Atlas-SNP	.											.	ZBTB40	87	.	0			c.G3711C						PASS	.	G	ASP/GLU,ASP/GLU	31,4375	36.8+/-68.6	0,31,2172	131.0	118.0	122.0		3711,3711	3.7	1.0	1	dbSNP_127	122	304,8296	110.2+/-170.6	6,292,4002	yes	missense,missense	ZBTB40	NM_001083621.1,NM_014870.3	45,45	6,323,6174	CC,CG,GG		3.5349,0.7036,2.5757	benign,benign	1237/1240,1237/1240	22852880	335,12671	2203	4300	6503	SO:0001583	missense	9923	exon19			TGGTGAGGCCAAA	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.3711G>C	1.37:g.22852880G>C	ENSP00000364798:p.Glu1237Asp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	41	0.018772893772893772	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	28	0.036939313984168866	G	15.08	2.726291	0.48833	0.007036	0.035349	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.09538	2.97;2.97;2.99	5.7	3.74	0.42951	.	0.000000	0.56097	D	0.000030	T	0.02156	0.0067	L	0.32530	0.975	0.33714	D	0.616155	P;P	0.46784	0.884;0.816	P;B	0.46208	0.507;0.31	T	0.19257	-1.0311	10	0.45353	T	0.12	-26.467	7.6071	0.28107	0.2788:0.0:0.7212:0.0	rs45502998;rs61741571	1125;1237	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	D	1237;1237;1125	ENSP00000384527:E1237D;ENSP00000364798:E1237D;ENSP00000363782:E1125D	ENSP00000363782:E1125D	E	+	3	2	ZBTB40	22725467	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.652000	0.37313	0.678000	0.31325	0.655000	0.94253	GAG	G|0.974;C|0.026	0.026	strong		0.597	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
CCDC144NL	339184	hgsc.bcm.edu	37	17	20799194	20799194	+	Missense_Mutation	SNP	A	A	G	rs9907420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:20799194A>G	ENST00000327925.5	-	1	259	c.140T>C	c.(139-141)tTg>tCg	p.L47S	RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000582324.1_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	47										large_intestine(3)|lung(3)|skin(1)	7						GGAGAAGCCCAAGGACCACTG	0.627													N|||	417	0.0832668	0.1089	0.0951	5008	,	,		16892	0.0149		0.1183	False		,,,				2504	0.0746				p.L47S		Atlas-SNP	.											.	CCDC144NL	34	.	0			c.T140C						PASS	.	G	SER/LEU	366,4040		24,318,1861	73.0	74.0	73.0		140	-0.7	0.0	17	dbSNP_119	73	1004,7596		66,872,3362	no	missense	CCDC144NL	NM_001004306.1	145	90,1190,5223	GG,GA,AA		11.6744,8.3069,10.5336	benign	47/222	20799194	1370,11636	2203	4300	6503	SO:0001583	missense	339184	exon1			AAGCCCAAGGACC		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.140T>C	17.37:g.20799194A>G	ENSP00000328054:p.Leu47Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_001004306		Missense_Mutation	SNP	ENST00000327925.5	37	CCDS32591.1	173	0.07921245421245421	37	0.07520325203252033	38	0.10497237569060773	8	0.013986013986013986	90	0.11873350923482849	N	0.960	-0.703586	0.03255	0.083069	0.116744	ENSG00000205212	ENST00000327925	T	0.11604	2.76	0.624	-0.71	0.11234	.	.	.	.	.	T	0.00039	0.0001	N	0.01874	-0.695	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.35624	-0.9781	8	0.02654	T	1	.	1.5829	0.02638	0.3306:0.3805:0.0:0.2888	rs9907420	47	Q6NUI1	C144L_HUMAN	S	47	ENSP00000328054:L47S	ENSP00000328054:L47S	L	-	2	0	CCDC144NL	20739786	0.003000	0.15002	0.001000	0.08648	0.000000	0.00434	-1.616000	0.02053	-0.960000	0.03613	0.000000	0.15137	TTG	A|0.897;G|0.103	0.103	strong		0.627	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306	
AVPR1B	553	hgsc.bcm.edu	37	1	206225011	206225011	+	Missense_Mutation	SNP	G	G	C	rs33990840	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:206225011G>C	ENST00000367126.4	+	1	1036	c.571G>C	c.(571-573)Ggc>Cgc	p.G191R	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	191			G -> R (in dbSNP:rs33990840). {ECO:0000269|Ref.7}.		activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	GGCAGACTTCGGCTTCCCTTG	0.627													C|||	297	0.0593051	0.1256	0.0403	5008	,	,		16287	0.006		0.0507	False		,,,				2504	0.047				p.G191R		Atlas-SNP	.											.	AVPR1B	47	.	0			c.G571C						PASS	.	C	ARG/GLY	401,4001		19,363,1819	52.0	51.0	51.0		571	5.0	1.0	1	dbSNP_126	51	401,8187		14,373,3907	yes	missense	AVPR1B	NM_000707.3	125	33,736,5726	CC,CG,GG		4.6693,9.1095,6.174	benign	191/425	206225011	802,12188	2201	4294	6495	SO:0001583	missense	553	exon1			GACTTCGGCTTCC	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.571G>C	1.37:g.206225011G>C	ENSP00000356094:p.Gly191Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	117	0.05357142857142857	57	0.11585365853658537	17	0.04696132596685083	4	0.006993006993006993	39	0.051451187335092345	C	10.34	1.323494	0.24080	0.091095	0.046693	ENSG00000198049	ENST00000367126	T	0.37058	1.22	5.9	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.538057	0.19162	N	0.121180	T	0.00210	0.0006	N	0.05124	-0.11	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.09377	0.004	T	0.19943	-1.0290	9	0.12430	T	0.62	-19.2633	4.1308	0.10148	0.2403:0.4391:0.2464:0.0742	rs33990840	191	P47901	V1BR_HUMAN	R	191	ENSP00000356094:G191R	ENSP00000356094:G191R	G	+	1	0	AVPR1B	204391634	0.042000	0.20092	1.000000	0.80357	0.980000	0.70556	0.194000	0.17135	0.823000	0.34589	-0.215000	0.12644	GGC	G|0.938;C|0.062	0.062	strong		0.627	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1877480	1877480	+	Missense_Mutation	SNP	T	T	G	rs17683288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:1877480T>G	ENST00000398564.1	+	25	3025	c.3025T>G	c.(3025-3027)Tcc>Gcc	p.S1009A	ARHGEF10_ENST00000262112.6_Missense_Mutation_p.S980A|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.S946A|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.S984A|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.S1008A			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1009					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CAGTCAAGGCTCCAAGAAAGT	0.433													T|||	153	0.0305511	0.0038	0.0389	5008	,	,		15810	0.001		0.0736	False		,,,				2504	0.047				p.S984A		Atlas-SNP	.											ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	0			c.T2950G						scavenged	.	T	ALA/SER	66,4340	61.7+/-98.7	1,64,2138	87.0	87.0	87.0		2950	2.7	1.0	8	dbSNP_123	87	611,7989	159.4+/-212.7	28,555,3717	yes	missense	ARHGEF10	NM_014629.2	99	29,619,5855	GG,GT,TT		7.1047,1.498,5.2053	possibly-damaging	984/1345	1877480	677,12329	2203	4300	6503	SO:0001583	missense	9639	exon25			CAAGGCTCCAAGA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3025T>G	8.37:g.1877480T>G	ENSP00000381571:p.Ser1009Ala	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	157	94	0.598726	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		76	0.0347985347985348	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	57	0.07519788918205805	T	3.915	-0.019235	0.07634	0.01498	0.071047	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.05;-0.05	5.08	2.66	0.31614	.	0.308232	0.36200	N	0.002727	T	0.05731	0.0150	L	0.50919	1.6	0.09310	P	0.999999999999999	B;B	0.21688	0.059;0.01	B;B	0.22753	0.041;0.011	T	0.34428	-0.9829	9	0.07813	T	0.8	-13.8843	12.2936	0.54833	0.0:0.0:0.2956:0.7044	rs17683288;rs56496515;rs57650527;rs17683288	946;984	O15013-7;O15013-5	.;.	A	984;946;1008;1009;980;628	ENSP00000340297:S984A;ENSP00000427909:S946A;ENSP00000431012:S1008A;ENSP00000381571:S1009A;ENSP00000262112:S980A;ENSP00000427768:S628A	ENSP00000262112:S980A	S	+	1	0	ARHGEF10	1864887	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	3.497000	0.53295	0.336000	0.23639	-0.258000	0.10820	TCC	T|0.954;G|0.046	0.046	strong		0.433	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
RGAG4	340526	hgsc.bcm.edu	37	X	71349774	71349774	+	Silent	SNP	T	T	C	rs12393722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:71349774T>C	ENST00000545866.1	-	1	1984	c.1617A>G	c.(1615-1617)ggA>ggG	p.G539G	RGAG4_ENST00000609883.1_Silent_p.G539G|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	539										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					CTTGGCGTTGTCCTAAACGAC	0.592													C|||	1454	0.385166	0.1021	0.4193	3775	,	,		13966	0.119		0.5964	False		,,,				2504	0.3149				p.G539G		Atlas-SNP	.											.	RGAG4	63	.	0			c.A1617G						PASS	.	C	,	813,2507		106,477,124,792,446	46.0	49.0	48.0		,1617	2.2	0.9	X	dbSNP_120	48	5125,1342		1484,736,1421,120,366	no	intron,coding-synonymous	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,	1590,1213,1545,912,812	CC,CT,C,TT,T		20.7515,24.488,39.3277	,	,539/570	71349774	5938,3849	1945	4127	6072	SO:0001819	synonymous_variant	340526	exon1			GCGTTGTCCTAAA	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.1617A>G	X.37:g.71349774T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Silent	SNP	ENST00000545866.1	37	CCDS55446.1																																																																																			T|0.599;C|0.401	0.401	strong		0.592	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
KIF20B	9585	hgsc.bcm.edu	37	10	91497631	91497631	+	Missense_Mutation	SNP	T	T	A	rs1062465	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91497631T>A	ENST00000371728.3	+	20	3098	c.3033T>A	c.(3031-3033)gaT>gaA	p.D1011E	KIF20B_ENST00000394289.2_Missense_Mutation_p.D1011E|KIF20B_ENST00000416354.1_Missense_Mutation_p.D1041E|KIF20B_ENST00000260753.4_Missense_Mutation_p.D971E|KIF20B_ENST00000478929.1_3'UTR	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	75	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	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	
LCT	3938	hgsc.bcm.edu	37	2	136555659	136555659	+	Missense_Mutation	SNP	T	T	C	rs2322659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:136555659T>C	ENST00000264162.2	-	13	4926	c.4916A>G	c.(4915-4917)aAt>aGt	p.N1639S		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1639	4 X approximate repeats.		N -> S (in dbSNP:rs2322659). {ECO:0000269|PubMed:1902057}.		carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCACCTCATTGTAATCTCC	0.582											OREG0014998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2217	0.442692	0.3011	0.4669	5008	,	,		19883	0.4623		0.6382	False		,,,				2504	0.3957				p.N1639S		Atlas-SNP	.											LCT,NS,carcinoma,-1,2	LCT	309	2	0			c.A4916G						PASS	.	T	SER/ASN	1794,2612		346,1102,755	121.0	108.0	113.0		4916	-8.9	0.0	2	dbSNP_100	113	6240,2360		2335,1570,395	yes	missense	LCT	NM_002299.2	46	2681,2672,1150	CC,CT,TT		27.4419,40.7172,38.2285	benign	1639/1928	136555659	8034,4972	2203	4300	6503	SO:0001583	missense	3938	exon13			ACCTCATTGTAAT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4916A>G	2.37:g.136555659T>C	ENSP00000264162:p.Asn1639Ser	Somatic	72	0	0	1626	WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	1066	0.4880952380952381	132	0.2682926829268293	180	0.4972375690607735	262	0.458041958041958	492	0.6490765171503958	T	9.982	1.228511	0.22542	0.407172	0.725581	ENSG00000115850	ENST00000264162	T	0.30182	1.54	5.76	-8.89	0.00785	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.634460	0.18103	N	0.151626	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B	0.15473	0.013	B	0.20767	0.031	T	0.37709	-0.9694	9	0.33940	T	0.23	0.1499	10.073	0.42345	0.0:0.2833:0.4665:0.2502	rs2322659;rs3739023;rs61091462;rs2322659	1639	P09848	LPH_HUMAN	S	1639	ENSP00000264162:N1639S	ENSP00000264162:N1639S	N	-	2	0	LCT	136272129	0.000000	0.05858	0.000000	0.03702	0.963000	0.63663	-0.869000	0.04232	-1.651000	0.01504	0.533000	0.62120	AAT	T|0.466;C|0.534	0.534	strong		0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
CAPRIN1	4076	hgsc.bcm.edu	37	11	34107955	34107955	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:34107955C>T	ENST00000341394.4	+	11	1415	c.1226C>T	c.(1225-1227)cCt>cTt	p.P409L	CAPRIN1_ENST00000532820.1_Missense_Mutation_p.P409L|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.P409L|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.P409L|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.P328L	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	409					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				CTGGTTTGCCCTCCAGGTTAG	0.363																																					p.P409L		Atlas-SNP	.											CAPRIN1_ENST00000389645,colon,carcinoma,+1,2	CAPRIN1	110	2	0			c.C1226T						scavenged	.						76.0	73.0	74.0					11																	34107955		2202	4298	6500	SO:0001583	missense	4076	exon11			TTTGCCCTCCAGG	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"""cytoplasmic activation/proliferation-associated protein-1"""	601178	"""membrane component, chromosome 11, surface marker 1"", ""GPI-anchored membrane protein 1"""	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.1226C>T	11.37:g.34107955C>T	ENSP00000340329:p.Pro409Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	2	0.0277778	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	37	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611244	0.87258	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	6.03	6.03	0.97812	.	0.048925	0.85682	D	0.000000	T	0.47414	0.1444	M	0.63843	1.955	0.80722	D	1	D;D	0.58268	0.982;0.959	P;P	0.57620	0.824;0.647	T	0.32348	-0.9910	10	0.72032	D	0.01	-7.4619	20.5753	0.99366	0.0:1.0:0.0:0.0	.	409;409	Q14444;Q14444-2	CAPR1_HUMAN;.	L	409;409;409;409;328	ENSP00000340329:P409L;ENSP00000374296:P409L;ENSP00000434150:P409L;ENSP00000434204:P409L;ENSP00000431581:P328L	ENSP00000340329:P409L	P	+	2	0	CAPRIN1	34064531	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.641000	0.67881	2.868000	0.98415	0.557000	0.71058	CCT	.	.	none		0.363	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:103124135T>G	ENST00000375735.2	+	66	10308	c.10164T>G	c.(10162-10164)acT>acG	p.T3388T	DYNC2H1_ENST00000398093.3_Silent_p.T3395T|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	3388	AAA 5. {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)		CCATTGTTACTGAGGTTAACT	0.348													T|||	907	0.18111	0.3752	0.1254	5008	,	,		15809	0.0933		0.1252	False		,,,				2504	0.1063				p.T3395T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10185G						PASS	.	T	,	1168,2482		189,790,846	109.0	105.0	106.0		10185,10164	0.5	1.0	11	dbSNP_120	106	955,7229		63,829,3200	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	252,1619,4046	GG,GT,TT		11.6691,32.0,17.9398	,	3395/4315,3388/4308	103124135	2123,9711	1825	4092	5917	SO:0001819	synonymous_variant	79659	exon67			TGTTACTGAGGTT	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.10164T>G	11.37:g.103124135T>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.824;G|0.176	0.176	strong		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
PCDH15	65217	hgsc.bcm.edu	37	10	55582905	55582905	+	Silent	SNP	G	G	T	rs10825114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:55582905G>T	ENST00000320301.6	-	33	4975	c.4581C>A	c.(4579-4581)ccC>ccA	p.P1527P	PCDH15_ENST00000395430.1_Silent_p.P1524P|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395433.1_Silent_p.P1504P|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Silent_p.P1529P|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_Silent_p.P1458P|PCDH15_ENST00000395432.2_Silent_p.P1487P|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000373965.2_Intron	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	95	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	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	
LPCAT3	10162	hgsc.bcm.edu	37	12	7091918	7091918	+	Silent	SNP	C	C	T	rs3764031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	124	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	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	
TTN	7273	hgsc.bcm.edu	37	2	179611851	179611851	+	Intron	SNP	C	C	T	rs72648910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611851C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.L5092L|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTATCTCTCCAGAGTCTCTC	0.527													T|||	200	0.0399361	0.1407	0.013	5008	,	,		15008	0.001		0.003	False		,,,				2504	0.001				p.L5092L		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,-2,1	TTN	18412	1	0			c.G15276A						PASS	.	T	,,,,	323,4077	759.4+/-412.9	21,281,1898	61.0	73.0	69.0		,,15276,,	-10.5	0.0	2	dbSNP_130	69	6,8592	810.5+/-407.1	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	21,287,6191	TT,TC,CC		0.0698,7.3409,2.5312	,,,,	,,5092/5605,,	179611851	329,12669	2200	4299	6499	SO:0001627	intron_variant	7273	exon46			TCTCTCCAGAGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5203G>A	2.37:g.179611851C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	148	32	0.216216	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.965;T|0.035	0.035	strong		0.527	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
UTS2	10911	hgsc.bcm.edu	37	1	7913029	7913029	+	Missense_Mutation	SNP	A	A	G	rs34305100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:7913029A>G	ENST00000361696.5	-	1	66	c.35T>C	c.(34-36)aTa>aCa	p.I12T	UTS2_ENST00000054668.5_Intron|UTS2_ENST00000377516.2_Missense_Mutation_p.I12T	NM_006786.3	NP_006777.1	O95399	UTS2_HUMAN	urotensin 2	12			I -> T (in dbSNP:rs34305100). {ECO:0000269|PubMed:12975309}.		muscle contraction (GO:0006936)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell differentiation (GO:0045597)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of heart rate (GO:0010460)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to testosterone (GO:0033574)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			kidney(1)|lung(4)|urinary_tract(1)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|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;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		TAAGAATCCTATGAAAAGCAA	0.413													A|||	416	0.0830671	0.0635	0.0994	5008	,	,		17758	0.0357		0.1839	False		,,,				2504	0.0429				p.I12T		Atlas-SNP	.											UTS2_ENST00000361696,NS,carcinoma,-1,1	UTS2	18	1	0			c.T35C						PASS	.	A	THR/ILE,	330,4076	169.4+/-200.1	11,308,1884	75.0	81.0	79.0		35,	2.8	0.0	1	dbSNP_126	79	1526,7074	285.9+/-297.4	139,1248,2913	yes	missense,intron	UTS2	NM_006786.3,NM_021995.2	89,	150,1556,4797	GG,GA,AA		17.7442,7.4898,14.2703	,	12/125,	7913029	1856,11150	2203	4300	6503	SO:0001583	missense	10911	exon1			AATCCTATGAAAA	AF104118	CCDS90.1, CCDS91.1	1p36	2013-02-28			ENSG00000049247	ENSG00000049247		"""Endogenous ligands"""	12636	protein-coding gene	gene with protein product	"""prepro U-II"""	604097				9861051, 10499587	Standard	NM_021995		Approved	UII, U-II, UCN2, PRO1068	uc001aos.3	O95399	OTTHUMG00000001218	ENST00000361696.5:c.35T>C	1.37:g.7913029A>G	ENSP00000355163:p.Ile12Thr	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	217	108	0.497696	NM_006786	Q5H8X7|Q6UXF6|Q9UKP7	Missense_Mutation	SNP	ENST00000361696.5	37	CCDS91.1	232	0.10622710622710622	29	0.05894308943089431	45	0.12430939226519337	18	0.03146853146853147	140	0.18469656992084432	A	11.02	1.517424	0.27123	0.074898	0.177442	ENSG00000049247	ENST00000377516;ENST00000400910;ENST00000361696	T;T	0.39592	1.07;1.15	5.2	2.83	0.33086	.	0.467176	0.22376	N	0.060863	T	0.00073	0.0002	L	0.38175	1.15	0.58432	P	1.0000000000287557E-6	B;B	0.23806	0.055;0.091	B;B	0.22386	0.018;0.039	T	0.10064	-1.0646	9	0.39692	T	0.17	-1.1173	4.3418	0.11113	0.6983:0.0:0.1556:0.1461	rs34305100	12;12	O95399;Q5H8X8	UTS2_HUMAN;.	T	12	ENSP00000366738:I12T;ENSP00000355163:I12T	ENSP00000355163:I12T	I	-	2	0	UTS2	7835616	0.003000	0.15002	0.000000	0.03702	0.031000	0.12232	1.875000	0.39578	0.370000	0.24538	0.528000	0.53228	ATA	A|0.874;G|0.126	0.126	strong		0.413	UTS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003612.1	NM_006786	
TNKS2	80351	hgsc.bcm.edu	37	10	93608142	93608142	+	Silent	SNP	G	G	A	rs3758499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:93608142G>A	ENST00000371627.4	+	19	2740	c.2361G>A	c.(2359-2361)gcG>gcA	p.A787A		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	787					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				TACCCTAGGCGGATGATGTCA	0.443													G|||	2015	0.402356	0.2375	0.4078	5008	,	,		17019	0.5456		0.3002	False		,,,				2504	0.5787				p.A787A		Atlas-SNP	.											.	TNKS2	103	.	0			c.G2361A						PASS	.	G		1047,3359	382.5+/-324.5	113,821,1269	65.0	61.0	62.0		2361	-6.9	1.0	10	dbSNP_107	62	2660,5940	429.1+/-356.1	387,1886,2027	no	coding-synonymous	TNKS2	NM_025235.3		500,2707,3296	AA,AG,GG		30.9302,23.7631,28.5022		787/1167	93608142	3707,9299	2203	4300	6503	SO:0001819	synonymous_variant	80351	exon19			CTAGGCGGATGAT	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2361G>A	10.37:g.93608142G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Silent	SNP	ENST00000371627.4	37	CCDS7417.1																																																																																			G|0.687;A|0.313	0.313	strong		0.443	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235	
PYROXD2	84795	hgsc.bcm.edu	37	10	100167396	100167396	+	Silent	SNP	G	G	A	rs12763326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100167396G>A	ENST00000370575.4	-	4	306	c.258C>T	c.(256-258)cgC>cgT	p.R86R	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	86							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GGTAGGACGCGCGGGAGAACT	0.622													g|||	2092	0.417732	0.5053	0.3775	5008	,	,		16640	0.4395		0.2376	False		,,,				2504	0.4908				p.R86R		Atlas-SNP	.											.	PYROXD2	43	.	0			c.C258T						PASS	.	A		2086,2320	569.8+/-382.7	481,1124,598	44.0	51.0	49.0		258	-5.8	0.9	10	dbSNP_121	49	2287,6313	384.7+/-341.2	316,1655,2329	no	coding-synonymous	PYROXD2	NM_032709.2		797,2779,2927	AA,AG,GG		26.593,47.3445,33.6229		86/582	100167396	4373,8633	2203	4300	6503	SO:0001819	synonymous_variant	84795	exon4			GGACGCGCGGGAG	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.258C>T	10.37:g.100167396G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	13	0.270833	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Silent	SNP	ENST00000370575.4	37	CCDS7474.1																																																																																			G|0.643;A|0.356	0.356	strong		0.622	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	
CTSF	8722	hgsc.bcm.edu	37	11	66335548	66335548	+	Silent	SNP	A	A	G	rs1127894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	46	9	0.195652		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	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	
IL12RB2	3595	hgsc.bcm.edu	37	1	67833643	67833643	+	Missense_Mutation	SNP	G	G	A	rs2307153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:67833643G>A	ENST00000262345.1	+	10	2034	c.1394G>A	c.(1393-1395)gGt>gAt	p.G465D	IL12RB2_ENST00000544434.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000541374.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000371000.1_Missense_Mutation_p.G465D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	465	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> D (in dbSNP:rs2307153). {ECO:0000269|Ref.3}.		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						CATCCAGGGGGTGACACACAG	0.527													G|||	37	0.00738818	0.0015	0.0101	5008	,	,		18311	0.001		0.0268	False		,,,				2504	0.0				p.G465D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1394A						PASS	.	G	ASP/GLY	19,4387	26.2+/-53.5	0,19,2184	155.0	138.0	144.0		1394	-3.2	0.0	1	dbSNP_100	144	163,8437	77.2+/-139.8	0,163,4137	yes	missense	IL12RB2	NM_001559.2	94	0,182,6321	AA,AG,GG		1.8953,0.4312,1.3994	benign	465/863	67833643	182,12824	2203	4300	6503	SO:0001583	missense	3595	exon10			CAGGGGGTGACAC	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.1394G>A	1.37:g.67833643G>A	ENSP00000262345:p.Gly465Asp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	6.679	0.493890	0.12702	0.004312	0.018953	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.02	-3.19	0.05171	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.541502	0.22419	N	0.060316	T	0.14960	0.0361	L	0.58101	1.795	0.09310	N	1	B;B;B;B	0.29301	0.011;0.0;0.241;0.002	B;B;B;B	0.26693	0.025;0.002;0.072;0.014	T	0.32929	-0.9888	10	0.16896	T	0.51	0.5509	2.0862	0.03646	0.2949:0.3687:0.22:0.1163	rs2307153;rs17097322;rs52799399;rs2307153	465;465;465;465	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	D	465	ENSP00000262345:G465D;ENSP00000360039:G465D;ENSP00000445276:G465D;ENSP00000442443:G465D	ENSP00000262345:G465D	G	+	2	0	IL12RB2	67606231	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.673000	0.05239	-0.876000	0.04017	-0.122000	0.15005	GGT	G|0.986;A|0.014	0.014	strong		0.527	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160453978A>G	ENST00000356956.1	+	9	1198	c.1050A>G	c.(1048-1050)tcA>tcG	p.S350S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	350					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTTAGGTTCATCCTATATTT	0.313													A|||	2123	0.423922	0.2405	0.3545	5008	,	,		20863	0.746		0.3489	False		,,,				2504	0.4663				p.S350S		Atlas-SNP	.											.	IGF2R	251	.	0			c.A1050G						PASS	.	A		1139,3265	378.0+/-322.7	132,875,1195	79.0	88.0	85.0		1050	-7.8	0.0	6	dbSNP_88	85	2790,5810	437.3+/-358.6	463,1864,1973	no	coding-synonymous	IGF2R	NM_000876.2		595,2739,3168	GG,GA,AA		32.4419,25.8629,30.2138		350/2492	160453978	3929,9075	2202	4300	6502	SO:0001819	synonymous_variant	3482	exon9			AGGTTCATCCTAT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1050A>G	6.37:g.160453978A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.643;G|0.357	0.357	strong		0.313	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
PTX4	390667	hgsc.bcm.edu	37	16	1537874	1537874	+	Missense_Mutation	SNP	G	G	A	rs7202502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1537874G>A	ENST00000447419.2	-	2	264	c.239C>T	c.(238-240)gCg>gTg	p.A80V	PTX4_ENST00000293922.1_Missense_Mutation_p.A75V|PTX4_ENST00000440447.2_Missense_Mutation_p.A80V			Q96A99	PTX4_HUMAN	pentraxin 4, long	80						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						GCTCTCTTCCGCCAGGCTCCG	0.632													G|||	532	0.10623	0.3147	0.0476	5008	,	,		16770	0.0119		0.0358	False		,,,				2504	0.0358				p.A75V		Atlas-SNP	.											PTX4,colon,carcinoma,0,1	PTX4	46	1	0			c.C224T						PASS	.	G	VAL/ALA	1235,3153		169,897,1128	93.0	95.0	94.0		224	-1.6	0.0	16	dbSNP_116	94	301,8279		6,289,3995	yes	missense	PTX4	NM_001013658.1	64	175,1186,5123	AA,AG,GG		3.5082,28.1449,11.8445	benign	75/474	1537874	1536,11432	2194	4290	6484	SO:0001583	missense	390667	exon2			TCTTCCGCCAGGC		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.239C>T	16.37:g.1537874G>A	ENSP00000445277:p.Ala80Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		200	0.09157509157509157	148	0.3008130081300813	20	0.055248618784530384	6	0.01048951048951049	26	0.03430079155672823	G	7.797	0.712742	0.15306	0.281449	0.035082	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05139	3.6;3.49	5.58	-1.58	0.08479	.	1.177010	0.06210	N	0.684847	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	P	0.42248	0.774	B	0.30572	0.117	T	0.42716	-0.9435	9	0.12103	T	0.63	.	0.4208	0.00456	0.2557:0.1407:0.3152:0.2884	rs7202502;rs56872109	75	Q96A99-2	.	V	80;75	ENSP00000445277:A80V;ENSP00000293922:A75V	ENSP00000293922:A75V	A	-	2	0	PTX4	1477875	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	0.197000	0.17197	-0.527000	0.06374	-0.251000	0.11542	GCG	G|0.894;A|0.106	0.106	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
SPTLC3	55304	hgsc.bcm.edu	37	20	13140720	13140720	+	Missense_Mutation	SNP	G	G	A	rs61738161	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:13140720G>A	ENST00000399002.2	+	11	1760	c.1486G>A	c.(1486-1488)Gca>Aca	p.A496T	SPTLC3_ENST00000378194.4_3'UTR	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	496					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						CACTCCCCTCGCAGAAGCTCG	0.488													G|||	139	0.0277556	0.0053	0.1354	5008	,	,		14294	0.001		0.0318	False		,,,				2504	0.0051				p.A496T		Atlas-SNP	.											.	SPTLC3	78	.	0			c.G1486A						PASS	.	G	THR/ALA	31,3621		0,31,1795	70.0	73.0	72.0		1486	1.5	0.6	20	dbSNP_129	72	291,7897		7,277,3810	yes	missense	SPTLC3	NM_018327.2	58	7,308,5605	AA,AG,GG		3.554,0.8488,2.7196	benign	496/553	13140720	322,11518	1826	4094	5920	SO:0001583	missense	55304	exon11			CCCCTCGCAGAAG	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.1486G>A	20.37:g.13140720G>A	ENSP00000381968:p.Ala496Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	73	0.033424908424908424	5	0.01016260162601626	40	0.11049723756906077	1	0.0017482517482517483	27	0.03562005277044855	G	14.05	2.420122	0.42918	0.008488	0.03554	ENSG00000172296	ENST00000399002	D	0.94966	-3.57	5.84	1.46	0.22682	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.243209	0.47455	N	0.000222	T	0.05502	0.0145	N	0.01109	-1.01	0.09310	P	0.99999999887093	B	0.16396	0.017	B	0.14023	0.01	T	0.54833	-0.8234	9	0.14656	T	0.56	-7.1844	1.3532	0.02177	0.2814:0.1603:0.4065:0.1518	rs61738161	496	Q9NUV7	SPTC3_HUMAN	T	496	ENSP00000381968:A496T	ENSP00000381968:A496T	A	+	1	0	SPTLC3	13088720	0.697000	0.27767	0.641000	0.29422	0.938000	0.57974	2.405000	0.44548	0.783000	0.33636	0.655000	0.94253	GCA	G|0.964;A|0.036	0.036	strong		0.488	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
MASTL	84930	hgsc.bcm.edu	37	10	27458886	27458886	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:27458886C>T	ENST00000375940.4	+	8	1055	c.998C>T	c.(997-999)gCa>gTa	p.A333V	MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000375946.4_Missense_Mutation_p.A333V|MASTL_ENST00000342386.6_Missense_Mutation_p.A333V			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	333	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGTGATGAAGCATTGGGCCCA	0.358																																					p.A333V		Atlas-SNP	.											.	MASTL	81	.	0			c.C998T						PASS	.						66.0	65.0	65.0					10																	27458886		2203	4300	6503	SO:0001583	missense	84930	exon8			ATGAAGCATTGGG	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.998C>T	10.37:g.27458886C>T	ENSP00000365107:p.Ala333Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	C	0.061	-1.224400	0.01530	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.65549	-0.02;-0.16;-0.02	5.28	2.44	0.29823	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.881451	0.10156	N	0.708985	T	0.46814	0.1412	L	0.38531	1.155	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.31194	-0.9952	10	0.25751	T	0.34	-2.2806	4.3382	0.11097	0.1893:0.5647:0.0:0.246	.	333;333;333	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	V	333	ENSP00000365113:A333V;ENSP00000343446:A333V;ENSP00000365107:A333V	ENSP00000343446:A333V	A	+	2	0	MASTL	27498892	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.005000	0.13129	0.370000	0.24538	-0.133000	0.14855	GCA	.	.	none		0.358	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
FBXW12	285231	hgsc.bcm.edu	37	3	48419898	48419898	+	Missense_Mutation	SNP	G	G	A	rs79525977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48419898G>A	ENST00000296438.5	+	6	683	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	RN7SL321P_ENST00000581742.1_RNA|FBXW12_ENST00000436231.1_Missense_Mutation_p.R9Q|FBXW12_ENST00000415155.1_Intron|FBXW12_ENST00000445170.1_Missense_Mutation_p.R147Q	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)		ACTATGGATCGGAAAAAAACT	0.488													G|||	94	0.01877	0.0068	0.0317	5008	,	,		19977	0.0		0.0616	False		,,,				2504	0.001				p.R166Q		Atlas-SNP	.											.	FBXW12	44	.	0			c.G497A						PASS	.	G	,GLN/ARG,GLN/ARG	39,4367	43.1+/-76.7	1,37,2165	92.0	80.0	85.0		,440,497	-8.5	0.0	3	dbSNP_131	85	410,8190	128.8+/-187.0	10,390,3900	yes	intron,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	,43,43	11,427,6065	AA,AG,GG		4.7674,0.8852,3.4523	,benign,benign	,147/446,166/465	48419898	449,12557	2203	4300	6503	SO:0001583	missense	285231	exon6			TGGATCGGAAAAA	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.497G>A	3.37:g.48419898G>A	ENSP00000296438:p.Arg166Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	62	0.632653	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	65	0.02976190476190476	6	0.012195121951219513	16	0.04419889502762431	0	0.0	43	0.05672823218997362	G	5.691	0.311973	0.10789	0.008852	0.047674	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170	T;T;T	0.62639	1.55;0.01;1.55	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	0.04003	0.0112	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.05451	-1.0884	10	0.25106	T	0.35	-0.4377	1.2043	0.01891	0.2549:0.3408:0.1265:0.2777	.	65;147;166	E9PCA2;E9PG36;Q6X9E4	.;.;FBW12_HUMAN	Q	65;166;9;147	ENSP00000296438:R166Q;ENSP00000413866:R9Q;ENSP00000406139:R147Q	ENSP00000296438:R166Q	R	+	2	0	FBXW12	48394902	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.832000	0.01696	-1.661000	0.01484	-2.476000	0.00200	CGG	G|0.964;A|0.036	0.036	strong		0.488	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102	
PLEC	5339	hgsc.bcm.edu	37	8	144992900	144992900	+	Silent	SNP	G	G	A	rs17062686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144992900G>A	ENST00000322810.4	-	32	11669	c.11500C>T	c.(11500-11502)Ctg>Ttg	p.L3834L	PLEC_ENST00000527096.1_Silent_p.L3720L|PLEC_ENST00000436759.2_Silent_p.L3724L|PLEC_ENST00000354958.2_Silent_p.L3675L|PLEC_ENST00000345136.3_Silent_p.L3697L|PLEC_ENST00000354589.3_Silent_p.L3697L|PLEC_ENST00000356346.3_Silent_p.L3683L|PLEC_ENST00000398774.2_Silent_p.L3665L|PLEC_ENST00000357649.2_Silent_p.L3701L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3834	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						GAACCGGGCAGGTAGACACCA	0.667													G|||	85	0.0169728	0.0023	0.0115	5008	,	,		16451	0.0		0.0517	False		,,,				2504	0.0225				p.L3834L		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11500T						PASS	.	G	,,,,,,,	32,3900		1,30,1935	20.0	26.0	24.0		11170,11047,11023,11500,10993,11089,11101,11089	-0.8	0.0	8	dbSNP_123	24	408,7866		8,392,3737	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	,,,,,,,	9,422,5672	AA,AG,GG		4.9311,0.8138,3.6048	,,,,,,,	3724/4575,3683/4534,3675/4526,3834/4685,3665/4516,3697/4548,3701/4552,3697/4548	144992900	440,11766	1966	4137	6103	SO:0001819	synonymous_variant	5339	exon32			CGGGCAGGTAGAC	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.11500C>T	8.37:g.144992900G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.970;A|0.030	0.030	strong		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
C10orf55	414236	hgsc.bcm.edu	37	10	75673101	75673101	+	Intron	SNP	T	T	C	rs2227564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:75673101T>C	ENST00000409178.1	-	3	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372762.4_Missense_Mutation_p.L105P|PLAU_ENST00000446342.1_Missense_Mutation_p.L124P|PLAU_ENST00000372764.3_Missense_Mutation_p.L141P	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					GGCCTAAAGCTGCTTGTCCAA	0.557													C|||	3883	0.775359	0.9902	0.7536	5008	,	,		20057	0.6349		0.7922	False		,,,				2504	0.6278				p.L141P		Atlas-SNP	.											.	PLAU	47	.	0			c.T422C	GRCh37	CM035594	PLAU	M	rs2227564	PASS	.	C	,PRO/LEU,PRO/LEU	4209,197	123.7+/-161.0	2011,187,5	132.0	125.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,371,422	3.1	0.0	10	dbSNP_98	127	6699,1901	338.3+/-322.7	2628,1443,229	yes	intron,missense,missense	PLAU,C10orf55	NM_001001791.2,NM_001145031.1,NM_002658.3	,98,98	4639,1630,234	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	22.1047,4.4712,16.131	,benign,benign	,124/415,141/432	75673101	10908,2098	2203	4300	6503	SO:0001627	intron_variant	5328	exon6			TAAAGCTGCTTGT		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-268A>G	10.37:g.75673101T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	37	CCDS53541.1	1740	0.7967032967032966	482	0.9796747967479674	271	0.7486187845303868	402	0.7027972027972028	585	0.7717678100263852	C	7.917	0.737699	0.15574	0.955288	0.778953	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	T;T;T	0.63913	-0.07;-0.07;-0.07	5.47	3.07	0.35406	.	0.394419	0.26975	N	0.021549	T	0.00012	0.0000	.	.	.	0.33829	P	0.369992	P;P	0.40602	0.676;0.723	P;P	0.56398	0.694;0.797	T	0.28996	-1.0026	8	0.36615	T	0.2	.	6.4544	0.21922	0.5304:0.3202:0.0:0.1494	rs2227564;rs2228228;rs17856426;rs56591699;rs57705546;rs2227564	124;105	E7ET40;E7ESM2	.;.	P	124;141;105;105	ENSP00000388474:L124P;ENSP00000361850:L141P;ENSP00000361848:L105P	ENSP00000361847:L105P	L	+	2	0	PLAU	75343107	0.055000	0.20627	0.005000	0.12908	0.045000	0.14185	0.567000	0.23608	0.045000	0.15804	-1.058000	0.02302	CTG	T|0.183;C|0.817	0.817	strong		0.557	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
FBXL16	146330	hgsc.bcm.edu	37	16	746884	746884	+	Silent	SNP	A	A	C	rs4984683	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:746884A>C	ENST00000397621.1	-	2	853	c.522T>G	c.(520-522)gtT>gtG	p.V174V	FBXL16_ENST00000562563.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.V174V|FBXL16_ENST00000562585.1_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	50	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	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	
LCT	3938	hgsc.bcm.edu	37	2	136594158	136594158	+	Silent	SNP	G	G	A	rs2236783	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:136594158G>A	ENST00000264162.2	-	1	592	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	194	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCACTGAGGGTCTGGAGTT	0.517													g|||	1745	0.348442	0.1233	0.402	5008	,	,		19559	0.372		0.5964	False		,,,				2504	0.3354				p.T194T		Atlas-SNP	.											.	LCT	309	.	0			c.C582T						PASS	.			1049,3357		122,805,1276	147.0	110.0	123.0		582	-0.4	0.0	2	dbSNP_98	123	6004,2596		2182,1640,478	no	coding-synonymous	LCT	NM_002299.2		2304,2445,1754	AA,AG,GG		30.186,23.8084,45.7712		194/1928	136594158	7053,5953	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon1			ACTGAGGGTCTGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.582C>T	2.37:g.136594158G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	199	83	0.417085	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.584;A|0.416	0.416	strong		0.517	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
MYOM3	127294	hgsc.bcm.edu	37	1	24417415	24417415	+	Missense_Mutation	SNP	T	T	C	rs6700245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24417415T>C	ENST00000374434.3	-	12	1466	c.1304A>G	c.(1303-1305)cAa>cGa	p.Q435R	MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Missense_Mutation_p.Q435R|MYOM3_ENST00000330966.7_Missense_Mutation_p.Q436R	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	435	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs6700245). {ECO:0000269|PubMed:14702039}.			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)		GACGAGGCCTTGGATTGGGCA	0.637													T|||	849	0.169529	0.239	0.1311	5008	,	,		17130	0.003		0.1759	False		,,,				2504	0.2679				p.Q435R		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1304G						PASS	.	T	ARG/GLN	818,3318		89,640,1339	96.0	106.0	102.0		1304	3.0	1.0	1	dbSNP_116	102	1344,7032		106,1132,2950	yes	missense	MYOM3	NM_152372.3	43	195,1772,4289	CC,CT,TT		16.0458,19.7776,17.2794	possibly-damaging	435/1438	24417415	2162,10350	2068	4188	6256	SO:0001583	missense	127294	exon12			AGGCCTTGGATTG	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.1304A>G	1.37:g.24417415T>C	ENSP00000363557:p.Gln435Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	260	0.11904761904761904	90	0.18292682926829268	57	0.1574585635359116	2	0.0034965034965034965	111	0.14643799472295516	T	11.82	1.751658	0.31046	0.197776	0.160458	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.56776	0.44;0.44;0.44	5.3	3.03	0.35002	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.531566	0.21490	N	0.073699	T	0.00039	0.0001	N	0.12887	0.27	0.09310	P	0.9999999873397	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.18263	0.021;0.007;0.009	T	0.13045	-1.0524	9	0.12766	T	0.61	.	3.636	0.08148	0.2217:0.1547:0.0:0.6236	rs6700245;rs61179261;rs6700245	92;435;435	Q6ZU56;Q5VTT5-2;Q5VTT5	.;.;MYOM3_HUMAN	R	435;436;435	ENSP00000363557:Q435R;ENSP00000332670:Q436R;ENSP00000328415:Q435R	ENSP00000328415:Q435R	Q	-	2	0	MYOM3	24290002	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	1.310000	0.33551	2.007000	0.58848	0.460000	0.39030	CAA	T|0.841;C|0.159	0.159	strong		0.637	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
WDR87	83889	hgsc.bcm.edu	37	19	38385707	38385707	+	Silent	SNP	G	G	A	rs189713744		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:38385707G>A	ENST00000303868.5	-	4	743	c.519C>T	c.(517-519)gcC>gcT	p.A173A	WDR87_ENST00000447313.2_Silent_p.A212A	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	173										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						TCTCACACAGGGCCAGGAGGG	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18587	0.0		0.0	False		,,,				2504	0.0				p.A173A		Atlas-SNP	.											.	WDR87	191	.	0			c.C519T						PASS	.	G		1,1383		0,1,691	52.0	56.0	55.0		519	-0.3	0.5	19		55	4,3178		0,4,1587	no	coding-synonymous	WDR87	NM_031951.3		0,5,2278	AA,AG,GG		0.1257,0.0723,0.1095		173/2874	38385707	5,4561	692	1591	2283	SO:0001819	synonymous_variant	83889	exon4			ACACAGGGCCAGG	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.519C>T	19.37:g.38385707G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			G|1.000;A|0.000	0.000	strong		0.607	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZNF835	90485	hgsc.bcm.edu	37	19	57176198	57176198	+	Silent	SNP	T	T	G	rs8108756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57176198T>G	ENST00000537055.2	-	2	600	c.369A>C	c.(367-369)tcA>tcC	p.S123S		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	123					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)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						AGATGAACGCTGAACAGTAGC	0.627													.|||	2330	0.465256	0.6377	0.4078	5008	,	,		14934	0.4692		0.3131	False		,,,				2504	0.4254				p.S123S		Atlas-SNP	.											.	ZNF835	106	.	0			c.A369C						PASS	.	G		2827,1579	461.1+/-352.8	919,989,295	73.0	86.0	82.0		369	-5.6	0.0	19	dbSNP_116	82	2609,5991	675.7+/-403.2	396,1817,2087	no	coding-synonymous	ZNF835	NM_001005850.2		1315,2806,2382	GG,GT,TT		30.3372,35.8375,41.7961		123/538	57176198	5436,7570	2203	4300	6503	SO:0001819	synonymous_variant	90485	exon2			GAACGCTGAACAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.369A>C	19.37:g.57176198T>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			T|0.587;G|0.413	0.413	strong		0.627	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
KIF13A	63971	hgsc.bcm.edu	37	6	17831419	17831419	+	Silent	SNP	G	G	A	rs2277080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17831419G>A	ENST00000259711.6	-	13	1419	c.1314C>T	c.(1312-1314)tcC>tcT	p.S438S	KIF13A_ENST00000378843.2_Silent_p.S438S|KIF13A_ENST00000378826.2_Silent_p.S438S|KIF13A_ENST00000378814.5_Silent_p.S438S|KIF13A_ENST00000378816.5_Silent_p.S438S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	438					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)			CCTTGATACCGGACATCTCCA	0.408													G|||	1199	0.239417	0.1566	0.1758	5008	,	,		22334	0.2004		0.2803	False		,,,				2504	0.3947				p.S438S		Atlas-SNP	.											.	KIF13A	276	.	0			c.C1314T						PASS	.	G	,,,	645,3153		59,527,1313	124.0	121.0	122.0		1314,1314,1314,1314	-7.8	0.2	6	dbSNP_100	122	2399,5857		341,1717,2070	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	400,2244,3383	AA,AG,GG		29.0577,16.9826,25.253	,,,	438/1771,438/1758,438/1750,438/1806	17831419	3044,9010	1899	4128	6027	SO:0001819	synonymous_variant	63971	exon13			GATACCGGACATC	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.1314C>T	6.37:g.17831419G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.777;A|0.223	0.223	strong		0.408	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
NCKAP5L	57701	hgsc.bcm.edu	37	12	50186585	50186585	+	Silent	SNP	T	T	C	rs138292278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:50186585T>C	ENST00000335999.6	-	11	3726	c.3525A>G	c.(3523-3525)acA>acG	p.T1175T		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1171	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCCGCTCCAGTGTGTGGGCGC	0.687													T|||	54	0.0107827	0.0023	0.0029	5008	,	,		11936	0.0		0.0109	False		,,,				2504	0.0389				p.T1175T		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.A3525G						PASS	.	T		10,3996		0,10,1993	9.0	12.0	11.0		3525	-7.7	0.6	12	dbSNP_134	11	76,8136		0,76,4030	no	coding-synonymous	NCKAP5L	NM_001037806.3		0,86,6023	CC,CT,TT		0.9255,0.2496,0.7039		1175/1335	50186585	86,12132	2003	4106	6109	SO:0001819	synonymous_variant	57701	exon11			CTCCAGTGTGTGG	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3525A>G	12.37:g.50186585T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	7.331	0.618991	0.14129	0.002496	0.009255	ENSG00000167566	ENST00000433948	.	.	.	4.3	-7.72	0.01250	.	0.000000	0.45126	D	0.000393	T	0.43831	0.1265	.	.	.	0.48040	D	0.999577	.	.	.	.	.	.	T	0.57201	-0.7852	6	0.72032	D	0.01	-11.3794	4.1532	0.10247	0.1022:0.264:0.1016:0.5322	.	.	.	.	A	890	.	ENSP00000402619:T890A	T	-	1	0	NCKAP5L	48472852	0.000000	0.05858	0.623000	0.29173	0.865000	0.49528	-6.231000	0.00075	-1.638000	0.01529	-1.226000	0.01582	ACT	T|0.993;C|0.007	0.007	strong		0.687	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
UCP1	7350	hgsc.bcm.edu	37	4	141483471	141483471	+	Missense_Mutation	SNP	T	T	A	rs2270565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:141483471T>A	ENST00000262999.3	-	5	760	c.685A>T	c.(685-687)Atg>Ttg	p.M229L		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	229			M -> L (in dbSNP:rs2270565). {ECO:0000269|PubMed:11317671}.		brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)	oxidative phosphorylation uncoupler activity (GO:0017077)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					GGGGAGGACATAGCTGTTGCG	0.463													T|||	361	0.0720847	0.0166	0.0893	5008	,	,		16412	0.0804		0.0785	False		,,,				2504	0.1196				p.M229L		Atlas-SNP	.											.	UCP1	33	.	0			c.A685T	GRCh37	CM011016	UCP1	M	rs2270565	PASS	.	T	LEU/MET	96,4310	78.8+/-117.2	0,96,2107	116.0	107.0	110.0		685	3.0	0.6	4	dbSNP_100	110	682,7918	169.6+/-220.9	20,642,3638	yes	missense	UCP1	NM_021833.4	15	20,738,5745	AA,AT,TT		7.9302,2.1788,5.9819	benign	229/308	141483471	778,12228	2203	4300	6503	SO:0001583	missense	7350	exon5			AGGACATAGCTGT	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"""Solute carriers"""	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.685A>T	4.37:g.141483471T>A	ENSP00000262999:p.Met229Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_021833	Q13218|Q4KMZ3|Q68G66	Missense_Mutation	SNP	ENST00000262999.3	37	CCDS3753.1	161	0.07371794871794872	11	0.022357723577235773	33	0.09116022099447514	55	0.09615384615384616	62	0.08179419525065963	T	8.518	0.868190	0.17250	0.021788	0.079302	ENSG00000109424	ENST00000262999	T	0.76968	-1.06	5.83	3.03	0.35002	Mitochondrial carrier domain (2);	0.211045	0.39615	N	0.001319	T	0.01287	0.0042	N	0.00462	-1.47	0.41057	P	0.014654999999999974	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08269	-1.0730	9	0.24483	T	0.36	.	7.3918	0.26913	0.0:0.1867:0.394:0.4194	rs2270565;rs17848357;rs52815735;rs2270565	228;229	Q4KMT7;P25874	.;UCP1_HUMAN	L	229	ENSP00000262999:M229L	ENSP00000262999:M229L	M	-	1	0	UCP1	141702921	0.977000	0.34250	0.635000	0.29338	0.253000	0.25986	0.936000	0.28938	0.767000	0.33267	-0.219000	0.12488	ATG	T|0.932;A|0.068	0.068	strong		0.463	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1		
CMPK1	51727	hgsc.bcm.edu	37	1	47799639	47799639	+	Missense_Mutation	SNP	G	G	C	rs7543016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:47799639G>C	ENST00000371873.5	+	1	171	c.22G>C	c.(22-24)Ggg>Cgg	p.G8R	CMPK1_ENST00000450808.2_Missense_Mutation_p.G8R|CMPK1_ENST00000471289.2_Missense_Mutation_p.G8R	NM_001136140.1|NM_016308.2	NP_001129612.1|NP_057392.1			cytidine monophosphate (UMP-CMP) kinase 1, cytosolic											endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(2)	8						CTGCCGCAGCGGGCTGCTCCA	0.726													C|||	2987	0.596446	0.8245	0.5893	5008	,	,		6280	0.5843		0.4602	False		,,,				2504	0.4458				p.G8R		Atlas-SNP	.											.	CMPK1	13	.	0			c.G22C						PASS	.	C	ARG/GLY,ARG/GLY	3307,1031		1310,687,172	9.0	9.0	9.0		22,22	2.9	0.0	1	dbSNP_116	9	4001,4503		1027,1947,1278	no	missense,missense	CMPK1	NM_001136140.1,NM_016308.2	125,125	2337,2634,1450	CC,CG,GG		47.0484,23.7667,43.093	benign,benign	8/180,8/229	47799639	7308,5534	2169	4252	6421	SO:0001583	missense	51727	exon1			CGCAGCGGGCTGC	AF070416	CCDS549.1, CCDS44135.1	1p34.1-p33	2008-02-05	2008-01-25	2008-01-25	ENSG00000162368	ENSG00000162368	2.7.4.14		18170	protein-coding gene	gene with protein product	"""UMP-CMP kinase"", ""Cytidine monophosphate kinase"""	191710	"""cytidylate kinase"""	CMPK		10462544	Standard	NM_016308		Approved	UMP-CMPK	uc001cri.3	P30085	OTTHUMG00000007849	ENST00000371873.5:c.22G>C	1.37:g.47799639G>C	ENSP00000360939:p.Gly8Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_016308		Missense_Mutation	SNP	ENST00000371873.5	37	CCDS549.1	1289	0.5902014652014652	390	0.7926829268292683	199	0.5497237569060773	340	0.5944055944055944	360	0.47493403693931396	C	3.287	-0.145854	0.06627	0.762333	0.470484	ENSG00000162368	ENST00000371873;ENST00000471289;ENST00000450808	T;T	0.73469	-0.75;0.15	4.8	2.91	0.33838	.	2.085520	0.01882	N	0.037956	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	0.41251	-0.9519	9	0.10111	T	0.7	5.8212	5.5177	0.16916	0.0:0.6134:0.1448:0.2417	rs7543016;rs17856470	8;8	E9PGI8;B2R6S5	.;.	R	8	ENSP00000360939:G8R;ENSP00000398192:G8R	ENSP00000360937:G8R	G	+	1	0	CMPK1	47572226	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.519000	0.22862	0.238000	0.21222	-0.365000	0.07479	GGG	G|0.428;C|0.572	0.572	strong		0.726	CMPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021646.2	NM_016308	
OR6C74	254783	hgsc.bcm.edu	37	12	55641255	55641255	+	Nonsense_Mutation	SNP	C	C	T	rs4522268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55641255C>T	ENST00000343870.4	+	1	274	c.184C>T	c.(184-186)Cga>Tga	p.R62*		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	62						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						TTTCTTCCTCCGAAATTTCTC	0.388													C|||	1180	0.235623	0.1483	0.2334	5008	,	,		18707	0.1171		0.333	False		,,,				2504	0.3773				p.R62X		Atlas-SNP	.											OR6C74,colon,carcinoma,0,6	OR6C74	52	6	0			c.C184T						PASS	.	C	stop/ARG	818,3588	324.8+/-298.8	65,688,1450	156.0	155.0	155.0		184	1.7	0.6	12	dbSNP_111	155	2719,5881	434.5+/-357.7	426,1867,2007	no	stop-gained	OR6C74	NM_001005490.1		491,2555,3457	TT,TC,CC		31.6163,18.5656,27.1951		62/313	55641255	3537,9469	2203	4300	6503	SO:0001587	stop_gained	254783	exon1			TTCCTCCGAAATT		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.184C>T	12.37:g.55641255C>T	ENSP00000342836:p.Arg62*	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	188	83	0.441489	NM_001005490		Nonsense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	495	0.22664835164835165	76	0.15447154471544716	98	0.27071823204419887	74	0.12937062937062938	247	0.3258575197889182	c	23.3	4.402942	0.83230	0.185656	0.316163	ENSG00000197706	ENST00000343870	.	.	.	4.83	1.73	0.24493	.	0.000000	0.43919	D	0.000516	.	.	.	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.628	0.17492	0.2419:0.5656:0.1184:0.0742	rs4522268;rs17382945;rs52829092;rs58701179;rs4522268	.	.	.	X	62	.	ENSP00000342836:R62X	R	+	1	2	OR6C74	53927522	0.000000	0.05858	0.611000	0.29010	0.940000	0.58332	-1.308000	0.02730	0.706000	0.31912	-0.234000	0.12200	CGA	C|0.743;N|0.000	.	strong		0.388	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
PTCHD2	57540	hgsc.bcm.edu	37	1	11589911	11589911	+	Silent	SNP	G	G	A	rs2076468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11589911G>A	ENST00000294484.6	+	15	3135	c.2997G>A	c.(2995-2997)ccG>ccA	p.P999P	PTCHD2_ENST00000389575.3_Silent_p.P999P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	999					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)		GCGGGAAGCCGGCGGTGCGGC	0.622													G|||	913	0.182308	0.0726	0.0994	5008	,	,		16735	0.4385		0.1064	False		,,,				2504	0.2035				p.P999P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G2997A						PASS	.	G		353,3581		18,317,1632	59.0	75.0	70.0		2997	-9.9	0.0	1	dbSNP_96	70	1166,7122		73,1020,3051	no	coding-synonymous	PTCHD2	NM_020780.1		91,1337,4683	AA,AG,GG		14.0685,8.9731,12.4284		999/1393	11589911	1519,10703	1967	4144	6111	SO:0001819	synonymous_variant	57540	exon15			GAAGCCGGCGGTG	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.2997G>A	1.37:g.11589911G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	127	56	0.440945	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1																																																																																			G|0.816;A|0.184	0.184	strong		0.622	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
SERPINC1	462	hgsc.bcm.edu	37	1	173878862	173878862	+	Silent	SNP	T	T	C	rs5877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:173878862T>C	ENST00000367698.3	-	5	1099	c.981A>G	c.(979-981)gtA>gtG	p.V327V	SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	327					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	GTTCCTTCTCTACCTTGGCCA	0.572													C|||	2731	0.545327	0.8366	0.4251	5008	,	,		20145	0.619		0.34	False		,,,				2504	0.3722				p.V327V		Atlas-SNP	.											.	SERPINC1	57	.	0			c.A981G	GRCh37	CD930906	SERPINC1	D	rs5877	PASS	.	C		3326,1080	391.4+/-328.1	1257,812,134	146.0	140.0	142.0		981	3.6	1.0	1	dbSNP_52	142	2964,5636	668.0+/-402.5	505,1954,1841	no	coding-synonymous	SERPINC1	NM_000488.3		1762,2766,1975	CC,CT,TT		34.4651,24.512,48.3623		327/465	173878862	6290,6716	2203	4300	6503	SO:0001819	synonymous_variant	462	exon5			CTTCTCTACCTTG	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.981A>G	1.37:g.173878862T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	137	46	0.335766	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Silent	SNP	ENST00000367698.3	37	CCDS1313.1																																																																																			T|0.474;C|0.526	0.526	strong		0.572	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	
ARHGEF35	445328	hgsc.bcm.edu	37	7	143884216	143884216	+	Missense_Mutation	SNP	G	G	C	rs200777966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143884216G>C	ENST00000378115.2	-	2	1390	c.1261C>G	c.(1261-1263)Ctg>Gtg	p.L421V	ARHGEF35_ENST00000543357.1_Missense_Mutation_p.L421V	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	421										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						CCTGGAAACAGGTCACAGTGA	0.587													-|||	6	0.00119808	0.0	0.0014	5008	,	,		17229	0.0		0.005	False		,,,				2504	0.0				p.L421V		Atlas-SNP	.											.	ARHGEF35	11	.	0			c.C1261G						PASS	.	G	VAL/LEU	4,4156		0,4,2076	8.0	9.0	8.0		1261	-4.7	0.0	7		8	33,8021		1,31,3995	no	missense	ARHGEF35	NM_001003702.2	32	1,35,6071	CC,CG,GG		0.4097,0.0962,0.3029	benign	421/485	143884216	37,12177	2080	4027	6107	SO:0001583	missense	445328	exon2			GAAACAGGTCACA	AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"""Rho guanine nucleotide exchange factors"""	33846	protein-coding gene	gene with protein product			"""Rho guanine nucleotide exchange factor (GEF) 5-like"""	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.1261C>G	7.37:g.143884216G>C	ENSP00000367355:p.Leu421Val	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	458	88	0.19214	NM_001003702	Q6ZUI2	Missense_Mutation	SNP	ENST00000378115.2	37	CCDS34770.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	4.049	0.006734	0.07866	9.62E-4	0.004097	ENSG00000213214	ENST00000378115;ENST00000543357	.	.	.	2.34	-4.67	0.03319	.	.	.	.	.	T	0.23688	0.0573	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	8	0.24483	T	0.36	.	4.1258	0.10126	0.3886:0.2006:0.4109:0.0	.	421	A5YM69	ARG35_HUMAN	V	421	.	ENSP00000367355:L421V	L	-	1	2	ARHGEF35	143515149	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-1.471000	0.02344	-1.282000	0.02396	-1.271000	0.01417	CTG	G|0.999;C|0.001	0.001	strong		0.587	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702	
SLC39A9	55334	hgsc.bcm.edu	37	14	69908982	69908982	+	Splice_Site	SNP	C	C	T	rs373683599		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:69908982C>T	ENST00000336643.5	+	3	1080	c.402C>T	c.(400-402)gaC>gaT	p.D134D	SLC39A9_ENST00000031146.4_Intron|SLC39A9_ENST00000557046.1_Splice_Site_p.D134D|SLC39A9_ENST00000556605.1_Splice_Site_p.D134D|SLC39A9_ENST00000555245.1_3'UTR	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	134					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.D134D(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		ATTCTACTGACGGTGAGTGGC	0.453																																					p.D134D		Atlas-SNP	.											SLC39A9,caecum,carcinoma,0,1	SLC39A9	27	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C402T						scavenged	.	C		0,4406		0,0,2203	285.0	248.0	260.0		402	-6.9	1.0	14		260	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	SLC39A9	NM_018375.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		134/308	69908982	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	55334	exon3			TACTGACGGTGAG		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"""Solute carriers"""	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.403+1C>T	14.37:g.69908982C>T		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	211	3	0.014218	NM_001252150	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Silent	SNP	ENST00000336643.5	37	CCDS9795.1																																																																																			.	.	weak		0.453	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375	Silent
ACKR4	51554	hgsc.bcm.edu	37	3	132319361	132319361	+	Silent	SNP	A	A	C	rs61748105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132319361A>C	ENST00000249887.2	+	2	216	c.120A>C	c.(118-120)gcA>gcC	p.A40A	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000355458.3_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	40					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										GAGAATTTGCAAAAGTTTTCC	0.353													A|||	172	0.034345	0.0113	0.0533	5008	,	,		21918	0.0129		0.0646	False		,,,				2504	0.0429				p.A40A		Atlas-SNP	.											.	CCRL1	30	.	0			c.A120C						PASS	.	A	,,	84,4322	70.3+/-108.2	0,84,2119	62.0	63.0	63.0		120,,120	-4.2	0.5	3	dbSNP_129	63	609,7991	157.9+/-211.5	17,575,3708	no	coding-synonymous,intron,coding-synonymous	CCRL1,ACAD11	NM_016557.2,NM_032169.4,NM_178445.1	,,	17,659,5827	CC,CA,AA		7.0814,1.9065,5.3283	,,	40/351,,40/351	132319361	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	51554	exon1			ATTTGCAAAAGTT	AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"""GPCR / Class A : Chemokine receptors : Atypical"""	1611	protein-coding gene	gene with protein product		606065	"""chemokine (C-C motif) receptor-like 1"""	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.120A>C	3.37:g.132319361A>C		Somatic	504	0	0		WXS	Illumina HiSeq	Phase_I	646	254	0.393189	NM_178445	B2R9U7	Silent	SNP	ENST00000249887.2	37	CCDS3075.1																																																																																			A|0.953;C|0.047	0.047	strong		0.353	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557	
PCNXL2	80003	hgsc.bcm.edu	37	1	233225848	233225848	+	Silent	SNP	T	T	C	rs12059884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:233225848T>C	ENST00000258229.9	-	23	4269	c.4035A>G	c.(4033-4035)acA>acG	p.T1345T		NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1345						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TGACATATGATGTGATGAAAA	0.413													T|||	669	0.133586	0.3548	0.1066	5008	,	,		17968	0.0		0.1014	False		,,,				2504	0.0245				p.T1345T		Atlas-SNP	.											.	PCNXL2	204	.	0			c.A4035G						PASS	.	T		1090,2644		175,740,952	115.0	110.0	112.0		4035	-11.7	0.0	1	dbSNP_120	112	1008,7208		59,890,3159	no	coding-synonymous	PCNXL2	NM_014801.3		234,1630,4111	CC,CT,TT		12.2687,29.1912,17.5565		1345/2138	233225848	2098,9852	1867	4108	5975	SO:0001819	synonymous_variant	80003	exon23			ATATGATGTGATG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4035A>G	1.37:g.233225848T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	124	46	0.370968	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																			T|0.854;C|0.146	0.146	strong		0.413	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
RASSF2	9770	hgsc.bcm.edu	37	20	4768282	4768282	+	Silent	SNP	G	G	A	rs6052876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4768282G>A	ENST00000379400.3	-	10	1005	c.810C>T	c.(808-810)taC>taT	p.Y270Y	RASSF2_ENST00000379376.2_Silent_p.Y270Y|RASSF2_ENST00000478553.1_5'UTR	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	270					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						AACTCACGTCGTAGGTGACTT	0.537													A|||	236	0.0471246	0.171	0.0115	5008	,	,		19617	0.0		0.0	False		,,,				2504	0.002				p.Y270Y	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.C810T						PASS	.	A	,	679,3727	763.0+/-413.2	61,557,1585	117.0	94.0	102.0		810,810	1.8	1.0	20	dbSNP_114	102	9,8591	818.9+/-406.8	0,9,4291	no	coding-synonymous,coding-synonymous	RASSF2	NM_014737.2,NM_170774.1	,	61,566,5876	AA,AG,GG		0.1047,15.4108,5.2899	,	270/327,270/327	4768282	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	9770	exon10			CACGTCGTAGGTG	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"""centromere protein 34"""	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.810C>T	20.37:g.4768282G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	37	CCDS13083.1																																																																																			G|0.954;A|0.046	0.046	strong		0.537	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737	
NEK5	341676	hgsc.bcm.edu	37	13	52667228	52667228	+	Silent	SNP	G	G	A	rs55715265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52667228G>A	ENST00000355568.4	-	13	1309	c.1170C>T	c.(1168-1170)taC>taT	p.Y390Y		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	390					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		TTTCCTGACCGTAATCCTCAA	0.363													g|||	155	0.0309505	0.0113	0.0231	5008	,	,		17266	0.0079		0.0358	False		,,,				2504	0.0818				p.Y390Y		Atlas-SNP	.											.	NEK5	189	.	0			c.C1170T						PASS	.	A		99,4307	79.9+/-118.3	0,99,2104	169.0	143.0	152.0		1170	-4.7	0.0	13	dbSNP_129	152	392,8208	126.7+/-185.1	9,374,3917	no	coding-synonymous	NEK5	NM_199289.1		9,473,6021	AA,AG,GG		4.5581,2.2469,3.7752		390/709	52667228	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	341676	exon13			CTGACCGTAATCC	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.1170C>T	13.37:g.52667228G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	NM_199289	Q5TAP5	Silent	SNP	ENST00000355568.4	37	CCDS31979.1																																																																																			G|0.967;A|0.033	0.033	strong		0.363	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
CLIP1	6249	hgsc.bcm.edu	37	12	122825398	122825398	+	Missense_Mutation	SNP	C	C	T	rs61954403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122825398C>T	ENST00000540338.1	-	10	2394	c.2353G>A	c.(2353-2355)Gaa>Aaa	p.E785K	CLIP1_ENST00000545889.1_Intron|CLIP1_ENST00000537178.1_Missense_Mutation_p.E739K|CLIP1_ENST00000361654.4_Intron|CLIP1_ENST00000302528.7_Missense_Mutation_p.E774K|CLIP1_ENST00000358808.2_Missense_Mutation_p.E774K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	785					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)		GATTTACCTTCGGAACTGGCT	0.388													C|||	33	0.00658946	0.0015	0.0144	5008	,	,		21925	0.0		0.0199	False		,,,				2504	0.001				p.E785K		Atlas-SNP	.											.	CLIP1	126	.	0			c.G2353A						PASS	.	C	LYS/GLU,LYS/GLU	15,4391	22.3+/-47.3	0,15,2188	141.0	139.0	140.0		2320,2215	5.7	1.0	12	dbSNP_129	140	130,8470	66.3+/-128.7	0,130,4170	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	56,56	0,145,6358	TT,TC,CC		1.5116,0.3404,1.1149	possibly-damaging,possibly-damaging	774/1428,739/1393	122825398	145,12861	2203	4300	6503	SO:0001583	missense	6249	exon11			TACCTTCGGAACT		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.2353G>A	12.37:g.122825398C>T	ENSP00000439093:p.Glu785Lys	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	C	26.0	4.699526	0.88830	0.003404	0.015116	ENSG00000130779	ENST00000302528;ENST00000358808;ENST00000537178;ENST00000540338	T;T;T;T	0.56275	0.56;0.56;0.57;0.47	5.73	5.73	0.89815	.	0.052582	0.85682	D	0.000000	T	0.48466	0.1501	M	0.64997	1.995	0.53005	D	0.999968	D;D;D	0.64830	0.994;0.994;0.977	P;P;P	0.53649	0.731;0.731;0.487	T	0.52094	-0.8621	10	0.29301	T	0.29	-19.7607	20.2602	0.98440	0.0:1.0:0.0:0.0	rs61954403	739;774;785	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	K	774;774;739;785	ENSP00000303585:E774K;ENSP00000351665:E774K;ENSP00000445531:E739K;ENSP00000439093:E785K	ENSP00000303585:E774K	E	-	1	0	CLIP1	121391351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.025000	0.57225	2.861000	0.98227	0.655000	0.94253	GAA	C|0.990;T|0.010	0.010	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
PER3	8863	hgsc.bcm.edu	37	1	7890117	7890117	+	Missense_Mutation	SNP	T	T	C	rs2640909	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:7890117T>C	ENST00000361923.2	+	18	3258	c.3083T>C	c.(3082-3084)aTg>aCg	p.M1028T	PER3_ENST00000377532.3_Missense_Mutation_p.M1037T|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1028	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		M -> T (only found in PER3.4 allele; dbSNP:rs2640909). {ECO:0000269|PubMed:11306557}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		ACACTGTCCATGGGATTGCCT	0.577													-|||	928	0.185304	0.0968	0.2853	5008	,	,		17789	0.0506		0.2932	False		,,,				2504	0.2618				p.M1028T		Atlas-SNP	.											.	PER3	95	.	0			c.T3083C						PASS	.	T	THR/MET	560,3846		36,488,1679	162.0	130.0	141.0		3083	-1.5	0.0	1	dbSNP_100	141	2539,6061		393,1753,2154	yes	missense	PER3	NM_016831.1	81	429,2241,3833	CC,CT,TT		29.5233,12.7099,23.8275	benign	1028/1202	7890117	3099,9907	2203	4300	6503	SO:0001583	missense	8863	exon18			TGTCCATGGGATT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3083T>C	1.37:g.7890117T>C	ENSP00000355031:p.Met1028Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	406	0.1858974358974359	58	0.11788617886178862	91	0.2513812154696133	38	0.06643356643356643	219	0.28891820580474936	-	0.008	-1.871084	0.00542	0.127099	0.295233	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.13538	2.58;2.58	0.77	-1.54	0.08584	Period circadian-like, C-terminal (1);	2.711880	0.01895	N	0.038848	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B;B;B	0.16396	0.0;0.0;0.0;0.017;0.0	B;B;B;B;B	0.15484	0.001;0.0;0.001;0.013;0.0	T	0.43475	-0.9389	9	0.13108	T	0.6	.	3.4008	0.07323	0.0:0.6486:0.0:0.3514	rs2640909;rs10779690;rs17374481;rs34042617;rs52837510;rs2640909	77;1028;1037;1037;1028	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	T	1037;1028;221	ENSP00000366755:M1037T;ENSP00000355031:M1028T	ENSP00000355031:M1028T	M	+	2	0	PER3	7812704	0.019000	0.18553	0.002000	0.10522	0.008000	0.06430	0.000000	0.12993	-0.216000	0.10048	-0.736000	0.03550	ATG	T|0.783;C|0.217	0.217	strong		0.577	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
CLEC12B	387837	hgsc.bcm.edu	37	12	10163379	10163379	+	Silent	SNP	C	C	T	rs1359083|rs386760228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10163379C>T	ENST00000338896.5	+	1	149	c.21C>T	c.(19-21)taC>taT	p.Y7Y	CLEC1B_ENST00000428126.2_Intron|CLEC12B_ENST00000396502.1_Silent_p.Y7Y	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						AAGTGACCTACGCGACACTCA	0.403													C|||	1332	0.265974	0.261	0.3487	5008	,	,		20658	0.1468		0.3966	False		,,,				2504	0.2025				p.Y7Y		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C21T						PASS	.	C	,	1291,3115	431.4+/-342.9	185,921,1097	61.0	57.0	59.0		21,21	-4.1	0.3	12	dbSNP_88	59	2999,5601	458.5+/-364.6	528,1943,1829	no	coding-synonymous,coding-synonymous	CLEC12B	NM_001129998.1,NM_205852.2	,	713,2864,2926	TT,TC,CC		34.8721,29.301,32.9848	,	7/277,7/233	10163379	4290,8716	2203	4300	6503	SO:0001819	synonymous_variant	387837	exon1			GACCTACGCGACA	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"""C-type lectin domain containing"""	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.21C>T	12.37:g.10163379C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001129998	Q6UWF2|Q6ZRG0	Silent	SNP	ENST00000338896.5	37	CCDS44830.1																																																																																			C|0.683;T|0.317	0.317	strong		0.403	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
DNAH10	196385	hgsc.bcm.edu	37	12	124265687	124265687	+	Missense_Mutation	SNP	T	T	C	rs11057353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124265687T>C	ENST00000409039.3	+	6	524	c.499T>C	c.(499-501)Tct>Cct	p.S167P		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	167	Stem. {ECO:0000250}.		S -> P (in dbSNP:rs11057353).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GGGAGTCACATCTGGAGAAGT	0.428													t|||	3572	0.713259	0.5348	0.7032	5008	,	,		16112	0.9573		0.6769	False		,,,				2504	0.7474				p.S167P		Atlas-SNP	.											.	DNAH10	888	.	0			c.T499C						PASS	.		PRO/SER	2468,1938	614.5+/-392.4	674,1120,409	112.0	122.0	118.0		499	-10.6	0.0	12	dbSNP_120	118	5418,3182	652.9+/-401.0	1737,1944,619	yes	missense	DNAH10	NM_207437.3	74	2411,3064,1028	CC,CT,TT		37.0,43.9855,39.3664	benign	167/4472	124265687	7886,5120	2203	4300	6503	SO:0001583	missense	196385	exon6			GTCACATCTGGAG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.499T>C	12.37:g.124265687T>C	ENSP00000386770:p.Ser167Pro	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	1556	0.7124542124542125	263	0.5345528455284553	248	0.6850828729281768	541	0.9458041958041958	504	0.6649076517150396	t	9.468	1.094813	0.20471	0.560145	0.63	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.3	-10.6	0.00265	.	.	.	.	.	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	0.28522	-1.0041	8	0.25751	T	0.34	.	15.1095	0.72343	0.0:0.6112:0.2248:0.164	rs11057353;rs52789374;rs59091251;rs11057353	167	Q8IVF4	DYH10_HUMAN	P	167	ENSP00000386770:S167P	ENSP00000386770:S167P	S	+	1	0	DNAH10	122831640	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.199000	0.01238	-2.568000	0.00469	-0.696000	0.03686	TCT	T|0.310;C|0.690	0.690	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
YARS	8565	hgsc.bcm.edu	37	1	33246709	33246709	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:33246709T>C	ENST00000373477.4	-	10	1988	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	360					apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	TGACCTCCTCTGGTTCTGAAT	0.527																																					p.P360P		Atlas-SNP	.											.	YARS	34	.	0			c.A1080G						PASS	.						128.0	117.0	120.0					1																	33246709		2203	4300	6503	SO:0001819	synonymous_variant	8565	exon10			CTCCTCTGGTTCT	U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	12840	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 1, cytoplasmic"""	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.1080A>G	1.37:g.33246709T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	37	CCDS368.1																																																																																			.	.	none		0.527	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680	
FGGY	55277	hgsc.bcm.edu	37	1	59787350	59787350	+	Missense_Mutation	SNP	T	T	G	rs835409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:59787350T>G	ENST00000303721.7	+	2	303	c.129T>G	c.(127-129)aaT>aaG	p.N43K	FGGY_ENST00000371212.1_Missense_Mutation_p.N43K|FGGY_ENST00000371218.4_Missense_Mutation_p.N43K|FGGY_ENST00000474476.1_Intron	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	43			N -> K (in dbSNP:rs835409).		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.N43K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					CAATTAAGAATTGGGAGCCCC	0.547													G|||	2340	0.467252	0.5477	0.4078	5008	,	,		18632	0.4782		0.3509	False		,,,				2504	0.5092				p.N43K		Atlas-SNP	.											FGGY_ENST00000303721,NS,carcinoma,0,1	FGGY	99	1	1	Substitution - Missense(1)	stomach(1)	c.T129G						PASS	.	G	LYS/ASN,LYS/ASN	1612,1524		406,800,362	59.0	57.0	57.0		129,129	0.1	0.0	1	dbSNP_86	57	2424,4738		428,1568,1585	yes	missense,missense	FGGY	NM_001113411.1,NM_018291.3	94,94	834,2368,1947	GG,GT,TT		33.8453,48.5969,39.1921	benign,benign	43/576,43/552	59787350	4036,6262	1568	3581	5149	SO:0001583	missense	55277	exon2			TAAGAATTGGGAG		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.129T>G	1.37:g.59787350T>G	ENSP00000305922:p.Asn43Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	37	CCDS611.2	983	0.4500915750915751	276	0.5609756097560976	149	0.4116022099447514	278	0.486013986013986	280	0.36939313984168864	G	10.43	1.348245	0.24426	0.514031	0.338453	ENSG00000172456	ENST00000413489;ENST00000371218;ENST00000303721;ENST00000371212	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.2	0.0513	0.14297	Carbohydrate kinase, FGGY, N-terminal (1);	0.376195	0.26567	N	0.023650	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999582564	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	0.44697	-0.9311	8	.	.	.	-0.5346	1.3217	0.02117	0.4209:0.1012:0.2026:0.2753	rs835409;rs1692529;rs3738173;rs60573002	43;43;43;43	Q96C11-3;B1AK94;F2Z2V1;Q96C11	.;.;.;FGGY_HUMAN	K	43	ENSP00000406607:N43K;ENSP00000360262:N43K;ENSP00000305922:N43K;ENSP00000360256:N43K	.	N	+	3	2	FGGY	59559938	0.000000	0.05858	0.030000	0.17652	0.980000	0.70556	-1.274000	0.02820	-0.384000	0.07845	-0.121000	0.15023	AAT	T|0.565;G|0.435	0.435	strong		0.547	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	
HHIPL2	79802	hgsc.bcm.edu	37	1	222712108	222712108	+	Missense_Mutation	SNP	G	G	T	rs116359984	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222712108G>T	ENST00000343410.6	-	5	1517	c.1459C>A	c.(1459-1461)Ctg>Atg	p.L487M		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	487					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		TAGATTGGCAGAACATCATCT	0.453													G|||	12	0.00239617	0.0	0.0086	5008	,	,		19989	0.0		0.006	False		,,,				2504	0.0				p.L487M		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C1459A						PASS	.	G	MET/LEU	3,4403	6.2+/-15.9	0,3,2200	118.0	97.0	104.0		1459	4.4	1.0	1	dbSNP_132	104	54,8546	33.3+/-86.6	1,52,4247	yes	missense	HHIPL2	NM_024746.3	15	1,55,6447	TT,TG,GG		0.6279,0.0681,0.4383	probably-damaging	487/725	222712108	57,12949	2203	4300	6503	SO:0001583	missense	79802	exon5			TTGGCAGAACATC	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1459C>A	1.37:g.222712108G>T	ENSP00000342118:p.Leu487Met	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	17.11	3.306873	0.60305	6.81E-4	0.006279	ENSG00000143512	ENST00000343410	T	0.13778	2.56	5.35	4.43	0.53597	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Glucose/Sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.153343	0.43416	D	0.000570	T	0.19886	0.0478	L	0.49513	1.565	0.42479	D	0.992857	D	0.89917	1.0	D	0.87578	0.998	T	0.00453	-1.1730	10	0.31617	T	0.26	-6.822	9.5251	0.39160	0.1591:0.0:0.8409:0.0	.	487	Q6UWX4	HIPL2_HUMAN	M	487	ENSP00000342118:L487M	ENSP00000342118:L487M	L	-	1	2	HHIPL2	220778731	1.000000	0.71417	0.994000	0.49952	0.530000	0.34684	6.212000	0.72188	2.472000	0.83506	0.591000	0.81541	CTG	G|0.995;T|0.005	0.005	strong		0.453	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
ZNF106	64397	hgsc.bcm.edu	37	15	42744094	42744094	+	Missense_Mutation	SNP	A	A	G	rs12440118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42744094A>G	ENST00000263805.4	-	2	633	c.307T>C	c.(307-309)Tgg>Cgg	p.W103R	ZNF106_ENST00000565611.1_Intron|ZNF106_ENST00000565380.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	103			W -> R (in dbSNP:rs12440118).		insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCTCGTCTCCATTGGGGTCGT	0.438													A|||	295	0.0589058	0.0068	0.1037	5008	,	,		18656	0.006		0.1362	False		,,,				2504	0.0726				p.W103R		Atlas-SNP	.											.	ZFP106	117	.	0			c.T307C						PASS	.	A	ARG/TRP	165,4241	109.9+/-148.2	1,163,2039	215.0	195.0	202.0		307	-4.6	0.2	15	dbSNP_120	202	1288,7310	256.1+/-280.7	103,1082,3114	yes	missense	ZFP106	NM_022473.1	101	104,1245,5153	GG,GA,AA		14.9802,3.7449,11.1735	benign	103/1884	42744094	1453,11551	2203	4299	6502	SO:0001583	missense	64397	exon2			GTCTCCATTGGGG	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.307T>C	15.37:g.42744094A>G	ENSP00000263805:p.Trp103Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	142	0.06501831501831502	4	0.008130081300813009	42	0.11602209944751381	0	0.0	96	0.1266490765171504	A	1.982	-0.433843	0.04669	0.037449	0.149802	ENSG00000103994	ENST00000263805	T	0.13420	2.59	5.44	-4.57	0.03421	.	0.644100	0.15631	N	0.252384	T	0.00039	0.0001	N	0.12746	0.255	0.22591	P	0.99895191	B	0.02656	0.0	B	0.01281	0.0	T	0.37056	-0.9722	9	0.06099	T	0.92	0.8154	6.0782	0.19927	0.2285:0.0:0.2073:0.5642	rs12440118;rs17709157;rs52810470;rs61196539;rs12440118	103	Q9H2Y7	ZF106_HUMAN	R	103	ENSP00000263805:W103R	ENSP00000263805:W103R	W	-	1	0	ZFP106	40531386	0.001000	0.12720	0.165000	0.22776	0.988000	0.76386	-0.349000	0.07731	-1.037000	0.03283	-0.282000	0.10007	TGG	A|0.907;G|0.093	0.093	strong		0.438	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276681	71276681	+	Silent	SNP	T	T	C	rs113879786		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:71276681T>C	ENST00000398531.1	+	1	73	c.48T>C	c.(46-48)ggT>ggC	p.G16G	KRTAP5-10_ENST00000376536.4_Silent_p.G16G	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	16						keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GCTGTGGGGGTTGTGGCTCCG	0.662																																					p.G16G		Atlas-SNP	.											.	KRTAP5-10	37	.	0			c.T48C						PASS	.						33.0	43.0	40.0					11																	71276681		2175	4274	6449	SO:0001819	synonymous_variant	387273	exon1			TGGGGGTTGTGGC	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.48T>C	11.37:g.71276681T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	82	20	0.243902	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			T|0.717;C|0.283	0.283	strong		0.662	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106499	31106499	+	Missense_Mutation	SNP	G	G	A	rs386698869|rs9263726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31106499G>A	ENST00000259881.9	+	5	399	c.110G>A	c.(109-111)cGt>cAt	p.R37H	PSORS1C1_ENST00000481450.2_Intron|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000547221.1_5'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	37			R -> H (in dbSNP:rs9263726). {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GAGGAAACTCGTCCCCCCCAC	0.562													G|||	561	0.112021	0.1626	0.1196	5008	,	,		17027	0.0625		0.1501	False		,,,				2504	0.0501				p.R37H		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.G110A						PASS	.						145.0	144.0	144.0					6																	31106499		1511	2709	4220	SO:0001583	missense	170679	exon5			AAACTCGTCCCCC	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.110G>A	6.37:g.31106499G>A	ENSP00000259881:p.Arg37His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	250	0.11446886446886446	77	0.1565040650406504	46	0.1270718232044199	30	0.05244755244755245	97	0.1279683377308707	G	8.017	0.758775	0.15846	.	.	ENSG00000204540	ENST00000259881	T	0.11495	2.77	2.44	-4.87	0.03123	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44847	-0.9301	8	0.87932	D	0	.	1.4358	0.02343	0.1331:0.3391:0.1802:0.3476	rs9263726;rs52792269;rs61603795;rs9263726	37	Q9UIG5	PS1C1_HUMAN	H	37	ENSP00000259881:R37H	ENSP00000259881:R37H	R	+	2	0	PSORS1C1	31214478	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-3.269000	0.00532	-2.470000	0.00530	-0.707000	0.03653	CGT	G|0.879;A|0.121	0.121	strong		0.562	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
AKAP11	11215	hgsc.bcm.edu	37	13	42872779	42872779	+	Silent	SNP	C	C	T	rs2273951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42872779C>T	ENST00000025301.2	+	7	637	c.462C>T	c.(460-462)taC>taT	p.Y154Y		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	154					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GTATAAGGTACACCTTGGACA	0.403													C|||	570	0.113818	0.0416	0.1297	5008	,	,		16782	0.123		0.1272	False		,,,				2504	0.1769				p.Y154Y		Atlas-SNP	.											.	AKAP11	146	.	0			c.C462T						PASS	.	C		281,4125	157.0+/-190.0	13,255,1935	192.0	164.0	174.0		462	0.9	1.0	13	dbSNP_100	174	1321,7279	259.9+/-283.0	94,1133,3073	no	coding-synonymous	AKAP11	NM_016248.3		107,1388,5008	TT,TC,CC		15.3605,6.3777,12.3174		154/1902	42872779	1602,11404	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon7			AAGGTACACCTTG	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.462C>T	13.37:g.42872779C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			C|0.887;T|0.113	0.113	strong		0.403	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
ACOXL	55289	hgsc.bcm.edu	37	2	111850515	111850515	+	Missense_Mutation	SNP	C	C	T	rs17041850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:111850515C>T	ENST00000389811.4	+	18	1828	c.1604C>T	c.(1603-1605)cCc>cTc	p.P535L	ACOXL_ENST00000439055.1_Missense_Mutation_p.P505L			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	535			P -> L (in dbSNP:rs17041850).		fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						TACTTGACTCCCATGGCCAGC	0.463													C|||	373	0.0744808	0.0129	0.0879	5008	,	,		15389	0.2331		0.0378	False		,,,				2504	0.0225				p.P505L		Atlas-SNP	.											ACOXL_ENST00000439055,right_upper_lobe,carcinoma,-1,2	ACOXL	93	2	0			c.C1514T						scavenged	.	C	LEU/PRO	95,4311	76.8+/-115.0	0,95,2108	95.0	92.0	93.0		1514	6.0	0.2	2	dbSNP_123	93	412,8188	130.3+/-188.3	11,390,3899	yes	missense	ACOXL	NM_001142807.1	98	11,485,6007	TT,TC,CC		4.7907,2.1562,3.8982	probably-damaging	505/581	111850515	507,12499	2203	4300	6503	SO:0001583	missense	55289	exon17			TGACTCCCATGGC		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.1604C>T	2.37:g.111850515C>T	ENSP00000374461:p.Pro535Leu	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		188	0.08608058608058608	6	0.012195121951219513	14	0.03867403314917127	144	0.2517482517482518	24	0.0316622691292876	C	16.59	3.166862	0.57476	0.021562	0.047907	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	T;T;T	0.47528	0.84;0.84;0.84	5.97	5.97	0.96955	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.64402	D	0.000007	T	0.00039	0.0001	M	0.79693	2.465	0.09310	P	1.0	D;D;P	0.56968	0.978;0.973;0.949	P;P;P	0.57620	0.823;0.73;0.824	T	0.00158	-1.1975	9	0.28530	T	0.3	-0.2987	17.9177	0.88957	0.0:1.0:0.0:0.0	rs17041850;rs59233521;rs17041850	505;505;535	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	L	535;505;356;343	ENSP00000374461:P535L;ENSP00000407761:P505L;ENSP00000387832:P343L	ENSP00000374461:P535L	P	+	2	0	ACOXL	111566986	0.070000	0.21116	0.216000	0.23742	0.193000	0.23685	2.041000	0.41213	2.828000	0.97474	0.655000	0.94253	CCC	C|0.930;T|0.070	0.070	strong		0.463	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
SALL3	27164	hgsc.bcm.edu	37	18	76753588	76753588	+	Missense_Mutation	SNP	A	A	G	rs7240860	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:76753588A>G	ENST00000537592.2	+	2	1597	c.1597A>G	c.(1597-1599)Act>Gct	p.T533A	SALL3_ENST00000575389.2_Missense_Mutation_p.T533A|SALL3_ENST00000536229.3_Missense_Mutation_p.T400A	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	533			T -> A (in dbSNP:rs7240860).		forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|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(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ACTGCCGCCCACTGTCCCTGG	0.741													A|||	3600	0.71885	0.3374	0.8242	5008	,	,		11859	0.9127		0.8459	False		,,,				2504	0.8292				p.T533A		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	0			c.A1597G						scavenged	.	A	ALA/THR	1821,2527		397,1027,750	12.0	11.0	11.0		1597	2.7	0.2	18	dbSNP_116	11	7027,1441		2953,1121,160	no	missense	SALL3	NM_171999.2	58	3350,2148,910	GG,GA,AA		17.017,41.8813,30.9613	possibly-damaging	533/1301	76753588	8848,3968	2174	4234	6408	SO:0001583	missense	27164	exon2			CCGCCCACTGTCC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1597A>G	18.37:g.76753588A>G	ENSP00000441823:p.Thr533Ala	Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	1629	0.7458791208791209	158	0.32113821138211385	307	0.8480662983425414	532	0.9300699300699301	632	0.8337730870712401	A	3.488	-0.104379	0.06967	0.418813	0.82983	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.10288	2.89	5.2	2.73	0.32206	.	0.000000	0.64402	D	0.000017	T	0.00012	0.0000	M	0.70842	2.15	0.09310	P	0.999999037973	P;P	0.52577	0.712;0.954	B;B	0.43950	0.396;0.437	T	0.11155	-1.0599	9	0.42905	T	0.14	-37.6074	8.1421	0.31089	0.7253:0.1343:0.0:0.1405	rs7240860	265;533	F5GXY4;Q9BXA9	.;SALL3_HUMAN	A	533;533;265	ENSP00000441823:T533A	ENSP00000299466:T533A	T	+	1	0	SALL3	74854576	1.000000	0.71417	0.204000	0.23530	0.006000	0.05464	4.407000	0.59754	0.267000	0.21916	-0.460000	0.05396	ACT	A|0.251;G|0.749	0.749	strong		0.741	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
MRPL1	65008	hgsc.bcm.edu	37	4	78792906	78792906	+	Missense_Mutation	SNP	C	C	T	rs373565703		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78792906C>T	ENST00000315567.8	+	2	369	c.40C>T	c.(40-42)Cat>Tat	p.H14Y		NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	14					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						AGCCTTGATACATCATCAAAG	0.303																																					p.H14Y		Atlas-SNP	.											.	MRPL1	37	.	0			c.C40T						PASS	.	C	TYR/HIS	0,4406		0,0,2203	82.0	77.0	78.0		40	2.6	1.0	4		78	2,8598	2.2+/-6.3	0,2,4298	no	missense	MRPL1	NM_020236.3	83	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	14/326	78792906	2,13004	2203	4300	6503	SO:0001583	missense	65008	exon2			TTGATACATCATC	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"""Mitochondrial ribosomal proteins / large subunits"""	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.40C>T	4.37:g.78792906C>T	ENSP00000315017:p.His14Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_020236	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	SNP	ENST00000315567.8	37	CCDS3583.2	.	.	.	.	.	.	.	.	.	.	C	8.711	0.912058	0.17907	0.0	2.33E-4	ENSG00000169288	ENST00000315567	T	0.49139	0.79	5.27	2.62	0.31277	Ribosomal protein L1, chordata (1);	1.288150	0.06367	U	0.712771	T	0.46034	0.1372	L	0.56769	1.78	0.25979	N	0.982403	B	0.30889	0.299	B	0.35278	0.199	T	0.38585	-0.9654	10	0.31617	T	0.26	-0.8796	6.1972	0.20555	0.0:0.6775:0.1532:0.1693	.	14	Q9BYD6	RM01_HUMAN	Y	14	ENSP00000315017:H14Y	ENSP00000315017:H14Y	H	+	1	0	MRPL1	79011930	0.405000	0.25336	0.956000	0.39512	0.721000	0.41392	0.268000	0.18571	0.442000	0.26555	-0.143000	0.13931	CAT	.	.	weak		0.303	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236	
TRPC4	7223	hgsc.bcm.edu	37	13	38225406	38225406	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:38225406A>G	ENST00000379705.3	-	8	2932	c.2075T>C	c.(2074-2076)aTa>aCa	p.I692T	TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000447043.1_Missense_Mutation_p.I692T|TRPC4_ENST00000358477.2_Missense_Mutation_p.I692T|TRPC4_ENST00000379679.1_Missense_Mutation_p.I519T|TRPC4_ENST00000355779.2_Missense_Mutation_p.I692T|TRPC4_ENST00000338947.5_Missense_Mutation_p.I519T|TRPC4_ENST00000379681.3_Missense_Mutation_p.I692T|TRPC4_ENST00000379673.2_Intron			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	692	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCTTACCCCTATTGTTCCAAA	0.363																																					p.I692T		Atlas-SNP	.											.	TRPC4	389	.	0			c.T2075C						PASS	.						130.0	127.0	128.0					13																	38225406		2203	4300	6503	SO:0001583	missense	7223	exon8			ACCCCTATTGTTC	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2075T>C	13.37:g.38225406A>G	ENSP00000369027:p.Ile692Thr	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	237	112	0.472574	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.097773	0.76870	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000447043	D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.7	5.7	0.88788	.	0.094472	0.64402	D	0.000001	D	0.83862	0.5346	L	0.42245	1.32	0.80722	D	1	B;P;P;P;P	0.51057	0.336;0.718;0.941;0.506;0.59	B;B;P;B;B	0.51777	0.253;0.215;0.679;0.333;0.25	D	0.83644	0.0152	10	0.40728	T	0.16	-26.2199	15.9668	0.79979	1.0:0.0:0.0:0.0	.	692;692;519;692;692	Q9UBN4-3;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	T	692;692;519;519;692;692;692	ENSP00000369027:I692T;ENSP00000369003:I692T;ENSP00000342580:I519T;ENSP00000369001:I519T;ENSP00000348025:I692T;ENSP00000351264:I692T;ENSP00000414316:I692T	ENSP00000342580:I519T	I	-	2	0	TRPC4	37123406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.310000	0.96267	2.182000	0.69389	0.459000	0.35465	ATA	.	.	none		0.363	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280759A>G	ENST00000368799.1	-	3	6638	c.6603T>C	c.(6601-6603)gaT>gaC	p.D2201D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2201	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)			GCCTAGAGCCATCTCCTGATT	0.552									Ichthyosis				-|||	1839	0.367212	0.472	0.3501	5008	,	,		27298	0.4454		0.1531	False		,,,				2504	0.3773				p.D2201D		Atlas-SNP	.											FLG,NS,carcinoma,-2,2	FLG	900	2	0			c.T6603C						scavenged	.	G		1706,2700		229,1248,726	444.0	388.0	407.0		6603	-4.9	0.0	1	dbSNP_100	407	945,7655		0,945,3355	no	coding-synonymous	FLG	NM_002016.1		229,2193,4081	GG,GA,AA		10.9884,38.7199,20.3829		2201/4062	152280759	2651,10355	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGAGCCATCTCCT	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.6603T>C	1.37:g.152280759A>G		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	364	97	0.266484	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.718;G|0.282	0.282	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PKHD1	5314	hgsc.bcm.edu	37	6	51947257	51947257	+	Silent	SNP	G	G	A	rs6901799	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:51947257G>A	ENST00000371117.3	-	4	489	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	PKHD1_ENST00000340994.4_Silent_p.L72L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	72	IPT/TIG 1; 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)					ACACTCCGCAGTGCGGGCACC	0.507													G|||	353	0.0704872	0.0651	0.0764	5008	,	,		19004	0.0367		0.1163	False		,,,				2504	0.0613				p.L72L		Atlas-SNP	.											.	PKHD1	927	.	0			c.C214T						PASS	.	G	,	356,4050	184.0+/-211.4	16,324,1863	163.0	168.0	166.0		214,214	-2.6	0.0	6	dbSNP_116	166	997,7603	214.8+/-254.3	65,867,3368	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	81,1191,5231	AA,AG,GG		11.593,8.0799,10.4029	,	72/4075,72/3397	51947257	1353,11653	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon4			TCCGCAGTGCGGG	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.214C>T	6.37:g.51947257G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.920;A|0.080	0.080	strong		0.507	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
BCL2L13	23786	hgsc.bcm.edu	37	22	18209718	18209718	+	Silent	SNP	C	C	T	rs2535688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:18209718C>T	ENST00000317582.5	+	7	1223	c.876C>T	c.(874-876)aaC>aaT	p.N292N	BCL2L13_ENST00000337612.5_Silent_p.N130N|BCL2L13_ENST00000485631.1_3'UTR|BCL2L13_ENST00000543133.1_Silent_p.N130N|BCL2L13_ENST00000538149.1_Silent_p.N168N|BCL2L13_ENST00000418951.2_3'UTR|BCL2L13_ENST00000355028.3_3'UTR	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	292					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		TAGACAGCAACGGAGCTGGAG	0.527													C|||	267	0.0533147	0.0061	0.0994	5008	,	,		22787	0.002		0.1421	False		,,,				2504	0.046				p.N316N		Atlas-SNP	.											.	BCL2L13	27	.	0			c.C948T						PASS	.	C		151,4255	105.2+/-143.6	5,141,2057	61.0	52.0	55.0		876	-7.7	0.6	22	dbSNP_100	55	1459,7141	277.1+/-292.7	116,1227,2957	no	coding-synonymous	BCL2L13	NM_015367.2		121,1368,5014	TT,TC,CC		16.9651,3.4271,12.3789		292/486	18209718	1610,11396	2203	4300	6503	SO:0001819	synonymous_variant	23786	exon6			CAGCAACGGAGCT	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.876C>T	22.37:g.18209718C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_001270726	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Silent	SNP	ENST00000317582.5	37	CCDS13746.1																																																																																			C|0.897;T|0.103	0.103	strong		0.527	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367	
BIN1	274	hgsc.bcm.edu	37	2	127811561	127811561	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127811561G>A	ENST00000316724.5	-	13	1570	c.1159C>T	c.(1159-1161)Cag>Tag	p.Q387*	BIN1_ENST00000409400.1_Intron|BIN1_ENST00000346226.3_Intron|BIN1_ENST00000357970.3_Nonsense_Mutation_p.Q344*|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000393041.3_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	387	Clathrin-binding.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		AGACTGGCCTGCTCCGAGAAA	0.642																																					p.Q387X		Atlas-SNP	.											.	BIN1	85	.	0			c.C1159T						PASS	.						22.0	24.0	23.0					2																	127811561		2107	4099	6206	SO:0001587	stop_gained	274	exon13			TGGCCTGCTCCGA	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1159C>T	2.37:g.127811561G>A	ENSP00000316779:p.Gln387*	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	162	67	0.41358	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Nonsense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	G	41	8.932924	0.99008	.	.	ENSG00000136717	ENST00000357970;ENST00000316724	.	.	.	5.36	4.39	0.52855	.	0.765384	0.12406	N	0.471717	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-22.063	9.5913	0.39548	0.0:0.2271:0.6314:0.1415	.	.	.	.	X	344;387	.	ENSP00000316779:Q387X	Q	-	1	0	BIN1	127528031	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.211000	0.42825	2.533000	0.85409	0.456000	0.33151	CAG	.	.	none		0.642	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
STXBP4	252983	hgsc.bcm.edu	37	17	53158492	53158492	+	Silent	SNP	G	G	A	rs8069999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:53158492G>A	ENST00000376352.2	+	16	1644	c.1437G>A	c.(1435-1437)gcG>gcA	p.A479A	STXBP4_ENST00000434978.2_Silent_p.A457A	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	479					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						CAACGCTGGCGCTTGAATCTA	0.378													g|||	947	0.189097	0.0613	0.1484	5008	,	,		17488	0.2431		0.2455	False		,,,				2504	0.2771				p.A479A		Atlas-SNP	.											.	STXBP4	41	.	0			c.G1437A						PASS	.	A		337,4069	176.2+/-205.4	17,303,1883	125.0	113.0	117.0		1437	-11.0	0.0	17	dbSNP_116	117	1976,6624	346.4+/-326.2	214,1548,2538	no	coding-synonymous	STXBP4	NM_178509.5		231,1851,4421	AA,AG,GG		22.9767,7.6487,17.7841		479/554	53158492	2313,10693	2203	4300	6503	SO:0001819	synonymous_variant	252983	exon16			GCTGGCGCTTGAA	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1437G>A	17.37:g.53158492G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	37	CCDS11584.2																																																																																			G|0.813;A|0.187	0.187	strong		0.378	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
FANCA	2175	hgsc.bcm.edu	37	16	89866043	89866043	+	Missense_Mutation	SNP	T	T	C	rs7190823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89866043T>C	ENST00000389301.3	-	9	826	c.796A>G	c.(796-798)Acg>Gcg	p.T266A	FANCA_ENST00000563673.1_Missense_Mutation_p.T266A|FANCA_ENST00000389302.3_Missense_Mutation_p.T266A|FANCA_ENST00000534992.1_Missense_Mutation_p.T266A|FANCA_ENST00000568369.1_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	101	2	0.019802		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	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		
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:99825348T>C	ENST00000254759.3	-	4	424	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	COQ3_ENST00000369240.1_5'Flank|COQ3_ENST00000369242.1_5'UTR|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	27	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	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	
FKBP15	23307	hgsc.bcm.edu	37	9	115931593	115931593	+	Silent	SNP	G	G	A	rs1128122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115931593G>A	ENST00000238256.3	-	26	3513	c.3396C>T	c.(3394-3396)acC>acT	p.T1132T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1132					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						TGTGGGGACCGGTGGAGCTAG	0.597													G|||	306	0.0611022	0.0363	0.0317	5008	,	,		19298	0.0387		0.0467	False		,,,				2504	0.1534				p.T1132T		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,-1,2	FKBP15	128	2	0			c.C3396T						PASS	.	G		187,4009		5,177,1916	73.0	77.0	76.0		3396	-1.1	0.0	9	dbSNP_86	76	534,7892		15,504,3694	no	coding-synonymous	FKBP15	NM_015258.1		20,681,5610	AA,AG,GG		6.3375,4.4566,5.7122		1132/1220	115931593	721,11901	2098	4213	6311	SO:0001819	synonymous_variant	23307	exon26			GGGACCGGTGGAG	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.3396C>T	9.37:g.115931593G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.953;A|0.047	0.047	strong		0.597	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
MED24	9862	hgsc.bcm.edu	37	17	38179492	38179492	+	Silent	SNP	A	A	G	rs2302777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38179492A>G	ENST00000394128.2	-	20	2223	c.2142T>C	c.(2140-2142)atT>atC	p.I714I	MED24_ENST00000356271.3_Silent_p.I701I|MED24_ENST00000394127.2_Silent_p.I701I|MED24_ENST00000394126.1_Silent_p.I739I|MED24_ENST00000501516.3_Silent_p.I733I	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	87	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	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	
OR8J1	219477	hgsc.bcm.edu	37	11	56128081	56128081	+	Missense_Mutation	SNP	A	A	G	rs10896290	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	165	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	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	
WNT16	51384	hgsc.bcm.edu	37	7	120969769	120969769	+	Missense_Mutation	SNP	G	G	A	rs2908004	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:120969769G>A	ENST00000222462.2	+	2	534	c.244G>A	c.(244-246)Ggg>Agg	p.G82R	WNT16_ENST00000361301.2_Missense_Mutation_p.G72R	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	82			G -> R (in dbSNP:rs2908004). {ECO:0000269|PubMed:11095990}.		bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					TCAGGAGTGCGGGAGCCAGTT	0.642													A|||	2556	0.510383	0.9228	0.4092	5008	,	,		13422	0.1766		0.4433	False		,,,				2504	0.4376				p.G82R		Atlas-SNP	.											WNT16_ENST00000361301,brain,glioma,0,2	WNT16	97	2	0			c.G244A						PASS	.	A	ARG/GLY,ARG/GLY	3692,714		1553,586,64	31.0	35.0	34.0		214,244	-0.8	0.9	7	dbSNP_101	34	3913,4687		907,2099,1294	yes	missense,missense	WNT16	NM_016087.2,NM_057168.1	125,125	2460,2685,1358	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.5,16.2052,41.527	benign,benign	72/356,82/366	120969769	7605,5401	2203	4300	6503	SO:0001583	missense	51384	exon2			GAGTGCGGGAGCC	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"""Wingless-type MMTV integration sites"""	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.244G>A	7.37:g.120969769G>A	ENSP00000222462:p.Gly82Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_057168	Q2M3G1|Q9Y5C0	Missense_Mutation	SNP	ENST00000222462.2	37	CCDS5781.1	1048	0.47985347985347987	456	0.926829268292683	160	0.4419889502762431	101	0.17657342657342656	331	0.4366754617414248	A	12.58	1.980316	0.34942	0.837948	0.455	ENSG00000002745	ENST00000361301;ENST00000222462;ENST00000414945	T;T	0.74842	-0.88;-0.88	4.87	-0.765	0.11023	.	0.162937	0.48767	N	0.000179	T	0.00012	0.0000	N	0.00496	-1.435	0.54753	P	1.0999999999983245E-5	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.43589	-0.9382	9	0.35671	T	0.21	.	12.1566	0.54081	0.3129:0.6182:0.0689:0.0	rs2908004;rs10364442;rs52797177;rs2908004	82;72	Q9UBV4;E9PH60	WNT16_HUMAN;.	R	72;82;23	ENSP00000355065:G72R;ENSP00000222462:G82R	ENSP00000222462:G82R	G	+	1	0	WNT16	120757005	0.413000	0.25400	0.879000	0.34478	0.855000	0.48748	1.051000	0.30417	-0.608000	0.05731	-1.126000	0.01995	GGG	G|0.462;A|0.538	0.538	strong		0.642	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
MAN2B1	4125	hgsc.bcm.edu	37	19	12774208	12774208	+	Missense_Mutation	SNP	G	G	C	rs1054486	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12774208G>C	ENST00000456935.2	-	6	872	c.832C>G	c.(832-834)Ctg>Gtg	p.L278V	MAN2B1_ENST00000221363.4_Missense_Mutation_p.L278V	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	278			L -> V (in dbSNP:rs1054486). {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						TCCTCCACCAGCGGCTGATCG	0.582													C|||	1199	0.239417	0.4115	0.2291	5008	,	,		17346	0.0337		0.3022	False		,,,				2504	0.1616				p.L278V		Atlas-SNP	.											.	MAN2B1	91	.	0			c.C832G						PASS	.	C	VAL/LEU,VAL/LEU	1655,2751	658.7+/-400.4	304,1047,852	113.0	93.0	100.0		832,832	-7.4	0.0	19	dbSNP_86	100	2488,6112	695.9+/-404.8	343,1802,2155	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	32,32	647,2849,3007	CC,CG,GG		28.9302,37.5624,31.8545	benign,benign	278/1012,278/1011	12774208	4143,8863	2203	4300	6503	SO:0001583	missense	4125	exon6			CCACCAGCGGCTG		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.832C>G	19.37:g.12774208G>C	ENSP00000395473:p.Leu278Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	503	0.2303113553113553	176	0.35772357723577236	84	0.23204419889502761	16	0.027972027972027972	227	0.2994722955145119	C	7.900	0.734163	0.15574	0.375624	0.289302	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.78364	-1.17;-1.17	5.64	-7.4	0.01397	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	1.114720	0.06958	N	0.815893	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.10222	-1.0639	9	0.13108	T	0.6	-2.9866	0.8562	0.01183	0.2026:0.1595:0.2824:0.3555	rs1054486;rs3195021;rs52820829;rs60806517;rs1054486	278;278	G5E928;O00754	.;MA2B1_HUMAN	V	278;217;278	ENSP00000395473:L278V;ENSP00000221363:L278V	ENSP00000221363:L278V	L	-	1	2	MAN2B1	12635208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.428000	0.06991	-1.472000	0.01883	-1.168000	0.01747	CTG	G|0.717;C|0.283	0.283	strong		0.582	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
GPR144	347088	hgsc.bcm.edu	37	9	127215778	127215778	+	Missense_Mutation	SNP	C	C	T	rs67997410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127215778C>T	ENST00000334810.1	+	4	802	c.802C>T	c.(802-804)Ctc>Ttc	p.L268F				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	268	Pentaxin.				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)			central_nervous_system(1)|endometrium(3)	4						GCGTCACGCCCTCAGCGGCAA	0.756													T|||	3825	0.763778	0.9486	0.7363	5008	,	,		6605	0.8631		0.5736	False		,,,				2504	0.6268				p.L268F		Atlas-SNP	.											GPR144,rectum,carcinoma,0,1	GPR144	33	1	0			c.C802T						PASS	.						4.0	5.0	4.0					9																	127215778		654	1509	2163	SO:0001583	missense	347088	exon4			CACGCCCTCAGCG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.802C>T	9.37:g.127215778C>T	ENSP00000335156:p.Leu268Phe	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	18	14	0.777778	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1591	0.7284798534798534	428	0.8699186991869918	247	0.6823204419889503	488	0.8531468531468531	428	0.5646437994722955	T	0.219	-1.029965	0.02045	.	.	ENSG00000180264	ENST00000334810	T	0.51817	0.69	3.81	2.61	0.31194	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00205	-1.85	0.52501	P	4.199999999998649E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.27606	-1.0069	8	0.12103	T	0.63	.	4.8806	0.13677	0.1631:0.0944:0.0:0.7425	.	268	Q7Z7M1	GP144_HUMAN	F	268	ENSP00000335156:L268F	ENSP00000335156:L268F	L	+	1	0	GPR144	126255599	1.000000	0.71417	0.629000	0.29254	0.351000	0.29236	3.633000	0.54295	-0.045000	0.13468	-0.817000	0.03123	CTC	C|0.271;T|0.729	0.729	strong		0.756	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
DGKH	160851	hgsc.bcm.edu	37	13	42772717	42772717	+	Silent	SNP	G	G	T	rs9533031	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42772717G>T	ENST00000337343.4	+	18	2292	c.2271G>T	c.(2269-2271)ccG>ccT	p.P757P	DGKH_ENST00000540693.1_Silent_p.P757P|DGKH_ENST00000379274.2_Silent_p.P621P|DGKH_ENST00000261491.5_Silent_p.P757P|DGKH_ENST00000536612.1_Silent_p.P621P|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Silent_p.P512P	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	757					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)		TTATTGACCCGGATCTAGATT	0.358													G|||	2012	0.401757	0.3608	0.3876	5008	,	,		18660	0.3492		0.5606	False		,,,				2504	0.3579				p.P757P		Atlas-SNP	.											.	DGKH	106	.	0			c.G2271T						PASS	.	G	,,,,	1816,2590	530.9+/-373.1	359,1098,746	135.0	126.0	129.0		2271,1863,1863,2271,2271	-9.1	0.7	13	dbSNP_119	129	4923,3677	621.5+/-397.2	1412,2099,789	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	,,,,	1771,3197,1535	TT,TG,GG		42.7558,41.2165,48.1855	,,,,	757/1165,621/1101,621/1085,757/1165,757/1221	42772717	6739,6267	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon19			TGACCCGGATCTA	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.2271G>T	13.37:g.42772717G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			G|0.519;T|0.481	0.481	strong		0.358	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
SP8	221833	hgsc.bcm.edu	37	7	20824953	20824953	+	Silent	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20824953G>C	ENST00000361443.4	-	3	666	c.429C>G	c.(427-429)ggC>ggG	p.G143G	SP8_ENST00000418710.2_Silent_p.G161G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	143					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						cgccgccgccgcccccgccgc	0.736																																					p.G161G		Atlas-SNP	.											.	SP8	43	.	0			c.C483G						PASS	.						2.0	2.0	2.0					7																	20824953		584	1454	2038	SO:0001819	synonymous_variant	221833	exon2			GCCGCCGCCCCCG		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.429C>G	7.37:g.20824953G>C		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	none		0.736	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
CSMD1	64478	hgsc.bcm.edu	37	8	2808730	2808730	+	Missense_Mutation	SNP	T	T	A	rs34337712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:2808730T>A	ENST00000520002.1	-	67	10665	c.10110A>T	c.(10108-10110)caA>caT	p.Q3370H	CSMD1_ENST00000602557.1_Missense_Mutation_p.Q3370H|CSMD1_ENST00000602723.1_Missense_Mutation_p.Q3193H|CSMD1_ENST00000537824.1_Missense_Mutation_p.Q3369H|CSMD1_ENST00000542608.1_Missense_Mutation_p.Q3192H|CSMD1_ENST00000400186.3_Missense_Mutation_p.Q3193H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3370			Q -> H (in dbSNP:rs34337712).			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)		GAGTGGCGGGTTGTCTTTTCC	0.478													T|||	107	0.0213658	0.0	0.0331	5008	,	,		15935	0.0		0.0726	False		,,,				2504	0.0112				p.Q3369H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A10107T						PASS	.	T	HIS/GLN	58,3764		0,58,1853	71.0	70.0	70.0		10107	-7.9	0.2	8	dbSNP_126	70	621,7587		23,575,3506	yes	missense	CSMD1	NM_033225.5	24	23,633,5359	AA,AT,TT		7.5658,1.5175,5.6442	benign	3369/3565	2808730	679,11351	1911	4104	6015	SO:0001583	missense	64478	exon66			GGCGGGTTGTCTT			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.10110A>T	8.37:g.2808730T>A	ENSP00000430733:p.Gln3370His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	26	0.288889	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		70|70	0.03205128205128205|0.03205128205128205	0|0	0.0|0.0	15|15	0.04143646408839779|0.04143646408839779	0|0	0.0|0.0	55|55	0.07255936675461741|0.07255936675461741	T|T	11.72|11.72	1.724179|1.724179	0.30593|0.30593	0.015175|0.015175	0.075658|0.075658	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.30448|.	1.53;1.74;1.77;1.53|.	5.2|5.2	-7.9|-7.9	0.01169|0.01169	.|.	0.149652|.	0.44285|.	D|.	0.000465|.	T|T	0.02929|0.02929	0.0087|0.0087	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	D|D	0.999999|0.999999	B;B;B|.	0.17268|.	0.0;0.021;0.007|.	B;B;B|.	0.19946|.	0.001;0.027;0.022|.	T|T	0.40534|0.40534	-0.9558|-0.9558	10|5	0.44086|.	T|.	0.13|.	.|.	7.2925|7.2925	0.26374|0.26374	0.1661:0.5758:0.0877:0.1704|0.1661:0.5758:0.0877:0.1704	rs34337712|rs34337712	3370;3370;3192|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	H|S	3193;3370;3231;3369;3192|2772	ENSP00000383047:Q3193H;ENSP00000430733:Q3370H;ENSP00000441462:Q3369H;ENSP00000446243:Q3192H|.	ENSP00000320445:Q3231H|.	Q|T	-|-	3|1	2|0	CSMD1|CSMD1	2796137|2796137	0.786000|0.786000	0.28738|0.28738	0.193000|0.193000	0.23327|0.23327	0.331000|0.331000	0.28603|0.28603	-0.078000|-0.078000	0.11375|0.11375	-0.678000|-0.678000	0.05224|0.05224	-0.312000|-0.312000	0.09012|0.09012	CAA|ACC	T|0.962;A|0.038	0.038	strong		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CNTRL	11064	hgsc.bcm.edu	37	9	123917045	123917045	+	Missense_Mutation	SNP	A	A	G	rs149632088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:123917045A>G	ENST00000373855.1	+	27	4479	c.4219A>G	c.(4219-4221)Ata>Gta	p.I1407V	CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.I1407V|CNTRL_ENST00000373850.1_Missense_Mutation_p.I855V|CNTRL_ENST00000373847.1_Missense_Mutation_p.I855V			Q7Z7A1	CNTRL_HUMAN	centriolin	1407					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						TGAACTAGAAATAGAAAAATC	0.343													A|||	2	0.000399361	0.0	0.0	5008	,	,		19659	0.0		0.002	False		,,,				2504	0.0				p.I1407V		Atlas-SNP	.											.	CNTRL	161	.	0			c.A4219G						PASS	.	A	VAL/ILE	2,4404	2.1+/-5.4	0,2,2201	65.0	62.0	63.0		4219	1.9	1.0	9	dbSNP_134	63	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CNTRL	NM_007018.4	29	0,5,6498	GG,GA,AA		0.0349,0.0454,0.0384	benign	1407/2326	123917045	5,13001	2203	4300	6503	SO:0001583	missense	11064	exon25			CTAGAAATAGAAA	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.4219A>G	9.37:g.123917045A>G	ENSP00000362962:p.Ile1407Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	9.257	1.042151	0.19748	4.54E-4	3.49E-4	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373847;ENST00000431571;ENST00000373845	T;T;T;T;T	0.77489	2.57;2.57;2.57;2.57;-1.1	5.58	1.93	0.25924	.	.	.	.	.	T	0.64023	0.2561	L	0.47716	1.5	0.24107	N	0.995855	B	0.20780	0.048	B	0.16289	0.015	T	0.50303	-0.8844	9	0.30078	T	0.28	.	0.594	0.00733	0.3991:0.2274:0.1411:0.2325	.	1407	Q7Z7A1	CNTRL_HUMAN	V	1407;1407;1407;163;855;855;76;76	ENSP00000362962:I1407V;ENSP00000238341:I1407V;ENSP00000362956:I855V;ENSP00000362953:I855V;ENSP00000413014:I76V	ENSP00000238341:I1407V	I	+	1	0	CNTRL	122956866	0.975000	0.34042	0.997000	0.53966	0.931000	0.56810	0.100000	0.15231	0.135000	0.18707	-0.250000	0.11733	ATA	A|0.999;G|0.001	0.001	strong		0.343	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
MTMR7	9108	hgsc.bcm.edu	37	8	17218629	17218629	+	Silent	SNP	G	G	A	rs1024355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17218629G>A	ENST00000180173.5	-	4	499	c.465C>T	c.(463-465)taC>taT	p.Y155Y	MTMR7_ENST00000521857.1_Silent_p.Y155Y	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	155	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				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)	p.Y155Y(1)		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)		CACTCACTCTGTAGTCTCTAT	0.463													G|||	980	0.195687	0.4864	0.134	5008	,	,		17037	0.0655		0.1541	False		,,,				2504	0.0235				p.Y155Y		Atlas-SNP	.											MTMR7,NS,carcinoma,-1,2	MTMR7	75	2	1	Substitution - coding silent(1)	stomach(1)	c.C465T						PASS	.	G		1622,2784	500.8+/-364.8	311,1000,892	131.0	118.0	122.0		465	4.6	1.0	8	dbSNP_86	122	1261,7339	251.4+/-277.9	93,1075,3132	no	coding-synonymous	MTMR7	NM_004686.4		404,2075,4024	AA,AG,GG		14.6628,36.8134,22.1667		155/661	17218629	2883,10123	2203	4300	6503	SO:0001819	synonymous_variant	9108	exon4			CACTCTGTAGTCT	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.465C>T	8.37:g.17218629G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_004686	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	37	CCDS34851.1																																																																																			G|0.778;A|0.222	0.222	strong		0.463	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
WDR33	55339	hgsc.bcm.edu	37	2	128528508	128528508	+	Silent	SNP	C	C	T	rs55916728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128528508C>T	ENST00000322313.4	-	2	206	c.48G>A	c.(46-48)agG>agA	p.R16R	WDR33_ENST00000393006.1_Silent_p.R16R|WDR33_ENST00000409658.3_Silent_p.R16R	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	16					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GGTGCTGGAACCTTGGCATAT	0.418													C|||	66	0.0131789	0.0008	0.0159	5008	,	,		16418	0.0		0.0527	False		,,,				2504	0.001				p.R16R		Atlas-SNP	.											.	WDR33	136	.	0			c.G48A						PASS	.	C	,,	45,4361	46.0+/-80.4	0,45,2158	102.0	100.0	101.0		48,48,48	5.5	1.0	2	dbSNP_129	101	389,8211	125.1+/-183.8	14,361,3925	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR33	NM_001006622.2,NM_001006623.2,NM_018383.4	,,	14,406,6083	TT,TC,CC		4.5233,1.0213,3.3369	,,	16/327,16/258,16/1337	128528508	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	55339	exon2			CTGGAACCTTGGC		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.48G>A	2.37:g.128528508C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_001006623	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			C|0.972;T|0.028	0.028	strong		0.418	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
SPEG	10290	hgsc.bcm.edu	37	2	220354108	220354108	+	Missense_Mutation	SNP	A	A	G	rs55760516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220354108A>G	ENST00000312358.7	+	36	8500	c.8368A>G	c.(8368-8370)Agg>Ggg	p.R2790G	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	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	82	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	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	
TBX4	9496	hgsc.bcm.edu	37	17	59560751	59560751	+	Silent	SNP	G	G	A	rs117324438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59560751G>A	ENST00000240335.1	+	8	1557	c.1512G>A	c.(1510-1512)aaG>aaA	p.K504K	TBX4_ENST00000393853.4_Silent_p.K505K	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	504					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GTGAGAGGAAGCCACCCTCGC	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		17921	0.0		0.003	False		,,,				2504	0.001				p.K504K		Atlas-SNP	.											.	TBX4	69	.	0			c.G1512A						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	69.0	69.0	69.0		1512	2.4	1.0	17	dbSNP_133	69	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous	TBX4	NM_018488.2		0,35,6468	AA,AG,GG		0.3023,0.2043,0.2691		504/546	59560751	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GAGGAAGCCACCC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1512G>A	17.37:g.59560751G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
CS	1431	hgsc.bcm.edu	37	12	56676233	56676233	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56676233G>A	ENST00000351328.3	-	6	749	c.559C>T	c.(559-561)Cag>Tag	p.Q187*	CS_ENST00000548567.1_Nonsense_Mutation_p.Q121*|CS_ENST00000542324.2_Nonsense_Mutation_p.Q174*	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	187				Q -> R (in Ref. 1; AAC25560). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		CTGATACCCTGTGCATATGCT	0.507																																					p.Q187X		Atlas-SNP	.											CS,NS,adenoma,+1,1	CS	44	1	0			c.C559T						scavenged	.						102.0	77.0	86.0					12																	56676233		2203	4300	6503	SO:0001587	stop_gained	1431	exon6			TACCCTGTGCATA		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.559C>T	12.37:g.56676233G>A	ENSP00000342056:p.Gln187*	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	197	7	0.035533	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Nonsense_Mutation	SNP	ENST00000351328.3	37	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444473	0.83993	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000546930;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000546554	.	.	.	4.79	2.95	0.34219	.	0.098661	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4858	14.6063	0.68481	0.0:0.7188:0.2812:0.0	.	.	.	.	X	121;187;174;112;121;121;121;121;151;137	.	ENSP00000342056:Q187X	Q	-	1	0	CS	54962500	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.603000	0.61105	0.695000	0.31675	-0.139000	0.14373	CAG	.	.	none		0.507	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
ERICH3	127254	hgsc.bcm.edu	37	1	75037845	75037845	+	Silent	SNP	A	A	G	rs12723334	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:75037845A>G	ENST00000326665.5	-	14	3767	c.3549T>C	c.(3547-3549)agT>agC	p.S1183S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1183	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						CTCTGGCTTCACTCAGTCTTT	0.517													N|||	1879	0.3752	0.2466	0.3314	5008	,	,		20208	0.5843		0.3549	False		,,,				2504	0.3855				p.S1183S		Atlas-SNP	.											.	C1orf173	380	.	0			c.T3549C						PASS	.	G		1103,3303	719.8+/-409.0	143,817,1243	144.0	141.0	142.0		3549	-8.7	0.0	1	dbSNP_121	142	3177,5423	653.5+/-401.1	598,1981,1721	no	coding-synonymous	C1orf173	NM_001002912.4		741,2798,2964	GG,GA,AA		36.9419,25.034,32.9079		1183/1531	75037845	4280,8726	2203	4300	6503	SO:0001819	synonymous_variant	127254	exon14			GGCTTCACTCAGT																												ENST00000326665.5:c.3549T>C	1.37:g.75037845A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	37	CCDS30755.1																																																																																			A|0.649;G|0.351	0.351	strong		0.517	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
ERICH3	127254	hgsc.bcm.edu	37	1	75055741	75055741	+	Missense_Mutation	SNP	A	A	C	rs74513893	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:75055741A>C	ENST00000326665.5	-	12	1968	c.1750T>G	c.(1750-1752)Tca>Gca	p.S584A	C1orf173_ENST00000420661.2_Missense_Mutation_p.S387A|RP4-612J11.1_ENST00000416017.1_RNA	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		584	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						CTTCTGGATGAGGTTGATGAA	0.393													A|||	7	0.00139776	0.0	0.0	5008	,	,		17217	0.0069		0.0	False		,,,				2504	0.0				p.S584A		Atlas-SNP	.											.	C1orf173	380	.	0			c.T1750G						PASS	.						39.0	35.0	36.0					1																	75055741		2203	4300	6503	SO:0001583	missense	127254	exon12			TGGATGAGGTTGA																												ENST00000326665.5:c.1750T>G	1.37:g.75055741A>C	ENSP00000322609:p.Ser584Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	A	13.45	2.240627	0.39598	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.22743	2.28;1.94	5.12	5.12	0.69794	.	.	.	.	.	T	0.23210	0.0561	L	0.55990	1.75	0.29460	N	0.857821	D;D	0.67145	0.996;0.996	D;D	0.77557	0.99;0.99	T	0.06092	-1.0846	9	0.18710	T	0.47	-11.9848	11.3405	0.49531	1.0:0.0:0.0:0.0	.	387;584	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	A	584;387	ENSP00000322609:S584A;ENSP00000398581:S387A	ENSP00000322609:S584A	S	-	1	0	C1orf173	74828329	1.000000	0.71417	0.771000	0.31576	0.030000	0.12068	4.765000	0.62271	1.931000	0.55961	0.443000	0.29094	TCA	A|0.999;C|0.001	0.001	strong		0.393	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
MFSD6	54842	hgsc.bcm.edu	37	2	191301368	191301368	+	Missense_Mutation	SNP	A	A	G	rs9646748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:191301368A>G	ENST00000392328.1	+	3	937	c.613A>G	c.(613-615)Agg>Ggg	p.R205G	MFSD6_ENST00000281416.7_Missense_Mutation_p.R205G	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	205			R -> G (in dbSNP:rs9646748). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:20123006, ECO:0000269|Ref.4}.		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						TTTGGAAACAAGGCTCAATGT	0.433													G|||	2466	0.492412	0.4266	0.6427	5008	,	,		22706	0.6181		0.4483	False		,,,				2504	0.3906				p.R205G		Atlas-SNP	.											.	MFSD6	58	.	0			c.A613G						PASS	.	G	GLY/ARG	1940,2466	617.9+/-393.1	445,1050,708	76.0	81.0	79.0		613	5.2	0.0	2	dbSNP_119	79	3755,4845	612.9+/-396.0	829,2097,1374	yes	missense	MFSD6	NM_017694.3	125	1274,3147,2082	GG,GA,AA		43.6628,44.0309,43.7875	benign	205/792	191301368	5695,7311	2203	4300	6503	SO:0001583	missense	54842	exon3			GAAACAAGGCTCA		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.613A>G	2.37:g.191301368A>G	ENSP00000376141:p.Arg205Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	1108	0.5073260073260073	199	0.40447154471544716	217	0.5994475138121547	352	0.6153846153846154	340	0.44854881266490765	G	0.303	-0.972835	0.02215	0.440309	0.436628	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.29917	1.55;1.55	5.25	5.25	0.73442	Major facilitator superfamily domain, general substrate transporter (1);	0.859177	0.10675	N	0.647079	T	0.00012	0.0000	N	0.01352	-0.895	0.36623	P	0.12414199999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.41052	-0.9530	9	0.13853	T	0.58	0.2618	13.3583	0.60642	0.0754:0.0:0.9246:0.0	rs9646748;rs59869310;rs9646748	205	Q6ZSS7	MFSD6_HUMAN	G	205	ENSP00000376141:R205G;ENSP00000281416:R205G	ENSP00000281416:R205G	R	+	1	2	MFSD6	191009613	0.002000	0.14202	0.002000	0.10522	0.010000	0.07245	1.232000	0.32636	1.468000	0.48064	-0.176000	0.13171	AGG	A|0.532;G|0.468	0.468	strong		0.433	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
FASTKD2	22868	hgsc.bcm.edu	37	2	207631461	207631461	+	Missense_Mutation	SNP	G	G	A	rs3762568	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207631461G>A	ENST00000236980.6	+	2	392	c.44G>A	c.(43-45)aGc>aAc	p.S15N	MDH1B_ENST00000449792.1_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.S15N|MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S15N|MDH1B_ENST00000392214.2_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	139	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	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	
GDPD2	54857	hgsc.bcm.edu	37	X	69652762	69652762	+	Splice_Site	SNP	A	A	G	rs2296542	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:69652762A>G	ENST00000374382.3	+	15	1790	c.1539A>G	c.(1537-1539)agA>agG	p.R513R	GDPD2_ENST00000472623.1_3'UTR|GDPD2_ENST00000538649.1_Splice_Site_p.R434R|GDPD2_ENST00000453994.2_Splice_Site_p.R564R|GDPD2_ENST00000536730.1_Splice_Site_p.R434R	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	513					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					CTCCCCACAGAAGATTTGTTA	0.498													G|||	3216	0.851921	0.4652	0.7161	3775	,	,		12942	0.6746		0.7217	False		,,,				2504	0.7137				p.R564R		Atlas-SNP	.											.	GDPD2	80	.	0			c.A1692G						PASS	.	G	,,,	2368,1467		635,749,349,248,222	80.0	67.0	71.0		1302,1692,1302,1539	4.0	0.9	X	dbSNP_100	71	6398,330		2194,230,1780,4,92	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	GDPD2	NM_001171191.1,NM_001171192.1,NM_001171193.1,NM_017711.3	,,,	2829,979,2129,252,314	GG,GA,G,AA,A		4.9049,38.2529,17.0122	,,,	434/461,564/591,434/461,513/540	69652762	8766,1797	2203	4300	6503	SO:0001630	splice_region_variant	54857	exon16			CCACAGAAGATTT	AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"""osteoblast differentiation promoting factor"""					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.1539-1A>G	X.37:g.69652762A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001171192	B4DRH4|B4DVC9|Q9NXJ6	Silent	SNP	ENST00000374382.3	37	CCDS14402.1																																																																																			A|0.161;G|0.839	0.839	strong		0.498	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711	Silent
HKR1	284459	hgsc.bcm.edu	37	19	37854580	37854580	+	Missense_Mutation	SNP	C	C	T	rs3745764	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37854580C>T	ENST00000324411.4	+	6	2152	c.1883C>T	c.(1882-1884)aCa>aTa	p.T628I	HKR1_ENST00000591134.1_Intron|HKR1_ENST00000589392.1_Missense_Mutation_p.T610I|HKR1_ENST00000591471.1_Missense_Mutation_p.T355I|HKR1_ENST00000544914.1_Missense_Mutation_p.T355I|HKR1_ENST00000541583.2_Missense_Mutation_p.T567I|HKR1_ENST00000392153.3_Missense_Mutation_p.T609I	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	628			T -> I (in dbSNP:rs3745764).		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)			CACCAGAGGACACATTCAGGA	0.507													C|||	943	0.188299	0.1067	0.1801	5008	,	,		21232	0.1627		0.2614	False		,,,				2504	0.2556				p.T628I		Atlas-SNP	.											.	HKR1	74	.	0			c.C1883T						PASS	.	C	ILE/THR	628,3778	273.1+/-271.2	54,520,1629	73.0	74.0	73.0		1883	-0.5	1.0	19	dbSNP_107	73	2192,6408	374.0+/-337.2	287,1618,2395	yes	missense	HKR1	NM_181786.2	89	341,2138,4024	TT,TC,CC		25.4884,14.2533,21.6823	benign	628/660	37854580	2820,10186	2203	4300	6503	SO:0001583	missense	284459	exon6			AGAGGACACATTC	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.1883C>T	19.37:g.37854580C>T	ENSP00000315505:p.Thr628Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	399|399	0.18269230769230768|0.18269230769230768	61|61	0.12398373983739837|0.12398373983739837	69|69	0.19060773480662985|0.19060773480662985	77|77	0.1346153846153846|0.1346153846153846	192|192	0.2532981530343008|0.2532981530343008	C|C	8.511|8.511	0.866564|0.866564	0.17250|0.17250	0.142533|0.142533	0.254884|0.254884	ENSG00000181666|ENSG00000181666	ENST00000542144|ENST00000544914;ENST00000414402;ENST00000392153;ENST00000324411;ENST00000541583	.|T;T;T;T	.|0.53640	.|0.61;0.61;0.61;0.61	2.96|2.96	-0.455|-0.455	0.12193|0.12193	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04636|0.04636	-0.2|-0.2	0.09310|0.09310	P|P	0.999999121925|0.999999121925	.|B;B;B;B	.|0.11235	.|0.0;0.004;0.001;0.001	.|B;B;B;B	.|0.19148	.|0.003;0.024;0.005;0.001	T|T	0.33828|0.33828	-0.9853|-0.9853	5|8	0.87932|0.09590	D|T	0|0.72	.|.	4.441|4.441	0.11573|0.11573	0.177:0.5389:0.0:0.284|0.177:0.5389:0.0:0.284	rs3745764;rs17585173;rs52828567;rs3745764|rs3745764;rs17585173;rs52828567;rs3745764	.|567;609;628;610	.|Q7Z6E1;P10072-2;P10072;B4DSY3	.|.;.;HKR1_HUMAN;.	Y|I	663|355;407;609;628;567	.|ENSP00000437774:T355I;ENSP00000375994:T609I;ENSP00000315505:T628I;ENSP00000438261:T567I	ENSP00000440633:H663Y|ENSP00000315505:T628I	H|T	+|+	1|2	0|0	HKR1|HKR1	42546420|42546420	0.000000|0.000000	0.05858|0.05858	0.979000|0.979000	0.43373|0.43373	0.992000|0.992000	0.81027|0.81027	-0.735000|-0.735000	0.04888|0.04888	0.077000|0.077000	0.16863|0.16863	0.650000|0.650000	0.86243|0.86243	CAC|ACA	C|0.794;T|0.206	0.206	strong		0.507	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
PRR21	643905	hgsc.bcm.edu	37	2	240981262	240981262	+	Missense_Mutation	SNP	A	A	C	rs6728493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240981262A>C	ENST00000408934.1	-	1	1137	c.1138T>G	c.(1138-1140)Tct>Gct	p.S380A		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	380			S -> A (in dbSNP:rs6728493).							NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						TACATGTTAGAAACAAGAAGA	0.463													a|||	2079	0.415136	0.4455	0.379	5008	,	,		22976	0.5754		0.332	False		,,,				2504	0.32				p.S380A		Atlas-SNP	.											.	PRR21	53	.	0			c.T1138G						PASS	.	A	ALA/SER	1685,2721	511.1+/-367.7	316,1053,834	74.0	72.0	73.0		1138	0.5	0.0	2	dbSNP_116	73	2727,5873	434.6+/-357.8	431,1865,2004	yes	missense	PRR21	NM_001080835.1	99	747,2918,2838	CC,CA,AA		31.7093,38.2433,33.9228	benign	380/390	240981262	4412,8594	2203	4300	6503	SO:0001583	missense	643905	exon1			TGTTAGAAACAAG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.1138T>G	2.37:g.240981262A>C	ENSP00000386166:p.Ser380Ala	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	954	0.4368131868131868	233	0.4735772357723577	135	0.3729281767955801	322	0.5629370629370629	264	0.3482849604221636	a	6.816	0.519647	0.13005	0.382433	0.317093	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.32753	1.44;1.44	0.483	0.483	0.16820	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.999999999950489E-6	P	0.39424	0.673	B	0.32022	0.139	T	0.41052	-0.9530	8	0.87932	D	0	.	2.636	0.04958	0.6216:0.0:0.3784:0.0	rs6728493;rs52815143;rs60219994;rs6728493	380	Q8WXC7	PRR21_HUMAN	A	380	ENSP00000386166:S380A;ENSP00000418240:S380A	ENSP00000386166:S380A	S	-	1	0	PRR21	240629935	0.000000	0.05858	0.013000	0.15412	0.040000	0.13550	0.106000	0.15354	0.424000	0.26061	0.413000	0.27773	TCT	A|0.620;C|0.380	0.380	strong		0.463	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
DSCAML1	57453	hgsc.bcm.edu	37	11	117391966	117391966	+	Silent	SNP	G	G	A	rs2276340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:117391966G>A	ENST00000321322.6	-	6	1273	c.1272C>T	c.(1270-1272)cgC>cgT	p.R424R	DSCAML1_ENST00000527706.1_Silent_p.R154R	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	364	Ig-like C2-type 5.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TGCTGAGCCCGCGGATGGAGA	0.652													G|||	1000	0.199681	0.0938	0.1888	5008	,	,		15433	0.253		0.1581	False		,,,				2504	0.3384				p.R424R		Atlas-SNP	.											DSCAML1,colon,carcinoma,-1,1	DSCAML1	286	1	0			c.C1272T						PASS	.	G		458,3944	216.8+/-235.3	25,408,1768	121.0	102.0	108.0		1272	0.5	1.0	11	dbSNP_100	108	1391,7201	268.5+/-287.9	102,1187,3007	no	coding-synonymous	DSCAML1	NM_020693.2		127,1595,4775	AA,AG,GG		16.1895,10.4044,14.2296		424/2114	117391966	1849,11145	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon6			GAGCCCGCGGATG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1272C>T	11.37:g.117391966G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.848;A|0.152	0.152	strong		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
USP1	7398	hgsc.bcm.edu	37	1	62907883	62907883	+	Silent	SNP	C	C	G	rs34521477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62907883C>G	ENST00000339950.4	+	4	1124	c.309C>G	c.(307-309)ccC>ccG	p.P103P	USP1_ENST00000371146.1_Silent_p.P103P	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	103	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		ATTTTTGTCCCGGTTTTAAAT	0.284													C|||	66	0.0131789	0.0023	0.0231	5008	,	,		16782	0.0		0.0398	False		,,,				2504	0.0072				p.P103P	Ovarian(122;1846 2315 3982 19504)	Atlas-SNP	.											.	USP1	51	.	0			c.C309G						PASS	.	C	,,	48,4350	41.6+/-74.8	1,46,2152	51.0	52.0	52.0		309,309,309	2.2	1.0	1	dbSNP_126	52	362,8222	106.4+/-167.3	10,342,3940	no	coding-synonymous,coding-synonymous,coding-synonymous	USP1	NM_001017415.1,NM_001017416.1,NM_003368.4	,,	11,388,6092	GG,GC,CC		4.2171,1.0914,3.1582	,,	103/786,103/786,103/786	62907883	410,12572	2199	4292	6491	SO:0001819	synonymous_variant	7398	exon4			TTGTCCCGGTTTT		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"""Ubiquitin-specific peptidases"""	12607	protein-coding gene	gene with protein product		603478	"""ubiquitin specific protease 1"""			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.309C>G	1.37:g.62907883C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Silent	SNP	ENST00000339950.4	37	CCDS621.1																																																																																			C|0.975;G|0.025	0.025	strong		0.284	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415	
HLTF	6596	hgsc.bcm.edu	37	3	148786085	148786085	+	Missense_Mutation	SNP	T	T	C	rs2305868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:148786085T>C	ENST00000310053.5	-	8	1125	c.932A>G	c.(931-933)aAc>aGc	p.N311S	HLTF_ENST00000494055.1_Missense_Mutation_p.N311S|HLTF_ENST00000465259.1_Missense_Mutation_p.N311S|HLTF_ENST00000392912.2_Missense_Mutation_p.N311S	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	311			N -> S (in dbSNP:rs2305868).		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)			ATCATGGAAGTTGGTAAGGAT	0.363													T|||	102	0.0203674	0.0038	0.0317	5008	,	,		17102	0.0278		0.0288	False		,,,				2504	0.0184				p.N311S		Atlas-SNP	.											.	HLTF	87	.	0			c.A932G						PASS	.	T	SER/ASN,SER/ASN	23,4383	30.8+/-60.4	0,23,2180	153.0	161.0	159.0		932,932	6.0	1.0	3	dbSNP_100	159	238,8362	97.0+/-158.7	4,230,4066	yes	missense,missense	HLTF	NM_003071.3,NM_139048.2	46,46	4,253,6246	CC,CT,TT		2.7674,0.522,2.0068	probably-damaging,probably-damaging	311/1010,311/1010	148786085	261,12745	2203	4300	6503	SO:0001583	missense	6596	exon8			TGGAAGTTGGTAA	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.932A>G	3.37:g.148786085T>C	ENSP00000308944:p.Asn311Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	33	0.340206	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	56	0.02564102564102564	0	0.0	15	0.04143646408839779	19	0.033216783216783216	22	0.029023746701846966	T	19.09	3.759929	0.69763	0.00522	0.027674	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000416117;ENST00000392913	D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2	6.01	6.01	0.97437	DEAD-like helicase (1);SNF2-related (1);	.	.	.	.	T	0.74809	0.3765	L	0.37630	1.12	0.50632	D	0.999883	B;P;P	0.42827	0.394;0.791;0.679	P;P;P	0.46917	0.531;0.462;0.461	T	0.81174	-0.1053	9	0.33141	T	0.24	-8.68	8.9767	0.35939	0.0:0.0817:0.0:0.9183	rs2305868;rs17729483;rs52828545;rs2305868	311;311;311	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	S	311;311;311;311;308;308	ENSP00000420745:N311S;ENSP00000308944:N311S;ENSP00000376644:N311S;ENSP00000420429:N311S	ENSP00000308944:N311S	N	-	2	0	HLTF	150268775	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.197000	0.65141	2.307000	0.77673	0.528000	0.53228	AAC	T|0.977;C|0.023	0.023	strong		0.363	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
P2RX4	5025	hgsc.bcm.edu	37	12	121666646	121666646	+	Missense_Mutation	SNP	A	A	G	rs25644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121666646A>G	ENST00000337233.4	+	7	1032	c.724A>G	c.(724-726)Agt>Ggt	p.S242G	P2RX4_ENST00000359949.7_Missense_Mutation_p.S258G|P2RX4_ENST00000541532.1_3'UTR|P2RX4_ENST00000543171.1_Missense_Mutation_p.S141G	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	242			S -> G (in dbSNP:rs25644). {ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGCAGGACACAGTTTCCAGGA	0.562													A|||	883	0.176318	0.1082	0.2579	5008	,	,		19320	0.2371		0.1322	False		,,,				2504	0.1933				p.S258G		Atlas-SNP	.											.	P2RX4	27	.	0			c.A772G						PASS	.	A	GLY/SER	529,3877	240.3+/-251.1	25,479,1699	102.0	104.0	103.0		724	5.3	1.0	12	dbSNP_72	103	1016,7584	217.3+/-256.0	61,894,3345	yes	missense	P2RX4	NM_002560.2	56	86,1373,5044	GG,GA,AA		11.814,12.0064,11.8791	benign	242/389	121666646	1545,11461	2203	4300	6503	SO:0001583	missense	5025	exon8			GGACACAGTTTCC	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.724A>G	12.37:g.121666646A>G	ENSP00000336607:p.Ser242Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	47	0.405172	NM_001256796	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Missense_Mutation	SNP	ENST00000337233.4	37	CCDS9214.1	364	0.16666666666666666	54	0.10975609756097561	80	0.22099447513812154	132	0.23076923076923078	98	0.12928759894459102	A	13.74	2.326604	0.41197	0.120064	0.11814	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000543171;ENST00000538701;ENST00000542067	T;T;T;T;T	0.04551	3.6;3.6;3.6;3.6;3.6	5.31	5.31	0.75309	.	0.126969	0.64402	D	0.000001	T	0.00012	0.0000	M	0.72894	2.215	0.39075	P	0.03920699999999999	B;B;B	0.26318	0.071;0.146;0.087	B;B;B	0.39935	0.209;0.314;0.314	T	0.32666	-0.9898	9	0.62326	D	0.03	-33.2719	10.5056	0.44832	0.9215:0.0:0.0785:0.0	rs25644;rs2230831;rs2303997;rs11065500;rs17846070;rs17859066;rs52797647;rs57149118;rs25644	215;258;242	F6RU17;E7EPF7;Q99571	.;.;P2RX4_HUMAN	G	242;258;141;112;215	ENSP00000336607:S242G;ENSP00000353032:S258G;ENSP00000438131:S141G;ENSP00000444033:S112G;ENSP00000438329:S215G	ENSP00000336607:S242G	S	+	1	0	P2RX4	120151029	0.941000	0.31946	1.000000	0.80357	0.456000	0.32438	2.153000	0.42282	2.012000	0.59069	0.260000	0.18958	AGT	A|0.860;G|0.140	0.140	strong		0.562	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567	
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840677	1840677	+	Missense_Mutation	SNP	C	C	T	rs181444163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1840677C>T	ENST00000331238.6	-	2	918	c.439G>A	c.(439-441)Ggc>Agc	p.G147S		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1									p.G147S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						CTGTGCAGGCCGCCAAAGACG	0.622													C|||	24	0.00479233	0.0091	0.0058	5008	,	,		18221	0.002		0.006	False		,,,				2504	0.0				p.G147S	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											RTN4RL1,NS,carcinoma,0,1	RTN4RL1	21	1	1	Substitution - Missense(1)	prostate(1)	c.G439A						PASS	.	C	SER/GLY	30,4296		0,30,2133	40.0	46.0	44.0		439	5.7	1.0	17		44	113,8417		1,111,4153	yes	missense	RTN4RL1	NM_178568.2	56	1,141,6286	TT,TC,CC		1.3247,0.6935,1.1123	probably-damaging	147/442	1840677	143,12713	2163	4265	6428	SO:0001583	missense	146760	exon2			GCAGGCCGCCAAA	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"""nogo-66 receptor homolog 2"""	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.439G>A	17.37:g.1840677C>T	ENSP00000330631:p.Gly147Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	27.1	4.803980	0.90623	0.006935	0.013247	ENSG00000185924	ENST00000331238	T	0.61510	0.1	5.72	5.72	0.89469	.	0.000000	0.40064	N	0.001187	T	0.66684	0.2814	L	0.56280	1.765	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.68213	-0.5468	10	0.44086	T	0.13	.	19.9443	0.97176	0.0:1.0:0.0:0.0	.	147	Q86UN2	R4RL1_HUMAN	S	147	ENSP00000330631:G147S	ENSP00000330631:G147S	G	-	1	0	RTN4RL1	1787427	1.000000	0.71417	0.964000	0.40570	0.955000	0.61496	7.484000	0.81180	2.717000	0.92951	0.644000	0.83932	GGC	C|0.995;T|0.005	0.005	strong		0.622	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
LRRN2	10446	hgsc.bcm.edu	37	1	204589101	204589101	+	Missense_Mutation	SNP	G	G	A	rs3789044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204589101G>A	ENST00000367175.1	-	1	2232	c.20C>T	c.(19-21)cCa>cTa	p.P7L	LRRN2_ENST00000367177.3_Missense_Mutation_p.P7L|LRRN2_ENST00000367176.3_Missense_Mutation_p.P7L|LRRN2_ENST00000496057.1_5'UTR			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	82	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	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	
RIN3	79890	hgsc.bcm.edu	37	14	93118229	93118229	+	Missense_Mutation	SNP	C	C	T	rs117068593	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:93118229C>T	ENST00000216487.7	+	6	994	c.835C>T	c.(835-837)Cgc>Tgc	p.R279C	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	279	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				GGCCCCACGccgcccaccacc	0.721													C|||	403	0.0804712	0.0053	0.098	5008	,	,		5561	0.003		0.1869	False		,,,				2504	0.1401				p.R279C		Atlas-SNP	.											.	RIN3	81	.	0			c.C835T						PASS	.	C	CYS/ARG	154,4250	102.5+/-141.1	3,148,2051	29.0	33.0	32.0		835	3.7	1.0	14	dbSNP_132	32	1687,6911	297.4+/-303.4	157,1373,2769	no	missense	RIN3	NM_024832.3	180	160,1521,4820	TT,TC,CC		19.6208,3.4968,14.1594	probably-damaging	279/986	93118229	1841,11161	2202	4299	6501	SO:0001583	missense	79890	exon6			CCACGCCGCCCAC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.835C>T	14.37:g.93118229C>T	ENSP00000216487:p.Arg279Cys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	55	36	0.654545	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	177	0.08104395604395605	3	0.006097560975609756	44	0.12154696132596685	1	0.0017482517482517483	129	0.17018469656992086	C	14.37	2.515668	0.44763	0.034968	0.196208	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.08008	3.14	4.65	3.65	0.41850	.	0.936394	0.08842	N	0.885755	T	0.00039	0.0001	L	0.60455	1.87	0.09310	P	0.9999999999954712	D;D	0.89917	1.0;1.0	D;D	0.64410	0.925;0.925	T	0.18461	-1.0336	9	0.51188	T	0.08	-13.9867	15.0459	0.71827	0.1521:0.8479:0.0:0.0	.	204;279	Q6ZRC2;Q8TB24	.;RIN3_HUMAN	C	279	ENSP00000216487:R279C	ENSP00000216487:R279C	R	+	1	0	RIN3	92187982	0.977000	0.34250	0.991000	0.47740	0.617000	0.37484	1.979000	0.40608	2.157000	0.67596	0.313000	0.20887	CGC	C|0.886;T|0.114	0.114	strong		0.721	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
DOCK1	1793	hgsc.bcm.edu	37	10	128807018	128807018	+	Silent	SNP	A	A	C	rs35541322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:128807018A>C	ENST00000280333.6	+	11	1117	c.1008A>C	c.(1006-1008)atA>atC	p.I336I	RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000594559.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA|RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.3_ENST00000601826.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	336					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)			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)		CAGATATAATAAATGGAAAAG	0.343													A|||	93	0.0185703	0.0045	0.0259	5008	,	,		18452	0.0		0.0567	False		,,,				2504	0.0123				p.I336I		Atlas-SNP	.											.	DOCK1	188	.	0			c.A1008C						PASS	.	A		38,3880		0,38,1921	79.0	78.0	78.0		963	1.2	1.0	10	dbSNP_126	78	501,7889		13,475,3707	no	coding-synonymous	DOCK1	NM_001380.3		13,513,5628	CC,CA,AA		5.9714,0.9699,4.3793		321/1851	128807018	539,11769	1959	4195	6154	SO:0001819	synonymous_variant	1793	exon11			TATAATAAATGGA	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.1008A>C	10.37:g.128807018A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				A|0.964;C|0.036	0.036	strong		0.343	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
AGPAT2	10555	hgsc.bcm.edu	37	9	139571430	139571430	+	Missense_Mutation	SNP	G	G	A	rs142993240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139571430G>A	ENST00000371696.2	-	3	540	c.475C>T	c.(475-477)Cgc>Tgc	p.R159C	AGPAT2_ENST00000538402.1_Missense_Mutation_p.R159C|AGPAT2_ENST00000371694.3_Missense_Mutation_p.R159C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	159					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CTGACCATGCGCTCGCCCAGG	0.672													g|||	15	0.00299521	0.0008	0.0014	5008	,	,		12176	0.0		0.008	False		,,,				2504	0.0051				p.R159C		Atlas-SNP	.											.	AGPAT2	17	.	0			c.C475T						PASS	.	G	CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	55.0	58.0	57.0		475,475	2.7	1.0	9	dbSNP_134	57	48,8552	31.2+/-83.2	0,48,4252	yes	missense,missense	AGPAT2	NM_001012727.1,NM_006412.3	180,180	0,54,6449	AA,AG,GG		0.5581,0.1362,0.4152	possibly-damaging,possibly-damaging	159/247,159/279	139571430	54,12952	2203	4300	6503	SO:0001583	missense	10555	exon3			CCATGCGCTCGCC	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	325	protein-coding gene	gene with protein product	"""LPAAT-beta"", ""lysophosphatidic acid acyltransferase, beta"""	603100	"""Berardinelli-Seip congenital lipodystrophy"", ""1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"""	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.475C>T	9.37:g.139571430G>A	ENSP00000360761:p.Arg159Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Missense_Mutation	SNP	ENST00000371696.2	37	CCDS7003.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.73	2.920536	0.52653	0.001362	0.005581	ENSG00000169692	ENST00000371694;ENST00000371696;ENST00000538402	D;D;D	0.93604	-3.25;-3.25;-3.25	4.75	2.66	0.31614	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.654070	0.14876	N	0.293250	D	0.93552	0.7942	M	0.83692	2.655	0.40657	D	0.98209	D;D	0.65815	0.994;0.995	P;P	0.59595	0.827;0.86	D	0.92032	0.5634	10	0.54805	T	0.06	-9.0385	6.8996	0.24275	0.0:0.1308:0.3813:0.488	.	159;159	O15120-2;O15120	.;PLCB_HUMAN	C	159	ENSP00000360759:R159C;ENSP00000360761:R159C;ENSP00000438919:R159C	ENSP00000360759:R159C	R	-	1	0	AGPAT2	138691251	0.999000	0.42202	0.977000	0.42913	0.479000	0.33129	2.180000	0.42537	0.978000	0.38470	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.672	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412	
RFPL3	10738	hgsc.bcm.edu	37	22	32754103	32754103	+	Missense_Mutation	SNP	A	A	C	rs58637580	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32754103A>C	ENST00000249007.4	+	1	250	c.45A>C	c.(43-45)caA>caC	p.Q15H	RFPL3_ENST00000397468.1_Intron|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	15							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TTTCACCTCAAGGAAATTTTC	0.463													N|||	724	0.144569	0.0265	0.0893	5008	,	,		20055	0.4583		0.0408	False		,,,				2504	0.1268				p.Q15H		Atlas-SNP	.											.	RFPL3	91	.	0			c.A45C						PASS	.	C	HIS/GLN,	138,4268	779.0+/-414.3	8,122,2073	114.0	113.0	113.0		45,	-1.3	0.0	22	dbSNP_129	113	418,8180	790.4+/-407.6	12,394,3893	no	missense,intron	RFPL3	NM_001098535.1,NM_006604.2	24,	20,516,5966	CC,CA,AA		4.8616,3.1321,4.2756	,	15/318,	32754103	556,12448	2203	4299	6502	SO:0001583	missense	10738	exon1			ACCTCAAGGAAAT	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.45A>C	22.37:g.32754103A>C	ENSP00000249007:p.Gln15His	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	215	96	0.446512	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	296	0.13553113553113552	7	0.014227642276422764	32	0.08839779005524862	227	0.3968531468531469	30	0.0395778364116095	C	0.203	-1.042871	0.01997	0.031321	0.048616	ENSG00000128276	ENST00000249007	T	0.52526	0.66	0.784	-1.26	0.09376	.	.	.	.	.	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	0.35798	-0.9774	8	0.02654	T	1	.	1.4237	0.02318	0.3217:0.2569:0.0:0.4214	rs58637580;rs61729173	15	O75679	RFPL3_HUMAN	H	15	ENSP00000249007:Q15H	ENSP00000249007:Q15H	Q	+	3	2	RFPL3	31084103	0.002000	0.14202	0.002000	0.10522	0.029000	0.11900	-2.692000	0.00830	-1.119000	0.02958	-2.543000	0.00179	CAA	A|0.883;C|0.108;T|0.009	0.108	strong		0.463	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
KIF26A	26153	hgsc.bcm.edu	37	14	104639519	104639519	+	Silent	SNP	C	C	G	rs61743517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104639519C>G	ENST00000423312.2	+	8	1626	c.1626C>G	c.(1624-1626)ctC>ctG	p.L542L	KIF26A_ENST00000315264.7_Silent_p.L403L	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	542	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)		CTGGCAGCCTCCAGGACACCC	0.731													C|||	111	0.0221645	0.0038	0.036	5008	,	,		13918	0.0		0.0577	False		,,,				2504	0.0235				p.L542L		Atlas-SNP	.											.	KIF26A	84	.	0			c.C1626G						PASS	.	C		48,3966		0,48,1959	13.0	19.0	17.0		1626	-5.6	0.1	14	dbSNP_129	17	521,7751		21,479,3636	no	coding-synonymous	KIF26A	NM_015656.1		21,527,5595	GG,GC,CC		6.2984,1.1958,4.6313		542/1883	104639519	569,11717	2007	4136	6143	SO:0001819	synonymous_variant	26153	exon8			CAGCCTCCAGGAC	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.1626C>G	14.37:g.104639519C>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.973;G|0.027	0.027	strong		0.731	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CAMKK2	10645	hgsc.bcm.edu	37	12	121691096	121691096	+	Missense_Mutation	SNP	G	G	A	rs1132780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121691096G>A	ENST00000324774.5	-	10	1915	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C	CAMKK2_ENST00000412367.2_Missense_Mutation_p.R363C|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000337174.3_Missense_Mutation_p.R363C|CAMKK2_ENST00000392473.2_Missense_Mutation_p.R363C|CAMKK2_ENST00000347034.2_Missense_Mutation_p.R363C|CAMKK2_ENST00000446440.2_Missense_Mutation_p.R363C|CAMKK2_ENST00000545538.1_Missense_Mutation_p.R150C|CAMKK2_ENST00000392474.2_Missense_Mutation_p.R363C|CAMKK2_ENST00000404169.3_Missense_Mutation_p.R363C|CAMKK2_ENST00000538733.1_Missense_Mutation_p.R363C|CAMKK2_ENST00000402834.4_Missense_Mutation_p.R363C	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	363	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> C (in dbSNP:rs1132780).		calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AAGATCTTGCGGGTCTCAGAG	0.562													G|||	1208	0.241214	0.2799	0.2839	5008	,	,		20324	0.2778		0.1491	False		,,,				2504	0.2157				p.R363C		Atlas-SNP	.											.	CAMKK2	87	.	0			c.C1087T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1234,3172	426.6+/-341.2	172,890,1141	104.0	77.0	86.0		1087,1087,1087,1087,1087,1087,1087	4.5	1.0	12	dbSNP_86	86	1114,7486	231.0+/-265.1	79,956,3265	yes	missense,missense,missense,missense,missense,missense,missense	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	180,180,180,180,180,180,180	251,1846,4406	AA,AG,GG		12.9535,28.0073,18.0532	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	363/589,363/542,363/499,363/534,363/491,363/546,363/542	121691096	2348,10658	2203	4300	6503	SO:0001583	missense	10645	exon10			TCTTGCGGGTCTC	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.1087C>T	12.37:g.121691096G>A	ENSP00000312741:p.Arg363Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	37	CCDS9216.1	498	0.22802197802197802	141	0.2865853658536585	94	0.2596685082872928	151	0.263986013986014	112	0.14775725593667546	G	13.21	2.169524	0.38315	0.280073	0.129535	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000545538;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473	T;T;T;T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	5.35	4.47	0.54385	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	L	0.35249	1.045	0.09310	P	0.99999881955	B;B;B;D;B;B;B;B	0.57899	0.036;0.036;0.036;0.981;0.063;0.036;0.045;0.036	B;B;B;P;B;B;B;B	0.53549	0.013;0.013;0.021;0.729;0.021;0.021;0.035;0.021	T	0.09618	-1.0666	9	0.72032	D	0.01	-0.1032	9.0375	0.36296	0.0785:0.0:0.7665:0.155	rs1132780;rs2230777;rs3193919;rs4980999;rs11548315;rs17418140;rs52829826;rs59056292;rs1132780	363;363;363;150;363;363;363;363	Q96RR4-6;Q96RR4-2;Q96RR4-7;F5GZ00;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;.;KKCC2_HUMAN;.	C	363;363;363;363;363;150;363;363;346;363;363	ENSP00000376266:R363C;ENSP00000321230:R363C;ENSP00000445944:R363C;ENSP00000336634:R363C;ENSP00000312741:R363C;ENSP00000441352:R150C;ENSP00000388368:R363C;ENSP00000384600:R363C;ENSP00000388273:R363C;ENSP00000376265:R363C	ENSP00000312741:R363C	R	-	1	0	CAMKK2	120175479	1.000000	0.71417	0.998000	0.56505	0.800000	0.45204	2.049000	0.41288	1.279000	0.44446	-0.119000	0.15052	CGC	G|0.795;A|0.205	0.205	strong		0.562	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
PEMT	10400	hgsc.bcm.edu	37	17	17409140	17409140	+	Missense_Mutation	SNP	G	G	A	rs140621950		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:17409140G>A	ENST00000395783.1	-	7	744	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	PEMT_ENST00000395781.2_3'UTR|RP11-524F11.1_ENST00000582325.1_RNA|PEMT_ENST00000395782.1_Missense_Mutation_p.R189W|PEMT_ENST00000255389.5_Missense_Mutation_p.R226W|PEMT_ENST00000484838.2_5'UTR|PEMT_ENST00000435340.2_3'UTR	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	189					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)		GCTTTCTGCCGGTAGATCTCA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		16588	0.0		0.001	False		,,,				2504	0.0				p.R226W		Atlas-SNP	.											.	PEMT	12	.	0			c.C676T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	63.0	57.0	59.0		565,676,565	2.3	1.0	17	dbSNP_134	59	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	101,101,101	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging	189/200,226/237,189/200	17409140	8,12998	2203	4300	6503	SO:0001583	missense	10400	exon7			TCTGCCGGTAGAT	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.565C>T	17.37:g.17409140G>A	ENSP00000379129:p.Arg189Trp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_148172	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460614	0.43736	4.54E-4	6.98E-4	ENSG00000133027	ENST00000255389;ENST00000395783;ENST00000395782	T;T;T	0.44482	0.92;0.92;0.92	3.29	2.3	0.28687	.	0.487586	0.21644	N	0.071298	T	0.61185	0.2327	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68192	0.927;0.956	T	0.64322	-0.6435	10	0.66056	D	0.02	-31.4459	9.9715	0.41757	0.0:0.0:0.7954:0.2046	.	226;189	Q9UBM1-2;Q9UBM1	.;PEMT_HUMAN	W	226;189;189	ENSP00000255389:R226W;ENSP00000379129:R189W;ENSP00000379128:R189W	ENSP00000255389:R226W	R	-	1	2	PEMT	17349865	1.000000	0.71417	0.989000	0.46669	0.268000	0.26511	2.878000	0.48515	0.946000	0.37632	0.561000	0.74099	CGG	G|0.999;A|0.001	0.001	strong		0.662	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183286	11183286	+	Missense_Mutation	SNP	G	G	C	rs10845294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11183286G>C	ENST00000390675.2	-	1	720	c.649C>G	c.(649-651)Caa>Gaa	p.Q217E	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	217			Q -> E (in dbSNP:rs10845294).		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						CTGGGATCTTGAGATCCTTTA	0.403													.|||	614	0.122604	0.1051	0.2161	5008	,	,		20987	0.0		0.2734	False		,,,				2504	0.0511				p.Q217E		Atlas-SNP	.											.	TAS2R31	24	.	0			c.C649G						PASS	.	G	GLU/GLN	590,3816		49,492,1662	152.0	159.0	157.0		649	-1.3	0.0	12	dbSNP_120	157	2206,6390		295,1616,2387	no	missense	TAS2R31	NM_176885.2	29	344,2108,4049	CC,CG,GG		25.6631,13.3908,21.5044	possibly-damaging	217/310	11183286	2796,10206	2203	4298	6501	SO:0001583	missense	259290	exon1			GATCTTGAGATCC	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.649C>G	12.37:g.11183286G>C	ENSP00000375093:p.Gln217Glu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	115	112	0.973913	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	359	0.16437728937728938	70	0.14227642276422764	76	0.20994475138121546	0	0.0	213	0.28100263852242746	.	10.69	1.420493	0.25639	0.133908	0.256631	ENSG00000256436	ENST00000390675	T	0.00724	5.78	2.62	-1.26	0.09376	.	.	.	.	.	T	0.00012	0.0000	M	0.79805	2.47	0.80722	P	0.0	P	0.41041	0.736	B	0.44278	0.445	T	0.43442	-0.9391	8	0.72032	D	0.01	.	3.0067	0.06031	0.1566:0.0:0.3795:0.4638	rs10845294	217	P59538	T2R31_HUMAN	E	217	ENSP00000375093:Q217E	ENSP00000375093:Q217E	Q	-	1	0	TAS2R31	11074553	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	0.317000	0.19487	-0.006000	0.14370	0.194000	0.17425	CAA	G|0.834;C|0.166	0.166	strong		0.403	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
LRP1	4035	hgsc.bcm.edu	37	12	57573261	57573261	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57573261T>C	ENST00000243077.3	+	29	5354	c.4888T>C	c.(4888-4890)Tac>Cac	p.Y1630H		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1630					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCAGCGTGTGTACTGGTCTGA	0.592																																					p.Y1630H		Atlas-SNP	.											LRP1,NS,carcinoma,0,1	LRP1	428	1	0			c.T4888C						scavenged	.						170.0	113.0	132.0					12																	57573261		2203	4300	6503	SO:0001583	missense	4035	exon29			CGTGTGTACTGGT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.4888T>C	12.37:g.57573261T>C	ENSP00000243077:p.Tyr1630His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	2	0.0148148	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.762130	0.89932	.	.	ENSG00000123384	ENST00000243077	D	0.99304	-5.72	4.5	4.5	0.54988	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.99554	0.9840	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97996	1.0357	10	0.87932	D	0	.	13.2022	0.59774	0.0:0.0:0.0:1.0	.	1630	Q07954	LRP1_HUMAN	H	1630	ENSP00000243077:Y1630H	ENSP00000243077:Y1630H	Y	+	1	0	LRP1	55859528	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.760000	0.85248	2.007000	0.58848	0.533000	0.62120	TAC	.	.	none		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PRKCZ	5590	hgsc.bcm.edu	37	1	1991014	1991014	+	IGR	SNP	A	A	G	rs1878745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1991014A>G								RP11-547D24.3 (9505 upstream) : PRKCZ (13886 downstream)														p.P106P(2)									CTGGCCTGCCATGTCCGGGAG	0.592													G|||	1190	0.23762	0.0719	0.2032	5008	,	,		18261	0.4752		0.1928	False		,,,				2504	0.2873				p.P106P		Atlas-SNP	.											PRKCZ_ENST00000378567,NS,carcinoma,+1,4	PRKCZ	84	4	2	Substitution - coding silent(2)	stomach(2)	c.A318G						PASS	.	G		404,4002	789.1+/-415.0	14,376,1813	91.0	77.0	82.0		318	-8.8	0.1	1	dbSNP_92	82	1587,7013	743.6+/-407.2	155,1277,2868	no	coding-synonymous	PRKCZ	NM_002744.4		169,1653,4681	GG,GA,AA		18.4535,9.1693,15.3083		106/593	1991014	1991,11015	2203	4300	6503	SO:0001628	intergenic_variant	5590	exon4			CCTGCCATGTCCG																													1.37:g.1991014A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_002744		Silent	SNP		37																																																																																				A|0.809;G|0.191	0.191	strong	0	0.592								
SELE	6401	hgsc.bcm.edu	37	1	169694918	169694918	+	Silent	SNP	A	A	G	rs5356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169694918A>G	ENST00000333360.7	-	13	1939	c.1800T>C	c.(1798-1800)gaT>gaC	p.D600D	SELE_ENST00000367776.1_Silent_p.D537D|SELE_ENST00000367779.4_Silent_p.D474D|SELE_ENST00000367782.4_Silent_p.D537D|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367775.1_Silent_p.D475D|SELE_ENST00000367780.4_Silent_p.D475D|SELE_ENST00000367781.4_Silent_p.D537D|SELE_ENST00000367774.1_Silent_p.D474D|SELE_ENST00000367777.1_Silent_p.D537D	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	600					actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	GGTAGCTTCCATCTGATTCAA	0.383													A|||	743	0.148363	0.0809	0.2363	5008	,	,		20461	0.1984		0.1252	False		,,,				2504	0.1493				p.D600D		Atlas-SNP	.											.	SELE	84	.	0			c.T1800C						PASS	.	A		343,4063	178.7+/-207.4	11,321,1871	123.0	116.0	118.0		1800	-6.7	0.0	1	dbSNP_52	118	816,7784	189.7+/-236.4	40,736,3524	no	coding-synonymous	SELE	NM_000450.2		51,1057,5395	GG,GA,AA		9.4884,7.7848,8.9113		600/611	169694918	1159,11847	2203	4300	6503	SO:0001819	synonymous_variant	6401	exon13			GCTTCCATCTGAT	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1800T>C	1.37:g.169694918A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	37	CCDS1283.1																																																																																			A|0.886;G|0.114	0.114	strong		0.383	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
C19orf40	91442	hgsc.bcm.edu	37	19	33467576	33467576	+	Silent	SNP	G	G	A	rs7258185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:33467576G>A	ENST00000588258.1	+	5	746	c.636G>A	c.(634-636)acG>acA	p.T212T	C19orf40_ENST00000590281.1_Silent_p.T212T|C19orf40_ENST00000590179.1_Silent_p.T117T|C19orf40_ENST00000589646.1_Silent_p.T117T	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	212	RuvA domain 2-like.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					CCTTCTTCACGCAGCCCAGGT	0.537								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1346	0.26877	0.3094	0.4366	5008	,	,		19432	0.1647		0.2157	False		,,,				2504	0.2566				p.T212T		Atlas-SNP	.											.	C19orf40	21	.	0			c.G636A						PASS	.	A		1337,3069	694.4+/-405.8	196,945,1062	83.0	75.0	78.0		636	-3.4	0.8	19	dbSNP_116	78	1979,6621	723.3+/-406.4	202,1575,2523	no	coding-synonymous	C19orf40	NM_152266.3		398,2520,3585	AA,AG,GG		23.0116,30.345,25.4959		212/216	33467576	3316,9690	2203	4300	6503	SO:0001819	synonymous_variant	91442	exon5			CTTCACGCAGCCC	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.636G>A	19.37:g.33467576G>A		Somatic	60	0	0	840	WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Silent	SNP	ENST00000588258.1	37	CCDS12426.1																																																																																			G|0.753;A|0.247	0.247	strong		0.537	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
NASP	4678	hgsc.bcm.edu	37	1	46073489	46073489	+	Silent	SNP	G	G	A	rs2230657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46073489G>A	ENST00000350030.3	+	6	993	c.906G>A	c.(904-906)ccG>ccA	p.P302P	NASP_ENST00000351223.3_Intron|NASP_ENST00000372052.4_Intron|NASP_ENST00000537798.1_Silent_p.P238P|NASP_ENST00000402363.3_Silent_p.P304P	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	103	3	0.0291262		WXS	Illumina HiSeq	Phase_I	82	82	1	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	
BNIPL	149428	hgsc.bcm.edu	37	1	151011325	151011325	+	Missense_Mutation	SNP	C	C	T	rs373344206|rs61751619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	87	0	0		WXS	Illumina HiSeq	Phase_I	135	82	0.607407	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	
ARC	23237	hgsc.bcm.edu	37	8	143694775	143694775	+	Silent	SNP	G	G	C	rs28686812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143694775G>C	ENST00000356613.2	-	1	2058	c.858C>G	c.(856-858)cgC>cgG	p.R286R	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				GGTCCAGCTCGCGCTGGATGG	0.647													G|||	2507	0.500599	0.5651	0.4928	5008	,	,		11277	0.3948		0.508	False		,,,				2504	0.5204				p.R286R		Atlas-SNP	.											ARC,NS,carcinoma,-2,1	ARC	34	1	0			c.C858G						scavenged	.	G		2389,2017	599.1+/-389.2	648,1093,462	35.0	35.0	35.0		858	-9.6	0.3	8	dbSNP_125	35	4182,4418	557.0+/-387.0	1032,2118,1150	no	coding-synonymous	ARC	NM_015193.3		1680,3211,1612	CC,CG,GG		48.6279,45.7785,49.4772		286/397	143694775	6571,6435	2203	4300	6503	SO:0001819	synonymous_variant	23237	exon1			CAGCTCGCGCTGG	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.858C>G	8.37:g.143694775G>C		Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_015193	B4DFL0|O60937	Silent	SNP	ENST00000356613.2	37	CCDS34950.1																																																																																			G|0.488;C|0.512	0.512	strong		0.647	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
ZNF645	158506	hgsc.bcm.edu	37	X	22291942	22291942	+	Silent	SNP	G	G	A	rs138094158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:22291942G>A	ENST00000323684.1	+	1	878	c.834G>A	c.(832-834)caG>caA	p.Q278Q		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	278	Pro-rich.				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						TTATACCTCAGAAACAGCATT	0.463													G|||	1	0.000264901	0.0	0.0	3775	,	,		16433	0.0		0.001	False		,,,				2504	0.0				p.Q278Q		Atlas-SNP	.											.	ZNF645	67	.	0			c.G834A						PASS	.	G		2,3833		0,2,0,1630,571	149.0	119.0	129.0		834	-5.1	0.0	X	dbSNP_134	129	28,6700		0,19,9,2409,1863	no	coding-synonymous	ZNF645	NM_152577.3		0,21,9,4039,2434	AA,AG,A,GG,G		0.4162,0.0522,0.284		278/426	22291942	30,10533	2203	4300	6503	SO:0001819	synonymous_variant	158506	exon1			ACCTCAGAAACAG	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.834G>A	X.37:g.22291942G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																			G|0.997;A|0.003	0.003	strong		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
TRPM6	140803	hgsc.bcm.edu	37	9	77377410	77377410	+	Missense_Mutation	SNP	C	C	T	rs3750425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:77377410C>T	ENST00000360774.1	-	26	4414	c.4177G>A	c.(4177-4179)Gtt>Att	p.V1393I	TRPM6_ENST00000361255.3_Missense_Mutation_p.V1388I|TRPM6_ENST00000449912.2_Missense_Mutation_p.V1388I|TRPM6_ENST00000451710.3_Missense_Mutation_p.V1393I|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.V1393I|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1393			V -> I (in dbSNP:rs3750425). {ECO:0000269|PubMed:17344846}.		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						TCAGAGACAACTGGGGTCTGC	0.527													c|||	883	0.176318	0.2958	0.0879	5008	,	,		19160	0.1548		0.0785	False		,,,				2504	0.2004				p.V1393I		Atlas-SNP	.											.	TRPM6	377	.	0			c.G4177A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1138,3268	405.1+/-333.4	166,806,1231	93.0	86.0	89.0		4162,4162,4177	0.4	0.0	9	dbSNP_107	89	732,7868	177.9+/-227.4	30,672,3598	yes	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	29,29,29	196,1478,4829	TT,TC,CC		8.5116,25.8284,14.378	benign,benign,benign	1388/2018,1388/2018,1393/2023	77377410	1870,11136	2203	4300	6503	SO:0001583	missense	140803	exon26			AGACAACTGGGGT	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.4177G>A	9.37:g.77377410C>T	ENSP00000354006:p.Val1393Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	303	0.13873626373626374	119	0.241869918699187	30	0.08287292817679558	89	0.1555944055944056	65	0.08575197889182058	c	8.299	0.819541	0.16607	0.258284	0.085116	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.55052	0.64;0.64;0.64;0.64;0.54	5.68	0.442	0.16582	.	2.390330	0.01144	N	0.006262	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.30973	0.029;0.302;0.05	B;B;B	0.27500	0.016;0.08;0.037	T	0.06516	-1.0822	9	0.09843	T	0.71	.	1.2411	0.01963	0.2303:0.4003:0.1124:0.257	rs3750425;rs52794331;rs56518046;rs59790880;rs3750425	1393;1388;1388	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	I	1393;1393;1388;1388;1393;1056;1056	ENSP00000354006:V1393I;ENSP00000407341:V1393I;ENSP00000396672:V1388I;ENSP00000354962:V1388I;ENSP00000366060:V1393I	ENSP00000309693:V1056I	V	-	1	0	TRPM6	76567230	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.484000	0.06528	0.080000	0.16959	-1.618000	0.00794	GTT	C|0.855;T|0.145	0.145	strong		0.527	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
IL34	146433	hgsc.bcm.edu	37	16	70694000	70694000	+	Nonsense_Mutation	SNP	C	C	A	rs4985556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70694000C>A	ENST00000288098.2	+	6	1022	c.639C>A	c.(637-639)taC>taA	p.Y213*	IL34_ENST00000429149.2_Nonsense_Mutation_p.Y213*|IL34_ENST00000566361.1_Nonsense_Mutation_p.Y188*|FLJ00418_ENST00000597002.1_5'Flank	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	213					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						CCCAGCTGTACCCTCCGCCCC	0.657													C|||	300	0.0599042	0.0053	0.0375	5008	,	,		13120	0.0665		0.1044	False		,,,				2504	0.0971				p.Y213X		Atlas-SNP	.											.	IL34	26	.	0			c.C639A						PASS	.	C	stop/TYR,stop/TYR,stop/TYR	105,4291	81.4+/-119.9	1,103,2094	74.0	83.0	80.0		636,639,639	0.4	0.1	16	dbSNP_111	80	1018,7582	215.9+/-255.1	60,898,3342	yes	stop-gained,stop-gained,stop-gained	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	,,	61,1001,5436	AA,AC,CC		11.8372,2.3885,8.6411	,,	212/242,213/243,213/243	70694000	1123,11873	2198	4300	6498	SO:0001587	stop_gained	146433	exon7			GCTGTACCCTCCG	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"""Interleukins and interleukin receptors"""	28529	protein-coding gene	gene with protein product		612081	"""chromosome 16 open reading frame 77"""	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.639C>A	16.37:g.70694000C>A	ENSP00000288098:p.Tyr213*	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	168	58	0.345238	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Nonsense_Mutation	SNP	ENST00000288098.2	37	CCDS10895.1	122	0.055860805860805864	2	0.0040650406504065045	14	0.03867403314917127	26	0.045454545454545456	80	0.10554089709762533	C	22.0	4.233060	0.79688	0.023885	0.118372	ENSG00000157368	ENST00000429149;ENST00000288098	.	.	.	4.8	0.394	0.16299	.	1.242800	0.05737	N	0.600667	.	.	.	.	.	.	0.42010	D	0.99093	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.5745	4.6997	0.12822	0.0:0.5589:0.158:0.2831	rs4985556;rs58625464;rs4985556	.	.	.	X	213	.	ENSP00000288098:Y213X	Y	+	3	2	IL34	69251501	0.001000	0.12720	0.072000	0.20136	0.013000	0.08279	0.237000	0.17985	0.082000	0.17018	-0.463000	0.05309	TAC	C|0.927;A|0.073	0.073	strong		0.657	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
SYNE1	23345	hgsc.bcm.edu	37	6	152722368	152722368	+	Missense_Mutation	SNP	A	A	G	rs138004884		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152722368A>G	ENST00000367255.5	-	47	7535	c.6934T>C	c.(6934-6936)Ttt>Ctt	p.F2312L	SYNE1_ENST00000341594.5_Missense_Mutation_p.F2349L|RP3-398G3.5_ENST00000458194.1_RNA|SYNE1_ENST00000423061.1_Missense_Mutation_p.F2319L|SYNE1_ENST00000265368.4_Missense_Mutation_p.F2312L|SYNE1_ENST00000448038.1_Missense_Mutation_p.F2319L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2312					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)		TCATTAATAAACTTCTCCACT	0.393										HNSCC(10;0.0054)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19585	0.0		0.001	False		,,,				2504	0.0				p.F2319L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T6955C						PASS	.	A	LEU/PHE,LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	147.0	129.0	135.0		6955,6934	5.6	1.0	6	dbSNP_134	135	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	22,22	0,9,6494	GG,GA,AA		0.093,0.0227,0.0692	benign,benign	2319/8750,2312/8798	152722368	9,12997	2203	4300	6503	SO:0001583	missense	23345	exon47			TAATAAACTTCTC	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.6934T>C	6.37:g.152722368A>G	ENSP00000356224:p.Phe2312Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	156	63	0.403846	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	14.92	2.678770	0.47886	2.27E-4	9.3E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	5.58	5.58	0.84498	.	0.101968	0.43919	D	0.000518	T	0.11623	0.0283	L	0.39633	1.23	0.80722	D	1	B;B;B;B	0.15141	0.012;0.002;0.002;0.002	B;B;B;B	0.13407	0.009;0.003;0.003;0.004	T	0.08848	-1.0702	10	0.16896	T	0.51	.	11.6415	0.51235	0.9288:0.0:0.0712:0.0	.	2295;2312;2312;2319	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	L	2312;2319;2312;2319;2349	ENSP00000356224:F2312L;ENSP00000396024:F2319L;ENSP00000265368:F2312L;ENSP00000390975:F2319L;ENSP00000341887:F2349L	ENSP00000265368:F2312L	F	-	1	0	SYNE1	152764061	1.000000	0.71417	0.963000	0.40424	0.921000	0.55340	5.286000	0.65639	2.133000	0.65898	0.482000	0.46254	TTT	A|0.999;G|0.001	0.001	strong		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3413868C>G	ENST00000356575.4	-	27	3636	c.3410G>C	c.(3409-3411)gGc>gCc	p.G1137A	MEGF6_ENST00000294599.4_Missense_Mutation_p.G946A	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1137	EGF-like 21. {ECO:0000255|PROSITE- ProRule:PRU00076}.		G -> A (in dbSNP:rs4648506). {ECO:0000269|PubMed:9693030}.			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)		GCAGGCAGCGCCAGGCGGGCA	0.716													C|||	1222	0.24401	0.146	0.3357	5008	,	,		12528	0.1865		0.3201	False		,,,				2504	0.2924				p.G1137A	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G3410C						PASS	.	C	ALA/GLY	547,3569		48,451,1559	8.0	13.0	11.0		3410	0.1	0.0	1	dbSNP_111	11	2204,6092		339,1526,2283	no	missense	MEGF6	NM_001409.3	60	387,1977,3842	GG,GC,CC		26.567,13.2896,22.164	possibly-damaging	1137/1542	3413868	2751,9661	2058	4148	6206	SO:0001583	missense	1953	exon27			GCAGCGCCAGGCG	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.3410G>C	1.37:g.3413868C>G	ENSP00000348982:p.Gly1137Ala	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	532	0.24358974358974358	83	0.16869918699186992	101	0.27900552486187846	130	0.22727272727272727	218	0.287598944591029	C	12.32	1.903437	0.33628	0.132896	0.26567	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.71934	-0.09;-0.61	4.36	0.0897	0.14460	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.182174	0.48286	N	0.000200	T	0.00012	0.0000	M	0.91663	3.23	0.40306	P	0.021338999999999997	P;P	0.51147	0.942;0.929	P;P	0.62435	0.902;0.841	T	0.05022	-1.0911	9	0.62326	D	0.03	-7.763	6.2955	0.21083	0.0:0.6314:0.1331:0.2355	rs4648506	1137;946	O75095;O75095-2	MEGF6_HUMAN;.	A	946;1137	ENSP00000294599:G946A;ENSP00000348982:G1137A	ENSP00000294599:G946A	G	-	2	0	MEGF6	3403728	0.002000	0.14202	0.000000	0.03702	0.135000	0.20990	0.253000	0.18296	-0.064000	0.13043	0.561000	0.74099	GGC	C|0.736;G|0.264	0.264	strong		0.716	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
BAGE2	85319	hgsc.bcm.edu	37	21	11058322	11058322	+	RNA	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11058322C>T	ENST00000470054.1	-	0	325							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								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)		AAATGCACATCGCTGAAAGGG	0.383																																					p.D40N		Atlas-SNP	.											.	.	.	.	0			c.G118A						PASS	.						92.0	70.0	77.0					21																	11058322		692	1591	2283			85318	exon3			GCACATCGCTGAA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058322C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	238	14	0.0588235	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				C|0.750;T|0.250	0.250	strong		0.383	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
ANK3	288	hgsc.bcm.edu	37	10	61828954	61828954	+	Silent	SNP	G	G	A	rs7923682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61828954G>A	ENST00000280772.2	-	37	11876	c.11685C>T	c.(11683-11685)tcC>tcT	p.S3895S	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3895					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)			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						TGGTTTTCTCGGATTGACTAA	0.388													G|||	49	0.00978435	0.0023	0.0144	5008	,	,		21552	0.0		0.0298	False		,,,				2504	0.0061				p.S3895S		Atlas-SNP	.											.	ANK3	703	.	0			c.C11685T						PASS	.	G	,,,	24,4382	30.8+/-60.4	0,24,2179	263.0	255.0	258.0		,,,11685	-3.6	0.2	10	dbSNP_116	258	286,8314	107.0+/-167.8	3,280,4017	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	3,304,6196	AA,AG,GG		3.3256,0.5447,2.3835	,,,	,,,3895/4378	61828954	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TTTCTCGGATTGA	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.11685C>T	10.37:g.61828954G>A		Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	487	241	0.494867	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			G|0.981;A|0.019	0.019	strong		0.388	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
TRUB1	142940	hgsc.bcm.edu	37	10	116719543	116719543	+	Missense_Mutation	SNP	G	G	A	rs7099565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	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	
KCTD8	386617	hgsc.bcm.edu	37	4	44176960	44176960	+	Silent	SNP	T	T	C	rs13143747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:44176960T>C	ENST00000360029.3	-	2	1552	c.1269A>G	c.(1267-1269)acA>acG	p.T423T		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	423					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						TGGACAGATTTGTTTCCCGGG	0.403										HNSCC(17;0.042)			T|||	198	0.0395367	0.0045	0.0389	5008	,	,		19523	0.0		0.0984	False		,,,				2504	0.0675				p.T423T		Atlas-SNP	.											KCTD8,NS,carcinoma,-1,1	KCTD8	96	1	0			c.A1269G						scavenged	.	T		92,4314	74.7+/-112.8	1,90,2112	209.0	219.0	215.0		1269	-4.7	1.0	4	dbSNP_121	215	970,7630	211.0+/-251.7	59,852,3389	no	coding-synonymous	KCTD8	NM_198353.2		60,942,5501	CC,CT,TT		11.2791,2.0881,8.1655		423/474	44176960	1062,11944	2203	4300	6503	SO:0001819	synonymous_variant	386617	exon2			CAGATTTGTTTCC	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 8"""				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1269A>G	4.37:g.44176960T>C		Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	37	CCDS3467.1																																																																																			T|0.929;C|0.071	0.071	strong		0.403	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1		
SVIL	6840	hgsc.bcm.edu	37	10	29779914	29779914	+	Missense_Mutation	SNP	C	C	T	rs148355552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29779914C>T	ENST00000355867.4	-	22	4806	c.4054G>A	c.(4054-4056)Gtt>Att	p.V1352I	SVIL_ENST00000535393.1_Missense_Mutation_p.V266I|SVIL_ENST00000538146.1_Missense_Mutation_p.V144I|SVIL_ENST00000375398.2_Missense_Mutation_p.V1352I|SVIL_ENST00000375400.3_Missense_Mutation_p.V926I	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1352					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)				TTGGGCCTAACTGCCCGCTTG	0.587													C|||	68	0.0135783	0.0	0.0144	5008	,	,		19004	0.001		0.0378	False		,,,				2504	0.0194				p.V1352I		Atlas-SNP	.											.	SVIL	226	.	0			c.G4054A						PASS	.	C	ILE/VAL,ILE/VAL	35,4371	40.0+/-72.8	0,35,2168	37.0	38.0	38.0		2776,4054	4.1	0.3	10	dbSNP_134	38	342,8258	113.9+/-173.9	2,338,3960	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	29,29	2,373,6128	TT,TC,CC		3.9767,0.7944,2.8987	probably-damaging,probably-damaging	926/1789,1352/2215	29779914	377,12629	2203	4300	6503	SO:0001583	missense	6840	exon22			GCCTAACTGCCCG	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.4054G>A	10.37:g.29779914C>T	ENSP00000348128:p.Val1352Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	C	19.54	3.847185	0.71603	0.007944	0.039767	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.28666	2.56;2.54;2.54;2.46;1.6	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	T	0.11537	0.0281	L	0.49350	1.555	0.52099	D	0.999949	B;B;B;P	0.40515	0.384;0.433;0.433;0.719	P;B;B;B	0.45753	0.492;0.131;0.3;0.443	T	0.11084	-1.0602	10	0.72032	D	0.01	-18.8293	16.543	0.84407	0.0:1.0:0.0:0.0	.	266;144;926;1352	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	I	926;1352;1352;266;306;144	ENSP00000364549:V926I;ENSP00000364547:V1352I;ENSP00000348128:V1352I;ENSP00000445472:V266I;ENSP00000440343:V144I	ENSP00000348128:V1352I	V	-	1	0	SVIL	29819920	1.000000	0.71417	0.283000	0.24790	0.451000	0.32288	5.822000	0.69265	2.110000	0.64415	0.485000	0.47835	GTT	C|0.979;T|0.021	0.021	strong		0.587	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
BTBD11	121551	hgsc.bcm.edu	37	12	108035903	108035903	+	Silent	SNP	T	T	C	rs9919712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:108035903T>C	ENST00000280758.5	+	14	3405	c.2877T>C	c.(2875-2877)gaT>gaC	p.D959D	BTBD11_ENST00000357167.4_Silent_p.D496D|BTBD11_ENST00000420571.2_Silent_p.D840D|BTBD11_ENST00000494235.2_Silent_p.D38D|BTBD11_ENST00000490090.2_Silent_p.D959D	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	137	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	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	
CCDC168	643677	hgsc.bcm.edu	37	13	103384824	103384824	+	Missense_Mutation	SNP	G	G	A	rs9300756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:103384824G>A	ENST00000322527.2	-	1	4335	c.4336C>T	c.(4336-4338)Cgt>Tgt	p.R1446C		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1446			R -> C (in dbSNP:rs9300756).														TGATCTTTACGTTTGGGAGAA	0.313													g|||	2938	0.586661	0.3654	0.6153	5008	,	,		19757	0.8442		0.6123	False		,,,				2504	0.5736				p.R6075C		Atlas-SNP	.											.	.	.	.	0			c.C18223T						PASS	.	G	CYS/ARG	562,822		118,326,248	137.0	100.0	111.0		18223	0.0	0.0	13	dbSNP_119	111	1908,1272		574,760,256	yes	missense	CCDC168	NM_001146197.1	180	692,1086,504	AA,AG,GG		40.0,40.6069,45.8808	benign	6075/7082	103384824	2470,2094	692	1590	2282	SO:0001583	missense	643677	exon4			CTTTACGTTTGGG		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.4336C>T	13.37:g.103384824G>A	ENSP00000320232:p.Arg1446Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		1338	0.6126373626373627	186	0.3780487804878049	210	0.580110497237569	473	0.8269230769230769	469	0.6187335092348285	g	3.276	-0.148121	0.06627	0.406069	0.6	ENSG00000175820	ENST00000322527	T	0.03689	3.84	2.62	0.0102	0.14082	.	.	.	.	.	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	0.02868	-1.1100	8	0.38643	T	0.18	.	4.9317	0.13921	0.7117:0.0:0.2883:0.0	rs9300756;rs52830042;rs59881186;rs9300756	1446	Q8NDH2	CC168_HUMAN	C	1446	ENSP00000320232:R1446C	ENSP00000320232:R1446C	R	-	1	0	CCDC168	102182825	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.080000	0.14802	0.010000	0.14839	-0.416000	0.06073	CGT	G|0.321;A|0.679	0.679	strong		0.313	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
DNHD1	144132	hgsc.bcm.edu	37	11	6554941	6554941	+	Missense_Mutation	SNP	C	C	A	rs4282961	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	95	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	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	
HLA-B	3106	hgsc.bcm.edu	37	6	31323262	31323262	+	Missense_Mutation	SNP	G	G	A	rs77665001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31323262G>A	ENST00000412585.2	-	4	755	c.727C>T	c.(727-729)Cgg>Tgg	p.R243W		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	243	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						TCGCCATCCCGCTGCCAGGTC	0.597									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R243W		Atlas-SNP	.											.	HLA-B	54	.	0			c.C727T						PASS	.						95.0	88.0	90.0					6																	31323262		2203	4300	6503	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	CATCCCGCTGCCA	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.727C>T	6.37:g.31323262G>A	ENSP00000399168:p.Arg243Trp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	32	0.22695	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	133	0.060897435897435896	29	0.05894308943089431	17	0.04696132596685083	44	0.07692307692307693	43	0.05672823218997362	N	11.80	1.747791	0.30955	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.03181	4.02	3.16	-0.095	0.13643	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.232653	0.21556	U	0.072641	T	0.01661	0.0053	M	0.80183	2.485	0.22989	N	0.998462	B	0.23540	0.087	B	0.14023	0.01	T	0.36504	-0.9745	10	0.72032	D	0.01	.	2.5362	0.04715	0.2793:0.0:0.3821:0.3386	.	243	P01889	1B07_HUMAN	W	243;122;122	ENSP00000399168:R243W	ENSP00000399168:R243W	R	-	1	2	HLA-B	31431241	0.022000	0.18835	0.712000	0.30502	0.703000	0.40648	0.052000	0.14163	0.183000	0.20059	0.442000	0.29010	CGG	A|0.049;G|0.951	0.049	strong		0.597	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
GRM8	2918	hgsc.bcm.edu	37	7	126542667	126542667	+	Missense_Mutation	SNP	A	A	T	rs78124913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:126542667A>T	ENST00000339582.2	-	6	1893	c.1085T>A	c.(1084-1086)tTc>tAc	p.F362Y	GRM8_ENST00000444921.2_Missense_Mutation_p.F362Y|GRM8_ENST00000405249.1_Missense_Mutation_p.F362Y|GRM8_ENST00000358373.3_Missense_Mutation_p.F362Y|GRM8_ENST00000480995.1_5'UTR			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	362			F -> Y. {ECO:0000269|Ref.6}.		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|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)	p.F362Y(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CTCCTCCCAGAATTCTGCAAA	0.378										HNSCC(24;0.065)			A|||	614	0.122604	0.0098	0.1369	5008	,	,		16946	0.2083		0.1481	False		,,,				2504	0.1503				p.F362Y		Atlas-SNP	.											GRM8,NS,carcinoma,0,1	GRM8	377	1	1	Substitution - Missense(1)	stomach(1)	c.T1085A						PASS	.	A	TYR/PHE,TYR/PHE	135,4271	96.7+/-135.4	5,125,2073	91.0	90.0	90.0		1085,1085	4.9	1.0	7	dbSNP_131	90	1068,7532	224.5+/-260.9	78,912,3310	no	missense,missense	GRM8	NM_000845.2,NM_001127323.1	22,22	83,1037,5383	TT,TA,AA		12.4186,3.064,9.2496	benign,benign	362/909,362/909	126542667	1203,11803	2203	4300	6503	SO:0001583	missense	2918	exon5			TCCCAGAATTCTG		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1085T>A	7.37:g.126542667A>T	ENSP00000344173:p.Phe362Tyr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	292	0.1336996336996337	5	0.01016260162601626	52	0.143646408839779	121	0.21153846153846154	114	0.1503957783641161	A	16.48	3.135052	0.56828	0.03064	0.124186	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.88	4.88	0.63580	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	L	0.36672	1.1	0.09310	P	0.999999464699	B;P;B	0.41450	0.077;0.75;0.035	B;P;B	0.45195	0.17;0.473;0.074	T	0.04242	-1.0966	9	0.23302	T	0.38	.	13.6821	0.62491	1.0:0.0:0.0:0.0	rs61755380	362;362;362	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	Y	362	ENSP00000344173:F362Y;ENSP00000409790:F362Y;ENSP00000351142:F362Y;ENSP00000385731:F362Y	ENSP00000344173:F362Y	F	-	2	0	GRM8	126329903	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.283000	0.95860	1.827000	0.53221	0.418000	0.28097	TTC	A|0.896;T|0.104	0.104	strong		0.378	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
BAZ2A	11176	hgsc.bcm.edu	37	12	56995907	56995907	+	Missense_Mutation	SNP	G	G	A	rs202169462		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56995907G>A	ENST00000551812.1	-	20	3693	c.3500C>T	c.(3499-3501)gCc>gTc	p.A1167V	BAZ2A_ENST00000179765.5_Missense_Mutation_p.A1135V|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Missense_Mutation_p.A1165V|BAZ2A_ENST00000379441.3_Missense_Mutation_p.A1137V	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1167					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						AGAGAAGAGGGCAGGGTTGAG	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18914	0.0		0.0	False		,,,				2504	0.0				p.A1167V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C3500T						PASS	.	G	VAL/ALA	0,3988		0,0,1994	18.0	19.0	18.0		3500	1.7	0.0	12		18	3,8319		0,3,4158	yes	missense	BAZ2A	NM_013449.3	64	0,3,6152	AA,AG,GG		0.036,0.0,0.0244	benign	1167/1906	56995907	3,12307	1994	4161	6155	SO:0001583	missense	11176	exon20			AAGAGGGCAGGGT	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.3500C>T	12.37:g.56995907G>A	ENSP00000446880:p.Ala1167Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	2.919	-0.223686	0.06061	0.0	3.6E-4	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.70164	-0.15;-0.15;-0.15;-0.46;-0.15	5.6	1.72	0.24424	.	0.512331	0.20956	N	0.082651	T	0.49133	0.1539	L	0.38531	1.155	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.29212	-1.0019	10	0.30854	T	0.27	.	4.9226	0.13878	0.239:0.0:0.6142:0.1468	.	1165;1167;1167	F8VU39;Q9UIF9-3;Q9UIF9	.;.;BAZ2A_HUMAN	V	1137;1135;1167;103;1165	ENSP00000368754:A1137V;ENSP00000179765:A1135V;ENSP00000446880:A1167V;ENSP00000448760:A103V;ENSP00000447941:A1165V	ENSP00000179765:A1135V	A	-	2	0	BAZ2A	55282174	0.008000	0.16893	0.000000	0.03702	0.010000	0.07245	1.643000	0.37217	0.123000	0.18342	-0.229000	0.12294	GCC	G|0.999;A|0.001	0.001	strong		0.512	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
ZDBF2	57683	hgsc.bcm.edu	37	2	207171311	207171311	+	Missense_Mutation	SNP	C	C	T	rs192597586	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207171311C>T	ENST00000374423.3	+	5	2445	c.2059C>T	c.(2059-2061)Cgt>Tgt	p.R687C		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	687							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CGAAATAGAGCGTCAGAAAGT	0.443													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20794	0.0		0.0	False		,,,				2504	0.0164				p.R687C		Atlas-SNP	.											.	ZDBF2	531	.	0			c.C2059T						PASS	.	C	CYS/ARG	3,3795		0,3,1896	79.0	78.0	78.0		2059	0.8	0.0	2		78	39,8211		0,39,4086	yes	missense	ZDBF2	NM_020923.1	180	0,42,5982	TT,TC,CC		0.4727,0.079,0.3486	benign	687/2355	207171311	42,12006	1899	4125	6024	SO:0001583	missense	57683	exon5			ATAGAGCGTCAGA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2059C>T	2.37:g.207171311C>T	ENSP00000363545:p.Arg687Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	10.35	1.324971	0.24080	7.9E-4	0.004727	ENSG00000204186	ENST00000374423	T	0.46063	0.88	4.51	0.754	0.18410	.	0.460073	0.16677	N	0.204098	T	0.11239	0.0274	N	0.08118	0	0.09310	N	1	B	0.26147	0.143	B	0.10450	0.005	T	0.09400	-1.0676	10	0.30078	T	0.28	.	1.5228	0.02519	0.1723:0.473:0.1669:0.1877	.	687	Q9HCK1	ZDBF2_HUMAN	C	687	ENSP00000363545:R687C	ENSP00000363545:R687C	R	+	1	0	ZDBF2	206879556	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.470000	0.02346	0.125000	0.18397	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.443	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
MEGF6	1953	hgsc.bcm.edu	37	1	3417545	3417545	+	Missense_Mutation	SNP	A	A	G	rs41303857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3417545A>G	ENST00000356575.4	-	20	2786	c.2560T>C	c.(2560-2562)Ttt>Ctt	p.F854L	MEGF6_ENST00000294599.4_Missense_Mutation_p.F749L	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	854	EGF-like 14. {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)		TGGCAGCTAAAGCCGGTCCAC	0.652													A|||	5	0.000998403	0.0	0.0029	5008	,	,		18548	0.0		0.003	False		,,,				2504	0.0				p.F854L	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.T2560C						PASS	.	A	LEU/PHE	4,3954		0,4,1975	36.0	45.0	42.0		2560	1.7	1.0	1	dbSNP_127	42	27,8299		0,27,4136	yes	missense	MEGF6	NM_001409.3	22	0,31,6111	GG,GA,AA		0.3243,0.1011,0.2524	benign	854/1542	3417545	31,12253	1979	4163	6142	SO:0001583	missense	1953	exon20			AGCTAAAGCCGGT	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.2560T>C	1.37:g.3417545A>G	ENSP00000348982:p.Phe854Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.886	-0.456687	0.04540	0.001011	0.003243	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.24538	1.85;1.85	4.98	1.73	0.24493	EGF-like, laminin (2);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.277593	0.32703	N	0.005760	T	0.06416	0.0165	N	0.00686	-1.255	0.24354	N	0.994905	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.002	T	0.32981	-0.9886	10	0.27082	T	0.32	-9.1415	6.1992	0.20567	0.241:0.0:0.6099:0.1491	rs41303857;rs61744087	854;749	O75095;O75095-2	MEGF6_HUMAN;.	L	749;854	ENSP00000294599:F749L;ENSP00000348982:F854L	ENSP00000294599:F749L	F	-	1	0	MEGF6	3407405	0.024000	0.19004	0.996000	0.52242	0.611000	0.37282	1.115000	0.31209	1.072000	0.40860	-0.366000	0.07423	TTT	A|0.998;G|0.002	0.002	strong		0.652	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
MADD	8567	hgsc.bcm.edu	37	11	47306630	47306630	+	Nonsense_Mutation	SNP	C	C	T	rs35233100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47306630C>T	ENST00000311027.5	+	13	2461	c.2296C>T	c.(2296-2298)Cga>Tga	p.R766*	MADD_ENST00000342922.4_Nonsense_Mutation_p.R766*|MADD_ENST00000402799.1_Intron|MADD_ENST00000406482.1_Intron|MADD_ENST00000407859.3_Intron|MADD_ENST00000395344.3_Intron|MADD_ENST00000349238.3_Nonsense_Mutation_p.R766*|MADD_ENST00000395336.3_Nonsense_Mutation_p.R766*|MADD_ENST00000402192.2_Nonsense_Mutation_p.R766*	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)		AGTGCGCCGGCGAATCTATGA	0.557													C|||	85	0.0169728	0.003	0.0288	5008	,	,		19633	0.0		0.0517	False		,,,				2504	0.0092				p.R766X		Atlas-SNP	.											.	MADD	172	.	0			c.C2296T						PASS	.	C	,,stop/ARG,stop/ARG,,,stop/ARG,,stop/ARG,stop/ARG	52,4350	52.9+/-88.7	0,52,2149	98.0	92.0	94.0		,,2296,2296,,,2296,,2296,2296	4.1	1.0	11	dbSNP_126	94	545,8051	150.9+/-205.7	21,503,3774	yes	intron,intron,stop-gained,stop-gained,intron,intron,stop-gained,intron,stop-gained,stop-gained	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	,,,,,,,,,	21,555,5923	TT,TC,CC		6.3402,1.1813,4.593	,,,,,,,,,	,,766/1648,766/1589,,,766/1609,,766/1582,766/1588	47306630	597,12401	2201	4298	6499	SO:0001587	stop_gained	8567	exon13			CGCCGGCGAATCT	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.2296C>T	11.37:g.47306630C>T	ENSP00000310933:p.Arg766*	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	14	0.297872	NM_130470		Nonsense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	48	0.02197802197802198	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	35	0.04617414248021108	C	41	9.028689	0.99040	0.011813	0.063402	ENSG00000110514	ENST00000342922;ENST00000349238;ENST00000311027;ENST00000395336;ENST00000402192	.	.	.	5.99	4.07	0.47477	.	0.296440	0.35151	N	0.003407	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0	16.6411	0.85127	0.0:0.7547:0.2452:0.0	rs35233100	.	.	.	X	766	.	ENSP00000310933:R766X	R	+	1	2	MADD	47263206	0.998000	0.40836	0.959000	0.39883	0.855000	0.48748	3.243000	0.51392	0.811000	0.34303	0.655000	0.94253	CGA	C|0.962;T|0.038	0.038	strong		0.557	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
LRCH4	4034	hgsc.bcm.edu	37	7	100172858	100172858	+	Missense_Mutation	SNP	C	C	T	rs3197597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100172858C>T	ENST00000310300.6	-	18	1976	c.1924G>A	c.(1924-1926)Gtg>Atg	p.V642M	LRCH4_ENST00000497245.1_Missense_Mutation_p.V190M|SAP25_ENST00000538735.1_5'Flank	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	26	0	0		WXS	Illumina HiSeq	Phase_I	31	21	0.677419	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	
CSTA	1475	hgsc.bcm.edu	37	3	122060404	122060404	+	Missense_Mutation	SNP	C	C	T	rs34173813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	36	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	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	
PIK3CA	5290	hgsc.bcm.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|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)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	PIK3CA_ENST00000263967,NS,carcinoma,0,745	PIK3CA	8460	745	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						scavenged	.						56.0	56.0	56.0					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	372	85	0.228495	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.	weak		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
ATG4B	23192	hgsc.bcm.edu	37	2	242610738	242610738	+	Silent	SNP	T	T	C	rs11538896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242610738T>C	ENST00000404914.3	+	12	1129	c.1026T>C	c.(1024-1026)ctT>ctC	p.L342L	ATG4B_ENST00000405546.3_Silent_p.L342L|ATG4B_ENST00000396411.3_Silent_p.L268L|ATG4B_ENST00000474739.2_Silent_p.L328L|ATG4B_ENST00000402096.1_Silent_p.L268L	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	342					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)		TGTCTCTGCTTGGAGGTGCCC	0.627													C|||	1027	0.205072	0.0787	0.2089	5008	,	,		19333	0.2966		0.2336	False		,,,				2504	0.2495				p.L342L	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.T1026C						PASS	.	C	,	413,3859		23,367,1746	65.0	71.0	69.0		1026,1026	-9.1	0.0	2	dbSNP_120	69	1876,6578		229,1418,2580	no	coding-synonymous,coding-synonymous	ATG4B	NM_013325.4,NM_178326.2	,	252,1785,4326	CC,CT,TT		22.1907,9.6676,17.9868	,	342/394,342/381	242610738	2289,10437	2136	4227	6363	SO:0001819	synonymous_variant	23192	exon12			TCTGCTTGGAGGT	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.1026T>C	2.37:g.242610738T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Silent	SNP	ENST00000404914.3	37	CCDS46564.1																																																																																			T|0.776;C|0.224	0.224	strong		0.627	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
IQCG	84223	hgsc.bcm.edu	37	3	197670652	197670652	+	Silent	SNP	G	G	A	rs3828371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:197670652G>A	ENST00000265239.6	-	4	703	c.279C>T	c.(277-279)tgC>tgT	p.C93C	IQCG_ENST00000480302.1_5'UTR|IQCG_ENST00000453254.1_Silent_p.C93C|IQCG_ENST00000455191.1_Silent_p.C93C	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	93						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)		TCTATACCACGCAGATGCTCT	0.413													G|||	340	0.0678914	0.0961	0.0187	5008	,	,		20049	0.0526		0.0507	False		,,,				2504	0.0982				p.C93C		Atlas-SNP	.											.	IQCG	44	.	0			c.C279T						PASS	.	G	,	437,3969	212.5+/-232.4	26,385,1792	120.0	120.0	120.0		279,279	1.5	0.0	3	dbSNP_107	120	387,8213	125.6+/-184.2	9,369,3922	no	coding-synonymous,coding-synonymous	IQCG	NM_001134435.1,NM_032263.3	,	35,754,5714	AA,AG,GG		4.5,9.9183,6.3355	,	93/444,93/444	197670652	824,12182	2203	4300	6503	SO:0001819	synonymous_variant	84223	exon4			TACCACGCAGATG	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.279C>T	3.37:g.197670652G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	72	0.571429	NM_032263	Q9BST2|Q9HAG8	Silent	SNP	ENST00000265239.6	37	CCDS3331.1																																																																																			G|0.937;A|0.063	0.063	strong		0.413	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263	
MAP3K8	1326	hgsc.bcm.edu	37	10	30728101	30728101	+	Silent	SNP	T	T	C	rs1042058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:30728101T>C	ENST00000263056.1	+	3	930	c.234T>C	c.(232-234)taT>taC	p.Y78Y	MAP3K8_ENST00000375322.2_Silent_p.Y78Y|MAP3K8_ENST00000375321.1_Silent_p.Y78Y|MAP3K8_ENST00000542547.1_Silent_p.Y78Y	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	78					cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				CAGTCAGATATGGAACTGTGG	0.408													T|||	1767	0.352835	0.0976	0.5187	5008	,	,		19327	0.3492		0.6044	False		,,,				2504	0.3252				p.Y78Y		Atlas-SNP	.											.	MAP3K8	46	.	0			c.T234C						PASS	.	T		694,3712	289.2+/-280.3	53,588,1562	133.0	116.0	122.0		234	-6.6	0.6	10	dbSNP_86	122	5188,3412	638.6+/-399.4	1581,2026,693	no	coding-synonymous	MAP3K8	NM_005204.3		1634,2614,2255	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	39.6744,15.7512,45.2253		78/468	30728101	5882,7124	2203	4300	6503	SO:0001819	synonymous_variant	1326	exon2			CAGATATGGAACT	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.234T>C	10.37:g.30728101T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_001244134	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Silent	SNP	ENST00000263056.1	37	CCDS7166.1																																																																																			T|0.582;C|0.418	0.418	strong		0.408	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204	
PHLPP2	23035	hgsc.bcm.edu	37	16	71712786	71712786	+	Silent	SNP	A	A	G	rs61733126	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:71712786A>G	ENST00000568954.1	-	8	1518	c.1140T>C	c.(1138-1140)ttT>ttC	p.F380F	PHLPP2_ENST00000360429.3_Silent_p.F380F|PHLPP2_ENST00000393524.2_Silent_p.F380F|PHLPP2_ENST00000567016.1_Silent_p.F415F|PHLPP2_ENST00000356272.3_Silent_p.F380F			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	380					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)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						GAATTTGACTAAAGTTGTTGA	0.408													A|||	804	0.160543	0.0121	0.0994	5008	,	,		18921	0.1766		0.1302	False		,,,				2504	0.4192				p.F380F		Atlas-SNP	.											.	PHLPP2	96	.	0			c.T1140C						PASS	.	A		112,4284	85.3+/-124.0	1,110,2087	81.0	78.0	79.0		1140	1.2	1.0	16	dbSNP_129	79	1052,7548	221.9+/-259.1	77,898,3325	no	coding-synonymous	PHLPP2	NM_015020.2		78,1008,5412	GG,GA,AA		12.2326,2.5478,8.9566		380/1324	71712786	1164,11832	2198	4300	6498	SO:0001819	synonymous_variant	23035	exon7			TTGACTAAAGTTG	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.1140T>C	16.37:g.71712786A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_015020	A1L374|Q9NV17|Q9Y2E3	Silent	SNP	ENST00000568954.1	37	CCDS32479.1																																																																																			A|0.899;G|0.101	0.101	strong		0.408	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020	
OR4K1	79544	hgsc.bcm.edu	37	14	20404736	20404736	+	Missense_Mutation	SNP	G	G	A	rs2792146	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20404736G>A	ENST00000285600.4	+	1	970	c.911G>A	c.(910-912)cGt>cAt	p.R304H		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, member 1	304			R -> H (in dbSNP:rs2792146). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		CTGAGAAACCGTCATGTGAAC	0.433													G|||	2151	0.429513	0.2617	0.4669	5008	,	,		22603	0.6101		0.4294	False		,,,				2504	0.4438				p.R304H		Atlas-SNP	.											.	OR4K1	108	.	0			c.G911A						PASS	.	G	HIS/ARG	1275,3131		125,1025,1053	71.0	79.0	76.0		911	-4.6	0.0	14	dbSNP_100	76	3532,5068		424,2684,1192	yes	missense	OR4K1	NM_001004063.2	29	549,3709,2245	AA,AG,GG		41.0698,28.9378,36.9599	benign	304/312	20404736	4807,8199	2203	4300	6503	SO:0001583	missense	79544	exon1			GAAACCGTCATGT		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"""GPCR / Class A : Olfactory receptors"""	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.911G>A	14.37:g.20404736G>A	ENSP00000285600:p.Arg304His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Missense_Mutation	SNP	ENST00000285600.4	37	CCDS32025.1	967	0.44276556776556775	140	0.2845528455284553	168	0.46408839779005523	348	0.6083916083916084	311	0.4102902374670185	.	1.788	-0.480168	0.04383	0.289378	0.410698	ENSG00000155249	ENST00000285600	T	0.39592	1.07	5.17	-4.59	0.03400	.	0.609210	0.15670	N	0.250404	T	0.00012	0.0000	L	0.38649	1.16	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.43925	-0.9361	9	0.34782	T	0.22	.	8.6915	0.34269	0.6043:0.0:0.2872:0.1086	rs2792146;rs3916625	304	Q8NGD4	OR4K1_HUMAN	H	304	ENSP00000285600:R304H	ENSP00000285600:R304H	R	+	2	0	OR4K1	19474576	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.082000	0.03400	-0.902000	0.03886	-1.686000	0.00732	CGT	G|0.548;A|0.452	0.452	strong		0.433	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1		
TIAM2	26230	hgsc.bcm.edu	37	6	155451352	155451352	+	Missense_Mutation	SNP	G	G	A	rs931312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:155451352G>A	ENST00000461783.3	+	6	2268	c.995G>A	c.(994-996)cGt>cAt	p.R332H	TIAM2_ENST00000360366.4_Missense_Mutation_p.R332H|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000318981.5_Missense_Mutation_p.R332H|TIAM2_ENST00000529824.2_Missense_Mutation_p.R332H|TIAM2_ENST00000456144.1_Missense_Mutation_p.R332H			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	332			R -> H (in dbSNP:rs931312).		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)		CTGAGCAACCGTGTCTCTTTT	0.577													G|||	1178	0.235224	0.0711	0.2464	5008	,	,		19702	0.3026		0.175	False		,,,				2504	0.4417				p.R332H		Atlas-SNP	.											.	TIAM2	161	.	0			c.G995A						PASS	.	G	HIS/ARG	496,3910	230.1+/-244.4	30,436,1737	83.0	79.0	81.0		995	5.0	0.4	6	dbSNP_86	81	1567,7033	293.5+/-301.4	137,1293,2870	yes	missense	TIAM2	NM_012454.3	29	167,1729,4607	AA,AG,GG		18.2209,11.2574,15.8619	probably-damaging	332/1702	155451352	2063,10943	2203	4300	6503	SO:0001583	missense	26230	exon3			GCAACCGTGTCTC		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.995G>A	6.37:g.155451352G>A	ENSP00000437188:p.Arg332His	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	440	0.20146520146520147	41	0.08333333333333333	86	0.23756906077348067	194	0.33916083916083917	119	0.15699208443271767	G	15.18	2.757389	0.49468	0.112574	0.182209	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.08282	3.22;3.11;3.2;3.22;3.24;3.2	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.72118	2.19	0.09310	P	1.0	D	0.89917	1.0	D	0.78314	0.991	T	0.00800	-1.1561	9	0.40728	T	0.16	.	16.8516	0.85995	0.0:0.0:1.0:0.0	rs931312;rs56418104;rs57922078;rs931312	332	Q8IVF5	TIAM2_HUMAN	H	332;578;332;332;332;332;332	ENSP00000437188:R332H;ENSP00000434901:R332H;ENSP00000407746:R332H;ENSP00000327315:R332H;ENSP00000353528:R332H;ENSP00000433348:R332H	ENSP00000327315:R332H	R	+	2	0	TIAM2	155493044	1.000000	0.71417	0.427000	0.26684	0.008000	0.06430	7.136000	0.77285	2.489000	0.83994	0.655000	0.94253	CGT	G|0.815;A|0.185	0.185	strong		0.577	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
FLG	2312	hgsc.bcm.edu	37	1	152276772	152276772	+	Missense_Mutation	SNP	C	C	A	rs72697000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276772C>A	ENST00000368799.1	-	3	10625	c.10590G>T	c.(10588-10590)agG>agT	p.R3530S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3530	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)			TCCTGCTTGTCCTGGGCCCCG	0.577									Ichthyosis				C|||	1455	0.290535	0.0113	0.3919	5008	,	,		18815	0.5853		0.1421	False		,,,				2504	0.4448				p.R3530S		Atlas-SNP	.											.	FLG	900	.	0			c.G10590T						PASS	.	C	SER/ARG	161,4245	108.2+/-146.6	2,157,2044	192.0	199.0	196.0		10590	-3.0	0.0	1	dbSNP_130	196	1264,7336	251.9+/-278.2	121,1022,3157	yes	missense	FLG	NM_002016.1	110	123,1179,5201	AA,AC,CC		14.6977,3.6541,10.9565	probably-damaging	3530/4062	152276772	1425,11581	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTTGTCCTGGGC	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.10590G>T	1.37:g.152276772C>A	ENSP00000357789:p.Arg3530Ser	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	263	147	0.558935	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	587	0.26877289377289376	9	0.018292682926829267	119	0.3287292817679558	347	0.6066433566433567	112	0.14775725593667546	C	10.62	1.400937	0.25291	0.036541	0.146977	ENSG00000143631	ENST00000368799	T	0.04406	3.63	3.63	-2.97	0.05530	.	.	.	.	.	T	0.04770	0.0129	M	0.76574	2.34	0.80722	P	0.0	D	0.71674	0.998	D	0.87578	0.998	T	0.26360	-1.0105	8	0.10377	T	0.69	.	4.3032	0.10933	0.1524:0.4281:0.0:0.4194	.	3530	P20930	FILA_HUMAN	S	3530	ENSP00000357789:R3530S	ENSP00000357789:R3530S	R	-	3	2	FLG	150543396	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.006000	0.00160	-0.437000	0.07243	-0.552000	0.04208	AGG	C|0.842;A|0.158	0.158	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ZZEF1	23140	hgsc.bcm.edu	37	17	4046101	4046101	+	Missense_Mutation	SNP	A	A	G	rs1454121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4046101A>G	ENST00000381638.2	-	1	213	c.89T>C	c.(88-90)gTc>gCc	p.V30A	ZZEF1_ENST00000574474.1_5'UTR|CYB5D2_ENST00000575251.1_5'Flank|CYB5D2_ENST00000573984.1_5'Flank|CYB5D2_ENST00000301391.3_5'Flank	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	30			V -> A (in dbSNP:rs1454121). {ECO:0000269|PubMed:14702039}.				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						CGTGCCCGAGACCGCGGCCCA	0.746													A|||	4028	0.804313	0.4781	0.8617	5008	,	,		11055	1.0		0.8529	False		,,,				2504	0.953				p.V30A		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T89C						PASS	.						2.0	2.0	2.0					17																	4046101		1609	3070	4679	SO:0001583	missense	23140	exon1			CCCGAGACCGCGG	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.89T>C	17.37:g.4046101A>G	ENSP00000371051:p.Val30Ala	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	1773	0.8118131868131868	254	0.516260162601626	308	0.850828729281768	572	1.0	639	0.8430079155672823	A	12.64	1.999923	0.35320	.	.	ENSG00000074755	ENST00000381638	T	0.18810	2.19	4.8	1.17	0.20885	.	0.614467	0.15724	N	0.247743	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	0.20107	-1.0285	9	0.33940	T	0.23	-2.2642	0.9962	0.01467	0.1675:0.1675:0.1581:0.5069	rs1454121	30;30	O43149-3;O43149	.;ZZEF1_HUMAN	A	30	ENSP00000371051:V30A	ENSP00000371051:V30A	V	-	2	0	ZZEF1	3992850	0.343000	0.24818	0.021000	0.16686	0.882000	0.50991	0.278000	0.18753	0.760000	0.33108	-0.527000	0.04329	GTC	A|0.188;G|0.812	0.812	strong		0.746	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
UGGT1	56886	hgsc.bcm.edu	37	2	128939817	128939817	+	Silent	SNP	G	G	A	rs1699	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128939817G>A	ENST00000259253.6	+	37	4244	c.4197G>A	c.(4195-4197)aaG>aaA	p.K1399K	UGGT1_ENST00000375990.3_Silent_p.K1375K	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1399	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						GGTTCTGGAAGTCAGGGTACT	0.438													G|||	2143	0.427915	0.4198	0.3775	5008	,	,		18387	0.3224		0.4105	False		,,,				2504	0.6012				p.K1399K		Atlas-SNP	.											.	UGGT1	126	.	0			c.G4197A						PASS	.	G		1781,2625	525.2+/-371.5	373,1035,795	100.0	102.0	102.0		4197	4.5	1.0	2	dbSNP_36	102	3664,4936	526.4+/-380.9	777,2110,1413	no	coding-synonymous	UGGT1	NM_020120.3		1150,3145,2208	AA,AG,GG		42.6047,40.4222,41.8653		1399/1556	128939817	5445,7561	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon37			CTGGAAGTCAGGG	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.4197G>A	2.37:g.128939817G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			G|0.589;A|0.411	0.411	strong		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
KIF13A	63971	hgsc.bcm.edu	37	6	17834213	17834213	+	Silent	SNP	T	T	C	rs4716190	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17834213T>C	ENST00000259711.6	-	12	1350	c.1245A>G	c.(1243-1245)agA>agG	p.R415R	KIF13A_ENST00000378843.2_Silent_p.R415R|KIF13A_ENST00000378826.2_Silent_p.R415R|KIF13A_ENST00000378814.5_Silent_p.R415R|KIF13A_ENST00000378816.5_Silent_p.R415R	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	415					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)			CTTCTGTTTTTCTCAGCTTCT	0.388													C|||	2349	0.46905	0.3797	0.536	5008	,	,		16523	0.4018		0.5308	False		,,,				2504	0.5481				p.R415R		Atlas-SNP	.											.	KIF13A	276	.	0			c.A1245G						PASS	.	C	,,,	1554,2130		344,866,632	154.0	142.0	145.0		1245,1245,1245,1245	3.8	1.0	6	dbSNP_111	145	4239,3941		1095,2049,946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	1439,2915,1578	CC,CT,TT		48.1785,42.1824,48.8284	,,,	415/1771,415/1758,415/1750,415/1806	17834213	5793,6071	1842	4090	5932	SO:0001819	synonymous_variant	63971	exon12			TGTTTTTCTCAGC	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.1245A>G	6.37:g.17834213T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			T|0.528;C|0.472	0.472	strong		0.388	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:76640781C>T	ENST00000369950.3	-	15	2321	c.2132G>A	c.(2131-2133)cGc>cAc	p.R711H	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TGGTTTGCAGCGACACTCCGC	0.567													C|||	962	0.192093	0.1293	0.2032	5008	,	,		18124	0.254		0.1809	False		,,,				2504	0.2168				p.R711H	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	0			c.G2132A						PASS	.	C	HIS/ARG	553,3853	249.3+/-256.8	36,481,1686	119.0	95.0	103.0		2132	1.2	1.0	6	dbSNP_107	103	1460,7140	278.6+/-293.5	118,1224,2958	yes	missense	IMPG1	NM_001563.2	29	154,1705,4644	TT,TC,CC		16.9767,12.5511,15.4775	probably-damaging	711/798	76640781	2013,10993	2203	4300	6503	SO:0001583	missense	3617	exon15			TTGCAGCGACACT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2132G>A	6.37:g.76640781C>T	ENSP00000358966:p.Arg711His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	442	0.20238095238095238	66	0.13414634146341464	68	0.1878453038674033	165	0.28846153846153844	143	0.18865435356200527	C	13.01	2.108235	0.37242	0.125511	0.169767	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.20463	2.07;2.15	5.45	1.18	0.20946	Epidermal growth factor-like, type 3 (1);	0.353536	0.24280	N	0.039906	T	0.04543	0.0124	L	0.46157	1.445	0.09310	P	0.9999999898373	P	0.52316	0.952	B	0.35770	0.21	T	0.33369	-0.9871	9	0.34782	T	0.22	.	3.7999	0.08754	0.2697:0.437:0.0:0.2933	rs3734313;rs52816738;rs61241500;rs3734313	711	Q17R60	IMPG1_HUMAN	H	711;72	ENSP00000358966:R711H;ENSP00000358968:R72H	ENSP00000358966:R711H	R	-	2	0	IMPG1	76697501	0.112000	0.22096	0.992000	0.48379	0.274000	0.26718	0.372000	0.20467	0.283000	0.22279	0.461000	0.40582	CGC	C|0.826;T|0.174	0.174	strong		0.567	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
ADGB	79747	hgsc.bcm.edu	37	6	146977963	146977963	+	Silent	SNP	A	A	C	rs79354452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	139	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	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	
RHOT2	89941	hgsc.bcm.edu	37	16	722548	722548	+	Silent	SNP	A	A	G	rs1128550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	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	
FAM208B	54906	hgsc.bcm.edu	37	10	5799613	5799613	+	Missense_Mutation	SNP	A	A	G	rs2275774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5799613A>G	ENST00000328090.5	+	17	7488	c.6863A>G	c.(6862-6864)aAg>aGg	p.K2288R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2288			K -> R (in dbSNP:rs2275774).														TCAGATGACAAGATACTAGAA	0.418													A|||	416	0.0830671	0.0212	0.0994	5008	,	,		21518	0.0595		0.1759	False		,,,				2504	0.0838				p.K2288R		Atlas-SNP	.											.	.	.	.	0			c.A6863G						PASS	.	A	ARG/LYS	156,3632		2,152,1740	243.0	230.0	234.0		6863	-3.2	0.0	10	dbSNP_100	234	1587,6647		160,1267,2690	yes	missense	FAM208B	NM_017782.4	26	162,1419,4430	GG,GA,AA		19.2737,4.1183,14.4984	benign	2288/2431	5799613	1743,10279	1894	4117	6011	SO:0001583	missense	54906	exon17			ATGACAAGATACT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.6863A>G	10.37:g.5799613A>G	ENSP00000328426:p.Lys2288Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	226	0.10347985347985347	14	0.028455284552845527	42	0.11602209944751381	35	0.06118881118881119	135	0.17810026385224276	A	7.930	0.740551	0.15642	0.041183	0.192737	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.42900	0.96	5.59	-3.17	0.05202	.	0.622148	0.15979	N	0.235401	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B	0.19200	0.034	B	0.14023	0.01	T	0.15983	-1.0418	9	0.27082	T	0.32	.	1.7479	0.02966	0.4115:0.2225:0.2581:0.1079	rs2275774;rs56581575;rs58161058;rs2275774	2288	Q5VWN6	F208B_HUMAN	R	2288;1483	ENSP00000328426:K2288R	ENSP00000328426:K2288R	K	+	2	0	C10orf18	5839619	0.000000	0.05858	0.005000	0.12908	0.046000	0.14306	-0.019000	0.12546	-0.495000	0.06659	0.533000	0.62120	AAG	A|0.887;G|0.113	0.113	strong		0.418	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
SLC22A14	9389	hgsc.bcm.edu	37	3	38357067	38357067	+	Missense_Mutation	SNP	T	T	C	rs34256819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38357067T>C	ENST00000273173.4	+	8	1488	c.1397T>C	c.(1396-1398)cTc>cCc	p.L466P	SLC22A14_ENST00000448498.1_Missense_Mutation_p.L466P	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	466			L -> P (in dbSNP:rs34256819).		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)		GGCCTCAGACTCAAGTGGCCA	0.587													T|||	4	0.000798722	0.0015	0.0	5008	,	,		19422	0.0		0.002	False		,,,				2504	0.0				p.L466P		Atlas-SNP	.											.	SLC22A14	64	.	0			c.T1397C						PASS	.	T	PRO/LEU	2,4404	4.2+/-10.8	0,2,2201	96.0	84.0	88.0		1397	3.7	0.1	3	dbSNP_126	88	32,8568	22.8+/-68.1	0,32,4268	yes	missense	SLC22A14	NM_004803.3	98	0,34,6469	CC,CT,TT		0.3721,0.0454,0.2614	probably-damaging	466/595	38357067	34,12972	2203	4300	6503	SO:0001583	missense	9389	exon8			TCAGACTCAAGTG	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.1397T>C	3.37:g.38357067T>C	ENSP00000273173:p.Leu466Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	106	31	0.292453	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	14.48	2.549489	0.45383	4.54E-4	0.003721	ENSG00000144671	ENST00000448498;ENST00000273173	T;T	0.66815	-0.23;-0.23	3.66	3.66	0.41972	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.270402	0.15269	U	0.271366	T	0.56426	0.1984	N	0.02011	-0.69	0.20638	N	0.999874	D	0.76494	0.999	D	0.69307	0.963	T	0.50276	-0.8847	10	0.87932	D	0	.	8.9423	0.35738	0.0:0.0:0.0:1.0	rs34256819	466	Q9Y267	S22AE_HUMAN	P	466	ENSP00000396283:L466P;ENSP00000273173:L466P	ENSP00000273173:L466P	L	+	2	0	SLC22A14	38332071	0.184000	0.23200	0.067000	0.19924	0.003000	0.03518	0.714000	0.25808	1.873000	0.54277	0.533000	0.62120	CTC	T|0.997;C|0.003	0.003	strong		0.587	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
PTPN5	84867	hgsc.bcm.edu	37	11	18751041	18751041	+	Silent	SNP	C	C	T	rs1550870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18751041C>T	ENST00000358540.2	-	14	1993	c.1563G>A	c.(1561-1563)gtG>gtA	p.V521V	RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396168.1_Silent_p.V497V|PTPN5_ENST00000396170.1_Silent_p.V489V|PTPN5_ENST00000396171.4_Silent_p.V521V|PTPN5_ENST00000396166.3_Silent_p.V127V|PTPN5_ENST00000396167.2_Silent_p.V489V|PTPN5_ENST00000477854.1_Silent_p.V325V	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	521	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GGATGTCCACCACACCCTCCT	0.667													C|||	1590	0.317492	0.3185	0.3055	5008	,	,		15381	0.2619		0.4423	False		,,,				2504	0.2536				p.V521V		Atlas-SNP	.											.	PTPN5	163	.	0			c.G1563A						PASS	.	C	,,	1410,2988	454.2+/-350.6	239,932,1028	47.0	46.0	46.0		1467,1563,1563	3.3	1.0	11	dbSNP_88	46	3945,4641	539.1+/-383.5	925,2095,1273	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	,,	1164,3027,2301	TT,TC,CC		45.9469,32.06,41.2431	,,	489/534,521/566,521/566	18751041	5355,7629	2199	4293	6492	SO:0001819	synonymous_variant	84867	exon14			GTCCACCACACCC	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.1563G>A	11.37:g.18751041C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Silent	SNP	ENST00000358540.2	37	CCDS7845.1																																																																																			C|0.633;T|0.367	0.367	strong		0.667	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
SKOR1	390598	hgsc.bcm.edu	37	15	68124665	68124665	+	Silent	SNP	C	C	A	rs72751453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:68124665C>A	ENST00000380035.2	+	6	2699	c.2641C>A	c.(2641-2643)Cgg>Agg	p.R881R	SKOR1_ENST00000554054.1_Silent_p.R853R|RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000341418.5_Silent_p.R784R|RP11-34F13.2_ENST00000502156.1_lincRNA|SKOR1_ENST00000389002.1_Silent_p.R837R|SKOR1_ENST00000554240.1_Silent_p.R842R			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	881					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GAAGCTGGAACGGGAATTTCA	0.552											OREG0023215	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	874	0.174521	0.1157	0.2291	5008	,	,		14590	0.003		0.3986	False		,,,				2504	0.1616				p.R784R		Atlas-SNP	.											.	SKOR1	144	.	0			c.C2350A						PASS	.	C		660,3740	280.5+/-275.4	51,558,1591	122.0	120.0	121.0		2509	4.4	1.0	15	dbSNP_130	121	3757,4839	534.5+/-382.6	828,2101,1369	no	coding-synonymous	SKOR1	NM_001031807.1		879,2659,2960	AA,AC,CC		43.7064,15.0,33.9874		837/922	68124665	4417,8579	2200	4298	6498	SO:0001819	synonymous_variant	390598	exon12			CTGGAACGGGAAT		CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"""SKI transcriptional corepressors"""	21326	protein-coding gene	gene with protein product	"""transcriptional corepressor CORL1"", ""functional smad suppressing element 15"", ""corepressor for LBX1"""	611273	"""Lbxcor1 homolog (mouse)"""	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2641C>A	15.37:g.68124665C>A		Somatic	70	0	0	1104	WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001258024	A6NIP4|A6NJY0|Q2VWA5	Silent	SNP	ENST00000380035.2	37																																																																																				C|0.702;A|0.298	0.298	strong		0.552	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807	
HK1	3098	hgsc.bcm.edu	37	10	71142492	71142492	+	Silent	SNP	C	C	T	rs140498607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:71142492C>T	ENST00000359426.6	+	10	1619	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	HK1_ENST00000404387.2_Silent_p.N509N|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Silent_p.N493N|HK1_ENST00000448642.2_Silent_p.N540N|HK1_ENST00000298649.3_Silent_p.N504N	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	505	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AGACGCACAACAATGCCGTGG	0.622													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19064	0.001		0.008	False		,,,				2504	0.001				p.N509N		Atlas-SNP	.											.	HK1	170	.	0			c.C1527T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	103.0	77.0	86.0		1515,1512,1527,1527,1479	-9.8	0.0	10	dbSNP_134	86	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	0,56,6447	TT,TC,CC		0.6279,0.0454,0.4306	,,,,	505/918,504/917,509/922,509/922,493/906	71142492	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon13			GCACAACAATGCC	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1515C>T	10.37:g.71142492C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21790040	21790040	+	Missense_Mutation	SNP	G	G	T	rs10151259	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:21790040G>T	ENST00000400017.2	+	13	1639	c.1639G>T	c.(1639-1641)Gct>Tct	p.A547S	RPGRIP1_ENST00000307974.4_5'Flank|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.A189S|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.A520S|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.A547S|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.A520S	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	547			A -> S (in CORD13; dbSNP:rs10151259). {ECO:0000269|PubMed:10958648, ECO:0000269|PubMed:12920076}.		eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GATGACAAAAGCTGACAATGA	0.393													G|||	838	0.167332	0.2315	0.1412	5008	,	,		20902	0.004		0.2366	False		,,,				2504	0.1963				p.A547S		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1639T	GRCh37	CM032029	RPGRIP1	M	rs10151259	PASS	.	G	SER/ALA	775,3007		86,603,1202	80.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1639	3.0	1.0	14	dbSNP_119	77	2017,6207		230,1557,2325	yes	missense	RPGRIP1	NM_020366.3	99	316,2160,3527	TT,TG,GG		24.5258,20.4918,23.255	probably-damaging	547/1287	21790040	2792,9214	1891	4112	6003	SO:0001583	missense	57096	exon13			ACAAAAGCTGACA	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1639G>T	14.37:g.21790040G>T	ENSP00000382895:p.Ala547Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	352	0.16117216117216118	115	0.23373983739837398	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	13.80	2.344142	0.41498	0.204918	0.245258	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000554303	T;T;T;T;T;T;T	0.79554	-0.1;-0.86;-0.9;-0.9;-0.47;-1.22;-1.28	4.86	3.04	0.35103	.	0.320649	0.34223	N	0.004147	T	0.00073	0.0002	L	0.52266	1.64	0.09310	P	0.99999999479642	D;D;D;D	0.89917	1.0;0.97;1.0;1.0	D;P;D;D	0.91635	0.999;0.747;0.999;0.998	T	0.14117	-1.0484	9	0.29301	T	0.29	-9.0074	5.6994	0.17873	0.1672:0.0:0.6767:0.1561	rs61722408	22;189;163;547	G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7	.;.;.;RPGR1_HUMAN	S	520;520;547;547;189;22;20	ENSP00000450445:A520S;ENSP00000451219:A520S;ENSP00000382895:A547S;ENSP00000206660:A547S;ENSP00000372391:A189S;ENSP00000451262:A22S;ENSP00000450426:A20S	ENSP00000206660:A547S	A	+	1	0	RPGRIP1	20859880	0.990000	0.36364	0.991000	0.47740	0.402000	0.30811	0.774000	0.26675	0.777000	0.33496	-0.384000	0.06662	GCT	A|0.059;C|0.298	.	strong		0.393	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
IGSF3	3321	hgsc.bcm.edu	37	1	117142707	117142707	+	Missense_Mutation	SNP	G	G	A	rs201515387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:117142707G>A	ENST00000369486.3	-	7	2650	c.1885C>T	c.(1885-1887)Cgc>Tgc	p.R629C	IGSF3_ENST00000318837.6_Missense_Mutation_p.R649C|IGSF3_ENST00000369483.1_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	62	0	0		WXS	Illumina HiSeq	Phase_I	72	4	0.0555556	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	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60241732	60241732	+	Silent	SNP	C	C	T	rs3744926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:60241732C>T	ENST00000269499.5	+	13	2836	c.2418C>T	c.(2416-2418)ccC>ccT	p.P806P	ZCCHC2_ENST00000586834.1_Silent_p.P485P	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	806						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						GTAGTACTCCCGCTTTGCATC	0.502													C|||	2415	0.482228	0.3056	0.4481	5008	,	,		20720	0.7817		0.33	False		,,,				2504	0.593				p.P806P		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.C2418T						PASS	.	C		1271,2821		226,819,1001	108.0	106.0	107.0		2418	-11.0	0.0	18	dbSNP_107	107	3184,5234		607,1970,1632	no	coding-synonymous	ZCCHC2	NM_017742.4		833,2789,2633	TT,TC,CC		37.8237,31.0606,35.6115		806/1179	60241732	4455,8055	2046	4209	6255	SO:0001819	synonymous_variant	54877	exon13			TACTCCCGCTTTG	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"""Zinc fingers, CCHC domain containing"""	22916	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 49"""	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.2418C>T	18.37:g.60241732C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			C|0.533;T|0.467	0.467	strong		0.502	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
SETDB2	83852	hgsc.bcm.edu	37	13	50057633	50057633	+	Silent	SNP	A	A	G	rs11619265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50057633A>G	ENST00000317257.8	+	11	2277	c.1452A>G	c.(1450-1452)caA>caG	p.Q484Q	SETDB2_ENST00000354234.4_Silent_p.Q472Q|SETDB2_ENST00000258672.5_Silent_p.Q472Q	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	484	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		CAAGAATTCAATATCATTCAG	0.299													A|||	2361	0.471446	0.4992	0.5	5008	,	,		12518	0.4762		0.5239	False		,,,				2504	0.3548				p.Q484Q		Atlas-SNP	.											.	SETDB2	48	.	0			c.A1452G						PASS	.	A	,	2289,2105		613,1063,521	24.0	25.0	25.0		1416,1452	-9.7	0.0	13	dbSNP_120	25	4657,3897		1303,2051,923	no	coding-synonymous,coding-synonymous	SETDB2	NM_001160308.1,NM_031915.2	,	1916,3114,1444	GG,GA,AA		45.5576,47.9062,46.3546	,	472/708,484/720	50057633	6946,6002	2197	4277	6474	SO:0001819	synonymous_variant	83852	exon11			AATTCAATATCAT	AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"""Chromatin-modifying enzymes / K-methyltransferases"""	20263	protein-coding gene	gene with protein product		607865	"""chromosome 13 open reading frame 4"""	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.1452A>G	13.37:g.50057633A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_031915	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Silent	SNP	ENST00000317257.8	37	CCDS9417.1																																																																																			A|0.477;G|0.523	0.523	strong		0.299	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329407	59329407	+	Splice_Site	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:59329407A>T	ENST00000399598.2	+	2	206		c.e2-1		UBXN2B_ENST00000522978.1_Splice_Site	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B							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						GTTATTATGTAGTTGGCCTTG	0.378																																					.		Atlas-SNP	.											.	UBXN2B	36	.	0			c.85-2A>T						PASS	.						87.0	79.0	81.0					8																	59329407		1877	4089	5966	SO:0001630	splice_region_variant	137886	exon2			TTATGTAGTTGGC	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.85-1A>T	8.37:g.59329407A>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_001077619	B3KWZ3	Splice_Site	SNP	ENST00000399598.2	37	CCDS43741.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063813	0.55432	.	.	ENSG00000215114	ENST00000399598	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7027	0.57043	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBXN2B	59491961	1.000000	0.71417	0.920000	0.36463	0.789000	0.44602	4.736000	0.62059	2.257000	0.74773	0.460000	0.39030	.	.	.	none		0.378	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	Intron
ZNF615	284370	hgsc.bcm.edu	37	19	52497250	52497250	+	Missense_Mutation	SNP	G	G	A	rs1978717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52497250G>A	ENST00000602063.1	-	6	1428	c.1079C>T	c.(1078-1080)aCt>aTt	p.T360I	ZNF615_ENST00000391795.3_Missense_Mutation_p.T365I|ZNF615_ENST00000376716.5_Missense_Mutation_p.T360I|ZNF615_ENST00000594083.1_Missense_Mutation_p.T371I|ZNF615_ENST00000598071.1_Missense_Mutation_p.T371I			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	360			T -> I (in dbSNP:rs1978717). {ECO:0000269|PubMed:14702039, 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)	p.T371I(1)|p.T360I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		ATGATGTGCAGTAAGACGCCT	0.388													A|||	2384	0.476038	0.6074	0.3977	5008	,	,		22199	0.3929		0.3121	False		,,,				2504	0.6084				p.T371I		Atlas-SNP	.											ZNF615,NS,carcinoma,0,2	ZNF615	111	2	2	Substitution - Missense(2)	stomach(2)	c.C1112T						PASS	.	A	ILE/THR,ILE/THR	2554,1852	534.5+/-374.0	718,1118,367	99.0	103.0	102.0		1112,1079	-3.4	0.0	19	dbSNP_92	102	2388,6212	700.1+/-405.1	323,1742,2235	yes	missense,missense	ZNF615	NM_001199324.1,NM_198480.3	89,89	1041,2860,2602	AA,AG,GG		27.7674,42.0336,37.9978	benign,benign	371/743,360/732	52497250	4942,8064	2203	4300	6503	SO:0001583	missense	284370	exon7			TGTGCAGTAAGAC	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1079C>T	19.37:g.52497250G>A	ENSP00000473089:p.Thr360Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	893	0.4088827838827839	297	0.6036585365853658	145	0.4005524861878453	204	0.35664335664335667	247	0.3258575197889182	A	0.001	-4.047464	0.00002	0.579664	0.277674	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.07908	3.15;3.15	3.08	-3.42	0.04825	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12422	0.21	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	0.38436	-0.9661	8	0.02654	T	1	.	9.9817	0.41817	0.2834:0.0:0.6046:0.112	rs1978717;rs52792656;rs56500541;rs59971178;rs1978717	367;371;360	Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;ZN615_HUMAN	I	360;370;365;370	ENSP00000365906:T360I;ENSP00000375672:T365I	ENSP00000347019:T370I	T	-	2	0	ZNF615	57189062	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.987000	0.03743	-2.010000	0.00953	-2.772000	0.00119	ACT	G|0.596;A|0.404	0.404	strong		0.388	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204425028	204425028	+	Silent	SNP	G	G	A	rs3765156	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204425028G>A	ENST00000367187.3	-	12	2455	c.1899C>T	c.(1897-1899)ttC>ttT	p.F633F	PIK3C2B_ENST00000496872.1_5'UTR|PIK3C2B_ENST00000424712.2_Silent_p.F633F	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	633					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|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)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CATAGACAGTGAAGGCCAGGG	0.617													G|||	1018	0.203275	0.0582	0.0865	5008	,	,		18514	0.3998		0.2078	False		,,,				2504	0.2751				p.F633F		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C1899T						PASS	.	G		314,4092	169.1+/-199.8	10,294,1899	65.0	63.0	63.0		1899	2.3	1.0	1	dbSNP_107	63	1493,7107	283.7+/-296.3	114,1265,2921	no	coding-synonymous	PIK3C2B	NM_002646.3		124,1559,4820	AA,AG,GG		17.3605,7.1266,13.8936		633/1635	204425028	1807,11199	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon12			GACAGTGAAGGCC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1899C>T	1.37:g.204425028G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.839;A|0.161	0.161	strong		0.617	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
GLI2	2736	hgsc.bcm.edu	37	2	121747429	121747429	+	Silent	SNP	A	A	G	rs10167980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:121747429A>G	ENST00000452319.1	+	14	3999	c.3939A>G	c.(3937-3939)ccA>ccG	p.P1313P	GLI2_ENST00000361492.4_Silent_p.P1313P|GLI2_ENST00000314490.11_Intron					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)				CTGGAGTGCCACCACCTCACC	0.652													A|||	2566	0.51238	0.3593	0.5865	5008	,	,		17670	0.4762		0.7286	False		,,,				2504	0.4816				p.P1313P		Atlas-SNP	.											.	GLI2	187	.	0			c.A3939G						PASS	.	A		1802,2600		376,1050,775	22.0	22.0	22.0		3939	-2.4	0.0	2	dbSNP_119	22	6311,2287		2324,1663,312	no	coding-synonymous	GLI2	NM_005270.4		2700,2713,1087	GG,GA,AA		26.5992,40.9359,37.5923		1313/1587	121747429	8113,4887	2201	4299	6500	SO:0001819	synonymous_variant	2736	exon13			AGTGCCACCACCT		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.3939A>G	2.37:g.121747429A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			A|0.400;G|0.600	0.600	strong		0.652	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
SELP	6403	hgsc.bcm.edu	37	1	169566308	169566308	+	Silent	SNP	G	G	A	rs6132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169566308G>A	ENST00000263686.6	-	11	1849	c.1812C>T	c.(1810-1812)aaC>aaT	p.N604N	SELP_ENST00000367794.2_Silent_p.N542N|SELP_ENST00000367788.2_Silent_p.N542N|SELP_ENST00000367793.2_Silent_p.N542N|SELP_ENST00000367786.2_Silent_p.N542N|SELP_ENST00000367791.2_Intron|SELP_ENST00000367792.2_Intron|SELP_ENST00000458599.2_Intron	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	604	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	GCTTAAAGCCGTTGTCACAAG	0.488													c|||	1097	0.21905	0.6589	0.1268	5008	,	,		16240	0.002		0.1193	False		,,,				2504	0.0164				p.N604N		Atlas-SNP	.											.	SELP	132	.	0			c.C1812T						PASS	.	T		2421,1985		680,1061,462	70.0	74.0	73.0		1812	-1.1	0.0	1	dbSNP_52	73	1005,7595		45,915,3340	no	coding-synonymous	SELP	NM_003005.3		725,1976,3802	AA,AG,GG		11.686,45.0522,26.3417		604/831	169566308	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	6403	exon11			AAAGCCGTTGTCA	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.1812C>T	1.37:g.169566308G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	173	42	0.242775	NM_003005	Q5R344|Q8IVD1	Silent	SNP	ENST00000263686.6	37	CCDS1282.1																																																																																			G|0.764;A|0.236	0.236	strong		0.488	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
SLC38A10	124565	hgsc.bcm.edu	37	17	79220224	79220224	+	Missense_Mutation	SNP	G	G	C	rs2725405	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79220224G>C	ENST00000374759.3	-	16	2875	c.2492C>G	c.(2491-2493)gCc>gGc	p.A831G		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	831			A -> G (in dbSNP:rs2725405). {ECO:0000269|PubMed:15498874}.		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)			TCTCAGCTTGGCCTGGGCTGC	0.701													G|||	2146	0.428514	0.025	0.4784	5008	,	,		14012	0.7004		0.4374	False		,,,				2504	0.6493				p.A831G		Atlas-SNP	.											.	SLC38A10	133	.	0			c.C2492G						PASS	.	G	GLY/ALA	327,3373		26,275,1549	11.0	13.0	13.0		2492	0.7	0.0	17	dbSNP_100	13	3573,4591		819,1935,1328	yes	missense	SLC38A10	NM_001037984.1	60	845,2210,2877	CC,CG,GG		43.7653,8.8378,32.8726	benign	831/1120	79220224	3900,7964	1850	4082	5932	SO:0001583	missense	124565	exon16			AGCTTGGCCTGGG	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.2492C>G	17.37:g.79220224G>C	ENSP00000363891:p.Ala831Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	37	CCDS42397.1	946	0.43315018315018317	25	0.0508130081300813	175	0.48342541436464087	410	0.7167832167832168	336	0.44327176781002636	G	12.76	2.033367	0.35893	0.088378	0.437653	ENSG00000157637	ENST00000374759;ENST00000540966	T;T	0.53640	2.93;0.61	3.98	0.68	0.17980	.	4.052290	0.01250	N	0.008853	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	P	0.39282	0.666	B	0.33339	0.162	T	0.45411	-0.9263	9	0.37606	T	0.19	-0.9264	5.2532	0.15532	0.1956:0.1672:0.6372:0.0	rs2725405	831	Q9HBR0	S38AA_HUMAN	G	831;217	ENSP00000363891:A831G;ENSP00000437601:A217G	ENSP00000363891:A831G	A	-	2	0	SLC38A10	76834819	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.368000	0.20399	0.336000	0.23639	0.467000	0.42956	GCC	G|0.561;C|0.439	0.439	strong		0.701	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
PTX4	390667	hgsc.bcm.edu	37	16	1536323	1536323	+	Silent	SNP	A	A	G	rs2667671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1536323A>G	ENST00000447419.2	-	3	1079	c.1054T>C	c.(1054-1056)Ttg>Ctg	p.L352L	PTX4_ENST00000293922.1_Silent_p.L347L|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	352	Pentaxin.					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						AGCAGCTGCAAGGGCAGCTCC	0.647													A|||	1553	0.310104	0.7057	0.1916	5008	,	,		16320	0.0665		0.2306	False		,,,				2504	0.1922				p.L347L		Atlas-SNP	.											PTX4,NS,carcinoma,0,1	PTX4	46	1	0			c.T1039C						PASS	.	A		2725,1673		852,1021,326	31.0	36.0	35.0		1039	2.5	0.9	16	dbSNP_100	35	1795,6805		191,1413,2696	no	coding-synonymous	PTX4	NM_001013658.1		1043,2434,3022	GG,GA,AA		20.8721,38.04,34.7746		347/474	1536323	4520,8478	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GCTGCAAGGGCAG		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.1054T>C	16.37:g.1536323A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				A|0.662;G|0.338	0.338	strong		0.647	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
NEO1	4756	hgsc.bcm.edu	37	15	73562532	73562532	+	Silent	SNP	C	C	T	rs2680348	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:73562532C>T	ENST00000339362.5	+	18	3123	c.2676C>T	c.(2674-2676)acC>acT	p.T892T	NEO1_ENST00000261908.6_Silent_p.T892T|NEO1_ENST00000558964.1_Silent_p.T892T|NEO1_ENST00000560262.1_Silent_p.T892T			Q92859	NEO1_HUMAN	neogenin 1	892	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						GATACTACACCGTCCGATGGA	0.453													C|||	383	0.0764776	0.1944	0.0504	5008	,	,		17833	0.0		0.0815	False		,,,				2504	0.0092				p.T892T		Atlas-SNP	.											.	NEO1	102	.	0			c.C2676T						PASS	.	C	,,	733,3663	303.0+/-287.7	64,605,1529	98.0	92.0	94.0		2676,2676,2676	-10.3	0.7	15	dbSNP_100	94	546,8048	150.6+/-205.5	19,508,3770	no	coding-synonymous,coding-synonymous,coding-synonymous	NEO1	NM_001172623.1,NM_001172624.1,NM_002499.3	,,	83,1113,5299	TT,TC,CC		6.3533,16.6742,9.846	,,	892/1409,892/1451,892/1462	73562532	1279,11711	2198	4297	6495	SO:0001819	synonymous_variant	4756	exon17			CTACACCGTCCGA	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2676C>T	15.37:g.73562532C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Silent	SNP	ENST00000339362.5	37	CCDS10247.1																																																																																			C|0.911;T|0.089	0.089	strong		0.453	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499	
KMT2C	58508	hgsc.bcm.edu	37	7	151962168	151962168	+	Missense_Mutation	SNP	C	C	A	rs138908625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151962168C>A	ENST00000262189.6	-	8	1357	c.1139G>T	c.(1138-1140)cGt>cTt	p.R380L	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380					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)	p.R380L(4)									CCAACCTGCACGTTTTAATGG	0.443																																					p.R380L		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,0,6	MLL3	1564	6	4	Substitution - Missense(4)	skin(4)	c.G1139T						scavenged	.	C	LEU/ARG	29,4377	25.3+/-52.1	0,29,2174	410.0	369.0	383.0		1139	4.7	1.0	7	dbSNP_134	383	15,8585	3.7+/-12.6	0,15,4285	no	missense	MLL3	NM_170606.2	102	0,44,6459	AA,AC,CC		0.1744,0.6582,0.3383	probably-damaging	380/4912	151962168	44,12962	2203	4300	6503	SO:0001583	missense	58508	exon8			CCTGCACGTTTTA	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.1139G>T	7.37:g.151962168C>A	ENSP00000262189:p.Arg380Leu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	279	38	0.136201	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.688003	0.48097	0.006582	0.001744	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98876	-5.2;-5.2	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38548	U	0.001645	D	0.98560	0.9519	M	0.74881	2.28	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	D	0.96263	0.9192	10	0.52906	T	0.07	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	380	Q8NEZ4	MLL3_HUMAN	L	380	ENSP00000262189:R380L;ENSP00000347325:R380L	ENSP00000262189:R380L	R	-	2	0	MLL3	151593101	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	6.039000	0.70972	2.271000	0.75665	0.557000	0.71058	CGT	C|0.500;A|0.500	0.500	weak		0.443	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
CACNA2D3	55799	hgsc.bcm.edu	37	3	54930794	54930794	+	Silent	SNP	C	C	T	rs17054524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:54930794C>T	ENST00000474759.1	+	26	2313	c.2265C>T	c.(2263-2265)ggC>ggT	p.G755G	CACNA2D3_ENST00000490478.1_Silent_p.G661G|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000415676.2_Silent_p.G755G|CACNA2D3_ENST00000288197.5_Silent_p.G755G	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	755						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)	TGAAAGCTGGCGACAAGGAGA	0.512													C|||	590	0.117812	0.1293	0.111	5008	,	,		19156	0.0536		0.1272	False		,,,				2504	0.1636				p.G755G		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.C2265T						PASS	.	C		496,3476		26,444,1516	132.0	133.0	132.0		2265	0.6	1.0	3	dbSNP_123	132	1146,7166		72,1002,3082	no	coding-synonymous	CACNA2D3	NM_018398.2		98,1446,4598	TT,TC,CC		13.7873,12.4874,13.367		755/1092	54930794	1642,10642	1986	4156	6142	SO:0001819	synonymous_variant	55799	exon26			AGCTGGCGACAAG	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.2265C>T	3.37:g.54930794C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	126	34	0.269841	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																			C|0.885;T|0.115	0.115	strong		0.512	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
KRT40	125115	hgsc.bcm.edu	37	17	39140417	39140417	+	Missense_Mutation	SNP	T	T	C	rs1510069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39140417T>C	ENST00000398486.2	-	3	269	c.109A>G	c.(109-111)Acc>Gcc	p.T37A	KRT40_ENST00000377755.4_Missense_Mutation_p.T37A	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	37	Head.		T -> A (in dbSNP:rs1510069).			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)				GTAGCACAGGTACCGGGGAGA	0.572													C|||	1808	0.361022	0.6861	0.2378	5008	,	,		19875	0.1716		0.2684	False		,,,				2504	0.2996				p.T37A		Atlas-SNP	.											.	KRT40	27	.	0			c.A109G						PASS	.	C	ALA/THR	2457,1719		745,967,376	51.0	58.0	56.0		109	-7.4	0.0	17	dbSNP_88	56	2313,6123		315,1683,2220	yes	missense	KRT40	NM_182497.3	58	1060,2650,2596	CC,CT,TT		27.4182,41.1638,37.8211	benign	37/432	39140417	4770,7842	2088	4218	6306	SO:0001583	missense	125115	exon3			CACAGGTACCGGG	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.109A>G	17.37:g.39140417T>C	ENSP00000381500:p.Thr37Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	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	3.450	-0.112292	0.06881	0.588362	0.274182	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.81739	-1.53;-1.53	5.13	-7.38	0.01407	.	0.769868	0.10675	N	0.647011	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24476	-1.0159	9	0.09590	T	0.72	.	11.0326	0.47783	0.0888:0.2759:0.0:0.6353	rs1510069;rs17647026;rs52806666	37	Q6A162	K1C40_HUMAN	A	37	ENSP00000366984:T37A;ENSP00000381500:T37A	ENSP00000366984:T37A	T	-	1	0	KRT40	36393943	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.113000	0.01331	-1.696000	0.01421	-0.983000	0.02560	ACC	C|0.339;N|0.005	0.339	strong		0.572	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
PRKRA	8575	hgsc.bcm.edu	37	2	179315757	179315757	+	Start_Codon_SNP	SNP	T	T	G	rs9406386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179315757T>G	ENST00000325748.4	-	1	201	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	PRKRA_ENST00000432031.2_5'Flank|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000470200.1_Intron|DFNB59_ENST00000375129.4_5'Flank|PRKRA_ENST00000438687.3_5'UTR|PRKRA_ENST00000487082.1_5'Flank	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	1	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CTCTGGGACATGGCGAGAAGG	0.746																																					p.M1L	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											.	PRKRA	56	.	0			c.A1C						PASS	.						6.0	9.0	8.0					2																	179315757		1711	3612	5323	SO:0001582	initiator_codon_variant	8575	exon1			GGGACATGGCGAG	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.1A>C	2.37:g.179315757T>G	ENSP00000318176:p.Met1Leu	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	37	CCDS2279.1	354	0.1620879120879121	36	0.07317073170731707	85	0.23480662983425415	70	0.12237762237762238	163	0.21503957783641162	T	17.06	3.292620	0.59976	.	.	ENSG00000180228	ENST00000325748	T	0.70164	-0.46	4.45	3.29	0.37713	.	0.824018	0.10788	N	0.634052	T	0.00039	0.0001	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04635	-1.0937	9	0.87932	D	0	.	6.5676	0.22521	0.0:0.1104:0.0:0.8896	rs9406386	1	O75569	PRKRA_HUMAN	L	1	ENSP00000318176:M1L	ENSP00000318176:M1L	M	-	1	0	PRKRA	179024003	0.994000	0.37717	0.921000	0.36526	0.909000	0.53808	1.278000	0.33179	0.853000	0.35312	0.338000	0.21704	ATG	T|0.825;G|0.175	0.175	strong		0.746	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Missense_Mutation
COL15A1	1306	hgsc.bcm.edu	37	9	101748234	101748234	+	Missense_Mutation	SNP	G	G	A	rs2075662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:101748234G>A	ENST00000375001.3	+	3	911	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	163	Laminin G-like.		R -> H (in dbSNP:rs2075662).		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)				AGGTGGAACCGCTTCGCCATG	0.607													G|||	1226	0.244808	0.3374	0.2637	5008	,	,		18975	0.1974		0.1551	False		,,,				2504	0.2474				p.R163H		Atlas-SNP	.											.	COL15A1	211	.	0			c.G488A						PASS	.	G	HIS/ARG	1389,3017	458.6+/-352.0	217,955,1031	104.0	98.0	100.0		488	1.2	1.0	9	dbSNP_96	100	1339,7261	262.4+/-284.4	100,1139,3061	yes	missense	COL15A1	NM_001855.3	29	317,2094,4092	AA,AG,GG		15.5698,31.5252,20.9749	benign	163/1389	101748234	2728,10278	2203	4300	6503	SO:0001583	missense	1306	exon3			GGAACCGCTTCGC	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.488G>A	9.37:g.101748234G>A	ENSP00000364140:p.Arg163His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	506	0.2316849816849817	163	0.3313008130081301	89	0.24585635359116023	125	0.21853146853146854	129	0.17018469656992086	G	10.30	1.312663	0.23908	0.315252	0.155698	ENSG00000204291	ENST00000375001;ENST00000536083	T	0.61742	0.08	5.25	1.22	0.21188	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.299857	0.37178	N	0.002213	T	0.00012	0.0000	L	0.47716	1.5	0.28555	P	0.9114195	B;B	0.24258	0.011;0.1	B;B	0.25291	0.016;0.059	T	0.28170	-1.0052	9	0.32370	T	0.25	-1.3674	8.0382	0.30506	0.3651:0.0:0.6349:0.0	rs2075662;rs2075662	163;133	P39059;B3KTP7	COFA1_HUMAN;.	H	163;133	ENSP00000364140:R163H	ENSP00000364140:R163H	R	+	2	0	COL15A1	100788055	0.286000	0.24305	0.970000	0.41538	0.432000	0.31715	2.443000	0.44881	0.020000	0.15106	0.650000	0.86243	CGC	G|0.772;A|0.227	0.227	strong		0.607	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
HIGD1C	613227	hgsc.bcm.edu	37	12	51354803	51354803	+	Silent	SNP	C	C	T	rs12306808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:51354803C>T	ENST00000398455.3	+	2	224	c.147C>T	c.(145-147)taC>taT	p.Y49Y		NM_001109619.1	NP_001103089.1	A8MV81	HIG1C_HUMAN	HIG1 hypoxia inducible domain family, member 1C	49	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.					integral component of membrane (GO:0016021)				lung(1)	1						AGCTAAAGTACAGAAGAGATC	0.418													C|||	1318	0.263179	0.1793	0.1585	5008	,	,		19096	0.494		0.163	False		,,,				2504	0.316				p.Y49Y		Atlas-SNP	.											.	HIGD1C	4	.	0			c.C147T						PASS	.	C		621,3197		54,513,1342	94.0	94.0	94.0		147	3.6	1.0	12	dbSNP_120	94	1276,6968		105,1066,2951	no	coding-synonymous	HIGD1C	NM_001109619.1		159,1579,4293	TT,TC,CC		15.4779,16.2651,15.7271		49/98	51354803	1897,10165	1909	4122	6031	SO:0001819	synonymous_variant	613227	exon2			AAAGTACAGAAGA	DQ029494	CCDS44882.1	12q13.12	2011-09-16	2009-03-17		ENSG00000214511	ENSG00000214511			28044	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1C"""				Standard	NM_001109619		Approved	Gm921	uc010smw.2	A8MV81	OTTHUMG00000169488	ENST00000398455.3:c.147C>T	12.37:g.51354803C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_001109619		Silent	SNP	ENST00000398455.3	37	CCDS44882.1																																																																																			C|0.758;T|0.242	0.242	strong		0.418	HIGD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404340.2	NM_001109619	
ERCC1	2067	hgsc.bcm.edu	37	19	45923598	45923598	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45923598A>G	ENST00000300853.3	-	4	1000	c.409T>C	c.(409-411)Tgt>Cgt	p.C137R	ERCC1_ENST00000013807.5_Missense_Mutation_p.C137R|ERCC1_ENST00000340192.7_Missense_Mutation_p.C137R|ERCC1_ENST00000423698.2_Missense_Mutation_p.C65R|ERCC1_ENST00000589165.1_Missense_Mutation_p.C137R|ERCC1_ENST00000591636.1_Missense_Mutation_p.C137R	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	137					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		AACAGGGCACAGGTGCTCTGG	0.617								Nucleotide excision repair (NER)																													p.C137R		Atlas-SNP	.											.	ERCC1	46	.	0			c.T409C						PASS	.						87.0	68.0	74.0					19																	45923598		2203	4300	6503	SO:0001583	missense	2067	exon4			GGGCACAGGTGCT		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.409T>C	19.37:g.45923598A>G	ENSP00000300853:p.Cys137Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	38	0.644068	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.572338	0.65765	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.52526	0.76;0.66;0.87;0.71	5.28	5.28	0.74379	Restriction endonuclease, type II-like (1);	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	M	0.91561	3.22	0.80722	D	1	P;B;P;P	0.43973	0.731;0.054;0.681;0.823	P;B;B;B	0.45913	0.497;0.064;0.32;0.399	T	0.71210	-0.4660	10	0.66056	D	0.02	-2.2056	11.5895	0.50938	1.0:0.0:0.0:0.0	.	137;65;137;137	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	R	137;137;65;137	ENSP00000300853:C137R;ENSP00000345203:C137R;ENSP00000394875:C65R;ENSP00000013807:C137R	ENSP00000013807:C137R	C	-	1	0	ERCC1	50615438	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.739000	0.84976	2.013000	0.59113	0.374000	0.22700	TGT	.	.	none		0.617	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24505722	24505722	+	RNA	SNP	C	C	G	rs8005834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24505722C>G	ENST00000558293.1	+	0	61					NR_102693.1																						GCACAAGGCGCGGCTACGAGG	0.662													G|||	2318	0.462859	0.6422	0.3444	5008	,	,		16247	0.5863		0.2157	False		,,,				2504	0.4315				p.R5G		Atlas-SNP	.											.	.	.	.	0			c.C13G						PASS	.	G	GLY/ARG	2570,1836		763,1044,396	43.0	43.0	43.0		13	1.0	0.0	14	dbSNP_116	43	1821,6779		200,1421,2679	no	missense	DHRS4L1	NM_001082488.1	125	963,2465,3075	GG,GC,CC		21.1744,41.6704,33.7613	benign	5/282	24505722	4391,8615	2203	4300	6503			728635	exon1			AAGGCGCGGCTAC																													14.37:g.24505722C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	37		957	0.4381868131868132	333	0.676829268292683	116	0.32044198895027626	351	0.6136363636363636	157	0.20712401055408972	-	6.585	0.476309	0.12521	0.583296	0.211744	ENSG00000225766	ENST00000397065	.	.	.	1.94	0.966	0.19667	.	.	.	.	.	T	0.00012	0.0000	N	0.02736	-0.51	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.34900	-0.9810	7	0.36615	T	0.2	.	7.5988	0.28065	0.0:0.5299:0.4701:0.0	rs8005834;rs52837552;rs8005834	5	P0CG22	DR4L1_HUMAN	G	5	.	ENSP00000380255:R5G	R	+	1	2	AL136295.1	23575562	0.000000	0.05858	0.008000	0.14137	0.064000	0.16182	-0.561000	0.05957	-0.022000	0.13986	-1.042000	0.02369	CGG	C|0.569;G|0.431	0.431	strong		0.662	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
RIN3	79890	hgsc.bcm.edu	37	14	93107590	93107590	+	Silent	SNP	C	C	T	rs34101393	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:93107590C>T	ENST00000216487.7	+	5	607	c.448C>T	c.(448-450)Ctg>Ttg	p.L150L	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	150	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CAGAGACTTACTGCCCTTCAC	0.592													C|||	144	0.028754	0.0076	0.0865	5008	,	,		19271	0.0		0.0586	False		,,,				2504	0.0153				p.L150L		Atlas-SNP	.											.	RIN3	81	.	0			c.C448T						PASS	.	C		73,4333	65.3+/-102.7	3,67,2133	130.0	102.0	111.0		448	4.0	1.0	14	dbSNP_126	111	560,8040	152.7+/-207.2	27,506,3767	no	coding-synonymous	RIN3	NM_024832.3		30,573,5900	TT,TC,CC		6.5116,1.6568,4.867		150/986	93107590	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	79890	exon5			GACTTACTGCCCT	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.448C>T	14.37:g.93107590C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			C|0.957;T|0.043	0.043	strong		0.592	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
KRT6B	3854	hgsc.bcm.edu	37	12	52843581	52843581	+	Silent	SNP	A	A	G	rs382894		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52843581A>G	ENST00000252252.3	-	4	920	c.873T>C	c.(871-873)ctT>ctC	p.L291L		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	291	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.L291L(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		TCTCATCTGTAAGAGTGTCTG	0.488																																					p.L291L		Atlas-SNP	.											KRT6B,NS,carcinoma,0,5	KRT6B	90	5	1	Substitution - coding silent(1)	prostate(1)	c.T873C						scavenged	.						186.0	173.0	177.0					12																	52843581		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon4			ATCTGTAAGAGTG	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.873T>C	12.37:g.52843581A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	204	10	0.0490196	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			A|1.000;|0.000	.	weak		0.488	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
NEK1	4750	hgsc.bcm.edu	37	4	170345893	170345893	+	Silent	SNP	C	C	T	rs7655924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:170345893C>T	ENST00000439128.2	-	29	3589	c.2949G>A	c.(2947-2949)ccG>ccA	p.P983P	NEK1_ENST00000507142.1_Silent_p.P1011P|NEK1_ENST00000511633.1_Silent_p.P967P|NEK1_ENST00000510533.1_Silent_p.P939P|NEK1_ENST00000512193.1_Silent_p.P914P	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	983					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		AAAATGGTTCCGGTTGCACAG	0.403													T|||	498	0.0994409	0.1936	0.0476	5008	,	,		18328	0.0308		0.0706	False		,,,				2504	0.1094				p.P1011P		Atlas-SNP	.											.	NEK1	203	.	0			c.G3033A						PASS	.	T	,,,,	551,3201		36,479,1361	121.0	115.0	117.0		3033,2901,2742,2817,2949	-1.7	0.6	4	dbSNP_116	117	518,7658		15,488,3585	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	,,,,	51,967,4946	TT,TC,CC		6.3356,14.6855,8.9621	,,,,	1011/1287,967/1243,914/1190,939/1215,983/1259	170345893	1069,10859	1876	4088	5964	SO:0001819	synonymous_variant	4750	exon31			TGGTTCCGGTTGC	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.2949G>A	4.37:g.170345893C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																			C|0.907;T|0.093	0.093	strong		0.403	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
ZNF189	7743	hgsc.bcm.edu	37	9	104170350	104170350	+	Silent	SNP	A	A	G	rs1047968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104170350A>G	ENST00000339664.2	+	3	429	c.300A>G	c.(298-300)acA>acG	p.T100T	ZNF189_ENST00000259395.4_Silent_p.T58T|ZNF189_ENST00000374861.3_Silent_p.T86T	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	100					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				GTAGAGAAACATTTGAACTTG	0.383													a|||	312	0.0623003	0.0265	0.0893	5008	,	,		18241	0.002		0.1153	False		,,,				2504	0.0992				p.T100T		Atlas-SNP	.											.	ZNF189	79	.	0			c.A300G						PASS	.	A	,	173,4233	112.9+/-151.0	1,171,2031	87.0	82.0	84.0		300,174	-0.3	1.0	9	dbSNP_86	84	925,7675	205.9+/-248.2	54,817,3429	no	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	55,988,5460	GG,GA,AA		10.7558,3.9265,8.4423	,	100/627,58/585	104170350	1098,11908	2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			AGAAACATTTGAA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.300A>G	9.37:g.104170350A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			A|0.931;G|0.069	0.069	strong		0.383	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
RABGAP1	23637	hgsc.bcm.edu	37	9	125748669	125748669	+	Silent	SNP	A	A	G	rs376096787		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:125748669A>G	ENST00000373647.4	+	4	695	c.561A>G	c.(559-561)tcA>tcG	p.S187S		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	187	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						TTACCCTTTCAGTGCCGAATG	0.438																																					p.S187S		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A561G						PASS	.	A		0,4406		0,0,2203	185.0	179.0	181.0		561	-10.1	0.1	9		181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RABGAP1	NM_012197.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		187/1070	125748669	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23637	exon4			CCTTTCAGTGCCG	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.561A>G	9.37:g.125748669A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.	.	weak		0.438	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
LRR1	122769	hgsc.bcm.edu	37	14	50074520	50074520	+	Missense_Mutation	SNP	C	C	T	rs7148147	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50074520C>T	ENST00000298288.6	+	3	1009	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	LRR1_ENST00000318317.4_Intron	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	229			R -> W (in dbSNP:rs7148147).		protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GAAGTCACTTCGGAGTTTGGA	0.408													C|||	863	0.172324	0.2625	0.3156	5008	,	,		19416	0.0268		0.2296	False		,,,				2504	0.0399				p.R229W		Atlas-SNP	.											.	LRR1	35	.	0			c.C685T						PASS	.	C	TRP/ARG,	1124,3282	401.5+/-332.0	138,848,1217	68.0	69.0	69.0		685,	5.1	1.0	14	dbSNP_116	69	1880,6720	333.7+/-320.7	218,1444,2638	yes	missense,intron	LRR1	NM_152329.3,NM_203467.1	101,	356,2292,3855	TT,TC,CC		21.8605,25.5107,23.097	possibly-damaging,	229/415,	50074520	3004,10002	2203	4300	6503	SO:0001583	missense	122769	exon3			TCACTTCGGAGTT	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"""LRR-repeat protein 1"""	609193	"""peptidylprolyl isomerase (cyclophilin)-like 5"""	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.685C>T	14.37:g.50074520C>T	ENSP00000298288:p.Arg229Trp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	37	CCDS9686.1	417	0.19093406593406592	120	0.24390243902439024	106	0.292817679558011	27	0.0472027972027972	164	0.21635883905013192	C	20.8	4.057746	0.76074	0.255107	0.218605	ENSG00000165501	ENST00000298288;ENST00000361579	T	0.20738	2.05	5.98	5.1	0.69264	.	0.495374	0.23999	N	0.042485	T	0.00012	0.0000	M	0.85542	2.76	0.09310	P	1.0	D;D	0.61697	0.99;0.99	P;P	0.54210	0.53;0.745	T	0.21381	-1.0247	9	0.52906	T	0.07	-0.0624	11.5755	0.50858	0.0:0.8641:0.0:0.1359	rs7148147;rs52803719;rs58585267;rs7148147	251;229	A8MSW2;Q96L50	.;LLR1_HUMAN	W	229;251	ENSP00000298288:R229W	ENSP00000298288:R229W	R	+	1	2	LRR1	49144270	1.000000	0.71417	0.990000	0.47175	0.966000	0.64601	4.636000	0.61339	1.571000	0.49722	-0.131000	0.14894	CGG	C|0.792;T|0.208	0.208	strong		0.408	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467	
FAM221B	392307	hgsc.bcm.edu	37	9	35826038	35826038	+	Missense_Mutation	SNP	T	T	C	rs13294245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35826038T>C	ENST00000423537.2	-	2	390	c.121A>G	c.(121-123)Aag>Gag	p.K41E	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	41			K -> E (in dbSNP:rs13294245). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(4)	7						GTGGAAGGCTTCAAGAAGCTT	0.537											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1203	0.240216	0.2474	0.2017	5008	,	,		20084	0.375		0.2008	False		,,,				2504	0.1595				p.K41E		Atlas-SNP	.											.	FAM221B	38	.	0			c.A121G						PASS	.		GLU/LYS	894,2904		111,672,1116	81.0	83.0	82.0		121	1.9	0.0	9	dbSNP_121	82	1590,6608		150,1290,2659	yes	missense	C9orf128	NM_001012446.2	56	261,1962,3775	CC,CT,TT		19.395,23.5387,20.7069	benign	41/403	35826038	2484,9512	1899	4099	5998	SO:0001583	missense	392307	exon2			AAGGCTTCAAGAA	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.121A>G	9.37:g.35826038T>C	ENSP00000415299:p.Lys41Glu	Somatic	76	0	0	858	WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001012446	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	572	0.2619047619047619	126	0.25609756097560976	82	0.2265193370165746	220	0.38461538461538464	144	0.18997361477572558	c	9.080	0.999048	0.19121	0.235387	0.19395	ENSG00000204930	ENST00000423537;ENST00000377984;ENST00000472182	T;T;T	0.26373	2.84;2.56;1.74	3.8	1.91	0.25777	.	0.511663	0.16358	N	0.217901	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	0.45659	-0.9246	9	0.02654	T	1	.	4.0585	0.09827	0.0:0.5692:0.2061:0.2248	rs13294245	41	A6H8Z2	CI128_HUMAN	E	41	ENSP00000415299:K41E;ENSP00000367222:K41E;ENSP00000420279:K41E	ENSP00000367222:K41E	K	-	1	0	C9orf128	35816038	0.001000	0.12720	0.019000	0.16419	0.374000	0.29953	-0.007000	0.12810	0.201000	0.20466	-0.779000	0.03376	AAG	T|0.758;C|0.242	0.242	strong		0.537	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446	
C2orf54	79919	hgsc.bcm.edu	37	2	241835379	241835379	+	Silent	SNP	G	G	A	rs12105122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	25	14	0.56	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	
ZNF668	79759	hgsc.bcm.edu	37	16	31072909	31072909	+	Missense_Mutation	SNP	G	G	A	rs8046978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:31072909G>A	ENST00000538906.1	-	3	2124	c.1340C>T	c.(1339-1341)gCa>gTa	p.A447V	ZNF668_ENST00000417110.2_Missense_Mutation_p.A33T|ZNF668_ENST00000426488.2_Missense_Mutation_p.A470V|ZNF668_ENST00000300849.4_Missense_Mutation_p.A447V|ZNF668_ENST00000539836.3_Missense_Mutation_p.A470V|ZNF668_ENST00000394983.2_Missense_Mutation_p.A447V|ZNF668_ENST00000535577.1_Missense_Mutation_p.A447V	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	447			A -> V (in dbSNP:rs8046978).		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(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGCCCCTGCTGCCGGGGCGGC	0.711													G|||	472	0.0942492	0.0386	0.1383	5008	,	,		13492	0.003		0.2336	False		,,,				2504	0.089				p.A470V	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1409T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	257,4127		6,245,1941	32.0	39.0	37.0		1340,1409,1340,1340	-1.8	0.0	16	dbSNP_116	37	1956,6638		208,1540,2549	no	missense,missense,missense,missense	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	64,64,64,64	214,1785,4490	AA,AG,GG		22.7601,5.8622,17.0519	benign,benign,benign,benign	447/620,470/643,447/620,447/620	31072909	2213,10765	2192	4297	6489	SO:0001583	missense	79759	exon4			CCTGCTGCCGGGG		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1340C>T	16.37:g.31072909G>A	ENSP00000440149:p.Ala447Val	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	265|265	0.12133699633699634|0.12133699633699634	31|31	0.06300813008130081|0.06300813008130081	58|58	0.16022099447513813|0.16022099447513813	0|0	0.0|0.0	176|176	0.23218997361477572|0.23218997361477572	G|G	7.430|7.430	0.638493|0.638493	0.14386|0.14386	0.058622|0.058622	0.227601|0.227601	ENSG00000232748|ENSG00000167394	ENST00000417110|ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	.|T;T;T;T;T	.|0.07444	.|3.19;3.2;3.2;3.2;3.2	4.63|4.63	-1.8|-1.8	0.07907|0.07907	.|.	0.914317|0.914317	0.08993|0.08993	N|N	0.864087|0.864087	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	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.47886|0.47886	-0.9082|-0.9082	6|9	0.87932|0.87932	D|D	0|0	-1.2257|-1.2257	4.0535|4.0535	0.09806|0.09806	0.1021:0.4895:0.2577:0.1507|0.1021:0.4895:0.2577:0.1507	rs8046978;rs8046978|rs8046978;rs8046978	.|447	.|Q96K58	.|ZN668_HUMAN	T|V	33|470;447;447;447;447	.|ENSP00000442573:A470V;ENSP00000441349:A447V;ENSP00000440149:A447V;ENSP00000378434:A447V;ENSP00000300849:A447V	ENSP00000391989:A33T|ENSP00000300849:A447V	A|A	+|-	1|2	0|0	AC135050.1|ZNF668	30980410|30980410	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.410000|0.410000	0.31052|0.31052	-0.300000|-0.300000	0.08243|0.08243	-0.091000|-0.091000	0.12440|0.12440	0.462000|0.462000	0.41574|0.41574	GCC|GCA	G|0.851;A|0.149	0.149	strong		0.711	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
F5	2153	hgsc.bcm.edu	37	1	169511755	169511755	+	Missense_Mutation	SNP	T	T	C	rs4524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169511755T>C	ENST00000367797.3	-	13	2774	c.2573A>G	c.(2572-2574)aAa>aGa	p.K858R	F5_ENST00000367796.3_Missense_Mutation_p.K863R	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	858	B.		K -> R (in dbSNP:rs4524). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	TTCTTGACTTTTGAATTCTCC	0.453													T|||	1336	0.266773	0.1679	0.3948	5008	,	,		21468	0.248		0.2535	False		,,,				2504	0.3425				p.K858R		Atlas-SNP	.											.	F5	301	.	0			c.A2573G						PASS	.	T	ARG/LYS	813,3593	321.3+/-297.0	68,677,1458	187.0	175.0	179.0		2573	-1.7	0.0	1	dbSNP_52	179	2355,6245	393.6+/-344.4	300,1755,2245	yes	missense	F5	NM_000130.4	26	368,2432,3703	CC,CT,TT		27.3837,18.4521,24.358	benign	858/2225	169511755	3168,9838	2203	4300	6503	SO:0001583	missense	2153	exon13			TGACTTTTGAATT	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.2573A>G	1.37:g.169511755T>C	ENSP00000356771:p.Lys858Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	262	155	0.591603	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	T	0.281	-0.986145	0.02180	0.184521	0.273837	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.19105	2.17;2.17	5.34	-1.7	0.08159	.	0.830320	0.10778	N	0.635169	T	0.01523	0.0049	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47711	-0.9096	9	0.15499	T	0.54	-3.9453	5.1617	0.15064	0.0:0.3402:0.1552:0.5046	rs4524;rs52817149;rs59950571;rs4524	858	P12259	FA5_HUMAN	R	858;863	ENSP00000356771:K858R;ENSP00000356770:K863R	ENSP00000356770:K863R	K	-	2	0	F5	167778379	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.454000	0.06770	-0.097000	0.12307	-1.534000	0.00916	AAA	T|0.760;C|0.240	0.240	strong		0.453	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
RTEL1	51750	hgsc.bcm.edu	37	20	62297400	62297400	+	Silent	SNP	T	T	C	rs73920935	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62297400T>C	ENST00000360203.5	+	7	907	c.582T>C	c.(580-582)atT>atC	p.I194I	RTEL1_ENST00000370018.3_Silent_p.I194I|RTEL1_ENST00000318100.4_Silent_p.I194I|RTEL1_ENST00000508582.2_Silent_p.I218I|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.I194I					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			TCCTGGACATTGAGGACTTGG	0.597													C|||	332	0.0662939	0.1188	0.0533	5008	,	,		17136	0.001		0.0855	False		,,,				2504	0.0521				p.I218I		Atlas-SNP	.											.	RTEL1	114	.	0			c.T654C						PASS	.	C	,	497,3909	779.5+/-414.4	23,451,1729	79.0	64.0	69.0		582,654	0.1	1.0	20	dbSNP_130	69	715,7885	786.9+/-407.6	36,643,3621	no	coding-synonymous,coding-synonymous	RTEL1	NM_016434.3,NM_032957.4	,	59,1094,5350	CC,CT,TT		8.314,11.2801,9.3188	,	194/1220,218/1244	62297400	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	51750	exon7			GGACATTGAGGAC	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.582T>C	20.37:g.62297400T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_032957		Silent	SNP	ENST00000360203.5	37																																																																																				T|0.915;C|0.085	0.085	strong		0.597	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
ANKRD44	91526	hgsc.bcm.edu	37	2	198001319	198001319	+	Silent	SNP	A	A	G	rs3731569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000282272.8_Silent_p.S78S|ANKRD44_ENST00000409919.1_Silent_p.S86S|ANKRD44_ENST00000450567.1_Silent_p.S61S|ANKRD44_ENST00000409153.1_Silent_p.S86S|ANKRD44_ENST00000539527.1_Silent_p.S14S			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	66	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	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	
NACC2	138151	hgsc.bcm.edu	37	9	138903671	138903671	+	Silent	SNP	A	A	G	rs9626|rs386739528	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:138903671A>G	ENST00000371753.1	-	5	1513	c.1455T>C	c.(1453-1455)ccT>ccC	p.P485P	NACC2_ENST00000277554.2_Silent_p.P485P			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	485					cellular protein complex localization (GO:0034629)|histone deacetylation (GO:0016575)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|posttranscriptional regulation of gene expression (GO:0010608)|protein homooligomerization (GO:0051260)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|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 transcription factor binding transcription factor activity (GO:0001076)			endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						GTGCCGCGGCAGGCGGGAACT	0.677													A|||	3440	0.686901	0.7905	0.6902	5008	,	,		12310	0.5694		0.6968	False		,,,				2504	0.6554				p.P485P		Atlas-SNP	.											.	NACC2	16	.	0			c.T1455C						PASS	.	A		3309,991		1298,713,139	8.0	8.0	8.0		1455	-1.2	0.1	9	dbSNP_52	8	5996,2320		2212,1572,374	no	coding-synonymous	NACC2	NM_144653.4		3510,2285,513	GG,GA,AA		27.898,23.0465,26.2445		485/588	138903671	9305,3311	2150	4158	6308	SO:0001819	synonymous_variant	138151	exon6			CGCGGCAGGCGGG	BC015649	CCDS6993.1	9q34.3	2013-01-09	2008-10-03	2008-10-03	ENSG00000148411	ENSG00000148411		"""BEN domain containing"", ""BTB/POZ domain containing"""	23846	protein-coding gene	gene with protein product	"""BEN domain containing 9"""	615786	"""BTB (POZ) domain containing 14A"""	BTBD14A		12477932	Standard	NM_144653		Approved	MGC23427, BEND9, BTBD31	uc004cgv.4	Q96BF6	OTTHUMG00000020921	ENST00000371753.1:c.1455T>C	9.37:g.138903671A>G		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			A|0.317;G|0.683	0.683	strong		0.677	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653	
OR10G9	219870	hgsc.bcm.edu	37	11	123894352	123894352	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:123894352C>T	ENST00000375024.1	+	1	633	c.633C>T	c.(631-633)ctC>ctT	p.L211L		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L211L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		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;0.0399)		GCTGCTTTCTCCTGATAGTGC	0.567																																					p.L211L		Atlas-SNP	.											OR10G9,NS,carcinoma,0,1	OR10G9	80	1	1	Substitution - coding silent(1)	lung(1)	c.C633T						scavenged	.						243.0	208.0	220.0					11																	123894352		2201	4299	6500	SO:0001819	synonymous_variant	219870	exon1			CTTTCTCCTGATA	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.633C>T	11.37:g.123894352C>T		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	324	4	0.0123457	NM_001001953		Silent	SNP	ENST00000375024.1	37	CCDS31703.1																																																																																			.	.	none		0.567	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
RELN	5649	hgsc.bcm.edu	37	7	103155864	103155864	+	Silent	SNP	A	A	G	rs56345626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:103155864A>G	ENST00000428762.1	-	50	8046	c.7887T>C	c.(7885-7887)ccT>ccC	p.P2629P	RELN_ENST00000343529.5_Silent_p.P2629P|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Silent_p.P2629P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2629					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTTTAGCATCAGGAGGGAGAA	0.478													A|||	876	0.17492	0.1339	0.1513	5008	,	,		18623	0.254		0.1849	False		,,,				2504	0.1554				p.P2629P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T7887C						PASS	.	A	,	560,3846	245.3+/-254.3	43,474,1686	48.0	49.0	49.0		7887,7887	1.5	1.0	7	dbSNP_129	49	1643,6957	299.9+/-304.7	156,1331,2813	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	199,1805,4499	GG,GA,AA		19.1047,12.7099,16.9383	,	2629/3461,2629/3459	103155864	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon50			AGCATCAGGAGGG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7887T>C	7.37:g.103155864A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			A|0.829;G|0.171	0.171	strong		0.478	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
KIF4B	285643	hgsc.bcm.edu	37	5	154395682	154395682	+	Missense_Mutation	SNP	G	G	A	rs41390849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:154395682G>A	ENST00000435029.4	+	1	2423	c.2263G>A	c.(2263-2265)Gtc>Atc	p.V755I		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	755	Interaction with PRC1. {ECO:0000250}.			V -> I (in Ref. 3; ABB92415). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TGAGGTTATGGTCAGTACTGA	0.458													G|||	621	0.124002	0.0053	0.0836	5008	,	,		20480	0.1895		0.1421	False		,,,				2504	0.227				p.V755I		Atlas-SNP	.											.	KIF4B	307	.	0			c.G2263A						PASS	.	G	ILE/VAL	125,4281	89.7+/-128.4	0,125,2078	86.0	83.0	84.0		2263	2.1	1.0	5	dbSNP_129	84	1247,7353	250.3+/-277.2	94,1059,3147	yes	missense	KIF4B	NM_001099293.1	29	94,1184,5225	AA,AG,GG		14.5,2.837,10.549	probably-damaging	755/1235	154395682	1372,11634	2203	4300	6503	SO:0001583	missense	285643	exon1			GTTATGGTCAGTA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2263G>A	5.37:g.154395682G>A	ENSP00000387875:p.Val755Ile	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	231	113	0.489177	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	226	0.10347985347985347	4	0.008130081300813009	31	0.0856353591160221	88	0.15384615384615385	103	0.1358839050131926	g	11.04	1.523021	0.27211	0.02837	0.145	ENSG00000226650	ENST00000435029	T	0.69561	-0.41	2.14	2.14	0.27477	.	.	.	.	.	T	0.00496	0.0016	L	0.55017	1.72	0.09310	P	0.99999470196	B	0.20368	0.044	B	0.22386	0.039	T	0.21008	-1.0258	8	0.31617	T	0.26	.	10.3225	0.43775	0.0:0.0:1.0:0.0	rs56080630;rs61734293	755	Q2VIQ3	KIF4B_HUMAN	I	755	ENSP00000387875:V755I	ENSP00000387875:V755I	V	+	1	0	KIF4B	154375875	1.000000	0.71417	0.995000	0.50966	0.503000	0.33858	6.159000	0.71856	1.138000	0.42230	0.563000	0.77884	GTC	G|0.888;A|0.112	0.112	strong		0.458	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
LRP1	4035	hgsc.bcm.edu	37	12	57588433	57588433	+	Silent	SNP	G	G	A	rs1800141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57588433G>A	ENST00000243077.3	+	50	8608	c.8142G>A	c.(8140-8142)acG>acA	p.T2714T	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2714	LDL-receptor class A 15. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TGAGCTGGACGTGTGACAAAG	0.622													g|||	483	0.0964457	0.0825	0.0548	5008	,	,		19511	0.251		0.0298	False		,,,				2504	0.0542				p.T2714T		Atlas-SNP	.											LRP1,colon,carcinoma,0,2	LRP1	428	2	0			c.G8142A						PASS	.			388,4018	196.0+/-220.5	9,370,1824	74.0	69.0	71.0		8142	-10.4	0.7	12	dbSNP_89	71	239,8361	96.6+/-158.3	7,225,4068	no	coding-synonymous	LRP1	NM_002332.2		16,595,5892	AA,AG,GG		2.7791,8.8062,4.8209		2714/4545	57588433	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon50			CTGGACGTGTGAC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.8142G>A	12.37:g.57588433G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			G|0.933;A|0.067	0.067	strong		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
MFI2	4241	hgsc.bcm.edu	37	3	196742243	196742243	+	Missense_Mutation	SNP	C	C	T	rs45625439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196742243C>T	ENST00000296350.5	-	9	1339	c.1226G>A	c.(1225-1227)cGg>cAg	p.R409Q		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	409	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				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)		CACCTGGATCCGCTCCATGCA	0.657													C|||	23	0.00459265	0.0	0.0043	5008	,	,		18548	0.0		0.0129	False		,,,				2504	0.0072				p.R409Q		Atlas-SNP	.											.	MFI2	88	.	0			c.G1226A						PASS	.	C	GLN/ARG	22,4348		0,22,2163	34.0	24.0	27.0		1226	-3.8	0.9	3	dbSNP_127	27	146,8408		2,142,4133	yes	missense	MFI2	NM_005929.5	43	2,164,6296	TT,TC,CC		1.7068,0.5034,1.2999	benign	409/739	196742243	168,12756	2185	4277	6462	SO:0001583	missense	4241	exon9			TGGATCCGCTCCA		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.1226G>A	3.37:g.196742243C>T	ENSP00000296350:p.Arg409Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	66	0.616822	NM_005929	Q9BQE2	Missense_Mutation	SNP	ENST00000296350.5	37	CCDS3325.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	12.39	1.923379	0.33908	0.005034	0.017068	ENSG00000163975	ENST00000296350	T	0.32272	1.46	5.72	-3.84	0.04256	.	1.025380	0.07685	N	0.937703	T	0.04907	0.0132	N	0.03177	-0.4	0.41333	D	0.987255	B	0.09022	0.002	B	0.08055	0.003	T	0.38001	-0.9681	10	0.14656	T	0.56	-10.756	5.8183	0.18514	0.183:0.3633:0.0:0.4537	rs45625439	409	P08582	TRFM_HUMAN	Q	409	ENSP00000296350:R409Q	ENSP00000296350:R409Q	R	-	2	0	MFI2	198226640	0.027000	0.19231	0.857000	0.33713	0.825000	0.46686	-0.069000	0.11542	-0.368000	0.08040	-1.320000	0.01293	CGG	C|0.991;T|0.009	0.009	strong		0.657	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
FCGBP	8857	hgsc.bcm.edu	37	19	40392347	40392347	+	Missense_Mutation	SNP	C	C	G	rs139175656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40392347C>G	ENST00000221347.6	-	16	8164	c.8157G>C	c.(8155-8157)caG>caC	p.Q2719H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2719				Q -> H (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.Q2719H(2)		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)			AGGGCTCCACCTGGCCTCCAG	0.592													G|||	1513	0.302117	0.2708	0.4164	5008	,	,		15565	0.2103		0.3688	False		,,,				2504	0.2894				p.Q2719H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	2	Substitution - Missense(2)	prostate(2)	c.G8157C						scavenged	.						17.0	16.0	17.0					19																	40392347		2135	4094	6229	SO:0001583	missense	8857	exon16			CTCCACCTGGCCT	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.8157G>C	19.37:g.40392347C>G	ENSP00000221347:p.Gln2719His	Somatic	430	3	0.00697674		WXS	Illumina HiSeq	Phase_I	15	13	0.866667	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	0.582	-0.836839	0.02692	.	.	ENSG00000090920	ENST00000221347	T	0.76709	-1.04	2.02	-2.46	0.06461	Uncharacterised domain, cysteine-rich (2);	1.468830	0.04141	N	0.319631	T	0.53818	0.1820	N	0.04063	-0.285	0.09310	N	1	B	0.14012	0.009	B	0.20577	0.03	T	0.33904	-0.9850	10	0.37606	T	0.19	.	2.9179	0.05759	0.1094:0.305:0.4189:0.1668	.	2719	Q9Y6R7	FCGBP_HUMAN	H	2719	ENSP00000221347:Q2719H	ENSP00000221347:Q2719H	Q	-	3	2	FCGBP	45084187	0.000000	0.05858	0.060000	0.19600	0.366000	0.29705	-3.718000	0.00384	-0.933000	0.03737	-0.702000	0.03669	CAG	C|0.333;G|0.667	0.667	strong		0.592	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CASZ1	54897	hgsc.bcm.edu	37	1	10725498	10725498	+	Silent	SNP	G	G	A	rs284322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	25	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	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	
KRT33B	3884	hgsc.bcm.edu	37	17	39525750	39525750	+	Missense_Mutation	SNP	C	C	T	rs12450621	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39525750C>T	ENST00000251646.3	-	1	302	c.253G>A	c.(253-255)Gag>Aag	p.E85K		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	85	Coil 1A.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				ATGAGGTTCTCCAGCTCCGCG	0.602													C|||	142	0.0283546	0.0023	0.0375	5008	,	,		18403	0.0		0.0537	False		,,,				2504	0.0603				p.E85K		Atlas-SNP	.											.	KRT33B	46	.	0			c.G253A						PASS	.	C	LYS/GLU	50,4356		0,50,2153	65.0	64.0	64.0		253	4.4	1.0	17	dbSNP_120	64	538,8056		19,500,3778	no	missense	KRT33B	NM_002279.3	56	19,550,5931	TT,TC,CC		6.2602,1.1348,4.5231	probably-damaging	85/405	39525750	588,12412	2203	4297	6500	SO:0001583	missense	3884	exon1			GGTTCTCCAGCTC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.253G>A	17.37:g.39525750C>T	ENSP00000251646:p.Glu85Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	58	0.026556776556776556	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	44	0.05804749340369393	N	27.6	4.846144	0.91277	0.011348	0.062602	ENSG00000131738	ENST00000251646	D	0.90069	-2.61	4.41	4.41	0.53225	Filament (1);	0.087756	0.49916	D	0.000131	D	0.82476	0.5045	H	0.97829	4.085	0.47009	D	0.999284	D	0.71674	0.998	D	0.73380	0.98	D	0.86523	0.1817	10	0.87932	D	0	.	16.522	0.84319	0.0:1.0:0.0:0.0	rs12450621	85	Q14525	KT33B_HUMAN	K	85	ENSP00000251646:E85K	ENSP00000251646:E85K	E	-	1	0	KRT33B	36779276	1.000000	0.71417	0.998000	0.56505	0.758000	0.43043	7.502000	0.81614	2.434000	0.82447	0.650000	0.86243	GAG	C|0.986;T|0.014	0.014	weak		0.602	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
CYP2A7	1549	hgsc.bcm.edu	37	19	41386033	41386033	+	Missense_Mutation	SNP	T	T	C	rs73032311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41386033T>C	ENST00000301146.4	-	4	1151	c.610A>G	c.(610-612)Atg>Gtg	p.M204V	CYP2A7_ENST00000291764.3_Missense_Mutation_p.M153V|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	204						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTAGCATCATGCTCAGCAGT	0.567													.|||	569	0.113618	0.0802	0.0807	5008	,	,		9800	0.1796		0.1441	False		,,,				2504	0.0828				p.M204V		Atlas-SNP	.											.	CYP2A7	71	.	0			c.A610G						PASS	.	T	VAL/MET,VAL/MET	408,3998	202.8+/-225.5	17,374,1812	163.0	136.0	145.0		610,457	0.8	0.0	19	dbSNP_131	145	1367,7233	267.1+/-287.1	131,1105,3064	yes	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	21,21	148,1479,4876	CC,CT,TT		15.8953,9.2601,13.6475	possibly-damaging,possibly-damaging	204/495,153/444	41386033	1775,11231	2203	4300	6503	SO:0001583	missense	1549	exon4			GCATCATGCTCAG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.610A>G	19.37:g.41386033T>C	ENSP00000301146:p.Met204Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	86	0.505882	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	299	0.13690476190476192	49	0.09959349593495935	32	0.08839779005524862	106	0.1853146853146853	112	0.14775725593667546	t	5.558	0.287753	0.10513	0.092601	0.158953	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.68331	-0.32;-0.32	1.95	0.761	0.18448	.	0.227903	0.43579	U	0.000551	T	0.00109	0.0003	L	0.37507	1.11	0.80722	P	0.0	B;B	0.24533	0.03;0.105	B;B	0.22386	0.036;0.039	T	0.02758	-1.1114	9	0.40728	T	0.16	.	4.8627	0.13592	0.2728:0.0:0.0:0.7272	.	153;204	F8W816;P20853	.;CP2A7_HUMAN	V	204;153	ENSP00000301146:M204V;ENSP00000291764:M153V	ENSP00000291764:M153V	M	-	1	0	CYP2A7	46077873	0.830000	0.29337	0.002000	0.10522	0.018000	0.09664	1.082000	0.30803	0.000000	0.14550	0.147000	0.16070	ATG	T|0.862;C|0.138	0.138	strong		0.567	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
GSDMB	55876	hgsc.bcm.edu	37	17	38062503	38062503	+	Missense_Mutation	SNP	T	T	C	rs35104165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38062503T>C	ENST00000394179.1	-	7	864	c.734A>G	c.(733-735)gAt>gGt	p.D245G	GSDMB_ENST00000394175.2_Missense_Mutation_p.D228G|GSDMB_ENST00000520542.1_Missense_Mutation_p.D241G|GSDMB_ENST00000360317.3_Missense_Mutation_p.D250G|GSDMB_ENST00000309481.7_Missense_Mutation_p.D237G|GSDMB_ENST00000418519.1_Missense_Mutation_p.D250G			Q8TAX9	GSDMB_HUMAN	gasdermin B	245			D -> G (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			cytoplasm (GO:0005737)		p.D228G(2)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						GTTTCTGGAATCCTCCGAACC	0.478													T|||	79	0.0157748	0.0038	0.0288	5008	,	,		19080	0.0		0.0358	False		,,,				2504	0.0184				p.D250G		Atlas-SNP	.											GSDMB_ENST00000418519,colon,carcinoma,0,8	GSDMB	87	8	2	Substitution - Missense(2)	breast(1)|pancreas(1)	c.A749G						PASS	.	T	GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP	40,4366	43.1+/-76.7	1,38,2164	102.0	90.0	94.0		710,749,722,683	2.7	0.0	17	dbSNP_126	94	324,8276	113.7+/-173.7	6,312,3982	yes	missense,missense,missense,missense	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	94,94,94,94	7,350,6146	CC,CT,TT		3.7674,0.9079,2.7987	benign,benign,benign,benign	237/404,250/417,241/408,228/395	38062503	364,12642	2203	4300	6503	SO:0001583	missense	55876	exon8			CTGGAATCCTCCG	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.734A>G	17.37:g.38062503T>C	ENSP00000377733:p.Asp245Gly	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Missense_Mutation	SNP	ENST00000394179.1	37		43|43	0.019688644688644688|0.019688644688644688	3|3	0.006097560975609756|0.006097560975609756	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	29|29	0.03825857519788918|0.03825857519788918	T|T	10.78|10.78	1.447317|1.447317	0.25987|0.25987	0.009079|0.009079	0.037674|0.037674	ENSG00000073605|ENSG00000073605	ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179|ENST00000420491	T;T;T;T;T|.	0.26810|.	1.71;1.71;1.71;1.71;1.71|.	3.78|3.78	2.66|2.66	0.31614|0.31614	.|.	0.346182|.	0.24061|.	N|.	0.041915|.	T|T	0.10723|0.10723	0.0262|0.0262	L|L	0.41824|0.41824	1.3|1.3	0.09310|0.09310	N|N	1|1	B;D;D;D|.	0.60160|.	0.012;0.987;0.987;0.987|.	B;P;P;P|.	0.56278|.	0.023;0.795;0.795;0.795|.	T|T	0.08638|0.08638	-1.0712|-1.0712	10|5	0.22109|.	T|.	0.4|.	.|.	7.3505|7.3505	0.26689|0.26689	0.0:0.0:0.2224:0.7775|0.0:0.0:0.2224:0.7775	rs35104165|rs35104165	241;250;237;228|.	B4DKK7;Q8TAX9-4;Q8TAX9-3;Q8TAX9-2|.	.;.;.;.|.	G|V	245;228;237;241;250;245|182	ENSP00000377729:D228G;ENSP00000312584:D237G;ENSP00000430157:D241G;ENSP00000415049:D250G;ENSP00000377733:D245G|.	ENSP00000312584:D237G|.	D|I	-|-	2|1	0|0	GSDMB|GSDMB	35316029|35316029	0.001000|0.001000	0.12720|0.12720	0.006000|0.006000	0.13384|0.13384	0.242000|0.242000	0.25591|0.25591	0.092000|0.092000	0.15066|0.15066	0.589000|0.589000	0.29677|0.29677	0.496000|0.496000	0.49642|0.49642	GAT|ATT	T|0.974;C|0.026	0.026	strong		0.478	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
CTBS	1486	hgsc.bcm.edu	37	1	85040070	85040070	+	Missense_Mutation	SNP	C	C	A	rs115347546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85040070C>A	ENST00000370630.5	-	1	77	c.29G>T	c.(28-30)cGc>cTc	p.R10L	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	10					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		AGAGACGAGGCGCCAGCGTCG	0.756													C|||	764	0.152556	0.1044	0.1196	5008	,	,		8545	0.0298		0.2157	False		,,,				2504	0.3027				p.R10L		Atlas-SNP	.											.	CTBS	24	.	0			c.G29T						PASS	.	C	LEU/ARG	247,3003		7,233,1385	3.0	3.0	3.0		29	4.5	0.1	1	dbSNP_132	3	1042,5984		70,902,2541	no	missense	CTBS	NM_004388.2	102	77,1135,3926	AA,AC,CC		14.8306,7.6,12.5438	benign	10/386	85040070	1289,8987	1625	3513	5138	SO:0001583	missense	1486	exon1			ACGAGGCGCCAGC	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.29G>T	1.37:g.85040070C>A	ENSP00000359664:p.Arg10Leu	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	295	0.13507326007326007	57	0.11585365853658537	56	0.15469613259668508	17	0.02972027972027972	165	0.21767810026385223	C	14.10	2.433412	0.43224	0.076	0.148306	ENSG00000117151	ENST00000370630	T	0.36878	1.23	4.46	4.46	0.54185	.	1.494160	0.04094	N	0.311836	T	0.10508	0.0257	N	0.16478	0.41	0.58432	P	1.0000000000287557E-6	P	0.35033	0.481	B	0.29716	0.106	T	0.02031	-1.1226	9	0.13853	T	0.58	0.9571	12.8155	0.57663	0.0:1.0:0.0:0.0	.	10	Q01459	DIAC_HUMAN	L	10	ENSP00000359664:R10L	ENSP00000359664:R10L	R	-	2	0	CTBS	84812658	0.000000	0.05858	0.115000	0.21578	0.011000	0.07611	-0.397000	0.07269	2.466000	0.83321	0.591000	0.81541	CGC	C|0.863;A|0.137	0.137	strong		0.756	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
MYBL2	4605	hgsc.bcm.edu	37	20	42331457	42331457	+	Missense_Mutation	SNP	A	A	G	rs2070235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42331457A>G	ENST00000217026.4	+	8	1406	c.1279A>G	c.(1279-1281)Agc>Ggc	p.S427G	MYBL2_ENST00000396863.4_Missense_Mutation_p.S403G	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	427			S -> G (in dbSNP:rs2070235). {ECO:0000269|PubMed:14702039}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CACTGAGAATAGCACCAGTCT	0.617													A|||	784	0.15655	0.3124	0.0807	5008	,	,		20014	0.1002		0.0885	False		,,,				2504	0.1278				p.S427G		Atlas-SNP	.											.	MYBL2	82	.	0			c.A1279G	GRCh37	CM087204	MYBL2	M	rs2070235	PASS	.	A	GLY/SER	1246,3160	427.6+/-341.6	191,864,1148	130.0	103.0	112.0		1279	2.7	1.0	20	dbSNP_96	112	738,7862	178.3+/-227.7	34,670,3596	yes	missense	MYBL2	NM_002466.2	56	225,1534,4744	GG,GA,AA		8.5814,28.2796,15.2545	benign	427/701	42331457	1984,11022	2203	4300	6503	SO:0001583	missense	4605	exon8			GAGAATAGCACCA		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1279A>G	20.37:g.42331457A>G	ENSP00000217026:p.Ser427Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	329	0.15064102564102563	160	0.3252032520325203	30	0.08287292817679558	68	0.11888111888111888	71	0.09366754617414248	A	8.745	0.919897	0.17982	0.282796	0.085814	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.14266	2.52;2.53	4.99	2.73	0.32206	.	0.407546	0.27442	N	0.019356	T	0.00012	0.0000	N	0.08118	0	0.32649	P	0.519701	B;P	0.42456	0.002;0.78	B;B	0.34931	0.004;0.192	T	0.48525	-0.9028	9	0.21540	T	0.41	-13.7789	6.8685	0.24106	0.7346:0.0:0.2654:0.0	rs2070235;rs2227938;rs52818546;rs58370135;rs2070235	403;427	F8W6N6;P10244	.;MYBB_HUMAN	G	403;427	ENSP00000380072:S403G;ENSP00000217026:S427G	ENSP00000217026:S427G	S	+	1	0	MYBL2	41764871	1.000000	0.71417	0.999000	0.59377	0.736000	0.42039	2.611000	0.46334	0.867000	0.35654	0.379000	0.24179	AGC	A|0.837;G|0.163	0.163	strong		0.617	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272479	11272479	+	Missense_Mutation	SNP	G	G	A	rs74163631		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11272479G>A	ENST00000409790.1	+	24	3324	c.3094G>A	c.(3094-3096)Gcc>Acc	p.A1032T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A119T	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									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						CACGCCGGCTGCCGCCTGCAC	0.687																																					p.A1032T		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3094A						PASS	.	G	THR/ALA	0,4094		0,0,2047	10.0	13.0	12.0		3094	-7.3	0.0	16	dbSNP_130	12	2,8338		0,2,4168	no	missense	CLEC16A	NM_015226.2	58	0,2,6215	AA,AG,GG		0.024,0.0,0.0161	benign	1032/1054	11272479	2,12432	2047	4170	6217	SO:0001583	missense	23274	exon23			CCGGCTGCCGCCT	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.3094G>A	16.37:g.11272479G>A	ENSP00000387122:p.Ala1032Thr	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109842	0.37242	0.0	2.4E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44083	0.93	4.4	-7.33	0.01431	.	1.036120	0.07675	N	0.936064	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.28350	0.208;0.002	B;B	0.22152	0.038;0.004	T	0.15723	-1.0427	10	0.49607	T	0.09	0.8435	1.4953	0.02465	0.3763:0.2341:0.2704:0.1192	.	119;1032	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1032;1032;119	ENSP00000387122:A1032T	ENSP00000371244:A119T	A	+	1	0	CLEC16A	11179980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.117000	0.10708	-1.280000	0.02402	-0.140000	0.14226	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
PTK2	5747	hgsc.bcm.edu	37	8	141840574	141840574	+	Silent	SNP	G	G	A	rs148611560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141840574G>A	ENST00000522684.1	-	8	874	c.645C>T	c.(643-645)gtC>gtT	p.V215V	PTK2_ENST00000535192.1_Silent_p.V215V|PTK2_ENST00000521059.1_Silent_p.V215V|PTK2_ENST00000517887.1_Silent_p.V259V|PTK2_ENST00000340930.3_Silent_p.V215V|PTK2_ENST00000519419.1_Silent_p.V259V|PTK2_ENST00000395218.2_Silent_p.V215V	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	215	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)			TAATTACCTTGACAGAATCCA	0.303													G|||	4	0.000798722	0.0	0.0029	5008	,	,		15534	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											.	PTK2	311	.	0			c.C711T						PASS	.	G	,,	3,4361		0,3,2179	30.0	31.0	30.0		645,711,645	5.2	1.0	8	dbSNP_134	30	18,8528		0,18,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	PTK2	NM_001199649.1,NM_005607.4,NM_153831.3	,,	0,21,6434	AA,AG,GG		0.2106,0.0687,0.1627	,,	215/1066,237/1075,215/1053	141840574	21,12889	2182	4273	6455	SO:0001819	synonymous_variant	5747	exon8			TACCTTGACAGAA	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.645C>T	8.37:g.141840574G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	165	82	0.49697	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	37	CCDS6381.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	9.907	1.208441	0.22205	6.87E-4	0.002106	ENSG00000169398	ENST00000519654	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4863	0.55874	0.0:0.1681:0.8319:0.0	.	.	.	.	X	226	.	.	Q	-	1	0	PTK2	141909756	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.739000	0.38217	2.618000	0.88619	0.655000	0.94253	CAA	G|0.998;A|0.002	0.002	strong		0.303	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
PIGF	5281	hgsc.bcm.edu	37	2	46839477	46839477	+	Silent	SNP	T	T	C	rs1824050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:46839477T>C	ENST00000281382.6	-	4	497	c.327A>G	c.(325-327)gcA>gcG	p.A109A	PIGF_ENST00000495933.1_5'UTR|PIGF_ENST00000306465.4_Silent_p.A109A	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F	109					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)	ethanolaminephosphotransferase activity (GO:0004307)			breast(1)|endometrium(1)|lung(1)|stomach(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATGTTTCCAATGCCAACCTAG	0.274													T|||	903	0.180312	0.0484	0.3213	5008	,	,		12823	0.121		0.2873	False		,,,				2504	0.2096				p.A109A		Atlas-SNP	.											.	PIGF	9	.	0			c.A327G						PASS	.	T	,	354,4006		19,316,1845	23.0	21.0	22.0		327,327	1.9	1.0	2	dbSNP_92	22	2457,6103		374,1709,2197	no	coding-synonymous,coding-synonymous	PIGF	NM_002643.3,NM_173074.2	,	393,2025,4042	CC,CT,TT		28.7033,8.1193,21.757	,	109/220,109/207	46839477	2811,10109	2180	4280	6460	SO:0001819	synonymous_variant	5281	exon4			TTCCAATGCCAAC		CCDS1827.1, CCDS1828.1	2p21-p16	2013-02-26	2006-06-28		ENSG00000151665	ENSG00000151665		"""Phosphatidylinositol glycan anchor biosynthesis"""	8962	protein-coding gene	gene with protein product		600153	"""phosphatidylinositol glycan, class F"""			8575782, 8463218	Standard	NM_173074		Approved		uc002rvd.3	Q07326	OTTHUMG00000128816	ENST00000281382.6:c.327A>G	2.37:g.46839477T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_002643	Q8WW20	Silent	SNP	ENST00000281382.6	37	CCDS1827.1																																																																																			T|0.798;C|0.202	0.202	strong		0.274	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074	
CCDC60	160777	hgsc.bcm.edu	37	12	119961587	119961587	+	Missense_Mutation	SNP	G	G	A	rs78218795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:119961587G>A	ENST00000327554.2	+	11	1658	c.1193G>A	c.(1192-1194)gGc>gAc	p.G398D	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	398										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)		CAGGAGGCTGGCTTCTGCCTG	0.483													G|||	156	0.0311502	0.0862	0.0274	5008	,	,		20637	0.001		0.0129	False		,,,				2504	0.0092				p.G398D		Atlas-SNP	.											.	CCDC60	84	.	0			c.G1193A						PASS	.	G	ASP/GLY	319,4087	170.1+/-200.6	11,297,1895	100.0	82.0	88.0		1193	4.2	1.0	12	dbSNP_131	88	148,8452	72.6+/-135.2	0,148,4152	yes	missense	CCDC60	NM_178499.3	94	11,445,6047	AA,AG,GG		1.7209,7.2401,3.5907	probably-damaging	398/551	119961587	467,12539	2203	4300	6503	SO:0001583	missense	160777	exon11			AGGCTGGCTTCTG	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.1193G>A	12.37:g.119961587G>A	ENSP00000333374:p.Gly398Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	60	0.027472527472527472	43	0.08739837398373984	7	0.019337016574585635	1	0.0017482517482517483	9	0.011873350923482849	G	16.22	3.061173	0.55432	0.072401	0.017209	ENSG00000183273	ENST00000327554	T	0.22743	1.94	4.16	4.16	0.48862	.	0.128128	0.35407	N	0.003225	T	0.01558	0.0050	L	0.55481	1.735	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	T	0.00032	-1.2278	9	.	.	.	-20.1692	11.8272	0.52273	0.0:0.0:1.0:0.0	.	398	Q8IWA6	CCD60_HUMAN	D	398	ENSP00000333374:G398D	.	G	+	2	0	CCDC60	118445970	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	2.598000	0.46223	2.156000	0.67533	0.655000	0.94253	GGC	G|0.968;A|0.032	0.032	strong		0.483	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
ASIC2	40	hgsc.bcm.edu	37	17	31618551	31618551	+	Intron	SNP	G	G	A	rs9890913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:31618551G>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Silent_p.L195L	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CGCGGAGGCAGGAAGAGGCGG	0.706													G|||	646	0.128994	0.1203	0.1888	5008	,	,		14494	0.1329		0.1014	False		,,,				2504	0.1227				p.L195L		Atlas-SNP	.											.	.	.	.	0			c.C583T						PASS	.	G	,	549,3819		38,473,1673	18.0	20.0	19.0		,583	4.7	1.0	17	dbSNP_119	19	718,7804		26,666,3569	no	intron,coding-synonymous	ACCN1	NM_001094.4,NM_183377.1	,	64,1139,5242	AA,AG,GG		8.4253,12.5687,9.8293	,	,195/564	31618551	1267,11623	2184	4261	6445	SO:0001627	intron_variant	40	exon1			GAGGCAGGAAGAG	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179466C>T	17.37:g.31618551G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																			G|0.896;A|0.104	0.104	strong		0.706	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
PRKX	5613	hgsc.bcm.edu	37	X	3631167	3631167	+	Missense_Mutation	SNP	A	A	G	rs3752362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:3631167A>G	ENST00000262848.5	-	1	482	c.128T>C	c.(127-129)gTg>gCg	p.V43A		NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	43			V -> A (in dbSNP:rs3752362).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CAGGCTGTACACAGGCGGCTC	0.751													N|||	2672	0.707815	0.736	0.4856	3775	,	,		7851	0.6944		0.2644	False		,,,				2504	0.4049				p.V43A		Atlas-SNP	.											.	PRKX	29	.	0			c.T128C						PASS	.	G	ALA/VAL	3226,436		1253,279,441,50,57	6.0	5.0	6.0		128	-0.4	0.0	X	dbSNP_107	6	2368,4079		373,1000,622,979,1121	yes	missense	PRKX	NM_005044.4	64	1626,1279,1063,1029,1178	GG,GA,G,AA,A		36.7303,11.9061,44.6632	benign	43/359	3631167	5594,4515	2080	4095	6175	SO:0001583	missense	5613	exon1			CTGTACACAGGCG		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.128T>C	X.37:g.3631167A>G	ENSP00000262848:p.Val43Ala	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	37	CCDS14125.1	1097	0.6612417118746232	255	0.8673469387755102	120	0.47619047619047616	261	0.8474025974025974	133	0.20336391437308868	G	2.016	-0.425905	0.04701	0.880939	0.367303	ENSG00000183943	ENST00000262848	T	0.07908	3.15	1.08	-0.453	0.12201	Protein kinase-like domain (1);	0.957488	0.08497	N	0.937090	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	0.07908	-1.0748	9	0.38643	T	0.18	.	1.5859	0.02644	0.284:0.0:0.3851:0.3309	rs3752362;rs57248025	43	P51817	PRKX_HUMAN	A	43	ENSP00000262848:V43A	ENSP00000262848:V43A	V	-	2	0	PRKX	3641167	0.007000	0.16637	0.001000	0.08648	0.016000	0.09150	-0.380000	0.07427	-0.338000	0.08413	-0.697000	0.03683	GTG	A|0.340;G|0.660	0.660	strong		0.751	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
IL4R	3566	hgsc.bcm.edu	37	16	27356203	27356203	+	Missense_Mutation	SNP	A	A	G	rs1805010	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:27356203A>G	ENST00000395762.2	+	5	482	c.223A>G	c.(223-225)Atc>Gtc	p.I75V	IL4R_ENST00000380922.3_Missense_Mutation_p.I60V|IL4R_ENST00000170630.2_Missense_Mutation_p.I75V|IL4R_ENST00000449195.1_Missense_Mutation_p.I75V|IL4R_ENST00000543915.2_Missense_Mutation_p.I75V	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	75			I -> F (in dbSNP:rs1805010).|I -> L (in dbSNP:rs1805010).|I -> V (associated with atopic asthma and cedar pollen sensitization; dbSNP:rs1805010). {ECO:0000269|PubMed:10390422, ECO:0000269|PubMed:14657871, ECO:0000269|PubMed:9070874, ECO:0000269|PubMed:9620765, 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						CCACACGTGTATCCCTGAGAA	0.632													G|||	2286	0.45647	0.4811	0.4251	5008	,	,		15543	0.5159		0.4254	False		,,,				2504	0.4162				p.I75V		Atlas-SNP	.											.	IL4R	70	.	0			c.A223G	GRCh37	CM983400	IL4R	M	rs1805010	PASS	.	G	VAL/ILE,VAL/ILE	2189,2205	589.1+/-387.1	542,1105,550	81.0	66.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	223,223	0.2	0.3	16	dbSNP_89	71	3853,4747	609.8+/-395.6	858,2137,1305	yes	missense,missense	IL4R	NM_000418.2,NM_001008699.1	29,29	1400,3242,1855	GG,GA,AA		44.8023,49.8179,46.4984	benign,benign	75/826,75/228	27356203	6042,6952	2197	4300	6497	SO:0001583	missense	3566	exon5			ACGTGTATCCCTG	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.223A>G	16.37:g.27356203A>G	ENSP00000379111:p.Ile75Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	1019	0.4665750915750916	240	0.4878048780487805	168	0.46408839779005523	296	0.5174825174825175	315	0.4155672823218997	G	0.017	-1.489913	0.01018	0.498179	0.448023	ENSG00000077238	ENST00000380925;ENST00000449195;ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19	3.4	0.172	0.15031	Interleukin-4 receptor alpha chain, N-terminal (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.415690	0.04499	N	0.380973	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	0.04013	0.001;0.001;0.0	T	0.43196	-0.9406	9	0.02654	T	1	-25.804	6.3201	0.21213	0.5679:0.0:0.4321:0.0	rs1805010;rs3024558;rs3116576;rs17513665;rs1805010	60;75;75	B4E076;P24394;P24394-2	.;IL4RA_HUMAN;.	V	75;75;75;75;60;75	ENSP00000410322:I75V;ENSP00000379111:I75V;ENSP00000441667:I75V;ENSP00000370309:I60V;ENSP00000170630:I75V	ENSP00000170630:I75V	I	+	1	0	IL4R	27263704	0.708000	0.27876	0.313000	0.25210	0.013000	0.08279	-0.173000	0.09854	-0.161000	0.10983	-0.642000	0.03964	ATC	A|0.524;G|0.476	0.476	strong		0.632	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
HAUS6	54801	hgsc.bcm.edu	37	9	19058734	19058734	+	Missense_Mutation	SNP	T	T	A	rs143374581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19058734T>A	ENST00000380502.3	-	16	2498	c.2031A>T	c.(2029-2031)gaA>gaT	p.E677D	HAUS6_ENST00000380496.1_Missense_Mutation_p.E541D	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	677					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)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GTGTTGGTGGTTCATCTATGT	0.388													T|||	5	0.000998403	0.0008	0.0	5008	,	,		20270	0.0		0.004	False		,,,				2504	0.0				p.E677D		Atlas-SNP	.											.	HAUS6	66	.	0			c.A2031T						PASS	.	T	ASP/GLU	5,4401	8.1+/-20.4	0,5,2198	111.0	110.0	110.0		2031	0.8	0.0	9	dbSNP_134	110	31,8569	21.0+/-64.5	1,29,4270	yes	missense	HAUS6	NM_017645.3	45	1,34,6468	AA,AT,TT		0.3605,0.1135,0.2768	benign	677/956	19058734	36,12970	2203	4300	6503	SO:0001583	missense	54801	exon16			TGGTGGTTCATCT	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.2031A>T	9.37:g.19058734T>A	ENSP00000369871:p.Glu677Asp	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	269	132	0.490706	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	0.652	-0.808955	0.02819	0.001135	0.003605	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.23552	1.9;1.91	5.06	0.783	0.18572	.	0.637390	0.16626	N	0.206243	T	0.15869	0.0382	L	0.39633	1.23	0.09310	N	0.999993	B;B;B	0.15930	0.009;0.015;0.009	B;B;B	0.16722	0.013;0.016;0.006	T	0.22312	-1.0220	10	0.22109	T	0.4	-2.834	3.737	0.08514	0.1151:0.0783:0.3907:0.4159	.	642;541;677	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	D	677;541	ENSP00000369871:E677D;ENSP00000369865:E541D	ENSP00000369865:E541D	E	-	3	2	HAUS6	19048734	0.000000	0.05858	0.019000	0.16419	0.207000	0.24258	-0.132000	0.10467	0.280000	0.22209	0.383000	0.25322	GAA	T|0.997;A|0.003	0.003	strong		0.388	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
ZNF561	93134	hgsc.bcm.edu	37	19	9721401	9721401	+	Silent	SNP	A	A	T	rs28445940	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9721401A>T	ENST00000302851.3	-	6	1299	c.936T>A	c.(934-936)acT>acA	p.T312T	ZNF561_ENST00000354661.4_Silent_p.T176T|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000424629.1_Silent_p.T243T	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	312					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)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TCCCACAGTAAGTACACTTGT	0.378													T|||	1411	0.281749	0.5	0.3775	5008	,	,		22239	0.0665		0.2107	False		,,,				2504	0.2137				p.T312T		Atlas-SNP	.											.	ZNF561	64	.	0			c.T936A						PASS	.	T		1828,2578	637.6+/-396.8	377,1074,752	134.0	124.0	128.0		936	-2.2	0.0	19	dbSNP_125	128	1704,6896	737.5+/-407.0	170,1364,2766	no	coding-synonymous	ZNF561	NM_152289.2		547,2438,3518	TT,TA,AA		19.814,41.4889,27.1567		312/487	9721401	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	93134	exon6			ACAGTAAGTACAC	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"""Zinc fingers, C2H2-type"", ""-"""	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.936T>A	19.37:g.9721401A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_152289	B4E2Q8|Q6PJS0	Silent	SNP	ENST00000302851.3	37	CCDS12216.2																																																																																			A|0.733;T|0.267	0.267	strong		0.378	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289	
TSC1	7248	hgsc.bcm.edu	37	9	135804239	135804239	+	Silent	SNP	G	G	A	rs145987906		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135804239G>A	ENST00000298552.3	-	3	242	c.21C>T	c.(19-21)gtC>gtT	p.V7V	TSC1_ENST00000545250.1_Silent_p.V7V|TSC1_ENST00000403810.1_Silent_p.V7V|TSC1_ENST00000440111.2_Silent_p.V7V|TSC1_ENST00000475903.1_5'UTR	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	7					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)			NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GAAGCTCCCCGACATTTGCTT	0.527			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.V7V		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	0			c.C21T						PASS	.						104.0	84.0	91.0					9																	135804239		2203	4300	6503	SO:0001819	synonymous_variant	7248	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTCCCCGACATTT	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.21C>T	9.37:g.135804239G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	52	0.634146	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			G|1.000;C|0.000	.	alt		0.527	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
NAPEPLD	222236	hgsc.bcm.edu	37	7	102760511	102760511	+	Missense_Mutation	SNP	A	A	C	rs12540583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102760511A>C	ENST00000417955.1	-	3	608	c.454T>G	c.(454-456)Tct>Gct	p.S152A	NAPEPLD_ENST00000341533.4_Missense_Mutation_p.S152A|NAPEPLD_ENST00000465647.1_Missense_Mutation_p.S152A|NAPEPLD_ENST00000455523.2_Missense_Mutation_p.S225A|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.S152A			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	152			S -> A (in dbSNP:rs12540583).		phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAGCACGAGAGCTAAAGATG	0.502													A|||	841	0.167931	0.0946	0.1844	5008	,	,		13891	0.2768		0.0974	False		,,,				2504	0.2157				p.S152A		Atlas-SNP	.											.	NAPEPLD	49	.	0			c.T454G						PASS	.	A	ALA/SER,ALA/SER	364,4042	185.7+/-212.7	12,340,1851	169.0	132.0	144.0		454,454	-4.7	0.1	7	dbSNP_120	144	890,7710	199.9+/-243.8	51,788,3461	yes	missense,missense	NAPEPLD	NM_001122838.1,NM_198990.4	99,99	63,1128,5312	CC,CA,AA		10.3488,8.2615,9.6417	benign,benign	152/394,152/394	102760511	1254,11752	2203	4300	6503	SO:0001583	missense	222236	exon3			CACGAGAGCTAAA	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"""	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.454T>G	7.37:g.102760511A>C	ENSP00000407112:p.Ser152Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	106	0.972477	NM_001122838	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	347	0.15888278388278387	60	0.12195121951219512	58	0.16022099447513813	159	0.27797202797202797	70	0.09234828496042216	A	13.41	2.228637	0.39399	0.082615	0.103488	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	5.93	-4.69	0.03299	.	0.645957	0.17297	N	0.179417	T	0.00039	0.0001	N	0.25332	0.735	0.48762	P	2.9800000000002047E-4	B;B	0.06786	0.001;0.0	B;B	0.15052	0.012;0.002	T	0.16660	-1.0395	9	0.44086	T	0.13	-5.2249	2.2767	0.04104	0.1181:0.2271:0.3677:0.2871	rs12540583;rs12540583	225;152	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	A	152;152;152;152;225	ENSP00000340093:S152A;ENSP00000407112:S152A;ENSP00000419188:S152A;ENSP00000392775:S152A;ENSP00000414364:S225A	ENSP00000340093:S152A	S	-	1	0	NAPEPLD	102547747	1.000000	0.71417	0.065000	0.19835	0.998000	0.95712	1.650000	0.37292	-0.455000	0.07054	0.482000	0.46254	TCT	A|0.876;C|0.124	0.124	strong		0.502	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990	
NASP	4678	hgsc.bcm.edu	37	1	46078884	46078884	+	Silent	SNP	C	C	T	rs2230659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46078884C>T	ENST00000350030.3	+	7	1557	c.1470C>T	c.(1468-1470)acC>acT	p.T490T	NASP_ENST00000351223.3_Silent_p.T151T|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000372052.4_Silent_p.T124T|NASP_ENST00000537798.1_Silent_p.T426T|NASP_ENST00000402363.3_Silent_p.T492T	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	490	Glu-rich (acidic).|Histone-binding.				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)					ATGATAAGACCGAAGAAATGC	0.373													C|||	3397	0.678315	0.7315	0.6499	5008	,	,		23108	0.6577		0.7177	False		,,,				2504	0.6074				p.T490T		Atlas-SNP	.											.	NASP	77	.	0			c.C1470T						PASS	.	C	,,	3292,1114	714.6+/-408.4	1236,820,147	96.0	96.0	96.0		1278,1470,453	3.4	1.0	1	dbSNP_98	96	6062,2538	690.8+/-404.5	2150,1762,388	no	coding-synonymous,coding-synonymous,coding-synonymous	NASP	NM_001195193.1,NM_002482.3,NM_152298.3	,,	3386,2582,535	TT,TC,CC		29.5116,25.2837,28.0793	,,	426/725,490/789,151/450	46078884	9354,3652	2203	4300	6503	SO:0001819	synonymous_variant	4678	exon7			TAAGACCGAAGAA	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.1470C>T	1.37:g.46078884C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	37	CCDS524.1	1487	0.6808608058608059	350	0.7113821138211383	243	0.6712707182320442	364	0.6363636363636364	530	0.6992084432717678	C	7.632	0.679121	0.14907	0.747163	0.704884	ENSG00000132780	ENST00000531612	.	.	.	5.72	3.39	0.38822	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.30534	-0.9975	3	.	.	.	-1.7389	9.544	0.39268	0.0:0.1394:0.0:0.8606	rs2230659;rs2991982;rs17410392;rs17849728;rs61546022;rs2230659	.	.	.	L	15	.	.	P	+	2	0	NASP	45851471	0.999000	0.42202	1.000000	0.80357	0.822000	0.46500	0.347000	0.20014	0.504000	0.28082	-0.295000	0.09555	CCG	C|0.295;T|0.705	0.705	strong		0.373	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
PRRC2A	7916	hgsc.bcm.edu	37	6	31602967	31602967	+	Missense_Mutation	SNP	G	G	A	rs1046089	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31602967G>A	ENST00000376033.2	+	22	5453	c.5219G>A	c.(5218-5220)cGt>cAt	p.R1740H	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R1740H	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1740	4 X 57 AA type A repeats.		R -> H (in dbSNP:rs1046089). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967, ECO:0000269|Ref.6}.			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						CGATCACAGCGTACAGACCGA	0.622													G|||	1954	0.390176	0.5431	0.3646	5008	,	,		17959	0.3512		0.3449	False		,,,				2504	0.2883				p.R1740H		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G5219A	GRCh37	CM090830	PRRC2A	M	rs1046089	PASS	.	G	HIS/ARG,HIS/ARG	2245,2161	594.2+/-388.2	578,1089,536	85.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5219,5219	5.5	1.0	6	dbSNP_86	83	2971,5629	460.2+/-365.1	516,1939,1845	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	29,29	1094,3028,2381	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.5465,49.0468,40.1046	probably-damaging,probably-damaging	1740/2158,1740/2158	31602967	5216,7790	2203	4300	6503	SO:0001583	missense	7916	exon22			CACAGCGTACAGA	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.5219G>A	6.37:g.31602967G>A	ENSP00000365201:p.Arg1740His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	81	26	0.320988	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	862	0.3946886446886447	262	0.532520325203252	127	0.35082872928176795	202	0.3531468531468531	271	0.3575197889182058	G	15.40	2.822060	0.50739	0.509532	0.345465	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01745	4.66;4.66	5.51	5.51	0.81932	.	0.218848	0.33075	N	0.005319	T	0.01592	0.0051	L	0.36672	1.1	0.27289	P	0.9578908	D	0.52996	0.957	P	0.46339	0.513	T	0.60131	-0.7323	9	0.87932	D	0	0.17	16.4508	0.83990	0.0:0.0:1.0:0.0	rs1046089;rs6913649;rs17207246;rs17845914;rs17857495;rs17858890;rs59917316;rs1046089	1740	P48634	PRC2A_HUMAN	H	1734;1723;1740;1740;965	ENSP00000365175:R1740H;ENSP00000365201:R1740H	ENSP00000365175:R1740H	R	+	2	0	PRRC2A	31710946	0.999000	0.42202	0.983000	0.44433	0.993000	0.82548	3.354000	0.52254	2.873000	0.98535	0.561000	0.74099	CGT	G|0.611;A|0.389	0.389	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
OR52E6	390078	hgsc.bcm.edu	37	11	5862845	5862845	+	Missense_Mutation	SNP	A	A	G	rs4592451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5862845A>G	ENST00000329322.5	-	1	282	c.283T>C	c.(283-285)Tct>Cct	p.S95P	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.S99P	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	95			S -> P (in dbSNP:rs4592451).			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(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTCCAAAAGATATTTCCTTG	0.468													A|||	1923	0.383986	0.3782	0.3184	5008	,	,		22268	0.4593		0.3728	False		,,,				2504	0.3722				p.S95P		Atlas-SNP	.											.	OR52E6	70	.	0			c.T283C						PASS	.	A	PRO/SER	1619,2783	499.1+/-364.3	294,1031,876	134.0	133.0	133.0		283	-4.4	0.0	11	dbSNP_111	133	3009,5583	464.1+/-366.1	533,1943,1820	yes	missense	OR52E6	NM_001005167.1	74	827,2974,2696	GG,GA,AA		35.0209,36.7787,35.6164	possibly-damaging	95/314	5862845	4628,8366	2201	4296	6497	SO:0001583	missense	390078	exon1			CAAAAGATATTTC	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.283T>C	11.37:g.5862845A>G	ENSP00000328878:p.Ser95Pro	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	879	0.4024725274725275	201	0.40853658536585363	120	0.3314917127071823	264	0.46153846153846156	294	0.38786279683377306	A	14.27	2.483961	0.44147	0.367787	0.350209	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.41400	1.0;1.0	3.64	-4.43	0.03568	GPCR, rhodopsin-like superfamily (1);	0.410878	0.20792	N	0.085583	T	0.00012	0.0000	M	0.73598	2.24	0.80722	P	0.0	P	0.48016	0.904	P	0.49597	0.616	T	0.27502	-1.0072	9	0.54805	T	0.06	.	5.397	0.16275	0.2086:0.4033:0.0:0.3881	rs4592451;rs52793358;rs4592451	95	Q96RD3	O52E6_HUMAN	P	95;99	ENSP00000328878:S95P;ENSP00000369279:S99P	ENSP00000328878:S95P	S	-	1	0	OR52E6	5819421	0.000000	0.05858	0.000000	0.03702	0.762000	0.43233	-4.844000	0.00179	-0.345000	0.08325	0.450000	0.29827	TCT	A|0.608;G|0.392	0.392	strong		0.468	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
ZBBX	79740	hgsc.bcm.edu	37	3	167051769	167051769	+	Missense_Mutation	SNP	T	T	C	rs11923054	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167051769T>C	ENST00000392766.2	-	10	873	c.533A>G	c.(532-534)aAa>aGa	p.K178R	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000455345.2_Missense_Mutation_p.K178R|ZBBX_ENST00000392767.2_Missense_Mutation_p.K178R|ZBBX_ENST00000307529.5_Missense_Mutation_p.K178R|ZBBX_ENST00000392764.1_Missense_Mutation_p.K149R	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	47	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	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	
ARHGAP40	343578	hgsc.bcm.edu	37	20	37257590	37257590	+	Silent	SNP	C	C	G	rs6070809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:37257590C>G	ENST00000373345.4	+	4	588	c.420C>G	c.(418-420)ggC>ggG	p.G140G		NM_001164431.1	NP_001157903.1	Q5TG30	RHG40_HUMAN	Rho GTPase activating protein 40	140					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(1)	1						CAGAGAATGGCGACTCCGGTA	0.532																																					p.G192G		Atlas-SNP	.											.	ARHGAP40	50	.	0			c.C576G						PASS	.	G		685,699		159,367,166	63.0	61.0	62.0		576	-4.3	0.0	20	dbSNP_114	62	986,2196		160,666,765	no	coding-synonymous	ARHGAP40	NM_001164431.1		319,1033,931	GG,GC,CC		30.9868,49.4942,36.5966		192/675	37257590	1671,2895	692	1591	2283	SO:0001819	synonymous_variant	343578	exon4			GAATGGCGACTCC	AL035419		20q11.23	2011-06-29	2010-04-14	2010-04-14	ENSG00000124143	ENSG00000124143		"""Rho GTPase activating proteins"""	16226	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 95"""	C20orf95			Standard	NM_001164431		Approved	dJ1100H13.4	uc021wdn.1	Q5TG30	OTTHUMG00000032453	ENST00000373345.4:c.420C>G	20.37:g.37257590C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	165	86	0.521212	NM_001164431		Silent	SNP	ENST00000373345.4	37		674	0.3086080586080586	264	0.5365853658536586	103	0.2845303867403315	85	0.1486013986013986	222	0.2928759894459103	G	4.501	0.092919	0.08632	0.494942	0.309868	ENSG00000124143	ENST00000243967	.	.	.	3.66	-4.34	0.03666	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	9.99999999995449E-6	.	.	.	.	.	.	T	0.42632	-0.9440	3	.	.	.	.	6.6039	0.22714	0.6053:0.1321:0.2626:0.0	rs6070809;rs6070809	.	.	.	G	81	.	.	R	+	1	2	ARHGAP40	36691004	0.000000	0.05858	0.006000	0.13384	0.082000	0.17680	-1.874000	0.01636	-1.319000	0.02286	-0.222000	0.12452	CGA	C|0.699;G|0.301	0.301	strong		0.532	ARHGAP40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_293123	
BRMS1	25855	hgsc.bcm.edu	37	11	66109033	66109033	+	Silent	SNP	T	T	C	rs11537993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:66109033T>C	ENST00000359957.3	-	3	361	c.201A>G	c.(199-201)ctA>ctG	p.L67L	RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Silent_p.L67L	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	67					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						ACTGCTTCTCTAGGTCCAGCA	0.592													T|||	705	0.140775	0.0234	0.17	5008	,	,		21312	0.0327		0.329	False		,,,				2504	0.1963				p.L67L	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.A201G						PASS	.	T	,	297,4103	162.5+/-194.5	13,271,1916	287.0	262.0	270.0		201,201	2.5	1.0	11	dbSNP_120	270	2854,5736	448.6+/-361.9	475,1904,1916	yes	coding-synonymous,coding-synonymous	BRMS1	NM_001024957.1,NM_015399.3	,	488,2175,3832	CC,CT,TT		33.2247,6.75,24.2571	,	67/291,67/247	66109033	3151,9839	2200	4295	6495	SO:0001819	synonymous_variant	25855	exon3			CTTCTCTAGGTCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.201A>G	11.37:g.66109033T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_015399	Q6IAI2	Silent	SNP	ENST00000359957.3	37	CCDS8135.1	346	0.15842490842490842	17	0.034552845528455285	75	0.20718232044198895	18	0.03146853146853147	236	0.3113456464379947	T	8.732	0.916870	0.17907	0.0675	0.332247	ENSG00000174744	ENST00000524699	.	.	.	4.44	2.55	0.30701	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.35674	-0.9779	3	.	.	.	-12.9533	8.2431	0.31671	0.0:0.7956:0.0:0.2044	rs11537993;rs11537993	.	.	.	G	30	.	.	R	-	1	2	BRMS1	65865609	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	1.938000	0.40203	0.608000	0.30000	-0.242000	0.12053	AGA	T|0.796;C|0.204	0.204	strong		0.592	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
DUS4L	11062	hgsc.bcm.edu	37	7	107217020	107217020	+	Missense_Mutation	SNP	G	G	A	rs6957510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:107217020G>A	ENST00000265720.3	+	7	1051	c.689G>A	c.(688-690)cGg>cAg	p.R230Q	RP4-593H12.1_ENST00000610269.1_RNA|DUS4L_ENST00000402620.1_Missense_Mutation_p.R109Q	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	230			R -> Q (in dbSNP:rs6957510).				flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						AATGTGTGGCGGATTACTGGG	0.358													G|||	138	0.0275559	0.0378	0.0202	5008	,	,		18986	0.001		0.0547	False		,,,				2504	0.0184				p.R230Q		Atlas-SNP	.											.	DUS4L	27	.	0			c.G689A						PASS	.	G	GLN/ARG	168,4238	112.1+/-150.2	1,166,2036	53.0	54.0	54.0		689	3.7	1.0	7	dbSNP_116	54	479,8121	138.9+/-195.6	13,453,3834	yes	missense	DUS4L	NM_181581.1	43	14,619,5870	AA,AG,GG		5.5698,3.813,4.9746	benign	230/318	107217020	647,12359	2203	4300	6503	SO:0001583	missense	11062	exon7			TGTGGCGGATTAC	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"""protein similar to E.coli yhdg and R. capsulatus nifR3"""						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.689G>A	7.37:g.107217020G>A	ENSP00000265720:p.Arg230Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001270419	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	37	CCDS5745.1	81	0.03708791208791209	29	0.05894308943089431	8	0.022099447513812154	0	0.0	44	0.05804749340369393	G	11.29	1.596039	0.28445	0.03813	0.055698	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.28255	1.62;1.62	6.01	3.68	0.42216	Aldolase-type TIM barrel (1);	0.418879	0.28273	N	0.015947	T	0.01387	0.0045	N	0.04203	-0.255	0.19775	N	0.999955	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13361	-1.0512	10	0.34782	T	0.22	.	9.9539	0.41655	0.8642:0.0:0.1358:0.0	rs6957510;rs52810758;rs57263488;rs6957510	230;230	A4D0R5;O95620	.;DUS4L_HUMAN	Q	230;109	ENSP00000265720:R230Q;ENSP00000385274:R109Q	ENSP00000265720:R230Q	R	+	2	0	DUS4L	107004256	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.087000	0.57671	1.109000	0.41680	-0.247000	0.11927	CGG	G|0.956;A|0.044	0.044	strong		0.358	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581	
ARFGAP2	84364	hgsc.bcm.edu	37	11	47185680	47185680	+	IGR	SNP	G	G	A	rs11039114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47185680G>A	ENST00000524782.1	-	0	2976				ARFGAP2_ENST00000395449.3_5'Flank|C11orf49_ENST00000378618.2_Silent_p.Q286Q	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CCTCACGGCAGCACAGAGCCA	0.607													G|||	776	0.154952	0.0174	0.1254	5008	,	,		17888	0.0744		0.2276	False		,,,				2504	0.3701				p.Q286Q		Atlas-SNP	.											.	C11orf49	41	.	0			c.G858A						PASS	.	G		211,4191	129.4+/-166.1	6,199,1996	57.0	56.0	56.0		858	5.3	1.0	11	dbSNP_120	56	1916,6682	339.0+/-323.0	196,1524,2579	no	coding-synonymous	C11orf49	NM_001003678.1		202,1723,4575	AA,AG,GG		22.2843,4.7933,16.3615		286/327	47185680	2127,10873	2201	4299	6500	SO:0001628	intergenic_variant	79096	exon9			ACGGCAGCACAGA	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"""ADP-ribosylation factor GTPase activating proteins"""	13504	protein-coding gene	gene with protein product		606908	"""zinc finger protein 289, ID1 regulated"""	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773		11.37:g.47185680G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001003678	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Silent	SNP	ENST00000524782.1	37	CCDS7926.1																																																																																			G|0.847;A|0.153	0.153	strong		0.607	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389	
AMZ1	155185	hgsc.bcm.edu	37	7	2752487	2752487	+	Missense_Mutation	SNP	G	G	A	rs7776970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	91	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	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	
PARP4	143	hgsc.bcm.edu	37	13	25016008	25016008	+	Silent	SNP	C	C	T	rs59195808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25016008C>T	ENST00000381989.3	-	30	3747	c.3642G>A	c.(3640-3642)gaG>gaA	p.E1214E		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1214					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)		CTTCTTGGGGCTCCCCCTGCC	0.433																																					p.E1214E		Atlas-SNP	.											.	PARP4	142	.	0			c.G3642A						PASS	.						50.0	52.0	52.0					13																	25016008		2203	4298	6501	SO:0001819	synonymous_variant	143	exon30			TTGGGGCTCCCCC	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.3642G>A	13.37:g.25016008C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			.	.	weak		0.433	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
EGF	1950	hgsc.bcm.edu	37	4	110901198	110901198	+	Missense_Mutation	SNP	G	G	A	rs2237051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:110901198G>A	ENST00000265171.5	+	14	2569	c.2124G>A	c.(2122-2124)atG>atA	p.M708I	EGF_ENST00000503392.1_Missense_Mutation_p.M708I|EGF_ENST00000509793.1_Missense_Mutation_p.M666I	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	137	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	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		
OR51I1	390063	hgsc.bcm.edu	37	11	5462085	5462085	+	Silent	SNP	G	G	A	rs11037444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5462085G>A	ENST00000380211.1	-	1	659	c.660C>T	c.(658-660)taC>taT	p.Y220Y	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_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	120	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	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	
GAS8	2622	hgsc.bcm.edu	37	16	90102835	90102835	+	Silent	SNP	A	A	G	rs868045	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:90102835A>G	ENST00000268699.4	+	6	719	c.597A>G	c.(595-597)gaA>gaG	p.E199E	GAS8_ENST00000536122.1_Silent_p.E174E|GAS8_ENST00000540721.1_3'UTR	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	199	Microtubule-binding.		E -> K (in dbSNP:rs868044).		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)		TGAGGGACGAACTCGACTTGC	0.542													G|||	1324	0.264377	0.3933	0.2493	5008	,	,		22057	0.0079		0.3907	False		,,,				2504	0.2352				p.E199E		Atlas-SNP	.											.	GAS8	29	.	0			c.A597G						PASS	.	G		1719,2677	648.6+/-398.7	337,1045,816	107.0	91.0	97.0		597	1.3	0.4	16	dbSNP_86	97	3532,5068	631.5+/-398.5	725,2082,1493	no	coding-synonymous	GAS8	NM_001481.2		1062,3127,2309	GG,GA,AA		41.0698,39.1037,40.4047		199/479	90102835	5251,7745	2198	4300	6498	SO:0001819	synonymous_variant	2622	exon6			GGACGAACTCGAC	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.597A>G	16.37:g.90102835A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			A|0.644;G|0.356	0.356	strong		0.542	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
GPER1	2852	hgsc.bcm.edu	37	7	1132384	1132384	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1132384G>A	ENST00000297469.3	+	2	1711	c.1020G>A	c.(1018-1020)gaG>gaA	p.E340E	GPER1_ENST00000397088.3_Silent_p.E340E|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000401670.1_Silent_p.E340E|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000397092.1_Silent_p.E340E|C7orf50_ENST00000397100.2_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	340					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)										TGTACATTGAGCAGAAAACAA	0.557																																					p.E340E		Atlas-SNP	.											.	GPER	25	.	0			c.G1020A						PASS	.						93.0	76.0	82.0					7																	1132384		2203	4300	6503	SO:0001819	synonymous_variant	2852	exon2			CATTGAGCAGAAA	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.1020G>A	7.37:g.1132384G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	174	64	0.367816	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			.	.	none		0.557	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
NSUN5	55695	hgsc.bcm.edu	37	7	72721583	72721583	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72721583G>T	ENST00000252594.6	-	3	403	c.388C>A	c.(388-390)Cca>Aca	p.P130T	NSUN5_ENST00000438747.2_Missense_Mutation_p.P130T|NSUN5_ENST00000428206.1_Missense_Mutation_p.P92T|NSUN5_ENST00000310326.8_Missense_Mutation_p.P130T			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	130					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				AGCTTACCTGGACCAGGCCTG	0.627																																					p.P130T		Atlas-SNP	.											.	NSUN5	47	.	0			c.C388A						PASS	.						65.0	54.0	58.0					7																	72721583		2203	4300	6503	SO:0001583	missense	55695	exon3			TACCTGGACCAGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.388C>A	7.37:g.72721583G>T	ENSP00000252594:p.Pro130Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	62	4	0.0645161	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	.	.	.	.	.	.	.	.	.	.	G	0.150	-1.092733	0.01858	.	.	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.13901	2.55;2.57;2.78;2.77	4.18	-3.05	0.05396	.	1.150850	0.06151	N	0.674063	T	0.08802	0.0218	L	0.39397	1.21	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.0;0.002	T	0.40869	-0.9540	10	0.12430	T	0.62	.	3.4709	0.07567	0.2185:0.4119:0.2641:0.1055	.	130;92;130;130	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	T	92;130;130;130	ENSP00000393081:P92T;ENSP00000252594:P130T;ENSP00000388464:P130T;ENSP00000309126:P130T	ENSP00000252594:P130T	P	-	1	0	NSUN5	72359519	0.000000	0.05858	0.036000	0.18154	0.102000	0.19082	-0.935000	0.03950	-0.472000	0.06881	-0.350000	0.07774	CCA	.	.	none		0.627	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
LRRC61	65999	hgsc.bcm.edu	37	7	150034378	150034378	+	Missense_Mutation	SNP	A	A	G	rs3735169	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150034378A>G	ENST00000359623.4	+	3	1016	c.428A>G	c.(427-429)aAc>aGc	p.N143S	LRRC61_ENST00000323078.7_Missense_Mutation_p.N143S|LRRC61_ENST00000493307.1_Missense_Mutation_p.N143S	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	143	LRRCT.		N -> S (in dbSNP:rs3735169). {ECO:0000269|PubMed:14702039}.							endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			CTCTGTGCCAACCCCTCCTAC	0.657													G|||	1294	0.258387	0.2625	0.1571	5008	,	,		18703	0.2897		0.2455	False		,,,				2504	0.3057				p.N143S		Atlas-SNP	.											.	LRRC61	17	.	0			c.A428G						PASS	.	G	SER/ASN,SER/ASN	1076,3330	719.7+/-409.0	128,820,1255	57.0	57.0	57.0		428,428	0.7	0.1	7	dbSNP_107	57	2198,6402	709.9+/-405.7	286,1626,2388	yes	missense,missense	LRRC61	NM_001142928.1,NM_023942.2	46,46	414,2446,3643	GG,GA,AA		25.5581,24.4212,25.173	benign,benign	143/260,143/260	150034378	3274,9732	2203	4300	6503	SO:0001583	missense	65999	exon2			GTGCCAACCCCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.428A>G	7.37:g.150034378A>G	ENSP00000352642:p.Asn143Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_023942	B3KUW0|D3DWY8	Missense_Mutation	SNP	ENST00000359623.4	37	CCDS5901.1	572	0.2619047619047619	118	0.23983739837398374	66	0.18232044198895028	182	0.3181818181818182	206	0.2717678100263852	G	0.012	-1.649709	0.00785	0.244212	0.255581	ENSG00000127399	ENST00000323078;ENST00000359623;ENST00000493307	T;T;T	0.22945	1.93;1.93;1.93	3.82	0.741	0.18336	.	0.276635	0.36591	N	0.002504	T	0.00012	0.0000	N	0.02158	-0.66	0.48452	P	3.429999999999822E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48352	-0.9043	9	0.18710	T	0.47	-7.5883	7.2278	0.26026	0.4766:0.0:0.5234:0.0	rs3735169;rs57401595;rs3735169	143	Q9BV99	LRC61_HUMAN	S	143	ENSP00000339047:N143S;ENSP00000352642:N143S;ENSP00000420560:N143S	ENSP00000339047:N143S	N	+	2	0	LRRC61	149665311	0.000000	0.05858	0.095000	0.20976	0.498000	0.33706	-0.123000	0.10611	-0.314000	0.08716	-0.665000	0.03846	AAC	A|0.744;G|0.256	0.256	strong		0.657	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
PTK2	5747	hgsc.bcm.edu	37	8	141685537	141685537	+	Intron	SNP	G	G	A	rs191246950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141685537G>A	ENST00000522684.1	-	28	2832				PTK2_ENST00000535192.1_Intron|PTK2_ENST00000521059.1_Intron|PTK2_ENST00000538769.1_Intron|PTK2_ENST00000430260.2_Intron|PTK2_ENST00000519465.1_Intron|PTK2_ENST00000517887.1_Intron|PTK2_ENST00000340930.3_Missense_Mutation_p.A875V|PTK2_ENST00000519419.1_Intron|PTK2_ENST00000395218.2_Missense_Mutation_p.A875V	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2						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)			ACTTCTTTCCGCCCAATTCTT	0.368													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19290	0.0		0.003	False		,,,				2504	0.0				p.A875V		Atlas-SNP	.											.	PTK2	311	.	0			c.C2624T						PASS	.	G	VAL/ALA,,	0,4406		0,0,2203	187.0	161.0	170.0		2624,,	-0.7	0.0	8		170	3,8595	3.0+/-9.4	0,3,4296	yes	missense,intron,intron	PTK2	NM_001199649.1,NM_005607.4,NM_153831.3	64,,	0,3,6499	AA,AG,GG		0.0349,0.0,0.0231	,,	875/1066,,	141685537	3,13001	2203	4299	6502	SO:0001627	intron_variant	5747	exon28			CTTTCCGCCCAAT	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.2602+21C>T	8.37:g.141685537G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	54	0.409091	NM_001199649	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	7.078	0.569753	0.13560	0.0	3.49E-4	ENSG00000169398	ENST00000395218;ENST00000340930	T;T	0.75589	-0.95;-0.93	4.39	-0.655	0.11439	.	.	.	.	.	T	0.53449	0.1797	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32455	-0.9906	8	0.28530	T	0.3	.	3.7898	0.08715	0.4383:0.2078:0.3539:0.0	.	875	B4E2N6	.	V	875	ENSP00000378644:A875V;ENSP00000341189:A875V	ENSP00000341189:A875V	A	-	2	0	PTK2	141754719	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.330000	0.07925	0.005000	0.14708	-0.302000	0.09304	GCG	G|0.998;A|0.002	0.002	strong		0.368	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
SHROOM3	57619	hgsc.bcm.edu	37	4	77662486	77662486	+	Missense_Mutation	SNP	G	G	T	rs71607374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77662486G>T	ENST00000296043.6	+	5	4113	c.3160G>T	c.(3160-3162)Gtg>Ttg	p.V1054L		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1054					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GGAGAGCAGCGTGGCCGACCG	0.687													G|||	189	0.0377396	0.031	0.0375	5008	,	,		11140	0.005		0.0905	False		,,,				2504	0.0266				p.V1054L		Atlas-SNP	.											SHROOM3,NS,carcinoma,0,1	SHROOM3	134	1	0			c.G3160T						PASS	.	G	LEU/VAL	145,4259		3,139,2060	17.0	18.0	18.0		3160	3.1	0.1	4	dbSNP_130	18	779,7817		33,713,3552	yes	missense	SHROOM3	NM_020859.3	32	36,852,5612	TT,TG,GG		9.0624,3.2925,7.1077	probably-damaging	1054/1997	77662486	924,12076	2202	4298	6500	SO:0001583	missense	57619	exon5			AGCAGCGTGGCCG	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.3160G>T	4.37:g.77662486G>T	ENSP00000296043:p.Val1054Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	107	0.04899267399267399	25	0.0508130081300813	17	0.04696132596685083	2	0.0034965034965034965	63	0.08311345646437995	G	12.89	2.074449	0.36566	0.032925	0.090624	ENSG00000138771	ENST00000296043	T	0.47528	0.84	4.91	3.11	0.35812	Apx/shroom, ASD1 (1);	0.896159	0.09325	N	0.817696	T	0.02929	0.0087	M	0.64404	1.975	0.31938	P	0.611326	P;B;B	0.39831	0.69;0.446;0.446	B;B;B	0.41466	0.358;0.257;0.257	T	0.23190	-1.0195	9	0.66056	D	0.02	-8.2468	11.3605	0.49640	0.0:0.1375:0.7195:0.143	.	878;1054;832	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	L	1054	ENSP00000296043:V1054L	ENSP00000296043:V1054L	V	+	1	0	SHROOM3	77881510	1.000000	0.71417	0.135000	0.22099	0.004000	0.04260	4.682000	0.61671	0.432000	0.26286	0.563000	0.77884	GTG	G|0.935;T|0.065	0.065	strong		0.687	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
FAT1	2195	hgsc.bcm.edu	37	4	187517758	187517758	+	Silent	SNP	G	G	A	rs3822060	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187517758G>A	ENST00000441802.2	-	25	13145	c.12936C>T	c.(12934-12936)ccC>ccT	p.P4312P	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4312					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGTTTGAAGGGGGTGGGGGAG	0.547										HNSCC(5;0.00058)			G|||	278	0.0555112	0.0023	0.1066	5008	,	,		15389	0.1538		0.0348	False		,,,				2504	0.0112				p.P4312P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C12936T						PASS	.	G		31,4093		0,31,2031	42.0	47.0	45.0		12936	-10.7	0.0	4	dbSNP_107	45	253,8155		3,247,3954	no	coding-synonymous	FAT1	NM_005245.3		3,278,5985	AA,AG,GG		3.009,0.7517,2.2662		4312/4589	187517758	284,12248	2062	4204	6266	SO:0001819	synonymous_variant	2195	exon25			TGAAGGGGGTGGG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12936C>T	4.37:g.187517758G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1	157	0.07188644688644688	2	0.0040650406504065045	23	0.06353591160220995	101	0.17657342657342656	31	0.040897097625329816	G	0.015	-1.543438	0.00934	0.007517	0.03009	ENSG00000083857	ENST00000512772	.	.	.	5.37	-10.7	0.00240	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999743339	.	.	.	.	.	.	T	0.56165	-0.8024	5	0.07325	T	0.83	.	9.8232	0.40896	0.1357:0.4098:0.3872:0.0672	rs3822060	.	.	.	S	80	.	ENSP00000424157:P80S	P	-	1	0	FAT1	187754752	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.133000	0.01308	-6.898000	0.00002	-3.755000	0.00021	CCC	G|0.938;A|0.062	0.062	strong		0.547	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609249	84609249	+	Silent	SNP	A	A	T	rs116948895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84609249A>T	ENST00000344803.2	+	4	3911	c.3864A>T	c.(3862-3864)ccA>ccT	p.P1288P		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1288					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CGAATTTCCCACCAGCTGTAA	0.557													A|||	30	0.00599042	0.0	0.0043	5008	,	,		18184	0.005		0.0149	False		,,,				2504	0.0072				p.P1288P		Atlas-SNP	.											.	.	.	.	0			c.A3864T						PASS	.	A		15,3903		0,15,1944	44.0	45.0	44.0		3864	-3.8	0.0	9	dbSNP_132	44	76,8228		1,74,4077	no	coding-synonymous	FAM75D1	NM_001001670.2		1,89,6021	TT,TA,AA		0.9152,0.3828,0.7446		1288/1577	84609249	91,12131	1959	4152	6111	SO:0001819	synonymous_variant	389763	exon4			TTTCCCACCAGCT		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.3864A>T	9.37:g.84609249A>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			A|0.993;T|0.007	0.007	strong		0.557	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39261693A>T	ENST00000391415.1	+	1	110	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.D18V(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						TGCGGCCAAGACCTCTGTCAG	0.627																																					p.D18V		Atlas-SNP	.											KRTAP4-9,NS,carcinoma,0,6	KRTAP4-9	110	6	1	Substitution - Missense(1)	endometrium(1)	c.A53T						scavenged	.						18.0	22.0	21.0					17																	39261693		692	1590	2282	SO:0001583	missense	100132386	exon1			GCCAAGACCTCTG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.53A>T	17.37:g.39261693A>T	ENSP00000375234:p.Asp18Val	Somatic	41	5	0.121951		WXS	Illumina HiSeq	Phase_I	37	7	0.189189	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	6.082	0.383461	0.11524	.	.	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32272	1.46	2.51	0.174	0.15040	.	.	.	.	.	T	0.25865	0.0630	M	0.64404	1.975	0.30580	P	0.762648	B	0.17852	0.024	B	0.14023	0.01	T	0.23154	-1.0196	8	0.45353	T	0.12	.	3.5681	0.07907	0.2702:0.2037:0.5261:0.0	.	18	Q9BYQ8	KRA49_HUMAN	V	18	ENSP00000375234:D18V	ENSP00000334461:D18V	D	+	2	0	KRTAP4-9	36515219	0.000000	0.05858	0.388000	0.26195	0.320000	0.28249	0.098000	0.15189	-0.245000	0.09625	0.155000	0.16302	GAC	T|1.000;|0.000	1.000	weak		0.627	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
FLG	2312	hgsc.bcm.edu	37	1	152280864	152280864	+	Silent	SNP	A	A	G	rs2184954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280864A>G	ENST00000368799.1	-	3	6533	c.6498T>C	c.(6496-6498)tcT>tcC	p.S2166S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2166	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)			GGCTGTGATGAGACCCTGAGT	0.557									Ichthyosis				-|||	2322	0.463658	0.5204	0.4524	5008	,	,		24600	0.6577		0.172	False		,,,				2504	0.4949				p.S2166S		Atlas-SNP	.											.	FLG	900	.	0			c.T6498C						PASS	.	G		2056,2350	607.5+/-391.0	471,1114,618	381.0	336.0	351.0		6498	-4.8	0.0	1	dbSNP_96	351	1453,7145	750.6+/-407.4	125,1203,2971	no	coding-synonymous	FLG	NM_002016.1		596,2317,3589	GG,GA,AA		16.8993,46.6636,26.984		2166/4062	152280864	3509,9495	2203	4299	6502	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGATGAGACCCT	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.6498T>C	1.37:g.152280864A>G		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	287	203	0.707317	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LGALS9	3965	hgsc.bcm.edu	37	17	25958304	25958304	+	Missense_Mutation	SNP	G	G	A	rs3751093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:25958304G>A	ENST00000395473.2	+	1	1481	c.13G>A	c.(13-15)Ggt>Agt	p.G5S	LGALS9_ENST00000448970.2_3'UTR|AC015688.3_ENST00000584605.1_Intron|LGALS9_ENST00000413914.2_5'UTR|LGALS9_ENST00000313648.6_Missense_Mutation_p.G5S|LGALS9_ENST00000310394.5_Missense_Mutation_p.G5S|LGALS9_ENST00000302228.5_Missense_Mutation_p.G5S	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	5			G -> S (in dbSNP:rs3751093). {ECO:0000269|PubMed:9642261, ECO:0000269|Ref.7}.		positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		GGCCTTCAGCGGTTCCCAGGC	0.577													G|||	1014	0.202476	0.1014	0.2767	5008	,	,		14825	0.2331		0.2008	False		,,,				2504	0.2566				p.G5S	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.G13A						PASS	.	G	SER/GLY,SER/GLY	568,3838	252.1+/-258.6	45,478,1680	68.0	67.0	67.0		13,13	-5.4	0.0	17	dbSNP_107	67	1808,6792	325.0+/-316.7	220,1368,2712	yes	missense,missense	LGALS9	NM_002308.3,NM_009587.2	56,56	265,1846,4392	AA,AG,GG		21.0233,12.8915,18.2685	benign,benign	5/324,5/356	25958304	2376,10630	2203	4300	6503	SO:0001583	missense	3965	exon1			TTCAGCGGTTCCC	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.13G>A	17.37:g.25958304G>A	ENSP00000378856:p.Gly5Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	170	77	0.452941	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	431	0.19734432234432234	45	0.09146341463414634	97	0.26795580110497236	143	0.25	146	0.19261213720316622	G	8.369	0.834917	0.16820	0.128915	0.210233	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394;ENST00000313648;ENST00000448970	T;T;T;T	0.03801	4.02;3.99;3.97;3.8	2.8	-5.36	0.02689	.	1.415160	0.04312	N	0.349115	T	0.00012	0.0000	N	0.11064	0.09	0.51482	P	7.100000000004325E-5	B;B;B	0.14012	0.009;0.003;0.0	B;B;B	0.15052	0.012;0.001;0.001	T	0.46569	-0.9182	9	0.08381	T	0.77	.	1.5284	0.02530	0.2392:0.1671:0.4281:0.1657	rs3751093;rs3751093	5;5;5	F8W9W4;Q3B8N1;O00182	.;.;LEG9_HUMAN	S	5	ENSP00000378856:G5S;ENSP00000306228:G5S;ENSP00000312259:G5S;ENSP00000318214:G5S	ENSP00000306228:G5S	G	+	1	0	LGALS9	22982431	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.980000	0.00663	-1.287000	0.02381	-0.217000	0.12591	GGT	G|0.811;A|0.189	0.189	strong		0.577	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
LMBR1	64327	hgsc.bcm.edu	37	7	156554830	156554830	+	Missense_Mutation	SNP	T	T	C	rs6957768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:156554830T>C	ENST00000353442.5	-	8	918	c.682A>G	c.(682-684)Aca>Gca	p.T228A	LMBR1_ENST00000354505.4_Missense_Mutation_p.T228A|LMBR1_ENST00000540390.1_Missense_Mutation_p.T207A|LMBR1_ENST00000359422.4_Missense_Mutation_p.T76A	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	228			T -> A (in dbSNP:rs6957768).		embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		ataCTTACTGTTGGCTTCACT	0.333													T|||	449	0.0896565	0.0938	0.0706	5008	,	,		16386	0.1339		0.0736	False		,,,				2504	0.0685				p.T228A		Atlas-SNP	.											.	LMBR1	35	.	0			c.A682G						PASS	.	T	ALA/THR	423,3983	205.2+/-227.1	21,381,1801	58.0	55.0	56.0		682	-5.4	0.7	7	dbSNP_116	56	453,8147	135.2+/-192.5	16,421,3863	yes	missense	LMBR1	NM_022458.3	58	37,802,5664	CC,CT,TT		5.2674,9.6005,6.7354	benign	228/491	156554830	876,12130	2203	4300	6503	SO:0001583	missense	64327	exon8			TTACTGTTGGCTT	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.682A>G	7.37:g.156554830T>C	ENSP00000326604:p.Thr228Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Missense_Mutation	SNP	ENST00000353442.5	37	CCDS5945.1	214	0.09798534798534798	49	0.09959349593495935	28	0.07734806629834254	83	0.1451048951048951	54	0.0712401055408971	T	9.680	1.149069	0.21288	0.096005	0.052674	ENSG00000105983	ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	4.79	-5.42	0.02640	LMBR1-like membrane protein (1);	0.159012	0.64402	N	0.000020	T	0.00109	0.0003	L	0.36672	1.1	0.22457	P	0.999086621	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.14023	0.01;0.004;0.009	T	0.22906	-1.0203	9	0.19147	T	0.46	0.0	12.3304	0.55035	0.0:0.4568:0.0:0.5432	rs6957768;rs52829970;rs59491940;rs6957768	207;228;228	B7Z633;Q8WVP7-3;Q8WVP7	.;.;LMBR1_HUMAN	A	228;76;226;228;207	ENSP00000326604:T228A;ENSP00000352392:T76A;ENSP00000408256:T226A;ENSP00000346500:T228A;ENSP00000445509:T207A	ENSP00000326604:T228A	T	-	1	0	LMBR1	156247591	0.994000	0.37717	0.725000	0.30721	0.996000	0.88848	1.004000	0.29822	-1.340000	0.02227	0.482000	0.46254	ACA	T|0.914;C|0.086	0.086	strong		0.333	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
CALML3	810	hgsc.bcm.edu	37	10	5567366	5567366	+	Silent	SNP	G	G	A	rs1142825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5567366G>A	ENST00000315238.1	+	1	443	c.318G>A	c.(316-318)ctG>ctA	p.L106L	CALML3-AS1_ENST00000542093.1_RNA|CALML3-AS1_ENST00000545372.1_RNA|CALML3-AS1_ENST00000543008.1_RNA|RP11-116G8.5_ENST00000442008.2_RNA	NM_005185.2	NP_005176.1	P27482	CALL3_HUMAN	calmodulin-like 3	106	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			endometrium(3)|lung(2)	5						CCGCCGAGCTGCGACACGTCA	0.647													G|||	2095	0.418331	0.5076	0.3156	5008	,	,		15693	0.6091		0.2455	False		,,,				2504	0.3517				p.L106L	Colon(173;2070 2647 27580 52203)	Atlas-SNP	.											.	CALML3	12	.	0			c.G318A						PASS	.	G		2067,2339	564.2+/-381.4	482,1103,618	76.0	58.0	64.0		318	1.8	1.0	10	dbSNP_86	64	2114,6486	359.3+/-331.5	259,1596,2445	no	coding-synonymous	CALML3	NM_005185.2		741,2699,3063	AA,AG,GG		24.5814,46.9133,32.1467		106/150	5567366	4181,8825	2203	4300	6503	SO:0001819	synonymous_variant	810	exon1			CGAGCTGCGACAC	X13461	CCDS7069.1	10p15.1	2013-01-10			ENSG00000178363	ENSG00000178363		"""EF-hand domain containing"""	1452	protein-coding gene	gene with protein product		114184				8476923	Standard	NM_005185		Approved	CLP	uc001iie.1	P27482	OTTHUMG00000017597	ENST00000315238.1:c.318G>A	10.37:g.5567366G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	45	16	0.355556	NM_005185	B2R9V6|Q5SQI4	Silent	SNP	ENST00000315238.1	37	CCDS7069.1																																																																																			G|0.641;A|0.359	0.359	strong		0.647	CALML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046555.1	NM_005185	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505141	37505141	+	Missense_Mutation	SNP	G	G	A	rs1200876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:37505141G>A	ENST00000602533.1	+	32	2833	c.2734G>A	c.(2734-2736)Gtt>Att	p.V912I	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.V912I|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.V1031I			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	111	0	0		WXS	Illumina HiSeq	Phase_I	89	55	0.617977	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	
SYNE2	23224	hgsc.bcm.edu	37	14	64469828	64469828	+	Missense_Mutation	SNP	C	C	T	rs17751301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64469828C>T	ENST00000344113.4	+	30	4389	c.4177C>T	c.(4177-4179)Cgg>Tgg	p.R1393W	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.R1393W|SYNE2_ENST00000358025.3_Missense_Mutation_p.R1393W	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1393			R -> W (in dbSNP:rs17751301).		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGATGCTGAACGGGGTGATGA	0.388													C|||	128	0.0255591	0.0038	0.0836	5008	,	,		18118	0.0		0.0477	False		,,,				2504	0.0174				p.R1393W		Atlas-SNP	.											.	SYNE2	577	.	0			c.C4177T						PASS	.	C	TRP/ARG,TRP/ARG	49,3653		0,49,1802	100.0	91.0	94.0		4177,4177	-3.2	0.0	14	dbSNP_123	94	580,7624		21,538,3543	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	101,101	21,587,5345	TT,TC,CC		7.0697,1.3236,5.2831	possibly-damaging,possibly-damaging	1393/6886,1393/6908	64469828	629,11277	1851	4102	5953	SO:0001583	missense	23224	exon30			GCTGAACGGGGTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.4177C>T	14.37:g.64469828C>T	ENSP00000341781:p.Arg1393Trp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	69	0.03159340659340659	1	0.0020325203252032522	29	0.08011049723756906	1	0.0017482517482517483	38	0.05013192612137203	C	0.837	-0.743245	0.03088	0.013236	0.070697	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57107	0.79;0.79;0.42	5.51	-3.22	0.05125	.	2.688840	0.01173	N	0.006902	T	0.02571	0.0078	L	0.36672	1.1	0.09310	N	0.999997	B;B	0.09022	0.001;0.002	B;B	0.04013	0.0;0.001	T	0.12192	-1.0557	10	0.62326	D	0.03	.	2.7479	0.05272	0.1022:0.3524:0.1367:0.4086	rs17751301;rs52835345;rs17751301	1393;1393	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	W	1393	ENSP00000350719:R1393W;ENSP00000341781:R1393W;ENSP00000452570:R1393W	ENSP00000261678:R1393W	R	+	1	2	SYNE2	63539581	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.053000	0.03500	-0.605000	0.05753	-0.907000	0.02831	CGG	C|0.961;T|0.039	0.039	strong		0.388	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
ZP3	7784	hgsc.bcm.edu	37	7	76069881	76069881	+	Missense_Mutation	SNP	A	A	G	rs2906998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76069881A>G	ENST00000394857.3	+	7	1071	c.1013A>G	c.(1012-1014)cAt>cGt	p.H338R	ZP3_ENST00000336517.4_Missense_Mutation_p.H287R|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.H162R	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	338					binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						AGGCAGCCTCATGTCATGAGC	0.537																																					p.H338R		Atlas-SNP	.											.	ZP3	32	.	0			c.A1013G						PASS	.						132.0	128.0	130.0					7																	76069881		2203	4300	6503	SO:0001583	missense	7784	exon7			AGCCTCATGTCAT	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1013A>G	7.37:g.76069881A>G	ENSP00000378326:p.His338Arg	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	179	14	0.0782123	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	9.044|9.044	0.990333|0.990333	0.18966|0.18966	.|.	.|.	ENSG00000188372|ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245|ENST00000394860	T;T;T|.	0.21031|.	2.61;2.82;2.03|.	4.68|4.68	-7.24|-7.24	0.01475|0.01475	.|.	1.306680|.	0.05708|.	N|.	0.595475|.	T|T	0.32912|0.32912	0.0845|0.0845	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.005;0.001|.	B;B|.	0.13407|.	0.009;0.001|.	T|T	0.38908|0.38908	-0.9639|-0.9639	10|5	0.23891|.	T|.	0.37|.	2.8954|2.8954	3.3471|3.3471	0.07139|0.07139	0.1819:0.4453:0.2607:0.1121|0.1819:0.4453:0.2607:0.1121	rs2906998|rs2906998	287;338|.	P21754-3;P21754|.	.;ZP3_HUMAN|.	R|V	287;338;338;162|172	ENSP00000337310:H287R;ENSP00000378326:H338R;ENSP00000411955:H162R|.	ENSP00000337310:H287R|.	H|M	+|+	2|1	0|0	ZP3|ZP3	75907817|75907817	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	-1.122000|-1.122000	0.03267|0.03267	-1.144000|-1.144000	0.02862|0.02862	0.459000|0.459000	0.35465|0.35465	CAT|ATG	A|0.885;G|0.115	0.115	strong		0.537	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
DDRGK1	65992	hgsc.bcm.edu	37	20	3180666	3180666	+	Missense_Mutation	SNP	C	C	A	rs35327491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3180666C>A	ENST00000354488.3	-	4	548	c.491G>T	c.(490-492)cGc>cTc	p.R164L	DDRGK1_ENST00000380201.2_Missense_Mutation_p.R164L	NM_023935.1	NP_076424.1	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1	164						endoplasmic reticulum (GO:0005783)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7						CTCCTCCAGGCGAAGCCGCTC	0.617													C|||	41	0.0081869	0.0	0.0144	5008	,	,		19093	0.002		0.0229	False		,,,				2504	0.0061				p.R164L		Atlas-SNP	.											.	DDRGK1	21	.	0			c.G491T						PASS	.	C	LEU/ARG	27,4379	30.8+/-60.4	0,27,2176	85.0	66.0	72.0		491	5.3	1.0	20	dbSNP_126	72	231,8369	95.2+/-157.0	5,221,4074	yes	missense	DDRGK1	NM_023935.1	102	5,248,6250	AA,AC,CC		2.686,0.6128,1.9837	possibly-damaging	164/315	3180666	258,12748	2203	4300	6503	SO:0001583	missense	65992	exon4			TCCAGGCGAAGCC	AL121891	CCDS13050.1	20p13	2011-08-18	2008-10-03	2008-10-03	ENSG00000198171	ENSG00000198171			16110	protein-coding gene	gene with protein product	"""Dashurin"""		"""chromosome 20 open reading frame 116"""	C20orf116		20036718, 20228063, 21494687	Standard	NM_023935		Approved	dJ1187M17.3	uc002wic.3	Q96HY6	OTTHUMG00000031732	ENST00000354488.3:c.491G>T	20.37:g.3180666C>A	ENSP00000346483:p.Arg164Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	38	23	0.605263	NM_023935	A6NIU5|C9JSZ5|Q9BW47	Missense_Mutation	SNP	ENST00000354488.3	37	CCDS13050.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	C	20.3	3.961337	0.74016	0.006128	0.02686	ENSG00000198171	ENST00000354488;ENST00000380213;ENST00000380201	T	0.50548	0.74	5.35	5.35	0.76521	.	0.059853	0.64402	D	0.000002	T	0.40595	0.1123	L	0.58101	1.795	0.58432	D	0.999995	D;D	0.89917	1.0;0.997	D;D	0.85130	0.997;0.995	T	0.56353	-0.7993	10	0.52906	T	0.07	-7.9057	14.5665	0.68179	0.0:1.0:0.0:0.0	rs35327491;rs62206135	164;164	Q96HY6-2;Q96HY6	.;DDRGK_HUMAN	L	164	ENSP00000346483:R164L	ENSP00000346483:R164L	R	-	2	0	DDRGK1	3128666	1.000000	0.71417	0.999000	0.59377	0.761000	0.43186	4.380000	0.59581	2.503000	0.84419	0.655000	0.94253	CGC	C|0.986;A|0.014	0.014	strong		0.617	DDRGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077709.2	NM_023935	
SLC2A14	144195	hgsc.bcm.edu	37	12	7967076	7967076	+	Silent	SNP	A	A	G	rs10845983	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7967076A>G	ENST00000543909.1	-	16	2158	c.1399T>C	c.(1399-1401)Ttg>Ctg	p.L467L	SLC2A14_ENST00000539924.1_Silent_p.L482L|SLC2A14_ENST00000542505.1_Silent_p.L108L|SLC2A14_ENST00000396589.2_Silent_p.L467L|SLC2A14_ENST00000431042.2_Silent_p.L444L|SLC2A14_ENST00000542546.1_Silent_p.L358L|SLC2A14_ENST00000340749.5_Silent_p.L444L|SLC2A14_ENST00000535295.1_Silent_p.L358L			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	98	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	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	
ACSS1	84532	hgsc.bcm.edu	37	20	25003705	25003705	+	Silent	SNP	A	A	C	rs41308619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25003705A>C	ENST00000323482.4	-	5	910	c.831T>G	c.(829-831)gtT>gtG	p.V277V	ACSS1_ENST00000542618.1_Silent_p.V156V|ACSS1_ENST00000432802.2_Silent_p.V277V|ACSS1_ENST00000537502.1_Silent_p.V194V	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	277				V -> M (in Ref. 4; AAH39261). {ECO:0000305}.	acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CTGGGGCGCAAACAGGGTCCT	0.612													C|||	176	0.0351438	0.0968	0.0274	5008	,	,		20418	0.0		0.0278	False		,,,				2504	0.001				p.V277V		Atlas-SNP	.											.	ACSS1	46	.	0			c.T831G						PASS	.	C		412,3994	787.6+/-414.9	19,374,1810	63.0	52.0	55.0		831	-1.6	0.0	20	dbSNP_127	55	188,8412	810.6+/-407.1	1,186,4113	no	coding-synonymous	ACSS1	NM_032501.2		20,560,5923	CC,CA,AA		2.186,9.3509,4.6133		277/690	25003705	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon5			GGCGCAAACAGGG		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.831T>G	20.37:g.25003705A>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	16	0.355556	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			A|0.960;C|0.040	0.040	strong		0.612	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
CDH15	1013	hgsc.bcm.edu	37	16	89259993	89259993	+	Silent	SNP	A	A	G	rs3815615	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89259993A>G	ENST00000289746.2	+	12	2036	c.1971A>G	c.(1969-1971)caA>caG	p.Q657Q		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	657					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)		ACGATGAGCAAGGAGGCGGGG	0.662													G|||	2503	0.4998	0.3389	0.3775	5008	,	,		8160	0.8333		0.4473	False		,,,				2504	0.5143				p.Q657Q		Atlas-SNP	.											.	CDH15	54	.	0			c.A1971G						PASS	.	G		1475,2877		257,961,958	21.0	20.0	21.0		1971	2.5	1.0	16	dbSNP_107	21	3643,4929		816,2011,1459	no	coding-synonymous	CDH15	NM_004933.2		1073,2972,2417	GG,GA,AA		42.4988,33.8925,39.6007		657/815	89259993	5118,7806	2176	4286	6462	SO:0001819	synonymous_variant	1013	exon12			TGAGCAAGGAGGC	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.1971A>G	16.37:g.89259993A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			A|0.565;G|0.435	0.435	strong		0.662	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
ZNF616	90317	hgsc.bcm.edu	37	19	52620269	52620269	+	Missense_Mutation	SNP	G	G	A	rs35582075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52620269G>A	ENST00000600228.1	-	4	409	c.148C>T	c.(148-150)Cct>Tct	p.P50S	ZNF616_ENST00000330123.5_3'UTR|ZNF616_ENST00000596290.1_Silent_p.L66L	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	50	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		P -> S (in dbSNP:rs35582075). {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(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		ACACATTTAGGAGAGATACCT	0.318													G|||	377	0.0752796	0.0038	0.1527	5008	,	,		17919	0.0982		0.1163	False		,,,				2504	0.0511				p.P50S		Atlas-SNP	.											.	ZNF616	109	.	0			c.C148T						PASS	.	G	SER/PRO	83,4323	68.1+/-105.8	1,81,2121	77.0	78.0	78.0		148	-1.5	0.0	19	dbSNP_126	78	968,7630	203.4+/-246.4	55,858,3386	yes	missense	ZNF616	NM_178523.3	74	56,939,5507	AA,AG,GG		11.2584,1.8838,8.0821	probably-damaging	50/782	52620269	1051,11953	2203	4299	6502	SO:0001583	missense	90317	exon4			ATTTAGGAGAGAT	AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"""Zinc fingers, C2H2-type"", ""-"""	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.148C>T	19.37:g.52620269G>A	ENSP00000471000:p.Pro50Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	191	0.08745421245421245	3	0.006097560975609756	40	0.11049723756906077	51	0.08916083916083917	97	0.1279683377308707	G	11.02	1.514713	0.27123	0.018838	0.112584	ENSG00000204611	ENST00000330123	.	.	.	1.08	-1.47	0.08772	Krueppel-associated box (3);	.	.	.	.	T	0.00073	0.0002	N	0.01522	-0.82	0.80722	P	0.0	B	0.17852	0.024	B	0.15052	0.012	T	0.33752	-0.9856	7	0.17832	T	0.49	.	2.4656	0.04552	0.2439:0.324:0.4321:0.0	rs35582075	50	Q08AN1	ZN616_HUMAN	S	50	.	ENSP00000328722:P50S	P	-	1	0	ZNF616	57312081	0.000000	0.05858	0.001000	0.08648	0.817000	0.46193	-0.647000	0.05397	-0.440000	0.07211	0.305000	0.20034	CCT	G|0.921;A|0.079	0.079	strong		0.318	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892	
MAGI2	9863	hgsc.bcm.edu	37	7	77789403	77789403	+	Silent	SNP	A	A	G	rs1009524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:77789403A>G	ENST00000354212.4	-	16	3037	c.2784T>C	c.(2782-2784)aaT>aaC	p.N928N	MAGI2_ENST00000522391.1_Silent_p.N928N|MAGI2_ENST00000419488.1_Silent_p.N914N	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	928	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CGAAGCCCTCATTCTCTTTGC	0.532													G|||	635	0.126797	0.1225	0.1297	5008	,	,		20786	0.1905		0.0944	False		,,,				2504	0.0982				p.N928N		Atlas-SNP	.											.	MAGI2	246	.	0			c.T2784C						PASS	.	G		513,3893	778.6+/-414.3	37,439,1727	106.0	96.0	100.0		2784	-1.2	1.0	7	dbSNP_86	100	881,7719	778.9+/-407.7	42,797,3461	no	coding-synonymous	MAGI2	NM_012301.3		79,1236,5188	GG,GA,AA		10.2442,11.6432,10.7181		928/1456	77789403	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	9863	exon16			GCCCTCATTCTCT	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.2784T>C	7.37:g.77789403A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	37	CCDS5594.1																																																																																			A|0.879;G|0.121	0.121	strong		0.532	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
ARMC1	55156	hgsc.bcm.edu	37	8	66525548	66525548	+	Silent	SNP	T	T	C	rs11559265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:66525548T>C	ENST00000276569.3	-	4	640	c.396A>G	c.(394-396)caA>caG	p.Q132Q	ARMC1_ENST00000458464.2_Intron|ARMC1_ENST00000523384.1_5'Flank	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	132					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			CCAGAAAAAATTGAGCTTTCC	0.393													C|||	1283	0.25619	0.0877	0.3228	5008	,	,		19145	0.379		0.3002	False		,,,				2504	0.2648				p.Q132Q		Atlas-SNP	.											.	ARMC1	22	.	0			c.A396G						PASS	.	C		542,3864	776.6+/-414.2	34,474,1695	152.0	140.0	144.0		396	5.9	1.0	8	dbSNP_120	144	2698,5902	682.6+/-403.8	398,1902,2000	no	coding-synonymous	ARMC1	NM_018120.4		432,2376,3695	CC,CT,TT		31.3721,12.3014,24.9116		132/283	66525548	3240,9766	2203	4300	6503	SO:0001819	synonymous_variant	55156	exon4			AAAAAATTGAGCT	BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"""Armadillo repeat containing"""	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.396A>G	8.37:g.66525548T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	154	86	0.558442	NM_018120	B4E2W7|Q9H018|Q9H820	Silent	SNP	ENST00000276569.3	37	CCDS6181.1																																																																																			T|0.731;C|0.269	0.269	strong		0.393	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120	
FAF1	11124	hgsc.bcm.edu	37	1	51121198	51121198	+	Silent	SNP	T	T	C	rs11205753	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:51121198T>C	ENST00000396153.2	-	8	1111	c.660A>G	c.(658-660)gtA>gtG	p.V220V	FAF1_ENST00000371778.4_Silent_p.V220V	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	220					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CATTTCTCTTTACCTATGAAA	0.373													T|||	462	0.0922524	0.0182	0.0706	5008	,	,		17097	0.001		0.1113	False		,,,				2504	0.2822				p.V220V		Atlas-SNP	.											.	FAF1	64	.	1	Whole gene deletion(1)	thyroid(1)	c.A660G						PASS	.	T		169,4237	113.3+/-151.4	3,163,2037	97.0	92.0	93.0		660	3.9	1.0	1	dbSNP_120	93	1109,7491	227.6+/-262.9	78,953,3269	no	coding-synonymous	FAF1	NM_007051.2		81,1116,5306	CC,CT,TT		12.8953,3.8357,9.8262		220/651	51121198	1278,11728	2203	4300	6503	SO:0001819	synonymous_variant	11124	exon8			TCTCTTTACCTAT	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.660A>G	1.37:g.51121198T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Silent	SNP	ENST00000396153.2	37	CCDS554.1																																																																																			T|0.918;C|0.082	0.082	strong		0.373	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	
GSTA4	2941	hgsc.bcm.edu	37	6	52850270	52850270	+	Missense_Mutation	SNP	T	T	C	rs151284340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:52850270T>C	ENST00000370959.1	-	4	368	c.251A>G	c.(250-252)aAg>aGg	p.K84R	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370960.1_Intron|GSTA4_ENST00000541324.1_Intron			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	84					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)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	CTTGAGGTTCTTGCCAAAGAG	0.488													T|||	6	0.00119808	0.0	0.0	5008	,	,		19004	0.0		0.006	False		,,,				2504	0.0				p.K84R		Atlas-SNP	.											GSTA4,right_upper_lobe,carcinoma,+1,1	GSTA4	20	1	0			c.A251G						PASS	.	T	ARG/LYS	0,4406		0,0,2203	187.0	150.0	162.0		251	-0.5	0.9	6	dbSNP_134	162	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GSTA4	NM_001512.3	26	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	benign	84/223	52850270	7,12999	2203	4300	6503	SO:0001583	missense	2941	exon4			AGGTTCTTGCCAA	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4629	protein-coding gene	gene with protein product		605450	"""glutathione S-transferase A4"""			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.251A>G	6.37:g.52850270T>C	ENSP00000359998:p.Lys84Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	153	62	0.405229	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Missense_Mutation	SNP	ENST00000370959.1	37	CCDS4948.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	14.82	2.649056	0.47362	0.0	8.14E-4	ENSG00000170899	ENST00000370963;ENST00000370959	T;T	0.35048	1.33;1.33	5.13	-0.516	0.11950	Glutathione S-transferase, C-terminal-like (1);Thioredoxin-like fold (1);	0.248733	0.46145	N	0.000302	T	0.16214	0.0390	M	0.62016	1.91	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.08493	-1.0719	10	0.48119	T	0.1	-15.3197	8.5879	0.33668	0.0:0.3374:0.0:0.6626	.	84	O15217	GSTA4_HUMAN	R	84	ENSP00000360002:K84R;ENSP00000359998:K84R	ENSP00000359998:K84R	K	-	2	0	GSTA4	52958229	0.443000	0.25641	0.914000	0.36105	0.981000	0.71138	0.582000	0.23834	-0.231000	0.09825	-0.376000	0.06991	AAG	T|0.999;C|0.001	0.001	strong		0.488	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4900095A>G	ENST00000404991.1	-	1	1530	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	448					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.N448N(1)		kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		GAATTTCAGAATTATCTGGCT	0.383													G|||	2269	0.453075	0.5537	0.3559	5008	,	,		21126	0.4117		0.341	False		,,,				2504	0.544				p.N449N		Atlas-SNP	.											PAPOLB,NS,carcinoma,0,1	PAPOLB	93	1	1	Substitution - coding silent(1)	stomach(1)	c.T1347C						PASS	.	G	,	2235,2083		607,1021,531	101.0	107.0	105.0		,1347	1.5	0.6	7	dbSNP_88	105	3327,5245		628,2071,1587	yes	intron,coding-synonymous	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,	1235,3092,2118	GG,GA,AA		38.8124,48.2399,43.1497	,	,449/638	4900095	5562,7328	2159	4286	6445	SO:0001819	synonymous_variant	56903	exon1			TTCAGAATTATCT	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1344T>C	7.37:g.4900095A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	306	87	0.284314	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																				A|0.574;G|0.426	0.426	strong		0.383	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
CEACAM7	1087	hgsc.bcm.edu	37	19	42192071	42192071	+	Silent	SNP	T	T	C	rs1860331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:42192071T>C	ENST00000006724.3	-	1	225	c.24A>G	c.(22-24)ccA>ccG	p.P8P	CEACAM7_ENST00000599715.1_Intron|CEACAM7_ENST00000401731.1_Silent_p.P8P|CEACAM7_ENST00000602225.1_Silent_p.P8P|CEACAM7_ENST00000338196.4_Silent_p.P8P	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	8						anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		ACACTCTGTATGGACAGGCTG	0.617													T|||	94	0.01877	0.0068	0.0692	5008	,	,		17673	0.0		0.0089	False		,,,				2504	0.0286				p.P8P		Atlas-SNP	.											.	CEACAM7	33	.	0			c.A24G						PASS	.	T		36,4370		0,36,2167	81.0	69.0	73.0		24	-3.3	0.0	19	dbSNP_92	73	96,8504		2,92,4206	no	coding-synonymous	CEACAM7	NM_006890.3		2,128,6373	CC,CT,TT		1.1163,0.8171,1.0149		8/266	42192071	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	1087	exon1			TCTGTATGGACAG	X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1819	protein-coding gene	gene with protein product	"""carcinoembryonic antigen gene family member 2"""			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.24A>G	19.37:g.42192071T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_006890	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Silent	SNP	ENST00000006724.3	37	CCDS12583.1																																																																																			T|0.988;C|0.012	0.012	strong		0.617	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44800176	44800176	+	Missense_Mutation	SNP	G	G	T	rs3735478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44800176G>T	ENST00000309315.4	+	9	1347	c.1224G>T	c.(1222-1224)ttG>ttT	p.L408F	ZMIZ2_ENST00000433667.1_Missense_Mutation_p.L376F|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.L350F|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.L382F|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.L408F	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	408			L -> F (in dbSNP:rs3735478). {ECO:0000269|PubMed:14702039}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TCAACTCCTTGCACTCATCGC	0.577													G|||	752	0.15016	0.0136	0.1873	5008	,	,		18823	0.1429		0.3042	False		,,,				2504	0.1575				p.L408F	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G1224T						PASS	.	G	PHE/LEU,PHE/LEU	232,3990		9,214,1888	156.0	160.0	159.0		1224,1146	2.6	1.0	7	dbSNP_107	159	2344,6154		356,1632,2261	yes	missense,missense	ZMIZ2	NM_031449.3,NM_174929.2	22,22	365,1846,4149	TT,TG,GG		27.583,5.495,20.2516	probably-damaging,probably-damaging	408/921,382/895	44800176	2576,10144	2111	4249	6360	SO:0001583	missense	83637	exon9			CTCCTTGCACTCA	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.1224G>T	7.37:g.44800176G>T	ENSP00000311778:p.Leu408Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	181	118	0.651934	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	387	0.1771978021978022	2	0.0040650406504065045	65	0.17955801104972377	76	0.13286713286713286	244	0.32189973614775724	G	16.81	3.226875	0.58668	0.05495	0.27583	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	5.53	2.59	0.31030	.	0.000000	0.45126	D	0.000398	T	0.00012	0.0000	L	0.51422	1.61	0.22034	P	0.999404254	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.78314	0.991;0.943;0.991	T	0.19418	-1.0306	9	0.25106	T	0.35	-6.0933	8.4087	0.32629	0.1428:0.1274:0.7298:0.0	rs3735478;rs3735478	382;408;350	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	F	350;408;408;376;382;408	ENSP00000409648:L350F;ENSP00000311778:L408F;ENSP00000414723:L408F;ENSP00000396601:L376F;ENSP00000265346:L382F	ENSP00000265346:L382F	L	+	3	2	ZMIZ2	44766701	1.000000	0.71417	0.995000	0.50966	0.767000	0.43475	0.844000	0.27654	0.705000	0.31890	0.561000	0.74099	TTG	G|0.821;T|0.179	0.179	strong		0.577	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
RBM12	10137	hgsc.bcm.edu	37	20	34243017	34243017	+	Silent	SNP	C	C	T	rs6121015	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34243017C>T	ENST00000374114.3	-	3	491	c.228G>A	c.(226-228)aaG>aaA	p.K76K	RBM12_ENST00000374104.3_Silent_p.K76K|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397442.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000352393.4_Intron|RBM12_ENST00000359646.1_Silent_p.K76K|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000397446.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	76						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GCATTTCCGTCTTACTACTCA	0.423											OREG0004046	type=REGULATORY REGION|Gene=RBM12|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1358	0.271166	0.4228	0.1844	5008	,	,		21996	0.1339		0.1899	False		,,,				2504	0.3528				p.K76K		Atlas-SNP	.											.	RBM12	93	.	0			c.G228A						PASS	.	T	,,,,,,,,	1733,2673	648.4+/-398.7	331,1071,801	180.0	160.0	167.0		228,228,,228,228,,,,	5.4	1.0	20	dbSNP_114	167	1640,6960	741.6+/-407.2	172,1296,2832	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,intron,intron,intron,intron	CPNE1,RBM12	NM_001198838.1,NM_001198840.1,NM_001198863.1,NM_006047.5,NM_152838.3,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,,,,	503,2367,3633	TT,TC,CC		19.0698,39.3327,25.9342	,,,,,,,,	76/933,76/933,,76/933,76/933,,,,	34243017	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	10137	exon2			TTCCGTCTTACTA	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.228G>A	20.37:g.34243017C>T		Somatic	241	2	0.00829876	846	WXS	Illumina HiSeq	Phase_I	255	253	0.992157	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	37	CCDS13261.1																																																																																			C|0.753;T|0.247	0.247	strong		0.423	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
BMP4	652	hgsc.bcm.edu	37	14	54417522	54417522	+	Missense_Mutation	SNP	A	A	G	rs17563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:54417522A>G	ENST00000245451.4	-	4	848	c.455T>C	c.(454-456)gTg>gCg	p.V152A	BMP4_ENST00000417573.1_Missense_Mutation_p.V152A|BMP4_ENST00000558984.1_Missense_Mutation_p.V152A|MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000559087.1_Missense_Mutation_p.V152A	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	152			V -> A (in dbSNP:rs17563). {ECO:0000269|PubMed:12404109, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19249007, ECO:0000269|PubMed:9701626}.		activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|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)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						AGAGGAGATCACCTCGTTCTC	0.512													A|||	1631	0.325679	0.1831	0.3617	5008	,	,		19089	0.2857		0.5497	False		,,,				2504	0.3037				p.V152A		Atlas-SNP	.											.	BMP4	45	.	0			c.T455C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	1138,3268		145,848,1210	45.0	42.0	43.0		455,455,455	4.1	1.0	14	dbSNP_63	43	4715,3885		1289,2137,874	yes	missense,missense,missense	BMP4	NM_001202.3,NM_130850.2,NM_130851.2	64,64,64	1434,2985,2084	GG,GA,AA		45.1744,25.8284,45.0023	probably-damaging,probably-damaging,probably-damaging	152/409,152/409,152/409	54417522	5853,7153	2203	4300	6503	SO:0001583	missense	652	exon4			GAGATCACCTCGT	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.455T>C	14.37:g.54417522A>G	ENSP00000245451:p.Val152Ala	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	37	CCDS9715.1	812	0.3717948717948718	99	0.20121951219512196	134	0.3701657458563536	152	0.26573426573426573	427	0.5633245382585752	A	12.19	1.864500	0.32977	0.258284	0.548256	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.64085	-0.08;-0.08	5.2	4.05	0.47172	Transforming growth factor-beta, N-terminal (1);	0.123114	0.56097	N	0.000032	T	0.00012	0.0000	L	0.44542	1.39	0.22842	P	0.99866552	B	0.09022	0.002	B	0.12156	0.007	T	0.46247	-0.9205	9	0.30078	T	0.28	.	9.1323	0.36852	0.9092:0.0:0.0908:0.0	rs17563;rs1048810;rs3829971;rs17845605;rs17858529;rs52814732;rs17563	152	P12644	BMP4_HUMAN	A	152	ENSP00000245451:V152A;ENSP00000394165:V152A	ENSP00000245451:V152A	V	-	2	0	BMP4	53487272	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.063000	0.64332	0.993000	0.38866	0.533000	0.62120	GTG	A|0.593;G|0.407	0.407	strong		0.512	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202	
LILRA4	23547	hgsc.bcm.edu	37	19	54849942	54849942	+	Missense_Mutation	SNP	G	G	A	rs534566751|rs2241384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54849942G>A	ENST00000291759.4	-	3	136	c.80C>T	c.(79-81)cCc>cTc	p.P27L	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	27	Ig-like C2-type 1.		P -> L (in dbSNP:rs2241384).		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)		GATGGGTTTGGGTAGGTTTTC	0.597											OREG0003656	type=REGULATORY REGION|Gene=LILRA4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	990	0.197684	0.1566	0.2133	5008	,	,		18609	0.2679		0.169	False		,,,				2504	0.1994				p.P27L		Atlas-SNP	.											.	LILRA4	91	.	0			c.C80T						PASS	.	A	LEU/PRO	701,3705		51,599,1553	50.0	49.0	50.0		80	-1.0	0.0	19	dbSNP_98	50	1421,7179		127,1167,3006	yes	missense	LILRA4	NM_012276.3	98	178,1766,4559	AA,AG,GG		16.5233,15.9101,16.3155	benign	27/500	54849942	2122,10884	2203	4300	6503	SO:0001583	missense	23547	exon3			GGTTTGGGTAGGT	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.80C>T	19.37:g.54849942G>A	ENSP00000291759:p.Pro27Leu	Somatic	25	0	0	1003	WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	420	0.19230769230769232	79	0.16056910569105692	76	0.20994475138121546	135	0.23601398601398602	130	0.17150395778364116	.	6.236	0.411693	0.11812	0.159101	0.165233	ENSG00000239961	ENST00000291759	T	0.13538	2.58	2.5	-1.05	0.10036	Immunoglobulin-like fold (1);	0.398226	0.21610	N	0.071815	T	0.00012	0.0000	M	0.80183	2.485	0.80722	P	0.0	B	0.20780	0.048	B	0.25759	0.063	T	0.18116	-1.0347	9	0.48119	T	0.1	.	4.7733	0.13166	0.2633:0.1811:0.5555:0.0	rs2241384;rs52794492;rs60249083;rs2241384	27	P59901	LIRA4_HUMAN	L	27	ENSP00000291759:P27L	ENSP00000291759:P27L	P	-	2	0	LILRA4	59541754	0.033000	0.19621	0.014000	0.15608	0.001000	0.01503	0.493000	0.22451	-0.466000	0.06943	-3.327000	0.00044	CCC	G|0.827;A|0.173	0.173	strong		0.597	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
AK9	221264	hgsc.bcm.edu	37	6	109827716	109827716	+	Missense_Mutation	SNP	C	C	T	rs2277114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:109827716C>T	ENST00000424296.2	-	35	4739	c.4663G>A	c.(4663-4665)Gta>Ata	p.V1555I	RP5-919F19.5_ENST00000423747.2_RNA|AL109947.2_ENST00000517228.1_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	159	0	0		WXS	Illumina HiSeq	Phase_I	143	79	0.552448	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	
TEP1	7011	hgsc.bcm.edu	37	14	20841707	20841707	+	Missense_Mutation	SNP	C	C	T	rs1713449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20841707C>T	ENST00000262715.5	-	46	6680	c.6640G>A	c.(6640-6642)Gtc>Atc	p.V2214I	TEP1_ENST00000556935.1_Missense_Mutation_p.V2106I|TEP1_ENST00000545983.1_Missense_Mutation_p.V552I	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2214			V -> I (in dbSNP:rs1713449).		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)		TCTAGCCCGACGGTTACCACC	0.552													T|||	1623	0.324081	0.4675	0.3646	5008	,	,		21201	0.3056		0.2187	False		,,,				2504	0.229				p.V2214I		Atlas-SNP	.											TEP1,NS,carcinoma,0,1	TEP1	224	1	0			c.G6640A						PASS	.	T	ILE/VAL	1806,2600	640.4+/-397.3	363,1080,760	74.0	67.0	69.0		6640	4.3	0.4	14	dbSNP_89	69	1767,6833	734.4+/-406.9	176,1415,2709	yes	missense	TEP1	NM_007110.4	29	539,2495,3469	TT,TC,CC		20.5465,40.9896,27.4719	benign	2214/2628	20841707	3573,9433	2203	4300	6503	SO:0001583	missense	7011	exon46			GCCCGACGGTTAC		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.6640G>A	14.37:g.20841707C>T	ENSP00000262715:p.Val2214Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	682	0.31227106227106227	226	0.45934959349593496	115	0.31767955801104975	169	0.29545454545454547	172	0.22691292875989447	T	4.632	0.117390	0.08881	0.409896	0.205465	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.56103	2.19;2.19;0.48	5.25	4.35	0.52113	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.575156	0.17401	N	0.175537	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.31209	0.002;0.002;0.313;0.001	B;B;B;B	0.27380	0.001;0.004;0.079;0.002	T	0.46638	-0.9177	9	0.23302	T	0.38	-0.1231	12.057	0.53540	0.0:0.9059:0.0:0.0941	rs1713449;rs2228024;rs59335611;rs1713449	552;2106;1557;2214	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	I	2214;2214;2106;552	ENSP00000262715:V2214I;ENSP00000452574:V2106I;ENSP00000438849:V552I	ENSP00000262715:V2214I	V	-	1	0	TEP1	19911547	0.047000	0.20315	0.434000	0.26772	0.140000	0.21249	1.561000	0.36342	0.601000	0.29879	-0.977000	0.02584	GTC	C|0.712;T|0.288	0.288	strong		0.552	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
SLC6A13	6540	hgsc.bcm.edu	37	12	333267	333267	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:333267G>A	ENST00000343164.4	-	11	1254	c.1202C>T	c.(1201-1203)gCg>gTg	p.A401V	SLC6A13_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Missense_Mutation_p.A309V	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	401					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)			GTCCACCAGCGCTGTCACCAG	0.557																																					p.A401V		Atlas-SNP	.											.	SLC6A13	62	.	0			c.C1202T						PASS	.						106.0	89.0	95.0					12																	333267		2203	4300	6503	SO:0001583	missense	6540	exon11			ACCAGCGCTGTCA	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.1202C>T	12.37:g.333267G>A	ENSP00000339260:p.Ala401Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059781	0.93846	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.78003	-1.14;-1.14	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.997	D;P;D	0.76071	0.987;0.893;0.941	D	0.89618	0.3846	10	0.87932	D	0	.	19.3766	0.94512	0.0:0.0:1.0:0.0	.	309;380;401	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	V	309;380;401	ENSP00000407104:A309V;ENSP00000339260:A401V	ENSP00000318097:A380V	A	-	2	0	SLC6A13	203528	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	7.876000	0.87215	2.596000	0.87737	0.491000	0.48974	GCG	.	.	none		0.557	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
DCAF11	80344	hgsc.bcm.edu	37	14	24587639	24587639	+	Missense_Mutation	SNP	G	G	A	rs3825584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24587639G>A	ENST00000446197.3	+	7	1347	c.620G>A	c.(619-621)cGt>cAt	p.R207H	RP11-468E2.6_ENST00000558325.1_5'Flank|DCAF11_ENST00000396941.4_Missense_Mutation_p.R181H|DCAF11_ENST00000559115.1_Missense_Mutation_p.R207H|DCAF11_ENST00000396936.1_Missense_Mutation_p.R107H|DCAF11_ENST00000560171.1_3'UTR	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	207			R -> H (in dbSNP:rs3825584). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.7}.		protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											GGCCGTTTCCGTAAATTCAAG	0.488													g|||	1989	0.397165	0.3351	0.4625	5008	,	,		23535	0.4355		0.3032	False		,,,				2504	0.4918				p.R207H		Atlas-SNP	.											.	.	.	.	0			c.G620A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	1405,3001	461.1+/-352.8	229,947,1027	134.0	126.0	129.0		620,620,542	-5.3	0.7	14	dbSNP_107	129	2340,6260	391.3+/-343.6	326,1688,2286	yes	missense,missense,missense	DCAF11	NM_001163484.1,NM_025230.4,NM_181357.2	29,29,29	555,2635,3313	AA,AG,GG		27.2093,31.8883,28.7944	benign,benign,benign	207/547,207/547,181/521	24587639	3745,9261	2203	4300	6503	SO:0001583	missense	80344	exon7			GTTTCCGTAAATT	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20258	protein-coding gene	gene with protein product		613317	"""WD repeat domain 23"""	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.620G>A	14.37:g.24587639G>A	ENSP00000415556:p.Arg207His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	141	62	0.439716	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	37	CCDS9610.1	791	0.36217948717948717	167	0.3394308943089431	162	0.44751381215469616	230	0.4020979020979021	232	0.30606860158311344	g	11.67	1.708956	0.30322	0.318883	0.272093	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396936;ENST00000396941	T;T	0.41065	1.01;1.01	5.4	-5.29	0.02747	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.537521	0.21749	N	0.069715	T	0.00012	0.0000	N	0.02539	-0.55	0.44603	P	0.0024290000000000145	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.0	T	0.48559	-0.9025	9	0.35671	T	0.21	-0.7512	13.2261	0.59914	0.4655:0.0:0.5345:0.0	rs3825584;rs58760613;rs3825584	181;107;207;207	Q8TEB1-2;Q8TEB1-3;A8K9T2;Q8TEB1	.;.;.;DCA11_HUMAN	H	207;181;107;181	ENSP00000380142:R107H;ENSP00000380146:R181H	ENSP00000323680:R207H	R	+	2	0	DCAF11	23657479	0.716000	0.27956	0.737000	0.30932	0.986000	0.74619	0.021000	0.13489	-1.098000	0.03038	-0.290000	0.09829	CGT	G|0.685;A|0.315	0.315	strong		0.488	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		
IGFALS	3483	hgsc.bcm.edu	37	16	1842209	1842209	+	Silent	SNP	A	A	G	rs3751893	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1842209A>G	ENST00000215539.3	-	2	320	c.210T>C	c.(208-210)gaT>gaC	p.D70D	IGFALS_ENST00000568221.1_Missense_Mutation_p.M81T|IGFALS_ENST00000415638.3_Silent_p.D108D			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	70	LRRNT.				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						CCGGGACTCCATCAGGCAGGC	0.677													G|||	3927	0.784145	0.8192	0.7781	5008	,	,		15269	0.7272		0.8032	False		,,,				2504	0.7802				p.D108D		Atlas-SNP	.											IGFALS,NS,carcinoma,0,1	IGFALS	29	1	0			c.T324C						PASS	.	G	,	3580,808		1463,654,77	27.0	29.0	28.0		324,210	-10.7	0.0	16	dbSNP_107	28	7065,1531		2901,1263,134	no	coding-synonymous,coding-synonymous	IGFALS	NM_001146006.1,NM_004970.2	,	4364,1917,211	GG,GA,AA		17.8106,18.4139,18.0145	,	108/644,70/606	1842209	10645,2339	2194	4298	6492	SO:0001819	synonymous_variant	3483	exon2			GACTCCATCAGGC	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.210T>C	16.37:g.1842209A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_001146006	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			A|0.191;G|0.809	0.809	strong		0.677	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
LSP1	4046	hgsc.bcm.edu	37	11	1887806	1887806	+	Intron	SNP	T	T	A	rs7938342	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1887806T>A	ENST00000311604.3	+	1	228				AC051649.12_ENST00000509204.1_RNA|LSP1_ENST00000405957.2_5'Flank|LSP1_ENST00000381775.1_Missense_Mutation_p.H34Q	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1						cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		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;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GCACACCTCATCCCAGCCTCC	0.657													T|||	3127	0.624401	0.531	0.7622	5008	,	,		13459	0.7688		0.6322	False		,,,				2504	0.4959				p.H34Q		Atlas-SNP	.											.	LSP1	59	.	0			c.T102A						PASS	.																																			SO:0001627	intron_variant	4046	exon2			ACCTCATCCCAGC	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.53+13379T>A	11.37:g.1887806T>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	1429	0.6543040293040293	268	0.5447154471544715	249	0.6878453038674033	460	0.8041958041958042	452	0.5963060686015831	t	12.20	1.867727	0.32977	.	.	ENSG00000130592	ENST00000381775	T	0.26518	1.73	1.8	-0.645	0.11475	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.35982	0.531	B	0.29598	0.104	T	0.42515	-0.9447	7	0.02654	T	1	.	4.2569	0.10721	0.0:0.3731:0.0:0.6269	rs7938342;rs57757026	34	E9PFP3	.	Q	34	ENSP00000371194:H34Q	ENSP00000371194:H34Q	H	+	3	2	LSP1	1844382	0.000000	0.05858	0.000000	0.03702	0.672000	0.39443	-1.399000	0.02506	-0.182000	0.10602	0.172000	0.16884	CAT	T|0.346;A|0.654	0.654	strong		0.657	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
ZNF583	147949	hgsc.bcm.edu	37	19	56935527	56935527	+	Silent	SNP	A	A	G	rs3810340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56935527A>G	ENST00000333201.9	+	5	1710	c.1500A>G	c.(1498-1500)gcA>gcG	p.A500A	ZNF583_ENST00000585612.1_Intron|ZNF583_ENST00000291598.7_Silent_p.A500A	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	500					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		GTGGGAAAGCATTTAGCTATA	0.398													C|||	3235	0.645966	0.5764	0.6282	5008	,	,		22156	0.873		0.5119	False		,,,				2504	0.6564				p.A500A		Atlas-SNP	.											.	ZNF583	83	.	0			c.A1500G						PASS	.	C	,,	2471,1935		691,1089,423	110.0	115.0	113.0		1500,1500,1500	0.2	0.9	19	dbSNP_107	113	4499,4101		1164,2171,965	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF583	NM_001159860.1,NM_001159861.1,NM_152478.2	,,	1855,3260,1388	GG,GA,AA		47.686,43.9174,46.4093	,,	500/570,500/570,500/570	56935527	6970,6036	2203	4300	6503	SO:0001819	synonymous_variant	147949	exon5			GAAAGCATTTAGC	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"""Zinc fingers, C2H2-type"", ""-"""	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1500A>G	19.37:g.56935527A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_001159861	O14850|Q2NKK3	Silent	SNP	ENST00000333201.9	37	CCDS12943.1																																																																																			A|0.423;G|0.577	0.577	strong		0.398	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478	
TMEM244	253582	hgsc.bcm.edu	37	6	130154686	130154686	+	Missense_Mutation	SNP	A	A	G	rs4629709	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:130154686A>G	ENST00000368143.1	-	4	320	c.238T>C	c.(238-240)Ttt>Ctt	p.F80L	TMEM244_ENST00000438392.1_Missense_Mutation_p.F80L	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	80			F -> L (in dbSNP:rs4629709).			integral component of membrane (GO:0016021)											GGAACAAAAAACAATCCACAA	0.348													G|||	3076	0.614217	0.6687	0.5101	5008	,	,		17740	0.3611		0.7744	False		,,,				2504	0.7106				p.F80L		Atlas-SNP	.											.	.	.	.	0			c.T238C						PASS	.	G	LEU/PHE	3062,1344	449.2+/-349.0	1062,938,203	126.0	122.0	123.0		238	4.8	0.9	6	dbSNP_111	123	7045,1555	290.1+/-299.6	2900,1245,155	yes	missense	C6orf191	NM_001010876.1	22	3962,2183,358	GG,GA,AA		18.0814,30.5039,22.2897	benign	80/129	130154686	10107,2899	2203	4300	6503	SO:0001583	missense	253582	exon4			CAAAAAACAATCC		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.238T>C	6.37:g.130154686A>G	ENSP00000357125:p.Phe80Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_001010876		Missense_Mutation	SNP	ENST00000368143.1	37	CCDS34536.1	1322	0.6053113553113553	334	0.6788617886178862	208	0.574585635359116	199	0.3479020979020979	581	0.7664907651715039	G	5.332	0.246588	0.10130	0.694961	0.819186	ENSG00000203756	ENST00000368143;ENST00000438392	T;T	0.33865	1.39;1.39	4.8	4.8	0.61643	.	0.085531	0.47852	N	0.000203	T	0.02494	0.0076	N	0.00621	-1.32	0.49213	P	2.3200000000000998E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41251	-0.9519	9	0.02654	T	1	-19.0081	7.7395	0.28833	0.0851:0.0:0.7547:0.1603	rs4629709;rs52812966;rs60692248;rs4629709	80	Q5VVB8	CF191_HUMAN	L	80	ENSP00000357125:F80L;ENSP00000403755:F80L	ENSP00000357125:F80L	F	-	1	0	C6orf191	130196379	0.885000	0.30320	0.927000	0.36925	0.974000	0.67602	0.230000	0.17852	1.147000	0.42369	-0.128000	0.14901	TTT	A|0.296;G|0.704	0.704	strong		0.348	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
TMCO6	55374	hgsc.bcm.edu	37	5	140023238	140023238	+	Missense_Mutation	SNP	C	C	G	rs17208187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140023238C>G	ENST00000394671.3	+	8	997	c.896C>G	c.(895-897)aCc>aGc	p.T299S	TMCO6_ENST00000537378.1_Missense_Mutation_p.T59S|NDUFA2_ENST00000510680.1_Intron|TMCO6_ENST00000252100.6_Missense_Mutation_p.T305S	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	299			T -> S (in dbSNP:rs17208187). {ECO:0000269|PubMed:15489334}.		protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCAGAAAACCGAGGATGCA	0.527													C|||	1037	0.207069	0.0605	0.2176	5008	,	,		19225	0.3016		0.2545	False		,,,				2504	0.2515				p.T299S		Atlas-SNP	.											.	TMCO6	30	.	0			c.C896G						PASS	.	C	SER/THR	320,3632		13,294,1669	140.0	142.0	142.0		896	2.4	0.3	5	dbSNP_123	142	2002,6328		248,1506,2411	yes	missense	TMCO6	NM_018502.3	58	261,1800,4080	GG,GC,CC		24.0336,8.0972,18.9057	benign	299/494	140023238	2322,9960	1976	4165	6141	SO:0001583	missense	55374	exon8			AGAAAACCGAGGA	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.896C>G	5.37:g.140023238C>G	ENSP00000378166:p.Thr299Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_018502	Q9BUU0|Q9P198	Missense_Mutation	SNP	ENST00000394671.3	37	CCDS4233.2	495	0.22664835164835165	34	0.06910569105691057	90	0.24861878453038674	166	0.2902097902097902	205	0.2704485488126649	C	0.007	-1.937287	0.00484	0.080972	0.240336	ENSG00000113119	ENST00000394671;ENST00000537378;ENST00000252100	T;T;T	0.41065	2.32;1.01;2.3	5.12	2.37	0.29283	Armadillo-like helical (1);Armadillo-type fold (1);	0.592775	0.17865	N	0.159399	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.39292	-0.9621	9	0.27785	T	0.31	-0.4379	6.1096	0.20094	0.0:0.6376:0.1383:0.2241	rs17208187;rs17849552;rs56597340;rs58706596;rs17208187	305;299	Q96DC7-2;Q96DC7	.;TMCO6_HUMAN	S	299;59;305	ENSP00000378166:T299S;ENSP00000444474:T59S;ENSP00000252100:T305S	ENSP00000252100:T305S	T	+	2	0	TMCO6	140003422	0.080000	0.21391	0.341000	0.25589	0.183000	0.23260	0.397000	0.20883	0.328000	0.23435	0.561000	0.74099	ACC	C|0.780;G|0.220	0.220	strong		0.527	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502	
PDZRN3	23024	hgsc.bcm.edu	37	3	73433369	73433369	+	Missense_Mutation	SNP	G	G	A	rs3205537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:73433369G>A	ENST00000263666.4	-	10	2462	c.2348C>T	c.(2347-2349)gCg>gTg	p.A783V	PDZRN3_ENST00000462146.2_Missense_Mutation_p.A440V|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000466780.1_Missense_Mutation_p.A440V|PDZRN3_ENST00000479530.1_Missense_Mutation_p.A500V|PDZRN3_ENST00000535920.1_Missense_Mutation_p.A505V	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	783			A -> V (in dbSNP:rs3205537). {ECO:0000269|PubMed:17974005}.		neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GATGCCCTCCGCCGCTCTCCT	0.647													G|||	1364	0.272364	0.0635	0.3415	5008	,	,		16006	0.4435		0.3549	False		,,,				2504	0.2444				p.A783V		Atlas-SNP	.											.	PDZRN3	196	.	0			c.C2348T						PASS	.	G	VAL/ALA	468,3938	217.8+/-236.0	30,408,1765	35.0	38.0	37.0		2348	4.1	0.2	3	dbSNP_105	37	2851,5749	440.9+/-359.6	471,1909,1920	yes	missense	PDZRN3	NM_015009.1	64	501,2317,3685	AA,AG,GG		33.1512,10.6219,25.519	possibly-damaging	783/1067	73433369	3319,9687	2203	4300	6503	SO:0001583	missense	23024	exon10			CCCTCCGCCGCTC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2348C>T	3.37:g.73433369G>A	ENSP00000263666:p.Ala783Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	709	0.32463369963369965	41	0.08333333333333333	119	0.3287292817679558	267	0.46678321678321677	282	0.3720316622691293	G	1.520	-0.547126	0.04024	0.106219	0.331512	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000492909	T;T;T;T;T;T	0.10099	2.91;3.61;3.5;3.5;3.62;3.58	4.93	4.05	0.47172	.	1.618580	0.02891	N	0.134123	T	0.00012	0.0000	L	0.57536	1.79	0.58432	P	5.000000000032756E-6	B;B;B;B	0.27286	0.005;0.011;0.003;0.174	B;B;B;B	0.14578	0.005;0.004;0.003;0.011	T	0.48536	-0.9027	9	0.23891	T	0.37	.	13.1789	0.59642	0.0793:0.0:0.9207:0.0	rs3205537;rs3732435;rs52810062;rs57871998;rs3205537	505;500;500;783	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	V	783;505;440;440;500;481	ENSP00000263666:A783V;ENSP00000442026:A505V;ENSP00000418168:A440V;ENSP00000418484:A440V;ENSP00000418624:A500V;ENSP00000419250:A481V	ENSP00000263666:A783V	A	-	2	0	PDZRN3	73516059	0.713000	0.27926	0.216000	0.23742	0.081000	0.17604	2.975000	0.49281	1.030000	0.39839	0.655000	0.94253	GCG	G|0.729;A|0.271	0.271	strong		0.647	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
CETP	1071	hgsc.bcm.edu	37	16	57015091	57015091	+	Missense_Mutation	SNP	G	G	C	rs5880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:57015091G>C	ENST00000566128.1	+	12	1240	c.973G>C	c.(973-975)Gcc>Ccc	p.A325P	CETP_ENST00000200676.3_Missense_Mutation_p.A390P|CETP_ENST00000379780.2_Missense_Mutation_p.A330P					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TACCGTCCAGGCCTCCTATTC	0.547													G|||	210	0.0419329	0.0038	0.0908	5008	,	,		17517	0.0089		0.0517	False		,,,				2504	0.0828				p.A390P		Atlas-SNP	.											.	CETP	50	.	0			c.G1168C	GRCh37	CM074726	CETP	M	rs5880	PASS	.	G	PRO/ALA	47,4349	47.5+/-82.1	0,47,2151	86.0	91.0	89.0		1168	2.9	0.9	16	dbSNP_52	89	450,8150	135.2+/-192.5	10,430,3860	yes	missense	CETP	NM_000078.2	27	10,477,6011	CC,CG,GG		5.2326,1.0692,3.8243	probably-damaging	390/494	57015091	497,12499	2198	4300	6498	SO:0001583	missense	1071	exon12			GTCCAGGCCTCCT	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.973G>C	16.37:g.57015091G>C	ENSP00000456276:p.Ala325Pro	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		74	0.03388278388278388	1	0.0020325203252032522	24	0.06629834254143646	4	0.006993006993006993	45	0.059366754617414245	G	13.22	2.172358	0.38315	0.010692	0.052326	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.09723	2.95;2.95	3.9	2.94	0.34122	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.000000	0.64402	U	0.000001	T	0.01353	0.0044	L	0.36672	1.1	0.37500	D	0.916714	D;D	0.89917	0.999;1.0	D;D	0.91635	0.997;0.999	T	0.01863	-1.1258	10	0.51188	T	0.08	-1.7718	7.8559	0.29483	0.1201:0.0:0.8799:0.0	rs5880;rs1801705;rs17245736;rs56814827;rs5880	330;390	P11597-2;P11597	.;CETP_HUMAN	P	390;330	ENSP00000200676:A390P;ENSP00000369106:A330P	ENSP00000200676:A390P	A	+	1	0	CETP	55572592	1.000000	0.71417	0.907000	0.35723	0.505000	0.33919	2.739000	0.47409	0.774000	0.33427	0.313000	0.20887	GCC	G|0.966;C|0.034	0.034	strong		0.547	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
VPS9D1	9605	hgsc.bcm.edu	37	16	89774870	89774870	+	Silent	SNP	C	C	T	rs369209003		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89774870C>T	ENST00000389386.3	-	14	1891	c.1767G>A	c.(1765-1767)tcG>tcA	p.S589S	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Silent_p.S519S	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	589	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCGCGCACTCCGACACCAGCT	0.657																																					p.S589S		Atlas-SNP	.											C16orf7,colon,carcinoma,-1,1	.	.	1	0			c.G1767A						PASS	.	C		0,4254		0,0,2127	27.0	34.0	31.0		1767	-10.3	0.5	16		31	1,8465		0,1,4232	no	coding-synonymous	C16orf7	NM_004913.2		0,1,6359	TT,TC,CC		0.0118,0.0,0.0079		589/632	89774870	1,12719	2127	4233	6360	SO:0001819	synonymous_variant	9605	exon14			GCACTCCGACACC	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1767G>A	16.37:g.89774870C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	205	104	0.507317	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			.	.	weak		0.657	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
MYH6	4624	hgsc.bcm.edu	37	14	23874523	23874523	+	Silent	SNP	C	C	T	rs2277474	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	73	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	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		
TXNDC2	84203	hgsc.bcm.edu	37	18	9886890	9886890	+	Silent	SNP	A	A	G	rs601874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:9886890A>G	ENST00000306084.6	+	2	613	c.414A>G	c.(412-414)tcA>tcG	p.S138S	TXNDC2_ENST00000536353.2_Silent_p.S71S|TXNDC2_ENST00000357775.5_Silent_p.S71S|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	138	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CCAAGTCCTCAGAAAAAGCCA	0.542													a|||	960	0.191693	0.2791	0.1628	5008	,	,		20464	0.001		0.2873	False		,,,				2504	0.1922				p.S138S		Atlas-SNP	.											.	TXNDC2	168	.	0			c.A414G						PASS	.	A	,	1147,3259	407.5+/-334.3	168,811,1224	129.0	127.0	128.0		414,213	-3.1	0.0	18	dbSNP_83	128	2413,6187	401.1+/-347.0	347,1719,2234	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	515,2530,3458	GG,GA,AA		28.0581,26.0327,27.372	,	138/554,71/487	9886890	3560,9446	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GTCCTCAGAAAAA	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.414A>G	18.37:g.9886890A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			A|0.762;G|0.238	0.238	strong		0.542	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
MAN2B1	4125	hgsc.bcm.edu	37	19	12772090	12772090	+	Missense_Mutation	SNP	C	C	T	rs1133330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12772090C>T	ENST00000456935.2	-	7	1050	c.1010G>A	c.(1009-1011)cGg>cAg	p.R337Q	MAN2B1_ENST00000495617.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.R337Q	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	125	1	0.008		WXS	Illumina HiSeq	Phase_I	127	127	1	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		
TIE1	7075	hgsc.bcm.edu	37	1	43784956	43784956	+	Silent	SNP	A	A	G	rs1199039|rs45475401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:43784956A>G	ENST00000372476.3	+	18	3052	c.2973A>G	c.(2971-2973)ctA>ctG	p.L991L	TIE1_ENST00000433781.2_Silent_p.L636L|TIE1_ENST00000473014.1_3'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	991	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGAGAACCTAGCCTCCAAGA	0.567													G|||	1131	0.225839	0.1815	0.3631	5008	,	,		20631	0.1478		0.3777	False		,,,				2504	0.1125				p.L991L		Atlas-SNP	.											.	TIE1	132	.	0			c.A2973G						PASS	.	G		904,3502	740.8+/-411.2	93,718,1392	118.0	110.0	113.0		2973	5.1	1.0	1	dbSNP_87	113	3360,5240	642.3+/-399.8	665,2030,1605	no	coding-synonymous	TIE1	NM_005424.2		758,2748,2997	GG,GA,AA		39.0698,20.5175,32.7849		991/1139	43784956	4264,8742	2203	4300	6503	SO:0001819	synonymous_variant	7075	exon18			GAACCTAGCCTCC	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.2973A>G	1.37:g.43784956A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	37	CCDS482.1																																																																																			A|0.697;G|0.303	0.303	strong		0.567	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651352	1651352	+	Silent	SNP	C	C	T	rs75391124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1651352C>T	ENST00000399676.2	+	1	320	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	94	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G94G(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)		CTTGCGGGGGCTCCAAGAGAG	0.667													-|||	308	0.0615016	0.0257	0.0634	5008	,	,		6470	0.0119		0.0994	False		,,,				2504	0.1207				p.G94G		Atlas-SNP	.											KRTAP5-5,NS,haematopoietic_neoplasm,0,1	KRTAP5-5	86	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C282T						scavenged	.	C		109,4295		1,107,2094	76.0	95.0	88.0		282	0.4	1.0	11	dbSNP_131	88	684,7910		29,626,3642	no	coding-synonymous	KRTAP5-5	NM_001001480.2		30,733,5736	TT,TC,CC		7.959,2.475,6.1009		94/238	1651352	793,12205	2202	4297	6499	SO:0001819	synonymous_variant	439915	exon1			CGGGGGCTCCAAG	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.282C>T	11.37:g.1651352C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			C|0.929;T|0.071	0.071	strong		0.667	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:32996805C>T	ENST00000399302.2	+	12	5318	c.4983C>T	c.(4981-4983)gtC>gtT	p.V1661V	QSER1_ENST00000527788.1_Silent_p.V1422V	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1661										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AGTTTGCTGTCGATCCAGAGA	0.308													c|||	295	0.0589058	0.0015	0.0994	5008	,	,		15385	0.005		0.1481	False		,,,				2504	0.0716				p.V1661V		Atlas-SNP	.											QSER1,caecum,carcinoma,0,1	QSER1	153	1	0			c.C4983T						PASS	.	T		98,3494		2,94,1700	97.0	92.0	93.0		4983	-2.5	1.0	11	dbSNP_120	93	1124,7000		72,980,3010	no	coding-synonymous	QSER1	NM_001076786.1		74,1074,4710	TT,TC,CC		13.8355,2.7283,10.4302		1661/1736	32996805	1222,10494	1796	4062	5858	SO:0001819	synonymous_variant	79832	exon12			TGCTGTCGATCCA	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.4983C>T	11.37:g.32996805C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	CCDS41631.1	158	0.07234432234432235	1	0.0020325203252032522	44	0.12154696132596685	3	0.005244755244755245	110	0.14511873350923482	c	7.557	0.663876	0.14710	0.027283	0.138355	ENSG00000060749	ENST00000524678	.	.	.	5.67	-2.55	0.06288	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21999	-1.0229	3	.	.	.	.	6.1626	0.20372	0.2699:0.3365:0.0:0.3936	rs11032076;rs17756863;rs61521589;rs11032076	.	.	.	L	682	.	.	S	+	2	0	QSER1	32953381	0.998000	0.40836	0.972000	0.41901	0.923000	0.55619	0.465000	0.22004	-0.725000	0.04901	-1.873000	0.00551	TCG	C|0.907;T|0.093	0.093	strong		0.308	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
MICAL3	57553	hgsc.bcm.edu	37	22	18300879	18300879	+	Silent	SNP	G	G	A	rs11704809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	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		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65348725	65348725	+	Silent	SNP	G	G	A	rs79021529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65348725G>A	ENST00000309295.4	+	8	1012	c.747G>A	c.(745-747)gtG>gtA	p.V249V		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	249						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						CAGCCCCTGTGAGTGCTCCTG	0.657													G|||	178	0.0355431	0.0045	0.0432	5008	,	,		15454	0.0		0.0924	False		,,,				2504	0.0501				p.V249V		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G747A						PASS	.	G		67,3785		0,67,1859	29.0	33.0	32.0		747	3.3	1.0	11	dbSNP_132	32	669,7547		24,621,3463	no	coding-synonymous	EHBP1L1	NM_001099409.1		24,688,5322	AA,AG,GG		8.1426,1.7394,6.0988		249/1524	65348725	736,11332	1926	4108	6034	SO:0001819	synonymous_variant	254102	exon8			CCCTGTGAGTGCT	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.747G>A	11.37:g.65348725G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.951;A|0.049	0.049	strong		0.657	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
ERAP1	51752	hgsc.bcm.edu	37	5	96116808	96116808	+	Silent	SNP	G	G	A	rs17481856	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:96116808G>A	ENST00000443439.2	-	17	2608	c.2542C>T	c.(2542-2544)Ctg>Ttg	p.L848L	ERAP1_ENST00000296754.3_Silent_p.L848L|ERAP1_ENST00000514604.1_5'Flank	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	848					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)		TGCCAGGCCAGTGGGTATCCT	0.398													A|||	299	0.0597045	0.0053	0.1138	5008	,	,		17033	0.0		0.1382	False		,,,				2504	0.0757				p.L848L		Atlas-SNP	.											.	ERAP1	59	.	0			c.C2542T						PASS	.	A	,,	103,4303	816.5+/-416.3	0,103,2100	99.0	105.0	103.0		2542,2542,2542	-5.5	0.0	5	dbSNP_123	103	1169,7431	764.7+/-407.6	63,1043,3194	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	63,1146,5294	AA,AG,GG		13.593,2.3377,9.7801	,,	848/942,848/942,848/949	96116808	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon17			AGGCCAGTGGGTA	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.2542C>T	5.37:g.96116808G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			G|0.917;A|0.083	0.083	strong		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
TRIM42	287015	hgsc.bcm.edu	37	3	140406947	140406947	+	Missense_Mutation	SNP	G	G	A	rs28594654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:140406947G>A	ENST00000286349.3	+	3	1614	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	475	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.		V -> M (in dbSNP:rs28594654).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AATAAACTACGTGCCCTTGGA	0.587													A|||	2006	0.400559	0.2655	0.5058	5008	,	,		19201	0.3899		0.5328	False		,,,				2504	0.3834				p.V475M		Atlas-SNP	.											.	TRIM42	143	.	0			c.G1423A						PASS	.	A	MET/VAL	1368,3038	691.2+/-405.4	218,932,1053	77.0	65.0	69.0		1423	1.8	0.9	3	dbSNP_125	69	4983,3617	521.9+/-380.0	1456,2071,773	yes	missense	TRIM42	NM_152616.4	21	1674,3003,1826	AA,AG,GG		42.0581,31.0486,48.8313	benign	475/724	140406947	6351,6655	2203	4300	6503	SO:0001583	missense	287015	exon3			AACTACGTGCCCT	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1423G>A	3.37:g.140406947G>A	ENSP00000286349:p.Val475Met	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	931	0.42628205128205127	148	0.3008130081300813	179	0.494475138121547	208	0.36363636363636365	396	0.5224274406332454	A	0.139	-1.104067	0.01828	0.310486	0.579419	ENSG00000155890	ENST00000286349	T	0.37752	1.18	5.63	1.79	0.24919	COS domain (1);	0.430834	0.23591	N	0.046556	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	0.44283	-0.9338	9	0.17832	T	0.49	-5.1999	4.4257	0.11501	0.4933:0.3337:0.1731:0.0	rs28594654	475	Q8IWZ5	TRI42_HUMAN	M	475	ENSP00000286349:V475M	ENSP00000286349:V475M	V	+	1	0	TRIM42	141889637	0.030000	0.19436	0.926000	0.36857	0.111000	0.19643	0.379000	0.20585	0.488000	0.27723	-0.254000	0.11334	GTG	G|0.527;A|0.473	0.473	strong		0.587	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
FLII	2314	hgsc.bcm.edu	37	17	18148485	18148485	+	Silent	SNP	G	G	A	rs7498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18148485G>A	ENST00000327031.4	-	30	4002	c.3777C>T	c.(3775-3777)caC>caT	p.H1259H	FLII_ENST00000379450.4_Silent_p.H1173H|FLII_ENST00000579294.1_Silent_p.H1248H|FLII_ENST00000578558.1_Missense_Mutation_p.T669M|FLII_ENST00000545457.2_Silent_p.H1204H	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1259					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CGCTCCAGGCGTGGAAGCAGC	0.627													A|||	1280	0.255591	0.2882	0.2622	5008	,	,		18123	0.3204		0.2435	False		,,,				2504	0.1524				p.H1259H		Atlas-SNP	.											.	FLII	79	.	0			c.C3777T						PASS	.	A		1213,3193	699.9+/-406.5	168,877,1158	85.0	93.0	90.0		3777	-7.1	0.6	17	dbSNP_52	90	2167,6433	706.2+/-405.5	271,1625,2404	no	coding-synonymous	FLII	NM_002018.2		439,2502,3562	AA,AG,GG		25.1977,27.5306,25.988		1259/1270	18148485	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon30			CCAGGCGTGGAAG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3777C>T	17.37:g.18148485G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.728;A|0.272	0.272	strong		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
OR52N2	390077	hgsc.bcm.edu	37	11	5842329	5842329	+	Missense_Mutation	SNP	T	T	G	rs74377989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5842329T>G	ENST00000317037.2	+	1	786	c.764T>G	c.(763-765)gTt>gGt	p.V255G	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, 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)			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)		ATCACCTATGTTGCTGCTTTT	0.443													T|||	204	0.0407348	0.0741	0.0259	5008	,	,		23394	0.002		0.0467	False		,,,				2504	0.0399				p.V255G		Atlas-SNP	.											.	OR52N2	58	.	0			c.T764G						PASS	.	T	GLY/VAL	338,4064	178.0+/-206.8	9,320,1872	210.0	165.0	180.0		764	5.0	0.0	11	dbSNP_132	180	576,8016	154.8+/-208.9	16,544,3736	yes	missense	OR52N2	NM_001005174.1	109	25,864,5608	GG,GT,TT		6.7039,7.6783,7.034	possibly-damaging	255/322	5842329	914,12080	2201	4296	6497	SO:0001583	missense	390077	exon1			CCTATGTTGCTGC	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.764T>G	11.37:g.5842329T>G	ENSP00000322801:p.Val255Gly	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	208	85	0.408654	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	82	0.037545787545787544	37	0.07520325203252033	12	0.03314917127071823	0	0.0	33	0.04353562005277045	T	7.460	0.644505	0.14451	0.076783	0.067039	ENSG00000180988	ENST00000317037	T	0.38077	1.16	6.09	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000183	T	0.02727	0.0082	M	0.62209	1.925	0.18873	N	0.999989	B	0.20550	0.046	B	0.32022	0.139	T	0.07966	-1.0745	10	0.62326	D	0.03	.	12.5707	0.56334	0.0:0.0:0.1392:0.8608	.	255	Q8NGI0	O52N2_HUMAN	G	255	ENSP00000322801:V255G	ENSP00000322801:V255G	V	+	2	0	OR52N2	5798905	0.000000	0.05858	0.036000	0.18154	0.012000	0.07955	0.723000	0.25939	1.109000	0.41680	0.523000	0.50628	GTT	T|0.939;G|0.061	0.061	strong		0.443	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
GTF2F1	2962	hgsc.bcm.edu	37	19	6392906	6392906	+	Missense_Mutation	SNP	G	G	T	rs151336104		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392906G>T	ENST00000394456.5	-	2	485	c.21C>A	c.(19-21)agC>agA	p.S7R	CTB-180A7.6_ENST00000599584.1_RNA|GTF2F1_ENST00000429701.2_5'Flank	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|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)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						CATTCTGGCTGCTAGGGCCCT	0.592											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.S7R		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C21A						PASS	.	G	ARG/SER	0,4406		0,0,2203	138.0	139.0	139.0		21	2.9	1.0	19	dbSNP_134	139	3,8597	2.2+/-6.3	0,3,4297	yes	missense	GTF2F1	NM_002096.2	110	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	7/518	6392906	3,13003	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGGCTGCTAGGG		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.21C>A	19.37:g.6392906G>T	ENSP00000377969:p.Ser7Arg	Somatic	70	0	0	633	WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.51	3.143568	0.57044	0.0	3.49E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.50001	0.76	5.07	2.86	0.33363	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.35566	0.0936	L	0.34521	1.04	0.80722	D	1	B	0.31040	0.305	B	0.33890	0.172	T	0.29941	-0.9995	10	0.59425	D	0.04	-8.1482	8.3825	0.32479	0.086:0.156:0.758:0.0	.	7	P35269	T2FA_HUMAN	R	7	ENSP00000377969:S7R	ENSP00000377969:S7R	S	-	3	2	GTF2F1	6343906	1.000000	0.71417	0.997000	0.53966	0.686000	0.39977	2.995000	0.49441	1.334000	0.45468	-0.282000	0.10007	AGC	G|0.999;T|0.001	0.001	strong		0.592	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
VPS36	51028	hgsc.bcm.edu	37	13	52997751	52997751	+	Silent	SNP	G	G	A	rs148697614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52997751G>A	ENST00000378060.4	-	10	825	c.798C>T	c.(796-798)ctC>ctT	p.L266L		NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	266					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		ACACCTCCGTGAGTGACATTA	0.308													G|||	10	0.00199681	0.0	0.0058	5008	,	,		15634	0.0		0.006	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	VPS36	38	.	0			c.C798T						PASS	.	G		8,4398		0,8,2195	113.0	116.0	115.0		798	-2.3	0.9	13	dbSNP_134	115	29,8571		0,29,4271	no	coding-synonymous	VPS36	NM_016075.2		0,37,6466	AA,AG,GG		0.3372,0.1816,0.2845		266/387	52997751	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	51028	exon10			CTCCGTGAGTGAC	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"""chromosome 13 open reading frame 9"", ""vacuolar protein sorting 36 homolog (yeast)"""	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.798C>T	13.37:g.52997751G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	16	6	0.375	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Silent	SNP	ENST00000378060.4	37	CCDS9434.1																																																																																			G|0.997;A|0.003	0.003	strong		0.308	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3		
MYO9B	4650	hgsc.bcm.edu	37	19	17212925	17212925	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17212925G>A	ENST00000594824.1	+	2	545	c.398G>A	c.(397-399)cGg>cAg	p.R133Q	MYO9B_ENST00000397274.2_Missense_Mutation_p.R133Q|CTD-2528A14.5_ENST00000597045.1_RNA|MYO9B_ENST00000595618.1_Missense_Mutation_p.R133Q			Q13459	MYO9B_HUMAN	myosin IXB	133					actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						ACAGCCACCCGGCGCCTAGTG	0.617																																					p.R133Q		Atlas-SNP	.											.	MYO9B	264	.	0			c.G398A						PASS	.						33.0	35.0	35.0					19																	17212925		2002	4174	6176	SO:0001583	missense	4650	exon2			CCACCCGGCGCCT		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.398G>A	19.37:g.17212925G>A	ENSP00000471367:p.Arg133Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		.	.	.	.	.	.	.	.	.	.	G	11.59	1.683444	0.29872	.	.	ENSG00000099331	ENST00000397274	D	0.84730	-1.89	5.62	3.5	0.40072	.	0.178051	0.27891	N	0.017422	T	0.79713	0.4493	L	0.52126	1.63	0.30811	N	0.738814	B;B;B	0.24651	0.108;0.108;0.064	B;B;B	0.17979	0.01;0.01;0.02	T	0.74475	-0.3653	10	0.37606	T	0.19	.	11.4579	0.50193	0.1454:0.0:0.8546:0.0	.	133;133;139	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	Q	133	ENSP00000380444:R133Q	ENSP00000380444:R133Q	R	+	2	0	MYO9B	17073925	1.000000	0.71417	0.977000	0.42913	0.326000	0.28443	3.417000	0.52714	0.747000	0.32809	-0.119000	0.15052	CGG	.	.	none		0.617	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
FHL5	9457	hgsc.bcm.edu	37	6	97058574	97058574	+	Missense_Mutation	SNP	G	G	A	rs2252816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	156	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	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	
KRT5	3852	hgsc.bcm.edu	37	12	52913668	52913668	+	Missense_Mutation	SNP	C	C	T	rs11170164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52913668C>T	ENST00000252242.4	-	1	803	c.413G>A	c.(412-414)gGa>gAa	p.G138E		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	138	Gly-rich.|Head.		G -> E (in dbSNP:rs11170164). {ECO:0000269|PubMed:7684424}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TTGGATACCTCCAGGAGGGCA	0.622													C|||	133	0.0265575	0.0045	0.0173	5008	,	,		15513	0.0		0.0676	False		,,,				2504	0.0481				p.G138E		Atlas-SNP	.											.	KRT5	88	.	0			c.G413A	GRCh37	CM076254	KRT5	M	rs11170164	PASS	.	C	GLU/GLY	71,4335	62.9+/-100.1	1,69,2133	151.0	145.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	413	5.4	1.0	12	dbSNP_120	147	639,7961	164.2+/-216.6	26,587,3687	yes	missense	KRT5	NM_000424.3	98	27,656,5820	TT,TC,CC		7.4302,1.6114,5.459	probably-damaging	138/591	52913668	710,12296	2203	4300	6503	SO:0001583	missense	3852	exon1			ATACCTCCAGGAG		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.413G>A	12.37:g.52913668C>T	ENSP00000252242:p.Gly138Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	152	86	0.565789	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	63	0.028846153846153848	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	56	0.07387862796833773	C	16.92	3.255260	0.59321	0.016114	0.074302	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000549420;ENST00000551275	D;T;D	0.95137	-3.31;-1.02;-3.62	5.45	5.45	0.79879	.	0.000000	0.56097	D	0.000026	T	0.75867	0.3908	M	0.90145	3.09	0.47621	D	0.999478	D	0.53312	0.959	P	0.46076	0.503	D	0.83396	0.0020	10	0.72032	D	0.01	.	19.2864	0.94072	0.0:1.0:0.0:0.0	rs11170164;rs60852362;rs11170164	138	P13647	K2C5_HUMAN	E	138;103;28;103	ENSP00000252242:G138E;ENSP00000447209:G28E;ENSP00000448041:G103E	ENSP00000252242:G138E	G	-	2	0	KRT5	51199935	.	.	1.000000	0.80357	0.869000	0.49853	.	.	2.559000	0.86315	0.655000	0.94253	GGA	C|0.956;T|0.044	0.044	strong		0.622	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
DISP2	85455	hgsc.bcm.edu	37	15	40661013	40661013	+	Silent	SNP	G	G	T	rs61734053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40661013G>T	ENST00000267889.3	+	8	2787	c.2700G>T	c.(2698-2700)ctG>ctT	p.L900L	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	900					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		ATGGCAGCCTGGCCGCCCTGG	0.602													G|||	157	0.0313498	0.0023	0.0692	5008	,	,		19025	0.0		0.0437	False		,,,				2504	0.0634				p.L900L		Atlas-SNP	.											.	DISP2	86	.	0			c.G2700T						PASS	.	G		55,4351	50.9+/-86.3	0,55,2148	37.0	38.0	38.0		2700	1.7	0.9	15	dbSNP_129	38	423,8177	129.3+/-187.4	5,413,3882	no	coding-synonymous	DISP2	NM_033510.1		5,468,6030	TT,TG,GG		4.9186,1.2483,3.6752		900/1402	40661013	478,12528	2203	4300	6503	SO:0001819	synonymous_variant	85455	exon8			CAGCCTGGCCGCC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2700G>T	15.37:g.40661013G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			G|0.965;T|0.035	0.035	strong		0.602	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
POFUT2	23275	hgsc.bcm.edu	37	21	46705621	46705621	+	Silent	SNP	G	G	A	rs2297285	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46705621G>A	ENST00000349485.5	-	2	380	c.354C>T	c.(352-354)ccC>ccT	p.P118P	POFUT2_ENST00000471540.1_5'Flank|BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000331343.7_Silent_p.P118P	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	118					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		ACTCGATGACGGGGATGTTTT	0.547													G|||	818	0.163339	0.0159	0.1196	5008	,	,		21057	0.1776		0.2485	False		,,,				2504	0.2914				p.P118P		Atlas-SNP	.											POFUT2,NS,carcinoma,-1,1	POFUT2	77	1	0			c.C354T						PASS	.	G	,	227,4179	135.7+/-171.8	3,221,1979	81.0	88.0	85.0		354,354	-9.3	0.3	21	dbSNP_100	85	2116,6484	363.6+/-333.2	267,1582,2451	no	coding-synonymous,coding-synonymous	POFUT2	NM_015227.4,NM_133635.4	,	270,1803,4430	AA,AG,GG		24.6047,5.1521,18.0148	,	118/425,118/430	46705621	2343,10663	2203	4300	6503	SO:0001819	synonymous_variant	23275	exon2			GATGACGGGGATG	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.354C>T	21.37:g.46705621G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			G|0.821;A|0.179	0.179	strong		0.547	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	
ALS2CL	259173	hgsc.bcm.edu	37	3	46713457	46713457	+	Silent	SNP	C	C	G	rs7625303	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46713457C>G	ENST00000318962.4	-	24	2684	c.2601G>C	c.(2599-2601)acG>acC	p.T867T	ALS2CL_ENST00000383742.3_Silent_p.T214T|ALS2CL_ENST00000415953.1_Silent_p.T867T	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	867	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCCTCGACACCGTGCCCTCAA	0.642													C|||	1254	0.250399	0.1483	0.2968	5008	,	,		17491	0.38		0.2197	False		,,,				2504	0.2536				p.T867T		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2601C						PASS	.	C	,,	723,3683	299.8+/-286.0	58,607,1538	124.0	103.0	110.0		2601,2601,642	-10.6	0.7	3	dbSNP_116	110	1848,6752	330.1+/-319.0	197,1454,2649	no	coding-synonymous,coding-synonymous,coding-synonymous	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	,,	255,2061,4187	GG,GC,CC		21.4884,16.4094,19.7678	,,	867/954,867/954,214/301	46713457	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	259173	exon24			CGACACCGTGCCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2601G>C	3.37:g.46713457C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	37	CCDS2743.1																																																																																			C|0.780;G|0.220	0.220	strong		0.642	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
ZNF224	7767	hgsc.bcm.edu	37	19	44611957	44611957	+	Silent	SNP	T	T	C	rs3746322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44611957T>C	ENST00000336976.6	+	6	1898	c.1644T>C	c.(1642-1644)agT>agC	p.S548S	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	548					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S548S(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				GTGGGAAGAGTTTTGGCTGGG	0.418													T|||	981	0.195887	0.3578	0.2277	5008	,	,		21037	0.0843		0.1074	False		,,,				2504	0.1605				p.S548S		Atlas-SNP	.											ZNF224,NS,carcinoma,0,1	ZNF224	70	1	1	Substitution - coding silent(1)	stomach(1)	c.T1644C						PASS	.	T		1340,3066	448.3+/-348.6	200,940,1063	101.0	95.0	97.0		1644	-5.7	0.0	19	dbSNP_107	97	681,7919	170.0+/-221.2	33,615,3652	no	coding-synonymous	ZNF224	NM_013398.2		233,1555,4715	CC,CT,TT		7.9186,30.4131,15.539		548/708	44611957	2021,10985	2203	4300	6503	SO:0001819	synonymous_variant	7767	exon6			GAAGAGTTTTGGC	AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1644T>C	19.37:g.44611957T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Silent	SNP	ENST00000336976.6	37	CCDS33046.1																																																																																			T|0.850;C|0.150	0.150	strong		0.418	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
CD302	9936	hgsc.bcm.edu	37	2	160628466	160628466	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160628466A>G	ENST00000259053.4	-	6	638	c.595T>C	c.(595-597)Tct>Cct	p.S199P	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S1784P|CD302_ENST00000480212.1_5'UTR|LY75_ENST00000554112.1_Missense_Mutation_p.S1840P|CD302_ENST00000429078.2_Missense_Mutation_p.S141P|LY75_ENST00000553424.1_Missense_Mutation_p.S1784P|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S1840P	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	199					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						GTGAAACGAGAATCAGAATGT	0.363																																					p.S1840P		Atlas-SNP	.											CD302,bladder,carcinoma,+1,1	.	.	1	0			c.T5518C						scavenged	.						108.0	110.0	110.0					2																	160628466		2203	4300	6503	SO:0001583	missense	100526664	exon39			AACGAGAATCAGA	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"""CD molecules"", ""C-type lectin domain containing"""	30843	protein-coding gene	gene with protein product	"""C-type lectin domain family 13, member A"""	612246	"""CD302 antigen"""			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.595T>C	2.37:g.160628466A>G	ENSP00000259053:p.Ser199Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	138	3	0.0217391	NM_001198759	A8K5G4|B4E2T9|Q15009	Missense_Mutation	SNP	ENST00000259053.4	37	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222486	0.58668	.	.	ENSG00000241399;ENSG00000241399;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000259053;ENST00000429078;ENST00000554112;ENST00000553424;ENST00000504764;ENST00000505052	T;T;T;T;T;T	0.32272	3.14;1.46;2.79;2.83;2.79;2.83	5.44	4.27	0.50696	.	0.335552	0.27088	N	0.020988	T	0.30103	0.0754	L	0.34521	1.04	0.09310	N	0.999999	D;P;P;P	0.62365	0.991;0.755;0.911;0.952	P;B;P;B	0.50490	0.642;0.295;0.576;0.372	T	0.07121	-1.0789	10	0.35671	T	0.21	-24.5918	10.4421	0.44472	0.836:0.164:0.0:0.0	.	141;1784;1840;199	B4E2T9;O60449-3;O60449-2;Q8IX05	.;.;.;CD302_HUMAN	P	199;141;1840;1784;1840;1784	ENSP00000259053:S199P;ENSP00000394301:S141P;ENSP00000451511:S1840P;ENSP00000451446:S1784P;ENSP00000423463:S1840P;ENSP00000421035:S1784P	ENSP00000259053:S199P	S	-	1	0	LY75;CD302;LY75-CD302	160336712	0.411000	0.25384	0.704000	0.30370	0.563000	0.35712	1.752000	0.38349	0.889000	0.36185	0.477000	0.44152	TCT	.	.	none		0.363	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880	
HK1	3098	hgsc.bcm.edu	37	10	71142420	71142420	+	Silent	SNP	G	G	A	rs748235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:71142420G>A	ENST00000359426.6	+	10	1547	c.1443G>A	c.(1441-1443)aaG>aaA	p.K481K	HK1_ENST00000404387.2_Silent_p.K485K|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Silent_p.K469K|HK1_ENST00000448642.2_Silent_p.K516K|HK1_ENST00000298649.3_Silent_p.K480K	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	481	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						ACCTCACCAAGGACATGCTGC	0.627													G|||	3900	0.778754	0.8896	0.6254	5008	,	,		17382	0.6409		0.7763	False		,,,				2504	0.8824				p.K485K		Atlas-SNP	.											.	HK1	170	.	0			c.G1455A						PASS	.	G	,,,,	3875,531	775.1+/-414.1	1701,473,29	69.0	59.0	62.0		1443,1440,1455,1455,1407	2.5	1.0	10	dbSNP_86	62	6791,1809	731.7+/-406.8	2691,1409,200	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	4392,1882,229	AA,AG,GG		21.0349,12.0517,17.9917	,,,,	481/918,480/917,485/922,485/922,469/906	71142420	10666,2340	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon13			CACCAAGGACATG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1443G>A	10.37:g.71142420G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			G|0.201;A|0.799	0.799	strong		0.627	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
DNAJC5B	85479	hgsc.bcm.edu	37	8	66992737	66992737	+	Silent	SNP	G	G	A	rs7006209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:66992737G>A	ENST00000276570.5	+	5	746	c.459G>A	c.(457-459)gtG>gtA	p.V153V	DNAJC5B_ENST00000519330.1_3'UTR	NM_033105.4	NP_149096.2	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 beta	153						membrane (GO:0016020)				endometrium(3)|large_intestine(6)|liver(1)|lung(6)|prostate(1)|skin(3)	20		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			ACTTCTATGTGTCCCCAGAGG	0.552													G|||	357	0.0712859	0.1944	0.0375	5008	,	,		20135	0.0		0.0487	False		,,,				2504	0.0256				p.V153V		Atlas-SNP	.											.	DNAJC5B	42	.	0			c.G459A						PASS	.	G		783,3623	310.2+/-291.5	70,643,1490	65.0	54.0	58.0		459	5.1	1.0	8	dbSNP_116	58	408,8192	128.5+/-186.7	11,386,3903	no	coding-synonymous	DNAJC5B	NM_033105.4		81,1029,5393	AA,AG,GG		4.7442,17.7712,9.1573		153/200	66992737	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	85479	exon5			CTATGTGTCCCCA	AF368276	CCDS6183.1	8q13.1	2012-10-02			ENSG00000147570	ENSG00000147570		"""Heat shock proteins / DNAJ (HSP40)"""	24138	protein-coding gene	gene with protein product		613945				12477932	Standard	NM_033105		Approved	MGC26226, CSP-beta	uc003xvs.1	Q9UF47	OTTHUMG00000164470	ENST00000276570.5:c.459G>A	8.37:g.66992737G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_033105	Q969Y8	Silent	SNP	ENST00000276570.5	37	CCDS6183.1																																																																																			G|0.909;A|0.091	0.091	strong		0.552	DNAJC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378915.1	NM_033105	
KMT2C	58508	hgsc.bcm.edu	37	7	151927016	151927016	+	Missense_Mutation	SNP	T	T	C	rs141049734		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151927016T>C	ENST00000262189.6	-	18	3186	c.2968A>G	c.(2968-2970)Agt>Ggt	p.S990G	KMT2C_ENST00000355193.2_Missense_Mutation_p.S990G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	990					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)	p.S990G(6)									ACCTTAATACTGACACAGTAT	0.363																																					p.S990G		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,0,6	MLL3	1564	6	6	Substitution - Missense(6)	skin(6)	c.A2968G						scavenged	.						31.0	25.0	27.0					7																	151927016		2166	4178	6344	SO:0001583	missense	58508	exon18			TAATACTGACACA	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.2968A>G	7.37:g.151927016T>C	ENSP00000262189:p.Ser990Gly	Somatic	390	1	0.0025641		WXS	Illumina HiSeq	Phase_I	403	39	0.0967742	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.72|12.72	2.022540|2.022540	0.35701|0.35701	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000418673|ENST00000262189;ENST00000355193	.|D;D	.|0.85339	.|-1.97;-1.97	4.67|4.67	4.67|4.67	0.58626|0.58626	.|Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	.|0.000000	.|0.48767	.|U	.|0.000180	T|T	0.82001|0.82001	0.4942|0.4942	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	D|D	1|1	.|D;B	.|0.63046	.|0.992;0.114	.|D;B	.|0.76071	.|0.987;0.083	D|D	0.83865|0.83865	0.0270|0.0270	5|10	.|0.33141	.|T	.|0.24	.|.	14.4054|14.4054	0.67079|0.67079	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|990;51	.|Q8NEZ4;Q8NEZ4-2	.|MLL3_HUMAN;.	R|G	145|990	.|ENSP00000262189:S990G;ENSP00000347325:S990G	.|ENSP00000262189:S990G	Q|S	-|-	2|1	0|0	MLL3|MLL3	151557949|151557949	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.888000|4.888000	0.63164|0.63164	1.866000|1.866000	0.54105|0.54105	0.377000|0.377000	0.23210|0.23210	CAG|AGT	.	.	weak		0.363	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ECM2	1842	hgsc.bcm.edu	37	9	95279985	95279985	+	Silent	SNP	C	C	A	rs968040	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:95279985C>A	ENST00000344604.5	-	3	614	c.465G>T	c.(463-465)ccG>ccT	p.P155P	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.P155P|ECM2_ENST00000375540.1_Silent_p.P155P	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	155	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						CGGAGCAGACCGGGCAGCATT	0.423													C|||	1676	0.334665	0.7557	0.2421	5008	,	,		18956	0.0893		0.2932	False		,,,				2504	0.1268				p.P155P		Atlas-SNP	.											.	ECM2	147	.	0			c.G465T						PASS	.	C	,,,	2918,1488	678.6+/-403.6	969,980,254	152.0	162.0	158.0		,465,465,465	-10.7	0.0	9	dbSNP_86	158	2496,6104	411.9+/-350.6	371,1754,2175	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	1340,2734,2429	AA,AC,CC		29.0233,33.7721,41.6269	,,,	,155/678,155/644,155/700	95279985	5414,7592	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon3			GCAGACCGGGCAG	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.465G>T	9.37:g.95279985C>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			C|0.602;A|0.398	0.398	strong		0.423	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
MUC20	200958	hgsc.bcm.edu	37	3	195453243	195453243	+	Missense_Mutation	SNP	C	C	T	rs3828408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195453243C>T	ENST00000447234.2	+	2	1895	c.1769C>T	c.(1768-1770)cCg>cTg	p.P590L	MUC20_ENST00000320736.6_Missense_Mutation_p.P419L|MUC20_ENST00000445522.2_Missense_Mutation_p.P555L|MUC20_ENST00000436408.1_Missense_Mutation_p.P590L	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	590	Involved in oligomerization.|Thr-rich.		P -> L (in dbSNP:rs3828408). {ECO:0000269|PubMed:15489334}.		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)		TCAGAGACACCGACCATGGAC	0.602																																					p.P419L		Atlas-SNP	.											.	MUC20	84	.	0			c.C1256T						PASS	.						63.0	59.0	60.0					3																	195453243		2047	4191	6238	SO:0001583	missense	200958	exon3			AGACACCGACCAT	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.1769C>T	3.37:g.195453243C>T	ENSP00000414350:p.Pro590Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	145	85	0.586207	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		683	0.31272893772893773	86	0.17479674796747968	120	0.3314917127071823	256	0.44755244755244755	221	0.29155672823219	C	11.91	1.779655	0.31502	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.11385	3.19;3.15;3.36;2.78	4.69	-1.57	0.08506	.	0.995724	0.08133	N	0.992892	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.23891	0.093	B	0.16722	0.016	T	0.46091	-0.9216	9	0.31617	T	0.26	1.2966	9.428	0.38592	0.0:0.7235:0.0:0.2765	rs3828408;rs4084964	419	E9PH32	.	L	590;419;590;555	ENSP00000414350:P590L;ENSP00000325431:P419L;ENSP00000396774:P590L;ENSP00000405629:P555L	ENSP00000325431:P419L	P	+	2	0	MUC20	196938914	0.087000	0.21565	0.000000	0.03702	0.002000	0.02628	0.258000	0.18387	-0.224000	0.09928	0.558000	0.71614	CCG	C|0.677;T|0.323	0.323	strong		0.602	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
PEAR1	375033	hgsc.bcm.edu	37	1	156878531	156878531	+	Silent	SNP	T	T	C	rs11264580	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156878531T>C	ENST00000338302.3	+	11	1425	c.1200T>C	c.(1198-1200)caT>caC	p.H400H	PEAR1_ENST00000292357.7_Silent_p.H400H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	400	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGGACACGCATGGGCCAGGGT	0.716													C|||	1118	0.223243	0.2617	0.1585	5008	,	,		14582	0.3135		0.1243	False		,,,				2504	0.226				p.H400H		Atlas-SNP	.											PEAR1,colon,carcinoma,0,1	PEAR1	118	1	0			c.T1200C						PASS	.	C		1033,3307		130,773,1267	16.0	15.0	15.0		1200	1.9	1.0	1	dbSNP_120	15	1014,7508		64,886,3311	no	coding-synonymous	PEAR1	NM_001080471.1		194,1659,4578	CC,CT,TT		11.8986,23.8018,15.9151		400/1038	156878531	2047,10815	2170	4261	6431	SO:0001819	synonymous_variant	375033	exon10			CACGCATGGGCCA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1200T>C	1.37:g.156878531T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	25	0.328947	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			T|0.780;C|0.220	0.220	strong		0.716	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
MUC5B	727897	hgsc.bcm.edu	37	11	1269627	1269627	+	Silent	SNP	C	C	T	rs4963056	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1269627C>T	ENST00000529681.1	+	31	11575	c.11517C>T	c.(11515-11517)acC>acT	p.T3839T	MUC5B_ENST00000447027.1_Silent_p.T3842T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3839	11 X approximate tandem repeats, Ser/Thr- rich.|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)		TGCTTACCACCACGGCCACCA	0.637													C|||	1690	0.33746	0.2126	0.3199	5008	,	,		16897	0.5962		0.2853	False		,,,				2504	0.3057				p.T3839T		Atlas-SNP	.											.	MUC5B	473	.	0			c.C11517T						PASS	.	C		831,3419		75,681,1369	156.0	183.0	174.0		11517	2.0	0.0	11	dbSNP_111	174	2509,5905		399,1711,2097	no	coding-synonymous	MUC5B	NM_002458.2		474,2392,3466	TT,TC,CC		29.8193,19.5529,26.374		3839/5763	1269627	3340,9324	2125	4207	6332	SO:0001819	synonymous_variant	727897	exon31			TACCACCACGGCC	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.11517C>T	11.37:g.1269627C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	218	85	0.389908	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.749;T|0.251	0.251	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GSDMB	55876	hgsc.bcm.edu	37	17	38062196	38062196	+	Missense_Mutation	SNP	G	G	A	rs2305480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38062196G>A	ENST00000394179.1	-	8	1046	c.916C>T	c.(916-918)Cca>Tca	p.P306S	GSDMB_ENST00000394175.2_Missense_Mutation_p.P289S|GSDMB_ENST00000520542.1_Missense_Mutation_p.P302S|GSDMB_ENST00000360317.3_Missense_Mutation_p.P311S|GSDMB_ENST00000309481.7_Missense_Mutation_p.P298S|GSDMB_ENST00000418519.1_Missense_Mutation_p.P311S			Q8TAX9	GSDMB_HUMAN	gasdermin B	306			P -> S (in dbSNP:rs2305480). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.P289S(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						GGCTTGTCTGGGTCCTCCATG	0.537													G|||	1436	0.286741	0.1074	0.3357	5008	,	,		16886	0.2817		0.4662	False		,,,				2504	0.3149				p.P311S		Atlas-SNP	.											GSDMB,NS,carcinoma,0,1	GSDMB	87	1	1	Substitution - Missense(1)	stomach(1)	c.C931T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	647,3759	274.9+/-272.2	49,549,1605	70.0	69.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	892,931,904,865	0.5	0.0	17	dbSNP_100	69	3808,4792	535.7+/-382.9	832,2144,1324	yes	missense,missense,missense,missense	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	74,74,74,74	881,2693,2929	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	44.2791,14.6845,34.2534	benign,benign,benign,benign	298/404,311/417,302/408,289/395	38062196	4455,8551	2203	4300	6503	SO:0001583	missense	55876	exon9			TGTCTGGGTCCTC	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.916C>T	17.37:g.38062196G>A	ENSP00000377733:p.Pro306Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Missense_Mutation	SNP	ENST00000394179.1	37		718	0.32875457875457875	53	0.10772357723577236	126	0.34806629834254144	180	0.3146853146853147	359	0.4736147757255937	G	0.915	-0.717902	0.03182	0.146845	0.442791	ENSG00000073605	ENST00000360317;ENST00000394175;ENST00000309481;ENST00000520542;ENST00000418519;ENST00000394179	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	3.8	0.469	0.16741	.	0.282386	0.24991	N	0.034000	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	P;B;P;B;B	0.46395	0.877;0.336;0.636;0.336;0.336	P;B;B;B;B	0.51615	0.675;0.087;0.404;0.143;0.087	T	0.41662	-0.9496	9	0.14252	T	0.57	.	5.491	0.16777	0.4151:0.0:0.5849:0.0	rs2305480;rs17677099;rs17845769;rs17858729;rs58161295;rs2305480	302;311;306;298;289	B4DKK7;Q8TAX9-4;Q8TAX9;Q8TAX9-3;Q8TAX9-2	.;.;GSDMB_HUMAN;.;.	S	306;289;298;302;311;306	ENSP00000377729:P289S;ENSP00000312584:P298S;ENSP00000430157:P302S;ENSP00000415049:P311S;ENSP00000377733:P306S	ENSP00000312584:P298S	P	-	1	0	GSDMB	35315722	0.032000	0.19561	0.001000	0.08648	0.002000	0.02628	0.422000	0.21296	0.325000	0.23359	-0.466000	0.05196	CCA	G|0.674;A|0.326	0.326	strong		0.537	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632717	32632717	+	Silent	SNP	G	G	A	rs1049073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632717G>A	ENST00000399084.1	-	3	415	c.237C>T	c.(235-237)taC>taT	p.Y79Y	HLA-DQB1_ENST00000434651.2_Silent_p.Y79Y|HLA-DQB1_ENST00000374943.4_Silent_p.Y79Y|HLA-DQB1_ENST00000399079.3_Silent_p.Y79Y|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	79	Beta-1.		Y -> F (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04 and allele DQB1*02:05; dbSNP:rs9274397).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCACCGCGCGGTACACCCCCA	0.637									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				G|||	1831	0.365615	0.1573	0.4222	5008	,	,		5390	0.5109		0.2952	False		,,,				2504	0.5297				p.Y79Y	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C237T						PASS	.	G		485,3767		63,359,1704	39.0	38.0	38.0		237	2.2	0.0	6	dbSNP_86	38	1761,6679		354,1053,2813	no	coding-synonymous	HLA-DQB1	NM_002123.4		417,1412,4517	AA,AG,GG		20.8649,11.4064,17.6962		79/262	32632717	2246,10446	2126	4220	6346	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CGCGCGGTACACC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.237C>T	6.37:g.32632717G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	23	16	0.695652	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			G|0.712;A|0.288	0.288	strong		0.637	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
ARFRP1	10139	hgsc.bcm.edu	37	20	62333231	62333231	+	Missense_Mutation	SNP	G	G	A	rs139547982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62333231G>A	ENST00000359715.5	-	5	934	c.368C>T	c.(367-369)gCg>gTg	p.A123V	ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000324228.2_Missense_Mutation_p.A123V|ARFRP1_ENST00000609142.1_Missense_Mutation_p.A123V|ARFRP1_ENST00000440854.1_Missense_Mutation_p.A123V|ARFRP1_ENST00000607873.1_Missense_Mutation_p.A76V			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	123					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			ACCGCACAGCGCCTCGCTGGT	0.687													G|||	2	0.000399361	0.0	0.0014	5008	,	,		15284	0.001		0.0	False		,,,				2504	0.0				p.A123V		Atlas-SNP	.											ARFRP1,colon,carcinoma,+1,1	ARFRP1	17	1	0			c.C368T						PASS	.	G	VAL/ALA,VAL/ALA	1,4167		0,1,2083	48.0	28.0	35.0		368,368	4.6	0.6	20	dbSNP_134	35	10,8152		0,10,4071	yes	missense,missense	ARFRP1	NM_001134758.1,NM_003224.3	64,64	0,11,6154	AA,AG,GG		0.1225,0.024,0.0892	benign,benign	123/174,123/202	62333231	11,12319	2084	4081	6165	SO:0001583	missense	10139	exon6			CACAGCGCCTCGC	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"""ADP-ribosylation factors"""	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.368C>T	20.37:g.62333231G>A	ENSP00000352746:p.Ala123Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	37	CCDS13533.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	G	11.15	1.552881	0.27739	2.4E-4	0.001225	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.63913	-0.07;-0.07;-0.07	5.53	4.57	0.56435	Small GTP-binding protein domain (1);	0.234257	0.42053	D	0.000776	T	0.41351	0.1155	L	0.33624	1.015	0.50467	D	0.999877	B	0.12630	0.006	B	0.12156	0.007	T	0.44757	-0.9307	10	0.51188	T	0.08	-29.5252	10.3719	0.44060	0.1489:0.0:0.8511:0.0	.	123	Q13795	ARFRP_HUMAN	V	123	ENSP00000403942:A123V;ENSP00000352746:A123V;ENSP00000326884:A123V	ENSP00000326884:A123V	A	-	2	0	ARFRP1	61803675	0.992000	0.36948	0.594000	0.28785	0.597000	0.36814	2.904000	0.48719	2.590000	0.87494	0.462000	0.41574	GCG	G|0.999;A|0.001	0.001	strong		0.687	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1		
ETS1	2113	hgsc.bcm.edu	37	11	128333503	128333503	+	Silent	SNP	T	T	C	rs2230004	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:128333503T>C	ENST00000319397.6	-	7	1320	c.1011A>G	c.(1009-1011)ctA>ctG	p.L337L	ETS1_ENST00000535549.1_Silent_p.L121L|ETS1_ENST00000526145.2_Silent_p.L250L|ETS1_ENST00000392668.4_Silent_p.L381L|ETS1_ENST00000531611.1_Intron|ETS1_ENST00000345075.4_Silent_p.L250L	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	337				SGPIQL -> RRPPAA (in Ref. 11; AAA52409). {ECO:0000305}.	angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|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)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		GAAACTGCCATAGCTGGATTG	0.468													C|||	2402	0.479633	0.4561	0.3646	5008	,	,		19297	0.5962		0.493	False		,,,				2504	0.4591				p.L381L		Atlas-SNP	.											.	ETS1	123	.	0			c.A1143G						PASS	.	C	,,	2090,2312	603.0+/-390.0	517,1056,628	106.0	104.0	105.0		1143,363,1011	5.9	1.0	11	dbSNP_116	105	4034,4560	596.3+/-393.6	932,2170,1195	no	coding-synonymous,coding-synonymous,coding-synonymous	ETS1	NM_001143820.1,NM_001162422.1,NM_005238.3	,,	1449,3226,1823	CC,CT,TT		46.9397,47.4784,47.1222	,,	381/486,121/226,337/442	128333503	6124,6872	2201	4297	6498	SO:0001819	synonymous_variant	2113	exon9			CTGCCATAGCTGG		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"""Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1"", ""ets protein"""	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.1011A>G	11.37:g.128333503T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	61	40	0.655738	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Silent	SNP	ENST00000319397.6	37	CCDS8475.1																																																																																			T|0.524;C|0.476	0.476	strong		0.468	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238	
FKBP15	23307	hgsc.bcm.edu	37	9	115933978	115933978	+	Silent	SNP	G	G	A	rs1128117|rs386737766	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115933978G>A	ENST00000238256.3	-	24	2658	c.2541C>T	c.(2539-2541)gcC>gcT	p.A847A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	847			A -> S (in dbSNP:rs1128116).		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						GGGCCTGGAGGGCTAAACACT	0.502													G|||	399	0.0796725	0.0991	0.0389	5008	,	,		11897	0.0387		0.0477	False		,,,				2504	0.1575				p.A847A		Atlas-SNP	.											.	FKBP15	128	.	0			c.C2541T						PASS	.	G		382,3380		14,354,1513	83.0	84.0	84.0		2541	-1.9	0.8	9	dbSNP_86	84	505,7723		15,475,3624	no	coding-synonymous	FKBP15	NM_015258.1		29,829,5137	AA,AG,GG		6.1376,10.1542,7.3978		847/1220	115933978	887,11103	1881	4114	5995	SO:0001819	synonymous_variant	23307	exon24			CTGGAGGGCTAAA	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.2541C>T	9.37:g.115933978G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.940;A|0.060	0.060	strong		0.502	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
UGT1A6	54578	hgsc.bcm.edu	37	2	234601965	234601965	+	Silent	SNP	A	A	G	rs1105880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234601965A>G	ENST00000305139.6	+	1	454	c.315A>G	c.(313-315)ctA>ctG	p.L105L	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_5'Flank|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	105					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	GATCATTCCTAACTGCTCCTC	0.448													G|||	1716	0.342652	0.3684	0.304	5008	,	,		21918	0.2242		0.333	False		,,,				2504	0.4673				p.L105L		Atlas-SNP	.											.	UGT1A6	63	.	0			c.A315G						PASS	.	G	,,,,,	1611,2795	663.2+/-401.2	308,995,900	91.0	82.0	85.0		315,,,,,	2.5	0.0	2	dbSNP_86	85	3078,5522	660.8+/-401.8	563,1952,1785	no	coding-synonymous,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2,NM_205862.1	,,,,,	871,2947,2685	GG,GA,AA		35.7907,36.5638,36.0526	,,,,,	105/533,,,,,	234601965	4689,8317	2203	4300	6503	SO:0001819	synonymous_variant	54578	exon1			ATTCCTAACTGCT	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.315A>G	2.37:g.234601965A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001072	A6NKK6|B8K289|Q96TE7	Silent	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			A|0.659;G|0.341	0.341	strong		0.448	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
DNAH5	1767	hgsc.bcm.edu	37	5	13829799	13829799	+	Silent	SNP	G	G	A	rs1348689	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13829799G>A	ENST00000265104.4	-	38	6368	c.6264C>T	c.(6262-6264)gcC>gcT	p.A2088A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2088	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)					CCTGCCGTCCGGCATAGCCAG	0.423									Kartagener syndrome				G|||	2220	0.443291	0.4705	0.4207	5008	,	,		21016	0.626		0.3698	False		,,,				2504	0.3098				p.A2088A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C6264T						PASS	.	G		2011,2395	561.5+/-380.7	451,1109,643	69.0	66.0	67.0		6264	-9.1	0.7	5	dbSNP_88	67	3135,5465	478.5+/-369.9	576,1983,1741	no	coding-synonymous	DNAH5	NM_001369.2		1027,3092,2384	AA,AG,GG		36.4535,45.6423,39.5664		2088/4625	13829799	5146,7860	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon38	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCGTCCGGCATAG	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.6264C>T	5.37:g.13829799G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DCPS	28960	hgsc.bcm.edu	37	11	126213242	126213242	+	Missense_Mutation	SNP	G	G	A	rs35836343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126213242G>A	ENST00000263579.4	+	5	1006	c.677G>A	c.(676-678)gGc>gAc	p.G226D	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	226					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)		CATCGCCGGGGCATCAGATCC	0.607													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18355	0.0		0.002	False		,,,				2504	0.0				p.G226D		Atlas-SNP	.											.	DCPS	33	.	0			c.G677A						PASS	.	G	ASP/GLY	5,4397	11.4+/-27.6	0,5,2196	84.0	62.0	69.0		677	0.2	1.0	11	dbSNP_126	69	66,8530	38.8+/-94.9	0,66,4232	yes	missense	DCPS	NM_014026.3	94	0,71,6428	AA,AG,GG		0.7678,0.1136,0.5462	possibly-damaging	226/338	126213242	71,12927	2201	4298	6499	SO:0001583	missense	28960	exon5			GCCGGGGCATCAG	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.677G>A	11.37:g.126213242G>A	ENSP00000263579:p.Gly226Asp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	11.16	1.556018	0.27827	0.001136	0.007678	ENSG00000110063	ENST00000263579	D	0.94966	-3.57	5.31	0.2	0.15181	Histidine triad-like motif (1);	0.269864	0.42548	N	0.000697	T	0.78272	0.4257	N	0.04820	-0.15	0.50171	D	0.999857	B	0.16603	0.018	B	0.30316	0.114	T	0.68667	-0.5348	10	0.02654	T	1	-8.8663	7.34	0.26632	0.3137:0.1113:0.5751:0.0	rs35836343	226	Q96C86	DCPS_HUMAN	D	226	ENSP00000263579:G226D	ENSP00000263579:G226D	G	+	2	0	DCPS	125718452	0.981000	0.34729	0.986000	0.45419	0.713000	0.41058	1.462000	0.35266	-0.091000	0.12440	-0.123000	0.14984	GGC	G|0.995;A|0.005	0.005	strong		0.607	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
KIF1B	23095	hgsc.bcm.edu	37	1	10364260	10364260	+	Intron	SNP	A	A	G	rs148481786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10364260A>G	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377081.1_Intron|RN7SL731P_ENST00000584329.1_RNA|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377083.1_Missense_Mutation_p.E1006G|KIF1B_ENST00000377093.4_Missense_Mutation_p.E1006G			O60333	KIF1B_HUMAN	kinesin family member 1B						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)		GAGAGCCAAGAAAAAGGGGGT	0.423													A|||	11	0.00219649	0.0	0.0029	5008	,	,		20281	0.0		0.007	False		,,,				2504	0.002				p.E1006G		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3017G						PASS	.	A	,GLY/GLU	2,4404	2.1+/-5.4	0,2,2201	108.0	117.0	114.0		,3017	4.4	0.9	1	dbSNP_134	114	52,8548	30.7+/-82.3	1,50,4249	yes	intron,missense	KIF1B	NM_015074.3,NM_183416.3	,98	1,52,6450	GG,GA,AA		0.6047,0.0454,0.4152	,	,1006/1154	10364260	54,12952	2203	4300	6503	SO:0001627	intron_variant	23095	exon21			GCCAAGAAAAAGG	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.2115+6956A>G	1.37:g.10364260A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	43	0.605634	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	11.72	1.722702	0.30503	4.54E-4	0.006047	ENSG00000054523	ENST00000377093;ENST00000377083	T;T	0.73152	-0.72;-0.72	5.48	4.36	0.52297	.	.	.	.	.	T	0.55513	0.1925	.	.	.	0.80722	D	1	B	0.34290	0.447	B	0.33690	0.168	T	0.61038	-0.7143	8	0.66056	D	0.02	.	9.7928	0.40717	0.9228:0.0:0.0772:0.0	.	1006	O60333-3	.	G	1006	ENSP00000366297:E1006G;ENSP00000366287:E1006G	ENSP00000366287:E1006G	E	+	2	0	KIF1B	10286847	0.933000	0.31639	0.938000	0.37757	0.716000	0.41182	1.714000	0.37961	0.931000	0.37242	0.533000	0.62120	GAA	A|0.994;G|0.006	0.006	strong		0.423	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
IFITM5	387733	hgsc.bcm.edu	37	11	299411	299411	+	Missense_Mutation	SNP	C	C	G	rs57285449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:299411C>G	ENST00000382614.2	-	1	115	c.80G>C	c.(79-81)gGg>gCg	p.G27A		NM_001025295.2	NP_001020466.1	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	27			G -> A (in dbSNP:rs57285449).		bone mineralization (GO:0030282)|regulation of bone mineralization (GO:0030500)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		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;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTGCGGGGCCCCCAGTGTGAG	0.682													c|||	2968	0.592652	0.7148	0.5922	5008	,	,		8718	0.6429		0.3479	False		,,,				2504	0.6278				p.G27A		Atlas-SNP	.											.	IFITM5	12	.	0			c.G80C						PASS	.	C	ALA/GLY	2610,1758		836,938,410	22.0	22.0	22.0		80	2.2	0.0	11	dbSNP_129	22	2407,6153		412,1583,2285	no	missense	IFITM5	NM_001025295.1	60	1248,2521,2695	GG,GC,CC		28.1192,40.2473,38.8072	probably-damaging	27/133	299411	5017,7911	2184	4280	6464	SO:0001583	missense	387733	exon1			GGGGCCCCCAGTG	AA463818, CR747200, DY654432	CCDS31323.1	11p15.5	2010-05-12			ENSG00000206013	ENSG00000206013			16644	protein-coding gene	gene with protein product		614757				11106657, 12659663, 18442316	Standard	NM_001025295		Approved	fragilis4, Hrmp1, BRIL	uc001low.2	A6NNB3	OTTHUMG00000165355	ENST00000382614.2:c.80G>C	11.37:g.299411C>G	ENSP00000372059:p.Gly27Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	33	0.33	NM_001025295		Missense_Mutation	SNP	ENST00000382614.2	37	CCDS31323.1	1064	0.48717948717948717	325	0.6605691056910569	166	0.4585635359116022	333	0.5821678321678322	240	0.316622691292876	C	5.600	0.295412	0.10622	0.597527	0.281192	ENSG00000206013	ENST00000382614	D	0.85556	-2.0	4.23	2.25	0.28309	.	0.185737	0.35179	N	0.003399	T	0.00012	0.0000	L	0.46157	1.445	0.38741	P	0.04611500000000002	B	0.12630	0.006	B	0.15484	0.013	T	0.48328	-0.9045	9	0.13853	T	0.58	-5.224	7.931	0.29901	0.0:0.6073:0.3018:0.0908	rs57285449;rs61876233	27	A6NNB3	IFM5_HUMAN	A	27	ENSP00000372059:G27A	ENSP00000372059:G27A	G	-	2	0	IFITM5	289411	0.603000	0.26924	0.029000	0.17559	0.033000	0.12548	1.221000	0.32503	0.203000	0.20529	0.561000	0.74099	GGG	C|0.546;G|0.454	0.454	strong		0.682	IFITM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383588.1	NM_001025295	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:173516903A>G	ENST00000367714.3	-	13	1904	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N	SLC9C2_ENST00000536496.1_Silent_p.N392N|SLC9C2_ENST00000466087.1_5'UTR	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	75	0	0		WXS	Illumina HiSeq	Phase_I	126	75	0.595238	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	
PALLD	23022	hgsc.bcm.edu	37	4	169433444	169433444	+	Silent	SNP	C	C	T	rs72695199	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169433444C>T	ENST00000505667.1	+	2	962	c.789C>T	c.(787-789)agC>agT	p.S263S	PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.S263S|PALLD_ENST00000333488.4_Silent_p.S140S			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	263					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AGCCCCACAGCGCCCTCCACT	0.567									Pancreatic Cancer, Familial Clustering of				C|||	287	0.0573083	0.0189	0.0778	5008	,	,		17753	0.0		0.1173	False		,,,				2504	0.092				p.S263S	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C789T						PASS	.	C	,	189,4217	118.4+/-156.1	9,171,2023	65.0	59.0	61.0		789,789	-10.4	0.0	4	dbSNP_130	61	1168,7432	238.9+/-270.2	76,1016,3208	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	85,1187,5231	TT,TC,CC		13.5814,4.2896,10.4336	,	263/1124,263/1107	169433444	1357,11649	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CCACAGCGCCCTC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.789C>T	4.37:g.169433444C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.907;T|0.093	0.093	strong		0.567	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
LATS2	26524	hgsc.bcm.edu	37	13	21562832	21562832	+	Missense_Mutation	SNP	C	C	T	rs2770928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21562832C>T	ENST00000382592.4	-	4	1492	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S	LATS2_ENST00000542899.1_Missense_Mutation_p.G363S|LATS2_ENST00000472754.1_5'Flank	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)		GAGGTGCTGCCCAATTCATAC	0.716													T|||	4258	0.85024	0.6876	0.9135	5008	,	,		9653	0.997		0.8767	False		,,,				2504	0.8466				p.G363S		Atlas-SNP	.											LATS2_ENST00000382592,NS,carcinoma,0,1	LATS2	176	1	0			c.G1087A						scavenged	.	T	SER/GLY	3174,1152		1175,824,164	25.0	27.0	26.0		1087	-1.1	0.0	13	dbSNP_100	26	7379,969		3255,869,50	yes	missense	LATS2	NM_014572.2	56	4430,1693,214	TT,TC,CC		11.6076,26.6297,16.735	benign	363/1089	21562832	10553,2121	2163	4174	6337	SO:0001583	missense	26524	exon4			TGCTGCCCAATTC	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.1087G>A	13.37:g.21562832C>T	ENSP00000372035:p.Gly363Ser	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	1898	0.8690476190476191	334	0.6788617886178862	330	0.9116022099447514	572	1.0	662	0.8733509234828496	T	4.469	0.087000	0.08583	0.733703	0.883924	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.57436	0.4;0.4	4.94	-1.07	0.09968	.	1.091720	0.06907	N	0.806929	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.47315	-0.9127	9	0.02654	T	1	.	11.4202	0.49976	0.0:0.4735:0.0:0.5265	rs2770928;rs60641998	363	Q9NRM7	LATS2_HUMAN	S	363	ENSP00000372035:G363S;ENSP00000441817:G363S	ENSP00000372035:G363S	G	-	1	0	LATS2	20460832	0.893000	0.30496	0.000000	0.03702	0.051000	0.14879	0.768000	0.26590	-0.622000	0.05626	-1.487000	0.00979	GGC	T|0.842;G|0.000;C|0.158;A|0.000	0.842	strong		0.716	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093311	1093311	+	Silent	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1093311C>A	ENST00000441003.2	+	30	5157	c.5130C>A	c.(5128-5130)acC>acA	p.T1710T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1677T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tgaccccaaccccaacaccca	0.637																																					p.T1710T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,2	MUC2	614	2	0			c.C5130A						scavenged	.						143.0	189.0	173.0					11																	1093311		1906	3557	5463	SO:0001819	synonymous_variant	4583	exon30			CCCAACCCCAACA	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.5130C>A	11.37:g.1093311C>A		Somatic	21	3	0.142857		WXS	Illumina HiSeq	Phase_I	36	5	0.138889	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR10K2	391107	hgsc.bcm.edu	37	1	158390378	158390378	+	Silent	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158390378A>T	ENST00000314902.2	-	1	278	c.279T>A	c.(277-279)tcT>tcA	p.S93S		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	93						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)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					AGCCCAGGAAAGAAATGGTCT	0.478																																					p.S93S		Atlas-SNP	.											OR10K2,rectum,carcinoma,-1,1	OR10K2	69	1	0			c.T279A						PASS	.						176.0	172.0	174.0					1																	158390378		2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			CAGGAAAGAAATG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.279T>A	1.37:g.158390378A>T		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	231	139	0.601732	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			.	.	none		0.478	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5231712T>A	ENST00000239316.4	+	1	294	c.189T>A	c.(187-189)cgT>cgA	p.R63R		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	63					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		AATCTGGACGTCCCAAAGGTG	0.512													A|||	1999	0.399161	0.7337	0.3775	5008	,	,		19844	0.2222		0.2883	False		,,,				2504	0.2587				p.R63R		Atlas-SNP	.											INSL4,bladder,carcinoma,+2,1	INSL4	20	1	0			c.T189A						scavenged	.	A		2877,1529	483.3+/-359.7	937,1003,263	46.0	46.0	46.0		189	0.4	0.0	9	dbSNP_52	46	2350,6250	701.5+/-405.2	305,1740,2255	no	coding-synonymous	INSL4	NM_002195.1		1242,2743,2518	AA,AT,TT		27.3256,34.7027,40.1891		63/140	5231712	5227,7779	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon1			TGGACGTCCCAAA		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.189T>A	9.37:g.5231712T>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			T|0.613;A|0.387	0.387	strong		0.512	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195	
KIF27	55582	hgsc.bcm.edu	37	9	86518796	86518796	+	Missense_Mutation	SNP	T	T	C	rs12001918	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:86518796T>C	ENST00000297814.2	-	4	780	c.637A>G	c.(637-639)Atc>Gtc	p.I213V	KIF27_ENST00000413982.1_Missense_Mutation_p.I213V|KIF27_ENST00000334204.2_Missense_Mutation_p.I213V	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	213	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		I -> V (in dbSNP:rs12001918).		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						CAAATGCTGATTGTAAAAATT	0.428													T|||	605	0.120807	0.146	0.0937	5008	,	,		19236	0.1071		0.1312	False		,,,				2504	0.1094				p.I213V		Atlas-SNP	.											.	KIF27	103	.	0			c.A637G						PASS	.	T	VAL/ILE	644,3762	276.6+/-273.2	51,542,1610	184.0	181.0	182.0		637	4.4	1.0	9	dbSNP_120	182	1181,7419	241.0+/-271.5	83,1015,3202	yes	missense	KIF27	NM_017576.1	29	134,1557,4812	CC,CT,TT		13.7326,14.6164,14.032	benign	213/1402	86518796	1825,11181	2203	4300	6503	SO:0001583	missense	55582	exon4			TGCTGATTGTAAA	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.637A>G	9.37:g.86518796T>C	ENSP00000297814:p.Ile213Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	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	8.680	0.904801	0.17760	0.146164	0.137326	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.76968	-1.06;-1.06;-1.06	5.57	4.44	0.53790	Kinesin, motor domain (5);	0.000000	0.64402	D	0.000016	T	0.01061	0.0035	N	0.25647	0.755	0.29845	P	0.82895	B;P;P	0.42692	0.394;0.763;0.787	B;B;P	0.54499	0.224;0.355;0.754	T	0.36601	-0.9741	9	0.28530	T	0.3	.	10.9173	0.47144	0.0:0.0732:0.0:0.9268	rs12001918;rs52810520;rs60740451;rs12001918	213;213;213	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	213	ENSP00000297814:I213V;ENSP00000401688:I213V;ENSP00000333928:I213V	ENSP00000297814:I213V	I	-	1	0	KIF27	85708616	0.971000	0.33674	0.999000	0.59377	0.997000	0.91878	1.695000	0.37763	2.109000	0.64355	0.482000	0.46254	ATC	T|0.869;C|0.131	0.131	strong		0.428	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
PXDN	7837	hgsc.bcm.edu	37	2	1652660	1652660	+	Silent	SNP	G	G	A	rs3811613	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:1652660G>A	ENST00000252804.4	-	17	2942	c.2892C>T	c.(2890-2892)aaC>aaT	p.N964N		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	964					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGGGGCTCTCGTTCTCGTCCC	0.721													G|||	1226	0.244808	0.1218	0.2709	5008	,	,		14999	0.2847		0.2823	False		,,,				2504	0.3129				p.N964N		Atlas-SNP	.											.	PXDN	255	.	0			c.C2892T						PASS	.	G		635,3533		56,523,1505	15.0	16.0	16.0		2892	-0.3	1.0	2	dbSNP_107	16	2507,5881		385,1737,2072	no	coding-synonymous	PXDN	NM_012293.1		441,2260,3577	AA,AG,GG		29.8879,15.2351,25.0239		964/1480	1652660	3142,9414	2084	4194	6278	SO:0001819	synonymous_variant	7837	exon17			GCTCTCGTTCTCG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2892C>T	2.37:g.1652660G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	24	18	0.75	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			G|0.761;A|0.239	0.239	strong		0.721	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
SHANK3	85358	hgsc.bcm.edu	37	22	51160581	51160581	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:51160581C>T	ENST00000414786.2	+	21	4505	c.4278C>T	c.(4276-4278)agC>agT	p.S1426S	SHANK3_ENST00000262795.3_Silent_p.S1456S|SHANK3_ENST00000445220.2_Silent_p.S1442S			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1440					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)		CCTCGGACAGCGAGCTCATGG	0.682																																					p.S1426S		Atlas-SNP	.											.	SHANK3	96	.	0			c.C4278T						PASS	.						14.0	19.0	17.0					22																	51160581		2085	4202	6287	SO:0001819	synonymous_variant	85358	exon21			GGACAGCGAGCTC	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.4278C>T	22.37:g.51160581C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	37																																																																																				.	.	none		0.682	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
PTPRO	5800	hgsc.bcm.edu	37	12	15679120	15679120	+	Silent	SNP	C	C	A	rs6488782	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	53	0	0		WXS	Illumina HiSeq	Phase_I	51	14	0.27451	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		
SLK	9748	hgsc.bcm.edu	37	10	105758670	105758670	+	Silent	SNP	A	A	G	rs10883960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	145	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	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	
HPS5	11234	hgsc.bcm.edu	37	11	18318354	18318354	+	Missense_Mutation	SNP	C	C	T	rs143784823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18318354C>T	ENST00000349215.3	-	12	1778	c.1501G>A	c.(1501-1503)Gga>Aga	p.G501R	HPS5_ENST00000438420.2_Missense_Mutation_p.G387R|HPS5_ENST00000531848.1_Missense_Mutation_p.G387R|HPS5_ENST00000352460.3_5'Flank|HPS5_ENST00000396253.3_Missense_Mutation_p.G387R	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	501					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CCTTCATTTCCGTGTGAGCCA	0.458									Hermansky-Pudlak syndrome				C|||	9	0.00179712	0.0	0.0	5008	,	,		17393	0.0		0.0089	False		,,,				2504	0.0				p.G501R		Atlas-SNP	.											.	HPS5	70	.	0			c.G1501A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	4,4394	8.1+/-20.4	0,4,2195	260.0	249.0	253.0		1159,1501,1159	2.8	0.0	11	dbSNP_134	253	32,8554	21.6+/-65.8	1,30,4262	yes	missense,missense,missense	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	125,125,125	1,34,6457	TT,TC,CC		0.3727,0.091,0.2773	benign,benign,benign	387/1016,501/1130,387/1016	18318354	36,12948	2199	4293	6492	SO:0001583	missense	11234	exon12	Familial Cancer Database	HPS, HPS1-8	CATTTCCGTGTGA	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.1501G>A	11.37:g.18318354C>T	ENSP00000265967:p.Gly501Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	178	81	0.455056	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.033	-1.322402	0.01320	9.1E-4	0.003727	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	T;T;T;T	0.53423	0.63;0.63;0.62;1.6	5.71	2.83	0.33086	.	1.416520	0.04002	N	0.296561	T	0.18425	0.0442	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20107	-1.0285	10	0.08179	T	0.78	.	7.3826	0.26864	0.0:0.6515:0.0:0.3485	.	501	Q9UPZ3	HPS5_HUMAN	R	387;387;501;387	ENSP00000379552:G387R;ENSP00000399590:G387R;ENSP00000265967:G501R;ENSP00000431758:G387R	ENSP00000265967:G501R	G	-	1	0	HPS5	18274930	0.000000	0.05858	0.002000	0.10522	0.108000	0.19459	0.521000	0.22893	0.347000	0.23924	-0.214000	0.12660	GGA	C|0.997;T|0.003	0.003	strong		0.458	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
KIAA1024	23251	hgsc.bcm.edu	37	15	79749789	79749789	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79749789G>A	ENST00000305428.3	+	2	1375	c.1300G>A	c.(1300-1302)Ggg>Agg	p.G434R		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	434						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						AAAACAAAATGGGCTCAAATC	0.483																																					p.G434R		Atlas-SNP	.											KIAA1024,NS,carcinoma,-1,1	KIAA1024	146	1	0			c.G1300A						scavenged	.						64.0	65.0	65.0					15																	79749789		2196	4293	6489	SO:0001583	missense	23251	exon2			CAAAATGGGCTCA	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.1300G>A	15.37:g.79749789G>A	ENSP00000307461:p.Gly434Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	3	0.0337079	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	6.196	0.404261	0.11754	.	.	ENSG00000169330	ENST00000305428	T	0.31510	1.49	4.81	2.73	0.32206	.	0.310563	0.36409	N	0.002609	T	0.21062	0.0507	L	0.35723	1.085	0.52501	D	0.99995	B	0.13594	0.008	B	0.14578	0.011	T	0.05115	-1.0905	9	.	.	.	.	9.8661	0.41145	0.0787:0.1388:0.7825:0.0	.	434	Q9UPX6	K1024_HUMAN	R	434	ENSP00000307461:G434R	.	G	+	1	0	KIAA1024	77536844	1.000000	0.71417	0.924000	0.36721	0.200000	0.23975	4.000000	0.57039	2.206000	0.71126	0.491000	0.48974	GGG	.	.	none		0.483	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
LRCH3	84859	hgsc.bcm.edu	37	3	197597044	197597044	+	Silent	SNP	C	C	T	rs77281724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:197597044C>T	ENST00000425562.2	+	18	1887	c.1887C>T	c.(1885-1887)ccC>ccT	p.P629P	LRCH3_ENST00000414675.2_Silent_p.P577P|LRCH3_ENST00000334859.4_Silent_p.P629P|LRCH3_ENST00000441090.2_Silent_p.P475P|LRCH3_ENST00000536618.1_Silent_p.P224P|LRCH3_ENST00000438796.2_Silent_p.P629P			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	629						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)		ATGCTTCACCCCTTCCTCCAT	0.443													C|||	506	0.101038	0.1596	0.0648	5008	,	,		20135	0.0069		0.1093	False		,,,				2504	0.136				p.P629P		Atlas-SNP	.											.	LRCH3	96	.	0			c.C1887T						PASS	.	C		548,3858	246.2+/-254.9	27,494,1682	129.0	137.0	134.0		1887	1.2	0.8	3	dbSNP_132	134	978,7622	211.4+/-252.0	52,874,3374	no	coding-synonymous	LRCH3	NM_032773.2		79,1368,5056	TT,TC,CC		11.3721,12.4376,11.733		629/713	197597044	1526,11480	2203	4300	6503	SO:0001819	synonymous_variant	84859	exon18			TTCACCCCTTCCT	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.1887C>T	3.37:g.197597044C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_032773	B4E0T7|Q96FP9|Q9NT52	Silent	SNP	ENST00000425562.2	37		191	0.08745421245421245	78	0.15853658536585366	22	0.06077348066298342	6	0.01048951048951049	85	0.11213720316622691	C	3.141	-0.176262	0.06380	0.124376	0.113721	ENSG00000186001	ENST00000428136	T	0.47528	0.84	5.19	1.25	0.21368	.	0.615691	0.15074	N	0.282036	T	0.00109	0.0003	.	.	.	0.09310	P	0.99999999467511	.	.	.	.	.	.	T	0.10613	-1.0622	6	0.22706	T	0.39	-0.7417	1.8562	0.03179	0.4717:0.2482:0.1542:0.1259	.	.	.	.	S	7	ENSP00000394763:P7S	ENSP00000394763:P7S	P	+	1	0	LRCH3	199081441	0.438000	0.25602	0.807000	0.32361	0.331000	0.28603	-0.359000	0.07632	0.167000	0.19631	-0.187000	0.12897	CCT	C|0.887;T|0.113	0.113	strong		0.443	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
CFAP221	200373	hgsc.bcm.edu	37	2	120409616	120409616	+	Missense_Mutation	SNP	G	G	T	rs11686014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:120409616G>T	ENST00000413369.3	+	23	2472	c.2385G>T	c.(2383-2385)atG>atT	p.M795I	PCDP1_ENST00000602047.1_Missense_Mutation_p.M509I	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					AATTCCCTATGTTGAACTACA	0.373													G|||	759	0.151558	0.2239	0.1196	5008	,	,		19768	0.126		0.1282	False		,,,				2504	0.1268				p.M795I		Atlas-SNP	.											.	.	.	.	0			c.G2385T						PASS	.	G	ILE/MET	962,3444	362.1+/-316.0	95,772,1336	117.0	115.0	116.0		1527	2.0	0.0	2	dbSNP_120	116	1070,7530	225.0+/-261.2	64,942,3294	yes	missense	PCDP1	NM_001029996.3	10	159,1714,4630	TT,TG,GG		12.4419,21.8339,15.6236	benign	509/555	120409616	2032,10974	2203	4300	6503	SO:0001583	missense	0	exon23			CCCTATGTTGAAC																												ENST00000413369.3:c.2385G>T	2.37:g.120409616G>T	ENSP00000393222:p.Met795Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	45	0.362903	NM_001271049		Missense_Mutation	SNP	ENST00000413369.3	37	CCDS33282.2	339|339	0.15521978021978022|0.15521978021978022	110|110	0.22357723577235772|0.22357723577235772	50|50	0.13812154696132597|0.13812154696132597	81|81	0.14160839160839161|0.14160839160839161	98|98	0.12928759894459102|0.12928759894459102	G|G	1.264|1.264	-0.614900|-0.614900	0.03663|0.03663	0.218339|0.218339	0.124419|0.124419	ENSG00000163075|ENSG00000163075	ENST00000443972|ENST00000295220;ENST00000413369	.|T	.|0.27557	.|1.66	4.85|4.85	1.95|1.95	0.26073|0.26073	.|.	.|0.927302	.|0.09187	.|N	.|0.836631	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.17474|0.17474	0.49|0.49	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.11235	.|0.004	.|B	.|0.06405	.|0.002	T|T	0.37709|0.37709	-0.9694|-0.9694	4|9	.|0.24483	.|T	.|0.36	-3.4952|-3.4952	3.7528|3.7528	0.08573|0.08573	0.092:0.1631:0.5766:0.1683|0.092:0.1631:0.5766:0.1683	rs11686014;rs52805001;rs57573271;rs11686014|rs11686014;rs52805001;rs57573271;rs11686014	.|795	.|Q4G0U5	.|PCDP1_HUMAN	F|I	354|509;795	.|ENSP00000393222:M795I	.|ENSP00000295220:M509I	C|M	+|+	2|3	0|0	AC069154.2|AC069154.2	120126086|120126086	0.001000|0.001000	0.12720|0.12720	0.006000|0.006000	0.13384|0.13384	0.644000|0.644000	0.38419|0.38419	0.226000|0.226000	0.17776|0.17776	0.615000|0.615000	0.30124|0.30124	-0.314000|-0.314000	0.08810|0.08810	TGT|ATG	G|0.845;T|0.155	0.155	strong		0.373	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1		
HIVEP3	59269	hgsc.bcm.edu	37	1	42047208	42047208	+	Missense_Mutation	SNP	C	C	G	rs17363472	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:42047208C>G	ENST00000372583.1	-	4	4146	c.3261G>C	c.(3259-3261)caG>caC	p.Q1087H	HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Missense_Mutation_p.Q1087H|HIVEP3_ENST00000247584.5_Missense_Mutation_p.Q1087H|HIVEP3_ENST00000429157.2_Missense_Mutation_p.Q1087H	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1087			Q -> H (in dbSNP:rs17363472).		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)				CAGAGGAAATCTGGGACAATG	0.607													C|||	245	0.0489217	0.0038	0.1153	5008	,	,		17657	0.002		0.0427	False		,,,				2504	0.1176				p.Q1087H		Atlas-SNP	.											.	HIVEP3	235	.	0			c.G3261C						PASS	.	C	HIS/GLN,HIS/GLN	64,4342	59.9+/-96.7	0,64,2139	58.0	66.0	63.0		3261,3261	3.9	0.7	1	dbSNP_123	63	499,8101	142.8+/-198.9	12,475,3813	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	24,24	12,539,5952	GG,GC,CC		5.8023,1.4526,4.3288	possibly-damaging,possibly-damaging	1087/2406,1087/2407	42047208	563,12443	2203	4300	6503	SO:0001583	missense	59269	exon4			GGAAATCTGGGAC	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.3261G>C	1.37:g.42047208C>G	ENSP00000361664:p.Gln1087His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	77	0.035256410256410256	2	0.0040650406504065045	39	0.10773480662983426	1	0.0017482517482517483	35	0.04617414248021108	C	0.012	-1.671318	0.00758	0.014526	0.058023	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05996	3.37;3.36;3.36;3.37	4.77	3.86	0.44501	.	0.388790	0.19076	N	0.123374	T	0.00144	0.0004	N	0.24115	0.695	0.38461	P	0.05277699999999996	P;P	0.41569	0.755;0.641	B;B	0.44224	0.444;0.259	T	0.52185	-0.8609	9	0.19590	T	0.45	0.4506	12.7726	0.57429	0.0:0.9196:0.0:0.0804	rs17363472;rs52801254;rs17363472	1087;1087	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	H	1087	ENSP00000361665:Q1087H;ENSP00000361664:Q1087H;ENSP00000247584:Q1087H;ENSP00000410828:Q1087H	ENSP00000247584:Q1087H	Q	-	3	2	HIVEP3	41819795	0.009000	0.17119	0.653000	0.29593	0.119000	0.20118	0.192000	0.17096	1.233000	0.43693	0.313000	0.20887	CAG	C|0.961;G|0.039	0.039	strong		0.607	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
ATRN	8455	hgsc.bcm.edu	37	20	3624848	3624848	+	Silent	SNP	C	C	T	rs34398666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	121	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	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	
ABCA13	154664	hgsc.bcm.edu	37	7	48315930	48315930	+	Missense_Mutation	SNP	G	G	C	rs74859514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:48315930G>C	ENST00000435803.1	+	17	6691	c.6667G>C	c.(6667-6669)Gca>Cca	p.A2223P		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2223					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						TTCTCAGGAAGCAGCTTGGAA	0.343													G|||	156	0.0311502	0.0045	0.0447	5008	,	,		17853	0.001		0.1024	False		,,,				2504	0.0153				p.A2223P		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G6667C						PASS	.	G	PRO/ALA	68,3578		0,68,1755	24.0	23.0	23.0		6667	3.2	0.0	7	dbSNP_132	23	747,7423		27,693,3365	yes	missense	ABCA13	NM_152701.3	27	27,761,5120	CC,CG,GG		9.1432,1.8651,6.8974	possibly-damaging	2223/5059	48315930	815,11001	1823	4085	5908	SO:0001583	missense	154664	exon17			CAGGAAGCAGCTT	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.6667G>C	7.37:g.48315930G>C	ENSP00000411096:p.Ala2223Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	149	38	0.255034	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	97	0.044413919413919416	7	0.014227642276422764	15	0.04143646408839779	0	0.0	75	0.09894459102902374	G	6.878	0.531385	0.13127	0.018651	0.091432	ENSG00000179869	ENST00000435803	T	0.30981	1.51	5.03	3.19	0.36642	.	0.444772	0.18764	N	0.131819	T	0.00666	0.0022	L	0.50333	1.59	0.49798	P	1.7900000000004024E-4	B	0.21309	0.054	B	0.20767	0.031	T	0.09292	-1.0681	8	.	.	.	.	9.5523	0.39317	0.1537:0.0:0.8463:0.0	.	2223	Q86UQ4	ABCAD_HUMAN	P	2223	ENSP00000411096:A2223P	.	A	+	1	0	ABCA13	48286476	0.930000	0.31532	0.015000	0.15790	0.034000	0.12701	1.981000	0.40628	0.508000	0.28173	0.491000	0.48974	GCA	G|0.939;C|0.061	0.061	strong		0.343	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZBTB40	9923	hgsc.bcm.edu	37	1	22852715	22852715	+	Silent	SNP	G	G	C	rs881646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22852715G>C	ENST00000375647.4	+	18	3753	c.3546G>C	c.(3544-3546)ccG>ccC	p.P1182P	ZBTB40_ENST00000374651.4_Silent_p.P1070P|ZBTB40_ENST00000404138.1_Silent_p.P1182P	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1182					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|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(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CCCCAGAGCCGGTGGCCCCGA	0.557													G|||	1593	0.318091	0.1225	0.2205	5008	,	,		17902	0.4692		0.3936	False		,,,				2504	0.4182				p.P1182P		Atlas-SNP	.											.	ZBTB40	87	.	0			c.G3546C						PASS	.	G	,	704,3702	293.3+/-282.5	61,582,1560	75.0	76.0	76.0		3546,3546	-11.4	0.0	1	dbSNP_86	76	3172,5428	479.8+/-370.2	572,2028,1700	no	coding-synonymous,coding-synonymous	ZBTB40	NM_001083621.1,NM_014870.3	,	633,2610,3260	CC,CG,GG		36.8837,15.9782,29.8016	,	1182/1240,1182/1240	22852715	3876,9130	2203	4300	6503	SO:0001819	synonymous_variant	9923	exon19			AGAGCCGGTGGCC	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.3546G>C	1.37:g.22852715G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																			G|0.692;C|0.308	0.308	strong		0.557	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
SLITRK1	114798	hgsc.bcm.edu	37	13	84454391	84454391	+	Missense_Mutation	SNP	T	T	A	rs150504822		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:84454391T>A	ENST00000377084.2	-	1	2137	c.1252A>T	c.(1252-1254)Act>Tct	p.T418S		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	418				T -> S (in Ref. 4; AAH51738). {ECO:0000305}.	adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		TTCTTGAAAGTGTTGTTCTCT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		21199	0.0		0.001	False		,,,				2504	0.0				p.T418S		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A1252T						PASS	.	T	SER/THR	0,4406		0,0,2203	225.0	217.0	220.0		1252	5.2	1.0	13	dbSNP_134	220	12,8588	9.1+/-34.3	0,12,4288	yes	missense	SLITRK1	NM_052910.1	58	0,12,6491	AA,AT,TT		0.1395,0.0,0.0923	benign	418/697	84454391	12,12994	2203	4300	6503	SO:0001583	missense	114798	exon1			TGAAAGTGTTGTT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1252A>T	13.37:g.84454391T>A	ENSP00000366288:p.Thr418Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	13.37	2.215492	0.39102	0.0	0.001395	ENSG00000178235	ENST00000377084	T	0.48201	0.82	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.36799	0.0980	N	0.05177	-0.1	0.51482	D	0.999926	B	0.24963	0.115	B	0.41174	0.349	T	0.36939	-0.9727	10	0.30854	T	0.27	-8.2603	13.9445	0.64075	0.0:0.0:0.0:1.0	.	418	Q96PX8	SLIK1_HUMAN	S	418	ENSP00000366288:T418S	ENSP00000366288:T418S	T	-	1	0	SLITRK1	83352392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.270000	0.58896	1.985000	0.57927	0.459000	0.35465	ACT	T|0.999;A|0.001	0.001	strong		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
ASB18	401036	hgsc.bcm.edu	37	2	237149941	237149941	+	Missense_Mutation	SNP	C	C	T	rs6756597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:237149941C>T	ENST00000409749.3	-	2	309	c.310G>A	c.(310-312)Gcc>Acc	p.A104T	ASB18_ENST00000330842.6_Missense_Mutation_p.A75T|AC079135.1_ENST00000415226.1_RNA	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	142	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	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	
PMFBP1	83449	hgsc.bcm.edu	37	16	72162966	72162966	+	Splice_Site	SNP	G	G	T	rs34832584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72162966G>T	ENST00000237353.10	-	13	2210	c.1949C>A	c.(1948-1950)aCg>aAg	p.T650K	PMFBP1_ENST00000355636.6_Splice_Site_p.T505K|PMFBP1_ENST00000537465.1_Splice_Site_p.T655K	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	655			K -> T (in dbSNP:rs34832584).			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)				CCCACTCACCGTCTTGTCTTT	0.552													G|||	436	0.0870607	0.0113	0.0634	5008	,	,		16413	0.0228		0.16	False		,,,				2504	0.1973				p.T650K		Atlas-SNP	.											.	PMFBP1	101	.	0			c.C1949A						PASS	.	G	LYS/THR,LYS/THR	154,4242	105.6+/-144.1	6,142,2050	144.0	145.0	145.0		1514,1949	2.2	1.0	16	dbSNP_126	145	1410,7190	271.7+/-289.7	126,1158,3016	yes	missense-near-splice,missense-near-splice	PMFBP1	NM_001160213.1,NM_031293.2	78,78	132,1300,5066	TT,TG,GG		16.3953,3.5032,12.0345	benign,benign	505/883,650/1008	72162966	1564,11432	2198	4300	6498	SO:0001630	splice_region_variant	83449	exon13			CTCACCGTCTTGT	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.1950+1C>A	16.37:g.72162966G>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	176	0.08058608058608059	8	0.016260162601626018	27	0.07458563535911603	11	0.019230769230769232	130	0.17150395778364116	G	3.613	-0.079076	0.07141	0.035032	0.163953	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.11063	2.81;2.81;2.81	4.55	2.15	0.27550	.	0.312733	0.28236	N	0.016094	T	0.00012	0.0000	N	0.19112	0.55	0.45354	P	0.0016570000000000196	P;B;P	0.37176	0.586;0.433;0.586	B;B;B	0.31442	0.13;0.13;0.13	T	0.37150	-0.9718	9	0.07325	T	0.83	-8.0813	5.4832	0.16735	0.7356:0.0:0.2644:0.0	rs34832584	655;650;655	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	K	655;650;505	ENSP00000443817:T655K;ENSP00000237353:T650K;ENSP00000347854:T505K	ENSP00000237353:T650K	T	-	2	0	PMFBP1	70720467	0.993000	0.37304	0.999000	0.59377	0.056000	0.15407	0.355000	0.20163	0.434000	0.26340	-0.345000	0.07892	ACG	G|0.890;T|0.110	0.110	strong		0.552	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	Missense_Mutation
ZNF395	55893	hgsc.bcm.edu	37	8	28206677	28206677	+	Silent	SNP	G	G	A	rs75444725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:28206677G>A	ENST00000344423.5	-	9	1526	c.1395C>T	c.(1393-1395)atC>atT	p.I465I	ZNF395_ENST00000523202.1_Silent_p.I465I|ZNF395_ENST00000523095.1_Silent_p.I465I	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	465					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)		GAGAAGTGACGATCAGATGAG	0.642													G|||	66	0.0131789	0.0	0.0187	5008	,	,		18436	0.003		0.0089	False		,,,				2504	0.0419				p.I465I		Atlas-SNP	.											.	ZNF395	54	.	0			c.C1395T						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	113.0	117.0	116.0		1395	-4.8	0.9	8	dbSNP_131	116	87,8513	50.2+/-110.2	1,85,4214	no	coding-synonymous	ZNF395	NM_018660.2		1,95,6407	AA,AG,GG		1.0116,0.227,0.7458		465/514	28206677	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	55893	exon9			AGTGACGATCAGA	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.1395C>T	8.37:g.28206677G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Silent	SNP	ENST00000344423.5	37	CCDS6067.1																																																																																			G|0.995;A|0.005	0.005	strong		0.642	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		
HOOK2	29911	hgsc.bcm.edu	37	19	12876964	12876964	+	Missense_Mutation	SNP	G	G	C	rs897804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12876964G>C	ENST00000397668.3	-	15	1537	c.1464C>G	c.(1462-1464)caC>caG	p.H488Q	HOOK2_ENST00000589965.1_Intron|HOOK2_ENST00000264827.5_Missense_Mutation_p.H488Q	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	488	Sufficient for interaction with microtubules.		H -> Q (in dbSNP:rs897804). {ECO:0000269|PubMed:15489334}.		early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						CATCCTCCAGGTGGCGCTGCA	0.706											OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1086	0.216853	0.0325	0.2939	5008	,	,		12044	0.2321		0.4394	False		,,,				2504	0.1667				p.H488Q		Atlas-SNP	.											HOOK2,NS,carcinoma,0,1	HOOK2	73	1	0			c.C1464G						PASS	.	G	GLN/HIS,GLN/HIS	323,3541		20,283,1629	10.0	13.0	12.0		1464,1464	3.7	1.0	19	dbSNP_87	12	3246,5000		672,1902,1549	no	missense,missense	HOOK2	NM_001100176.1,NM_013312.2	24,24	692,2185,3178	CC,CG,GG		39.3645,8.3592,29.4715	benign,benign	488/718,488/720	12876964	3569,8541	1932	4123	6055	SO:0001583	missense	29911	exon15			CTCCAGGTGGCGC	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"""hook homolog 2 (Drosophila)"""			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1464C>G	19.37:g.12876964G>C	ENSP00000380785:p.His488Gln	Somatic	20	0	0	683	WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_001100176	O60562	Missense_Mutation	SNP	ENST00000397668.3	37	CCDS42508.1	599	0.2742673992673993	19	0.03861788617886179	120	0.3314917127071823	121	0.21153846153846154	339	0.4472295514511873	G	13.50	2.255926	0.39896	0.083592	0.393645	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.15718	2.4;2.4	4.77	3.69	0.42338	.	0.449885	0.22723	N	0.056436	T	0.00012	0.0000	N	0.04959	-0.14	0.32618	P	0.5237350000000001	B;B	0.15473	0.01;0.013	B;B	0.14023	0.006;0.01	T	0.47935	-0.9078	9	0.20046	T	0.44	-30.7248	6.3	0.21107	0.1135:0.3067:0.5798:0.0	rs897804;rs17850914;rs897804	488;488	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	Q	488	ENSP00000380785:H488Q;ENSP00000264827:H488Q	ENSP00000264827:H488Q	H	-	3	2	HOOK2	12737964	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.363000	0.34159	2.174000	0.68829	0.467000	0.42956	CAC	G|0.729;C|0.271	0.271	strong		0.706	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312	
OR2T33	391195	hgsc.bcm.edu	37	1	248436857	248436857	+	Missense_Mutation	SNP	C	C	T	rs137984104		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248436857C>T	ENST00000318021.2	-	1	281	c.260G>A	c.(259-261)aGt>aAt	p.S87N		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S87N(1)		NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|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;0.0245)			GATGGCCTTACTTCCGGTCAA	0.572																																					p.S87N		Atlas-SNP	.											OR2T33,extremity,malignant_melanoma,0,2	OR2T33	133	2	1	Substitution - Missense(1)	skin(1)	c.G260A						scavenged	.						96.0	86.0	89.0					1																	248436857		2203	4297	6500	SO:0001583	missense	391195	exon1			GCCTTACTTCCGG		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"""GPCR / Class A : Olfactory receptors"""	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.260G>A	1.37:g.248436857C>T	ENSP00000324687:p.Ser87Asn	Somatic	531	6	0.0112994		WXS	Illumina HiSeq	Phase_I	528	21	0.0397727	NM_001004695	B2RNN0	Missense_Mutation	SNP	ENST00000318021.2	37	CCDS31109.1	280	0.1282051282051282	21	0.042682926829268296	47	0.1298342541436464	136	0.23776223776223776	76	0.10026385224274406	-	0.156	-1.086530	0.01873	.	.	ENSG00000177212	ENST00000318021	T	0.03004	4.08	2.7	-5.39	0.02664	GPCR, rhodopsin-like superfamily (1);	0.665350	0.12301	N	0.481086	T	0.00012	0.0000	N	0.25380	0.74	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45571	-0.9252	10	0.07175	T	0.84	.	1.5682	0.02609	0.34:0.3409:0.1141:0.205	.	87	Q8NG76	O2T33_HUMAN	N	87	ENSP00000324687:S87N	ENSP00000324687:S87N	S	-	2	0	OR2T33	246503480	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.484000	0.02316	-2.190000	0.00757	-0.528000	0.04320	AGT	T|1.000;|0.000	1.000	weak		0.572	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695	
TTI2	80185	hgsc.bcm.edu	37	8	33369994	33369994	+	Silent	SNP	A	A	G	rs3098657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:33369994A>G	ENST00000431156.2	-	2	756	c.138T>C	c.(136-138)aaT>aaC	p.N46N	TTI2_ENST00000519356.1_5'Flank|SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000520636.1_Silent_p.N46N|TTI2_ENST00000360742.5_Silent_p.N46N	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	46																	CATCTTTTACATTGCCTCGTC	0.507													G|||	2899	0.578874	0.6702	0.4957	5008	,	,		17050	0.5565		0.6551	False		,,,				2504	0.4591				p.N46N		Atlas-SNP	.											.	.	.	.	0			c.T138C						PASS	.	G	,	2955,1451	468.9+/-355.3	999,957,247	72.0	73.0	73.0		138,138	0.2	0.0	8	dbSNP_103	73	5578,3022	463.9+/-366.1	1807,1964,529	yes	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	2806,2921,776	GG,GA,AA		35.1395,32.9324,34.3918	,	46/509,46/509	33369994	8533,4473	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon2			TTTTACATTGCCT	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.138T>C	8.37:g.33369994A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																			A|0.369;G|0.631	0.631	strong		0.507	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
DMXL2	23312	hgsc.bcm.edu	37	15	51795172	51795172	+	Silent	SNP	G	G	A	rs12592889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51795172G>A	ENST00000251076.5	-	17	3110	c.2823C>T	c.(2821-2823)aaC>aaT	p.N941N	DMXL2_ENST00000449909.3_Intron|DMXL2_ENST00000543779.2_Silent_p.N941N	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	941						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.N941N(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AAGAATCTACGTTCTTCTGTC	0.378													A|||	2060	0.411342	0.3011	0.4813	5008	,	,		16613	0.4077		0.5159	False		,,,				2504	0.407				p.N941N		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	1	1	Substitution - coding silent(1)	stomach(1)	c.C2823T						scavenged	.	A	,,	1548,2842	669.4+/-402.2	277,994,924	89.0	93.0	92.0		2823,,2823	-0.2	0.0	15	dbSNP_120	92	4328,4258	573.8+/-389.9	1103,2122,1068	no	coding-synonymous,intron,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1380,3116,1992	AA,AG,GG		49.5924,35.262,45.2836	,,	941/3038,,941/3037	51795172	5876,7100	2195	4293	6488	SO:0001819	synonymous_variant	23312	exon17			ATCTACGTTCTTC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2823C>T	15.37:g.51795172G>A		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			G|0.548;A|0.452	0.452	strong		0.378	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
ANKK1	255239	hgsc.bcm.edu	37	11	113270160	113270160	+	Missense_Mutation	SNP	A	A	G	rs2734849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:113270160A>G	ENST00000303941.3	+	8	1563	c.1469A>G	c.(1468-1470)cAt>cGt	p.H490R		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	490			H -> R (in dbSNP:rs2734849). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		CCCAACCTGCATGAGGCTGAG	0.597													A|||	1227	0.245008	0.1044	0.3098	5008	,	,		19763	0.0625		0.504	False		,,,				2504	0.3108				p.H490R		Atlas-SNP	.											.	ANKK1	83	.	0			c.A1469G	GRCh37	CM085118	ANKK1	M	rs2734849	PASS	.	A	ARG/HIS	665,3379		50,565,1407	16.0	18.0	17.0		1469	-9.3	0.0	11	dbSNP_100	17	4205,4177		1089,2027,1075	yes	missense	ANKK1	NM_178510.1	29	1139,2592,2482	GG,GA,AA		49.833,16.4441,39.192	benign	490/766	113270160	4870,7556	2022	4191	6213	SO:0001583	missense	255239	exon8			ACCTGCATGAGGC	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1469A>G	11.37:g.113270160A>G	ENSP00000306678:p.His490Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	598	0.27380952380952384	59	0.11991869918699187	131	0.36187845303867405	33	0.057692307692307696	375	0.4947229551451187	A	0.017	-1.494949	0.01009	0.164441	0.50167	ENSG00000170209	ENST00000303941	T	0.14893	2.47	4.66	-9.31	0.00646	Ankyrin repeat-containing domain (3);	1.164800	0.06415	N	0.721278	T	0.00012	0.0000	N	0.00188	-1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48490	-0.9031	9	0.08837	T	0.75	1.1889	17.9493	0.89047	0.871:0.0:0.129:0.0	rs2734849;rs52793977;rs59959221;rs2734849	490	Q8NFD2	ANKK1_HUMAN	R	490	ENSP00000306678:H490R	ENSP00000306678:H490R	H	+	2	0	ANKK1	112775370	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.114000	0.10757	-2.467000	0.00532	-0.379000	0.06801	CAT	A|0.725;G|0.275	0.275	strong		0.597	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
LRRC18	474354	hgsc.bcm.edu	37	10	50121784	50121784	+	Silent	SNP	T	T	C	rs10776653|rs386743529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50121784T>C	ENST00000374160.3	-	1	493	c.417A>G	c.(415-417)acA>acG	p.T139T	RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron|LRRC18_ENST00000298124.3_Silent_p.T139T	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	139						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						GGGCCCCCAGTGTGGTGGGCA	0.592													C|||	3131	0.6252	0.68	0.5346	5008	,	,		19514	0.7292		0.494	False		,,,				2504	0.6431				p.T139T		Atlas-SNP	.											.	LRRC18	52	.	0			c.A417G						PASS	.	C	,	2774,1632	471.7+/-356.1	881,1012,310	74.0	74.0	74.0		417,	-12.0	0.0	10	dbSNP_120	74	4252,4348	578.0+/-390.6	1049,2154,1097	no	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	1930,3166,1407	CC,CT,TT		49.4419,37.0404,45.9788	,	139/262,	50121784	7026,5980	2203	4300	6503	SO:0001819	synonymous_variant	474354	exon1			CCCCAGTGTGGTG	AY358137	CCDS31197.1	10q11.23	2011-02-10			ENSG00000165383	ENSG00000165383			23199	protein-coding gene	gene with protein product							Standard	NM_001006939		Approved	UNQ933, MGC34773, UNQ9338, VKGE9338	uc001jhd.3	Q8N456	OTTHUMG00000018182	ENST00000374160.3:c.417A>G	10.37:g.50121784T>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_001006939	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																			T|0.454;C|0.546	0.546	strong		0.592	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
GPR98	84059	hgsc.bcm.edu	37	5	90012379	90012379	+	Missense_Mutation	SNP	G	G	A	rs13157270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	134	0	0		WXS	Illumina HiSeq	Phase_I	158	59	0.373418	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	
DCAF6	55827	hgsc.bcm.edu	37	1	168013850	168013850	+	Missense_Mutation	SNP	T	T	C	rs11558511	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:168013850T>C	ENST00000312263.6	+	13	1844	c.1640T>C	c.(1639-1641)gTg>gCg	p.V547A	DCAF6_ENST00000367843.3_Missense_Mutation_p.V567A|DCAF6_ENST00000367840.3_Missense_Mutation_p.V624A|DCAF6_ENST00000432587.2_Missense_Mutation_p.V593A	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	547			V -> A (in dbSNP:rs11558511). {ECO:0000269|PubMed:15489334}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TCAGAGGATGTGACAAAATAT	0.373													T|||	924	0.184505	0.0545	0.1383	5008	,	,		18636	0.2044		0.2823	False		,,,				2504	0.272				p.V624A		Atlas-SNP	.											.	DCAF6	99	.	0			c.T1871C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	383,4023	192.6+/-218.0	13,357,1833	104.0	105.0	105.0		1640,1871,1778,1700	2.5	0.9	1	dbSNP_120	105	2364,6236	394.6+/-344.7	324,1716,2260	yes	missense,missense,missense,missense	DCAF6	NM_001017977.2,NM_001198956.1,NM_001198957.1,NM_018442.3	64,64,64,64	337,2073,4093	CC,CT,TT		27.4884,8.6927,21.121	benign,benign,benign,benign	547/861,624/952,593/921,567/881	168013850	2747,10259	2203	4300	6503	SO:0001583	missense	55827	exon15			AGGATGTGACAAA	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.1640T>C	1.37:g.168013850T>C	ENSP00000311949:p.Val547Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	414	0.18956043956043955	24	0.04878048780487805	62	0.1712707182320442	117	0.20454545454545456	211	0.2783641160949868	T	3.734	-0.054977	0.07362	0.086927	0.274884	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	4.91	2.53	0.30540	WD40 repeat-like-containing domain (1);	1.234980	0.05717	N	0.597043	T	0.02807	0.0084	N	0.03608	-0.345	0.09310	P	1.0	B;B;B;B	0.12013	0.001;0.001;0.005;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.35624	-0.9781	9	0.07175	T	0.84	.	2.2628	0.04071	0.2191:0.2799:0.0:0.501	rs11558511;rs17855508;rs56482202;rs11558511	593;624;547;567	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	A	567;593;547;624	ENSP00000356817:V567A;ENSP00000396238:V593A;ENSP00000311949:V547A;ENSP00000356814:V624A	ENSP00000311949:V547A	V	+	2	0	DCAF6	166280474	0.002000	0.14202	0.895000	0.35142	0.932000	0.56968	-0.106000	0.10890	0.704000	0.31869	0.533000	0.62120	GTG	C|0.196;N|0.000	0.196	strong		0.373	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
RGAG4	340526	hgsc.bcm.edu	37	X	71349753	71349753	+	Silent	SNP	G	G	A	rs12397326		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:71349753G>A	ENST00000545866.1	-	1	2005	c.1638C>T	c.(1636-1638)cgC>cgT	p.R546R	RGAG4_ENST00000609883.1_Silent_p.R546R|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	546										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					GCACAGGGGGGCGTCTTCGAA	0.602													G|||	1160	0.307285	0.0386	0.3775	3775	,	,		13445	0.0298		0.5934	False		,,,				2504	0.2249				p.R546R		Atlas-SNP	.											.	RGAG4	63	.	0			c.C1638T						PASS	.	G	,	507,2759		47,335,78,966,492	38.0	43.0	41.0		,1638	-4.0	0.1	X	dbSNP_120	41	5072,1385		1458,749,1407,126,384	no	intron,coding-synonymous	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,	1505,1084,1485,1092,876	AA,AG,A,GG,G		21.4496,15.5236,42.6206	,	,546/570	71349753	5579,4144	1918	4124	6042	SO:0001819	synonymous_variant	340526	exon1			AGGGGGGCGTCTT	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.1638C>T	X.37:g.71349753G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Silent	SNP	ENST00000545866.1	37	CCDS55446.1																																																																																			G|0.616;A|0.384	0.384	strong		0.602	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
KRT3	3850	hgsc.bcm.edu	37	12	53189446	53189446	+	Silent	SNP	C	C	T	rs117364830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53189446C>T	ENST00000417996.2	-	1	455	c.381G>A	c.(379-381)ggG>ggA	p.G127G	KRT3_ENST00000309505.3_Silent_p.G127G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	127	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						agccaccagcccctccaaagc	0.632																																					p.G127G		Atlas-SNP	.											KRT3,NS,carcinoma,0,1	KRT3	65	1	0			c.G381A						PASS	.						148.0	189.0	175.0					12																	53189446		2189	4287	6476	SO:0001819	synonymous_variant	3850	exon1			ACCAGCCCCTCCA		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.381G>A	12.37:g.53189446C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	17	0.207317	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																			C|0.971;T|0.029	0.029	strong		0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
HAO2	51179	hgsc.bcm.edu	37	1	119923724	119923724	+	Silent	SNP	T	T	C	rs2275607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:119923724T>C	ENST00000325945.3	+	2	89	c.16T>C	c.(16-18)Ttg>Ctg	p.L6L	HAO2_ENST00000361035.4_Silent_p.L19L	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	6	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		CTTGGTGTGTTTGACAGACTT	0.473													T|||	1794	0.358227	0.0817	0.5216	5008	,	,		20465	0.4504		0.5298	False		,,,				2504	0.3446				p.L6L		Atlas-SNP	.											.	HAO2	62	.	0			c.T16C						PASS	.	T	,	816,3590		129,558,1516	189.0	179.0	183.0		16,16	-9.5	0.6	1	dbSNP_100	183	4447,4153		1166,2115,1019	no	coding-synonymous,coding-synonymous	HAO2	NM_001005783.1,NM_016527.2	,	1295,2673,2535	CC,CT,TT		48.2907,18.5202,40.4659	,	6/352,6/352	119923724	5263,7743	2203	4300	6503	SO:0001819	synonymous_variant	51179	exon3			GTGTGTTTGACAG	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"""(S)-2-hydroxy-acid oxidase"", ""glycolate oxidase"", ""long-chain L-2-hydroxy acid oxidase"", ""growth-inhibiting protein 16"""	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.16T>C	1.37:g.119923724T>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001005783	Q2TU86|Q5QP00|Q9UJS6	Silent	SNP	ENST00000325945.3	37	CCDS901.1																																																																																			C|0.420;G|0.000;T|0.579	0.420	strong		0.473	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511732	99511732	+	Missense_Mutation	SNP	A	A	G	rs61743493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:99511732A>G	ENST00000378919.6	-	5	771	c.566T>C	c.(565-567)aTg>aCg	p.M189T	PGPEP1L_ENST00000535714.1_Missense_Mutation_p.M135T|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	189							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						TGGAAGGACCATGGTTGAGTT	0.498													A|||	81	0.0161741	0.0061	0.0187	5008	,	,		17707	0.0238		0.0298	False		,,,				2504	0.0061				p.M189T		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.T566C						PASS	.	A	THR/MET,THR/MET	36,3772		0,36,1868	61.0	59.0	60.0		566,404	-5.5	0.0	15	dbSNP_129	60	333,7873		5,323,3775	yes	missense,missense	PGPEP1L	NM_001102612.2,NM_001167902.1	81,81	5,359,5643	GG,GA,AA		4.058,0.9454,3.0714	benign,benign	189/197,135/143	99511732	369,11645	1904	4103	6007	SO:0001583	missense	145814	exon5			AGGACCATGGTTG		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.566T>C	15.37:g.99511732A>G	ENSP00000368199:p.Met189Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	51	0.023351648351648352	3	0.006097560975609756	7	0.019337016574585635	14	0.024475524475524476	27	0.03562005277044855	A	3.128	-0.179079	0.06380	0.009454	0.04058	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.31247	1.5	5.24	-5.53	0.02552	.	.	.	.	.	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26503	-1.0101	9	0.87932	D	0	.	3.2736	0.06891	0.476:0.1066:0.3093:0.1081	.	189	A6NFU8	PGPIL_HUMAN	T	189;182	ENSP00000368199:M189T	ENSP00000368199:M189T	M	-	2	0	PGPEP1L	97329255	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.617000	0.05584	-0.679000	0.05217	-0.899000	0.02877	ATG	A|0.974;G|0.026	0.026	strong		0.498	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
HIVEP1	3096	hgsc.bcm.edu	37	6	12123249	12123249	+	Missense_Mutation	SNP	A	A	G	rs2228220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:12123249A>G	ENST00000379388.2	+	4	3553	c.3221A>G	c.(3220-3222)aAt>aGt	p.N1074S	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1074			N -> S (in dbSNP:rs2228220). {ECO:0000269|PubMed:2106471}.		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)				CCTAAACATAATGTTACCATA	0.433													A|||	737	0.147165	0.1793	0.1009	5008	,	,		18841	0.13		0.1163	False		,,,				2504	0.1861				p.N1074S		Atlas-SNP	.											.	HIVEP1	242	.	0			c.A3221G						PASS	.	A	SER/ASN	574,3168		51,472,1348	64.0	63.0	63.0		3221	-0.5	0.0	6	dbSNP_98	63	725,7469		33,659,3405	yes	missense	HIVEP1	NM_002114.2	46	84,1131,4753	GG,GA,AA		8.8479,15.3394,10.883	benign	1074/2719	12123249	1299,10637	1871	4097	5968	SO:0001583	missense	3096	exon4			AACATAATGTTAC	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.3221A>G	6.37:g.12123249A>G	ENSP00000368698:p.Asn1074Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	276	0.12637362637362637	91	0.18495934959349594	41	0.1132596685082873	62	0.10839160839160839	82	0.10817941952506596	A	0.011	-1.696664	0.00725	0.153394	0.088479	ENSG00000095951	ENST00000379388	T	0.27557	1.66	5.87	-0.523	0.11924	.	1.266190	0.05938	N	0.636543	T	0.05593	0.0147	N	0.17674	0.51	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.36065	-0.9763	8	.	.	.	-0.1788	4.9242	0.13885	0.2551:0.5127:0.1367:0.0955	rs2228220;rs3800502;rs59573488;rs2228220	1074	P15822	ZEP1_HUMAN	S	1074	ENSP00000368698:N1074S	.	N	+	2	0	HIVEP1	12231235	0.000000	0.05858	0.000000	0.03702	0.575000	0.36095	-0.027000	0.12371	-0.314000	0.08716	0.533000	0.62120	AAT	A|0.870;G|0.130	0.130	strong		0.433	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
ZNF10	7556	hgsc.bcm.edu	37	12	133732624	133732624	+	Silent	SNP	C	C	T	rs3763151	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133732624C>T	ENST00000248211.6	+	5	1014	c.792C>T	c.(790-792)ccC>ccT	p.P264P	CTD-2140B24.4_ENST00000540096.2_Intron|ZNF10_ENST00000402932.2_Intron|ZNF10_ENST00000426665.2_Silent_p.P264P|ZNF268_ENST00000416488.1_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	264				Missing (in Ref. 1). {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)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		GAGAGAAACCCTATGAATGTA	0.388													C|||	1468	0.293131	0.4402	0.2608	5008	,	,		21351	0.1111		0.34	False		,,,				2504	0.2566				p.P264P		Atlas-SNP	.											.	ZNF10	58	.	0			c.C792T						PASS	.	C		1811,2595	527.8+/-372.2	357,1097,749	66.0	67.0	67.0		792	0.4	1.0	12	dbSNP_107	67	2834,5766	444.5+/-360.7	491,1852,1957	no	coding-synonymous	ZNF10	NM_015394.4		848,2949,2706	TT,TC,CC		32.9535,41.103,35.7143		264/574	133732624	4645,8361	2203	4300	6503	SO:0001819	synonymous_variant	7556	exon5			GAAACCCTATGAA	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"""Zinc fingers, C2H2-type"", ""-"""	12879	protein-coding gene	gene with protein product		194538	"""zinc finger protein 10 (KOX 1)"""			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.792C>T	12.37:g.133732624C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_015394	B2RBS1|Q8TC91	Silent	SNP	ENST00000248211.6	37	CCDS9283.1																																																																																			C|0.668;T|0.332	0.332	strong		0.388	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394	
MED24	9862	hgsc.bcm.edu	37	17	38178679	38178679	+	Missense_Mutation	SNP	G	G	A	rs149459087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38178679G>A	ENST00000394128.2	-	22	2572	c.2491C>T	c.(2491-2493)Cgc>Tgc	p.R831C	MED24_ENST00000356271.3_Missense_Mutation_p.R818C|MED24_ENST00000394127.2_Missense_Mutation_p.R818C|MED24_ENST00000394126.1_Missense_Mutation_p.R856C|MED24_ENST00000501516.3_Missense_Mutation_p.R850C	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	831					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)					TTCTTCTGGCGGGTGGACGCC	0.587													G|||	3	0.000599042	0.0	0.0	5008	,	,		18089	0.0		0.003	False		,,,				2504	0.0				p.R831C		Atlas-SNP	.											.	MED24	89	.	0			c.C2491T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	43.0	40.0	41.0		2452,2491	5.5	1.0	17	dbSNP_134	41	27,8573	19.2+/-60.6	0,27,4273	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	180,180	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging,probably-damaging	818/977,831/990	38178679	29,12977	2203	4300	6503	SO:0001583	missense	9862	exon22			TCTGGCGGGTGGA	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.2491C>T	17.37:g.38178679G>A	ENSP00000377686:p.Arg831Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	G|G	13.32|13.32	2.201336|2.201336	0.38905|0.38905	4.54E-4|4.54E-4	0.00314|0.00314	ENSG00000008838|ENSG00000008838	ENST00000422942|ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	.|T;T;T	.|0.48836	.|0.8;0.8;0.8	5.48|5.48	5.48|5.48	0.80851|0.80851	.|Mediator complex, subunit Med24, N-terminal (1);	.|0.054745	.|0.85682	.|D	.|0.000000	T|T	0.58481|0.58481	0.2125|0.2125	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.76494	.|0.98;0.995;0.998;0.999;0.98	.|P;P;P;P;P	.|0.60345	.|0.606;0.817;0.799;0.873;0.606	T|T	0.60321|0.60321	-0.7286|-0.7286	5|10	.|0.59425	.|D	.|0.04	-17.5546|-17.5546	10.1133|10.1133	0.42576|0.42576	0.0719:0.0:0.7899:0.1382|0.0719:0.0:0.7899:0.1382	.|.	.|741;741;818;831;773	.|F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.|.;.;.;MED24_HUMAN;.	L|C	85|831;831;831;781;818;773;741	.|ENSP00000377686:R831C;ENSP00000443344:R781C;ENSP00000377685:R818C	.|ENSP00000348610:R831C	P|R	-|-	2|1	0|0	MED24|MED24	35432205|35432205	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.566000|0.566000	0.35808|0.35808	3.807000|3.807000	0.55591|0.55591	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.998;A|0.002	0.002	strong		0.587	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
URB2	9816	hgsc.bcm.edu	37	1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	rs41310553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229787055G>A	ENST00000258243.2	+	8	4359	c.4223G>A	c.(4222-4224)cGg>cAg	p.R1408Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1408						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						CGGGAAGGGCGGCAGAAGGAC	0.388													G|||	41	0.0081869	0.0083	0.0159	5008	,	,		17462	0.0		0.0139	False		,,,				2504	0.0051				p.R1408Q		Atlas-SNP	.											.	URB2	152	.	0			c.G4223A						PASS	.	G	GLN/ARG	58,4348	56.8+/-93.2	0,58,2145	87.0	84.0	85.0		4223	4.9	1.0	1	dbSNP_127	85	149,8451	72.9+/-135.5	1,147,4152	yes	missense	URB2	NM_014777.2	43	1,205,6297	AA,AG,GG		1.7326,1.3164,1.5916	probably-damaging	1408/1525	229787055	207,12799	2203	4300	6503	SO:0001583	missense	9816	exon8			AAGGGCGGCAGAA	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.4223G>A	1.37:g.229787055G>A	ENSP00000258243:p.Arg1408Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	20	0.009157509157509158	3	0.006097560975609756	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	25.7	4.661699	0.88154	0.013164	0.017326	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.45668	0.89;0.89	5.78	4.86	0.63082	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.116848	0.53938	D	0.000042	T	0.46210	0.1381	M	0.69823	2.125	0.40363	D	0.97926	D	0.89917	1.0	D	0.69824	0.966	T	0.59968	-0.7354	9	.	.	.	-18.2991	14.7398	0.69445	0.0695:0.0:0.9305:0.0	rs41310553	1408	Q14146	URB2_HUMAN	Q	1408;24	ENSP00000258243:R1408Q;ENSP00000395107:R24Q	.	R	+	2	0	URB2	227853678	0.967000	0.33354	0.971000	0.41717	0.989000	0.77384	5.262000	0.65501	1.435000	0.47434	0.655000	0.94253	CGG	G|0.986;A|0.014	0.014	strong		0.388	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
NEK1	4750	hgsc.bcm.edu	37	4	170477125	170477125	+	Missense_Mutation	SNP	G	G	A	rs34540355	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:170477125G>A	ENST00000439128.2	-	16	2028	c.1388C>T	c.(1387-1389)gCt>gTt	p.A463V	NEK1_ENST00000507142.1_Missense_Mutation_p.A463V|NEK1_ENST00000511633.1_Missense_Mutation_p.A463V|NEK1_ENST00000510533.1_Missense_Mutation_p.A463V|NEK1_ENST00000512193.1_Missense_Mutation_p.A438V	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	463			A -> V (in dbSNP:rs34540355). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TTTCCATTTAGCTTCATTATC	0.388													G|||	81	0.0161741	0.0008	0.0317	5008	,	,		19501	0.0		0.0497	False		,,,				2504	0.0082				p.A463V		Atlas-SNP	.											.	NEK1	203	.	0			c.C1388T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	38,3678		1,36,1821	158.0	142.0	147.0		1388,1388,1313,1388,1388	4.0	0.2	4	dbSNP_126	147	470,7746		11,448,3649	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	64,64,64,64,64	12,484,5470	AA,AG,GG		5.7205,1.0226,4.2575	benign,benign,benign,benign,benign	463/1287,463/1243,438/1190,463/1215,463/1259	170477125	508,11424	1858	4108	5966	SO:0001583	missense	4750	exon16			CATTTAGCTTCAT	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.1388C>T	4.37:g.170477125G>A	ENSP00000408020:p.Ala463Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_012224	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	47	0.02152014652014652	0	0.0	14	0.03867403314917127	0	0.0	33	0.04353562005277045	G	12.30	1.896204	0.33442	0.010226	0.057205	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.69561	-0.38;-0.32;-0.34;-0.41;-0.36	5.66	3.95	0.45737	.	0.279103	0.30949	N	0.008542	T	0.14141	0.0342	L	0.53249	1.67	0.26899	N	0.967153	B;B;B;B;B;B	0.15473	0.002;0.004;0.013;0.01;0.013;0.01	B;B;B;B;B;B	0.21546	0.005;0.011;0.035;0.011;0.035;0.006	T	0.19745	-1.0296	10	0.31617	T	0.26	.	9.2614	0.37614	0.2176:0.0:0.7824:0.0	rs34540355	463;438;463;463;463;463	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	V	463;463;463;463;438	ENSP00000408020:A463V;ENSP00000423332:A463V;ENSP00000427653:A463V;ENSP00000424757:A463V;ENSP00000424938:A438V	ENSP00000408020:A463V	A	-	2	0	NEK1	170713700	0.731000	0.28111	0.249000	0.24280	0.796000	0.44982	1.494000	0.35616	0.767000	0.33267	0.585000	0.79938	GCT	G|0.975;A|0.025	0.025	strong		0.388	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
GDF9	2661	hgsc.bcm.edu	37	5	132198199	132198199	+	Silent	SNP	G	G	A	rs254286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:132198199G>A	ENST00000378673.2	-	3	1313	c.447C>T	c.(445-447)acC>acT	p.T149T	GDF9_ENST00000296875.2_Silent_p.T149T|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	149					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)			AGTGTTCAACGGTAGTAATGC	0.383													G|||	2283	0.455871	0.3313	0.4885	5008	,	,		19646	0.2897		0.5994	False		,,,				2504	0.6247				p.T149T		Atlas-SNP	.											.	GDF9	50	.	0			c.C447T	GRCh37	CM056327	GDF9	M	rs254286	PASS	.	G		1582,2820	454.2+/-350.6	287,1008,906	76.0	79.0	78.0		447	-4.7	0.0	5	dbSNP_79	78	4988,3612	615.5+/-396.4	1439,2110,751	no	coding-synonymous	GDF9	NM_005260.3		1726,3118,1657	AA,AG,GG		42.0,35.9382,49.4693		149/455	132198199	6570,6432	2201	4300	6501	SO:0001819	synonymous_variant	2661	exon2			TTCAACGGTAGTA		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.447C>T	5.37:g.132198199G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	NM_005260	Q4VAW5	Silent	SNP	ENST00000378673.2	37	CCDS4162.1																																																																																			G|0.516;A|0.484	0.484	strong		0.383	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
APLP1	333	hgsc.bcm.edu	37	19	36370092	36370092	+	Silent	SNP	C	C	T	rs138562956		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36370092C>T	ENST00000221891.4	+	16	2022	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	APLP1_ENST00000537454.2_Silent_p.Y570Y|APLP1_ENST00000586861.1_Silent_p.Y603Y|RN7SL402P_ENST00000465059.1_RNA	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	609					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGAAGCCCTACGGGGCTATCA	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17200	0.0		0.001	False		,,,				2504	0.0				p.Y610Y		Atlas-SNP	.											.	APLP1	77	.	0			c.C1830T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	55.0	58.0	57.0		1830,1827	-1.7	1.0	19	dbSNP_134	57	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous	APLP1	NM_001024807.1,NM_005166.3	,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,	610/652,609/651	36370092	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	333	exon16			GCCCTACGGGGCT	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"""amyloid-like protein 1"", ""amyloid precursor-like protein 1"""	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1830C>T	19.37:g.36370092C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_001024807	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																			C|0.999;T|0.001	0.001	strong		0.652	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
MFF	56947	hgsc.bcm.edu	37	2	228194481	228194481	+	Missense_Mutation	SNP	G	G	T	rs3211098|rs386655869	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:228194481G>T	ENST00000353339.3	+	3	461	c.20G>T	c.(19-21)aGt>aTt	p.S7I	MFF_ENST00000524634.1_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000409616.1_5'UTR|MFF_ENST00000409565.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7I|MFF_ENST00000349901.7_Intron|MFF_ENST00000476924.1_Intron	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						GGAACAAGCAGTGACACATCA	0.363													G|||	1364	0.272364	0.0961	0.2493	5008	,	,		17526	0.245		0.3748	False		,,,				2504	0.4499				p.S7I		Atlas-SNP	.											.	MFF	48	.	0			c.G20T						PASS	.	G	ILE/SER	516,3890		31,454,1718	125.0	117.0	120.0		20	3.1	1.0	2	dbSNP_105	120	2985,5615		552,1881,1867	yes	missense	MFF	NM_020194.4	142	583,2335,3585	TT,TG,GG		34.7093,11.7113,26.9183	possibly-damaging	7/343	228194481	3501,9505	2203	4300	6503	SO:0001583	missense	56947	exon3			CAAGCAGTGACAC	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.20G>T	2.37:g.228194481G>T	ENSP00000302037:p.Ser7Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	SNP	ENST00000353339.3	37	CCDS2465.1	428	0.19597069597069597	32	0.06504065040650407	88	0.2430939226519337	106	0.1853146853146853	202	0.26649076517150394	G	11.95	1.792561	0.31685	0.117113	0.347093	ENSG00000168958	ENST00000353339;ENST00000436237;ENST00000443428;ENST00000392059	T;T;T;T	0.61859	1.35;0.07;1.34;1.35	5.97	3.1	0.35709	.	0.300115	0.29253	N	0.012695	T	0.00012	0.0000	N	0.22421	0.69	0.39157	P	0.037660999999999945	B	0.23058	0.079	B	0.21546	0.035	T	0.38672	-0.9650	8	.	.	.	-1.6615	7.0809	0.25231	0.0813:0.0:0.6137:0.305	rs3211098;rs10190875;rs60557422;rs3211098	7	Q9GZY8	MFF_HUMAN	I	7	ENSP00000302037:S7I;ENSP00000411386:S7I;ENSP00000391829:S7I;ENSP00000375912:S7I	.	S	+	2	0	MFF	227902725	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.061000	0.41403	0.365000	0.24400	0.650000	0.86243	AGT	G|0.737;T|0.263	0.263	strong		0.363	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
ABCA10	10349	hgsc.bcm.edu	37	17	67150088	67150088	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:67150088C>A	ENST00000269081.4	-	33	4758	c.3849G>T	c.(3847-3849)ttG>ttT	p.L1283F	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1283	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GGCAGTACCCCAAGAACTTGA	0.483																																					p.L1283F		Atlas-SNP	.											ABCA10,NS,carcinoma,-2,1	ABCA10	209	1	0			c.G3849T						scavenged	.						123.0	107.0	112.0					17																	67150088		2203	4300	6503	SO:0001583	missense	10349	exon33			GTACCCCAAGAAC	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"""ATP binding cassette transporters / subfamily A"""	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3849G>T	17.37:g.67150088C>A	ENSP00000269081:p.Leu1283Phe	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	127	3	0.023622	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695554	0.48202	.	.	ENSG00000154263	ENST00000269081	D	0.94330	-3.4	3.67	2.6	0.31112	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.428114	0.11772	U	0.531072	D	0.94581	0.8254	L	0.41961	1.31	0.32302	N	0.564881	D;D	0.89917	0.998;1.0	D;D	0.87578	0.993;0.998	D	0.92643	0.6126	10	0.56958	D	0.05	.	11.7127	0.51635	0.2775:0.7225:0.0:0.0	.	275;1283	B4DPV2;Q8WWZ4	.;ABCAA_HUMAN	F	1283	ENSP00000269081:L1283F	ENSP00000269081:L1283F	L	-	3	2	ABCA10	64661683	0.683000	0.27633	0.916000	0.36221	0.764000	0.43329	0.057000	0.14279	1.861000	0.53984	0.514000	0.50259	TTG	.	.	none		0.483	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	
IGDCC4	57722	hgsc.bcm.edu	37	15	65703625	65703625	+	Missense_Mutation	SNP	C	C	G	rs34355056	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65703625C>G	ENST00000352385.2	-	2	363	c.154G>C	c.(154-156)Gct>Cct	p.A52P		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	52	Ig-like C2-type 1.		A -> P (in dbSNP:rs34355056).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						AGCACTGCAGCCTGCTCTGGG	0.647													C|||	723	0.144369	0.233	0.196	5008	,	,		18791	0.0417		0.1471	False		,,,				2504	0.091				p.A52P		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G154C						PASS	.	C	PRO/ALA	935,3467	350.8+/-311.0	96,743,1362	39.0	37.0	38.0		154	3.0	0.4	15	dbSNP_126	38	1263,7335	245.1+/-274.1	89,1085,3125	yes	missense	IGDCC4	NM_020962.1	27	185,1828,4487	GG,GC,CC		14.6895,21.2403,16.9077	benign	52/1251	65703625	2198,10802	2201	4299	6500	SO:0001583	missense	57722	exon2			CTGCAGCCTGCTC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.154G>C	15.37:g.65703625C>G	ENSP00000319623:p.Ala52Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	295	0.13507326007326007	103	0.20934959349593496	50	0.13812154696132597	32	0.055944055944055944	110	0.14511873350923482	C	1.856	-0.463746	0.04476	0.212403	0.146895	ENSG00000103742	ENST00000352385	T	0.76448	-1.02	5.07	3.0	0.34707	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.528595	0.18896	N	0.128174	T	0.00073	0.0002	N	0.16037	0.36	0.40067	P	0.024035999999999946	B	0.14805	0.011	B	0.16722	0.016	T	0.03086	-1.1074	9	0.16896	T	0.51	-2.9139	6.3413	0.21324	0.3286:0.585:0.0:0.0864	rs34355056	52	Q8TDY8	IGDC4_HUMAN	P	52	ENSP00000319623:A52P	ENSP00000319623:A52P	A	-	1	0	IGDCC4	63490678	0.414000	0.25408	0.448000	0.26945	0.113000	0.19764	0.420000	0.21263	1.088000	0.41272	0.563000	0.77884	GCT	C|0.845;G|0.155	0.155	strong		0.647	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
CFAP74	85452	hgsc.bcm.edu	37	1	1888193	1888193	+	IGR	SNP	C	C	A	rs3820011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1888193C>A								TMEM52 (37481 upstream) : C1orf222 (31369 downstream)																							ACGTAGCTGCCGAAGTCAATG	0.622													C|||	936	0.186901	0.1067	0.232	5008	,	,		19634	0.2282		0.2455	False		,,,				2504	0.1605				p.G628C		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1882T						PASS	.	C	CYS/GLY	566,3756		44,478,1639	55.0	60.0	58.0		1882	4.8	1.0	1	dbSNP_107	58	2242,6272		294,1654,2309	yes	missense	KIAA1751	NM_001080484.1	159	338,2132,3948	AA,AC,CC		26.3331,13.0958,21.876	probably-damaging	628/763	1888193	2808,10028	2161	4257	6418	SO:0001628	intergenic_variant	85452	exon17			AGCTGCCGAAGTC																													1.37:g.1888193C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001080484		Missense_Mutation	SNP		37		514	0.23534798534798534	66	0.13414634146341464	89	0.24585635359116023	162	0.28321678321678323	197	0.2598944591029024	C	19.64	3.865871	0.71949	0.130958	0.263331	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000001	T	0.00039	0.0001	M	0.79258	2.445	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00348	-1.1799	8	0.87932	D	0	-32.4849	15.6211	0.76808	0.0:1.0:0.0:0.0	rs3820011;rs17372244;rs57075302;rs3820011	628;628	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	C	628;75	.	ENSP00000270720:G628C	G	-	1	0	C1orf222	1878053	1.000000	0.71417	0.993000	0.49108	0.683000	0.39861	5.452000	0.66638	2.352000	0.79861	0.655000	0.94253	GGC	C|0.775;A|0.225	0.225	strong	0	0.622								
DKK4	27121	hgsc.bcm.edu	37	8	42231786	42231786	+	Silent	SNP	G	G	A	rs2073664	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:42231786G>A	ENST00000220812.2	-	4	693	c.507C>T	c.(505-507)gtC>gtT	p.V169V		NM_014420.2	NP_055235.1	Q9UBT3	DKK4_HUMAN	dickkopf WNT signaling pathway inhibitor 4	169	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|large_intestine(7)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|Lung(22;0.00597)|LUSC - Lung squamous cell carcinoma(45;0.024)			CCTCCAAAAGGACTGGCTTAC	0.493													G|||	1525	0.304513	0.7224	0.1009	5008	,	,		17908	0.1657		0.0875	False		,,,				2504	0.2505				p.V169V		Atlas-SNP	.											.	DKK4	28	.	0			c.C507T						PASS	.	G		2570,1836	636.4+/-396.6	745,1080,378	88.0	87.0	87.0		507	2.2	0.9	8	dbSNP_96	87	630,7970	161.7+/-214.6	24,582,3694	no	coding-synonymous	DKK4	NM_014420.2		769,1662,4072	AA,AG,GG		7.3256,41.6704,24.604		169/225	42231786	3200,9806	2203	4300	6503	SO:0001819	synonymous_variant	27121	exon4			CAAAAGGACTGGC	AF177397	CCDS6130.1	8p11.2-p11.1	2013-05-15	2013-05-15		ENSG00000104371	ENSG00000104371			2894	protein-coding gene	gene with protein product		605417	"""dickkopf (Xenopus laevis) homolog 4"", ""dickkopf homolog 4 (Xenopus laevis)"""			10570958, 11701963	Standard	NM_014420		Approved		uc003xpb.3	Q9UBT3	OTTHUMG00000164167	ENST00000220812.2:c.507C>T	8.37:g.42231786G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_014420	Q3KNX0|Q9Y4C3	Silent	SNP	ENST00000220812.2	37	CCDS6130.1																																																																																			G|0.739;A|0.261	0.261	strong		0.493	DKK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377563.1		
SLC27A6	28965	hgsc.bcm.edu	37	5	128301971	128301971	+	Silent	SNP	T	T	C	rs2577541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:128301971T>C	ENST00000262462.4	+	1	1151	c.141T>C	c.(139-141)taT>taC	p.Y47Y	SLC27A6_ENST00000395266.1_Silent_p.Y47Y|SLC27A6_ENST00000506176.1_Silent_p.Y47Y			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	47					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		TGAAGAAGTATGAAAAGAGAG	0.448													C|||	1019	0.203474	0.171	0.255	5008	,	,		20526	0.0585		0.3678	False		,,,				2504	0.1912				p.Y47Y		Atlas-SNP	.											.	SLC27A6	112	.	0			c.T141C						PASS	.	C	,	952,3454	735.5+/-410.7	88,776,1339	123.0	123.0	123.0		141,141	3.5	0.0	5	dbSNP_100	123	3252,5348	649.1+/-400.6	619,2014,1667	no	coding-synonymous,coding-synonymous	SLC27A6	NM_001017372.1,NM_014031.3	,	707,2790,3006	CC,CT,TT		37.814,21.6069,32.3235	,	47/620,47/620	128301971	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	28965	exon1			GAAGTATGAAAAG	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.141T>C	5.37:g.128301971T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Silent	SNP	ENST00000262462.4	37	CCDS4145.1																																																																																			T|0.719;C|0.281	0.281	strong		0.448	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
CALHM3	119395	hgsc.bcm.edu	37	10	105238527	105238527	+	Missense_Mutation	SNP	C	C	T	rs372176967		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:105238527C>T	ENST00000369783.4	-	1	470	c.263G>A	c.(262-264)cGg>cAg	p.R88Q	RP11-225H22.5_ENST00000453753.1_RNA	NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	88					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						GTCCTTCCTCCGGTGCCCTGC	0.677																																					p.R88Q		Atlas-SNP	.											.	CALHM3	46	.	0			c.G263A						PASS	.	C	GLN/ARG	0,1384		0,0,692	18.0	23.0	21.0		263	5.7	1.0	10		21	1,3181		0,1,1590	no	missense	CALHM3	NM_001129742.1	43	0,1,2282	TT,TC,CC		0.0314,0.0,0.0219	probably-damaging	88/345	105238527	1,4565	692	1591	2283	SO:0001583	missense	119395	exon1			TTCCTCCGGTGCC	BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.263G>A	10.37:g.105238527C>T	ENSP00000358798:p.Arg88Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001129742	Q5W090|Q8IXR2	Missense_Mutation	SNP	ENST00000369783.4	37	CCDS44476.1	.	.	.	.	.	.	.	.	.	.	C	36	5.855923	0.97030	0.0	3.14E-4	ENSG00000183128	ENST00000369783	T	0.18502	2.21	5.65	5.65	0.86999	.	0.060452	0.64402	D	0.000006	T	0.44519	0.1297	M	0.74647	2.275	0.53688	D	0.999972	D	0.89917	1.0	D	0.72338	0.977	T	0.14783	-1.0460	10	0.40728	T	0.16	-12.0254	19.7261	0.96164	0.0:1.0:0.0:0.0	.	88	Q86XJ0-2	.	Q	88	ENSP00000358798:R88Q	ENSP00000358798:R88Q	R	-	2	0	CALHM3	105228517	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.371000	0.79600	2.667000	0.90743	0.561000	0.74099	CGG	.	.	none		0.677	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
L1TD1	54596	hgsc.bcm.edu	37	1	62675619	62675619	+	Silent	SNP	C	C	T	rs4625314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62675619C>T	ENST00000498273.1	+	4	1468	c.1173C>T	c.(1171-1173)gcC>gcT	p.A391A	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	391	Glu-rich.							p.A391A(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						ATGAAGAGGCCTCAGGGATGG	0.493													C|||	1495	0.298522	0.2769	0.3473	5008	,	,		16813	0.1091		0.492	False		,,,				2504	0.2894				p.A391A		Atlas-SNP	.											L1TD1,NS,carcinoma,0,1	L1TD1	114	1	1	Substitution - coding silent(1)	stomach(1)	c.C1173T						PASS	.	C	,	1485,2921	448.1+/-348.6	247,991,965	60.0	67.0	64.0		1173,1173	-2.5	0.0	1	dbSNP_111	64	4405,4193	563.7+/-388.2	1145,2115,1039	no	coding-synonymous,coding-synonymous	L1TD1	NM_001164835.1,NM_019079.4	,	1392,3106,2004	TT,TC,CC		48.7672,33.704,45.2938	,	391/866,391/866	62675619	5890,7114	2203	4299	6502	SO:0001819	synonymous_variant	54596	exon5			AGAGGCCTCAGGG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1173C>T	1.37:g.62675619C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			C|0.605;T|0.395	0.395	strong		0.493	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
OR2A14	135941	hgsc.bcm.edu	37	7	143826603	143826603	+	Missense_Mutation	SNP	G	G	T	rs2961160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	176	2	0.0113636		WXS	Illumina HiSeq	Phase_I	169	59	0.349112	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		
CCDC114	93233	hgsc.bcm.edu	37	19	48821757	48821757	+	Missense_Mutation	SNP	G	G	A	rs16981988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48821757G>A	ENST00000315396.7	-	3	818	c.136C>T	c.(136-138)Cgg>Tgg	p.R46W	CCDC114_ENST00000497803.1_5'UTR	NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	46					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)		TCCCGAAGCCGCTTGACCTGG	0.662													G|||	160	0.0319489	0.0605	0.0303	5008	,	,		17279	0.0		0.0249	False		,,,				2504	0.0348				p.R46W		Atlas-SNP	.											.	CCDC114	100	.	0			c.C136T						PASS	.	G	TRP/ARG	63,1321		3,57,632	23.0	26.0	25.0		136	-0.6	1.0	19	dbSNP_123	25	91,3091		0,91,1500	yes	missense	CCDC114	NM_144577.3	101	3,148,2132	AA,AG,GG		2.8598,4.552,3.3728	probably-damaging	46/671	48821757	154,4412	692	1591	2283	SO:0001583	missense	93233	exon3			GAAGCCGCTTGAC	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.136C>T	19.37:g.48821757G>A	ENSP00000318429:p.Arg46Trp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	70	0.03205128205128205	36	0.07317073170731707	13	0.03591160220994475	2	0.0034965034965034965	19	0.025065963060686015	G	18.20	3.571425	0.65765	0.04552	0.028598	ENSG00000105479	ENST00000315396	T	0.25579	1.79	4.56	-0.634	0.11516	.	.	.	.	.	T	0.03220	0.0094	L	0.32530	0.975	0.32806	D	0.50074	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.30504	-0.9976	9	0.72032	D	0.01	-23.6886	11.1491	0.48447	0.0:0.0:0.3483:0.6517	rs16981988	46;46	Q96M63;Q96M63-5	CC114_HUMAN;.	W	46	ENSP00000318429:R46W	ENSP00000318429:R46W	R	-	1	2	CCDC114	53513569	1.000000	0.71417	0.996000	0.52242	0.656000	0.38851	0.342000	0.19926	0.231000	0.21079	-0.302000	0.09304	CGG	G|0.970;A|0.030	0.030	strong		0.662	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T	rs200516145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549582G>T	ENST00000360004.5	-	3	509	c.404C>A	c.(403-405)aCc>aAc	p.T135N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	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)|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						CAGGGGCTGGGTCTTTGAAGG	0.507										Multiple Myeloma(14;0.17)																											p.T135N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C404A						PASS	.						67.0	84.0	78.0					6																	32549582		1510	2709	4219	SO:0001583	missense	3123	exon3			GGCTGGGTCTTTG	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.404C>A	6.37:g.32549582G>T	ENSP00000353099:p.Thr135Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	172	22	0.127907	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740603	0.30865	.	.	ENSG00000196126	ENST00000360004	T	0.02863	4.13	3.87	2.92	0.33932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.06781	0.0173	M	0.76574	2.34	0.26397	N	0.97649	D	0.76494	0.999	D	0.87578	0.998	T	0.02632	-1.1131	10	0.87932	D	0	.	10.9743	0.47456	0.0:0.0:0.8139:0.1861	.	135	P01911	2B1F_HUMAN	N	135	ENSP00000353099:T135N	ENSP00000353099:T135N	T	-	2	0	HLA-DRB1	32657560	0.030000	0.19436	0.762000	0.31397	0.139000	0.21198	1.809000	0.38922	1.883000	0.54544	0.453000	0.30009	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ZZEF1	23140	hgsc.bcm.edu	37	17	3979949	3979949	+	Silent	SNP	G	G	A	rs7207986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3979949G>A	ENST00000381638.2	-	21	3340	c.3216C>T	c.(3214-3216)ccC>ccT	p.P1072P	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1072							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						GTCCTCCTTCGGGGCCACTAC	0.547													G|||	845	0.16873	0.1551	0.1513	5008	,	,		16692	0.1825		0.1789	False		,,,				2504	0.1748				p.P1072P		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C3216T						PASS	.	G		725,3681	297.8+/-285.0	50,625,1528	40.0	38.0	39.0		3216	-0.7	1.0	17	dbSNP_116	39	1544,7056	286.3+/-297.7	131,1282,2887	no	coding-synonymous	ZZEF1	NM_015113.3		181,1907,4415	AA,AG,GG		17.9535,16.4548,17.4458		1072/2962	3979949	2269,10737	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon21			TCCTTCGGGGCCA	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.3216C>T	17.37:g.3979949G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			G|0.820;A|0.180	0.180	strong		0.547	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
LAD1	3898	hgsc.bcm.edu	37	1	201358304	201358304	+	Missense_Mutation	SNP	C	C	A	rs3738281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201358304C>A	ENST00000391967.2	-	2	467	c.166G>T	c.(166-168)Gcc>Tcc	p.A56S	LAD1_ENST00000367313.3_Missense_Mutation_p.A70S	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	56			A -> S (in dbSNP:rs3738281).			basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						GAAGCAGAGGCCTGCCGGTCT	0.602													C|||	890	0.177716	0.357	0.0735	5008	,	,		18618	0.1081		0.0944	False		,,,				2504	0.1667				p.A56S		Atlas-SNP	.											.	LAD1	42	.	0			c.G166T						PASS	.	C	SER/ALA	1396,3010	457.6+/-351.7	217,962,1024	73.0	72.0	73.0		166	1.0	0.0	1	dbSNP_107	73	882,7718	198.5+/-242.8	48,786,3466	yes	missense	LAD1	NM_005558.3	99	265,1748,4490	AA,AC,CC		10.2558,31.6841,17.515	benign	56/518	201358304	2278,10728	2203	4300	6503	SO:0001583	missense	3898	exon2			CAGAGGCCTGCCG	U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.166G>T	1.37:g.201358304C>A	ENSP00000375829:p.Ala56Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	84	0.651163	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	346	0.15842490842490842	181	0.3678861788617886	31	0.0856353591160221	56	0.0979020979020979	78	0.10290237467018469	C	0.120	-1.126198	0.01770	0.316841	0.102558	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.11604	2.77;2.76	5.17	0.998	0.19857	.	1.789730	0.04429	U	0.368840	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.25563	0.038;0.129	B;B	0.27608	0.034;0.081	T	0.43637	-0.9379	9	0.07175	T	0.84	0.041	5.2288	0.15410	0.1438:0.6204:0.1457:0.0901	rs3738281;rs11539493;rs56846552;rs3738281	70;56	E9PDI4;O00515	.;LAD1_HUMAN	S	56;70	ENSP00000375829:A56S;ENSP00000356282:A70S	ENSP00000356282:A70S	A	-	1	0	LAD1	199624927	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.218000	0.02976	-0.080000	0.12685	-0.978000	0.02582	GCC	C|0.826;A|0.174	0.174	strong		0.602	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73076590	73076590	+	Silent	SNP	C	C	T	rs61749197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73076590C>T	ENST00000263674.3	+	19	6056	c.5706C>T	c.(5704-5706)ccC>ccT	p.P1902P		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1902					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|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)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P1902P(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TCACTCCTCCCGTGCACAGGA	0.577													C|||	162	0.0323482	0.0068	0.0418	5008	,	,		22002	0.003		0.0924	False		,,,				2504	0.0286				p.P1902P		Atlas-SNP	.											ARHGEF17,mucosal,malignant_melanoma,+1,2	ARHGEF17	117	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C5706T						PASS	.	C		81,4319	70.3+/-108.2	0,81,2119	140.0	107.0	118.0		5706	-11.6	0.5	11	dbSNP_129	118	788,7798	184.9+/-232.8	36,716,3541	no	coding-synonymous	ARHGEF17	NM_014786.3		36,797,5660	TT,TC,CC		9.1777,1.8409,6.6918		1902/2064	73076590	869,12117	2200	4293	6493	SO:0001819	synonymous_variant	9828	exon19			TCCTCCCGTGCAC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5706C>T	11.37:g.73076590C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																			C|0.941;T|0.059	0.059	strong		0.577	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
KIF1B	23095	hgsc.bcm.edu	37	1	10421878	10421878	+	Silent	SNP	A	A	G	rs12125492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10421878A>G	ENST00000377086.1	+	40	4501	c.4299A>G	c.(4297-4299)ccA>ccG	p.P1433P	KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000377081.1_Silent_p.P1433P|KIF1B_ENST00000263934.6_Silent_p.P1387P			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	55	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	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		
EML4	27436	hgsc.bcm.edu	37	2	42515437	42515437	+	Missense_Mutation	SNP	A	A	G	rs28651764	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:42515437A>G	ENST00000318522.5	+	11	1455	c.1193A>G	c.(1192-1194)aAg>aGg	p.K398R	EML4_ENST00000402711.2_Missense_Mutation_p.K340R|EML4_ENST00000401738.3_Missense_Mutation_p.K409R	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	38	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	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	
CPO	130749	hgsc.bcm.edu	37	2	207834049	207834049	+	Silent	SNP	G	G	C	rs139758524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207834049G>C	ENST00000272852.3	+	9	1060	c.1014G>C	c.(1012-1014)ctG>ctC	p.L338L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	338						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		AGGCTGTGCTGTCAGTCCTGG	0.542																																					p.L338L		Atlas-SNP	.											.	CPO	42	.	0			c.G1014C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	164.0	129.0	141.0		1014	-0.4	0.3	2	dbSNP_134	141	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CPO	NM_173077.2		0,5,6498	CC,CG,GG		0.0465,0.0227,0.0384		338/375	207834049	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGTGCTGTCAGTC		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.1014G>C	2.37:g.207834049G>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			G|1.000;C|0.000	0.000	strong		0.542	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
C2orf54	79919	hgsc.bcm.edu	37	2	241828012	241828012	+	Silent	SNP	T	T	C	rs6708304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241828012T>C	ENST00000388934.4	-	4	1106	c.948A>G	c.(946-948)gaA>gaG	p.E316E	C2orf54_ENST00000402775.2_Silent_p.E148E|C2orf54_ENST00000307486.8_Silent_p.E167E	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	99	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	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	
COL4A2	1284	hgsc.bcm.edu	37	13	111098226	111098226	+	Silent	SNP	C	C	T	rs4103	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:111098226C>T	ENST00000360467.5	+	17	1314	c.1008C>T	c.(1006-1008)ccC>ccT	p.P336P		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	336	Triple-helical region.				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)			CCCGGGGACCCAAGGTGAGCC	0.537													C|||	2418	0.482827	0.3714	0.464	5008	,	,		18286	0.5625		0.5139	False		,,,				2504	0.5327				p.P336P		Atlas-SNP	.											COL4A2,colon,carcinoma,0,1	COL4A2	178	1	0			c.C1008T						scavenged	.	C		1538,2346		313,912,717	99.0	102.0	101.0		1008	0.9	0.9	13	dbSNP_36	101	4411,3849		1174,2063,893	no	coding-synonymous	COL4A2	NM_001846.2		1487,2975,1610	TT,TC,CC		46.5981,39.5984,48.9872		336/1713	111098226	5949,6195	1942	4130	6072	SO:0001819	synonymous_variant	1284	exon17			GGGACCCAAGGTG	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.1008C>T	13.37:g.111098226C>T		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	72	22	0.305556	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			C|0.496;T|0.504	0.504	strong		0.537	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
KRT38	8687	hgsc.bcm.edu	37	17	39595537	39595537	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39595537G>A	ENST00000246646.3	-	3	649	c.650C>T	c.(649-651)gCg>gTg	p.A217V		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	217	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GGCCAGGGTCGCATCATCCAG	0.637																																					p.A217V		Atlas-SNP	.											.	KRT38	63	.	0			c.C650T						PASS	.						83.0	75.0	78.0					17																	39595537		2203	4300	6503	SO:0001583	missense	8687	exon3			AGGGTCGCATCAT	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.650C>T	17.37:g.39595537G>A	ENSP00000246646:p.Ala217Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	89	5	0.0561798	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928753	0.34002	.	.	ENSG00000171360	ENST00000246646	D	0.90004	-2.6	4.31	3.11	0.35812	Filament (1);	1.672080	0.04241	N	0.336988	D	0.85961	0.5819	L	0.45051	1.395	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.71217	-0.4658	10	0.72032	D	0.01	.	7.6159	0.28158	0.8792:0.0:0.1208:0.0	.	217	O76015	KRT38_HUMAN	V	217	ENSP00000246646:A217V	ENSP00000246646:A217V	A	-	2	0	KRT38	36849063	0.044000	0.20184	0.710000	0.30468	0.780000	0.44128	3.320000	0.51991	0.590000	0.29694	0.484000	0.47621	GCG	.	.	none		0.637	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
GALC	2581	hgsc.bcm.edu	37	14	88431898	88431898	+	Silent	SNP	C	C	T	rs12888666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88431898C>T	ENST00000261304.2	-	9	1090	c.984G>A	c.(982-984)caG>caA	p.Q328Q	GALC_ENST00000393568.4_Silent_p.Q305Q|GALC_ENST00000393569.2_Silent_p.Q302Q|GALC_ENST00000544807.2_Silent_p.Q272Q	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	328					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCCATGGCTCCTGGGCCGTCA	0.443													C|||	1658	0.33107	0.0794	0.4236	5008	,	,		14935	0.5327		0.3429	False		,,,				2504	0.3855				p.Q328Q		Atlas-SNP	.											.	GALC	48	.	0			c.G984A						PASS	.	C	,,	459,3401		30,399,1501	85.0	91.0	89.0		984,915,906	5.3	1.0	14	dbSNP_121	89	2882,5396		491,1900,1748	no	coding-synonymous,coding-synonymous,coding-synonymous	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	,,	521,2299,3249	TT,TC,CC		34.8152,11.8912,27.5251	,,	328/686,305/663,302/660	88431898	3341,8797	1930	4139	6069	SO:0001819	synonymous_variant	2581	exon9			TGGCTCCTGGGCC	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"""Krabbe disease"""	606890	"""galactosylceramidase (Krabbe disease)"""				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.984G>A	14.37:g.88431898C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	37	CCDS9878.2																																																																																			C|0.646;T|0.354	0.354	strong		0.443	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
ENG	2022	hgsc.bcm.edu	37	9	130586688	130586688	+	Silent	SNP	G	G	A	rs3739817|rs45439096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:130586688G>A	ENST00000373203.4	-	8	1429	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	ENG_ENST00000344849.3_Silent_p.T343T|RP11-228B15.4_ENST00000425991.1_RNA|RP11-228B15.4_ENST00000439298.1_RNA|ENG_ENST00000480266.1_5'UTR	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	343	Ser/Thr-rich.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						TGGGAGGAGTGGTCTGGATCG	0.597									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia				G|||	404	0.0806709	0.0439	0.0562	5008	,	,		15497	0.0188		0.0656	False		,,,				2504	0.227				p.T343T		Atlas-SNP	.											.	ENG	44	.	0			c.C1029T						PASS	.	G	,	198,4208	124.1+/-161.4	8,182,2013	109.0	91.0	97.0		1029,1029	2.5	1.0	9	dbSNP_107	97	691,7909	172.3+/-223.0	28,635,3637	no	coding-synonymous,coding-synonymous	ENG	NM_000118.2,NM_001114753.1	,	36,817,5650	AA,AG,GG		8.0349,4.4939,6.8353	,	343/626,343/659	130586688	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	2022	exon8	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	AGGAGTGGTCTGG	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.1029C>T	9.37:g.130586688G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																			G|0.920;A|0.080	0.080	strong		0.597	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
TAF1C	9013	hgsc.bcm.edu	37	16	84212571	84212571	+	Silent	SNP	C	C	A	rs1804500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84212571C>A	ENST00000567759.1	-	14	2768	c.2586G>T	c.(2584-2586)cgG>cgT	p.R862R	TAF1C_ENST00000378541.4_Silent_p.R862R|TAF1C_ENST00000570117.1_Silent_p.R530R|TAF1C_ENST00000566732.1_Silent_p.R836R|TAF1C_ENST00000541676.1_Silent_p.R769R|TAF1C_ENST00000341690.6_Silent_p.R768R	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	862					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)	p.R862R(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GAGGCTTCTTCCGGAGGGGCT	0.647													C|||	1372	0.273962	0.0923	0.4092	5008	,	,		14562	0.372		0.341	False		,,,				2504	0.2536				p.R862R		Atlas-SNP	.											TAF1C,NS,carcinoma,0,1	TAF1C	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G2586T						PASS	.	C	,	589,3811	258.0+/-262.2	43,503,1654	48.0	53.0	51.0		2586,2304	0.9	0.2	16	dbSNP_89	51	3045,5555	465.6+/-366.6	554,1937,1809	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	597,2440,3463	AA,AC,CC		35.407,13.3864,27.9538	,	862/870,768/776	84212571	3634,9366	2200	4300	6500	SO:0001819	synonymous_variant	9013	exon14			CTTCTTCCGGAGG	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.2586G>T	16.37:g.84212571C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			C|0.709;A|0.291	0.291	strong		0.647	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
COMMD1	150684	hgsc.bcm.edu	37	2	62362995	62362995	+	Silent	SNP	T	T	C	rs9096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:62362995T>C	ENST00000311832.5	+	3	524	c.492T>C	c.(490-492)gaT>gaC	p.D164D	AC018462.2_ENST00000421323.1_RNA|COMMD1_ENST00000472729.1_3'UTR|AC018462.2_ENST00000425966.2_RNA	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	164	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.				copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.L161_K167delLEFDEVK(2)		large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			TGGAATTTGATGAGGTCAAAG	0.413													T|||	230	0.0459265	0.0303	0.0605	5008	,	,		18464	0.0		0.1342	False		,,,				2504	0.0133				p.D164D		Atlas-SNP	.											.	COMMD1	17	.	2	Deletion - In frame(2)	liver(2)	c.T492C						PASS	.	T		174,4232	113.8+/-151.8	4,166,2033	131.0	129.0	130.0		492	5.8	1.0	2	dbSNP_52	130	1098,7502	229.0+/-263.8	66,966,3268	no	coding-synonymous	COMMD1	NM_152516.2		70,1132,5301	CC,CT,TT		12.7674,3.9492,9.7801		164/191	62362995	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	150684	exon3			ATTTGATGAGGTC	BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163			23024	protein-coding gene	gene with protein product	"""copper metabolism gene MURR1"""	607238	"""chromosome 2 open reading frame 5 (MURR1)"""	C2orf5		9001233, 11809725	Standard	NM_152516		Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.492T>C	2.37:g.62362995T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_152516	B4DFQ4|Q96GS0	Silent	SNP	ENST00000311832.5	37	CCDS1869.1	140	0.0641025641025641	19	0.03861788617886179	29	0.08011049723756906	0	0.0	92	0.12137203166226913	T	10.46	1.356079	0.24598	0.039492	0.127674	ENSG00000173163	ENST00000458337;ENST00000427417;ENST00000444166	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7528	0.57318	0.0:0.0:0.0:1.0	rs9096;rs1045302;rs3185192	.	.	.	R	12;12;6	.	.	X	+	1	0	COMMD1	62216499	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.541000	0.53618	2.326000	0.78906	0.472000	0.43445	TGA	T|0.906;C|0.094	0.094	strong		0.413	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251607.2	NM_152516	
LRRK1	79705	hgsc.bcm.edu	37	15	101598200	101598200	+	Silent	SNP	G	G	A	rs11857803	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:101598200G>A	ENST00000388948.3	+	29	4892	c.4533G>A	c.(4531-4533)ccG>ccA	p.P1511P	LRRK1_ENST00000284395.5_Silent_p.P1508P|RP11-505E24.2_ENST00000559857.1_RNA	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)			CTCAGCGACCGCTGGCCCTGT	0.582													G|||	1594	0.318291	0.3071	0.2839	5008	,	,		19623	0.128		0.4493	False		,,,				2504	0.4192				p.P1511P		Atlas-SNP	.											.	LRRK1	310	.	0			c.G4533A						PASS	.	G		1283,2719		215,853,933	79.0	82.0	81.0		4533	-7.6	0.8	15	dbSNP_120	81	3865,4491		920,2025,1233	no	coding-synonymous	LRRK1	NM_024652.3		1135,2878,2166	AA,AG,GG		46.2542,32.059,41.6572		1511/2016	101598200	5148,7210	2001	4178	6179	SO:0001819	synonymous_variant	79705	exon29			GCGACCGCTGGCC	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.4533G>A	15.37:g.101598200G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.633;A|0.367	0.367	strong		0.582	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
DHX57	90957	hgsc.bcm.edu	37	2	39082344	39082344	+	Missense_Mutation	SNP	T	T	C	rs7598922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	157	0	0		WXS	Illumina HiSeq	Phase_I	162	85	0.524691	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	
TFCP2	7024	hgsc.bcm.edu	37	12	51500329	51500329	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:51500329C>T	ENST00000257915.5	-	8	1354	c.896G>A	c.(895-897)aGc>aAc	p.S299N	TFCP2_ENST00000548115.1_Missense_Mutation_p.S248N|TFCP2_ENST00000307660.4_Missense_Mutation_p.S248N|TFCP2_ENST00000549867.1_Missense_Mutation_p.S299N	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	299	DNA-binding.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AGAAAAACTGCTATGGGAACT	0.368																																					p.S299N		Atlas-SNP	.											.	TFCP2	49	.	0			c.G896A						PASS	.						81.0	79.0	80.0					12																	51500329		2203	4300	6503	SO:0001583	missense	7024	exon8			AAACTGCTATGGG	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.896G>A	12.37:g.51500329C>T	ENSP00000257915:p.Ser299Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	4	0.0677966	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	37	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.019071	0.35606	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.45276	2.22;0.91;2.24;0.9;2.24	5.53	4.64	0.57946	Sterile alpha motif/pointed domain (1);	0.047786	0.85682	D	0.000000	T	0.19765	0.0475	N	0.03194	-0.395	0.40060	D	0.975885	B;B;B;B	0.23990	0.0;0.095;0.0;0.0	B;B;B;B	0.26416	0.002;0.069;0.001;0.001	T	0.09840	-1.0656	10	0.19147	T	0.46	-8.47	10.179	0.42957	0.0:0.8443:0.0:0.1557	.	248;299;299;299	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	N	299;248;299;248;201	ENSP00000257915:S299N;ENSP00000304411:S248N;ENSP00000449742:S299N;ENSP00000447991:S248N;ENSP00000449280:S201N	ENSP00000257915:S299N	S	-	2	0	TFCP2	49786596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.788000	0.26872	1.482000	0.48325	0.655000	0.94253	AGC	.	.	none		0.368	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	
LAMA5	3911	hgsc.bcm.edu	37	20	60887468	60887468	+	Silent	SNP	G	G	A	rs16985970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60887468G>A	ENST00000252999.3	-	68	9414	c.9348C>T	c.(9346-9348)acC>acT	p.T3116T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3116					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)			GCAGGTCGGCGGTGCAGCCGG	0.697													.|||	433	0.0864617	0.0204	0.0331	5008	,	,		15056	0.2054		0.0775	False		,,,				2504	0.1002				p.T3116T		Atlas-SNP	.											.	LAMA5	268	.	0			c.C9348T						PASS	.			104,4266		0,104,2081	26.0	26.0	26.0		9348	-8.5	0.0	20	dbSNP_123	26	681,7891		33,615,3638	no	coding-synonymous	LAMA5	NM_005560.3		33,719,5719	AA,AG,GG		7.9445,2.3799,6.0655		3116/3696	60887468	785,12157	2185	4286	6471	SO:0001819	synonymous_variant	3911	exon68			GTCGGCGGTGCAG	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.9348C>T	20.37:g.60887468G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.928;A|0.072	0.072	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CALCOCO1	57658	hgsc.bcm.edu	37	12	54109659	54109659	+	Missense_Mutation	SNP	C	C	T	rs3741659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:54109659C>T	ENST00000550804.1	-	9	1238	c.1178G>A	c.(1177-1179)aGg>aAg	p.R393K	CALCOCO1_ENST00000548263.1_Missense_Mutation_p.R393K|CALCOCO1_ENST00000262059.4_Missense_Mutation_p.R393K|CALCOCO1_ENST00000430117.2_Missense_Mutation_p.R308K			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	393			R -> K (in dbSNP:rs3741659). {ECO:0000269|PubMed:14702039}.		intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						CTCAGCCAGCCTGCCGTTAAC	0.602													C|||	876	0.17492	0.1203	0.1354	5008	,	,		19930	0.2698		0.17	False		,,,				2504	0.184				p.R393K		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.G1178A						PASS	.	C	LYS/ARG,LYS/ARG	581,3825	258.6+/-262.5	42,497,1664	53.0	50.0	51.0		923,1178	4.9	1.0	12	dbSNP_107	51	1189,7411	241.4+/-271.8	81,1027,3192	yes	missense,missense	CALCOCO1	NM_001143682.1,NM_020898.2	26,26	123,1524,4856	TT,TC,CC		13.8256,13.1866,13.6091	benign,benign	308/607,393/692	54109659	1770,11236	2203	4300	6503	SO:0001583	missense	57658	exon9			GCCAGCCTGCCGT	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"""coiled-coil leucine zipper coactivator 1"", ""inorganic pyrophosphatase activator"""					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.1178G>A	12.37:g.54109659C>T	ENSP00000449960:p.Arg393Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Missense_Mutation	SNP	ENST00000550804.1	37	CCDS8864.1	416	0.19047619047619047	61	0.12398373983739837	48	0.13259668508287292	183	0.31993006993006995	124	0.16358839050131926	C	13.16	2.154064	0.38021	0.131866	0.138256	ENSG00000012822	ENST00000342760;ENST00000430117;ENST00000262059;ENST00000413257;ENST00000548263;ENST00000550804;ENST00000549935	T;T;T;T	0.08896	3.04;3.04;3.04;3.04	4.91	4.91	0.64330	.	0.000000	0.44688	D	0.000426	T	0.00012	0.0000	N	0.16368	0.405	0.37567	P	0.08072900000000005	B;B;B;B;B;B	0.28667	0.219;0.025;0.1;0.039;0.025;0.122	B;B;B;B;B;B	0.24541	0.054;0.022;0.017;0.042;0.022;0.03	T	0.49916	-0.8888	9	0.18276	T	0.48	-23.3552	7.5434	0.27753	0.0:0.8258:0.0:0.1742	rs3741659;rs52825391;rs56753282;rs3741659	386;308;393;393;308;393	B4DG60;E9PAU0;Q9P1Z2-3;Q9P1Z2-2;E7EPK7;Q9P1Z2	.;.;.;.;.;CACO1_HUMAN	K	70;308;393;331;393;393;386	ENSP00000397189:R308K;ENSP00000262059:R393K;ENSP00000447647:R393K;ENSP00000449960:R393K	ENSP00000262059:R393K	R	-	2	0	CALCOCO1	52395926	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.970000	0.49240	2.713000	0.92767	0.655000	0.94253	AGG	C|0.829;T|0.171	0.171	strong		0.602	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634373	32634373	+	Silent	SNP	C	C	T	rs9274522	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32634373C>T	ENST00000399082.3	-	1	56	c.12G>A	c.(10-12)aaG>aaA	p.K4K	HLA-DQB1_ENST00000434651.2_Silent_p.K4K|HLA-DQB1_ENST00000374943.4_Silent_p.K4K|HLA-DQB1_ENST00000399079.3_Silent_p.K4K|HLA-DQB1_ENST00000399084.1_Silent_p.K4K			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	4					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GCAAAGCCTTCTTCCAAGACA	0.532									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				c|||	1621	0.323682	0.3722	0.3458	5008	,	,		14244	0.2381		0.3608	False		,,,				2504	0.2924				p.K4K	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G12A						PASS	.						39.0	38.0	38.0					6																	32634373		1927	4107	6034	SO:0001819	synonymous_variant	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AGCCTTCTTCCAA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.12G>A	6.37:g.32634373C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				C|0.670;T|0.330	0.330	strong		0.532	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181082	19181082	+	Silent	SNP	A	A	C	rs28470550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19181082A>C	ENST00000375371.3	-	3	903	c.882T>G	c.(880-882)acT>acG	p.T294T	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	294					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ACACGGCGCCAGTGAAGTTCT	0.637													C|||	1196	0.238818	0.2602	0.2536	5008	,	,		18981	0.1032		0.3201	False		,,,				2504	0.2556				p.T294T		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,2	TAS1R2	134	2	0			c.T882G						scavenged	.	C		1096,3310	717.7+/-408.7	130,836,1237	56.0	54.0	55.0		882	-9.8	0.0	1	dbSNP_125	55	2810,5790	674.9+/-403.2	449,1912,1939	no	coding-synonymous	TAS1R2	NM_152232.2		579,2748,3176	CC,CA,AA		32.6744,24.8752,30.0323		294/840	19181082	3906,9100	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon3			GGCGCCAGTGAAG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.882T>G	1.37:g.19181082A>C		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	69	43	0.623188	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			A|0.717;C|0.283	0.283	strong		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
RFX4	5992	hgsc.bcm.edu	37	12	107141265	107141265	+	Missense_Mutation	SNP	G	G	A	rs61743416	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:107141265G>A	ENST00000392842.1	+	16	2098	c.1684G>A	c.(1684-1686)Gct>Act	p.A562T	RFX4_ENST00000229387.5_Missense_Mutation_p.A468T|RFX4_ENST00000357881.4_Missense_Mutation_p.A571T|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	562					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						GACGACGGCTGCTGGGTCCCC	0.498													G|||	54	0.0107827	0.0023	0.0202	5008	,	,		19904	0.0099		0.0109	False		,,,				2504	0.0164				p.A571T		Atlas-SNP	.											.	RFX4	218	.	0			c.G1711A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	22,4384	29.9+/-59.1	0,22,2181	104.0	94.0	97.0		1711,1402,1684	5.4	1.0	12	dbSNP_129	97	101,8499	55.2+/-116.2	0,101,4199	yes	missense,missense,missense	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	58,58,58	0,123,6380	AA,AG,GG		1.1744,0.4993,0.9457	benign,benign,benign	571/745,468/642,562/736	107141265	123,12883	2203	4300	6503	SO:0001583	missense	5992	exon16			ACGGCTGCTGGGT	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1684G>A	12.37:g.107141265G>A	ENSP00000376585:p.Ala562Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Missense_Mutation	SNP	ENST00000392842.1	37	CCDS9106.1	24	0.01098901098901099	2	0.0040650406504065045	10	0.027624309392265192	2	0.0034965034965034965	10	0.013192612137203167	G	20.7	4.034562	0.75617	0.004993	0.011744	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000229387	T;T;T	0.64618	-0.1;-0.11;0.89	5.45	5.45	0.79879	.	0.101606	0.64402	D	0.000002	T	0.26557	0.0649	N	0.14661	0.345	0.58432	D	0.999996	P;P;P	0.41313	0.634;0.745;0.487	B;B;B	0.40444	0.298;0.329;0.124	T	0.45789	-0.9237	10	0.45353	T	0.12	-13.2519	19.3053	0.94158	0.0:0.0:1.0:0.0	rs61743416	468;571;562	B2RDW4;Q33E94-2;Q33E94	.;.;RFX4_HUMAN	T	562;571;468	ENSP00000376585:A562T;ENSP00000350552:A571T;ENSP00000229387:A468T	ENSP00000229387:A468T	A	+	1	0	RFX4	105665395	1.000000	0.71417	0.952000	0.39060	0.981000	0.71138	9.098000	0.94202	2.562000	0.86427	0.655000	0.94253	GCT	G|0.990;A|0.010	0.010	strong		0.498	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
OR7G2	390882	hgsc.bcm.edu	37	19	9213079	9213079	+	Missense_Mutation	SNP	A	A	C	rs4804401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9213079A>C	ENST00000305456.2	-	1	903	c.904T>G	c.(904-906)Ttc>Gtc	p.F302V		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, 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)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						ATTTGAGGGAACACAGAATAC	0.453													-|||	1665	0.332468	0.1051	0.2853	5008	,	,		20121	0.5575		0.3718	False		,,,				2504	0.4008				p.F302V	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											.	OR7G2	48	.	0			c.T904G						PASS	.	C	VAL/PHE	645,3761	766.0+/-413.4	40,565,1598	125.0	109.0	115.0		904	3.1	0.1	19	dbSNP_111	115	3016,5584	663.7+/-402.1	528,1960,1812	yes	missense	OR7G2	NM_001005193.1	50	568,2525,3410	CC,CA,AA		35.0698,14.6391,28.1485	benign	302/346	9213079	3661,9345	2203	4300	6503	SO:0001583	missense	390882	exon1			GAGGGAACACAGA		CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"""GPCR / Class A : Olfactory receptors"""	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.904T>G	19.37:g.9213079A>C	ENSP00000303822:p.Phe302Val	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_001005193	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	767	0.35119047619047616	63	0.12804878048780488	101	0.27900552486187846	323	0.5646853146853147	280	0.36939313984168864	c	0.016	-1.515691	0.00975	0.146391	0.350698	ENSG00000170923	ENST00000305456	T	0.00014	9.18	3.14	3.14	0.36123	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33875	N	0.004468	T	0.00012	0.0000	N	0.00010	-3.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26608	-1.0098	9	0.02654	T	1	.	11.3342	0.49494	0.1843:0.8157:0.0:0.0	rs4804401;rs17238753;rs59110665;rs4804401	281	Q8NG99	OR7G2_HUMAN	V	302	ENSP00000303822:F302V	ENSP00000303822:F302V	F	-	1	0	OR7G2	9074079	0.000000	0.05858	0.055000	0.19348	0.003000	0.03518	-4.165000	0.00282	0.948000	0.37687	-0.395000	0.06472	TTC	A|0.683;C|0.317	0.317	strong		0.453	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1		
AHCTF1	25909	hgsc.bcm.edu	37	1	247007232	247007232	+	Splice_Site	SNP	T	T	A	rs148600466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247007232T>A	ENST00000391829.2	-	34	6515		c.e34-2		AHCTF1_ENST00000326225.3_Splice_Site|AHCTF1_ENST00000366508.1_Splice_Site|AHCTF1_ENST00000470300.1_Splice_Site			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1						cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TTTTTTTAGCTAAAAAAAGTT	0.303													T|||	19	0.00379393	0.0	0.0101	5008	,	,		13414	0.0		0.0109	False		,,,				2504	0.001				.	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.6419-2A>T						PASS	.	T		19,4381	20.2+/-43.8	0,19,2181	44.0	44.0	44.0			4.2	0.9	1	dbSNP_134	44	102,8494	43.6+/-101.6	1,100,4197	no	splice-3	AHCTF1	NM_015446.4		1,119,6378	AA,AT,TT		1.1866,0.4318,0.9311			247007232	121,12875	2200	4298	6498	SO:0001630	splice_region_variant	25909	exon35			TTTAGCTAAAAAA		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6392-2A>T	1.37:g.247007232T>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Splice_Site	SNP	ENST00000391829.2	37		13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	8	0.010554089709762533	T	13.05	2.121636	0.37436	0.004318	0.011866	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	.	.	.	5.29	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8575	0.41094	0.0:0.0781:0.0:0.9219	.	.	.	.	.	-1	.	.	.	-	.	.	AHCTF1	245073855	1.000000	0.71417	0.937000	0.37676	0.546000	0.35178	3.504000	0.53347	0.955000	0.37878	-0.326000	0.08463	.	T|0.992;A|0.008	0.008	strong		0.303	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	Intron
RHOBTB1	9886	hgsc.bcm.edu	37	10	62645873	62645873	+	Silent	SNP	A	A	G	rs2271128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:62645873A>G	ENST00000337910.5	-	7	1909	c.1572T>C	c.(1570-1572)agT>agC	p.S524S	RHOBTB1_ENST00000357917.4_Silent_p.S524S	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	524	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					CACGTACCTCACTGTTGGCAC	0.478													A|||	255	0.0509185	0.0023	0.0793	5008	,	,		21464	0.1052		0.0328	False		,,,				2504	0.0593				p.S524S		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.T1572C						PASS	.	A	,	29,4377	35.2+/-66.4	0,29,2174	205.0	179.0	188.0		1572,1572	1.9	1.0	10	dbSNP_100	188	323,8277	114.2+/-174.2	13,297,3990	no	coding-synonymous,coding-synonymous	RHOBTB1	NM_001242359.1,NM_014836.4	,	13,326,6164	GG,GA,AA		3.7558,0.6582,2.7064	,	524/697,524/697	62645873	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	9886	exon7			TACCTCACTGTTG	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"""BTB/POZ domain containing"""	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1572T>C	10.37:g.62645873A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_014836		Silent	SNP	ENST00000337910.5	37	CCDS7261.1																																																																																			A|0.962;G|0.038	0.038	strong		0.478	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1		
BNC2	54796	hgsc.bcm.edu	37	9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	rs117452684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:16419519G>A	ENST00000380672.4	-	7	2825	c.2768C>T	c.(2767-2769)gCc>gTc	p.A923V	BNC2_ENST00000545497.1_Missense_Mutation_p.A828V|BNC2_ENST00000380667.2_Missense_Mutation_p.A856V	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GGGGTGCTGGGCACCATATAT	0.572													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		16876	0.0		0.0288	False		,,,				2504	0.0092				p.A923V		Atlas-SNP	.											.	BNC2	166	.	0			c.C2768T						PASS	.	G	VAL/ALA	30,4376	36.0+/-67.5	0,30,2173	83.0	87.0	86.0		2768	5.5	1.0	9	dbSNP_132	86	293,8307	107.0+/-167.8	3,287,4010	yes	missense	BNC2	NM_017637.5	64	3,317,6183	AA,AG,GG		3.407,0.6809,2.4835	benign	923/1100	16419519	323,12683	2203	4300	6503	SO:0001583	missense	54796	exon7			TGCTGGGCACCAT	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2768C>T	9.37:g.16419519G>A	ENSP00000370047:p.Ala923Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	G	13.60	2.286262	0.40494	0.006809	0.03407	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.31510	1.49;1.5;1.5	5.5	5.5	0.81552	.	0.166180	0.51477	D	0.000083	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P;P;B	0.41673	0.578;0.759;0.18	B;B;B	0.39027	0.158;0.288;0.051	T	0.01844	-1.1262	10	0.27082	T	0.32	-9.5452	14.94	0.70986	0.0:0.1426:0.8574:0.0	.	828;923;688	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	V	923;856;828	ENSP00000370047:A923V;ENSP00000370042:A856V;ENSP00000444640:A828V	ENSP00000370042:A856V	A	-	2	0	BNC2	16409519	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.336000	0.52113	2.586000	0.87340	0.591000	0.81541	GCC	G|0.979;A|0.021	0.021	strong		0.572	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
SH3BP1	23616	hgsc.bcm.edu	37	22	38039708	38039708	+	Silent	SNP	T	T	C	rs1894529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38039708T>C	ENST00000357436.4	+	7	844	c.531T>C	c.(529-531)ggT>ggC	p.G177G	SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000442465.2_Silent_p.G177G|SH3BP1_ENST00000336738.5_Silent_p.G177G|SH3BP1_ENST00000599616.1_Silent_p.G113G|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	177	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)	p.G177G(1)		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)					GCAGCCCGGGTAGTCACAGCC	0.587											OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	473	0.0944489	0.1641	0.0591	5008	,	,		20123	0.0139		0.0616	False		,,,				2504	0.1421				p.G177G		Atlas-SNP	.											SH3BP1,NS,carcinoma,0,1	SH3BP1	41	1	1	Substitution - coding silent(1)	stomach(1)	c.T531C						PASS	.	C		693,3713	758.0+/-412.8	52,589,1562	149.0	116.0	127.0		531	-2.2	0.0	22	dbSNP_92	127	657,7943	788.9+/-407.6	29,599,3672	no	coding-synonymous	SH3BP1	NM_018957.3		81,1188,5234	CC,CT,TT		7.6395,15.7286,10.3798		177/702	38039708	1350,11656	2203	4300	6503	SO:0001819	synonymous_variant	23616	exon7			CCCGGGTAGTCAC		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.531T>C	22.37:g.38039708T>C		Somatic	52	0	0	875	WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			T|0.906;C|0.094	0.094	strong		0.587	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
WDR90	197335	hgsc.bcm.edu	37	16	705360	705360	+	Missense_Mutation	SNP	T	T	C	rs3803697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:705360T>C	ENST00000293879.4	+	15	1610	c.1610T>C	c.(1609-1611)gTg>gCg	p.V537A	WDR90_ENST00000549091.1_Missense_Mutation_p.V537A|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	537			V -> A (in dbSNP:rs3803697). {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)				CGTGGCGGGGTGCTGCGTTCC	0.706													C|||	3489	0.696685	0.8744	0.5965	5008	,	,		15360	0.9841		0.3757	False		,,,				2504	0.5613				p.V537A		Atlas-SNP	.											WDR90,colon,carcinoma,0,3	WDR90	107	3	0			c.T1610C						PASS	.	C	ALA/VAL	3355,989		1322,711,139	17.0	29.0	25.0		1610	-9.3	0.0	16	dbSNP_107	25	3028,5518		558,1912,1803	yes	missense	WDR90	NM_145294.4	64	1880,2623,1942	CC,CT,TT		35.4318,22.767,49.519	benign	537/1749	705360	6383,6507	2172	4273	6445	SO:0001583	missense	197335	exon15			GCGGGGTGCTGCG	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.1610T>C	16.37:g.705360T>C	ENSP00000293879:p.Val537Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	15	13	0.866667	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	1465	0.6707875457875457	417	0.8475609756097561	197	0.5441988950276243	562	0.9825174825174825	289	0.3812664907651715	C	0.015	-1.540982	0.00934	0.77233	0.354318	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.26067	1.8;1.76	4.67	-9.34	0.00636	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	1.118960	0.07045	N	0.830877	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.23261	-1.0193	9	0.07813	T	0.8	.	1.8074	0.03084	0.3135:0.1797:0.0853:0.4215	rs3803697	537;537;538;537	F8VUX9;Q96KV7;C9JMK1;Q96KV7-3	.;WDR90_HUMAN;.;.	A	537	ENSP00000448122:V537A;ENSP00000293879:V537A	ENSP00000293879:V537A	V	+	2	0	WDR90	645361	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.586000	0.05787	-3.437000	0.00163	-2.865000	0.00100	GTG	T|0.374;C|0.626	0.626	strong		0.706	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
SALL2	6297	hgsc.bcm.edu	37	14	21993638	21993638	+	Missense_Mutation	SNP	G	G	C	rs2242527	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:21993638G>C	ENST00000327430.3	-	2	518	c.224C>G	c.(223-225)tCt>tGt	p.S75C	SALL2_ENST00000538754.1_Missense_Mutation_p.S73C|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000317492.5_Missense_Mutation_p.S75C|SALL2_ENST00000450879.2_Missense_Mutation_p.S73C	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	223	0	0		WXS	Illumina HiSeq	Phase_I	228	110	0.482456	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	
MCTP1	79772	hgsc.bcm.edu	37	5	94230358	94230358	+	Missense_Mutation	SNP	C	C	T	rs9885412	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:94230358C>T	ENST00000515393.1	-	11	1834	c.1835G>A	c.(1834-1836)aGa>aAa	p.R612K	MCTP1_ENST00000505208.1_Missense_Mutation_p.R391K|MCTP1_ENST00000312216.8_Missense_Mutation_p.R391K|MCTP1_ENST00000505078.1_Missense_Mutation_p.R128K|MCTP1_ENST00000429576.2_Missense_Mutation_p.R345K	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	612			R -> K (in dbSNP:rs9885412). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		ACGTACATATCTCTTTAATAT	0.473													C|||	495	0.0988419	0.1029	0.0807	5008	,	,		20252	0.0704		0.1103	False		,,,				2504	0.1237				p.R612K		Atlas-SNP	.											.	MCTP1	110	.	0			c.G1835A						PASS	.	C	LYS/ARG,LYS/ARG	463,3943	219.7+/-237.4	33,397,1773	132.0	109.0	117.0		1172,1835	5.4	1.0	5	dbSNP_119	117	971,7629	210.4+/-251.3	49,873,3378	yes	missense,missense	MCTP1	NM_001002796.2,NM_024717.4	26,26	82,1270,5151	TT,TC,CC		11.2907,10.5084,11.0257	benign,benign	391/779,612/1000	94230358	1434,11572	2203	4300	6503	SO:0001583	missense	79772	exon11			ACATATCTCTTTA		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1835G>A	5.37:g.94230358C>T	ENSP00000424126:p.Arg612Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	37	CCDS34203.1	199	0.09111721611721611	50	0.1016260162601626	35	0.09668508287292818	32	0.055944055944055944	82	0.10817941952506596	C	17.32	3.360489	0.61403	0.105084	0.112907	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509;ENST00000512425;ENST00000505208;ENST00000506568	T;T;T;T;T;T;T;T	0.77358	-1.09;-0.79;-0.04;-0.98;-0.79;-0.92;-1.08;-0.71	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.10723	0.0262	L	0.55017	1.72	0.09310	P	0.999999999075779	D;D;P	0.67145	0.994;0.996;0.923	D;D;P	0.77557	0.977;0.99;0.599	T	0.61749	-0.6999	9	0.07482	T	0.82	-14.4605	19.4941	0.95064	0.0:1.0:0.0:0.0	rs9885412;rs17852723;rs52810316;rs9885412	612;345;391	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	K	612;345;128;391;332;273;391;213	ENSP00000424126:R612K;ENSP00000391639:R345K;ENSP00000426417:R128K;ENSP00000308957:R391K;ENSP00000423410:R332K;ENSP00000431075:R273K;ENSP00000426438:R391K;ENSP00000426294:R213K	ENSP00000308957:R391K	R	-	2	0	MCTP1	94256114	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	7.238000	0.78173	2.682000	0.91365	0.591000	0.81541	AGA	C|0.895;T|0.105	0.105	strong		0.473	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
DOCK2	1794	hgsc.bcm.edu	37	5	169127097	169127097	+	Silent	SNP	C	C	A	rs2112703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169127097C>A	ENST00000256935.8	+	13	1292	c.1212C>A	c.(1210-1212)acC>acA	p.T404T		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	404					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGACAGGACCACCGTGGTGG	0.567													C|||	609	0.121605	0.0363	0.0893	5008	,	,		17531	0.122		0.2048	False		,,,				2504	0.1738				p.T404T		Atlas-SNP	.											.	DOCK2	389	.	0			c.C1212A						PASS	.	C		323,4083	171.9+/-202.1	18,287,1898	160.0	146.0	151.0		1212	1.6	1.0	5	dbSNP_96	151	1783,6817	322.8+/-315.7	197,1389,2714	no	coding-synonymous	DOCK2	NM_004946.2		215,1676,4612	AA,AC,CC		20.7326,7.3309,16.1925		404/1831	169127097	2106,10900	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon13			CAGGACCACCGTG	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.1212C>A	5.37:g.169127097C>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			C|0.852;A|0.148	0.148	strong		0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
DNAH8	1769	hgsc.bcm.edu	37	6	38957853	38957853	+	Silent	SNP	A	A	G	rs3737094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:38957853A>G	ENST00000359357.3	+	86	12722	c.12468A>G	c.(12466-12468)ttA>ttG	p.L4156L	DNAH8_ENST00000441566.1_Silent_p.L4120L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4156					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						AAATCCCCTTATGCAAAACCT	0.383													G|||	1646	0.328674	0.3124	0.3429	5008	,	,		18987	0.252		0.4443	False		,,,				2504	0.3006				p.L4373L		Atlas-SNP	.											DNAH8_ENST00000359357,NS,adenoma,0,2	DNAH8	1239	2	0			c.A13119G						PASS	.	G		1467,2939	679.5+/-403.7	268,931,1004	174.0	165.0	168.0		13119	-1.2	0.2	6	dbSNP_107	168	3844,4756	609.6+/-395.6	850,2144,1306	no	coding-synonymous	DNAH8	NM_001206927.1		1118,3075,2310	GG,GA,AA		44.6977,33.2955,40.835		4373/4708	38957853	5311,7695	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon88			CCCCTTATGCAAA	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.12468A>G	6.37:g.38957853A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				A|0.618;G|0.382	0.382	strong		0.383	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
ZP3	7784	hgsc.bcm.edu	37	7	76069886	76069886	+	Missense_Mutation	SNP	A	A	G	rs2906997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76069886A>G	ENST00000394857.3	+	7	1076	c.1018A>G	c.(1018-1020)Atg>Gtg	p.M340V	ZP3_ENST00000336517.4_Missense_Mutation_p.M289V|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.M164V	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	340			M -> V (in dbSNP:rs2906997).		binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GCCTCATGTCATGAGCCAGTG	0.542																																					p.M340V		Atlas-SNP	.											.	ZP3	32	.	0			c.A1018G						PASS	.						134.0	129.0	131.0					7																	76069886		2203	4300	6503	SO:0001583	missense	7784	exon7			CATGTCATGAGCC	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1018A>G	7.37:g.76069886A>G	ENSP00000378326:p.Met340Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	184	17	0.0923913	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	N	2.901	-0.227591	0.06022	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.20463	2.66;2.88;2.07	4.27	-5.46	0.02608	.	2.545950	0.01889	N	0.038399	T	0.04952	0.0133	N	0.00483	-1.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23368	-1.0190	10	0.29301	T	0.29	1.7081	2.1536	0.03806	0.4579:0.2402:0.1865:0.1154	rs2906997;rs2906997	289;340	P21754-3;P21754	.;ZP3_HUMAN	V	289;340;340;164	ENSP00000337310:M289V;ENSP00000378326:M340V;ENSP00000411955:M164V	ENSP00000337310:M289V	M	+	1	0	ZP3	75907822	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.029000	0.01430	-1.516000	0.01782	-1.163000	0.01768	ATG	A|0.912;G|0.088	0.088	strong		0.542	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
USH1C	10083	hgsc.bcm.edu	37	11	17522638	17522638	+	Silent	SNP	G	G	A	rs10832796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17522638G>A	ENST00000318024.4	-	18	1548	c.1440C>T	c.(1438-1440)gtC>gtT	p.V480V	USH1C_ENST00000527720.1_Silent_p.V449V|USH1C_ENST00000529563.1_5'UTR|USH1C_ENST00000527020.1_Silent_p.V461V|USH1C_ENST00000005226.7_Silent_p.V780V	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	480	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CAGCAGAAACGACCACCTTCC	0.592													G|||	954	0.190495	0.0234	0.1902	5008	,	,		18565	0.2837		0.3171	False		,,,				2504	0.1902				p.V780V		Atlas-SNP	.											.	USH1C	157	.	0			c.C2340T						PASS	.	G	,	264,4136	148.0+/-182.4	8,248,1944	78.0	63.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1440,2340	-6.1	0.9	11	dbSNP_120	68	2489,6097	407.0+/-349.0	348,1793,2152	no	coding-synonymous,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	356,2041,4096	AA,AG,GG		28.9891,6.0,21.1998	,	480/553,780/900	17522638	2753,10233	2200	4293	6493	SO:0001819	synonymous_variant	10083	exon23			AGAAACGACCACC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1440C>T	11.37:g.17522638G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			G|0.784;A|0.216	0.216	strong		0.592	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
PKD1L2	114780	hgsc.bcm.edu	37	16	81211570	81211570	+	RNA	SNP	T	T	C	rs143824762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81211570T>C	ENST00000527937.1	-	0	319				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA			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						GTCCTCCCCATAGGCATGCCT	0.592													T|||	10	0.00199681	0.0	0.0029	5008	,	,		18450	0.0		0.007	False		,,,				2504	0.001				p.Y760C		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A2279G						PASS	.	T	CYS/TYR,CYS/TYR	4,4006		0,4,2001	43.0	43.0	43.0		2279,2279	4.9	1.0	16	dbSNP_134	43	26,8340		0,26,4157	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	194,194	0,30,6158	CC,CT,TT		0.3108,0.0998,0.2424	probably-damaging,probably-damaging	760/992,760/2460	81211570	30,12346	2005	4183	6188			114780	exon14			TCCCCATAGGCAT	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.81211570T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	13.84	2.357767	0.41801	9.98E-4	0.003108	ENSG00000166473	ENST00000531391;ENST00000337114	T;T	0.69561	-0.41;-0.41	4.89	4.89	0.63831	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.418664	0.17665	N	0.166183	T	0.80003	0.4544	.	.	.	0.28529	N	0.912673	D;D	0.89917	1.0;0.996	D;P	0.70935	0.971;0.863	T	0.75019	-0.3465	9	0.87932	D	0	-4.73	12.1197	0.53885	0.0:0.0:0.0:1.0	.	760;760	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	C	75;760	ENSP00000436309:Y75C;ENSP00000337397:Y760C	ENSP00000337397:Y760C	Y	-	2	0	PKD1L2	79769071	0.963000	0.33076	0.984000	0.44739	0.338000	0.28826	3.995000	0.57001	1.858000	0.53909	0.449000	0.29647	TAT	T|0.998;C|0.002	0.002	strong		0.592	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
VWA3B	200403	hgsc.bcm.edu	37	2	98809432	98809432	+	Missense_Mutation	SNP	T	T	C	rs74735968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:98809432T>C	ENST00000477737.1	+	11	1742	c.1538T>C	c.(1537-1539)aTt>aCt	p.I513T	VWA3B_ENST00000435344.1_Missense_Mutation_p.I513T|VWA3B_ENST00000451075.2_Missense_Mutation_p.I363T	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	513	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.									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						TACATTCTCATTGACACGTCT	0.428													T|||	84	0.0167732	0.0	0.0115	5008	,	,		22387	0.0		0.0666	False		,,,				2504	0.0092				p.I513T		Atlas-SNP	.											.	VWA3B	138	.	0			c.T1538C						PASS	.	T	THR/ILE	57,3841		0,57,1892	172.0	160.0	164.0		1538	5.5	1.0	2	dbSNP_131	164	477,7843		10,457,3693	yes	missense	VWA3B	NM_144992.4	89	10,514,5585	CC,CT,TT		5.7332,1.4623,4.3706	probably-damaging	513/1295	98809432	534,11684	1949	4160	6109	SO:0001583	missense	200403	exon11			TTCTCATTGACAC	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.1538T>C	2.37:g.98809432T>C	ENSP00000417955:p.Ile513Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	61	0.027930402930402932	0	0.0	4	0.011049723756906077	0	0.0	57	0.07519788918205805	T	15.40	2.822694	0.50739	0.014623	0.057332	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	D;T;D	0.81996	-1.56;1.64;-1.56	5.5	5.5	0.81552	von Willebrand factor, type A (3);	0.077125	0.53938	D	0.000059	T	0.48642	0.1511	M	0.85197	2.74	0.31224	N	0.697125	D;D;D;D	0.89917	1.0;1.0;1.0;0.997	D;D;D;D	0.97110	0.985;1.0;0.987;0.913	T	0.76597	-0.2901	10	0.87932	D	0	.	14.5903	0.68359	0.0:0.0:0.0:1.0	.	363;513;513;513	B7Z7Q7;Q502W6;Q502W6-8;Q502W6-6	.;VWA3B_HUMAN;.;.	T	513;513;363	ENSP00000401959:I513T;ENSP00000417955:I513T;ENSP00000389463:I363T	ENSP00000388158:I513T	I	+	2	0	VWA3B	98175864	1.000000	0.71417	0.987000	0.45799	0.289000	0.27227	5.140000	0.64807	2.096000	0.63516	0.528000	0.53228	ATT	T|0.964;C|0.036	0.036	strong		0.428	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
FAT2	2196	hgsc.bcm.edu	37	5	150947128	150947128	+	Silent	SNP	G	G	A	rs34166097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150947128G>A	ENST00000261800.5	-	1	1377	c.1365C>T	c.(1363-1365)gcC>gcT	p.A455A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	455	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)			TGAAGAGGGGGGCATGGTTGT	0.557													G|||	79	0.0157748	0.0008	0.0259	5008	,	,		19350	0.001		0.0527	False		,,,				2504	0.0061				p.A455A		Atlas-SNP	.											.	FAT2	465	.	0			c.C1365T						PASS	.	G		36,4370	41.6+/-74.8	0,36,2167	125.0	124.0	125.0		1365	2.8	1.0	5	dbSNP_126	125	414,8186	129.5+/-187.6	7,400,3893	no	coding-synonymous	FAT2	NM_001447.2		7,436,6060	AA,AG,GG		4.814,0.8171,3.4599		455/4350	150947128	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GAGGGGGGCATGG	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.1365C>T	5.37:g.150947128G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	152	62	0.407895	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
ALG12	79087	hgsc.bcm.edu	37	22	50301476	50301476	+	Silent	SNP	T	T	C	rs8135963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50301476T>C	ENST00000330817.6	-	7	1158	c.885A>G	c.(883-885)gcA>gcG	p.A295A		NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	295					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)		TGAAGCCCAGTGCCAGCACCG	0.622													C|||	2014	0.402157	0.8253	0.1902	5008	,	,		18089	0.1806		0.2097	False		,,,				2504	0.407				p.A295A		Atlas-SNP	.											ALG12,NS,carcinoma,0,1	ALG12	35	1	0			c.A885G						PASS	.	C		3136,1270	432.8+/-343.4	1121,894,188	136.0	125.0	129.0		885	-9.6	0.0	22	dbSNP_116	129	1850,6750	730.8+/-406.8	201,1448,2651	yes	coding-synonymous	ALG12	NM_024105.3		1322,2342,2839	CC,CT,TT		21.5116,28.8243,38.3362		295/489	50301476	4986,8020	2203	4300	6503	SO:0001819	synonymous_variant	79087	exon7			GCCCAGTGCCAGC	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.885A>G	22.37:g.50301476T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_024105	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	Silent	SNP	ENST00000330817.6	37	CCDS14081.1	754	0.34523809523809523	409	0.8313008130081301	74	0.20441988950276244	107	0.18706293706293706	164	0.21635883905013192	C	0.366	-0.936583	0.02340	0.711757	0.215116	ENSG00000182858	ENST00000486602	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.14643	-1.0465	3	.	.	.	-9.9376	1.8826	0.03231	0.1691:0.3659:0.1762:0.2889	rs8135963;rs60186810;rs8135963	.	.	.	A	31	.	.	T	-	1	0	ALG12	48687480	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.665000	0.00106	-3.134000	0.00235	-3.324000	0.00044	ACT	T|0.617;C|0.383	0.383	strong		0.622	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317405.2	NM_024105	
QRICH2	84074	hgsc.bcm.edu	37	17	74289648	74289648	+	Missense_Mutation	SNP	G	G	A	rs118098530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74289648G>A	ENST00000262765.5	-	4	841	c.662C>T	c.(661-663)cCa>cTa	p.P221L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	221										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACGACGATCTGGCCTTAGATG	0.547													G|||	31	0.0061901	0.0	0.0086	5008	,	,		23912	0.0		0.0239	False		,,,				2504	0.001				p.P221L		Atlas-SNP	.											.	QRICH2	143	.	0			c.C662T						PASS	.	G	LEU/PRO	21,4385	28.1+/-56.4	0,21,2182	136.0	102.0	113.0		662	-0.7	0.0	17	dbSNP_132	113	226,8374	95.0+/-156.8	1,224,4075	yes	missense	QRICH2	NM_032134.1	98	1,245,6257	AA,AG,GG		2.6279,0.4766,1.8991	benign	221/1664	74289648	247,12759	2203	4300	6503	SO:0001583	missense	84074	exon4			CGATCTGGCCTTA	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.662C>T	17.37:g.74289648G>A	ENSP00000262765:p.Pro221Leu	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	261	115	0.440613	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	22	0.010073260073260074	0	0.0	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	7.287	0.610371	0.14066	0.004766	0.026279	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.20069	2.1	3.93	-0.743	0.11105	.	.	.	.	.	T	0.03390	0.0098	L	0.39020	1.185	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.005	T	0.37911	-0.9685	9	0.02654	T	1	-0.3034	4.0087	0.09613	0.2955:0.0:0.5197:0.1848	.	221;221	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	221	ENSP00000262765:P221L	ENSP00000262765:P221L	P	-	2	0	QRICH2	71801243	0.297000	0.24408	0.003000	0.11579	0.059000	0.15707	0.061000	0.14366	-0.173000	0.10761	0.563000	0.77884	CCA	G|0.984;A|0.016	0.016	strong		0.547	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
MYOM2	9172	hgsc.bcm.edu	37	8	2054171	2054171	+	Silent	SNP	C	C	T	rs3817705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:2054171C>T	ENST00000262113.4	+	22	3015	c.2874C>T	c.(2872-2874)atC>atT	p.I958I	MYOM2_ENST00000523438.1_Silent_p.I383I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	958	Ig-like C2-type 3.				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)		GGTTTAAAATCGAAACCGTGG	0.448													C|||	1277	0.254992	0.1006	0.3098	5008	,	,		17185	0.2282		0.4135	False		,,,				2504	0.2894				p.I958I		Atlas-SNP	.											.	MYOM2	251	.	0			c.C2874T						PASS	.	C		679,3727	285.7+/-278.4	50,579,1574	100.0	99.0	100.0		2874	-8.0	0.0	8	dbSNP_107	100	3484,5116	510.1+/-377.4	715,2054,1531	no	coding-synonymous	MYOM2	NM_003970.2		765,2633,3105	TT,TC,CC		40.5116,15.4108,32.0083		958/1466	2054171	4163,8843	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon22			TAAAATCGAAACC		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.2874C>T	8.37:g.2054171C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			C|0.707;T|0.293	0.293	strong		0.448	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
LAMA5	3911	hgsc.bcm.edu	37	20	60899513	60899513	+	Missense_Mutation	SNP	C	C	A	rs148177752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60899513C>A	ENST00000252999.3	-	42	5693	c.5627G>T	c.(5626-5628)gGc>gTc	p.G1876V		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1876	Laminin EGF-like 17. {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)			GACGCCAGAGCCAGGGAGGCA	0.622													.|||	5	0.000998403	0.0008	0.0	5008	,	,		18736	0.0		0.004	False		,,,				2504	0.0				p.G1876V		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5627T						PASS	.	C	VAL/GLY	10,4384	15.5+/-35.6	1,8,2188	42.0	36.0	38.0		5627	4.2	1.0	20	dbSNP_134	38	54,8532	31.2+/-83.2	1,52,4240	yes	missense	LAMA5	NM_005560.3	109	2,60,6428	AA,AC,CC		0.6289,0.2276,0.4931	probably-damaging	1876/3696	60899513	64,12916	2197	4293	6490	SO:0001583	missense	3911	exon42			CCAGAGCCAGGGA	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.5627G>T	20.37:g.60899513C>A	ENSP00000252999:p.Gly1876Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	18.61	3.660047	0.67586	0.002276	0.006289	ENSG00000130702	ENST00000252999	T	0.60424	0.19	4.25	4.25	0.50352	TNFR/CD27/30/40/95 cysteine-rich region (1);EGF-like, laminin (3);	0.000000	0.85682	U	0.000000	T	0.62636	0.2444	L	0.46567	1.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66638	-0.5873	10	0.36615	T	0.2	.	16.9991	0.86377	0.0:1.0:0.0:0.0	.	1876	O15230	LAMA5_HUMAN	V	1876	ENSP00000252999:G1876V	ENSP00000252999:G1876V	G	-	2	0	LAMA5	60332908	1.000000	0.71417	0.995000	0.50966	0.568000	0.35870	4.553000	0.60753	2.074000	0.62210	0.579000	0.79373	GGC	C|0.996;A|0.004	0.004	strong		0.622	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SYVN1	84447	hgsc.bcm.edu	37	11	64897292	64897292	+	Missense_Mutation	SNP	C	C	T	rs141712194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64897292C>T	ENST00000377190.3	-	14	1598	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	SYVN1_ENST00000307289.6_Missense_Mutation_p.A450T|SYVN1_ENST00000526060.1_Missense_Mutation_p.A501T|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_Missense_Mutation_p.A501T	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	502					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)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TGCAGCCGGGCCTCCAGGTGC	0.657													c|||	2	0.000399361	0.0	0.0	5008	,	,		17978	0.0		0.002	False		,,,				2504	0.0				p.A502T		Atlas-SNP	.											.	SYVN1	55	.	0			c.G1504A						PASS	.	C	THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	40.0	45.0	43.0		1504,1501	3.8	1.0	11	dbSNP_134	43	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense	SYVN1	NM_172230.2,NM_032431.2	58,58	0,5,6493	TT,TC,CC		0.0465,0.0227,0.0385	benign,benign	502/618,501/617	64897292	5,12991	2201	4297	6498	SO:0001583	missense	84447	exon14			GCCGGGCCTCCAG	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1504G>A	11.37:g.64897292C>T	ENSP00000366395:p.Ala502Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	37	CCDS31605.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.41	3.616870	0.66672	2.27E-4	4.65E-4	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060	T;T;T;T	0.15718	2.43;2.4;2.52;2.4	4.75	3.82	0.43975	.	0.062439	0.64402	D	0.000006	T	0.40719	0.1128	M	0.78049	2.395	0.80722	D	1	D;B;B	0.67145	0.996;0.361;0.247	D;B;B	0.77557	0.99;0.293;0.153	T	0.32052	-0.9921	10	0.54805	T	0.06	-14.4894	12.007	0.53265	0.1742:0.8258:0.0:0.0	.	450;501;502	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	T	502;501;502;450;501	ENSP00000366395:A502T;ENSP00000294256:A501T;ENSP00000302035:A450T;ENSP00000436984:A501T	ENSP00000294256:A501T	A	-	1	0	SYVN1	64653868	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.189000	0.77747	1.213000	0.43380	0.561000	0.74099	GCC	C|0.999;T|0.001	0.001	strong		0.657	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
PIGN	23556	hgsc.bcm.edu	37	18	59770033	59770033	+	Silent	SNP	C	C	T	rs12326381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	36	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	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	
CPNE1	8904	hgsc.bcm.edu	37	20	34214173	34214173	+	Missense_Mutation	SNP	G	G	A	rs11543239	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34214173G>A	ENST00000317619.3	-	18	1998	c.1604C>T	c.(1603-1605)cCc>cTc	p.P535L	CPNE1_ENST00000397445.1_Missense_Mutation_p.P535L|CPNE1_ENST00000397442.1_Missense_Mutation_p.P479L|CPNE1_ENST00000397443.1_Missense_Mutation_p.P535L|CPNE1_ENST00000352393.4_Missense_Mutation_p.P535L|CPNE1_ENST00000317677.5_Missense_Mutation_p.P540L|CPNE1_ENST00000397446.1_Missense_Mutation_p.P535L			Q99829	CPNE1_HUMAN	copine I	535			P -> L (in dbSNP:rs11543239).		lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CTAGGCCTGGGGGGCCTGTGC	0.617													G|||	449	0.0896565	0.1036	0.0274	5008	,	,		16724	0.0516		0.0507	False		,,,				2504	0.1943				p.P540L		Atlas-SNP	.											.	CPNE1	44	.	0			c.C1619T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	468,3938	222.3+/-239.2	24,420,1759	98.0	115.0	109.0		1601,1619,1604,1604,1604,1604	5.6	0.0	20	dbSNP_120	109	443,8157	133.8+/-191.2	18,407,3875	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	98,98,98,98,98,98	42,827,5634	AA,AG,GG		5.1512,10.6219,7.0045	benign,benign,benign,benign,benign,benign	534/537,540/543,535/538,535/538,535/538,535/538	34214173	911,12095	2203	4300	6503	SO:0001583	missense	8904	exon16			GCCTGGGGGGCCT	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1604C>T	20.37:g.34214173G>A	ENSP00000326126:p.Pro535Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	141	0.06456043956043957	62	0.12601626016260162	14	0.03867403314917127	22	0.038461538461538464	43	0.05672823218997362	G	11.03	1.518339	0.27211	0.106219	0.051512	ENSG00000214078	ENST00000352393;ENST00000415920;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442	T;T;T;T;T;T;T;T	0.40756	3.49;1.02;3.48;3.49;3.49;3.49;3.49;3.4	5.55	5.55	0.83447	.	7.547470	0.02290	U	0.070255	T	0.00440	0.0014	N	0.24115	0.695	0.80722	P	0.0	B;B;B;B	0.13594	0.008;0.008;0.005;0.008	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.03344	-1.1046	9	0.87932	D	0	0.043	14.8729	0.70471	0.0:0.0:1.0:0.0	rs11543239;rs52809653;rs11543239	540;479;535;515	B0QZ18;A6PVH9;Q99829;Q59EI4	.;.;CPNE1_HUMAN;.	L	535;175;540;535;535;535;535;479	ENSP00000336945:P535L;ENSP00000396069:P175L;ENSP00000317257:P540L;ENSP00000326126:P535L;ENSP00000380588:P535L;ENSP00000380587:P535L;ENSP00000380585:P535L;ENSP00000380584:P479L	ENSP00000326126:P535L	P	-	2	0	CPNE1	33677587	0.978000	0.34361	0.016000	0.15963	0.151000	0.21798	2.727000	0.47311	2.885000	0.99019	0.655000	0.94253	CCC	G|0.925;A|0.075	0.075	strong		0.617	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
MX1	4599	hgsc.bcm.edu	37	21	42812891	42812891	+	Silent	SNP	C	C	T	rs467960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:42812891C>T	ENST00000398600.2	+	11	1694	c.669C>T	c.(667-669)atC>atT	p.I223I	AP001610.5_ENST00000411427.1_RNA|MX1_ENST00000455164.2_Silent_p.I223I|MX1_ENST00000398598.3_Silent_p.I223I|MX1_ENST00000288383.6_Silent_p.I200I	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	223	Dynamin-type G.|GTPase domain (Globular).				apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				ATGTGGACATCGCCACCACAG	0.572													C|||	1777	0.354832	0.3313	0.4424	5008	,	,		16676	0.1062		0.5706	False		,,,				2504	0.3589				p.I223I		Atlas-SNP	.											.	MX1	58	.	0			c.C669T						PASS	.	C	,,	1536,2870	485.8+/-360.4	277,982,944	110.0	102.0	104.0		669,669,669	-2.1	1.0	21	dbSNP_80	104	4955,3645	623.6+/-397.5	1390,2175,735	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	1667,3157,1679	TT,TC,CC		42.3837,34.8616,49.9077	,,	223/663,223/663,223/663	42812891	6491,6515	2203	4300	6503	SO:0001819	synonymous_variant	4599	exon11			GGACATCGCCACC		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.669C>T	21.37:g.42812891C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																			C|0.547;T|0.453	0.453	strong		0.572	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
BTNL2	56244	hgsc.bcm.edu	37	6	32363844	32363844	+	Silent	SNP	C	C	T	rs9268480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32363844C>T	ENST00000374993.1	-	5	1049	c.1050G>A	c.(1048-1050)caG>caA	p.Q350Q	BTNL2_ENST00000374995.3_Silent_p.Q256Q|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000429232.2_Silent_p.Q257Q|BTNL2_ENST00000414363.1_Silent_p.Q140Q|BTNL2_ENST00000454136.3_Silent_p.Q350Q|BTNL2_ENST00000540315.1_Silent_p.Q140Q|BTNL2_ENST00000544175.1_Silent_p.Q73Q	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	350	Ig-like V-type 3.					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						AACTGGCCTCCTGGTAGACAT	0.468													c|||	1040	0.207668	0.1672	0.3127	5008	,	,		20109	0.1141		0.2734	False		,,,				2504	0.2168				p.Q350Q		Atlas-SNP	.											.	BTNL2	50	.	0			c.G1050A						PASS	.			520,2500		44,432,1034	79.0	84.0	82.0	http://omim.org/entry/604519|http://www.ncbi.nlm.nih.gov/pubmed?term	1050	1.4	1.0	6	dbSNP_118	82	1526,3890		200,1126,1382	no	coding-synonymous	BTNL2	NM_019602.1		244,1558,2416	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	28.1758,17.2185,24.2532		350/456	32363844	2046,6390	1510	2708	4218	SO:0001819	synonymous_variant	56244	exon5			GGCCTCCTGGTAG	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.1050G>A	6.37:g.32363844C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	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|0.785;N|0.000	.	strong		0.468	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
TAS2R4	50832	hgsc.bcm.edu	37	7	141478574	141478574	+	Missense_Mutation	SNP	G	G	C	rs2234001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141478574G>C	ENST00000247881.2	+	1	333	c.286G>C	c.(286-288)Gtc>Ctc	p.V96L	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	96			V -> L (in dbSNP:rs2234001).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		CTCGAGCAGTGTCTGGTTTGT	0.423													C|||	2637	0.526558	0.3192	0.5793	5008	,	,		21049	0.745		0.4722	False		,,,				2504	0.6002				p.V96L		Atlas-SNP	.											.	TAS2R4	25	.	0			c.G286C						PASS	.	C	LEU/VAL	1575,2831	493.1+/-362.6	314,947,942	218.0	192.0	201.0		286	2.7	0.9	7	dbSNP_98	201	4274,4326	575.0+/-390.2	1055,2164,1081	yes	missense	TAS2R4	NM_016944.1	32	1369,3111,2023	CC,CG,GG		49.6977,35.7467,44.9716	benign	96/300	141478574	5849,7157	2203	4300	6503	SO:0001583	missense	50832	exon1			AGCAGTGTCTGGT	AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.286G>C	7.37:g.141478574G>C	ENSP00000247881:p.Val96Leu	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	1150	0.5265567765567766	166	0.33739837398373984	204	0.56353591160221	427	0.7465034965034965	353	0.4656992084432718	g	0.015	-1.567101	0.00895	0.357467	0.496977	ENSG00000127364	ENST00000247881	T	0.00631	6.09	5.52	2.73	0.32206	.	0.169609	0.35805	N	0.002963	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.10451	-1.0629	9	0.02654	T	1	.	10.3055	0.43678	0.0:0.5464:0.382:0.0716	rs2234001;rs3735278;rs17523539;rs52815299;rs2234001	96	Q9NYW5	TA2R4_HUMAN	L	96	ENSP00000247881:V96L	ENSP00000247881:V96L	V	+	1	0	TAS2R4	141125043	0.000000	0.05858	0.918000	0.36340	0.152000	0.21847	0.138000	0.16016	0.147000	0.19030	-0.876000	0.02978	GTC	G|0.508;C|0.492	0.492	strong		0.423	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
MID2	11043	hgsc.bcm.edu	37	X	107159291	107159291	+	Missense_Mutation	SNP	C	C	A	rs12849510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:107159291C>A	ENST00000262843.6	+	6	1681	c.1133C>A	c.(1132-1134)gCc>gAc	p.A378D	RP6-191P20.4_ENST00000430140.1_RNA|MID2_ENST00000443968.2_Missense_Mutation_p.A378D	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	55	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	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	
MGMT	4255	hgsc.bcm.edu	37	10	131506283	131506283	+	Missense_Mutation	SNP	C	C	T	rs12917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:131506283C>T	ENST00000306010.7	+	3	375	c.343C>T	c.(343-345)Ctt>Ttt	p.L115F	MGMT_ENST00000462672.1_3'UTR	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	84					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	CGTGCCGGCTCTTCACCATCC	0.552								Direct reversal of damage					C|||	743	0.148363	0.1619	0.1974	5008	,	,		17175	0.1062		0.1382	False		,,,				2504	0.1493				p.L115F		Atlas-SNP	.											.	MGMT	32	.	0			c.C343T	GRCh37	CM065311	MGMT	M	rs12917	PASS	.	C	PHE/LEU	660,3746	281.9+/-276.2	47,566,1590	112.0	109.0	110.0		343	1.9	0.0	10	dbSNP_52	110	1092,7508	229.4+/-264.1	74,944,3282	yes	missense	MGMT	NM_002412.3	22	121,1510,4872	TT,TC,CC		12.6977,14.9796,13.4707	benign	115/239	131506283	1752,11254	2203	4300	6503	SO:0001583	missense	4255	exon3			CCGGCTCTTCACC	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.343C>T	10.37:g.131506283C>T	ENSP00000302111:p.Leu115Phe	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_002412	Q5VY78	Missense_Mutation	SNP	ENST00000306010.7	37	CCDS7660.2	329	0.15064102564102563	84	0.17073170731707318	75	0.20718232044198895	67	0.11713286713286714	103	0.1358839050131926	C	11.77	1.738340	0.30774	0.149796	0.126977	ENSG00000170430	ENST00000306010	T	0.13778	2.56	4.79	1.89	0.25635	.	0.277525	0.34906	N	0.003582	T	0.00012	0.0000	L	0.40543	1.245	0.25052	P	0.99112594	P	0.38473	0.633	B	0.34652	0.187	T	0.39482	-0.9612	9	0.34782	T	0.22	.	2.222	0.03974	0.2548:0.3868:0.0:0.3584	rs12917;rs1042400;rs2257841;rs3181860;rs4986979;rs16909784;rs57527955;rs12917	115	B4DEE8	.	F	115	ENSP00000302111:L115F	ENSP00000302111:L115F	L	+	1	0	MGMT	131396273	0.592000	0.26832	0.018000	0.16275	0.070000	0.16714	1.037000	0.30241	0.717000	0.32145	0.655000	0.94253	CTT	C|0.858;T|0.142	0.142	strong		0.552	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
LPIN2	9663	hgsc.bcm.edu	37	18	2929103	2929103	+	Missense_Mutation	SNP	G	G	A	rs104895500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:2929103G>A	ENST00000261596.4	-	10	1748	c.1510C>T	c.(1510-1512)Ctt>Ttt	p.L504F		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	504					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TTGTCTATAAGTCCAGGGTTT	0.294													G|||	10	0.00199681	0.0008	0.0043	5008	,	,		16858	0.0		0.005	False		,,,				2504	0.001				p.L504F		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1510T	GRCh37	CM082924	LPIN2	M	rs104895500	PASS	.	G	PHE/LEU	5,4399	11.4+/-27.6	0,5,2197	126.0	139.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1510	6.0	1.0	18	dbSNP_132	135	39,8555	25.7+/-73.6	0,39,4258	yes	missense	LPIN2	NM_014646.2	22	0,44,6455	AA,AG,GG		0.4538,0.1135,0.3385	benign	504/897	2929103	44,12954	2202	4297	6499	SO:0001583	missense	9663	exon10			CTATAAGTCCAGG	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1510C>T	18.37:g.2929103G>A	ENSP00000261596:p.Leu504Phe	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	100	28	0.28	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	24.1	4.489970	0.84962	0.001135	0.004538	ENSG00000101577	ENST00000261596	D	0.83419	-1.72	6.03	6.03	0.97812	.	0.051415	0.85682	D	0.000000	D	0.83175	0.5197	M	0.75615	2.305	0.52099	D	0.99994	P	0.52842	0.956	P	0.50049	0.629	D	0.86195	0.1615	10	0.72032	D	0.01	.	15.2928	0.73879	0.0:0.0:0.86:0.14	.	504	Q92539	LPIN2_HUMAN	F	504	ENSP00000261596:L504F	ENSP00000261596:L504F	L	-	1	0	LPIN2	2919103	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.723000	0.74742	2.861000	0.98227	0.655000	0.94253	CTT	G|0.998;A|0.002	0.002	strong		0.294	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646	
E2F7	144455	hgsc.bcm.edu	37	12	77438436	77438436	+	Silent	SNP	T	T	C	rs2242384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:77438436T>C	ENST00000322886.7	-	6	1204	c.969A>G	c.(967-969)ccA>ccG	p.P323P	E2F7_ENST00000416496.2_Silent_p.P323P	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	323					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|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 involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|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)	p.P323P(1)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TACTATGGTCTGGGGCATCTT	0.403													C|||	951	0.189896	0.1036	0.2464	5008	,	,		17986	0.1647		0.2575	False		,,,				2504	0.2229				p.P323P		Atlas-SNP	.											E2F7_ENST00000322886,NS,carcinoma,0,1	E2F7	201	1	1	Substitution - coding silent(1)	stomach(1)	c.A969G						PASS	.	C		586,3820	772.6+/-413.9	50,486,1667	180.0	172.0	174.0		969	-12.1	0.1	12	dbSNP_98	174	2369,6231	702.1+/-405.3	306,1757,2237	no	coding-synonymous	E2F7	NM_203394.2		356,2243,3904	CC,CT,TT		27.5465,13.3,22.7203		323/912	77438436	2955,10051	2203	4300	6503	SO:0001819	synonymous_variant	144455	exon6			ATGGTCTGGGGCA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.969A>G	12.37:g.77438436T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1	432	0.1978021978021978	51	0.10365853658536585	91	0.2513812154696133	95	0.1660839160839161	195	0.25725593667546176	C	7.117	0.577118	0.13686	0.133	0.275465	ENSG00000165891	ENST00000551058	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21627	P	0.999618366	.	.	.	.	.	.	T	0.06698	-1.0812	3	.	.	.	-7.7333	11.7418	0.51796	0.1909:0.5119:0.0:0.2972	rs2242384;rs17760343;rs58868311;rs2242384	.	.	.	R	201	.	.	Q	-	2	0	E2F7	75962567	0.000000	0.05858	0.095000	0.20976	0.924000	0.55760	-4.852000	0.00178	-2.400000	0.00579	-1.874000	0.00550	CAG	T|0.792;C|0.208	0.208	strong		0.403	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
SORBS2	8470	hgsc.bcm.edu	37	4	186541301	186541301	+	Silent	SNP	A	A	G	rs61753946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186541301A>G	ENST00000284776.7	-	14	3017	c.2508T>C	c.(2506-2508)cgT>cgC	p.R836R	SORBS2_ENST00000449407.2_Silent_p.R380R|SORBS2_ENST00000431808.1_Silent_p.R836R|SORBS2_ENST00000319471.9_Silent_p.R467R|SORBS2_ENST00000355634.5_Silent_p.R936R|SORBS2_ENST00000393528.3_Silent_p.R402R|SORBS2_ENST00000437304.2_Silent_p.R560R|SORBS2_ENST00000448662.2_Silent_p.R397R|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000418609.1_Silent_p.R740R	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	836					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TAGGGGACTCACGGTCTATTG	0.458													A|||	207	0.0413339	0.0045	0.049	5008	,	,		17283	0.0		0.1044	False		,,,				2504	0.0634				p.R936R	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.T2808C						PASS	.	A	,,,,,,,	98,4308	79.3+/-117.8	2,94,2107	183.0	174.0	177.0		1140,1401,1191,1680,2220,684,1206,2508	-12.3	0.0	4	dbSNP_129	177	942,7658	207.6+/-249.3	52,838,3410	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	54,932,5517	GG,GA,AA		10.9535,2.2242,7.9963	,,,,,,,	380/645,467/732,397/662,560/825,740/1005,228/493,402/667,836/1101	186541301	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	8470	exon17			GGACTCACGGTCT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2508T>C	4.37:g.186541301A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1	97	0.044413919413919416	4	0.008130081300813009	18	0.049723756906077346	0	0.0	75	0.09894459102902374	A	9.046	0.990773	0.18966	0.022242	0.109535	ENSG00000154556	ENST00000438278	.	.	.	6.17	-12.3	0.00002	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999582921	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.6773	2.4451	0.04504	0.3107:0.1332:0.0902:0.4659	.	.	.	.	R	253	.	.	X	-	1	0	SORBS2	186778295	0.000000	0.05858	0.000000	0.03702	0.962000	0.63368	-4.297000	0.00257	-4.750000	0.00033	-1.155000	0.01812	TGA	A|0.927;G|0.073	0.073	strong		0.458	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
LATS2	26524	hgsc.bcm.edu	37	13	21562948	21562948	+	Missense_Mutation	SNP	G	G	A	rs558614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21562948G>A	ENST00000382592.4	-	4	1376	c.971C>T	c.(970-972)gCg>gTg	p.A324V	LATS2_ENST00000542899.1_Missense_Mutation_p.A324V|LATS2_ENST00000472754.1_5'Flank	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	25	24	0.96	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		
CYP2D6	1565	hgsc.bcm.edu	37	22	42523636	42523636	+	Splice_Site	SNP	C	C	A	rs1135831|rs3915951		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42523636C>A	ENST00000360608.5	-	7	1100	c.986G>T	c.(985-987)cGc>cTc	p.R329L	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Splice_Site_p.R329L|CYP2D6_ENST00000359033.4_Splice_Site_p.R278L	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	329			R -> L (in dbSNP:rs3915951).		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)	p.R278L(5)|p.R329L(4)		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)	TTGGACACGGCCTGGACAGAC	0.602																																					p.R329L		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,11	CYP2D6	104	11	9	Substitution - Missense(9)	prostate(6)|large_intestine(2)|NS(1)	c.G986T						scavenged	.						73.0	56.0	62.0					22																	42523636		2201	4299	6500	SO:0001630	splice_region_variant	1565	exon7			ACACGGCCTGGAC	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.986-1G>T	22.37:g.42523636C>A		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	131	34	0.259542	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669463	0.47677	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.79940	-1.32;-1.32;4.99	4.93	3.91	0.45181	.	.	.	.	.	T	0.76435	0.3987	M	0.67953	2.075	0.41700	D	0.989391	B;B;B	0.15473	0.004;0.013;0.002	B;B;B	0.26693	0.013;0.072;0.013	T	0.72174	-0.4370	9	0.48119	T	0.1	.	5.5275	0.16967	0.1599:0.672:0.0:0.1681	rs3915951	329;278;329	C1ID54;Q6NXU8;Q6NWU0	.;.;.	L	329;329;275;278;278	ENSP00000353820:R329L;ENSP00000374620:R329L;ENSP00000351927:R278L	ENSP00000351927:R278L	R	-	2	0	CYP2D6	40853580	0.444000	0.25649	0.954000	0.39281	0.844000	0.47949	0.448000	0.21726	1.070000	0.40811	0.555000	0.69702	CGC	C|0.500;A|0.500	0.500	weak		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		Missense_Mutation
DHRS4	10901	hgsc.bcm.edu	37	14	24435538	24435538	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24435538C>A	ENST00000313250.5	+	6	781	c.578C>A	c.(577-579)aCc>aAc	p.T193N	DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.T141N|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.T159N|DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000397073.2_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	193					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)	p.T193N(1)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGGCCTGACCAAGACCCTG	0.502																																					p.T193N		Atlas-SNP	.											DHRS4,NS,carcinoma,0,1	DHRS4	22	1	1	Substitution - Missense(1)	kidney(1)	c.C578A						scavenged	.						181.0	156.0	165.0					14																	24435538		2200	4300	6500	SO:0001583	missense	10901	exon6			GCCTGACCAAGAC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.578C>A	14.37:g.24435538C>A	ENSP00000326219:p.Thr193Asn	Somatic	671	1	0.00149031		WXS	Illumina HiSeq	Phase_I	735	28	0.0380952	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	c	11.36	1.615720	0.28801	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.32023	1.47;1.47	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.115238	0.56097	N	0.000021	T	0.47691	0.1459	H	0.95504	3.68	0.80722	D	1	B;B	0.25105	0.118;0.023	B;B	0.32342	0.073;0.144	T	0.52155	-0.8613	10	0.54805	T	0.06	.	10.3016	0.43656	0.1993:0.8007:0.0:0.0	.	159;193	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	193;141	ENSP00000326219:T193N;ENSP00000404147:T141N	ENSP00000326219:T193N	T	+	2	0	DHRS4	23505378	1.000000	0.71417	0.992000	0.48379	0.683000	0.39861	3.158000	0.50723	0.608000	0.30000	-0.202000	0.12741	ACC	.	.	none		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
PRTG	283659	hgsc.bcm.edu	37	15	55965666	55965666	+	Silent	SNP	A	A	G	rs75403514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:55965666A>G	ENST00000389286.4	-	10	1802	c.1755T>C	c.(1753-1755)agT>agC	p.S585S		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)		CCAGGTAGACACTGTCAGGTT	0.522													A|||	13	0.00259585	0.0	0.0014	5008	,	,		14634	0.0		0.0109	False		,,,				2504	0.001				p.S585S		Atlas-SNP	.											.	PRTG	110	.	0			c.T1755C						PASS	.	A		11,3823		0,11,1906	87.0	88.0	87.0		1755	-0.2	1.0	15	dbSNP_131	87	119,8139		4,111,4014	no	coding-synonymous	PRTG	NM_173814.4		4,122,5920	GG,GA,AA		1.441,0.2869,1.0751		585/1151	55965666	130,11962	1917	4129	6046	SO:0001819	synonymous_variant	283659	exon10			GTAGACACTGTCA	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.1755T>C	15.37:g.55965666A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_173814		Silent	SNP	ENST00000389286.4	37	CCDS42040.1																																																																																			A|0.994;G|0.006	0.006	strong		0.522	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
THAP3	90326	hgsc.bcm.edu	37	1	6693097	6693097	+	Missense_Mutation	SNP	A	A	G	rs3174820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6693097A>G	ENST00000054650.4	+	6	838	c.680A>G	c.(679-681)cAg>cGg	p.Q227R	THAP3_ENST00000307896.6_Missense_Mutation_p.Q226R|THAP3_ENST00000377627.3_Intron|DNAJC11_ENST00000465508.1_5'Flank	NM_001195753.1	NP_001182682.1	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated protein 3	227				Q -> R (in Ref. 3; AAH05114/AAH92427). {ECO:0000305}.			DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|large_intestine(1)|prostate(1)	4	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|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;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		AAAGGGCACCAGGGACTCCAG	0.637													A|||	1855	0.370407	0.3086	0.3429	5008	,	,		17358	0.3889		0.332	False		,,,				2504	0.4939				p.Q227R		Atlas-SNP	.											.	THAP3	43	.	0			c.A680G						PASS	.	A	ARG/GLN,ARG/GLN,	537,1213		84,369,422	15.0	16.0	16.0		677,680,	-7.5	0.0	1	dbSNP_105	16	1372,2610		232,908,851	no	missense,missense,intron	THAP3	NM_001195752.1,NM_001195753.1,NM_138350.3	43,43,	316,1277,1273	GG,GA,AA		34.455,30.6857,33.3043	,,	226/239,227/240,	6693097	1909,3823	875	1991	2866	SO:0001583	missense	90326	exon6			GGCACCAGGGACT	BC022081	CCDS86.1, CCDS55572.1, CCDS55573.1	1p36.1	2013-01-25			ENSG00000041988	ENSG00000041988		"""THAP (C2CH-type zinc finger) domain containing"""	20855	protein-coding gene	gene with protein product		612532				12575992	Standard	NM_138350		Approved		uc001aod.3	Q8WTV1	OTTHUMG00000001440	ENST00000054650.4:c.680A>G	1.37:g.6693097A>G	ENSP00000054650:p.Gln227Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_001195753	Q569K1|Q5TH66|Q5TH67|Q8N8T6|Q9BSC7|Q9Y3H2|Q9Y3H3	Missense_Mutation	SNP	ENST00000054650.4	37	CCDS55572.1	726	0.3324175824175824	139	0.28252032520325204	115	0.31767955801104975	219	0.38286713286713286	253	0.3337730870712401	A	0.017	-1.510745	0.00984	0.306857	0.34455	ENSG00000041988	ENST00000054650;ENST00000307896	D;D	0.94330	-3.4;-3.4	3.75	-7.5	0.01351	.	5.936390	0.00357	N	0.000020	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	0.44251	-0.9340	9	0.07325	T	0.83	-18.8905	1.2862	0.02051	0.3402:0.3301:0.169:0.1607	rs3174820;rs52816457;rs58034382;rs3174820	226;227	Q8WTV1-3;Q8WTV1	.;THAP3_HUMAN	R	227;226	ENSP00000054650:Q227R;ENSP00000311537:Q226R	ENSP00000054650:Q227R	Q	+	2	0	THAP3	6615684	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.490000	0.00975	-3.278000	0.00198	-0.414000	0.06135	CAG	A|0.662;G|0.338	0.338	strong		0.637	THAP3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004203.1	NM_138350	
TYRO3	7301	hgsc.bcm.edu	37	15	41857307	41857307	+	Missense_Mutation	SNP	G	G	A	rs141641556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41857307G>A	ENST00000263798.3	+	6	975	c.751G>A	c.(751-753)Ggc>Agc	p.G251S	TYRO3_ENST00000559066.1_Missense_Mutation_p.G206S	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	251	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AGGTGCTGATGGCCGAGCTCT	0.592													G|||	42	0.00838658	0.0	0.0202	5008	,	,		20484	0.0		0.0268	False		,,,				2504	0.001				p.G251S		Atlas-SNP	.											TYRO3_ENST00000263798,NS,haematopoietic_neoplasm,0,2	TYRO3	169	2	0			c.G751A						scavenged	.	G	SER/GLY	8,4398	15.5+/-35.6	0,8,2195	94.0	84.0	87.0		751	4.9	0.6	15	dbSNP_134	87	128,8472	63.5+/-125.6	0,128,4172	yes	missense	TYRO3	NM_006293.3	56	0,136,6367	AA,AG,GG		1.4884,0.1816,1.0457	probably-damaging	251/891	41857307	136,12870	2203	4300	6503	SO:0001583	missense	7301	exon6			GCTGATGGCCGAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.751G>A	15.37:g.41857307G>A	ENSP00000263798:p.Gly251Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	6	0.136364	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	31	5.104713	0.94245	0.001816	0.014884	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.60920	0.15	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41712	D	0.000828	T	0.59266	0.2181	L	0.55103	1.725	0.58432	D	0.999997	D	0.64830	0.994	P	0.58970	0.849	T	0.64689	-0.6348	10	0.51188	T	0.08	-23.6363	13.5493	0.61723	0.0:0.0:1.0:0.0	.	251	Q06418	TYRO3_HUMAN	S	183;251	ENSP00000263798:G251S	ENSP00000263798:G251S	G	+	1	0	TYRO3	39644599	1.000000	0.71417	0.626000	0.29213	0.989000	0.77384	6.282000	0.72639	2.581000	0.87130	0.563000	0.77884	GGC	G|0.992;A|0.008	0.008	strong		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
CDA	978	hgsc.bcm.edu	37	1	20945055	20945055	+	Silent	SNP	C	C	T	rs1048977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20945055C>T	ENST00000375071.3	+	4	617	c.435C>T	c.(433-435)acC>acT	p.T145T	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	145					cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.T145T(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|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)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	TGCAGAAGACCCAGTGACAGC	0.587													C|||	1558	0.311102	0.379	0.317	5008	,	,		18751	0.244		0.3231	False		,,,				2504	0.272				p.T145T	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											CDA,NS,carcinoma,0,1	CDA	19	1	1	Substitution - coding silent(1)	stomach(1)	c.C435T						PASS	.	C		1744,2662	518.0+/-369.6	349,1046,808	71.0	61.0	65.0		435	1.7	0.0	1	dbSNP_86	65	2708,5892	431.7+/-356.9	429,1850,2021	no	coding-synonymous	CDA	NM_001785.2		778,2896,2829	TT,TC,CC		31.4884,39.5824,34.2304		145/147	20945055	4452,8554	2203	4300	6503	SO:0001819	synonymous_variant	978	exon4			GAAGACCCAGTGA	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.435C>T	1.37:g.20945055C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_001785		Silent	SNP	ENST00000375071.3	37	CCDS210.1																																																																																			C|0.671;T|0.329	0.329	strong		0.587	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	
SCUBE1	80274	hgsc.bcm.edu	37	22	43607040	43607040	+	Silent	SNP	G	G	A	rs138988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43607040G>A	ENST00000360835.4	-	18	2397	c.2271C>T	c.(2269-2271)atC>atT	p.I757I	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	757					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CGGGGCAGCGGATGCAGCGGT	0.647													G|||	252	0.0503195	0.0552	0.036	5008	,	,		15874	0.0		0.1352	False		,,,				2504	0.0184				p.I757I		Atlas-SNP	.											.	SCUBE1	105	.	0			c.C2271T						PASS	.	G		307,4093	165.4+/-196.9	9,289,1902	172.0	136.0	148.0		2271	1.7	1.0	22	dbSNP_78	148	976,7622	211.4+/-252.0	53,870,3376	no	coding-synonymous	SCUBE1	NM_173050.3		62,1159,5278	AA,AG,GG		11.3515,6.9773,9.8707		757/989	43607040	1283,11715	2200	4299	6499	SO:0001819	synonymous_variant	80274	exon18			GCAGCGGATGCAG		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2271C>T	22.37:g.43607040G>A		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	286	162	0.566434	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																			G|0.910;A|0.090	0.090	strong		0.647	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
CNGA1	1259	hgsc.bcm.edu	37	4	47938879	47938879	+	Silent	SNP	G	G	A	rs17573673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:47938879G>A	ENST00000514170.1	-	11	1951	c.1632C>T	c.(1630-1632)ttC>ttT	p.F544F	CNGA1_ENST00000544810.1_Silent_p.F544F|CNGA1_ENST00000402813.3_Silent_p.F613F|CNGA1_ENST00000420489.2_Silent_p.F544F|CNGA1_ENST00000358519.4_Silent_p.F544F			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	544					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	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)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TGATCTCACCGAAGTAGCTGC	0.448													G|||	194	0.038738	0.0023	0.0375	5008	,	,		22533	0.005		0.0736	False		,,,				2504	0.0879				p.F613F		Atlas-SNP	.											.	CNGA1	74	.	0			c.C1839T						PASS	.	G	,	75,4319	59.3+/-96.0	1,73,2123	111.0	112.0	112.0		1632,1839	-7.1	0.9	4	dbSNP_123	112	723,7875	171.4+/-222.4	26,671,3602	no	coding-synonymous,coding-synonymous	CNGA1	NM_000087.3,NM_001142564.1	,	27,744,5725	AA,AG,GG		8.4089,1.7069,6.1422	,	544/691,613/760	47938879	798,12194	2197	4299	6496	SO:0001819	synonymous_variant	1259	exon10			CTCACCGAAGTAG	M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.1632C>T	4.37:g.47938879G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	67	0.598214	NM_001142564	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Silent	SNP	ENST00000514170.1	37	CCDS43226.1																																																																																			G|0.953;A|0.047	0.047	strong		0.448	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087	
ZNF681	148213	hgsc.bcm.edu	37	19	23927604	23927604	+	Missense_Mutation	SNP	T	T	C	rs147282314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23927604T>C	ENST00000402377.3	-	4	889	c.748A>G	c.(748-750)Aga>Gga	p.R250G	ZNF681_ENST00000395385.3_Missense_Mutation_p.R181G	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AGTTTGTCTCTAGTATAAATT	0.348													T|||	4	0.000798722	0.003	0.0	5008	,	,		18422	0.0		0.0	False		,,,				2504	0.0				p.R250G		Atlas-SNP	.											.	ZNF681	76	.	0			c.A748G						PASS	.	T	GLY/ARG	10,4396		0,10,2193	97.0	96.0	97.0		748	-3.2	0.0	19	dbSNP_134	97	0,8600		0,0,4300	no	missense	ZNF681	NM_138286.2	125	0,10,6493	CC,CT,TT		0.0,0.227,0.0769	benign	250/646	23927604	10,12996	2203	4300	6503	SO:0001583	missense	148213	exon4			TGTCTCTAGTATA	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.748A>G	19.37:g.23927604T>C	ENSP00000384000:p.Arg250Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	0.010	-1.745110	0.00675	0.00227	0.0	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07908	3.29;3.15	1.6	-3.2	0.05156	Zinc finger, C2H2 (1);	.	.	.	.	T	0.01156	0.0038	N	0.00387	-1.565	0.20703	N	0.999865	B	0.02656	0.0	B	0.01281	0.0	T	0.38607	-0.9653	9	0.02654	T	1	.	9.6115	0.39665	0.0:0.7478:0.0:0.2522	.	250	Q96N22	ZN681_HUMAN	G	250;181	ENSP00000384000:R250G;ENSP00000378783:R181G	ENSP00000378783:R181G	R	-	1	2	ZNF681	23719444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.592000	0.23984	-1.681000	0.01448	-1.783000	0.00646	AGA	T|0.999;C|0.001	0.001	strong		0.348	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
ITGA2	3673	hgsc.bcm.edu	37	5	52369002	52369002	+	Silent	SNP	G	G	A	rs3212327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52369002G>A	ENST00000296585.5	+	20	2627	c.2484G>A	c.(2482-2484)acG>acA	p.T828T		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	828					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)				TTTCAGTAACGCTGAAAAATA	0.353													G|||	522	0.104233	0.2035	0.0663	5008	,	,		19385	0.0317		0.0885	False		,,,				2504	0.0879				p.T828T		Atlas-SNP	.											.	ITGA2	211	.	0			c.G2484A						PASS	.	G		802,3604	321.5+/-297.2	65,672,1466	121.0	116.0	117.0		2484	-2.5	0.5	5	dbSNP_106	117	828,7772	191.8+/-238.0	40,748,3512	no	coding-synonymous	ITGA2	NM_002203.3		105,1420,4978	AA,AG,GG		9.6279,18.2025,12.5327		828/1182	52369002	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon20			AGTAACGCTGAAA		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.2484G>A	5.37:g.52369002G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			G|0.880;A|0.120	0.120	strong		0.353	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
PRKAG3	53632	hgsc.bcm.edu	37	2	219695487	219695487	+	Missense_Mutation	SNP	G	G	C	rs692243	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:219695487G>C	ENST00000529249.1	-	3	526	c.211C>G	c.(211-213)Cca>Gca	p.P71A	PRKAG3_ENST00000545803.1_5'UTR|PRKAG3_ENST00000392098.3_Missense_Mutation_p.P71A|PRKAG3_ENST00000439262.2_Missense_Mutation_p.P46A			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	71			P -> A (in dbSNP:rs692243). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17878938}.		cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	TGACCTGGTGGCTCCCCTTCC	0.612													G|||	908	0.18131	0.0605	0.1758	5008	,	,		18442	0.4018		0.1471	False		,,,				2504	0.1564				p.P71A		Atlas-SNP	.											PRKAG3,NS,carcinoma,+1,1	PRKAG3	47	1	0			c.C211G						PASS	.	G	ALA/PRO	365,4041	186.0+/-213.0	15,335,1853	148.0	122.0	130.0		211	1.9	0.1	2	dbSNP_83	130	1532,7068	288.8+/-298.9	148,1236,2916	yes	missense	PRKAG3	NM_017431.2	27	163,1571,4769	CC,CG,GG		17.814,8.2842,14.5856	benign	71/490	219695487	1897,11109	2203	4300	6503	SO:0001583	missense	53632	exon3			CTGGTGGCTCCCC	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.211C>G	2.37:g.219695487G>C	ENSP00000436068:p.Pro71Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	448	0.20512820512820512	47	0.09552845528455285	55	0.15193370165745856	228	0.3986013986013986	118	0.15567282321899736	G	12.42	1.933641	0.34096	0.082842	0.17814	ENSG00000115592	ENST00000439262;ENST00000529249;ENST00000392098;ENST00000430489	D;D;T;T	0.83914	-1.66;-1.78;-0.05;0.79	4.78	1.91	0.25777	.	0.360067	0.23775	N	0.044685	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D;B;B	0.63880	0.993;0.287;0.189	P;B;B	0.55545	0.778;0.124;0.058	T	0.22347	-1.0219	9	0.19147	T	0.46	-0.0387	5.0549	0.14527	0.167:0.1924:0.6406:0.0	rs692243;rs832678;rs17848621;rs52808491;rs59655878;rs692243	71;46;71	B4DUK8;Q9UGI9-2;Q9UGI9	.;.;AAKG3_HUMAN	A	46;71;71;71	ENSP00000397133:P46A;ENSP00000436068:P71A;ENSP00000375947:P71A;ENSP00000416100:P71A	ENSP00000233944:P71A	P	-	1	0	PRKAG3	219403731	0.446000	0.25665	0.091000	0.20842	0.449000	0.32228	1.419000	0.34793	0.992000	0.38840	0.655000	0.94253	CCA	G|0.835;C|0.165	0.165	strong		0.612	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1		
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629859	32629859	+	Silent	SNP	A	A	G	rs1049130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629859A>G	ENST00000399082.3	-	2	320	c.276T>C	c.(274-276)aaT>aaC	p.N92N	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.N182N|HLA-DQB1_ENST00000374943.4_Silent_p.N182N|HLA-DQB1_ENST00000399079.3_Silent_p.N182N|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Silent_p.N182N			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	182	Beta-1.		Y -> N (in allele DQB1*06:16).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCCAGTCACCATTCCTAATAA	0.567									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	3333	0.665535	0.5363	0.7046	5008	,	,		16815	0.8423		0.5885	False		,,,				2504	0.7096				p.N182N	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T546C						PASS	.	G		2204,2190		579,1046,572	54.0	58.0	57.0		546	-6.3	0.3	6	dbSNP_86	57	4604,3996		1245,2114,941	no	coding-synonymous	HLA-DQB1	NM_002123.4		1824,3160,1513	GG,GA,AA		46.4651,49.8407,47.6066		182/262	32629859	6808,6186	2197	4300	6497	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTCACCATTCCTA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.276T>C	6.37:g.32629859A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				A|0.380;G|0.620	0.620	strong		0.567	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
ASIC3	9311	hgsc.bcm.edu	37	7	150747937	150747937	+	Silent	SNP	C	C	A	rs3217353|rs11977275|rs200386051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150747937C>A	ENST00000349064.5	+	4	1104	c.906C>A	c.(904-906)ccC>ccA	p.P302P	ASIC3_ENST00000357922.4_Silent_p.P302P|ASIC3_ENST00000297512.8_Silent_p.P302P	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	302					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										TAGGCTCccccagccccagcc	0.642													C|||	719	0.14357	0.1573	0.1254	5008	,	,		11840	0.0139		0.1779	False		,,,				2504	0.2362				p.P302P		Atlas-SNP	.											.	.	.	.	0			c.C906A						PASS	.	C	,,	740,3664		73,594,1535	17.0	20.0	19.0		906,906,906	2.6	0.9	7	dbSNP_120	19	1786,6814		193,1400,2707	no	coding-synonymous,coding-synonymous,coding-synonymous	ACCN3	NM_004769.2,NM_020321.2,NM_020322.2	,,	266,1994,4242	AA,AC,CC		20.7674,16.8029,19.4248	,,	302/532,302/550,302/544	150747937	2526,10478	2202	4300	6502	SO:0001819	synonymous_variant	9311	exon4			CTCCCCCAGCCCC	AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	101	protein-coding gene	gene with protein product	"""testis sodium channel 1"""	611741	"""amiloride-sensitive cation channel 3, testis"", ""amiloride-sensitive cation channel 3"""	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.906C>A	7.37:g.150747937C>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Silent	SNP	ENST00000349064.5	37	CCDS5916.1																																																																																			C|0.842;A|0.158	0.158	strong		0.642	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769	
AGAP1	116987	hgsc.bcm.edu	37	2	236708166	236708166	+	Splice_Site	SNP	C	C	T	rs2292708	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:236708166C>T	ENST00000304032.8	+	8	1537	c.957C>T	c.(955-957)acC>acT	p.T319T	AGAP1_ENST00000409538.1_Splice_Site_p.T584T|AGAP1_ENST00000428334.2_Splice_Site_p.T158T|AGAP1_ENST00000409457.1_Splice_Site_p.T319T|AGAP1_ENST00000336665.5_Splice_Site_p.T319T	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	319					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)	p.T319T(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACCTGTTCACCGTGAGTGTCA	0.542													C|||	960	0.191693	0.0295	0.4063	5008	,	,		18911	0.2708		0.2624	False		,,,				2504	0.1043				p.T319T		Atlas-SNP	.											AGAP1,NS,carcinoma,0,1	AGAP1	95	1	1	Substitution - coding silent(1)	prostate(1)	c.C957T						PASS	.	C	,	293,4113	159.6+/-192.1	14,265,1924	94.0	79.0	84.0		957,957	-2.0	1.0	2	dbSNP_100	84	2504,6096	412.1+/-350.7	374,1756,2170	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	AGAP1	NM_001037131.2,NM_014914.4	,	388,2021,4094	TT,TC,CC		29.1163,6.65,21.5055	,	319/858,319/805	236708166	2797,10209	2203	4300	6503	SO:0001630	splice_region_variant	116987	exon8			GTTCACCGTGAGT	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.957+1C>T	2.37:g.236708166C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Silent	SNP	ENST00000304032.8	37	CCDS33408.1																																																																																			C|0.787;T|0.213	0.213	strong		0.542	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	Silent
HGFAC	3083	hgsc.bcm.edu	37	4	3446091	3446091	+	Missense_Mutation	SNP	G	G	T	rs3748034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	32	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	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		
TMEM171	134285	hgsc.bcm.edu	37	5	72427404	72427404	+	Missense_Mutation	SNP	C	C	G	rs61746311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:72427404C>G	ENST00000454765.2	+	4	1295	c.822C>G	c.(820-822)gaC>gaG	p.D274E	TMEM171_ENST00000287773.5_Missense_Mutation_p.D273E|RP11-232L2.2_ENST00000508255.1_RNA			Q8WVE6	TM171_HUMAN	transmembrane protein 171	274						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)		CTGAAAGAGACTGTGAATCTA	0.453													C|||	157	0.0313498	0.0045	0.0288	5008	,	,		16136	0.001		0.0855	False		,,,				2504	0.045				p.D274E	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.C822G						PASS	.	C	GLU/ASP,GLU/ASP	69,4337	63.5+/-100.7	0,69,2134	83.0	83.0	83.0		819,822	-10.1	0.0	5	dbSNP_129	83	653,7947	166.4+/-218.3	21,611,3668	yes	missense,missense	TMEM171	NM_001161342.1,NM_173490.6	45,45	21,680,5802	GG,GC,CC		7.593,1.566,5.5513	benign,benign	273/324,274/325	72427404	722,12284	2203	4300	6503	SO:0001583	missense	134285	exon4			AAGAGACTGTGAA	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.822C>G	5.37:g.72427404C>G	ENSP00000415030:p.Asp274Glu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	74	0.03388278388278388	2	0.0040650406504065045	11	0.03038674033149171	1	0.0017482517482517483	60	0.079155672823219	C	7.679	0.688559	0.14973	0.01566	0.07593	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.25579	1.79;1.79	5.07	-10.1	0.00402	.	0.731992	0.12240	N	0.486577	T	0.00754	0.0025	L	0.60455	1.87	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.004	T	0.06552	-1.0820	10	0.18276	T	0.48	-1.3882	5.6598	0.17662	0.1371:0.3851:0.3565:0.1212	rs61746311	273;274	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	E	274;273	ENSP00000415030:D274E;ENSP00000287773:D273E	ENSP00000287773:D273E	D	+	3	2	TMEM171	72463160	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.440000	0.00233	-4.094000	0.00074	-0.471000	0.05019	GAC	C|0.948;G|0.051;T|0.000	0.051	strong		0.453	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
OR51B6	390058	hgsc.bcm.edu	37	11	5372751	5372751	+	Missense_Mutation	SNP	A	A	C	rs4910755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5372751A>C	ENST00000380219.1	+	1	14	c.14A>C	c.(13-15)aAg>aCg	p.K5T	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	5			K -> T (in dbSNP:rs4910755). {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)			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)		GGGCTCAATAAGTCTGCTTCC	0.433													A|||	1178	0.235224	0.3283	0.2349	5008	,	,		21631	0.0863		0.2644	False		,,,				2504	0.2331				p.K5T		Atlas-SNP	.											.	OR51B6	53	.	0			c.A14C						PASS	.	A	THR/LYS	1298,3104	441.0+/-346.2	177,944,1080	78.0	67.0	71.0		14	-4.6	0.0	11	dbSNP_111	71	2268,6326	381.2+/-339.9	310,1648,2339	yes	missense	OR51B6	NM_001004750.1	78	487,2592,3419	CC,CA,AA		26.3905,29.4866,27.4392	benign	5/313	5372751	3566,9430	2201	4297	6498	SO:0001583	missense	390058	exon1			TCAATAAGTCTGC		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.14A>C	11.37:g.5372751A>C	ENSP00000369568:p.Lys5Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	160	0.3252032520325203	90	0.24861878453038674	30	0.05244755244755245	192	0.2532981530343008	A	5.628	0.300519	0.10678	0.294866	0.263905	ENSG00000176239	ENST00000380219	T	0.00316	8.13	4.63	-4.64	0.03349	.	2.386480	0.01623	N	0.023135	T	0.00012	0.0000	N	0.03294	-0.36	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11446	-1.0587	9	0.10377	T	0.69	.	0.8917	0.01255	0.3948:0.1828:0.2435:0.1789	rs4910755;rs59085266;rs4910755	5	Q9H340	O51B6_HUMAN	T	5	ENSP00000369568:K5T	ENSP00000369568:K5T	K	+	2	0	OR51B6	5329327	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.699000	0.05087	-0.615000	0.05679	-0.460000	0.05396	AAG	A|0.770;C|0.230	0.230	strong		0.433	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
DPYD	1806	hgsc.bcm.edu	37	1	97547947	97547947	+	Missense_Mutation	SNP	T	T	A	rs67376798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:97547947T>A	ENST00000370192.3	-	22	2946	c.2846A>T	c.(2845-2847)gAt>gTt	p.D949V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	949	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	CATTTCTTCATCAATCATAGC	0.388													T|||	11	0.00219649	0.0008	0.0029	5008	,	,		18701	0.0		0.007	False		,,,				2504	0.001				p.D949V		Atlas-SNP	.											.	DPYD	219	.	0			c.A2846T	GRCh37	CM003590	DPYD	M	rs67376798	PASS	.	T	VAL/ASP	4,4402	9.9+/-24.2	0,4,2199	242.0	220.0	228.0		2846	5.8	1.0	1	dbSNP_130	228	47,8553	30.7+/-82.3	1,45,4254	yes	missense	DPYD	NM_000110.3	152	1,49,6453	AA,AT,TT		0.5465,0.0908,0.3921	probably-damaging	949/1026	97547947	51,12955	2203	4300	6503	SO:0001583	missense	1806	exon22			TCTTCATCAATCA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2846A>T	1.37:g.97547947T>A	ENSP00000359211:p.Asp949Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	23.4	4.406204	0.83230	9.08E-4	0.005465	ENSG00000188641	ENST00000370192	D	0.93019	-3.15	5.82	5.82	0.92795	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97170	0.9075	M	0.93763	3.455	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	D	0.98134	1.0432	10	0.87932	D	0	-25.8976	16.1779	0.81874	0.0:0.0:0.0:1.0	.	949	Q12882	DPYD_HUMAN	V	949	ENSP00000359211:D949V	ENSP00000359211:D949V	D	-	2	0	DPYD	97320535	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.841000	0.86834	2.216000	0.71823	0.533000	0.62120	GAT	T|0.996;A|0.004	0.004	strong		0.388	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
F13A1	2162	hgsc.bcm.edu	37	6	6318795	6318795	+	Missense_Mutation	SNP	C	C	A	rs5985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	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	
PLXNA4	91584	hgsc.bcm.edu	37	7	131817850	131817850	+	Silent	SNP	T	T	C	rs75848889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:131817850T>C	ENST00000359827.3	-	31	6509	c.5547A>G	c.(5545-5547)gcA>gcG	p.A1849A	PLXNA4_ENST00000321063.4_Silent_p.A1849A			Q9HCM2	PLXA4_HUMAN	plexin A4	1849					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TCTCTGAGAGTGCACTCATGG	0.522													T|||	655	0.130791	0.0303	0.2853	5008	,	,		17858	0.0962		0.0984	False		,,,				2504	0.226				p.A1849A		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A5547G						PASS	.	T		151,4231		2,147,2042	137.0	140.0	139.0		5547	-10.5	0.1	7	dbSNP_131	139	859,7739		48,763,3488	no	coding-synonymous	PLXNA4	NM_020911.1		50,910,5530	CC,CT,TT		9.9907,3.4459,7.7812		1849/1895	131817850	1010,11970	2191	4299	6490	SO:0001819	synonymous_variant	91584	exon31			TGAGAGTGCACTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.5547A>G	7.37:g.131817850T>C		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			T|0.898;C|0.102	0.102	strong		0.522	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
GSX2	170825	hgsc.bcm.edu	37	4	54966667	54966667	+	Silent	SNP	C	C	T	rs3194383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:54966667C>T	ENST00000326902.2	+	1	470	c.156C>T	c.(154-156)tcC>tcT	p.S52S	GSX2_ENST00000503800.1_Silent_p.S52S|FIP1L1_ENST00000507166.1_Intron	NM_133267.2	NP_573574.1	Q9BZM3	GSX2_HUMAN	GS homeobox 2	52					forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|hindbrain morphogenesis (GO:0021575)|neuron fate specification (GO:0048665)|olfactory bulb interneuron differentiation (GO:0021889)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|spinal cord association neuron differentiation (GO:0021527)|subpallium neuron fate commitment (GO:0060163)|telencephalon regionalization (GO:0021978)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(2)|lung(2)	6	all_cancers(7;0.00671)|Lung NSC(11;0.0154)|all_neural(26;0.0209)|Glioma(25;0.08)|all_epithelial(27;0.147)		LUSC - Lung squamous cell carcinoma(32;0.00216)			GCTGCCCGTCCCGCAAGAGCG	0.726													C|||	3006	0.60024	0.2859	0.7219	5008	,	,		11378	0.8423		0.6143	False		,,,				2504	0.6748				p.S52S		Atlas-SNP	.											.	GSX2	27	.	0			c.C156T						PASS	.	C		1479,2923		236,1007,958	24.0	24.0	24.0		156	1.6	1.0	4	dbSNP_105	24	5294,3304		1650,1994,655	no	coding-synonymous	GSX2	NM_133267.2		1886,3001,1613	TT,TC,CC		38.4275,33.5984,47.9		52/305	54966667	6773,6227	2201	4299	6500	SO:0001819	synonymous_variant	170825	exon1			CCCGTCCCGCAAG		CCDS3494.1	4q12	2012-03-09			ENSG00000180613	ENSG00000180613		"""Homeoboxes / ANTP class : HOXL subclass"""	24959	protein-coding gene	gene with protein product						11861295, 12205114	Standard	NM_133267		Approved	Gsh2	uc010igp.1	Q9BZM3	OTTHUMG00000128696	ENST00000326902.2:c.156C>T	4.37:g.54966667C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_133267		Silent	SNP	ENST00000326902.2	37	CCDS3494.1																																																																																			C|0.456;T|0.544	0.544	strong		0.726	GSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250595.1	NM_133267	
PRPF40A	55660	hgsc.bcm.edu	37	2	153533260	153533260	+	Silent	SNP	G	G	A	rs11544718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:153533260G>A	ENST00000410080.1	-	10	1231	c.690C>T	c.(688-690)gcC>gcT	p.A230A		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	257					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TAGGGACTGGGGCTGTTGATG	0.468													G|||	773	0.154353	0.0295	0.098	5008	,	,		18533	0.2659		0.1789	False		,,,				2504	0.2229				p.A230A		Atlas-SNP	.											PRPF40A_ENST00000410080,caecum,carcinoma,0,3	PRPF40A	149	3	0			c.C690T						PASS	.	G		134,2936		1,132,1402	122.0	117.0	119.0		690	4.1	1.0	2	dbSNP_120	119	975,5029		74,827,2101	no	coding-synonymous	PRPF40A	NM_017892.3		75,959,3503	AA,AG,GG		16.2392,4.3648,12.2217		230/931	153533260	1109,7965	1535	3002	4537	SO:0001819	synonymous_variant	55660	exon10			GACTGGGGCTGTT	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"""formin-binding protein 3"", ""formin binding protein 3"", ""PRP40 pre-mRNA processing factor 40 homolog A (yeast)"""	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.690C>T	2.37:g.153533260G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	234	113	0.482906	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Silent	SNP	ENST00000410080.1	37	CCDS46430.1																																																																																			T|0.000;G|0.835;C|0.000;A|0.164	0.164	strong		0.468	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575	
C20orf173	140873	hgsc.bcm.edu	37	20	34116282	34116282	+	Missense_Mutation	SNP	T	T	C	rs7261862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34116282T>C	ENST00000246199.2	-	3	699	c.421A>G	c.(421-423)Aag>Gag	p.K141E	C20orf173_ENST00000374345.4_Missense_Mutation_p.K194E|C20orf173_ENST00000444723.1_Missense_Mutation_p.K194E|RP3-477O4.5_ENST00000422009.1_RNA			Q96LM9	CT173_HUMAN	chromosome 20 open reading frame 173	141			K -> E (in dbSNP:rs7261862). {ECO:0000269|PubMed:14702039}.							haematopoietic_and_lymphoid_tissue(1)|skin(1)	2						TCCATCACCTTATCACTTAGA	0.562													C|||	1140	0.227636	0.3132	0.1772	5008	,	,		19285	0.1419		0.16	False		,,,				2504	0.3057				p.K194E		Atlas-SNP	.											.	C20orf173	19	.	0			c.A580G						PASS	.	C	GLU/LYS	397,987		58,281,353	115.0	98.0	103.0		580	1.3	0.0	20	dbSNP_116	103	540,2642		54,432,1105	yes	missense	C20orf173	NM_001145350.1	56	112,713,1458	CC,CT,TT		16.9705,28.685,20.5212	benign	194/203	34116282	937,3629	692	1591	2283	SO:0001583	missense	140873	exon4			TCACCTTATCACT	AL121586	CCDS46594.1	20q11.22	2012-10-30			ENSG00000125975	ENSG00000125975			16166	protein-coding gene	gene with protein product							Standard	NM_001145350		Approved	dJ477O4.4	uc010zvf.1	Q96LM9	OTTHUMG00000032340	ENST00000246199.2:c.421A>G	20.37:g.34116282T>C	ENSP00000246199:p.Lys141Glu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	197	97	0.492386	NM_001145350	A6PVJ1|Q2M293|Q5JWS4|Q9H449	Missense_Mutation	SNP	ENST00000246199.2	37		407	0.18635531135531136	151	0.30691056910569103	69	0.19060773480662985	74	0.12937062937062938	113	0.14907651715039577	C	5.657	0.305826	0.10733	0.28685	0.169705	ENSG00000125975	ENST00000246199;ENST00000444723	T;T	0.45276	0.9;0.98	3.33	1.31	0.21738	.	.	.	.	.	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	0.40059	-0.9583	8	0.02654	T	1	.	5.993	0.19478	0.0:0.6508:0.0:0.3492	rs7261862;rs58056225;rs7261862	194;141	E9PFA0;Q96LM9	.;CT173_HUMAN	E	141;194	ENSP00000246199:K141E;ENSP00000403566:K194E	ENSP00000246199:K141E	K	-	1	0	C20orf173	33579696	0.000000	0.05858	0.017000	0.16124	0.035000	0.12851	-0.128000	0.10531	0.085000	0.17107	-0.213000	0.12676	AAG	T|0.793;C|0.207	0.207	strong		0.562	C20orf173-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078874.6	NM_001145350	
MICALL1	85377	hgsc.bcm.edu	37	22	38323700	38323700	+	Missense_Mutation	SNP	C	C	T	rs2272829	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38323700C>T	ENST00000215957.6	+	9	1874	c.1748C>T	c.(1747-1749)cCc>cTc	p.P583L	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	583	Pro-rich.		P -> L (in dbSNP:rs2272829).		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)					GGCCTTGCCCCCAGGACCAGG	0.642													C|||	309	0.0617013	0.1195	0.0202	5008	,	,		15652	0.0496		0.0159	False		,,,				2504	0.0726				p.P583L		Atlas-SNP	.											.	MICALL1	53	.	0			c.C1748T						PASS	.	C	LEU/PRO	481,3925	224.9+/-240.9	26,429,1748	93.0	98.0	96.0		1748	3.0	0.2	22	dbSNP_100	96	174,8426	78.6+/-141.3	2,170,4128	yes	missense	MICALL1	NM_033386.3	98	28,599,5876	TT,TC,CC		2.0233,10.9169,5.0361	probably-damaging	583/864	38323700	655,12351	2203	4300	6503	SO:0001583	missense	85377	exon9			TTGCCCCCAGGAC	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.1748C>T	22.37:g.38323700C>T	ENSP00000215957:p.Pro583Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	103	0.04716117216117216	48	0.0975609756097561	8	0.022099447513812154	32	0.055944055944055944	15	0.01978891820580475	C	10.47	1.358833	0.24598	0.109169	0.020233	ENSG00000100139	ENST00000215957;ENST00000402631	T;T	0.56941	0.43;1.8	5.2	3.01	0.34805	.	0.697298	0.12245	N	0.486132	T	0.01124	0.0037	M	0.67953	2.075	0.80722	P	0.0	B	0.26002	0.139	B	0.17433	0.018	T	0.11131	-1.0600	9	0.20046	T	0.44	.	9.9042	0.41366	0.1175:0.6636:0.2189:0.0	rs2272829	583	Q8N3F8	MILK1_HUMAN	L	583;10	ENSP00000215957:P583L;ENSP00000384608:P10L	ENSP00000215957:P583L	P	+	2	0	MICALL1	36653646	0.002000	0.14202	0.181000	0.23098	0.280000	0.26924	1.588000	0.36633	2.432000	0.82394	0.555000	0.69702	CCC	C|0.949;T|0.051	0.051	strong		0.642	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
SELP	6403	hgsc.bcm.edu	37	1	169566326	169566326	+	Silent	SNP	G	G	A	rs6135	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169566326G>A	ENST00000263686.6	-	11	1831	c.1794C>T	c.(1792-1794)tgC>tgT	p.C598C	SELP_ENST00000367794.2_Silent_p.C536C|SELP_ENST00000367788.2_Silent_p.C536C|SELP_ENST00000367793.2_Silent_p.C536C|SELP_ENST00000367786.2_Silent_p.C536C|SELP_ENST00000367791.2_Intron|SELP_ENST00000367792.2_Intron|SELP_ENST00000458599.2_Intron	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	598	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	AAGAGAAATGGCAGGTGGAGC	0.502													G|||	1098	0.219249	0.6589	0.1268	5008	,	,		15867	0.002		0.1203	False		,,,				2504	0.0164				p.C598C		Atlas-SNP	.											.	SELP	132	.	0			c.C1794T						PASS	.	G		2425,1981	619.6+/-393.4	680,1065,458	67.0	70.0	69.0		1794	-0.0	0.8	1	dbSNP_52	69	1004,7596	215.2+/-254.6	45,914,3341	no	coding-synonymous	SELP	NM_003005.3		725,1979,3799	AA,AG,GG		11.6744,44.9614,26.3648		598/831	169566326	3429,9577	2203	4300	6503	SO:0001819	synonymous_variant	6403	exon11			GAAATGGCAGGTG	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.1794C>T	1.37:g.169566326G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	161	41	0.254658	NM_003005	Q5R344|Q8IVD1	Silent	SNP	ENST00000263686.6	37	CCDS1282.1																																																																																			G|0.774;A|0.226	0.226	strong		0.502	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
F11	2160	hgsc.bcm.edu	37	4	187201211	187201211	+	Silent	SNP	A	A	G	rs5974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187201211A>G	ENST00000403665.2	+	8	1153	c.801A>G	c.(799-801)acA>acG	p.T267T	F11_ENST00000264692.4_Silent_p.T215T	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	267	Apple 3. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	TGCCCAGTACACGCATTAAAA	0.388													A|||	837	0.167133	0.2579	0.1398	5008	,	,		19090	0.0387		0.163	False		,,,				2504	0.2004				p.T267T		Atlas-SNP	.											F11,colon,carcinoma,+1,1	F11	65	1	0			c.A801G						PASS	.	A		949,3457	358.6+/-314.5	113,723,1367	80.0	80.0	80.0		801	-5.1	0.3	4	dbSNP_52	80	1214,7386	244.3+/-273.6	89,1036,3175	no	coding-synonymous	F11	NM_000128.3		202,1759,4542	GG,GA,AA		14.1163,21.5388,16.6308		267/626	187201211	2163,10843	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon8			CAGTACACGCATT	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.801A>G	4.37:g.187201211A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1	317	0.14514652014652016	114	0.23170731707317074	61	0.1685082872928177	22	0.038461538461538464	120	0.158311345646438	A	1.280	-0.610683	0.03690	0.215388	0.141163	ENSG00000088926	ENST00000452239	.	.	.	5.63	-5.12	0.02893	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	.	.	.	.	.	.	T	0.31251	-0.9950	3	.	.	.	.	4.8271	0.13421	0.6382:0.1749:0.0636:0.1234	rs5974;rs56560313;rs60184336;rs5974	.	.	.	R	83	.	.	H	+	2	0	F11	187438205	0.000000	0.05858	0.252000	0.24328	0.167000	0.22549	-0.992000	0.03724	-0.481000	0.06792	0.524000	0.50904	CAC	A|0.837;G|0.163	0.163	strong		0.388	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
FBN3	84467	hgsc.bcm.edu	37	19	8160334	8160334	+	Missense_Mutation	SNP	G	G	A	rs12608849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8160334G>A	ENST00000600128.1	-	46	6124	c.5710C>T	c.(5710-5712)Ctc>Ttc	p.L1904F	FBN3_ENST00000601739.1_Missense_Mutation_p.L1904F|FBN3_ENST00000270509.2_Missense_Mutation_p.L1904F			Q75N90	FBN3_HUMAN	fibrillin 3	1904	EGF-like 30; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> F (in dbSNP:rs12608849).|L -> P (in dbSNP:rs12608849). {ECO:0000269|PubMed:15221638}.			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						GCTGTGTTGAGGCAATGGCCA	0.552													G|||	1550	0.309505	0.0613	0.2767	5008	,	,		18064	0.4881		0.2843	False		,,,				2504	0.5102				p.L1904F		Atlas-SNP	.											.	FBN3	300	.	0			c.C5710T						PASS	.	G	PHE/LEU	413,3993	203.1+/-225.7	22,369,1812	118.0	83.0	95.0		5710	-0.7	1.0	19	dbSNP_120	95	2173,6427	371.5+/-336.3	289,1595,2416	yes	missense	FBN3	NM_032447.3	22	311,1964,4228	AA,AG,GG		25.2674,9.3736,19.8831	benign	1904/2810	8160334	2586,10420	2203	4300	6503	SO:0001583	missense	84467	exon45			TGTTGAGGCAATG		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.5710C>T	19.37:g.8160334G>A	ENSP00000470498:p.Leu1904Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	159	85	0.534591	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	629	0.288003663003663	34	0.06910569105691057	105	0.2900552486187845	275	0.4807692307692308	215	0.2836411609498681	G	1.717	-0.497540	0.04291	0.093736	0.252674	ENSG00000142449	ENST00000270509	D	0.87809	-2.3	4.68	-0.659	0.11424	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.119782	0.53938	U	0.000046	T	0.00012	0.0000	N	0.25789	0.76	0.37245	P	0.09371399999999996	B	0.21688	0.059	B	0.23275	0.045	T	0.33033	-0.9884	9	0.27082	T	0.32	.	3.9566	0.09393	0.0885:0.1042:0.416:0.3914	rs12608849;rs52826951;rs60158242;rs12608849	1904	Q75N90	FBN3_HUMAN	F	1904	ENSP00000270509:L1904F	ENSP00000270509:L1904F	L	-	1	0	FBN3	8066334	0.022000	0.18835	0.960000	0.40013	0.804000	0.45430	0.137000	0.15995	0.053000	0.16036	-0.211000	0.12701	CTC	G|0.757;A|0.243	0.243	strong		0.552	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
STAB2	55576	hgsc.bcm.edu	37	12	104025446	104025446	+	Silent	SNP	G	G	A	rs147053330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104025446G>A	ENST00000388887.2	+	6	762	c.558G>A	c.(556-558)gcG>gcA	p.A186A		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						GCTACTCTGCGTACACTGGCC	0.468													g|||	13	0.00259585	0.0	0.0	5008	,	,		19013	0.001		0.0119	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											.	STAB2	370	.	0			c.G558A						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	229.0	174.0	193.0		558	-9.4	0.0	12	dbSNP_134	193	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous	STAB2	NM_017564.9		0,72,6431	AA,AG,GG		0.7907,0.0908,0.5536		186/2552	104025446	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon6			CTCTGCGTACACT	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.558G>A	12.37:g.104025446G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			G|0.994;A|0.006	0.006	strong		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
OR4D2	124538	hgsc.bcm.edu	37	17	56247101	56247101	+	Missense_Mutation	SNP	C	C	A	rs60994383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56247101C>A	ENST00000545221.1	+	1	85	c.85C>A	c.(85-87)Cta>Ata	p.L29I		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	29			L -> I (in dbSNP:rs60994383).			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(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						TTTCCTGTTTCTAATGTTCCT	0.483													C|||	1178	0.235224	0.3775	0.1599	5008	,	,		20152	0.1657		0.2147	False		,,,				2504	0.1892				p.L29I		Atlas-SNP	.											.	OR4D2	48	.	0			c.C85A						PASS	.	C	ILE/LEU	1567,2839	490.4+/-361.8	275,1017,911	159.0	141.0	147.0		85	-5.0	0.9	17	dbSNP_129	147	1963,6637	346.7+/-326.3	234,1495,2571	yes	missense	OR4D2	NM_001004707.3	5	509,2512,3482	AA,AC,CC		22.8256,35.5651,27.1413	benign	29/308	56247101	3530,9476	2203	4300	6503	SO:0001583	missense	124538	exon1			CTGTTTCTAATGT		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.85C>A	17.37:g.56247101C>A	ENSP00000441354:p.Leu29Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	498	0.22802197802197802	178	0.3617886178861789	66	0.18232044198895028	90	0.15734265734265734	164	0.21635883905013192	C	4.031	0.003271	0.07866	0.355651	0.228256	ENSG00000255713	ENST00000545221	T	0.00272	8.36	5.4	-5.02	0.02982	.	0.596543	0.13642	N	0.372932	T	0.00012	0.0000	L	0.28014	0.82	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.31475	-0.9942	9	0.42905	T	0.14	-0.2109	2.2874	0.04130	0.2069:0.334:0.3064:0.1527	rs60994383;rs62083702	29	P58180	OR4D2_HUMAN	I	29	ENSP00000441354:L29I	ENSP00000441354:L29I	L	+	1	2	OR4D2	53602100	0.000000	0.05858	0.947000	0.38551	0.016000	0.09150	-2.547000	0.00931	-0.561000	0.06094	-1.610000	0.00802	CTA	C|0.745;A|0.255	0.255	strong		0.483	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
DGKQ	1609	hgsc.bcm.edu	37	4	961397	961397	+	Silent	SNP	C	C	T	rs2305487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:961397C>T	ENST00000273814.3	-	8	1000	c.927G>A	c.(925-927)gtG>gtA	p.V309V	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	309					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)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCTTCTTCTCACCGCGTCGT	0.687													c|||	161	0.0321486	0.0015	0.0403	5008	,	,		10295	0.0605		0.0467	False		,,,				2504	0.0235				p.V309V	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.G927A						PASS	.			35,4367	40.0+/-72.8	0,35,2166	61.0	59.0	60.0		927	2.2	0.2	4	dbSNP_100	60	372,8228	121.5+/-180.6	7,358,3935	no	coding-synonymous	DGKQ	NM_001347.2		7,393,6101	TT,TC,CC		4.3256,0.7951,3.1303		309/943	961397	407,12595	2201	4300	6501	SO:0001819	synonymous_variant	1609	exon8			TCTTCTCACCGCG	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.927G>A	4.37:g.961397C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	165	92	0.557576	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	37	CCDS3342.1																																																																																			T|0.037;G|0.000;C|0.963	0.037	strong		0.687	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
CACNG6	59285	hgsc.bcm.edu	37	19	54501527	54501527	+	Silent	SNP	G	G	A	rs34604090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54501527G>A	ENST00000252729.2	+	2	956	c.366G>A	c.(364-366)acG>acA	p.T122T	CACNG6_ENST00000352529.1_Intron|CACNG6_ENST00000346968.2_Silent_p.T122T	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	122					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		TCTTCACCACGGGGGAGAATG	0.522													G|||	454	0.090655	0.2126	0.0591	5008	,	,		18577	0.0258		0.0586	False		,,,				2504	0.0481				p.T122T		Atlas-SNP	.											CACNG6,colon,carcinoma,0,1	CACNG6	42	1	0			c.G366A						PASS	.	G	,,	850,3556		84,682,1437	104.0	91.0	95.0		,366,366	0.6	1.0	19	dbSNP_126	95	610,7990		23,564,3713	no	intron,coding-synonymous,coding-synonymous	CACNG6	NM_031897.2,NM_145814.1,NM_145815.1	,,	107,1246,5150	AA,AG,GG		7.093,19.2919,11.2256	,,	,122/261,122/215	54501527	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	59285	exon2			CACCACGGGGGAG	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"""Calcium channel subunits"""	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.366G>A	19.37:g.54501527G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	10	0.277778	NM_145815		Silent	SNP	ENST00000252729.2	37	CCDS12870.1																																																																																			G|0.899;A|0.101	0.101	strong		0.522	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1		
PANK1	53354	hgsc.bcm.edu	37	10	91344169	91344169	+	Silent	SNP	G	G	A	rs1063943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	71	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	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			
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:128182074G>A	ENST00000469083.1	-	2	2572	c.15C>T	c.(13-15)taC>taT	p.Y5Y	DNAJB8_ENST00000319153.3_Silent_p.Y5Y|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	5	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CCAGCACTTCGTAGTAGTTAG	0.632													G|||	1540	0.307508	0.1316	0.3573	5008	,	,		16196	0.4891		0.2753	False		,,,				2504	0.3558				p.Y5Y		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C15T						PASS	.	G		658,3748	268.6+/-268.5	48,562,1593	55.0	57.0	56.0		15	0.9	1.0	3	dbSNP_101	56	2275,6325	374.6+/-337.4	318,1639,2343	no	coding-synonymous	DNAJB8	NM_153330.2		366,2201,3936	AA,AG,GG		26.4535,14.9342,22.5511		5/233	128182074	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			CACTTCGTAGTAG		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.15C>T	3.37:g.128182074G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	163	161	0.98773	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			G|0.724;A|0.276	0.276	strong		0.632	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
PROP1	5626	hgsc.bcm.edu	37	5	177419967	177419967	+	Missense_Mutation	SNP	C	C	T	rs1800197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:177419967C>T	ENST00000308304.2	-	3	732	c.424G>A	c.(424-426)Gcc>Acc	p.A142T		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	142			A -> T (in dbSNP:rs1800197).		blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.A142T(1)		endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|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)			CTGGAAAAGGCGGCAGGAGAC	0.587													C|||	1025	0.204673	0.1218	0.3012	5008	,	,		16521	0.0972		0.2664	False		,,,				2504	0.2955				p.A142T		Atlas-SNP	.											PROP1,NS,carcinoma,0,1	PROP1	28	1	1	Substitution - Missense(1)	stomach(1)	c.G424A						PASS	.	C	THR/ALA	574,3832		38,498,1667	154.0	141.0	145.0		424	-7.5	0.4	5	dbSNP_89	145	2523,6077		382,1759,2159	yes	missense	PROP1	NM_006261.4	58	420,2257,3826	TT,TC,CC		29.3372,13.0277,23.8121	benign	142/227	177419967	3097,9909	2203	4300	6503	SO:0001583	missense	5626	exon3			AAAAGGCGGCAGG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.424G>A	5.37:g.177419967C>T	ENSP00000311290:p.Ala142Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_006261		Missense_Mutation	SNP	ENST00000308304.2	37	CCDS4430.1	439	0.20100732600732601	79	0.16056910569105692	110	0.30386740331491713	45	0.07867132867132867	205	0.2704485488126649	.	0.010	-1.783005	0.00634	0.130277	0.293372	ENSG00000175325	ENST00000308304	D	0.90504	-2.68	3.75	-7.49	0.01355	.	0.374024	0.19648	N	0.109300	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	0.32241	-0.9914	9	0.18276	T	0.48	-6.671	4.5819	0.12262	0.0986:0.4276:0.0992:0.3745	rs1800197;rs2233786;rs17240663;rs52809470;rs57963305;rs1800197	142	O75360	PROP1_HUMAN	T	142	ENSP00000311290:A142T	ENSP00000311290:A142T	A	-	1	0	PROP1	177352573	0.000000	0.05858	0.424000	0.26647	0.026000	0.11368	-0.814000	0.04486	-2.936000	0.00299	-1.446000	0.01064	GCC	C|0.785;T|0.214	0.214	strong		0.587	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
SHARPIN	81858	hgsc.bcm.edu	37	8	145154257	145154257	+	Missense_Mutation	SNP	C	C	G	rs11541804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145154257C>G	ENST00000398712.2	-	6	1281	c.845G>C	c.(844-846)aGc>aCc	p.S282T	SHARPIN_ENST00000533948.1_5'Flank	NM_030974.3	NP_112236.3	Q9H0F6	SHRPN_HUMAN	SHANK-associated RH domain interactor	282	Interaction with SHANK1. {ECO:0000250}.|Ubiquitin-like.		S -> T (in dbSNP:rs11541804).		apoptotic nuclear changes (GO:0030262)|brain development (GO:0007420)|keratinization (GO:0031424)|mitochondrion organization (GO:0007005)|negative regulation of inflammatory response (GO:0050728)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein homooligomerization (GO:0051260)|protein linear polyubiquitination (GO:0097039)|regulation of CD40 signaling pathway (GO:2000348)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|LUBAC complex (GO:0071797)|postsynaptic density (GO:0014069)	polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(2)|ovary(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;4.1e-42)|Epithelial(56;1.58e-40)|all cancers(56;6.12e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGAGGCAAGGCTGCGCTCAGG	0.642													C|||	139	0.0277556	0.0045	0.0303	5008	,	,		20220	0.0		0.0835	False		,,,				2504	0.0286				p.S282T		Atlas-SNP	.											.	SHARPIN	16	.	0			c.G845C						PASS	.	C	THR/SER	65,4227		2,61,2083	56.0	66.0	63.0		845	4.6	1.0	8	dbSNP_120	63	684,7818		33,618,3600	yes	missense	SHARPIN	NM_030974.3	58	35,679,5683	GG,GC,CC		8.0452,1.5144,5.8543	probably-damaging	282/388	145154257	749,12045	2146	4251	6397	SO:0001583	missense	81858	exon6			GCAAGGCTGCGCT	AL136816	CCDS43777.1	8q24.3	2005-08-09				ENSG00000179526			25321	protein-coding gene	gene with protein product		611885				11178875, 12753155	Standard	NM_030974		Approved	DKFZP434N1923, SIPL1	uc003zba.3	Q9H0F6		ENST00000398712.2:c.845G>C	8.37:g.145154257C>G	ENSP00000381698:p.Ser282Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_030974	A6NEG3|C0L3L2|D3DWL3|Q8IXF5|Q8IXF6|Q8N2E7|Q8TB25|Q9BUE4	Missense_Mutation	SNP	ENST00000398712.2	37	CCDS43777.1	77	0.035256410256410256	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	62	0.08179419525065963	C	13.36	2.214536	0.39102	0.015144	0.080452	ENSG00000179526	ENST00000398712;ENST00000359551	T;T	0.34859	1.34;1.34	4.63	4.63	0.57726	.	0.108957	0.64402	D	0.000006	T	0.03053	0.0090	L	0.31207	0.915	0.41223	D	0.986525	D	0.76494	0.999	D	0.78314	0.991	T	0.00770	-1.1573	10	0.15066	T	0.55	.	12.8664	0.57941	0.0:1.0:0.0:0.0	rs11541804	282	Q9H0F6	SHRPN_HUMAN	T	282	ENSP00000381698:S282T;ENSP00000352551:S282T	ENSP00000352551:S282T	S	-	2	0	SHARPIN	145226245	1.000000	0.71417	0.996000	0.52242	0.450000	0.32258	5.141000	0.64814	2.424000	0.82194	0.555000	0.69702	AGC	C|0.939;G|0.061	0.061	strong		0.642	SHARPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382901.1	NM_030974	
GLI2	2736	hgsc.bcm.edu	37	2	121746956	121746956	+	Missense_Mutation	SNP	G	G	T	rs3738880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:121746956G>T	ENST00000452319.1	+	14	3526	c.3466G>T	c.(3466-3468)Gcc>Tcc	p.A1156S	GLI2_ENST00000361492.4_Missense_Mutation_p.A1156S|GLI2_ENST00000314490.11_Intron					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)				CACCGTAGACGCCCTGGCCAG	0.612													G|||	2549	0.508986	0.3578	0.5836	5008	,	,		17208	0.4722		0.7247	False		,,,				2504	0.4765				p.A1156S		Atlas-SNP	.											.	GLI2	187	.	0			c.G3466T						PASS	.	G	SER/ALA	1801,2555		392,1017,769	27.0	25.0	26.0		3466	0.0	0.2	2	dbSNP_107	26	6231,2297		2304,1623,337	yes	missense	GLI2	NM_005270.4	99	2696,2640,1106	TT,TG,GG		26.9348,41.3453,37.6591	benign	1156/1587	121746956	8032,4852	2178	4264	6442	SO:0001583	missense	2736	exon13			GTAGACGCCCTGG		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.3466G>T	2.37:g.121746956G>T	ENSP00000390436:p.Ala1156Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	1224	0.5604395604395604	180	0.36585365853658536	215	0.5939226519337016	285	0.4982517482517482	544	0.7176781002638523	G	2.076	-0.411771	0.04799	0.413453	0.730652	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.14144	2.53;2.53	4.87	0.0393	0.14204	.	0.833216	0.11014	N	0.609104	T	0.00012	0.0000	L	0.39633	1.23	0.80722	P	0.0	B;B	0.29341	0.156;0.242	B;B	0.25140	0.018;0.058	T	0.16188	-1.0411	8	.	.	.	.	6.8098	0.23799	0.4893:0.1217:0.389:0.0	rs3738880;rs3738880	1156;811	P10070;P10070-2	GLI2_HUMAN;.	S	1156	ENSP00000390436:A1156S;ENSP00000354586:A1156S	.	A	+	1	0	GLI2	121463426	0.000000	0.05858	0.182000	0.23118	0.760000	0.43138	-0.368000	0.07543	-0.176000	0.10707	0.449000	0.29647	GCC	G|0.411;T|0.589	0.589	strong		0.612	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
MUC2	4583	hgsc.bcm.edu	37	11	1093393	1093393	+	Missense_Mutation	SNP	G	G	A	rs199525790		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1093393G>A	ENST00000441003.2	+	30	5239	c.5212G>A	c.(5212-5214)Ggc>Agc	p.G1738S	MUC2_ENST00000333592.6_Missense_Mutation_p.G26S|MUC2_ENST00000359061.5_Missense_Mutation_p.G1705S|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.647																																					p.G1738S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G5212A						PASS	.						167.0	217.0	200.0					11																	1093393		1999	3870	5869	SO:0001583	missense	4583	exon30			CCCACCGGCACAC	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.5212G>A	11.37:g.1093393G>A	ENSP00000415183:p.Gly1738Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	4	0.0952381	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	0.322	-0.961495	0.02249	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.16743	3.21;3.25;2.32	0.677	-1.35	0.09114	.	381.381000	0.01358	N	0.012136	T	0.08537	0.0212	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21861	-1.0233	9	0.12430	T	0.62	.	4.7623	0.13113	0.7467:0.0:0.2533:0.0	.	1738	E7EUV1	.	S	1738;1705;26	ENSP00000415183:G1738S;ENSP00000351956:G1705S;ENSP00000331373:G26S	ENSP00000331373:G26S	G	+	1	0	MUC2	1083393	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.042000	0.13949	-0.796000	0.04456	-1.112000	0.02068	GGC	.	.	weak		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FAM153B	202134	hgsc.bcm.edu	37	5	175530780	175530780	+	Missense_Mutation	SNP	C	C	T	rs200265244		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:175530780C>T	ENST00000253490.4	+	14	814	c.757C>T	c.(757-759)Cgt>Tgt	p.R253C	FAM153B_ENST00000515817.1_Missense_Mutation_p.R176C|FAM153B_ENST00000512862.1_Missense_Mutation_p.R44C|FAM153B_ENST00000510151.1_Missense_Mutation_p.R176C			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	253										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)		AGTTCCACAACGTGGTACGTA	0.473																																					p.R176C		Atlas-SNP	.											.	FAM153B	28	.	0			c.C526T						PASS	.	C	CYS/ARG	5,4401	8.1+/-20.4	0,5,2198	78.0	80.0	79.0		757	-2.2	0.0	5		79	29,8565	15.3+/-51.7	0,29,4268	no	missense	FAM153B	NM_001079529.2	180	0,34,6466	TT,TC,CC		0.3374,0.1135,0.2615	possibly-damaging	253/388	175530780	34,12966	2203	4297	6500	SO:0001583	missense	202134	exon13			CCACAACGTGGTA	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.757C>T	5.37:g.175530780C>T	ENSP00000253490:p.Arg253Cys	Somatic	913	1	0.00109529		WXS	Illumina HiSeq	Phase_I	923	206	0.223185	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	C	4.556	0.103267	0.08731	0.001135	0.003374	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	1.12	-2.24	0.06909	.	.	.	.	.	T	0.16642	0.0400	N	0.14661	0.345	0.09310	N	1	B	0.19200	0.034	B	0.04013	0.001	T	0.16748	-1.0392	8	0.51188	T	0.08	.	2.2521	0.04046	0.4486:0.3196:0.2318:0.0	.	253	P0C7A2	F153B_HUMAN	C	176;253	.	ENSP00000253490:R253C	R	+	1	0	FAM153B	175463386	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-2.175000	0.01263	-0.591000	0.05859	-1.402000	0.01139	CGT	C|0.999;T|0.001	0.001	weak		0.473	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570557	570557	+	Silent	SNP	T	T	C	rs11537754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:570557T>C	ENST00000262305.4	+	13	2503	c.2115T>C	c.(2113-2115)tcT>tcC	p.S705S	RAB11FIP3_ENST00000457159.1_Silent_p.S750S|RAB11FIP3_ENST00000450428.1_Silent_p.S409S	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	705	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.				cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CAGCCTTCTCTGAGTCCCTGG	0.592													C|||	3961	0.790935	0.8381	0.6902	5008	,	,		22357	0.9911		0.5398	False		,,,				2504	0.8507				p.S705S	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.T2115C						PASS	.	C	,	3351,1051	386.8+/-326.2	1280,791,130	156.0	144.0	148.0		1227,2115	-8.9	0.0	16	dbSNP_120	148	4640,3960	550.6+/-385.8	1267,2106,927	no	coding-synonymous,coding-synonymous	RAB11FIP3	NM_001142272.1,NM_014700.3	,	2547,2897,1057	CC,CT,TT		46.0465,23.8755,38.5402	,	409/461,705/757	570557	7991,5011	2201	4300	6501	SO:0001819	synonymous_variant	9727	exon13			CTTCTCTGAGTCC	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.2115T>C	16.37:g.570557T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			T|0.353;C|0.647	0.647	strong		0.592	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700	
ISG15	9636	hgsc.bcm.edu	37	1	949608	949608	+	Missense_Mutation	SNP	G	G	A	rs1921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:949608G>A	ENST00000379389.4	+	2	399	c.248G>A	c.(247-249)aGc>aAc	p.S83N	RP11-54O7.11_ENST00000458555.1_RNA	NM_005101.3	NP_005092.1	P05161	ISG15_HUMAN	ISG15 ubiquitin-like modifier	83	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		S -> N (in dbSNP:rs1921). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of erythrocyte differentiation (GO:0045648)|regulation of interferon-gamma production (GO:0032649)|response to type I interferon (GO:0034340)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular region (GO:0005576)	protein tag (GO:0031386)			endometrium(1)|lung(1)|upper_aerodigestive_tract(1)	3	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;4.05e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.54e-23)|Colorectal(212;5.37e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00238)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GAACCTCTGAGCATCCTGGTG	0.662													g|||	1697	0.338858	0.4387	0.2709	5008	,	,		18347	0.1845		0.3926	False		,,,				2504	0.3558				p.S83N		Atlas-SNP	.											.	ISG15	10	.	0			c.G248A						PASS	.	A	ASN/SER	1827,2579	528.4+/-372.4	388,1051,764	62.0	58.0	59.0		248	-2.4	0.2	1	dbSNP_36	59	3396,5204	497.7+/-374.6	670,2056,1574	yes	missense	ISG15	NM_005101.3	46	1058,3107,2338	AA,AG,GG		39.4884,41.4662,40.1584	benign	83/166	949608	5223,7783	2203	4300	6503	SO:0001583	missense	9636	exon2			CTCTGAGCATCCT	BC009507	CCDS6.1	1p36.33	2008-02-05	2006-04-28	2006-04-28	ENSG00000187608	ENSG00000187608			4053	protein-coding gene	gene with protein product		147571	"""interferon, alpha-inducible protein (clone IFI-15K)"""	G1P2		3087979	Standard	NM_005101		Approved	IFI15, UCRP	uc001acj.4	P05161	OTTHUMG00000040777	ENST00000379389.4:c.248G>A	1.37:g.949608G>A	ENSP00000368699:p.Ser83Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_005101	Q5SVA4|Q7Z2G2|Q96GF0	Missense_Mutation	SNP	ENST00000379389.4	37	CCDS6.1	742	0.33974358974358976	210	0.4268292682926829	109	0.3011049723756906	118	0.2062937062937063	305	0.4023746701846966	g	2.900	-0.227652	0.06022	0.414662	0.394884	ENSG00000187608	ENST00000379389	T	0.28895	1.59	3.99	-2.36	0.06663	Ubiquitin supergroup (1);Ubiquitin (1);	3.314280	0.00669	N	0.000631	T	0.00012	0.0000	L	0.41236	1.265	0.58432	P	1.0000000000287557E-6	B	0.14438	0.01	B	0.10450	0.005	T	0.48525	-0.9028	9	0.87932	D	0	-21.9	9.972	0.41761	0.6559:0.0:0.3441:0.0	rs1921;rs4890;rs17651;rs1126669;rs3813185;rs17837903;rs17856313;rs52792478;rs56610207;rs59370406	83	P05161	ISG15_HUMAN	N	83	ENSP00000368699:S83N	ENSP00000368699:S83N	S	+	2	0	ISG15	939471	0.000000	0.05858	0.204000	0.23530	0.152000	0.21847	-1.538000	0.02204	-0.675000	0.05246	-0.925000	0.02716	AGC	A|0.360;C|0.000;G|0.640	0.360	strong		0.662	ISG15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097989.1	NM_005101	
ITGA2	3673	hgsc.bcm.edu	37	5	52369086	52369086	+	Silent	SNP	G	G	A	rs3213805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52369086G>A	ENST00000296585.5	+	20	2711	c.2568G>A	c.(2566-2568)ctG>ctA	p.L856L		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	856					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)				CATTCTCCCTGCCGGTATGTG	0.373													G|||	475	0.0948482	0.2027	0.0663	5008	,	,		20554	0.0188		0.0885	False		,,,				2504	0.0542				p.L856L		Atlas-SNP	.											ITGA2_ENST00000296585,NS,carcinoma,0,1	ITGA2	211	1	0			c.G2568A						PASS	.	G		795,3611	319.9+/-296.3	63,669,1471	192.0	191.0	191.0		2568	3.0	1.0	5	dbSNP_106	191	827,7773	192.0+/-238.1	40,747,3513	no	coding-synonymous	ITGA2	NM_002203.3		103,1416,4984	AA,AG,GG		9.6163,18.0436,12.4712		856/1182	52369086	1622,11384	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon20			CTCCCTGCCGGTA		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.2568G>A	5.37:g.52369086G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			G|0.883;A|0.117	0.117	strong		0.373	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
OR7A17	26333	hgsc.bcm.edu	37	19	14991459	14991459	+	Missense_Mutation	SNP	C	C	T	rs13345394	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14991459C>T	ENST00000327462.2	-	1	805	c.709G>A	c.(709-711)Gca>Aca	p.A237T		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	237			A -> T (in dbSNP:rs13345394).			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)					GTGGAAAATGCCTTGTACTTC	0.498													.|||	230	0.0459265	0.1036	0.0476	5008	,	,		20481	0.0159		0.0149	False		,,,				2504	0.0297				p.A237T		Atlas-SNP	.											.	OR7A17	37	.	0			c.G709A						PASS	.	C	THR/ALA	400,4006	199.4+/-223.0	16,368,1819	110.0	97.0	102.0		709	2.3	0.3	19	dbSNP_121	102	250,8350	99.5+/-161.0	3,244,4053	no	missense	OR7A17	NM_030901.1	58	19,612,5872	TT,TC,CC		2.907,9.0785,4.9977	benign	237/310	14991459	650,12356	2203	4300	6503	SO:0001583	missense	26333	exon1			AAAATGCCTTGTA	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.709G>A	19.37:g.14991459C>T	ENSP00000328144:p.Ala237Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_030901	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	37	CCDS12319.1	68	0.031135531135531136	33	0.06707317073170732	16	0.04419889502762431	8	0.013986013986013986	11	0.014511873350923483	c	12.62	1.991591	0.35131	0.090785	0.02907	ENSG00000185385	ENST00000327462	T	0.00357	7.89	3.37	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38548	U	0.001647	T	0.00039	0.0001	L	0.61218	1.895	0.26061	N	0.981357	D	0.64830	0.994	D	0.66602	0.945	T	0.48445	-0.9035	10	0.87932	D	0	.	9.8486	0.41043	0.207:0.793:0.0:0.0	rs13345394	237	O14581	OR7AH_HUMAN	T	237	ENSP00000328144:A237T	ENSP00000328144:A237T	A	-	1	0	OR7A17	14852459	1.000000	0.71417	0.335000	0.25508	0.029000	0.11900	3.726000	0.54977	0.756000	0.33013	-0.578000	0.04140	GCA	C|0.959;T|0.041	0.041	strong		0.498	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
UGT1A3	54659	hgsc.bcm.edu	37	2	234637853	234637853	+	Silent	SNP	G	G	A	rs6706232	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234637853G>A	ENST00000482026.1	+	1	100	c.81G>A	c.(79-81)gaG>gaA	p.E27E	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Silent_p.E27E|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	27					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	CCTGGGCTGAGAGTGGAAAGG	0.632													g|||	2867	0.572484	0.8336	0.5187	5008	,	,		17738	0.3571		0.4145	False		,,,				2504	0.6421				p.E27E		Atlas-SNP	.											UGT1A3,colon,carcinoma,0,1	UGT1A3	91	1	0			c.G81A						PASS	.	A	,,,,,,,,	3293,1113	397.9+/-330.6	1240,813,150	60.0	60.0	60.0		,,,,,,81,,	-1.4	0.0	2	dbSNP_116	60	3867,4733	608.6+/-395.4	840,2187,1273	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,	2080,3000,1423	AA,AG,GG		44.9651,25.261,44.9485	,,,,,,,,	,,,,,,27/535,,	234637853	7160,5846	2203	4300	6503	SO:0001819	synonymous_variant	54659	exon1			GGCTGAGAGTGGA	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"""UDP glucuronosyltransferases"""	12535	other	complex locus constituent		606428	"""UDP glycosyltransferase 1 family, polypeptide A3"""			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.81G>A	2.37:g.234637853G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_019093	B8K287	Silent	SNP	ENST00000482026.1	37	CCDS2509.1																																																																																			G|0.480;A|0.520	0.520	strong		0.632	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208515	81208515	+	RNA	SNP	G	G	A	rs12596941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81208515G>A	ENST00000527937.1	-	0	469				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA			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						GTCTCCGAGTGCCACCTGTTA	0.557													G|||	1013	0.202276	0.0068	0.2104	5008	,	,		20376	0.3046		0.2247	False		,,,				2504	0.3323				p.A863V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2588T						PASS	.	G	VAL/ALA,VAL/ALA	202,3868		5,192,1838	50.0	47.0	48.0		2588,2588	0.4	0.0	16	dbSNP_120	48	1882,6504		214,1454,2525	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	64,64	219,1646,4363	AA,AG,GG		22.4422,4.9631,16.7309	benign,benign	863/992,863/2460	81208515	2084,10372	2035	4193	6228			114780	exon16			CCGAGTGCCACCT	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.81208515G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		445	0.20375457875457875	7	0.014227642276422764	77	0.212707182320442	181	0.31643356643356646	180	0.23746701846965698	G	9.620	1.133700	0.21123	0.049631	0.224422	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.29655	1.56;1.56;1.56	4.7	0.362	0.16113	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2.898440	0.00953	N	0.002980	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.28933	0.078;0.228;0.216	B;B;B	0.27796	0.025;0.083;0.074	T	0.33240	-0.9876	8	0.42905	T	0.14	-0.0057	6.5899	0.22642	0.0:0.5186:0.3065:0.1748	rs12596941;rs52800976;rs12596941	119;863;863	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	V	178;863;119	ENSP00000436309:A178V;ENSP00000337397:A863V;ENSP00000432818:A119V	ENSP00000337397:A863V	A	-	2	0	PKD1L2	79766016	0.000000	0.05858	0.029000	0.17559	0.022000	0.10575	0.054000	0.14205	0.151000	0.19162	-0.321000	0.08615	GCA	G|0.789;A|0.211	0.211	strong		0.557	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
ABCB5	340273	hgsc.bcm.edu	37	7	20778646	20778646	+	Missense_Mutation	SNP	G	G	A	rs6461515	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20778646G>A	ENST00000404938.2	+	24	3560	c.2908G>A	c.(2908-2910)Gaa>Aaa	p.E970K	ABCB5_ENST00000258738.6_Missense_Mutation_p.E525K	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	970	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		E -> K (in dbSNP:rs6461515). {ECO:0000269|PubMed:12960149, ECO:0000269|PubMed:15760339, ECO:0000269|PubMed:22306008, ECO:0000269|Ref.5, ECO:0000269|Ref.8}.		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						GGCCATCGGAGAAACGCTCGT	0.423													G|||	3790	0.756789	0.6392	0.8573	5008	,	,		18616	0.8214		0.8241	False		,,,				2504	0.7086				p.E970K		Atlas-SNP	.											.	ABCB5	357	.	0			c.G2908A						PASS	.	G	LYS/GLU,LYS/GLU	2933,1473	677.0+/-403.3	973,987,243	65.0	62.0	63.0		2908,1573	4.1	1.0	7	dbSNP_116	63	7131,1469	749.1+/-407.4	2940,1251,109	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	56,56	3913,2238,352	AA,AG,GG		17.0814,33.4317,22.6203	benign,benign	970/1258,525/813	20778646	10064,2942	2203	4300	6503	SO:0001583	missense	340273	exon24			ATCGGAGAAACGC	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.2908G>A	7.37:g.20778646G>A	ENSP00000384881:p.Glu970Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	1752	0.8021978021978022	326	0.6626016260162602	307	0.8480662983425414	495	0.8653846153846154	624	0.8232189973614775	G	11.45	1.643741	0.29246	0.665683	0.829186	ENSG00000004846	ENST00000404938;ENST00000258738	T;T	0.80304	-1.36;-1.36	4.99	4.11	0.48088	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.189347	0.35708	N	0.003027	T	0.00012	0.0000	L	0.34521	1.04	0.32639	P	0.520975	B	0.22211	0.066	B	0.23419	0.046	T	0.36456	-0.9747	9	0.42905	T	0.14	.	7.6846	0.28534	0.186:0.0:0.814:0.0	rs6461515;rs17143317;rs52829521;rs59299440;rs6461515	525	Q2M3G0	ABCB5_HUMAN	K	970;525	ENSP00000384881:E970K;ENSP00000258738:E525K	ENSP00000258738:E525K	E	+	1	0	ABCB5	20745171	0.922000	0.31269	1.000000	0.80357	0.525000	0.34531	0.885000	0.28227	1.490000	0.48466	0.484000	0.47621	GAA	G|0.210;A|0.790	0.790	strong		0.423	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
GNL2	29889	hgsc.bcm.edu	37	1	38061396	38061396	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38061396T>C	ENST00000373062.3	-	1	126	c.28A>G	c.(28-30)Agc>Ggc	p.S10G		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	10					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TTGATGGTGCTCCGTCCTTTG	0.587																																					p.S10G		Atlas-SNP	.											.	GNL2	58	.	0			c.A28G						PASS	.						143.0	112.0	123.0					1																	38061396		2203	4300	6503	SO:0001583	missense	29889	exon1			TGGTGCTCCGTCC	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.28A>G	1.37:g.38061396T>C	ENSP00000362153:p.Ser10Gly	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	165	9	0.0545455	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494496	0.64186	.	.	ENSG00000134697	ENST00000373062	T	0.24723	1.84	5.01	5.01	0.66863	.	0.073396	0.85682	D	0.000000	T	0.21186	0.0510	L	0.51422	1.61	0.54753	D	0.999985	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.08207	-1.0733	10	0.33141	T	0.24	-17.281	6.6224	0.22810	0.1386:0.0758:0.0:0.7856	.	10;10	Q5T0F3;Q13823	.;NOG2_HUMAN	G	10	ENSP00000362153:S10G	ENSP00000362153:S10G	S	-	1	0	GNL2	37833983	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.138000	0.42140	2.102000	0.63906	0.533000	0.62120	AGC	.	.	none		0.587	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	
TMEM129	92305	hgsc.bcm.edu	37	4	1719294	1719294	+	Silent	SNP	T	T	C	rs2236786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:1719294T>C	ENST00000382936.3	-	3	1282	c.789A>G	c.(787-789)acA>acG	p.T263T	TMEM129_ENST00000536901.1_Silent_p.T263T|TMEM129_ENST00000303277.2_Intron	NM_001127266.1	NP_001120738.1	A0AVI4	TM129_HUMAN	transmembrane protein 129, E3 ubiquitin protein ligase	263					protein ubiquitination (GO:0016567)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(23;0.00765)			GGGAGGCAAATGTCTCCAGGA	0.682													T|||	786	0.156949	0.0129	0.2651	5008	,	,		18069	0.1468		0.2137	False		,,,				2504	0.227				p.T263T		Atlas-SNP	.											.	TMEM129	10	.	0			c.A789G						PASS	.	T	,	48,1336		0,48,644	59.0	68.0	65.0		789,	-9.2	0.5	4	dbSNP_98	65	637,2545		57,523,1011	yes	coding-synonymous,intron	TMEM129	NM_001127266.1,NM_138385.3	,	57,571,1655	CC,CT,TT		20.0189,3.4682,15.0022	,	263/363,	1719294	685,3881	692	1591	2283	SO:0001819	synonymous_variant	92305	exon3			GGCAAATGTCTCC	BC009331	CCDS3351.1, CCDS46998.1	4p16.3	2014-07-25	2014-07-25		ENSG00000168936	ENSG00000168936			25137	protein-coding gene	gene with protein product		615975	"""transmembrane protein 129"""			24807418, 25030448	Standard	NM_138385		Approved	D4S2561E	uc003gdn.3	A0AVI4	OTTHUMG00000121150	ENST00000382936.3:c.789A>G	4.37:g.1719294T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001127266	A6NH49|A6NI98|D3DVP8	Silent	SNP	ENST00000382936.3	37	CCDS46998.1																																																																																			T|0.851;C|0.149	0.149	strong		0.682	TMEM129-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350724.1	NM_138385	
DNAH9	1770	hgsc.bcm.edu	37	17	11511457	11511457	+	Silent	SNP	C	C	T	rs11078022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:11511457C>T	ENST00000262442.4	+	2	497	c.429C>T	c.(427-429)ccC>ccT	p.P143P	DNAH9_ENST00000454412.2_Silent_p.P143P|DNAH9_ENST00000579828.1_Silent_p.P143P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	143	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)		TTGTTCTACCCGTCCTGGCCA	0.483													C|||	2220	0.443291	0.1664	0.5648	5008	,	,		18842	0.5417		0.4235	False		,,,				2504	0.6503				p.P143P		Atlas-SNP	.											.	DNAH9	695	.	0			c.C429T						PASS	.	C		940,3466	357.1+/-313.8	103,734,1366	137.0	136.0	136.0		429	-11.4	0.0	17	dbSNP_120	136	3560,5040	516.7+/-378.9	761,2038,1501	no	coding-synonymous	DNAH9	NM_001372.3		864,2772,2867	TT,TC,CC		41.3953,21.3345,34.5994		143/4487	11511457	4500,8506	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon2			TCTACCCGTCCTG	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.429C>T	17.37:g.11511457C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.626;N|0.000	.	strong		0.483	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
OR4A5	81318	hgsc.bcm.edu	37	11	51412379	51412379	+	Missense_Mutation	SNP	T	T	C	rs10902343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:51412379T>C	ENST00000319760.6	-	1	69	c.17A>G	c.(16-18)aAt>aGt	p.N6S		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	6			N -> S (in dbSNP:rs10902343).			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)				TTCTGTAATATTGTTATTCTG	0.408													.|||	978	0.195288	0.1611	0.1671	5008	,	,		18518	0.2282		0.0954	False		,,,				2504	0.3303				p.N6S		Atlas-SNP	.											.	OR4A5	116	.	0			c.A17G						PASS	.	T	SER/ASN	691,3707		61,569,1569	25.0	24.0	24.0		17	2.2	0.4	11	dbSNP_120	24	882,7698		55,772,3463	no	missense	OR4A5	NM_001005272.3	46	116,1341,5032	CC,CT,TT		10.2797,15.7117,12.1205	benign	6/316	51412379	1573,11405	2199	4290	6489	SO:0001583	missense	81318	exon1			GTAATATTGTTAT	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.17A>G	11.37:g.51412379T>C	ENSP00000367664:p.Asn6Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	27	0.675	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	354	0.1620879120879121	89	0.18089430894308944	53	0.1464088397790055	145	0.2534965034965035	67	0.08839050131926121	.	3.473	-0.107446	0.06924	0.157117	0.102797	ENSG00000221840	ENST00000319760	T	0.00011	9.37	2.16	2.16	0.27623	.	0.000000	0.49916	D	0.000123	T	0.00012	0.0000	N	0.13272	0.32	0.58432	P	1.0000000000287557E-6	B	0.28128	0.201	B	0.28305	0.088	T	0.00172	-1.1958	9	0.49607	T	0.09	.	8.2487	0.31704	0.0:0.0:0.0:1.0	rs10902343;rs52824781;rs10902343	6	Q8NH83	OR4A5_HUMAN	S	6	ENSP00000367664:N6S	ENSP00000367664:N6S	N	-	2	0	OR4A5	51268955	0.000000	0.05858	0.370000	0.25965	0.132000	0.20833	0.007000	0.13174	1.259000	0.44117	0.136000	0.15936	AAT	T|0.864;C|0.136	0.136	strong		0.408	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
ABCC3	8714	hgsc.bcm.edu	37	17	48761053	48761053	+	Missense_Mutation	SNP	G	G	A	rs11568591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48761053G>A	ENST00000285238.8	+	27	3970	c.3890G>A	c.(3889-3891)cGc>cAc	p.R1297H		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1297	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> H (in dbSNP:rs11568591).		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)	TATTCTGTGCGCTACCGGCCG	0.662													g|||	99	0.0197684	0.0045	0.0476	5008	,	,		18448	0.0		0.0557	False		,,,				2504	0.0041				p.R1297H		Atlas-SNP	.											ABCC3,NS,carcinoma,+1,2	ABCC3	138	2	0			c.G3890A						PASS	.		HIS/ARG	75,4331	65.8+/-103.3	3,69,2131	124.0	112.0	116.0		3890	5.9	1.0	17	dbSNP_123	116	542,8058	149.2+/-204.3	10,522,3768	yes	missense	ABCC3	NM_003786.3	29	13,591,5899	AA,AG,GG		6.3023,1.7022,4.744	probably-damaging	1297/1528	48761053	617,12389	2203	4300	6503	SO:0001583	missense	8714	exon27			CTGTGCGCTACCG	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.3890G>A	17.37:g.48761053G>A	ENSP00000285238:p.Arg1297His	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	67	0.030677655677655676	3	0.006097560975609756	22	0.06077348066298342	0	0.0	42	0.055408970976253295	g	35	5.496309	0.96355	0.017022	0.063023	ENSG00000108846	ENST00000285238	D	0.90788	-2.73	5.94	5.94	0.96194	ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.78947	0.4364	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84861	0.0819	10	0.87932	D	0	-23.8467	20.3705	0.98891	0.0:0.0:1.0:0.0	rs11568591;rs17643133;rs52818811;rs61701650;rs11568591	1297	O15438	MRP3_HUMAN	H	1297	ENSP00000285238:R1297H	ENSP00000285238:R1297H	R	+	2	0	ABCC3	46116052	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	9.790000	0.99075	2.821000	0.97095	0.651000	0.88453	CGC	G|0.964;A|0.036	0.036	strong		0.662	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
DCAF17	80067	hgsc.bcm.edu	37	2	172330393	172330393	+	Silent	SNP	A	A	G	rs3731983	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:172330393A>G	ENST00000375255.3	+	10	1326	c.999A>G	c.(997-999)caA>caG	p.Q333Q	DCAF17_ENST00000468592.1_3'UTR|DCAF17_ENST00000539783.1_Intron	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	333					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						ATGGGATCCAAGAAATGGATT	0.338													A|||	1035	0.206669	0.146	0.2767	5008	,	,		20111	0.1885		0.1948	False		,,,				2504	0.2699				p.Q333Q		Atlas-SNP	.											.	DCAF17	41	.	0			c.A999G						PASS	.	A	,	772,3634	303.0+/-287.7	78,616,1509	80.0	77.0	78.0		,999	1.8	1.0	2	dbSNP_107	78	1719,6881	308.4+/-308.9	164,1391,2745	no	intron,coding-synonymous	DCAF17	NM_001164821.1,NM_025000.3	,	242,2007,4254	GG,GA,AA		19.9884,17.5216,19.1527	,	,333/521	172330393	2491,10515	2203	4300	6503	SO:0001819	synonymous_variant	80067	exon10			GATCCAAGAAATG	AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"""DDB1 and CUL4 associated factors"""	25784	protein-coding gene	gene with protein product	"""Woodhouse-Sakati syndrome"""	612515	"""chromosome 2 open reading frame 37"""	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.999A>G	2.37:g.172330393A>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	191	101	0.528796	NM_025000	B2RTW5|Q53TN3|Q9H908	Silent	SNP	ENST00000375255.3	37	CCDS2243.2	432	0.1978021978021978	75	0.1524390243902439	88	0.2430939226519337	134	0.23426573426573427	135	0.17810026385224276	A	0.948	-0.707301	0.03230	0.175216	0.199884	ENSG00000115827	ENST00000339506;ENST00000431110	.	.	.	5.53	1.75	0.24633	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999993463	.	.	.	.	.	.	T	0.07501	-1.0769	3	.	.	.	-10.5591	11.8954	0.52654	0.6933:0.0:0.3067:0.0	rs3731983;rs61472742;rs3731983	.	.	.	R	84;35	.	.	K	+	2	0	DCAF17	172038639	0.996000	0.38824	0.996000	0.52242	0.277000	0.26821	0.496000	0.22499	-0.190000	0.10465	-1.139000	0.01908	AAG	A|0.804;G|0.196	0.196	strong		0.338	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000	
HELZ2	85441	hgsc.bcm.edu	37	20	62193019	62193019	+	Silent	SNP	C	C	T	rs11551684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	100	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	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	
HELB	92797	hgsc.bcm.edu	37	12	66725160	66725160	+	Missense_Mutation	SNP	C	C	T	rs1185244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:66725160C>T	ENST00000247815.4	+	12	2956	c.2897C>T	c.(2896-2898)cCg>cTg	p.P966L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	966			P -> L (in dbSNP:rs1185244). {ECO:0000269|PubMed:14702039}.		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)		GCAGATTTTCCGTCCCCACGG	0.502													c|||	2393	0.477835	0.382	0.6138	5008	,	,		19343	0.5585		0.4205	False		,,,				2504	0.4867				p.P966L		Atlas-SNP	.											.	HELB	90	.	0			c.C2897T						PASS	.	C	LEU/PRO	1686,2720	512.1+/-368.0	333,1020,850	67.0	61.0	63.0		2897	2.4	0.0	12	dbSNP_87	63	3712,4888	530.2+/-381.7	805,2102,1393	yes	missense	HELB	NM_033647.2	98	1138,3122,2243	TT,TC,CC		43.1628,38.266,41.5039	benign	966/1088	66725160	5398,7608	2203	4300	6503	SO:0001583	missense	92797	exon12			ATTTTCCGTCCCC	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.2897C>T	12.37:g.66725160C>T	ENSP00000247815:p.Pro966Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	1088	0.4981684981684982	214	0.4349593495934959	208	0.574585635359116	338	0.5909090909090909	328	0.43271767810026385	c	8.303	0.820277	0.16678	0.38266	0.431628	ENSG00000127311	ENST00000247815	T	0.12039	2.72	5.24	2.41	0.29592	.	0.765215	0.11887	N	0.519971	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.16166	0.016	B	0.06405	0.002	T	0.33752	-0.9856	8	.	.	.	-1.1376	7.2998	0.26413	0.1454:0.6934:0.0:0.1611	rs1185244;rs1691825;rs17180686;rs1185244	966	Q8NG08	HELB_HUMAN	L	966	ENSP00000247815:P966L	.	P	+	2	0	HELB	65011427	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.076000	0.14712	0.216000	0.20781	-1.836000	0.00589	CCG	C|0.561;T|0.439	0.439	strong		0.502	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
SLC25A12	8604	hgsc.bcm.edu	37	2	172671648	172671648	+	Missense_Mutation	SNP	A	A	C	rs200754828		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:172671648A>C	ENST00000422440.2	-	10	1032	c.995T>G	c.(994-996)cTg>cGg	p.L332R	SLC25A12_ENST00000392592.4_Missense_Mutation_p.L225R	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	332					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	AACTGAGCCCAGAGTGAATCT	0.473																																					p.L332R		Atlas-SNP	.											.	SLC25A12	59	.	0			c.T995G						PASS	.						86.0	81.0	83.0					2																	172671648		2203	4300	6503	SO:0001583	missense	8604	exon10			GAGCCCAGAGTGA	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"""Solute carriers"", ""EF-hand domain containing"""	10982	protein-coding gene	gene with protein product		603667	"""solute carrier family 25 (mitochondrial carrier, Aralar), member 12"""			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.995T>G	2.37:g.172671648A>C	ENSP00000388658:p.Leu332Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	215	95	0.44186	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	a	23.6	4.440914	0.83993	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.80033	-1.33;-1.33	5.47	5.47	0.80525	Mitochondrial carrier domain (2);	0.140827	0.49305	D	0.000150	D	0.88187	0.6369	M	0.63208	1.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.89300	0.3625	10	0.72032	D	0.01	-1.9365	15.5193	0.75854	1.0:0.0:0.0:0.0	.	225;332	B3KR64;O75746	.;CMC1_HUMAN	R	332;225	ENSP00000388658:L332R;ENSP00000376371:L225R	ENSP00000376371:L225R	L	-	2	0	SLC25A12	172379894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.869000	0.92326	2.054000	0.61138	0.482000	0.46254	CTG	A|0.999;C|0.001	0.001	weak		0.473	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	
BAGE2	85319	hgsc.bcm.edu	37	21	11049621	11049621	+	RNA	SNP	G	G	A	rs28441174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11049621G>A	ENST00000470054.1	-	0	487							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								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)		ATCTTCCTTCGCTATAATTAA	0.368													g|||	470	0.0938498	0.1558	0.0533	5008	,	,		116266	0.0268		0.0626	False		,,,				2504	0.1401				p.R94X		Atlas-SNP	.											.	.	.	.	0			c.C280T						PASS	.						139.0	99.0	111.0					21																	11049621		692	1591	2283			85318	exon4			TCCTTCGCTATAA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049621G>A		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	336	39	0.116071	NM_182481	A8K925|Q08ER0	Nonsense_Mutation	SNP	ENST00000470054.1	37																																																																																				G|0.643;A|0.357	0.357	strong		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
SLC22A24	283238	hgsc.bcm.edu	37	11	62902146	62902146	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:62902146A>G	ENST00000417740.1	-	2	938	c.497T>C	c.(496-498)cTt>cCt	p.L166P	SLC22A24_ENST00000326192.5_Missense_Mutation_p.L166P	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	166					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						CCTGTCTGAAAGATGGCCATA	0.383																																					p.L166P		Atlas-SNP	.											.	SLC22A24	31	.	0			c.T497C						PASS	.						93.0	72.0	79.0					11																	62902146		692	1591	2283	SO:0001583	missense	283238	exon2			TCTGAAAGATGGC		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.497T>C	11.37:g.62902146A>G	ENSP00000396586:p.Leu166Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	160	49	0.30625	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		.	.	.	.	.	.	.	.	.	.	A	18.12	3.553416	0.65425	.	.	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.85013	-1.93;-0.36	3.52	3.52	0.40303	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.237783	0.35615	U	0.003083	D	0.93631	0.7966	H	0.95043	3.615	0.35699	D	0.815434	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.994	D	0.95896	0.8911	10	0.87932	D	0	.	10.166	0.42879	1.0:0.0:0.0:0.0	.	166;166	Q8N4F4;C9JC66	S22AO_HUMAN;.	P	166	ENSP00000396586:L166P;ENSP00000321549:L166P	ENSP00000321549:L166P	L	-	2	0	SLC22A24	62658722	0.140000	0.22579	0.047000	0.18901	0.691000	0.40173	5.090000	0.64498	1.474000	0.48178	0.321000	0.21382	CTT	.	.	none		0.383	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
HRNR	388697	hgsc.bcm.edu	37	1	152189038	152189038	+	Silent	SNP	A	A	G	rs145118416	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152189038A>G	ENST00000368801.2	-	3	5142	c.5067T>C	c.(5065-5067)taT>taC	p.Y1689Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1689					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGCTGACCATAGCGGGAAG	0.617																																					p.Y1689Y		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.T5067C						scavenged	.	A		321,2979		2,317,1331	67.0	73.0	71.0		5067	-0.7	0.0	1	dbSNP_134	71	363,6063		1,361,2851	no	coding-synonymous	HRNR	NM_001009931.1		3,678,4182	GG,GA,AA		5.6489,9.7273,7.0327		1689/2851	152189038	684,9042	1650	3213	4863	SO:0001819	synonymous_variant	388697	exon3			CTGACCATAGCGG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5067T>C	1.37:g.152189038A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	90	16	0.177778	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			A|0.968;G|0.032	0.032	strong		0.617	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PGM3	5238	hgsc.bcm.edu	37	6	83881740	83881740	+	Silent	SNP	T	T	C	rs542948	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:83881740T>C	ENST00000283977.4	-	10	1164	c.1038A>G	c.(1036-1038)gaA>gaG	p.E346E	PGM3_ENST00000512866.1_Silent_p.E427E|PGM3_ENST00000513973.1_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	74	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	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	
PLXDC1	57125	hgsc.bcm.edu	37	17	37243927	37243927	+	Silent	SNP	A	A	G	rs12602945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:37243927A>G	ENST00000315392.4	-	8	1051	c.840T>C	c.(838-840)taT>taC	p.Y280Y	PLXDC1_ENST00000539608.1_Silent_p.Y207Y|PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000444911.2_Silent_p.Y240Y|PLXDC1_ENST00000394316.2_Silent_p.Y280Y	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	45	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	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	
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248309020G>A	ENST00000366476.1	+	1	571	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	191						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(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	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;0.0388)			CTCATGCAATGACACATCAAT	0.418																																					p.D191N		Atlas-SNP	.											OR2M5,NS,carcinoma,0,2	OR2M5	117	2	0			c.G571A						scavenged	.						284.0	272.0	276.0					1																	248309020		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCAATGACACAT		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.571G>A	1.37:g.248309020G>A	ENSP00000355432:p.Asp191Asn	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	276	11	0.0398551	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	13.27	2.186763	0.38609	.	.	ENSG00000162727	ENST00000366476	T	0.00231	8.49	3.05	-0.584	0.11702	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33691	U	0.004660	T	0.00178	0.0005	M	0.63843	1.955	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.40739	-0.9547	10	0.52906	T	0.07	.	6.3472	0.21355	0.2028:0.2355:0.5617:0.0	.	191	A3KFT3	OR2M5_HUMAN	N	191	ENSP00000355432:D191N	ENSP00000355432:D191N	D	+	1	0	OR2M5	246375643	0.002000	0.14202	0.001000	0.08648	0.566000	0.35808	0.608000	0.24223	-0.004000	0.14419	0.492000	0.49549	GAC	G|0.996;A|0.004	0.004	strong		0.418	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
SERPINB8	5271	hgsc.bcm.edu	37	18	61650865	61650865	+	Silent	SNP	G	G	A	rs11537989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:61650865G>A	ENST00000397985.2	+	5	733	c.477G>A	c.(475-477)ctG>ctA	p.L159L	SERPINB8_ENST00000542677.1_5'UTR|SERPINB8_ENST00000353706.2_Silent_p.L159L|SERPINB8_ENST00000397988.3_Silent_p.L159L	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	85	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	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	
LAMC3	10319	hgsc.bcm.edu	37	9	133946909	133946909	+	Silent	SNP	G	G	A	rs10901344	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133946909G>A	ENST00000361069.4	+	18	3241	c.3108G>A	c.(3106-3108)ggG>ggA	p.G1036G	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1036	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		TGACGGAGGGGTGGCTCCAAG	0.612													G|||	1467	0.292931	0.1619	0.3285	5008	,	,		19182	0.1944		0.4115	False		,,,				2504	0.4243				p.G1036G		Atlas-SNP	.											.	LAMC3	167	.	0			c.G3108A						PASS	.	G		868,3538	337.0+/-304.7	86,696,1421	95.0	84.0	88.0		3108	2.0	1.0	9	dbSNP_120	88	3487,5113	509.4+/-377.3	717,2053,1530	no	coding-synonymous	LAMC3	NM_006059.3		803,2749,2951	AA,AG,GG		40.5465,19.7004,33.4845		1036/1576	133946909	4355,8651	2203	4300	6503	SO:0001819	synonymous_variant	10319	exon18			GGAGGGGTGGCTC	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3108G>A	9.37:g.133946909G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			G|0.683;A|0.317	0.317	strong		0.612	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
CD300LG	146894	hgsc.bcm.edu	37	17	41926023	41926023	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:41926023G>A	ENST00000317310.4	+	2	182	c.141G>A	c.(139-141)cgG>cgA	p.R47R	CD300LG_ENST00000293396.8_Silent_p.R47R|CD300LG_ENST00000377203.4_Silent_p.R47R|CD300LG_ENST00000588884.1_Silent_p.R47R|CD300LG_ENST00000539718.1_Silent_p.R47R|CD300LG_ENST00000586233.1_Silent_p.R47R	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	47	Ig-like V-type.				immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GGGACCACCGGAAGTACTGGT	0.577																																					p.R47R		Atlas-SNP	.											.	CD300LG	46	.	0			c.G141A						PASS	.						85.0	72.0	77.0					17																	41926023		2203	4300	6503	SO:0001819	synonymous_variant	146894	exon2			CCACCGGAAGTAC	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.141G>A	17.37:g.41926023G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_001168323	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	37	CCDS11470.1																																																																																			.	.	none		0.577	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273	
COL27A1	85301	hgsc.bcm.edu	37	9	116931445	116931445	+	Missense_Mutation	SNP	T	T	C	rs2808770	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:116931445T>C	ENST00000356083.3	+	3	2001	c.1610T>C	c.(1609-1611)aTt>aCt	p.I537T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	537	Pro-rich.		I -> T (in dbSNP:rs2808770). {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						AAGAAGCCCATTGGATCGGAA	0.627													C|||	1091	0.217851	0.3048	0.183	5008	,	,		14995	0.1339		0.2992	False		,,,				2504	0.1278				p.I537T		Atlas-SNP	.											.	COL27A1	200	.	0			c.T1610C						PASS	.	C	THR/ILE	1367,3039	690.7+/-405.3	211,945,1047	87.0	107.0	100.0		1610	4.5	0.7	9	dbSNP_100	100	2409,6191	699.2+/-405.1	328,1753,2219	yes	missense	COL27A1	NM_032888.2	89	539,2698,3266	CC,CT,TT		28.0116,31.0259,29.0328	benign	537/1861	116931445	3776,9230	2203	4300	6503	SO:0001583	missense	85301	exon3			AGCCCATTGGATC	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.1610T>C	9.37:g.116931445T>C	ENSP00000348385:p.Ile537Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	513	0.2348901098901099	157	0.31910569105691056	74	0.20441988950276244	70	0.12237762237762238	212	0.2796833773087071	C	6.209	0.406695	0.11754	0.310259	0.280116	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.90732	-2.47;-2.72	5.41	4.51	0.55191	.	.	.	.	.	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	0.04128	-1.0975	8	0.07990	T	0.79	.	8.4602	0.32923	0.0:0.8205:0.0:0.1795	rs2808770;rs52809082;rs57844925;rs2808770	537;484	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	T	537;537;484;484	ENSP00000348385:I537T;ENSP00000391328:I484T	ENSP00000348385:I537T	I	+	2	0	COL27A1	115971266	0.000000	0.05858	0.709000	0.30452	0.168000	0.22595	0.053000	0.14184	0.670000	0.31165	-0.213000	0.12676	ATT	C|0.259;N|0.000	0.259	strong		0.627	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
ACSS3	79611	hgsc.bcm.edu	37	12	81627238	81627238	+	Silent	SNP	C	C	T	rs1921038	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:81627238C>T	ENST00000548058.1	+	13	2617	c.1707C>T	c.(1705-1707)ggC>ggT	p.G569G	ACSS3_ENST00000548324.1_Silent_p.G251G|ACSS3_ENST00000261206.3_Silent_p.G568G			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	569						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TTTCTGCAGGCGCCATTGAAG	0.393													T|||	886	0.176917	0.1029	0.1801	5008	,	,		18410	0.2321		0.2207	False		,,,				2504	0.1728				p.G569G		Atlas-SNP	.											.	ACSS3	118	.	0			c.C1707T						PASS	.	T		539,3867	776.8+/-414.2	35,469,1699	199.0	195.0	197.0		1707	-1.2	1.0	12	dbSNP_92	197	1833,6767	731.2+/-406.8	207,1419,2674	no	coding-synonymous	ACSS3	NM_024560.2		242,1888,4373	TT,TC,CC		21.314,12.2333,18.2377		569/687	81627238	2372,10634	2203	4300	6503	SO:0001819	synonymous_variant	79611	exon13			TGCAGGCGCCATT		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1707C>T	12.37:g.81627238C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_024560	Q8NC66	Silent	SNP	ENST00000548058.1	37	CCDS9022.1																																																																																			C|0.811;T|0.189	0.189	strong		0.393	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
ACAT2	39	hgsc.bcm.edu	37	6	160198359	160198359	+	Silent	SNP	C	C	T	rs3464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160198359C>T	ENST00000367048.4	+	7	2543	c.783C>T	c.(781-783)gtC>gtT	p.V261V	ACAT2_ENST00000472052.1_3'UTR|SNORA20_ENST00000384662.1_RNA|ACAT2_ENST00000541436.1_Silent_p.V290V	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	261					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)		CTGCAGCTGTCGTTCTTATGA	0.423													C|||	1308	0.261182	0.1755	0.2161	5008	,	,		20467	0.4266		0.2127	False		,,,				2504	0.2883				p.V261V		Atlas-SNP	.											.	ACAT2	32	.	0			c.C783T						PASS	.	C		840,3566	333.3+/-302.9	89,662,1452	155.0	147.0	150.0		783	3.3	1.0	6	dbSNP_36	150	1500,7100	284.7+/-296.8	140,1220,2940	no	coding-synonymous	ACAT2	NM_005891.2		229,1882,4392	TT,TC,CC		17.4419,19.0649,17.9917		261/398	160198359	2340,10666	2203	4300	6503	SO:0001819	synonymous_variant	39	exon7			AGCTGTCGTTCTT	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.783C>T	6.37:g.160198359C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	127	0.954887	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Silent	SNP	ENST00000367048.4	37	CCDS5268.1																																																																																			C|0.797;T|0.203	0.203	strong		0.423	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891	
A2M	2	hgsc.bcm.edu	37	12	9232268	9232268	+	Missense_Mutation	SNP	T	T	C	rs669	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:9232268T>C	ENST00000318602.7	-	24	3305	c.2998A>G	c.(2998-3000)Atc>Gtc	p.I1000V	A2M_ENST00000542567.1_5'UTR	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1000			I -> V (in dbSNP:rs669). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15611997, ECO:0000269|PubMed:1707161, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:2581245}.		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)	TTGGACTTGATCTCTGGAGTA	0.428													T|||	1274	0.254393	0.329	0.3919	5008	,	,		-128	0.0823		0.3191	False		,,,				2504	0.1667				p.I1000V		Atlas-SNP	.											.	A2M	180	.	0			c.A2998G	GRCh37	CM980001	A2M	M	rs669	PASS	.	T	VAL/ILE	1235,2855		186,863,996	100.0	95.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2998	0.1	0.1	12	dbSNP_36	97	2776,5682		453,1870,1906	yes	missense	A2M	NM_000014.4	29	639,2733,2902	CC,CT,TT		32.821,30.1956,31.9653	benign	1000/1475	9232268	4011,8537	2045	4229	6274	SO:0001583	missense	2	exon24			ACTTGATCTCTGG	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.2998A>G	12.37:g.9232268T>C	ENSP00000323929:p.Ile1000Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	580	0.26556776556776557	144	0.2926829268292683	143	0.39502762430939226	41	0.07167832167832168	252	0.3324538258575198	T	7.920	0.738315	0.15574	0.301956	0.32821	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.37235	1.21	5.08	0.0893	0.14458	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.434068	0.23369	N	0.048939	T	0.00012	0.0000	L	0.41632	1.29	0.80722	P	0.0	B	0.16802	0.019	B	0.17979	0.02	T	0.43845	-0.9366	9	0.39692	T	0.17	.	5.7456	0.18118	0.0:0.1936:0.1402:0.6662	rs669;rs10432;rs1049149;rs2228223;rs3168556;rs10743597;rs17354152;rs17853961;rs52792261;rs57589145;rs669	1000	P01023	A2MG_HUMAN	V	1000;1015	ENSP00000323929:I1000V	ENSP00000323929:I1000V	I	-	1	0	A2M	9123535	0.243000	0.23878	0.141000	0.22245	0.589000	0.36550	0.910000	0.28571	-0.137000	0.11455	-0.456000	0.05471	ATC	T|0.745;C|0.255	0.255	strong		0.428	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
MGMT	4255	hgsc.bcm.edu	37	10	131265545	131265545	+	Silent	SNP	C	C	T	rs16906252	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:131265545C>T	ENST00000306010.7	+	1	98	c.66C>T	c.(64-66)cgC>cgT	p.R22R		NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	0					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	TCGCGGTGCGCACCGTTTGCG	0.731								Direct reversal of damage					C|||	123	0.0245607	0.0015	0.0288	5008	,	,		9189	0.0		0.0616	False		,,,				2504	0.0399				p.R22R		Atlas-SNP	.											.	MGMT	32	.	0			c.C66T	GRCh37	CR075258	MGMT	R	rs16906252	PASS	.	C		22,2814		0,22,1396	6.0	7.0	7.0		66	3.2	0.0	10	dbSNP_123	7	390,6204		5,380,2912	no	coding-synonymous	MGMT	NM_002412.3		5,402,4308	TT,TC,CC		5.9145,0.7757,4.369		22/239	131265545	412,9018	1418	3297	4715	SO:0001819	synonymous_variant	4255	exon1			GGTGCGCACCGTT	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.66C>T	10.37:g.131265545C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_002412	Q5VY78	Silent	SNP	ENST00000306010.7	37	CCDS7660.2																																																																																			C|0.966;T|0.034	0.034	strong		0.731	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
OR52E6	390078	hgsc.bcm.edu	37	11	5862984	5862984	+	Missense_Mutation	SNP	G	G	C	rs10769272	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5862984G>C	ENST00000329322.5	-	1	143	c.144C>G	c.(142-144)ttC>ttG	p.F48L	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.F52L	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	48			F -> L (in dbSNP:rs10769272).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F52L(1)|p.F48L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATCACAAAGAAGATAGCAG	0.483													C|||	1924	0.384185	0.379	0.3184	5008	,	,		20915	0.4593		0.3728	False		,,,				2504	0.3722				p.F48L		Atlas-SNP	.											OR52E6,NS,carcinoma,0,1	OR52E6	70	1	2	Substitution - Missense(2)	prostate(2)	c.C144G						PASS	.	C	LEU/PHE	1620,2782	652.3+/-399.4	294,1032,875	120.0	120.0	120.0		144	-7.3	0.0	11	dbSNP_120	120	3010,5582	662.7+/-402.0	533,1944,1819	yes	missense	OR52E6	NM_001005167.1	22	827,2976,2694	CC,CG,GG		35.0326,36.8015,35.6318	benign	48/314	5862984	4630,8364	2201	4296	6497	SO:0001583	missense	390078	exon1			CACAAAGAAGATA	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.144C>G	11.37:g.5862984G>C	ENSP00000328878:p.Phe48Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	879	0.4024725274725275	201	0.40853658536585363	120	0.3314917127071823	264	0.46153846153846156	294	0.38786279683377306	C	0.015	-1.558484	0.00910	0.368015	0.350326	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00482	8.17;7.1	3.64	-7.27	0.01461	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	N	0.000475	T	0.00012	0.0000	N	0.00022	-2.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33085	-0.9882	9	0.02654	T	1	.	4.0047	0.09595	0.163:0.1201:0.4805:0.2364	rs10769272;rs52812932;rs10769272	48	Q96RD3	O52E6_HUMAN	L	48;52	ENSP00000328878:F48L;ENSP00000369279:F52L	ENSP00000328878:F48L	F	-	3	2	OR52E6	5819560	0.000000	0.05858	0.001000	0.08648	0.436000	0.31835	-7.918000	0.00027	-1.655000	0.01497	-0.231000	0.12243	TTC	G|0.607;C|0.393	0.393	strong		0.483	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
KCTD9	54793	hgsc.bcm.edu	37	8	25287397	25287397	+	Silent	SNP	T	T	C	rs1812594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	321	0	0		WXS	Illumina HiSeq	Phase_I	318	166	0.522013	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	
OR10H1	26539	hgsc.bcm.edu	37	19	15918455	15918455	+	Silent	SNP	G	G	A	rs61739573	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:15918455G>A	ENST00000334920.2	-	1	481	c.393C>T	c.(391-393)cgC>cgT	p.R131R		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	131						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)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GCACGTTGTAGCGCAGGGGGT	0.637													.|||	964	0.192492	0.0416	0.2032	5008	,	,		19525	0.1905		0.3072	False		,,,				2504	0.273				p.R131R		Atlas-SNP	.											OR10H1,NS,carcinoma,-2,1	OR10H1	59	1	0			c.C393T						scavenged	.	G		326,4080		15,296,1892	68.0	56.0	60.0		393	3.7	1.0	19	dbSNP_129	60	2491,6109		372,1747,2181	no	coding-synonymous	OR10H1	NM_013940.2		387,2043,4073	AA,AG,GG		28.9651,7.399,21.6592		131/319	15918455	2817,10189	2203	4300	6503	SO:0001819	synonymous_variant	26539	exon1			GTTGTAGCGCAGG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.393C>T	19.37:g.15918455G>A		Somatic	140	2	0.0142857		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			G|0.794;A|0.206	0.206	strong		0.637	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
RPGRIP1	57096	hgsc.bcm.edu	37	14	21792811	21792811	+	Silent	SNP	G	G	A	rs9322965	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:21792811G>A	ENST00000400017.2	+	14	1797	c.1797G>A	c.(1795-1797)ccG>ccA	p.P599P	RPGRIP1_ENST00000307974.4_Missense_Mutation_p.R8H|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000206660.6_Silent_p.P599P|RPGRIP1_ENST00000557771.1_Silent_p.P561P	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	599					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GCACCCGACCGTTGTCGTTAT	0.478													G|||	925	0.184704	0.2421	0.1427	5008	,	,		21117	0.0188		0.2336	False		,,,				2504	0.2577				p.P599P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1797A						PASS	.	G		835,3111		96,643,1234	125.0	117.0	120.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1797	3.2	0.1	14	dbSNP_119	120	1996,6294		228,1540,2377	no	coding-synonymous	RPGRIP1	NM_020366.3		324,2183,3611	AA,AG,GG		24.0772,21.1607,23.1366		599/1287	21792811	2831,9405	1973	4145	6118	SO:0001819	synonymous_variant	57096	exon14			CCGACCGTTGTCG	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1797G>A	14.37:g.21792811G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1	357	0.16346153846153846	115	0.23373983739837398	56	0.15469613259668508	6	0.01048951048951049	180	0.23746701846965698	G	8.657	0.899673	0.17686	0.211607	0.240772	ENSG00000092200	ENST00000307974	T	0.79454	-1.27	5.28	3.17	0.36434	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.04320	-1.0960	7	0.37606	T	0.19	-0.1041	2.6329	0.04950	0.2604:0.0:0.3544:0.3852	rs9322965;rs59052867;rs9322965	8	Q96KN7-3	.	H	8	ENSP00000309721:R8H	ENSP00000309721:R8H	R	+	2	0	RPGRIP1	20862651	0.000000	0.05858	0.052000	0.19188	0.972000	0.66771	-0.363000	0.07593	0.534000	0.28695	0.655000	0.94253	CGT	G|0.856;A|0.144	0.144	strong		0.478	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
KRT35	3886	hgsc.bcm.edu	37	17	39633354	39633354	+	Missense_Mutation	SNP	C	C	T	rs12451652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39633354C>T	ENST00000393989.1	-	7	1364	c.1322G>A	c.(1321-1323)tGc>tAc	p.C441Y	KRT35_ENST00000246639.2_Missense_Mutation_p.C411Y	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	441	Tail.		C -> Y (in dbSNP:rs12451652).		anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				GCGGGGGCTGCAGTTTGTGCG	0.622													C|||	871	0.173922	0.0741	0.1225	5008	,	,		15175	0.2956		0.172	False		,,,				2504	0.2219				p.C441Y		Atlas-SNP	.											.	KRT35	58	.	0			c.G1322A						PASS	.	C	TYR/CYS	350,3512		14,322,1595	45.0	52.0	50.0		1322	4.4	1.0	17	dbSNP_120	50	1397,6857		107,1183,2837	no	missense	KRT35	NM_002280.4	194	121,1505,4432	TT,TC,CC		16.9251,9.0627,14.419	benign	441/456	39633354	1747,10369	1931	4127	6058	SO:0001583	missense	3886	exon7			GGGCTGCAGTTTG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.1322G>A	17.37:g.39633354C>T	ENSP00000377558:p.Cys441Tyr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	382	0.1749084249084249	36	0.07317073170731707	50	0.13812154696132597	164	0.2867132867132867	132	0.1741424802110818	C	12.96	2.095527	0.36952	0.090627	0.169251	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.83075	-1.68;-1.6	5.41	4.43	0.53597	.	0.094013	0.47852	D	0.000220	T	0.00039	0.0001	M	0.84219	2.685	0.29739	P	0.8372580000000001	B	0.14805	0.011	B	0.18561	0.022	T	0.11179	-1.0598	9	0.72032	D	0.01	.	11.9926	0.53184	0.0:0.8264:0.1736:0.0	rs12451652;rs59654549;rs12451652	441	Q92764	KRT35_HUMAN	Y	411;441	ENSP00000246639:C411Y;ENSP00000377558:C441Y	ENSP00000246639:C411Y	C	-	2	0	KRT35	36886880	0.991000	0.36638	0.996000	0.52242	0.696000	0.40369	1.906000	0.39887	1.496000	0.48567	0.563000	0.77884	TGC	C|0.825;T|0.175	0.175	strong		0.622	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
MAU2	23383	hgsc.bcm.edu	37	19	19449686	19449686	+	Silent	SNP	G	G	T	rs2074090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19449686G>T	ENST00000392313.6	+	5	668	c.489G>T	c.(487-489)tcG>tcT	p.S163S	MAU2_ENST00000586189.3_Intron|MAU2_ENST00000262815.8_Silent_p.S163S	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	163					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						ACCTGGTGTCGGCCTGTGACC	0.572													G|||	2625	0.524161	0.348	0.5418	5008	,	,		18843	0.6677		0.674	False		,,,				2504	0.4479				p.S163S		Atlas-SNP	.											MAU2,NS,malignant_melanoma,+1,1	MAU2	38	1	0			c.G489T						PASS	.	G		1576,2408		307,962,723	88.0	99.0	95.0		489	-10.8	0.4	19	dbSNP_96	95	5475,2843		1802,1871,486	no	coding-synonymous	MAU2	NM_015329.3		2109,2833,1209	TT,TG,GG		34.1789,39.5582,42.6841		163/614	19449686	7051,5251	1992	4159	6151	SO:0001819	synonymous_variant	23383	exon5			GGTGTCGGCCTGT	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"""sister chromatid cohesion 4"""	614560	"""KIAA0892"", ""MAU2 chromatid cohesion factor homolog (C. elegans)"""	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.489G>T	19.37:g.19449686G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_015329	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Silent	SNP	ENST00000392313.6	37	CCDS32969.2																																																																																			G|0.437;T|0.563	0.563	strong		0.572	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329	
TAS2R5	54429	hgsc.bcm.edu	37	7	141490238	141490238	+	Missense_Mutation	SNP	G	G	T	rs2227264	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141490238G>T	ENST00000247883.4	+	1	222	c.77G>T	c.(76-78)aGc>aTc	p.S26I		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	26			S -> I (in dbSNP:rs2227264).		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)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GGAAATGGAAGCCTGGTGGTC	0.512													t|||	2266	0.452476	0.2065	0.5648	5008	,	,		20485	0.7014		0.4672	False		,,,				2504	0.4335				p.S26I		Atlas-SNP	.											.	TAS2R5	33	.	0			c.G77T						PASS	.	T	ILE/SER	1124,3282	717.0+/-408.7	149,826,1228	96.0	96.0	96.0		77	3.4	0.0	7	dbSNP_98	96	4239,4361	582.2+/-391.4	1039,2161,1100	yes	missense	TAS2R5	NM_018980.2	142	1188,2987,2328	TT,TG,GG		49.2907,25.5107,41.2348	benign	26/300	141490238	5363,7643	2203	4300	6503	SO:0001583	missense	54429	exon1			ATGGAAGCCTGGT	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.77G>T	7.37:g.141490238G>T	ENSP00000247883:p.Ser26Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	167	74	0.443114	NM_018980	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	1069	0.48946886446886445	120	0.24390243902439024	196	0.5414364640883977	404	0.7062937062937062	349	0.4604221635883905	T	3.131	-0.178496	0.06380	0.255107	0.492907	ENSG00000127366	ENST00000247883	T	0.35236	1.32	4.59	3.43	0.39272	.	.	.	.	.	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	0.27905	-1.0060	8	0.45353	T	0.12	.	4.8795	0.13672	0.0:0.0979:0.1869:0.7152	rs2227264;rs17523954;rs52799831;rs2227264	26	Q9NYW4	TA2R5_HUMAN	I	26	ENSP00000247883:S26I	ENSP00000247883:S26I	S	+	2	0	TAS2R5	141136707	0.000000	0.05858	0.012000	0.15200	0.004000	0.04260	-0.001000	0.12947	0.279000	0.22186	-0.256000	0.11100	AGC	G|0.549;N|0.000	.	strong		0.512	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1		
SLC5A1	6523	hgsc.bcm.edu	37	22	32506041	32506041	+	Silent	SNP	A	A	G	rs17683704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32506041A>G	ENST00000266088.4	+	15	2086	c.1836A>G	c.(1834-1836)ctA>ctG	p.L612L	SLC5A1_ENST00000543737.1_Silent_p.L485L	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	612					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TTTGTGGGCTAGAGCAGCACG	0.463													G|||	111	0.0221645	0.003	0.0259	5008	,	,		20404	0.0		0.0606	False		,,,				2504	0.0286				p.L612L		Atlas-SNP	.											.	SLC5A1	80	.	0			c.A1836G						PASS	.	G		61,4345	820.8+/-416.4	0,61,2142	158.0	135.0	143.0		1836	5.6	1.0	22	dbSNP_123	143	602,7998	792.5+/-407.5	20,562,3718	no	coding-synonymous	SLC5A1	NM_000343.3		20,623,5860	GG,GA,AA		7.0,1.3845,5.0976		612/665	32506041	663,12343	2203	4300	6503	SO:0001819	synonymous_variant	6523	exon15			TGGGCTAGAGCAG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1836A>G	22.37:g.32506041A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Silent	SNP	ENST00000266088.4	37	CCDS13902.1																																																																																			A|0.954;G|0.046	0.046	strong		0.463	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
IL7R	3575	hgsc.bcm.edu	37	5	35876274	35876274	+	Missense_Mutation	SNP	A	A	G	rs3194051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:35876274A>G	ENST00000303115.3	+	8	1195	c.1066A>G	c.(1066-1068)Atc>Gtc	p.I356V	IL7R_ENST00000343305.4_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	356			I -> V (in dbSNP:rs3194051). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2038316, ECO:0000269|PubMed:2317865}.		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)			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)			GGATGTAGTCATCACTCCAGA	0.507			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						A|||	1106	0.220847	0.348	0.1816	5008	,	,		18793	0.0625		0.2823	False		,,,				2504	0.1769				p.I356V		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.A1066G						PASS	.	A	VAL/ILE	1542,2864	485.7+/-360.4	269,1004,930	89.0	85.0	86.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1066	3.2	0.0	5	dbSNP_105	86	2271,6329	383.8+/-340.9	301,1669,2330	yes	missense	IL7R	NM_002185.2	29	570,2673,3260	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	26.407,34.9977,29.3172	benign	356/460	35876274	3813,9193	2203	4300	6503	SO:0001583	missense	3575	exon8			GTAGTCATCACTC	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.1066A>G	5.37:g.35876274A>G	ENSP00000306157:p.Ile356Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	493	0.22573260073260074	164	0.3333333333333333	81	0.22375690607734808	28	0.04895104895104895	220	0.29023746701846964	A	4.605	0.112367	0.08831	0.349977	0.26407	ENSG00000168685	ENST00000303115;ENST00000505875	T;T	0.33438	1.88;1.41	5.6	3.23	0.37069	.	0.345580	0.27437	N	0.019361	T	0.00012	0.0000	L	0.56769	1.78	0.58432	P	4.000000000004E-6	B	0.20368	0.044	B	0.19148	0.024	T	0.43734	-0.9373	9	0.13108	T	0.6	-24.3005	6.0166	0.19607	0.6534:0.1963:0.0:0.1503	rs3194051;rs16902513;rs52816604;rs58270601;rs3194051	356	P16871	IL7RA_HUMAN	V	356;122	ENSP00000306157:I356V;ENSP00000420923:I122V	ENSP00000306157:I356V	I	+	1	0	IL7R	35912031	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.576000	0.23744	0.408000	0.25621	0.533000	0.62120	ATC	A|0.740;G|0.260	0.260	strong		0.507	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
LRP1B	53353	hgsc.bcm.edu	37	2	141093340	141093340	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:141093340T>A	ENST00000389484.3	-	78	12931	c.11960A>T	c.(11959-11961)gAt>gTt	p.D3987V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3987					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)		TCTAGAATGATCAGTCCAGTA	0.463										TSP Lung(27;0.18)																											p.D3987V	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,-1,1	LRP1B	1315	1	0			c.A11960T						scavenged	.						144.0	135.0	138.0					2																	141093340		2203	4300	6503	SO:0001583	missense	53353	exon78			GAATGATCAGTCC	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.11960A>T	2.37:g.141093340T>A	ENSP00000374135:p.Asp3987Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	134	2	0.0149254	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.4|26.4	4.733784|4.733784	0.89482|0.89482	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977	D|.	0.93247|.	-3.19|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);|.	0.130534|.	0.48767|.	D|.	0.000167|.	T|T	0.80539|0.80539	0.4642|0.4642	M|M	0.88377|0.88377	2.95|2.95	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.80764|.	0.994|.	D|D	0.84102|0.84102	0.0396|0.0396	10|5	0.87932|.	D|.	0|.	.|.	15.509|15.509	0.75766|0.75766	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3987|.	Q9NZR2|.	LRP1B_HUMAN|.	V|F	3987;3925|219	ENSP00000374135:D3987V|.	ENSP00000374135:D3987V|.	D|I	-|-	2|1	0|0	LRP1B|LRP1B	140809810|140809810	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.563000|7.563000	0.82314|0.82314	2.119000|2.119000	0.64992|0.64992	0.528000|0.528000	0.53228|0.53228	GAT|ATC	.	.	none		0.463	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
HELZ2	85441	hgsc.bcm.edu	37	20	62196033	62196033	+	Missense_Mutation	SNP	C	C	T	rs3810487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	30	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	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	
CALU	813	hgsc.bcm.edu	37	7	128388648	128388648	+	Missense_Mutation	SNP	G	G	A	rs2290228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:128388648G>A	ENST00000249364.4	+	2	113	c.11G>A	c.(10-12)cGa>cAa	p.R4Q	CALU_ENST00000538546.1_Intron|CALU_ENST00000449187.2_Missense_Mutation_p.R4Q|CALU_ENST00000535011.2_Missense_Mutation_p.R4Q|CALU_ENST00000542996.2_Missense_Mutation_p.R12Q|CALU_ENST00000479257.1_Missense_Mutation_p.R12Q|CALU_ENST00000535623.1_Missense_Mutation_p.R12Q	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	98	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	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	
FAT4	79633	hgsc.bcm.edu	37	4	126241335	126241335	+	Missense_Mutation	SNP	C	C	G	rs36052762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:126241335C>G	ENST00000394329.3	+	1	3782	c.3769C>G	c.(3769-3771)Cag>Gag	p.Q1257E		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1257	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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						TGAAGAAAGACAGTTTGCTAT	0.373													C|||	544	0.108626	0.0234	0.1571	5008	,	,		19121	0.2014		0.0477	False		,,,				2504	0.1564				p.Q1257E		Atlas-SNP	.											.	FAT4	1752	.	0			c.C3769G						PASS	.	C	GLU/GLN	93,3617		4,85,1766	65.0	62.0	63.0		3769	3.9	1.0	4	dbSNP_126	63	364,7842		4,356,3743	yes	missense	FAT4	NM_024582.4	29	8,441,5509	GG,GC,CC		4.4358,2.5067,3.8352	benign	1257/4982	126241335	457,11459	1855	4103	5958	SO:0001583	missense	79633	exon1			GAAAGACAGTTTG	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.3769C>G	4.37:g.126241335C>G	ENSP00000377862:p.Gln1257Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	208	0.09523809523809523	12	0.024390243902439025	48	0.13259668508287292	117	0.20454545454545456	31	0.040897097625329816	C	3.596	-0.082671	0.07141	0.025067	0.044358	ENSG00000196159	ENST00000394329	T	0.01106	5.33	4.81	3.89	0.44902	Cadherin (4);Cadherin-like (1);	0.000000	0.33040	U	0.005344	T	0.00012	0.0000	L	0.28274	0.84	0.09310	P	0.9999999999999951	B	0.21309	0.054	B	0.27500	0.08	T	0.62756	-0.6787	9	0.25751	T	0.34	.	15.6179	0.76780	0.1466:0.8534:0.0:0.0	rs36052762	1257	Q6V0I7	FAT4_HUMAN	E	1257	ENSP00000377862:Q1257E	ENSP00000377862:Q1257E	Q	+	1	0	FAT4	126460785	0.997000	0.39634	1.000000	0.80357	0.979000	0.70002	3.553000	0.53713	2.503000	0.84419	0.561000	0.74099	CAG	C|0.920;G|0.080	0.080	strong		0.373	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FCAR	2204	hgsc.bcm.edu	37	19	55396900	55396900	+	Silent	SNP	A	A	G	rs1865096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55396900A>G	ENST00000355524.3	+	3	334	c.324A>G	c.(322-324)agA>agG	p.R108R	FCAR_ENST00000353758.4_Intron|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000359272.4_Silent_p.R96R|FCAR_ENST00000391726.3_Silent_p.R96R|FCAR_ENST00000391723.3_Silent_p.R96R|FCAR_ENST00000391725.3_Silent_p.R108R|FCAR_ENST00000469767.1_Silent_p.R108R|FCAR_ENST00000345937.4_Silent_p.R108R|FCAR_ENST00000391724.3_Silent_p.R96R	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	108					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		GGCACTACAGATTCCGGTACA	0.458													.|||	3703	0.739417	0.8933	0.6167	5008	,	,		17121	0.7341		0.7157	False		,,,				2504	0.6483				p.R108R		Atlas-SNP	.											FCAR_ENST00000433231,colon,carcinoma,0,2	FCAR	110	2	0			c.A324G	GRCh37	CM044227	FCAR	M	rs1865096	PASS	.	G	,,,,,,,,	3767,639	275.7+/-272.7	1605,557,41	71.0	64.0	66.0		324,324,324,288,288,288,,288,324	2.1	0.0	19	dbSNP_92	66	6311,2289	386.1+/-341.7	2311,1689,300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	FCAR	NM_002000.2,NM_133269.2,NM_133271.2,NM_133272.2,NM_133273.2,NM_133274.2,NM_133277.2,NM_133278.2,NM_133279.2	,,,,,,,,	3916,2246,341	GG,GA,AA		26.6163,14.503,22.5127	,,,,,,,,	108/288,108/266,108/192,96/276,96/180,96/210,,96/254,108/240	55396900	10078,2928	2203	4300	6503	SO:0001819	synonymous_variant	2204	exon3			CTACAGATTCCGG	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.324A>G	19.37:g.55396900A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_133279	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Silent	SNP	ENST00000355524.3	37	CCDS12907.1																																																																																			A|0.234;G|0.766	0.766	strong		0.458	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595183	140595183	+	Silent	SNP	G	G	T	rs2910330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	152	0	0		WXS	Illumina HiSeq	Phase_I	136	61	0.448529	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	
SLC5A12	159963	hgsc.bcm.edu	37	11	26694979	26694979	+	Silent	SNP	A	A	G	rs4369354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:26694979A>G	ENST00000396005.3	-	14	1986	c.1677T>C	c.(1675-1677)tgT>tgC	p.C559C		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	559					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GCTGAACTCCACACCAGCATA	0.408													G|||	2118	0.422923	0.4448	0.3127	5008	,	,		19336	0.3502		0.4881	False		,,,				2504	0.4796				p.C559C		Atlas-SNP	.											SLC5A12,colon,carcinoma,-2,1	SLC5A12	134	1	0			c.T1677C						PASS	.	G		1797,2329		404,989,670	142.0	145.0	144.0		1677	1.9	1.0	11	dbSNP_111	144	4258,4184		1086,2086,1049	no	coding-synonymous	SLC5A12	NM_178498.3		1490,3075,1719	GG,GA,AA		49.5617,43.5531,48.1779		559/619	26694979	6055,6513	2063	4221	6284	SO:0001819	synonymous_variant	159963	exon14			AACTCCACACCAG	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1677T>C	11.37:g.26694979A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			A|0.555;G|0.445	0.445	strong		0.408	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
FLNB	2317	hgsc.bcm.edu	37	3	58080639	58080639	+	Silent	SNP	C	C	T	rs141151998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58080639C>T	ENST00000295956.4	+	5	1029	c.864C>T	c.(862-864)gaC>gaT	p.D288D	FLNB_ENST00000490882.1_Silent_p.D288D|FLNB_ENST00000429972.2_Silent_p.D288D|FLNB_ENST00000493452.1_Silent_p.D119D|FLNB_ENST00000419752.2_Silent_p.D119D|FLNB_ENST00000358537.3_Silent_p.D288D|FLNB_ENST00000357272.4_Silent_p.D288D|FLNB_ENST00000348383.5_Silent_p.D288D	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	288					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)		GGCAAGGAGACGTGATGGTGT	0.542																																					p.D288D		Atlas-SNP	.											FLNB_ENST00000490882,NS,carcinoma,0,2	FLNB	430	2	0			c.C864T						PASS	.	C	,,,	0,4406		0,0,2203	213.0	194.0	201.0		864,864,864,864	-7.8	0.3	3	dbSNP_134	201	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	288/2634,288/2592,288/2579,288/2603	58080639	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon5			AGGAGACGTGATG	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.864C>T	3.37:g.58080639C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	123	43	0.349593	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|0.999;T|0.001	0.001	strong		0.542	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
INSC	387755	hgsc.bcm.edu	37	11	15243047	15243047	+	Missense_Mutation	SNP	G	G	A	rs61745838	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:15243047G>A	ENST00000379554.3	+	8	1031	c.985G>A	c.(985-987)Gac>Aac	p.D329N	INSC_ENST00000447214.2_3'UTR|INSC_ENST00000424273.1_Missense_Mutation_p.D240N|INSC_ENST00000528567.1_Missense_Mutation_p.D282N|INSC_ENST00000379556.3_Missense_Mutation_p.D282N|INSC_ENST00000525218.1_Missense_Mutation_p.D240N|INSC_ENST00000530161.1_Missense_Mutation_p.D282N	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	329					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GTGCTTGGCCGACATCCTGAC	0.622													G|||	80	0.0159744	0.0015	0.0202	5008	,	,		17254	0.0		0.0338	False		,,,				2504	0.0307				p.D329N		Atlas-SNP	.											INSC,NS,carcinoma,0,1	INSC	104	1	0			c.G985A						PASS	.	G	ASN/ASP,ASN/ASP	32,4228		0,32,2098	59.0	66.0	64.0		985,844	3.4	0.9	11	dbSNP_129	64	373,8117		14,345,3886	yes	missense,missense	INSC	NM_001031853.3,NM_001042536.1	23,23	14,377,5984	AA,AG,GG		4.3934,0.7512,3.1765	probably-damaging,probably-damaging	329/580,282/533	15243047	405,12345	2130	4245	6375	SO:0001583	missense	387755	exon8			TTGGCCGACATCC	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.985G>A	11.37:g.15243047G>A	ENSP00000368872:p.Asp329Asn	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	33	0.01510989010989011	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	24	0.0316622691292876	G	15.86	2.956639	0.53293	0.007512	0.043934	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000528567;ENST00000530161;ENST00000525218	T;T;T;T;T;T	0.48522	0.81;0.81;0.82;0.81;0.81;0.82	5.24	3.38	0.38709	Armadillo-like helical (1);Armadillo-type fold (1);	0.047194	0.85682	N	0.000000	T	0.25419	0.0618	M	0.61703	1.905	0.58432	D	0.999999	B;D;B;B	0.76494	0.142;0.999;0.131;0.016	B;P;B;B	0.57009	0.055;0.811;0.042;0.016	T	0.41963	-0.9479	10	0.62326	D	0.03	-24.3802	11.3416	0.49535	0.1473:0.0:0.8527:0.0	rs61745838	317;240;282;329	Q1MX18-5;Q1MX18-4;A0PJX5;Q1MX18	.;.;.;INSC_HUMAN	N	329;282;240;282;282;240	ENSP00000368872:D329N;ENSP00000368874:D282N;ENSP00000389161:D240N;ENSP00000435022:D282N;ENSP00000436194:D282N;ENSP00000436113:D240N	ENSP00000368872:D329N	D	+	1	0	INSC	15199623	1.000000	0.71417	0.888000	0.34837	0.796000	0.44982	6.239000	0.72356	0.596000	0.29794	-0.137000	0.14449	GAC	G|0.975;A|0.025	0.025	strong		0.622	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
THSD1	55901	hgsc.bcm.edu	37	13	52952575	52952575	+	Silent	SNP	G	G	A	rs9536042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52952575G>A	ENST00000258613.4	-	5	1708	c.1530C>T	c.(1528-1530)gcC>gcT	p.A510A	THSD1_ENST00000544466.1_Silent_p.A131A|THSD1_ENST00000349258.4_Silent_p.A457A	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	510					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CGCTGCCAGAGGCATCATCCT	0.607													G|||	354	0.0706869	0.1687	0.0288	5008	,	,		15959	0.0079		0.0388	False		,,,				2504	0.0654				p.A510A		Atlas-SNP	.											.	THSD1	89	.	0			c.C1530T						PASS	.	G	,	574,3832	254.0+/-259.7	40,494,1669	94.0	96.0	95.0		1530,1371	0.1	0.0	13	dbSNP_119	95	443,8157	134.9+/-192.2	11,421,3868	no	coding-synonymous,coding-synonymous	THSD1	NM_018676.3,NM_199263.2	,	51,915,5537	AA,AG,GG		5.1512,13.0277,7.8195	,	510/853,457/800	52952575	1017,11989	2203	4300	6503	SO:0001819	synonymous_variant	55901	exon5			GCCAGAGGCATCA	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1530C>T	13.37:g.52952575G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Silent	SNP	ENST00000258613.4	37	CCDS9432.1																																																																																			G|0.933;A|0.067	0.067	strong		0.607	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24423090A>G	ENST00000313250.5	+	1	296	c.93A>G	c.(91-93)gcA>gcG	p.A31A	DHRS4_ENST00000543741.2_Silent_p.A31A|DHRS4_ENST00000397075.3_Silent_p.A31A|DHRS4_ENST00000559632.1_Silent_p.A31A|DHRS4_ENST00000382761.3_Silent_p.A13A|DHRS4_ENST00000421831.1_Silent_p.A13A|DHRS4_ENST00000558263.1_Silent_p.A31A|DHRS4_ENST00000558581.1_Silent_p.A31A|DHRS4_ENST00000397074.3_Silent_p.A31A|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_Silent_p.A13A|DHRS4_ENST00000397073.2_Silent_p.A13A	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	31			A -> T (in dbSNP:rs1043442).		alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	ACCCGCTCGCAAATAAGGTGG	0.662													.|||	1415	0.282548	0.7973	0.1254	5008	,	,		15599	0.1359		0.0875	False		,,,				2504	0.0501				p.A31A		Atlas-SNP	.											.	DHRS4	22	.	0			c.A93G						PASS	.	G		3004,1398		1049,906,246	28.0	36.0	33.0		93	0.5	0.5	14	dbSNP_100	33	810,7782		36,738,3522	no	coding-synonymous	DHRS4	NM_021004.2		1085,1644,3768	GG,GA,AA		9.4274,31.7583,29.352		31/279	24423090	3814,9180	2201	4296	6497	SO:0001819	synonymous_variant	10901	exon1			GCTCGCAAATAAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.93A>G	14.37:g.24423090A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			A|0.694;G|0.306	0.306	strong		0.662	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
HR	55806	hgsc.bcm.edu	37	8	21984596	21984596	+	Silent	SNP	C	C	T	rs78489044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:21984596C>T	ENST00000381418.4	-	3	2839	c.1359G>A	c.(1357-1359)tcG>tcA	p.S453S	HR_ENST00000312841.8_Silent_p.S453S	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	453					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)		TGTTCCCTATCGATGTGTCCC	0.662													C|||	18	0.00359425	0.0	0.0029	5008	,	,		13123	0.0		0.0159	False		,,,				2504	0.0				p.S453S		Atlas-SNP	.											HR,colon,carcinoma,-1,1	HR	71	1	0			c.G1359A						PASS	.	C	,	9,4345		0,9,2168	73.0	78.0	76.0		1359,1359	-11.7	0.0	8	dbSNP_132	76	104,8402		0,104,4149	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	0,113,6317	TT,TC,CC		1.2227,0.2067,0.8787	,	453/1190,453/1135	21984596	113,12747	2177	4253	6430	SO:0001819	synonymous_variant	55806	exon3			CCCTATCGATGTG	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.1359G>A	8.37:g.21984596C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			C|0.992;T|0.008	0.008	strong		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
EFCAB6	64800	hgsc.bcm.edu	37	22	44083442	44083442	+	Missense_Mutation	SNP	T	T	C	rs5764214	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:44083442T>C	ENST00000262726.7	-	11	1304	c.1051A>G	c.(1051-1053)Act>Gct	p.T351A	EFCAB6_ENST00000396231.2_Missense_Mutation_p.T199A|EFCAB6_ENST00000358439.4_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	351			T -> A (in dbSNP:rs5764214). {ECO:0000269|PubMed:14702039}.		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)				TTGATTTTAGTGGTGGCTTTA	0.328													T|||	2082	0.415735	0.5053	0.2867	5008	,	,		14884	0.2669		0.4573	False		,,,				2504	0.4969				p.T351A		Atlas-SNP	.											.	EFCAB6	177	.	0			c.A1051G						PASS	.	T	ALA/THR,ALA/THR	2205,2201	587.5+/-386.7	547,1111,545	59.0	59.0	59.0		1051,595	-3.8	0.0	22	dbSNP_114	59	4081,4519	559.1+/-387.3	944,2193,1163	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	58,58	1491,3304,1708	CC,CT,TT		47.4535,49.9546,48.3315	benign,benign	351/1502,199/1350	44083442	6286,6720	2203	4300	6503	SO:0001583	missense	64800	exon11			TTTTAGTGGTGGC	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.1051A>G	22.37:g.44083442T>C	ENSP00000262726:p.Thr351Ala	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	49	0.368421	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	830	0.38003663003663	237	0.4817073170731707	118	0.3259668508287293	136	0.23776223776223776	339	0.4472295514511873	T	6.692	0.496279	0.12762	0.500454	0.474535	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.07688	3.17;3.17	4.68	-3.84	0.04256	.	1.984030	0.02128	N	0.056195	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.46190	-0.9209	9	0.18710	T	0.47	0.2565	13.2868	0.60247	0.0:0.6849:0.0:0.3151	rs5764214;rs7284270;rs52791933;rs5764214	351;351	Q5THR3-6;Q5THR3	.;EFCB6_HUMAN	A	199;351	ENSP00000379533:T199A;ENSP00000262726:T351A	ENSP00000262726:T351A	T	-	1	0	EFCAB6	42414775	0.000000	0.05858	0.001000	0.08648	0.958000	0.62258	-1.233000	0.02934	-0.759000	0.04684	0.533000	0.62120	ACT	T|0.603;C|0.397	0.397	strong		0.328	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
ZNF749	388567	hgsc.bcm.edu	37	19	57955885	57955885	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57955885C>G	ENST00000334181.4	+	3	1619	c.1369C>G	c.(1369-1371)Cag>Gag	p.Q457E	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	457					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.Q457E(1)|p.Q370E(1)		breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		AGTTCAGCACCAGAAAATCCA	0.423																																					p.Q457E		Atlas-SNP	.											ZNF749,right_upper_lobe,carcinoma,0,14	ZNF749	75	14	2	Substitution - Missense(2)	endometrium(2)	c.C1369G						scavenged	.						92.0	89.0	90.0					19																	57955885		2203	4300	6503	SO:0001583	missense	388567	exon3			CAGCACCAGAAAA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1369C>G	19.37:g.57955885C>G	ENSP00000333980:p.Gln457Glu	Somatic	137	3	0.0218978		WXS	Illumina HiSeq	Phase_I	147	3	0.0204082	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410685	0.25465	.	.	ENSG00000186230	ENST00000334181	T	0.07327	3.2	1.62	0.523	0.17060	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06826	0.0174	L	0.38649	1.16	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.33904	-0.9850	9	0.52906	T	0.07	.	5.9852	0.19430	0.5886:0.4114:0.0:0.0	.	457	O43361	ZN749_HUMAN	E	457	ENSP00000333980:Q457E	ENSP00000333980:Q457E	Q	+	1	0	ZNF749	62647697	.	.	0.001000	0.08648	0.750000	0.42670	.	.	0.202000	0.20498	0.650000	0.86243	CAG	.	.	none		0.423	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
HSPG2	3339	hgsc.bcm.edu	37	1	22214127	22214127	+	Silent	SNP	A	A	G	rs2229478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	135	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	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	
IGFN1	91156	hgsc.bcm.edu	37	1	201181920	201181920	+	Silent	SNP	G	G	T	rs12060924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201181920G>T	ENST00000335211.4	+	12	8029	c.7899G>T	c.(7897-7899)ggG>ggT	p.G2633G	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_5'UTR	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	94	0	0		WXS	Illumina HiSeq	Phase_I	136	78	0.573529	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	
CYB5R3	1727	hgsc.bcm.edu	37	22	43032742	43032742	+	Silent	SNP	C	C	T	rs5996200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43032742C>T	ENST00000352397.5	-	2	384	c.132G>A	c.(130-132)ccG>ccA	p.P44P	CYB5R3_ENST00000407623.3_Silent_p.P21P|CYB5R3_ENST00000361740.4_Silent_p.P77P|CYB5R3_ENST00000407332.1_Silent_p.P21P|CYB5R3_ENST00000402438.1_Silent_p.P21P|CYB5R3_ENST00000396303.3_Silent_p.P21P	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	44	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				blood circulation (GO:0008015)|cholesterol biosynthetic process (GO:0006695)|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)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|hemoglobin complex (GO:0005833)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|FAD binding (GO:0071949)|flavin adenine dinucleotide binding (GO:0050660)|NAD binding (GO:0051287)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6					Flavin adenine dinucleotide(DB03147)	TGAGCCGCAGCGGGTACTTGA	0.632													C|||	369	0.0736821	0.0961	0.0951	5008	,	,		16206	0.001		0.1531	False		,,,				2504	0.0215				p.P77P		Atlas-SNP	.											CYB5R3_ENST00000361740,bladder,carcinoma,-1,2	CYB5R3	31	2	0			c.G231A						scavenged	.	C	,,,,	482,3924	221.0+/-238.3	29,424,1750	44.0	42.0	43.0		132,63,231,63,63	-2.2	1.0	22	dbSNP_114	43	1336,7264	256.5+/-280.9	97,1142,3061	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CYB5R3	NM_000398.6,NM_001129819.2,NM_001171660.1,NM_001171661.1,NM_007326.4	,,,,	126,1566,4811	TT,TC,CC		15.5349,10.9396,13.9782	,,,,	44/302,21/279,77/335,21/279,21/279	43032742	1818,11188	2203	4300	6503	SO:0001819	synonymous_variant	1727	exon2			CCGCAGCGGGTAC	M16461	CCDS14040.1, CCDS33658.1, CCDS54535.1	22q13.2	2012-10-02		2005-07-13	ENSG00000100243	ENSG00000100243	1.6.2.2		2873	protein-coding gene	gene with protein product		613213	"""diaphorase (NADH) (cytochrome b-5 reductase)"""	DIA1		2479590, 3268037	Standard	NM_001129819		Approved		uc011aps.2	P00387	OTTHUMG00000150745	ENST00000352397.5:c.132G>A	22.37:g.43032742C>T		Somatic	31	1	0.0322581		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Silent	SNP	ENST00000352397.5	37	CCDS33658.1																																																																																			C|0.882;T|0.118	0.118	strong		0.632	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1		
VPS51	738	hgsc.bcm.edu	37	11	64877197	64877197	+	Silent	SNP	C	C	T	rs61736623	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64877197C>T	ENST00000279281.3	+	7	1772	c.1680C>T	c.(1678-1680)ccC>ccT	p.P560P	AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000345348.5_5'Flank|TM7SF2_ENST00000540748.1_5'Flank|TM7SF2_ENST00000279263.7_5'Flank|VPS51_ENST00000527646.1_3'UTR	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	560					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CAGTGACGCCCGTGAGCACGC	0.642													c|||	140	0.0279553	0.003	0.0389	5008	,	,		19211	0.0655		0.0348	False		,,,				2504	0.0082				p.P560P		Atlas-SNP	.											.	.	.	.	0			c.C1680T						PASS	.	T		31,4361		0,31,2165	26.0	22.0	23.0		1680	-9.6	0.0	11	dbSNP_129	23	275,8299		3,269,4015	no	coding-synonymous	C11orf2	NM_013265.2		3,300,6180	TT,TC,CC		3.2074,0.7058,2.36		560/783	64877197	306,12660	2196	4287	6483	SO:0001819	synonymous_variant	738	exon7			GACGCCCGTGAGC	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"""fat-free homolog (zebrafish)"""	615738	"""chromosome 11 open reading frame 3"", ""chromosome 11 open reading frame 2"""	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.1680C>T	11.37:g.64877197C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Silent	SNP	ENST00000279281.3	37	CCDS8093.1	64	0.029304029304029304	4	0.008130081300813009	13	0.03591160220994475	19	0.033216783216783216	28	0.036939313984168866	c	0.838	-0.743015	0.03088	0.007058	0.032074	ENSG00000149823	ENST00000526856	.	.	.	4.8	-9.61	0.00550	.	0.055231	0.85682	D	0.000000	T	0.16428	0.0395	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59364	-0.7468	6	0.24483	T	0.36	-15.4675	10.0775	0.42368	0.0824:0.124:0.0816:0.712	rs61736623	.	.	.	L	58	.	ENSP00000435629:P58L	P	+	2	0	C11orf2	64633773	0.000000	0.05858	0.014000	0.15608	0.127000	0.20565	-4.504000	0.00224	-2.406000	0.00574	-0.974000	0.02594	CCG	C|0.974;T|0.026	0.026	strong		0.642	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265	
ITGB8	3696	hgsc.bcm.edu	37	7	20418678	20418678	+	Silent	SNP	C	C	T	rs3735619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20418678C>T	ENST00000222573.4	+	4	1077	c.393C>T	c.(391-393)gcC>gcT	p.A131A	SNORD56_ENST00000363883.1_RNA|ITGB8_ENST00000537992.1_5'UTR	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	131					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)	p.A131A(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AACTAGGAGCCGAAGCTAATT	0.323													C|||	803	0.160343	0.0998	0.072	5008	,	,		12866	0.4107		0.1004	False		,,,				2504	0.1084				p.A131A		Atlas-SNP	.											ITGB8,NS,carcinoma,0,1	ITGB8	159	1	1	Substitution - coding silent(1)	stomach(1)	c.C393T						PASS	.	C		490,3804		34,422,1691	61.0	71.0	67.0		393	-4.2	1.0	7	dbSNP_107	67	816,7754		41,734,3510	no	coding-synonymous	ITGB8	NM_002214.2		75,1156,5201	TT,TC,CC		9.5216,11.4113,10.1524		131/770	20418678	1306,11558	2147	4285	6432	SO:0001819	synonymous_variant	3696	exon4			AGGAGCCGAAGCT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.393C>T	7.37:g.20418678C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	126	78	0.619048	NM_002214	A4D133|B4DHD4	Silent	SNP	ENST00000222573.4	37	CCDS5370.1																																																																																			C|0.849;N|0.000	.	strong		0.323	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
CEP170B	283638	hgsc.bcm.edu	37	14	105352910	105352910	+	Silent	SNP	G	G	A	rs373896765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105352910G>A	ENST00000414716.3	+	12	2562	c.2334G>A	c.(2332-2334)acG>acA	p.T778T	CEP170B_ENST00000418279.1_Silent_p.T708T|CEP170B_ENST00000556508.1_Silent_p.T708T|CEP170B_ENST00000453495.1_Silent_p.T779T	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	778						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGGGGCCCACGTGGAGCAGGG	0.682																																					p.T778T		Atlas-SNP	.											.	.	.	.	0			c.G2334A						PASS	.	G	,	0,3656		0,0,1828	9.0	11.0	10.0		2334,2124	-6.8	0.0	14		10	3,8099		0,3,4048	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	0,3,5876	AA,AG,GG		0.037,0.0,0.0255	,	778/1555,708/1520	105352910	3,11755	1828	4051	5879	SO:0001819	synonymous_variant	283638	exon12			GCCCACGTGGAGC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.2334G>A	14.37:g.105352910G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			.	.	weak		0.682	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
WNT8A	7478	hgsc.bcm.edu	37	5	137426447	137426447	+	Silent	SNP	G	G	A	rs6596422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:137426447G>A	ENST00000398754.1	+	6	746	c.741G>A	c.(739-741)gcG>gcA	p.A247A	WNT8A_ENST00000506684.1_Silent_p.A265A	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	247					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCGCAGAGGCGGAACTGATCT	0.557													G|||	2352	0.469649	0.3185	0.4337	5008	,	,		20730	0.5843		0.494	False		,,,				2504	0.5562				p.A247A		Atlas-SNP	.											WNT8A,colon,carcinoma,+1,1	WNT8A	36	1	0			c.G741A						PASS	.	G		1317,2647		226,865,891	53.0	58.0	57.0		741	-8.1	0.3	5	dbSNP_116	57	3953,4385		939,2075,1155	no	coding-synonymous	WNT8A	NM_058244.2		1165,2940,2046	AA,AG,GG		47.4095,33.224,42.8386		247/352	137426447	5270,7032	1982	4169	6151	SO:0001819	synonymous_variant	7478	exon6			AGAGGCGGAACTG	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"""Wingless-type MMTV integration sites"""	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.741G>A	5.37:g.137426447G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_058244	Q96S51	Silent	SNP	ENST00000398754.1	37	CCDS43368.1																																																																																			G|0.519;A|0.481	0.481	strong		0.557	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244	
SEMA6D	80031	hgsc.bcm.edu	37	15	48063076	48063076	+	Silent	SNP	T	T	C	rs568215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:48063076T>C	ENST00000316364.5	+	19	2755	c.2316T>C	c.(2314-2316)ccT>ccC	p.P772P	SEMA6D_ENST00000358066.4_Silent_p.P710P|SEMA6D_ENST00000354744.4_Silent_p.P716P|SEMA6D_ENST00000389433.2_Silent_p.P753P|SEMA6D_ENST00000558014.1_Silent_p.P710P|SEMA6D_ENST00000389432.2_Silent_p.P729P|SEMA6D_ENST00000536845.2_Silent_p.P772P|SEMA6D_ENST00000537942.1_Silent_p.P710P|SEMA6D_ENST00000389428.3_Silent_p.P697P|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000355997.3_3'UTR	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	772					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTGCTCTTCCTACTCCTGAGT	0.527													C|||	3985	0.795727	0.9811	0.6527	5008	,	,		17316	0.8442		0.6352	False		,,,				2504	0.7618				p.P772P		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T2316C						PASS	.	C	,,,,,	4037,357	169.8+/-200.3	1859,319,19	59.0	61.0	60.0		2130,2130,2091,2148,2316,	-1.1	1.0	15	dbSNP_83	60	5223,3371	484.6+/-371.4	1598,2027,672	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3	SEMA6D	NM_001198999.1,NM_020858.1,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,	3457,2346,691	CC,CT,TT		39.225,8.1247,28.7034	,,,,,	710/1012,710/1012,697/999,716/1018,772/1074,	48063076	9260,3728	2197	4297	6494	SO:0001819	synonymous_variant	80031	exon19			TCTTCCTACTCCT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2316T>C	15.37:g.48063076T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			T|0.258;C|0.742	0.742	strong		0.527	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
TNK2	10188	hgsc.bcm.edu	37	3	195591056	195591056	+	Missense_Mutation	SNP	C	C	T	rs13433937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195591056C>T	ENST00000333602.6	-	15	3730	c.3113G>A	c.(3112-3114)cGc>cAc	p.R1038H	TNK2_ENST00000428187.1_Missense_Mutation_p.R1040H|TNK2_ENST00000392400.1_Missense_Mutation_p.R1038H|TNK2_ENST00000381916.2_Missense_Mutation_p.R1086H	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	1038			R -> H (in dbSNP:rs13433937). {ECO:0000269|PubMed:17344846}.	Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CGCATCTCAGCGCCTAGAGAA	0.602													C|||	81	0.0161741	0.0091	0.0288	5008	,	,		18139	0.002		0.0417	False		,,,				2504	0.0051				p.R1086H		Atlas-SNP	.											.	TNK2	246	.	0			c.G3257A						PASS	.	C	HIS/ARG,HIS/ARG	74,4332	65.8+/-103.3	1,72,2130	98.0	97.0	97.0		3113,3257	3.8	1.0	3	dbSNP_121	97	419,8181	129.5+/-187.6	12,395,3893	yes	missense,missense	TNK2	NM_005781.4,NM_001010938.1	29,29	13,467,6023	TT,TC,CC		4.8721,1.6795,3.7906	benign,benign	1038/1039,1086/1087	195591056	493,12513	2203	4300	6503	SO:0001583	missense	10188	exon15			TCTCAGCGCCTAG	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.3113G>A	3.37:g.195591056C>T	ENSP00000329425:p.Arg1038His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	48	0.02197802197802198	6	0.012195121951219513	8	0.022099447513812154	0	0.0	34	0.044854881266490766	C	16.12	3.032572	0.54790	0.016795	0.048721	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000416152;ENST00000428187;ENST00000392400	T;T;T;T;T	0.76448	-0.96;-1.02;2.75;-0.99;-0.96	4.69	3.81	0.43845	.	0.590344	0.18136	N	0.150561	T	0.33147	0.0853	L	0.29908	0.895	0.80722	D	1	B;B;B;D	0.57571	0.241;0.354;0.241;0.98	B;B;B;P	0.50231	0.011;0.037;0.011;0.635	T	0.60398	-0.7271	10	0.87932	D	0	.	8.4736	0.32999	0.0:0.8955:0.0:0.1045	rs13433937;rs52800150;rs13433937	1038;1086;1040;565	Q07912;Q07912-3;C9J1X3;B3KXJ4	ACK1_HUMAN;.;.;.	H	1038;1086;607;1040;1038	ENSP00000329425:R1038H;ENSP00000371341:R1086H;ENSP00000398614:R607H;ENSP00000392546:R1040H;ENSP00000376201:R1038H	ENSP00000329425:R1038H	R	-	2	0	TNK2	197075453	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	3.548000	0.53670	1.339000	0.45563	0.655000	0.94253	CGC	C|0.969;T|0.031	0.031	strong		0.602	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
TTLL13P	440307	hgsc.bcm.edu	37	15	90796558	90796558	+	Missense_Mutation	SNP	G	G	A	rs12912620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90796558G>A	ENST00000561573.1	+	4	640	c.376G>A	c.(376-378)Gct>Act	p.A126T	TTLL13_ENST00000438251.1_Missense_Mutation_p.A126T|TTLL13_ENST00000339615.5_Missense_Mutation_p.A126T																							GACAGACTGCGCTGTCTCACT	0.567													G|||	1983	0.395966	0.1838	0.4265	5008	,	,		19364	0.6885		0.2654	False		,,,				2504	0.4939				p.A126T		Atlas-SNP	.											TTLL13,brain,glioma,0,1	TTLL13	44	1	0			c.G376A						PASS	.	G	THR/ALA	844,3554	333.1+/-302.8	78,688,1433	150.0	98.0	116.0		376	3.1	1.0	15	dbSNP_121	116	2244,6352	375.5+/-337.8	277,1690,2331	yes	missense	TTLL13	NM_001029964.2	58	355,2378,3764	AA,AG,GG		26.1052,19.1905,23.7648	benign	126/460	90796558	3088,9906	2199	4298	6497	SO:0001583	missense	440307	exon4			GACTGCGCTGTCT																												ENST00000561573.1:c.376G>A	15.37:g.90796558G>A	ENSP00000456615:p.Ala126Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001029964		Missense_Mutation	SNP	ENST00000561573.1	37		791	0.36217948717948717	90	0.18292682926829268	137	0.3784530386740331	365	0.6381118881118881	199	0.262532981530343	G	14.71	2.616673	0.46736	0.191905	0.261052	ENSG00000213471	ENST00000438251;ENST00000339615	T;T	0.03772	3.82;3.81	5.41	3.08	0.35506	.	0.079729	0.53938	D	0.000052	T	0.00012	0.0000	L	0.34521	1.04	0.42541	P	0.0069270000000000165	B	0.22800	0.075	B	0.19148	0.024	T	0.10474	-1.0628	9	0.17832	T	0.49	.	8.1054	0.30883	0.1239:0.0:0.2625:0.6136	rs12912620;rs58063391;rs12912620	126	A6NNM8-2	.	T	126	ENSP00000413362:A126T;ENSP00000345294:A126T	ENSP00000345294:A126T	A	+	1	0	TTLL13	88597562	1.000000	0.71417	0.998000	0.56505	0.768000	0.43524	2.384000	0.44362	0.352000	0.24053	-1.527000	0.00925	GCT	G|0.710;A|0.290	0.290	strong		0.567	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1		
ZNF44	51710	hgsc.bcm.edu	37	19	12383540	12383540	+	Silent	SNP	G	G	C	rs56056044	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:12383540G>C	ENST00000356109.5	-	5	1792	c.1674C>G	c.(1672-1674)ggC>ggG	p.G558G	ZNF44_ENST00000355684.5_Silent_p.G510G	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	558					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		TGAAGGCTTTGCCACAAATTT	0.383													C|||	1022	0.204073	0.2269	0.1556	5008	,	,		20476	0.2569		0.168	False		,,,				2504	0.1902				p.G558G		Atlas-SNP	.											.	ZNF44	55	.	0			c.C1674G						PASS	.	C	,	876,3128		99,678,1225	56.0	57.0	57.0		1674,1530	-2.0	0.0	19	dbSNP_129	57	1345,7091		101,1143,2974	no	coding-synonymous,coding-synonymous	ZNF44	NM_001164276.1,NM_016264.3	,	200,1821,4199	CC,CG,GG		15.9436,21.8781,17.8537	,	558/664,510/616	12383540	2221,10219	2002	4218	6220	SO:0001819	synonymous_variant	51710	exon5			GGCTTTGCCACAA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1674C>G	19.37:g.12383540G>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Silent	SNP	ENST00000356109.5	37	CCDS54223.1																																																																																			G|0.778;C|0.222	0.222	strong		0.383	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264	
SCFD1	23256	hgsc.bcm.edu	37	14	31099738	31099738	+	Missense_Mutation	SNP	A	A	G	rs229150	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31099738A>G	ENST00000458591.2	+	3	415	c.188A>G	c.(187-189)aAg>aGg	p.K63R	SCFD1_ENST00000396629.2_Intron|SCFD1_ENST00000421551.3_Intron|SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000544052.2_5'UTR	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	63			K -> R (in dbSNP:rs229150). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		CTATCTGTGAAGGAGCTAAGA	0.323													A|||	2893	0.577676	0.7935	0.5029	5008	,	,		17065	0.7103		0.3608	False		,,,				2504	0.4254				p.K63R		Atlas-SNP	.											SCFD1,NS,carcinoma,0,1	SCFD1	43	1	0			c.A188G						PASS	.	A	ARG/LYS,	3123,1283	699.6+/-406.5	1127,869,207	152.0	159.0	157.0		188,	5.6	1.0	14	dbSNP_79	157	2940,5658	457.1+/-364.2	506,1928,1865	yes	missense,utr-5	SCFD1	NM_016106.2,NM_182835.1	26,	1633,2797,2072	GG,GA,AA		34.194,29.1194,46.6241	benign,	63/643,	31099738	6063,6941	2203	4299	6502	SO:0001583	missense	23256	exon3			CTGTGAAGGAGCT	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.188A>G	14.37:g.31099738A>G	ENSP00000390783:p.Lys63Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	1221	0.5590659340659341	388	0.7886178861788617	169	0.46685082872928174	405	0.708041958041958	259	0.341688654353562	A	15.51	2.853519	0.51270	0.708806	0.34194	ENSG00000092108	ENST00000458591;ENST00000557076	T;T	0.29917	1.55;1.55	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.49126	1.545	0.09310	P	1.0	B	0.17667	0.023	B	0.32928	0.155	T	0.25676	-1.0125	9	0.42905	T	0.14	-17.8222	15.7861	0.78304	1.0:0.0:0.0:0.0	rs229150;rs230378;rs17362188;rs17851559;rs52794734;rs60052190;rs229150	63	Q8WVM8	SCFD1_HUMAN	R	63;38	ENSP00000390783:K63R;ENSP00000450755:K38R	ENSP00000309417:K71R	K	+	2	0	SCFD1	30169489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.719000	0.91436	2.129000	0.65627	0.528000	0.53228	AAG	G|0.519;N|0.000	0.519	strong		0.323	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
MEGF6	1953	hgsc.bcm.edu	37	1	3418391	3418391	+	Silent	SNP	C	C	T	rs4648508	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3418391C>T	ENST00000356575.4	-	18	2509	c.2283G>A	c.(2281-2283)ccG>ccA	p.P761P	MEGF6_ENST00000294599.4_Silent_p.P656P	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	761	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)		TCCTCCCCGGCGGACACCGGC	0.706													C|||	1433	0.286142	0.1914	0.2882	5008	,	,		13912	0.3056		0.336	False		,,,				2504	0.3415				p.P761P	Ovarian(73;978 3658)	Atlas-SNP	.											MEGF6,colon,carcinoma,0,2	MEGF6	91	2	0			c.G2283A						PASS	.	C		753,3243		71,611,1316	22.0	30.0	27.0		2283	-7.2	0.2	1	dbSNP_111	27	2575,5717		410,1755,1981	no	coding-synonymous	MEGF6	NM_001409.3		481,2366,3297	TT,TC,CC		31.054,18.8438,27.0833		761/1542	3418391	3328,8960	1998	4146	6144	SO:0001819	synonymous_variant	1953	exon18			CCCCGGCGGACAC	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.2283G>A	1.37:g.3418391C>T		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	255	250	0.980392	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			C|0.703;T|0.297	0.297	strong		0.706	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
ZNF468	90333	hgsc.bcm.edu	37	19	53344919	53344919	+	Missense_Mutation	SNP	T	T	G	rs58239286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:53344919T>G	ENST00000595646.1	-	4	748	c.628A>C	c.(628-630)Atg>Ctg	p.M210L	ZNF468_ENST00000390651.4_Missense_Mutation_p.M157L|ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000396409.4_Missense_Mutation_p.M157L|ZNF28_ENST00000594602.1_Intron			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	210					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)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		TTTTCTCTCATGTGTACTTCC	0.323													-|||	1114	0.222444	0.3238	0.1326	5008	,	,		20903	0.0605		0.1491	False		,,,				2504	0.3916				p.M210L		Atlas-SNP	.											.	ZNF468	46	.	0			c.A628C						PASS	.	T	LEU/MET,LEU/MET	1348,3058	442.9+/-346.8	205,938,1060	85.0	86.0	86.0		628,469	0.3	0.0	19	dbSNP_129	86	1599,7001	294.2+/-301.7	152,1295,2853	yes	missense,missense	ZNF468	NM_001008801.1,NM_199132.1	15,15	357,2233,3913	GG,GT,TT		18.593,30.5946,22.6588	benign,benign	210/523,157/470	53344919	2947,10059	2203	4300	6503	SO:0001583	missense	90333	exon4			CTCTCATGTGTAC	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.628A>C	19.37:g.53344919T>G	ENSP00000470381:p.Met210Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	58	0.604167	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	368	0.1684981684981685	162	0.32926829268292684	59	0.16298342541436464	32	0.055944055944055944	115	0.1517150395778364	t	6.884	0.532532	0.13127	0.305946	0.18593	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	T;T	0.13901	2.55;2.55	1.38	0.328	0.15918	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.45877	-0.9231	8	0.66056	D	0.02	.	4.4541	0.11635	0.0:0.2097:0.0:0.7903	rs58239286;rs61744274	210	Q5VIY5	ZN468_HUMAN	L	210;157;157	ENSP00000379690:M157L;ENSP00000445669:M157L	ENSP00000243639:M210L	M	-	1	0	ZNF468	58036731	0.128000	0.22383	0.000000	0.03702	0.153000	0.21895	0.706000	0.25690	0.043000	0.15746	0.147000	0.16070	ATG	T|0.795;G|0.205	0.205	strong		0.323	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
POPDC3	64208	hgsc.bcm.edu	37	6	105609468	105609468	+	Missense_Mutation	SNP	C	C	T	rs11961225	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:105609468C>T	ENST00000254765.3	-	2	595	c.317G>A	c.(316-318)cGa>cAa	p.R106Q	POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA|BVES-AS1_ENST00000369120.2_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	122	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	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	
KIF20B	9585	hgsc.bcm.edu	37	10	91498318	91498318	+	Silent	SNP	A	A	G	rs1886998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91498318A>G	ENST00000371728.3	+	20	3785	c.3720A>G	c.(3718-3720)aaA>aaG	p.K1240K	KIF20B_ENST00000394289.2_Silent_p.K1240K|KIF20B_ENST00000416354.1_Silent_p.K1270K|KIF20B_ENST00000260753.4_Silent_p.K1200K|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1240					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						AAGATATGAAACATTTACTTC	0.279													G|||	1788	0.357029	0.4796	0.219	5008	,	,		18501	0.3085		0.2326	False		,,,				2504	0.4673				p.K1200K		Atlas-SNP	.											.	KIF20B	191	.	0			c.A3600G						PASS	.	G		1867,2279		421,1025,627	38.0	42.0	41.0		3600	-3.0	0.0	10	dbSNP_92	41	1941,6525		216,1509,2508	no	coding-synonymous	KIF20B	NM_016195.2		637,2534,3135	GG,GA,AA		22.927,45.0314,30.1935		1200/1781	91498318	3808,8804	2073	4233	6306	SO:0001819	synonymous_variant	9585	exon20			TATGAAACATTTA	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.3720A>G	10.37:g.91498318A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				A|0.706;G|0.294	0.294	strong		0.279	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
WWC1	23286	hgsc.bcm.edu	37	5	167891830	167891830	+	Silent	SNP	T	T	C	rs3203960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:167891830T>C	ENST00000265293.4	+	21	3515	c.3013T>C	c.(3013-3015)Ttg>Ctg	p.L1005L	WWC1_ENST00000521089.1_Silent_p.L1011L|WWC1_ENST00000522140.1_3'UTR	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	1005	Interaction with histone H3.				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)		GCACAGCCAATTGACCCAGGA	0.602													C|||	1698	0.339058	0.4009	0.3329	5008	,	,		17703	0.0407		0.4463	False		,,,				2504	0.4571				p.L1011L		Atlas-SNP	.											.	WWC1	98	.	0			c.T3031C						PASS	.	C	,,	1734,2672	647.5+/-398.6	333,1068,802	76.0	73.0	74.0		3031,3031,3013	5.1	1.0	5	dbSNP_105	74	3581,5019	627.1+/-397.9	764,2053,1483	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	1097,3121,2285	CC,CT,TT		41.6395,39.3554,40.8658	,,	1011/1120,1011/1119,1005/1114	167891830	5315,7691	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon21			AGCCAATTGACCC	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.3013T>C	5.37:g.167891830T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001161662	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	695	0.3182234432234432	197	0.40040650406504064	130	0.35911602209944754	17	0.02972027972027972	351	0.4630606860158311	C	6.375	0.437319	0.12104	0.393554	0.416395	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44050	-0.9353	3	.	.	.	.	13.9056	0.63834	0.0:0.9268:0.0:0.0732	rs3203960;rs17633483;rs17845558;rs17858456;rs60748229;rs3203960	.	.	.	T	972;781	.	.	I	+	2	0	WWC1	167824408	1.000000	0.71417	1.000000	0.80357	0.506000	0.33950	1.673000	0.37534	1.189000	0.43028	-0.227000	0.12334	ATT	T|0.625;C|0.375	0.375	strong		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
CHAMP1	283489	hgsc.bcm.edu	37	13	115090019	115090019	+	Silent	SNP	G	G	A	rs3813131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115090019G>A	ENST00000361283.1	+	3	1011	c.702G>A	c.(700-702)ccG>ccA	p.P234P		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	234	Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CTCATTTCCCGGAAACATTGG	0.527													g|||	984	0.196486	0.3578	0.1787	5008	,	,		19683	0.1062		0.0835	False		,,,				2504	0.2004				p.P234P		Atlas-SNP	.											.	.	.	.	0			c.G702A						PASS	.	A	,,	1256,3150	431.2+/-342.8	173,910,1120	88.0	101.0	97.0		702,702,702	2.4	1.0	13	dbSNP_107	97	606,7994	159.4+/-212.7	21,564,3715	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF828	NM_001164144.1,NM_001164145.1,NM_032436.2	,,	194,1474,4835	AA,AG,GG		7.0465,28.5066,14.3165	,,	234/813,234/813,234/813	115090019	1862,11144	2203	4300	6503	SO:0001819	synonymous_variant	283489	exon3			TTTCCCGGAAACA	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.702G>A	13.37:g.115090019G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	37	CCDS9545.1																																																																																			G|0.835;A|0.165	0.165	strong		0.527	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
GLI4	2738	hgsc.bcm.edu	37	8	144358381	144358381	+	Missense_Mutation	SNP	G	G	A	rs1056148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144358381G>A	ENST00000523522.1	+	3	577	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	GLI4_ENST00000523812.1_3'UTR|GLI4_ENST00000340042.1_Missense_Mutation_p.A180T|ZFP41_ENST00000522452.1_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	27	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	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		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604885	33604885	+	Splice_Site	SNP	C	C	T	rs2273117	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	31	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	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
ABL1	25	hgsc.bcm.edu	37	9	133761001	133761001	+	Silent	SNP	A	A	G	rs1056171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133761001A>G	ENST00000318560.5	+	11	3705	c.3324A>G	c.(3322-3324)ccA>ccG	p.P1108P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1108	F-actin-binding.				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)	GCAGTGGTCCAGCGGCCACTC	0.557			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								G|||	3276	0.654153	0.882	0.6974	5008	,	,		18771	0.5952		0.4881	False		,,,				2504	0.547				p.P1127P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	0			c.A3381G						scavenged	.	G	,	3592,814	300.1+/-286.2	1470,652,81	29.0	34.0	32.0		3324,3381	-10.5	0.2	9	dbSNP_86	32	4015,4585	586.5+/-392.0	924,2167,1209	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	2394,2819,1290	GG,GA,AA		46.686,18.4748,41.5116	,	1108/1131,1127/1150	133761001	7607,5399	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			TGGTCCAGCGGCC	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.3324A>G	9.37:g.133761001A>G		Somatic	108	2	0.0185185		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.391;G|0.609	0.609	strong		0.557	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
DSE	29940	hgsc.bcm.edu	37	6	116720487	116720487	+	Missense_Mutation	SNP	C	C	T	rs10485183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116720487C>T	ENST00000331677.3	+	3	518	c.74C>T	c.(73-75)aCc>aTc	p.T25I	DSE_ENST00000359564.2_Missense_Mutation_p.T25I|DSE_ENST00000452085.3_Missense_Mutation_p.T25I|DSE_ENST00000537543.1_Missense_Mutation_p.T44I|DSE_ENST00000540275.1_3'UTR			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	25			T -> I (in dbSNP:rs10485183).		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)		GCCTACATCACCGACGAGAAC	0.512													C|||	684	0.136581	0.0908	0.2046	5008	,	,		18041	0.0169		0.2734	False		,,,				2504	0.1329				p.T25I		Atlas-SNP	.											DSE,rectum,carcinoma,-1,1	DSE	98	1	0			c.C74T						PASS	.	C	ILE/THR,ILE/THR	607,3799	264.7+/-266.2	39,529,1635	89.0	78.0	82.0		74,74	4.8	0.2	6	dbSNP_119	82	2783,5817	441.7+/-359.9	455,1873,1972	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	89,89	494,2402,3607	TT,TC,CC		32.3605,13.7767,26.0649	benign,benign	25/959,25/959	116720487	3390,9616	2203	4300	6503	SO:0001583	missense	29940	exon2			ACATCACCGACGA	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.74C>T	6.37:g.116720487C>T	ENSP00000332151:p.Thr25Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	361	0.1652930402930403	48	0.0975609756097561	90	0.24861878453038674	17	0.02972027972027972	206	0.2717678100263852	C	12.67	2.007432	0.35415	0.137767	0.323605	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.65	4.77	0.60923	.	0.345981	0.33610	N	0.004734	T	0.14141	0.0342	L	0.36672	1.1	0.29795	P	0.832921	B;B	0.27791	0.189;0.062	B;B	0.33254	0.16;0.048	T	0.06267	-1.0836	9	0.52906	T	0.07	-9.9049	16.6514	0.85203	0.0:0.8702:0.1298:0.0	rs10485183;rs10485183	44;25	B7Z765;Q9UL01	.;DSE_HUMAN	I	25;25;44;25;25	ENSP00000397597:T25I;ENSP00000404049:T25I;ENSP00000441152:T44I;ENSP00000332151:T25I;ENSP00000352567:T25I	ENSP00000332151:T25I	T	+	2	0	DSE	116827180	0.001000	0.12720	0.234000	0.24042	0.710000	0.40934	0.555000	0.23422	1.593000	0.50029	0.655000	0.94253	ACC	C|0.500;T|0.500	0.500	strong		0.512	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
CXorf58	254158	hgsc.bcm.edu	37	X	23928489	23928489	+	Missense_Mutation	SNP	C	C	T	rs2707164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:23928489C>T	ENST00000379211.3	+	2	619	c.70C>T	c.(70-72)Cgc>Tgc	p.R24C	APOO_ENST00000379220.3_5'Flank|APOO_ENST00000379226.4_5'Flank	NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	24			R -> C (in dbSNP:rs2707164). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						ACAAAAAGTTCGCAGAGTACA	0.373													C|||	1397	0.370066	0.1505	0.4294	3775	,	,		15069	0.2381		0.5139	False		,,,				2504	0.1462				p.R24C		Atlas-SNP	.											.	CXorf58	53	.	0			c.C70T						PASS	.	C	CYS/ARG,CYS/ARG	942,2893		112,572,146,948,425	131.0	96.0	108.0		70,70	-0.7	0.0	X	dbSNP_100	108	4745,1983		1222,987,1314,219,558	yes	missense,missense	CXorf58	NM_001169574.1,NM_152761.2	180,180	1334,1559,1460,1167,983	TT,TC,T,CC,C		29.4738,24.5632,46.1611	probably-damaging,probably-damaging	24/331,24/333	23928489	5687,4876	2203	4300	6503	SO:0001583	missense	254158	exon2			AAAGTTCGCAGAG	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.70C>T	X.37:g.23928489C>T	ENSP00000368511:p.Arg24Cys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_152761		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	772	0.4653405666063894	69	0.15065502183406113	104	0.4126984126984127	99	0.21153846153846154	260	0.49429657794676807	C	6.635	0.485625	0.12641	0.245632	0.705262	ENSG00000165182	ENST00000379211	T	0.32753	1.44	3.44	-0.668	0.11392	.	1.597720	0.03958	N	0.289533	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.67145	0.996	P	0.47573	0.55	T	0.42932	-0.9422	9	0.37606	T	0.19	10.0265	6.5671	0.22519	0.0:0.3254:0.5532:0.1214	rs2707164;rs17322469;rs52793631;rs58445345;rs2707164	24	Q96LI9	CX058_HUMAN	C	24	ENSP00000368511:R24C	ENSP00000368511:R24C	R	+	1	0	CXorf58	23838410	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.158000	0.16422	-0.274000	0.09232	0.600000	0.82982	CGC	0|0.003;T|0.491	0.491	strong		0.373	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	
FNDC1	84624	hgsc.bcm.edu	37	6	159621087	159621087	+	Missense_Mutation	SNP	C	C	T	rs62432291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:159621087C>T	ENST00000297267.9	+	3	564	c.364C>T	c.(364-366)Cct>Tct	p.P122S	FNDC1_ENST00000340366.6_Missense_Mutation_p.P122S	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	122	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.			P -> S (in Ref. 4; AAI50608). {ECO:0000305}.	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)		AGTGAGCCGTCCTGTTTACAG	0.478													C|||	147	0.029353	0.0038	0.0793	5008	,	,		16665	0.001		0.0517	False		,,,				2504	0.0348				p.P122S		Atlas-SNP	.											.	FNDC1	250	.	0			c.C364T						PASS	.	C	SER/PRO	54,3840		0,54,1893	85.0	85.0	85.0		364	5.9	1.0	6	dbSNP_129	85	489,7787		17,455,3666	yes	missense	FNDC1	NM_032532.2	74	17,509,5559	TT,TC,CC		5.9087,1.3867,4.4618	probably-damaging	122/1895	159621087	543,11627	1947	4138	6085	SO:0001583	missense	84624	exon3			AGCCGTCCTGTTT	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.364C>T	6.37:g.159621087C>T	ENSP00000297267:p.Pro122Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	54|54	0.024725274725274724|0.024725274725274724	3|3	0.006097560975609756|0.006097560975609756	18|18	0.049723756906077346|0.049723756906077346	1|1	0.0017482517482517483|0.0017482517482517483	32|32	0.04221635883905013|0.04221635883905013	C|C	18.49|18.49	3.634974|3.634974	0.67130|0.67130	0.013867|0.013867	0.059087|0.059087	ENSG00000164694|ENSG00000164694	ENST00000297267;ENST00000340366|ENST00000329629	T;T|.	0.56611|.	0.45;0.45|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Fibronectin, type III (2);Immunoglobulin-like fold (1);|.	0.179987|.	0.38058|.	N|.	0.001838|.	T|T	0.27454|0.27454	0.0674|0.0674	N|N	0.19112|0.19112	0.55|0.55	0.32528|0.32528	N|N	0.535278|0.535278	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.16837|0.16837	-1.0389|-1.0389	10|5	0.87932|.	D|.	0|.	-14.3351|-14.3351	15.8813|15.8813	0.79207|0.79207	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs62432291|rs62432291	122;122|.	Q4ZHG4-2;Q4ZHG4|.	.;FNDC1_HUMAN|.	S|F	122|80	ENSP00000297267:P122S;ENSP00000342460:P122S|.	ENSP00000297267:P122S|.	P|S	+|+	1|2	0|0	FNDC1|FNDC1	159541075|159541075	0.997000|0.997000	0.39634|0.39634	0.965000|0.965000	0.40720|0.40720	0.954000|0.954000	0.61252|0.61252	3.083000|3.083000	0.50136|0.50136	2.821000|2.821000	0.97095|0.97095	0.650000|0.650000	0.86243|0.86243	CCT|TCC	C|0.972;T|0.028	0.028	strong		0.478	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
ZNF230	7773	hgsc.bcm.edu	37	19	44515492	44515492	+	Missense_Mutation	SNP	T	T	A	rs6413542	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44515492T>A	ENST00000429154.2	+	5	1529	c.1301T>A	c.(1300-1302)tTc>tAc	p.F434Y		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	434			F -> Y (in dbSNP:rs6413542).		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)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				CACCGGTCTTTCTGTAAAGAC	0.428													T|||	27	0.00539137	0.0	0.0014	5008	,	,		16061	0.0		0.0239	False		,,,				2504	0.002				p.F434Y	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.T1301A						PASS	.	T	TYR/PHE	4,4402	8.1+/-20.4	0,4,2199	53.0	58.0	56.0		1301	-1.1	0.0	19	dbSNP_116	56	95,8505	49.8+/-109.6	0,95,4205	yes	missense	ZNF230	NM_006300.3	22	0,99,6404	AA,AT,TT		1.1047,0.0908,0.7612	benign	434/475	44515492	99,12907	2203	4300	6503	SO:0001583	missense	7773	exon5			GGTCTTTCTGTAA	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"""Zinc fingers, C2H2-type"", ""-"""	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.1301T>A	19.37:g.44515492T>A	ENSP00000409318:p.Phe434Tyr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	23	0.010531135531135532	0	0.0	0	0.0	0	0.0	23	0.030343007915567283	T	0.541	-0.853455	0.02630	9.08E-4	0.011047	ENSG00000159882	ENST00000429154	T	0.14640	2.49	2.55	-1.12	0.09808	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01156	0.0038	N	0.02751	-0.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42799	-0.9430	9	0.09590	T	0.72	.	2.3511	0.04283	0.2475:0.0:0.2858:0.4666	rs6413542;rs52791695;rs6413542	434	Q9UIE0	ZN230_HUMAN	Y	434	ENSP00000409318:F434Y	ENSP00000409318:F434Y	F	+	2	0	ZNF230	49207332	0.000000	0.05858	0.000000	0.03702	0.423000	0.31445	-0.228000	0.09114	-0.182000	0.10602	-1.285000	0.01374	TTC	T|0.992;A|0.008	0.008	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
SLC9C2	284525	hgsc.bcm.edu	37	1	173516871	173516871	+	Missense_Mutation	SNP	G	G	C	rs16846206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:173516871G>C	ENST00000367714.3	-	13	1936	c.1514C>G	c.(1513-1515)gCt>gGt	p.A505G	SLC9C2_ENST00000536496.1_Missense_Mutation_p.A403G|SLC9C2_ENST00000466087.1_5'UTR	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	90	0	0		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	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	
KIF20B	9585	hgsc.bcm.edu	37	10	91470834	91470834	+	Silent	SNP	A	A	C	rs1048057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91470834A>C	ENST00000371728.3	+	6	672	c.607A>C	c.(607-609)Agg>Cgg	p.R203R	KIF20B_ENST00000394289.2_Silent_p.R203R|KIF20B_ENST00000416354.1_Silent_p.R203R|KIF20B_ENST00000260753.4_Silent_p.R203R	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	203	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.R203R(1)		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						AGAATACTTAAGGTTATCATC	0.323													C|||	2321	0.463458	0.5749	0.3847	5008	,	,		20058	0.5665		0.2396	False		,,,				2504	0.4928				p.R203R		Atlas-SNP	.											KIF20B,NS,carcinoma,0,1	KIF20B	191	1	1	Substitution - coding silent(1)	stomach(1)	c.A607C						PASS	.	C		2405,2001	551.7+/-378.3	654,1097,452	67.0	72.0	70.0		607	3.5	1.0	10	dbSNP_86	70	2076,6522	715.3+/-406.0	237,1602,2460	no	coding-synonymous	KIF20B	NM_016195.2		891,2699,2912	CC,CA,AA		24.1452,45.4153,34.4586		203/1781	91470834	4481,8523	2203	4299	6502	SO:0001819	synonymous_variant	9585	exon6			TACTTAAGGTTAT	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.607A>C	10.37:g.91470834A>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				A|0.632;C|0.368	0.368	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
DEPDC7	91614	hgsc.bcm.edu	37	11	33054856	33054856	+	Missense_Mutation	SNP	C	C	T	rs17852859	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:33054856C>T	ENST00000241051.3	+	9	1483	c.1391C>T	c.(1390-1392)aCa>aTa	p.T464I	DEPDC7_ENST00000311388.3_Missense_Mutation_p.T455I	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	464			T -> I (in dbSNP:rs17852859). {ECO:0000269|PubMed:15489334}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						TCCAACAATACAGAGAAGACA	0.308													C|||	70	0.0139776	0.0015	0.0216	5008	,	,		17100	0.0		0.0447	False		,,,				2504	0.0082				p.T464I		Atlas-SNP	.											.	DEPDC7	94	.	0			c.C1391T						PASS	.	C	ILE/THR,ILE/THR	28,3590		1,26,1782	71.0	68.0	69.0		1391,1364	2.3	0.1	11	dbSNP_123	69	328,7800		11,306,3747	yes	missense,missense	DEPDC7	NM_001077242.1,NM_139160.2	89,89	12,332,5529	TT,TC,CC		4.0354,0.7739,3.0308	benign,benign	464/512,455/503	33054856	356,11390	1809	4064	5873	SO:0001583	missense	91614	exon9			ACAATACAGAGAA		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.1391C>T	11.37:g.33054856C>T	ENSP00000241051:p.Thr464Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Missense_Mutation	SNP	ENST00000241051.3	37	CCDS41632.1	41	0.018772893772893772	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	33	0.04353562005277045	C	0.730	-0.780275	0.02929	0.007739	0.040354	ENSG00000121690	ENST00000241051;ENST00000311388	D;D	0.83673	-1.75;-1.75	5.33	2.33	0.28932	.	0.341223	0.33753	N	0.004594	T	0.35008	0.0917	N	0.13043	0.29	0.09310	N	1	B;B	0.13594	0.008;0.002	B;B	0.13407	0.009;0.002	T	0.46020	-0.9221	10	0.45353	T	0.12	-21.0409	8.2954	0.31982	0.1273:0.7382:0.0:0.1345	rs17852859	455;464	G5E941;Q96QD5	.;DEPD7_HUMAN	I	464;455	ENSP00000241051:T464I;ENSP00000308971:T455I	ENSP00000241051:T464I	T	+	2	0	DEPDC7	33011432	0.000000	0.05858	0.116000	0.21606	0.013000	0.08279	0.099000	0.15210	0.279000	0.22186	0.460000	0.39030	ACA	C|0.977;T|0.023	0.023	strong		0.308	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
CTNNAL1	8727	hgsc.bcm.edu	37	9	111755008	111755008	+	Silent	SNP	C	C	T	rs2297581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111755008C>T	ENST00000325551.4	-	3	509	c.423G>A	c.(421-423)gtG>gtA	p.V141V	CTNNAL1_ENST00000374595.4_Silent_p.V141V|CTNNAL1_ENST00000325580.6_Silent_p.V141V|RNA5-8SP3_ENST00000364357.1_RNA|CTNNAL1_ENST00000374593.4_Silent_p.V141V	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	141					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		CAGCCTTTATCACTCCTGTTT	0.378													C|||	993	0.198283	0.0166	0.3228	5008	,	,		21396	0.3145		0.2674	False		,,,				2504	0.1646				p.V141V		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.G423A						PASS	.	C		255,4151	145.4+/-180.2	16,223,1964	128.0	120.0	123.0		423	-7.3	0.9	9	dbSNP_100	123	2434,6166	402.8+/-347.6	333,1768,2199	no	coding-synonymous	CTNNAL1	NM_003798.2		349,1991,4163	TT,TC,CC		28.3023,5.7876,20.6751		141/735	111755008	2689,10317	2203	4300	6503	SO:0001819	synonymous_variant	8727	exon3			CTTTATCACTCCT	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"""alpha-catulin"", ""alpha2-catulin"""	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.423G>A	9.37:g.111755008C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	215	107	0.497674	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Silent	SNP	ENST00000325551.4	37	CCDS6775.1																																																																																			C|0.775;A|0.002	.	strong		0.378	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798	
TRMT2A	27037	hgsc.bcm.edu	37	22	20103263	20103263	+	Missense_Mutation	SNP	G	G	T	rs9605067|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103263G>T	ENST00000252136.7	-	3	1028	c.640C>A	c.(640-642)Ctc>Atc	p.L214I	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.L214I|RANBP1_ENST00000430524.1_5'Flank|RANBP1_ENST00000331821.3_5'Flank|TRMT2A_ENST00000439169.2_Missense_Mutation_p.L214I|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.L214I	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	214					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						CTCTGCTCGAGCAGCCAGGGC	0.637													G|||	59	0.0117812	0.0023	0.013	5008	,	,		17914	0.0		0.0378	False		,,,				2504	0.0092				p.L214I		Atlas-SNP	.											.	TRMT2A	34	.	0			c.C640A						PASS	.	G	ILE/LEU,ILE/LEU	27,4377	33.5+/-64.1	1,25,2176	45.0	42.0	43.0		640,640	-1.0	0.3	22	dbSNP_119	43	326,8274	113.7+/-173.7	12,302,3986	yes	missense,missense	TRMT2A	NM_022727.4,NM_182984.3	5,5	13,327,6162	TT,TG,GG		3.7907,0.6131,2.7145	benign,benign	214/626,214/626	20103263	353,12651	2202	4300	6502	SO:0001583	missense	27037	exon3			GCTCGAGCAGCCA	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.640C>A	22.37:g.20103263G>T	ENSP00000252136:p.Leu214Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	37	CCDS13774.1	32	0.014652014652014652	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	9.951	1.220275	0.22457	0.006131	0.037907	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169	T;T;T	0.44482	0.92;0.92;0.92	5.37	-1.03	0.10102	.	0.284900	0.40385	N	0.001117	T	0.05868	0.0153	L	0.43923	1.385	0.22796	N	0.998726	B;B;B;B	0.10296	0.003;0.001;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.001	T	0.04621	-1.0938	10	0.25106	T	0.35	-17.0401	0.75	0.00989	0.4301:0.1753:0.2184:0.1762	rs9605067	214;214;214;214	B4E213;F2Z2W7;Q8IZ69-2;Q8IZ69	.;.;.;TRM2A_HUMAN	I	214	ENSP00000252136:L214I;ENSP00000385807:L214I;ENSP00000395738:L214I	ENSP00000252136:L214I	L	-	1	0	TRMT2A	18483263	1.000000	0.71417	0.273000	0.24645	0.285000	0.27093	2.279000	0.43435	0.010000	0.14839	-0.273000	0.10243	CTC	G|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
OR52I2	143502	hgsc.bcm.edu	37	11	4608542	4608542	+	Missense_Mutation	SNP	C	C	T	rs1847632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4608542C>T	ENST00000312614.4	+	1	522	c.500C>T	c.(499-501)aCg>aTg	p.T167M		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	167			T -> M (in dbSNP:rs1847632).			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(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGAATTCTCACGCCTCAAGTG	0.512													C|||	2061	0.411542	0.2852	0.4121	5008	,	,		23130	0.5585		0.326	False		,,,				2504	0.5184				p.T167M		Atlas-SNP	.											.	OR52I2	50	.	0			c.C500T						PASS	.	C	MET/THR	1210,3192	413.5+/-336.5	186,838,1177	64.0	65.0	65.0		500	3.3	0.8	11	dbSNP_92	65	2416,6180	398.8+/-346.2	348,1720,2230	no	missense	OR52I2	NM_001005170.2	81	534,2558,3407	TT,TC,CC		28.1061,27.4875,27.8966	probably-damaging	167/351	4608542	3626,9372	2201	4298	6499	SO:0001583	missense	143502	exon1			TTCTCACGCCTCA	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.500C>T	11.37:g.4608542C>T	ENSP00000308764:p.Thr167Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	155	71	0.458065	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	851	0.38965201465201466	118	0.23983739837398374	140	0.3867403314917127	330	0.5769230769230769	263	0.3469656992084433	C	8.772	0.926203	0.18056	0.274875	0.281061	ENSG00000226288	ENST00000312614	T	0.45668	0.89	4.18	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000314	T	0.00012	0.0000	H	0.95679	3.705	0.40828	P	0.016430999999999973	D	0.89917	1.0	D	0.68943	0.961	T	0.48175	-0.9058	9	0.87932	D	0	-12.5133	6.9968	0.24786	0.0:0.7261:0.1779:0.0959	rs1847632;rs61277460;rs1847632	167	Q8NH67	O52I2_HUMAN	M	167	ENSP00000308764:T167M	ENSP00000308764:T167M	T	+	2	0	OR52I2	4565118	0.055000	0.20627	0.810000	0.32431	0.089000	0.18198	0.878000	0.28126	0.984000	0.38629	-0.168000	0.13345	ACG	C|0.676;T|0.324	0.324	strong		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
KLC2	64837	hgsc.bcm.edu	37	11	66031660	66031660	+	Silent	SNP	C	C	T	rs1151539	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:66031660C>T	ENST00000417856.1	+	8	1329	c.1086C>T	c.(1084-1086)gaC>gaT	p.D362D	KLC2_ENST00000394078.1_Intron|KLC2_ENST00000394067.2_Silent_p.D362D|RP11-867G23.1_ENST00000530805.1_RNA|KLC2_ENST00000394065.2_Silent_p.D223D|KLC2_ENST00000394066.2_Silent_p.D285D|KLC2_ENST00000316924.5_Silent_p.D362D|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000421552.1_Silent_p.D285D	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	362					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						GGCCCGATGACCCCAATGTGG	0.592													C|||	1664	0.332268	0.205	0.5086	5008	,	,		17224	0.252		0.4841	False		,,,				2504	0.3057				p.D362D		Atlas-SNP	.											.	KLC2	50	.	0			c.C1086T						PASS	.	C	,,,	1083,3301		137,809,1246	28.0	22.0	24.0		855,1086,1086,1086	2.4	1.0	11	dbSNP_87	24	3972,4602		920,2132,1235	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLC2	NM_001134774.1,NM_001134775.1,NM_001134776.1,NM_022822.2	,,,	1057,2941,2481	TT,TC,CC		46.3261,24.7035,39.0106	,,,	285/546,362/623,362/623,362/623	66031660	5055,7903	2192	4287	6479	SO:0001819	synonymous_variant	64837	exon8			CGATGACCCCAAT	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.1086C>T	11.37:g.66031660C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_022822	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Silent	SNP	ENST00000417856.1	37	CCDS8130.1																																																																																			C|0.642;T|0.358	0.358	strong		0.592	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
CLYBL	171425	hgsc.bcm.edu	37	13	100518580	100518580	+	Missense_Mutation	SNP	A	A	G	rs3783185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:100518580A>G	ENST00000376360.1	+	6	748	c.721A>G	c.(721-723)Ata>Gta	p.I241V	CLYBL_ENST00000339105.4_Missense_Mutation_p.I241V|CLYBL_ENST00000444838.2_Missense_Mutation_p.I207V|CLYBL_ENST00000376355.3_Missense_Mutation_p.I207V|CLYBL_ENST00000376354.1_Missense_Mutation_p.I207V			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	241			I -> V (in dbSNP:rs3783185). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TCTCCAAGCCATAGATCTGGT	0.478													A|||	4132	0.82508	0.9047	0.7536	5008	,	,		15807	0.877		0.7356	False		,,,				2504	0.8067				p.I241V		Atlas-SNP	.											CLYBL,NS,adenoma,0,1	CLYBL	48	1	0			c.A721G						scavenged	.	A	VAL/ILE	3843,563	774.4+/-414.0	1680,483,40	104.0	103.0	103.0		721	3.2	1.0	13	dbSNP_107	103	6081,2519	693.9+/-404.7	2134,1813,353	yes	missense	CLYBL	NM_206808.2	29	3814,2296,393	GG,GA,AA		29.2907,12.778,23.6968	benign	241/341	100518580	9924,3082	2203	4300	6503	SO:0001583	missense	171425	exon6			CAAGCCATAGATC	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.721A>G	13.37:g.100518580A>G	ENSP00000365538:p.Ile241Val	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	1765	0.8081501831501832	430	0.8739837398373984	277	0.7651933701657458	509	0.8898601398601399	549	0.7242744063324539	A	15.23	2.772797	0.49680	0.87222	0.707093	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105;ENST00000419700	T;T;T;T;T;T	0.56103	1.37;1.37;1.37;1.37;1.37;0.48	5.66	3.17	0.36434	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.040925	0.85682	N	0.000000	T	0.00012	0.0000	M	0.62016	1.91	0.09310	P	0.99999839348	B;B	0.24368	0.102;0.058	B;B	0.43950	0.437;0.232	T	0.14980	-1.0453	9	0.40728	T	0.16	-2.533	10.0377	0.42139	0.8009:0.0:0.1991:0.0	rs3783185;rs17474250;rs56419906;rs59153602;rs3783185	207;241	B4DU60;Q8N0X4	.;CLYBL_HUMAN	V	207;241;207;207;241;4	ENSP00000365533:I207V;ENSP00000365538:I241V;ENSP00000404768:I207V;ENSP00000365532:I207V;ENSP00000342991:I241V;ENSP00000396574:I4V	ENSP00000342991:I241V	I	+	1	0	CLYBL	99316581	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	4.849000	0.62882	0.479000	0.27511	0.477000	0.44152	ATA	A|0.202;G|0.798	0.798	strong		0.478	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
ZNF598	90850	hgsc.bcm.edu	37	16	2049003	2049003	+	Missense_Mutation	SNP	A	A	T	rs2286468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2049003A>T	ENST00000563630.1	-	10	2250	c.2008T>A	c.(2008-2010)Tgt>Agt	p.C670S	ZNF598_ENST00000431526.1_Missense_Mutation_p.C725S|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Missense_Mutation_p.C670S			Q86UK7	ZN598_HUMAN	zinc finger protein 598	725	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						CTGGGGACACAGGCCGGGTGG	0.706													A|||	1235	0.246605	0.4682	0.1282	5008	,	,		9816	0.3194		0.1382	False		,,,				2504	0.0675				p.C725S		Atlas-SNP	.											.	ZNF598	55	.	0			c.T2173A						PASS	.	A	SER/CYS	1181,2311		207,767,772	4.0	5.0	4.0		2175	2.9	0.7	16	dbSNP_100	4	873,6775		77,719,3028	no	missense	ZNF598	NM_178167.2	112	284,1486,3800	TT,TA,AA		11.4147,33.8202,18.4381	possibly-damaging	725/905	2049003	2054,9086	1746	3824	5570	SO:0001583	missense	90850	exon12			GGACACAGGCCGG	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.2008T>A	16.37:g.2049003A>T	ENSP00000455882:p.Cys670Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		557	0.25503663003663	214	0.4349593495934959	50	0.13812154696132597	191	0.3339160839160839	102	0.1345646437994723	.	0.016	-1.513109	0.00975	0.338202	0.114147	ENSG00000167962	ENST00000431526	T	0.15372	2.43	3.99	2.87	0.33458	.	0.541948	0.21004	N	0.081811	T	0.00012	0.0000	M	0.63428	1.95	0.40947	P	0.015480999999999967	B;B	0.20671	0.047;0.015	B;B	0.15484	0.013;0.009	T	0.45920	-0.9228	9	0.09590	T	0.72	-6.8235	4.7271	0.12946	0.6104:0.1836:0.0:0.206	rs2286468;rs59198711	725;717	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	S	725	ENSP00000411409:C725S	ENSP00000411409:C725S	C	-	1	0	ZNF598	1989004	0.433000	0.25562	0.655000	0.29622	0.325000	0.28411	0.888000	0.28268	0.854000	0.35336	0.529000	0.55759	TGT	A|0.743;T|0.257	0.257	strong		0.706	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
ATF1	466	hgsc.bcm.edu	37	12	51213433	51213433	+	Silent	SNP	A	A	G	rs17291650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:51213433A>G	ENST00000262053.3	+	7	709	c.687A>G	c.(685-687)gaA>gaG	p.E229E	ATF1_ENST00000539132.1_Silent_p.E94E	NM_005171.4	NP_005162.1	P18846	ATF1_HUMAN	activating transcription factor 1	229	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular protein complex assembly (GO:0043623)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to cobalt ion (GO:0032025)|response to organic cyclic compound (GO:0014070)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 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)		EWSR1/ATF1(347)|FUS/ATF1(4)	breast(1)|large_intestine(1)|ovary(2)	4					Pseudoephedrine(DB00852)	CTGCTCGAGAATGTCGCAGAA	0.323			T	"""EWSR1, FUS"""	"""malignant melanoma of soft parts , angiomatoid fibrous histiocytoma """								A|||	183	0.0365415	0.0038	0.0403	5008	,	,		17695	0.0		0.0885	False		,,,				2504	0.0624				p.E229E		Atlas-SNP	.		Dom	yes		12	12q13	466	activating transcription factor 1		"""E, M"""	.	ATF1	32	.	0			c.A687G						PASS	.	A		81,4325	66.4+/-103.9	1,79,2123	45.0	48.0	47.0	http://www.ncbi.nlm.nih.gov/pubmed?term	687	0.6	1.0	12	dbSNP_123	47	796,7800	179.0+/-228.3	36,724,3538	yes	coding-synonymous	ATF1	NM_005171.4		37,803,5661	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	9.2601,1.8384,6.7451		229/272	51213433	877,12125	2203	4298	6501	SO:0001819	synonymous_variant	466	exon7			TCGAGAATGTCGC	BC029619	CCDS8803.1	12q13	2014-05-13			ENSG00000123268	ENSG00000123268		"""basic leucine zipper proteins"""	783	protein-coding gene	gene with protein product		123803				8401579	Standard	NM_005171		Approved	TREB36	uc001rww.4	P18846		ENST00000262053.3:c.687A>G	12.37:g.51213433A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	81	48	0.592593	NM_005171	B4DRF9|P25168|Q9H4A8	Silent	SNP	ENST00000262053.3	37	CCDS8803.1																																																																																			A|0.944;G|0.056	0.056	strong		0.323	ATF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404285.1	NM_005171	
USP15	9958	hgsc.bcm.edu	37	12	62778065	62778065	+	Silent	SNP	A	A	G	rs2044846	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:62778065A>G	ENST00000280377.5	+	11	1513	c.1455A>G	c.(1453-1455)ccA>ccG	p.P485P	USP15_ENST00000393654.3_Silent_p.P460P|USP15_ENST00000353364.3_Silent_p.P456P	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	485	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)		GAATGGATCCACTTACCAAAC	0.308													G|||	2806	0.560304	0.5212	0.5634	5008	,	,		13820	0.5813		0.6332	False		,,,				2504	0.5143				p.P485P	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.A1455G						PASS	.	G		2353,2053	558.7+/-380.1	643,1067,493	66.0	59.0	62.0		1368	0.1	1.0	12	dbSNP_94	62	5368,3230	482.7+/-370.9	1696,1976,627	no	coding-synonymous	USP15	NM_006313.1		2339,3043,1120	GG,GA,AA		37.5669,46.5956,40.626		456/953	62778065	7721,5283	2203	4299	6502	SO:0001819	synonymous_variant	9958	exon11			GGATCCACTTACC	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.1455A>G	12.37:g.62778065A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	53	0.929825	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1																																																																																			A|0.415;G|0.585	0.585	strong		0.308	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
OR4D11	219986	hgsc.bcm.edu	37	11	59271210	59271210	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:59271210C>T	ENST00000313253.1	+	1	162	c.162C>T	c.(160-162)cgC>cgT	p.R54R		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	54						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(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						GTGAGTCTCGCCTTCACACCC	0.488																																					p.R54R		Atlas-SNP	.											OR4D11,NS,carcinoma,+1,3	OR4D11	62	3	0			c.C162T						scavenged	.						206.0	201.0	203.0					11																	59271210		2201	4295	6496	SO:0001819	synonymous_variant	219986	exon1			GTCTCGCCTTCAC	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.162C>T	11.37:g.59271210C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	165	2	0.0121212	NM_001004706		Silent	SNP	ENST00000313253.1	37	CCDS31563.1																																																																																			.	.	none		0.488	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32141460	32141460	+	Silent	SNP	T	T	C	rs2799021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32141460T>C	ENST00000344936.2	-	6	1389	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	ARHGAP12_ENST00000375245.4_Silent_p.E338E|ARHGAP12_ENST00000311380.4_Silent_p.E338E|ARHGAP12_ENST00000375250.5_Silent_p.E385E|ARHGAP12_ENST00000396144.4_Silent_p.E385E	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	385	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				GCAATTCCCATTCTGACCGAG	0.333													T|||	1161	0.231829	0.0545	0.2954	5008	,	,		15238	0.4127		0.2048	False		,,,				2504	0.2679				p.E385E		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.A1155G						PASS	.	T		371,4035	187.8+/-214.3	16,339,1848	100.0	99.0	99.0		1155	2.1	1.0	10	dbSNP_100	99	1826,6774	327.9+/-318.0	191,1444,2665	no	coding-synonymous	ARHGAP12	NM_018287.5		207,1783,4513	CC,CT,TT		21.2326,8.4203,16.8922		385/847	32141460	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	94134	exon6			TTCCCATTCTGAC	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1155A>G	10.37:g.32141460T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_001270696	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	T	9.049	0.991719	0.18966	0.084203	0.212326	ENSG00000165322	ENST00000454919	.	.	.	5.85	2.14	0.27477	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38672	-0.9650	3	.	.	.	.	10.3205	0.43762	0.0:0.2537:0.0:0.7463	rs2799021;rs17572817;rs56514703;rs2799021	.	.	.	V	61	.	.	M	-	1	0	ARHGAP12	32181466	0.998000	0.40836	0.997000	0.53966	0.961000	0.63080	0.386000	0.20702	0.108000	0.17862	0.455000	0.32223	ATG	T|0.798;C|0.202	0.202	strong		0.333	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
PDE11A	50940	hgsc.bcm.edu	37	2	178936475	178936475	+	Silent	SNP	G	G	A	rs78496158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:178936475G>A	ENST00000286063.6	-	1	1007	c.690C>T	c.(688-690)tgC>tgT	p.C230C	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	230	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CCACCATAAGGCAGACAAAGA	0.473									Primary Pigmented Nodular Adrenocortical Disease, Familial				G|||	85	0.0169728	0.0015	0.0058	5008	,	,		21161	0.0		0.0229	False		,,,				2504	0.0573				p.C230C		Atlas-SNP	.											.	PDE11A	283	.	0			c.C690T						PASS	.	G	,	29,4377	35.2+/-66.4	0,29,2174	95.0	81.0	86.0		,690	3.6	1.0	2	dbSNP_131	86	245,8355	98.1+/-159.7	4,237,4059	no	intron,coding-synonymous	PDE11A	NM_001077197.1,NM_016953.3	,	4,266,6233	AA,AG,GG		2.8488,0.6582,2.1067	,	,230/934	178936475	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	CATAAGGCAGACA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.690C>T	2.37:g.178936475G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1																																																																																			G|0.981;A|0.019	0.019	strong		0.473	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
PCLO	27445	hgsc.bcm.edu	37	7	82582846	82582846	+	Missense_Mutation	SNP	C	C	T	rs10954696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:82582846C>T	ENST00000333891.9	-	5	7760	c.7423G>A	c.(7423-7425)Gtt>Att	p.V2475I	PCLO_ENST00000423517.2_Missense_Mutation_p.V2475I|PCLO_ENST00000437081.1_5'Flank	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						ATTCTTGTAACAGGTAATCCA	0.443													C|||	1604	0.320288	0.1021	0.389	5008	,	,		12115	0.4425		0.3608	False		,,,				2504	0.3988				p.V2475I		Atlas-SNP	.											.	PCLO	1506	.	0			c.G7423A						PASS	.	C	ILE/VAL,ILE/VAL	536,3374		40,456,1459	128.0	126.0	127.0		7423,7423	2.6	0.5	7	dbSNP_120	127	2995,5295		544,1907,1694	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	29,29	584,2363,3153	TT,TC,CC		36.1279,13.7084,28.9426	benign,benign	2475/5143,2475/4936	82582846	3531,8669	1955	4145	6100	SO:0001583	missense	27445	exon5			TTGTAACAGGTAA	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.7423G>A	7.37:g.82582846C>T	ENSP00000334319:p.Val2475Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	711	0.32554945054945056	46	0.09349593495934959	135	0.3729281767955801	253	0.4423076923076923	277	0.3654353562005277	C	0.307	-0.970320	0.02232	0.137084	0.361279	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.37;2.36	4.52	2.62	0.31277	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.22457	P	0.999085595	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.41928	-0.9481	8	0.87932	D	0	.	8.8003	0.34905	0.0:0.7328:0.0:0.2672	rs10954696;rs58069415;rs10954696	2475;2475	Q9Y6V0-5;Q9Y6V0-6	.;.	I	2406;2475;2475	ENSP00000334319:V2475I;ENSP00000388393:V2475I	ENSP00000334319:V2475I	V	-	1	0	PCLO	82420782	0.000000	0.05858	0.546000	0.28166	0.091000	0.18340	-0.776000	0.04674	0.847000	0.35167	0.484000	0.47621	GTT	C|0.674;T|0.326	0.326	strong		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
VPS13A	23230	hgsc.bcm.edu	37	9	79853068	79853068	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:79853068T>C	ENST00000360280.3	+	18	2006	c.1746T>C	c.(1744-1746)tgT>tgC	p.C582C	VPS13A_ENST00000357409.5_Silent_p.C582C|VPS13A_ENST00000376636.3_Silent_p.C582C|VPS13A_ENST00000376634.4_Silent_p.C582C	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	582					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CTCAGAGGTGTATCATAGAAG	0.313																																					p.C582C		Atlas-SNP	.											VPS13A_ENST00000376634,NS,carcinoma,0,3	VPS13A	735	3	0			c.T1746C						scavenged	.						69.0	73.0	71.0					9																	79853068		2203	4297	6500	SO:0001819	synonymous_variant	23230	exon18			GAGGTGTATCATA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.1746T>C	9.37:g.79853068T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	131	3	0.0229008	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			.	.	none		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
MYH6	4624	hgsc.bcm.edu	37	14	23858232	23858232	+	Silent	SNP	C	C	T	rs451794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23858232C>T	ENST00000356287.3	-	28	4040	c.4011G>A	c.(4009-4011)tcG>tcA	p.S1337S	MIR208A_ENST00000362287.1_RNA|MYH6_ENST00000405093.3_Silent_p.S1337S			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1337					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)		CATGCCGGGCCGACTGCAGTG	0.667													C|||	174	0.0347444	0.0083	0.0432	5008	,	,		14843	0.0		0.1064	False		,,,				2504	0.0266				p.S1337S		Atlas-SNP	.											.	MYH6	274	.	0			c.G4011A						PASS	.	C		109,4297		1,107,2095	33.0	32.0	32.0		4011	-9.5	0.4	14	dbSNP_80	32	1008,7592		64,880,3356	no	coding-synonymous	MYH6	NM_002471.3		65,987,5451	TT,TC,CC		11.7209,2.4739,8.5883		1337/1940	23858232	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon29			CCGGGCCGACTGC	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.4011G>A	14.37:g.23858232C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			C|0.921;T|0.079	0.079	strong		0.667	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
MUC16	94025	hgsc.bcm.edu	37	19	9070079	9070079	+	Silent	SNP	C	C	G	rs1559170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9070079C>G	ENST00000397910.4	-	3	17570	c.17367G>C	c.(17365-17367)acG>acC	p.T5789T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5791	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						TCTCCTCAGACGTCCTGGTGT	0.458													C|||	966	0.192891	0.2602	0.1859	5008	,	,		22214	0.2679		0.0845	False		,,,				2504	0.1411				p.T5789T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G17367C						PASS	.	C		909,3047		108,693,1177	153.0	146.0	148.0		17367	-2.4	0.0	19	dbSNP_88	148	648,7684		26,596,3544	no	coding-synonymous	MUC16	NM_024690.2		134,1289,4721	GG,GC,CC		7.7772,22.9778,12.6709		5789/14508	9070079	1557,10731	1978	4166	6144	SO:0001819	synonymous_variant	94025	exon3			CTCAGACGTCCTG	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.17367G>C	19.37:g.9070079C>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.805;G|0.195	0.195	strong		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DISP2	85455	hgsc.bcm.edu	37	15	40662501	40662501	+	Silent	SNP	G	G	A	rs4514650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40662501G>A	ENST00000267889.3	+	8	4275	c.4188G>A	c.(4186-4188)acG>acA	p.T1396T	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	1396					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GCACTCACACGTCAGGCTATA	0.662													G|||	1260	0.251597	0.1112	0.3242	5008	,	,		19087	0.5327		0.0934	False		,,,				2504	0.2628				p.T1396T		Atlas-SNP	.											.	DISP2	86	.	0			c.G4188A						PASS	.	G		505,3883		27,451,1716	31.0	36.0	35.0		4188	-8.5	0.6	15	dbSNP_111	35	728,7836		26,676,3580	no	coding-synonymous	DISP2	NM_033510.1		53,1127,5296	AA,AG,GG		8.5007,11.5087,9.5198		1396/1402	40662501	1233,11719	2194	4282	6476	SO:0001819	synonymous_variant	85455	exon8			TCACACGTCAGGC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.4188G>A	15.37:g.40662501G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			G|0.832;A|0.168	0.168	strong		0.662	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
TBC1D4	9882	hgsc.bcm.edu	37	13	75866284	75866284	+	Missense_Mutation	SNP	G	G	A	rs9600455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:75866284G>A	ENST00000377636.3	-	19	3786	c.3440C>T	c.(3439-3441)aCg>aTg	p.T1147M	TBC1D4_ENST00000431480.2_Missense_Mutation_p.T1139M|TBC1D4_ENST00000377625.2_Missense_Mutation_p.T1084M|TBC1D4_ENST00000478591.1_5'Flank|TBC1D4_ENST00000425511.1_Missense_Mutation_p.T311M	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1147			T -> M (in dbSNP:rs9600455).		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)	p.T1147M(1)		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)		ATCAGGTAGCGTGTTTTTAAG	0.323													G|||	182	0.0363419	0.0023	0.0706	5008	,	,		15425	0.0		0.1133	False		,,,				2504	0.0164				p.T1147M		Atlas-SNP	.											TBC1D4,NS,lymphoid_neoplasm,0,1	TBC1D4	142	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C3440T						PASS	.	G	MET/THR	76,3552		1,74,1739	76.0	74.0	74.0		3440	3.9	0.0	13	dbSNP_119	74	979,7167		68,843,3162	yes	missense	TBC1D4	NM_014832.2	81	69,917,4901	AA,AG,GG		12.0182,2.0948,8.9604	possibly-damaging	1147/1299	75866284	1055,10719	1814	4073	5887	SO:0001583	missense	9882	exon19			GGTAGCGTGTTTT	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.3440C>T	13.37:g.75866284G>A	ENSP00000366863:p.Thr1147Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	120	0.054945054945054944	0	0.0	33	0.09116022099447514	0	0.0	87	0.11477572559366754	G	14.20	2.463807	0.43736	0.020948	0.120182	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	5.63	3.87	0.44632	Rab-GAP/TBC domain (1);	0.079267	0.53938	D	0.000052	T	0.00210	0.0006	L	0.60455	1.87	0.33130	P	0.45700799999999997	B;P;B;B	0.42785	0.135;0.79;0.26;0.166	B;B;B;B	0.29353	0.016;0.101;0.038;0.02	T	0.14200	-1.0481	9	0.56958	D	0.05	-9.219	7.0733	0.25191	0.141:0.0:0.7189:0.1401	rs9600455;rs52825604;rs9600455	311;1084;1139;1147	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	M	1147;1139;1084;311	ENSP00000366863:T1147M;ENSP00000395986:T1139M;ENSP00000366852:T1084M;ENSP00000390654:T311M	ENSP00000366852:T1084M	T	-	2	0	TBC1D4	74764285	1.000000	0.71417	0.003000	0.11579	0.992000	0.81027	4.605000	0.61119	0.695000	0.31675	0.650000	0.86243	ACG	G|0.929;A|0.071	0.071	strong		0.323	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
KRT39	390792	hgsc.bcm.edu	37	17	39122797	39122797	+	Silent	SNP	G	G	A	rs10491137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39122797G>A	ENST00000355612.2	-	1	347	c.312C>T	c.(310-312)aaC>aaT	p.N104N	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	104	Coil 1A.|Rod.					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)				CAAGGCGCTCGTTCAAGATTT	0.448													G|||	838	0.167332	0.2466	0.1628	5008	,	,		20361	0.0327		0.159	False		,,,				2504	0.2106				p.N104N		Atlas-SNP	.											.	KRT39	53	.	0			c.C312T						PASS	.	G		975,3431	365.1+/-317.3	109,757,1337	209.0	211.0	210.0		312	-4.7	0.0	17	dbSNP_119	210	1356,7236	264.3+/-285.5	108,1140,3048	no	coding-synonymous	KRT39	NM_213656.3		217,1897,4385	AA,AG,GG		15.7821,22.1289,17.9335		104/492	39122797	2331,10667	2203	4296	6499	SO:0001819	synonymous_variant	390792	exon1			GCGCTCGTTCAAG	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.312C>T	17.37:g.39122797G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	208	107	0.514423	NM_213656	B2RXK6|Q6IFU6	Silent	SNP	ENST00000355612.2	37	CCDS11382.1																																																																																			G|0.826;A|0.174	0.174	strong		0.448	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18143261	18143261	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:18143261A>G	ENST00000435364.3	+	6	1684	c.1343A>G	c.(1342-1344)cAg>cGg	p.Q448R	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.Q447R|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.Q320R	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	448					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGGAAGCCTCAGCTGGAGAAG	0.502																																					p.Q448R		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A1343G						PASS	.						71.0	74.0	73.0					20																	18143261		2203	4300	6503	SO:0001583	missense	57325	exon6			AGCCTCAGCTGGA	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"""cysteine rich protein 2 binding protein"", ""ATAC component 2 homolog (Drosophila)"""					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1343A>G	20.37:g.18143261A>G	ENSP00000392318:p.Gln448Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	4.422	0.078067	0.08485	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.15017	2.46;2.46;2.46;2.47	6.17	0.00674	0.14068	.	0.384216	0.28859	N	0.013905	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.38628	-0.9652	10	0.16420	T	0.52	-20.6595	7.114	0.25407	0.3473:0.3538:0.0:0.2988	.	320;448	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	R	448;447;448;320	ENSP00000278816:Q448R;ENSP00000366909:Q447R;ENSP00000392318:Q448R;ENSP00000425909:Q320R	ENSP00000278816:Q448R	Q	+	2	0	CSRP2BP	18091261	0.192000	0.23301	0.001000	0.08648	0.983000	0.72400	0.681000	0.25320	-0.235000	0.09767	0.533000	0.62120	CAG	.	.	none		0.502	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
ZNF335	63925	hgsc.bcm.edu	37	20	44578674	44578674	+	Silent	SNP	T	T	A	rs16990951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44578674T>A	ENST00000322927.2	-	23	3622	c.3522A>T	c.(3520-3522)ccA>ccT	p.P1174P	ZNF335_ENST00000426788.1_Silent_p.P1019P	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1174					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)				GTAGCCGCTCTGGGCCCAGGA	0.612													T|||	1133	0.226238	0.3313	0.1009	5008	,	,		19525	0.3294		0.1004	False		,,,				2504	0.1963				p.P1174P		Atlas-SNP	.											.	ZNF335	115	.	0			c.A3522T						PASS	.	T		1162,3244	403.1+/-332.6	139,884,1180	36.0	35.0	35.0		3522	-2.2	1.0	20	dbSNP_123	35	987,7613	211.0+/-251.7	50,887,3363	no	coding-synonymous	ZNF335	NM_022095.3		189,1771,4543	AA,AT,TT		11.4767,26.3731,16.5231		1174/1343	44578674	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	63925	exon23			CCGCTCTGGGCCC	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.3522A>T	20.37:g.44578674T>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			T|0.821;A|0.179	0.179	strong		0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
C11orf16	56673	hgsc.bcm.edu	37	11	8947179	8947179	+	Silent	SNP	G	G	A	rs2568077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	113	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	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	
PRDM11	56981	hgsc.bcm.edu	37	11	45203848	45203848	+	Silent	SNP	G	G	A	rs1078931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:45203848G>A	ENST00000530656.1	+	3	273	c.273G>A	c.(271-273)aaG>aaA	p.K91K	PRDM11_ENST00000424263.2_Silent_p.K57K|PRDM11_ENST00000263765.4_Silent_p.K91K			Q9NQV5	PRD11_HUMAN	PR domain containing 11	91							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						AGAAACTGAAGGGGAAGCGCG	0.582													G|||	628	0.125399	0.2625	0.121	5008	,	,		18537	0.0		0.1292	False		,,,				2504	0.0685				p.K57K	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.G171A						PASS	.	G		940,3466	351.3+/-311.2	100,740,1363	77.0	72.0	74.0		273	3.1	1.0	11	dbSNP_86	74	1071,7527	220.9+/-258.5	75,921,3303	no	coding-synonymous	PRDM11	NM_020229.2		175,1661,4666	AA,AG,GG		12.4564,21.3345,15.4645		91/512	45203848	2011,10993	2203	4299	6502	SO:0001819	synonymous_variant	56981	exon3			ACTGAAGGGGAAG	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.273G>A	11.37:g.45203848G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_001256695	Q8N9F1	Silent	SNP	ENST00000530656.1	37																																																																																				G|0.854;A|0.146	0.146	strong		0.582	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
COX10	1352	hgsc.bcm.edu	37	17	14095348	14095348	+	Silent	SNP	G	G	A	rs587780910		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:14095348G>A	ENST00000261643.3	+	6	815	c.738G>A	c.(736-738)ccG>ccA	p.P246P	COX10_ENST00000537334.1_Silent_p.P29P|COX10_ENST00000536205.1_Silent_p.P54P	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	246					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)		GTGCTGTTCCGGGAGTTGCCA	0.502																																					p.P246P		Atlas-SNP	.											COX10,NS,carcinoma,+1,1	COX10	36	1	0			c.G738A						scavenged	.						123.0	118.0	120.0					17																	14095348		2203	4300	6503	SO:0001819	synonymous_variant	1352	exon6			TGTTCCGGGAGTT	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.738G>A	17.37:g.14095348G>A		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	114	14	0.122807	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			T|0.054;A|0.946	0.946	alt		0.502	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
KMT2C	58508	hgsc.bcm.edu	37	7	151932997	151932997	+	Missense_Mutation	SNP	C	C	T	rs199831680		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151932997C>T	ENST00000262189.6	-	16	2892	c.2674G>A	c.(2674-2676)Gga>Aga	p.G892R	KMT2C_ENST00000355193.2_Missense_Mutation_p.G892R	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	892					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)										CTCCGCTTTCCTGGAAATCCA	0.488																																					p.G892R		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,+1,4	MLL3	1564	4	0			c.G2674A						scavenged	.						32.0	33.0	33.0					7																	151932997		2203	4296	6499	SO:0001583	missense	58508	exon16			GCTTTCCTGGAAA	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.2674G>A	7.37:g.151932997C>T	ENSP00000262189:p.Gly892Arg	Somatic	64	4	0.0625		WXS	Illumina HiSeq	Phase_I	55	6	0.109091	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.2|22.2	4.254300|4.254300	0.80135|0.80135	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193|ENST00000418673	D;D|.	0.89746|.	-2.54;-2.56|.	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	0.000000|.	0.46145|.	D|.	0.000320|.	T|T	0.72301|0.72301	0.3443|0.3443	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.70894|0.70894	-0.4748|-0.4748	10|5	0.87932|.	D|.	0|.	.|.	17.0444|17.0444	0.86498|0.86498	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	892|.	Q8NEZ4|.	MLL3_HUMAN|.	R|K	892|47	ENSP00000262189:G892R;ENSP00000347325:G892R|.	ENSP00000262189:G892R|.	G|R	-|-	1|2	0|0	MLL3|MLL3	151563930|151563930	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.268000|7.268000	0.78473|0.78473	2.530000|2.530000	0.85305|0.85305	0.650000|0.650000	0.86243|0.86243	GGA|AGG	C|0.998;T|0.002	0.002	weak		0.488	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539186	110539186	+	Missense_Mutation	SNP	G	G	A	rs1783174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:110539186G>A	ENST00000378402.5	+	77	12762	c.12658G>A	c.(12658-12660)Gtt>Att	p.V4220I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4220			V -> I (in dbSNP:rs1783174).		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)			TAGCTGTCTGGTTGGAAGAAT	0.403										HNSCC(38;0.096)			A|||	1427	0.284944	0.3464	0.3991	5008	,	,		18077	0.3244		0.1402	False		,,,				2504	0.229				p.V4220I		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G12658A						PASS	.	A	ILE/VAL	1263,2715		200,863,926	91.0	96.0	94.0		12658	-9.2	0.0	8	dbSNP_89	94	1345,7035		118,1109,2963	yes	missense	PKHD1L1	NM_177531.4	29	318,1972,3889	AA,AG,GG		16.0501,31.7496,21.1037	benign	4220/4244	110539186	2608,9750	1989	4190	6179	SO:0001583	missense	93035	exon77			TGTCTGGTTGGAA	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.12658G>A	8.37:g.110539186G>A	ENSP00000367655:p.Val4220Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	570	0.260989010989011	150	0.3048780487804878	119	0.3287292817679558	193	0.3374125874125874	108	0.1424802110817942	A	0.784	-0.761348	0.02996	0.317496	0.160501	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85861	-2.04;-1.89	5.64	-9.18	0.00688	.	0.938892	0.08808	N	0.890675	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	0.04128	-1.0975	9	0.07482	T	0.82	.	9.2526	0.37564	0.1675:0.1037:0.6181:0.1107	rs1783174;rs3200931;rs52800227;rs58003000;rs1783174	4220	Q86WI1	PKHL1_HUMAN	I	4220;1148	ENSP00000367655:V4220I;ENSP00000437376:V1148I	ENSP00000367655:V4220I	V	+	1	0	PKHD1L1	110608362	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	-1.952000	0.01528	-1.635000	0.01535	-2.208000	0.00301	GTT	G|0.742;A|0.258	0.258	strong		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
OR7G2	390882	hgsc.bcm.edu	37	19	9213132	9213132	+	Missense_Mutation	SNP	A	A	G	rs12610094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9213132A>G	ENST00000305456.2	-	1	850	c.851T>C	c.(850-852)gTg>gCg	p.V284A		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	263						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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						GTCAGTAACCACAGAACTAAT	0.468													-|||	2026	0.404553	0.2057	0.3588	5008	,	,		20333	0.5903		0.4245	False		,,,				2504	0.4939				p.V284A	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											.	OR7G2	48	.	0			c.T851C						PASS	.	G	ALA/VAL	1026,3380	727.2+/-409.8	110,806,1287	115.0	101.0	106.0		851	-0.5	0.0	19	dbSNP_120	106	3576,5024	627.8+/-398.0	757,2062,1481	yes	missense	OR7G2	NM_001005193.1	64	867,2868,2768	GG,GA,AA		41.5814,23.2864,35.3837	benign	284/346	9213132	4602,8404	2203	4300	6503	SO:0001583	missense	390882	exon1			GTAACCACAGAAC		CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"""GPCR / Class A : Olfactory receptors"""	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.851T>C	19.37:g.9213132A>G	ENSP00000303822:p.Val284Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001005193	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	883	0.4043040293040293	102	0.2073170731707317	124	0.3425414364640884	337	0.5891608391608392	320	0.42216358839050133	g	0.014	-1.585771	0.00872	0.232864	0.415814	ENSG00000170923	ENST00000305456	T	0.00042	8.84	3.14	-0.483	0.12075	GPCR, rhodopsin-like superfamily (1);	0.983847	0.08234	N	0.977019	T	0.00012	0.0000	N	0.00108	-2.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	9	0.02654	T	1	.	4.7739	0.13169	0.2769:0.0:0.5741:0.149	rs12610094;rs17238760;rs52807732;rs56575652;rs59255517;rs12610094	263	Q8NG99	OR7G2_HUMAN	A	284	ENSP00000303822:V284A	ENSP00000303822:V284A	V	-	2	0	OR7G2	9074132	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.935000	0.01550	-0.196000	0.10366	-0.401000	0.06369	GTG	A|0.620;G|0.380	0.380	strong		0.468	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1		
HEXIM1	10614	hgsc.bcm.edu	37	17	43227214	43227214	+	Silent	SNP	T	T	C	rs1044977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:43227214T>C	ENST00000332499.2	+	1	2531	c.657T>C	c.(655-657)gaT>gaC	p.D219D	AC002117.1_ENST00000452741.1_RNA|AC002117.1_ENST00000589950.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	219	Autoinhibitory acidic region; in absence of 7SK snRNA interacts with the basic region preventing interaction with P-TEFb and modulating subcellular localization.				heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AGGAGCCGGATCTCAAAACCG	0.617											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	995	0.198682	0.0477	0.196	5008	,	,		14687	0.2183		0.2734	False		,,,				2504	0.3078				p.D219D		Atlas-SNP	.											.	HEXIM1	25	.	0			c.T657C						PASS	.	T		337,4069	167.6+/-198.6	6,325,1872	44.0	48.0	46.0		657	-1.8	1.0	17	dbSNP_86	46	2093,6507	346.0+/-326.0	243,1607,2450	no	coding-synonymous	HEXIM1	NM_006460.2		249,1932,4322	CC,CT,TT		24.3372,7.6487,18.6837		219/360	43227214	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	10614	exon1			GCCGGATCTCAAA	AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834			24953	protein-coding gene	gene with protein product		607328				12119119, 12832472	Standard	NM_006460		Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.657T>C	17.37:g.43227214T>C		Somatic	46	0	0	914	WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_006460	B2R8Y5	Silent	SNP	ENST00000332499.2	37	CCDS11495.1																																																																																			T|0.817;C|0.183	0.183	strong		0.617	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460	
MMP15	4324	hgsc.bcm.edu	37	16	58079165	58079165	+	Missense_Mutation	SNP	G	G	A	rs3743563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:58079165G>A	ENST00000219271.3	+	10	2610	c.1825G>A	c.(1825-1827)Ggg>Agg	p.G609R		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	609			G -> R (in dbSNP:rs3743563). {ECO:0000269|PubMed:9119382, ECO:0000269|Ref.2}.		cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G609R(2)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CAACAAGGACGGGGGCAGCCG	0.701													G|||	996	0.198882	0.0318	0.3963	5008	,	,		11871	0.3462		0.1829	False		,,,				2504	0.1493				p.G609R		Atlas-SNP	.											MMP15,hand,carcinoma,0,3	MMP15	58	3	2	Substitution - Missense(2)	central_nervous_system(1)|skin(1)	c.G1825A						PASS	.	G	ARG/GLY	308,4086	156.6+/-189.7	15,278,1904	105.0	117.0	113.0		1825	3.7	1.0	16	dbSNP_107	113	1645,6955	282.4+/-295.5	161,1323,2816	yes	missense	MMP15	NM_002428.2	125	176,1601,4720	AA,AG,GG		19.1279,7.0096,15.03	possibly-damaging	609/670	58079165	1953,11041	2197	4300	6497	SO:0001583	missense	4324	exon10			AAGGACGGGGGCA	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"""matrix metalloproteinase 15 (membrane-inserted)"""			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1825G>A	16.37:g.58079165G>A	ENSP00000219271:p.Gly609Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	482	0.2206959706959707	24	0.04878048780487805	111	0.30662983425414364	199	0.3479020979020979	148	0.19525065963060687	G	13.06	2.125616	0.37533	0.070096	0.191279	ENSG00000102996	ENST00000219271	T	0.28069	1.63	4.65	3.69	0.42338	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.368453	0.32081	N	0.006618	T	0.00012	0.0000	N	0.21448	0.665	0.35109	P	0.23400299999999996	B	0.23854	0.092	B	0.19946	0.027	T	0.45804	-0.9236	9	0.17369	T	0.5	.	8.5638	0.33527	0.1046:0.0:0.8954:0.0	rs3743563;rs3743563	609	P51511	MMP15_HUMAN	R	609	ENSP00000219271:G609R	ENSP00000219271:G609R	G	+	1	0	MMP15	56636666	1.000000	0.71417	0.982000	0.44146	0.606000	0.37113	6.421000	0.73353	1.184000	0.42957	0.555000	0.69702	GGG	G|0.829;A|0.171	0.171	strong		0.701	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
RPUSD4	84881	hgsc.bcm.edu	37	11	126074192	126074192	+	Silent	SNP	A	A	G	rs2276312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126074192A>G	ENST00000298317.4	-	6	881	c.828T>C	c.(826-828)tcT>tcC	p.S276S	RPUSD4_ENST00000533628.1_Silent_p.S245S|RPUSD4_ENST00000534393.1_5'Flank	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	276					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)		CCAATCCAAAAGACAAGTGAA	0.423													A|||	1298	0.259185	0.0408	0.3242	5008	,	,		18746	0.623		0.1143	False		,,,				2504	0.2822				p.S276S		Atlas-SNP	.											.	RPUSD4	36	.	0			c.T828C						PASS	.	A	,	315,4087	161.4+/-193.6	14,287,1900	109.0	106.0	107.0		735,828	-4.4	1.0	11	dbSNP_100	107	1002,7596	203.0+/-246.1	55,892,3352	no	coding-synonymous,coding-synonymous	RPUSD4	NM_001144827.1,NM_032795.2	,	69,1179,5252	GG,GA,AA		11.6539,7.1558,10.1308	,	245/347,276/378	126074192	1317,11683	2201	4299	6500	SO:0001819	synonymous_variant	84881	exon6			TCCAAAAGACAAG	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.828T>C	11.37:g.126074192A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_032795	E9PML2|Q96K56	Silent	SNP	ENST00000298317.4	37	CCDS8469.1																																																																																			A|0.818;G|0.182	0.182	strong		0.423	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795	
METTL7B	196410	hgsc.bcm.edu	37	12	56077740	56077740	+	Silent	SNP	C	C	T	rs11615467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	86	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	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	
HLA-DOB	3112	hgsc.bcm.edu	37	6	32783086	32783086	+	Silent	SNP	A	A	G	rs7383287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32783086A>G	ENST00000438763.2	-	2	192	c.96T>C	c.(94-96)gaT>gaC	p.D32D	TAP2_ENST00000452392.2_Intron	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	32	Beta-1.				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)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						GAATCACAAAATCTTCTGGAA	0.458													A|||	663	0.132388	0.1831	0.1268	5008	,	,		20437	0.0308		0.1839	False		,,,				2504	0.1196				p.D32D		Atlas-SNP	.											.	HLA-DOB	17	.	0			c.T96C						PASS	.	A		806,3600	322.3+/-297.6	83,640,1480	102.0	100.0	101.0		96	4.3	1.0	6	dbSNP_116	101	1822,6778	325.4+/-316.9	209,1404,2687	yes	coding-synonymous	HLA-DOB	NM_002120.3		292,2044,4167	GG,GA,AA		21.186,18.2932,20.2061		32/274	32783086	2628,10378	2203	4300	6503	SO:0001819	synonymous_variant	3112	exon2			CACAAAATCTTCT		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.96T>C	6.37:g.32783086A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Silent	SNP	ENST00000438763.2	37	CCDS4754.1	270	0.12362637362637363	61	0.12398373983739837	45	0.12430939226519337	20	0.03496503496503497	144	0.18997361477572558	A	10.40	1.339479	0.24339	0.182932	0.21186	ENSG00000241106	ENST00000447394	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	T	0.42743	0.1216	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41787	-0.9489	3	.	.	.	.	11.651	0.51288	1.0:0.0:0.0:0.0	rs7383287;rs17429396;rs29029540;rs45459295;rs60007806;rs7383287	.	.	.	L	19	.	.	F	-	1	0	HLA-DOB	32891064	0.981000	0.34729	1.000000	0.80357	0.992000	0.81027	0.298000	0.19120	1.907000	0.55213	0.486000	0.48141	TTT	A|0.838;G|0.162	0.162	strong		0.458	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120	
ALOX12	239	hgsc.bcm.edu	37	17	6913652	6913652	+	Silent	SNP	G	G	A	rs312462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6913652G>A	ENST00000251535.6	+	14	1955	c.1902G>A	c.(1900-1902)ctG>ctA	p.L634L	RNASEK_ENST00000402093.1_5'Flank|RNASEK_ENST00000548577.1_5'Flank|AC027763.2_ENST00000399540.2_Intron|RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000575727.1_Intron|RNASEK_ENST00000552321.1_5'Flank|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000573939.1_Intron	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	634	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|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 endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						TGGAAAAGCTGGAAAAGGAGA	0.483													G|||	597	0.119209	0.0613	0.0879	5008	,	,		20045	0.129		0.0865	False		,,,				2504	0.2434				p.L634L		Atlas-SNP	.											.	ALOX12	49	.	0			c.G1902A						PASS	.	G		291,4115	158.9+/-191.5	9,273,1921	75.0	80.0	78.0		1902	-0.1	0.8	17	dbSNP_79	78	863,7737	193.1+/-238.9	50,763,3487	no	coding-synonymous	ALOX12	NM_000697.2		59,1036,5408	AA,AG,GG		10.0349,6.6046,8.8728		634/664	6913652	1154,11852	2203	4300	6503	SO:0001819	synonymous_variant	239	exon14			AAAGCTGGAAAAG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1902G>A	17.37:g.6913652G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	NM_000697	O95569|Q6ISF8|Q9UQM4	Silent	SNP	ENST00000251535.6	37	CCDS11084.1																																																																																			G|0.898;A|0.102	0.102	strong		0.483	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
SORBS2	8470	hgsc.bcm.edu	37	4	186544879	186544879	+	Silent	SNP	G	G	C	rs61910743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186544879G>C	ENST00000284776.7	-	13	2201	c.1692C>G	c.(1690-1692)ccC>ccG	p.P564P	SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000431808.1_Silent_p.P564P|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000355634.5_Silent_p.P664P|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000418609.1_Silent_p.P468P	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	564					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GGCCCCGAGCGGGGGGGCCGC	0.577													G|||	247	0.0493211	0.0522	0.0403	5008	,	,		13984	0.0		0.0845	False		,,,				2504	0.0665				p.P664P	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2,right_lower_lobe,carcinoma,-2,1	SORBS2	300	1	0			c.C1992G						PASS	.	G	,,,,,,,	204,4180		3,198,1991	23.0	30.0	28.0		,,,,1404,,,1692	0.2	0.5	4	dbSNP_129	28	689,7857		32,625,3616	no	intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	35,823,5607	CC,CG,GG		8.0623,4.6533,6.9064	,,,,,,,	,,,,468/1005,,,564/1101	186544879	893,12037	2192	4273	6465	SO:0001819	synonymous_variant	8470	exon16			CCGAGCGGGGGGG		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1692C>G	4.37:g.186544879G>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																			G|0.919;C|0.081	0.081	strong		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
FAM185A	222234	hgsc.bcm.edu	37	7	102389710	102389710	+	Missense_Mutation	SNP	A	A	T	rs147397718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102389710A>T	ENST00000413034.2	+	1	56	c.56A>T	c.(55-57)cAg>cTg	p.Q19L	FAM185A_ENST00000409231.3_Missense_Mutation_p.Q19L|FAM185A_ENST00000481697.1_3'UTR	NM_001145268.1	NP_001138740	Q8N0U4	F185A_HUMAN	family with sequence similarity 185, member A	19										kidney(1)	1						TGTCTCCGTCAGGTCCGACTG	0.667													.|||	448	0.0894569	0.0688	0.0231	5008	,	,		16037	0.1954		0.0437	False		,,,				2504	0.1022				p.Q19L		Atlas-SNP	.											FAM185A_ENST00000413034,NS,carcinoma,0,2	FAM185A	10	2	0			c.A56T						scavenged	.						6.0	9.0	8.0					7																	102389710		672	1566	2238	SO:0001583	missense	222234	exon1			TCCGTCAGGTCCG	BC029175	CCDS47676.1, CCDS47677.1	7q22.1	2009-07-09			ENSG00000222011	ENSG00000222011			22412	protein-coding gene	gene with protein product							Standard	NM_001145268		Approved	MGC35361	uc011klf.2	Q8N0U4	OTTHUMG00000154140	ENST00000413034.2:c.56A>T	7.37:g.102389710A>T	ENSP00000395340:p.Gln19Leu	Somatic	120	3	0.025		WXS	Illumina HiSeq	Phase_I	194	190	0.979381	NM_001145269	A8MUR7|B4DQD3|C9IZ91	Missense_Mutation	SNP	ENST00000413034.2	37	CCDS47676.1	193	0.08836996336996338	36	0.07317073170731707	11	0.03038674033149171	107	0.18706293706293706	39	0.051451187335092345	A	7.672	0.687154	0.14973	.	.	ENSG00000222011	ENST00000409231;ENST00000418198;ENST00000413034	T;T;T	0.73575	-0.76;-0.76;-0.76	3.51	1.53	0.23141	.	1.965010	0.04113	U	0.314863	T	0.00178	0.0005	N	0.22421	0.69	0.80722	P	0.0	B;B	0.19935	0.04;0.024	B;B	0.19148	0.024;0.01	T	0.06661	-1.0814	9	0.66056	D	0.02	0.6102	5.4838	0.16739	0.2602:0.0:0.7398:0.0	.	19;19	Q8N0U4-3;Q8N0U4	.;F185A_HUMAN	L	19	ENSP00000387066:Q19L;ENSP00000410034:Q19L;ENSP00000395340:Q19L	ENSP00000387066:Q19L	Q	+	2	0	FAM185A	102176946	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.215000	0.02985	0.123000	0.18342	0.443000	0.29094	CAG	A|0.920;T|0.080	0.080	strong		0.667	FAM185A-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349482.1	NM_001145268	
INSR	3643	hgsc.bcm.edu	37	19	7166376	7166376	+	Silent	SNP	C	C	T	rs2059806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7166376C>T	ENST00000302850.5	-	8	1792	c.1650G>A	c.(1648-1650)gcG>gcA	p.A550A	INSR_ENST00000341500.5_Silent_p.A550A	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	550					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.A550A(1)		breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TGGAACCACACGCATCCTGCC	0.552													c|||	1226	0.244808	0.1793	0.2363	5008	,	,		19405	0.2798		0.2853	False		,,,				2504	0.2618				p.A550A		Atlas-SNP	.											INSR,NS,carcinoma,0,1	INSR	265	1	1	Substitution - coding silent(1)	stomach(1)	c.G1650A	GRCh37	CM004252	INSR	M	rs2059806	PASS	.	T	,	855,3551	335.5+/-303.9	87,681,1435	99.0	74.0	83.0		1650,1650	-10.2	0.0	19	dbSNP_94	83	2078,6522	359.6+/-331.6	252,1574,2474	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	339,2255,3909	TT,TC,CC		24.1628,19.4054,22.5511	,	550/1383,550/1371	7166376	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon8			ACCACACGCATCC	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.1650G>A	19.37:g.7166376C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			C|0.767;T|0.233	0.233	strong		0.552	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
H6PD	9563	hgsc.bcm.edu	37	1	9307033	9307033	+	Silent	SNP	G	G	A	rs7524046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	71	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	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	
ADCY2	108	hgsc.bcm.edu	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:7520881G>T	ENST00000338316.4	+	3	528	c.439G>T	c.(439-441)Gtg>Ttg	p.V147L		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	147			V -> L (in dbSNP:rs13166360). {ECO:0000269|PubMed:15489334}.		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						CATCTTCGTGGTGTACACCAT	0.507													G|||	459	0.0916534	0.0545	0.0994	5008	,	,		21118	0.0		0.2117	False		,,,				2504	0.1074				p.V147L		Atlas-SNP	.											.	ADCY2	337	.	0			c.G439T						PASS	.	G	LEU/VAL	390,4016	194.7+/-219.5	22,346,1835	179.0	124.0	143.0		439	5.4	1.0	5	dbSNP_121	143	2139,6461	367.0+/-334.5	269,1601,2430	yes	missense	ADCY2	NM_020546.2	32	291,1947,4265	TT,TG,GG		24.8721,8.8516,19.4449	possibly-damaging	147/1092	7520881	2529,10477	2203	4300	6503	SO:0001583	missense	108	exon3			TTCGTGGTGTACA	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.439G>T	5.37:g.7520881G>T	ENSP00000342952:p.Val147Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	236	0.10805860805860806	30	0.06097560975609756	41	0.1132596685082873	0	0.0	165	0.21767810026385223	G	20.9	4.072518	0.76415	0.088516	0.248721	ENSG00000078295	ENST00000338316	T	0.76186	-1.0	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.64997	1.995	0.09310	P	1.0	P	0.37525	0.598	B	0.37888	0.26	T	0.01652	-1.1303	9	0.54805	T	0.06	.	16.4516	0.83993	0.0:0.0:1.0:0.0	rs13166360;rs17826984;rs60134556;rs13166360	147	Q08462	ADCY2_HUMAN	L	147	ENSP00000342952:V147L	ENSP00000342952:V147L	V	+	1	0	ADCY2	7573881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.996000	0.70639	2.545000	0.85829	0.650000	0.86243	GTG	G|0.850;T|0.150	0.150	strong		0.507	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
SYNPO2	171024	hgsc.bcm.edu	37	4	119944611	119944611	+	Silent	SNP	G	G	T	rs1459058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:119944611G>T	ENST00000429713.2	+	2	314	c.132G>T	c.(130-132)ggG>ggT	p.G44G	SYNPO2_ENST00000448416.2_Silent_p.G44G|SYNPO2_ENST00000434046.2_Silent_p.G44G|SYNPO2_ENST00000307142.4_Silent_p.G44G	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	44	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					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						AAGCCTCTGGGTCTGGGCTCT	0.433													G|||	2063	0.411941	0.1906	0.4784	5008	,	,		17996	0.4524		0.503	False		,,,				2504	0.5286				p.G44G		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G132T						PASS	.	G	,,	1018,3388	377.1+/-322.3	129,760,1314	92.0	77.0	82.0		132,132,132	0.8	0.7	4	dbSNP_88	82	4276,4324	575.3+/-390.2	1049,2178,1073	no	coding-synonymous,coding-synonymous,coding-synonymous	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	,,	1178,2938,2387	TT,TG,GG		49.7209,23.1049,40.7043	,,	44/1094,44/1110,44/1262	119944611	5294,7712	2203	4300	6503	SO:0001819	synonymous_variant	171024	exon2			CTCTGGGTCTGGG	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.132G>T	4.37:g.119944611G>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	205	98	0.478049	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Silent	SNP	ENST00000429713.2	37	CCDS47129.1																																																																																			G|0.594;T|0.406	0.406	strong		0.433	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
JAK1	3716	hgsc.bcm.edu	37	1	65310489	65310489	+	Silent	SNP	T	T	C	rs2230588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	84	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	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	
BNIP3	664	hgsc.bcm.edu	37	10	133786586	133786586	+	Silent	SNP	T	T	C	rs1050704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:133786586T>C	ENST00000368636.4	-	3	358	c.234A>G	c.(232-234)agA>agG	p.R78R	BNIP3_ENST00000540159.1_Silent_p.R78R	NM_004052.2	NP_004043.2	Q12983	BNIP3_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3	78					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|brown fat cell differentiation (GO:0050873)|cell death (GO:0008219)|cellular response to cobalt ion (GO:0071279)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|intrinsic apoptotic signaling pathway in response to hypoxia (GO:1990144)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|negative regulation of membrane potential (GO:0045837)|negative regulation of mitochondrial fusion (GO:0010637)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane permeability (GO:0046902)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase binding (GO:0051020)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		TTTCAGAAGCTCTGTTGGTAT	0.423													T|||	362	0.0722843	0.0726	0.1081	5008	,	,		20538	0.0198		0.1233	False		,,,				2504	0.0481				p.R78R		Atlas-SNP	.											.	BNIP3	13	.	0			c.A234G						PASS	.	T		379,4027	190.5+/-216.4	19,341,1843	233.0	217.0	223.0		234	3.0	0.1	10	dbSNP_86	223	1186,7414	240.4+/-271.1	85,1016,3199	no	coding-synonymous	BNIP3	NM_004052.2		104,1357,5042	CC,CT,TT		13.7907,8.6019,12.0329		78/195	133786586	1565,11441	2203	4300	6503	SO:0001819	synonymous_variant	664	exon3			AGAAGCTCTGTTG	U15174	CCDS7663.1	10q26.3	2003-11-05	2002-08-29		ENSG00000176171	ENSG00000176171			1084	protein-coding gene	gene with protein product		603293	"""BCL2/adenovirus E1B 19kD-interacting protein 3"""			7954800	Standard	NM_004052		Approved	Nip3	uc001lkv.1	Q12983	OTTHUMG00000019278	ENST00000368636.4:c.234A>G	10.37:g.133786586T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_004052	O14620|Q96GP0	Silent	SNP	ENST00000368636.4	37	CCDS7663.1																																																																																			.	.	weak		0.423	BNIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051039.1		
OSGEP	55644	hgsc.bcm.edu	37	14	20916958	20916958	+	Silent	SNP	T	T	C	rs938883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20916958T>C	ENST00000206542.4	-	6	991	c.570A>G	c.(568-570)ctA>ctG	p.L190L	OSGEP_ENST00000554249.1_Silent_p.L8L|OSGEP_ENST00000555656.1_5'UTR|RP11-203M5.7_ENST00000555435.1_RNA	NM_017807.3	NP_060277.1			O-sialoglycoprotein endopeptidase									p.L190L(1)		endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(4)|stomach(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)		GCAGCTCAACTAGCTTCTTGC	0.483													T|||	2482	0.495607	0.5613	0.4121	5008	,	,		18430	0.4276		0.5835	False		,,,				2504	0.4458				p.L190L		Atlas-SNP	.											OSGEP,NS,carcinoma,0,1	OSGEP	31	1	1	Substitution - coding silent(1)	stomach(1)	c.A570G						PASS	.	T		2398,2008	614.1+/-392.3	642,1114,447	131.0	105.0	114.0		570	-3.1	1.0	14	dbSNP_86	114	4852,3748	616.2+/-396.5	1372,2108,820	no	coding-synonymous	OSGEP	NM_017807.3		2014,3222,1267	CC,CT,TT		43.5814,45.5742,44.2565		190/336	20916958	7250,5756	2203	4300	6503	SO:0001819	synonymous_variant	55644	exon6			CTCAACTAGCTTC	AB050442	CCDS9549.1	14q12	2010-03-19			ENSG00000092094	ENSG00000092094	3.4.24.57		18028	protein-coding gene	gene with protein product		610107				12039036	Standard	NM_017807		Approved	PRSMG1, GCPL1, OSGEP1, KAE1	uc001vxf.3	Q9NPF4	OTTHUMG00000029543	ENST00000206542.4:c.570A>G	14.37:g.20916958T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	32	0.4	NM_017807		Silent	SNP	ENST00000206542.4	37	CCDS9549.1																																																																																			T|0.458;C|0.542	0.542	strong		0.483	OSGEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073635.3	NM_017807	
PRR25	388199	hgsc.bcm.edu	37	16	863336	863336	+	Silent	SNP	T	T	C	rs11860086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:863336T>C	ENST00000301698.1	+	3	684	c.684T>C	c.(682-684)gcT>gcC	p.A228A		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	228										large_intestine(1)|lung(1)|skin(1)	3						TCCCCTCTGCTATTGCTGCGG	0.726													C|||	1984	0.396166	0.8442	0.3473	5008	,	,		13095	0.245		0.1064	False		,,,				2504	0.2791				p.A228A		Atlas-SNP	.											.	PRR25	27	.	0			c.T684C						PASS	.	C		2629,1401		879,871,265	10.0	12.0	11.0		684	0.2	0.0	16	dbSNP_120	11	864,7408		53,758,3325	no	coding-synonymous	PRR25	NM_001013638.1		932,1629,3590	CC,CT,TT		10.4449,34.7643,28.3938		228/403	863336	3493,8809	2015	4136	6151	SO:0001819	synonymous_variant	388199	exon3			CTCTGCTATTGCT	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.684T>C	16.37:g.863336T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_001013638		Silent	SNP	ENST00000301698.1	37	CCDS45372.1																																																																																			T|0.671;C|0.329	0.329	strong		0.726	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
MUC16	94025	hgsc.bcm.edu	37	19	8995959	8995959	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8995959G>T	ENST00000397910.4	-	62	41485	c.41282C>A	c.(41281-41283)aCc>aAc	p.T13761N	MUC16_ENST00000380951.5_Missense_Mutation_p.T402N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13763				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						CTCACTGCTGGTGGTGGACAC	0.527																																					p.T13761N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41282A						PASS	.						89.0	78.0	81.0					19																	8995959		1947	4143	6090	SO:0001583	missense	94025	exon62			CTGCTGGTGGTGG	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.41282C>A	19.37:g.8995959G>T	ENSP00000381008:p.Thr13761Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	14	0.311111	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.099|6.099	0.386626|0.386626	0.11524|0.11524	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.35973	.|1.28;1.28	1.84|1.84	0.727|0.727	0.18254|0.18254	.|.	.|.	.|.	.|.	.|.	T|T	0.53254|0.53254	0.1785|0.1785	M|M	0.81239|0.81239	2.535|2.535	.|.	.|.	.|.	.|B;D	.|0.53745	.|0.099;0.962	.|B;D	.|0.66716	.|0.007;0.946	T|T	0.58142|0.58142	-0.7688|-0.7688	4|8	.|0.44086	.|T	.|0.13	-3.0332|-3.0332	5.3761|5.3761	0.16166|0.16166	0.0:0.0:0.6654:0.3346|0.0:0.0:0.6654:0.3346	.|.	.|21406;13761	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	T|N	601|13761;402	.|ENSP00000381008:T13761N;ENSP00000370338:T402N	.|ENSP00000370338:T402N	P|T	-|-	1|2	0|0	MUC16|MUC16	8856959|8856959	0.002000|0.002000	0.14202|0.14202	0.034000|0.034000	0.17996|0.17996	0.195000|0.195000	0.23768|0.23768	0.094000|0.094000	0.15107|0.15107	0.320000|0.320000	0.23234|0.23234	0.455000|0.455000	0.32223|0.32223	CCA|ACC	.	.	none		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SYNE1	23345	hgsc.bcm.edu	37	6	152694184	152694184	+	Silent	SNP	T	T	C	rs6913579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152694184T>C	ENST00000367255.5	-	59	10096	c.9495A>G	c.(9493-9495)gaA>gaG	p.E3165E	SYNE1_ENST00000341594.5_Silent_p.E3204E|SYNE1_ENST00000423061.1_Silent_p.E3172E|SYNE1_ENST00000265368.4_Silent_p.E3165E|SYNE1_ENST00000448038.1_Silent_p.E3172E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3165					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)		CTAGAGCAGATTCTTTTTGGT	0.378										HNSCC(10;0.0054)			T|||	2345	0.468251	0.4365	0.536	5008	,	,		17998	0.4613		0.5308	False		,,,				2504	0.4059				p.E3172E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A9516G						PASS	.	T	,	2184,2222	585.1+/-386.2	541,1102,560	187.0	198.0	194.0		9516,9495	3.0	1.0	6	dbSNP_116	194	4694,3906	605.6+/-395.0	1320,2054,926	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	1861,3156,1486	CC,CT,TT		45.4186,49.5688,47.1167	,	3172/8750,3165/8798	152694184	6878,6128	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon59			AGCAGATTCTTTT	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.9495A>G	6.37:g.152694184T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_033071	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	1021|1021	0.4674908424908425|0.4674908424908425	203|203	0.41260162601626016|0.41260162601626016	184|184	0.5082872928176796|0.5082872928176796	237|237	0.4143356643356643|0.4143356643356643	397|397	0.5237467018469657|0.5237467018469657	T|T	4.796|4.796	0.148083|0.148083	0.09134|0.09134	0.495688|0.495688	0.545814|0.545814	ENSG00000131018|ENSG00000131018	ENST00000469439|ENST00000454018	.|.	.|.	.|.	5.74|5.74	3.04|3.04	0.35103|0.35103	.|.	.|.	.|.	.|.	.|.	T|T	0.38957|0.38957	0.1060|0.1060	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999984213|0.9999999999984213	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25537|0.25537	-1.0129|-1.0129	3|3	.|.	.|.	.|.	.|.	10.8986|10.8986	0.47038|0.47038	0.0:0.1482:0.0:0.8518|0.0:0.1482:0.0:0.8518	rs6913579;rs6913579|rs6913579;rs6913579	.|.	.|.	.|.	V|S	30|282	.|.	.|.	I|N	-|-	1|2	0|0	SYNE1|SYNE1	152735877|152735877	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.639000|0.639000	0.38242|0.38242	0.825000|0.825000	0.27393|0.27393	1.007000|1.007000	0.39238|0.39238	0.533000|0.533000	0.62120|0.62120	ATC|AAT	T|0.507;C|0.493	0.493	strong		0.378	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TIMD4	91937	hgsc.bcm.edu	37	5	156346506	156346506	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:156346506G>A	ENST00000274532.2	-	9	1155	c.1099C>T	c.(1099-1101)Cat>Tat	p.H367Y	TIMD4_ENST00000407087.3_Missense_Mutation_p.H339Y|TIMD4_ENST00000406964.1_Missense_Mutation_p.H69Y	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	367						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCTTCCATGCTGCACGTCA	0.428																																					p.H367Y		Atlas-SNP	.											TIMD4,NS,carcinoma,+1,1	TIMD4	94	1	0			c.C1099T						scavenged	.						202.0	172.0	182.0					5																	156346506		2203	4300	6503	SO:0001583	missense	91937	exon9			TTCCATGCTGCAC	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"""Immunoglobulin superfamily / V-set domain containing"""	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.1099C>T	5.37:g.156346506G>A	ENSP00000274532:p.His367Tyr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	220	3	0.0136364	NM_138379	B5MCL9	Missense_Mutation	SNP	ENST00000274532.2	37	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.471959	0.43942	.	.	ENSG00000145850	ENST00000274532;ENST00000406964;ENST00000407087	T;T;T	0.69435	-0.4;-0.4;-0.4	4.66	2.47	0.30058	.	1.224140	0.06005	N	0.648587	T	0.57301	0.2044	N	0.19112	0.55	0.09310	N	1	D;P	0.56968	0.978;0.952	P;P	0.45913	0.497;0.497	T	0.52403	-0.8580	10	0.66056	D	0.02	-0.1368	9.1932	0.37211	0.0:0.0:0.5289:0.4711	.	339;367	B5MCL9;Q96H15	.;TIMD4_HUMAN	Y	367;69;339	ENSP00000274532:H367Y;ENSP00000385882:H69Y;ENSP00000385973:H339Y	ENSP00000274532:H367Y	H	-	1	0	TIMD4	156279084	0.005000	0.15991	0.003000	0.11579	0.005000	0.04900	1.387000	0.34430	1.064000	0.40671	0.561000	0.74099	CAT	.	.	none		0.428	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379	
ALDH1L2	160428	hgsc.bcm.edu	37	12	105434467	105434467	+	Silent	SNP	C	C	T	rs11112330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:105434467C>T	ENST00000258494.9	-	16	2009	c.1869G>A	c.(1867-1869)acG>acA	p.T623T	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	623	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)	p.T623T(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CAGTCAAGGGCGTGACCTGAG	0.483													C|||	1527	0.304912	0.1384	0.2622	5008	,	,		17193	0.2619		0.3748	False		,,,				2504	0.5327				p.T623T		Atlas-SNP	.											ALDH1L2,NS,carcinoma,0,1	ALDH1L2	71	1	1	Substitution - coding silent(1)	stomach(1)	c.G1869A						PASS	.	C		759,3647	309.7+/-291.2	57,645,1501	209.0	203.0	205.0		1869	-5.0	0.9	12	dbSNP_120	205	3278,5322	491.9+/-373.2	622,2034,1644	no	coding-synonymous	ALDH1L2	NM_001034173.3		679,2679,3145	TT,TC,CC		38.1163,17.2265,31.0395		623/924	105434467	4037,8969	2203	4300	6503	SO:0001819	synonymous_variant	160428	exon16			CAAGGGCGTGACC	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.1869G>A	12.37:g.105434467C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Silent	SNP	ENST00000258494.9	37	CCDS31891.1																																																																																			C|0.698;T|0.302	0.302	strong		0.483	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294	
OR4C15	81309	hgsc.bcm.edu	37	11	55322638	55322638	+	Missense_Mutation	SNP	C	C	T	rs12225462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55322638C>T	ENST00000314644.2	+	1	856	c.856C>T	c.(856-858)Cgc>Tgc	p.R286C		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	232						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						TTCTGAAGGGCGCTGGAAAGC	0.443										HNSCC(20;0.049)			c|||	909	0.18151	0.0794	0.1744	5008	,	,		17916	0.2331		0.1004	False		,,,				2504	0.3548				p.R286C		Atlas-SNP	.											.	OR4C15	145	.	0			c.C856T						PASS	.	C	CYS/ARG	414,3988	203.1+/-225.7	23,368,1810	221.0	203.0	209.0		856	3.0	0.0	11	dbSNP_120	209	937,7655	206.2+/-248.4	57,823,3416	yes	missense	OR4C15	NM_001001920.1	180	80,1191,5226	TT,TC,CC		10.9055,9.4048,10.3971	probably-damaging	286/371	55322638	1351,11643	2201	4296	6497	SO:0001583	missense	81309	exon1			GAAGGGCGCTGGA	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.856C>T	11.37:g.55322638C>T	ENSP00000324958:p.Arg286Cys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	307	0.14056776556776557	39	0.07926829268292683	56	0.15469613259668508	143	0.25	69	0.09102902374670185	C	10.11	1.259426	0.23051	0.094048	0.109055	ENSG00000181939	ENST00000314644	T	0.00337	8.05	5.02	3.01	0.34805	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.92833	3.35	0.80722	P	0.0	D	0.76494	0.999	D	0.67900	0.954	T	0.42783	-0.9431	8	0.72032	D	0.01	.	11.0258	0.47744	0.4667:0.5333:0.0:0.0	rs12225462;rs52823838;rs57466201;rs12225462	232	Q8NGM1	OR4CF_HUMAN	C	286	ENSP00000324958:R286C	ENSP00000324958:R286C	R	+	1	0	OR4C15	55079214	0.000000	0.05858	0.018000	0.16275	0.119000	0.20118	0.179000	0.16840	1.298000	0.44778	0.385000	0.25706	CGC	C|0.874;T|0.126	0.126	strong		0.443	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
KRT40	125115	hgsc.bcm.edu	37	17	39134528	39134528	+	Missense_Mutation	SNP	G	G	A	rs16968862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39134528G>A	ENST00000398486.2	-	9	1377	c.1217C>T	c.(1216-1218)tCg>tTg	p.S406L	AC004231.2_ENST00000418393.1_RNA|KRT40_ENST00000377755.4_Missense_Mutation_p.S406L	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	406	Tail.		S -> L (in dbSNP:rs16968862).			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)				GCATGTGGTCGAACATGGGCT	0.438													G|||	743	0.148363	0.2451	0.1037	5008	,	,		19413	0.0317		0.1292	False		,,,				2504	0.1892				p.S406L		Atlas-SNP	.											.	KRT40	27	.	0			c.C1217T						PASS	.	G	LEU/SER	786,3080		76,634,1223	100.0	110.0	107.0		1217	5.2	0.0	17	dbSNP_123	107	1061,7227		79,903,3162	yes	missense	KRT40	NM_182497.3	145	155,1537,4385	AA,AG,GG		12.8016,20.3311,15.1966	benign	406/432	39134528	1847,10307	1933	4144	6077	SO:0001583	missense	125115	exon9			GTGGTCGAACATG	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.1217C>T	17.37:g.39134528G>A	ENSP00000381500:p.Ser406Leu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	285	0.1304945054945055	122	0.24796747967479674	38	0.10497237569060773	22	0.038461538461538464	103	0.1358839050131926	G	14.84	2.655613	0.47467	0.203311	0.128016	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.82893	-1.66;-1.66	5.2	5.2	0.72013	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	P	0.51240	0.943	B	0.44085	0.44	T	0.08743	-1.0707	8	0.54805	T	0.06	.	14.5864	0.68328	0.0:0.0:1.0:0.0	rs16968862	406	Q6A162	K1C40_HUMAN	L	406	ENSP00000366984:S406L;ENSP00000381500:S406L	ENSP00000366984:S406L	S	-	2	0	KRT40	36388054	0.173000	0.23056	0.016000	0.15963	0.060000	0.15804	4.394000	0.59671	2.584000	0.87258	0.650000	0.86243	TCG	G|0.870;A|0.130	0.130	strong		0.438	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
TSEN54	283989	hgsc.bcm.edu	37	17	73517536	73517536	+	Missense_Mutation	SNP	G	G	A	rs79508780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73517536G>A	ENST00000333213.6	+	7	604	c.568G>A	c.(568-570)Gtg>Atg	p.V190M		NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	190					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)			GGATGCCAGCGTGCAGCACTT	0.622													G|||	114	0.0227636	0.0015	0.0231	5008	,	,		17829	0.0		0.0596	False		,,,				2504	0.0368				p.V190M		Atlas-SNP	.											TSEN54,NS,carcinoma,-2,1	TSEN54	27	1	0			c.G568A						PASS	.	G	MET/VAL	51,4355	51.6+/-87.1	0,51,2152	97.0	87.0	90.0		568	-1.7	0.0	17	dbSNP_131	90	494,8106	143.0+/-199.1	7,480,3813	yes	missense	TSEN54	NM_207346.2	21	7,531,5965	AA,AG,GG		5.7442,1.1575,4.1904	benign	190/527	73517536	545,12461	2203	4300	6503	SO:0001583	missense	283989	exon7			GCCAGCGTGCAGC	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.568G>A	17.37:g.73517536G>A	ENSP00000327487:p.Val190Met	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	59	0.027014652014652016	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	47	0.06200527704485488	G	2.490	-0.317750	0.05386	0.011575	0.057442	ENSG00000182173	ENST00000434205;ENST00000333213	T	0.57273	0.41	5.63	-1.71	0.08133	.	1.141700	0.06213	N	0.685374	T	0.03608	0.0103	N	0.22421	0.69	0.09310	N	1	P	0.51653	0.947	B	0.35182	0.197	T	0.11891	-1.0569	10	0.40728	T	0.16	-0.6814	5.7897	0.18353	0.4542:0.0:0.3547:0.1911	.	190	Q7Z6J9	SEN54_HUMAN	M	89;190	ENSP00000327487:V190M	ENSP00000327487:V190M	V	+	1	0	TSEN54	71029131	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	0.022000	0.13511	0.026000	0.15269	-0.982000	0.02568	GTG	A|0.040;C|0.000;G|0.960	0.040	strong		0.622	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
DYTN	391475	hgsc.bcm.edu	37	2	207527656	207527656	+	Missense_Mutation	SNP	A	A	G	rs201792178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207527656A>G	ENST00000452335.2	-	11	1720	c.1604T>C	c.(1603-1605)aTg>aCg	p.M535T		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	535						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GAAGGCATCCATAAGTTTTGA	0.433													A|||	2	0.000399361	0.0	0.0014	5008	,	,		21916	0.0		0.001	False		,,,				2504	0.0				p.M535T		Atlas-SNP	.											DYTN_ENST00000452335,colon,carcinoma,-1,1	DYTN	168	1	0			c.T1604C						PASS	.	A	THR/MET	5,3917		0,5,1956	277.0	273.0	274.0		1604	-2.1	0.0	2		274	42,8238		0,42,4098	yes	missense	DYTN	NM_001093730.1	81	0,47,6054	GG,GA,AA		0.5072,0.1275,0.3852	benign	535/579	207527656	47,12155	1961	4140	6101	SO:0001583	missense	391475	exon11			GCATCCATAAGTT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1604T>C	2.37:g.207527656A>G	ENSP00000396593:p.Met535Thr	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	2.601	-0.292930	0.05568	0.001275	0.005072	ENSG00000232125	ENST00000452335	T	0.14640	2.49	5.13	-2.14	0.07123	.	.	.	.	.	T	0.03695	0.0105	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44267	-0.9339	9	0.15066	T	0.55	-0.1195	4.7275	0.12948	0.392:0.0:0.4418:0.1662	.	535	A2CJ06	DYTN_HUMAN	T	535	ENSP00000396593:M535T	ENSP00000396593:M535T	M	-	2	0	DYTN	207235901	0.114000	0.22134	0.020000	0.16555	0.244000	0.25665	0.144000	0.16135	-0.124000	0.11724	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.433	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
GIPC1	10755	hgsc.bcm.edu	37	19	14590236	14590236	+	Silent	SNP	C	C	T	rs3815715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14590236C>T	ENST00000393033.4	-	7	1025	c.756G>A	c.(754-756)acG>acA	p.T252T	GIPC1_ENST00000393029.3_Silent_p.T155T|GIPC1_ENST00000393028.1_Silent_p.T155T|GIPC1_ENST00000586027.1_Silent_p.T252T|GIPC1_ENST00000345425.2_Silent_p.T252T|GIPC1_ENST00000591349.1_Silent_p.T155T	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	252					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						GATCCTCCACCGTGGCGGGGC	0.622													c|||	1539	0.307308	0.1195	0.2536	5008	,	,		12956	0.6448		0.2555	False		,,,				2504	0.3047				p.T252T	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											GIPC1,NS,carcinoma,0,1	GIPC1	21	1	0			c.G756A						PASS	.	C	,,,,,	566,3768		50,466,1651	7.0	9.0	9.0		756,465,756,465,756,465	-8.1	0.9	19	dbSNP_107	9	2343,6163		364,1615,2274	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GIPC1	NM_005716.2,NM_202467.1,NM_202468.1,NM_202469.1,NM_202470.1,NM_202494.1	,,,,,	414,2081,3925	TT,TC,CC		27.5453,13.0595,22.6558	,,,,,	252/334,155/237,252/334,155/237,252/334,155/237	14590236	2909,9931	2167	4253	6420	SO:0001819	synonymous_variant	10755	exon6			CTCCACCGTGGCG	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.756G>A	19.37:g.14590236C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	CCDS12310.1																																																																																			C|0.678;T|0.322	0.322	strong		0.622	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462926	37462926	+	Silent	SNP	G	G	A	rs2235321	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37462926G>A	ENST00000346753.3	-	17	2333	c.2217C>T	c.(2215-2217)taC>taT	p.Y739Y	TMPRSS6_ENST00000381792.2_Silent_p.Y752Y|TMPRSS6_ENST00000406856.1_Silent_p.Y752Y|TMPRSS6_ENST00000406725.1_Silent_p.Y730Y	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	739	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	p.Y739Y(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GCGTCACCTGGTAGCGATAGA	0.607													G|||	1783	0.35603	0.41	0.2118	5008	,	,		20113	0.4087		0.4245	False		,,,				2504	0.2607				p.Y739Y		Atlas-SNP	.											TMPRSS6,NS,carcinoma,0,1	TMPRSS6	99	1	1	Substitution - coding silent(1)	stomach(1)	c.C2217T						PASS	.	G		1850,2556	536.1+/-374.4	378,1094,731	133.0	98.0	110.0		2217	3.7	1.0	22	dbSNP_98	110	3223,5377	485.3+/-371.6	616,1991,1693	yes	coding-synonymous	TMPRSS6	NM_153609.2		994,3085,2424	AA,AG,GG		37.4767,41.9882,39.0051		739/812	37462926	5073,7933	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon17			CACCTGGTAGCGA	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.2217C>T	22.37:g.37462926G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.622;A|0.377	0.377	strong		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
PCDH19	57526	hgsc.bcm.edu	37	X	99661969	99661969	+	Silent	SNP	G	G	A	rs1953337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:99661969G>A	ENST00000373034.4	-	1	3302	c.1627C>T	c.(1627-1629)Ctg>Ttg	p.L543L	PCDH19_ENST00000255531.7_Silent_p.L543L|PCDH19_ENST00000420881.2_Silent_p.L543L	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> P (in EIEE9; disease features overlapping with Dravet syndrome). {ECO:0000269|PubMed:19214208}.		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						TTGCTTTGCAGTGAGGGAAGG	0.587													G|||	325	0.0860927	0.0204	0.121	3775	,	,		13359	0.001		0.1819	False		,,,				2504	0.0307				p.L543L		Atlas-SNP	.											.	PCDH19	269	.	0			c.C1627T						PASS	.	G	,,	179,3568		4,148,23,1436,548	129.0	126.0	127.0		1627,1627,1627	4.0	0.9	X	dbSNP_92	127	1917,4749		226,956,509,1231,1331	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDH19	NM_001105243.1,NM_001184880.1,NM_020766.2	,,	230,1104,532,2667,1879	AA,AG,A,GG,G		28.7579,4.7772,20.1287	,,	543/1102,543/1149,543/1101	99661969	2096,8317	2159	4253	6412	SO:0001819	synonymous_variant	57526	exon1			TTTGCAGTGAGGG	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.1627C>T	X.37:g.99661969G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																			G|0.881;A|0.119	0.119	strong		0.587	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
EVC2	132884	hgsc.bcm.edu	37	4	5642347	5642347	+	Missense_Mutation	SNP	G	G	C	rs141287105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:5642347G>C	ENST00000344408.5	-	10	1417	c.1364C>G	c.(1363-1365)aCa>aGa	p.T455R	EVC2_ENST00000310917.2_Missense_Mutation_p.T375R|EVC2_ENST00000344938.1_Missense_Mutation_p.T455R	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	455					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						ACATTCAGCTGTCAATGCCAC	0.433													G|||	10	0.00199681	0.0	0.0014	5008	,	,		22461	0.0		0.0089	False		,,,				2504	0.0				p.T455R		Atlas-SNP	.											.	EVC2	202	.	0			c.C1364G						PASS	.	G	ARG/THR,ARG/THR	5,4401	9.9+/-24.2	0,5,2198	367.0	327.0	341.0		1124,1364	3.3	0.8	4	dbSNP_134	341	65,8535	39.8+/-96.3	1,63,4236	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	71,71	1,68,6434	CC,CG,GG		0.7558,0.1135,0.5382	probably-damaging,probably-damaging	375/1229,455/1309	5642347	70,12936	2203	4300	6503	SO:0001583	missense	132884	exon10			TCAGCTGTCAATG	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.1364C>G	4.37:g.5642347G>C	ENSP00000342144:p.Thr455Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	151	66	0.437086	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	G	16.55	3.154339	0.57259	0.001135	0.007558	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.78707	-1.2;-1.2;-1.2	4.25	3.34	0.38264	.	0.344939	0.27677	N	0.018315	T	0.75671	0.3881	M	0.67953	2.075	0.38779	D	0.954725	D	0.56746	0.977	P	0.54544	0.755	T	0.77814	-0.2448	10	0.22706	T	0.39	-4.8253	12.9472	0.58379	0.0:0.0:0.8385:0.1615	.	455	Q86UK5	LBN_HUMAN	R	455;375;455	ENSP00000339954:T455R;ENSP00000311683:T375R;ENSP00000342144:T455R	ENSP00000311683:T375R	T	-	2	0	EVC2	5693248	1.000000	0.71417	0.807000	0.32361	0.767000	0.43475	4.192000	0.58378	2.074000	0.62210	0.591000	0.81541	ACA	G|0.995;C|0.005	0.005	strong		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
TRIM42	287015	hgsc.bcm.edu	37	3	140407260	140407260	+	Missense_Mutation	SNP	C	C	A	rs9876490	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:140407260C>A	ENST00000286349.3	+	3	1927	c.1736C>A	c.(1735-1737)gCa>gAa	p.A579E		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	579			A -> E (in dbSNP:rs9876490).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGTGCTGGAGCAGACAGCCAG	0.572													C|||	2017	0.402756	0.2723	0.5072	5008	,	,		17094	0.3899		0.5328	False		,,,				2504	0.3845				p.A579E		Atlas-SNP	.											.	TRIM42	143	.	0			c.C1736A						PASS	.	C	GLU/ALA	1382,3024	455.5+/-351.0	224,934,1045	83.0	83.0	83.0		1736	-1.2	0.0	3	dbSNP_119	83	4982,3618	625.7+/-397.7	1455,2072,773	yes	missense	TRIM42	NM_152616.4	107	1679,3006,1818	AA,AC,CC		42.0698,31.3663,48.9313	benign	579/724	140407260	6364,6642	2203	4300	6503	SO:0001583	missense	287015	exon3			CTGGAGCAGACAG	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.1736C>A	3.37:g.140407260C>A	ENSP00000286349:p.Ala579Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	100	61	0.61	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	933	0.4271978021978022	150	0.3048780487804878	179	0.494475138121547	208	0.36363636363636365	396	0.5224274406332454	C	5.246	0.230904	0.09969	0.313663	0.579302	ENSG00000155890	ENST00000286349	T	0.39229	1.09	5.52	-1.19	0.09585	.	2.154850	0.04497	U	0.380605	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14438	0.01	B	0.18263	0.021	T	0.46978	-0.9152	9	0.38643	T	0.18	-16.6172	5.1633	0.15073	0.0:0.378:0.2726:0.3494	rs9876490;rs52813579;rs60498709;rs9876490	579	Q8IWZ5	TRI42_HUMAN	E	579	ENSP00000286349:A579E	ENSP00000286349:A579E	A	+	2	0	TRIM42	141889950	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.208000	0.17415	-0.118000	0.11851	-0.140000	0.14226	GCA	C|0.542;A|0.458	0.458	strong		0.572	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
H6PD	9563	hgsc.bcm.edu	37	1	9324213	9324213	+	Missense_Mutation	SNP	C	C	T	rs17368528	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9324213C>T	ENST00000377403.2	+	5	1963	c.1661C>T	c.(1660-1662)cCg>cTg	p.P554L	H6PD_ENST00000602477.1_Missense_Mutation_p.P565L	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	554	6-phosphogluconolactonase.		P -> L (in dbSNP:rs17368528).		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)		CGAGAGAGCCCGCTGGTCTCC	0.652													C|||	485	0.096845	0.0053	0.1138	5008	,	,		15585	0.0685		0.1302	False		,,,				2504	0.2035				p.P554L		Atlas-SNP	.											H6PD,NS,carcinoma,-1,1	H6PD	71	1	0			c.C1661T						PASS	.	C	LEU/PRO	100,4300		1,98,2101	22.0	28.0	26.0		1661	4.8	0.9	1	dbSNP_123	26	1054,7542		63,928,3307	yes	missense	H6PD	NM_004285.3	98	64,1026,5408	TT,TC,CC		12.2615,2.2727,8.8797	probably-damaging	554/792	9324213	1154,11842	2200	4298	6498	SO:0001583	missense	9563	exon5			AGAGCCCGCTGGT	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.1661C>T	1.37:g.9324213C>T	ENSP00000366620:p.Pro554Leu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	185	0.08470695970695971	6	0.012195121951219513	45	0.12430939226519337	38	0.06643356643356643	96	0.1266490765171504	C	14.06	2.423691	0.43020	0.022727	0.122615	ENSG00000049239	ENST00000377403	D	0.98164	-4.76	5.67	4.76	0.60689	.	0.275476	0.42682	D	0.000664	T	0.30727	0.0774	M	0.67953	2.075	0.21652	P	0.999602907	P	0.48640	0.913	B	0.35688	0.208	T	0.69468	-0.5137	9	0.66056	D	0.02	-50.9557	13.1468	0.59467	0.0:0.9238:0.0:0.0762	rs17368528;rs52818643;rs17368528	554	O95479	G6PE_HUMAN	L	554	ENSP00000366620:P554L	ENSP00000366620:P554L	P	+	2	0	H6PD	9246800	0.890000	0.30428	0.913000	0.36048	0.619000	0.37552	1.817000	0.39002	2.677000	0.91161	0.561000	0.74099	CCG	C|0.916;N|0.000	.	strong		0.652	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
HLA-B	3106	hgsc.bcm.edu	37	6	31324051	31324051	+	Missense_Mutation	SNP	C	C	A	rs41551018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324051C>A	ENST00000412585.2	-	3	540	c.512G>T	c.(511-513)tGg>tTg	p.W171L		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	171	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						GGCCGCCTCCCACTTGCGCTG	0.667									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	340	0.0678914	0.0749	0.0576	5008	,	,		12515	0.12		0.0577	False		,,,				2504	0.0225				p.W171L		Atlas-SNP	.											.	HLA-B	54	.	0			c.G512T						PASS	.	C	LEU/TRP	195,4123		0,195,1964	29.0	20.0	23.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	512	1.3	0.3	6	dbSNP_127	23	375,8059		5,365,3847	no	missense	HLA-B	NM_005514.6	61	5,560,5811	AA,AC,CC		4.4463,4.516,4.4699		171/363	31324051	570,12182	2159	4217	6376	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GCCTCCCACTTGC	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.512G>T	6.37:g.31324051C>A	ENSP00000399168:p.Trp171Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	204	59	0.289216	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	163	0.07463369963369963	36	0.07317073170731707	19	0.052486187845303865	68	0.11888111888111888	40	0.052770448548812667	N	9.115	1.007573	0.19199	0.04516	0.044463	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00015	9.14;9.14	3.18	1.3	0.21679	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.000000	0.37012	U	0.002282	T	0.00073	0.0002	M	0.86740	2.835	0.31286	P	0.6900200000000001	P;B	0.48230	0.907;0.01	B;B	0.40741	0.339;0.017	T	0.20739	-1.0266	9	0.72032	D	0.01	.	9.3439	0.38096	0.3857:0.6143:0.0:0.0	rs41551018	171;171	P30480;P01889	1B42_HUMAN;1B07_HUMAN	L	171;50;50;182	ENSP00000399168:W171L;ENSP00000405931:W182L	ENSP00000399168:W171L	W	-	2	0	HLA-B	31432030	0.955000	0.32602	0.325000	0.25375	0.005000	0.04900	0.352000	0.20113	0.177000	0.19895	-0.898000	0.02899	TGG	C|0.943;A|0.057	0.057	strong		0.667	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
EPHA2	1969	hgsc.bcm.edu	37	1	16458339	16458339	+	Silent	SNP	G	G	A	rs112285834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16458339G>A	ENST00000358432.5	-	14	2506	c.2352C>T	c.(2350-2352)acC>acT	p.T784T		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	784	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	CCTCCGGGGCGGTCCAGCGGA	0.647													G|||	14	0.00279553	0.0	0.0014	5008	,	,		17168	0.0		0.0129	False		,,,				2504	0.0				p.T784T		Atlas-SNP	.											.	EPHA2	102	.	0			c.C2352T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	49.0	46.0	47.0		2352	-8.9	0.7	1	dbSNP_132	47	138,8462	68.0+/-130.5	0,138,4162	no	coding-synonymous	EPHA2	NM_004431.3		0,152,6351	AA,AG,GG		1.6047,0.3177,1.1687		784/977	16458339	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon14			CGGGGCGGTCCAG	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.2352C>T	1.37:g.16458339G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	79	28	0.35443	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.990;A|0.010	0.010	strong		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
HELZ2	85441	hgsc.bcm.edu	37	20	62191558	62191558	+	Silent	SNP	G	G	A	rs3810479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	36	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	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	
FLG	2312	hgsc.bcm.edu	37	1	152281228	152281228	+	Missense_Mutation	SNP	C	C	G	rs7546186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281228C>G	ENST00000368799.1	-	3	6169	c.6134G>C	c.(6133-6135)aGt>aCt	p.S2045T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2045	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)			CTCACTGTCACTGGCCTGACT	0.562									Ichthyosis																												p.S2045T		Atlas-SNP	.											.	FLG	900	.	0			c.G6134C						PASS	.	A	THR/SER	1445,2961		0,1445,758	497.0	422.0	448.0		6134	2.4	0.0	1	dbSNP_116	448	1127,7467		0,1127,3170	no	missense	FLG	NM_002016.1	58	0,2572,3928	GG,GC,CC		13.1138,32.7962,19.7846	possibly-damaging	2045/4062	152281228	2572,10428	2203	4297	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGTCACTGGCCT	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.6134G>C	1.37:g.152281228C>G	ENSP00000357789:p.Ser2045Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	264	94	0.356061	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	4.788	0.146596	0.09134	0.327962	0.131138	ENSG00000143631	ENST00000368799	T	0.08008	3.14	3.29	2.37	0.29283	.	.	.	.	.	T	0.06371	0.0164	M	0.66939	2.045	0.09310	N	1	P	0.47677	0.899	P	0.53266	0.722	T	0.27468	-1.0073	9	0.15499	T	0.54	-11.6761	8.0203	0.30406	0.2436:0.7564:0.0:0.0	rs7546186	2045	P20930	FILA_HUMAN	T	2045	ENSP00000357789:S2045T	ENSP00000357789:S2045T	S	-	2	0	FLG	150547852	0.044000	0.20184	0.010000	0.14722	0.001000	0.01503	1.514000	0.35834	0.726000	0.32339	-0.333000	0.08304	AGT	C|0.969;G|0.031	0.031	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
JAK3	3718	hgsc.bcm.edu	37	19	17945696	17945696	+	Missense_Mutation	SNP	C	C	T	rs3213409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17945696C>T	ENST00000527670.1	-	15	2193	c.2164G>A	c.(2164-2166)Gtc>Atc	p.V722I	JAK3_ENST00000534444.1_Missense_Mutation_p.V722I|JAK3_ENST00000458235.1_Missense_Mutation_p.V722I			P52333	JAK3_HUMAN	Janus kinase 3	722	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in dbSNP:rs3213409). {ECO:0000269|PubMed:10982185, ECO:0000269|PubMed:14615376, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.V722I(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGCATGGTGACGCCACTAAAC	0.627		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""								C|||	18	0.00359425	0.0023	0.0014	5008	,	,		16598	0.0		0.007	False		,,,				2504	0.0072				p.V722I		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3,NS,haematopoietic_neoplasm,0,2	JAK3	341	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2164A	GRCh37	CM000172	JAK3	M	rs3213409	PASS	.	C	ILE/VAL	9,4397	14.3+/-33.2	1,7,2195	82.0	88.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2164	0.2	0.0	19	dbSNP_106	86	114,8486	61.0+/-122.8	2,110,4188	yes	missense	JAK3	NM_000215.3	29	3,117,6383	TT,TC,CC		1.3256,0.2043,0.9457	benign	722/1125	17945696	123,12883	2203	4300	6503	SO:0001583	missense	3718	exon16			TGGTGACGCCACT	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2164G>A	19.37:g.17945696C>T	ENSP00000432511:p.Val722Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	0	0.0	5	0.006596306068601583	C	8.473	0.857929	0.17178	0.002043	0.013256	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;T	0.61980	0.06;0.06;0.06	4.89	0.248	0.15526	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.618726	0.15813	N	0.243360	T	0.33147	0.0853	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.003;0.004	T	0.24977	-1.0145	10	0.62326	D	0.03	-7.2327	7.7407	0.28839	0.0:0.6163:0.0:0.3837	rs3213409;rs52813014;rs3213409	722;722	P52333-2;P52333	.;JAK3_HUMAN	I	722	ENSP00000391676:V722I;ENSP00000432511:V722I;ENSP00000436421:V722I	ENSP00000391676:V722I	V	-	1	0	JAK3	17806696	0.011000	0.17503	0.000000	0.03702	0.008000	0.06430	1.524000	0.35942	-0.126000	0.11682	0.555000	0.69702	GTC	C|0.991;T|0.009	0.009	strong		0.627	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656805	46656805	+	Silent	SNP	G	G	A	rs6519994	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46656805G>A	ENST00000253255.5	-	1	2414	c.2415C>T	c.(2413-2415)atC>atT	p.I805I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	805	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CAGTACTCACGATTTCTATTT	0.368													G|||	1190	0.23762	0.6505	0.1297	5008	,	,		20491	0.001		0.161	False		,,,				2504	0.0787				p.I805I		Atlas-SNP	.											PKDREJ,caecum,carcinoma,0,1	PKDREJ	195	1	0			c.C2415T						PASS	.	G		2514,1890	617.9+/-393.1	710,1094,398	66.0	72.0	70.0		2415	-10.2	0.0	22	dbSNP_116	70	1254,7346	249.2+/-276.5	88,1078,3134	no	coding-synonymous	PKDREJ	NM_006071.1		798,2172,3532	AA,AG,GG		14.5814,42.9155,28.9757		805/2254	46656805	3768,9236	2202	4300	6502	SO:0001819	synonymous_variant	10343	exon1			ACTCACGATTTCT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2415C>T	22.37:g.46656805G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.732;A|0.268	0.268	strong		0.368	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
MACF1	23499	hgsc.bcm.edu	37	1	39835817	39835817	+	Missense_Mutation	SNP	A	A	G	rs2296172	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:39835817A>G	ENST00000372915.3	+	50	13156	c.13069A>G	c.(13069-13071)Atg>Gtg	p.M4357V	MACF1_ENST00000564288.1_Missense_Mutation_p.M4352V|MACF1_ENST00000361689.2_Missense_Mutation_p.M2290V|MACF1_ENST00000545844.1_Missense_Mutation_p.M2290V|MACF1_ENST00000567887.1_Missense_Mutation_p.M4389V|MACF1_ENST00000317713.7_Missense_Mutation_p.M2290V|MACF1_ENST00000539005.1_Missense_Mutation_p.M2290V|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000289893.4_Missense_Mutation_p.M2792V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4357			M -> V (in dbSNP:rs2296172). {ECO:0000269|PubMed:10559237}.		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GGAAACTTCTATGAGTGCTAA	0.433													A|||	592	0.118211	0.0121	0.2046	5008	,	,		20675	0.1587		0.1948	False		,,,				2504	0.0798				p.M2290V		Atlas-SNP	.											.	MACF1	909	.	0			c.A6868G						PASS	.	A	VAL/MET,VAL/MET	194,4212	122.1+/-159.5	1,192,2010	69.0	68.0	68.0		6868,8374	0.3	1.0	1	dbSNP_100	68	1919,6681	339.9+/-323.4	231,1457,2612	yes	missense,missense	MACF1	NM_012090.4,NM_033044.3	21,21	232,1649,4622	GG,GA,AA		22.314,4.4031,16.2463	benign,benign	2290/5431,2792/5939	39835817	2113,10893	2203	4300	6503	SO:0001583	missense	23499	exon47			ACTTCTATGAGTG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13069A>G	1.37:g.39835817A>G	ENSP00000362006:p.Met4357Val	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		320|320	0.14652014652014653|0.14652014652014653	8|8	0.016260162601626018|0.016260162601626018	76|76	0.20994475138121546|0.20994475138121546	89|89	0.1555944055944056|0.1555944055944056	147|147	0.19393139841688653|0.19393139841688653	A|A	1.600|1.600	-0.526671|-0.526671	0.04141|0.04141	0.044031|0.044031	0.22314|0.22314	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.59364|.	0.3;0.33;0.3;0.27;0.4;1.43|.	5.37|5.37	0.348|0.348	0.16026|0.16026	.|.	0.777656|.	0.11516|.	N|.	0.556259|.	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	0.9999999709851|0.9999999709851	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.06405|.	0.002;0.001;0.001;0.002|.	T|T	0.37934|0.37934	-0.9684|-0.9684	9|4	0.06099|.	T|.	0.92|.	.|.	0.2216|0.2216	0.00168|0.00168	0.2976:0.2744:0.1754:0.2526|0.2976:0.2744:0.1754:0.2526	rs2296172;rs57700239;rs2296172|rs2296172;rs57700239;rs2296172	4357;2290;2290;2255|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	V|C	2290;4357;2290;2290;2290;2792|1423	ENSP00000439537:M2290V;ENSP00000362006:M4357V;ENSP00000354573:M2290V;ENSP00000313438:M2290V;ENSP00000444364:M2290V;ENSP00000289893:M2792V|.	ENSP00000289893:M2792V|.	M|Y	+|+	1|2	0|0	MACF1|MACF1	39608404|39608404	0.850000|0.850000	0.29656|0.29656	0.996000|0.996000	0.52242|0.52242	0.949000|0.949000	0.60115|0.60115	0.193000|0.193000	0.17116|0.17116	0.021000|0.021000	0.15133|0.15133	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.855;G|0.145	0.145	strong		0.433	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
NUSAP1	51203	hgsc.bcm.edu	37	15	41672384	41672384	+	Silent	SNP	A	A	G	rs7168431	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41672384A>G	ENST00000559596.1	+	11	1413	c.1326A>G	c.(1324-1326)taA>taG	p.*442*	NUSAP1_ENST00000450318.1_Silent_p.*403*|NUSAP1_ENST00000560177.1_Silent_p.*441*|NUSAP1_ENST00000450592.2_Silent_p.*379*|NUSAP1_ENST00000560747.1_Silent_p.*440*|NUSAP1_ENST00000414849.2_Silent_p.*441*|NUSAP1_ENST00000260359.6_Silent_p.*427*|NUSAP1_ENST00000558123.1_3'UTR			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	0					establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		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;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		CTGAAGATTAATAATTTTTTA	0.373													A|||	579	0.115615	0.0091	0.1542	5008	,	,		19315	0.0079		0.2714	False		,,,				2504	0.183				p.X442X		Atlas-SNP	.											.	NUSAP1	32	.	0			c.A1326G						PASS	.	A	,,	186,3440		8,170,1635	71.0	80.0	77.0		1209,1326,1323	-1.1	0.0	15	dbSNP_116	77	2091,6035		252,1587,2224	no	coding-synonymous,coding-synonymous,coding-synonymous	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	,,	260,1757,3859	GG,GA,AA		25.7322,5.1296,19.3754	,,	403/403,442/442,441/441	41672384	2277,9475	1813	4063	5876	SO:0001819	synonymous_variant	51203	exon11			AGATTAATAATTT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.1326A>G	15.37:g.41672384A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_016359	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Silent	SNP	ENST00000559596.1	37	CCDS45234.1																																																																																			A|0.876;G|0.124	0.124	strong		0.373	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
OR5D14	219436	hgsc.bcm.edu	37	11	55563336	55563336	+	Missense_Mutation	SNP	A	A	T	rs76383258	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55563336A>T	ENST00000335605.1	+	1	305	c.305A>T	c.(304-306)cAg>cTg	p.Q102L		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	102						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(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TGCATGATGCAGTACTTCCTG	0.448													a|||	972	0.194089	0.121	0.1758	5008	,	,		20717	0.2381		0.1024	False		,,,				2504	0.3548				p.Q102L		Atlas-SNP	.											OR5D14,NS,carcinoma,+1,1	OR5D14	116	1	0			c.A305T						scavenged	.	A	LEU/GLN	564,3836	251.5+/-258.2	39,486,1675	146.0	120.0	129.0		305	3.9	0.1	11	dbSNP_131	129	932,7660	205.4+/-247.8	55,822,3419	yes	missense	OR5D14	NM_001004735.1	113	94,1308,5094	TT,TA,AA		10.8473,12.8182,11.5148	probably-damaging	102/315	55563336	1496,11496	2200	4296	6496	SO:0001583	missense	219436	exon1			TGATGCAGTACTT	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.305A>T	11.37:g.55563336A>T	ENSP00000334456:p.Gln102Leu	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	320	0.14652014652014653	50	0.1016260162601626	56	0.15469613259668508	144	0.2517482517482518	70	0.09234828496042216	a	14.24	2.475783	0.44044	0.128182	0.108473	ENSG00000186113	ENST00000335605	T	0.00470	7.2	5.08	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000640	T	0.00012	0.0000	H	0.97564	4.03	0.23616	P	0.99728045	P	0.51537	0.946	P	0.56916	0.809	T	0.11991	-1.0565	9	0.87932	D	0	-11.5909	11.0361	0.47802	0.8436:0.1564:0.0:0.0	.	102	Q8NGL3	OR5DE_HUMAN	L	102	ENSP00000334456:Q102L	ENSP00000334456:Q102L	Q	+	2	0	OR5D14	55319912	1.000000	0.71417	0.126000	0.21872	0.023000	0.10783	5.512000	0.67030	0.768000	0.33290	0.523000	0.50628	CAG	A|0.873;T|0.127	0.127	strong		0.448	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
XIRP2	129446	hgsc.bcm.edu	37	2	168099555	168099555	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:168099555C>T	ENST00000409195.1	+	9	1742	c.1653C>T	c.(1651-1653)gaC>gaT	p.D551D	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Silent_p.D329D|XIRP2_ENST00000295237.9_Silent_p.D551D|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	376					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACACAAATGACAGTTCTCAAA	0.398																																					p.D551D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C1653T						PASS	.						43.0	40.0	41.0					2																	168099555		1842	4094	5936	SO:0001819	synonymous_variant	129446	exon9			AAATGACAGTTCT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1653C>T	2.37:g.168099555C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	71	21	0.295775	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			.	.	none		0.398	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
KIAA1598	57698	hgsc.bcm.edu	37	10	118713596	118713596	+	Silent	SNP	G	G	A	rs117277365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118713596G>A	ENST00000355371.4	-	5	890	c.393C>T	c.(391-393)gcC>gcT	p.A131A	KIAA1598_ENST00000392903.2_Silent_p.A131A|KIAA1598_ENST00000392901.4_Silent_p.A71A|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000260777.10_Silent_p.A131A	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	131					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		AAGTCTCGGCGGCACCGTCTG	0.403													G|||	3	0.000599042	0.0	0.0	5008	,	,		17591	0.0		0.003	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	KIAA1598	74	.	0			c.C393T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	136.0	118.0	124.0		393,393	-8.1	0.0	10	dbSNP_133	124	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	KIAA1598	NM_001127211.1,NM_018330.5	,	0,12,6491	AA,AG,GG		0.093,0.0908,0.0923	,	131/632,131/457	118713596	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	57698	exon5			CTCGGCGGCACCG	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.393C>T	10.37:g.118713596G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	21	0.276316	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Silent	SNP	ENST00000355371.4	37	CCDS44482.1																																																																																			G|0.999;A|0.001	0.001	strong		0.403	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	
GTSE1	51512	hgsc.bcm.edu	37	22	46712077	46712077	+	Silent	SNP	C	C	T	rs9615947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46712077C>T	ENST00000454366.1	+	7	1412	c.1200C>T	c.(1198-1200)gtC>gtT	p.V400V		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	381					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CCAAGCGGGTCGATGTTTCTG	0.657													C|||	203	0.0405351	0.0038	0.0576	5008	,	,		12399	0.003		0.1223	False		,,,				2504	0.0327				p.V400V	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1200T						PASS	.	C		82,4324		2,78,2123	32.0	36.0	35.0		1200	-7.1	0.0	22	dbSNP_119	35	900,7696		48,804,3446	no	coding-synonymous	GTSE1	NM_016426.6		50,882,5569	TT,TC,CC		10.47,1.8611,7.5527		400/740	46712077	982,12020	2203	4298	6501	SO:0001819	synonymous_variant	51512	exon7			GCGGGTCGATGTT	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1200C>T	22.37:g.46712077C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.933;T|0.067	0.067	strong		0.657	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
TAS1R2	80834	hgsc.bcm.edu	37	1	19184077	19184077	+	Silent	SNP	A	A	G	rs68081213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19184077A>G	ENST00000375371.3	-	2	252	c.231T>C	c.(229-231)ttT>ttC	p.F77F	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	77					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CCTCCACCGCAAAGCGCATGG	0.547													-|||	1381	0.275759	0.3631	0.2853	5008	,	,		23250	0.1052		0.326	False		,,,				2504	0.2751				p.F77F		Atlas-SNP	.											.	TAS1R2	134	.	0			c.T231C						PASS	.			1451,2955		238,975,990	128.0	94.0	105.0		231	-2.2	1.0	1	dbSNP_130	105	2887,5713		471,1945,1884	no	coding-synonymous	TAS1R2	NM_152232.2		709,2920,2874	GG,GA,AA		33.5698,32.9324,33.3538		77/840	19184077	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon2			CACCGCAAAGCGC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.231T>C	1.37:g.19184077A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			A|0.684;G|0.316	0.316	strong		0.547	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
FLG	2312	hgsc.bcm.edu	37	1	152281142	152281142	+	Missense_Mutation	SNP	C	C	G	rs141120727	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281142C>G	ENST00000368799.1	-	3	6255	c.6220G>C	c.(6220-6222)Gag>Cag	p.E2074Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2074	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)			CGTGCGGACTCTTTGTGGCTC	0.557									Ichthyosis				-|||	13	0.00259585	0.0	0.0014	5008	,	,		29807	0.0		0.0089	False		,,,				2504	0.0031				p.E2074Q		Atlas-SNP	.											FLG,NS,lymphoid_neoplasm,0,1	FLG	900	1	0			c.G6220C						PASS	.	C	GLN/GLU	13,4393	20.2+/-43.8	0,13,2190	328.0	270.0	290.0		6220	-4.2	0.0	1	dbSNP_134	290	101,8499	57.2+/-118.5	2,97,4201	no	missense	FLG	NM_002016.1	29	2,110,6391	GG,GC,CC		1.1744,0.2951,0.8765	benign	2074/4062	152281142	114,12892	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGGACTCTTTGTG	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.6220G>C	1.37:g.152281142C>G	ENSP00000357789:p.Glu2074Gln	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	429	94	0.219114	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	c	4.095	0.015596	0.07959	0.002951	0.011744	ENSG00000143631	ENST00000368799	T	0.01685	4.69	2.33	-4.18	0.03846	.	.	.	.	.	T	0.00724	0.0024	M	0.75447	2.3	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.42155	-0.9468	9	0.18276	T	0.48	.	7.3479	0.26674	0.0:0.2262:0.6352:0.1386	.	2074	P20930	FILA_HUMAN	Q	2074	ENSP00000357789:E2074Q	ENSP00000357789:E2074Q	E	-	1	0	FLG	150547766	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.212000	0.09319	-0.825000	0.04290	-0.494000	0.04653	GAG	C|0.993;G|0.007	0.007	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PKD1L1	168507	hgsc.bcm.edu	37	7	47920345	47920345	+	Silent	SNP	G	G	A	rs62447081	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	74	0	0		WXS	Illumina HiSeq	Phase_I	143	98	0.685315	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	
PNP	4860	hgsc.bcm.edu	37	14	20940626	20940626	+	Silent	SNP	C	C	T	rs1130650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0		WXS	Illumina HiSeq	Phase_I	62	44	0.709677	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	
SEMA3A	10371	hgsc.bcm.edu	37	7	83590852	83590852	+	Silent	SNP	T	T	C	rs797821	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:83590852T>C	ENST00000265362.4	-	17	2465	c.2151A>G	c.(2149-2151)acA>acG	p.T717T	SEMA3A_ENST00000436949.1_Silent_p.T717T	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	717					apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ACTCATCCATTGTGTTGAGAT	0.468													C|||	3065	0.612021	0.475	0.6902	5008	,	,		19046	0.6915		0.6412	False		,,,				2504	0.6299				p.T717T		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A2151G						PASS	.	C		2179,2227	591.6+/-387.6	531,1117,555	195.0	170.0	178.0		2151	-11.6	0.2	7	dbSNP_86	178	5411,3189	482.4+/-370.9	1682,2047,571	no	coding-synonymous	SEMA3A	NM_006080.2		2213,3164,1126	CC,CT,TT		37.0814,49.4553,41.6423		717/772	83590852	7590,5416	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon17			ATCCATTGTGTTG	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.2151A>G	7.37:g.83590852T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	234	102	0.435897	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			T|0.401;G|0.006	.	strong		0.468	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
CTNNAL1	8727	hgsc.bcm.edu	37	9	111727670	111727670	+	Missense_Mutation	SNP	C	C	G	rs7021366	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111727670C>G	ENST00000325551.4	-	11	1665	c.1579G>C	c.(1579-1581)Gaa>Caa	p.E527Q	CTNNAL1_ENST00000374595.4_Missense_Mutation_p.E527Q|CTNNAL1_ENST00000374594.1_5'Flank|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.E443Q	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	527			E -> Q (in dbSNP:rs7021366). {ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		CGTCTTCCTTCAAACACGTCA	0.333													C|||	991	0.197883	0.0166	0.3199	5008	,	,		17796	0.3155		0.2694	False		,,,				2504	0.1616				p.E527Q		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.G1579C						PASS	.	C	GLN/GLU	259,4147	146.5+/-181.1	16,227,1960	173.0	158.0	163.0		1579	5.9	1.0	9	dbSNP_116	163	2442,6158	404.1+/-348.0	334,1774,2192	yes	missense	CTNNAL1	NM_003798.2	29	350,2001,4152	GG,GC,CC		28.3953,5.8783,20.7673	benign	527/735	111727670	2701,10305	2203	4300	6503	SO:0001583	missense	8727	exon11			TTCCTTCAAACAC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"""alpha-catulin"", ""alpha2-catulin"""	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.1579G>C	9.37:g.111727670C>G	ENSP00000320434:p.Glu527Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	494	0.2261904761904762	13	0.026422764227642278	98	0.27071823204419887	182	0.3181818181818182	201	0.26517150395778366	C	13.82	2.352183	0.41700	0.058783	0.283953	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580	T;T;T	0.27720	1.67;1.8;1.65	5.91	5.91	0.95273	.	0.143577	0.64402	D	0.000006	T	0.00012	0.0000	L	0.32530	0.975	0.31394	P	0.677511	B;D;B;B;B	0.67145	0.19;0.996;0.19;0.011;0.19	B;D;B;B;B	0.63877	0.076;0.919;0.076;0.025;0.076	T	0.33292	-0.9874	9	0.17369	T	0.5	-16.4177	17.7923	0.88558	0.0:1.0:0.0:0.0	rs7021366;rs17802108;rs7021366	527;443;527;527;527	B2RBI4;Q9UBT7-3;B3KMX6;Q9UBT7-2;Q9UBT7	.;.;.;.;CTNL1_HUMAN	Q	527;527;443	ENSP00000363723:E527Q;ENSP00000320434:E527Q;ENSP00000323351:E443Q	ENSP00000320434:E527Q	E	-	1	0	CTNNAL1	110767491	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.063000	0.71162	2.793000	0.96121	0.655000	0.94253	GAA	C|0.786;G|0.214	0.214	strong		0.333	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798	
LCT	3938	hgsc.bcm.edu	37	2	136575199	136575199	+	Silent	SNP	G	G	T	rs6719488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:136575199G>T	ENST00000264162.2	-	6	1429	c.1419C>A	c.(1417-1419)ggC>ggA	p.G473G	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	473	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGTAGGCAACGCCTGGGAGGC	0.637													G|||	1783	0.35603	0.1195	0.4323	5008	,	,		18831	0.3998		0.5954	False		,,,				2504	0.3303				p.G473G		Atlas-SNP	.											.	LCT	309	.	0			c.C1419A						PASS	.	G		1040,3366		120,800,1283	55.0	49.0	51.0		1419	-11.5	0.0	2	dbSNP_116	51	5998,2602		2180,1638,482	no	coding-synonymous	LCT	NM_002299.2		2300,2438,1765	TT,TG,GG		30.2558,23.6042,45.8865		473/1928	136575199	7038,5968	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon6			GGCAACGCCTGGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1419C>A	2.37:g.136575199G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.592;T|0.408	0.408	strong		0.637	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
TCP11L1	55346	hgsc.bcm.edu	37	11	33083263	33083263	+	Silent	SNP	G	G	A	rs61889262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:33083263G>A	ENST00000334274.4	+	7	1363	c.963G>A	c.(961-963)ccG>ccA	p.P321P	TCP11L1_ENST00000432887.1_Silent_p.P321P|TCP11L1_ENST00000531632.2_Silent_p.P321P|TCP11L1_ENST00000324357.9_Silent_p.P100P	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	321						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TCCAGAGGCCGTTCCCCGAAG	0.522													G|||	75	0.014976	0.0015	0.0274	5008	,	,		19596	0.0		0.0457	False		,,,				2504	0.0082				p.P321P		Atlas-SNP	.											.	TCP11L1	40	.	0			c.G963A						PASS	.	G	,	35,4369	37.6+/-69.7	1,33,2168	30.0	28.0	29.0		963,963	-8.1	0.4	11	dbSNP_129	29	343,8253	110.2+/-170.6	10,323,3965	no	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	11,356,6133	AA,AG,GG		3.9902,0.7947,2.9077	,	321/510,321/510	33083263	378,12622	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon7			GAGGCCGTTCCCC	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.963G>A	11.37:g.33083263G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	37	CCDS7882.1																																																																																			G|0.975;A|0.025	0.025	strong		0.522	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
PATE1	160065	hgsc.bcm.edu	37	11	125617606	125617606	+	Missense_Mutation	SNP	G	G	A	rs537916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125617606G>A	ENST00000305738.5	+	4	148	c.136G>A	c.(136-138)Gtt>Att	p.V46I	PATE1_ENST00000437148.2_Missense_Mutation_p.V34I	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	46			V -> I (in dbSNP:rs537916).			extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						GATAGAAATTGTTCAGTGTAG	0.493													G|||	1373	0.274161	0.2073	0.2925	5008	,	,		21088	0.2282		0.334	False		,,,				2504	0.3374				p.V46I		Atlas-SNP	.											.	PATE1	21	.	0			c.G136A						PASS	.	G	ILE/VAL	1010,3392	374.9+/-321.4	128,754,1319	89.0	85.0	87.0		136	-6.2	0.0	11	dbSNP_83	87	3043,5555	468.7+/-367.4	533,1977,1789	yes	missense	PATE1	NM_138294.2	29	661,2731,3108	AA,AG,GG		35.392,22.9441,31.1769	benign	46/127	125617606	4053,8947	2201	4299	6500	SO:0001583	missense	160065	exon4			GAAATTGTTCAGT	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.136G>A	11.37:g.125617606G>A	ENSP00000307164:p.Val46Ile	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	37	CCDS8464.1	594	0.27197802197802196	99	0.20121951219512196	101	0.27900552486187846	139	0.243006993006993	255	0.33641160949868076	G	7.495	0.651394	0.14516	0.229441	0.35392	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.27557	1.66;1.66	4.19	-6.17	0.02091	.	1.053100	0.07597	N	0.923050	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.12837	0.005;0.008	T	0.36578	-0.9742	9	0.26408	T	0.33	-0.0242	13.5369	0.61652	0.8035:0.0:0.1965:0.0	rs537916;rs1365079;rs58817293	34;46	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	I	46;34	ENSP00000307164:V46I;ENSP00000396056:V34I	ENSP00000307164:V46I	V	+	1	0	PATE1	125122816	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-1.626000	0.02035	-1.459000	0.01914	-0.140000	0.14226	GTT	G|0.697;A|0.303	0.303	strong		0.493	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294	
USP18	11274	hgsc.bcm.edu	37	22	18650682	18650682	+	Missense_Mutation	SNP	C	C	T	rs3180408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:18650682C>T	ENST00000215794.7	+	6	936	c.506C>T	c.(505-507)aCg>aTg	p.T169M		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	169	USP.		T -> M (in dbSNP:rs3180408). {ECO:0000269|Ref.7}.		cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.T169M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GCCCTGTATACGATCCGGGTG	0.547													c|||	1489	0.297324	0.3979	0.2997	5008	,	,		16115	0.1637		0.3072	False		,,,				2504	0.2873				p.T169M		Atlas-SNP	.											USP18,NS,carcinoma,0,1	USP18	22	1	1	Substitution - Missense(1)	stomach(1)	c.C506T						PASS	.	C	MET/THR	1709,2697		320,1069,814	121.0	94.0	103.0		506	-3.1	0.0	22	dbSNP_105	103	2965,5635		496,1973,1831	no	missense	USP18	NM_017414.3	81	816,3042,2645	TT,TC,CC		34.4767,38.788,35.9373	benign	169/373	18650682	4674,8332	2203	4300	6503	SO:0001583	missense	11274	exon6			TGTATACGATCCG	AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"""Ubiquitin-specific peptidases"""	12616	protein-coding gene	gene with protein product		607057	"""ubiquitin specific protease 18"""			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.506C>T	22.37:g.18650682C>T	ENSP00000215794:p.Thr169Met	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	614	0.28113553113553114	173	0.3516260162601626	107	0.2955801104972376	92	0.16083916083916083	242	0.31926121372031663	.	2.520	-0.311064	0.05458	0.38788	0.344767	ENSG00000184979	ENST00000215794;ENST00000441683	T	0.31769	1.48	5.62	-3.07	0.05363	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.540147	0.20380	N	0.093467	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P	0.36789	0.57	B	0.33521	0.165	T	0.40270	-0.9572	9	0.46703	T	0.11	.	7.1474	0.25591	0.0:0.5396:0.1135:0.347	rs3180408;rs3210451;rs3180408	169	Q9UMW8	UBP18_HUMAN	M	169;1	ENSP00000215794:T169M	ENSP00000215794:T169M	T	+	2	0	USP18	17030682	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-0.757000	0.04697	-1.789000	0.00628	ACG	C|0.674;N|0.000	.	strong		0.547	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
TTC30A	92104	hgsc.bcm.edu	37	2	178482594	178482594	+	Missense_Mutation	SNP	G	G	T	rs61742858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:178482594G>T	ENST00000355689.5	-	1	1100	c.836C>A	c.(835-837)cCc>cAc	p.P279H	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	279				P -> H (in Ref. 1; BAF85084). {ECO:0000305}.	cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			CTCTGCCCTGGGTGGCATGTC	0.502													G|||	395	0.0788738	0.0068	0.1542	5008	,	,		21302	0.001		0.2346	False		,,,				2504	0.0429				p.P279H		Atlas-SNP	.											.	TTC30A	60	.	0			c.C836A						PASS	.	G	HIS/PRO	186,4220	118.8+/-156.5	3,180,2020	127.0	138.0	134.0		836	4.9	0.6	2	dbSNP_129	134	1891,6709	334.7+/-321.1	209,1473,2618	no	missense	TTC30A	NM_152275.3	77	212,1653,4638	TT,TG,GG		21.9884,4.2215,15.9696	probably-damaging	279/666	178482594	2077,10929	2203	4300	6503	SO:0001583	missense	92104	exon1			GCCCTGGGTGGCA	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.836C>A	2.37:g.178482594G>T	ENSP00000347915:p.Pro279His	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	393	189	0.480916	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	254	0.1163003663003663	5	0.01016260162601626	58	0.16022099447513813	0	0.0	191	0.2519788918205805	G	15.69	2.908034	0.52333	0.042215	0.219884	ENSG00000197557	ENST00000355689	T	0.22945	1.93	5.78	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.93016	3.37	0.09310	P	0.99999999776138	D	0.89917	1.0	D	0.97110	1.0	T	0.03662	-1.1015	9	0.87932	D	0	.	14.871	0.70456	0.0686:0.0:0.9314:0.0	.	279	Q86WT1	TT30A_HUMAN	H	279	ENSP00000347915:P279H	ENSP00000347915:P279H	P	-	2	0	TTC30A	178190840	1.000000	0.71417	0.625000	0.29200	0.995000	0.86356	4.219000	0.58561	1.472000	0.48140	0.549000	0.68633	CCC	G|0.847;T|0.153	0.153	strong		0.502	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
JUP	3728	hgsc.bcm.edu	37	17	39925713	39925713	+	Missense_Mutation	SNP	C	C	T	rs41283425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39925713C>T	ENST00000393931.3	-	3	543	c.425G>A	c.(424-426)cGc>cAc	p.R142H	JUP_ENST00000310706.5_Missense_Mutation_p.R142H|JUP_ENST00000393930.1_Missense_Mutation_p.R142H|JUP_ENST00000540235.1_Missense_Mutation_p.R142H	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	142	Interaction with DSC1 and DSG1.		R -> H (in dbSNP:rs41283425). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GGGCAGGGCGCGAGTGGCCAG	0.652													C|||	120	0.0239617	0.0023	0.0331	5008	,	,		18035	0.0		0.0567	False		,,,				2504	0.0378				p.R142H	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.G425A						PASS	.	C	HIS/ARG,HIS/ARG	49,4357	45.3+/-79.5	1,47,2155	26.0	25.0	26.0		425,425	5.5	1.0	17	dbSNP_127	26	500,8100	137.9+/-194.8	10,480,3810	yes	missense,missense	JUP	NM_002230.2,NM_021991.2	29,29	11,527,5965	TT,TC,CC		5.814,1.1121,4.2211	possibly-damaging,possibly-damaging	142/746,142/746	39925713	549,12457	2203	4300	6503	SO:0001583	missense	3728	exon3			AGGGCGCGAGTGG	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.425G>A	17.37:g.39925713C>T	ENSP00000377508:p.Arg142His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	37	CCDS11407.1	61	0.027930402930402932	0	0.0	15	0.04143646408839779	0	0.0	46	0.06068601583113457	c	34	5.375802	0.95923	0.011121	0.05814	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35913	0.0948	M	0.73430	2.235	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;P	0.79784	0.993;0.901	T	0.67628	-0.5622	10	0.72032	D	0.01	-47.1096	18.4331	0.90633	0.0:1.0:0.0:0.0	rs41283425	142;142	B4DE59;P14923	.;PLAK_HUMAN	H	142	ENSP00000441751:R142H;ENSP00000377507:R142H;ENSP00000311113:R142H;ENSP00000377508:R142H;ENSP00000389886:R142H;ENSP00000394146:R142H;ENSP00000411449:R142H;ENSP00000401034:R142H	ENSP00000311113:R142H	R	-	2	0	JUP	37179239	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.809000	0.86057	2.593000	0.87608	0.556000	0.70494	CGC	C|0.962;T|0.038	0.038	strong		0.652	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		
WDR90	197335	hgsc.bcm.edu	37	16	705844	705844	+	Silent	SNP	T	T	C	rs8051645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:705844T>C	ENST00000293879.4	+	17	1921	c.1921T>C	c.(1921-1923)Ttg>Ctg	p.L641L	WDR90_ENST00000549091.1_Silent_p.L641L|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	641										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GGACGGCTTCTTGCGGCTCTG	0.687													C|||	3471	0.693091	0.8616	0.5937	5008	,	,		17245	0.9841		0.3767	False		,,,				2504	0.5613				p.L641L		Atlas-SNP	.											.	WDR90	107	.	0			c.T1921C						PASS	.	C		3319,1005		1297,725,140	26.0	32.0	30.0		1921	1.6	0.1	16	dbSNP_116	30	3044,5470		568,1908,1781	no	coding-synonymous	WDR90	NM_145294.4		1865,2633,1921	CC,CT,TT		35.7529,23.2424,49.5638		641/1749	705844	6363,6475	2162	4257	6419	SO:0001819	synonymous_variant	197335	exon17			GGCTTCTTGCGGC	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.1921T>C	16.37:g.705844T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			T|0.367;C|0.633	0.633	strong		0.687	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
NOC4L	79050	hgsc.bcm.edu	37	12	132631855	132631855	+	Silent	SNP	C	C	T	rs11543305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:132631855C>T	ENST00000330579.1	+	4	416	c.375C>T	c.(373-375)ttC>ttT	p.F125F	DDX51_ENST00000397333.3_5'Flank	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	125					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		TCCTGAAGTTCGTGCAGCTGG	0.647													C|||	218	0.0435304	0.0061	0.072	5008	,	,		17936	0.0		0.1064	False		,,,				2504	0.0542				p.F125F		Atlas-SNP	.											.	NOC4L	31	.	0			c.C375T						PASS	.	C		98,4264		2,94,2085	31.0	31.0	31.0		375	-3.3	1.0	12	dbSNP_120	31	957,7611		50,857,3377	no	coding-synonymous	NOC4L	NM_024078.1		52,951,5462	TT,TC,CC		11.1695,2.2467,8.1593		125/517	132631855	1055,11875	2181	4284	6465	SO:0001819	synonymous_variant	79050	exon4			GAAGTTCGTGCAG		CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.375C>T	12.37:g.132631855C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_024078	Q8N2S5|Q96I14	Silent	SNP	ENST00000330579.1	37	CCDS9277.1																																																																																			C|0.928;T|0.072	0.072	strong		0.647	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1	NM_024078	
ZNF497	162968	hgsc.bcm.edu	37	19	58868480	58868480	+	Missense_Mutation	SNP	G	G	T	rs12609654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58868480G>T	ENST00000311044.3	-	3	710	c.522C>A	c.(520-522)caC>caA	p.H174Q	ZNF497_ENST00000425453.3_Missense_Mutation_p.H174Q|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|CTD-2619J13.9_ENST00000599952.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000600686.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	174			H -> Q (in dbSNP:rs12609654). {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)			central_nervous_system(2)|lung(3)|skin(2)	7		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0278)		TGAGCTGCGAGTGCGCGCGGA	0.677													G|||	1917	0.382788	0.4856	0.3746	5008	,	,		15859	0.1825		0.4006	False		,,,				2504	0.4376				p.H174Q		Atlas-SNP	.											.	ZNF497	22	.	0			c.C522A						PASS	.	G	GLN/HIS,GLN/HIS	2210,2196	561.4+/-380.7	560,1090,553	31.0	25.0	27.0		522,522	-0.6	0.0	19	dbSNP_120	27	3902,4696	524.8+/-380.6	869,2164,1266	yes	missense,missense	ZNF497	NM_001207009.1,NM_198458.2	24,24	1429,3254,1819	TT,TG,GG		45.3826,49.8411,47.0009	benign,benign	174/499,174/499	58868480	6112,6892	2203	4299	6502	SO:0001583	missense	162968	exon2			CTGCGAGTGCGCG	AK126727	CCDS12977.1	19q13.43	2013-01-08			ENSG00000174586	ENSG00000174586		"""Zinc fingers, C2H2-type"""	23714	protein-coding gene	gene with protein product							Standard	NM_198458		Approved	FLJ44773	uc002qsi.2	Q6ZNH5		ENST00000311044.3:c.522C>A	19.37:g.58868480G>T	ENSP00000311183:p.His174Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_001207009	Q05AG8|Q0VF48|Q6ZTD2|Q9UIA8	Missense_Mutation	SNP	ENST00000311044.3	37	CCDS12977.1	802	0.36721611721611724	236	0.4796747967479675	157	0.43370165745856354	108	0.1888111888111888	301	0.3970976253298153	G	13.05	2.120431	0.37436	0.501589	0.453826	ENSG00000174586	ENST00000311044;ENST00000425453;ENST00000391697	T;T	0.35605	1.3;1.3	0.62	-0.577	0.11727	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	P	0.35107	0.484	B	0.22880	0.042	T	0.46911	-0.9157	8	0.44086	T	0.13	.	5.7584	0.18186	0.2752:0.0:0.7248:0.0	rs12609654;rs58652230;rs12609654	174	Q6ZNH5	ZN497_HUMAN	Q	174;174;19	ENSP00000311183:H174Q;ENSP00000402815:H174Q	ENSP00000311183:H174Q	H	-	3	2	ZNF497	63560292	0.000000	0.05858	0.004000	0.12327	0.420000	0.31355	-1.525000	0.02231	-0.298000	0.08921	0.205000	0.17691	CAC	G|0.561;T|0.439	0.439	strong		0.677	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	NM_198458	
SIDT1	54847	hgsc.bcm.edu	37	3	113323787	113323787	+	Silent	SNP	G	G	A	rs3732797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:113323787G>A	ENST00000264852.4	+	14	2094	c.1368G>A	c.(1366-1368)gcG>gcA	p.A456A	SIDT1_ENST00000393830.3_Silent_p.A456A|SIDT1_ENST00000463226.1_3'UTR	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	456					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGTTTTACGCGCTGCCCGTGA	0.473													G|||	226	0.0451278	0.0068	0.0591	5008	,	,		15729	0.0407		0.0994	False		,,,				2504	0.0358				p.A456A		Atlas-SNP	.											.	SIDT1	99	.	0			c.G1368A						PASS	.	G		61,4345	58.7+/-95.3	1,59,2143	128.0	119.0	122.0		1368	-6.4	1.0	3	dbSNP_107	122	859,7741	195.9+/-241.0	51,757,3492	no	coding-synonymous	SIDT1	NM_017699.2		52,816,5635	AA,AG,GG		9.9884,1.3845,7.0737		456/828	113323787	920,12086	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon14			TTACGCGCTGCCC	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1368G>A	3.37:g.113323787G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			G|0.931;A|0.069	0.069	strong		0.473	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
NLRP4	147945	hgsc.bcm.edu	37	19	56392920	56392920	+	Silent	SNP	C	C	T	rs12975929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56392920C>T	ENST00000301295.6	+	10	3374	c.2952C>T	c.(2950-2952)gaC>gaT	p.D984D	NLRP4_ENST00000587891.1_Silent_p.D909D|NLRP4_ENST00000346986.5_Silent_p.D928D	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	984					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)		CCATCACAGACGACTGTGACA	0.473													C|||	1111	0.221845	0.0151	0.3256	5008	,	,		17030	0.2589		0.2376	False		,,,				2504	0.3732				p.D984D		Atlas-SNP	.											.	NLRP4	331	.	0			c.C2952T						PASS	.	C		231,4175	137.3+/-173.1	3,225,1975	92.0	75.0	81.0		2952	-3.2	0.0	19	dbSNP_121	81	1961,6639	345.9+/-325.9	222,1517,2561	no	coding-synonymous	NLRP4	NM_134444.4		225,1742,4536	TT,TC,CC		22.8023,5.2429,16.8538		984/995	56392920	2192,10814	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon10			CACAGACGACTGT	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.2952C>T	19.37:g.56392920C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.817;T|0.183	0.183	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
MAP9	79884	hgsc.bcm.edu	37	4	156273768	156273768	+	Missense_Mutation	SNP	T	T	C	rs2305050	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156273768T>C	ENST00000311277.4	-	13	2064	c.1801A>G	c.(1801-1803)Aat>Gat	p.N601D	AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000593387.2_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.N577D|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000601977.1_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	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	139	139	1	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	
CUL3	8452	hgsc.bcm.edu	37	2	225365109	225365109	+	Silent	SNP	T	T	A	rs41373148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:225365109T>A	ENST00000264414.4	-	11	1919	c.1581A>T	c.(1579-1581)gcA>gcT	p.A527A	CUL3_ENST00000344951.4_Silent_p.A461A|CUL3_ENST00000409777.1_Silent_p.A503A|CUL3_ENST00000409096.1_Silent_p.A503A	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	527					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CATGTCTTGGTGCTGGTGGGA	0.403													T|||	27	0.00539137	0.0015	0.0043	5008	,	,		16507	0.0		0.0169	False		,,,				2504	0.0051				p.A533A		Atlas-SNP	.											.	CUL3	96	.	0			c.A1599T						PASS	.	T		18,4388	26.2+/-53.5	0,18,2185	206.0	186.0	193.0		1581	3.6	1.0	2	dbSNP_127	193	154,8446	74.2+/-136.8	3,148,4149	no	coding-synonymous	CUL3	NM_003590.3		3,166,6334	AA,AT,TT		1.7907,0.4085,1.3225		527/769	225365109	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon11			TCTTGGTGCTGGT	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1581A>T	2.37:g.225365109T>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	37	CCDS2462.1																																																																																			T|0.987;A|0.013	0.013	strong		0.403	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
TLE6	79816	hgsc.bcm.edu	37	19	2989697	2989697	+	Silent	SNP	T	T	C	rs6510730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2989697T>C	ENST00000246112.4	+	13	1359	c.1158T>C	c.(1156-1158)gaT>gaC	p.D386D	TLE6_ENST00000452088.1_Silent_p.D263D|TLE6_ENST00000478073.2_3'UTR	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	386					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		AGGCcctggatgccaacctgg	0.642													t|||	1482	0.295927	0.6679	0.2104	5008	,	,		18258	0.0149		0.2942	False		,,,				2504	0.1452				p.D386D		Atlas-SNP	.											.	TLE6	68	.	0			c.T1158C						PASS	.	C	,	2677,1729	649.1+/-398.8	807,1063,333	70.0	74.0	73.0		1158,789	-5.1	0.0	19	dbSNP_116	73	2392,6208	398.0+/-345.9	334,1724,2242	no	coding-synonymous,coding-synonymous	TLE6	NM_001143986.1,NM_024760.2	,	1141,2787,2575	CC,CT,TT		27.814,39.2419,38.9743	,	386/573,263/450	2989697	5069,7937	2203	4300	6503	SO:0001819	synonymous_variant	79816	exon13			CCTGGATGCCAAC	AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"""WD repeat domain containing"""	30788	protein-coding gene	gene with protein product		612399	"""transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"""			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.1158T>C	19.37:g.2989697T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	158	84	0.531646	NM_001143986	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1																																																																																			T|0.637;C|0.363	0.363	strong		0.642	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
PHF2	5253	hgsc.bcm.edu	37	9	96407983	96407983	+	Silent	SNP	C	C	T	rs9695734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:96407983C>T	ENST00000359246.4	+	4	739	c.372C>T	c.(370-372)acC>acT	p.T124T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	124					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		ACGGCTTCACCGAGCCCATCC	0.622													C|||	530	0.105831	0.1241	0.0764	5008	,	,		20102	0.0506		0.161	False		,,,				2504	0.1022				p.T124T		Atlas-SNP	.											PHF2,NS,carcinoma,0,1	PHF2	113	1	0			c.C372T						PASS	.	C		536,3870	244.3+/-253.7	28,480,1695	81.0	75.0	77.0		372	-9.2	0.2	9	dbSNP_119	77	1498,7102	284.7+/-296.8	119,1260,2921	yes	coding-synonymous	PHF2	NM_005392.3		147,1740,4616	TT,TC,CC		17.4186,12.1652,15.6389		124/1097	96407983	2034,10972	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			CTTCACCGAGCCC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.372C>T	9.37:g.96407983C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			C|0.853;T|0.147	0.147	strong		0.622	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
FUZ	80199	hgsc.bcm.edu	37	19	50312653	50312653	+	Silent	SNP	C	C	T	rs2305921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50312653C>T	ENST00000313777.4	-	6	835	c.672G>A	c.(670-672)ctG>ctA	p.L224L	AC006942.4_ENST00000600669.1_RNA|FUZ_ENST00000534008.1_5'Flank|FUZ_ENST00000528094.1_Silent_p.L188L|FUZ_ENST00000533418.1_Silent_p.L174L|FUZ_ENST00000445575.2_Silent_p.L224L	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN	fuzzy planar cell polarity protein	224					cilium assembly (GO:0042384)|embryonic body morphogenesis (GO:0010172)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of planar polarity (GO:0001736)|hair follicle development (GO:0001942)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)|negative regulation of neural crest formation (GO:0090301)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|positive regulation of cilium assembly (GO:0045724)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(3)	4		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)		TCCCGTGCGGCAGGTACACCG	0.736													C|||	656	0.13099	0.1793	0.0865	5008	,	,		13586	0.1399		0.1183	False		,,,				2504	0.1012				p.L224L		Atlas-SNP	.											.	FUZ	18	.	0			c.G672A						PASS	.	C	,	513,3175		37,439,1368	3.0	5.0	4.0		564,672	3.0	1.0	19	dbSNP_100	4	786,6290		53,680,2805	no	coding-synonymous,coding-synonymous	FUZ	NM_001171937.1,NM_025129.4	,	90,1119,4173	TT,TC,CC		11.108,13.91,12.068	,	188/383,224/419	50312653	1299,9465	1844	3538	5382	SO:0001819	synonymous_variant	80199	exon6			GTGCGGCAGGTAC	BC016793	CCDS12781.1, CCDS54293.1	19q13.33	2013-03-05	2013-03-05			ENSG00000010361			26219	protein-coding gene	gene with protein product		610622	"""fuzzy homolog (Drosophila)"""			21761479	Standard	NM_001171937		Approved	FLJ22688, Fy	uc002ppq.2	Q9BT04		ENST00000313777.4:c.672G>A	19.37:g.50312653C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_025129	B2RD86|B5MDH0|Q6PJY0|Q9H613	Silent	SNP	ENST00000313777.4	37	CCDS12781.1																																																																																			C|0.866;T|0.134	0.134	strong		0.736	FUZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393986.1	NM_025129	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:103152919G>A	ENST00000375735.2	+	72	10917	c.10773G>A	c.(10771-10773)acG>acA	p.T3591T	DYNC2H1_ENST00000398093.3_Silent_p.T3598T|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	3591					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)		AATGGGATACGTTTACAGGTG	0.284													G|||	970	0.19369	0.4198	0.1282	5008	,	,		15088	0.0913		0.1272	False		,,,				2504	0.1084				p.T3598T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G10794A						PASS	.	G	,	1299,2303		234,831,736	87.0	88.0	88.0		10794,10773	-11.7	0.6	11	dbSNP_120	88	952,7168		62,828,3170	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	296,1659,3906	AA,AG,GG		11.7241,36.0633,19.2032	,	3598/4315,3591/4308	103152919	2251,9471	1801	4060	5861	SO:0001819	synonymous_variant	79659	exon73			GGATACGTTTACA	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.10773G>A	11.37:g.103152919G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			G|0.808;A|0.192	0.192	strong		0.284	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
MAPK4	5596	hgsc.bcm.edu	37	18	48190440	48190440	+	Missense_Mutation	SNP	G	G	A	rs3752087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:48190440G>A	ENST00000400384.2	+	2	1148	c.112G>A	c.(112-114)Gtg>Atg	p.V38M	MAPK4_ENST00000588540.1_Missense_Mutation_p.V38M|MAPK4_ENST00000592595.1_Missense_Mutation_p.V38M|MAPK4_ENST00000540640.1_Intron	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	38	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> M (in dbSNP:rs3752087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		GCTGTCGGCCGTGGACAGCCG	0.607													G|||	1540	0.307508	0.1135	0.2579	5008	,	,		18211	0.4187		0.4354	False		,,,				2504	0.3589				p.V38M		Atlas-SNP	.											.	MAPK4	75	.	0			c.G112A						PASS	.	G	MET/VAL	650,3578		49,552,1513	76.0	85.0	82.0		112	-4.1	0.0	18	dbSNP_107	82	3335,5101		641,2053,1524	yes	missense	MAPK4	NM_002747.3	21	690,2605,3037	AA,AG,GG		39.533,15.3737,31.4672	benign	38/588	48190440	3985,8679	2114	4218	6332	SO:0001583	missense	5596	exon2			TCGGCCGTGGACA	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"""Mitogen-activated protein kinase cascade / Kinases"""	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.112G>A	18.37:g.48190440G>A	ENSP00000383234:p.Val38Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	116	73	0.62931	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	37	CCDS42437.1	723	0.33104395604395603	67	0.13617886178861788	112	0.30939226519337015	244	0.42657342657342656	300	0.39577836411609496	G	7.874	0.728811	0.15507	0.153737	0.39533	ENSG00000141639	ENST00000400384	T	0.45668	0.89	5.87	-4.07	0.03975	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.280120	0.05161	N	0.497703	T	0.00012	0.0000	L	0.49571	1.57	0.80722	P	0.0	P;P	0.50819	0.939;0.939	P;P	0.53549	0.729;0.729	T	0.31081	-0.9956	9	0.51188	T	0.08	-13.4551	14.0949	0.65013	0.5273:0.0:0.4727:0.0	rs3752087;rs58014467;rs3752087	38;38	Q0VG04;P31152	.;MK04_HUMAN	M	38	ENSP00000383234:V38M	ENSP00000383234:V38M	V	+	1	0	MAPK4	46444438	0.002000	0.14202	0.005000	0.12908	0.112000	0.19704	0.262000	0.18460	-0.635000	0.05531	-1.332000	0.01269	GTG	G|0.665;A|0.335	0.335	strong		0.607	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747	
MGAM	8972	hgsc.bcm.edu	37	7	141755358	141755358	+	Splice_Site	SNP	T	T	C	rs67998329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	92	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	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
GNPDA1	10007	hgsc.bcm.edu	37	5	141391532	141391532	+	Silent	SNP	G	G	A	rs164080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141391532G>A	ENST00000508177.1	-	1	827	c.69C>T	c.(67-69)cgC>cgT	p.R23R	GNPDA1_ENST00000311337.6_Silent_p.R23R|GNPDA1_ENST00000513454.1_Silent_p.R23R|GNPDA1_ENST00000542860.1_Silent_p.R23R|GNPDA1_ENST00000503794.1_Silent_p.R23R|GNPDA1_ENST00000500692.2_Silent_p.R23R|GNPDA1_ENST00000458112.2_Silent_p.R23R			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	23					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucosamine catabolic process (GO:0006043)|N-acetylglucosamine metabolic process (GO:0006044)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)	p.R23R(1)		central_nervous_system(1)|lung(1)|skin(3)|stomach(1)	6		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGGATGATGCGGTTCCTGA	0.567											OREG0016880	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2728	0.544728	0.671	0.4352	5008	,	,		19378	0.625		0.4612	False		,,,				2504	0.455				p.R23R		Atlas-SNP	.											GNPDA1,NS,carcinoma,0,1	GNPDA1	16	1	1	Substitution - coding silent(1)	stomach(1)	c.C69T						scavenged	.	G		2771,1635	659.9+/-400.6	883,1005,315	113.0	106.0	108.0		69	-0.2	1.0	5	dbSNP_79	108	3927,4673	547.6+/-385.2	889,2149,1262	no	coding-synonymous	GNPDA1	NM_005471.4		1772,3154,1577	AA,AG,GG		45.6628,37.1085,48.5007		23/290	141391532	6698,6308	2203	4300	6503	SO:0001819	synonymous_variant	10007	exon2			GATGATGCGGTTC	AF048826	CCDS4272.1	5q21	2008-02-05	2003-10-17	2003-10-22	ENSG00000113552	ENSG00000113552	3.5.99.6		4417	protein-coding gene	gene with protein product	"""glucosamine-6-phosphate deaminase"", ""oscillin"""	601798	"""glucosamine-6-phosphate isomerase"""	GNPI		9714720, 9438414	Standard	NM_005471		Approved	GNPDA, HLN, GPI, KIAA0060	uc010jgh.3	P46926	OTTHUMG00000129657	ENST00000508177.1:c.69C>T	5.37:g.141391532G>A		Somatic	164	2	0.0121951	1663	WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_005471	B7Z3X4|D3DQE7	Silent	SNP	ENST00000508177.1	37	CCDS4272.1																																																																																			G|0.454;A|0.546	0.546	strong		0.567	GNPDA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370631.1	NM_005471	
PER3	8863	hgsc.bcm.edu	37	1	7887579	7887579	+	Missense_Mutation	SNP	C	C	G	rs228697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:7887579C>G	ENST00000361923.2	+	17	2741	c.2566C>G	c.(2566-2568)Cct>Gct	p.P856A	PER3_ENST00000377532.3_Missense_Mutation_p.P864A|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	856	Pro-rich.		P -> A (in dbSNP:rs228697). {ECO:0000269|PubMed:11306557}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTGACCCCCCTGTCTGTCC	0.547													C|||	302	0.0603035	0.0098	0.0692	5008	,	,		19911	0.0427		0.0964	False		,,,				2504	0.1033				p.P856A		Atlas-SNP	.											.	PER3	95	.	0			c.C2566G						PASS	.	C	ALA/PRO	102,4304	80.4+/-118.8	0,102,2101	201.0	197.0	198.0		2566	-2.6	0.0	1	dbSNP_79	198	897,7703	201.4+/-244.9	51,795,3454	yes	missense	PER3	NM_016831.1	27	51,897,5555	GG,GC,CC		10.4302,2.315,7.6811	benign	856/1202	7887579	999,12007	2203	4300	6503	SO:0001583	missense	8863	exon17			GACCCCCCTGTCT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2566C>G	1.37:g.7887579C>G	ENSP00000355031:p.Pro856Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	141	0.06456043956043957	3	0.006097560975609756	29	0.08011049723756906	30	0.05244755244755245	79	0.10422163588390501	C	9.849	1.193105	0.21954	0.02315	0.104302	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.10763	2.84;2.85	4.32	-2.59	0.06209	.	3.975590	0.00837	N	0.001717	T	0.00241	0.0007	L	0.46157	1.445	0.80722	P	0.0	B;B;B;B	0.30914	0.199;0.199;0.3;0.199	B;B;B;B	0.31290	0.06;0.06;0.127;0.06	T	0.20042	-1.0287	9	0.24483	T	0.36	.	0.4792	0.00545	0.2482:0.2832:0.243:0.2255	rs228697;rs480069;rs52826465;rs228697	856;864;864;856	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	A	864;856;67	ENSP00000366755:P864A;ENSP00000355031:P856A	ENSP00000355031:P856A	P	+	1	0	PER3	7810166	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.057000	0.14279	-0.823000	0.04301	-0.263000	0.10527	CCT	C|0.925;G|0.075	0.075	strong		0.547	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
CLEC18B	497190	hgsc.bcm.edu	37	16	74451961	74451961	+	Missense_Mutation	SNP	G	G	A	rs151079980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74451961G>A	ENST00000339953.5	-	3	573	c.452C>T	c.(451-453)aCg>aTg	p.T151M		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	151	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T151K(1)		endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						ACTCACCTGCGTGTAGTGGGT	0.592																																					p.T151M		Atlas-SNP	.											CLEC18B,NS,carcinoma,0,4	CLEC18B	45	4	1	Substitution - Missense(1)	lung(1)	c.C452T						scavenged	.						9.0	10.0	9.0					16																	74451961		1775	3623	5398	SO:0001583	missense	497190	exon3			ACCTGCGTGTAGT	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.452C>T	16.37:g.74451961G>A	ENSP00000341051:p.Thr151Met	Somatic	396	1	0.00252525		WXS	Illumina HiSeq	Phase_I	271	21	0.0774908	NM_001011880	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	91	0.041666666666666664	5	0.01016260162601626	17	0.04696132596685083	20	0.03496503496503497	49	0.06464379947229551	g	16.79	3.221692	0.58560	.	.	ENSG00000140839	ENST00000429489;ENST00000339953;ENST00000268492	T	0.16073	2.37	3.57	3.57	0.40892	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.09686	0.0238	H	0.95982	3.75	0.46113	D	0.998879	D;D	0.89917	0.999;1.0	D;D	0.66716	0.943;0.946	T	0.45920	-0.9228	10	0.66056	D	0.02	.	10.55	0.45083	0.0:0.0:1.0:0.0	.	151;151	C9JSV1;Q6UXF7	.;CL18B_HUMAN	M	151	ENSP00000341051:T151M	ENSP00000268492:T151M	T	-	2	0	CLEC18B	73009462	1.000000	0.71417	0.986000	0.45419	0.699000	0.40488	5.199000	0.65152	1.821000	0.53095	0.531000	0.56144	ACG	G|0.968;A|0.032	0.032	strong		0.592	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
CDA	978	hgsc.bcm.edu	37	1	20915701	20915701	+	Missense_Mutation	SNP	A	A	C	rs2072671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20915701A>C	ENST00000375071.3	+	1	261	c.79A>C	c.(79-81)Aag>Cag	p.K27Q	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	27	CMP/dCMP deaminase zinc-binding.		K -> Q (in dbSNP:rs2072671). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8422236}.		cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|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)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	GGAGGCCAAGAAGTCAGCCTA	0.627													A|||	965	0.192692	0.0673	0.3055	5008	,	,		18529	0.122		0.3141	False		,,,				2504	0.2301				p.K27Q	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.A79C	GRCh37	CM984152	CDA	M	rs2072671	PASS	.	A	GLN/LYS	456,3950	216.1+/-234.9	27,402,1774	65.0	58.0	60.0		79	4.0	1.0	1	dbSNP_96	60	2978,5622	462.3+/-365.7	511,1956,1833	yes	missense	CDA	NM_001785.2	53	538,2358,3607	CC,CA,AA		34.6279,10.3495,26.4032	benign	27/147	20915701	3434,9572	2203	4300	6503	SO:0001583	missense	978	exon1			GCCAAGAAGTCAG	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.79A>C	1.37:g.20915701A>C	ENSP00000364212:p.Lys27Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	37	CCDS210.1	467	0.21382783882783882	39	0.07926829268292683	103	0.2845303867403315	76	0.13286713286713286	249	0.32849604221635886	A	13.74	2.326085	0.41197	0.103495	0.346279	ENSG00000158825	ENST00000375071	T	0.42131	0.98	5.14	3.98	0.46160	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.280120	0.39544	N	0.001322	T	0.00012	0.0000	N	0.17248	0.465	0.21184	P	0.999763501	B	0.11235	0.004	B	0.10450	0.005	T	0.38824	-0.9643	9	0.21014	T	0.42	.	7.7946	0.29140	0.9042:0.0:0.0958:0.0	rs2072671;rs57221291;rs2072671	27	P32320	CDD_HUMAN	Q	27	ENSP00000364212:K27Q	ENSP00000364212:K27Q	K	+	1	0	CDA	20788288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.604000	0.36804	2.169000	0.68431	0.459000	0.35465	AAG	A|0.766;C|0.234	0.234	strong		0.627	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	
MCM10	55388	hgsc.bcm.edu	37	10	13234356	13234356	+	Missense_Mutation	SNP	A	A	T	rs7905784	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13234356A>T	ENST00000484800.2	+	12	1724	c.1621A>T	c.(1621-1623)Aca>Tca	p.T541S	MCM10_ENST00000378714.3_Missense_Mutation_p.T540S|MCM10_ENST00000378694.1_Missense_Mutation_p.T540S			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	541			T -> S (in dbSNP:rs7905784). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGCCAAAGCCACAGCTTCAGG	0.542													A|||	321	0.0640974	0.0688	0.0648	5008	,	,		19284	0.0139		0.1431	False		,,,				2504	0.0276				p.T541S		Atlas-SNP	.											.	MCM10	76	.	0			c.A1621T						PASS	.	A	SER/THR,SER/THR	388,4018	193.6+/-218.7	15,358,1830	149.0	118.0	128.0		1618,1621	4.4	0.1	10	dbSNP_116	128	1258,7342	252.5+/-278.5	86,1086,3128	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	58,58	101,1444,4958	TT,TA,AA		14.6279,8.8062,12.6557	benign,benign	540/875,541/876	13234356	1646,11360	2203	4300	6503	SO:0001583	missense	55388	exon12			AAAGCCACAGCTT	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1621A>T	10.37:g.13234356A>T	ENSP00000418268:p.Thr541Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	191	0.08745421245421245	38	0.07723577235772358	31	0.0856353591160221	12	0.02097902097902098	110	0.14511873350923482	A	0.019	-1.465822	0.01053	0.088062	0.146279	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.28666	1.6;1.6;1.6	5.52	4.38	0.52667	Replication factor Mcm10 (1);	0.940200	0.09247	N	0.828350	T	0.00073	0.0002	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.11329	0.006;0.003;0.005	T	0.37056	-0.9722	9	0.08837	T	0.75	-11.0297	3.0826	0.06267	0.6331:0.1467:0.0794:0.1408	rs7905784;rs52819774;rs7905784	540;540;541	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	S	540;541;541;540	ENSP00000367986:T540S;ENSP00000418268:T541S;ENSP00000367966:T540S	ENSP00000354945:T541S	T	+	1	0	MCM10	13274362	0.205000	0.23458	0.061000	0.19648	0.006000	0.05464	2.074000	0.41529	0.912000	0.36772	-0.345000	0.07892	ACA	A|0.889;T|0.111	0.111	strong		0.542	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
A4GNT	51146	hgsc.bcm.edu	37	3	137850003	137850003	+	Silent	SNP	A	A	G	rs2724691	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137850003A>G	ENST00000236709.3	-	2	297	c.96T>C	c.(94-96)tgT>tgC	p.C32C		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	32					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						AAGAAGGCAAACAGAAGAGGC	0.557													G|||	3075	0.614018	0.5946	0.719	5008	,	,		16574	0.5476		0.662	False		,,,				2504	0.5849				p.C32C		Atlas-SNP	.											.	A4GNT	42	.	0			c.T96C						PASS	.	G		2648,1758	521.2+/-370.5	794,1060,349	85.0	84.0	84.0		96	3.6	0.0	3	dbSNP_100	84	5754,2846	447.4+/-361.5	1918,1918,464	no	coding-synonymous	A4GNT	NM_016161.2		2712,2978,813	GG,GA,AA		33.093,39.9001,35.399		32/341	137850003	8402,4604	2203	4300	6503	SO:0001819	synonymous_variant	51146	exon2			AGGCAAACAGAAG	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.96T>C	3.37:g.137850003A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_016161	Q0VDK1|Q0VDK2	Silent	SNP	ENST00000236709.3	37	CCDS3097.1																																																																																			A|0.366;C|0.003	.	strong		0.557	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	
FBN3	84467	hgsc.bcm.edu	37	19	8176919	8176919	+	Silent	SNP	C	C	T	rs4804264	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8176919C>T	ENST00000600128.1	-	31	4317	c.3903G>A	c.(3901-3903)ccG>ccA	p.P1301P	FBN3_ENST00000601739.1_Silent_p.P1301P|FBN3_ENST00000270509.2_Silent_p.P1301P			Q75N90	FBN3_HUMAN	fibrillin 3	1301	EGF-like 19; 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						TGAAACTCCCCGGGATGTTGA	0.597													C|||	3452	0.689297	0.6604	0.719	5008	,	,		12420	0.7847		0.5298	False		,,,				2504	0.773				p.P1301P		Atlas-SNP	.											.	FBN3	300	.	0			c.G3903A						PASS	.	C		2841,1565	668.8+/-402.1	923,995,285	142.0	121.0	128.0		3903	-8.7	0.1	19	dbSNP_111	128	4495,4105	591.7+/-392.9	1154,2187,959	no	coding-synonymous	FBN3	NM_032447.3		2077,3182,1244	TT,TC,CC		47.7326,35.5197,43.5953		1301/2810	8176919	7336,5670	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon30			ACTCCCCGGGATG		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.3903G>A	19.37:g.8176919C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.388;N|0.000	.	strong		0.597	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
WDR17	116966	hgsc.bcm.edu	37	4	177098285	177098285	+	Missense_Mutation	SNP	G	G	A	rs17625943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:177098285G>A	ENST00000280190.4	+	29	3799	c.3643G>A	c.(3643-3645)Gct>Act	p.A1215T	WDR17_ENST00000508596.1_Missense_Mutation_p.A1176T|WDR17_ENST00000393643.2_Missense_Mutation_p.A1191T|WDR17_ENST00000507824.2_Missense_Mutation_p.A1190T			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1215			A -> T (in dbSNP:rs17625943). {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)		TGCATGGAGAGCTTGCACACA	0.373													G|||	1305	0.260583	0.2519	0.4164	5008	,	,		15205	0.2569		0.2624	False		,,,				2504	0.1636				p.A1215T		Atlas-SNP	.											WDR17,rectum,carcinoma,-1,1	WDR17	198	1	0			c.G3643A						PASS	.	G	THR/ALA,THR/ALA	1062,3344	369.5+/-319.1	140,782,1281	61.0	62.0	61.0		3643,3526	4.1	1.0	4	dbSNP_123	61	2190,6408	368.6+/-335.1	282,1626,2391	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	58,58	422,2408,3672	AA,AG,GG		25.471,24.1035,25.0077	benign,benign	1215/1323,1176/1284	177098285	3252,9752	2203	4299	6502	SO:0001583	missense	116966	exon29			TGGAGAGCTTGCA	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.3643G>A	4.37:g.177098285G>A	ENSP00000280190:p.Ala1215Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	623|623	0.28525641025641024|0.28525641025641024	139|139	0.28252032520325204|0.28252032520325204	137|137	0.3784530386740331|0.3784530386740331	161|161	0.28146853146853146|0.28146853146853146	186|186	0.24538258575197888|0.24538258575197888	G|G	21.1|21.1	4.105116|4.105116	0.77096|0.77096	0.241035|0.241035	0.25471|0.25471	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.54479|.	0.57;0.57;0.57|.	5.94|5.94	4.11|4.11	0.48088|0.48088	.|.	0.192654|.	0.43579|.	D|.	0.000542|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69823|0.69823	2.125|2.125	0.19775|0.19775	P|P	0.9999589415|0.9999589415	P;P;P|.	0.41910|.	0.764;0.764;0.764|.	B;B;B|.	0.39503|.	0.301;0.235;0.235|.	T|T	0.10451|0.10451	-1.0629|-1.0629	9|4	0.62326|.	D|.	0.03|.	-16.1407|-16.1407	14.9963|14.9963	0.71433|0.71433	0.0:0.0:0.7179:0.2821|0.0:0.0:0.7179:0.2821	rs17625943;rs52821017;rs17625943|rs17625943;rs52821017;rs17625943	1191;1176;1215|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	T|N	1176;1191;1215;1191|449	ENSP00000422763:A1176T;ENSP00000377258:A1191T;ENSP00000280190:A1215T|.	ENSP00000280190:A1215T|.	A|S	+|+	1|2	0|0	WDR17|WDR17	177335279|177335279	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	5.753000|5.753000	0.68736|0.68736	1.470000|1.470000	0.48102|0.48102	0.644000|0.644000	0.83932|0.83932	GCT|AGC	G|0.743;A|0.257	0.257	strong		0.373	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
OR10X1	128367	hgsc.bcm.edu	37	1	158549420	158549420	+	Silent	SNP	C	C	T	rs863361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158549420C>T	ENST00000368150.1	-	1	269	c.270G>A	c.(268-270)acG>acA	p.T90T		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, 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)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					CGATGGTCAGCGTATAGCAGG	0.493													T|||	2596	0.518371	0.6324	0.4164	5008	,	,		21121	0.5853		0.4732	False		,,,				2504	0.4141				p.T90T		Atlas-SNP	.											OR10X1,face,carcinoma,-2,1	OR10X1	96	1	0			c.G270A						scavenged	.	T		2726,1680	510.9+/-367.7	824,1078,301	106.0	100.0	102.0		270	-7.3	0.0	1	dbSNP_86	102	3829,4771	612.1+/-395.9	876,2077,1347	no	coding-synonymous	OR10X1	NM_001004477.1		1700,3155,1648	TT,TC,CC		44.5233,38.1298,49.6002		90/327	158549420	6555,6451	2203	4300	6503	SO:0001819	synonymous_variant	128367	exon1			GGTCAGCGTATAG	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.270G>A	1.37:g.158549420C>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	183	58	0.31694	NM_001004477	Q6IFR8	Silent	SNP	ENST00000368150.1	37	CCDS30900.1																																																																																			C|0.471;T|0.529	0.529	strong		0.493	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
UGT1A7	54577	hgsc.bcm.edu	37	2	234591205	234591205	+	Missense_Mutation	SNP	T	T	C	rs11692021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234591205T>C	ENST00000373426.3	+	1	622	c.622T>C	c.(622-624)Tgg>Cgg	p.W208R	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	208			W -> R (in allele UGT1A7*3 and allele UGT1A7*4; dbSNP:rs11692021). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906}.		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GGAGAGAGTATGGAACCACAT	0.453													T|||	1491	0.297724	0.2496	0.2637	5008	,	,		19491	0.1964		0.3598	False		,,,				2504	0.4274				p.W208R		Atlas-SNP	.											.	UGT1A7	74	.	0			c.T622C	GRCh37	CM004345	UGT1A7	M	rs11692021	PASS	.	T	,,ARG/TRP,	1211,3195	422.5+/-339.8	180,851,1172	176.0	185.0	182.0		,,622,	-8.3	0.0	2	dbSNP_120	182	3331,5269	496.2+/-374.2	653,2025,1622	no	intron,intron,missense,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A9	NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2	,,101,	833,2876,2794	CC,CT,TT		38.7326,27.4852,34.9223	,,,	,,208/531,	234591205	4542,8464	2203	4300	6503	SO:0001583	missense	54577	exon1			AGAGTATGGAACC	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.622T>C	2.37:g.234591205T>C	ENSP00000362525:p.Trp208Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	202	103	0.509901	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	636	0.29120879120879123	118	0.23983739837398374	113	0.31215469613259667	130	0.22727272727272727	275	0.3627968337730871	T	0.584	-0.835946	0.02713	0.274852	0.387326	ENSG00000244122	ENST00000373426	T	0.05786	3.39	4.16	-8.32	0.00996	.	.	.	.	.	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32268	-0.9913	8	0.36615	T	0.2	.	3.594	0.08000	0.4615:0.2944:0.1316:0.1125	rs11692021;rs17863779;rs57605148	208;208	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	R	208	ENSP00000362525:W208R	ENSP00000362525:W208R	W	+	1	0	UGT1A7	234255944	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	-4.177000	0.00279	-4.859000	0.00029	-1.814000	0.00607	TGG	T|0.683;C|0.317	0.317	strong		0.453	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
HECW1	23072	hgsc.bcm.edu	37	7	43506059	43506059	+	Silent	SNP	A	A	G	rs2304329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:43506059A>G	ENST00000395891.2	+	15	3410	c.2805A>G	c.(2803-2805)gaA>gaG	p.E935E	HECW1_ENST00000453890.1_Silent_p.E901E	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	935					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						TAAGGAGAGAAGGGTCACTTT	0.473													A|||	2781	0.555312	0.5098	0.5533	5008	,	,		16370	0.3879		0.6352	False		,,,				2504	0.7086				p.E935E		Atlas-SNP	.											.	HECW1	540	.	0			c.A2805G						PASS	.	A		2032,1862		531,970,446	110.0	103.0	105.0		2805	-0.8	1.0	7	dbSNP_100	105	5225,3043		1676,1873,585	no	coding-synonymous	HECW1	NM_015052.3		2207,2843,1031	GG,GA,AA		36.8045,47.8172,40.3305		935/1607	43506059	7257,4905	1947	4134	6081	SO:0001819	synonymous_variant	23072	exon15			GAGAGAAGGGTCA	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.2805A>G	7.37:g.43506059A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.416;G|0.584	0.584	strong		0.473	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
UGDH	7358	hgsc.bcm.edu	37	4	39515736	39515736	+	Silent	SNP	A	A	G	rs10019532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:39515736A>G	ENST00000316423.6	-	3	573	c.231T>C	c.(229-231)gaT>gaC	p.D77D	UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000506179.1_Silent_p.D77D|UGDH_ENST00000501493.2_Silent_p.D77D	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	77					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						CTTTGATGGCATCATCAATAT	0.284													A|||	1430	0.285543	0.4826	0.1599	5008	,	,		18043	0.4067		0.1044	False		,,,				2504	0.1697				p.D77D		Atlas-SNP	.											.	UGDH	52	.	0			c.T231C						PASS	.	A	,,	1889,2511	520.4+/-370.3	407,1075,718	69.0	79.0	75.0		231,,231	-0.2	1.0	4	dbSNP_119	75	847,7739	192.3+/-238.3	37,773,3483	no	coding-synonymous,utr-5,coding-synonymous	UGDH	NM_001184700.1,NM_001184701.1,NM_003359.3	,,	444,1848,4201	GG,GA,AA		9.8649,42.9318,21.0688	,,	77/428,,77/495	39515736	2736,10250	2200	4293	6493	SO:0001819	synonymous_variant	7358	exon3			GATGGCATCATCA	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.231T>C	4.37:g.39515736A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	37	CCDS3455.1																																																																																			A|0.768;G|0.232	0.232	strong		0.284	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
F5	2153	hgsc.bcm.edu	37	1	169498975	169498975	+	Missense_Mutation	SNP	T	T	C	rs6030	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169498975T>C	ENST00000367797.3	-	16	5491	c.5290A>G	c.(5290-5292)Atg>Gtg	p.M1764V	F5_ENST00000367796.3_Missense_Mutation_p.M1769V	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1764	F5/8 type A 3.|Plastocyanin-like 6.		M -> V (in dbSNP:rs6030). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3110773, ECO:0000269|PubMed:7874144}.		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)	CTCATGTCCATAGGCATGTTG	0.393													C|||	1546	0.308706	0.1732	0.4885	5008	,	,		19732	0.2837		0.3111	False		,,,				2504	0.3875				p.M1764V		Atlas-SNP	.											.	F5	301	.	0			c.A5290G	GRCh37	CM070090	F5	M	rs6030	PASS	.	C	VAL/MET	878,3528	744.5+/-411.6	87,704,1412	154.0	148.0	150.0		5290	-2.9	0.2	1	dbSNP_52	150	2886,5714	672.0+/-402.9	453,1980,1867	yes	missense	F5	NM_000130.4	21	540,2684,3279	CC,CT,TT		33.5581,19.9274,28.9405	benign	1764/2225	169498975	3764,9242	2203	4300	6503	SO:0001583	missense	2153	exon16			TGTCCATAGGCAT	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.5290A>G	1.37:g.169498975T>C	ENSP00000356771:p.Met1764Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	639	0.2925824175824176	102	0.2073170731707317	161	0.4447513812154696	137	0.2395104895104895	239	0.3153034300791557	C	0.020	-1.433840	0.01108	0.199274	0.335581	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98602	-5.02;-5.02	5.32	-2.86	0.05717	Cupredoxin (2);	0.908379	0.09456	N	0.799742	T	0.78729	0.4329	N	0.03608	-0.345	0.19945	P	0.999945	B	0.02656	0.0	B	0.01281	0.0	T	0.72293	-0.4336	9	0.02654	T	1	-0.243	3.2522	0.06819	0.0923:0.1961:0.2724:0.4392	rs6030;rs3830171;rs17579170;rs61682329;rs6030	1764	P12259	FA5_HUMAN	V	1764;1769	ENSP00000356771:M1764V;ENSP00000356770:M1769V	ENSP00000356770:M1769V	M	-	1	0	F5	167765599	0.000000	0.05858	0.189000	0.23252	0.981000	0.71138	-2.414000	0.01037	-0.913000	0.03832	-0.226000	0.12346	ATG	T|0.711;C|0.288	0.288	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
PIGQ	9091	hgsc.bcm.edu	37	16	633125	633125	+	Missense_Mutation	SNP	T	T	C	rs1045277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:633125T>C	ENST00000026218.5	+	10	1862	c.1774T>C	c.(1774-1776)Tgt>Cgt	p.C592R	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	592			C -> R (in dbSNP:rs1045277).		C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GCGCATGTCCTGTGCTTTGTG	0.637													C|||	2658	0.530751	0.4758	0.4885	5008	,	,		19817	0.6369		0.4324	False		,,,				2504	0.6268				p.C592R		Atlas-SNP	.											PIGQ,colon,carcinoma,0,2	PIGQ	43	2	0			c.T1774C						PASS	.	C	,ARG/CYS	2069,2333	602.2+/-389.9	496,1077,628	92.0	91.0	92.0		,1774	1.7	0.0	16	dbSNP_86	92	3525,5075	630.3+/-398.3	725,2075,1500	yes	utr-3,missense	PIGQ	NM_004204.3,NM_148920.1	,180	1221,3152,2128	CC,CT,TT		40.9884,47.0014,43.0242	,benign	,592/761	633125	5594,7408	2201	4300	6501	SO:0001583	missense	9091	exon10			ATGTCCTGTGCTT	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1774T>C	16.37:g.633125T>C	ENSP00000026218:p.Cys592Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	1136	0.5201465201465202	253	0.5142276422764228	179	0.494475138121547	360	0.6293706293706294	344	0.45382585751978893	C	1.168	-0.641783	0.03531	0.470014	0.409884	ENSG00000007541	ENST00000026218	T	0.22743	1.94	1.68	1.68	0.24146	.	.	.	.	.	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	0.34329	-0.9833	7	.	.	.	1.0596	4.2548	0.10712	0.0:0.7913:0.0:0.2087	rs1045277;rs3826234;rs61457146;rs1045277	162;592	B3KRR7;Q9BRB3	.;PIGQ_HUMAN	R	592	ENSP00000026218:C592R	.	C	+	1	0	PIGQ	573126	0.000000	0.05858	0.003000	0.11579	0.163000	0.22366	-2.106000	0.01338	0.306000	0.22856	-0.479000	0.04858	TGT	T|0.534;C|0.466	0.466	strong		0.637	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
ZNF189	7743	hgsc.bcm.edu	37	9	104171856	104171856	+	Silent	SNP	C	C	T	rs17772514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104171856C>T	ENST00000339664.2	+	3	1935	c.1806C>T	c.(1804-1806)gaC>gaT	p.D602D	ZNF189_ENST00000259395.4_Silent_p.D560D|ZNF189_ENST00000374861.3_Silent_p.D588D	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	602					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				ATGAATGTGACGCTTGTGGTG	0.418													C|||	198	0.0395367	0.0023	0.0634	5008	,	,		21051	0.002		0.0785	False		,,,				2504	0.0716				p.D602D		Atlas-SNP	.											.	ZNF189	79	.	0			c.C1806T						PASS	.	C	,	62,4344	52.9+/-88.7	1,60,2142	77.0	82.0	80.0		1806,1680	0.6	1.0	9	dbSNP_123	80	689,7909	170.4+/-221.6	28,633,3638	no	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	29,693,5780	TT,TC,CC		8.0135,1.4072,5.7751	,	602/627,560/585	104171856	751,12253	2203	4299	6502	SO:0001819	synonymous_variant	7743	exon3			ATGTGACGCTTGT	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1806C>T	9.37:g.104171856C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			C|0.953;T|0.047	0.047	strong		0.418	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
DNAH2	146754	hgsc.bcm.edu	37	17	7735934	7735934	+	Missense_Mutation	SNP	G	G	A	rs61745181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7735934G>A	ENST00000572933.1	+	83	14224	c.12764G>A	c.(12763-12765)cGg>cAg	p.R4255Q	DNAH2_ENST00000389173.2_Missense_Mutation_p.R4255Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4255					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)				GCCTGGACCCGGGACTTGGCC	0.547													G|||	575	0.114816	0.0038	0.2478	5008	,	,		16887	0.1409		0.0616	False		,,,				2504	0.1984				p.R4255Q		Atlas-SNP	.											.	DNAH2	498	.	0			c.G12764A						PASS	.	G	GLN/ARG	99,4307	78.3+/-116.7	3,93,2107	93.0	100.0	98.0		12764	5.4	1.0	17	dbSNP_129	98	653,7947	166.7+/-218.6	18,617,3665	yes	missense	DNAH2	NM_020877.2	43	21,710,5772	AA,AG,GG		7.593,2.2469,5.7819	possibly-damaging	4255/4428	7735934	752,12254	2203	4300	6503	SO:0001583	missense	146754	exon82			GGACCCGGGACTT	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.12764G>A	17.37:g.7735934G>A	ENSP00000458355:p.Arg4255Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	194	0.08882783882783883	4	0.008130081300813009	68	0.1878453038674033	80	0.13986013986013987	42	0.055408970976253295	G	25.5	4.642337	0.87859	0.022469	0.07593	ENSG00000183914	ENST00000389173	T	0.08008	3.14	5.41	5.41	0.78517	Dynein heavy chain (1);	0.065840	0.64402	D	0.000020	T	0.00039	0.0001	L	0.52364	1.645	0.09310	P	1.0	P	0.52692	0.955	P	0.51079	0.658	T	0.50800	-0.8785	9	0.13470	T	0.59	.	17.9726	0.89118	0.0:0.0:1.0:0.0	rs61745181	4255	Q9P225	DYH2_HUMAN	Q	4255	ENSP00000373825:R4255Q	ENSP00000373825:R4255Q	R	+	2	0	DNAH2	7676659	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.481000	0.73608	2.546000	0.85860	0.591000	0.81541	CGG	G|0.935;A|0.065	0.065	strong		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
UNC5B	219699	hgsc.bcm.edu	37	10	73051388	73051388	+	Silent	SNP	T	T	C	rs3740460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:73051388T>C	ENST00000335350.6	+	10	1910	c.1494T>C	c.(1492-1494)gaT>gaC	p.D498D	UNC5B_ENST00000373192.4_Silent_p.D487D	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	498					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GCCTGGCAGATGGGGCTGACC	0.642													t|||	972	0.194089	0.2088	0.1657	5008	,	,		17689	0.2014		0.1272	False		,,,				2504	0.2556				p.D498D		Atlas-SNP	.											.	UNC5B	123	.	0			c.T1494C						PASS	.			794,3612	318.8+/-295.8	78,638,1487	53.0	54.0	54.0		1494	-8.5	0.4	10	dbSNP_107	54	1056,7544	223.7+/-260.4	62,932,3306	no	coding-synonymous	UNC5B	NM_170744.4		140,1570,4793	CC,CT,TT		12.2791,18.0209,14.2242		498/946	73051388	1850,11156	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon10			GGCAGATGGGGCT	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1494T>C	10.37:g.73051388T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			T|0.845;C|0.155	0.155	strong		0.642	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
PNN	5411	hgsc.bcm.edu	37	14	39648629	39648629	+	Silent	SNP	C	C	T	rs11558739	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:39648629C>T	ENST00000216832.4	+	8	823	c.756C>T	c.(754-756)acC>acT	p.T252T	PNN_ENST00000557680.1_3'UTR	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	252	Glu-rich.|Necessary for interaction with RNPS1.|Sufficient for PSAP complex assembly.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.T252T(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		GTCCAGCTACCCAAAAACTAA	0.338													C|||	624	0.124601	0.1566	0.1614	5008	,	,		16751	0.0734		0.1123	False		,,,				2504	0.1207				p.T252T		Atlas-SNP	.											PNN,NS,carcinoma,0,1	PNN	67	1	1	Substitution - coding silent(1)	stomach(1)	c.C756T						PASS	.	C		605,3801	240.9+/-251.5	37,531,1635	61.0	64.0	63.0		756	2.9	1.0	14	dbSNP_120	63	1075,7525	219.5+/-257.5	61,953,3286	no	coding-synonymous	PNN	NM_002687.3		98,1484,4921	TT,TC,CC		12.5,13.7313,12.9171		252/718	39648629	1680,11326	2203	4300	6503	SO:0001819	synonymous_variant	5411	exon8			AGCTACCCAAAAA	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.756C>T	14.37:g.39648629C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	126	48	0.380952	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Silent	SNP	ENST00000216832.4	37	CCDS9671.1																																																																																			C|0.870;T|0.130	0.130	strong		0.338	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687	
FAM129A	116496	hgsc.bcm.edu	37	1	184765000	184765000	+	Missense_Mutation	SNP	G	G	A	rs12750174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:184765000G>A	ENST00000367511.3	-	14	2091	c.1898C>T	c.(1897-1899)tCg>tTg	p.S633L	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	633			S -> L (in dbSNP:rs12750174).		negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						TTTGGCCAACGAGCTAGGGAC	0.542													G|||	36	0.0071885	0.0008	0.013	5008	,	,		18580	0.0		0.0199	False		,,,				2504	0.0061				p.S633L		Atlas-SNP	.											.	FAM129A	98	.	0			c.C1898T						PASS	.	G	LEU/SER	33,4373	38.4+/-70.7	1,31,2171	73.0	74.0	73.0		1898	2.2	0.0	1	dbSNP_121	73	258,8342	100.8+/-162.1	3,252,4045	yes	missense	FAM129A	NM_052966.2	145	4,283,6216	AA,AG,GG		3.0,0.749,2.2374	benign	633/929	184765000	291,12715	2203	4300	6503	SO:0001583	missense	116496	exon14			GCCAACGAGCTAG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1898C>T	1.37:g.184765000G>A	ENSP00000356481:p.Ser633Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	113	37	0.327434	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	12.15	1.850516	0.32699	0.00749	0.03	ENSG00000135842	ENST00000367511	T	0.10960	2.82	5.05	2.18	0.27775	.	0.917868	0.09180	N	0.837556	T	0.01976	0.0062	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.44360	-0.9333	10	0.25751	T	0.34	1.4829	8.3421	0.32249	0.243:0.0:0.757:0.0	rs12750174;rs52830752;rs12750174	633	Q9BZQ8	NIBAN_HUMAN	L	633	ENSP00000356481:S633L	ENSP00000356481:S633L	S	-	2	0	FAM129A	183031623	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	1.554000	0.36266	0.184000	0.20083	0.561000	0.74099	TCG	G|0.981;A|0.019	0.019	strong		0.542	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
OR4K17	390436	hgsc.bcm.edu	37	14	20586042	20586042	+	Missense_Mutation	SNP	G	G	C	rs8005245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20586042G>C	ENST00000315543.4	+	1	477	c.477G>C	c.(475-477)aaG>aaC	p.K159N		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	131						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)		CCATTTGTAAGCCCCTACACT	0.458													G|||	2141	0.427516	0.3268	0.4135	5008	,	,		20287	0.5437		0.4294	False		,,,				2504	0.4519				p.K159N		Atlas-SNP	.											.	OR4K17	58	.	0			c.G477C						PASS	.	G	ASN/LYS	1596,2810		285,1026,892	185.0	156.0	166.0		477	2.0	1.0	14	dbSNP_116	166	3585,5015		736,2113,1451	yes	missense	OR4K17	NM_001004715.1	94	1021,3139,2343	CC,CG,GG		41.686,36.2233,39.8355	probably-damaging	159/344	20586042	5181,7825	2203	4300	6503	SO:0001583	missense	390436	exon1			TTGTAAGCCCCTA		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.477G>C	14.37:g.20586042G>C	ENSP00000319197:p.Lys159Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	37	CCDS32030.1	928	0.4249084249084249	147	0.29878048780487804	152	0.4198895027624309	307	0.5367132867132867	322	0.42480211081794195	.	13.61	2.287217	0.40494	0.362233	0.41686	ENSG00000176230	ENST00000315543	T	0.00392	7.58	2.86	1.95	0.26073	GPCR, rhodopsin-like superfamily (1);	0.561453	0.12470	U	0.466129	T	0.00012	0.0000	L	0.39566	1.225	0.39937	P	0.02563700000000002	D	0.69078	0.997	D	0.64687	0.928	T	0.09885	-1.0654	9	0.72032	D	0.01	.	5.0304	0.14407	0.1331:0.3717:0.4952:0.0	rs8005245;rs17308178;rs52832107;rs8005245	131	Q8NGC6	OR4KH_HUMAN	N	159	ENSP00000319197:K159N	ENSP00000319197:K159N	K	+	3	2	OR4K17	19655882	0.000000	0.05858	0.963000	0.40424	0.765000	0.43378	-6.214000	0.00075	0.511000	0.28236	0.404000	0.27445	AAG	G|0.599;C|0.401	0.401	strong		0.458	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
OR4B1	119765	hgsc.bcm.edu	37	11	48238549	48238549	+	Missense_Mutation	SNP	G	G	A	rs11606506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:48238549G>A	ENST00000309562.2	+	1	206	c.188G>A	c.(187-189)tGc>tAc	p.C63Y		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	63			C -> Y (in dbSNP:rs11606506).			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(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						TTCCTTAGCTGCCTGTCCTTG	0.498													a|||	1373	0.274161	0.171	0.1916	5008	,	,		20453	0.3869		0.174	False		,,,				2504	0.4591				p.C63Y		Atlas-SNP	.											.	OR4B1	52	.	0			c.G188A						PASS	.	A	TYR/CYS	769,3633	753.4+/-412.4	70,629,1502	188.0	171.0	177.0		188	0.1	0.4	11	dbSNP_120	177	1522,7074	747.4+/-407.3	129,1264,2905	yes	missense	OR4B1	NM_001005470.1	194	199,1893,4407	AA,AG,GG		17.7059,17.4693,17.6258	benign	63/310	48238549	2291,10707	2201	4298	6499	SO:0001583	missense	119765	exon1			TTAGCTGCCTGTC	AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"""GPCR / Class A : Olfactory receptors"""	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.188G>A	11.37:g.48238549G>A	ENSP00000311605:p.Cys63Tyr	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	237	113	0.476793	NM_001005470	Q6IF75|Q96R64	Missense_Mutation	SNP	ENST00000309562.2	37	CCDS31485.1	482	0.2206959706959707	87	0.17682926829268292	68	0.1878453038674033	192	0.3356643356643357	135	0.17810026385224276	A	0.003	-2.546631	0.00140	0.174693	0.177059	ENSG00000175619	ENST00000309562	T	0.02944	4.1	5.4	0.102	0.14522	GPCR, rhodopsin-like superfamily (1);	0.915675	0.09180	N	0.837530	T	0.00012	0.0000	N	0.00377	-1.585	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42481	-0.9449	9	0.02654	T	1	.	2.0648	0.03600	0.3133:0.3957:0.1573:0.1337	rs11606506;rs52792165;rs60487265;rs11606506	63	Q8NGF8	OR4B1_HUMAN	Y	63	ENSP00000311605:C63Y	ENSP00000311605:C63Y	C	+	2	0	OR4B1	48195125	0.000000	0.05858	0.391000	0.26233	0.168000	0.22595	1.481000	0.35476	-0.569000	0.06030	-0.775000	0.03384	TGC	G|0.796;A|0.204	0.204	strong		0.498	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470	
FBN3	84467	hgsc.bcm.edu	37	19	8154990	8154990	+	Silent	SNP	C	C	T	rs35002391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8154990C>T	ENST00000600128.1	-	49	6591	c.6177G>A	c.(6175-6177)gaG>gaA	p.E2059E	FBN3_ENST00000601739.1_Silent_p.E2059E|FBN3_ENST00000270509.2_Silent_p.E2059E			Q75N90	FBN3_HUMAN	fibrillin 3	2059	TB 8.					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						CACCGCTGCCCTCCTGGGGAC	0.632													C|||	1228	0.245208	0.3691	0.219	5008	,	,		18512	0.0724		0.337	False		,,,				2504	0.18				p.E2059E		Atlas-SNP	.											.	FBN3	300	.	0			c.G6177A						PASS	.	C		1599,2807	488.0+/-361.1	299,1001,903	39.0	41.0	40.0		6177	0.3	1.0	19	dbSNP_126	40	3155,5445	472.1+/-368.3	586,1983,1731	no	coding-synonymous	FBN3	NM_032447.3		885,2984,2634	TT,TC,CC		36.686,36.2914,36.5524		2059/2810	8154990	4754,8252	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon48			GCTGCCCTCCTGG		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.6177G>A	19.37:g.8154990C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1	574	0.26282051282051283	181	0.3678861788617886	89	0.24585635359116023	48	0.08391608391608392	256	0.33773087071240104	C	0.118	-1.128823	0.01756	0.362914	0.36686	ENSG00000142449	ENST00000341066	.	.	.	3.83	0.32	0.15878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999917993	.	.	.	.	.	.	T	0.39461	-0.9613	4	0.22706	T	0.39	.	11.4047	0.49892	0.0:0.6267:0.0:0.3733	rs35002391	.	.	.	K	179	.	ENSP00000341317:R179K	R	-	2	0	FBN3	8060990	0.033000	0.19621	0.998000	0.56505	0.071000	0.16799	-0.251000	0.08818	-0.046000	0.13446	-1.598000	0.00824	AGG	C|0.668;T|0.332	0.332	strong		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PUS3	83480	hgsc.bcm.edu	37	11	125763746	125763746	+	Missense_Mutation	SNP	C	C	G	rs3088241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125763746C>G	ENST00000530811.1	-	3	1425	c.1380G>C	c.(1378-1380)gaG>gaC	p.E460D	HYLS1_ENST00000425380.2_Intron|PUS3_ENST00000227474.3_Missense_Mutation_p.E460D|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	460			E -> D (in dbSNP:rs3088241). {ECO:0000269|PubMed:15489334}.		tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	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;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		AATTAGTATTCTCTTCCTCTA	0.413													C|||	2297	0.458666	0.3933	0.4236	5008	,	,		19356	0.5327		0.501	False		,,,				2504	0.4519				p.E460D		Atlas-SNP	.											.	PUS3	33	.	0			c.G1380C						PASS	.	C	,ASP/GLU,	1779,2623	526.5+/-371.9	355,1069,777	211.0	201.0	205.0		,1380,	-2.1	0.1	11	dbSNP_102	205	4289,4309	577.5+/-390.6	1071,2147,1081	yes	intron,missense,intron	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	,45,	1426,3216,1858	GG,GC,CC		49.8837,40.4134,46.6769	,possibly-damaging,	,460/482,	125763746	6068,6932	2201	4299	6500	SO:0001583	missense	83480	exon4			AGTATTCTCTTCC	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.1380G>C	11.37:g.125763746C>G	ENSP00000432386:p.Glu460Asp	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	274	116	0.423358	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	1056	0.4835164835164835	196	0.3983739837398374	154	0.425414364640884	322	0.5629370629370629	384	0.5065963060686016	C	8.796	0.931769	0.18131	0.404134	0.498837	ENSG00000110060	ENST00000227474;ENST00000530811	T;T	0.31247	1.5;1.5	4.92	-2.14	0.07123	.	0.667480	0.14995	N	0.286428	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.46062	-0.9218	9	0.20046	T	0.44	-10.5276	6.2703	0.20951	0.0:0.5046:0.1624:0.3331	rs3088241;rs17795488;rs17849865;rs17858239;rs3088241	460	Q9BZE2	PUS3_HUMAN	D	460	ENSP00000227474:E460D;ENSP00000432386:E460D	ENSP00000227474:E460D	E	-	3	2	PUS3	125268956	0.340000	0.24792	0.138000	0.22173	0.363000	0.29612	-0.041000	0.12084	-0.433000	0.07286	0.591000	0.81541	GAG	C|0.522;G|0.478	0.478	strong		0.413	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307	
GALR1	2587	hgsc.bcm.edu	37	18	74962645	74962645	+	Silent	SNP	T	T	C	rs5374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:74962645T>C	ENST00000299727.3	+	1	141	c.141T>C	c.(139-141)ggT>ggC	p.G47G		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	47					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		TCGCGCTGGGTGTGCTGGGCA	0.687													C|||	2453	0.489816	0.4493	0.4438	5008	,	,		14410	0.374		0.665	False		,,,				2504	0.5164				p.G47G		Atlas-SNP	.											GALR1,colon,carcinoma,0,2	GALR1	53	2	0			c.T141C						scavenged	.	C		2102,2304	592.2+/-387.7	502,1098,603	36.0	34.0	34.0		141	1.8	1.0	18	dbSNP_52	34	5546,3052	463.8+/-366.1	1786,1974,539	yes	coding-synonymous	GALR1	NM_001480.3		2288,3072,1142	CC,CT,TT		35.4966,47.7077,41.1873		47/350	74962645	7648,5356	2203	4299	6502	SO:0001819	synonymous_variant	2587	exon1			GCTGGGTGTGCTG	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.141T>C	18.37:g.74962645T>C		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001480	Q4VBL7	Silent	SNP	ENST00000299727.3	37	CCDS12012.1																																																																																			T|0.442;C|0.558	0.558	strong		0.687	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
GPATCH1	55094	hgsc.bcm.edu	37	19	33617583	33617583	+	Silent	SNP	C	C	T	rs6510356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:33617583C>T	ENST00000170564.2	+	19	3023	c.2709C>T	c.(2707-2709)agC>agT	p.S903S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	903					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CCGACAGCAGCGACAGCCAGA	0.488											OREG0025410	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1298	0.259185	0.4387	0.134	5008	,	,		16215	0.1716		0.1163	False		,,,				2504	0.3425				p.S903S	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C2709T						PASS	.	C		1821,2585	533.0+/-373.6	379,1063,761	86.0	83.0	84.0		2709	-4.2	0.7	19	dbSNP_116	84	1008,7592	216.3+/-255.4	50,908,3342	no	coding-synonymous	GPATCH1	NM_018025.2		429,1971,4103	TT,TC,CC		11.7209,41.33,21.7515		903/932	33617583	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon19			CAGCAGCGACAGC	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2709C>T	19.37:g.33617583C>T		Somatic	25	0	0	841	WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.792;N|0.001	.	strong		0.488	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
BRWD1	54014	hgsc.bcm.edu	37	21	40641858	40641858	+	Silent	SNP	T	T	G	rs61740760	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:40641858T>G	ENST00000333229.2	-	15	1824	c.1497A>C	c.(1495-1497)acA>acC	p.T499T	BRWD1_ENST00000380800.3_Silent_p.T499T|BRWD1_ENST00000342449.3_Silent_p.T499T	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	499					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)				TGGTACCTTTTGTAATATCCC	0.353													T|||	50	0.00998403	0.0023	0.0115	5008	,	,		15942	0.0		0.0368	False		,,,				2504	0.002				p.T499T	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A1497C						PASS	.	T	,	25,4381	31.7+/-61.6	0,25,2178	116.0	110.0	112.0		1497,1497	3.2	1.0	21	dbSNP_129	112	280,8320	105.4+/-166.3	5,270,4025	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	5,295,6203	GG,GT,TT		3.2558,0.5674,2.3451	,	499/2321,499/2270	40641858	305,12701	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon15			ACCTTTTGTAATA	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.1497A>C	21.37:g.40641858T>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	163	80	0.490798	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	34	0.015567765567765568	0	0.0	6	0.016574585635359115	0	0.0	28	0.036939313984168866	T	9.400	1.077745	0.20227	0.005674	0.032558	ENSG00000185658	ENST00000455867	.	.	.	5.57	3.15	0.36227	.	.	.	.	.	T	0.16471	0.0396	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07986	-1.0744	4	.	.	.	-10.8021	3.5033	0.07681	0.1241:0.069:0.256:0.5509	.	.	.	.	Q	211	.	.	K	-	1	0	BRWD1	39563728	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	0.332000	0.19751	0.380000	0.24823	0.455000	0.32223	AAA	T|0.978;G|0.022	0.022	strong		0.353	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
OR5W2	390148	hgsc.bcm.edu	37	11	55681336	55681336	+	Silent	SNP	G	G	A	rs11231529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	115	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	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	
DHX38	9785	hgsc.bcm.edu	37	16	72132832	72132832	+	Silent	SNP	G	G	A	rs150221434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72132832G>A	ENST00000268482.3	+	6	1280	c.771G>A	c.(769-771)gtG>gtA	p.V257V	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	257					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)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CCAGGTCTGTGAGGGGCAAGT	0.582													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19641	0.0		0.002	False		,,,				2504	0.0				p.V257V	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G771A						PASS	.	G		1,4395	2.1+/-5.4	0,1,2197	53.0	53.0	53.0		771	2.8	1.0	16	dbSNP_134	53	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DHX38	NM_014003.3		0,18,6480	AA,AG,GG		0.1977,0.0227,0.1385		257/1228	72132832	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon6			GTCTGTGAGGGGC	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.771G>A	16.37:g.72132832G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
LRP2	4036	hgsc.bcm.edu	37	2	170060670	170060670	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170060670G>C	ENST00000263816.3	-	42	8112	c.7827C>G	c.(7825-7827)gaC>gaG	p.D2609E		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2609					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)"""	GTGTGTACAAGTCAGTCCAGT	0.473																																					p.D2609E		Atlas-SNP	.											.	LRP2	751	.	0			c.C7827G						PASS	.						165.0	174.0	171.0					2																	170060670		2203	4300	6503	SO:0001583	missense	4036	exon42			GTACAAGTCAGTC		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.7827C>G	2.37:g.170060670G>C	ENSP00000263816:p.Asp2609Glu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	153	48	0.313726	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200151	0.58126	.	.	ENSG00000081479	ENST00000263816	D	0.92446	-3.04	5.78	3.01	0.34805	Six-bladed beta-propeller, TolB-like (1);	0.093401	0.64402	N	0.000001	D	0.93677	0.7980	H	0.95504	3.68	0.80722	D	1	D	0.53745	0.962	P	0.44394	0.448	D	0.91687	0.5363	10	0.87932	D	0	.	7.2942	0.26383	0.1959:0.0:0.6833:0.1207	.	2609	P98164	LRP2_HUMAN	E	2609	ENSP00000263816:D2609E	ENSP00000263816:D2609E	D	-	3	2	LRP2	169768916	1.000000	0.71417	0.553000	0.28255	0.357000	0.29423	3.438000	0.52871	0.364000	0.24374	-0.857000	0.03018	GAC	.	.	none		0.473	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
UBE2I	7329	hgsc.bcm.edu	37	16	1364365	1364365	+	Silent	SNP	A	A	G	rs4610	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1364365A>G	ENST00000355803.4	+	3	689	c.138A>G	c.(136-138)ccA>ccG	p.P46P	UBE2I_ENST00000402301.1_Silent_p.P46P|UBE2I_ENST00000325437.5_Silent_p.P46P|UBE2I_ENST00000566587.1_Silent_p.P46P|UBE2I_ENST00000397515.2_Silent_p.P46P|UBE2I_ENST00000403747.2_Silent_p.P46P|UBE2I_ENST00000397514.3_Silent_p.P46P|UBE2I_ENST00000406620.1_Silent_p.P46P	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	46					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				GCGCCATTCCAGGAAAGAAAG	0.577													A|||	696	0.138978	0.1634	0.2262	5008	,	,		17411	0.0456		0.1382	False		,,,				2504	0.1411				p.P46P		Atlas-SNP	.											.	UBE2I	15	.	0			c.A138G						PASS	.	A	,,,	691,3707	286.3+/-278.7	58,575,1566	67.0	65.0	66.0		138,138,138,138	-4.0	0.7	16	dbSNP_52	66	1228,7372	246.2+/-274.8	87,1054,3159	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UBE2I	NM_003345.4,NM_194259.2,NM_194260.2,NM_194261.2	,,,	145,1629,4725	GG,GA,AA		14.2791,15.7117,14.7638	,,,	46/159,46/159,46/159,46/159	1364365	1919,11079	2199	4300	6499	SO:0001819	synonymous_variant	7329	exon3			CATTCCAGGAAAG	D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"""Ubiquitin-conjugating enzymes E2"""	12485	protein-coding gene	gene with protein product		601661	"""ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)"", ""ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"""			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.138A>G	16.37:g.1364365A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_003345	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Silent	SNP	ENST00000355803.4	37	CCDS10433.1																																																																																			A|0.870;G|0.130	0.130	strong		0.577	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345	
OR2T35	403244	hgsc.bcm.edu	37	1	248801592	248801592	+	Missense_Mutation	SNP	C	C	T	rs78622116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248801592C>T	ENST00000317450.3	-	1	967	c.968G>A	c.(967-969)gGc>gAc	p.G323D		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G323D(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)			TCCCTGCTAGCCCTTCCTGAT	0.542																																					p.G323D		Atlas-SNP	.											OR2T35,caecum,carcinoma,0,1	OR2T35	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G968A						scavenged	.						21.0	6.0	12.0					1																	248801592		1918	2711	4629	SO:0001583	missense	403244	exon1			TGCTAGCCCTTCC	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.968G>A	1.37:g.248801592C>T	ENSP00000324369:p.Gly323Asp	Somatic	10	3	0.3		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_001001827	Q6IEY7	Missense_Mutation	SNP	ENST00000317450.3	37	CCDS31123.1	1586	0.7261904761904762	244	0.4959349593495935	286	0.7900552486187845	451	0.7884615384615384	605	0.7981530343007915	.	4.951	0.176629	0.09443	.	.	ENSG00000177151	ENST00000317450	T	0.01647	4.71	0.75	0.75	0.18387	.	.	.	.	.	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	0.03259	-1.1055	8	0.56958	D	0.05	.	2.9607	0.05891	0.0:0.3203:0.0:0.6797	.	323	Q8NGX2	O2T35_HUMAN	D	323	ENSP00000324369:G323D	ENSP00000324369:G323D	G	-	2	0	OR2T35	246868215	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	0.032000	0.13732	-0.215000	0.10063	-1.461000	0.01025	GGC	C|0.245;T|0.755	0.755	strong		0.542	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	
TTC28	23331	hgsc.bcm.edu	37	22	28559120	28559120	+	Silent	SNP	G	G	C	rs17486417	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:28559120G>C	ENST00000397906.2	-	6	1542	c.1401C>G	c.(1399-1401)ctC>ctG	p.L467L		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	467					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CCCGGTCCTTGAGATCCTCAG	0.552													G|||	678	0.135383	0.0794	0.0821	5008	,	,		18257	0.1736		0.1342	False		,,,				2504	0.2106				p.L467L		Atlas-SNP	.											.	TTC28	84	.	0			c.C1401G						PASS	.	G		116,1268		5,106,581	47.0	38.0	41.0		1401	2.6	1.0	22	dbSNP_123	41	450,2732		25,400,1166	no	coding-synonymous	TTC28	NM_001145418.1		30,506,1747	CC,CG,GG		14.142,8.3815,12.396		467/2482	28559120	566,4000	692	1591	2283	SO:0001819	synonymous_variant	23331	exon6			GTCCTTGAGATCC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1401C>G	22.37:g.28559120G>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.870;C|0.128	0.128	strong		0.552	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
FOXN1	8456	hgsc.bcm.edu	37	17	26851602	26851602	+	Missense_Mutation	SNP	C	C	T	rs2071587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26851602C>T	ENST00000226247.2	+	2	234	c.205C>T	c.(205-207)Cgc>Tgc	p.R69C	FOXN1_ENST00000579795.1_Missense_Mutation_p.R69C	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	69			R -> C (in dbSNP:rs2071587).		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)					ACACAGCCCCCGCATTGCGTC	0.652													C|||	535	0.106829	0.0045	0.2378	5008	,	,		14582	0.1905		0.1203	False		,,,				2504	0.0521				p.R69C		Atlas-SNP	.											FOXN1,NS,carcinoma,-1,3	FOXN1	51	3	0			c.C205T						PASS	.	C	CYS/ARG	103,4303	80.4+/-118.8	1,101,2101	45.0	49.0	48.0		205	3.3	1.0	17	dbSNP_96	48	653,7947	161.1+/-214.1	23,607,3670	yes	missense	FOXN1	NM_003593.2	180	24,708,5771	TT,TC,CC		7.593,2.3377,5.8127	benign	69/649	26851602	756,12250	2203	4300	6503	SO:0001583	missense	8456	exon2			AGCCCCCGCATTG	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.205C>T	17.37:g.26851602C>T	ENSP00000226247:p.Arg69Cys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	37	CCDS11232.1	276	0.12637362637362637	6	0.012195121951219513	74	0.20441988950276244	118	0.2062937062937063	78	0.10290237467018469	C	11.77	1.737541	0.30774	0.023377	0.07593	ENSG00000109101	ENST00000226247	D	0.92446	-3.04	5.54	3.3	0.37823	.	0.063200	0.64402	D	0.000002	T	0.00241	0.0007	N	0.08118	0	0.30571	P	0.7635270000000001	B	0.17268	0.021	B	0.04013	0.001	T	0.30592	-0.9973	9	0.72032	D	0.01	.	7.1547	0.25630	0.7:0.1597:0.0:0.1403	rs2071587;rs60721475;rs2071587	69	O15353	FOXN1_HUMAN	C	69	ENSP00000226247:R69C	ENSP00000226247:R69C	R	+	1	0	FOXN1	23875729	0.993000	0.37304	0.974000	0.42286	0.361000	0.29550	1.912000	0.39946	0.467000	0.27218	-0.397000	0.06425	CGC	C|0.914;T|0.086	0.086	strong		0.652	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
TULP4	56995	hgsc.bcm.edu	37	6	158924595	158924595	+	Silent	SNP	A	A	G	rs3749853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	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	
GNAT3	346562	hgsc.bcm.edu	37	7	80088041	80088041	+	Silent	SNP	G	G	A	rs2074674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:80088041G>A	ENST00000398291.3	-	8	1104	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	337					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)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						CTGTAACTGCGTCAAACACAA	0.338													A|||	2341	0.467452	0.4168	0.4481	5008	,	,		16205	0.7421		0.3201	False		,,,				2504	0.4182				p.D337D		Atlas-SNP	.											GNAT3_ENST00000398291,NS,carcinoma,0,2	GNAT3	65	2	0			c.C1011T						PASS	.	A		1537,2159		327,883,638	80.0	80.0	80.0		1011	3.2	1.0	7	dbSNP_96	80	2628,5574		444,1740,1917	no	coding-synonymous	GNAT3	NM_001102386.1		771,2623,2555	AA,AG,GG		32.041,41.5855,35.0059		337/355	80088041	4165,7733	1848	4101	5949	SO:0001819	synonymous_variant	346562	exon8			AACTGCGTCAAAC		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.1011C>T	7.37:g.80088041G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	37	CCDS47625.1																																																																																			G|0.553;A|0.447	0.447	strong		0.338	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136305530	136305530	+	Missense_Mutation	SNP	C	C	G	rs28647808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136305530C>G	ENST00000371929.3	+	16	2296	c.1852C>G	c.(1852-1854)Ccc>Gcc	p.P618A	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.P587A|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.P290A|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.P618A	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	618	Spacer.		P -> A (in dbSNP:rs28647808). {ECO:0000269|PubMed:11586351, ECO:0000269|PubMed:19055667, 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)		CACCACCTACCCCTCCCTCCT	0.652													C|||	162	0.0323482	0.0053	0.036	5008	,	,		18262	0.0198		0.0825	False		,,,				2504	0.0276				p.P618A		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C1852G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	79,4327	68.7+/-106.4	1,77,2125	119.0	85.0	97.0		1852,1759,1852	5.1	1.0	9	dbSNP_125	97	742,7858	178.5+/-227.8	37,668,3595	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	27,27,27	38,745,5720	GG,GC,CC		8.6279,1.793,6.3125	probably-damaging,probably-damaging,probably-damaging	618/1428,587/1341,618/1372	136305530	821,12185	2203	4300	6503	SO:0001583	missense	11093	exon16			ACCTACCCCTCCC	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.1852C>G	9.37:g.136305530C>G	ENSP00000360997:p.Pro618Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	96	0.04395604395604396	3	0.006097560975609756	14	0.03867403314917127	12	0.02097902097902098	67	0.08839050131926121	C	21.8	4.204993	0.79127	0.01793	0.086279	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.67523	-0.26;-0.27;-0.25;0.22	5.12	5.12	0.69794	.	.	.	.	.	T	0.19927	0.0479	M	0.85945	2.785	0.20403	P	0.9999036639	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.985;0.996	T	0.63060	-0.6721	8	0.45353	T	0.12	.	17.1153	0.86687	0.0:1.0:0.0:0.0	rs28647808;rs36221218	618;587;618;290	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	A	618;618;587;290	ENSP00000360997:P618A;ENSP00000347927:P618A;ENSP00000348997:P587A;ENSP00000444504:P290A	ENSP00000347927:P618A	P	+	1	0	ADAMTS13	135295351	1.000000	0.71417	0.996000	0.52242	0.617000	0.37484	6.389000	0.73199	2.377000	0.81083	0.491000	0.48974	CCC	C|0.939;G|0.061	0.061	strong		0.652	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
CD1E	913	hgsc.bcm.edu	37	1	158324425	158324425	+	Missense_Mutation	SNP	A	A	G	rs1065457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158324425A>G	ENST00000368167.3	+	2	556	c.317A>G	c.(316-318)cAg>cGg	p.Q106R	CD1E_ENST00000368163.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368161.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368155.3_Missense_Mutation_p.Q106R|CD1E_ENST00000368166.3_Intron|CD1E_ENST00000368156.1_Missense_Mutation_p.Q106R|CD1E_ENST00000368160.3_Missense_Mutation_p.Q106R|CD1E_ENST00000464822.1_Intron|CD1E_ENST00000444681.2_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Intron|CD1E_ENST00000368165.3_Missense_Mutation_p.Q106R|CD1E_ENST00000434258.1_Missense_Mutation_p.Q104R	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	106			Q -> R (in allele CD1E*02, allele CD1E*05 and CD1E*06; dbSNP:rs1065457). {ECO:0000269|PubMed:10488738, ECO:0000269|PubMed:10948205, ECO:0000269|PubMed:12144626}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					AGTTTTATCCAGATAGTGCAA	0.428													G|||	3087	0.616414	0.8964	0.415	5008	,	,		22018	0.6617		0.3579	False		,,,				2504	0.6002				p.Q106R		Atlas-SNP	.											.	CD1E	129	.	0			c.A317G	GRCh37	CM067657	CD1E	M	rs1065457	PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN,,,ARG/GLN,ARG/GLN,,,,,ARG/GLN,ARG/GLN	3006,842		1166,674,84	63.0	63.0	63.0		317,317,317,,,317,317,,,,,317,317	-5.5	0.0	1	dbSNP_86	63	2869,5465		492,1885,1790	yes	missense,missense,missense,intron,intron,missense,missense,intron,intron,intron,intron,missense,missense	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	43,43,43,,,43,43,,,,,43,43	1658,2559,1874	GG,GA,AA		34.4252,21.8815,48.2269	benign,benign,benign,,,benign,benign,,,,,benign,benign	106/377,106/291,106/322,,,106/299,106/232,,,,,106/287,106/389	158324425	5875,6307	1924	4167	6091	SO:0001583	missense	913	exon2			TTATCCAGATAGT	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.317A>G	1.37:g.158324425A>G	ENSP00000357149:p.Gln106Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	167	92	0.550898	NM_001185107	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	1208	0.5531135531135531	431	0.8760162601626016	143	0.39502762430939226	364	0.6363636363636364	270	0.3562005277044855	G	0.955	-0.705122	0.03255	0.781185	0.344252	ENSG00000158488	ENST00000434258;ENST00000368167;ENST00000368165;ENST00000368163;ENST00000368160;ENST00000368161;ENST00000368156;ENST00000368155	T;T;T;T;T;T;T;T	0.16457	2.34;2.34;3.63;2.34;2.34;2.34;3.83;3.73	3.8	-5.46	0.02608	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	4.005330	0.00702	N	0.000789	T	0.00875	0.0029	N	0.02674	-0.535	0.80722	P	0.0	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	0.04013	0.001;0.0;0.0;0.001;0.0;0.001;0.0;0.001	T	0.24012	-1.0172	9	0.02654	T	1	2.1543	0.268	0.00227	0.3302:0.2288:0.221:0.2199	rs1065457;rs57813521;rs1065457	104;106;106;106;106;106;106;106	E7ET31;P15812-5;P15812-7;P15812-2;P15812;P15812-3;P15812-6;P15812-4	.;.;.;.;CD1E_HUMAN;.;.;.	R	104;106;106;106;106;106;106;106	ENSP00000401957:Q104R;ENSP00000357149:Q106R;ENSP00000357147:Q106R;ENSP00000357145:Q106R;ENSP00000357142:Q106R;ENSP00000357143:Q106R;ENSP00000357138:Q106R;ENSP00000357137:Q106R	ENSP00000357137:Q106R	Q	+	2	0	CD1E	156591049	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.010000	0.00314	-1.710000	0.01397	-0.213000	0.12676	CAG	A|0.437;G|0.563	0.563	strong		0.428	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
EHBP1	23301	hgsc.bcm.edu	37	2	63101560	63101560	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:63101560A>G	ENST00000263991.5	+	11	1665	c.1183A>G	c.(1183-1185)Agg>Ggg	p.R395G	EHBP1_ENST00000354487.3_Missense_Mutation_p.R360G|EHBP1_ENST00000405289.1_Missense_Mutation_p.R360G|EHBP1_ENST00000431489.1_Missense_Mutation_p.R360G|EHBP1_ENST00000405015.3_Missense_Mutation_p.R360G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	395			R -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			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)			AGAAACTGAAAGGCGAGTGAA	0.378																																					p.R395G		Atlas-SNP	.											EHBP1,caecum,carcinoma,0,11	EHBP1	127	11	0			c.A1183G						scavenged	.						98.0	108.0	104.0					2																	63101560		2203	4300	6503	SO:0001583	missense	23301	exon11			ACTGAAAGGCGAG	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.1183A>G	2.37:g.63101560A>G	ENSP00000263991:p.Arg395Gly	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	163	3	0.0184049	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242526	0.39598	.	.	ENSG00000115504	ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T	0.74002	-0.8;-0.8;-0.79;-0.79;-0.79	5.13	3.95	0.45737	.	0.467690	0.24752	N	0.035895	T	0.62073	0.2398	L	0.43152	1.355	0.37765	D	0.926455	P;B;B	0.35684	0.515;0.13;0.009	B;B;B	0.29862	0.108;0.022;0.031	T	0.59984	-0.7351	10	0.20046	T	0.44	.	12.0596	0.53555	0.8503:0.1497:0.0:0.0	.	360;360;395	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	G	360;360;395;360;360	ENSP00000384143:R360G;ENSP00000403783:R360G;ENSP00000263991:R395G;ENSP00000346482:R360G;ENSP00000385524:R360G	ENSP00000263991:R395G	R	+	1	2	EHBP1	62955064	1.000000	0.71417	0.992000	0.48379	0.964000	0.63967	3.296000	0.51802	0.884000	0.36064	0.528000	0.53228	AGG	.	.	none		0.378	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
C16orf71	146562	hgsc.bcm.edu	37	16	4796393	4796393	+	Missense_Mutation	SNP	A	A	G	rs737700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4796393A>G	ENST00000299320.5	+	7	1539	c.1061A>G	c.(1060-1062)cAg>cGg	p.Q354R	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.Q368R	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	354			Q -> R (in dbSNP:rs737700). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						TCAAGGAAGCAGGGCTCCCAG	0.572													G|||	2834	0.565895	0.4682	0.5692	5008	,	,		20659	0.6786		0.6481	False		,,,				2504	0.4949				p.Q354R		Atlas-SNP	.											C16orf71,NS,carcinoma,0,1	C16orf71	46	1	0			c.A1061G						PASS	.	G	ARG/GLN	2308,2086	569.0+/-382.5	617,1074,506	51.0	53.0	53.0		1061	-6.6	0.0	16	dbSNP_86	53	5681,2919	450.8+/-362.5	1877,1927,496	yes	missense	C16orf71	NM_139170.2	43	2494,3001,1002	GG,GA,AA		33.9419,47.4738,38.5178	benign	354/521	4796393	7989,5005	2197	4300	6497	SO:0001583	missense	146562	exon7			GGAAGCAGGGCTC	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.1061A>G	16.37:g.4796393A>G	ENSP00000299320:p.Gln354Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	1355	0.6204212454212454	251	0.5101626016260162	204	0.56353591160221	407	0.7115384615384616	493	0.6503957783641161	G	0.059	-1.227684	0.01518	0.525262	0.660581	ENSG00000166246	ENST00000299320;ENST00000411541	T	0.06294	3.32	3.3	-6.6	0.01824	.	2.256840	0.02402	N	0.080735	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	0.30995	-0.9959	9	0.19590	T	0.45	2.6361	3.002	0.06017	0.113:0.4976:0.2293:0.1602	rs737700;rs17857045;rs60363277;rs737700	354	Q8IYS4	CP071_HUMAN	R	354;109	ENSP00000299320:Q354R	ENSP00000299320:Q354R	Q	+	2	0	C16orf71	4736394	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.218000	0.02976	-2.323000	0.00639	-2.018000	0.00433	CAG	A|0.391;G|0.609	0.609	strong		0.572	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
CDH13	1012	hgsc.bcm.edu	37	16	83636136	83636136	+	Silent	SNP	G	G	A	rs371581191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:83636136G>A	ENST00000566620.1	+	8	1328	c.1038G>A	c.(1036-1038)acG>acA	p.T346T	CDH13_ENST00000268613.10_Silent_p.T393T|CDH13_ENST00000428848.3_Silent_p.T307T	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	346	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TAACAGGCACGGCCACAGCCA	0.458													G|||	4	0.000798722	0.0	0.0	5008	,	,		15867	0.0		0.003	False		,,,				2504	0.001				p.T393T		Atlas-SNP	.											.	CDH13	97	.	0			c.G1179A						PASS	.	G	,,,	1,3891		0,1,1945	182.0	184.0	183.0		1179,921,276,1038	-12.0	0.0	16		183	20,8320		0,20,4150	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,21,6095	AA,AG,GG		0.2398,0.0257,0.1717	,,,	393/761,307/675,92/460,346/714	83636136	21,12211	1946	4170	6116	SO:0001819	synonymous_variant	1012	exon9			AGGCACGGCCACA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1038G>A	16.37:g.83636136G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			.	.	weak		0.458	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
GAB2	9846	hgsc.bcm.edu	37	11	77930345	77930345	+	Silent	SNP	T	T	C	rs2450122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	84	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	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	
ETFB	2109	hgsc.bcm.edu	37	19	51856469	51856469	+	Missense_Mutation	SNP	G	G	A	rs147353781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51856469G>A	ENST00000309244.4	-	3	383	c.292C>T	c.(292-294)Cgc>Tgc	p.R98C	CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.R189C|CTD-2616J11.11_ENST00000600067.1_3'UTR	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	98					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)		GGACCCAAGCGTTCTGCTTCT	0.637													g|||	2	0.000399361	0.0	0.0014	5008	,	,		16497	0.0		0.001	False		,,,				2504	0.0				p.R189C		Atlas-SNP	.											ETFB_ENST00000309244,NS,carcinoma,0,2	ETFB	46	2	0			c.C565T						PASS	.		CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	112.0	99.0	104.0		565,292	3.0	0.1	19	dbSNP_134	104	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	ETFB	NM_001014763.1,NM_001985.2	180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	probably-damaging,probably-damaging	189/347,98/256	51856469	15,12991	2203	4300	6503	SO:0001583	missense	2109	exon2			CCAAGCGTTCTGC	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.292C>T	19.37:g.51856469G>A	ENSP00000311930:p.Arg98Cys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	13.39	2.223595	0.39300	4.54E-4	0.001512	ENSG00000105379	ENST00000309244;ENST00000354232	D;D	0.82803	-1.65;-1.65	5.18	3.0	0.34707	Electron transfer flavoprotein, alpha/beta-subunit, N-terminal (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.416981	0.27315	N	0.019921	T	0.81389	0.4812	L	0.39898	1.24	0.09310	N	0.999997	B;D	0.58620	0.218;0.983	B;P	0.55667	0.369;0.781	T	0.71774	-0.4491	10	0.72032	D	0.01	.	6.2267	0.20711	0.088:0.0:0.5739:0.3381	.	98;189	P38117;P38117-2	ETFB_HUMAN;.	C	98;189	ENSP00000311930:R98C;ENSP00000346173:R189C	ENSP00000311930:R98C	R	-	1	0	ETFB	56548281	0.020000	0.18652	0.107000	0.21349	0.673000	0.39480	1.050000	0.30404	0.561000	0.29186	-0.233000	0.12211	CGC	G|0.999;A|0.001	0.001	strong		0.637	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
PREX1	57580	hgsc.bcm.edu	37	20	47307618	47307618	+	Silent	SNP	G	G	A	rs3746820	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	142	0	0		WXS	Illumina HiSeq	Phase_I	180	176	0.977778	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	
GNG8	94235	hgsc.bcm.edu	37	19	47137459	47137459	+	Silent	SNP	C	C	T	rs12974613	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47137459C>T	ENST00000300873.4	-	2	89	c.87G>A	c.(85-87)gtG>gtA	p.V29V		NM_033258.1	NP_150283.1	O14610	GBGT2_HUMAN	guanine nucleotide binding protein (G protein), gamma 8	29					G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|phototransduction (GO:0007602)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)						Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.000621)|Epithelial(262;0.0171)|GBM - Glioblastoma multiforme(486;0.0325)		CTGCCTGCGACACCTGCGAGC	0.682													c|||	1057	0.211062	0.2595	0.1988	5008	,	,		10534	0.0635		0.341	False		,,,				2504	0.1728				p.V29V	Colon(120;3580 4883)	Atlas-SNP	.											.	GNG8	2	.	0			c.G87A						PASS	.			1231,3171	400.6+/-331.6	166,899,1136	36.0	36.0	36.0		87	4.1	1.0	19	dbSNP_121	36	2963,5637	432.3+/-357.1	516,1931,1853	no	coding-synonymous	GNG8	NM_033258.1		682,2830,2989	TT,TC,CC		34.4535,27.9646,32.2566		29/71	47137459	4194,8808	2201	4300	6501	SO:0001819	synonymous_variant	94235	exon2			CTGCGACACCTGC	AF493875	CCDS12687.1	19q13.32	2008-07-10				ENSG00000167414			19664	protein-coding gene	gene with protein product						10819326	Standard	NM_033258		Approved		uc010xyd.2	Q9UK08		ENST00000300873.4:c.87G>A	19.37:g.47137459C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	37	0.606557	NM_033258	B2R746|D3DTW5	Silent	SNP	ENST00000300873.4	37	CCDS12687.1																																																																																			C|0.728;T|0.272	0.272	strong		0.682	GNG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466587.1		
AKT1	207	hgsc.bcm.edu	37	14	105239894	105239894	+	Silent	SNP	C	C	T	rs1130233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000349310.3_Silent_p.E242E|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000544168.1_Silent_p.E180E			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	114	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	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	
PGS1	9489	hgsc.bcm.edu	37	17	76423151	76423151	+	IGR	SNP	C	C	T	rs3209030	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:76423151C>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000585328.1_Silent_p.P4204P|DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.P4232P	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TGAAAGTCTCCGGAATCTTCT	0.562													C|||	416	0.0830671	0.1127	0.0605	5008	,	,		18579	0.0317		0.0895	False		,,,				2504	0.1053				p.P4209P	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.G12627A						PASS	.	C		352,4054		15,322,1866	44.0	35.0	38.0		12627	-9.9	0.3	17	dbSNP_105	38	787,7809		45,697,3556	no	coding-synonymous	DNAH17	NM_173628.3		60,1019,5422	TT,TC,CC		9.1554,7.9891,8.7602		4209/4463	76423151	1139,11863	2203	4298	6501	SO:0001628	intergenic_variant	8632	exon78			AGTCTCCGGAATC		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76423151C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			C|0.914;T|0.086	0.086	strong		0.562	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
MIB2	142678	hgsc.bcm.edu	37	1	1564064	1564064	+	Missense_Mutation	SNP	G	G	A	rs201947158		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1564064G>A	ENST00000357210.4	+	16	2554	c.2338G>A	c.(2338-2340)Gcc>Acc	p.A780T	MIB2_ENST00000518681.1_Missense_Mutation_p.A772T|MIB2_ENST00000505820.2_Missense_Mutation_p.A837T|MIB2_ENST00000360522.4_Missense_Mutation_p.A745T|MIB2_ENST00000520777.1_Missense_Mutation_p.A833T|MIB2_ENST00000378708.1_Missense_Mutation_p.A686T|MIB2_ENST00000378710.3_Missense_Mutation_p.A744T|MIB2_ENST00000378712.1_Missense_Mutation_p.A657T|MIB2_ENST00000504599.1_Missense_Mutation_p.A736T|MIB2_ENST00000355826.5_Missense_Mutation_p.A823T	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	780					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCTGATGGGGCCGGGGGGGA	0.716													.|||	1	0.000199681	0.0	0.0	5008	,	,		15533	0.0		0.001	False		,,,				2504	0.0				p.A837T		Atlas-SNP	.											.	MIB2	62	.	0			c.G2509A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	3,3915		0,3,1956	7.0	10.0	9.0		2497,2467,2314,1969,2509	2.9	1.0	1		9	26,8118		0,26,4046	yes	missense,missense,missense,missense,missense	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	58,58,58,58,58	0,29,6002	AA,AG,GG		0.3193,0.0766,0.2404	benign,benign,benign,benign,benign	833/1067,823/1057,772/1006,657/754,837/1071	1564064	29,12033	1959	4072	6031	SO:0001583	missense	142678	exon16			GATGGGGCCGGGG	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	30577	protein-coding gene	gene with protein product		611141	"""zinc finger, ZZ type with ankyrin repeat domain 1"", ""mindbomb homolog 2 (Drosophila)"""	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.2338G>A	1.37:g.1564064G>A	ENSP00000349741:p.Ala780Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_080875	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.810|8.810	0.934982|0.934982	0.18206|0.18206	7.66E-4|7.66E-4	0.003193|0.003193	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599;ENST00000378708|ENST00000514234	T;T;T;T;T;T;T;T;T;T|T	0.66995|0.35421	1.26;1.28;1.27;1.28;1.27;1.27;1.26;-0.24;1.28;1.3|1.31	3.83|3.83	2.91|2.91	0.33838|0.33838	Ankyrin repeat-containing domain (1);|.	0.626746|.	0.15520|.	N|.	0.258115|.	T|T	0.32645|0.32645	0.0836|0.0836	L|L	0.36672|0.36672	1.1|1.1	0.26411|0.26411	N|N	0.976259|0.976259	B;B;B;B;P;P;B|.	0.37122|.	0.433;0.011;0.126;0.011;0.583;0.575;0.015|.	B;B;B;B;B;B;B|.	0.36845|.	0.234;0.013;0.05;0.021;0.08;0.108;0.014|.	T|T	0.21895|0.21895	-1.0232|-1.0232	10|7	0.29301|0.56958	T|D	0.29|0.05	-2.4025|-2.4025	7.3783|7.3783	0.26841|0.26841	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	.|.	745;686;657;772;833;766;780|.	Q96AX9-5;F2Z2L2;B3KXY1;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9|.	.;.;.;.;.;.;MIB2_HUMAN|.	T|D	833;780;745;744;823;772;837;657;736;686|595	ENSP00000428660:A833T;ENSP00000349741:A780T;ENSP00000353713:A745T;ENSP00000367982:A744T;ENSP00000348081:A823T;ENSP00000428264:A772T;ENSP00000426103:A837T;ENSP00000367984:A657T;ENSP00000426128:A736T;ENSP00000367980:A686T|ENSP00000427680:G595D	ENSP00000348081:A823T|ENSP00000427680:G595D	A|G	+|+	1|2	0|0	MIB2|MIB2	1553927|1553927	0.894000|0.894000	0.30519|0.30519	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	0.434000|0.434000	0.21494|0.21494	0.817000|0.817000	0.34445|0.34445	0.491000|0.491000	0.48974|0.48974	GCC|GGC	.	.	weak		0.716	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	
FNDC7	163479	hgsc.bcm.edu	37	1	109268441	109268441	+	Missense_Mutation	SNP	G	G	A	rs11582005	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:109268441G>A	ENST00000370017.3	+	6	1203	c.926G>A	c.(925-927)aGt>aAt	p.S309N	FNDC7_ENST00000271311.2_Missense_Mutation_p.S310N	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	309	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> N (in dbSNP:rs11582005).			extracellular region (GO:0005576)		p.S76N(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GCTTGGTCCAGTGTAGATCTG	0.468													g|||	849	0.169529	0.3215	0.0865	5008	,	,		13449	0.0992		0.1412	False		,,,				2504	0.1247				p.S309N		Atlas-SNP	.											FNDC7,NS,carcinoma,0,1	FNDC7	113	1	1	Substitution - Missense(1)	stomach(1)	c.G926A						PASS	.	A	ASN/SER	1308,3098	442.5+/-346.7	205,898,1100	153.0	134.0	140.0		926	-8.0	0.0	1	dbSNP_120	140	1301,7299	258.3+/-282.0	100,1101,3099	yes	missense	FNDC7	NM_001144937.1	46	305,1999,4199	AA,AG,GG		15.1279,29.6868,20.06	benign	309/734	109268441	2609,10397	2203	4300	6503	SO:0001583	missense	163479	exon6			GGTCCAGTGTAGA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.926G>A	1.37:g.109268441G>A	ENSP00000359034:p.Ser309Asn	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	365	0.1671245421245421	162	0.32926829268292684	32	0.08839779005524862	60	0.1048951048951049	111	0.14643799472295516	g	1.406	-0.576763	0.03854	0.296868	0.151279	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.23147	1.92;1.92	5.9	-8.02	0.01118	Fibronectin, type III (3);	0.712224	0.14967	N	0.288052	T	0.04452	0.0122	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.22765	-1.0207	9	0.28530	T	0.3	-2.9951	14.2542	0.66040	0.3755:0.0844:0.5401:0.0	rs11582005;rs52796157;rs59157354;rs11582005	310;309	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	N	309;310	ENSP00000359034:S309N;ENSP00000271311:S310N	ENSP00000271311:S310N	S	+	2	0	FNDC7	109069964	0.000000	0.05858	0.001000	0.08648	0.816000	0.46133	-1.892000	0.01610	-2.225000	0.00724	-2.021000	0.00431	AGT	G|0.816;A|0.184	0.184	strong		0.468	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
LRRCC1	85444	hgsc.bcm.edu	37	8	86057707	86057707	+	Silent	SNP	A	A	G	rs62525428	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:86057707A>G	ENST00000360375.3	+	19	3209	c.3060A>G	c.(3058-3060)caA>caG	p.Q1020Q	LRRCC1_ENST00000414626.2_Silent_p.Q1000Q	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1020					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AAATTAAGCAACTTGCTTTTG	0.299													A|||	286	0.0571086	0.0083	0.0389	5008	,	,		12994	0.0159		0.0905	False		,,,				2504	0.1442				p.Q1020Q		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A3060G						PASS	.	A		71,3547		0,71,1738	55.0	52.0	53.0		3060	4.0	1.0	8	dbSNP_129	53	898,7228		42,814,3207	no	coding-synonymous	LRRCC1	NM_033402.4		42,885,4945	GG,GA,AA		11.0509,1.9624,8.251		1020/1033	86057707	969,10775	1809	4063	5872	SO:0001819	synonymous_variant	85444	exon19			TAAGCAACTTGCT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3060A>G	8.37:g.86057707A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	216	97	0.449074	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Silent	SNP	ENST00000360375.3	37	CCDS43750.1																																																																																			A|0.926;G|0.074	0.074	strong		0.299	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
C12orf71	728858	hgsc.bcm.edu	37	12	27234914	27234914	+	Missense_Mutation	SNP	G	G	A	rs61741737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:27234914G>A	ENST00000429849.2	-	1	533	c.503C>T	c.(502-504)cCg>cTg	p.P168L		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	168										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						AACCATTTCCGGAGGGGAGCC	0.443													G|||	885	0.176717	0.2852	0.1225	5008	,	,		22242	0.1042		0.1491	False		,,,				2504	0.1718				p.P168L		Atlas-SNP	.											.	C12orf71	20	.	0			c.C503T						PASS	.	G	LEU/PRO	965,2745		127,711,1017	29.0	28.0	28.0		503	1.0	0.0	12	dbSNP_129	28	996,7240		64,868,3186	yes	missense	C12orf71	NM_001080406.1	98	191,1579,4203	AA,AG,GG		12.0932,26.0108,16.4155	possibly-damaging	168/270	27234914	1961,9985	1855	4118	5973	SO:0001583	missense	728858	exon1			ATTTCCGGAGGGG		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.503C>T	12.37:g.27234914G>A	ENSP00000413728:p.Pro168Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_001080406		Missense_Mutation	SNP	ENST00000429849.2	37	CCDS44851.1	359	0.16437728937728938	137	0.2784552845528455	43	0.11878453038674033	63	0.11013986013986014	116	0.15303430079155672	G	12.50	1.956711	0.34565	0.260108	0.120932	ENSG00000214700	ENST00000398815;ENST00000429849	T	0.48201	0.82	2.96	0.984	0.19773	.	0.608457	0.12468	U	0.466274	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.49862	0.929	B	0.40506	0.331	T	0.22941	-1.0202	9	0.87932	D	0	-6.8683	2.9651	0.05905	0.155:0.0:0.5722:0.2728	rs61741737	168	A8MTZ7	CL071_HUMAN	L	168	ENSP00000413728:P168L	ENSP00000381796:P168L	P	-	2	0	C12orf71	27126181	0.292000	0.24362	0.018000	0.16275	0.077000	0.17291	0.286000	0.18902	0.539000	0.28788	0.205000	0.17691	CCG	G|0.847;A|0.153	0.153	strong		0.443	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
PCDH12	51294	hgsc.bcm.edu	37	5	141335241	141335241	+	Silent	SNP	A	A	G	rs164073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141335241A>G	ENST00000231484.3	-	1	3386	c.2176T>C	c.(2176-2178)Ttg>Ctg	p.L726L	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	726					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGATGCCCAACAGTACAGCC	0.572													G|||	3907	0.780152	0.941	0.719	5008	,	,		19313	0.8581		0.5765	False		,,,				2504	0.7352				p.L726L		Atlas-SNP	.											.	PCDH12	133	.	0			c.T2176C						PASS	.	G		3824,582	254.9+/-260.3	1670,484,49	66.0	55.0	59.0		2176	2.4	0.9	5	dbSNP_79	59	4808,3792	536.3+/-383.0	1360,2088,852	no	coding-synonymous	PCDH12	NM_016580.2		3030,2572,901	GG,GA,AA		44.093,13.2093,33.6306		726/1185	141335241	8632,4374	2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			TGCCCAACAGTAC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2176T>C	5.37:g.141335241A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																			A|0.299;G|0.701	0.701	strong		0.572	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
C2orf54	79919	hgsc.bcm.edu	37	2	241831005	241831005	+	Silent	SNP	C	C	T	rs10195453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241831005C>T	ENST00000388934.4	-	2	848	c.690G>A	c.(688-690)agG>agA	p.R230R	C2orf54_ENST00000402775.2_Silent_p.R62R|C2orf54_ENST00000307486.8_Silent_p.R81R	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	66	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	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	
TMEM155	132332	hgsc.bcm.edu	37	4	122682720	122682720	+	Missense_Mutation	SNP	C	C	T	rs138330999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:122682720C>T	ENST00000337677.5	-	5	743	c.185G>A	c.(184-186)cGc>cAc	p.R62H	TMEM155_ENST00000394396.1_Missense_Mutation_p.R62H|TMEM155_ENST00000394394.1_Missense_Mutation_p.R62H	NM_152399.2	NP_689612.2	Q4W5P6	TM155_HUMAN	transmembrane protein 155	62						extracellular region (GO:0005576)				breast(1)|lung(5)	6						CCCCTGCAAGCGAACCAAAAA	0.378													C|||	18	0.00359425	0.0008	0.0072	5008	,	,		18627	0.0		0.0109	False		,,,				2504	0.001				p.R62H		Atlas-SNP	.											TMEM155,NS,carcinoma,0,1	TMEM155	17	1	0			c.G185A						scavenged	.	C	HIS/ARG	9,4397	15.5+/-35.6	0,9,2194	61.0	63.0	62.0		185	-1.0	1.0	4	dbSNP_134	62	90,8510	49.8+/-109.6	2,86,4212	yes	missense	TMEM155	NM_152399.2	29	2,95,6406	TT,TC,CC		1.0465,0.2043,0.7612	possibly-damaging	62/131	122682720	99,12907	2203	4300	6503	SO:0001583	missense	132332	exon5			TGCAAGCGAACCA	AK055396	CCDS3721.1	4q27	2008-02-05			ENSG00000164112	ENSG00000164112			26418	protein-coding gene	gene with protein product							Standard	NM_152399		Approved	FLJ30834	uc003idx.1	Q4W5P6	OTTHUMG00000133035	ENST00000337677.5:c.185G>A	4.37:g.122682720C>T	ENSP00000336987:p.Arg62His	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_152399	D3DNW9|Q96NI2	Missense_Mutation	SNP	ENST00000337677.5	37	CCDS3721.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	11.78	1.741976	0.30865	0.002043	0.010465	ENSG00000164112	ENST00000394396;ENST00000337677;ENST00000394394;ENST00000514885	T;T;T;T	0.58797	0.46;0.46;0.46;0.31	5.23	-0.983	0.10263	.	0.327069	0.22175	N	0.063597	T	0.21427	0.0516	N	0.04508	-0.205	0.24235	N	0.995385	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	10	0.87932	D	0	-2.2114	6.5437	0.22394	0.0:0.0903:0.4863:0.4235	.	62	Q4W5P6	TM155_HUMAN	H	62	ENSP00000377919:R62H;ENSP00000336987:R62H;ENSP00000377917:R62H;ENSP00000422869:R62H	ENSP00000336987:R62H	R	-	2	0	TMEM155	122902170	0.974000	0.33945	0.992000	0.48379	0.996000	0.88848	0.148000	0.16224	0.114000	0.18032	-0.290000	0.09829	CGC	C|0.995;T|0.005	0.005	strong		0.378	TMEM155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256637.2	NM_152399	
LZTR1	8216	hgsc.bcm.edu	37	22	21337325	21337325	+	Silent	SNP	G	G	A	rs13054014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	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	
MICAL1	64780	hgsc.bcm.edu	37	6	109768295	109768295	+	Silent	SNP	G	G	A	rs910730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	63	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	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	
CD6	923	hgsc.bcm.edu	37	11	60785352	60785352	+	Silent	SNP	A	A	G	rs1050922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60785352A>G	ENST00000313421.7	+	11	1890	c.1704A>G	c.(1702-1704)tcA>tcG	p.S568S	CD6_ENST00000344028.5_Silent_p.S536S|CD6_ENST00000352009.5_Silent_p.S536S|CD6_ENST00000346437.4_Silent_p.S495S|CD6_ENST00000452451.2_Silent_p.S527S	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	568					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GCACCTCTTCAGGGGAGGATT	0.567													G|||	2338	0.466853	0.6407	0.4236	5008	,	,		18405	0.1736		0.6849	False		,,,				2504	0.3405				p.S568S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,bladder,carcinoma,+1,2	CD6	122	2	0			c.A1704G						scavenged	.	G		2860,1546	486.9+/-360.8	930,1000,273	78.0	79.0	78.0		1704	-10.6	0.0	11	dbSNP_86	78	5745,2853	449.2+/-362.0	1924,1897,478	no	coding-synonymous	CD6	NM_006725.3		2854,2897,751	GG,GA,AA		33.1821,35.0885,33.8281		568/669	60785352	8605,4399	2203	4299	6502	SO:0001819	synonymous_variant	923	exon11			CTCTTCAGGGGAG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1704A>G	11.37:g.60785352A>G		Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1																																																																																			A|0.418;G|0.582	0.582	strong		0.567	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
OBSCN	84033	hgsc.bcm.edu	37	1	228495867	228495867	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228495867G>A	ENST00000422127.1	+	47	12566	c.12522G>A	c.(12520-12522)gaG>gaA	p.E4174E	OBSCN_ENST00000570156.2_Silent_p.E5131E|OBSCN_ENST00000284548.11_Silent_p.E4174E|OBSCN_ENST00000366707.4_Silent_p.E1808E|OBSCN_ENST00000366709.4_Silent_p.E1293E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4174	Ig-like 43.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGGCCGATGAGGATGTTGAGT	0.597																																					p.E5131E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G15393A						PASS	.						92.0	104.0	100.0					1																	228495867		2171	4258	6429	SO:0001819	synonymous_variant	84033	exon58			CGATGAGGATGTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12522G>A	1.37:g.228495867G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
C2orf83	56918	hgsc.bcm.edu	37	2	228476140	228476140	+	Nonsense_Mutation	SNP	C	C	T	rs2176186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:228476140C>T	ENST00000264387.4	-	3	509	c.423G>A	c.(421-423)tgG>tgA	p.W141*	C2orf83_ENST00000409066.1_3'UTR	NM_020161.3	NP_064546.3	Q53S99	CB083_HUMAN	chromosome 2 open reading frame 83	141					transport (GO:0006810)	membrane (GO:0016020)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(2)	11						TAGAATGGCTCCAGAGCACCG	0.473													T|||	1572	0.313898	0.2254	0.3401	5008	,	,		18581	0.4058		0.2753	False		,,,				2504	0.3599				p.W141X		Atlas-SNP	.											.	C2orf83	15	.	0			c.G423A						PASS	.	T	,stop/TRP	1024,3382	727.6+/-409.9	113,798,1292	159.0	154.0	156.0		,423	-1.8	0.0	2	dbSNP_96	156	2628,5972	687.1+/-404.2	382,1864,2054	yes	utr-3,stop-gained	C2orf83	NM_001162483.1,NM_020161.3	,	495,2662,3346	TT,TC,CC		30.5581,23.241,28.0793	,	,141/151	228476140	3652,9354	2203	4300	6503	SO:0001587	stop_gained	56918	exon3			ATGGCTCCAGAGC		CCDS33388.1, CCDS54434.1	2q36.3	2008-09-16			ENSG00000042304	ENSG00000042304			25344	protein-coding gene	gene with protein product							Standard	NM_020161		Approved	DKFZp547H025	uc002vph.3	Q53S99	OTTHUMG00000153550	ENST00000264387.4:c.423G>A	2.37:g.228476140C>T	ENSP00000264387:p.Trp141*	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	232	232	1	NM_020161	A2RRG6|B8ZZI8|Q9NPW4	Nonsense_Mutation	SNP	ENST00000264387.4	37	CCDS33388.1	671	0.30723443223443225	112	0.22764227642276422	117	0.32320441988950277	241	0.42132867132867136	201	0.26517150395778366	T	9.224	1.034135	0.19590	0.23241	0.305581	ENSG00000042304	ENST00000264387	.	.	.	2.28	-1.83	0.07833	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0887	0.09960	0.0:0.4167:0.2121:0.3712	rs2176186;rs3762469;rs60183513;rs2176186	.	.	.	X	141	.	ENSP00000264387:W141X	W	-	3	0	C2orf83	228184384	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.799000	0.27028	-0.890000	0.03945	-1.480000	0.00990	TGG	C|0.703;T|0.297	0.297	strong		0.473	C2orf83-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331607.1	NM_020161	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726774	32726774	+	Missense_Mutation	SNP	C	C	T	rs200716952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32726774C>T	ENST00000437316.2	-	3	562	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.A167T|HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.A167T			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	171	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|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)|toxic substance binding (GO:0015643)	p.A167T(1)		endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACAACACCGGCTGTCTCCTCC	0.542																																					p.A167T		Atlas-SNP	.											HLA-DQB2,NS,carcinoma,0,4	HLA-DQB2	22	4	1	Substitution - Missense(1)	kidney(1)	c.G499A						scavenged	.																																			SO:0001583	missense	3120	exon3			CACCGGCTGTCTC	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.499G>A	6.37:g.32726774C>T	ENSP00000396330:p.Ala167Thr	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	128	23	0.179688	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	C	10.03	1.238159	0.22711	.	.	ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527	T;T;T	0.02812	4.15;4.15;4.15	3.43	2.56	0.30785	.	0.330401	0.23935	U	0.043113	T	0.00967	0.0032	L	0.33189	0.99	0.23425	N	0.997708	B;B	0.19073	0.001;0.033	B;B	0.26310	0.014;0.068	T	0.47394	-0.9121	10	0.33940	T	0.23	.	8.9215	0.35615	0.0:0.8839:0.0:0.1161	.	167;167	A2ADX3;Q5SR06	.;.	T	167	ENSP00000396330:A167T;ENSP00000410512:A167T;ENSP00000390431:A167T	ENSP00000390431:A167T	A	-	1	0	HLA-DQB2	32834752	0.000000	0.05858	0.869000	0.34112	0.359000	0.29487	0.045000	0.14013	0.784000	0.33661	-0.333000	0.08304	GCC	C|0.997;T|0.003	0.003	weak		0.542	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
NACAD	23148	hgsc.bcm.edu	37	7	45123977	45123977	+	Missense_Mutation	SNP	G	G	A	rs61740884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45123977G>A	ENST00000490531.2	-	2	1821	c.1802C>T	c.(1801-1803)gCt>gTt	p.A601V		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	601					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CGGTGTCATAGCGGAGTCCTG	0.607													g|||	79	0.0157748	0.0008	0.0274	5008	,	,		22313	0.0		0.0517	False		,,,				2504	0.0072				p.A601V		Atlas-SNP	.											NACAD,NS,carcinoma,-1,1	NACAD	44	1	0			c.C1802T						PASS	.	G	VAL/ALA	18,1366		0,18,674	42.0	39.0	40.0		1802	1.1	0.0	7	dbSNP_129	40	168,3014		3,162,1426	yes	missense	NACAD	NM_001146334.1	64	3,180,2100	AA,AG,GG		5.2797,1.3006,4.0736	benign	601/1563	45123977	186,4380	692	1591	2283	SO:0001583	missense	23148	exon2			GTCATAGCGGAGT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1802C>T	7.37:g.45123977G>A	ENSP00000420477:p.Ala601Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	106	69	0.650943	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	57	0.0260989010989011	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	42	0.055408970976253295	g	2.276	-0.365964	0.05069	0.013006	0.052797	ENSG00000136274	ENST00000490531	T	0.12255	2.7	2.09	1.13	0.20643	.	.	.	.	.	T	0.00754	0.0025	N	0.24115	0.695	0.09310	N	1	B	0.18310	0.027	B	0.06405	0.002	T	0.39057	-0.9632	9	0.29301	T	0.29	.	4.132	0.10154	0.4124:0.0:0.5876:0.0	.	601	O15069	NACAD_HUMAN	V	601	ENSP00000420477:A601V	ENSP00000420477:A601V	A	-	2	0	NACAD	45090502	0.006000	0.16342	0.001000	0.08648	0.139000	0.21198	0.904000	0.28491	0.178000	0.19917	0.306000	0.20318	GCT	G|0.968;A|0.032	0.032	strong		0.607	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
MICALL2	79778	hgsc.bcm.edu	37	7	1478495	1478495	+	Silent	SNP	A	A	G	rs4492283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1478495A>G	ENST00000297508.7	-	10	2278	c.2103T>C	c.(2101-2103)ccT>ccC	p.P701P	MICALL2_ENST00000405088.4_Silent_p.P489P|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	701	Forms an intramolecular interaction with the N-terminal CH and LIM zinc-binding domains-containing region keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CCTGAAGGTGAGGTTTCTTCT	0.627													G|||	1268	0.253195	0.5605	0.3098	5008	,	,		16920	0.0288		0.1362	False		,,,				2504	0.1493				p.P701P		Atlas-SNP	.											.	MICALL2	63	.	0			c.T2103C						PASS	.			2164,2242	590.0+/-387.3	512,1140,551	82.0	80.0	81.0		2103	-4.1	0.0	7	dbSNP_111	81	1443,7157	749.2+/-407.4	119,1205,2976	no	coding-synonymous	MICALL2	NM_182924.3		631,2345,3527	GG,GA,AA		16.7791,49.1148,27.7334		701/905	1478495	3607,9399	2203	4300	6503	SO:0001819	synonymous_variant	79778	exon10			AAGGTGAGGTTTC	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2103T>C	7.37:g.1478495A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			A|0.738;G|0.262	0.262	strong		0.627	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
OR2A5	393046	hgsc.bcm.edu	37	7	143747870	143747870	+	Missense_Mutation	SNP	A	A	G	rs2961144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143747870A>G	ENST00000408906.2	+	1	410	c.376A>G	c.(376-378)Atc>Gtc	p.I126V		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	126			I -> V (in dbSNP:rs2961144).			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)					GTACATGGCTATCTGCCACCC	0.498													A|||	1481	0.295727	0.5318	0.2695	5008	,	,		22246	0.0079		0.2903	False		,,,				2504	0.2975				p.I126V		Atlas-SNP	.											.	OR2A5	78	.	0			c.A376G						PASS	.	A	VAL/ILE	1970,2278		480,1010,634	181.0	185.0	183.0		376	5.2	1.0	7	dbSNP_101	183	2685,5801		428,1829,1986	yes	missense	OR2A5	NM_012365.1	29	908,2839,2620	GG,GA,AA		31.6403,46.3748,36.5557	possibly-damaging	126/312	143747870	4655,8079	2124	4243	6367	SO:0001583	missense	393046	exon1			ATGGCTATCTGCC	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.376A>G	7.37:g.143747870A>G	ENSP00000386208:p.Ile126Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	538	0.24633699633699635	232	0.4715447154471545	101	0.27900552486187846	0	0.0	205	0.2704485488126649	A	13.91	2.378807	0.42207	0.463748	0.316403	ENSG00000221836	ENST00000408906	T	0.50813	0.73	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32563	U	0.005924	T	0.00012	0.0000	M	0.71296	2.17	0.27740	P	0.9445097	D	0.54207	0.965	P	0.51385	0.668	T	0.50980	-0.8763	9	0.15499	T	0.54	.	13.1424	0.59442	1.0:0.0:0.0:0.0	rs2961144;rs52833438;rs60301672;rs2961144	126	Q96R48	OR2A5_HUMAN	V	126	ENSP00000386208:I126V	ENSP00000386208:I126V	I	+	1	0	OR2A5	143378803	1.000000	0.71417	0.998000	0.56505	0.404000	0.30871	5.947000	0.70242	2.202000	0.70862	0.455000	0.32223	ATC	A|0.713;G|0.287	0.287	strong		0.498	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458893	39458893	+	Missense_Mutation	SNP	G	G	A	rs758741	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39458893G>A	ENST00000391353.1	-	1	210	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	71	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GCTGGAAGGCGGGTAGGTTGA	0.547													A|||	1164	0.232428	0.2859	0.1484	5008	,	,		23883	0.3204		0.1879	False		,,,				2504	0.1748				p.R71C		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.C211T						PASS	.																																			SO:0001583	missense	100533177	exon1			GAAGGCGGGTAGG		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.211C>T	17.37:g.39458893G>A	ENSP00000375148:p.Arg71Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		498	0.22802197802197802	124	0.25203252032520324	58	0.16022099447513813	175	0.30594405594405594	141	0.18601583113456466	A	0.003	-2.566138	0.00134	.	.	ENSG00000212658	ENST00000391353	.	.	.	5.49	4.41	0.53225	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.38628	-0.9652	4	0.02654	T	1	.	3.9785	0.09484	0.6829:0.0:0.1639:0.1532	rs758741;rs61634168;rs758741	.	.	.	C	71	.	ENSP00000375148:R71C	R	-	1	0	KRTAP29-1	36712419	0.968000	0.33430	0.085000	0.20634	0.004000	0.04260	0.877000	0.28106	0.370000	0.24538	-1.815000	0.00603	CGC	G|0.768;A|0.232	0.232	strong		0.547	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
GAK	2580	hgsc.bcm.edu	37	4	843695	843695	+	Silent	SNP	A	A	G	rs76111882|rs8093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:843695A>G	ENST00000314167.4	-	27	3929	c.3819T>C	c.(3817-3819)gcT>gcC	p.A1273A	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.A1194A	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1273	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		CGGGGTGCACAGCCAGCACCG	0.726													a|||	4010	0.800719	0.8918	0.6369	5008	,	,		11851	0.877		0.671	False		,,,				2504	0.8487				p.A1273A		Atlas-SNP	.											.	GAK	104	.	0			c.T3819C						PASS	.	G		3856,542		1696,464,39	17.0	18.0	18.0		3819	-9.1	0.1	4	dbSNP_52	18	5883,2711		2028,1827,442	no	coding-synonymous	GAK	NM_005255.2		3724,2291,481	GG,GA,AA		31.5453,12.3238,25.0385		1273/1312	843695	9739,3253	2199	4297	6496	SO:0001819	synonymous_variant	2580	exon27			GTGCACAGCCAGC	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.3819T>C	4.37:g.843695A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	1636	0.7490842490842491	420	0.8536585365853658	226	0.6243093922651933	484	0.8461538461538461	506	0.6675461741424802	a	0.556	-0.847528	0.02651	0.876762	0.684547	ENSG00000178950	ENST00000511980	.	.	.	4.56	-9.13	0.00704	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999880066	.	.	.	.	.	.	T	0.16512	-1.0400	3	.	.	.	-19.8857	2.0039	0.03473	0.429:0.2136:0.2148:0.1425	rs8093;rs1134910;rs3197278;rs3816672;rs17359324;rs60405968;rs8093	.	.	.	P	429	.	.	L	-	2	0	GAK	833695	0.000000	0.05858	0.094000	0.20943	0.014000	0.08584	-4.755000	0.00190	-2.434000	0.00554	-1.578000	0.00866	CTG	A|0.228;G|0.772	0.772	strong		0.726	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470138	24470138	+	Nonsense_Mutation	SNP	C	C	T	rs1811890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24470138C>T	ENST00000335125.6	+	4	601	c.475C>T	c.(475-477)Cga>Tga	p.R159*	DHRS4L2_ENST00000382755.4_Nonsense_Mutation_p.R157*|DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000558753.1_Intron|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Intron|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000534993.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	157						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		AATGGAGAAACGAGGGTACAG	0.547													c|||	645	0.128794	0.0416	0.1138	5008	,	,		21065	0.2232		0.0795	False		,,,				2504	0.2106				p.R159X		Atlas-SNP	.											DHRS4L2,NS,carcinoma,-1,1	DHRS4L2	29	1	0			c.C475T						PASS	.	C	stop/ARG,stop/ARG,,stop/ARG	172,4222		6,160,2031	70.0	76.0	74.0		289,172,,475	2.8	1.0	14	dbSNP_92	74	606,7988		11,584,3702	no	stop-gained,stop-gained,intron,stop-gained	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	17,744,5733	TT,TC,CC		7.0514,3.9144,5.9901	,,,	97/171,58/132,,159/233	24470138	778,12210	2197	4297	6494	SO:0001587	stop_gained	317749	exon4			GAGAAACGAGGGT		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.475C>T	14.37:g.24470138C>T	ENSP00000334801:p.Arg159*	Somatic	378	1	0.0026455		WXS	Illumina HiSeq	Phase_I	512	153	0.298828	NM_198083	Q3YLD4	Nonsense_Mutation	SNP	ENST00000335125.6	37	CCDS9606.2	257	0.11767399267399267	29	0.05894308943089431	40	0.11049723756906077	134	0.23426573426573427	54	0.0712401055408971	-	33	5.247139	0.95305	0.039144	0.070514	ENSG00000187630	ENST00000348916;ENST00000335125;ENST00000382755	.	.	.	3.76	2.84	0.33178	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.09310	P	0.999999999590057	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1511	0.42794	0.2015:0.7985:0.0:0.0	rs1811890;rs58573619;rs1811890	.	.	.	X	97;159;157	.	ENSP00000334801:R159X	R	+	1	2	DHRS4L2	23539978	1.000000	0.71417	0.999000	0.59377	0.668000	0.39293	2.341000	0.43983	0.536000	0.28733	0.194000	0.17425	CGA	.	.	weak		0.547	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
NSUN2	54888	hgsc.bcm.edu	37	5	6604787	6604787	+	Silent	SNP	C	C	T	rs13181449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:6604787C>T	ENST00000264670.6	-	16	2060	c.1749G>A	c.(1747-1749)acG>acA	p.T583T	NSUN2_ENST00000539938.1_Silent_p.T347T|NSUN2_ENST00000506139.1_Silent_p.T548T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	583					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTTTGATCCCCGTGTTAATAA	0.453													C|||	1112	0.222045	0.0371	0.1427	5008	,	,		19971	0.4623		0.1899	False		,,,				2504	0.3139				p.T583T		Atlas-SNP	.											.	NSUN2	82	.	0			c.G1749A						PASS	.	C	,	255,4151	145.0+/-179.8	8,239,1956	81.0	83.0	83.0		1644,1749	-10.7	0.0	5	dbSNP_121	83	1753,6847	316.6+/-312.8	186,1381,2733	yes	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	194,1620,4689	TT,TC,CC		20.3837,5.7876,15.439	,	548/733,583/768	6604787	2008,10998	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon16			GATCCCCGTGTTA	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1749G>A	5.37:g.6604787C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			C|0.819;T|0.181	0.181	strong		0.453	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566903	206566903	+	Splice_Site	SNP	G	G	A	rs2987927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:206566903G>A	ENST00000414007.1	+	3	284	c.284G>A	c.(283-285)cGt>cAt	p.R95H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	235	F-BAR domain.				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)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CCTTTTCAGCGTCAAGCCAAG	0.408													g|||	3	0.000599042	0.0	0.0014	5008	,	,		35930	0.0		0.002	False		,,,				2504	0.0				p.H82H		Atlas-SNP	.											.	.	.	.	0			c.A245A						PASS	.						78.0	67.0	70.0					1																	206566903		1899	4122	6021	SO:0001630	splice_region_variant	100996712	exon3			TTCAGCGTCAAGC	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.283-1G>A	1.37:g.206566903G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	213	38	0.178404	NM_001271887		Silent	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	g	32	5.192443	0.94960	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.55930	0.49	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.75925	0.3916	.	.	.	0.80722	D	1.000000	D;D;D	0.89917	1.0;0.996;0.958	D;P;B	0.83275	0.996;0.728;0.425	T	0.78645	-0.2123	8	0.87932	D	0	.	19.5856	0.95488	0.0:0.0:1.0:0.0	rs2987927;rs4844666	82;235;235	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	149;95	ENSP00000390898:R95H	ENSP00000390898:R95H	R	+	2	0	SRGAP2	204633526	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.864000	0.99589	2.625000	0.88918	0.555000	0.69702	CGT	G|0.500;A|0.500	0.500	weak		0.408	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	Missense_Mutation
CCDC109B	55013	hgsc.bcm.edu	37	4	110603784	110603784	+	Silent	SNP	T	T	C	rs3733611	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:110603784T>C	ENST00000394650.4	+	5	631	c.498T>C	c.(496-498)tcT>tcC	p.S166S		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	166					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		ACATGAAATCTTTGGTTCACA	0.428													C|||	3477	0.694289	0.8585	0.6153	5008	,	,		18835	0.5179		0.6551	False		,,,				2504	0.7505				p.S166S		Atlas-SNP	.											.	CCDC109B	47	.	0			c.T498C						PASS	.	C		3602,804	320.4+/-296.6	1474,654,75	126.0	124.0	125.0		498	1.2	0.0	4	dbSNP_107	125	5710,2890	453.4+/-363.2	1898,1914,488	no	coding-synonymous	CCDC109B	NM_017918.4		3372,2568,563	CC,CT,TT		33.6047,18.2478,28.4023		166/337	110603784	9312,3694	2203	4300	6503	SO:0001819	synonymous_variant	55013	exon5			GAAATCTTTGGTT	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.498T>C	4.37:g.110603784T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_017918	A8K4Y3|Q6IAC1	Silent	SNP	ENST00000394650.4	37	CCDS3683.2																																																																																			C|0.694;N|0.000	0.694	strong		0.428	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
GSDMB	55876	hgsc.bcm.edu	37	17	38064469	38064469	+	Silent	SNP	T	T	C	rs11078928	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38064469T>C	ENST00000394179.1	-	6	802	c.672A>G	c.(670-672)ttA>ttG	p.L224L	GSDMB_ENST00000394175.2_Intron|GSDMB_ENST00000520542.1_Splice_Site|GSDMB_ENST00000360317.3_Splice_Site|GSDMB_ENST00000309481.7_Intron|GSDMB_ENST00000418519.1_Splice_Site			Q8TAX9	GSDMB_HUMAN	gasdermin B	224						cytoplasm (GO:0005737)		p.?(1)		breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						AATGAATATCTAAACCAGCAC	0.433													T|||	1430	0.285543	0.1036	0.3357	5008	,	,		15743	0.2817		0.4652	False		,,,				2504	0.3149				.		Atlas-SNP	.											GSDMB_ENST00000418519,NS,carcinoma,0,1	GSDMB	87	1	1	Unknown(1)	stomach(1)	c.662-2A>G						PASS	.	T	,,,	186,1198		10,166,516	78.0	64.0	68.0		,,,	2.1	0.0	17	dbSNP_120	68	1391,1791		295,801,495	yes	intron,splice-3,splice-3,intron	GSDMB	NM_001042471.1,NM_001165958.1,NM_001165959.1,NM_018530.2	,,,	305,967,1011	CC,CT,TT		43.7146,13.4393,34.5379	,,,	,,,	38064469	1577,2989	692	1591	2283	SO:0001819	synonymous_variant	55876	exon7			AATATCTAAACCA	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.672A>G	17.37:g.38064469T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_001165958	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Splice_Site	SNP	ENST00000394179.1	37		713	0.32646520146520147	51	0.10365853658536585	124	0.3425414364640884	180	0.3146853146853147	358	0.47229551451187335	T	2.921	-0.223260	0.06061	0.134393	0.437146	ENSG00000073605	ENST00000420491;ENST00000520542;ENST00000418519	.	.	.	3.19	2.11	0.27256	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3471	0.32279	0.0:0.0:0.1986:0.8014	rs11078928;rs17852277	.	.	.	.	-1	.	.	.	-	.	.	GSDMB	35317995	0.022000	0.18835	0.001000	0.08648	0.003000	0.03518	0.732000	0.26072	0.144000	0.18951	-1.524000	0.00929	.	T|0.651;C|0.349	0.349	strong		0.433	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
SCAF8	22828	hgsc.bcm.edu	37	6	155123273	155123273	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:155123273T>C	ENST00000367178.3	+	7	1351	c.775T>C	c.(775-777)Ttt>Ctt	p.F259L	SCAF8_ENST00000417268.1_Missense_Mutation_p.F259L|SCAF8_ENST00000367186.4_Missense_Mutation_p.F325L	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	259	Gln-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						GGGAGTCTCCTTTAACAAGGT	0.343																																					p.F259L		Atlas-SNP	.											.	SCAF8	122	.	0			c.T775C						PASS	.						48.0	45.0	46.0					6																	155123273		2203	4300	6503	SO:0001583	missense	22828	exon7			GTCTCCTTTAACA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.775T>C	6.37:g.155123273T>C	ENSP00000356146:p.Phe259Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	4	0.0470588	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430469	0.62844	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.54675	0.6;0.6;0.56	5.75	5.75	0.90469	.	0.205984	0.41938	U	0.000799	T	0.23289	0.0563	L	0.27053	0.805	0.52501	D	0.999959	B;B;B;B	0.18610	0.029;0.029;0.006;0.015	B;B;B;B	0.17433	0.018;0.018;0.007;0.01	T	0.11131	-1.0600	10	0.35671	T	0.21	.	10.3929	0.44184	0.0:0.073:0.0:0.927	.	304;325;337;259	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	L	259;259;325	ENSP00000356146:F259L;ENSP00000413098:F259L;ENSP00000356154:F325L	ENSP00000356146:F259L	F	+	1	0	SCAF8	155164965	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	5.971000	0.70440	2.188000	0.69820	0.528000	0.53228	TTT	.	.	none		0.343	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	
RLN3	117579	hgsc.bcm.edu	37	19	14141666	14141666	+	Missense_Mutation	SNP	G	G	T	rs78161395	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	102	0	0		WXS	Illumina HiSeq	Phase_I	99	94	0.949495	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		
ANP32E	81611	hgsc.bcm.edu	37	1	150199123	150199123	+	Silent	SNP	G	G	T	rs7522034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150199123G>T	ENST00000314136.8	-	5	867	c.498C>A	c.(496-498)ggC>ggA	p.G166G	ANP32E_ENST00000533654.1_Missense_Mutation_p.A111E|ANP32E_ENST00000369114.5_Intron|ANP32E_ENST00000436748.2_Silent_p.G125G|ANP32E_ENST00000369116.4_Silent_p.G34G|ANP32E_ENST00000369115.2_Silent_p.G34G|ANP32E_ENST00000369119.3_Silent_p.G118G	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	166	Asp/Glu-rich (highly acidic).				histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-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)			CATCTTCATCGCCATCTTTAA	0.418													T|||	3015	0.602037	0.9228	0.4683	5008	,	,		19153	0.5456		0.4304	False		,,,				2504	0.498				p.G166G		Atlas-SNP	.											ANP32E,NS,adenoma,0,1	ANP32E	28	1	0			c.C498A						scavenged	.	T	,,	3621,785	315.8+/-294.3	1488,645,70	109.0	98.0	102.0		375,354,498	-3.2	1.0	1	dbSNP_116	102	3578,5022	627.1+/-397.9	744,2090,1466	no	coding-synonymous,coding-synonymous,coding-synonymous	ANP32E	NM_001136478.2,NM_001136479.1,NM_030920.3	,,	2232,2735,1536	TT,TG,GG		41.6047,17.8166,44.6486	,,	125/228,118/221,166/269	150199123	7199,5807	2203	4300	6503	SO:0001819	synonymous_variant	81611	exon5			TTCATCGCCATCT	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"""ANP32 acidic nuclear phosphoproteins"""	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.498C>A	1.37:g.150199123G>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_030920	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	Silent	SNP	ENST00000314136.8	37	CCDS946.1	1220	0.5586080586080586	445	0.9044715447154471	157	0.43370165745856354	288	0.5034965034965035	330	0.43535620052770446	T	0.022	-1.416738	0.01136	0.821834	0.416047	ENSG00000143401	ENST00000533654	T	0.00333	8.07	4.71	-3.24	0.05094	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999945053	B	0.02656	0.0	B	0.01281	0.0	T	0.06285	-1.0835	7	0.15066	T	0.55	.	1.3997	0.02268	0.3882:0.0817:0.2172:0.3129	rs7522034;rs60000686;rs7522034	111	E9PLC4	.	E	111	ENSP00000435215:A111E	ENSP00000435215:A111E	A	-	2	0	ANP32E	148465747	0.993000	0.37304	0.988000	0.46212	0.046000	0.14306	0.015000	0.13355	-0.475000	0.06852	-0.363000	0.07495	GCG	G|0.433;T|0.567	0.567	strong		0.418	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974415	22974415	+	Silent	SNP	G	G	A	rs11780526	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22974415G>A	ENST00000356864.3	+	5	1183	c.651G>A	c.(649-651)ccG>ccA	p.P217P	TNFRSF10C_ENST00000540813.1_Silent_p.P115P	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	217					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)	p.P217P(2)		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)		CCACCAGCCCGGGGACTCCTG	0.607																																					p.P217P		Atlas-SNP	.											TNFRSF10C,NS,carcinoma,0,1	TNFRSF10C	30	1	2	Substitution - coding silent(2)	prostate(2)	c.G651A						PASS	.						54.0	58.0	57.0					8																	22974415		2203	4296	6499	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.651G>A	8.37:g.22974415G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			G|0.893;A|0.107	0.107	strong		0.607	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
GAB2	9846	hgsc.bcm.edu	37	11	77930447	77930447	+	Silent	SNP	G	G	A	rs61749244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77930447G>A	ENST00000361507.4	-	10	1987	c.1902C>T	c.(1900-1902)tcC>tcT	p.S634S	GAB2_ENST00000340149.2_Silent_p.S596S	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	634					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)	p.S634S(1)	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)			CAGAGGTGACGGATGAAGTAG	0.567													g|||	31	0.0061901	0.0023	0.013	5008	,	,		22020	0.0		0.0149	False		,,,				2504	0.0041				p.S634S		Atlas-SNP	.											GAB2,rectum,carcinoma,-2,4	GAB2	63	4	1	Substitution - coding silent(1)	ovary(1)	c.C1902T						PASS	.	G	,	25,4375	31.7+/-61.6	0,25,2175	121.0	98.0	106.0		1788,1902	-10.7	0.0	11	dbSNP_129	106	236,8348	96.3+/-158.1	3,230,4059	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	3,255,6234	AA,AG,GG		2.7493,0.5682,2.0102	,	596/639,634/677	77930447	261,12723	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon10			GGTGACGGATGAA	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.1902C>T	11.37:g.77930447G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
TSTD2	158427	hgsc.bcm.edu	37	9	100388119	100388119	+	Missense_Mutation	SNP	G	G	T	rs10817858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100388119G>T	ENST00000341170.4	-	3	708	c.326C>A	c.(325-327)gCt>gAt	p.A109D	TSTD2_ENST00000354801.2_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	109			A -> D (in dbSNP:rs10817858).					p.A109D(1)		large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						TAAAATAGAAGCTGTCTGGTG	0.423													G|||	1089	0.217452	0.0991	0.1167	5008	,	,		19402	0.253		0.2177	False		,,,				2504	0.4121				p.A109D		Atlas-SNP	.											TSTD2,NS,carcinoma,0,1	TSTD2	42	1	1	Substitution - Missense(1)	stomach(1)	c.C326A						PASS	.	G	ASP/ALA	496,3910	229.4+/-244.0	22,452,1729	161.0	154.0	156.0		326	1.8	0.1	9	dbSNP_120	156	1640,6960	303.6+/-306.5	150,1340,2810	yes	missense	TSTD2	NM_139246.4	126	172,1792,4539	TT,TG,GG		19.0698,11.2574,16.4232	benign	109/517	100388119	2136,10870	2203	4300	6503	SO:0001583	missense	158427	exon3			ATAGAAGCTGTCT	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.326C>A	9.37:g.100388119G>T	ENSP00000342499:p.Ala109Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	389	0.17811355311355312	53	0.10772357723577236	40	0.11049723756906077	133	0.23251748251748253	163	0.21503957783641162	G	12.26	1.885639	0.33255	0.112574	0.190698	ENSG00000136925	ENST00000341170	T	0.32272	1.46	4.8	1.8	0.24995	.	0.832652	0.11148	N	0.594432	T	0.00012	0.0000	L	0.51422	1.61	0.53688	P	2.599999999997049E-5	B	0.17038	0.02	B	0.14578	0.011	T	0.34900	-0.9810	9	0.12430	T	0.62	-0.337	1.6494	0.02768	0.1632:0.1405:0.4078:0.2885	rs10817858;rs56741257;rs10817858	109	Q5T7W7	TSTD2_HUMAN	D	109	ENSP00000342499:A109D	ENSP00000342499:A109D	A	-	2	0	TSTD2	99427940	0.001000	0.12720	0.087000	0.20705	0.959000	0.62525	0.262000	0.18460	0.258000	0.21686	0.563000	0.77884	GCT	G|0.832;T|0.168	0.168	strong		0.423	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
TNIK	23043	hgsc.bcm.edu	37	3	170928936	170928936	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:170928936T>C	ENST00000436636.2	-	4	619	c.275A>G	c.(274-276)aAg>aGg	p.K92R	TNIK_ENST00000369326.5_Missense_Mutation_p.K92R|TNIK_ENST00000475336.1_Missense_Mutation_p.K92R|TNIK_ENST00000284483.8_Missense_Mutation_p.K92R|TNIK_ENST00000470834.1_Missense_Mutation_p.K92R|TNIK_ENST00000357327.5_Missense_Mutation_p.K92R|TNIK_ENST00000538048.1_Missense_Mutation_p.K92R|TNIK_ENST00000341852.6_Missense_Mutation_p.K92R|TNIK_ENST00000460047.1_Missense_Mutation_p.K92R|TNIK_ENST00000488470.1_Missense_Mutation_p.K92R	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			TGGTGGGTTCTTTTTGATAAA	0.353																																					p.K92R		Atlas-SNP	.											TNIK_ENST00000436636,NS,carcinoma,-1,4	TNIK	313	4	0			c.A275G						scavenged	.						120.0	115.0	116.0					3																	170928936		1830	4093	5923	SO:0001583	missense	23043	exon4			GGGTTCTTTTTGA	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.275A>G	3.37:g.170928936T>C	ENSP00000399511:p.Lys92Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	164	6	0.0365854	NM_001161562	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263209	0.80358	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834;ENST00000468757	T;T;T;T;T;T;T;T;T;T;T	0.76578	1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;1.82;-1.03	6.16	6.16	0.99307	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	0.80363	0.4609	N	0.16903	0.455	0.80722	D	1	B;P;B;B;P;P;B;P	0.46859	0.077;0.86;0.342;0.289;0.86;0.86;0.342;0.885	B;P;B;B;P;P;B;D	0.65140	0.046;0.888;0.385;0.2;0.888;0.888;0.385;0.932	D	0.83367	0.0005	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	92;92;92;92;92;92;92;92	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	R	92;92;92;92;92;92;92;92;92;92;66	ENSP00000399511:K92R;ENSP00000358332:K92R;ENSP00000443278:K92R;ENSP00000345352:K92R;ENSP00000284483:K92R;ENSP00000418156:K92R;ENSP00000349880:K92R;ENSP00000418916:K92R;ENSP00000418378:K92R;ENSP00000419990:K92R;ENSP00000417338:K66R	ENSP00000284483:K92R	K	-	2	0	TNIK	172411630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.243000	0.72384	2.367000	0.80283	0.528000	0.53228	AAG	.	.	none		0.353	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
PIGN	23556	hgsc.bcm.edu	37	18	59814324	59814324	+	Missense_Mutation	SNP	G	G	C	rs9320001	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:59814324G>C	ENST00000357637.5	-	9	1100	c.685C>G	c.(685-687)Cac>Gac	p.H229D	PIGN_ENST00000400334.3_Missense_Mutation_p.H229D	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	229			H -> D (in dbSNP:rs9320001). {ECO:0000269|PubMed:15489334}.		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)				TTAATATTGTGCTTGTAGTCT	0.289													C|||	4243	0.847244	0.885	0.7896	5008	,	,		16424	0.9345		0.7435	False		,,,				2504	0.8538				p.H229D		Atlas-SNP	.											.	PIGN	62	.	0			c.C685G						PASS	.	C	ASP/HIS,ASP/HIS	3151,439		1376,399,20	62.0	56.0	58.0		685,685	3.7	0.9	18	dbSNP_119	58	6121,2011		2320,1481,265	yes	missense,missense	PIGN	NM_012327.5,NM_176787.4	81,81	3696,1880,285	CC,CG,GG		24.7295,12.2284,20.9009	benign,benign	229/932,229/932	59814324	9272,2450	1795	4066	5861	SO:0001583	missense	23556	exon9			TATTGTGCTTGTA	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.685C>G	18.37:g.59814324G>C	ENSP00000350263:p.His229Asp	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	37	CCDS45879.1	1812	0.8296703296703297	433	0.8800813008130082	283	0.7817679558011049	534	0.9335664335664335	562	0.741424802110818	C	0.013	-1.629729	0.00813	0.877716	0.752705	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.68903	-0.36;-0.36	5.5	3.71	0.42584	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.269430	0.42821	N	0.000642	T	0.00012	0.0000	N	0.01140	-0.99	0.49915	P	1.64000000000053E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.35201	-0.9798	8	.	.	.	-1.8571	7.5845	0.27985	0.0:0.6816:0.1197:0.1987	rs9320001;rs17856806;rs52805265;rs9320001	229	O95427	PIGN_HUMAN	D	229	ENSP00000350263:H229D;ENSP00000383188:H229D	.	H	-	1	0	PIGN	57965304	0.997000	0.39634	0.887000	0.34795	0.263000	0.26337	1.765000	0.38481	0.385000	0.24970	-0.187000	0.12897	CAC	G|0.194;C|0.806	0.806	strong		0.289	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257266	114257266	+	Missense_Mutation	SNP	C	C	T	rs142136016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	209	0	0		WXS	Illumina HiSeq	Phase_I	306	59	0.19281	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	
MUC16	94025	hgsc.bcm.edu	37	19	9068530	9068530	+	Missense_Mutation	SNP	C	C	T	rs7250080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9068530C>T	ENST00000397910.4	-	3	19119	c.18916G>A	c.(18916-18918)Gtg>Atg	p.V6306M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6308	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						GTGGTCCCCACATTGGCCACT	0.463													C|||	949	0.189497	0.2458	0.1888	5008	,	,		20887	0.2679		0.0845	False		,,,				2504	0.1411				p.V6306M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G18916A						PASS	.	C	MET/VAL	876,3138		97,682,1228	201.0	190.0	193.0		18916	1.1	0.0	19	dbSNP_116	193	648,7702		26,596,3553	yes	missense	MUC16	NM_024690.2	21	123,1278,4781	TT,TC,CC		7.7605,21.8236,12.3261	probably-damaging	6306/14508	9068530	1524,10840	2007	4175	6182	SO:0001583	missense	94025	exon3			TCCCCACATTGGC	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.18916G>A	19.37:g.9068530C>T	ENSP00000381008:p.Val6306Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	214	106	0.495327	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	397	0.18177655677655677	100	0.2032520325203252	60	0.16574585635359115	169	0.29545454545454547	68	0.08970976253298153	c	3.020	-0.201996	0.06219	0.218236	0.077605	ENSG00000181143	ENST00000397910	T	0.33654	1.4	2.13	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	D	0.53462	0.96	B	0.41299	0.353	T	0.37244	-0.9714	8	0.87932	D	0	.	4.8461	0.13514	0.0:0.8122:0.0:0.1878	rs7250080;rs52814554;rs60352912;rs7250080	6306	B5ME49	.	M	6306	ENSP00000381008:V6306M	ENSP00000381008:V6306M	V	-	1	0	MUC16	8929530	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.485000	0.02314	0.447000	0.26695	0.195000	0.17529	GTG	C|0.827;T|0.173	0.173	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ABCA8	10351	hgsc.bcm.edu	37	17	66924083	66924083	+	Missense_Mutation	SNP	G	G	A	rs35621847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66924083G>A	ENST00000269080.2	-	9	1384	c.1247C>T	c.(1246-1248)gCg>gTg	p.A416V	ABCA8_ENST00000586539.1_Missense_Mutation_p.A416V|ABCA8_ENST00000430352.2_Missense_Mutation_p.A416V	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	416			A -> V (in dbSNP:rs35621847). {ECO:0000269|PubMed:15489334}.		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)					AAAGTAAATCGCCAATGCCAG	0.318													G|||	198	0.0395367	0.0083	0.0418	5008	,	,		16327	0.0		0.0626	False		,,,				2504	0.0971				p.A416V		Atlas-SNP	.											.	ABCA8	213	.	0			c.C1247T						PASS	.	G	VAL/ALA	71,4335	60.5+/-97.4	0,71,2132	50.0	50.0	50.0		1247	-3.5	0.0	17	dbSNP_126	50	565,8035	152.8+/-207.3	17,531,3752	yes	missense	ABCA8	NM_007168.2	64	17,602,5884	AA,AG,GG		6.5698,1.6114,4.8901	benign	416/1582	66924083	636,12370	2203	4300	6503	SO:0001583	missense	10351	exon9			TAAATCGCCAATG	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.1247C>T	17.37:g.66924083G>A	ENSP00000269080:p.Ala416Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	59	0.59596	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	74	0.03388278388278388	4	0.008130081300813009	18	0.049723756906077346	0	0.0	52	0.06860158311345646	G	10.99	1.506787	0.26949	0.016114	0.065698	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000542396	D;D	0.89681	-2.55;-2.55	4.93	-3.47	0.04753	.	0.804077	0.10961	N	0.615030	T	0.28863	0.0716	N	0.21545	0.675	0.09310	N	1	B;B;B;B	0.25169	0.119;0.072;0.094;0.062	B;B;B;B	0.30105	0.027;0.052;0.111;0.081	T	0.55354	-0.8154	10	0.44086	T	0.13	.	11.1094	0.48223	0.6192:0.0:0.3808:0.0	rs35621847	355;416;416;416	F5H6Z4;B4DJ11;C9JQE6;O94911	.;.;.;ABCA8_HUMAN	V	416;416;355;47	ENSP00000269080:A416V;ENSP00000402814:A416V	ENSP00000269080:A416V	A	-	2	0	ABCA8	64435678	0.000000	0.05858	0.001000	0.08648	0.564000	0.35744	-0.063000	0.11655	-0.438000	0.07232	-0.143000	0.13931	GCG	G|0.956;A|0.044	0.044	strong		0.318	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
PRDM10	56980	hgsc.bcm.edu	37	11	129785594	129785594	+	Silent	SNP	G	G	A	rs3734073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:129785594G>A	ENST00000360871.3	-	16	2718	c.2487C>T	c.(2485-2487)ccC>ccT	p.P829P	PRDM10_ENST00000526082.1_Silent_p.P747P|PRDM10_ENST00000528746.1_Silent_p.P803P|PRDM10_ENST00000423662.2_Silent_p.P747P|PRDM10_ENST00000358825.5_Silent_p.P833P|PRDM10_ENST00000304538.6_Silent_p.P743P	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	833					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		GACAGCAGACGGGAGGGGTGG	0.597													G|||	1149	0.229433	0.1218	0.2896	5008	,	,		16915	0.1567		0.3231	False		,,,				2504	0.3108				p.P833P		Atlas-SNP	.											PRDM10,colon,carcinoma,0,1	PRDM10	120	1	0			c.C2499T						PASS	.	G	,,,	726,3676	300.7+/-286.5	64,598,1539	104.0	101.0	102.0		2499,2487,2241,2229	-7.1	0.7	11	dbSNP_107	102	2773,5821	441.1+/-359.7	439,1895,1963	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	503,2493,3502	AA,AG,GG		32.2667,16.4925,26.9237	,,,	833/1161,829/1157,747/1062,743/1024	129785594	3499,9497	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon17			GCAGACGGGAGGG	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2487C>T	11.37:g.129785594G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			G|0.729;A|0.271	0.271	strong		0.597	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462754	21462754	+	Silent	SNP	A	A	G	rs451242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:21462754A>G	ENST00000281523.2	-	8	1658	c.1140T>C	c.(1138-1140)ccT>ccC	p.P380P		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	380						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						GAATGGGTCCAGGAGCTGGCC	0.502													A|||	4012	0.801118	0.7368	0.8098	5008	,	,		11101	0.8988		0.7584	False		,,,				2504	0.8252				p.P380P		Atlas-SNP	.											.	ZNF385D	93	.	0			c.T1140C						PASS	.	A		3339,1067	722.3+/-409.3	1281,777,145	48.0	46.0	46.0		1140	-11.6	0.0	3	dbSNP_80	46	6497,2103	714.6+/-406.0	2461,1575,264	no	coding-synonymous	ZNF385D	NM_024697.2		3742,2352,409	GG,GA,AA		24.4535,24.217,24.3734		380/396	21462754	9836,3170	2203	4300	6503	SO:0001819	synonymous_variant	79750	exon8			GGGTCCAGGAGCT	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.1140T>C	3.37:g.21462754A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_024697		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																			G|0.765;A|0.235	0.765	strong		0.502	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
KLKB1	3818	hgsc.bcm.edu	37	4	187173012	187173012	+	Missense_Mutation	SNP	T	T	G	rs4253301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187173012T>G	ENST00000264690.6	+	10	1328	c.1141T>G	c.(1141-1143)Tct>Gct	p.S381A	KLKB1_ENST00000513864.1_Missense_Mutation_p.S381A	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	381			S -> A (in dbSNP:rs4253301). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TGGGGACAACTCTGGTGAGTA	0.423													.|||	565	0.112819	0.0484	0.1095	5008	,	,		21668	0.0675		0.1342	False		,,,				2504	0.227				p.S381A		Atlas-SNP	.											KLKB1_ENST00000264690,bladder,carcinoma,-1,2	KLKB1	155	2	0			c.T1141G						PASS	.	T	ALA/SER	275,4131	153.7+/-187.2	5,265,1933	122.0	127.0	125.0		1141	-2.6	0.6	4	dbSNP_111	125	1004,7596	215.3+/-254.7	70,864,3366	yes	missense	KLKB1	NM_000892.3	99	75,1129,5299	GG,GT,TT		11.6744,6.2415,9.8339	benign	381/639	187173012	1279,11727	2203	4300	6503	SO:0001583	missense	3818	exon10			GACAACTCTGGTG	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1141T>G	4.37:g.187173012T>G	ENSP00000264690:p.Ser381Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	205	0.09386446886446886	18	0.036585365853658534	48	0.13259668508287292	35	0.06118881118881119	104	0.13720316622691292	t	11.95	1.792986	0.31685	0.062415	0.116744	ENSG00000164344	ENST00000264690;ENST00000513864;ENST00000418715	D;D	0.92752	-2.47;-3.1	5.15	-2.63	0.06133	.	0.575398	0.16596	N	0.207553	T	0.01976	0.0062	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.34015	0.028;0.304;0.435	B;B;B	0.27887	0.01;0.077;0.084	T	0.49103	-0.8974	9	0.20046	T	0.44	.	0.948	0.01369	0.2601:0.3092:0.1211:0.3096	rs4253301;rs52817049;rs58196317;rs4253301	343;381;381	E7EQA8;A8K9A9;P03952	.;.;KLKB1_HUMAN	A	381;381;343	ENSP00000264690:S381A;ENSP00000424469:S381A	ENSP00000264690:S381A	S	+	1	0	KLKB1	187410006	0.218000	0.23608	0.578000	0.28575	0.687000	0.40016	0.685000	0.25378	-0.204000	0.10235	-0.348000	0.07805	TCT	T|0.904;G|0.096	0.096	strong		0.423	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
WNT8B	7479	hgsc.bcm.edu	37	10	102222957	102222957	+	Missense_Mutation	SNP	G	G	C	rs3793771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102222957G>C	ENST00000343737.5	+	1	160	c.32G>C	c.(31-33)tGt>tCt	p.C11S		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	11			C -> S (in dbSNP:rs3793771).		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)		GTGTACATCTGTCTTTTCACC	0.428													C|||	933	0.186302	0.2012	0.1873	5008	,	,		18427	0.129		0.2008	False		,,,				2504	0.2096				p.C11S		Atlas-SNP	.											.	WNT8B	31	.	0			c.G32C						PASS	.	C	SER/CYS	894,3512	740.5+/-411.2	80,734,1389	141.0	135.0	137.0		32	4.7	1.0	10	dbSNP_107	137	1950,6650	725.0+/-406.5	222,1506,2572	yes	missense	WNT8B	NM_003393.3	112	302,2240,3961	CC,CG,GG		22.6744,20.2905,21.8668	benign	11/352	102222957	2844,10162	2203	4300	6503	SO:0001583	missense	7479	exon1			ACATCTGTCTTTT	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.32G>C	10.37:g.102222957G>C	ENSP00000340677:p.Cys11Ser	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_003393	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	37	CCDS7494.1	410	0.18772893772893773	85	0.17276422764227642	70	0.19337016574585636	88	0.15384615384615385	167	0.22031662269129287	C	6.745	0.506185	0.12883	0.202905	0.226744	ENSG00000075290	ENST00000343737	T	0.73047	-0.71	5.85	4.72	0.59763	.	0.610680	0.17969	N	0.155936	T	0.00039	0.0001	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06552	-1.0820	9	0.13470	T	0.59	.	8.145	0.31106	0.0:0.0712:0.1356:0.7932	rs3793771;rs17733373;rs3793771	11	Q93098	WNT8B_HUMAN	S	11	ENSP00000340677:C11S	ENSP00000340677:C11S	C	+	2	0	WNT8B	102212947	0.988000	0.35896	0.992000	0.48379	0.703000	0.40648	1.476000	0.35420	0.486000	0.27676	-1.145000	0.01858	TGT	G|0.799;C|0.201	0.201	strong		0.428	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
MYO10	4651	hgsc.bcm.edu	37	5	16877739	16877739	+	Silent	SNP	G	G	A	rs185323430		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16877739G>A	ENST00000513610.1	-	2	553	c.99C>T	c.(97-99)gtC>gtT	p.V33V	MYO10_ENST00000507288.1_Silent_p.V33V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	33					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTGTCCGGAAGACGACGATGC	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		18799	0.0		0.001	False		,,,				2504	0.0				p.V33V		Atlas-SNP	.											.	MYO10	198	.	0			c.C99T						PASS	.	G		0,4024		0,0,2012	104.0	105.0	105.0		99	2.5	1.0	5		105	6,8338		0,6,4166	no	coding-synonymous	MYO10	NM_012334.2		0,6,6178	AA,AG,GG		0.0719,0.0,0.0485		33/2059	16877739	6,12362	2012	4172	6184	SO:0001819	synonymous_variant	4651	exon2			CCGGAAGACGACG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.99C>T	5.37:g.16877739G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
ALG1	56052	hgsc.bcm.edu	37	16	5127460	5127460	+	Missense_Mutation	SNP	T	T	G	rs112668461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5127460T>G	ENST00000262374.5	+	5	585	c.554T>G	c.(553-555)tTt>tGt	p.F185C	ALG1_ENST00000588623.1_Missense_Mutation_p.F74C|ALG1_ENST00000544428.1_Missense_Mutation_p.F74C	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	185					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)				GAGAAGTTCTTTGGGCGCCTG	0.557													T|||	73	0.0145767	0.0545	0.0014	5008	,	,		15459	0.0		0.0	False		,,,				2504	0.0				p.F185C		Atlas-SNP	.											.	ALG1	35	.	0			c.T554G						PASS	.	T	CYS/PHE	179,4215	115.9+/-153.8	4,171,2022	102.0	92.0	96.0		554	-0.3	0.1	16	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	205	4,172,6321	GG,GT,TT		0.0116,4.0737,1.3853	benign	185/465	5127460	180,12814	2197	4300	6497	SO:0001583	missense	56052	exon5			AGTTCTTTGGGCG	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.554T>G	16.37:g.5127460T>G	ENSP00000262374:p.Phe185Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	T	10.06	1.246611	0.22796	0.040737	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	D;D	0.86297	-2.1;-2.1	5.79	-0.341	0.12639	.	0.364426	0.34223	N	0.004141	T	0.55529	0.1926	L	0.45422	1.42	0.54753	D	0.999989	B;B	0.22746	0.011;0.074	B;B	0.22152	0.009;0.038	T	0.64166	-0.6471	10	0.49607	T	0.09	-2.3162	14.4032	0.67063	0.0:0.0:0.338:0.662	.	74;185	B4DP08;Q9BT22	.;ALG1_HUMAN	C	185;74	ENSP00000262374:F185C;ENSP00000440019:F74C	ENSP00000262374:F185C	F	+	2	0	ALG1	5067461	0.953000	0.32496	0.133000	0.22050	0.575000	0.36095	1.537000	0.36083	-0.348000	0.08286	0.459000	0.35465	TTT	T|0.982;G|0.018	0.018	strong		0.557	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
OR4N2	390429	hgsc.bcm.edu	37	14	20295779	20295779	+	Missense_Mutation	SNP	C	C	G	rs11621884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	246	0	0		WXS	Illumina HiSeq	Phase_I	303	62	0.20462	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		
FAM189A1	23359	hgsc.bcm.edu	37	15	29416901	29416901	+	Missense_Mutation	SNP	A	A	G	rs2279482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:29416901A>G	ENST00000261275.4	-	10	1291	c.1292T>C	c.(1291-1293)gTg>gCg	p.V431A		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	431			V -> A (in dbSNP:rs2279482).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GCTCCCAGGCACAGCCTCAGA	0.562													a|||	858	0.171326	0.2315	0.1153	5008	,	,		16403	0.2202		0.0775	False		,,,				2504	0.1759				p.V431A		Atlas-SNP	.											.	FAM189A1	20	.	0			c.T1292C						PASS	.	G	ALA/VAL	311,1073		40,231,421	63.0	69.0	67.0		1292	-3.4	0.0	15	dbSNP_100	67	231,2951		9,213,1369	yes	missense	FAM189A1	NM_015307.1	64	49,444,1790	GG,GA,AA		7.2596,22.4711,11.8703	benign	431/540	29416901	542,4024	692	1591	2283	SO:0001583	missense	23359	exon10			CCAGGCACAGCCT		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.1292T>C	15.37:g.29416901A>G	ENSP00000261275:p.Val431Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	330	0.1510989010989011	113	0.22967479674796748	40	0.11049723756906077	122	0.21328671328671328	55	0.07255936675461741	a	0.012	-1.672619	0.00758	0.224711	0.072596	ENSG00000104059	ENST00000261275	T	0.09630	2.96	4.28	-3.41	0.04839	.	2.367780	0.01632	N	0.023592	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	0.43294	-0.9400	9	0.15066	T	0.55	-18.2153	3.3831	0.07261	0.2555:0.1122:0.508:0.1243	rs2279482;rs59311904;rs2279482	431	O60320	F1891_HUMAN	A	431	ENSP00000261275:V431A	ENSP00000261275:V431A	V	-	2	0	FAM189A1	27204193	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.411000	0.07530	-3.557000	0.00030	GTG	A|0.843;G|0.157	0.157	strong		0.562	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
SYT2	127833	hgsc.bcm.edu	37	1	202569600	202569600	+	Silent	SNP	C	C	T	rs115267501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202569600C>T	ENST00000367267.1	-	7	996	c.804G>A	c.(802-804)ccG>ccA	p.P268P	SYT2_ENST00000367268.4_Silent_p.P268P	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	268	Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	CCAGCTTCTCCGGCTGTCCAG	0.567											OREG0014101	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	101	0.0201677	0.0015	0.0389	5008	,	,		21141	0.0		0.0567	False		,,,				2504	0.0153				p.P268P		Atlas-SNP	.											.	SYT2	51	.	0			c.G804A						PASS	.	C	,	43,4363	43.8+/-77.6	1,41,2161	73.0	69.0	70.0		804,804	-0.1	1.0	1	dbSNP_132	70	367,8233	122.0+/-181.0	12,343,3945	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	13,384,6106	TT,TC,CC		4.2674,0.9759,3.1524	,	268/420,268/420	202569600	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon7			CTTCTCCGGCTGT	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.804G>A	1.37:g.202569600C>T		Somatic	55	0	0	2130	WXS	Illumina HiSeq	Phase_I	74	23	0.310811	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			C|0.967;T|0.033	0.033	strong		0.567	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
MERTK	10461	hgsc.bcm.edu	37	2	112765973	112765973	+	Silent	SNP	A	A	G	rs1131244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	54	0	0		WXS	Illumina HiSeq	Phase_I	45	45	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		
ITGAX	3687	hgsc.bcm.edu	37	16	31382470	31382470	+	Silent	SNP	A	A	G	rs138137251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:31382470A>G	ENST00000268296.4	+	15	1897	c.1776A>G	c.(1774-1776)caA>caG	p.Q592Q	ITGAX_ENST00000562522.1_Silent_p.Q592Q	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	592					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						GCGGGGGTCAAGACCTCACCC	0.642													A|||	32	0.00638978	0.0015	0.0173	5008	,	,		17052	0.0		0.0169	False		,,,				2504	0.001				p.Q592Q		Atlas-SNP	.											.	ITGAX	198	.	0			c.A1776G						PASS	.	A		4,4390	8.1+/-20.4	0,4,2193	56.0	63.0	61.0		1776	3.3	1.0	16	dbSNP_134	61	112,8488	57.9+/-119.4	0,112,4188	no	coding-synonymous	ITGAX	NM_000887.3		0,116,6381	GG,GA,AA		1.3023,0.091,0.8927		592/1164	31382470	116,12878	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GGGTCAAGACCTC	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.1776A>G	16.37:g.31382470A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			A|0.991;G|0.009	0.009	strong		0.642	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
TG	7038	hgsc.bcm.edu	37	8	133984058	133984058	+	Missense_Mutation	SNP	C	C	T	rs2076740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:133984058C>T	ENST00000220616.4	+	33	6035	c.5995C>T	c.(5995-5997)Cgg>Tgg	p.R1999W	TG_ENST00000377869.1_Missense_Mutation_p.R1942W|TG_ENST00000542445.1_Missense_Mutation_p.R369W|TG_ENST00000519543.1_Missense_Mutation_p.R153W	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1999			R -> W (in dbSNP:rs2076740). {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)		ATGTGAACGACGGTGCGATGC	0.493													C|||	1665	0.332468	0.5408	0.2493	5008	,	,		19511	0.1627		0.3559	False		,,,				2504	0.2607				p.R1999W		Atlas-SNP	.											.	TG	416	.	0			c.C5995T						PASS	.	C	TRP/ARG	2194,2212	588.3+/-386.9	544,1106,553	129.0	114.0	119.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5995	-0.2	0.0	8	dbSNP_96	119	2901,5699	454.1+/-363.4	469,1963,1868	yes	missense	TG	NM_003235.4	101	1013,3069,2421	TT,TC,CC		33.7326,49.7957,39.1742	benign	1999/2769	133984058	5095,7911	2203	4300	6503	SO:0001583	missense	7038	exon33			GAACGACGGTGCG	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.5995C>T	8.37:g.133984058C>T	ENSP00000220616:p.Arg1999Trp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	721|721	0.3301282051282051|0.3301282051282051	246|246	0.5|0.5	99|99	0.27348066298342544|0.27348066298342544	107|107	0.18706293706293706|0.18706293706293706	269|269	0.3548812664907652|0.3548812664907652	C|C	4.432|4.432	0.079891|0.079891	0.08533|0.08533	0.497957|0.497957	0.337326|0.337326	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543|ENST00000519178	T;T;T;T|.	0.66099|.	-0.18;-0.19;-0.05;-0.05|.	5.55|5.55	-0.156|-0.156	0.13391|0.13391	.|.	1.194990|.	0.06265|.	N|.	0.694711|.	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;B;B|.	0.18013|.	0.025;0.003;0.005|.	B;B;B|.	0.11329|.	0.006;0.002;0.003|.	T|T	0.48043|0.48043	-0.9069|-0.9069	9|4	0.45353|.	T|.	0.12|.	.|.	4.5318|4.5318	0.12008|0.12008	0.2776:0.474:0.0:0.2484|0.2776:0.474:0.0:0.2484	rs2076740;rs2228589;rs2293209;rs11535853;rs52833903;rs57636340;rs11535853|rs2076740;rs2228589;rs2293209;rs11535853;rs52833903;rs57636340;rs11535853	153;369;1999|.	E7EVM0;F5GWW5;P01266|.	.;.;THYG_HUMAN|.	W|M	1942;805;1999;369;153|454	ENSP00000367100:R1942W;ENSP00000220616:R1999W;ENSP00000441693:R369W;ENSP00000430430:R153W|.	ENSP00000220616:R1999W|.	R|T	+|+	1|2	2|0	TG|TG	134053240|134053240	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.031000|0.031000	0.12232|0.12232	0.050000|0.050000	0.14120|0.14120	0.036000|0.036000	0.15547|0.15547	-0.137000|-0.137000	0.14449|0.14449	CGG|ACG	C|0.628;T|0.372	0.372	strong		0.493	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
UBXN6	80700	hgsc.bcm.edu	37	19	4457650	4457650	+	Silent	SNP	C	C	T	rs1044510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4457650C>T	ENST00000301281.6	-	1	169	c.45G>A	c.(43-45)aaG>aaA	p.K15K	UBXN6_ENST00000394765.3_5'Flank|CTB-50L17.9_ENST00000592034.1_RNA|CTB-50L17.16_ENST00000591414.1_lincRNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	15						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						GTCCCGCGCTCTTGAACTTGA	0.697													C|||	2034	0.40615	0.3374	0.4294	5008	,	,		3297	0.6171		0.2763	False		,,,				2504	0.3988				p.K15K		Atlas-SNP	.											.	UBXN6	27	.	0			c.G45A						PASS	.	C		1456,2946	448.5+/-348.7	253,950,998	34.0	31.0	32.0		45	3.1	1.0	19	dbSNP_86	32	2433,6161	385.4+/-341.5	334,1765,2198	no	coding-synonymous	UBXN6	NM_025241.2		587,2715,3196	TT,TC,CC		28.3104,33.0759,29.9246		15/442	4457650	3889,9107	2201	4297	6498	SO:0001819	synonymous_variant	80700	exon1			CGCGCTCTTGAAC	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.45G>A	19.37:g.4457650C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	37	CCDS12129.1																																																																																			C|0.660;T|0.340	0.340	strong		0.697	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
ZNF70	7621	hgsc.bcm.edu	37	22	24086107	24086107	+	Silent	SNP	A	A	G	rs5759985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:24086107A>G	ENST00000341976.3	-	2	1681	c.1221T>C	c.(1219-1221)atT>atC	p.I407I		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	407					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)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TATAGTGCTCAATGAGGGCTG	0.582													g|||	2787	0.55651	0.7927	0.4006	5008	,	,		18529	0.6865		0.3579	False		,,,				2504	0.4182				p.I407I		Atlas-SNP	.											ZNF70,NS,carcinoma,-1,1	ZNF70	49	1	0			c.T1221C						PASS	.	G		3262,1144	405.8+/-333.6	1225,812,166	124.0	119.0	121.0		1221	-5.1	0.4	22	dbSNP_114	121	3116,5484	658.5+/-401.6	596,1924,1780	no	coding-synonymous	ZNF70	NM_021916.2		1821,2736,1946	GG,GA,AA		36.2326,25.9646,49.0389		407/447	24086107	6378,6628	2203	4300	6503	SO:0001819	synonymous_variant	7621	exon2			GTGCTCAATGAGG	X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"""Zinc fingers, C2H2-type"""	13140	protein-coding gene	gene with protein product		194544	"""zinc finger protein 70 (Cos17)"""			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.1221T>C	22.37:g.24086107A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																			A|0.481;G|0.519	0.519	strong		0.582	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33541216	33541216	+	Missense_Mutation	SNP	G	G	C	rs111814125		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33541216G>C	ENST00000290943.6	+	7	976	c.880G>C	c.(880-882)Ggt>Cgt	p.G294R		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	294								p.G294R(1)		NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						aagaaaagaaGGTGCAAAAGG	0.343																																					p.G294R		Atlas-SNP	.											ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	1	Substitution - Missense(1)	prostate(1)	c.G880C						scavenged	.																																			SO:0001583	missense	441459	exon7			AAAGAAGGTGCAA			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.880G>C	9.37:g.33541216G>C	ENSP00000290943:p.Gly294Arg	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	225	32	0.142222	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	37		.	.	.	.	.	.	.	.	.	.	g	0.030	-1.339649	0.01277	.	.	ENSG00000230453	ENST00000290943	T	0.26660	1.72	0.225	0.225	0.15325	.	.	.	.	.	T	0.18087	0.0434	.	.	.	0.23076	N	0.998333	.	.	.	.	.	.	T	0.34625	-0.9821	4	0.19147	T	0.46	.	.	.	.	.	.	.	.	R	294	ENSP00000290943:G294R	ENSP00000290943:G294R	G	+	1	0	ANKRD18B	33531216	0.013000	0.17824	0.008000	0.14137	0.008000	0.06430	0.337000	0.19841	0.300000	0.22699	0.305000	0.20034	GGT	G|0.500;C|0.500	0.500	weak		0.343	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
SEC31B	25956	hgsc.bcm.edu	37	10	102247408	102247408	+	Missense_Mutation	SNP	C	C	A	rs2298075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102247408C>A	ENST00000370345.3	-	26	3602	c.3505G>T	c.(3505-3507)Gct>Tct	p.A1169S		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1169			A -> S (in dbSNP:rs2298075).		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		ATGAGGACAGCCTTCAGGATA	0.562													C|||	946	0.188898	0.2088	0.1888	5008	,	,		20238	0.129		0.2018	False		,,,				2504	0.2106				p.A1169S		Atlas-SNP	.											SEC31B,NS,carcinoma,0,2	SEC31B	84	2	0			c.G3505T						PASS	.	C	SER/ALA	908,3498	347.2+/-309.4	82,744,1377	49.0	41.0	44.0		3505	1.2	0.9	10	dbSNP_100	44	1955,6645	338.2+/-322.6	225,1505,2570	yes	missense	SEC31B	NM_015490.3	99	307,2249,3947	AA,AC,CC		22.7326,20.6083,22.0129	benign	1169/1180	102247408	2863,10143	2203	4300	6503	SO:0001583	missense	25956	exon26			GGACAGCCTTCAG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3505G>T	10.37:g.102247408C>A	ENSP00000359370:p.Ala1169Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	415	0.190018315018315	89	0.18089430894308944	71	0.19613259668508287	88	0.15384615384615385	167	0.22031662269129287	C	7.962	0.747208	0.15710	0.206083	0.227326	ENSG00000075826	ENST00000370345	T	0.49432	0.78	4.45	1.23	0.21249	.	0.487653	0.22268	N	0.062301	T	0.00012	0.0000	N	0.03050	-0.425	0.09310	P	0.9999999999717782	B;B	0.17038	0.02;0.012	B;B	0.16289	0.015;0.007	T	0.20438	-1.0275	9	0.45353	T	0.12	-2.4525	7.7526	0.28907	0.2984:0.6126:0.0:0.089	rs2298075;rs17672195;rs52835061;rs59609476;rs2298075	1168;1169	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	S	1169	ENSP00000359370:A1169S	ENSP00000359370:A1169S	A	-	1	0	SEC31B	102237398	1.000000	0.71417	0.924000	0.36721	0.103000	0.19146	3.426000	0.52778	0.477000	0.27464	0.561000	0.74099	GCT	C|0.795;A|0.205	0.205	strong		0.562	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
KIAA1755	85449	hgsc.bcm.edu	37	20	36856616	36856616	+	Missense_Mutation	SNP	G	G	A	rs16987188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36856616G>A	ENST00000279024.4	-	6	2169	c.1898C>T	c.(1897-1899)gCg>gTg	p.A633V		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	633			A -> V (in dbSNP:rs16987188).							breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AATCAGGACCGCCAGCCCCTT	0.612													G|||	269	0.0537141	0.0893	0.0259	5008	,	,		17350	0.0456		0.0249	False		,,,				2504	0.0634				p.A633V		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1898T						PASS	.	G	VAL/ALA	380,4026	189.5+/-215.6	19,342,1842	44.0	40.0	42.0		1898	-0.5	0.5	20	dbSNP_123	42	275,8325	102.5+/-163.7	7,261,4032	yes	missense	KIAA1755	NM_001029864.1	64	26,603,5874	AA,AG,GG		3.1977,8.6246,5.0361	benign	633/1201	36856616	655,12351	2203	4300	6503	SO:0001583	missense	85449	exon6			AGGACCGCCAGCC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1898C>T	20.37:g.36856616G>A	ENSP00000279024:p.Ala633Val	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	103	0.04716117216117216	48	0.0975609756097561	14	0.03867403314917127	24	0.04195804195804196	17	0.022427440633245383	G	0.487	-0.877142	0.02550	0.086246	0.031977	ENSG00000149633	ENST00000279024;ENST00000373398	T	0.14266	2.52	4.8	-0.471	0.12119	.	0.949823	0.08653	N	0.913657	T	0.00241	0.0007	L	0.28115	0.83	0.80722	P	0.0	B	0.13594	0.008	B	0.12837	0.008	T	0.44877	-0.9299	9	0.14252	T	0.57	.	8.381	0.32472	0.5547:0.0:0.4453:0.0	rs16987188;rs52805884;rs16987188	633	Q5JYT7	K1755_HUMAN	V	633;180	ENSP00000279024:A633V	ENSP00000279024:A633V	A	-	2	0	KIAA1755	36290030	0.003000	0.15002	0.546000	0.28166	0.186000	0.23388	0.141000	0.16076	-0.220000	0.09988	-0.812000	0.03155	GCG	G|0.949;A|0.051	0.051	strong		0.612	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
LRRC36	55282	hgsc.bcm.edu	37	16	67381383	67381383	+	Intron	SNP	G	G	C	rs79636320	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:67381383G>C	ENST00000329956.6	+	4	410				LRRC36_ENST00000563303.1_Intron|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000435835.3_Missense_Mutation_p.R5P|LRRC36_ENST00000290940.7_5'UTR|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	88	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	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	
HS6ST1	9394	hgsc.bcm.edu	37	2	129025860	129025860	+	Missense_Mutation	SNP	C	C	T	rs147436494		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:129025860C>T	ENST00000259241.6	-	2	1125	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	371					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)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		GCTCCTCAGGCGCTGCTCCCT	0.677																																					p.R371H		Atlas-SNP	.											HS6ST1,NS,carcinoma,0,2	HS6ST1	31	2	0			c.G1112A						scavenged	.						32.0	41.0	38.0					2																	129025860		2097	4251	6348	SO:0001583	missense	9394	exon2			CTCAGGCGCTGCT	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.1112G>A	2.37:g.129025860C>T	ENSP00000259241:p.Arg371His	Somatic	129	7	0.0542636		WXS	Illumina HiSeq	Phase_I	164	31	0.189024	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	591	0.2706043956043956	87	0.17682926829268292	106	0.292817679558011	168	0.2937062937062937	230	0.3034300791556728	C	28.0	4.883726	0.91814	.	.	ENSG00000136720	ENST00000259241	D	0.85339	-1.97	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.74647	2.275	0.09310	P	0.99999999795479	D	0.76494	0.999	D	0.76071	0.987	T	0.00000	-1.3594	8	.	.	.	-12.2845	17.1367	0.86742	0.0:1.0:0.0:0.0	.	371	O60243	H6ST1_HUMAN	H	371	ENSP00000259241:R371H	.	R	-	2	0	HS6ST1	128742330	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.243000	0.78219	2.099000	0.63709	0.462000	0.41574	CGC	C|0.729;T|0.271	0.271	strong		0.677	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
RUFY1	80230	hgsc.bcm.edu	37	5	179036433	179036433	+	Silent	SNP	G	G	A	rs17355294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:179036433G>A	ENST00000319449.4	+	18	2052	c.2040G>A	c.(2038-2040)ctG>ctA	p.L680L	RUFY1_ENST00000393438.2_Silent_p.L572L|RUFY1_ENST00000437570.2_Silent_p.L572L|RUFY1_ENST00000508797.1_3'UTR|RUFY1_ENST00000377001.2_3'UTR	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	680					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAACGAGCTGGCCCTGCCCT	0.647										HNSCC(44;0.11)			G|||	1361	0.271765	0.2912	0.3084	5008	,	,		15099	0.1706		0.4284	False		,,,				2504	0.1626				p.L680L		Atlas-SNP	.											.	RUFY1	101	.	0			c.G2040A						PASS	.	G	,,	1450,2956		244,962,997	79.0	61.0	67.0		1716,1716,2040	1.2	1.0	5	dbSNP_123	67	3769,4831		852,2065,1383	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	1096,3027,2380	AA,AG,GG		43.8256,32.9097,40.1276	,,	572/601,572/601,680/709	179036433	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon18			CGAGCTGGCCCTG	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.2040G>A	5.37:g.179036433G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2																																																																																			G|0.620;A|0.380	0.380	strong		0.647	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
COG1	9382	hgsc.bcm.edu	37	17	71197439	71197439	+	Silent	SNP	C	C	T	rs1551036	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:71197439C>T	ENST00000299886.4	+	7	1553	c.1473C>T	c.(1471-1473)agC>agT	p.S491S		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	491					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)			CCTGGGTCAGCGTGGCAAACC	0.532													C|||	660	0.131789	0.0083	0.1225	5008	,	,		20222	0.1746		0.1958	False		,,,				2504	0.1953				p.S491S		Atlas-SNP	.											.	COG1	46	.	0			c.C1473T						PASS	.	C		172,4234	112.5+/-150.6	5,162,2036	139.0	129.0	132.0		1473	-2.5	0.0	17	dbSNP_88	132	1661,6939	304.5+/-307.0	178,1305,2817	no	coding-synonymous	COG1	NM_018714.2		183,1467,4853	TT,TC,CC		19.314,3.9038,14.0935		491/981	71197439	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	9382	exon7			GGTCAGCGTGGCA		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.1473C>T	17.37:g.71197439C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	37	CCDS11692.1																																																																																			C|0.867;N|0.001	.	strong		0.532	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
USP24	23358	hgsc.bcm.edu	37	1	55538462	55538462	+	Silent	SNP	C	C	T	rs17410294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55538462C>T	ENST00000294383.6	-	65	7598	c.7599G>A	c.(7597-7599)aaG>aaA	p.K2533K	USP24_ENST00000407756.1_Silent_p.K2373K|USP24_ENST00000484447.1_5'UTR	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2533					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						CAGTTACCTTCTTCTGTAGCC	0.428													C|||	326	0.0650958	0.0287	0.0764	5008	,	,		18938	0.003		0.161	False		,,,				2504	0.0716				p.K2533K		Atlas-SNP	.											.	USP24	323	.	0			c.G7599A						PASS	.	C		210,3656		8,194,1731	53.0	53.0	53.0		7599	3.1	1.0	1	dbSNP_123	53	1262,7030		107,1048,2991	no	coding-synonymous	USP24	NM_015306.2		115,1242,4722	TT,TC,CC		15.2195,5.432,12.1073		2533/2621	55538462	1472,10686	1933	4146	6079	SO:0001819	synonymous_variant	23358	exon65			TACCTTCTTCTGT	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.7599G>A	1.37:g.55538462C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			C|0.916;T|0.084	0.084	strong		0.428	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
PRPF38B	55119	hgsc.bcm.edu	37	1	109242617	109242617	+	Missense_Mutation	SNP	A	A	G	rs147907392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:109242617A>G	ENST00000370025.4	+	6	1885	c.1616A>G	c.(1615-1617)cAt>cGt	p.H539R	PRPF38B_ENST00000370021.1_Missense_Mutation_p.H428R	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	539					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		GAAAAACAGCATAAAAACAAA	0.378																																					p.H539R		Atlas-SNP	.											.	PRPF38B	55	.	0			c.A1616G						PASS	.	A	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	99.0	105.0	103.0		1616	2.6	0.1	1	dbSNP_134	103	3,8595	3.0+/-9.4	0,3,4296	yes	missense	PRPF38B	NM_018061.2	29	0,4,6498	GG,GA,AA		0.0349,0.0227,0.0308	benign	539/547	109242617	4,13000	2203	4299	6502	SO:0001583	missense	55119	exon6			AACAGCATAAAAA	AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"""PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"""				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.1616A>G	1.37:g.109242617A>G	ENSP00000359042:p.His539Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_018061	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation	SNP	ENST00000370025.4	37	CCDS788.1	.	.	.	.	.	.	.	.	.	.	A	3.445	-0.113310	0.06881	2.27E-4	3.49E-4	ENSG00000134186	ENST00000370025;ENST00000370021	T;T	0.28255	1.62;2.63	5.0	2.62	0.31277	.	0.721070	0.12939	N	0.426764	T	0.04318	0.0119	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.44205	-0.9343	10	0.15952	T	0.53	.	3.5441	0.07821	0.6531:0.1392:0.0743:0.1334	.	539	Q5VTL8	PR38B_HUMAN	R	539;428	ENSP00000359042:H539R;ENSP00000359038:H428R	ENSP00000359038:H428R	H	+	2	0	PRPF38B	109044140	0.998000	0.40836	0.127000	0.21898	0.592000	0.36648	2.211000	0.42825	0.248000	0.21435	0.379000	0.24179	CAT	A|1.000;G|0.000	0.000	strong		0.378	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061	
PARP4	143	hgsc.bcm.edu	37	13	25009297	25009297	+	Missense_Mutation	SNP	G	G	T	rs1050112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25009297G>T	ENST00000381989.3	-	31	4087	c.3982C>A	c.(3982-3984)Ccc>Acc	p.P1328T		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1328				P -> T (in Ref. 1; AAD47250, 2; AAC62491 and 3; BAA11494). {ECO:0000305}.	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)		GCAGTCGGGGGAAGATAGGAA	0.493													g|||	1928	0.384984	0.4849	0.3473	5008	,	,		19272	0.3601		0.4115	False		,,,				2504	0.2751				p.P1328T		Atlas-SNP	.											.	PARP4	142	.	0			c.C3982A						PASS	.	G	THR/PRO	2075,2331	570.1+/-382.8	471,1133,599	84.0	91.0	89.0		3982	-4.7	0.0	13	dbSNP_86	89	3204,5396	483.3+/-371.1	594,2016,1690	yes	missense	PARP4	NM_006437.3	38	1065,3149,2289	TT,TG,GG		37.2558,47.0949,40.589	benign	1328/1725	25009297	5279,7727	2203	4300	6503	SO:0001583	missense	143	exon31			TCGGGGGAAGATA	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.3982C>A	13.37:g.25009297G>T	ENSP00000371419:p.Pro1328Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	144	132	0.916667	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	842	0.38553113553113555	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	314	0.41424802110817943	g	0.123	-1.122756	0.01785	0.470949	0.372558	ENSG00000102699	ENST00000381989	T	0.01705	4.68	2.34	-4.69	0.03299	.	18.580100	0.00559	U	0.000278	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13145	0.007	B	0.12156	0.007	T	0.43572	-0.9383	9	0.15499	T	0.54	.	8.7913	0.34852	0.4246:0.0:0.5754:0.0	rs1050112;rs3190396;rs3742175;rs58385276;rs1050112	1328	Q9UKK3	PARP4_HUMAN	T	1328	ENSP00000371419:P1328T	ENSP00000371419:P1328T	P	-	1	0	PARP4	23907297	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.632000	0.24583	-1.483000	0.01858	-1.800000	0.00619	CCC	G|0.603;T|0.397	0.397	strong		0.493	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
FABP6	2172	hgsc.bcm.edu	37	5	159659273	159659273	+	Missense_Mutation	SNP	C	C	T	rs1130435	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:159659273C>T	ENST00000402432.3	+	2	364	c.236C>T	c.(235-237)aCg>aTg	p.T79M	FABP6_ENST00000393982.1_Missense_Mutation_p.T128M|FABP6_ENST00000393980.4_Missense_Mutation_p.T128M	NM_001445.2	NP_001436.1	P51161	FABP6_HUMAN	fatty acid binding protein 6, ileal	79			T -> M (in dbSNP:rs1130435).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(1)|lung(2)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGGGCAAGACGTTCAAGGTG	0.582													C|||	2328	0.464856	0.4629	0.4092	5008	,	,		16993	0.494		0.3966	False		,,,				2504	0.547				p.T128M	Colon(29;562 677 12756 16385 20992)	Atlas-SNP	.											.	FABP6	37	.	0			c.C383T						PASS	.	C	MET/THR,MET/THR,MET/THR	2042,2364	542.8+/-376.1	484,1074,645	43.0	32.0	36.0		383,383,236	3.5	1.0	5	dbSNP_86	36	3443,5157	476.8+/-369.5	697,2049,1554	yes	missense,missense,missense	FABP6	NM_001040442.1,NM_001130958.1,NM_001445.2	81,81,81	1181,3123,2199	TT,TC,CC		40.0349,46.3459,42.1728	benign,benign,benign	128/178,128/178,79/129	159659273	5485,7521	2203	4300	6503	SO:0001583	missense	2172	exon5			GCAAGACGTTCAA	U19869	CCDS4349.1, CCDS43393.1	5q23-q35	2013-03-01	2008-08-01		ENSG00000170231	ENSG00000170231		"""Fatty acid binding protein family"""	3561	protein-coding gene	gene with protein product	"""illeal lipid-binding protein"", ""ileal bile acid binding protein"", ""gastrotropin"""	600422				7894165, 7619861	Standard	NM_001130958		Approved	I-15P, ILLBP, I-BAP, ILBP3, I-BABP, ILBP, I-BALB	uc003lxx.1	P51161	OTTHUMG00000130329	ENST00000402432.3:c.236C>T	5.37:g.159659273C>T	ENSP00000385433:p.Thr79Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001130958	Q07DR7|Q8TBI3|Q9UGI7	Missense_Mutation	SNP	ENST00000402432.3	37	CCDS4349.1	954	0.4368131868131868	222	0.45121951219512196	154	0.425414364640884	282	0.493006993006993	296	0.39050131926121373	C	9.909	1.208885	0.22205	0.463459	0.400349	ENSG00000170231	ENST00000393980;ENST00000393982;ENST00000402432	T;T;T	0.23147	1.92;1.92;1.92	4.64	3.48	0.39840	Calycin-like (1);Cytosolic fatty-acid binding (1);Calycin (1);	0.046714	0.85682	D	0.000000	T	0.00012	0.0000	L	0.27053	0.805	0.45899	P	0.0012539999999999774	B;B	0.29886	0.037;0.26	B;B	0.17979	0.008;0.02	T	0.46062	-0.9218	9	0.51188	T	0.08	-38.2958	9.6938	0.40145	0.8224:0.1776:0.0:0.0	rs1130435;rs2229417;rs3189270;rs13161018;rs17416281;rs52803411;rs61698143;rs13161018	79;128	P51161;P51161-2	FABP6_HUMAN;.	M	128;128;79	ENSP00000377549:T128M;ENSP00000377551:T128M;ENSP00000385433:T79M	ENSP00000377549:T128M	T	+	2	0	FABP6	159591851	1.000000	0.71417	1.000000	0.80357	0.374000	0.29953	5.108000	0.64609	0.805000	0.34159	-0.525000	0.04345	ACG	C|0.576;T|0.424	0.424	strong		0.582	FABP6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320505.2	NM_001040442	
SPINK4	27290	hgsc.bcm.edu	37	9	33240225	33240225	+	Missense_Mutation	SNP	G	G	A	rs706107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33240225G>A	ENST00000379721.3	+	1	64	c.19G>A	c.(19-21)Gta>Ata	p.V7I	SPINK4_ENST00000379723.1_Intron|SPINK4_ENST00000379725.1_Intron	NM_014471.1	NP_055286.1	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	7			V -> I (in dbSNP:rs706107).		response to drug (GO:0042493)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			CCGCCAGTGGGTAATCGCCCT	0.607													G|||	1904	0.380192	0.7148	0.2622	5008	,	,		17914	0.2569		0.2485	False		,,,				2504	0.274				p.V7I		Atlas-SNP	.											.	SPINK4	7	.	0			c.G19A						PASS	.	G	ILE/VAL	2832,1574	640.5+/-397.3	918,996,289	69.0	60.0	63.0		19	-7.2	0.0	9	dbSNP_86	63	2010,6588	334.9+/-321.2	226,1558,2515	yes	missense	SPINK4	NM_014471.1	29	1144,2554,2804	AA,AG,GG		23.3775,35.724,37.2347	benign	7/87	33240225	4842,8162	2203	4299	6502	SO:0001583	missense	27290	exon1			CAGTGGGTAATCG	AF048700	CCDS6536.1	9p13.3	2011-08-31	2005-08-17		ENSG00000122711	ENSG00000122711		"""Serine peptidase inhibitors, Kazal type"""	16646	protein-coding gene	gene with protein product		613929	"""serine protease inhibitor, Kazal type 4"""			1400298, 17333166	Standard	NM_014471		Approved	PEC-60, MGC133107	uc003zsh.3	O60575	OTTHUMG00000019762	ENST00000379721.3:c.19G>A	9.37:g.33240225G>A	ENSP00000369045:p.Val7Ile	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_014471	Q2YDT7	Missense_Mutation	SNP	ENST00000379721.3	37	CCDS6536.1	766	0.3507326007326007	331	0.6727642276422764	104	0.287292817679558	148	0.25874125874125875	183	0.24142480211081793	G	2.626	-0.287494	0.05605	0.64276	0.233775	ENSG00000122711	ENST00000379721	T	0.68025	-0.3	4.26	-7.22	0.01485	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.799999999996249E-5	B	0.14438	0.01	B	0.08055	0.003	T	0.41840	-0.9486	7	0.07990	T	0.79	.	0.5067	0.00588	0.328:0.2853:0.1523:0.2344	rs706107;rs3818828;rs61549733;rs706107	7	O60575	ISK4_HUMAN	I	7	ENSP00000369045:V7I	ENSP00000369045:V7I	V	+	1	0	SPINK4	33230225	0.008000	0.16893	0.000000	0.03702	0.009000	0.06853	-0.667000	0.05274	-1.612000	0.01579	0.462000	0.41574	GTA	G|0.621;A|0.379	0.379	strong		0.607	SPINK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052035.1	NM_014471	
NUP188	23511	hgsc.bcm.edu	37	9	131768786	131768786	+	Silent	SNP	G	G	A	rs150379581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131768786G>A	ENST00000372577.2	+	44	5100	c.5079G>A	c.(5077-5079)acG>acA	p.T1693T	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1693					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)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						TGTAGAGCACGCTGCTGTCCA	0.642											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	24	0.00479233	0.0008	0.0072	5008	,	,		15926	0.0		0.0169	False		,,,				2504	0.001				p.T1693T		Atlas-SNP	.											.	NUP188	140	.	0			c.G5079A						PASS	.	G		13,4393	21.2+/-45.6	0,13,2190	59.0	66.0	64.0		5079	-10.4	0.6	9	dbSNP_134	64	136,8464	67.7+/-130.1	0,136,4164	no	coding-synonymous	NUP188	NM_015354.1		0,149,6354	AA,AG,GG		1.5814,0.2951,1.1456		1693/1750	131768786	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon44			GAGCACGCTGCTG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.5079G>A	9.37:g.131768786G>A		Somatic	108	0	0	1590	WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			G|0.990;A|0.010	0.010	strong		0.642	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
PWP2	5822	hgsc.bcm.edu	37	21	45528919	45528919	+	Missense_Mutation	SNP	G	G	A	rs2020945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45528919G>A	ENST00000291576.7	+	2	200	c.73G>A	c.(73-75)Gat>Aat	p.D25N		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	25			D -> N (in dbSNP:rs2020945). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8661145, ECO:0000269|PubMed:8893822, ECO:0000269|PubMed:8973917, ECO:0000269|PubMed:9196060, ECO:0000269|Ref.7}.		signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		TTTTACCTGCGATGGAAATTC	0.373													G|||	2865	0.572085	0.2466	0.6729	5008	,	,		19909	0.6994		0.8201	False		,,,				2504	0.5542				p.D25N		Atlas-SNP	.											.	PWP2	64	.	0			c.G73A						PASS	.	G	ASN/ASP	1425,2981	462.3+/-353.2	236,953,1014	133.0	109.0	117.0		73	3.9	0.5	21	dbSNP_94	117	6948,1652	740.6+/-407.1	2826,1296,178	yes	missense	PWP2	NM_005049.2	23	3062,2249,1192	AA,AG,GG		19.2093,32.3423,35.622	benign	25/920	45528919	8373,4633	2203	4300	6503	SO:0001583	missense	5822	exon2			ACCTGCGATGGAA		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.73G>A	21.37:g.45528919G>A	ENSP00000291576:p.Asp25Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	1399	0.6405677655677655	127	0.258130081300813	253	0.6988950276243094	403	0.7045454545454546	616	0.8126649076517151	G	19.24	3.788775	0.70337	0.323423	0.807907	ENSG00000241945	ENST00000291576;ENST00000456705	T;T	0.66995	-0.24;1.06	4.75	3.87	0.44632	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.43923	1.385	0.21950	P	0.999457184	P	0.39940	0.696	B	0.25291	0.059	T	0.26538	-1.0100	9	0.45353	T	0.12	-3.7742	13.3146	0.60399	0.0778:0.0:0.9222:0.0	rs2020945;rs17851024;rs17858319;rs61711661;rs2020945	25	Q15269	PWP2_HUMAN	N	25	ENSP00000291576:D25N;ENSP00000411749:D25N	ENSP00000291576:D25N	D	+	1	0	PWP2	44353347	1.000000	0.71417	0.538000	0.28064	0.462000	0.32619	7.217000	0.77982	1.135000	0.42183	0.563000	0.77884	GAT	G|0.379;A|0.621	0.621	strong		0.373	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
COL3A1	1281	hgsc.bcm.edu	37	2	189859312	189859312	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:189859312G>A	ENST00000304636.3	+	19	1509	c.1339G>A	c.(1339-1341)Ggt>Agt	p.G447S	COL3A1_ENST00000317840.5_Missense_Mutation_p.G447S	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	447	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)	CGGACCACGTGGTGAACGCGT	0.393																																					p.G447S		Atlas-SNP	.											COL3A1,NS,malignant_melanoma,-1,1	COL3A1	292	1	0			c.G1339A						PASS	.						102.0	101.0	101.0					2																	189859312		2203	4300	6503	SO:0001583	missense	1281	exon19			CCACGTGGTGAAC	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.1339G>A	2.37:g.189859312G>A	ENSP00000304408:p.Gly447Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	122	36	0.295082	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	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907297	0.92107	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99607	-6.27;-6.27	6.17	6.17	0.99709	.	0.000000	0.52532	D	0.000067	D	0.99806	0.9916	H	0.96048	3.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97394	0.9991	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	447	P02461	CO3A1_HUMAN	S	447	ENSP00000304408:G447S;ENSP00000315243:G447S	ENSP00000304408:G447S	G	+	1	0	COL3A1	189567557	1.000000	0.71417	0.983000	0.44433	0.945000	0.59286	9.550000	0.98110	2.941000	0.99782	0.655000	0.94253	GGT	.	.	none		0.393	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
MAN2B2	23324	hgsc.bcm.edu	37	4	6606864	6606864	+	Missense_Mutation	SNP	A	A	G	rs2301788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:6606864A>G	ENST00000285599.3	+	11	1658	c.1622A>G	c.(1621-1623)aAc>aGc	p.N541S	MAN2B2_ENST00000504248.1_Missense_Mutation_p.N490S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	541			N -> S (in dbSNP:rs2301788). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.		mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CGGCACTACAACATCAGACCC	0.597													G|||	2683	0.535743	0.4871	0.5159	5008	,	,		17173	0.6151		0.495	False		,,,				2504	0.5757				p.N541S		Atlas-SNP	.											MAN2B2,NS,carcinoma,0,1	MAN2B2	80	1	0			c.A1622G						scavenged	.	G	SER/ASN	2158,2248	595.1+/-388.4	525,1108,570	105.0	107.0	106.0		1622	-1.5	0.0	4	dbSNP_100	106	4409,4191	569.8+/-389.3	1114,2181,1005	yes	missense	MAN2B2	NM_015274.1	46	1639,3289,1575	GG,GA,AA		48.7326,48.9787,49.5079	benign	541/1010	6606864	6567,6439	2203	4300	6503	SO:0001583	missense	23324	exon11			ACTACAACATCAG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1622A>G	4.37:g.6606864A>G	ENSP00000285599:p.Asn541Ser	Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	1157|1157	0.5297619047619048|0.5297619047619048	240|240	0.4878048780487805|0.4878048780487805	188|188	0.5193370165745856|0.5193370165745856	353|353	0.6171328671328671|0.6171328671328671	376|376	0.49604221635883905|0.49604221635883905	G|G	5.544|5.544	0.285181|0.285181	0.10513|0.10513	0.489787|0.489787	0.512674|0.512674	ENSG00000013288|ENSG00000013288	ENST00000285599;ENST00000504248|ENST00000505907	T;T|.	0.77750|.	-1.12;-1.12|.	4.28|4.28	-1.52|-1.52	0.08637|0.08637	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);|.	1.311970|.	0.04623|.	N|.	0.402386|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00707|0.00707	-1.245|-1.245	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|T	0.39251|0.39251	-0.9623|-0.9623	9|4	0.22109|.	T|.	0.4|.	-0.0112|-0.0112	3.2455|3.2455	0.06796|0.06796	0.462:0.1076:0.3222:0.1082|0.462:0.1076:0.3222:0.1082	rs2301788;rs52821833;rs59598692;rs2301788|rs2301788;rs52821833;rs59598692;rs2301788	490;541;541|.	E9PCD7;Q9Y2E5;Q9Y2E5-2|.	.;MA2B2_HUMAN;.|.	S|A	541;490|540	ENSP00000285599:N541S;ENSP00000423129:N490S|.	ENSP00000285599:N541S|.	N|T	+|+	2|1	0|0	MAN2B2|MAN2B2	6657765|6657765	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.038000|0.038000	0.13279|0.13279	-0.287000|-0.287000	0.08388|0.08388	-0.588000|-0.588000	0.05882|0.05882	-0.320000|-0.320000	0.08662|0.08662	AAC|ACA	A|0.484;G|0.516	0.516	strong		0.597	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
DLC1	10395	hgsc.bcm.edu	37	8	12958025	12958025	+	Silent	SNP	C	C	A	rs3739298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000520226.1_Silent_p.A96A|DLC1_ENST00000358919.2_Silent_p.A170A	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	21	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	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	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552067	32552067	+	Silent	SNP	C	C	T	rs17882603	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32552067C>T	ENST00000360004.5	-	2	294	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	63	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						CGGACTCCTCCTGGTTATAGA	0.607										Multiple Myeloma(14;0.17)			c|||	2521	0.503395	0.5038	0.6383	5008	,	,		9430	0.4583		0.5686	False		,,,				2504	0.3865				p.Q63Q		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G189A						PASS	.	T		1945,2439		480,985,727	35.0	33.0	34.0		189	-2.2	0.0	6	dbSNP_124	34	4031,4533		1094,1843,1345	no	coding-synonymous	HLA-DRB1	NM_002124.3		1574,2828,2072	TT,TC,CC		47.0691,44.3659,46.1538		63/267	32552067	5976,6972	2192	4282	6474	SO:0001819	synonymous_variant	3123	exon2			CTCCTCCTGGTTA	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.189G>A	6.37:g.32552067C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			C|0.548;T|0.452	0.452	strong		0.607	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FAM208A	23272	hgsc.bcm.edu	37	3	56658871	56658871	+	Missense_Mutation	SNP	T	T	C	rs2291498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56658871T>C	ENST00000493960.2	-	22	4313	c.4303A>G	c.(4303-4305)Ata>Gta	p.I1435V	FAM208A_ENST00000355628.5_Missense_Mutation_p.I1374V|FAM208A_ENST00000431842.2_Missense_Mutation_p.I998V|FAM208A_ENST00000485156.1_Intron	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1435			I -> V (in dbSNP:rs2291498). {ECO:0000269|PubMed:11149944}.				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						AAAAAGACTATGTGTCGTTGC	0.383													T|||	1464	0.292332	0.326	0.1744	5008	,	,		19153	0.377		0.1054	False		,,,				2504	0.4356				p.I1435V		Atlas-SNP	.											.	FAM208A	113	.	0			c.A4303G						PASS	.	T	VAL/ILE,VAL/ILE	1410,2996	460.9+/-352.8	228,954,1021	116.0	116.0	116.0		4303,2992	1.8	0.9	3	dbSNP_100	116	886,7714	198.9+/-243.1	48,790,3462	yes	missense,missense	FAM208A	NM_001112736.1,NM_015224.3	29,29	276,1744,4483	CC,CT,TT		10.3023,32.0018,17.6534	benign,benign	1435/1513,998/1234	56658871	2296,10710	2203	4300	6503	SO:0001583	missense	23272	exon22			AGACTATGTGTCG	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.4303A>G	3.37:g.56658871T>C	ENSP00000417509:p.Ile1435Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	239	95	0.39749	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	508	0.2326007326007326	168	0.34146341463414637	64	0.17679558011049723	206	0.36013986013986016	70	0.09234828496042216	T	6.411	0.443887	0.12164	0.320018	0.103023	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.46819	0.86;0.86;0.86	5.7	1.82	0.25136	.	0.162090	0.42420	N	0.000702	T	0.00012	0.0000	N	0.24115	0.695	0.45607	P	0.0014579999999999593	B;B;B;B	0.15473	0.003;0.007;0.012;0.013	B;B;B;B	0.17979	0.009;0.016;0.02;0.004	T	0.41556	-0.9502	9	0.13108	T	0.6	-2.097	5.6455	0.17586	0.1198:0.2551:0.0:0.6251	rs2291498;rs52804263;rs58959416;rs2291498	1435;1374;998;1435	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	V	998;1435;1374	ENSP00000399410:I998V;ENSP00000417509:I1435V;ENSP00000347845:I1374V	ENSP00000347845:I1374V	I	-	1	0	C3orf63	56633911	0.719000	0.27986	0.930000	0.37139	0.966000	0.64601	-0.123000	0.10611	0.982000	0.38575	0.533000	0.62120	ATA	T|0.785;C|0.215	0.215	strong		0.383	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
HOMEZ	57594	hgsc.bcm.edu	37	14	23745533	23745533	+	Missense_Mutation	SNP	C	C	T	rs10131813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23745533C>T	ENST00000357460.5	-	2	1068	c.904G>A	c.(904-906)Gcc>Acc	p.A302T	HOMEZ_ENST00000431326.2_Missense_Mutation_p.A304T|HOMEZ_ENST00000561013.1_Missense_Mutation_p.A304T	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	302				A -> T (in Ref. 5; AAI30393). {ECO:0000305}.	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)	p.A302T(1)		endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GGTTTAGAGGCGGCAGTAGCT	0.537																																					p.A302T		Atlas-SNP	.											HOMEZ_ENST00000357460,NS,carcinoma,0,3	HOMEZ	80	3	1	Substitution - Missense(1)	stomach(1)	c.G904A						PASS	.	C	THR/ALA	1556,2546		291,974,786	40.0	45.0	43.0		904	-2.6	1.0	14	dbSNP_119	43	3585,4767		752,2081,1343	yes	missense	HOMEZ	NM_020834.2	58	1043,3055,2129	TT,TC,CC		42.9239,37.9327,41.2799	benign	302/551	23745533	5141,7313	2051	4176	6227	SO:0001583	missense	57594	exon2			TAGAGGCGGCAGT	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.904G>A	14.37:g.23745533C>T	ENSP00000350049:p.Ala302Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	67	0.744444	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	756	0.34615384615384615	192	0.3902439024390244	105	0.2900552486187845	174	0.3041958041958042	285	0.3759894459102902	C	0.005	-2.212362	0.00289	0.379327	0.429239	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.20738	2.05;2.05	6.04	-2.58	0.06228	.	0.255590	0.39687	N	0.001291	T	0.00012	0.0000	N	0.01576	-0.805	0.48632	P	3.1400000000003647E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37454	-0.9705	9	0.02654	T	1	-8.6359	6.3652	0.21451	0.1417:0.4002:0.0:0.4581	rs10131813;rs17846379;rs17859416;rs52832578;rs59669643;rs10131813	304;302	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	T	302;304	ENSP00000350049:A302T;ENSP00000406579:A304T	ENSP00000350049:A302T	A	-	1	0	HOMEZ	22815373	0.961000	0.32948	0.955000	0.39395	0.034000	0.12701	0.194000	0.17135	-0.248000	0.09583	-1.155000	0.01812	GCC	C|0.636;N|0.001	.	strong		0.537	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
SPINK5	11005	hgsc.bcm.edu	37	5	147499616	147499616	+	Silent	SNP	C	C	T	rs17704908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:147499616C>T	ENST00000256084.7	+	25	2400	c.2358C>T	c.(2356-2358)ctC>ctT	p.L786L	SPINK5_ENST00000398454.1_Silent_p.L786L|SPINK5_ENST00000359874.3_Silent_p.L786L	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	786	Kazal-like 12. {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)			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)			ATGGAAAACTCATCTGCACTC	0.378													T|||	2441	0.48742	0.3139	0.6311	5008	,	,		20079	0.4821		0.5915	False		,,,				2504	0.5184				p.L786L		Atlas-SNP	.											.	SPINK5	245	.	0			c.C2358T						PASS	.	T	,,	1379,2315		249,881,717	79.0	70.0	73.0		2358,2358,2358	-2.0	0.0	5	dbSNP_123	73	5039,3149		1525,1989,580	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1774,2870,1297	TT,TC,CC		38.4587,37.3308,45.9855	,,	786/1095,786/917,786/1065	147499616	6418,5464	1847	4094	5941	SO:0001819	synonymous_variant	11005	exon25			AAAACTCATCTGC	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.2358C>T	5.37:g.147499616C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			C|0.489;T|0.511	0.511	strong		0.378	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
RPL3L	6123	hgsc.bcm.edu	37	16	1996629	1996629	+	Silent	SNP	C	C	T	rs74930354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1996629C>T	ENST00000268661.7	-	7	1042	c.948G>A	c.(946-948)ccG>ccA	p.P316P		NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	316					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)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						GCCTCACCAGCGGTGTGATGG	0.637													C|||	231	0.0461262	0.0726	0.0303	5008	,	,		19745	0.0069		0.0189	False		,,,				2504	0.09				p.P316P		Atlas-SNP	.											.	RPL3L	42	.	0			c.G948A						PASS	.	C		214,4184	129.8+/-166.5	3,208,1988	46.0	45.0	46.0		948	-9.1	0.0	16	dbSNP_131	46	194,8404	82.9+/-145.4	5,184,4110	no	coding-synonymous	RPL3L	NM_005061.2		8,392,6098	TT,TC,CC		2.2563,4.8658,3.1394		316/408	1996629	408,12588	2199	4299	6498	SO:0001819	synonymous_variant	6123	exon7			CACCAGCGGTGTG	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.948G>A	16.37:g.1996629C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_005061		Silent	SNP	ENST00000268661.7	37	CCDS10450.1																																																																																			C|0.970;T|0.030	0.030	strong		0.637	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
MYO3A	53904	hgsc.bcm.edu	37	10	26385578	26385578	+	Silent	SNP	G	G	A	rs41279908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:26385578G>A	ENST00000265944.5	+	17	1909	c.1743G>A	c.(1741-1743)gaG>gaA	p.E581E	MYO3A_ENST00000543632.1_Silent_p.E581E	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	581	Myosin motor.				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)			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						AATTAATTGAGCAATGTTTCA	0.299													G|||	287	0.0573083	0.0651	0.0706	5008	,	,		14714	0.004		0.1223	False		,,,				2504	0.0256				p.E581E		Atlas-SNP	.											.	MYO3A	371	.	0			c.G1743A						PASS	.	G		362,4042	176.6+/-205.7	12,338,1852	82.0	92.0	88.0		1743	2.1	1.0	10	dbSNP_127	88	1014,7582	213.6+/-253.5	61,892,3345	no	coding-synonymous	MYO3A	NM_017433.4		73,1230,5197	AA,AG,GG		11.7962,8.2198,10.5846		581/1617	26385578	1376,11624	2202	4298	6500	SO:0001819	synonymous_variant	53904	exon17			AATTGAGCAATGT	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.1743G>A	10.37:g.26385578G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			G|0.909;A|0.091	0.091	strong		0.299	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
PTPRQ	374462	hgsc.bcm.edu	37	12	80900348	80900348	+	Splice_Site	SNP	T	T	G	rs7965277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	27	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	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
CFAP74	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	IGR	SNP	G	G	A	rs28575980	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1887245G>A								TMEM52 (36533 upstream) : C1orf222 (32317 downstream)																							AGCTGGTGGCGGCTTTGTCAT	0.562													G|||	908	0.18131	0.1044	0.219	5008	,	,		17542	0.2292		0.2316	False		,,,				2504	0.1575				p.A687A		Atlas-SNP	.											KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	0			c.C2061T						PASS	.	G		517,3601		38,441,1580	44.0	48.0	47.0		2061	-1.6	0.0	1	dbSNP_125	47	2075,6339		258,1559,2390	no	coding-synonymous	KIAA1751	NM_001080484.1		296,2000,3970	AA,AG,GG		24.6613,12.5546,20.6831		687/763	1887245	2592,9940	2059	4207	6266	SO:0001628	intergenic_variant	85452	exon18			GGTGGCGGCTTTG																													1.37:g.1887245G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_001080484		Silent	SNP		37		480	0.21978021978021978	59	0.11991869918699187	82	0.2265193370165746	159	0.27797202797202797	180	0.23746701846965698	G	3.005	-0.205185	0.06180	0.125546	0.246613	ENSG00000142609	ENST00000493316	.	.	.	2.8	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.35724	-0.9777	3	.	.	.	-1.4405	5.1203	0.14856	0.3205:0.1589:0.5206:0.0	rs28575980;rs61496843	.	.	.	L	93	.	.	P	-	2	0	C1orf222	1877105	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.129000	0.15830	-0.723000	0.04915	-1.119000	0.02030	CCG	G|0.777;A|0.223	0.223	strong	0	0.562								
TRABD2B	388630	hgsc.bcm.edu	37	1	48459907	48459907	+	Silent	SNP	C	C	T	rs3814006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:48459907C>T	ENST00000606738.2	-	2	570	c.465G>A	c.(463-465)gcG>gcA	p.A155A	TRABD2B_ENST00000435576.2_5'Flank	NM_001194986.1	NP_001181915.1	A6NFA1	TIKI2_HUMAN	TraB domain containing 2B	155					metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|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)										CCCAGTTGCCCGCGATGGCAT	0.612													C|||	830	0.165735	0.0144	0.2233	5008	,	,		19246	0.253		0.2793	False		,,,				2504	0.1227				p.A155A		Atlas-SNP	.											RP11-543D5.3,NS,carcinoma,0,1	.	.	1	0			c.G465A						PASS	.																																			SO:0001819	synonymous_variant	388630	exon2			GTTGCCCGCGATG		CCDS58000.1	1p33	2012-07-04			ENSG00000204018				44200	protein-coding gene	gene with protein product		614913					Standard	NM_001194986		Approved		uc021ong.1	A6NFA1	OTTHUMG00000007960	ENST00000606738.2:c.465G>A	1.37:g.48459907C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_001194986	I6U4Y0	Silent	SNP	ENST00000606738.2	37	CCDS58000.1																																																																																			C|0.817;T|0.183	0.183	strong		0.612	TRABD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021842.3	NM_001194986	
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161132777G>A	ENST00000289865.8	+	6	1183	c.962G>A	c.(961-963)gGc>gAc	p.G321D	USP21_ENST00000368002.3_Missense_Mutation_p.G321D|USP21_ENST00000368001.1_Missense_Mutation_p.G321D	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	321	USP.		G -> D (in dbSNP:rs17356051).		histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AACCGCCGAGGCCGCCGGGCT	0.582													G|||	107	0.0213658	0.0008	0.0231	5008	,	,		16906	0.0		0.0746	False		,,,				2504	0.0153				p.G321D		Atlas-SNP	.											.	USP21	63	.	0			c.G962A						PASS	.	G	ASP/GLY,ASP/GLY	46,4360	46.7+/-81.2	0,46,2157	56.0	64.0	61.0		962,962	3.8	1.0	1	dbSNP_123	61	504,8096	143.9+/-199.8	11,482,3807	yes	missense,missense	USP21	NM_001014443.2,NM_012475.4	94,94	11,528,5964	AA,AG,GG		5.8605,1.044,4.2288	possibly-damaging,possibly-damaging	321/566,321/566	161132777	550,12456	2203	4300	6503	SO:0001583	missense	27005	exon6			GCCGAGGCCGCCG	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.962G>A	1.37:g.161132777G>A	ENSP00000289865:p.Gly321Asp	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	66	0.03021978021978022	0	0.0	11	0.03038674033149171	0	0.0	55	0.07255936675461741	G	15.82	2.945230	0.53079	0.01044	0.058605	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.29917	1.55;1.55;1.55	4.72	3.8	0.43715	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.377030	0.03429	U	0.207571	T	0.29355	0.0731	L	0.41079	1.255	0.41560	D	0.988622	D	0.76494	0.999	D	0.67231	0.95	T	0.47071	-0.9145	10	0.10111	T	0.7	.	12.152	0.54055	0.0853:0.0:0.9147:0.0	rs17356051	321	Q9UK80	UBP21_HUMAN	D	321	ENSP00000356981:G321D;ENSP00000289865:G321D;ENSP00000356980:G321D	ENSP00000289865:G321D	G	+	2	0	USP21	159399401	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.474000	0.53129	1.202000	0.43218	0.455000	0.32223	GGC	G|0.960;A|0.040	0.040	strong		0.582	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
IGFN1	91156	hgsc.bcm.edu	37	1	201166383	201166383	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs4915221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201166383G>A	ENST00000295591.8	+	0	435				IGFN1_ENST00000451870.2_Missense_Mutation_p.R102H|IGFN1_ENST00000335211.4_Missense_Mutation_p.R102H			Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1							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						GATCTGTACCGCTGCACAGCA	0.547													g|||	3669	0.732628	0.8101	0.5735	5008	,	,		22538	0.8562		0.5547	False		,,,				2504	0.7965				p.R102H		Atlas-SNP	.											.	IGFN1	220	.	0			c.G305A						PASS	.	A	HIS/ARG	1065,319		406,253,33	146.0	135.0	138.0		305	3.2	1.0	1	dbSNP_111	138	1812,1370		519,774,298	yes	missense	IGFN1	NM_001164586.1	29	925,1027,331	AA,AG,GG		43.0547,23.0491,36.9908		102/3709	201166383	2877,1689	692	1591	2283			91156	exon5			TGTACCGCTGCAC	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	ENST00000295591.8:c.-8216G>A	1.37:g.201166383G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000295591.8	37		1519	0.6955128205128205	387	0.7865853658536586	212	0.585635359116022	493	0.8618881118881119	427	0.5633245382585752	g	13.61	2.290057	0.40494	0.769509	0.569453	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.44083	0.93;0.93	5.04	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	M	0.68952	2.095	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.10941	-1.0608	6	0.32370	T	0.25	.	7.9743	0.30145	0.1909:0.0:0.8091:0.0	rs4915221;rs17461911;rs52829174;rs56471819;rs60470802;rs4915221	.	.	.	H	102	ENSP00000334714:R102H;ENSP00000398386:R102H	ENSP00000334714:R102H	R	+	2	0	IGFN1	199433006	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	0.498000	0.22530	0.545000	0.28902	-1.004000	0.02495	CGC	G|0.289;A|0.710	0.710	strong		0.547	IGFN1-201	KNOWN	basic	protein_coding	protein_coding		NM_178275	
APC	324	hgsc.bcm.edu	37	5	112162854	112162854	+	Silent	SNP	T	T	C	rs2229992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112162854T>C	ENST00000457016.1	+	12	1838	c.1458T>C	c.(1456-1458)taT>taC	p.Y486Y	APC_ENST00000508376.2_Silent_p.Y486Y|CTC-554D6.1_ENST00000520401.1_5'Flank|APC_ENST00000257430.4_Silent_p.Y486Y			P25054	APC_HUMAN	adenomatous polyposis coli	486	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTGAAATGTATGGGCTTACTA	0.368		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			T|||	2554	0.509984	0.1619	0.6671	5008	,	,		17461	0.6647		0.5795	False		,,,				2504	0.638				p.Y486Y	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,colon,carcinoma,0,1	APC	4158	1	1	Unknown(1)	skin(1)	c.T1458C	GRCh37	CM990152	APC	M	rs2229992	PASS	.	T	,,	934,3470	356.6+/-313.6	103,728,1371	131.0	117.0	122.0	http://omim.org/entry/114500	1458,1458,1404	0.7	1.0	5	dbSNP_98	122	5076,3524	632.0+/-398.6	1516,2044,740	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1619,2772,2111	CC,CT,TT		40.9767,21.208,46.2165	,,	486/2844,486/2844,468/2826	112162854	6010,6994	2202	4300	6502	SO:0001819	synonymous_variant	324	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AATGTATGGGCTT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1458T>C	5.37:g.112162854T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			A|0.002;C|0.475	0.475	strong		0.368	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
CTDP1	9150	hgsc.bcm.edu	37	18	77475455	77475455	+	Silent	SNP	G	G	A	rs11549119	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	23	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	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	
RP1L1	94137	hgsc.bcm.edu	37	8	10465097	10465097	+	Missense_Mutation	SNP	C	C	T	rs4354268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	92	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	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		
NAA60	79903	hgsc.bcm.edu	37	16	3533577	3533577	+	Silent	SNP	C	C	G	rs1137454	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:3533577C>G	ENST00000407558.4	+	6	855	c.552C>G	c.(550-552)ggC>ggG	p.G184G	NAA60_ENST00000572942.1_Intron|NAA60_ENST00000570551.1_3'UTR|LA16c-306E5.3_ENST00000574423.2_RNA|NAA60_ENST00000570819.1_Intron|NAA60_ENST00000424546.2_Silent_p.G191G|NAA60_ENST00000577013.1_Intron|NAA60_ENST00000610180.1_Silent_p.G184G|NAA60_ENST00000576916.1_Intron|NAA60_ENST00000575076.1_Silent_p.G184G|NAA60_ENST00000608993.1_Silent_p.G119G|NAA60_ENST00000360862.5_Silent_p.G119G|NAA60_ENST00000421765.3_Intron|NAA60_ENST00000572584.1_Silent_p.G184G|NAA60_ENST00000573580.1_Silent_p.G119G|NAA60_ENST00000414063.2_Silent_p.G184G|NAA60_ENST00000608722.1_Silent_p.G184G			Q9H7X0	NAA60_HUMAN	N(alpha)-acetyltransferase 60, NatF catalytic subunit	184					cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|histone H4 acetylation (GO:0043967)|N-terminal peptidyl-methionine acetylation (GO:0017196)|nucleosome assembly (GO:0006334)	Golgi membrane (GO:0000139)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)	7						TCAACGGCGGCCACCCTCCCT	0.517													C|||	3583	0.715455	0.77	0.6888	5008	,	,		18750	0.7411		0.67	False		,,,				2504	0.681				p.G184G		Atlas-SNP	.											.	NAA60	21	.	0			c.C552G						PASS	.	C	,,	2989,915		1142,705,105	90.0	90.0	90.0		552,552,552	3.3	1.0	16	dbSNP_86	90	5636,2664		1925,1786,439	no	coding-synonymous,coding-synonymous,coding-synonymous	NAA60	NM_001083600.1,NM_001083601.1,NM_024845.2	,,	3067,2491,544	GG,GC,CC		32.0964,23.4375,29.3265	,,	184/243,184/243,184/243	3533577	8625,3579	1952	4150	6102	SO:0001819	synonymous_variant	79903	exon5			CGGCGGCCACCCT		CCDS45396.1	16p13.3	2012-07-13	2011-08-02	2011-08-02	ENSG00000122390	ENSG00000122390	2.3.1.48, 2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	25875	protein-coding gene	gene with protein product		614246	"""N-acetyltransferase 15 (GCN5-related, putative)"""	NAT15		12975309, 21750686	Standard	NM_001083600		Approved	FLJ14154	uc010btm.3	Q9H7X0	OTTHUMG00000150268	ENST00000407558.4:c.552C>G	16.37:g.3533577C>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_001083600	B3KRQ0|B4DLZ0|B4DPZ8|B4DYC4|D3DUC2|E7EQ65|Q6IA31|Q6UX26	Silent	SNP	ENST00000407558.4	37	CCDS45396.1																																																																																			C|0.294;G|0.706	0.706	strong		0.517	NAA60-001	KNOWN	NMD_exception|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317235.2	NM_024845	
UGT2B17	7367	hgsc.bcm.edu	37	4	69417570	69417570	+	Silent	SNP	A	A	G	rs28374627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69417570A>G	ENST00000317746.2	-	4	1107	c.1065T>C	c.(1063-1065)taT>taC	p.Y355Y		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	355					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	GTAACCACTTATACAGTCGAG	0.348													G|||	2992	0.597444	0.3563	0.5274	5008	,	,		7632	0.7897		0.7296	False		,,,				2504	0.6391				p.Y355Y	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.T1065C						PASS	.	G		1633,2543		532,569,987	96.0	84.0	88.0		1065	-1.2	0.0	4	dbSNP_125	88	5142,2692		2121,900,896	no	coding-synonymous	UGT2B17	NM_001077.3		2653,1469,1883	GG,GA,AA		34.363,39.1044,43.5887		355/531	69417570	6775,5235	2088	3917	6005	SO:0001819	synonymous_variant	7367	exon4			CCACTTATACAGT	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1065T>C	4.37:g.69417570A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	278	128	0.460432	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			.	.	weak		0.348	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
MUC16	94025	hgsc.bcm.edu	37	19	9015351	9015351	+	Missense_Mutation	SNP	G	G	A	rs201449501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9015351G>A	ENST00000397910.4	-	30	38440	c.38237C>T	c.(38236-38238)cCt>cTt	p.P12746L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12748	SEA 5. {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						AGAGTACAGAGGGCCAACACT	0.512													-|||	7	0.00139776	0.0008	0.0	5008	,	,		20370	0.003		0.001	False		,,,				2504	0.002				p.P12746L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38237T						PASS	.	G	LEU/PRO	0,4000		0,0,2000	153.0	130.0	137.0		38237	-1.6	0.0	19	dbSNP_134	137	4,8338		0,4,4167	no	missense	MUC16	NM_024690.2	98	0,4,6167	AA,AG,GG		0.048,0.0,0.0324	possibly-damaging	12746/14508	9015351	4,12338	2000	4171	6171	SO:0001583	missense	94025	exon30			TACAGAGGGCCAA	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.38237C>T	19.37:g.9015351G>A	ENSP00000381008:p.Pro12746Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	18	0.160714	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	10.49	1.365631	0.24684	0.0	4.8E-4	ENSG00000181143	ENST00000397910	T	0.38077	1.16	2.82	-1.58	0.08479	.	.	.	.	.	T	0.39759	0.1090	.	.	.	.	.	.	P	0.50710	0.938	P	0.50270	0.636	T	0.52419	-0.8578	7	0.87932	D	0	.	8.0693	0.30680	0.0:0.0:0.3447:0.6553	.	12746	B5ME49	.	L	12746	ENSP00000381008:P12746L	ENSP00000381008:P12746L	P	-	2	0	MUC16	8876351	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.413000	0.21148	-0.376000	0.07943	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	weak		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
UNC5B	219699	hgsc.bcm.edu	37	10	73046625	73046625	+	Splice_Site	SNP	C	C	T	rs7069294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:73046625C>T	ENST00000335350.6	+	5	1148	c.732C>T	c.(730-732)taC>taT	p.Y244Y	UNC5B_ENST00000373192.4_Splice_Site_p.Y244Y	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	244					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						TCATCGTCTACGGTGCGGGCC	0.657													C|||	393	0.0784744	0.0726	0.1138	5008	,	,		20286	0.0675		0.0507	False		,,,				2504	0.1012				p.Y244Y		Atlas-SNP	.											.	UNC5B	123	.	0			c.C732T						PASS	.	C		326,4080	173.4+/-203.2	8,310,1885	104.0	101.0	102.0		732	-7.6	0.9	10	dbSNP_116	102	415,8185	129.8+/-187.9	11,393,3896	yes	coding-synonymous-near-splice	UNC5B	NM_170744.4		19,703,5781	TT,TC,CC		4.8256,7.399,5.6974		244/946	73046625	741,12265	2203	4300	6503	SO:0001630	splice_region_variant	219699	exon5			CGTCTACGGTGCG	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.733+1C>T	10.37:g.73046625C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			C|0.942;T|0.058	0.058	strong		0.657	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	Silent
TPRX1	284355	hgsc.bcm.edu	37	19	48305651	48305651	+	Missense_Mutation	SNP	G	G	A	rs62130758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48305651G>A	ENST00000322175.3	-	2	772	c.617C>T	c.(616-618)cCg>cTg	p.P206L	TPRX1_ENST00000543508.1_Missense_Mutation_p.P196L|TPRX1_ENST00000535759.1_Missense_Mutation_p.P303L	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	206	Gly-rich.			P -> L (in Ref. 1; BAC05130). {ECO:0000305}.		nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctgggatcgggcctgggat	0.677													G|||	1483	0.296126	0.4561	0.2104	5008	,	,		13150	0.2123		0.2177	False		,,,				2504	0.3078				p.P206L	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C617T						PASS	.	G	LEU/PRO	1202,2398		185,832,783	13.0	10.0	11.0		617	-0.8	0.0	19	dbSNP_129	11	1235,5609		116,1003,2303	no	missense	TPRX1	NM_198479.2	98	301,1835,3086	AA,AG,GG		18.045,33.3889,23.334	possibly-damaging	206/412	48305651	2437,8007	1800	3422	5222	SO:0001583	missense	284355	exon2			GGGATCGGGCCTG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.617C>T	19.37:g.48305651G>A	ENSP00000323455:p.Pro206Leu	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	513	0.2348901098901099	178	0.3617886178861789	78	0.2154696132596685	106	0.1853146853146853	151	0.19920844327176782	-	5.425	0.263536	0.10294	0.333889	0.18045	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.66099	-0.19;-0.19;-0.19	0.401	-0.802	0.10889	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.40197	0.706	B	0.22753	0.041	T	0.30966	-0.9960	7	0.72032	D	0.01	.	.	.	.	rs62130758	206	Q8N7U7	TPRX1_HUMAN	L	206;303;196	ENSP00000323455:P206L;ENSP00000438832:P303L;ENSP00000438712:P196L	ENSP00000323455:P206L	P	-	2	0	TPRX1	52997463	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.060000	0.11712	-0.483000	0.06772	-0.485000	0.04761	CCG	G|0.764;A|0.236	0.236	strong		0.677	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
TTC37	9652	hgsc.bcm.edu	37	5	94861118	94861118	+	Missense_Mutation	SNP	G	G	C	rs17084873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:94861118G>C	ENST00000358746.2	-	15	1607	c.1309C>G	c.(1309-1311)Cta>Gta	p.L437V		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	437			L -> V (in dbSNP:rs17084873).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						TCTGCTTGTAGATAGTCCTTT	0.343													G|||	1211	0.241813	0.4228	0.1772	5008	,	,		16642	0.12		0.1779	False		,,,				2504	0.2342				p.L437V		Atlas-SNP	.											.	TTC37	128	.	0			c.C1309G						PASS	.	G	VAL/LEU	1710,2694	512.2+/-368.0	347,1016,839	92.0	101.0	98.0		1309	3.9	1.0	5	dbSNP_123	98	1410,7190	271.1+/-289.3	129,1152,3019	yes	missense	TTC37	NM_014639.3	32	476,2168,3858	CC,CG,GG		16.3953,38.8283,23.9926	benign	437/1565	94861118	3120,9884	2202	4300	6502	SO:0001583	missense	9652	exon15			CTTGTAGATAGTC	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.1309C>G	5.37:g.94861118G>C	ENSP00000351596:p.Leu437Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	167	73	0.437126	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	464	0.21245421245421245	185	0.37601626016260165	71	0.19613259668508287	72	0.1258741258741259	136	0.17941952506596306	G	7.515	0.655409	0.14580	0.388283	0.163953	ENSG00000198677	ENST00000358746;ENST00000514952	T;T	0.76060	0.31;-0.99	5.68	3.87	0.44632	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.623141	0.16503	N	0.211579	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.10296	0.002;0.003	B;B	0.11329	0.004;0.006	T	0.27673	-1.0067	9	0.39692	T	0.17	.	5.5873	0.17281	0.2238:0.315:0.4612:0.0	rs17084873;rs17084873	389;437	D6RCE2;Q6PGP7	.;TTC37_HUMAN	V	437;389	ENSP00000351596:L437V;ENSP00000423742:L389V	ENSP00000351596:L437V	L	-	1	2	TTC37	94886874	0.760000	0.28428	0.992000	0.48379	0.929000	0.56500	1.085000	0.30840	0.727000	0.32360	0.561000	0.74099	CTA	G|0.773;C|0.227	0.227	strong		0.343	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
FASTKD1	79675	hgsc.bcm.edu	37	2	170417031	170417031	+	Silent	SNP	T	T	C	rs35933910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170417031T>C	ENST00000453153.2	-	5	1183	c.837A>G	c.(835-837)caA>caG	p.Q279Q	FASTKD1_ENST00000453929.2_Silent_p.Q279Q	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	279					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AACTATTAAATTGTAGAAATT	0.284													T|||	175	0.0349441	0.0008	0.0086	5008	,	,		16183	0.1111		0.0288	False		,,,				2504	0.0276				p.Q279Q		Atlas-SNP	.											.	FASTKD1	86	.	0			c.A837G						PASS	.	T		30,4334		0,30,2152	47.0	54.0	51.0		837	-0.8	1.0	2	dbSNP_126	51	297,8277		3,291,3993	no	coding-synonymous	FASTKD1	NM_024622.3		3,321,6145	CC,CT,TT		3.464,0.6874,2.5274		279/848	170417031	327,12611	2182	4287	6469	SO:0001819	synonymous_variant	79675	exon5			ATTAAATTGTAGA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.837A>G	2.37:g.170417031T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			T|0.967;C|0.033	0.033	strong		0.284	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
AGBL2	79841	hgsc.bcm.edu	37	11	47712213	47712213	+	Missense_Mutation	SNP	C	C	T	rs7941404	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:47712213C>T	ENST00000525123.1	-	10	1331	c.1046G>A	c.(1045-1047)cGc>cAc	p.R349H	AGBL2_ENST00000298861.4_Missense_Mutation_p.R349H|AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000357610.3_Missense_Mutation_p.R349H|AGBL2_ENST00000528244.1_Missense_Mutation_p.R311H	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	349			R -> H (in dbSNP:rs7941404).			cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						GCCAATATTGCGGGTGTTGGC	0.468													C|||	195	0.0389377	0.0061	0.0648	5008	,	,		20653	0.0		0.1252	False		,,,				2504	0.0164				p.R349H		Atlas-SNP	.											AGBL2,caecum,carcinoma,-1,1	AGBL2	73	1	0			c.G1046A						scavenged	.	C	HIS/ARG	126,4276	92.5+/-131.2	1,124,2076	137.0	130.0	132.0		1046	-0.4	0.0	11	dbSNP_116	132	1191,7405	243.2+/-272.9	80,1031,3187	yes	missense	AGBL2	NM_024783.3	29	81,1155,5263	TT,TC,CC		13.8553,2.8623,10.1323	benign	349/903	47712213	1317,11681	2201	4298	6499	SO:0001583	missense	79841	exon10			ATATTGCGGGTGT		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1046G>A	11.37:g.47712213C>T	ENSP00000435582:p.Arg349His	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	121	0.0554029304029304	2	0.0040650406504065045	26	0.0718232044198895	0	0.0	93	0.12269129287598944	C	0.040	-1.287887	0.01387	0.028623	0.138553	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244;ENST00000532595	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.72	-0.361	0.12564	.	1.009670	0.07907	N	0.973673	T	0.00109	0.0003	N	0.05383	-0.06	0.80722	P	0.0	B;B	0.11235	0.001;0.004	B;B	0.06405	0.002;0.002	T	0.34079	-0.9843	9	0.02654	T	1	-4.9958	10.9986	0.47591	0.0:0.4528:0.0:0.5472	rs7941404;rs52838057;rs56962476;rs7941404	311;349	F6U0I4;Q5U5Z8	.;CBPC2_HUMAN	H	349;349;349;311;293	ENSP00000435582:R349H;ENSP00000350228:R349H;ENSP00000298861:R349H;ENSP00000436630:R311H;ENSP00000436063:R293H	ENSP00000298861:R349H	R	-	2	0	AGBL2	47668789	0.000000	0.05858	0.001000	0.08648	0.432000	0.31715	-0.368000	0.07543	-0.086000	0.12550	-0.302000	0.09304	CGC	C|0.916;T|0.084	0.084	strong		0.468	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
FLG	2312	hgsc.bcm.edu	37	1	152278689	152278689	+	Silent	SNP	C	C	A	rs57672167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152278689C>A	ENST00000368799.1	-	3	8708	c.8673G>T	c.(8671-8673)gtG>gtT	p.V2891V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2891	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)			TGTCCTGGCTCACACTGGATC	0.552									Ichthyosis				A|||	1985	0.396366	0.3147	0.4337	5008	,	,		31121	0.6101		0.171	False		,,,				2504	0.4918				p.V2891V		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.G8673T						PASS	.	A		847,3219		243,361,1429	85.0	137.0	120.0		8673	-5.2	0.0	1	dbSNP_129	120	1434,7156		126,1182,2987	no	coding-synonymous	FLG	NM_002016.1		369,1543,4416	AA,AC,CC		16.6938,20.8313,18.0231		2891/4062	152278689	2281,10375	2033	4295	6328	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGCTCACACTG	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.8673G>T	1.37:g.152278689C>A		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	537	399	0.743017	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			C|0.688;A|0.312	0.312	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CFAP46	54777	hgsc.bcm.edu	37	10	134735672	134735672	+	Silent	SNP	A	A	G	rs7915371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:134735672A>G	ENST00000368586.5	-	13	1642	c.1542T>C	c.(1540-1542)aaT>aaC	p.N514N	TTC40_ENST00000368582.2_Silent_p.N514N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCAGGCCTGCATTCACCAGGA	0.572													G|||	2678	0.534744	0.6558	0.6081	5008	,	,		18661	0.3542		0.4712	False		,,,				2504	0.5706				p.N514N		Atlas-SNP	.											.	TTC40	100	.	0			c.T1542C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon13			GCCTGCATTCACC																												ENST00000368586.5:c.1542T>C	10.37:g.134735672A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.515;G|0.485	0.485	strong		0.572	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
E2F2	1870	hgsc.bcm.edu	37	1	23847464	23847464	+	Missense_Mutation	SNP	C	C	A	rs2075995	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23847464C>A	ENST00000361729.2	-	4	1104	c.678G>T	c.(676-678)caG>caT	p.Q226H	E2F2_ENST00000487237.1_5'Flank	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	226	Dimerization. {ECO:0000255}.		Q -> H (in dbSNP:rs2075995). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		TCTGGATGAGCTGGTCCAAGG	0.577													C|||	1779	0.355232	0.062	0.4092	5008	,	,		15948	0.5992		0.5089	False		,,,				2504	0.3037				p.Q226H		Atlas-SNP	.											E2F2,colon,carcinoma,-2,1	E2F2	31	1	0			c.G678T						PASS	.	C	HIS/GLN	564,3842	250.0+/-257.2	40,484,1679	112.0	101.0	105.0		678	5.1	1.0	1	dbSNP_96	105	4324,4276	579.2+/-390.8	1079,2166,1055	yes	missense	E2F2	NM_004091.3	24	1119,2650,2734	AA,AC,CC		49.7209,12.8007,37.5827	probably-damaging	226/438	23847464	4888,8118	2203	4300	6503	SO:0001583	missense	1870	exon4			GATGAGCTGGTCC	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.678G>T	1.37:g.23847464C>A	ENSP00000355249:p.Gln226His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	926	0.423992673992674	32	0.06504065040650407	136	0.3756906077348066	367	0.6416083916083916	391	0.5158311345646438	C	14.92	2.679578	0.47886	0.128007	0.502791	ENSG00000007968	ENST00000361729	D	0.85556	-2.0	5.97	5.06	0.68205	.	0.171574	0.45867	D	0.000332	T	0.00012	0.0000	L	0.54323	1.7	0.26452	P	0.9755961	D	0.59357	0.985	P	0.51415	0.669	T	0.50988	-0.8762	9	0.24483	T	0.36	-21.0358	14.1362	0.65289	0.0:0.9271:0.0:0.0729	rs2075995;rs2228221;rs3218171;rs17846515;rs17859587;rs57250008;rs2075995	226	Q14209	E2F2_HUMAN	H	226	ENSP00000355249:Q226H	ENSP00000355249:Q226H	Q	-	3	2	E2F2	23720051	0.943000	0.32029	1.000000	0.80357	0.981000	0.71138	0.027000	0.13621	1.521000	0.48983	0.655000	0.94253	CAG	C|0.614;A|0.386	0.386	strong		0.577	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974370	22974370	+	Silent	SNP	G	G	A	rs151239314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22974370G>A	ENST00000356864.3	+	5	1138	c.606G>A	c.(604-606)ccG>ccA	p.P202P	TNFRSF10C_ENST00000540813.1_Silent_p.P100P	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	202					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)		CCACCAGCCCGGGGACTCCTG	0.642																																					p.P202P		Atlas-SNP	.											TNFRSF10C,colon,carcinoma,0,2	TNFRSF10C	30	2	0			c.G606A						scavenged	.						57.0	72.0	67.0					8																	22974370		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.606G>A	8.37:g.22974370G>A		Somatic	104	7	0.0673077		WXS	Illumina HiSeq	Phase_I	98	13	0.132653	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			G|0.882;A|0.118	0.118	strong		0.642	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
CRELD2	79174	hgsc.bcm.edu	37	22	50313438	50313438	+	Silent	SNP	T	T	C	rs9616388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50313438T>C	ENST00000328268.4	+	3	347	c.273T>C	c.(271-273)aaT>aaC	p.N91N	CRELD2_ENST00000403427.3_Silent_p.N91N|CRELD2_ENST00000404488.3_Silent_p.N91N|CRELD2_ENST00000407217.3_Silent_p.N91N|ALG12_ENST00000330817.6_5'Flank	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	91						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)	p.N91N(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TCGAATGCAATCAGATGCTAG	0.562													C|||	1251	0.2498	0.3994	0.1354	5008	,	,		18561	0.1052		0.1978	False		,,,				2504	0.3313				p.N91N		Atlas-SNP	.											CRELD2_ENST00000404488,NS,carcinoma,0,3	CRELD2	57	3	1	Substitution - coding silent(1)	stomach(1)	c.T273C						PASS	.	C	,	1526,2876	658.8+/-400.5	263,1000,938	40.0	41.0	41.0		273,273	3.2	0.7	22	dbSNP_119	41	1682,6918	730.4+/-406.8	176,1330,2794	no	coding-synonymous,coding-synonymous	CRELD2	NM_001135101.1,NM_024324.3	,	439,2330,3732	CC,CT,TT		19.5581,34.6661,24.6731	,	91/403,91/354	50313438	3208,9794	2201	4300	6501	SO:0001819	synonymous_variant	79174	exon3			ATGCAATCAGATG	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.273T>C	22.37:g.50313438T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Silent	SNP	ENST00000328268.4	37	CCDS14082.1																																																																																			T|0.754;C|0.246	0.246	strong		0.562	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
CKAP2	26586	hgsc.bcm.edu	37	13	53035665	53035665	+	Missense_Mutation	SNP	T	T	A	rs35975899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:53035665T>A	ENST00000378037.5	+	4	797	c.707T>A	c.(706-708)aTg>aAg	p.M236K	CKAP2_ENST00000378034.3_Missense_Mutation_p.M235K|CKAP2_ENST00000490903.1_Missense_Mutation_p.M187K|CKAP2_ENST00000258607.5_Missense_Mutation_p.M235K	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		TCCTCCAATATGACTGCCACT	0.423													t|||	149	0.0297524	0.0166	0.0231	5008	,	,		19720	0.0079		0.0388	False		,,,				2504	0.0654				p.M236K		Atlas-SNP	.											.	CKAP2	51	.	0			c.T707A						PASS	.	T	LYS/MET,LYS/MET	117,4289		0,117,2086	104.0	94.0	97.0		707,704	-7.7	0.0	13	dbSNP_126	97	435,8165		12,411,3877	yes	missense,missense	CKAP2	NM_001098525.1,NM_018204.3	95,95	12,528,5963	AA,AT,TT		5.0581,2.6555,4.2442	benign,benign	236/684,235/683	53035665	552,12454	2203	4300	6503	SO:0001583	missense	26586	exon4			CCAATATGACTGC	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.707T>A	13.37:g.53035665T>A	ENSP00000367276:p.Met236Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_001098525		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	53	0.024267399267399268	7	0.014227642276422764	10	0.027624309392265192	7	0.012237762237762238	29	0.03825857519788918	.	0.514	-0.865276	0.02590	0.026555	0.050581	ENSG00000136108	ENST00000398044;ENST00000258607;ENST00000378034;ENST00000378037;ENST00000490903	T;T;T;T	0.20598	2.37;2.06;2.39;2.39	5.62	-7.65	0.01281	.	1.522930	0.03307	N	0.189991	T	0.01870	0.0059	L	0.36672	1.1	0.09310	N	1	P;P;B;B	0.37864	0.61;0.61;0.241;0.435	B;B;B;B	0.38500	0.201;0.275;0.08;0.08	T	0.20273	-1.0280	9	.	.	.	3.4253	2.374	0.04337	0.2076:0.3943:0.2108:0.1873	rs35975899;rs61959700	187;236;235;236	E9PD90;Q8WWK9;B2RMQ4;A8MYU4	.;CKAP2_HUMAN;.;.	K	236;235;235;236;187	ENSP00000258607:M235K;ENSP00000367273:M235K;ENSP00000367276:M236K;ENSP00000417830:M187K	.	M	+	2	0	CKAP2	51933666	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.438000	0.06905	-0.865000	0.04073	0.528000	0.53228	ATG	T|0.964;A|0.036	0.036	strong		0.423	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2		
MTMR10	54893	hgsc.bcm.edu	37	15	31234064	31234064	+	Missense_Mutation	SNP	C	C	T	rs6493352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:31234064C>T	ENST00000435680.1	-	16	2040	c.1943G>A	c.(1942-1944)cGt>cAt	p.R648H	MTMR10_ENST00000425768.1_3'UTR|MTMR10_ENST00000314404.8_Intron|FAN1_ENST00000362065.4_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	648	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.		R -> H (in dbSNP:rs6493352).				phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TCCAGAGACACGTGGCAGAAT	0.522													C|||	733	0.146366	0.2383	0.1441	5008	,	,		18890	0.0218		0.1879	False		,,,				2504	0.1094				p.R648H		Atlas-SNP	.											.	MTMR10	74	.	0			c.G1943A						PASS	.	C	,HIS/ARG	856,3098		104,648,1225	115.0	118.0	117.0		,1943	-4.1	0.0	15	dbSNP_116	117	1398,6930		101,1196,2867	yes	utr-3,missense	FAN1,MTMR10	NM_014967.4,NM_017762.2	,29	205,1844,4092	TT,TC,CC		16.7867,21.649,18.3521	,benign	,648/778	31234064	2254,10028	1977	4164	6141	SO:0001583	missense	54893	exon16			GAGACACGTGGCA	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.1943G>A	15.37:g.31234064C>T	ENSP00000402537:p.Arg648His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	174	81	0.465517	NM_017762	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	342	0.1565934065934066	120	0.24390243902439024	65	0.17955801104972377	16	0.027972027972027972	141	0.18601583113456466	C	12.98	2.101218	0.37048	0.21649	0.167867	ENSG00000166912	ENST00000435680	T	0.42900	0.96	5.67	-4.13	0.03904	Myotubularin phosphatase domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.04994	-0.135	0.45464	P	0.0015690000000000426	B	0.02656	0.0	B	0.04013	0.001	T	0.36553	-0.9743	8	0.11485	T	0.65	.	8.6044	0.33764	0.0947:0.4011:0.0:0.5041	rs6493352;rs60398231;rs6493352	648	Q9NXD2	MTMRA_HUMAN	H	648	ENSP00000402537:R648H	ENSP00000402537:R648H	R	-	2	0	MTMR10	29021356	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.622000	0.05553	-1.288000	0.02378	-0.136000	0.14681	CGT	C|0.844;T|0.156	0.156	strong		0.522	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
WDR66	144406	hgsc.bcm.edu	37	12	122372183	122372183	+	Missense_Mutation	SNP	G	G	A	rs77540055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122372183G>A	ENST00000288912.4	+	5	1773	c.919G>A	c.(919-921)Gtc>Atc	p.V307I	WDR66_ENST00000397454.2_Missense_Mutation_p.V307I	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	307							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)		CTGCCTCTGCGTCAGTGAAGA	0.527													G|||	172	0.034345	0.003	0.0375	5008	,	,		19010	0.0496		0.0457	False		,,,				2504	0.047				p.V307I	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,caecum,carcinoma,0,1	WDR66	143	1	0			c.G919A						PASS	.	G	ILE/VAL,ILE/VAL	40,4036		2,36,2000	74.0	78.0	77.0		919,919	-5.8	0.0	12	dbSNP_131	77	380,7974		14,352,3811	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	29,29	16,388,5811	AA,AG,GG		4.5487,0.9814,3.3789	benign,benign	307/942,307/1150	122372183	420,12010	2038	4177	6215	SO:0001583	missense	144406	exon5			CTCTGCGTCAGTG	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.919G>A	12.37:g.122372183G>A	ENSP00000288912:p.Val307Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	69	0.03159340659340659	3	0.006097560975609756	15	0.04143646408839779	20	0.03496503496503497	31	0.040897097625329816	G	9.960	1.222419	0.22457	0.009814	0.045487	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.59083	0.29;0.29	5.05	-5.79	0.02354	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.636624	0.15986	N	0.235056	T	0.07954	0.0199	N	0.21097	0.63	0.22066	N	0.999387	B	0.15473	0.013	B	0.17979	0.02	T	0.03761	-1.1006	10	0.18710	T	0.47	.	16.0506	0.80760	0.0984:0.0956:0.806:0.0	.	307	Q8TBY9	WDR66_HUMAN	I	307	ENSP00000288912:V307I;ENSP00000380595:V307I	ENSP00000288912:V307I	V	+	1	0	WDR66	120856566	0.548000	0.26473	0.034000	0.17996	0.288000	0.27193	-0.029000	0.12329	-1.655000	0.01497	-0.672000	0.03802	GTC	G|0.960;A|0.040	0.040	strong		0.527	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
NLRP1	22861	hgsc.bcm.edu	37	17	5425077	5425077	+	Missense_Mutation	SNP	T	T	C	rs11651270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:5425077T>C	ENST00000572272.1	-	13	3549	c.3550A>G	c.(3550-3552)Atg>Gtg	p.M1184V	NLRP1_ENST00000269280.4_Missense_Mutation_p.M1184V|NLRP1_ENST00000345221.3_Missense_Mutation_p.M1184V|NLRP1_ENST00000577119.1_Missense_Mutation_p.M1154V|NLRP1_ENST00000262467.5_Missense_Mutation_p.M1188V|NLRP1_ENST00000354411.3_Missense_Mutation_p.M1154V			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1184			M -> V (in dbSNP:rs11651270). {ECO:0000269|PubMed:11270363, ECO:0000269|PubMed:17974005}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AAGTGGGCCATTTGGAACAGG	0.478													C|||	2093	0.417931	0.4841	0.4294	5008	,	,		17171	0.2768		0.4612	False		,,,				2504	0.4213				p.M1188V		Atlas-SNP	.											.	NLRP1	358	.	0			c.A3562G						PASS	.	C	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	2249,2157	566.0+/-381.8	582,1085,536	53.0	58.0	56.0		3562,3550,3550,3460,3460	2.3	0.2	17	dbSNP_120	56	4028,4572	591.8+/-392.9	934,2160,1206	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	1516,3245,1742	CC,CT,TT		46.8372,48.956,48.2623	benign,benign,benign,benign,benign	1188/1376,1184/1430,1184/1474,1154/1444,1154/1400	5425077	6277,6729	2203	4300	6503	SO:0001583	missense	22861	exon13			GGGCCATTTGGAA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3550A>G	17.37:g.5425077T>C	ENSP00000460475:p.Met1184Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	886	0.4056776556776557	253	0.5142276422764228	140	0.3867403314917127	152	0.26573426573426573	341	0.449868073878628	C	0.051	-1.251336	0.01469	0.51044	0.468372	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82	4.3	2.26	0.28386	.	0.226772	0.22584	N	0.058166	T	0.00012	0.0000	N	0.00041	-2.485	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	0.43310	-0.9399	9	0.02654	T	1	.	6.0509	0.19785	0.0:0.6519:0.1609:0.1872	rs11651270;rs57152836;rs11651270	1154;1154;1184;1184;1188	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	V	1188;1188;1184;1154;1184;450	ENSP00000442029:M1188V;ENSP00000262467:M1188V;ENSP00000269280:M1184V;ENSP00000346390:M1154V;ENSP00000324366:M1184V	ENSP00000262467:M1188V	M	-	1	0	NLRP1	5365801	0.004000	0.15560	0.153000	0.22517	0.983000	0.72400	0.439000	0.21575	0.565000	0.29255	-0.124000	0.14976	ATG	T|0.542;C|0.458	0.458	strong		0.478	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
CCNE1	898	hgsc.bcm.edu	37	19	30314666	30314666	+	Silent	SNP	C	C	T	rs7257694	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:30314666C>T	ENST00000262643.3	+	12	1494	c.1215C>T	c.(1213-1215)agC>agT	p.S405S	CCNE1_ENST00000357943.5_Silent_p.S362S|CCNE1_ENST00000444983.2_Silent_p.S390S	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	405					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			AGCAGAGCAGCGGGCCGGAAA	0.587			A		serous ovarian								C|||	966	0.192891	0.0825	0.2378	5008	,	,		14611	0.1012		0.3549	False		,,,				2504	0.2382				p.S405S		Atlas-SNP	.		Dom	yes		19	19q12	898	cyclin E1		E	.	CCNE1	49	.	0			c.C1215T						PASS	.	C		489,3917	227.8+/-242.9	35,419,1749	74.0	73.0	73.0		1215	-7.4	0.0	19	dbSNP_116	73	3353,5247	497.8+/-374.6	674,2005,1621	no	coding-synonymous	CCNE1	NM_001238.2		709,2424,3370	TT,TC,CC		38.9884,11.0985,29.5402		405/411	30314666	3842,9164	2203	4300	6503	SO:0001819	synonymous_variant	898	exon12			GAGCAGCGGGCCG	M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"""cyclin Es"", ""cyclin Et"""	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.1215C>T	19.37:g.30314666C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_001238	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Silent	SNP	ENST00000262643.3	37	CCDS12419.1																																																																																			C|0.724;T|0.276	0.276	strong		0.587	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238	
NLRP4	147945	hgsc.bcm.edu	37	19	56392875	56392875	+	Silent	SNP	T	T	G	rs302456	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	44	22	0.5	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	
OR52B6	340980	hgsc.bcm.edu	37	11	5602438	5602438	+	Missense_Mutation	SNP	T	T	A	rs541562623|rs2341432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602438T>A	ENST00000345043.2	+	1	332	c.332T>A	c.(331-333)cTc>cAc	p.L111H	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	111			L -> H (in dbSNP:rs2341432).			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)		GGTTATAGCCTCATTTCCTTT	0.502														3581	0.715056	0.7352	0.67	5008	,	,		23317	0.9802		0.4761	False		,,,				2504	0.6922				p.L111H		Atlas-SNP	.											.	OR52B6	37	.	0			c.T332A						PASS	.	A	HIS/LEU	3064,1328	394.9+/-329.4	1077,910,209	109.0	110.0	109.0		332	2.7	0.0	11	dbSNP_100	109	4023,4567	578.8+/-390.8	936,2151,1208	yes	missense	OR52B6	NM_001005162.2	99	2013,3061,1417	AA,AT,TT		46.8335,30.2368,45.409	benign	111/336	5602438	7087,5895	2196	4295	6491	SO:0001583	missense	340980	exon1			ATAGCCTCATTTC	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.332T>A	11.37:g.5602438T>A	ENSP00000341581:p.Leu111His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	1483	0.6790293040293041	348	0.7073170731707317	227	0.6270718232044199	553	0.9667832167832168	355	0.4683377308707124	A	3.783	-0.045281	0.07452	0.697632	0.468335	ENSG00000187747	ENST00000345043	T	0.00554	6.64	5.15	2.71	0.32032	GPCR, rhodopsin-like superfamily (1);	0.686748	0.11712	N	0.536805	T	0.00012	0.0000	N	0.10707	0.03	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38265	-0.9669	9	0.41790	T	0.15	.	5.9086	0.19014	0.5833:0.1517:0.0:0.265	rs2341432;rs16933200;rs52836118;rs60418242;rs2341432	111	Q8NGF0	O52B6_HUMAN	H	111	ENSP00000341581:L111H	ENSP00000341581:L111H	L	+	2	0	OR52B6	5559014	0.000000	0.05858	0.000000	0.03702	0.293000	0.27360	0.473000	0.22132	0.400000	0.25396	-0.265000	0.10407	CTC	T|0.358;A|0.642	0.642	strong		0.502	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
KRT75	9119	hgsc.bcm.edu	37	12	52827740	52827740	+	Missense_Mutation	SNP	G	G	C	rs2232386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52827740G>C	ENST00000252245.5	-	1	569	c.349C>G	c.(349-351)Ccc>Gcc	p.P117A		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	117	Gly-rich.|Head.		P -> A (in dbSNP:rs2232386).		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CCTCCAGGGGGACACACGGGG	0.612													G|||	647	0.129193	0.0726	0.2262	5008	,	,		15852	0.1548		0.1213	False		,,,				2504	0.1186				p.P117A		Atlas-SNP	.											.	KRT75	75	.	0			c.C349G						PASS	.	G	ALA/PRO	388,4018	195.3+/-220.0	18,352,1833	116.0	119.0	118.0		349	2.9	0.0	12	dbSNP_98	118	935,7665	204.9+/-247.5	54,827,3419	yes	missense	KRT75	NM_004693.2	27	72,1179,5252	CC,CG,GG		10.8721,8.8062,10.1722	possibly-damaging	117/552	52827740	1323,11683	2203	4300	6503	SO:0001583	missense	9119	exon1			CAGGGGGACACAC	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.349C>G	12.37:g.52827740G>C	ENSP00000252245:p.Pro117Ala	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	286	0.13095238095238096	36	0.07317073170731707	65	0.17955801104972377	95	0.1660839160839161	90	0.11873350923482849	G	5.471	0.271891	0.10349	0.088062	0.108721	ENSG00000170454	ENST00000252245	T	0.74106	-0.81	5.74	2.87	0.33458	.	0.116168	0.38778	N	0.001573	T	0.00356	0.0011	M	0.61703	1.905	0.80722	P	0.0	P	0.41498	0.752	P	0.46208	0.507	T	0.14727	-1.0462	9	0.54805	T	0.06	.	7.8082	0.29215	0.1445:0.0:0.7251:0.1304	rs2232386;rs17716647;rs52833224;rs2232386	117	O95678	K2C75_HUMAN	A	117	ENSP00000252245:P117A	ENSP00000252245:P117A	P	-	1	0	KRT75	51114007	0.000000	0.05858	0.007000	0.13788	0.094000	0.18550	0.052000	0.14163	0.322000	0.23283	-0.152000	0.13540	CCC	G|0.888;C|0.112	0.112	strong		0.612	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
CASD1	64921	hgsc.bcm.edu	37	7	94180691	94180691	+	Silent	SNP	T	T	C	rs10280457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	97	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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	
SPA17	53340	hgsc.bcm.edu	37	11	124564252	124564252	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124564252A>G	ENST00000532692.1	+	4	1787	c.366A>G	c.(364-366)caA>caG	p.Q122Q	SIAE_ENST00000525730.1_5'UTR|SPA17_ENST00000524614.1_3'UTR|SPA17_ENST00000227135.2_Silent_p.Q122Q			Q15506	SP17_HUMAN	sperm autoantigenic protein 17	122	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				binding of sperm to zona pellucida (GO:0007339)|epithelial cilium movement (GO:0003351)|single fertilization (GO:0007338)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|primary cilium (GO:0072372)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	5	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)		TCAAAATCCAAGCTGCCTTCC	0.413																																					p.Q122Q		Atlas-SNP	.											SPA17,NS,malignant_melanoma,+2,1	SPA17	16	1	0			c.A366G						PASS	.						94.0	96.0	96.0					11																	124564252		2201	4299	6500	SO:0001819	synonymous_variant	53340	exon5			AATCCAAGCTGCC	AF334735	CCDS8450.1	11q24.2	2009-03-12			ENSG00000064199	ENSG00000064199			11210	protein-coding gene	gene with protein product	"""cancer/testis antigen 22"""	608621				8688458	Standard	NM_017425		Approved	SP17, CT22	uc001qap.3	Q15506	OTTHUMG00000165927	ENST00000532692.1:c.366A>G	11.37:g.124564252A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_017425	B2R4F2|Q9BXF7	Silent	SNP	ENST00000532692.1	37	CCDS8450.1																																																																																			.	.	none		0.413	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387075.1	NM_017425	
EBLN2	55096	hgsc.bcm.edu	37	3	73111998	73111998	+	Missense_Mutation	SNP	C	C	T	rs1060584	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:73111998C>T	ENST00000533473.1	+	1	1189	c.766C>T	c.(766-768)Ctt>Ttt	p.L256F	PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	256										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						AATGTTCACACTTCTATTTGG	0.428													T|||	2634	0.525958	0.618	0.3689	5008	,	,		22212	0.4504		0.508	False		,,,				2504	0.6094				p.L256F		Atlas-SNP	.											.	EBLN2	18	.	0			c.C766T						PASS	.	T	PHE/LEU,	2428,1434		764,900,267	191.0	196.0	195.0		766,	-0.7	0.0	3	dbSNP_86	195	4235,4021		1083,2069,976	yes	missense,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	22,	1847,2969,1243	TT,TC,CC		48.704,37.131,45.0157	benign,	256/273,	73111998	6663,5455	1931	4128	6059	SO:0001583	missense	55096	exon1			TTCACACTTCTAT		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.766C>T	3.37:g.73111998C>T	ENSP00000432104:p.Leu256Phe	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	1072	0.4908424908424908	301	0.6117886178861789	143	0.39502762430939226	248	0.43356643356643354	380	0.5013192612137203	T	1.100	-0.661497	0.03454	0.62869	0.51296	ENSG00000255423	ENST00000533473	.	.	.	0.468	-0.722	0.11184	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	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	0.41680	-0.9495	6	0.24483	T	0.36	.	.	.	.	rs1060584;rs3172277;rs3732436;rs61042197;rs1060584	256	Q6P2I7	EBLN2_HUMAN	F	256	.	ENSP00000432104:L256F	L	+	1	0	EBLN2	73194688	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	-0.622000	0.05553	-1.287000	0.02381	-1.305000	0.01319	CTT	C|0.490;T|0.510	0.510	strong		0.428	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
SEMA6B	10501	hgsc.bcm.edu	37	19	4550183	4550183	+	Missense_Mutation	SNP	G	G	A	rs142864702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4550183G>A	ENST00000586582.1	-	12	1533	c.1223C>T	c.(1222-1224)gCg>gTg	p.A408V	SEMA6B_ENST00000586965.1_Missense_Mutation_p.A408V|SEMA6B_ENST00000301293.3_Missense_Mutation_p.A408V	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	408	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CGAGGGCACCGCCTCGTCCAT	0.657													G|||	12	0.00239617	0.0	0.0101	5008	,	,		18713	0.002		0.003	False		,,,				2504	0.0				p.A408V		Atlas-SNP	.											SEMA6B,NS,carcinoma,+1,1	SEMA6B	51	1	0			c.C1223T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	70.0	56.0	61.0		1223	2.2	1.0	19	dbSNP_134	61	20,8580		0,20,4280	yes	missense	SEMA6B	NM_032108.3	64	0,20,6483	AA,AG,GG		0.2326,0.0,0.1538	possibly-damaging	408/889	4550183	20,12986	2203	4300	6503	SO:0001583	missense	10501	exon12			GGCACCGCCTCGT	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1223C>T	19.37:g.4550183G>A	ENSP00000467290:p.Ala408Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	1	0.0013192612137203166	.	21.8	4.204157	0.79127	0.0	0.002326	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10573	2.86	2.17	2.17	0.27698	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.196139	0.42964	U	0.000634	T	0.17492	0.0420	L	0.58925	1.835	0.42906	D	0.994242	D;D	0.89917	0.997;1.0	P;D	0.64321	0.484;0.924	T	0.03384	-1.1042	10	0.87932	D	0	.	12.0039	0.53248	0.0:0.0:1.0:0.0	.	408;408	B4DT36;Q9H3T3	.;SEM6B_HUMAN	V	408	ENSP00000301293:A408V	ENSP00000301292:A408V	A	-	2	0	SEMA6B	4501183	0.999000	0.42202	0.996000	0.52242	0.933000	0.57130	9.245000	0.95431	1.580000	0.49851	0.478000	0.44815	GCG	G|0.999;A|0.001	0.001	strong		0.657	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
IKZF3	22806	hgsc.bcm.edu	37	17	37944519	37944519	+	Missense_Mutation	SNP	C	C	G	rs112301322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:37944519C>G	ENST00000346872.3	-	6	762	c.701G>C	c.(700-702)gGg>gCg	p.G234A	IKZF3_ENST00000377945.3_Intron|IKZF3_ENST00000377944.3_Missense_Mutation_p.G91A|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000467757.1_Missense_Mutation_p.G178A|IKZF3_ENST00000351680.3_Intron|IKZF3_ENST00000377958.2_Missense_Mutation_p.G147A|IKZF3_ENST00000350532.3_Missense_Mutation_p.G234A|IKZF3_ENST00000535189.1_Missense_Mutation_p.G200A|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000439167.2_Intron|IKZF3_ENST00000439016.2_Intron|IKZF3_ENST00000346243.3_Intron	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	234					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|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)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACCAGTGTCCCCTGGGTCAGT	0.463													C|||	70	0.0139776	0.003	0.0274	5008	,	,		19399	0.0		0.0308	False		,,,				2504	0.0164				p.G234A		Atlas-SNP	.											IKZF3,rectum,carcinoma,0,1	IKZF3	79	1	0			c.G701C						scavenged	.	C	ALA/GLY,ALA/GLY,,ALA/GLY,,	32,4374	37.6+/-69.7	1,30,2172	132.0	101.0	111.0		701,533,,701,,	2.9	0.0	17	dbSNP_132	111	273,8327	104.0+/-165.0	3,267,4030	yes	missense,missense,intron,missense,intron,intron	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	60,60,,60,,	4,297,6202	GG,GC,CC		3.1744,0.7263,2.3451	benign,benign,,benign,,	234/510,178/454,,234/471,,	37944519	305,12701	2203	4300	6503	SO:0001583	missense	22806	exon6			GTGTCCCCTGGGT	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13178	protein-coding gene	gene with protein product		606221	"""zinc finger protein, subfamily 1A, 3 (Aiolos)"""	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.701G>C	17.37:g.37944519C>G	ENSP00000344544:p.Gly234Ala	Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	36|36	0.016483516483516484|0.016483516483516484	2|2	0.0040650406504065045|0.0040650406504065045	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	25|25	0.032981530343007916|0.032981530343007916	C|C	1.864|1.864	-0.461818|-0.461818	0.04508|0.04508	0.007263|0.007263	0.031744|0.031744	ENSG00000161405|ENSG00000161405	ENST00000488188;ENST00000377944;ENST00000377958;ENST00000535189;ENST00000350532;ENST00000467757|ENST00000439016	T;T;T;T;T|.	0.08896|.	3.25;3.04;3.3;3.24;4.29|.	6.04|6.04	2.93|2.93	0.34026|0.34026	.|.	0.232813|0.232813	0.30575|0.30575	N|N	0.009333|0.009333	T|T	0.04952|0.04952	0.0133|0.0133	N|N	0.08118|0.08118	0|0	0.18873|0.18873	N|N	0.999984|0.999984	B;B;B;B;B;B|.	0.33171|.	0.4;0.041;0.007;0.002;0.004;0.006|.	B;B;B;B;B;B|.	0.28011|.	0.085;0.026;0.009;0.007;0.007;0.008|.	T|T	0.16867|0.16867	-1.0388|-1.0388	10|7	0.18710|0.18276	T|T	0.47|0.48	-8.0392|-8.0392	4.9351|4.9351	0.13937|0.13937	0.1251:0.6226:0.1207:0.1316|0.1251:0.6226:0.1207:0.1316	.|.	147;91;200;234;178;234|.	Q9UKT9-9;Q9UKT9-10;Q9UKT9-7;Q9UKT9-4;Q9UKT9-2;Q9UKT9|.	.;.;.;.;.;IKZF3_HUMAN|.	A|R	234;91;147;200;234;178|188	ENSP00000367179:G91A;ENSP00000367194:G147A;ENSP00000438972:G200A;ENSP00000344471:G234A;ENSP00000420463:G178A|.	ENSP00000344471:G234A|ENSP00000403027:G188R	G|G	-|-	2|1	0|0	IKZF3|IKZF3	35198045|35198045	0.751000|0.751000	0.28327|0.28327	0.011000|0.011000	0.14972|0.14972	0.055000|0.055000	0.15305|0.15305	2.583000|2.583000	0.46094|0.46094	0.418000|0.418000	0.25898|0.25898	0.563000|0.563000	0.77884|0.77884	GGG|GGG	C|0.979;G|0.021	0.021	strong		0.463	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481	
OR52N2	390077	hgsc.bcm.edu	37	11	5842081	5842081	+	Silent	SNP	G	G	A	rs73394378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5842081G>A	ENST00000317037.2	+	1	538	c.516G>A	c.(514-516)cgG>cgA	p.R172R	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, 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)			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)		CCTATTGCCGGGGGAACTTCA	0.522													G|||	204	0.0407348	0.0749	0.0259	5008	,	,		22597	0.001		0.0467	False		,,,				2504	0.0399				p.R172R		Atlas-SNP	.											.	OR52N2	58	.	0			c.G516A						PASS	.	G		340,4062	178.7+/-207.4	9,322,1870	250.0	225.0	233.0		516	-8.3	0.0	11	dbSNP_130	233	576,8016	154.8+/-208.9	16,544,3736	no	coding-synonymous	OR52N2	NM_001005174.1		25,866,5606	AA,AG,GG		6.7039,7.7238,7.0494		172/322	5842081	916,12078	2201	4296	6497	SO:0001819	synonymous_variant	390077	exon1			TTGCCGGGGGAAC	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.516G>A	11.37:g.5842081G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	NM_001005174	Q6IFF9	Silent	SNP	ENST00000317037.2	37	CCDS31399.1																																																																																			G|0.939;A|0.061	0.061	strong		0.522	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
AMPH	273	hgsc.bcm.edu	37	7	38433726	38433726	+	Missense_Mutation	SNP	T	T	G	rs35024632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:38433726T>G	ENST00000356264.2	-	18	1702	c.1487A>C	c.(1486-1488)aAg>aCg	p.K496T	AMPH_ENST00000428293.2_Missense_Mutation_p.K454T|AMPH_ENST00000325590.5_Missense_Mutation_p.K454T|AMPH_ENST00000471913.1_5'UTR	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	496			K -> T (in dbSNP:rs35024632). {ECO:0000269|PubMed:15489334}.		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						GACAGTGGCCTTCTCCGCCTC	0.577													T|||	351	0.0700879	0.0008	0.0519	5008	,	,		18146	0.1825		0.0726	False		,,,				2504	0.0583				p.K496T		Atlas-SNP	.											.	AMPH	157	.	0			c.A1487C						PASS	.	T	THR/LYS,THR/LYS	50,4356	52.9+/-88.7	1,48,2154	120.0	110.0	113.0		1487,1361	2.1	0.9	7	dbSNP_126	113	634,7966	164.2+/-216.6	34,566,3700	yes	missense,missense	AMPH	NM_001635.3,NM_139316.2	78,78	35,614,5854	GG,GT,TT		7.3721,1.1348,5.2591	benign,benign	496/696,454/654	38433726	684,12322	2203	4300	6503	SO:0001583	missense	273	exon18			GTGGCCTTCTCCG		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.1487A>C	7.37:g.38433726T>G	ENSP00000348602:p.Lys496Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	96	63	0.65625	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	184|184	0.08424908424908426|0.08424908424908426	0|0	0.0|0.0	19|19	0.052486187845303865|0.052486187845303865	111|111	0.19405594405594406|0.19405594405594406	54|54	0.0712401055408971|0.0712401055408971	T|T	9.076|9.076	0.998033|0.998033	0.19043|0.19043	0.011348|0.011348	0.073721|0.073721	ENSG00000078053|ENSG00000078053	ENST00000441628|ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	T|T;T;T	0.34667|0.61040	1.35|0.17;0.18;0.14	5.93|5.93	2.1|2.1	0.27182|0.27182	.|.	.|0.544311	.|0.19498	.|N	.|0.112820	T|T	0.00109|0.00109	0.0003|0.0003	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	P|P	0.0|0.0	.|D;B;B;P	.|0.67145	.|0.996;0.274;0.323;0.925	.|P;B;B;P	.|0.59948	.|0.866;0.072;0.079;0.52	T|T	0.05257|0.05257	-1.0896|-1.0896	6|9	0.13853|0.27082	T|T	0.58|0.32	-27.4888|-27.4888	3.6841|3.6841	0.08321|0.08321	0.0:0.199:0.1936:0.6074|0.0:0.199:0.1936:0.6074	rs35024632|rs35024632	.|542;454;496;384	.|Q8NFL6;P49418-2;P49418;Q8NFL4	.|.;.;AMPH_HUMAN;.	D|T	378|454;496;454;398	ENSP00000415085:E378D|ENSP00000317441:K454T;ENSP00000348602:K496T;ENSP00000390734:K454T	ENSP00000415085:E378D|ENSP00000317441:K454T	E|K	-|-	3|2	2|0	AMPH|AMPH	38400251|38400251	0.378000|0.378000	0.25114|0.25114	0.894000|0.894000	0.35097|0.35097	0.444000|0.444000	0.32077|0.32077	1.415000|1.415000	0.34748|0.34748	1.076000|1.076000	0.40961|0.40961	0.460000|0.460000	0.39030|0.39030	GAA|AAG	T|0.934;G|0.066	0.066	strong		0.577	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
SPATA25	128497	hgsc.bcm.edu	37	20	44515322	44515322	+	Missense_Mutation	SNP	C	C	T	rs76638086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515322C>T	ENST00000372519.3	-	2	562	c.518G>A	c.(517-519)cGg>cAg	p.R173Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	173					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GTCCTCTTCCCGAACTCCTGG	0.652													C|||	12	0.00239617	0.0008	0.0072	5008	,	,		18142	0.0		0.005	False		,,,				2504	0.001				p.R173Q		Atlas-SNP	.											.	.	.	.	0			c.G518A						PASS	.	C	GLN/ARG	7,4399	11.4+/-27.6	0,7,2196	62.0	64.0	64.0		518	3.6	1.0	20	dbSNP_132	64	36,8564	25.1+/-72.6	0,36,4264	yes	missense	C20orf165	NM_080608.3	43	0,43,6460	TT,TC,CC		0.4186,0.1589,0.3306	probably-damaging	173/228	44515322	43,12963	2203	4300	6503	SO:0001583	missense	128497	exon2			TCTTCCCGAACTC	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 165"""	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.518G>A	20.37:g.44515322C>T	ENSP00000361597:p.Arg173Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	20.8	4.042836	0.75732	0.001589	0.004186	ENSG00000149634	ENST00000372519	T	0.56941	0.43	5.55	3.63	0.41609	.	0.134112	0.33515	N	0.004823	T	0.28797	0.0714	L	0.34521	1.04	0.31251	N	0.693996	B	0.30021	0.265	B	0.23852	0.049	T	0.42050	-0.9474	10	0.87932	D	0	-13.3192	6.8348	0.23931	0.0:0.6984:0.1454:0.1562	.	173	Q9BR10	CT165_HUMAN	Q	173	ENSP00000361597:R173Q	ENSP00000361597:R173Q	R	-	2	0	C20orf165	43948729	0.718000	0.27976	1.000000	0.80357	0.974000	0.67602	0.589000	0.23939	0.908000	0.36671	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.652	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1		
TBX4	9496	hgsc.bcm.edu	37	17	59560463	59560463	+	Silent	SNP	C	C	T	rs7218485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59560463C>T	ENST00000240335.1	+	8	1269	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TBX4_ENST00000589449.1_Intron|TBX4_ENST00000393853.4_Silent_p.D409D	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	408					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CTGGGGTGGACGACCTGCCCC	0.597													C|||	579	0.115615	0.1135	0.0764	5008	,	,		16721	0.1151		0.0994	False		,,,				2504	0.1636				p.D408D		Atlas-SNP	.											TBX4,colon,carcinoma,0,2	TBX4	69	2	0			c.C1224T						PASS	.	C		486,3920	227.2+/-242.5	24,438,1741	88.0	77.0	81.0		1224	-3.8	1.0	17	dbSNP_116	81	899,7701	200.2+/-244.0	47,805,3448	no	coding-synonymous	TBX4	NM_018488.2		71,1243,5189	TT,TC,CC		10.4535,11.0304,10.6489		408/546	59560463	1385,11621	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GGTGGACGACCTG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1224C>T	17.37:g.59560463C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			C|0.886;T|0.114	0.114	strong		0.597	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
PDLIM1	9124	hgsc.bcm.edu	37	10	96997820	96997820	+	Silent	SNP	A	A	G	rs1049814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	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		
PIGQ	9091	hgsc.bcm.edu	37	16	633353	633353	+	Missense_Mutation	SNP	T	T	C	rs710924|rs71391136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:633353T>C	ENST00000026218.5	+	10	2090	c.2002T>C	c.(2002-2004)Tgt>Cgt	p.C668R	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	668			C -> R (in dbSNP:rs710924).|C -> Y (in dbSNP:rs710925).		C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)	p.C668R(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GCCCACCCTGTGTACCCAGGT	0.692													C|||	2657	0.530551	0.4743	0.4885	5008	,	,		16791	0.6379		0.4324	False		,,,				2504	0.6268				p.C668R		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	1	Substitution - Missense(1)	prostate(1)	c.T2002C						PASS	.	C	ARG/CYS,	1968,2434		486,996,719	45.0	53.0	50.0		2002,	1.3	0.0	16	dbSNP_86	50	3354,5242		723,1908,1667	yes	missense,utr-3	PIGQ	NM_148920.1,NM_004204.3	180,	1209,2904,2386	CC,CT,TT		39.0181,44.707,40.9448	possibly-damaging,	668/761,	633353	5322,7676	2201	4298	6499	SO:0001583	missense	9091	exon10			ACCCTGTGTACCC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.2002T>C	16.37:g.633353T>C	ENSP00000026218:p.Cys668Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	1035	0.4739010989010989	231	0.4695121951219512	169	0.46685082872928174	325	0.5681818181818182	310	0.40897097625329815	C	0.015	-1.571008	0.00895	0.44707	0.390181	ENSG00000007541	ENST00000026218	T	0.22743	1.94	2.39	1.29	0.21616	.	.	.	.	.	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	0.40794	-0.9544	7	.	.	.	.	5.1028	0.14768	0.0:0.6231:0.0:0.3769	rs710924;rs60515732;rs710924	238;668	B3KRR7;Q9BRB3	.;PIGQ_HUMAN	R	668	ENSP00000026218:C668R	.	C	+	1	0	PIGQ	573354	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.893000	0.00708	-0.082000	0.12640	-0.479000	0.04858	TGT	CA|0.500;TG|0.500	.	alt		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
PARP4	143	hgsc.bcm.edu	37	13	25009485	25009485	+	Missense_Mutation	SNP	C	C	G	rs1050110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25009485C>G	ENST00000381989.3	-	31	3899	c.3794G>C	c.(3793-3795)gGc>gCc	p.G1265A		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1265			G -> A (in dbSNP:rs1050110). {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)		TACACCTAAGCCATCCTCTTC	0.368													g|||	1935	0.386382	0.4856	0.3473	5008	,	,		20414	0.3601		0.4175	False		,,,				2504	0.2751				p.G1265A		Atlas-SNP	.											.	PARP4	142	.	0			c.G3794C						PASS	.	G	ALA/GLY	2096,2310	602.4+/-389.9	484,1128,591	81.0	87.0	85.0		3794	-2.1	0.0	13	dbSNP_86	85	3204,5396	651.7+/-400.9	595,2014,1691	no	missense	PARP4	NM_006437.3	60	1079,3142,2282	GG,GC,CC		37.2558,47.5715,40.7504	benign	1265/1725	25009485	5300,7706	2203	4300	6503	SO:0001583	missense	143	exon31			CCTAAGCCATCCT	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.3794G>C	13.37:g.25009485C>G	ENSP00000371419:p.Gly1265Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	847	0.38782051282051283	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	319	0.420844327176781	g	0	-2.709352	0.00094	0.475715	0.372558	ENSG00000102699	ENST00000381989	T	0.01584	4.75	1.95	-2.08	0.07254	.	11.803900	0.01079	N	0.004944	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	9	0.07990	T	0.79	.	4.05	0.09791	0.0:0.3716:0.2351:0.3933	rs1050110;rs3190393;rs3742173;rs1050110	1265	Q9UKK3	PARP4_HUMAN	A	1265	ENSP00000371419:G1265A	ENSP00000371419:G1265A	G	-	2	0	PARP4	23907485	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.921000	0.00693	-1.265000	0.02449	-1.962000	0.00476	GGC	.	.	weak		0.368	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
C1orf162	128346	hgsc.bcm.edu	37	1	112018657	112018657	+	Missense_Mutation	SNP	G	G	A	rs6703267	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:112018657G>A	ENST00000343534.5	+	2	257	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	C1orf162_ENST00000369718.3_Missense_Mutation_p.G3S|C1orf162_ENST00000464591.1_3'UTR	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	71	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	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	
ZNF835	90485	hgsc.bcm.edu	37	19	57175121	57175121	+	Silent	SNP	G	G	A	rs115625349	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57175121G>A	ENST00000537055.2	-	2	1677	c.1446C>T	c.(1444-1446)gcC>gcT	p.A482A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	482					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)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						AGAAGCTGAAGGCCTTCCCGC	0.642													.|||	408	0.0814696	0.233	0.0346	5008	,	,		16940	0.0258		0.0099	False		,,,				2504	0.0409				p.A482A		Atlas-SNP	.											.	ZNF835	106	.	0			c.C1446T						PASS	.	G		929,3477	333.6+/-303.0	99,731,1373	123.0	137.0	133.0		1446	1.9	1.0	19	dbSNP_132	133	164,8436	76.6+/-139.3	1,162,4137	no	coding-synonymous	ZNF835	NM_001005850.2		100,893,5510	AA,AG,GG		1.907,21.0849,8.4038		482/538	57175121	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	90485	exon2			GCTGAAGGCCTTC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1446C>T	19.37:g.57175121G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			G|0.942;A|0.058	0.058	strong		0.642	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
LAMB4	22798	hgsc.bcm.edu	37	7	107738882	107738882	+	Silent	SNP	G	G	A	rs1735499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:107738882G>A	ENST00000388781.3	-	11	1409	c.1326C>T	c.(1324-1326)taC>taT	p.Y442Y	LAMB4_ENST00000388780.3_Silent_p.Y442Y|LAMB4_ENST00000205386.4_Silent_p.Y442Y|LAMB4_ENST00000418464.1_Silent_p.Y442Y|LAMB4_ENST00000414450.2_Silent_p.Y442Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	442	Laminin EGF-like 3. {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						CGCTTAGTCCGTAGTGGTTGG	0.577													G|||	1535	0.30651	0.2458	0.3689	5008	,	,		15217	0.2649		0.3767	False		,,,				2504	0.3149				p.Y442Y		Atlas-SNP	.											.	LAMB4	253	.	0			c.C1326T						PASS	.	G		1191,3215	416.5+/-337.6	182,827,1194	137.0	117.0	124.0		1326	-7.7	0.4	7	dbSNP_89	124	3375,5225	500.2+/-375.2	694,1987,1619	no	coding-synonymous	LAMB4	NM_007356.2		876,2814,2813	AA,AG,GG		39.2442,27.0313,35.1069		442/1762	107738882	4566,8440	2203	4300	6503	SO:0001819	synonymous_variant	22798	exon11			TAGTCCGTAGTGG	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.1326C>T	7.37:g.107738882G>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			T|0.052;G|0.532;C|0.144;A|0.272	0.272	strong		0.577	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
PIGN	23556	hgsc.bcm.edu	37	18	59781800	59781800	+	Silent	SNP	A	A	G	rs13381627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	51	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	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	
LIME1	54923	hgsc.bcm.edu	37	20	62369997	62369997	+	Missense_Mutation	SNP	C	C	T	rs1151625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62369997C>T	ENST00000309546.3	+	6	719	c.632C>T	c.(631-633)cCa>cTa	p.P211L	LIME1_ENST00000490824.1_3'UTR|RP4-583P15.15_ENST00000490623.2_3'UTR|SLC2A4RG_ENST00000266077.2_5'Flank|RP4-583P15.14_ENST00000476221.1_3'UTR|RP4-583P15.14_ENST00000467211.1_Intron	NM_017806.2	NP_060276.2	Q9H400	LIME1_HUMAN	Lck interacting transmembrane adaptor 1	211			P -> L (in dbSNP:rs1151625).		B cell receptor signaling pathway (GO:0050853)|T cell receptor signaling pathway (GO:0050852)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|liver(1)	3	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					AGGAGGGACCCAGGACCCACC	0.657													C|||	129	0.0257588	0.0038	0.0403	5008	,	,		15525	0.005		0.0835	False		,,,				2504	0.0072				p.P211L		Atlas-SNP	.											.	LIME1	13	.	0			c.C632T						PASS	.	C	LEU/PRO	73,4323		0,73,2125	25.0	32.0	30.0		632	-0.0	0.0	20	dbSNP_87	30	652,7946		26,600,3673	yes	missense	LIME1	NM_017806.2	98	26,673,5798	TT,TC,CC		7.5832,1.6606,5.5795	probably-damaging	211/296	62369997	725,12269	2198	4299	6497	SO:0001583	missense	54923	exon6			GGGACCCAGGACC	AK000413	CCDS13536.1	20q13.33	2010-05-11			ENSG00000203896	ENSG00000203896			26016	protein-coding gene	gene with protein product		609809				12477932	Standard	NM_017806		Approved	FLJ20406, dJ583P15.4, LIME	uc002ygp.4	Q9H400	OTTHUMG00000032999	ENST00000309546.3:c.632C>T	20.37:g.62369997C>T	ENSP00000309521:p.Pro211Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_017806	E1P5K5|E1P5K6|Q5JWJ2|Q6XYB3|Q9NX69	Missense_Mutation	SNP	ENST00000309546.3	37	CCDS13536.1	89	0.04075091575091575	3	0.006097560975609756	20	0.055248618784530384	4	0.006993006993006993	62	0.08179419525065963	c	10.07	1.250553	0.22880	0.016606	0.075832	ENSG00000203896	ENST00000309546	T	0.39592	1.07	3.15	-0.00527	0.14018	.	.	.	.	.	T	0.01320	0.0043	N	0.19112	0.55	0.09310	N	0.999996	B	0.14012	0.009	B	0.10450	0.005	T	0.10636	-1.0621	9	0.62326	D	0.03	.	6.8833	0.24185	0.0:0.4222:0.0:0.5778	rs1151625;rs1758202;rs52803152;rs60606264;rs1151625	211	Q9H400	LIME1_HUMAN	L	211	ENSP00000309521:P211L	ENSP00000309521:P211L	P	+	2	0	LIME1	61840441	0.000000	0.05858	0.000000	0.03702	0.817000	0.46193	0.051000	0.14141	-0.075000	0.12798	0.457000	0.33378	CCA	C|0.944;T|0.056	0.056	strong		0.657	LIME1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080225.1	NM_017806	
NELFA	7469	hgsc.bcm.edu	37	4	1986542	1986542	+	Silent	SNP	C	C	T	rs2234570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:1986542C>T	ENST00000411638.2	-	8	1044	c.1029G>A	c.(1027-1029)acG>acA	p.T343T	NELFA_ENST00000542778.1_Silent_p.T208T|NELFA_ENST00000382882.3_Silent_p.T354T|MIR943_ENST00000401286.1_RNA	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	343					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										CACCTGGGGGCGTCTCGGAGC	0.672													C|||	1296	0.258786	0.0076	0.1844	5008	,	,		18187	0.5952		0.1938	False		,,,				2504	0.3712				p.T354T		Atlas-SNP	.											.	.	.	.	0			c.G1062A						PASS	.	C		171,4193		4,163,2015	45.0	45.0	45.0		1062	-10.3	0.0	4	dbSNP_98	45	1455,7085		115,1225,2930	no	coding-synonymous	WHSC2	NM_005663.4		119,1388,4945	TT,TC,CC		17.0375,3.9184,12.6007		354/540	1986542	1626,11278	2182	4270	6452	SO:0001819	synonymous_variant	7469	exon8			TGGGGGCGTCTCG	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"""Wolf-Hirschhorn syndrome candidate 2"""	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.1029G>A	4.37:g.1986542C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_005663	A2A2T1|O95392	Silent	SNP	ENST00000411638.2	37		554	0.25366300366300365	6	0.012195121951219513	62	0.1712707182320442	336	0.5874125874125874	150	0.19788918205804748	C	3.052	-0.195068	0.06259	0.039184	0.170375	ENSG00000185049	ENST00000453740	.	.	.	5.13	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999884854	.	.	.	.	.	.	T	0.26155	-1.0111	3	.	.	.	-5.5093	1.6002	0.02672	0.1559:0.2889:0.199:0.3562	rs2234570;rs3185642;rs17410658;rs17849665;rs2234570	.	.	.	H	244	.	.	R	-	2	0	WHSC2	1956340	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	-3.469000	0.00460	-3.653000	0.00126	-0.176000	0.13171	CGC	C|0.820;T|0.180	0.180	strong		0.672	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
FBXO7	25793	hgsc.bcm.edu	37	22	32875190	32875190	+	Missense_Mutation	SNP	G	G	A	rs11107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32875190G>A	ENST00000266087.7	+	2	672	c.345G>A	c.(343-345)atG>atA	p.M115I	FBXO7_ENST00000382058.3_Missense_Mutation_p.M36I|FBXO7_ENST00000397426.1_Start_Codon_SNP_p.M1I|FBXO7_ENST00000465418.1_3'UTR	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	115	Important for interaction with PINK1.		M -> I (in dbSNP:rs11107). {ECO:0000269|PubMed:10531035, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18513678}.		cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGACTAGCATGCAGGATGAAC	0.448													g|||	2441	0.48742	0.4047	0.5663	5008	,	,		17154	0.6915		0.3748	False		,,,				2504	0.4489				p.M115I		Atlas-SNP	.											.	FBXO7	131	.	0			c.G345A						PASS	.	G	ILE/MET,ILE/MET	1640,2766	501.8+/-365.1	307,1026,870	93.0	92.0	92.0		108,345	-3.6	0.0	22	dbSNP_52	92	3202,5398	483.2+/-371.1	572,2058,1670	yes	missense,missense	FBXO7	NM_001033024.1,NM_012179.3	10,10	879,3084,2540	AA,AG,GG		37.2326,37.222,37.229	benign,benign	36/444,115/523	32875190	4842,8164	2203	4300	6503	SO:0001583	missense	25793	exon2			TAGCATGCAGGAT	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.345G>A	22.37:g.32875190G>A	ENSP00000266087:p.Met115Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	1067	0.48855311355311354	185	0.37601626016260165	193	0.5331491712707183	396	0.6923076923076923	293	0.3865435356200528	g	0.741	-0.776340	0.02951	0.37222	0.372326	ENSG00000100225	ENST00000266087;ENST00000452138;ENST00000382058;ENST00000397426;ENST00000444207	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	4.53	-3.63	0.04529	.	1.881220	0.01957	N	0.043074	T	0.00012	0.0000	N	0.00138	-2.015	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	0.47368	-0.9123	9	0.37606	T	0.19	0.134	0.4433	0.00489	0.2236:0.1582:0.2575:0.3607	rs11107;rs710174;rs3171628;rs17350295;rs17771677;rs17850310;rs52811518;rs58963810;rs11107	36;115;1	Q9Y3I1-2;Q9Y3I1;Q5TI86	.;FBX7_HUMAN;.	I	115;36;36;1;1	ENSP00000266087:M115I;ENSP00000388547:M36I;ENSP00000371490:M36I;ENSP00000380571:M1I;ENSP00000404388:M1I	ENSP00000266087:M115I	M	+	3	0	FBXO7	31205190	0.000000	0.05858	0.000000	0.03702	0.231000	0.25187	-0.024000	0.12435	-0.629000	0.05575	-0.578000	0.04140	ATG	G|0.577;N|0.000	.	strong		0.448	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
HEPH	9843	hgsc.bcm.edu	37	X	65427124	65427124	+	Silent	SNP	A	A	G	rs809363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:65427124A>G	ENST00000343002.2	+	13	3043	c.2379A>G	c.(2377-2379)acA>acG	p.T793T	HEPH_ENST00000519389.1_Silent_p.T847T|HEPH_ENST00000336279.5_Silent_p.T526T|HEPH_ENST00000441993.2_Silent_p.T796T|HEPH_ENST00000374727.3_Silent_p.T796T|HEPH_ENST00000419594.1_Silent_p.T604T			Q9BQS7	HEPH_HUMAN	hephaestin	793	Plastocyanin-like 5.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						CTGATGGTACATTCAGGATCC	0.473													A|||	928	0.245828	0.4395	0.1744	3775	,	,		11159	0.001		0.159	False		,,,				2504	0.0665				p.T847T		Atlas-SNP	.											.	HEPH	224	.	0			c.A2541G						PASS	.	A	,,	1958,1877		424,811,299,397,272	121.0	99.0	106.0		2388,1578,2541	0.6	1.0	X	dbSNP_86	106	1431,5297		107,764,453,1557,1419	no	coding-synonymous,coding-synonymous,coding-synonymous	HEPH	NM_001130860.2,NM_014799.2,NM_138737.3	,,	531,1575,752,1954,1691	GG,GA,G,AA,A		21.2693,48.9439,32.0837	,,	796/1161,526/892,847/1213	65427124	3389,7174	2203	4300	6503	SO:0001819	synonymous_variant	9843	exon14			TGGTACATTCAGG	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.2379A>G	X.37:g.65427124A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	37																																																																																				A|0.687;0|0.002	.	strong		0.473	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	
BCAT2	587	hgsc.bcm.edu	37	19	49303070	49303070	+	Missense_Mutation	SNP	G	G	C	rs11548193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49303070G>C	ENST00000316273.6	-	6	569	c.557C>G	c.(556-558)aCg>aGg	p.T186R	BCAT2_ENST00000545387.2_Missense_Mutation_p.T94R|BCAT2_ENST00000598162.1_Missense_Mutation_p.T186R|BCAT2_ENST00000599246.1_Missense_Mutation_p.T94R|BCAT2_ENST00000402551.1_Missense_Mutation_p.T146R|BCAT2_ENST00000597011.1_Missense_Mutation_p.T146R	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	186			T -> R (in dbSNP:rs11548193). {ECO:0000269|PubMed:8702755, ECO:0000269|PubMed:9165094}.		branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-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;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	GAGCGCGCGCGTGGGCTGGCT	0.701													G|||	355	0.0708866	0.0076	0.1037	5008	,	,		14201	0.0		0.2177	False		,,,				2504	0.0552				p.T186R		Atlas-SNP	.											.	BCAT2	35	.	0			c.C557G						PASS	.	G	ARG/THR,ARG/THR	187,4087		11,165,1961	20.0	18.0	19.0		281,557	2.0	0.0	19	dbSNP_120	19	1658,6738		153,1352,2693	no	missense,missense	BCAT2	NM_001164773.1,NM_001190.3	71,71	164,1517,4654	CC,CG,GG		19.7475,4.3753,14.562	benign,benign	94/301,186/393	49303070	1845,10825	2137	4198	6335	SO:0001583	missense	587	exon6			GCGCGCGTGGGCT	U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"""branched chain aminotransferase 2, mitochondrial"""	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.557C>G	19.37:g.49303070G>C	ENSP00000322991:p.Thr186Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	208	0.09523809523809523	3	0.006097560975609756	43	0.11878453038674033	0	0.0	162	0.21372031662269128	G	8.463	0.855676	0.17106	0.043753	0.197475	ENSG00000105552	ENST00000316273;ENST00000545387;ENST00000402551	T;T;T	0.16597	2.33;2.33;2.33	4.24	1.97	0.26223	.	0.784748	0.11673	N	0.540689	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B;B;B;B	0.22080	0.064;0.064;0.015;0.064	B;B;B;B	0.29176	0.099;0.099;0.026;0.099	T	0.37407	-0.9707	9	0.15952	T	0.53	-0.0452	12.1372	0.53979	0.0:0.3239:0.6761:0.0	rs11548193	146;186;94;186	B3KSI3;Q53EW7;O15382-2;O15382	.;.;.;BCAT2_HUMAN	R	186;94;146	ENSP00000322991:T186R;ENSP00000440973:T94R;ENSP00000385161:T146R	ENSP00000322991:T186R	T	-	2	0	BCAT2	53994882	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	1.033000	0.30191	0.502000	0.28037	0.561000	0.74099	ACG	G|0.904;C|0.096	0.096	strong		0.701	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726756	32726756	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32726756A>G	ENST00000437316.2	-	3	580	c.517T>C	c.(517-519)Tcc>Ccc	p.S173P	HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.S173P|HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.S173P			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	177	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|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)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						CTAATGAGGGAGGTGGACACA	0.547																																					p.S173P		Atlas-SNP	.											.	HLA-DQB2	22	.	0			c.T517C						PASS	.																																			SO:0001583	missense	3120	exon3			TGAGGGAGGTGGA	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.517T>C	6.37:g.32726756A>G	ENSP00000396330:p.Ser173Pro	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	14	0.126126	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	A	0.001	-3.015517	0.00042	.	.	ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527	T;T;T	0.00599	6.3;6.3;6.3	3.43	0.281	0.15687	.	0.777035	0.10865	N	0.625646	T	0.00039	0.0001	N	0.00221	-1.82	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.10917	-1.0609	10	0.28530	T	0.3	.	4.2619	0.10745	0.2399:0.2957:0.4644:0.0	.	173;173	A2ADX3;Q5SR06	.;.	P	173	ENSP00000396330:S173P;ENSP00000410512:S173P;ENSP00000390431:S173P	ENSP00000390431:S173P	S	-	1	0	HLA-DQB2	32834734	0.000000	0.05858	0.188000	0.23233	0.053000	0.15095	0.295000	0.19065	0.267000	0.21916	-1.585000	0.00851	TCC	.	.	none		0.547	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
MTPAP	55149	hgsc.bcm.edu	37	10	30629226	30629226	+	Missense_Mutation	SNP	G	G	A	rs1047991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:30629226G>A	ENST00000263063.4	-	3	527	c.484C>T	c.(484-486)Cgc>Tgc	p.R162C	MTPAP_ENST00000358107.4_Missense_Mutation_p.R292C|MTPAP_ENST00000488290.1_5'UTR	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	162			R -> C (in dbSNP:rs1047991).		cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)			breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GACCGTACGCGTGACCGTTCA	0.413													G|||	1094	0.21845	0.1929	0.121	5008	,	,		19041	0.2103		0.2495	False		,,,				2504	0.2986				p.R162C		Atlas-SNP	.											.	MTPAP	113	.	0			c.C484T						PASS	.	G	CYS/ARG	935,3471	356.6+/-313.6	99,737,1367	126.0	113.0	117.0		484	-10.2	0.0	10	dbSNP_86	117	2476,6124	408.5+/-349.5	376,1724,2200	yes	missense	MTPAP	NM_018109.3	180	475,2461,3567	AA,AG,GG		28.7907,21.2211,26.2264	benign	162/583	30629226	3411,9595	2203	4300	6503	SO:0001583	missense	55149	exon3			GTACGCGTGACCG	AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"""TUTase1"""	613669	"""PAP associated domain containing 1"""	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.484C>T	10.37:g.30629226G>A	ENSP00000263063:p.Arg162Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_018109	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Missense_Mutation	SNP	ENST00000263063.4	37	CCDS7165.1	455	0.20833333333333334	71	0.1443089430894309	57	0.1574585635359116	137	0.2395104895104895	190	0.25065963060686014	G	7.660	0.684719	0.14973	0.212211	0.287907	ENSG00000107951	ENST00000358107;ENST00000263063;ENST00000417581;ENST00000421701	T;T;T;T	0.45276	2.02;2.02;2.02;0.9	5.08	-10.2	0.00374	.	3.461010	0.00794	N	0.001365	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.18013	0.001;0.025;0.001	B;B;B	0.09377	0.001;0.004;0.001	T	0.12502	-1.0545	9	0.52906	T	0.07	13.6516	5.5208	0.16931	0.2334:0.0678:0.4959:0.2028	rs1047991;rs3187968;rs17295129;rs17569747;rs61559846;rs1047991	124;292;162	Q5T851;Q9NVV4-2;Q9NVV4	.;.;PAPD1_HUMAN	C	292;162;97;124	ENSP00000350820:R292C;ENSP00000263063:R162C;ENSP00000404392:R97C;ENSP00000394118:R124C	ENSP00000263063:R162C	R	-	1	0	MTPAP	30669232	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.273000	0.00531	-4.256000	0.00061	-3.879000	0.00017	CGC	G|0.755;A|0.245	0.245	strong		0.413	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109	
ST14	6768	hgsc.bcm.edu	37	11	130066261	130066261	+	Missense_Mutation	SNP	C	C	A	rs17667603	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:130066261C>A	ENST00000278742.5	+	10	1559	c.1141C>A	c.(1141-1143)Cgc>Agc	p.R381S		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	381	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.		R -> S (in dbSNP:rs17667603). {ECO:0000269|Ref.4}.		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)	TGTGAAGGTGCGCTTCAAATT	0.607													C|||	160	0.0319489	0.0265	0.0389	5008	,	,		14529	0.0		0.0845	False		,,,				2504	0.0133				p.R381S		Atlas-SNP	.											.	ST14	82	.	0			c.C1141A						PASS	.	C	SER/ARG	178,4224		4,170,2027	71.0	57.0	62.0		1141	1.4	0.8	11	dbSNP_123	62	653,7941		21,611,3665	yes	missense	ST14	NM_021978.3	110	25,781,5692	AA,AC,CC		7.5983,4.0436,6.3943	possibly-damaging	381/856	130066261	831,12165	2201	4297	6498	SO:0001583	missense	6768	exon10			AAGGTGCGCTTCA	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.1141C>A	11.37:g.130066261C>A	ENSP00000278742:p.Arg381Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	85	0.03891941391941392	12	0.024390243902439025	17	0.04696132596685083	0	0.0	56	0.07387862796833773	C	10.01	1.233600	0.22626	0.040436	0.075983	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.17054	2.3	4.62	1.44	0.22558	CUB (5);	0.984165	0.08241	N	0.976043	T	0.00608	0.0020	L	0.35644	1.08	0.29742	P	0.837043	B	0.20887	0.049	B	0.24394	0.053	T	0.37798	-0.9690	9	0.26408	T	0.33	.	3.5592	0.07875	0.1649:0.5744:0.1596:0.1011	rs17667603;rs52826539;rs17667603	381	Q9Y5Y6	ST14_HUMAN	S	381;283	ENSP00000278742:R381S	ENSP00000278742:R381S	R	+	1	0	ST14	129571471	0.021000	0.18746	0.821000	0.32701	0.349000	0.29174	0.237000	0.17985	-0.001000	0.14495	0.655000	0.94253	CGC	C|0.949;A|0.051	0.051	strong		0.607	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
COPE	11316	hgsc.bcm.edu	37	19	19017862	19017862	+	Missense_Mutation	SNP	G	G	A	rs10330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19017862G>A	ENST00000262812.4	-	4	398	c.350C>T	c.(349-351)aCc>aTc	p.T117I	COPE_ENST00000351079.4_Intron|COPE_ENST00000600932.1_Missense_Mutation_p.T117I|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000349893.4_Missense_Mutation_p.T117I|COPE_ENST00000598969.1_Intron	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	83	0	0		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	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	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331094	28331094	+	Missense_Mutation	SNP	G	G	A	rs17856167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:28331094G>A	ENST00000377255.3	+	5	862	c.565G>A	c.(565-567)Gtg>Atg	p.V189M	ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.V189M|ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.V41M	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	189			V -> M (in dbSNP:rs17856167). {ECO:0000269|Ref.1}.		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						CCAGGTCCCCGTGCTTGCCCA	0.517													g|||	486	0.0970447	0.1415	0.0807	5008	,	,		17926	0.1349		0.0457	False		,,,				2504	0.0624				p.V189M		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.G565A						PASS	.	A	MET/VAL,MET/VAL,MET/VAL	474,3932		25,424,1754	88.0	77.0	81.0		565,121,565	-1.1	0.0	6	dbSNP_123	81	381,8219		3,375,3922	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	21,21,21	28,799,5676	AA,AG,GG		4.4302,10.7581,6.5739	benign,benign,benign	189/539,41/391,189/539	28331094	855,12151	2203	4300	6503	SO:0001583	missense	80317	exon4			GTCCCCGTGCTTG	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.565G>A	6.37:g.28331094G>A	ENSP00000366465:p.Val189Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	202	0.0924908424908425	65	0.13211382113821138	26	0.0718232044198895	82	0.14335664335664336	29	0.03825857519788918	.	1.357	-0.589719	0.03799	0.107581	0.044302	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.05649	3.47;3.41;3.47	1.98	-1.09	0.09904	.	.	.	.	.	T	0.00552	0.0018	N	0.08118	0	0.80722	P	0.0	P	0.46277	0.875	B	0.25759	0.063	T	0.45775	-0.9238	8	0.27785	T	0.31	.	2.0626	0.03596	0.3365:0.0:0.4072:0.2563	rs17856167;rs17856167	189	Q9BRR0	ZKSC3_HUMAN	M	189;41;189	ENSP00000252211:V189M;ENSP00000341883:V41M;ENSP00000366465:V189M	ENSP00000252211:V189M	V	+	1	0	ZKSCAN3	28439073	0.000000	0.05858	0.023000	0.16930	0.051000	0.14879	-0.316000	0.08071	-0.350000	0.08262	-0.213000	0.12676	GTG	G|0.921;A|0.079	0.079	strong		0.517	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
UBR4	23352	hgsc.bcm.edu	37	1	19499560	19499560	+	Missense_Mutation	SNP	T	T	C	rs16862578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19499560T>C	ENST00000375254.3	-	25	3346	c.3319A>G	c.(3319-3321)Acc>Gcc	p.T1107A	UBR4_ENST00000375217.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375226.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375267.2_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						scavenged	.	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	89	2	0.0224719		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	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	
CSN3	1448	hgsc.bcm.edu	37	4	71115060	71115060	+	Missense_Mutation	SNP	G	G	A	rs3775739	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71115060G>A	ENST00000304954.3	+	4	519	c.433G>A	c.(433-435)Gct>Act	p.A145T		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)				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						ACCTACACCAGCTCCTGCCAC	0.458													A|||	745	0.148762	0.0091	0.0879	5008	,	,		17226	0.2857		0.1402	False		,,,				2504	0.2485				p.A145T		Atlas-SNP	.											.	CSN3	43	.	0			c.G433A						PASS	.	A	THR/ALA	167,4239	811.1+/-416.0	5,157,2041	71.0	69.0	70.0		433	-3.6	0.0	4	dbSNP_107	70	1185,7415	764.3+/-407.6	82,1021,3197	yes	missense	CSN3	NM_005212.2	58	87,1178,5238	AA,AG,GG		13.7791,3.7903,10.3952	benign	145/183	71115060	1352,11654	2203	4300	6503	SO:0001583	missense	1448	exon4			ACACCAGCTCCTG	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.433G>A	4.37:g.71115060G>A	ENSP00000304822:p.Ala145Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000304954.3	37	CCDS3538.1	315	0.14423076923076922	4	0.008130081300813009	41	0.1132596685082873	162	0.28321678321678323	108	0.1424802110817942	A	0.224	-1.026583	0.02045	0.037903	0.137791	ENSG00000171209	ENST00000304954	T	0.21543	2.0	4.32	-3.61	0.04556	.	1.093820	0.06981	N	0.819843	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.37572	-0.9700	9	0.02654	T	1	-11.8062	9.109	0.36716	0.3016:0.0:0.5822:0.1162	rs3775739;rs52798047;rs58688596;rs3775739	145	P07498	CASK_HUMAN	T	145	ENSP00000304822:A145T	ENSP00000304822:A145T	A	+	1	0	CSN3	71149649	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.670000	0.05256	-1.597000	0.01609	-2.688000	0.00140	GCT	G|0.881;A|0.119	0.119	strong		0.458	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212	
FRAS1	80144	hgsc.bcm.edu	37	4	79387586	79387586	+	Silent	SNP	A	A	G	rs34840208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:79387586A>G	ENST00000264895.6	+	50	7694	c.7254A>G	c.(7252-7254)aaA>aaG	p.K2418K		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2418					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						AAGGGGGAAAAGAGGTGAGGG	0.502													A|||	1571	0.313698	0.1059	0.268	5008	,	,		22102	0.4702		0.2654	False		,,,				2504	0.5153				p.K2418K		Atlas-SNP	.											.	FRAS1	779	.	0			c.A7254G						PASS	.	A		499,3511		30,439,1536	38.0	38.0	38.0		7254	2.2	1.0	4	dbSNP_126	38	2081,6297		252,1577,2360	no	coding-synonymous	FRAS1	NM_025074.6		282,2016,3896	GG,GA,AA		24.8389,12.4439,20.8266		2418/4013	79387586	2580,9808	2005	4189	6194	SO:0001819	synonymous_variant	80144	exon50			GGGAAAAGAGGTG	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.7254A>G	4.37:g.79387586A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	636	0.29120879120879123	55	0.11178861788617886	95	0.26243093922651933	278	0.486013986013986	208	0.27440633245382584	A	7.897	0.733586	0.15574	0.124439	0.248389	ENSG00000138759	ENST00000512123	.	.	.	4.86	2.18	0.27775	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999919645	.	.	.	.	.	.	T	0.48864	-0.8997	3	.	.	.	.	8.6299	0.33913	0.7309:0.0:0.2691:0.0	rs34840208;rs62308120	.	.	.	G	647	.	.	R	+	1	2	FRAS1	79606610	0.990000	0.36364	0.995000	0.50966	0.757000	0.42996	0.354000	0.20146	0.342000	0.23796	0.477000	0.44152	AGA	A|0.709;G|0.291	0.291	strong		0.502	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PRR5	55615	hgsc.bcm.edu	37	22	45075741	45075741	+	Missense_Mutation	SNP	C	C	T	rs74960825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45075741C>T	ENST00000403581.1	+	2	671	c.62C>T	c.(61-63)cCg>cTg	p.P21L	PRR5_ENST00000006251.7_Intron	NM_001198721.1	NP_001185650.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	0	Interaction with RICTOR.				cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		GAAAAGATGCCGGCGCAGCCT	0.602													C|||	10	0.00199681	0.0008	0.0043	5008	,	,		15072	0.0		0.006	False		,,,				2504	0.0				p.P21L		Atlas-SNP	.											.	PRR5	75	.	0			c.C62T						PASS	.	C	,,,LEU/PRO,	0,1750		0,0,875	10.0	11.0	10.0		,,,62,	-1.5	0.0	22	dbSNP_131	10	21,3953		0,21,1966	yes	intron,intron,intron,missense,intron	PRR5	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3	,,,98,	0,21,2841	TT,TC,CC		0.5284,0.0,0.3669	,,,,	,,,21/412,	45075741	21,5703	875	1987	2862	SO:0001583	missense	55615	exon2			AGATGCCGGCGCA	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000403581.1:c.62C>T	22.37:g.45075741C>T	ENSP00000384848:p.Pro21Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000403581.1	37	CCDS56232.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	1.807	-0.475651	0.04414	0.0	0.005284	ENSG00000186654	ENST00000403581	T	0.32515	1.45	1.09	-1.49	0.08718	.	.	.	.	.	T	0.09555	0.0235	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20174	-1.0283	9	0.87932	D	0	.	4.4212	0.11481	0.0:0.534:0.0:0.466	.	21	B1AHF6	.	L	21	ENSP00000384848:P21L	ENSP00000384848:P21L	P	+	2	0	PRR5	43454405	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.017000	0.12590	-0.536000	0.06298	-0.474000	0.04947	CCG	C|0.996;T|0.004	0.004	strong		0.602	PRR5-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318199.1	NM_001017528	
TRIM6	117854	hgsc.bcm.edu	37	11	5632212	5632212	+	Silent	SNP	G	G	A	rs10769124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5632212G>A	ENST00000278302.5	+	8	1247	c.1107G>A	c.(1105-1107)ctG>ctA	p.L369L	TRIM6_ENST00000380097.3_Silent_p.L397L|TRIM6_ENST00000380107.1_Silent_p.L343L|TRIM6_ENST00000507320.1_Silent_p.L194L|TRIM6_ENST00000506134.1_Silent_p.L194L|TRIM6_ENST00000515022.1_Silent_p.L194L|TRIM6_ENST00000481603.1_3'UTR|AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Intron|TRIM6_ENST00000445329.1_Silent_p.L194L	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	369	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)		CCTGGATCCTGGGGGTATGCA	0.493													G|||	3952	0.789137	0.6044	0.7622	5008	,	,		20805	0.998		0.662	False		,,,				2504	0.9734				p.L397L		Atlas-SNP	.											.	TRIM6	55	.	0			c.G1191A						PASS	.	G	,,,,	2793,1609	663.3+/-401.2	905,983,313	121.0	119.0	120.0		1191,,582,582,1107	2.3	1.0	11	dbSNP_120	120	6137,2457	696.7+/-404.9	2188,1761,348	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	,,,,	3093,2744,661	AA,AG,GG		28.5897,36.5516,31.2865	,,,,	397/517,,194/314,194/314,369/489	5632212	8930,4066	2201	4297	6498	SO:0001819	synonymous_variant	117854	exon8			GATCCTGGGGGTA	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.1107G>A	11.37:g.5632212G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_001003818	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Silent	SNP	ENST00000278302.5	37	CCDS31390.1																																																																																			G|0.300;A|0.700	0.700	strong		0.493	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
OR52N1	79473	hgsc.bcm.edu	37	11	5809673	5809673	+	Missense_Mutation	SNP	C	C	T	rs10769224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5809673C>T	ENST00000317078.1	-	1	373	c.374G>A	c.(373-375)tGt>tAt	p.C125Y	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	125			C -> Y (in dbSNP:rs10769224).			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)		GATGGCCACACAGTGGTCCAG	0.507													T|||	1611	0.321685	0.4576	0.2738	5008	,	,		24514	0.2004		0.332	False		,,,				2504	0.2863				p.C125Y		Atlas-SNP	.											.	OR52N1	70	.	0			c.G374A						PASS	.	T	TYR/CYS	1894,2508	628.7+/-395.1	396,1102,703	159.0	137.0	144.0		374	2.1	0.9	11	dbSNP_120	144	2640,5952	686.7+/-404.1	396,1848,2052	yes	missense	OR52N1	NM_001001913.1	194	792,2950,2755	TT,TC,CC		30.7263,43.0259,34.893	benign	125/321	5809673	4534,8460	2201	4296	6497	SO:0001583	missense	79473	exon1			GCCACACAGTGGT	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.374G>A	11.37:g.5809673C>T	ENSP00000322823:p.Cys125Tyr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	37	CCDS31398.1	667	0.30540293040293043	217	0.4410569105691057	94	0.2596685082872928	109	0.19055944055944055	247	0.3258575197889182	T	0.003	-2.437657	0.00182	0.430259	0.307263	ENSG00000181001	ENST00000317078	T	0.21543	2.0	4.58	2.13	0.27403	GPCR, rhodopsin-like superfamily (1);	0.151595	0.30584	N	0.009313	T	0.00012	0.0000	N	0.00014	-2.9	0.46981	P	7.260000000000044E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43442	-0.9391	9	0.02654	T	1	.	5.1575	0.15042	0.2755:0.0789:0.0:0.6457	rs10769224;rs52827772;rs61031410;rs10769224	125	Q8NH53	O52N1_HUMAN	Y	125	ENSP00000322823:C125Y	ENSP00000322823:C125Y	C	-	2	0	OR52N1	5766249	0.030000	0.19436	0.875000	0.34327	0.091000	0.18340	0.193000	0.17116	0.018000	0.15052	-0.326000	0.08463	TGT	C|0.675;T|0.325	0.325	strong		0.507	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
WDR90	197335	hgsc.bcm.edu	37	16	711905	711905	+	Silent	SNP	A	A	G	rs2301426	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	58	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	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	
ETV7	51513	hgsc.bcm.edu	37	6	36341294	36341294	+	Silent	SNP	C	C	T	rs3213530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:36341294C>T	ENST00000340181.4	-	4	610	c.369G>A	c.(367-369)ggG>ggA	p.G123G	ETV7_ENST00000373738.1_Silent_p.G68G|ETV7_ENST00000339796.5_Silent_p.G123G|ETV7_ENST00000373737.4_Silent_p.G123G|ETV7_ENST00000538992.1_5'UTR	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	123					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)	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 RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						CAAAAAAGGGCCCACACACCA	0.627													C|||	1094	0.21845	0.2179	0.3415	5008	,	,		11130	0.2391		0.1501	False		,,,				2504	0.181				p.G123G		Atlas-SNP	.											.	ETV7	31	.	0			c.G369A						PASS	.	C	,,,,,,,	871,3531		87,697,1417	28.0	25.0	26.0		369,204,192,369,204,126,,369	-2.0	0.1	6	dbSNP_106	26	1331,7267		105,1121,3073	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	,,,,,,,	192,1818,4490	TT,TC,CC		15.4803,19.7865,16.9385	,,,,,,,	123/318,68/287,64/283,123/265,68/263,42/261,,123/342	36341294	2202,10798	2201	4299	6500	SO:0001819	synonymous_variant	51513	exon4			AAAGGGCCCACAC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"""TEL2 oncogene"""	605255	"""ets variant gene 7 (TEL2 oncogene)"""			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.369G>A	6.37:g.36341294C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Silent	SNP	ENST00000340181.4	37	CCDS4819.1																																																																																			C|0.813;T|0.187	0.187	strong		0.627	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
DNHD1	144132	hgsc.bcm.edu	37	11	6559961	6559961	+	Silent	SNP	G	G	A	rs118078642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6559961G>A	ENST00000527990.2	+	14	3246	c.3246G>A	c.(3244-3246)gaG>gaA	p.E1082E	DNHD1_ENST00000254579.6_Silent_p.E1082E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1082					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)		TCCTGGGGGAGTTTCGCAGCT	0.602													G|||	13	0.00259585	0.0	0.0072	5008	,	,		17960	0.0		0.007	False		,,,				2504	0.001				p.E1082E		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3246A						PASS	.	G		6,1376		0,6,685	13.0	13.0	13.0		3246	3.2	1.0	11	dbSNP_132	13	31,3151		0,31,1560	no	coding-synonymous	DNHD1	NM_144666.2		0,37,2245	AA,AG,GG		0.9742,0.4342,0.8107		1082/4754	6559961	37,4527	691	1591	2282	SO:0001819	synonymous_variant	144132	exon16			GGGGGAGTTTCGC	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.3246G>A	11.37:g.6559961G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	44	0.656716	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
WDR35	57539	hgsc.bcm.edu	37	2	20135283	20135283	+	Silent	SNP	T	T	C	rs6741091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:20135283T>C	ENST00000345530.3	-	22	2644	c.2529A>G	c.(2527-2529)gaA>gaG	p.E843E	WDR35_ENST00000281405.4_Silent_p.E832E|WDR35_ENST00000416055.2_Silent_p.E408E	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	843					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)				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)					TCTCTAACCCTTCATAATCCT	0.348													C|||	2558	0.510783	0.472	0.4597	5008	,	,		15149	0.623		0.4026	False		,,,				2504	0.5951				p.E843E		Atlas-SNP	.											.	WDR35	92	.	0			c.A2529G						PASS	.	C	,	1990,2416	614.2+/-392.3	473,1044,686	106.0	103.0	104.0		2529,2496	-4.0	0.2	2	dbSNP_116	104	3599,5001	625.0+/-397.7	757,2085,1458	no	coding-synonymous,coding-synonymous	WDR35	NM_001006657.1,NM_020779.3	,	1230,3129,2144	CC,CT,TT		41.8488,45.1657,42.9725	,	843/1182,832/1171	20135283	5589,7417	2203	4300	6503	SO:0001819	synonymous_variant	57539	exon22			TAACCCTTCATAA	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.2529A>G	2.37:g.20135283T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Silent	SNP	ENST00000345530.3	37	CCDS33152.1																																																																																			T|0.533;C|0.467	0.467	strong		0.348	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42386630	42386630	+	Missense_Mutation	SNP	G	G	T	rs75734921	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42386630G>T	ENST00000290472.3	-	1	122	c.28C>A	c.(28-30)Cct>Act	p.P10T		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	10	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.			P -> T (in Ref. 1; BAC67158). {ECO:0000305}.	glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGGTGGCCAGGTGGTCCCCCA	0.617													G|||	228	0.0455272	0.0234	0.072	5008	,	,		17431	0.001		0.1044	False		,,,				2504	0.0419				p.P10T		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.C28A						PASS	.	G	THR/PRO	184,4222	120.0+/-157.7	1,182,2020	116.0	94.0	101.0		28	4.4	0.8	15	dbSNP_132	101	898,7700	200.7+/-244.4	42,814,3443	yes	missense	PLA2G4D	NM_178034.3	38	43,996,5463	TT,TG,GG		10.4443,4.1761,8.3205	benign	10/819	42386630	1082,11922	2203	4299	6502	SO:0001583	missense	283748	exon1			GGCCAGGTGGTCC	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.28C>A	15.37:g.42386630G>T	ENSP00000290472:p.Pro10Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	126	0.057692307692307696	15	0.03048780487804878	29	0.08011049723756906	0	0.0	82	0.10817941952506596	G	8.831	0.939844	0.18281	0.041761	0.104443	ENSG00000159337	ENST00000290472	T	0.01192	5.2	4.4	4.4	0.53042	C2 membrane targeting protein (1);	0.723471	0.12616	N	0.453410	T	0.00039	0.0001	L	0.55481	1.735	0.41402	P	0.012317000000000022	P	0.38335	0.627	B	0.26614	0.071	T	0.54370	-0.8304	9	0.30854	T	0.27	-0.0898	12.6888	0.56962	0.0:0.0:1.0:0.0	.	10	Q86XP0	PA24D_HUMAN	T	10	ENSP00000290472:P10T	ENSP00000290472:P10T	P	-	1	0	PLA2G4D	40173922	0.015000	0.18098	0.759000	0.31340	0.316000	0.28119	0.165000	0.16564	2.441000	0.82636	0.655000	0.94253	CCT	G|0.922;T|0.078	0.078	strong		0.617	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833378	27833378	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27833378C>T	ENST00000357320.2	+	1	345	c.246C>T	c.(244-246)cgC>cgT	p.R82R		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	82						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						TTATCCCGCGCCACTTGCAGC	0.637																																					p.R82R		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C246T						PASS	.						112.0	113.0	113.0					6																	27833378		2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CCCGCGCCACTTG	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.246C>T	6.37:g.27833378C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			.	.	none		0.637	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
SLC4A11	83959	hgsc.bcm.edu	37	20	3218634	3218634	+	5'Flank	SNP	G	G	C	rs3810562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3218634G>C	ENST00000380056.3	-	0	0				SLC4A11_ENST00000380059.3_Missense_Mutation_p.P26R|SLC4A11_ENST00000539553.2_Intron	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	101	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	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		
EFHB	151651	hgsc.bcm.edu	37	3	19962044	19962044	+	Missense_Mutation	SNP	G	G	A	rs13078867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:19962044G>A	ENST00000295824.9	-	2	966	c.805C>T	c.(805-807)Cca>Tca	p.P269S	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Missense_Mutation_p.P139S	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	269			P -> S (in dbSNP:rs13078867).				calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TAACCAACTGGAATAACTTTT	0.373													G|||	956	0.190895	0.0734	0.1758	5008	,	,		16758	0.2143		0.2495	False		,,,				2504	0.2761				p.P269S		Atlas-SNP	.											.	EFHB	186	.	0			c.C805T						PASS	.	G	SER/PRO	433,3973	211.5+/-231.7	22,389,1792	80.0	81.0	81.0		805	4.9	0.1	3	dbSNP_121	81	2224,6376	377.8+/-338.7	280,1664,2356	yes	missense	EFHB	NM_144715.3	74	302,2053,4148	AA,AG,GG		25.8605,9.8275,20.429	probably-damaging	269/834	19962044	2657,10349	2203	4300	6503	SO:0001583	missense	151651	exon2			CAACTGGAATAAC	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.805C>T	3.37:g.19962044G>A	ENSP00000295824:p.Pro269Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	426	0.19505494505494506	44	0.08943089430894309	63	0.17403314917127072	121	0.21153846153846154	198	0.2612137203166227	G	17.37	3.373042	0.61624	0.098275	0.258605	ENSG00000163576	ENST00000295824;ENST00000344838;ENST00000389256	T;T;T	0.26957	1.7;1.8;2.0	5.75	4.88	0.63580	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.72894	2.215	0.37975	P	0.06657100000000005	P;P	0.46142	0.873;0.675	P;B	0.47673	0.554;0.32	T	0.19712	-1.0297	8	.	.	.	-12.5966	12.1223	0.53897	0.0804:0.0:0.9196:0.0	rs13078867;rs52802880;rs58072698;rs13078867	139;269	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	S	269;139;269	ENSP00000295824:P269S;ENSP00000342263:P139S;ENSP00000373908:P269S	.	P	-	1	0	EFHB	19937048	1.000000	0.71417	0.055000	0.19348	0.929000	0.56500	4.533000	0.60615	1.438000	0.47492	0.655000	0.94253	CCA	G|0.804;A|0.196	0.196	strong		0.373	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
OMP	4975	hgsc.bcm.edu	37	11	76814110	76814110	+	Silent	SNP	G	G	A	rs2233549	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76814110G>A	ENST00000529803.1	+	1	225	c.225G>A	c.(223-225)ccG>ccA	p.P75P	CAPN5_ENST00000529629.1_Intron|CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000456580.2_Intron|CAPN5_ENST00000278559.3_Intron	NM_006189.1	NP_006180.1	P47874	OMP_HUMAN	olfactory marker protein	75					neurogenesis (GO:0022008)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						TGGACAAGCCGGGCAAGGTCA	0.622													G|||	1199	0.239417	0.1952	0.2061	5008	,	,		17152	0.2321		0.2107	False		,,,				2504	0.3599				p.P75P		Atlas-SNP	.											OMP,NS,carcinoma,+2,1	OMP	14	1	0			c.G225A						scavenged	.	G	,	794,3570		65,664,1453	54.0	65.0	61.0		,225	-7.9	0.6	11	dbSNP_98	61	1673,6867		168,1337,2765	no	intron,coding-synonymous	CAPN5,OMP	NM_004055.4,NM_006189.1	,	233,2001,4218	AA,AG,GG		19.5902,18.1943,19.1181	,	,75/164	76814110	2467,10437	2182	4270	6452	SO:0001819	synonymous_variant	4975	exon1			CAAGCCGGGCAAG	U01212	CCDS53682.1	11q14-q21	2008-07-21				ENSG00000254550			8136	protein-coding gene	gene with protein product		164340				8499899	Standard	NM_006189		Approved		uc010rsk.2	P47874		ENST00000529803.1:c.225G>A	11.37:g.76814110G>A		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_006189	Q562G2	Silent	SNP	ENST00000529803.1	37	CCDS53682.1																																																																																			G|0.790;A|0.210	0.210	strong		0.622	OMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382570.1	NM_006189	
SESTD1	91404	hgsc.bcm.edu	37	2	179979930	179979930	+	Silent	SNP	T	T	C	rs2289993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179979930T>C	ENST00000428443.3	-	16	2017	c.1701A>G	c.(1699-1701)caA>caG	p.Q567Q		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	567							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|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)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AGCGCAAAGATTGGCATAACA	0.388													T|||	972	0.194089	0.2882	0.1081	5008	,	,		17715	0.0645		0.166	False		,,,				2504	0.2904				p.Q567Q		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1701G						PASS	.	T		1082,3324	391.7+/-328.2	128,826,1249	71.0	63.0	66.0		1701	0.9	1.0	2	dbSNP_100	66	1358,7242	265.8+/-286.4	112,1134,3054	no	coding-synonymous	SESTD1	NM_178123.4		240,1960,4303	CC,CT,TT		15.7907,24.5574,18.7606		567/697	179979930	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon16			CAAAGATTGGCAT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1701A>G	2.37:g.179979930T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.810;C|0.190	0.190	strong		0.388	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
CMYA5	202333	hgsc.bcm.edu	37	5	79086883	79086883	+	Missense_Mutation	SNP	G	G	A	rs1129770	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79086883G>A	ENST00000446378.2	+	11	11811	c.11780G>A	c.(11779-11781)cGg>cAg	p.R3927Q	CTC-431G16.2_ENST00000421252.2_RNA	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3927	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> Q (in dbSNP:rs1129770). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		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)		GAGAGGAGACGGCTGACGGAG	0.517													G|||	596	0.11901	0.0726	0.1066	5008	,	,		18826	0.0942		0.2018	False		,,,				2504	0.1309				p.R3927Q		Atlas-SNP	.											.	CMYA5	643	.	0			c.G11780A						PASS	.	G	GLN/ARG	404,3684		16,372,1656	62.0	60.0	61.0		11780	6.1	1.0	5	dbSNP_86	61	1515,6905		138,1239,2833	yes	missense	CMYA5	NM_153610.3	43	154,1611,4489	AA,AG,GG		17.9929,9.8826,15.3422	probably-damaging	3927/4070	79086883	1919,10589	2044	4210	6254	SO:0001583	missense	202333	exon11			GGAGACGGCTGAC	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.11780G>A	5.37:g.79086883G>A	ENSP00000394770:p.Arg3927Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	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	267	0.12225274725274725	27	0.054878048780487805	38	0.10497237569060773	59	0.10314685314685315	143	0.18865435356200527	G	24.3	4.511938	0.85389	0.098826	0.179929	ENSG00000164309	ENST00000446378	T	0.20463	2.07	6.06	6.06	0.98353	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00039	0.0001	L	0.49350	1.555	0.39798	P	0.027464000000000044	D	0.89917	1.0	D	0.66497	0.944	T	0.25710	-1.0124	8	0.72032	D	0.01	.	5.9675	0.19332	0.1701:0.1628:0.6671:0.0	rs1129770;rs2287675;rs3188025;rs17392236;rs17412292;rs52809107;rs59804203;rs1129770	3927	Q8N3K9	CMYA5_HUMAN	Q	3927	ENSP00000394770:R3927Q	ENSP00000394770:R3927Q	R	+	2	0	CMYA5	79122639	0.941000	0.31946	1.000000	0.80357	0.927000	0.56198	3.175000	0.50855	2.882000	0.98803	0.655000	0.94253	CGG	G|0.884;A|0.116	0.116	strong		0.517	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ARHGAP4	393	hgsc.bcm.edu	37	X	153175295	153175295	+	Missense_Mutation	SNP	C	C	A	rs2070099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153175295C>A	ENST00000350060.5	-	19	2355	c.2314G>T	c.(2314-2316)Gta>Tta	p.V772L	ARHGAP4_ENST00000537206.1_Missense_Mutation_p.V749L|ARHGAP4_ENST00000393721.1_Missense_Mutation_p.V594L|ARHGAP4_ENST00000370028.3_Missense_Mutation_p.V812L|ARHGAP4_ENST00000467421.1_5'UTR|ARHGAP4_ENST00000370016.1_Missense_Mutation_p.V751L	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	772	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGCCGCAGTACGTCCCCCCGC	0.706													C|||	117	0.0309934	0.0023	0.0187	3775	,	,		8955	0.0		0.0328	False		,,,				2504	0.0695				p.V812L		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.G2434T						PASS	.	C	LEU/VAL,LEU/VAL	24,3789		0,20,4,1608,553	12.0	14.0	14.0		2434,2314	-0.3	0.0	X	dbSNP_96	14	266,6431		3,177,83,2242,1770	no	missense,missense	ARHGAP4	NM_001164741.1,NM_001666.4	32,32	3,197,87,3850,2323	AA,AC,A,CC,C		3.9719,0.6294,2.7593	benign,benign	812/987,772/947	153175295	290,10220	2185	4275	6460	SO:0001583	missense	393	exon20			GCAGTACGTCCCC	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"""Rho GTPase activating proteins"""	674	protein-coding gene	gene with protein product	"""Rho-GAP hematopoietic protein C1"""	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.2314G>T	X.37:g.153175295C>A	ENSP00000203786:p.Val772Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_001164741	Q14144|Q86UY3	Missense_Mutation	SNP	ENST00000350060.5	37	CCDS14736.1	27	0.0162748643761302	1	0.0020325203252032522	5	0.013888888888888888	0	0.0	19	0.02526595744680851	C	0.038	-1.297525	0.01364	0.006294	0.039719	ENSG00000089820	ENST00000393721;ENST00000370028;ENST00000350060;ENST00000370016;ENST00000537206	T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66	4.44	-0.296	0.12824	Src homology-3 domain (4);	0.625045	0.12235	N	0.487041	T	0.05181	0.0138	N	0.05619	-0.005	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.003	T	0.13415	-1.0510	10	0.22109	T	0.4	.	4.9253	0.13891	0.151:0.4538:0.0:0.3952	rs2070099	812;772	Q86UY3;P98171	.;RHG04_HUMAN	L	594;812;772;751;749	ENSP00000377322:V594L;ENSP00000359045:V812L;ENSP00000203786:V772L;ENSP00000359033:V751L;ENSP00000444169:V749L	ENSP00000203786:V772L	V	-	1	0	ARHGAP4	152828489	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.319000	0.08039	-0.084000	0.12595	-0.301000	0.09380	GTA	C|0.979;A|0.021	0.021	strong		0.706	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115526177	115526177	+	Silent	SNP	A	A	G	rs10885500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115526177A>G	ENST00000369310.3	+	2	580	c.18A>G	c.(16-18)caA>caG	p.Q6Q	PLEKHS1_ENST00000369312.4_5'UTR|PLEKHS1_ENST00000361048.1_Silent_p.Q12Q	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	6																	TAGGCAAACAATTTACATTTT	0.338													A|||	1168	0.233227	0.0234	0.4625	5008	,	,		18429	0.1379		0.4175	False		,,,				2504	0.2628				p.Q12Q		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.A36G						PASS	.	A	,,,	381,4023	190.2+/-216.2	23,335,1844	74.0	77.0	76.0		,,36,18	3.1	0.8	10	dbSNP_120	76	3479,5117	507.1+/-376.8	719,2041,1538	no	utr-5,intron,coding-synonymous,coding-synonymous	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	,,,	742,2376,3382	GG,GA,AA		40.4723,8.6512,29.6923	,,,	,,12/364,6/466	115526177	3860,9140	2202	4298	6500	SO:0001819	synonymous_variant	79949	exon3			CAAACAATTTACA	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.18A>G	10.37:g.115526177A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000369310.3	37	CCDS53580.1																																																																																			A|0.729;G|0.271	0.271	strong		0.338	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
CEP120	153241	hgsc.bcm.edu	37	5	122682348	122682348	+	Silent	SNP	A	A	G	rs1047438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:122682348A>G	ENST00000306467.5	-	20	3130	c.2826T>C	c.(2824-2826)gaT>gaC	p.D942D	CEP120_ENST00000328236.5_Silent_p.D942D|CEP120_ENST00000306481.6_Silent_p.D916D			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	942					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)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						TCAAATAATCATCCAAACCTT	0.428													A|||	3419	0.682708	0.7209	0.6729	5008	,	,		16546	0.5923		0.7406	False		,,,				2504	0.6718				p.D942D		Atlas-SNP	.											CEP120,colon,carcinoma,0,1	CEP120	72	1	0			c.T2826C						PASS	.	A	,	3362,1044	726.1+/-409.7	1289,784,130	182.0	185.0	184.0		2748,2826	1.6	1.0	5	dbSNP_86	184	6127,2473	695.6+/-404.8	2181,1765,354	no	coding-synonymous,coding-synonymous	CEP120	NM_001166226.1,NM_153223.3	,	3470,2549,484	GG,GA,AA		28.7558,23.695,27.0414	,	916/961,942/987	122682348	9489,3517	2203	4300	6503	SO:0001819	synonymous_variant	153241	exon21			ATAATCATCCAAA	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.2826T>C	5.37:g.122682348A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	37	CCDS4134.2																																																																																			G|0.709;N|0.000	0.709	strong		0.428	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
FLG	2312	hgsc.bcm.edu	37	1	152286002	152286002	+	Missense_Mutation	SNP	T	T	C	rs386635459|rs2011331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152286002T>C	ENST00000368799.1	-	3	1395	c.1360A>G	c.(1360-1362)Aca>Gca	p.T454A	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	454	Ser-rich.		T -> A (in dbSNP:rs2011331).		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)			CGGCCACGTGTGGACTCTTGG	0.587									Ichthyosis				-|||	2324	0.464058	0.5204	0.4539	5008	,	,		18904	0.6587		0.173	False		,,,				2504	0.4939				p.T454A		Atlas-SNP	.											.	FLG	900	.	0			c.A1360G						PASS	.	C	ALA/THR	2058,2348		473,1112,618	201.0	196.0	198.0		1360	-6.9	0.0	1	dbSNP_92	198	1461,7139		126,1209,2965	no	missense	FLG	NM_002016.1	58	599,2321,3583	CC,CT,TT		16.9884,46.709,27.0567	benign	454/4062	152286002	3519,9487	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CACGTGTGGACTC	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.1360A>G	1.37:g.152286002T>C	ENSP00000357789:p.Thr454Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	263	161	0.612167	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	869	0.39789377289377287	240	0.4878048780487805	136	0.3756906077348066	360	0.6293706293706294	133	0.17546174142480211	-	3.629	-0.075933	0.07184	0.46709	0.169884	ENSG00000143631	ENST00000368799	T	0.02197	4.4	3.43	-6.86	0.01676	.	.	.	.	.	T	0.00210	0.0006	N	0.05230	-0.09	0.80722	P	0.0	B	0.19935	0.04	B	0.11329	0.006	T	0.48559	-0.9025	8	0.05620	T	0.96	.	0.0862	0.00036	0.2681:0.2448:0.199:0.2881	rs60352258	454	P20930	FILA_HUMAN	A	454	ENSP00000357789:T454A	ENSP00000357789:T454A	T	-	1	0	FLG	150552626	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.855000	0.00729	-3.086000	0.00249	-1.512000	0.00943	ACA	T|0.667;C|0.333	0.333	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SAMD4A	23034	hgsc.bcm.edu	37	14	55243152	55243152	+	Silent	SNP	C	C	T	rs1951437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:55243152C>T	ENST00000554335.1	+	11	2601	c.1938C>T	c.(1936-1938)ccC>ccT	p.P646P	SAMD4A_ENST00000392067.3_Silent_p.P646P|SAMD4A_ENST00000555192.1_Silent_p.P237P|SAMD4A_ENST00000251091.5_Silent_p.P558P|SAMD4A_ENST00000357634.3_Silent_p.P645P			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	646					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TTGCCAACCCCGGGGGCAGCA	0.587													C|||	124	0.0247604	0.0008	0.0231	5008	,	,		15289	0.001		0.0437	False		,,,				2504	0.0634				p.P646P		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C1938T						PASS	.	C	,,	37,4369	42.3+/-75.8	0,37,2166	102.0	115.0	110.0		1671,711,1935	-6.3	0.6	14	dbSNP_92	110	354,8246	118.1+/-177.6	7,340,3953	no	coding-synonymous,coding-synonymous,coding-synonymous	SAMD4A	NM_001161576.2,NM_001161577.1,NM_015589.5	,,	7,377,6119	TT,TC,CC		4.1163,0.8398,3.0063	,,	557/630,237/346,645/718	55243152	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	23034	exon10			CAACCCCGGGGGC	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1938C>T	14.37:g.55243152C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Silent	SNP	ENST00000554335.1	37	CCDS32084.2																																																																																			C|0.974;T|0.026	0.026	strong		0.587	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
POLE	5426	hgsc.bcm.edu	37	12	133253995	133253995	+	Missense_Mutation	SNP	G	G	A	rs5744751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133253995G>A	ENST00000320574.5	-	8	798	c.755C>T	c.(754-756)gCt>gTt	p.A252V	POLE_ENST00000535270.1_Missense_Mutation_p.A225V	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	252			A -> V (in dbSNP:rs5744751).		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)	TACCGGAAAAGCATTTCCTCG	0.423								DNA polymerases (catalytic subunits)					G|||	285	0.0569089	0.0045	0.0447	5008	,	,		20247	0.1052		0.1004	False		,,,				2504	0.0419				p.A252V		Atlas-SNP	.											.	POLE	416	.	0			c.C755T						PASS	.	G	VAL/ALA	70,4336	64.7+/-102.0	0,70,2133	115.0	109.0	111.0		755	5.6	1.0	12	dbSNP_114	111	923,7677	205.5+/-247.9	59,805,3436	yes	missense	POLE	NM_006231.2	64	59,875,5569	AA,AG,GG		10.7326,1.5887,7.6349	benign	252/2287	133253995	993,12013	2203	4300	6503	SO:0001583	missense	5426	exon8			GGAAAAGCATTTC		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.755C>T	12.37:g.133253995G>A	ENSP00000322570:p.Ala252Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	157	0.07188644688644688	2	0.0040650406504065045	20	0.055248618784530384	57	0.09965034965034965	78	0.10290237467018469	G	12.78	2.041642	0.35989	0.015887	0.107326	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	5.64	5.64	0.86602	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.113409	0.64402	D	0.000009	T	0.00178	0.0005	N	0.16166	0.38	0.21950	P	0.999454457	B;B	0.13145	0.005;0.007	B;B	0.19946	0.016;0.027	T	0.47289	-0.9129	9	0.27082	T	0.32	.	19.7069	0.96076	0.0:0.0:1.0:0.0	rs5744751;rs52830930;rs60851699;rs5744751	225;252	F5H1D6;Q07864	.;DPOE1_HUMAN	V	252;263;225;32;187	ENSP00000322570:A252V;ENSP00000406383:A263V;ENSP00000445753:A225V;ENSP00000442519:A32V	ENSP00000322570:A252V	A	-	2	0	POLE	131764068	1.000000	0.71417	0.957000	0.39632	0.028000	0.11728	5.457000	0.66672	2.654000	0.90174	0.563000	0.77884	GCT	G|0.928;A|0.072	0.072	strong		0.423	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
SH2D2A	9047	hgsc.bcm.edu	37	1	156784982	156784982	+	Missense_Mutation	SNP	T	T	C	rs926103	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156784982T>C	ENST00000368199.3	-	3	308	c.155A>G	c.(154-156)aAc>aGc	p.N52S	NTRK1_ENST00000392302.2_5'Flank|SH2D2A_ENST00000368198.3_Missense_Mutation_p.N34S|SH2D2A_ENST00000392306.2_Missense_Mutation_p.N52S|SH2D2A_ENST00000495306.1_5'UTR	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A	52			N -> S (in dbSNP:rs926103). {ECO:0000269|PubMed:10692392, ECO:0000269|PubMed:10752626, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15592455, ECO:0000269|PubMed:9468509, ECO:0000269|Ref.4}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATTCCCTGTGTTGGAGGCAGC	0.617													T|||	2973	0.59365	0.3192	0.6297	5008	,	,		17540	0.8155		0.662	False		,,,				2504	0.6401				p.N52S		Atlas-SNP	.											SH2D2A_ENST00000392306,NS,carcinoma,0,2	SH2D2A	78	2	0			c.A155G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1686,2720		330,1026,847	26.0	24.0	25.0		155,101,71,155,155	-9.9	0.0	1	dbSNP_86	25	5505,3095		1791,1923,586	yes	missense,missense,missense,missense,missense	SH2D2A	NM_001161441.1,NM_001161442.1,NM_001161443.1,NM_001161444.1,NM_003975.3	46,46,46,46,46	2121,2949,1433	CC,CT,TT		35.9884,38.266,44.7101	benign,benign,benign,benign,benign	52/400,34/372,24/362,52/390,52/390	156784982	7191,5815	2203	4300	6503	SO:0001583	missense	9047	exon3			CCTGTGTTGGAGG	AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"""SH2 domain containing"""	10821	protein-coding gene	gene with protein product	"""T lymphocyte specific adaptor protein"", ""T cell specific adapter protein TSAd"", ""T cell specific adpater protein TSAd"""	604514	"""SH2 domain protein 2A"""			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.155A>G	1.37:g.156784982T>C	ENSP00000357182:p.Asn52Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	237	234	0.987342	NM_003975	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Missense_Mutation	SNP	ENST00000368199.3	37	CCDS1159.1	1349	0.6176739926739927	154	0.3130081300813008	234	0.6464088397790055	464	0.8111888111888111	497	0.6556728232189973	T	0.142	-1.101109	0.01843	0.38266	0.640116	ENSG00000027869	ENST00000368199;ENST00000368198;ENST00000392306	T;T;T	0.54866	0.59;0.55;1.01	4.94	-9.87	0.00470	.	3.198450	0.00760	N	0.001137	T	0.05135	0.0137	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	0.15780	-1.0425	9	0.06099	T	0.92	2.6197	0.9938	0.01462	0.1594:0.239:0.209:0.3925	rs926103;rs3748807;rs17850866;rs926103	52;34;52	Q9NP31-2;Q5VZS4;Q9NP31	.;.;SH22A_HUMAN	S	52;34;52	ENSP00000357182:N52S;ENSP00000357181:N34S;ENSP00000376123:N52S	ENSP00000357181:N34S	N	-	2	0	SH2D2A	155051606	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.442000	0.02407	-2.789000	0.00357	-1.847000	0.00572	AAC	T|0.445;C|0.555	0.555	strong		0.617	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975	
DHX57	90957	hgsc.bcm.edu	37	2	39050141	39050141	+	Silent	SNP	A	A	C	rs3770681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	66	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	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	
COPS3	8533	hgsc.bcm.edu	37	17	17168164	17168164	+	Silent	SNP	G	G	A	rs3182911	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:17168164G>A	ENST00000268717.5	-	6	679	c.573C>T	c.(571-573)atC>atT	p.I191I	COPS3_ENST00000539941.2_Silent_p.I171I|COPS3_ENST00000439936.2_Silent_p.I171I	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	191					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)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GCCCAGTATAGATCATCCCTC	0.358													G|||	2435	0.486222	0.3215	0.5317	5008	,	,		18745	0.6558		0.5119	False		,,,				2504	0.4755				p.I191I		Atlas-SNP	.											.	COPS3	41	.	0			c.C573T						PASS	.	G	,	1436,2970	466.0+/-354.4	239,958,1006	93.0	89.0	90.0		513,573	3.8	1.0	17	dbSNP_105	90	4292,4308	575.5+/-390.2	1062,2168,1070	no	coding-synonymous,coding-synonymous	COPS3	NM_001199125.1,NM_003653.3	,	1301,3126,2076	AA,AG,GG		49.907,32.5919,44.0412	,	171/404,191/424	17168164	5728,7278	2203	4300	6503	SO:0001819	synonymous_variant	8533	exon6			AGTATAGATCATC	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3"", ""COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"""			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.573C>T	17.37:g.17168164G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000268717.5	37	CCDS11183.1																																																																																			G|0.540;N|0.000	.	strong		0.358	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2		
OR5R1	219479	hgsc.bcm.edu	37	11	56185327	56185327	+	Missense_Mutation	SNP	T	T	C	rs7933772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56185327T>C	ENST00000312253.1	-	1	381	c.382A>G	c.(382-384)Agt>Ggt	p.S128G		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	128			S -> G (in dbSNP:rs7933772).			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)					TGCAGGGGACTACAGATGGCG	0.478													T|||	1391	0.277756	0.5378	0.1816	5008	,	,		21435	0.123		0.2664	False		,,,				2504	0.1656				p.S128G		Atlas-SNP	.											.	OR5R1	83	.	0			c.A382G						PASS	.	T	GLY/SER	2203,2199	587.9+/-386.8	567,1069,565	106.0	104.0	105.0		382	4.7	0.3	11	dbSNP_116	105	2394,6196	397.6+/-345.8	320,1754,2221	yes	missense	OR5R1	NM_001004744.1	56	887,2823,2786	CC,CT,TT		27.8696,49.9546,35.3833	benign	128/325	56185327	4597,8395	2201	4295	6496	SO:0001583	missense	219479	exon1			GGGGACTACAGAT	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.382A>G	11.37:g.56185327T>C	ENSP00000308595:p.Ser128Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	600	0.27472527472527475	249	0.5060975609756098	63	0.17403314917127072	80	0.13986013986013987	208	0.27440633245382584	T	14.94	2.686423	0.47991	0.500454	0.278696	ENSG00000174942	ENST00000312253	T	0.00478	7.13	5.78	4.66	0.58398	GPCR, rhodopsin-like superfamily (1);	0.200266	0.24488	U	0.038084	T	0.00012	0.0000	M	0.64997	1.995	0.58432	P	1.999999999946489E-6	B	0.22909	0.077	B	0.26614	0.071	T	0.16988	-1.0384	9	0.72032	D	0.01	-0.2935	10.9674	0.47421	0.0:0.0737:0.0:0.9263	rs7933772;rs52833006;rs58645970;rs7933772	128	Q8NH85	OR5R1_HUMAN	G	128	ENSP00000308595:S128G	ENSP00000308595:S128G	S	-	1	0	OR5R1	55941903	0.000000	0.05858	0.329000	0.25429	0.907000	0.53573	0.565000	0.23578	2.211000	0.71520	0.391000	0.25812	AGT	C|0.324;N|0.000	0.324	strong		0.478	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:74497152G>A	ENST00000287097.5	+	21	2645	c.2533G>A	c.(2533-2535)Gtc>Atc	p.V845I	CD109_ENST00000422508.2_Missense_Mutation_p.V768I|CD109_ENST00000437994.2_Missense_Mutation_p.V845I			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	63	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	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	
CWF19L2	143884	hgsc.bcm.edu	37	11	107299631	107299631	+	Missense_Mutation	SNP	G	G	A	rs659040	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:107299631G>A	ENST00000282251.5	-	8	1354	c.1327C>T	c.(1327-1329)Cac>Tac	p.H443Y	CWF19L2_ENST00000433523.1_Missense_Mutation_p.H443Y	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	443			H -> Y (in dbSNP:rs659040). {ECO:0000269|PubMed:15489334}.				catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		ACATGTTGGTGTTCATCAGTA	0.403													A|||	574	0.114617	0.1604	0.1369	5008	,	,		17579	0.002		0.2227	False		,,,				2504	0.0419				p.H443Y		Atlas-SNP	.											.	CWF19L2	135	.	0			c.C1327T						PASS	.	A	TYR/HIS	771,3631	752.5+/-412.3	76,619,1506	241.0	232.0	235.0		1327	-3.7	0.0	11	dbSNP_83	235	1880,6716	728.1+/-406.7	209,1462,2627	yes	missense	CWF19L2	NM_152434.2	83	285,2081,4133	AA,AG,GG		21.8706,17.5148,20.3954	benign	443/895	107299631	2651,10347	2201	4298	6499	SO:0001583	missense	143884	exon8			GTTGGTGTTCATC	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1327C>T	11.37:g.107299631G>A	ENSP00000282251:p.His443Tyr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	82	0.565517	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	287	0.13141025641025642	73	0.1483739837398374	50	0.13812154696132597	1	0.0017482517482517483	163	0.21503957783641162	A	0.052	-1.248631	0.01469	0.175148	0.218706	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.21361	2.01;2.01	5.02	-3.67	0.04476	.	2.765330	0.00769	N	0.001196	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	0.33624	-0.9861	9	0.51188	T	0.08	5.6759	2.3012	0.04162	0.2483:0.3046:0.3315:0.1156	rs659040;rs52817546;rs58584040;rs659040	443	Q2TBE0	C19L2_HUMAN	Y	443	ENSP00000282251:H443Y;ENSP00000387533:H443Y	ENSP00000282251:H443Y	H	-	1	0	CWF19L2	106804841	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.808000	0.01732	-0.716000	0.04962	-1.120000	0.02017	CAC	G|0.822;A|0.178	0.178	strong		0.403	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
IL17RD	54756	hgsc.bcm.edu	37	3	57136585	57136585	+	Missense_Mutation	SNP	C	C	T	rs17057718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	106	0	0		WXS	Illumina HiSeq	Phase_I	140	47	0.335714	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	
SDHA	6389	hgsc.bcm.edu	37	5	256508	256508	+	Silent	SNP	C	C	T	rs3211499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	102	7	0.0686275	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	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60027236	60027236	+	Silent	SNP	C	C	T	rs12721430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:60027236C>T	ENST00000586569.1	+	6	608	c.570C>T	c.(568-570)tcC>tcT	p.S190S	TNFRSF11A_ENST00000269485.7_Silent_p.S190S	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	190					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				CAGAGAAATCCGATGCGGTTT	0.448													C|||	8	0.00159744	0.0	0.0029	5008	,	,		19769	0.0		0.004	False		,,,				2504	0.002				p.S190S		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.C570T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	116.0	105.0	109.0		570	-2.3	1.0	18	dbSNP_121	109	40,8560	25.7+/-73.6	0,40,4260	no	coding-synonymous	TNFRSF11A	NM_003839.2		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		190/617	60027236	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	8792	exon6			GAAATCCGATGCG	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.570C>T	18.37:g.60027236C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	160	114	0.7125	NM_001270951	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	37	CCDS11980.1																																																																																			C|0.997;T|0.003	0.003	strong		0.448	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
KDM5A	5927	hgsc.bcm.edu	37	12	427575	427575	+	Missense_Mutation	SNP	A	A	G	rs11062385	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:427575A>G	ENST00000399788.2	-	19	2956	c.2594T>C	c.(2593-2595)aTg>aCg	p.M865T	KDM5A_ENST00000382815.4_Missense_Mutation_p.M865T	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	865			M -> T (in dbSNP:rs11062385).		chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GGTTTCATCCATCATGGCCTC	0.393			T	NUP98	AML								A|||	1768	0.353035	0.3321	0.3199	5008	,	,		21745	0.5109		0.2326	False		,,,				2504	0.3661				p.M865T		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	.	KDM5A	307	.	0			c.T2594C						PASS	.	A	THR/MET	1180,2546		203,774,886	108.0	105.0	106.0		2594	4.0	1.0	12	dbSNP_120	106	2085,6131		276,1533,2299	yes	missense	KDM5A	NM_001042603.1	81	479,2307,3185	GG,GA,AA		25.3773,31.6694,27.3405	benign	865/1691	427575	3265,8677	1863	4108	5971	SO:0001583	missense	5927	exon19			TCATCCATCATGG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.2594T>C	12.37:g.427575A>G	ENSP00000382688:p.Met865Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	768	0.3516483516483517	181	0.3678861788617886	116	0.32044198895027626	289	0.5052447552447552	182	0.24010554089709762	A	6.591	0.477457	0.12521	0.316694	0.253773	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.39997	1.05;1.05;1.05	5.18	3.99	0.46301	Lysine-specific demethylase-like domain (1);	0.270105	0.38217	N	0.001762	T	0.00012	0.0000	N	0.01874	-0.695	0.32953	P	0.479989	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.001;0.004	T	0.46965	-0.9153	9	0.21014	T	0.42	-7.7721	6.1802	0.20468	0.7533:0.1572:0.0895:0.0	rs11062385;rs52835808;rs60765971;rs11062385	865;865;865	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	T	484;824;865;865;484	ENSP00000382688:M865T;ENSP00000372265:M865T;ENSP00000440622:M484T	ENSP00000261253:M484T	M	-	2	0	KDM5A	297836	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.908000	0.56355	0.760000	0.33108	0.482000	0.46254	ATG	A|0.651;G|0.349	0.349	strong		0.393	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
FABP1	2168	hgsc.bcm.edu	37	2	88424066	88424066	+	Missense_Mutation	SNP	T	T	C	rs2241883	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:88424066T>C	ENST00000295834.3	-	3	378	c.280A>G	c.(280-282)Act>Gct	p.T94A	FABP1_ENST00000495375.1_5'UTR|FABP1_ENST00000393750.3_Missense_Mutation_p.T94A	NM_001443.2	NP_001434.1	P07148	FABPL_HUMAN	fatty acid binding protein 1, liver	94			T -> A (in dbSNP:rs2241883). {ECO:0000269|PubMed:3838313}.		cellular lipid metabolic process (GO:0044255)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|intestinal absorption (GO:0050892)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)	apical cortex (GO:0045179)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|peroxisomal matrix (GO:0005782)	antioxidant activity (GO:0016209)|bile acid binding (GO:0032052)|chromatin binding (GO:0003682)|drug binding (GO:0008144)|fatty acid binding (GO:0005504)|long-chain fatty acid transporter activity (GO:0005324)|phospholipid binding (GO:0005543)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	6						TTTTTGAAAGTTGTCACCAGT	0.517													T|||	1118	0.223243	0.1392	0.3458	5008	,	,		20701	0.2073		0.3479	False		,,,				2504	0.138				p.T94A		Atlas-SNP	.											.	FABP1	23	.	0			c.A280G	GRCh37	CM042701	FABP1	M	rs2241883	PASS	.	T	ALA/THR	736,3670	304.4+/-288.4	68,600,1535	197.0	154.0	168.0		280	1.4	0.9	2	dbSNP_98	168	2774,5826	439.8+/-359.3	473,1828,1999	yes	missense	FABP1	NM_001443.2	58	541,2428,3534	CC,CT,TT		32.2558,16.7045,26.9875	benign	94/128	88424066	3510,9496	2203	4300	6503	SO:0001583	missense	2168	exon3			TGAAAGTTGTCAC	M10617	CCDS2001.1	2p11	2013-03-01			ENSG00000163586	ENSG00000163586		"""Fatty acid binding protein family"""	3555	protein-coding gene	gene with protein product		134650				3012800, 17698986	Standard	NM_001443		Approved	L-FABP	uc002sst.2	P07148	OTTHUMG00000130312	ENST00000295834.3:c.280A>G	2.37:g.88424066T>C	ENSP00000295834:p.Thr94Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	93	33	0.354839	NM_001443		Missense_Mutation	SNP	ENST00000295834.3	37	CCDS2001.1	577	0.2641941391941392	61	0.12398373983739837	130	0.35911602209944754	127	0.22202797202797203	259	0.341688654353562	T	7.875	0.729033	0.15507	0.167045	0.322558	ENSG00000163586	ENST00000295834;ENST00000393750	T;T	0.13196	2.61;2.61	5.5	1.35	0.21983	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.647546	0.17155	N	0.184882	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.13407	0.009;0.002	T	0.44892	-0.9298	9	0.10636	T	0.68	.	6.2319	0.20740	0.3971:0.0:0.1367:0.4662	rs2241883;rs59305633;rs2241883	94;94	A8MW49;P07148	.;FABPL_HUMAN	A	94	ENSP00000295834:T94A;ENSP00000377351:T94A	ENSP00000295834:T94A	T	-	1	0	FABP1	88205181	0.001000	0.12720	0.885000	0.34714	0.923000	0.55619	0.541000	0.23207	0.404000	0.25506	0.533000	0.62120	ACT	A|0.004;C|0.254	0.254	strong		0.517	FABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252660.1	NM_001443	
C17orf49	124944	hgsc.bcm.edu	37	17	6920257	6920257	+	Silent	SNP	C	C	T	rs11078662	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6920257C>T	ENST00000439424.2	+	5	514	c.438C>T	c.(436-438)tcC>tcT	p.S146S	C17orf49_ENST00000547709.1_Intron|MIR497HG_ENST00000385194.1_RNA|C17orf49_ENST00000552775.1_Silent_p.S120S|C17orf49_ENST00000546760.1_Intron|C17orf49_ENST00000552402.1_Silent_p.S112S|MIR497HG_ENST00000443997.1_RNA|RP11-589P10.7_ENST00000572547.1_RNA|C17orf49_ENST00000546495.1_Silent_p.S146S|MIR497HG_ENST00000572453.1_RNA|RNASEK-C17orf49_ENST00000547302.2_Missense_Mutation_p.P187L|MIR497HG_ENST00000385056.1_RNA|AC040977.1_ENST00000593646.1_5'Flank	NM_001142798.2|NM_174893.3	NP_001136270.1|NP_777553.1	Q8IXM2	BAP18_HUMAN	chromosome 17 open reading frame 49	146					chromatin modification (GO:0016568)	MLL1 complex (GO:0071339)|NURF complex (GO:0016589)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|ovary(1)	4						TGAACGACTCCGATGCCAACA	0.557													C|||	452	0.0902556	0.0061	0.3228	5008	,	,		18117	0.1171		0.0716	False		,,,				2504	0.0307				p.S146S		Atlas-SNP	.											.	C17orf49	28	.	0			c.C438T						PASS	.	C	,,	80,4326	70.3+/-108.2	1,78,2124	157.0	147.0	151.0		438,336,438	-7.8	0.9	17	dbSNP_120	151	590,8010	156.4+/-210.3	16,558,3726	no	coding-synonymous,coding-synonymous,coding-synonymous	C17orf49	NM_001142798.2,NM_001142799.2,NM_174893.3	,,	17,636,5850	TT,TC,CC		6.8605,1.8157,5.1515	,,	146/193,112/139,146/173	6920257	670,12336	2203	4300	6503	SO:0001819	synonymous_variant	124944	exon5			CGACTCCGATGCC	AK055800	CCDS32542.1, CCDS45595.1, CCDS45596.1	17p13.1	2013-02-11			ENSG00000258315	ENSG00000258315			28737	protein-coding gene	gene with protein product	"""BPTF associated protein of 18 kDa"", ""human embryo lung cellular protein interacting with SARS-CoV nsp-10"""						Standard	NM_174893		Approved	MGC49942, BAP18, HEPIS		Q8IXM2	OTTHUMG00000170147	ENST00000439424.2:c.438C>T	17.37:g.6920257C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_174893	B4DIV3|C9J4G0|E9PB29	Silent	SNP	ENST00000439424.2	37	CCDS32542.1	253	0.11584249084249085	5	0.01016260162601626	102	0.281767955801105	88	0.15384615384615385	58	0.07651715039577836	C	8.613	0.889572	0.17540	0.018157	0.068605	ENSG00000161939	ENST00000547302	.	.	.	5.3	-7.84	0.01196	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29119	-1.0022	3	.	.	.	-13.9179	8.0932	0.30813	0.1136:0.2858:0.5238:0.0768	rs11078662;rs11078662	.	.	.	L	187	.	.	P	+	2	0	C17orf49	6860981	0.099000	0.21834	0.928000	0.36995	0.897000	0.52465	-0.961000	0.03845	-0.756000	0.04703	-0.150000	0.13652	CCG	T|0.072;G|0.000;C|0.928	0.072	strong		0.557	C17orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407666.1	NM_174893	
SLC52A3	113278	hgsc.bcm.edu	37	20	744415	744415	+	Missense_Mutation	SNP	G	G	A	rs3746804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:744415G>A	ENST00000217254.7	-	3	1041	c.800C>T	c.(799-801)cCg>cTg	p.P267L	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Missense_Mutation_p.P267L	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	267			P -> L (in dbSNP:rs3746804). {ECO:0000269|PubMed:15489334}.		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)										CTCTTCCCGCGGCCGGATGGA	0.647													G|||	913	0.182308	0.1346	0.1167	5008	,	,		19203	0.255		0.2018	False		,,,				2504	0.1984				p.P267L		Atlas-SNP	.											.	.	.	.	0			c.C800T						PASS	.	G	LEU/PRO	713,3693	296.1+/-284.1	61,591,1551	50.0	50.0	50.0		800	0.1	0.2	20	dbSNP_107	50	1837,6763	329.2+/-318.6	215,1407,2678	yes	missense	C20orf54	NM_033409.3	98	276,1998,4229	AA,AG,GG		21.3605,16.1825,19.6063	benign	267/470	744415	2550,10456	2203	4300	6503	SO:0001583	missense	113278	exon3			TCCCGCGGCCGGA	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.800C>T	20.37:g.744415G>A	ENSP00000217254:p.Pro267Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	466	0.21336996336996336	83	0.16869918699186992	42	0.11602209944751381	183	0.31993006993006995	158	0.20844327176781002	G	6.760	0.509184	0.12883	0.161825	0.213605	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.72942	-0.63;-0.7	4.95	0.143	0.14820	.	0.889113	0.10011	N	0.727169	T	0.00012	0.0000	N	0.19112	0.55	0.54753	P	1.0999999999983245E-5	B;B	0.16396	0.01;0.017	B;B	0.08055	0.003;0.001	T	0.17018	-1.0383	9	0.25106	T	0.35	-0.336	4.1083	0.10047	0.3612:0.0:0.4742:0.1646	rs3746804;rs17855409;rs61573051;rs3746804	267;267	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	L	267	ENSP00000217254:P267L;ENSP00000371370:P267L	ENSP00000217254:P267L	P	-	2	0	C20orf54	692415	0.000000	0.05858	0.154000	0.22540	0.797000	0.45037	0.461000	0.21940	0.466000	0.27193	0.561000	0.74099	CCG	G|0.794;A|0.206	0.206	strong		0.647	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
RCBTB1	55213	hgsc.bcm.edu	37	13	50123688	50123688	+	Silent	SNP	G	G	T	rs3751382	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50123688G>T	ENST00000378302.2	-	9	1211	c.951C>A	c.(949-951)tcC>tcA	p.S317S	RCBTB1_ENST00000258646.3_Silent_p.S317S|RCBTB1_ENST00000546015.1_Silent_p.S317S	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	317					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GGAGGATCACGGACTGACCCC	0.632													G|||	1567	0.312899	0.5023	0.1311	5008	,	,		17415	0.2788		0.167	False		,,,				2504	0.3712				p.S317S		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C951A						PASS	.	G		1988,2418	558.0+/-379.9	443,1102,658	94.0	71.0	79.0		951	-7.7	0.9	13	dbSNP_107	79	1262,7338	250.0+/-277.0	81,1100,3119	no	coding-synonymous	RCBTB1	NM_018191.3		524,2202,3777	TT,TG,GG		14.6744,45.1203,24.9885		317/532	50123688	3250,9756	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon9			GATCACGGACTGA	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.951C>A	13.37:g.50123688G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			G|0.471;T|0.529	0.529	strong		0.632	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
LAMA5	3911	hgsc.bcm.edu	37	20	60927412	60927412	+	Silent	SNP	G	G	A	rs624313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60927412G>A	ENST00000252999.3	-	4	639	c.573C>T	c.(571-573)tcC>tcT	p.S191S	LAMA5_ENST00000370677.3_Silent_p.S191S|RP11-157P1.5_ENST00000456721.2_RNA|RP11-157P1.5_ENST00000477848.1_RNA|LAMA5_ENST00000370692.3_Silent_p.S191S|RP11-157P1.5_ENST00000478167.1_RNA|RP11-157P1.5_ENST00000487421.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	191	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)			AGTCCCTCTTGGAGGCTGCGG	0.692													g|||	2599	0.51897	0.1036	0.6369	5008	,	,		12934	0.7341		0.6581	False		,,,				2504	0.6319				p.S191S		Atlas-SNP	.											LAMA5,NS,carcinoma,0,2	LAMA5	268	2	0			c.C573T						PASS	.			906,3484	327.7+/-300.2	110,686,1399	36.0	34.0	35.0		573	2.9	1.0	20	dbSNP_83	35	5787,2797	655.1+/-401.2	1962,1863,467	no	coding-synonymous	LAMA5	NM_005560.3		2072,2549,1866	AA,AG,GG		32.5839,20.6378,48.4122		191/3696	60927412	6693,6281	2195	4292	6487	SO:0001819	synonymous_variant	3911	exon4			CCTCTTGGAGGCT	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.573C>T	20.37:g.60927412G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.486;A|0.514	0.514	strong		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
OPRM1	4988	hgsc.bcm.edu	37	6	154428666	154428666	+	Intron	SNP	C	C	T	rs677830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:154428666C>T	ENST00000330432.7	+	4	1401				OPRM1_ENST00000414028.2_Intron|OPRM1_ENST00000435918.2_Intron|OPRM1_ENST00000522236.1_Intron|OPRM1_ENST00000452687.2_Intron|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000522555.1_Intron|OPRM1_ENST00000337049.4_Intron|OPRM1_ENST00000434900.2_Intron|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000419506.2_Nonsense_Mutation_p.Q411*|OPRM1_ENST00000524163.1_Intron	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|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 cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	caatgcagggcagtctccatt	0.408													C|||	751	0.14996	0.143	0.1859	5008	,	,		19562	0.0734		0.2266	False		,,,				2504	0.1339				p.Q411X		Atlas-SNP	.											.	OPRM1	241	.	0			c.C1231T						PASS	.						136.0	128.0	131.0					6																	154428666		692	1591	2283	SO:0001627	intron_variant	4988	exon4			GCAGGGCAGTCTC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"""GPCR / Class A : Opioid receptors"""	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.1165-11152C>T	6.37:g.154428666C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001145286	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Nonsense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	363	0.1662087912087912	85	0.17276422764227642	65	0.17955801104972377	44	0.07692307692307693	169	0.22295514511873352	C	8.345	0.829563	0.16749	.	.	ENSG00000112038	ENST00000419506	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	rs677830;rs1067691;rs59977603;rs677830	.	.	.	X	411	.	ENSP00000403549:Q411X	Q	+	1	0	OPRM1	154470358	0.005000	0.15991	0.024000	0.17045	0.025000	0.11179	-0.687000	0.05156	0.300000	0.22699	0.305000	0.20034	CAG	C|0.837;T|0.163	0.163	strong		0.408	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
BRICD5	283870	hgsc.bcm.edu	37	16	2259393	2259393	+	Silent	SNP	C	C	G	rs1129185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2259393C>G	ENST00000562360.1	-	5	752	c.753G>C	c.(751-753)gtG>gtC	p.V251V	MLST8_ENST00000301725.7_3'UTR|MLST8_ENST00000397124.1_3'UTR|MLST8_ENST00000382450.4_3'UTR|MLST8_ENST00000564088.1_3'UTR|MLST8_ENST00000301724.10_3'UTR|RP11-304L19.8_ENST00000561544.1_lincRNA|MLST8_ENST00000569417.1_3'UTR|BRICD5_ENST00000328540.3_Silent_p.V219V			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	251						integral component of membrane (GO:0016021)											AGCAGACCGACACGCAGATGT	0.642													C|||	107	0.0213658	0.0023	0.0504	5008	,	,		17393	0.0		0.0487	False		,,,				2504	0.0204				p.V219V		Atlas-SNP	.											.	.	.	.	0			c.G657C						PASS	.	C	,,,,	63,4333	57.4+/-93.9	0,63,2135	70.0	67.0	68.0		,,,,657	0.2	0.1	16	dbSNP_86	68	545,8055	150.7+/-205.6	16,513,3771	no	utr-3,utr-3,utr-3,utr-3,coding-synonymous	MLST8,C16orf79	NM_001199173.1,NM_001199174.1,NM_001199175.1,NM_022372.4,NM_182563.3	,,,,	16,576,5906	GG,GC,CC		6.3372,1.4331,4.6784	,,,,	,,,,219/229	2259393	608,12388	2198	4300	6498	SO:0001819	synonymous_variant	283870	exon6			GACCGACACGCAG	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.753G>C	16.37:g.2259393C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_182563	C9J7K2|Q8IXU9	Silent	SNP	ENST00000562360.1	37	CCDS10463.1																																																																																			C|0.956;G|0.044	0.044	strong		0.642	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563	
ZNF778	197320	hgsc.bcm.edu	37	16	89289624	89289624	+	Silent	SNP	G	G	A	rs12920028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89289624G>A	ENST00000433976.2	+	4	509	c.177G>A	c.(175-177)ctG>ctA	p.L59L	ZNF778_ENST00000306502.6_5'UTR	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	59	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(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GGACTTTACTGGACCCATCTC	0.532													G|||	577	0.115216	0.1846	0.0677	5008	,	,		21800	0.0972		0.0626	False		,,,				2504	0.1278				p.L59L		Atlas-SNP	.											.	ZNF778	67	.	0			c.G177A						PASS	.	G	,	791,3605	314.4+/-293.6	67,657,1474	139.0	138.0	138.0		177,177	1.6	0.3	16	dbSNP_121	138	545,8055	149.5+/-204.6	17,511,3772	no	coding-synonymous,coding-synonymous	ZNF778	NM_001201407.1,NM_182531.3	,	84,1168,5246	AA,AG,GG		6.3372,17.9936,10.2801	,	59/758,59/730	89289624	1336,11660	2198	4300	6498	SO:0001819	synonymous_variant	197320	exon4			TTTACTGGACCCA	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.177G>A	16.37:g.89289624G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_182531	Q08AG0	Silent	SNP	ENST00000433976.2	37	CCDS45550.1																																																																																			G|0.901;A|0.099	0.099	strong		0.532	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
OR10X1	128367	hgsc.bcm.edu	37	1	158549422	158549422	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158549422T>C	ENST00000368150.1	-	1	267	c.268A>G	c.(268-270)Acg>Gcg	p.T90A		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, 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)	p.T90A(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					ATGGTCAGCGTATAGCAGGTC	0.493																																					p.T90A		Atlas-SNP	.											OR10X1,face,carcinoma,0,1	OR10X1	96	1	1	Substitution - Missense(1)	skin(1)	c.A268G						scavenged	.						108.0	101.0	103.0					1																	158549422		2203	4300	6503	SO:0001583	missense	128367	exon1			TCAGCGTATAGCA	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.268A>G	1.37:g.158549422T>C	ENSP00000357132:p.Thr90Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	182	3	0.0164835	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.684660	0.47991	.	.	ENSG00000186400	ENST00000368150	T	0.00578	6.44	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000120	T	0.00967	0.0032	M	0.65320	2	0.29286	N	0.869699	D	0.71674	0.998	D	0.77004	0.989	T	0.41840	-0.9486	10	0.87932	D	0	.	10.2406	0.43310	0.0:0.0:0.1663:0.8337	.	90	Q8NGY0	O10X1_HUMAN	A	90	ENSP00000357132:T90A	ENSP00000357132:T90A	T	-	1	0	OR10X1	156816046	0.000000	0.05858	0.991000	0.47740	0.338000	0.28826	0.277000	0.18734	2.139000	0.66308	0.528000	0.53228	ACG	.	.	none		0.493	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
FAM205A	259308	hgsc.bcm.edu	37	9	34728065	34728065	+	Missense_Mutation	SNP	G	G	A	rs75766630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34728065G>A	ENST00000378788.3	-	3	244	c.205C>T	c.(205-207)Cgg>Tgg	p.R69W		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	69						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GCTTCTTCCCGGGAACGTCTC	0.458													G|||	271	0.0541134	0.1483	0.0159	5008	,	,		19456	0.0109		0.0189	False		,,,				2504	0.0348				p.R69W		Atlas-SNP	.											.	FAM205A	45	.	0			c.C205T						PASS	.	G	TRP/ARG	173,1211		9,155,528	86.0	86.0	86.0		205	0.4	0.0	9	dbSNP_131	86	60,3122		1,58,1532	yes	missense	FAM205A	NM_001141917.1	101	10,213,2060	AA,AG,GG		1.8856,12.5,5.1029	benign	69/1336	34728065	233,4333	692	1591	2283	SO:0001583	missense	259308	exon3			CTTCCCGGGAACG		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.205C>T	9.37:g.34728065G>A	ENSP00000417711:p.Arg69Trp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	74	0.03388278388278388	52	0.10569105691056911	7	0.019337016574585635	1	0.0017482517482517483	14	0.018469656992084433	G	10.84	1.462993	0.26248	0.125	0.018856	ENSG00000205108	ENST00000378788	T	0.24723	1.84	4.46	0.398	0.16319	.	.	.	.	.	T	0.00241	0.0007	L	0.38175	1.15	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21930	-1.0231	9	0.49607	T	0.09	.	3.9596	0.09405	0.3036:0.1779:0.5185:0.0	.	69	Q6ZU69	F205A_HUMAN	W	69	ENSP00000417711:R69W	ENSP00000417711:R69W	R	-	1	2	RP11-195F19.10	34718065	0.001000	0.12720	0.001000	0.08648	0.833000	0.47200	-0.141000	0.10327	-0.020000	0.14032	-0.133000	0.14855	CGG	G|0.970;A|0.030	0.030	strong		0.458	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
CLMN	79789	hgsc.bcm.edu	37	14	95660242	95660242	+	Silent	SNP	A	A	G	rs1128468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95660242A>G	ENST00000298912.4	-	12	2897	c.2784T>C	c.(2782-2784)taT>taC	p.Y928Y	CLMN_ENST00000556441.1_5'UTR|CLMN_ENST00000557215.1_5'UTR	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	928					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TCAACTGAACATAGCTAAAAT	0.373													A|||	757	0.151158	0.0915	0.0648	5008	,	,		16060	0.3333		0.0706	False		,,,				2504	0.1881				p.Y928Y		Atlas-SNP	.											.	CLMN	103	.	0			c.T2784C						PASS	.	A		454,3952	218.1+/-236.3	22,410,1771	110.0	104.0	106.0		2784	4.9	1.0	14	dbSNP_86	106	684,7916	171.0+/-222.0	26,632,3642	no	coding-synonymous	CLMN	NM_024734.3		48,1042,5413	GG,GA,AA		7.9535,10.3041,8.7498		928/1003	95660242	1138,11868	2203	4300	6503	SO:0001819	synonymous_variant	79789	exon12			CTGAACATAGCTA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2784T>C	14.37:g.95660242A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Silent	SNP	ENST00000298912.4	37	CCDS9933.1																																																																																			A|0.884;G|0.116	0.116	strong		0.373	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
ZFYVE9	9372	hgsc.bcm.edu	37	1	52703491	52703491	+	Missense_Mutation	SNP	G	G	C	rs35385323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:52703491G>C	ENST00000371591.1	+	3	533	c.402G>C	c.(400-402)aaG>aaC	p.K134N	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.K134N|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.K134N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	134					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TGGGAGAGAAGAAATGTGGAA	0.403													G|||	320	0.0638978	0.1135	0.0403	5008	,	,		22542	0.003		0.0517	False		,,,				2504	0.089				p.K134N		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.G402C						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS	421,3985	205.2+/-227.1	15,391,1797	80.0	79.0	80.0		402,402,402	3.9	1.0	1	dbSNP_126	80	470,8130	138.7+/-195.5	13,444,3843	yes	missense,missense,missense	ZFYVE9	NM_004799.2,NM_007323.1,NM_007324.2	94,94,94	28,835,5640	CC,CG,GG		5.4651,9.5552,6.8507	benign,benign,benign	134/1426,134/763,134/1367	52703491	891,12115	2203	4300	6503	SO:0001583	missense	9372	exon4			AGAGAAGAAATGT	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.402G>C	1.37:g.52703491G>C	ENSP00000360647:p.Lys134Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	115	0.052655677655677656	57	0.11585365853658537	15	0.04143646408839779	1	0.0017482517482517483	42	0.055408970976253295	G	11.18	1.563362	0.27915	0.095552	0.054651	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.55413	1.01;0.52;1.01;1.01	5.77	3.86	0.44501	.	0.407035	0.22551	N	0.058597	T	0.00412	0.0013	N	0.19112	0.55	0.41685	P	0.01068800000000003	P;B;P	0.41848	0.493;0.361;0.763	B;B;B	0.33620	0.109;0.051;0.167	T	0.06661	-1.0814	9	0.46703	T	0.11	.	5.8879	0.18892	0.2158:0.1414:0.6427:0.0	rs35385323;rs61753388	134;134;134	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	N	134	ENSP00000349737:K134N;ENSP00000355358:K134N;ENSP00000287727:K134N;ENSP00000360647:K134N	ENSP00000287727:K134N	K	+	3	2	ZFYVE9	52476079	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.776000	0.26704	0.756000	0.33013	0.655000	0.94253	AAG	G|0.935;C|0.065	0.065	strong		0.403	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
GLRX3	10539	hgsc.bcm.edu	37	10	131934747	131934747	+	Missense_Mutation	SNP	G	G	C	rs13991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:131934747G>C	ENST00000368644.1	+	1	85	c.63G>C	c.(61-63)caG>caC	p.Q21H	GLRX3_ENST00000331244.5_Missense_Mutation_p.Q21H	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	21	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		Q -> H (in dbSNP:rs13991). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CAGCCGGGCAGTTTGAGGAGC	0.726													G|||	814	0.16254	0.1233	0.0893	5008	,	,		9451	0.1091		0.2326	False		,,,				2504	0.2505				p.Q21H		Atlas-SNP	.											TXNL2,NS,carcinoma,0,2	GLRX3	39	2	0			c.G63C						PASS	.	G	HIS/GLN,HIS/GLN	308,2812		15,278,1267	7.0	10.0	9.0		63,63	2.9	1.0	10	dbSNP_52	9	885,4637		75,735,1951	no	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	24,24	90,1013,3218	CC,CG,GG		16.0268,9.8718,13.8047	possibly-damaging,possibly-damaging	21/336,21/336	131934747	1193,7449	1560	2761	4321	SO:0001583	missense	10539	exon1			CGGGCAGTTTGAG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.63G>C	10.37:g.131934747G>C	ENSP00000357633:p.Gln21His	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	334	0.15293040293040294	64	0.13008130081300814	39	0.10773480662983426	52	0.09090909090909091	179	0.23614775725593667	G	16.20	3.054661	0.55325	0.098718	0.160268	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.14893	2.47;2.47	3.85	2.92	0.33932	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.077404	0.53938	D	0.000052	T	0.00012	0.0000	L	0.50993	1.605	0.20307	P	0.999915407	P	0.39862	0.692	P	0.50590	0.645	T	0.33954	-0.9848	9	0.24483	T	0.36	-2.8845	8.5365	0.33366	0.0:0.0:0.7694:0.2306	rs13991;rs1047395;rs3187400;rs13991	21	O76003	GLRX3_HUMAN	H	21	ENSP00000330836:Q21H;ENSP00000357633:Q21H	ENSP00000330836:Q21H	Q	+	3	2	GLRX3	131824737	0.996000	0.38824	0.997000	0.53966	0.810000	0.45777	0.140000	0.16056	0.802000	0.34089	0.313000	0.20887	CAG	G|0.849;C|0.151	0.151	strong		0.726	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955515	18955515	+	Missense_Mutation	SNP	A	A	G	rs138263314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18955515A>G	ENST00000302797.3	-	1	1041	c.817T>C	c.(817-819)Ttc>Ctc	p.F273L	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'Flank	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	273					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCCACGAAGAAGTAAATGATG	0.493													A|||	102	0.0203674	0.0015	0.0605	5008	,	,		27612	0.0		0.0318	False		,,,				2504	0.0266				p.F273L		Atlas-SNP	.											MRGPRX1,NS,carcinoma,+1,1	MRGPRX1	84	1	0			c.T817C						scavenged	.	A	LEU/PHE	23,4365		0,23,2171	78.0	76.0	77.0		817	1.1	0.4	11	dbSNP_134	77	203,8367		0,203,4082	no	missense	MRGPRX1	NM_147199.3	22	0,226,6253	GG,GA,AA		2.3687,0.5242,1.7441	possibly-damaging	273/323	18955515	226,12732	2194	4285	6479	SO:0001583	missense	259249	exon1			CGAAGAAGTAAAT		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.817T>C	11.37:g.18955515A>G	ENSP00000305766:p.Phe273Leu	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	85	29	0.341176	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	49	0.022435897435897436	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	24	0.0316622691292876	.	17.20	3.328525	0.60743	0.005242	0.023687	ENSG00000170255	ENST00000302797	T	0.35421	1.31	2.28	1.06	0.20224	.	0.210366	0.32753	N	0.005690	T	0.08179	0.0204	M	0.83692	2.655	0.25544	N	0.987152	D	0.59357	0.985	P	0.53518	0.728	T	0.04178	-1.0971	10	0.32370	T	0.25	.	6.7944	0.23717	0.7627:0.2373:0.0:0.0	.	273	Q96LB2	MRGX1_HUMAN	L	273	ENSP00000305766:F273L	ENSP00000305766:F273L	F	-	1	0	MRGPRX1	18912091	0.218000	0.23608	0.370000	0.25965	0.402000	0.30811	0.633000	0.24598	0.270000	0.21984	0.402000	0.26972	TTC	A|0.980;G|0.020	0.020	strong		0.493	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632714	32632714	+	Silent	SNP	G	G	C	rs3210148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32632714G>C	ENST00000399084.1	-	3	418	c.240C>G	c.(238-240)cgC>cgG	p.R80R	HLA-DQB1_ENST00000434651.2_Silent_p.R80R|HLA-DQB1_ENST00000374943.4_Silent_p.R80R|HLA-DQB1_ENST00000399079.3_Silent_p.R80R|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	80	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GCGTCACCGCGCGGTACACCC	0.637									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	4215	0.841653	0.7496	0.8674	5008	,	,		5285	0.9395		0.7942	False		,,,				2504	0.8957				p.R80R	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C240G						PASS	.	C		2911,1327		1276,359,484	38.0	38.0	38.0		240	3.1	0.0	6	dbSNP_105	38	5890,2528		2647,596,966	no	coding-synonymous	HLA-DQB1	NM_002123.4		3923,955,1450	CC,CG,GG		30.0309,31.3119,30.4599		80/262	32632714	8801,3855	2119	4209	6328	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CACCGCGCGGTAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.240C>G	6.37:g.32632714G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			G|0.427;C|0.573	0.573	strong		0.637	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
CRELD1	78987	hgsc.bcm.edu	37	3	9985656	9985656	+	Intron	SNP	C	C	T	rs3774207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9985656C>T	ENST00000383811.3	+	10	1647				CRELD1_ENST00000326434.5_Silent_p.H373H|CRELD1_ENST00000452070.1_Intron|CRELD1_ENST00000489674.1_Intron|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	120	0	0		WXS	Illumina HiSeq	Phase_I	156	54	0.346154	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	
CCND1	595	hgsc.bcm.edu	37	11	69462802	69462802	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:69462802G>A	ENST00000227507.2	+	4	842	c.615G>A	c.(613-615)gcG>gcA	p.A205A	CCND1_ENST00000536559.1_3'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	205					canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	TGGTGGCAGCGGGGAGCGTGG	0.607			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)																											p.A205A	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	CCND1,NS,carcinoma,0,1	CCND1	107	1	0			c.G615A						PASS	.						112.0	111.0	112.0					11																	69462802		2200	4294	6494	SO:0001819	synonymous_variant	595	exon4			GGCAGCGGGGAGC	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.615G>A	11.37:g.69462802G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	none		0.607	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	
IPO13	9670	hgsc.bcm.edu	37	1	44422622	44422622	+	Silent	SNP	C	C	T	rs17402858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44422622C>T	ENST00000372343.3	+	5	1907	c.1245C>T	c.(1243-1245)gaC>gaT	p.D415D	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	415					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				GGTCCTCAGACGAGAAGGAGC	0.517													C|||	110	0.0219649	0.0015	0.0403	5008	,	,		20579	0.0		0.0527	False		,,,				2504	0.0276				p.D415D		Atlas-SNP	.											.	IPO13	86	.	0			c.C1245T						PASS	.	C		28,4378	33.5+/-64.1	0,28,2175	62.0	60.0	60.0		1245	-7.4	0.8	1	dbSNP_123	60	354,8246	117.4+/-177.0	10,334,3956	no	coding-synonymous	IPO13	NM_014652.3		10,362,6131	TT,TC,CC		4.1163,0.6355,2.9371		415/964	44422622	382,12624	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon5			CTCAGACGAGAAG	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1245C>T	1.37:g.44422622C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			C|0.973;T|0.027	0.027	strong		0.517	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249984	3249984	+	Missense_Mutation	SNP	C	C	T	rs12295710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	49	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	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	
APLF	200558	hgsc.bcm.edu	37	2	68729931	68729931	+	Silent	SNP	A	A	G	rs112136813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:68729931A>G	ENST00000303795.4	+	3	408	c.237A>G	c.(235-237)ctA>ctG	p.L79L		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	79	FHA-like.				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						AGCCAAATCTATGGTGCTATT	0.338													A|||	137	0.0273562	0.0038	0.0144	5008	,	,		16672	0.0357		0.0398	False		,,,				2504	0.047				p.L79L		Atlas-SNP	.											.	APLF	69	.	0			c.A237G						PASS	.	A		30,4376	36.8+/-68.6	0,30,2173	112.0	111.0	111.0		237	-5.0	0.0	2	dbSNP_132	111	334,8266	115.0+/-174.9	8,318,3974	no	coding-synonymous	APLF	NM_173545.2		8,348,6147	GG,GA,AA		3.8837,0.6809,2.7987		79/512	68729931	364,12642	2203	4300	6503	SO:0001819	synonymous_variant	200558	exon3			AAATCTATGGTGC	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.237A>G	2.37:g.68729931A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Silent	SNP	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.972;G|0.028	0.028	strong		0.338	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
SSRP1	6749	hgsc.bcm.edu	37	11	57100225	57100225	+	Silent	SNP	A	A	G	rs2230650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:57100225A>G	ENST00000278412.2	-	6	908	c.642T>C	c.(640-642)taT>taC	p.Y214Y		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	214					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TCCGAATGTCATAACGACCAC	0.522													A|||	37	0.00738818	0.0008	0.0058	5008	,	,		22752	0.0		0.0258	False		,,,				2504	0.0061				p.Y214Y	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.T642C						PASS	.	A		32,4370	38.4+/-70.7	0,32,2169	93.0	89.0	90.0		642	-3.9	0.8	11	dbSNP_98	90	274,8318	104.8+/-165.8	4,266,4026	no	coding-synonymous	SSRP1	NM_003146.2		4,298,6195	GG,GA,AA		3.189,0.7269,2.3549		214/710	57100225	306,12688	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon6			AATGTCATAACGA	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 80 kDa subunit"""	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.642T>C	11.37:g.57100225A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			A|0.978;G|0.022	0.022	strong		0.522	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
KIF21A	55605	hgsc.bcm.edu	37	12	39735348	39735348	+	Missense_Mutation	SNP	C	C	A	rs79089655	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:39735348C>A	ENST00000361418.5	-	14	1895	c.1880G>T	c.(1879-1881)gGt>gTt	p.G627V	KIF21A_ENST00000541463.2_Missense_Mutation_p.G614V|KIF21A_ENST00000544797.2_Missense_Mutation_p.G614V|KIF21A_ENST00000361961.3_Missense_Mutation_p.G614V|KIF21A_ENST00000395670.3_Missense_Mutation_p.G627V			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	627					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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				AGAACTTTCACCCCCATCAAT	0.378													C|||	81	0.0161741	0.0	0.0187	5008	,	,		18852	0.0		0.0417	False		,,,				2504	0.0266				p.G627V		Atlas-SNP	.											.	KIF21A	238	.	0			c.G1880T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	38,4368	41.6+/-74.8	0,38,2165	117.0	114.0	115.0		1841,1880,1841,1841	3.7	1.0	12	dbSNP_131	115	390,8210	124.1+/-182.9	12,366,3922	yes	missense,missense,missense,missense	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	109,109,109,109	12,404,6087	AA,AC,CC		4.5349,0.8625,3.2908	benign,benign,benign,benign	614/1638,627/1675,614/1622,614/1662	39735348	428,12578	2203	4300	6503	SO:0001583	missense	55605	exon14			CTTTCACCCCCAT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1880G>T	12.37:g.39735348C>A	ENSP00000354878:p.Gly627Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	45	0.020604395604395604	0	0.0	7	0.019337016574585635	0	0.0	38	0.05013192612137203	C	10.10	1.258070	0.23051	0.008625	0.045349	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36	5.5	3.65	0.41850	.	0.289256	0.24534	N	0.037688	T	0.11580	0.0282	N	0.14661	0.345	0.43982	D	0.996675	B;B;B;B	0.29162	0.235;0.0;0.0;0.0	B;B;B;B	0.37304	0.246;0.001;0.001;0.002	T	0.07481	-1.0770	10	0.27082	T	0.32	.	2.1801	0.03872	0.1913:0.5129:0.1254:0.1704	.	614;614;627;614	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;KI21A_HUMAN;.	V	614;627;627;614;627;614	ENSP00000354851:G614V;ENSP00000379029:G627V;ENSP00000445606:G614V;ENSP00000354878:G627V;ENSP00000438075:G614V	ENSP00000344501:G627V	G	-	2	0	KIF21A	38021615	1.000000	0.71417	0.993000	0.49108	0.744000	0.42396	2.088000	0.41663	0.656000	0.30886	0.655000	0.94253	GGT	C|0.971;A|0.029	0.029	strong		0.378	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
SORD	6652	hgsc.bcm.edu	37	15	45365724	45365724	+	Missense_Mutation	SNP	C	C	T	rs76283634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45365724C>T	ENST00000267814.9	+	9	1250	c.1070C>T	c.(1069-1071)cCc>cTc	p.P357L	SORD_ENST00000558580.1_Missense_Mutation_p.P336L|SORD_ENST00000559562.1_3'UTR|RP11-109D20.2_ENST00000560967.1_RNA	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	357					fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		GACCAGAATCCCTGATGTTAA	0.488																																					p.P357L		Atlas-SNP	.											.	SORD	24	.	0			c.C1070T						PASS	.	C	LEU/PRO	1953,2293		271,1411,441	48.0	60.0	56.0		1070	4.5	1.0	15	dbSNP_131	56	1439,7157		0,1439,2859	yes	missense	SORD	NM_003104.5	98	271,2850,3300	TT,TC,CC		16.7403,45.9962,26.4133	probably-damaging	357/358	45365724	3392,9450	2123	4298	6421	SO:0001583	missense	6652	exon9			AGAATCCCTGATG		CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.1070C>T	15.37:g.45365724C>T	ENSP00000267814:p.Pro357Leu	Somatic	456	0	0		WXS	Illumina HiSeq	Phase_I	584	176	0.30137	NM_003104	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	37	CCDS10116.1	651	0.2980769230769231	302	0.6138211382113821	90	0.24861878453038674	109	0.19055944055944055	150	0.19788918205804748	C	22.0	4.229049	0.79688	0.459962	0.167403	ENSG00000140263	ENST00000267814	T	0.02050	4.48	5.46	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.99999999988807	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.06862	-1.0803	9	0.87932	D	0	-5.8678	13.1766	0.59630	0.0:0.9229:0.0:0.0771	rs2412946;rs2467833	278;357	B4DKI2;Q00796	.;DHSO_HUMAN	L	357	ENSP00000267814:P357L	ENSP00000267814:P357L	P	+	2	0	SORD	43153016	1.000000	0.71417	0.955000	0.39395	0.796000	0.44982	4.587000	0.60991	1.305000	0.44909	0.563000	0.77884	CCC	C|0.918;T|0.082	0.082	strong		0.488	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3		
C8orf34	116328	hgsc.bcm.edu	37	8	69699756	69699756	+	Missense_Mutation	SNP	G	G	A	rs16935065	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:69699756G>A	ENST00000539993.1	+	12	1825	c.1276G>A	c.(1276-1278)Gca>Aca	p.A426T	C8orf34_ENST00000325233.3_Missense_Mutation_p.A170T|C8orf34_ENST00000518698.1_Missense_Mutation_p.A512T|C8orf34_ENST00000337103.4_Missense_Mutation_p.A401T			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	426			A -> T (in dbSNP:rs16935065). {ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			AGGAGTGGAAGCAGAACAAGA	0.353													G|||	843	0.168331	0.2784	0.0965	5008	,	,		17608	0.124		0.1521	False		,,,				2504	0.1329				p.A512T		Atlas-SNP	.											.	C8orf34	170	.	0			c.G1534A						PASS	.	G	THR/ALA	1040,3364	379.7+/-323.4	130,780,1292	110.0	99.0	102.0		1534	-0.3	1.0	8	dbSNP_123	102	1339,7261	258.4+/-282.1	99,1141,3060	yes	missense	C8orf34	NM_052958.2	58	229,1921,4352	AA,AG,GG		15.5698,23.6149,18.2944	benign	512/539	69699756	2379,10625	2202	4300	6502	SO:0001583	missense	116328	exon12			GTGGAAGCAGAAC	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"""vestibule 1"""						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.1276G>A	8.37:g.69699756G>A	ENSP00000438159:p.Ala426Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	37		356	0.163003663003663	124	0.25203252032520324	34	0.09392265193370165	72	0.1258741258741259	126	0.1662269129287599	G	17.35	3.368334	0.61513	0.236149	0.155698	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000337103;ENST00000325233	T;T;T;T	0.54675	0.58;0.65;0.64;0.56	5.36	-0.339	0.12647	.	0.700302	0.12960	N	0.425071	T	0.00012	0.0000	N	0.19112	0.55	0.38403	P	0.05427199999999999	B	0.02656	0.0	B	0.06405	0.002	T	0.25916	-1.0118	8	.	.	.	-3.0872	5.0911	0.14708	0.3637:0.2059:0.4304:0.0	rs16935065;rs52799884;rs16935065	426	Q49A92	CH034_HUMAN	T	512;426;401;170	ENSP00000427820:A512T;ENSP00000438159:A426T;ENSP00000337174:A401T;ENSP00000319532:A170T	.	A	+	1	0	C8orf34	69862310	0.998000	0.40836	0.956000	0.39512	0.994000	0.84299	0.396000	0.20867	0.006000	0.14734	0.655000	0.94253	GCA	G|0.813;A|0.187	0.187	strong		0.353	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	
KIF20B	9585	hgsc.bcm.edu	37	10	91484780	91484780	+	Silent	SNP	G	G	A	rs386746405|rs8181361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91484780G>A	ENST00000371728.3	+	15	1931	c.1866G>A	c.(1864-1866)gaG>gaA	p.E622E	KIF20B_ENST00000394289.2_Silent_p.E622E|KIF20B_ENST00000416354.1_Silent_p.E622E|KIF20B_ENST00000260753.4_Silent_p.E622E|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	622					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						TTTGAAGGGAGACTCTGCTTC	0.333													A|||	1788	0.357029	0.4796	0.219	5008	,	,		18112	0.3085		0.2326	False		,,,				2504	0.4673				p.E622E		Atlas-SNP	.											.	KIF20B	191	.	0			c.G1866A						PASS	.	A		1998,2408	614.7+/-392.4	492,1014,697	102.0	107.0	105.0		1866	2.0	1.0	10	dbSNP_117	105	2003,6597	721.9+/-406.4	222,1559,2519	no	coding-synonymous	KIF20B	NM_016195.2		714,2573,3216	AA,AG,GG		23.2907,45.3473,30.7627		622/1781	91484780	4001,9005	2203	4300	6503	SO:0001819	synonymous_variant	9585	exon15			AAGGGAGACTCTG	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.1866G>A	10.37:g.91484780G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				G|0.688;A|0.312	0.312	strong		0.333	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
AHCTF1	25909	hgsc.bcm.edu	37	1	247006051	247006051	+	Missense_Mutation	SNP	G	G	C	rs12410563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247006051G>C	ENST00000391829.2	-	35	6676	c.6553C>G	c.(6553-6555)Ctg>Gtg	p.L2185V	AHCTF1_ENST00000326225.3_Missense_Mutation_p.L2194V|AHCTF1_ENST00000366508.1_Missense_Mutation_p.L2220V|AHCTF1_ENST00000470300.1_Intron			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2185	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.		L -> V (in dbSNP:rs12410563).		cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GGCTTTCCCAGAGTTTCTACT	0.343													C|||	1079	0.215455	0.2201	0.3357	5008	,	,		14969	0.1706		0.2197	False		,,,				2504	0.1656				p.L2194V	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6580G						PASS	.	C	VAL/LEU	918,3488	738.7+/-411.0	83,752,1368	226.0	206.0	213.0		6580	-0.1	0.0	1	dbSNP_120	213	1848,6752	730.1+/-406.7	202,1444,2654	yes	missense	AHCTF1	NM_015446.4	32	285,2196,4022	CC,CG,GG		21.4884,20.8352,21.2671	benign	2194/2276	247006051	2766,10240	2203	4300	6503	SO:0001583	missense	25909	exon35			TTCCCAGAGTTTC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6553C>G	1.37:g.247006051G>C	ENSP00000375705:p.Leu2185Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		503	0.2303113553113553	107	0.21747967479674796	118	0.3259668508287293	112	0.1958041958041958	166	0.21899736147757257	C	0	-2.750109	0.00086	0.208352	0.214884	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.22743	1.94;1.94;1.94	5.06	-0.129	0.13502	.	0.730444	0.12588	N	0.455812	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45220	-0.9276	9	0.12766	T	0.61	0.0995	5.9971	0.19499	0.0:0.5018:0.1262:0.372	rs12410563;rs12410563	2220;2185	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	V	2220;2194;2185	ENSP00000355464:L2220V;ENSP00000355465:L2194V;ENSP00000375705:L2185V	ENSP00000355465:L2194V	L	-	1	2	AHCTF1	245072674	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.286000	0.08399	-0.188000	0.10499	-1.295000	0.01343	CTG	G|0.784;C|0.216	0.216	strong		0.343	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
DZIP1	22873	hgsc.bcm.edu	37	13	96239805	96239805	+	Missense_Mutation	SNP	G	G	A	rs11070136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96239805G>A	ENST00000376829.2	-	20	3057	c.2206C>T	c.(2206-2208)Ccc>Tcc	p.P736S	DZIP1_ENST00000361396.2_Missense_Mutation_p.P717S|DZIP1_ENST00000347108.3_Missense_Mutation_p.P736S|DZIP1_ENST00000361156.3_Missense_Mutation_p.P717S	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	736			P -> S (in dbSNP:rs11070136). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P717S(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GCGGGCTTGGGAGAATCATCA	0.542													G|||	1346	0.26877	0.3207	0.2248	5008	,	,		19768	0.1558		0.3618	False		,,,				2504	0.2505				p.P736S		Atlas-SNP	.											DZIP1,NS,carcinoma,0,1	DZIP1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2206T						PASS	.	G	SER/PRO,SER/PRO	1323,3083	444.7+/-347.4	190,943,1070	161.0	140.0	147.0		2149,2206	2.6	1.0	13	dbSNP_120	147	2927,5673	456.3+/-364.0	498,1931,1871	yes	missense,missense	DZIP1	NM_014934.3,NM_198968.2	74,74	688,2874,2941	AA,AG,GG		34.0349,30.0272,32.6772	benign,benign	717/849,736/868	96239805	4250,8756	2203	4300	6503	SO:0001583	missense	22873	exon20			GCTTGGGAGAATC	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2206C>T	13.37:g.96239805G>A	ENSP00000366025:p.Pro736Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	27	0.3375	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	619	0.2834249084249084	160	0.3252032520325203	103	0.2845303867403315	80	0.13986013986013987	276	0.3641160949868074	G	0.013	-1.609554	0.00842	0.300272	0.340349	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.34	2.63	0.31362	.	0.434403	0.26116	N	0.026258	T	0.00012	0.0000	L	0.43923	1.385	0.50467	P	1.2900000000004574E-4	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.004	T	0.44081	-0.9351	9	0.17369	T	0.5	-9.4551	4.96	0.14061	0.2465:0.1776:0.5759:0.0	rs11070136;rs52809482;rs56641201;rs60157457;rs11070136	717;736	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	S	736;717;717;736	ENSP00000257312:P736S;ENSP00000355018:P717S;ENSP00000355175:P717S;ENSP00000366025:P736S	ENSP00000257312:P736S	P	-	1	0	DZIP1	95037806	0.995000	0.38212	0.968000	0.41197	0.094000	0.18550	0.739000	0.26173	1.244000	0.43870	0.650000	0.86243	CCC	G|0.704;A|0.296	0.296	strong		0.542	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
MMP26	56547	hgsc.bcm.edu	37	11	5010905	5010905	+	Missense_Mutation	SNP	A	A	G	rs2499953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5010905A>G	ENST00000380390.1	+	3	343	c.127A>G	c.(127-129)Aag>Gag	p.K43E	MMP26_ENST00000300762.1_Missense_Mutation_p.K43E|MMP26_ENST00000477339.1_3'UTR			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	43			K -> E (in dbSNP:rs2499953). {ECO:0000269|PubMed:10801841, ECO:0000269|PubMed:11389678}.		collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	TTTCCTGACCAAGAAGGAGTC	0.463													A|||	835	0.166733	0.2761	0.1614	5008	,	,		20022	0.2788		0.0308	False		,,,				2504	0.047				p.K43E		Atlas-SNP	.											.	MMP26	49	.	0			c.A127G						PASS	.	A	GLU/LYS	1080,3322	391.0+/-327.9	124,832,1245	51.0	46.0	48.0		127	1.1	0.3	11	dbSNP_100	48	187,8409	81.8+/-144.4	0,187,4111	yes	missense	MMP26	NM_021801.3	56	124,1019,5356	GG,GA,AA		2.1754,24.5343,9.7477	benign	43/262	5010905	1267,11731	2201	4298	6499	SO:0001583	missense	56547	exon2			CTGACCAAGAAGG	AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"""matrilysin 2"""	605470	"""matrix metalloproteinase 26"""			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.127A>G	11.37:g.5010905A>G	ENSP00000369753:p.Lys43Glu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_021801	Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	37	CCDS7752.1	398	0.18223443223443223	165	0.3353658536585366	50	0.13812154696132597	155	0.270979020979021	28	0.036939313984168866	A	14.50	2.554534	0.45487	0.245343	0.021754	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.37752	1.18;1.18	3.73	1.1	0.20463	Metallopeptidase, catalytic domain (1);	1.171060	0.06617	N	0.756722	T	0.00012	0.0000	L	0.41710	1.295	0.80722	P	0.0	B	0.21821	0.061	B	0.19148	0.024	T	0.34477	-0.9827	9	0.05721	T	0.95	-3.9917	3.2952	0.06964	0.6787:0.0:0.1187:0.2026	rs2499953;rs3763879;rs52823770;rs59422657;rs2499953	43	Q9NRE1	MMP26_HUMAN	E	43	ENSP00000369753:K43E;ENSP00000300762:K43E	ENSP00000300762:K43E	K	+	1	0	MMP26	4967481	0.011000	0.17503	0.274000	0.24659	0.463000	0.32649	0.368000	0.20399	0.325000	0.23359	0.455000	0.32223	AAG	A|0.858;G|0.142	0.142	strong		0.463	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801	
LRWD1	222229	hgsc.bcm.edu	37	7	102108532	102108532	+	Silent	SNP	G	G	A	rs73189880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102108532G>A	ENST00000292616.5	+	6	854	c.702G>A	c.(700-702)cgG>cgA	p.R234R	MIR5090_ENST00000582533.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	234					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						CCTTGAAACGGCCAGACGACG	0.692													G|||	607	0.121206	0.0068	0.1081	5008	,	,		15819	0.1399		0.1461	False		,,,				2504	0.2403				p.R234R		Atlas-SNP	.											LRWD1,NS,carcinoma,0,1	LRWD1	41	1	0			c.G702A						PASS	.	G		135,4267	92.5+/-131.2	0,135,2066	38.0	43.0	41.0		702	-0.4	0.0	7	dbSNP_130	41	1219,7377	229.4+/-264.1	82,1055,3161	no	coding-synonymous	LRWD1	NM_152892.1		82,1190,5227	AA,AG,GG		14.181,3.0668,10.417		234/648	102108532	1354,11644	2201	4298	6499	SO:0001819	synonymous_variant	222229	exon6			GAAACGGCCAGAC	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.702G>A	7.37:g.102108532G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			G|0.901;A|0.099	0.099	strong		0.692	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
SCAPER	49855	hgsc.bcm.edu	37	15	76726465	76726465	+	Missense_Mutation	SNP	G	G	T	rs1607017|rs34441478	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:76726465G>T	ENST00000563290.1	-	26	3360	c.3265C>A	c.(3265-3267)Ccc>Acc	p.P1089T	SCAPER_ENST00000538941.2_Missense_Mutation_p.P843T|SCAPER_ENST00000324767.7_Missense_Mutation_p.P1089T			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1089			P -> T (in dbSNP:rs1607017). {ECO:0000269|PubMed:10819331, ECO:0000269|Ref.7}.			endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						CCTTGTGAGGGTTTGTTTTTC	0.398													G|||	1783	0.35603	0.0938	0.3372	5008	,	,		16225	0.6131		0.327	False		,,,				2504	0.4888				p.P1089T		Atlas-SNP	.											.	SCAPER	160	.	0			c.C3265A						PASS	.	G	THR/PRO,THR/PRO	464,3200		23,418,1391	115.0	104.0	108.0		3265,2527	3.0	1.0	15	dbSNP_88	108	2519,5643		387,1745,1949	yes	missense,missense	SCAPER	NM_020843.2,NM_001145923.1	38,38	410,2163,3340	TT,TG,GG		30.8625,12.6638,25.2241	benign,benign	1089/1401,843/1155	76726465	2983,8843	1832	4081	5913	SO:0001583	missense	49855	exon25			GTGAGGGTTTGTT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3265C>A	15.37:g.76726465G>T	ENSP00000454973:p.Pro1089Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	753	0.3447802197802198	43	0.08739837398373984	130	0.35911602209944754	334	0.583916083916084	246	0.3245382585751979	G	7.381	0.628737	0.14257	0.126638	0.308625	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.22743	1.96;1.94	5.93	2.97	0.34412	.	0.429133	0.27306	N	0.019963	T	0.00012	0.0000	L	0.57536	1.79	0.31641	P	0.648053	B;B	0.21071	0.007;0.051	B;B	0.18871	0.007;0.023	T	0.39981	-0.9587	9	0.30078	T	0.28	.	5.7223	0.17995	0.2163:0.2696:0.5142:0.0	rs1607017;rs52823383;rs1607017	1088;843	Q9BY12;F5H7X8	SCAPE_HUMAN;.	T	1089;843;1111	ENSP00000326924:P1089T;ENSP00000442190:P843T	ENSP00000303560:P1111T	P	-	1	0	SCAPER	74513520	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	0.687000	0.25407	0.815000	0.34398	0.655000	0.94253	CCC	G|0.674;T|0.326	0.326	strong		0.398	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	
NKIRAS1	28512	hgsc.bcm.edu	37	3	23934772	23934772	+	Silent	SNP	G	G	A	rs3762775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:23934772G>A	ENST00000443659.2	-	4	1170	c.393C>T	c.(391-393)gaC>gaT	p.D131D	NKIRAS1_ENST00000425478.2_Silent_p.D131D|NKIRAS1_ENST00000416026.2_Silent_p.D131D|NKIRAS1_ENST00000421515.2_Silent_p.D131D|NKIRAS1_ENST00000415901.2_Silent_p.D131D|NKIRAS1_ENST00000388759.3_Silent_p.D131D|NKIRAS1_ENST00000412028.1_Silent_p.D131D|NKIRAS1_ENST00000437230.1_Silent_p.D131D			Q9NYS0	KBRS1_HUMAN	NFKB inhibitor interacting Ras-like 1	131					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	7						CCACTTCAGCGTCCACTTGTC	0.413													G|||	767	0.153155	0.2799	0.1772	5008	,	,		20287	0.003		0.0676	False		,,,				2504	0.2076				p.D131D		Atlas-SNP	.											.	NKIRAS1	18	.	0			c.C393T						PASS	.	G		1061,3345	385.4+/-325.7	123,815,1265	189.0	159.0	169.0		393	-10.3	0.2	3	dbSNP_107	169	575,8025	154.8+/-208.9	13,549,3738	no	coding-synonymous	NKIRAS1	NM_020345.3		136,1364,5003	AA,AG,GG		6.686,24.0808,12.5788		131/193	23934772	1636,11370	2203	4300	6503	SO:0001819	synonymous_variant	28512	exon5			TTCAGCGTCCACT	AF229839	CCDS33717.1	3p24.1	2014-05-09	2004-05-20		ENSG00000197885	ENSG00000197885			17899	protein-coding gene	gene with protein product		604496	"""NFKB inhibitor interacting Ras-like protein 1"""			10657303	Standard	NM_020345		Approved	KBRAS1, kappaB-Ras1	uc003ccj.3	Q9NYS0	OTTHUMG00000155605	ENST00000443659.2:c.393C>T	3.37:g.23934772G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	169	104	0.615385	NM_020345	Q96K18	Silent	SNP	ENST00000443659.2	37	CCDS33717.1																																																																																			G|0.868;A|0.132	0.132	strong		0.413	NKIRAS1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340876.2	NM_020345	
ANXA13	312	hgsc.bcm.edu	37	8	124710729	124710729	+	Missense_Mutation	SNP	C	C	T	rs2294013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:124710729C>T	ENST00000419625.1	-	4	329	c.257G>A	c.(256-258)cGt>cAt	p.R86H	ANXA13_ENST00000262219.6_Missense_Mutation_p.R127H	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	86			R -> H (in dbSNP:rs2294013).		cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			CTCGCTGGGACGGTCCAGAAG	0.577													C|||	1172	0.234026	0.2118	0.2133	5008	,	,		19804	0.1935		0.34	False		,,,				2504	0.2117				p.R127H		Atlas-SNP	.											.	ANXA13	38	.	0			c.G380A						PASS	.	C	HIS/ARG,HIS/ARG	939,3467	357.1+/-313.8	107,725,1371	126.0	118.0	121.0		380,257	-0.2	0.0	8	dbSNP_100	121	2895,5705	454.3+/-363.5	502,1891,1907	yes	missense,missense	ANXA13	NM_001003954.1,NM_004306.2	29,29	609,2616,3278	TT,TC,CC		33.6628,21.3118,29.4787	benign,benign	127/358,86/317	124710729	3834,9172	2203	4300	6503	SO:0001583	missense	312	exon5			CTGGGACGGTCCA	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.257G>A	8.37:g.124710729C>T	ENSP00000390809:p.Arg86His	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	37	CCDS47917.1	534	0.2445054945054945	101	0.20528455284552846	90	0.24861878453038674	93	0.16258741258741258	250	0.32981530343007914	C	13.84	2.358382	0.41801	0.213118	0.336628	ENSG00000104537	ENST00000262219;ENST00000419625;ENST00000520519	T;T;T	0.22134	3.56;1.97;3.56	5.67	-0.199	0.13220	.	0.389731	0.31589	N	0.007400	T	0.00012	0.0000	L	0.40543	1.245	0.53688	P	2.8000000000028002E-5	B;B	0.17268	0.002;0.021	B;B	0.16722	0.003;0.016	T	0.42965	-0.9420	9	0.62326	D	0.03	.	6.8696	0.24113	0.1174:0.5038:0.0:0.3788	rs2294013;rs17341816;rs60830097;rs2294013	86;127	P27216;P27216-2	ANX13_HUMAN;.	H	127;86;57	ENSP00000262219:R127H;ENSP00000390809:R86H;ENSP00000429358:R57H	ENSP00000262219:R127H	R	-	2	0	ANXA13	124779910	0.003000	0.15002	0.005000	0.12908	0.981000	0.71138	0.044000	0.13992	0.030000	0.15379	0.561000	0.74099	CGT	C|0.733;T|0.267	0.267	strong		0.577	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
MEFV	4210	hgsc.bcm.edu	37	16	3293880	3293880	+	Missense_Mutation	SNP	A	A	G	rs11466045	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:3293880A>G	ENST00000219596.1	-	9	1811	c.1772T>C	c.(1771-1773)aTt>aCt	p.I591T	MEFV_ENST00000339854.4_Missense_Mutation_p.I411T|MEFV_ENST00000536379.1_Missense_Mutation_p.I380T|MEFV_ENST00000541159.1_Silent_p.D438D	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	591	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		I -> T (in arFMF; unknown pathological significance; dbSNP:rs11466045). {ECO:0000269|PubMed:12124996}.		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						CTGAGCGCCAATCAGCTCCGG	0.507													A|||	22	0.00439297	0.0	0.0043	5008	,	,		19043	0.0		0.0179	False		,,,				2504	0.001				p.I591T		Atlas-SNP	.											.	MEFV	170	.	0			c.T1772C	GRCh37	CM015289	MEFV	M	rs11466045	PASS	.	A	THR/ILE,	9,4385	15.5+/-35.6	0,9,2188	47.0	49.0	48.0		1772,1314	-7.4	0.0	16	dbSNP_120	48	131,8469	66.0+/-128.3	0,131,4169	yes	missense,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	89,	0,140,6357	GG,GA,AA		1.5233,0.2048,1.0774	benign,	591/782,438/446	3293880	140,12854	2197	4300	6497	SO:0001583	missense	4210	exon9			GCGCCAATCAGCT	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.1772T>C	16.37:g.3293880A>G	ENSP00000219596:p.Ile591Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	CCDS10498.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	A	0.354	-0.943270	0.02322	0.002048	0.015233	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379	T;T;T	0.62941	-0.01;0.42;0.43	4.92	-7.43	0.01383	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	1.794070	0.02665	N	0.107974	T	0.17023	0.0409	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17349	-1.0372	10	0.10636	T	0.68	-12.7302	5.5811	0.17250	0.1755:0.1235:0.5795:0.1215	rs11466045;rs52809680;rs11466045	591	O15553	MEFV_HUMAN	T	591;591;411;380	ENSP00000219596:I591T;ENSP00000339639:I411T;ENSP00000445079:I380T	ENSP00000219596:I591T	I	-	2	0	MEFV	3233881	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.995000	0.03712	-1.022000	0.03346	-0.993000	0.02533	ATT	A|0.990;G|0.010	0.010	strong		0.507	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
OR10Z1	128368	hgsc.bcm.edu	37	1	158577167	158577167	+	Silent	SNP	A	A	T	rs2427808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158577167A>T	ENST00000361284.1	+	1	939	c.939A>T	c.(937-939)ggA>ggT	p.G313G		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	313						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)					TGGGTAAAGGATGAAGGTTAC	0.488													A|||	548	0.109425	0.0461	0.098	5008	,	,		19696	0.0794		0.1332	False		,,,				2504	0.2096				p.G313G		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A939T						PASS	.	A		306,4100	165.1+/-196.6	12,282,1909	89.0	91.0	90.0		939	1.9	0.7	1	dbSNP_100	90	1113,7487	229.7+/-264.3	88,937,3275	no	coding-synonymous	OR10Z1	NM_001004478.1		100,1219,5184	TT,TA,AA		12.9419,6.9451,10.9103		313/314	158577167	1419,11587	2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			TAAAGGATGAAGG	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.939A>T	1.37:g.158577167A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_001004478	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	37	CCDS30901.1																																																																																			A|0.898;T|0.102	0.102	strong		0.488	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
EFCAB6	64800	hgsc.bcm.edu	37	22	44079645	44079645	+	Silent	SNP	T	T	C	rs8141450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:44079645T>C	ENST00000262726.7	-	12	1486	c.1233A>G	c.(1231-1233)gcA>gcG	p.A411A	EFCAB6_ENST00000396231.2_Silent_p.A259A|EFCAB6_ENST00000358439.4_Intron	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	411	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.A411A(1)		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)				TTATCAGTAATGCTTTCTTCA	0.363													T|||	405	0.0808706	0.0083	0.0807	5008	,	,		22720	0.0327		0.1481	False		,,,				2504	0.1595				p.A411A		Atlas-SNP	.											EFCAB6,NS,carcinoma,0,1	EFCAB6	177	1	1	Substitution - coding silent(1)	stomach(1)	c.A1233G						scavenged	.	T	,	119,4287	89.7+/-128.4	2,115,2086	275.0	244.0	254.0		1233,777	-6.3	0.0	22	dbSNP_116	254	1210,7390	245.6+/-274.3	85,1040,3175	no	coding-synonymous,coding-synonymous	EFCAB6	NM_022785.3,NM_198856.2	,	87,1155,5261	CC,CT,TT		14.0698,2.7009,10.2184	,	411/1502,259/1350	44079645	1329,11677	2203	4300	6503	SO:0001819	synonymous_variant	64800	exon12			CAGTAATGCTTTC	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.1233A>G	22.37:g.44079645T>C		Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Silent	SNP	ENST00000262726.7	37	CCDS14049.1																																																																																			T|0.909;C|0.091	0.091	strong		0.363	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
PSMD3	5709	hgsc.bcm.edu	37	17	38137364	38137364	+	Silent	SNP	G	G	A	rs3087852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38137364G>A	ENST00000264639.4	+	1	315	c.141G>A	c.(139-141)tcG>tcA	p.S47S	PSMD3_ENST00000541736.1_Intron	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	47					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 protein catabolic process (GO:0042176)|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)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					GTGGCGGGTCGACGGGGGAGG	0.711											OREG0024385	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2630	0.52516	0.677	0.5259	5008	,	,		12464	0.4325		0.4563	False		,,,				2504	0.4857				p.S47S	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.G141A						PASS	.	A		2556,1346		884,788,279	10.0	17.0	15.0		141	-4.1	0.0	17	dbSNP_102	15	3869,3747		1069,1731,1008	no	coding-synonymous	PSMD3	NM_002809.2		1953,2519,1287	AA,AG,GG		49.1991,34.4951,44.2177		47/535	38137364	6425,5093	1951	3808	5759	SO:0001819	synonymous_variant	5709	exon1			CGGGTCGACGGGG	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.141G>A	17.37:g.38137364G>A		Somatic	66	0	0	875	WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	37	CCDS11356.1																																																																																			G|0.491;A|0.509	0.509	strong		0.711	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
ZFHX4	79776	hgsc.bcm.edu	37	8	77616519	77616519	+	Missense_Mutation	SNP	G	G	C	rs56261025	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:77616519G>C	ENST00000521891.2	+	2	644	c.196G>C	c.(196-198)Gtt>Ctt	p.V66L	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000518282.1_Missense_Mutation_p.V66L|ZFHX4_ENST00000050961.6_Missense_Mutation_p.V66L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.V66L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	66					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)			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)			GGGTTTCAGCGTTGAGAATGC	0.488										HNSCC(33;0.089)			G|||	70	0.0139776	0.0023	0.0187	5008	,	,		19093	0.0		0.0487	False		,,,				2504	0.0051				p.V66L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G196C						PASS	.	G	LEU/VAL	28,4140		1,26,2057	99.0	106.0	104.0		196	-2.6	0.0	8	dbSNP_129	104	329,8121		6,317,3902	yes	missense	ZFHX4	NM_024721.4	32	7,343,5959	CC,CG,GG		3.8935,0.6718,2.8293	benign	66/3617	77616519	357,12261	2084	4225	6309	SO:0001583	missense	79776	exon2			TTCAGCGTTGAGA		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.196G>C	8.37:g.77616519G>C	ENSP00000430497:p.Val66Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	51	0.023351648351648352	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	43	0.05672823218997362	G	2.338	-0.351766	0.05173	0.006718	0.038935	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000520307;ENST00000523885;ENST00000517585;ENST00000523809;ENST00000518282	T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.53	-2.56	0.06268	.	0.365437	0.19334	U	0.116828	T	0.00998	0.0033	N	0.08118	0	0.25403	N	0.988427	B;B;B;B	0.24483	0.002;0.0;0.004;0.104	B;B;B;B	0.20184	0.004;0.002;0.008;0.028	T	0.13124	-1.0521	10	0.29301	T	0.29	.	2.4741	0.04571	0.3445:0.1097:0.4333:0.1126	rs56261025;rs61729522	66;66;66;66	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	L	66	ENSP00000430497:V66L;ENSP00000399605:V66L;ENSP00000050961:V66L;ENSP00000428525:V66L;ENSP00000429495:V66L;ENSP00000427775:V66L;ENSP00000427739:V66L;ENSP00000430848:V66L	ENSP00000050961:V66L	V	+	1	0	ZFHX4	77779074	0.733000	0.28132	0.001000	0.08648	0.751000	0.42716	0.116000	0.15561	-0.739000	0.04809	0.655000	0.94253	GTT	A|0.002;C|0.025;G|0.973	0.025	strong		0.488	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863108	30863108	+	Missense_Mutation	SNP	A	A	G	rs12471868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:30863108A>G	ENST00000309052.4	+	7	1077	c.868A>G	c.(868-870)Ata>Gta	p.I290V	LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000540623.1_Missense_Mutation_p.I252V|LCLAT1_ENST00000379509.3_Missense_Mutation_p.I252V	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	290			I -> V (in dbSNP:rs12471868).		cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						CCGGTATCCAATAGACACCCT	0.512													A|||	844	0.16853	0.0923	0.2205	5008	,	,		19969	0.2232		0.1183	False		,,,				2504	0.2301				p.I290V		Atlas-SNP	.											.	LCLAT1	51	.	0			c.A868G						PASS	.	A	VAL/ILE,VAL/ILE	375,4031	190.9+/-216.7	20,335,1848	93.0	88.0	89.0		754,868	-7.0	0.0	2	dbSNP_120	89	1150,7450	236.8+/-268.9	94,962,3244	yes	missense,missense	LCLAT1	NM_001002257.1,NM_182551.3	29,29	114,1297,5092	GG,GA,AA		13.3721,8.5111,11.7254	benign,benign	252/377,290/415	30863108	1525,11481	2203	4300	6503	SO:0001583	missense	253558	exon7			TATCCAATAGACA	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.868A>G	2.37:g.30863108A>G	ENSP00000310551:p.Ile290Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_182551	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	331	0.15155677655677655	41	0.08333333333333333	74	0.20441988950276244	119	0.20804195804195805	97	0.1279683377308707	A	0.008	-1.886745	0.00527	0.085111	0.133721	ENSG00000172954	ENST00000379509;ENST00000444270;ENST00000309052;ENST00000540623	T;T;T	0.53640	0.61;0.61;0.61	5.77	-6.96	0.01622	.	0.419198	0.27126	N	0.020818	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.21861	-1.0233	9	0.13108	T	0.6	-1.6084	12.2763	0.54737	0.2097:0.0:0.7143:0.076	rs12471868;rs52802369;rs61598697;rs12471868	290	Q6UWP7	LCLT1_HUMAN	V	252;252;290;252	ENSP00000368823:I252V;ENSP00000310551:I290V;ENSP00000442857:I252V	ENSP00000310551:I290V	I	+	1	0	LCLAT1	30716612	0.023000	0.18921	0.000000	0.03702	0.048000	0.14542	0.249000	0.18216	-1.202000	0.02655	-0.379000	0.06801	ATA	A|0.870;G|0.130	0.130	strong		0.512	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	
FLG	2312	hgsc.bcm.edu	37	1	152277717	152277717	+	Silent	SNP	C	C	A	rs9436066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152277717C>A	ENST00000368799.1	-	3	9680	c.9645G>T	c.(9643-9645)gtG>gtT	p.V3215V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3215	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)			TGTCCTGGCTCACACTGGATC	0.557									Ichthyosis				A|||	2352	0.469649	0.5212	0.4524	5008	,	,		19788	0.6835		0.173	False		,,,				2504	0.4969				p.V3215V		Atlas-SNP	.											.	FLG	900	.	0			c.G9645T						PASS	.	A		1977,2427		470,1037,695	115.0	142.0	133.0		9645	-5.4	0.0	1	dbSNP_119	133	1292,7288		130,1032,3128	no	coding-synonymous	FLG	NM_002016.1		600,2069,3823	AA,AC,CC		15.0583,44.891,25.1771		3215/4062	152277717	3269,9715	2202	4290	6492	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGCTCACACTG	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.9645G>T	1.37:g.152277717C>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	205	117	0.570732	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			C|0.695;A|0.305	0.305	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CCDC61	729440	hgsc.bcm.edu	37	19	46518651	46518651	+	Missense_Mutation	SNP	A	A	G	rs7895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46518651A>G	ENST00000595358.1	+	7	860	c.811A>G	c.(811-813)Acg>Gcg	p.T271A	CCDC61_ENST00000536603.1_Intron|CCDC61_ENST00000594087.1_Intron|CCDC61_ENST00000263284.2_Missense_Mutation_p.T328A	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	271						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		CCGGCTGAAGACGCTGACCAG	0.721													A|||	575	0.114816	0.053	0.0663	5008	,	,		6141	0.1081		0.1392	False		,,,				2504	0.2147				p.T271A		Atlas-SNP	.											.	CCDC61	32	.	0			c.A811G						PASS	.		ALA/THR	188,3606		4,180,1713	14.0	16.0	16.0		982	0.1	0.8	19	dbSNP_52	16	995,7003		50,895,3054	yes	missense	CCDC61	NM_001080402.1	58	54,1075,4767	GG,GA,AA		12.4406,4.9552,10.0322	benign	328/532	46518651	1183,10609	1897	3999	5896	SO:0001583	missense	729440	exon7			CTGAAGACGCTGA		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.811A>G	19.37:g.46518651A>G	ENSP00000471454:p.Thr271Ala	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	224	0.10256410256410256	27	0.054878048780487805	28	0.07734806629834254	71	0.12412587412587413	98	0.12928759894459102	A	12.21	1.868702	0.32977	0.049552	0.124406	ENSG00000104983	ENST00000263284	.	.	.	3.86	0.117	0.14652	.	0.282143	0.36303	N	0.002663	T	0.00300	0.0009	L	0.36672	1.1	0.09310	P	0.99999999003817	B	0.02656	0.0	B	0.06405	0.002	T	0.03184	-1.1063	8	0.38643	T	0.18	-7.0451	3.1397	0.06451	0.5895:0.0:0.2303:0.1802	rs7895;rs17349438	271	Q9Y6R9	CCD61_HUMAN	A	328	.	ENSP00000263284:T328A	T	+	1	0	CCDC61	51210491	0.995000	0.38212	0.816000	0.32577	0.823000	0.46562	1.816000	0.38992	0.058000	0.16222	0.249000	0.18162	ACG	A|0.897;G|0.103	0.103	strong		0.721	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
SLFN13	146857	hgsc.bcm.edu	37	17	33768199	33768199	+	Silent	SNP	G	G	A	rs1822403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33768199G>A	ENST00000285013.6	-	6	2384	c.2109C>T	c.(2107-2109)gaC>gaT	p.D703D	SLFN13_ENST00000542635.1_Silent_p.D703D|SLFN13_ENST00000360502.2_Silent_p.D385D|SLFN13_ENST00000533791.1_Silent_p.D703D|SLFN13_ENST00000526861.1_Silent_p.D703D|SLFN13_ENST00000534689.1_Silent_p.D385D	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	703						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.D703D(1)		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)		TCTGAAAGTAGTCCAGAAAGA	0.478													G|||	1854	0.370208	0.5068	0.3314	5008	,	,		16920	0.3849		0.3688	False		,,,				2504	0.1994				p.D703D		Atlas-SNP	.											SLFN13,NS,carcinoma,0,1	SLFN13	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C2109T						PASS	.	G		2104,2302	565.2+/-381.6	518,1068,617	129.0	136.0	133.0		2109	2.4	1.0	17	dbSNP_92	133	3222,5378	484.4+/-371.4	610,2002,1688	no	coding-synonymous	SLFN13	NM_144682.5		1128,3070,2305	AA,AG,GG		37.4651,47.7531,40.9503		703/898	33768199	5326,7680	2203	4300	6503	SO:0001819	synonymous_variant	146857	exon6			AAAGTAGTCCAGA	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.2109C>T	17.37:g.33768199G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																			.	.	weak		0.478	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
SIRPB1	10326	hgsc.bcm.edu	37	20	1600524	1600524	+	Missense_Mutation	SNP	T	T	C	rs1535882	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1600524T>C	ENST00000381605.4	-	1	131	c.67A>G	c.(67-69)Aga>Gga	p.R23G	SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000279477.7_Missense_Mutation_p.R23G|SIRPB1_ENST00000381603.3_Missense_Mutation_p.R23G|SIRPB1_ENST00000568365.1_Missense_Mutation_p.R23G|RP4-576H24.4_ENST00000564763.1_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	56	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	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	
KLHL21	9903	hgsc.bcm.edu	37	1	6659505	6659505	+	Silent	SNP	G	G	A	rs2232460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6659505G>A	ENST00000377658.4	-	2	1080	c.1029C>T	c.(1027-1029)tcC>tcT	p.S343S	KLHL21_ENST00000463043.1_5'UTR|KLHL21_ENST00000467612.1_5'UTR|KLHL21_ENST00000377663.3_Silent_p.S343S	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	343					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|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;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		GGGAGCCATCGGACCCACCTG	0.632													G|||	1740	0.347444	0.267	0.3127	5008	,	,		19334	0.38		0.3171	False		,,,				2504	0.4785				p.S343S		Atlas-SNP	.											KLHL21,NS,carcinoma,0,1	KLHL21	27	1	0			c.C1029T						scavenged	.	G		1186,3220	405.8+/-333.6	171,844,1188	43.0	41.0	42.0		1029	-9.8	0.0	1	dbSNP_98	42	2908,5692	448.5+/-361.8	480,1948,1872	no	coding-synonymous	KLHL21	NM_014851.2		651,2792,3060	AA,AG,GG		33.814,26.9178,31.4778		343/598	6659505	4094,8912	2203	4300	6503	SO:0001819	synonymous_variant	9903	exon2			GCCATCGGACCCA	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"""Kelch-like"", ""BTB/POZ domain containing"""	29041	protein-coding gene	gene with protein product			"""kelch-like 21 (Drosophila)"""				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1029C>T	1.37:g.6659505G>A		Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Silent	SNP	ENST00000377658.4	37	CCDS30575.1																																																																																			G|0.689;A|0.311	0.311	strong		0.632	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851	
PECR	55825	hgsc.bcm.edu	37	2	216923679	216923679	+	Missense_Mutation	SNP	C	C	T	rs1429148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	113	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	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	
ABCA13	154664	hgsc.bcm.edu	37	7	48313510	48313510	+	Missense_Mutation	SNP	A	A	G	rs17547830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	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	
DOCK8	81704	hgsc.bcm.edu	37	9	370244	370244	+	Silent	SNP	A	A	G	rs913703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:370244A>G	ENST00000453981.1	+	16	1924	c.1812A>G	c.(1810-1812)aaA>aaG	p.K604K	DOCK8_ENST00000469391.1_Silent_p.K536K|DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000432829.2_Silent_p.K536K|DOCK8_ENST00000382329.1_Silent_p.K71K			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	604	DHR-1.				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)		TCTTTGGAAAATCCAGCGGGC	0.388													G|||	1081	0.215855	0.2859	0.2133	5008	,	,		20473	0.0804		0.2326	False		,,,				2504	0.2454				p.K604K		Atlas-SNP	.											.	DOCK8	401	.	0			c.A1812G						PASS	.	G	,,	1184,3222	711.3+/-408.0	150,884,1169	104.0	104.0	104.0		1608,1608,1812	1.8	1.0	9	dbSNP_86	104	2091,6509	717.4+/-406.2	253,1585,2462	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	403,2469,3631	GG,GA,AA		24.314,26.8724,25.1807	,,	536/2000,536/2032,604/2100	370244	3275,9731	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon16			TGGAAAATCCAGC	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.1812A>G	9.37:g.370244A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			A|0.770;G|0.230	0.230	strong		0.388	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
F5	2153	hgsc.bcm.edu	37	1	169512120	169512120	+	Silent	SNP	G	G	A	rs6016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169512120G>A	ENST00000367797.3	-	13	2409	c.2208C>T	c.(2206-2208)atC>atT	p.I736I	F5_ENST00000367796.3_Silent_p.I741I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	736	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)	GGAATGACCTGATTCCTAATG	0.428													A|||	1316	0.26278	0.1679	0.3948	5008	,	,		20914	0.248		0.2535	False		,,,				2504	0.3221				p.I736I		Atlas-SNP	.											.	F5	301	.	0			c.C2208T						PASS	.	A		813,3593	750.9+/-412.2	68,677,1458	227.0	210.0	216.0		2208	-2.7	0.9	1	dbSNP_52	216	2355,6245	702.8+/-405.3	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2434,3702	AA,AG,GG		27.3837,18.4521,24.358		736/2225	169512120	3168,9838	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGACCTGATTCCT	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.2208C>T	1.37:g.169512120G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	163	99	0.607362	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.758;A|0.242	0.242	strong		0.428	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ERGIC3	51614	hgsc.bcm.edu	37	20	34144746	34144746	+	Silent	SNP	A	A	G	rs8825|rs17845241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34144746A>G	ENST00000348547.2	+	11	959	c.882A>G	c.(880-882)gtA>gtG	p.V294V	ERGIC3_ENST00000279052.6_Silent_p.V299V|ERGIC3_ENST00000447986.1_Silent_p.V309V|ERGIC3_ENST00000357394.4_Silent_p.V299V	NM_015966.2	NP_057050.1	Q9Y282	ERGI3_HUMAN	ERGIC and golgi 3	294					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)	16	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CACCCCAGGTACTGAGGACAA	0.607													A|||	805	0.160743	0.2685	0.1182	5008	,	,		18196	0.0794		0.0865	False		,,,				2504	0.2055				p.V299V		Atlas-SNP	.											.	ERGIC3	41	.	0			c.A897G						PASS	.	A	,	1176,3230	411.1+/-335.6	148,880,1175	46.0	40.0	42.0		882,897	2.1	1.0	20	dbSNP_52	42	714,7886	174.0+/-224.4	35,644,3621	no	coding-synonymous,coding-synonymous	ERGIC3	NM_015966.2,NM_198398.1	,	183,1524,4796	GG,GA,AA		8.3023,26.6909,14.5318	,	294/384,299/389	34144746	1890,11116	2203	4300	6503	SO:0001819	synonymous_variant	51614	exon12			CCAGGTACTGAGG	AF077030	CCDS13257.1, CCDS13258.1	20q11.22	2013-09-19	2006-01-19	2006-01-19	ENSG00000125991	ENSG00000125991			15927	protein-coding gene	gene with protein product			"""serologically defined breast cancer antigen 84"", ""chromosome 20 open reading frame 47"""	SDBCAG84, C20orf47		10810093	Standard	NM_015966		Approved	CGI-54, PRO0989, NY-BR-84, Erv46	uc002xcs.3	Q9Y282	OTTHUMG00000032346	ENST00000348547.2:c.882A>G	20.37:g.34144746A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_198398	Q5JWS3|Q6ZWP7|Q9H276|Q9P1L3	Silent	SNP	ENST00000348547.2	37	CCDS13257.1	294|294	0.1346153846153846|0.1346153846153846	142|142	0.2886178861788618|0.2886178861788618	53|53	0.1464088397790055|0.1464088397790055	32|32	0.055944055944055944|0.055944055944055944	67|67	0.08839050131926121|0.08839050131926121	A|A	11.99|11.99	1.805097|1.805097	0.31961|0.31961	0.266909|0.266909	0.083023|0.083023	ENSG00000125991|ENSG00000125991	ENST00000413587;ENST00000451605|ENST00000416206;ENST00000442139	.|.	.|.	.|.	5.36|5.36	2.13|2.13	0.27403|0.27403	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999956|0.9999999999999956	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34153|0.34153	-0.9840|-0.9840	3|3	.|.	.|.	.|.	-33.0283|-33.0283	4.1626|4.1626	0.10291|0.10291	0.0785:0.1371:0.5024:0.2819|0.0785:0.1371:0.5024:0.2819	rs8825;rs1135935;rs3198951;rs11554457;rs17423412;rs61341895;rs8825|rs8825;rs1135935;rs3198951;rs11554457;rs17423412;rs61341895;rs8825	.|.	.|.	.|.	A|C	296;41|308;84	.|.	.|.	T|Y	+|+	1|2	0|0	ERGIC3|ERGIC3	33608160|33608160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	2.983000|2.983000	0.49345|0.49345	0.621000|0.621000	0.30232|0.30232	-0.142000|-0.142000	0.14014|0.14014	ACT|TAC	A|0.855;G|0.145	0.145	strong		0.607	ERGIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078880.2	NM_015966	
TNRC18	84629	hgsc.bcm.edu	37	7	5427652	5427652	+	Silent	SNP	G	G	A	rs4720623	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5427652G>A	ENST00000430969.1	-	5	2151	c.1803C>T	c.(1801-1803)gcC>gcT	p.A601A	TNRC18_ENST00000399537.4_Silent_p.A601A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	601							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CAGGGCGCACGGCCACGGCGT	0.667													G|||	2102	0.419728	0.7693	0.3703	5008	,	,		12690	0.1756		0.2535	False		,,,				2504	0.4049				p.A601A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C1803T						PASS	.	G		2598,1330		889,820,255	6.0	8.0	7.0		1803	-5.4	0.7	7	dbSNP_111	7	2219,5961		360,1499,2231	no	coding-synonymous	TNRC18	NM_001080495.2		1249,2319,2486	AA,AG,GG		27.1271,33.8595,39.7836		601/2969	5427652	4817,7291	1964	4090	6054	SO:0001819	synonymous_variant	84629	exon5			GCGCACGGCCACG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1803C>T	7.37:g.5427652G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	92	23	0.25	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.633;A|0.367	0.367	strong		0.667	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
ZNF8	7554	hgsc.bcm.edu	37	19	58806083	58806083	+	Silent	SNP	T	T	C	rs260471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58806083T>C	ENST00000196548.5	+	4	1040	c.909T>C	c.(907-909)caT>caC	p.H303H	ZNF8_ENST00000608843.1_Silent_p.H303H|AC010642.1_ENST00000591325.1_3'UTR			P17098	ZNF8_HUMAN	zinc finger protein 8	303					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		TCGTCCAGCATGAGCGCATCC	0.527													C|||	1888	0.376997	0.4523	0.3271	5008	,	,		21527	0.499		0.2445	False		,,,				2504	0.3211				p.H303H		Atlas-SNP	.											.	ZNF8	60	.	0			c.T909C						PASS	.	C		1849,2557	635.3+/-396.4	393,1063,747	91.0	90.0	91.0		909	-1.9	1.0	19	dbSNP_79	91	2394,6206	701.0+/-405.2	308,1778,2214	no	coding-synonymous	ZNF8	NM_021089.2		701,2841,2961	CC,CT,TT		27.8372,41.9655,32.6234		303/576	58806083	4243,8763	2203	4300	6503	SO:0001819	synonymous_variant	7554	exon4			CCAGCATGAGCGC	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"""Zinc fingers, C2H2-type"", ""-"""	13154	protein-coding gene	gene with protein product		194532	"""zinc finger protein 8 (clone HF.18)"""			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.909T>C	19.37:g.58806083T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_021089	Q6PI99	Silent	SNP	ENST00000196548.5	37	CCDS12974.1																																																																																			T|0.652;C|0.348	0.348	strong		0.527	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089	
DNAJB6	10049	hgsc.bcm.edu	37	7	157202683	157202683	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:157202683G>A	ENST00000262177.4	+	9	1091	c.886G>A	c.(886-888)Gcg>Acg	p.A296T	DNAJB6_ENST00000443280.1_Missense_Mutation_p.A181T|DNAJB6_ENST00000452797.2_Missense_Mutation_p.A247T	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	296					intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGACCCCCTCGCGTCCGCAGC	0.701																																					p.A296T	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.G886A						PASS	.						6.0	5.0	5.0					7																	157202683		2018	3994	6012	SO:0001583	missense	10049	exon9			CCCCTCGCGTCCG	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"""Heat shock proteins / DNAJ (HSP40)"""	14888	protein-coding gene	gene with protein product		611332	"""limb girdle muscular dystrophy 1D (autosomal dominant)"""	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.886G>A	7.37:g.157202683G>A	ENSP00000262177:p.Ala296Thr	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	37	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226791	0.58668	.	.	ENSG00000105993	ENST00000262177;ENST00000452797;ENST00000443280	T;T;T	0.63255	0.39;-0.03;-0.02	4.5	-5.97	0.02227	.	3.940110	0.01650	N	0.024503	T	0.36054	0.0953	N	0.08118	0	0.09310	N	1	B;B;B;B	0.33494	0.0;0.414;0.001;0.001	B;B;B;B	0.24006	0.0;0.05;0.001;0.001	T	0.32107	-0.9919	10	0.45353	T	0.12	.	8.0691	0.30678	0.668:0.2188:0.1132:0.0	.	181;247;296;296	E9PH18;B4DN73;A8KAG0;O75190	.;.;.;DNJB6_HUMAN	T	296;247;181	ENSP00000262177:A296T;ENSP00000402270:A247T;ENSP00000396267:A181T	ENSP00000262177:A296T	A	+	1	0	DNAJB6	156895444	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.031000	0.03578	-1.112000	0.02984	-0.140000	0.14226	GCG	.	.	none		0.701	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2		
OR4C46	119749	hgsc.bcm.edu	37	11	51515912	51515912	+	Missense_Mutation	SNP	C	C	T	rs77689730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:51515912C>T	ENST00000328188.1	+	1	631	c.631C>T	c.(631-633)Ctc>Ttc	p.L211F		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						AAACTTTGCCCTCCTGCTGGT	0.517													.|||	978	0.195288	0.1626	0.1671	5008	,	,		20373	0.2262		0.0954	False		,,,				2504	0.3303				p.L211F		Atlas-SNP	.											OR4C46,NS,carcinoma,-2,1	OR4C46	96	1	0			c.C631T						PASS	.	C	PHE/LEU	708,3694		58,592,1551	123.0	106.0	111.0		631	0.3	0.0	11	dbSNP_131	111	902,7690		54,794,3448	yes	missense	OR4C46	NM_001004703.1	22	112,1386,4999	TT,TC,CC		10.4981,16.0836,12.3903	benign	211/310	51515912	1610,11384	2201	4296	6497	SO:0001583	missense	119749	exon1			TTTGCCCTCCTGC		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.631C>T	11.37:g.51515912C>T	ENSP00000329056:p.Leu211Phe	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	354	0.1620879120879121	89	0.18089430894308944	53	0.1464088397790055	145	0.2534965034965035	67	0.08839050131926121	.	0.623	-0.820491	0.02755	0.160836	0.104981	ENSG00000185926	ENST00000328188	T	0.42131	0.98	2.47	0.291	0.15732	GPCR, rhodopsin-like superfamily (1);	0.425624	0.17845	N	0.160070	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.20988	0.05	B	0.29077	0.098	T	0.28618	-1.0038	9	0.51188	T	0.08	.	4.736	0.12988	0.2095:0.6582:0.0:0.1323	.	211	A6NHA9	O4C46_HUMAN	F	211	ENSP00000329056:L211F	ENSP00000329056:L211F	L	+	1	0	OR4C46	51372488	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.168000	0.01270	-0.027000	0.13873	-1.492000	0.00969	CTC	C|0.864;T|0.136	0.136	strong		0.517	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
CCDC14	64770	hgsc.bcm.edu	37	3	123634046	123634046	+	Silent	SNP	G	G	A	rs2700373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:123634046G>A	ENST00000488653.2	-	13	2532	c.2442C>T	c.(2440-2442)agC>agT	p.S814S	CCDC14_ENST00000310351.4_Silent_p.S654S|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000433542.2_Silent_p.S773S|CCDC14_ENST00000485727.1_Silent_p.S614S|CCDC14_ENST00000489746.1_Silent_p.S614S			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	814					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		CAGCAAGTCCGCTGTTGCTGA	0.428													A|||	4219	0.842452	0.9539	0.8689	5008	,	,		20223	0.8859		0.7137	False		,,,				2504	0.7607				p.S773S		Atlas-SNP	.											.	CCDC14	97	.	0			c.C2319T						PASS	.	A		4075,331	173.0+/-202.9	1888,299,16	61.0	61.0	61.0		2319	1.3	0.0	3	dbSNP_100	61	6438,2162	369.4+/-335.5	2410,1618,272	no	coding-synonymous	CCDC14	NM_022757.4		4298,1917,288	AA,AG,GG		25.1395,7.5125,19.1681		773/913	123634046	10513,2493	2203	4300	6503	SO:0001819	synonymous_variant	64770	exon12			AAGTCCGCTGTTG	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2442C>T	3.37:g.123634046G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Silent	SNP	ENST00000488653.2	37																																																																																				G|0.166;A|0.834	0.834	strong		0.428	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
CDKN2D	1032	hgsc.bcm.edu	37	19	10676423	10676423	+	IGR	SNP	G	G	A	rs3745245	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10676423G>A	ENST00000393599.2	-	0	1422				KRI1_ENST00000361821.5_Silent_p.S48S|KRI1_ENST00000312962.6_Silent_p.S52S|KRI1_ENST00000537964.1_5'UTR	NM_001800.3|NM_079421.2	NP_001791.1|NP_524145.1	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)						autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to retinoic acid (GO:0032526)|response to UV (GO:0009411)|response to vitamin D (GO:0033280)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)			endometrium(3)|lung(2)|ovary(1)	6			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			CCGACTCGGAGCTGGAGTCGC	0.716													g|||	3035	0.60603	0.7474	0.4726	5008	,	,		11812	0.3472		0.7773	False		,,,				2504	0.6002				p.S52S		Atlas-SNP	.											KRI1,rectum,carcinoma,0,1	KRI1	65	1	0			c.C156T						PASS	.			3281,1103		1238,805,149	17.0	18.0	18.0		156	2.1	1.0	19	dbSNP_107	18	6392,2178		2405,1582,298	no	coding-synonymous	KRI1	NM_023008.3		3643,2387,447	AA,AG,GG		25.4142,25.1597,25.3281		52/710	10676423	9673,3281	2192	4285	6477	SO:0001628	intergenic_variant	65095	exon2			CTCGGAGCTGGAG		CCDS12244.1	19p13	2013-01-10				ENSG00000129355		"""Ankyrin repeat domain containing"""	1790	protein-coding gene	gene with protein product		600927				8575754	Standard	NM_079421		Approved	INK4D, p19	uc002mpa.3	P55273			19.37:g.10676423G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_023008	Q13102|Q6FGE9	Silent	SNP	ENST00000393599.2	37	CCDS12244.1																																																																																			G|0.330;A|0.670	0.670	strong		0.716	CDKN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452030.1	NM_079421	
FNDC1	84624	hgsc.bcm.edu	37	6	159650978	159650978	+	Missense_Mutation	SNP	A	A	G	rs509648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	95	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	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	
TYRO3	7301	hgsc.bcm.edu	37	15	41857303	41857303	+	Silent	SNP	T	T	C	rs2277536	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41857303T>C	ENST00000263798.3	+	6	971	c.747T>C	c.(745-747)gcT>gcC	p.A249A	TYRO3_ENST00000559066.1_Silent_p.A204A	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	249	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TGCCAGGTGCTGATGGCCGAG	0.592													T|||	1338	0.267173	0.1959	0.4063	5008	,	,		20524	0.1736		0.3082	False		,,,				2504	0.319				p.A249A		Atlas-SNP	.											.	TYRO3	169	.	0			c.T747C						PASS	.	T		890,3516		81,728,1394	94.0	84.0	88.0		747	-0.1	1.0	15	dbSNP_100	88	2455,6145		285,1885,2130	no	coding-synonymous	TYRO3	NM_006293.3		366,2613,3524	CC,CT,TT		28.5465,20.1997,25.7189		249/891	41857303	3345,9661	2203	4300	6503	SO:0001819	synonymous_variant	7301	exon6			AGGTGCTGATGGC	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.747T>C	15.37:g.41857303T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_006293	O14953|Q86VR3	Silent	SNP	ENST00000263798.3	37	CCDS10080.1																																																																																			T|0.736;C|0.264	0.264	strong		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
SEC31B	25956	hgsc.bcm.edu	37	10	102265815	102265815	+	Silent	SNP	A	A	G	rs2295773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102265815A>G	ENST00000370345.3	-	9	1123	c.1026T>C	c.(1024-1026)caT>caC	p.H342H	SEC31B_ENST00000370329.5_Silent_p.H345H|SEC31B_ENST00000451524.1_Silent_p.H342H|SEC31B_ENST00000535773.1_Silent_p.H185H	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	342					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCTGTCTCATATGCTGGACTT	0.542													G|||	927	0.185104	0.1997	0.1844	5008	,	,		19940	0.1319		0.1909	False		,,,				2504	0.2147				p.H342H		Atlas-SNP	.											SEC31B,colon,carcinoma,-2,1	SEC31B	84	1	0			c.T1026C						PASS	.	G		858,3548	744.3+/-411.5	86,686,1431	183.0	186.0	185.0		1026	3.1	1.0	10	dbSNP_100	185	1893,6707	728.3+/-406.7	216,1461,2623	no	coding-synonymous	SEC31B	NM_015490.3		302,2147,4054	GG,GA,AA		22.0116,19.4734,21.1518		342/1180	102265815	2751,10255	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon9			TCTCATATGCTGG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1026T>C	10.37:g.102265815A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			A|0.807;G|0.193	0.193	strong		0.542	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
SLC12A9	56996	hgsc.bcm.edu	37	7	100454796	100454796	+	Missense_Mutation	SNP	G	G	A	rs143666254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100454796G>A	ENST00000354161.3	+	5	880	c.755G>A	c.(754-756)gGc>gAc	p.G252D	SLC12A9_ENST00000428758.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000540482.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000415287.1_Missense_Mutation_p.G163D|SLC12A9_ENST00000275729.3_Missense_Mutation_p.G163D	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	252					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					GACAACTTGGGCGGTGAGCTG	0.652													G|||	7	0.00139776	0.0008	0.0029	5008	,	,		15798	0.0		0.004	False		,,,				2504	0.0				p.G252D		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G755A						PASS	.	G	ASP/GLY	6,4398		0,6,2196	43.0	48.0	46.0		755	0.7	0.2	7	dbSNP_134	46	59,8537		0,59,4239	yes	missense	SLC12A9	NM_020246.2	94	0,65,6435	AA,AG,GG		0.6864,0.1362,0.5	probably-damaging	252/915	100454796	65,12935	2202	4298	6500	SO:0001583	missense	56996	exon5			ACTTGGGCGGTGA	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.755G>A	7.37:g.100454796G>A	ENSP00000275730:p.Gly252Asp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	2.002	-0.429266	0.04701	0.001362	0.006864	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161	D;D;D;D;D	0.98862	-5.19;-5.19;-5.19;-5.19;-5.19	4.65	0.708	0.18144	Amino acid permease domain (1);	0.458827	0.21438	N	0.074528	D	0.94470	0.8220	L	0.41710	1.295	0.19775	N	0.99995	B;B	0.24132	0.098;0.002	B;B	0.32149	0.141;0.024	D	0.89635	0.3858	10	0.36615	T	0.2	.	5.9914	0.19465	0.2529:0.3003:0.4469:0.0	.	163;252	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	D	252;252;163;163;252	ENSP00000443702:G252D;ENSP00000408301:G252D;ENSP00000275729:G163D;ENSP00000413796:G163D;ENSP00000275730:G252D	ENSP00000275729:G163D	G	+	2	0	SLC12A9	100292732	0.059000	0.20769	0.160000	0.22671	0.005000	0.04900	0.363000	0.20301	-0.175000	0.10725	-1.943000	0.00494	GGC	G|0.996;A|0.004	0.004	strong		0.652	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
THADA	63892	hgsc.bcm.edu	37	2	43819139	43819139	+	Silent	SNP	A	A	G	rs17031095	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43819139A>G	ENST00000405006.4	-	3	474	c.123T>C	c.(121-123)caT>caC	p.H41H	THADA_ENST00000402360.2_Silent_p.H41H|THADA_ENST00000404790.1_Silent_p.H41H|THADA_ENST00000403856.1_Silent_p.H41H|THADA_ENST00000415080.2_5'UTR|THADA_ENST00000405975.2_Silent_p.H41H	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	41										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)				GTTGCACACAATGTAACAGCA	0.313													A|||	577	0.115216	0.2337	0.0793	5008	,	,		16040	0.0079		0.1074	False		,,,				2504	0.0992				p.H41H		Atlas-SNP	.											.	THADA	131	.	0			c.T123C						PASS	.	A	,	699,2989		60,579,1205	59.0	54.0	56.0		123,123	-9.3	0.0	2	dbSNP_123	56	1087,7075		77,933,3071	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	137,1512,4276	GG,GA,AA		13.3178,18.9534,15.0717	,	41/1954,41/1954	43819139	1786,10064	1844	4081	5925	SO:0001819	synonymous_variant	63892	exon3			CACACAATGTAAC	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.123T>C	2.37:g.43819139A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1																																																																																			A|0.886;G|0.114	0.114	strong		0.313	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
PFKP	5214	hgsc.bcm.edu	37	10	3150898	3150898	+	Silent	SNP	C	C	T	rs11251721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:3150898C>T	ENST00000381125.4	+	9	952	c.876C>T	c.(874-876)gtC>gtT	p.V292V	PFKP_ENST00000381075.2_Silent_p.V284V	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	292	N-terminal catalytic PFK domain 1.				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)		TGCAGCTTGTCGTCACGCAGC	0.562													c|||	692	0.138179	0.1543	0.2075	5008	,	,		17981	0.0536		0.2018	False		,,,				2504	0.089				p.V292V		Atlas-SNP	.											.	PFKP	182	.	0			c.C876T						PASS	.	T	,	704,3702	294.4+/-283.1	65,574,1564	132.0	114.0	120.0		852,876	-5.7	0.1	10	dbSNP_120	120	1731,6869	315.7+/-312.4	172,1387,2741	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	237,1961,4305	TT,TC,CC		20.1279,15.9782,18.7221	,	284/777,292/785	3150898	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon9			GCTTGTCGTCACG	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.876C>T	10.37:g.3150898C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.826;T|0.174	0.174	strong		0.562	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
PLEKHA1	59338	hgsc.bcm.edu	37	10	124189197	124189197	+	Missense_Mutation	SNP	A	A	G	rs1045216	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:124189197A>G	ENST00000368990.3	+	12	1089	c.958A>G	c.(958-960)Acc>Gcc	p.T320A	PLEKHA1_ENST00000433307.1_Missense_Mutation_p.T320A|PLEKHA1_ENST00000538022.1_3'UTR|PLEKHA1_ENST00000368989.2_Silent_p.P333P|PLEKHA1_ENST00000368988.1_Silent_p.P333P	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	320			T -> A (in dbSNP:rs1045216). {ECO:0000269|PubMed:11001876, ECO:0000269|Ref.4}.		androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAACGCAGCCACCGCCACCTC	0.542													G|||	3740	0.746805	0.8321	0.745	5008	,	,		17071	0.8155		0.5895	False		,,,				2504	0.7239				p.T320A		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.A958G						PASS	.	G	ALA/THR,,ALA/THR	3495,911	349.0+/-310.2	1396,703,104	86.0	77.0	80.0		958,,958	4.8	0.1	10	dbSNP_86	80	5183,3417	504.5+/-376.2	1558,2067,675	yes	missense,utr-3,missense	PLEKHA1	NM_001001974.2,NM_001195608.1,NM_021622.4	58,,58	2954,2770,779	GG,GA,AA		39.7326,20.6764,33.2769	benign,,benign	320/405,,320/405	124189197	8678,4328	2203	4300	6503	SO:0001583	missense	59338	exon12			GCAGCCACCGCCA	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"""Pleckstrin homology (PH) domain containing"""	14335	protein-coding gene	gene with protein product	"""tandem PH domain containing protein-1"""	607772	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"""			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.958A>G	10.37:g.124189197A>G	ENSP00000357986:p.Thr320Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	37	CCDS7629.1	1571	0.7193223443223443	395	0.8028455284552846	265	0.7320441988950276	457	0.798951048951049	454	0.5989445910290238	G	1.391	-0.580748	0.03854	0.793236	0.602674	ENSG00000107679	ENST00000368990;ENST00000409427;ENST00000433307	T;T	0.05319	3.46;3.46	5.71	4.81	0.61882	.	0.968694	0.08615	N	0.919389	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999999927212	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	9	0.02654	T	1	-2.568	6.7268	0.23361	0.2111:0.1282:0.6607:0.0	rs1045216;rs3185078;rs52798853;rs60697358;rs1045216	320	Q9HB21	PKHA1_HUMAN	A	320	ENSP00000357986:T320A;ENSP00000394416:T320A	ENSP00000357986:T320A	T	+	1	0	PLEKHA1	124179187	0.913000	0.31002	0.134000	0.22075	0.197000	0.23852	1.192000	0.32150	0.899000	0.36444	-0.128000	0.14901	ACC	A|0.314;G|0.686	0.686	strong		0.542	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974	
MUC17	140453	hgsc.bcm.edu	37	7	100677409	100677409	+	Silent	SNP	G	G	A	rs150735476	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100677409G>A	ENST00000306151.4	+	3	2776	c.2712G>A	c.(2710-2712)tcG>tcA	p.S904S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	904	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)					AAGCCCGTTCGTCTCCTACAA	0.527													A|||	890	0.177716	0.2292	0.0865	5008	,	,		30785	0.1954		0.0964	False		,,,				2504	0.2382				p.S904S		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G2712A						scavenged	.	A		373,4033	760.0+/-412.9	0,373,1830	319.0	301.0	307.0		2712	-0.7	0.0	7	dbSNP_134	307	291,8309	788.8+/-407.6	0,291,4009	no	coding-synonymous	MUC17	NM_001040105.1		0,664,5839	AA,AG,GG		3.3837,8.4657,5.1053		904/4494	100677409	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CCGTTCGTCTCCT	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.2712G>A	7.37:g.100677409G>A		Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	49	4	0.0816327	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.957;A|0.043	0.043	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SCYL2	55681	hgsc.bcm.edu	37	12	100708367	100708367	+	Missense_Mutation	SNP	C	C	T	rs33968174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:100708367C>T	ENST00000360820.2	+	8	1507	c.1070C>T	c.(1069-1071)cCa>cTa	p.P357L		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	357			P -> L (in dbSNP:rs33968174). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		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						AAAGGACTGCCAAAGGTTCTA	0.318													C|||	177	0.0353435	0.0061	0.0461	5008	,	,		16528	0.0		0.1103	False		,,,				2504	0.0266				p.P357L		Atlas-SNP	.											.	SCYL2	99	.	0			c.C1070T						PASS	.	C	LEU/PRO	87,4319	68.7+/-106.4	1,85,2117	65.0	65.0	65.0		1070	5.4	1.0	12	dbSNP_126	65	1026,7568	217.1+/-255.9	64,898,3335	yes	missense	SCYL2	NM_017988.4	98	65,983,5452	TT,TC,CC		11.9386,1.9746,8.5615	probably-damaging	357/930	100708367	1113,11887	2203	4297	6500	SO:0001583	missense	55681	exon8			GACTGCCAAAGGT	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.1070C>T	12.37:g.100708367C>T	ENSP00000354061:p.Pro357Leu	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	224	102	0.455357	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	111	0.050824175824175824	7	0.014227642276422764	20	0.055248618784530384	0	0.0	84	0.11081794195250659	C	29.3	4.997584	0.93227	0.019746	0.119386	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.30714	1.52;1.52	5.43	5.43	0.79202	Armadillo-like helical (1);Protein kinase-like domain (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00815	0.0027	L	0.55103	1.725	0.80722	D	1	D	0.67145	0.996	D	0.63877	0.919	T	0.01702	-1.1292	10	0.07325	T	0.83	.	19.6166	0.95636	0.0:1.0:0.0:0.0	rs33968174	357	Q6P3W7	SCYL2_HUMAN	L	357;184;357	ENSP00000448366:P357L;ENSP00000354061:P357L	ENSP00000258506:P184L	P	+	2	0	SCYL2	99232498	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.568000	0.82369	2.721000	0.93114	0.655000	0.94253	CCA	C|0.924;T|0.076	0.076	strong		0.318	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
SEC31B	25956	hgsc.bcm.edu	37	10	102269085	102269085	+	Missense_Mutation	SNP	C	C	A	rs3793706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102269085C>A	ENST00000370345.3	-	4	484	c.387G>T	c.(385-387)ttG>ttT	p.L129F	SEC31B_ENST00000370329.5_Missense_Mutation_p.L129F|NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000557395.1_Intron|SEC31B_ENST00000451524.1_Missense_Mutation_p.L129F|SEC31B_ENST00000535773.1_Intron	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	129			L -> F (in dbSNP:rs3793706). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGAAAGGATTCAAGTCGAGGG	0.493											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	972	0.194089	0.23	0.1873	5008	,	,		18265	0.1319		0.1928	False		,,,				2504	0.2157				p.L129F		Atlas-SNP	.											.	SEC31B	84	.	0			c.G387T						PASS	.	A	PHE/LEU	1058,3348	723.6+/-409.4	131,796,1276	161.0	169.0	166.0		387	4.8	1.0	10	dbSNP_107	166	1899,6701	727.9+/-406.7	216,1467,2617	yes	missense	SEC31B	NM_015490.3	22	347,2263,3893	AA,AC,CC		22.0814,24.0127,22.7357	benign	129/1180	102269085	2957,10049	2203	4300	6503	SO:0001583	missense	25956	exon4			AGGATTCAAGTCG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.387G>T	10.37:g.102269085C>A	ENSP00000359370:p.Leu129Phe	Somatic	115	0	0	1365	WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	415	0.190018315018315	89	0.18089430894308944	72	0.19889502762430938	94	0.16433566433566432	160	0.21108179419525067	A	3.549	-0.092094	0.07053	0.240127	0.220814	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.51325	0.71;0.71;0.71	5.9	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.044767	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00053	-2.39	0.38832	P	0.04412700000000003	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	0.29882	-0.9997	9	0.02654	T	1	-10.7429	1.3668	0.02202	0.5458:0.1513:0.1581:0.1448	rs3793706;rs61612790;rs3793706	129;129;129;129	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	F	129	ENSP00000359370:L129F;ENSP00000391178:L129F;ENSP00000359354:L129F	ENSP00000359354:L129F	L	-	3	2	SEC31B	102259075	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	0.670000	0.25157	0.501000	0.28013	-0.362000	0.07510	TTG	C|0.796;A|0.204	0.204	strong		0.493	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
IL1RAP	3556	hgsc.bcm.edu	37	3	190363594	190363594	+	Silent	SNP	G	G	A	rs34879831	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:190363594G>A	ENST00000412504.2	+	10	1560	c.1308G>A	c.(1306-1308)aaG>aaA	p.K436K	IL1RAP_ENST00000439062.1_Silent_p.K436K|IL1RAP_ENST00000443369.2_Silent_p.K436K|IL1RAP_ENST00000317757.3_Silent_p.K436K|IL1RAP_ENST00000447382.1_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	101	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	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		
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276909	71276909	+	Silent	SNP	G	G	A	rs71272260|rs12289712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:71276909G>A	ENST00000398531.1	+	1	301	c.276G>A	c.(274-276)ggG>ggA	p.G92G	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	92	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						GCTCCAAGGGGGGCTGTGGCT	0.677																																					p.G92G		Atlas-SNP	.											KRTAP5-10,rectum,carcinoma,0,3	KRTAP5-10	37	3	0			c.G276A						PASS	.						35.0	54.0	47.0					11																	71276909		2068	4190	6258	SO:0001819	synonymous_variant	387273	exon1			CAAGGGGGGCTGT	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.276G>A	11.37:g.71276909G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	8	0.148148	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			A|0.153;G|0.847	0.153	strong		0.677	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
UCP2	7351	hgsc.bcm.edu	37	11	73689104	73689104	+	Missense_Mutation	SNP	G	G	A	rs660339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73689104G>A	ENST00000310473.3	-	4	1006	c.164C>T	c.(163-165)gCc>gTc	p.A55V	UCP2_ENST00000536983.1_Missense_Mutation_p.A55V|UCP2_ENST00000542615.1_5'Flank	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	44	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	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	
DNAJC11	55735	hgsc.bcm.edu	37	1	6705944	6705944	+	Missense_Mutation	SNP	C	C	T	rs12137794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6705944C>T	ENST00000377577.5	-	8	922	c.799G>A	c.(799-801)Gtg>Atg	p.V267M	DNAJC11_ENST00000294401.7_Missense_Mutation_p.V267M|DNAJC11_ENST00000349363.6_Missense_Mutation_p.V229M|DNAJC11_ENST00000542246.1_Missense_Mutation_p.V229M|DNAJC11_ENST00000377573.5_Missense_Mutation_p.V177M|DNAJC11_ENST00000465508.1_5'Flank	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	267			V -> M (in dbSNP:rs12137794). {ECO:0000269|PubMed:14702039}.			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)		AGGTAGCCCACGGTGTTCTTG	0.557													C|||	221	0.0441294	0.0038	0.1282	5008	,	,		18682	0.0		0.0795	False		,,,				2504	0.0481				p.V267M		Atlas-SNP	.											.	DNAJC11	93	.	0			c.G799A						PASS	.	C	MET/VAL	75,4331	65.8+/-103.3	1,73,2129	187.0	172.0	177.0		799	4.2	1.0	1	dbSNP_120	177	708,7892	174.5+/-224.7	22,664,3614	yes	missense	DNAJC11	NM_018198.3	21	23,737,5743	TT,TC,CC		8.2326,1.7022,6.0203	benign	267/560	6705944	783,12223	2203	4300	6503	SO:0001583	missense	55735	exon8			AGCCCACGGTGTT	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.799G>A	1.37:g.6705944C>T	ENSP00000366800:p.Val267Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	87	0.03983516483516483	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	61	0.08047493403693931	C	12.89	2.072584	0.36566	0.017022	0.082326	ENSG00000007923	ENST00000377577;ENST00000451196;ENST00000349363;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T;T;T	0.33216	2.51;1.84;1.42;2.53;2.25;1.92;2.19	5.27	4.25	0.50352	.	0.042873	0.85682	D	0.000000	T	0.00496	0.0016	N	0.03608	-0.345	0.43503	D	0.995757	B;B;B;B	0.28783	0.007;0.222;0.005;0.011	B;B;B;B	0.17722	0.003;0.019;0.01;0.005	T	0.30238	-0.9985	10	0.21014	T	0.42	0.3111	3.8383	0.08903	0.0:0.679:0.0:0.321	rs12137794;rs59410624;rs12137794	177;243;267;267	B4DGD5;Q5TH61;Q9NVH1-3;Q9NVH1	.;.;.;DJC11_HUMAN	M	267;243;229;267;229;177;297	ENSP00000366800:V267M;ENSP00000415871:V243M;ENSP00000326304:V229M;ENSP00000294401:V267M;ENSP00000444020:V229M;ENSP00000366796:V177M;ENSP00000410194:V297M	ENSP00000294401:V267M	V	-	1	0	DNAJC11	6628531	1.000000	0.71417	0.957000	0.39632	0.994000	0.84299	5.648000	0.67930	2.472000	0.83506	0.650000	0.86243	GTG	C|0.951;T|0.049	0.049	strong		0.557	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
BRD8	10902	hgsc.bcm.edu	37	5	137500665	137500665	+	Missense_Mutation	SNP	G	G	A	rs11750814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:137500665G>A	ENST00000254900.5	-	12	1840	c.1469C>T	c.(1468-1470)aCg>aTg	p.T490M	BRD8_ENST00000515014.1_5'Flank|BRD8_ENST00000230901.5_Missense_Mutation_p.T563M|BRD8_ENST00000402931.1_Missense_Mutation_p.T490M|BRD8_ENST00000455658.2_Missense_Mutation_p.T449M|BRD8_ENST00000411594.2_Missense_Mutation_p.T493M	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	490			T -> M (in dbSNP:rs11750814). {ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTTGTTTTCCGTTTCCTCAAA	0.547													G|||	584	0.116613	0.0582	0.098	5008	,	,		22487	0.0159		0.173	False		,,,				2504	0.2546				p.T563M		Atlas-SNP	.											.	BRD8	192	.	0			c.C1688T						PASS	.	G	MET/THR,MET/THR,MET/THR	363,4043	186.4+/-213.3	18,327,1858	231.0	206.0	214.0		1478,1688,1469	5.6	1.0	5	dbSNP_120	214	1496,7104	284.0+/-296.4	113,1270,2917	yes	missense,missense,missense	BRD8	NM_001164326.1,NM_006696.3,NM_139199.1	81,81,81	131,1597,4775	AA,AG,GG		17.3953,8.2388,14.2934	probably-damaging,probably-damaging,probably-damaging	493/867,563/952,490/1236	137500665	1859,11147	2203	4300	6503	SO:0001583	missense	10902	exon13			TTTTCCGTTTCCT	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.1469C>T	5.37:g.137500665G>A	ENSP00000254900:p.Thr490Met	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	311	141	0.453376	NM_006696	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	215|215	0.09844322344322344|0.09844322344322344	31|31	0.06300813008130081|0.06300813008130081	37|37	0.10220994475138122|0.10220994475138122	7|7	0.012237762237762238|0.012237762237762238	140|140	0.18469656992084432|0.18469656992084432	G|G	18.00|18.00	3.525817|3.525817	0.64860|0.64860	0.082388|0.082388	0.173953|0.173953	ENSG00000112983|ENSG00000112983	ENST00000441656|ENST00000254900;ENST00000454473;ENST00000418329;ENST00000230901;ENST00000402931;ENST00000411594;ENST00000239899;ENST00000455658	.|T;T;T;T;T;T;T	.|0.31769	.|1.88;1.48;1.48;1.63;1.63;1.48;1.62	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	.|0.559762	.|0.18897	.|N	.|0.128122	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.08118|0.08118	0|0	0.25009|0.25009	P|P	0.99141681|0.99141681	.|D;D;D;D;P;D;D	.|0.63880	.|0.971;0.971;0.968;0.969;0.924;0.969;0.993	.|B;B;B;P;B;B;B	.|0.44732	.|0.305;0.224;0.183;0.459;0.34;0.34;0.443	T|T	0.13282|0.13282	-1.0515|-1.0515	4|9	.|0.62326	.|D	.|0.03	-13.9432|-13.9432	18.6837|18.6837	0.91556|0.91556	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs11750814;rs56497211;rs61087195;rs11750814|rs11750814;rs56497211;rs61087195;rs11750814	.|449;474;563;493;384;563;490	.|F8W820;B4DN43;A8K1N6;Q9H0E9-4;Q9H0E9-3;Q9H0E9-2;Q9H0E9	.|.;.;.;.;.;.;BRD8_HUMAN	W|M	484|490;519;488;563;490;493;384;449	.|ENSP00000254900:T490M;ENSP00000398067:T519M;ENSP00000398873:T488M;ENSP00000230901:T563M;ENSP00000384845:T490M;ENSP00000394330:T493M;ENSP00000408396:T449M	.|ENSP00000230901:T563M	R|T	-|-	1|2	2|0	BRD8|BRD8	137528564|137528564	0.997000|0.997000	0.39634|0.39634	0.994000|0.994000	0.49952|0.49952	0.922000|0.922000	0.55478|0.55478	4.899000|4.899000	0.63245|0.63245	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	CGG|ACG	G|0.879;A|0.121	0.121	strong		0.547	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696	
USP4	7375	hgsc.bcm.edu	37	3	49343175	49343175	+	Silent	SNP	G	G	A	rs2230929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	140	0	0		WXS	Illumina HiSeq	Phase_I	185	114	0.616216	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	
TCF7	6932	hgsc.bcm.edu	37	5	133477951	133477951	+	Silent	SNP	G	G	A	rs34995273	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:133477951G>A	ENST00000321584.4	+	6	907	c.711G>A	c.(709-711)gtG>gtA	p.V237V	TCF7_ENST00000395029.1_Silent_p.V237V|TCF7_ENST00000378564.1_Silent_p.V237V|TCF7_ENST00000518915.1_Silent_p.V122V|TCF7_ENST00000321603.6_Silent_p.V237V|TCF7_ENST00000342854.5_Silent_p.V237V|TCF7_ENST00000432532.2_Silent_p.V122V|TCF7_ENST00000520958.1_Silent_p.V122V|TCF7_ENST00000378560.4_Silent_p.V122V|TCF7_ENST00000395023.1_Silent_p.V122V			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	237					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGGCCATTGTGCCCCCCTCAG	0.582													G|||	18	0.00359425	0.0	0.0043	5008	,	,		14925	0.0		0.0119	False		,,,				2504	0.0031				p.V237V		Atlas-SNP	.											.	TCF7	81	.	0			c.G711A						PASS	.	G	,,,,	16,4390	23.3+/-48.9	0,16,2187	72.0	67.0	69.0		366,711,366,366,366	4.3	1.0	5	dbSNP_126	69	120,8480	62.1+/-124.0	3,114,4183	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF7	NM_001134851.2,NM_003202.3,NM_201632.3,NM_201634.3,NM_213648.3	,,,,	3,130,6370	AA,AG,GG		1.3953,0.3631,1.0457	,,,,	122/270,237/385,122/270,122/269,122/270	133477951	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	6932	exon6			CATTGTGCCCCCC	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.711G>A	5.37:g.133477951G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_003202	B3KSH3|Q86WR9|Q9UKI4	Silent	SNP	ENST00000321584.4	37		11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	9.479	1.097594	0.20552	0.003631	0.013953	ENSG00000081059	ENST00000517855	.	.	.	6.08	4.26	0.50523	.	.	.	.	.	T	0.47673	0.1458	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47535	-0.9110	4	.	.	.	.	6.5899	0.22642	0.1518:0.0:0.7055:0.1427	rs34995273	.	.	.	T	26	.	.	A	+	1	0	TCF7	133505850	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	2.344000	0.44010	0.859000	0.35456	-0.140000	0.14226	GCC	G|0.991;A|0.009	0.009	strong		0.582	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634	
ANO8	57719	hgsc.bcm.edu	37	19	17439320	17439320	+	Missense_Mutation	SNP	C	C	T	rs76655932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17439320C>T	ENST00000159087.4	-	13	2035	c.1877G>A	c.(1876-1878)cGg>cAg	p.R626Q		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	626	Glu-rich.				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)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						gggccgacgccgccccgcgcc	0.716													C|||	241	0.048123	0.0514	0.0519	5008	,	,		7642	0.001		0.1034	False		,,,				2504	0.0327				p.R626Q		Atlas-SNP	.											.	ANO8	67	.	0			c.G1877A						PASS	.	C	GLN/ARG	196,4018		3,190,1914	6.0	5.0	5.0		1877	3.9	0.9	19	dbSNP_131	5	791,7537		26,739,3399	no	missense	ANO8	NM_020959.2	43	29,929,5313	TT,TC,CC		9.4981,4.6512,7.8696	benign	626/1233	17439320	987,11555	2107	4164	6271	SO:0001583	missense	57719	exon13			CGACGCCGCCCCG	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.1877G>A	19.37:g.17439320C>T	ENSP00000159087:p.Arg626Gln	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	127	0.05815018315018315	35	0.07113821138211382	16	0.04419889502762431	0	0.0	76	0.10026385224274406	C	11.07	1.529749	0.27387	0.046512	0.094981	ENSG00000074855	ENST00000159087	T	0.62498	0.02	5.03	3.93	0.45458	.	0.300667	0.29100	N	0.013150	T	0.01287	0.0042	N	0.17594	0.5	0.80722	P	0.0	B	0.20988	0.05	B	0.13407	0.009	T	0.07654	-1.0761	9	0.31617	T	0.26	.	8.1545	0.31160	0.0:0.8475:0.0:0.1525	.	626	Q9HCE9	ANO8_HUMAN	Q	626	ENSP00000159087:R626Q	ENSP00000159087:R626Q	R	-	2	0	ANO8	17300320	0.001000	0.12720	0.905000	0.35620	0.354000	0.29330	0.118000	0.15605	2.368000	0.80403	0.478000	0.44815	CGG	C|0.940;T|0.060	0.060	strong		0.716	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
PTPN12	5782	hgsc.bcm.edu	37	7	77247821	77247821	+	Missense_Mutation	SNP	G	G	A	rs9640663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:77247821G>A	ENST00000248594.6	+	12	1236	c.964G>A	c.(964-966)Gtc>Atc	p.V322I	PTPN12_ENST00000415482.2_Missense_Mutation_p.V203I|PTPN12_ENST00000435495.2_Missense_Mutation_p.V192I	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	322			V -> I (in dbSNP:rs9640663). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1472029, ECO:0000269|PubMed:18669648, ECO:0000269|Ref.5}.		protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TGAAAACATGGTCAGCTCCAT	0.353													G|||	3943	0.78734	0.8729	0.7695	5008	,	,		15802	0.9048		0.6252	False		,,,				2504	0.7301				p.V322I		Atlas-SNP	.											PTPN12,rectum,carcinoma,0,1	PTPN12	83	1	0			c.G964A						scavenged	.	G	ILE/VAL,ILE/VAL,ILE/VAL	3643,763	755.1+/-412.5	1510,623,70	115.0	119.0	118.0		607,574,964	3.4	1.0	7	dbSNP_119	118	5049,3551	629.9+/-398.3	1521,2007,772	yes	missense,missense,missense	PTPN12	NM_001131008.1,NM_001131009.1,NM_002835.3	29,29,29	3031,2630,842	AA,AG,GG		41.2907,17.3173,33.1693	benign,benign,benign	203/662,192/651,322/781	77247821	8692,4314	2203	4300	6503	SO:0001583	missense	5782	exon12			AACATGGTCAGCT		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.964G>A	7.37:g.77247821G>A	ENSP00000248594:p.Val322Ile	Somatic	23	1	0.0434783		WXS	Illumina HiSeq	Phase_I	41	31	0.756098	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	1661	0.7605311355311355	424	0.8617886178861789	266	0.7348066298342542	508	0.8881118881118881	463	0.6108179419525066	G	12.04	1.817478	0.32145	0.826827	0.587093	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.34472	1.36;1.36;1.36	5.21	3.41	0.39046	.	0.432581	0.24759	N	0.035823	T	0.00012	0.0000	N	0.17674	0.51	0.39781	P	0.027707000000000037	B	0.02656	0.0	B	0.06405	0.002	T	0.23048	-1.0199	9	0.15066	T	0.55	.	9.1932	0.37211	0.2234:0.0:0.7766:0.0	rs9640663;rs17382002;rs17854591;rs58031922;rs9640663	322	Q05209	PTN12_HUMAN	I	322;203;203;192	ENSP00000248594:V322I;ENSP00000392429:V203I;ENSP00000397991:V192I	ENSP00000248594:V322I	V	+	1	0	PTPN12	77085757	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	2.143000	0.42187	0.696000	0.31696	0.467000	0.42956	GTC	G|0.277;A|0.722	0.722	strong		0.353	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
DOCK8	81704	hgsc.bcm.edu	37	9	390512	390512	+	Silent	SNP	C	C	T	rs2297075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:390512C>T	ENST00000453981.1	+	24	3028	c.2916C>T	c.(2914-2916)acC>acT	p.T972T	DOCK8_ENST00000469391.1_Silent_p.T872T|DOCK8_ENST00000382331.1_Silent_p.T274T|DOCK8_ENST00000432829.2_Silent_p.T904T|DOCK8_ENST00000382329.1_Silent_p.T439T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	972					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)		TGGTCAGCACCGGAATGGTGA	0.433													T|||	1277	0.254992	0.3964	0.245	5008	,	,		21549	0.0972		0.2495	False		,,,				2504	0.2393				p.T972T		Atlas-SNP	.											DOCK8_ENST00000453981,NS,adenoma,0,2	DOCK8	401	2	0			c.C2916T						PASS	.	T	,,	1592,2814	664.8+/-401.4	290,1012,901	256.0	215.0	229.0		2616,2712,2916	0.1	1.0	9	dbSNP_100	229	2115,6485	716.0+/-406.1	261,1593,2446	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	551,2605,3347	TT,TC,CC		24.593,36.1325,28.5022	,,	872/2000,904/2032,972/2100	390512	3707,9299	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon24			CAGCACCGGAATG	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.2916C>T	9.37:g.390512C>T		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	258	152	0.589147	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.729;T|0.271	0.271	strong		0.433	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
INSR	3643	hgsc.bcm.edu	37	19	7125297	7125297	+	Silent	SNP	G	G	A	rs1799817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7125297G>A	ENST00000302850.5	-	17	3397	c.3255C>T	c.(3253-3255)caC>caT	p.H1085H	INSR_ENST00000341500.5_Silent_p.H1073H	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1085	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	GACTCACCACGTGATGGCAGG	0.607													g|||	1465	0.292532	0.23	0.232	5008	,	,		20275	0.4464		0.2157	False		,,,				2504	0.3405				p.H1085H		Atlas-SNP	.											.	INSR	265	.	0			c.C3255T						PASS	.	A	,	971,3435	367.3+/-318.2	100,771,1332	104.0	79.0	88.0		3255,3219	-7.5	0.4	19	dbSNP_89	88	1511,7089	285.9+/-297.4	122,1267,2911	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	222,2038,4243	AA,AG,GG		17.5698,22.0381,19.0835	,	1085/1383,1073/1371	7125297	2482,10524	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon17			CACCACGTGATGG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.3255C>T	19.37:g.7125297G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			G|0.771;A|0.229	0.229	strong		0.607	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
SLC39A12	221074	hgsc.bcm.edu	37	10	18280214	18280214	+	Silent	SNP	T	T	A	rs59434947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:18280214T>A	ENST00000377369.2	+	8	1677	c.1404T>A	c.(1402-1404)ctT>ctA	p.L468L	SLC39A12_ENST00000539911.1_Silent_p.L334L|SLC39A12_ENST00000377374.4_Silent_p.L468L|SLC39A12_ENST00000377371.3_Silent_p.L468L	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	468					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TTATTCTTCTTGTATCACCAA	0.308													T|||	706	0.140974	0.4342	0.0432	5008	,	,		16604	0.0357		0.0099	False		,,,				2504	0.0573				p.L468L		Atlas-SNP	.											.	SLC39A12	181	.	0			c.T1404A						PASS	.	T	,	1546,2860	474.1+/-356.9	268,1010,925	76.0	85.0	82.0		1404,1404	-7.6	0.4	10	dbSNP_129	82	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous,coding-synonymous	SLC39A12	NM_001145195.1,NM_152725.3	,	268,1057,5178	AA,AT,TT		0.5465,35.0885,12.2482	,	468/692,468/655	18280214	1593,11413	2203	4300	6503	SO:0001819	synonymous_variant	221074	exon8			TCTTCTTGTATCA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1404T>A	10.37:g.18280214T>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	37	CCDS44362.1																																																																																			T|0.888;A|0.112	0.112	strong		0.308	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
MKI67	4288	hgsc.bcm.edu	37	10	129903802	129903802	+	Missense_Mutation	SNP	A	A	G	rs11016073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:129903802A>G	ENST00000368654.3	-	13	6677	c.6302T>C	c.(6301-6303)aTa>aCa	p.I2101T	MKI67_ENST00000368653.3_Missense_Mutation_p.I1741T	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2101	16 X 122 AA approximate repeats.		I -> T (in dbSNP:rs11016073).		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)				TTTGCAGGCTATTTTGGTAGT	0.493													A|||	766	0.152955	0.0166	0.1542	5008	,	,		20790	0.2262		0.2276	False		,,,				2504	0.184				p.I2101T		Atlas-SNP	.											MKI67,NS,carcinoma,+1,1	MKI67	363	1	0			c.T6302C						PASS	.	A	THR/ILE,THR/ILE	242,4164	141.9+/-177.2	6,230,1967	323.0	316.0	318.0		5222,6302	-8.9	0.0	10	dbSNP_120	318	1874,6726	334.2+/-320.9	205,1464,2631	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	89,89	211,1694,4598	GG,GA,AA		21.7907,5.4925,16.2694	benign,benign	1741/2897,2101/3257	129903802	2116,10890	2203	4300	6503	SO:0001583	missense	4288	exon13			CAGGCTATTTTGG	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.6302T>C	10.37:g.129903802A>G	ENSP00000357643:p.Ile2101Thr	Somatic	348	1	0.00287356		WXS	Illumina HiSeq	Phase_I	371	189	0.509434	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	364	0.16666666666666666	11	0.022357723577235773	59	0.16298342541436464	116	0.20279720279720279	178	0.23482849604221637	A	14.06	2.423156	0.43020	0.054925	0.217907	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03468	3.92;3.92	4.43	-8.87	0.00792	.	7.783340	0.00166	N	0.000004	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.15473	0.01;0.01;0.013	B;B;B	0.15870	0.008;0.008;0.014	T	0.41305	-0.9516	9	0.14252	T	0.57	.	7.1603	0.25661	0.1776:0.1033:0.5803:0.1388	rs11016073;rs52835413;rs59373454;rs11016073	2100;1741;2101	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	T	2101;1741;2100	ENSP00000357643:I2101T;ENSP00000357642:I1741T	ENSP00000357642:I1741T	I	-	2	0	MKI67	129793792	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.759000	0.04761	-2.820000	0.00344	-0.912000	0.02778	ATA	A|0.842;G|0.158	0.158	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
SEC14L5	9717	hgsc.bcm.edu	37	16	5061113	5061113	+	Silent	SNP	G	G	A	rs116849014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5061113G>A	ENST00000251170.7	+	15	1998	c.1818G>A	c.(1816-1818)cgG>cgA	p.R606R	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	606	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						ATGTGACCCGGTGGCCCGGCG	0.657													G|||	28	0.00559105	0.0	0.0029	5008	,	,		15446	0.0		0.0229	False		,,,				2504	0.0031				p.R606R		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1818A						PASS	.	G		6,3994		0,6,1994	20.0	24.0	23.0		1818	-0.5	1.0	16	dbSNP_132	23	175,8173		5,165,4004	no	coding-synonymous	SEC14L5	NM_014692.1		5,171,5998	AA,AG,GG		2.0963,0.15,1.4658		606/697	5061113	181,12167	2000	4174	6174	SO:0001819	synonymous_variant	9717	exon15			GACCCGGTGGCCC	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1818G>A	16.37:g.5061113G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			G|0.990;A|0.010	0.010	strong		0.657	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548544	32548544	+	Missense_Mutation	SNP	T	T	G	rs199873800	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32548544T>G	ENST00000360004.5	-	4	847	c.742A>C	c.(742-744)Atc>Ctc	p.I248L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	248					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						CTGAAGTAGATGAACAGCCCG	0.547										Multiple Myeloma(14;0.17)																											p.I248L		Atlas-SNP	.											HLA-DRB1,NS,haematopoietic_neoplasm,0,1	HLA-DRB1	41	1	0			c.A742C						PASS	.						86.0	100.0	95.0					6																	32548544		1511	2709	4220	SO:0001583	missense	3123	exon4			AGTAGATGAACAG	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.742A>C	6.37:g.32548544T>G	ENSP00000353099:p.Ile248Leu	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	277	28	0.101083	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	16.04	3.009505	0.54361	.	.	ENSG00000196126	ENST00000360004	T	0.00638	6.04	3.98	-6.48	0.01896	.	0.413267	0.26923	N	0.021810	T	0.00552	0.0018	L	0.58510	1.815	0.19300	N	0.99997	B;B;D	0.59357	0.009;0.002;0.985	B;B;D	0.66716	0.021;0.005;0.946	T	0.51252	-0.8729	10	0.87932	D	0	.	1.2914	0.02061	0.2749:0.3631:0.1397:0.2223	.	248;248;248	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	L	248	ENSP00000353099:I248L	ENSP00000353099:I248L	I	-	1	0	HLA-DRB1	32656522	0.003000	0.15002	0.067000	0.19924	0.641000	0.38312	-1.853000	0.01666	-0.703000	0.05049	0.372000	0.22366	ATC	T|0.954;G|0.046	0.046	strong		0.547	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
RUFY4	285180	hgsc.bcm.edu	37	2	218940418	218940418	+	Silent	SNP	C	C	T	rs4674246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	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	
SPATA21	374955	hgsc.bcm.edu	37	1	16736327	16736327	+	Missense_Mutation	SNP	G	G	A	rs41269197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16736327G>A	ENST00000335496.1	-	6	838	c.356C>T	c.(355-357)cCg>cTg	p.P119L	SPATA21_ENST00000540400.1_Missense_Mutation_p.P96L|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	119	Pro-rich.						calcium ion binding (GO:0005509)			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)		GGTGGGCACCGGGGTCAGGGT	0.682													G|||	116	0.0231629	0.0015	0.0346	5008	,	,		13933	0.001		0.0686	False		,,,				2504	0.0204				p.P119L		Atlas-SNP	.											.	SPATA21	47	.	0			c.C356T						PASS	.	G	LEU/PRO	53,4353	49.6+/-84.7	0,53,2150	31.0	39.0	36.0		356	2.2	0.0	1	dbSNP_127	36	550,8050	148.6+/-203.8	22,506,3772	yes	missense	SPATA21	NM_198546.1	98	22,559,5922	AA,AG,GG		6.3953,1.2029,4.6363	probably-damaging	119/470	16736327	603,12403	2203	4300	6503	SO:0001583	missense	374955	exon6			GGCACCGGGGTCA		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.356C>T	1.37:g.16736327G>A	ENSP00000335612:p.Pro119Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	68	0.031135531135531136	1	0.0020325203252032522	12	0.03314917127071823	1	0.0017482517482517483	54	0.0712401055408971	G	13.99	2.401897	0.42613	0.012029	0.063953	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.69806	-0.39;-0.43	4.07	2.16	0.27623	.	0.145674	0.32401	N	0.006141	T	0.07908	0.0198	L	0.29908	0.895	0.09310	N	1	D;P	0.57899	0.981;0.943	P;B	0.46253	0.509;0.235	T	0.08146	-1.0736	10	0.87932	D	0	-3.4136	7.2518	0.26154	0.1024:0.1774:0.7202:0.0	rs41269197	96;119	F5GXP5;Q7Z572	.;SPT21_HUMAN	L	119;96	ENSP00000335612:P119L;ENSP00000440046:P96L	ENSP00000335612:P119L	P	-	2	0	SPATA21	16608914	0.016000	0.18221	0.007000	0.13788	0.010000	0.07245	1.688000	0.37690	1.049000	0.40321	-0.527000	0.04329	CCG	G|0.960;A|0.040	0.040	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
PGLYRP4	57115	hgsc.bcm.edu	37	1	153320401	153320401	+	Missense_Mutation	SNP	G	G	A	rs12096209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:153320401G>A	ENST00000359650.5	-	2	72	c.8C>T	c.(7-9)cCg>cTg	p.P3L	PGLYRP4_ENST00000490266.1_5'UTR|PGLYRP4_ENST00000368739.3_Missense_Mutation_p.P3L	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	3			P -> L (in dbSNP:rs12096209). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			AAGAAGCCACGGCAGCATCCC	0.522													G|||	396	0.0790735	0.2247	0.0476	5008	,	,		19002	0.0		0.0398	False		,,,				2504	0.0266				p.P3L		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.C8T						PASS	.	G	LEU/PRO	839,3567	330.7+/-301.6	66,707,1430	49.0	51.0	51.0		8	-1.3	0.2	1	dbSNP_120	51	520,8080	146.0+/-201.7	9,502,3789	yes	missense	PGLYRP4	NM_020393.2	98	75,1209,5219	AA,AG,GG		6.0465,19.0422,10.449	benign	3/374	153320401	1359,11647	2203	4300	6503	SO:0001583	missense	57115	exon2			AGCCACGGCAGCA	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.8C>T	1.37:g.153320401G>A	ENSP00000352672:p.Pro3Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	156	0.07142857142857142	114	0.23170731707317074	16	0.04419889502762431	0	0.0	26	0.03430079155672823	G	11.30	1.597676	0.28445	0.190422	0.060465	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.04502	3.61;3.61	3.39	-1.28	0.09318	.	1.717000	0.03732	N	0.253599	T	0.00666	0.0022	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B	0.15473	0.013;0.006	B;B	0.11329	0.006;0.002	T	0.47086	-0.9144	9	0.14656	T	0.56	-6.1628	3.7862	0.08702	0.5119:0.2348:0.2533:0.0	rs12096209;rs61382871	3;3	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	L	3	ENSP00000357728:P3L;ENSP00000352672:P3L	ENSP00000352672:P3L	P	-	2	0	PGLYRP4	151587025	0.000000	0.05858	0.187000	0.23214	0.674000	0.39518	-1.156000	0.03160	-0.241000	0.09681	-0.258000	0.10820	CCG	G|0.905;A|0.095	0.095	strong		0.522	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
APOB	338	hgsc.bcm.edu	37	2	21245813	21245813	+	Silent	SNP	G	G	A	rs1801700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21245813G>A	ENST00000233242.1	-	18	2833	c.2706C>T	c.(2704-2706)aaC>aaT	p.N902N		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	902	Heparin-binding.				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)					AGAAGTTGGTGTTCATCTGGA	0.517													G|||	81	0.0161741	0.0008	0.0231	5008	,	,		18975	0.0		0.0467	False		,,,				2504	0.0174				p.N902N		Atlas-SNP	.											.	APOB	761	.	0			c.C2706T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	101.0	96.0	98.0		2706	2.7	1.0	2	dbSNP_89	98	416,8184	129.2+/-187.3	11,394,3895	no	coding-synonymous	APOB	NM_000384.2		11,441,6051	AA,AG,GG		4.8372,1.0667,3.5599		902/4564	21245813	463,12543	2203	4300	6503	SO:0001819	synonymous_variant	338	exon18			GTTGGTGTTCATC	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.2706C>T	2.37:g.21245813G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	136	56	0.411765	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.970;A|0.030	0.030	strong		0.517	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ZDBF2	57683	hgsc.bcm.edu	37	2	207170026	207170026	+	Silent	SNP	T	T	C	rs77622365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170026T>C	ENST00000374423.3	+	5	1160	c.774T>C	c.(772-774)aaT>aaC	p.N258N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	258							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAGAATCAAATAGGAAATCTT	0.368													T|||	115	0.0229633	0.0734	0.0159	5008	,	,		18712	0.0		0.006	False		,,,				2504	0.001				p.N258N		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T774C						PASS	.	T		243,3413		8,227,1593	29.0	28.0	29.0		774	-3.9	0.0	2	dbSNP_132	29	71,8095		0,71,4012	no	coding-synonymous	ZDBF2	NM_020923.1		8,298,5605	CC,CT,TT		0.8695,6.6466,2.6561		258/2355	207170026	314,11508	1828	4083	5911	SO:0001819	synonymous_variant	57683	exon5			ATCAAATAGGAAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.774T>C	2.37:g.207170026T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999261	83999261	+	Silent	SNP	C	C	A	rs35132222	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:83999261C>A	ENST00000343939.2	+	7	1715	c.1332C>A	c.(1330-1332)ctC>ctA	p.L444L	OSGIN1_ENST00000393306.1_Silent_p.L361L|OSGIN1_ENST00000361711.3_Silent_p.L361L|NECAB2_ENST00000305202.4_5'Flank			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	444					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						ACCGCAGCCTCCCCAGGCACC	0.622													C|||	313	0.0625	0.0045	0.0778	5008	,	,		17833	0.0159		0.1491	False		,,,				2504	0.089				p.L361L		Atlas-SNP	.											OSGIN1,colon,carcinoma,+2,1	OSGIN1	33	1	0			c.C1083A						PASS	.	C	,,	120,4280	89.2+/-127.9	5,110,2085	97.0	88.0	91.0		1332,1083,1083	1.1	1.0	16	dbSNP_126	91	1203,7397	242.1+/-272.2	91,1021,3188	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	96,1131,5273	AA,AC,CC		13.9884,2.7273,10.1769	,,	444/561,361/478,361/478	83999261	1323,11677	2200	4300	6500	SO:0001819	synonymous_variant	29948	exon6			CAGCCTCCCCAGG	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.1332C>A	16.37:g.83999261C>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	164	80	0.487805	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				C|0.902;A|0.098	0.098	strong		0.622	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
OR7G2	390882	hgsc.bcm.edu	37	19	9213026	9213026	+	Silent	SNP	T	T	C	rs4804400	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9213026T>C	ENST00000305456.2	-	1	956	c.957A>G	c.(955-957)aaA>aaG	p.K319K		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	298						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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						TCAAGGTTCCTTTCATGTCCT	0.443													-|||	1667	0.332867	0.1059	0.2853	5008	,	,		20747	0.5575		0.3718	False		,,,				2504	0.4018				p.K319K	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											.	OR7G2	48	.	0			c.A957G						PASS	.	C		644,3762	765.7+/-413.4	40,564,1599	131.0	115.0	121.0		957	-0.2	0.0	19	dbSNP_111	121	3013,5587	663.3+/-402.1	528,1957,1815	no	coding-synonymous	OR7G2	NM_001005193.1		568,2521,3414	CC,CT,TT		35.0349,14.6164,28.1178		319/346	9213026	3657,9349	2203	4300	6503	SO:0001819	synonymous_variant	390882	exon1			GGTTCCTTTCATG		CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"""GPCR / Class A : Olfactory receptors"""	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.957A>G	19.37:g.9213026T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_001005193	Q6IFJ4|Q96RA0	Silent	SNP	ENST00000305456.2	37	CCDS32897.1																																																																																			T|0.687;C|0.313	0.313	strong		0.443	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1		
CR2	1380	hgsc.bcm.edu	37	1	207646322	207646322	+	Silent	SNP	G	G	A	rs1048971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	112	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	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	
RNF215	200312	hgsc.bcm.edu	37	22	30782731	30782731	+	Silent	SNP	G	G	A	rs12171261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:30782731G>A	ENST00000382363.3	-	2	377	c.303C>T	c.(301-303)gcC>gcT	p.A101A		NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	101						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						CCTCCTGCTCGGCATCCACGA	0.642													G|||	1301	0.259784	0.1445	0.2651	5008	,	,		15674	0.3492		0.1769	False		,,,				2504	0.4049				p.A101A		Atlas-SNP	.											.	RNF215	19	.	0			c.C303T						PASS	.	G		696,3710	286.9+/-279.0	49,598,1556	41.0	41.0	41.0		303	-7.2	0.3	22	dbSNP_120	41	1515,7085	276.3+/-292.2	148,1219,2933	no	coding-synonymous	RNF215	NM_001017981.1		197,1817,4489	AA,AG,GG		17.6163,15.7966,16.9998		101/378	30782731	2211,10795	2203	4300	6503	SO:0001819	synonymous_variant	200312	exon2			CTGCTCGGCATCC		CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999		"""RING-type (C3HC4) zinc fingers"""	33434	protein-coding gene	gene with protein product							Standard	NM_001017981		Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.303C>T	22.37:g.30782731G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_001017981	A6NEL1	Silent	SNP	ENST00000382363.3	37	CCDS33633.1	534	0.2445054945054945	77	0.1565040650406504	108	0.2983425414364641	208	0.36363636363636365	141	0.18601583113456466	G	8.155	0.788180	0.16258	0.157966	0.176163	ENSG00000099999	ENST00000215798	.	.	.	4.46	-7.2	0.01495	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.3004	5.239	0.15462	0.2394:0.0977:0.5663:0.0966	rs12171261	.	.	.	X	39	.	.	R	-	1	2	RNF215	29112731	0.000000	0.05858	0.306000	0.25113	0.578000	0.36192	-1.251000	0.02882	-1.480000	0.01865	-0.145000	0.13849	CGA	G|0.810;A|0.190	0.190	strong		0.642	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320960.1	NM_001017981	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629904	32629904	+	Silent	SNP	A	A	G	rs1049086|rs386699586	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629904A>G	ENST00000399082.3	-	2	275	c.231T>C	c.(229-231)gaT>gaC	p.D77D	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.D167D|HLA-DQB1_ENST00000374943.4_Silent_p.D167D|HLA-DQB1_ENST00000399079.3_Silent_p.D167D|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Silent_p.D167D			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	167	Beta-1.		E -> G (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:05, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:10, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:14, allele DQB1*03:15, allele DQB1*03:17, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:01, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; dbSNP:rs1049083). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCTCCTCCTGATCATTCCGAA	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				a|||	3134	0.625799	0.5174	0.7205	5008	,	,		14307	0.6756		0.5984	False		,,,				2504	0.682				p.D167D	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T501C						PASS	.	G		2206,2140		632,942,599	39.0	40.0	40.0		501	-1.0	0.9	6	dbSNP_86	40	4967,3609		1579,1809,900	no	coding-synonymous	HLA-DQB1	NM_002123.4		2211,2751,1499	GG,GA,AA		42.0826,49.2407,44.49		167/262	32629904	7173,5749	2173	4288	6461	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CTCCTGATCATTC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.231T>C	6.37:g.32629904A>G		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	39	37	0.948718	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				A|0.394;G|0.606	0.606	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657261	46657261	+	Silent	SNP	A	A	G	rs6007747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46657261A>G	ENST00000253255.5	-	1	1958	c.1959T>C	c.(1957-1959)gaT>gaC	p.D653D		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	653	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CTCCTAGAGAATCATAGACCT	0.463													G|||	1229	0.245407	0.6785	0.134	5008	,	,		15446	0.001		0.16	False		,,,				2504	0.0787				p.D653D		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T1959C						PASS	.	G		2648,1758		791,1066,346	67.0	74.0	72.0		1959	0.8	0.4	22	dbSNP_114	72	1257,7343		90,1077,3133	no	coding-synonymous	PKDREJ	NM_006071.1		881,2143,3479	GG,GA,AA		14.6163,39.9001,30.0246		653/2254	46657261	3905,9101	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TAGAGAATCATAG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1959T>C	22.37:g.46657261A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.721;G|0.279	0.279	strong		0.463	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CBWD6	644019	hgsc.bcm.edu	37	9	69256816	69256816	+	Silent	SNP	G	G	A	rs62557779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:69256816G>A	ENST00000377457.5	-	3	420	c.315C>T	c.(313-315)aaC>aaT	p.N105N	CBWD6_ENST00000382399.4_Silent_p.N105N|CBWD6_ENST00000377441.1_Silent_p.N105N|CBWD6_ENST00000377449.1_Silent_p.N69N	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	105							ATP binding (GO:0005524)			lung(4)	4						AGAGGCAACCGTTTCTAAGTT	0.378													.|||	1986	0.396565	0.1921	0.5288	5008	,	,		16370	0.4712		0.5686	False		,,,				2504	0.3252				p.N105N		Atlas-SNP	.											.	CBWD6	19	.	0			c.C315T						PASS	.						86.0	93.0	90.0					9																	69256816		2193	4267	6460	SO:0001819	synonymous_variant	644019	exon3			GCAACCGTTTCTA		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.315C>T	9.37:g.69256816G>A		Somatic	1003	1	0.000997009		WXS	Illumina HiSeq	Phase_I	2037	309	0.151694	NM_001085457		Silent	SNP	ENST00000377457.5	37	CCDS43827.1																																																																																			G|0.525;A|0.475	0.475	strong		0.378	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	
CCDC186	55088	hgsc.bcm.edu	37	10	115922774	115922774	+	Missense_Mutation	SNP	G	G	A	rs1061159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115922774G>A	ENST00000369287.3	-	2	520	c.254C>T	c.(253-255)aCa>aTa	p.T85I	C10orf118_ENST00000369285.3_Missense_Mutation_p.T85I|C10orf118_ENST00000369286.1_Missense_Mutation_p.T85I	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		85			T -> I (in dbSNP:rs1061159). {ECO:0000269|PubMed:14996095, ECO:0000269|PubMed:15489334}.							NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		TTCTGAGCCTGTGTCTGTTTT	0.333													A|||	1038	0.207268	0.3434	0.2349	5008	,	,		19563	0.0585		0.2505	False		,,,				2504	0.1125				p.T85I		Atlas-SNP	.											.	C10orf118	70	.	0			c.C254T						PASS	.	A	ILE/THR	1395,3011	680.6+/-403.9	208,979,1016	84.0	87.0	86.0		254	-9.5	0.1	10	dbSNP_86	86	2024,6576	719.2+/-406.3	246,1532,2522	yes	missense	C10orf118	NM_018017.2	89	454,2511,3538	AA,AG,GG		23.5349,31.6614,26.2879	benign	85/899	115922774	3419,9587	2203	4300	6503	SO:0001583	missense	55088	exon2			GAGCCTGTGTCTG																												ENST00000369287.3:c.254C>T	10.37:g.115922774G>A	ENSP00000358293:p.Thr85Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	459	0.21016483516483517	152	0.3089430894308943	92	0.2541436464088398	34	0.05944055944055944	181	0.23878627968337732	A	0.074	-1.196215	0.01594	0.316614	0.235349	ENSG00000165813	ENST00000369287;ENST00000430353;ENST00000369286;ENST00000369285	T;T;T	0.32753	1.87;1.44;1.44	5.65	-9.53	0.00575	.	1.254280	0.05071	N	0.481642	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	0.21793	-1.0235	9	0.20519	T	0.43	.	19.1548	0.93506	0.1006:0.1643:0.7351:0.0	rs1061159;rs3167863;rs52837087;rs60892464;rs1061159	85	Q7Z3E2	CJ118_HUMAN	I	85;191;85;85	ENSP00000358293:T85I;ENSP00000358292:T85I;ENSP00000358291:T85I	ENSP00000358291:T85I	T	-	2	0	C10orf118	115912764	0.000000	0.05858	0.051000	0.19133	0.029000	0.11900	-0.821000	0.04452	-1.547000	0.01715	-1.781000	0.00649	ACA	G|0.762;N|0.000	.	strong		0.333	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
KCNV2	169522	hgsc.bcm.edu	37	9	2718534	2718534	+	Silent	SNP	C	C	G	rs12237048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	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	
AGMAT	79814	hgsc.bcm.edu	37	1	15909850	15909850	+	Missense_Mutation	SNP	C	C	G	rs6429757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15909850C>G	ENST00000375826.3	-	2	455	c.313G>C	c.(313-315)Ggg>Cgg	p.G105R	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	105			G -> R (in dbSNP:rs6429757). {ECO:0000269|PubMed:11804860, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		TTGACTGTCCCAAGCATCACT	0.527													G|||	3171	0.633187	0.9017	0.5274	5008	,	,		18672	0.6359		0.5288	False		,,,				2504	0.4499				p.G105R	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G313C						PASS	.	G	ARG/GLY	3749,657	279.0+/-274.6	1598,553,52	63.0	57.0	59.0		313	-1.4	0.0	1	dbSNP_116	59	4755,3845	541.2+/-384.0	1338,2079,883	yes	missense	AGMAT	NM_024758.4	125	2936,2632,935	GG,GC,CC		44.7093,14.9115,34.6148	benign	105/353	15909850	8504,4502	2203	4300	6503	SO:0001583	missense	79814	exon2			CTGTCCCAAGCAT	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.313G>C	1.37:g.15909850C>G	ENSP00000364986:p.Gly105Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	1383	0.6332417582417582	428	0.8699186991869918	193	0.5331491712707183	344	0.6013986013986014	418	0.5514511873350924	G	0.008	-1.909524	0.00508	0.850885	0.552907	ENSG00000116771	ENST00000375826	D	0.84800	-1.9	5.13	-1.41	0.08941	Ureohydrolase domain (1);	0.051023	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00405	-1.535	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34900	-0.9810	9	0.02654	T	1	-8.5468	3.7841	0.08692	0.0764:0.1895:0.3075:0.4267	rs6429757;rs17856129;rs56615894;rs6429757	105	Q9BSE5	SPEB_HUMAN	R	105	ENSP00000364986:G105R	ENSP00000364986:G105R	G	-	1	0	AGMAT	15782437	0.997000	0.39634	0.010000	0.14722	0.138000	0.21146	0.598000	0.24074	-0.321000	0.08627	-0.986000	0.02555	GGG	C|0.348;G|0.652	0.652	strong		0.527	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57176304T>G	ENST00000537055.2	-	2	494	c.263A>C	c.(262-264)gAg>gCg	p.E88A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	88			E -> A (in dbSNP:rs12460400). {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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CTTCGGGCTCTCCCCAGGCGC	0.637													.|||	2007	0.400759	0.4123	0.3732	5008	,	,		15470	0.4702		0.3121	False		,,,				2504	0.4243				p.E88A		Atlas-SNP	.											.	ZNF835	106	.	0			c.A263C						PASS	.	T	ALA/GLU	1630,2550		347,936,807	54.0	59.0	57.0		263	-1.0	0.0	19	dbSNP_120	57	2524,5938		380,1764,2087	no	missense	ZNF835	NM_001005850.2	107	727,2700,2894	GG,GT,TT		29.8275,38.9952,32.8587	benign	88/538	57176304	4154,8488	2090	4231	6321	SO:0001583	missense	90485	exon2			GGGCTCTCCCCAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.263A>C	19.37:g.57176304T>G	ENSP00000444747:p.Glu88Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	847	0.38782051282051283	215	0.4369918699186992	127	0.35082872928176795	264	0.46153846153846156	241	0.3179419525065963	T	6.640	0.486634	0.12641	0.389952	0.298275	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06849	3.25	2.58	-1.04	0.10068	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.44605	-0.9317	8	0.72032	D	0.01	.	2.9659	0.05908	0.0:0.2978:0.2397:0.4625	rs12460400	110	Q9Y2P0	ZN835_HUMAN	A	110;88	ENSP00000444747:E88A	ENSP00000341756:E110A	E	-	2	0	ZNF835	61868116	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.149000	0.10204	-0.483000	0.06772	0.459000	0.35465	GAG	T|0.628;G|0.372	0.372	strong		0.637	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
CLEC3B	7123	hgsc.bcm.edu	37	3	45077123	45077123	+	Missense_Mutation	SNP	G	G	A	rs13963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:45077123G>A	ENST00000296130.4	+	3	496	c.316G>A	c.(316-318)Ggc>Agc	p.G106S	CLEC3B_ENST00000428034.1_Missense_Mutation_p.G64S|CLEC3B_ENST00000490386.1_3'UTR|RNU5B-3P_ENST00000516601.1_RNA	NM_003278.2	NP_003269.2	P05452	TETN_HUMAN	C-type lectin domain family 3, member B	106	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		G -> S (in dbSNP:rs13963). {ECO:0000269|PubMed:1354271, ECO:0000269|PubMed:1511740, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3427041, ECO:0000269|Ref.3}.		bone mineralization (GO:0030282)|cellular response to organic substance (GO:0071310)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ossification (GO:0001503)|positive regulation of plasminogen activation (GO:0010756)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)|kringle domain binding (GO:0036143)			endometrium(1)|lung(3)	4				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Tenecteplase(DB00031)	GGGCACCCTGGGCACCCCTCA	0.637													G|||	2822	0.563498	0.4002	0.5144	5008	,	,		15918	0.8591		0.3817	False		,,,				2504	0.7014				p.G106S	GBM(139;1487 3263 30871)	Atlas-SNP	.											.	CLEC3B	15	.	0			c.G316A						PASS	.	G	SER/GLY	1708,2698	511.2+/-367.7	331,1046,826	47.0	46.0	46.0		316	-0.1	1.0	3	dbSNP_52	46	3484,5116	508.9+/-377.2	690,2104,1506	yes	missense	CLEC3B	NM_003278.2	56	1021,3150,2332	AA,AG,GG		40.5116,38.7653,39.92	benign	106/203	45077123	5192,7814	2203	4300	6503	SO:0001583	missense	7123	exon3			ACCCTGGGCACCC		CCDS2726.1	3p22-p21.3	2010-04-27	2005-02-09	2005-02-09	ENSG00000163815	ENSG00000163815		"""C-type lectin domain containing"""	11891	protein-coding gene	gene with protein product		187520	"""tetranectin (plasminogen binding protein)"""	TNA			Standard	NM_003278		Approved	TN	uc003cok.4	P05452	OTTHUMG00000133087	ENST00000296130.4:c.316G>A	3.37:g.45077123G>A	ENSP00000296130:p.Gly106Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_003278	Q6FGX6	Missense_Mutation	SNP	ENST00000296130.4	37	CCDS2726.1	1177	0.5389194139194139	199	0.40447154471544716	178	0.49171270718232046	499	0.8723776223776224	301	0.3970976253298153	G	9.397	1.076946	0.20227	0.387653	0.405116	ENSG00000163815	ENST00000296130;ENST00000428034	T;T	0.18174	2.23;2.23	4.53	-0.0541	0.13815	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.324435	0.36854	N	0.002366	T	0.00012	0.0000	N	0.03224	-0.385	0.31816	P	0.626606	B	0.24186	0.099	B	0.29353	0.101	T	0.06770	-1.0808	9	0.27082	T	0.32	-15.8475	8.7078	0.34365	0.6061:0.0:0.3939:0.0	rs13963;rs3188726;rs17077143;rs17850716;rs13963	106	P05452	TETN_HUMAN	S	106;64	ENSP00000296130:G106S;ENSP00000396013:G64S	ENSP00000296130:G106S	G	+	1	0	CLEC3B	45052127	1.000000	0.71417	0.996000	0.52242	0.395000	0.30598	1.497000	0.35649	0.121000	0.18284	-0.258000	0.10820	GGC	G|0.539;A|0.461	0.461	strong		0.637	CLEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256745.1	NM_003278	
DOLK	22845	hgsc.bcm.edu	37	9	131708710	131708710	+	Silent	SNP	G	G	A	rs148646968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131708710G>A	ENST00000372586.3	-	1	1188	c.873C>T	c.(871-873)ctC>ctT	p.L291L	RP11-101E3.5_ENST00000482796.1_Intron|NUP188_ENST00000372577.2_5'Flank	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	291					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)			breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGTCTGGAAGAGAAACTGAA	0.577													G|||	2	0.000399361	0.0	0.0	5008	,	,		18331	0.0		0.002	False		,,,				2504	0.0				p.L291L		Atlas-SNP	.											DOLK,colon,carcinoma,-2,1	DOLK	39	1	0			c.C873T						PASS	.	G		0,4406		0,0,2203	71.0	77.0	75.0		873	0.7	1.0	9	dbSNP_134	75	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	DOLK	NM_014908.3		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		291/539	131708710	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	22845	exon1			CTGGAAGAGAAAC	AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"""dolichol kinase 1"""	610746	"""transmembrane protein 15"""	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.873C>T	9.37:g.131708710G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_014908	Q5SRE6	Silent	SNP	ENST00000372586.3	37	CCDS6915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908	
SPTA1	6708	hgsc.bcm.edu	37	1	158584091	158584091	+	Missense_Mutation	SNP	A	A	G	rs952094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158584091A>G	ENST00000368147.4	-	49	6974	c.6794T>C	c.(6793-6795)aTc>aCc	p.I2265T	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2265			I -> T (in dbSNP:rs952094).		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)					CACACCTTTGATGTCCCTGAA	0.333													G|||	2535	0.50619	0.4228	0.5202	5008	,	,		17099	0.6319		0.5636	False		,,,				2504	0.4202				p.I2265T		Atlas-SNP	.											.	SPTA1	720	.	0			c.T6794C						PASS	.	G	THR/ILE	1554,2056		323,908,574	67.0	65.0	65.0		6794	1.3	0.7	1	dbSNP_86	65	4396,3734		1214,1968,883	yes	missense	SPTA1	NM_003126.2	89	1537,2876,1457	GG,GA,AA		45.9287,43.0471,49.3186	benign	2265/2420	158584091	5950,5790	1805	4065	5870	SO:0001583	missense	6708	exon49			CCTTTGATGTCCC	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.6794T>C	1.37:g.158584091A>G	ENSP00000357129:p.Ile2265Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	134	36	0.268657	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	1199	0.548992673992674	229	0.4654471544715447	188	0.5193370165745856	344	0.6013986013986014	438	0.5778364116094987	G	0.007	-1.972266	0.00457	0.430471	0.540713	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49432	0.94;0.78	5.53	1.28	0.21552	EF-hand-like domain (1);	.	.	.	.	T	0.04998	0.0134	N	0.02247	-0.625	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.39761	-0.9598	8	0.02654	T	1	.	7.2407	0.26094	0.3063:0.1189:0.5748:0.0	rs952094;rs52828265;rs59527173;rs952094	2265	P02549	SPTA1_HUMAN	T	2265;2262	ENSP00000357130:I2265T;ENSP00000357129:I2262T	ENSP00000357129:I2262T	I	-	2	0	SPTA1	156850715	1.000000	0.71417	0.663000	0.29738	0.186000	0.23388	2.478000	0.45189	0.144000	0.18951	-0.724000	0.03597	ATC	A|0.461;G|0.539	0.539	strong		0.333	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
TEP1	7011	hgsc.bcm.edu	37	14	20837701	20837701	+	Missense_Mutation	SNP	G	G	C	rs938886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20837701G>C	ENST00000262715.5	-	53	7498	c.7458C>G	c.(7456-7458)atC>atG	p.I2486M	TEP1_ENST00000556935.1_Missense_Mutation_p.I2378M	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2486			I -> M (in dbSNP:rs938886).		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)		GGTTCCATAGGATCCCATCAG	0.507													C|||	1699	0.339257	0.5129	0.3718	5008	,	,		18936	0.3065		0.2237	False		,,,				2504	0.2342				p.I2486M		Atlas-SNP	.											.	TEP1	224	.	0			c.C7458G						PASS	.	C	MET/ILE	1925,2481	624.5+/-394.3	436,1053,714	140.0	133.0	135.0		7458	2.8	0.9	14	dbSNP_86	135	1780,6820	733.8+/-406.9	176,1428,2696	yes	missense	TEP1	NM_007110.4	10	612,2481,3410	CC,CG,GG		20.6977,43.6904,28.4869	benign	2486/2628	20837701	3705,9301	2203	4300	6503	SO:0001583	missense	7011	exon53			CCATAGGATCCCA		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.7458C>G	14.37:g.20837701G>C	ENSP00000262715:p.Ile2486Met	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	243	115	0.473251	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	710|710|710	0.3250915750915751|0.3250915750915751|0.3250915750915751	246|246|246	0.5|0.5|0.5	118|118|118	0.3259668508287293|0.3259668508287293|0.3259668508287293	169|169|169	0.29545454545454547|0.29545454545454547|0.29545454545454547	177|177|177	0.23350923482849603|0.23350923482849603|0.23350923482849603	C|C|C	1.075|1.075|1.075	-0.668871|-0.668871|-0.668871	0.03403|0.03403|0.03403	0.436904|0.436904|0.436904	0.206977|0.206977|0.206977	ENSG00000129566|ENSG00000129566|ENSG00000129566	ENST00000262715;ENST00000556935|ENST00000553984|ENST00000359243	T;T|.|.	0.36340|.|.	1.26;1.26|.|.	5.82|5.82|5.82	2.82|2.82|2.82	0.32997|0.32997|0.32997	.|.|.	0.474590|.|.	0.23096|.|.	N|.|.	0.051971|.|.	T|T|T	0.00012|0.00012|0.00012	0.0000|0.0000|0.0000	N|N|N	0.01048|0.01048|0.01048	-1.04|-1.04|-1.04	0.09310|0.09310|0.09310	P|P|P	0.99999074952|0.99999074952|0.99999074952	B;B;B|.|.	0.02656|.|.	0.0;0.0;0.0|.|.	B;B;B|.|.	0.06405|.|.	0.0;0.002;0.0|.|.	T|T|T	0.37478|0.37478|0.37478	-0.9704|-0.9704|-0.9704	9|4|5	0.18276|.|0.44086	T|.|T	0.48|.|0.13	-4.4158|-4.4158|-4.4158	9.0619|9.0619|9.0619	0.36440|0.36440|0.36440	0.2591:0.4878:0.2531:0.0|0.2591:0.4878:0.2531:0.0|0.2591:0.4878:0.2531:0.0	rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886|rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886|rs938886;rs1713445;rs2228025;rs17110682;rs52804129;rs58609794;rs938886	2378;1829;2486|.|.	G3V5X7;G3V2A4;Q99973|.|.	.;.;TEP1_HUMAN|.|.	M|A|C	2486;2378|143|2479	ENSP00000262715:I2486M;ENSP00000452574:I2378M|.|.	ENSP00000262715:I2486M|.|ENSP00000352180:S2479C	I|P|S	-|-|-	3|1|2	3|0|0	TEP1|TEP1|TEP1	19907541|19907541|19907541	0.561000|0.561000|0.561000	0.26578|0.26578|0.26578	0.937000|0.937000|0.937000	0.37676|0.37676|0.37676	0.953000|0.953000|0.953000	0.61014|0.61014|0.61014	0.569000|0.569000|0.569000	0.23638|0.23638|0.23638	0.788000|0.788000|0.788000	0.33755|0.33755|0.33755	-0.187000|-0.187000|-0.187000	0.12897|0.12897|0.12897	ATC|CCT|TCC	G|0.702;C|0.297	0.297	strong		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
OR8U1	219417	hgsc.bcm.edu	37	11	56143966	56143966	+	Silent	SNP	C	C	T	rs12291978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56143966C>T	ENST00000302270.1	+	1	867	c.867C>T	c.(865-867)atC>atT	p.I289I		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, 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)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					ATCCCTTAATCTATAGCCTCC	0.368													T|||	1006	0.200879	0.2481	0.1571	5008	,	,		18503	0.1369		0.2654	False		,,,				2504	0.1677				p.I289I		Atlas-SNP	.											.	OR8U1	59	.	0			c.C867T						PASS	.	C		961,2933		138,685,1124	129.0	133.0	132.0		867	2.8	1.0	11	dbSNP_120	132	2286,6030		301,1684,2173	no	coding-synonymous	OR8U1	NM_001005204.1		439,2369,3297	TT,TC,CC		27.4892,24.679,26.593		289/310	56143966	3247,8963	1947	4158	6105	SO:0001819	synonymous_variant	219417	exon1			CTTAATCTATAGC	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.867C>T	11.37:g.56143966C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_001005204		Silent	SNP	ENST00000302270.1	37	CCDS41647.1																																																																																			C|0.738;T|0.262	0.262	strong		0.368	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
DRD5	1816	hgsc.bcm.edu	37	4	9784853	9784853	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:9784853C>G	ENST00000304374.2	+	1	1596	c.1200C>G	c.(1198-1200)atC>atG	p.I400M		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	400					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.I400M(2)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	ACCAAGACATCGTCTTCCACA	0.592																																					p.I400M		Atlas-SNP	.											DRD5,NS,carcinoma,0,2	DRD5	119	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.C1200G						scavenged	.						97.0	78.0	84.0					4																	9784853		2203	4300	6503	SO:0001583	missense	1816	exon1			AGACATCGTCTTC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1200C>G	4.37:g.9784853C>G	ENSP00000306129:p.Ile400Met	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	4	0.0283688	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	c	2.136	-0.397995	0.04865	.	.	ENSG00000169676	ENST00000304374	T	0.65364	-0.15	4.73	-9.46	0.00597	.	0.191884	0.44688	D	0.000429	T	0.27098	0.0664	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.04650	-1.0936	10	0.33141	T	0.24	.	5.418	0.16384	0.1584:0.2933:0.4256:0.1227	.	400	P21918	DRD5_HUMAN	M	400	ENSP00000306129:I400M	ENSP00000306129:I400M	I	+	3	3	DRD5	9393951	0.000000	0.05858	0.000000	0.03702	0.163000	0.22366	-2.589000	0.00900	-1.894000	0.01105	-1.614000	0.00798	ATC	.	.	none		0.592	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
ZNF311	282890	hgsc.bcm.edu	37	6	28963248	28963248	+	Missense_Mutation	SNP	T	T	G	rs6456880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:28963248T>G	ENST00000377179.3	-	7	2043	c.1531A>C	c.(1531-1533)Aag>Cag	p.K511Q	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	511			K -> Q (in dbSNP:rs6456880). {ECO:0000269|PubMed:14574404}.		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)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						AGGCAGTGCTTATCTTGGAAG	0.463													G|||	3341	0.667133	0.9539	0.5692	5008	,	,		23712	0.6508		0.4354	False		,,,				2504	0.6043				p.K511Q		Atlas-SNP	.											ZNF311,colon,carcinoma,0,2	ZNF311	59	2	0			c.A1531C						PASS	.	G	GLN/LYS	2586,436		1113,360,38	87.0	83.0	84.0		1531	1.8	0.0	6	dbSNP_116	84	2247,3171		468,1311,930	yes	missense	ZNF311	NM_001010877.2	53	1581,1671,968	GG,GT,TT		41.4729,14.4275,42.737	benign	511/667	28963248	4833,3607	1511	2709	4220	SO:0001583	missense	282890	exon7			AGTGCTTATCTTG	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.1531A>C	6.37:g.28963248T>G	ENSP00000366384:p.Lys511Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	37	CCDS34357.1	1350	0.6181318681318682	467	0.9491869918699187	203	0.5607734806629834	375	0.6555944055944056	305	0.4023746701846966	G	0.364	-0.938000	0.02340	0.855725	0.414729	ENSG00000197935	ENST00000377179;ENST00000535083	T	0.13538	2.58	3.69	1.82	0.25136	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03053	0.0090	L	0.38692	1.165	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41875	-0.9484	8	0.30854	T	0.27	-0.5211	5.6026	0.17361	0.0993:0.0:0.4055:0.4951	rs6456880;rs17340289;rs59778525;rs6456880	511	Q5JNZ3	ZN311_HUMAN	Q	511;419	ENSP00000366384:K511Q	ENSP00000366384:K511Q	K	-	1	0	ZNF311	29071227	0.021000	0.18746	0.000000	0.03702	0.035000	0.12851	0.492000	0.22435	0.009000	0.14813	-0.195000	0.12781	AAG	G|0.602;N|0.000	0.602	strong		0.463	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
CUL7	9820	hgsc.bcm.edu	37	6	43008298	43008298	+	Silent	SNP	C	C	T	rs2273917	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	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	
SLC39A4	55630	hgsc.bcm.edu	37	8	145641328	145641328	+	Missense_Mutation	SNP	C	C	T	rs17855765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145641328C>T	ENST00000301305.3	-	2	445	c.340G>A	c.(340-342)Gct>Act	p.A114T	SLC39A4_ENST00000276833.5_Missense_Mutation_p.A89T|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	114			A -> T (in dbSNP:rs17855765). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)			CCAGCCCGAGCGTCCTCACAG	0.721													C|||	1874	0.374201	0.2761	0.379	5008	,	,		14156	0.37		0.5209	False		,,,				2504	0.3569				p.A114T		Atlas-SNP	.											SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	2	0			c.G340A						PASS	.	C	THR/ALA,THR/ALA	1238,3114		198,842,1136	13.0	15.0	15.0		265,340	-3.7	0.0	8	dbSNP_123	15	4378,4180		1181,2016,1082	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	58,58	1379,2858,2218	TT,TC,CC		48.8432,28.4467,43.5012	benign,benign	89/623,114/648	145641328	5616,7294	2176	4279	6455	SO:0001583	missense	55630	exon2			CCCGAGCGTCCTC	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.340G>A	8.37:g.145641328C>T	ENSP00000301305:p.Ala114Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	952	0.4358974358974359	162	0.32926829268292684	149	0.4116022099447514	230	0.4020979020979021	411	0.5422163588390502	C	6.069	0.380958	0.11466	0.284467	0.511568	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.56941	0.43;0.43	4.3	-3.67	0.04476	.	0.827299	0.10373	N	0.682547	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;P	0.43352	0.429;0.804	B;B	0.31101	0.039;0.124	T	0.43343	-0.9397	9	0.25106	T	0.35	-14.0618	10.6355	0.45563	0.0:0.492:0.0:0.508	rs17855765;rs61412194;rs17855765	114;89	Q6P5W5;A6NDY5	S39A4_HUMAN;.	T	89;114	ENSP00000276833:A89T;ENSP00000301305:A114T	ENSP00000276833:A89T	A	-	1	0	SLC39A4	145612136	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.006000	0.03671	-0.547000	0.06207	0.306000	0.20318	GCT	C|0.574;T|0.426	0.426	strong		0.721	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
FBN2	2201	hgsc.bcm.edu	37	5	127680130	127680130	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:127680130T>G	ENST00000508053.1	-	31	4264	c.3290A>C	c.(3289-3291)aAa>aCa	p.K1097T	FBN2_ENST00000262464.4_Missense_Mutation_p.K1097T|FBN2_ENST00000508989.1_Missense_Mutation_p.K1064T			P35556	FBN2_HUMAN	fibrillin 2	1097	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		GCAACGGCATTTGAAGCTTCC	0.423																																					p.K1097T		Atlas-SNP	.											.	FBN2	858	.	0			c.A3290C						PASS	.						144.0	139.0	141.0					5																	127680130		2203	4300	6503	SO:0001583	missense	2201	exon25			CGGCATTTGAAGC	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.3290A>C	5.37:g.127680130T>G	ENSP00000424571:p.Lys1097Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	9.363	1.068611	0.20067	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.86865	-2.18;-2.18;-2.18	4.26	4.26	0.50523	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.076495	0.50627	D	0.000108	T	0.79341	0.4429	N	0.04116	-0.275	0.38313	D	0.943307	P;P	0.47677	0.899;0.503	P;B	0.51701	0.677;0.296	T	0.78884	-0.2028	10	0.17369	T	0.5	.	14.4286	0.67233	0.0:0.0:0.0:1.0	.	1064;1097	D6RJI3;P35556	.;FBN2_HUMAN	T	1097;1097;1064	ENSP00000262464:K1097T;ENSP00000424571:K1097T;ENSP00000425596:K1064T	ENSP00000262464:K1097T	K	-	2	0	FBN2	127708029	0.954000	0.32549	1.000000	0.80357	0.011000	0.07611	1.122000	0.31295	2.148000	0.66965	0.454000	0.30748	AAA	.	.	none		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
SNPH	9751	hgsc.bcm.edu	37	20	1285933	1285933	+	Silent	SNP	G	G	A	rs3795139	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1285933G>A	ENST00000381873.3	+	6	956	c.720G>A	c.(718-720)ggG>ggA	p.G240G	SNPH_ENST00000381867.1_Silent_p.G284G	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	240					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CTGAGGATGGGGCAGACAGTG	0.672													G|||	1973	0.39397	0.3979	0.3314	5008	,	,		17209	0.5407		0.3201	False		,,,				2504	0.3579				p.G240G		Atlas-SNP	.											.	SNPH	89	.	0			c.G720A						PASS	.	G		1676,2726		316,1044,841	27.0	27.0	27.0		720	-0.2	0.4	20	dbSNP_107	27	2477,6113		357,1763,2175	no	coding-synonymous	SNPH	NM_014723.2		673,2807,3016	AA,AG,GG		28.8359,38.0736,31.9658		240/495	1285933	4153,8839	2201	4295	6496	SO:0001819	synonymous_variant	9751	exon6			GGATGGGGCAGAC		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.720G>A	20.37:g.1285933G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_014723	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																			G|0.650;A|0.350	0.350	strong		0.672	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
NCR3	259197	hgsc.bcm.edu	37	6	31557640	31557640	+	Missense_Mutation	SNP	C	C	T	rs11575840	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31557640C>T	ENST00000340027.5	-	2	570	c.307G>A	c.(307-309)Gcc>Acc	p.A103T	NCR3_ENST00000376071.4_Missense_Mutation_p.A78T|NCR3_ENST00000376072.3_Missense_Mutation_p.A103T|NCR3_ENST00000376073.4_Missense_Mutation_p.A103T|NCR3_ENST00000491161.1_5'UTR	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3	103	Ig-like.		A -> T (in dbSNP:rs11575840).		cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)				cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						TAGATGCTGGCGTCATGGCCT	0.632													C|||	54	0.0107827	0.0015	0.0144	5008	,	,		20018	0.002		0.0229	False		,,,				2504	0.0174				p.A103T		Atlas-SNP	.											.	NCR3	21	.	0			c.G307A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	15,3007		0,15,1496	140.0	125.0	131.0		307,307,307	-2.7	0.0	6	dbSNP_120	131	113,5305		1,111,2597	yes	missense,missense,missense	NCR3	NM_001145466.1,NM_001145467.1,NM_147130.2	58,58,58	1,126,4093	TT,TC,CC		2.0856,0.4964,1.5166	benign,benign,benign	103/178,103/191,103/202	31557640	128,8312	1511	2709	4220	SO:0001583	missense	259197	exon2			TGCTGGCGTCATG	AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19077	protein-coding gene	gene with protein product		611550	"""lymphocyte antigen 117"""	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123	ENST00000340027.5:c.307G>A	6.37:g.31557640C>T	ENSP00000342156:p.Ala103Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_001145466	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Missense_Mutation	SNP	ENST00000340027.5	37	CCDS34397.1	28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	2	0.0034965034965034965	18	0.023746701846965697	C	3.675	-0.066682	0.07273	0.004964	0.020856	ENSG00000204475	ENST00000340027;ENST00000376073;ENST00000376072;ENST00000376071	T;T;T;T	0.62788	-0.0;-0.0;-0.0;4.16	4.01	-2.69	0.06022	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.707951	0.12172	N	0.492913	T	0.11665	0.0284	N	0.14661	0.345	0.09310	N	1	B;B;B	0.27351	0.056;0.069;0.176	B;B;B	0.14578	0.006;0.011;0.011	T	0.26677	-1.0096	10	0.09338	T	0.73	-0.0807	4.1705	0.10327	0.167:0.3946:0.0:0.4384	rs11575840;rs17200803;rs17550840;rs11575840	103;103;103	O14931-2;Q05D23;O14931	.;.;NCTR3_HUMAN	T	103;103;103;78	ENSP00000342156:A103T;ENSP00000365241:A103T;ENSP00000365240:A103T;ENSP00000365239:A78T	ENSP00000342156:A103T	A	-	1	0	NCR3	31665619	0.000000	0.05858	0.000000	0.03702	0.595000	0.36748	-1.539000	0.02202	-0.742000	0.04790	0.585000	0.79938	GCC	C|0.982;T|0.018	0.018	strong		0.632	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076210.2		
MEP1A	4224	hgsc.bcm.edu	37	6	46793175	46793175	+	Silent	SNP	G	G	A	rs6920863	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	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	
ZNF880	400713	hgsc.bcm.edu	37	19	52876385	52876385	+	Missense_Mutation	SNP	G	G	A	rs14048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52876385G>A	ENST00000422689.2	+	2	49	c.34G>A	c.(34-36)Gtg>Atg	p.V12M	ZNF880_ENST00000424032.2_Missense_Mutation_p.V12M|ZNF880_ENST00000600321.1_Missense_Mutation_p.V12M|ZNF880_ENST00000344085.5_Missense_Mutation_p.V12M|ZNF880_ENST00000595099.1_3'UTR|ZNF880_ENST00000597976.1_Missense_Mutation_p.V12M	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	12	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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						ATTCAGGGACGTGGCCATAGA	0.453													g|||	202	0.0403355	0.0061	0.0303	5008	,	,		15687	0.0		0.1163	False		,,,				2504	0.0573				p.V12M		Atlas-SNP	.											.	ZNF880	45	.	0			c.G34A						PASS	.	G	MET/VAL	33,1351		0,33,659	117.0	101.0	106.0		34	1.6	0.9	19	dbSNP_52	106	343,2839		17,309,1265	no	missense	ZNF880	NM_001145434.1	21	17,342,1924	AA,AG,GG		10.7794,2.3844,8.2348	probably-damaging	12/578	52876385	376,4190	692	1591	2283	SO:0001583	missense	400713	exon2			AGGGACGTGGCCA	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.34G>A	19.37:g.52876385G>A	ENSP00000406318:p.Val12Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	25	0.328947	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	109	0.04990842490842491	5	0.01016260162601626	14	0.03867403314917127	0	0.0	90	0.11873350923482849	g	9.241	1.038238	0.19669	0.023844	0.107794	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	T;T;T	0.10382	2.88;2.88;2.88	1.61	1.61	0.23674	Krueppel-associated box (4);	.	.	.	.	T	0.00524	0.0017	H	0.95539	3.685	0.51012	P	9.199999999998099E-5	D	0.76494	0.999	P	0.59357	0.856	T	0.11275	-1.0594	8	0.66056	D	0.02	.	8.2474	0.31698	0.0:0.0:1.0:0.0	rs14048;rs1129900;rs3177668;rs3188205;rs11546948;rs17296839;rs17355912	12	Q6PDB4	ZN880_HUMAN	M	12	ENSP00000414470:V12M;ENSP00000343625:V12M;ENSP00000406318:V12M	ENSP00000343625:V12M	V	+	1	0	ZNF880	57568197	0.985000	0.35326	0.861000	0.33841	0.107000	0.19398	1.214000	0.32419	0.870000	0.35726	0.305000	0.20034	GTG	G|0.941;A|0.059	0.059	strong		0.453	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74196686	74196686	+	Silent	SNP	T	T	C	rs2075025	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	37	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	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	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360625	71360625	+	Missense_Mutation	SNP	G	G	T	rs1813160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71360625G>T	ENST00000244230.2	+	2	1039	c.687G>T	c.(685-687)gaG>gaT	p.E229D	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.E229D	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	229	Poly-Glu.		E -> D (in dbSNP:rs1813160).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						ATAATGATGAGGAGGAGGAAG	0.323													g|||	1782	0.355831	0.4251	0.4035	5008	,	,		19873	0.2738		0.2982	False		,,,				2504	0.3722				p.E229D		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G687T						PASS	.	G	ASP/GLU	1653,2753	483.2+/-359.6	298,1057,848	72.0	79.0	76.0		687	-5.8	0.0	2	dbSNP_92	76	2557,6043	408.0+/-349.4	400,1757,2143	yes	missense	MPHOSPH10	NM_005791.2	45	698,2814,2991	TT,TG,GG		29.7326,37.517,32.3697	possibly-damaging	229/682	71360625	4210,8796	2203	4300	6503	SO:0001583	missense	10199	exon2			TGATGAGGAGGAG	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.687G>T	2.37:g.71360625G>T	ENSP00000244230:p.Glu229Asp	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	252	121	0.480159	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	751	0.34386446886446886	214	0.4349593495934959	139	0.3839779005524862	180	0.3146853146853147	218	0.287598944591029	G	0.023	-1.395481	0.01175	0.37517	0.297326	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.09723	2.95;2.95	4.88	-5.84	0.02318	.	1.151000	0.06097	N	0.664775	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B	0.10296	0.003	B	0.16289	0.015	T	0.49244	-0.8960	9	0.10377	T	0.69	.	5.1731	0.15120	0.0813:0.0935:0.2794:0.5458	rs1813160;rs35147470;rs52810143;rs58460570;rs1813160	229	O00566	MPP10_HUMAN	D	229;89	ENSP00000244230:E229D;ENSP00000393034:E89D	ENSP00000244230:E229D	E	+	3	2	MPHOSPH10	71214133	0.017000	0.18338	0.001000	0.08648	0.189000	0.23516	-2.557000	0.00924	-0.696000	0.05098	-1.893000	0.00533	GAG	G|0.673;T|0.327	0.327	strong		0.323	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
HERC2	8924	hgsc.bcm.edu	37	15	28419695	28419695	+	Silent	SNP	T	T	C	rs149592795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28419695T>C	ENST00000261609.7	-	65	10011	c.9903A>G	c.(9901-9903)acA>acG	p.T3301T		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.T3301T(1)		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)		CTTGCACGAGTGTGGGCTTCC	0.562													t|||	336	0.0670927	0.0598	0.0634	5008	,	,		22598	0.0198		0.1183	False		,,,				2504	0.0757				p.T3301T		Atlas-SNP	.											HERC2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HERC2	501	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A9903G						PASS	.						87.0	58.0	68.0					15																	28419695		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon65			CACGAGTGTGGGC	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.9903A>G	15.37:g.28419695T>C		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	401	80	0.199501	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			T|0.915;C|0.085	0.085	strong		0.562	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
HRNR	388697	hgsc.bcm.edu	37	1	152187276	152187276	+	Missense_Mutation	SNP	C	C	T	rs199952550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152187276C>T	ENST00000368801.2	-	3	6904	c.6829G>A	c.(6829-6831)Ggt>Agt	p.G2277S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2277					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCATGCTGACCGTGGCTGGAA	0.572																																					p.G2277S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.G6829A						scavenged	.						5.0	7.0	7.0					1																	152187276		1607	3791	5398	SO:0001583	missense	388697	exon3			GCTGACCGTGGCT	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6829G>A	1.37:g.152187276C>T	ENSP00000357791:p.Gly2277Ser	Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	364	38	0.104396	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	8.412	0.844499	0.16963	.	.	ENSG00000197915	ENST00000368801	T	0.16196	2.36	3.98	-0.207	0.13189	.	.	.	.	.	T	0.01765	0.0056	N	0.19112	0.55	0.09310	N	1	D	0.52996	0.957	B	0.34242	0.178	T	0.38672	-0.9650	9	0.09590	T	0.72	.	6.592	0.22651	0.0:0.5599:0.0:0.4401	.	2277	Q86YZ3	HORN_HUMAN	S	2277	ENSP00000357791:G2277S	ENSP00000357791:G2277S	G	-	1	0	HRNR	150453900	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.276000	0.08514	-0.129000	0.11620	0.650000	0.86243	GGT	C|0.993;T|0.007	0.007	strong		0.572	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
FLVCR1	28982	hgsc.bcm.edu	37	1	213068595	213068595	+	Missense_Mutation	SNP	C	C	T	rs3207090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:213068595C>T	ENST00000366971.4	+	10	1829	c.1631C>T	c.(1630-1632)aCg>aTg	p.T544M	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	544			T -> M (in dbSNP:rs3207090). {ECO:0000269|PubMed:15489334}.		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)		GAACCAAAAACGGTTATGTTG	0.383													C|||	1900	0.379393	0.1316	0.2781	5008	,	,		18284	0.4583		0.5	False		,,,				2504	0.5808				p.T544M	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											FLVCR1,rectum,carcinoma,0,2	FLVCR1	31	2	0			c.C1631T						PASS	.	C	MET/THR	920,3486	351.6+/-311.3	102,716,1385	116.0	108.0	111.0		1631	-2.6	0.0	1	dbSNP_105	111	4086,4514	560.3+/-387.6	986,2114,1200	yes	missense	FLVCR1	NM_014053.3	81	1088,2830,2585	TT,TC,CC		47.5116,20.8806,38.4899	possibly-damaging	544/556	213068595	5006,8000	2203	4300	6503	SO:0001583	missense	28982	exon10			CAAAAACGGTTAT	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.1631C>T	1.37:g.213068595C>T	ENSP00000355938:p.Thr544Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	43	0.377193	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	37	CCDS1510.1	848|848	0.3882783882783883|0.3882783882783883	85|85	0.17276422764227642|0.17276422764227642	120|120	0.3314917127071823|0.3314917127071823	273|273	0.4772727272727273|0.4772727272727273	370|370	0.48812664907651715|0.48812664907651715	C|C	5.834|5.834	0.338073|0.338073	0.11013|0.11013	0.208806|0.208806	0.475116|0.475116	ENSG00000162769|ENSG00000162769	ENST00000419102|ENST00000366971	.|D	.|0.82619	.|-1.63	4.88|4.88	-2.58|-2.58	0.06228|0.06228	.|.	.|1.686840	.|0.03088	.|N	.|0.159422	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.45634	.|0.863	.|B	.|0.35240	.|0.198	T|T	0.26883|0.26883	-1.0090|-1.0090	4|9	.|0.59425	.|D	.|0.04	-16.4378|-16.4378	3.3478|3.3478	0.07141|0.07141	0.3494:0.2632:0.0:0.3874|0.3494:0.2632:0.0:0.3874	rs3207090;rs17857350;rs52790363;rs60120981;rs3207090|rs3207090;rs17857350;rs52790363;rs60120981;rs3207090	.|544	.|Q9Y5Y0	.|FLVC1_HUMAN	W|M	343|544	.|ENSP00000355938:T544M	.|ENSP00000355938:T544M	R|T	+|+	1|2	2|0	FLVCR1|FLVCR1	211135218|211135218	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	-0.358000|-0.358000	0.07641|0.07641	-0.118000|-0.118000	0.11851|0.11851	-0.274000|-0.274000	0.10170|0.10170	CGG|ACG	C|0.616;T|0.384	0.384	strong		0.383	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	
WNK1	65125	hgsc.bcm.edu	37	12	936230	936230	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:936230A>T	ENST00000315939.6	+	3	1598	c.955A>T	c.(955-957)Atg>Ttg	p.M319L	WNK1_ENST00000447667.2_Missense_Mutation_p.M319L|WNK1_ENST00000535572.1_Missense_Mutation_p.M319L|WNK1_ENST00000537687.1_Missense_Mutation_p.M319L|WNK1_ENST00000530271.2_Missense_Mutation_p.M319L	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			GTTTAAAGTGATGAAGATCAA	0.358																																					p.M319L	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.A955T						PASS	.						102.0	99.0	100.0					12																	936230		2203	4300	6503	SO:0001583	missense	65125	exon3			AAAGTGATGAAGA	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.955A>T	12.37:g.936230A>T	ENSP00000313059:p.Met319Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	17	0.182796	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	34	5.350017	0.95830	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.59638	0.25;0.25;0.25;0.25;0.25	5.54	5.54	0.83059	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.44644	0.1303	N	0.00337	-1.62	0.80722	D	1	P;P;B	0.52692	0.944;0.955;0.252	P;D;B	0.68353	0.866;0.957;0.157	T	0.73385	-0.3999	10	0.66056	D	0.02	-15.3692	15.6803	0.77364	1.0:0.0:0.0:0.0	.	319;319;319	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	L	319	ENSP00000441972:M319L;ENSP00000313059:M319L;ENSP00000444465:M319L;ENSP00000392542:M319L;ENSP00000433548:M319L	ENSP00000313059:M319L	M	+	1	0	WNK1	806491	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.339000	0.96797	2.115000	0.64714	0.482000	0.46254	ATG	.	.	none		0.358	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
MED16	10025	hgsc.bcm.edu	37	19	868115	868115	+	Missense_Mutation	SNP	C	C	T	rs13090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:868115C>T	ENST00000589119.1	-	15	2619	c.2620G>A	c.(2620-2622)Gag>Aag	p.E874K	MED16_ENST00000325464.1_Missense_Mutation_p.E874K|MED16_ENST00000395808.3_3'UTR|MED16_ENST00000269814.4_3'UTR|MED16_ENST00000312090.6_3'UTR			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	874			E -> K (in dbSNP:rs13090).		androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		GGACGGTCCTCTGGATGCAGA	0.672													c|||	1201	0.239816	0.4334	0.2075	5008	,	,		14335	0.0327		0.2783	False		,,,				2504	0.1748				p.E874K		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	1	0			c.G2620A						PASS	.		LYS/GLU	1733,2661	500.3+/-364.7	341,1051,805	35.0	34.0	35.0		2620	-0.5	0.0	19	dbSNP_52	35	2419,6171	389.6+/-343.0	340,1739,2216	yes	missense	MED16	NM_005481.2	56	681,2790,3021	TT,TC,CC		28.1607,39.4401,31.9778	benign	874/878	868115	4152,8832	2197	4295	6492	SO:0001583	missense	10025	exon16			GGTCCTCTGGATG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2620G>A	19.37:g.868115C>T	ENSP00000464810:p.Glu874Lys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	540	0.24725274725274726	225	0.4573170731707317	85	0.23480662983425415	21	0.03671328671328671	209	0.2757255936675462	c	7.534	0.659189	0.14645	0.394401	0.281607	ENSG00000175221	ENST00000325464	T	0.32988	1.43	0.652	-0.498	0.12019	.	7739.210000	0.00166	U	0.000003	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.13594	0.008	B	0.04013	0.001	T	0.46512	-0.9186	8	0.40728	T	0.16	.	.	.	.	rs13090;rs61664660;rs13090	874	Q9Y2X0	MED16_HUMAN	K	874	ENSP00000325612:E874K	ENSP00000325612:E874K	E	-	1	0	MED16	819115	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	-0.075000	0.11431	-0.185000	0.10550	0.457000	0.33378	GAG	C|0.702;T|0.298	0.298	strong		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
SPEF2	79925	hgsc.bcm.edu	37	5	35646784	35646784	+	Missense_Mutation	SNP	A	A	G	rs80010329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:35646784A>G	ENST00000356031.3	+	5	755	c.601A>G	c.(601-603)Aga>Gga	p.R201G	SPEF2_ENST00000282469.6_Missense_Mutation_p.R201G|SPEF2_ENST00000509059.1_Missense_Mutation_p.R201G|SPEF2_ENST00000440995.2_Missense_Mutation_p.R201G	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	201					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)			CTTAAACAGAAGACGACAAAA	0.318													A|||	44	0.00878594	0.0008	0.0043	5008	,	,		16656	0.001		0.007	False		,,,				2504	0.0327				p.R201G		Atlas-SNP	.											.	SPEF2	324	.	0			c.A601G						PASS	.	A	GLY/ARG,GLY/ARG	9,4397	14.3+/-33.2	0,9,2194	104.0	111.0	109.0		601,601	5.8	1.0	5	dbSNP_131	109	66,8532	39.8+/-96.3	0,66,4233	yes	missense,missense	SPEF2	NM_024867.3,NM_144722.3	125,125	0,75,6427	GG,GA,AA		0.7676,0.2043,0.5767	probably-damaging,probably-damaging	201/1823,201/515	35646784	75,12929	2203	4299	6502	SO:0001583	missense	79925	exon5			AACAGAAGACGAC	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.601A>G	5.37:g.35646784A>G	ENSP00000348314:p.Arg201Gly	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	172	73	0.424419	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	18.98	3.738481	0.69304	0.002043	0.007676	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000510777;ENST00000440995	T;T;T;T;T	0.23147	2.44;3.29;3.14;1.92;3.29	5.76	5.76	0.90799	.	0.106914	0.64402	D	0.000010	T	0.38374	0.1038	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.78314	0.991;0.931;0.936	T	0.37033	-0.9723	10	0.62326	D	0.03	.	11.5326	0.50618	0.8504:0.1496:0.0:0.0	.	201;201;201	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	G	201;201;201;144;201	ENSP00000282469:R201G;ENSP00000348314:R201G;ENSP00000421593:R201G;ENSP00000426259:R144G;ENSP00000412125:R201G	ENSP00000282469:R201G	R	+	1	2	SPEF2	35682541	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.892000	0.63193	2.209000	0.71365	0.533000	0.62120	AGA	A|0.995;G|0.005	0.005	strong		0.318	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
ANK3	288	hgsc.bcm.edu	37	10	61831984	61831984	+	Missense_Mutation	SNP	G	G	T	rs11599164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61831984G>T	ENST00000280772.2	-	37	8846	c.8655C>A	c.(8653-8655)caC>caA	p.H2885Q	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2885			H -> Q (in dbSNP:rs11599164).		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)			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						TACTCTCAGGGTGACCAATGT	0.373													G|||	157	0.0313498	0.0053	0.049	5008	,	,		20093	0.0		0.1044	False		,,,				2504	0.0112				p.H2885Q		Atlas-SNP	.											.	ANK3	703	.	0			c.C8655A						PASS	.	G	,,,GLN/HIS	83,4321	64.1+/-101.4	2,79,2121	76.0	79.0	78.0		,,,8655	5.7	1.0	10	dbSNP_120	78	934,7664	198.5+/-242.8	60,814,3425	yes	intron,intron,intron,missense	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,24	62,893,5546	TT,TG,GG		10.863,1.8847,7.8219	,,,benign	,,,2885/4378	61831984	1017,11985	2202	4299	6501	SO:0001583	missense	288	exon37			CTCAGGGTGACCA	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.8655C>A	10.37:g.61831984G>T	ENSP00000280772:p.His2885Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	105	0.04807692307692308	3	0.006097560975609756	22	0.06077348066298342	0	0.0	80	0.10554089709762533	G	7.724	0.697850	0.15106	0.018847	0.10863	ENSG00000151150	ENST00000280772	T	0.65364	-0.15	5.73	5.73	0.89815	.	0.333501	0.21774	N	0.069311	T	0.00967	0.0032	N	0.14661	0.345	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.01424	-1.1358	10	0.23891	T	0.37	.	10.9362	0.47247	0.1286:0.0:0.8714:0.0	rs11599164;rs17208469;rs52837259;rs61286680;rs11599164	2885	Q12955	ANK3_HUMAN	Q	2885	ENSP00000280772:H2885Q	ENSP00000280772:H2885Q	H	-	3	2	ANK3	61501990	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.096000	0.41738	2.708000	0.92522	0.555000	0.69702	CAC	G|0.934;T|0.066	0.066	strong		0.373	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
USP30	84749	hgsc.bcm.edu	37	12	109520769	109520769	+	Missense_Mutation	SNP	A	A	G	rs16939904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109520769A>G	ENST00000257548.5	+	11	1163	c.1070A>G	c.(1069-1071)cAc>cGc	p.H357R	USP30_ENST00000392784.2_Missense_Mutation_p.H326R	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	357	USP.		H -> R (in dbSNP:rs16939904).		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						TACAAGTACCACCTCCTTGGA	0.562													A|||	318	0.0634984	0.0098	0.0288	5008	,	,		19787	0.13		0.1054	False		,,,				2504	0.0491				p.H357R		Atlas-SNP	.											.	USP30	48	.	0			c.A1070G						PASS	.	A	ARG/HIS	80,4326	69.2+/-107.0	0,80,2123	95.0	77.0	83.0		1070	0.1	1.0	12	dbSNP_123	83	713,7887	175.0+/-225.2	34,645,3621	yes	missense	USP30	NM_032663.3	29	34,725,5744	GG,GA,AA		8.2907,1.8157,6.0972	benign	357/518	109520769	793,12213	2203	4300	6503	SO:0001583	missense	84749	exon11			AGTACCACCTCCT	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.1070A>G	12.37:g.109520769A>G	ENSP00000257548:p.His357Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	37	CCDS9123.2	177	0.08104395604395605	9	0.018292682926829267	14	0.03867403314917127	76	0.13286713286713286	78	0.10290237467018469	A	2.271	-0.366972	0.05069	0.018157	0.082907	ENSG00000135093	ENST00000392784;ENST00000257548	T;T	0.29142	1.58;1.58	5.04	0.0531	0.14305	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.812498	0.11957	N	0.513197	T	0.00144	0.0004	N	0.04746	-0.17	0.33810	P	0.372193	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32640	-0.9899	9	0.19590	T	0.45	-9.0099	11.9733	0.53075	0.3742:0.0:0.6258:0.0	rs16939904;rs52822414;rs56478323;rs61087620;rs16939904	357;326	Q70CQ3;B3KUS5	UBP30_HUMAN;.	R	326;357	ENSP00000376535:H326R;ENSP00000257548:H357R	ENSP00000257548:H357R	H	+	2	0	USP30	108005152	0.002000	0.14202	0.985000	0.45067	0.993000	0.82548	-0.011000	0.12721	-0.159000	0.11021	0.459000	0.35465	CAC	A|0.928;G|0.072	0.072	strong		0.562	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663	
STRADB	55437	hgsc.bcm.edu	37	2	202342402	202342402	+	Silent	SNP	G	G	T	rs12990557	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:202342402G>T	ENST00000194530.3	+	8	974	c.609G>T	c.(607-609)ctG>ctT	p.L203L	STRADB_ENST00000392249.2_Silent_p.L203L	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	203	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						TCTCTGGCCTGTCCCATCTGC	0.478													G|||	2363	0.471845	0.2239	0.4986	5008	,	,		589	0.494		0.5865	False		,,,				2504	0.6472				p.L203L		Atlas-SNP	.											.	STRADB	33	.	0			c.G609T						PASS	.	G	,	1179,3227	415.4+/-337.2	149,881,1173	128.0	126.0	127.0		609,609	3.3	1.0	2	dbSNP_121	127	5115,3477	633.7+/-398.8	1518,2079,699	no	coding-synonymous,coding-synonymous	STRADB	NM_001206864.1,NM_018571.5	,	1667,2960,1872	TT,TG,GG		40.4679,26.759,48.4228	,	203/378,203/419	202342402	6294,6704	2203	4296	6499	SO:0001819	synonymous_variant	55437	exon8			TGGCCTGTCCCAT	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"""	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.609G>T	2.37:g.202342402G>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	226	216	0.955752	NM_001206864	Q5BKY7|Q9P1L0	Silent	SNP	ENST00000194530.3	37	CCDS2348.1																																																																																			G|0.513;T|0.487	0.487	strong		0.478	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571	
HYDIN	54768	hgsc.bcm.edu	37	16	71163693	71163693	+	Silent	SNP	A	A	G	rs4788770	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:71163693A>G	ENST00000393567.2	-	9	1227	c.1077T>C	c.(1075-1077)gaT>gaC	p.D359D	HYDIN_ENST00000393550.2_Silent_p.D359D|HYDIN_ENST00000321489.5_Silent_p.D359D|HYDIN_ENST00000448089.2_Silent_p.D359D|HYDIN_ENST00000448691.1_Silent_p.D359D|HYDIN_ENST00000538248.1_Silent_p.D386D|HYDIN_ENST00000541601.1_Silent_p.D376D|HYDIN_ENST00000288168.10_Silent_p.D376D	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	359					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)				CATCAGTCTCATCCTTCTCCT	0.453																																					p.D386D		Atlas-SNP	.											.	HYDIN	788	.	0			c.T1158C						PASS	.						21.0	21.0	21.0					16																	71163693		2197	4279	6476	SO:0001819	synonymous_variant	54768	exon9			AGTCTCATCCTTC	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.1077T>C	16.37:g.71163693A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	129	53	0.410853	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			A|0.625;G|0.375	0.375	strong		0.453	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HDGFL1	154150	hgsc.bcm.edu	37	6	22570064	22570064	+	Missense_Mutation	SNP	C	C	T	rs2076506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:22570064C>T	ENST00000230012.3	+	1	387	c.260C>T	c.(259-261)aCg>aTg	p.T87M	HDGFL1_ENST00000510882.2_Missense_Mutation_p.T87M	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	87			T -> M (in dbSNP:rs2076506).							kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					AACAACCCCACGGTCCAGGCC	0.652													C|||	955	0.190695	0.0567	0.2493	5008	,	,		12678	0.3879		0.0865	False		,,,				2504	0.2342				p.T87M		Atlas-SNP	.											.	HDGFL1	33	.	0			c.C260T						PASS	.	C	MET/THR	301,4105		13,275,1915	27.0	26.0	26.0		260	1.4	0.0	6	dbSNP_96	26	711,7887		27,657,3615	yes	missense	HDGFL1	NM_138574.2	81	40,932,5530	TT,TC,CC		8.2694,6.8316,7.7822	possibly-damaging	87/252	22570064	1012,11992	2203	4299	6502	SO:0001583	missense	154150	exon1			ACCCCACGGTCCA	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"""PWWP domain containing 1"""	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.260C>T	6.37:g.22570064C>T	ENSP00000230012:p.Thr87Met	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_138574	Q96MJ6	Missense_Mutation	SNP	ENST00000230012.3	37	CCDS34347.1	375	0.1717032967032967	29	0.05894308943089431	70	0.19337016574585636	213	0.3723776223776224	63	0.08311345646437995	C	10.33	1.320124	0.23994	0.068316	0.082694	ENSG00000112273	ENST00000230012;ENST00000510882	T;T	0.70749	-0.51;-0.51	3.28	1.38	0.22167	.	0.258413	0.37261	N	0.002180	T	0.33673	0.0871	L	0.42245	1.32	0.80722	P	0.0	D	0.53745	0.962	B	0.38378	0.272	T	0.31779	-0.9931	9	0.51188	T	0.08	-40.4351	1.6909	0.02852	0.2123:0.453:0.2077:0.127	rs2076506;rs56879815;rs2076506	87	Q5TGJ6	HDGL1_HUMAN	M	87	ENSP00000230012:T87M;ENSP00000442129:T87M	ENSP00000230012:T87M	T	+	2	0	HDGFL1	22678043	0.000000	0.05858	0.007000	0.13788	0.424000	0.31475	-0.161000	0.10026	0.352000	0.24053	0.491000	0.48974	ACG	C|0.862;T|0.138	0.138	strong		0.652	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574	
FREM1	158326	hgsc.bcm.edu	37	9	14859356	14859356	+	Silent	SNP	T	T	C	rs10961757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:14859356T>C	ENST00000380880.3	-	4	1239	c.456A>G	c.(454-456)caA>caG	p.Q152Q	FREM1_ENST00000422223.2_Silent_p.Q152Q|FREM1_ENST00000380881.4_Silent_p.Q152Q			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	152					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)		TATCAATCGCTTGGGACAAGC	0.473													T|||	1244	0.248403	0.1483	0.2435	5008	,	,		19125	0.5367		0.164	False		,,,				2504	0.1769				p.Q152Q		Atlas-SNP	.											.	FREM1	261	.	0			c.A456G						PASS	.	T		557,3241		49,459,1391	133.0	131.0	131.0		456	3.4	0.8	9	dbSNP_120	131	1259,6989		117,1025,2982	no	coding-synonymous	FREM1	NM_144966.5		166,1484,4373	CC,CT,TT		15.2643,14.6656,15.0755		152/2180	14859356	1816,10230	1899	4124	6023	SO:0001819	synonymous_variant	158326	exon5			AATCGCTTGGGAC	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.456A>G	9.37:g.14859356T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			T|0.752;C|0.248	0.248	strong		0.473	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
MUC16	94025	hgsc.bcm.edu	37	19	9077060	9077060	+	Silent	SNP	C	C	T	rs2591596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9077060C>T	ENST00000397910.4	-	3	10589	c.10386G>A	c.(10384-10386)gtG>gtA	p.V3462V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3463	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						AGGGCAGAGACACTAGTGAGG	0.498													T|||	1244	0.248403	0.2012	0.2118	5008	,	,		22404	0.249		0.3121	False		,,,				2504	0.272				p.V3462V		Atlas-SNP	.											.	MUC16	4315	.	0			c.G10386A						PASS	.	T		893,3339		107,679,1330	131.0	128.0	129.0		10386	-0.7	0.0	19	dbSNP_100	129	2433,6021		353,1727,2147	no	coding-synonymous	MUC16	NM_024690.2		460,2406,3477	TT,TC,CC		28.7793,21.1011,26.2179		3462/14508	9077060	3326,9360	2116	4227	6343	SO:0001819	synonymous_variant	94025	exon3			CAGAGACACTAGT	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.10386G>A	19.37:g.9077060C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.743;T|0.257	0.257	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
AGMAT	79814	hgsc.bcm.edu	37	1	15904318	15904318	+	Silent	SNP	C	C	T	rs11544523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15904318C>T	ENST00000375826.3	-	5	904	c.762G>A	c.(760-762)tcG>tcA	p.S254S	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	254					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAACCAGCGACTTCATCC	0.537													C|||	1189	0.23742	0.4493	0.1873	5008	,	,		21655	0.0565		0.2177	False		,,,				2504	0.1933				p.S254S	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G762A						PASS	.	C		1892,2514	543.7+/-376.3	400,1092,711	83.0	75.0	77.0		762	-10.8	0.4	1	dbSNP_120	77	1922,6678	339.6+/-323.3	198,1526,2576	yes	coding-synonymous	AGMAT	NM_024758.4		598,2618,3287	TT,TC,CC		22.3488,42.9414,29.3249		254/353	15904318	3814,9192	2203	4300	6503	SO:0001819	synonymous_variant	79814	exon5			AACCAGCGACTTC	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.762G>A	1.37:g.15904318C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_024758	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	37	CCDS160.1																																																																																			C|0.729;T|0.271	0.271	strong		0.537	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
DMRT2	10655	hgsc.bcm.edu	37	9	1056728	1056728	+	Missense_Mutation	SNP	G	G	C	rs3824419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:1056728G>C	ENST00000358146.2	+	3	1141	c.1141G>C	c.(1141-1143)Gca>Cca	p.A381P	DMRT2_ENST00000382251.3_Missense_Mutation_p.A381P|DMRT2_ENST00000302441.6_Missense_Mutation_p.A381P|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000259622.6_3'UTR			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	381			A -> P (in dbSNP:rs3824419). {ECO:0000269|PubMed:15489334}.		embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		CTTGAAGGGAGCACGAGTCCA	0.577													G|||	1736	0.346645	0.1528	0.4222	5008	,	,		19498	0.4762		0.3489	False		,,,				2504	0.4192				p.A381P		Atlas-SNP	.											DMRT2_ENST00000302441,NS,carcinoma,0,2	DMRT2	70	2	0			c.G1141C						PASS	.	G	,,PRO/ALA	823,3583	328.0+/-300.3	83,657,1463	90.0	86.0	88.0		,,1141	-1.6	0.0	9	dbSNP_107	88	2956,5644	459.2+/-364.8	521,1914,1865	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,27	604,2571,3328	CC,CG,GG		34.3721,18.6791,29.0558	,,benign	,,381/562	1056728	3779,9227	2203	4300	6503	SO:0001583	missense	10655	exon4			AAGGGAGCACGAG	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"""terra-like protein"""	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.1141G>C	9.37:g.1056728G>C	ENSP00000350865:p.Ala381Pro	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	751	0.34386446886446886	60	0.12195121951219512	139	0.3839779005524862	284	0.4965034965034965	268	0.35356200527704484	G	6.760	0.509175	0.12883	0.186791	0.343721	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.23754	1.89;1.89;1.89	5.78	-1.62	0.08372	.	0.746171	0.13395	N	0.391098	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.31730	0.337	B	0.25759	0.063	T	0.46176	-0.9210	9	0.33141	T	0.24	0.1605	1.5529	0.02578	0.4335:0.1001:0.275:0.1914	rs3824419;rs17722173;rs60311434;rs3824419	381	Q9Y5R5	DMRT2_HUMAN	P	381	ENSP00000371686:A381P;ENSP00000305785:A381P;ENSP00000350865:A381P	ENSP00000305785:A381P	A	+	1	0	DMRT2	1046728	0.004000	0.15560	0.003000	0.11579	0.472000	0.32918	0.457000	0.21875	-0.150000	0.11195	-0.156000	0.13503	GCA	G|0.685;C|0.315	0.315	strong		0.577	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
NT5DC3	51559	hgsc.bcm.edu	37	12	104171742	104171742	+	Silent	SNP	C	C	T	rs17034524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104171742C>T	ENST00000392876.3	-	14	1552	c.1512G>A	c.(1510-1512)ctG>ctA	p.L504L		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	504						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.L429L(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						GGAGGCAGCTCAGAGACGCCA	0.587													C|||	1124	0.224441	0.087	0.2104	5008	,	,		15043	0.4375		0.1829	False		,,,				2504	0.2434				p.L504L		Atlas-SNP	.											NT5DC3,NS,carcinoma,0,1	NT5DC3	113	1	1	Substitution - coding silent(1)	stomach(1)	c.G1512A						PASS	.	C		419,3987	206.2+/-227.9	23,373,1807	78.0	79.0	78.0		1512	3.9	1.0	12	dbSNP_123	78	1453,7147	278.3+/-293.3	119,1215,2966	no	coding-synonymous	NT5DC3	NM_001031701.2		142,1588,4773	TT,TC,CC		16.8953,9.5098,14.3934		504/549	104171742	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon14			GCAGCTCAGAGAC	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1512G>A	12.37:g.104171742C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			C|0.815;T|0.185	0.185	strong		0.587	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
C22orf42	150297	hgsc.bcm.edu	37	22	32554996	32554996	+	Silent	SNP	C	C	T	rs12160688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32554996C>T	ENST00000382097.3	-	1	279	c.207G>A	c.(205-207)acG>acA	p.T69T	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	69										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GCATCTTCGGCGTCTTCGGGA	0.557													.|||	266	0.053115	0.1089	0.0403	5008	,	,		18046	0.0		0.0666	False		,,,				2504	0.0276				p.T69T		Atlas-SNP	.											C22orf42,NS,carcinoma,-2,1	C22orf42	37	1	0			c.G207A						PASS	.	C		341,4065	176.6+/-205.7	16,309,1878	174.0	170.0	171.0		207		0.0	22	dbSNP_120	171	610,7990	158.2+/-211.7	20,570,3710	no	coding-synonymous	C22orf42	NM_001010859.1		36,879,5588	TT,TC,CC		7.093,7.7394,7.312		69/252	32554996	951,12055	2203	4300	6503	SO:0001819	synonymous_variant	150297	exon1			CTTCGGCGTCTTC	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.207G>A	22.37:g.32554996C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	219	92	0.420091	NM_001010859	A4QPH5	Silent	SNP	ENST00000382097.3	37	CCDS33639.1																																																																																			C|0.930;T|0.070	0.070	strong		0.557	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
KRTAP2-4	85294	hgsc.bcm.edu	37	17	39221816	39221816	+	Nonsense_Mutation	SNP	C	C	T	rs200049107		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39221816C>T	ENST00000394015.2	-	1	315	c.282G>A	c.(280-282)tgG>tgA	p.W94*		NM_033184.3	NP_149440.1	Q9BYR9	KRA24_HUMAN	keratin associated protein 2-4	94	10 X 5 AA repeats of C-C-[CDPQRW]- [ADPRS]-[CIPSTV].					keratin filament (GO:0045095)		p.W94*(1)		skin(1)	1		Breast(137;0.000496)|Myeloproliferative disorder(1115;0.204)	STAD - Stomach adenocarcinoma(17;0.000371)			AGGTGGTGGCCCAGCAGCAGG	0.716																																					p.W94X		Atlas-SNP	.											KRTAP2-4,trunk,malignant_melanoma,0,1	KRTAP2-4	2	1	1	Substitution - Nonsense(1)	skin(1)	c.G282A						scavenged	.						9.0	9.0	9.0					17																	39221816		1454	3133	4587	SO:0001587	stop_gained	85294	exon1			GGTGGCCCAGCAG	AJ406930		17q21.2	2012-04-19			ENSG00000213417	ENSG00000213417		"""Keratin associated proteins"""	18891	protein-coding gene	gene with protein product						11279113	Standard	NM_033184		Approved	KAP2.4	uc002hvy.3	Q9BYR9	OTTHUMG00000133594	ENST00000394015.2:c.282G>A	17.37:g.39221816C>T	ENSP00000377583:p.Trp94*	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	17	4	0.235294	NM_033184	Q495J2	Nonsense_Mutation	SNP	ENST00000394015.2	37	CCDS32648.1	.	.	.	.	.	.	.	.	.	.	.	25.2	4.608564	0.87258	.	.	ENSG00000213417	ENST00000394015	.	.	.	5.58	5.58	0.84498	.	0.187904	0.26119	U	0.026230	.	.	.	.	.	.	0.58432	D	0.999994	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	15.0735	0.72059	0.0:1.0:0.0:0.0	.	.	.	.	X	94	.	ENSP00000377583:W94X	W	-	3	0	KRTAP2-4	36475342	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	0.989000	0.29629	2.624000	0.88883	0.655000	0.94253	TGG	.	.	weak		0.716	KRTAP2-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257698.1	NM_033184	
POLE2	5427	hgsc.bcm.edu	37	14	50131846	50131846	+	Silent	SNP	G	G	T	rs3218791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50131846G>T	ENST00000216367.5	-	8	711	c.612C>A	c.(610-612)gtC>gtA	p.V204V	POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000554396.1_Silent_p.V204V|POLE2_ENST00000539565.2_Silent_p.V178V	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	204					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|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)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	GGTCTAGTTGGACTGTTCCAG	0.279													T|||	1039	0.207468	0.4939	0.1657	5008	,	,		17661	0.0268		0.2127	False		,,,				2504	0.0307				p.V204V		Atlas-SNP	.											.	POLE2	36	.	0			c.C612A						PASS	.	T	,,	1928,2472	601.4+/-389.7	419,1090,691	46.0	46.0	46.0		534,612,612	2.9	1.0	14	dbSNP_106	46	1683,6905	723.2+/-406.4	170,1343,2781	no	coding-synonymous,coding-synonymous,coding-synonymous	POLE2	NM_001197330.1,NM_001197331.1,NM_002692.3	,,	589,2433,3472	TT,TG,GG		19.5971,43.8182,27.8026	,,	178/502,204/503,204/528	50131846	3611,9377	2200	4294	6494	SO:0001819	synonymous_variant	5427	exon8			TAGTTGGACTGTT	AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"""DNA polymerases"""	9178	protein-coding gene	gene with protein product	"""DNA polymerase epsilon subunit B"""	602670	"""polymerase (DNA directed), epsilon 2 (p59 subunit)"""			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.612C>A	14.37:g.50131846G>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001197331	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Silent	SNP	ENST00000216367.5	37	CCDS32073.1																																																																																			G|0.766;T|0.234	0.234	strong		0.279	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410512.1	NM_002692	
TBP	6908	hgsc.bcm.edu	37	6	170871061	170871061	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:170871061G>A	ENST00000392092.2	+	3	516	c.237G>A	c.(235-237)caG>caA	p.Q79Q	TBP_ENST00000230354.6_Silent_p.Q79Q|TBP_ENST00000540980.1_Silent_p.Q59Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	79	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)	p.Q79Q(2)		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	0.582																																					p.Q79Q		Atlas-SNP	.											TBP,caecum,carcinoma,0,5	TBP	58	5	2	Substitution - coding silent(2)	prostate(1)|endometrium(1)	c.G237A						PASS	.						12.0	17.0	15.0					6																	170871061		1930	3791	5721	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.237G>A	6.37:g.170871061G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	36	7	0.194444	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			.	.	none		0.582	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
KMT2C	58508	hgsc.bcm.edu	37	7	151970951	151970951	+	Splice_Site	SNP	C	C	T	rs201009236		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151970951C>T	ENST00000262189.6	-	7	1069	c.851G>A	c.(850-852)cGa>cAa	p.R284Q	KMT2C_ENST00000355193.2_Splice_Site_p.R284Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	284					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)										AAATGCACATCGCTGAAAGGG	0.393																																					p.R284Q		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,12	MLL3	1564	12	0			c.G851A						scavenged	.						54.0	51.0	52.0					7																	151970951		2202	4299	6501	SO:0001630	splice_region_variant	58508	exon7			GCACATCGCTGAA	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.850-1G>A	7.37:g.151970951C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	165	14	0.0848485	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.551821	0.45487	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.70631	-0.5;-0.5	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.258206	0.20689	N	0.087494	T	0.78381	0.4274	M	0.69463	2.115	0.80722	D	1	D	0.58970	0.984	P	0.52159	0.691	T	0.81093	-0.1089	10	0.59425	D	0.04	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	284	Q8NEZ4	MLL3_HUMAN	Q	284	ENSP00000262189:R284Q;ENSP00000347325:R284Q	ENSP00000262189:R284Q	R	-	2	0	MLL3	151601884	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.773000	0.55333	2.423000	0.82170	0.650000	0.86243	CGA	C|0.750;T|0.250	0.250	strong		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		Missense_Mutation
MON2	23041	hgsc.bcm.edu	37	12	62979216	62979216	+	Silent	SNP	G	G	A	rs11174557	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:62979216G>A	ENST00000393632.2	+	33	5233	c.4842G>A	c.(4840-4842)agG>agA	p.R1614R	MON2_ENST00000552738.1_Silent_p.R1585R|MON2_ENST00000393630.3_Silent_p.R1615R|MON2_ENST00000280379.6_Silent_p.R1615R|MON2_ENST00000546600.1_Silent_p.R1614R|MON2_ENST00000393629.2_Silent_p.R1608R|MON2_ENST00000551397.1_5'Flank	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1614					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTTTAAAGAGGTCCCAAGATG	0.348													G|||	390	0.0778754	0.0129	0.1095	5008	,	,		17108	0.0169		0.1859	False		,,,				2504	0.0951				p.R1614R		Atlas-SNP	.											.	MON2	160	.	0			c.G4842A						PASS	.	G		167,4239	109.5+/-147.8	8,151,2044	74.0	71.0	72.0		4842	0.9	1.0	12	dbSNP_120	72	1564,7036	293.4+/-301.3	130,1304,2866	no	coding-synonymous	MON2	NM_015026.2		138,1455,4910	AA,AG,GG		18.186,3.7903,13.3092		1614/1718	62979216	1731,11275	2203	4300	6503	SO:0001819	synonymous_variant	23041	exon33			AAAGAGGTCCCAA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4842G>A	12.37:g.62979216G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	CCDS31849.1																																																																																			G|0.884;A|0.116	0.116	strong		0.348	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
PRKCB	5579	hgsc.bcm.edu	37	16	24202458	24202458	+	Silent	SNP	C	C	T	rs3729904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	104	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	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	
MUC16	94025	hgsc.bcm.edu	37	19	9063935	9063935	+	Silent	SNP	G	G	A	rs2252675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9063935G>A	ENST00000397910.4	-	3	23714	c.23511C>T	c.(23509-23511)agC>agT	p.S7837S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7839	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)		p.S7837S(2)|p.S3470S(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						CTTCAGAGCCGCTGGACTCCC	0.542													G|||	1053	0.210264	0.0628	0.2003	5008	,	,		20983	0.249		0.3101	False		,,,				2504	0.274				p.S7837S		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - coding silent(3)	stomach(3)	c.C23511T						PASS	.			418,3682		24,370,1656	75.0	74.0	74.0		23511	-3.4	0.0	19	dbSNP_100	74	2390,6004		338,1714,2145	no	coding-synonymous	MUC16	NM_024690.2		362,2084,3801	AA,AG,GG		28.4727,10.1951,22.4748		7837/14508	9063935	2808,9686	2050	4197	6247	SO:0001819	synonymous_variant	94025	exon3			AGAGCCGCTGGAC	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.23511C>T	19.37:g.9063935G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.772;A|0.228	0.228	strong		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GALNT4	8693	hgsc.bcm.edu	37	12	89917518	89917518	+	Missense_Mutation	SNP	A	A	G	rs2230281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:89917518A>G	ENST00000529983.2	-	1	1065	c.809T>C	c.(808-810)aTa>aCa	p.I270T	POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000549035.1_Intron|GALNT4_ENST00000413530.1_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.I267T	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	270			I -> T (in dbSNP:rs2230281). {ECO:0000269|PubMed:14702039}.		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)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						GGGCTCCCCTATCTGCATATA	0.448													G|||	3674	0.733626	0.7428	0.6513	5008	,	,		20509	0.7361		0.7217	False		,,,				2504	0.7894				p.I270T		Atlas-SNP	.											.	GALNT4	38	.	0			c.T809C						PASS	.	G	,THR/ILE,,THR/ILE,	2854,924		1076,702,111	59.0	59.0	59.0		,800,,809,	4.6	0.9	12	dbSNP_98	59	5960,2264		2173,1614,325	yes	intron,missense,intron,missense,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,89,,89,	3249,2316,436	GG,GA,AA		27.5292,24.4574,26.5622	,benign,,benign,	,267/576,,270/579,	89917518	8814,3188	1889	4112	6001	SO:0001583	missense	8693	exon1			TCCCCTATCTGCA	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.809T>C	12.37:g.89917518A>G	ENSP00000436604:p.Ile270Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	1603	0.7339743589743589	367	0.7459349593495935	227	0.6270718232044199	457	0.798951048951049	552	0.7282321899736148	G	5.791	0.330207	0.10956	0.755426	0.724708	ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000529983	T;T	0.61040	0.14;0.14	5.56	4.59	0.56863	Glycosyl transferase, family 2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.00289	-1.7	0.45690	P	0.0013929999999999776	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33828	-0.9853	8	0.33141	T	0.24	.	11.5105	0.50490	0.0729:0.0:0.7941:0.133	rs2230281;rs3803127;rs52821019;rs60934578;rs2230281	267;270	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	T	267;270	ENSP00000447852:I267T;ENSP00000436604:I270T	ENSP00000436604:I270T	I	-	2	0	GALNT4;RP11-1109F11.4	88441649	1.000000	0.71417	0.874000	0.34290	0.959000	0.62525	5.606000	0.67641	1.366000	0.46076	-0.119000	0.15052	ATA	G|0.754;N|0.000	0.754	strong		0.448	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
DCTD	1635	hgsc.bcm.edu	37	4	183815688	183815688	+	Silent	SNP	A	A	G	rs4742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:183815688A>G	ENST00000438320.2	-	4	605	c.315T>C	c.(313-315)gtT>gtC	p.V105V	DCTD_ENST00000357067.3_Silent_p.V116V|DCTD_ENST00000510370.1_Silent_p.V105V	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	105					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	GGAACAAGGCAACATACATAC	0.463													A|||	1556	0.310703	0.5182	0.1974	5008	,	,		20632	0.2202		0.2913	False		,,,				2504	0.2239				p.V116V		Atlas-SNP	.											.	DCTD	30	.	0			c.T348C						PASS	.	A	,	2254,2152	595.3+/-388.4	592,1070,541	199.0	159.0	172.0		348,315	-5.9	0.3	4	dbSNP_52	172	2636,5964	426.0+/-355.2	399,1838,2063	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	991,2908,2604	GG,GA,AA		30.6512,48.8425,37.598	,	116/190,105/179	183815688	4890,8116	2203	4300	6503	SO:0001819	synonymous_variant	1635	exon4			CAAGGCAACATAC	L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.315T>C	4.37:g.183815688A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	159	71	0.446541	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																			T|0.125;G|0.280;C|0.062;A|0.534	0.280	strong		0.463	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
NUDT8	254552	hgsc.bcm.edu	37	11	67395714	67395714	+	Silent	SNP	C	C	T	rs7124513	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:67395714C>T	ENST00000376693.2	-	4	423	c.414G>A	c.(412-414)gaG>gaA	p.E138E	RP11-655M14.13_ENST00000533311.1_lincRNA|NUDT8_ENST00000301490.4_3'UTR	NM_001243750.1	NP_001230679.1	Q8WV74	NUDT8_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 8	138	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|prostate(1)|skin(1)	4						GTGCAAACACCTCATCTACCT	0.617													C|||	1166	0.232827	0.1815	0.4496	5008	,	,		20782	0.127		0.332	False		,,,				2504	0.1554				p.E138E		Atlas-SNP	.											.	NUDT8	12	.	0			c.G414A						PASS	.	C		340,1406		28,284,561	43.0	42.0	43.0			-1.5	1.0	11	dbSNP_116	43	1238,2732		203,832,950	no	utr-3	NUDT8	NM_181843.2		231,1116,1511	TT,TC,CC		31.1839,19.4731,27.6067			67395714	1578,4138	873	1985	2858	SO:0001819	synonymous_variant	254552	exon4			AAACACCTCATCT	AI743601	CCDS8174.1, CCDS58151.1	11q13.2	2008-07-21			ENSG00000167799	ENSG00000167799		"""Nudix motif containing"""	8055	protein-coding gene	gene with protein product						11415433	Standard	NM_181843		Approved	FLJ41567	uc001omo.2	Q8WV74	OTTHUMG00000167292	ENST00000376693.2:c.414G>A	11.37:g.67395714C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_001243750	Q6ZW59	Silent	SNP	ENST00000376693.2	37	CCDS58151.1																																																																																			C|0.746;T|0.254	0.254	strong		0.617	NUDT8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394036.1	NM_181843	
ARHGAP20	57569	hgsc.bcm.edu	37	11	110450382	110450382	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:110450382C>T	ENST00000260283.4	-	16	3572	c.3288G>A	c.(3286-3288)agG>agA	p.R1096R	ARHGAP20_ENST00000529591.1_Silent_p.R639R|ARHGAP20_ENST00000357139.3_Silent_p.R1070R|ARHGAP20_ENST00000528829.1_Silent_p.R1060R|ARHGAP20_ENST00000527598.1_Silent_p.R1060R|ARHGAP20_ENST00000533353.1_Silent_p.R1070R|ARHGAP20_ENST00000524756.1_Silent_p.R1073R	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	1096					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R1096R(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CTTCAGCTGCCCTTAAGGGCA	0.522																																					p.R1096R		Atlas-SNP	.											ARHGAP20,NS,carcinoma,0,1	ARHGAP20	150	1	1	Substitution - coding silent(1)	prostate(1)	c.G3288A						scavenged	.						73.0	76.0	75.0					11																	110450382		2201	4298	6499	SO:0001819	synonymous_variant	57569	exon16			AGCTGCCCTTAAG	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.3288G>A	11.37:g.110450382C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	2	0.0246914	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Silent	SNP	ENST00000260283.4	37	CCDS31673.1																																																																																			.	.	none		0.522	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
DNAH5	1767	hgsc.bcm.edu	37	5	13845045	13845045	+	Silent	SNP	G	G	A	rs10041113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13845045G>A	ENST00000265104.4	-	32	5276	c.5172C>T	c.(5170-5172)gcC>gcT	p.A1724A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1724	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)					TCTCTAGAAGGGCAGGATCTG	0.443									Kartagener syndrome				A|||	2277	0.454673	0.5174	0.4092	5008	,	,		18672	0.622		0.3598	False		,,,				2504	0.3272				p.A1724A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5172T						PASS	.	A		2201,2205	588.0+/-386.8	546,1109,548	84.0	88.0	87.0		5172	-1.3	0.4	5	dbSNP_119	87	2993,5607	664.8+/-402.2	512,1969,1819	no	coding-synonymous	DNAH5	NM_001369.2		1058,3078,2367	AA,AG,GG		34.8023,49.9546,39.9354		1724/4625	13845045	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon32	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAGAAGGGCAGGA	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.5172C>T	5.37:g.13845045G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	52	33	0.634615	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
GPR110	266977	hgsc.bcm.edu	37	6	46977277	46977277	+	Silent	SNP	G	G	A	rs16875406	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46977277G>A	ENST00000371253.2	-	11	2109	c.1894C>T	c.(1894-1896)Ctg>Ttg	p.L632L	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.L435L	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	632					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						AAGAGGGACAGGGCTATGTTC	0.458													G|||	274	0.0547125	0.1672	0.0303	5008	,	,		23603	0.0		0.0249	False		,,,				2504	0.0072				p.L632L		Atlas-SNP	.											.	GPR110	102	.	0			c.C1894T						PASS	.	G		660,3746	281.4+/-275.9	58,544,1601	133.0	98.0	110.0		1894	2.2	1.0	6	dbSNP_123	110	302,8298	109.0+/-169.6	7,288,4005	no	coding-synonymous	GPR110	NM_153840.2		65,832,5606	AA,AG,GG		3.5116,14.9796,7.3966		632/911	46977277	962,12044	2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			GGGACAGGGCTAT	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.1894C>T	6.37:g.46977277G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	145	84	0.57931	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			G|0.932;A|0.068	0.068	strong		0.458	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
RTEL1	51750	hgsc.bcm.edu	37	20	62293272	62293272	+	Missense_Mutation	SNP	A	A	G	rs3848668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62293272A>G	ENST00000360203.5	+	4	696	c.371A>G	c.(370-372)aAc>aGc	p.N124S	RTEL1_ENST00000370018.3_Missense_Mutation_p.N124S|RTEL1_ENST00000318100.4_Missense_Mutation_p.N124S|RTEL1_ENST00000508582.2_Missense_Mutation_p.N124S|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.N124S					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			CAGGTCATCAACGAGCTTCGG	0.552													A|||	177	0.0353435	0.0038	0.0504	5008	,	,		18072	0.001		0.0845	False		,,,				2504	0.0521				p.N124S		Atlas-SNP	.											.	RTEL1	114	.	0			c.A371G						PASS	.	A	SER/ASN,SER/ASN	77,4329	68.7+/-106.4	0,77,2126	147.0	113.0	125.0		371,371	2.8	0.0	20	dbSNP_108	125	712,7888	174.3+/-224.6	36,640,3624	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	46,46	36,717,5750	GG,GA,AA		8.2791,1.7476,6.0664	benign,benign	124/1220,124/1244	62293272	789,12217	2203	4300	6503	SO:0001583	missense	51750	exon4			TCATCAACGAGCT	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.371A>G	20.37:g.62293272A>G	ENSP00000353332:p.Asn124Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		88	0.040293040293040296	3	0.006097560975609756	22	0.06077348066298342	0	0.0	63	0.08311345646437995	A	0.049	-1.256084	0.01457	0.017476	0.082791	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000356810	T;T;T;T;T	0.70986	0.99;0.99;-0.53;0.99;-0.45	4.84	2.77	0.32553	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	1.399430	0.03967	N	0.290957	T	0.03608	0.0103	N	0.02865	-0.47	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.11329	0.004;0.006;0.004;0.002	T	0.10800	-1.0614	10	0.11485	T	0.65	-0.7426	7.8064	0.29204	0.2891:0.0:0.7109:0.0	rs3848668;rs56544488;rs3848668	124;124;124;124	Q9NZ71-7;D6RBA3;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	S	124	ENSP00000359035:N124S;ENSP00000322287:N124S;ENSP00000424307:N124S;ENSP00000353332:N124S;ENSP00000349265:N124S	ENSP00000349265:N124S	N	+	2	0	AL353715.1	61763716	0.005000	0.15991	0.020000	0.16555	0.038000	0.13279	1.489000	0.35562	0.447000	0.26695	-0.624000	0.04008	AAC	A|0.946;G|0.054	0.054	strong		0.552	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
DENND4C	55667	hgsc.bcm.edu	37	9	19352096	19352096	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19352096G>A	ENST00000380432.2	+	20	3699	c.3666G>A	c.(3664-3666)atG>atA	p.M1222I	DENND4C_ENST00000434457.2_Missense_Mutation_p.M1507I|DENND4C_ENST00000602925.1_Missense_Mutation_p.M1458I			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1222					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CAAGAGGCATGAAAGGGCAAG	0.348																																					p.M1458I		Atlas-SNP	.											.	DENND4C	120	.	0			c.G4374A						PASS	.						148.0	138.0	141.0					9																	19352096		2203	4300	6503	SO:0001583	missense	55667	exon24			AGGCATGAAAGGG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3666G>A	9.37:g.19352096G>A	ENSP00000369797:p.Met1222Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	19	0.202128	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	5.514	0.279774	0.10458	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024;ENST00000380424	T;T	0.20881	2.05;2.04	5.27	-2.51	0.06365	.	1.303380	0.04496	N	0.380371	T	0.09818	0.0241	N	0.11560	0.145	0.28170	N	0.928596	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	0.28902	-1.0029	10	0.34782	T	0.22	-0.4352	2.7946	0.05397	0.1982:0.2628:0.4155:0.1235	.	552;1222;404;1222	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	I	1222;695;404;552;695;404;219;93	ENSP00000305795:M695I;ENSP00000443804:M552I	ENSP00000305795:M695I	M	+	3	0	DENND4C	19342096	0.685000	0.27652	0.809000	0.32408	0.994000	0.84299	0.215000	0.17562	-0.207000	0.10187	0.655000	0.94253	ATG	.	.	none		0.348	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
DSC2	1824	hgsc.bcm.edu	37	18	28673565	28673565	+	Silent	SNP	T	T	C	rs12954874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	55	0	0		WXS	Illumina HiSeq	Phase_I	74	48	0.648649	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	
RRP36	88745	hgsc.bcm.edu	37	6	42992825	42992825	+	Missense_Mutation	SNP	C	C	G	rs3749903	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:42992825C>G	ENST00000244496.5	+	2	243	c.233C>G	c.(232-234)gCt>gGt	p.A78G		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	78			A -> G (in dbSNP:rs3749903).		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						AAGAAACAAGCTTCTAGACCA	0.433													G|||	1721	0.34365	0.7133	0.2421	5008	,	,		22689	0.2123		0.1223	False		,,,				2504	0.2791				p.A78G		Atlas-SNP	.											.	RRP36	20	.	0			c.C233G						PASS	.	G	GLY/ALA	2782,1624	499.5+/-364.4	882,1018,303	132.0	118.0	122.0		233	-2.4	0.0	6	dbSNP_107	122	1118,7482	767.9+/-407.6	65,988,3247	yes	missense	RRP36	NM_033112.2	60	947,2006,3550	GG,GC,CC		13.0,36.8588,29.9862	benign	78/260	42992825	3900,9106	2203	4300	6503	SO:0001583	missense	88745	exon2			AACAAGCTTCTAG	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.233C>G	6.37:g.42992825C>G	ENSP00000244496:p.Ala78Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_033112	Q9BRF6|Q9P0C8	Missense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	642	0.29395604395604397	343	0.6971544715447154	80	0.22099447513812154	121	0.21153846153846154	98	0.12928759894459102	G	0.013	-1.630591	0.00813	0.631412	0.13	ENSG00000124541	ENST00000244496	T	0.48201	0.82	4.82	-2.4	0.06583	.	1.291000	0.04995	N	0.468096	T	0.07052	0.0179	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11991	-1.0565	9	0.20046	T	0.44	.	1.8773	0.03221	0.2792:0.3881:0.201:0.1316	rs3749903;rs52827172;rs58983673;rs3749903	78	Q96EU6	RRP36_HUMAN	G	78	ENSP00000244496:A78G	ENSP00000244496:A78G	A	+	2	0	RRP36	43100803	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.006000	0.13152	-0.500000	0.06614	-1.130000	0.01982	GCT	C|0.705;G|0.295	0.295	strong		0.433	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
IL4R	3566	hgsc.bcm.edu	37	16	27373964	27373964	+	Missense_Mutation	SNP	T	T	C	rs1805012	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000170630.2_Missense_Mutation_p.C431R|IL4R_ENST00000543915.2_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	63	0	0		WXS	Illumina HiSeq	Phase_I	71	25	0.352113	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		
OBSL1	23363	hgsc.bcm.edu	37	2	220420785	220420785	+	Silent	SNP	G	G	A	rs3087971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220420785G>A	ENST00000404537.1	-	14	4622	c.4566C>T	c.(4564-4566)tgC>tgT	p.C1522C	OBSL1_ENST00000603926.1_Silent_p.C1522C|OBSL1_ENST00000265318.4_Missense_Mutation_p.A1389V|OBSL1_ENST00000373876.1_Silent_p.C1430C|OBSL1_ENST00000265317.5_Silent_p.C421C	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1522	Ig-like 12.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGTGGCTCTCGCAGCCGTAGG	0.632													G|||	1148	0.229233	0.2224	0.2983	5008	,	,		15387	0.2837		0.2734	False		,,,				2504	0.0879				p.C1522C		Atlas-SNP	.											.	OBSL1	120	.	0			c.C4566T						PASS	.	G	,	944,3286		124,696,1295	41.0	45.0	43.0		4566,4566	-6.8	0.7	2	dbSNP_102	43	2355,6105		334,1687,2209	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	458,2383,3504	AA,AG,GG		27.8369,22.3168,25.9968	,	1522/1544,1522/1897	220420785	3299,9391	2115	4230	6345	SO:0001819	synonymous_variant	23363	exon14			GCTCTCGCAGCCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4566C>T	2.37:g.220420785G>A		Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	286	136	0.475524	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1	576	0.26373626373626374	93	0.18902439024390244	104	0.287292817679558	171	0.29895104895104896	208	0.27440633245382584	G	1.900	-0.453356	0.04540	0.223168	0.278369	ENSG00000124006	ENST00000265318;ENST00000456147	T	0.56941	0.43	4.39	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42041	P	0.008920999999999957	.	.	.	.	.	.	T	0.39860	-0.9593	5	0.87932	D	0	.	14.8475	0.70270	0.569:0.0:0.431:0.0	rs3087971	.	.	.	V	1389;424	ENSP00000265318:A1389V	ENSP00000265318:A1389V	A	-	2	0	OBSL1	220129029	0.000000	0.05858	0.679000	0.29978	0.262000	0.26303	-2.148000	0.01292	-1.935000	0.01049	-0.458000	0.05436	GCG	G|0.730;A|0.270	0.270	strong		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
PKDREJ	10343	hgsc.bcm.edu	37	22	46656479	46656479	+	Missense_Mutation	SNP	A	A	G	rs6519993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46656479A>G	ENST00000253255.5	-	1	2740	c.2741T>C	c.(2740-2742)cTc>cCc	p.L914P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	914			L -> P (in dbSNP:rs6519993).		acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CCAAGGAAAGAGGTCATTTGT	0.418													G|||	1229	0.245407	0.6785	0.134	5008	,	,		22048	0.001		0.16	False		,,,				2504	0.0787				p.L914P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2741C						PASS	.	G	PRO/LEU	2650,1756	517.3+/-369.4	793,1064,346	106.0	111.0	109.0		2741	5.3	1.0	22	dbSNP_116	109	1256,7344	758.5+/-407.5	88,1080,3132	yes	missense	PKDREJ	NM_006071.1	98	881,2144,3478	GG,GA,AA		14.6047,39.8547,30.0323	benign	914/2254	46656479	3906,9100	2203	4300	6503	SO:0001583	missense	10343	exon1			GGAAAGAGGTCAT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2741T>C	22.37:g.46656479A>G	ENSP00000253255:p.Leu914Pro	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	477	0.2184065934065934	309	0.6280487804878049	55	0.15193370165745856	0	0.0	113	0.14907651715039577	G	1.467	-0.560725	0.03939	0.601453	0.146047	ENSG00000130943	ENST00000253255	T	0.30714	1.52	5.33	5.33	0.75918	.	0.307994	0.28398	N	0.015492	T	0.00012	0.0000	N	0.00392	-1.555	0.30026	P	0.813909	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	-28.6325	13.3236	0.60447	0.0774:0.0:0.9226:0.0	rs6519993;rs52835982;rs61529203;rs6519993	914	Q9NTG1	PKDRE_HUMAN	P	914	ENSP00000253255:L914P	ENSP00000253255:L914P	L	-	2	0	PKDREJ	45035143	1.000000	0.71417	0.965000	0.40720	0.372000	0.29890	4.073000	0.57570	1.411000	0.46957	-0.119000	0.15052	CTC	A|0.724;G|0.276	0.276	strong		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
MUC16	94025	hgsc.bcm.edu	37	19	9026257	9026257	+	Silent	SNP	G	G	A	rs62118274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9026257G>A	ENST00000397910.4	-	14	36932	c.36729C>T	c.(36727-36729)taC>taT	p.Y12243Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12245	SEA 2. {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						TGTCCTCCTCGTACTGCAGGT	0.537													A|||	597	0.119209	0.2088	0.0692	5008	,	,		20456	0.1617		0.0457	False		,,,				2504	0.0654				p.Y12243Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C36729T						PASS	.	G		729,3403		67,595,1404	240.0	217.0	224.0		36729	-4.6	0.0	19	dbSNP_129	224	335,8079		4,327,3876	no	coding-synonymous	MUC16	NM_024690.2		71,922,5280	AA,AG,GG		3.9815,17.6428,8.4808		12243/14508	9026257	1064,11482	2066	4207	6273	SO:0001819	synonymous_variant	94025	exon14			CTCCTCGTACTGC	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.36729C>T	19.37:g.9026257G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.902;A|0.098	0.098	strong		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ATP1B2	482	hgsc.bcm.edu	37	17	7557419	7557419	+	Silent	SNP	A	A	G	rs1642763	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7557419A>G	ENST00000250111.4	+	4	803	c.396A>G	c.(394-396)ggA>ggG	p.G132G		NM_001678.3	NP_001669.3	P14415	AT1B2_HUMAN	ATPase, Na+/K+ transporting, beta 2 polypeptide	132					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.0?(2)|p.?(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|pancreas(1)	10		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)		GCCGCCCTGGACGCTATTACG	0.547													G|||	3956	0.789936	0.9183	0.8084	5008	,	,		19189	0.6687		0.7843	False		,,,				2504	0.7342				p.G132G		Atlas-SNP	.											.	ATP1B2	24	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|bone(1)	c.A396G						PASS	.	G		3830,576	255.2+/-260.5	1671,488,44	162.0	161.0	162.0		396	-1.2	1.0	17	dbSNP_89	162	6582,2018	353.5+/-329.1	2513,1556,231	yes	coding-synonymous	ATP1B2	NM_001678.3		4184,2044,275	GG,GA,AA		23.4651,13.0731,19.9446		132/291	7557419	10412,2594	2203	4300	6503	SO:0001819	synonymous_variant	482	exon4			CCCTGGACGCTAT	U45945	CCDS32550.1	17p13.1	2012-10-22			ENSG00000129244	ENSG00000129244	3.6.3.9	"""ATPases / P-type"""	805	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit beta-2"", ""sodium pump subunit beta-2"", ""sodium-potassium ATPase subunit beta 2 (non-catalytic)"""	182331				1699290	Standard	NM_001678		Approved	AMOG	uc002gif.1	P14415		ENST00000250111.4:c.396A>G	17.37:g.7557419A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001678	A0AV17|A8K278|D3DTQ2|O60444	Silent	SNP	ENST00000250111.4	37	CCDS32550.1																																																																																			A|0.209;C|0.004	.	strong		0.547	ATP1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440234.1	NM_001678	
TECPR1	25851	hgsc.bcm.edu	37	7	97852399	97852399	+	Missense_Mutation	SNP	G	G	A	rs11762014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:97852399G>A	ENST00000447648.2	-	21	3130	c.2831C>T	c.(2830-2832)cCg>cTg	p.P944L	TECPR1_ENST00000379795.3_Missense_Mutation_p.P946L|TECPR1_ENST00000479975.1_5'UTR			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	75	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	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	
ASTE1	28990	hgsc.bcm.edu	37	3	130743812	130743812	+	Silent	SNP	G	G	A	rs35558913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:130743812G>A	ENST00000264992.3	-	3	780	c.339C>T	c.(337-339)taC>taT	p.Y113Y	NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000510769.1_5'Flank|ASTE1_ENST00000514044.1_Silent_p.Y113Y|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000412440.2_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	113					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						AGGGACATACGTACCCACTCC	0.443													A|||	834	0.166534	0.1157	0.1369	5008	,	,		19760	0.131		0.2197	False		,,,				2504	0.2382				p.Y113Y		Atlas-SNP	.											.	ASTE1	67	.	0			c.C339T						PASS	.	A		627,3779	767.6+/-413.5	40,547,1616	113.0	106.0	108.0		339	2.9	0.5	3	dbSNP_126	108	1854,6746	730.0+/-406.7	195,1464,2641	no	coding-synonymous	ASTE1	NM_014065.2		235,2011,4257	AA,AG,GG		21.5581,14.2306,19.0758		113/680	130743812	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	28990	exon3			ACATACGTACCCA	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.339C>T	3.37:g.130743812G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	125	78	0.624	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Silent	SNP	ENST00000264992.3	37	CCDS3068.1																																																																																			G|0.817;A|0.183	0.183	strong		0.443	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065	
THBS4	7060	hgsc.bcm.edu	37	5	79351852	79351852	+	Silent	SNP	A	A	T	rs71594659|rs438042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79351852A>T	ENST00000350881.2	+	3	727	c.537A>T	c.(535-537)ccA>ccT	p.P179P	THBS4_ENST00000511733.1_Silent_p.P88P|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	179	Laminin G-like.				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)	p.P179P(1)		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)		AGAGGAAGCCACAGGTAGGAA	0.537													A|||	2852	0.569489	0.6536	0.5476	5008	,	,		17271	0.5139		0.5527	False		,,,				2504	0.546				p.P179P		Atlas-SNP	.											THBS4,NS,carcinoma,0,1	THBS4	82	1	1	Substitution - coding silent(1)	stomach(1)	c.A537T						PASS	.	A		2744,1660		894,956,352	20.0	24.0	23.0		537	-3.2	1.0	5	dbSNP_80	23	4236,4362		1063,2110,1126	no	coding-synonymous	THBS4	NM_003248.4		1957,3066,1478	TT,TA,AA		49.2673,37.693,46.316		179/962	79351852	6980,6022	2202	4299	6501	SO:0001819	synonymous_variant	7060	exon3			GAAGCCACAGGTA		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.537A>T	5.37:g.79351852A>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	28	0.341463	NM_003248	B2R909|Q86TG2	Silent	SNP	ENST00000350881.2	37	CCDS4049.1																																																																																			ACAGGTAGG|0.500;TCAGGTAAA|0.500	.	alt		0.537	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
LRIT2	340745	hgsc.bcm.edu	37	10	85984323	85984323	+	Missense_Mutation	SNP	G	G	A	rs11200925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85984323G>A	ENST00000372113.4	-	2	663	c.658C>T	c.(658-660)Ctc>Ttc	p.L220F	LRIT2_ENST00000538192.1_Missense_Mutation_p.L220F	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	220	LRRCT.		L -> F (in dbSNP:rs11200925).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						ATGACTGGGAGGGTAATGGAC	0.542													G|||	936	0.186901	0.0522	0.232	5008	,	,		21650	0.2907		0.2346	False		,,,				2504	0.181				p.L220F		Atlas-SNP	.											.	LRIT2	81	.	0			c.C658T						PASS	.	G	PHE/LEU	379,4027	193.3+/-218.5	11,357,1835	77.0	78.0	78.0		658	-0.1	0.0	10	dbSNP_120	78	1933,6667	340.4+/-323.6	197,1539,2564	yes	missense	LRIT2	NM_001017924.2	22	208,1896,4399	AA,AG,GG		22.4767,8.6019,17.7764	possibly-damaging	220/551	85984323	2312,10694	2203	4300	6503	SO:0001583	missense	340745	exon2			CTGGGAGGGTAAT		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.658C>T	10.37:g.85984323G>A	ENSP00000361185:p.Leu220Phe	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	432	0.1978021978021978	34	0.06910569105691057	93	0.2569060773480663	141	0.2465034965034965	164	0.21635883905013192	G	12.48	1.949383	0.34377	0.086019	0.224767	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.54071	0.59;0.59	6.17	-0.0674	0.13760	Cysteine-rich flanking region, C-terminal (1);	0.270193	0.42964	N	0.000636	T	0.00012	0.0000	L	0.48642	1.525	0.58432	P	1.999999999946489E-6	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.001	T	0.11991	-1.0565	9	0.37606	T	0.19	.	2.747	0.05270	0.2534:0.1091:0.5163:0.1211	rs11200925;rs17339092;rs52812362;rs57406188;rs11200925	220;220	B7ZME6;A6NDA9	.;LRIT2_HUMAN	F	220	ENSP00000361185:L220F;ENSP00000438264:L220F	ENSP00000361185:L220F	L	-	1	0	LRIT2	85974303	1.000000	0.71417	0.000000	0.03702	0.991000	0.79684	4.488000	0.60300	-0.264000	0.09365	0.655000	0.94253	CTC	G|0.817;A|0.183	0.183	strong		0.542	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
CALCOCO1	57658	hgsc.bcm.edu	37	12	54110197	54110197	+	Silent	SNP	A	A	G	rs2277369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:54110197A>G	ENST00000550804.1	-	8	912	c.852T>C	c.(850-852)gcT>gcC	p.A284A	CALCOCO1_ENST00000548263.1_Silent_p.A284A|CALCOCO1_ENST00000262059.4_Silent_p.A284A|CALCOCO1_ENST00000430117.2_Intron			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	284					intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						CTTGGAGCTCAGCCTGAGGGA	0.537													A|||	541	0.108027	0.0098	0.1239	5008	,	,		20669	0.2966		0.0239	False		,,,				2504	0.1217				p.A284A		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.T852C						PASS	.	A	,	47,4359	47.5+/-82.1	0,47,2156	71.0	59.0	63.0		,852	1.8	1.0	12	dbSNP_100	63	176,8424	80.1+/-142.7	0,176,4124	no	intron,coding-synonymous	CALCOCO1	NM_001143682.1,NM_020898.2	,	0,223,6280	GG,GA,AA		2.0465,1.0667,1.7146	,	,284/692	54110197	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	57658	exon8			GAGCTCAGCCTGA	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"""coiled-coil leucine zipper coactivator 1"", ""inorganic pyrophosphatase activator"""					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.852T>C	12.37:g.54110197A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Silent	SNP	ENST00000550804.1	37	CCDS8864.1																																																																																			A|0.937;G|0.063	0.063	strong		0.537	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898	
ZNF350	59348	hgsc.bcm.edu	37	19	52472295	52472295	+	Silent	SNP	A	A	G	rs4986773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52472295A>G	ENST00000243644.4	-	3	332	c.105T>C	c.(103-105)gaT>gaC	p.D35D	ZNF350_ENST00000600703.1_5'UTR|HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	35	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)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		CCAACATCACATCCCGGTACA	0.547													G|||	2293	0.457867	0.6762	0.3012	5008	,	,		15686	0.2966		0.2962	False		,,,				2504	0.6063				p.D35D		Atlas-SNP	.											.	ZNF350	48	.	0			c.T105C						PASS	.	G		2752,1654	506.2+/-366.3	855,1042,306	196.0	174.0	182.0		105	-6.9	0.2	19	dbSNP_111	182	2278,6322	707.5+/-405.6	298,1682,2320	no	coding-synonymous	ZNF350	NM_021632.3		1153,2724,2626	GG,GA,AA		26.4884,37.5397,38.6745		35/533	52472295	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	59348	exon3			CATCACATCCCGG	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.105T>C	19.37:g.52472295A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	37	CCDS12845.1																																																																																			A|0.608;G|0.392	0.392	strong		0.547	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
C5orf45	51149	hgsc.bcm.edu	37	5	179269011	179269011	+	Silent	SNP	G	G	C	rs61736195	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:179269011G>C	ENST00000292586.6	-	5	435	c.345C>G	c.(343-345)tcC>tcG	p.S115S	C5orf45_ENST00000376931.2_Silent_p.S60S|C5orf45_ENST00000403396.2_Silent_p.S157S|C5orf45_ENST00000523084.1_5'UTR|C5orf45_ENST00000518235.1_Silent_p.S115S|C5orf45_ENST00000518219.1_Silent_p.S115S|C5orf45_ENST00000523267.1_5'UTR|C5orf45_ENST00000521333.1_Intron|C5orf45_ENST00000520698.1_Silent_p.S60S	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	115										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						CCAGTTCTTGGGAGTCCTTTT	0.498													G|||	78	0.0155751	0.0408	0.0058	5008	,	,		19451	0.0		0.0129	False		,,,				2504	0.0072				p.S115S		Atlas-SNP	.											.	C5orf45	23	.	0			c.C345G						PASS	.	G	,	142,4264	98.9+/-137.6	2,138,2063	264.0	283.0	277.0		180,345	-1.4	0.0	5	dbSNP_129	277	90,8510	51.5+/-111.7	0,90,4210	no	coding-synonymous,coding-synonymous	C5orf45	NM_001017987.2,NM_016175.3	,	2,228,6273	CC,CG,GG		1.0465,3.2229,1.7838	,	60/289,115/344	179269011	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	51149	exon5			TTCTTGGGAGTCC		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.345C>G	5.37:g.179269011G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Silent	SNP	ENST00000292586.6	37	CCDS34319.1																																																																																			G|0.974;C|0.026	0.026	strong		0.498	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
CRTAM	56253	hgsc.bcm.edu	37	11	122742050	122742050	+	Silent	SNP	T	T	C	rs34242434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	130	0	0		WXS	Illumina HiSeq	Phase_I	154	83	0.538961	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	
POMT1	10585	hgsc.bcm.edu	37	9	134386781	134386781	+	Missense_Mutation	SNP	G	G	A	rs4740164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134386781G>A	ENST00000372228.3	+	10	1158	c.979G>A	c.(979-981)Gtc>Atc	p.V327I	POMT1_ENST00000404875.2_Missense_Mutation_p.V188I|POMT1_ENST00000402686.3_Missense_Mutation_p.V305I|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000541219.1_Missense_Mutation_p.V83I|POMT1_ENST00000354713.4_Missense_Mutation_p.V275I|POMT1_ENST00000341012.7_Missense_Mutation_p.V251I|POMT1_ENST00000419118.2_Missense_Mutation_p.V153I|POMT1_ENST00000423007.1_Missense_Mutation_p.V305I	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	327	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.		V -> I (in dbSNP:rs4740164).		carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		TGGGTCCCAGGTCACTCTGAG	0.522													G|||	263	0.052516	0.0091	0.1398	5008	,	,		19380	0.0704		0.0577	False		,,,				2504	0.0256				p.V327I		Atlas-SNP	.											.	POMT1	59	.	0			c.G979A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	92,4314	75.7+/-113.9	2,88,2113	127.0	110.0	116.0		913,751,913,562,979	3.3	1.0	9	dbSNP_111	116	399,8201	128.0+/-186.3	11,377,3912	yes	missense,missense,missense,missense,missense	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	29,29,29,29,29	13,465,6025	AA,AG,GG		4.6395,2.0881,3.7752	benign,benign,benign,benign,benign	305/726,251/672,305/726,188/609,327/748	134386781	491,12515	2203	4300	6503	SO:0001583	missense	10585	exon10			TCCCAGGTCACTC	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.979G>A	9.37:g.134386781G>A	ENSP00000361302:p.Val327Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Missense_Mutation	SNP	ENST00000372228.3	37	CCDS6943.1	134|134	0.06135531135531135|0.06135531135531135	6|6	0.012195121951219513|0.012195121951219513	40|40	0.11049723756906077|0.11049723756906077	45|45	0.07867132867132867|0.07867132867132867	43|43	0.05672823218997362|0.05672823218997362	G|G	6.330|6.330	0.428917|0.428917	0.11987|0.11987	0.020881|0.020881	0.046395|0.046395	ENSG00000130714|ENSG00000130714	ENST00000372221;ENST00000415075|ENST00000423007;ENST00000404875;ENST00000341012;ENST00000441334;ENST00000372228;ENST00000402686;ENST00000419118;ENST00000541219;ENST00000354713	D|D;D;D;D;D;D;D;D;D	0.90676|0.84800	-2.71|-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9;-1.9	5.37|5.37	3.28|3.28	0.37604|0.37604	.|MIR motif (2);MIR (1);	.|0.170150	.|0.51477	.|N	.|0.000098	T|T	0.02193|0.02193	0.0068|0.0068	N|N	0.05124|0.05124	-0.11|-0.11	0.42656|0.42656	D|D	0.993469|0.993469	.|B;B;B;B;B	.|0.18013	.|0.0;0.001;0.001;0.025;0.003	.|B;B;B;B;B	.|0.18561	.|0.003;0.007;0.007;0.022;0.014	T|T	0.28744|0.28744	-1.0034|-1.0034	7|10	0.36615|0.02654	T|T	0.2|1	-29.4106|-29.4106	4.3415|4.3415	0.11112|0.11112	0.4331:0.0:0.5669:0.0|0.4331:0.0:0.5669:0.0	rs4740164;rs52828463;rs4740164|rs4740164;rs52828463;rs4740164	.|30;275;83;327;305	.|B4DU61;B4DTW4;B4DI80;Q9Y6A1;Q9Y6A1-2	.|.;.;.;POMT1_HUMAN;.	D|I	102|305;188;251;210;327;305;153;83;275	ENSP00000405149:G102D|ENSP00000404119:V305I;ENSP00000384531:V188I;ENSP00000343034:V251I;ENSP00000395060:V210I;ENSP00000361302:V327I;ENSP00000385797:V305I;ENSP00000403032:V153I;ENSP00000440895:V83I;ENSP00000346748:V275I	ENSP00000361295:G102D|ENSP00000343034:V251I	G|V	+|+	2|1	0|0	POMT1|POMT1	133376602|133376602	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	4.817000|4.817000	0.62650|0.62650	1.258000|1.258000	0.44101|0.44101	0.563000|0.563000	0.77884|0.77884	GGT|GTC	G|0.954;A|0.046	0.046	strong		0.522	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
SLC4A7	9497	hgsc.bcm.edu	37	3	27478899	27478899	+	Silent	SNP	A	A	G	rs2029618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:27478899A>G	ENST00000295736.5	-	4	451	c.381T>C	c.(379-381)taT>taC	p.Y127Y	SLC4A7_ENST00000428386.1_Silent_p.Y127Y|SLC4A7_ENST00000440156.1_Silent_p.Y136Y|SLC4A7_ENST00000425128.2_Silent_p.Y132Y|SLC4A7_ENST00000437179.1_Silent_p.Y132Y|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000446700.1_Silent_p.Y132Y|SLC4A7_ENST00000454389.1_Silent_p.Y136Y|SLC4A7_ENST00000455077.1_Silent_p.Y132Y|SLC4A7_ENST00000445684.1_Silent_p.Y136Y|SLC4A7_ENST00000435667.2_Silent_p.Y136Y	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	127					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)	CTTTCCATTCATATTCTTCTC	0.398													A|||	520	0.103834	0.1543	0.1081	5008	,	,		16933	0.0446		0.1531	False		,,,				2504	0.0429				p.Y132Y		Atlas-SNP	.											.	SLC4A7	119	.	0			c.T396C						PASS	.	A		664,3742	280.2+/-275.2	44,576,1583	164.0	163.0	163.0		381	-2.6	0.9	3	dbSNP_94	163	1241,7359	249.3+/-276.6	93,1055,3152	no	coding-synonymous	SLC4A7	NM_003615.3		137,1631,4735	GG,GA,AA		14.4302,15.0704,14.6471		127/1215	27478899	1905,11101	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon4			CCATTCATATTCT	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.381T>C	3.37:g.27478899A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			A|0.867;G|0.133	0.133	strong		0.398	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
CELSR1	9620	hgsc.bcm.edu	37	22	46787697	46787697	+	Missense_Mutation	SNP	A	A	G	rs6008795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46787697A>G	ENST00000262738.3	-	15	5980	c.5981T>C	c.(5980-5982)cTc>cCc	p.L1994P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1994	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		L -> P (in dbSNP:rs6008795).		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)		CTGGGCTAGGAGCTTGTAGTA	0.637													G|||	996	0.198882	0.475	0.1153	5008	,	,		16332	0.001		0.159	False		,,,				2504	0.1299				p.L1994P		Atlas-SNP	.											.	CELSR1	242	.	0			c.T5981C						PASS	.	G	PRO/LEU	1735,2669		364,1007,831	26.0	34.0	31.0		5981	3.5	1.0	22	dbSNP_114	31	1185,7415		75,1035,3190	yes	missense	CELSR1	NM_014246.1	98	439,2042,4021	GG,GA,AA		13.7791,39.396,22.4546	benign	1994/3015	46787697	2920,10084	2202	4300	6502	SO:0001583	missense	9620	exon15			GCTAGGAGCTTGT	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.5981T>C	22.37:g.46787697A>G	ENSP00000262738:p.Leu1994Pro	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	387	0.1771978021978022	225	0.4573170731707317	43	0.11878453038674033	1	0.0017482517482517483	118	0.15567282321899736	G	0.012	-1.661256	0.00772	0.39396	0.137791	ENSG00000075275	ENST00000262738	T	0.70399	-0.48	4.52	3.5	0.40072	.	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00256	-1.76	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42292	-0.9460	9	0.02654	T	1	.	10.5204	0.44916	0.1619:0.0:0.8381:0.0	rs6008795;rs7290902;rs61043581;rs6008795	315;1994	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	1994	ENSP00000262738:L1994P	ENSP00000262738:L1994P	L	-	2	0	CELSR1	45166361	1.000000	0.71417	0.978000	0.43139	0.018000	0.09664	6.135000	0.71696	0.379000	0.24794	-0.355000	0.07637	CTC	A|0.783;G|0.217	0.217	strong		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
NFYC	4802	hgsc.bcm.edu	37	1	41232588	41232588	+	Splice_Site	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41232588A>G	ENST00000308733.5	+	8	834		c.e8-1		NFYC_ENST00000372651.1_Intron|NFYC_ENST00000372653.1_Intron|NFYC_ENST00000456393.2_Intron|NFYC_ENST00000425457.2_Splice_Site|NFYC_ENST00000372654.1_Intron|NFYC_ENST00000483091.1_Splice_Site|NFYC_ENST00000427410.2_Intron|NFYC_ENST00000372652.1_Intron|NFYC_ENST00000447388.3_Intron|NFYC_ENST00000440226.3_Intron			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma						cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			CTTGTTCTCAAGGGGCAAAGA	0.498																																					.		Atlas-SNP	.											.	NFYC	39	.	0			c.829-2A>G						PASS	.						85.0	83.0	84.0					1																	41232588		692	1591	2283	SO:0001630	splice_region_variant	4802	exon9			TTCTCAAGGGGCA	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.829-1A>G	1.37:g.41232588A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	5	0.0724638	NM_001142588	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Splice_Site	SNP	ENST00000308733.5	37		.	.	.	.	.	.	.	.	.	.	A	7.622	0.677071	0.14841	.	.	ENSG00000066136	ENST00000425457;ENST00000308733	.	.	.	5.43	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.21355	N	0.999718	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7246	0.23348	0.7231:0.0:0.2769:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NFYC	41005175	0.005000	0.15991	0.003000	0.11579	0.043000	0.13939	0.938000	0.28965	0.077000	0.16863	0.379000	0.24179	.	.	.	none		0.498	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223	Intron
NUDT9	53343	hgsc.bcm.edu	37	4	88344154	88344154	+	Missense_Mutation	SNP	C	C	A	rs146952902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88344154C>A	ENST00000302174.4	+	1	421	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	33					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CCGCGGCATCCAGGCGTTCAG	0.592													C|||	11	0.00219649	0.0	0.0014	5008	,	,		15253	0.0		0.006	False		,,,				2504	0.0041				p.Q33K		Atlas-SNP	.											.	NUDT9	21	.	0			c.C97A						PASS	.	C	LYS/GLN,	5,4401	9.9+/-24.2	0,5,2198	57.0	57.0	57.0		97,	2.7	0.0	4	dbSNP_134	57	32,8568	22.2+/-67.0	0,32,4268	yes	missense,intron	NUDT9	NM_024047.3,NM_198038.1	53,	0,37,6466	AA,AC,CC		0.3721,0.1135,0.2845	benign,	33/351,	88344154	37,12969	2203	4300	6503	SO:0001583	missense	53343	exon1			GGCATCCAGGCGT	AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"""Nudix motif containing"""	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.97C>A	4.37:g.88344154C>A	ENSP00000303575:p.Gln33Lys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000302174.4	37	CCDS3620.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	9.675	1.147631	0.21288	0.001135	0.003721	ENSG00000170502	ENST00000302174;ENST00000440591	T;T	0.75589	-0.95;2.6	3.56	2.71	0.32032	.	0.536650	0.17871	N	0.159179	T	0.44498	0.1296	N	0.08118	0	0.21897	N	0.99949	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44726	-0.9309	10	0.51188	T	0.08	0.1088	9.1276	0.36826	0.0:0.7534:0.2466:0.0	.	33;33	Q96KB3;Q9BW91	.;NUDT9_HUMAN	K	33	ENSP00000303575:Q33K;ENSP00000410270:Q33K	ENSP00000303575:Q33K	Q	+	1	0	NUDT9	88563178	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	0.585000	0.23879	1.048000	0.40298	0.484000	0.47621	CAG	C|0.997;A|0.003	0.003	strong		0.592	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2		
OVGP1	5016	hgsc.bcm.edu	37	1	111957592	111957592	+	Missense_Mutation	SNP	A	A	G	rs56294468|rs376377993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	124	2	0.016129		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	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	
RBFA	79863	hgsc.bcm.edu	37	18	77805856	77805856	+	Missense_Mutation	SNP	A	A	C	rs3744872	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:77805856A>C	ENST00000306735.5	+	7	871	c.733A>C	c.(733-735)Aac>Cac	p.N245H	RBFA_ENST00000262197.7_Silent_p.S216S|RP11-795F19.5_ENST00000564012.1_Intron|RP11-795F19.5_ENST00000569722.1_Intron	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	245			N -> H (in dbSNP:rs3744872). {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						TGAGGCGCTCAACAAGCAGAT	0.577													A|||	1952	0.389776	0.2458	0.4697	5008	,	,		19105	0.4821		0.3161	False		,,,				2504	0.5082				p.N245H		Atlas-SNP	.											.	RBFA	27	.	0			c.A733C						PASS	.	A	,HIS/ASN	1012,3394	370.3+/-319.5	124,764,1315	66.0	74.0	71.0		648,733	2.1	1.0	18	dbSNP_107	71	2528,6072	410.2+/-350.1	368,1792,2140	yes	coding-synonymous,missense	RBFA	NM_001171967.1,NM_024805.2	,68	492,2556,3455	CC,CA,AA		29.3953,22.9687,27.2182	,possibly-damaging	216/243,245/344	77805856	3540,9466	2203	4300	6503	SO:0001583	missense	79863	exon7			GCGCTCAACAAGC	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.733A>C	18.37:g.77805856A>C	ENSP00000305696:p.Asn245His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	63	0.605769	NM_024805	Q6PF07|Q8WZ65|Q9H776	Missense_Mutation	SNP	ENST00000306735.5	37	CCDS12021.1	801	0.36675824175824173	140	0.2845528455284553	158	0.43646408839779005	272	0.4755244755244755	231	0.30474934036939316	A	9.760	1.169886	0.21621	0.229687	0.293953	ENSG00000101546	ENST00000306735	T	0.27104	1.69	4.78	2.11	0.27256	.	0.540708	0.18128	N	0.150828	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999114157	P	0.42735	0.788	B	0.37731	0.257	T	0.49263	-0.8958	8	0.40728	T	0.16	-21.9528	10.1421	0.42740	0.6149:0.3851:0.0:0.0	rs3744872;rs17846552;rs17859627;rs59885162;rs3744872	245	Q8N0V3	RBFA_HUMAN	H	245	ENSP00000305696:N245H	ENSP00000305696:N245H	N	+	1	0	RBFA	75906844	1.000000	0.71417	0.983000	0.44433	0.175000	0.22909	1.650000	0.37292	0.741000	0.32674	0.533000	0.62120	AAC	A|0.688;C|0.312	0.312	strong		0.577	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
HLA-A	3105	hgsc.bcm.edu	37	6	29910538	29910538	+	Silent	SNP	C	C	T	rs1136657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910538C>T	ENST00000396634.1	+	4	419	c.78C>T	c.(76-78)tcC>tcT	p.S26S	HLA-A_ENST00000376806.5_Silent_p.S26S|HLA-A_ENST00000376809.5_Silent_p.S26S|HLA-A_ENST00000376802.2_Silent_p.S26S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	26	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCCCAGGCTCCCACTCCATGA	0.721									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.S26S		Atlas-SNP	.											HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	0			c.C78T						PASS	.						13.0	12.0	12.0					6																	29910538		2164	4231	6395	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGCTCCCACTCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.78C>T	6.37:g.29910538C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	55	13	0.236364	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.821;T|0.179	0.179	strong		0.721	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ZNF383	163087	hgsc.bcm.edu	37	19	37733771	37733771	+	Silent	SNP	A	A	C	rs12974332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37733771A>C	ENST00000589413.1	+	8	1216	c.633A>C	c.(631-633)tcA>tcC	p.S211S	ZNF383_ENST00000352998.3_Silent_p.S211S|ZNF383_ENST00000590503.1_Silent_p.S211S			Q8NA42	ZN383_HUMAN	zinc finger protein 383	211					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTTGTGGTTCACATGTTACTC	0.363													A|||	71	0.0141773	0.0008	0.0216	5008	,	,		19729	0.0		0.0487	False		,,,				2504	0.0061				p.S211S		Atlas-SNP	.											.	ZNF383	42	.	0			c.A633C						PASS	.	A		54,4352	53.6+/-89.4	0,54,2149	63.0	66.0	65.0		633	1.6	1.0	19	dbSNP_121	65	448,8152	135.4+/-192.6	20,408,3872	no	coding-synonymous	ZNF383	NM_152604.1		20,462,6021	CC,CA,AA		5.2093,1.2256,3.8598		211/476	37733771	502,12504	2203	4300	6503	SO:0001819	synonymous_variant	163087	exon5			TGGTTCACATGTT	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"""Zinc fingers, C2H2-type"", ""-"""	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.633A>C	19.37:g.37733771A>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_152604	Q6X2C7	Silent	SNP	ENST00000589413.1	37	CCDS12501.1																																																																																			A|0.967;C|0.033	0.033	strong		0.363	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604	
ESYT3	83850	hgsc.bcm.edu	37	3	138191232	138191232	+	Missense_Mutation	SNP	G	G	A	rs10935282	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	31	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	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	
WDFY3	23001	hgsc.bcm.edu	37	4	85612823	85612823	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:85612823T>C	ENST00000295888.4	-	60	9572	c.9165A>G	c.(9163-9165)gcA>gcG	p.A3055A	WDFY3_ENST00000322366.6_Silent_p.A3038A	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3055	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AACTGAGGTCTGCATAGCCCC	0.413																																					p.A3055A		Atlas-SNP	.											.	WDFY3	314	.	0			c.A9165G						PASS	.						121.0	108.0	113.0					4																	85612823		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon60			GAGGTCTGCATAG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9165A>G	4.37:g.85612823T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																			.	.	none		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
ZNF189	7743	hgsc.bcm.edu	37	9	104171523	104171523	+	Silent	SNP	A	A	G	rs45455902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104171523A>G	ENST00000339664.2	+	3	1602	c.1473A>G	c.(1471-1473)aaA>aaG	p.K491K	ZNF189_ENST00000259395.4_Silent_p.K449K|ZNF189_ENST00000374861.3_Silent_p.K477K	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	491					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TCTGTGGGAAAAGCTTCAGCC	0.423													A|||	198	0.0395367	0.0023	0.0634	5008	,	,		19868	0.002		0.0785	False		,,,				2504	0.0716				p.K491K		Atlas-SNP	.											.	ZNF189	79	.	0			c.A1473G						PASS	.	A	,	63,4343	57.4+/-93.9	1,61,2141	88.0	94.0	92.0		1473,1347	4.5	1.0	9	dbSNP_127	92	691,7909	172.3+/-223.0	28,635,3637	yes	coding-synonymous,coding-synonymous	ZNF189	NM_003452.2,NM_197977.1	,	29,696,5778	GG,GA,AA		8.0349,1.4299,5.7973	,	491/627,449/585	104171523	754,12252	2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			TGGGAAAAGCTTC	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.1473A>G	9.37:g.104171523A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			A|0.952;G|0.048	0.048	strong		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
ZNF773	374928	hgsc.bcm.edu	37	19	58017753	58017753	+	Missense_Mutation	SNP	C	C	A	rs201340833|rs61731281|rs386811330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58017753C>A	ENST00000282292.4	+	4	430	c.290C>A	c.(289-291)gCa>gAa	p.A97E	ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.A96E	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)		AAGGCTGAGGCAGCTGCTGAG	0.488													A|||	859	0.171526	0.2716	0.1484	5008	,	,		22832	0.1002		0.2018	False		,,,				2504	0.0951				p.A97E		Atlas-SNP	.											.	ZNF773	62	.	0			c.C290A						PASS	.						84.0	87.0	86.0					19																	58017753		2203	4300	6503	SO:0001583	missense	374928	exon4			CTGAGGCAGCTGC	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.290C>A	19.37:g.58017753C>A	ENSP00000282292:p.Ala97Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.856327	0.00558	.	.	ENSG00000152439	ENST00000282292	T	0.05649	3.41	1.25	1.25	0.21368	.	.	.	.	.	T	0.02929	0.0087	N	0.05280	-0.08	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46789	-0.9166	9	0.28530	T	0.3	.	5.476	0.16695	0.7127:0.2873:0.0:0.0	rs61731281	96;97	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	E	97	ENSP00000282292:A97E	ENSP00000282292:A97E	A	+	2	0	ZNF773	62709565	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.333000	0.19768	0.000000	0.14550	-0.824000	0.03097	GCA	C|0.813;A|0.187	0.187	strong		0.488	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542	
RARS2	57038	hgsc.bcm.edu	37	6	88240570	88240570	+	Missense_Mutation	SNP	C	C	T	rs35862137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88240570C>T	ENST00000369536.5	-	9	748	c.703G>A	c.(703-705)Gtg>Atg	p.V235M		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	235					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)		AGTGCTTGCACATCGCCCAGT	0.423													C|||	103	0.0205671	0.0023	0.0144	5008	,	,		17954	0.0		0.0437	False		,,,				2504	0.047				p.V235M		Atlas-SNP	.											.	RARS2	61	.	0			c.G703A						PASS	.	C	MET/VAL	49,4357	50.9+/-86.3	0,49,2154	197.0	183.0	187.0		703	-5.6	0.0	6	dbSNP_126	187	374,8226	123.1+/-182.0	3,368,3929	yes	missense	RARS2	NM_020320.3	21	3,417,6083	TT,TC,CC		4.3488,1.1121,3.2523	benign	235/579	88240570	423,12583	2203	4300	6503	SO:0001583	missense	57038	exon9			CTTGCACATCGCC	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.703G>A	6.37:g.88240570C>T	ENSP00000358549:p.Val235Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	43	0.019688644688644688	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	35	0.04617414248021108	C	6.736	0.504662	0.12822	0.011121	0.043488	ENSG00000146282	ENST00000369536	T	0.63096	-0.02	6.17	-5.62	0.02481	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	1.575680	0.02623	N	0.103390	T	0.21921	0.0528	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.14023	0.01	T	0.34925	-0.9809	10	0.66056	D	0.02	.	4.7575	0.13092	0.0958:0.4426:0.2598:0.2017	rs35862137	235	Q5T160	SYRM_HUMAN	M	235	ENSP00000358549:V235M	ENSP00000358549:V235M	V	-	1	0	RARS2	88297289	0.000000	0.05858	0.001000	0.08648	0.076000	0.17211	-1.073000	0.03430	-0.377000	0.07930	-0.345000	0.07892	GTG	C|0.973;T|0.027	0.027	strong		0.423	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
ADCY7	113	hgsc.bcm.edu	37	16	50342658	50342658	+	Silent	SNP	C	C	T	rs17289102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:50342658C>T	ENST00000394697.2	+	17	2356	c.2016C>T	c.(2014-2016)gcC>gcT	p.A672A	ADCY7_ENST00000537579.1_3'UTR|ADCY7_ENST00000566433.2_Silent_p.A672A|ADCY7_ENST00000538642.1_Silent_p.A672A|ADCY7_ENST00000254235.3_Silent_p.A672A			P51828	ADCY7_HUMAN	adenylate cyclase 7	672					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 ethanol (GO:0071361)|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)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|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)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TGACCCTGGCCGTCCTGACCA	0.642													C|||	490	0.0978435	0.025	0.1009	5008	,	,		17502	0.0119		0.2515	False		,,,				2504	0.1247				p.A672A		Atlas-SNP	.											ADCY7,NS,carcinoma,0,1	ADCY7	90	1	0			c.C2016T						PASS	.	C		271,4125	152.5+/-186.2	14,243,1941	52.0	49.0	50.0		2016	-5.0	0.0	16	dbSNP_123	50	2215,6385	374.0+/-337.2	276,1663,2361	yes	coding-synonymous	ADCY7	NM_001114.3		290,1906,4302	TT,TC,CC		25.7558,6.1647,19.129		672/1081	50342658	2486,10510	2198	4300	6498	SO:0001819	synonymous_variant	113	exon16			CCTGGCCGTCCTG	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2016C>T	16.37:g.50342658C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|0.842;T|0.158	0.158	strong		0.642	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
MUSK	4593	hgsc.bcm.edu	37	9	113457726	113457726	+	Silent	SNP	G	G	A	rs10980531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:113457726G>A	ENST00000374448.4	+	4	536	c.402G>A	c.(400-402)gaG>gaA	p.E134E	MUSK_ENST00000374440.3_Silent_p.E16E|MUSK_ENST00000374439.1_Silent_p.E16E|MUSK_ENST00000189978.5_Silent_p.E134E|MUSK_ENST00000416899.2_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	82	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	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			
COL5A3	50509	hgsc.bcm.edu	37	19	10085054	10085054	+	Missense_Mutation	SNP	G	G	A	rs3815745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10085054G>A	ENST00000264828.3	-	46	3458	c.3373C>T	c.(3373-3375)Ccc>Tcc	p.P1125S		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1125	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			AGGCCTGGGGGTCCCCGGCGC	0.612													G|||	731	0.145966	0.0688	0.1282	5008	,	,		16599	0.2202		0.2078	False		,,,				2504	0.1227				p.P1125S		Atlas-SNP	.											.	COL5A3	243	.	0			c.C3373T						PASS	.	G	SER/PRO	398,4008	196.4+/-220.7	10,378,1815	41.0	45.0	43.0		3373	4.9	1.0	19	dbSNP_107	43	1949,6651	341.7+/-324.1	210,1529,2561	yes	missense	COL5A3	NM_015719.3	74	220,1907,4376	AA,AG,GG		22.6628,9.0331,18.0455	probably-damaging	1125/1746	10085054	2347,10659	2203	4300	6503	SO:0001583	missense	50509	exon46			CTGGGGGTCCCCG	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3373C>T	19.37:g.10085054G>A	ENSP00000264828:p.Pro1125Ser	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	20	14	0.7	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	395	0.18086080586080586	41	0.08333333333333333	52	0.143646408839779	141	0.2465034965034965	161	0.21240105540897097	G	20.8	4.046628	0.75846	0.090331	0.226628	ENSG00000080573	ENST00000264828	D	0.95756	-3.8	4.89	4.89	0.63831	.	0.082278	0.50627	D	0.000105	T	0.00328	0.0010	L	0.35593	1.075	0.26776	P	0.9697033	D	0.63880	0.993	D	0.67725	0.953	T	0.21381	-1.0247	9	0.12430	T	0.62	.	15.5331	0.75980	0.0:0.0:1.0:0.0	rs3815745	1125	P25940	CO5A3_HUMAN	S	1125	ENSP00000264828:P1125S	ENSP00000264828:P1125S	P	-	1	0	COL5A3	9946054	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	6.794000	0.75135	2.246000	0.74042	0.313000	0.20887	CCC	G|0.822;A|0.178	0.178	strong		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
CARD10	29775	hgsc.bcm.edu	37	22	37900762	37900762	+	Silent	SNP	G	G	A	rs3817805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37900762G>A	ENST00000403299.1	-	9	1614	c.1398C>T	c.(1396-1398)tcC>tcT	p.S466S	CARD10_ENST00000406271.3_Silent_p.S180S|CARD10_ENST00000251973.5_Silent_p.S466S			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	466					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					ACAGGGAATGGGAGGAGGCAC	0.622													G|||	657	0.13119	0.0197	0.1441	5008	,	,		18194	0.2708		0.1064	False		,,,				2504	0.1544				p.S466S		Atlas-SNP	.											.	CARD10	55	.	0			c.C1398T						PASS	.	G		88,4318	70.9+/-108.8	1,86,2116	53.0	40.0	45.0		1398	3.3	1.0	22	dbSNP_107	45	914,7686	200.4+/-244.2	28,858,3414	no	coding-synonymous	CARD10	NM_014550.3		29,944,5530	AA,AG,GG		10.6279,1.9973,7.7041		466/1033	37900762	1002,12004	2203	4300	6503	SO:0001819	synonymous_variant	29775	exon8			GGAATGGGAGGAG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1398C>T	22.37:g.37900762G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			G|0.894;A|0.106	0.106	strong		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
FAM179A	165186	hgsc.bcm.edu	37	2	29225463	29225463	+	Silent	SNP	C	C	T	rs370488483		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29225463C>T	ENST00000379558.4	+	5	840	c.489C>T	c.(487-489)gcC>gcT	p.A163A	FAM179A_ENST00000403861.2_Silent_p.A163A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	163										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						TCCCCCGAGCCACCTCTCAGA	0.632																																					p.A163A		Atlas-SNP	.											.	FAM179A	106	.	0			c.C489T						PASS	.	C		1,3891		0,1,1945	23.0	28.0	27.0		489	-0.5	0.1	2		27	7,8255		0,7,4124	no	coding-synonymous	FAM179A	NM_199280.2		0,8,6069	TT,TC,CC		0.0847,0.0257,0.0658		163/1020	29225463	8,12146	1946	4131	6077	SO:0001819	synonymous_variant	165186	exon5			CCGAGCCACCTCT	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.489C>T	2.37:g.29225463C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			.	.	weak		0.632	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
MST1L	11223	hgsc.bcm.edu	37	1	17084152	17084152	+	RNA	SNP	C	C	T	rs202123117	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17084152C>T	ENST00000455405.2	-	0	560							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										ATTACCCGTACCTGCAGTGAG	0.562													.|||	138	0.0275559	0.0023	0.0288	5008	,	,		80178	0.0159		0.0517	False		,,,				2504	0.0481				p.G590D		Atlas-SNP	.											Q13209_HUMAN,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.G1769A						scavenged	.																																					11223	exon14			CCCGTACCTGCAG	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.17084152C>T		Somatic	747	1	0.00133869		WXS	Illumina HiSeq	Phase_I	1073	103	0.0959925	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	10.17	1.277638	0.23307	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.335271	0.21488	N	0.073725	T	0.63581	0.2523	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.67150	-0.5743	6	0.36615	T	0.2	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	.	590;616	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	D	590;616	.	ENSP00000439273:G590D	G	-	2	0	MST1P9	16956739	0.996000	0.38824	0.190000	0.23270	0.000000	0.00434	2.021000	0.41020	0.502000	0.28037	0.000000	0.15137	GGT	C|0.973;T|0.027	0.027	strong		0.562	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
MYOM3	127294	hgsc.bcm.edu	37	1	24409191	24409191	+	Missense_Mutation	SNP	C	C	T	rs4320729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24409191C>T	ENST00000374434.3	-	17	2146	c.1984G>A	c.(1984-1986)Ggg>Agg	p.G662R	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Missense_Mutation_p.G662R|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.G663R	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	662	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> R (in dbSNP:rs4320729). {ECO:0000269|PubMed:14702039, 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)		GTCCTCAGCCCGGGAACTGTA	0.537													C|||	1286	0.256789	0.0159	0.3213	5008	,	,		20504	0.4266		0.4364	False		,,,				2504	0.1769				p.G662R		Atlas-SNP	.											.	MYOM3	131	.	0			c.G1984A						PASS	.	C	ARG/GLY	335,3707		19,297,1705	54.0	57.0	56.0		1984	5.4	0.9	1	dbSNP_111	56	3520,4872		728,2064,1404	yes	missense	MYOM3	NM_152372.3	125	747,2361,3109	TT,TC,CC		41.9447,8.288,31.0037	probably-damaging	662/1438	24409191	3855,8579	2021	4196	6217	SO:0001583	missense	127294	exon17			TCAGCCCGGGAAC	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.1984G>A	1.37:g.24409191C>T	ENSP00000363557:p.Gly662Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	706	0.3232600732600733	10	0.02032520325203252	108	0.2983425414364641	248	0.43356643356643354	340	0.44854881266490765	C	18.80	3.701981	0.68501	0.08288	0.419447	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.61980	0.06;0.06;0.06	5.41	5.41	0.78517	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.104378	0.64402	D	0.000003	T	0.00012	0.0000	M	0.78801	2.425	0.21782	P	0.999544475	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.21314	-1.0249	9	0.62326	D	0.03	.	19.1966	0.93691	0.0:1.0:0.0:0.0	rs4320729;rs52799837;rs57980115;rs4320729	662;662	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	R	662;663;662	ENSP00000363557:G662R;ENSP00000332670:G663R;ENSP00000328415:G662R	ENSP00000328415:G662R	G	-	1	0	MYOM3	24281778	1.000000	0.71417	0.922000	0.36590	0.308000	0.27856	5.783000	0.68982	2.546000	0.85860	0.557000	0.71058	GGG	C|0.679;T|0.321	0.321	strong		0.537	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
KRT73	319101	hgsc.bcm.edu	37	12	53010024	53010024	+	Silent	SNP	C	C	T	rs61736101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53010024C>T	ENST00000305748.3	-	2	622	c.588G>A	c.(586-588)acG>acA	p.T196T	RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	196	Coil 1B.|Rod.					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)		CCCCAGACAGCGTCTCCAGCT	0.602													C|||	423	0.0844649	0.208	0.0605	5008	,	,		21505	0.0288		0.0477	False		,,,				2504	0.0297				p.T196T		Atlas-SNP	.											KRT73,NS,malignant_melanoma,-1,3	KRT73	101	3	0			c.G588A						PASS	.	C		756,3650	308.6+/-290.6	59,638,1506	177.0	159.0	165.0		588	-3.0	0.3	12	dbSNP_129	165	418,8182	130.7+/-188.6	11,396,3893	no	coding-synonymous	KRT73	NM_175068.2		70,1034,5399	TT,TC,CC		4.8605,17.1584,9.0266		196/541	53010024	1174,11832	2203	4300	6503	SO:0001819	synonymous_variant	319101	exon2			AGACAGCGTCTCC	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.588G>A	12.37:g.53010024C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_175068	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																			C|0.917;T|0.083	0.083	strong		0.602	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
SLC18B1	116843	hgsc.bcm.edu	37	6	133105120	133105120	+	Missense_Mutation	SNP	C	C	T	rs6926101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:133105120C>T	ENST00000275227.4	-	6	706	c.610G>A	c.(610-612)Gtc>Atc	p.V204I	SLC18B1_ENST00000367918.1_Intron|SLC18B1_ENST00000538764.1_Missense_Mutation_p.V78I	NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	204			V -> I (in dbSNP:rs6926101).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)											AGCAAAACGACGCATCCCAGA	0.373													T|||	934	0.186502	0.525	0.0576	5008	,	,		13411	0.0268		0.0616	False		,,,				2504	0.1135				p.V204I		Atlas-SNP	.											.	.	.	.	0			c.G610A						PASS	.	T	ILE/VAL	1969,2437	619.6+/-393.4	436,1097,670	117.0	121.0	120.0		610	-9.1	0.6	6	dbSNP_116	120	424,8176	800.6+/-407.4	11,402,3887	yes	missense	C6orf192	NM_052831.2	29	447,1499,4557	TT,TC,CC		4.9302,44.6891,18.3992	benign	204/457	133105120	2393,10613	2203	4300	6503	SO:0001583	missense	116843	exon6			AAACGACGCATCC	AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	Standard	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.610G>A	6.37:g.133105120C>T	ENSP00000275227:p.Val204Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_052831	A8K1K3|B3KW77|Q6ISF2	Missense_Mutation	SNP	ENST00000275227.4	37	CCDS5163.1	361	0.1652930402930403	274	0.556910569105691	25	0.06906077348066299	10	0.017482517482517484	52	0.06860158311345646	T	1.326	-0.598232	0.03744	0.446891	0.049302	ENSG00000146409	ENST00000275227;ENST00000538764	T;T	0.58210	0.35;0.35	5.53	-9.11	0.00711	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.676968	0.15904	N	0.238903	T	0.06645	0.0170	N	0.11427	0.14	0.80722	P	0.0	B;B	0.15473	0.013;0.004	B;B	0.09377	0.003;0.004	T	0.18555	-1.0333	9	0.17369	T	0.5	-2.2202	3.6149	0.08074	0.3298:0.3896:0.1701:0.1105	rs6926101;rs52812882;rs60262769;rs6926101	78;204	B7Z1S5;Q6NT16	.;CF192_HUMAN	I	204;78	ENSP00000275227:V204I;ENSP00000444098:V78I	ENSP00000275227:V204I	V	-	1	0	C6orf192	133146813	0.000000	0.05858	0.576000	0.28549	0.240000	0.25518	-3.041000	0.00632	-1.375000	0.02129	-2.402000	0.00224	GTC	C|0.812;T|0.188	0.188	strong		0.373	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1	NM_052831	
MSH6	2956	hgsc.bcm.edu	37	2	48025764	48025764	+	Silent	SNP	C	C	T	rs1800937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48025764C>T	ENST00000234420.5	+	4	794	c.642C>T	c.(640-642)taC>taT	p.Y214Y	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR|MSH6_ENST00000540021.1_Silent_p.Y84Y	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	214					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)			GCACAACTTACGTAACAGATA	0.358			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	143	0.0285543	0.0038	0.0432	5008	,	,		21755	0.0		0.1034	False		,,,				2504	0.0041				p.Y214Y		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.C642T	GRCh37	CM085566|CM990714	MSH6	M	rs1800937	PASS	.	C		98,4308	77.8+/-116.1	1,96,2106	72.0	71.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	642	-6.3	0.0	2	dbSNP_89	71	801,7799	184.3+/-232.3	33,735,3532	no	coding-synonymous	MSH6	NM_000179.2		34,831,5638	TT,TC,CC		9.314,2.2242,6.9122		214/1361	48025764	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	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	AACTTACGTAACA	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.642C>T	2.37:g.48025764C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			C|0.942;T|0.058	0.058	strong		0.358	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
SLC35G3	146861	hgsc.bcm.edu	37	17	33521276	33521276	+	Silent	SNP	C	C	T	rs34540158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33521276C>T	ENST00000297307.5	-	1	136	c.51G>A	c.(49-51)tcG>tcA	p.S17S	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	17						integral component of membrane (GO:0016021)		p.S17S(1)									CGGAGGGCGGCGATGGGTGTG	0.667													C|||	664	0.132588	0.2504	0.0447	5008	,	,		15278	0.2034		0.0109	False		,,,				2504	0.0879				p.S17S		Atlas-SNP	.											AMAC1,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G51A						PASS	.	C		962,3444	364.1+/-316.8	116,730,1357	65.0	64.0	65.0		51		0.4	17	dbSNP_126	65	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous	SLC35G3	NM_152462.2		116,801,5586	TT,TC,CC		0.8256,21.8339,7.9425		17/339	33521276	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	146861	exon1			GGGCGGCGATGGG	AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"""Solute carriers"""	26848	protein-coding gene	gene with protein product			"""transmembrane protein 21A"", ""acyl-malonyl condensing enzyme 1"""	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.51G>A	17.37:g.33521276C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	91	0.52907	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	37	CCDS11293.1																																																																																			C|0.910;T|0.090	0.090	strong		0.667	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462	
TMC5	79838	hgsc.bcm.edu	37	16	19455468	19455468	+	Missense_Mutation	SNP	G	G	T	rs72785308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19455468G>T	ENST00000396229.2	+	4	1603	c.854G>T	c.(853-855)aGt>aTt	p.S285I	TMC5_ENST00000541464.1_Missense_Mutation_p.S285I|TMC5_ENST00000542583.2_Missense_Mutation_p.S285I|TMC5_ENST00000381414.4_Missense_Mutation_p.S285I	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	285					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CCCGTGGGCAGTCTTTGGGGA	0.498													A|||	130	0.0259585	0.0552	0.0216	5008	,	,		21858	0.001		0.0388	False		,,,				2504	0.002				p.S285I		Atlas-SNP	.											.	TMC5	169	.	0			c.G854T						PASS	.	A	ILE/SER,ILE/SER	213,3647		4,205,1721	123.0	121.0	122.0		854,854	2.0	0.0	16	dbSNP_130	122	302,7978		5,292,3843	yes	missense,missense	TMC5	NM_001105248.1,NM_001105249.1	142,142	9,497,5564	TT,TG,GG		3.6473,5.5181,4.2422	benign,benign	285/1007,285/949	19455468	515,11625	1930	4140	6070	SO:0001583	missense	79838	exon4			TGGGCAGTCTTTG	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.854G>T	16.37:g.19455468G>T	ENSP00000379531:p.Ser285Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	68	0.031135531135531136	33	0.06707317073170732	8	0.022099447513812154	0	0.0	27	0.03562005277044855	A	3.261	-0.151276	0.06585	0.055181	0.036473	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.24	1.99	0.26369	.	2.630760	0.01185	N	0.007191	T	0.01254	0.0041	N	0.00823	-1.155	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.08806	-1.0704	10	0.28530	T	0.3	-2.0782	1.3006	0.02078	0.1884:0.1001:0.1777:0.5338	.	285;285;285	F5GYU8;Q6UXY8;Q6UXY8-2	.;TMC5_HUMAN;.	I	285	ENSP00000441227:S285I;ENSP00000370822:S285I;ENSP00000379531:S285I;ENSP00000446274:S285I	ENSP00000370822:S285I	S	+	2	0	TMC5	19362969	0.005000	0.15991	0.003000	0.11579	0.028000	0.11728	0.192000	0.17096	0.093000	0.17368	-1.372000	0.01188	AGT	G|0.969;T|0.031	0.031	strong		0.498	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
RFX4	5992	hgsc.bcm.edu	37	12	107113769	107113769	+	Silent	SNP	G	G	A	rs17038732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:107113769G>A	ENST00000392842.1	+	12	1584	c.1170G>A	c.(1168-1170)gaG>gaA	p.E390E	RFX4_ENST00000229387.5_Silent_p.E296E|RFX4_ENST00000357881.4_Silent_p.E399E|RP11-482D24.3_ENST00000552415.1_RNA|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	390	Necessary for dimerization.				cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TCTTGGAGGAGCAGTCTCCCA	0.502													G|||	353	0.0704872	0.1944	0.0519	5008	,	,		17906	0.0099		0.0199	False		,,,				2504	0.0307				p.E399E		Atlas-SNP	.											.	RFX4	218	.	0			c.G1197A						PASS	.	G	,,	706,3700	294.4+/-283.1	60,586,1557	210.0	187.0	195.0		1197,888,1170	-0.2	1.0	12	dbSNP_123	195	158,8442	75.1+/-137.7	0,158,4142	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	60,744,5699	AA,AG,GG		1.8372,16.0236,6.6431	,,	399/745,296/642,390/736	107113769	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon12			GGAGGAGCAGTCT	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1170G>A	12.37:g.107113769G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			G|0.928;A|0.072	0.072	strong		0.502	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
SNX18	112574	hgsc.bcm.edu	37	5	53815560	53815560	+	Missense_Mutation	SNP	A	A	C	rs13162502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:53815560A>C	ENST00000326277.3	+	1	1968	c.1778A>C	c.(1777-1779)aAg>aCg	p.K593T	SNX18_ENST00000381410.4_Intron|SNX18_ENST00000343017.6_Intron	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	593	BAR.		K -> T (in dbSNP:rs13162502). {ECO:0000269|PubMed:15489334}.		cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CTAGAGTGTAAGTTGGATTGC	0.483													a|||	587	0.117212	0.0582	0.0908	5008	,	,		20372	0.0655		0.1928	False		,,,				2504	0.1912				p.K593T		Atlas-SNP	.											.	SNX18	102	.	0			c.A1778C						PASS	.	A	,,THR/LYS	339,4067	178.3+/-207.1	15,309,1879	72.0	73.0	73.0		,,1778	-6.1	0.0	5	dbSNP_121	73	1536,7064	288.1+/-298.6	150,1236,2914	yes	intron,intron,missense	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,78	165,1545,4793	CC,CA,AA		17.8605,7.6941,14.4164	,,	,,593/629	53815560	1875,11131	2203	4300	6503	SO:0001583	missense	112574	exon1			AGTGTAAGTTGGA	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1778A>C	5.37:g.53815560A>C	ENSP00000317332:p.Lys593Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	250	0.11446886446886446	27	0.054878048780487805	41	0.1132596685082873	36	0.06293706293706294	146	0.19261213720316622	A	8.380	0.837333	0.16891	0.076941	0.178605	ENSG00000178996	ENST00000326277	T	0.12774	2.65	3.06	-6.12	0.02124	.	0.272352	0.33401	U	0.004955	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	0.31447	-0.9943	8	.	.	.	0.9985	0.6291	0.00791	0.2273:0.1391:0.2332:0.4005	rs13162502;rs52817422;rs59638761;rs13162502	593	Q96RF0	SNX18_HUMAN	T	593	ENSP00000317332:K593T	.	K	+	2	0	SNX18	53851317	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.933000	0.01553	-2.532000	0.00491	-0.669000	0.03829	AAG	A|0.866;C|0.134	0.134	strong		0.483	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
COPG1	22820	hgsc.bcm.edu	37	3	128976396	128976396	+	Silent	SNP	T	T	C	rs4927910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:128976396T>C	ENST00000314797.6	+	9	767	c.663T>C	c.(661-663)caT>caC	p.H221H		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	221					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)	p.H221H(1)									TCACACGGCATGGCCTTAAGT	0.542													C|||	1285	0.256589	0.6104	0.1671	5008	,	,		22890	0.1081		0.0835	False		,,,				2504	0.1728				p.H221H		Atlas-SNP	.											COPG,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T663C						PASS	.	C		2293,2113	576.8+/-384.3	597,1099,507	195.0	186.0	189.0		663	-6.5	0.6	3	dbSNP_111	189	907,7693	778.2+/-407.7	47,813,3440	no	coding-synonymous	COPG	NM_016128.3		644,1912,3947	CC,CT,TT		10.5465,47.9573,24.604		221/875	128976396	3200,9806	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon9			ACGGCATGGCCTT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.663T>C	3.37:g.128976396T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	166	64	0.385542	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			T|0.755;C|0.245	0.245	strong		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
PSG11	5680	hgsc.bcm.edu	37	19	43529027	43529027	+	Silent	SNP	A	A	G	rs1058958|rs34787457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43529027A>G	ENST00000401740.1	-	2	349	c.246T>C	c.(244-246)taT>taC	p.Y82Y	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Silent_p.Y82Y|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	82	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CGTCTACTACATATGATGTAA	0.438													.|||	3220	0.642971	0.6415	0.4942	5008	,	,		21207	0.9871		0.4751	False		,,,				2504	0.5685				p.Y82Y		Atlas-SNP	.											.	PSG11	57	.	0			c.T246C						PASS	.	A	,,	2792,1606		955,882,362	157.0	155.0	155.0		,246,	0.9	0.0	19	dbSNP_86	155	3707,4885		901,1905,1490	no	intron,coding-synonymous,intron	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	,,	1856,2787,1852	GG,GA,AA		43.1448,36.5166,49.9692	,,	,82/336,	43529027	6499,6491	2199	4296	6495	SO:0001819	synonymous_variant	5680	exon2			TACTACATATGAT	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.246T>C	19.37:g.43529027A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000401740.1	37	CCDS12614.2																																																																																			A|0.479;G|0.521	0.521	strong		0.438	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
ACD	65057	hgsc.bcm.edu	37	16	67691515	67691515	+	Silent	SNP	C	C	A	rs14920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:67691515C>A	ENST00000393919.4	-	12	1893	c.1629G>T	c.(1627-1629)ccG>ccT	p.P543P	ACD_ENST00000219251.8_Silent_p.P540P			Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog (mouse)	543					intracellular protein transport (GO:0006886)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of single-stranded telomeric DNA binding (GO:0060381)|positive regulation of telomerase activity (GO:0051973)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	17		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CGTCTCACATCGGAGTTGGCT	0.532													C|||	93	0.0185703	0.0045	0.0245	5008	,	,		19752	0.0		0.0616	False		,,,				2504	0.0082				p.P543P		Atlas-SNP	.											.	ACD	34	.	0			c.G1629T						PASS	.	C	,,	56,4340	54.9+/-90.9	1,54,2143	92.0	88.0	89.0		1629,1581,1620	3.2	0.8	16	dbSNP_52	89	431,8169	132.2+/-189.8	14,403,3883	no	coding-synonymous,coding-synonymous,coding-synonymous	ACD	NM_001082486.1,NM_001082487.1,NM_022914.2	,,	15,457,6026	AA,AC,CC		5.0116,1.2739,3.7473	,,	543/545,527/529,540/542	67691515	487,12509	2198	4300	6498	SO:0001819	synonymous_variant	65057	exon12			TCACATCGGAGTT	AF070535	CCDS10842.1, CCDS42181.1	16q22	2012-08-23			ENSG00000102977	ENSG00000102977			25070	protein-coding gene	gene with protein product	"""TIN2 interacting protein 1"", ""POT1 and TIN2 organizing protein"""	609377				15231715, 15181449	Standard	NM_001082486		Approved	Ptop, Pip1, Tpp1, Tint1	uc002etq.4	Q96AP0	OTTHUMG00000137547	ENST00000393919.4:c.1629G>T	16.37:g.67691515C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_001082486	Q562H5|Q9H8F9	Silent	SNP	ENST00000393919.4	37	CCDS42181.1																																																																																			C|0.968;A|0.032	0.032	strong		0.532	ACD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268880.1	NM_022914	
FCN2	2220	hgsc.bcm.edu	37	9	137775155	137775155	+	Silent	SNP	T	T	C	rs4520243	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	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	
SERPINB10	5273	hgsc.bcm.edu	37	18	61584726	61584726	+	Missense_Mutation	SNP	G	G	T	rs143009235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:61584726G>T	ENST00000238508.3	+	3	264	c.205G>T	c.(205-207)Gac>Tac	p.D69Y		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	69					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)				AGTCAAATGTGACCCTGAAAG	0.274													G|||	18	0.00359425	0.003	0.0058	5008	,	,		15269	0.0		0.0099	False		,,,				2504	0.0				p.D69Y		Atlas-SNP	.											.	SERPINB10	53	.	0			c.G205T						PASS	.	G	TYR/ASP	4,4382		0,4,2189	33.0	33.0	33.0		205	-4.8	0.0	18	dbSNP_134	33	64,8478		0,64,4207	yes	missense	SERPINB10	NM_005024.1	160	0,68,6396	TT,TG,GG		0.7492,0.0912,0.526		69/398	61584726	68,12860	2193	4271	6464	SO:0001583	missense	5273	exon2			AAATGTGACCCTG	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.205G>T	18.37:g.61584726G>T	ENSP00000238508:p.Asp69Tyr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	34	0.330097	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	15	0.006868131868131868	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	4.514	0.095366	0.08681	9.12E-4	0.007492	ENSG00000242550	ENST00000238508	D	0.85088	-1.94	5.1	-4.8	0.03190	Serpin domain (3);	1.218670	0.05583	N	0.573270	T	0.55305	0.1912	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.50466	-0.8825	9	.	.	.	.	7.1303	0.25497	0.3286:0.0:0.4743:0.1971	.	69;69	P48595;B2RC45	SPB10_HUMAN;.	Y	69	ENSP00000238508:D69Y	.	D	+	1	0	SERPINB10	59735706	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.633000	0.05483	-0.892000	0.03935	-0.813000	0.03139	GAC	G|0.993;T|0.007	0.007	strong		0.274	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
ZBTB39	9880	hgsc.bcm.edu	37	12	57397250	57397250	+	Silent	SNP	G	G	C	rs145214115		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57397250G>C	ENST00000300101.2	-	2	1537	c.1452C>G	c.(1450-1452)gtC>gtG	p.V484V		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	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)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						GCTGGTCGCAGACACTGCAGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V484V		Atlas-SNP	.											.	ZBTB39	58	.	0			c.C1452G						PASS	.	G		0,4406		0,0,2203	58.0	52.0	54.0		1452	0.1	0.9	12	dbSNP_134	54	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB39	NM_014830.2		0,2,6501	CC,CG,GG		0.0233,0.0,0.0154		484/713	57397250	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9880	exon2			GTCGCAGACACTG	AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1452C>G	12.37:g.57397250G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_014830	A7MD38|Q9UD98	Silent	SNP	ENST00000300101.2	37	CCDS31839.1																																																																																			G|0.999;C|0.001	0.001	strong		0.547	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830	
NCOR2	9612	hgsc.bcm.edu	37	12	124821696	124821696	+	Silent	SNP	C	C	T	rs2229842	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124821696C>T	ENST00000405201.1	-	38	5718	c.5718G>A	c.(5716-5718)ccG>ccA	p.P1906P	NCOR2_ENST00000404121.2_Silent_p.P1467P|NCOR2_ENST00000397355.1_Silent_p.P1897P|NCOR2_ENST00000356219.3_Silent_p.P1913P|NCOR2_ENST00000429285.2_Silent_p.P1896P|NCOR2_ENST00000404621.1_Silent_p.P1896P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1917					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)	p.P1906P(1)		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)		ATGTGGCAGCCGGGCGAACGG	0.672													c|||	1279	0.255391	0.1694	0.245	5008	,	,		14363	0.5079		0.1302	False		,,,				2504	0.2474				p.P1906P		Atlas-SNP	.											NCOR2_ENST00000405201,caecum,carcinoma,0,1	NCOR2	475	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G5718A						PASS	.		,,	552,3316		30,492,1412	11.0	16.0	14.0		5688,5688,5718	-8.7	0.3	12	dbSNP_98	14	1024,6994		60,904,3045	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	90,1396,4457	TT,TC,CC		12.7713,14.2709,13.2593	,,	1896/2459,1896/2505,1906/2515	124821696	1576,10310	1934	4009	5943	SO:0001819	synonymous_variant	9612	exon40			GGCAGCCGGGCGA	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.5718G>A	12.37:g.124821696C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2	519	0.23763736263736263	71	0.1443089430894309	74	0.20441988950276244	271	0.4737762237762238	103	0.1358839050131926	c	7.338	0.620237	0.14193	0.142709	0.127713	ENSG00000196498	ENST00000440187	.	.	.	4.36	-8.71	0.00848	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.24333	P	0.99499456	.	.	.	.	.	.	T	0.40701	-0.9549	3	.	.	.	-13.2026	4.7644	0.13125	0.1575:0.1151:0.121:0.6065	rs2229842;rs3741511	.	.	.	S	141	.	.	G	-	1	0	NCOR2	123387649	0.000000	0.05858	0.343000	0.25615	0.797000	0.45037	-4.763000	0.00189	-1.562000	0.01682	-0.265000	0.10407	GGC	C|0.762;T|0.238	0.238	strong		0.672	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
ZNF208	7757	hgsc.bcm.edu	37	19	22156943	22156943	+	Missense_Mutation	SNP	G	G	A	rs12462668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22156943G>A	ENST00000397126.4	-	4	1041	c.893C>T	c.(892-894)tCg>tTg	p.S298L	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	298			S -> L (in dbSNP:rs12462668).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGTAAGAGTCGAGACCTTACT	0.388													g|||	851	0.169928	0.1543	0.2104	5008	,	,		20470	0.1895		0.1113	False		,,,				2504	0.2025				p.S298L		Atlas-SNP	.											.	ZNF208	817	.	0			c.C893T						PASS	.	G	LEU/SER	532,3728		42,448,1640	57.0	61.0	60.0		893	1.6	0.0	19	dbSNP_120	60	1132,7406		83,966,3220	no	missense	ZNF208	NM_007153.3	145	125,1414,4860	AA,AG,GG		13.2584,12.4883,13.002	probably-damaging	298/1281	22156943	1664,11134	2130	4269	6399	SO:0001583	missense	7757	exon4			AGAGTCGAGACCT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.893C>T	19.37:g.22156943G>A	ENSP00000380315:p.Ser298Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	358	0.16391941391941392	89	0.18089430894308944	67	0.1850828729281768	116	0.20279720279720279	86	0.11345646437994723	G	9.262	1.043511	0.19748	0.124883	0.132584	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.17691	2.26	2.76	1.61	0.23674	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.48589	0.912	B	0.27715	0.082	T	0.36335	-0.9752	7	0.59425	D	0.04	.	9.138	0.36886	0.0:0.0:0.7794:0.2206	rs12462668;rs52829010;rs12462668	298	O43345	ZN208_HUMAN	L	298	ENSP00000380315:S298L	ENSP00000380315:S298L	S	-	2	0	ZNF208	21948783	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.118000	0.03280	0.111000	0.17947	0.306000	0.20318	TCG	G|0.839;A|0.161	0.161	strong		0.388	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
UGT2A1	10941	hgsc.bcm.edu	37	4	70462042	70462042	+	Missense_Mutation	SNP	C	C	T	rs4148301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:70462042C>T	ENST00000503640.1	-	3	977	c.922G>A	c.(922-924)Gga>Aga	p.G308R	UGT2A1_ENST00000512704.1_Intron|UGT2A2_ENST00000457664.2_Missense_Mutation_p.G317R|UGT2A1_ENST00000286604.4_Intron|UGT2A1_ENST00000502343.1_Intron|UGT2A1_ENST00000514019.1_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	94	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	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	
KSR1	8844	hgsc.bcm.edu	37	17	25909805	25909805	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:25909805A>G	ENST00000319524.6	+	4	654	c.654A>G	c.(652-654)gcA>gcG	p.A218A	KSR1_ENST00000398988.3_Silent_p.A81A|KSR1_ENST00000268763.6_Silent_p.A81A|KSR1_ENST00000509603.2_Silent_p.A218A			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	218					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TGGGCAGAGCAGGCAACAGCG	0.682																																					p.A81A	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											KSR1_ENST00000319524,caecum,carcinoma,+2,2	KSR1	151	2	0			c.A243G						scavenged	.						28.0	35.0	33.0					17																	25909805		2084	4205	6289	SO:0001819	synonymous_variant	8844	exon5			CAGAGCAGGCAAC	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.654A>G	17.37:g.25909805A>G		Somatic	125	4	0.032		WXS	Illumina HiSeq	Phase_I	116	3	0.0258621	NM_014238	F8WEA9|H7BYU0|Q13476	Silent	SNP	ENST00000319524.6	37																																																																																				.	.	none		0.682	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
EXOSC1	51013	hgsc.bcm.edu	37	10	99205731	99205731	+	Silent	SNP	A	A	G	rs4919098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99205731A>G	ENST00000370902.3	-	1	43	c.12T>C	c.(10-12)ccT>ccC	p.P4P	ZDHHC16_ENST00000353979.3_5'Flank|EXOSC1_ENST00000370886.5_Silent_p.P4P|EXOSC1_ENST00000370885.4_Silent_p.P4P|EXOSC1_ENST00000485122.2_Silent_p.P4P|ZDHHC16_ENST00000370842.2_5'Flank|ZDHHC16_ENST00000345745.5_5'Flank|ZDHHC16_ENST00000370854.3_5'Flank|ZDHHC16_ENST00000352634.4_5'Flank|ZDHHC16_ENST00000393760.1_5'Flank|EXOSC1_ENST00000471049.1_5'Flank|ZDHHC16_ENST00000370846.4_5'Flank	NM_016046.3	NP_057130.1	Q9Y3B2	EXOS1_HUMAN	exosome component 1	4					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)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|lung(5)	7		Renal(717;0.000147)|Colorectal(252;0.00205)|Ovarian(717;0.00965)		all cancers(201;8.29e-42)|Epithelial(162;5.7e-33)|BRCA - Breast invasive adenocarcinoma(275;0.000315)|Kidney(138;0.000832)|KIRC - Kidney renal clear cell carcinoma(50;0.00269)|STAD - Stomach adenocarcinoma(243;0.202)		AGTATCTCACAGGTGGCGCCA	0.557											OREG0020413	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	479	0.095647	0.0938	0.111	5008	,	,		17552	0.0764		0.1223	False		,,,				2504	0.0798				p.P4P		Atlas-SNP	.											.	EXOSC1	8	.	0			c.T12C						PASS	.	G		482,3924	782.5+/-414.6	33,416,1754	108.0	99.0	102.0		12	-3.7	0.8	10	dbSNP_111	102	1157,7443	765.0+/-407.6	81,995,3224	no	coding-synonymous	EXOSC1	NM_016046.3		114,1411,4978	GG,GA,AA		13.4535,10.9396,12.6019		4/196	99205731	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	51013	exon1			TCTCACAGGTGGC	AF151866	CCDS7459.1	10q24	2004-03-26			ENSG00000171311	ENSG00000171311			17286	protein-coding gene	gene with protein product	"""CSL4 exosomal core protein homolog (yeast)"""	606493				11812149, 11719186	Standard	XR_246092		Approved	hCsl4p, Csl4p, CSL4, Ski4p, SKI4, CGI-108, p13	uc001kni.3	Q9Y3B2	OTTHUMG00000018854	ENST00000370902.3:c.12T>C	10.37:g.99205731A>G		Somatic	65	0	0	1341	WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_016046	B2R9B3|Q5JTH3	Silent	SNP	ENST00000370902.3	37	CCDS7459.1																																																																																			A|0.888;G|0.112	0.112	strong		0.557	EXOSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049680.1		
ZBTB46	140685	hgsc.bcm.edu	37	20	62422080	62422080	+	Missense_Mutation	SNP	T	T	C	rs2281929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62422080T>C	ENST00000245663.4	-	2	181	c.31A>G	c.(31-33)Acg>Gcg	p.T11A	ZBTB46_ENST00000395104.1_Missense_Mutation_p.T11A|ZBTB46_ENST00000302995.2_Missense_Mutation_p.T11A|ZBTB46_ENST00000480766.1_5'Flank	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	11			T -> A (in dbSNP:rs2281929). {ECO:0000269|PubMed:15489334}.		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)					TAGTGGGACGTGATTTCCATA	0.567													C|||	1266	0.252796	0.2678	0.1931	5008	,	,		20715	0.4613		0.1243	False		,,,				2504	0.1922				p.T11A		Atlas-SNP	.											ZBTB46,NS,carcinoma,+1,2	ZBTB46	72	2	0			c.A31G						PASS	.	C	ALA/THR	1084,3322		134,816,1253	42.0	29.0	33.0		31	2.2	1.0	20	dbSNP_100	33	1005,7593		60,885,3354	yes	missense	ZBTB46	NM_025224.3	58	194,1701,4607	CC,CT,TT		11.6888,24.6028,16.0643	benign	11/590	62422080	2089,10915	2203	4299	6502	SO:0001583	missense	140685	exon2			GGGACGTGATTTC	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.31A>G	20.37:g.62422080T>C	ENSP00000245663:p.Thr11Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	513	0.2348901098901099	109	0.22154471544715448	57	0.1574585635359116	249	0.4353146853146853	98	0.12928759894459102	C	0.040	-1.289329	0.01387	0.246028	0.116888	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.70631	-0.5;-0.5;-0.5	5.39	2.25	0.28309	BTB/POZ fold (2);	0.216998	0.40818	N	0.001002	T	0.00012	0.0000	N	0.05306	-0.075	0.40220	P	0.02227699999999999	B	0.02656	0.0	B	0.06405	0.002	T	0.43605	-0.9381	9	0.24483	T	0.36	.	5.1718	0.15114	0.0:0.5358:0.1392:0.3251	rs2281929;rs17857409;rs57058623;rs2281929	11	Q86UZ6	ZBT46_HUMAN	A	11	ENSP00000245663:T11A;ENSP00000303102:T11A;ENSP00000378536:T11A	ENSP00000245663:T11A	T	-	1	0	ZBTB46	61892524	0.991000	0.36638	0.986000	0.45419	0.418000	0.31294	0.272000	0.18644	-0.022000	0.13986	-1.082000	0.02213	ACG	T|0.799;C|0.201	0.201	strong		0.567	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
SEMA3C	10512	hgsc.bcm.edu	37	7	80427495	80427495	+	Silent	SNP	C	C	A	rs1880959	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:80427495C>A	ENST00000265361.3	-	11	1605	c.1044G>T	c.(1042-1044)gtG>gtT	p.V348V	SEMA3C_ENST00000419255.2_Silent_p.V348V|SEMA3C_ENST00000544525.1_Silent_p.V366V|SEMA3C_ENST00000536800.1_Silent_p.V200V	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	348	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GCCCATTAAACACAGTCTGTA	0.393													C|||	237	0.0473243	0.0666	0.0504	5008	,	,		13404	0.001		0.0915	False		,,,				2504	0.0215				p.V348V		Atlas-SNP	.											SEMA3C,NS,carcinoma,-2,1	SEMA3C	106	1	0			c.G1044T						PASS	.	C		375,4031	186.4+/-213.3	19,337,1847	60.0	60.0	60.0		1044	2.8	1.0	7	dbSNP_92	60	810,7790	186.3+/-233.8	28,754,3518	no	coding-synonymous	SEMA3C	NM_006379.3		47,1091,5365	AA,AC,CC		9.4186,8.5111,9.1112		348/752	80427495	1185,11821	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon11			ATTAAACACAGTC	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1044G>T	7.37:g.80427495C>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	137	64	0.467153	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			C|0.925;A|0.075	0.075	strong		0.393	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
TRIM6	117854	hgsc.bcm.edu	37	11	5625847	5625847	+	Silent	SNP	A	A	G	rs3751006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5625847A>G	ENST00000278302.5	+	3	647	c.507A>G	c.(505-507)aaA>aaG	p.K169K	TRIM6_ENST00000380097.3_Silent_p.K197K|TRIM6_ENST00000380107.1_Silent_p.K143K|TRIM6_ENST00000507320.1_5'UTR|TRIM6_ENST00000506134.1_5'UTR|TRIM6_ENST00000515022.1_Intron|AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Silent_p.K197K|TRIM6_ENST00000445329.1_5'UTR	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	169					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)		GAGAGAAGAAAACATCCTGGA	0.468													G|||	3505	0.69988	0.7171	0.6556	5008	,	,		20342	0.7212		0.5865	False		,,,				2504	0.8027				p.K197K		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A591G						PASS	.	G	,,,,	3172,1230	424.9+/-340.6	1123,926,152	109.0	109.0	109.0		591,591,,,507	0.6	0.0	11	dbSNP_107	109	5341,3253	488.7+/-372.4	1674,1993,630	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	,,,,	2797,2919,782	GG,GA,AA		37.852,27.9418,34.4952	,,,,	197/517,197/843,,,169/489	5625847	8513,4483	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon3			GAAGAAAACATCC	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.507A>G	11.37:g.5625847A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001003819	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Silent	SNP	ENST00000278302.5	37	CCDS31390.1																																																																																			A|0.329;G|0.671	0.671	strong		0.468	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
SPTY2D1	144108	hgsc.bcm.edu	37	11	18633897	18633897	+	Missense_Mutation	SNP	T	T	C	rs35411689	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18633897T>C	ENST00000336349.5	-	4	2085	c.1850A>G	c.(1849-1851)aAg>aGg	p.K617R	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	617			K -> R (in dbSNP:rs35411689). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.					p.K617R(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TCTAATGTGCTTGGATATTTC	0.333													T|||	514	0.102636	0.0091	0.0605	5008	,	,		16987	0.2232		0.0974	False		,,,				2504	0.1401				p.K617R		Atlas-SNP	.											SPTY2D1,NS,carcinoma,0,1	SPTY2D1	72	1	1	Substitution - Missense(1)	stomach(1)	c.A1850G						PASS	.	T	ARG/LYS	94,4304	76.8+/-115.0	0,94,2105	133.0	131.0	132.0		1850	3.7	1.0	11	dbSNP_126	132	714,7872	174.2+/-224.5	27,660,3606	yes	missense	SPTY2D1	NM_194285.2	26	27,754,5711	CC,CT,TT		8.3159,2.1373,6.223	possibly-damaging	617/686	18633897	808,12176	2199	4293	6492	SO:0001583	missense	144108	exon4			ATGTGCTTGGATA	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1850A>G	11.37:g.18633897T>C	ENSP00000337991:p.Lys617Arg	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	249	0.11401098901098901	9	0.018292682926829267	22	0.06077348066298342	136	0.23776223776223776	82	0.10817941952506596	T	15.32	2.797273	0.50208	0.021373	0.083159	ENSG00000179119	ENST00000336349	T	0.47528	0.84	5.99	3.67	0.42095	.	0.092812	0.64402	N	0.000001	T	0.00012	0.0000	L	0.43757	1.38	0.21933	P	0.99946053	P	0.34724	0.465	B	0.33568	0.166	T	0.15925	-1.0420	9	0.27785	T	0.31	-6.5418	10.2959	0.43625	0.0:0.1332:0.0:0.8668	rs35411689	617	Q68D10	SPT2_HUMAN	R	617	ENSP00000337991:K617R	ENSP00000337991:K617R	K	-	2	0	SPTY2D1	18590473	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.257000	0.43240	0.514000	0.28300	0.533000	0.62120	AAG	T|0.921;C|0.079	0.079	strong		0.333	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285	
OR13H1	347468	hgsc.bcm.edu	37	X	130678844	130678844	+	Missense_Mutation	SNP	A	A	C	rs655415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:130678844A>C	ENST00000338616.3	+	1	895	c.797A>C	c.(796-798)tAc>tCc	p.Y266S		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	266			Y -> S (in dbSNP:rs655415). {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(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					TCCAAGTCCTACCCTGACCAG	0.458													C|||	2627	0.695894	0.6346	0.4049	3775	,	,		10047	0.4841		0.4583	False		,,,				2504	0.5706				p.Y266S		Atlas-SNP	.											.	OR13H1	41	.	0			c.A797C						PASS	.	C	SER/TYR	3151,684		1096,484,475,52,96	119.0	111.0	113.0		797	4.9	0.0	X	dbSNP_83	113	4237,2491		953,1145,1186,330,686	yes	missense	OR13H1	NM_001004486.1	144	2049,1629,1661,382,782	CC,CA,C,AA,A		37.0244,17.8357,30.0577	benign	266/309	130678844	7388,3175	2203	4300	6503	SO:0001583	missense	347468	exon1			AGTCCTACCCTGA		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.797A>C	X.37:g.130678844A>C	ENSP00000340748:p.Tyr266Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Missense_Mutation	SNP	ENST00000338616.3	37	CCDS35396.1	1094	0.6594333936106088	209	0.6966666666666667	106	0.4076923076923077	187	0.4869791666666667	242	0.44814814814814813	C	0	-2.735259	0.00089	0.821643	0.629756	ENSG00000171054	ENST00000338616	T	0.00015	9.15	4.87	4.87	0.63330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39407	N	0.001374	T	0.00012	0.0000	N	0.00007	-3.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34950	-0.9808	9	0.02654	T	1	.	9.5077	0.39058	0.3837:0.6163:0.0:0.0	rs655415;rs52802619;rs58879001;rs655415	266	Q8NG92	O13H1_HUMAN	S	266	ENSP00000340748:Y266S	ENSP00000340748:Y266S	Y	+	2	0	OR13H1	130506525	0.000000	0.05858	0.010000	0.14722	0.063000	0.16089	0.570000	0.23653	1.058000	0.40530	-0.178000	0.13098	TAC	A|0.292;0|0.012	.	strong		0.458	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1		
HAGHL	84264	hgsc.bcm.edu	37	16	778820	778820	+	Silent	SNP	G	G	A	rs12448432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:778820G>A	ENST00000341413.4	+	7	806	c.525G>A	c.(523-525)acG>acA	p.T175T	HAGHL_ENST00000561546.1_Silent_p.T175T|HAGHL_ENST00000389703.3_Silent_p.T175T|CCDC78_ENST00000293889.6_5'Flank|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564537.1_Missense_Mutation_p.A202T|HAGHL_ENST00000564545.1_Missense_Mutation_p.A84T|HAGHL_ENST00000549114.1_Missense_Mutation_p.A202T			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	175							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				ACGAGCACACGCTTAGCAACC	0.667													G|||	1975	0.394369	0.1573	0.4625	5008	,	,		9189	0.7569		0.2376	False		,,,				2504	0.454				p.T175T	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.G525A						PASS	.	G		563,3815	238.7+/-250.0	32,499,1658	26.0	27.0	26.0		525	-8.2	0.0	16	dbSNP_120	26	1796,6786	299.9+/-304.7	197,1402,2692	no	coding-synonymous	HAGHL	NM_032304.2		229,1901,4350	AA,AG,GG		20.9275,12.8598,18.2022		175/283	778820	2359,10601	2189	4291	6480	SO:0001819	synonymous_variant	84264	exon6			GCACACGCTTAGC	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.525G>A	16.37:g.778820G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37		865	0.39606227106227104	82	0.16666666666666666	148	0.4088397790055249	436	0.7622377622377622	199	0.262532981530343	G	15.03	2.712967	0.48517	0.128598	0.209275	ENSG00000103253	ENST00000549114;ENST00000389701	D	0.87103	-2.21	4.27	-8.21	0.01041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999590043	B	0.11235	0.004	B	0.12837	0.008	T	0.34551	-0.9824	6	.	.	.	-20.0695	1.828	0.03125	0.4147:0.1648:0.2828:0.1376	rs12448432;rs61367184;rs12448432	202	Q6PII5-3	.	T	202;203	ENSP00000447170:A202T	.	A	+	1	0	HAGHL	718821	0.002000	0.14202	0.002000	0.10522	0.426000	0.31534	-1.023000	0.03607	-1.455000	0.01923	-0.258000	0.10820	GCT	G|0.733;A|0.267	0.267	strong		0.667	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
RBM5	10181	hgsc.bcm.edu	37	3	50147061	50147061	+	Silent	SNP	G	G	A	rs116604207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:50147061G>A	ENST00000347869.3	+	15	1393	c.1218G>A	c.(1216-1218)gcG>gcA	p.A406A	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	406	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCACCTCAGCGGCTGTAGTGT	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		14240	0.0		0.002	False		,,,				2504	0.0				p.A406A		Atlas-SNP	.											.	RBM5	76	.	0			c.G1218A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	203.0	183.0	190.0		1218	-12.1	0.5	3	dbSNP_132	190	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	RBM5	NM_005778.2		0,21,6482	AA,AG,GG		0.2326,0.0227,0.1615		406/816	50147061	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon15			CTCAGCGGCTGTA	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1218G>A	3.37:g.50147061G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	193	69	0.357513	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			G|0.998;A|0.002	0.002	strong		0.488	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
SSFA2	6744	hgsc.bcm.edu	37	2	182780874	182780874	+	Missense_Mutation	SNP	C	C	T	rs17647806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:182780874C>T	ENST00000431877.2	+	11	2686	c.2507C>T	c.(2506-2508)cCa>cTa	p.P836L	SSFA2_ENST00000428267.2_Missense_Mutation_p.P683L|SSFA2_ENST00000409136.1_Missense_Mutation_p.P345L|SSFA2_ENST00000320370.7_Missense_Mutation_p.P836L|SSFA2_ENST00000409001.1_Missense_Mutation_p.P836L	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	836			P -> L (in dbSNP:rs17647806). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14702039}.			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)			CGGCTTGCTCCACCACCAATG	0.542													C|||	117	0.0233626	0.0038	0.0259	5008	,	,		17717	0.0		0.0437	False		,,,				2504	0.0511				p.P836L		Atlas-SNP	.											.	SSFA2	130	.	0			c.C2507T						PASS	.	C	LEU/PRO,LEU/PRO	49,4357	50.9+/-86.3	0,49,2154	111.0	123.0	119.0		2507,2507	4.6	0.0	2	dbSNP_123	119	459,8141	137.0+/-194.0	16,427,3857	yes	missense,missense	SSFA2	NM_001130445.1,NM_006751.5	98,98	16,476,6011	TT,TC,CC		5.3372,1.1121,3.9059	probably-damaging,probably-damaging	836/1260,836/1257	182780874	508,12498	2203	4300	6503	SO:0001583	missense	6744	exon11			TTGCTCCACCACC	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.2507C>T	2.37:g.182780874C>T	ENSP00000388731:p.Pro836Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	44	0.020146520146520148	5	0.01016260162601626	8	0.022099447513812154	0	0.0	31	0.040897097625329816	C	13.01	2.110096	0.37242	0.011121	0.053372	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.20332	2.32;2.08;2.31;2.32;2.13	5.43	4.55	0.56014	.	0.249441	0.40908	D	0.000995	T	0.07188	0.0182	M	0.67953	2.075	0.29493	N	0.855498	D;D;P;P;D	0.53312	0.959;0.959;0.787;0.787;0.959	P;P;B;B;P	0.50659	0.647;0.647;0.372;0.372;0.647	T	0.04128	-1.0975	10	0.87932	D	0	-3.0934	16.1437	0.81548	0.0:0.8662:0.1338:0.0	rs17647806;rs52810715;rs17647806	683;345;836;836;836	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	L	836;836;836;683;345	ENSP00000388731:P836L;ENSP00000314669:P836L;ENSP00000387319:P836L;ENSP00000409867:P683L;ENSP00000386916:P345L	ENSP00000314669:P836L	P	+	2	0	SSFA2	182489119	0.172000	0.23043	0.005000	0.12908	0.125000	0.20455	2.683000	0.46943	1.269000	0.44280	0.655000	0.94253	CCA	C|0.966;T|0.034	0.034	strong		0.542	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
SLC1A2	6506	hgsc.bcm.edu	37	11	35327748	35327748	+	Silent	SNP	C	C	T	rs752949	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:35327748C>T	ENST00000278379.3	-	5	885	c.603G>A	c.(601-603)ccG>ccA	p.P201P	SLC1A2_ENST00000395753.1_Silent_p.P192P|SLC1A2_ENST00000395750.1_Silent_p.P192P|SLC1A2_ENST00000606205.1_Silent_p.P201P	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	201					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			CCTCCTCGTCCGGCGGTGGTG	0.502											OREG0020883	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	904	0.180511	0.1415	0.2464	5008	,	,		18901	0.1905		0.2624	False		,,,				2504	0.092				p.P201P	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-SNP	.											SLC1A2,NS,carcinoma,-1,1	SLC1A2	54	1	0			c.G603A						PASS	.	T	,	619,3785	768.6+/-413.6	45,529,1628	93.0	86.0	88.0		576,603	-3.3	0.0	11	dbSNP_92	88	2095,6501	717.2+/-406.2	251,1593,2454	no	coding-synonymous,coding-synonymous	SLC1A2	NM_001195728.1,NM_004171.3	,	296,2122,4082	TT,TC,CC		24.3718,14.0554,20.8769	,	192/566,201/575	35327748	2714,10286	2202	4298	6500	SO:0001819	synonymous_variant	6506	exon5			CTCGTCCGGCGGT	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.603G>A	11.37:g.35327748C>T		Somatic	49	0	0	854	WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	Silent	SNP	ENST00000278379.3	37	CCDS31459.1																																																																																			C|0.786;T|0.214	0.214	strong		0.502	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171	
FBN3	84467	hgsc.bcm.edu	37	19	8212263	8212263	+	Silent	SNP	G	G	A	rs11878432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8212263G>A	ENST00000600128.1	-	2	516	c.102C>T	c.(100-102)gaC>gaT	p.D34D	FBN3_ENST00000601739.1_Silent_p.D34D|FBN3_ENST00000270509.2_Silent_p.D34D			Q75N90	FBN3_HUMAN	fibrillin 3	34						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						CCAAGGCCCCGTCCCAGCGGC	0.692													G|||	1058	0.211262	0.1135	0.2075	5008	,	,		14258	0.2163		0.3499	False		,,,				2504	0.1984				p.D34D		Atlas-SNP	.											.	FBN3	300	.	0			c.C102T						PASS	.	G		724,3650		69,586,1532	11.0	13.0	12.0		102	-9.6	0.0	19	dbSNP_120	12	2897,5663		520,1857,1903	no	coding-synonymous	FBN3	NM_032447.3		589,2443,3435	AA,AG,GG		33.8435,16.5524,27.996		34/2810	8212263	3621,9313	2187	4280	6467	SO:0001819	synonymous_variant	84467	exon1			GGCCCCGTCCCAG		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.102C>T	19.37:g.8212263G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.760;A|0.240	0.240	strong		0.692	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
FLG	2312	hgsc.bcm.edu	37	1	152285930	152285930	+	Missense_Mutation	SNP	G	G	A	rs11584340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152285930G>A	ENST00000368799.1	-	3	1467	c.1432C>T	c.(1432-1434)Cct>Tct	p.P478S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	478	Ser-rich.		P -> S (in dbSNP:rs11584340).		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)			GCAGAGTCAGGCTGTTCATGA	0.612									Ichthyosis				-|||	1726	0.344649	0.1286	0.4222	5008	,	,		18652	0.6062		0.171	False		,,,				2504	0.4908				p.P478S		Atlas-SNP	.											.	FLG	900	.	0			c.C1432T	GRCh37	CM084968	FLG	M	rs11584340	PASS	.	A	SER/PRO	615,3791		44,527,1632	220.0	210.0	214.0		1432	-3.1	0.0	1	dbSNP_120	214	1444,7156		124,1196,2980	yes	missense	FLG	NM_002016.1	74	168,1723,4612	AA,AG,GG		16.7907,13.9582,15.8312	benign	478/4062	152285930	2059,10947	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTCAGGCTGTTC	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.1432C>T	1.37:g.152285930G>A	ENSP00000357789:p.Pro478Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	237	153	0.64557	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	684	0.3131868131868132	72	0.14634146341463414	125	0.3453038674033149	355	0.6206293706293706	132	0.1741424802110818	-	4.251	0.045625	0.08196	0.139582	0.167907	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00873	5.59	3.05	-3.12	0.05282	.	.	.	.	.	T	0.00073	0.0002	N	0.00260	-1.75	0.80722	P	0.0	B	0.17038	0.02	B	0.21360	0.034	T	0.30149	-0.9988	8	0.02654	T	1	.	3.0665	0.06217	0.3181:0.0:0.3425:0.3394	rs11584340;rs52819317;rs11584340	478	P20930	FILA_HUMAN	S	478;10	ENSP00000357789:P478S	ENSP00000357789:P478S	P	-	1	0	FLG	150552554	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.893000	0.01609	-1.350000	0.02199	-1.441000	0.01070	CCT	G|0.785;A|0.215	0.215	strong		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PRRT3	285368	hgsc.bcm.edu	37	3	9988175	9988175	+	Silent	SNP	C	C	T	rs61740128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9988175C>T	ENST00000412055.1	-	4	2811	c.2682G>A	c.(2680-2682)ggG>ggA	p.G894G	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	894						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						CAGCGGCTGCCCCGTCGGGTG	0.687													C|||	119	0.023762	0.003	0.0115	5008	,	,		13195	0.001		0.0437	False		,,,				2504	0.0634				p.G894G		Atlas-SNP	.											.	PRRT3	35	.	0			c.G2682A						PASS	.	C		15,3439		0,15,1712	3.0	6.0	5.0		2682	3.5	0.0	3	dbSNP_129	5	184,7442		0,184,3629	no	coding-synonymous	PRRT3	NM_207351.3		0,199,5341	TT,TC,CC		2.4128,0.4343,1.796		894/982	9988175	199,10881	1727	3813	5540	SO:0001819	synonymous_variant	285368	exon4			GGCTGCCCCGTCG	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.2682G>A	3.37:g.9988175C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	70	47	0.671429	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Silent	SNP	ENST00000412055.1	37	CCDS43049.1																																																																																			C|0.983;T|0.017	0.017	strong		0.687	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
FAM151B	167555	hgsc.bcm.edu	37	5	79817898	79817898	+	Silent	SNP	A	A	G	rs2431224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79817898A>G	ENST00000282226.4	+	5	767	c.612A>G	c.(610-612)agA>agG	p.R204R	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	204										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		TCCCTGTCAGAGCAGCATTAG	0.348													A|||	152	0.0303514	0.0038	0.0461	5008	,	,		18692	0.003		0.0636	False		,,,				2504	0.0491				p.R204R		Atlas-SNP	.											.	FAM151B	25	.	0			c.A612G						PASS	.	A		82,4324	70.3+/-108.2	1,80,2122	163.0	144.0	150.0		612	-0.0	1.0	5	dbSNP_100	150	673,7927	168.7+/-220.2	24,625,3651	no	coding-synonymous	FAM151B	NM_205548.2		25,705,5773	GG,GA,AA		7.8256,1.8611,5.805		204/277	79817898	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	167555	exon5			TGTCAGAGCAGCA		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.612A>G	5.37:g.79817898A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_205548	A2RRE4	Silent	SNP	ENST00000282226.4	37	CCDS4051.1																																																																																			A|0.954;G|0.046	0.046	strong		0.348	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548	
GSTO2	119391	hgsc.bcm.edu	37	10	106039185	106039185	+	Missense_Mutation	SNP	A	A	G	rs156697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:106039185A>G	ENST00000338595.2	+	5	744	c.424A>G	c.(424-426)Aat>Gat	p.N142D	GSTO2_ENST00000429569.2_Intron|GSTO2_ENST00000369707.2_Missense_Mutation_p.N114D|GSTO2_ENST00000401888.2_Missense_Mutation_p.N142D|GSTO2_ENST00000450629.2_Intron|GSTO2_ENST00000477078.2_3'UTR	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	142	GST C-terminal.		N -> D (in dbSNP:rs156697). {ECO:0000269|PubMed:12618591}.		cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	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.N142D(1)		NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	AGAATGCACTAATCTGAAGGC	0.527													G|||	2207	0.440695	0.8048	0.2752	5008	,	,		21195	0.255		0.3668	False		,,,				2504	0.3333				p.N142D		Atlas-SNP	.											GSTO2,NS,carcinoma,0,1	GSTO2	23	1	1	Substitution - Missense(1)	stomach(1)	c.A424G						PASS	.	G	,ASP/ASN,,ASP/ASN	3273,1133	405.8+/-333.6	1225,823,155	150.0	132.0	138.0		,340,,424	4.0	0.1	10	dbSNP_79	138	2929,5671	669.5+/-402.7	498,1933,1869	yes	intron,missense,intron,missense	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,23,,23	1723,2756,2024	GG,GA,AA		34.0581,25.7149,47.6857	,benign,,benign	,114/216,,142/244	106039185	6202,6804	2203	4300	6503	SO:0001583	missense	119391	exon5			TGCACTAATCTGA	AY191318	CCDS7556.1, CCDS53574.1, CCDS53575.1	10q25.1	2012-06-21			ENSG00000065621	ENSG00000065621	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	23064	protein-coding gene	gene with protein product		612314				12618591	Standard	NM_001191013		Approved		uc001kyb.3	Q9H4Y5	OTTHUMG00000019006	ENST00000338595.2:c.424A>G	10.37:g.106039185A>G	ENSP00000345023:p.Asn142Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Missense_Mutation	SNP	ENST00000338595.2	37	CCDS7556.1	936	0.42857142857142855	399	0.8109756097560976	114	0.3149171270718232	152	0.26573426573426573	271	0.3575197889182058	G	0.500	-0.871174	0.02570	0.742851	0.340581	ENSG00000065621	ENST00000369708;ENST00000338595;ENST00000401888;ENST00000369707	T;T;T	0.12774	2.65;3.17;2.65	5.87	3.96	0.45880	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.333001	0.34986	N	0.003530	T	0.00012	0.0000	N	0.01048	-1.04	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.16660	-1.0395	9	0.12103	T	0.63	-7.1748	7.3566	0.26723	0.1496:0.1367:0.7137:0.0	rs156697;rs601755;rs11565111;rs17826262;rs60436392;rs156697	142	Q9H4Y5	GSTO2_HUMAN	D	142;142;142;114	ENSP00000345023:N142D;ENSP00000386011:N142D;ENSP00000358721:N114D	ENSP00000345023:N142D	N	+	1	0	GSTO2	106029175	0.009000	0.17119	0.081000	0.20488	0.253000	0.25986	0.748000	0.26305	0.851000	0.35264	-0.733000	0.03571	AAT	A|0.537;G|0.463	0.463	strong		0.527	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17961345	17961345	+	Silent	SNP	C	C	T	rs34725104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17961345C>T	ENST00000361221.3	+	18	1920	c.1761C>T	c.(1759-1761)atC>atT	p.I587I	ARHGEF10L_ENST00000375420.3_Silent_p.I345I|ARHGEF10L_ENST00000375408.3_Silent_p.I360I|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000452522.1_Silent_p.I548I|ARHGEF10L_ENST00000167825.4_Silent_p.I290I|ARHGEF10L_ENST00000375415.1_Silent_p.I548I|ARHGEF10L_ENST00000434513.1_Silent_p.I582I	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	587						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)		AGCTGGAGATCAGCAGCCTGG	0.667													C|||	407	0.08127	0.0061	0.0965	5008	,	,		15918	0.0724		0.1859	False		,,,				2504	0.0736				p.I587I		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C1761T						PASS	.	C	,	177,4229	113.3+/-151.4	5,167,2031	39.0	40.0	39.0		1644,1761	2.9	1.0	1	dbSNP_126	39	1643,6957	296.2+/-302.8	158,1327,2815	no	coding-synonymous,coding-synonymous	ARHGEF10L	NM_001011722.2,NM_018125.3	,	163,1494,4846	TT,TC,CC		19.1047,4.0172,13.9935	,	548/1241,587/1280	17961345	1820,11186	2203	4300	6503	SO:0001819	synonymous_variant	55160	exon18			GGAGATCAGCAGC	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.1761C>T	1.37:g.17961345C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	37	CCDS182.1																																																																																			C|0.874;T|0.126	0.126	strong		0.667	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
MCCC2	64087	hgsc.bcm.edu	37	5	70888804	70888804	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:70888804G>A	ENST00000340941.6	+	2	310	c.181G>A	c.(181-183)Gag>Aag	p.E61K	MCCC2_ENST00000509358.2_Missense_Mutation_p.E61K|MCCC2_ENST00000323375.8_Missense_Mutation_p.E61K	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	61	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|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 matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	TGAACGAGTGGAGCATATAAA	0.348																																					p.E61K		Atlas-SNP	.											.	MCCC2	47	.	0			c.G181A						PASS	.						69.0	67.0	67.0					5																	70888804		2203	4300	6503	SO:0001583	missense	64087	exon2			CGAGTGGAGCATA	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"""methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"""				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.181G>A	5.37:g.70888804G>A	ENSP00000343657:p.Glu61Lys	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	256	137	0.535156	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Missense_Mutation	SNP	ENST00000340941.6	37	CCDS34184.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.327666	0.24080	.	.	ENSG00000131844	ENST00000340941;ENST00000509358;ENST00000323375	D;D;D	0.98090	-4.71;-4.71;-4.71	4.73	0.197	0.15164	Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.297876	0.35903	N	0.002915	D	0.96015	0.8702	M	0.69185	2.1	0.34463	D	0.701963	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	D	0.92607	0.6096	10	0.36615	T	0.2	-1.2046	16.3491	0.83195	0.0:0.3931:0.6069:0.0	.	61;61	D6RDF7;Q9HCC0	.;MCCB_HUMAN	K	61	ENSP00000343657:E61K;ENSP00000420994:E61K;ENSP00000327308:E61K	ENSP00000327308:E61K	E	+	1	0	MCCC2	70924560	0.999000	0.42202	0.001000	0.08648	0.001000	0.01503	0.986000	0.29590	0.062000	0.16340	-0.153000	0.13522	GAG	.	.	none		0.348	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4		
PTCH2	8643	hgsc.bcm.edu	37	1	45292173	45292173	+	Missense_Mutation	SNP	G	G	A	rs11573590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45292173G>A	ENST00000372192.3	-	18	3093	c.2963C>T	c.(2962-2964)aCg>aTg	p.T988M	PTCH2_ENST00000447098.2_Missense_Mutation_p.T988M	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	988			T -> M (in dbSNP:rs11573590). {ECO:0000269|Ref.5}.		epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GAGGCCAGCCGTCCAGGGGTT	0.637									Basal Cell Nevus syndrome				G|||	315	0.0628994	0.0015	0.0937	5008	,	,		19263	0.1677		0.0219	False		,,,				2504	0.0583				p.T988M		Atlas-SNP	.											PTCH2,NS,carcinoma,0,1	PTCH2	96	1	0			c.C2963T						PASS	.	G	MET/THR,MET/THR	31,4373	36.8+/-68.6	1,29,2172	35.0	35.0	35.0		2963,2963	0.3	0.4	1	dbSNP_120	35	178,8422	80.6+/-143.3	0,178,4122	yes	missense,missense	PTCH2	NM_001166292.1,NM_003738.4	81,81	1,207,6294	AA,AG,GG		2.0698,0.7039,1.6072	probably-damaging,probably-damaging	988/1147,988/1204	45292173	209,12795	2202	4300	6502	SO:0001583	missense	8643	exon18	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	CCAGCCGTCCAGG	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2963C>T	1.37:g.45292173G>A	ENSP00000361266:p.Thr988Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	126	0.057692307692307696	1	0.0020325203252032522	20	0.055248618784530384	84	0.14685314685314685	21	0.027704485488126648	G	14.13	2.444673	0.43429	0.007039	0.020698	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.86366	-2.11;-2.11	4.73	0.354	0.16063	.	0.122950	0.37577	N	0.002036	T	0.03390	0.0098	L	0.56199	1.76	0.28260	P	0.9248696	P;P	0.47106	0.843;0.89	B;P	0.55923	0.408;0.787	T	0.58640	-0.7601	9	0.66056	D	0.02	-28.2945	9.4813	0.38902	0.3114:0.0:0.6886:0.0	rs11573590;rs11573590	988;988	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	M	988	ENSP00000389703:T988M;ENSP00000361266:T988M	ENSP00000361266:T988M	T	-	2	0	PTCH2	45064760	1.000000	0.71417	0.364000	0.25888	0.984000	0.73092	3.651000	0.54431	-0.012000	0.14223	-0.137000	0.14449	ACG	G|0.962;A|0.038	0.038	strong		0.637	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
FLG	2312	hgsc.bcm.edu	37	1	152276282	152276282	+	Missense_Mutation	SNP	C	C	G	rs55707024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276282C>G	ENST00000368799.1	-	3	11115	c.11080G>C	c.(11080-11082)Gag>Cag	p.E3694Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3694	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.E3694Q(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)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	911	0.181909	0.0772	0.232	5008	,	,		20697	0.3452		0.1004	False		,,,				2504	0.2035				p.E3694Q		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,1	FLG	900	1	1	Substitution - Missense(1)	skin(1)	c.G11080C						scavenged	.						50.0	56.0	54.0					1																	152276282		2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	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.11080G>C	1.37:g.152276282C>G	ENSP00000357789:p.Glu3694Gln	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	249	32	0.128514	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	8.701	0.909632	0.17833	.	.	ENSG00000143631	ENST00000368799	T	0.01787	4.64	2.52	-3.46	0.04767	.	.	.	.	.	T	0.01454	0.0047	M	0.75447	2.3	0.09310	N	1	D	0.65815	0.995	P	0.61070	0.883	T	0.34254	-0.9836	9	0.20519	T	0.43	.	0.3502	0.00348	0.1921:0.291:0.2301:0.2868	rs55707024;rs58436539	3694	P20930	FILA_HUMAN	Q	3694	ENSP00000357789:E3694Q	ENSP00000357789:E3694Q	E	-	1	0	FLG	150542906	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.189000	0.03061	-0.738000	0.04817	0.552000	0.68991	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
B4GALT3	8703	hgsc.bcm.edu	37	1	161143801	161143801	+	Silent	SNP	G	G	A	rs3813619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161143801G>A	ENST00000319769.5	-	5	750	c.528C>T	c.(526-528)aaC>aaT	p.N176N	B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Silent_p.N176N	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	176					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	GCACCCCAACGTTCAACAGTT	0.507													G|||	320	0.0638978	0.0454	0.0533	5008	,	,		20572	0.0675		0.0666	False		,,,				2504	0.09				p.N176N		Atlas-SNP	.											.	B4GALT3	39	.	0			c.C528T						PASS	.	G	,,	186,4220	118.8+/-156.5	2,182,2019	107.0	88.0	94.0		528,528,528	-4.0	1.0	1	dbSNP_107	94	552,8048	152.1+/-206.7	20,512,3768	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	,,	22,694,5787	AA,AG,GG		6.4186,4.2215,5.6743	,,	176/394,176/394,176/394	161143801	738,12268	2203	4300	6503	SO:0001819	synonymous_variant	8703	exon5			CCCAACGTTCAAC	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.528C>T	1.37:g.161143801G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	54	16	0.296296	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Silent	SNP	ENST00000319769.5	37	CCDS1222.1																																																																																			G|0.946;A|0.054	0.054	strong		0.507	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
MADCAM1	8174	hgsc.bcm.edu	37	19	501900	501900	+	Missense_Mutation	SNP	C	C	A	rs3745925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:501900C>A	ENST00000215637.3	+	4	945	c.899C>A	c.(898-900)cCc>cAc	p.P300H	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000382683.4_Intron|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P81H	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	300	Mucin-like.		P -> H (in dbSNP:rs3745925).		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)		CAGGCTGGGCCCACGCAGGGA	0.667													C|||	1088	0.217252	0.2103	0.2017	5008	,	,		11442	0.3224		0.2386	False		,,,				2504	0.1074				p.P300H		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C899A						PASS	.	C	HIS/PRO,	870,3470		95,680,1395	8.0	9.0	8.0		899,	-0.8	0.0	19	dbSNP_107	8	1715,6805		191,1333,2736	yes	missense,intron	MADCAM1	NM_130760.2,NM_130762.2	77,	286,2013,4131	AA,AC,CC		20.1291,20.0461,20.1011	probably-damaging,	300/383,	501900	2585,10275	2170	4260	6430	SO:0001583	missense	8174	exon4			CTGGGCCCACGCA	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.899C>A	19.37:g.501900C>A	ENSP00000215637:p.Pro300His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	566	0.2591575091575092	102	0.2073170731707317	82	0.2265193370165746	192	0.3356643356643357	190	0.25065963060686014	c	0.244	-1.011721	0.02095	0.200461	0.201291	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10382	2.88	1.75	-0.825	0.10809	.	1.969940	0.03219	U	0.177235	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.67145	0.996	P	0.46172	0.506	T	0.28964	-1.0027	9	0.46703	T	0.11	.	0.5786	0.00708	0.2459:0.3319:0.2439:0.1782	rs3745925;rs58652856;rs3745925	300	Q13477	MADCA_HUMAN	H	324;316;308;300	ENSP00000215637:P300H	ENSP00000215637:P300H	P	+	2	0	MADCAM1	452900	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.049000	0.14099	-0.143000	0.11334	0.650000	0.86243	CCC	C|0.760;A|0.240	0.240	strong		0.667	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
UGGT2	55757	hgsc.bcm.edu	37	13	96555149	96555149	+	Missense_Mutation	SNP	C	C	T	rs33949518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96555149C>T	ENST00000376747.3	-	21	2531	c.2461G>A	c.(2461-2463)Gct>Act	p.A821T		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	821			A -> T (in dbSNP:rs33949518). {ECO:0000269|PubMed:10694380}.		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						GAGTAAATAGCTGTAGCAATT	0.328													C|||	576	0.115016	0.1399	0.1167	5008	,	,		17475	0.0526		0.1819	False		,,,				2504	0.0757				p.A821T		Atlas-SNP	.											.	UGGT2	127	.	0			c.G2461A						PASS	.	C	THR/ALA	604,3798	256.7+/-261.4	43,518,1640	93.0	101.0	99.0		2461	4.8	1.0	13	dbSNP_126	99	1397,7199	268.2+/-287.7	123,1151,3024	yes	missense	UGGT2	NM_020121.3	58	166,1669,4664	TT,TC,CC		16.2517,13.721,15.3947	benign	821/1517	96555149	2001,10997	2201	4298	6499	SO:0001583	missense	55757	exon21			AAATAGCTGTAGC	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.2461G>A	13.37:g.96555149C>T	ENSP00000365938:p.Ala821Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	292	0.1336996336996337	77	0.1565040650406504	57	0.1574585635359116	25	0.043706293706293704	133	0.17546174142480211	C	12.92	2.081586	0.36758	0.13721	0.162517	ENSG00000102595	ENST00000376747	T	0.08634	3.07	5.66	4.81	0.61882	.	0.435762	0.25408	N	0.030896	T	0.00039	0.0001	M	0.76328	2.33	0.24946	P	0.99182671	B	0.20887	0.049	B	0.19946	0.027	T	0.28839	-1.0031	9	0.15952	T	0.53	-15.4287	12.3074	0.54910	0.1409:0.7379:0.1212:0.0	rs33949518;rs58131245;rs33949518	821	Q9NYU1	UGGG2_HUMAN	T	821	ENSP00000365938:A821T	ENSP00000365938:A821T	A	-	1	0	UGGT2	95353150	1.000000	0.71417	0.992000	0.48379	0.826000	0.46750	2.713000	0.47194	1.384000	0.46424	-0.172000	0.13284	GCT	C|0.858;T|0.142	0.142	strong		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
TTC39B	158219	hgsc.bcm.edu	37	9	15188106	15188106	+	Missense_Mutation	SNP	T	T	C	rs1407977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:15188106T>C	ENST00000512701.2	-	14	1294	c.1258A>G	c.(1258-1260)Att>Gtt	p.I420V	TTC39B_ENST00000355694.2_Missense_Mutation_p.I354V|TTC39B_ENST00000507285.1_Missense_Mutation_p.I255V|TTC39B_ENST00000297615.5_Missense_Mutation_p.I351V|TTC39B_ENST00000380850.4_Missense_Mutation_p.I407V|TTC39B_ENST00000507993.1_Missense_Mutation_p.I255V			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	420			I -> V (in dbSNP:rs1407977). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						TGAACTGAAATGCATTTTTGA	0.343													t|||	3869	0.772564	0.8548	0.7089	5008	,	,		22606	0.9236		0.5964	False		,,,				2504	0.7321				p.I420V		Atlas-SNP	.											TTC39B_ENST00000512701,NS,carcinoma,0,1	TTC39B	83	1	0			c.A1258G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	3546,860	744.3+/-411.5	1436,674,93	145.0	138.0	140.0		1252,1219,1051,763,1258	2.8	1.0	9	dbSNP_88	140	5084,3514	632.1+/-398.6	1486,2112,701	yes	missense,missense,missense,missense,missense	TTC39B	NM_001168339.1,NM_001168340.1,NM_001168341.1,NM_001168342.1,NM_152574.2	29,29,29,29,29	2922,2786,794	CC,CT,TT		40.87,19.5188,33.6358	benign,benign,benign,benign,benign	418/681,407/670,351/614,255/518,420/683	15188106	8630,4374	2203	4299	6502	SO:0001583	missense	158219	exon14			CTGAAATGCATTT	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1258A>G	9.37:g.15188106T>C	ENSP00000422496:p.Ile420Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_152574	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	37	CCDS6477.2	1665	0.7623626373626373	430	0.8739837398373984	243	0.6712707182320442	535	0.9353146853146853	457	0.6029023746701847	t	1.742	-0.491464	0.04322	0.804812	0.5913	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	T;T;T;T;T;T	0.52754	0.93;0.99;0.65;0.65;0.99;0.99	5.4	2.85	0.33270	Tetratricopeptide-like helical (1);	0.115474	0.56097	N	0.000029	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.9999999999999394	B;B;B;B	0.09022	0.002;0.0;0.002;0.0	B;B;B;B	0.15052	0.012;0.007;0.01;0.007	T	0.33343	-0.9872	9	0.15066	T	0.55	-11.1261	12.6299	0.56651	0.0:0.0795:0.0:0.9205	rs1407977;rs17325022;rs52814502;rs57577773;rs1407977	351;407;420;354	F5H705;E9PAQ9;E9PE60;Q5VTQ0	.;.;.;TT39B_HUMAN	V	407;351;354;420;255;255	ENSP00000370231:I407V;ENSP00000297615:I351V;ENSP00000347920:I354V;ENSP00000422496:I420V;ENSP00000426539:I255V;ENSP00000423392:I255V	ENSP00000297615:I351V	I	-	1	0	TTC39B	15178106	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	1.742000	0.38248	0.342000	0.23796	-1.067000	0.02272	ATT	T|0.284;C|0.716	0.716	strong		0.343	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
NUP153	9972	hgsc.bcm.edu	37	6	17675553	17675553	+	Silent	SNP	T	T	C	rs61748704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17675553T>C	ENST00000262077.2	-	4	629	c.630A>G	c.(628-630)ccA>ccG	p.P210P	NUP153_ENST00000537253.1_Silent_p.P210P	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	210					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 RNA export from nucleus (GO:0046832)|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 entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			GTTCAGCTTCTGGGGACCACA	0.418													T|||	69	0.013778	0.0182	0.0187	5008	,	,		15245	0.0		0.0179	False		,,,				2504	0.0143				p.P210P		Atlas-SNP	.											.	NUP153	116	.	0			c.A630G						PASS	.	T		81,4325	69.8+/-107.6	0,81,2122	151.0	151.0	151.0		630	2.1	1.0	6	dbSNP_129	151	227,8373	93.5+/-155.5	2,223,4075	no	coding-synonymous	NUP153	NM_005124.2		2,304,6197	CC,CT,TT		2.6395,1.8384,2.3681		210/1476	17675553	308,12698	2203	4300	6503	SO:0001819	synonymous_variant	9972	exon4			AGCTTCTGGGGAC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.630A>G	6.37:g.17675553T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	37	CCDS4541.1																																																																																			T|0.978;C|0.022	0.022	strong		0.418	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
FLNB	2317	hgsc.bcm.edu	37	3	58118555	58118555	+	Missense_Mutation	SNP	G	G	A	rs12632456	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58118555G>A	ENST00000295956.4	+	26	4576	c.4411G>A	c.(4411-4413)Gtg>Atg	p.V1471M	FLNB_ENST00000490882.1_Missense_Mutation_p.V1502M|FLNB_ENST00000429972.2_Missense_Mutation_p.V1471M|FLNB_ENST00000493452.1_Missense_Mutation_p.V1302M|FLNB_ENST00000419752.2_Missense_Mutation_p.V1302M|FLNB_ENST00000358537.3_Missense_Mutation_p.V1471M|FLNB_ENST00000357272.4_Missense_Mutation_p.V1471M|FLNB_ENST00000348383.5_Missense_Mutation_p.V1471M	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1471	Interaction with FBLP1.		V -> M (in dbSNP:rs12632456). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		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)		GCCAGTGAACGTGGTGGACAA	0.512													G|||	3046	0.608227	0.6422	0.4813	5008	,	,		23390	0.9692		0.2833	False		,,,				2504	0.6145				p.V1502M		Atlas-SNP	.											.	FLNB	430	.	0			c.G4504A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	2573,1833	636.4+/-396.6	741,1091,371	148.0	127.0	134.0		4504,4411,4411,4411	2.8	0.7	3	dbSNP_120	134	2109,6491	363.6+/-333.2	265,1579,2456	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	21,21,21,21	1006,2670,2827	AA,AG,GG		24.5233,41.6024,35.9988	benign,benign,benign,benign	1502/2634,1471/2592,1471/2579,1471/2603	58118555	4682,8324	2203	4300	6503	SO:0001583	missense	2317	exon27			GTGAACGTGGTGG	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.4411G>A	3.37:g.58118555G>A	ENSP00000295956:p.Val1471Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	94	34	0.361702	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1232	0.5641025641025641	315	0.6402439024390244	153	0.42265193370165743	554	0.9685314685314685	210	0.2770448548812665	G	18.29	3.592206	0.66219	0.583976	0.245233	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.81	2.75	0.32379	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.199780	0.43110	D	0.000613	T	0.00012	0.0000	M	0.83774	2.66	0.25432	P	0.9881714	P;P;B;B;P;P	0.46395	0.877;0.588;0.382;0.057;0.807;0.807	B;B;B;B;B;B	0.43536	0.37;0.194;0.278;0.055;0.423;0.423	T	0.33828	-0.9853	9	0.49607	T	0.09	.	5.5883	0.17287	0.3207:0.1285:0.5508:0.0	rs12632456;rs52793889;rs61428936;rs12632456	1471;1502;1302;1302;1471;1471	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	M	1471;1502;1471;1471;1471;1471;1302;1302	ENSP00000295956:V1471M;ENSP00000420213:V1502M;ENSP00000351339:V1471M;ENSP00000415599:V1471M;ENSP00000232447:V1471M;ENSP00000349819:V1471M;ENSP00000418510:V1302M;ENSP00000414532:V1302M	ENSP00000295956:V1471M	V	+	1	0	FLNB	58093595	1.000000	0.71417	0.669000	0.29828	0.915000	0.54546	2.951000	0.49089	0.228000	0.21019	0.557000	0.71058	GTG	G|0.538;A|0.462	0.462	strong		0.512	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
TBX6	6911	hgsc.bcm.edu	37	16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	rs56098093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000279386.2_Missense_Mutation_p.G162S|TBX6_ENST00000553607.1_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47.0	52.0	50.0		484	5.8	1.0	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	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.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
CMBL	134147	hgsc.bcm.edu	37	5	10282396	10282396	+	Silent	SNP	A	A	G	rs10067744	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	104	0	0		WXS	Illumina HiSeq	Phase_I	140	55	0.392857	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	
MAGEC1	9947	hgsc.bcm.edu	37	X	140994419	140994419	+	Missense_Mutation	SNP	T	T	C	rs138268726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:140994419T>C	ENST00000285879.4	+	4	1515	c.1229T>C	c.(1228-1230)aTt>aCt	p.I410T	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	410										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)					CCTCTCCAGATTCCTATGACC	0.483										HNSCC(15;0.026)			-|||	284	0.0752318	0.0401	0.0533	3775	,	,		13350	0.0337		0.0577	False		,,,				2504	0.1043				p.I410T		Atlas-SNP	.											.	MAGEC1	317	.	0			c.T1229C						PASS	.	T	THR/ILE	190,3643		12,134,32,1486,537	118.0	129.0	126.0		1229		0.0	X	dbSNP_134	126	634,6086		24,425,161,1979,1703	no	missense	MAGEC1	NM_005462.4	89	36,559,193,3465,2240	CC,CT,C,TT,T		9.4345,4.957,7.8082	possibly-damaging	410/1143	140994419	824,9729	2201	4292	6493	SO:0001583	missense	9947	exon4			TCCAGATTCCTAT	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.1229T>C	X.37:g.140994419T>C	ENSP00000285879:p.Ile410Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	113	105	0.929204	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	107	0.0644966847498493	19	0.03991596638655462	11	0.03197674418604651	10	0.017793594306049824	33	0.045205479452054796	t	0.313	-0.966724	0.02232	0.04957	0.094345	ENSG00000155495	ENST00000285879	T	0.03801	3.8	.	.	.	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	P	0.38110	0.618	B	0.25759	0.063	T	0.47302	-0.9128	7	0.66056	D	0.02	.	4.5609	0.12160	0.0:5.0E-4:0.0:0.9995	.	410	O60732	MAGC1_HUMAN	T	410	ENSP00000285879:I410T	ENSP00000285879:I410T	I	+	2	0	MAGEC1	140822085	0.000000	0.05858	0.021000	0.16686	0.021000	0.10359	0.010000	0.13242	0.127000	0.18452	0.126000	0.15802	ATT	T|0.932;C|0.068	0.068	strong		0.483	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
TRIM59	286827	hgsc.bcm.edu	37	3	160156951	160156951	+	Silent	SNP	C	C	T	rs1141023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:160156951C>T	ENST00000309784.4	-	3	206	c.21G>A	c.(19-21)gaG>gaA	p.E7E	TRIM59_ENST00000543469.1_Silent_p.E7E|RP11-432B6.3_ENST00000483754.1_Silent_p.E7E	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	7					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GACAAGTTAACTCTTCCTCAA	0.328													C|||	412	0.0822684	0.0045	0.1009	5008	,	,		18066	0.0397		0.1839	False		,,,				2504	0.1135				p.E7E		Atlas-SNP	.											.	TRIM59	42	.	0			c.G21A						PASS	.	C		168,4236	101.2+/-139.8	4,160,2038	40.0	39.0	40.0		21	2.0	1.0	3	dbSNP_86	40	1742,6852	284.4+/-296.6	178,1386,2733	no	coding-synonymous	TRIM59	NM_173084.2		182,1546,4771	TT,TC,CC		20.27,3.8147,14.6946		7/404	160156951	1910,11088	2202	4297	6499	SO:0001819	synonymous_variant	286827	exon3			AGTTAACTCTTCC	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	30834	protein-coding gene	gene with protein product			"""tripartite motif-containing 57"", ""tripartite motif-containing 59"""	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.21G>A	3.37:g.160156951C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	169	100	0.591716	NM_173084	A8K5G9|D3DNL9	Silent	SNP	ENST00000309784.4	37	CCDS3190.1																																																																																			C|0.882;T|0.118	0.118	strong		0.328	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084	
CCDC181	57821	hgsc.bcm.edu	37	1	169391154	169391154	+	Missense_Mutation	SNP	A	A	G	rs3820059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169391154A>G	ENST00000367806.3	-	3	667	c.515T>C	c.(514-516)tTt>tCt	p.F172S	CCDC181_ENST00000545005.1_Missense_Mutation_p.F172S|CCDC181_ENST00000367805.3_Missense_Mutation_p.F172S|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	172			F -> S (in dbSNP:rs3820059). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			nucleus (GO:0005634)											ATAATTTTTAAAAGTAGTAGT	0.353													G|||	3450	0.688898	0.6422	0.7176	5008	,	,		19760	0.9236		0.669	False		,,,				2504	0.5102				p.F172S		Atlas-SNP	.											.	C1orf114	67	.	0			c.T515C						PASS	.	G	SER/PHE	2829,1577	481.0+/-359.0	900,1029,274	70.0	76.0	74.0		515	1.7	0.0	1	dbSNP_107	74	5549,3047	465.3+/-366.5	1770,2009,519	yes	missense	C1orf114	NM_021179.1	155	2670,3038,793	GG,GA,AA		35.4467,35.7921,35.5638	benign	172/509	169391154	8378,4624	2203	4298	6501	SO:0001583	missense	57821	exon3			TTTTTAAAAGTAG	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.515T>C	1.37:g.169391154A>G	ENSP00000356780:p.Phe172Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		1629	0.7458791208791209	319	0.6483739837398373	263	0.7265193370165746	534	0.9335664335664335	513	0.6767810026385225	G	0.003	-2.535484	0.00143	0.642079	0.645533	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.19938	2.12;2.12;2.12;2.11	5.24	1.67	0.24075	.	1.102760	0.06633	N	0.759632	T	0.02304	0.0071	N	0.08118	0	0.09310	P	0.999993	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.0;0.0	T	0.44050	-0.9353	9	0.17832	T	0.49	0.091	2.0448	0.03558	0.1177:0.2061:0.1257:0.5505	rs3820059;rs17517260;rs17856743;rs52790033;rs58672233;rs3820059	172;172;172	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	S	172	ENSP00000356779:F172S;ENSP00000356780:F172S;ENSP00000442297:F172S;ENSP00000411000:F172S	ENSP00000356779:F172S	F	-	2	0	C1orf114	167657778	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	0.118000	0.15605	0.026000	0.15269	-1.625000	0.00788	TTT	A|0.308;G|0.692	0.692	strong		0.353	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	
PLXNB1	5364	hgsc.bcm.edu	37	3	48461313	48461313	+	Silent	SNP	C	C	G	rs2362450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48461313C>G	ENST00000358536.4	-	11	2651	c.2382G>C	c.(2380-2382)ccG>ccC	p.P794P	PLXNB1_ENST00000456774.1_Intron|PLXNB1_ENST00000296440.6_Silent_p.P794P|PLXNB1_ENST00000358459.4_Intron|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	794	Pro-rich.				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)		CTACCTCTGACGGTGACAGCG	0.657													G|||	2165	0.432308	0.6399	0.3357	5008	,	,		14003	0.3135		0.4652	False		,,,				2504	0.3088				p.P794P		Atlas-SNP	.											PLXNB1,colon,carcinoma,-2,1	PLXNB1	150	1	0			c.G2382C						PASS	.	G	,	2736,1668		872,992,338	13.0	16.0	15.0		2382,2382	3.7	0.8	3	dbSNP_100	15	4083,4505		994,2095,1205	no	coding-synonymous,coding-synonymous	PLXNB1	NM_001130082.1,NM_002673.4	,	1866,3087,1543	GG,GC,CC		47.5431,37.8747,47.5139	,	794/2136,794/2136	48461313	6819,6173	2202	4294	6496	SO:0001819	synonymous_variant	5364	exon11			CTCTGACGGTGAC	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.2382G>C	3.37:g.48461313C>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	157	85	0.541401	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	37	CCDS2765.1																																																																																			C|0.517;G|0.483	0.483	strong		0.657	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
PWP2	5822	hgsc.bcm.edu	37	21	45538647	45538647	+	Silent	SNP	T	T	C	rs756553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45538647T>C	ENST00000291576.7	+	9	1111	c.984T>C	c.(982-984)atT>atC	p.I328I		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	328					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		TCTGCAGCATTTCAGATCAGA	0.597													C|||	3016	0.602236	0.3517	0.6801	5008	,	,		16395	0.7014		0.8231	False		,,,				2504	0.5562				p.I328I		Atlas-SNP	.											.	PWP2	64	.	0			c.T984C						PASS	.	C		1762,2644	645.6+/-398.2	358,1046,799	111.0	92.0	99.0		984	2.8	1.0	21	dbSNP_86	99	6953,1647	304.0+/-306.7	2832,1289,179	no	coding-synonymous	PWP2	NM_005049.2		3190,2335,978	CC,CT,TT		19.1512,39.9909,32.9925		328/920	45538647	8715,4291	2203	4300	6503	SO:0001819	synonymous_variant	5822	exon9			CAGCATTTCAGAT		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.984T>C	21.37:g.45538647T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_005049	B2RAG8|Q96A77	Silent	SNP	ENST00000291576.7	37	CCDS33579.1																																																																																			T|0.327;C|0.673	0.673	strong		0.597	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
QRICH2	84074	hgsc.bcm.edu	37	17	74290008	74290008	+	Missense_Mutation	SNP	G	G	T	rs62621822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74290008G>T	ENST00000262765.5	-	4	481	c.302C>A	c.(301-303)cCa>cAa	p.P101Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	101										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTCAATACTTGGTTGCTTGGT	0.527													G|||	37	0.00738818	0.0	0.0101	5008	,	,		18679	0.0		0.0278	False		,,,				2504	0.002				p.P101Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.C302A						PASS	.	G	GLN/PRO	25,4381	31.7+/-61.6	0,25,2178	104.0	104.0	104.0		302	0.7	0.0	17	dbSNP_129	104	252,8348	100.8+/-162.1	1,250,4049	yes	missense	QRICH2	NM_032134.1	76	1,275,6227	TT,TG,GG		2.9302,0.5674,2.1298	probably-damaging	101/1664	74290008	277,12729	2203	4300	6503	SO:0001583	missense	84074	exon4			ATACTTGGTTGCT	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.302C>A	17.37:g.74290008G>T	ENSP00000262765:p.Pro101Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	G	11.32	1.603688	0.28534	0.005674	0.029302	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.09630	2.96	3.74	0.655	0.17839	.	.	.	.	.	T	0.06781	0.0173	M	0.66939	2.045	0.09310	N	1	D;P	0.58268	0.982;0.899	P;P	0.54889	0.763;0.571	T	0.06625	-1.0816	9	0.72032	D	0.01	-0.0019	5.8311	0.18581	0.3459:0.0:0.6541:0.0	rs62621822	101;101	B5MD94;Q9H0J4	.;QRIC2_HUMAN	Q	101	ENSP00000262765:P101Q	ENSP00000262765:P101Q	P	-	2	0	QRICH2	71801603	0.000000	0.05858	0.000000	0.03702	0.147000	0.21601	0.394000	0.20834	0.197000	0.20387	-0.251000	0.11542	CCA	G|0.982;T|0.018	0.018	strong		0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
MED16	10025	hgsc.bcm.edu	37	19	890165	890165	+	Silent	SNP	G	G	A	rs6678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:890165G>A	ENST00000589119.1	-	2	248	c.249C>T	c.(247-249)gcC>gcT	p.A83A	MED16_ENST00000606828.1_Intron|MED16_ENST00000325464.1_Silent_p.A83A|MED16_ENST00000395808.3_Silent_p.A83A|MED16_ENST00000269814.4_Silent_p.A83A|MED16_ENST00000312090.6_Silent_p.A83A			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	83					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		GGCAGGTGATGGCCTCGTGGT	0.682													G|||	891	0.177915	0.2693	0.1931	5008	,	,		17255	0.0208		0.2604	False		,,,				2504	0.1207				p.A83A		Atlas-SNP	.											.	MED16	61	.	0			c.C249T						PASS	.	G		1045,3267		149,747,1260	87.0	69.0	75.0		249	1.2	1.0	19	dbSNP_52	75	2043,6395		254,1535,2430	no	coding-synonymous	MED16	NM_005481.2		403,2282,3690	AA,AG,GG		24.2119,24.2347,24.2196		83/878	890165	3088,9662	2156	4219	6375	SO:0001819	synonymous_variant	10025	exon3			GGTGATGGCCTCG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.249C>T	19.37:g.890165G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.765;A|0.235	0.235	strong		0.682	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
CYSLTR2	57105	hgsc.bcm.edu	37	13	49281554	49281554	+	Missense_Mutation	SNP	A	A	G	rs41347648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:49281554A>G	ENST00000282018.3	+	1	604	c.601A>G	c.(601-603)Atg>Gtg	p.M201V		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	201					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	GCTGCAGACCATGAACTATAT	0.478													A|||	35	0.00698882	0.0015	0.0202	5008	,	,		20528	0.0		0.0129	False		,,,				2504	0.0061				p.M201V		Atlas-SNP	.											.	CYSLTR2	55	.	0			c.A601G	GRCh37	CM034033	CYSLTR2	M	rs41347648	PASS	.	A	VAL/MET	21,4385	27.2+/-55.0	0,21,2182	118.0	115.0	116.0		601	0.6	0.0	13	dbSNP_127	116	217,8383	91.6+/-153.7	0,217,4083	yes	missense	CYSLTR2	NM_020377.2	21	0,238,6265	GG,GA,AA		2.5233,0.4766,1.8299	benign	201/347	49281554	238,12768	2203	4300	6503	SO:0001583	missense	57105	exon1			CAGACCATGAACT	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"""GPCR / Class A : Leukotriene receptors"""	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.601A>G	13.37:g.49281554A>G	ENSP00000282018:p.Met201Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_020377	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	CCDS9412.1	17	0.007783882783882784	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	9	0.011873350923482849	A	2.924	-0.222489	0.06061	0.004766	0.025233	ENSG00000152207	ENST00000282018	T	0.35789	1.29	5.89	0.547	0.17202	GPCR, rhodopsin-like superfamily (1);	0.489617	0.20222	N	0.096662	T	0.08268	0.0206	L	0.37466	1.105	0.21740	N	0.999567	B	0.22983	0.078	B	0.22152	0.038	T	0.13229	-1.0517	10	0.25106	T	0.35	.	6.5752	0.22562	0.5058:0.1926:0.0:0.3017	rs41347648;rs61735176	201	Q9NS75	CLTR2_HUMAN	V	201	ENSP00000282018:M201V	ENSP00000282018:M201V	M	+	1	0	CYSLTR2	48179555	0.000000	0.05858	0.016000	0.15963	0.094000	0.18550	-0.370000	0.07523	-0.119000	0.11830	0.533000	0.62120	ATG	A|0.985;G|0.015	0.015	strong		0.478	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1		
IGSF5	150084	hgsc.bcm.edu	37	21	41137499	41137499	+	Silent	SNP	A	A	G	rs12626544	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:41137499A>G	ENST00000380588.4	+	3	241	c.138A>G	c.(136-138)caA>caG	p.Q46Q	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	46	Ig-like V-type 1.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				AAGGCCCCCAAAATGCAAGAG	0.493													A|||	1983	0.395966	0.2027	0.5389	5008	,	,		19833	0.4702		0.3926	False		,,,				2504	0.4826				p.Q46Q		Atlas-SNP	.											.	IGSF5	62	.	0			c.A138G						PASS	.	A		992,3414	370.0+/-319.4	118,756,1329	56.0	55.0	55.0		138	3.2	1.0	21	dbSNP_120	55	2972,5628	456.2+/-364.0	528,1916,1856	no	coding-synonymous	IGSF5	NM_001080444.1		646,2672,3185	GG,GA,AA		34.5581,22.5148,30.4782		46/408	41137499	3964,9042	2203	4300	6503	SO:0001819	synonymous_variant	150084	exon3			CCCCCAAAATGCA		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.138A>G	21.37:g.41137499A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001080444		Silent	SNP	ENST00000380588.4	37	CCDS33562.1																																																																																			A|0.661;G|0.339	0.339	strong		0.493	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
FAM25A	643161	hgsc.bcm.edu	37	10	88782111	88782111	+	Silent	SNP	C	C	T	rs61857037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88782111C>T	ENST00000343959.4	+	2	133	c.114C>T	c.(112-114)caC>caT	p.H38H	RP11-96C23.14_ENST00000444180.3_RNA	NM_001146157.2	NP_001139629.1	B3EWG3	FM25A_HUMAN	family with sequence similarity 25, member A	38										stomach(1)	1						TGGTGGGACACGCCAAGGAGA	0.602													.|||	585	0.116813	0.1218	0.1729	5008	,	,		20466	0.0883		0.0795	False		,,,				2504	0.138				p.H38H		Atlas-SNP	.											FAM25A,colon,carcinoma,0,1	FAM25A	4	1	0			c.C114T						PASS	.						38.0	35.0	36.0					10																	88782111		692	1591	2283	SO:0001819	synonymous_variant	643161	exon2			GGGACACGCCAAG		CCDS44451.1	10q23.2	2008-08-13			ENSG00000188100	ENSG00000188100			23436	protein-coding gene	gene with protein product							Standard	NM_001146157		Approved	bA96C23.5	uc010qmo.2	B3EWG3	OTTHUMG00000018664	ENST00000343959.4:c.114C>T	10.37:g.88782111C>T		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_001146157	B2RV02|Q5VTM1	Silent	SNP	ENST00000343959.4	37	CCDS44451.1	180	0.08241758241758242	58	0.11788617886178862	46	0.1270718232044199	36	0.06293706293706294	40	0.052770448548812667	T	1.966	-0.437763	0.04636	.	.	ENSG00000188100	ENST00000343959	.	.	.	3.93	-3.72	0.04411	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.21604	P	0.99962918	.	.	.	.	.	.	T	0.22208	-1.0223	3	.	.	.	-2.8604	10.3976	0.44209	0.0:0.6636:0.1311:0.2053	rs61857037	.	.	.	C	45	.	.	R	+	1	0	FAM25A	88772091	0.000000	0.05858	0.257000	0.24404	0.117000	0.20001	-2.997000	0.00654	-1.067000	0.03160	-0.540000	0.04249	CGC	C|0.913;T|0.087	0.087	strong		0.602	FAM25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049182.2		
UPF3A	65110	hgsc.bcm.edu	37	13	115064423	115064423	+	Missense_Mutation	SNP	G	G	A	rs3752107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115064423G>A	ENST00000375299.3	+	8	1011	c.955G>A	c.(955-957)Gca>Aca	p.A319T	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Missense_Mutation_p.A286T	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	319					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)		TGCCCCCGGTGCAGTCGTAAA	0.547													G|||	273	0.0545128	0.0136	0.0389	5008	,	,		17352	0.0357		0.0746	False		,,,				2504	0.1196				p.A319T		Atlas-SNP	.											UPF3A,colon,carcinoma,0,1	UPF3A	47	1	0			c.G955A						PASS	.	G	THR/ALA,THR/ALA	93,4313	75.2+/-113.4	1,91,2111	53.0	51.0	52.0		955,856	-1.2	0.0	13	dbSNP_107	52	529,8071	147.1+/-202.6	19,491,3790	no	missense,missense	UPF3A	NM_023011.3,NM_080687.2	58,58	20,582,5901	AA,AG,GG		6.1512,2.1108,4.7824	benign,benign	319/477,286/444	115064423	622,12384	2203	4300	6503	SO:0001583	missense	65110	exon8			CCCGGTGCAGTCG	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.955G>A	13.37:g.115064423G>A	ENSP00000364448:p.Ala319Thr	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	243	117	0.481481	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Missense_Mutation	SNP	ENST00000375299.3	37	CCDS9543.1	110	0.05036630036630037	11	0.022357723577235773	15	0.04143646408839779	26	0.045454545454545456	58	0.07651715039577836	G	4.682	0.126748	0.08931	0.021108	0.061512	ENSG00000169062	ENST00000375299;ENST00000351487;ENST00000543577	T;T	0.80909	-1.43;1.64	4.08	-1.17	0.09648	.	0.751533	0.12508	N	0.462684	T	0.07773	0.0195	N	0.15975	0.35	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.03423	-1.1038	9	.	.	.	-1.1725	10.6354	0.45563	0.2261:0.0:0.7739:0.0	rs3752107;rs9525320	286;319	Q9H1J1-2;Q9H1J1	.;REN3A_HUMAN	T	319;286;118	ENSP00000364448:A319T;ENSP00000329592:A286T	.	A	+	1	0	UPF3A	114082525	0.302000	0.24454	0.000000	0.03702	0.000000	0.00434	2.210000	0.42816	-0.212000	0.10109	-1.000000	0.02509	GCA	G|0.949;A|0.051	0.051	strong		0.547	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
COL6A3	1293	hgsc.bcm.edu	37	2	238247734	238247734	+	Missense_Mutation	SNP	C	C	G	rs36104025	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238247734C>G	ENST00000295550.4	-	39	8943	c.8491G>C	c.(8491-8493)Gat>Cat	p.D2831H	COL6A3_ENST00000347401.3_Missense_Mutation_p.D2630H|COL6A3_ENST00000409809.1_Missense_Mutation_p.D2625H|COL6A3_ENST00000472056.1_Missense_Mutation_p.D2224H|COL6A3_ENST00000353578.4_Missense_Mutation_p.D2625H|COL6A3_ENST00000346358.4_Missense_Mutation_p.D2631H	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2831	Nonhelical region.		D -> H (in dbSNP:rs36104025). {ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:17886299, ECO:0000269|PubMed:9536084}.		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)		TTCCTGATATCTGGGGACAAG	0.333													C|||	163	0.0325479	0.0083	0.0447	5008	,	,		19123	0.0		0.0716	False		,,,				2504	0.0501				p.D2831H		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8491C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	83,4323	69.8+/-107.6	4,75,2124	71.0	70.0	70.0		8491,6670,7873	5.1	1.0	2	dbSNP_126	70	853,7747	194.7+/-240.0	48,757,3495	yes	missense,missense,missense	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	81,81,81	52,832,5619	GG,GC,CC		9.9186,1.8838,7.1967	probably-damaging,probably-damaging,probably-damaging	2831/3178,2224/2571,2625/2972	238247734	936,12070	2203	4300	6503	SO:0001583	missense	1293	exon39			TGATATCTGGGGA	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.8491G>C	2.37:g.238247734C>G	ENSP00000295550:p.Asp2831His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	90	0.04120879120879121	6	0.012195121951219513	16	0.04419889502762431	0	0.0	68	0.08970976253298153	C	14.74	2.624546	0.46840	0.018838	0.099186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.89939	-2.59;-2.57;-2.55;-2.56;-2.55;-2.55	5.09	5.09	0.68999	.	0.118877	0.36893	N	0.002355	T	0.40839	0.1133	M	0.64997	1.995	0.53688	D	0.999971	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.921;0.964;0.997	T	0.72906	-0.4150	10	0.72032	D	0.01	.	18.52	0.90948	0.0:1.0:0.0:0.0	rs36104025	2224;2625;2831	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	H	2831;2630;2625;2224;2625;2631	ENSP00000295550:D2831H;ENSP00000315609:D2630H;ENSP00000315873:D2625H;ENSP00000418285:D2224H;ENSP00000386844:D2625H;ENSP00000295546:D2631H	ENSP00000295550:D2831H	D	-	1	0	COL6A3	237912473	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.416000	0.66417	2.378000	0.81104	0.655000	0.94253	GAT	C|0.942;G|0.058	0.058	strong		0.333	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
OR8U1	219417	hgsc.bcm.edu	37	11	56143977	56143977	+	Missense_Mutation	SNP	A	A	G	rs12272403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:56143977A>G	ENST00000302270.1	+	1	878	c.878A>G	c.(877-879)cAg>cGg	p.Q293R		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	293			Q -> R (in dbSNP:rs12272403).			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)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					TATAGCCTCCAGAATAAGGAG	0.373													G|||	1608	0.321086	0.5484	0.2363	5008	,	,		18009	0.1379		0.3579	False		,,,				2504	0.2249				p.Q293R		Atlas-SNP	.											.	OR8U1	59	.	0			c.A878G						PASS	.	G	ARG/GLN	1936,1866		511,914,476	119.0	123.0	122.0		878	4.8	0.6	11	dbSNP_120	122	2968,5300		510,1948,1676	yes	missense	OR8U1	NM_001005204.1	43	1021,2862,2152	GG,GA,AA		35.8974,49.0794,40.6297	benign	293/310	56143977	4904,7166	1901	4134	6035	SO:0001583	missense	219417	exon1			GCCTCCAGAATAA	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.878A>G	11.37:g.56143977A>G	ENSP00000304188:p.Gln293Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	40	25	0.625	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	762	0.3489010989010989	254	0.516260162601626	92	0.2541436464088398	126	0.2202797202797203	290	0.38258575197889183	G	0.009	-1.832186	0.00579	0.509206	0.358974	ENSG00000172199	ENST00000302270	T	0.00342	8.03	5.69	4.78	0.61160	.	0.000000	0.47093	N	0.000242	T	0.00012	0.0000	N	0.00001	-3.68	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	9	0.02654	T	1	.	9.794	0.40724	0.2092:0.0:0.7908:0.0	rs12272403;rs60622359;rs12272403	293	Q8NH10	OR8U1_HUMAN	R	293	ENSP00000304188:Q293R	ENSP00000304188:Q293R	Q	+	2	0	OR8U1	55900553	0.799000	0.28903	0.596000	0.28811	0.001000	0.01503	3.683000	0.54663	0.792000	0.33850	-0.200000	0.12747	CAG	A|0.655;G|0.345	0.345	strong		0.373	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
MUC4	4585	hgsc.bcm.edu	37	3	195513126	195513126	+	Silent	SNP	G	G	A	rs62282488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195513126G>A	ENST00000463781.3	-	2	5784	c.5325C>T	c.(5323-5325)acC>acT	p.T1775T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1775T	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)		CAGGAAGTGGGGTGGCGTGAG	0.592													.|||	468	0.0934505	0.0144	0.1023	5008	,	,		35328	0.0466		0.1958	False		,,,				2504	0.137				p.T1775T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5325T						PASS	.	G	,,	38,1346		0,38,654	62.0	60.0	60.0		,5325,		0.0	3	dbSNP_129	60	548,2634		55,438,1098	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	55,476,1752	AA,AG,GG		17.2219,2.7457,12.834	,,	,1775/5413,	195513126	586,3980	692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			AAGTGGGGTGGCG	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.5325C>T	3.37:g.195513126G>A		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	438	72	0.164384	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.897;A|0.103	0.103	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RABGGTA	5875	hgsc.bcm.edu	37	14	24736027	24736027	+	Silent	SNP	G	G	A	rs14193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24736027G>A	ENST00000399409.3	-	14	1905	c.1422C>T	c.(1420-1422)cgC>cgT	p.R474R	RABGGTA_ENST00000560777.1_Silent_p.R83R|RABGGTA_ENST00000216840.6_Silent_p.R474R|RABGGTA_ENST00000559586.1_5'Flank	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	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	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	
TNFAIP8L3	388121	hgsc.bcm.edu	37	15	51350287	51350287	+	Missense_Mutation	SNP	T	T	G	rs78897873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51350287T>G	ENST00000327536.5	-	3	769	c.670A>C	c.(670-672)Aat>Cat	p.N224H	RP11-108K3.1_ENST00000559909.1_lincRNA	NM_207381.2	NP_997264.2	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 3	224										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)		TGCAGGAGATTGGAGAGCACG	0.542													T|||	79	0.0157748	0.0015	0.0216	5008	,	,		21984	0.0		0.0547	False		,,,				2504	0.0072				p.N224H		Atlas-SNP	.											.	TNFAIP8L3	30	.	0			c.A670C						PASS	.	T	HIS/ASN	41,4351	44.6+/-78.6	0,41,2155	87.0	75.0	79.0		670	-1.4	1.0	15	dbSNP_131	79	434,8152	132.6+/-190.3	9,416,3868	yes	missense	TNFAIP8L3	NM_207381.2	68	9,457,6023	GG,GT,TT		5.0547,0.9335,3.66	benign	224/293	51350287	475,12503	2196	4293	6489	SO:0001583	missense	388121	exon3			GGAGATTGGAGAG	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.670A>C	15.37:g.51350287T>G	ENSP00000328016:p.Asn224His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_207381	Q6ZWD1	Missense_Mutation	SNP	ENST00000327536.5	37	CCDS32241.1	52	0.023809523809523808	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	40	0.052770448548812667	T	15.77	2.932509	0.52866	0.009335	0.050547	ENSG00000183578	ENST00000327536	T	0.30448	1.53	5.55	-1.38	0.09027	.	0.483471	0.25347	N	0.031328	T	0.02119	0.0066	N	0.19112	0.55	0.20403	N	0.999901	B	0.26547	0.152	B	0.19391	0.025	T	0.11251	-1.0595	10	0.49607	T	0.09	-0.6704	6.1644	0.20382	0.0:0.2665:0.5113:0.2222	.	224	Q5GJ75	TP8L3_HUMAN	H	224	ENSP00000328016:N224H	ENSP00000328016:N224H	N	-	1	0	TNFAIP8L3	49137579	1.000000	0.71417	0.988000	0.46212	0.729000	0.41735	2.126000	0.42026	0.048000	0.15891	0.455000	0.32223	AAT	T|0.968;G|0.032	0.032	strong		0.542	TNFAIP8L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418661.1	NM_207381	
SLC22A18	5002	hgsc.bcm.edu	37	11	2929502	2929502	+	Missense_Mutation	SNP	G	G	A	rs143044180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2929502G>A	ENST00000380574.1	+	3	615	c.184G>A	c.(184-186)Ggc>Agc	p.G62S	SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62S|SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	62					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)		CATTGCCTTCGGCTACCTGCA	0.617																																					p.G62S		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184A						PASS	.						86.0	82.0	84.0					11																	2929502		2202	4299	6501	SO:0001583	missense	5002	exon3			GCCTTCGGCTACC	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.184G>A	11.37:g.2929502G>A	ENSP00000369948:p.Gly62Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935071	0.52866	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.84442	0.1;0.1;-0.06;0.1;-1.85	4.27	3.34	0.38264	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	D	0.87128	0.6100	L	0.56340	1.77	0.52501	D	0.999959	D;D	0.71674	0.991;0.998	P;P	0.62740	0.461;0.906	D	0.86466	0.1782	10	0.59425	D	0.04	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	62	ENSP00000307859:G62S;ENSP00000311139:G62S;ENSP00000392072:G62S;ENSP00000369948:G62S;ENSP00000433019:G62S	ENSP00000311139:G62S	G	+	1	0	SLC22A18	2886078	1.000000	0.71417	0.933000	0.37362	0.037000	0.13140	2.882000	0.48546	2.105000	0.64084	0.491000	0.48974	GGC	G|0.998;T|0.002	.	alt		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
COL4A3	1285	hgsc.bcm.edu	37	2	228135631	228135631	+	Missense_Mutation	SNP	C	C	T	rs28381984	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:228135631C>T	ENST00000396578.3	+	25	1883	c.1721C>T	c.(1720-1722)cCg>cTg	p.P574L	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	574	Triple-helical region.		P -> L (in dbSNP:rs28381984). {ECO:0000269|PubMed:8083201}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CCTGGAACTCCGGGAGTGAAA	0.507													C|||	2003	0.39996	0.152	0.4409	5008	,	,		17505	0.4752		0.4732	False		,,,				2504	0.5532				p.P574L		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,-1,2	COL4A3	293	2	0			c.C1721T						PASS	.	C	LEU/PRO	782,2936		92,598,1169	54.0	58.0	56.0		1721	5.8	0.1	2	dbSNP_125	56	3848,4336		917,2014,1161	yes	missense	COL4A3	NM_000091.4	98	1009,2612,2330	TT,TC,CC		47.0186,21.0328,38.901	probably-damaging	574/1671	228135631	4630,7272	1859	4092	5951	SO:0001583	missense	1285	exon25			GAACTCCGGGAGT		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1721C>T	2.37:g.228135631C>T	ENSP00000379823:p.Pro574Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	856	0.39194139194139194	81	0.16463414634146342	161	0.4447513812154696	266	0.46503496503496505	348	0.45910290237467016	C	19.26	3.793365	0.70452	0.210328	0.470186	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93076	-3.16	5.8	5.8	0.92144	.	0.108401	0.41605	D	0.000847	T	0.00012	0.0000	M	0.77103	2.36	0.09310	P	0.999999516562	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.944;0.987;1.0;0.998	T	0.00000	-1.3321	9	0.59425	D	0.04	.	16.9678	0.86290	0.0:1.0:0.0:0.0	rs28381984;rs58545005;rs28381984	574;574;574;574	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	L	574	ENSP00000379823:P574L	ENSP00000323334:P574L	P	+	2	0	COL4A3	227843875	0.367000	0.25023	0.130000	0.21974	0.769000	0.43574	2.193000	0.42658	2.740000	0.93945	0.650000	0.86243	CCG	C|0.604;T|0.396	0.396	strong		0.507	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
NCR2	9436	hgsc.bcm.edu	37	6	41303995	41303995	+	Missense_Mutation	SNP	A	A	G	rs9471577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:41303995A>G	ENST00000373089.5	+	2	311	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	NCR2_ENST00000373086.3_Missense_Mutation_p.M75V|NCR2_ENST00000373083.4_Missense_Mutation_p.M75V	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	75	Ig-like.		M -> V (in dbSNP:rs9471577).		cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					GCCCAGGACGATGGCTTGGAC	0.542													G|||	883	0.176318	0.2436	0.1023	5008	,	,		20277	0.3036		0.0795	False		,,,				2504	0.1063				p.M75V		Atlas-SNP	.											.	NCR2	44	.	0			c.A223G						PASS	.	G	VAL/MET,VAL/MET,VAL/MET	920,3486	738.6+/-411.0	91,738,1374	72.0	70.0	70.0		223,223,223	-0.5	0.0	6	dbSNP_119	70	641,7959	790.6+/-407.6	32,577,3691	yes	missense,missense,missense	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	21,21,21	123,1315,5065	GG,GA,AA		7.4535,20.8806,12.0022	benign,benign,benign	75/271,75/259,75/277	41303995	1561,11445	2203	4300	6503	SO:0001583	missense	9436	exon2			AGGACGATGGCTT	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.223A>G	6.37:g.41303995A>G	ENSP00000362181:p.Met75Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Missense_Mutation	SNP	ENST00000373089.5	37	CCDS4855.1	382	0.1749084249084249	91	0.18495934959349594	38	0.10497237569060773	193	0.3374125874125874	60	0.079155672823219	G	0.007	-1.941822	0.00479	0.208806	0.074535	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	T;T;T	0.64618	-0.11;-0.11;-0.11	3.44	-0.532	0.11890	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.12561	0.0305	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	0.12553	-1.0543	8	0.24483	T	0.36	.	0.567	0.00689	0.1731:0.317:0.1769:0.333	rs9471577;rs9471577	75;75;75	O95944-3;O95944-2;O95944	.;.;NCTR2_HUMAN	V	75	ENSP00000362175:M75V;ENSP00000362181:M75V;ENSP00000362178:M75V	ENSP00000362175:M75V	M	+	1	0	NCR2	41411973	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.408000	0.02485	-0.271000	0.09272	-0.762000	0.03455	ATG	A|0.858;G|0.142	0.142	strong		0.542	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
NDUFA10	4705	hgsc.bcm.edu	37	2	240946766	240946766	+	Silent	SNP	T	T	C	rs13848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240946766T>C	ENST00000252711.2	-	7	871	c.771A>G	c.(769-771)caA>caG	p.Q257Q	NDUFA10_ENST00000307300.4_Silent_p.Q287Q|NDUFA10_ENST00000404554.1_Silent_p.Q257Q	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	257					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)	16		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)		TTGCAGAATATTGTAAAACCT	0.308													C|||	1784	0.35623	0.2867	0.4424	5008	,	,		21733	0.4702		0.4115	False		,,,				2504	0.2147				p.Q257Q		Atlas-SNP	.											.	NDUFA10	40	.	0			c.A771G						PASS	.	C		1284,3120	693.8+/-405.7	184,916,1102	88.0	86.0	86.0		771	1.7	0.0	2	dbSNP_52	86	3496,5100	631.6+/-398.5	716,2064,1518	no	coding-synonymous	NDUFA10	NM_004544.3		900,2980,2620	CC,CT,TT		40.6701,29.1553,36.7692		257/356	240946766	4780,8220	2202	4298	6500	SO:0001819	synonymous_variant	4705	exon7			AGAATATTGTAAA	AF087661	CCDS2531.1	2q37.3	2011-07-04	2002-08-29		ENSG00000130414	ENSG00000130414		"""Mitochondrial respiratory chain complex / Complex I"""	7684	protein-coding gene	gene with protein product	"""complex I 42kDa subunit"""	603835	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)"""			9878551	Standard	NM_004544		Approved	CI-42k	uc002vyn.3	O95299	OTTHUMG00000133350	ENST00000252711.2:c.771A>G	2.37:g.240946766T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_004544	Q8WXC9	Silent	SNP	ENST00000252711.2	37	CCDS2531.1	899|899	0.4116300366300366|0.4116300366300366	149|149	0.30284552845528456|0.30284552845528456	167|167	0.4613259668508287|0.4613259668508287	250|250	0.4370629370629371|0.4370629370629371	333|333	0.4393139841688654|0.4393139841688654	C|C	2.675|2.675	-0.276745|-0.276745	0.05679|0.05679	0.291553|0.291553	0.406701|0.406701	ENSG00000130414|ENSG00000130414	ENST00000444548|ENST00000443626	.|D	.|0.94457	.|-3.43	4.54|4.54	1.66|1.66	0.24008|0.24008	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48901|0.48901	P|P	2.750000000000252E-4|2.750000000000252E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.00035|0.00035	-1.2263|-1.2263	3|5	.|0.56958	.|D	.|0.05	-1.9108|-1.9108	7.6453|7.6453	0.28316|0.28316	0.0:0.606:0.0:0.394|0.0:0.606:0.0:0.394	rs13848;rs1138444;rs1802467;rs3202343;rs11541495;rs17343510;rs17357973;rs17809870;rs17844982;rs17857736;rs58574753;rs3828304;rs1138444|rs13848;rs1138444;rs1802467;rs3202343;rs11541495;rs17343510;rs17357973;rs17809870;rs17844982;rs17857736;rs58574753;rs3828304;rs1138444	.|.	.|.	.|.	V|S	28|190	.|ENSP00000411527:N190S	.|ENSP00000411527:N190S	I|N	-|-	1|2	0|0	NDUFA10|NDUFA10	240595439|240595439	0.055000|0.055000	0.20627|0.20627	0.013000|0.013000	0.15412|0.15412	0.000000|0.000000	0.00434|0.00434	-0.303000|-0.303000	0.08210|0.08210	0.139000|0.139000	0.18822|0.18822	-1.050000|-1.050000	0.02344|0.02344	ATA|AAT	A|0.120;C|0.311	0.311	strong		0.308	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544	
F5	2153	hgsc.bcm.edu	37	1	169529973	169529973	+	Silent	SNP	C	C	T	rs6029	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169529973C>T	ENST00000367797.3	-	4	606	c.405G>A	c.(403-405)gcG>gcA	p.A135A	F5_ENST00000546081.1_5'UTR|F5_ENST00000367796.3_Silent_p.A135A	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	135	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)	CCATCTTCTCCGCAGGGAATG	0.522													C|||	1997	0.398762	0.584	0.2882	5008	,	,		16887	0.6647		0.1819	False		,,,				2504	0.1759				p.A135A		Atlas-SNP	.											.	F5	301	.	0			c.G405A						PASS	.	C		2249,2157	596.6+/-388.7	572,1105,526	133.0	111.0	119.0		405	-3.1	0.0	1	dbSNP_52	119	1517,7083	285.9+/-297.4	132,1253,2915	no	coding-synonymous	F5	NM_000130.4		704,2358,3441	TT,TC,CC		17.6395,48.956,28.9559		135/2225	169529973	3766,9240	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon4			CTTCTCCGCAGGG	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.405G>A	1.37:g.169529973C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	160	61	0.38125	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			C|0.653;T|0.347	0.347	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
CFAP46	54777	hgsc.bcm.edu	37	10	134738232	134738232	+	Silent	SNP	A	A	G	rs4075501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:134738232A>G	ENST00000368586.5	-	11	1324	c.1224T>C	c.(1222-1224)gcT>gcC	p.A408A	TTC40_ENST00000368582.2_Silent_p.A408A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCGCAACGCCAGCCAGGGGCT	0.677													G|||	2670	0.533147	0.7035	0.6153	5008	,	,		16344	0.3512		0.4722	False		,,,				2504	0.4949				p.A408A		Atlas-SNP	.											.	TTC40	100	.	0			c.T1224C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon11			AACGCCAGCCAGG																												ENST00000368586.5:c.1224T>C	10.37:g.134738232A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.499;G|0.501	0.501	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ZBTB46	140685	hgsc.bcm.edu	37	20	62421622	62421622	+	Silent	SNP	A	A	G	rs755017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62421622A>G	ENST00000245663.4	-	2	639	c.489T>C	c.(487-489)gcT>gcC	p.A163A	ZBTB46_ENST00000395104.1_Silent_p.A163A|ZBTB46_ENST00000302995.2_Silent_p.A163A|ZBTB46_ENST00000480766.1_5'Flank	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	163					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)					TGCTCCTCCCAGCCATCACGG	0.632													G|||	1328	0.265176	0.3116	0.1974	5008	,	,		20170	0.4623		0.1243	False		,,,				2504	0.1922				p.A163A		Atlas-SNP	.											ZBTB46,caecum,carcinoma,0,1	ZBTB46	72	1	0			c.T489C						PASS	.	G		1198,3208	673.7+/-402.8	173,852,1178	26.0	24.0	24.0		489	-9.6	0.0	20	dbSNP_86	24	1003,7597	749.4+/-407.4	61,881,3358	no	coding-synonymous	ZBTB46	NM_025224.3		234,1733,4536	GG,GA,AA		11.6628,27.1902,16.923		163/590	62421622	2201,10805	2203	4300	6503	SO:0001819	synonymous_variant	140685	exon2			CCTCCCAGCCATC	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.489T>C	20.37:g.62421622A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			A|0.797;G|0.203	0.203	strong		0.632	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
IGFN1	91156	hgsc.bcm.edu	37	1	201166435	201166435	+	Silent	SNP	T	T	C	rs11589317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201166435T>C	ENST00000335211.4	+	5	487	c.357T>C	c.(355-357)acT>acC	p.T119T	IGFN1_ENST00000451870.2_Silent_p.T119T|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	119	Ig-like 1.					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						TGAGACTCACTGTCATCGAAG	0.572													C|||	4345	0.867612	0.8623	0.7939	5008	,	,		21947	0.8552		0.9364	False		,,,				2504	0.8691				p.T119T		Atlas-SNP	.											.	IGFN1	220	.	0			c.T357C						PASS	.	C		1186,198		504,178,10	169.0	158.0	161.0		357	-10.3	0.3	1	dbSNP_120	161	2948,234		1369,210,12	no	coding-synonymous	IGFN1	NM_001164586.1		1873,388,22	CC,CT,TT		7.3539,14.3064,9.4612		119/3709	201166435	4134,432	692	1591	2283	SO:0001819	synonymous_variant	91156	exon5			ACTCACTGTCATC	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.357T>C	1.37:g.201166435T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																			T|0.124;C|0.876	0.876	strong		0.572	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
SCN1B	6324	hgsc.bcm.edu	37	19	35524939	35524939	+	Intron	SNP	C	C	A	rs67701503	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35524939C>A	ENST00000262631.5	+	3	585				CTD-2527I21.9_ENST00000601692.1_RNA|SCN1B_ENST00000595652.1_Intron|SCN1B_ENST00000596348.1_Intron|SCN1B_ENST00000415950.3_Missense_Mutation_p.S248R	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit						axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	tgtctctgagccaaagggttg	0.552													C|||	638	0.127396	0.0885	0.1311	5008	,	,		21003	0.1825		0.1461	False		,,,				2504	0.1012				p.S248R		Atlas-SNP	.											.	SCN1B	32	.	0			c.C744A						PASS	.	C	,ARG/SER	190,2062		9,172,945	88.0	99.0	95.0		,744	1.9	0.1	19	dbSNP_130	95	640,3758		42,556,1601	yes	intron,missense	SCN1B	NM_001037.4,NM_199037.3	,110	51,728,2546	AA,AC,CC		14.5521,8.4369,12.4812	,benign	,248/269	35524939	830,5820	1126	2199	3325	SO:0001627	intron_variant	6324	exon3			TCTGAGCCAAAGG		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10586	protein-coding gene	gene with protein product		600235	"""sodium channel, voltage-gated, type I, beta polypeptide"", ""sodium channel, voltage-gated, type I, beta"""			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.448+296C>A	19.37:g.35524939C>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	188	94	0.5	NM_199037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	37	CCDS12441.1	291	0.13324175824175824	33	0.06707317073170732	49	0.13535911602209943	93	0.16258741258741258	116	0.15303430079155672	C	14.15	2.449285	0.43531	0.084369	0.145521	ENSG00000105711	ENST00000415950	D	0.89617	-2.54	2.95	1.88	0.25563	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.31530	-0.9940	6	.	.	.	.	7.8587	0.29497	0.0:0.7425:0.2575:0.0	.	248	Q07699-2	.	R	248	ENSP00000396915:S248R	.	S	+	3	2	SCN1B	40216779	0.410000	0.25376	0.081000	0.20488	0.064000	0.16182	0.080000	0.14802	0.769000	0.33313	0.549000	0.68633	AGC	C|0.866;A|0.134	0.134	strong		0.552	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1		
SLC39A12	221074	hgsc.bcm.edu	37	10	18242311	18242311	+	Missense_Mutation	SNP	A	A	G	rs10764176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:18242311A>G	ENST00000377369.2	+	2	379	c.106A>G	c.(106-108)Agc>Ggc	p.S36G	SLC39A12_ENST00000539911.1_Intron|SLC39A12_ENST00000377374.4_Missense_Mutation_p.S36G|SLC39A12_ENST00000377371.3_Missense_Mutation_p.S36G	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	36			S -> G (in dbSNP:rs10764176). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16311021}.		regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GGATAGCAGAAGCCGTGGGAG	0.522													G|||	1329	0.265375	0.3048	0.2017	5008	,	,		16816	0.1548		0.2883	False		,,,				2504	0.3476				p.S36G		Atlas-SNP	.											.	SLC39A12	181	.	0			c.A106G						PASS	.	G	GLY/SER,GLY/SER	1326,3080	696.0+/-406.0	212,902,1089	94.0	92.0	93.0		106,106	-8.4	0.0	10	dbSNP_120	93	2564,6036	690.9+/-404.5	406,1752,2142	yes	missense,missense	SLC39A12	NM_001145195.1,NM_152725.3	56,56	618,2654,3231	GG,GA,AA		29.814,30.0953,29.9093	benign,benign	36/692,36/655	18242311	3890,9116	2203	4300	6503	SO:0001583	missense	221074	exon2			AGCAGAAGCCGTG		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.106A>G	10.37:g.18242311A>G	ENSP00000366586:p.Ser36Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	37	CCDS44362.1	515	0.2358058608058608	144	0.2926829268292683	83	0.2292817679558011	69	0.12062937062937062	219	0.28891820580474936	G	7.046	0.563593	0.13498	0.300953	0.29814	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371	T;T;T	0.22134	1.97;1.97;1.97	5.51	-8.36	0.00980	.	1.473130	0.03220	N	0.177415	T	0.00012	0.0000	N	0.17474	0.49	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	0.36187	-0.9758	9	0.12430	T	0.62	1.4047	5.8728	0.18812	0.627:0.1529:0.083:0.137	rs10764176;rs60194653;rs10764176	36;36;36	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	G	36	ENSP00000366586:S36G;ENSP00000366591:S36G;ENSP00000366588:S36G	ENSP00000366586:S36G	S	+	1	0	SLC39A12	18282317	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.865000	0.01649	-1.186000	0.02713	-0.119000	0.15052	AGC	A|0.724;G|0.276	0.276	strong		0.522	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
TTN	7273	hgsc.bcm.edu	37	2	179498303	179498303	+	Silent	SNP	T	T	C	rs16866425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179498303T>C	ENST00000591111.1	-	182	38084	c.37860A>G	c.(37858-37860)aaA>aaG	p.K12620K	TTN_ENST00000589042.1_Silent_p.K14261K|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.K11693K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342175.6_Silent_p.K5388K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.K5321K|TTN_ENST00000460472.2_Silent_p.K5196K|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12620	Ig-like 84.				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)			CTTTGAACCATTTCACTGGTA	0.428													T|||	548	0.109425	0.1566	0.1556	5008	,	,		19292	0.0228		0.0328	False		,,,				2504	0.181				p.K14261K		Atlas-SNP	.											.	TTN	18412	.	0			c.A42783G						PASS	.	T	,,,	538,3268		40,458,1405	99.0	92.0	94.0		15588,35079,15963,16164	3.6	1.0	2	dbSNP_123	94	174,8086		4,166,3960	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	44,624,5365	CC,CT,TT		2.1065,14.1356,5.9009	,,,	5196/26927,11693/33424,5321/27052,5388/27119	179498303	712,11354	1903	4130	6033	SO:0001819	synonymous_variant	7273	exon232			GAACCATTTCACT	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.37860A>G	2.37:g.179498303T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	194	95	0.489691	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|0.000;C|0.061;T|0.938	0.061	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SLFN5	162394	hgsc.bcm.edu	37	17	33592194	33592194	+	Missense_Mutation	SNP	C	C	G	rs117695297	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33592194C>G	ENST00000299977.4	+	5	2111	c.1963C>G	c.(1963-1965)Cgt>Ggt	p.R655G	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	655					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)		TCAGAATTTCCGTACTGAAGA	0.458													C|||	126	0.0251597	0.0008	0.0101	5008	,	,		21296	0.0675		0.007	False		,,,				2504	0.044				p.R655G		Atlas-SNP	.											.	SLFN5	92	.	0			c.C1963G						PASS	.	C	GLY/ARG	14,4392	21.2+/-45.6	0,14,2189	145.0	141.0	143.0		1963	0.1	0.9	17	dbSNP_132	143	93,8507	51.5+/-111.7	1,91,4208	yes	missense	SLFN5	NM_144975.3	125	1,105,6397	GG,GC,CC		1.0814,0.3177,0.8227	probably-damaging	655/892	33592194	107,12899	2203	4300	6503	SO:0001583	missense	162394	exon5			AATTTCCGTACTG	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.1963C>G	17.37:g.33592194C>G	ENSP00000299977:p.Arg655Gly	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	46	0.021062271062271064	1	0.0020325203252032522	1	0.0027624309392265192	38	0.06643356643356643	6	0.0079155672823219	c	11.85	1.762705	0.31228	0.003177	0.010814	ENSG00000166750	ENST00000299977	D	0.86230	-2.09	3.27	0.0504	0.14293	Domain of unknown function DUF2075 (1);	0.593314	0.14081	N	0.342734	T	0.40645	0.1125	M	0.69358	2.11	0.58432	D	0.999996	D	0.58970	0.984	P	0.50162	0.633	T	0.66760	-0.5842	10	0.48119	T	0.1	.	5.7102	0.17931	0.0:0.6283:0.0:0.3717	.	655	Q08AF3	SLFN5_HUMAN	G	655	ENSP00000299977:R655G	ENSP00000299977:R655G	R	+	1	0	SLFN5	30616307	0.322000	0.24634	0.903000	0.35520	0.964000	0.63967	0.495000	0.22483	-0.054000	0.13266	-0.145000	0.13849	CGT	C|0.988;G|0.012	0.012	strong		0.458	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
AIRE	326	hgsc.bcm.edu	37	21	45709568	45709568	+	Silent	SNP	C	C	T	rs1055311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:45709568C>T	ENST00000291582.5	+	6	808	c.681C>T	c.(679-681)ggC>ggT	p.G227G	AIRE_ENST00000329347.4_5'Flank|AIRE_ENST00000355347.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	227	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		TCCAGGTTGGCGGGGAGTTCT	0.647									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	589	0.117612	0.0182	0.2248	5008	,	,		15544	0.005		0.2624	False		,,,				2504	0.1431				p.G227G		Atlas-SNP	.											.	AIRE	61	.	0			c.C681T						PASS	.	T		260,4146	783.2+/-414.6	5,250,1948	46.0	52.0	50.0		681	-3.1	0.6	21	dbSNP_86	50	2368,6230	690.4+/-404.4	338,1692,2269	no	coding-synonymous	AIRE	NM_000383.2		343,1942,4217	TT,TC,CC		27.5413,5.901,20.2092		227/546	45709568	2628,10376	2203	4299	6502	SO:0001819	synonymous_variant	326	exon6	Familial Cancer Database	APECED	GGTTGGCGGGGAG	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.681C>T	21.37:g.45709568C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			C|0.833;T|0.167	0.167	strong		0.647	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
HMMR	3161	hgsc.bcm.edu	37	5	162909716	162909716	+	Missense_Mutation	SNP	C	C	T	rs299295	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:162909716C>T	ENST00000358715.3	+	13	1487	c.1451C>T	c.(1450-1452)gCg>gTg	p.A484V	HMMR_ENST00000393915.4_Missense_Mutation_p.A485V|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000353866.3_Missense_Mutation_p.A469V|HMMR_ENST00000432118.2_Missense_Mutation_p.A398V|RP11-80G7.1_ENST00000514724.2_RNA			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	484			A -> V (in dbSNP:rs299295). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	CAGGAAAAAGCGGCCAAGGCT	0.373													T|||	1080	0.215655	0.2905	0.1888	5008	,	,		17356	0.0724		0.2525	False		,,,				2504	0.2434				p.A485V		Atlas-SNP	.											.	HMMR	64	.	0			c.C1454T						PASS	.	T	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1278,3128	700.3+/-406.6	154,970,1079	74.0	76.0	75.0		1454,1193,1451,1406	4.3	0.6	5	dbSNP_79	75	2046,6554	719.4+/-406.3	257,1532,2511	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	64,64,64,64	411,2502,3590	TT,TC,CC		23.7907,29.0059,25.5574	benign,benign,benign,benign	485/726,398/639,484/725,469/710	162909716	3324,9682	2203	4300	6503	SO:0001583	missense	3161	exon13			AAAAAGCGGCCAA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1451C>T	5.37:g.162909716C>T	ENSP00000351554:p.Ala484Val	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	290	142	0.489655	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	426	0.19505494505494506	128	0.2601626016260163	76	0.20994475138121546	29	0.050699300699300696	193	0.2546174142480211	T	0.015	-1.548218	0.00926	0.290059	0.237907	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.03717	3.83;3.83;3.83;3.83;3.83	5.43	4.27	0.50696	.	0.709479	0.14135	N	0.339134	T	0.00012	0.0000	N	0.00289	-1.7	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	0.40403	-0.9565	9	0.02654	T	1	-5.128	8.1855	0.31337	0.0:0.1757:0.0:0.8243	rs299295;rs3172948;rs52793826;rs61629152;rs299295	398;485;469;484	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	V	370;469;485;461;398;484	ENSP00000400527:A370V;ENSP00000185942:A469V;ENSP00000377492:A485V;ENSP00000402673:A398V;ENSP00000351554:A484V	ENSP00000185942:A469V	A	+	2	0	HMMR	162842294	0.611000	0.26992	0.574000	0.28523	0.001000	0.01503	2.306000	0.43673	1.068000	0.40764	-0.269000	0.10298	GCG	C|0.774;N|0.000	.	strong		0.373	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
FCRLB	127943	hgsc.bcm.edu	37	1	161697068	161697068	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161697068C>T	ENST00000367948.2	+	8	1112	c.897C>T	c.(895-897)gcC>gcT	p.A299A	FCRLB_ENST00000367945.1_Missense_Mutation_p.P244L|FCRLB_ENST00000367944.3_Missense_Mutation_p.P258S|FCRLB_ENST00000336830.5_Missense_Mutation_p.P265S|FCRLB_ENST00000392158.1_Silent_p.A299A|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367946.3_Missense_Mutation_p.P251L			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	299					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)			CCACCACCGCCCCAGCTCCAT	0.662																																					p.A299A		Atlas-SNP	.											.	FCRLB	35	.	0			c.C897T						PASS	.						22.0	25.0	24.0					1																	161697068		2203	4299	6502	SO:0001819	synonymous_variant	127943	exon6			CACCGCCCCAGCT	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.897C>T	1.37:g.161697068C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	4	0.0615385	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	37	CCDS30927.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.08|17.08	3.296672|3.296672	0.60086|0.60086	.|.	.|.	ENSG00000162746|ENSG00000162746	ENST00000367946;ENST00000367945|ENST00000336830;ENST00000367944	T;T|T;T	0.02032|0.02369	4.49;4.51|4.32;4.35	4.07|4.07	-3.13|-3.13	0.05266|0.05266	.|.	.|.	.|.	.|.	.|.	T|T	0.00666|0.00666	0.0022|0.0022	.|.	.|.	.|.	0.19300|0.19300	N|N	0.999978|0.999978	B;B|B;B;B	0.06786|0.25312	0.001;0.001|0.123;0.005;0.005	B;B|B;B;B	0.04013|0.20955	0.001;0.001|0.032;0.002;0.002	T|T	0.46610|0.46610	-0.9179|-0.9179	8|8	0.62326|0.87932	D|D	0.03|0	.|.	2.4538|2.4538	0.04524|0.04524	0.143:0.2488:0.4213:0.1869|0.143:0.2488:0.4213:0.1869	.|.	244;251|302;258;265	Q6BAA4-5;Q6BAA4-4|Q96DP6;Q6BAA4-3;Q6BAA4-2	.;.|.;.;.	L|S	251;244|265;258	ENSP00000356923:P251L;ENSP00000356922:P244L|ENSP00000338598:P265S;ENSP00000356921:P258S	ENSP00000356922:P244L|ENSP00000338598:P265S	P|P	+|+	2|1	0|0	FCRLB|FCRLB	159963692|159963692	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.913000|-0.913000	0.04042|0.04042	-0.994000|-0.994000	0.03463|0.03463	-0.519000|-0.519000	0.04390|0.04390	CCC|CCC	.	.	none		0.662	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43585253C>T	ENST00000406487.1	-	2	308	c.210G>A	c.(208-210)ggG>ggA	p.G70G	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	70	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G70G(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)				CCCTGATTTGCCCTTTGTACC	0.433																																					p.G70G		Atlas-SNP	.											PSG2,NS,carcinoma,0,2	PSG2	84	2	2	Substitution - coding silent(2)	prostate(2)	c.G210A						scavenged	.						92.0	96.0	94.0					19																	43585253		2201	4285	6486	SO:0001819	synonymous_variant	5670	exon2			GATTTGCCCTTTG		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.210G>A	19.37:g.43585253C>T		Somatic	130	2	0.0153846		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.433	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
DNAH6	1768	hgsc.bcm.edu	37	2	84896628	84896628	+	Silent	SNP	G	G	A	rs17708884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:84896628G>A	ENST00000237449.6	+	37	6308	c.6300G>A	c.(6298-6300)gtG>gtA	p.V2100V	DNAH6_ENST00000389394.3_Silent_p.V2100V|DNAH6_ENST00000398278.2_Silent_p.V2100V|DNAH6_ENST00000602588.1_Silent_p.V121V			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2100	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)			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						TAACTGGAGTGGGCAAGGTAG	0.423													G|||	313	0.0625	0.0113	0.1282	5008	,	,		19963	0.004		0.1312	False		,,,				2504	0.0746				p.V2100V		Atlas-SNP	.											DNAH6,colon,carcinoma,+1,1	DNAH6	194	1	0			c.G6300A						PASS	.	G		40,1344		0,40,652	94.0	80.0	84.0		6300	-5.0	1.0	2	dbSNP_123	84	449,2733		36,377,1178	no	coding-synonymous	DNAH6	NM_001370.1		36,417,1830	AA,AG,GG		14.1106,2.8902,10.7096		2100/4159	84896628	489,4077	692	1591	2283	SO:0001819	synonymous_variant	1768	exon38			TGGAGTGGGCAAG	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.6300G>A	2.37:g.84896628G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.926;A|0.074	0.074	strong		0.423	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
CXCR5	643	hgsc.bcm.edu	37	11	118765267	118765267	+	Silent	SNP	G	G	C	rs598207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:118765267G>C	ENST00000292174.4	+	2	1190	c.1014G>C	c.(1012-1014)acG>acC	p.T338T	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	338					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)		GGCTCCTGACGAAGCTGGGCT	0.627													C|||	1611	0.321685	0.4992	0.4366	5008	,	,		20978	0.2212		0.2714	False		,,,				2504	0.1554				p.T338T		Atlas-SNP	.											.	CXCR5	34	.	0			c.G1014C						PASS	.	C	,	1982,2418	615.4+/-392.6	452,1078,670	60.0	55.0	57.0		1014,879	3.2	1.0	11	dbSNP_83	57	2306,6284	704.3+/-405.4	324,1658,2313	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	776,2736,2983	CC,CG,GG		26.8452,45.0455,33.01	,	338/373,293/328	118765267	4288,8702	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGACGAAGCTG	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.1014G>C	11.37:g.118765267G>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	25	18	0.72	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.684;C|0.316	0.316	strong		0.627	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
ERAL1	26284	hgsc.bcm.edu	37	17	27185827	27185827	+	Silent	SNP	C	C	T	rs2242345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:27185827C>T	ENST00000254928.5	+	7	1042	c.945C>T	c.(943-945)gaC>gaT	p.D315D	MIR144_ENST00000581873.1_lincRNA|MIR144_ENST00000384886.1_lincRNA|MIR144_ENST00000385059.1_lincRNA	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	315	Era-type G.				ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			GCCAGGAGGACGTGAAAACAC	0.488													T|||	3862	0.771166	0.8835	0.6873	5008	,	,		20704	0.749		0.8052	False		,,,				2504	0.6667				p.D315D		Atlas-SNP	.											.	ERAL1	28	.	0			c.C945T						PASS	.	T		3817,589	253.4+/-259.3	1668,481,54	126.0	130.0	128.0		945	2.5	1.0	17	dbSNP_98	128	6900,1700	301.2+/-305.3	2770,1360,170	no	coding-synonymous	ERAL1	NM_005702.2		4438,1841,224	TT,TC,CC		19.7674,13.3681,17.5996		315/438	27185827	10717,2289	2203	4300	6503	SO:0001819	synonymous_variant	26284	exon7			GGAGGACGTGAAA	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"""Era (E. coli G-protein homolog)-like 1"", ""Era G-protein-like 1 (E. coli)"""			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.945C>T	17.37:g.27185827C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Silent	SNP	ENST00000254928.5	37	CCDS11244.1																																																																																			C|0.197;T|0.803	0.803	strong		0.488	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2		
LRRC43	254050	hgsc.bcm.edu	37	12	122674758	122674758	+	Silent	SNP	G	G	A	rs4758651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122674758G>A	ENST00000339777.4	+	5	772	c.744G>A	c.(742-744)cgG>cgA	p.R248R	LRRC43_ENST00000425921.1_Silent_p.R63R	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	248										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)		GGACCCTCCGGCACCTGCGAC	0.657													G|||	3251	0.649161	0.3404	0.6383	5008	,	,		19152	0.9008		0.7326	False		,,,				2504	0.729				p.R248R		Atlas-SNP	.											.	LRRC43	105	.	0			c.G744A						PASS	.	G	,	1780,2540		374,1032,754	89.0	101.0	97.0		744,189	-1.9	0.0	12	dbSNP_111	97	6169,2345		2247,1675,335	no	coding-synonymous,coding-synonymous	LRRC43	NM_001098519.1,NM_152759.4	,	2621,2707,1089	AA,AG,GG		27.5429,41.2037,38.063	,	248/657,63/472	122674758	7949,4885	2160	4257	6417	SO:0001819	synonymous_variant	254050	exon5			CCTCCGGCACCTG	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.744G>A	12.37:g.122674758G>A		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																			G|0.305;N|0.003	.	strong		0.657	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
JMY	133746	hgsc.bcm.edu	37	5	78573790	78573790	+	Missense_Mutation	SNP	A	A	T	rs13182512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:78573790A>T	ENST00000396137.4	+	2	1552	c.1090A>T	c.(1090-1092)Atg>Ttg	p.M364L		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	364			M -> L (in dbSNP:rs13182512). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		CTTGTATCAGATGGAGGATGA	0.438													A|||	2407	0.480631	0.3646	0.5562	5008	,	,		17393	0.4851		0.6243	False		,,,				2504	0.4315				p.M364L		Atlas-SNP	.											.	JMY	82	.	0			c.A1090T						PASS	.	A	LEU/MET	1539,2297		328,883,707	110.0	106.0	108.0		1090	-4.7	1.0	5	dbSNP_121	108	5085,3163		1584,1917,623	yes	missense	JMY	NM_152405.4	15	1912,2800,1330	TT,TA,AA		38.3487,40.1199,45.1837	benign	364/989	78573790	6624,5460	1918	4124	6042	SO:0001583	missense	133746	exon2			TATCAGATGGAGG	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1090A>T	5.37:g.78573790A>T	ENSP00000379441:p.Met364Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	1138	0.5210622710622711	207	0.42073170731707316	191	0.5276243093922652	265	0.4632867132867133	475	0.6266490765171504	A	3.901	-0.022008	0.07634	0.401199	0.616513	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.07021	3.23	5.37	-4.71	0.03279	.	0.357771	0.31709	N	0.007197	T	0.00012	0.0000	L	0.36672	1.1	0.37339	P	0.08970500000000003	B	0.06786	0.001	B	0.06405	0.002	T	0.38373	-0.9664	9	0.32370	T	0.25	.	5.5033	0.16840	0.2347:0.5041:0.0633:0.1979	rs13182512;rs52808458;rs58775933;rs13182512	364	Q8N9B5	JMY_HUMAN	L	364	ENSP00000379441:M364L	ENSP00000282259:M364L	M	+	1	0	JMY	78609546	1.000000	0.71417	0.976000	0.42696	0.963000	0.63663	1.365000	0.34182	-0.624000	0.05611	-1.251000	0.01509	ATG	A|0.466;T|0.534	0.534	strong		0.438	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
HCN4	10021	hgsc.bcm.edu	37	15	73615878	73615878	+	Silent	SNP	C	C	T	rs117819825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:73615878C>T	ENST00000261917.3	-	8	3549	c.2556G>A	c.(2554-2556)ccG>ccA	p.P852P		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	852					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)		AGGATGAAGACGGTGTGTCCA	0.682													C|||	138	0.0275559	0.0023	0.0821	5008	,	,		14196	0.0		0.0348	False		,,,				2504	0.044				p.P852P		Atlas-SNP	.											.	HCN4	150	.	0			c.G2556A						PASS	.	C		51,4345	50.2+/-85.5	1,49,2148	56.0	57.0	57.0		2556	-5.1	0.6	15	dbSNP_132	57	419,8165	123.2+/-182.1	11,397,3884	no	coding-synonymous	HCN4	NM_005477.2		12,446,6032	TT,TC,CC		4.8812,1.1601,3.621		852/1204	73615878	470,12510	2198	4292	6490	SO:0001819	synonymous_variant	10021	exon8			TGAAGACGGTGTG	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.2556G>A	15.37:g.73615878C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			C|0.965;T|0.035	0.035	strong		0.682	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
STRA6	64220	hgsc.bcm.edu	37	15	74487969	74487969	+	Intron	SNP	A	A	T	rs971756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:74487969A>T	ENST00000323940.5	-	6	676				STRA6_ENST00000535552.1_Intron|STRA6_ENST00000395105.4_Intron|STRA6_ENST00000574278.1_Intron|STRA6_ENST00000563965.1_Intron|STRA6_ENST00000416286.3_Intron|STRA6_ENST00000574439.1_Intron|STRA6_ENST00000423167.2_Intron|STRA6_ENST00000432245.2_Missense_Mutation_p.L152M|STRA6_ENST00000449139.2_Intron	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6						adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						actagtctcaactctgtgatc	0.483													A|||	273	0.0545128	0.0076	0.0692	5008	,	,		20852	0.0		0.1809	False		,,,				2504	0.0337				p.L152M		Atlas-SNP	.											.	STRA6	66	.	0			c.T454A						PASS	.	A	,,,MET/LEU,,,,	99,2545		2,95,1225	172.0	166.0	168.0		,,,454,,,,	-2.4	0.0	15	dbSNP_86	168	1006,3606		108,790,1408	yes	intron,intron,intron,missense,intron,intron,intron,intron	STRA6	NM_001142617.1,NM_001142618.1,NM_001142619.1,NM_001142620.1,NM_001199040.1,NM_001199041.1,NM_001199042.1,NM_022369.3	,,,15,,,,	110,885,2633	TT,TA,AA		21.8127,3.7443,15.2288	,,,,,,,	,,,152/160,,,,	74487969	1105,6151	1322	2306	3628	SO:0001627	intron_variant	64220	exon6			GTCTCAACTCTGT	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.430+23T>A	15.37:g.74487969A>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001142620	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	171	0.0782967032967033	5	0.01016260162601626	28	0.07734806629834254	0	0.0	138	0.1820580474934037	A	10.87	1.472402	0.26423	0.037443	0.218127	ENSG00000137868	ENST00000432245	T	0.80123	-1.34	3.18	-2.4	0.06583	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	P	0.47677	0.899	B	0.42422	0.387	T	0.03576	-1.1023	7	0.87932	D	0	.	4.0381	0.09738	0.342:0.3467:0.3113:0.0	rs971756;rs971756	152	Q9BX79-2	.	M	152	ENSP00000407176:L152M	ENSP00000407176:L152M	L	-	1	2	STRA6	72275022	0.002000	0.14202	0.000000	0.03702	0.138000	0.21146	0.416000	0.21198	-0.530000	0.06349	-0.464000	0.05259	TTG	A|0.928;T|0.072	0.072	strong		0.483	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
TIAF1	9220	hgsc.bcm.edu	37	17	27401176	27401176	+	Silent	SNP	G	G	C	rs1049848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:27401176G>C	ENST00000359450.6	-	1	4699	c.42C>G	c.(40-42)ctC>ctG	p.L14L	TIAF1_ENST00000408971.2_Silent_p.L14L|MYO18A_ENST00000354329.4_3'UTR|MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000533112.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR|MYO18A_ENST00000531253.1_3'UTR	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1	14					apoptotic process (GO:0006915)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of apoptotic process (GO:0043066)	nucleus (GO:0005634)				kidney(1)|lung(1)|urinary_tract(1)	3	Lung NSC(42;0.015)		Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CAGCTGCACAGAGAAAGGACT	0.597													G|||	24	0.00479233	0.0	0.0	5008	,	,		16628	0.001		0.0209	False		,,,				2504	0.002				p.L14L		Atlas-SNP	.											.	TIAF1	9	.	0			c.C42G						PASS	.	G	,,	18,4388	25.3+/-52.1	0,18,2185	50.0	51.0	51.0		42,,	1.7	0.0	17	dbSNP_86	51	135,8465	68.7+/-131.2	1,133,4166	no	coding-synonymous,utr-3,utr-3	TIAF1,MYO18A	NM_004740.3,NM_078471.3,NM_203318.1	,,	1,151,6351	CC,CG,GG		1.5698,0.4085,1.1764	,,	14/116,,	27401176	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	9220	exon1			TGCACAGAGAAAG	AF105277	CCDS32599.1	17q11.2	2006-08-07				ENSG00000221995			11803	protein-coding gene	gene with protein product		609517				9918798	Standard	NM_004740		Approved		uc002hdv.1	O95411		ENST00000359450.6:c.42C>G	17.37:g.27401176G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_004740	A2RRE2|Q6PEG2	Silent	SNP	ENST00000359450.6	37	CCDS32599.1																																																																																			G|0.988;C|0.012	0.012	strong		0.597	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	NM_004740	
MYLK	4638	hgsc.bcm.edu	37	3	123452838	123452838	+	Silent	SNP	G	G	A	rs4678047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:123452838G>A	ENST00000475616.1	-	7	1004	c.1005C>T	c.(1003-1005)acC>acT	p.T335T	MYLK_ENST00000360772.3_Silent_p.T335T|MYLK_ENST00000360304.3_Silent_p.T335T|MYLK_ENST00000359169.1_Silent_p.T335T|MYLK_ENST00000346322.5_Silent_p.T335T			Q15746	MYLK_HUMAN	myosin light chain kinase	335					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		GAAGGACCGGGGTCTGCGGGG	0.642													G|||	3169	0.632788	0.3623	0.7262	5008	,	,		15445	0.9375		0.6491	False		,,,				2504	0.6012				p.T335T		Atlas-SNP	.											.	MYLK	224	.	0			c.C1005T						PASS	.	G	,,,	1727,2679	507.6+/-366.7	336,1055,812	54.0	59.0	57.0		1005,1005,1005,1005	0.3	0.0	3	dbSNP_111	57	5743,2857	663.9+/-402.1	1923,1897,480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	2259,2952,1292	AA,AG,GG		33.2209,39.1966,42.565	,,,	335/1915,335/1846,335/1864,335/1795	123452838	7470,5536	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon10			GACCGGGGTCTGC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.1005C>T	3.37:g.123452838G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	114	110	0.964912	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																			A|0.608;G|0.392	0.608	strong		0.642	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
ABCA8	10351	hgsc.bcm.edu	37	17	66878099	66878099	+	Missense_Mutation	SNP	C	C	T	rs34987539	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66878099C>T	ENST00000269080.2	-	29	3868	c.3731G>A	c.(3730-3732)tGt>tAt	p.C1244Y	ABCA8_ENST00000586539.1_Missense_Mutation_p.C1284Y|ABCA8_ENST00000430352.2_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	38	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	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	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625686	74625686	+	Missense_Mutation	SNP	A	A	G	rs8077382	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	331	166	0.501511	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	
TXLNG	55787	hgsc.bcm.edu	37	X	16859628	16859628	+	Silent	SNP	G	G	A	rs5924530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	119	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	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	
OR51B6	390058	hgsc.bcm.edu	37	11	5372856	5372856	+	Missense_Mutation	SNP	A	A	G	rs4910756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5372856A>G	ENST00000380219.1	+	1	119	c.119A>G	c.(118-120)aAt>aGt	p.N40S	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	40			N -> S (in dbSNP:rs4910756). {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)			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)		CTTCTTGGCAATGGCACTCTT	0.473													A|||	755	0.150759	0.2254	0.1556	5008	,	,		22235	0.0188		0.2147	False		,,,				2504	0.1166				p.N40S		Atlas-SNP	.											.	OR51B6	53	.	0			c.A119G						PASS	.	A	SER/ASN	869,3533	340.5+/-306.2	85,699,1417	174.0	138.0	150.0		119	4.0	1.0	11	dbSNP_111	150	1824,6770	327.2+/-317.7	205,1414,2678	yes	missense	OR51B6	NM_001004750.1	46	290,2113,4095	GG,GA,AA		21.2241,19.741,20.7218	probably-damaging	40/313	5372856	2693,10303	2201	4297	6498	SO:0001583	missense	390058	exon1			TTGGCAATGGCAC		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.119A>G	11.37:g.5372856A>G	ENSP00000369568:p.Asn40Ser	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	320	0.14652014652014653	100	0.2032520325203252	59	0.16298342541436464	4	0.006993006993006993	157	0.20712401055408972	A	18.26	3.584023	0.65992	0.19741	0.212241	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.75477	-0.94	5.15	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000025	T	0.00271	0.0008	H	0.96805	3.885	0.27891	P	0.9393456	P	0.35307	0.494	B	0.41202	0.35	T	0.36504	-0.9745	9	0.72032	D	0.01	.	9.8577	0.41094	0.9186:0.0:0.0814:0.0	rs4910756;rs17186878;rs52833327;rs58240740;rs4910756	40	Q9H340	O51B6_HUMAN	S	39;40	ENSP00000369568:N40S	ENSP00000369568:N40S	N	+	2	0	OR51B6	5329432	1.000000	0.71417	0.962000	0.40283	0.949000	0.60115	6.909000	0.75735	0.978000	0.38470	0.455000	0.32223	AAT	A|0.824;G|0.176	0.176	strong		0.473	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
FLG	2312	hgsc.bcm.edu	37	1	152281690	152281690	+	Missense_Mutation	SNP	C	C	T	rs12407748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281690C>T	ENST00000368799.1	-	3	5707	c.5672G>A	c.(5671-5673)cGg>cAg	p.R1891Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1891	Ser-rich.		R -> Q (in dbSNP:rs12407748).		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)			GCTGTCGGCCCGAGAGGAAGC	0.567									Ichthyosis				C|||	1440	0.28754	0.0113	0.3905	5008	,	,		19138	0.5843		0.1421	False		,,,				2504	0.4315				p.R1891Q		Atlas-SNP	.											.	FLG	900	.	0			c.G5672A						PASS	.	C	GLN/ARG	162,4244	108.6+/-147.0	2,158,2043	272.0	275.0	274.0		5672	-3.6	0.0	1	dbSNP_120	274	1242,7358	249.3+/-276.6	97,1048,3155	no	missense	FLG	NM_002016.1	43	99,1206,5198	TT,TC,CC		14.4419,3.6768,10.795	possibly-damaging	1891/4062	152281690	1404,11602	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCGGCCCGAGAGG	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.5672G>A	1.37:g.152281690C>T	ENSP00000357789:p.Arg1891Gln	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	267	160	0.599251	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	549	0.25137362637362637	9	0.018292682926829267	114	0.3149171270718232	316	0.5524475524475524	110	0.14511873350923482	C	4.339	0.062313	0.08388	0.036768	0.144419	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03358	3.96	1.78	-3.57	0.04612	.	.	.	.	.	T	0.00524	0.0017	N	0.13235	0.315	0.80722	P	0.0	P	0.39250	0.665	B	0.33890	0.172	T	0.39272	-0.9622	8	0.08599	T	0.76	.	7.8311	0.29342	0.0:0.7145:0.0:0.2855	rs12407748;rs35359555;rs12407748	1891	P20930	FILA_HUMAN	Q	1891;126	ENSP00000357789:R1891Q	ENSP00000271820:R126Q	R	-	2	0	FLG	150548314	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.006000	0.00315	-1.013000	0.03383	-1.309000	0.01313	CGG	C|0.851;T|0.149	0.149	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610008	32610008	+	Silent	SNP	C	C	T	rs2308890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32610008C>T	ENST00000343139.5	+	3	693	c.591C>T	c.(589-591)gaC>gaT	p.D197D	HLA-DQA1_ENST00000374949.2_Silent_p.D197D|HLA-DQA1_ENST00000395363.1_Silent_p.D197D	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	196	Alpha-2.|Ig-like C1-type.		K -> E (in allele DQA1*02:01, allele DQA1*03:01, allele DQA1*03:02, allele DQA1*03:03, allele DQA1*04:01, allele DQA1*04:02, allele DQA1*04:04, allele DQA1*06:01 and allele DQA1*06:02).|K -> Q (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05 and allele DQA1*01:07).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGGGCCTGGACCAGCCTCTTC	0.448													.|||	1472	0.29393	0.1959	0.3833	5008	,	,		13880	0.3333		0.3201	False		,,,				2504	0.2955				p.D197D		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C591T						PASS	.	T		623,2391		125,373,1009	100.0	105.0	103.0		591	-8.2	0.0	6	dbSNP_123	103	1761,3651		417,927,1362	no	coding-synonymous	HLA-DQA1	NM_002122.3		542,1300,2371	TT,TC,CC		32.5388,20.6702,28.2934		197/256	32610008	2384,6042	1507	2706	4213	SO:0001819	synonymous_variant	3117	exon3			CCTGGACCAGCCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.591C>T	6.37:g.32610008C>T		Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	122	97	0.795082	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	598	0.27380952380952384	67	0.13617886178861788	109	0.3011049723756906	193	0.3374125874125874	229	0.3021108179419525	.	0.690	-0.794762	0.02862	0.206702	0.325388	ENSG00000196735	ENST00000486548	.	.	.	4.08	-8.17	0.01057	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.20703	P	0.999863693	.	.	.	.	.	.	T	0.19614	-1.0300	3	.	.	.	.	2.8614	0.05588	0.1097:0.1325:0.3147:0.4432	rs2308890;rs9272752	.	.	.	I	170	.	.	T	+	2	0	HLA-DQA1	32717986	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-6.856000	0.00051	-1.995000	0.00971	-0.753000	0.03488	ACC	C|0.717;T|0.283	0.283	strong		0.448	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
RP1	6101	hgsc.bcm.edu	37	8	55541513	55541513	+	Missense_Mutation	SNP	T	T	C	rs414352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55541513T>C	ENST00000220676.1	+	4	5219	c.5071T>C	c.(5071-5073)Tct>Cct	p.S1691P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1691	Poly-Ser.		S -> P (in dbSNP:rs414352). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TAGTAGTTCATCTATGTTGCA	0.403													C|||	1397	0.278954	0.1687	0.3069	5008	,	,		20686	0.4415		0.2714	False		,,,				2504	0.2485				p.S1691P	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.T5071C						PASS	.	C	PRO/SER	883,3523	740.2+/-411.2	91,701,1411	163.0	166.0	165.0		5071	3.7	0.5	8	dbSNP_80	165	2341,6259	702.6+/-405.3	304,1733,2263	yes	missense	RP1	NM_006269.1	74	395,2434,3674	CC,CT,TT		27.2209,20.0409,24.7886	benign	1691/2157	55541513	3224,9782	2203	4300	6503	SO:0001583	missense	6101	exon4			AGTTCATCTATGT	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5071T>C	8.37:g.55541513T>C	ENSP00000220676:p.Ser1691Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	665	0.30448717948717946	110	0.22357723577235772	109	0.3011049723756906	250	0.4370629370629371	196	0.25857519788918204	C	3.533	-0.095342	0.07010	0.200409	0.272209	ENSG00000104237	ENST00000220676	T	0.21734	1.99	5.64	3.7	0.42460	.	0.647529	0.13571	N	0.378089	T	0.00012	0.0000	L	0.41236	1.265	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.20519	T	0.43	.	4.4777	0.11752	0.1745:0.6254:0.0:0.2001	rs414352;rs16920625;rs52799326;rs57524481;rs414352	1691	P56715	RP1_HUMAN	P	1691	ENSP00000220676:S1691P	ENSP00000220676:S1691P	S	+	1	0	RP1	55704066	0.011000	0.17503	0.460000	0.27093	0.374000	0.29953	-0.231000	0.09069	0.230000	0.21059	-0.119000	0.15052	TCT	C|0.269;N|0.000	0.269	strong		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
ZNF350	59348	hgsc.bcm.edu	37	19	52468203	52468203	+	Missense_Mutation	SNP	T	T	A	rs2278415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52468203T>A	ENST00000243644.4	-	5	1730	c.1503A>T	c.(1501-1503)agA>agT	p.R501S	ZNF350_ENST00000600703.1_5'Flank|HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	501			R -> S (in dbSNP:rs2278415). {ECO:0000269|PubMed:11090615, ECO:0000269|PubMed:12872252, ECO:0000269|PubMed:14702039}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		GTGCAAATCCTCTGTTATCTC	0.468													T|||	880	0.175719	0.1029	0.1297	5008	,	,		20681	0.2331		0.1471	False		,,,				2504	0.2771				p.R501S		Atlas-SNP	.											.	ZNF350	48	.	0			c.A1503T	GRCh37	CM074642	ZNF350	M	rs2278415	PASS	.	T	SER/ARG	631,3775	273.1+/-271.2	52,527,1624	106.0	90.0	96.0		1503	2.0	0.0	19	dbSNP_100	96	1096,7504	228.9+/-263.8	72,952,3276	yes	missense	ZNF350	NM_021632.3	110	124,1479,4900	AA,AT,TT		12.7442,14.3214,13.2785	benign	501/533	52468203	1727,11279	2203	4300	6503	SO:0001583	missense	59348	exon5			AAATCCTCTGTTA	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1503A>T	19.37:g.52468203T>A	ENSP00000243644:p.Arg501Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_021632	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	37	CCDS12845.1	339	0.15521978021978022	61	0.12398373983739837	39	0.10773480662983426	117	0.20454545454545456	122	0.16094986807387862	T	14.47	2.543957	0.45280	0.143214	0.127442	ENSG00000256683	ENST00000243644	T	0.05258	3.47	3.04	1.96	0.26148	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.22080	0.064	B	0.20955	0.032	T	0.41106	-0.9527	8	0.66056	D	0.02	.	7.2522	0.26156	0.1986:0.0:0.0:0.8014	rs2278415;rs17835584;rs52811528;rs2278415	501	Q9GZX5	ZN350_HUMAN	S	501	ENSP00000243644:R501S	ENSP00000243644:R501S	R	-	3	2	ZNF350	57160015	0.000000	0.05858	0.003000	0.11579	0.667000	0.39255	-0.260000	0.08708	0.234000	0.21139	0.402000	0.26972	AGA	T|0.844;A|0.156	0.156	strong		0.468	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
TRHDE	29953	hgsc.bcm.edu	37	12	72956782	72956782	+	Silent	SNP	C	C	T	rs79522035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:72956782C>T	ENST00000261180.4	+	9	1965	c.1869C>T	c.(1867-1869)atC>atT	p.I623I	TRHDE_ENST00000549138.1_3'UTR	NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	623					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						TCTATGATATCAGTGCTAAAA	0.308													C|||	95	0.0189696	0.0	0.0317	5008	,	,		15397	0.0		0.0467	False		,,,				2504	0.0266				p.I623I		Atlas-SNP	.											.	TRHDE	194	.	0			c.C1869T						PASS	.	C		31,4375	38.4+/-70.7	0,31,2172	85.0	91.0	89.0		1869	2.2	1.0	12	dbSNP_131	89	340,8250	117.0+/-176.6	7,326,3962	no	coding-synonymous	TRHDE	NM_013381.2		7,357,6134	TT,TC,CC		3.9581,0.7036,2.8547		623/1025	72956782	371,12625	2203	4295	6498	SO:0001819	synonymous_variant	29953	exon9			TGATATCAGTGCT	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.1869C>T	12.37:g.72956782C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	190	93	0.489474	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	37	CCDS9004.1																																																																																			C|0.974;T|0.026	0.026	strong		0.308	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	
HKR1	284459	hgsc.bcm.edu	37	19	37854273	37854273	+	Missense_Mutation	SNP	G	G	A	rs141902493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:37854273G>A	ENST00000324411.4	+	6	1845	c.1576G>A	c.(1576-1578)Gta>Ata	p.V526I	HKR1_ENST00000591134.1_Intron|HKR1_ENST00000589392.1_Missense_Mutation_p.V508I|HKR1_ENST00000591471.1_Missense_Mutation_p.V253I|HKR1_ENST00000544914.1_Missense_Mutation_p.V253I|HKR1_ENST00000541583.2_Missense_Mutation_p.V465I|HKR1_ENST00000392153.3_Missense_Mutation_p.V507I	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	526					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)			GAAGCCATTTGTATGTGCTGA	0.522													G|||	8	0.00159744	0.0	0.0	5008	,	,		22399	0.0		0.006	False		,,,				2504	0.002				p.V526I		Atlas-SNP	.											.	HKR1	74	.	0			c.G1576A						PASS	.	G	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	71.0	66.0	68.0		1576	2.6	0.7	19	dbSNP_134	68	44,8556	29.0+/-79.6	1,42,4257	yes	missense	HKR1	NM_181786.2	29	1,46,6456	AA,AG,GG		0.5116,0.0908,0.3691	benign	526/660	37854273	48,12958	2203	4300	6503	SO:0001583	missense	284459	exon6			CCATTTGTATGTG	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.1576G>A	19.37:g.37854273G>A	ENSP00000315505:p.Val526Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	3.125	-0.179759	0.06380	9.08E-4	0.005116	ENSG00000181666	ENST00000544914;ENST00000414402;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	T;T;T;T	0.18810	2.19;2.19;2.19;2.19	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07007	0.0178	N	0.13327	0.33	0.46078	D	0.998854	B;P;B;P	0.43826	0.005;0.791;0.033;0.818	B;B;B;B	0.40506	0.021;0.331;0.01;0.266	T	0.09773	-1.0659	9	0.35671	T	0.21	-4.4029	3.3358	0.07101	0.1403:0.0:0.5995:0.2602	.	465;507;526;508	Q7Z6E1;P10072-2;P10072;B4DSY3	.;.;HKR1_HUMAN;.	I	253;305;507;562;526;465	ENSP00000437774:V253I;ENSP00000375994:V507I;ENSP00000315505:V526I;ENSP00000438261:V465I	ENSP00000315505:V526I	V	+	1	0	HKR1	42546113	0.000000	0.05858	0.686000	0.30086	0.232000	0.25224	-3.551000	0.00433	1.756000	0.51951	0.650000	0.86243	GTA	G|0.997;A|0.003	0.003	strong		0.522	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195936382	195936382	+	Silent	SNP	G	G	A	rs11719281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195936382G>A	ENST00000296326.3	-	3	352	c.273C>T	c.(271-273)tcC>tcT	p.S91S	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	91						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		CCTGCTCAGCGGAGCCTGGCG	0.692													G|||	712	0.142173	0.2254	0.098	5008	,	,		18877	0.1637		0.1362	False		,,,				2504	0.045				p.S91S		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.C273T						PASS	.	G		789,3303		76,637,1333	29.0	37.0	34.0		273	1.0	0.3	3	dbSNP_120	34	1035,7321		76,883,3219	no	coding-synonymous	ZDHHC19	NM_001039617.1		152,1520,4552	AA,AG,GG		12.3863,19.2815,14.653		91/310	195936382	1824,10624	2046	4178	6224	SO:0001819	synonymous_variant	131540	exon3			CTCAGCGGAGCCT	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"""Zinc fingers, DHHC-type"""	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.273C>T	3.37:g.195936382G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	103	66	0.640777	NM_001039617	A8MSY6|B3KVI1	Silent	SNP	ENST00000296326.3	37	CCDS43190.1																																																																																			G|0.851;A|0.149	0.149	strong		0.692	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42360950	42360950	+	Missense_Mutation	SNP	C	C	T	rs750051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42360950C>T	ENST00000290472.3	-	20	2514	c.2420G>A	c.(2419-2421)cGg>cAg	p.R807Q		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	807	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> Q (in dbSNP:rs750051).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CTCTAGAGTCCGGTGCTTCAG	0.637													C|||	222	0.0443291	0.0144	0.0749	5008	,	,		20155	0.0		0.1083	False		,,,				2504	0.0429				p.R807Q		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.G2420A						PASS	.	C	GLN/ARG	163,4243	106.0+/-144.5	1,161,2041	34.0	29.0	31.0		2420	1.5	0.1	15	dbSNP_86	31	965,7633	197.9+/-242.4	47,871,3381	yes	missense	PLA2G4D	NM_178034.3	43	48,1032,5422	TT,TC,CC		11.2235,3.6995,8.6743	probably-damaging	807/819	42360950	1128,11876	2203	4299	6502	SO:0001583	missense	283748	exon20			AGAGTCCGGTGCT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.2420G>A	15.37:g.42360950C>T	ENSP00000290472:p.Arg807Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	129	0.059065934065934064	10	0.02032520325203252	31	0.0856353591160221	0	0.0	88	0.11609498680738786	C	13.66	2.304059	0.40795	0.036995	0.112235	ENSG00000159337	ENST00000290472	T	0.01613	4.73	4.35	1.47	0.22746	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (1);	0.399001	0.20201	N	0.097100	T	0.00039	0.0001	M	0.65498	2.005	0.80722	P	0.0	B	0.26445	0.149	B	0.11329	0.006	T	0.32851	-0.9891	9	0.72032	D	0.01	-15.085	4.0893	0.09962	0.0:0.5497:0.1869:0.2633	rs750051;rs17747341;rs58606400;rs750051	807	Q86XP0	PA24D_HUMAN	Q	807	ENSP00000290472:R807Q	ENSP00000290472:R807Q	R	-	2	0	PLA2G4D	40148242	0.007000	0.16637	0.146000	0.22360	0.034000	0.12701	-0.248000	0.08854	0.758000	0.33059	0.655000	0.94253	CGG	C|0.926;T|0.074	0.074	strong		0.637	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
ZNF490	57474	hgsc.bcm.edu	37	19	12692001	12692001	+	Silent	SNP	G	G	A	rs3745651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	23	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29910700	29910700	+	Silent	SNP	G	G	T	rs1059452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29910700G>T	ENST00000396634.1	+	4	581	c.240G>T	c.(238-240)ggG>ggT	p.G80G	HLA-A_ENST00000376806.5_Silent_p.G80G|HLA-A_ENST00000376809.5_Silent_p.G80G|HLA-A_ENST00000376802.2_Silent_p.G80G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	80	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGCAGGAGGGGCCGGAGTATT	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.G80G		Atlas-SNP	.											.	HLA-A	89	.	0			c.G240T						PASS	.						61.0	64.0	63.0					6																	29910700		2203	4300	6503	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGAGGGGCCGGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.240G>T	6.37:g.29910700G>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	212	37	0.174528	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.769;T|0.231	0.231	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SLC6A17	388662	hgsc.bcm.edu	37	1	110738296	110738296	+	Silent	SNP	G	G	A	rs2784140	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:110738296G>A	ENST00000331565.4	+	10	2066	c.1581G>A	c.(1579-1581)tcG>tcA	p.S527S		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	527					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)	p.S527S(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		ATGACTACTCGGCCACCCTGC	0.532													G|||	1451	0.289736	0.0439	0.3847	5008	,	,		20344	0.3016		0.4543	False		,,,				2504	0.3732				p.S527S		Atlas-SNP	.											SLC6A17,NS,carcinoma,0,1	SLC6A17	86	1	1	Substitution - coding silent(1)	stomach(1)	c.G1581A						PASS	.	G		505,3901	234.2+/-247.1	28,449,1726	104.0	86.0	92.0		1581	-1.0	1.0	1	dbSNP_100	92	4276,4324	575.3+/-390.2	1098,2080,1122	no	coding-synonymous	SLC6A17	NM_001010898.2		1126,2529,2848	AA,AG,GG		49.7209,11.4616,36.76		527/728	110738296	4781,8225	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon10			CTACTCGGCCACC		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1581G>A	1.37:g.110738296G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			G|0.658;A|0.342	0.342	strong		0.532	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
SNAP23	8773	hgsc.bcm.edu	37	15	42820589	42820589	+	Silent	SNP	G	G	A	rs1060291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42820589G>A	ENST00000249647.3	+	6	864	c.396G>A	c.(394-396)acG>acA	p.T132T	SNAP23_ENST00000564153.1_Intron|SNAP23_ENST00000397138.1_Intron|SNAP23_ENST00000349777.1_Intron	NM_003825.3	NP_003816.2	O00161	SNP23_HUMAN	synaptosomal-associated protein, 23kDa	132					exocytosis (GO:0006887)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	azurophil granule (GO:0042582)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|synapse (GO:0045202)				large_intestine(1)|lung(1)	2		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)		AACCAACAACGGGAGCAGCCA	0.458													A|||	1416	0.282748	0.6611	0.2061	5008	,	,		14604	0.0079		0.2227	False		,,,				2504	0.1708				p.T132T		Atlas-SNP	.											SNAP23,colon,carcinoma,+1,1	SNAP23	15	1	0			c.G396A						PASS	.	A	,	2567,1839	535.6+/-374.3	751,1065,387	76.0	64.0	68.0		396,	-3.2	0.0	15	dbSNP_86	68	2086,6512	716.4+/-406.1	277,1532,2490	no	coding-synonymous,intron	SNAP23	NM_003825.3,NM_130798.2	,	1028,2597,2877	AA,AG,GG		24.2615,41.7385,35.7813	,	132/212,	42820589	4653,8351	2203	4299	6502	SO:0001819	synonymous_variant	8773	exon6			AACAACGGGAGCA	Y09567	CCDS10087.1, CCDS10088.1	15q14	2004-01-19	2002-08-29		ENSG00000092531	ENSG00000092531			11131	protein-coding gene	gene with protein product		602534	"""synaptosomal-associated protein, 23kD"""			9070898, 8663154	Standard	NM_003825		Approved	SNAP23A, SNAP23B, HsT17016	uc001zpz.2	O00161	OTTHUMG00000130625	ENST00000249647.3:c.396G>A	15.37:g.42820589G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_003825	O00162|Q13602|Q6IAE3	Silent	SNP	ENST00000249647.3	37	CCDS10087.1																																																																																			G|0.678;A|0.322	0.322	strong		0.458	SNAP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253111.4	NM_003825	
CIDEC	63924	hgsc.bcm.edu	37	3	9920138	9920138	+	Silent	SNP	G	G	C	rs17851444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9920138G>C	ENST00000336832.2	-	2	172	c.33C>G	c.(31-33)ctC>ctG	p.L11L	CIDEC_ENST00000383817.1_Silent_p.L11L|CIDEC_ENST00000430427.1_Silent_p.L11L|CIDEC_ENST00000455015.1_5'UTR|CIDEC_ENST00000443115.1_Silent_p.L11L|CIDEC_ENST00000423850.1_5'UTR	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	11					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)					ACTTGGGGTAGAGAAGGCTAA	0.498													G|||	426	0.0850639	0.0484	0.0605	5008	,	,		21255	0.0437		0.1292	False		,,,				2504	0.1493				p.L24L		Atlas-SNP	.											.	CIDEC	22	.	0			c.C72G						PASS	.	G	,,,	242,4164	141.9+/-177.2	10,222,1971	179.0	142.0	154.0		33,33,72,33	0.7	1.0	3	dbSNP_123	154	1135,7465	233.3+/-266.6	78,979,3243	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	88,1201,5214	CC,CG,GG		13.1977,5.4925,10.5874	,,,	11/249,11/239,24/252,11/239	9920138	1377,11629	2203	4300	6503	SO:0001819	synonymous_variant	63924	exon2			GGGGTAGAGAAGG		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.33C>G	3.37:g.9920138G>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	180	107	0.594444	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1																																																																																			G|0.895;C|0.105	0.105	strong		0.498	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
AMZ2	51321	hgsc.bcm.edu	37	17	66253095	66253095	+	Silent	SNP	T	T	A	rs7105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66253095T>A	ENST00000359904.3	+	7	2200	c.1068T>A	c.(1066-1068)gcT>gcA	p.A356A	AMZ2_ENST00000577985.1_Silent_p.A356A|AMZ2_ENST00000577273.1_3'UTR|AMZ2_ENST00000359783.4_Silent_p.A298A|AMZ2_ENST00000392720.2_Silent_p.A356A|AMZ2_ENST00000577866.1_Silent_p.A356A|ARSG_ENST00000448504.2_5'Flank|AMZ2_ENST00000580753.1_Silent_p.A356A	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	75	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	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	
HIPK1	204851	hgsc.bcm.edu	37	1	114515717	114515717	+	Silent	SNP	G	G	A	rs2358996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000369554.2_Silent_p.A1027A|HIPK1_ENST00000369553.1_Silent_p.A678A|HIPK1_ENST00000369561.4_Silent_p.A1038A|HIPK1_ENST00000369555.2_Silent_p.A1027A|HIPK1_ENST00000406344.1_Silent_p.A678A			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	64	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	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	
OSBP2	23762	hgsc.bcm.edu	37	22	31285190	31285190	+	Missense_Mutation	SNP	C	C	G	rs35702187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:31285190C>G	ENST00000332585.6	+	6	1549	c.1445C>G	c.(1444-1446)aCa>aGa	p.T482R	OSBP2_ENST00000403222.3_Missense_Mutation_p.T316R|OSBP2_ENST00000446658.2_Missense_Mutation_p.T481R|OSBP2_ENST00000401475.1_Missense_Mutation_p.T115R|OSBP2_ENST00000535268.1_Missense_Mutation_p.T26R|OSBP2_ENST00000437268.2_Missense_Mutation_p.T224R|OSBP2_ENST00000382310.3_Missense_Mutation_p.T482R|OSBP2_ENST00000407373.1_Missense_Mutation_p.T309R	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	482					lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						AGCACCGGGACAAGTTCCGTG	0.572													C|||	11	0.00219649	0.0	0.0072	5008	,	,		19944	0.0		0.005	False		,,,				2504	0.001				p.T482R		Atlas-SNP	.											.	OSBP2	52	.	0			c.C1445G						PASS	.	C	ARG/THR	2,3908		0,2,1953	51.0	55.0	54.0		1445	3.8	0.0	22	dbSNP_126	54	65,8227		0,65,4081	yes	missense	OSBP2	NM_030758.3	71	0,67,6034	GG,GC,CC		0.7839,0.0512,0.5491	benign	482/917	31285190	67,12135	1955	4146	6101	SO:0001583	missense	23762	exon6			CCGGGACAAGTTC		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.1445C>G	22.37:g.31285190C>G	ENSP00000332576:p.Thr482Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Missense_Mutation	SNP	ENST00000332585.6	37	CCDS43002.1	8|8	0.003663003663003663|0.003663003663003663	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	6.047|6.047	0.377098|0.377098	0.11466|0.11466	5.12E-4|5.12E-4	0.007839|0.007839	ENSG00000184792|ENSG00000184792	ENST00000454145;ENST00000453621;ENST00000431368|ENST00000403222;ENST00000407373;ENST00000332585;ENST00000382310;ENST00000446658;ENST00000401475;ENST00000424224;ENST00000437268;ENST00000535268;ENST00000452656	.|T;T;T;T;T;T;T;T	.|0.44881	.|0.91;0.91;1.49;1.47;1.46;0.93;0.93;0.97	4.81|4.81	3.79|3.79	0.43588|0.43588	.|.	.|1.571790	.|0.03812	.|N	.|0.266088	T|T	0.20700|0.20700	0.0498|0.0498	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B;B;B;B;B;B	.|0.30634	.|0.288;0.01;0.088;0.19;0.088;0.19;0.19	.|B;B;B;B;B;B;B	.|0.30943	.|0.113;0.004;0.045;0.053;0.045;0.122;0.122	T|T	0.22487|0.22487	-1.0215|-1.0215	5|10	.|0.24483	.|T	.|0.36	.|.	5.8851|5.8851	0.18876|0.18876	0.1893:0.7143:0.0:0.0964|0.1893:0.7143:0.0:0.0964	rs35702187|rs35702187	.|224;482;316;224;309;481;482	.|F5H2A3;B4DFA8;B4DKE4;B4DK24;Q6ZN50;Q0VF99;Q969R2	.|.;.;.;.;.;.;OSBP2_HUMAN	E|R	154;153;154|316;309;482;482;481;115;116;224;26;113	.|ENSP00000384213:T316R;ENSP00000385237:T309R;ENSP00000332576:T482R;ENSP00000371747:T482R;ENSP00000392080:T481R;ENSP00000385254:T115R;ENSP00000389200:T224R;ENSP00000438713:T26R	.|ENSP00000332576:T482R	Q|T	+|+	1|2	0|0	OSBP2|OSBP2	29615190|29615190	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	0.901000|0.901000	0.28445|0.28445	1.255000|1.255000	0.44051|0.44051	0.563000|0.563000	0.77884|0.77884	CAA|ACA	C|0.995;G|0.005	0.005	strong		0.572	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
MST1L	11223	hgsc.bcm.edu	37	1	17087521	17087521	+	RNA	SNP	G	G	A	rs11589598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17087521G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GCCAAGGCCCGGGCACCACCG	0.617																																					p.P48P		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	0			c.C144T						PASS	.																																					11223	exon2			AGGCCCGGGCACC	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.17087521G>A		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	348	57	0.163793	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				G|0.833;A|0.167	0.167	strong		0.617	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SLC7A8	23428	hgsc.bcm.edu	37	14	23652004	23652004	+	Silent	SNP	G	G	A	rs1884545	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23652004G>A	ENST00000316902.7	-	1	845	c.120C>T	c.(118-120)atC>atT	p.I40I	C14orf164_ENST00000399910.1_5'Flank|SLC7A8_ENST00000469263.1_Silent_p.I40I	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	40					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TGACCAATCCGATCTCTTTCT	0.597													G|||	284	0.0567093	0.0219	0.0807	5008	,	,		16034	0.004		0.1064	False		,,,				2504	0.09				p.I40I		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C120T						PASS	.	G		216,4190	131.0+/-167.6	8,200,1995	130.0	111.0	117.0		120	1.8	1.0	14	dbSNP_92	117	1139,7461	236.0+/-268.3	72,995,3233	no	coding-synonymous	SLC7A8	NM_012244.2		80,1195,5228	AA,AG,GG		13.2442,4.9024,10.4183		40/536	23652004	1355,11651	2203	4300	6503	SO:0001819	synonymous_variant	23428	exon1			CAATCCGATCTCT	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.120C>T	14.37:g.23652004G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1																																																																																			G|0.934;A|0.066	0.066	strong		0.597	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
KIF20B	9585	hgsc.bcm.edu	37	10	91503660	91503660	+	Silent	SNP	A	A	G	rs1126480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91503660A>G	ENST00000371728.3	+	22	4076	c.4011A>G	c.(4009-4011)aaA>aaG	p.K1337K	KIF20B_ENST00000394289.2_Silent_p.K1337K|KIF20B_ENST00000416354.1_Silent_p.K1367K|KIF20B_ENST00000260753.4_Silent_p.K1297K|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1337					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						TAGATATGAAACAGCGAACCA	0.308													A|||	1772	0.353834	0.4697	0.2147	5008	,	,		14368	0.3085		0.2326	False		,,,				2504	0.4673				p.K1297K		Atlas-SNP	.											KIF20B_ENST00000416354,adrenal_gland,adrenal_cortical_adenoma,0,2	KIF20B	191	2	0			c.A3891G						PASS	.	A		2024,2380	550.2+/-378.0	472,1080,650	81.0	92.0	88.0		3891	5.4	1.0	10	dbSNP_86	88	2002,6596	347.3+/-326.5	221,1560,2518	no	coding-synonymous	KIF20B	NM_016195.2		693,2640,3168	GG,GA,AA		23.2845,45.9582,30.9645		1297/1781	91503660	4026,8976	2202	4299	6501	SO:0001819	synonymous_variant	9585	exon22			TATGAAACAGCGA	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.4011A>G	10.37:g.91503660A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				A|0.701;G|0.299	0.299	strong		0.308	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
BCKDHA	593	hgsc.bcm.edu	37	19	41930396	41930396	+	Silent	SNP	A	A	G	rs4674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41930396A>G	ENST00000269980.2	+	9	1589	c.1221A>G	c.(1219-1221)ctA>ctG	p.L407L	B3GNT8_ENST00000601379.1_5'Flank|BCKDHA_ENST00000457836.2_Silent_p.L410L|CTC-435M10.3_ENST00000540732.1_Silent_p.L441L|BCKDHA_ENST00000595085.1_Silent_p.L441L|CTC-435M10.6_ENST00000598887.1_RNA	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	407					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						ACCCCAACCTACTCTTCTCAG	0.647													G|||	3090	0.617013	0.8548	0.4885	5008	,	,		16180	0.4345		0.5924	False		,,,				2504	0.6002				p.L407L		Atlas-SNP	.											.	BCKDHA	36	.	0			c.A1221G						PASS	.	G	,	3571,835	331.8+/-302.1	1447,677,79	113.0	106.0	108.0		1221,1218	2.9	1.0	19	dbSNP_52	108	5234,3366	499.5+/-375.0	1610,2014,676	no	coding-synonymous,coding-synonymous	BCKDHA	NM_000709.3,NM_001164783.1	,	3057,2691,755	GG,GA,AA		39.1395,18.9514,32.3005	,	407/446,406/445	41930396	8805,4201	2203	4300	6503	SO:0001819	synonymous_variant	593	exon9			CAACCTACTCTTC	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.1221A>G	19.37:g.41930396A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	CCDS12581.1																																																																																			A|0.349;G|0.651	0.651	strong		0.647	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
DNAJC15	29103	hgsc.bcm.edu	37	13	43597865	43597865	+	Missense_Mutation	SNP	A	A	G	rs12015	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:43597865A>G	ENST00000379221.2	+	1	527	c.103A>G	c.(103-105)Aga>Gga	p.R35G	DNAJC15_ENST00000474320.1_3'UTR	NM_013238.2	NP_037370.2	Q9Y5T4	DJC15_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 15	35			R -> G (in dbSNP:rs11617079). {ECO:0000269|PubMed:11358853, ECO:0000269|PubMed:15489334}.		cellular response to starvation (GO:0009267)|negative regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902957)|negative regulation of protein complex assembly (GO:0031333)|protein transport (GO:0015031)|regulation of lipid metabolic process (GO:0019216)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(1)|urinary_tract(1)	4		Lung NSC(96;4.3e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0737)		CGACCAGCAGAGACTGGTGAG	0.632													G|||	1181	0.235823	0.4281	0.2219	5008	,	,		8065	0.1002		0.2535	False		,,,				2504	0.1074				p.R35G		Atlas-SNP	.											DNAJC15_ENST00000379221,NS,carcinoma,0,2	DNAJC15	16	2	0			c.A103G						PASS	.	G	GLY/ARG	1795,2609		375,1045,782	19.0	20.0	20.0		103	0.6	0.0	13	dbSNP_120	20	2062,6538		279,1504,2517	yes	missense	DNAJC15	NM_013238.2	125	654,2549,3299	GG,GA,AA		23.9767,40.7584,29.6601	benign	35/151	43597865	3857,9147	2202	4300	6502	SO:0001583	missense	29103	exon1			CAGCAGAGACTGG	AF126743	CCDS9388.1	13q14.1	2011-09-02	2005-06-30	2005-06-30	ENSG00000120675	ENSG00000120675		"""Heat shock proteins / DNAJ (HSP40)"""	20325	protein-coding gene	gene with protein product		615339	"""DnaJ (Hsp40) homolog, subfamily D, member 1"""	DNAJD1		11358853	Standard	NM_013238		Approved	MCJ	uc001uyy.3	Q9Y5T4	OTTHUMG00000016813	ENST00000379221.2:c.103A>G	13.37:g.43597865A>G	ENSP00000368523:p.Arg35Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_013238	B2R4L0|Q5T219|Q6X963	Missense_Mutation	SNP	ENST00000379221.2	37	CCDS9388.1	521	0.23855311355311357	180	0.36585365853658536	79	0.21823204419889503	65	0.11363636363636363	197	0.2598944591029024	G	5.877	0.345947	0.11126	0.407584	0.239767	ENSG00000120675	ENST00000379221	T	0.44881	0.91	4.56	0.561	0.17285	.	0.816791	0.11028	N	0.607571	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46582	-0.9181	9	0.19590	T	0.45	-19.9861	4.356	0.11178	0.4233:0.1645:0.4122:0.0	rs11617079;rs17856341;rs59811457;rs11617079	35	Q9Y5T4	DJC15_HUMAN	G	35	ENSP00000368523:R35G	ENSP00000368523:R35G	R	+	1	2	DNAJC15	42495865	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.682000	0.05185	-0.381000	0.07882	-0.166000	0.13349	AGA	A|0.735;G|0.265	0.265	strong		0.632	DNAJC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044709.2	NM_013238	
FAM21C	253725	hgsc.bcm.edu	37	10	46254776	46254776	+	Missense_Mutation	SNP	A	A	C	rs199848673		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:46254776A>C	ENST00000336378.4	+	17	1680	c.1562A>C	c.(1561-1563)tAc>tCc	p.Y521S	FAM21C_ENST00000374362.2_Missense_Mutation_p.Y521S|FAM21C_ENST00000359860.4_Missense_Mutation_p.Y465S|FAM21C_ENST00000537517.1_Missense_Mutation_p.Y497S|FAM21C_ENST00000540872.1_Missense_Mutation_p.Y521S	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	521				Y -> S (in Ref. 1; BAA25518 and 2; BAG64168). {ECO:0000305}.	retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)		p.Y520S(3)|p.Y521S(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						ACCTTATCTTACAGCAAAAAT	0.413																																					p.Y521S		Atlas-SNP	.											FAM21C,NS,carcinoma,0,6	FAM21C	68	6	5	Substitution - Missense(5)	prostate(4)|skin(1)	c.A1562C						PASS	.	C	SER/TYR,SER/TYR,SER/TYR	254,3222		29,196,1513	61.0	73.0	69.0		1562,1490,1562	3.3	0.7	10	dbSNP_134	69	410,7550		58,294,3628	yes	missense,missense,missense	FAM21C	NM_001169106.1,NM_001169107.1,NM_015262.2	144,144,144	87,490,5141	CC,CA,AA		5.1508,7.3072,5.8062	benign,benign,benign	521/1280,497/1246,521/1321	46254776	664,10772	1738	3980	5718	SO:0001583	missense	253725	exon17			TATCTTACAGCAA		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1562A>C	10.37:g.46254776A>C	ENSP00000337541:p.Tyr521Ser	Somatic	405	0	0		WXS	Illumina HiSeq	Phase_I	335	22	0.0656716	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Missense_Mutation	SNP	ENST00000336378.4	37		.	.	.	.	.	.	.	.	.	.	C	0.006	-2.057382	0.00390	0.073072	0.051508	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000537517;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.26	3.26	0.37387	.	0.662706	0.15995	N	0.234623	T	0.00496	0.0016	N	0.00099	-2.14	0.54753	P	1.4999999999987246E-5	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	0.25950	-1.0117	8	0.02654	T	1	0.2567	9.8043	0.40783	0.2076:0.7924:0.0:0.0	.	497;521;521;466	F5H871;Q9Y4E1-4;Q9Y4E1;Q9Y4E1-3	.;.;FA21C_HUMAN;.	S	521;521;497;521;521;465;433	.	ENSP00000337541:Y521S	Y	+	2	0	FAM21C	45574782	0.554000	0.26522	0.660000	0.29694	0.197000	0.23852	2.157000	0.42320	0.721000	0.32231	-0.488000	0.04728	TAC	A|0.300;C|0.700	0.700	strong		0.413	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
PPP2R3B	28227	hgsc.bcm.edu	37	X	322257	322257	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:322257G>A	ENST00000390665.3	-	2	411	c.393C>T	c.(391-393)ccC>ccT	p.P131P		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	131					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(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)				GGCGTCCTCTGGGGAAGTAGA	0.597													g|||	1193	0.238219	0.1694	0.2435	5008	,	,		17361	0.2103		0.3579	False		,,,				2504	0.2331				p.P131P		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.C393T						PASS	.	G		863,3417		92,679,1369	196.0	234.0	221.0		393	-1.1	0.0	X	dbSNP_134	221	2983,5523		509,1965,1779	no	coding-synonymous	PPP2R3B	NM_013239.4		601,2644,3148	AA,AG,GG		35.0694,20.1636,30.0798		131/576	322257	3846,8940	2140	4253	6393	SO:0001819	synonymous_variant	28227	exon2			TCCTCTGGGGAAG	AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"""Pseudoautosomal regions / PAR1"", ""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	13417	protein-coding gene	gene with protein product		300339	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"""	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.393C>T	X.37:g.322257G>A		Somatic	455	0	0		WXS	Illumina HiSeq	Phase_I	309	301	0.97411	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Silent	SNP	ENST00000390665.3	37	CCDS14104.1																																																																																			G|0.704;A|0.296	0.296	strong		0.597	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239	
KRT19	3880	hgsc.bcm.edu	37	17	39684321	39684321	+	Missense_Mutation	SNP	G	G	C	rs4602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39684321G>C	ENST00000361566.3	-	1	239	c.179C>G	c.(178-180)gCc>gGc	p.A60G		NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	60	Head.		A -> G (in dbSNP:rs4602). {ECO:0000269|PubMed:10623642, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:2447559, ECO:0000269|PubMed:2448790, ECO:0000269|PubMed:2469734}.		cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				GCCGCCGTAGGCCCCCGAGGA	0.726													C|||	3746	0.748003	0.6445	0.7896	5008	,	,		12585	0.9187		0.6471	False		,,,				2504	0.7863				p.A60G		Atlas-SNP	.											KRT19,colon,carcinoma,-1,1	KRT19	41	1	0			c.C179G						scavenged	.	C	GLY/ALA	2720,1596		894,932,332	17.0	23.0	21.0		179	4.4	1.0	17	dbSNP_52	21	5361,3111		1756,1849,631	no	missense	KRT19	NM_002276.4	60	2650,2781,963	CC,CG,GG		36.721,36.9787,36.8079		60/401	39684321	8081,4707	2158	4236	6394	SO:0001583	missense	3880	exon1			CCGTAGGCCCCCG		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.179C>G	17.37:g.39684321G>C	ENSP00000355124:p.Ala60Gly	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	36	10	0.277778	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	37	CCDS11399.1	1594	0.7298534798534798	313	0.6361788617886179	269	0.7430939226519337	533	0.9318181818181818	479	0.6319261213720316	C	2.730	-0.264716	0.05754	0.630213	0.63279	ENSG00000171345	ENST00000361566;ENST00000455635	T;T	0.81330	-1.48;-1.07	4.39	4.39	0.52855	.	0.426572	0.19926	N	0.102967	T	0.00012	0.0000	N	0.00237	-1.79	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40040	-0.9584	9	0.13853	T	0.58	.	14.8587	0.70362	0.0:0.8554:0.1446:0.0	rs4602;rs3188663;rs16967073;rs17856215;rs58113253	60	P08727	K1C19_HUMAN	G	60	ENSP00000355124:A60G;ENSP00000408759:A60G	ENSP00000355124:A60G	A	-	2	0	KRT19	36937847	0.005000	0.15991	1.000000	0.80357	0.129000	0.20672	0.256000	0.18351	1.213000	0.43380	-0.216000	0.12614	GCC	G|0.335;C|0.665	0.665	strong		0.726	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777422	18777422	+	Silent	SNP	G	G	A	rs45579937	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	43	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	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		
TP53BP2	7159	hgsc.bcm.edu	37	1	223991959	223991959	+	Missense_Mutation	SNP	G	G	A	rs61749337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223991959G>A	ENST00000343537.7	-	6	857	c.566C>T	c.(565-567)gCt>gTt	p.A189V	TP53BP2_ENST00000498843.1_5'Flank|TP53BP2_ENST00000391878.2_Missense_Mutation_p.A60V	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	183					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)		CTGATTCTCAGCTATTTCTTT	0.393													G|||	18	0.00359425	0.0	0.0072	5008	,	,		19407	0.0		0.0129	False		,,,				2504	0.0				p.A189V		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C566T						PASS	.	G	VAL/ALA,VAL/ALA	13,4391	20.2+/-43.8	0,13,2189	184.0	184.0	184.0		566,179	5.3	0.9	1	dbSNP_129	184	117,8483	61.7+/-123.6	0,117,4183	yes	missense,missense	TP53BP2	NM_001031685.2,NM_005426.2	64,64	0,130,6372	AA,AG,GG		1.3605,0.2952,0.9997	probably-damaging,probably-damaging	189/1135,60/1006	223991959	130,12874	2202	4300	6502	SO:0001583	missense	7159	exon6			TTCTCAGCTATTT	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.566C>T	1.37:g.223991959G>A	ENSP00000341957:p.Ala189Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	13.93	2.383745	0.42308	0.002952	0.013605	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.31769	1.48;1.48	5.35	5.35	0.76521	.	0.099855	0.64402	D	0.000001	T	0.29524	0.0736	N	0.17674	0.51	0.80722	D	1	D;B	0.76494	0.999;0.376	D;B	0.80764	0.994;0.113	T	0.02721	-1.1119	10	0.02654	T	1	.	19.4317	0.94772	0.0:0.0:1.0:0.0	rs61749337	189;183	B4DG66;Q13625	.;ASPP2_HUMAN	V	60;189	ENSP00000375750:A60V;ENSP00000341957:A189V	ENSP00000341957:A189V	A	-	2	0	TP53BP2	222058582	1.000000	0.71417	0.919000	0.36401	0.980000	0.70556	5.551000	0.67274	2.668000	0.90789	0.591000	0.81541	GCT	G|0.990;A|0.010	0.010	strong		0.393	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
HK3	3101	hgsc.bcm.edu	37	5	176314459	176314459	+	Silent	SNP	G	G	A	rs2278492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176314459G>A	ENST00000292432.5	-	11	1684	c.1593C>T	c.(1591-1593)gaC>gaT	p.D531D		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	531	Catalytic.|Hexokinase type-1 2.			PD -> LT (in Ref. 4; AAC50422). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACCGCTGCCGTCAGGGGTGG	0.672													A|||	1669	0.333267	0.1793	0.4452	5008	,	,		17657	0.3948		0.327	False		,,,				2504	0.4049				p.D531D		Atlas-SNP	.											.	HK3	210	.	0			c.C1593T						PASS	.	A		974,3432	716.2+/-408.6	109,756,1338	32.0	35.0	34.0		1593	-1.5	0.6	5	dbSNP_100	34	2941,5659	657.9+/-401.5	511,1919,1870	no	coding-synonymous	HK3	NM_002115.2		620,2675,3208	AA,AG,GG		34.1977,22.1062,30.1015		531/924	176314459	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	3101	exon11			GCTGCCGTCAGGG		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1593C>T	5.37:g.176314459G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.694;A|0.306	0.306	strong		0.672	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
GUCY1A2	2977	hgsc.bcm.edu	37	11	106647222	106647222	+	Silent	SNP	G	G	A	rs34690080	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:106647222G>A	ENST00000526355.2	-	6	2247	c.1779C>T	c.(1777-1779)gcC>gcT	p.A593A	GUCY1A2_ENST00000347596.2_Silent_p.A614A|GUCY1A2_ENST00000282249.2_Silent_p.A593A	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	593	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TCATCTTCAAGGCCATCAGAG	0.478													G|||	252	0.0503195	0.0212	0.0389	5008	,	,		18798	0.0784		0.0547	False		,,,				2504	0.0644				p.A593A		Atlas-SNP	.											GUCY1A2,NS,carcinoma,-1,2	GUCY1A2	180	2	0			c.C1779T						PASS	.	G		134,4268	95.7+/-134.4	4,126,2071	111.0	94.0	100.0		1779	3.9	1.0	11	dbSNP_126	100	413,8183	128.8+/-187.0	9,395,3894	no	coding-synonymous	GUCY1A2	NM_000855.1		13,521,5965	AA,AG,GG		4.8046,3.0441,4.2083		593/733	106647222	547,12451	2201	4298	6499	SO:0001819	synonymous_variant	2977	exon6			CTTCAAGGCCATC	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.1779C>T	11.37:g.106647222G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_000855	A1L4C4|B7ZLT5	Silent	SNP	ENST00000526355.2	37	CCDS8335.1																																																																																			G|0.953;A|0.047	0.047	strong		0.478	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
CXXC1	30827	hgsc.bcm.edu	37	18	47810351	47810351	+	Silent	SNP	A	A	G	rs7228084	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:47810351A>G	ENST00000285106.6	-	10	2040	c.1326T>C	c.(1324-1326)acT>acC	p.T442T	MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000589940.1_Silent_p.T442T|MBD1_ENST00000347968.3_5'Flank|CXXC1_ENST00000412036.2_Silent_p.T446T|MBD1_ENST00000269468.5_5'Flank|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000590208.1_5'Flank|MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000424334.2_5'Flank|CXXC1_ENST00000587396.1_5'Flank|MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000339998.6_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	442					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)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						CCTGAAGGCGAGTGCGGGCAC	0.602													A|||	3578	0.714457	0.5953	0.7709	5008	,	,		21331	0.7907		0.7396	False		,,,				2504	0.7311				p.T446T		Atlas-SNP	.											.	CXXC1	50	.	0			c.T1338C						PASS	.	A	,	2734,1672	655.2+/-399.9	847,1040,316	107.0	97.0	100.0		1338,1326	-5.3	1.0	18	dbSNP_116	100	6192,2408	698.7+/-405.0	2230,1732,338	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	3077,2772,654	GG,GA,AA		28.0,37.9483,31.3701	,	446/661,442/657	47810351	8926,4080	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon10			AAGGCGAGTGCGG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.1326T>C	18.37:g.47810351A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			A|0.305;G|0.695	0.695	strong		0.602	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
FCHO1	23149	hgsc.bcm.edu	37	19	17885880	17885880	+	Silent	SNP	C	C	T	rs2287855	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17885880C>T	ENST00000596536.1	+	14	1219	c.936C>T	c.(934-936)ccC>ccT	p.P312P	FCHO1_ENST00000597512.1_Silent_p.P319P|FCHO1_ENST00000252771.7_Silent_p.P312P|FCHO1_ENST00000389133.4_Silent_p.P312P|FCHO1_ENST00000539407.1_Silent_p.P312P|FCHO1_ENST00000595033.1_Silent_p.P262P|FCHO1_ENST00000600676.1_Silent_p.P312P|FCHO1_ENST00000594202.1_Silent_p.P312P|FCHO1_ENST00000596951.1_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	101	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	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	
OR2S2	56656	hgsc.bcm.edu	37	9	35957669	35957669	+	Missense_Mutation	SNP	T	T	C	rs2233564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35957669T>C	ENST00000341959.2	-	1	482	c.427A>G	c.(427-429)Atg>Gtg	p.M143V		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	143			M -> V (in dbSNP:rs2233564).		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(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GCCATGGGCATGTAGGCAGCC	0.537													C|||	1588	0.317093	0.4017	0.2896	5008	,	,		23981	0.2976		0.2793	False		,,,				2504	0.2812				p.M143V	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.A427G						PASS	.	C	VAL/MET	1741,2665	647.6+/-398.6	328,1085,790	91.0	80.0	84.0		427	2.1	0.3	9	dbSNP_98	84	2837,5763	674.6+/-403.1	509,1819,1972	yes	missense	OR2S2	NM_019897.2	21	837,2904,2762	CC,CT,TT		32.9884,39.5143,35.1991	benign	143/320	35957669	4578,8428	2203	4300	6503	SO:0001583	missense	56656	exon1			TGGGCATGTAGGC	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.427A>G	9.37:g.35957669T>C	ENSP00000344040:p.Met143Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	700	0.32051282051282054	206	0.4186991869918699	121	0.3342541436464088	163	0.28496503496503495	210	0.2770448548812665	C	0.001	-3.007357	0.00043	0.395143	0.329884	ENSG00000122718	ENST00000341959	T	0.34667	1.35	3.98	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.149772	0.30547	N	0.009391	T	0.00012	0.0000	N	0.00459	-1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44345	-0.9334	9	0.02654	T	1	.	3.956	0.09390	0.0:0.5234:0.1778:0.2988	rs2233564;rs3739616;rs52803098;rs2233564	143	Q9NQN1	OR2S1_HUMAN	V	143	ENSP00000344040:M143V	ENSP00000344040:M143V	M	-	1	0	OR2S2	35947669	0.000000	0.05858	0.335000	0.25508	0.040000	0.13550	-1.843000	0.01680	0.236000	0.21180	-0.119000	0.15052	ATG	T|0.657;C|0.343	0.343	strong		0.537	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
MGA	23269	hgsc.bcm.edu	37	15	42041712	42041712	+	Silent	SNP	G	G	A	rs2695163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42041712G>A	ENST00000570161.1	+	16	5907	c.5907G>A	c.(5905-5907)aaG>aaA	p.K1969K	MGA_ENST00000566586.1_Silent_p.K1760K|MGA_ENST00000389936.4_Silent_p.K1930K|MGA_ENST00000545763.1_Silent_p.K1760K|MGA_ENST00000219905.7_Silent_p.K1969K			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTCAGATGAAGAGAGAATCTC	0.438													G|||	3510	0.700879	0.3699	0.8055	5008	,	,		21069	0.8909		0.8161	False		,,,				2504	0.7597				p.K1969K		Atlas-SNP	.											.	MGA	264	.	0			c.G5907A						PASS	.	G	,	1681,2059		371,939,560	43.0	41.0	41.0		5280,5907	0.1	1.0	15	dbSNP_100	41	6656,1554		2707,1242,156	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	3078,2181,716	AA,AG,GG		18.9281,44.9465,30.2343	,	1760/2857,1969/3066	42041712	8337,3613	1870	4105	5975	SO:0001819	synonymous_variant	23269	exon17			GATGAAGAGAGAA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5907G>A	15.37:g.42041712G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			G|0.275;A|0.725	0.725	strong		0.438	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
NPR2	4882	hgsc.bcm.edu	37	9	35792423	35792423	+	Silent	SNP	T	T	C	rs2228580	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35792423T>C	ENST00000342694.2	+	1	273	c.18T>C	c.(16-18)ctT>ctC	p.L6L		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	6					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TGCCATCACTTCTGCTGTTGG	0.677													C|||	1570	0.313498	0.4985	0.2334	5008	,	,		12482	0.3819		0.2028	False		,,,				2504	0.1636				p.L6L		Atlas-SNP	.											.	NPR2	162	.	0			c.T18C						PASS	.	C		2004,2400		469,1066,667	21.0	23.0	22.0		18	2.2	1.0	9	dbSNP_98	22	1743,6853		170,1403,2725	no	coding-synonymous	NPR2	NM_003995.3		639,2469,3392	CC,CT,TT		20.2769,45.5041,28.8231		6/1048	35792423	3747,9253	2202	4298	6500	SO:0001819	synonymous_variant	4882	exon1			ATCACTTCTGCTG	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.18T>C	9.37:g.35792423T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																			T|0.691;C|0.309	0.309	strong		0.677	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
FLG	2312	hgsc.bcm.edu	37	1	152281948	152281948	+	Missense_Mutation	SNP	G	G	A	rs12405241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281948G>A	ENST00000368799.1	-	3	5449	c.5414C>T	c.(5413-5415)gCg>gTg	p.A1805V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1805	Ser-rich.		A -> V (in dbSNP:rs12405241).		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)			CTCTTGGGACGCTGAGTGCCT	0.592									Ichthyosis				G|||	1440	0.28754	0.0113	0.3905	5008	,	,		20549	0.5843		0.1421	False		,,,				2504	0.4315				p.A1805V		Atlas-SNP	.											.	FLG	900	.	0			c.C5414T						PASS	.	G	VAL/ALA	161,4245	108.2+/-146.6	2,157,2044	311.0	321.0	317.0		5414	-3.6	0.0	1	dbSNP_120	317	1240,7356	248.9+/-276.4	97,1046,3155	no	missense	FLG	NM_002016.1	64	99,1203,5199	AA,AG,GG		14.4253,3.6541,10.7753	probably-damaging	1805/4062	152281948	1401,11601	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGCTGAGT	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.5414C>T	1.37:g.152281948G>A	ENSP00000357789:p.Ala1805Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	282	173	0.613475	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	574	0.26282051282051283	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	112	0.14775725593667546	G	9.606	1.130070	0.21041	0.036541	0.144253	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01821	4.62	2.68	-3.56	0.04626	.	.	.	.	.	T	0.01254	0.0041	L	0.49350	1.555	0.80722	P	0.0	D	0.76494	0.999	D	0.68621	0.959	T	0.36383	-0.9750	8	0.25106	T	0.35	.	0.7622	0.01009	0.3595:0.1924:0.2946:0.1534	rs12405241;rs57429267	1805	P20930	FILA_HUMAN	V	1805;40	ENSP00000357789:A1805V	ENSP00000271820:A40V	A	-	2	0	FLG	150548572	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.623000	0.00109	-0.903000	0.03881	-1.464000	0.01018	GCG	G|0.839;A|0.161	0.161	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
USH2A	7399	hgsc.bcm.edu	37	1	215916563	215916563	+	Missense_Mutation	SNP	G	G	A	rs11120616	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:215916563G>A	ENST00000307340.3	-	59	11890	c.11504C>T	c.(11503-11505)aCt>aTt	p.T3835I	USH2A_ENST00000366943.2_Missense_Mutation_p.T3835I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3835	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I (in dbSNP:rs11120616). {ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|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)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.T3835I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGTGAATGGAGTCAAATTTTC	0.393										HNSCC(13;0.011)			G|||	724	0.144569	0.149	0.1931	5008	,	,		9956	0.0843		0.2346	False		,,,				2504	0.0736				p.T3835I		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	1	1	Substitution - Missense(1)	stomach(1)	c.C11504T						PASS	.	G	ILE/THR	628,3778	269.8+/-269.2	42,544,1617	139.0	133.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11504	4.9	1.0	1	dbSNP_120	135	2005,6595	351.9+/-328.4	237,1531,2532	yes	missense	USH2A	NM_206933.2	89	279,2075,4149	AA,AG,GG		23.314,14.2533,20.2445	benign	3835/5203	215916563	2633,10373	2203	4300	6503	SO:0001583	missense	7399	exon59			AATGGAGTCAAAT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11504C>T	1.37:g.215916563G>A	ENSP00000305941:p.Thr3835Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	392	0.1794871794871795	83	0.16869918699186992	80	0.22099447513812154	57	0.09965034965034965	172	0.22691292875989447	G	12.76	2.036066	0.35893	0.142533	0.23314	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.58210	0.35;0.35	4.94	4.94	0.65067	Fibronectin, type III (4);Immunoglobulin-like fold (1);	1.047120	0.07615	N	0.926035	T	0.00039	0.0001	L	0.34521	1.04	0.50039	P	1.5399999999998748E-4	B	0.21381	0.055	B	0.24701	0.055	T	0.02244	-1.1189	9	0.35671	T	0.21	.	11.5737	0.50850	0.0:0.0:0.7026:0.2974	rs11120616;rs52823661;rs61208500;rs11120616	3835	O75445	USH2A_HUMAN	I	3835	ENSP00000305941:T3835I;ENSP00000355910:T3835I	ENSP00000305941:T3835I	T	-	2	0	USH2A	213983186	0.919000	0.31177	0.996000	0.52242	0.781000	0.44180	1.348000	0.33987	2.706000	0.92434	0.655000	0.94253	ACT	G|0.807;A|0.193	0.193	strong		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
NLRP13	126204	hgsc.bcm.edu	37	19	56410222	56410222	+	Silent	SNP	C	C	T	rs302827	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56410222C>T	ENST00000342929.3	-	10	2870	c.2871G>A	c.(2869-2871)ttG>ttA	p.L957L	NLRP13_ENST00000588751.1_Silent_p.L957L	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	957							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)		CTCCCAAATCCAAGATTTTCA	0.438													C|||	1395	0.278554	0.1626	0.2493	5008	,	,		20206	0.4246		0.2803	False		,,,				2504	0.3037				p.L957L		Atlas-SNP	.											.	NLRP13	220	.	0			c.G2871A						PASS	.	C		720,3686	299.8+/-286.0	61,598,1544	178.0	150.0	159.0		2871	0.7	0.0	19	dbSNP_79	159	2504,6096	409.9+/-350.0	366,1772,2162	no	coding-synonymous	NLRP13	NM_176810.2		427,2370,3706	TT,TC,CC		29.1163,16.3414,24.7886		957/1044	56410222	3224,9782	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon10			CAAATCCAAGATT	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.2871G>A	19.37:g.56410222C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			C|0.739;T|0.261	0.261	strong		0.438	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
TEP1	7011	hgsc.bcm.edu	37	14	20871901	20871901	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20871901C>T	ENST00000262715.5	-	6	1215	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	392	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				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)		GGGTGGCCGGCGGGGGTGTCT	0.627																																					p.R392H		Atlas-SNP	.											TEP1,NS,carcinoma,-1,1	TEP1	224	1	0			c.G1175A						PASS	.						57.0	69.0	65.0					14																	20871901		2203	4300	6503	SO:0001583	missense	7011	exon6			GGCCGGCGGGGGT		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.1175G>A	14.37:g.20871901C>T	ENSP00000262715:p.Arg392His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	c	12.44	1.939881	0.34189	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.19250	2.16	5.54	-2.45	0.06481	TROVE (2);	0.558259	0.18672	N	0.134420	T	0.19446	0.0467	M	0.74258	2.255	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.19811	-1.0294	10	0.51188	T	0.08	-0.5193	5.7588	0.18188	0.0:0.4309:0.2237:0.3453	.	392	Q99973	TEP1_HUMAN	H	392	ENSP00000262715:R392H	ENSP00000262715:R392H	R	-	2	0	TEP1	19941741	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.167000	0.03126	-0.499000	0.06623	-0.119000	0.15052	CGC	.	.	none		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
HLA-A	3105	hgsc.bcm.edu	37	6	29911119	29911119	+	Missense_Mutation	SNP	G	G	T	rs3173419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29911119G>T	ENST00000396634.1	+	5	759	c.418G>T	c.(418-420)Gac>Tac	p.D140Y	HLA-A_ENST00000376806.5_Missense_Mutation_p.D140Y|HLA-A_ENST00000376809.5_Missense_Mutation_p.D140Y|HLA-A_ENST00000376802.2_Missense_Mutation_p.D140Y			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTACCGGCAGGACGCCTACGA	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	2088	0.416933	0.3646	0.536	5008	,	,		11816	0.497		0.4344	False		,,,				2504	0.3027				p.D140Y		Atlas-SNP	.											.	HLA-A	89	.	0			c.G418T						PASS	.	C	TYR/ASP	1066,1926		301,464,731	36.0	27.0	30.0		418	-7.6	0.0	6	dbSNP_105	30	1887,3509		429,1029,1240	no	missense	HLA-A	NM_002116.7	160	730,1493,1971	TT,TG,GG		34.9703,35.6283,35.2051	benign	140/366	29911119	2953,5435	1496	2698	4194	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGCAGGACGCCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.418G>T	6.37:g.29911119G>T	ENSP00000379873:p.Asp140Tyr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	128	28	0.21875	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	951	0.43543956043956045	186	0.3780487804878049	176	0.4861878453038674	289	0.5052447552447552	300	0.39577836411609496	.	0.012	-1.652752	0.00785	0.356283	0.349703	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00007	9.64;9.64;9.64;9.64	3.78	-7.56	0.01322	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	79.907900	0.01339	U	0.011517	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B;B	0.27166	0.17;0.013;0.005;0.034;0.013;0.013	B;B;B;B;B;B	0.30572	0.047;0.038;0.045;0.117;0.117;0.038	T	0.23691	-1.0181	8	0.02654	T	1	.	5.3314	0.15934	0.102:0.2286:0.5197:0.1496	rs3173419;rs3175999;rs16896879;rs28749152;rs41549418	19;140;140;140;140;140	B4DVB9;P13746;Q5SRN7;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;.;1A36_HUMAN;1A03_HUMAN	Y	140	ENSP00000379873:D140Y;ENSP00000366002:D140Y;ENSP00000366005:D140Y;ENSP00000365998:D140Y	ENSP00000365998:D140Y	D	+	1	0	HLA-A	30019098	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-9.138000	0.00013	-2.332000	0.00632	-4.658000	0.00004	GAC	C|0.006;G|0.577;T|0.416	0.416	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
NLRP5	126206	hgsc.bcm.edu	37	19	56549532	56549532	+	Silent	SNP	A	A	G	rs306447	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56549532A>G	ENST00000390649.3	+	10	2757	c.2757A>G	c.(2755-2757)agA>agG	p.R919R		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	919					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.R919R(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		ATGCCTTGAGAGTCTCCCAGT	0.522													G|||	1518	0.303115	0.4834	0.1758	5008	,	,		21896	0.3016		0.2406	False		,,,				2504	0.2157				p.R919R		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.A2757G						PASS	.	G		1782,2452		384,1014,719	133.0	134.0	134.0		2757	-2.2	0.0	19	dbSNP_79	134	1872,6602		218,1436,2583	no	coding-synonymous	NLRP5	NM_153447.4		602,2450,3302	GG,GA,AA		22.0911,42.0879,28.7535		919/1201	56549532	3654,9054	2117	4237	6354	SO:0001819	synonymous_variant	126206	exon10			CTTGAGAGTCTCC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2757A>G	19.37:g.56549532A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			A|0.693;G|0.307	0.307	strong		0.522	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
DHRS1	115817	hgsc.bcm.edu	37	14	24760764	24760764	+	Missense_Mutation	SNP	G	G	A	rs10134537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24760764G>A	ENST00000288111.7	-	7	998	c.722C>T	c.(721-723)aCa>aTa	p.T241I	DHRS1_ENST00000396813.1_Missense_Mutation_p.T241I|DHRS1_ENST00000559088.1_5'UTR	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	241			T -> I (in dbSNP:rs10134537).			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)		AACTTCACCTGTTGCCAAAGC	0.507													G|||	469	0.0936502	0.1384	0.0735	5008	,	,		21757	0.0893		0.0636	False		,,,				2504	0.0828				p.T241I		Atlas-SNP	.											.	DHRS1	21	.	0			c.C722T						PASS	.	G	ILE/THR,ILE/THR	545,3861	247.5+/-255.7	32,481,1690	234.0	233.0	234.0		722,722	6.0	1.0	14	dbSNP_119	234	602,7998	158.3+/-211.8	24,554,3722	yes	missense,missense	DHRS1	NM_001136050.2,NM_138452.2	89,89	56,1035,5412	AA,AG,GG		7.0,12.3695,8.819	possibly-damaging,possibly-damaging	241/314,241/314	24760764	1147,11859	2203	4300	6503	SO:0001583	missense	115817	exon7			TCACCTGTTGCCA	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.722C>T	14.37:g.24760764G>A	ENSP00000288111:p.Thr241Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Missense_Mutation	SNP	ENST00000288111.7	37	CCDS9623.1	181	0.08287545787545787	54	0.10975609756097561	30	0.08287292817679558	43	0.07517482517482517	54	0.0712401055408971	G	16.95	3.264429	0.59431	0.123695	0.07	ENSG00000157379	ENST00000288111;ENST00000396813	D;D	0.89746	-2.56;-2.56	5.97	5.97	0.96955	NAD(P)-binding domain (1);	0.108837	0.64402	D	0.000007	T	0.12774	0.0310	M	0.75264	2.295	0.23585	P	0.99735537	B	0.31752	0.338	B	0.33042	0.157	T	0.65265	-0.6210	9	0.48119	T	0.1	-7.9814	15.9136	0.79491	0.0:0.0:1.0:0.0	rs10134537;rs60832143;rs10134537	241	Q96LJ7	DHRS1_HUMAN	I	241	ENSP00000288111:T241I;ENSP00000380027:T241I	ENSP00000288111:T241I	T	-	2	0	DHRS1	23830604	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.736000	0.55052	2.835000	0.97688	0.591000	0.81541	ACA	G|0.913;A|0.087	0.087	strong		0.507	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
CBLB	868	hgsc.bcm.edu	37	3	105464766	105464766	+	Silent	SNP	G	G	A	rs9657906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:105464766G>A	ENST00000264122.4	-	6	1161	c.840C>T	c.(838-840)ccC>ccT	p.P280P	CBLB_ENST00000405772.1_Silent_p.P280P|CBLB_ENST00000394027.3_Silent_p.P302P|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000403724.1_Silent_p.P280P	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	280	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P280P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						CTTACCTTCCGGGTTTGGTGC	0.383			Mis S		AML								G|||	35	0.00698882	0.0038	0.0058	5008	,	,		16074	0.0		0.0179	False		,,,				2504	0.0082				p.P280P	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	1	Substitution - coding silent(1)	lung(1)	c.C840T						PASS	.	G		18,4388	24.3+/-50.5	0,18,2185	139.0	149.0	145.0		840	0.8	1.0	3	dbSNP_119	145	175,8425	80.1+/-142.7	2,171,4127	no	coding-synonymous	CBLB	NM_170662.3		2,189,6312	AA,AG,GG		2.0349,0.4085,1.4839		280/983	105464766	193,12813	2203	4300	6503	SO:0001819	synonymous_variant	868	exon6			CCTTCCGGGTTTG	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.840C>T	3.37:g.105464766G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	51	0.689189	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			G|0.987;A|0.013	0.013	strong		0.383	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
BCLAF1	9774	hgsc.bcm.edu	37	6	136589448	136589448	+	Missense_Mutation	SNP	C	C	A	rs78267720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:136589448C>A	ENST00000531224.1	-	10	2501	c.2249G>T	c.(2248-2250)cGa>cTa	p.R750L	BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R750L|BCLAF1_ENST00000530767.1_Missense_Mutation_p.R577L|BCLAF1_ENST00000527759.1_Missense_Mutation_p.R748L|BCLAF1_ENST00000353331.4_Missense_Mutation_p.R748L|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R748L|BCLAF1_ENST00000031135.9_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	750	Poly-Ser.				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)		GGATGAAGATCGAGAATGATC	0.343																																					p.R750L	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,bladder,carcinoma,-1,1	BCLAF1	203	1	0			c.G2249T						scavenged	.						106.0	91.0	97.0					6																	136589448		2203	4300	6503	SO:0001583	missense	9774	exon10			GAAGATCGAGAAT	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.2249G>T	6.37:g.136589448C>A	ENSP00000435210:p.Arg750Leu	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	118	25	0.211864	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529872	0.64860	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54	4.97	4.97	0.65823	.	0.000000	0.47852	D	0.000213	T	0.20455	0.0492	L	0.47190	1.495	0.80722	D	1	D;D;D;D;D	0.71674	0.991;0.998;0.991;0.991;0.991	P;D;P;P;P	0.69654	0.771;0.965;0.771;0.771;0.771	T	0.00752	-1.1581	10	0.35671	T	0.21	-3.7893	16.7666	0.85525	0.0:1.0:0.0:0.0	.	748;78;748;750;577	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	L	750;748;750;577;748;748	ENSP00000435210:R750L;ENSP00000229446:R748L;ENSP00000435441:R750L;ENSP00000436501:R577L;ENSP00000434826:R748L;ENSP00000376159:R748L	ENSP00000229446:R748L	R	-	2	0	BCLAF1	136631141	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.587000	0.60991	2.478000	0.83669	0.484000	0.47621	CGA	C|0.811;A|0.190	0.190	strong		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
OR52E6	390078	hgsc.bcm.edu	37	11	5863013	5863013	+	Missense_Mutation	SNP	T	T	C	rs4362173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5863013T>C	ENST00000329322.5	-	1	114	c.115A>G	c.(115-117)Att>Gtt	p.I39V	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.I43V	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	39			I -> V (in dbSNP:rs4362173).			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(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGAGTGCAATAAGATACACA	0.468													C|||	1924	0.384185	0.379	0.3184	5008	,	,		20747	0.4593		0.3728	False		,,,				2504	0.3722				p.I39V		Atlas-SNP	.											.	OR52E6	70	.	0			c.A115G						PASS	.	C	VAL/ILE	1625,2775	632.2+/-395.8	300,1025,875	119.0	119.0	119.0		115	-3.2	0.0	11	dbSNP_111	119	3011,5581	659.9+/-401.7	534,1943,1819	yes	missense	OR52E6	NM_001005167.1	29	834,2968,2694	CC,CT,TT		35.0442,36.9318,35.6835	benign	39/314	5863013	4636,8356	2200	4296	6496	SO:0001583	missense	390078	exon1			GTGCAATAAGATA	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.115A>G	11.37:g.5863013T>C	ENSP00000328878:p.Ile39Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	879	0.4024725274725275	201	0.40853658536585363	120	0.3314917127071823	264	0.46153846153846156	294	0.38786279683377306	C	0	-2.611809	0.00120	0.369318	0.350442	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00253	8.43;8.43	3.64	-3.21	0.05140	.	0.674836	0.13488	N	0.384173	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.23048	-1.0199	9	0.02654	T	1	.	7.5924	0.28029	0.1155:0.2699:0.0:0.6146	rs4362173;rs52822593;rs4362173	39	Q96RD3	O52E6_HUMAN	V	39;43	ENSP00000328878:I39V;ENSP00000369279:I43V	ENSP00000328878:I39V	I	-	1	0	OR52E6	5819589	0.000000	0.05858	0.002000	0.10522	0.119000	0.20118	-5.184000	0.00143	-0.999000	0.03442	-0.229000	0.12294	ATT	T|0.606;C|0.394	0.394	strong		0.468	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792003	8792003	+	Silent	SNP	C	C	T	rs9915880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8792003C>T	ENST00000447110.1	-	10	1225	c.1101G>A	c.(1099-1101)tcG>tcA	p.S367S	PIK3R5_ENST00000581552.1_Silent_p.S367S|PIK3R5_ENST00000584803.1_Silent_p.S367S	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	367				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	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						GGGCCGGCCCCGAGGCCTGGG	0.627													c|||	1017	0.203075	0.2995	0.2853	5008	,	,		18342	0.001		0.2833	False		,,,				2504	0.1401				p.S367S	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.G1101A						PASS	.	C	,	1297,3109	432.8+/-343.4	203,891,1109	72.0	75.0	74.0		1101,1101	-9.0	0.1	17	dbSNP_119	74	2686,5914	427.5+/-355.6	414,1858,2028	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	617,2749,3137	TT,TC,CC		31.2326,29.4371,30.6243	,	367/881,367/881	8792003	3983,9023	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CGGCCCCGAGGCC	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.1101G>A	17.37:g.8792003C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			C|0.736;T|0.264	0.264	strong		0.627	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
ARL2	402	hgsc.bcm.edu	37	11	64789222	64789222	+	Silent	SNP	C	C	T	rs61736632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64789222C>T	ENST00000246747.4	+	5	545	c.450C>T	c.(448-450)caC>caT	p.H150H	RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000533729.1_Silent_p.H123H|ARL2_ENST00000529384.1_Silent_p.H150H	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	150					cell cycle (GO:0007049)|centrosome organization (GO:0051297)|GTP catabolic process (GO:0006184)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of GTPase activity (GO:0034260)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of microtubule polymerization (GO:0031116)|regulation of microtubule polymerization (GO:0031113)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|tubulin complex assembly (GO:0007021)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|GTPase inhibitor activity (GO:0005095)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						TCCGCAGCCACCACTGGTGCA	0.642													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		17847	0.0		0.0129	False		,,,				2504	0.002				p.H150H		Atlas-SNP	.											.	ARL2	11	.	0			c.C450T						PASS	.	C	,	10,4392	16.8+/-37.8	0,10,2191	47.0	40.0	42.0		369,450	4.5	1.0	11	dbSNP_129	42	112,8482	58.7+/-120.3	0,112,4185	no	coding-synonymous,coding-synonymous	ARL2	NM_001199745.1,NM_001667.3	,	0,122,6376	TT,TC,CC		1.3032,0.2272,0.9388	,	123/158,150/185	64789222	122,12874	2201	4297	6498	SO:0001819	synonymous_variant	402	exon5			CAGCCACCACTGG	AF493888	CCDS8088.1, CCDS55770.1	11q13	2014-05-09			ENSG00000213465	ENSG00000213465		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	693	protein-coding gene	gene with protein product		601175				8415637, 9253601	Standard	NM_001667		Approved	ARFL2	uc001och.4	P36404	OTTHUMG00000165728	ENST00000246747.4:c.450C>T	11.37:g.64789222C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_001667	G3V184|Q9BUK8	Silent	SNP	ENST00000246747.4	37	CCDS8088.1																																																																																			C|0.992;T|0.008	0.008	strong		0.642	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667	
CNTLN	54875	hgsc.bcm.edu	37	9	17135115	17135115	+	Silent	SNP	C	C	T	rs41306071	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000262360.5_Silent_p.L18L|CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000425824.1_Silent_p.L18L			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	56	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	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	
TRIM66	9866	hgsc.bcm.edu	37	11	8671296	8671296	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8671296C>T	ENST00000299550.6	-	3	342	c.148G>A	c.(148-150)Gga>Aga	p.G50R	TRIM66_ENST00000402157.2_Missense_Mutation_p.G50R|TRIM66_ENST00000531498.1_5'UTR	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	50						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						CCTGGAGATCCCTTCTGGGCC	0.587																																					p.G50R		Atlas-SNP	.											.	TRIM66	45	.	0			c.G148A						PASS	.						57.0	61.0	60.0					11																	8671296		692	1591	2283	SO:0001583	missense	9866	exon3			GAGATCCCTTCTG	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.148G>A	11.37:g.8671296C>T	ENSP00000299550:p.Gly50Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		.	.	.	.	.	.	.	.	.	.	C	12.59	1.984321	0.35036	.	.	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.65549	-0.16;-0.15	5.69	4.78	0.61160	Zinc finger, PHD-type (1);	0.108635	0.41712	N	0.000827	T	0.50377	0.1612	L	0.27053	0.805	0.32346	N	0.559062	B;B	0.24768	0.047;0.111	B;B	0.24269	0.052;0.039	T	0.54214	-0.8327	10	0.25106	T	0.35	-4.1626	16.8115	0.85722	0.0:0.8713:0.1286:0.0	.	50;50	O15016;B5MCJ9	TRI66_HUMAN;.	R	50	ENSP00000299550:G50R;ENSP00000384876:G50R	ENSP00000299550:G50R	G	-	1	0	TRIM66	8627872	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	2.886000	0.48578	1.393000	0.46605	0.655000	0.94253	GGA	.	.	none		0.587	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
KRT6B	3854	hgsc.bcm.edu	37	12	52841765	52841765	+	Silent	SNP	G	G	A	rs388626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52841765G>A	ENST00000252252.3	-	7	1268	c.1221C>T	c.(1219-1221)gcC>gcT	p.A407A		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	407	Coil 2.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CAGCAATGGCGGCCTGTAGGT	0.537													G|||	2592	0.517572	0.4781	0.572	5008	,	,		21821	0.6825		0.505	False		,,,				2504	0.3753				p.A407A		Atlas-SNP	.											.	KRT6B	90	.	0			c.C1221T						PASS	.	G		1978,2428	558.4+/-380.0	438,1102,663	74.0	68.0	70.0		1221	-4.8	0.0	12	dbSNP_80	70	4228,4372	571.5+/-389.6	1031,2166,1103	no	coding-synonymous	KRT6B	NM_005555.3		1469,3268,1766	AA,AG,GG		49.1628,44.8933,47.7164		407/565	52841765	6206,6800	2203	4300	6503	SO:0001819	synonymous_variant	3854	exon7			AATGGCGGCCTGT	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.1221C>T	12.37:g.52841765G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			G|0.488;A|0.512	0.512	strong		0.537	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
STAT3	6774	hgsc.bcm.edu	37	17	40498635	40498635	+	Silent	SNP	C	C	T	rs146184566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40498635C>T	ENST00000264657.5	-	3	537	c.225G>A	c.(223-225)tcG>tcA	p.S75S	STAT3_ENST00000585517.1_Silent_p.S75S|STAT3_ENST00000404395.3_Silent_p.S75S|STAT3_ENST00000389272.3_5'UTR|STAT3_ENST00000588969.1_Silent_p.S75S	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	75					acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|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)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|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 regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		AGAGAACATTCGACTCTTGCA	0.478									Hyperimmunoglobulin E Recurrent Infection Syndrome				C|||	10	0.00199681	0.0076	0.0	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S75S		Atlas-SNP	.											STAT3,NS,carcinoma,0,1	STAT3	268	1	0			c.G225A						PASS	.	C	,,	7,4399	11.4+/-27.6	0,7,2196	225.0	220.0	222.0		225,225,225	-11.0	0.7	17	dbSNP_134	222	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	STAT3	NM_003150.3,NM_139276.2,NM_213662.1	,,	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	,,	75/770,75/771,75/723	40498635	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6774	exon3	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	AACATTCGACTCT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.225G>A	17.37:g.40498635C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Silent	SNP	ENST00000264657.5	37	CCDS32656.1																																																																																			C|0.999;T|0.001	0.001	strong		0.478	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
SAP30BP	29115	hgsc.bcm.edu	37	17	73702135	73702135	+	Silent	SNP	G	G	A	rs56144802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73702135G>A	ENST00000584667.1	+	10	965	c.708G>A	c.(706-708)acG>acA	p.T236T	SAP30BP_ENST00000355423.3_Silent_p.T220T	NM_013260.6	NP_037392.1			SAP30 binding protein											kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)	17	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ccaacgccacgtccaccacca	0.577													G|||	118	0.0235623	0.003	0.0331	5008	,	,		17530	0.0		0.0378	False		,,,				2504	0.0542				p.T236T		Atlas-SNP	.											.	SAP30BP	30	.	0			c.G708A						PASS	.	G		38,4368	41.6+/-74.8	0,38,2165	133.0	83.0	100.0		708	-11.6	0.0	17	dbSNP_129	100	409,8191	126.2+/-184.7	13,383,3904	no	coding-synonymous	SAP30BP	NM_013260.6		13,421,6069	AA,AG,GG		4.7558,0.8625,3.4369		236/309	73702135	447,12559	2203	4300	6503	SO:0001819	synonymous_variant	29115	exon10			CGCCACGTCCACC	AY082382	CCDS11726.1	17q25.1	2006-01-05				ENSG00000161526			30785	protein-coding gene	gene with protein product		610218				15496587	Standard	NM_013260		Approved	HCNGP, HTRG, HTRP	uc002jpe.3	Q9UHR5		ENST00000584667.1:c.708G>A	17.37:g.73702135G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_013260		Silent	SNP	ENST00000584667.1	37	CCDS11726.1																																																																																			G|0.972;A|0.028	0.028	strong		0.577	SAP30BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448227.1	NM_013260	
HELZ2	85441	hgsc.bcm.edu	37	20	62193733	62193733	+	Missense_Mutation	SNP	C	C	T	rs370768380		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62193733C>T	ENST00000467148.1	-	9	6374	c.6305G>A	c.(6304-6306)cGc>cAc	p.R2102H	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1533H	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2102					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)										TTCCTCCTTGCGGCTGGGGGT	0.682																																					p.R2102H		Atlas-SNP	.											PRIC285,colon,carcinoma,0,1	.	.	1	0			c.G6305A						PASS	.	C	HIS/ARG,HIS/ARG	0,4222		0,0,2111	8.0	9.0	9.0		6305,4598	4.2	1.0	20		9	1,8395		0,1,4197	no	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	29,29	0,1,6308	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging,probably-damaging	2102/2650,1533/2081	62193733	1,12617	2111	4198	6309	SO:0001583	missense	85441	exon10			TCCTTGCGGCTGG	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.6305G>A	20.37:g.62193733C>T	ENSP00000417401:p.Arg2102His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227358	0.79576	0.0	1.19E-4	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.84800	-1.9;-1.72	4.15	4.15	0.48705	.	0.311695	0.30043	N	0.010556	D	0.91233	0.7237	M	0.74258	2.255	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.74348	0.961;0.983	D	0.92378	0.5911	10	0.87932	D	0	-31.3164	13.9239	0.63950	0.0:1.0:0.0:0.0	.	2102;1533	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	H	1533;2102	ENSP00000393257:R1533H;ENSP00000417401:R2102H	ENSP00000393257:R1533H	R	-	2	0	RP4-697K14.7	61664177	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.523000	0.45580	1.867000	0.54127	0.313000	0.20887	CGC	.	.	weak		0.682	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
TRPM3	80036	hgsc.bcm.edu	37	9	73150918	73150918	+	Missense_Mutation	SNP	C	C	T	rs41287373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000358082.3_Missense_Mutation_p.R1554K|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Missense_Mutation_p.R1564K|TRPM3_ENST00000408909.2_Missense_Mutation_p.R1551K|TRPM3_ENST00000377106.1_Missense_Mutation_p.R1564K|TRPM3_ENST00000396280.5_Missense_Mutation_p.R1541K|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			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	124	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	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	
DLX5	1749	hgsc.bcm.edu	37	7	96653684	96653684	+	Silent	SNP	G	G	C	rs61753628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:96653684G>C	ENST00000222598.4	-	1	725	c.252C>G	c.(250-252)gcC>gcG	p.A84A	DLX5_ENST00000493764.1_5'UTR|DLX5_ENST00000486603.2_Silent_p.A84A	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	84					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|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)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	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)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGTAGCTCCCGGCGGAGCCGT	0.627													G|||	4	0.000798722	0.0	0.0014	5008	,	,		14915	0.0		0.002	False		,,,				2504	0.001				p.A84A		Atlas-SNP	.											DLX5,caecum,carcinoma,0,1	DLX5	52	1	0			c.C252G						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	51.0	52.0	52.0		252	3.1	1.0	7	dbSNP_129	52	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	DLX5	NM_005221.5		0,8,6495	CC,CG,GG		0.0814,0.0227,0.0615		84/290	96653684	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	1749	exon1			GCTCCCGGCGGAG		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"""Homeoboxes / ANTP class : NKL subclass"""	2918	protein-coding gene	gene with protein product		600028	"""distal-less homeo box 5"""			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.252C>G	7.37:g.96653684G>C		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_005221	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																			G|0.994;C|0.006	0.006	strong		0.627	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2		
TCEB3	6924	hgsc.bcm.edu	37	1	24083494	24083494	+	Silent	SNP	C	C	T	rs2076345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24083494C>T	ENST00000418390.2	+	10	2485	c.2214C>T	c.(2212-2214)agC>agT	p.S738S	TCEB3_ENST00000609199.1_Silent_p.S712S	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	738					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CCGCCAGTAGCATCAGCTTTA	0.577													C|||	1004	0.200479	0.0885	0.2421	5008	,	,		20319	0.2698		0.3101	False		,,,				2504	0.138				p.S738S		Atlas-SNP	.											.	TCEB3	61	.	0			c.C2214T						PASS	.	C		581,3825	258.0+/-262.2	39,503,1661	176.0	170.0	172.0		2214	3.5	1.0	1	dbSNP_96	172	2655,5945	426.8+/-355.4	400,1855,2045	no	coding-synonymous	TCEB3	NM_003198.2		439,2358,3706	TT,TC,CC		30.8721,13.1866,24.8808		738/799	24083494	3236,9770	2203	4300	6503	SO:0001819	synonymous_variant	6924	exon10			CAGTAGCATCAGC	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.2214C>T	1.37:g.24083494C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	179	96	0.536313	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	37	CCDS239.2																																																																																			C|0.764;T|0.236	0.236	strong		0.577	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152284505C>G	ENST00000368799.1	-	3	2892	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	953	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)			GAATGTCCCTCACTGTCACTG	0.572									Ichthyosis				-|||	685	0.136781	0.3707	0.0576	5008	,	,		22374	0.0694		0.0258	False		,,,				2504	0.0603				p.E953Q		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.G2857C						scavenged	.	G	GLN/GLU	442,3964		4,434,1765	302.0	283.0	290.0		2857	2.1	0.0	1	dbSNP_134	290	5,8595		0,5,4295	no	missense	FLG	NM_002016.1	29	4,439,6060	GG,GC,CC		0.0581,10.0318,3.4369	probably-damaging	953/4062	152284505	447,12559	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	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.2857G>C	1.37:g.152284505C>G	ENSP00000357789:p.Glu953Gln	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	280	14	0.05	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	7.629	0.678402	0.14841	0.100318	5.81E-4	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.08008	3.14	4.22	2.12	0.27331	.	.	.	.	.	T	0.03477	0.0100	N	0.11724	0.165	0.09310	N	1	D	0.61697	0.99	P	0.61201	0.885	T	0.41770	-0.9490	9	0.25751	T	0.34	.	6.5814	0.22596	0.2048:0.5963:0.1989:0.0	.	953	P20930	FILA_HUMAN	Q	953;160	ENSP00000357789:E953Q	ENSP00000357789:E953Q	E	-	1	0	FLG	150551129	0.000000	0.05858	0.004000	0.12327	0.029000	0.11900	-0.312000	0.08113	0.743000	0.32719	0.473000	0.43528	GAG	.	.	weak		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178581859	178581859	+	Silent	SNP	G	G	A	rs2278221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178581859G>A	ENST00000251582.7	-	7	1295	c.1194C>T	c.(1192-1194)gaC>gaT	p.D398D	ADAMTS2_ENST00000274609.5_Silent_p.D398D	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	398	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)		AGGAGAAGCCGTCCTCATGGT	0.642													G|||	1144	0.228435	0.0446	0.2925	5008	,	,		19306	0.3185		0.2475	False		,,,				2504	0.319				p.D398D		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C1194T						PASS	.	G	,	347,4059	177.6+/-206.5	13,321,1869	59.0	47.0	51.0		1194,1194	-3.6	1.0	5	dbSNP_100	51	2084,6516	354.4+/-329.5	269,1546,2485	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	282,1867,4354	AA,AG,GG		24.2326,7.8756,18.6914	,	398/1212,398/567	178581859	2431,10575	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon7			GAAGCCGTCCTCA	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.1194C>T	5.37:g.178581859G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			G|0.802;A|0.198	0.198	strong		0.642	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
CCDC14	64770	hgsc.bcm.edu	37	3	123665902	123665902	+	Missense_Mutation	SNP	T	T	G	rs17310144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:123665902T>G	ENST00000488653.2	-	8	1183	c.1093A>C	c.(1093-1095)Acg>Ccg	p.T365P	CCDC14_ENST00000310351.4_Missense_Mutation_p.T205P|CCDC14_ENST00000483247.1_Intron|CCDC14_ENST00000433542.2_Missense_Mutation_p.T324P|CCDC14_ENST00000485727.1_Missense_Mutation_p.T165P|CCDC14_ENST00000489746.1_Missense_Mutation_p.T165P			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	365			T -> P (in dbSNP:rs17310144). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		TCCAGATGCGTTTCTTTTCCA	0.403													T|||	1495	0.298522	0.0998	0.4035	5008	,	,		19041	0.1002		0.5676	False		,,,				2504	0.4202				p.T324P		Atlas-SNP	.											.	CCDC14	97	.	0			c.A970C						PASS	.	T	PRO/THR	834,3572	331.0+/-301.8	82,670,1451	227.0	209.0	215.0		970	-2.2	0.0	3	dbSNP_123	215	5345,3255	649.9+/-400.7	1662,2021,617	yes	missense	CCDC14	NM_022757.4	38	1744,2691,2068	GG,GT,TT		37.8488,18.9287,47.5088	possibly-damaging	324/913	123665902	6179,6827	2203	4300	6503	SO:0001583	missense	64770	exon7			GATGCGTTTCTTT	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.1093A>C	3.37:g.123665902T>G	ENSP00000420180:p.Thr365Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	37		689	0.31547619047619047	52	0.10569105691056911	170	0.4696132596685083	46	0.08041958041958042	421	0.5554089709762533	T	12.21	1.869719	0.33069	0.189287	0.621512	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000426152	T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.96	4.3	-2.21	0.06973	.	0.618090	0.15154	N	0.277539	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;P;P	0.47677	0.899;0.899;0.899	B;B;B	0.41813	0.367;0.367;0.367	T	0.42447	-0.9451	9	0.30078	T	0.28	.	10.2117	0.43145	0.0:0.435:0.0:0.565	rs17310144;rs17853981;rs52835558;rs17310144	365;324;165	Q49A88;Q49A88-6;Q49A88-4	CCD14_HUMAN;.;.	P	365;205;165;165;324;346;91	ENSP00000420180:T365P;ENSP00000312031:T205P;ENSP00000418002:T165P;ENSP00000418403:T165P;ENSP00000395706:T324P;ENSP00000386866:T346P;ENSP00000414655:T91P	ENSP00000312031:T205P	T	-	1	0	CCDC14	125148592	0.000000	0.05858	0.021000	0.16686	0.434000	0.31775	0.108000	0.15396	-0.253000	0.09514	0.533000	0.62120	ACG	T|0.623;G|0.377	0.377	strong		0.403	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
SLC7A7	9056	hgsc.bcm.edu	37	14	23248112	23248112	+	Silent	SNP	A	A	G	rs1805061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23248112A>G	ENST00000397532.3	-	4	1185	c.660T>C	c.(658-660)ggT>ggC	p.G220G	SLC7A7_ENST00000554061.1_5'UTR|SLC7A7_ENST00000285850.7_Silent_p.G220G|SLC7A7_ENST00000554517.1_5'UTR|SLC7A7_ENST00000397529.2_Silent_p.G220G|SLC7A7_ENST00000397528.4_Silent_p.G220G|SLC7A7_ENST00000555702.1_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	104	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	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		
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104123911C>T	ENST00000388887.2	+	49	5304	c.5100C>T	c.(5098-5100)aaC>aaT	p.N1700N		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						TGTATATAAACAATAAGGCTA	0.338													T|||	1424	0.284345	0.6702	0.2522	5008	,	,		17391	0.0367		0.1511	False		,,,				2504	0.1779				p.N1700N		Atlas-SNP	.											.	STAB2	370	.	0			c.C5100T						PASS	.	T		2627,1779	525.4+/-371.6	785,1057,361	120.0	140.0	134.0		5100	3.4	1.0	12	dbSNP_120	134	1197,7403	763.6+/-407.6	76,1045,3179	no	coding-synonymous	STAB2	NM_017564.9		861,2102,3540	TT,TC,CC		13.9186,40.3768,29.4018		1700/2552	104123911	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon49			TATAAACAATAAG	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.5100C>T	12.37:g.104123911C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.717;T|0.283	0.283	strong		0.338	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
TMC7	79905	hgsc.bcm.edu	37	16	19056695	19056695	+	Silent	SNP	C	C	T	rs137989665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19056695C>T	ENST00000304381.5	+	11	1618	c.1488C>T	c.(1486-1488)taC>taT	p.Y496Y	TMC7_ENST00000569532.1_Silent_p.Y496Y|TMC7_ENST00000421369.3_Silent_p.Y386Y	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	496					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						AGGAAATGTACAAGCTGATGA	0.493																																					p.Y496Y		Atlas-SNP	.											.	TMC7	75	.	0			c.C1488T						PASS	.	C	,	0,4394		0,0,2197	163.0	131.0	142.0		1158,1488	2.9	1.0	16	dbSNP_134	142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMC7	NM_001160364.1,NM_024847.3	,	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	,	386/614,496/724	19056695	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	79905	exon11			AATGTACAAGCTG	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1488C>T	16.37:g.19056695C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	156	69	0.442308	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	37	CCDS10573.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
GLP1R	2740	hgsc.bcm.edu	37	6	39034072	39034072	+	Missense_Mutation	SNP	G	G	A	rs6923761	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:39034072G>A	ENST00000373256.4	+	5	545	c.502G>A	c.(502-504)Ggc>Agc	p.G168S		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	168			G -> S (in dbSNP:rs6923761). {ECO:0000269|Ref.7}.		activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)			breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	GATCCTCCTCGGCTTCAGGTA	0.577													G|||	605	0.120807	0.0144	0.1729	5008	,	,		19884	0.0069		0.333	False		,,,				2504	0.1268				p.G168S		Atlas-SNP	.											.	GLP1R	64	.	0			c.G502A						PASS	.	G	SER/GLY	289,4117	159.6+/-192.1	12,265,1926	120.0	93.0	102.0		502	-2.1	0.0	6	dbSNP_116	102	2896,5704	452.4+/-362.9	528,1840,1932	yes	missense	GLP1R	NM_002062.3	56	540,2105,3858	AA,AG,GG		33.6744,6.5592,24.4887	benign	168/464	39034072	3185,9821	2203	4300	6503	SO:0001583	missense	2740	exon5			CTCCTCGGCTTCA		CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.502G>A	6.37:g.39034072G>A	ENSP00000362353:p.Gly168Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_002062	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	336	0.15384615384615385	11	0.022357723577235773	69	0.19060773480662985	4	0.006993006993006993	252	0.3324538258575198	G	5.606	0.296605	0.10622	0.065592	0.336744	ENSG00000112164	ENST00000373256	T	0.35789	1.29	4.95	-2.09	0.07232	GPCR, family 2-like (1);	1.053100	0.07412	N	0.892596	T	0.05868	0.0153	N	0.11131	0.1	0.50313	P	1.3700000000005375E-4	B	0.06786	0.001	B	0.13407	0.009	T	0.37641	-0.9697	9	0.21014	T	0.42	.	7.5642	0.27868	0.3703:0.1327:0.497:0.0	rs6923761;rs17339269;rs52795843;rs60911077;rs6923761	168	P43220	GLP1R_HUMAN	S	168	ENSP00000362353:G168S	ENSP00000362353:G168S	G	+	1	0	GLP1R	39142050	0.061000	0.20836	0.040000	0.18447	0.505000	0.33919	0.342000	0.19926	-0.385000	0.07833	0.650000	0.86243	GGC	A|0.199;G|0.801	0.199	strong		0.577	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
FAT1	2195	hgsc.bcm.edu	37	4	187540654	187540654	+	Silent	SNP	T	T	A	rs3796647	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187540654T>A	ENST00000441802.2	-	10	7295	c.7086A>T	c.(7084-7086)gcA>gcT	p.A2362A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2362	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CACCATCAACTGCCCTCACAA	0.488										HNSCC(5;0.00058)			A|||	341	0.0680911	0.003	0.1499	5008	,	,		20319	0.1786		0.0338	False		,,,				2504	0.0194				p.A2362A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A7086T						PASS	.	A		41,4215		0,41,2087	106.0	109.0	108.0		7086	-0.2	0.1	4	dbSNP_107	108	255,8231		4,247,3992	no	coding-synonymous	FAT1	NM_005245.3		4,288,6079	AA,AT,TT		3.0049,0.9633,2.323		2362/4589	187540654	296,12446	2128	4243	6371	SO:0001819	synonymous_variant	2195	exon10			ATCAACTGCCCTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7086A>T	4.37:g.187540654T>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.927;A|0.073	0.073	strong		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
NEB	4703	hgsc.bcm.edu	37	2	152499143	152499143	+	Missense_Mutation	SNP	C	C	T	rs35974308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:152499143C>T	ENST00000172853.10	-	60	8465	c.8318G>A	c.(8317-8319)cGg>cAg	p.R2773Q	NEB_ENST00000397345.3_Missense_Mutation_p.R2773Q|NEB_ENST00000427231.2_Missense_Mutation_p.R2773Q|NEB_ENST00000409198.1_Missense_Mutation_p.R2773Q|NEB_ENST00000603639.1_Missense_Mutation_p.R2773Q|NEB_ENST00000604864.1_Missense_Mutation_p.R2773Q			P20929	NEBU_HUMAN	nebulin	2773			R -> Q (in dbSNP:rs35974308).		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)		GGCATCTACCCGCATGTCATA	0.383													C|||	103	0.0205671	0.003	0.0086	5008	,	,		20553	0.0139		0.0258	False		,,,				2504	0.0542				p.R2773Q		Atlas-SNP	.											.	NEB	1697	.	0			c.G8318A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	21,3741		0,21,1860	88.0	84.0	85.0		8318,8318,8318	6.2	0.9	2	dbSNP_126	85	234,7984		4,226,3879	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	43,43,43	4,247,5739	TT,TC,CC		2.8474,0.5582,2.1285	probably-damaging,probably-damaging,probably-damaging	2773/8526,2773/8526,2773/6670	152499143	255,11725	1881	4109	5990	SO:0001583	missense	4703	exon60			TCTACCCGCATGT	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.8318G>A	2.37:g.152499143C>T	ENSP00000172853:p.Arg2773Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	7	0.012237762237762238	23	0.030343007915567283	C	18.81	3.703758	0.68501	0.005582	0.028474	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.09723	3.19;3.13;3.13;2.95	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	M	0.91354	3.2	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.11792	-1.0573	10	0.36615	T	0.2	.	20.8794	0.99867	0.0:1.0:0.0:0.0	rs35974308	2773	P20929	NEBU_HUMAN	Q	2773	ENSP00000386259:R2773Q;ENSP00000380505:R2773Q;ENSP00000416578:R2773Q;ENSP00000172853:R2773Q	ENSP00000172853:R2773Q	R	-	2	0	NEB	152207389	0.992000	0.36948	0.925000	0.36789	0.006000	0.05464	3.918000	0.56432	2.941000	0.99782	0.655000	0.94253	CGG	C|0.981;T|0.019	0.019	strong		0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
PJA2	9867	hgsc.bcm.edu	37	5	108713982	108713982	+	Silent	SNP	T	T	C	rs12523186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:108713982T>C	ENST00000361189.2	-	4	1445	c.1206A>G	c.(1204-1206)gcA>gcG	p.A402A	PJA2_ENST00000511624.1_5'Flank|PJA2_ENST00000361557.3_Silent_p.A402A	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	402					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)		CTTGCCTTCCTGCTGTGGCTC	0.408													T|||	1628	0.32508	0.0643	0.4726	5008	,	,		20694	0.0565		0.5915	False		,,,				2504	0.5757				p.A402A		Atlas-SNP	.											.	PJA2	53	.	0			c.A1206G						PASS	.	T		690,3714	286.9+/-279.0	54,582,1566	204.0	179.0	187.0		1206	-2.2	0.3	5	dbSNP_120	187	5097,3503	632.8+/-398.7	1517,2063,720	no	coding-synonymous	PJA2	NM_014819.4		1571,2645,2286	CC,CT,TT		40.7326,15.6676,44.5017		402/709	108713982	5787,7217	2202	4300	6502	SO:0001819	synonymous_variant	9867	exon4			CCTTCCTGCTGTG	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.1206A>G	5.37:g.108713982T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Silent	SNP	ENST00000361189.2	37	CCDS4099.1																																																																																			T|0.606;C|0.394	0.394	strong		0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
SH3TC1	54436	hgsc.bcm.edu	37	4	8229378	8229378	+	Silent	SNP	C	C	A	rs139890356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:8229378C>A	ENST00000245105.3	+	12	2024	c.1957C>A	c.(1957-1959)Cgg>Agg	p.R653R	SH3TC1_ENST00000539824.1_Silent_p.R577R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	653										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGGCGCTGCGGCGGGCGGT	0.726																																					p.R653R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C1957A						PASS	.						12.0	13.0	13.0					4																	8229378		1842	3696	5538	SO:0001819	synonymous_variant	54436	exon12			GCGCTGCGGCGGG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.1957C>A	4.37:g.8229378C>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			C|0.996;T|0.004	.	alt		0.726	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
TWISTNB	221830	hgsc.bcm.edu	37	7	19744417	19744417	+	Silent	SNP	T	T	C	rs11543308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:19744417T>C	ENST00000222567.5	-	2	451	c.381A>G	c.(379-381)ccA>ccG	p.P127P	MIR3146_ENST00000580367.1_RNA	NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	127					transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						GCTTCTGCCCTGGTTCAGGGC	0.333													C|||	515	0.102835	0.1884	0.1484	5008	,	,		15492	0.0526		0.0388	False		,,,				2504	0.0726				p.P127P		Atlas-SNP	.											.	TWISTNB	63	.	0			c.A381G						PASS	.	C		686,3720	739.3+/-411.1	51,584,1568	64.0	64.0	64.0		381	-3.6	1.0	7	dbSNP_131	64	337,8263	792.2+/-407.5	11,315,3974	no	coding-synonymous	TWISTNB	NM_001002926.1		62,899,5542	CC,CT,TT		3.9186,15.5697,7.8656		127/339	19744417	1023,11983	2203	4300	6503	SO:0001819	synonymous_variant	221830	exon2			CTGCCCTGGTTCA	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.381A>G	7.37:g.19744417T>C		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	248	172	0.693548	NM_001002926	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			T|0.918;C|0.082	0.082	strong		0.333	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1		
CTAGE5	4253	hgsc.bcm.edu	37	14	39818145	39818145	+	Missense_Mutation	SNP	G	G	A	rs1060878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:39818145G>A	ENST00000280083.3	+	23	2526	c.2212G>A	c.(2212-2214)Ggg>Agg	p.G738R	CTAGE5_ENST00000341749.3_Missense_Mutation_p.G726R|CTAGE5_ENST00000348007.3_Missense_Mutation_p.G695R|CTAGE5_ENST00000556148.1_Missense_Mutation_p.G663R|CTAGE5_ENST00000341502.5_Missense_Mutation_p.G738R|CTAGE5_ENST00000557038.1_Missense_Mutation_p.G658R|CTAGE5_ENST00000396165.4_Missense_Mutation_p.G709R|CTAGE5_ENST00000553383.1_3'UTR|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.G709R|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.G1273R|CTAGE5_ENST00000553352.1_Missense_Mutation_p.G709R|CTAGE5_ENST00000396158.2_Missense_Mutation_p.G743R			O15320	CTGE5_HUMAN	CTAGE family, member 5	738	Pro-rich.		G -> R (in dbSNP:rs1060878). {ECO:0000269|PubMed:12839582, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9356211}.		positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TTTTCCACCAGGGGATTTCCC	0.438													A|||	1556	0.310703	0.2973	0.2839	5008	,	,		17576	0.1587		0.3837	False		,,,				2504	0.4294				p.G743R		Atlas-SNP	.											.	CTAGE5	75	.	0			c.G2227A						PASS	.	A	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1388,3016		214,960,1028	69.0	75.0	73.0		2212,2176,2083,2125	3.8	1.0	14	dbSNP_86	73	3173,5425		612,1949,1738	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	826,2909,2766	AA,AG,GG		36.9039,31.5168,35.0792	benign,benign,benign,benign	738/805,726/793,695/762,709/776	39818145	4561,8441	2202	4299	6501	SO:0001583	missense	4253	exon23			CCACCAGGGGATT	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2212G>A	14.37:g.39818145G>A	ENSP00000280083:p.Gly738Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	642	0.29395604395604397	156	0.3170731707317073	101	0.27900552486187846	95	0.1660839160839161	290	0.38258575197889183	A	0.424	-0.907019	0.02434	0.315168	0.369039	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	4.95	3.81	0.43845	.	0.000000	0.36444	N	0.002599	T	0.00012	0.0000	N	0.00034	-2.56	0.58432	P	2.9999999999752447E-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	0.001;0.001;0.001;0.001;0.001	T	0.41805	-0.9488	8	.	.	.	.	4.5122	0.11917	0.6562:0.1657:0.1781:0.0	rs1060878;rs1804861;rs3201810;rs57745043	743;695;738;666;726	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	R	1273;726;658;709;738;743;738;663;695;709	ENSP00000452252:G1273R;ENSP00000343897:G726R;ENSP00000450869:G658R;ENSP00000379468:G709R;ENSP00000339286:G738R;ENSP00000379462:G743R;ENSP00000280083:G738R;ENSP00000452562:G663R;ENSP00000343912:G695R;ENSP00000450449:G709R	.	G	+	1	0	CTAGE5;RP11-407N17.3	38887896	1.000000	0.71417	0.998000	0.56505	0.671000	0.39405	1.555000	0.36277	0.329000	0.23460	-0.254000	0.11334	GGG	G|0.654;A|0.346	0.346	strong		0.438	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
PDPR	55066	hgsc.bcm.edu	37	16	70172890	70172890	+	Missense_Mutation	SNP	C	C	T	rs112617700		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70172890C>T	ENST00000288050.4	+	11	2236	c.1279C>T	c.(1279-1281)Cgc>Tgc	p.R427C	PDPR_ENST00000398122.3_Missense_Mutation_p.R327C|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000568530.1_Missense_Mutation_p.R427C	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	427					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)	p.R427C(1)		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)		CCAGAGCAGCCGCACCTTTCT	0.512																																					p.R427C		Atlas-SNP	.											PDPR,colon,carcinoma,-1,2	PDPR	66	2	1	Substitution - Missense(1)	stomach(1)	c.C1279T						scavenged	.						20.0	21.0	21.0					16																	70172890		1801	4043	5844	SO:0001583	missense	55066	exon11			AGCAGCCGCACCT		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.1279C>T	16.37:g.70172890C>T	ENSP00000288050:p.Arg427Cys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	185	35	0.189189	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	287	0.13141025641025642	69	0.1402439024390244	43	0.11878453038674033	51	0.08916083916083917	124	0.16358839050131926	C	29.1	4.978510	0.92982	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	D;D	0.85773	-2.03;-2.03	4.42	4.42	0.53409	.	0.119515	0.64402	D	0.000017	T	0.03136	0.0092	M	0.77406	2.37	0.80722	D	1	D;D	0.89917	1.0;0.998	P;P	0.56216	0.794;0.676	T	0.26087	-1.0113	10	0.72032	D	0.01	.	16.0044	0.80349	0.0:1.0:0.0:0.0	.	155;427	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	C	427;327;155	ENSP00000288050:R427C;ENSP00000381190:R327C	ENSP00000205055:R155C	R	+	1	0	PDPR	68730391	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	7.645000	0.83430	1.985000	0.57927	0.455000	0.32223	CGC	C|0.870;T|0.130	0.130	strong		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
PMFBP1	83449	hgsc.bcm.edu	37	16	72170408	72170408	+	Missense_Mutation	SNP	C	C	A	rs35781168	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72170408C>A	ENST00000237353.10	-	9	1403	c.1142G>T	c.(1141-1143)cGg>cTg	p.R381L	PMFBP1_ENST00000355636.6_Missense_Mutation_p.R236L|PMFBP1_ENST00000537465.1_Missense_Mutation_p.R381L	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	381			R -> L (in dbSNP:rs35781168).			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)				CTCCTGCAGCCGGCACTGCAG	0.547													C|||	23	0.00459265	0.0	0.0029	5008	,	,		20957	0.0		0.0159	False		,,,				2504	0.0051				p.R381L		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G1142T						PASS	.	C	LEU/ARG,LEU/ARG	7,4389	12.9+/-30.5	0,7,2191	125.0	115.0	118.0		707,1142	-1.5	0.3	16	dbSNP_126	118	130,8470	66.0+/-128.3	1,128,4171	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	102,102	1,135,6362	AA,AC,CC		1.5116,0.1592,1.0542	probably-damaging,probably-damaging	236/883,381/1008	72170408	137,12859	2198	4300	6498	SO:0001583	missense	83449	exon9			TGCAGCCGGCACT	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.1142G>T	16.37:g.72170408C>A	ENSP00000237353:p.Arg381Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	17.56	3.421157	0.62622	0.001592	0.015116	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.14144	2.54;2.55;2.53	5.21	-1.49	0.08718	.	0.642755	0.13016	N	0.420490	T	0.07728	0.0194	L	0.36672	1.1	0.09310	N	1	P;P;P	0.47841	0.872;0.901;0.872	B;P;B	0.50970	0.441;0.655;0.441	T	0.15925	-1.0420	10	0.66056	D	0.02	-4.5634	9.3035	0.37861	0.0:0.3994:0.0:0.6006	rs35781168	381;381;381	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	L	381;381;236	ENSP00000443817:R381L;ENSP00000237353:R381L;ENSP00000347854:R236L	ENSP00000237353:R381L	R	-	2	0	PMFBP1	70727909	0.033000	0.19621	0.319000	0.25293	0.249000	0.25844	-0.102000	0.10956	-0.050000	0.13356	-0.222000	0.12452	CGG	C|0.990;A|0.010	0.010	strong		0.547	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
EEF2	1938	hgsc.bcm.edu	37	19	3982967	3982967	+	Silent	SNP	G	G	A	rs2230561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3982967G>A	ENST00000309311.6	-	4	538	c.450C>T	c.(448-450)cgC>cgT	p.R150R	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	150	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCTTGATGCGCTCGGCAA	0.642													G|||	330	0.0658946	0.0045	0.0533	5008	,	,		16936	0.0218		0.0974	False		,,,				2504	0.1708				p.R150R	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C450T						PASS	.	G		69,4335	62.3+/-99.4	1,67,2134	45.0	35.0	38.0		450	1.6	1.0	19	dbSNP_98	38	825,7773	185.6+/-233.3	37,751,3511	yes	coding-synonymous	EEF2	NM_001961.3		38,818,5645	AA,AG,GG		9.5953,1.5668,6.8759		150/859	3982967	894,12108	2202	4299	6501	SO:0001819	synonymous_variant	1938	exon4			CTTGATGCGCTCG	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.450C>T	19.37:g.3982967G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			G|0.937;A|0.063	0.063	strong		0.642	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
TMEM177	80775	hgsc.bcm.edu	37	2	120438515	120438515	+	Missense_Mutation	SNP	G	G	C	rs11684353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:120438515G>C	ENST00000424086.1	+	2	559	c.86G>C	c.(85-87)gGa>gCa	p.G29A	TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000401466.1_Missense_Mutation_p.G29A|TMEM177_ENST00000409951.1_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	110	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	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	
ARRDC4	91947	hgsc.bcm.edu	37	15	98513845	98513845	+	Missense_Mutation	SNP	T	T	C	rs2130882	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:98513845T>C	ENST00000268042.6	+	7	1236	c.1072T>C	c.(1072-1074)Tca>Cca	p.S358P	ARRDC4_ENST00000538249.1_Missense_Mutation_p.S271P	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	358			S -> P (in dbSNP:rs2130882). {ECO:0000269|PubMed:15489334}.		positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			AGATGTGGTATCAGAGGAAGA	0.403													T|||	2099	0.419129	0.0545	0.5043	5008	,	,		16140	0.5486		0.4811	False		,,,				2504	0.6544				p.S358P		Atlas-SNP	.											ARRDC4,colon,carcinoma,0,1	ARRDC4	30	1	0			c.T1072C						scavenged	.	T	PRO/SER	511,3883	233.3+/-246.5	36,439,1722	99.0	87.0	91.0		1072	4.3	1.0	15	dbSNP_96	91	4362,4234	581.6+/-391.2	1096,2170,1032	yes	missense	ARRDC4	NM_183376.2	74	1132,2609,2754	CC,CT,TT		49.2555,11.6295,37.5135	probably-damaging	358/419	98513845	4873,8117	2197	4298	6495	SO:0001583	missense	91947	exon7			GTGGTATCAGAGG	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.1072T>C	15.37:g.98513845T>C	ENSP00000268042:p.Ser358Pro	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_183376	Q6NSI9	Missense_Mutation	SNP	ENST00000268042.6	37	CCDS10377.1	900	0.41208791208791207	38	0.07723577235772358	174	0.48066298342541436	320	0.5594405594405595	368	0.48548812664907653	T	14.26	2.483797	0.44147	0.116295	0.507445	ENSG00000140450	ENST00000538249;ENST00000268042	T;T	0.10382	2.88;3.05	5.49	4.35	0.52113	Immunoglobulin E-set (1);	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	L	0.42686	1.345	0.23162	P	0.99819883	D;D	0.71674	0.998;0.995	P;P	0.60682	0.878;0.876	T	0.30416	-0.9979	9	0.17832	T	0.49	-5.5959	12.0812	0.53671	0.129:0.0:0.0:0.871	rs2130882;rs3759829;rs17852599;rs52814015;rs58570136;rs2130882	358;271	Q8NCT1;F5H824	ARRD4_HUMAN;.	P	271;358	ENSP00000443774:S271P;ENSP00000268042:S358P	ENSP00000268042:S358P	S	+	1	0	ARRDC4	96314849	1.000000	0.71417	0.965000	0.40720	0.753000	0.42808	3.886000	0.56190	0.994000	0.38892	-0.336000	0.08194	TCA	C|0.387;N|0.001	0.387	strong		0.403	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376	
NUP205	23165	hgsc.bcm.edu	37	7	135269656	135269656	+	Missense_Mutation	SNP	G	G	A	rs61459701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135269656G>A	ENST00000285968.6	+	8	1145	c.1119G>A	c.(1117-1119)atG>atA	p.M373I	NUP205_ENST00000440390.2_Missense_Mutation_p.M167I	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	373					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TGTTCCTCATGGAATCTGTAG	0.398													G|||	176	0.0351438	0.0333	0.049	5008	,	,		16359	0.003		0.0467	False		,,,				2504	0.0491				p.M373I		Atlas-SNP	.											.	NUP205	198	.	0			c.G1119A						PASS	.	G	ILE/MET	109,4297	36.8+/-68.6	2,105,2096	80.0	72.0	75.0		1119	-6.1	0.6	7	dbSNP_129	75	223,8377	35.3+/-89.8	4,215,4081	yes	missense	NUP205	NM_015135.2	10	6,320,6177	AA,AG,GG		2.593,2.4739,2.5527	benign	373/2013	135269656	332,12674	2203	4300	6503	SO:0001583	missense	23165	exon8			CCTCATGGAATCT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1119G>A	7.37:g.135269656G>A	ENSP00000285968:p.Met373Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	61	20	0.327869	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	51	0.023351648351648352	10	0.02032520325203252	16	0.04419889502762431	2	0.0034965034965034965	23	0.030343007915567283	G	11.64	1.698742	0.30142	0.024739	0.02593	ENSG00000155561	ENST00000285968;ENST00000440390	T;T	0.28895	1.59;1.59	5.53	-6.05	0.02172	.	0.144073	0.64402	D	0.000008	T	0.02304	0.0071	N	0.08118	0	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.17899	-1.0354	10	0.22109	T	0.4	-28.4751	10.8116	0.46551	0.0:0.1971:0.5398:0.2631	rs61459701;rs61751962	373	Q92621	NU205_HUMAN	I	373;167	ENSP00000285968:M373I;ENSP00000401983:M167I	ENSP00000285968:M373I	M	+	3	0	NUP205	134920196	0.047000	0.20315	0.628000	0.29241	0.896000	0.52359	-1.195000	0.03043	-0.903000	0.03881	-0.362000	0.07510	ATG	G|0.964;A|0.036	0.036	strong		0.398	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
HLA-DRA	3122	hgsc.bcm.edu	37	6	32411646	32411646	+	Missense_Mutation	SNP	T	T	G	rs58547911|rs7192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32411646T>G	ENST00000374982.5	+	4	722	c.649T>G	c.(649-651)Ttg>Gtg	p.L217V	HLA-DRA_ENST00000395388.2_Missense_Mutation_p.L242V			P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	242					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|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)|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)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|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 protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						CATCAAGGGATTGCGCAAAAG	0.537									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of				G|||	3303	0.659545	0.5998	0.6902	5008	,	,		19093	0.6865		0.6332	False		,,,				2504	0.7178				p.L242V		Atlas-SNP	.											HLA-DRA,colon,carcinoma,0,1	HLA-DRA	34	1	0			c.T724G						PASS	.	G	VAL/LEU	1752,1270		486,780,245	146.0	132.0	137.0	http://omim.org/entry/142395	724	-7.3	0.0	6	dbSNP_52	137	3292,2126		996,1300,413	yes	missense	HLA-DRA	NM_019111.4	32	1482,2080,658	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	39.2396,42.0251,40.237	benign	242/255	32411646	5044,3396	1511	2709	4220	SO:0001583	missense	3122	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;	AAGGGATTGCGCA		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000374982.5:c.649T>G	6.37:g.32411646T>G	ENSP00000364121:p.Leu217Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_019111	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000374982.5	37		1380	0.6318681318681318	286	0.5813008130081301	238	0.6574585635359116	389	0.6800699300699301	467	0.6160949868073878	.	8.697	0.908903	0.17833	0.579749	0.607604	ENSG00000204287	ENST00000395388;ENST00000374982	T;T	0.01787	4.64;4.91	5.36	-7.3	0.01446	.	1.413030	0.04205	N	0.330761	T	0.00384	0.0012	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45891	-0.9230	8	0.35671	T	0.21	.	4.0215	0.09668	0.5796:0.0938:0.1373:0.1893	rs7192;rs3175097;rs9268661;rs17349282;rs52820028;rs60904659;rs7192	217	Q30118	.	V	242;217	ENSP00000378786:L242V;ENSP00000364121:L217V	ENSP00000364121:L217V	L	+	1	2	HLA-DRA	32519624	0.002000	0.14202	0.000000	0.03702	0.035000	0.12851	-0.101000	0.10973	-1.957000	0.01021	-1.194000	0.01681	TTG	T|0.376;G|0.624	0.624	strong		0.537	HLA-DRA-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000076587.3	NM_019111	
LYZ	4069	hgsc.bcm.edu	37	12	69744014	69744014	+	Missense_Mutation	SNP	C	C	A	rs1800973	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:69744014C>A	ENST00000261267.2	+	2	331	c.263C>A	c.(262-264)aCc>aAc	p.T88N	LYZ_ENST00000548839.1_Missense_Mutation_p.T88N|LYZ_ENST00000549690.1_Missense_Mutation_p.T88N	NM_000239.2	NP_000230.1	P61626	LYSC_HUMAN	lysozyme	88			T -> N (in dbSNP:rs1800973).		cell wall macromolecule catabolic process (GO:0016998)|cytolysis (GO:0019835)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|lysozyme activity (GO:0003796)			endometrium(2)|lung(1)|upper_aerodigestive_tract(1)	4	all_epithelial(5;2.98e-35)|Lung NSC(4;9.93e-33)|all_lung(4;5.66e-31)|Breast(13;2.56e-06)|Esophageal squamous(21;0.187)		Epithelial(6;8.26e-19)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00503)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)		L-Aspartic Acid(DB00128)	GATGGCAAAACCCCAGGAGCA	0.403													C|||	73	0.0145767	0.0008	0.0288	5008	,	,		16479	0.0		0.0437	False		,,,				2504	0.0082				p.T88N		Atlas-SNP	.											.	LYZ	7	.	0			c.C263A	GRCh37	CM060322	LYZ	M	rs1800973	PASS	.	C	ASN/THR	56,4350	54.2+/-90.2	1,54,2148	152.0	133.0	139.0		263	5.9	1.0	12	dbSNP_89	139	600,8000	155.7+/-209.7	21,558,3721	yes	missense	LYZ	NM_000239.2	65	22,612,5869	AA,AC,CC		6.9767,1.271,5.0438	probably-damaging	88/149	69744014	656,12350	2203	4300	6503	SO:0001583	missense	4069	exon2			GCAAAACCCCAGG	X14008	CCDS8989.1	12q15	2014-09-17	2010-04-29			ENSG00000090382	3.2.1.17		6740	protein-coding gene	gene with protein product	"""renal amyloidosis"""	153450	"""lysozyme (renal amyloidosis)"""			8464497, 2546758	Standard	NM_000239		Approved		uc001suw.2	P61626	OTTHUMG00000169342	ENST00000261267.2:c.263C>A	12.37:g.69744014C>A	ENSP00000261267:p.Thr88Asn	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_000239	P00695|Q13170|Q9UCF8	Missense_Mutation	SNP	ENST00000261267.2	37	CCDS8989.1	46	0.021062271062271064	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	31	0.040897097625329816	C	15.08	2.728201	0.48833	0.01271	0.069767	ENSG00000090382	ENST00000261267;ENST00000549690;ENST00000548839	T;T;T	0.70516	-0.49;-0.49;-0.49	5.94	5.94	0.96194	Lysozyme-like domain (1);	0.049482	0.85682	D	0.000000	T	0.38108	0.1028	M	0.81341	2.54	0.58432	D	0.999999	D	0.56746	0.977	D	0.74023	0.982	T	0.68573	-0.5373	9	.	.	.	.	17.8674	0.88799	0.0:1.0:0.0:0.0	rs1800973;rs52807071;rs59962001;rs1800973	88	P61626	LYSC_HUMAN	N	88	ENSP00000261267:T88N;ENSP00000449898:T88N;ENSP00000449969:T88N	.	T	+	2	0	LYZ	68030281	0.981000	0.34729	1.000000	0.80357	0.089000	0.18198	2.441000	0.44864	2.820000	0.97059	0.650000	0.86243	ACC	C|0.961;A|0.039	0.039	strong		0.403	LYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403624.2	NM_000239	
TMEM175	84286	hgsc.bcm.edu	37	4	951947	951947	+	Missense_Mutation	SNP	T	T	C	rs34311866	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:951947T>C	ENST00000264771.4	+	11	1363	c.1178T>C	c.(1177-1179)aTg>aCg	p.M393T	TMEM175_ENST00000508204.1_Missense_Mutation_p.M311T|TMEM175_ENST00000515740.1_Missense_Mutation_p.M277T	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	393			M -> T (in dbSNP:rs34311866).			integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CAGCTGGCCATGTGGACCACG	0.672													T|||	701	0.139976	0.0083	0.0879	5008	,	,		17754	0.131		0.1869	False		,,,				2504	0.316				p.M393T		Atlas-SNP	.											.	TMEM175	44	.	0			c.T1178C						PASS	.	T	THR/MET	156,4242	95.3+/-134.0	3,150,2046	31.0	31.0	31.0		1178	0.8	0.0	4	dbSNP_126	31	1629,6963	277.5+/-292.9	166,1297,2833	no	missense	TMEM175	NM_032326.2	81	169,1447,4879	CC,CT,TT		18.9595,3.5471,13.7413	benign	393/505	951947	1785,11205	2199	4296	6495	SO:0001583	missense	84286	exon11			TGGCCATGTGGAC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.1178T>C	4.37:g.951947T>C	ENSP00000264771:p.Met393Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	37	CCDS3341.1	252	0.11538461538461539	3	0.006097560975609756	27	0.07458563535911603	71	0.12412587412587413	151	0.19920844327176782	T	4.032	0.003419	0.07866	0.035471	0.189595	ENSG00000127419	ENST00000264771;ENST00000515740;ENST00000508204	T;T;T	0.42131	1.56;1.55;0.98	4.65	0.788	0.18601	.	0.350017	0.27802	N	0.017788	T	0.00039	0.0001	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.15235	-1.0444	9	0.72032	D	0.01	-2.1276	7.5233	0.27641	0.0:0.3491:0.0:0.6509	rs34311866	311;393	D3DVN5;Q9BSA9	.;TM175_HUMAN	T	393;277;311	ENSP00000264771:M393T;ENSP00000427039:M277T;ENSP00000423669:M311T	ENSP00000264771:M393T	M	+	2	0	TMEM175	941947	0.999000	0.42202	0.014000	0.15608	0.001000	0.01503	1.299000	0.33424	-0.078000	0.12730	0.402000	0.26972	ATG	T|0.874;C|0.126	0.126	strong		0.672	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	
KMT2C	58508	hgsc.bcm.edu	37	7	151970859	151970859	+	Missense_Mutation	SNP	C	C	T	rs149992209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151970859C>T	ENST00000262189.6	-	7	1161	c.943G>A	c.(943-945)Ggc>Agc	p.G315S	KMT2C_ENST00000355193.2_Missense_Mutation_p.G315S	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.G315S		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,14	MLL3	1564	14	0			c.G943A						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>A	7.37:g.151970859C>T	ENSP00000262189:p.Gly315Ser	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	288	24	0.0833333	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265939	0.80358	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.72615	-0.67;-0.67	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.45606	D	0.000359	D	0.85999	0.5828	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87947	0.2721	10	0.59425	D	0.04	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	315	Q8NEZ4	MLL3_HUMAN	S	315	ENSP00000262189:G315S;ENSP00000347325:G315S	ENSP00000262189:G315S	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	0.006	strong		0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
VSX2	338917	hgsc.bcm.edu	37	14	74711883	74711883	+	Silent	SNP	C	C	T	rs35435463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74711883C>T	ENST00000261980.2	+	3	561	c.471C>T	c.(469-471)tcC>tcT	p.S157S		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	157					cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		TCTTTACCTCCTACCAGCTAG	0.547													C|||	1302	0.259984	0.0628	0.4755	5008	,	,		14812	0.0754		0.5129	False		,,,				2504	0.3037				p.S157S		Atlas-SNP	.											.	VSX2	32	.	0			c.C471T						PASS	.	C		564,3842	252.4+/-258.8	37,490,1676	57.0	50.0	52.0		471	4.8	1.0	14	dbSNP_126	52	4487,4113	590.0+/-392.6	1192,2103,1005	no	coding-synonymous	VSX2	NM_182894.2		1229,2593,2681	TT,TC,CC		47.8256,12.8007,38.8359		157/362	74711883	5051,7955	2203	4300	6503	SO:0001819	synonymous_variant	338917	exon3			TACCTCCTACCAG	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"""Homeoboxes / PRD class"""	1975	protein-coding gene	gene with protein product		142993	"""C elegans ceh-10 homeo domain-containing homolog"", ""ceh-10 homeo domain containing homolog (C. elegans)"", ""ceh-10 homeodomain containing homolog (C. elegans)"""	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.471C>T	14.37:g.74711883C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_182894	A1A4X6	Silent	SNP	ENST00000261980.2	37	CCDS9827.1																																																																																			C|0.634;T|0.366	0.366	strong		0.547	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894	
FSIP2	401024	hgsc.bcm.edu	37	2	186678633	186678633	+	Missense_Mutation	SNP	C	C	T	rs17826666	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:186678633C>T	ENST00000424728.1	+	18	20189	c.20189C>T	c.(20188-20190)aCt>aTt	p.T6730I	FSIP2_ENST00000343098.5_Missense_Mutation_p.T6819I			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6730				T -> I (in Ref. 2; BX648733). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						ATTGAAAGTACTGAAGCAATC	0.403													C|||	265	0.0529153	0.0038	0.0634	5008	,	,		19953	0.0079		0.1004	False		,,,				2504	0.1094				p.T6819I		Atlas-SNP	.											.	FSIP2	251	.	0			c.C20456T						PASS	.	C	ILE/THR	72,3748		0,72,1838	89.0	85.0	86.0		20456	-5.7	0.0	2	dbSNP_123	86	776,7482		27,722,3380	yes	missense	FSIP2	NM_173651.2	89	27,794,5218	TT,TC,CC		9.3969,1.8848,7.021	benign	6819/6997	186678633	848,11230	1910	4129	6039	SO:0001583	missense	401024	exon18			AAAGTACTGAAGC	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.20189C>T	2.37:g.186678633C>T	ENSP00000401306:p.Thr6730Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	162	89	0.549383	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		120	0.054945054945054944	4	0.008130081300813009	27	0.07458563535911603	4	0.006993006993006993	85	0.11213720316622691	C	3.880	-0.026082	0.07589	0.018848	0.093969	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39229	1.09;1.09	5.29	-5.67	0.02444	.	1.038600	0.07609	N	0.925119	T	0.00468	0.0015	N	0.12182	0.205	0.80722	P	0.0	.	.	.	.	.	.	T	0.19128	-1.0315	7	0.21014	T	0.42	.	13.0578	0.58990	0.0:0.6171:0.0:0.3829	rs17826666;rs17826666	.	.	.	I	6819;6730	ENSP00000344403:T6819I;ENSP00000401306:T6730I	ENSP00000344403:T6819I	T	+	2	0	FSIP2	186386878	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.829000	0.01701	-1.109000	0.02996	-1.036000	0.02392	ACT	C|0.944;T|0.056	0.056	strong		0.403	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
UBR5	51366	hgsc.bcm.edu	37	8	103306033	103306033	+	Silent	SNP	T	T	C	rs16869352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:103306033T>C	ENST00000520539.1	-	34	4995	c.4389A>G	c.(4387-4389)gtA>gtG	p.V1463V	UBR5_ENST00000521922.1_Silent_p.V1457V|UBR5_ENST00000220959.4_Silent_p.V1463V|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	1463					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)			ATGCTTGGAATACACGCTTGC	0.398													T|||	122	0.024361	0.0045	0.0216	5008	,	,		22490	0.0198		0.0626	False		,,,				2504	0.0184				p.V1463V	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.A4389G						PASS	.	T		55,4351	54.2+/-90.2	0,55,2148	90.0	74.0	79.0		4389	-2.4	1.0	8	dbSNP_123	79	573,8027	154.2+/-208.4	19,535,3746	no	coding-synonymous	UBR5	NM_015902.5		19,590,5894	CC,CT,TT		6.6628,1.2483,4.8285		1463/2800	103306033	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	51366	exon34			TTGGAATACACGC	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.4389A>G	8.37:g.103306033T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			T|0.957;C|0.043	0.043	strong		0.398	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
RBM19	9904	hgsc.bcm.edu	37	12	114362515	114362515	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:114362515C>T	ENST00000545145.2	-	18	2370	c.2292G>A	c.(2290-2292)aaG>aaA	p.K764K	RBM19_ENST00000392561.3_Silent_p.K764K|RBM19_ENST00000261741.5_Silent_p.K764K	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	764	RRM 5. {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)			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)					CTTTGTTCTTCTTCTTGGAGA	0.448																																					p.K764K		Atlas-SNP	.											RBM19,right_upper_lobe,carcinoma,-2,1	RBM19	117	1	0			c.G2292A						scavenged	.						192.0	186.0	188.0					12																	114362515		2203	4300	6503	SO:0001819	synonymous_variant	9904	exon18			GTTCTTCTTCTTG	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.2292G>A	12.37:g.114362515C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			.	.	none		0.448	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SLC39A3	29985	hgsc.bcm.edu	37	19	2732986	2732986	+	Silent	SNP	T	T	C	rs759073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2732986T>C	ENST00000269740.4	-	3	1037	c.708A>G	c.(706-708)gtA>gtG	p.V236V	AC006538.4_ENST00000586572.1_Intron|SLC39A3_ENST00000545664.1_Silent_p.V236V	NM_144564.4	NP_653165.2	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter), member 3	236					transmembrane transport (GO:0055085)	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(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10		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)		TCATGGCGCTTACGGTGACCG	0.736													C|||	3132	0.625399	0.907	0.3905	5008	,	,		14002	0.6468		0.4414	False		,,,				2504	0.5787				p.V236V		Atlas-SNP	.											SLC39A3,NS,carcinoma,0,1	SLC39A3	20	1	0			c.A708G						scavenged	.	C		3669,719		1542,585,67	19.0	22.0	21.0		708	2.4	1.0	19	dbSNP_86	21	3873,4701		921,2031,1335	no	coding-synonymous	SLC39A3	NM_144564.4		2463,2616,1402	CC,CT,TT		45.1714,16.3856,41.8145		236/315	2732986	7542,5420	2194	4287	6481	SO:0001819	synonymous_variant	29985	exon3			GGCGCTTACGGTG	AF052125	CCDS12093.1, CCDS45909.1	19p13.3	2013-05-22			ENSG00000141873	ENSG00000141873		"""Solute carriers"""	17128	protein-coding gene	gene with protein product		612168				10681536	Standard	NM_144564		Approved	ZIP3	uc002lwg.3	Q9BRY0		ENST00000269740.4:c.708A>G	19.37:g.2732986T>C		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_144564	B3KMJ3|Q8WUG1	Silent	SNP	ENST00000269740.4	37	CCDS12093.1																																																																																			T|0.411;C|0.589	0.589	strong		0.736	SLC39A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451354.2		
AKNAD1	254268	hgsc.bcm.edu	37	1	109369915	109369915	+	Missense_Mutation	SNP	G	G	T	rs7551421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:109369915G>T	ENST00000370001.3	-	11	2116	c.1848C>A	c.(1846-1848)aaC>aaA	p.N616K	AKNAD1_ENST00000357393.4_Missense_Mutation_p.N323K|AKNAD1_ENST00000369994.1_Missense_Mutation_p.N586K|AKNAD1_ENST00000369995.3_Missense_Mutation_p.N616K	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	616			N -> K (in dbSNP:rs7551421). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)		p.N616K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TTTTCTCCACGTTTTGCTTCC	0.378													T|||	2520	0.503195	0.6331	0.5288	5008	,	,		16967	0.2649		0.5805	False		,,,				2504	0.4755				p.N616K		Atlas-SNP	.											AKNAD1,NS,carcinoma,-2,2	AKNAD1	83	2	1	Substitution - Missense(1)	stomach(1)	c.C1848A						PASS	.	T	LYS/ASN	2802,1604	495.1+/-363.2	896,1010,297	152.0	158.0	156.0		1848	-7.4	0.0	1	dbSNP_116	156	5195,3403	501.8+/-375.5	1582,2031,686	yes	missense	AKNAD1	NM_152763.3	94	2478,3041,983	TT,TG,GG		39.579,36.4049,38.5035	benign	616/837	109369915	7997,5007	2203	4299	6502	SO:0001583	missense	254268	exon11			CTCCACGTTTTGC	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.1848C>A	1.37:g.109369915G>T	ENSP00000359018:p.Asn616Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	1112	0.5091575091575091	316	0.6422764227642277	205	0.5662983425414365	152	0.26573426573426573	439	0.579155672823219	T	0.038	-1.296348	0.01364	0.635951	0.60421	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.0	-7.42	0.01388	.	0.949771	0.08698	N	0.906845	T	0.00552	0.0018	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	0.36792	-0.9733	9	0.02654	T	1	-0.0014	2.3068	0.04176	0.2031:0.2145:0.4134:0.169	rs7551421;rs52829264;rs58082587;rs7551421	323;616	B4DET8;Q5T1N1	.;AKND1_HUMAN	K	616;323;586;616	ENSP00000359018:N616K;ENSP00000349968:N323K;ENSP00000359011:N586K;ENSP00000359012:N616K	ENSP00000349968:N323K	N	-	3	2	AKNAD1	109171438	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.357000	0.02607	-2.161000	0.00785	-1.554000	0.00893	AAC	G|0.440;N|0.001	.	strong		0.378	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
EFS	10278	hgsc.bcm.edu	37	14	23830042	23830042	+	Splice_Site	SNP	T	T	C	rs2231798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23830042T>C	ENST00000216733.3	-	2	626	c.19A>G	c.(19-21)Acc>Gcc	p.T7A	EFS_ENST00000351354.3_Intron|EFS_ENST00000429593.2_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	54	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	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
TRIOBP	11078	hgsc.bcm.edu	37	22	38120542	38120542	+	Missense_Mutation	SNP	C	C	T	rs142024473	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38120542C>T	ENST00000406386.3	+	7	2234	c.1979C>T	c.(1978-1980)gCc>gTc	p.A660V		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	660					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)					GATCCCAGAGCCTCCTCTCCT	0.582													C|||	238	0.047524	0.0484	0.0375	5008	,	,		20601	0.001		0.0368	False		,,,				2504	0.1125				p.A660V		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C1979T						PASS	.	C	VAL/ALA	219,3727		10,199,1764	165.0	184.0	178.0		1979	3.3	0.2	22	dbSNP_134	178	372,7956		4,364,3796	no	missense	TRIOBP	NM_001039141.2	64	14,563,5560	TT,TC,CC		4.4669,5.5499,4.8151	benign	660/2366	38120542	591,11683	1973	4164	6137	SO:0001583	missense	11078	exon7			CCAGAGCCTCCTC	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.1979C>T	22.37:g.38120542C>T	ENSP00000384312:p.Ala660Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	160	66	0.4125	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	73	0.033424908424908424	28	0.056910569105691054	16	0.04419889502762431	0	0.0	29	0.03825857519788918	C	9.758	1.169225	0.21621	0.055499	0.044669	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20598	2.06	5.44	3.29	0.37713	.	.	.	.	.	T	0.01835	0.0058	L	0.46157	1.445	0.49798	P	1.7999999999995797E-4	B	0.19200	0.034	B	0.14023	0.01	T	0.04579	-1.0941	8	0.41790	T	0.15	.	8.0188	0.30398	0.0:0.7526:0.1592:0.0881	.	660	Q9H2D6	TARA_HUMAN	V	660	ENSP00000384312:A660V	ENSP00000384312:A660V	A	+	2	0	TRIOBP	36450488	0.875000	0.30112	0.194000	0.23346	0.160000	0.22226	0.882000	0.28186	1.281000	0.44480	0.460000	0.39030	GCC	C|0.963;T|0.037	0.037	strong		0.582	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
LRRC6	23639	hgsc.bcm.edu	37	8	133584558	133584558	+	Missense_Mutation	SNP	A	A	G	rs9297853	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:133584558A>G	ENST00000519595.1	-	12	1495	c.1397T>C	c.(1396-1398)aTt>aCt	p.I466T	LRRC6_ENST00000250173.1_Missense_Mutation_p.I466T|LRRC6_ENST00000518642.1_3'UTR			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	466			I -> T (in dbSNP:rs9297853).		cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			GATGTTTCAAATCAGCGGAGG	0.468													A|||	721	0.14397	0.326	0.0893	5008	,	,		17839	0.0466		0.0875	False		,,,				2504	0.0951				p.I466T		Atlas-SNP	.											.	LRRC6	58	.	0			c.T1397C						PASS	.	A	THR/ILE	1297,3109	439.2+/-345.6	198,901,1104	225.0	206.0	212.0		1397	5.7	0.6	8	dbSNP_119	212	832,7768	192.1+/-238.2	38,756,3506	yes	missense	LRRC6	NM_012472.3	89	236,1657,4610	GG,GA,AA		9.6744,29.4371,16.3694	probably-damaging	466/467	133584558	2129,10877	2203	4300	6503	SO:0001583	missense	23639	exon12			TTTCAAATCAGCG	U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"""leucine rich testes protein"""	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.1397T>C	8.37:g.133584558A>G	ENSP00000429791:p.Ile466Thr	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	258	147	0.569767	NM_012472	Q13648|Q4G183	Missense_Mutation	SNP	ENST00000519595.1	37		286	0.13095238095238096	153	0.31097560975609756	36	0.09944751381215469	23	0.04020979020979021	74	0.09762532981530343	A	15.36	2.810633	0.50421	0.294371	0.096744	ENSG00000129295	ENST00000519595;ENST00000522789;ENST00000250173	T;T;T	0.60040	0.22;0.34;0.22	5.69	5.69	0.88448	.	0.250357	0.41294	D	0.000910	T	0.00012	0.0000	M	0.72894	2.215	0.27459	P	0.9531937	D	0.54964	0.969	P	0.52856	0.711	T	0.08391	-1.0724	9	0.87932	D	0	.	12.3338	0.55054	1.0:0.0:0.0:0.0	rs9297853;rs52822837;rs57953540;rs9297853	466	Q86X45	LRRC6_HUMAN	T	466;206;466	ENSP00000429791:I466T;ENSP00000428015:I206T;ENSP00000250173:I466T	ENSP00000250173:I466T	I	-	2	0	LRRC6	133653740	0.999000	0.42202	0.576000	0.28549	0.116000	0.19942	5.469000	0.66749	2.162000	0.67917	0.533000	0.62120	ATT	A|0.843;G|0.157	0.157	strong		0.468	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	135	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	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	
RPUSD4	84881	hgsc.bcm.edu	37	11	126081403	126081403	+	Missense_Mutation	SNP	T	T	C	rs2282580	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126081403T>C	ENST00000298317.4	-	1	184	c.131A>G	c.(130-132)cAg>cGg	p.Q44R	FAM118B_ENST00000533050.1_5'UTR|RPUSD4_ENST00000533628.1_Missense_Mutation_p.Q44R|RPUSD4_ENST00000534393.1_5'Flank|FAM118B_ENST00000529731.1_5'Flank|FAM118B_ENST00000360194.4_5'Flank|RNU4-86P_ENST00000410135.1_RNA|RP11-50B3.4_ENST00000532866.1_RNA	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	56	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	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	
APC	324	hgsc.bcm.edu	37	5	112176559	112176559	+	Silent	SNP	T	T	G	rs866006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176559T>G	ENST00000457016.1	+	16	5648	c.5268T>G	c.(5266-5268)tcT>tcG	p.S1756S	APC_ENST00000508376.2_Silent_p.S1756S|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.S1756S			P25054	APC_HUMAN	adenomatous polyposis coli	1756	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CATCTGCGTCTTCTTCTGCAC	0.398		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			t|||	3340	0.666933	0.5197	0.7161	5008	,	,		19571	0.8165		0.6004	False		,,,				2504	0.7454				p.S1756S	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5268G						PASS	.	G	,,	2326,2078	584.6+/-386.1	621,1084,497	55.0	54.0	54.0	http://omim.org/entry/114500	5268,5268,5214	-2.5	0.2	5	dbSNP_86	54	5319,3279	623.8+/-397.5	1680,1959,660	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2301,3043,1157	GG,GT,TT		38.1368,47.1844,41.2014	,,	1756/2844,1756/2844,1738/2826	112176559	7645,5357	2202	4299	6501	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TGCGTCTTCTTCT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5268T>G	5.37:g.112176559T>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			T|0.384;G|0.616	0.616	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
ADCY6	112	hgsc.bcm.edu	37	12	49162439	49162439	+	Missense_Mutation	SNP	C	C	G	rs200204618		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49162439C>G	ENST00000307885.4	-	21	4136	c.3442G>C	c.(3442-3444)Gtg>Ctg	p.V1148L	ADCY6_ENST00000550422.1_Missense_Mutation_p.V1095L|ADCY6_ENST00000357869.3_Missense_Mutation_p.V1095L|RP11-579D7.2_ENST00000548742.1_RNA	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	1148					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						ACCTTGACCACCCCTCGACAC	0.607																																					p.V1148L		Atlas-SNP	.											.	ADCY6	81	.	0			c.G3442C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	104.0	88.0	93.0		3442,3283	4.2	1.0	12		93	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ADCY6	NM_015270.3,NM_020983.2	32,32	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	benign,benign	1148/1169,1095/1116	49162439	2,13004	2203	4300	6503	SO:0001583	missense	112	exon21			TGACCACCCCTCG		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.3442G>C	12.37:g.49162439C>G	ENSP00000311405:p.Val1148Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_015270	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	37	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735662	0.30774	0.0	2.33E-4	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.80738	-1.41;-1.41;-1.41	5.12	4.23	0.50019	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.246243	0.32563	N	0.005938	T	0.56834	0.2012	N	0.01679	-0.765	0.47778	D	0.999511	B;B	0.13594	0.007;0.008	B;B	0.15484	0.012;0.013	T	0.53165	-0.8477	10	0.19590	T	0.45	.	15.4765	0.75485	0.0:0.86:0.14:0.0	.	1095;1148	O43306-2;O43306	.;ADCY6_HUMAN	L	1095;1095;1148	ENSP00000350536:V1095L;ENSP00000446730:V1095L;ENSP00000311405:V1148L	ENSP00000311405:V1148L	V	-	1	0	ADCY6	47448706	0.944000	0.32072	1.000000	0.80357	0.994000	0.84299	1.300000	0.33436	1.491000	0.48482	-0.223000	0.12442	GTG	.	.	weak		0.607	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
KLHL33	123103	hgsc.bcm.edu	37	14	20898308	20898308	+	Missense_Mutation	SNP	C	C	T	rs17242648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	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	
URGCP	55665	hgsc.bcm.edu	37	7	43916491	43916491	+	Silent	SNP	G	G	A	rs2232109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:43916491G>A	ENST00000453200.1	-	6	3064	c.2571C>T	c.(2569-2571)gaC>gaT	p.D857D	URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Silent_p.D848D|URGCP_ENST00000443736.1_Silent_p.D814D|URGCP_ENST00000223341.7_Silent_p.D814D|URGCP_ENST00000447717.3_Silent_p.D814D|URGCP_ENST00000336086.6_Silent_p.D814D|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	857	VLIG-type G.				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						CCCGGAAGCCGTCGCCCTGTT	0.642													G|||	366	0.0730831	0.028	0.0908	5008	,	,		18388	0.0149		0.1292	False		,,,				2504	0.1237				p.D857D		Atlas-SNP	.											.	URGCP	170	.	0			c.C2571T						PASS	.	G	,,,	193,3793		3,187,1803	29.0	30.0	30.0		2571,2442,,2544	-6.8	0.0	7	dbSNP_98	30	1068,7278		57,954,3162	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	60,1141,4965	AA,AG,GG		12.7965,4.8419,10.2254	,,,	857/932,814/889,,848/923	43916491	1261,11071	1993	4173	6166	SO:0001819	synonymous_variant	55665	exon6			GAAGCCGTCGCCC		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.2571C>T	7.37:g.43916491G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	107	34	0.317757	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			G|0.918;A|0.082	0.082	strong		0.642	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
CCDC39	339829	hgsc.bcm.edu	37	3	180365956	180365956	+	Silent	SNP	G	G	A	rs6769457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:180365956G>A	ENST00000442201.2	-	10	1478	c.1359C>T	c.(1357-1359)agC>agT	p.S453S	CCDC39_ENST00000273654.4_Silent_p.S537S	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	453					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|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)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CATCTACCTGGCTGTACATAA	0.343													A|||	1597	0.31889	0.7375	0.2911	5008	,	,		18222	0.004		0.2515	False		,,,				2504	0.1667				p.S453S		Atlas-SNP	.											.	CCDC39	242	.	0			c.C1359T						PASS	.	A		2333,1391		731,871,260	74.0	72.0	72.0		1359	1.5	1.0	3	dbSNP_116	72	1803,6395		198,1407,2494	no	coding-synonymous	CCDC39	NM_181426.1		929,2278,2754	AA,AG,GG		21.9932,37.3523,34.6922		453/942	180365956	4136,7786	1862	4099	5961	SO:0001819	synonymous_variant	339829	exon10			TACCTGGCTGTAC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1359C>T	3.37:g.180365956G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	37	CCDS46964.1																																																																																			G|0.678;A|0.322	0.322	strong		0.343	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs200702907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22574357C>G	ENST00000357774.5	-	4	1801	c.1680G>C	c.(1678-1680)aaG>aaC	p.K560N		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	560					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.K560N(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				ATTTGGAAATCTTTGCAATGT	0.323																																					p.K560N		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,0,4	ZNF98	230	4	2	Substitution - Missense(2)	prostate(2)	c.G1680C						scavenged	.						21.0	16.0	17.0					19																	22574357		1774	3947	5721	SO:0001583	missense	148198	exon4			GGAAATCTTTGCA		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1680G>C	19.37:g.22574357C>G	ENSP00000350418:p.Lys560Asn	Somatic	492	0	0		WXS	Illumina HiSeq	Phase_I	522	73	0.139847	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.422641	0.00186	.	.	ENSG00000197360	ENST00000357774	T	0.07688	3.17	1.39	0.147	0.14838	.	.	.	.	.	T	0.02193	0.0068	N	0.03000	-0.44	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41858	-0.9485	9	0.05959	T	0.93	.	0.0912	0.00040	0.3312:0.2373:0.1958:0.2357	.	560	A6NK75	ZNF98_HUMAN	N	560	ENSP00000350418:K560N	ENSP00000350418:K560N	K	-	3	2	ZNF98	22366197	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-2.155000	0.01284	-0.971000	0.03564	-0.764000	0.03450	AAG	C|0.500;G|0.500	0.500	weak		0.323	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
MUC4	4585	hgsc.bcm.edu	37	3	195511294	195511294	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195511294G>T	ENST00000463781.3	-	2	7616	c.7157C>A	c.(7156-7158)cCt>cAt	p.P2386H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2386H	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	0.582																																					p.P2386H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C7157A						PASS	.						23.0	27.0	26.0					3																	195511294		677	1585	2262	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.7157C>A	3.37:g.195511294G>T	ENSP00000417498:p.Pro2386His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	248	10	0.0403226	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	3.986	-0.005498	0.07773	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.39;1.44	.	.	.	.	.	.	.	.	T	0.31979	0.0814	N	0.19112	0.55	0.09310	N	1	D	0.54964	0.969	P	0.55667	0.781	T	0.14282	-1.0478	7	.	.	.	.	6.7067	0.23254	2.0E-4:0.0:0.9998:0.0	.	2386	E7ESK3	.	H	2386	ENSP00000417498:P2386H;ENSP00000420243:P2386H	.	P	-	2	0	MUC4	196995689	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.286000	0.18902	0.488000	0.27723	0.064000	0.15345	CCT	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
STARD7	56910	hgsc.bcm.edu	37	2	96859034	96859034	+	Silent	SNP	A	A	G	rs997547	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:96859034A>G	ENST00000337288.5	-	4	989	c.606T>C	c.(604-606)atT>atC	p.I202I	STARD7_ENST00000462501.1_Intron	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	202	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.					mitochondrion (GO:0005739)	lipid binding (GO:0008289)	p.I127I(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						CATCCCTCTCAATCACCTCCA	0.423													a|||	536	0.107029	0.0189	0.0793	5008	,	,		18024	0.0863		0.1511	False		,,,				2504	0.2219				p.I202I		Atlas-SNP	.											STARD7,NS,carcinoma,0,1	STARD7	49	1	1	Substitution - coding silent(1)	stomach(1)	c.T606C						PASS	.	A		174,4232	114.2+/-152.2	3,168,2032	146.0	136.0	139.0		606	-3.0	1.0	2	dbSNP_86	139	1247,7353	250.4+/-277.3	95,1057,3148	no	coding-synonymous	STARD7	NM_020151.3		98,1225,5180	GG,GA,AA		14.5,3.9492,10.9257		202/371	96859034	1421,11585	2203	4300	6503	SO:0001819	synonymous_variant	56910	exon4			CCTCTCAATCACC	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"""StAR-related lipid transfer (START) domain containing"""	18063	protein-coding gene	gene with protein product			"""START domain containing 7"""				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.606T>C	2.37:g.96859034A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	178	77	0.432584	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Silent	SNP	ENST00000337288.5	37	CCDS2017.2																																																																																			A|0.904;G|0.096	0.096	strong		0.423	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2		
GJA4	2701	hgsc.bcm.edu	37	1	35259946	35259946	+	Silent	SNP	G	G	A	rs1764389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35259946G>A	ENST00000342280.4	+	2	220	c.132G>A	c.(130-132)gtG>gtA	p.V44V		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	44					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)		p.V44V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GCGAGTCAGTGTGGGGTGACG	0.602													G|||	1182	0.236022	0.4796	0.1614	5008	,	,		18859	0.1349		0.2197	False		,,,				2504	0.0808				p.V44V		Atlas-SNP	.											GJA4,NS,carcinoma,0,1	GJA4	25	1	1	Substitution - coding silent(1)	stomach(1)	c.G132A						scavenged	.	G		1917,2489	547.9+/-377.4	415,1087,701	163.0	142.0	149.0		132	1.2	1.0	1	dbSNP_89	149	1733,6867	315.0+/-312.1	173,1387,2740	no	coding-synonymous	GJA4	NM_002060.2		588,2474,3441	AA,AG,GG		20.1512,43.5089,28.064		44/334	35259946	3650,9356	2203	4300	6503	SO:0001819	synonymous_variant	2701	exon2			GTCAGTGTGGGGT	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.132G>A	1.37:g.35259946G>A		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Silent	SNP	ENST00000342280.4	37	CCDS30669.1																																																																																			G|0.731;A|0.269	0.269	strong		0.602	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
PLIN4	729359	hgsc.bcm.edu	37	19	4511860	4511860	+	Silent	SNP	G	G	A	rs79731243	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4511860G>A	ENST00000301286.3	-	3	2069	c.2070C>T	c.(2068-2070)ctC>ctT	p.L690L		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	690	27 X 33 AA approximate tandem repeat.					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						CTGCCCCCATGAGCCCAGTAG	0.587																																					p.L690L		Atlas-SNP	.											.	PLIN4	191	.	0			c.C2070T						PASS	.	G		156,4150		1,154,1998	240.0	258.0	252.0		2070	0.2	0.0	19	dbSNP_131	252	508,7980		0,508,3736	no	coding-synonymous	PLIN4	NM_001080400.1		1,662,5734	AA,AG,GG		5.9849,3.6229,5.1899		690/1358	4511860	664,12130	2153	4244	6397	SO:0001819	synonymous_variant	729359	exon3			CCCCATGAGCCCA	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.2070C>T	19.37:g.4511860G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	247	52	0.210526	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.912;A|0.088	0.088	strong		0.587	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
FREM1	158326	hgsc.bcm.edu	37	9	14824799	14824799	+	Silent	SNP	G	G	A	rs12236053	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:14824799G>A	ENST00000380880.3	-	11	2856	c.2073C>T	c.(2071-2073)agC>agT	p.S691S	FREM1_ENST00000422223.2_Silent_p.S691S|FREM1_ENST00000380881.4_Silent_p.S692S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	691					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)		GATACCTGTGGCTGAAGGAGA	0.358													G|||	761	0.151957	0.2156	0.0821	5008	,	,		16773	0.1716		0.0994	False		,,,				2504	0.1493				p.S691S		Atlas-SNP	.											.	FREM1	261	.	0			c.C2073T						PASS	.	G		650,3036		66,518,1259	43.0	41.0	42.0		2073	-1.4	0.4	9	dbSNP_120	42	1012,7160		58,896,3132	no	coding-synonymous	FREM1	NM_144966.5		124,1414,4391	AA,AG,GG		12.3837,17.6343,14.0159		691/2180	14824799	1662,10196	1843	4086	5929	SO:0001819	synonymous_variant	158326	exon12			CCTGTGGCTGAAG	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.2073C>T	9.37:g.14824799G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.831;A|0.169	0.169	strong		0.358	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
ITFG3	83986	hgsc.bcm.edu	37	16	304514	304514	+	Silent	SNP	C	C	T	rs3213508	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:304514C>T	ENST00000399932.3	+	3	553	c.102C>T	c.(100-102)aaC>aaT	p.N34N	ITFG3_ENST00000600536.1_Silent_p.N34N|ITFG3_ENST00000301679.2_Silent_p.N34N|ITFG3_ENST00000442458.2_Silent_p.N34N|ITFG3_ENST00000301678.3_Silent_p.N34N|ITFG3_ENST00000450082.2_Silent_p.N34N	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	34						cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				ATGAGGATAACGTGAAAAGCG	0.483											OREG0003695	type=REGULATORY REGION|Gene=C16orf9|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	992	0.198083	0.1437	0.2378	5008	,	,		16496	0.3244		0.1421	False		,,,				2504	0.1708				p.N34N		Atlas-SNP	.											.	ITFG3	42	.	0			c.C102T						PASS	.	C		507,3163		34,439,1362	122.0	134.0	131.0		102	1.5	0.0	16	dbSNP_106	131	1305,6853		103,1099,2877	no	coding-synonymous	ITFG3	NM_032039.2		137,1538,4239	TT,TC,CC		15.9966,13.8147,15.3196		34/553	304514	1812,10016	1835	4079	5914	SO:0001819	synonymous_variant	83986	exon3			GGATAACGTGAAA	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 9"""	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.102C>T	16.37:g.304514C>T		Somatic	60	0	0	587	WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Silent	SNP	ENST00000399932.3	37	CCDS10402.1																																																																																			C|0.801;T|0.199	0.199	strong		0.483	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039	
NOD2	64127	hgsc.bcm.edu	37	16	50753892	50753892	+	Missense_Mutation	SNP	G	G	A	rs201831159		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:50753892G>A	ENST00000300589.2	+	7	2792	c.2687G>A	c.(2686-2688)cGa>cAa	p.R896Q		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	896					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)				GAGGGGCTCCGAGGCAACACC	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		18894	0.0		0.001	False		,,,				2504	0.0				p.R896Q		Atlas-SNP	.											.	NOD2	118	.	0			c.G2687A						PASS	.						75.0	80.0	78.0					16																	50753892		2198	4300	6498	SO:0001583	missense	64127	exon7			GGCTCCGAGGCAA	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.2687G>A	16.37:g.50753892G>A	ENSP00000300589:p.Arg896Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	8.658	0.899935	0.17686	.	.	ENSG00000167207	ENST00000526417;ENST00000300589;ENST00000431240	T	0.52983	0.64	5.91	3.31	0.37934	.	0.369818	0.23142	N	0.051460	T	0.30479	0.0766	L	0.47716	1.5	0.09310	N	1	P;P	0.50066	0.788;0.931	B;B	0.37267	0.245;0.091	T	0.13282	-1.0515	10	0.18710	T	0.47	.	5.1538	0.15025	0.367:0.0:0.633:0.0	.	869;896	Q9HC29-2;Q9HC29	.;NOD2_HUMAN	Q	869;896;36	ENSP00000300589:R896Q	ENSP00000300589:R896Q	R	+	2	0	NOD2	49311393	0.115000	0.22152	0.283000	0.24790	0.014000	0.08584	0.496000	0.22499	1.161000	0.42604	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	strong		0.597	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
NLRP4	147945	hgsc.bcm.edu	37	19	56370166	56370166	+	Silent	SNP	C	C	T	rs379327	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56370166C>T	ENST00000301295.6	+	3	1829	c.1407C>T	c.(1405-1407)caC>caT	p.H469H	NLRP4_ENST00000587891.1_Silent_p.H394H|NLRP4_ENST00000346986.5_Silent_p.H469H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	469	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)		TCAAGAGCCACCTTGATCATC	0.473													C|||	522	0.104233	0.0061	0.196	5008	,	,		19960	0.1647		0.1093	False		,,,				2504	0.1043				p.H469H		Atlas-SNP	.											NLRP4_ENST00000301295,right_upper_lobe,carcinoma,+1,1	NLRP4	331	1	0			c.C1407T						PASS	.	C		98,4308	77.3+/-115.6	1,96,2106	142.0	140.0	141.0		1407	0.6	0.0	19	dbSNP_80	141	1037,7563	220.6+/-258.3	74,889,3337	no	coding-synonymous	NLRP4	NM_134444.4		75,985,5443	TT,TC,CC		12.0581,2.2242,8.7267		469/995	56370166	1135,11871	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GAGCCACCTTGAT	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.1407C>T	19.37:g.56370166C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.899;T|0.101	0.101	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
CSTL1	128817	hgsc.bcm.edu	37	20	23424660	23424660	+	Silent	SNP	G	G	C	rs12625959	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23424660G>C	ENST00000246020.2	+	2	329	c.309G>C	c.(307-309)ctG>ctC	p.L103L	CSTL1_ENST00000347397.1_Silent_p.L103L			Q9H114	CST1L_HUMAN	cystatin-like 1	103						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					CCTGCCCCCTGCAAAGCAAGA	0.463													G|||	851	0.169928	0.4713	0.0432	5008	,	,		21258	0.0823		0.0577	False		,,,				2504	0.0583				p.L103L		Atlas-SNP	.											.	CSTL1	30	.	0			c.G309C						PASS	.	G		1785,2621	527.1+/-372.1	355,1075,773	111.0	96.0	101.0		309	1.8	0.5	20	dbSNP_120	101	461,8139	137.9+/-194.8	14,433,3853	no	coding-synonymous	CSTL1	NM_138283.1		369,1508,4626	CC,CG,GG		5.3605,40.5129,17.269		103/146	23424660	2246,10760	2203	4300	6503	SO:0001819	synonymous_variant	128817	exon3			CCCCCTGCAAAGC	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.309G>C	20.37:g.23424660G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_138283	Q17RA8|Q64FF7	Silent	SNP	ENST00000246020.2	37	CCDS13153.1																																																																																			G|0.837;C|0.163	0.163	strong		0.463	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
PYGB	5834	hgsc.bcm.edu	37	20	25255338	25255338	+	Silent	SNP	C	C	T	rs2227894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25255338C>T	ENST00000216962.4	+	5	749	c.639C>T	c.(637-639)ggC>ggT	p.G213G		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	213					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CCCCCGACGGCGTGAAGTGGC	0.632													C|||	613	0.122404	0.3253	0.062	5008	,	,		18316	0.0645		0.0567	False		,,,				2504	0.0184				p.G213G		Atlas-SNP	.											PYGB,NS,carcinoma,+2,1	PYGB	84	1	0			c.C639T						PASS	.	C		1287,3119	437.2+/-344.9	185,917,1101	88.0	100.0	96.0		639	-8.1	0.0	20	dbSNP_98	96	391,8209	125.5+/-184.1	7,377,3916	no	coding-synonymous	PYGB	NM_002862.3		192,1294,5017	TT,TC,CC		4.5465,29.2102,12.9017		213/844	25255338	1678,11328	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon5			CGACGGCGTGAAG		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.639C>T	20.37:g.25255338C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	17	5	0.294118	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			C|0.873;G|0.000;T|0.126	0.126	strong		0.632	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
ALDH5A1	7915	hgsc.bcm.edu	37	6	24503590	24503590	+	Missense_Mutation	SNP	C	C	T	rs2760118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24503590C>T	ENST00000357578.3	+	3	683	c.538C>T	c.(538-540)Cac>Tac	p.H180Y	ALDH5A1_ENST00000546278.1_Missense_Mutation_p.H92Y|ALDH5A1_ENST00000348925.2_Missense_Mutation_p.H180Y|ALDH5A1_ENST00000491546.1_Missense_Mutation_p.H152Y	NM_001080.3	NP_001071.1	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5 family, member A1	180			H -> Y (83% of activity; dbSNP:rs2760118). {ECO:0000269|PubMed:14635103, ECO:0000269|PubMed:14702039}.		acetate metabolic process (GO:0006083)|central nervous system development (GO:0007417)|galactosylceramide metabolic process (GO:0006681)|gamma-aminobutyric acid catabolic process (GO:0009450)|glucose metabolic process (GO:0006006)|glucosylceramide metabolic process (GO:0006678)|glutamate metabolic process (GO:0006536)|glutamine metabolic process (GO:0006541)|glutathione metabolic process (GO:0006749)|glycerophospholipid metabolic process (GO:0006650)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|respiratory electron transport chain (GO:0022904)|short-chain fatty acid metabolic process (GO:0046459)|succinate metabolic process (GO:0006105)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	protein homodimerization activity (GO:0042803)|succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777)|succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|skin(2)|urinary_tract(1)	20					Chlormerodrin(DB00534)|Succinic acid(DB00139)|Valproic Acid(DB00313)	AGACATTATCCACACCCCGGC	0.567													T|||	1576	0.314696	0.466	0.219	5008	,	,		19092	0.1667		0.3231	False		,,,				2504	0.3221				p.H180Y		Atlas-SNP	.											.	ALDH5A1	42	.	0			c.C538T	GRCh37	CM083577	ALDH5A1	M	rs2760118	PASS	.	T	TYR/HIS,TYR/HIS	1937,2469	622.5+/-394.0	430,1077,696	49.0	49.0	49.0		538,538	-0.0	0.0	6	dbSNP_100	49	2891,5709	671.4+/-402.8	470,1951,1879	yes	missense,missense	ALDH5A1	NM_001080.3,NM_170740.1	83,83	900,3028,2575	TT,TC,CC		33.6163,43.9628,37.1213	benign,benign	180/536,180/549	24503590	4828,8178	2203	4300	6503	SO:0001583	missense	7915	exon3			ATTATCCACACCC	L34820	CCDS4555.1, CCDS4556.1	6p22	2013-06-03	2008-07-31		ENSG00000112294	ENSG00000112294	1.2.1.24	"""Aldehyde dehydrogenases"""	408	protein-coding gene	gene with protein product	"""succinate-semialdehyde dehydrogenase"""	610045				7814412, 9059628	Standard	NM_001080		Approved	SSADH, SSDH	uc003nef.3	P51649	OTTHUMG00000014356	ENST00000357578.3:c.538C>T	6.37:g.24503590C>T	ENSP00000350191:p.His180Tyr	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_001080	B2RD26|G5E949|Q546H9|Q8N3W6	Missense_Mutation	SNP	ENST00000357578.3	37	CCDS4555.1	670	0.3067765567765568	224	0.45528455284552843	91	0.2513812154696133	105	0.18356643356643357	250	0.32981530343007914	T	5.650	0.304590	0.10678	0.439628	0.336163	ENSG00000112294	ENST00000357578;ENST00000546278;ENST00000491546;ENST00000348925	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.22	-0.0441	0.13856	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.816074	0.11105	N	0.599274	T	0.31513	0.0799	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04737	-1.0930	9	0.51188	T	0.08	0.2889	1.8122	0.03092	0.1336:0.3194:0.3093:0.2376	rs2760118;rs3765309;rs52829319;rs60953148;rs2760118	180;180	P51649;G5E949	SSDH_HUMAN;.	Y	180;92;152;180	ENSP00000350191:H180Y;ENSP00000438193:H92Y;ENSP00000417687:H152Y;ENSP00000314649:H180Y	ENSP00000314649:H180Y	H	+	1	0	ALDH5A1	24611569	0.029000	0.19370	0.013000	0.15412	0.241000	0.25554	0.812000	0.27211	-0.423000	0.07394	-0.269000	0.10298	CAC	C|0.656;T|0.344	0.344	strong		0.567	ALDH5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040007.2		
DNHD1	144132	hgsc.bcm.edu	37	11	6580495	6580495	+	Silent	SNP	G	G	A	rs72901756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6580495G>A	ENST00000527990.2	+	26	9501	c.9501G>A	c.(9499-9501)caG>caA	p.Q3167Q	DNHD1_ENST00000254579.6_Silent_p.Q3167Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3167					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)		TGGAACAGCAGCTGAAAGACT	0.483													G|||	364	0.0726837	0.0204	0.1037	5008	,	,		21689	0.0159		0.0736	False		,,,				2504	0.1789				p.Q3167Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9501A						PASS	.	G		45,1339		1,43,648	106.0	90.0	95.0		9501	2.5	0.9	11	dbSNP_130	95	339,2843		20,299,1272	no	coding-synonymous	DNHD1	NM_144666.2		21,342,1920	AA,AG,GG		10.6537,3.2514,8.41		3167/4754	6580495	384,4182	692	1591	2283	SO:0001819	synonymous_variant	144132	exon28			ACAGCAGCTGAAA	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.9501G>A	11.37:g.6580495G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.957;A|0.043	0.043	strong		0.483	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PRRC2B	84726	hgsc.bcm.edu	37	9	134340444	134340444	+	Missense_Mutation	SNP	A	A	G	rs201633009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134340444A>G	ENST00000357304.4	+	11	1754	c.1699A>G	c.(1699-1701)Aac>Gac	p.N567D	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.N567D|PRRC2B_ENST00000405995.1_Missense_Mutation_p.N567D	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	567							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						TCCCCAGGAAAACGGCCCTGC	0.572													A|||	2	0.000399361	0.0	0.0029	5008	,	,		17186	0.0		0.0	False		,,,				2504	0.0				p.N567D		Atlas-SNP	.											.	PRRC2B	266	.	0			c.A1699G						PASS	.	A	ASP/ASN	0,3984		0,0,1992	41.0	47.0	45.0		1699	5.5	1.0	9		45	13,8289		1,11,4139	yes	missense	PRRC2B	NM_013318.3	23	1,11,6131	GG,GA,AA		0.1566,0.0,0.1058	probably-damaging	567/2230	134340444	13,12273	1992	4151	6143	SO:0001583	missense	84726	exon11			CAGGAAAACGGCC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1699A>G	9.37:g.134340444A>G	ENSP00000349856:p.Asn567Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.185233	0.57909	0.0	0.001566	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.48	5.48	0.80851	.	0.000000	0.44483	U	0.000450	T	0.31827	0.0809	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.01914	-1.1248	10	0.26408	T	0.33	-2.5709	14.7458	0.69490	1.0:0.0:0.0:0.0	.	567	Q5JSZ5	PRC2B_HUMAN	D	567;567;567;107	ENSP00000384606:N567D;ENSP00000349856:N567D;ENSP00000398853:N567D;ENSP00000391063:N107D	ENSP00000349856:N567D	N	+	1	0	PRRC2B	133330265	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	4.399000	0.59703	2.075000	0.62263	0.459000	0.35465	AAC	A|0.994;G|0.006	0.006	strong		0.572	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609097	32609097	+	Silent	SNP	T	T	C	rs553033826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609097T>C	ENST00000343139.5	+	2	195	c.93T>C	c.(91-93)gtT>gtC	p.V31V	HLA-DQA1_ENST00000374949.2_Silent_p.V31V|HLA-DQA1_ENST00000395363.1_Silent_p.V31V	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	31	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTGACCACGTTGCCTCTTGTG	0.463													.|||	967	0.193091	0.2171	0.2522	5008	,	,		17644	0.1339		0.2396	False		,,,				2504	0.1319				p.V31V		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.T93C						PASS	.	T		919,3487		123,673,1407	147.0	125.0	132.0		93	-0.5	0.0	6	dbSNP_118	132	2114,6474		330,1454,2510	no	coding-synonymous	HLA-DQA1	NM_002122.3		453,2127,3917	CC,CT,TT		24.6157,20.8579,23.3415		31/256	32609097	3033,9961	2203	4294	6497	SO:0001819	synonymous_variant	3117	exon2			CCACGTTGCCTCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.93T>C	6.37:g.32609097T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	59	54	0.915254	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	449	0.20558608058608058	104	0.21138211382113822	96	0.26519337016574585	88	0.15384615384615385	161	0.21240105540897097	.	2.891	-0.229734	0.06022	0.208579	0.246157	ENSG00000196735	ENST00000486548	.	.	.	3.84	-0.455	0.12193	.	.	.	.	.	T	0.07593	0.0191	.	.	.	0.44789	P	0.002206999999999959	.	.	.	.	.	.	T	0.32955	-0.9887	3	.	.	.	.	1.1609	0.01805	0.1526:0.1993:0.1463:0.5018	rs9272688;rs12722044;rs17412258	.	.	.	S	4	.	.	L	+	2	0	HLA-DQA1	32717075	0.372000	0.25064	0.013000	0.15412	0.005000	0.04900	-0.091000	0.11146	-0.119000	0.11830	-1.777000	0.00654	TTG	T|0.743;C|0.257	0.257	strong		0.463	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
SHMT2	6472	hgsc.bcm.edu	37	12	57627074	57627074	+	Silent	SNP	G	G	T	rs2229717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57627074G>T	ENST00000328923.3	+	8	1421	c.969G>T	c.(967-969)ctG>ctT	p.L323L	SHMT2_ENST00000393827.4_Silent_p.L227L|SHMT2_ENST00000449049.3_Silent_p.L302L|SHMT2_ENST00000414700.3_Silent_p.L302L|SHMT2_ENST00000553474.1_Silent_p.L302L|SHMT2_ENST00000557487.1_Silent_p.L313L	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	323					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	TCCCATCCCTGCAGGGGGGCC	0.582													g|||	434	0.0866613	0.0371	0.0591	5008	,	,		20268	0.2272		0.0507	False		,,,				2504	0.0654				p.L323L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.G969T						PASS	.	A	,,,,	122,4284	89.2+/-127.9	1,120,2082	52.0	55.0	54.0		939,906,906,906,969	0.6	1.0	12	dbSNP_98	54	291,8309	107.6+/-168.3	10,271,4019	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SHMT2	NM_001166356.1,NM_001166357.1,NM_001166358.1,NM_001166359.1,NM_005412.5	,,,,	11,391,6101	TT,TG,GG		3.3837,2.769,3.1755	,,,,	313/495,302/484,302/484,302/484,323/505	57627074	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	6472	exon8			ATCCCTGCAGGGG	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.969G>T	12.37:g.57627074G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Silent	SNP	ENST00000328923.3	37	CCDS8934.1	165	0.07554945054945054	18	0.036585365853658534	17	0.04696132596685083	90	0.15734265734265734	40	0.052770448548812667	g	7.809	0.715364	0.15306	0.02769	0.033837	ENSG00000182199	ENST00000557529	.	.	.	4.58	0.592	0.17471	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16335	-1.0406	3	.	.	.	-0.6784	1.6307	0.02732	0.2524:0.1406:0.4627:0.1443	rs2229717	.	.	.	S	123	.	.	A	+	1	0	SHMT2	55913341	0.195000	0.23338	0.968000	0.41197	0.882000	0.50991	-0.481000	0.06552	0.021000	0.15133	-0.222000	0.12452	GCA	G|0.952;T|0.048	0.048	strong		0.582	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
FSCB	84075	hgsc.bcm.edu	37	14	44974189	44974189	+	Missense_Mutation	SNP	C	C	A	rs11621923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:44974189C>A	ENST00000340446.4	-	1	2293	c.2002G>T	c.(2002-2004)Gct>Tct	p.A668S	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	668	Ala-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TGAACTTCAGCGGGGGCCTCC	0.617																																					p.A668S		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.G2002T						PASS	.						10.0	12.0	11.0					14																	44974189		2171	4287	6458	SO:0001583	missense	84075	exon1			CTTCAGCGGGGGC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2002G>T	14.37:g.44974189C>A	ENSP00000344579:p.Ala668Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	42	0.823529	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	839	0.3841575091575092	172	0.34959349593495936	128	0.35359116022099446	225	0.39335664335664333	314	0.41424802110817943	C	8.835	0.940852	0.18281	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.12039	2.72	4.24	-8.48	0.00935	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B	0.25105	0.118	B	0.24155	0.051	T	0.44982	-0.9292	8	0.14656	T	0.56	-0.0478	4.397	0.11367	0.4313:0.2556:0.2435:0.0696	rs11621923	668	Q5H9T9	FSCB_HUMAN	S	668;561	ENSP00000344579:A668S	ENSP00000344579:A668S	A	-	1	0	FSCB	44043939	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-1.504000	0.02275	-1.989000	0.00979	-0.719000	0.03609	GCT	C|0.624;A|0.376	0.376	strong		0.617	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
TTC28	23331	hgsc.bcm.edu	37	22	28378472	28378472	+	Silent	SNP	A	A	G	rs5762430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:28378472A>G	ENST00000397906.2	-	23	7324	c.7183T>C	c.(7183-7185)Ttg>Ctg	p.L2395L	TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000425112.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000454996.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000419253.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000430525.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2395					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						GACAAATTCAACAGACTGAGG	0.547													A|||	1307	0.260982	0.3086	0.1542	5008	,	,		16213	0.2887		0.1521	False		,,,				2504	0.3558				p.L2395L		Atlas-SNP	.											.	TTC28	84	.	0			c.T7183C						PASS	.	A		395,989		52,291,349	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/pubmed?term	7183	-3.3	0.0	22	dbSNP_114	57	601,2581		54,493,1044	no	coding-synonymous	TTC28	NM_001145418.1		106,784,1393	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.8875,28.5405,21.8134		2395/2482	28378472	996,3570	692	1591	2283	SO:0001819	synonymous_variant	23331	exon23			AATTCAACAGACT	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.7183T>C	22.37:g.28378472A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			A|0.754;G|0.246	0.246	strong		0.547	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
C19orf35	374872	hgsc.bcm.edu	37	19	2278755	2278755	+	Missense_Mutation	SNP	C	C	T	rs73518414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2278755C>T	ENST00000342063.3	-	3	533	c.440G>A	c.(439-441)cGt>cAt	p.R147H		NM_198532.2	NP_940934.1	Q6ZS72	CS035_HUMAN	chromosome 19 open reading frame 35	147										large_intestine(1)|lung(5)|pancreas(1)|prostate(1)	8				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)		ATAGATGGTACGGAGGCCCTG	0.721													C|||	1786	0.356629	0.3691	0.4078	5008	,	,		11853	0.5496		0.1312	False		,,,				2504	0.3364				p.R147H		Atlas-SNP	.											.	C19orf35	18	.	0			c.G440A						PASS	.	C	HIS/ARG	1293,2969		171,951,1009	6.0	8.0	7.0		440	0.6	0.0	19	dbSNP_130	7	1007,7373		69,869,3252	no	missense	C19orf35	NM_198532.2	29	240,1820,4261	TT,TC,CC		12.0167,30.3379,18.1933	benign	147/474	2278755	2300,10342	2131	4190	6321	SO:0001583	missense	374872	exon3			ATGGTACGGAGGC	AK127680	CCDS12087.1	19p13.3	2012-10-26			ENSG00000188305	ENSG00000188305			24793	protein-coding gene	gene with protein product							Standard	NM_198532		Approved	FLJ45778	uc002lvn.2	Q6ZS72	OTTHUMG00000178460	ENST00000342063.3:c.440G>A	19.37:g.2278755C>T	ENSP00000345102:p.Arg147His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_198532		Missense_Mutation	SNP	ENST00000342063.3	37	CCDS12087.1	694	0.31776556776556775	167	0.3394308943089431	120	0.3314917127071823	304	0.5314685314685315	103	0.1358839050131926	C	11.80	1.747421	0.30955	0.303379	0.120167	ENSG00000188305	ENST00000342063	T	0.16743	2.32	4.16	0.647	0.17796	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.37478	-0.9704	8	0.72032	D	0.01	.	4.7369	0.12993	0.0:0.6131:0.1756:0.2114	.	147	Q6ZS72	CS035_HUMAN	H	147	ENSP00000345102:R147H	ENSP00000345102:R147H	R	-	2	0	C19orf35	2229755	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.208000	0.17415	-0.088000	0.12506	-0.860000	0.03012	CGT	C|0.681;T|0.319	0.319	strong		0.721	C19orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442080.1	NM_198532	
SLCO4A1	28231	hgsc.bcm.edu	37	20	61299525	61299525	+	Silent	SNP	G	G	A	rs34985812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61299525G>A	ENST00000370507.1	+	8	1896	c.1800G>A	c.(1798-1800)acG>acA	p.T600T	SLCO4A1_ENST00000217159.1_Silent_p.T600T|RP11-93B14.5_ENST00000451648.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|RP11-93B14.5_ENST00000433126.1_RNA|SLCO4A1_ENST00000470412.1_3'UTR			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	600					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CTGCACTAACGGCAACTCTAC	0.517											OREG0026115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	87	0.0173722	0.0038	0.0274	5008	,	,		20944	0.0		0.0477	False		,,,				2504	0.0153				p.T600T	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											.	SLCO4A1	65	.	0			c.G1800A						PASS	.	G		54,4352	54.9+/-90.9	0,54,2149	117.0	118.0	118.0		1800	-8.6	0.1	20	dbSNP_126	118	435,8165	132.0+/-189.7	11,413,3876	no	coding-synonymous	SLCO4A1	NM_016354.3		11,467,6025	AA,AG,GG		5.0581,1.2256,3.7598		600/723	61299525	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	28231	exon9			ACTAACGGCAACT	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.1800G>A	20.37:g.61299525G>A		Somatic	132	0	0	1052	WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Silent	SNP	ENST00000370507.1	37	CCDS13501.1	51	0.023351648351648352	3	0.006097560975609756	11	0.03038674033149171	0	0.0	37	0.048812664907651716	G	7.446	0.641786	0.14451	0.012256	0.050581	ENSG00000101187	ENST00000370512	.	.	.	4.94	-8.57	0.00900	.	.	.	.	.	T	0.06690	0.0171	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43426	-0.9392	5	0.30078	T	0.28	.	0.6937	0.00896	0.2502:0.1421:0.2701:0.3376	rs34985812;rs56467268;rs34985812	.	.	.	S	586	.	ENSP00000359543:G586S	G	+	1	0	SLCO4A1	60769970	0.000000	0.05858	0.085000	0.20634	0.859000	0.49053	-3.473000	0.00459	-1.090000	0.03069	-0.424000	0.05967	GGC	G|0.964;A|0.036	0.036	strong		0.517	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
ATXN3L	92552	hgsc.bcm.edu	37	X	13337059	13337059	+	Missense_Mutation	SNP	C	C	T	rs4830842	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:13337059C>T	ENST00000380622.2	-	1	1459	c.995G>A	c.(994-996)gGc>gAc	p.G332D	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	332			G -> D (in dbSNP:rs4830842). {ECO:0000269|PubMed:11450850, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTGTACTGTGCCTTCACTGAT	0.403													T|||	2467	0.65351	0.6339	0.5288	3775	,	,		14767	0.6349		0.2475	False		,,,				2504	0.3814				p.G332D		Atlas-SNP	.											.	ATXN3L	64	.	0			c.G995A						PASS	.	T	ASP/GLY	2003,624		618,364,403,77,106	196.0	163.0	173.0		995	0.8	0.0	X	dbSNP_111	173	1862,3636		213,884,552,819,1114	yes	missense	ATXN3L	NM_001135995.1	94	831,1248,955,896,1220	TT,TC,T,CC,C		33.8669,23.7533,47.5692	benign	332/356	13337059	3865,4260	1568	3582	5150	SO:0001583	missense	92552	exon1			ACTGTGCCTTCAC		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.995G>A	X.37:g.13337059C>T	ENSP00000369996:p.Gly332Asp	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_001135995	B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	CCDS48080.1	1036	0.6244725738396625	214	0.7328767123287672	121	0.4959016393442623	234	0.7048192771084337	124	0.19682539682539682	T	0.004	-2.384494	0.00202	0.762467	0.338669	ENSG00000123594	ENST00000380622	T	0.13657	2.57	0.793	0.793	0.18632	.	0.067617	0.64402	N	0.000011	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	0.30416	-0.9979	8	0.02654	T	1	.	.	.	.	rs4830842;rs17322136;rs58346436;rs4830842	332	Q9H3M9	ATX3L_HUMAN	D	332	ENSP00000369996:G332D	ENSP00000369996:G332D	G	-	2	0	ATXN3L	13246980	0.013000	0.17824	0.008000	0.14137	0.003000	0.03518	-0.055000	0.11807	-0.243000	0.09653	-0.631000	0.03989	GGC	C|0.321;0|0.030	.	strong		0.403	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995	
TMEM259	91304	hgsc.bcm.edu	37	19	1014398	1014398	+	Silent	SNP	A	A	G	rs7146	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1014398A>G	ENST00000356663.3	-	2	421	c.300T>C	c.(298-300)caT>caC	p.H100H	TMEM259_ENST00000333175.5_Silent_p.H100H	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	100						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											TGTCACGCACATGCTCCAGGC	0.652													N|||	3381	0.67512	0.8154	0.5231	5008	,	,		17015	0.5308		0.6799	False		,,,				2504	0.7372				p.H100H		Atlas-SNP	.											.	.	.	.	0			c.T300C						PASS	.	G	,	3502,904	334.1+/-303.3	1390,722,91	34.0	33.0	33.0		300,300	-2.2	1.0	19	dbSNP_52	33	5726,2872	435.4+/-358.0	1923,1880,496	no	coding-synonymous,coding-synonymous	C19orf6	NM_001033026.1,NM_033420.3	,	3313,2602,587	GG,GA,AA		33.4031,20.5175,29.0372	,	100/621,100/409	1014398	9228,3776	2203	4299	6502	SO:0001819	synonymous_variant	91304	exon2			ACGCACATGCTCC	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.300T>C	19.37:g.1014398A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			A|0.317;G|0.683	0.683	strong		0.652	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
HLA-B	3106	hgsc.bcm.edu	37	6	31324104	31324104	+	Silent	SNP	G	G	A	rs281864624		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324104G>A	ENST00000412585.2	-	3	487	c.459C>T	c.(457-459)gaC>gaT	p.D153D		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	153	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						AGGAGCGCAGGTCCTCGTTCA	0.701									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.D153D		Atlas-SNP	.											.	HLA-B	54	.	0			c.C459T						PASS	.						31.0	22.0	25.0					6																	31324104		2114	4208	6322	SO:0001819	synonymous_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GCGCAGGTCCTCG	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.459C>T	6.37:g.31324104G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	185	46	0.248649	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.820;A|0.180	0.180	weak		0.701	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	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	
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105930406G>A	ENST00000331320.7	+	13	1328	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	MTA1_ENST00000405646.1_Missense_Mutation_p.V355I|MTA1_ENST00000406191.1_Missense_Mutation_p.V372I|MTA1_ENST00000435036.2_5'UTR	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	372			V -> I (in dbSNP:rs4983413).		circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.V372I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		CGTCAACAACGTCAAGGCCGG	0.617													G|||	1427	0.284944	0.0121	0.3314	5008	,	,		12491	0.622		0.2366	False		,,,				2504	0.3231				p.V372I		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	1	1	Substitution - Missense(1)	stomach(1)	c.G1114A						PASS	.	G	ILE/VAL,ILE/VAL	233,4173	138.0+/-173.8	9,215,1979	73.0	76.0	75.0		1114,1114	1.7	1.0	14	dbSNP_111	75	1995,6605	349.7+/-327.5	235,1525,2540	yes	missense,missense	MTA1	NM_001203258.1,NM_004689.3	29,29	244,1740,4519	AA,AG,GG		23.1977,5.2882,17.1306	benign,benign	372/431,372/716	105930406	2228,10778	2203	4300	6503	SO:0001583	missense	9112	exon13			AACAACGTCAAGG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1114G>A	14.37:g.105930406G>A	ENSP00000333633:p.Val372Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	37	CCDS32169.1	655	0.2999084249084249	11	0.022357723577235773	110	0.30386740331491713	360	0.6293706293706294	174	0.22955145118733508	G	12.92	2.082237	0.36758	0.052882	0.231977	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.30981	1.52;1.52;1.51;1.53	4.61	1.66	0.24008	.	0.396957	0.27080	N	0.021022	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.99999999865637	B;B	0.31274	0.164;0.317	B;B	0.26202	0.036;0.067	T	0.36187	-0.9758	9	0.36615	T	0.2	-21.1079	7.0619	0.25131	0.1661:0.1403:0.6937:0.0	rs4983413;rs60510827;rs4983413	164;372	Q59FW1;Q13330	.;MTA1_HUMAN	I	281;372;372;355;164	ENSP00000333633:V372I;ENSP00000385702:V372I;ENSP00000384180:V355I;ENSP00000394106:V164I	ENSP00000333633:V372I	V	+	1	0	MTA1	105001451	0.813000	0.29090	0.972000	0.41901	0.734000	0.41952	1.456000	0.35201	0.366000	0.24427	0.563000	0.77884	GTC	G|0.782;A|0.218	0.218	strong		0.617	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
LHX9	56956	hgsc.bcm.edu	37	1	197896728	197896728	+	Silent	SNP	T	T	C	rs12046958	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:197896728T>C	ENST00000367387.4	+	4	1166	c.741T>C	c.(739-741)aaT>aaC	p.N247N	LHX9_ENST00000367390.3_Silent_p.N238N|LHX9_ENST00000367391.1_Silent_p.N238N|LHX9_ENST00000561173.1_Silent_p.N253N|LHX9_ENST00000337020.2_Silent_p.N247N	NM_020204.2	NP_064589.2	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	247					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.N247N(1)		endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						CAGGTTGTAATGAGAATGAGG	0.493													T|||	1342	0.267971	0.1959	0.3545	5008	,	,		18498	0.4067		0.1859	False		,,,				2504	0.2454				p.N247N		Atlas-SNP	.											LHX9,NS,carcinoma,0,1	LHX9	144	1	1	Substitution - coding silent(1)	stomach(1)	c.T741C						PASS	.	T	,	819,3587	326.7+/-299.7	80,659,1464	286.0	288.0	288.0		714,741	-3.6	1.0	1	dbSNP_120	288	1625,6975	301.4+/-305.4	151,1323,2826	no	coding-synonymous,coding-synonymous	LHX9	NM_001014434.1,NM_020204.2	,	231,1982,4290	CC,CT,TT		18.8953,18.5883,18.7913	,	238/389,247/398	197896728	2444,10562	2203	4300	6503	SO:0001819	synonymous_variant	56956	exon4			TTGTAATGAGAAT	AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"""Homeoboxes / LIM class"""	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367387.4:c.741T>C	1.37:g.197896728T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	164	69	0.420732	NM_020204	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	ENST00000367387.4	37	CCDS1393.1																																																																																			T|0.773;C|0.227	0.227	strong		0.493	LHX9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086547.2	NM_020204	
KNDC1	85442	hgsc.bcm.edu	37	10	135012429	135012429	+	Missense_Mutation	SNP	T	T	A	rs386749477|rs3008390	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:135012429T>A	ENST00000304613.3	+	14	2438	c.2417T>A	c.(2416-2418)gTt>gAt	p.V806D	KNDC1_ENST00000368571.2_Missense_Mutation_p.V741D|KNDC1_ENST00000368572.2_Missense_Mutation_p.V806D			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	806	Pro-rich.			V -> D (in Ref. 1; BAD12625). {ECO:0000305}.	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)		CCACCTGGAGTTGCTTCCGGG	0.746													T|||	2004	0.40016	0.1604	0.3919	5008	,	,		10760	0.5476		0.4195	False		,,,				2504	0.5583				p.V806D		Atlas-SNP	.											.	KNDC1	155	.	0			c.T2417A						PASS	.		ASP/VAL	526,2634		71,384,1125	4.0	5.0	4.0		2417	-1.3	0.0	10	dbSNP_101	4	2723,4467		626,1471,1498	yes	missense	KNDC1	NM_152643.6	152	697,1855,2623	AA,AT,TT		37.872,16.6456,31.3913	benign	806/1750	135012429	3249,7101	1580	3595	5175	SO:0001583	missense	85442	exon14			CTGGAGTTGCTTC	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.2417T>A	10.37:g.135012429T>A	ENSP00000304437:p.Val806Asp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	884	0.40476190476190477	86	0.17479674796747968	139	0.3839779005524862	333	0.5821678321678322	326	0.43007915567282323	T	4.682	0.126733	0.08931	0.166456	0.37872	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18174	2.82;2.82;2.23	3.43	-1.31	0.09230	.	1.661170	0.03733	N	0.253684	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;P;B	0.45827	0.867;0.531;0.244	B;B;B	0.41271	0.352;0.107;0.05	T	0.45614	-0.9249	9	0.12103	T	0.63	.	3.9153	0.09220	0.0:0.3422:0.3942:0.2636	rs3008390;rs61587518	806;741;806	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	D	806;806;741	ENSP00000304437:V806D;ENSP00000357561:V806D;ENSP00000357560:V741D	ENSP00000304437:V806D	V	+	2	0	KNDC1	134862419	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.817000	0.27281	-0.241000	0.09681	0.255000	0.18592	GTT	T|0.596;A|0.404	0.404	strong		0.746	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
OR5B12	390191	hgsc.bcm.edu	37	11	58207203	58207203	+	Missense_Mutation	SNP	C	C	T	rs11229457|rs386753911	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:58207203C>T	ENST00000302572.2	-	1	443	c.422G>A	c.(421-423)tGc>tAc	p.C141Y		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	141			C -> R (in dbSNP:rs4938895). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.|C -> Y (in dbSNP:rs11229457).			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)				TATGGCCAGGCAAGCACATAC	0.473													C|||	1119	0.223442	0.2708	0.2032	5008	,	,		20166	0.1438		0.2097	False		,,,				2504	0.2699				p.C141Y		Atlas-SNP	.											.	OR5B12	80	.	0			c.G422A						PASS	.	C	TYR/CYS	1033,3369	375.1+/-321.5	104,825,1272	135.0	128.0	131.0		422	2.5	0.0	11	dbSNP_120	131	1846,6744	321.6+/-315.2	199,1448,2648	yes	missense	OR5B12	NM_001004733.2	194	303,2273,3920	TT,TC,CC		21.4901,23.4666,22.1598	benign	141/315	58207203	2879,10113	2201	4295	6496	SO:0001583	missense	390191	exon1			GCCAGGCAAGCAC	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.422G>A	11.37:g.58207203C>T	ENSP00000306657:p.Cys141Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	407	0.18635531135531136	127	0.258130081300813	57	0.1574585635359116	81	0.14160839160839161	142	0.18733509234828497	C	0.001	-3.150305	0.00029	0.234666	0.214901	ENSG00000172362	ENST00000302572	T	0.00084	8.75	4.44	2.46	0.29980	GPCR, rhodopsin-like superfamily (1);	0.766506	0.11955	N	0.513292	T	0.00012	0.0000	N	0.21097	0.63	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.13361	-1.0512	9	0.02654	T	1	-16.6186	4.2654	0.10761	0.259:0.5239:0.1357:0.0815	rs11229457;rs60468483;rs11229457	141	Q96R08	OR5BC_HUMAN	Y	141	ENSP00000306657:C141Y	ENSP00000306657:C141Y	C	-	2	0	OR5B12	57963779	0.000000	0.05858	0.021000	0.16686	0.072000	0.16883	-1.307000	0.02733	0.560000	0.29169	0.462000	0.41574	TGC	C|0.782;T|0.218	0.218	strong		0.473	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
SPPL2A	84888	hgsc.bcm.edu	37	15	51041909	51041909	+	Missense_Mutation	SNP	C	C	T	rs145832874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51041909C>T	ENST00000261854.5	-	2	375	c.101G>A	c.(100-102)gGa>gAa	p.G34E	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	34					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)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TGTGCCATTTCCAGACGCATG	0.403													C|||	13	0.00259585	0.0	0.0043	5008	,	,		20240	0.0		0.002	False		,,,				2504	0.0082				p.G34E	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.G101A						PASS	.	C	GLU/GLY	0,4392		0,0,2196	137.0	129.0	132.0		101	3.8	1.0	15	dbSNP_134	132	14,8574	11.2+/-40.8	0,14,4280	yes	missense	SPPL2A	NM_032802.3	98	0,14,6476	TT,TC,CC		0.163,0.0,0.1079	benign	34/521	51041909	14,12966	2196	4294	6490	SO:0001583	missense	84888	exon2			CCATTTCCAGACG		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.101G>A	15.37:g.51041909C>T	ENSP00000261854:p.Gly34Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	37	CCDS10138.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.84	2.951845	0.53293	0.0	0.00163	ENSG00000138600	ENST00000261854	T	0.10960	2.82	5.72	3.8	0.43715	.	0.291695	0.39909	N	0.001238	T	0.06050	0.0157	L	0.36672	1.1	0.32630	N	0.522116	B	0.17038	0.02	B	0.16289	0.015	T	0.04413	-1.0953	10	0.45353	T	0.12	-4.7508	8.2699	0.31838	0.0:0.7246:0.1402:0.1353	.	34	Q8TCT8	PSL2_HUMAN	E	34	ENSP00000261854:G34E	ENSP00000261854:G34E	G	-	2	0	AC012100.1	48829201	0.998000	0.40836	0.995000	0.50966	0.954000	0.61252	1.261000	0.32980	1.384000	0.46424	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.403	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
ALDH3A1	218	hgsc.bcm.edu	37	17	19644472	19644472	+	Silent	SNP	A	A	T	rs2072330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:19644472A>T	ENST00000457500.2	-	5	1070	c.741T>A	c.(739-741)ccT>ccA	p.P247P	RP11-311F12.2_ENST00000580884.1_RNA|ALDH3A1_ENST00000444455.1_Silent_p.P247P|ALDH3A1_ENST00000485231.1_5'Flank|ALDH3A1_ENST00000395555.3_Silent_p.P247P|ALDH3A1_ENST00000225740.6_Silent_p.P247P|ALDH3A1_ENST00000494157.2_Silent_p.P174P	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	247					aging (GO:0007568)|cellular aldehyde metabolic process (GO:0006081)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|alcohol dehydrogenase (NADP+) activity (GO:0008106)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)		GGATGTAGTCAGGGGCCACGC	0.532													A|||	1456	0.290735	0.0923	0.3934	5008	,	,		11377	0.2956		0.3907	False		,,,				2504	0.3783				p.P247P		Atlas-SNP	.											.	ALDH3A1	40	.	0			c.T741A						PASS	.	A	,,	550,3856	246.8+/-255.3	33,484,1686	87.0	76.0	80.0		741,741,741	-10.4	0.1	17	dbSNP_96	80	3376,5224	502.0+/-375.6	640,2096,1564	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH3A1	NM_000691.4,NM_001135167.1,NM_001135168.1	,,	673,2580,3250	TT,TA,AA		39.2558,12.483,30.1861	,,	247/454,247/454,247/454	19644472	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	218	exon5			GTAGTCAGGGGCC	M74542	CCDS11212.1	17p11.2	2010-05-07	2010-05-07		ENSG00000108602	ENSG00000108602	1.2.1.5	"""Aldehyde dehydrogenases"""	405	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase, dimeric NADP-preferring"""	100660		ALDH3		7774944, 1737758	Standard	NM_000691		Approved		uc010cqu.3	P30838	OTTHUMG00000059469	ENST00000457500.2:c.741T>A	17.37:g.19644472A>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_001135168	A8K828|Q9BT37	Silent	SNP	ENST00000457500.2	37	CCDS11212.1																																																																																			A|0.701;T|0.299	0.299	strong		0.532	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4	NM_000691	
NUP210	23225	hgsc.bcm.edu	37	3	13367406	13367406	+	Silent	SNP	C	C	T	rs665064	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13367406C>T	ENST00000254508.5	-	33	4615	c.4533G>A	c.(4531-4533)tcG>tcA	p.S1511S		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1511					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)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TGCTGTTGGCCGAGGAGCTCC	0.617													C|||	2402	0.479633	0.18	0.5764	5008	,	,		17667	0.6696		0.4771	False		,,,				2504	0.6227				p.S1511S		Atlas-SNP	.											NUP210,bladder,carcinoma,-1,1	NUP210	182	1	0			c.G4533A						scavenged	.	C		1082,3324	389.3+/-327.3	124,834,1245	97.0	91.0	93.0		4533	-5.8	0.8	3	dbSNP_83	93	3915,4685	547.6+/-385.2	899,2117,1284	no	coding-synonymous	NUP210	NM_024923.2		1023,2951,2529	TT,TC,CC		45.5233,24.5574,38.4207		1511/1888	13367406	4997,8009	2203	4300	6503	SO:0001819	synonymous_variant	23225	exon33			GTTGGCCGAGGAG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4533G>A	3.37:g.13367406C>T		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			C|0.581;T|0.419	0.419	strong		0.617	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000401046.3_5'UTR|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_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	39	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	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	
TGFB2	7042	hgsc.bcm.edu	37	1	218520315	218520315	+	Missense_Mutation	SNP	G	G	A	rs10482721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:218520315G>A	ENST00000366930.4	+	1	739	c.272G>A	c.(271-273)cGc>cAc	p.R91H	TGFB2_ENST00000366929.4_Missense_Mutation_p.R91H|RP11-224O19.2_ENST00000414452.1_RNA	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	91			R -> H (in dbSNP:rs10482721). {ECO:0000269|PubMed:11528528, ECO:0000269|Ref.4}.		activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCCTGCGAGCGCGAGAGGAGC	0.577													G|||	4	0.000798722	0.0	0.0029	5008	,	,		17473	0.0		0.002	False		,,,				2504	0.0				p.R91H		Atlas-SNP	.											.	TGFB2	102	.	0			c.G272A						PASS	.	G	HIS/ARG,HIS/ARG	5,4393		0,5,2194	23.0	21.0	22.0		272,272	5.4	1.0	1	dbSNP_119	22	43,8543		1,41,4251	yes	missense,missense	TGFB2	NM_001135599.2,NM_003238.3	29,29	1,46,6445	AA,AG,GG		0.5008,0.1137,0.3697	possibly-damaging,possibly-damaging	91/443,91/415	218520315	48,12936	2199	4293	6492	SO:0001583	missense	7042	exon1			GCGAGCGCGAGAG	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"""Endogenous ligands"""	11768	protein-coding gene	gene with protein product	"""prepro-transforming growth factor beta-2"""	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.272G>A	1.37:g.218520315G>A	ENSP00000355897:p.Arg91His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	29.8	5.041172	0.93685	0.001137	0.005008	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.64618	-0.11;-0.11	5.45	5.45	0.79879	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68311	0.2987	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.995;0.984;1.0	P;P;D	0.81914	0.855;0.767;0.995	T	0.71941	-0.4440	10	0.52906	T	0.07	.	13.7098	0.62661	0.0732:0.0:0.9268:0.0	rs10482721	91;91;92	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	H	91	ENSP00000355897:R91H;ENSP00000355896:R91H	ENSP00000355896:R91H	R	+	2	0	TGFB2	216586938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.548000	0.73896	2.837000	0.97791	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.577	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238	
SBNO2	22904	hgsc.bcm.edu	37	19	1110829	1110829	+	Silent	SNP	G	G	A	rs2302109	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	181	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	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	
CLCNKA	1187	hgsc.bcm.edu	37	1	16356497	16356497	+	Silent	SNP	C	C	G	rs7411607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16356497C>G	ENST00000331433.4	+	14	1354	c.1335C>G	c.(1333-1335)gcC>gcG	p.A445A	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Silent_p.A445A|CLCNKA_ENST00000439316.2_Silent_p.A402A|CLCNKA_ENST00000420078.1_Silent_p.A445A			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	445					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	AGGCTCTTGCCGTCGCCTTCC	0.667													T|||	267	0.0533147	0.0809	0.0447	5008	,	,		17236	0.006		0.0755	False		,,,				2504	0.0481				p.A445A		Atlas-SNP	.											.	CLCNKA	56	.	0			c.C1335G						PASS	.	T	,	374,4032		14,346,1843	55.0	51.0	53.0		1335,1335	3.3	0.1	1	dbSNP_116	53	771,7829		40,691,3569	no	coding-synonymous,coding-synonymous	CLCNKA	NM_001042704.1,NM_004070.3	,	54,1037,5412	GG,GC,CC		8.9651,8.4884,8.8036	,	445/687,445/688	16356497	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	1187	exon14			TCTTGCCGTCGCC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1335C>G	1.37:g.16356497C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Silent	SNP	ENST00000331433.4	37	CCDS167.1																																																																																			C|0.926;G|0.074	0.074	strong		0.667	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105.0	108.0	107.0		1929	2.1	1.0	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	84	0.595745	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
ANKEF1	63926	hgsc.bcm.edu	37	20	10036202	10036202	+	Missense_Mutation	SNP	G	G	A	rs6087119	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:10036202G>A	ENST00000378380.3	+	10	2554	c.2225G>A	c.(2224-2226)cGg>cAg	p.R742Q	ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000421143.2_RNA|AL109754.1_ENST00000408554.2_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.R742Q|SNAP25-AS1_ENST00000603542.1_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	742			R -> Q (in dbSNP:rs6087119).				calcium ion binding (GO:0005509)										AGGGAACTACGGCGAGAGAGG	0.468													G|||	246	0.0491214	0.0461	0.0548	5008	,	,		16857	0.0		0.1113	False		,,,				2504	0.0358				p.R742Q		Atlas-SNP	.											.	.	.	.	0			c.G2225A						PASS	.	G	GLN/ARG,GLN/ARG	270,4136	151.8+/-185.6	16,238,1949	94.0	87.0	90.0		2225,2225	2.3	0.0	20	dbSNP_114	90	1087,7513	227.5+/-262.8	73,941,3286	yes	missense,missense	ANKRD5	NM_022096.4,NM_198798.1	43,43	89,1179,5235	AA,AG,GG		12.6395,6.128,10.4336	benign,benign	742/777,742/777	10036202	1357,11649	2203	4300	6503	SO:0001583	missense	63926	exon10			AACTACGGCGAGA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.2225G>A	20.37:g.10036202G>A	ENSP00000367631:p.Arg742Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	138	0.06318681318681318	29	0.05894308943089431	25	0.06906077348066299	0	0.0	84	0.11081794195250659	G	14.54	2.566519	0.45694	0.06128	0.126395	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.69685	-0.42;-0.42	5.64	2.33	0.28932	.	0.265080	0.37053	N	0.002276	T	0.00754	0.0025	L	0.58101	1.795	0.34684	D	0.725046	B	0.22851	0.076	B	0.14578	0.011	T	0.11372	-1.0590	10	0.11485	T	0.65	-9.5472	6.4593	0.21948	0.153:0.0:0.542:0.305	rs6087119;rs52796690;rs59484797;rs6087119	742	Q9NU02	ANKR5_HUMAN	Q	742	ENSP00000367644:R742Q;ENSP00000367631:R742Q	ENSP00000367631:R742Q	R	+	2	0	ANKRD5	9984202	0.021000	0.18746	0.045000	0.18777	0.793000	0.44817	1.143000	0.31553	0.237000	0.21200	0.655000	0.94253	CGG	G|0.913;A|0.087	0.087	strong		0.468	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
ITGB5	3693	hgsc.bcm.edu	37	3	124515308	124515308	+	Silent	SNP	A	A	G	rs1803825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124515308A>G	ENST00000296181.4	-	10	1916	c.1620T>C	c.(1618-1620)ttT>ttC	p.F540F		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	540	Cysteine-rich tandem repeats.				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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AGATCTTGCCAAACTCGCTCT	0.592													G|||	1686	0.336661	0.4788	0.3473	5008	,	,		20842	0.3194		0.1879	False		,,,				2504	0.3078				p.F540F		Atlas-SNP	.											.	ITGB5	66	.	0			c.T1620C						PASS	.	G		1841,2565	634.7+/-396.3	385,1071,747	123.0	111.0	115.0		1620	0.2	1.0	3	dbSNP_89	115	1725,6875	736.7+/-407.0	174,1377,2749	no	coding-synonymous	ITGB5	NM_002213.3		559,2448,3496	GG,GA,AA		20.0581,41.7839,27.4181		540/800	124515308	3566,9440	2203	4300	6503	SO:0001819	synonymous_variant	3693	exon10			CTTGCCAAACTCG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1620T>C	3.37:g.124515308A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	17	0.278689	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	37	CCDS3030.1	674	0.3086080586080586	234	0.47560975609756095	110	0.30386740331491713	194	0.33916083916083917	136	0.17941952506596306	G	7.501	0.652613	0.14580	0.417839	0.200581	ENSG00000082781	ENST00000481591	.	.	.	5.26	0.242	0.15498	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48340	-0.9044	3	.	.	.	.	6.595	0.22667	0.4816:0.0:0.4031:0.1153	rs1803825;rs17850113;rs1803825	.	.	.	S	230	.	.	L	-	2	0	ITGB5	125997998	0.001000	0.12720	0.994000	0.49952	0.591000	0.36615	-1.263000	0.02850	-0.106000	0.12110	-0.213000	0.12676	TTG	A|0.723;G|0.277	0.277	strong		0.592	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
ZNF324	25799	hgsc.bcm.edu	37	19	58983321	58983321	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58983321C>T	ENST00000536459.2	+	4	2171	c.1462C>T	c.(1462-1464)Cgc>Tgc	p.R488C	ZNF446_ENST00000596341.1_5'Flank|ZNF324_ENST00000196482.3_Missense_Mutation_p.R488C|ZNF324_ENST00000535298.1_Missense_Mutation_p.R265C			O75467	Z324A_HUMAN	zinc finger protein 324	488					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(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		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)		GCAGTGTGGCCGCGCCTTCCG	0.692																																					p.R488C		Atlas-SNP	.											ZNF324,NS,carcinoma,-2,1	ZNF324	46	1	0			c.C1462T						PASS	.						32.0	34.0	34.0					19																	58983321		2201	4299	6500	SO:0001583	missense	25799	exon4			TGTGGCCGCGCCT	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"""Zinc fingers, C2H2-type"", ""-"""	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1462C>T	19.37:g.58983321C>T	ENSP00000444812:p.Arg488Cys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_014347	B3KRX1	Missense_Mutation	SNP	ENST00000536459.2	37	CCDS12981.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268427	0.40095	.	.	ENSG00000083812	ENST00000196482;ENST00000536459;ENST00000539101;ENST00000535298	T;T;T	0.19806	2.12;2.12;2.12	3.84	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39475	N	0.001353	T	0.46386	0.1390	M	0.87547	2.89	0.45108	D	0.998126	D	0.69078	0.997	P	0.62740	0.906	T	0.53933	-0.8368	10	0.87932	D	0	.	11.5508	0.50719	0.0:1.0:0.0:0.0	.	488	O75467	Z324A_HUMAN	C	488;488;478;265	ENSP00000196482:R488C;ENSP00000444812:R488C;ENSP00000439588:R265C	ENSP00000196482:R488C	R	+	1	0	ZNF324	63675133	0.016000	0.18221	0.998000	0.56505	0.157000	0.22087	0.719000	0.25881	2.433000	0.82419	0.400000	0.26472	CGC	.	.	none		0.692	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347	
SDR42E1	93517	hgsc.bcm.edu	37	16	82033022	82033022	+	Silent	SNP	A	A	G	rs11861598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:82033022A>G	ENST00000328945.5	-	3	1003	c.876T>C	c.(874-876)ttT>ttC	p.F292F	SDR42E1_ENST00000534209.1_5'Flank	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	292					steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						TCTCTGTTAGAAAAGCAAAGC	0.483													A|||	243	0.0485224	0.1596	0.0173	5008	,	,		20516	0.001		0.0129	False		,,,				2504	0.0061				p.F292F		Atlas-SNP	.											.	SDR42E1	26	.	0			c.T876C						PASS	.	A		538,3326		32,474,1426	70.0	68.0	69.0		876	4.3	1.0	16	dbSNP_120	69	77,8211		0,77,4067	no	coding-synonymous	SDR42E1	NM_145168.2		32,551,5493	GG,GA,AA		0.9291,13.9234,5.0609		292/394	82033022	615,11537	1932	4144	6076	SO:0001819	synonymous_variant	93517	exon3			TGTTAGAAAAGCA	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.876T>C	16.37:g.82033022A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_145168	B2RDS1|Q9P0D1	Silent	SNP	ENST00000328945.5	37	CCDS42205.1																																																																																			A|0.956;G|0.044	0.044	strong		0.483	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168	
IDI2	91734	hgsc.bcm.edu	37	10	1068639	1068639	+	Silent	SNP	C	C	T	rs13377037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:1068639C>T	ENST00000277517.1	-	3	283	c.219G>A	c.(217-219)acG>acA	p.T73T	IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	73	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)			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)		ACGTGACTTTCGTGTCCGACC	0.522													C|||	501	0.10004	0.1483	0.1182	5008	,	,		18980	0.1081		0.0815	False		,,,				2504	0.0327				p.T73T		Atlas-SNP	.											.	IDI2	20	.	0			c.G219A						PASS	.	C		590,3816	259.2+/-262.9	34,522,1647	127.0	100.0	109.0		219	-5.2	0.0	10	dbSNP_121	109	670,7930	168.6+/-220.1	29,612,3659	no	coding-synonymous	IDI2	NM_033261.2		63,1134,5306	TT,TC,CC		7.7907,13.3908,9.6878		73/228	1068639	1260,11746	2203	4300	6503	SO:0001819	synonymous_variant	91734	exon3			GACTTTCGTGTCC	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.219G>A	10.37:g.1068639C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_033261		Silent	SNP	ENST00000277517.1	37	CCDS7055.1																																																																																			C|0.900;N|0.000	.	strong		0.522	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
NCOA7	135112	hgsc.bcm.edu	37	6	126210395	126210395	+	Missense_Mutation	SNP	T	T	G	rs6919947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:126210395T>G	ENST00000368357.3	+	10	1547	c.1195T>G	c.(1195-1197)Tct>Gct	p.S399A	NCOA7_ENST00000229634.9_Missense_Mutation_p.S284A|NCOA7_ENST00000392477.2_Missense_Mutation_p.S399A	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	399			S -> A (in dbSNP:rs6919947). {ECO:0000269|PubMed:11971969, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		CGACACTTCTTCTGCATTTGA	0.433													G|||	2396	0.478435	0.4024	0.4899	5008	,	,		20109	0.5903		0.5189	False		,,,				2504	0.4162				p.S399A		Atlas-SNP	.											.	NCOA7	92	.	0			c.T1195G						PASS	.	G	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	1895,2511	610.6+/-391.6	411,1073,719	57.0	60.0	59.0		1162,1195,1195,850,1195	-7.8	0.0	6	dbSNP_116	59	4329,4271	571.1+/-389.5	1092,2145,1063	yes	missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_181782.4	99,99,99,99,99	1503,3218,1782	GG,GT,TT		49.6628,43.0095,47.8548	benign,benign,benign,benign,benign	388/932,399/943,399/943,284/828,399/943	126210395	6224,6782	2203	4300	6503	SO:0001583	missense	135112	exon10			ACTTCTTCTGCAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1195T>G	6.37:g.126210395T>G	ENSP00000357341:p.Ser399Ala	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	1134	0.5192307692307693	198	0.4024390243902439	184	0.5082872928176796	357	0.6241258741258742	395	0.521108179419525	G	0.005	-2.154608	0.00325	0.430095	0.503372	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.29397	2.81;2.81;2.81;1.57	4.63	-7.76	0.01232	.	1.855050	0.02104	N	0.054209	T	0.01661	0.0053	N	0.01874	-0.695	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	0.09207	-1.0685	9	0.02654	T	1	0.7746	3.8292	0.08867	0.5446:0.0911:0.0925:0.2718	rs6919947;rs13217790;rs17807774;rs59024241;rs6919947	388;388;399	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	A	399;399;284;197	ENSP00000357341:S399A;ENSP00000376269:S399A;ENSP00000229634:S284A;ENSP00000389186:S197A	ENSP00000229634:S284A	S	+	1	0	NCOA7	126252088	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.657000	0.05335	-2.239000	0.00711	-1.084000	0.02203	TCT	T|0.507;G|0.493	0.493	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
GUCY2F	2986	hgsc.bcm.edu	37	X	108708552	108708552	+	Missense_Mutation	SNP	A	A	G	rs12008095	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:108708552A>G	ENST00000218006.2	-	3	1142	c.851T>C	c.(850-852)cTg>cCg	p.L284P		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	284			L -> P (in dbSNP:rs12008095). {ECO:0000269|PubMed:17344846}.		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)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						ACTGTAGAGCAGGGCATCATA	0.478													A|||	611	0.161854	0.0113	0.1412	3775	,	,		15658	0.0377		0.2913	False		,,,				2504	0.1708				p.L284P		Atlas-SNP	.											.	GUCY2F	178	.	0			c.T851C						PASS	.	A	PRO/LEU	273,3562		7,222,37,1403,534	176.0	137.0	151.0		851	3.9	1.0	X	dbSNP_120	151	2470,4258		318,1142,692,968,1180	yes	missense	GUCY2F	NM_001522.2	98	325,1364,729,2371,1714	GG,GA,G,AA,A		36.7122,7.1186,25.968	probably-damaging	284/1109	108708552	2743,7820	2203	4300	6503	SO:0001583	missense	2986	exon3			TAGAGCAGGGCAT	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.851T>C	X.37:g.108708552A>G	ENSP00000218006:p.Leu284Pro	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	319	0.19228450874020495	5	0.0102880658436214	43	0.1303030303030303	9	0.016129032258064516	162	0.26557377049180325	A	18.24	3.579314	0.65878	0.071186	0.367122	ENSG00000101890	ENST00000218006	D	0.83837	-1.77	3.94	3.94	0.45596	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.79475	2.455	0.09310	P	0.999999999739281	P	0.51240	0.943	P	0.58577	0.841	T	0.00542	-1.1680	9	0.35671	T	0.21	.	10.183	0.42980	1.0:0.0:0.0:0.0	rs12008095;rs52818490;rs57978660;rs12008095	284	P51841	GUC2F_HUMAN	P	284	ENSP00000218006:L284P	ENSP00000218006:L284P	L	-	2	0	GUCY2F	108595208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.579000	0.90781	1.764000	0.52075	0.486000	0.48141	CTG	A|0.790;0|0.012	.	strong		0.478	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
NPY2R	4887	hgsc.bcm.edu	37	4	156135676	156135676	+	Silent	SNP	C	C	T	rs1047214	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:156135676C>T	ENST00000329476.3	+	2	1074	c.585C>T	c.(583-585)atC>atT	p.I195I	NPY2R_ENST00000506608.1_Silent_p.I195I	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	195					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TTGAGATCATCCCGGACTTTG	0.512													T|||	3507	0.70028	0.9395	0.5014	5008	,	,		21126	0.8115		0.5447	False		,,,				2504	0.5634				p.I195I		Atlas-SNP	.											.	NPY2R	87	.	0			c.C585T	GRCh37	CM057405	NPY2R	M	rs1047214	PASS	.	T		3841,565	248.4+/-256.2	1684,473,46	101.0	102.0	102.0		585	-6.2	0.2	4	dbSNP_86	102	4559,4041	556.1+/-386.8	1206,2147,947	no	coding-synonymous	NPY2R	NM_000910.2		2890,2620,993	TT,TC,CC		46.9884,12.8234,35.4144		195/382	156135676	8400,4606	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			GATCATCCCGGAC	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.585C>T	4.37:g.156135676C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.329;N|0.000	.	strong		0.512	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94341267	94341267	+	Silent	SNP	A	A	G	rs2273165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:94341267A>G	ENST00000436063.2	-	3	1797	c.1740T>C	c.(1738-1740)ttT>ttC	p.F580F	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	580	TdBR region; mediates interaction with DNTT.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TATCTGCATTAAAATTAATAT	0.363													G|||	2673	0.533746	0.5378	0.4337	5008	,	,		15809	0.621		0.4225	False		,,,				2504	0.6237				p.F580F		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T1740C						PASS	.	G		1895,1789		462,971,409	202.0	173.0	182.0		1740	-0.2	1.0	1	dbSNP_100	182	3509,4671		723,2063,1304	no	coding-synonymous	DNTTIP2	NM_014597.4		1185,3034,1713	GG,GA,AA		42.8973,48.5613,45.5496		580/757	94341267	5404,6460	1842	4090	5932	SO:0001819	synonymous_variant	30836	exon3			TGCATTAAAATTA	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1740T>C	1.37:g.94341267A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																			A|0.510;G|0.490	0.490	strong		0.363	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
RHOU	58480	hgsc.bcm.edu	37	1	228871693	228871693	+	Silent	SNP	C	C	T	rs3738073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228871693C>T	ENST00000366691.3	+	1	870	c.204C>T	c.(202-204)agC>agT	p.S68S		NM_021205.5	NP_067028.1			ras homolog family member U											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	13	Breast(184;0.162)	Prostate(94;0.183)				TGGTGGTGAGCTACACCACCA	0.751													c|||	646	0.128994	0.0893	0.0951	5008	,	,		7479	0.0427		0.172	False		,,,				2504	0.2515				p.S68S		Atlas-SNP	.											.	RHOU	20	.	0			c.C204T						PASS	.			451,3945		35,381,1782	20.0	25.0	23.0		204	3.7	1.0	1	dbSNP_107	23	1682,6908		177,1328,2790	no	coding-synonymous	RHOU	NM_021205.5		212,1709,4572	TT,TC,CC		19.5809,10.2593,16.4254		68/259	228871693	2133,10853	2198	4295	6493	SO:0001819	synonymous_variant	58480	exon1			GGTGAGCTACACC		CCDS1575.1	1q42.11-q42.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000116574	ENSG00000116574			17794	protein-coding gene	gene with protein product	"""Ryu GTPase"", ""Wnt-1 responsive Cdc42 homolog"", ""2310026M05Rik"", ""GTP-binding protein like 1"", ""CDC42-like GTPase"", ""GTP-binding protein SB128"", ""ras-like gene family member U"""	606366	"""ras homolog gene family, member U"""	ARHU		11459829	Standard	NM_021205		Approved	WRCH-1, DJ646B12.2, FLJ10616, WRCH1, CDC42L1, hG28K, fJ646B12.2	uc001htf.3	Q7L0Q8	OTTHUMG00000037919	ENST00000366691.3:c.204C>T	1.37:g.228871693C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_021205		Silent	SNP	ENST00000366691.3	37	CCDS1575.1																																																																																			T|0.149;G|0.000;C|0.851	0.149	strong		0.751	RHOU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092555.1	NM_021205	
MUC16	94025	hgsc.bcm.edu	37	19	9048895	9048895	+	Missense_Mutation	SNP	A	A	C	rs2012761	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9048895A>C	ENST00000397910.4	-	5	32939	c.32736T>G	c.(32734-32736)agT>agG	p.S10912R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10914	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						CTTCCCCATGACTGGTGGCCA	0.507													A|||	798	0.159345	0.1415	0.1801	5008	,	,		24394	0.2619		0.0865	False		,,,				2504	0.138				p.S10912R		Atlas-SNP	.											.	MUC16	4315	.	0			c.T32736G						PASS	.		ARG/SER	513,3295		39,435,1430	118.0	106.0	110.0		32736	-1.2	0.0	19	dbSNP_92	110	641,7619		25,591,3514	yes	missense	MUC16	NM_024690.2	110	64,1026,4944	CC,CA,AA		7.7603,13.4716,9.5625	benign	10912/14508	9048895	1154,10914	1904	4130	6034	SO:0001583	missense	94025	exon5			CCCATGACTGGTG	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.32736T>G	19.37:g.9048895A>C	ENSP00000381008:p.Ser10912Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	346	0.15842490842490842	52	0.10569105691056911	56	0.15469613259668508	168	0.2937062937062937	70	0.09234828496042216	a	7.695	0.691851	0.15039	0.134716	0.077603	ENSG00000181143	ENST00000397910	T	0.02656	4.21	3.53	-1.16	0.09678	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	.	.	.	B	0.24823	0.112	B	0.20767	0.031	T	0.44967	-0.9293	8	0.87932	D	0	.	2.3433	0.04265	0.4026:0.0:0.2254:0.372	rs2012761;rs17000719;rs41313145;rs2012761	10912	B5ME49	.	R	10912	ENSP00000381008:S10912R	ENSP00000381008:S10912R	S	-	3	2	MUC16	8909895	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	0.433000	0.21477	-0.365000	0.08076	0.378000	0.23410	AGT	A|0.849;C|0.151	0.151	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NLRP7	199713	hgsc.bcm.edu	37	19	55451256	55451256	+	Missense_Mutation	SNP	G	G	T	rs79513034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451256G>T	ENST00000590030.1	-	3	971	c.931C>A	c.(931-933)Ctc>Atc	p.L311I	NLRP7_ENST00000340844.2_Missense_Mutation_p.L311I|NLRP7_ENST00000588756.1_Missense_Mutation_p.L311I|NLRP7_ENST00000446217.1_Missense_Mutation_p.L339I|NLRP7_ENST00000328092.5_Missense_Mutation_p.L311I|NLRP7_ENST00000592784.1_Missense_Mutation_p.L311I|NLRP7_ENST00000448121.2_Missense_Mutation_p.L311I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	311	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TGCGCCAGGAGCTGGAGGTCC	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16625	0.0		0.0219	False		,,,				2504	0.0				p.L311I		Atlas-SNP	.											.	NLRP7	411	.	0			c.C931A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU	3,4403	6.2+/-15.9	0,3,2200	38.0	38.0	38.0		931,931,931	-1.9	0.0	19	dbSNP_131	38	135,8465	60.2+/-122.0	1,133,4166	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	5,5,5	1,136,6366	TT,TG,GG		1.5698,0.0681,1.061	benign,benign,benign	311/1038,311/1010,311/981	55451256	138,12868	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGGAGCTGGAG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.931C>A	19.37:g.55451256G>T	ENSP00000465520:p.Leu311Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.165	0.029214	0.08054	6.81E-4	0.015698	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	1.77	-1.85	0.07784	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.46678	0.1405	L	0.39397	1.21	0.09310	N	1	P;P;P	0.39601	0.68;0.68;0.63	B;B;B	0.40066	0.318;0.318;0.212	T	0.47045	-0.9147	9	0.17369	T	0.5	.	3.7385	0.08520	0.2934:0.4095:0.2972:0.0	.	339;311;311	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	I	311;311;311;339	ENSP00000329568:L311I;ENSP00000409137:L311I;ENSP00000339491:L311I;ENSP00000414273:L339I	ENSP00000329568:L311I	L	-	1	0	NLRP7	60143068	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.029000	0.12329	-0.432000	0.07297	-0.368000	0.07277	CTC	G|0.989;T|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
TCEA3	6920	hgsc.bcm.edu	37	1	23720501	23720501	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23720501C>T	ENST00000450454.2	-	8	796	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	230	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				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)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ACTTCATGTCCGTGCTCTTGA	0.632																																					p.T230T		Atlas-SNP	.											.	TCEA3	20	.	0			c.G690A						PASS	.						68.0	69.0	69.0					1																	23720501		1970	4143	6113	SO:0001819	synonymous_variant	6920	exon8			CATGTCCGTGCTC	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.690G>A	1.37:g.23720501C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	109	26	0.238532	NM_003196	A8K2K7|Q5DR83	Silent	SNP	ENST00000450454.2	37	CCDS44086.1																																																																																			.	.	none		0.632	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	
ZC3H13	23091	hgsc.bcm.edu	37	13	46559703	46559703	+	Silent	SNP	T	T	C	rs17067518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:46559703T>C	ENST00000242848.4	-	10	1797	c.1449A>G	c.(1447-1449)agA>agG	p.R483R	ZC3H13_ENST00000282007.3_Silent_p.R483R			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	483	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R483R(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		TGCTATAATCTCTCATCTCCC	0.527													C|||	147	0.029353	0.0234	0.013	5008	,	,		16606	0.0367		0.0109	False		,,,				2504	0.0603				p.R483R	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											ZC3H13,NS,carcinoma,0,1	ZC3H13	197	1	1	Substitution - coding silent(1)	stomach(1)	c.A1449G						scavenged	.	C		87,4319	818.4+/-416.3	1,85,2117	175.0	174.0	174.0		1449	2.5	1.0	13	dbSNP_123	174	92,8508	815.4+/-407.0	1,90,4209	no	coding-synonymous	ZC3H13	NM_015070.3		2,175,6326	CC,CT,TT		1.0698,1.9746,1.3763		483/1565	46559703	179,12827	2203	4300	6503	SO:0001819	synonymous_variant	23091	exon10			ATAATCTCTCATC	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1449A>G	13.37:g.46559703T>C		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37																																																																																				T|0.981;C|0.019	0.019	strong		0.527	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
KLF17	128209	hgsc.bcm.edu	37	1	44595410	44595410	+	Missense_Mutation	SNP	A	A	G	rs2485652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44595410A>G	ENST00000372299.3	+	2	525	c.467A>G	c.(466-468)aAt>aGt	p.N156S	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	156			N -> S (in dbSNP:rs2485652). {ECO:0000269|PubMed:15489334}.		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)					ATGCCCCCCAATGGGCTGCCA	0.562													A|||	1380	0.275559	0.0915	0.2594	5008	,	,		16923	0.4236		0.3966	False		,,,				2504	0.2587				p.N156S		Atlas-SNP	.											.	KLF17	92	.	0			c.A467G						PASS	.	A	SER/ASN	636,3770	270.4+/-269.6	47,542,1614	32.0	36.0	34.0		467	-9.3	0.0	1	dbSNP_100	34	3204,5396	473.2+/-368.5	593,2018,1689	yes	missense	KLF17	NM_173484.3	46	640,2560,3303	GG,GA,AA		37.2558,14.4349,29.5248	benign	156/390	44595410	3840,9166	2203	4300	6503	SO:0001583	missense	128209	exon2			CCCCCAATGGGCT	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.467A>G	1.37:g.44595410A>G	ENSP00000361373:p.Asn156Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	696	0.31868131868131866	49	0.09959349593495935	107	0.2955801104972376	252	0.4405594405594406	288	0.37994722955145116	A	0.027	-1.362961	0.01235	0.144349	0.372558	ENSG00000171872	ENST00000372299	T	0.07688	3.17	4.64	-9.27	0.00659	.	1.710450	0.03115	N	0.163023	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42310	-0.9459	9	0.05833	T	0.94	.	8.5854	0.33655	0.5506:0.1851:0.2643:0.0	rs2485652;rs17854589;rs56961994;rs2485652	156	Q5JT82	KLF17_HUMAN	S	156	ENSP00000361373:N156S	ENSP00000361373:N156S	N	+	2	0	KLF17	44367997	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.032000	0.01426	-2.352000	0.00616	-2.144000	0.00337	AAT	A|0.702;G|0.298	0.298	strong		0.562	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
ALAD	210	hgsc.bcm.edu	37	9	116153900	116153900	+	Silent	SNP	A	A	G	rs1139488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	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	
STAB1	23166	hgsc.bcm.edu	37	3	52540773	52540773	+	Silent	SNP	T	T	C	rs1010553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52540773T>C	ENST00000321725.6	+	18	1972	c.1896T>C	c.(1894-1896)ggT>ggC	p.G632G		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	632	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCGCCAATGGTGTGATCCACA	0.667													C|||	3199	0.638778	0.8601	0.4265	5008	,	,		18395	0.5446		0.4682	False		,,,				2504	0.7628				p.G632G		Atlas-SNP	.											STAB1,trunk,malignant_melanoma,+1,1	STAB1	178	1	0			c.T1896C						scavenged	.	C		3617,789	311.1+/-291.9	1492,633,78	63.0	58.0	60.0		1896	-9.9	0.1	3	dbSNP_86	60	4119,4479	585.3+/-391.9	1009,2101,1189	no	coding-synonymous	STAB1	NM_015136.2		2501,2734,1267	CC,CT,TT		47.9065,17.9074,40.5106		632/2571	52540773	7736,5268	2203	4299	6502	SO:0001819	synonymous_variant	23166	exon18			CAATGGTGTGATC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.1896T>C	3.37:g.52540773T>C		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	196	65	0.331633	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			T|0.407;C|0.593	0.593	strong		0.667	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
ZNF335	63925	hgsc.bcm.edu	37	20	44578961	44578961	+	Silent	SNP	A	A	G	rs3746503	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44578961A>G	ENST00000322927.2	-	22	3484	c.3384T>C	c.(3382-3384)ccT>ccC	p.P1128P	ZNF335_ENST00000426788.1_Silent_p.P973P	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1128					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)				TCCTCCCATCAGGACTGTGCA	0.587													A|||	783	0.15635	0.0855	0.072	5008	,	,		17543	0.3294		0.0954	False		,,,				2504	0.1963				p.P1128P		Atlas-SNP	.											.	ZNF335	115	.	0			c.T3384C						PASS	.	A		262,4144	148.0+/-182.4	6,250,1947	93.0	97.0	96.0		3384	-7.5	0.2	20	dbSNP_107	96	939,7661	206.9+/-248.8	49,841,3410	no	coding-synonymous	ZNF335	NM_022095.3		55,1091,5357	GG,GA,AA		10.9186,5.9464,9.2342		1128/1343	44578961	1201,11805	2203	4300	6503	SO:0001819	synonymous_variant	63925	exon22			CCCATCAGGACTG	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.3384T>C	20.37:g.44578961A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			A|0.879;G|0.121	0.121	strong		0.587	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
OR8S1	341568	hgsc.bcm.edu	37	12	48919659	48919659	+	Missense_Mutation	SNP	T	T	C	rs4075258|rs71439450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	134	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	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		
COL6A2	1292	hgsc.bcm.edu	37	21	47537804	47537804	+	Missense_Mutation	SNP	C	C	G	rs199929757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47537804C>G	ENST00000300527.4	+	12	1174	c.1070C>G	c.(1069-1071)cCg>cGg	p.P357R	COL6A2_ENST00000409416.1_Missense_Mutation_p.P357R|COL6A2_ENST00000397763.1_Missense_Mutation_p.P357R|COL6A2_ENST00000310645.5_Missense_Mutation_p.P357R|COL6A2_ENST00000357838.4_Missense_Mutation_p.P357R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	357	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)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GACGGTTACCCGGGGGAAGCA	0.682													C|||	3	0.000599042	0.0	0.0014	5008	,	,		16264	0.0		0.002	False		,,,				2504	0.0				p.P357R		Atlas-SNP	.											.	COL6A2	351	.	0			c.C1070G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO	2,4388	2.1+/-5.4	0,2,2193	50.0	48.0	48.0		1070,1070,1070	2.6	0.1	21		48	14,8574	9.1+/-34.3	0,14,4280	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	103,103,103	0,16,6473	GG,GC,CC		0.163,0.0456,0.1233	benign,benign,benign	357/1020,357/919,357/829	47537804	16,12962	2195	4294	6489	SO:0001583	missense	1292	exon12			GTTACCCGGGGGA	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1070C>G	21.37:g.47537804C>G	ENSP00000300527:p.Pro357Arg	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	31	0.688889	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	2.941	-0.218840	0.06101	4.56E-4	0.00163	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16;-4.16	4.46	2.59	0.31030	.	0.302904	0.36303	N	0.002665	D	0.94463	0.8218	L	0.46741	1.465	0.49915	D	0.999832	P;P;B	0.44877	0.81;0.845;0.111	P;P;B	0.47626	0.552;0.504;0.103	D	0.91557	0.5261	10	0.44086	T	0.13	-0.2304	9.7478	0.40457	0.0:0.8421:0.0:0.1579	.	357;357;357	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	R	357	ENSP00000300527:P357R;ENSP00000350497:P357R;ENSP00000312529:P357R;ENSP00000387115:P357R;ENSP00000380870:P357R	ENSP00000300527:P357R	P	+	2	0	COL6A2	46362232	0.902000	0.30710	0.087000	0.20705	0.104000	0.19210	2.090000	0.41682	0.411000	0.25702	0.305000	0.20034	CCG	C|0.996;G|0.005	0.005	strong		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
GALNT15	117248	hgsc.bcm.edu	37	3	16268974	16268974	+	Silent	SNP	T	T	A	rs15767	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:16268974T>A	ENST00000339732.5	+	10	2390	c.1887T>A	c.(1885-1887)cgT>cgA	p.R629R	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	629	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				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)										AGCAGTGGCGTTTTGACCAGA	0.443													A|||	1808	0.361022	0.5287	0.3876	5008	,	,		18046	0.2034		0.3887	False		,,,				2504	0.2495				p.R629R		Atlas-SNP	.											GALNTL2,colon,carcinoma,0,4	.	.	4	0			c.T1887A						PASS	.	A		2148,2258	596.7+/-388.7	516,1116,571	125.0	123.0	123.0		1887	-2.8	0.5	3	dbSNP_52	123	3240,5360	650.3+/-400.7	610,2020,1670	no	coding-synonymous	GALNTL2	NM_054110.4		1126,3136,2241	AA,AT,TT		37.6744,48.7517,41.427		629/640	16268974	5388,7618	2203	4300	6503	SO:0001819	synonymous_variant	117248	exon10			GTGGCGTTTTGAC	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.1887T>A	3.37:g.16268974T>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Silent	SNP	ENST00000339732.5	37	CCDS33711.1	850	0.3891941391941392	277	0.5630081300813008	157	0.43370165745856354	129	0.22552447552447552	287	0.3786279683377309	A	2.572	-0.299389	0.05532	0.487517	0.376744	ENSG00000131386	ENST00000543679	.	.	.	5.4	-2.78	0.05859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999670301	.	.	.	.	.	.	T	0.44802	-0.9304	4	0.37606	T	0.19	.	7.3671	0.26779	0.413:0.0:0.4636:0.1233	rs15767;rs712871;rs1394909;rs3188637;rs17356739;rs15767	.	.	.	D	159	.	ENSP00000445852:V159D	V	+	2	0	GALNTL2	16243978	0.001000	0.12720	0.540000	0.28089	0.098000	0.18820	-0.374000	0.07484	-0.719000	0.04942	-0.257000	0.10917	GTT	T|0.600;A|0.400	0.400	strong		0.443	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249183	71249183	+	Missense_Mutation	SNP	T	T	C	rs55921335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	92	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	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	
GPANK1	7918	hgsc.bcm.edu	37	6	31630241	31630241	+	Silent	SNP	C	C	T	rs7992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31630241C>T	ENST00000375906.1	-	4	1557	c.873G>A	c.(871-873)agG>agA	p.R291R	C6orf47_ENST00000375911.1_5'Flank|GPANK1_ENST00000375895.2_Silent_p.R291R|GPANK1_ENST00000375893.2_Silent_p.R291R|GPANK1_ENST00000375896.4_Silent_p.R291R|GPANK1_ENST00000375900.4_Silent_p.R291R|C6orf47-AS1_ENST00000422049.1_RNA|Y_RNA_ENST00000364337.1_RNA|CSNK2B_ENST00000375885.4_5'Flank	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	145	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	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	
FFAR3	2865	hgsc.bcm.edu	37	19	35850022	35850022	+	Missense_Mutation	SNP	A	A	G	rs149009291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35850022A>G	ENST00000327809.4	+	2	431	c.230A>G	c.(229-231)aAt>aGt	p.N77S	FFAR3_ENST00000594310.1_Missense_Mutation_p.N77S	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	77					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|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 glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			GAGGCAGCCAATGGCATGCAC	0.632																																					p.N77S	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											.	FFAR3	40	.	0			c.A230G						PASS	.						33.0	29.0	30.0					19																	35850022		2197	4263	6460	SO:0001583	missense	2865	exon2			CAGCCAATGGCAT	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.230A>G	19.37:g.35850022A>G	ENSP00000328230:p.Asn77Ser	Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	367	192	0.523161	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.497958	0.00157	.	.	ENSG00000185897	ENST00000327809	T	0.71579	-0.58	5.52	-6.53	0.01866	GPCR, rhodopsin-like superfamily (1);	0.719489	0.14208	N	0.334232	T	0.34424	0.0897	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.46789	-0.9166	9	0.06625	T	0.88	-1.1157	9.116	0.36758	0.5692:0.103:0.3278:0.0	.	77	O14843	FFAR3_HUMAN	S	77	ENSP00000328230:N77S	ENSP00000328230:N77S	N	+	2	0	FFAR3	40541862	0.000000	0.05858	0.007000	0.13788	0.023000	0.10783	-2.334000	0.01107	-0.933000	0.03737	-1.294000	0.01345	AAT	A|0.891;G|0.109	0.109	strong		0.632	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:66618342A>G	ENST00000319212.4	+	12	1891	c.1841A>G	c.(1840-1842)gAt>gGt	p.D614G	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Missense_Mutation_p.D531G	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	614			D -> G (in dbSNP:rs3803412). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAAGACTTGGATGAGAAGAGC	0.453													A|||	1258	0.251198	0.0953	0.3199	5008	,	,		19288	0.3165		0.2952	False		,,,				2504	0.3006				p.D614G		Atlas-SNP	.											.	DIS3L	175	.	0			c.A1841G						PASS	.	A	GLY/ASP,GLY/ASP	608,3794	264.7+/-266.2	35,538,1628	121.0	113.0	116.0		1841,1592	5.3	0.7	15	dbSNP_107	116	2617,5981	423.7+/-354.4	397,1823,2079	yes	missense,missense	DIS3L	NM_001143688.1,NM_133375.3	94,94	432,2361,3707	GG,GA,AA		30.4373,13.8119,24.8077	benign,benign	614/1055,531/972	66618342	3225,9775	2201	4299	6500	SO:0001583	missense	115752	exon12			ACTTGGATGAGAA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"""DIS3 mitotic control homolog (S. cerevisiae)-like"""			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1841A>G	15.37:g.66618342A>G	ENSP00000321711:p.Asp614Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	37	CCDS45286.1	551	0.2522893772893773	46	0.09349593495934959	106	0.292817679558011	172	0.3006993006993007	227	0.2994722955145119	A	9.152	1.016533	0.19355	0.138119	0.304373	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.25250	1.81;1.81	5.31	5.31	0.75309	Ribonuclease II/R (2);	0.391663	0.30999	N	0.008458	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	1.0	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.11329	0.006;0.003;0.003	T	0.41088	-0.9528	9	0.36615	T	0.2	-17.8793	14.4288	0.67236	1.0:0.0:0.0:0.0	rs3803412;rs52810111;rs3803412	614;480;614	Q8TF46;Q8TF46-2;Q8TF46-3	DI3L1_HUMAN;.;.	G	531;614	ENSP00000321583:D531G;ENSP00000321711:D614G	ENSP00000321583:D531G	D	+	2	0	DIS3L	64405396	1.000000	0.71417	0.712000	0.30502	0.337000	0.28794	4.706000	0.61845	1.991000	0.58162	0.379000	0.24179	GAT	A|0.760;G|0.240	0.240	strong		0.453	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
SAT2	112483	hgsc.bcm.edu	37	17	7530271	7530271	+	Silent	SNP	C	C	T	rs858520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7530271C>T	ENST00000269298.5	-	4	513	c.294G>A	c.(292-294)ccG>ccA	p.P98P	SHBG_ENST00000572182.1_Intron|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000570547.1_Intron|SAT2_ENST00000573566.1_Intron|SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000576728.1_Intron|SAT2_ENST00000380466.2_5'UTR|SHBG_ENST00000572262.1_Intron	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	98	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	CCCGATATTCCGGCATCACAT	0.557													C|||	1359	0.271366	0.0182	0.2695	5008	,	,		17324	0.3155		0.3887	False		,,,				2504	0.4489				p.P98P		Atlas-SNP	.											.	SAT2	8	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.G294A						PASS	.	C		331,4075	172.7+/-202.6	14,303,1886	71.0	69.0	70.0		294	-11.5	0.0	17	dbSNP_86	70	3338,5262	484.3+/-371.4	671,1996,1633	no	coding-synonymous	SAT2	NM_133491.3		685,2299,3519	TT,TC,CC		38.814,7.5125,28.2101		98/171	7530271	3669,9337	2203	4300	6503	SO:0001819	synonymous_variant	112483	exon4			ATATTCCGGCATC	AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"""diamine N-acetyltransferase 2"""	611463	"""spermidine/spermine N1-acetyltransferase 2"""			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.294G>A	17.37:g.7530271C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_133491		Silent	SNP	ENST00000269298.5	37	CCDS11116.1																																																																																			C|0.723;T|0.277	0.277	strong		0.557	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491	
NRD1	4898	hgsc.bcm.edu	37	1	52264064	52264064	+	Silent	SNP	A	A	G	rs1770791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:52264064A>G	ENST00000354831.7	-	24	2854	c.2665T>C	c.(2665-2667)Ttg>Ctg	p.L889L	NRD1_ENST00000544028.1_Silent_p.L689L|NRD1_ENST00000352171.7_Silent_p.L821L|RP4-657D16.3_ENST00000588291.1_RNA|RP4-657D16.3_ENST00000586761.1_RNA|RP4-657D16.6_ENST00000607338.1_RNA|NRD1_ENST00000485608.1_5'UTR|RP4-657D16.3_ENST00000591675.1_RNA|NRD1_ENST00000539524.1_Silent_p.L757L	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	820					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						GCATATTCCAAGATTAAAAGC	0.393													G|||	1799	0.359225	0.6657	0.3732	5008	,	,		19295	0.1508		0.2435	False		,,,				2504	0.2689				p.L889L		Atlas-SNP	.											.	NRD1	89	.	0			c.T2665C						PASS	.	G	,,	2589,1817	530.3+/-372.9	743,1103,357	63.0	62.0	62.0		2461,2269,2665	3.8	1.0	1	dbSNP_89	62	2078,6522	717.4+/-406.2	252,1574,2474	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	995,2677,2831	GG,GA,AA		24.1628,41.2392,35.8834	,,	821/1152,757/1088,889/1220	52264064	4667,8339	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon24			ATTCCAAGATTAA	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2665T>C	1.37:g.52264064A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	159	65	0.408805	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1	738	0.33791208791208793	320	0.6504065040650406	131	0.36187845303867405	105	0.18356643356643357	182	0.24010554089709762	G	9.188	1.025351	0.19433	0.587608	0.241628	ENSG00000078618	ENST00000440943	.	.	.	5.64	3.76	0.43208	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45804	-0.9236	4	.	.	.	-6.2813	10.5457	0.45058	0.3166:0.0:0.6834:0.0	rs1770791;rs58390176;rs1770791	.	.	.	P	235	.	.	L	-	2	0	NRD1	52036652	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.464000	0.35288	0.489000	0.27749	-0.748000	0.03510	CTT	G|0.360;N|0.000	0.360	strong		0.393	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
SOHLH2	54937	hgsc.bcm.edu	37	13	36744910	36744910	+	Missense_Mutation	SNP	C	C	T	rs2296968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:36744910C>T	ENST00000379881.3	-	10	1103	c.1015G>A	c.(1015-1017)Gcc>Acc	p.A339T	CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.A416T|SOHLH2_ENST00000554962.1_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	102	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	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	
PODXL2	50512	hgsc.bcm.edu	37	3	127379270	127379270	+	Silent	SNP	C	C	T	rs920232	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	91	0	0		WXS	Illumina HiSeq	Phase_I	140	86	0.614286	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	
OR52I2	143502	hgsc.bcm.edu	37	11	4608116	4608116	+	Missense_Mutation	SNP	T	T	C	rs7128702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4608116T>C	ENST00000312614.4	+	1	96	c.74T>C	c.(73-75)cTt>cCt	p.L25P		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	25			L -> P (in dbSNP:rs7128702).			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(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAAGTCTCACTTGTGATGCTG	0.448													C|||	537	0.107228	0.3071	0.0778	5008	,	,		23320	0.0		0.0547	False		,,,				2504	0.0225				p.L25P		Atlas-SNP	.											.	OR52I2	50	.	0			c.T74C						PASS	.	C	PRO/LEU	1132,3270	715.2+/-408.4	161,810,1230	128.0	119.0	122.0		74	-3.2	0.0	11	dbSNP_116	122	559,8037	793.7+/-407.5	27,505,3766	yes	missense	OR52I2	NM_001005170.2	98	188,1315,4996	CC,CT,TT		6.503,25.7156,13.0097	benign	25/351	4608116	1691,11307	2201	4298	6499	SO:0001583	missense	143502	exon1			TCTCACTTGTGAT	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.74T>C	11.37:g.4608116T>C	ENSP00000308764:p.Leu25Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Missense_Mutation	SNP	ENST00000312614.4	37	CCDS31355.1	257	0.11767399267399267	183	0.3719512195121951	35	0.09668508287292818	0	0.0	39	0.051451187335092345	C	2.509	-0.313477	0.05422	0.257156	0.06503	ENSG00000226288	ENST00000312614	T	0.00623	6.15	3.96	-3.25	0.05079	.	1.052770	0.07667	N	0.934846	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	0.13872	-1.0493	9	0.30854	T	0.27	-4.0E-4	7.3368	0.26615	0.112:0.3516:0.0:0.5364	rs7128702;rs56514321;rs59244112;rs7128702	25	Q8NH67	O52I2_HUMAN	P	25	ENSP00000308764:L25P	ENSP00000308764:L25P	L	+	2	0	OR52I2	4564692	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.813000	0.04491	-0.962000	0.03604	-3.310000	0.00045	CTT	T|0.870;C|0.130	0.130	strong		0.448	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
ZNF853	54753	hgsc.bcm.edu	37	7	6661256	6661256	+	Missense_Mutation	SNP	C	C	G	rs11971880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6661256C>G	ENST00000457543.3	+	3	1192	c.634C>G	c.(634-636)Cag>Gag	p.Q212E		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	212	Gln-rich.		Q -> E (in dbSNP:rs11971880).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						ggaacagttacagcagcagca	0.512													C|||	493	0.0984425	0.1558	0.0994	5008	,	,		25510	0.0546		0.0855	False		,,,				2504	0.0787				p.Q212E		Atlas-SNP	.											.	ZNF853	32	.	0			c.C634G						PASS	.	C	GLU/GLN	212,1172		17,178,497	85.0	95.0	92.0		634	3.0	0.0	7	dbSNP_120	92	322,2860		12,298,1281	yes	missense	ZNF853	NM_017560.1	29	29,476,1778	GG,GC,CC		10.1194,15.3179,11.6951	probably-damaging	212/660	6661256	534,4032	692	1591	2283	SO:0001583	missense	54753	exon3			CAGTTACAGCAGC	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.634C>G	7.37:g.6661256C>G	ENSP00000455585:p.Gln212Glu	Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	267	184	0.689139	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			C|0.905;G|0.095	0.095	strong		0.512	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
OSBPL3	26031	hgsc.bcm.edu	37	7	24903139	24903139	+	Silent	SNP	C	C	T	rs17851558	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:24903139C>T	ENST00000313367.2	-	8	1204	c.753G>A	c.(751-753)tcG>tcA	p.S251S	OSBPL3_ENST00000431825.2_Silent_p.S251S|OSBPL3_ENST00000352860.1_Silent_p.S251S|OSBPL3_ENST00000396431.1_Silent_p.S251S|OSBPL3_ENST00000409069.1_Silent_p.S251S|OSBPL3_ENST00000396429.1_Silent_p.S251S|OSBPL3_ENST00000353930.1_Silent_p.S251S	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	251					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TAGCTGGTGCCGAGTATGTCC	0.552													C|||	140	0.0279553	0.0068	0.0331	5008	,	,		21168	0.0		0.0915	False		,,,				2504	0.0164				p.S251S		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G753A						PASS	.	C	,,,	84,4322	73.1+/-111.1	0,84,2119	204.0	173.0	184.0		753,753,753,753	-7.6	0.8	7	dbSNP_123	184	843,7757	193.0+/-238.8	41,761,3498	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL3	NM_015550.2,NM_145320.1,NM_145321.1,NM_145322.1	,,,	41,845,5617	TT,TC,CC		9.8023,1.9065,7.1275	,,,	251/888,251/857,251/852,251/821	24903139	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	26031	exon8			TGGTGCCGAGTAT	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.753G>A	7.37:g.24903139C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	167	115	0.688623	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	37	CCDS5390.1																																																																																			C|0.940;T|0.060	0.060	strong		0.552	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
ZNF705A	440077	hgsc.bcm.edu	37	12	8329700	8329700	+	Missense_Mutation	SNP	A	A	C	rs10743253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	190	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	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	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604430	80604430	+	Silent	SNP	C	C	T	rs1055383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:80604430C>T	ENST00000254037.2	+	2	3590	c.435C>T	c.(433-435)gcC>gcT	p.A145A	ZCCHC9_ENST00000438268.2_Silent_p.A145A|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Silent_p.A145A|ZCCHC9_ENST00000380199.5_Silent_p.A145A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	145					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		ATTGCCCCGCCGCCCTTGAAA	0.478													C|||	694	0.138578	0.0991	0.304	5008	,	,		14056	0.0149		0.1849	False		,,,				2504	0.1544				p.A145A		Atlas-SNP	.											ZCCHC9,caecum,carcinoma,+1,1	ZCCHC9	26	1	0			c.C435T						PASS	.	C	,,	499,3907	230.7+/-244.8	30,439,1734	85.0	86.0	86.0		435,435,435	-7.0	0.6	5	dbSNP_86	86	1694,6906	310.6+/-310.0	180,1334,2786	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	,,	210,1773,4520	TT,TC,CC		19.6977,11.3255,16.8614	,,	145/272,145/272,145/272	80604430	2193,10813	2203	4300	6503	SO:0001819	synonymous_variant	84240	exon3			CCCCGCCGCCCTT	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.435C>T	5.37:g.80604430C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			C|0.842;T|0.158	0.158	strong		0.478	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
FAM208B	54906	hgsc.bcm.edu	37	10	5784151	5784151	+	Missense_Mutation	SNP	A	A	G	rs45575338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5784151A>G	ENST00000328090.5	+	14	3044	c.2419A>G	c.(2419-2421)Atc>Gtc	p.I807V	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	807			I -> V (in dbSNP:rs45575338).														TCAGAACAAAATCATACGATC	0.398													G|||	704	0.140575	0.0719	0.2378	5008	,	,		18896	0.1498		0.1909	False		,,,				2504	0.1033				p.I807V		Atlas-SNP	.											C10orf18,NS,carcinoma,-2,1	.	.	1	0			c.A2419G						scavenged	.	G	VAL/ILE	281,3451		10,261,1595	125.0	114.0	117.0		2419	4.7	0.1	10	dbSNP_127	117	1714,6484		184,1346,2569	yes	missense	FAM208B	NM_017782.4	29	194,1607,4164	GG,GA,AA		20.9075,7.5295,16.7225	benign	807/2431	5784151	1995,9935	1866	4099	5965	SO:0001583	missense	54906	exon14			AACAAAATCATAC	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.2419A>G	10.37:g.5784151A>G	ENSP00000328426:p.Ile807Val	Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	376	0.17216117216117216	38	0.07723577235772358	91	0.2513812154696133	101	0.17657342657342656	146	0.19261213720316622	G	0.530	-0.858420	0.02610	0.075295	0.209075	ENSG00000108021	ENST00000328090	T	0.03524	3.9	5.57	4.66	0.58398	.	0.229969	0.30538	N	0.009413	T	0.00012	0.0000	N	0.00088	-2.19	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38178	-0.9673	9	0.02654	T	1	.	4.2655	0.10761	0.1442:0.1241:0.6039:0.1278	rs45575338	807	Q5VWN6	F208B_HUMAN	V	807	ENSP00000328426:I807V	ENSP00000328426:I807V	I	+	1	0	C10orf18	5824157	0.152000	0.22762	0.139000	0.22197	0.842000	0.47809	0.156000	0.16382	0.718000	0.32166	-0.119000	0.15052	ATC	A|0.816;G|0.184	0.184	strong		0.398	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
ASB7	140460	hgsc.bcm.edu	37	15	101169694	101169694	+	Silent	SNP	A	A	G	rs61752833	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:101169694A>G	ENST00000332783.7	+	5	1049	c.264A>G	c.(262-264)gcA>gcG	p.A88A	ASB7_ENST00000343276.4_Silent_p.A88A|ASB7_ENST00000558747.1_Intron	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	88					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			TTCACTATGCAGCCATGCATG	0.468													A|||	67	0.0133786	0.0008	0.0187	5008	,	,		20273	0.0		0.0398	False		,,,				2504	0.0133				p.A88A		Atlas-SNP	.											.	ASB7	32	.	0			c.A264G						PASS	.	A	,	33,4373	38.4+/-70.7	0,33,2170	57.0	58.0	57.0		264,264	-1.8	1.0	15	dbSNP_129	57	281,8319	104.0+/-165.0	6,269,4025	no	coding-synonymous,coding-synonymous	ASB7	NM_024708.3,NM_198243.2	,	6,302,6195	GG,GA,AA		3.2674,0.749,2.4143	,	88/275,88/319	101169694	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	140460	exon5			CTATGCAGCCATG		CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"""Ankyrin repeat domain containing"""	17182	protein-coding gene	gene with protein product		615052	"""ankyrin repeat and SOCS box-containing 7"""				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.264A>G	15.37:g.101169694A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_024708	A8K1E5|Q6GSJ6|Q7Z4S3	Silent	SNP	ENST00000332783.7	37	CCDS10387.1																																																																																			A|0.978;G|0.022	0.022	strong		0.468	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708	
FSCB	84075	hgsc.bcm.edu	37	14	44974922	44974922	+	Missense_Mutation	SNP	A	A	T	rs3825632	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:44974922A>T	ENST00000340446.4	-	1	1560	c.1269T>A	c.(1267-1269)gaT>gaA	p.D423E	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	423			D -> E (in dbSNP:rs3825632). {ECO:0000269|PubMed:11230166}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GAGGCTGAACATCAGCAAGGG	0.517													T|||	2204	0.440096	0.4735	0.3977	5008	,	,		17653	0.3869		0.4553	False		,,,				2504	0.4642				p.D423E		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.T1269A						PASS	.	T	GLU/ASP	1907,2453		439,1029,712	27.0	29.0	29.0		1269	-1.9	0.0	14	dbSNP_107	29	4026,4554		996,2034,1260	yes	missense	FSCB	NM_032135.3	45	1435,3063,1972	TT,TA,AA		46.9231,43.7385,45.8501	benign	423/826	44974922	5933,7007	2180	4290	6470	SO:0001583	missense	84075	exon1			CTGAACATCAGCA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1269T>A	14.37:g.44974922A>T	ENSP00000344579:p.Asp423Glu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	944	0.43223443223443225	222	0.45121951219512196	136	0.3756906077348066	241	0.42132867132867136	345	0.4551451187335092	T	1.412	-0.575357	0.03882	0.437385	0.469231	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.11712	2.75	4.67	-1.88	0.07713	.	.	.	.	.	T	0.00012	0.0000	N	0.00152	-1.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	8	0.02654	T	1	1.2389	0.638	0.00806	0.3943:0.2492:0.135:0.2216	rs3825632;rs3825632	423	Q5H9T9	FSCB_HUMAN	E	423	ENSP00000344579:D423E	ENSP00000344579:D423E	D	-	3	2	FSCB	44044672	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-2.011000	0.01452	-0.509000	0.06532	-1.179000	0.01719	GAT	A|0.560;T|0.440	0.440	strong		0.517	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
PPIE	10450	hgsc.bcm.edu	37	1	40207580	40207580	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:40207580C>T	ENST00000324379.5	+	4	207	c.188C>T	c.(187-189)gCt>gTt	p.A63V	PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000372830.1_Missense_Mutation_p.A63V|PPIE_ENST00000470213.1_Missense_Mutation_p.A63V|PPIE_ENST00000356511.2_Missense_Mutation_p.A63V	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	63	Poly-Ala.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-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;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCTGCAGCAGCTATCGACAAC	0.423																																					p.A63V		Atlas-SNP	.											.	PPIE	33	.	0			c.C188T						PASS	.						146.0	146.0	146.0					1																	40207580		2203	4300	6503	SO:0001583	missense	10450	exon4			CAGCAGCTATCGA	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"""RNA binding motif (RRM) containing"""	9258	protein-coding gene	gene with protein product	"""peptidyl-prolyl cis-trans isomerase E"", ""cyclophilin 33"", ""cyclophilin E"", ""PPIase E"", ""rotamase E"", ""peptidylprolyl isomerase E, isoform 1"""	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.188C>T	1.37:g.40207580C>T	ENSP00000312769:p.Ala63Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	182	81	0.445055	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	37	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255577	0.95336	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000470213;ENST00000372830	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.7	4.7	0.59300	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.93716	0.7992	M	0.84082	2.675	0.80722	D	1	D;D;D	0.76494	0.999;0.971;0.995	D;P;D	0.74023	0.982;0.783;0.951	D	0.94503	0.7711	10	0.87932	D	0	-15.1861	17.7685	0.88485	0.0:1.0:0.0:0.0	.	63;63;63	Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;PPIE_HUMAN	V	63	ENSP00000312769:A63V;ENSP00000348904:A63V;ENSP00000431714:A63V;ENSP00000361918:A63V	ENSP00000312769:A63V	A	+	2	0	PPIE	39980167	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.808000	0.75206	2.619000	0.88677	0.561000	0.74099	GCT	.	.	none		0.423	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112	
SON	6651	hgsc.bcm.edu	37	21	34925689	34925689	+	Silent	SNP	G	G	A	rs61739710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000381679.4_Silent_p.L1384L|SON_ENST00000290239.6_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	151	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	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	
MUC16	94025	hgsc.bcm.edu	37	19	9075584	9075584	+	Silent	SNP	T	T	A	rs2547069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9075584T>A	ENST00000397910.4	-	3	12065	c.11862A>T	c.(11860-11862)acA>acT	p.T3954T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3956	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.T3954T(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						TGACCCAGCCTGTGGTCTCTA	0.512													T|||	1054	0.210463	0.0628	0.2046	5008	,	,		20855	0.249		0.3101	False		,,,				2504	0.272				p.T3954T		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.A11862T						PASS	.	T		409,3615		23,363,1626	70.0	67.0	68.0		11862	-4.2	0.0	19	dbSNP_100	68	2400,5928		340,1720,2104	no	coding-synonymous	MUC16	NM_024690.2		363,2083,3730	AA,AT,TT		28.8184,10.164,22.7413		3954/14508	9075584	2809,9543	2012	4164	6176	SO:0001819	synonymous_variant	94025	exon3			CCAGCCTGTGGTC	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.11862A>T	19.37:g.9075584T>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	304	159	0.523026	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.771;A|0.229	0.229	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DCDC2	51473	hgsc.bcm.edu	37	6	24205236	24205236	+	Silent	SNP	G	G	A	rs9467075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24205236G>A	ENST00000378454.3	-	8	1318	c.1017C>T	c.(1015-1017)gtC>gtT	p.V339V	DCDC2_ENST00000378450.3_Silent_p.V92V	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	339					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TTACCTGATCGACTGGAACCT	0.398													G|||	583	0.116414	0.1218	0.1182	5008	,	,		19059	0.0417		0.1451	False		,,,				2504	0.1554				p.V339V		Atlas-SNP	.											.	DCDC2	53	.	0			c.C1017T						PASS	.	G	,	632,3774	275.2+/-272.4	41,550,1612	238.0	220.0	226.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1017,1017	-12.1	0.0	6	dbSNP_119	226	1276,7322	253.2+/-279.0	99,1078,3122	no	coding-synonymous,coding-synonymous	DCDC2	NM_001195610.1,NM_016356.3	,	140,1628,4734	AA,AG,GG		14.8407,14.3441,14.6724	,	339/477,339/477	24205236	1908,11096	2203	4299	6502	SO:0001819	synonymous_variant	51473	exon9			CTGATCGACTGGA	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.1017C>T	6.37:g.24205236G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1																																																																																			G|0.867;A|0.133	0.133	strong		0.398	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
PMS2	5395	hgsc.bcm.edu	37	7	6043386	6043386	+	Silent	SNP	G	G	A	rs12532895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6043386G>A	ENST00000265849.7	-	4	393	c.288C>T	c.(286-288)gcC>gcT	p.A96A	PMS2_ENST00000441476.2_Intron|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Silent_p.A96A|Y_RNA_ENST00000365120.1_RNA|PMS2_ENST00000406569.3_Silent_p.A96A	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	96					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)		GAGTTAGGTCGGCAAACTCTT	0.403			"""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|||	569	0.113618	0.0113	0.0504	5008	,	,		16647	0.3284		0.0338	False		,,,				2504	0.1575				p.A96A		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.C288T						PASS	.	G		54,2794		0,54,1370	55.0	63.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	288	-1.1	1.0	7	dbSNP_120	60	136,4768		0,136,2316	no	coding-synonymous	PMS2	NM_000535.5		0,190,3686	AA,AG,GG		2.7732,1.8961,2.451		96/863	6043386	190,7562	1424	2452	3876	SO:0001819	synonymous_variant	5395	exon4	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	TAGGTCGGCAAAC		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.288C>T	7.37:g.6043386G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																			G|0.942;A|0.058	0.058	strong		0.403	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
PKD1L2	114780	hgsc.bcm.edu	37	16	81219187	81219187	+	RNA	SNP	C	C	T	rs13339342	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81219187C>T	ENST00000525539.1	-	0	1906				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						AACAGCCAGGCGCAGGGTGAC	0.642													c|||	762	0.152157	0.1309	0.1585	5008	,	,		16480	0.0417		0.168	False		,,,				2504	0.274				p.R636H		Atlas-SNP	.											PKD1L2_ENST00000525539,NS,carcinoma,-1,2	PKD1L2	361	2	0			c.G1907A						PASS	.	T	HIS/ARG,HIS/ARG	551,3597		37,477,1560	35.0	45.0	42.0		1907,1907	-9.7	0.0	16	dbSNP_121	42	1377,7047		113,1151,2948	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	150,1628,4508	TT,TC,CC		16.3462,13.2835,15.3357	benign,benign	636/992,636/2460	81219187	1928,10644	2074	4212	6286			114780	exon11			GCCAGGCGCAGGG	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.81219187C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		264	0.12087912087912088	62	0.12601626016260162	56	0.15469613259668508	23	0.04020979020979021	123	0.16226912928759896	c	8.903	0.956878	0.18507	0.132835	0.163462	ENSG00000166473	ENST00000337114	T	0.70749	-0.51	4.83	-9.66	0.00534	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.252640	0.05331	N	0.528415	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	B;B	0.23316	0.011;0.083	B;B	0.22386	0.007;0.039	T	0.01839	-1.1263	8	0.20046	T	0.44	-3.9833	9.6762	0.40043	0.0:0.2218:0.185:0.5933	rs13339342;rs52836229;rs13339342	636;636	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	H	636	ENSP00000337397:R636H	ENSP00000337397:R636H	R	-	2	0	PKD1L2	79776688	0.000000	0.05858	0.014000	0.15608	0.622000	0.37654	-1.453000	0.02383	-1.677000	0.01455	-0.229000	0.12294	CGC	C|0.865;T|0.135	0.135	strong		0.642	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
LRIT2	340745	hgsc.bcm.edu	37	10	85984423	85984423	+	Silent	SNP	C	C	T	rs11200926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85984423C>T	ENST00000372113.4	-	2	563	c.558G>A	c.(556-558)ggG>ggA	p.G186G	LRIT2_ENST00000538192.1_Silent_p.G186G	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	186						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						GAATCTCAGCCCCACAGTCAG	0.547													C|||	1041	0.207867	0.0522	0.2911	5008	,	,		19595	0.3452		0.2346	False		,,,				2504	0.1902				p.G186G		Atlas-SNP	.											.	LRIT2	81	.	0			c.G558A						PASS	.	C		386,4020	195.3+/-220.0	12,362,1829	56.0	53.0	54.0		558	0.7	0.0	10	dbSNP_120	54	1936,6664	340.4+/-323.6	199,1538,2563	no	coding-synonymous	LRIT2	NM_001017924.2		211,1900,4392	TT,TC,CC		22.5116,8.7608,17.8533		186/551	85984423	2322,10684	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon2			CTCAGCCCCACAG		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.558G>A	10.37:g.85984423C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			C|0.806;T|0.194	0.194	strong		0.547	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
NUP54	53371	hgsc.bcm.edu	37	4	77065580	77065580	+	Silent	SNP	T	T	C	rs11558469	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77065580T>C	ENST00000264883.3	-	2	254	c.114A>G	c.(112-114)gcA>gcG	p.A38A	NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000514987.1_Silent_p.A38A|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	38	9 X 2 AA repeats of F-G.|Gly-rich.|Thr-rich.				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 targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.A38A(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						AAAAGCTGAATGCAGAACCTG	0.358													t|||	776	0.154952	0.0567	0.1282	5008	,	,		16392	0.3512		0.1312	False		,,,				2504	0.1288				p.A38A		Atlas-SNP	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A114G						scavenged	.	C		308,4098	166.2+/-197.5	15,278,1910	91.0	89.0	90.0		114	-8.4	0.8	4	dbSNP_120	90	1299,7301	257.2+/-281.3	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	CC,CT,TT		15.1047,6.9905,12.3558		38/508	77065580	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon2			GCTGAATGCAGAA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.114A>G	4.37:g.77065580T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			T|0.865;C|0.135	0.135	strong		0.358	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
PCDHB15	56121	hgsc.bcm.edu	37	5	140626790	140626790	+	Silent	SNP	A	A	C	rs3096082	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140626790A>C	ENST00000231173.3	+	1	1644	c.1644A>C	c.(1642-1644)cgA>cgC	p.R548R		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	548	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)			CGCTGGTGCGAGTGCTGGTGC	0.711													a|||	1006	0.200879	0.3797	0.1441	5008	,	,		15407	0.0913		0.1571	False		,,,				2504	0.1575				p.R548R		Atlas-SNP	.											.	PCDHB15	138	.	0			c.A1644C						PASS	.						32.0	40.0	38.0					5																	140626790		2200	4296	6496	SO:0001819	synonymous_variant	56121	exon1			GGTGCGAGTGCTG	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.1644A>C	5.37:g.140626790A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			A|0.846;C|0.154	0.154	strong		0.711	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
NLRP1	22861	hgsc.bcm.edu	37	17	5485367	5485367	+	Missense_Mutation	SNP	A	A	T	rs12150220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:5485367A>T	ENST00000572272.1	-	3	463	c.464T>A	c.(463-465)cTc>cAc	p.L155H	NLRP1_ENST00000269280.4_Missense_Mutation_p.L155H|NLRP1_ENST00000345221.3_Missense_Mutation_p.L155H|NLRP1_ENST00000577119.1_Missense_Mutation_p.L155H|NLRP1_ENST00000262467.5_Missense_Mutation_p.L155H|NLRP1_ENST00000354411.3_Missense_Mutation_p.L155H|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	155			L -> H (associated with susceptibility to vitiligo and vitiligo-associated autoimmune diseases; dbSNP:rs12150220). {ECO:0000269|PubMed:11270363, ECO:0000269|PubMed:17377159}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.L155H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTGGTAGAGGAGTGAGGCAGA	0.478													A|||	962	0.192093	0.034	0.3674	5008	,	,		18435	0.0308		0.4443	False		,,,				2504	0.1881				p.L155H		Atlas-SNP	.											NLRP1,NS,carcinoma,0,1	NLRP1	358	1	1	Substitution - Missense(1)	prostate(1)	c.T464A	GRCh37	CM074383	NLRP1	M	rs12150220	PASS	.	A	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	437,3969	204.8+/-226.9	24,389,1790	34.0	37.0	36.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	464,464,464,464,464	-1.1	0.0	17	dbSNP_120	36	3884,4716	530.3+/-381.8	877,2130,1293	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	99,99,99,99,99	901,2519,3083	TT,TA,AA		45.1628,9.9183,33.2231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	155/1376,155/1430,155/1474,155/1444,155/1400	5485367	4321,8685	2203	4300	6503	SO:0001583	missense	22861	exon3			TAGAGGAGTGAGG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.464T>A	17.37:g.5485367A>T	ENSP00000460475:p.Leu155His	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	504	0.23076923076923078	20	0.04065040650406504	131	0.36187845303867405	19	0.033216783216783216	334	0.44063324538258575	A	11.80	1.745635	0.30955	0.099183	0.451628	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	2.85	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;D;D;D;D	0.69078	0.997;0.997;0.994;0.997;0.994	P;P;P;P;P	0.57548	0.823;0.823;0.669;0.823;0.669	T	0.37197	-0.9716	8	0.41790	T	0.15	.	0.4436	0.00490	0.4246:0.2228:0.1358:0.2168	rs12150220;rs52798470;rs12150220	155;155;155;155;155	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	H	155	ENSP00000442029:L155H;ENSP00000262467:L155H;ENSP00000269280:L155H;ENSP00000346390:L155H;ENSP00000324366:L155H	ENSP00000262467:L155H	L	-	2	0	NLRP1	5426091	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.072000	0.03434	-0.277000	0.09193	0.459000	0.35465	CTC	A|0.737;T|0.263	0.263	strong		0.478	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
FAT1	2195	hgsc.bcm.edu	37	4	187630590	187630590	+	Missense_Mutation	SNP	G	G	A	rs3733415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187630590G>A	ENST00000441802.2	-	2	601	c.392C>T	c.(391-393)gCg>gTg	p.A131V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	131	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> V (in dbSNP:rs3733415).		actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTTTGTTCGCGCCTCCACATT	0.408										HNSCC(5;0.00058)			G|||	1309	0.261382	0.3994	0.1239	5008	,	,		20463	0.2768		0.1302	False		,,,				2504	0.2914				p.A131V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C392T						PASS	.	G	VAL/ALA	1402,2736		250,902,917	144.0	149.0	147.0		392	5.2	0.8	4	dbSNP_107	147	1171,7263		85,1001,3131	yes	missense	FAT1	NM_005245.3	64	335,1903,4048	AA,AG,GG		13.8843,33.8811,20.4661	possibly-damaging	131/4589	187630590	2573,9999	2069	4217	6286	SO:0001583	missense	2195	exon2			GTTCGCGCCTCCA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.392C>T	4.37:g.187630590G>A	ENSP00000406229:p.Ala131Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	484	0.2216117216117216	180	0.36585365853658536	53	0.1464088397790055	158	0.2762237762237762	93	0.12269129287598944	G	14.53	2.563244	0.45694	0.338811	0.138843	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.60171	0.21;0.21	5.2	5.2	0.72013	Cadherin (3);Cadherin-like (1);	0.241563	0.39985	N	0.001215	T	0.00012	0.0000	M	0.78801	2.425	0.23555	P	0.99742699	P	0.48016	0.904	B	0.38428	0.273	T	0.24368	-1.0162	9	0.72032	D	0.01	.	18.5053	0.90894	0.0:0.0:1.0:0.0	rs3733415;rs17692796;rs52790898;rs61279118;rs3733415	131	Q14517	FAT1_HUMAN	V	131	ENSP00000406229:A131V;ENSP00000423736:A131V	ENSP00000260147:A131V	A	-	2	0	FAT1	187867584	1.000000	0.71417	0.783000	0.31826	0.257000	0.26127	6.182000	0.71995	2.704000	0.92352	0.591000	0.81541	GCG	G|0.762;A|0.238	0.238	strong		0.408	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869396	36869396	+	Silent	SNP	G	G	A	rs41282822	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36869396G>A	ENST00000279024.4	-	3	1408	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	379										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGTCCAGTGCGTCCTCAAGGA	0.547													G|||	161	0.0321486	0.0741	0.0231	5008	,	,		17811	0.002		0.0209	False		,,,				2504	0.0245				p.D379D		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1137T						PASS	.	G		328,4078	166.2+/-197.5	13,302,1888	112.0	118.0	116.0		1137	-0.8	0.0	20	dbSNP_127	116	215,8385	88.4+/-150.7	4,207,4089	no	coding-synonymous	KIAA1755	NM_001029864.1		17,509,5977	AA,AG,GG		2.5,7.4444,4.175		379/1201	36869396	543,12463	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CAGTGCGTCCTCA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1137C>T	20.37:g.36869396G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.961;A|0.039	0.039	strong		0.547	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
ZNF229	7772	hgsc.bcm.edu	37	19	44932972	44932972	+	Missense_Mutation	SNP	C	C	T	rs1434579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44932972C>T	ENST00000588931.1	-	6	2417	c.1984G>A	c.(1984-1986)Gga>Aga	p.G662R	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.G656R|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	662			G -> R (in dbSNP:rs1434579). {ECO:0000269|Ref.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)|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)				AAGCCCTTTCCGCACTCTTGG	0.493													C|||	1442	0.287939	0.0484	0.2608	5008	,	,		22657	0.3294		0.3598	False		,,,				2504	0.5143				p.G662R		Atlas-SNP	.											ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	0			c.G1984A						PASS	.	C	ARG/GLY	393,3919		20,353,1783	126.0	127.0	127.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1984	3.5	0.0	19	dbSNP_88	127	2912,5640		507,1898,1871	yes	missense	ZNF229	NM_014518.2	125	527,2251,3654	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.0505,9.1141,25.6919	probably-damaging	662/826	44932972	3305,9559	2156	4276	6432	SO:0001583	missense	7772	exon6			CCTTTCCGCACTC	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.1984G>A	19.37:g.44932972C>T	ENSP00000466519:p.Gly662Arg	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	570	0.260989010989011	20	0.04065040650406504	94	0.2596685082872928	182	0.3181818181818182	274	0.36147757255936674	C	22.8	4.337383	0.81911	0.091141	0.340505	ENSG00000167383	ENST00000291187	.	.	.	3.5	3.5	0.40072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.81497	2.545	0.26784	P	0.969539	D	0.89917	1.0	D	0.67231	0.95	T	0.04005	-1.0985	7	0.59425	D	0.04	.	14.1802	0.65568	0.0:1.0:0.0:0.0	rs1434579;rs17347602;rs52817635;rs59210988;rs1434579	662	Q9UJW7	ZN229_HUMAN	R	662	.	ENSP00000291187:G662R	G	-	1	0	ZNF229	49624812	0.197000	0.23362	0.030000	0.17652	0.143000	0.21401	1.720000	0.38022	1.677000	0.50941	0.609000	0.83330	GGA	C|0.728;T|0.272	0.272	strong		0.493	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
SLC5A12	159963	hgsc.bcm.edu	37	11	26705310	26705310	+	Silent	SNP	A	A	G	rs3924551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:26705310A>G	ENST00000396005.3	-	11	1611	c.1302T>C	c.(1300-1302)aaT>aaC	p.N434N		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	434					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TTACCTTCCAATTCACAAAAG	0.512													G|||	2179	0.435104	0.3185	0.3689	5008	,	,		17943	0.3472		0.6342	False		,,,				2504	0.5256				p.N434N		Atlas-SNP	.											SLC5A12,NS,carcinoma,0,1	SLC5A12	134	1	0			c.T1302C						PASS	.	G		1423,2351		277,869,741	61.0	58.0	59.0		1302	5.6	1.0	11	dbSNP_108	59	5099,3155		1582,1935,610	no	coding-synonymous	SLC5A12	NM_178498.3		1859,2804,1351	GG,GA,AA		38.2239,37.7054,45.7765		434/619	26705310	6522,5506	1887	4127	6014	SO:0001819	synonymous_variant	159963	exon11			CTTCCAATTCACA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1302T>C	11.37:g.26705310A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			A|0.542;G|0.458	0.458	strong		0.512	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
SEC16B	89866	hgsc.bcm.edu	37	1	177902753	177902753	+	Missense_Mutation	SNP	G	G	C	rs591120	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177902753G>C	ENST00000308284.6	-	21	2679	c.2590C>G	c.(2590-2592)Cca>Gca	p.P864A	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	864			P -> A (in dbSNP:rs591120). {ECO:0000269|PubMed:17974005}.		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						ATACTTCGTGGTCTAGCAGCC	0.468													C|||	2048	0.408946	0.4644	0.4409	5008	,	,		20099	0.2808		0.4463	False		,,,				2504	0.4049				p.P864A		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2590G						PASS	.	C	ALA/PRO	1777,2067		402,973,547	56.0	57.0	57.0		2590	2.7	0.0	1	dbSNP_83	57	3541,4735		771,1999,1368	yes	missense	SEC16B	NM_033127.2	27	1173,2972,1915	CC,CG,GG		42.7864,46.2279,43.8779	benign	864/1061	177902753	5318,6802	1922	4138	6060	SO:0001583	missense	89866	exon21			TTCGTGGTCTAGC	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.2590C>G	1.37:g.177902753G>C	ENSP00000308339:p.Pro864Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	29	0.295918	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	899	0.4116300366300366	215	0.4369918699186992	144	0.39779005524861877	199	0.3479020979020979	341	0.449868073878628	C	7.408	0.634161	0.14322	0.462279	0.427864	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.12039	2.72	5.65	2.73	0.32206	.	0.628825	0.15398	N	0.264476	T	0.00012	0.0000	N	0.00246	-1.78	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	0.43196	-0.9406	9	0.06236	T	0.91	0.5442	4.338	0.11095	0.1591:0.4825:0.2788:0.0796	rs591120;rs3813650;rs17360447;rs52790094;rs591120	419;865;864	B1AM07;B1AM08;Q96JE7	.;.;SC16B_HUMAN	A	864;548;579	ENSP00000308339:P864A	ENSP00000239472:P579A	P	-	1	0	AL359075.1	176169376	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.320000	0.08028	0.052000	0.16007	-0.120000	0.15030	CCA	G|0.588;C|0.412	0.412	strong		0.468	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
SWAP70	23075	hgsc.bcm.edu	37	11	9749645	9749645	+	Silent	SNP	A	A	C	rs397686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9749645A>C	ENST00000318950.6	+	5	791	c.688A>C	c.(688-690)Aga>Cga	p.R230R	SWAP70_ENST00000447399.2_Silent_p.R172R	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	230	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		R -> G (in dbSNP:rs397686).		isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		CTGGACTGAAAGATGGTTTGT	0.348													C|||	1295	0.258586	0.3306	0.183	5008	,	,		19581	0.1726		0.3211	False		,,,				2504	0.2393				p.R230R		Atlas-SNP	.											.	SWAP70	40	.	0			c.A688C						PASS	.	C		1479,2923	678.1+/-403.5	243,993,965	131.0	128.0	129.0		688	6.0	1.0	11	dbSNP_80	129	3002,5586	665.0+/-402.2	516,1970,1808	no	coding-synonymous	SWAP70	NM_015055.2		759,2963,2773	CC,CA,AA		34.9558,33.5984,34.4958		230/586	9749645	4481,8509	2201	4294	6495	SO:0001819	synonymous_variant	23075	exon5			ACTGAAAGATGGT	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.688A>C	11.37:g.9749645A>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Silent	SNP	ENST00000318950.6	37	CCDS31426.1																																																																																			C|0.309;A|0.691	0.309	strong		0.348	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
SIRT1	23411	hgsc.bcm.edu	37	10	69666598	69666598	+	Silent	SNP	T	T	C	rs2273773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69666598T>C	ENST00000212015.6	+	5	1047	c.994T>C	c.(994-996)Ttg>Ctg	p.L332L	SIRT1_ENST00000432464.1_Silent_p.L37L|SIRT1_ENST00000403579.1_Silent_p.L29L|SIRT1_ENST00000406900.1_Silent_p.L29L	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	332	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ATTCATAGCCTTGTCAGATAA	0.383													T|||	637	0.127196	0.0204	0.1297	5008	,	,		16893	0.3115		0.0755	False		,,,				2504	0.1329				p.L332L		Atlas-SNP	.											.	SIRT1	38	.	0			c.T994C						PASS	.	T	,	134,4272	95.7+/-134.4	1,132,2070	88.0	87.0	87.0		109,994	5.3	1.0	10	dbSNP_100	87	524,8076	145.7+/-201.4	13,498,3789	no	coding-synonymous,coding-synonymous	SIRT1	NM_001142498.1,NM_012238.4	,	14,630,5859	CC,CT,TT		6.093,3.0413,5.0592	,	37/453,332/748	69666598	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	23411	exon5			ATAGCCTTGTCAG	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.994T>C	10.37:g.69666598T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Silent	SNP	ENST00000212015.6	37	CCDS7273.1																																																																																			T|0.910;C|0.090	0.090	strong		0.383	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
PIGN	23556	hgsc.bcm.edu	37	18	59768375	59768375	+	Silent	SNP	A	A	G	rs17714063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	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	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329652	8329652	+	Missense_Mutation	SNP	A	A	G	rs10743251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	192	0	0		WXS	Illumina HiSeq	Phase_I	181	82	0.453039	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	
PJA2	9867	hgsc.bcm.edu	37	5	108714298	108714298	+	Missense_Mutation	SNP	T	T	C	rs1045706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:108714298T>C	ENST00000361189.2	-	4	1129	c.890A>G	c.(889-891)cAa>cGa	p.Q297R	PJA2_ENST00000511624.1_5'Flank|PJA2_ENST00000361557.3_Missense_Mutation_p.Q297R	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	297			Q -> R (in dbSNP:rs1045706). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.		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)		ATTGGTATTTTGTTCACTACA	0.413													T|||	1607	0.320887	0.0643	0.4712	5008	,	,		22030	0.0565		0.5895	False		,,,				2504	0.5573				p.Q297R		Atlas-SNP	.											.	PJA2	53	.	0			c.A890G						PASS	.	T	ARG/GLN	690,3714	287.8+/-279.5	54,582,1566	139.0	147.0	144.0		890	2.9	1.0	5	dbSNP_86	144	5090,3510	632.9+/-398.7	1512,2066,722	yes	missense	PJA2	NM_014819.4	43	1566,2648,2288	CC,CT,TT		40.814,15.6676,44.4479	possibly-damaging	297/709	108714298	5780,7224	2202	4300	6502	SO:0001583	missense	9867	exon4			GTATTTTGTTCAC	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.890A>G	5.37:g.108714298T>C	ENSP00000354775:p.Gln297Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	685	0.31364468864468864	41	0.08333333333333333	169	0.46685082872928174	25	0.043706293706293704	450	0.5936675461741425	T	0.040	-1.287968	0.01387	0.156676	0.59186	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05513	3.43;3.43	5.61	2.88	0.33553	.	0.384034	0.24922	N	0.034535	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	8.000000000008E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.46105	-0.9215	9	0.07030	T	0.85	-15.05	1.7421	0.02955	0.2484:0.0888:0.1186:0.5443	rs1045706;rs3805437;rs17410526;rs17856899;rs52814571;rs56932049;rs1045706	297	O43164	PJA2_HUMAN	R	297	ENSP00000354775:Q297R;ENSP00000355284:Q297R	ENSP00000354775:Q297R	Q	-	2	0	PJA2	108742197	0.147000	0.22687	0.961000	0.40146	0.108000	0.19459	0.437000	0.21543	1.054000	0.40438	-0.274000	0.10170	CAA	T|0.639;C|0.361	0.361	strong		0.413	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558212	140558212	+	Missense_Mutation	SNP	A	A	C	rs2950845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	431	1	0.00232019		WXS	Illumina HiSeq	Phase_I	295	80	0.271186	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	
CDH8	1006	hgsc.bcm.edu	37	16	61687701	61687701	+	Silent	SNP	C	C	T	rs16963768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:61687701C>T	ENST00000577390.1	-	12	3165	c.2211G>A	c.(2209-2211)acG>acA	p.T737T	CDH8_ENST00000299345.6_Intron|CDH8_ENST00000577730.1_Intron	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	737					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)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATGGCGGGGCCGTGGGATCAT	0.507													T|||	537	0.107228	0.2095	0.1009	5008	,	,		14956	0.0198		0.1262	False		,,,				2504	0.044				p.T737T		Atlas-SNP	.											CDH8,rectum,carcinoma,-1,1	CDH8	273	1	0			c.G2211A						PASS	.	T		882,3524	742.8+/-411.4	89,704,1410	64.0	70.0	68.0		2211	-5.6	0.7	16	dbSNP_123	68	1081,7519	769.3+/-407.6	71,939,3290	no	coding-synonymous	CDH8	NM_001796.4		160,1643,4700	TT,TC,CC		12.5698,20.0182,15.093		737/800	61687701	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	1006	exon12			CGGGGCCGTGGGA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.2211G>A	16.37:g.61687701C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			C|0.868;N|0.000	.	strong		0.507	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
C17orf78	284099	hgsc.bcm.edu	37	17	35743010	35743010	+	Missense_Mutation	SNP	C	C	G	rs1714987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:35743010C>G	ENST00000300618.4	+	4	505	c.455C>G	c.(454-456)aCt>aGt	p.T152S	ACACA_ENST00000353139.5_Intron|ACACA_ENST00000416895.1_Intron|C17orf78_ENST00000586700.1_Intron|RP11-378E13.3_ENST00000592238.1_RNA|ACACA_ENST00000589665.1_5'Flank	NM_173625.3	NP_775896.3	Q8N4C9	CQ078_HUMAN	chromosome 17 open reading frame 78	152			T -> S (in dbSNP:rs1714987). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.T152S(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(1)	6		Breast(25;0.00295)|Ovarian(249;0.15)				TTTCCCACCACTGCCCCTTCT	0.388													C|||	1584	0.316294	0.2526	0.2493	5008	,	,		15541	0.5377		0.1918	False		,,,				2504	0.3497				p.T152S		Atlas-SNP	.											C17orf78,NS,carcinoma,0,1	C17orf78	23	1	1	Substitution - Missense(1)	stomach(1)	c.C455G						PASS	.	C	SER/THR,,	875,2713		118,639,1037	54.0	49.0	51.0		455,,	1.9	0.0	17	dbSNP_89	51	1471,6647		146,1179,2734	yes	missense,intron,intron	ACACA,C17orf78	NM_173625.3,NM_198834.1,NM_198839.1	58,,	264,1818,3771	GG,GC,CC		18.1202,24.3868,20.041	possibly-damaging,,	152/276,,	35743010	2346,9360	1794	4059	5853	SO:0001583	missense	284099	exon4			CCACCACTGCCCC	BC034672	CCDS45655.1	17q12	2014-05-06			ENSG00000167230	ENSG00000278505			26831	protein-coding gene	gene with protein product						14702039	Standard	NM_173625		Approved	FLJ39647	uc002hns.3	Q8N4C9	OTTHUMG00000188467	ENST00000300618.4:c.455C>G	17.37:g.35743010C>G	ENSP00000300618:p.Thr152Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_173625	Q8N8D2	Missense_Mutation	SNP	ENST00000300618.4	37	CCDS45655.1	695	0.3182234432234432	145	0.29471544715447157	91	0.2513812154696133	316	0.5524475524475524	143	0.18865435356200527	C	8.831	0.940004	0.18281	0.243868	0.181202	ENSG00000167230	ENST00000300618	T	0.48201	0.82	4.94	1.87	0.25490	.	0.660665	0.13966	N	0.350483	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.15930	0.015	B	0.16289	0.015	T	0.46775	-0.9167	9	0.26408	T	0.33	-1.6736	7.1964	0.25855	0.0:0.7231:0.0:0.2769	rs1714987;rs17846097;rs17859100;rs52823794;rs57014482;rs1714987	152	Q8N4C9	CQ078_HUMAN	S	152	ENSP00000300618:T152S	ENSP00000300618:T152S	T	+	2	0	C17orf78	32817123	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.114000	0.10757	0.375000	0.24679	0.655000	0.94253	ACT	C|0.700;G|0.300	0.300	strong		0.388	C17orf78-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451570.2	NM_173625	
SPATA25	128497	hgsc.bcm.edu	37	20	44515244	44515244	+	Missense_Mutation	SNP	C	C	T	rs146744825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515244C>T	ENST00000372519.3	-	2	640	c.596G>A	c.(595-597)cGg>cAg	p.R199Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	199					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGCTCCCACCGCGCCCCCTC	0.612													c|||	57	0.0113818	0.0015	0.0764	5008	,	,		16944	0.0		0.002	False		,,,				2504	0.0				p.R199Q		Atlas-SNP	.											.	.	.	.	0			c.G596A						PASS	.	T	GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	65.0	70.0	68.0		596	-5.7	0.0	20	dbSNP_134	68	22,8578	16.6+/-54.9	0,22,4278	yes	missense	C20orf165	NM_080608.3	43	0,35,6468	TT,TC,CC		0.2558,0.2951,0.2691	benign	199/228	44515244	35,12971	2203	4300	6503	SO:0001583	missense	128497	exon2			TCCCACCGCGCCC	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 165"""	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.596G>A	20.37:g.44515244C>T	ENSP00000361597:p.Arg199Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	34	0.015567765567765568	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	1	0.0013192612137203166	c	0.495	-0.873413	0.02570	0.002951	0.002558	ENSG00000149634	ENST00000372519	T	0.40756	1.02	5.55	-5.74	0.02391	.	1.042410	0.07602	N	0.923760	T	0.00754	0.0025	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.33085	-0.9882	10	0.09338	T	0.73	-0.1318	15.7642	0.78114	0.0:0.2044:0.0:0.7956	.	199	Q9BR10	CT165_HUMAN	Q	199	ENSP00000361597:R199Q	ENSP00000361597:R199Q	R	-	2	0	C20orf165	43948651	0.000000	0.05858	0.002000	0.10522	0.099000	0.18886	-1.573000	0.02134	-1.357000	0.02180	-1.552000	0.00895	CGG	C|0.994;T|0.006	0.006	strong		0.612	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581889	84581889	+	Silent	SNP	G	G	A	rs12439867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:84581889G>A	ENST00000286744.5	+	16	1970	c.1746G>A	c.(1744-1746)ccG>ccA	p.P582P	ADAMTSL3_ENST00000567476.1_Silent_p.P582P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	582	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			CGTGTGGGCCGGGTGTGCAGG	0.567													G|||	1935	0.386382	0.4871	0.4914	5008	,	,		17531	0.3294		0.2117	False		,,,				2504	0.4141				p.P582P		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.G1746A						PASS	.	G		1938,2468	547.0+/-377.2	422,1094,687	87.0	81.0	83.0		1746	-9.8	0.0	15	dbSNP_120	83	1812,6788	324.9+/-316.7	184,1444,2672	no	coding-synonymous	ADAMTSL3	NM_207517.2		606,2538,3359	AA,AG,GG		21.0698,43.9855,28.8328		582/1692	84581889	3750,9256	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon16			TGGGCCGGGTGTG	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1746G>A	15.37:g.84581889G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			G|0.688;A|0.312	0.312	strong		0.567	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
TLN1	7094	hgsc.bcm.edu	37	9	35712003	35712003	+	Splice_Site	SNP	G	G	A	rs2295795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35712003G>A	ENST00000314888.9	-	28	4033	c.3680C>T	c.(3679-3681)tCg>tTg	p.S1227L	TLN1_ENST00000540444.1_Splice_Site_p.S1227L	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1227			S -> L (in dbSNP:rs2295795). {ECO:0000269|Ref.1}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTCCTACCGAGTCACTCAG	0.597													G|||	1009	0.201478	0.0197	0.268	5008	,	,		18282	0.3383		0.2704	False		,,,				2504	0.1881				p.S1227L		Atlas-SNP	.											.	TLN1	185	.	0			c.C3680T						PASS	.	G	LEU/SER	280,4126	155.5+/-188.7	14,252,1937	54.0	49.0	51.0		3680	4.9	1.0	9	dbSNP_100	51	2408,6192	398.5+/-346.1	332,1744,2224	yes	missense-near-splice	TLN1	NM_006289.3	145	346,1996,4161	AA,AG,GG		28.0,6.355,20.6674	benign	1227/2542	35712003	2688,10318	2203	4300	6503	SO:0001630	splice_region_variant	7094	exon28			CCTACCGAGTCAC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3681+1C>T	9.37:g.35712003G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	20	15	0.75	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	521	0.23855311355311357	12	0.024390243902439025	100	0.27624309392265195	213	0.3723776223776224	196	0.25857519788918204	G	16.00	2.999336	0.54147	0.06355	0.28	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.12147	2.71;2.71	5.82	4.92	0.64577	.	0.356696	0.30492	N	0.009506	T	0.00012	0.0000	L	0.54323	1.7	0.20403	P	0.9999095468	B	0.09022	0.002	B	0.04013	0.001	T	0.46978	-0.9152	9	0.32370	T	0.25	-0.5518	16.3893	0.83528	0.0:0.0:0.8673:0.1327	rs2295795;rs17260374;rs60567288;rs2295795	1227	Q9Y490	TLN1_HUMAN	L	1227	ENSP00000316029:S1227L;ENSP00000442981:S1227L	ENSP00000316029:S1227L	S	-	2	0	TLN1	35702003	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.695000	0.84257	1.466000	0.48025	-0.169000	0.13324	TCG	G|0.785;A|0.215	0.215	strong		0.597	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation
TMEM161A	54929	hgsc.bcm.edu	37	19	19230816	19230816	+	Missense_Mutation	SNP	T	T	C	rs45467802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19230816T>C	ENST00000162044.9	-	12	1427	c.1363A>G	c.(1363-1365)Atc>Gtc	p.I455V	TMEM161A_ENST00000450333.2_Missense_Mutation_p.I352V|TMEM161A_ENST00000587583.2_Missense_Mutation_p.I430V	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	455				I -> V (in Ref. 2; BAG53402). {ECO:0000305}.	cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GTCCACCAGATGAGGTAGGCC	0.662													T|||	243	0.0485224	0.0477	0.0331	5008	,	,		15175	0.0446		0.0437	False		,,,				2504	0.0695				p.I455V		Atlas-SNP	.											.	TMEM161A	37	.	0			c.A1363G						PASS	.	T	VAL/ILE	231,4151		4,223,1964	20.0	21.0	20.0		1363	3.5	1.0	19	dbSNP_127	20	406,8160		11,384,3888	yes	missense	TMEM161A	NM_017814.1	29	15,607,5852	CC,CT,TT		4.7397,5.2716,4.9197	benign	455/480	19230816	637,12311	2191	4283	6474	SO:0001583	missense	54929	exon12			ACCAGATGAGGTA	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.1363A>G	19.37:g.19230816T>C	ENSP00000162044:p.Ile455Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_017814	B3KUE0|G5E9M6|Q7L2Y1	Missense_Mutation	SNP	ENST00000162044.9	37	CCDS12393.1	319	0.14606227106227107	104	0.21138211382113822	37	0.10220994475138122	65	0.11363636363636363	113	0.14907651715039577	T	11.76	1.735741	0.30774	0.052716	0.047397	ENSG00000064545	ENST00000450333;ENST00000162044	.	.	.	4.53	3.48	0.39840	.	0.051611	0.85682	D	0.000000	T	0.00039	0.0001	N	0.22421	0.69	0.33292	P	0.436354	B;B	0.14012	0.009;0.0	B;B	0.11329	0.006;0.002	T	0.10917	-1.0609	8	0.36615	T	0.2	-15.4835	7.5498	0.27790	0.0:0.1139:0.0:0.8861	rs45467802;rs61739370	352;455	G5E9M6;Q9NX61	.;T161A_HUMAN	V	352;455	.	ENSP00000162044:I455V	I	-	1	0	TMEM161A	19091816	1.000000	0.71417	0.998000	0.56505	0.343000	0.28985	1.729000	0.38115	0.602000	0.29896	0.260000	0.18958	ATC	T|0.911;C|0.089	0.089	strong		0.662	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814	
EFS	10278	hgsc.bcm.edu	37	14	23826822	23826822	+	Silent	SNP	C	C	T	rs2231809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23826822C>T	ENST00000216733.3	-	6	1906	c.1299G>A	c.(1297-1299)ctG>ctA	p.L433L	EFS_ENST00000351354.3_Silent_p.L340L|EFS_ENST00000429593.2_Silent_p.L264L|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	90	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	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		
CDC16	8881	hgsc.bcm.edu	37	13	115030714	115030714	+	Splice_Site	SNP	T	T	C	rs8809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115030714T>C	ENST00000356221.3	+	17	1710	c.1602T>C	c.(1600-1602)atT>atC	p.I534I	CDC16_ENST00000360383.3_Splice_Site_p.I534I|CDC16_ENST00000375312.3_Splice_Site_p.I389I|CDC16_ENST00000375308.1_Splice_Site_p.I440I|CDC16_ENST00000375310.1_Splice_Site_p.I440I|CDC16_ENST00000252457.5_Splice_Site_p.I533I|CDC16_ENST00000252458.6_Splice_Site_p.I389I|CDC16_ENST00000461716.1_3'UTR			Q13042	CDC16_HUMAN	cell division cycle 16	534					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)			AAGCTTATATTGGTAAGATAA	0.358													C|||	1850	0.369409	0.6868	0.2853	5008	,	,		19363	0.1567		0.2565	False		,,,				2504	0.3354				p.I534I		Atlas-SNP	.											.	CDC16	50	.	0			c.T1602C						PASS	.	C	,	2645,1761	524.3+/-371.3	796,1053,354	283.0	264.0	270.0		1602,1602	-4.7	0.7	13	dbSNP_116	270	1962,6638	724.1+/-406.5	227,1508,2565	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CDC16	NM_001078645.1,NM_003903.3	,	1023,2561,2919	CC,CT,TT		22.814,39.9682,35.4221	,	534/621,534/621	115030714	4607,8399	2203	4300	6503	SO:0001630	splice_region_variant	8881	exon17			TTATATTGGTAAG	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.1603+1T>C	13.37:g.115030714T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			T|0.661;C|0.339	0.339	strong		0.358	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	Silent
MYOM3	127294	hgsc.bcm.edu	37	1	24409165	24409165	+	Silent	SNP	C	C	T	rs4320728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24409165C>T	ENST00000374434.3	-	17	2172	c.2010G>A	c.(2008-2010)gaG>gaA	p.E670E	RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000329601.7_Silent_p.E670E|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Silent_p.E671E	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	670	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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)		TGACACAAAACTCGTACTCCT	0.572													C|||	924	0.184505	0.1929	0.1398	5008	,	,		19098	0.1925		0.1332	False		,,,				2504	0.2495				p.E670E		Atlas-SNP	.											.	MYOM3	131	.	0			c.G2010A						PASS	.	C		638,3500		48,542,1479	55.0	61.0	59.0		2010	2.5	1.0	1	dbSNP_111	59	1088,7332		63,962,3185	no	coding-synonymous	MYOM3	NM_152372.3		111,1504,4664	TT,TC,CC		12.9216,15.4181,13.7442		670/1438	24409165	1726,10832	2069	4210	6279	SO:0001819	synonymous_variant	127294	exon17			ACAAAACTCGTAC	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.2010G>A	1.37:g.24409165C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			C|0.844;T|0.156	0.156	strong		0.572	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
COL22A1	169044	hgsc.bcm.edu	37	8	139701209	139701209	+	Missense_Mutation	SNP	G	G	T	rs4909444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:139701209G>T	ENST00000303045.6	-	37	3259	c.2813C>A	c.(2812-2814)gCt>gAt	p.A938D	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.A938D	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	938	Collagen-like 8.|Gly-rich.|Pro-rich.		A -> D (in dbSNP:rs4909444). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GAGGCCGGGAGCACCCTGTGG	0.517										HNSCC(7;0.00092)			G|||	1461	0.291733	0.2534	0.3012	5008	,	,		19616	0.1835		0.34	False		,,,				2504	0.3988				p.A938D		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2813A						PASS	.	G	ASP/ALA	1269,3137	434.1+/-343.8	198,873,1132	130.0	118.0	122.0		2813	2.7	0.4	8	dbSNP_111	122	2821,5779	444.9+/-360.8	474,1873,1953	yes	missense	COL22A1	NM_152888.1	126	672,2746,3085	TT,TG,GG		32.8023,28.8016,31.447	benign	938/1627	139701209	4090,8916	2203	4300	6503	SO:0001583	missense	169044	exon37			CCGGGAGCACCCT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2813C>A	8.37:g.139701209G>T	ENSP00000303153:p.Ala938Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	638	0.29212454212454214	142	0.2886178861788618	116	0.32044198895027626	119	0.20804195804195805	261	0.34432717678100266	G	0.686	-0.796225	0.02862	0.288016	0.328023	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.93488	-3.23;-3.23	3.63	2.74	0.32292	.	0.979358	0.08299	U	0.967174	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B;B	0.21905	0.062;0.037	B;B	0.17098	0.017;0.007	T	0.17837	-1.0356	9	0.13470	T	0.59	.	6.2583	0.20885	0.138:0.0:0.862:0.0	rs4909444;rs17445739;rs52804110;rs60475514;rs4909444	938;938	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	D	938;938;651	ENSP00000303153:A938D;ENSP00000387655:A938D	ENSP00000303153:A938D	A	-	2	0	COL22A1	139770391	0.034000	0.19679	0.361000	0.25849	0.153000	0.21895	1.251000	0.32862	2.017000	0.59298	0.542000	0.68232	GCT	G|0.699;T|0.301	0.301	strong		0.517	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
FBXO42	54455	hgsc.bcm.edu	37	1	16577908	16577908	+	Missense_Mutation	SNP	G	G	C	rs12069239	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16577908G>C	ENST00000375592.3	-	10	1627	c.1411C>G	c.(1411-1413)Cct>Gct	p.P471A		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	471			P -> A (in dbSNP:rs12069239). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		TATCCTTCAGGAGCAGATGGA	0.488													C|||	1356	0.270767	0.4312	0.2133	5008	,	,		18995	0.1746		0.334	False		,,,				2504	0.1288				p.P471A		Atlas-SNP	.											.	FBXO42	53	.	0			c.C1411G						PASS	.	C	ALA/PRO	1864,2542	606.0+/-390.6	379,1106,718	43.0	48.0	46.0		1411	0.7	0.9	1	dbSNP_120	46	3084,5516	650.2+/-400.7	532,2020,1748	yes	missense	FBXO42	NM_018994.1	27	911,3126,2466	CC,CG,GG		35.8605,42.3059,38.044	benign	471/718	16577908	4948,8058	2203	4300	6503	SO:0001583	missense	54455	exon10			CTTCAGGAGCAGA	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1411C>G	1.37:g.16577908G>C	ENSP00000364742:p.Pro471Ala	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	652	0.29853479853479853	226	0.45934959349593496	90	0.24861878453038674	91	0.1590909090909091	245	0.3232189973614776	C	4.337	0.061879	0.08339	0.423059	0.358605	ENSG00000037637	ENST00000375592;ENST00000456164;ENST00000444116	T;T;T	0.39406	3.68;1.08;1.08	5.51	0.736	0.18307	.	0.696895	0.14389	N	0.322664	T	0.00012	0.0000	N	0.08118	0	0.50813	P	1.0900000000002574E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.46386	-0.9195	9	0.12766	T	0.61	-1.4499	1.5643	0.02601	0.3635:0.3387:0.1141:0.1838	rs12069239;rs52791447;rs12069239	471	Q6P3S6	FBX42_HUMAN	A	471;189;189	ENSP00000364742:P471A;ENSP00000415663:P189A;ENSP00000412416:P189A	ENSP00000364742:P471A	P	-	1	0	FBXO42	16450495	0.013000	0.17824	0.937000	0.37676	0.989000	0.77384	0.097000	0.15168	-0.343000	0.08351	-0.127000	0.14921	CCT	G|0.654;C|0.346	0.346	strong		0.488	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
TP53BP2	7159	hgsc.bcm.edu	37	1	223991119	223991119	+	Missense_Mutation	SNP	G	G	T	rs34683843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:223991119G>T	ENST00000343537.7	-	7	976	c.685C>A	c.(685-687)Caa>Aaa	p.Q229K	TP53BP2_ENST00000498843.1_5'Flank|TP53BP2_ENST00000391879.2_5'Flank|TP53BP2_ENST00000391878.2_Missense_Mutation_p.Q100K	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	223					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)		CTCTGTTTTTGCTGGAACAAA	0.448													G|||	177	0.0353435	0.003	0.036	5008	,	,		17547	0.0179		0.0895	False		,,,				2504	0.0409				p.Q229K		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C685A						PASS	.	G	LYS/GLN,LYS/GLN	65,4341	59.9+/-96.7	1,63,2139	94.0	85.0	88.0		685,298	6.2	1.0	1	dbSNP_126	88	761,7839	180.6+/-229.5	30,701,3569	yes	missense,missense	TP53BP2	NM_001031685.2,NM_005426.2	53,53	31,764,5708	TT,TG,GG		8.8488,1.4753,6.3509	possibly-damaging,possibly-damaging	229/1135,100/1006	223991119	826,12180	2203	4300	6503	SO:0001583	missense	7159	exon7			GTTTTTGCTGGAA	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.685C>A	1.37:g.223991119G>T	ENSP00000341957:p.Gln229Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	102	0.046703296703296704	3	0.006097560975609756	17	0.04696132596685083	7	0.012237762237762238	75	0.09894459102902374	G	35	5.545199	0.96488	0.014753	0.088488	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.29142	1.58;1.58	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.02688	0.0081	M	0.68317	2.08	0.80722	D	1	D;D	0.63880	0.993;0.987	D;P	0.67548	0.952;0.824	T	0.00412	-1.1755	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:0.0:1.0:0.0	rs34683843;rs61749336	229;223	B4DG66;Q13625	.;ASPP2_HUMAN	K	100;229	ENSP00000375750:Q100K;ENSP00000341957:Q229K	ENSP00000341957:Q229K	Q	-	1	0	TP53BP2	222057742	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.441000	0.97557	2.941000	0.99782	0.655000	0.94253	CAA	G|0.944;T|0.056	0.056	strong		0.448	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
SLC30A4	7782	hgsc.bcm.edu	37	15	45778828	45778828	+	Silent	SNP	G	G	A	rs145466606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45778828G>A	ENST00000261867.4	-	7	1430	c.1116C>T	c.(1114-1116)gcC>gcT	p.A372A	RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	372					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TGTGAACTATGGCAGTAGATT	0.373																																					p.A372A		Atlas-SNP	.											.	SLC30A4	25	.	0			c.C1116T						PASS	.	G		1,4395		0,1,2197	131.0	135.0	134.0		1116	4.6	1.0	15	dbSNP_134	134	8,8588	6.4+/-24.3	0,8,4290	no	coding-synonymous	SLC30A4	NM_013309.4		0,9,6487	AA,AG,GG		0.0931,0.0227,0.0693		372/430	45778828	9,12983	2198	4298	6496	SO:0001819	synonymous_variant	7782	exon7			AACTATGGCAGTA		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"""Solute carriers"""	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.1116C>T	15.37:g.45778828G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1		
EFCAB13	124989	hgsc.bcm.edu	37	17	45451894	45451894	+	Missense_Mutation	SNP	G	G	A	rs4968318	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45451894G>A	ENST00000331493.2	+	12	1345	c.934G>A	c.(934-936)Gta>Ata	p.V312I	EFCAB13_ENST00000517484.1_Missense_Mutation_p.V216I	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	312			V -> I (in dbSNP:rs4968318). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										GTTATCAAGTGTAGCAGGATG	0.279													A|||	3114	0.621805	0.7519	0.5317	5008	,	,		16412	0.5903		0.6034	False		,,,				2504	0.5613				p.V312I		Atlas-SNP	.											.	.	.	.	0			c.G934A						PASS	.	A	ILE/VAL,ILE/VAL	3176,1208		1163,850,179	32.0	36.0	34.0		646,934	-8.0	0.0	17	dbSNP_111	34	5226,3300		1668,1890,705	yes	missense,missense	C17orf57	NM_001195192.1,NM_152347.4	29,29	2831,2740,884	AA,AG,GG		38.7051,27.5547,34.9187	benign,benign	216/785,312/974	45451894	8402,4508	2192	4263	6455	SO:0001583	missense	124989	exon12			TCAAGTGTAGCAG	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.934G>A	17.37:g.45451894G>A	ENSP00000332111:p.Val312Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	1372	0.6282051282051282	343	0.6971544715447154	216	0.5966850828729282	361	0.6311188811188811	452	0.5963060686015831	A	0.044	-1.272243	0.01421	0.724453	0.612949	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.64438	0.26;-0.1	4.02	-8.04	0.01110	.	3.018340	0.01263	N	0.009260	T	0.00012	0.0000	N	0.19112	0.55	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;0.0	T	0.33033	-0.9884	9	0.02654	T	1	-12.1637	1.6133	0.02698	0.4474:0.1675:0.2154:0.1697	rs4968318;rs52803438;rs60032644;rs4968318	264;312;216	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	I	312;216;264	ENSP00000332111:V312I;ENSP00000430048:V216I	ENSP00000332111:V312I	V	+	1	0	C17orf57	42806893	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-3.603000	0.00417	-3.238000	0.00207	-2.097000	0.00363	GTA	G|0.358;A|0.642	0.642	strong		0.279	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
FBXO16	157574	hgsc.bcm.edu	37	8	28304767	28304767	+	Missense_Mutation	SNP	G	G	T	rs7016831|rs386723954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:28304767G>T	ENST00000380254.2	-	7	912	c.764C>A	c.(763-765)aCc>aAc	p.T255N	FBXO16_ENST00000518734.1_Missense_Mutation_p.T243N|RP11-181B11.2_ENST00000523935.1_RNA|FBXO16_ENST00000346498.2_Missense_Mutation_p.T243N|RP11-181B11.2_ENST00000518819.1_RNA	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	255			T -> N (in dbSNP:rs7016831).	MT -> IN (in Ref. 3; AAI02028). {ECO:0000305}.						large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		GAAGTCTGGGGTCATTTGGTT	0.348													G|||	464	0.0926518	0.2965	0.0274	5008	,	,		19250	0.0		0.0358	False		,,,				2504	0.0174				p.T255N		Atlas-SNP	.											.	FBXO16	29	.	0			c.C764A						PASS	.	G	ASN/THR	927,3479		117,693,1393	168.0	166.0	166.0		764	2.1	1.0	8	dbSNP_116	166	315,8285		5,305,3990	yes	missense	FBXO16	NM_172366.2	65	122,998,5383	TT,TG,GG		3.6628,21.0395,9.5494	benign	255/293	28304767	1242,11764	2203	4300	6503	SO:0001583	missense	157574	exon7			TCTGGGGTCATTT	AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"""F-boxes /  ""other"""""	13618	protein-coding gene	gene with protein product		608519	"""F-box only protein 16"""			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.764C>A	8.37:g.28304767G>T	ENSP00000369604:p.Thr255Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Missense_Mutation	SNP	ENST00000380254.2	37	CCDS6068.1	166	0.076007326007326	129	0.2621951219512195	8	0.022099447513812154	1	0.0017482517482517483	28	0.036939313984168866	G	9.249	1.040345	0.19669	0.210395	0.036628	ENSG00000214050	ENST00000380254;ENST00000346498;ENST00000518734	T;T;T	0.14893	2.49;2.47;2.49	5.01	2.07	0.26955	.	1.824990	0.03729	N	0.253071	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999999874268	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.38628	-0.9652	9	0.32370	T	0.25	-14.3367	4.1093	0.10052	0.2047:0.0:0.6154:0.1799	rs7016831;rs58436952;rs7016831	243;255	Q3T1B2;Q8IX29	.;FBX16_HUMAN	N	255;243;243	ENSP00000369604:T255N;ENSP00000341416:T243N;ENSP00000429687:T243N	ENSP00000341416:T243N	T	-	2	0	FBXO16	28360686	0.993000	0.37304	0.994000	0.49952	0.561000	0.35649	0.753000	0.26376	0.183000	0.20059	0.591000	0.81541	ACC	C|0.006;G|0.897;T|0.096	0.096	strong		0.348	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366	
MYO9A	4649	hgsc.bcm.edu	37	15	72170400	72170400	+	Missense_Mutation	SNP	G	G	A	rs148435644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72170400G>A	ENST00000356056.5	-	31	6384	c.5912C>T	c.(5911-5913)tCa>tTa	p.S1971L	MYO9A_ENST00000564571.1_Missense_Mutation_p.S1971L|MYO9A_ENST00000444904.1_Missense_Mutation_p.S1952L|MYO9A_ENST00000424560.1_Missense_Mutation_p.S2042L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1971	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTGCAATCTGAAGTCTTGAA	0.343													G|||	56	0.0111821	0.0	0.0317	5008	,	,		16355	0.0		0.0338	False		,,,				2504	0.0				p.S1971L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C5912T						PASS	.	G	LEU/SER	24,4374	29.9+/-59.1	1,22,2176	62.0	64.0	63.0		5912	0.1	0.5	15	dbSNP_134	63	287,8307	105.6+/-166.5	6,275,4016	yes	missense	MYO9A	NM_006901.2	145	7,297,6192	AA,AG,GG		3.3395,0.5457,2.3938	benign	1971/2549	72170400	311,12681	2199	4297	6496	SO:0001583	missense	4649	exon31			CAATCTGAAGTCT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5912C>T	15.37:g.72170400G>A	ENSP00000348349:p.Ser1971Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	0	0.0	25	0.032981530343007916	G	1.667	-0.509968	0.04231	0.005457	0.033395	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83591	-1.74;-1.73;-1.74	5.21	0.132	0.14762	.	.	.	.	.	T	0.31544	0.0800	N	0.01297	-0.9	0.20926	N	0.999826	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33979	-0.9847	9	0.22706	T	0.39	.	9.0444	0.36338	0.8015:0.0:0.1985:0.0	.	2042;1971	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	L	1971;2042;1952	ENSP00000348349:S1971L;ENSP00000399162:S2042L;ENSP00000398250:S1952L	ENSP00000348349:S1971L	S	-	2	0	MYO9A	69957454	0.999000	0.42202	0.470000	0.27216	0.826000	0.46750	2.312000	0.43726	0.174000	0.19809	0.591000	0.81541	TCA	G|0.977;A|0.023	0.023	strong		0.343	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
DDC	1644	hgsc.bcm.edu	37	7	50531015	50531015	+	Missense_Mutation	SNP	G	G	A	rs142110773		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:50531015G>A	ENST00000444124.2	-	14	1557	c.1357C>T	c.(1357-1359)Cgc>Tgc	p.R453C	DDC_ENST00000426377.1_Missense_Mutation_p.R375C|DDC_ENST00000431062.1_Missense_Mutation_p.R360C|DDC_ENST00000357936.5_Missense_Mutation_p.R453C	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	453					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)	TCCACCGTGCGAGAACAGATG	0.537																																					p.R453C		Atlas-SNP	.											DDC,NS,carcinoma,0,1	DDC	100	1	0			c.C1357T						scavenged	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	125.0	109.0	114.0		1357,1357,1243,1213,1123,1078	5.4	0.1	7	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	DDC	NM_000790.3,NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,NM_001242889.1	180,180,180,180,180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/481,453/481,415/443,405/433,375/403,360/388	50531015	1,13005	2203	4300	6503	SO:0001583	missense	1644	exon14			CCGTGCGAGAACA		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.1357C>T	7.37:g.50531015G>A	ENSP00000403644:p.Arg453Cys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	281	4	0.0142349	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058852	0.55325	0.0	1.16E-4	ENSG00000132437	ENST00000357936;ENST00000431062;ENST00000426377;ENST00000444124	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.44	5.44	0.79542	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.67608	0.2911	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	P;P	0.59889	0.865;0.865	T	0.75786	-0.3195	10	0.87932	D	0	-31.1202	14.1447	0.65344	0.0:0.0:0.85:0.15	.	453;453	Q53Y41;P20711	.;DDC_HUMAN	C	453;360;375;453	ENSP00000350616:R453C;ENSP00000399184:R360C;ENSP00000395069:R375C;ENSP00000403644:R453C	ENSP00000350616:R453C	R	-	1	0	DDC	50498509	1.000000	0.71417	0.096000	0.21009	0.176000	0.22953	7.349000	0.79376	2.540000	0.85666	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	weak		0.537	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
TECTA	7007	hgsc.bcm.edu	37	11	121038810	121038810	+	Silent	SNP	C	C	T	rs2155369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	204	0	0		WXS	Illumina HiSeq	Phase_I	210	111	0.528571	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	
KIAA1109	84162	hgsc.bcm.edu	37	4	123276961	123276961	+	Silent	SNP	G	G	A	rs62321696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:123276961G>A	ENST00000264501.4	+	83	14689	c.14316G>A	c.(14314-14316)ctG>ctA	p.L4772L	KIAA1109_ENST00000388738.3_Silent_p.L4772L			Q2LD37	K1109_HUMAN	KIAA1109	4772					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)				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						AGCTAAATCTGCTTCGTAATG	0.348													A|||	238	0.047524	0.0613	0.0504	5008	,	,		13254	0.002		0.0815	False		,,,				2504	0.0389				p.L4772L		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G14316A						PASS	.	A		233,3489		8,217,1636	95.0	91.0	92.0		14316	-5.4	0.2	4	dbSNP_129	92	593,7577		22,549,3514	no	coding-synonymous	KIAA1109	NM_015312.3		30,766,5150	AA,AG,GG		7.2583,6.2601,6.9458		4772/5006	123276961	826,11066	1861	4085	5946	SO:0001819	synonymous_variant	84162	exon81			AAATCTGCTTCGT	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.14316G>A	4.37:g.123276961G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	105	0.04807692307692308	26	0.052845528455284556	19	0.052486187845303865	0	0.0	60	0.079155672823219	A	2.391	-0.339773	0.05243	0.062601	0.072583	ENSG00000138688	ENST00000306802	.	.	.	5.43	-5.36	0.02689	.	.	.	.	.	T	0.04634	0.0126	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37079	-0.9721	4	.	.	.	.	9.5996	0.39596	0.2523:0.0:0.5483:0.1994	rs62321696	.	.	.	Y	1148	.	.	C	+	2	0	KIAA1109	123496411	0.005000	0.15991	0.150000	0.22450	0.502000	0.33828	-0.867000	0.04241	-1.292000	0.02366	-2.121000	0.00349	TGC	G|0.946;A|0.054	0.054	strong		0.348	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KRR1	11103	hgsc.bcm.edu	37	12	75900588	75900588	+	Silent	SNP	A	A	G	rs2070162	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:75900588A>G	ENST00000229214.4	-	3	390	c.367T>C	c.(367-369)Tta>Cta	p.L123L	KRR1_ENST00000438169.2_Silent_p.L123L	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	123					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CTCCTTGCTAACAGTTTTATC	0.388													A|||	1163	0.232228	0.1936	0.3588	5008	,	,		17068	0.121		0.2336	False		,,,				2504	0.3078				p.L123L		Atlas-SNP	.											.	KRR1	37	.	0			c.T367C						PASS	.	A		898,3508	345.4+/-308.5	99,700,1404	125.0	120.0	122.0		367	5.5	1.0	12	dbSNP_96	122	2145,6455	367.7+/-334.8	271,1603,2426	no	coding-synonymous	KRR1	NM_007043.6		370,2303,3830	GG,GA,AA		24.9419,20.3813,23.3969		123/382	75900588	3043,9963	2203	4300	6503	SO:0001819	synonymous_variant	11103	exon3			TTGCTAACAGTTT	U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"""HIV-1 rev binding protein 2"", ""HIV-1 Rev binding protein 2"""	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.367T>C	12.37:g.75900588A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_007043	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																			A|0.777;G|0.223	0.223	strong		0.388	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043	
KRT40	125115	hgsc.bcm.edu	37	17	39134455	39134455	+	Silent	SNP	G	G	A	rs2271277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	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	
NQO1	1728	hgsc.bcm.edu	37	16	69745145	69745145	+	Missense_Mutation	SNP	G	G	A	rs1800566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:69745145G>A	ENST00000320623.5	-	6	1070	c.559C>T	c.(559-561)Cct>Tct	p.P187S	snoU13_ENST00000459361.1_RNA|NQO1_ENST00000561500.1_Missense_Mutation_p.P149S|NQO1_ENST00000564043.1_Missense_Mutation_p.P166S|NQO1_ENST00000379046.2_Missense_Mutation_p.P149S|NQO1_ENST00000379047.3_Missense_Mutation_p.P153S|NQO1_ENST00000439109.2_Missense_Mutation_p.P115S|CTD-2033A16.1_ENST00000562696.1_RNA	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	187			P -> S (lack of activity; dbSNP:rs1800566). {ECO:0000269|PubMed:10447260, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1737339, ECO:0000269|Ref.3}.		aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)	p.P187S(1)		autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	GTCAGTTGAGGTTCTAAGACT	0.458													G|||	1447	0.288938	0.1755	0.3329	5008	,	,		21129	0.4187		0.2107	False		,,,				2504	0.3579				p.P187S		Atlas-SNP	.											NQO1,NS,carcinoma,0,1	NQO1	21	1	1	Substitution - Missense(1)	stomach(1)	c.C559T	GRCh37	CM950861	NQO1	M	rs1800566	PASS	.	G	SER/PRO,SER/PRO,SER/PRO	856,3540	334.4+/-303.4	77,702,1419	154.0	160.0	158.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	559,457,445	5.4	1.0	16	dbSNP_89	158	1709,6891	311.2+/-310.2	177,1355,2768	yes	missense,missense,missense	NQO1	NM_000903.2,NM_001025433.1,NM_001025434.1	74,74,74	254,2057,4187	AA,AG,GG		19.8721,19.4722,19.7368	possibly-damaging,possibly-damaging,possibly-damaging	187/275,153/241,149/237	69745145	2565,10431	2198	4300	6498	SO:0001583	missense	1728	exon6			GTTGAGGTTCTAA	M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"""diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"""	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.559C>T	16.37:g.69745145G>A	ENSP00000319788:p.Pro187Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_000903	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Missense_Mutation	SNP	ENST00000320623.5	37	CCDS10883.1	604	0.2765567765567766	88	0.17886178861788618	120	0.3314917127071823	243	0.42482517482517484	153	0.20184696569920843	G	23.7	4.442223	0.83993	0.194722	0.198721	ENSG00000181019	ENST00000320623;ENST00000379047;ENST00000379046;ENST00000439109	T;T;T;T	0.09723	2.95;3.11;3.11;3.11	5.41	5.41	0.78517	Flavodoxin-like fold (1);	0.050537	0.85682	D	0.000000	T	0.00012	0.0000	M	0.68593	2.085	0.09310	P	0.999999999882097	D;P;B	0.89917	1.0;0.77;0.438	D;B;B	0.91635	0.999;0.356;0.167	T	0.48536	-0.9027	9	0.46703	T	0.11	-14.2172	18.3313	0.90270	0.0:0.0:1.0:0.0	rs1800566;rs4134727;rs4149351;rs57135274;rs1800566	115;153;187	B4DLR8;B7ZAD1;P15559	.;.;NQO1_HUMAN	S	187;153;149;115	ENSP00000319788:P187S;ENSP00000368335:P153S;ENSP00000368334:P149S;ENSP00000398330:P115S	ENSP00000319788:P187S	P	-	1	0	NQO1	68302646	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.220000	0.95180	2.696000	0.92011	0.655000	0.94253	CCT	G|0.761;A|0.239	0.239	strong		0.458	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2		
TTLL12	23170	hgsc.bcm.edu	37	22	43572354	43572354	+	Missense_Mutation	SNP	C	C	T	rs11704935	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43572354C>T	ENST00000216129.6	-	6	952	c.889G>A	c.(889-891)Gtg>Atg	p.V297M	TTLL12_ENST00000484118.1_5'Flank	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	297			V -> M (in dbSNP:rs11704935).		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)				GGGTGCACCACGGGGTTGATG	0.587													C|||	140	0.0279553	0.0068	0.0692	5008	,	,		16106	0.0		0.0726	False		,,,				2504	0.0102				p.V297M		Atlas-SNP	.											.	TTLL12	50	.	0			c.G889A						PASS	.	C	MET/VAL	75,4327	61.7+/-98.7	1,73,2127	56.0	51.0	53.0		889	3.1	0.0	22	dbSNP_120	53	795,7803	176.3+/-226.2	42,711,3546	yes	missense	TTLL12	NM_015140.3	21	43,784,5673	TT,TC,CC		9.2463,1.7038,6.6923	benign	297/645	43572354	870,12130	2201	4299	6500	SO:0001583	missense	23170	exon6			GCACCACGGGGTT	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.889G>A	22.37:g.43572354C>T	ENSP00000216129:p.Val297Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	80	0.03663003663003663	6	0.012195121951219513	29	0.08011049723756906	0	0.0	45	0.059366754617414245	C	10.46	1.357432	0.24598	0.017038	0.092463	ENSG00000100304	ENST00000216129;ENST00000423379	T	0.47869	0.83	5.22	3.06	0.35304	.	1.047670	0.07415	N	0.893049	T	0.01454	0.0047	L	0.34521	1.04	0.80722	P	0.0	B;P	0.43701	0.353;0.815	B;B	0.40165	0.048;0.321	T	0.06661	-1.0814	9	0.34782	T	0.22	-2.3719	5.0279	0.14395	0.118:0.5693:0.2218:0.0908	rs11704935	297;297	B1AH89;Q14166	.;TTL12_HUMAN	M	297	ENSP00000216129:V297M	ENSP00000216129:V297M	V	-	1	0	TTLL12	41902298	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.024000	0.13555	1.193000	0.43086	0.655000	0.94253	GTG	C|0.945;G|0.000;T|0.055	0.055	strong		0.587	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
SYNE3	161176	hgsc.bcm.edu	37	14	95884323	95884323	+	Missense_Mutation	SNP	G	G	A	rs12434757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95884323G>A	ENST00000334258.5	-	17	2782	c.2768C>T	c.(2767-2769)gCg>gTg	p.A923V	SYNE3_ENST00000557275.1_Missense_Mutation_p.A918V|SYNE3_ENST00000554873.1_Missense_Mutation_p.A680V	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	923	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.		A -> V (in dbSNP:rs12434757). {ECO:0000269|PubMed:14702039}.		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						CACACAGCACGCCCTCCGGAA	0.672													A|||	2755	0.55012	0.5	0.5461	5008	,	,		14315	0.5		0.659	False		,,,				2504	0.5603				p.A923V		Atlas-SNP	.											SYNE3_ENST00000334258,NS,carcinoma,0,6	SYNE3	130	6	0			c.C2768T						scavenged	.	A	VAL/ALA	2281,2125	574.6+/-383.8	587,1107,509	56.0	50.0	52.0		2768	2.3	0.7	14	dbSNP_120	52	5839,2761	437.0+/-358.5	1983,1873,444	yes	missense	C14orf49	NM_152592.3	64	2570,2980,953	AA,AG,GG		32.1047,48.2297,37.5673	benign	923/976	95884323	8120,4886	2203	4300	6503	SO:0001583	missense	161176	exon17			CAGCACGCCCTCC	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.2768C>T	14.37:g.95884323G>A	ENSP00000334308:p.Ala923Val	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	1226	0.5613553113553114	235	0.47764227642276424	201	0.5552486187845304	287	0.5017482517482518	503	0.6635883905013192	A	3.580	-0.085774	0.07097	0.517703	0.678953	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.19532	2.14;2.14;2.14	4.67	2.34	0.29019	Klarsicht/ANC-1/syne-1 homology (2);	0.365080	0.17018	N	0.190232	T	0.00012	0.0000	N	0.00621	-1.32	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.42716	-0.9435	9	0.02654	T	1	-7.063	8.5717	0.33574	0.5683:0.0:0.4317:0.0	rs12434757;rs58866555;rs12434757	918;923	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	V	923;680;918	ENSP00000334308:A923V;ENSP00000452154:A680V;ENSP00000450562:A918V	ENSP00000334308:A923V	A	-	2	0	C14orf49	94954076	0.532000	0.26346	0.703000	0.30354	0.897000	0.52465	1.201000	0.32259	-0.092000	0.12417	-1.115000	0.02055	GCG	G|0.410;A|0.590	0.590	strong		0.672	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
TKT	7086	hgsc.bcm.edu	37	3	53269046	53269046	+	Silent	SNP	T	T	C	rs1051485|rs200778000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:53269046T>C	ENST00000462138.1	-	5	670	c.582A>G	c.(580-582)ccA>ccG	p.P194P	TKT_ENST00000423525.2_Silent_p.P194P|TKT_ENST00000296289.6_Silent_p.P147P|TKT_ENST00000423516.1_Silent_p.P202P|TKT_ENST00000461139.1_5'Flank			P29401	TKT_HUMAN	transketolase	194					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)		GGTGCTGCAGTGGGGCCGGGT	0.592													C|||	880	0.175719	0.1165	0.1427	5008	,	,		15418	0.1567		0.168	False		,,,				2504	0.3067				p.P202P	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.A606G						PASS	.	C	,	664,3742	764.2+/-413.3	55,554,1594	86.0	88.0	88.0		582,582	-11.1	0.0	3	dbSNP_86	88	1662,6938	740.5+/-407.1	161,1340,2799	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	216,1894,4393	CC,CT,TT		19.3256,15.0704,17.8841	,	194/624,194/624	53269046	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon6			CTGCAGTGGGGCC		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.582A>G	3.37:g.53269046T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	140	49	0.35	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			T|0.837;C|0.163	0.163	strong		0.592	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197499	39197499	+	Nonsense_Mutation	SNP	G	G	A	rs3213755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39197499G>A	ENST00000306271.4	-	1	214	c.151C>T	c.(151-153)Cag>Tag	p.Q51*		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	51			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)			AAGCTGGTCTGGCAGCAGCTT	0.612																																					p.Q51X		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.C151T	GRCh37	CM067999	KRTAP1-1	M	rs3213755	PASS	.	G	stop/GLN	743,3287		55,633,1327	75.0	86.0	83.0		151	3.6	1.0	17	dbSNP_106	83	1292,7138		100,1092,3023	yes	stop-gained	KRTAP1-1	NM_030967.2		155,1725,4350	AA,AG,GG		15.3262,18.4367,16.3323		51/178	39197499	2035,10425	2015	4215	6230	SO:0001587	stop_gained	81851	exon1			TGGTCTGGCAGCA	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.151C>T	17.37:g.39197499G>A	ENSP00000305975:p.Gln51*	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_030967	A6NC32|Q96S60|Q96S67	Nonsense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	426	0.19505494505494506	87	0.17682926829268292	84	0.23204419889502761	151	0.263986013986014	104	0.13720316622691292	G	21.1	4.100620	0.76983	0.184367	0.153262	ENSG00000188581	ENST00000306271;ENST00000543328	.	.	.	3.6	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999401316	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	7.1567	0.25641	0.1206:0.0:0.8794:0.0	rs3213755	.	.	.	X	51;41	.	ENSP00000305975:Q51X	Q	-	1	0	KRTAP1-1	36451025	0.237000	0.23815	1.000000	0.80357	0.931000	0.56810	-0.153000	0.10144	2.339000	0.79563	0.650000	0.86243	CAG	G|0.804;A|0.196	0.196	strong		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39915758	39915758	+	Missense_Mutation	SNP	C	C	G	rs31728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39915758C>G	ENST00000409794.3	+	19	4835	c.3985C>G	c.(3985-3987)Cca>Gca	p.P1329A	PLEKHG2_ENST00000409797.2_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.P1300A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1329			P -> A (in dbSNP:rs31728). {ECO:0000269|PubMed:14702039, 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)			ACCACCTCCCCCAGCCAGGCG	0.741													C|||	2966	0.592252	0.677	0.5058	5008	,	,		12399	0.6002		0.5338	False		,,,				2504	0.591				p.P1329A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C3985G						PASS	.	C	ALA/PRO	2632,1246		918,796,225	8.0	9.0	9.0		3985	3.0	1.0	19	dbSNP_76	9	4249,3771		1209,1831,970	yes	missense	PLEKHG2	NM_022835.2	27	2127,2627,1195	GG,GC,CC		47.02,32.13,42.1668	probably-damaging	1329/1387	39915758	6881,5017	1939	4010	5949	SO:0001583	missense	64857	exon19			CCTCCCCCAGCCA	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.3985C>G	19.37:g.39915758C>G	ENSP00000386733:p.Pro1329Ala	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	1222	0.5595238095238095	320	0.6504065040650406	185	0.511049723756906	317	0.5541958041958042	400	0.5277044854881267	C	15.66	2.898814	0.52227	0.6787	0.5298	ENSG00000090924	ENST00000409794;ENST00000425673	T;T	0.80123	-1.23;-1.34	5.27	3.03	0.35002	.	0.000000	0.41823	D	0.000812	T	0.00012	0.0000	M	0.65975	2.015	0.09310	P	0.9999999999449904	P;D	0.76494	0.582;0.999	B;D	0.78314	0.134;0.991	T	0.53279	-0.8461	8	.	.	.	.	9.1948	0.37222	0.1601:0.6839:0.156:0.0	rs31728;rs519317;rs17845458;rs17856425;rs17858334;rs59097129;rs31728	1300;1329	Q9H7P9-3;Q9H7P9	.;PKHG2_HUMAN	A	1329;1300	ENSP00000386733:P1329A;ENSP00000392906:P1300A	.	P	+	1	0	PLEKHG2	44607598	0.189000	0.23263	0.995000	0.50966	0.270000	0.26580	1.115000	0.31209	2.481000	0.83766	0.655000	0.94253	CCA	C|0.443;G|0.557	0.557	strong		0.741	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
AGO2	27161	hgsc.bcm.edu	37	8	141551407	141551407	+	Silent	SNP	G	G	A	rs2293939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141551407G>A	ENST00000220592.5	-	15	2002	c.1890C>T	c.(1888-1890)cgC>cgT	p.R630R	AGO2_ENST00000519980.1_Silent_p.R630R	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	630	Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|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)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GCTGCTGCACGCGCACGGTGG	0.617													G|||	1139	0.227436	0.0567	0.281	5008	,	,		17732	0.3581		0.2684	False		,,,				2504	0.2434				p.R630R		Atlas-SNP	.											.	.	.	.	0			c.C1890T						PASS	.	G	,	416,3990	198.4+/-222.2	24,368,1811	83.0	64.0	71.0		1890,1890	-9.1	0.3	8	dbSNP_100	71	2303,6297	379.1+/-339.1	314,1675,2311	no	coding-synonymous,coding-synonymous	EIF2C2	NM_001164623.1,NM_012154.3	,	338,2043,4122	AA,AG,GG		26.7791,9.4417,20.9057	,	630/826,630/860	141551407	2719,10287	2203	4300	6503	SO:0001819	synonymous_variant	27161	exon15			CTGCACGCGCACG	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1890C>T	8.37:g.141551407G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	32	23	0.71875	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	37	CCDS6380.1																																																																																			G|0.783;A|0.217	0.217	strong		0.617	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
BMP7	655	hgsc.bcm.edu	37	20	55803299	55803299	+	Silent	SNP	C	C	T	rs41274738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:55803299C>T	ENST00000395863.3	-	2	1102	c.597G>A	c.(595-597)caG>caA	p.Q199Q	BMP7_ENST00000395864.3_Silent_p.Q199Q|BMP7_ENST00000450594.2_Silent_p.Q199Q	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	199					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|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 localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			CCAAGTGCTCCTGGAGCACCT	0.577													C|||	87	0.0173722	0.0023	0.0144	5008	,	,		19796	0.0		0.0427	False		,,,				2504	0.0317				p.Q199Q		Atlas-SNP	.											.	BMP7	60	.	0			c.G597A						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	116.0	118.0	118.0		597	4.7	1.0	20	dbSNP_127	118	347,8253	117.7+/-177.3	5,337,3958	no	coding-synonymous	BMP7	NM_001719.2		5,364,6134	TT,TC,CC		4.0349,0.6128,2.8756		199/432	55803299	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	655	exon2			GTGCTCCTGGAGC		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1074	protein-coding gene	gene with protein product	"""osteogenic protein 1"""	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.597G>A	20.37:g.55803299C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_001719	Q9H512|Q9NTQ7	Silent	SNP	ENST00000395863.3	37	CCDS13455.1	40	0.018315018315018316	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	30	0.0395778364116095	C	9.707	1.156075	0.21454	0.006128	0.040349	ENSG00000101144	ENST00000433911	.	.	.	5.63	4.69	0.59074	.	.	.	.	.	T	0.30759	0.0775	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47611	-0.9104	4	.	.	.	.	11.6317	0.51178	0.0:0.8577:0.0:0.1423	rs41274738;rs61733435	.	.	.	R	85	.	.	G	-	1	0	BMP7	55236706	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.665000	0.54532	1.381000	0.46364	0.655000	0.94253	GGA	C|0.974;T|0.026	0.026	strong		0.577	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2		
MROH9	80133	hgsc.bcm.edu	37	1	170959029	170959029	+	Silent	SNP	C	C	T	rs16863922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:170959029C>T	ENST00000367758.3	+	11	1012	c.913C>T	c.(913-915)Ctg>Ttg	p.L305L	MROH9_ENST00000367759.4_Silent_p.L305L	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	305																	TTACAGGCAACTGTGTGATAA	0.413													T|||	1032	0.20607	0.4047	0.1873	5008	,	,		20225	0.001		0.2227	False		,,,				2504	0.1452				p.L305L		Atlas-SNP	.											.	.	.	.	0			c.C913T						PASS	.	T	,	1362,2426		259,844,791	198.0	186.0	189.0		913,913	-4.3	0.0	1	dbSNP_123	189	1707,6533		185,1337,2598	no	coding-synonymous,coding-synonymous	C1orf129	NM_001163629.1,NM_025063.2	,	444,2181,3389	TT,TC,CC		20.716,35.9556,25.5155	,	305/862,305/574	170959029	3069,8959	1894	4120	6014	SO:0001819	synonymous_variant	80133	exon11			AGGCAACTGTGTG	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.913C>T	1.37:g.170959029C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	173	103	0.595376	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																			C|0.806;T|0.194	0.194	strong		0.413	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
NAALAD2	10003	hgsc.bcm.edu	37	11	89868755	89868755	+	Silent	SNP	G	G	A	rs10734123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:89868755G>A	ENST00000534061.1	+	2	341	c.111G>A	c.(109-111)acG>acA	p.T37T	NAALAD2_ENST00000375944.3_Silent_p.T37T|NAALAD2_ENST00000321955.4_Silent_p.T37T|NAALAD2_ENST00000525171.1_Silent_p.T37T	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	37					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)	p.T37T(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TCAAAGAAACGACCACTTCTG	0.353													A|||	2558	0.510783	0.6815	0.5389	5008	,	,		17278	0.4177		0.3648	False		,,,				2504	0.5061				p.T37T		Atlas-SNP	.											NAALAD2,NS,carcinoma,0,1	NAALAD2	113	1	1	Substitution - coding silent(1)	stomach(1)	c.G111A						PASS	.	A		2652,1750	521.5+/-370.6	797,1058,346	104.0	105.0	104.0		111	1.4	0.1	11	dbSNP_120	104	3041,5557	662.9+/-402.0	554,1933,1812	no	coding-synonymous	NAALAD2	NM_005467.3		1351,2991,2158	AA,AG,GG		35.3687,39.7547,43.7923		37/741	89868755	5693,7307	2201	4299	6500	SO:0001819	synonymous_variant	10003	exon2			AGAAACGACCACT	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase III"""	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.111G>A	11.37:g.89868755G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Silent	SNP	ENST00000534061.1	37	CCDS8288.1																																																																																			G|0.541;A|0.459	0.459	strong		0.353	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467	
CERS4	79603	hgsc.bcm.edu	37	19	8321946	8321946	+	Silent	SNP	T	T	C	rs36247	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8321946T>C	ENST00000251363.5	+	9	1026	c.726T>C	c.(724-726)tcT>tcC	p.S242S	CERS4_ENST00000559336.1_Silent_p.S242S|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000558331.1_Silent_p.S191S|CERS4_ENST00000559450.1_Silent_p.S242S	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	242	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)										ACGATTCCTCTGACTACCTGC	0.602													C|||	2191	0.4375	0.4259	0.3862	5008	,	,		17309	0.4504		0.328	False		,,,				2504	0.589				p.S242S		Atlas-SNP	.											.	.	.	.	0			c.T726C						PASS	.	C		1879,2527	630.2+/-395.4	415,1049,739	223.0	210.0	214.0		726	-9.5	0.0	19	dbSNP_76	214	2769,5831	678.9+/-403.5	449,1871,1980	no	coding-synonymous	CERS4	NM_024552.2		864,2920,2719	CC,CT,TT		32.1977,42.6464,35.7374		242/395	8321946	4648,8358	2203	4300	6503	SO:0001819	synonymous_variant	79603	exon9			TTCCTCTGACTAC		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.726T>C	19.37:g.8321946T>C		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	37	CCDS12197.1																																																																																			T|0.623;C|0.376	0.376	strong		0.602	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
LTA	4049	hgsc.bcm.edu	37	6	31540556	31540556	+	Missense_Mutation	SNP	T	T	C	rs2229094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	50	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	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		
TEKT1	83659	hgsc.bcm.edu	37	17	6704121	6704121	+	Missense_Mutation	SNP	C	C	T	rs2271233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6704121C>T	ENST00000338694.2	-	7	1123	c.994G>A	c.(994-996)Gtc>Atc	p.V332I	TEKT1_ENST00000535086.1_Missense_Mutation_p.V186I	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	332			V -> I (in dbSNP:rs2271233).			cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TATTGTGCGACATCACGACAC	0.562											OREG0024124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	255	0.0509185	0.0015	0.0403	5008	,	,		19687	0.0516		0.0746	False		,,,				2504	0.1002				p.V332I		Atlas-SNP	.											TEKT1,rectum,carcinoma,+2,1	TEKT1	49	1	0			c.G994A						PASS	.	C	ILE/VAL	68,4338	61.7+/-98.7	1,66,2136	232.0	208.0	216.0		994	1.5	0.0	17	dbSNP_100	216	694,7906	172.2+/-222.9	30,634,3636	yes	missense	TEKT1	NM_053285.1	29	31,700,5772	TT,TC,CC		8.0698,1.5433,5.8588	benign	332/419	6704121	762,12244	2203	4300	6503	SO:0001583	missense	83659	exon7			GTGCGACATCACG		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.994G>A	17.37:g.6704121C>T	ENSP00000341346:p.Val332Ile	Somatic	122	0	0	636	WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	88	0.040293040293040296	1	0.0020325203252032522	20	0.055248618784530384	8	0.013986013986013986	59	0.07783641160949868	C	10.03	1.239842	0.22711	0.015433	0.080698	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.02472	4.28;4.28	5.85	1.46	0.22682	.	0.545369	0.19348	N	0.116471	T	0.00144	0.0004	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39542	-0.9609	9	0.35671	T	0.21	.	5.0249	0.14379	0.0:0.5096:0.1422:0.3482	rs2271233;rs17202721;rs52797408;rs60310395;rs2271233	332	Q969V4	TEKT1_HUMAN	I	332;186	ENSP00000341346:V332I;ENSP00000444142:V186I	ENSP00000341346:V332I	V	-	1	0	TEKT1	6644845	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.230000	0.09083	0.119000	0.18210	0.655000	0.94253	GTC	C|0.951;T|0.049	0.049	strong		0.562	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
MYO16	23026	hgsc.bcm.edu	37	13	109793177	109793177	+	Silent	SNP	G	G	A	rs150813880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:109793177G>A	ENST00000357550.2	+	31	4592	c.4551G>A	c.(4549-4551)aaG>aaA	p.K1517K	MYO16_ENST00000356711.2_Silent_p.K1517K	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)			TGGAGGTGAAGAAGCTGCCAG	0.706													G|||	109	0.0217652	0.0008	0.0447	5008	,	,		5637	0.0198		0.0209	False		,,,				2504	0.0368				p.K1539K		Atlas-SNP	.											.	MYO16	285	.	0			c.G4617A						PASS	.	G	,	21,4365		0,21,2172	17.0	21.0	20.0		4617,4551	-6.1	0.2	13	dbSNP_134	20	196,8366		4,188,4089	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	4,209,6261	AA,AG,GG		2.2892,0.4788,1.6759	,	1539/1881,1517/1859	109793177	217,12731	2193	4281	6474	SO:0001819	synonymous_variant	23026	exon32			GGTGAAGAAGCTG		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.4551G>A	13.37:g.109793177G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			G|0.984;A|0.016	0.016	strong		0.706	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
SH3GL1	6455	hgsc.bcm.edu	37	19	4362691	4362691	+	Silent	SNP	G	G	C	rs243261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4362691G>C	ENST00000269886.3	-	8	949	c.771C>G	c.(769-771)ccC>ccG	p.P257P	AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000417295.2_Silent_p.P209P|SH3GL1_ENST00000598564.1_Silent_p.P193P	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	257					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		CCCGGGGCTTGGGCTTATACT	0.652			T	MLL	AL								G|||	1961	0.391573	0.3434	0.4063	5008	,	,		17905	0.6042		0.2744	False		,,,				2504	0.3476				p.P257P	NSCLC(94;1152 2133 30346 33362)	Atlas-SNP	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.C771G						PASS	.	G	,,	1506,2900		270,966,967	58.0	56.0	57.0		627,579,771	-0.3	1.0	19	dbSNP_79	57	2423,6177		333,1757,2210	no	coding-synonymous,coding-synonymous,coding-synonymous	SH3GL1	NM_001199943.1,NM_001199944.1,NM_003025.3	,,	603,2723,3177	CC,CG,GG		28.1744,34.1807,30.2091	,,	209/321,193/305,257/369	4362691	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	6455	exon8			GGGCTTGGGCTTA		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.771C>G	19.37:g.4362691G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	37	CCDS32874.1																																																																																			G|0.684;C|0.316	0.316	strong		0.652	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
EIF3L	51386	hgsc.bcm.edu	37	22	38251629	38251629	+	Silent	SNP	C	C	G	rs11551384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38251629C>G	ENST00000412331.2	+	4	933	c.351C>G	c.(349-351)gcC>gcG	p.A117A	EIF3L_ENST00000381683.6_Silent_p.A117A|EIF3L_ENST00000476955.1_Intron|EIF3L_ENST00000406934.1_Intron	NM_016091.3	NP_057175.1			eukaryotic translation initiation factor 3, subunit L											kidney(2)|large_intestine(3)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						AGGCTGAAGCCATTGCTCCAC	0.448													C|||	307	0.0613019	0.0847	0.0375	5008	,	,		20009	0.0357		0.0477	False		,,,				2504	0.0869				p.A117A		Atlas-SNP	.											.	EIF3L	35	.	0			c.C351G						PASS	.	C	,	387,4019	194.0+/-219.0	22,343,1838	61.0	58.0	59.0		351,351	1.5	1.0	22	dbSNP_120	59	498,8102	142.3+/-198.5	15,468,3817	no	coding-synonymous,coding-synonymous	EIF3L	NM_001242923.1,NM_016091.3	,	37,811,5655	GG,GC,CC		5.7907,8.7835,6.8046	,	117/517,117/565	38251629	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	51386	exon4			TGAAGCCATTGCT	AF083243	CCDS13960.1, CCDS56230.1	22q	2012-12-20	2009-01-07	2009-01-07	ENSG00000100129	ENSG00000100129			18138	protein-coding gene	gene with protein product			"""eukaryotic translation initiation factor 3, subunit 6 interacting protein"", ""eukaryotic translation initiation factor 3, subunit E interacting protein"""	EIF3S6IP, EIF3EIP		11042152, 11590142	Standard	NM_016091		Approved	HSPC021, HSPC025, EIF3S11	uc003auf.3	Q9Y262	OTTHUMG00000150671	ENST00000412331.2:c.351C>G	22.37:g.38251629C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001242923		Silent	SNP	ENST00000412331.2	37	CCDS13960.1																																																																																			C|0.938;G|0.062	0.062	strong		0.448	EIF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319551.2	NM_016091	
RASGEF1C	255426	hgsc.bcm.edu	37	5	179529124	179529124	+	Silent	SNP	G	G	A	rs7725201	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:179529124G>A	ENST00000393371.2	-	12	1619	c.1323C>T	c.(1321-1323)taC>taT	p.Y441Y	RASGEF1C_ENST00000522500.1_Silent_p.Y290Y|RASGEF1C_ENST00000361132.4_Silent_p.Y441Y			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	441	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTCACTTTCGTAAGAAGCCA	0.443													A|||	4137	0.826078	0.8139	0.7882	5008	,	,		19228	0.7966		0.7684	False		,,,				2504	0.9591				p.Y441Y		Atlas-SNP	.											.	RASGEF1C	81	.	0			c.C1323T						PASS	.	A		3502,904	351.1+/-311.1	1384,734,85	91.0	83.0	85.0		1323	4.0	1.0	5	dbSNP_116	85	6706,1894	336.8+/-322.0	2617,1472,211	no	coding-synonymous	RASGEF1C	NM_175062.3		4001,2206,296	AA,AG,GG		22.0233,20.5175,21.5131		441/467	179529124	10208,2798	2203	4300	6503	SO:0001819	synonymous_variant	255426	exon13			ACTTTCGTAAGAA	AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090			27400	protein-coding gene	gene with protein product						12477932	Standard	XM_006714839		Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.1323C>T	5.37:g.179529124G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_175062	D3DWQ7|Q7Z4T0|Q8NA49	Silent	SNP	ENST00000393371.2	37	CCDS4452.1																																																																																			G|0.210;A|0.790	0.790	strong		0.443	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062	
PLEKHN1	84069	hgsc.bcm.edu	37	1	909419	909419	+	Silent	SNP	C	C	T	rs28548431	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:909419C>T	ENST00000379409.2	+	13	1827	c.1797C>T	c.(1795-1797)gaC>gaT	p.D599D	PLEKHN1_ENST00000379407.3_Silent_p.D512D|PLEKHN1_ENST00000379410.3_Silent_p.D547D			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	599										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)		AGCCCCCAGACGCCCCTCAGC	0.711													C|||	557	0.111222	0.0598	0.0778	5008	,	,		12060	0.0962		0.1839	False		,,,				2504	0.1452				p.D547D		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C1641T						PASS	.	C	,	243,3865		12,219,1823	5.0	7.0	6.0		1536,1641	1.0	0.0	1	dbSNP_125	6	1524,6692		147,1230,2731	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	159,1449,4554	TT,TC,CC		18.5492,5.9153,14.3379	,	512/577,547/612	909419	1767,10557	2054	4108	6162	SO:0001819	synonymous_variant	84069	exon14			CCCAGACGCCCCT	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.1797C>T	1.37:g.909419C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_032129	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37																																																																																				C|0.887;T|0.113	0.113	strong		0.711	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
JMY	133746	hgsc.bcm.edu	37	5	78596044	78596044	+	Silent	SNP	T	T	C	rs10514159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:78596044T>C	ENST00000396137.4	+	5	2058	c.1596T>C	c.(1594-1596)gaT>gaC	p.D532D		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	532	Interaction with p300/EP300. {ECO:0000250}.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		ATTATTATGATCTGCAACTTC	0.358													C|||	3404	0.679712	0.9372	0.585	5008	,	,		15309	0.6319		0.6163	False		,,,				2504	0.5133				p.D532D		Atlas-SNP	.											JMY_ENST00000396137,NS,carcinoma,+2,4	JMY	82	4	0			c.T1596C						scavenged	.	C		3335,435		1474,387,24	120.0	115.0	117.0		1596	-1.4	1.0	5	dbSNP_119	117	5067,3195		1574,1919,638	no	coding-synonymous	JMY	NM_152405.4		3048,2306,662	CC,CT,TT		38.671,11.5385,30.1695		532/989	78596044	8402,3630	1885	4131	6016	SO:0001819	synonymous_variant	133746	exon5			TTATGATCTGCAA	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1596T>C	5.37:g.78596044T>C		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_152405	A1L4P5|B5MDS2|B5MDT0	Silent	SNP	ENST00000396137.4	37	CCDS4047.3																																																																																			T|0.348;C|0.652	0.652	strong		0.358	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
EVC	2121	hgsc.bcm.edu	37	4	5721049	5721049	+	Silent	SNP	A	A	G	rs35870680	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:5721049A>G	ENST00000264956.6	+	2	433	c.249A>G	c.(247-249)tcA>tcG	p.S83S	EVC_ENST00000509451.1_Silent_p.S83S|EVC_ENST00000382674.2_Silent_p.S83S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	83					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)				GCTCCCCATCAAGGAGGAGGA	0.502													G|||	348	0.0694888	0.0076	0.0692	5008	,	,		19872	0.001		0.16	False		,,,				2504	0.1309				p.S83S		Atlas-SNP	.											.	EVC	90	.	0			c.A249G						PASS	.	G		135,4271	813.8+/-416.2	2,131,2070	222.0	216.0	218.0		249	-5.5	0.0	4	dbSNP_126	218	1286,7314	758.9+/-407.5	82,1122,3096	no	coding-synonymous	EVC	NM_153717.2		84,1253,5166	GG,GA,AA		14.9535,3.064,10.9257		83/993	5721049	1421,11585	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon2			CCCATCAAGGAGG	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.249A>G	4.37:g.5721049A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	58	0.610526	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			A|0.893;G|0.107	0.107	strong		0.502	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
BEND7	222389	hgsc.bcm.edu	37	10	13481466	13481466	+	Silent	SNP	C	C	T	rs76298779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13481466C>T	ENST00000396900.2	-	9	1265	c.1266G>A	c.(1264-1266)ccG>ccA	p.P422P	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.P371P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	422						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CACTCCCACCCGGCAGAACAG	0.527													C|||	142	0.0283546	0.1036	0.0072	5008	,	,		21405	0.0		0.0	False		,,,				2504	0.0				p.P371P		Atlas-SNP	.											.	BEND7	85	.	0			c.G1113A						PASS	.	C		389,4017	193.6+/-218.7	15,359,1829	56.0	50.0	52.0		1113	1.2	0.0	10	dbSNP_131	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	BEND7	NM_152751.2		15,361,6127	TT,TC,CC		0.0233,8.8289,3.0063		371/469	13481466	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon9			CCCACCCGGCAGA	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1266G>A	10.37:g.13481466C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				C|0.965;T|0.035	0.035	strong		0.527	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22846623G>A	ENST00000456783.2	+	4	396	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	51					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.R51Q(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TATTTTGCCCGAGACCTTTGG	0.284													N|||	1067	0.213059	0.4054	0.134	5008	,	,		14205	0.1736		0.1362	False		,,,				2504	0.1288				p.R51Q		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G152A						scavenged	.						18.0	20.0	20.0					19																	22846623		1801	4095	5896	SO:0001583	missense	57615	exon4			TTGCCCGAGACCT	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.152G>A	19.37:g.22846623G>A	ENSP00000413660:p.Arg51Gln	Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	34	11	0.323529	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	409	0.18727106227106227	166	0.33739837398373984	54	0.14917127071823205	99	0.17307692307692307	90	0.11873350923482849	.	0.007	-1.940811	0.00479	.	.	ENSG00000229676	ENST00000456783	T	0.06687	3.27	1.12	-0.367	0.12541	.	.	.	.	.	T	0.00012	0.0000	N	0.00014	-2.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	8	0.02654	T	1	.	4.7284	0.12952	0.4846:0.0:0.5154:0.0	.	51	Q9P255	ZN492_HUMAN	Q	51	ENSP00000413660:R51Q	ENSP00000413660:R51Q	R	+	2	0	ZNF492	22638463	0.000000	0.05858	0.053000	0.19242	0.052000	0.14988	-0.921000	0.04008	-0.964000	0.03595	-0.974000	0.02594	CGA	G|0.827;A|0.173	0.173	strong		0.284	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
TEDDM1	127670	hgsc.bcm.edu	37	1	182369233	182369233	+	Missense_Mutation	SNP	A	A	G	rs6674281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:182369233A>G	ENST00000367565.1	-	1	518	c.388T>C	c.(388-390)Tat>Cat	p.Y130H		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	130			Y -> H (in dbSNP:rs6674281).			integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						AGCAGAGAATAAACGTGCAGC	0.512													G|||	3396	0.678115	0.761	0.6124	5008	,	,		22039	0.8294		0.5417	False		,,,				2504	0.5971				p.Y130H		Atlas-SNP	.											.	TEDDM1	32	.	0			c.T388C						PASS	.	G	HIS/TYR	3281,1125	402.8+/-332.5	1230,821,152	147.0	146.0	147.0		388	5.1	0.0	1	dbSNP_116	147	4445,4155	566.7+/-388.7	1151,2143,1006	yes	missense	TEDDM1	NM_172000.3	83	2381,2964,1158	GG,GA,AA		48.314,25.5334,40.5966	benign	130/274	182369233	7726,5280	2203	4300	6503	SO:0001583	missense	127670	exon1			GAGAATAAACGTG	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"""putative membrane protein HE9"", ""transmembrane protein 45C"", ""epididymal protein 9"""						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.388T>C	1.37:g.182369233A>G	ENSP00000356536:p.Tyr130His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_172000	Q8IVJ0	Missense_Mutation	SNP	ENST00000367565.1	37	CCDS30953.1	1442	0.6602564102564102	362	0.7357723577235772	222	0.6132596685082873	461	0.8059440559440559	397	0.5237467018469657	G	0.012	-1.684426	0.00745	0.744666	0.51686	ENSG00000203730	ENST00000367565	T	0.31769	1.48	5.05	5.05	0.67936	.	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00017	-2.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40136	-0.9579	9	0.02654	T	1	-45.4785	11.5331	0.50622	0.0864:0.0:0.9136:0.0	rs6674281;rs17463348;rs58719880;rs6674281	130	Q5T9Z0	TEDM1_HUMAN	H	130	ENSP00000356536:Y130H	ENSP00000356536:Y130H	Y	-	1	0	TEDDM1	180635856	0.922000	0.31269	0.020000	0.16555	0.001000	0.01503	3.052000	0.49893	1.368000	0.46115	-0.119000	0.15052	TAT	A|0.364;G|0.636	0.636	strong		0.512	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000	
BSN	8927	hgsc.bcm.edu	37	3	49689642	49689642	+	Missense_Mutation	SNP	C	C	T	rs150021639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49689642C>T	ENST00000296452.4	+	5	2767	c.2653C>T	c.(2653-2655)Cct>Tct	p.P885S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	885					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)		CAGGCCTGAGCCTAGCCAAGA	0.652													C|||	34	0.00678914	0.0023	0.0058	5008	,	,		17544	0.0		0.0249	False		,,,				2504	0.002				p.P885S		Atlas-SNP	.											.	BSN	272	.	0			c.C2653T						PASS	.	C	SER/PRO	12,4394	19.1+/-41.9	0,12,2191	25.0	26.0	26.0		2653	1.3	1.0	3	dbSNP_134	26	152,8446	71.6+/-134.2	0,152,4147	yes	missense	BSN	NM_003458.3	74	0,164,6338	TT,TC,CC		1.7679,0.2724,1.2612	benign	885/3927	49689642	164,12840	2203	4299	6502	SO:0001583	missense	8927	exon5			CCTGAGCCTAGCC	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.2653C>T	3.37:g.49689642C>T	ENSP00000296452:p.Pro885Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	154	87	0.564935	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	24	0.01098901098901099	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	5.535	0.283703	0.10458	0.002724	0.017679	ENSG00000164061	ENST00000296452	T	0.15256	2.44	4.81	1.26	0.21427	.	1.048100	0.07469	N	0.901973	T	0.02083	0.0065	N	0.02011	-0.69	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.40757	-0.9546	10	0.08179	T	0.78	.	0.9669	0.01407	0.2611:0.3854:0.1373:0.2161	.	885	Q9UPA5	BSN_HUMAN	S	885	ENSP00000296452:P885S	ENSP00000296452:P885S	P	+	1	0	BSN	49664646	0.991000	0.36638	0.979000	0.43373	0.947000	0.59692	1.573000	0.36472	0.253000	0.21552	-0.225000	0.12378	CCT	C|0.987;T|0.013	0.013	strong		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
FOSB	2354	hgsc.bcm.edu	37	19	45971961	45971961	+	Silent	SNP	C	C	G	rs2282695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45971961C>G	ENST00000353609.3	+	1	709	c.117C>G	c.(115-117)gcC>gcG	p.A39A	FOSB_ENST00000585836.1_Silent_p.A39A|FOSB_ENST00000590335.1_Silent_p.A39A|FOSB_ENST00000591858.1_Silent_p.A39A|FOSB_ENST00000443841.2_Silent_p.A39A|FOSB_ENST00000586615.1_5'Flank|FOSB_ENST00000417353.2_Silent_p.A39A|FOSB_ENST00000592811.1_5'Flank|ERCC1_ENST00000423698.2_Intron|FOSB_ENST00000592436.1_Silent_p.A39A	NM_006732.2	NP_006723.2	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	39					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	13		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		CCACCGCCGCCGCCTCCCAGG	0.542													C|||	1990	0.397364	0.6362	0.1931	5008	,	,		14631	0.2292		0.3449	False		,,,				2504	0.4468				p.A39A		Atlas-SNP	.											.	FOSB	29	.	0			c.C117G						PASS	.		,	2435,1965		701,1033,466	39.0	50.0	46.0		117,117	4.3	1.0	19	dbSNP_100	46	2736,5856		480,1776,2040	no	coding-synonymous,coding-synonymous	FOSB	NM_001114171.1,NM_006732.2	,	1181,2809,2506	GG,GC,CC		31.8436,44.6591,39.8014	,	39/303,39/339	45971961	5171,7821	2200	4296	6496	SO:0001819	synonymous_variant	2354	exon1			CGCCGCCGCCTCC		CCDS12664.1, CCDS46113.1	19q13.3	2013-01-10						"""basic leucine zipper proteins"""	3797	protein-coding gene	gene with protein product	"""oncogene FOS-B"", ""activator protein 1"""	164772				1301997	Standard	NM_006732		Approved	G0S3, GOSB, GOS3, AP-1, MGC42291, DKFZp686C0818	uc002pbx.4	P53539		ENST00000353609.3:c.117C>G	19.37:g.45971961C>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001114171	A8K9K5|A8VJE1|A8VJE6|A8VJF0|A8VJF3|A8VJF7|A8VJG1|A8VJG5|A8VJG9|E7EPR6|E9PHJ3|K7EMJ6|Q49AD7	Silent	SNP	ENST00000353609.3	37	CCDS12664.1																																																																																			C|0.632;G|0.368	0.368	strong		0.542	FOSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459561.1	NM_006732	
LAMC3	10319	hgsc.bcm.edu	37	9	133946915	133946915	+	Silent	SNP	C	C	G	rs10901345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133946915C>G	ENST00000361069.4	+	18	3247	c.3114C>G	c.(3112-3114)ctC>ctG	p.L1038L	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1038	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		AGGGGTGGCTCCAAGGGTCCG	0.612													G|||	1468	0.293131	0.1619	0.3285	5008	,	,		19022	0.1954		0.4115	False		,,,				2504	0.4243				p.L1038L		Atlas-SNP	.											.	LAMC3	167	.	0			c.C3114G						PASS	.	G		868,3538	744.6+/-411.6	86,696,1421	92.0	81.0	85.0		3114	3.5	1.0	9	dbSNP_120	85	3487,5113	634.6+/-398.9	717,2053,1530	no	coding-synonymous	LAMC3	NM_006059.3		803,2749,2951	GG,GC,CC		40.5465,19.7004,33.4845		1038/1576	133946915	4355,8651	2203	4300	6503	SO:0001819	synonymous_variant	10319	exon18			GTGGCTCCAAGGG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3114C>G	9.37:g.133946915C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			C|0.671;G|0.329	0.329	strong		0.612	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
PTPRF	5792	hgsc.bcm.edu	37	1	44072066	44072066	+	Silent	SNP	C	C	T	rs10890266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000372413.3_Silent_p.P1204P|PTPRF_ENST00000438120.1_Silent_p.P1204P|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.P561P	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	69	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	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		
PRODH2	58510	hgsc.bcm.edu	37	19	36297966	36297966	+	Missense_Mutation	SNP	T	T	A	rs145964090		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36297966T>A	ENST00000301175.3	-	6	900	c.883A>T	c.(883-885)Agc>Tgc	p.S295C		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	295					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCAGGCGGCTGAGGGAGGCC	0.632																																					p.S295C		Atlas-SNP	.											.	PRODH2	68	.	0			c.A883T						PASS	.						20.0	23.0	22.0					19																	36297966		2135	4152	6287	SO:0001583	missense	58510	exon6			GGCGGCTGAGGGA	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.883A>T	19.37:g.36297966T>A	ENSP00000301175:p.Ser295Cys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	13	0.183099	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.962256	0.34659	.	.	ENSG00000250799	ENST00000301175	T	0.28895	1.59	5.11	1.81	0.25067	Proline dehydrogenase (1);	.	.	.	.	T	0.39064	0.1064	M	0.64404	1.975	0.19775	N	0.99996	D	0.60575	0.988	P	0.53689	0.732	T	0.20075	-1.0286	9	0.72032	D	0.01	.	5.7629	0.18211	0.0:0.0858:0.327:0.5873	.	295	Q9UF12	PROD2_HUMAN	C	295	ENSP00000301175:S295C	ENSP00000301175:S295C	S	-	1	0	PRODH2	40989806	0.362000	0.24980	0.313000	0.25210	0.052000	0.14988	0.545000	0.23268	0.134000	0.18681	-0.313000	0.08912	AGC	.	.	weak		0.632	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
MUC2	4583	hgsc.bcm.edu	37	11	1093354	1093354	+	Missense_Mutation	SNP	T	T	A	rs56290335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1093354T>A	ENST00000441003.2	+	30	5200	c.5173T>A	c.(5173-5175)Tcc>Acc	p.S1725T	MUC2_ENST00000333592.6_Missense_Mutation_p.S13T|MUC2_ENST00000359061.5_Missense_Mutation_p.S1692T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.S1725T(1)|p.S1692T(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)	gacacccatctccaccaccac	0.647																																					p.S1725T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	stomach(2)	c.T5173A						scavenged	.						207.0	244.0	231.0					11																	1093354		1965	3771	5736	SO:0001583	missense	4583	exon30			CCCATCTCCACCA	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.5173T>A	11.37:g.1093354T>A	ENSP00000415183:p.Ser1725Thr	Somatic	22	8	0.363636		WXS	Illumina HiSeq	Phase_I	32	12	0.375	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	0.005	-2.130853	0.00338	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.05580	3.56;3.42;3.71	1.49	-2.99	0.05497	.	0.209755	0.18974	U	0.126050	T	0.02156	0.0067	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40232	-0.9574	9	0.07813	T	0.8	.	3.3544	0.07164	0.3578:0.2012:0.0:0.441	rs56290335;rs61051760	1725	E7EUV1	.	T	1725;1692;13	ENSP00000415183:S1725T;ENSP00000351956:S1692T;ENSP00000331373:S13T	ENSP00000331373:S13T	S	+	1	0	MUC2	1083354	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.518000	0.06267	-2.490000	0.00517	-1.234000	0.01563	TCC	T|0.500;A|0.500	0.500	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CYP4F3	4051	hgsc.bcm.edu	37	19	15763721	15763721	+	Silent	SNP	G	G	A	rs1805042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:15763721G>A	ENST00000221307.8	+	9	1121	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	CYP4F3_ENST00000586182.2_Silent_p.V358V|CYP4F3_ENST00000585846.1_Silent_p.V358V|CYP4F3_ENST00000591058.1_Silent_p.V358V	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	358					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)	p.V358V(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						GGCAGGAGGTGCAAGAGCTTC	0.597													.|||	2580	0.515176	0.643	0.5663	5008	,	,		18400	0.6577		0.3509	False		,,,				2504	0.3282				p.V358V		Atlas-SNP	.											CYP4F3,NS,carcinoma,0,1	CYP4F3	69	1	1	Substitution - coding silent(1)	stomach(1)	c.G1074A						PASS	.	G	,,	2626,1780		800,1026,377	110.0	90.0	97.0		1074,1074,1074	0.2	0.6	19	dbSNP_111	97	3046,5554		551,1944,1805	no	coding-synonymous,coding-synonymous,coding-synonymous	CYP4F3	NM_000896.2,NM_001199208.1,NM_001199209.1	,,	1351,2970,2182	AA,AG,GG		35.4186,40.3995,43.6106	,,	358/521,358/521,358/521	15763721	5672,7334	2203	4300	6503	SO:0001819	synonymous_variant	4051	exon9			GGAGGTGCAAGAG	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.1074G>A	19.37:g.15763721G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	28	0.329412	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			G|0.523;A|0.477	0.477	strong		0.597	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32120678	32120678	+	Silent	SNP	C	C	T	rs2808100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32120678C>T	ENST00000344936.2	-	10	1671	c.1437G>A	c.(1435-1437)ggG>ggA	p.G479G	ARHGAP12_ENST00000375245.4_Silent_p.G427G|ARHGAP12_ENST00000311380.4_Silent_p.G427G|ARHGAP12_ENST00000375250.5_Silent_p.G449G|ARHGAP12_ENST00000396144.4_Silent_p.G474G	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	479	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				GAACCTTTTTCCCATTTTCAG	0.274													C|||	1211	0.241813	0.0908	0.2983	5008	,	,		16121	0.4127		0.2048	False		,,,				2504	0.2679				p.G479G		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.G1437A						PASS	.	C		476,3924	189.2+/-215.4	28,420,1752	116.0	109.0	111.0		1437	0.1	1.0	10	dbSNP_100	111	1747,6849	274.5+/-291.2	190,1367,2741	no	coding-synonymous	ARHGAP12	NM_018287.5		218,1787,4493	TT,TC,CC		20.3234,10.8182,17.1053		479/847	32120678	2223,10773	2200	4298	6498	SO:0001819	synonymous_variant	94134	exon10			CTTTTTCCCATTT	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1437G>A	10.37:g.32120678C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	205	93	0.453659	NM_018287	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	37	CCDS7170.1	522	0.23901098901098902	44	0.08943089430894309	90	0.24861878453038674	219	0.38286713286713286	169	0.22295514511873352	c	9.190	1.025724	0.19512	0.108182	0.203234	ENSG00000165322	ENST00000454919	.	.	.	5.51	0.0976	0.14494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999265	.	.	.	.	.	.	T	0.43572	-0.9383	3	.	.	.	.	5.5115	0.16884	0.1213:0.5113:0.0:0.3674	rs2808100;rs17582188;rs2808100	.	.	.	K	150	.	.	E	-	1	0	ARHGAP12	32160684	0.897000	0.30589	0.995000	0.50966	0.995000	0.86356	-0.141000	0.10327	-0.165000	0.10908	0.580000	0.79431	GAA	C|0.799;T|0.201	0.201	strong		0.274	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
SCARA5	286133	hgsc.bcm.edu	37	8	27767231	27767231	+	Missense_Mutation	SNP	C	C	G	rs17058207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:27767231C>G	ENST00000354914.3	-	5	1431	c.946G>C	c.(946-948)Gat>Cat	p.D316H	SCARA5_ENST00000518030.1_Missense_Mutation_p.D273H|SCARA5_ENST00000301906.4_Missense_Mutation_p.D273H|SCARA5_ENST00000524352.1_Missense_Mutation_p.D316H|SCARA5_ENST00000380385.2_Missense_Mutation_p.D91H|RP11-597M17.1_ENST00000517735.1_RNA	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	316	Collagen-like.		D -> H (in dbSNP:rs17058207). {ECO:0000269|Ref.3}.		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)		TTTCCTTCATCCCCCTGATCA	0.577													c|||	918	0.183307	0.1634	0.0706	5008	,	,		18293	0.376		0.0924	False		,,,				2504	0.1851				p.D316H		Atlas-SNP	.											.	SCARA5	53	.	0			c.G946C						PASS	.		HIS/ASP	589,3639		41,507,1566	94.0	62.0	73.0		946	-1.9	0.2	8	dbSNP_123	73	637,7529		27,583,3473	yes	missense	SCARA5	NM_173833.5	81	68,1090,5039	GG,GC,CC		7.8006,13.9309,9.8919	benign	316/496	27767231	1226,11168	2114	4083	6197	SO:0001583	missense	286133	exon5			CTTCATCCCCCTG	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.946G>C	8.37:g.27767231C>G	ENSP00000346990:p.Asp316His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	387	0.1771978021978022	100	0.2032520325203252	22	0.06077348066298342	191	0.3339160839160839	74	0.09762532981530343	C	7.087	0.571454	0.13623	0.139309	0.078006	ENSG00000168079	ENST00000354914;ENST00000380385;ENST00000517320;ENST00000524352;ENST00000518030;ENST00000301906	D;D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18;-3.18	4.99	-1.85	0.07784	.	0.751599	0.13024	N	0.419834	T	0.00012	0.0000	L	0.28014	0.82	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	0.001;0.003;0.003;0.002	T	0.04885	-1.0920	9	0.12766	T	0.61	.	5.1821	0.15165	0.0:0.2863:0.166:0.5477	rs17058207;rs52827400;rs57572280;rs17058207	91;316;273;316	Q6ZMJ2-4;Q6ZMJ2-2;Q6ZMJ2-3;Q6ZMJ2	.;.;.;SCAR5_HUMAN	H	316;91;116;316;273;273	ENSP00000346990:D316H;ENSP00000369746:D91H;ENSP00000428663:D316H;ENSP00000430713:D273H;ENSP00000301906:D273H	ENSP00000301906:D273H	D	-	1	0	SCARA5	27823150	0.039000	0.19947	0.178000	0.23040	0.949000	0.60115	-0.072000	0.11486	-0.045000	0.13468	-0.291000	0.09656	GAT	C|0.835;G|0.165	0.165	strong		0.577	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
POMC	5443	hgsc.bcm.edu	37	2	25384113	25384113	+	Missense_Mutation	SNP	T	T	C	rs80326661	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25384113T>C	ENST00000405623.1	-	3	1096	c.641A>G	c.(640-642)gAg>gGg	p.E214G	POMC_ENST00000264708.3_Missense_Mutation_p.E214G|POMC_ENST00000395826.2_Missense_Mutation_p.E214G|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000380794.1_Missense_Mutation_p.E214G			P01189	COLI_HUMAN	proopiomelanocortin	214			E -> G (in dbSNP:rs80326661). {ECO:0000269|PubMed:9768693}.		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)	GTCCTTCTTCTCGGCCGCCAC	0.697													T|||	7	0.00139776	0.0	0.0	5008	,	,		15787	0.0		0.007	False		,,,				2504	0.0				p.E214G	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											POMC,colon,carcinoma,-1,1	POMC	33	1	0			c.A641G	GRCh37	CM984056	POMC	M	rs80326661	scavenged	.	T	GLY/GLU,GLY/GLU	6,4400	8.1+/-20.4	0,6,2197	24.0	26.0	25.0		641,641	-2.6	0.3	2	dbSNP_131	25	62,8538	35.9+/-90.5	0,62,4238	yes	missense,missense	POMC	NM_000939.2,NM_001035256.1	98,98	0,68,6435	CC,CT,TT		0.7209,0.1362,0.5228	possibly-damaging,possibly-damaging	214/268,214/268	25384113	68,12938	2203	4300	6503	SO:0001583	missense	5443	exon4			TTCTTCTCGGCCG		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.641A>G	2.37:g.25384113T>C	ENSP00000384092:p.Glu214Gly	Somatic	25	1	0.04		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	37	CCDS1717.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	8.778	0.927470	0.18056	0.001362	0.007209	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.80033	-1.32;-1.32;-1.32;-1.32;-1.33	4.94	-2.56	0.06268	.	0.859913	0.10550	N	0.661521	T	0.65281	0.2676	M	0.80183	2.485	0.23657	N	0.997187	P	0.36086	0.536	B	0.27380	0.079	T	0.62685	-0.6802	10	0.87932	D	0	-23.9239	1.564	0.02601	0.3754:0.0782:0.2568:0.2896	.	214	P01189	COLI_HUMAN	G	214	ENSP00000370171:E214G;ENSP00000384092:E214G;ENSP00000264708:E214G;ENSP00000379170:E214G;ENSP00000387993:E214G	ENSP00000264708:E214G	E	-	2	0	POMC	25237617	0.001000	0.12720	0.348000	0.25681	0.190000	0.23558	-0.012000	0.12699	-0.317000	0.08677	-0.379000	0.06801	GAG	T|0.996;C|0.004	0.004	strong		0.697	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256	
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:170037572G>A	ENST00000284637.9	-	10	2328	c.1987C>T	c.(1987-1989)Cca>Tca	p.P663S	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	663			P -> S (in dbSNP:rs3811813).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		GAAGTCAGTGGAGCAGCTGCT	0.622													G|||	462	0.0922524	0.0083	0.062	5008	,	,		19880	0.0813		0.1362	False		,,,				2504	0.1933				p.P663S		Atlas-SNP	.											SH3RF1,NS,carcinoma,+2,1	SH3RF1	60	1	0			c.C1987T						PASS	.	G	SER/PRO	166,4240	109.1+/-147.4	3,160,2040	61.0	52.0	55.0		1987	1.4	0.0	4	dbSNP_107	55	1098,7502	228.7+/-263.7	80,938,3282	yes	missense	SH3RF1	NM_020870.3	74	83,1098,5322	AA,AG,GG		12.7674,3.7676,9.7186	benign	663/889	170037572	1264,11742	2203	4300	6503	SO:0001583	missense	57630	exon10			TCAGTGGAGCAGC	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"""RING-type (C3HC4) zinc fingers"""	17650	protein-coding gene	gene with protein product	"""plenty of SH3 domains"""		"""SH3 multiple domains 2"""	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1987C>T	4.37:g.170037572G>A	ENSP00000284637:p.Pro663Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	37	CCDS34099.1	177	0.08104395604395605	5	0.01016260162601626	28	0.07734806629834254	39	0.06818181818181818	105	0.13852242744063326	G	0.259	-1.000945	0.02128	0.037676	0.127674	ENSG00000154447	ENST00000284637	T	0.10960	2.82	5.24	1.38	0.22167	.	0.261100	0.27563	N	0.018810	T	0.00039	0.0001	N	0.00926	-1.1	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43572	-0.9383	9	0.02654	T	1	-1.1484	5.8399	0.18627	0.7065:0.1407:0.1528:0.0	rs3811813;rs60713833;rs3811813	663	Q7Z6J0	SH3R1_HUMAN	S	663	ENSP00000284637:P663S	ENSP00000284637:P663S	P	-	1	0	SH3RF1	170274147	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	3.648000	0.54410	0.009000	0.14813	-0.378000	0.06908	CCA	G|0.906;A|0.094	0.094	strong		0.622	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	
C16orf89	146556	hgsc.bcm.edu	37	16	5097947	5097947	+	Missense_Mutation	SNP	A	A	G	rs1127920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5097947A>G	ENST00000315997.5	-	7	1088	c.887T>C	c.(886-888)tTa>tCa	p.L296S	C16orf89_ENST00000422873.1_Missense_Mutation_p.L334S|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Missense_Mutation_p.L296S|C16orf89_ENST00000350219.4_Missense_Mutation_p.L334S|C16orf89_ENST00000474471.3_Missense_Mutation_p.L328S	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	296			L -> S (in dbSNP:rs1127920). {ECO:0000269|PubMed:15489334}.			cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						AGCTTTAGATAATTCTTCATC	0.328													A|||	1132	0.226038	0.0325	0.4337	5008	,	,		18221	0.2034		0.3678	False		,,,				2504	0.2178				p.L296S		Atlas-SNP	.											.	C16orf89	64	.	0			c.T887C						PASS	.	A	SER/LEU,SER/LEU	324,3282		13,298,1492	63.0	56.0	58.0		887,887	-2.8	0.0	16	dbSNP_86	58	2784,5348		479,1826,1761	yes	missense,missense	C16orf89	NM_001098514.2,NM_152459.4	145,145	492,2124,3253	GG,GA,AA		34.2351,8.985,26.4781	possibly-damaging,possibly-damaging	296/362,296/403	5097947	3108,8630	1803	4066	5869	SO:0001583	missense	146556	exon7			TTAGATAATTCTT		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.887T>C	16.37:g.5097947A>G	ENSP00000324672:p.Leu296Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Missense_Mutation	SNP	ENST00000315997.5	37	CCDS42116.2	558	0.2554945054945055	21	0.042682926829268296	141	0.38950276243093923	113	0.19755244755244755	283	0.3733509234828496	A	14.34	2.506853	0.44558	0.08985	0.342351	ENSG00000153446	ENST00000474471;ENST00000472572;ENST00000477550;ENST00000422873;ENST00000350219;ENST00000315997	T;T;T;T	0.40225	1.17;1.04;1.04;1.17	3.59	-2.84	0.05751	.	1.396170	0.04946	N	0.459453	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.38922	0.651;0.617	B;B	0.42282	0.212;0.382	T	0.18745	-1.0327	9	0.56958	D	0.05	-23.7719	1.8854	0.03237	0.269:0.1639:0.4064:0.1607	rs1127920;rs3210909;rs9674145;rs11558485;rs17846054;rs17859047;rs52830272;rs9674145	296;334	Q6UX73;G3V0F0	CP089_HUMAN;.	S	328;296;296;334;334;328	ENSP00000417158:L328S;ENSP00000420566:L296S;ENSP00000390402:L334S;ENSP00000283478:L334S	ENSP00000324672:L328S	L	-	2	0	C16orf89	5037948	0.000000	0.05858	0.000000	0.03702	0.621000	0.37620	-0.056000	0.11787	-0.796000	0.04456	0.459000	0.35465	TTA	T|0.086;G|0.260	0.260	strong		0.328	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
PAK7	57144	hgsc.bcm.edu	37	20	9547018	9547018	+	Missense_Mutation	SNP	C	C	G	rs11700112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:9547018C>G	ENST00000378429.3	-	6	1550	c.1004G>C	c.(1003-1005)cGa>cCa	p.R335P	PAK7_ENST00000378423.1_Missense_Mutation_p.R335P|PAK7_ENST00000353224.5_Missense_Mutation_p.R335P	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	335	Linker.		R -> P (in dbSNP:rs11700112). {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)			CATCTGTGCTCGATCGTAATC	0.537													C|||	583	0.116414	0.0499	0.1787	5008	,	,		20027	0.2381		0.0954	False		,,,				2504	0.0583				p.R335P		Atlas-SNP	.											.	PAK7	194	.	0			c.G1004C	GRCh37	CM065365	PAK7	M	rs11700112	PASS	.	C	PRO/ARG,PRO/ARG	235,4171	138.4+/-174.2	9,217,1977	104.0	106.0	105.0		1004,1004	5.0	1.0	20	dbSNP_120	105	814,7786	189.4+/-236.2	40,734,3526	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	103,103	49,951,5503	GG,GC,CC		9.4651,5.3336,8.0655	benign,benign	335/720,335/720	9547018	1049,11957	2203	4300	6503	SO:0001583	missense	57144	exon5			TGTGCTCGATCGT	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.1004G>C	20.37:g.9547018C>G	ENSP00000367686:p.Arg335Pro	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	305	0.13965201465201466	19	0.03861788617886179	71	0.19613259668508287	146	0.25524475524475526	69	0.09102902374670185	C	13.14	2.148585	0.37923	0.053336	0.094651	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.73575	-0.76;-0.76;-0.76	5.94	5.0	0.66597	.	0.129994	0.53938	D	0.000045	T	0.00039	0.0001	L	0.40543	1.245	0.09310	P	0.9999999490538	P;B	0.43477	0.808;0.0	P;B	0.46718	0.525;0.0	T	0.00783	-1.1568	8	.	.	.	.	15.1715	0.72878	0.0:0.9326:0.0:0.0674	rs11700112;rs11700112	335;335	B0AZM9;Q9P286	.;PAK7_HUMAN	P	335;335;335;283	ENSP00000367686:R335P;ENSP00000322957:R335P;ENSP00000367679:R335P	.	R	-	2	0	PAK7	9495018	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.261000	0.65496	1.519000	0.48950	0.591000	0.81541	CGA	C|0.888;G|0.112;T|0.000	0.112	strong		0.537	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
ERAP1	51752	hgsc.bcm.edu	37	5	96139595	96139595	+	Missense_Mutation	SNP	G	G	A	rs72773968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:96139595G>A	ENST00000443439.2	-	2	101	c.35C>T	c.(34-36)aCc>aTc	p.T12I	ERAP1_ENST00000296754.3_Missense_Mutation_p.T12I|CTD-2260A17.3_ENST00000606346.1_RNA|CTD-2260A17.3_ENST00000606656.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	12				T -> I (in Ref. 1; AAF07395 and 2; AAK37777/AAK37778). {ECO:0000305}.	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)		AAATGACATGGTTGCAAGGGA	0.428													G|||	358	0.0714856	0.0053	0.1643	5008	,	,		22426	0.004		0.1382	False		,,,				2504	0.0961				p.T12I		Atlas-SNP	.											.	ERAP1	59	.	0			c.C35T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	104,4302	80.9+/-119.3	0,104,2099	85.0	79.0	81.0		35,35,35	2.5	0.0	5	dbSNP_130	81	1175,7425	239.7+/-270.7	63,1049,3188	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	89,89,89	63,1153,5287	AA,AG,GG		13.6628,2.3604,9.8339	possibly-damaging,possibly-damaging,possibly-damaging	12/942,12/942,12/949	96139595	1279,11727	2203	4300	6503	SO:0001583	missense	51752	exon2			GACATGGTTGCAA	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.35C>T	5.37:g.96139595G>A	ENSP00000406304:p.Thr12Ile	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	155	0.07097069597069597	3	0.006097560975609756	56	0.15469613259668508	1	0.0017482517482517483	95	0.12532981530343007	G	12.45	1.943106	0.34283	0.023604	0.136628	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384;ENST00000507154	T;T;T	0.36157	5.03;5.03;1.27	5.31	2.49	0.30216	.	1.245050	0.05408	N	0.541989	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	P;P	0.41188	0.624;0.741	B;B	0.41988	0.206;0.372	T	0.27191	-1.0081	9	0.32370	T	0.25	.	14.431	0.67251	0.0:0.5976:0.4024:0.0	.	12;12	Q9NZ08;Q9NZ08-2	ERAP1_HUMAN;.	I	12	ENSP00000296754:T12I;ENSP00000406304:T12I;ENSP00000421697:T12I	ENSP00000296754:T12I	T	-	2	0	ERAP1	96165351	0.029000	0.19370	0.000000	0.03702	0.010000	0.07245	0.728000	0.26013	0.211000	0.20683	0.561000	0.74099	ACC	G|0.911;A|0.089	0.089	strong		0.428	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
FLNA	2316	hgsc.bcm.edu	37	X	153594535	153594535	+	Missense_Mutation	SNP	G	G	A	rs36051194		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153594535G>A	ENST00000369850.3	-	9	1522	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M	FLNA_ENST00000422373.1_Missense_Mutation_p.T429M|FLNA_ENST00000344736.4_Missense_Mutation_p.T429M|FLNA_ENST00000360319.4_Missense_Mutation_p.T429M	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	429			T -> M. {ECO:0000269|PubMed:12612583}.		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)					AGGCTCTACCGTGCCCTTCTG	0.682													G|||	16	0.00423841	0.0	0.0058	3775	,	,		12254	0.0		0.0119	False		,,,				2504	0.0				p.T429M		Atlas-SNP	.											.	FLNA	373	.	0			c.C1286T	GRCh37	CM065185	FLNA	M	rs36051194	PASS	.		MET/THR,MET/THR	9,3653		0,7,2,1539,568	48.0	53.0	51.0		1286,1286	3.8	0.3	X	dbSNP_126	51	107,6462		0,74,33,2305,1778	yes	missense,missense	FLNA	NM_001110556.1,NM_001456.3	81,81	0,81,35,3844,2346	AA,AG,A,GG,G		1.6289,0.2458,1.1338	probably-damaging,probably-damaging	429/2648,429/2640	153594535	116,10115	2116	4190	6306	SO:0001583	missense	2316	exon9			TCTACCGTGCCCT	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.1286C>T	X.37:g.153594535G>A	ENSP00000358866:p.Thr429Met	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	52	0.928571	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	8	0.004822182037371911	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	4.764	0.142126	0.09083	0.002458	0.016289	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.68	3.81	0.43845	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83626	0.5295	M	0.78285	2.405	0.80722	D	1	P;D	0.69078	0.839;0.997	B;D	0.62955	0.281;0.909	D	0.84840	0.0807	10	0.40728	T	0.16	.	11.1083	0.48216	0.096:0.0:0.904:0.0	rs36051194	429;429	P21333-2;P21333	.;FLNA_HUMAN	M	429;402;429;429;429	ENSP00000353467:T429M;ENSP00000416926:T429M;ENSP00000358866:T429M;ENSP00000358863:T429M	ENSP00000358863:T429M	T	-	2	0	FLNA	153247729	1.000000	0.71417	0.266000	0.24541	0.038000	0.13279	3.356000	0.52269	0.763000	0.33175	0.464000	0.42555	ACG	G|0.995;A|0.005	0.005	strong		0.682	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
FMN2	56776	hgsc.bcm.edu	37	1	240371085	240371085	+	Silent	SNP	A	A	T	rs71646826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.						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	50	2	0.04		WXS	Illumina HiSeq	Phase_I	75	19	0.253333	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	
MED16	10025	hgsc.bcm.edu	37	19	871135	871135	+	Silent	SNP	A	A	G	rs1683569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:871135A>G	ENST00000589119.1	-	12	2216	c.2217T>C	c.(2215-2217)gtT>gtC	p.V739V	MED16_ENST00000606828.1_5'Flank|MED16_ENST00000325464.1_Silent_p.V739V|MED16_ENST00000395808.3_Silent_p.V739V|MED16_ENST00000269814.4_Missense_Mutation_p.L675S|MED16_ENST00000312090.6_Silent_p.V758V			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	739					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		GCAGGCGGCTAACCAGGCCGT	0.701													g|||	1326	0.264776	0.5008	0.2205	5008	,	,		12505	0.0317		0.2873	False		,,,				2504	0.1943				p.V739V		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	1	0			c.T2217C						PASS	.			1482,2440		291,900,770	9.0	11.0	10.0		2217	3.1	1.0	19	dbSNP_89	10	1843,5871		223,1397,2237	no	coding-synonymous	MED16	NM_005481.2		514,2297,3007	GG,GA,AA		23.8916,37.7868,28.5751		739/878	871135	3325,8311	1961	3857	5818	SO:0001819	synonymous_variant	10025	exon13			GCGGCTAACCAGG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2217T>C	19.37:g.871135A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1	567	0.25961538461538464	240	0.4878048780487805	89	0.24585635359116023	20	0.03496503496503497	218	0.287598944591029	g	18.38	3.611665	0.66558	0.377868	0.238916	ENSG00000175221	ENST00000269814	.	.	.	4.13	3.06	0.35304	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47065	P	6.960000000000299E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44711	-0.9310	6	0.09590	T	0.72	-40.3568	9.783	0.40660	0.177:0.0:0.823:0.0	rs1683569;rs59662712;rs1683569	675	Q9Y2X0-4	.	S	675	.	ENSP00000269814:L675S	L	-	2	0	MED16	822135	1.000000	0.71417	0.984000	0.44739	0.793000	0.44817	2.176000	0.42500	0.718000	0.32166	-0.258000	0.10820	TTA	A|0.743;G|0.257	0.257	strong		0.701	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
CATSPERG	57828	hgsc.bcm.edu	37	19	38861333	38861333	+	Silent	SNP	G	G	A	rs1052375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:38861333G>A	ENST00000409235.3	+	29	3496	c.3381G>A	c.(3379-3381)ccG>ccA	p.P1127P	CATSPERG_ENST00000215069.4_3'UTR|CATSPERG_ENST00000410018.1_Silent_p.P1087P	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	102	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	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	
BCAR1	9564	hgsc.bcm.edu	37	16	75269534	75269534	+	Silent	SNP	C	C	T	rs3743613	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:75269534C>T	ENST00000162330.5	-	5	1389	c.1263G>A	c.(1261-1263)ccG>ccA	p.P421P	BCAR1_ENST00000535626.2_Silent_p.P273P|BCAR1_ENST00000418647.3_Silent_p.P467P|BCAR1_ENST00000393422.2_Silent_p.P439P|BCAR1_ENST00000546196.1_Silent_p.P392P|BCAR1_ENST00000420641.3_Silent_p.P439P|BCAR1_ENST00000393420.6_Silent_p.P439P|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000542031.2_Silent_p.P419P|BCAR1_ENST00000538440.2_Silent_p.P421P	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	78	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	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	
CRHR1	1394	hgsc.bcm.edu	37	17	43906973	43906973	+	Missense_Mutation	SNP	G	G	A	rs75638861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:43906973G>A	ENST00000398285.3	+	6	481	c.481G>A	c.(481-483)Gtg>Atg	p.V161M	CRHR1_ENST00000352855.5_Intron|CRHR1_ENST00000577353.1_Intron|CRHR1_ENST00000314537.5_Intron|CRHR1_ENST00000293493.7_Intron|CRHR1_ENST00000339069.5_Intron	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	161					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)		AGCCCTGGAGGTGGGGGCTCC	0.622													G|||	19	0.00379393	0.0008	0.0101	5008	,	,		18683	0.0		0.0089	False		,,,				2504	0.002				p.V161M	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.G481A						PASS	.	G	MET/VAL,,,	1,1383		0,1,691	32.0	38.0	36.0		481,,,	0.2	0.0	17	dbSNP_131	36	40,3142		0,40,1551	yes	missense,intron,intron,intron	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	21,,,	0,41,2242	AA,AG,GG		1.2571,0.0723,0.8979	,,,	161/445,,,	43906973	41,4525	692	1591	2283	SO:0001583	missense	1394	exon6			CTGGAGGTGGGGG	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.481G>A	17.37:g.43906973G>A	ENSP00000381333:p.Val161Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Missense_Mutation	SNP	ENST00000398285.3	37	CCDS45712.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	G	6.788	0.514380	0.12944	7.23E-4	0.012571	ENSG00000120088	ENST00000398285	T	0.39406	1.08	2.4	0.201	0.15186	GPCR, family 2-like (1);	1.915210	0.03115	U	0.163033	T	0.17408	0.0418	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22977	-1.0201	10	0.66056	D	0.02	.	3.9886	0.09527	0.4946:0.0:0.5054:0.0	.	161	P34998	CRFR1_HUMAN	M	161	ENSP00000381333:V161M	ENSP00000381333:V161M	V	+	1	0	CRHR1	41262754	0.000000	0.05858	0.005000	0.12908	0.046000	0.14306	-0.088000	0.11198	0.058000	0.16222	0.491000	0.48974	GTG	G|0.994;A|0.006	0.006	strong		0.622	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
PTPLA	9200	hgsc.bcm.edu	37	10	17659149	17659149	+	Missense_Mutation	SNP	C	C	T	rs7895850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:17659149C>T	ENST00000361271.3	-	1	227	c.190G>A	c.(190-192)Gag>Aag	p.E64K	PTPLA_ENST00000326961.6_Missense_Mutation_p.E64K	NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	64			E -> K (in dbSNP:rs7895850). {ECO:0000269|PubMed:10644438, ECO:0000269|PubMed:11054553, ECO:0000269|PubMed:15489334}.|E -> Q (in dbSNP:rs7895850). {ECO:0000269|PubMed:11054553}.		fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						CGCCTCCGCTCGCCGGGAGCC	0.766													T|||	4465	0.891573	0.9599	0.879	5008	,	,		6575	0.7679		0.8897	False		,,,				2504	0.9376				p.E64K		Atlas-SNP	.											.	PTPLA	34	.	0			c.G190A						PASS	.	T	LYS/GLN/GLU	2648,64,0		1292,64,0,0,0,0	2.0	4.0	4.0		190	2.0	0.1	10	dbSNP_116	4	4685,237,0		2230,225,0,6,0,0	no	missense	PTPLA	NM_014241.3	29,56	3522,289,0,6,0,0	TT,TG,TC,GG,GC,CC		4.8151,2.3599,3.9429	benign	64/289	17659149	7333,301,0	1356	2461	3817	SO:0001583	missense	9200	exon1			TCCGCTCGCCGGG	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.190G>A	10.37:g.17659149C>T	ENSP00000355308:p.Glu64Lys	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	2169	0.9931318681318682	491	0.9979674796747967	360	0.994475138121547	568	0.993006993006993	750	0.9894459102902374	T	9.049	0.991537	0.18966	0.976401	0.951849	ENSG00000165996	ENST00000361271;ENST00000326961	T;T	0.13657	2.86;2.57	3.35	2.04	0.26737	.	0.660756	0.13666	N	0.371221	T	0.00012	0.0000	N	0.00186	-1.895	0.58432	P	5.999999999950489E-6	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24584	-1.0156	9	0.02654	T	1	-20.0823	3.214	0.06692	0.0:0.1393:0.2442:0.6165	rs7895850;rs17856330	64;64;64	A6NP58;B0YJ81-2;B0YJ81	.;.;HACD1_HUMAN	K	64	ENSP00000355308:E64K;ENSP00000322923:E64K	ENSP00000322923:E64K	E	-	1	0	PTPLA	17699155	1.000000	0.71417	0.050000	0.19076	0.003000	0.03518	1.138000	0.31491	0.439000	0.26476	-0.381000	0.06696	GAG	C|0.007;G|0.002;T|0.991	0.991	strong		0.766	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
OR2D3	120775	hgsc.bcm.edu	37	11	6942695	6942695	+	Missense_Mutation	SNP	C	C	T	rs12806437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	210	0	0		WXS	Illumina HiSeq	Phase_I	258	137	0.531008	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	
MAPKBP1	23005	hgsc.bcm.edu	37	15	42115747	42115747	+	Missense_Mutation	SNP	G	G	C	rs3959569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42115747G>C	ENST00000456763.2	+	30	3915	c.3719G>C	c.(3718-3720)cGt>cCt	p.R1240P	RP11-23P13.4_ENST00000512295.1_RNA|RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R1117P|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.R1073P|MAPKBP1_ENST00000514566.1_Intron|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R1234P	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1240			R -> P (in dbSNP:rs3959569). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15491607, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9628581}.							breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GCTGATGGCCGTCCGTCTCGG	0.617													g|||	1172	0.234026	0.0371	0.4121	5008	,	,		19490	0.1796		0.3479	False		,,,				2504	0.3129				p.R1240P		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.G3719C						PASS	.	G	PRO/ARG,PRO/ARG	418,3988		28,362,1813	68.0	63.0	64.0		3719,3701	-0.6	0.0	15	dbSNP_108	64	2858,5742		464,1930,1906	yes	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	103,103	492,2292,3719	CC,CG,GG		33.2326,9.4871,25.1884	benign,benign	1240/1515,1234/1509	42115747	3276,9730	2203	4300	6503	SO:0001583	missense	23005	exon30			ATGGCCGTCCGTC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.3719G>C	15.37:g.42115747G>C	ENSP00000393099:p.Arg1240Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	524	0.23992673992673993	20	0.04065040650406504	140	0.3867403314917127	92	0.16083916083916083	272	0.35883905013192613	.	9.525	1.109421	0.20714	0.094871	0.332326	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763	T;T;T;T	0.42131	1.18;1.32;0.98;1.23	5.82	-0.625	0.11548	.	1.160040	0.05950	N	0.638738	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P;B;B;B	0.34615	0.0;0.459;0.337;0.002;0.002	B;B;B;B;B	0.38712	0.001;0.28;0.147;0.002;0.004	T	0.39165	-0.9627	9	0.33141	T	0.24	2.2892	7.306	0.26447	0.3584:0.1107:0.5308:0.0	rs3959569;rs56957727	1073;1117;1073;1240;1234	F8WC21;O60336-3;B4DYK7;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	P	1234;1117;1073;1240	ENSP00000397570:R1234P;ENSP00000221214:R1117P;ENSP00000260357:R1073P;ENSP00000393099:R1240P	ENSP00000221214:R1117P	R	+	2	0	MAPKBP1	39903039	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.783000	0.04638	-0.686000	0.05170	-2.487000	0.00196	CGT	G|0.740;C|0.260	0.260	strong		0.617	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
TM9SF2	9375	hgsc.bcm.edu	37	13	100181829	100181829	+	Silent	SNP	T	T	C	rs34302265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:100181829T>C	ENST00000376387.4	+	4	632	c.442T>C	c.(442-444)Ttg>Ctg	p.L148L	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	148					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					AAGCATGTTATTGAATTATCA	0.303													T|||	16	0.00319489	0.003	0.0029	5008	,	,		18094	0.001		0.008	False		,,,				2504	0.001				p.L148L		Atlas-SNP	.											.	TM9SF2	52	.	0			c.T442C						PASS	.	T		6,4398	11.4+/-27.6	0,6,2196	96.0	99.0	98.0		442	3.4	1.0	13	dbSNP_126	98	44,8544	27.9+/-77.7	0,44,4250	no	coding-synonymous	TM9SF2	NM_004800.1		0,50,6446	CC,CT,TT		0.5123,0.1362,0.3849		148/664	100181829	50,12942	2202	4294	6496	SO:0001819	synonymous_variant	9375	exon4			ATGTTATTGAATT	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.442T>C	13.37:g.100181829T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_004800	A8K399|Q2TAY5	Silent	SNP	ENST00000376387.4	37	CCDS9493.1																																																																																			T|0.995;C|0.005	0.005	strong		0.303	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
CLEC18B	497190	hgsc.bcm.edu	37	16	74444863	74444863	+	Missense_Mutation	SNP	G	G	A	rs148861848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74444863G>A	ENST00000339953.5	-	9	1175	c.1054C>T	c.(1054-1056)Cgc>Tgc	p.R352C		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	352	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GTCTCCAGGCGGCCCAGATAG	0.587																																					p.R352C		Atlas-SNP	.											CLEC18B,NS,haematopoietic_neoplasm,0,1	CLEC18B	45	1	0			c.C1054T						scavenged	.						2.0	2.0	2.0					16																	74444863		689	1379	2068	SO:0001583	missense	497190	exon9			CCAGGCGGCCCAG	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.1054C>T	16.37:g.74444863G>A	ENSP00000341051:p.Arg352Cys	Somatic	626	0	0		WXS	Illumina HiSeq	Phase_I	596	69	0.115772	NM_001011880	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	N	17.05	3.291101	0.59976	.	.	ENSG00000140839	ENST00000429489;ENST00000339953	T	0.56103	0.48	3.14	3.14	0.36123	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.446501	0.24806	N	0.035446	T	0.65344	0.2682	M	0.68952	2.095	0.41433	D	0.987878	D;D	0.89917	1.0;1.0	D;D	0.65773	0.938;0.938	T	0.68823	-0.5307	10	0.87932	D	0	.	9.6467	0.39872	0.0:0.0:1.0:0.0	.	352;352	C9JSV1;Q6UXF7	.;CL18B_HUMAN	C	352	ENSP00000341051:R352C	ENSP00000341051:R352C	R	-	1	0	CLEC18B	73002364	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.802000	0.62539	1.602000	0.50124	0.425000	0.28330	CGC	G|0.958;A|0.042	0.042	strong		0.587	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
HBEGF	1839	hgsc.bcm.edu	37	5	139722345	139722345	+	Silent	SNP	G	G	A	rs2074611	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:139722345G>A	ENST00000230990.6	-	3	575	c.273C>T	c.(271-273)caC>caT	p.H91H	HBEGF_ENST00000507104.1_Silent_p.H91H	NM_001945.2	NP_001936.1	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	91					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)|muscle organ development (GO:0007517)|negative regulation of elastin biosynthetic process (GO:0051545)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of wound healing (GO:0090303)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.H91H(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)	7			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTTTTCCCGTGCTCCTCCT	0.463													G|||	646	0.128994	0.2292	0.0591	5008	,	,		20476	0.1012		0.0646	False		,,,				2504	0.138				p.H91H		Atlas-SNP	.											HBEGF,NS,carcinoma,0,1	HBEGF	12	1	1	Substitution - coding silent(1)	stomach(1)	c.C273T						scavenged	.	G		802,3604	323.4+/-298.1	71,660,1472	357.0	372.0	367.0		273	-3.0	0.0	5	dbSNP_96	367	611,7989	160.0+/-213.2	17,577,3706	no	coding-synonymous	HBEGF	NM_001945.2		88,1237,5178	AA,AG,GG		7.1047,18.2025,10.8642		91/209	139722345	1413,11593	2203	4300	6503	SO:0001819	synonymous_variant	1839	exon3			TTTCCCGTGCTCC		CCDS4223.1	5q23	2012-10-02	2005-01-14	2005-01-14	ENSG00000113070	ENSG00000113070			3059	protein-coding gene	gene with protein product	"""Diphtheria toxin receptor (heparin-binding EGF-like growth factor)"", ""heparin-binding epidermal growth factor"""	126150	"""diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)"""	HEGFL, DTS, DTR		7590736, 12163414	Standard	NM_001945		Approved		uc003lfi.3	Q99075	OTTHUMG00000129496	ENST00000230990.6:c.273C>T	5.37:g.139722345G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	181	81	0.447514	NM_001945	B2R821	Silent	SNP	ENST00000230990.6	37	CCDS4223.1																																																																																			T|0.002;G|0.881;C|0.008;A|0.110	0.110	strong		0.463	HBEGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251665.2	NM_001945	
CFAP46	54777	hgsc.bcm.edu	37	10	134736076	134736076	+	Missense_Mutation	SNP	T	T	G	rs4880288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:134736076T>G	ENST00000368586.5	-	12	1493	c.1393A>C	c.(1393-1395)Atc>Ctc	p.I465L	TTC40_ENST00000368582.2_Missense_Mutation_p.I465L	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GCCATCTGGATCCTGTCCCGG	0.692													G|||	2822	0.563498	0.7511	0.6311	5008	,	,		15443	0.3542		0.4742	False		,,,				2504	0.5695				p.I465L		Atlas-SNP	.											.	TTC40	100	.	0			c.A1393C						PASS	.																																			SO:0001583	missense	54777	exon12			TCTGGATCCTGTC																												ENST00000368586.5:c.1393A>C	10.37:g.134736076T>G	ENSP00000357575:p.Ile465Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	1123	0.5141941391941391	345	0.7012195121951219	219	0.6049723756906077	211	0.3688811188811189	348	0.45910290237467016	G	0.004	-2.263662	0.00262	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.30448	3.5;1.53	3.28	1.22	0.21188	.	0.218401	0.29342	N	0.012439	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39742	-0.9599	6	0.02654	T	1	-11.0966	9.8203	0.40878	0.0:0.0:0.4419:0.5581	rs4880288	.	.	.	L	465	ENSP00000357575:I465L;ENSP00000357571:I465L	ENSP00000357571:I465L	I	-	1	0	C10orf93	134586066	0.084000	0.21492	0.000000	0.03702	0.008000	0.06430	1.285000	0.33261	-0.088000	0.12506	-0.358000	0.07595	ATC	T|0.485;G|0.515	0.515	strong		0.692	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
F5	2153	hgsc.bcm.edu	37	1	169551682	169551682	+	Silent	SNP	T	T	C	rs6028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169551682T>C	ENST00000367797.3	-	2	438	c.237A>G	c.(235-237)caA>caG	p.Q79Q	F5_ENST00000546081.1_Intron|F5_ENST00000367796.3_Silent_p.Q79Q	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	79	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)	p.Q79Q(1)		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)	AAATGGTAGATTGTGGTTTTT	0.269													t|||	1134	0.226438	0.028	0.3501	5008	,	,		15692	0.2044		0.2942	False		,,,				2504	0.3599				p.Q79Q		Atlas-SNP	.											F5,NS,carcinoma,0,1	F5	301	1	1	Substitution - coding silent(1)	stomach(1)	c.A237G						PASS	.	C		311,4043		14,283,1880	32.0	32.0	32.0		237	3.3	0.2	1	dbSNP_52	32	2331,6177		315,1701,2238	no	coding-synonymous	F5	NM_000130.4		329,1984,4118	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	27.3977,7.1429,20.5411		79/2225	169551682	2642,10220	2177	4254	6431	SO:0001819	synonymous_variant	2153	exon2			GGTAGATTGTGGT	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.237A>G	1.37:g.169551682T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	80	0.601504	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			C|0.214;N|0.000	0.214	strong		0.269	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140787850	140787850	+	Silent	SNP	C	C	T	rs62378453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140787850C>T	ENST00000520790.1	+	1	81	c.81C>T	c.(79-81)ccC>ccT	p.P27P	PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_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)																									p.P27P		Atlas-SNP	.											PCDHGB6,NS,carcinoma,0,1	PCDHGB6	120	1	1	Substitution - coding silent(1)	stomach(1)	c.C81T						scavenged	.						37.0	40.0	39.0					5																	140787850		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>T	5.37:g.140787850C>T		Somatic	146	0	0	1659	WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	37	CCDS54929.1																																																																																			C|0.906;G|0.094	.	alt		0.647	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
PKP3	11187	hgsc.bcm.edu	37	11	396915	396915	+	Silent	SNP	C	C	T	rs12419281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:396915C>T	ENST00000331563.2	+	3	490	c.414C>T	c.(412-414)aaC>aaT	p.N138N	PKP3_ENST00000530695.1_3'UTR	NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	138					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)		CAGCCCACAACGGGGGCAGCG	0.711													c|||	2238	0.446885	0.2912	0.4784	5008	,	,		14468	0.4296		0.5467	False		,,,				2504	0.5501				p.N138N		Atlas-SNP	.											.	PKP3	36	.	0			c.C414T						PASS	.			1461,2847		268,925,961	9.0	10.0	10.0		414	-0.8	0.9	11	dbSNP_120	10	4659,3863		1353,1953,955	no	coding-synonymous	PKP3	NM_007183.2		1621,2878,1916	TT,TC,CC		45.3297,33.9136,47.7007		138/798	396915	6120,6710	2154	4261	6415	SO:0001819	synonymous_variant	11187	exon3			CCACAACGGGGGC	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.414C>T	11.37:g.396915C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1																																																																																			C|0.573;T|0.427	0.427	strong		0.711	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
EML5	161436	hgsc.bcm.edu	37	14	89205265	89205265	+	Missense_Mutation	SNP	T	T	C	rs17188228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	74	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	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		
VWA5B1	127731	hgsc.bcm.edu	37	1	20671961	20671961	+	Missense_Mutation	SNP	G	G	A	rs11582960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20671961G>A	ENST00000375079.2	+	17	2835	c.2639G>A	c.(2638-2640)cGc>cAc	p.R880H	VWA5B1_ENST00000289815.8_Missense_Mutation_p.R880H|VWA5B1_ENST00000375083.4_Missense_Mutation_p.R880H|VWA5B1_ENST00000525343.1_3'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	880				R -> H (in Ref. 3; AAI01381). {ECO:0000305}.		extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						TCCAACCGCCGCTACCAAGTG	0.557													G|||	1511	0.301717	0.2443	0.3458	5008	,	,		16591	0.3532		0.3181	False		,,,				2504	0.2781				p.R880H		Atlas-SNP	.											VWA5B1,colon,carcinoma,0,1	VWA5B1	44	1	0			c.G2639A						PASS	.	G	HIS/ARG	342,1042		37,268,387	34.0	29.0	30.0		2639	5.3	1.0	1	dbSNP_120	30	1056,2126		168,720,703	yes	missense	VWA5B1	NM_001039500.2	29	205,988,1090	AA,AG,GG		33.1867,24.711,30.6176	probably-damaging	880/1216	20671961	1398,3168	692	1591	2283	SO:0001583	missense	127731	exon17			ACCGCCGCTACCA	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.2639G>A	1.37:g.20671961G>A	ENSP00000364220:p.Arg880His	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		693	0.3173076923076923	101	0.20528455284552846	125	0.3453038674033149	238	0.4160839160839161	229	0.3021108179419525	G	20.2	3.952435	0.73787	0.24711	0.331867	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.12774	3.01;2.65;3.01	5.28	5.28	0.74379	.	0.070917	0.56097	D	0.000025	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999999999946	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.991;0.999;0.983	T	0.48864	-0.8997	9	0.87932	D	0	-10.357	16.3895	0.83528	0.0:0.0:1.0:0.0	rs11582960;rs52789768;rs11582960	880;880;880	Q5TIE3;Q5TIE3-5;Q5TIE3-2	VW5B1_HUMAN;.;.	H	880	ENSP00000289815:R880H;ENSP00000364224:R880H;ENSP00000364220:R880H	ENSP00000289815:R880H	R	+	2	0	VWA5B1	20544548	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.758000	0.68776	2.470000	0.83445	0.573000	0.79308	CGC	G|0.696;A|0.304	0.304	strong		0.557	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
CMYA5	202333	hgsc.bcm.edu	37	5	79025157	79025157	+	Missense_Mutation	SNP	A	A	G	rs10942901	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79025157A>G	ENST00000446378.2	+	2	600	c.569A>G	c.(568-570)gAt>gGt	p.D190G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	190			D -> G (in dbSNP:rs10942901). {ECO:0000269|PubMed:17974005}.		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)		GGCATTTATGATAAAGCAAGA	0.393													A|||	835	0.166733	0.1036	0.1902	5008	,	,		17856	0.2202		0.1471	False		,,,				2504	0.2004				p.D190G		Atlas-SNP	.											.	CMYA5	643	.	0			c.A569G						PASS	.	A	GLY/ASP	388,3280		23,342,1469	45.0	44.0	44.0		569	4.9	0.0	5	dbSNP_120	44	1184,7008		98,988,3010	yes	missense	CMYA5	NM_153610.3	94	121,1330,4479	GG,GA,AA		14.4531,10.578,13.2546	probably-damaging	190/4070	79025157	1572,10288	1834	4096	5930	SO:0001583	missense	202333	exon2			TTTATGATAAAGC	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.569A>G	5.37:g.79025157A>G	ENSP00000394770:p.Asp190Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	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	341	0.15613553113553114	48	0.0975609756097561	67	0.1850828729281768	114	0.1993006993006993	112	0.14775725593667546	A	11.26	1.587130	0.28268	0.10578	0.144531	ENSG00000164309	ENST00000446378	T	0.65549	-0.16	6.06	4.88	0.63580	.	0.255650	0.28082	N	0.016672	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	P	0.48407	0.91	P	0.45099	0.469	T	0.25222	-1.0138	9	0.87932	D	0	.	3.4618	0.07536	0.6482:0.1413:0.0751:0.1354	rs10942901;rs10942901	190	Q8N3K9	CMYA5_HUMAN	G	190	ENSP00000394770:D190G	ENSP00000394770:D190G	D	+	2	0	CMYA5	79060913	0.975000	0.34042	0.020000	0.16555	0.282000	0.26991	1.489000	0.35562	1.073000	0.40885	0.533000	0.62120	GAT	A|0.832;G|0.162	0.162	strong		0.393	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
P4HB	5034	hgsc.bcm.edu	37	17	79803101	79803101	+	Silent	SNP	A	A	G	rs1130674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79803101A>G	ENST00000331483.4	-	10	1587	c.1365T>C	c.(1363-1365)atT>atC	p.I455I	RP11-498C9.2_ENST00000576784.1_RNA|P4HB_ENST00000472244.1_5'Flank|P4HB_ENST00000439918.2_Silent_p.I411I|P4HB_ENST00000576390.1_Intron	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	455	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			CGTTGTAATCAATGACCTGTG	0.597													G|||	1257	0.250998	0.3555	0.3184	5008	,	,		19752	0.2857		0.173	False		,,,				2504	0.1063				p.I455I	Colon(49;444 983 1296 7887 42561)	Atlas-SNP	.											.	P4HB	43	.	0			c.T1365C						PASS	.	G		1426,2978	676.6+/-403.3	232,962,1008	85.0	77.0	80.0		1365	-6.7	0.5	17	dbSNP_86	80	1683,6915	735.2+/-406.9	157,1369,2773	no	coding-synonymous	P4HB	NM_000918.3		389,2331,3781	GG,GA,AA		19.5743,32.3797,23.9117		455/509	79803101	3109,9893	2202	4299	6501	SO:0001819	synonymous_variant	5034	exon10			GTAATCAATGACC	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"""Protein disulfide isomerases"""	8548	protein-coding gene	gene with protein product	"""protein disulfide isomerase-associated 1"", ""protein disulfide isomerase family A, member 1"", ""collagen prolyl 4-hydroxylase beta"""	176790	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"""	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.1365T>C	17.37:g.79803101A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Silent	SNP	ENST00000331483.4	37	CCDS11787.1	621	0.28434065934065933	182	0.3699186991869919	103	0.2845303867403315	197	0.34440559440559443	139	0.18337730870712401	G	6.436	0.448536	0.12223	0.323797	0.195743	ENSG00000185624	ENST00000415593	.	.	.	5.16	-6.65	0.01795	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999385941	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4552	0.61195	0.7337:0.0:0.182:0.0842	rs56057239	.	.	.	R	221	.	.	X	-	1	0	P4HB	77396390	0.224000	0.23674	0.500000	0.27589	0.556000	0.35491	-0.470000	0.06639	-1.621000	0.01562	-0.930000	0.02707	TGA	A|0.736;G|0.264	0.264	strong		0.597	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918	
KY	339855	hgsc.bcm.edu	37	3	134369767	134369767	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:134369767G>A	ENST00000423778.2	-	1	97	c.36C>T	c.(34-36)atC>atT	p.I12I	KY_ENST00000508956.1_Silent_p.I12I|KY_ENST00000503669.1_Silent_p.I12I	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	12					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						GCAGCATGTCGATAGATACAG	0.647																																					p.I12I		Atlas-SNP	.											.	KY	92	.	0			c.C36T						PASS	.						58.0	65.0	63.0					3																	134369767		2131	4236	6367	SO:0001819	synonymous_variant	339855	exon1			CATGTCGATAGAT	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.36C>T	3.37:g.134369767G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	190	37	0.194737	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			.	.	none		0.647	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
MMAB	326625	hgsc.bcm.edu	37	12	110011229	110011229	+	Silent	SNP	G	G	T	rs10774774|rs36013132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:110011229G>T	ENST00000545712.2	-	1	450	c.57C>A	c.(55-57)cgC>cgA	p.R19R	MVK_ENST00000535044.1_3'UTR|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000539575.1_5'Flank|MVK_ENST00000541384.1_5'Flank|MVK_ENST00000539696.1_5'Flank|MVK_ENST00000228510.3_5'Flank|MMAB_ENST00000540016.1_Silent_p.R19R|MVK_ENST00000392727.3_5'Flank	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	19			R -> H (in dbSNP:rs10774775).|R -> Q (in dbSNP:rs36013132). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CGAAGCACCCGCGCAGGCCAA	0.711													G|||	1427	0.284944	0.438	0.2939	5008	,	,		13025	0.1607		0.2853	False		,,,				2504	0.1994				p.R19R		Atlas-SNP	.											.	MMAB	16	.	0			c.C57A						PASS	.	G		1718,2668		356,1006,831	16.0	17.0	16.0		57	2.0	0.4	12	dbSNP_120	16	2294,6298		372,1550,2374	no	coding-synonymous	MMAB	NM_052845.3		728,2556,3205	TT,TG,GG		26.6993,39.1701,30.9139		19/251	110011229	4012,8966	2193	4296	6489	SO:0001819	synonymous_variant	326625	exon1			GCACCCGCGCAGG	AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"""ATP:cob(I)alamin adenosyltransferase"", ""cilia and flagella associated protein 23"""	607568	"""methylmalonic aciduria (cobalamin deficiency) type B"""			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.57C>A	12.37:g.110011229G>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_052845	C5HU05|Q9BSH0	Silent	SNP	ENST00000545712.2	37	CCDS9131.1																																																																																			.	.	alt		0.711	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2		
USP4	7375	hgsc.bcm.edu	37	3	49321424	49321424	+	Missense_Mutation	SNP	T	T	C	rs41290700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49321424T>C	ENST00000265560.4	-	19	2582	c.2536A>G	c.(2536-2538)Atc>Gtc	p.I846V	USP4_ENST00000351842.4_Missense_Mutation_p.I799V	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	846	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)			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)		ACCCACCTGATTGGGAATTCT	0.463													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22007	0.0		0.005	False		,,,				2504	0.0051				p.I846V		Atlas-SNP	.											.	USP4	72	.	0			c.A2536G						PASS	.	T	VAL/ILE,VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	133.0	130.0	131.0		2536,2395	3.3	1.0	3	dbSNP_127	131	59,8541	36.9+/-92.0	0,59,4241	yes	missense,missense	USP4	NM_003363.3,NM_199443.2	29,29	0,67,6436	CC,CT,TT		0.686,0.1816,0.5151	benign,benign	846/964,799/917	49321424	67,12939	2203	4300	6503	SO:0001583	missense	7375	exon19			ACCTGATTGGGAA	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.2536A>G	3.37:g.49321424T>C	ENSP00000265560:p.Ile846Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	147	54	0.367347	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	37	CCDS2793.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	12.07|12.07	1.827377|1.827377	0.32329|0.32329	0.001816|0.001816	0.00686|0.00686	ENSG00000114316|ENSG00000114316	ENST00000351842;ENST00000265560|ENST00000431357	T;T|.	0.33654|.	1.4;1.4|.	5.63|5.63	3.35|3.35	0.38373|0.38373	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);|.	0.097121|.	0.64402|.	N|.	0.000002|.	T|T	0.31104|0.31104	0.0786|0.0786	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.12156|.	0.003;0.007;0.003|.	T|T	0.10200|0.10200	-1.0640|-1.0640	10|5	0.29301|.	T|.	0.29|.	.|.	4.7623|4.7623	0.13113|0.13113	0.0:0.5066:0.0:0.4934|0.0:0.5066:0.0:0.4934	rs41290700|rs41290700	799;846;846|.	Q13107-2;Q13107;Q08AK7|.	.;UBP4_HUMAN;.|.	V|S	799;846|584	ENSP00000341028:I799V;ENSP00000265560:I846V|.	ENSP00000265560:I846V|.	I|N	-|-	1|2	0|0	USP4|USP4	49296428|49296428	0.963000|0.963000	0.33076|0.33076	0.998000|0.998000	0.56505|0.56505	0.743000|0.743000	0.42351|0.42351	1.848000|1.848000	0.39309|0.39309	1.176000|1.176000	0.42840|0.42840	-0.408000|-0.408000	0.06270|0.06270	ATC|AAT	T|0.995;C|0.005	0.005	strong		0.463	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
RASGRF2	5924	hgsc.bcm.edu	37	5	80409729	80409729	+	Silent	SNP	T	T	C	rs10942942	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:80409729T>C	ENST00000265080.4	+	15	2527	c.2460T>C	c.(2458-2460)agT>agC	p.S820S	CTD-2193P3.2_ENST00000508993.1_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	820					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S820S(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TAAAACGAAGTATTCAAAAAG	0.478													T|||	2185	0.436302	0.612	0.3271	5008	,	,		21389	0.254		0.4394	False		,,,				2504	0.4611				p.S820S		Atlas-SNP	.											RASGRF2,NS,carcinoma,0,1	RASGRF2	165	1	1	Substitution - coding silent(1)	prostate(1)	c.T2460C						PASS	.	T		2588,1818	630.2+/-395.4	771,1046,386	61.0	60.0	61.0		2460	3.8	1.0	5	dbSNP_120	61	3901,4699	543.2+/-384.4	881,2139,1280	no	coding-synonymous	RASGRF2	NM_006909.1		1652,3185,1666	CC,CT,TT		45.3605,41.2619,49.8924		820/1238	80409729	6489,6517	2203	4300	6503	SO:0001819	synonymous_variant	5924	exon15			ACGAAGTATTCAA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2460T>C	5.37:g.80409729T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																			T|0.521;C|0.479	0.479	strong		0.478	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
PRR15	222171	hgsc.bcm.edu	37	7	29606288	29606288	+	Missense_Mutation	SNP	C	C	T	rs10271996	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:29606288C>T	ENST00000319694.2	+	2	1055	c.343C>T	c.(343-345)Ccg>Tcg	p.P115S		NM_175887.2	NP_787083.1	Q8IV56	PRR15_HUMAN	proline rich 15	115			P -> S (in dbSNP:rs10271996).		multicellular organismal development (GO:0007275)					endometrium(1)|lung(1)|skin(1)	3						GGGCAGGTCCCCGGAGGAGGC	0.657													C|||	2130	0.425319	0.4682	0.3573	5008	,	,		12362	0.5288		0.3449	False		,,,				2504	0.3916				p.P115S		Atlas-SNP	.											.	PRR15	6	.	0			c.C343T						PASS	.	C	SER/PRO	1965,2399		476,1013,693	7.0	8.0	8.0		343	-0.8	0.0	7	dbSNP_119	8	2969,5567		591,1787,1890	yes	missense	PRR15	NM_175887.2	74	1067,2800,2583	TT,TC,CC		34.7821,45.0275,38.2481	benign	115/130	29606288	4934,7966	2182	4268	6450	SO:0001583	missense	222171	exon2			AGGTCCCCGGAGG	BC029131	CCDS5421.1	7p15.1	2006-08-21			ENSG00000176532	ENSG00000176532			22310	protein-coding gene	gene with protein product						12477932	Standard	NM_175887		Approved		uc003tac.1	Q8IV56	OTTHUMG00000128555	ENST00000319694.2:c.343C>T	7.37:g.29606288C>T	ENSP00000317836:p.Pro115Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	92	61	0.663043	NM_175887		Missense_Mutation	SNP	ENST00000319694.2	37	CCDS5421.1	892	0.4084249084249084	233	0.4735772357723577	113	0.31215469613259667	295	0.5157342657342657	251	0.3311345646437995	C	4.974	0.180903	0.09443	0.450275	0.347821	ENSG00000176532	ENST00000319694	T	0.49139	0.79	4.63	-0.84	0.10755	.	1.228850	0.05969	N	0.642086	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.44574	-0.9319	9	0.08599	T	0.76	7.0E-4	4.1388	0.10183	0.0:0.3404:0.3302:0.3294	rs10271996	115	Q8IV56	PRR15_HUMAN	S	115	ENSP00000317836:P115S	ENSP00000317836:P115S	P	+	1	0	PRR15	29572813	0.001000	0.12720	0.001000	0.08648	0.368000	0.29767	0.138000	0.16016	-0.384000	0.07845	0.491000	0.48974	CCG	A|0.000;C|0.590;G|0.000;T|0.409	0.409	strong		0.657	PRR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250402.2	NM_175887	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136287582	136287582	+	Missense_Mutation	SNP	C	C	T	rs34024143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136287582C>T	ENST00000371929.3	+	1	463	c.19C>T	c.(19-21)Cgg>Tgg	p.R7W	ADAMTS13_ENST00000356589.2_Missense_Mutation_p.R7W|ADAMTS13_ENST00000371911.3_Missense_Mutation_p.R7W|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_Missense_Mutation_p.R7W|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.R7W	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	7			R -> W (does not affect protein secretion; dbSNP:rs34024143). {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)		GCGTCACCCCCGGGCAAGATG	0.632													C|||	264	0.0527157	0.0356	0.0735	5008	,	,		16616	0.006		0.1262	False		,,,				2504	0.0337				p.R7W		Atlas-SNP	.											ADAMTS13,colon,carcinoma,-2,1	ADAMTS13	113	1	0			c.C19T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	228,4178	136.5+/-172.5	3,222,1978	84.0	78.0	80.0		19,19,19	-6.6	0.0	9	dbSNP_126	80	1071,7529	225.5+/-261.6	66,939,3295	yes	missense,missense,missense	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	101,101,101	69,1161,5273	TT,TC,CC		12.4535,5.1748,9.9877	benign,benign,benign	7/1428,7/1341,7/1372	136287582	1299,11707	2203	4300	6503	SO:0001583	missense	11093	exon1			CACCCCCGGGCAA	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.19C>T	9.37:g.136287582C>T	ENSP00000360997:p.Arg7Trp	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_139026	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	153	0.07005494505494506	26	0.052845528455284556	26	0.0718232044198895	5	0.008741258741258742	96	0.1266490765171504	C	9.203	1.028867	0.19512	0.051748	0.124535	ENSG00000160323	ENST00000371929;ENST00000371916;ENST00000355699;ENST00000356589;ENST00000371911	T;T;T;T;D	0.85339	-0.13;-1.45;-0.17;-0.2;-1.97	3.35	-6.55	0.01854	.	.	.	.	.	T	0.01061	0.0035	N	0.04880	-0.145	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	0.11421	-1.0588	8	0.45353	T	0.12	.	1.1031	0.01688	0.1589:0.3274:0.1622:0.3515	rs34024143;rs36218241	7;7;7;7	Q76LX8;Q76LX8-3;Q76LX8-2;E7EV88	ATS13_HUMAN;.;.;.	W	7	ENSP00000360997:R7W;ENSP00000360984:R7W;ENSP00000347927:R7W;ENSP00000348997:R7W;ENSP00000360979:R7W	ENSP00000347927:R7W	R	+	1	2	ADAMTS13	135277403	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.569000	0.02142	-1.237000	0.02539	-1.311000	0.01308	CGG	C|0.905;T|0.095	0.095	strong		0.632	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
CDH9	1007	hgsc.bcm.edu	37	5	26885964	26885964	+	Silent	SNP	T	T	G	rs35328154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55.0	58.0	57.0		1641	-4.3	1.0	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1641A>C	5.37:g.26885964T>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
CFAP46	54777	hgsc.bcm.edu	37	10	134624504	134624504	+	Silent	SNP	C	C	T	rs2274429	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:134624504C>T	ENST00000368586.5	-	56	7633	c.7533G>A	c.(7531-7533)gcG>gcA	p.A2511A	TTC40_ENST00000263170.5_Silent_p.A672A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GGTAGGACCGCGCCAGGTCCA	0.662													C|||	1658	0.33107	0.0983	0.219	5008	,	,		17397	0.6181		0.3419	False		,,,				2504	0.4182				p.A2511A		Atlas-SNP	.											.	TTC40	100	.	0			c.G7533A						PASS	.	C		627,3775		51,525,1625	65.0	45.0	52.0		2469	-5.7	0.0	10	dbSNP_100	52	2894,5706		473,1948,1879	no	coding-synonymous	C10orf92	NM_001200049.1		524,2473,3504	TT,TC,CC		33.6512,14.2435,27.0804		823/1028	134624504	3521,9481	2201	4300	6501	SO:0001819	synonymous_variant	54777	exon56			GGACCGCGCCAGG																												ENST00000368586.5:c.7533G>A	10.37:g.134624504C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.701;T|0.299	0.299	strong		0.662	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
UGT2B17	7367	hgsc.bcm.edu	37	4	69433479	69433479	+	Splice_Site	SNP	C	C	G	rs145791375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69433479C>G	ENST00000317746.2	-	1	766	c.724G>C	c.(724-726)Gga>Cga	p.G242R		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	242					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	CACGACTTACCTAGAACTTCA	0.323													C|||	2	0.000399361	0.0	0.0	5008	,	,		10536	0.0		0.002	False		,,,				2504	0.0				p.G242R	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.G724C						PASS	.	C	ARG/GLY	2,4188		0,2,2093	100.0	109.0	106.0		724	2.7	0.7	4	dbSNP_134	106	6,7868		2,2,3933	yes	missense-near-splice	UGT2B17	NM_001077.3	125	2,4,6026	GG,GC,CC		0.0762,0.0477,0.0663		242/531	69433479	8,12056	2095	3937	6032	SO:0001630	splice_region_variant	7367	exon1			ACTTACCTAGAAC	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.724+1G>C	4.37:g.69433479C>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_001077		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	14.66	2.602420	0.46423	4.77E-4	7.62E-4	ENSG00000197888	ENST00000317746	T	0.60424	0.19	2.66	2.66	0.31614	.	0.000000	0.64402	U	0.000005	T	0.69967	0.3170	M	0.85777	2.775	0.30173	N	0.801107	.	.	.	.	.	.	T	0.70927	-0.4739	7	.	.	.	.	11.1206	0.48287	0.0:1.0:0.0:0.0	.	.	.	.	R	242	ENSP00000320401:G242R	.	G	-	1	0	UGT2B17	69116074	1.000000	0.71417	0.673000	0.29887	0.022000	0.10575	6.023000	0.70848	1.516000	0.48900	0.499000	0.49734	GGA	C|0.999;G|0.001	0.001	strong		0.323	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	Missense_Mutation
USP6NL	9712	hgsc.bcm.edu	37	10	11504752	11504752	+	Silent	SNP	T	T	C	rs12570211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:11504752T>C	ENST00000609104.1	-	15	2569	c.2175A>G	c.(2173-2175)ccA>ccG	p.P725P	USP6NL_ENST00000277575.5_Silent_p.P742P|USP6NL_ENST00000379237.2_Silent_p.P748P	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	725					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						AATCCACTGGTGGAATGATCA	0.478													t|||	498	0.0994409	0.0234	0.062	5008	,	,		21454	0.1319		0.0656	False		,,,				2504	0.2301				p.P742P		Atlas-SNP	.											.	USP6NL	57	.	0			c.A2226G						PASS	.	T	,	95,3711		1,93,1809	90.0	89.0	89.0		2226,2175	-2.3	1.0	10	dbSNP_120	89	516,7744		18,480,3632	no	coding-synonymous,coding-synonymous	USP6NL	NM_001080491.2,NM_014688.2	,	19,573,5441	CC,CT,TT		6.247,2.4961,5.0638	,	742/846,725/829	11504752	611,11455	1903	4130	6033	SO:0001819	synonymous_variant	9712	exon14			CACTGGTGGAATG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.2175A>G	10.37:g.11504752T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Silent	SNP	ENST00000609104.1	37	CCDS53492.1																																																																																			T|0.917;C|0.083	0.083	strong		0.478	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
APC	324	hgsc.bcm.edu	37	5	112176756	112176756	+	Missense_Mutation	SNP	T	T	A	rs459552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176756T>A	ENST00000457016.1	+	16	5845	c.5465T>A	c.(5464-5466)gTc>gAc	p.V1822D	APC_ENST00000508376.2_Missense_Mutation_p.V1822D|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.V1822D			P25054	APC_HUMAN	adenomatous polyposis coli	1822	Ser-rich.		V -> D (in dbSNP:rs459552). {ECO:0000269|PubMed:1651562, ECO:0000269|PubMed:1678319, ECO:0000269|PubMed:9950360, ECO:0000269|Ref.4}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AATTCCAAGGTCTTCAATGAT	0.328		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	4334	0.865415	0.9909	0.8184	5008	,	,		19820	0.9008		0.7654	False		,,,				2504	0.7955				p.V1822D	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5465A	GRCh37	CM990164	APC	M	rs459552	PASS	.	A	ASP/VAL,ASP/VAL,ASP/VAL	4164,238	135.3+/-171.4	1973,218,10	67.0	63.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5465,5465,5411	3.6	1.0	5	dbSNP_80	64	6579,2021	339.4+/-323.1	2529,1521,250	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	152,152,152	4502,1739,260	AA,AT,TT		23.5,5.4066,17.3743	benign,benign,benign	1822/2844,1822/2844,1804/2826	112176756	10743,2259	2201	4300	6501	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	CCAAGGTCTTCAA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5465T>A	5.37:g.112176756T>A	ENSP00000413133:p.Val1822Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	1883	0.8621794871794872	486	0.9878048780487805	296	0.8176795580110497	514	0.8986013986013986	587	0.7744063324538258	A	0.069	-1.206578	0.01568	0.945934	0.765	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.87809	-2.3;-2.3;-2.3	6.07	3.59	0.41128	.	0.187419	0.47093	N	0.000244	T	0.00012	0.0000	N	0.01352	-0.895	0.40534	P	0.019048999999999983	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42085	-0.9472	8	.	.	.	-1.4078	9.3995	0.38424	0.6507:0.2365:0.0:0.1128	rs459552;rs52814776;rs56587573;rs459552	1824;1822	Q4LE70;P25054	.;APC_HUMAN	D	1822	ENSP00000413133:V1822D;ENSP00000257430:V1822D;ENSP00000427089:V1822D	.	V	+	2	0	APC	112204655	1.000000	0.71417	0.987000	0.45799	0.796000	0.44982	3.653000	0.54446	0.139000	0.18822	-0.265000	0.10407	GTC	T|0.151;A|0.849	0.849	strong		0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	129	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	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	
WNT7A	7476	hgsc.bcm.edu	37	3	13896284	13896284	+	Silent	SNP	C	C	T	rs12639607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:13896284C>T	ENST00000285018.4	-	3	619	c.315G>A	c.(313-315)gcG>gcA	p.A105A		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	105					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CGTAGGTGAACGCAGCCTCCC	0.627													c|||	1109	0.221446	0.0257	0.1916	5008	,	,		19482	0.5813		0.17	False		,,,				2504	0.1892				p.A105A		Atlas-SNP	.											WNT7A,caecum,carcinoma,-1,3	WNT7A	70	3	0			c.G315A						PASS	.	T		270,4136	801.7+/-415.6	7,256,1940	64.0	63.0	63.0		315	0.6	1.0	3	dbSNP_120	63	1563,7037	744.7+/-407.2	133,1297,2870	no	coding-synonymous	WNT7A	NM_004625.3		140,1553,4810	TT,TC,CC		18.1744,6.128,14.0935		105/350	13896284	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	7476	exon3			GGTGAACGCAGCC	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.315G>A	3.37:g.13896284C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	37	CCDS2616.1																																																																																			C|0.826;T|0.174	0.174	strong		0.627	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
Unknown	0	hgsc.bcm.edu	37	7	63679733	63679733	+	IGR	SNP	A	A	G	rs10270226	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:63679733A>G								GUSBP6 (68634 upstream) : ZNF679 (9118 downstream)																							GCCAGAGCAGAGCATAAAAGA	0.323													.|||	3369	0.672724	0.6702	0.6873	5008	,	,		17661	0.7798		0.6471	False		,,,				2504	0.5818				p.S102G		Atlas-SNP	.											.	.	.	.	0			c.A304G						PASS	.						34.0	27.0	29.0					7																	63679733		692	1588	2280	SO:0001628	intergenic_variant	730291	exon4			GAGCAGAGCATAA																													7.37:g.63679733A>G		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	161	158	0.981366	NM_001159524		Missense_Mutation	SNP		37																																																																																				A|0.311;G|0.689	0.689	strong	0	0.323								
HLA-B	3106	hgsc.bcm.edu	37	6	31324604	31324604	+	Silent	SNP	T	T	C	rs9266179|rs200186034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324604T>C	ENST00000412585.2	-	2	232	c.204A>G	c.(202-204)agA>agG	p.R68R		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	68	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.E69fs*8(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCGGCTCCTCTCTCGGACTCG	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R68R		Atlas-SNP	.											.	HLA-B	54	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.A204G						PASS	.						33.0	33.0	33.0					6																	31324604		2015	3950	5965	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CTCCTCTCTCGGA	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.204A>G	6.37:g.31324604T>C		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	35	33	0.942857	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.435;C|0.565	0.565	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
USH2A	7399	hgsc.bcm.edu	37	1	215914826	215914826	+	Missense_Mutation	SNP	T	T	C	rs35309576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:215914826T>C	ENST00000307340.3	-	60	11988	c.11602A>G	c.(11602-11604)Atg>Gtg	p.M3868V	USH2A_ENST00000366943.2_Missense_Mutation_p.M3868V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3868	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.		M -> V (in dbSNP:rs35309576). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|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)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.M3868V(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTAAGATCCATTGGGGCTGCT	0.383										HNSCC(13;0.011)			T|||	798	0.159345	0.2027	0.196	5008	,	,		15397	0.0843		0.2356	False		,,,				2504	0.0736				p.M3868V		Atlas-SNP	.											USH2A,NS,carcinoma,0,2	USH2A	1168	2	1	Substitution - Missense(1)	stomach(1)	c.A11602G						PASS	.	T	VAL/MET	835,3571	328.0+/-300.3	82,671,1450	115.0	116.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11602	-9.7	0.0	1	dbSNP_126	116	2006,6594	350.3+/-327.8	238,1530,2532	yes	missense	USH2A	NM_206933.2	21	320,2201,3982	CC,CT,TT		23.3256,18.9514,21.8438	benign	3868/5203	215914826	2841,10165	2203	4300	6503	SO:0001583	missense	7399	exon60			GATCCATTGGGGC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.11602A>G	1.37:g.215914826T>C	ENSP00000305941:p.Met3868Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	52	14	0.269231	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	425	0.1945970695970696	114	0.23170731707317074	81	0.22375690607734808	57	0.09965034965034965	173	0.22823218997361477	T	5.460	0.270032	0.10349	0.189514	0.233256	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.12361	2.69;2.69	5.38	-9.68	0.00528	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.951410	0.08631	N	0.917001	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.24483	T	0.36	.	7.5708	0.27907	0.1504:0.535:0.1184:0.1961	rs35309576	3868	O75445	USH2A_HUMAN	V	3868	ENSP00000305941:M3868V;ENSP00000355910:M3868V	ENSP00000305941:M3868V	M	-	1	0	USH2A	213981449	0.000000	0.05858	0.000000	0.03702	0.757000	0.42996	-2.392000	0.01056	-1.693000	0.01427	-1.303000	0.01326	ATG	T|0.785;C|0.215	0.215	strong		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LRRC61	65999	hgsc.bcm.edu	37	7	150034184	150034184	+	Silent	SNP	T	T	C	rs3735170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150034184T>C	ENST00000359623.4	+	3	822	c.234T>C	c.(232-234)gcT>gcC	p.A78A	LRRC61_ENST00000323078.7_Silent_p.A78A|LRRC61_ENST00000493307.1_Silent_p.A78A	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	78										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCAGCTAGCTGTGCTCAATG	0.647													C|||	1295	0.258586	0.2625	0.1571	5008	,	,		17325	0.2907		0.2455	False		,,,				2504	0.3057				p.A78A		Atlas-SNP	.											LRRC61,rectum,carcinoma,0,1	LRRC61	17	1	0			c.T234C						PASS	.	C	,	1062,3342	697.3+/-406.2	129,804,1269	49.0	46.0	47.0		234,234	-7.1	0.0	7	dbSNP_107	47	2188,6412	681.9+/-403.8	286,1616,2398	no	coding-synonymous,coding-synonymous	LRRC61	NM_001142928.1,NM_023942.2	,	415,2420,3667	CC,CT,TT		25.4419,24.1144,24.9923	,	78/260,78/260	150034184	3250,9754	2202	4300	6502	SO:0001819	synonymous_variant	65999	exon2			GCTAGCTGTGCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.234T>C	7.37:g.150034184T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_023942	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																			T|0.745;C|0.255	0.255	strong		0.647	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
ZNF718	255403	hgsc.bcm.edu	37	4	155713	155713	+	lincRNA	SNP	A	A	G	rs7440274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:155713A>G	ENST00000510175.1	+	0	1148							Q3SXZ3	ZN718_HUMAN	zinc finger protein 718						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		CTGCATAATCATAAGAAAATT	0.348													A|||	957	0.191094	0.1551	0.2406	5008	,	,		20246	0.1528		0.1759	False		,,,				2504	0.2597				p.H413R		Atlas-SNP	.											.	.	.	.	0			c.A1238G						PASS	.	A	ARG/HIS	587,3559		39,509,1525	33.0	38.0	36.0		1049	1.0	0.0	4	dbSNP_116	36	1348,7154		108,1132,3011	no	missense	ZNF718	NM_001039127.3	29	147,1641,4536	GG,GA,AA		15.8551,14.1582,15.2989	possibly-damaging	350/416	155713	1935,10713	2073	4251	6324			255403	exon4			ATAATCATAAGAA	AK096662	CCDS75078.1, CCDS75079.1	4p16.3	2011-05-24			ENSG00000250312	ENSG00000250312		"""Zinc fingers, C2H2-type"""	26889	protein-coding gene	gene with protein product							Standard	XM_005278364		Approved	FLJ90036	uc003fzt.4	Q3SXZ3	OTTHUMG00000159873		4.37:g.155713A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_001039127	Q3SXZ4|Q3SXZ5	Missense_Mutation	SNP	ENST00000510175.1	37																																																																																				A|0.831;G|0.169	0.169	strong		0.348	ZNF718-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000357865.3	NM_001039127	
POLR1B	84172	hgsc.bcm.edu	37	2	113333238	113333238	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113333238T>C	ENST00000263331.5	+	15	3920	c.3340T>C	c.(3340-3342)Tat>Cat	p.Y1114H	POLR1B_ENST00000417433.2_Missense_Mutation_p.Y1058H|POLR1B_ENST00000409894.3_Missense_Mutation_p.Y931H|POLR1B_ENST00000537335.1_Missense_Mutation_p.Y903H|POLR1B_ENST00000541869.1_Missense_Mutation_p.Y1152H	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	1114					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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						TTCTGTGCCTTATGTTTTTCG	0.423																																					p.Y1114H	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											.	POLR1B	95	.	0			c.T3340C						PASS	.						122.0	114.0	117.0					2																	113333238		2203	4300	6503	SO:0001583	missense	84172	exon15			GTGCCTTATGTTT	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.3340T>C	2.37:g.113333238T>C	ENSP00000263331:p.Tyr1114His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.925462	0.52759	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.37	5.37	0.77165	RNA polymerase Rpb2, domain 7 (1);	0.108910	0.64402	D	0.000004	D	0.87669	0.6235	M	0.78637	2.42	0.80722	D	1	P;D;B;B	0.76494	0.476;0.999;0.274;0.183	B;D;B;B	0.83275	0.178;0.996;0.225;0.2	D	0.88914	0.3361	10	0.62326	D	0.03	-21.3681	14.3792	0.66900	0.0:0.0:0.0:1.0	.	1152;931;1058;1114	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	H	1114;1152;931;903;1058	ENSP00000263331:Y1114H;ENSP00000444136:Y1152H;ENSP00000387143:Y931H;ENSP00000437914:Y903H;ENSP00000405358:Y1058H	ENSP00000263331:Y1114H	Y	+	1	0	POLR1B	113049709	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	5.887000	0.69751	2.030000	0.59900	0.455000	0.32223	TAT	.	.	none		0.423	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
CERS5	91012	hgsc.bcm.edu	37	12	50537815	50537815	+	Missense_Mutation	SNP	A	A	G	rs7302981	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:50537815A>G	ENST00000317551.6	-	2	347	c.223T>C	c.(223-225)Tgt>Cgt	p.C75R	CERS5_ENST00000422340.2_Missense_Mutation_p.C17R	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	75			C -> R (in dbSNP:rs7302981).		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)										ATGCCAATACAGAGTGCACAG	0.388													G|||	4041	0.806909	0.9251	0.7493	5008	,	,		19453	0.9077		0.6024	False		,,,				2504	0.7945				p.C75R		Atlas-SNP	.											LASS5,colon,carcinoma,+1,1	.	.	1	0			c.T223C						PASS	.	G	ARG/CYS	3869,537	242.8+/-252.7	1697,475,31	123.0	121.0	122.0		223	3.1	1.0	12	dbSNP_116	122	5324,3276	491.4+/-373.1	1674,1976,650	yes	missense	CERS5	NM_147190.2	180	3371,2451,681	GG,GA,AA		38.093,12.1879,29.3172	benign	75/393	50537815	9193,3813	2203	4300	6503	SO:0001583	missense	91012	exon2			CAATACAGAGTGC		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"""Homeoboxes / CERS class"""	23749	protein-coding gene	gene with protein product		615335	"""LAG1 longevity assurance homolog 5 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 5"""	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.223T>C	12.37:g.50537815A>G	ENSP00000325485:p.Cys75Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	47	13	0.276596	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	37	CCDS8801.1	1679	0.7687728937728938	451	0.9166666666666666	253	0.6988950276243094	519	0.9073426573426573	456	0.6015831134564644	G	5.065	0.197665	0.09652	0.878121	0.61907	ENSG00000139624	ENST00000317551;ENST00000422340	T;T	0.67698	-0.28;2.89	4.0	3.11	0.35812	.	0.636734	0.17358	N	0.177173	T	0.00012	0.0000	N	0.00268	-1.735	0.40776	P	0.016866000000000048	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32771	-0.9894	9	0.25106	T	0.35	-0.4992	7.1507	0.25608	0.1627:0.0:0.6912:0.1461	rs7302981;rs17273303;rs52837285;rs61017558;rs7302981	17;75	B4DV54;Q8N5B7	.;CERS5_HUMAN	R	75;17	ENSP00000325485:C75R;ENSP00000389050:C17R	ENSP00000325485:C75R	C	-	1	0	CERS5	48824082	0.003000	0.15002	1.000000	0.80357	0.737000	0.42083	0.620000	0.24403	0.663000	0.31027	-0.766000	0.03442	TGT	A|0.260;G|0.740	0.740	strong		0.388	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190	
STKLD1	169436	hgsc.bcm.edu	37	9	136269143	136269143	+	Missense_Mutation	SNP	G	G	A	rs17150554	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136269143G>A	ENST00000371957.3	+	16	1810	c.1703G>A	c.(1702-1704)cGg>cAg	p.R568Q	C9orf96_ENST00000371955.1_Missense_Mutation_p.R101Q	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		568			R -> Q (in dbSNP:rs17150554).				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)		AATGCCTACCGGGGACTGGCC	0.607											OREG0019586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	162	0.0323482	0.0045	0.0403	5008	,	,		17509	0.0198		0.0815	False		,,,				2504	0.0266				p.R568Q		Atlas-SNP	.											C9orf96_ENST00000371957,NS,carcinoma,0,2	C9orf96	77	2	0			c.G1703A						scavenged	.	G	GLN/ARG	74,4332	66.4+/-103.9	1,72,2130	48.0	49.0	48.0		1703	3.1	1.0	9	dbSNP_123	48	732,7868	175.9+/-225.9	37,658,3605	yes	missense	C9orf96	NM_153710.3	43	38,730,5735	AA,AG,GG		8.5116,1.6795,6.1971	probably-damaging	568/681	136269143	806,12200	2203	4300	6503	SO:0001583	missense	169436	exon16			CCTACCGGGGACT																												ENST00000371957.3:c.1703G>A	9.37:g.136269143G>A	ENSP00000361025:p.Arg568Gln	Somatic	91	1	0.010989	1624	WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	97	0.044413919413919416	3	0.006097560975609756	16	0.04419889502762431	12	0.02097902097902098	66	0.0870712401055409	G	15.68	2.905428	0.52333	0.016795	0.085116	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.51574	0.7;0.79	5.12	3.07	0.35406	Armadillo-like helical (1);Armadillo-type fold (1);	0.108809	0.39909	N	0.001223	T	0.01156	0.0038	L	0.50333	1.59	0.38264	P	0.05803999999999998	P	0.40250	0.709	B	0.23716	0.048	T	0.16837	-1.0389	9	0.54805	T	0.06	-35.4068	6.0443	0.19752	0.1013:0.0:0.5425:0.3562	rs17150554;rs52833361;rs17150554	568	Q8NE28	SGK71_HUMAN	Q	568;101	ENSP00000361025:R568Q;ENSP00000361023:R101Q	ENSP00000361023:R101Q	R	+	2	0	C9orf96	135258964	0.960000	0.32886	0.983000	0.44433	0.640000	0.38277	1.589000	0.36644	1.116000	0.41820	0.555000	0.69702	CGG	G|0.947;A|0.053	0.053	strong		0.607	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
HELQ	113510	hgsc.bcm.edu	37	4	84364751	84364751	+	Silent	SNP	A	A	G	rs7665103	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:84364751A>G	ENST00000295488.3	-	6	1644	c.1482T>C	c.(1480-1482)atT>atC	p.I494I	HELQ_ENST00000510985.1_Silent_p.I427I	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	494	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						CACTCATACCAATAATTTGAG	0.294								Other identified genes with known or suspected DNA repair function					A|||	2543	0.507788	0.4493	0.5447	5008	,	,		18714	0.6736		0.3787	False		,,,				2504	0.5225				p.I494I		Atlas-SNP	.											.	HELQ	95	.	0			c.T1482C						PASS	.	A		1950,2446	539.4+/-375.3	460,1030,708	63.0	63.0	63.0		1482	0.6	1.0	4	dbSNP_116	63	3504,5094	502.8+/-375.8	713,2078,1508	no	coding-synonymous	HELQ	NM_133636.2		1173,3108,2216	GG,GA,AA		40.7537,44.3585,41.9732		494/1102	84364751	5454,7540	2198	4299	6497	SO:0001819	synonymous_variant	113510	exon6			CATACCAATAATT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1482T>C	4.37:g.84364751A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.558;G|0.442	0.442	strong		0.294	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
COL6A2	1292	hgsc.bcm.edu	37	21	47545826	47545826	+	Silent	SNP	C	C	T	rs13046639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47545826C>T	ENST00000300527.4	+	26	2201	c.2097C>T	c.(2095-2097)ggC>ggT	p.G699G	COL6A2_ENST00000409416.1_Silent_p.G699G|COL6A2_ENST00000397763.1_Silent_p.G699G|COL6A2_ENST00000310645.5_Silent_p.G699G|COL6A2_ENST00000357838.4_Silent_p.G699G	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	699	Nonhelical region.|VWFA 2. {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)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GGATTGCGGGCGGCACCTGGA	0.612													C|||	1973	0.39397	0.208	0.6383	5008	,	,		14617	0.4306		0.5109	False		,,,				2504	0.3139				p.G699G		Atlas-SNP	.											.	COL6A2	351	.	0			c.C2097T						PASS	.	C	,,	1062,3344	387.2+/-326.4	148,766,1289	76.0	70.0	72.0		2097,2097,2097	-8.4	0.0	21	dbSNP_121	72	4304,4296	576.8+/-390.4	1048,2208,1044	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	1196,2974,2333	TT,TC,CC		49.9535,24.1035,41.2579	,,	699/1020,699/919,699/829	47545826	5366,7640	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			TGCGGGCGGCACC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2097C>T	21.37:g.47545826C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	155	0.974843	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.584;T|0.416	0.416	strong		0.612	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
TMEM140	55281	hgsc.bcm.edu	37	7	134849209	134849209	+	Missense_Mutation	SNP	C	C	T	rs292500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:134849209C>T	ENST00000275767.3	+	2	239	c.16C>T	c.(16-18)Cct>Tct	p.P6S	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	6			P -> S (in dbSNP:rs292500).			integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CGGCCCAAGGCCTCGGTGGCG	0.587													C|||	81	0.0161741	0.0015	0.0331	5008	,	,		19474	0.0		0.0348	False		,,,				2504	0.0215				p.P6S		Atlas-SNP	.											.	TMEM140	18	.	0			c.C16T						PASS	.	C	SER/PRO	41,4365	44.6+/-78.6	0,41,2162	109.0	98.0	102.0		16	1.1	0.0	7	dbSNP_79	102	333,8267	116.1+/-175.8	8,317,3975	no	missense	TMEM140	NM_018295.3	74	8,358,6137	TT,TC,CC		3.8721,0.9305,2.8756	possibly-damaging	6/186	134849209	374,12632	2203	4300	6503	SO:0001583	missense	55281	exon2			CCAAGGCCTCGGT	AK001862	CCDS5837.1	7q33	2006-03-17			ENSG00000146859	ENSG00000146859			21870	protein-coding gene	gene with protein product							Standard	NM_018295		Approved	FLJ11000	uc003vsi.3	Q9NV12	OTTHUMG00000155413	ENST00000275767.3:c.16C>T	7.37:g.134849209C>T	ENSP00000275767:p.Pro6Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	81	0.613636	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	38	0.0173992673992674	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	21	0.027704485488126648	C	11.02	1.514817	0.27123	0.009305	0.038721	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.18174	2.23	5.68	1.06	0.20224	.	1.335970	0.04845	N	0.441179	T	0.03136	0.0092	L	0.44542	1.39	0.09310	N	1	B	0.20052	0.041	B	0.14578	0.011	T	0.32719	-0.9896	10	0.15499	T	0.54	0.2321	7.0434	0.25033	0.0:0.5556:0.2658:0.1786	rs292500;rs1647803;rs10351539;rs17856621	6	Q9NV12	TM140_HUMAN	S	6	ENSP00000275767:P6S	ENSP00000275767:P6S	P	+	1	0	TMEM140	134499749	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	0.289000	0.18957	0.275000	0.22094	0.563000	0.77884	CCT	C|0.975;T|0.025	0.025	strong		0.587	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
XCL1	6375	hgsc.bcm.edu	37	1	168549362	168549362	+	Silent	SNP	G	G	A	rs149760054	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:168549362G>A	ENST00000367818.3	+	2	288	c.123G>A	c.(121-123)ccG>ccA	p.P41P		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	41					cell-cell signaling (GO:0007267)|cellular response to interleukin-4 (GO:0071353)|cellular response to transforming growth factor beta stimulus (GO:0071560)|immune response (GO:0006955)|mature natural killer cell chemotaxis (GO:0035782)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T-helper 1 cell activation (GO:2000518)|negative regulation of T-helper 1 type immune response (GO:0002826)|negative regulation of transcription, DNA-templated (GO:0045892)|neutrophil chemotaxis (GO:0030593)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000566)|positive regulation of granzyme A production (GO:2000513)|positive regulation of granzyme B production (GO:0071663)|positive regulation of immunoglobulin production in mucosal tissue (GO:2000558)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 cell cytokine production (GO:2000556)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of thymocyte migration (GO:2000412)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of inflammatory response (GO:0050727)|release of sequestered calcium ion into cytosol (GO:0051209)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|protein homodimerization activity (GO:0042803)			kidney(2)|lung(7)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.208)					AGCGACTGCCGGTTAGCAGAA	0.468													A|||	80	0.0159744	0.0083	0.0115	5008	,	,		18330	0.0169		0.0229	False		,,,				2504	0.0215				p.P41P		Atlas-SNP	.											XCL1,colon,carcinoma,+2,1	XCL1	16	1	0			c.G123A						PASS	.	A		28,4378	823.4+/-416.5	0,28,2175	158.0	147.0	151.0		123	-6.8	0.0	1	dbSNP_134	151	108,8492	814.4+/-407.0	0,108,4192	no	coding-synonymous	XCL1	NM_002995.2		0,136,6367	AA,AG,GG		1.2558,0.6355,1.0457		41/115	168549362	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	6375	exon2			ACTGCCGGTTAGC	D43768	CCDS1274.1	1q24.2	2014-01-30	2002-08-22	2002-08-23	ENSG00000143184	ENSG00000143184		"""Endogenous ligands"""	10645	protein-coding gene	gene with protein product		600250	"""small inducible cytokine subfamily C, member 1 (lymphotactin)"""	LTN, SCYC1		7602097, 7875320	Standard	NM_002995		Approved	LPTN, ATAC, SCM-1a, SCM-1, lymphotactin	uc001gfo.2	P47992	OTTHUMG00000034548	ENST00000367818.3:c.123G>A	1.37:g.168549362G>A		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	297	194	0.653199	NM_002995	Q52MA8	Silent	SNP	ENST00000367818.3	37	CCDS1274.1																																																																																			G|0.987;A|0.013	0.013	strong		0.468	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995	
SEC16B	89866	hgsc.bcm.edu	37	1	177901655	177901655	+	Silent	SNP	G	G	A	rs3748792	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177901655G>A	ENST00000308284.6	-	24	3071	c.2982C>T	c.(2980-2982)ggC>ggT	p.G994G	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	994					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						CAACCCCAGCGCCCGCAGCTG	0.647													G|||	1142	0.228035	0.2655	0.2637	5008	,	,		16662	0.1052		0.2604	False		,,,				2504	0.2454				p.G994G		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2982T						PASS	.	G		1091,3003		154,783,1110	10.0	15.0	13.0		2982	-1.0	0.0	1	dbSNP_107	13	1769,6457		211,1347,2555	no	coding-synonymous	SEC16B	NM_033127.2		365,2130,3665	AA,AG,GG		21.505,26.6488,23.2143		994/1061	177901655	2860,9460	2047	4113	6160	SO:0001819	synonymous_variant	89866	exon24			CCCAGCGCCCGCA	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.2982C>T	1.37:g.177901655G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	120	33	0.275	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.786;A|0.214	0.214	strong		0.647	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
LCP2	3937	hgsc.bcm.edu	37	5	169675739	169675739	+	Missense_Mutation	SNP	A	A	G	rs187889192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169675739A>G	ENST00000046794.5	-	21	2179	c.1564T>C	c.(1564-1566)Tac>Cac	p.Y522H	C5orf58_ENST00000517575.1_Intron|LCP2_ENST00000521416.1_Missense_Mutation_p.Y317H	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		GTGCACTGGTATCTGGAACCT	0.458													A|||	3	0.000599042	0.0008	0.0	5008	,	,		17968	0.0		0.002	False		,,,				2504	0.0				p.Y522H		Atlas-SNP	.											.	LCP2	133	.	0			c.T1564C						PASS	.	A	HIS/TYR	1,3959		0,1,1979	308.0	298.0	302.0		1564	3.1	1.0	5		302	42,8248		0,42,4103	yes	missense	LCP2	NM_005565.3	83	0,43,6082	GG,GA,AA		0.5066,0.0253,0.351	possibly-damaging	522/534	169675739	43,12207	1980	4145	6125	SO:0001583	missense	3937	exon21			ACTGGTATCTGGA		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.1564T>C	5.37:g.169675739A>G	ENSP00000046794:p.Tyr522His	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	16.03	3.006340	0.54361	2.53E-4	0.005066	ENSG00000043462	ENST00000046794;ENST00000521416	T;T	0.42513	0.97;0.98	5.82	3.07	0.35406	SH2 motif (1);	0.191452	0.43260	D	0.000595	T	0.12050	0.0293	N	0.01874	-0.695	0.31418	N	0.674662	P;P	0.47910	0.902;0.902	B;B	0.44278	0.445;0.445	T	0.04216	-1.0968	10	0.29301	T	0.29	-19.8141	5.4042	0.16312	0.5846:0.0:0.0818:0.3337	.	317;522	E7ESF6;Q13094	.;LCP2_HUMAN	H	522;317	ENSP00000046794:Y522H;ENSP00000428871:Y317H	ENSP00000046794:Y522H	Y	-	1	0	LCP2	169608317	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.042000	0.41222	0.971000	0.38288	0.482000	0.46254	TAC	A|0.999;G|0.001	0.001	strong		0.458	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
SELP	6403	hgsc.bcm.edu	37	1	169582317	169582317	+	Missense_Mutation	SNP	C	C	T	rs6125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169582317C>T	ENST00000263686.6	-	5	662	c.625G>A	c.(625-627)Gtg>Atg	p.V209M	SELP_ENST00000367794.2_Missense_Mutation_p.V209M|SELP_ENST00000367788.2_Missense_Mutation_p.V209M|SELP_ENST00000367793.2_Missense_Mutation_p.V209M|SELP_ENST00000367786.2_Missense_Mutation_p.V209M|SELP_ENST00000367791.2_Missense_Mutation_p.V209M|SELP_ENST00000367792.2_Missense_Mutation_p.V209M|SELP_ENST00000458599.2_Missense_Mutation_p.V209M	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	209	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> M (in dbSNP:rs6125). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.2}.		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)	TTCATGAGCACGTGTTGAGGG	0.468													C|||	283	0.0565096	0.0454	0.0504	5008	,	,		19846	0.0079		0.0537	False		,,,				2504	0.1288				p.V209M		Atlas-SNP	.											.	SELP	132	.	0			c.G625A						PASS	.	C	MET/VAL	179,4227	115.9+/-153.8	4,171,2028	87.0	78.0	81.0		625	0.3	0.0	1	dbSNP_52	81	466,8134	138.3+/-195.1	22,422,3856	yes	missense	SELP	NM_003005.3	21	26,593,5884	TT,TC,CC		5.4186,4.0626,4.9592	benign	209/831	169582317	645,12361	2203	4300	6503	SO:0001583	missense	6403	exon5			TGAGCACGTGTTG	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.625G>A	1.37:g.169582317C>T	ENSP00000263686:p.Val209Met	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	41	0.759259	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	87|87	0.03983516483516483|0.03983516483516483	18|18	0.036585365853658534|0.036585365853658534	23|23	0.06353591160220995|0.06353591160220995	4|4	0.006993006993006993|0.006993006993006993	42|42	0.055408970976253295|0.055408970976253295	C|C	12.60|12.60	1.985953|1.985953	0.35036|0.35036	0.040626|0.040626	0.054186|0.054186	ENSG00000174175|ENSG00000174175	ENST00000446728|ENST00000367795;ENST00000367790;ENST00000426706;ENST00000367789;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367792;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599	.|T;T;T;T;T;T;T	.|0.49432	.|0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.98|5.98	0.329|0.329	0.15924|0.15924	.|Complement control module (2);Sushi/SCR/CCP (2);	.|0.848590	.|0.10237	.|N	.|0.698874	T|T	0.18130|0.18130	0.0435|0.0435	L|L	0.49126|0.49126	1.545|1.545	0.09310|0.09310	N|N	1|1	.|P;P;P	.|0.41947	.|0.636;0.766;0.563	.|B;B;B	.|0.38880	.|0.21;0.284;0.087	T|T	0.08289|0.08289	-1.0729|-1.0729	5|10	.|0.33940	.|T	.|0.23	-3.6584|-3.6584	4.5764|4.5764	0.12236|0.12236	0.0:0.4261:0.1553:0.4186|0.0:0.4261:0.1553:0.4186	rs6125;rs59751202;rs6125|rs6125;rs59751202;rs6125	.|209;209;209	.|Q6NUL9;P16109;G3V1U2	.|.;LYAM3_HUMAN;.	H|M	208|209;209;208;209;209;209;209;209;209;209;209;209;194	.|ENSP00000263686:V209M;ENSP00000356767:V209M;ENSP00000356768:V209M;ENSP00000356766:V209M;ENSP00000356765:V209M;ENSP00000356762:V209M;ENSP00000356760:V209M	.|ENSP00000263686:V209M	R|V	-|-	2|1	0|0	SELP|SELP	167848941|167848941	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.097000|0.097000	0.18754|0.18754	-0.354000|-0.354000	0.07681|0.07681	0.423000|0.423000	0.26033|0.26033	0.655000|0.655000	0.94253|0.94253	CGT|GTG	C|0.952;T|0.048	0.048	strong		0.468	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
CNDP1	84735	hgsc.bcm.edu	37	18	72238472	72238472	+	Missense_Mutation	SNP	C	C	A	rs73973908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72238472C>A	ENST00000358821.3	+	7	1036	c.808C>A	c.(808-810)Cat>Aat	p.H270N	CNDP1_ENST00000582365.1_Missense_Mutation_p.H227N	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	270						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.H270N(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)		TGGCATCCTTCATGAACCAAT	0.413													C|||	809	0.161542	0.2262	0.1297	5008	,	,		22319	0.1419		0.1282	False		,,,				2504	0.1513				p.H270N	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											CNDP1,NS,carcinoma,0,1	CNDP1	98	1	1	Substitution - Missense(1)	stomach(1)	c.C808A						PASS	.	C	ASN/HIS	860,3546	340.7+/-306.4	84,692,1427	240.0	206.0	218.0		808	-11.6	0.0	18	dbSNP_130	218	1166,7434	238.3+/-269.8	87,992,3221	yes	missense	CNDP1	NM_032649.5	68	171,1684,4648	AA,AC,CC		13.5581,19.5188,15.5774	benign	270/508	72238472	2026,10980	2203	4300	6503	SO:0001583	missense	84735	exon7			ATCCTTCATGAAC		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.808C>A	18.37:g.72238472C>A	ENSP00000351682:p.His270Asn	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	319	114	0.357367	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	332	0.152014652014652	99	0.20121951219512196	44	0.12154696132596685	84	0.14685314685314685	105	0.13852242744063326	C	12.02	1.812873	0.32053	0.195188	0.135581	ENSG00000150656	ENST00000358821	T	0.56776	0.44	5.82	-11.6	0.00059	Peptidase M20, dimerisation (1);	0.576924	0.19497	N	0.112834	T	0.00039	0.0001	L	0.28649	0.875	0.58432	P	5.000000000032756E-6	B	0.14805	0.011	B	0.17722	0.019	T	0.48525	-0.9028	9	0.49607	T	0.09	-4.675	32.931	0.99999	0.0939:0.9061:0.0:0.0	.	270	Q96KN2	CNDP1_HUMAN	N	270	ENSP00000351682:H270N	ENSP00000351682:H270N	H	+	1	0	CNDP1	70389452	0.000000	0.05858	0.000000	0.03702	0.891000	0.51852	-0.509000	0.06336	-2.037000	0.00920	-0.467000	0.05162	CAT	C|0.848;A|0.152	0.152	strong		0.413	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
OR8S1	341568	hgsc.bcm.edu	37	12	48919660	48919660	+	Silent	SNP	G	G	A	rs35367885|rs71439450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	132	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	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		
PODN	127435	hgsc.bcm.edu	37	1	53547800	53547800	+	Silent	SNP	A	A	G	rs371150672|rs6687909	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:53547800A>G	ENST00000312553.5	+	10	1960	c.1953A>G	c.(1951-1953)gaA>gaG	p.E651E	RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000371500.3_Silent_p.E632E|PODN_ENST00000395871.2_Silent_p.E509E	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	603					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)	p.E659delE(1)		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						aggaggaggaagaggaggagg	0.532													A|||	1077	0.215056	0.3918	0.1268	5008	,	,		19205	0.2629		0.0149	False		,,,				2504	0.1953				p.E651E		Atlas-SNP	.											.	PODN	86	.	1	Deletion - In frame(1)	prostate(1)	c.A1953G						PASS	.	A	,,,	1216,3190		217,782,1204	49.0	50.0	49.0		1896,1896,1527,1953	-9.2	0.0	1	dbSNP_116	49	101,8499		0,101,4199	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	217,883,5403	GG,GA,AA		1.1744,27.5987,10.1261	,,,	632/643,632/643,509/520,651/662	53547800	1317,11689	2203	4300	6503	SO:0001819	synonymous_variant	127435	exon10			GGAGGAAGAGGAG	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.1953A>G	1.37:g.53547800A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			A|0.855;G|0.145	0.145	strong		0.532	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
OR51B6	390058	hgsc.bcm.edu	37	11	5373170	5373170	+	Missense_Mutation	SNP	C	C	G	rs5006886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373170C>G	ENST00000380219.1	+	1	433	c.433C>G	c.(433-435)Cgg>Ggg	p.R145G	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	145			R -> G (in dbSNP:rs5006886). {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)			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)		GATTGGTGTGCGGGTATTGAC	0.478													G|||	1170	0.233626	0.326	0.2349	5008	,	,		23785	0.0863		0.2644	False		,,,				2504	0.228				p.R145G		Atlas-SNP	.											OR51B6,caecum,carcinoma,-1,1	OR51B6	53	1	0			c.C433G						scavenged	.	G	GLY/ARG	1267,3135	694.8+/-405.9	173,921,1107	162.0	133.0	142.0		433	5.0	0.0	11	dbSNP_113	142	2260,6334	704.9+/-405.4	310,1640,2347	yes	missense	OR51B6	NM_001004750.1	125	483,2561,3454	GG,GC,CC		26.2974,28.7824,27.1391	benign	145/313	5373170	3527,9469	2201	4297	6498	SO:0001583	missense	390058	exon1			GGTGTGCGGGTAT		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.433C>G	11.37:g.5373170C>G	ENSP00000369568:p.Arg145Gly	Somatic	191	4	0.0209424		WXS	Illumina HiSeq	Phase_I	186	58	0.311828	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	G	0.009	-1.810739	0.00600	0.287824	0.262974	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.33865	1.39	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.415428	0.20723	N	0.086862	T	0.00012	0.0000	N	0.00015	-2.885	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	9	0.12103	T	0.63	.	14.4601	0.67442	0.0:0.1483:0.8517:0.0	rs5006886;rs52816653;rs5006886	145	Q9H340	O51B6_HUMAN	G	144;145	ENSP00000369568:R145G	ENSP00000369568:R145G	R	+	1	2	OR51B6	5329746	0.000000	0.05858	0.033000	0.17914	0.234000	0.25298	0.344000	0.19962	1.353000	0.45828	-0.371000	0.07208	CGG	C|0.755;G|0.245	0.245	strong		0.478	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435058	7435058	+	Missense_Mutation	SNP	C	C	T	rs60816800	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7435058C>T	ENST00000319098.4	-	1	1642	c.1549G>A	c.(1549-1551)Gct>Act	p.A517T	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	517					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						TGTTCCCCAGCGTGGAGGTGC	0.597													C|||	516	0.103035	0.0144	0.1282	5008	,	,		20237	0.0764		0.1909	False		,,,				2504	0.1421				p.A517T		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G1549A						PASS	.	C	THR/ALA,	149,3999		3,143,1928	22.0	25.0	24.0		1549,	-2.3	0.0	4	dbSNP_129	24	1497,6867		126,1245,2811	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	58,	129,1388,4739	TT,TC,CC		17.8981,3.5921,13.1554	benign,	517/522,	7435058	1646,10866	2074	4182	6256	SO:0001583	missense	768239	exon1			CCCCAGCGTGGAG	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.1549G>A	4.37:g.7435058C>T	ENSP00000317445:p.Ala517Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	235	0.10760073260073261	9	0.018292682926829267	52	0.143646408839779	33	0.057692307692307696	141	0.18601583113456466	C	4.446	0.082652	0.08533	0.035921	0.178981	ENSG00000178597	ENST00000319098	T	0.66638	-0.22	2.65	-2.31	0.06765	.	.	.	.	.	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	8	0.10636	T	0.68	.	4.4357	0.11549	0.1609:0.4725:0.0:0.3667	rs60816800;rs61730429	517	Q6NUJ1	SAPL1_HUMAN	T	517	ENSP00000317445:A517T	ENSP00000317445:A517T	A	-	1	0	PSAPL1	7485959	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.780000	0.00773	-1.078000	0.03117	-1.119000	0.02030	GCT	C|0.893;T|0.107	0.107	strong		0.597	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
GPD1L	23171	hgsc.bcm.edu	37	3	32181723	32181723	+	Missense_Mutation	SNP	A	A	G	rs72552293	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:32181723A>G	ENST00000282541.5	+	4	571	c.370A>G	c.(370-372)Ata>Gta	p.I124V		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	124			I -> V (in SIDS; significant reduction of sodium current when coexpressed with SCN5A in HEK cells; dbSNP:rs72552293). {ECO:0000269|PubMed:17967976}.		carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						CTTGTAGGGCATAGACGAGGG	0.483													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20191	0.0		0.003	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.											.	GPD1L	25	.	0			c.A370G	GRCh37	CM074889	GPD1L	M	rs72552293	PASS	.	A	VAL/ILE	0,4406		0,0,2203	172.0	184.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	370	3.9	1.0	3	dbSNP_130	180	14,8586	10.5+/-38.8	0,14,4286	yes	missense	GPD1L	NM_015141.3	29	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign	124/352	32181723	14,12992	2203	4300	6503	SO:0001583	missense	23171	exon4			TAGGGCATAGACG	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.370A>G	3.37:g.32181723A>G	ENSP00000282541:p.Ile124Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	42	0.381818	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.632	-0.518627	0.04171	0.0	0.001628	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.59772	0.24;0.24;0.42;0.24	5.06	3.87	0.44632	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.042492	0.85682	D	0.000000	T	0.31979	0.0814	N	0.11818	0.18	0.54753	A	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.10377	T	0.69	-17.6846	7.0731	0.25189	0.7746:0.15:0.0753:0.0	.	124	Q8N335	GPD1L_HUMAN	V	85;124;77;85	ENSP00000393861:I85V;ENSP00000282541:I124V;ENSP00000408770:I77V;ENSP00000416518:I85V	ENSP00000282541:I124V	I	+	1	0	GPD1L	32156727	0.908000	0.30866	0.992000	0.48379	0.825000	0.46686	2.058000	0.41374	0.979000	0.38497	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.483	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
MEP1A	4224	hgsc.bcm.edu	37	6	46801071	46801071	+	Missense_Mutation	SNP	G	G	T	rs2274658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	73	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	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	
TBRG4	9238	hgsc.bcm.edu	37	7	45148667	45148667	+	Missense_Mutation	SNP	G	G	A	rs2304693	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45148667G>A	ENST00000258770.3	-	2	291	c.170C>T	c.(169-171)cCg>cTg	p.P57L	TBRG4_ENST00000471142.1_5'UTR|SNORA5B_ENST00000363786.1_RNA|TBRG4_ENST00000395655.4_Missense_Mutation_p.P57L|TBRG4_ENST00000494076.1_Missense_Mutation_p.P57L|TBRG4_ENST00000361278.3_Missense_Mutation_p.P57L	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	57			P -> L (in dbSNP:rs2304693). {ECO:0000269|PubMed:17974005}.		cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.P57L(1)		cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						CTTCTCCACCGGCTCCATCAA	0.567													G|||	633	0.126398	0.0083	0.2205	5008	,	,		19238	0.1766		0.161	False		,,,				2504	0.1319				p.P68L		Atlas-SNP	.											TBRG4,NS,carcinoma,0,1	TBRG4	52	1	1	Substitution - Missense(1)	stomach(1)	c.C203T						scavenged	.	G	LEU/PRO,LEU/PRO,LEU/PRO	169,4237	112.1+/-150.2	4,161,2038	113.0	104.0	107.0		170,170,170	-1.6	0.0	7	dbSNP_100	107	1442,7158	275.4+/-291.8	125,1192,2983	yes	missense,missense,missense	TBRG4	NM_004749.2,NM_030900.2,NM_199122.1	98,98,98	129,1353,5021	AA,AG,GG		16.7674,3.8357,12.3866	benign,benign,benign	57/632,57/522,57/522	45148667	1611,11395	2203	4300	6503	SO:0001583	missense	9238	exon2			TCCACCGGCTCCA	AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"""FAST kinase domains 4"", ""cell cycle progression 2 protein"""	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.170C>T	7.37:g.45148667G>A	ENSP00000258770:p.Pro57Leu	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	237	80	0.337553	NM_001261834	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Missense_Mutation	SNP	ENST00000258770.3	37	CCDS5501.1	308	0.14102564102564102	7	0.014227642276422764	69	0.19060773480662985	103	0.18006993006993008	129	0.17018469656992086	G	0.005	-2.226503	0.00283	0.038357	0.167674	ENSG00000136270	ENST00000258770;ENST00000361278;ENST00000395655;ENST00000494076;ENST00000478532;ENST00000461363;ENST00000475893;ENST00000482285;ENST00000495078	T;T;T;T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66	5.52	-1.62	0.08372	.	1.978000	0.01960	N	0.043251	T	0.00012	0.0000	N	0.00162	-1.95	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	0.37197	-0.9716	9	0.11182	T	0.66	.	0.1625	0.00105	0.2962:0.2485:0.2142:0.2411	rs2304693;rs11541071;rs17550455;rs60101505;rs2304693	68;57;57	B4DU42;Q969Z0-2;Q969Z0	.;.;TBRG4_HUMAN	L	57;57;57;57;57;3;57;57;57	ENSP00000258770:P57L;ENSP00000354992:P57L;ENSP00000379016:P57L;ENSP00000420597:P57L;ENSP00000418631:P57L;ENSP00000417743:P3L;ENSP00000417324:P57L;ENSP00000417967:P57L;ENSP00000417071:P57L	ENSP00000258770:P57L	P	-	2	0	TBRG4	45115192	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.010000	0.13242	-0.524000	0.06400	-1.117000	0.02048	CCG	G|0.875;A|0.125	0.125	strong		0.567	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900	
XIRP2	129446	hgsc.bcm.edu	37	2	168041152	168041152	+	Splice_Site	SNP	T	T	C	rs16853169	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:168041152T>C	ENST00000409728.1	+	4	750		c.e4+2		XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_5'Flank|XIRP2_ENST00000295237.9_Intron|XIRP2_ENST00000409195.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_5'Flank|XIRP2_ENST00000420519.1_Splice_Site	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2						actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						cttatatttgtaaggttctcg	0.433													T|||	514	0.102636	0.1286	0.0735	5008	,	,		19459	0.0665		0.0825	False		,,,				2504	0.1462				.		Atlas-SNP	.											.	XIRP2	914	.	0			c.661+2T>C						PASS	.																																			SO:0001630	splice_region_variant	129446	exon4			TATTTGTAAGGTT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.661+2T>C	2.37:g.168041152T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Splice_Site	SNP	ENST00000409728.1	37	CCDS56143.1																																																																																			T|0.904;C|0.096	0.096	strong		0.433	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	Intron
MYPN	84665	hgsc.bcm.edu	37	10	69902800	69902800	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69902800A>T	ENST00000358913.5	+	3	1494	c.1006A>T	c.(1006-1008)Aca>Tca	p.T336S	MYPN_ENST00000373675.3_Missense_Mutation_p.T336S|MYPN_ENST00000540630.1_Missense_Mutation_p.T336S|MYPN_ENST00000354393.2_Missense_Mutation_p.T61S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	336	Ig-like 1.|Interaction with CARP.				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						TGAAGAGGACACAGGACGCTA	0.443																																					p.T336S		Atlas-SNP	.											.	MYPN	189	.	0			c.A1006T						PASS	.						118.0	107.0	111.0					10																	69902800		2203	4300	6503	SO:0001583	missense	84665	exon3			GAGGACACAGGAC	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.1006A>T	10.37:g.69902800A>T	ENSP00000351790:p.Thr336Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	A	32	5.115153	0.94339	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630;ENST00000373675	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.59	5.59	0.84812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.53286	0.1787	N	0.01188	-0.97	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	D;D;D;D	0.87578	0.987;0.996;0.998;0.996	T	0.64706	-0.6344	9	.	.	.	.	15.7811	0.78260	1.0:0.0:0.0:0.0	.	336;336;61;336	F5GWA6;Q86TC9-3;Q86TC9-2;Q86TC9	.;.;.;MYPN_HUMAN	S	61;61;336;336;336	ENSP00000346369:T61S;ENSP00000351790:T336S;ENSP00000441668:T336S;ENSP00000362779:T336S	.	T	+	1	0	MYPN	69572806	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.253000	0.95501	2.123000	0.65237	0.533000	0.62120	ACA	.	.	none		0.443	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43861081	43861081	+	Missense_Mutation	SNP	T	T	G	rs62536501		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:43861081T>G	ENST00000377564.3	+	13	2348	c.1955T>G	c.(1954-1956)cTc>cGc	p.L652R		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	652	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.			L -> R (in Ref. 1; BAB70782). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.L652R(2)		central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						GGGCACCCGCTCTCGGCTGTG	0.746																																					p.L652R		Atlas-SNP	.											CNTNAP3B,NS,carcinoma,0,2	CNTNAP3B	37	2	2	Substitution - Missense(2)	prostate(2)	c.T1955G						scavenged	.																																			SO:0001583	missense	728577	exon13			ACCCGCTCTCGGC	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.1955T>G	9.37:g.43861081T>G	ENSP00000366787:p.Leu652Arg	Somatic	6	1	0.166667		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	966|966	0.4423076923076923|0.4423076923076923	215|215	0.4369918699186992|0.4369918699186992	144|144	0.39779005524861877|0.39779005524861877	274|274	0.479020979020979|0.479020979020979	333|333	0.4393139841688654|0.4393139841688654	G|G	0.440|0.440	-0.899156|-0.899156	0.02472|0.02472	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377564;ENST00000341990;ENST00000403166|ENST00000377561	T|.	0.09255|.	3.0|.	1.94|1.94	-3.89|-3.89	0.04193|0.04193	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02916|0.02916	-0.46|-0.46	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44329|0.44329	-0.9335|-0.9335	6|4	0.25751|.	T|.	0.34|.	.|.	4.9769|4.9769	0.14146|0.14146	0.3832:0.0:0.46:0.1569|0.3832:0.0:0.46:0.1569	rs62536501|rs62536501	.|.	.|.	.|.	R|A	652;652;558|701	ENSP00000366787:L652R|.	ENSP00000340890:L652R|.	L|S	+|+	2|1	0|0	CNTNAP3B|CNTNAP3B	43801077|43801077	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	0.143000|0.143000	0.16115|0.16115	-1.863000|-1.863000	0.01150|0.01150	-1.467000|-1.467000	0.01014|0.01014	CTC|TCT	T|0.555;G|0.445	0.445	strong		0.746	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
RNF130	55819	hgsc.bcm.edu	37	5	179498595	179498595	+	Silent	SNP	C	C	T	rs3749821	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:179498595C>T	ENST00000261947.4	-	1	506	c.108G>A	c.(106-108)acG>acA	p.T36T	RNF130_ENST00000521389.1_Silent_p.T36T|RNF130_ENST00000522208.2_Silent_p.T36T	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGATGAGCGCCGTGTAGTACT	0.751													C|||	2993	0.597644	0.4092	0.6758	5008	,	,		7633	0.621		0.6193	False		,,,				2504	0.7505				p.T36T	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.G108A						PASS	.	C		1858,2406		455,948,729	11.0	12.0	12.0		108	1.0	1.0	5	dbSNP_107	12	5377,3081		1751,1875,603	no	coding-synonymous	RNF130	NM_018434.4		2206,2823,1332	TT,TC,CC		36.4271,43.5741,43.13		36/420	179498595	7235,5487	2132	4229	6361	SO:0001819	synonymous_variant	55819	exon1			GAGCGCCGTGTAG	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"""RING-type (C3HC4) zinc fingers"""	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.108G>A	5.37:g.179498595C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				T|0.569;C|0.431;A|0.000	0.569	strong		0.751	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	
IGFALS	3483	hgsc.bcm.edu	37	16	1838640	1838640	+	IGR	SNP	T	T	C	rs344359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1838640T>C	ENST00000215539.3	-	0	2116				NUBP2_ENST00000568706.1_Silent_p.P106P|NUBP2_ENST00000543305.1_Silent_p.P106P|NUBP2_ENST00000565987.1_Silent_p.P187P|NUBP2_ENST00000262302.9_Silent_p.P247P			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						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						AGGAGTTCCCTGGGAGCCCCG	0.672													C|||	4121	0.822883	0.9599	0.7896	5008	,	,		15484	0.7232		0.8022	False		,,,				2504	0.7853				p.P247P		Atlas-SNP	.											.	NUBP2	25	.	0			c.T741C						PASS	.	C		4097,293	155.2+/-188.4	1911,275,9	35.0	30.0	32.0		741	0.2	0.0	16	dbSNP_79	32	7065,1531	271.1+/-289.3	2903,1259,136	no	coding-synonymous	NUBP2	NM_012225.2		4814,1534,145	CC,CT,TT		17.8106,6.6743,14.0459		247/272	1838640	11162,1824	2195	4298	6493	SO:0001628	intergenic_variant	10101	exon7			GTTCCCTGGGAGC	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		16.37:g.1838640T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_012225	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			T|0.153;C|0.847	0.847	strong		0.672	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
BCKDHA	593	hgsc.bcm.edu	37	19	41928652	41928652	+	Silent	SNP	C	C	T	rs284652|rs112312448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41928652C>T	ENST00000269980.2	+	7	1340	c.972C>T	c.(970-972)ttC>ttT	p.F324F	BCKDHA_ENST00000535632.1_3'UTR|BCKDHA_ENST00000457836.2_Silent_p.F302F|CTC-435M10.3_ENST00000540732.1_Silent_p.F358F|BCKDHA_ENST00000595085.1_Silent_p.F358F|CTC-435M10.6_ENST00000598887.1_RNA	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	324					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						ACCAGCCCTTCCTCATCGAGG	0.587													C|||	3087	0.616414	0.8548	0.4885	5008	,	,		17759	0.4325		0.5924	False		,,,				2504	0.5992				p.F324F		Atlas-SNP	.											.	BCKDHA	36	.	0			c.C972T						PASS	.	C	,	3568,838	744.4+/-411.6	1444,680,79	55.0	53.0	54.0		972,969	5.7	1.0	19	dbSNP_79	54	5225,3375	639.6+/-399.5	1610,2005,685	no	coding-synonymous,coding-synonymous	BCKDHA	NM_000709.3,NM_001164783.1	,	3054,2685,764	TT,TC,CC		39.2442,19.0195,32.3927	,	324/446,323/445	41928652	8793,4213	2203	4300	6503	SO:0001819	synonymous_variant	593	exon7			GCCCTTCCTCATC	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.972C>T	19.37:g.41928652C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	CCDS12581.1																																																																																			C|0.348;T|0.652	0.652	strong		0.587	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
KIF1A	547	hgsc.bcm.edu	37	2	241702599	241702599	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241702599G>A	ENST00000320389.7	-	20	2064	c.1906C>T	c.(1906-1908)Cag>Tag	p.Q636*	KIF1A_ENST00000498729.2_Nonsense_Mutation_p.Q645*	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	636					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)		TCCATCTCCTGCTTCATGTCG	0.672																																					p.Q645X		Atlas-SNP	.											.	KIF1A	152	.	0			c.C1933T						PASS	.						24.0	27.0	26.0					2																	241702599		2151	4252	6403	SO:0001587	stop_gained	547	exon21			TCTCCTGCTTCAT	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.1906C>T	2.37:g.241702599G>A	ENSP00000322791:p.Gln636*	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	52	16	0.307692	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Nonsense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	42	9.413377	0.99164	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	.	.	.	3.81	2.91	0.33838	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	11.8555	0.52435	0.089:0.0:0.911:0.0	.	.	.	.	X	636;645;645;645	.	ENSP00000322791:Q636X	Q	-	1	0	KIF1A	241351272	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.644000	0.83416	0.695000	0.31675	0.467000	0.42956	CAG	.	.	none		0.672	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
RASAL1	8437	hgsc.bcm.edu	37	12	113554946	113554946	+	Silent	SNP	G	G	A	rs34456143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:113554946G>A	ENST00000261729.5	-	9	978	c.663C>T	c.(661-663)acC>acT	p.T221T	RASAL1_ENST00000548055.1_Silent_p.T221T|RASAL1_ENST00000546530.1_Silent_p.T221T|RASAL1_ENST00000446861.3_Silent_p.T221T|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	221					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)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TCTGCTGGAGGGTCTTTGGAG	0.632													G|||	277	0.0553115	0.0083	0.085	5008	,	,		18411	0.0		0.1511	False		,,,				2504	0.0562				p.T221T		Atlas-SNP	.											.	RASAL1	89	.	0			c.C663T						PASS	.	G	,,	150,4256	104.7+/-143.2	2,146,2055	52.0	49.0	50.0		663,663,663	2.5	0.9	12	dbSNP_126	50	1279,7321	253.6+/-279.2	93,1093,3114	no	coding-synonymous,coding-synonymous,coding-synonymous	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	,,	95,1239,5169	AA,AG,GG		14.8721,3.4044,10.9872	,,	221/807,221/777,221/805	113554946	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	8437	exon9			CTGGAGGGTCTTT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.663C>T	12.37:g.113554946G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																			G|0.898;A|0.102	0.102	strong		0.632	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
SCN10A	6336	hgsc.bcm.edu	37	3	38768247	38768247	+	Silent	SNP	G	G	A	rs59468016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38768247G>A	ENST00000449082.2	-	16	2936	c.2937C>T	c.(2935-2937)ggC>ggT	p.G979G		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	979					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)			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)	CATCCCTGGGGCCTCTGGGAG	0.567													G|||	954	0.190495	0.0151	0.1081	5008	,	,		19690	0.373		0.2525	False		,,,				2504	0.2342				p.G979G		Atlas-SNP	.											.	SCN10A	359	.	0			c.C2937T						PASS	.	G		224,4182	133.7+/-170.0	7,210,1986	68.0	67.0	68.0		2937	1.1	0.6	3	dbSNP_129	68	2248,6352	381.0+/-339.9	295,1658,2347	no	coding-synonymous	SCN10A	NM_006514.2		302,1868,4333	AA,AG,GG		26.1395,5.084,19.0066		979/1957	38768247	2472,10534	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon16			CCTGGGGCCTCTG	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.2937C>T	3.37:g.38768247G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.796;A|0.204	0.204	strong		0.567	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
NEURL4	84461	hgsc.bcm.edu	37	17	7224921	7224921	+	Missense_Mutation	SNP	C	C	G	rs3809813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7224921C>G	ENST00000399464.2	-	18	3072	c.3057G>C	c.(3055-3057)caG>caC	p.Q1019H	NEURL4_ENST00000570460.1_Missense_Mutation_p.Q995H|RP11-542C16.2_ENST00000575474.1_5'Flank|NEURL4_ENST00000315614.7_Missense_Mutation_p.Q1017H|NEURL4_ENST00000574120.1_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1019	NHR 5. {ECO:0000255|PROSITE- ProRule:PRU00400}.		Q -> H (in dbSNP:rs3809813). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCCTCTGGAGCTGCCCATCAC	0.647													C|||	1029	0.205471	0.0091	0.2507	5008	,	,		18683	0.3819		0.163	False		,,,				2504	0.3006				p.Q1019H		Atlas-SNP	.											.	NEURL4	192	.	0			c.G3057C						PASS	.	C	HIS/GLN,HIS/GLN	123,4079		1,121,1979	78.0	87.0	84.0		3051,3057	0.7	1.0	17	dbSNP_107	84	1128,7308		78,972,3168	yes	missense,missense	NEURL4	NM_001005408.1,NM_032442.2	24,24	79,1093,5147	GG,GC,CC		13.3713,2.9272,9.8987	benign,benign	1017/1561,1019/1563	7224921	1251,11387	2101	4218	6319	SO:0001583	missense	84461	exon18			CTGGAGCTGCCCA		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.3057G>C	17.37:g.7224921C>G	ENSP00000382390:p.Gln1019His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	445	0.20375457875457875	9	0.018292682926829267	95	0.26243093922651933	207	0.3618881118881119	134	0.17678100263852242	C	6.723	0.502080	0.12822	0.029272	0.133713	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.30714	1.52;1.52	5.0	0.713	0.18173	NEUZ (2);	0.370692	0.28420	N	0.015411	T	0.00012	0.0000	L	0.59436	1.845	0.36725	P	0.11861999999999995	B;P	0.42785	0.002;0.79	B;B	0.31751	0.001;0.135	T	0.47045	-0.9147	9	0.15066	T	0.55	-9.5649	5.8763	0.18830	0.0:0.4857:0.2727:0.2417	rs3809813;rs3809813	1017;1019	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	H	1017;1019	ENSP00000319826:Q1017H;ENSP00000382390:Q1019H	ENSP00000319826:Q1017H	Q	-	3	2	NEURL4	7165645	0.502000	0.26107	1.000000	0.80357	0.999000	0.98932	-0.472000	0.06623	0.359000	0.24239	0.655000	0.94253	CAG	C|0.809;G|0.191	0.191	strong		0.647	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
PAK6	56924	hgsc.bcm.edu	37	15	40564441	40564441	+	Missense_Mutation	SNP	G	G	A	rs150100570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40564441G>A	ENST00000542403.2	+	4	986	c.875G>A	c.(874-876)cGa>cAa	p.R292Q	PAK6_ENST00000260404.4_Missense_Mutation_p.R292Q|PAK6_ENST00000441369.1_Missense_Mutation_p.R292Q|PAK6_ENST00000455577.2_Missense_Mutation_p.R292Q|PAK6_ENST00000560346.1_Missense_Mutation_p.R292Q|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000453867.1_Missense_Mutation_p.R292Q	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	292	Linker.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		TCCTCTTTCCGACCGCCGCAG	0.637																																					p.R292Q		Atlas-SNP	.											PAK6,NS,adenocarcinoma,+1,1	PAK6	49	1	0			c.G875A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	68.0	84.0	79.0		875,875,875	3.1	0.9	15	dbSNP_134	79	16,8584	10.5+/-38.8	0,16,4284	yes	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	43,43,43	0,16,6487	AA,AG,GG		0.186,0.0,0.123	possibly-damaging,possibly-damaging,possibly-damaging	292/682,292/682,292/682	40564441	16,12990	2203	4300	6503	SO:0001583	missense	56924	exon5			CTTTCCGACCGCC	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"""p21(CDKN1A)-activated kinase 6"""			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.875G>A	15.37:g.40564441G>A	ENSP00000439597:p.Arg292Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.529004	0.27387	0.0	0.00186	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.74842	-0.81;-0.81;-0.88;-0.81;-0.81	5.02	3.14	0.36123	.	0.683340	0.13547	N	0.379732	T	0.57799	0.2078	L	0.27053	0.805	0.37769	D	0.926619	B;B	0.21905	0.037;0.062	B;B	0.10450	0.002;0.005	T	0.47947	-0.9077	10	0.15499	T	0.54	.	9.1394	0.36894	0.2362:0.0:0.7638:0.0	.	292;292	Q9NQU5;G5E9R2	PAK6_HUMAN;.	Q	292	ENSP00000406873:R292Q;ENSP00000401153:R292Q;ENSP00000409465:R292Q;ENSP00000260404:R292Q;ENSP00000439597:R292Q	ENSP00000260404:R292Q	R	+	2	0	PAK6	38351733	0.340000	0.24792	0.917000	0.36280	0.835000	0.47333	0.975000	0.29449	0.632000	0.30432	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.637	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1		
D2HGDH	728294	hgsc.bcm.edu	37	2	242690745	242690745	+	Missense_Mutation	SNP	C	C	T	rs1105273	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242690745C>T	ENST00000321264.4	+	8	1291	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	D2HGDH_ENST00000486953.1_Intron|D2HGDH_ENST00000403782.1_Missense_Mutation_p.A227V	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	102	0	0		WXS	Illumina HiSeq	Phase_I	106	61	0.575472	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	
HLA-C	3107	hgsc.bcm.edu	37	6	31238880	31238880	+	Missense_Mutation	SNP	C	C	T	rs1050357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31238880C>T	ENST00000376228.5	-	3	603	c.589G>A	c.(589-591)Gag>Aag	p.E197K	HLA-C_ENST00000383329.3_Missense_Mutation_p.E197K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	197	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						TTCCCGTTCTCCAGGTATCTG	0.672																																					p.E197K		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.G589A						PASS	.						52.0	44.0	47.0					6																	31238880		2202	4297	6499	SO:0001583	missense	3107	exon3			CGTTCTCCAGGTA	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.589G>A	6.37:g.31238880C>T	ENSP00000365402:p.Glu197Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	100	25	0.25	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	250|250	0.11446886446886446|0.11446886446886446	26|26	0.052845528455284556|0.052845528455284556	32|32	0.08839779005524862|0.08839779005524862	110|110	0.19230769230769232|0.19230769230769232	82|82	0.10817941952506596|0.10817941952506596	.|.	14.40|14.40	2.525317|2.525317	0.44969|0.44969	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00864|.	5.6;5.6|.	2.71|2.71	2.71|2.71	0.32032|0.32032	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	0.857122|.	0.09529|.	U|.	0.789762|.	T|T	0.68604|0.68604	0.3019|0.3019	M|M	0.89904|0.89904	3.07|3.07	0.32236|0.32236	P|P	0.573324|0.573324	B;B;B;B|.	0.09022|.	0.001;0.001;0.0;0.002|.	B;B;B;B|.	0.13407|.	0.009;0.003;0.003;0.006|.	T|T	0.74438|0.74438	-0.3665|-0.3665	9|4	0.62326|.	D|.	0.03|.	.|.	11.5435|11.5435	0.50679|0.50679	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs1050357;rs3180652;rs12721964|rs1050357;rs3180652;rs12721964	197;197;197;197|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	K|E	197;197;197;234|196	ENSP00000365402:E197K;ENSP00000372819:E197K|.	ENSP00000365402:E197K|.	E|G	-|-	1|2	0|0	HLA-C|HLA-C	31346859|31346859	0.001000|0.001000	0.12720|0.12720	0.990000|0.990000	0.47175|0.47175	0.087000|0.087000	0.18053|0.18053	-0.307000|-0.307000	0.08167|0.08167	1.826000|1.826000	0.53198|0.53198	0.305000|0.305000	0.20034|0.20034	GAG|GGA	C|0.913;T|0.087	0.087	strong		0.672	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
CNNM1	26507	hgsc.bcm.edu	37	10	101147692	101147692	+	Missense_Mutation	SNP	G	G	A	rs2298316	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101147692G>A	ENST00000356713.4	+	8	2745	c.2456G>A	c.(2455-2457)cGg>cAg	p.R819Q	CNNM1_ENST00000370528.3_Missense_Mutation_p.R748Q|CNNM1_ENST00000370534.4_Missense_Mutation_p.R475Q|CNNM1_ENST00000446890.1_Missense_Mutation_p.R748Q	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	819			R -> Q (in dbSNP:rs2298316).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CCCACAACCCGGGGCACACCC	0.627													G|||	193	0.0385383	0.0015	0.0937	5008	,	,		18890	0.003		0.1074	False		,,,				2504	0.0153				p.R819Q		Atlas-SNP	.											.	CNNM1	101	.	0			c.G2456A						PASS	.	G	GLN/ARG	101,4305	80.9+/-119.3	0,101,2102	48.0	49.0	49.0		2456	5.1	1.0	10	dbSNP_100	49	914,7686	201.6+/-245.0	60,794,3446	yes	missense	CNNM1	NM_020348.2	43	60,895,5548	AA,AG,GG		10.6279,2.2923,7.8041	possibly-damaging	819/952	101147692	1015,11991	2203	4300	6503	SO:0001583	missense	26507	exon8			CAACCCGGGGCAC	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2456G>A	10.37:g.101147692G>A	ENSP00000349147:p.Arg819Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	114	0.0521978021978022	2	0.0040650406504065045	35	0.09668508287292818	1	0.0017482517482517483	76	0.10026385224274406	G	12.71	2.020394	0.35606	0.022923	0.106279	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.05	5.05	0.67936	.	0.101382	0.37761	N	0.001952	T	0.00440	0.0014	L	0.40543	1.245	0.35302	P	0.21687199999999995	P;P;P	0.48640	0.489;0.883;0.913	B;B;B	0.40602	0.096;0.334;0.201	T	0.07328	-1.0778	9	0.07030	T	0.85	-14.0957	16.9713	0.86301	0.0:0.0:1.0:0.0	rs2298316;rs52818796;rs57619431;rs2298316	475;819;819	F5H5J0;Q9NRU3-2;Q9NRU3	.;.;CNNM1_HUMAN	Q	819;748;748;475;272	ENSP00000349147:R819Q;ENSP00000406492:R748Q;ENSP00000359559:R748Q;ENSP00000359565:R475Q	ENSP00000349147:R819Q	R	+	2	0	CNNM1	101137682	0.869000	0.29996	1.000000	0.80357	0.971000	0.66376	2.716000	0.47219	2.493000	0.84123	0.655000	0.94253	CGG	G|0.935;A|0.065	0.065	strong		0.627	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
SH2D4A	63898	hgsc.bcm.edu	37	8	19192332	19192332	+	Silent	SNP	G	G	T	rs56005620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:19192332G>T	ENST00000265807.3	+	4	888	c.477G>T	c.(475-477)tcG>tcT	p.S159S	SH2D4A_ENST00000518040.1_Silent_p.S114S|SH2D4A_ENST00000519207.1_Silent_p.S159S	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	159					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AGCAAGGATCGAGGCCAGCAC	0.483													T|||	1531	0.305711	0.5809	0.1945	5008	,	,		17983	0.2073		0.167	False		,,,				2504	0.2566				p.S159S		Atlas-SNP	.											SH2D4A,NS,carcinoma,+1,3	SH2D4A	49	3	0			c.G477T						scavenged	.	T	,,	2229,2177	585.4+/-386.2	560,1109,534	98.0	94.0	95.0		477,342,477	-10.8	0.0	8	dbSNP_129	95	1608,6992	742.3+/-407.2	155,1298,2847	no	coding-synonymous,coding-synonymous,coding-synonymous	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	,,	715,2407,3381	TT,TG,GG		18.6977,49.4099,29.5018	,,	159/455,114/410,159/455	19192332	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	63898	exon4			AGGATCGAGGCCA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.477G>T	8.37:g.19192332G>T		Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	54	13	0.240741	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	37	CCDS6009.1																																																																																			G|0.718;T|0.282	0.282	strong		0.483	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178555097	178555097	+	Missense_Mutation	SNP	C	C	T	rs35445112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178555097C>T	ENST00000251582.7	-	17	2581	c.2480G>A	c.(2479-2481)cGg>cAg	p.R827Q		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	827	Spacer.		R -> Q (in dbSNP:rs35445112).		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)		CAGTGAGACCCGGGTGTCTCC	0.582													C|||	57	0.0113818	0.0008	0.0288	5008	,	,		17570	0.0		0.0348	False		,,,				2504	0.001				p.R827Q		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G2480A						PASS	.	C	GLN/ARG	28,4378	34.3+/-65.2	0,28,2175	142.0	115.0	124.0		2480	3.4	0.9	5	dbSNP_126	124	324,8276	113.9+/-173.9	7,310,3983	yes	missense	ADAMTS2	NM_014244.4	43	7,338,6158	TT,TC,CC		3.7674,0.6355,2.7064	possibly-damaging	827/1212	178555097	352,12654	2203	4300	6503	SO:0001583	missense	9509	exon17			GAGACCCGGGTGT	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.2480G>A	5.37:g.178555097C>T	ENSP00000251582:p.Arg827Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	14	0.311111	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	39	0.017857142857142856	0	0.0	11	0.03038674033149171	0	0.0	28	0.036939313984168866	C	11.16	1.556824	0.27827	0.006355	0.037674	ENSG00000087116	ENST00000251582	T	0.52057	0.68	4.55	3.4	0.38934	ADAM-TS Spacer 1 (1);	0.127203	0.34178	N	0.004196	T	0.10380	0.0254	L	0.54323	1.7	0.44668	D	0.997657	B	0.19706	0.038	B	0.15484	0.013	T	0.16129	-1.0413	10	0.30854	T	0.27	.	3.7292	0.08487	0.0:0.6429:0.0:0.3571	rs35445112;rs61751562	827	O95450	ATS2_HUMAN	Q	827	ENSP00000251582:R827Q	ENSP00000251582:R827Q	R	-	2	0	ADAMTS2	178487703	1.000000	0.71417	0.887000	0.34795	0.058000	0.15608	3.942000	0.56614	2.232000	0.73038	0.462000	0.41574	CGG	C|0.975;T|0.025	0.025	strong		0.582	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
CETP	1071	hgsc.bcm.edu	37	16	57017319	57017319	+	Missense_Mutation	SNP	G	G	A	rs1800777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:57017319G>A	ENST00000566128.1	+	15	1475	c.1208G>A	c.(1207-1209)cGa>cAa	p.R403Q	CETP_ENST00000200676.3_Missense_Mutation_p.R468Q|CETP_ENST00000379780.2_Missense_Mutation_p.R408Q					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						ATTATCACTCGAGATGTGAGT	0.587													g|||	132	0.0263578	0.003	0.0879	5008	,	,		19061	0.0		0.0398	False		,,,				2504	0.0276				p.R468Q		Atlas-SNP	.											CETP,NS,malignant_melanoma,+1,1	CETP	50	1	0			c.G1403A	GRCh37	CM973107	CETP	M	rs1800777	PASS	.		GLN/ARG	37,4359	40.8+/-73.8	0,37,2161	90.0	83.0	85.0		1403	-5.3	0.0	16	dbSNP_89	85	334,8266	115.7+/-175.5	5,324,3971	yes	missense	CETP	NM_000078.2	43	5,361,6132	AA,AG,GG		3.8837,0.8417,2.8547	benign	468/494	57017319	371,12625	2198	4300	6498	SO:0001583	missense	1071	exon15			TCACTCGAGATGT	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.1208G>A	16.37:g.57017319G>A	ENSP00000456276:p.Arg403Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		57	0.0260989010989011	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	33	0.04353562005277045	g	4.403	0.074481	0.08485	0.008417	0.038837	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.09350	2.99;2.99	2.88	-5.34	0.02705	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.983616	0.08267	N	0.972066	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.04013	0.001;0.001	T	0.43507	-0.9387	10	0.25751	T	0.34	-0.6986	5.0619	0.14560	0.6114:0.0:0.2095:0.1791	rs1800777;rs52789663;rs1800777	408;468	P11597-2;P11597	.;CETP_HUMAN	Q	468;408	ENSP00000200676:R468Q;ENSP00000369106:R408Q	ENSP00000200676:R468Q	R	+	2	0	CETP	55574820	0.001000	0.12720	0.004000	0.12327	0.001000	0.01503	-0.607000	0.05648	-1.163000	0.02793	-0.261000	0.10672	CGA	G|0.973;A|0.027	0.027	strong		0.587	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
LAMB4	22798	hgsc.bcm.edu	37	7	107738948	107738948	+	Silent	SNP	G	G	A	rs451252	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:107738948G>A	ENST00000388781.3	-	11	1343	c.1260C>T	c.(1258-1260)gcC>gcT	p.A420A	LAMB4_ENST00000388780.3_Silent_p.A420A|LAMB4_ENST00000205386.4_Silent_p.A420A|LAMB4_ENST00000418464.1_Silent_p.A420A|LAMB4_ENST00000414450.2_Silent_p.A420A	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	420	Laminin EGF-like 3. {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						GGCACTGGCCGGCCACAGACC	0.567													G|||	1531	0.305711	0.2458	0.3689	5008	,	,		15850	0.2609		0.3767	False		,,,				2504	0.3149				p.A420A		Atlas-SNP	.											.	LAMB4	253	.	0			c.C1260T						PASS	.	G		1190,3216	416.3+/-337.5	182,826,1195	122.0	106.0	111.0		1260	-8.4	0.2	7	dbSNP_80	111	3374,5226	500.2+/-375.2	694,1986,1620	no	coding-synonymous	LAMB4	NM_007356.2		876,2812,2815	AA,AG,GG		39.2326,27.0086,35.0915		420/1762	107738948	4564,8442	2203	4300	6503	SO:0001819	synonymous_variant	22798	exon11			CTGGCCGGCCACA	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.1260C>T	7.37:g.107738948G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			G|0.674;A|0.326	0.326	strong		0.567	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
CEBPZ	10153	hgsc.bcm.edu	37	2	37438993	37438993	+	Silent	SNP	G	G	A	rs1137437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	161	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	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	
CSMD1	64478	hgsc.bcm.edu	37	8	3076959	3076959	+	Missense_Mutation	SNP	T	T	C	rs28455997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:3076959T>C	ENST00000520002.1	-	30	5048	c.4493A>G	c.(4492-4494)aAc>aGc	p.N1498S	CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Missense_Mutation_p.N1498S|CSMD1_ENST00000602723.1_Missense_Mutation_p.N1498S|CSMD1_ENST00000537824.1_Missense_Mutation_p.N1497S|CSMD1_ENST00000539096.1_Missense_Mutation_p.N1497S|CSMD1_ENST00000542608.1_Missense_Mutation_p.N1497S|CSMD1_ENST00000400186.3_Missense_Mutation_p.N1498S			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	15	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	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	
PTX4	390667	hgsc.bcm.edu	37	16	1536535	1536535	+	Missense_Mutation	SNP	C	C	T	rs2745098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1536535C>T	ENST00000447419.2	-	3	867	c.842G>A	c.(841-843)aGg>aAg	p.R281K	PTX4_ENST00000293922.1_Missense_Mutation_p.R276K|PTX4_ENST00000440447.2_Missense_Mutation_p.G133R			Q96A99	PTX4_HUMAN	pentraxin 4, long	281	Pentaxin.		R -> K (in dbSNP:rs2745098).			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						GACCACGTTCCTGGTGGAGGC	0.657													T|||	2486	0.496406	0.7474	0.3228	5008	,	,		18995	0.5238		0.3738	False		,,,				2504	0.3783				p.R276K		Atlas-SNP	.											.	PTX4	46	.	0			c.G827A						PASS	.	T	LYS/ARG	2968,1430	459.2+/-352.2	993,982,224	51.0	52.0	52.0		827	4.5	0.0	16	dbSNP_100	52	3169,5431	648.3+/-400.5	558,2053,1689	yes	missense	PTX4	NM_001013658.1	26	1551,3035,1913	TT,TC,CC		36.8488,32.5148,47.215	benign	276/474	1536535	6137,6861	2199	4300	6499	SO:0001583	missense	390667	exon3			ACGTTCCTGGTGG		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.842G>A	16.37:g.1536535C>T	ENSP00000445277:p.Arg281Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		1079	0.49404761904761907	342	0.6951219512195121	116	0.32044198895027626	321	0.5611888111888111	300	0.39577836411609496	T	6.812	0.518886	0.13005	0.674852	0.368488	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.62364	0.03;0.03	5.58	4.48	0.54585	.	0.658399	0.15448	N	0.261830	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	0.46816	-0.9164	9	0.02654	T	1	.	6.1276	0.20187	0.1495:0.0796:0.0:0.7709	rs2745098;rs56885857;rs2745098	276	Q96A99-2	.	K	281;276	ENSP00000445277:R281K;ENSP00000293922:R276K	ENSP00000293922:R276K	R	-	2	0	PTX4	1476536	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	0.247000	0.18179	0.396000	0.25283	-0.254000	0.11334	AGG	C|0.507;T|0.493	0.493	strong		0.657	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363078	42363078	+	Missense_Mutation	SNP	T	T	C	rs77186114	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363078T>C	ENST00000290472.3	-	18	1974	c.1880A>G	c.(1879-1881)tAc>tGc	p.Y627C		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	627	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GTCAAGCTGGTAGTCTGGTGG	0.612													C|||	222	0.0443291	0.0144	0.0749	5008	,	,		17538	0.0		0.1083	False		,,,				2504	0.0429				p.Y627C		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.A1880G						PASS	.	C	CYS/TYR	163,4241	789.3+/-415.0	1,161,2040	67.0	72.0	70.0		1880	2.8	0.0	15	dbSNP_131	70	949,7649	754.2+/-407.5	41,867,3391	yes	missense	PLA2G4D	NM_178034.3	194	42,1028,5431	CC,CT,TT		11.0375,3.7012,8.5525	benign	627/819	42363078	1112,11890	2202	4299	6501	SO:0001583	missense	283748	exon18			AGCTGGTAGTCTG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1880A>G	15.37:g.42363078T>C	ENSP00000290472:p.Tyr627Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	128	0.05860805860805861	10	0.02032520325203252	31	0.0856353591160221	0	0.0	87	0.11477572559366754	C	6.825	0.521411	0.13005	0.037012	0.110375	ENSG00000159337	ENST00000290472	T	0.10099	2.91	4.85	2.85	0.33270	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.047240	0.07501	N	0.907297	T	0.00073	0.0002	N	0.00500	-1.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40794	-0.9544	9	0.30854	T	0.27	-2.7487	3.5029	0.07680	0.2347:0.4346:0.2484:0.0823	.	627	Q86XP0	PA24D_HUMAN	C	627	ENSP00000290472:Y627C	ENSP00000290472:Y627C	Y	-	2	0	PLA2G4D	40150370	0.000000	0.05858	0.014000	0.15608	0.050000	0.14768	-0.040000	0.12104	0.637000	0.30526	-0.154000	0.13518	TAC	T|0.926;C|0.074	0.074	strong		0.612	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
SNIP1	79753	hgsc.bcm.edu	37	1	38019747	38019747	+	Silent	SNP	C	C	T	rs2273013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38019747C>T	ENST00000296215.6	-	1	156	c.84G>A	c.(82-84)gtG>gtA	p.V28V	SNIP1_ENST00000468040.1_Intron|DNALI1_ENST00000541606.1_5'Flank|DNALI1_ENST00000296218.7_5'Flank	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	28					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				CCTGCTTCACCACCACCCCCG	0.701													C|||	1148	0.229233	0.0643	0.2896	5008	,	,		11462	0.3938		0.2177	False		,,,				2504	0.2515				p.V28V		Atlas-SNP	.											SNIP1,NS,carcinoma,0,1	SNIP1	44	1	0			c.G84A						PASS	.	C		338,4066		16,306,1880	34.0	32.0	33.0		84	2.7	1.0	1	dbSNP_100	33	1572,7024		142,1288,2868	no	coding-synonymous	SNIP1	NM_024700.2		158,1594,4748	TT,TC,CC		18.2876,7.6748,14.6923		28/397	38019747	1910,11090	2202	4298	6500	SO:0001819	synonymous_variant	79753	exon1			CTTCACCACCACC		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.84G>A	1.37:g.38019747C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_024700	Q96SP9|Q9H9T7	Silent	SNP	ENST00000296215.6	37	CCDS419.1																																																																																			C|0.822;T|0.178	0.178	strong		0.701	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700	
DPYSL5	56896	hgsc.bcm.edu	37	2	27169842	27169842	+	Silent	SNP	C	C	A	rs11126784	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:27169842C>A	ENST00000288699.6	+	13	1832	c.1674C>A	c.(1672-1674)ggC>ggA	p.G558G	DPYSL5_ENST00000401478.1_Silent_p.G558G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	558					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCCGGAGGCAGGTCGAGTG	0.637													c|||	2879	0.57488	0.4175	0.4625	5008	,	,		19717	0.7083		0.6262	False		,,,				2504	0.6769				p.G558G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.C1674A						PASS	.	C		1939,2467	549.4+/-377.8	444,1051,708	81.0	66.0	71.0		1674	5.7	1.0	2	dbSNP_120	71	5253,3347	640.6+/-399.6	1600,2053,647	no	coding-synonymous	DPYSL5	NM_020134.3		2044,3104,1355	AA,AC,CC		38.9186,44.0082,44.7024		558/565	27169842	7192,5814	2203	4300	6503	SO:0001819	synonymous_variant	56896	exon13			CGGAGGCAGGTCG	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.1674C>A	2.37:g.27169842C>A		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	134	131	0.977612	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			C|0.438;A|0.562	0.562	strong		0.637	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518214	161518214	+	Missense_Mutation	SNP	T	T	C	rs148181339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000443193.1_Missense_Mutation_p.I141V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.I106V|FCGR3A_ENST00000367969.3_Missense_Mutation_p.I142V|FCGR3A_ENST00000476031.1_5'UTR	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						PASS	.						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	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	471	160	0.339703	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	
SSH1	54434	hgsc.bcm.edu	37	12	109182049	109182049	+	Silent	SNP	T	T	C	rs3741778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109182049T>C	ENST00000326495.5	-	15	2958	c.2865A>G	c.(2863-2865)acA>acG	p.T955T	SSH1_ENST00000360239.3_Silent_p.T643T	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	955	Interaction with YWHAG.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAATCTCCTGTGTCCGCTGCT	0.632													t|||	2547	0.508586	0.7073	0.5216	5008	,	,		15710	0.6359		0.2962	False		,,,				2504	0.318				p.T955T		Atlas-SNP	.											.	SSH1	144	.	0			c.A2865G						PASS	.	C		2883,1523	627.6+/-394.9	957,969,277	79.0	92.0	88.0		2865	-7.7	0.3	12	dbSNP_107	88	2595,6005	392.2+/-343.9	406,1783,2111	no	coding-synonymous	SSH1	NM_018984.3		1363,2752,2388	CC,CT,TT		30.1744,34.5665,42.119		955/1050	109182049	5478,7528	2203	4300	6503	SO:0001819	synonymous_variant	54434	exon15			CTCCTGTGTCCGC	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.2865A>G	12.37:g.109182049T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_018984	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1																																																																																			T|0.550;C|0.450	0.450	strong		0.632	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	
SPATS1	221409	hgsc.bcm.edu	37	6	44310854	44310854	+	Missense_Mutation	SNP	G	G	A	rs10948132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	42	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	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	
FOXD4	2298	hgsc.bcm.edu	37	9	117696	117696	+	Missense_Mutation	SNP	G	G	A	rs9406415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	260	0	0		WXS	Illumina HiSeq	Phase_I	197	48	0.243655	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	
HLX	3142	hgsc.bcm.edu	37	1	221057646	221057646	+	Missense_Mutation	SNP	C	C	T	rs2738755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:221057646C>T	ENST00000366903.6	+	4	2568	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L	HLX_ENST00000549319.1_Missense_Mutation_p.P142L	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	356			P -> L (in dbSNP:rs2738755). {ECO:0000269|Ref.4}.		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)		GGTGGAGCCCCGGCTGCGGAT	0.662													C|||	1496	0.298722	0.4675	0.2911	5008	,	,		12585	0.0952		0.34	False		,,,				2504	0.2434				p.P356L		Atlas-SNP	.											.	HLX	67	.	0			c.C1067T						PASS	.	C	LEU/PRO	1884,2522	523.8+/-371.2	406,1072,725	34.0	37.0	36.0		1067	2.0	0.0	1	dbSNP_100	36	3017,5583	450.2+/-362.3	516,1985,1799	yes	missense	HLX	NM_021958.3	98	922,3057,2524	TT,TC,CC		35.0814,42.7599,37.6826	benign	356/489	221057646	4901,8105	2203	4300	6503	SO:0001583	missense	3142	exon4			GAGCCCCGGCTGC	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.1067C>T	1.37:g.221057646C>T	ENSP00000355870:p.Pro356Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	633	0.28983516483516486	220	0.44715447154471544	97	0.26795580110497236	60	0.1048951048951049	256	0.33773087071240104	C	7.496	0.651577	0.14516	0.427599	0.350814	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	T;T;T	0.66460	-0.21;0.6;3.34	3.96	2.02	0.26589	.	0.805437	0.10844	N	0.627919	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B	0.22414	0.069	B	0.12156	0.007	T	0.38779	-0.9645	9	0.51188	T	0.08	-2.1735	7.0076	0.24846	0.0:0.7202:0.1767:0.1031	rs2738755;rs3738181;rs9431029;rs60265970;rs2738755	356	Q14774	HLX_HUMAN	L	356;89;142	ENSP00000355870:P356L;ENSP00000408248:P89L;ENSP00000449882:P142L	ENSP00000355870:P356L	P	+	2	0	HLX	219124269	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.957000	0.29215	0.264000	0.21851	0.561000	0.74099	CCG	C|0.651;T|0.349	0.349	strong		0.662	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
MACROD2	140733	hgsc.bcm.edu	37	20	15967390	15967390	+	Missense_Mutation	SNP	C	C	T	rs41275442	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:15967390C>T	ENST00000310348.4	+	14	1004	c.1004C>T	c.(1003-1005)aCg>aTg	p.T335M	MACROD2_ENST00000217246.4_Missense_Mutation_p.T335M|MACROD2_ENST00000407045.3_5'UTR|MACROD2_ENST00000402914.1_Missense_Mutation_p.T100M|MACROD2_ENST00000378058.3_Missense_Mutation_p.T100M			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	335	Glu-rich.		T -> M (in dbSNP:rs41275442).		brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AATGATTCAACGAAGAATGAA	0.338													C|||	384	0.0766773	0.0076	0.121	5008	,	,		19157	0.0238		0.167	False		,,,				2504	0.1002				p.T335M		Atlas-SNP	.											.	MACROD2	34	.	0			c.C1004T						PASS	.	C	MET/THR,MET/THR	189,4217	118.0+/-155.7	6,177,2020	62.0	59.0	60.0		299,1004	-6.7	0.0	20	dbSNP_127	60	1609,6991	294.4+/-301.9	156,1297,2847	yes	missense,missense	MACROD2	NM_001033087.1,NM_080676.5	81,81	162,1474,4867	TT,TC,CC		18.7093,4.2896,13.8244	probably-damaging,probably-damaging	100/214,335/426	15967390	1798,11208	2203	4300	6503	SO:0001583	missense	140733	exon14			ATTCAACGAAGAA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1004C>T	20.37:g.15967390C>T	ENSP00000309809:p.Thr335Met	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	193	0.08836996336996338	5	0.01016260162601626	52	0.143646408839779	8	0.013986013986013986	128	0.16886543535620052	C	3.983	-0.005976	0.07773	0.042896	0.187093	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058	T;T;T;T	0.46063	2.48;2.5;0.88;0.88	5.92	-6.69	0.01772	.	1.480440	0.03889	N	0.278341	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	B;B	0.15719	0.008;0.014	B;B	0.11329	0.002;0.006	T	0.12656	-1.0539	9	0.30078	T	0.28	1.507	6.8409	0.23963	0.103:0.1336:0.102:0.6614	rs41275442	335;335	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	M	335;335;100;100	ENSP00000217246:T335M;ENSP00000309809:T335M;ENSP00000385290:T100M;ENSP00000367297:T100M	ENSP00000217246:T335M	T	+	2	0	MACROD2	15915390	0.000000	0.05858	0.000000	0.03702	0.349000	0.29174	-3.589000	0.00422	-1.070000	0.03149	-0.941000	0.02677	ACG	C|0.869;T|0.131	0.131	strong		0.338	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
SLC8A2	6543	hgsc.bcm.edu	37	19	47935572	47935572	+	Silent	SNP	G	G	A	rs7259674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47935572G>A	ENST00000236877.6	-	9	2636	c.2241C>T	c.(2239-2241)caC>caT	p.H747H	SLC8A2_ENST00000542837.1_Silent_p.H503H|SLC8A2_ENST00000601757.1_5'Flank|SLC8A2_ENST00000539381.1_Silent_p.H210H	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	747					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)		AGGCCCAGCCGTGGCAGTACT	0.642													.|||	425	0.0848642	0.0688	0.0663	5008	,	,		18918	0.122		0.1252	False		,,,				2504	0.0399				p.H747H		Atlas-SNP	.											.	SLC8A2	77	.	0			c.C2241T						PASS	.	G		309,4097	164.7+/-196.3	10,289,1904	100.0	84.0	90.0		2241	-7.8	0.8	19	dbSNP_116	90	1059,7541	223.7+/-260.4	56,947,3297	no	coding-synonymous	SLC8A2	NM_015063.2		66,1236,5201	AA,AG,GG		12.314,7.0132,10.5182		747/922	47935572	1368,11638	2203	4300	6503	SO:0001819	synonymous_variant	6543	exon9			CCAGCCGTGGCAG	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.2241C>T	19.37:g.47935572G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_015063	B4DYQ9	Silent	SNP	ENST00000236877.6	37	CCDS33065.1																																																																																			G|0.890;A|0.110	0.110	strong		0.642	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1		
PBLD	64081	hgsc.bcm.edu	37	10	70044031	70044031	+	Missense_Mutation	SNP	T	T	C	rs4142048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70044031T>C	ENST00000358769.2	-	10	972	c.770A>G	c.(769-771)cAc>cGc	p.H257R	PBLD_ENST00000336578.1_Missense_Mutation_p.H224R|PBLD_ENST00000309049.4_Missense_Mutation_p.H257R	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	84	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	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	
POP1	10940	hgsc.bcm.edu	37	8	99153088	99153088	+	Missense_Mutation	SNP	A	A	C	rs17184326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:99153088A>C	ENST00000401707.2	+	11	1647	c.1566A>C	c.(1564-1566)aaA>aaC	p.K522N	POP1_ENST00000349693.3_Missense_Mutation_p.K522N	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	522			K -> N (in dbSNP:rs17184326).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			AGAAGTCCAAAGCTTTGCCCA	0.418													A|||	515	0.102835	0.1641	0.0951	5008	,	,		17452	0.001		0.1392	False		,,,				2504	0.093				p.K522N		Atlas-SNP	.											.	POP1	85	.	0			c.A1566C	GRCh37	CM067452	POP1	M	rs17184326	PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS	776,3630	309.4+/-291.0	72,632,1499	83.0	86.0	85.0		1566,1566,1566	4.2	0.8	8	dbSNP_123	85	1224,7376	246.5+/-274.9	77,1070,3153	yes	missense,missense,missense	POP1	NM_001145860.1,NM_001145861.1,NM_015029.2	94,94,94	149,1702,4652	CC,CA,AA		14.2326,17.6123,15.3775	possibly-damaging,possibly-damaging,possibly-damaging	522/1025,522/1025,522/1025	99153088	2000,11006	2203	4300	6503	SO:0001583	missense	10940	exon11			GTCCAAAGCTTTG	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1566A>C	8.37:g.99153088A>C	ENSP00000385787:p.Lys522Asn	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	228	0.1043956043956044	90	0.18292682926829268	32	0.08839779005524862	0	0.0	106	0.13984168865435356	A	16.88	3.244265	0.59103	0.176123	0.142326	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.44482	0.92;0.92	5.59	4.23	0.50019	.	0.248471	0.40640	N	0.001052	T	0.00109	0.0003	M	0.78456	2.415	0.28215	P	0.9267864	P	0.41597	0.756	B	0.36289	0.221	T	0.15694	-1.0428	9	0.54805	T	0.06	-9.6686	9.0274	0.36239	0.8558:0.0:0.1442:0.0	rs17184326;rs17856354;rs52808856;rs17184326	522	Q99575	POP1_HUMAN	N	522	ENSP00000385787:K522N;ENSP00000339529:K522N	ENSP00000339529:K522N	K	+	3	2	POP1	99222264	1.000000	0.71417	0.779000	0.31741	0.922000	0.55478	5.790000	0.69038	2.127000	0.65507	0.529000	0.55759	AAA	A|0.859;C|0.141	0.141	strong		0.418	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69343287	69343287	+	Missense_Mutation	SNP	A	A	G	rs976002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69343287A>G	ENST00000305363.4	+	8	972	c.908A>G	c.(907-909)tAt>tGt	p.Y303C		NM_014058.3	NP_054777.2	Q9UL52	TM11E_HUMAN	transmembrane protease, serine 11E	303	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		Y -> C (in dbSNP:rs976002).		cognition (GO:0050890)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|lung(19)|pancreas(1)|skin(3)	24						GATGCATCCTATGAGTTTCAA	0.413													A|||	953	0.190296	0.2133	0.317	5008	,	,		17693	0.0873		0.1879	False		,,,				2504	0.1779				p.Y303C		Atlas-SNP	.											.	TMPRSS11E	40	.	0			c.A908G						PASS	.	A	CYS/TYR	969,3437	365.9+/-317.6	113,743,1347	264.0	253.0	257.0		908	3.0	0.2	4	dbSNP_86	257	1988,6612	349.7+/-327.5	232,1524,2544	yes	missense	TMPRSS11E	NM_014058.3	194	345,2267,3891	GG,GA,AA		23.1163,21.9927,22.7357	possibly-damaging	303/424	69343287	2957,10049	2203	4300	6503	SO:0001583	missense	28983	exon8			CATCCTATGAGTT	AF064819	CCDS33993.1	4q13.2	2010-04-13			ENSG00000087128	ENSG00000087128		"""Serine peptidases / Transmembrane"""	24465	protein-coding gene	gene with protein product		610399	"""transmembrane protease, serine 11E2"""	TMPRSS11E2		15328353	Standard	NM_014058		Approved	DESC1	uc003hdz.4	Q9UL52	OTTHUMG00000160438	ENST00000305363.4:c.908A>G	4.37:g.69343287A>G	ENSP00000307519:p.Tyr303Cys	Somatic	570	1	0.00175439		WXS	Illumina HiSeq	Phase_I	565	278	0.492035	NM_014058	A6NL71|Q14DC8|Q6UW31	Missense_Mutation	SNP	ENST00000305363.4	37	CCDS33993.1	405	0.18543956043956045	114	0.23170731707317074	100	0.27624309392265195	47	0.08216783216783216	144	0.18997361477572558	A	13.72	2.322425	0.41096	0.219927	0.231163	ENSG00000087128	ENST00000305363	D	0.88586	-2.4	5.42	3.0	0.34707	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.627472	0.13933	N	0.352776	T	0.00039	0.0001	L	0.42245	1.32	0.80722	P	0.0	D	0.59767	0.986	P	0.50109	0.631	T	0.00064	-1.2150	9	0.45353	T	0.12	.	7.8692	0.29556	0.8285:0.0:0.1715:0.0	.	303	Q9UL52	TM11E_HUMAN	C	303	ENSP00000307519:Y303C	ENSP00000307519:Y303C	Y	+	2	0	TMPRSS11E	69025882	0.004000	0.15560	0.204000	0.23530	0.777000	0.43975	2.022000	0.41030	0.884000	0.36064	0.477000	0.44152	TAT	A|0.789;G|0.211	0.211	strong		0.413	TMPRSS11E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360584.1	NM_014058	
PRRG2	5639	hgsc.bcm.edu	37	19	50091798	50091798	+	Missense_Mutation	SNP	G	G	T	rs2288920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50091798G>T	ENST00000246794.5	+	5	515	c.346G>T	c.(346-348)Ggt>Tgt	p.G116C	PRRG2_ENST00000596700.1_Intron	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	116			G -> C (in dbSNP:rs2288920).			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		GGGGCTGACAGGTGGCATCCT	0.652													T|||	1494	0.298323	0.4849	0.2622	5008	,	,		16533	0.1905		0.171	False		,,,				2504	0.3139				p.G116C		Atlas-SNP	.											.	PRRG2	13	.	0			c.G346T						PASS	.	T	CYS/GLY	1855,2547		395,1065,741	41.0	33.0	35.0		346	1.9	0.0	19	dbSNP_100	35	1523,7065		124,1275,2895	yes	missense	PRRG2	NM_000951.2	159	519,2340,3636	TT,TG,GG		17.734,42.1399,26.0046	benign	116/203	50091798	3378,9612	2201	4294	6495	SO:0001583	missense	5639	exon5			CTGACAGGTGGCA		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.346G>T	19.37:g.50091798G>T	ENSP00000246794:p.Gly116Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_000951	Q6IBF8	Missense_Mutation	SNP	ENST00000246794.5	37	CCDS12773.1	544	0.2490842490842491	218	0.44308943089430897	83	0.2292817679558011	119	0.20804195804195805	124	0.16358839050131926	T	2.900	-0.227794	0.06022	0.421399	0.17734	ENSG00000126460	ENST00000246794;ENST00000543867	D	0.97256	-4.31	5.48	1.92	0.25849	.	0.772653	0.11182	N	0.590830	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	0.01281	0.0;0.0	T	0.10917	-1.0609	9	0.39692	T	0.17	-1.6363	13.7371	0.62824	0.0:0.0:0.7095:0.2904	rs2288920;rs17856738;rs58269970;rs2288920	93;116	F5GZ13;O14669	.;TMG2_HUMAN	C	116;93	ENSP00000246794:G116C	ENSP00000246794:G116C	G	+	1	0	PRRG2	54783610	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.274000	0.18680	0.038000	0.15604	-0.362000	0.07510	GGT	G|0.723;T|0.277	0.277	strong		0.652	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951	
PARD3	56288	hgsc.bcm.edu	37	10	34620220	34620220	+	Silent	SNP	C	C	T	rs3781128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:34620220C>T	ENST00000374789.3	-	19	2992	c.2667G>A	c.(2665-2667)tcG>tcA	p.S889S	PARD3_ENST00000350537.4_Silent_p.S843S|PARD3_ENST00000466092.1_5'UTR|PARD3_ENST00000544292.1_Silent_p.S602S|PARD3_ENST00000340077.5_Silent_p.S886S|PARD3_ENST00000374773.1_Silent_p.S856S|PARD3_ENST00000374788.3_Silent_p.S886S|PARD3_ENST00000545260.1_Silent_p.S799S|PARD3_ENST00000374776.1_Silent_p.S843S|PARD3_ENST00000346874.4_Silent_p.S889S|PARD3_ENST00000374794.3_Silent_p.S814S|PARD3_ENST00000545693.1_Silent_p.S873S|PARD3_ENST00000374790.3_Silent_p.S829S	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	889	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GACTCTCCAACGAGCTTGACT	0.493													T|||	2753	0.54972	0.7254	0.5173	5008	,	,		15913	0.3919		0.4761	False		,,,				2504	0.5736				p.S889S		Atlas-SNP	.											.	PARD3	131	.	0			c.G2667A						PASS	.	T	,,,,,,,,,,	3105,1301	440.8+/-346.1	1111,883,209	72.0	67.0	69.0		2658,2619,2667,2529,2529,2397,2442,2658,2565,2529,2667	-10.9	0.0	10	dbSNP_107	69	4031,4569	596.6+/-393.6	926,2179,1195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_001184792.1,NM_001184793.1,NM_001184794.1,NM_019619.3	,,,,,,,,,,	2037,3062,1404	TT,TC,CC		46.8721,29.5279,45.133	,,,,,,,,,,	886/1354,873/1341,889/1320,843/1311,843/1274,799/1267,814/1245,886/1032,855/1001,843/989,889/1357	34620220	7136,5870	2203	4300	6503	SO:0001819	synonymous_variant	56288	exon19			CTCCAACGAGCTT	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2667G>A	10.37:g.34620220C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001184787	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			C|0.459;T|0.541	0.541	strong		0.493	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549531	32549531	+	Missense_Mutation	SNP	T	T	C	rs112796209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549531T>C	ENST00000360004.5	-	3	560	c.455A>G	c.(454-456)tAt>tGt	p.Y152C		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	152	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)|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						GCTGCCTGGATAGAAACCACT	0.532										Multiple Myeloma(14;0.17)																											p.Y152C		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A455G						PASS	.						101.0	120.0	113.0					6																	32549531		1511	2709	4220	SO:0001583	missense	3123	exon3			CCTGGATAGAAAC	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.455A>G	6.37:g.32549531T>C	ENSP00000353099:p.Tyr152Cys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	232	33	0.142241	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	15.26	2.782128	0.49891	.	.	ENSG00000196126	ENST00000360004	T	0.04317	3.65	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.113906	0.64402	D	0.000009	T	0.18882	0.0453	H	0.96398	3.815	0.44275	D	0.997133	D	0.89917	1.0	D	0.97110	1.0	T	0.02813	-1.1107	10	0.87932	D	0	.	6.8165	0.23833	0.2079:0.0:0.0:0.7921	.	152	P01911	2B1F_HUMAN	C	152	ENSP00000353099:Y152C	ENSP00000353099:Y152C	Y	-	2	0	HLA-DRB1	32657509	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.404000	0.44539	1.535000	0.49220	0.372000	0.22366	TAT	T|0.921;C|0.079	0.079	strong		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ANKS1A	23294	hgsc.bcm.edu	37	6	35048829	35048829	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:35048829G>A	ENST00000360359.3	+	17	2741	c.2603G>A	c.(2602-2604)gGg>gAg	p.G868E	ANKS1A_ENST00000470698.1_3'UTR|ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	868					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCTGCACTGGGCGGTCGGCA	0.617																																					p.G868E		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2603A						PASS	.						119.0	102.0	108.0					6																	35048829		2203	4300	6503	SO:0001583	missense	23294	exon17			GCACTGGGCGGTC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2603G>A	6.37:g.35048829G>A	ENSP00000353518:p.Gly868Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	27	0.27	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.838812	0.51057	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.40756	1.02	5.28	2.37	0.29283	.	0.133303	0.33591	N	0.004742	T	0.49508	0.1561	M	0.68952	2.095	0.80722	D	1	D;B;P	0.67145	0.996;0.104;0.884	D;B;B	0.63703	0.917;0.04;0.432	T	0.59521	-0.7439	10	0.87932	D	0	-8.113	15.4348	0.75137	0.0:0.4714:0.5286:0.0	.	194;194;868	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	E	868;194	ENSP00000353518:G868E	ENSP00000353518:G868E	G	+	2	0	ANKS1A	35156807	0.765000	0.28485	0.008000	0.14137	0.101000	0.19017	0.901000	0.28445	0.561000	0.29186	-0.211000	0.12701	GGG	.	.	none		0.617	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
CD6	923	hgsc.bcm.edu	37	11	60776103	60776103	+	Silent	SNP	T	T	C	rs61899223	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60776103T>C	ENST00000313421.7	+	4	753	c.567T>C	c.(565-567)acT>acC	p.T189T	CD6_ENST00000344028.5_Silent_p.T189T|CD6_ENST00000352009.5_Silent_p.T189T|CD6_ENST00000545105.1_Intron|CD6_ENST00000346437.4_Silent_p.T189T|CD6_ENST00000452451.2_Silent_p.T189T	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	189	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GCGATGACACTTGGGACCTGG	0.711													T|||	795	0.158746	0.2693	0.1081	5008	,	,		15451	0.0764		0.1382	False		,,,				2504	0.1513				p.T189T	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.T567C						PASS	.	T		1091,3307		152,787,1260	47.0	34.0	38.0		567	-8.0	0.0	11	dbSNP_129	38	1154,7444		71,1012,3216	no	coding-synonymous	CD6	NM_006725.3		223,1799,4476	CC,CT,TT		13.4217,24.8067,17.2745		189/669	60776103	2245,10751	2199	4299	6498	SO:0001819	synonymous_variant	923	exon4			TGACACTTGGGAC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.567T>C	11.37:g.60776103T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1	286	0.13095238095238096	115	0.23373983739837398	45	0.12430939226519337	35	0.06118881118881119	91	0.12005277044854881	T	1.073	-0.669235	0.03403	0.248067	0.134217	ENSG00000013725	ENST00000538611	.	.	.	4.0	-8.0	0.01126	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999330317	.	.	.	.	.	.	T	0.15009	-1.0452	3	.	.	.	.	6.2436	0.20805	0.1516:0.5662:0.1209:0.1613	rs61899223	.	.	.	P	33	.	.	L	+	2	0	CD6	60532679	0.000000	0.05858	0.037000	0.18230	0.011000	0.07611	-0.993000	0.03720	-2.159000	0.00787	-1.231000	0.01572	CTT	T|0.838;C|0.162	0.162	strong		0.711	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
TYK2	7297	hgsc.bcm.edu	37	19	10475652	10475652	+	Missense_Mutation	SNP	C	C	A	rs2304256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10475652C>A	ENST00000525621.1	-	8	1565	c.1084G>T	c.(1084-1086)Gtc>Ttc	p.V362F	TYK2_ENST00000264818.6_Missense_Mutation_p.V362F|TYK2_ENST00000524462.1_Missense_Mutation_p.V177F|TYK2_ENST00000529370.1_Missense_Mutation_p.V362F	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	362	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		V -> F (in dbSNP:rs2304256). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2216457, ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|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 tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GGCTGGCCGACTGCCTTGTGA	0.617													C|||	1331	0.265775	0.0893	0.1945	5008	,	,		15329	0.5238		0.2624	False		,,,				2504	0.2924				p.V362F		Atlas-SNP	.											.	TYK2	126	.	0			c.G1084T	GRCh37	CM050351	TYK2	M	rs2304256	PASS	.	C	PHE/VAL	510,3896	233.9+/-246.9	34,442,1727	43.0	43.0	43.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1084	-0.8	0.0	19	dbSNP_100	43	2411,6189	398.1+/-346.0	329,1753,2218	yes	missense	TYK2	NM_003331.4	50	363,2195,3945	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	28.0349,11.5751,22.4589	benign	362/1188	10475652	2921,10085	2203	4300	6503	SO:0001583	missense	7297	exon8			GGCCGACTGCCTT		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.1084G>T	19.37:g.10475652C>A	ENSP00000431885:p.Val362Phe	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	627	0.28708791208791207	61	0.12398373983739837	85	0.23480662983425415	271	0.4737762237762238	210	0.2770448548812665	C	10.11	1.260535	0.23051	0.115751	0.280349	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529370	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	4.19	-0.832	0.10785	FERM domain (1);	1.288840	0.05643	N	0.583836	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B	0.33694	0.421;0.015	B;B	0.28991	0.097;0.021	T	0.46965	-0.9153	9	0.56958	D	0.05	-2.2569	6.2456	0.20815	0.0:0.5268:0.2881:0.1851	rs2304256;rs2304256	362;362	E9PPF2;P29597	.;TYK2_HUMAN	F	177;362;362;109;362	ENSP00000433203:V177F;ENSP00000431885:V362F;ENSP00000264818:V362F;ENSP00000432728:V362F	ENSP00000264818:V362F	V	-	1	0	TYK2	10336652	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.040000	0.12104	-0.107000	0.12088	-1.338000	0.01255	GTC	C|0.745;A|0.247	0.247	strong		0.617	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
ZFHX3	463	hgsc.bcm.edu	37	16	72829616	72829616	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72829616C>T	ENST00000268489.5	-	9	7637	c.6965G>A	c.(6964-6966)cGa>cAa	p.R2322Q	ZFHX3_ENST00000397992.5_Missense_Mutation_p.R1408Q	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2322					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)				GTTGCTTGTTCGAATGTATCT	0.453																																					p.R2322Q		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,1	ZFHX3	404	1	0			c.G6965A						scavenged	.						137.0	130.0	133.0					16																	72829616		2198	4300	6498	SO:0001583	missense	463	exon9			CTTGTTCGAATGT	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.6965G>A	16.37:g.72829616C>T	ENSP00000268489:p.Arg2322Gln	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	198	3	0.0151515	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105087	0.77096	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.79033	-1.23;-1.19	5.65	5.65	0.86999	.	0.000000	0.41712	D	0.000826	D	0.86037	0.5837	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.86343	0.1706	10	0.66056	D	0.02	.	19.722	0.96147	0.0:1.0:0.0:0.0	.	2322	Q15911	ZFHX3_HUMAN	Q	2322;1408	ENSP00000268489:R2322Q;ENSP00000438926:R1408Q	ENSP00000268489:R2322Q	R	-	2	0	ZFHX3	71387117	1.000000	0.71417	0.978000	0.43139	0.938000	0.57974	7.818000	0.86416	2.657000	0.90304	0.561000	0.74099	CGA	.	.	none		0.453	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920119	51920119	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51920119G>A	ENST00000339313.5	-	3	623	c.507C>T	c.(505-507)gcC>gcT	p.A169A	SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.A169A|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Silent_p.A169A|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000525998.1_Silent_p.A169A|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000439889.2_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	169	Ig-like C2-type 1.				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)		ATTCCTCAAAGGCCCAGTTAA	0.597																																					p.A169A		Atlas-SNP	.											SIGLEC10,NS,carcinoma,-1,1	SIGLEC10	112	1	0			c.C507T						scavenged	.						98.0	99.0	98.0					19																	51920119		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon3			CTCAAAGGCCCAG	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.507C>T	19.37:g.51920119G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	140	2	0.0142857	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			.	.	none		0.597	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
NCOA1	8648	hgsc.bcm.edu	37	2	24929851	24929851	+	Silent	SNP	A	A	T	rs3731628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:24929851A>T	ENST00000406961.1	+	13	2164	c.1512A>T	c.(1510-1512)ccA>ccT	p.P504P	NCOA1_ENST00000407230.1_Silent_p.P353P|NCOA1_ENST00000395856.3_Silent_p.P504P|NCOA1_ENST00000538539.1_Silent_p.P504P|NCOA1_ENST00000288599.5_Silent_p.P504P|NCOA1_ENST00000405141.1_Silent_p.P504P|NCOA1_ENST00000348332.3_Silent_p.P504P			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	504	Interaction with STAT3.|Ser-rich.				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)					CCAGGATGCCAAACAATTCCT	0.423			T	PAX3	alveolar rhadomyosarcoma								A|||	540	0.107827	0.1399	0.0692	5008	,	,		21783	0.131		0.0755	False		,,,				2504	0.1012				p.P504P		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.A1512T						PASS	.	A	,,	530,3876	240.3+/-251.1	25,480,1698	84.0	89.0	87.0		1512,1512,1512	-2.8	1.0	2	dbSNP_107	87	533,8067	148.3+/-203.6	16,501,3783	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOA1	NM_003743.4,NM_147223.2,NM_147233.2	,,	41,981,5481	TT,TA,AA		6.1977,12.0291,8.1732	,,	504/1442,504/1400,504/1441	24929851	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	8648	exon11			GATGCCAAACAAT	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.1512A>T	2.37:g.24929851A>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	139	53	0.381295	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	37	CCDS1712.1																																																																																			A|0.914;T|0.086	0.086	strong		0.423	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
ABCA5	23461	hgsc.bcm.edu	37	17	67287358	67287358	+	Splice_Site	SNP	A	A	G	rs57367176	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:67287358A>G	ENST00000392676.3	-	12	1669	c.1605T>C	c.(1603-1605)gaT>gaC	p.D535D	ABCA5_ENST00000392677.2_Splice_Site_p.D535D|ABCA5_ENST00000588877.1_Splice_Site_p.D535D			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	535	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	AAAACTCACCATCAGAAGGTG	0.343													A|||	161	0.0321486	0.0023	0.0461	5008	,	,		14298	0.0079		0.0447	False		,,,				2504	0.0746				p.D535D		Atlas-SNP	.											.	ABCA5	162	.	0			c.T1605C						PASS	.	A	,	42,4362	46.0+/-80.4	0,42,2160	76.0	73.0	74.0		1605,1605	2.9	1.0	17	dbSNP_129	74	345,8255	117.4+/-177.0	8,329,3963	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ABCA5	NM_018672.3,NM_172232.2	,	8,371,6123	GG,GA,AA		4.0116,0.9537,2.976	,	535/1643,535/1643	67287358	387,12617	2202	4300	6502	SO:0001630	splice_region_variant	23461	exon11			CTCACCATCAGAA	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1606+1T>C	17.37:g.67287358A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Silent	SNP	ENST00000392676.3	37	CCDS11685.1																																																																																			A|0.971;G|0.029	0.029	strong		0.343	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	Silent
MUC4	4585	hgsc.bcm.edu	37	3	195511116	195511116	+	Silent	SNP	A	A	G	rs200940092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195511116A>G	ENST00000463781.3	-	2	7794	c.7335T>C	c.(7333-7335)caT>caC	p.H2445H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2445H	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)		GAGGGGTGGCATGACCTGTGG	0.587																																					p.H2445H		Atlas-SNP	.											MUC4_ENST00000463781,caecum,carcinoma,-2,1	MUC4	1505	1	0			c.T7335C						scavenged	.						46.0	45.0	45.0					3																	195511116		675	1590	2265	SO:0001819	synonymous_variant	4585	exon2			GGTGGCATGACCT	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.7335T>C	3.37:g.195511116A>G		Somatic	157	4	0.0254777		WXS	Illumina HiSeq	Phase_I	319	45	0.141066	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.965;G|0.034	0.034	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DISP2	85455	hgsc.bcm.edu	37	15	40656724	40656724	+	Silent	SNP	C	C	T	rs72733418	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40656724C>T	ENST00000267889.3	+	4	669	c.582C>T	c.(580-582)ccC>ccT	p.P194P		NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	194					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCCGGCTGCCCGACTTCTCCA	0.637													C|||	38	0.00758786	0.0212	0.0014	5008	,	,		18401	0.0		0.008	False		,,,				2504	0.001				p.P194P		Atlas-SNP	.											.	DISP2	86	.	0			c.C582T						PASS	.	C		120,4286	88.2+/-126.9	0,120,2083	56.0	59.0	58.0		582	-9.8	0.0	15	dbSNP_130	58	66,8534	40.8+/-97.7	0,66,4234	no	coding-synonymous	DISP2	NM_033510.1		0,186,6317	TT,TC,CC		0.7674,2.7236,1.4301		194/1402	40656724	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	85455	exon4			GCTGCCCGACTTC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.582C>T	15.37:g.40656724C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			C|0.987;T|0.013	0.013	strong		0.637	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
SLC7A5	8140	hgsc.bcm.edu	37	16	87885369	87885369	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:87885369C>T	ENST00000261622.4	-	2	690	c.625G>A	c.(625-627)Gcc>Acc	p.A209T	SLC7A5_ENST00000565644.1_5'UTR	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	209					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	ATGATCAGGGCCAGGGCCAGG	0.667																																					p.A209T		Atlas-SNP	.											.	SLC7A5	28	.	0			c.G625A						PASS	.						40.0	38.0	38.0					16																	87885369		2197	4300	6497	SO:0001583	missense	8140	exon2			TCAGGGCCAGGGC	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"""CD molecules"", ""Solute carriers"""	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.625G>A	16.37:g.87885369C>T	ENSP00000261622:p.Ala209Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	171	48	0.280702	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	37	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.378913	0.61735	.	.	ENSG00000103257	ENST00000261622	D	0.90620	-2.7	5.17	5.17	0.71159	Amino acid permease domain (1);	0.499292	0.20200	N	0.097117	D	0.88157	0.6361	L	0.56280	1.765	0.23361	N	0.997833	B	0.22003	0.063	B	0.19666	0.026	T	0.81609	-0.0855	10	0.72032	D	0.01	.	12.7141	0.57105	0.1645:0.8355:0.0:0.0	.	209	Q01650	LAT1_HUMAN	T	209	ENSP00000261622:A209T	ENSP00000261622:A209T	A	-	1	0	SLC7A5	86442870	0.088000	0.21588	0.710000	0.30468	0.944000	0.59088	1.045000	0.30341	2.386000	0.81285	0.655000	0.94253	GCC	.	.	none		0.667	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
TMTC4	84899	hgsc.bcm.edu	37	13	101287404	101287404	+	Silent	SNP	G	G	A	rs2297943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:101287404G>A	ENST00000376234.3	-	10	1380	c.1191C>T	c.(1189-1191)ccC>ccT	p.P397P	TMTC4_ENST00000342624.5_Silent_p.P416P|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Silent_p.P286P	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	397						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)					GGTTACTCGCGGGGAGAAATG	0.488													.|||	1331	0.265775	0.0378	0.3617	5008	,	,		19380	0.3343		0.3598	False		,,,				2504	0.3384				p.P416P		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1248T						PASS	.	G	,	392,4014	192.6+/-218.0	19,354,1830	41.0	38.0	39.0		1191,1248	1.3	1.0	13	dbSNP_100	39	2920,5680	449.5+/-362.1	497,1926,1877	no	coding-synonymous,coding-synonymous	TMTC4	NM_001079669.1,NM_032813.2	,	516,2280,3707	AA,AG,GG		33.9535,8.897,25.4652	,	397/742,416/761	101287404	3312,9694	2203	4300	6503	SO:0001819	synonymous_variant	84899	exon11			ACTCGCGGGGAGA		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.1191C>T	13.37:g.101287404G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			G|0.737;A|0.263	0.263	strong		0.488	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
OR4C13	283092	hgsc.bcm.edu	37	11	49974670	49974670	+	Silent	SNP	C	C	T	rs16914589	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49974670C>T	ENST00000555099.1	+	1	728	c.696C>T	c.(694-696)caC>caT	p.H232H		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	232						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(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						AGGCAAGGCACGAAGCCCTCT	0.478													C|||	936	0.186901	0.2345	0.1484	5008	,	,		17650	0.1627		0.0845	False		,,,				2504	0.2802				p.H232H		Atlas-SNP	.											.	OR4C13	96	.	0			c.C696T						PASS	.	C		885,3517		87,711,1403	184.0	154.0	164.0		696	-2.2	0.1	11	dbSNP_123	164	748,7844		33,682,3581	no	coding-synonymous	OR4C13	NM_001001955.2		120,1393,4984	TT,TC,CC		8.7058,20.1045,12.5673		232/310	49974670	1633,11361	2201	4296	6497	SO:0001819	synonymous_variant	283092	exon1			AAGGCACGAAGCC	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"""GPCR / Class A : Olfactory receptors"""	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.696C>T	11.37:g.49974670C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	199	99	0.497487	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Silent	SNP	ENST00000555099.1	37	CCDS31495.1																																																																																			C|0.868;T|0.132	0.132	strong		0.478	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955	
OSBPL3	26031	hgsc.bcm.edu	37	7	24843979	24843979	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:24843979C>T	ENST00000313367.2	-	22	2973	c.2522G>A	c.(2521-2523)cGg>cAg	p.R841Q	OSBPL3_ENST00000431825.2_Missense_Mutation_p.R774Q|OSBPL3_ENST00000352860.1_Missense_Mutation_p.R810Q|OSBPL3_ENST00000396431.1_Missense_Mutation_p.R810Q|OSBPL3_ENST00000409069.1_Missense_Mutation_p.R774Q|OSBPL3_ENST00000396429.1_Missense_Mutation_p.R805Q|OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000353930.1_Missense_Mutation_p.R805Q	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	841					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TTCTAAGACCCGCCGCCTTTC	0.458																																					p.R841Q		Atlas-SNP	.											OSBPL3,NS,carcinoma,-1,1	OSBPL3	100	1	0			c.G2522A						scavenged	.						157.0	130.0	139.0					7																	24843979		2203	4300	6503	SO:0001583	missense	26031	exon22			AAGACCCGCCGCC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2522G>A	7.37:g.24843979C>T	ENSP00000315410:p.Arg841Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	212	3	0.0141509	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045765	0.75846	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.73	5.73	0.89815	.	0.062226	0.64402	D	0.000003	T	0.36276	0.0961	M	0.68952	2.095	0.36978	D	0.894133	P;P;B;P	0.43607	0.648;0.775;0.216;0.812	B;B;B;P	0.45681	0.207;0.207;0.065;0.49	T	0.47983	-0.9074	10	0.66056	D	0.02	-22.4894	7.4957	0.27487	0.0:0.8035:0.0:0.1965	.	774;810;805;841	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	Q	841;810;805;774;810;805;774	ENSP00000315410:R841Q;ENSP00000315331:R810Q;ENSP00000315277:R805Q;ENSP00000389779:R774Q;ENSP00000379708:R810Q;ENSP00000379706:R805Q;ENSP00000386953:R774Q	ENSP00000315410:R841Q	R	-	2	0	OSBPL3	24810504	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	1.581000	0.36558	2.700000	0.92200	0.655000	0.94253	CGG	.	.	none		0.458	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
GP6	51206	hgsc.bcm.edu	37	19	55526373	55526373	+	Silent	SNP	G	G	C	rs2304166	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55526373G>C	ENST00000417454.1	-	8	963	c.936C>G	c.(934-936)ctC>ctG	p.L312L	GP6_ENST00000310373.3_Missense_Mutation_p.P314A|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.L294L	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	312					blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		GGAGGGGCGGGAGGGGCGGAA	0.657													G|||	1926	0.384585	0.2012	0.5663	5008	,	,		13801	0.2411		0.6093	False		,,,				2504	0.4202				p.P314A		Atlas-SNP	.											GP6,colon,carcinoma,0,1	GP6	55	1	0			c.C940G						PASS	.	G	ALA/PRO,	916,2878		125,666,1106	15.0	18.0	17.0		940,936	2.7	0.9	19	dbSNP_100	17	4939,3277		1506,1927,675	yes	missense,coding-synonymous	GP6	NM_001083899.1,NM_016363.4	27,	1631,2593,1781	CC,CG,GG		39.8856,24.1434,48.751	probably-damaging,	314/621,312/340	55526373	5855,6155	1897	4108	6005	SO:0001819	synonymous_variant	51206	exon8			GGGCGGGAGGGGC	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.936C>G	19.37:g.55526373G>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_001083899	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	925	0.42353479853479853	131	0.266260162601626	214	0.5911602209944752	124	0.21678321678321677	456	0.6015831134564644	g	13.95	2.391030	0.42410	0.241434	0.601144	ENSG00000088053	ENST00000310373	T	0.00566	6.55	2.65	2.65	0.31530	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999677	D	0.89917	1.0	D	0.83275	0.996	T	0.00341	-1.1804	7	0.27082	T	0.32	.	8.9559	0.35818	0.0:0.0:1.0:0.0	rs2304166;rs60037271	314	Q9HCN6-3	.	A	314	ENSP00000308782:P314A	ENSP00000308782:P314A	P	-	1	0	GP6	60218185	0.742000	0.28228	0.944000	0.38274	0.034000	0.12701	0.423000	0.21313	1.778000	0.52293	0.561000	0.74099	CCC	G|0.538;C|0.462	0.462	strong		0.657	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
PRKCB	5579	hgsc.bcm.edu	37	16	23847575	23847575	+	Silent	SNP	C	C	A	rs75964872	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:23847575C>A	ENST00000321728.7	+	1	254	c.79C>A	c.(79-81)Cgg>Agg	p.R27R	PRKCB_ENST00000498058.1_Silent_p.R27R|PRKCB_ENST00000303531.7_Silent_p.R27R	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	27					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)	AGGCGCCCTCCGGCAGAAGAA	0.672													C|||	1084	0.216454	0.3865	0.33	5008	,	,		8484	0.0565		0.1899	False		,,,				2504	0.0982				p.R27R		Atlas-SNP	.											PRKCB_ENST00000321728,NS,carcinoma,0,3	PRKCB	383	3	0			c.C79A						PASS	.	C	,	1603,2791	490.1+/-361.7	293,1017,887	69.0	61.0	64.0		79,79	0.6	1.0	16	dbSNP_131	64	1689,6911	307.6+/-308.5	170,1349,2781	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	463,2366,3668	AA,AC,CC		19.6395,36.4816,25.3348	,	27/674,27/672	23847575	3292,9702	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon1			GCCCTCCGGCAGA	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.79C>A	16.37:g.23847575C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			C|0.761;A|0.239	0.239	strong		0.672	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
VPS8	23355	hgsc.bcm.edu	37	3	184573555	184573555	+	Silent	SNP	C	C	T	rs6443999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184573555C>T	ENST00000437079.3	+	14	1263	c.1092C>T	c.(1090-1092)taC>taT	p.Y364Y	VPS8_ENST00000436792.2_Silent_p.Y362Y|VPS8_ENST00000287546.4_Silent_p.Y364Y|VPS8_ENST00000446204.2_Silent_p.Y362Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	364							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TACAAAATTACGTGAATCCCA	0.383													T|||	2776	0.554313	0.6755	0.4611	5008	,	,		19524	0.6587		0.3559	False		,,,				2504	0.5532				p.Y364Y		Atlas-SNP	.											.	VPS8	109	.	0			c.C1092T						PASS	.	T	,	2329,1489		698,933,278	211.0	206.0	207.0		1092,1086	-0.8	0.6	3	dbSNP_116	207	2693,5563		449,1795,1884	no	coding-synonymous,coding-synonymous	VPS8	NM_001009921.2,NM_015303.3	,	1147,2728,2162	TT,TC,CC		32.6187,38.9995,41.5935	,	364/1429,362/1427	184573555	5022,7052	1909	4128	6037	SO:0001819	synonymous_variant	23355	exon13			AAATTACGTGAAT	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1092C>T	3.37:g.184573555C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Silent	SNP	ENST00000437079.3	37	CCDS46971.1																																																																																			C|0.471;T|0.529	0.529	strong		0.383	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
DCPS	28960	hgsc.bcm.edu	37	11	126215507	126215507	+	Silent	SNP	G	G	A	rs139354381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126215507G>A	ENST00000263579.4	+	6	1342	c.1013G>A	c.(1012-1014)tGa>tAa	p.*338*	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	0					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)		CAGCAAAGCTGAATTAACTCA	0.502													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18179	0.0		0.002	False		,,,				2504	0.0				p.X338X		Atlas-SNP	.											.	DCPS	33	.	0			c.G1013A						PASS	.	G		5,4397	8.1+/-20.4	0,5,2196	73.0	78.0	76.0		1013	5.2	1.0	11	dbSNP_134	76	73,8523	39.8+/-96.3	0,73,4225	no	coding-synonymous	DCPS	NM_014026.3		0,78,6421	AA,AG,GG		0.8492,0.1136,0.6001		338/338	126215507	78,12920	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon6			AAAGCTGAATTAA	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.1013G>A	11.37:g.126215507G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			G|0.995;A|0.005	0.005	strong		0.502	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
WWC3	55841	hgsc.bcm.edu	37	X	10085227	10085227	+	Silent	SNP	T	T	C	rs7058143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085227T>C	ENST00000380861.4	+	11	1519	c.1128T>C	c.(1126-1128)cgT>cgC	p.R376R	WWC3_ENST00000454666.1_Silent_p.R376R	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	376	Ser-rich.				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)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CCTCCAGCCGTGGGTCTCTGG	0.672													C|||	774	0.205033	0.5401	0.0648	3775	,	,		12301	0.0		0.0149	False		,,,				2504	0.0				p.R376R		Atlas-SNP	.											.	WWC3	142	.	0			c.T1128C						PASS	.	C		2272,1558		575,780,342,277,224	36.0	44.0	41.0		1128	-3.3	0.3	X	dbSNP_116	41	142,6583		0,105,37,2323,1832	no	coding-synonymous	WWC3	NM_015691.3		575,885,379,2600,2056	CC,CT,C,TT,T		2.1115,40.6789,22.8707		376/1093	10085227	2414,8141	2198	4297	6495	SO:0001819	synonymous_variant	55841	exon11			CAGCCGTGGGTCT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1128T>C	X.37:g.10085227T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			0|0.004;C|0.221	0.221	strong		0.672	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
THADA	63892	hgsc.bcm.edu	37	2	43801712	43801712	+	Silent	SNP	A	A	G	rs11899823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43801712A>G	ENST00000405006.4	-	11	1843	c.1492T>C	c.(1492-1494)Ttg>Ctg	p.L498L	THADA_ENST00000402360.2_Silent_p.L498L|THADA_ENST00000404790.1_Silent_p.L498L|THADA_ENST00000403856.1_Silent_p.L498L|THADA_ENST00000415080.2_Silent_p.L208L|THADA_ENST00000405975.2_Silent_p.L498L|THADA_ENST00000330266.7_Silent_p.L208L	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	498										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)				ATGGTTTCCAAGAGGTCACTT	0.408													A|||	1726	0.344649	0.3986	0.2305	5008	,	,		18843	0.2649		0.34	False		,,,				2504	0.4397				p.L498L		Atlas-SNP	.											.	THADA	131	.	0			c.T1492C						PASS	.	A	,	1357,2341		247,863,739	89.0	87.0	88.0		1492,1492	4.7	1.0	2	dbSNP_120	88	2781,5413		468,1845,1784	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	715,2708,2523	GG,GA,AA		33.9395,36.6955,34.7965	,	498/1954,498/1954	43801712	4138,7754	1849	4097	5946	SO:0001819	synonymous_variant	63892	exon11			TTTCCAAGAGGTC	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.1492T>C	2.37:g.43801712A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1																																																																																			A|0.666;G|0.334	0.334	strong		0.408	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
SGSH	6448	hgsc.bcm.edu	37	17	78184393	78184393	+	Missense_Mutation	SNP	C	C	T	rs7503034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78184393C>T	ENST00000326317.6	-	8	1453	c.1367G>A	c.(1366-1368)cGc>cAc	p.R456H	SGSH_ENST00000534910.1_Missense_Mutation_p.R253H	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	456			R -> H (does not affect enzyme activity; cells transfected with the mutant enzyme contain a 62 kDa precursor and a 56 kDa mature form as cells transfected with the wild-type enzyme; dbSNP:rs7503034). {ECO:0000269|PubMed:11182930, ECO:0000269|PubMed:12000360, ECO:0000269|PubMed:12702166, ECO:0000269|PubMed:15637719, ECO:0000269|PubMed:9158154, ECO:0000269|PubMed:9554748}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CTGAGCAAAGCGCGGGTCGGT	0.672													C|||	1732	0.345847	0.2126	0.4769	5008	,	,		18116	0.3998		0.3032	False		,,,				2504	0.4213				p.R456H		Atlas-SNP	.											.	SGSH	27	.	0			c.G1367A						PASS	.	C	HIS/ARG	973,3433	351.6+/-311.3	98,777,1328	32.0	34.0	33.0		1367	-6.9	0.0	17	dbSNP_116	33	2850,5750	435.0+/-357.9	447,1956,1897	yes	missense	SGSH	NM_000199.3	29	545,2733,3225	TT,TC,CC		33.1395,22.0835,29.3941	benign	456/503	78184393	3823,9183	2203	4300	6503	SO:0001583	missense	6448	exon8			GCAAAGCGCGGGT	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"""sulfamidase"", ""mucopolysaccharidosis type IIIA"""	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.1367G>A	17.37:g.78184393C>T	ENSP00000314606:p.Arg456His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_000199	A8K5E2	Missense_Mutation	SNP	ENST00000326317.6	37	CCDS11770.1	713	0.32646520146520147	103	0.20934959349593496	161	0.4447513812154696	212	0.3706293706293706	237	0.31266490765171506	C	5.737	0.320438	0.10845	0.220835	0.331395	ENSG00000181523	ENST00000326317;ENST00000534910	T;T	0.77489	-1.1;-1.1	4.89	-6.91	0.01649	Alkaline-phosphatase-like, core domain (1);	1.486580	0.03365	N	0.198071	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.10730	-1.0617	9	0.45353	T	0.12	-3.0403	10.126	0.42649	0.0:0.3472:0.0928:0.56	rs7503034;rs52793683;rs60961709;rs7503034	456	P51688	SPHM_HUMAN	H	456;253	ENSP00000314606:R456H;ENSP00000437778:R253H	ENSP00000314606:R456H	R	-	2	0	SGSH	75798988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.308000	0.08156	-1.268000	0.02439	-1.090000	0.02178	CGC	C|0.701;N|0.000	.	strong		0.672	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199	
ZNF91	7644	hgsc.bcm.edu	37	19	23543095	23543095	+	Missense_Mutation	SNP	T	T	C	rs296093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23543095T>C	ENST00000300619.7	-	4	2891	c.2686A>G	c.(2686-2688)Acc>Gcc	p.T896A	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.T864A	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	896			T -> A (in dbSNP:rs296093).		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)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TCAGTAAGGGTTGAGGACCAG	0.353													T|||	863	0.172324	0.1884	0.0418	5008	,	,		21466	0.3472		0.0636	False		,,,				2504	0.1748				p.T896A		Atlas-SNP	.											.	ZNF91	349	.	0			c.A2686G						PASS	.	T	ALA/THR	709,3657	265.9+/-266.9	50,609,1524	68.0	74.0	72.0		2686	-2.7	0.0	19	dbSNP_79	72	460,8124	134.3+/-191.7	10,440,3842	no	missense	ZNF91	NM_003430.2	58	60,1049,5366	CC,CT,TT		5.3588,16.2391,9.027	possibly-damaging	896/1192	23543095	1169,11781	2183	4292	6475	SO:0001583	missense	7644	exon4			TAAGGGTTGAGGA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2686A>G	19.37:g.23543095T>C	ENSP00000300619:p.Thr896Ala	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	376	0.17216117216117216	101	0.20528455284552846	17	0.04696132596685083	203	0.3548951048951049	55	0.07255936675461741	T	0.008	-1.893581	0.00522	0.162391	0.053588	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.14640	2.49;2.49	1.34	-2.69	0.06022	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16266	0.395	0.80722	P	0.0	B;P	0.37370	0.097;0.592	B;B	0.35550	0.061;0.205	T	0.36986	-0.9725	8	0.07990	T	0.79	.	5.1758	0.15133	0.0:0.4361:0.3618:0.2021	rs296093;rs52836218;rs296093	864;896	Q05481-2;Q05481	.;ZNF91_HUMAN	A	896;864	ENSP00000300619:T896A;ENSP00000380272:T864A	ENSP00000300619:T896A	T	-	1	0	ZNF91	23334935	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.039000	0.03550	-1.698000	0.01418	-1.193000	0.01689	ACC	T|0.862;C|0.138	0.138	strong		0.353	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
ZFHX3	463	hgsc.bcm.edu	37	16	72827758	72827758	+	Silent	SNP	T	T	C	rs699444	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72827758T>C	ENST00000268489.5	-	9	9495	c.8823A>G	c.(8821-8823)ggA>ggG	p.G2941G	ZFHX3_ENST00000397992.5_Silent_p.G2027G|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2941					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)				CAGGCCGATCTCCGCTGTCAC	0.522													C|||	4611	0.920727	0.9917	0.8746	5008	,	,		20415	0.998		0.833	False		,,,				2504	0.8681				p.G2941G		Atlas-SNP	.											ZFHX3,colon,carcinoma,-2,1	ZFHX3	404	1	0			c.A8823G						PASS	.	C	,	4254,142	98.9+/-137.6	2058,138,2	62.0	60.0	60.0		6081,8823	5.1	1.0	16	dbSNP_86	60	7203,1397	269.0+/-288.2	3035,1133,132	no	coding-synonymous,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	5093,1271,134	CC,CT,TT		16.2442,3.2302,11.8421	,	2027/2790,2941/3704	72827758	11457,1539	2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			CCGATCTCCGCTG	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.8823A>G	16.37:g.72827758T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	96	0.979592	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			A|0.000;C|0.883	0.883	strong		0.522	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
LCT	3938	hgsc.bcm.edu	37	2	136546110	136546110	+	Silent	SNP	A	A	G	rs2278544	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:136546110A>G	ENST00000264162.2	-	17	5578	c.5568T>C	c.(5566-5568)gcT>gcC	p.A1856A		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1856					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	TGGTGGGTCCAGCATCTAGGA	0.562													A|||	2211	0.441494	0.2912	0.4784	5008	,	,		17785	0.4395		0.6561	False		,,,				2504	0.3998				p.A1856A		Atlas-SNP	.											.	LCT	309	.	0			c.T5568C						PASS	.	A		1734,2672	519.9+/-370.1	326,1082,795	88.0	83.0	85.0		5568	-2.8	0.0	2	dbSNP_100	85	6466,2134	715.2+/-406.0	2479,1508,313	no	coding-synonymous	LCT	NM_002299.2		2805,2590,1108	GG,GA,AA		24.814,39.3554,36.9522		1856/1928	136546110	8200,4806	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon17			GGGTCCAGCATCT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.5568T>C	2.37:g.136546110A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			A|0.458;G|0.542	0.542	strong		0.562	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
MYO7A	4647	hgsc.bcm.edu	37	11	76922868	76922868	+	Silent	SNP	C	C	T	rs41298757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76922868C>T	ENST00000409709.3	+	46	6512	c.6240C>T	c.(6238-6240)tcC>tcT	p.S2080S	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.S2031S|MYO7A_ENST00000458637.2_Silent_p.S2042S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2080	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CCCCATAGTCCATCGTCGCCT	0.627													C|||	80	0.0159744	0.0038	0.0173	5008	,	,		19295	0.0		0.0507	False		,,,				2504	0.0123				p.S2080S		Atlas-SNP	.											.	MYO7A	164	.	0			c.C6240T						PASS	.	C	,	39,4353	38.4+/-70.7	1,37,2158	46.0	47.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6240,6126	0.5	0.9	11	dbSNP_127	47	371,8199	119.7+/-179.0	11,349,3925	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	12,386,6083	TT,TC,CC		4.3291,0.888,3.1631	,	2080/2216,2042/2176	76922868	410,12552	2196	4285	6481	SO:0001819	synonymous_variant	4647	exon46			ATAGTCCATCGTC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6240C>T	11.37:g.76922868C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			C|0.975;T|0.025	0.025	strong		0.627	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
SLK	9748	hgsc.bcm.edu	37	10	105763026	105763026	+	Missense_Mutation	SNP	C	C	T	rs3740469	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:105763026C>T	ENST00000369755.3	+	9	2635	c.2090C>T	c.(2089-2091)aCt>aTt	p.T697I	SLK_ENST00000335753.4_Missense_Mutation_p.T697I	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	697			T -> I (in dbSNP:rs3740469). {ECO:0000269|PubMed:17344846}.		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)		CCTGAAGTTACTGTAGTTTCA	0.358													C|||	821	0.163938	0.0688	0.2147	5008	,	,		19569	0.1379		0.2256	False		,,,				2504	0.2198				p.T697I	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.C2090T						PASS	.	C	ILE/THR	470,3936	218.7+/-236.7	30,410,1763	69.0	71.0	70.0		2090	3.5	0.0	10	dbSNP_107	70	2065,6535	356.6+/-330.4	232,1601,2467	yes	missense	SLK	NM_014720.2	89	262,2011,4230	TT,TC,CC		24.0116,10.6673,19.491	possibly-damaging	697/1236	105763026	2535,10471	2203	4300	6503	SO:0001583	missense	9748	exon9			AAGTTACTGTAGT		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.2090C>T	10.37:g.105763026C>T	ENSP00000358770:p.Thr697Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	340	0.15567765567765568	31	0.06300813008130081	67	0.1850828729281768	78	0.13636363636363635	164	0.21635883905013192	C	3.803	-0.041303	0.07452	0.106673	0.240116	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69435	-0.4;-0.39	5.71	3.54	0.40534	Protein kinase-like domain (1);	0.452476	0.25264	N	0.031929	T	0.00039	0.0001	N	0.16478	0.41	0.48040	P	4.3000000000004146E-4	B;B	0.10296	0.003;0.002	B;B	0.09377	0.004;0.002	T	0.06144	-1.0843	9	0.48119	T	0.1	.	13.2602	0.60101	0.0:0.8499:0.0:0.1501	rs3740469;rs52790565;rs61191900;rs3740469	697;697	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	I	697	ENSP00000336824:T697I;ENSP00000358770:T697I	ENSP00000336824:T697I	T	+	2	0	SLK	105753016	0.001000	0.12720	0.022000	0.16811	0.181000	0.23173	0.268000	0.18571	1.430000	0.47334	0.555000	0.69702	ACT	C|0.822;T|0.178	0.178	strong		0.358	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
PELP1	27043	hgsc.bcm.edu	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4576620C>T	ENST00000574876.1	-	15	1787	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000301396.4_Silent_p.P734P|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000572293.1_Silent_p.P640P|PELP1_ENST00000436683.2_Silent_p.P443P			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	97	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	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	
TPO	7173	hgsc.bcm.edu	37	2	1426844	1426844	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:1426844G>T	ENST00000345913.4	+	3	213	c.122G>T	c.(121-123)aGc>aTc	p.S41I	TPO_ENST00000497517.2_Intron|TPO_ENST00000346956.3_Missense_Mutation_p.S41I|TPO_ENST00000382198.1_Missense_Mutation_p.S41I|TPO_ENST00000382269.3_Missense_Mutation_p.S41I|TPO_ENST00000382201.3_Missense_Mutation_p.S41I|TPO_ENST00000329066.4_Missense_Mutation_p.S41I|TPO_ENST00000337415.3_Missense_Mutation_p.S41I|TPO_ENST00000539820.1_Missense_Mutation_p.S41I|TPO_ENST00000349624.3_Missense_Mutation_p.S41I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	41					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)	CGTGTCTCTAGCGTCTTGGAG	0.572																																					p.S41I		Atlas-SNP	.											.	TPO	224	.	0			c.G122T						PASS	.						124.0	99.0	108.0					2																	1426844		2203	4300	6503	SO:0001583	missense	7173	exon3			TCTCTAGCGTCTT		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.122G>T	2.37:g.1426844G>T	ENSP00000318820:p.Ser41Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	58	37	0.637931	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274665	0.23307	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	3.72	-0.276	0.12902	.	2.391560	0.01734	N	0.029009	T	0.59865	0.2225	L	0.54323	1.7	0.09310	N	1	P;P;D;P;P	0.65815	0.846;0.545;0.995;0.911;0.761	P;B;P;P;B	0.58172	0.466;0.206;0.834;0.563;0.276	T	0.40001	-0.9586	10	0.33940	T	0.23	-1.8372	3.7622	0.08609	0.3281:0.185:0.4869:0.0	.	41;41;41;41;41	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	I	41	ENSP00000371704:S41I;ENSP00000337263:S41I;ENSP00000318820:S41I;ENSP00000263886:S41I;ENSP00000332044:S41I;ENSP00000444840:S41I;ENSP00000329869:S41I;ENSP00000371636:S41I;ENSP00000390994:S41I;ENSP00000371633:S41I	ENSP00000329869:S41I	S	+	2	0	TPO	1405851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-0.075000	0.12798	-0.373000	0.07131	AGC	.	.	none		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
ZPBP2	124626	hgsc.bcm.edu	37	17	38024626	38024626	+	Silent	SNP	C	C	T	rs11557466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38024626C>T	ENST00000348931.4	+	1	210	c.19C>T	c.(19-21)Cta>Tta	p.L7L	ZPBP2_ENST00000377940.3_Silent_p.L7L|ZPBP2_ENST00000584588.1_Silent_p.L7L	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	7					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)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			AACGTGCGTCCTACTCTCCGC	0.692													C|||	1455	0.290535	0.115	0.3415	5008	,	,		14820	0.2827		0.4722	False		,,,				2504	0.3129				p.L7L		Atlas-SNP	.											.	ZPBP2	33	.	0			c.C19T						PASS	.	C	,	673,3733	285.7+/-278.4	49,575,1579	85.0	77.0	80.0		19,19	2.0	0.7	17	dbSNP_120	80	3867,4733	542.3+/-384.2	856,2155,1289	no	coding-synonymous,coding-synonymous	ZPBP2	NM_198844.2,NM_199321.2	,	905,2730,2868	TT,TC,CC		44.9651,15.2746,34.907	,	7/317,7/339	38024626	4540,8466	2203	4300	6503	SO:0001819	synonymous_variant	124626	exon1			TGCGTCCTACTCT	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.19C>T	17.37:g.38024626C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			C|0.658;T|0.342	0.342	strong		0.692	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
HLA-G	3135	hgsc.bcm.edu	37	6	29797406	29797406	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29797406G>A	ENST00000360323.6	+	4	855	c.831G>A	c.(829-831)gaG>gaA	p.E277E	HLA-G_ENST00000428701.1_Silent_p.E277E|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Silent_p.E185E|HLA-G_ENST00000376828.2_Silent_p.E282E			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	93	0	0		WXS	Illumina HiSeq	Phase_I	93	15	0.16129	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	
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:149799216T>C	ENST00000435030.1	+	7	899	c.531T>C	c.(529-531)ccT>ccC	p.P177P	KIF5C_ENST00000414838.2_Silent_p.P82P			O60282	KIF5C_HUMAN	kinesin family member 5C	177	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TGTCGAGCCCTGAGGAAGTCA	0.488													C|||	750	0.14976	0.3427	0.1037	5008	,	,		19701	0.0347		0.1064	False		,,,				2504	0.0849				p.P177P		Atlas-SNP	.											.	KIF5C	166	.	0			c.T531C						PASS	.	C		1115,2823		164,787,1018	74.0	73.0	73.0		242	-11.0	0.0	2	dbSNP_129	73	765,7533		44,677,3428	no	coding-synonymous	KIF5C	NM_004522.1		208,1464,4446	CC,CT,TT		9.2191,28.3139,15.3645		177/958	149799216	1880,10356	1969	4149	6118	SO:0001819	synonymous_variant	3800	exon7			GAGCCCTGAGGAA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.531T>C	2.37:g.149799216T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				T|0.860;C|0.140	0.140	strong		0.488	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
GNB1L	54584	hgsc.bcm.edu	37	22	19808874	19808874	+	Missense_Mutation	SNP	G	G	A	rs36070348	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19808874G>A	ENST00000329517.6	-	3	241	c.5C>T	c.(4-6)aCg>aTg	p.T2M	GNB1L_ENST00000403325.1_Missense_Mutation_p.T2M|GNB1L_ENST00000460402.1_Intron|GNB1L_ENST00000405009.1_Missense_Mutation_p.T2M	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	2					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					GCAGGGGGCCGTCATGCTGGG	0.657													G|||	162	0.0323482	0.0015	0.0115	5008	,	,		17868	0.0139		0.0288	False		,,,				2504	0.1115				p.T2M		Atlas-SNP	.											.	GNB1L	34	.	0			c.C5T						PASS	.	G	MET/THR	31,4373		0,31,2171	39.0	48.0	44.0		5	3.7	0.2	22	dbSNP_126	44	246,8348		3,240,4054	yes	missense	GNB1L	NM_053004.2	81	3,271,6225	AA,AG,GG		2.8625,0.7039,2.1311	benign	2/328	19808874	277,12721	2202	4297	6499	SO:0001583	missense	54584	exon3			GGGGCCGTCATGC	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.5C>T	22.37:g.19808874G>A	ENSP00000331313:p.Thr2Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	CCDS13768.1	33	0.01510989010989011	0	0.0	2	0.0055248618784530384	11	0.019230769230769232	20	0.026385224274406333	G	15.97	2.990646	0.54041	0.007039	0.028625	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009;ENST00000453108	T;T;T;T	0.62941	1.12;1.12;-0.01;0.47	4.73	3.7	0.42460	.	2.937810	0.03052	N	0.154737	T	0.24160	0.0585	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.14578	0.011	T	0.34304	-0.9834	10	0.62326	D	0.03	0.5498	11.0733	0.48016	0.0886:0.0:0.9114:0.0	rs36070348;rs61752241	2	Q9BYB4	GNB1L_HUMAN	M	2	ENSP00000331313:T2M;ENSP00000385154:T2M;ENSP00000384626:T2M;ENSP00000389412:T2M	ENSP00000331313:T2M	T	-	2	0	GNB1L	18188874	0.226000	0.23696	0.248000	0.24265	0.378000	0.30076	0.600000	0.24104	1.104000	0.41587	0.313000	0.20887	ACG	G|0.983;A|0.017	0.017	strong		0.657	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
ZHX2	22882	hgsc.bcm.edu	37	8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	rs9649951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:123964819G>A	ENST00000314393.4	+	3	1904	c.1069G>A	c.(1069-1071)Gtg>Atg	p.V357M		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	357	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.		V -> M (in dbSNP:rs9649951).		mRNA catabolic process (GO:0006402)|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)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	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)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCCCACAAAGGTGACGCAGCC	0.617													G|||	50	0.00998403	0.0015	0.0144	5008	,	,		17314	0.001		0.0258	False		,,,				2504	0.0112				p.V357M	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G1069A						PASS	.	G	MET/VAL	41,4365	45.3+/-79.5	0,41,2162	77.0	64.0	69.0		1069	1.4	0.4	8	dbSNP_119	69	373,8227	123.1+/-182.0	6,361,3933	yes	missense	ZHX2	NM_014943.3	21	6,402,6095	AA,AG,GG		4.3372,0.9305,3.1831	benign	357/838	123964819	414,12592	2203	4300	6503	SO:0001583	missense	22882	exon3			ACAAAGGTGACGC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1069G>A	8.37:g.123964819G>A	ENSP00000314709:p.Val357Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	17	0.022427440633245383	G	6.657	0.489767	0.12702	0.009305	0.043372	ENSG00000178764	ENST00000314393	T	0.17370	2.28	5.62	1.42	0.22433	.	0.551628	0.20995	N	0.081968	T	0.02119	0.0066	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.40728	T	0.16	-6.6533	8.5687	0.33556	0.636:0.0:0.364:0.0	rs9649951;rs9649951	357	Q9Y6X8	ZHX2_HUMAN	M	357	ENSP00000314709:V357M	ENSP00000314709:V357M	V	+	1	0	ZHX2	124034000	1.000000	0.71417	0.392000	0.26245	0.782000	0.44232	1.466000	0.35310	0.008000	0.14787	-0.361000	0.07541	GTG	G|0.974;A|0.026	0.026	strong		0.617	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
ORC2	4999	hgsc.bcm.edu	37	2	201785837	201785837	+	Silent	SNP	G	G	A	rs2307362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:201785837G>A	ENST00000234296.2	-	14	1422	c.1173C>T	c.(1171-1173)ctC>ctT	p.L391L		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	391					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						AATTGTGGATGAGAAGGAAGA	0.363													G|||	960	0.191693	0.4486	0.147	5008	,	,		16745	0.0139		0.1928	False		,,,				2504	0.0583				p.L391L		Atlas-SNP	.											.	ORC2	48	.	0			c.C1173T						PASS	.	G		1639,2767	502.2+/-365.2	305,1029,869	75.0	72.0	73.0		1173	-2.0	1.0	2	dbSNP_100	73	1469,7131	279.9+/-294.2	110,1249,2941	no	coding-synonymous	ORC2	NM_006190.4		415,2278,3810	AA,AG,GG		17.0814,37.1993,23.8967		391/578	201785837	3108,9898	2203	4300	6503	SO:0001819	synonymous_variant	4999	exon14			GTGGATGAGAAGG		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"""origin recognition complex, subunit 2 (yeast homolog)-like"", ""origin recognition complex, subunit 2-like (yeast)"", ""origin recognition complex, subunit 2 homolog (yeast)"""	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1173C>T	2.37:g.201785837G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_006190	Q13204|Q53TX5	Silent	SNP	ENST00000234296.2	37	CCDS2334.1																																																																																			G|0.783;A|0.217	0.217	strong		0.363	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190	
FLG	2312	hgsc.bcm.edu	37	1	152280170	152280170	+	Missense_Mutation	SNP	C	C	G	rs71625201	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280170C>G	ENST00000368799.1	-	3	7227	c.7192G>C	c.(7192-7194)Gag>Cag	p.E2398Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2398	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)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	1655	0.330471	0.1135	0.4092	5008	,	,		20923	0.5665		0.169	False		,,,				2504	0.4908				p.E2398Q		Atlas-SNP	.											.	FLG	900	.	0			c.G7192C						PASS	.	C	GLN/GLU	584,3820	250.6+/-257.6	42,500,1660	70.0	74.0	72.0		7192	-3.5	0.0	1	dbSNP_130	72	1418,7138	262.7+/-284.6	121,1176,2981	no	missense	FLG	NM_002016.1	29	163,1676,4641	GG,GC,CC		16.5732,13.2607,15.4475	benign	2398/4062	152280170	2002,10958	2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	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.7192G>C	1.37:g.152280170C>G	ENSP00000357789:p.Glu2398Gln	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	246	106	0.430894	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	602	0.27564102564102566	64	0.13008130081300814	116	0.32044198895027626	294	0.513986013986014	128	0.16886543535620052	C	10.08	1.253118	0.22965	0.132607	0.165732	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01787	4.64	3.76	-3.46	0.04767	.	.	.	.	.	T	0.00815	0.0027	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.39522	-0.9610	8	0.33141	T	0.24	.	4.314	0.10984	0.0:0.2844:0.322:0.3937	.	2398	P20930	FILA_HUMAN	Q	2398;308	ENSP00000357789:E2398Q	ENSP00000271820:E308Q	E	-	1	0	FLG	150546794	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.310000	0.02725	-0.408000	0.07565	-0.494000	0.04653	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SLC26A10	65012	hgsc.bcm.edu	37	12	58019495	58019495	+	Silent	SNP	C	C	T	rs774894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:58019495C>T	ENST00000320442.4	+	14	1970	c.1659C>T	c.(1657-1659)agC>agT	p.S553S	SLC26A10_ENST00000379218.2_3'UTR|SLC26A10_ENST00000490243.1_3'UTR	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	553						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					GCACCAGGAGCGGGAGCCAGG	0.602													c|||	129	0.0257588	0.0666	0.0086	5008	,	,		18716	0.0		0.0189	False		,,,				2504	0.0164				p.S553S		Atlas-SNP	.											.	SLC26A10	89	.	0			c.C1659T						PASS	.	T		282,4124		15,252,1936	41.0	45.0	44.0		1659	-2.1	0.0	12	dbSNP_86	44	155,8445		0,155,4145	no	coding-synonymous	SLC26A10	NM_133489.2		15,407,6081	TT,TC,CC		1.8023,6.4004,3.36		553/564	58019495	437,12569	2203	4300	6503	SO:0001819	synonymous_variant	65012	exon14			CAGGAGCGGGAGC		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"""Solute carriers"""	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1659C>T	12.37:g.58019495C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Silent	SNP	ENST00000320442.4	37	CCDS8949.2																																																																																			C|0.965;T|0.035	0.035	strong		0.602	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
SCUBE2	57758	hgsc.bcm.edu	37	11	9069046	9069046	+	Missense_Mutation	SNP	G	G	A	rs3751055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9069046G>A	ENST00000309263.3	-	15	1844	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	SCUBE2_ENST00000457346.2_Missense_Mutation_p.T620M|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T465M|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T620M|RP11-467K18.2_ENST00000531592.1_RNA			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	591			T -> M (in dbSNP:rs3751055). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T591M(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTTTCTGAGCGTGCGGATGGC	0.562													G|||	773	0.154353	0.0507	0.062	5008	,	,		19886	0.256		0.1272	False		,,,				2504	0.2832				p.T620M		Atlas-SNP	.											SCUBE2,NS,carcinoma,0,1	SCUBE2	102	1	1	Substitution - Missense(1)	stomach(1)	c.C1859T						PASS	.	G	MET/THR,MET/THR	291,4111	160.0+/-192.4	11,269,1921	90.0	75.0	80.0		1394,1859	2.0	0.6	11	dbSNP_107	80	1204,7388	242.8+/-272.6	87,1030,3179	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	81,81	98,1299,5100	AA,AG,GG		14.013,6.6106,11.5053	benign,benign	465/808,620/972	9069046	1495,11499	2201	4296	6497	SO:0001583	missense	57758	exon16			CTGAGCGTGCGGA	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.1772C>T	11.37:g.9069046G>A	ENSP00000310658:p.Thr591Met	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	154	86	0.558442	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		311	0.1423992673992674	34	0.06910569105691057	33	0.09116022099447514	140	0.24475524475524477	104	0.13720316622691292	G	15.50	2.851660	0.51270	0.066106	0.14013	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;D;T	0.84370	-1.3;-1.41;-1.84;-1.48	5.07	2.03	0.26663	.	0.256195	0.44902	D	0.000419	T	0.00109	0.0003	L	0.45352	1.415	0.20926	P	0.999825555	P;P;P	0.46706	0.883;0.852;0.875	B;P;P	0.50162	0.407;0.633;0.534	T	0.01488	-1.1342	9	0.33141	T	0.24	.	7.8988	0.29723	0.1473:0.1337:0.719:0.0	rs3751055;rs52811192;rs58729419;rs3751055	465;620;591	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	M	620;591;465;620	ENSP00000390481:T620M;ENSP00000310658:T591M;ENSP00000415187:T465M;ENSP00000429969:T620M	ENSP00000310658:T591M	T	-	2	0	SCUBE2	9025622	1.000000	0.71417	0.556000	0.28293	0.935000	0.57460	4.686000	0.61700	0.594000	0.29761	0.655000	0.94253	ACG	G|0.865;A|0.135	0.135	strong		0.562	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
CEP70	80321	hgsc.bcm.edu	37	3	138289221	138289221	+	Missense_Mutation	SNP	C	C	T	rs1673607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:138289221C>T	ENST00000264982.3	-	6	670	c.404G>A	c.(403-405)aGt>aAt	p.S135N	CEP70_ENST00000481834.1_Missense_Mutation_p.S135N|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000484888.1_Missense_Mutation_p.S135N|CEP70_ENST00000464035.1_Missense_Mutation_p.S135N|CEP70_ENST00000542237.1_Missense_Mutation_p.S115N|CEP70_ENST00000489254.1_Intron	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	135			S -> N (in dbSNP:rs1673607). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		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						GCAAGCCCTACTTAGTGATTC	0.368													T|||	3459	0.690695	0.5923	0.7061	5008	,	,		18718	0.9425		0.5338	False		,,,				2504	0.7147				p.S135N		Atlas-SNP	.											.	CEP70	51	.	0			c.G404A						PASS	.	T	ASN/SER	2629,1775	524.9+/-371.5	780,1069,353	148.0	139.0	142.0		404	-0.5	1.0	3	dbSNP_89	142	4739,3857	541.6+/-384.0	1322,2095,881	yes	missense	CEP70	NM_024491.2	46	2102,3164,1234	TT,TC,CC		44.8697,40.3043,43.3231	benign	135/598	138289221	7368,5632	2202	4298	6500	SO:0001583	missense	80321	exon6			GCCCTACTTAGTG	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.404G>A	3.37:g.138289221C>T	ENSP00000264982:p.Ser135Asn	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	305	180	0.590164	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	37	CCDS3102.1	1487	0.6808608058608059	293	0.5955284552845529	238	0.6574585635359116	543	0.9493006993006993	413	0.5448548812664907	T	0.197	-1.047852	0.01981	0.596957	0.551303	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035	T;T;T;T;T;T;T;T	0.46451	1.44;1.44;1.44;1.44;1.44;0.87;0.87;0.88	4.98	-0.474	0.12108	.	0.608657	0.17900	N	0.158213	T	0.00012	0.0000	N	0.01277	-0.915	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	0.24297	-1.0164	9	0.07325	T	0.83	-10.1296	4.2353	0.10623	0.1737:0.3805:0.0:0.4458	rs1673607;rs17845490;rs17856867;rs17858371;rs52817699;rs56945954;rs1673607	115;135;135	F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;CEP70_HUMAN	N	135;115;135;117;135;114;115;135	ENSP00000264982:S135N;ENSP00000444128:S115N;ENSP00000419231:S135N;ENSP00000419833:S117N;ENSP00000417465:S135N;ENSP00000418131:S114N;ENSP00000417819:S115N;ENSP00000419743:S135N	ENSP00000264982:S135N	S	-	2	0	CEP70	139771911	0.994000	0.37717	0.989000	0.46669	0.193000	0.23685	0.029000	0.13666	-0.140000	0.11394	-1.017000	0.02453	AGT	C|0.378;T|0.622	0.622	strong		0.368	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
POLE	5426	hgsc.bcm.edu	37	12	133212582	133212582	+	Silent	SNP	G	G	A	rs5744990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133212582G>A	ENST00000320574.5	-	42	5750	c.5707C>T	c.(5707-5709)Ctg>Ttg	p.L1903L	POLE_ENST00000535270.1_Silent_p.L1876L|POLE_ENST00000434528.3_5'UTR	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	67	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	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	
MUC16	94025	hgsc.bcm.edu	37	19	9058907	9058907	+	Missense_Mutation	SNP	G	G	C	rs1833777	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9058907G>C	ENST00000397910.4	-	3	28742	c.28539C>G	c.(28537-28539)caC>caG	p.H9513Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9515	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						TTTCAAAAACGTGAATTGCCT	0.478													C|||	2098	0.41893	0.3593	0.3934	5008	,	,		21029	0.503		0.3946	False		,,,				2504	0.456				p.H9513Q		Atlas-SNP	.											MUC16_ENST00000397910,caecum,carcinoma,-2,2	MUC16	4315	2	0			c.C28539G						PASS	.	C	GLN/HIS	1482,2484		305,872,806	150.0	146.0	147.0		28539	-4.4	0.0	19	dbSNP_92	147	3047,5285		551,1945,1670	yes	missense	MUC16	NM_024690.2	24	856,2817,2476	CC,CG,GG		36.5699,37.3676,36.8271	benign	9513/14508	9058907	4529,7769	1983	4166	6149	SO:0001583	missense	94025	exon3			AAAAACGTGAATT	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.28539C>G	19.37:g.9058907G>C	ENSP00000381008:p.His9513Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	908	0.4157509157509158	176	0.35772357723577236	146	0.40331491712707185	284	0.4965034965034965	302	0.39841688654353563	c	1.009	-0.688602	0.03328	0.373676	0.365699	ENSG00000181143	ENST00000397910	T	0.25912	1.77	2.22	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	8	0.87932	D	0	.	0.8809	0.01234	0.1622:0.2737:0.2988:0.2654	rs1833777;rs1833777	9513	B5ME49	.	Q	9513	ENSP00000381008:H9513Q	ENSP00000381008:H9513Q	H	-	3	2	MUC16	8919907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.662000	0.00400	-3.470000	0.00157	-2.130000	0.00343	CAC	G|0.589;C|0.411	0.411	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NEK10	152110	hgsc.bcm.edu	37	3	27297816	27297816	+	Silent	SNP	G	G	C	rs3213930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:27297816G>C	ENST00000429845.2	-	24	2423	c.2061C>G	c.(2059-2061)acC>acG	p.T687T	NEK10_ENST00000357467.2_Silent_p.T84T|NEK10_ENST00000341435.5_Silent_p.T687T			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	687	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						CAACCACAGAGGTGAGTTTAC	0.343													C|||	2967	0.592452	0.9728	0.6138	5008	,	,		17152	0.2292		0.5388	False		,,,				2504	0.4928				p.T687T		Atlas-SNP	.											NEK10_ENST00000429845,NS,adenoma,0,3	NEK10	271	3	0			c.C2061G						PASS	.	C		3949,455	216.4+/-235.1	1779,391,32	122.0	119.0	120.0		2061	-6.9	0.6	3	dbSNP_106	120	4680,3920	547.0+/-385.1	1274,2132,894	no	coding-synonymous	NEK10	NM_199347.2		3053,2523,926	CC,CG,GG		45.5814,10.3315,33.6435		687/713	27297816	8629,4375	2202	4300	6502	SO:0001819	synonymous_variant	152110	exon24			CACAGAGGTGAGT	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.2061C>G	3.37:g.27297816G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		1234|1234	0.565018315018315|0.565018315018315	474|474	0.9634146341463414|0.9634146341463414	231|231	0.638121546961326|0.638121546961326	124|124	0.21678321678321677|0.21678321678321677	405|405	0.5343007915567283|0.5343007915567283	C|C	8.233|8.233	0.805083|0.805083	0.16467|0.16467	0.896685|0.896685	0.544186|0.544186	ENSG00000163491|ENSG00000163491	ENST00000435584|ENST00000424275	.|.	.|.	.|.	4.96|4.96	-6.92|-6.92	0.01644|0.01644	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999360013|0.999999999360013	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.04333|0.04333	-1.0959|-1.0959	3|3	.|.	.|.	.|.	.|.	10.3913|10.3913	0.44171|0.44171	0.0:0.5312:0.2116:0.2572|0.0:0.5312:0.2116:0.2572	rs3213930;rs17629794;rs61091103;rs3213930|rs3213930;rs17629794;rs61091103;rs3213930	.|.	.|.	.|.	V|R	144|174	.|.	.|.	L|P	-|-	1|2	0|0	NEK10|NEK10	27272820|27272820	0.017000|0.017000	0.18338|0.18338	0.642000|0.642000	0.29436|0.29436	0.971000|0.971000	0.66376|0.66376	-1.914000|-1.914000	0.01579|0.01579	-2.119000|-2.119000	0.00827|0.00827	-1.295000|-1.295000	0.01343|0.01343	CTC|CCT	G|0.368;C|0.632	0.632	strong		0.343	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
PSMD7	5713	hgsc.bcm.edu	37	16	74334016	74334016	+	Silent	SNP	C	C	T	rs140080000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74334016C>T	ENST00000219313.4	+	2	218	c.78C>T	c.(76-78)atC>atT	p.I26I	PSMD7_ENST00000567958.1_Silent_p.I26I|PSMD7_ENST00000540379.1_5'UTR|PSMD7_ENST00000568615.2_Silent_p.I26I	NM_002811.4	NP_002802.2	P51665	PSMD7_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	26	MPN.				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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	15						CATTCAGAATCGGCAAGGTTG	0.418													C|||	3	0.000599042	0.0	0.0	5008	,	,		19257	0.0		0.002	False		,,,				2504	0.001				p.I26I		Atlas-SNP	.											.	PSMD7	29	.	0			c.C78T						PASS	.	C		1,4395	2.1+/-5.4	0,1,2197	129.0	108.0	115.0		78	-0.2	1.0	16	dbSNP_134	115	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	PSMD7	NM_002811.4		0,15,6483	TT,TC,CC		0.1628,0.0227,0.1154		26/325	74334016	15,12981	2198	4300	6498	SO:0001819	synonymous_variant	5713	exon2			CAGAATCGGCAAG	D50063	CCDS10910.1	16q22.3	2010-10-15	2007-07-06		ENSG00000103035	ENSG00000103035		"""Proteasome (prosome, macropain) subunits"""	9565	protein-coding gene	gene with protein product	"""Mov34 homolog"""	157970	"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homolog)"""			7755639	Standard	NM_002811		Approved	S12, P40, MOV34, Rpn8	uc002fcq.3	P51665	OTTHUMG00000137601	ENST00000219313.4:c.78C>T	16.37:g.74334016C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_002811	D3DWS9|Q6PKI2|Q96E97	Silent	SNP	ENST00000219313.4	37	CCDS10910.1																																																																																			C|0.999;T|0.001	0.001	strong		0.418	PSMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269010.2	NM_002811	
ALKBH5	54890	hgsc.bcm.edu	37	17	18088094	18088094	+	Silent	SNP	C	C	T	rs11078411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18088094C>T	ENST00000399138.4	+	1	542	c.537C>T	c.(535-537)caC>caT	p.H179H	ALKBH5_ENST00000541285.1_Intron|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	179					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|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)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					TGGTGGAGCACCGCGTCATCC	0.667													C|||	899	0.179513	0.3011	0.1873	5008	,	,		16289	0.0119		0.2078	False		,,,				2504	0.1534				p.H179H	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C537T						PASS	.	C		1136,3026		162,812,1107	34.0	39.0	38.0		537	5.0	1.0	17	dbSNP_120	38	1748,6626		174,1400,2613	no	coding-synonymous	ALKBH5	NM_017758.3		336,2212,3720	TT,TC,CC		20.8741,27.2946,23.0057		179/395	18088094	2884,9652	2081	4187	6268	SO:0001819	synonymous_variant	54890	exon1			GGAGCACCGCGTC	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.537C>T	17.37:g.18088094C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	37	CCDS42272.1																																																																																			C|0.787;T|0.213	0.213	strong		0.667	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557497	32557497	+	Missense_Mutation	SNP	C	C	T	rs111934004		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32557497C>T	ENST00000360004.5	-	1	128	c.23G>A	c.(22-24)gGa>gAa	p.G8E		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	8					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						GCAGGAGCCTCCAGGGAGCTT	0.592										Multiple Myeloma(14;0.17)																											p.G8E		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G23A						PASS	.						81.0	96.0	90.0					6																	32557497		1511	2709	4220	SO:0001583	missense	3123	exon1			GAGCCTCCAGGGA	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.23G>A	6.37:g.32557497C>T	ENSP00000353099:p.Gly8Glu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	157	23	0.146497	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	15.35	2.808305	0.50421	.	.	ENSG00000196126	ENST00000360004	T	0.00265	8.39	4.68	0.718	0.18202	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00178	0.0005	M	0.69823	2.125	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.42832	-0.9428	9	0.87932	D	0	.	4.7199	0.12913	0.0:0.4558:0.3496:0.1945	.	8	P01911	2B1F_HUMAN	E	8	ENSP00000353099:G8E	ENSP00000353099:G8E	G	-	2	0	HLA-DRB1	32665475	0.000000	0.05858	0.003000	0.11579	0.026000	0.11368	0.820000	0.27323	0.595000	0.29777	0.462000	0.41574	GGA	C|0.500;T|0.500	0.500	weak		0.592	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SMCO2	341346	hgsc.bcm.edu	37	12	27654898	27654898	+	Silent	SNP	C	C	T	rs61731840	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:27654898C>T	ENST00000535986.1	+	8	876	c.876C>T	c.(874-876)acC>acT	p.T292T	SMCO2_ENST00000298876.4_Silent_p.T242T|SMCO2_ENST00000416383.1_Silent_p.T292T			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	292						integral component of membrane (GO:0016021)											ATGTCCTCACCGTCACTGGAC	0.403													C|||	587	0.117212	0.0318	0.1282	5008	,	,		20543	0.0327		0.2336	False		,,,				2504	0.1922				p.T292T		Atlas-SNP	.											.	.	.	.	0			c.C876T						PASS	.	C		79,1287		10,59,614	259.0	219.0	231.0		876	1.6	0.0	12	dbSNP_129	231	806,2374		121,564,905	no	coding-synonymous	C12orf70	NM_001145010.1		131,623,1519	TT,TC,CC		25.3459,5.7833,19.4677		292/344	27654898	885,3661	683	1590	2273	SO:0001819	synonymous_variant	0	exon9			CCTCACCGTCACT		CCDS44852.1	12p11.23	2013-03-11	2013-03-11	2013-03-11	ENSG00000165935	ENSG00000165935			34448	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 70"""	C12orf70			Standard	NM_001145010		Approved	LOC341346	uc010sjq.2	A6NFE2	OTTHUMG00000169205	ENST00000535986.1:c.876C>T	12.37:g.27654898C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			C|0.842;T|0.158	0.158	strong		0.403	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
CCDC17	149483	hgsc.bcm.edu	37	1	46087577	46087577	+	Missense_Mutation	SNP	G	G	A	rs3014242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46087577G>A	ENST00000528266.1	-	8	1205	c.1058C>T	c.(1057-1059)cCg>cTg	p.P353L	CCDC17_ENST00000343901.2_Missense_Mutation_p.P321L|CCDC17_ENST00000464739.1_Intron|CCDC17_ENST00000421127.2_Missense_Mutation_p.P344L|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	353	Pro-rich.		P -> L (in dbSNP:rs3014242). {ECO:0000269|PubMed:14702039}.							kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TGGTGGCAGCGGTGGTGCCAC	0.652													G|||	3391	0.677117	0.7292	0.6542	5008	,	,		15821	0.6518		0.7177	False		,,,				2504	0.6074				p.P353L		Atlas-SNP	.											.	CCDC17	54	.	0			c.C1058T						PASS	.	G	LEU/PRO,LEU/PRO	3289,1117		1237,815,151	24.0	28.0	27.0		1058,1031	2.2	0.3	1	dbSNP_101	27	6067,2533		2157,1753,390	yes	missense,missense	CCDC17	NM_001114938.2,NM_001190182.1	98,98	3394,2568,541	AA,AG,GG		29.4535,25.3518,28.064	benign,benign	353/623,344/614	46087577	9356,3650	2203	4300	6503	SO:0001583	missense	149483	exon8			GGCAGCGGTGGTG		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1058C>T	1.37:g.46087577G>A	ENSP00000432172:p.Pro353Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	1435	0.657051282051282	336	0.6829268292682927	245	0.6767955801104972	346	0.6048951048951049	508	0.6701846965699209	G	11.62	1.692373	0.30052	0.746482	0.705465	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.22743	1.97;1.94;1.96	5.11	2.19	0.27852	.	0.226304	0.39020	N	0.001493	T	0.00012	0.0000	N	0.16368	0.405	0.24084	P	0.99593518	B;B;B	0.26041	0.061;0.14;0.017	B;B;B	0.20767	0.012;0.031;0.004	T	0.40905	-0.9538	9	0.02654	T	1	-15.0227	5.7458	0.18120	0.1531:0.0:0.5756:0.2713	rs3014242;rs59643129;rs3014242	353;344;321	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	L	344;321;353	ENSP00000389415:P344L;ENSP00000341451:P321L;ENSP00000432172:P353L	ENSP00000341451:P321L	P	-	2	0	CCDC17	45860164	0.570000	0.26651	0.272000	0.24630	0.000000	0.00434	1.045000	0.30341	0.262000	0.21774	-0.137000	0.14449	CCG	G|0.318;A|0.682	0.682	strong		0.652	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
SP110	3431	hgsc.bcm.edu	37	2	231072709	231072709	+	Missense_Mutation	SNP	C	C	T	rs1365776	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231072709C>T	ENST00000358662.4	-	8	973	c.895G>A	c.(895-897)Gga>Aga	p.G299R	SP110_ENST00000540870.1_Missense_Mutation_p.G305R|SP110_ENST00000392048.3_Missense_Mutation_p.G299R|SP110_ENST00000486146.2_5'UTR|SP110_ENST00000258382.5_Missense_Mutation_p.G299R|SP110_ENST00000338556.3_Missense_Mutation_p.G51R|SP110_ENST00000258381.6_Missense_Mutation_p.G299R	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	299			G -> R (in dbSNP:rs1365776). {ECO:0000269|PubMed:10913195, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16803959, ECO:0000269|PubMed:16816019, ECO:0000269|PubMed:7693701}.		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)		atcttaccTCCTGGGAGGCTT	0.388													T|||	4019	0.802516	0.9592	0.7839	5008	,	,		21369	0.8978		0.6262	False		,,,				2504	0.6871				p.G305R		Atlas-SNP	.											.	SP110	105	.	0			c.G913A						PASS	.	T	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3941,461	201.1+/-224.2	1762,417,22	117.0	111.0	113.0		913,895,895,895	-0.1	0.0	2	dbSNP_88	113	5186,3408	472.2+/-368.3	1587,2012,698	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	125,125,125,125	3349,2429,720	TT,TC,CC		39.6556,10.4725,29.7707	benign,benign,benign,benign	305/556,299/690,299/550,299/714	231072709	9127,3869	2201	4297	6498	SO:0001583	missense	3431	exon9			TACCTCCTGGGAG	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.895G>A	2.37:g.231072709C>T	ENSP00000351488:p.Gly299Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	1720	0.7875457875457875	457	0.9288617886178862	279	0.7707182320441989	512	0.8951048951048951	472	0.6226912928759895	T	3.079	-0.189485	0.06299	0.895275	0.603444	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.65916	1.22;1.09;-0.18;0.01;0.0;2.45	3.62	-0.142	0.13448	.	1.611900	0.04182	N	0.326734	T	0.00012	0.0000	N	0.03608	-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	0.04013	0.0;0.0;0.0;0.001	T	0.31194	-0.9952	9	0.19147	T	0.46	.	4.0173	0.09649	0.0:0.344:0.2061:0.4499	rs1365776;rs59533753;rs1365776	299;305;299;299	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	R	299;299;299;299;305;51	ENSP00000258381:G299R;ENSP00000351488:G299R;ENSP00000375902:G299R;ENSP00000258382:G299R;ENSP00000439558:G305R;ENSP00000344049:G51R	ENSP00000258381:G299R	G	-	1	0	SP110	230780953	0.001000	0.12720	0.000000	0.03702	0.183000	0.23260	-0.226000	0.09139	-0.289000	0.09038	-0.360000	0.07572	GGA	T|0.642;G|0.024	0.642	strong		0.388	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:125889526C>T	ENST00000392693.3	-	4	611	c.484G>A	c.(484-486)Gaa>Aaa	p.E162K	CDON_ENST00000263577.7_Missense_Mutation_p.E162K	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	162	Ig-like C2-type 2.		E -> K (in dbSNP:rs3740909).		anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E162K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GTGGAATGTTCCAGCCATTTT	0.463													T|||	561	0.112021	0.1142	0.1225	5008	,	,		16614	0.127		0.0885	False		,,,				2504	0.1104				p.E162K		Atlas-SNP	.											CDON,NS,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	stomach(1)	c.G484A						PASS	.	T	LYS/GLU	545,3857	775.6+/-414.1	39,467,1695	147.0	151.0	149.0		484	4.0	0.9	11	dbSNP_107	149	739,7859	785.5+/-407.6	30,679,3590	yes	missense	CDON	NM_016952.4	56	69,1146,5285	TT,TC,CC		8.595,12.3807,9.8769	benign	162/1265	125889526	1284,11716	2201	4299	6500	SO:0001583	missense	50937	exon4			AATGTTCCAGCCA	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.484G>A	11.37:g.125889526C>T	ENSP00000376458:p.Glu162Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	235|235	0.10760073260073261|0.10760073260073261	59|59	0.11991869918699187|0.11991869918699187	42|42	0.11602209944751381|0.11602209944751381	63|63	0.11013986013986014|0.11013986013986014	71|71	0.09366754617414248|0.09366754617414248	T|T	6.637|6.637	0.485978|0.485978	0.12641|0.12641	0.123807|0.123807	0.08595|0.08595	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577;ENST00000531586|ENST00000534661	T;T;T|.	0.60548|.	2.7;2.7;0.18|.	5.33|5.33	4.03|4.03	0.46877|0.46877	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.362364|.	0.23589|.	N|.	0.046564|.	T|T	0.00552|0.00552	0.0018|0.0018	L|L	0.35793|0.35793	1.09|1.09	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.11329|.	0.0;0.006;0.003|.	T|T	0.12889|0.12889	-1.0530|-1.0530	9|4	0.02654|.	T|.	1|.	-5.3068|-5.3068	4.0763|4.0763	0.09906|0.09906	0.0:0.2693:0.1793:0.5514|0.0:0.2693:0.1793:0.5514	rs3740909;rs58697958;rs3740909|rs3740909;rs58697958;rs3740909	162;162;162|.	E9PRD8;Q4KMG0;Q4KMG0-2|.	.;CDON_HUMAN;.|.	K|E	162|137	ENSP00000376458:E162K;ENSP00000263577:E162K;ENSP00000434212:E162K|.	ENSP00000263577:E162K|.	E|G	-|-	1|2	0|0	CDON|CDON	125394736|125394736	1.000000|1.000000	0.71417|0.71417	0.903000|0.903000	0.35520|0.35520	0.969000|0.969000	0.65631|0.65631	1.933000|1.933000	0.40153|0.40153	0.961000|0.961000	0.38030|0.38030	-0.361000|-0.361000	0.07541|0.07541	GAA|GGA	C|0.896;N|0.000	.	strong		0.463	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
OR2J3	442186	hgsc.bcm.edu	37	6	29080344	29080344	+	Missense_Mutation	SNP	G	G	A	rs3749977	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	266	0	0		WXS	Illumina HiSeq	Phase_I	244	120	0.491803	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		
ARHGEF19	128272	hgsc.bcm.edu	37	1	16532498	16532498	+	Missense_Mutation	SNP	G	G	A	rs41269185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16532498G>A	ENST00000270747.3	-	8	1515	c.1379C>T	c.(1378-1380)cCg>cTg	p.P460L	ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	460	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		GCGGAAGGCCGGGCAGTGGTC	0.657													G|||	183	0.0365415	0.0038	0.062	5008	,	,		16369	0.0		0.1034	False		,,,				2504	0.0317				p.P460L		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C1379T						PASS	.	G	LEU/PRO	101,4305		2,97,2104	45.0	44.0	44.0		1379	4.7	0.9	1	dbSNP_127	44	1029,7569		61,907,3331	yes	missense	ARHGEF19	NM_153213.3	98	63,1004,5435	AA,AG,GG		11.9679,2.2923,8.6896	probably-damaging	460/803	16532498	1130,11874	2203	4299	6502	SO:0001583	missense	128272	exon8			AAGGCCGGGCAGT	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.1379C>T	1.37:g.16532498G>A	ENSP00000270747:p.Pro460Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	162	65	0.401235	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	106|106	0.048534798534798536|0.048534798534798536	3|3	0.006097560975609756|0.006097560975609756	29|29	0.08011049723756906|0.08011049723756906	0|0	0.0|0.0	74|74	0.09762532981530343|0.09762532981530343	G|G	20.6|20.6	4.013593|4.013593	0.75161|0.75161	0.022923|0.022923	0.119679|0.119679	ENSG00000142632|ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607;ENST00000441785|ENST00000449495	T;T;T|.	0.32515|.	1.45;1.45;2.17|.	4.66|4.66	4.66|4.66	0.58398|0.58398	Dbl homology (DH) domain (5);|.	0.077475|.	0.51477|.	D|.	0.000082|.	T|T	0.01627|0.01627	0.0052|0.0052	L|L	0.48986|0.48986	1.54|1.54	0.09310|0.09310	P|P	0.99999809875|0.99999809875	D|.	0.76494|.	0.999|.	D|.	0.74348|.	0.983|.	T|T	0.19712|0.19712	-1.0297|-1.0297	9|4	0.66056|.	D|.	0.02|.	.|.	15.048|15.048	0.71841|0.71841	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs41269185;rs61749280|rs41269185;rs61749280	460|.	Q8IW93|.	ARHGJ_HUMAN|.	L|W	460;460;460;143|149	ENSP00000270747:P460L;ENSP00000396001:P460L;ENSP00000414370:P143L|.	ENSP00000270747:P460L|.	P|R	-|-	2|1	0|2	ARHGEF19|ARHGEF19	16405085|16405085	1.000000|1.000000	0.71417|0.71417	0.948000|0.948000	0.38648|0.38648	0.963000|0.963000	0.63663|0.63663	8.216000|8.216000	0.89764|0.89764	2.129000|2.129000	0.65627|0.65627	0.561000|0.561000	0.74099|0.74099	CCG|CGG	G|0.923;A|0.077	0.077	strong		0.657	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
LDLRAD2	401944	hgsc.bcm.edu	37	1	22141030	22141030	+	Silent	SNP	C	C	T	rs75506362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22141030C>T	ENST00000344642.2	+	2	412	c.225C>T	c.(223-225)gaC>gaT	p.D75D	LDLRAD2_ENST00000543870.1_Silent_p.D75D	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain containing 2	75						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(3)	6		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)		CCCCCGGCGACCGGATCCGCT	0.736													C|||	745	0.148762	0.1051	0.0778	5008	,	,		10817	0.2937		0.0746	False		,,,				2504	0.1851				p.D75D		Atlas-SNP	.											LDLRAD2,NS,carcinoma,0,1	LDLRAD2	17	1	0			c.C225T						PASS	.	C		463,3905		29,405,1750	19.0	23.0	22.0		225	2.9	0.9	1	dbSNP_131	22	576,7954		9,558,3698	no	coding-synonymous	LDLRAD2	NM_001013693.2		38,963,5448	TT,TC,CC		6.7526,10.5998,8.0555		75/273	22141030	1039,11859	2184	4265	6449	SO:0001819	synonymous_variant	401944	exon2			CGGCGACCGGATC	AL590103	CCDS30624.1	1p36.12	2008-02-05	2005-10-07		ENSG00000187942	ENSG00000187942			32071	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 2"""				Standard	NM_001013693		Approved		uc001bfg.1	Q5SZI1	OTTHUMG00000002675	ENST00000344642.2:c.225C>T	1.37:g.22141030C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001013693	B9EJB3|Q6ZSN5	Silent	SNP	ENST00000344642.2	37	CCDS30624.1																																																																																			C|0.901;T|0.099	0.099	strong		0.736	LDLRAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007601.1	NM_001013693	
CYP3A43	64816	hgsc.bcm.edu	37	7	99459256	99459256	+	Silent	SNP	C	C	T	rs17342647	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000342499.4_Silent_p.A209A|CYP3A43_ENST00000222382.5_Silent_p.A349A|CYP3A43_ENST00000444905.1_Silent_p.A96A|CYP3A43_ENST00000415413.1_Silent_p.A138A|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000312017.5_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	144	0	0		WXS	Illumina HiSeq	Phase_I	188	93	0.494681	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		
NOTCH4	4855	hgsc.bcm.edu	37	6	32188642	32188642	+	Silent	SNP	T	T	C	rs520688|rs71556915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	101	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	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		
OR4K1	79544	hgsc.bcm.edu	37	14	20403909	20403909	+	Silent	SNP	T	T	C	rs2792148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20403909T>C	ENST00000285600.4	+	1	143	c.84T>C	c.(82-84)ttT>ttC	p.F28F		NM_001004063.2	NP_001004063.2	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K, 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)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(24)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		TTTTCTTTTTTGCCATCTTCT	0.368													T|||	1345	0.26857	0.0605	0.3213	5008	,	,		25635	0.2331		0.4016	False		,,,				2504	0.4121				p.F28F		Atlas-SNP	.											.	OR4K1	108	.	0			c.T84C						PASS	.	T		486,3920		18,450,1735	337.0	372.0	360.0		84	3.5	0.9	14	dbSNP_100	360	3183,5417		379,2425,1496	no	coding-synonymous	OR4K1	NM_001004063.2		397,2875,3231	CC,CT,TT		37.0116,11.0304,28.2101		28/312	20403909	3669,9337	2203	4300	6503	SO:0001819	synonymous_variant	79544	exon1			CTTTTTTGCCATC		CCDS32025.1	14q11.2	2013-09-23			ENSG00000155249	ENSG00000155249		"""GPCR / Class A : Olfactory receptors"""	14726	protein-coding gene	gene with protein product							Standard	NM_001004063		Approved		uc001vwj.2	Q8NGD4	OTTHUMG00000170633	ENST00000285600.4:c.84T>C	14.37:g.20403909T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	315	164	0.520635	NM_001004063	B9EKV9|Q8NGD6|Q96R73	Silent	SNP	ENST00000285600.4	37	CCDS32025.1																																																																																			T|0.729;C|0.271	0.271	strong		0.368	OR4K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409881.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:1388553A>G	ENST00000324803.4	+	1	3214	c.254A>G	c.(253-255)cAc>cGc	p.H85R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	85					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGGAGTGCCCACCTGCTCACA	0.647																																					p.H85R		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	0			c.A254G						scavenged	.						276.0	239.0	251.0					4																	1388553		2203	4300	6503	SO:0001583	missense	285464	exon1			GTGCCCACCTGCT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.254A>G	4.37:g.1388553A>G	ENSP00000323978:p.His85Arg	Somatic	101	8	0.0792079		WXS	Illumina HiSeq	Phase_I	101	4	0.039604	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	N	2.225	-0.377390	0.05000	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.22336	1.96	1.11	0.176	0.15049	.	.	.	.	.	T	0.08223	0.0205	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41734	-0.9492	9	0.11485	T	0.65	.	5.3685	0.16127	0.3874:0.0:0.6126:0.0	.	85	Q8N1N5	CRPAK_HUMAN	R	85;78	ENSP00000323978:H85R	ENSP00000323978:H85R	H	+	2	0	CRIPAK	1378553	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.861000	0.00726	-0.365000	0.08076	-1.123000	0.02005	CAC	.	.	none		0.647	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
FOXD4	2298	hgsc.bcm.edu	37	9	116800	116800	+	Nonstop_Mutation	SNP	C	C	G	rs79220013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	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	
ADCYAP1	116	hgsc.bcm.edu	37	18	909561	909561	+	Silent	SNP	A	A	G	rs2231187	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:909561A>G	ENST00000579794.1	+	4	734	c.456A>G	c.(454-456)aaA>aaG	p.K152K	RP11-672L10.3_ENST00000582554.1_RNA|RP11-672L10.2_ENST00000581719.2_RNA|ADCYAP1_ENST00000450565.3_Silent_p.K152K	NM_001117.3	NP_001108.2	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary)	152	Important for receptor binding.				activation of adenylate cyclase activity (GO:0007190)|ATP metabolic process (GO:0046034)|behavioral fear response (GO:0001662)|cAMP-mediated signaling (GO:0019933)|cell-cell signaling (GO:0007267)|cellular response to glucocorticoid stimulus (GO:0071385)|female pregnancy (GO:0007565)|histamine secretion (GO:0001821)|negative regulation of acute inflammatory response to antigenic stimulus (GO:0002865)|negative regulation of acute inflammatory response to non-antigenic stimulus (GO:0002878)|negative regulation of cell cycle (GO:0045786)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of Rho GTPase activity (GO:0034259)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|pituitary gland development (GO:0021983)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of somatostatin secretion (GO:0090274)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)|regulation of postsynaptic membrane potential (GO:0060078)|regulation of protein localization (GO:0032880)|response to ethanol (GO:0045471)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|terminal bouton (GO:0043195)	neuropeptide hormone activity (GO:0005184)|peptide hormone receptor binding (GO:0051428)|pituitary adenylate cyclase activating polypeptide activity (GO:0016521)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CTGTCAAGAAATACTTGGCGG	0.557													A|||	1014	0.202476	0.0802	0.2709	5008	,	,		11583	0.2411		0.3191	False		,,,				2504	0.1595				p.C152W		Atlas-SNP	.											ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	0			c.T456G						PASS	.	A	,	548,3858	241.8+/-252.1	36,476,1691	99.0	118.0	111.0		456,456	5.2	1.0	18	dbSNP_98	111	2798,5802	435.4+/-358.0	454,1890,1956	no	coding-synonymous,coding-synonymous	ADCYAP1	NM_001099733.1,NM_001117.3	,	490,2366,3647	GG,GA,AA		32.5349,12.4376,25.7266	,	152/177,152/177	909561	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	116	exon4			CAAGAAATACTTG	S83513	CCDS11825.1	18p11	2013-02-28			ENSG00000141433	ENSG00000141433		"""Endogenous ligands"""	241	protein-coding gene	gene with protein product	"""prepro-PACAP"""	102980				1730060	Standard	NM_001099733		Approved	PACAP	uc010dkh.4	P18509	OTTHUMG00000131479	ENST00000579794.1:c.456A>G	18.37:g.909561A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	168	104	0.619048	NM_001117	B2R7N4|Q52LQ0	Missense_Mutation	SNP	ENST00000579794.1	37	CCDS11825.1																																																																																			A|0.757;C|0.001	.	strong		0.557	ADCYAP1-003	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440765.3	NM_001117	
ZNF440	126070	hgsc.bcm.edu	37	19	11942771	11942771	+	Silent	SNP	G	G	A	rs436411	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	33	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	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	
USP10	9100	hgsc.bcm.edu	37	16	84778690	84778690	+	Silent	SNP	C	C	T	rs1812062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84778690C>T	ENST00000219473.7	+	4	716	c.603C>T	c.(601-603)ccC>ccT	p.P201P	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.P205P	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	201					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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GTGACATGCCCCCGTCAGTTA	0.542													C|||	1406	0.280751	0.2337	0.121	5008	,	,		17581	0.4107		0.1531	False		,,,				2504	0.455				p.P205P		Atlas-SNP	.											.	USP10	51	.	0			c.C615T						PASS	.	C		800,3184		77,646,1269	31.0	30.0	30.0		603	-5.5	0.0	16	dbSNP_92	30	1136,7192		76,984,3104	no	coding-synonymous	USP10	NM_005153.2		153,1630,4373	TT,TC,CC		13.6407,20.0803,15.7245		201/799	84778690	1936,10376	1992	4164	6156	SO:0001819	synonymous_variant	9100	exon5			CATGCCCCCGTCA	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.603C>T	16.37:g.84778690C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			C|0.773;T|0.227	0.227	strong		0.542	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
PQLC2	54896	hgsc.bcm.edu	37	1	19652063	19652063	+	Silent	SNP	G	G	A	rs11558390	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19652063G>A	ENST00000375153.3	+	4	1009	c.369G>A	c.(367-369)acG>acA	p.T123T	PQLC2_ENST00000400548.2_Silent_p.T58T|PQLC2_ENST00000375155.3_Silent_p.T123T	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	123					amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		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;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGTTCAGGACGCGCCCCTCTC	0.592													A|||	1032	0.20607	0.1589	0.183	5008	,	,		13556	0.0833		0.2873	False		,,,				2504	0.3292				p.T123T		Atlas-SNP	.											.	PQLC2	34	.	0			c.G369A						PASS	.	A	,,	808,3598	749.0+/-412.0	75,658,1470	95.0	78.0	84.0		369,174,369	-11.3	0.0	1	dbSNP_120	84	2479,6121	695.5+/-404.8	368,1743,2189	no	coding-synonymous,coding-synonymous,coding-synonymous	PQLC2	NM_001040125.1,NM_001040126.1,NM_017765.2	,,	443,2401,3659	AA,AG,GG		28.8256,18.3386,25.273	,,	123/292,58/227,123/292	19652063	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	54896	exon4			CAGGACGCGCCCC	BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.369G>A	1.37:g.19652063G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001040125	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Silent	SNP	ENST00000375153.3	37	CCDS195.2																																																																																			G|0.771;A|0.229	0.229	strong		0.592	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
GSDMA	284110	hgsc.bcm.edu	37	17	38122680	38122680	+	Missense_Mutation	SNP	G	G	T	rs7212938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38122680G>T	ENST00000301659.4	+	3	500	c.382G>T	c.(382-384)Gtg>Ttg	p.V128L		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	128			V -> L (in dbSNP:rs7212938). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17471240}.		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CCTGGAGACCGTGCAGGAGAG	0.612																																					p.V128L		Atlas-SNP	.											.	GSDMA	26	.	0			c.G382T						PASS	.	T	LEU/VAL	3285,769		1341,603,83	75.0	84.0	81.0		382	-2.3	0.0	17	dbSNP_116	81	4194,4166		1064,2066,1050	yes	missense	GSDMA	NM_178171.4	32	2405,2669,1133	TT,TG,GG		49.8325,18.9689,39.7535	benign	128/446	38122680	7479,4935	2027	4180	6207	SO:0001583	missense	284110	exon3			GAGACCGTGCAGG	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.382G>T	17.37:g.38122680G>T	ENSP00000301659:p.Val128Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	88	86	0.977273	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	1304	0.5970695970695971	431	0.8760162601626016	161	0.4447513812154696	314	0.548951048951049	398	0.525065963060686	T	9.654	1.142349	0.21205	0.810311	0.501675	ENSG00000167914	ENST00000301659	T	0.09163	3.01	5.5	-2.32	0.06745	.	0.141436	0.31612	N	0.007345	T	0.00012	0.0000	N	0.00092	-2.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18713	-1.0328	9	0.02654	T	1	-3.4177	2.8183	0.05464	0.1342:0.4029:0.1384:0.3245	rs7212938;rs12950659;rs58173345;rs7212938	128	Q96QA5	GSDMA_HUMAN	L	128	ENSP00000301659:V128L	ENSP00000301659:V128L	V	+	1	0	GSDMA	35376206	0.009000	0.17119	0.027000	0.17364	0.743000	0.42351	-0.611000	0.05622	-0.902000	0.03886	-0.362000	0.07510	GTG	G|0.378;T|0.622	0.622	strong		0.612	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
SH3BP1	23616	hgsc.bcm.edu	37	22	38051355	38051355	+	Silent	SNP	G	G	A	rs762989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38051355G>A	ENST00000357436.4	+	18	2083	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	SH3BP1_ENST00000599616.1_Intron|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	590					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)					CTCCAGCCCCGCCCTTGCCCC	0.741													G|||	975	0.194688	0.2867	0.3055	5008	,	,		4753	0.0833		0.1799	False		,,,				2504	0.1217				p.P590P		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G1770A						PASS	.	G		606,2448		46,514,967	3.0	4.0	4.0		1770	-1.0	0.0	22	dbSNP_86	4	739,5643		39,661,2491	no	coding-synonymous	SH3BP1	NM_018957.3		85,1175,3458	AA,AG,GG		11.5794,19.8428,14.2539		590/702	38051355	1345,8091	1527	3191	4718	SO:0001819	synonymous_variant	23616	exon18			AGCCCCGCCCTTG		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.1770G>A	22.37:g.38051355G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			G|0.825;A|0.175	0.175	strong		0.741	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
KCNA7	3743	hgsc.bcm.edu	37	19	49574125	49574125	+	Missense_Mutation	SNP	G	G	C	rs1611775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49574125G>C	ENST00000221444.1	-	2	921	c.566C>G	c.(565-567)cCg>cGg	p.P189R		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	189			P -> R (in dbSNP:rs1611775). {ECO:0000269|PubMed:11896454, ECO:0000269|Ref.3}.		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)	GCCATTCAGCGGAGCGGGGAA	0.547													C|||	1839	0.367212	0.4818	0.3228	5008	,	,		18986	0.3323		0.328	False		,,,				2504	0.32				p.P189R	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.C566G						PASS	.	C	ARG/PRO	2030,2376	607.3+/-390.9	466,1098,639	46.0	36.0	39.0		566	3.5	0.4	19	dbSNP_89	39	2966,5634	663.0+/-402.0	523,1920,1857	yes	missense	KCNA7	NM_031886.2	103	989,3018,2496	CC,CG,GG		34.4884,46.0735,38.413	benign	189/457	49574125	4996,8010	2203	4300	6503	SO:0001583	missense	3743	exon2			TTCAGCGGAGCGG	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.566C>G	19.37:g.49574125G>C	ENSP00000221444:p.Pro189Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	800	0.3663003663003663	242	0.491869918699187	142	0.39226519337016574	176	0.3076923076923077	240	0.316622691292876	C	6.584	0.476006	0.12521	0.460735	0.344884	ENSG00000104848	ENST00000221444	D	0.97529	-4.42	4.54	3.5	0.40072	.	2.254190	0.02318	N	0.072711	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42916	-0.9423	9	0.14252	T	0.57	.	6.4921	0.22121	0.0:0.7137:0.1845:0.1018	rs1611775;rs3810189;rs61592783;rs1611775	189	Q96RP8	KCNA7_HUMAN	R	189	ENSP00000221444:P189R	ENSP00000221444:P189R	P	-	2	0	KCNA7	54265937	0.001000	0.12720	0.408000	0.26446	0.528000	0.34623	0.098000	0.15189	0.477000	0.27464	-0.647000	0.03941	CCG	G|0.625;C|0.375	0.375	strong		0.547	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10885920T>C	ENST00000254488.2	+	5	711	c.645T>C	c.(643-645)tcT>tcC	p.S215S		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	215					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|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 binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	TGGCCATCTCTGACGGGATCG	0.597													t|||	1874	0.374201	0.3011	0.2161	5008	,	,		19545	0.4276		0.325	False		,,,				2504	0.5808				p.S215S		Atlas-SNP	.											SLC6A11,NS,adenoma,0,1	SLC6A11	87	1	0			c.T645C						PASS	.	T		1369,3037	453.8+/-350.4	214,941,1048	100.0	86.0	91.0		645	-11.5	0.0	3	dbSNP_100	91	2893,5707	454.0+/-363.4	495,1903,1902	yes	coding-synonymous	SLC6A11	NM_014229.1		709,2844,2950	CC,CT,TT		33.6395,31.0713,32.7695		215/633	10885920	4262,8744	2203	4300	6503	SO:0001819	synonymous_variant	6538	exon5			CATCTCTGACGGG	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.645T>C	3.37:g.10885920T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																			T|0.655;C|0.345	0.345	strong		0.597	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
TCF20	6942	hgsc.bcm.edu	37	22	42609148	42609148	+	Missense_Mutation	SNP	T	T	C	rs5758651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42609148T>C	ENST00000359486.3	-	1	2300	c.2164A>G	c.(2164-2166)Agt>Ggt	p.S722G	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.S722G	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	68	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	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	
C6orf195	154386	hgsc.bcm.edu	37	6	2623930	2623930	+	Missense_Mutation	SNP	G	G	A	rs9503233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	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	
EIF2AK1	27102	hgsc.bcm.edu	37	7	6098685	6098685	+	Silent	SNP	C	C	T	rs112759781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6098685C>T	ENST00000199389.6	-	1	176	c.30G>A	c.(28-30)aaG>aaA	p.K10K	RNU6-218P_ENST00000517120.1_RNA|EIF2AK1_ENST00000536084.1_5'UTR	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	10					negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CCTCTTCGCGCTTGCGGACCC	0.751													C|||	25	0.00499201	0.0	0.0043	5008	,	,		10883	0.002		0.005	False		,,,				2504	0.0153				p.K10K		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.G30A						PASS	.	C	,	11,4071		0,11,2030	5.0	8.0	7.0		30,30	3.9	0.0	7	dbSNP_132	7	91,7955		1,89,3933	no	coding-synonymous,coding-synonymous	EIF2AK1	NM_001134335.1,NM_014413.3	,	1,100,5963	TT,TC,CC		1.131,0.2695,0.841	,	10/630,10/631	6098685	102,12026	2041	4023	6064	SO:0001819	synonymous_variant	27102	exon1			TTCGCGCTTGCGG	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.30G>A	7.37:g.6098685C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	39	31	0.794872	NM_001134335	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Silent	SNP	ENST00000199389.6	37	CCDS5345.1																																																																																			C|0.500;T|0.500	0.500	weak		0.751	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
PPP1R9A	55607	hgsc.bcm.edu	37	7	94539536	94539536	+	Silent	SNP	C	C	T	rs12536183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:94539536C>T	ENST00000433881.1	+	2	643	c.111C>T	c.(109-111)ccC>ccT	p.P37P	PPP1R9A_ENST00000340694.4_Silent_p.P37P|PPP1R9A_ENST00000456331.2_Silent_p.P37P|PPP1R9A_ENST00000433360.1_Silent_p.P37P|PPP1R9A_ENST00000289495.5_Silent_p.P37P|PPP1R9A_ENST00000424654.1_Silent_p.P37P			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	37	Actin-binding.				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)			TTGACAAACCCAAGTCAGATG	0.453										HNSCC(28;0.073)			C|||	549	0.109625	0.0182	0.2248	5008	,	,		19522	0.1448		0.0964	False		,,,				2504	0.1288				p.P37P		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.C111T						PASS	.	C	,,,,	154,4252	105.2+/-143.6	4,146,2053	51.0	50.0	50.0		111,111,111,111,111	4.6	1.0	7	dbSNP_120	50	731,7869	177.8+/-227.3	31,669,3600	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP1R9A	NM_001166160.1,NM_001166161.1,NM_001166162.1,NM_001166163.1,NM_017650.2	,,,,	35,815,5653	TT,TC,CC		8.5,3.4952,6.8046	,,,,	37/1375,37/1297,37/1254,37/1091,37/1099	94539536	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	55607	exon2			CAAACCCAAGTCA	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.111C>T	7.37:g.94539536C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Silent	SNP	ENST00000433881.1	37	CCDS34683.1																																																																																			C|0.915;T|0.085	0.085	strong		0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
ALPK3	57538	hgsc.bcm.edu	37	15	85402610	85402610	+	Silent	SNP	G	G	A	rs34122391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:85402610G>A	ENST00000258888.5	+	7	4727	c.4560G>A	c.(4558-4560)gaG>gaA	p.E1520E		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1520	Ig-like 2.				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)			CAGTGGGCGAGGTGGGCAGGA	0.557													G|||	466	0.0930511	0.0893	0.0216	5008	,	,		19824	0.1994		0.0378	False		,,,				2504	0.0961				p.E1520E		Atlas-SNP	.											.	ALPK3	289	.	0			c.G4560A						PASS	.	G		368,4038	185.0+/-212.2	22,324,1857	65.0	57.0	60.0		4560	1.7	1.0	15	dbSNP_126	60	288,8310	104.2+/-165.2	5,278,4016	no	coding-synonymous	ALPK3	NM_020778.4		27,602,5873	AA,AG,GG		3.3496,8.3522,5.0446		1520/1908	85402610	656,12348	2203	4299	6502	SO:0001819	synonymous_variant	57538	exon7			GGGCGAGGTGGGC	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.4560G>A	15.37:g.85402610G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			G|0.941;A|0.059	0.059	strong		0.557	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
CBLN1	869	hgsc.bcm.edu	37	16	49314837	49314837	+	Silent	SNP	T	T	G	rs61735589	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:49314837T>G	ENST00000219197.6	-	2	746	c.381A>C	c.(379-381)atA>atC	p.I127I	CBLN1_ENST00000536749.1_Silent_p.I127I	NM_004352.3	NP_004343.1	P23435	CBLN1_HUMAN	cerebellin 1 precursor	127	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Necessary for interaction with CBLN3, and homotrimerization. {ECO:0000250}.				cerebellar granule cell differentiation (GO:0021707)|heterophilic cell-cell adhesion (GO:0007157)|nervous system development (GO:0007399)|positive regulation of synapse assembly (GO:0051965)|protein secretion (GO:0009306)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|extracellular region (GO:0005576)|postsynaptic membrane (GO:0045211)				breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(37;0.0766)|all_lung(18;0.24)				GGCTGACCTGTATGGTTTGTC	0.587													G|||	291	0.058107	0.0976	0.0346	5008	,	,		17485	0.0595		0.0497	False		,,,				2504	0.0286				p.I127I		Atlas-SNP	.											.	CBLN1	26	.	0			c.A381C						PASS	.	G		408,3992	788.5+/-414.9	17,374,1809	113.0	120.0	118.0		381	0.1	1.0	16	dbSNP_129	118	543,8057	794.7+/-407.5	14,515,3771	no	coding-synonymous	CBLN1	NM_004352.3		31,889,5580	GG,GT,TT		6.314,9.2727,7.3154		127/194	49314837	951,12049	2200	4300	6500	SO:0001819	synonymous_variant	869	exon2			GACCTGTATGGTT	M58583	CCDS10736.1	16q12.1	2008-02-05			ENSG00000102924	ENSG00000102924			1543	protein-coding gene	gene with protein product		600432				7877445, 1704129	Standard	NM_004352		Approved		uc002efq.3	P23435	OTTHUMG00000133148	ENST00000219197.6:c.381A>C	16.37:g.49314837T>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_004352	B2RAN9|P02682|Q52M09	Silent	SNP	ENST00000219197.6	37	CCDS10736.1																																																																																			T|0.937;G|0.063	0.063	strong		0.587	CBLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256845.4	NM_004352	
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:67064654A>G	ENST00000315962.4	+	8	1401	c.1028A>G	c.(1027-1029)aAa>aGa	p.K343R	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.K343R|TRIM55_ENST00000353317.5_Missense_Mutation_p.K343R	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	343			K -> R (in dbSNP:rs7843605).		signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.K343R(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			gaaggagaaaaagaaggagaa	0.413													G|||	1069	0.213458	0.6664	0.0908	5008	,	,		21464	0.0		0.0915	False		,,,				2504	0.0337				p.K343R		Atlas-SNP	.											TRIM55,NS,carcinoma,0,1	TRIM55	91	1	1	Substitution - Missense(1)	prostate(1)	c.A1028G						PASS	.	G	ARG/LYS,ARG/LYS,ARG/LYS,	2573,1833	510.9+/-367.7	761,1051,391	41.0	38.0	39.0		1028,1028,1028,	-1.8	0.0	8	dbSNP_116	39	825,7775	768.5+/-407.6	43,739,3518	no	missense,missense,missense,intron	TRIM55	NM_033058.2,NM_184085.1,NM_184086.1,NM_184087.1	26,26,26,	804,1790,3909	GG,GA,AA		9.593,41.6024,26.1264	benign,benign,benign,	343/541,343/549,343/453,	67064654	3398,9608	2203	4300	6503	SO:0001583	missense	84675	exon8			GAGAAAAAGAAGG	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1028A>G	8.37:g.67064654A>G	ENSP00000323913:p.Lys343Arg	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_184086	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	423	0.1936813186813187	312	0.6341463414634146	35	0.09668508287292818	0	0.0	76	0.10026385224274406	G	0.158	-1.083948	0.01888	0.583976	0.09593	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	T;T;T	0.27720	1.66;1.66;1.65	3.94	-1.8	0.07907	.	1.469880	0.04195	N	0.329017	T	0.00012	0.0000	N	0.08118	0	0.46901	P	7.540000000000324E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43845	-0.9366	9	0.24483	T	0.36	.	1.822	0.03112	0.5064:0.1493:0.1936:0.1507	rs7843605;rs52811956;rs7843605	343;343;343	Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;TRI55_HUMAN;.	R	343	ENSP00000323913:K343R;ENSP00000297348:K343R;ENSP00000276573:K343R	ENSP00000276573:K343R	K	+	2	0	TRIM55	67227208	0.055000	0.20627	0.000000	0.03702	0.040000	0.13550	-0.476000	0.06591	-0.529000	0.06358	-0.192000	0.12808	AAA	A|0.741;G|0.259	0.259	strong		0.413	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
VWA5B1	127731	hgsc.bcm.edu	37	1	20678551	20678551	+	Silent	SNP	A	A	G	rs230182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20678551A>G	ENST00000375079.2	+	21	3238	c.3042A>G	c.(3040-3042)ctA>ctG	p.L1014L	VWA5B1_ENST00000289815.8_Silent_p.L983L|VWA5B1_ENST00000525343.1_3'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	1014						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						TGCACAGGCTAAATCTCAACA	0.577													A|||	178	0.0355431	0.003	0.0908	5008	,	,		17611	0.0079		0.0845	False		,,,				2504	0.0184				p.L1009L		Atlas-SNP	.											.	VWA5B1	44	.	0			c.A3027G						PASS	.	A		18,1366		0,18,674	50.0	58.0	55.0		3027	1.6	0.4	1	dbSNP_79	55	251,2931		8,235,1348	no	coding-synonymous	VWA5B1	NM_001039500.2		8,253,2022	GG,GA,AA		7.8881,1.3006,5.8914		1009/1216	20678551	269,4297	692	1591	2283	SO:0001819	synonymous_variant	127731	exon21			CAGGCTAAATCTC	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.3042A>G	1.37:g.20678551A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				A|0.952;G|0.048	0.048	strong		0.577	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
SSPO	23145	hgsc.bcm.edu	37	7	149523195	149523195	+	RNA	SNP	C	C	G	rs78492471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:149523195C>G	ENST00000378016.2	+	0	14281							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGTGTGCCCACACCAGGAGTG	0.617													C|||	237	0.0473243	0.0053	0.0764	5008	,	,		20689	0.001		0.1421	False		,,,				2504	0.0337				p.H4760D		Atlas-SNP	.											NM_198455_2,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.C14278G						PASS	.	C	ASP/HIS	101,3991		0,101,1945	39.0	46.0	44.0		14297	0.6	0.0	7	dbSNP_131	44	1131,7237		86,959,3139	yes	missense	SSPO	NM_198455.2	81	86,1060,5084	GG,GC,CC		13.5158,2.4682,9.8876	benign	4760/5148	149523195	1232,11228	2046	4184	6230			23145	exon101			TGCCCACACCAGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149523195C>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.919;G|0.081	0.081	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
USP32	84669	hgsc.bcm.edu	37	17	58285542	58285542	+	Missense_Mutation	SNP	G	G	A	rs147413172	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	324	0	0		WXS	Illumina HiSeq	Phase_I	454	125	0.27533	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	
WIPI1	55062	hgsc.bcm.edu	37	17	66449122	66449122	+	Missense_Mutation	SNP	G	G	A	rs883541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66449122G>A	ENST00000262139.5	-	2	91	c.92C>T	c.(91-93)aCt>aTt	p.T31I	WIPI1_ENST00000546360.1_Intron|WIPI1_ENST00000589459.1_Intron	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	31			T -> I (in dbSNP:rs883541). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15602573}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						TTTAGTTCCAGTTGCTAGGGA	0.483													A|||	3687	0.736222	0.8533	0.6902	5008	,	,		19881	0.5337		0.7634	False		,,,				2504	0.7914				p.T31I		Atlas-SNP	.											WIPI1,NS,carcinoma,-1,1	WIPI1	46	1	0			c.C92T						PASS	.	A	ILE/THR	3648,758	310.2+/-291.5	1503,642,58	115.0	105.0	109.0		92	5.0	1.0	17	dbSNP_86	109	6620,1980	347.0+/-326.4	2532,1556,212	yes	missense	WIPI1	NM_017983.5	89	4035,2198,270	AA,AG,GG		23.0233,17.2038,21.0518	benign	31/447	66449122	10268,2738	2203	4300	6503	SO:0001583	missense	55062	exon2			GTTCCAGTTGCTA		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"""WD repeat domain containing"""	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.92C>T	17.37:g.66449122G>A	ENSP00000262139:p.Thr31Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_017983	Q8IXM5|Q9NWF8	Missense_Mutation	SNP	ENST00000262139.5	37	CCDS11677.1	1571	0.7193223443223443	416	0.8455284552845529	252	0.6961325966850829	319	0.5576923076923077	584	0.7704485488126649	A	10.85	1.467786	0.26335	0.827962	0.769767	ENSG00000070540	ENST00000262139	T	0.57907	0.37	6.11	5.02	0.67125	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.124232	0.56097	N	0.000034	T	0.00012	0.0000	N	0.00272	-1.73	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35943	-0.9768	9	0.33141	T	0.24	-2.5392	8.2244	0.31560	0.7993:0.1336:0.0671:0.0	rs883541;rs17857203;rs56802435;rs883541	31	Q5MNZ9	WIPI1_HUMAN	I	31	ENSP00000262139:T31I	ENSP00000262139:T31I	T	-	2	0	WIPI1	63960717	1.000000	0.71417	0.960000	0.40013	0.606000	0.37113	6.391000	0.73208	0.536000	0.28733	-0.254000	0.11334	ACT	G|0.243;A|0.757	0.757	strong		0.483	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983	
SPTA1	6708	hgsc.bcm.edu	37	1	158582646	158582646	+	Silent	SNP	T	T	C	rs2251969	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158582646T>C	ENST00000368147.4	-	51	7275	c.7095A>G	c.(7093-7095)gcA>gcG	p.A2365A	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2365	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)					ACTTGCCCTCTGCCAGGGCTT	0.443													C|||	2528	0.504792	0.4183	0.5202	5008	,	,		19129	0.6319		0.5626	False		,,,				2504	0.4202				p.A2365A		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,2	SPTA1	720	2	0			c.A7095G						scavenged	.	C		1681,2167		361,959,604	130.0	125.0	126.0		7095	0.2	1.0	1	dbSNP_100	126	4498,3782		1247,2004,889	no	coding-synonymous	SPTA1	NM_003126.2		1608,2963,1493	CC,CT,TT		45.6763,43.685,49.0518		2365/2420	158582646	6179,5949	1924	4140	6064	SO:0001819	synonymous_variant	6708	exon51			GCCCTCTGCCAGG	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.7095A>G	1.37:g.158582646T>C		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	108	34	0.314815	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			T|0.458;C|0.542	0.542	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
DUSP13	51207	hgsc.bcm.edu	37	10	76855421	76855421	+	Silent	SNP	G	G	A	rs3740316	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:76855421G>A	ENST00000472493.2	-	3	384	c.306C>T	c.(304-306)atC>atT	p.I102I	DUSP13_ENST00000607009.1_5'Flank|DUSP13_ENST00000478873.2_Silent_p.I238I|DUSP13_ENST00000605915.1_Silent_p.I124I|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000607131.1_Silent_p.I195I|DUSP13_ENST00000372700.3_Silent_p.I152I|DUSP13_ENST00000464872.1_Intron|DUSP13_ENST00000491677.2_Silent_p.I231I	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	102					meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CGTCCGCCTCGATGCCATAGT	0.557													G|||	1068	0.213259	0.233	0.2406	5008	,	,		21358	0.2649		0.166	False		,,,				2504	0.1626				p.I195I	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C585T						PASS	.	G	,,,	952,3454	360.6+/-315.3	96,760,1347	265.0	217.0	233.0		,456,585,306	-4.5	0.9	10	dbSNP_107	233	1353,7247	263.4+/-285.0	93,1167,3040	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,,,	189,1927,4387	AA,AG,GG		15.7326,21.6069,17.7226	,,,	,152/249,195/292,102/199	76855421	2305,10701	2203	4300	6503	SO:0001819	synonymous_variant	51207	exon5			CGCCTCGATGCCA	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000472493.2:c.306C>T	10.37:g.76855421G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Silent	SNP	ENST00000472493.2	37	CCDS7346.1																																																																																			G|0.795;A|0.205	0.205	strong		0.557	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
PLA2G4F	255189	hgsc.bcm.edu	37	15	42439376	42439376	+	Silent	SNP	G	G	A	rs4923929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42439376G>A	ENST00000382396.4	-	13	1451	c.1365C>T	c.(1363-1365)agC>agT	p.S455S	PLA2G4F_ENST00000397272.3_Silent_p.S457S			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	455	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		TGAGGGACACGCTGTGGCCAC	0.582													G|||	2052	0.409744	0.534	0.3718	5008	,	,		17590	0.246		0.496	False		,,,				2504	0.3487				p.S455S		Atlas-SNP	.											PLA2G4F,NS,carcinoma,0,1	PLA2G4F	75	1	0			c.C1365T						PASS	.	G		2322,2084	604.0+/-390.2	600,1122,481	58.0	53.0	55.0		1365	-5.2	0.0	15	dbSNP_111	55	4084,4514	559.5+/-387.4	978,2128,1193	no	coding-synonymous	PLA2G4F	NM_213600.3		1578,3250,1674	AA,AG,GG		47.4994,47.2991,49.2618		455/850	42439376	6406,6598	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon13			GGACACGCTGTGG		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1365C>T	15.37:g.42439376G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.534;A|0.466	0.466	strong		0.582	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
ANKRD50	57182	hgsc.bcm.edu	37	4	125590478	125590478	+	Silent	SNP	T	T	C	rs1874748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:125590478T>C	ENST00000504087.1	-	4	4991	c.3954A>G	c.(3952-3954)ccA>ccG	p.P1318P	ANKRD50_ENST00000515641.1_Silent_p.P1139P	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1318										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTTGTTTAGGTGGTGCAGCAG	0.398													T|||	1070	0.213658	0.2292	0.1816	5008	,	,		19308	0.2421		0.16	False		,,,				2504	0.2413				p.P1318P		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A3954G						PASS	.	T	,	969,3437	363.1+/-316.4	99,771,1333	145.0	146.0	146.0		3417,3954	-10.4	0.0	4	dbSNP_92	146	1303,7297	257.5+/-281.5	107,1089,3104	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	206,1860,4437	CC,CT,TT		15.1512,21.9927,17.4689	,	1139/1251,1318/1430	125590478	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			TTTAGGTGGTGCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3954A>G	4.37:g.125590478T>C		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	215	110	0.511628	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			T|0.820;C|0.180	0.180	strong		0.398	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
CPVL	54504	hgsc.bcm.edu	37	7	29152371	29152371	+	Silent	SNP	G	G	A	rs323182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:29152371G>A	ENST00000409850.1	-	7	883	c.237C>T	c.(235-237)acC>acT	p.T79T	CPVL_ENST00000265394.5_Silent_p.T79T|CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Silent_p.T79T			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	79						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						TCTTATTCACGGTGAGGAAGC	0.478													G|||	400	0.0798722	0.1513	0.0778	5008	,	,		15771	0.0337		0.0984	False		,,,				2504	0.0133				p.T79T		Atlas-SNP	.											.	CPVL	60	.	0			c.C237T						PASS	.	G	,	612,3794	267.4+/-267.8	48,516,1639	108.0	98.0	101.0		237,237	-11.7	0.4	7	dbSNP_79	101	1011,7589	216.3+/-255.4	63,885,3352	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	111,1401,4991	AA,AG,GG		11.7558,13.8901,12.4789	,	79/477,79/477	29152371	1623,11383	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon3			ATTCACGGTGAGG	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.237C>T	7.37:g.29152371G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	178	40	0.224719	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			G|0.887;A|0.113	0.113	strong		0.478	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134501410	134501410	+	Missense_Mutation	SNP	C	C	T	rs200547421		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134501410C>T	ENST00000372189.3	-	10	1673	c.1550G>A	c.(1549-1551)gGt>gAt	p.G517D	RAPGEF1_ENST00000481260.1_5'Flank|RAPGEF1_ENST00000372190.3_Missense_Mutation_p.G535D|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.G534D	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	517					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GGCTGAGGAACCTCCATGCTG	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18229	0.0		0.0	False		,,,				2504	0.0				p.G535D		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1604A						PASS	.	C	ASP/GLY,ASP/GLY	0,4064		0,0,2032	79.0	84.0	82.0		1550,1604	1.9	0.5	9		82	12,8340		1,10,4165	yes	missense,missense	RAPGEF1	NM_005312.2,NM_198679.1	94,94	1,10,6197	TT,TC,CC		0.1437,0.0,0.0966	benign,benign	517/1078,535/1096	134501410	12,12404	2032	4176	6208	SO:0001583	missense	2889	exon10			GAGGAACCTCCAT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1550G>A	9.37:g.134501410C>T	ENSP00000361263:p.Gly517Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397773	0.42512	0.0	0.001437	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000372191;ENST00000357686	T;T;T	0.25749	1.78;1.78;1.78	5.07	1.9	0.25705	.	0.158578	0.56097	D	0.000029	T	0.10937	0.0267	N	0.03608	-0.345	0.22675	N	0.998864	B;B;B	0.25235	0.121;0.072;0.118	B;B;B	0.32980	0.031;0.046;0.156	T	0.39057	-0.9632	10	0.13853	T	0.58	.	9.0597	0.36427	0.0:0.4277:0.4828:0.0895	.	534;517;535	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	D	517;534;411;517;535;497;443;212;534	ENSP00000361269:G534D;ENSP00000361263:G517D;ENSP00000361264:G535D	ENSP00000266110:G517D	G	-	2	0	RAPGEF1	133491231	0.026000	0.19158	0.521000	0.27850	0.981000	0.71138	0.914000	0.28624	0.488000	0.27723	0.655000	0.94253	GGT	C|0.993;T|0.007	0.007	strong		0.537	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
KIRREL	55243	hgsc.bcm.edu	37	1	158057633	158057633	+	Silent	SNP	C	C	G	rs36008419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158057633C>G	ENST00000359209.6	+	6	817	c.750C>G	c.(748-750)ccC>ccG	p.P250P	KIRREL_ENST00000368172.1_Silent_p.P48P|KIRREL_ENST00000360089.4_Silent_p.P86P|KIRREL_ENST00000392272.2_Silent_p.P147P|KIRREL_ENST00000416935.2_Silent_p.P150P|KIRREL_ENST00000368173.3_Silent_p.P250P			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	250	Ig-like C2-type 3.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)	p.P86P(1)|p.P250P(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CAGCCAACCCCGAGATCTTGG	0.597											OREG0013906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1144	0.228435	0.2935	0.2277	5008	,	,		17136	0.2401		0.1938	False		,,,				2504	0.1646				p.P250P		Atlas-SNP	.											KIRREL_ENST00000368173,NS,carcinoma,0,2	KIRREL	346	2	2	Substitution - coding silent(2)	stomach(2)	c.C750G						PASS	.	C		1196,3210	412.8+/-336.2	162,872,1169	49.0	45.0	47.0		750	-11.2	0.0	1	dbSNP_126	47	1811,6789	319.7+/-314.3	182,1447,2671	no	coding-synonymous	KIRREL	NM_018240.5		344,2319,3840	GG,GC,CC		21.0581,27.1448,23.1201		250/758	158057633	3007,9999	2203	4300	6503	SO:0001819	synonymous_variant	55243	exon6			CAACCCCGAGATC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.750C>G	1.37:g.158057633C>G		Somatic	70	0	0	1790	WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	37	CCDS1172.2																																																																																			C|0.762;G|0.238	0.238	strong		0.597	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
CCND1	595	hgsc.bcm.edu	37	11	69462856	69462856	+	Silent	SNP	C	C	T	rs3862792	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:69462856C>T	ENST00000227507.2	+	4	896	c.669C>T	c.(667-669)ttC>ttT	p.F223F	CCND1_ENST00000536559.1_3'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	223					canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	CCAACAACTTCCTGTCCTACT	0.602			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)			C|||	415	0.0828674	0.152	0.0447	5008	,	,		18880	0.0298		0.0328	False		,,,				2504	0.1227				p.F223F	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	.	CCND1	107	.	0			c.C669T						PASS	.	C		540,3860	245.3+/-254.3	33,474,1693	124.0	111.0	115.0		669	3.2	1.0	11	dbSNP_108	115	231,8357	94.5+/-156.4	4,223,4067	no	coding-synonymous	CCND1	NM_053056.2		37,697,5760	TT,TC,CC		2.6898,12.2727,5.9362		223/296	69462856	771,12217	2200	4294	6494	SO:0001819	synonymous_variant	595	exon4			CAACTTCCTGTCC	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.669C>T	11.37:g.69462856C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			C|0.931;T|0.069	0.069	strong		0.602	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	
BFSP1	631	hgsc.bcm.edu	37	20	17475311	17475311	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:17475311C>T	ENST00000377873.3	-	8	1445	c.1406G>A	c.(1405-1407)cGg>cAg	p.R469Q	BFSP1_ENST00000377868.2_Missense_Mutation_p.R344Q|BFSP1_ENST00000536626.1_Missense_Mutation_p.R330Q|BFSP1_ENST00000544874.1_Missense_Mutation_p.R330Q	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	469	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CAGCACGTGCCGCTCTTTGGT	0.522																																					p.R469Q		Atlas-SNP	.											BFSP1,colon,carcinoma,0,1	BFSP1	55	1	0			c.G1406A						scavenged	.						81.0	79.0	80.0					20																	17475311		2203	4300	6503	SO:0001583	missense	631	exon8			ACGTGCCGCTCTT	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1406G>A	20.37:g.17475311C>T	ENSP00000367104:p.Arg469Gln	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	199	5	0.0251256	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Missense_Mutation	SNP	ENST00000377873.3	37	CCDS13126.1	.	.	.	.	.	.	.	.	.	.	C	16.73	3.203006	0.58234	.	.	ENSG00000125864	ENST00000377873;ENST00000377868;ENST00000536626;ENST00000544874	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.21	1.04	0.20106	.	0.237751	0.43260	N	0.000589	T	0.34774	0.0909	L	0.46157	1.445	0.40748	D	0.982895	P;D	0.59357	0.545;0.985	B;B	0.41571	0.071;0.36	T	0.12116	-1.0560	10	0.56958	D	0.05	-7.3666	5.5729	0.17206	0.1385:0.6323:0.0:0.2293	.	344;469	Q12934-2;Q12934	.;BFSP1_HUMAN	Q	469;344;330;330	ENSP00000367104:R469Q;ENSP00000367099:R344Q;ENSP00000442522:R330Q;ENSP00000439870:R330Q	ENSP00000367099:R344Q	R	-	2	0	BFSP1	17423311	0.988000	0.35896	0.656000	0.29637	0.747000	0.42532	2.846000	0.48262	-0.039000	0.13602	-0.140000	0.14226	CGG	.	.	none		0.522	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
INTS8	55656	hgsc.bcm.edu	37	8	95888307	95888307	+	Silent	SNP	C	C	T	rs1129152	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:95888307C>T	ENST00000523731.1	+	24	2827	c.2694C>T	c.(2692-2694)gcC>gcT	p.A898A	INTS8_ENST00000447247.1_Silent_p.A881A	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	898					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					TGTAGGTGGCCATTTTATGTC	0.299													C|||	2354	0.470048	0.2511	0.5288	5008	,	,		19137	0.6528		0.4573	False		,,,				2504	0.5491				p.A898A		Atlas-SNP	.											.	INTS8	92	.	0			c.C2694T						PASS	.	C		1206,3196	395.8+/-329.8	189,828,1184	88.0	93.0	91.0		2694	3.3	1.0	8	dbSNP_86	91	3547,5049	509.3+/-377.2	729,2089,1480	no	coding-synonymous	INTS8	NM_017864.2		918,2917,2664	TT,TC,CC		41.2634,27.3966,36.5672		898/996	95888307	4753,8245	2201	4298	6499	SO:0001819	synonymous_variant	55656	exon24			GGTGGCCATTTTA	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"""chromosome 8 open reading frame 52"""	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2694C>T	8.37:g.95888307C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	1043	0.4775641025641026	139	0.28252032520325204	197	0.5441988950276243	360	0.6293706293706294	347	0.4577836411609499	C	8.736	0.917867	0.17982	0.273966	0.412634	ENSG00000164941	ENST00000520526	.	.	.	5.67	3.32	0.38043	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40701	-0.9549	3	.	.	.	-29.7653	3.4379	0.07453	0.5358:0.271:0.0717:0.1216	rs1129152;rs2290389;rs3186706;rs11538719;rs17411821;rs17663895;rs59844557;rs1129152	.	.	.	L	703	.	.	P	+	2	0	INTS8	95957483	0.840000	0.29493	1.000000	0.80357	0.984000	0.73092	-0.005000	0.12855	0.526000	0.28541	-0.467000	0.05162	CCA	C|0.581;T|0.419	0.419	strong		0.299	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864	
FARP2	9855	hgsc.bcm.edu	37	2	242371101	242371101	+	Missense_Mutation	SNP	C	C	T	rs757978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	77	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	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		
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:74497009A>G	ENST00000287097.5	+	21	2502	c.2390A>G	c.(2389-2391)aAt>aGt	p.N797S	CD109_ENST00000422508.2_Missense_Mutation_p.N720S|CD109_ENST00000437994.2_Missense_Mutation_p.N797S			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	48	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	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	
FHOD3	80206	hgsc.bcm.edu	37	18	34324091	34324091	+	Missense_Mutation	SNP	G	G	A	rs2303510	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:34324091G>A	ENST00000359247.4	+	19	3400	c.3400G>A	c.(3400-3402)Gta>Ata	p.V1134I	FHOD3_ENST00000590592.1_Missense_Mutation_p.V1326I|FHOD3_ENST00000591635.1_Missense_Mutation_p.V347I|FHOD3_ENST00000257209.4_Missense_Mutation_p.V1151I|FHOD3_ENST00000445677.1_Missense_Mutation_p.V1113I|FHOD3_ENST00000592128.1_Missense_Mutation_p.V130I	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1134	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.			V -> I (in Ref. 6; AAH81563). {ECO:0000305}.	actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CACCATGGTGGTAGAAAACTT	0.542													G|||	1884	0.376198	0.41	0.389	5008	,	,		19762	0.3204		0.3042	False		,,,				2504	0.453				p.V1151I		Atlas-SNP	.											.	FHOD3	210	.	0			c.G3451A						PASS	.	G	ILE/VAL	1817,2589	531.7+/-373.3	352,1113,738	101.0	91.0	94.0		3451	5.3	1.0	18	dbSNP_100	94	2806,5794	444.0+/-360.5	473,1860,1967	yes	missense	FHOD3	NM_025135.2	29	825,2973,2705	AA,AG,GG		32.6279,41.2392,35.5451	possibly-damaging	1151/1440	34324091	4623,8383	2203	4300	6503	SO:0001583	missense	80206	exon20			ATGGTGGTAGAAA	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3400G>A	18.37:g.34324091G>A	ENSP00000352186:p.Val1134Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		729	0.33379120879120877	189	0.38414634146341464	131	0.36187845303867405	188	0.32867132867132864	221	0.29155672823219	G	20.9	4.066190	0.76187	0.412392	0.326279	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.16196	2.36;2.36;2.36	5.29	5.29	0.74685	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.25286	0.73	0.09310	P	0.999999828311	B;D;D;B	0.56521	0.047;0.976;0.962;0.033	B;P;P;B	0.49799	0.145;0.488;0.622;0.12	T	0.56098	-0.8035	9	0.38643	T	0.18	.	17.5052	0.87743	0.0:0.0:1.0:0.0	rs2303510;rs2303510	355;1113;1134;1151	E7ETX5;Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;.;FHOD3_HUMAN;.	I	1151;1134;1113	ENSP00000257209:V1151I;ENSP00000352186:V1134I;ENSP00000411430:V1113I	ENSP00000257209:V1151I	V	+	1	0	FHOD3	32578089	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.884000	0.87274	2.451000	0.82905	0.563000	0.77884	GTA	G|0.653;A|0.347	0.347	strong		0.542	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
CD6	923	hgsc.bcm.edu	37	11	60776307	60776307	+	Silent	SNP	G	G	C	rs79848107|rs386754116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60776307G>C	ENST00000313421.7	+	4	957	c.771G>C	c.(769-771)gcG>gcC	p.A257A	CD6_ENST00000344028.5_Silent_p.A257A|CD6_ENST00000352009.5_Silent_p.A257A|CD6_ENST00000545105.1_Intron|CD6_ENST00000346437.4_Silent_p.A257A|CD6_ENST00000452451.2_Silent_p.A257A	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	257	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		A -> V (in dbSNP:rs2074225). {ECO:0000269|PubMed:17371992, ECO:0000269|PubMed:1919444, ECO:0000269|PubMed:9013954}.		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						ACGCGGGCGCGGTGTGCTCAG	0.652													G|||	834	0.166534	0.298	0.1095	5008	,	,		15908	0.0764		0.1382	False		,,,				2504	0.1513				p.A257A	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,NS,carcinoma,0,2	CD6	122	2	0			c.G771C						PASS	.						14.0	14.0	14.0					11																	60776307		2194	4286	6480	SO:0001819	synonymous_variant	923	exon4			GGGCGCGGTGTGC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.771G>C	11.37:g.60776307G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1	287	0.13141025641025642	120	0.24390243902439024	44	0.12154696132596685	35	0.06118881118881119	88	0.11609498680738786	G	0.743	-0.775758	0.02951	.	.	ENSG00000013725	ENST00000538611	.	.	.	4.42	-4.17	0.03857	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.29238	P	0.872832	.	.	.	.	.	.	T	0.20840	-1.0263	3	.	.	.	.	9.121	0.36786	0.2071:0.5517:0.2412:0.0	.	.	.	.	P	101	.	.	R	+	2	0	CD6	60532883	0.198000	0.23374	0.008000	0.14137	0.038000	0.13279	-0.013000	0.12678	-1.223000	0.02584	-0.175000	0.13238	CGG	G|0.870;C|0.130	0.130	strong		0.652	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000270452.2_Missense_Mutation_p.F418L|LILRB4_ENST00000391733.3_Missense_Mutation_p.F419L	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	191	2	0.0104712		WXS	Illumina HiSeq	Phase_I	199	7	0.0351759	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		
RRBP1	6238	hgsc.bcm.edu	37	20	17610535	17610535	+	Silent	SNP	C	C	T	rs11551701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:17610535C>T	ENST00000377813.1	-	9	2985	c.2682G>A	c.(2680-2682)acG>acA	p.T894T	RRBP1_ENST00000455029.2_Silent_p.T235T|RRBP1_ENST00000377807.2_Silent_p.T461T|RRBP1_ENST00000360807.4_Silent_p.T461T|RRBP1_ENST00000246043.4_Silent_p.T894T			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	894					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						GGCTGCTCTGCGTGTGGCACA	0.716													C|||	384	0.0766773	0.0991	0.049	5008	,	,		13649	0.0655		0.0835	False		,,,				2504	0.0706				p.T461T		Atlas-SNP	.											.	RRBP1	157	.	0			c.G1383A						PASS	.	C	,	388,4018	175.9+/-205.1	27,334,1842	27.0	28.0	27.0		1383,1383	-8.8	0.0	20	dbSNP_120	27	659,7935	161.1+/-214.1	34,591,3672	no	coding-synonymous,coding-synonymous	RRBP1	NM_001042576.1,NM_004587.2	,	61,925,5514	TT,TC,CC		7.6681,8.8062,8.0538	,	461/978,461/978	17610535	1047,11953	2203	4297	6500	SO:0001819	synonymous_variant	6238	exon9			GCTCTGCGTGTGG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.2682G>A	20.37:g.17610535C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Silent	SNP	ENST00000377813.1	37																																																																																				C|0.925;T|0.075	0.075	strong		0.716	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
HLA-B	3106	hgsc.bcm.edu	37	6	31324586	31324586	+	Silent	SNP	C	C	T	rs1050556|rs281864598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324586C>T	ENST00000412585.2	-	2	250	c.222G>A	c.(220-222)ccG>ccA	p.P74P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	74	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						GCTCTATCCACGGCGCCCGCG	0.662									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	3211	0.641174	0.5855	0.6383	5008	,	,		7989	0.7133		0.5417	False		,,,				2504	0.7464				p.P74P		Atlas-SNP	.											.	HLA-B	54	.	0			c.G222A						PASS	.	T		1533,2743		437,659,1042	42.0	41.0	41.0		222	-4.5	0.0	6	dbSNP_86	41	2590,5718		796,998,2360	no	coding-synonymous	HLA-B	NM_005514.6		1233,1657,3402	TT,TC,CC		31.1748,35.8513,32.7638		74/363	31324586	4123,8461	2138	4154	6292	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	TATCCACGGCGCC	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.222G>A	6.37:g.31324586C>T		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.533;C|0.467	0.533	strong		0.662	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
OR11H1	81061	hgsc.bcm.edu	37	22	16449539	16449539	+	Missense_Mutation	SNP	A	A	G	rs199856986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:16449539A>G	ENST00000252835.4	-	1	266	c.266T>C	c.(265-267)gTc>gCc	p.V89A		NM_001005239.1	NP_001005239.1	Q8NG94	O11H1_HUMAN	olfactory receptor, family 11, subfamily H, member 1	89						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(3)|lung(4)|skin(1)	11	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.208)		Kidney(3;0.00216)|KIRC - Kidney renal clear cell carcinoma(3;0.00244)|Lung(27;0.0724)|COAD - Colon adenocarcinoma(3;0.211)		TGTAGAAGAGACATACCATAT	0.418																																					p.V89A		Atlas-SNP	.											OR11H1,NS,carcinoma,0,5	OR11H1	44	5	0			c.T266C						scavenged	.						1.0	1.0	1.0					22																	16449539		71	200	271	SO:0001583	missense	81061	exon1			GAAGAGACATACC	AP000535, AF399611	CCDS74807.1	22q11.1	2012-08-09			ENSG00000130538	ENSG00000130538		"""GPCR / Class A : Olfactory receptors"""	15404	protein-coding gene	gene with protein product						12213199	Standard	NM_001005239		Approved	OR22-1	uc011agd.2	Q8NG94	OTTHUMG00000030069	ENST00000252835.4:c.266T>C	22.37:g.16449539A>G	ENSP00000252835:p.Val89Ala	Somatic	340	2	0.00588235		WXS	Illumina HiSeq	Phase_I	515	72	0.139806	NM_001005239	Q6IEX0|Q96R32	Missense_Mutation	SNP	ENST00000252835.4	37	CCDS33594.1	.	.	.	.	.	.	.	.	.	.	a	9.377	1.072113	0.20147	.	.	ENSG00000130538	ENST00000252835	T	0.00418	7.49	2.19	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37715	N	0.001976	T	0.00328	0.0010	L	0.47078	1.49	0.09310	N	1	P	0.42409	0.779	B	0.40636	0.335	T	0.53158	-0.8478	10	0.37606	T	0.19	.	8.3461	0.32275	1.0:0.0:0.0:0.0	.	89	Q8NG94	O11H1_HUMAN	A	89	ENSP00000252835:V89A	ENSP00000252835:V89A	V	-	2	0	OR11H1	14829539	0.000000	0.05858	0.990000	0.47175	0.581000	0.36288	0.456000	0.21859	0.966000	0.38159	0.302000	0.19851	GTC	.	.	weak		0.418	OR11H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074923.2	NM_001005239	
TKT	7086	hgsc.bcm.edu	37	3	53259850	53259850	+	Silent	SNP	C	C	T	rs3163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000296289.6_Silent_p.P551P|TKT_ENST00000423516.1_Silent_p.P606P|TKT_ENST00000461139.1_5'UTR			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	89	0	0		WXS	Illumina HiSeq	Phase_I	107	37	0.345794	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		
SCAI	286205	hgsc.bcm.edu	37	9	127764305	127764305	+	Silent	SNP	G	G	A	rs764304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127764305G>A	ENST00000336505.6	-	12	1141	c.1083C>T	c.(1081-1083)agC>agT	p.S361S	SCAI_ENST00000373549.4_Silent_p.S384S|SCAI_ENST00000487795.1_5'UTR	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	361					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.S384S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TCAGAAGCACGCTATTGGCAG	0.418													G|||	765	0.152756	0.0877	0.1138	5008	,	,		19547	0.1121		0.2555	False		,,,				2504	0.2045				p.S384S		Atlas-SNP	.											SCAI,NS,carcinoma,0,1	SCAI	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C1152T						PASS	.	G	,	366,3438		15,336,1551	107.0	103.0	105.0		1083,1152	-4.7	0.9	9	dbSNP_86	105	1893,6347		203,1487,2430	no	coding-synonymous,coding-synonymous	SCAI	NM_001144877.2,NM_173690.4	,	218,1823,3981	AA,AG,GG		22.9733,9.6215,18.7562	,	361/607,384/630	127764305	2259,9785	1902	4120	6022	SO:0001819	synonymous_variant	286205	exon13			AAGCACGCTATTG	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1083C>T	9.37:g.127764305G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	37	CCDS48017.1																																																																																			G|0.838;A|0.162	0.162	strong		0.418	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
TMEM176B	28959	hgsc.bcm.edu	37	7	150490238	150490238	+	Missense_Mutation	SNP	G	G	A	rs17256042	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150490238G>A	ENST00000447204.2	-	5	910	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	TMEM176B_ENST00000326442.5_Missense_Mutation_p.R180W|TMEM176B_ENST00000450753.2_Missense_Mutation_p.R143W|TMEM176B_ENST00000434545.1_Missense_Mutation_p.R180W|TMEM176B_ENST00000429904.2_Missense_Mutation_p.R180W|TMEM176B_ENST00000492607.1_Missense_Mutation_p.R180W	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	180			R -> W (in dbSNP:rs17256042).		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGACTTCGCCGCATCCATCTG	0.512													G|||	99	0.0197684	0.0076	0.0317	5008	,	,		21434	0.001		0.0577	False		,,,				2504	0.0082				p.R180W		Atlas-SNP	.											TMEM176B,NS,carcinoma,+1,2	TMEM176B	36	2	0			c.C538T						scavenged	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	44,4362	48.2+/-83.0	1,42,2160	150.0	125.0	133.0		538,538,427,538	-2.4	0.0	7	dbSNP_123	133	458,8142	137.1+/-194.1	13,432,3855	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	101,101,101,101	14,474,6015	AA,AG,GG		5.3256,0.9986,3.8598	probably-damaging,probably-damaging,probably-damaging,probably-damaging	180/271,180/271,143/234,180/271	150490238	502,12504	2203	4300	6503	SO:0001583	missense	28959	exon5			TTCGCCGCATCCA	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.538C>T	7.37:g.150490238G>A	ENSP00000410269:p.Arg180Trp	Somatic	167	2	0.011976		WXS	Illumina HiSeq	Phase_I	180	73	0.405556	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	60	0.027472527472527472	5	0.01016260162601626	14	0.03867403314917127	0	0.0	41	0.05408970976253298	G	11.90	1.776134	0.31411	0.009986	0.053256	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.02498	4.27;4.27;4.27;4.27;4.27;4.27	3.1	-2.36	0.06663	.	1.402630	0.04900	N	0.451178	T	0.00845	0.0028	L	0.57536	1.79	0.09310	N	1	D;D	0.60575	0.988;0.988	P;P	0.51266	0.664;0.541	T	0.22906	-1.0203	10	0.54805	T	0.06	1.2904	2.7714	0.05335	0.2776:0.0:0.331:0.3914	rs17256042;rs52810663;rs58586485;rs17256042	143;180	E9PAV4;Q3YBM2	.;T176B_HUMAN	W	180;180;180;180;180;143;180	ENSP00000419258:R180W;ENSP00000318409:R180W;ENSP00000410269:R180W;ENSP00000413531:R180W;ENSP00000397810:R180W;ENSP00000404831:R143W	ENSP00000318409:R180W	R	-	1	2	TMEM176B	150121171	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.341000	0.19909	-0.672000	0.05266	0.280000	0.19369	CGG	G|0.964;A|0.036	0.036	strong		0.512	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
SCN7A	6332	hgsc.bcm.edu	37	2	167262353	167262353	+	Missense_Mutation	SNP	C	C	G	rs3791251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:167262353C>G	ENST00000409855.1	-	25	4912	c.4786G>C	c.(4786-4788)Gtt>Ctt	p.V1596L		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1596			V -> L (in dbSNP:rs3791251).		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)	ATTTCTGAAACAACTTTCTCC	0.418													G|||	378	0.0754792	0.031	0.0288	5008	,	,		18649	0.1121		0.0775	False		,,,				2504	0.1288				p.V1596L		Atlas-SNP	.											.	SCN7A	410	.	0			c.G4786C						PASS	.	G	LEU/VAL	167,3595		3,161,1717	168.0	165.0	166.0		4786	1.6	0.5	2	dbSNP_107	166	803,7421		39,725,3348	yes	missense	SCN7A	NM_002976.3	32	42,886,5065	GG,GC,CC		9.7641,4.4391,8.0928	benign	1596/1683	167262353	970,11016	1881	4112	5993	SO:0001583	missense	6332	exon25			CTGAAACAACTTT	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.4786G>C	2.37:g.167262353C>G	ENSP00000386796:p.Val1596Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	154	0.07051282051282051	9	0.018292682926829267	10	0.027624309392265192	79	0.1381118881118881	56	0.07387862796833773	G	2.352	-0.348732	0.05208	0.044391	0.097641	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.96427	-4.01	4.51	1.57	0.23409	.	0.443058	0.19214	N	0.119842	T	0.03095	0.0091	N	0.00583	-1.355	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.57797	-0.7749	9	0.30078	T	0.28	.	9.0712	0.36493	0.0:0.1307:0.4321:0.4372	rs3791251;rs52802159;rs3791251	1596	Q01118	SCN7A_HUMAN	L	1596	ENSP00000386796:V1596L	ENSP00000259060:V1596L	V	-	1	0	SCN7A	166970599	0.000000	0.05858	0.516000	0.27786	0.134000	0.20937	-0.387000	0.07361	-0.020000	0.14032	-0.824000	0.03097	GTT	C|0.920;G|0.080	0.080	strong		0.418	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
F5	2153	hgsc.bcm.edu	37	1	169511555	169511555	+	Missense_Mutation	SNP	T	T	C	rs6032	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169511555T>C	ENST00000367797.3	-	13	2974	c.2773A>G	c.(2773-2775)Aag>Gag	p.K925E	F5_ENST00000367796.3_Missense_Mutation_p.K930E	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	925	2 X 17 AA tandem repeats.|B.		K -> E (in dbSNP:rs6032). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	GGAGGGTCCTTCCAGGGCCTC	0.478													C|||	1316	0.26278	0.1679	0.3948	5008	,	,		20989	0.248		0.2535	False		,,,				2504	0.3221				p.K925E		Atlas-SNP	.											F5,colon,carcinoma,+2,1	F5	301	1	0			c.A2773G						PASS	.	C	GLU/LYS	812,3594	748.8+/-412.0	67,678,1458	105.0	111.0	109.0		2773	-5.1	0.0	1	dbSNP_52	109	2355,6245	701.7+/-405.2	300,1755,2245	yes	missense	F5	NM_000130.4	56	367,2433,3703	CC,CT,TT		27.3837,18.4294,24.3503	benign	925/2225	169511555	3167,9839	2203	4300	6503	SO:0001583	missense	2153	exon13			GGTCCTTCCAGGG	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.2773A>G	1.37:g.169511555T>C	ENSP00000356771:p.Lys925Glu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	203	125	0.615764	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	C	2.099	-0.406537	0.04832	0.184294	0.273837	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.18016	2.24;2.24	5.11	-5.14	0.02875	.	0.944141	0.08852	N	0.884318	T	0.02083	0.0065	N	0.11427	0.14	0.09310	P	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	.	17.3504	0.87322	0.0:0.8069:0.0:0.1931	rs6032;rs52829643;rs6032	925	P12259	FA5_HUMAN	E	925;930	ENSP00000356771:K925E;ENSP00000356770:K930E	ENSP00000356770:K930E	K	-	1	0	F5	167778179	0.000000	0.05858	0.002000	0.10522	0.092000	0.18411	-0.987000	0.03743	-1.326000	0.02266	-1.306000	0.01317	AAG	T|0.758;C|0.242	0.242	strong		0.478	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ACTR8	93973	hgsc.bcm.edu	37	3	53905308	53905308	+	Silent	SNP	T	T	C	rs1046677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:53905308T>C	ENST00000335754.3	-	11	1618	c.1518A>G	c.(1516-1518)ggA>ggG	p.G506G	ACTR8_ENST00000482349.1_Silent_p.G395G|ACTR8_ENST00000231909.7_Silent_p.G211G|ACTR8_ENST00000488802.1_5'Flank	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	506					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		CCAGGGCTTTTCCTTCAAACA	0.547													C|||	3467	0.692292	0.7186	0.6196	5008	,	,		19990	0.9444		0.4523	False		,,,				2504	0.6953				p.G506G		Atlas-SNP	.											ACTR8_ENST00000231909,NS,carcinoma,-2,2	ACTR8	56	2	0			c.A1518G						PASS	.	C		2977,1429	464.5+/-353.9	1009,959,235	103.0	100.0	101.0		1518	-2.5	0.9	3	dbSNP_86	101	3771,4829	614.9+/-396.3	814,2143,1343	no	coding-synonymous	ACTR8	NM_022899.4		1823,3102,1578	CC,CT,TT		43.8488,32.433,48.1163		506/625	53905308	6748,6258	2203	4300	6503	SO:0001819	synonymous_variant	93973	exon11			GGCTTTTCCTTCA		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1518A>G	3.37:g.53905308T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	279	107	0.383513	NM_022899	B3KSW7|Q8N566|Q9H663	Silent	SNP	ENST00000335754.3	37	CCDS2875.1	1456	0.6666666666666666	363	0.7378048780487805	223	0.6160220994475138	541	0.9458041958041958	329	0.4340369393139842	C	9.636	1.137708	0.21123	0.67567	0.438488	ENSG00000113812	ENST00000486794	.	.	.	5.67	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.19976	-1.0289	3	.	.	.	-11.7537	7.8427	0.29408	0.0:0.2982:0.3936:0.3082	rs1046677;rs17641862;rs17846012;rs17858996;rs57230247;rs1046677	.	.	.	G	260	.	.	E	-	2	0	ACTR8	53880348	0.916000	0.31088	0.936000	0.37596	0.958000	0.62258	-0.016000	0.12613	-0.796000	0.04456	-1.551000	0.00897	GAA	T|0.410;C|0.590	0.590	strong		0.547	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	
GLI2	2736	hgsc.bcm.edu	37	2	121747406	121747406	+	Missense_Mutation	SNP	G	G	A	rs12711538	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:121747406G>A	ENST00000452319.1	+	14	3976	c.3916G>A	c.(3916-3918)Gat>Aat	p.D1306N	GLI2_ENST00000361492.4_Missense_Mutation_p.D1306N|GLI2_ENST00000314490.11_Intron					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)				TGGGGTCCCCGATTCAGCCCT	0.642													A|||	2840	0.567093	0.5681	0.5951	5008	,	,		18427	0.4712		0.7247	False		,,,				2504	0.4826				p.D1306N		Atlas-SNP	.											.	GLI2	187	.	0			c.G3916A						PASS	.	A	ASN/ASP	2536,1864		740,1056,404	23.0	23.0	23.0		3916	2.1	0.0	2	dbSNP_121	23	6262,2336		2289,1684,326	yes	missense	GLI2	NM_005270.4	23	3029,2740,730	AA,AG,GG		27.1691,42.3636,32.3127	benign	1306/1587	121747406	8798,4200	2200	4299	6499	SO:0001583	missense	2736	exon13			GTCCCCGATTCAG		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.3916G>A	2.37:g.121747406G>A	ENSP00000390436:p.Asp1306Asn	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	1298	0.5943223443223443	257	0.5223577235772358	217	0.5994475138121547	283	0.49475524475524474	541	0.7137203166226913	A	0.017	-1.502030	0.00992	0.576364	0.728309	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.13307	2.6;2.6	4.5	2.13	0.27403	.	0.742484	0.12604	N	0.454393	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20207	-1.0282	8	.	.	.	.	9.0523	0.36383	0.699:0.0:0.301:0.0	rs12711538;rs12711538	1306;961	P10070;P10070-2	GLI2_HUMAN;.	N	1306	ENSP00000390436:D1306N;ENSP00000354586:D1306N	.	D	+	1	0	GLI2	121463876	0.006000	0.16342	0.000000	0.03702	0.685000	0.39939	2.156000	0.42310	-0.006000	0.14370	-0.556000	0.04195	GAT	G|0.360;A|0.640	0.640	strong		0.642	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
OR2B6	26212	hgsc.bcm.edu	37	6	27925456	27925456	+	Silent	SNP	T	T	C	rs904142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27925456T>C	ENST00000244623.1	+	1	438	c.438T>C	c.(436-438)gcT>gcC	p.A146A		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	146						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						AGTTGGCAGCTGCATCCTGGG	0.493													T|||	296	0.0591054	0.0265	0.111	5008	,	,		17472	0.0843		0.0119	False		,,,				2504	0.089				p.A146A		Atlas-SNP	.											.	OR2B6	48	.	0			c.T438C						PASS	.	T		98,4308	79.3+/-117.8	1,96,2106	103.0	105.0	105.0		438	1.2	1.0	6	dbSNP_86	105	228,8372	93.5+/-155.5	3,222,4075	no	coding-synonymous	OR2B6	NM_012367.1		4,318,6181	CC,CT,TT		2.6512,2.2242,2.5065		146/314	27925456	326,12680	2203	4300	6503	SO:0001819	synonymous_variant	26212	exon1			GGCAGCTGCATCC	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.438T>C	6.37:g.27925456T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_012367	O43883|Q6IF89|Q9H5B0	Silent	SNP	ENST00000244623.1	37	CCDS4642.1																																																																																			T|0.963;C|0.037	0.037	strong		0.493	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1		
NPAS2	4862	hgsc.bcm.edu	37	2	101594191	101594191	+	Missense_Mutation	SNP	C	C	T	rs11541353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:101594191C>T	ENST00000335681.5	+	15	1697	c.1412C>T	c.(1411-1413)tCg>tTg	p.S471L	NPAS2_ENST00000542504.1_Missense_Mutation_p.S536L|AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA|AC016738.3_ENST00000433012.1_RNA	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	471			S -> L (susceptibility to seasonal affective disorder (SAD) and diurnal preference; dbSNP:rs11541353). {ECO:0000269|PubMed:9012850}.		cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTTCCCCATCGTCCTGCGAC	0.627													C|||	414	0.0826677	0.0696	0.0922	5008	,	,		17197	0.001		0.17	False		,,,				2504	0.0879				p.S471L		Atlas-SNP	.											.	NPAS2	88	.	0			c.C1412T	GRCh37	CM035892	NPAS2	M	rs11541353	PASS	.	C	LEU/SER	382,4024	193.0+/-218.2	14,354,1835	101.0	103.0	102.0		1412	5.7	0.0	2	dbSNP_120	102	1565,7035	293.9+/-301.6	166,1233,2901	yes	missense	NPAS2	NM_002518.3	145	180,1587,4736	TT,TC,CC		18.1977,8.67,14.97	benign	471/825	101594191	1947,11059	2203	4300	6503	SO:0001583	missense	4862	exon15			CCCCATCGTCCTG	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1412C>T	2.37:g.101594191C>T	ENSP00000338283:p.Ser471Leu	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	25	11	0.44	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	203	0.09294871794871795	46	0.09349593495934959	37	0.10220994475138122	0	0.0	120	0.158311345646438	C	8.842	0.942506	0.18281	0.0867	0.181977	ENSG00000170485	ENST00000335681;ENST00000542504;ENST00000450763	T;T;T	0.32023	3.47;3.45;1.47	5.69	5.69	0.88448	.	1.520810	0.03482	N	0.215274	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.19817	0.039;0.002;0.007	B;B;B	0.12837	0.008;0.0;0.004	T	0.03773	-1.1005	9	0.23891	T	0.37	.	12.2995	0.54866	0.0:0.92:0.0:0.08	rs11541353	536;471;471	F5H027;A0PJF9;Q99743	.;.;NPAS2_HUMAN	L	471;536;70	ENSP00000338283:S471L;ENSP00000438428:S536L;ENSP00000392125:S70L	ENSP00000338283:S471L	S	+	2	0	NPAS2	100960623	0.006000	0.16342	0.007000	0.13788	0.307000	0.27823	2.026000	0.41069	2.677000	0.91161	0.655000	0.94253	TCG	C|0.870;T|0.130	0.130	strong		0.627	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
PRKRA	8575	hgsc.bcm.edu	37	2	179300871	179300871	+	Splice_Site	SNP	C	C	T	rs200649428		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179300871C>T	ENST00000325748.4	-	7	985		c.e7+1		AC009948.5_ENST00000454488.1_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000432031.2_Splice_Site|PRKRA_ENST00000438687.3_Splice_Site|AC009948.5_ENST00000436616.2_RNA|PRKRA_ENST00000487082.1_Splice_Site	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator						cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			AAAAATCATACCTATATCCAA	0.294																																					.	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,caecum,carcinoma,0,1	PRKRA	56	1	0			c.709+1G>A						PASS	.						64.0	72.0	69.0					2																	179300871		2203	4299	6502	SO:0001630	splice_region_variant	8575	exon8			ATCATACCTATAT	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.784+1G>A	2.37:g.179300871C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	11	0.305556	NM_001139518	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Splice_Site	SNP	ENST00000325748.4	37	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432561	0.83776	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9579	0.86264	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKRA	179009117	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.411000	0.73298	2.739000	0.93911	0.655000	0.94253	.	.	.	weak		0.294	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Intron
COL4A4	1286	hgsc.bcm.edu	37	2	227954599	227954599	+	Missense_Mutation	SNP	G	G	A	rs2229814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:227954599G>A	ENST00000396625.3	-	21	1651	c.1444C>T	c.(1444-1446)Cca>Tca	p.P482S	COL4A4_ENST00000329662.7_Missense_Mutation_p.P482S	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	482	Triple-helical region.		P -> S (in dbSNP:rs2229814). {ECO:0000269|PubMed:11961012, ECO:0000269|PubMed:12631110}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|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(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCTCCTTTTGGGCCTCTTCCT	0.483													A|||	2747	0.548522	0.5113	0.6081	5008	,	,		13414	0.5198		0.498	False		,,,				2504	0.638				p.P482S		Atlas-SNP	.											.	COL4A4	215	.	0			c.C1444T						PASS	.	A	SER/PRO	1967,1779		523,921,429	118.0	108.0	111.0		1444	0.3	0.8	2	dbSNP_98	111	4115,4087		1044,2027,1030	yes	missense	COL4A4	NM_000092.4	74	1567,2948,1459	AA,AG,GG		49.8293,47.4907,49.0961	benign	482/1691	227954599	6082,5866	1873	4101	5974	SO:0001583	missense	1286	exon21			CTTTTGGGCCTCT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1444C>T	2.37:g.227954599G>A	ENSP00000379866:p.Pro482Ser	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	1130	0.5173992673992674	244	0.4959349593495935	212	0.585635359116022	287	0.5017482517482518	387	0.5105540897097626	A	0.121	-1.125898	0.01770	0.525093	0.501707	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.90133	-2.62;-2.53	5.74	0.339	0.15979	.	.	.	.	.	T	0.00012	0.0000	M	0.80332	2.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48536	-0.9027	8	0.09590	T	0.72	.	1.2219	0.01926	0.3311:0.2894:0.0874:0.2921	rs2229814;rs3736633;rs17644431;rs52828973;rs3736633	482	P53420	CO4A4_HUMAN	S	482	ENSP00000379866:P482S;ENSP00000328553:P482S	ENSP00000328553:P482S	P	-	1	0	COL4A4	227662843	0.533000	0.26354	0.750000	0.31169	0.512000	0.34134	0.624000	0.24462	0.089000	0.17243	-0.360000	0.07572	CCA	G|0.449;T|0.045	.	strong		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
NRAP	4892	hgsc.bcm.edu	37	10	115374670	115374670	+	Silent	SNP	A	A	G	rs3121453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115374670A>G	ENST00000359988.3	-	28	3358	c.3114T>C	c.(3112-3114)gaT>gaC	p.D1038D	NRAP_ENST00000360478.3_Silent_p.D1003D|NRAP_ENST00000369360.3_Silent_p.D1011D|NRAP_ENST00000369358.4_Silent_p.D1046D	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	108	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	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	
JRK	8629	hgsc.bcm.edu	37	8	143747389	143747389	+	RNA	SNP	G	G	A	rs34288113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143747389G>A	ENST00000507178.2	-	0	421							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ctccaggcgcgtgcagatgtc	0.627													G|||	102	0.0203674	0.003	0.0173	5008	,	,		19841	0.0308		0.0437	False		,,,				2504	0.0112				p.T30M		Atlas-SNP	.											.	.	.	.	0			c.C89T						PASS	.	G	MET/THR,MET/THR	35,4207		0,35,2086	48.0	58.0	55.0		89,89	0.9	0.1	8	dbSNP_126	55	424,8012		8,408,3802	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	81,81	8,443,5888	AA,AG,GG		5.0261,0.8251,3.6204	possibly-damaging,possibly-damaging	30/557,30/569	143747389	459,12219	2121	4218	6339			8629	exon2			AGGCGCGTGCAGA	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143747389G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				G|0.972;A|0.028	0.028	strong		0.627	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:13150531T>C	ENST00000319217.7	-	25	3856	c.3609A>G	c.(3607-3609)aaA>aaG	p.K1203K	MPDZ_ENST00000536827.1_Silent_p.K1203K|MPDZ_ENST00000381022.2_Silent_p.K1203K|MPDZ_ENST00000538841.1_Silent_p.K95K|MPDZ_ENST00000541718.1_Silent_p.K1203K|MPDZ_ENST00000381015.4_Silent_p.K1203K|MPDZ_ENST00000546205.1_Silent_p.K1217K|MPDZ_ENST00000447879.1_Silent_p.K1203K	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	85	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	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	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65197767	65197767	+	Silent	SNP	G	G	A	rs229624	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:65197767G>A	ENST00000394691.1	+	7	876	c.729G>A	c.(727-729)aaG>aaA	p.K243K	PLEKHG3_ENST00000247226.7_Silent_p.K187K			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	243	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		AAATTGCCAAGCATTTTGATG	0.572													G|||	619	0.123602	0.1067	0.0965	5008	,	,		20433	0.0308		0.1849	False		,,,				2504	0.1984				p.K187K		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.G561A						PASS	.	G		510,3896	235.2+/-247.8	36,438,1729	181.0	161.0	168.0		561	-3.7	1.0	14	dbSNP_79	168	1692,6908	310.5+/-309.9	154,1384,2762	no	coding-synonymous	PLEKHG3	NM_015549.1		190,1822,4491	AA,AG,GG		19.6744,11.5751,16.9306		187/1164	65197767	2202,10804	2203	4300	6503	SO:0001819	synonymous_variant	26030	exon5			TGCCAAGCATTTT	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.729G>A	14.37:g.65197767G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	37																																																																																				G|0.853;A|0.147	0.147	strong		0.572	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
ADAM12	8038	hgsc.bcm.edu	37	10	127737930	127737930	+	Silent	SNP	G	G	A	rs2292692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127737930G>A	ENST00000368679.4	-	16	2127	c.1818C>T	c.(1816-1818)ccC>ccT	p.P606P	ADAM12_ENST00000368676.4_Silent_p.P606P|ADAM12_ENST00000467145.1_5'Flank	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	606	Cys-rich.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CTTGCTGCAGGGGGATGTTTG	0.562													g|||	618	0.123403	0.1256	0.1513	5008	,	,		18562	0.0278		0.162	False		,,,				2504	0.1595				p.P606P		Atlas-SNP	.											.	ADAM12	388	.	0			c.C1818T						PASS	.	A	,	562,3844	249.6+/-257.0	29,504,1670	109.0	113.0	112.0		1818,1818	-10.1	0.1	10	dbSNP_100	112	1161,7439	237.4+/-269.2	76,1009,3215	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	105,1513,4885	AA,AG,GG		13.5,12.7553,13.2477	,	606/910,606/739	127737930	1723,11283	2203	4300	6503	SO:0001819	synonymous_variant	8038	exon16			CTGCAGGGGGATG	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1818C>T	10.37:g.127737930G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			G|0.869;A|0.131	0.131	strong		0.562	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
DCP1A	55802	hgsc.bcm.edu	37	3	53321631	53321631	+	Silent	SNP	A	A	C	rs9628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:53321631A>C	ENST00000607628.1	-	10	1831	c.1722T>G	c.(1720-1722)gtT>gtG	p.V574V	RN7SL821P_ENST00000579907.1_RNA|DCP1A_ENST00000606822.1_Silent_p.V536V|DCP1A_ENST00000294241.6_Silent_p.V572V|DCP1A_ENST00000480258.1_5'UTR	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	572					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)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		TCTTGGTCAGAACCTGCAAGT	0.433													C|||	1964	0.392173	0.4766	0.353	5008	,	,		17374	0.1845		0.4155	False		,,,				2504	0.4959				p.V572V		Atlas-SNP	.											.	DCP1A	30	.	0			c.T1716G						PASS	.	C		1764,2056		411,942,557	159.0	156.0	157.0		1722	1.6	1.0	3	dbSNP_52	157	3415,4835		673,2069,1383	no	coding-synonymous	DCP1A	NM_018403.5		1084,3011,1940	CC,CA,AA		41.3939,46.178,42.908		574/585	53321631	5179,6891	1910	4125	6035	SO:0001819	synonymous_variant	55802	exon10			GGTCAGAACCTGC	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"""DCP1 decapping enzyme homolog A (S. cerevisiae)"""				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.1722T>G	3.37:g.53321631A>C		Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	196	196	1	NM_018403	B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	37																																																																																				A|0.644;C|0.356	0.356	strong		0.433	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403	
KDM4C	23081	hgsc.bcm.edu	37	9	7170006	7170006	+	Intron	SNP	G	G	A	rs7022348	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:7170006G>A	ENST00000381309.3	+	21	3559				KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S1037N|KDM4C_ENST00000428870.2_Intron	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	109	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	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	
OR2T12	127064	hgsc.bcm.edu	37	1	248458760	248458760	+	Missense_Mutation	SNP	C	C	A	rs12135684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	3	0.00874636		WXS	Illumina HiSeq	Phase_I	320	153	0.478125	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	
C21orf91	54149	hgsc.bcm.edu	37	21	19169155	19169155	+	Missense_Mutation	SNP	G	G	C	rs1047978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:19169155G>C	ENST00000400558.3	-	3	498	c.408C>G	c.(406-408)gaC>gaG	p.D136E	AL109761.5_ENST00000428689.1_RNA|C21orf91_ENST00000400559.3_Missense_Mutation_p.D136E|C21orf91_ENST00000284881.4_Missense_Mutation_p.D136E|C21orf91_ENST00000493464.1_5'UTR	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)		GTACTTGGGAGTCAAACTGTG	0.388													G|||	1305	0.260583	0.0431	0.3112	5008	,	,		17958	0.3383		0.3996	False		,,,				2504	0.2955				p.D136E		Atlas-SNP	.											.	C21orf91	21	.	0			c.C408G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP	258,3392		9,240,1576	135.0	122.0	126.0		408,408,408	3.4	1.0	21	dbSNP_86	126	2813,5373		495,1823,1775	yes	missense,missense,missense	C21orf91	NM_001100420.1,NM_001100421.1,NM_017447.3	45,45,45	504,2063,3351	CC,CG,GG		34.3635,7.0685,25.9463	probably-damaging,probably-damaging,probably-damaging	136/298,136/222,136/297	19169155	3071,8765	1825	4093	5918	SO:0001583	missense	54149	exon3			TTGGGAGTCAAAC	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.408C>G	21.37:g.19169155G>C	ENSP00000383403:p.Asp136Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_017447		Missense_Mutation	SNP	ENST00000400558.3	37	CCDS42909.1	655	0.2999084249084249	25	0.0508130081300813	118	0.3259668508287293	211	0.3688811188811189	301	0.3970976253298153	G	18.17	3.565398	0.65651	0.070685	0.343635	ENSG00000154642	ENST00000284881;ENST00000400559;ENST00000400558;ENST00000405964	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	6.16	3.36	0.38483	.	0.083092	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.09310	P	0.9999999999974772	P;D	0.52996	0.946;0.957	B;P	0.47376	0.41;0.545	T	0.46414	-0.9193	8	.	.	.	-20.4981	9.6083	0.39648	0.2714:0.0:0.7286:0.0	rs1047978;rs3174905;rs17695314;rs17845464;rs17858342;rs52816870;rs1047978	136;136	Q9NYK6-3;Q9NYK6	.;EURL_HUMAN	E	136	ENSP00000284881:D136E;ENSP00000383404:D136E;ENSP00000383403:D136E;ENSP00000385566:D136E	.	D	-	3	2	C21orf91	18091026	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.841000	0.27613	0.924000	0.37069	0.650000	0.86243	GAC	G|0.690;C|0.310	0.310	strong		0.388	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447	
CR2	1380	hgsc.bcm.edu	37	1	207646462	207646462	+	Missense_Mutation	SNP	G	G	A	rs17615	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	117	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	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	
C3orf22	152065	hgsc.bcm.edu	37	3	126268918	126268918	+	Silent	SNP	G	G	A	rs869463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:126268918G>A	ENST00000318225.2	-	4	597	c.219C>T	c.(217-219)ctC>ctT	p.L73L		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	73										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CTGGAGCCCCGAGCCTAGAGA	0.607													G|||	873	0.174321	0.0356	0.2695	5008	,	,		17005	0.255		0.2485	False		,,,				2504	0.135				p.L73L		Atlas-SNP	.											.	C3orf22	17	.	0			c.C219T						PASS	.	G		355,4051	182.9+/-210.6	13,329,1861	75.0	65.0	69.0		219	-1.6	0.0	3	dbSNP_86	69	2056,6544	356.3+/-330.2	241,1574,2485	no	coding-synonymous	C3orf22	NM_152533.1		254,1903,4346	AA,AG,GG		23.907,8.0572,18.5376		73/142	126268918	2411,10595	2203	4300	6503	SO:0001819	synonymous_variant	152065	exon4			AGCCCCGAGCCTA		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.219C>T	3.37:g.126268918G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	127	81	0.637795	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	37	CCDS3040.1																																																																																			G|0.805;A|0.195	0.195	strong		0.607	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
RNF122	79845	hgsc.bcm.edu	37	8	33416222	33416222	+	Silent	SNP	C	C	T	rs3735951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:33416222C>T	ENST00000256257.1	-	2	494	c.93G>A	c.(91-93)caG>caA	p.Q31Q		NM_024787.2	NP_079063.2	Q9H9V4	RN122_HUMAN	ring finger protein 122	31						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)		GCGGAAGGTCCTGGAAACTGA	0.483													T|||	3057	0.610423	0.8548	0.5029	5008	,	,		20095	0.499		0.5855	False		,,,				2504	0.4969				p.Q31Q		Atlas-SNP	.											.	RNF122	17	.	0			c.G93A						PASS	.	T		3563,843	331.2+/-301.9	1440,683,80	120.0	109.0	113.0		93	-7.7	0.6	8	dbSNP_107	113	5104,3496	511.3+/-377.7	1509,2086,705	no	coding-synonymous	RNF122	NM_024787.2		2949,2769,785	TT,TC,CC		40.6512,19.133,33.3615		31/156	33416222	8667,4339	2203	4300	6503	SO:0001819	synonymous_variant	79845	exon2			AAGGTCCTGGAAA	AK022588	CCDS6091.1	8p12	2013-01-09			ENSG00000133874	ENSG00000133874		"""RING-type (C3HC4) zinc fingers"""	21147	protein-coding gene	gene with protein product							Standard	NM_024787		Approved	FLJ12526	uc003xjo.1	Q9H9V4	OTTHUMG00000163960	ENST00000256257.1:c.93G>A	8.37:g.33416222C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_024787	Q52LK3	Silent	SNP	ENST00000256257.1	37	CCDS6091.1																																																																																			C|0.357;T|0.643	0.643	strong		0.483	RNF122-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376562.1	NM_024787	
TIMM21	29090	hgsc.bcm.edu	37	18	71816278	71816278	+	Missense_Mutation	SNP	G	G	A	rs3737512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:71816278G>A	ENST00000169551.6	+	1	533	c.235G>A	c.(235-237)Ggc>Agc	p.G79S	FBXO15_ENST00000269500.5_5'Flank|TIMM21_ENST00000580087.1_Missense_Mutation_p.G79S|FBXO15_ENST00000419743.2_5'Flank	NM_014177.2	NP_054896.2	Q9BVV7	TIM21_HUMAN	translocase of inner mitochondrial membrane 21 homolog (yeast)	79			G -> S (in dbSNP:rs3737512).		cellular protein metabolic process (GO:0044267)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane presequence translocase complex (GO:0005744)		p.G79S(1)									AAAGGAGGATGGCAGCAAACA	0.483													A|||	629	0.125599	0.2587	0.0548	5008	,	,		17804	0.1319		0.0417	False		,,,				2504	0.0757				p.G79S		Atlas-SNP	.											C18orf55,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G235A						PASS	.	A	SER/GLY	925,3481	738.5+/-411.0	100,725,1378	70.0	75.0	74.0		235	-3.5	0.0	18	dbSNP_107	74	308,8292	805.8+/-407.3	5,298,3997	yes	missense	C18orf55	NM_014177.2	56	105,1023,5375	AA,AG,GG		3.5814,20.9941,9.4802	benign	79/249	71816278	1233,11773	2203	4300	6503	SO:0001583	missense	29090	exon1			GAGGATGGCAGCA	BC000892	CCDS12003.1	18q22.3	2011-11-25	2011-11-25	2011-11-25	ENSG00000075336	ENSG00000075336			25010	protein-coding gene	gene with protein product		615180	"""chromosome 18 open reading frame 55"""	C18orf55		11042152	Standard	NM_014177		Approved	HSPC154, TIM21	uc010dqr.1	Q9BVV7	OTTHUMG00000132844	ENST00000169551.6:c.235G>A	18.37:g.71816278G>A	ENSP00000169551:p.Gly79Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_014177	Q9P010	Missense_Mutation	SNP	ENST00000169551.6	37	CCDS12003.1	272	0.12454212454212454	131	0.266260162601626	24	0.06629834254143646	83	0.1451048951048951	34	0.044854881266490766	A	0.046	-1.267748	0.01433	0.209941	0.035814	ENSG00000075336	ENST00000169551	T	0.41758	0.99	4.75	-3.53	0.04667	.	0.917798	0.09473	N	0.797497	T	0.00012	0.0000	N	0.04686	-0.185	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41556	-0.9502	9	0.11794	T	0.64	-0.3654	11.0144	0.47681	0.1835:0.1371:0.6793:0.0	rs3737512;rs52816198;rs57185450;rs3737512	79	Q9BVV7	TI21L_HUMAN	S	79	ENSP00000169551:G79S	ENSP00000169551:G79S	G	+	1	0	C18orf55	69967258	0.000000	0.05858	0.006000	0.13384	0.074000	0.17049	-0.574000	0.05868	-0.980000	0.03524	-0.254000	0.11334	GGC	G|0.891;A|0.109	0.109	strong		0.483	TIMM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256318.1	NM_014177	
OR8H3	390152	hgsc.bcm.edu	37	11	55890736	55890736	+	Silent	SNP	A	A	G	rs11604579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55890736A>G	ENST00000313472.3	+	1	888	c.888A>G	c.(886-888)gaA>gaG	p.E296E		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	296						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)					GAAACAGAGAAGTGAAAAATG	0.368													A|||	354	0.0706869	0.0234	0.0562	5008	,	,		17665	0.0873		0.0954	False		,,,				2504	0.1022				p.E296E		Atlas-SNP	.											OR8H3,NS,carcinoma,+2,1	OR8H3	92	1	0			c.A888G						PASS	.	A		121,4281		2,117,2082	95.0	100.0	98.0		888	-1.4	1.0	11	dbSNP_120	98	614,7974		46,522,3726	no	coding-synonymous	OR8H3	NM_001005201.1		48,639,5808	GG,GA,AA		7.1495,2.7488,5.6582		296/313	55890736	735,12255	2201	4294	6495	SO:0001819	synonymous_variant	390152	exon1			CAGAGAAGTGAAA	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.888A>G	11.37:g.55890736A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	119	46	0.386555	NM_001005201	Q6IFB7	Silent	SNP	ENST00000313472.3	37	CCDS31519.1																																																																																			A|0.924;G|0.076	0.076	strong		0.368	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
COL15A1	1306	hgsc.bcm.edu	37	9	101767315	101767315	+	Missense_Mutation	SNP	G	G	A	rs35934703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:101767315G>A	ENST00000375001.3	+	9	1759	c.1336G>A	c.(1336-1338)Ggg>Agg	p.G446R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	446	4 X tandem repeats.|Nonhelical region 1 (NC1).		G -> R (in dbSNP:rs35934703).		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)				CCAGAGCCTCGGGGAAGAGGC	0.652													g|||	802	0.160144	0.0983	0.134	5008	,	,		18333	0.2927		0.0785	False		,,,				2504	0.2096				p.G446R		Atlas-SNP	.											.	COL15A1	211	.	0			c.G1336A						PASS	.		ARG/GLY	490,3916	219.4+/-237.2	24,442,1737	41.0	42.0	42.0		1336	-0.6	0.0	9	dbSNP_126	42	701,7899	167.7+/-219.4	29,643,3628	yes	missense	COL15A1	NM_001855.3	125	53,1085,5365	AA,AG,GG		8.1512,11.1212,9.1573	benign	446/1389	101767315	1191,11815	2203	4300	6503	SO:0001583	missense	1306	exon9			AGCCTCGGGGAAG	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.1336G>A	9.37:g.101767315G>A	ENSP00000364140:p.Gly446Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	344	0.1575091575091575	49	0.09959349593495935	42	0.11602209944751381	188	0.32867132867132864	65	0.08575197889182058	g	2.409	-0.335893	0.05278	0.111212	0.081512	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89050	-2.46	3.21	-0.633	0.11519	.	5.313430	0.01370	N	0.012554	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	0.10245	-1.0638	9	0.27082	T	0.32	-0.3511	5.9749	0.19373	0.5231:0.0:0.4769:0.0	rs35934703;rs57389704	446	P39059	COFA1_HUMAN	R	446;416	ENSP00000364140:G446R	ENSP00000364140:G446R	G	+	1	0	COL15A1	100807136	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.267000	0.18552	-0.131000	0.11578	-1.073000	0.02249	GGG	G|0.887;A|0.113	0.113	strong		0.652	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
SCN10A	6336	hgsc.bcm.edu	37	3	38768300	38768300	+	Missense_Mutation	SNP	T	T	C	rs57326399	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38768300T>C	ENST00000449082.2	-	16	2883	c.2884A>G	c.(2884-2886)Att>Gtt	p.I962V		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	962					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.I962V(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)	TTGGCAGCAATGTGGTTCTCA	0.602													C|||	1055	0.210663	0.0862	0.1153	5008	,	,		19922	0.373		0.2545	False		,,,				2504	0.2342				p.I962V		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - Missense(1)	prostate(1)	c.A2884G						PASS	.	C	VAL/ILE	482,3924	782.1+/-414.5	24,434,1745	60.0	62.0	61.0		2884	-4.2	0.1	3	dbSNP_129	61	2253,6347	708.4+/-405.7	296,1661,2343	yes	missense	SCN10A	NM_006514.2	29	320,2095,4088	CC,CT,TT		26.1977,10.9396,21.0288	benign	962/1957	38768300	2735,10271	2203	4300	6503	SO:0001583	missense	6336	exon16			CAGCAATGTGGTT	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.2884A>G	3.37:g.38768300T>C	ENSP00000390600:p.Ile962Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	504	0.23076923076923078	35	0.07113821138211382	47	0.1298342541436464	231	0.40384615384615385	191	0.2519788918205805	C	10.05	1.245153	0.22796	0.109396	0.261977	ENSG00000185313	ENST00000449082	D	0.83837	-1.77	5.2	-4.17	0.03857	Sodium ion transport-associated (1);	6.869170	0.00447	N	0.000087	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.34103	0.437	B	0.33799	0.17	T	0.04522	-1.0945	9	0.49607	T	0.09	.	6.3619	0.21433	0.0:0.2379:0.3312:0.4309	rs57326399;rs62242441	962	Q9Y5Y9	SCNAA_HUMAN	V	962	ENSP00000390600:I962V	ENSP00000390600:I962V	I	-	1	0	SCN10A	38743304	0.000000	0.05858	0.093000	0.20910	0.059000	0.15707	0.052000	0.14163	-0.612000	0.05701	-1.337000	0.01257	ATT	T|0.779;C|0.221	0.221	strong		0.602	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
H6PD	9563	hgsc.bcm.edu	37	1	9324571	9324571	+	Silent	SNP	T	T	C	rs9434742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9324571T>C	ENST00000377403.2	+	5	2321	c.2019T>C	c.(2017-2019)taT>taC	p.Y673Y	H6PD_ENST00000602477.1_Silent_p.Y684Y	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	673	6-phosphogluconolactonase.				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)		CCCAGATCTATGCCAGGGAGA	0.652													C|||	2018	0.402955	0.497	0.4207	5008	,	,		18852	0.1657		0.4115	False		,,,				2504	0.499				p.Y673Y		Atlas-SNP	.											H6PD,NS,carcinoma,0,1	H6PD	71	1	0			c.T2019C						PASS	.	C		2150,2256	582.9+/-385.7	526,1098,579	53.0	56.0	55.0		2019	-8.9	0.0	1	dbSNP_119	55	3408,5188	627.4+/-398.0	653,2102,1543	no	coding-synonymous	H6PD	NM_004285.3		1179,3200,2122	CC,CT,TT		39.6463,48.7971,42.7473		673/792	9324571	5558,7444	2203	4298	6501	SO:0001819	synonymous_variant	9563	exon5			GATCTATGCCAGG	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.2019T>C	1.37:g.9324571T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			T|0.603;C|0.397	0.397	strong		0.652	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
PLOD1	5351	hgsc.bcm.edu	37	1	12024235	12024235	+	Silent	SNP	C	C	T	rs1130529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12024235C>T	ENST00000196061.4	+	12	1233	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N	PLOD1_ENST00000376369.3_Silent_p.N449N	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	402					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	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)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CCCTCAGGAACGTCATTGCCC	0.622													C|||	1745	0.348442	0.2693	0.3545	5008	,	,		15315	0.3839		0.3151	False		,,,				2504	0.4489				p.N402N		Atlas-SNP	.											.	PLOD1	75	.	0			c.C1206T						PASS	.	C		1281,3125	435.9+/-344.5	182,917,1104	150.0	144.0	146.0		1206	-5.4	1.0	1	dbSNP_86	146	2761,5839	439.9+/-359.4	458,1845,1997	no	coding-synonymous	PLOD1	NM_000302.3		640,2762,3101	TT,TC,CC		32.1047,29.074,31.078		402/728	12024235	4042,8964	2203	4300	6503	SO:0001819	synonymous_variant	5351	exon12			CAGGAACGTCATT	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.1206C>T	1.37:g.12024235C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_000302	B4DR87|Q96AV9|Q9H132	Silent	SNP	ENST00000196061.4	37	CCDS142.1																																																																																			C|0.687;N|0.001	.	strong		0.622	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726675	25726675	+	Silent	SNP	G	G	A	rs9358871	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	72	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	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	
FOXP1	27086	hgsc.bcm.edu	37	3	71096114	71096114	+	Missense_Mutation	SNP	G	G	C	rs146606219		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:71096114G>C	ENST00000318789.4	-	10	1168	c.643C>G	c.(643-645)Ccc>Gcc	p.P215A	FOXP1_ENST00000484350.1_Missense_Mutation_p.P139A|FOXP1_ENST00000475937.1_Missense_Mutation_p.P215A|FOXP1_ENST00000472382.1_5'UTR|FOXP1_ENST00000468577.1_Missense_Mutation_p.P215A|FOXP1_ENST00000493089.1_Missense_Mutation_p.P215A|FOXP1_ENST00000491238.1_Missense_Mutation_p.P217A|FOXP1_ENST00000498215.1_Missense_Mutation_p.P215A	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	215	Gln-rich.		P -> A (in dbSNP:rs146606219). {ECO:0000269|PubMed:19352412, ECO:0000269|PubMed:20848658, ECO:0000269|PubMed:20950788}.		negative regulation of transcription, DNA-templated (GO:0045892)|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)	p.P215S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GGTTGAAGGGGAAGGGCAGGC	0.517			T	PAX5	ALL								G|||	1	0.000199681	0.0	0.0	5008	,	,		19705	0.0		0.001	False		,,,				2504	0.0				p.P217A		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	FOXP1,NS,carcinoma,0,1	FOXP1	104	1	1	Substitution - Missense(1)	endometrium(1)	c.C649G						PASS	.	G	ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	177.0	181.0	180.0		643	6.0	1.0	3	dbSNP_134	180	22,8578	15.3+/-51.7	0,22,4278	yes	missense	FOXP1	NM_032682.5	27	0,24,6479	CC,CG,GG		0.2558,0.0454,0.1845	benign	215/678	71096114	24,12982	2203	4300	6503	SO:0001583	missense	27086	exon5			GAAGGGGAAGGGC	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.643C>G	3.37:g.71096114G>C	ENSP00000318902:p.Pro215Ala	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	161	90	0.559006	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	37	CCDS2914.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.6	4.554029	0.86231	4.54E-4	0.002558	ENSG00000114861	ENST00000318789;ENST00000318796;ENST00000475937;ENST00000339693;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577;ENST00000485326;ENST00000497553	T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;1.13	6.03	6.03	0.97812	.	0.195111	0.56097	D	0.000031	T	0.64483	0.2602	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.993	D;D;D;D	0.76071	0.987;0.981;0.956;0.956	T	0.61322	-0.7086	10	0.52906	T	0.07	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	214;215;139;215	A3KMG1;G5E9V8;Q8NAN6;Q9H334	.;.;.;FOXP1_HUMAN	A	215;115;215;215;111;217;215;215;139;215;115;115	ENSP00000318902:P215A;ENSP00000419393:P215A;ENSP00000418225:P111A;ENSP00000420736:P217A;ENSP00000418524:P215A;ENSP00000418102:P215A;ENSP00000417857:P139A;ENSP00000418883:P215A;ENSP00000417941:P115A;ENSP00000418784:P115A	ENSP00000318902:P215A	P	-	1	0	FOXP1	71178804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.878000	0.92393	2.854000	0.98071	0.655000	0.94253	CCC	G|0.998;C|0.002	0.002	strong		0.517	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682	
DCHS1	8642	hgsc.bcm.edu	37	11	6643976	6643976	+	Silent	SNP	C	C	T	rs7122587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6643976C>T	ENST00000299441.3	-	21	9342	c.8931G>A	c.(8929-8931)caG>caA	p.Q2977Q	RP11-732A19.9_ENST00000545572.1_RNA|RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2977					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGGTGCTGCCTGTGACATTG	0.622													C|||	982	0.196086	0.3487	0.1816	5008	,	,		17200	0.0714		0.2157	False		,,,				2504	0.1084				p.Q2977Q		Atlas-SNP	.											.	DCHS1	277	.	0			c.G8931A						PASS	.	C		1390,3006		225,940,1033	53.0	44.0	47.0		8931	2.7	1.0	11	dbSNP_116	47	1707,6869		171,1365,2752	yes	coding-synonymous	DCHS1	NM_003737.2		396,2305,3785	TT,TC,CC		19.9044,31.6197,23.8745		2977/3299	6643976	3097,9875	2198	4288	6486	SO:0001819	synonymous_variant	8642	exon21			TGCTGCCTGTGAC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8931G>A	11.37:g.6643976C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.764;T|0.236	0.236	strong		0.622	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
LRP3	4037	hgsc.bcm.edu	37	19	33696897	33696897	+	Silent	SNP	C	C	T	rs11084712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:33696897C>T	ENST00000253193.7	+	5	1423	c.1221C>T	c.(1219-1221)ggC>ggT	p.G407G	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	407					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					GTGCCAGCGGCCGAGACGAGC	0.682													C|||	1298	0.259185	0.1672	0.3761	5008	,	,		13617	0.2262		0.2207	False		,,,				2504	0.3742				p.G407G		Atlas-SNP	.											LRP3,rectum,carcinoma,0,2	LRP3	46	2	0			c.C1221T						PASS	.	C		667,3667		52,563,1552	9.0	9.0	9.0		1221	3.0	1.0	19	dbSNP_120	9	1559,6947		146,1267,2840	no	coding-synonymous	LRP3	NM_002333.3		198,1830,4392	TT,TC,CC		18.3282,15.3899,17.3364		407/771	33696897	2226,10614	2167	4253	6420	SO:0001819	synonymous_variant	4037	exon5			CAGCGGCCGAGAC	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.1221C>T	19.37:g.33696897C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_002333	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																			C|0.769;T|0.231	0.231	strong		0.682	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
SEMA4G	57715	hgsc.bcm.edu	37	10	102738766	102738766	+	Silent	SNP	T	T	C	rs118166648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102738766T>C	ENST00000370250.4	+	7	1177	c.804T>C	c.(802-804)cgT>cgC	p.R268R	SEMA4G_ENST00000519756.1_Intron|SEMA4G_ENST00000517724.1_Silent_p.R268R|SEMA4G_ENST00000210633.3_Silent_p.R268R|MRPL43_ENST00000370241.3_Silent_p.T177T|MRPL43_ENST00000318325.2_3'UTR|RP11-108L7.4_ENST00000447344.1_RNA	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	268	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		GTGTGGCTCGTGTCTGCAAGG	0.617													T|||	172	0.034345	0.0076	0.0836	5008	,	,		15654	0.001		0.0825	False		,,,				2504	0.0204				p.R268R		Atlas-SNP	.											SEMA4G,colon,carcinoma,+1,2	SEMA4G	55	2	0			c.T804C						scavenged	.	T	,,	92,4314	74.7+/-112.8	0,92,2111	53.0	42.0	45.0		804,804,	-3.5	1.0	10	dbSNP_132	45	736,7864	176.6+/-226.4	28,680,3592	no	coding-synonymous,coding-synonymous,utr-3	SEMA4G,MRPL43	NM_001203244.1,NM_017893.3,NM_176792.2	,,	28,772,5703	CC,CT,TT		8.5581,2.0881,6.3663	,,	268/703,268/844,	102738766	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	57715	exon7			GGCTCGTGTCTGC	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.804T>C	10.37:g.102738766T>C		Somatic	88	3	0.0340909		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_001203244	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Silent	SNP	ENST00000370250.4	37																																																																																				T|0.944;C|0.056	0.056	strong		0.617	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		
PCLO	27445	hgsc.bcm.edu	37	7	82581859	82581859	+	Missense_Mutation	SNP	C	C	T	rs976714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:82581859C>T	ENST00000333891.9	-	5	8747	c.8410G>A	c.(8410-8412)Gca>Aca	p.A2804T	PCLO_ENST00000423517.2_Missense_Mutation_p.A2804T|PCLO_ENST00000437081.1_5'Flank	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						GTGTAACTTGCACTAGCTGTG	0.458													C|||	1603	0.320088	0.1029	0.389	5008	,	,		21680	0.4405		0.3608	False		,,,				2504	0.3988				p.A2804T		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,2	PCLO	1506	2	0			c.G8410A						PASS	.	C	THR/ALA,THR/ALA	565,3531		41,483,1524	200.0	176.0	184.0		8410,8410	-5.0	0.1	7	dbSNP_86	184	3018,5356		549,1920,1718	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	58,58	590,2403,3242	TT,TC,CC		36.0401,13.7939,28.733	benign,benign	2804/5143,2804/4936	82581859	3583,8887	2048	4187	6235	SO:0001583	missense	27445	exon5			AACTTGCACTAGC	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.8410G>A	7.37:g.82581859C>T	ENSP00000334319:p.Ala2804Thr	Somatic	351	1	0.002849		WXS	Illumina HiSeq	Phase_I	359	355	0.988858	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	711	0.32554945054945056	46	0.09349593495934959	135	0.3729281767955801	253	0.4423076923076923	277	0.3654353562005277	C	6.515	0.463151	0.12402	0.137939	0.360401	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16743	2.32;2.32	5.69	-5.02	0.02982	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48293	-0.9048	8	0.87932	D	0	.	1.6918	0.02853	0.2103:0.2657:0.0973:0.4267	rs976714;rs10350430;rs61026231;rs976714	2804;2804	Q9Y6V0-5;Q9Y6V0-6	.;.	T	2735;2804;2804	ENSP00000334319:A2804T;ENSP00000388393:A2804T	ENSP00000334319:A2804T	A	-	1	0	PCLO	82419795	0.000000	0.05858	0.067000	0.19924	0.627000	0.37826	-1.275000	0.02817	-0.998000	0.03446	-0.793000	0.03317	GCA	C|0.673;T|0.327	0.327	strong		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
TTLL5	23093	hgsc.bcm.edu	37	14	76232469	76232469	+	Silent	SNP	C	C	T	rs61741261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:76232469C>T	ENST00000298832.9	+	20	1978	c.1773C>T	c.(1771-1773)gtC>gtT	p.V591V	TTLL5_ENST00000554510.1_Silent_p.V100V|TTLL5_ENST00000557636.1_Silent_p.V605V|TTLL5_ENST00000556893.1_Silent_p.V142V|TTLL5_ENST00000555422.1_3'UTR	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	591					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		AGGAAGAAGTCGCATTAGATA	0.398													c|||	6	0.00119808	0.0	0.0	5008	,	,		16548	0.0		0.006	False		,,,				2504	0.0				p.V591V		Atlas-SNP	.											.	TTLL5	102	.	0			c.C1773T						PASS	.			0,4406		0,0,2203	86.0	82.0	83.0		1773	-3.9	0.1	14	dbSNP_129	83	17,8583	13.3+/-46.6	0,17,4283	no	coding-synonymous	TTLL5	NM_015072.4		0,17,6486	TT,TC,CC		0.1977,0.0,0.1307		591/1282	76232469	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23093	exon20			AGAAGTCGCATTA	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.1773C>T	14.37:g.76232469C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Silent	SNP	ENST00000298832.9	37	CCDS32124.1																																																																																			C|0.998;T|0.002	0.002	strong		0.398	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
RP1L1	94137	hgsc.bcm.edu	37	8	10466482	10466482	+	Missense_Mutation	SNP	G	G	A	rs13267180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	91	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	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		
ZNF615	284370	hgsc.bcm.edu	37	19	52496149	52496149	+	Missense_Mutation	SNP	C	C	T	rs16983353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52496149C>T	ENST00000602063.1	-	6	2529	c.2180G>A	c.(2179-2181)aGg>aAg	p.R727K	ZNF615_ENST00000391795.3_Missense_Mutation_p.R732K|ZNF615_ENST00000376716.5_Missense_Mutation_p.R727K|ZNF615_ENST00000594083.1_Missense_Mutation_p.R738K|ZNF615_ENST00000598071.1_Missense_Mutation_p.R738K			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	727			R -> K (in dbSNP:rs16983353). {ECO:0000269|PubMed:14702039, 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)	p.R738K(1)|p.R727K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTGAATTCTCCTGTGTTTAAC	0.423													T|||	2391	0.477436	0.6074	0.3977	5008	,	,		19636	0.3948		0.3131	False		,,,				2504	0.6125				p.R738K		Atlas-SNP	.											ZNF615,NS,carcinoma,0,2	ZNF615	111	2	2	Substitution - Missense(2)	stomach(2)	c.G2213A						PASS	.	T	LYS/ARG,LYS/ARG	2556,1850	537.3+/-374.7	720,1116,367	170.0	182.0	178.0		2213,2180	2.5	0.0	19	dbSNP_123	178	2386,6214	700.9+/-405.2	321,1744,2235	yes	missense,missense	ZNF615	NM_001199324.1,NM_198480.3	26,26	1041,2860,2602	TT,TC,CC		27.7442,41.9882,37.9978	benign,benign	738/743,727/732	52496149	4942,8064	2203	4300	6503	SO:0001583	missense	284370	exon7			ATTCTCCTGTGTT	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.2180G>A	19.37:g.52496149C>T	ENSP00000473089:p.Arg727Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	893	0.4088827838827839	297	0.6036585365853658	145	0.4005524861878453	204	0.35664335664335667	247	0.3258575197889182	T	7.455	0.643567	0.14451	0.580118	0.277442	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.35236	1.32;1.32	3.53	2.5	0.30297	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04959	-0.14	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	0.40156	-0.9578	8	0.42905	T	0.14	.	6.1118	0.20104	0.0:0.2239:0.0:0.7761	rs16983353;rs52803934;rs59945485;rs16983353	734;738;727	Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;ZN615_HUMAN	K	727;737;732;681	ENSP00000365906:R727K;ENSP00000375672:R732K	ENSP00000347019:R737K	R	-	2	0	ZNF615	57187961	0.000000	0.05858	0.003000	0.11579	0.730000	0.41778	-0.207000	0.09384	0.108000	0.17862	-0.254000	0.11334	AGG	C|0.595;T|0.405	0.405	strong		0.423	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
KIF4B	285643	hgsc.bcm.edu	37	5	154396505	154396505	+	Missense_Mutation	SNP	G	G	A	rs60928118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:154396505G>A	ENST00000435029.4	+	1	3246	c.3086G>A	c.(3085-3087)cGt>cAt	p.R1029H		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	1029	Globular. {ECO:0000250}.|Interaction with PRC1. {ECO:0000250}.			R -> H (in Ref. 3; ABB92415). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAACCTTCTCGTGTTAAAGAA	0.423													G|||	789	0.157548	0.0885	0.111	5008	,	,		23558	0.1895		0.166	False		,,,				2504	0.2423				p.R1029H		Atlas-SNP	.											.	KIF4B	307	.	0			c.G3086A						PASS	.	G	HIS/ARG	443,3963	211.2+/-231.4	23,397,1783	124.0	126.0	125.0		3086	1.8	1.0	5	dbSNP_129	125	1463,7137	280.1+/-294.3	130,1203,2967	yes	missense	KIF4B	NM_001099293.1	29	153,1600,4750	AA,AG,GG		17.0116,10.0545,14.6548	benign	1029/1235	154396505	1906,11100	2203	4300	6503	SO:0001583	missense	285643	exon1			CTTCTCGTGTTAA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.3086G>A	5.37:g.154396505G>A	ENSP00000387875:p.Arg1029His	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	300	136	0.453333	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	309	0.14148351648351648	59	0.11991869918699187	41	0.1132596685082873	88	0.15384615384615385	121	0.15963060686015831	G	10.43	1.349050	0.24426	0.100545	0.170116	ENSG00000226650	ENST00000435029	T	0.69040	-0.37	1.77	1.77	0.24775	.	.	.	.	.	T	0.00271	0.0008	M	0.61703	1.905	0.25967	P	0.9825413	B	0.20887	0.049	B	0.09377	0.004	T	0.22103	-1.0226	8	0.66056	D	0.02	.	7.0054	0.24833	0.0:0.0:1.0:0.0	rs60928118;rs61734294	1029	Q2VIQ3	KIF4B_HUMAN	H	1029	ENSP00000387875:R1029H	ENSP00000387875:R1029H	R	+	2	0	KIF4B	154376698	0.827000	0.29292	0.972000	0.41901	0.950000	0.60333	1.504000	0.35726	1.290000	0.44636	0.563000	0.77884	CGT	G|0.858;A|0.142	0.142	strong		0.423	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
OR6C74	254783	hgsc.bcm.edu	37	12	55641295	55641295	+	Missense_Mutation	SNP	A	A	G	rs4388990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55641295A>G	ENST00000343870.4	+	1	314	c.224A>G	c.(223-225)tAc>tGc	p.Y75C		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	75			Y -> C (in dbSNP:rs4388990).			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						ACAACTGTCTACATTCCCAAA	0.403													G|||	1181	0.235823	0.149	0.2334	5008	,	,		19409	0.1171		0.333	False		,,,				2504	0.3773				p.Y75C		Atlas-SNP	.											.	OR6C74	52	.	0			c.A224G						PASS	.	G	CYS/TYR	818,3588	324.5+/-298.6	65,688,1450	173.0	174.0	174.0		224	2.9	0.0	12	dbSNP_111	174	2719,5881	434.2+/-357.7	426,1867,2007	yes	missense	OR6C74	NM_001005490.1	194	491,2555,3457	GG,GA,AA		31.6163,18.5656,27.1951	benign	75/313	55641295	3537,9469	2203	4300	6503	SO:0001583	missense	254783	exon1			CTGTCTACATTCC		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.224A>G	12.37:g.55641295A>G	ENSP00000342836:p.Tyr75Cys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	184	79	0.429348	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	495	0.22664835164835165	76	0.15447154471544716	98	0.27071823204419887	74	0.12937062937062938	247	0.3258575197889182	a	0.003	-2.548705	0.00140	0.185656	0.316163	ENSG00000197706	ENST00000343870	T	0.00882	5.58	4.83	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	N	0.000024	T	0.00012	0.0000	N	0.00507	-1.42	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	9	0.02654	T	1	.	3.4523	0.07503	0.0764:0.2412:0.3214:0.361	rs4388990;rs17382973;rs52809662;rs60288258;rs4388990	75	A6NCV1	O6C74_HUMAN	C	75	ENSP00000342836:Y75C	ENSP00000342836:Y75C	Y	+	2	0	OR6C74	53927562	0.000000	0.05858	0.009000	0.14445	0.351000	0.29236	-0.367000	0.07553	0.300000	0.22699	-0.229000	0.12294	TAC	A|0.750;G|0.250	0.250	strong		0.403	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
COL4A1	1282	hgsc.bcm.edu	37	13	110813709	110813709	+	Silent	SNP	G	G	A	rs1133219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	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		
MYO18A	399687	hgsc.bcm.edu	37	17	27425132	27425132	+	Silent	SNP	C	C	T	rs71369700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:27425132C>T	ENST00000527372.1	-	25	4161	c.3981G>A	c.(3979-3981)aaG>aaA	p.K1327K	MYO18A_ENST00000354329.4_Silent_p.K1327K|MYO18A_ENST00000533112.1_Silent_p.K1327K|MYO18A_ENST00000531253.1_Silent_p.K1327K	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1327					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCTGCAGTTCCTTCATCTCCT	0.602													C|||	21	0.00419329	0.0	0.0	5008	,	,		20280	0.001		0.0179	False		,,,				2504	0.002				p.K1327K	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G3981A						PASS	.	C	,	12,4302		0,12,2145	123.0	135.0	131.0		3981,3981	-1.5	1.0	17	dbSNP_130	131	112,8404		1,110,4147	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	1,122,6292	TT,TC,CC		1.3152,0.2782,0.9665	,	1327/2055,1327/2040	27425132	124,12706	2157	4258	6415	SO:0001819	synonymous_variant	399687	exon25			CAGTTCCTTCATC	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.3981G>A	17.37:g.27425132C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			C|0.991;T|0.009	0.009	strong		0.602	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
TRMU	55687	hgsc.bcm.edu	37	22	46731689	46731689	+	Missense_Mutation	SNP	G	G	T	rs11090865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46731689G>T	ENST00000290846.4	+	1	368	c.28G>T	c.(28-30)Gcc>Tcc	p.A10S	TRMU_ENST00000381019.3_Missense_Mutation_p.A10S|TRMU_ENST00000424260.2_5'Flank	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	10			A -> S (decreased activity; dbSNP:rs11090865). {ECO:0000269|PubMed:16826519, ECO:0000269|PubMed:19732863}.		tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		CGTCGTGTGCGCCCTGTCCGG	0.751													G|||	529	0.105631	0.2436	0.0692	5008	,	,		10046	0.001		0.1223	False		,,,				2504	0.0358				p.A10S		Atlas-SNP	.											.	TRMU	23	.	0			c.G28T	GRCh37	CM063224	TRMU	M	rs11090865	PASS	.	G	SER/ALA	847,3317		81,685,1316	7.0	9.0	8.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	28	4.5	1.0	22	dbSNP_120	8	805,7339		37,731,3304	yes	missense	TRMU	NM_018006.4	99	118,1416,4620	TT,TG,GG		9.8846,20.341,13.4222	probably-damaging	10/422	46731689	1652,10656	2082	4072	6154	SO:0001583	missense	55687	exon1			GTGTGCGCCCTGT	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"""tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase """	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.28G>T	22.37:g.46731689G>T	ENSP00000290846:p.Ala10Ser	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	36	28	0.777778	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	37	CCDS14075.1	237	0.10851648351648352	111	0.22560975609756098	32	0.08839779005524862	0	0.0	94	0.12401055408970976	G	34	5.364808	0.95877	0.20341	0.098846	ENSG00000100416	ENST00000290846;ENST00000381019	T;T	0.68479	-0.33;-0.33	4.49	4.49	0.54785	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.00178	0.0005	H	0.94345	3.525	0.09310	P	1.0	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.80764	0.981;0.968;0.994	T	0.02437	-1.1159	9	0.87932	D	0	-6.6109	16.1042	0.81209	0.0:0.0:1.0:0.0	rs11090865;rs11090865	10;10;10	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	S	10	ENSP00000290846:A10S;ENSP00000370407:A10S	ENSP00000290846:A10S	A	+	1	0	TRMU	45110353	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	7.674000	0.83992	2.308000	0.77769	0.467000	0.42956	GCC	G|0.890;T|0.110	0.110	strong		0.751	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006	
PRR14	78994	hgsc.bcm.edu	37	16	30666367	30666367	+	Missense_Mutation	SNP	C	C	T	rs3747481	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30666367C>T	ENST00000542965.2	+	7	1532	c.1076C>T	c.(1075-1077)cCg>cTg	p.P359L	PRR14_ENST00000300835.4_Missense_Mutation_p.P359L|PRR14_ENST00000571654.1_Intron			Q9BWN1	PRR14_HUMAN	proline rich 14	359	Pro-rich.		P -> L (in dbSNP:rs3747481). {ECO:0000269|PubMed:15489334}.							breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CGACCACGGCCGCGGCGGCAC	0.706													C|||	1827	0.364816	0.438	0.2017	5008	,	,		12033	0.1062		0.2773	False		,,,				2504	0.7382				p.P359L		Atlas-SNP	.											.	PRR14	45	.	0			c.C1076T						PASS	.	C	LEU/PRO	1781,2607		360,1061,773	25.0	31.0	29.0		1076	4.4	1.0	16	dbSNP_107	29	2266,6326		306,1654,2336	yes	missense	PRR14	NM_024031.2	98	666,2715,3109	TT,TC,CC		26.3734,40.588,31.1787	probably-damaging	359/586	30666367	4047,8933	2194	4296	6490	SO:0001583	missense	78994	exon8			CACGGCCGCGGCG	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1076C>T	16.37:g.30666367C>T	ENSP00000441641:p.Pro359Leu	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_024031	Q8WTX2	Missense_Mutation	SNP	ENST00000542965.2	37	CCDS10687.1	547	0.25045787545787546	211	0.42886178861788615	76	0.20994475138121546	49	0.08566433566433566	211	0.2783641160949868	C	17.54	3.414049	0.62511	0.40588	0.263734	ENSG00000156858	ENST00000287463;ENST00000300835;ENST00000542965	T;T	0.62639	0.01;0.01	5.37	4.42	0.53409	.	0.646742	0.15365	N	0.266168	T	0.00012	0.0000	M	0.69823	2.125	0.25924	P	0.9830724	B	0.26041	0.14	B	0.23419	0.046	T	0.32719	-0.9896	9	0.49607	T	0.09	-5.2848	7.1976	0.25862	0.1676:0.7454:0.0:0.087	rs3747481;rs17845665;rs17858601;rs60779979;rs3747481	359	Q9BWN1	PRR14_HUMAN	L	332;359;359	ENSP00000300835:P359L;ENSP00000441641:P359L	ENSP00000287463:P332L	P	+	2	0	PRR14	30573868	0.756000	0.28383	0.953000	0.39169	0.994000	0.84299	1.134000	0.31442	1.257000	0.44085	0.563000	0.77884	CCG	C|0.701;T|0.299	0.299	strong		0.706	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031	
LZIC	84328	hgsc.bcm.edu	37	1	9995633	9995633	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9995633G>A	ENST00000377223.1	-	4	401	c.154C>T	c.(154-156)Caa>Taa	p.Q52*	LZIC_ENST00000400903.2_Nonsense_Mutation_p.Q52*|LZIC_ENST00000377213.1_Nonsense_Mutation_p.Q52*|LZIC_ENST00000541052.1_Nonsense_Mutation_p.Q73*	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	52					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		TCACTTAGTTGCTCCAGAGTT	0.333																																					p.Q52X		Atlas-SNP	.											.	LZIC	11	.	0			c.C154T						PASS	.						151.0	157.0	155.0					1																	9995633		2203	4299	6502	SO:0001587	stop_gained	84328	exon3			TTAGTTGCTCCAG	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.154C>T	1.37:g.9995633G>A	ENSP00000366430:p.Gln52*	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	5	0.0510204	NM_032368	B2R6F0|B4E2N0|Q96IU1	Nonsense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	.	.	.	.	.	.	.	.	.	.	G	39	7.297898	0.98196	.	.	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6655	0.95891	0.0:0.0:1.0:0.0	.	.	.	.	X	52;52;73;52	.	.	Q	-	1	0	LZIC	9918220	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.716000	0.98752	2.652000	0.90054	0.491000	0.48974	CAA	.	.	none		0.333	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368	
HRNR	388697	hgsc.bcm.edu	37	1	152192555	152192555	+	Missense_Mutation	SNP	T	T	C	rs41266134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152192555T>C	ENST00000368801.2	-	3	1625	c.1550A>G	c.(1549-1551)tAt>tGt	p.Y517C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	517			Y -> C (in dbSNP:rs41266134).		establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGCTGACCATAGCTGGAAGA	0.582													T|||	1464	0.292332	0.0242	0.3905	5008	,	,		23145	0.5962		0.1412	False		,,,				2504	0.4274				p.Y517C		Atlas-SNP	.											.	HRNR	403	.	0			c.A1550G						PASS	.	T	CYS/TYR	206,4200	126.6+/-163.6	3,200,2000	260.0	249.0	253.0		1550	-6.0	0.0	1	dbSNP_127	253	1241,7359	249.2+/-276.5	96,1049,3155	yes	missense	HRNR	NM_001009931.1	194	99,1249,5155	CC,CT,TT		14.4302,4.6754,11.1256	benign	517/2851	152192555	1447,11559	2203	4300	6503	SO:0001583	missense	388697	exon3			TGACCATAGCTGG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1550A>G	1.37:g.152192555T>C	ENSP00000357791:p.Tyr517Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	58	0.690476	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	582	0.2664835164835165	13	0.026422764227642278	119	0.3287292817679558	338	0.5909090909090909	112	0.14775725593667546	T	2.829	-0.243134	0.05906	0.046754	0.144302	ENSG00000197915	ENST00000368801	T	0.01725	4.67	3.01	-6.02	0.02192	.	.	.	.	.	T	0.00300	0.0009	N	0.14661	0.345	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.46952	-0.9154	8	0.38643	T	0.18	.	0.3516	0.00350	0.3025:0.2331:0.2662:0.1982	rs41266134	517	Q86YZ3	HORN_HUMAN	C	517	ENSP00000357791:Y517C	ENSP00000357791:Y517C	Y	-	2	0	HRNR	150459179	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-6.023000	0.00085	-1.875000	0.01132	-0.515000	0.04445	TAT	T|0.836;C|0.164	0.164	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204403659	204403659	+	Silent	SNP	A	A	G	rs3747636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204403659A>G	ENST00000367187.3	-	25	4150	c.3594T>C	c.(3592-3594)aaT>aaC	p.N1198N	PIK3C2B_ENST00000424712.2_Silent_p.N1170N|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1198	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|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)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGATGTTGTCATTATGTCGGT	0.537													G|||	2028	0.404952	0.525	0.2666	5008	,	,		23776	0.5089		0.2594	False		,,,				2504	0.3834				p.N1198N		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T3594C						PASS	.	G		2104,2302	601.4+/-389.7	495,1114,594	92.0	71.0	78.0		3594	-7.8	0.4	1	dbSNP_107	78	1876,6724	728.1+/-406.7	189,1498,2613	no	coding-synonymous	PIK3C2B	NM_002646.3		684,2612,3207	GG,GA,AA		21.814,47.7531,30.6013		1198/1635	204403659	3980,9026	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon25			GTTGTCATTATGT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3594T>C	1.37:g.204403659A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	54	0.350649	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			A|0.650;G|0.350	0.350	strong		0.537	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
HIF3A	64344	hgsc.bcm.edu	37	19	46823702	46823702	+	Missense_Mutation	SNP	A	A	G	rs3764609	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000300862.3_Missense_Mutation_p.Q341R|HIF3A_ENST00000339613.2_Missense_Mutation_p.Q287R|HIF3A_ENST00000472815.1_Missense_Mutation_p.Q274R|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000600383.1_Missense_Mutation_p.Q274R|HIF3A_ENST00000420102.2_Missense_Mutation_p.Q292R	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	34	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	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		
TAF6	6878	hgsc.bcm.edu	37	7	99711386	99711386	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99711386A>C	ENST00000344095.4	-	4	775	c.250T>G	c.(250-252)Tat>Gat	p.Y84D	TAF6_ENST00000452041.1_Missense_Mutation_p.Y84D|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000418432.2_Missense_Mutation_p.Y27D|TAF6_ENST00000472509.1_Missense_Mutation_p.Y141D|TAF6_ENST00000453269.2_Missense_Mutation_p.Y84D|TAF6_ENST00000437822.2_Missense_Mutation_p.Y121D|TAF6_ENST00000497233.1_5'Flank	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	84					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|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)|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)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGGAAGCCATAGAGTGGCTGT	0.607																																					p.Y121D		Atlas-SNP	.											.	TAF6	55	.	0			c.T361G						PASS	.						33.0	35.0	35.0					7																	99711386		2203	4300	6503	SO:0001583	missense	6878	exon4			AGCCATAGAGTGG		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"""TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD"", ""transcription initiation factor TFIID 70 kD subunit"""	602955	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"""	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.250T>G	7.37:g.99711386A>C	ENSP00000344537:p.Tyr84Asp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	8	0.153846	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	37	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758276	0.69763	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822;ENST00000493322;ENST00000440225;ENST00000452438;ENST00000523306;ENST00000449571;ENST00000520135;ENST00000451699	T;T;T;T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.5	4.35	0.52113	Histone-fold (1);	0.057225	0.64402	D	0.000001	T	0.69006	0.3063	M	0.92219	3.285	0.58432	D	0.99999	P;P;P;P;D;P	0.58970	0.865;0.753;0.639;0.491;0.984;0.919	P;P;P;P;P;P	0.58520	0.642;0.71;0.516;0.54;0.84;0.516	T	0.73493	-0.3965	10	0.62326	D	0.03	-2.7986	9.3794	0.38304	0.9156:0.0:0.0844:0.0	.	121;84;74;84;84;27	B4DT11;P49848-2;A4D299;P49848;C9JTY6;B3KUR4	.;.;.;TAF6_HUMAN;.;.	D	84;141;84;84;27;121;84;84;84;74;84;74;84	ENSP00000389575:Y84D;ENSP00000419760:Y141D;ENSP00000416396:Y84D;ENSP00000344537:Y84D;ENSP00000399982:Y121D;ENSP00000419555:Y84D;ENSP00000410012:Y84D;ENSP00000412346:Y84D;ENSP00000428639:Y74D;ENSP00000390073:Y84D;ENSP00000428071:Y74D;ENSP00000406315:Y84D	ENSP00000344537:Y84D	Y	-	1	0	TAF6	99549322	1.000000	0.71417	0.821000	0.32701	0.907000	0.53573	8.627000	0.90974	0.939000	0.37446	0.456000	0.33151	TAT	.	.	none		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641	
DNHD1	144132	hgsc.bcm.edu	37	11	6561270	6561270	+	Silent	SNP	A	A	G	rs10839577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	69	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	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	
FLG	2312	hgsc.bcm.edu	37	1	152284549	152284549	+	Missense_Mutation	SNP	G	G	C	rs141646551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152284549G>C	ENST00000368799.1	-	3	2848	c.2813C>G	c.(2812-2814)aCa>aGa	p.T938R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	938	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.T938R(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)			GCGCCTGCTTGTCCTGGACCC	0.572									Ichthyosis				-|||	170	0.0339457	0.0	0.0403	5008	,	,		21979	0.0754		0.007	False		,,,				2504	0.0603				p.T938R		Atlas-SNP	.											FLG,rectum,NS,0,1	FLG	900	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2813G						scavenged	.						325.0	297.0	306.0					1																	152284549		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGCTTGTCCTGG	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.2813C>G	1.37:g.152284549G>C	ENSP00000357789:p.Thr938Arg	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	334	22	0.0658683	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	5.712	0.315925	0.10789	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.04083	3.71	3.85	0.458	0.16670	.	.	.	.	.	T	0.01124	0.0037	L	0.38531	1.155	0.09310	N	1	B	0.14805	0.011	B	0.23018	0.043	T	0.48163	-0.9059	9	0.30854	T	0.27	.	2.2232	0.03978	0.119:0.1996:0.4931:0.1882	.	938	P20930	FILA_HUMAN	R	938;145	ENSP00000357789:T938R	ENSP00000357789:T938R	T	-	2	0	FLG	150551173	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.641000	0.02007	0.119000	0.18210	0.473000	0.43528	ACA	G|0.989;C|0.011	0.011	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CARD11	84433	hgsc.bcm.edu	37	7	2983886	2983886	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:2983886T>G	ENST00000396946.4	-	5	1047	c.644A>C	c.(643-645)aAg>aCg	p.K215T	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					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)		CGCCATGTTCTTCTCCTCACT	0.572			Mis		DLBCL																																p.K215T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,colon,carcinoma,-1,6	CARD11	339	6	0			c.A644C						PASS	.						187.0	114.0	139.0					7																	2983886		2203	4300	6503	SO:0001583	missense	84433	exon5			ATGTTCTTCTCCT	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.644A>C	7.37:g.2983886T>G	ENSP00000380150:p.Lys215Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	251	36	0.143426	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705011	0.68615	.	.	ENSG00000198286	ENST00000396946	T	0.37915	1.17	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	L	0.57536	1.79	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	T	0.58836	-0.7566	10	0.66056	D	0.02	-28.1579	13.4982	0.61438	0.0:0.0:0.0:1.0	.	215	Q9BXL7	CAR11_HUMAN	T	215	ENSP00000380150:K215T	ENSP00000380150:K215T	K	-	2	0	CARD11	2950412	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	5.720000	0.68470	1.650000	0.50662	0.459000	0.35465	AAG	.	.	none		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1983782	1983782	+	Silent	SNP	C	C	T	rs758160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000585732.1_Intron|CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000585708.1_Silent_p.P558P|CACNA2D4_ENST00000587995.1_Silent_p.P597P|CACNA2D4_ENST00000588077.1_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	325	0	0		WXS	Illumina HiSeq	Phase_I	278	117	0.420863	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		
SLC25A37	51312	hgsc.bcm.edu	37	8	23423669	23423669	+	Missense_Mutation	SNP	A	A	G	rs2942194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	25	0.409836	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	
THOC1	9984	hgsc.bcm.edu	37	18	264039	264039	+	Silent	SNP	C	C	A	rs376944925		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264039C>A	ENST00000261600.6	-	4	250	c.243G>T	c.(241-243)ggG>ggT	p.G81G	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	81					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CAGTTACTCCCCCAATAGCAA	0.358																																					p.G81G		Atlas-SNP	.											.	THOC1	43	.	0			c.G243T						PASS	.	C		0,3690		0,0,1845	86.0	74.0	78.0		243	4.3	1.0	18		78	5,8171		0,5,4083	no	coding-synonymous	THOC1	NM_005131.2		0,5,5928	AA,AC,CC		0.0612,0.0,0.0421		81/658	264039	5,11861	1845	4088	5933	SO:0001819	synonymous_variant	9984	exon4			TACTCCCCCAATA	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"""THO complex subunits"""	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.243G>T	18.37:g.264039C>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	179	62	0.346369	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.358	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131	
ZNF536	9745	hgsc.bcm.edu	37	19	31039256	31039256	+	Silent	SNP	C	C	T	rs111707808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039256C>T	ENST00000355537.3	+	4	2877	c.2730C>T	c.(2728-2730)aaC>aaT	p.N910N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	910					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TTGTGAGCAACGGTGTGAATT	0.498													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		21120	0.005		0.0338	False		,,,				2504	0.135				p.N910N		Atlas-SNP	.											ZNF536,colon,carcinoma,+1,1	ZNF536	424	1	0			c.C2730T						scavenged	.	C		161,4245	108.6+/-147.0	2,157,2044	178.0	183.0	181.0		2730	-0.6	1.0	19	dbSNP_132	181	287,8313	106.8+/-167.6	5,277,4018	no	coding-synonymous	ZNF536	NM_014717.1		7,434,6062	TT,TC,CC		3.3372,3.6541,3.4446		910/1301	31039256	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			GAGCAACGGTGTG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.2730C>T	19.37:g.31039256C>T		Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																			C|0.970;T|0.030	0.030	strong		0.498	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
HSPG2	3339	hgsc.bcm.edu	37	1	22214040	22214040	+	Silent	SNP	G	G	A	rs41310388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22214040G>A	ENST00000374695.3	-	8	910	c.831C>T	c.(829-831)ccC>ccT	p.P277P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	277					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)	p.P277P(1)		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)	TGACGGAACCGGGAAGCAGGG	0.647													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		14680	0.0		0.0179	False		,,,				2504	0.0082				p.P277P		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	1	Substitution - coding silent(1)	prostate(1)	c.C831T						PASS	.	G		14,4392	20.2+/-43.8	0,14,2189	81.0	99.0	93.0		831	-4.3	0.0	1	dbSNP_127	93	138,8462	66.7+/-129.0	1,136,4163	no	coding-synonymous	HSPG2	NM_005529.5		1,150,6352	AA,AG,GG		1.6047,0.3177,1.1687		277/4392	22214040	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon8			GGAACCGGGAAGC	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.831C>T	1.37:g.22214040G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	16.74	3.206474	0.58343	0.003177	0.016047	ENSG00000142798	ENST00000412328;ENST00000374673	T;D	0.92249	0.51;-3.0	4.62	-4.32	0.03688	.	0.000000	0.37623	N	0.002018	T	0.72503	0.3468	.	.	.	0.49915	D	0.999833	B	0.20780	0.048	B	0.17098	0.017	T	0.55805	-0.8083	9	0.27785	T	0.31	.	7.5881	0.28004	0.6013:0.1275:0.2712:0.0	rs41310388	200	Q5SZI5	.	L	200;104	ENSP00000405412:P200L;ENSP00000363805:P104L	ENSP00000363805:P104L	P	-	2	0	HSPG2	22086627	0.011000	0.17503	0.000000	0.03702	0.013000	0.08279	-0.065000	0.11617	-1.198000	0.02669	-0.379000	0.06801	CCG	G|0.989;A|0.011	0.011	strong		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SPATA3	130560	hgsc.bcm.edu	37	2	231861056	231861056	+	Silent	SNP	A	A	C	rs72362780		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231861056A>C	ENST00000452881.1	+	1	216	c.108A>C	c.(106-108)acA>acC	p.T36T	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Silent_p.T36T|SPATA3_ENST00000455816.1_Silent_p.T36T|SPATA3_ENST00000424440.1_Silent_p.T36T			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	36										endometrium(2)|lung(1)	3						CTGAATCCACACCACAGCAGC	0.577																																					p.T36T		Atlas-SNP	.											SPATA3,rectum,carcinoma,0,1	SPATA3	52	1	0			c.A108C						scavenged	.						133.0	139.0	137.0					2																	231861056		692	1591	2283	SO:0001819	synonymous_variant	130560	exon1			ATCCACACCACAG	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.108A>C	2.37:g.231861056A>C		Somatic	67	4	0.0597015		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_139073	Q86WX5|Q8N9Y6	Silent	SNP	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	none		0.577	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
RECQL5	9400	hgsc.bcm.edu	37	17	73627539	73627539	+	Missense_Mutation	SNP	T	T	C	rs820196	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73627539T>C	ENST00000317905.5	-	9	1598	c.1439A>G	c.(1438-1440)gAc>gGc	p.D480G	RECQL5_ENST00000423245.2_Missense_Mutation_p.D453G|RECQL5_ENST00000443199.2_5'UTR|SMIM5_ENST00000375215.3_5'Flank	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	480			D -> G (in dbSNP:rs820196).		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)			CCTGCTGAAGTCCCCGTAGCC	0.662								Other identified genes with known or suspected DNA repair function					C|||	1331	0.265775	0.1936	0.3112	5008	,	,		17901	0.2758		0.2445	False		,,,				2504	0.3425				p.D480G		Atlas-SNP	.											.	RECQL5	77	.	0			c.A1439G						PASS	.	C	GLY/ASP	677,3399		51,575,1412	49.0	52.0	51.0		1439	6.0	1.0	17	dbSNP_86	51	1829,6547		220,1389,2579	yes	missense	RECQL5	NM_004259.6	94	271,1964,3991	CC,CT,TT		21.8362,16.6094,20.1253	benign	480/992	73627539	2506,9946	2038	4188	6226	SO:0001583	missense	9400	exon9			CTGAAGTCCCCGT	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.1439A>G	17.37:g.73627539T>C	ENSP00000317636:p.Asp480Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	175	82	0.468571	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	37	CCDS42380.1	557	0.25503663003663	96	0.1951219512195122	99	0.27348066298342544	176	0.3076923076923077	186	0.24538258575197888	C	16.45	3.125715	0.56721	0.166094	0.218362	ENSG00000108469	ENST00000443199;ENST00000423245;ENST00000317905	T	0.56275	0.47	5.97	5.97	0.96955	.	0.119814	0.56097	N	0.000031	T	0.00012	0.0000	N	0.00566	-1.37	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23511	-1.0186	9	0.15952	T	0.53	-13.5569	12.407	0.55445	0.0:0.8655:0.0:0.1345	rs820196;rs1661738;rs61587854;rs820196	480;453	O94762;Q6P4G0	RECQ5_HUMAN;.	G	75;480;480	ENSP00000317636:D480G	ENSP00000317636:D480G	D	-	2	0	RECQL5	71139134	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	2.326000	0.43849	1.555000	0.49500	-0.119000	0.15052	GAC	T|0.746;C|0.254	0.254	strong		0.662	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
ABCA12	26154	hgsc.bcm.edu	37	2	215851303	215851303	+	Silent	SNP	A	A	G	rs34351934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:215851303A>G	ENST00000272895.7	-	28	4345	c.4126T>C	c.(4126-4128)Ttg>Ctg	p.L1376L	ABCA12_ENST00000389661.4_Silent_p.L1058L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1376	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		GGCCCCAGCAATGAAGTAATA	0.408													A|||	1037	0.207069	0.4312	0.255	5008	,	,		15281	0.0407		0.0924	False		,,,				2504	0.1595				p.L1376L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,+2,1	ABCA12	368	1	0			c.T4126C						PASS	.	A	,	1664,2742	506.9+/-366.5	316,1032,855	71.0	68.0	69.0		3172,4126	2.1	1.0	2	dbSNP_126	69	871,7729	197.6+/-242.2	47,777,3476	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	363,1809,4331	GG,GA,AA		10.1279,37.7667,19.491	,	1058/2278,1376/2596	215851303	2535,10471	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon28			CCAGCAATGAAGT	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.4126T>C	2.37:g.215851303A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			A|0.807;G|0.193	0.193	strong		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
OR51F1	256892	hgsc.bcm.edu	37	11	4791111	4791111	+	Missense_Mutation	SNP	T	T	C	rs17324812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4791111T>C	ENST00000380383.1	-	1	57	c.58A>G	c.(58-60)Acc>Gcc	p.T20A	OR51F1_ENST00000343430.3_Missense_Mutation_p.T13A|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	20			T -> A (in dbSNP:rs17324812).			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(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		AACAAGAAGGTTGGAAATTTA	0.448													T|||	681	0.135982	0.0091	0.1427	5008	,	,		20080	0.0635		0.2485	False		,,,				2504	0.2618				p.T13A		Atlas-SNP	.											.	OR51F1	60	.	0			c.A37G						PASS	.	T	ALA/THR	213,4189		4,205,1992	40.0	44.0	43.0		37	0.8	0.9	11	dbSNP_123	43	2311,6285		308,1695,2295	yes	missense	OR51F1	NM_001004752.1	58	312,1900,4287	CC,CT,TT		26.8846,4.8387,19.4184	benign	13/313	4791111	2524,10474	2201	4298	6499	SO:0001583	missense	256892	exon1			AGAAGGTTGGAAA	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"""GPCR / Class A : Olfactory receptors"""	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.58A>G	11.37:g.4791111T>C	ENSP00000369744:p.Thr20Ala	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	140	82	0.585714	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		284	0.13003663003663005	10	0.02032520325203252	56	0.15469613259668508	38	0.06643356643356643	180	0.23746701846965698	T	11.72	1.721629	0.30503	0.048387	0.268846	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00325	8.1;8.1	4.81	0.84	0.18912	.	0.270733	0.25848	N	0.027919	T	0.00012	0.0000	M	0.73372	2.23	0.45318	P	0.0016880000000000228	B	0.12013	0.005	B	0.11329	0.006	T	0.41342	-0.9514	9	0.39692	T	0.17	.	4.146	0.10215	0.1493:0.1733:0.0:0.6774	rs17324812;rs52822566;rs59975624;rs17324812	20	A6NGY5	O51F1_HUMAN	A	13;20	ENSP00000345163:T13A;ENSP00000369744:T20A	ENSP00000345163:T13A	T	-	1	0	OR51F1	4747687	0.000000	0.05858	0.888000	0.34837	0.934000	0.57294	-0.930000	0.03972	0.316000	0.23135	0.477000	0.44152	ACC	T|0.834;C|0.166	0.166	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
LAMA3	3909	hgsc.bcm.edu	37	18	21496533	21496533	+	Silent	SNP	C	C	T	rs61751706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21496533C>T	ENST00000313654.9	+	60	8038	c.7797C>T	c.(7795-7797)gaC>gaT	p.D2599D	LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000399516.3_Silent_p.D2543D|LAMA3_ENST00000587184.1_Silent_p.D934D|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2599	Laminin G-like 2. {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)					AAGAGTCAGACAAAAATTATT	0.423													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18308	0.0		0.004	False		,,,				2504	0.0				p.D2599D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7797T						PASS	.	C	,,,	5,4401	9.9+/-24.2	0,5,2198	161.0	149.0	153.0		2970,7629,2802,7797	5.2	1.0	18	dbSNP_129	153	60,8540	37.8+/-93.5	1,58,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	1,63,6439	TT,TC,CC		0.6977,0.1135,0.4998	,,,	990/1725,2543/3278,934/1669,2599/3334	21496533	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon60			GTCAGACAAAAAT	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.7797C>T	18.37:g.21496533C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
L1TD1	54596	hgsc.bcm.edu	37	1	62676612	62676612	+	Silent	SNP	A	A	G	rs66958136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62676612A>G	ENST00000498273.1	+	4	2461	c.2166A>G	c.(2164-2166)aaA>aaG	p.K722K	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	722								p.K722K(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						acataattaaagaaataattg	0.358													G|||	792	0.158147	0.0825	0.3199	5008	,	,		20205	0.0704		0.2922	False		,,,				2504	0.0982				p.K722K		Atlas-SNP	.											L1TD1,NS,carcinoma,0,2	L1TD1	114	2	2	Substitution - coding silent(2)	ovary(1)|stomach(1)	c.A2166G						PASS	.	G	,	314,2912		19,276,1318	36.0	38.0	37.0		2166,2166	-4.0	0.0	1	dbSNP_130	37	1482,4316		190,1102,1607	no	coding-synonymous,coding-synonymous	L1TD1	NM_001164835.1,NM_019079.4	,	209,1378,2925	GG,GA,AA		25.5605,9.7334,19.9025	,	722/866,722/866	62676612	1796,7228	1613	2899	4512	SO:0001819	synonymous_variant	54596	exon5			AATTAAAGAAATA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.2166A>G	1.37:g.62676612A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	220	215	0.977273	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			A|0.804;G|0.196	0.196	strong		0.358	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
GSG2	83903	hgsc.bcm.edu	37	17	3628759	3628759	+	Missense_Mutation	SNP	A	A	G	rs146480185		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3628759A>G	ENST00000325418.4	+	1	1549	c.1530A>G	c.(1528-1530)atA>atG	p.I510M	ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	510	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CCGTAGCCATAAAAATCATTG	0.443																																					p.I510M		Atlas-SNP	.											.	GSG2	48	.	0			c.A1530G						PASS	.	A	,MET/ILE	0,4406		0,0,2203	68.0	66.0	67.0		,1530	2.6	1.0	17	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,10	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,benign	,510/799	3628759	1,13005	2203	4300	6503	SO:0001583	missense	83903	exon1			AGCCATAAAAATC	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.1530A>G	17.37:g.3628759A>G	ENSP00000325290:p.Ile510Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	A	9.753	1.167938	0.21621	0.0	1.16E-4	ENSG00000177602	ENST00000325418	T	0.68624	-0.34	4.87	2.62	0.31277	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.249150	0.20240	N	0.096308	T	0.56202	0.1969	L	0.33093	0.98	0.30357	N	0.784223	B	0.13145	0.007	B	0.31946	0.138	T	0.57625	-0.7779	10	0.87932	D	0	-37.732	7.5752	0.27931	0.8258:0.0:0.1742:0.0	.	510	Q8TF76	HASP_HUMAN	M	510	ENSP00000325290:I510M	ENSP00000325290:I510M	I	+	3	3	GSG2	3575508	1.000000	0.71417	0.997000	0.53966	0.594000	0.36715	0.746000	0.26275	0.420000	0.25954	0.533000	0.62120	ATA	A|1.000;G|0.000	0.000	weak		0.443	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854479	12854479	+	Missense_Mutation	SNP	C	C	G	rs1063775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12854479C>G	ENST00000332296.7	+	3	806	c.703C>G	c.(703-705)Cgc>Ggc	p.R235G	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	235					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)		GAAGAATCTTCGCAAACTCGT	0.438													c|||	502	0.10024	0.115	0.0519	5008	,	,		29731	0.0685		0.0785	False		,,,				2504	0.1697				p.R235G		Atlas-SNP	.											PRAMEF1,NS,carcinoma,-1,2	PRAMEF1	78	2	0			c.C703G						scavenged	.						158.0	163.0	161.0					1																	12854479		2203	4300	6503	SO:0001583	missense	65121	exon3			AATCTTCGCAAAC	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.703C>G	1.37:g.12854479C>G	ENSP00000332134:p.Arg235Gly	Somatic	289	18	0.0622837		WXS	Illumina HiSeq	Phase_I	311	63	0.202572	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	6.921	0.539576	0.13250	.	.	ENSG00000116721	ENST00000332296	T	0.21543	2.0	1.61	1.61	0.23674	.	2.269980	0.01911	N	0.039880	T	0.27594	0.0678	M	0.74467	2.265	0.09310	N	0.999992	B	0.09022	0.002	B	0.06405	0.002	T	0.26916	-1.0089	10	0.39692	T	0.17	.	6.6557	0.22986	0.0:1.0:0.0:0.0	.	235	O95521	PRAM1_HUMAN	G	235	ENSP00000332134:R235G	ENSP00000332134:R235G	R	+	1	0	PRAMEF1	12777066	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.124000	0.10595	1.196000	0.43129	0.436000	0.28706	CGC	C|0.811;G|0.187;T|0.002	0.187	strong		0.438	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
IL15RA	3601	hgsc.bcm.edu	37	10	6002368	6002368	+	Missense_Mutation	SNP	T	T	G	rs2228059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:6002368T>G	ENST00000379977.3	-	4	642	c.545A>C	c.(544-546)aAc>aCc	p.N182T	IL15RA_ENST00000397248.2_Missense_Mutation_p.N146T|IL15RA_ENST00000397255.3_Missense_Mutation_p.N182T|IL15RA_ENST00000379971.1_Missense_Mutation_p.N84T|IL15RA_ENST00000397250.2_Missense_Mutation_p.N84T|IL15RA_ENST00000530685.1_Missense_Mutation_p.N149T|IL15RA_ENST00000397251.3_Missense_Mutation_p.N117T|IL15RA_ENST00000534292.1_5'UTR|IL15RA_ENST00000525219.2_Missense_Mutation_p.N146T|IL15RA_ENST00000528354.1_Missense_Mutation_p.N149T			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	182			N -> T (in dbSNP:rs2228059). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8530383, ECO:0000269|Ref.3}.		cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						GAGTTCCCAGTTCTTGGCTGT	0.582													G|||	2757	0.550519	0.7549	0.4928	5008	,	,		17662	0.4266		0.4632	False		,,,				2504	0.5327				p.N268T		Atlas-SNP	.											.	IL15RA	17	.	0			c.A803C						PASS	.	G	THR/ASN,THR/ASN	3167,1239	427.4+/-341.5	1138,891,174	150.0	150.0	150.0		545,446	1.1	0.0	10	dbSNP_98	150	4202,4398	585.2+/-391.8	1030,2142,1128	yes	missense,missense	IL15RA	NM_002189.3,NM_172200.2	65,65	2168,3033,1302	GG,GT,TT		48.8605,28.1207,43.3415	benign,benign	182/268,149/235	6002368	7369,5637	2203	4300	6503	SO:0001583	missense	3601	exon5			TCCCAGTTCTTGG	U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"""Interleukins and interleukin receptors"", ""CD molecules"""	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.545A>C	10.37:g.6002368T>G	ENSP00000369312:p.Asn182Thr	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_001256765	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Missense_Mutation	SNP	ENST00000379977.3	37	CCDS7074.1	1131|1131	0.5178571428571429|0.5178571428571429	350|350	0.7113821138211383|0.7113821138211383	180|180	0.4972375690607735|0.4972375690607735	243|243	0.42482517482517484|0.42482517482517484	358|358	0.47229551451187335|0.47229551451187335	G|G	0.003|0.003	-2.573351|-2.573351	0.00131|0.00131	0.718793|0.718793	0.488605|0.488605	ENSG00000134470|ENSG00000134470	ENST00000397246;ENST00000397251;ENST00000379977;ENST00000397248;ENST00000319465;ENST00000528354;ENST00000397250;ENST00000379971;ENST00000530685;ENST00000397255;ENST00000525219;ENST00000429135;ENST00000453922|ENST00000435171;ENST00000447291;ENST00000532039	T;T;T;T;T;T;T;T;T;T|.	0.38722|.	1.58;1.58;1.58;1.58;1.58;1.12;2.11;1.58;2.34;1.58|.	4.08|4.08	1.13|1.13	0.20643|0.20643	.|.	0.846228|.	0.10233|.	N|.	0.699439|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00583|0.00583	-1.355|-1.355	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.0;0.0;0.001|.	T|T	0.29336|0.29336	-1.0015|-1.0015	9|4	0.02654|.	T|.	1|.	-5.1834|-5.1834	3.5341|3.5341	0.07788|0.07788	0.1957:0.0:0.4597:0.3446|0.1957:0.0:0.4597:0.3446	rs2228059;rs3136617;rs17320992;rs17846697;rs17859798;rs52796202;rs61551851;rs2228059|rs2228059;rs3136617;rs17320992;rs17846697;rs17859798;rs52796202;rs61551851;rs2228059	149;182;146|.	Q13261-3;Q13261;E7ETI1|.	.;I15RA_HUMAN;.|.	T|P	146;117;182;146;146;149;84;84;149;182;117;149;145|58;85;87	ENSP00000380423:N117T;ENSP00000369312:N182T;ENSP00000380421:N146T;ENSP00000435454:N149T;ENSP00000380422:N84T;ENSP00000369306:N84T;ENSP00000435995:N149T;ENSP00000380426:N182T;ENSP00000395113:N149T;ENSP00000405107:N145T|.	ENSP00000322245:N146T|.	N|T	-|-	2|1	0|0	IL15RA|IL15RA	6042374|6042374	0.009000|0.009000	0.17119|0.17119	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.097000|0.097000	0.15168|0.15168	-0.084000|-0.084000	0.12595|0.12595	-0.217000|-0.217000	0.12591|0.12591	AAC|ACT	T|0.460;G|0.540	0.540	strong		0.582	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189	
RPL7A	6130	hgsc.bcm.edu	37	9	136216882	136216882	+	Silent	SNP	G	G	A	rs7700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136216882G>A	ENST00000323345.6	+	4	420	c.390G>A	c.(388-390)acG>acA	p.T130T	SNORD36B_ENST00000363961.1_RNA|RPL7A_ENST00000315731.4_Silent_p.T15T|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000371999.1_5'Flank|MED22_ENST00000471524.1_5'Flank|SNORD24_ENST00000383884.1_RNA|RPL7A_ENST00000463740.1_3'UTR|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000491289.1_5'Flank|SNORD36A_ENST00000362874.1_RNA|SURF1_ENST00000495952.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	130					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)|ribosome biogenesis (GO:0042254)|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)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		ACGTCCCAACGAAGAGACCAC	0.557													G|||	153	0.0305511	0.003	0.0389	5008	,	,		19124	0.0198		0.0795	False		,,,				2504	0.0225				p.T130T		Atlas-SNP	.											.	RPL7A	9	.	0			c.G390A						PASS	.	G		75,4331	66.4+/-103.9	1,73,2129	58.0	63.0	61.0		390	-8.4	0.8	9	dbSNP_52	61	706,7894	171.4+/-222.4	32,642,3626	no	coding-synonymous	RPL7A	NM_000972.2		33,715,5755	AA,AG,GG		8.2093,1.7022,6.0049		130/267	136216882	781,12225	2203	4300	6503	SO:0001819	synonymous_variant	6130	exon4			CCCAACGAAGAGA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"""L ribosomal proteins"""	10364	protein-coding gene	gene with protein product	"""surfeit 3"", ""PLA-X polypeptide"", ""surfeit locus protein 3"", ""60S ribosomal protein L7a"", "";"", ""thyroid hormone receptor uncoupling protein"""	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.390G>A	9.37:g.136216882G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_000972	P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	37	CCDS6965.1																																																																																			G|0.942;A|0.058	0.058	strong		0.557	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	
HLX	3142	hgsc.bcm.edu	37	1	221057739	221057739	+	Missense_Mutation	SNP	C	C	G	rs11578466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:221057739C>G	ENST00000366903.6	+	4	2661	c.1160C>G	c.(1159-1161)gCc>gGc	p.A387G	HLX_ENST00000549319.1_Missense_Mutation_p.A173G	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	387	Ser-rich.		A -> G (in dbSNP:rs11578466).		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)		CTGGACATGGCCCCCAGCGAC	0.652													C|||	374	0.0746805	0.0719	0.1066	5008	,	,		15491	0.001		0.162	False		,,,				2504	0.0419				p.A387G		Atlas-SNP	.											.	HLX	67	.	0			c.C1160G						PASS	.	C	GLY/ALA	351,4055	169.4+/-200.1	11,329,1863	58.0	52.0	54.0		1160	3.2	1.0	1	dbSNP_120	54	1287,7313	245.7+/-274.4	100,1087,3113	yes	missense	HLX	NM_021958.3	60	111,1416,4976	GG,GC,CC		14.9651,7.9664,12.5942	possibly-damaging	387/489	221057739	1638,11368	2203	4300	6503	SO:0001583	missense	3142	exon4			ACATGGCCCCCAG	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.1160C>G	1.37:g.221057739C>G	ENSP00000355870:p.Ala387Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	86	0.573333	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	214	0.09798534798534798	46	0.09349593495934959	43	0.11878453038674033	0	0.0	125	0.16490765171503957	C	17.06	3.292686	0.59976	0.079664	0.149651	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;T;T	0.90676	-2.71;0.61;0.61	5.03	3.16	0.36331	.	0.487636	0.18752	N	0.132160	T	0.01061	0.0035	N	0.12746	0.255	0.30258	P	0.79347	B	0.15141	0.012	B	0.18263	0.021	T	0.39941	-0.9589	9	0.35671	T	0.21	-14.8358	8.3626	0.32367	0.0:0.7502:0.0:0.2498	rs11578466;rs11578466	387	Q14774	HLX_HUMAN	G	387;120;173	ENSP00000355870:A387G;ENSP00000408248:A120G;ENSP00000449882:A173G	ENSP00000355870:A387G	A	+	2	0	HLX	219124362	0.747000	0.28283	1.000000	0.80357	0.933000	0.57130	1.083000	0.30815	0.642000	0.30620	0.561000	0.74099	GCC	C|0.877;G|0.123	0.123	strong		0.652	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
HLA-A	3105	hgsc.bcm.edu	37	6	29912147	29912147	+	Silent	SNP	C	C	T	rs1059686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29912147C>T	ENST00000396634.1	+	6	1209	c.868C>T	c.(868-870)Ctg>Ttg	p.L290L	HLA-A_ENST00000376806.5_Silent_p.L290L|HLA-A_ENST00000376809.5_Silent_p.L290L|HLA-A_ENST00000376802.2_Silent_p.L290L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	290	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCATGAGGGTCTGCCCAAGCC	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.L290L		Atlas-SNP	.											.	HLA-A	89	.	0			c.C868T						PASS	.	C		786,2236		78,630,803	67.0	59.0	62.0		868	3.7	1.0	6	dbSNP_86	62	1703,3715		244,1215,1250	no	coding-synonymous	HLA-A	NM_002116.7		322,1845,2053	TT,TC,CC		31.4323,26.0093,29.4905		290/366	29912147	2489,5951	1511	2709	4220	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGGGTCTGCCCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.868C>T	6.37:g.29912147C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	113	43	0.380531	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.711;T|0.289	0.289	strong		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PLK2	10769	hgsc.bcm.edu	37	5	57755703	57755703	+	Silent	SNP	C	C	T	rs3211270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	96	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	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	
TMEM91	641649	hgsc.bcm.edu	37	19	41889748	41889748	+	Silent	SNP	T	T	C	rs12602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41889748T>C	ENST00000392002.2	+	4	1149	c.489T>C	c.(487-489)gcT>gcC	p.A163A	TMEM91_ENST00000447302.2_Intron|TMEM91_ENST00000544232.1_Intron|CTC-435M10.3_ENST00000604424.1_Intron|CTC-435M10.3_ENST00000540732.1_Intron|TMEM91_ENST00000436170.2_Intron|TMEM91_ENST00000413014.2_Intron|TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000356385.4_3'UTR|BCKDHA_ENST00000595085.1_Intron|TMEM91_ENST00000542945.1_3'UTR|TMEM91_ENST00000539627.1_3'UTR	NM_001098821.1	NP_001092291.1	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91	163					hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						TGACCCTGGCTGCCTACCTTG	0.697													C|||	3097	0.618411	0.8691	0.4784	5008	,	,		11887	0.4306		0.5924	False		,,,				2504	0.5992				p.A163A		Atlas-SNP	.											.	TMEM91	22	.	0			c.T489C						PASS	.	C	,,,,,	3357,709		1383,591,59	25.0	31.0	29.0		,489,,,,	-4.1	0.9	19	dbSNP_52	29	5133,3231		1588,1957,637	no	utr-3,coding-synonymous,intron,intron,intron,intron	TMEM91	NM_001042595.2,NM_001098821.1,NM_001098822.1,NM_001098823.1,NM_001098824.1,NM_001098825.1	,,,,,	2971,2548,696	CC,CT,TT		38.6298,17.4373,31.6975	,,,,,	,163/173,,,,	41889748	8490,3940	2033	4182	6215	SO:0001819	synonymous_variant	641649	exon4			CCTGGCTGCCTAC	AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16							32393	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 6"""					12477932	Standard	NM_001098824		Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000392002.2:c.489T>C	19.37:g.41889748T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001098821	C9J9D1|C9JZ62|C9K046|Q6P434	Silent	SNP	ENST00000392002.2	37	CCDS42571.1																																																																																			T|0.374;C|0.626	0.626	strong		0.697	TMEM91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398302.2		
FDFT1	2222	hgsc.bcm.edu	37	8	11667253	11667253	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11667253A>G	ENST00000220584.4	+	3	497	c.275A>G	c.(274-276)aAg>aGg	p.K92R	FDFT1_ENST00000528643.1_Missense_Mutation_p.K7R|FDFT1_ENST00000525900.1_Missense_Mutation_p.K85R|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000443614.2_Missense_Mutation_p.K92R|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000528812.1_Missense_Mutation_p.K28R|FDFT1_ENST00000530664.1_Missense_Mutation_p.K28R|FDFT1_ENST00000525777.1_Missense_Mutation_p.K7R	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	92					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)		AGTGTGGAAAAGAAGGTCCCG	0.473																																					p.K92R		Atlas-SNP	.											.	FDFT1	25	.	0			c.A275G						PASS	.						138.0	115.0	123.0					8																	11667253		2203	4300	6503	SO:0001583	missense	2222	exon3			TGGAAAAGAAGGT	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.275A>G	8.37:g.11667253A>G	ENSP00000220584:p.Lys92Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Missense_Mutation	SNP	ENST00000220584.4	37	CCDS5985.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479017	0.26511	.	.	ENSG00000079459	ENST00000530337;ENST00000220584;ENST00000443614;ENST00000525900;ENST00000528812;ENST00000530664;ENST00000528643;ENST00000525777	D;D;D;D;D;D;T;T	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-0.57;-0.57	4.91	-1.99	0.07457	Terpenoid synthase (2);	0.360845	0.31760	N	0.007118	T	0.66436	0.2789	L	0.42245	1.32	0.09310	N	0.999998	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.47100	-0.9143	10	0.25106	T	0.35	-7.7419	0.1655	0.00108	0.2664:0.2386:0.2384:0.2566	.	92;149;85;92	B4DJE5;B4DND3;E9PNM1;P37268	.;.;.;FDFT_HUMAN	R	92;92;92;85;28;28;7;7	ENSP00000431852:K92R;ENSP00000220584:K92R;ENSP00000390367:K92R;ENSP00000434714:K85R;ENSP00000431749:K28R;ENSP00000432331:K28R;ENSP00000431649:K7R;ENSP00000436069:K7R	ENSP00000220584:K92R	K	+	2	0	FDFT1	11704662	0.008000	0.16893	0.000000	0.03702	0.943000	0.58893	0.527000	0.22987	-0.398000	0.07679	0.402000	0.26972	AAG	.	.	none		0.473	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
PSMB1	5689	hgsc.bcm.edu	37	6	170862300	170862300	+	Missense_Mutation	SNP	G	G	C	rs12717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:170862300G>C	ENST00000262193.6	-	1	129	c.31C>G	c.(31-33)Cct>Gct	p.P11A	PSMB1_ENST00000462957.1_5'Flank|TBP_ENST00000392092.2_5'Flank|TBP_ENST00000230354.6_5'Flank|TBP_ENST00000540980.1_5'Flank	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	11			P -> A (in dbSNP:rs12717). {ECO:0000269|PubMed:15489334}.		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)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TCTCTGCCAGGAGCCGAATAC	0.597													G|||	2254	0.45008	0.2708	0.3991	5008	,	,		17181	0.7728		0.4085	False		,,,				2504	0.4387				p.P11A		Atlas-SNP	.											.	PSMB1	12	.	0			c.C31G						PASS	.	G	ALA/PRO	1308,3098	433.1+/-343.5	184,940,1079	42.0	38.0	39.0		31	0.4	0.0	6	dbSNP_52	39	3350,5248	485.3+/-371.6	656,2038,1605	yes	missense	PSMB1	NM_002793.3	27	840,2978,2684	CC,CG,GG		38.9625,29.6868,35.8197	benign	11/242	170862300	4658,8346	2203	4299	6502	SO:0001583	missense	5689	exon1			TGCCAGGAGCCGA	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"""Proteasome (prosome, macropain) subunits"""	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.31C>G	6.37:g.170862300G>C	ENSP00000262193:p.Pro11Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_002793	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	37	CCDS34577.1	1049	0.4803113553113553	143	0.29065040650406504	152	0.4198895027624309	450	0.7867132867132867	304	0.40105540897097625	G	10.34	1.324311	0.24080	0.296868	0.389625	ENSG00000008018	ENST00000262193;ENST00000392093	T	0.24538	1.85	4.37	0.413	0.16401	.	1.016080	0.07851	N	0.964623	T	0.04227	0.0117	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42498	-0.9448	9	0.25751	T	0.34	0.0024	6.0254	0.19652	0.1757:0.2916:0.5328:0.0	rs12717;rs1049686;rs3189890;rs17354871;rs17655245;rs17849329;rs17860781;rs52804979;rs60717301;rs12717	11	P20618	PSB1_HUMAN	A	11;16	ENSP00000262193:P11A	ENSP00000262193:P11A	P	-	1	0	PSMB1	170704225	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	0.024000	0.13555	-0.128000	0.11641	0.563000	0.77884	CCT	G|0.580;C|0.420	0.420	strong		0.597	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793	
OPN3	23596	hgsc.bcm.edu	37	1	241755348	241755348	+	IGR	SNP	C	C	T	rs1053230	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:241755348C>T	ENST00000366554.2	-	0	2620				KMO_ENST00000366558.3_Missense_Mutation_p.R439C|KMO_ENST00000366557.4_Missense_Mutation_p.R418C|OPN3_ENST00000469376.1_5'Flank|KMO_ENST00000366559.4_Missense_Mutation_p.R452C	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3						detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			ATCTTTCCTCCGCTTGAGAAG	0.448													C|||	582	0.116214	0.0091	0.1282	5008	,	,		19206	0.0526		0.2237	False		,,,				2504	0.2076				p.R452C		Atlas-SNP	.											KMO,NS,adenoma,0,1	KMO	69	1	0			c.C1354T						PASS	.	C	CYS/ARG	192,4214	121.3+/-158.8	2,188,2013	174.0	148.0	157.0		1354	0.3	0.0	1	dbSNP_86	157	1945,6655	343.5+/-324.9	212,1521,2567	yes	missense	KMO	NM_003679.3	180	214,1709,4580	TT,TC,CC		22.6163,4.3577,16.4309	benign	452/487	241755348	2137,10869	2203	4300	6503	SO:0001628	intergenic_variant	8564	exon15			TTCCTCCGCTTGA	AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"""GPCR / Class A : Opsin receptors"""	14007	protein-coding gene	gene with protein product	"""panopsin"", ""protein phosphatase 1, regulatory subunit 116"""	606695	"""encephalopsin"""	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691		1.37:g.241755348C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_003679	Q8IX08|Q9Y344	Missense_Mutation	SNP	ENST00000366554.2	37	CCDS31072.1	271|271	0.12408424908424909|0.12408424908424909	5|5	0.01016260162601626|0.01016260162601626	55|55	0.15193370165745856|0.15193370165745856	37|37	0.06468531468531469|0.06468531468531469	174|174	0.22955145118733508|0.22955145118733508	C|C	4.393|4.393	0.072607|0.072607	0.08436|0.08436	0.043577|0.043577	0.226163|0.226163	ENSG00000117009|ENSG00000117009	ENST00000366555|ENST00000366559;ENST00000366558;ENST00000366557	.|T;T;T	.|0.44482	.|0.92;0.92;0.95	5.4|5.4	0.337|0.337	0.15966|0.15966	.|.	.|1.582250	.|0.02739	.|N	.|0.116117	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.12372|0.12372	-1.0550|-1.0550	4|9	.|0.38643	.|T	.|0.18	.|.	7.3222|7.3222	0.26533|0.26533	0.0:0.3956:0.0:0.6044|0.0:0.3956:0.0:0.6044	rs1053230;rs58727153;rs1053230|rs1053230;rs58727153;rs1053230	.|452	.|O15229	.|KMO_HUMAN	L|C	137|452;439;418	.|ENSP00000355517:R452C;ENSP00000355516:R439C;ENSP00000355515:R418C	.|ENSP00000355515:R418C	P|R	+|+	2|1	0|0	KMO|KMO	239821971|239821971	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.265000|0.265000	0.18515|0.18515	0.139000|0.139000	0.18822|0.18822	-0.247000|-0.247000	0.11927|0.11927	CCG|CGC	C|0.853;T|0.147	0.147	strong		0.448	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322	
TRMT1	55621	hgsc.bcm.edu	37	19	13218417	13218417	+	Silent	SNP	T	T	C	rs148858467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13218417T>C	ENST00000592062.1	-	15	2124	c.1554A>G	c.(1552-1554)ccA>ccG	p.P518P	TRMT1_ENST00000357720.4_Silent_p.P518P|TRMT1_ENST00000221504.8_Silent_p.P489P|TRMT1_ENST00000437766.1_Silent_p.P518P			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	518							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		TGCGGAACGCTGGGCTAGTCT	0.592													T|||	9	0.00179712	0.0	0.0043	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.0				p.P518P		Atlas-SNP	.											.	TRMT1	31	.	0			c.A1554G						PASS	.	T	,,	4,4402	8.1+/-20.4	0,4,2199	64.0	39.0	48.0		1554,1467,1554	-8.0	0.0	19	dbSNP_134	48	75,8523	41.2+/-98.3	0,75,4224	no	coding-synonymous,coding-synonymous,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,79,6423	CC,CT,TT		0.8723,0.0908,0.6075	,,	518/660,489/631,518/660	13218417	79,12925	2203	4299	6502	SO:0001819	synonymous_variant	55621	exon14			GAACGCTGGGCTA	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1554A>G	19.37:g.13218417T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			T|0.995;C|0.005	0.005	strong		0.592	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722	
NKAPL	222698	hgsc.bcm.edu	37	6	28227633	28227633	+	Missense_Mutation	SNP	C	C	T	rs9461446	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:28227633C>T	ENST00000343684.3	+	1	536	c.484C>T	c.(484-486)Cat>Tat	p.H162Y	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	162			H -> Y (in dbSNP:rs9461446).							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						AGAGGTAACGCATCAGAAAAG	0.453													C|||	368	0.0734824	0.0613	0.0793	5008	,	,		18791	0.122		0.0308	False		,,,				2504	0.0798				p.H162Y		Atlas-SNP	.											.	NKAPL	72	.	0			c.C484T						PASS	.	C	TYR/HIS	217,4189	127.0+/-164.0	9,199,1995	69.0	77.0	74.0		484	-1.6	0.0	6	dbSNP_119	74	374,8226	120.6+/-179.8	8,358,3934	yes	missense	NKAPL	NM_001007531.1	83	17,557,5929	TT,TC,CC		4.3488,4.9251,4.5441	benign	162/403	28227633	591,12415	2203	4300	6503	SO:0001583	missense	222698	exon1			GTAACGCATCAGA	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.484C>T	6.37:g.28227633C>T	ENSP00000345716:p.His162Tyr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	148	0.06776556776556776	27	0.054878048780487805	26	0.0718232044198895	74	0.12937062937062938	21	0.027704485488126648	C	2.959	-0.215066	0.06101	0.049251	0.043488	ENSG00000189134	ENST00000343684	T	0.13538	2.58	4.77	-1.61	0.08399	.	1.858370	0.02915	N	0.137246	T	0.02119	0.0066	N	0.22421	0.69	0.80722	P	0.0	B	0.32829	0.386	B	0.25759	0.063	T	0.37079	-0.9721	9	0.24483	T	0.36	-0.4569	4.6059	0.12378	0.357:0.3546:0.2884:0.0	rs9461446;rs52789464;rs59183411;rs9461446	162	Q5M9Q1	NKAPL_HUMAN	Y	162	ENSP00000345716:H162Y	ENSP00000345716:H162Y	H	+	1	0	NKAPL	28335612	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.220000	0.17660	-0.127000	0.11661	-0.262000	0.10625	CAT	C|0.941;T|0.059	0.059	strong		0.453	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
PAK2	5062	hgsc.bcm.edu	37	3	196529902	196529902	+	Missense_Mutation	SNP	G	G	C	rs201465227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196529902G>C	ENST00000327134.3	+	4	625	c.303G>C	c.(301-303)caG>caC	p.Q101H		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	101	Autoregulatory region. {ECO:0000250}.|GTPase-binding. {ECO:0000250}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGCCAGAACAGTGGGCTCGAT	0.373																																					p.Q101H		Atlas-SNP	.											PAK2_ENST00000327134,colon,carcinoma,0,4	PAK2	113	4	0			c.G303C						scavenged	.						82.0	72.0	76.0					3																	196529902		2203	4300	6503	SO:0001583	missense	5062	exon4			AGAACAGTGGGCT	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.303G>C	3.37:g.196529902G>C	ENSP00000314067:p.Gln101His	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	166	12	0.0722892	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480973	0.63849	.	.	ENSG00000180370	ENST00000327134	D	0.86366	-2.11	5.51	1.7	0.24286	PAK-box/P21-Rho-binding (2);	0.000000	0.85682	D	0.000000	D	0.92283	0.7552	M	0.91090	3.175	0.52099	D	0.999949	D	0.60160	0.987	P	0.61275	0.886	D	0.90843	0.4725	10	0.72032	D	0.01	.	6.8738	0.24135	0.4882:0.0:0.5118:0.0	.	101	Q13177	PAK2_HUMAN	H	101	ENSP00000314067:Q101H	ENSP00000314067:Q101H	Q	+	3	2	PAK2	198014299	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.826000	0.27407	0.705000	0.31890	-0.253000	0.11424	CAG	G|0.914;C|0.086	0.086	strong		0.373	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
PPP1R12B	4660	hgsc.bcm.edu	37	1	202411697	202411697	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202411697A>G	ENST00000608999.1	+	12	1817	c.1664A>G	c.(1663-1665)aAa>aGa	p.K555R	PPP1R12B_ENST00000336894.4_Missense_Mutation_p.K555R|RP11-175B9.2_ENST00000602961.1_RNA	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	555					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			ACTTACTTGAAAAGGTACCAG	0.458																																					p.K555R		Atlas-SNP	.											PPP1R12B,caecum,carcinoma,0,1	PPP1R12B	100	1	0			c.A1664G						scavenged	.						72.0	70.0	70.0					1																	202411697		2203	4300	6503	SO:0001583	missense	4660	exon12			ACTTGAAAAGGTA	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1664A>G	1.37:g.202411697A>G	ENSP00000476755:p.Lys555Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	3	0.0309278	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	37	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	A	13.13	2.144335	0.37825	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	T;T	0.39229	1.09;1.09	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000003	T	0.25938	0.0632	N	0.20328	0.56	0.80722	D	1	B;B	0.13145	0.007;0.007	B;B	0.13407	0.004;0.009	T	0.09952	-1.0651	10	0.02654	T	1	.	14.4598	0.67440	1.0:0.0:0.0:0.0	.	555;555	O60237;F8W8M3	MYPT2_HUMAN;.	R	555	ENSP00000384496:K555R;ENSP00000337897:K555R	ENSP00000337897:K555R	K	+	2	0	PPP1R12B	200678320	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.278000	0.43426	2.154000	0.67381	0.460000	0.39030	AAA	.	.	none		0.458	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	
DEFA4	1669	hgsc.bcm.edu	37	8	6793581	6793581	+	Silent	SNP	A	A	G	rs2738100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:6793581A>G	ENST00000297435.2	-	3	379	c.255T>C	c.(253-255)ggT>ggC	p.G85G		NM_001925.1	NP_001916.1	P12838	DEF4_HUMAN	defensin, alpha 4, corticostatin	85					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	10				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		AACTCACACCACCAATGAGGC	0.517													A|||	2311	0.461462	0.6172	0.2853	5008	,	,		21089	0.4593		0.3648	False		,,,				2504	0.4775				p.G85G		Atlas-SNP	.											.	DEFA4	19	.	0			c.T255C						PASS	.	A		2319,2087		590,1139,474	143.0	124.0	130.0		255	0.2	0.0	8	dbSNP_100	130	3267,5333		620,2027,1653	no	coding-synonymous	DEFA4	NM_001925.1		1210,3166,2127	GG,GA,AA		37.9884,47.3672,42.9494		85/98	6793581	5586,7420	2203	4300	6503	SO:0001819	synonymous_variant	1669	exon3			CACACCACCAATG	X65977	CCDS5961.1	8p23.1	2007-02-20			ENSG00000164821	ENSG00000164821		"""Defensins, alpha"""	2763	protein-coding gene	gene with protein product		601157		DEF4		8469233	Standard	NM_001925		Approved	HP-4	uc003wqu.1	P12838	OTTHUMG00000090382	ENST00000297435.2:c.255T>C	8.37:g.6793581A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001925	Q6EZF8	Silent	SNP	ENST00000297435.2	37	CCDS5961.1																																																																																			G|0.438;A|0.562	0.438	strong		0.517	DEFA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206754.1	NM_001925	
TTN	7273	hgsc.bcm.edu	37	2	179455352	179455352	+	Missense_Mutation	SNP	C	C	T	rs141973925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179455352C>T	ENST00000591111.1	-	254	56401	c.56177G>A	c.(56176-56178)cGg>cAg	p.R18726Q	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R20367Q|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R17799Q|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R11494Q|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R11427Q|TTN_ENST00000460472.2_Missense_Mutation_p.R11302Q|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18726	Fibronectin type-III 35. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q. {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)			TTTGATGGGCCGGCAAGCTTT	0.433													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		22262	0.0		0.003	False		,,,				2504	0.0				p.R20367Q		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+1,5	TTN	18412	5	0			c.G61100A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	5,3765		0,5,1880	109.0	107.0	107.0		33905,53396,34280,34481	6.1	1.0	2	dbSNP_134	107	35,8191		0,35,4078	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	43,43,43,43	0,40,5958	TT,TC,CC		0.4255,0.1326,0.3334	probably-damaging,probably-damaging,probably-damaging,probably-damaging	11302/26927,17799/33424,11427/27052,11494/27119	179455352	40,11956	1885	4113	5998	SO:0001583	missense	7273	exon304			ATGGGCCGGCAAG	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.56177G>A	2.37:g.179455352C>T	ENSP00000465570:p.Arg18726Gln	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	344	179	0.520349	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		3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	15.40	2.821552	0.50633	0.001326	0.004255	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	6.11	6.11	0.99139	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.60818	0.2298	L	0.43923	1.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.992;0.992;0.992;0.992	T	0.59101	-0.7517	9	0.87932	D	0	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	11302;11427;11494;18726	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	17799;11302;11494;11427;11300	ENSP00000343764:R17799Q;ENSP00000434586:R11302Q;ENSP00000340554:R11494Q;ENSP00000352154:R11427Q	ENSP00000340554:R11494Q	R	-	2	0	TTN	179163598	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.976000	0.70484	2.906000	0.99361	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SMCHD1	23347	hgsc.bcm.edu	37	18	2740714	2740714	+	Silent	SNP	A	A	G	rs12327477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	94	36	0.382979	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		
ZNF268	10795	hgsc.bcm.edu	37	12	133778887	133778887	+	Silent	SNP	G	G	A	rs75772856	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133778887G>A	ENST00000536435.2	+	6	945	c.615G>A	c.(613-615)acG>acA	p.T205T	CTD-2140B24.4_ENST00000540096.2_3'UTR|ZNF268_ENST00000228289.5_Silent_p.T205T|ZNF268_ENST00000541211.2_Missense_Mutation_p.R163H|ZNF268_ENST00000537565.1_Silent_p.T44T|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000542711.2_Missense_Mutation_p.R96H|ZNF268_ENST00000416488.1_3'UTR|ZNF268_ENST00000539248.2_Missense_Mutation_p.R131H|ZNF268_ENST00000536899.2_Missense_Mutation_p.R64H|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000592241.1_3'UTR	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	205					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)		AATGTGGCACGCATGGAAAGA	0.338													g|||	48	0.00958466	0.0	0.0072	5008	,	,		21313	0.0		0.0278	False		,,,				2504	0.0153				p.R163H		Atlas-SNP	.											.	ZNF268	71	.	0			c.G488A						PASS	.	G	,,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,,,	9,3651		0,9,1821	67.0	68.0	67.0		615,366,392,191,488,287,,615,	-4.6	0.0	12	dbSNP_132	67	160,7998		1,158,3920	yes	coding-synonymous,coding-synonymous,missense,missense,missense,missense,utr-3,coding-synonymous,utr-3	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	,,29,29,29,29,,,	1,167,5741	AA,AG,GG		1.9613,0.2459,1.43	,,,,,,,,	205/948,122/865,131/136,64/69,163/168,96/101,,205/948,	133778887	169,11649	1830	4079	5909	SO:0001819	synonymous_variant	10795	exon5			TGGCACGCATGGA	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.615G>A	12.37:g.133778887G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	54	18	0.333333	NM_001165885	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	25	0.011446886446886446	0	0.0	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	G	11.82	1.751871	0.31046	0.002459	0.019613	ENSG00000090612	ENST00000536435;ENST00000542711;ENST00000536899	.	.	.	3.79	-4.56	0.03431	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23440	-1.0188	4	.	.	.	.	4.4841	0.11781	0.191:0.0:0.2934:0.5157	.	.	.	.	H	163;96;64	.	.	R	+	2	0	ZNF268	132288960	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.052000	0.03503	-0.961000	0.03609	-0.387000	0.06579	CGC	G|0.988;A|0.012	0.012	strong		0.338	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
MUC4	4585	hgsc.bcm.edu	37	3	195516730	195516730	+	Missense_Mutation	SNP	G	G	A	rs74547899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195516730G>A	ENST00000463781.3	-	2	2180	c.1721C>T	c.(1720-1722)aCt>aTt	p.T574I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T574I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	579					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)		AGCCTCTCCAGTGGTCCCCGT	0.537													g|||	40	0.00798722	0.0008	0.0072	5008	,	,		17776	0.0		0.0308	False		,,,				2504	0.0031				p.T574I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C1721T						PASS	.		,,ILE/THR	24,3974		0,24,1975	314.0	299.0	304.0		,,1721	0.0	0.0	3	dbSNP_132	304	251,8073		3,245,3914	yes	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,89	3,269,5889	AA,AG,GG		3.0154,0.6003,2.2318	,,benign	,,574/5413	195516730	275,12047	1999	4162	6161	SO:0001583	missense	4585	exon2			TCTCCAGTGGTCC	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.1721C>T	3.37:g.195516730G>A	ENSP00000417498:p.Thr574Ile	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	277	165	0.595668	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	29	0.013278388278388278	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	25	0.032981530343007916	-	3.304	-0.142305	0.06669	0.006003	0.030154	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.45668	0.89;0.91	1.99	0.0303	0.14166	.	.	.	.	.	T	0.08223	0.0205	L	0.38175	1.15	0.09310	N	1	B;P	0.35923	0.215;0.528	B;B	0.20955	0.032;0.024	T	0.07654	-1.0761	9	0.48119	T	0.1	.	3.204	0.06659	0.1777:0.282:0.5403:0.0	.	574;579	E7ESK3;Q99102	.;MUC4_HUMAN	I	574;574;548	ENSP00000417498:T574I;ENSP00000420243:T574I	ENSP00000376209:T548I	T	-	2	0	MUC4	197001125	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	0.580000	0.23803	0.002000	0.14630	0.459000	0.35465	ACT	G|0.983;A|0.017	0.017	strong		0.537	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ARHGAP22	58504	hgsc.bcm.edu	37	10	49687800	49687800	+	Silent	SNP	G	G	A	rs4080665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:49687800G>A	ENST00000249601.4	-	4	626	c.330C>T	c.(328-330)gcC>gcT	p.A110A	ARHGAP22_ENST00000417912.2_Silent_p.A110A|ARHGAP22_ENST00000435790.2_Silent_p.A116A|ARHGAP22_ENST00000374172.1_5'UTR|ARHGAP22_ENST00000374170.1_Silent_p.A20A|ARHGAP22_ENST00000417247.2_Silent_p.A20A	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	110	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCCGCTCCCCGGCACCACCTG	0.662													G|||	3953	0.789337	0.4894	0.8761	5008	,	,		17059	0.9425		0.8678	False		,,,				2504	0.8947				p.A116A		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.C348T						PASS	.	G		2434,1968		691,1052,458	16.0	16.0	16.0		330	2.5	1.0	10	dbSNP_108	16	7310,1286		3114,1082,102	no	coding-synonymous	ARHGAP22	NM_021226.2		3805,2134,560	AA,AG,GG		14.9604,44.707,25.0346		110/699	49687800	9744,3254	2201	4298	6499	SO:0001819	synonymous_variant	58504	exon4			CTCCCCGGCACCA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.330C>T	10.37:g.49687800G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001256025	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Silent	SNP	ENST00000249601.4	37	CCDS7227.1																																																																																			G|0.233;A|0.767	0.767	strong		0.662	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166862233	166862233	+	Silent	SNP	T	T	C	rs2230730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000405189.3_Silent_p.T348T|RPS6KA2_ENST00000503859.1_Silent_p.T445T|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						scavenged	.	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	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	136	68	0.5	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	
IL6ST	3572	hgsc.bcm.edu	37	5	55251889	55251889	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:55251889C>T	ENST00000381298.2	-	10	1543	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.A411T|IL6ST_ENST00000381294.3_Missense_Mutation_p.A411T|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000502326.3_Missense_Mutation_p.A411T|IL6ST_ENST00000522633.2_3'UTR	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	411	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)				AAAACAGCTGCATCTGATTTG	0.413			O		hepatocellular ca																																p.A411T		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.G1231A						PASS	.						142.0	131.0	135.0					5																	55251889		2203	4300	6503	SO:0001583	missense	3572	exon10			CAGCTGCATCTGA	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.1231G>A	5.37:g.55251889C>T	ENSP00000370698:p.Ala411Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	1.910	-0.450848	0.04572	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.43688	0.94;0.94;0.94	5.86	0.727	0.18254	Long hematopoietin receptor, Gp130 family 2, conserved site (1);Fibronectin, type III (2);	0.981590	0.08384	N	0.954070	T	0.40956	0.1138	M	0.71036	2.16	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.41251	-0.9519	10	0.56958	D	0.05	.	6.7334	0.23395	0.0:0.3836:0.3238:0.2926	.	411;411;411	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	T	411	ENSP00000370698:A411T;ENSP00000338799:A411T;ENSP00000370694:A411T	ENSP00000338799:A411T	A	-	1	0	IL6ST	55287646	0.007000	0.16637	0.002000	0.10522	0.162000	0.22319	-0.060000	0.11712	0.166000	0.19597	-0.145000	0.13849	GCA	.	.	none		0.413	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
PRRT3	285368	hgsc.bcm.edu	37	3	9991101	9991101	+	Missense_Mutation	SNP	C	C	G	rs55847233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9991101C>G	ENST00000412055.1	-	2	828	c.699G>C	c.(697-699)ttG>ttC	p.L233F	PRRT3-AS1_ENST00000431558.1_RNA|PRRT3_ENST00000411976.2_Missense_Mutation_p.L233F	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	40	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	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	
SRFBP1	153443	hgsc.bcm.edu	37	5	121355961	121355961	+	Silent	SNP	G	G	A	rs55708726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:121355961G>A	ENST00000339397.4	+	6	603	c.531G>A	c.(529-531)gcG>gcA	p.A177A		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AAATATTGGCGAAGAAACCAA	0.343																																					p.A177A		Atlas-SNP	.											.	SRFBP1	47	.	0			c.G531A						PASS	.	G		328,3396		14,300,1548	112.0	103.0	106.0		531	-1.9	0.9	5	dbSNP_129	106	1111,7063		81,949,3057	no	coding-synonymous	SRFBP1	NM_152546.2		95,1249,4605	AA,AG,GG		13.5919,8.8077,12.0945		177/430	121355961	1439,10459	1862	4087	5949	SO:0001819	synonymous_variant	153443	exon6			ATTGGCGAAGAAA	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.531G>A	5.37:g.121355961G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_152546		Silent	SNP	ENST00000339397.4	37	CCDS43354.1																																																																																			G|0.890;A|0.110	0.110	strong		0.343	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152284854A>G	ENST00000368799.1	-	3	2543	c.2508T>C	c.(2506-2508)gaT>gaC	p.D836D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	836	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)			TGTCCTGACCATCTTGGGATG	0.592									Ichthyosis				-|||	2370	0.473243	0.5567	0.4553	5008	,	,		20739	0.6558		0.173	False		,,,				2504	0.4939				p.D836D		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.T2508C						PASS	.	C		2208,2198		542,1124,537	320.0	318.0	319.0		2508	-5.9	0.0	1	dbSNP_103	319	1462,7138		126,1210,2964	no	coding-synonymous	FLG	NM_002016.1		668,2334,3501	GG,GA,AA		17.0,49.8865,28.2177		836/4062	152284854	3670,9336	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCATCTTGG	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.2508T>C	1.37:g.152284854A>G		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	253	145	0.573123	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.687;G|0.313	0.313	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ATM	472	hgsc.bcm.edu	37	11	108163487	108163487	+	Silent	SNP	C	C	T	rs1800889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:108163487C>T	ENST00000452508.2	+	31	4767	c.4578C>T	c.(4576-4578)ccC>ccT	p.P1526P	ATM_ENST00000278616.4_Silent_p.P1526P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1526					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|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)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CACTTATACCCCTTGTGTATG	0.358			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			C|||	77	0.0153754	0.003	0.0288	5008	,	,		18654	0.0		0.0398	False		,,,				2504	0.0133				p.P1526P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.C4578T						PASS	.	C		43,4359	44.6+/-78.6	0,43,2158	197.0	173.0	181.0		4578	-0.5	0.9	11	dbSNP_89	181	438,8158	133.0+/-190.5	21,396,3881	no	coding-synonymous	ATM	NM_000051.3		21,439,6039	TT,TC,CC		5.0954,0.9768,3.7006		1526/3057	108163487	481,12517	2201	4298	6499	SO:0001819	synonymous_variant	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	TATACCCCTTGTG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4578C>T	11.37:g.108163487C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	139	69	0.496403	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																			C|0.972;T|0.028	0.028	strong		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
LRRCC1	85444	hgsc.bcm.edu	37	8	86021994	86021994	+	Missense_Mutation	SNP	G	G	A	rs62525422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:86021994G>A	ENST00000360375.3	+	2	418	c.269G>A	c.(268-270)tGc>tAc	p.C90Y	LRRCC1_ENST00000414626.2_Missense_Mutation_p.C70Y	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	90				C -> Y (in Ref. 1; BAB21855 and 2; BAG63888). {ECO:0000305}.	mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ACAAAACTGTGCACATTAAAT	0.308													G|||	283	0.0565096	0.0083	0.0389	5008	,	,		14924	0.0149		0.0905	False		,,,				2504	0.1421				p.C90Y		Atlas-SNP	.											.	LRRCC1	212	.	0			c.G269A						PASS	.	G	TYR/CYS	73,3603		0,73,1765	60.0	55.0	57.0		269	5.5	1.0	8	dbSNP_129	57	898,7258		42,814,3222	yes	missense	LRRCC1	NM_033402.4	194	42,887,4987	AA,AG,GG		11.0103,1.9859,8.2066	probably-damaging	90/1033	86021994	971,10861	1838	4078	5916	SO:0001583	missense	85444	exon2			AACTGTGCACATT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.269G>A	8.37:g.86021994G>A	ENSP00000353538:p.Cys90Tyr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	140	56	0.4	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	99	0.04532967032967033	4	0.008130081300813009	16	0.04419889502762431	7	0.012237762237762238	72	0.09498680738786279	G	14.18	2.457495	0.43634	0.019859	0.110103	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.09163	3.01;3.01	5.52	5.52	0.82312	.	0.185354	0.26871	N	0.022066	T	0.00210	0.0006	N	0.08118	0	0.33173	P	0.45148299999999997	D;P	0.54964	0.969;0.91	P;P	0.51135	0.66;0.544	T	0.31280	-0.9949	9	0.54805	T	0.06	-0.1137	12.7415	0.57255	0.075:0.0:0.925:0.0	rs62525422	70;90	Q9C099-2;Q9C099	.;LRCC1_HUMAN	Y	90;70	ENSP00000353538:C90Y;ENSP00000394695:C70Y	ENSP00000353538:C90Y	C	+	2	0	LRRCC1	86209246	1.000000	0.71417	0.997000	0.53966	0.186000	0.23388	5.294000	0.65687	2.582000	0.87167	0.591000	0.81541	TGC	G|0.925;A|0.075	0.075	strong		0.308	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
TTC39C	125488	hgsc.bcm.edu	37	18	21662974	21662974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21662974C>T	ENST00000317571.3	+	6	1149	c.913C>T	c.(913-915)Ctt>Ttt	p.L305F	TTC39C_ENST00000304621.6_Missense_Mutation_p.L244F|RP11-403A21.3_ENST00000578443.1_RNA	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	305										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						GGAAATTCTCCTTAAAAAAGA	0.413																																					p.L305F		Atlas-SNP	.											.	TTC39C	83	.	0			c.C913T						PASS	.						135.0	138.0	137.0					18																	21662974		2203	4300	6503	SO:0001583	missense	125488	exon6			ATTCTCCTTAAAA	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.913C>T	18.37:g.21662974C>T	ENSP00000323645:p.Leu305Phe	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	163	34	0.208589	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831199	0.50845	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.76578	-1.03;-1.03	5.7	5.7	0.88788	.	0.377714	0.30556	N	0.009377	T	0.58708	0.2141	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.18263	0.021	T	0.59857	-0.7375	10	0.56958	D	0.05	-23.3579	11.3611	0.49644	0.1316:0.725:0.1435:0.0	.	305	Q8N584	TT39C_HUMAN	F	244;305	ENSP00000306598:L244F;ENSP00000323645:L305F	ENSP00000306598:L244F	L	+	1	0	TTC39C	19916972	0.889000	0.30405	0.998000	0.56505	0.994000	0.84299	1.412000	0.34714	2.681000	0.91329	0.557000	0.71058	CTT	.	.	none		0.413	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
LRP1	4035	hgsc.bcm.edu	37	12	57579390	57579390	+	Silent	SNP	C	C	T	rs149556819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57579390C>T	ENST00000243077.3	+	41	7006	c.6540C>T	c.(6538-6540)tgC>tgT	p.C2180C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2180	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGCGGGCCTGCGCCTGTGCCC	0.672																																					p.C2180C		Atlas-SNP	.											.	LRP1	428	.	0			c.C6540T						PASS	.	C		2,4402	4.2+/-10.8	0,2,2200	31.0	28.0	29.0		6540	-4.2	1.0	12	dbSNP_134	29	0,8594		0,0,4297	no	coding-synonymous	LRP1	NM_002332.2		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		2180/4545	57579390	2,12996	2202	4297	6499	SO:0001819	synonymous_variant	4035	exon41			GGCCTGCGCCTGT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.6540C>T	12.37:g.57579390C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
ZNF516	9658	hgsc.bcm.edu	37	18	74091718	74091718	+	Silent	SNP	G	G	A	rs17059302	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:74091718G>A	ENST00000443185.2	-	4	2669	c.2352C>T	c.(2350-2352)cgC>cgT	p.R784R	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	784					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)		TGCAGCTGACGCGGTGCCAGA	0.587													G|||	867	0.173123	0.2821	0.1369	5008	,	,		18104	0.1825		0.0746	False		,,,				2504	0.1431				p.R784R		Atlas-SNP	.											.	ZNF516	102	.	0			c.C2352T						PASS	.	G		900,3210		108,684,1263	33.0	37.0	36.0		2352	-2.1	0.3	18	dbSNP_123	36	686,7702		35,616,3543	no	coding-synonymous	ZNF516	NM_014643.3		143,1300,4806	AA,AG,GG		8.1784,21.8978,12.69		784/1164	74091718	1586,10912	2055	4194	6249	SO:0001819	synonymous_variant	9658	exon4			GCTGACGCGGTGC	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.2352C>T	18.37:g.74091718G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	73	0.722772	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				G|0.852;A|0.148	0.148	strong		0.587	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
HK3	3101	hgsc.bcm.edu	37	5	176314639	176314639	+	Silent	SNP	G	G	A	rs6875296	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176314639G>A	ENST00000292432.5	-	11	1504	c.1413C>T	c.(1411-1413)gcC>gcT	p.A471A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	471	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGCAGCCACGGCAGTCACCA	0.652													G|||	1518	0.303115	0.0756	0.4294	5008	,	,		15488	0.3929		0.326	False		,,,				2504	0.4049				p.A471A		Atlas-SNP	.											HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	0			c.C1413T						scavenged	.	G		559,3847	239.9+/-250.9	34,491,1678	35.0	33.0	34.0		1413	-8.9	0.0	5	dbSNP_116	34	2929,5669	439.3+/-359.2	506,1917,1876	no	coding-synonymous	HK3	NM_002115.2		540,2408,3554	AA,AG,GG		34.0661,12.6872,26.8225		471/924	176314639	3488,9516	2203	4299	6502	SO:0001819	synonymous_variant	3101	exon11			AGCCACGGCAGTC		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1413C>T	5.37:g.176314639G>A		Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.724;A|0.276	0.276	strong		0.652	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
JAKMIP3	282973	hgsc.bcm.edu	37	10	133918420	133918420	+	Silent	SNP	G	G	A	rs11146177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:133918420G>A	ENST00000298622.4	+	1	246	c.108G>A	c.(106-108)caG>caA	p.Q36Q		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	36						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)		CAGACATCCAGATCGAGCTGC	0.662													G|||	809	0.161542	0.1293	0.1081	5008	,	,		16530	0.2014		0.2008	False		,,,				2504	0.1616				p.Q36Q		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G108A						PASS	.	G		506,3668		31,444,1612	19.0	24.0	23.0		108	2.9	1.0	10	dbSNP_120	23	1569,6871		158,1253,2809	no	coding-synonymous	JAKMIP3	NM_001105521.2		189,1697,4421	AA,AG,GG		18.59,12.1227,16.45		36/845	133918420	2075,10539	2087	4220	6307	SO:0001819	synonymous_variant	282973	exon1			CATCCAGATCGAG	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.108G>A	10.37:g.133918420G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			G|0.837;A|0.163	0.163	strong		0.662	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280471C>G	ENST00000368799.1	-	3	6926	c.6891G>C	c.(6889-6891)gaG>gaC	p.E2297D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2297	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)			GTCTGGAGCTCTCTGCAGAGT	0.547									Ichthyosis																												p.E2297D		Atlas-SNP	.											.	FLG	900	.	0			c.G6891C						PASS	.	C	ASP/GLU	403,4003		10,383,1810	272.0	285.0	281.0		6891	-4.0	0.0	1	dbSNP_131	281	921,7679		0,921,3379	no	missense	FLG	NM_002016.1	45	10,1304,5189	GG,GC,CC		10.7093,9.1466,10.1799	benign	2297/4062	152280471	1324,11682	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGAGCTCTCTGCA	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.6891G>C	1.37:g.152280471C>G	ENSP00000357789:p.Glu2297Asp	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	608	224	0.368421	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	4.465	0.086112	0.08583	0.091466	0.107093	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.00760	5.73	3.12	-3.95	0.04118	.	.	.	.	.	T	0.00109	0.0003	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28073	-1.0055	8	0.02654	T	1	.	8.7493	0.34605	0.1106:0.6338:0.2556:0.0	.	2297	P20930	FILA_HUMAN	D	2297;207	ENSP00000357789:E2297D	ENSP00000271820:E207D	E	-	3	2	FLG	150547095	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.925000	0.03992	-0.492000	0.06687	-1.941000	0.00496	GAG	.	.	weak		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14991643G>A	ENST00000327462.2	-	1	621	c.525C>T	c.(523-525)ccC>ccT	p.P175P		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	175						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)					AGAAAAAGTGGGGGATTTCCA	0.483													.|||	1390	0.277556	0.438	0.2349	5008	,	,		21572	0.2867		0.2356	False		,,,				2504	0.1247				p.P175P		Atlas-SNP	.											.	OR7A17	37	.	0			c.C525T						PASS	.	G		1723,2683	516.7+/-369.2	350,1023,830	91.0	86.0	88.0		525	-2.2	0.6	19	dbSNP_119	88	1945,6655	341.3+/-324.0	215,1515,2570	no	coding-synonymous	OR7A17	NM_030901.1		565,2538,3400	AA,AG,GG		22.6163,39.1058,28.2024		175/310	14991643	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			AAAGTGGGGGATT	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.525C>T	19.37:g.14991643G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			G|0.709;A|0.291	0.291	strong		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
NAV3	89795	hgsc.bcm.edu	37	12	78598891	78598891	+	Silent	SNP	G	G	A	rs9971904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:78598891G>A	ENST00000397909.2	+	39	7184	c.7011G>A	c.(7009-7011)ccG>ccA	p.P2337P	NAV3_ENST00000536525.2_Silent_p.P2315P|NAV3_ENST00000266692.7_Silent_p.P2138P|NAV3_ENST00000228327.6_Silent_p.P2315P|NAV3_ENST00000541270.1_Silent_p.P167P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2337						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGCACATTCCGCAAACTGACA	0.433										HNSCC(70;0.22)			G|||	3184	0.635783	0.6392	0.585	5008	,	,		16118	0.8006		0.4334	False		,,,				2504	0.7055				p.P2315P		Atlas-SNP	.											.	NAV3	506	.	0			c.G6945A						PASS	.	G		2348,1670		703,942,364	78.0	86.0	84.0		6945	-4.6	0.4	12	dbSNP_119	84	3316,5056		639,2038,1509	no	coding-synonymous	NAV3	NM_014903.4		1342,2980,1873	AA,AG,GG		39.6082,41.563,45.7143		2315/2364	78598891	5664,6726	2009	4186	6195	SO:0001819	synonymous_variant	89795	exon38			CATTCCGCAAACT	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.7011G>A	12.37:g.78598891G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	47	45	0.957447	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		1321	0.6048534798534798	312	0.6341463414634146	204	0.56353591160221	478	0.8356643356643356	327	0.4313984168865435	G	0.018	-1.483281	0.01027	0.58437	0.396082	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.3	-4.56	0.03431	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22626	-1.0211	3	.	.	.	-4.5325	3.6867	0.08331	0.4497:0.3009:0.0606:0.1888	rs9971904;rs56442146;rs58843251;rs9971904	.	.	.	T	1210;205	.	.	A	+	1	0	NAV3	77123022	0.831000	0.29352	0.381000	0.26106	0.000000	0.00434	0.050000	0.14120	-1.079000	0.03113	-4.833000	0.00003	GCA	G|0.427;A|0.573	0.573	strong		0.433	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
NUTM1	256646	hgsc.bcm.edu	37	15	34648935	34648935	+	Missense_Mutation	SNP	G	G	T	rs57115249	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:34648935G>T	ENST00000333756.4	+	7	2797	c.2642G>T	c.(2641-2643)aGt>aTt	p.S881I	NUTM1_ENST00000438749.3_Missense_Mutation_p.S899I|NUTM1_ENST00000537011.1_Missense_Mutation_p.S909I	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	881						cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCTGAAGCCAGTCAAGAGGCA	0.498													G|||	606	0.121006	0.0053	0.2248	5008	,	,		22446	0.2867		0.0577	False		,,,				2504	0.0982				p.S881I		Atlas-SNP	.											.	C15orf55	110	.	0			c.G2642T						PASS	.	G	ILE/SER	97,4305	78.3+/-116.7	0,97,2104	55.0	52.0	53.0		2642	3.9	0.0	15	dbSNP_129	53	623,7973	161.7+/-214.6	17,589,3692	yes	missense	C15orf55	NM_175741.1	142	17,686,5796	TT,TG,GG		7.2476,2.2035,5.5393	probably-damaging	881/1133	34648935	720,12278	2201	4298	6499	SO:0001583	missense	256646	exon7			AAGCCAGTCAAGA	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.2642G>T	15.37:g.34648935G>T	ENSP00000329448:p.Ser881Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	288	0.13186813186813187	5	0.01016260162601626	76	0.20994475138121546	166	0.2902097902097902	41	0.05408970976253298	G	18.01	3.527509	0.64860	0.022035	0.072476	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.12984	2.65;2.63;2.65	4.81	3.89	0.44902	.	1.699820	0.02548	N	0.095317	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D;D;D	0.67145	0.994;0.996;0.994	P;D;P	0.63381	0.823;0.914;0.823	T	0.09378	-1.0677	9	0.72032	D	0.01	.	10.9934	0.47561	0.0:0.1881:0.8119:0.0	rs57115249	899;909;881	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	I	909;899;881	ENSP00000444896:S909I;ENSP00000407031:S899I;ENSP00000329448:S881I	ENSP00000329448:S881I	S	+	2	0	C15orf55	32436227	0.012000	0.17670	0.037000	0.18230	0.281000	0.26958	1.184000	0.32053	1.229000	0.43630	0.650000	0.86243	AGT	G|0.923;T|0.077	0.077	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
CNP	1267	hgsc.bcm.edu	37	17	40125864	40125864	+	Silent	SNP	G	G	A	rs2070106	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40125864G>A	ENST00000393892.3	+	4	1332	c.1188G>A	c.(1186-1188)ggG>ggA	p.G396G	CNP_ENST00000393888.1_Silent_p.G376G|CNP_ENST00000591072.1_Silent_p.G161G|CNP_ENST00000472031.1_3'UTR	NM_033133.4	NP_149124.3	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	396					adult locomotory behavior (GO:0008344)|aging (GO:0007568)|axonogenesis (GO:0007409)|cyclic nucleotide catabolic process (GO:0009214)|microtubule cytoskeleton organization (GO:0000226)|oligodendrocyte differentiation (GO:0048709)|regulation of mitochondrial membrane permeability (GO:0046902)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule (GO:0005874)|microvillus (GO:0005902)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|myelin sheath abaxonal region (GO:0035748)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity (GO:0004113)|cyclic nucleotide binding (GO:0030551)|RNA binding (GO:0003723)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	9		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)		TCTTCACGGGGTACTACGGGA	0.597													G|||	1378	0.27516	0.0756	0.2406	5008	,	,		15024	0.4157		0.2843	False		,,,				2504	0.4151				p.G396G		Atlas-SNP	.											.	CNP	58	.	0			c.G1188A						PASS	.	G		406,3668		17,372,1648	34.0	39.0	37.0		1188	-10.4	0.1	17	dbSNP_96	37	2688,5692		438,1812,1940	no	coding-synonymous	CNP	NM_033133.4		455,2184,3588	AA,AG,GG		32.0764,9.9656,24.8434		396/422	40125864	3094,9360	2037	4190	6227	SO:0001819	synonymous_variant	1267	exon4			CACGGGGTACTAC		CCDS11414.2	17q21	2008-02-05			ENSG00000173786	ENSG00000173786	3.1.4.37		2158	protein-coding gene	gene with protein product		123830				1322358	Standard	XM_006721701		Approved		uc002hyl.1	P09543	OTTHUMG00000133502	ENST00000393892.3:c.1188G>A	17.37:g.40125864G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_033133		Silent	SNP	ENST00000393892.3	37	CCDS11414.2																																																																																			G|0.731;A|0.269	0.269	strong		0.597	CNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257443.2		
LRRFIP1	9208	hgsc.bcm.edu	37	2	238662005	238662005	+	Silent	SNP	T	T	C	rs200278632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238662005T>C	ENST00000392000.4	+	8	654	c.537T>C	c.(535-537)gcT>gcC	p.A179A	LRRFIP1_ENST00000244815.5_Silent_p.A155A|LRRFIP1_ENST00000289175.6_Silent_p.A123A|LRRFIP1_ENST00000308482.9_Silent_p.A307A	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	179					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TTTCCAATGCTCAGCTAGACA	0.388																																					p.A307A		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.T921C						PASS	.						89.0	88.0	89.0					2																	238662005		2203	4300	6503	SO:0001819	synonymous_variant	9208	exon15			CAATGCTCAGCTA	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.537T>C	2.37:g.238662005T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	12	0.266667	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			T|1.000;C|0.000	0.000	strong		0.388	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
GSTM2	2946	hgsc.bcm.edu	37	1	110211956	110211956	+	Silent	SNP	C	C	T	rs592792	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:110211956C>T	ENST00000241337.4	+	4	272	c.222C>T	c.(220-222)aaC>aaT	p.N74N	GSTM2_ENST00000369829.2_Silent_p.N74N|GSTM2_ENST00000414179.2_5'UTR|GSTM2_ENST00000464206.1_3'UTR|GSTM2_ENST00000369827.3_Silent_p.N72N|GSTM2_ENST00000442650.1_Silent_p.N74N|GSTM2_ENST00000369831.2_Silent_p.N74N|GSTM2_ENST00000460717.3_Silent_p.N74N	NM_000848.3	NP_000839.1	P28161	GSTM2_HUMAN	glutathione S-transferase mu 2 (muscle)	74	GST N-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|cellular response to caffeine (GO:0071313)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|nitrobenzene metabolic process (GO:0018916)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|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)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|relaxation of cardiac muscle (GO:0055119)|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)|sarcoplasmic reticulum (GO:0016529)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			kidney(1)|large_intestine(2)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	11		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0122)|Colorectal(144;0.0129)|Epithelial(280;0.0146)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.047)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	CCCAGAGCAACGCCATCCTGC	0.597													C|||	470	0.0938498	0.1634	0.0836	5008	,	,		19402	0.001		0.1481	False		,,,				2504	0.047				p.N74N		Atlas-SNP	.											.	GSTM2	45	.	0			c.C222T						PASS	.	C	,	717,3689	299.3+/-285.7	55,607,1541	244.0	205.0	218.0		222,222	-2.1	1.0	1	dbSNP_83	218	1212,7388	245.6+/-274.3	77,1058,3165	no	coding-synonymous,coding-synonymous	GSTM2	NM_000848.3,NM_001142368.1	,	132,1665,4706	TT,TC,CC		14.093,16.2733,14.8316	,	74/219,74/192	110211956	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	2946	exon4			GAGCAACGCCATC	M63509	CCDS808.1, CCDS44192.1	1p13.3	2012-06-21	2008-11-26		ENSG00000213366	ENSG00000213366	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4634	protein-coding gene	gene with protein product		138380	"""glutathione S-transferase M2 (muscle)"""			2034681, 2345169	Standard	NM_000848		Approved	GST4		P28161	OTTHUMG00000011638	ENST00000241337.4:c.222C>T	1.37:g.110211956C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_001142368	B4DRY4|E9PEM9|Q2M318|Q5TZY5|Q8WWE1	Silent	SNP	ENST00000241337.4	37	CCDS808.1																																																																																			T|0.128;G|0.006	0.128	strong		0.597	GSTM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032167.2	NM_000848	
PHYHIPL	84457	hgsc.bcm.edu	37	10	61005204	61005204	+	Silent	SNP	C	C	T	rs138490289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61005204C>T	ENST00000373880.4	+	5	1248	c.984C>T	c.(982-984)gtC>gtT	p.V328V	PHYHIPL_ENST00000373878.3_Silent_p.V302V	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	328						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						CCCAGGATGTCATTTTAGAAG	0.433													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18642	0.0		0.0	False		,,,				2504	0.0				p.V328V		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.C984T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	75.0	70.0	72.0		906,984	2.7	1.0	10	dbSNP_134	72	18,8582	14.6+/-50.1	0,18,4282	no	coding-synonymous,coding-synonymous	PHYHIPL	NM_001143774.1,NM_032439.3	,	0,20,6483	TT,TC,CC		0.2093,0.0454,0.1538	,	302/351,328/377	61005204	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84457	exon5			GGATGTCATTTTA	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"""Fibronectin type III domain containing"""	29378	protein-coding gene	gene with protein product			"""phytanoyl-CoA hydroxylase interacting protein-like"""			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.984C>T	10.37:g.61005204C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Silent	SNP	ENST00000373880.4	37	CCDS7254.1																																																																																			C|0.998;T|0.002	0.002	strong		0.433	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439	
SORD	6652	hgsc.bcm.edu	37	15	45361180	45361180	+	Missense_Mutation	SNP	A	A	T	rs55739437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45361180A>T	ENST00000267814.9	+	7	896	c.716A>T	c.(715-717)cAg>cTg	p.Q239L	SORD_ENST00000558580.1_Missense_Mutation_p.Q218L	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	239			Q -> L (in dbSNP:rs55739437). {ECO:0000269|PubMed:7782086}.		fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		GTAGAAGGTCAGCTGGGGTGC	0.582													.|||	1678	0.335064	0.6664	0.2867	5008	,	,		12388	0.2202		0.1799	False		,,,				2504	0.1994				p.Q239L		Atlas-SNP	.											.	SORD	24	.	0			c.A716T						PASS	.	T	LEU/GLN	2459,1937		652,1155,391	33.0	38.0	36.0		716	4.7	0.1	15	dbSNP_129	36	1338,7258		46,1246,3006	yes	missense	SORD	NM_003104.5	113	698,2401,3397	TT,TA,AA		15.5654,44.0628,29.2257	benign	239/358	45361180	3797,9195	2198	4298	6496	SO:0001583	missense	6652	exon7			AAGGTCAGCTGGG		CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.716A>T	15.37:g.45361180A>T	ENSP00000267814:p.Gln239Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	184	72	0.391304	NM_003104	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	37	CCDS10116.1	503	0.2303113553113553	287	0.5833333333333334	70	0.19337016574585636	64	0.11188811188811189	82	0.10817941952506596	T	7.574	0.667425	0.14710	0.559372	0.155654	ENSG00000140263	ENST00000267814	T	0.04234	3.67	4.74	4.74	0.60224	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.335846	0.28459	N	0.015261	T	0.00012	0.0000	N	0.00670	-1.27	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15464	-1.0436	9	0.21014	T	0.42	-13.1845	10.1157	0.42589	0.1501:0.0:0.0:0.8499	rs55739437;rs62621228	160;239	B4DKI2;Q00796	.;DHSO_HUMAN	L	239	ENSP00000267814:Q239L	ENSP00000267814:Q239L	Q	+	2	0	SORD	43148472	0.996000	0.38824	0.078000	0.20375	0.622000	0.37654	2.525000	0.45598	0.669000	0.31146	-0.527000	0.04329	CAG	A|0.734;T|0.266	0.266	strong		0.582	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3		
YTHDC2	64848	hgsc.bcm.edu	37	5	112888882	112888882	+	Missense_Mutation	SNP	A	A	T	rs72805422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112888882A>T	ENST00000161863.4	+	13	1906	c.1693A>T	c.(1693-1695)Aca>Tca	p.T565S	YTHDC2_ENST00000515883.1_Missense_Mutation_p.T565S	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	565					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)		tttCAGTGCTACACTGGAATT	0.338													T|||	1644	0.328275	0.5968	0.4251	5008	,	,		11965	0.2083		0.1909	False		,,,				2504	0.1616				p.T565S		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A1693T						PASS	.	T	SER/THR	2243,2061		604,1035,513	17.0	17.0	17.0		1693	5.7	1.0	5	dbSNP_130	17	1434,7012		137,1160,2926	yes	missense	YTHDC2	NM_022828.3	58	741,2195,3439	TT,TA,AA		16.9785,47.8857,28.8392	benign	565/1431	112888882	3677,9073	2152	4223	6375	SO:0001583	missense	64848	exon13			AGTGCTACACTGG	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.1693A>T	5.37:g.112888882A>T	ENSP00000161863:p.Thr565Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	715	0.3273809523809524	314	0.6382113821138211	134	0.3701657458563536	123	0.21503496503496503	144	0.18997361477572558	T	5.005	0.186645	0.09547	0.521143	0.169785	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.63255	-0.03;-0.03	5.7	5.7	0.88788	Ankyrin repeat-containing domain (4);	0.087379	0.50627	N	0.000118	T	0.00012	0.0000	N	0.02802	-0.49	0.53688	P	2.2999999999995246E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.40059	-0.9583	9	0.06757	T	0.87	.	12.3136	0.54942	0.127:0.0:0.0:0.873	.	565	Q9H6S0	YTDC2_HUMAN	S	565;565;475	ENSP00000161863:T565S;ENSP00000423101:T565S	ENSP00000161863:T565S	T	+	1	0	YTHDC2	112916781	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.364000	0.66110	0.986000	0.38683	-0.265000	0.10407	ACA	A|0.671;T|0.329	0.329	strong		0.338	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
SPDYE1	285955	hgsc.bcm.edu	37	7	44046900	44046900	+	Silent	SNP	G	G	A	rs147853765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44046900G>A	ENST00000258704.3	+	5	803	c.666G>A	c.(664-666)gaG>gaA	p.E222E	AC004951.6_ENST00000447643.1_lincRNA|POLR2J4_ENST00000427076.1_RNA|RP5-1165K10.2_ENST00000454572.1_RNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	222										endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						AGGACGACGAGGACTCCAAAC	0.552													g|||	26	0.00519169	0.0	0.0115	5008	,	,		19923	0.0		0.0159	False		,,,				2504	0.002				p.E222E		Atlas-SNP	.											.	SPDYE1	29	.	0			c.G666A						PASS	.	G		18,4388		0,18,2185	110.0	109.0	110.0		666		0.4	7	dbSNP_134	110	148,8442		1,146,4148	no	coding-synonymous	SPDYE1	NM_175064.2		1,164,6333	AA,AG,GG		1.7229,0.4085,1.2773		222/337	44046900	166,12830	2203	4295	6498	SO:0001819	synonymous_variant	285955	exon5			CGACGAGGACTCC	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.666G>A	7.37:g.44046900G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	235	55	0.234043	NM_175064	Q9NTH5	Silent	SNP	ENST00000258704.3	37	CCDS5475.1																																																																																			G|0.984;A|0.016	0.016	strong		0.552	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064	
RGL3	57139	hgsc.bcm.edu	37	19	11508177	11508177	+	Missense_Mutation	SNP	G	G	A	rs2291516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	77	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	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	
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:114282496C>T	ENST00000545145.2	-	23	2840	c.2762G>A	c.(2761-2763)cGg>cAg	p.R921Q	RBM19_ENST00000392561.3_Missense_Mutation_p.R921Q|RBM19_ENST00000261741.5_Missense_Mutation_p.R921Q	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	921			R -> Q (in dbSNP:rs2075387). {ECO:0000269|PubMed:11230166}.		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)					GGCCGTCTTCCGCCGCAGGGC	0.647													C|||	1100	0.219649	0.1815	0.2032	5008	,	,		17432	0.131		0.3002	False		,,,				2504	0.2914				p.R921Q		Atlas-SNP	.											.	RBM19	117	.	0			c.G2762A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	776,3630	286.9+/-279.0	78,620,1505	35.0	32.0	33.0		2762,2762,2762	5.1	1.0	12	dbSNP_96	33	2321,6279	356.9+/-330.5	326,1669,2305	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	43,43,43	404,2289,3810	TT,TC,CC		26.9884,17.6123,23.8121	possibly-damaging,possibly-damaging,possibly-damaging	921/961,921/961,921/961	114282496	3097,9909	2203	4300	6503	SO:0001583	missense	9904	exon23			GTCTTCCGCCGCA	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.2762G>A	12.37:g.114282496C>T	ENSP00000442053:p.Arg921Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	486	0.22252747252747251	100	0.2032520325203252	74	0.20441988950276244	78	0.13636363636363635	234	0.3087071240105541	C	21.4	4.143675	0.77888	0.176123	0.269884	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05258	3.47;3.47;3.47	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.99999854926	D	0.69078	0.997	P	0.59595	0.86	T	0.43475	-0.9389	9	0.56958	D	0.05	-9.4086	18.1548	0.89687	0.0:1.0:0.0:0.0	rs2075387;rs60062169;rs2075387	921	Q9Y4C8	RBM19_HUMAN	Q	921	ENSP00000442053:R921Q;ENSP00000376344:R921Q;ENSP00000261741:R921Q	ENSP00000261741:R921Q	R	-	2	0	RBM19	112766879	1.000000	0.71417	0.999000	0.59377	0.194000	0.23727	4.408000	0.59761	2.368000	0.80403	0.561000	0.74099	CGG	C|0.781;T|0.219	0.219	strong		0.647	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
PTPRD	5789	hgsc.bcm.edu	37	9	8518143	8518143	+	Silent	SNP	T	T	C	rs7026388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:8518143T>C	ENST00000381196.4	-	18	1791	c.1248A>G	c.(1246-1248)gcA>gcG	p.A416A	PTPRD_ENST00000397611.3_Silent_p.A413A|PTPRD_ENST00000537002.1_Silent_p.A413A|PTPRD_ENST00000360074.4_Silent_p.A403A|PTPRD_ENST00000358503.5_Silent_p.A403A|PTPRD_ENST00000355233.5_Silent_p.A416A|PTPRD_ENST00000486161.1_Silent_p.A416A|PTPRD_ENST00000397617.3_Silent_p.A406A|PTPRD_ENST00000397606.3_Silent_p.A406A|PTPRD_ENST00000540109.1_Silent_p.A416A|PTPRD_ENST00000356435.5_Silent_p.A416A	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	416					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)			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)		CACTGGATGGTGCTTGCTCTG	0.517										TSP Lung(15;0.13)			C|||	1539	0.307308	0.4418	0.2695	5008	,	,		18246	0.3919		0.164	False		,,,				2504	0.2127				p.A416A		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A1248G						PASS	.	C	,,,,,	1682,2724	653.8+/-399.6	330,1022,851	162.0	155.0	157.0		1239,1218,1248,1248,1248,1230	-10.6	0.4	9	dbSNP_116	157	1345,7255	756.3+/-407.5	115,1115,3070	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,,,,	445,2137,3921	CC,CT,TT		15.6395,38.1752,23.2739	,,,,,	413/1503,406/1506,416/1913,416/1506,416/1507,410/1497	8518143	3027,9979	2203	4300	6503	SO:0001819	synonymous_variant	5789	exon10			GGATGGTGCTTGC	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.1248A>G	9.37:g.8518143T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	177	91	0.514124	NM_130392	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	CCDS43786.1																																																																																			C|0.268;N|0.000	0.268	strong		0.517	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:81769581C>T	ENST00000549396.1	-	10	1285	c.1125G>A	c.(1123-1125)ctG>ctA	p.L375L	RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000407050.4_Silent_p.L301L|PPFIA2_ENST00000550584.2_Silent_p.L375L|PPFIA2_ENST00000333447.7_Silent_p.L357L|PPFIA2_ENST00000549325.1_Silent_p.L357L|PPFIA2_ENST00000548586.1_Silent_p.L375L|PPFIA2_ENST00000443686.3_Silent_p.L276L|PPFIA2_ENST00000552948.1_Silent_p.L375L|PPFIA2_ENST00000550359.2_Silent_p.L222L|PPFIA2_ENST00000545296.2_5'UTR	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	136	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	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		
FAM219A	203259	hgsc.bcm.edu	37	9	34401049	34401049	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34401049C>T	ENST00000445726.1	-	6	777	c.471G>A	c.(469-471)gaG>gaA	p.E157E	FAM219A_ENST00000297620.4_Silent_p.E140E|FAM219A_ENST00000379084.1_Silent_p.E139E|FAM219A_ENST00000379089.1_Silent_p.E155E|FAM219A_ENST00000379081.1_Silent_p.E128E|FAM219A_ENST00000379087.1_Silent_p.E138E|FAM219A_ENST00000379080.1_Silent_p.E144E	NM_001184940.1|NM_001184941.1	NP_001171869.1|NP_001171870.1	Q8IW50	F219A_HUMAN	family with sequence similarity 219, member A	157																	GGTCTAGGTCCTCGTCGTCGG	0.617																																					p.E157E		Atlas-SNP	.											.	FAM219A	3	.	0			c.G471A						PASS	.						119.0	105.0	110.0					9																	34401049		2203	4300	6503	SO:0001819	synonymous_variant	203259	exon6			TAGGTCCTCGTCG	AK096350	CCDS6556.1, CCDS55304.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164970	ENSG00000164970			19920	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 25"""	C9orf25		9110174, 8619474	Standard	NM_147202		Approved	bA573M23.5, FLJ39031	uc011lok.2	Q8IW50	OTTHUMG00000019822	ENST00000445726.1:c.471G>A	9.37:g.34401049C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	4	0.0833333	NM_001184940	A2A364|B4DFE1|B4DSR8|Q5T590|Q5T591|Q5T592|Q5T594|Q5T595|Q8TAZ8	Silent	SNP	ENST00000445726.1	37	CCDS55304.1																																																																																			.	.	none		0.617	FAM219A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001184940	
COG5	10466	hgsc.bcm.edu	37	7	107002504	107002504	+	Missense_Mutation	SNP	T	T	C	rs34087251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:107002504T>C	ENST00000347053.3	-	10	1143	c.1093A>G	c.(1093-1095)Att>Gtt	p.I365V	COG5_ENST00000393603.2_Missense_Mutation_p.I365V|COG5_ENST00000297135.3_Missense_Mutation_p.I365V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	365			I -> V (in dbSNP:rs34087251).		intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						ATGAAACAAATGTGAGAAACA	0.299													T|||	188	0.0375399	0.0719	0.0202	5008	,	,		20211	0.001		0.0596	False		,,,				2504	0.0184				p.I365V		Atlas-SNP	.											.	COG5	78	.	0			c.A1093G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	343,4057	172.7+/-202.6	7,329,1864	84.0	81.0	82.0		1093,1093,1093	1.6	0.8	7	dbSNP_126	82	485,8113	139.4+/-196.0	13,459,3827	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	29,29,29	20,788,5691	CC,CT,TT		5.6408,7.7955,6.3702	benign,benign,benign	365/824,365/861,365/840	107002504	828,12170	2200	4299	6499	SO:0001583	missense	10466	exon10			AACAAATGTGAGA	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1093A>G	7.37:g.107002504T>C	ENSP00000334703:p.Ile365Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	89	0.04075091575091575	36	0.07317073170731707	6	0.016574585635359115	0	0.0	47	0.06200527704485488	T	5.221	0.226268	0.09916	0.077955	0.056408	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.27890	1.64;1.64;1.64	5.31	1.64	0.23874	.	0.241766	0.43260	N	0.000592	T	0.00496	0.0016	N	0.01257	-0.925	0.25624	N	0.986362	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.28586	-1.0039	10	0.20519	T	0.43	-8.4971	9.951	0.41638	0.0:0.4246:0.0:0.5754	rs34087251	365;365	Q9UP83;Q9UP83-2	COG5_HUMAN;.	V	365	ENSP00000334703:I365V;ENSP00000297135:I365V;ENSP00000377228:I365V	ENSP00000297135:I365V	I	-	1	0	COG5	106789740	0.455000	0.25736	0.825000	0.32803	0.987000	0.75469	0.867000	0.27968	0.094000	0.17404	0.533000	0.62120	ATT	T|0.947;C|0.053	0.053	strong		0.299	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
B4GALNT3	283358	hgsc.bcm.edu	37	12	662448	662448	+	Silent	SNP	T	T	C	rs758790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:662448T>C	ENST00000266383.5	+	14	1372	c.1359T>C	c.(1357-1359)ctT>ctC	p.L453L		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	453					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)			CCAGGATGCTTGAGGGAAGAC	0.572													C|||	4243	0.847244	0.944	0.7968	5008	,	,		18199	0.8958		0.659	False		,,,				2504	0.8957				p.L453L		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T1359C						PASS	.	C		3990,416	198.1+/-222.0	1808,374,21	76.0	86.0	83.0		1359	-0.9	0.0	12	dbSNP_86	83	5560,3040	456.3+/-364.0	1803,1954,543	no	coding-synonymous	B4GALNT3	NM_173593.3		3611,2328,564	CC,CT,TT		35.3488,9.4417,26.5724		453/999	662448	9550,3456	2203	4300	6503	SO:0001819	synonymous_variant	283358	exon14			GATGCTTGAGGGA	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.1359T>C	12.37:g.662448T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			T|0.225;C|0.775	0.775	strong		0.572	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
SVIL	6840	hgsc.bcm.edu	37	10	29821523	29821523	+	Silent	SNP	T	T	C	rs1328323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29821523T>C	ENST00000355867.4	-	8	2525	c.1773A>G	c.(1771-1773)aaA>aaG	p.K591K	SVIL_ENST00000375398.2_Silent_p.K591K|SVIL_ENST00000375400.3_Intron	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	128	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	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		
KIAA1024	23251	hgsc.bcm.edu	37	15	79748603	79748603	+	Silent	SNP	C	C	T	rs7183867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79748603C>T	ENST00000305428.3	+	2	189	c.114C>T	c.(112-114)ttC>ttT	p.F38F		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	38						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						GTGCCCGGTTCGACCTGTCGC	0.473													C|||	941	0.187899	0.5287	0.0634	5008	,	,		16769	0.0823		0.0636	False		,,,				2504	0.0521				p.F38F		Atlas-SNP	.											.	KIAA1024	146	.	0			c.C114T						PASS	.	C		1963,2429	555.4+/-379.2	442,1079,675	116.0	110.0	112.0		114	-8.4	0.0	15	dbSNP_116	112	537,8049	148.8+/-204.0	15,507,3771	no	coding-synonymous	KIAA1024	NM_015206.2		457,1586,4446	TT,TC,CC		6.2544,44.6949,19.2634		38/917	79748603	2500,10478	2196	4293	6489	SO:0001819	synonymous_variant	23251	exon2			CCGGTTCGACCTG	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.114C>T	15.37:g.79748603C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																			C|0.813;T|0.187	0.187	strong		0.473	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
PRUNE	58497	hgsc.bcm.edu	37	1	150999737	150999737	+	Silent	SNP	A	A	G	rs11204762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150999737A>G	ENST00000271620.3	+	6	864	c.708A>G	c.(706-708)aaA>aaG	p.K236K	PRUNE_ENST00000467771.1_3'UTR|PRUNE_ENST00000271619.8_Silent_p.K77K|PRUNE_ENST00000368936.1_Silent_p.K54K|PRUNE_ENST00000368934.1_Silent_p.K54K|PRUNE_ENST00000368935.1_Silent_p.K4K|PRUNE_ENST00000368937.1_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	87	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	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	
FAM208A	23272	hgsc.bcm.edu	37	3	56667682	56667682	+	Missense_Mutation	SNP	G	G	C	rs9835332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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	
OR7A10	390892	hgsc.bcm.edu	37	19	14951889	14951889	+	Silent	SNP	A	A	G	rs3752194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14951889A>G	ENST00000248058.1	-	1	800	c.801T>C	c.(799-801)aaT>aaC	p.N267N		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	267						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)					CTGTGTGTGAATTGTGGGTGG	0.473													.|||	508	0.101438	0.0893	0.1499	5008	,	,		20026	0.1438		0.0586	False		,,,				2504	0.0838				p.N267N		Atlas-SNP	.											.	OR7A10	33	.	0			c.T801C						PASS	.	A		298,4108	161.8+/-193.9	12,274,1917	98.0	90.0	93.0		801	-5.5	0.0	19	dbSNP_107	93	510,8090	145.6+/-201.3	17,476,3807	no	coding-synonymous	OR7A10	NM_001005190.1		29,750,5724	GG,GA,AA		5.9302,6.7635,6.2125		267/310	14951889	808,12198	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			GTGTGAATTGTGG		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.801T>C	19.37:g.14951889A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			A|0.922;G|0.078	0.078	strong		0.473	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
TRAF7	84231	hgsc.bcm.edu	37	16	2222286	2222286	+	Silent	SNP	C	C	T	rs11547311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2222286C>T	ENST00000326181.6	+	8	702	c.570C>T	c.(568-570)caC>caT	p.H190H		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	190					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACTGCCGGCACGGCTGCCGGG	0.647													C|||	152	0.0303514	0.0038	0.0663	5008	,	,		13645	0.0		0.0795	False		,,,				2504	0.0215				p.H190H		Atlas-SNP	.											.	TRAF7	158	.	0			c.C570T						PASS	.	C		68,4324	57.4+/-93.9	1,66,2129	36.0	38.0	37.0		570	-0.6	1.0	16	dbSNP_120	37	659,7939	164.9+/-217.2	21,617,3661	no	coding-synonymous	TRAF7	NM_032271.2		22,683,5790	TT,TC,CC		7.6646,1.5483,5.5966		190/671	2222286	727,12263	2196	4299	6495	SO:0001819	synonymous_variant	84231	exon8			CCGGCACGGCTGC	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.570C>T	16.37:g.2222286C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	37	CCDS10461.1																																																																																			C|0.945;T|0.055	0.055	strong		0.647	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271	
ADAD2	161931	hgsc.bcm.edu	37	16	84229436	84229436	+	Silent	SNP	G	G	A	rs62049905	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84229436G>A	ENST00000315906.5	+	7	1120	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.S438S	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	356	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CCCCCACCTCGGAAGGTGGCC	0.706													G|||	1575	0.314497	0.2784	0.4438	5008	,	,		14714	0.2292		0.3211	False		,,,				2504	0.3528				p.S438S		Atlas-SNP	.											ADAD2,NS,carcinoma,0,1	ADAD2	46	1	0			c.G1314A						PASS	.	G	,	1219,3093		170,879,1107	14.0	16.0	15.0		1068,1314	-9.4	0.0	16	dbSNP_129	15	2560,5934		420,1720,2107	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	590,2599,3214	AA,AG,GG		30.1389,28.2699,29.5096	,	356/584,438/666	84229436	3779,9027	2156	4247	6403	SO:0001819	synonymous_variant	161931	exon8			CACCTCGGAAGGT	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1068G>A	16.37:g.84229436G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			G|0.696;A|0.304	0.304	strong		0.706	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
PIGN	23556	hgsc.bcm.edu	37	18	59814268	59814268	+	Silent	SNP	G	G	A	rs9320000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	224	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	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	
OR5H1	26341	hgsc.bcm.edu	37	3	97851900	97851900	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	375	1	0.00266667		WXS	Illumina HiSeq	Phase_I	456	20	0.0438596	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	
OMA1	115209	hgsc.bcm.edu	37	1	59002221	59002221	+	Silent	SNP	T	T	C	rs7537470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:59002221T>C	ENST00000371226.3	-	3	806	c.693A>G	c.(691-693)gaA>gaG	p.E231E	DAB1_ENST00000485760.1_Intron|OMA1_ENST00000467063.1_5'UTR|OMA1_ENST00000358603.2_Silent_p.E231E	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	231					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)					GTCTGAACTGTTCTTTCCCCA	0.353													c|||	736	0.146965	0.2307	0.1023	5008	,	,		17939	0.1399		0.1193	False		,,,				2504	0.1012				p.E231E		Atlas-SNP	.											.	OMA1	50	.	0			c.A693G						PASS	.	C		803,3601	746.7+/-411.8	71,661,1470	75.0	76.0	76.0		693	0.8	1.0	1	dbSNP_116	76	1045,7555	769.4+/-407.6	64,917,3319	no	coding-synonymous	OMA1	NM_145243.3		135,1578,4789	CC,CT,TT		12.1512,18.2334,14.211		231/525	59002221	1848,11156	2202	4300	6502	SO:0001819	synonymous_variant	115209	exon3			GAACTGTTCTTTC	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.693A>G	1.37:g.59002221T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Silent	SNP	ENST00000371226.3	37	CCDS608.1	312	0.14285714285714285	102	0.2073170731707317	45	0.12430939226519337	80	0.13986013986013987	85	0.11213720316622691	c	8.760	0.923311	0.18056	0.182334	0.121512	ENSG00000162600	ENST00000421528	.	.	.	5.39	0.76	0.18442	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999997031	.	.	.	.	.	.	T	0.11060	-1.0603	3	.	.	.	-21.7632	11.8447	0.52376	0.0:0.2815:0.0:0.7185	rs7537470;rs60200867;rs7537470	.	.	.	A	73	.	.	T	-	1	0	OMA1	58774809	0.949000	0.32298	0.998000	0.56505	0.898000	0.52572	-0.072000	0.11486	0.007000	0.14760	-0.244000	0.11960	ACA	T|0.862;C|0.138	0.138	strong		0.353	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243	
RAB11FIP4	84440	hgsc.bcm.edu	37	17	29857460	29857460	+	Silent	SNP	G	G	A	rs61731602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:29857460G>A	ENST00000325874.8	+	14	1999	c.1770G>A	c.(1768-1770)gcG>gcA	p.A590A	RAB11FIP4_ENST00000394744.2_Silent_p.A488A	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	590	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				CTCTGGCTGCGGAGATAGACA	0.592													G|||	457	0.091254	0.0113	0.2003	5008	,	,		17485	0.0833		0.174	False		,,,				2504	0.045				p.A590A		Atlas-SNP	.											.	RAB11FIP4	65	.	0			c.G1770A						PASS	.	G		152,4254	104.3+/-142.8	6,140,2057	88.0	89.0	88.0		1770	-10.9	0.7	17	dbSNP_129	88	1406,7194	269.7+/-288.6	120,1166,3014	no	coding-synonymous	RAB11FIP4	NM_032932.3		126,1306,5071	AA,AG,GG		16.3488,3.4498,11.9791		590/638	29857460	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	84440	exon14			GGCTGCGGAGATA	AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.1770G>A	17.37:g.29857460G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
NUP205	23165	hgsc.bcm.edu	37	7	135329690	135329690	+	Silent	SNP	T	T	C	rs12540688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:135329690T>C	ENST00000285968.6	+	40	5633	c.5607T>C	c.(5605-5607)gcT>gcC	p.A1869A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1869					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.A1869A(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TCTCCACTGCTCAGAAATATG	0.388											OREG0018343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1258	0.251198	0.2428	0.196	5008	,	,		18544	0.253		0.1968	False		,,,				2504	0.3558				p.A1869A		Atlas-SNP	.											NUP205,NS,carcinoma,0,1	NUP205	198	1	1	Substitution - coding silent(1)	stomach(1)	c.T5607C						PASS	.	C		1068,3338		139,790,1274	159.0	144.0	149.0		5607	1.2	0.5	7	dbSNP_120	149	1612,6988		153,1306,2841	no	coding-synonymous	NUP205	NM_015135.2		292,2096,4115	CC,CT,TT		18.7442,24.2397,20.6059		1869/2013	135329690	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon40			CACTGCTCAGAAA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5607T>C	7.37:g.135329690T>C		Somatic	118	0	0	1617	WXS	Illumina HiSeq	Phase_I	116	116	1	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			T|0.778;C|0.222	0.222	strong		0.388	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
BST1	683	hgsc.bcm.edu	37	4	15709252	15709252	+	Missense_Mutation	SNP	G	G	A	rs2302464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15709252G>A	ENST00000265016.4	+	3	629	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	BST1_ENST00000382346.3_Missense_Mutation_p.R160Q	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	145			R -> Q (in dbSNP:rs2302464).		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.R145Q(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						AGCTGGTGTCGACAGAAAAAT	0.443													G|||	396	0.0790735	0.0287	0.0259	5008	,	,		14972	0.2232		0.0199	False		,,,				2504	0.0971				p.R145Q		Atlas-SNP	.											BST1,NS,carcinoma,0,1	BST1	30	1	1	Substitution - Missense(1)	stomach(1)	c.G434A						PASS	.	G	GLN/ARG	201,4205	125.3+/-162.5	4,193,2006	114.0	109.0	110.0		434	3.8	1.0	4	dbSNP_100	110	228,8372	94.2+/-156.2	1,226,4073	yes	missense	BST1	NM_004334.2	43	5,419,6079	AA,AG,GG		2.6512,4.562,3.2985	probably-damaging	145/319	15709252	429,12577	2203	4300	6503	SO:0001583	missense	683	exon3			GGTGTCGACAGAA	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.434G>A	4.37:g.15709252G>A	ENSP00000265016:p.Arg145Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	143	82	0.573427	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	172|172	0.07875457875457875|0.07875457875457875	10|10	0.02032520325203252|0.02032520325203252	11|11	0.03038674033149171|0.03038674033149171	136|136	0.23776223776223776|0.23776223776223776	15|15	0.01978891820580475|0.01978891820580475	G|G	17.72|17.72	3.459767|3.459767	0.63401|0.63401	0.04562|0.04562	0.026512|0.026512	ENSG00000109743|ENSG00000109743	ENST00000505785|ENST00000265016;ENST00000382346	.|T;T	.|0.17854	.|2.25;2.25	5.62|5.62	3.84|3.84	0.44239|0.44239	.|.	.|0.124747	.|0.53938	.|D	.|0.000054	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.68952|0.68952	2.095|2.095	0.28171|0.28171	P|P	0.9285529|0.9285529	.|D	.|0.89917	.|1.0	.|P	.|0.52909	.|0.713	T|T	0.21484|0.21484	-1.0244|-1.0244	4|9	.|0.45353	.|T	.|0.12	-4.1085|-4.1085	8.1902|8.1902	0.31363|0.31363	0.0858:0.1559:0.7582:0.0|0.0858:0.1559:0.7582:0.0	rs2302464;rs11548109;rs52836531;rs58881266;rs2302464|rs2302464;rs11548109;rs52836531;rs58881266;rs2302464	.|145	.|Q10588	.|BST1_HUMAN	N|Q	41|145;160	.|ENSP00000265016:R145Q;ENSP00000371783:R160Q	.|ENSP00000265016:R145Q	D|R	+|+	1|2	0|0	BST1|BST1	15318350|15318350	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.737000|0.737000	0.42083|0.42083	3.645000|3.645000	0.54389|0.54389	1.373000|1.373000	0.46208|0.46208	0.591000|0.591000	0.81541|0.81541	GAC|CGA	G|0.944;A|0.056	0.056	strong		0.443	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
MYO7A	4647	hgsc.bcm.edu	37	11	76853783	76853783	+	Missense_Mutation	SNP	T	T	C	rs1052030	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76853783T>C	ENST00000409709.3	+	3	319	c.47T>C	c.(46-48)tTg>tCg	p.L16S	MYO7A_ENST00000409893.1_Missense_Mutation_p.L16S|MYO7A_ENST00000409619.2_Missense_Mutation_p.L5S|MYO7A_ENST00000458637.2_Missense_Mutation_p.L16S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	16			L -> S (in USH1B; heterozygosity approaching 50%; dbSNP:rs1052030). {ECO:0000269|PubMed:15660226}.		actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GACCTGAGATTGGGGCAGGAG	0.612													C|||	2572	0.513578	0.8109	0.3775	5008	,	,		18560	0.4812		0.341	False		,,,				2504	0.4192				p.L16S		Atlas-SNP	.											.	MYO7A	164	.	0			c.T47C	GRCh37	CM050716|CM990894	MYO7A	M	rs1052030	PASS	.	C	SER/LEU,SER/LEU,SER/LEU	3006,1148		1104,798,175	77.0	88.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	47,47,47	3.9	0.8	11	dbSNP_86	85	2871,5517		494,1883,1817	yes	missense,missense,missense	MYO7A	NM_000260.3,NM_001127179.2,NM_001127180.1	145,145,145	1598,2681,1992	CC,CT,TT		34.2275,27.636,46.8586	benign,benign,benign	16/2216,16/1179,16/2176	76853783	5877,6665	2077	4194	6271	SO:0001583	missense	4647	exon3			TGAGATTGGGGCA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.47T>C	11.37:g.76853783T>C	ENSP00000386331:p.Leu16Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	1061	0.4858058608058608	388	0.7886178861788617	157	0.43370165745856354	270	0.47202797202797203	246	0.3245382585751979	C	3.679	-0.065832	0.07273	0.72364	0.342275	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.87412	-2.17;-2.25;-2.17;-2.18	4.84	3.91	0.45181	.	0.142236	0.45126	N	0.000387	T	0.00012	0.0000	N	0.00500	-1.43	0.53688	P	2.599999999997049E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45308	-0.9270	9	0.13470	T	0.59	.	10.384	0.44129	0.0:0.7921:0.1347:0.0732	rs1052030;rs1801156;rs3740761;rs60249649;rs1052030	16;16;16	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	S	16;16;16;5;15;15;15;15	ENSP00000386331:L16S;ENSP00000386689:L16S;ENSP00000392185:L16S;ENSP00000386635:L5S	ENSP00000345075:L15S	L	+	2	0	MYO7A	76531431	1.000000	0.71417	0.847000	0.33407	0.961000	0.63080	4.469000	0.60169	0.636000	0.30508	-0.355000	0.07637	TTG	T|0.491;C|0.509	0.509	strong		0.612	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
CHD4	1108	hgsc.bcm.edu	37	12	6711147	6711147	+	Missense_Mutation	SNP	C	C	A	rs71584865|rs1639122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:6711147C>A	ENST00000357008.2	-	4	580	c.417G>T	c.(415-417)gaG>gaT	p.E139D	CHD4_ENST00000309577.6_Missense_Mutation_p.E139D|CHD4_ENST00000544484.1_Missense_Mutation_p.E136D|CHD4_ENST00000544040.1_Missense_Mutation_p.E132D	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	139	Poly-Asp.		E -> D (in dbSNP:rs1639122). {ECO:0000269|PubMed:7575689}.		ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						CATCATCAtcctcctcctcct	0.453													.|||	2770	0.553115	0.9009	0.3617	5008	,	,		21676	0.4821		0.4066	False		,,,				2504	0.4427				p.E139D	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											CHD4_ENST00000357008,colon,carcinoma,0,3	CHD4	539	3	0			c.G417T						PASS	.	A	ASP/GLU	3616,764		1521,574,95	36.0	37.0	37.0		417	-8.1	0.2	12	dbSNP_89	37	3488,5078		774,1940,1569	yes	missense	CHD4	NM_001273.2	45	2295,2514,1664	AA,AC,CC		40.7191,17.4429,45.1259	benign	139/1913	6711147	7104,5842	2190	4283	6473	SO:0001583	missense	1108	exon4			ATCATCCTCCTCC	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.417G>T	12.37:g.6711147C>A	ENSP00000349508:p.Glu139Asp	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	1161	0.5315934065934066	435	0.8841463414634146	152	0.4198895027624309	255	0.4458041958041958	319	0.420844327176781	A	0.018	-1.471809	0.01044	0.825571	0.407191	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	D;D;D;D;T	0.90261	-2.64;-2.63;-2.64;-2.63;0.95	5.73	-8.15	0.01065	.	0.348573	0.28877	N	0.013860	T	0.00012	0.0000	N	0.05383	-0.06	0.47094	P	6.819999999999604E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47699	-0.9097	9	0.02654	T	1	.	2.3791	0.04349	0.1933:0.3889:0.2142:0.2036	rs1639122;rs52837269;rs61283931;rs1639122	139;139;132	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	D	136;132;139;139;113;139	ENSP00000440392:E136D;ENSP00000440542:E132D;ENSP00000312419:E139D;ENSP00000349508:E139D;ENSP00000437506:E139D	ENSP00000312419:E139D	E	-	3	2	CHD4	6581408	0.000000	0.05858	0.152000	0.22495	0.039000	0.13416	-2.782000	0.00772	-2.141000	0.00805	-0.996000	0.02517	GAG	C|0.440;A|0.560	0.560	strong		0.453	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
KMT2B	9757	hgsc.bcm.edu	37	19	36218478	36218478	+	Silent	SNP	C	C	T	rs11670414	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36218478C>T	ENST00000222270.7	+	16	4257	c.4257C>T	c.(4255-4257)ggC>ggT	p.G1419G	KMT2B_ENST00000420124.1_Silent_p.G1419G|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1419					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGCTCCAGGGCCTGCTGAGCT	0.741													C|||	892	0.178115	0.1929	0.0663	5008	,	,		15191	0.1776		0.1213	False		,,,				2504	0.2965				p.G1419G		Atlas-SNP	.											.	MLL4	229	.	0			c.C4257T						PASS	.	C		639,3147		48,543,1302	26.0	29.0	28.0		4257	1.9	1.0	19	dbSNP_120	28	1072,7104		64,944,3080	no	coding-synonymous	MLL4	NM_014727.1		112,1487,4382	TT,TC,CC		13.1115,16.878,14.3036		1419/2716	36218478	1711,10251	1893	4088	5981	SO:0001819	synonymous_variant	8085	exon16			CCAGGGCCTGCTG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4257C>T	19.37:g.36218478C>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			C|0.856;T|0.144	0.144	strong		0.741	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
OR6P1	128366	hgsc.bcm.edu	37	1	158533224	158533224	+	Silent	SNP	A	A	G	rs12081915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158533224A>G	ENST00000334632.1	-	1	170	c.171T>C	c.(169-171)cgT>cgC	p.R57R		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	57						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(4)|lung(1)	6						AGTACATGGGACGATGAAGGC	0.448													G|||	2637	0.526558	0.6611	0.4193	5008	,	,		19703	0.5863		0.4742	False		,,,				2504	0.4131				p.R57R		Atlas-SNP	.											OR6P1,NS,carcinoma,-1,1	OR6P1	47	1	0			c.T171C						scavenged	.	G		891,493		278,335,79	43.0	49.0	47.0		171	0.9	1.0	1	dbSNP_120	47	1456,1726		348,760,483	no	coding-synonymous	OR6P1	NM_001160325.1		626,1095,562	GG,GA,AA		45.7574,35.6214,48.5983		57/318	158533224	2347,2219	692	1591	2283	SO:0001819	synonymous_variant	128366	exon1			CATGGGACGATGA	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.171T>C	1.37:g.158533224A>G		Somatic	67	2	0.0298507		WXS	Illumina HiSeq	Phase_I	69	20	0.289855	NM_001160325	Q6IFR9	Silent	SNP	ENST00000334632.1	37	CCDS53391.1																																																																																			A|0.441;G|0.558	0.558	strong		0.448	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
NCLN	56926	hgsc.bcm.edu	37	19	3186085	3186085	+	Silent	SNP	G	G	T	rs11551095	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3186085G>T	ENST00000246117.4	+	1	488	c.57G>T	c.(55-57)ccG>ccT	p.P19P	NCLN_ENST00000590671.1_Intron	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	19				P -> L (in Ref. 6; CAG38597). {ECO:0000305}.	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)		CTTGTCTGCCGCTCGGCTTCA	0.721													g|||	2771	0.553315	0.6006	0.5288	5008	,	,		9423	0.5238		0.5318	False		,,,				2504	0.5593				p.P19P		Atlas-SNP	.											NCLN,NS,carcinoma,0,1	NCLN	27	1	0			c.G57T						PASS	.	T		2654,1752	620.9+/-393.6	810,1034,359	48.0	34.0	39.0		57	-1.7	1.0	19	dbSNP_120	39	4550,4050	574.3+/-390.0	1199,2152,949	no	coding-synonymous	NCLN	NM_020170.3		2009,3186,1308	TT,TG,GG		47.093,39.764,44.6102		19/564	3186085	7204,5802	2203	4300	6503	SO:0001819	synonymous_variant	56926	exon1			TCTGCCGCTCGGC	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.57G>T	19.37:g.3186085G>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			G|0.450;T|0.550	0.550	strong		0.721	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
PSG11	5680	hgsc.bcm.edu	37	19	43529026	43529026	+	Missense_Mutation	SNP	C	C	T	rs2471952|rs34787457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43529026C>T	ENST00000401740.1	-	2	350	c.247G>A	c.(247-249)Gta>Ata	p.V83I	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.V83I|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	83	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CCGTCTACTACATATGATGTA	0.438													.|||	3215	0.641973	0.6407	0.4928	5008	,	,		21422	0.9871		0.4722	False		,,,				2504	0.5685				p.V83I		Atlas-SNP	.											.	PSG11	57	.	0			c.G247A						PASS	.	C	,ILE/VAL,	2792,1606		954,884,361	159.0	156.0	157.0		,247,	-1.6	0.0	19	dbSNP_100	157	3705,4887		899,1907,1490	no	intron,missense,intron	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	,29,	1853,2791,1851	TT,TC,CC		43.1215,36.5166,49.9846	,,	,83/336,	43529026	6497,6493	2199	4296	6495	SO:0001583	missense	5680	exon2			CTACTACATATGA	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.247G>A	19.37:g.43529026C>T	ENSP00000384995:p.Val83Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	1207	0.5526556776556777	246	0.5	161	0.4447513812154696	501	0.8758741258741258	299	0.3944591029023747	c	2.568	-0.300368	0.05532	0.634834	0.431215	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.67345	-0.26;-0.26	0.929	-1.65	0.08291	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.17379	0.485	0.80722	P	0.0	B	0.11235	0.004	B	0.24394	0.053	T	0.22382	-1.0218	8	0.34782	T	0.22	.	3.9341	0.09298	0.0:0.4493:0.0:0.5507	rs2471952	83	Q9UQ72	PSG11_HUMAN	I	83	ENSP00000319140:V83I;ENSP00000384995:V83I	ENSP00000319140:V83I	V	-	1	0	PSG11	48220866	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.856000	0.00729	-0.586000	0.05898	0.184000	0.17185	GTA	CA|0.500;TG|0.500	.	alt		0.438	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
BTN1A1	696	hgsc.bcm.edu	37	6	26501897	26501897	+	Silent	SNP	T	T	C	rs1321479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26501897T>C	ENST00000244513.6	+	2	225	c.159T>C	c.(157-159)tcT>tcC	p.S53S		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	53	Ig-like V-type 1.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						GTCGCCTGTCTCCGAACGCGA	0.657													C|||	2834	0.565895	0.5136	0.5879	5008	,	,		14855	0.7312		0.4423	False		,,,				2504	0.5777				p.S53S		Atlas-SNP	.											BTN1A1,colon,carcinoma,0,1	BTN1A1	68	1	0			c.T159C						scavenged	.	C		2285,2117		600,1085,516	34.0	36.0	35.0		159	1.6	0.0	6	dbSNP_88	35	4004,4584		990,2024,1280	no	coding-synonymous	BTN1A1	NM_001732.2		1590,3109,1796	CC,CT,TT		46.6232,48.0918,48.4142		53/527	26501897	6289,6701	2201	4294	6495	SO:0001819	synonymous_variant	696	exon2			CCTGTCTCCGAAC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.159T>C	6.37:g.26501897T>C		Somatic	47	2	0.0425532		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Silent	SNP	ENST00000244513.6	37	CCDS4614.1																																																																																			T|0.485;C|0.515	0.515	strong		0.657	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
RNASEL	6041	hgsc.bcm.edu	37	1	182554557	182554557	+	Missense_Mutation	SNP	C	C	T	rs486907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:182554557C>T	ENST00000367559.3	-	2	1638	c.1385G>A	c.(1384-1386)cGa>cAa	p.R462Q	RNASEL_ENST00000444138.1_Missense_Mutation_p.R462Q|RNASEL_ENST00000539397.1_Missense_Mutation_p.R462Q	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	462	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (risk factor for prostate cancer; reduced enzymatic activity; dbSNP:rs486907). {ECO:0000269|PubMed:11799394, ECO:0000269|PubMed:11941539, ECO:0000269|PubMed:17344846}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CAGGACATTTCGGGCAAATTC	0.453													C|||	1155	0.230631	0.0666	0.2233	5008	,	,		20473	0.2421		0.3708	False		,,,				2504	0.3016				p.R462Q		Atlas-SNP	.											.	RNASEL	83	.	0			c.G1385A	GRCh37	CM020962	RNASEL	M	rs486907	PASS	.	C	GLN/ARG	587,3819	257.7+/-262.0	42,503,1658	129.0	127.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1385	0.1	0.0	1	dbSNP_83	128	3065,5535	471.5+/-368.1	516,2033,1751	yes	missense	RNASEL	NM_021133.3	43	558,2536,3409	TT,TC,CC		35.6395,13.3227,28.0793	probably-damaging	462/742	182554557	3652,9354	2203	4300	6503	SO:0001583	missense	6041	exon2			ACATTTCGGGCAA	L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1385G>A	1.37:g.182554557C>T	ENSP00000356530:p.Arg462Gln	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	282	282	1	NM_021133	Q5W0L2|Q6AI46	Missense_Mutation	SNP	ENST00000367559.3	37	CCDS1347.1	533	0.24404761904761904	26	0.052845528455284556	93	0.2569060773480663	135	0.23601398601398602	279	0.36807387862796836	C	22.0	4.225120	0.79576	0.133227	0.356395	ENSG00000135828	ENST00000367559;ENST00000444138;ENST00000543858;ENST00000539397	T;T;T	0.20463	2.07;2.07;2.07	5.95	0.0561	0.14318	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.497265	0.17966	N	0.156039	T	0.00012	0.0000	M	0.76574	2.34	0.80722	P	0.0	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.59825	0.864;0.864;0.864	T	0.36138	-0.9760	9	0.18276	T	0.48	-4.1493	0.4865	0.00557	0.1814:0.2702:0.1788:0.3696	rs486907;rs3738580;rs52825450;rs60634396;rs486907	462;462;462	Q5W0L2;Q6AI46;Q05823	.;.;RN5A_HUMAN	Q	462;462;106;462	ENSP00000356530:R462Q;ENSP00000411147:R462Q;ENSP00000440844:R462Q	ENSP00000356530:R462Q	R	-	2	0	RNASEL	180821180	0.001000	0.12720	0.001000	0.08648	0.188000	0.23474	0.217000	0.17603	0.102000	0.17638	0.650000	0.86243	CGA	C|0.737;T|0.263	0.263	strong		0.453	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1	NM_021133	
MUC7	4589	hgsc.bcm.edu	37	4	71347171	71347171	+	Missense_Mutation	SNP	C	C	T	rs147763101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71347171C>T	ENST00000304887.5	+	3	900	c.710C>T	c.(709-711)gCc>gTc	p.A237V	MUC7_ENST00000413702.1_Missense_Mutation_p.A237V|MUC7_ENST00000456088.1_Missense_Mutation_p.A237V	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	237	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)		p.A237V(1)		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)			ACCACAGCTGCCCCACCCACA	0.587																																					p.A237V		Atlas-SNP	.											MUC7,trunk,malignant_melanoma,0,1	MUC7	91	1	1	Substitution - Missense(1)	skin(1)	c.C710T						scavenged	.						387.0	316.0	340.0					4																	71347171		2203	4300	6503	SO:0001583	missense	4589	exon4			CAGCTGCCCCACC	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.710C>T	4.37:g.71347171C>T	ENSP00000302021:p.Ala237Val	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	199	22	0.110553	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	c	9.877	1.200531	0.22121	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.59772	0.24;0.24;0.24	2.03	1.17	0.20885	.	.	.	.	.	T	0.39911	0.1096	N	0.19112	0.55	0.20975	N	0.999817	P	0.50943	0.94	B	0.43809	0.432	T	0.17198	-1.0377	8	.	.	.	-1.8774	6.8415	0.23965	0.0:0.8404:0.0:0.1596	.	237	Q8TAX7	MUC7_HUMAN	V	237	ENSP00000407422:A237V;ENSP00000400585:A237V;ENSP00000302021:A237V	.	A	+	2	0	MUC7	71381760	0.004000	0.15560	0.026000	0.17262	0.070000	0.16714	0.994000	0.29693	0.392000	0.25172	-0.150000	0.13652	GCC	C|0.991;T|0.010	0.010	strong		0.587	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
TNC	3371	hgsc.bcm.edu	37	9	117808785	117808785	+	Missense_Mutation	SNP	T	T	A	rs2104772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:117808785T>A	ENST00000350763.4	-	17	5440	c.5029A>T	c.(5029-5031)Ata>Tta	p.I1677L	TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000346706.3_Missense_Mutation_p.I1131L|TNC_ENST00000341037.4_Missense_Mutation_p.I1495L|TNC_ENST00000542877.1_Missense_Mutation_p.I1314L|TNC_ENST00000423613.2_Intron|TNC_ENST00000535648.1_Missense_Mutation_p.I1222L|TNC_ENST00000481475.1_5'Flank|TNC_ENST00000340094.3_Missense_Mutation_p.I1313L	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	246	0	0		WXS	Illumina HiSeq	Phase_I	206	109	0.529126	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	
DYTN	391475	hgsc.bcm.edu	37	2	207564562	207564562	+	Missense_Mutation	SNP	T	T	A	rs112735024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564562T>A	ENST00000452335.2	-	7	724	c.608A>T	c.(607-609)gAg>gTg	p.E203V	Y_RNA_ENST00000384589.1_RNA|DYTN_ENST00000477734.1_5'UTR	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	203						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GATGGGAGGCTCAGATTGGAC	0.507													T|||	16	0.00319489	0.0076	0.0058	5008	,	,		18067	0.0		0.002	False		,,,				2504	0.0				p.E203V		Atlas-SNP	.											.	DYTN	168	.	0			c.A608T						PASS	.	T	VAL/GLU	44,3860		1,42,1909	76.0	82.0	80.0		608	3.6	1.0	2	dbSNP_132	80	51,8255		0,51,4102	yes	missense	DYTN	NM_001093730.1	121	1,93,6011	AA,AT,TT		0.614,1.127,0.7781	probably-damaging	203/579	207564562	95,12115	1952	4153	6105	SO:0001583	missense	391475	exon7			GGAGGCTCAGATT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.608A>T	2.37:g.207564562T>A	ENSP00000396593:p.Glu203Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	16.99	3.273329	0.59649	0.01127	0.00614	ENSG00000232125	ENST00000452335	T	0.77620	-1.11	5.89	3.58	0.41010	EF-hand domain, type 2 (1);	.	.	.	.	D	0.83450	0.5257	M	0.84433	2.695	0.36672	D	0.878551	D	0.89917	1.0	D	0.79784	0.993	D	0.88043	0.2782	9	0.87932	D	0	-12.5875	9.3049	0.37870	0.0:0.1712:0.0:0.8288	.	203	A2CJ06	DYTN_HUMAN	V	203	ENSP00000396593:E203V	ENSP00000396593:E203V	E	-	2	0	DYTN	207272807	1.000000	0.71417	0.998000	0.56505	0.413000	0.31143	2.499000	0.45372	2.254000	0.74563	0.459000	0.35465	GAG	T|0.997;A|0.003	0.003	strong		0.507	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
SIN3B	23309	hgsc.bcm.edu	37	19	16973724	16973724	+	Silent	SNP	G	G	A	rs143287291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:16973724G>A	ENST00000379803.1	+	10	1310	c.1296G>A	c.(1294-1296)tcG>tcA	p.S432S	SIN3B_ENST00000248054.5_Intron|SIN3B_ENST00000595541.1_5'Flank	NM_015260.2	NP_056075.1			SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCCAGGGTTCGTGGACAGACG	0.527													.|||	22	0.00439297	0.0	0.0072	5008	,	,		19490	0.0		0.0119	False		,,,				2504	0.0051				p.S432S		Atlas-SNP	.											SIN3B,NS,malignant_melanoma,+1,1	SIN3B	90	1	0			c.G1296A						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	254.0	236.0	242.0		1296	-0.3	0.0	19	dbSNP_134	242	86,8514	49.8+/-109.6	1,84,4215	no	coding-synonymous	SIN3B	NM_015260.2		1,93,6409	AA,AG,GG		1.0,0.2043,0.7304		432/1163	16973724	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	23309	exon10			GGGTTCGTGGACA	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000379803.1:c.1296G>A	19.37:g.16973724G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	NM_015260		Silent	SNP	ENST00000379803.1	37	CCDS32946.1																																																																																			G|0.992;A|0.008	0.008	strong		0.527	SIN3B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462848.1	NM_015260	
MOGAT1	116255	hgsc.bcm.edu	37	2	223559089	223559089	+	Missense_Mutation	SNP	T	T	C	rs1868024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:223559089T>C	ENST00000446656.3	+	4	487	c.487T>C	c.(487-489)Tca>Cca	p.S163P		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	163			S -> P (in dbSNP:rs1868024).		diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		AGGGCTGGTTTCAGTTTCCAA	0.358													T|||	1151	0.229832	0.3654	0.2349	5008	,	,		19517	0.1161		0.2336	False		,,,				2504	0.1564				p.S163P	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.T487C						PASS	.	T	PRO/SER	1281,2449		236,809,820	64.0	65.0	65.0		487	3.0	1.0	2	dbSNP_92	65	1786,6392		202,1382,2505	yes	missense	MOGAT1	NM_058165.2	74	438,2191,3325	CC,CT,TT		21.8391,34.3432,25.7558	benign	163/336	223559089	3067,8841	1865	4089	5954	SO:0001583	missense	116255	exon4			CTGGTTTCAGTTT	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.487T>C	2.37:g.223559089T>C	ENSP00000406674:p.Ser163Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_058165	Q6IEE5	Missense_Mutation	SNP	ENST00000446656.3	37	CCDS46524.1	494	0.2261904761904762	165	0.3353658536585366	94	0.2596685082872928	65	0.11363636363636363	170	0.22427440633245382	T	0.052	-1.247371	0.01481	0.343432	0.218391	ENSG00000124003	ENST00000446656	D	0.91894	-2.93	5.42	2.96	0.34315	.	0.086801	0.49916	D	0.000132	T	0.00012	0.0000	L	0.33710	1.025	0.20873	P	0.999830245	B	0.17465	0.022	B	0.29598	0.104	T	0.03433	-1.1037	9	0.23891	T	0.37	-7.6214	7.6937	0.28581	0.1246:0.0686:0.0:0.8067	rs1868024;rs17507996;rs52814175;rs61034242;rs1868024	163	Q96PD6	MOGT1_HUMAN	P	163	ENSP00000406674:S163P	ENSP00000406674:S163P	S	+	1	0	MOGAT1	223267333	1.000000	0.71417	0.985000	0.45067	0.321000	0.28281	2.651000	0.46674	1.049000	0.40321	0.523000	0.50628	TCA	C|0.221;N|0.001	0.221	strong		0.358	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	
MCAM	4162	hgsc.bcm.edu	37	11	119185677	119185677	+	Missense_Mutation	SNP	T	T	C	rs34587557	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119185677T>C	ENST00000264036.4	-	3	280	c.266A>G	c.(265-267)gAg>gGg	p.E89G	MCAM_ENST00000530144.2_5'UTR|MCAM_ENST00000392814.1_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	89	Ig-like V-type 1.		E -> G (in dbSNP:rs34587557). {ECO:0000269|Ref.5}.		anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		GAGCCGCTGCTCGTACTCCCC	0.642													T|||	104	0.0207668	0.0	0.049	5008	,	,		18799	0.0		0.0477	False		,,,				2504	0.0225				p.E89G		Atlas-SNP	.											MCAM,NS,carcinoma,0,1	MCAM	57	1	0			c.A266G						PASS	.	T	GLY/GLU	36,4360	39.2+/-71.8	0,36,2162	67.0	73.0	71.0		266	5.4	1.0	11	dbSNP_126	71	465,8125	136.7+/-193.7	11,443,3841	yes	missense	MCAM	NM_006500.2	98	11,479,6003	CC,CT,TT		5.4133,0.8189,3.858	benign	89/647	119185677	501,12485	2198	4295	6493	SO:0001583	missense	4162	exon3			CGCTGCTCGTACT	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6934	protein-coding gene	gene with protein product	"""Gicerin"""	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.266A>G	11.37:g.119185677T>C	ENSP00000264036:p.Glu89Gly	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Missense_Mutation	SNP	ENST00000264036.4	37	CCDS31690.1	44	0.020146520146520148	0	0.0	15	0.04143646408839779	0	0.0	29	0.03825857519788918	T	17.27	3.347132	0.61183	0.008189	0.054133	ENSG00000076706	ENST00000264036	T	0.65178	-0.14	5.41	5.41	0.78517	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.16685	0.0401	L	0.40543	1.245	0.80722	D	1	B	0.16603	0.018	B	0.29077	0.098	T	0.26087	-1.0113	9	0.33940	T	0.23	-6.7672	11.83	0.52290	0.0:0.0:0.0:1.0	rs34587557	89	P43121	MUC18_HUMAN	G	89	ENSP00000264036:E89G	ENSP00000264036:E89G	E	-	2	0	MCAM	118690887	0.866000	0.29940	1.000000	0.80357	0.937000	0.57800	0.893000	0.28336	2.040000	0.60383	0.459000	0.35465	GAG	T|0.968;C|0.032	0.032	strong		0.642	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2		
MAPT	4137	hgsc.bcm.edu	37	17	44061025	44061025	+	Silent	SNP	C	C	T	rs63750222	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:44061025C>T	ENST00000571987.1	+	5	855	c.855C>T	c.(853-855)gaC>gaT	p.D285D	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000262410.5_Silent_p.D285D|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Silent_p.D285D|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Silent_p.D285D|MAPT_ENST00000535772.1_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)	CAGAGCCCGACGGGCCCAGTG	0.627													C|||	549	0.109625	0.0371	0.1599	5008	,	,		15767	0.2054		0.1213	False		,,,				2504	0.0613				p.D285D		Atlas-SNP	.											.	MAPT	135	.	0			c.C855T						PASS	.	C	,,,,,,,	213,4193	126.6+/-163.6	4,205,1994	39.0	44.0	42.0		855,,,,,,855,	-10.9	0.0	17	dbSNP_130	42	1028,7572	213.9+/-253.7	66,896,3338	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous,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	,,,,,,,	70,1101,5332	TT,TC,CC		11.9535,4.8343,9.5417	,,,,,,,	285/777,,,,,,285/759,	44061025	1241,11765	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon6			GCCCGACGGGCCC	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.855C>T	17.37:g.44061025C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			C|0.896;T|0.104	0.104	strong		0.627	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
CHST13	166012	hgsc.bcm.edu	37	3	126260608	126260608	+	Silent	SNP	G	G	T	rs6766712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:126260608G>T	ENST00000319340.2	+	3	263	c.213G>T	c.(211-213)cgG>cgT	p.R71R		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	71					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)		AGGTGCACCGGCAGCGGCGCG	0.736													G|||	1195	0.238618	0.2579	0.2983	5008	,	,		9581	0.255		0.2525	False		,,,				2504	0.1391				p.R71R		Atlas-SNP	.											CHST13,NS,carcinoma,0,1	CHST13	21	1	0			c.G213T						scavenged	.	G		1018,3082		137,744,1169	6.0	6.0	6.0		213	0.3	1.0	3	dbSNP_116	6	1785,6069		251,1283,2393	no	coding-synonymous	CHST13	NM_152889.2		388,2027,3562	TT,TG,GG		22.7273,24.8293,23.4482		71/342	126260608	2803,9151	2050	3927	5977	SO:0001819	synonymous_variant	166012	exon3			GCACCGGCAGCGG	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.213G>T	3.37:g.126260608G>T		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			G|0.739;T|0.261	0.261	strong		0.736	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
KMT2D	8085	hgsc.bcm.edu	37	12	49445949	49445949	+	Missense_Mutation	SNP	G	G	T	rs367925817		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49445949G>T	ENST00000301067.7	-	10	1516	c.1517C>A	c.(1516-1518)cCa>cAa	p.P506Q		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	506	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|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)										TGATTCAGGTGGGGGAGACAG	0.612																																					p.P506Q		Atlas-SNP	.											.	MLL2	1173	.	0			c.C1517A						PASS	.	G	GLN/PRO	0,4072		0,0,2036	48.0	55.0	52.0		1517	-0.0	1.0	12		52	1,8375		0,1,4187	no	missense	MLL2	NM_003482.3	76	0,1,6223	TT,TG,GG		0.0119,0.0,0.0080	possibly-damaging	506/5538	49445949	1,12447	2036	4188	6224	SO:0001583	missense	8085	exon10			TCAGGTGGGGGAG	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.1517C>A	12.37:g.49445949G>T	ENSP00000301067:p.Pro506Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	6.497	0.459924	0.12342	0.0	1.19E-4	ENSG00000167548	ENST00000301067	T	0.79653	-1.29	4.2	-0.0106	0.13996	.	.	.	.	.	T	0.57301	0.2044	N	0.08118	0	0.09310	N	1	P	0.34462	0.454	B	0.34722	0.188	T	0.53851	-0.8380	9	0.87932	D	0	.	0.6454	0.00817	0.2995:0.1688:0.3582:0.1735	.	506	O14686	MLL2_HUMAN	Q	506	ENSP00000301067:P506Q	ENSP00000301067:P506Q	P	-	2	0	MLL2	47732216	0.015000	0.18098	0.993000	0.49108	0.853000	0.48598	0.189000	0.17037	0.178000	0.19917	-0.678000	0.03780	CCA	.	.	weak		0.612	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
CASP1	834	hgsc.bcm.edu	37	11	104900488	104900488	+	Silent	SNP	G	G	A	rs580253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:104900488G>A	ENST00000533400.1	-	6	801	c.766C>T	c.(766-768)Cta>Tta	p.L256L	CASP1_ENST00000593315.1_Silent_p.L235L|CASP1_ENST00000446369.1_Silent_p.L163L|CASP1_ENST00000527979.1_Silent_p.L219L|CASP1_ENST00000598974.1_Silent_p.L256L|CASP1_ENST00000525825.1_Silent_p.L235L|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000526568.1_Silent_p.L163L|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000594519.1_Silent_p.L163L|CASP1_ENST00000393136.4_Silent_p.L235L|CASP1_ENST00000436863.3_Silent_p.L256L|CASP1_ENST00000534497.1_Silent_p.L163L|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000528974.1_Silent_p.L217L	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	256					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TTGAGTTGTAGTATATCTGGG	0.468													.|||	580	0.115815	0.0893	0.2464	5008	,	,		19797	0.006		0.1759	False		,,,				2504	0.1104				p.L256L	NSCLC(41;1246 1743 4934)	Atlas-SNP	.											.	CASP1	53	.	0			c.C766T						PASS	.	A	,,,,	420,3984		18,384,1800	140.0	125.0	130.0		703,766,487,487,	1.1	0.0	11	dbSNP_83	130	1409,7189		125,1159,3015	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	CASP1	NM_001223.3,NM_033292.2,NM_033293.2,NM_033294.2,NM_033295.2	,,,,	143,1543,4815	AA,AG,GG		16.3875,9.5368,14.0671	,,,,	235/384,256/405,163/312,163/264,	104900488	1829,11173	2202	4299	6501	SO:0001819	synonymous_variant	834	exon6			GTTGTAGTATATC	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.766C>T	11.37:g.104900488G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	184	83	0.451087	NM_001257118	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																			G|0.867;A|0.133	0.133	strong		0.468	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292	
PTX4	390667	hgsc.bcm.edu	37	16	1537455	1537455	+	Missense_Mutation	SNP	T	T	C	rs112830794|rs2667673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1537455T>C	ENST00000447419.2	-	2	683	c.658A>G	c.(658-660)Agg>Ggg	p.R220G	PTX4_ENST00000293922.1_Missense_Mutation_p.R215G|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	220			R -> G (in dbSNP:rs2667673).			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						GGGGGGCCCCTGTGCTCAGAG	0.692													C|||	2683	0.535743	0.8896	0.3314	5008	,	,		13751	0.5238		0.3757	False		,,,				2504	0.3793				p.R215G		Atlas-SNP	.											.	PTX4	46	.	0			c.A643G						PASS	.	C	GLY/ARG	3474,900		1415,644,128	15.0	19.0	18.0		643	-10.1	0.0	16	dbSNP_100	18	2674,5902		536,1602,2150	no	missense	PTX4	NM_001013658.1	125	1951,2246,2278	CC,CT,TT		31.18,20.5761,47.4749	benign	215/474	1537455	6148,6802	2187	4288	6475	SO:0001583	missense	390667	exon2			GGCCCCTGTGCTC		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.658A>G	16.37:g.1537455T>C	ENSP00000445277:p.Arg220Gly	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		1169	0.5352564102564102	429	0.8719512195121951	120	0.3314917127071823	318	0.5559440559440559	302	0.39841688654353563	C	7.233	0.599711	0.13939	0.794239	0.3118	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06528	3.46;3.29	5.04	-10.1	0.00402	.	2.463480	0.01259	N	0.009118	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.34279	-0.9835	9	0.19147	T	0.46	.	3.9047	0.09177	0.0914:0.3026:0.3716:0.2344	rs2667673;rs58416337	215	Q96A99-2	.	G	220;215	ENSP00000445277:R220G;ENSP00000293922:R215G	ENSP00000293922:R215G	R	-	1	2	PTX4	1477456	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.619000	0.00412	-3.768000	0.00109	-2.517000	0.00185	AGG	T|0.479;C|0.521	0.521	strong		0.692	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
FAIM	55179	hgsc.bcm.edu	37	3	138329862	138329862	+	Intron	SNP	G	G	A	rs811322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:138329862G>A	ENST00000393035.2	+	1	87				FAIM_ENST00000393034.2_Intron|FAIM_ENST00000360570.3_Intron|FAIM_ENST00000338446.4_Silent_p.P21P	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule						apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						TGGTATCTCCGGACTCTGCCA	0.463													A|||	3538	0.70647	0.5492	0.7262	5008	,	,		17908	0.9802		0.5567	False		,,,				2504	0.7771				p.P21P		Atlas-SNP	.											.	FAIM	27	.	0			c.G63A						PASS	.	A	,,,	2501,1905	545.4+/-376.8	704,1093,406	199.0	191.0	194.0		63,,,	2.1	0.0	3	dbSNP_86	194	4922,3678	526.6+/-381.0	1438,2046,816	no	coding-synonymous,intron,intron,intron	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	,,,	2142,3139,1222	AA,AG,GG		42.7674,43.2365,42.9263	,,,	21/214,,,	138329862	7423,5583	2203	4300	6503	SO:0001627	intron_variant	55179	exon2			ATCTCCGGACTCT	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.-23+2083G>A	3.37:g.138329862G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	220	146	0.663636	NM_001033030	Q6IAN2	Silent	SNP	ENST00000393035.2	37	CCDS3103.1																																																																																			A|0.616;C|0.002	0.616	strong		0.463	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2341194	2341194	+	Silent	SNP	T	T	C	rs2071680	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2341194T>C	ENST00000290974.2	-	4	846	c.507A>G	c.(505-507)gcA>gcG	p.A169A	ZFYVE28_ENST00000515312.1_Silent_p.A99A|ZFYVE28_ENST00000503000.1_Silent_p.A169A|ZFYVE28_ENST00000515169.1_Silent_p.A99A|ZFYVE28_ENST00000509171.1_Silent_p.A122A|ZFYVE28_ENST00000511071.1_Silent_p.A169A	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	151	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	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	
MYH6	4624	hgsc.bcm.edu	37	14	23861811	23861811	+	Missense_Mutation	SNP	A	A	G	rs365990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	149	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	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		
RARG	5916	hgsc.bcm.edu	37	12	53605496	53605496	+	Silent	SNP	C	C	T	rs61754163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53605496C>T	ENST00000425354.2	-	10	1816	c.1329G>A	c.(1327-1329)ggG>ggA	p.G443G	RARG_ENST00000338561.5_Silent_p.G432G|RARG_ENST00000394426.1_Silent_p.G443G|RARG_ENST00000327550.3_Silent_p.G371G|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000543726.1_Silent_p.G421G	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	443					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	TGCCCTGGCCCCCAGGAACCT	0.627													C|||	125	0.0249601	0.0061	0.0418	5008	,	,		17427	0.0		0.0696	False		,,,				2504	0.0184				p.G443G		Atlas-SNP	.											.	RARG	53	.	0			c.G1329A						PASS	.	C	,	76,4330	65.3+/-102.7	2,72,2129	35.0	33.0	34.0		1329,1296	2.7	0.0	12	dbSNP_129	34	710,7890	168.6+/-220.1	24,662,3614	no	coding-synonymous,coding-synonymous	RARG	NM_000966.5,NM_001042728.2	,	26,734,5743	TT,TC,CC		8.2558,1.7249,6.0434	,	443/455,432/444	53605496	786,12220	2203	4300	6503	SO:0001819	synonymous_variant	5916	exon10			CTGGCCCCCAGGA	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.1329G>A	12.37:g.53605496C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Silent	SNP	ENST00000425354.2	37	CCDS8850.1																																																																																			C|0.949;T|0.051	0.051	strong		0.627	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966	
OR5D14	219436	hgsc.bcm.edu	37	11	55563900	55563900	+	Missense_Mutation	SNP	T	T	C	rs297055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55563900T>C	ENST00000335605.1	+	1	869	c.869T>C	c.(868-870)cTg>cCg	p.L290P		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	290			L -> P (in dbSNP:rs297055).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L290P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTGAACCCTCTGATCTACAGC	0.408													t|||	1086	0.216853	0.326	0.1844	5008	,	,		17041	0.1458		0.2525	False		,,,				2504	0.1288				p.L290P		Atlas-SNP	.											OR5D14,NS,carcinoma,-1,3	OR5D14	116	3	1	Substitution - Missense(1)	stomach(1)	c.T869C						scavenged	.	T	PRO/LEU	1414,2986	451.6+/-349.7	252,910,1038	55.0	54.0	55.0		869	5.1	1.0	11	dbSNP_79	55	2204,6388	368.9+/-335.3	305,1594,2397	yes	missense	OR5D14	NM_001004735.1	98	557,2504,3435	CC,CT,TT		25.6518,32.1364,27.8479	probably-damaging	290/315	55563900	3618,9374	2200	4296	6496	SO:0001583	missense	219436	exon1			ACCCTCTGATCTA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.869T>C	11.37:g.55563900T>C	ENSP00000334456:p.Leu290Pro	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	524	0.23992673992673993	171	0.3475609756097561	66	0.18232044198895028	87	0.1520979020979021	200	0.2638522427440633	t	14.05	2.420915	0.42918	0.321364	0.256518	ENSG00000186113	ENST00000335605	T	0.46451	0.87	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35179	N	0.003382	T	0.00012	0.0000	M	0.90369	3.11	0.44966	P	0.0020139999999999603	P	0.49559	0.925	P	0.45712	0.491	T	0.22208	-1.0223	9	0.87932	D	0	-13.9526	13.7086	0.62654	0.0:0.0:0.0:1.0	rs297055;rs52801945;rs60885889;rs297055	290	Q8NGL3	OR5DE_HUMAN	P	290	ENSP00000334456:L290P	ENSP00000334456:L290P	L	+	2	0	OR5D14	55320476	0.122000	0.22280	1.000000	0.80357	0.991000	0.79684	3.008000	0.49544	1.916000	0.55485	0.523000	0.50628	CTG	T|0.746;C|0.254	0.254	strong		0.408	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
MUC16	94025	hgsc.bcm.edu	37	19	9075969	9075969	+	Missense_Mutation	SNP	C	C	T	rs2591593	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9075969C>T	ENST00000397910.4	-	3	11680	c.11477G>A	c.(11476-11478)gGg>gAg	p.G3826E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3827	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.G3826E(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						GGGCACCTGCCCTGGATGTGC	0.507													C|||	1243	0.248203	0.2005	0.2118	5008	,	,		21707	0.249		0.3121	False		,,,				2504	0.272				p.G3826E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - Missense(2)	stomach(2)	c.G11477A						PASS	.	C	GLU/GLY	852,3266		98,656,1305	209.0	197.0	201.0		11477	-0.6	0.0	19	dbSNP_100	201	2423,5995		347,1729,2133	yes	missense	MUC16	NM_024690.2	98	445,2385,3438	TT,TC,CC		28.7836,20.6897,26.1248	possibly-damaging	3826/14508	9075969	3275,9261	2059	4209	6268	SO:0001583	missense	94025	exon3			ACCTGCCCTGGAT	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.11477G>A	19.37:g.9075969C>T	ENSP00000381008:p.Gly3826Glu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	163	69	0.423313	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	c	4.377	0.069544	0.08436	0.206897	0.287836	ENSG00000181143	ENST00000397910	T	0.03553	3.89	1.67	-0.571	0.11749	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.38370	0.628	B	0.28232	0.087	T	0.49753	-0.8906	8	0.87932	D	0	.	4.0285	0.09698	0.0:0.5788:0.0:0.4212	rs2591593;rs17418331;rs52808109;rs60034029;rs2591593	3826	B5ME49	.	E	3826	ENSP00000381008:G3826E	ENSP00000381008:G3826E	G	-	2	0	MUC16	8936969	0.000000	0.05858	0.001000	0.08648	0.179000	0.23085	-0.107000	0.10873	-0.095000	0.12351	0.205000	0.17691	GGG	C|0.750;T|0.250	0.250	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000192	52000192	+	Missense_Mutation	SNP	A	A	G	rs144032115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52000192A>G	ENST00000291707.3	-	7	1596	c.1541T>C	c.(1540-1542)gTg>gCg	p.V514A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.V396A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	514					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCCCACGCCCACTGCTGGCCT	0.582													N|||	5	0.000998403	0.0015	0.0	5008	,	,		19279	0.0		0.001	False		,,,				2504	0.002				p.V514A		Atlas-SNP	.											SIGLEC12,NS,haematopoietic_neoplasm,0,1	SIGLEC12	243	1	0			c.T1541C						PASS	.	G	ALA/VAL,ALA/VAL	0,4406		0,0,2203	164.0	127.0	140.0		1187,1541	-2.7	0.0	19	dbSNP_134	140	5,8595		0,5,4295	no	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	64,64	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign,benign	396/478,514/596	52000192	5,13001	2203	4300	6503	SO:0001583	missense	89858	exon7			ACGCCCACTGCTG	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""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"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1541T>C	19.37:g.52000192A>G	ENSP00000291707:p.Val514Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	132	15	0.113636	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.001	-3.340068	0.00017	0.0	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35789	1.29	1.34	-2.69	0.06022	.	.	.	.	.	T	0.10981	0.0268	N	0.03194	-0.395	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10894	-1.0610	9	0.11485	T	0.65	.	0.7864	0.01049	0.2935:0.3354:0.2021:0.169	.	514;396	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	514	ENSP00000291707:V514A	ENSP00000291707:V514A	V	-	2	0	SIGLEC12	56692004	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.050000	0.00156	-3.045000	0.00262	-1.416000	0.01114	GTG	A|1.000;G|0.000	0.000	strong		0.582	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
PIK3CD	5293	hgsc.bcm.edu	37	1	9784423	9784423	+	Silent	SNP	C	C	T	rs11121484	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9784423C>T	ENST00000377346.4	+	22	3003	c.2808C>T	c.(2806-2808)taC>taT	p.Y936Y	PIK3CD_ENST00000536656.1_Silent_p.Y960Y|PIK3CD_ENST00000361110.2_Silent_p.Y960Y	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	936	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|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 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	TCCTCACCTACGACTTTGTCC	0.517													T|||	1532	0.305911	0.5983	0.219	5008	,	,		21084	0.131		0.0755	False		,,,				2504	0.3896				p.Y936Y		Atlas-SNP	.											.	PIK3CD	86	.	0			c.C2808T						PASS	.	T		2271,2135	578.2+/-384.6	588,1095,520	104.0	117.0	113.0		2808	-3.2	1.0	1	dbSNP_120	113	727,7873	786.7+/-407.6	33,661,3606	no	coding-synonymous	PIK3CD	NM_005026.3		621,1756,4126	TT,TC,CC		8.4535,48.4567,23.0509		936/1045	9784423	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	5293	exon22			CACCTACGACTTT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2808C>T	1.37:g.9784423C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	37	CCDS104.1																																																																																			C|0.800;T|0.200	0.200	strong		0.517	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507010	24507010	+	RNA	SNP	C	C	A	rs12587718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24507010C>A	ENST00000558293.1	+	0	176					NR_102693.1																						GGTAGTCAGCCGCCGGAAGCA	0.637													A|||	1669	0.333267	0.6483	0.1916	5008	,	,		17227	0.3274		0.1193	False		,,,				2504	0.2342				p.R63S		Atlas-SNP	.											.	.	.	.	0			c.C187A						PASS	.	A	SER/ARG	2452,1954		696,1060,447	34.0	35.0	34.0		187	3.3	1.0	14	dbSNP_120	34	936,7664		50,836,3414	no	missense	DHRS4L1	NM_001082488.1	110	746,1896,3861	AA,AC,CC		10.8837,44.3486,26.0495	benign	63/282	24507010	3388,9618	2203	4300	6503			728635	exon2			GTCAGCCGCCGGA																													14.37:g.24507010C>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	170	166	0.976471	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	37		662	0.3031135531135531	318	0.6463414634146342	71	0.19613259668508287	191	0.3339160839160839	82	0.10817941952506596	-	7.162	0.585944	0.13749	0.556514	0.108837	ENSG00000225766	ENST00000397065	.	.	.	3.31	3.31	0.37934	NAD(P)-binding domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.00107	-2.115	.	.	.	B	0.06786	0.001	B	0.01281	0.0	T	0.45862	-0.9232	7	0.02654	T	1	.	8.0999	0.30850	0.7943:0.2057:0.0:0.0	rs12587718;rs58779867	63	P0CG22	DR4L1_HUMAN	S	63	.	ENSP00000380255:R63S	R	+	1	0	AL136295.1	23576850	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	5.800000	0.69108	0.473000	0.27368	-0.814000	0.03130	CGC	C|0.731;A|0.269	0.269	strong		0.637	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
RB1CC1	9821	hgsc.bcm.edu	37	8	53555069	53555069	+	Silent	SNP	A	A	G	rs2305427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Silent_p.R1393R	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	160	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	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	
MORN3	283385	hgsc.bcm.edu	37	12	122092181	122092181	+	Splice_Site	SNP	C	C	T	rs11043312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122092181C>T	ENST00000355329.3	-	3	632	c.462G>A	c.(460-462)ctG>ctA	p.L154L		NM_173855.4	NP_776254.3	Q6PF18	MORN3_HUMAN	MORN repeat containing 3	154						nucleus (GO:0005634)				breast(2)|large_intestine(1)|lung(4)|skin(1)|stomach(1)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)		GGCACTCACTCAGGCGCAGCA	0.701													C|||	173	0.0345447	0.0129	0.0418	5008	,	,		8235	0.002		0.0915	False		,,,				2504	0.0337				p.L154L		Atlas-SNP	.											.	MORN3	20	.	0			c.G462A						PASS	.	C		99,4291		3,93,2099	38.0	26.0	30.0		462	1.5	1.0	12	dbSNP_120	30	728,7846		28,672,3587	yes	coding-synonymous-near-splice	MORN3	NM_173855.4		31,765,5686	TT,TC,CC		8.4908,2.2551,6.3792		154/241	122092181	827,12137	2195	4287	6482	SO:0001630	splice_region_variant	283385	exon3			CTCACTCAGGCGC	BC057760	CCDS31917.1	12q24.31	2006-01-17			ENSG00000139714	ENSG00000139714			29807	protein-coding gene	gene with protein product							Standard	NM_173855		Approved		uc001uax.3	Q6PF18	OTTHUMG00000169075	ENST00000355329.3:c.463+1G>A	12.37:g.122092181C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_173855	Q86YQ9	Silent	SNP	ENST00000355329.3	37	CCDS31917.1																																																																																			C|0.950;T|0.050	0.050	strong		0.701	MORN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402154.1	NM_173855	Silent
SCUBE2	57758	hgsc.bcm.edu	37	11	9082068	9082068	+	Missense_Mutation	SNP	G	G	A	rs35703942|rs72547298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9082068G>A	ENST00000309263.3	-	8	926	c.854C>T	c.(853-855)aCg>aTg	p.T285M	SCUBE2_ENST00000457346.2_Missense_Mutation_p.T285M|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T285M|RP11-467K18.2_ENST00000521394.2_RNA|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T285M			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	285						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GACAGCACACGTTTCTGGCAA	0.498													G|||	14	0.00279553	0.0	0.0029	5008	,	,		23726	0.0		0.0089	False		,,,				2504	0.0031				p.T285M		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C854T						PASS	.	G	MET/THR,MET/THR	12,4390	19.1+/-41.9	0,12,2189	143.0	133.0	136.0		854,854	5.9	1.0	11	dbSNP_130	136	92,8500	51.9+/-112.3	3,86,4207	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	81,81	3,98,6396	AA,AG,GG		1.0708,0.2726,0.8004	probably-damaging,probably-damaging	285/808,285/972	9082068	104,12890	2201	4296	6497	SO:0001583	missense	57758	exon8			GCACACGTTTCTG	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.854C>T	11.37:g.9082068G>A	ENSP00000310658:p.Thr285Met	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_001170690	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	G|G	23.8|23.8	4.462764|4.462764	0.84425|0.84425	0.002726|0.002726	0.010708|0.010708	ENSG00000175356|ENSG00000175356	ENST00000519788;ENST00000531429|ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	.|T;T;D;D	.|0.84589	.|-1.34;-1.41;-1.87;-1.53	5.94|5.94	5.94|5.94	0.96194|0.96194	.|Epidermal growth factor-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91885|0.91885	0.7431|0.7431	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.999;1.0;0.999	D|D	0.92305|0.92305	0.5853|0.5853	5|10	.|0.72032	.|D	.|0.01	.|.	20.3736|20.3736	0.98901|0.98901	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|285;285;285	.|Q9NQ36-3;Q9NQ36-2;Q9NQ36	.|.;.;SCUB2_HUMAN	C|M	9;50|285	.|ENSP00000390481:T285M;ENSP00000310658:T285M;ENSP00000415187:T285M;ENSP00000429969:T285M	.|ENSP00000310658:T285M	R|T	-|-	1|2	0|0	SCUBE2|SCUBE2	9038644|9038644	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.916000|0.916000	0.54674|0.54674	9.869000|9.869000	0.99810|0.99810	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CGT|ACG	G|0.994;A|0.006	0.006	strong		0.498	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
DTX1	1840	hgsc.bcm.edu	37	12	113532885	113532885	+	Silent	SNP	C	C	T	rs12426056	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:113532885C>T	ENST00000257600.3	+	7	1928	c.1425C>T	c.(1423-1425)taC>taT	p.Y475Y	DTX1_ENST00000547974.1_3'UTR	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	475					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						AGGCCATCTACGGGGAGAAGA	0.657													C|||	284	0.0567093	0.0113	0.085	5008	,	,		17700	0.001		0.1511	False		,,,				2504	0.0583				p.Y475Y		Atlas-SNP	.											.	DTX1	83	.	0			c.C1425T						PASS	.	C		161,4245	108.2+/-146.6	2,157,2044	54.0	53.0	54.0		1425	-0.4	1.0	12	dbSNP_120	54	1285,7315	252.3+/-278.5	95,1095,3110	no	coding-synonymous	DTX1	NM_004416.2		97,1252,5154	TT,TC,CC		14.9419,3.6541,11.1179		475/621	113532885	1446,11560	2203	4300	6503	SO:0001819	synonymous_variant	1840	exon7			CATCTACGGGGAG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.1425C>T	12.37:g.113532885C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			C|0.902;T|0.098	0.098	strong		0.657	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
MCM10	55388	hgsc.bcm.edu	37	10	13230934	13230934	+	Silent	SNP	C	C	T	rs7904071	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13230934C>T	ENST00000484800.2	+	10	1375	c.1272C>T	c.(1270-1272)agC>agT	p.S424S	MCM10_ENST00000378714.3_Silent_p.S423S|MCM10_ENST00000378694.1_Silent_p.S423S			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	424					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AGAAGCTCAGCGCAAAGCGTG	0.557													C|||	205	0.0409345	0.0053	0.0576	5008	,	,		18242	0.0		0.1421	False		,,,				2504	0.0153				p.S424S		Atlas-SNP	.											.	MCM10	76	.	0			c.C1272T						PASS	.	C	,	133,4273	95.7+/-134.4	3,127,2073	142.0	131.0	134.0		1269,1272	-11.7	0.3	10	dbSNP_116	134	1236,7364	249.4+/-276.7	82,1072,3146	no	coding-synonymous,coding-synonymous	MCM10	NM_018518.4,NM_182751.2	,	85,1199,5219	TT,TC,CC		14.3721,3.0186,10.5259	,	423/875,424/876	13230934	1369,11637	2203	4300	6503	SO:0001819	synonymous_variant	55388	exon10			GCTCAGCGCAAAG	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1272C>T	10.37:g.13230934C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	37	CCDS7096.1																																																																																			C|0.909;T|0.091	0.091	strong		0.557	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
CCHCR1	54535	hgsc.bcm.edu	37	6	31110786	31110786	+	Silent	SNP	T	T	A	rs12364	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31110786T>A	ENST00000376266.5	-	17	2300	c.2178A>T	c.(2176-2178)gcA>gcT	p.A726A	CCHCR1_ENST00000396268.3_Silent_p.A815A|CCHCR1_ENST00000396263.2_Silent_p.A673A|CCHCR1_ENST00000451521.2_Silent_p.A779A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	726					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						CAGGTGCAGATGCTGAACACT	0.537													T|||	714	0.142572	0.1596	0.1369	5008	,	,		20599	0.0952		0.173	False		,,,				2504	0.1411				p.A815A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A2445T						PASS	.	T	,,	518,2500		36,446,1027	292.0	339.0	322.0		2337,2445,2178	-6.8	0.0	6	dbSNP_52	322	897,4521		78,741,1890	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	114,1187,2917	AA,AT,TT		16.5559,17.1637,16.7734	,,	779/836,815/872,726/783	31110786	1415,7021	1509	2709	4218	SO:0001819	synonymous_variant	54535	exon17			TGCAGATGCTGAA	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.2178A>T	6.37:g.31110786T>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			T|0.846;A|0.154	0.154	strong		0.537	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701423	8701423	+	Missense_Mutation	SNP	A	A	G	rs34184531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8701423A>G	ENST00000329805.4	-	1	1244	c.1016T>C	c.(1015-1017)aTt>aCt	p.I339T		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	339						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						GGGAAAGGCAATGCTCACCAG	0.597													A|||	875	0.17472	0.1384	0.1499	5008	,	,		17836	0.13		0.2316	False		,,,				2504	0.229				p.I339T		Atlas-SNP	.											.	MFSD6L	46	.	0			c.T1016C						PASS	.	A	THR/ILE	662,3744	279.6+/-274.9	48,566,1589	72.0	71.0	71.0		1016	-0.6	0.0	17	dbSNP_126	71	1967,6633	344.9+/-325.5	215,1537,2548	yes	missense	MFSD6L	NM_152599.3	89	263,2103,4137	GG,GA,AA		22.8721,15.025,20.2137	benign	339/587	8701423	2629,10377	2203	4300	6503	SO:0001583	missense	162387	exon1			AAGGCAATGCTCA	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1016T>C	17.37:g.8701423A>G	ENSP00000330051:p.Ile339Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_152599	Q6YL34|Q8NA76	Missense_Mutation	SNP	ENST00000329805.4	37	CCDS11146.1	398	0.18223443223443223	89	0.18089430894308944	63	0.17403314917127072	67	0.11713286713286714	179	0.23614775725593667	A	0.432	-0.902668	0.02453	0.15025	0.228721	ENSG00000185156	ENST00000329805	D	0.89123	-2.47	5.3	-0.563	0.11778	Major facilitator superfamily domain, general substrate transporter (1);	0.969423	0.08470	N	0.941105	T	0.00073	0.0002	N	0.04508	-0.205	0.80722	P	0.0	B	0.14438	0.01	B	0.15052	0.012	T	0.01382	-1.1369	9	0.15066	T	0.55	-19.0848	10.3679	0.44035	0.5125:0.0:0.4875:0.0	rs34184531	339	Q8IWD5	MFS6L_HUMAN	T	339	ENSP00000330051:I339T	ENSP00000330051:I339T	I	-	2	0	MFSD6L	8642148	0.001000	0.12720	0.007000	0.13788	0.320000	0.28249	0.331000	0.19733	-0.300000	0.08895	0.533000	0.62120	ATT	A|0.802;G|0.198	0.198	strong		0.597	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
EFEMP2	30008	hgsc.bcm.edu	37	11	65638719	65638719	+	Silent	SNP	G	G	A	rs633800	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65638719G>A	ENST00000307998.6	-	4	506	c.276C>T	c.(274-276)caC>caT	p.H92H	EFEMP2_ENST00000528176.1_Silent_p.H92H	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	92					blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		GTCCCTCGCCGTGTAGGTCGT	0.647													G|||	1608	0.321086	0.0953	0.3127	5008	,	,		17334	0.2262		0.503	False		,,,				2504	0.5429				p.H92H		Atlas-SNP	.											.	EFEMP2	42	.	0			c.C276T						PASS	.	G		703,3699	293.0+/-282.3	52,599,1550	95.0	105.0	102.0		276	-2.5	0.7	11	dbSNP_83	102	4451,4141	588.0+/-392.3	1139,2173,984	no	coding-synonymous	EFEMP2	NM_016938.4		1191,2772,2534	AA,AG,GG		48.196,15.97,39.6645		92/444	65638719	5154,7840	2201	4296	6497	SO:0001819	synonymous_variant	30008	exon4			CTCGCCGTGTAGG	AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"""Fibulins"""	3219	protein-coding gene	gene with protein product	"""fibulin 4"""	604633	"""EGF-containing fibulin-like extracellular matrix protein 2"""			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.276C>T	11.37:g.65638719G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_016938	A8K7R4|B3KM31|B3KQT1|O75967	Silent	SNP	ENST00000307998.6	37	CCDS8116.1																																																																																			G|0.642;A|0.358	0.358	strong		0.647	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938	
NAA25	80018	hgsc.bcm.edu	37	12	112486213	112486213	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112486213C>T	ENST00000261745.4	-	16	2011	c.1763G>A	c.(1762-1764)gGt>gAt	p.G588D		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	588						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						CTCAAATGCACCATATTTGTA	0.388																																					p.G588D		Atlas-SNP	.											.	NAA25	105	.	0			c.G1763A						PASS	.						111.0	106.0	108.0					12																	112486213		2203	4300	6503	SO:0001583	missense	80018	exon16			AATGCACCATATT	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.1763G>A	12.37:g.112486213C>T	ENSP00000261745:p.Gly588Asp	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	57	4	0.0701754	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545698	0.86022	.	.	ENSG00000111300	ENST00000261745	T	0.53857	0.6	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.75722	0.3888	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.75442	-0.3316	10	0.40728	T	0.16	-12.8941	19.5841	0.95484	0.0:1.0:0.0:0.0	.	588;588	A8K8X0;Q14CX7	.;NAA25_HUMAN	D	588	ENSP00000261745:G588D	ENSP00000261745:G588D	G	-	2	0	NAA25	110970596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.604000	0.88044	0.655000	0.94253	GGT	.	.	none		0.388	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
REEP3	221035	hgsc.bcm.edu	37	10	65380587	65380587	+	Silent	SNP	A	A	G	rs1133386	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:65380587A>G	ENST00000373758.4	+	8	909	c.726A>G	c.(724-726)tcA>tcG	p.S242S	REEP3_ENST00000298249.4_Silent_p.S227S	NM_001001330.2	NP_001001330.1	Q6NUK4	REEP3_HUMAN	receptor accessory protein 3	242					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)				endometrium(1)|large_intestine(2)|lung(3)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					GGTACGGGTCACTAAAATACA	0.303													A|||	40	0.00798722	0.0008	0.013	5008	,	,		13795	0.001		0.0219	False		,,,				2504	0.0072				p.S242S		Atlas-SNP	.											.	REEP3	14	.	0			c.A726G						PASS	.	A		15,3621		0,15,1803	78.0	69.0	72.0		726	2.2	1.0	10	dbSNP_86	72	167,7979		5,157,3911	no	coding-synonymous	REEP3	NM_001001330.2		5,172,5714	GG,GA,AA		2.0501,0.4125,1.5447		242/256	65380587	182,11600	1818	4073	5891	SO:0001819	synonymous_variant	221035	exon8			CGGGTCACTAAAA	BC057832	CCDS44411.1	10q21.3	2011-01-05	2006-02-07	2006-02-07	ENSG00000165476	ENSG00000165476		"""Receptor accessory proteins"""	23711	protein-coding gene	gene with protein product		609348	"""chromosome 10 open reading frame 74"""	C10orf74		16271481, 15550249	Standard	NM_001001330		Approved		uc001jmt.3	Q6NUK4	OTTHUMG00000018318	ENST00000373758.4:c.726A>G	10.37:g.65380587A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001001330	Q5JQR5|Q5QGT2|Q6PEW8|Q6PJY4	Silent	SNP	ENST00000373758.4	37	CCDS44411.1																																																																																			A|0.988;G|0.012	0.012	strong		0.303	REEP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001001330	
OTUD7A	161725	hgsc.bcm.edu	37	15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	rs76704217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:31776837C>G	ENST00000307050.4	-	11	1533	c.1441G>C	c.(1441-1443)Gtg>Ctg	p.V481L	OTUD7A_ENST00000382902.1_Missense_Mutation_p.V488L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	481					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)		TTGCTGCACACCGAATCGCGG	0.642													C|||	57	0.0113818	0.0015	0.0173	5008	,	,		19876	0.001		0.0378	False		,,,				2504	0.0041				p.V481L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.G1441C						PASS	.	C	LEU/VAL	30,4354		0,30,2162	80.0	57.0	64.0		1441	2.4	1.0	15	dbSNP_131	64	415,8183		14,387,3898	yes	missense	OTUD7A	NM_130901.1	32	14,417,6060	GG,GC,CC		4.8267,0.6843,3.4278	benign	481/927	31776837	445,12537	2192	4299	6491	SO:0001583	missense	161725	exon11			TGCACACCGAATC	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.1441G>C	15.37:g.31776837C>G	ENSP00000305926:p.Val481Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	45	0.020604395604395604	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	C	14.83	2.652700	0.47362	0.006843	0.048267	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.34472	1.37;1.36	4.35	2.4	0.29515	.	0.175056	0.50627	D	0.000102	T	0.06005	0.0156	M	0.69823	2.125	0.28750	N	0.90147	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	10	0.51188	T	0.08	-32.5726	3.9645	0.09424	0.0:0.5203:0.2199:0.2599	.	488;481	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	L	481;488	ENSP00000305926:V481L;ENSP00000372358:V488L	ENSP00000305926:V481L	V	-	1	0	OTUD7A	29564129	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	2.060000	0.41394	0.936000	0.37367	0.655000	0.94253	GTG	C|0.970;G|0.030	0.030	strong		0.642	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
JRK	8629	hgsc.bcm.edu	37	8	143746416	143746416	+	RNA	SNP	A	A	G	rs754957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143746416A>G	ENST00000507178.2	-	0	1394							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tgtagcgggcatgggggccct	0.612													G|||	2671	0.533347	0.7209	0.3213	5008	,	,		18399	0.5188		0.3917	False		,,,				2504	0.591				p.H354H		Atlas-SNP	.											.	.	.	.	0			c.T1062C						PASS	.	G	,	2462,1536		789,884,326	8.0	9.0	9.0		1062,1062	-0.7	0.0	8	dbSNP_86	9	3105,5209		657,1791,1709	yes	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	1446,2675,2035	GG,GA,AA		37.3466,38.4192,45.216	,	354/557,354/569	143746416	5567,6745	1999	4157	6156			8629	exon2			GCGGGCATGGGGG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746416A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.478;G|0.522	0.522	strong		0.612	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
KIAA1958	158405	hgsc.bcm.edu	37	9	115337154	115337154	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115337154A>G	ENST00000337530.6	+	2	1090	c.794A>G	c.(793-795)gAc>gGc	p.D265G	KIAA1958_ENST00000536272.1_Missense_Mutation_p.D265G|KIAA1958_ENST00000374244.3_Missense_Mutation_p.D265G	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	265										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						ACGGAGCTAGACCCACACGGT	0.547																																					p.D265G		Atlas-SNP	.											KIAA1958_ENST00000374244,NS,carcinoma,+1,3	KIAA1958	52	3	0			c.A794G						PASS	.						239.0	211.0	221.0					9																	115337154		2203	4300	6503	SO:0001583	missense	158405	exon2			AGCTAGACCCACA	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.794A>G	9.37:g.115337154A>G	ENSP00000336940:p.Asp265Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	5	0.0490196	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	37	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999186	0.54147	.	.	ENSG00000165185	ENST00000337530;ENST00000374244;ENST00000536272	T;T;T	0.41758	0.99;0.99;0.99	6.07	6.07	0.98685	.	0.067648	0.64402	D	0.000011	T	0.33059	0.0850	N	0.14661	0.345	0.58432	D	0.999991	P;P	0.46395	0.877;0.734	B;B	0.43194	0.411;0.321	T	0.24297	-1.0164	10	0.66056	D	0.02	-10.9977	16.6288	0.85011	1.0:0.0:0.0:0.0	.	265;265	B7ZKW6;Q8N8K9	.;K1958_HUMAN	G	265	ENSP00000336940:D265G;ENSP00000363362:D265G;ENSP00000440504:D265G	ENSP00000336940:D265G	D	+	2	0	KIAA1958	114376975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.696000	0.74598	2.326000	0.78906	0.533000	0.62120	GAC	.	.	none		0.547	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465	
SAMD15	161394	hgsc.bcm.edu	37	14	77844869	77844869	+	Missense_Mutation	SNP	A	A	G	rs4903576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77844869A>G	ENST00000216471.4	+	1	1394	c.1108A>G	c.(1108-1110)Aaa>Gaa	p.K370E	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	370			K -> E (in dbSNP:rs4903576).					p.K370E(1)		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						GTCAAATGAGAAAAAAAATCC	0.388													G|||	2620	0.523163	0.9259	0.4841	5008	,	,		19467	0.0893		0.497	False		,,,				2504	0.4806				p.K370E		Atlas-SNP	.											SAMD15,NS,carcinoma,0,1	SAMD15	60	1	1	Substitution - Missense(1)	stomach(1)	c.A1108G						PASS	.	G	GLU/LYS	3738,668	261.0+/-264.0	1601,536,66	77.0	80.0	79.0		1108	2.4	0.0	14	dbSNP_111	79	4015,4585	579.8+/-390.9	954,2107,1239	yes	missense	SAMD15	NM_001010860.1	56	2555,2643,1305	GG,GA,AA		46.686,15.1611,40.3891	benign	370/675	77844869	7753,5253	2203	4300	6503	SO:0001583	missense	161394	exon1			AATGAGAAAAAAA	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.1108A>G	14.37:g.77844869A>G	ENSP00000216471:p.Lys370Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	1066	0.4880952380952381	451	0.9166666666666666	197	0.5441988950276243	43	0.07517482517482517	375	0.4947229551451187	G	0.279	-0.987681	0.02162	0.848389	0.46686	ENSG00000100583	ENST00000216471	T	0.30714	1.52	5.35	2.43	0.29744	.	1.460450	0.04946	N	0.459412	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	0.33471	-0.9867	9	0.02654	T	1	.	4.4543	0.11635	0.2564:0.0:0.5899:0.1537	rs4903576;rs57517281;rs4903576	370	Q9P1V8	SAM15_HUMAN	E	370	ENSP00000216471:K370E	ENSP00000216471:K370E	K	+	1	0	SAMD15	76914622	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.524000	0.06222	0.262000	0.21774	-0.227000	0.12334	AAA	A|0.446;G|0.554	0.554	strong		0.388	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373452	80373452	+	Silent	SNP	C	C	T	rs4789769	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80373452C>T	ENST00000313056.5	-	2	277	c.126G>A	c.(124-126)ccG>ccA	p.P42P	Y_RNA_ENST00000364369.1_RNA|HEXDC_ENST00000337014.6_5'Flank|OGFOD3_ENST00000329197.5_Silent_p.P42P	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	43	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	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	
UGT2B17	7367	hgsc.bcm.edu	37	4	69433714	69433714	+	Silent	SNP	C	C	T	rs34664906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69433714C>T	ENST00000317746.2	-	1	531	c.489G>A	c.(487-489)gaG>gaA	p.E163E		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	163					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TGTTAAGTAGCTCAGCCAGCA	0.443													C|||	1417	0.282947	0.3306	0.4798	5008	,	,		8754	0.0476		0.3549	False		,,,				2504	0.2474				p.E163E	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											UGT2B17,NS,carcinoma,-1,1	UGT2B17	34	1	0			c.G489A						PASS	.	C		1402,2780		435,532,1124	177.0	173.0	174.0		489	1.8	0.3	4	dbSNP_126	174	3313,4597		1164,985,1806	no	coding-synonymous	UGT2B17	NM_001077.3		1599,1517,2930	TT,TC,CC		41.8837,33.5246,38.9927		163/531	69433714	4715,7377	2091	3955	6046	SO:0001819	synonymous_variant	7367	exon1			AAGTAGCTCAGCC	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.489G>A	4.37:g.69433714C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	226	225	0.995575	NM_001077		Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																			C|0.694;T|0.306	0.306	strong		0.443	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	
ESR2	2100	hgsc.bcm.edu	37	14	64724051	64724051	+	Silent	SNP	C	C	T	rs1256049	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64724051C>T	ENST00000341099.4	-	6	1401	c.984G>A	c.(982-984)gtG>gtA	p.V328V	ESR2_ENST00000353772.3_Silent_p.V328V|ESR2_ENST00000542956.1_Silent_p.V328V|ESR2_ENST00000553796.1_Silent_p.V328V|ESR2_ENST00000555278.1_Silent_p.V328V|ESR2_ENST00000357782.2_Silent_p.V328V|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000267525.6_Intron|ESR2_ENST00000554572.1_Silent_p.V328V|ESR2_ENST00000557772.1_Silent_p.V328V|ESR2_ENST00000358599.5_Silent_p.V328V	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	328	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.V328V(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CCAAGAGCCGCACTTGGTCGA	0.572													C|||	649	0.129593	0.1029	0.0346	5008	,	,		15483	0.4028		0.0358	False		,,,				2504	0.0481				p.V328V		Atlas-SNP	.											ESR2,NS,carcinoma,0,1	ESR2	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G984A	GRCh37	CM010232	ESR2	M	rs1256049	PASS	.	C	,,,,	396,4010	198.7+/-222.5	14,368,1821	105.0	106.0	105.0		984,984,984,984,984	1.7	1.0	14	dbSNP_87	105	297,8303	109.0+/-169.6	5,287,4008	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR2	NM_001040275.1,NM_001040276.1,NM_001214902.1,NM_001214903.1,NM_001437.2	,,,,	19,655,5829	TT,TC,CC		3.4535,8.9877,5.3283	,,,,	328/496,328/496,328/482,328/473,328/531	64724051	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	2100	exon5			GAGCCGCACTTGG	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.984G>A	14.37:g.64724051C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Silent	SNP	ENST00000341099.4	37	CCDS9762.1																																																																																			C|0.909;T|0.091	0.091	strong		0.572	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1		
ABCA2	20	hgsc.bcm.edu	37	9	139916833	139916833	+	Silent	SNP	T	T	G	rs35590326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139916833T>G	ENST00000371605.3	-	5	681	c.534A>C	c.(532-534)gcA>gcC	p.A178A	ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000341511.6_Silent_p.A179A|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	123	9	0.0731707		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	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	
KCNIP4	80333	hgsc.bcm.edu	37	4	20751343	20751343	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:20751343T>C	ENST00000382152.2	-	5	538	c.371A>G	c.(370-372)tAt>tGt	p.Y124C	KCNIP4_ENST00000509207.1_Missense_Mutation_p.Y62C|KCNIP4_ENST00000382148.3_Missense_Mutation_p.Y99C|PACRGL_ENST00000507634.1_Intron|KCNIP4_ENST00000382150.4_Missense_Mutation_p.Y103C|KCNIP4_ENST00000359001.5_Missense_Mutation_p.Y62C|KCNIP4_ENST00000447367.2_Missense_Mutation_p.Y90C|KCNIP4_ENST00000382149.4_5'UTR	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	124	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				AAAATGTGCATATGTTGTAGA	0.368																																					p.Y104C		Atlas-SNP	.											.	KCNIP4	85	.	0			c.A311G						PASS	.						114.0	105.0	108.0					4																	20751343		2203	4300	6503	SO:0001583	missense	80333	exon4			TGTGCATATGTTG	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"""EF-hand domain containing"""	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.371A>G	4.37:g.20751343T>C	ENSP00000371587:p.Tyr124Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	4	0.0833333	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Missense_Mutation	SNP	ENST00000382152.2	37	CCDS43216.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628173	0.66901	.	.	ENSG00000185774	ENST00000382148;ENST00000447367;ENST00000382150;ENST00000413487;ENST00000382152;ENST00000509207;ENST00000359001	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.24	5.24	0.73138	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.92880	3.355	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.999	T	0.67715	-0.5599	10	0.87932	D	0	.	14.1041	0.65078	0.0:0.0:0.0:1.0	.	99;103;107;124	Q3YAB9;Q3YAC0;Q3YAB7;Q6PIL6	.;.;.;KCIP4_HUMAN	C	99;90;103;62;124;62;62	ENSP00000371583:Y99C;ENSP00000399080:Y90C;ENSP00000371585:Y103C;ENSP00000371587:Y124C;ENSP00000423257:Y62C;ENSP00000351892:Y62C	ENSP00000351892:Y62C	Y	-	2	0	KCNIP4	20360441	1.000000	0.71417	0.997000	0.53966	0.725000	0.41563	7.662000	0.83803	1.974000	0.57490	0.482000	0.46254	TAT	.	.	none		0.368	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221	
TMEM14E	645843	hgsc.bcm.edu	37	3	152058449	152058449	+	Missense_Mutation	SNP	A	A	G	rs13077912	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:152058449A>G	ENST00000408960.3	-	1	330	c.245T>C	c.(244-246)cTa>cCa	p.L82P	MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000324210.5_Intron|MBNL1_ENST00000492948.1_Intron|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000485910.1_Intron|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000282486.6_Intron|MBNL1_ENST00000463374.1_Intron|MBNL1_ENST00000545754.1_Intron|MBNL1_ENST00000282488.7_Intron|MBNL1_ENST00000357472.3_Intron|MBNL1_ENST00000493459.1_Intron	NM_001123228.1	NP_001116700.1	Q6UXP3	TM14E_HUMAN	transmembrane protein 14E	82			L -> P (in dbSNP:rs13077912).			integral component of membrane (GO:0016021)				lung(1)	1						CCAGAGTGTTAGAATCTTATT	0.443													A|||	346	0.0690895	0.0484	0.085	5008	,	,		19975	0.0099		0.161	False		,,,				2504	0.0521				p.L82P		Atlas-SNP	.											.	TMEM14E	6	.	0			c.T245C						PASS	.	A	PRO/LEU,,,,,,,	189,2947		8,173,1387	111.0	98.0	102.0		245,,,,,,,	0.9	0.0	3	dbSNP_121	102	1123,6041		95,933,2554	yes	missense,intron,intron,intron,intron,intron,intron,intron	MBNL1,TMEM14E	NM_001123228.1,NM_021038.3,NM_207292.1,NM_207293.1,NM_207294.1,NM_207295.1,NM_207296.1,NM_207297.1	98,,,,,,,	103,1106,3941	GG,GA,AA		15.6756,6.0268,12.7379	probably-damaging,,,,,,,	82/126,,,,,,,	152058449	1312,8988	1568	3582	5150	SO:0001583	missense	645843	exon1			AGTGTTAGAATCT		CCDS43161.1	3q25.1	2011-09-15			ENSG00000221962	ENSG00000221962			34386	protein-coding gene	gene with protein product							Standard	NM_001123228		Approved		uc010hvo.3	Q6UXP3	OTTHUMG00000159652	ENST00000408960.3:c.245T>C	3.37:g.152058449A>G	ENSP00000386163:p.Leu82Pro	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	152	95	0.625	NM_001123228		Missense_Mutation	SNP	ENST00000408960.3	37	CCDS43161.1	188	0.08608058608058608	27	0.054878048780487805	38	0.10497237569060773	5	0.008741258741258742	118	0.15567282321899736	A	11.16	1.557587	0.27827	0.060268	0.156756	ENSG00000221962	ENST00000408960	T	0.35421	1.31	2.12	0.919	0.19392	.	.	.	.	.	T	0.00144	0.0004	N	0.19112	0.55	0.80722	P	0.0	D	0.76494	0.999	D	0.66497	0.944	T	0.06935	-1.0799	8	0.45353	T	0.12	.	3.901	0.09161	0.8047:0.0:0.1953:0.0	rs13077912;rs52798054;rs13077912	82	Q6UXP3	TM14E_HUMAN	P	82	ENSP00000386163:L82P	ENSP00000386163:L82P	L	-	2	0	TMEM14E	153541139	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.111000	0.15458	0.249000	0.21456	-0.361000	0.07541	CTA	A|0.902;G|0.098	0.098	strong		0.443	TMEM14E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356703.1	NM_001123228	
SRRM4	84530	hgsc.bcm.edu	37	12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	rs7297606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	18	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	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	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634350	32634350	+	Missense_Mutation	SNP	T	T	C	rs1049057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32634350T>C	ENST00000399082.3	-	1	79	c.35A>G	c.(34-36)gAc>gGc	p.D12G	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.D12G|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.D12G|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.D12G|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.D12G			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	12			G -> D (in allele DQB1*05:01, allele DQB1*05:02, allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs1049057).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TACCCGAAGGTCTCCGGGGAT	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				t|||	3031	0.605232	0.4818	0.7089	5008	,	,		11450	0.6657		0.5755	False		,,,				2504	0.6667				p.D12G	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.A35G						PASS	.	C	GLY/ASP	1428,2438		461,506,966	50.0	48.0	49.0		35	1.7	0.0	6	dbSNP_86	49	3721,4489		1409,903,1793	yes	missense	HLA-DQB1	NM_002123.4	94	1870,1409,2759	CC,CT,TT		45.3228,36.9374,42.6383	benign	12/262	32634350	5149,6927	1933	4105	6038	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CGAAGGTCTCCGG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.35A>G	6.37:g.32634350T>C	ENSP00000382032:p.Asp12Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		1225	0.5608974358974359	193	0.39227642276422764	236	0.6519337016574586	398	0.6958041958041958	398	0.525065963060686	.	0.021	-1.421267	0.01126	0.369374	0.453228	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03386	3.95;8.5;8.5;8.5;8.5	3.59	1.68	0.24146	.	.	.	.	.	T	0.00384	0.0012	.	.	.	0.80722	P	0.0	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.44081	-0.9351	7	0.02654	T	1	.	3.1383	0.06447	0.2174:0.5424:0.0:0.2402	rs1049057;rs3189133;rs9274521;rs12722099;rs16868461	22;12;12;12	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	G	12	ENSP00000382032:D12G;ENSP00000382029:D12G;ENSP00000364080:D12G;ENSP00000407332:D12G;ENSP00000382034:D12G	ENSP00000364080:D12G	D	-	2	0	HLA-DQB1	32742328	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.328000	0.19681	0.003000	0.14656	-0.368000	0.07277	GAC	T|0.417;C|0.583	0.583	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
WWC2	80014	hgsc.bcm.edu	37	4	184207192	184207192	+	Missense_Mutation	SNP	C	C	T	rs148189381		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184207192C>T	ENST00000403733.3	+	20	3320	c.3121C>T	c.(3121-3123)Cgc>Tgc	p.R1041C	WWC2_ENST00000513834.1_Missense_Mutation_p.R992C|WWC2_ENST00000508747.1_Missense_Mutation_p.R169C|WWC2_ENST00000504005.1_Missense_Mutation_p.R723C|WWC2_ENST00000448232.2_Missense_Mutation_p.R1065C	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1041					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)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CACCGAACGCCGCAGTTTGAG	0.448																																					p.R1041C		Atlas-SNP	.											.	WWC2	78	.	0			c.C3121T						PASS	.	C	CYS/ARG	0,4404		0,0,2202	73.0	63.0	67.0		3121	4.4	1.0	4	dbSNP_134	67	1,8599		0,1,4299	no	missense	WWC2	NM_024949.5	180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1041/1193	184207192	1,13003	2202	4300	6502	SO:0001583	missense	80014	exon20			GAACGCCGCAGTT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3121C>T	4.37:g.184207192C>T	ENSP00000384222:p.Arg1041Cys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897272	0.72639	0.0	1.16E-4	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.23	4.39	0.52855	.	0.082358	0.50627	D	0.000117	T	0.71350	0.3329	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.998	T	0.73672	-0.3909	10	0.54805	T	0.06	-15.2741	9.6331	0.39791	0.1967:0.7307:0.0:0.0726	.	1065;1041;169;992	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	C	1041;992;1065;723;169	ENSP00000384222:R1041C;ENSP00000425054:R992C;ENSP00000398577:R1065C;ENSP00000427569:R723C;ENSP00000420835:R169C	ENSP00000384222:R1041C	R	+	1	0	WWC2	184444186	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.516000	0.45520	1.443000	0.47586	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.448	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
GRAP2	9402	hgsc.bcm.edu	37	22	40366924	40366924	+	Missense_Mutation	SNP	C	C	T	rs149718626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:40366924C>T	ENST00000344138.4	+	8	1092	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	GRAP2_ENST00000399090.2_Missense_Mutation_p.R164W|GRAP2_ENST00000543252.1_Missense_Mutation_p.R237W|GRAP2_ENST00000407075.3_Missense_Mutation_p.R277W|GRAP2_ENST00000540310.1_Missense_Mutation_p.R211W|GRAP2_ENST00000544756.1_Missense_Mutation_p.R205W	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	277	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GCGGTGGGCCCGGGCGCTGTA	0.657																																					p.R277W		Atlas-SNP	.											.	GRAP2	29	.	0			c.C829T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	42.0	44.0	43.0		829	0.6	0.9	22	dbSNP_134	43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	GRAP2	NM_004810.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	277/331	40366924	2,13004	2203	4300	6503	SO:0001583	missense	9402	exon8			TGGGCCCGGGCGC	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"""SH2 domain containing"""	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.829C>T	22.37:g.40366924C>T	ENSP00000339186:p.Arg277Trp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786068	0.70337	0.0	2.33E-4	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.52983	0.64;1.37;0.64;0.64;0.64;0.64	5.45	0.607	0.17564	Src homology-3 domain (5);	0.508670	0.20690	N	0.087471	T	0.69513	0.3119	M	0.92649	3.33	0.40772	D	0.983098	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.998	D;P;D;P;P	0.68765	0.96;0.817;0.921;0.877;0.817	T	0.73257	-0.4040	10	0.66056	D	0.02	-14.6978	8.7497	0.34609	0.5226:0.4077:0.0:0.0697	.	164;277;211;251;277	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	W	277;237;251;211;205;164;277	ENSP00000339186:R277W;ENSP00000446350:R237W;ENSP00000444734:R211W;ENSP00000442195:R205W;ENSP00000382040:R164W;ENSP00000385607:R277W	ENSP00000339186:R277W	R	+	1	2	GRAP2	38696870	0.999000	0.42202	0.932000	0.37286	0.880000	0.50808	0.823000	0.27366	0.593000	0.29745	0.557000	0.71058	CGG	C|1.000;T|0.000	0.000	strong		0.657	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810	
OR6C74	254783	hgsc.bcm.edu	37	12	55641075	55641075	+	Missense_Mutation	SNP	A	A	G	rs7301705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55641075A>G	ENST00000343870.4	+	1	94	c.4A>G	c.(4-6)Aga>Gga	p.R2G		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	2			R -> G (in dbSNP:rs7301705).			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						ATCAACTATGAGAAACCATAC	0.318													A|||	1105	0.220647	0.1248	0.2291	5008	,	,		16842	0.0794		0.333	False		,,,				2504	0.3742				p.R2G		Atlas-SNP	.											.	OR6C74	52	.	0			c.A4G						PASS	.	A	GLY/ARG	688,3716	271.3+/-270.1	48,592,1562	101.0	99.0	100.0		4	-0.7	0.1	12	dbSNP_116	100	2714,5886	416.3+/-352.1	425,1864,2011	yes	missense	OR6C74	NM_001005490.1	125	473,2456,3573	GG,GA,AA		31.5581,15.6222,26.1612	benign	2/313	55641075	3402,9602	2202	4300	6502	SO:0001583	missense	254783	exon1			ACTATGAGAAACC		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.4A>G	12.37:g.55641075A>G	ENSP00000342836:p.Arg2Gly	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	454	0.2078754578754579	66	0.13414634146341464	95	0.26243093922651933	46	0.08041958041958042	247	0.3258575197889182	a	10.26	1.302047	0.23736	0.156222	0.315581	ENSG00000197706	ENST00000343870	T	0.01665	4.7	4.83	-0.667	0.11395	.	0.415391	0.20729	N	0.086750	T	0.00012	0.0000	N	0.16368	0.405	0.53005	P	3.900000000001125E-5	B	0.10296	0.003	B	0.19946	0.027	T	0.46610	-0.9179	9	0.40728	T	0.16	.	5.0269	0.14389	0.495:0.2724:0.2326:0.0	rs7301705;rs52817965;rs61689751;rs7301705	2	A6NCV1	O6C74_HUMAN	G	2	ENSP00000342836:R2G	ENSP00000342836:R2G	R	+	1	2	OR6C74	53927342	0.376000	0.25098	0.080000	0.20451	0.147000	0.21601	-0.260000	0.08708	-0.178000	0.10672	0.450000	0.29827	AGA	A|0.753;G|0.247	0.247	strong		0.318	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
CYP2A7	1549	hgsc.bcm.edu	37	19	41384702	41384702	+	Missense_Mutation	SNP	T	T	C	rs117539170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:41384702T>C	ENST00000301146.4	-	5	1335	c.794A>G	c.(793-795)cAg>cGg	p.Q265R	CYP2A7_ENST00000291764.3_Missense_Mutation_p.Q214R|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	265						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GATGAAGTCCTGTGGGGAATT	0.572													.|||	699	0.139577	0.1664	0.1052	5008	,	,		18540	0.0456		0.2336	False		,,,				2504	0.1278				p.Q265R		Atlas-SNP	.											.	CYP2A7	71	.	0			c.A794G						PASS	.						122.0	92.0	103.0					19																	41384702		2203	4299	6502	SO:0001583	missense	1549	exon5			AAGTCCTGTGGGG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.794A>G	19.37:g.41384702T>C	ENSP00000301146:p.Gln265Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	219	113	0.515982	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	284	0.13003663003663005	73	0.1483739837398374	36	0.09944751381215469	16	0.027972027972027972	159	0.20976253298153033	C	0.267	-0.995466	0.02145	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.64260	-0.09;-0.09	2.18	2.18	0.27775	.	0.117868	0.53938	N	0.000051	T	0.00012	0.0000	N	0.00098	-2.145	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.22977	-1.0201	9	0.02654	T	1	.	6.4282	0.21782	0.0:0.8412:0.0:0.1588	.	214;265	F8W816;P20853	.;CP2A7_HUMAN	R	265;214	ENSP00000301146:Q265R;ENSP00000291764:Q214R	ENSP00000291764:Q214R	Q	-	2	0	CYP2A7	46076542	0.002000	0.14202	0.033000	0.17914	0.219000	0.24729	1.278000	0.33179	0.257000	0.21650	-1.160000	0.01791	CAG	T|0.870;C|0.130	0.130	strong		0.572	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
DNAJC13	23317	hgsc.bcm.edu	37	3	132218623	132218623	+	Missense_Mutation	SNP	G	G	T	rs3762672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132218623G>T	ENST00000260818.6	+	38	4635	c.4387G>T	c.(4387-4389)Gct>Tct	p.A1463S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1463			A -> S (in dbSNP:rs3762672). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9734811}.		osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CTTGACTCGTGCTAGTAAACC	0.423													T|||	3701	0.739018	0.9796	0.513	5008	,	,		17576	0.8839		0.4891	False		,,,				2504	0.682				p.A1463S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.G4387T						PASS	.	T	SER/ALA	3918,488	228.5+/-243.3	1744,430,29	221.0	230.0	227.0		4387	5.2	1.0	3	dbSNP_107	227	4130,4470	590.3+/-392.7	1012,2106,1182	yes	missense	DNAJC13	NM_015268.3	99	2756,2536,1211	TT,TG,GG		48.0233,11.0758,38.1209	benign	1463/2244	132218623	8048,4958	2203	4300	6503	SO:0001583	missense	23317	exon38			ACTCGTGCTAGTA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4387G>T	3.37:g.132218623G>T	ENSP00000260818:p.Ala1463Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	1587	0.7266483516483516	477	0.9695121951219512	197	0.5441988950276243	535	0.9353146853146853	378	0.49868073878627966	T	9.154	1.017079	0.19355	0.889242	0.480233	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.44881	0.91	5.17	5.17	0.71159	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00094	-2.165	0.47374	P	5.979999999999874E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41734	-0.9492	9	0.02654	T	1	.	12.5822	0.56397	0.0:0.0:0.139:0.8609	rs3762672;rs17411585;rs52836147;rs60113069;rs3762672	1463	O75165	DJC13_HUMAN	S	1463;110	ENSP00000260818:A1463S	ENSP00000260818:A1463S	A	+	1	0	DNAJC13	133701313	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.799000	0.69101	0.901000	0.36495	-0.375000	0.07067	GCT	G|0.315;T|0.685	0.685	strong		0.423	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
MSGN1	343930	hgsc.bcm.edu	37	2	17998331	17998331	+	Silent	SNP	T	T	C	rs13001625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	54	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	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	
CRYGB	1419	hgsc.bcm.edu	37	2	209007559	209007559	+	Missense_Mutation	SNP	T	T	G	rs796287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209007559T>G	ENST00000260988.4	-	3	378	c.331A>C	c.(331-333)Atc>Ctc	p.I111L		NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B	111	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.		I -> L (in dbSNP:rs796287). {ECO:0000269|PubMed:12011157, ECO:0000269|PubMed:12676897, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2777080, ECO:0000269|PubMed:4065573}.		lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		TGAACAGAGATACAGTCGTCT	0.517													G|||	3228	0.644569	0.6203	0.5447	5008	,	,		17939	0.5952		0.7326	False		,,,				2504	0.7086				p.I111L		Atlas-SNP	.											.	CRYGB	24	.	0			c.A331C						PASS	.	G	LEU/ILE	2978,1428	465.9+/-354.3	1033,912,258	145.0	145.0	145.0		331	0.5	0.1	2	dbSNP_86	145	6334,2266	384.1+/-341.0	2333,1668,299	yes	missense	CRYGB	NM_005210.3	5	3366,2580,557	GG,GT,TT		26.3488,32.4103,28.4023	benign	111/176	209007559	9312,3694	2203	4300	6503	SO:0001583	missense	1419	exon3			CAGAGATACAGTC		CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"""crystallin, gamma 1-2"""	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.331A>C	2.37:g.209007559T>G	ENSP00000260988:p.Ile111Leu	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	211	210	0.995261	NM_005210	Q17RB5|Q53ST2	Missense_Mutation	SNP	ENST00000260988.4	37	CCDS2380.1	1385	0.6341575091575091	319	0.6483739837398373	206	0.569060773480663	315	0.5506993006993007	545	0.7189973614775725	G	10.87	1.474126	0.26423	0.675897	0.736512	ENSG00000182187	ENST00000260988	T	0.75589	-0.95	4.64	0.468	0.16732	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.463806	0.25377	N	0.031104	T	0.00012	0.0000	N	0.01668	-0.77	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44559	-0.9320	9	0.54805	T	0.06	.	9.4649	0.38806	0.0:0.128:0.3464:0.5255	rs796287;rs17641392;rs58328262;rs796287	111	P07316	CRGB_HUMAN	L	111	ENSP00000260988:I111L	ENSP00000260988:I111L	I	-	1	0	CRYGB	208715804	0.005000	0.15991	0.102000	0.21198	0.613000	0.37349	0.827000	0.27421	-0.247000	0.09597	-0.217000	0.12591	ATC	G|0.655;N|0.000	0.655	strong		0.517	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256473.2	NM_005210	
PDCD4	27250	hgsc.bcm.edu	37	10	112654238	112654238	+	Silent	SNP	C	C	T	rs41292602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:112654238C>T	ENST00000280154.7	+	10	1441	c.1167C>T	c.(1165-1167)tcC>tcT	p.S389S	PDCD4_ENST00000393104.2_Silent_p.S378S	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	389	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		TATTAAAGTCCCTTTGGAAGT	0.284													C|||	9	0.00179712	0.0008	0.0014	5008	,	,		17286	0.0		0.007	False		,,,				2504	0.0				p.S389S	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.C1167T						PASS	.	C	,,	3,4399	2.1+/-5.4	0,3,2198	87.0	97.0	93.0		1125,1167,1134	-7.2	0.5	10	dbSNP_127	93	45,8529	27.9+/-77.7	0,45,4242	no	coding-synonymous,coding-synonymous,coding-synonymous	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	,,	0,48,6440	TT,TC,CC		0.5248,0.0682,0.3699	,,	375/456,389/470,378/459	112654238	48,12928	2201	4287	6488	SO:0001819	synonymous_variant	27250	exon10			AAAGTCCCTTTGG	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1167C>T	10.37:g.112654238C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																			C|0.997;T|0.003	0.003	strong		0.284	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
CD164L2	388611	hgsc.bcm.edu	37	1	27709020	27709020	+	Missense_Mutation	SNP	T	T	C	rs2504779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27709020T>C	ENST00000374030.1	-	2	366	c.226A>G	c.(226-228)Atg>Gtg	p.M76V	CD164L2_ENST00000374027.3_Missense_Mutation_p.M76V|CD164L2_ENST00000374025.3_Missense_Mutation_p.M76V			Q6UWJ8	C16L2_HUMAN	CD164 sialomucin-like 2	76			M -> V (in dbSNP:rs2504779).			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TGCTCCCACATGCAGCTGGAG	0.657													C|||	1686	0.336661	0.6082	0.0764	5008	,	,		13151	0.3998		0.1362	False		,,,				2504	0.2955				p.M76V		Atlas-SNP	.											.	CD164L2	13	.	0			c.A226G						PASS	.	C	VAL/MET	2321,2085	569.4+/-382.6	620,1081,502	43.0	45.0	45.0		226	3.6	0.8	1	dbSNP_100	45	838,7762	780.3+/-407.7	32,774,3494	yes	missense	CD164L2	NM_207397.2	21	652,1855,3996	CC,CT,TT		9.7442,47.3218,24.2888	benign	76/174	27709020	3159,9847	2203	4300	6503	SO:0001583	missense	388611	exon2			CCCACATGCAGCT	AY358761	CCDS302.1	1p36.11	2008-02-05			ENSG00000174950	ENSG00000174950			32043	protein-coding gene	gene with protein product							Standard	XM_005245868		Approved		uc001boc.3	Q6UWJ8	OTTHUMG00000003395	ENST00000374030.1:c.226A>G	1.37:g.27709020T>C	ENSP00000363142:p.Met76Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_207397	B2RPJ0|Q5JXD6	Missense_Mutation	SNP	ENST00000374030.1	37		618	0.28296703296703296	288	0.5853658536585366	30	0.08287292817679558	199	0.3479020979020979	101	0.13324538258575197	C	0.006	-2.098954	0.00360	0.526782	0.097442	ENSG00000174950	ENST00000374030;ENST00000374027;ENST00000374025	T;T;T	0.35421	1.31;1.31;1.31	4.5	3.58	0.41010	.	0.000000	0.43919	N	0.000517	T	0.00012	0.0000	N	0.00119	-2.075	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46638	-0.9177	9	0.02654	T	1	-13.4328	6.4453	0.21873	0.0:0.7181:0.1819:0.1	rs2504779;rs59160788;rs2504779	76	Q6UWJ8	C16L2_HUMAN	V	76	ENSP00000363142:M76V;ENSP00000363139:M76V;ENSP00000363137:M76V	ENSP00000363137:M76V	M	-	1	0	CD164L2	27581607	0.854000	0.29725	0.772000	0.31596	0.039000	0.13416	0.367000	0.20382	0.524000	0.28502	-0.227000	0.12334	ATG	T|0.731;C|0.269	0.269	strong		0.657	CD164L2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009518.1	NM_207397	
HUS1	3364	hgsc.bcm.edu	37	7	48004962	48004962	+	Silent	SNP	C	C	T	rs1056663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:48004962C>T	ENST00000258774.5	-	8	857	c.834G>A	c.(832-834)gcG>gcA	p.A278A	HUS1_ENST00000432325.1_Silent_p.A257A	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	278					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)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				GCTAGGACAGCGCAGGGATGA	0.488								Direct reversal of damage;Other conserved DNA damage response genes					c|||	2120	0.423323	0.2799	0.4928	5008	,	,		20745	0.5119		0.5189	False		,,,				2504	0.3783				p.A278A	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.G834A						PASS	.	G		1389,3017	457.8+/-351.8	236,917,1050	164.0	129.0	141.0		834	-10.3	0.0	7	dbSNP_86	141	4384,4216	584.4+/-391.7	1096,2192,1012	no	coding-synonymous	HUS1	NM_004507.3		1332,3109,2062	TT,TC,CC		49.0233,31.5252,44.3872		278/281	48004962	5773,7233	2203	4300	6503	SO:0001819	synonymous_variant	3364	exon8			GGACAGCGCAGGG	Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"""hus1+-like protein"""	603760	"""HUS1 (S. pombe) checkpoint homolog"""			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.834G>A	7.37:g.48004962C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_004507	B4DFI9	Silent	SNP	ENST00000258774.5	37	CCDS34635.1																																																																																			C|0.560;T|0.440	0.440	strong		0.488	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507	
SLC4A10	57282	hgsc.bcm.edu	37	2	162696414	162696414	+	Silent	SNP	C	C	T	rs2084543	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:162696414C>T	ENST00000446997.1	+	4	486	c.393C>T	c.(391-393)gaC>gaT	p.D131D	SLC4A10_ENST00000421911.1_Silent_p.D131D|SLC4A10_ENST00000272716.5_Silent_p.D131D|SLC4A10_ENST00000535165.1_Silent_p.D131D|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000375514.5_Silent_p.D142D|SLC4A10_ENST00000415876.2_Silent_p.D131D	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	131					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	AAGGTGAGGACGCTGAGTGGC	0.418													T|||	348	0.0694888	0.003	0.0605	5008	,	,		16826	0.1319		0.0825	False		,,,				2504	0.0879				p.D142D		Atlas-SNP	.											.	SLC4A10	309	.	0			c.C426T						PASS	.	T	,,	61,4193		1,59,2067	136.0	139.0	138.0		393,426,393	3.2	1.0	2	dbSNP_96	138	574,7942		18,538,3702	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A10	NM_001178015.1,NM_001178016.1,NM_022058.3	,,	19,597,5769	TT,TC,CC		6.7403,1.4339,4.9726	,,	131/1119,142/1100,131/1089	162696414	635,12135	2127	4258	6385	SO:0001819	synonymous_variant	57282	exon5			TGAGGACGCTGAG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"""Solute carriers"""	13811	protein-coding gene	gene with protein product		605556	"""solute carrier family 4, sodium bicarbonate transporter-like, member 10"""			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.393C>T	2.37:g.162696414C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	37	CCDS54411.1																																																																																			C|0.922;T|0.078	0.078	strong		0.418	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058	
STPG1	90529	hgsc.bcm.edu	37	1	24718079	24718079	+	Missense_Mutation	SNP	C	C	A	rs560219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24718079C>A	ENST00000374409.1	-	3	415	c.161G>T	c.(160-162)aGt>aTt	p.S54I	STPG1_ENST00000337248.4_Missense_Mutation_p.S54I|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000003583.8_Intron|STPG1_ENST00000440416.1_Intron	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	54					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTTGGCTTGACTATTGAATCC	0.403											OREG0013240	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1173	0.234225	0.1906	0.2248	5008	,	,		18080	0.3145		0.2416	False		,,,				2504	0.2096				p.S54I		Atlas-SNP	.											.	.	.	.	0			c.G161T						PASS	.																																			SO:0001583	missense	90529	exon3			GCTTGACTATTGA	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.161G>T	1.37:g.24718079C>A	ENSP00000363530:p.Ser54Ile	Somatic	63	0	0	773	WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	544|544	0.2490842490842491|0.2490842490842491	103|103	0.20934959349593496|0.20934959349593496	88|88	0.2430939226519337|0.2430939226519337	176|176	0.3076923076923077|0.3076923076923077	177|177	0.23350923482849603|0.23350923482849603	C|C	14.40|14.40	2.522665|2.522665	0.44866|0.44866	.|.	.|.	ENSG00000001460|ENSG00000001460	ENST00000374409;ENST00000337248;ENST00000437986|ENST00000435187	.|.	.|.	.|.	5.39|5.39	4.47|4.47	0.54385|0.54385	.|.	0.342231|.	0.29286|.	N|.	0.012599|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.74881|0.74881	2.28|2.28	0.09310|0.09310	P|P	0.9999999999999184|0.9999999999999184	B|.	0.12630|.	0.006|.	B|.	0.09377|.	0.004|.	T|T	0.04840|0.04840	-1.0923|-1.0923	8|4	0.59425|.	D|.	0.04|.	-2.4253|-2.4253	11.8682|11.8682	0.52505|0.52505	0.1747:0.8253:0.0:0.0|0.1747:0.8253:0.0:0.0	rs560219;rs1064840;rs3170834;rs560219|rs560219;rs1064840;rs3170834;rs560219	54|.	Q5TH74|.	CA201_HUMAN|.	I|F	54|31	.|.	ENSP00000337461:S54I|.	S|V	-|-	2|1	0|0	C1orf201|C1orf201	24590666|24590666	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	2.445000|2.445000	0.44899|0.44899	1.404000|1.404000	0.46819|0.46819	-0.169000|-0.169000	0.13324|0.13324	AGT|GTC	C|0.758;A|0.242	0.242	strong		0.403	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
DCLRE1B	64858	hgsc.bcm.edu	37	1	114449662	114449662	+	Silent	SNP	T	T	C	rs3761936	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:114449662T>C	ENST00000369563.3	+	2	680	c.234T>C	c.(232-234)caT>caC	p.H78H	DCLRE1B_ENST00000466480.1_Intron|AP4B1_ENST00000369566.3_5'Flank|AP4B1_ENST00000369567.1_5'Flank|AP4B1_ENST00000369569.1_5'Flank|AP4B1_ENST00000256658.4_5'Flank	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	78					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		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)		GTGAGAGCCATGTATTACCCC	0.483								Other identified genes with known or suspected DNA repair function					T|||	1219	0.243411	0.0151	0.3833	5008	,	,		16672	0.5903		0.1928	False		,,,				2504	0.1472				p.H78H		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.T234C						PASS	.	T		185,4221	116.7+/-154.6	9,167,2027	255.0	225.0	235.0		234	0.4	1.0	1	dbSNP_107	235	1500,7100	284.0+/-296.4	130,1240,2930	no	coding-synonymous	DCLRE1B	NM_022836.3		139,1407,4957	CC,CT,TT		17.4419,4.1988,12.9556		78/533	114449662	1685,11321	2203	4300	6503	SO:0001819	synonymous_variant	64858	exon2			GAGCCATGTATTA	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.234T>C	1.37:g.114449662T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_022836	Q9H9E5	Silent	SNP	ENST00000369563.3	37	CCDS866.1																																																																																			C|0.191;N|0.000	0.191	strong		0.483	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836	
LILRA6	79168	hgsc.bcm.edu	37	19	54744358	54744358	+	Nonsense_Mutation	SNP	A	A	C	rs1052992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000419410.2_Nonsense_Mutation_p.Y350*|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron	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	211	8	0.0379147		WXS	Illumina HiSeq	Phase_I	286	33	0.115385	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	
FAM83G	644815	hgsc.bcm.edu	37	17	18907198	18907198	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18907198C>T	ENST00000388995.6	-	2	380	c.157G>A	c.(157-159)Gag>Aag	p.E53K	FAM83G_ENST00000345041.4_Missense_Mutation_p.E53K|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.E53K|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395643.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	53					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGGATGTTCTCCCGCTTGAGC	0.672																																					p.E53K		Atlas-SNP	.											.	FAM83G	51	.	0			c.G157A						PASS	.						35.0	41.0	39.0					17																	18907198		2015	4183	6198	SO:0001583	missense	644815	exon2			TGTTCTCCCGCTT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.157G>A	17.37:g.18907198C>T	ENSP00000373647:p.Glu53Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658749	0.47467	.	.	ENSG00000188522	ENST00000388995;ENST00000345041;ENST00000399096	T;T	0.15487	2.42;2.42	5.01	5.01	0.66863	.	0.392245	0.26746	N	0.022701	T	0.31040	0.0784	M	0.84511	2.7	0.34765	D	0.733098	P	0.34934	0.476	B	0.36186	0.219	T	0.53732	-0.8397	10	0.87932	D	0	-36.4032	18.3131	0.90207	0.0:1.0:0.0:0.0	.	53	A6ND36	FA83G_HUMAN	K	53	ENSP00000373647:E53K;ENSP00000343279:E53K	ENSP00000343279:E53K	E	-	1	0	FAM83G	18847923	0.905000	0.30787	1.000000	0.80357	0.987000	0.75469	1.035000	0.30216	2.332000	0.79248	0.491000	0.48974	GAG	.	.	none		0.672	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
UBTD2	92181	hgsc.bcm.edu	37	5	171639152	171639152	+	Missense_Mutation	SNP	C	C	T	rs17074452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:171639152C>T	ENST00000393792.2	-	3	792	c.387G>A	c.(385-387)atG>atA	p.M129I		NM_152277.2	NP_689490.2	Q8WUN7	UBTD2_HUMAN	ubiquitin domain containing 2	129			M -> I (in dbSNP:rs17074452).			cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTTCCTCTATCATGTTGATTG	0.463													C|||	30	0.00599042	0.0	0.013	5008	,	,		20884	0.0		0.0199	False		,,,				2504	0.001				p.M129I		Atlas-SNP	.											.	UBTD2	26	.	0			c.G387A						PASS	.	C	ILE/MET	20,4386	27.2+/-55.0	0,20,2183	136.0	126.0	129.0		387	5.1	1.0	5	dbSNP_123	129	212,8388	89.9+/-152.1	1,210,4089	yes	missense	UBTD2	NM_152277.2	10	1,230,6272	TT,TC,CC		2.4651,0.4539,1.7838	benign	129/235	171639152	232,12774	2203	4300	6503	SO:0001583	missense	92181	exon3			CTCTATCATGTTG	AF251700	CCDS4379.2	5q35.1	2008-10-30			ENSG00000168246	ENSG00000168246			24463	protein-coding gene	gene with protein product	"""dendritic cell derived ubiquitin like protein"""	610174				12507522	Standard	NM_152277		Approved	DC-UbP, MGC30022	uc003mbp.1	Q8WUN7	OTTHUMG00000130519	ENST00000393792.2:c.387G>A	5.37:g.171639152C>T	ENSP00000377381:p.Met129Ile	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	171	95	0.555556	NM_152277	Q8TDQ3	Missense_Mutation	SNP	ENST00000393792.2	37	CCDS4379.2	24	0.01098901098901099	0	0.0	7	0.019337016574585635	0	0.0	17	0.022427440633245383	C	17.44	3.391192	0.62066	0.004539	0.024651	ENSG00000168246	ENST00000393792	T	0.39787	1.06	5.96	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.14527	0.0351	N	0.17901	0.54	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04693	-1.0933	10	0.15952	T	0.53	.	13.1696	0.59591	0.0:0.923:0.0:0.077	rs17074452;rs52816309;rs17074452	129	Q8WUN7	UBTD2_HUMAN	I	129	ENSP00000377381:M129I	ENSP00000377381:M129I	M	-	3	0	UBTD2	171571757	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.888000	0.69758	1.533000	0.49186	0.655000	0.94253	ATG	C|0.983;T|0.017	0.017	strong		0.463	UBTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252936.1	NM_152277	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363480	42363480	+	Missense_Mutation	SNP	G	G	A	rs17747505	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363480G>A	ENST00000290472.3	-	17	1811	c.1717C>T	c.(1717-1719)Cgg>Tgg	p.R573W		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	573	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> W (in dbSNP:rs17747505).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GCCTCCAGCCGCGAGGAGGTC	0.627													G|||	223	0.0445288	0.0144	0.0749	5008	,	,		16774	0.001		0.1083	False		,,,				2504	0.0429				p.R573W		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.C1717T						PASS	.	G	TRP/ARG	168,4236	108.6+/-147.0	1,166,2035	24.0	29.0	27.0		1717	-7.0	0.0	15	dbSNP_123	27	968,7630	200.9+/-244.5	45,878,3376	yes	missense	PLA2G4D	NM_178034.3	101	46,1044,5411	AA,AG,GG		11.2584,3.8147,8.7371	benign	573/819	42363480	1136,11866	2202	4299	6501	SO:0001583	missense	283748	exon17			CCAGCCGCGAGGA	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1717C>T	15.37:g.42363480G>A	ENSP00000290472:p.Arg573Trp	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	128	0.05860805860805861	10	0.02032520325203252	31	0.0856353591160221	0	0.0	87	0.11477572559366754	G	9.049	0.991657	0.18966	0.038147	0.112584	ENSG00000159337	ENST00000290472	T	0.04603	3.59	3.85	-6.98	0.01611	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.685400	0.02743	N	0.116527	T	0.00073	0.0002	N	0.11651	0.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.66056	D	0.02	2.8874	1.2673	0.02013	0.1887:0.2474:0.3329:0.231	rs17747505;rs17747505	573	Q86XP0	PA24D_HUMAN	W	573	ENSP00000290472:R573W	ENSP00000290472:R573W	R	-	1	2	PLA2G4D	40150772	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.107000	0.03316	-1.446000	0.01945	-0.251000	0.11542	CGG	G|0.925;A|0.075	0.075	strong		0.627	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2307121	2307121	+	Missense_Mutation	SNP	G	G	A	rs61742112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2307121G>A	ENST00000290974.2	-	8	1285	c.946C>T	c.(946-948)Cct>Tct	p.P316S	RP11-478C1.7_ENST00000510632.1_RNA|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.P246S|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.P286S	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	316					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						GGCCCCTCAGGGGGGAGAGGG	0.657													G|||	211	0.0421326	0.0091	0.0663	5008	,	,		18981	0.0		0.1272	False		,,,				2504	0.0256				p.P316S		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C946T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	119,4287	81.9+/-120.4	3,113,2087	38.0	42.0	41.0		856,736,946	1.1	0.0	4	dbSNP_129	41	1107,7489	216.4+/-255.5	70,967,3261	yes	missense,missense,missense	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	74,74,74	73,1080,5348	AA,AG,GG		12.8781,2.7009,9.4293	benign,benign,benign	286/858,246/818,316/888	2307121	1226,11776	2203	4298	6501	SO:0001583	missense	57732	exon8			CCTCAGGGGGGAG	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.946C>T	4.37:g.2307121G>A	ENSP00000290974:p.Pro316Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	37	CCDS33942.1	140	0.0641025641025641	8	0.016260162601626018	35	0.09668508287292818	0	0.0	97	0.1279683377308707	G	2.740	-0.262423	0.05791	0.027009	0.128781	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.58060	0.37;0.36;0.37	4.85	1.12	0.20585	.	0.391533	0.28618	N	0.014715	T	0.00412	0.0013	L	0.47716	1.5	0.23483	P	0.99758385	B;B	0.10296	0.003;0.0	B;B	0.12156	0.007;0.001	T	0.03887	-1.0995	9	0.34782	T	0.22	.	3.6557	0.08220	0.1448:0.3585:0.3743:0.1224	.	286;316	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	S	316;286;246	ENSP00000290974:P316S;ENSP00000425706:P286S;ENSP00000426299:P246S	ENSP00000290974:P316S	P	-	1	0	ZFYVE28	2276919	0.276000	0.24211	0.001000	0.08648	0.005000	0.04900	0.232000	0.17891	0.007000	0.14760	-0.949000	0.02662	CCT	A|0.086;C|0.000;G|0.914	0.086	strong		0.657	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
HBP1	26959	hgsc.bcm.edu	37	7	106836344	106836344	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:106836344G>A	ENST00000222574.4	+	9	1319	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	HBP1_ENST00000485846.1_Missense_Mutation_p.R378H|HBP1_ENST00000468410.1_Missense_Mutation_p.R378H|HBP1_ENST00000461963.1_3'UTR|CTA-363E19.2_ENST00000607036.1_RNA	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	378					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CGCCAGCGTCGTGCATCTTTG	0.388																																					p.R388H		Atlas-SNP	.											.	HBP1	31	.	0			c.G1163A						PASS	.						87.0	85.0	86.0					7																	106836344		2203	4300	6503	SO:0001583	missense	26959	exon9			AGCGTCGTGCATC	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.1133G>A	7.37:g.106836344G>A	ENSP00000222574:p.Arg378His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	37	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355207	0.95854	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.99369	-5.78;-5.78;-5.78	5.96	5.96	0.96718	.	0.044632	0.85682	D	0.000000	D	0.98896	0.9626	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.999	D;D;P	0.65773	0.913;0.938;0.869	D	0.99925	1.1280	10	0.72032	D	0.01	-14.0183	20.4084	0.99013	0.0:0.0:1.0:0.0	.	388;378;378	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	H	378;378;378;370	ENSP00000420500:R378H;ENSP00000222574:R378H;ENSP00000418738:R378H	ENSP00000222574:R378H	R	+	2	0	HBP1	106623580	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.950000	0.87804	2.833000	0.97629	0.650000	0.86243	CGT	.	.	none		0.388	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
SCN7A	6332	hgsc.bcm.edu	37	2	167269629	167269629	+	Silent	SNP	T	T	G	rs33922582	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	224	222	0.991071	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		
OR2G3	81469	hgsc.bcm.edu	37	1	247769062	247769062	+	Missense_Mutation	SNP	A	A	G	rs61748963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247769062A>G	ENST00000320002.2	+	1	207	c.175A>G	c.(175-177)Atg>Gtg	p.M59V	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	59						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)			TCATACCCCAATGTACTTTTT	0.423													A|||	288	0.057508	0.0053	0.0994	5008	,	,		21406	0.005		0.1083	False		,,,				2504	0.1002				p.M59V		Atlas-SNP	.											OR2G3,NS,carcinoma,-2,2	OR2G3	108	2	0			c.A175G						PASS	.	A	VAL/MET	109,4297	83.9+/-122.4	1,107,2095	268.0	260.0	263.0		175	3.8	0.8	1	dbSNP_129	263	1048,7552	223.0+/-259.9	74,900,3326	yes	missense	OR2G3	NM_001001914.1	21	75,1007,5421	GG,GA,AA		12.186,2.4739,8.8959	probably-damaging	59/310	247769062	1157,11849	2203	4300	6503	SO:0001583	missense	81469	exon1			ACCCCAATGTACT	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.175A>G	1.37:g.247769062A>G	ENSP00000326301:p.Met59Val	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	337	156	0.462908	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	134	0.06135531135531135	3	0.006097560975609756	46	0.1270718232044199	2	0.0034965034965034965	83	0.10949868073878628	A	9.626	1.135224	0.21123	0.024739	0.12186	ENSG00000177476	ENST00000320002	T	0.09350	2.99	3.79	3.79	0.43588	GPCR, rhodopsin-like superfamily (1);	0.149295	0.29572	U	0.011778	T	0.00271	0.0008	H	0.95917	3.74	0.38059	P	0.06399999999999995	B	0.24963	0.115	B	0.29077	0.098	T	0.06734	-1.0810	9	0.87932	D	0	.	10.8362	0.46688	1.0:0.0:0.0:0.0	rs61748963	59	Q8NGZ4	OR2G3_HUMAN	V	59	ENSP00000326301:M59V	ENSP00000326301:M59V	M	+	1	0	OR2G3	245835685	1.000000	0.71417	0.785000	0.31869	0.054000	0.15201	7.298000	0.78815	1.719000	0.51432	0.398000	0.26397	ATG	A|0.914;G|0.086	0.086	strong		0.423	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
ERCC6	2074	hgsc.bcm.edu	37	10	50732280	50732280	+	Missense_Mutation	SNP	C	C	T	rs2228528	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50732280C>T	ENST00000355832.5	-	5	1274	c.1196G>A	c.(1195-1197)gGt>gAt	p.G399D	PGBD3_ENST00000374127.3_5'Flank|PGBD3_ENST00000603152.1_Missense_Mutation_p.G399D|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.G399D|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.G399D	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	399			G -> D (in dbSNP:rs2228528). {ECO:0000269|PubMed:9443879, ECO:0000269|Ref.3}.		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)			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						ATAGTCAGTACCATCTCCAGA	0.547								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	1191	0.237819	0.1793	0.2378	5008	,	,		17237	0.4911		0.1581	False		,,,				2504	0.138				p.L399H		Atlas-SNP	.											.	ERCC6	162	.	0			c.T1196A						PASS	.	C	ASP/GLY,	729,3677	302.1+/-287.2	62,605,1536	72.0	70.0	70.0		1196,	-3.8	0.0	10	dbSNP_98	70	1382,7218	268.2+/-287.7	112,1158,3030	yes	missense,utr-5	ERCC6,PGBD3	NM_000124.2,NM_170753.2	94,	174,1763,4566	TT,TC,CC		16.0698,16.5456,16.231	benign,	399/1494,	50732280	2111,10895	2203	4300	6503	SO:0001583	missense	2074	exon5			TCAGTACCATCTC	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.1196G>A	10.37:g.50732280C>T	ENSP00000348089:p.Gly399Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	553	0.2532051282051282	83	0.16869918699186992	75	0.20718232044198895	276	0.4825174825174825	119	0.15699208443271767	C	7.256	0.604123	0.14002	0.165456	0.160698	ENSG00000225830;ENSG00000258838;ENSG00000258838	ENST00000355832;ENST00000515869;ENST00000447839	D;T;T	0.81579	-1.51;3.62;3.62	5.93	-3.85	0.04243	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.54753	P	1.8999999999991246E-5	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.18967	-1.0320	8	0.06757	T	0.87	-1.3641	9.5029	0.39028	0.0:0.26:0.1064:0.6336	rs2228528;rs3829171;rs61043658;rs2228528	399;399	E7EV46;Q03468	.;ERCC6_HUMAN	D	399	ENSP00000348089:G399D;ENSP00000423550:G399D;ENSP00000387966:G399D	ENSP00000348089:G399D	G	-	2	0	ERCC6;RP11-123B3.6	50402286	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.130000	0.15850	-0.609000	0.05724	-0.140000	0.14226	GGT	C|0.794;T|0.206	0.206	strong		0.547	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
POLR2H	5437	hgsc.bcm.edu	37	3	184082931	184082931	+	Silent	SNP	T	T	C	rs11556518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184082931T>C	ENST00000456318.1	+	4	1217	c.168T>C	c.(166-168)ttT>ttC	p.F56F	POLR2H_ENST00000443489.1_Silent_p.F20F|POLR2H_ENST00000452961.1_Silent_p.F20F|POLR2H_ENST00000430783.1_Silent_p.F56F|POLR2H_ENST00000438240.1_Silent_p.F20F|POLR2H_ENST00000429568.1_Silent_p.F56F|POLR2H_ENST00000296223.3_Silent_p.F56F|EIF2B5_ENST00000444495.1_Intron	NM_001278699.1	NP_001265628.1	P52434	RPAB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide H	56					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|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 II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|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)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GTGACAAGTTTCGGTTGGTCA	0.418													C|||	430	0.0858626	0.1256	0.0288	5008	,	,		20699	0.128		0.0686	False		,,,				2504	0.047				p.F56F		Atlas-SNP	.											.	POLR2H	17	.	0			c.T168C						PASS	.	T		485,3921	226.5+/-242.0	31,423,1749	203.0	186.0	192.0		168	1.8	1.0	3	dbSNP_120	192	550,8050	150.7+/-205.6	17,516,3767	no	coding-synonymous	POLR2H	NM_006232.2		48,939,5516	CC,CT,TT		6.3953,11.0077,7.9579		56/151	184082931	1035,11971	2203	4300	6503	SO:0001819	synonymous_variant	5437	exon3			CAAGTTTCGGTTG		CCDS3264.1, CCDS63861.1, CCDS63862.1, CCDS63859.1, CCDS63860.1	3q28	2013-01-21			ENSG00000163882	ENSG00000163882		"""RNA polymerase subunits"""	9195	protein-coding gene	gene with protein product		606023					Standard	NM_001278698		Approved	RPB8	uc003fok.2	P52434	OTTHUMG00000156746	ENST00000456318.1:c.168T>C	3.37:g.184082931T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	194	68	0.350515	NM_006232	C9J413|C9JBJ6|C9JCU7|C9JUA8|P53802|Q969R0	Silent	SNP	ENST00000456318.1	37	CCDS3264.1																																																																																			T|0.918;C|0.082	0.082	strong		0.418	POLR2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345558.1	NM_006232	
SIX5	147912	hgsc.bcm.edu	37	19	46269076	46269076	+	Missense_Mutation	SNP	G	G	A	rs2014576	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.5_ENST00000592217.2_RNA	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	25	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	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	
GABRR1	2569	hgsc.bcm.edu	37	6	89888744	89888744	+	Silent	SNP	C	C	T	rs1796743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:89888744C>T	ENST00000454853.2	-	10	1295	c.1185G>A	c.(1183-1185)gcG>gcA	p.A395A	GABRR1_ENST00000369451.3_Silent_p.A308A|GABRR1_ENST00000435811.1_Silent_p.A378A	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	395					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)	CGTCCAGCATCGCAGTGCGGG	0.552													C|||	2284	0.45607	0.4977	0.4265	5008	,	,		18475	0.631		0.34	False		,,,				2504	0.3599				p.A395A		Atlas-SNP	.											.	GABRR1	63	.	0			c.G1185A						PASS	.	C		2079,2327	571.2+/-383.0	498,1083,622	93.0	80.0	84.0		1185	1.6	0.1	6	dbSNP_89	84	2838,5762	447.1+/-361.4	467,1904,1929	yes	coding-synonymous	GABRR1	NM_002042.3		965,2987,2551	TT,TC,CC		33.0,47.1857,37.8056		395/480	89888744	4917,8089	2203	4300	6503	SO:0001819	synonymous_variant	2569	exon10			CAGCATCGCAGTG		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.1185G>A	6.37:g.89888744C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_002042	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Silent	SNP	ENST00000454853.2	37	CCDS5019.2																																																																																			C|0.582;T|0.418	0.418	strong		0.552	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
ADCK4	79934	hgsc.bcm.edu	37	19	41220529	41220529	+	Silent	SNP	C	C	T	rs11673492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	101	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	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	
TARBP1	6894	hgsc.bcm.edu	37	1	234529570	234529570	+	Silent	SNP	G	G	A	rs2175593	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:234529570G>A	ENST00000040877.1	-	27	4256	c.4257C>T	c.(4255-4257)gtC>gtT	p.V1419V	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1419					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)			TATCTGCTTCGACCAAATTAG	0.383													G|||	2524	0.503994	0.6089	0.5677	5008	,	,		17325	0.494		0.4334	False		,,,				2504	0.3998				p.V1419V		Atlas-SNP	.											.	TARBP1	111	.	0			c.C4257T						PASS	.	G		2501,1905	621.0+/-393.7	735,1031,437	61.0	66.0	64.0		4257	-9.0	0.0	1	dbSNP_96	64	3675,4925	524.7+/-380.6	779,2117,1404	no	coding-synonymous	TARBP1	NM_005646.3		1514,3148,1841	AA,AG,GG		42.7326,43.2365,47.4858		1419/1622	234529570	6176,6830	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon27			TGCTTCGACCAAA		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.4257C>T	1.37:g.234529570G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			G|0.519;A|0.481	0.481	strong		0.383	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491840	110491840	+	Missense_Mutation	SNP	C	C	G	rs1783147	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:110491840C>G	ENST00000378402.5	+	54	9254	c.9150C>G	c.(9148-9150)caC>caG	p.H3050Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3050	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.		H -> Q (in dbSNP:rs1783147).		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)			CTGTACCTCACCCAGGGGCAA	0.343										HNSCC(38;0.096)			C|||	2132	0.425719	0.382	0.5202	5008	,	,		20404	0.3284		0.337	False		,,,				2504	0.6094				p.H3050Q		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C9150G						PASS	.	C	GLN/HIS	1380,2312		286,808,752	102.0	91.0	94.0		9150	-3.4	0.1	8	dbSNP_89	94	2940,5224		558,1824,1700	yes	missense	PKHD1L1	NM_177531.4	24	844,2632,2452	GG,GC,CC		36.0118,37.3781,36.4372	benign	3050/4244	110491840	4320,7536	1846	4082	5928	SO:0001583	missense	93035	exon54			ACCTCACCCAGGG	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.9150C>G	8.37:g.110491840C>G	ENSP00000367655:p.His3050Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	800	0.3663003663003663	171	0.3475609756097561	178	0.49171270718232046	195	0.3409090909090909	256	0.33773087071240104	C	3.578	-0.086257	0.07097	0.373781	0.360118	ENSG00000205038	ENST00000378402	D	0.87887	-2.31	5.88	-3.42	0.04825	G8 domain (2);	1.091090	0.06978	N	0.819430	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	0.15925	-1.0420	9	0.06625	T	0.88	.	1.9072	0.03279	0.1153:0.2046:0.2997:0.3804	rs1783147;rs17447503;rs52824856;rs58215772;rs1783147	3050	Q86WI1	PKHL1_HUMAN	Q	3050	ENSP00000367655:H3050Q	ENSP00000367655:H3050Q	H	+	3	2	PKHD1L1	110561016	0.121000	0.22262	0.067000	0.19924	0.989000	0.77384	0.097000	0.15168	-0.330000	0.08514	0.655000	0.94253	CAC	C|0.626;G|0.374	0.374	strong		0.343	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
GTSE1	51512	hgsc.bcm.edu	37	22	46704243	46704243	+	Silent	SNP	C	C	T	rs6008598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46704243C>T	ENST00000454366.1	+	4	377	c.165C>T	c.(163-165)ttC>ttT	p.F55F		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	36					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		AAGTCTTCTTCGGACCCTTTG	0.388													C|||	750	0.14976	0.3858	0.0951	5008	,	,		17943	0.002		0.1302	False		,,,				2504	0.0419				p.F55F	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C165T						PASS	.	C		1512,2894	479.0+/-358.4	277,958,968	92.0	100.0	97.0		165	0.7	0.9	22	dbSNP_114	97	957,7643	208.9+/-250.2	53,851,3396	no	coding-synonymous	GTSE1	NM_016426.6		330,1809,4364	TT,TC,CC		11.1279,34.3168,18.9835		55/740	46704243	2469,10537	2203	4300	6503	SO:0001819	synonymous_variant	51512	exon4			CTTCTTCGGACCC	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.165C>T	22.37:g.46704243C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.821;T|0.179	0.179	strong		0.388	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
LANCL3	347404	hgsc.bcm.edu	37	X	37431597	37431597	+	Silent	SNP	G	G	T	rs186317346		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:37431597G>T	ENST00000378619.3	+	1	693	c.474G>T	c.(472-474)gcG>gcT	p.A158A	LANCL3_ENST00000378621.3_Silent_p.A158A|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	158							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						CCGTCTGCGCGCCGGTCTCCT	0.697													G|||	47	0.0124503	0.0008	0.0173	3775	,	,		10148	0.0		0.0278	False		,,,				2504	0.0061				p.A158A		Atlas-SNP	.											.	LANCL3	42	.	0			c.G474T						PASS	.						3.0	3.0	3.0					X																	37431597		1840	3527	5367	SO:0001819	synonymous_variant	347404	exon1			CTGCGCGCCGGTC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.474G>T	X.37:g.37431597G>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_001170331	A6NHE3	Silent	SNP	ENST00000378619.3	37	CCDS55398.1																																																																																			G|0.981;T|0.019	0.019	strong		0.697	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32834186	32834186	+	Missense_Mutation	SNP	T	T	G	rs2249769	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:32834186T>G	ENST00000420878.3	-	5	1168	c.713A>C	c.(712-714)cAa>cCa	p.Q238P	ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000261333.6_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.Q238P	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	238			Q -> P (in dbSNP:rs2249769).		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)			large_intestine(5)|lung(3)|urinary_tract(1)	9						ATTTCCCTTTTGCTTCTTAGA	0.483													T|||	562	0.11222	0.1301	0.1254	5008	,	,		19783	0.2252		0.0358	False		,,,				2504	0.0409				p.Q238P		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.A713C						PASS	.	T	PRO/GLN,PRO/GLN,	544,3862	244.7+/-253.9	29,486,1688	166.0	164.0	165.0		713,713,	0.1	0.0	18	dbSNP_100	165	312,8288	111.2+/-171.5	11,290,3999	yes	missense,missense,intron	ZNF397,ZSCAN30	NM_001112734.2,NM_001166012.1,NM_032347.2	76,76,	40,776,5687	GG,GT,TT		3.6279,12.3468,6.5816	benign,benign,	238/495,238/495,	32834186	856,12150	2203	4300	6503	SO:0001583	missense	100101467	exon5			CCCTTTTGCTTCT	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.713A>C	18.37:g.32834186T>G	ENSP00000392371:p.Gln238Pro	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	232	144	0.62069	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	260	0.11904761904761904	67	0.13617886178861788	47	0.1298342541436464	125	0.21853146853146854	21	0.027704485488126648	T	3.509	-0.100225	0.06967	0.123468	0.036279	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.07327	3.2;3.2	4.1	0.0779	0.14410	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.47535	-0.9110	8	0.31617	T	0.26	.	4.3293	0.11055	0.3586:0.0:0.3564:0.285	rs2249769;rs17737745;rs52803218;rs2249769	238	Q86W11	ZSC30_HUMAN	P	238;238;173	ENSP00000392371:Q238P;ENSP00000329738:Q238P	ENSP00000329738:Q238P	Q	-	2	0	ZSCAN30	31088184	0.000000	0.05858	0.001000	0.08648	0.582000	0.36321	0.465000	0.22004	-0.146000	0.11274	0.523000	0.50628	CAA	T|0.892;G|0.108	0.108	strong		0.483	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
DNA2	1763	hgsc.bcm.edu	37	10	70225504	70225504	+	Silent	SNP	G	G	T	rs3758626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70225504G>T	ENST00000358410.3	-	4	557	c.507C>A	c.(505-507)gcC>gcA	p.A169A	DNA2_ENST00000399179.2_Silent_p.A169A|DNA2_ENST00000399180.2_Silent_p.A255A	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	58	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	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		
MYCT1	80177	hgsc.bcm.edu	37	6	153043035	153043035	+	Missense_Mutation	SNP	G	G	A	rs17710008	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	196	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	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	
APC	324	hgsc.bcm.edu	37	5	112176325	112176325	+	Silent	SNP	G	G	A	rs42427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176325G>A	ENST00000457016.1	+	16	5414	c.5034G>A	c.(5032-5034)ggG>ggA	p.G1678G	APC_ENST00000508376.2_Silent_p.G1678G|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.G1678G			P25054	APC_HUMAN	adenomatous polyposis coli	1678	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTAGAGGAGGGGCACAGTCAG	0.443		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			g|||	3339	0.666733	0.5189	0.7176	5008	,	,		20292	0.8165		0.6024	False		,,,				2504	0.7423				p.G1678G	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.G5034A						PASS	.	T	,,	2333,2071	603.2+/-390.1	625,1083,494	60.0	59.0	59.0	http://omim.org/entry/114500	5034,5034,4980	1.3	0.2	5	dbSNP_76	59	5341,3259	648.4+/-400.5	1692,1957,651	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2317,3040,1145	AA,AG,GG		37.8953,47.0254,40.9874	,,	1678/2844,1678/2844,1660/2826	112176325	7674,5330	2202	4300	6502	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AGGAGGGGCACAG	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5034G>A	5.37:g.112176325G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.379;A|0.621	0.621	strong		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
NEK3	4752	hgsc.bcm.edu	37	13	52707924	52707924	+	Missense_Mutation	SNP	A	A	C	rs200805375		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52707924A>C	ENST00000400357.2	-	13	2579	c.1286T>G	c.(1285-1287)cTg>cGg	p.L429R	NEK3_ENST00000452082.2_Missense_Mutation_p.L450R|NEK3_ENST00000339406.3_Missense_Mutation_p.L446R|NEK3_ENST00000378101.2_Missense_Mutation_p.L446R			P51956	NEK3_HUMAN	NIMA-related kinase 3	446					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		TTCTTCAGACAGGGGGCCTTT	0.418																																					p.L446R		Atlas-SNP	.											.	NEK3	41	.	0			c.T1337G						PASS	.	A	ARG/LEU,ARG/LEU	0,3778		0,0,1889	43.0	40.0	41.0		1286,1336	3.8	1.0	13		41	2,8224		0,2,4111	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	102,102	0,2,6000	CC,CA,AA		0.0243,0.0,0.0167	probably-damaging,probably-damaging	429/490,446/507	52707924	2,12002	1889	4113	6002	SO:0001583	missense	4752	exon15			TCAGACAGGGGGC	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1286T>G	13.37:g.52707924A>C	ENSP00000383210:p.Leu429Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012638	0.54468	0.0	2.43E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.78816	-1.03;-1.03;-1.21;-1.11;-1.04	4.99	3.78	0.43462	.	0.141261	0.48767	D	0.000177	D	0.85796	0.5780	M	0.74258	2.255	0.34463	D	0.702004	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.89208	0.3562	10	0.87932	D	0	.	9.7246	0.40324	0.8455:0.0:0.0:0.1545	.	446;450;423	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	R	446;446;429;450;423	ENSP00000339429:L446R;ENSP00000367341:L446R;ENSP00000383210:L429R;ENSP00000404197:L450R;ENSP00000448716:L423R	ENSP00000339429:L446R	L	-	2	0	NEK3	51605925	1.000000	0.71417	0.998000	0.56505	0.625000	0.37756	5.553000	0.67287	0.807000	0.34208	0.383000	0.25322	CTG	A|0.999;C|0.001	0.001	weak		0.418	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
DFNB31	25861	hgsc.bcm.edu	37	9	117169033	117169033	+	Missense_Mutation	SNP	A	A	G	rs942519	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	63	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	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	
CLIP4	79745	hgsc.bcm.edu	37	2	29356567	29356567	+	Silent	SNP	G	G	C	rs17749904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000401605.1_Silent_p.L138L|CLIP4_ENST00000401617.2_Silent_p.L31L	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	87	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	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	
NCOA5	57727	hgsc.bcm.edu	37	20	44691350	44691350	+	Silent	SNP	T	T	G	rs1537028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44691350T>G	ENST00000290231.6	-	8	1493	c.1329A>C	c.(1327-1329)acA>acC	p.T443T		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TGGCCGTCACTGTGCCACTAT	0.567													T|||	1996	0.398562	0.289	0.4856	5008	,	,		16946	0.5675		0.3479	False		,,,				2504	0.363				p.T443T		Atlas-SNP	.											.	NCOA5	58	.	0			c.A1329C						PASS	.	T		1125,3281	401.3+/-331.9	147,831,1225	114.0	119.0	118.0		1329	-7.1	0.3	20	dbSNP_88	118	2790,5810	441.8+/-359.9	456,1878,1966	no	coding-synonymous	NCOA5	NM_020967.2		603,2709,3191	GG,GT,TT		32.4419,25.5334,30.1015		443/580	44691350	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	57727	exon8			CGTCACTGTGCCA		CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"""coactivator independent of AF-2"""					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.1329A>C	20.37:g.44691350T>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	209	86	0.411483	NM_020967	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Silent	SNP	ENST00000290231.6	37	CCDS13392.1																																																																																			A|0.003;C|0.002	.	strong		0.567	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967	
LACC1	144811	hgsc.bcm.edu	37	13	44457984	44457984	+	Silent	SNP	A	A	G	rs9533673	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:44457984A>G	ENST00000441843.1	+	4	1304	c.819A>G	c.(817-819)agA>agG	p.R273R	LACC1_ENST00000325686.6_Silent_p.R273R	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	273																	CAAATCAGAGAGGAGTCACAA	0.413													A|||	324	0.0646965	0.1029	0.0793	5008	,	,		15921	0.0		0.1014	False		,,,				2504	0.0317				p.R273R		Atlas-SNP	.											.	.	.	.	0			c.A819G						PASS	.	A	,	476,3930	222.3+/-239.2	25,426,1752	115.0	109.0	111.0		819,819	1.7	1.0	13	dbSNP_119	111	871,7729	196.5+/-241.4	51,769,3480	no	coding-synonymous,coding-synonymous	LACC1	NM_001128303.1,NM_153218.2	,	76,1195,5232	GG,GA,AA		10.1279,10.8034,10.3568	,	273/431,273/431	44457984	1347,11659	2203	4300	6503	SO:0001819	synonymous_variant	144811	exon4			TCAGAGAGGAGTC	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.819A>G	13.37:g.44457984A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_001128303	A2A3Z6|Q8N8X5	Silent	SNP	ENST00000441843.1	37	CCDS9391.1																																																																																			A|0.903;G|0.097	0.097	strong		0.413	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218	
CDC45	8318	hgsc.bcm.edu	37	22	19482035	19482035	+	Intron	SNP	C	C	G	rs151216373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19482035C>G	ENST00000407835.1	+	7	798				CDC45_ENST00000263201.1_Intron|CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000437685.2_Missense_Mutation_p.S183C|CDC45_ENST00000404724.3_Intron			O75419	CDC45_HUMAN	cell division cycle 45						DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|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)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						GCCAGTGGCTCTGGGAGTGAA	0.562													C|||	19	0.00379393	0.0	0.0159	5008	,	,		14122	0.0		0.008	False		,,,				2504	0.0				p.S183C		Atlas-SNP	.											.	CDC45	48	.	0			c.C548G						PASS	.																																			SO:0001627	intron_variant	8318	exon7			GTGGCTCTGGGAG	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.542+130C>G	22.37:g.19482035C>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Missense_Mutation	SNP	ENST00000407835.1	37	CCDS13762.1	16	0.007326007326007326	0	0.0	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	10.30	1.312792	0.23908	.	.	ENSG00000093009	ENST00000437685	T	0.23754	1.89	4.21	-2.11	0.07187	.	.	.	.	.	T	0.07908	0.0198	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25363	-1.0134	9	0.59425	D	0.04	.	4.7364	0.12989	0.0:0.4021:0.3216:0.2763	.	183	E9PDH7	.	C	183	ENSP00000405726:S183C	ENSP00000405726:S183C	S	+	2	0	CDC45	17862035	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.293000	0.08320	-0.352000	0.08237	-0.136000	0.14681	TCT	C|0.993;G|0.007	0.007	strong		0.562	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
CPA1	1357	hgsc.bcm.edu	37	7	130022041	130022041	+	Silent	SNP	C	C	T	rs968404	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	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	
PRPF8	10594	hgsc.bcm.edu	37	17	1578939	1578939	+	Silent	SNP	C	C	T	rs33965342	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	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		
OR6B3	150681	hgsc.bcm.edu	37	2	240984789	240984789	+	Missense_Mutation	SNP	C	C	T	rs12465491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240984789C>T	ENST00000319423.4	-	1	700	c.701G>A	c.(700-702)tGc>tAc	p.C234Y	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	234			C -> Y (in dbSNP:rs12465491).			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(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GGCTCTCCAGCAGCCGGTGGC	0.582													c|||	1495	0.298522	0.2247	0.2089	5008	,	,		19653	0.5595		0.3042	False		,,,				2504	0.1871				p.C234Y		Atlas-SNP	.											.	OR6B3	37	.	0			c.G701A						PASS	.	C	TYR/CYS	793,3397		72,649,1374	47.0	54.0	52.0		701	1.1	0.0	2	dbSNP_120	52	2261,6199		309,1643,2278	no	missense	OR6B3	NM_173351.1	194	381,2292,3652	TT,TC,CC		26.7258,18.926,24.1423	benign	234/332	240984789	3054,9596	2095	4230	6325	SO:0001583	missense	150681	exon1			CTCCAGCAGCCGG		CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"""GPCR / Class A : Olfactory receptors"""	15042	protein-coding gene	gene with protein product			"""olfactory receptor, family 6, subfamily B, member 3 pseudogene"""	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.701G>A	2.37:g.240984789C>T	ENSP00000322435:p.Cys234Tyr	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	188	105	0.558511	NM_173351	Q6IFH3	Missense_Mutation	SNP	ENST00000319423.4	37	CCDS42837.1	771	0.35302197802197804	127	0.258130081300813	87	0.24033149171270718	316	0.5524475524475524	241	0.3179419525065963	c	2.572	-0.299476	0.05532	0.18926	0.267258	ENSG00000178586	ENST00000319423	T	0.00076	8.76	3.88	1.06	0.20224	GPCR, rhodopsin-like superfamily (1);	0.290468	0.24350	N	0.039282	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B	0.20671	0.047	B	0.33121	0.158	T	0.26360	-1.0105	9	0.72032	D	0.01	.	4.943	0.13975	0.1697:0.6368:0.0:0.1935	rs12465491;rs59155230	234	Q8NGW1	OR6B3_HUMAN	Y	234	ENSP00000322435:C234Y	ENSP00000322435:C234Y	C	-	2	0	OR6B3	240633462	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.629000	0.24538	0.206000	0.20587	-0.249000	0.11873	TGC	C|0.680;T|0.320	0.320	strong		0.582	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1		
LYPD2	137797	hgsc.bcm.edu	37	8	143833850	143833850	+	Missense_Mutation	SNP	G	G	A	rs11775636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143833850G>A	ENST00000359228.3	-	1	102	c.20C>T	c.(19-21)gCg>gTg	p.A7V		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	7			A -> V (in dbSNP:rs11775636).	RLA -> QLV (in Ref. 3; AAI19020). {ECO:0000305}.		anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CGCCAGGAGCGCCAGCCGCGT	0.682													G|||	1250	0.249601	0.205	0.1628	5008	,	,		12740	0.4018		0.1899	False		,,,				2504	0.2761				p.A7V		Atlas-SNP	.											.	LYPD2	18	.	0			c.C20T						PASS	.	G	VAL/ALA	922,3480	334.4+/-303.4	96,730,1375	42.0	48.0	46.0		20	-8.4	0.0	8	dbSNP_120	46	1545,7049	280.2+/-294.4	146,1253,2898	no	missense	LYPD2	NM_205545.1	64	242,1983,4273	AA,AG,GG		17.9777,20.945,18.9828	benign	7/126	143833850	2467,10529	2201	4297	6498	SO:0001583	missense	137797	exon1			AGGAGCGCCAGCC	AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.20C>T	8.37:g.143833850G>A	ENSP00000352163:p.Ala7Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	207	193	0.932367	NM_205545	A8K2R6|Q0VD64|Q0VF31	Missense_Mutation	SNP	ENST00000359228.3	37	CCDS6388.1	535	0.24496336996336995	102	0.2073170731707317	59	0.16298342541436464	226	0.3951048951048951	148	0.19525065963060687	G	1.377	-0.584380	0.03827	0.20945	0.179777	ENSG00000197353	ENST00000359228	D	0.82344	-1.6	4.29	-8.41	0.00961	.	2.015980	0.02437	N	0.084164	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.04153	-1.0973	9	0.11182	T	0.66	.	8.5047	0.33179	0.5165:0.1013:0.3822:0.0	rs11775636;rs61033355	7	Q6UXB3	LYPD2_HUMAN	V	7	ENSP00000352163:A7V	ENSP00000352163:A7V	A	-	2	0	LYPD2	143830852	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.198000	0.01239	-1.930000	0.01056	-0.739000	0.03532	GCG	G|0.791;A|0.209	0.209	strong		0.682	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545	
HLA-A	3105	hgsc.bcm.edu	37	6	29911115	29911115	+	Silent	SNP	G	G	C	rs66488547|rs1059498|rs12721717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29911115G>C	ENST00000396634.1	+	5	755	c.414G>C	c.(412-414)cgG>cgC	p.R138R	HLA-A_ENST00000376806.5_Silent_p.R138R|HLA-A_ENST00000376809.5_Silent_p.R138R|HLA-A_ENST00000376802.2_Silent_p.R138R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	138	Alpha-2.		Q -> R (in allele A*31:03, allele A*31:04 and allele A*31:06).		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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGGGTACCGGCAGGACGCCT	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	2088	0.416933	0.3646	0.536	5008	,	,		11640	0.497		0.4344	False		,,,				2504	0.3027				p.R138R		Atlas-SNP	.											.	HLA-A	89	.	0			c.G414C						PASS	.						33.0	25.0	28.0					6																	29911115		1489	2696	4185	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTACCGGCAGGAC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.414G>C	6.37:g.29911115G>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	123	23	0.186992	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1	944	0.43223443223443225	183	0.3719512195121951	172	0.47513812154696133	290	0.506993006993007	299	0.3944591029023747	a	0.249	-1.007698	0.02112	.	.	ENSG00000206503	ENST00000355767	.	.	.	3.78	-7.56	0.01322	.	.	.	.	.	.	.	.	.	.	.	0.53688	P	2.8999999999945736E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.9334	0.19152	0.1782:0.1516:0.5545:0.1158	rs12721717;rs16896874;rs28749151;rs41556422	.	.	.	.	-1	.	.	.	+	.	.	HLA-A	30019094	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-12.409000	0.00002	-3.751000	0.00111	-2.593000	0.00164	.	A|0.005;C|0.418;G|0.576	0.418	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2983138	2983138	+	Silent	SNP	C	C	T	rs2074363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2983138C>T	ENST00000253928.9	+	5	1209	c.804C>T	c.(802-804)gcC>gcT	p.A268A	FLYWCH1_ENST00000416288.2_Silent_p.A267A|FLYWCH1_ENST00000399667.2_Silent_p.A268A			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	50	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	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	
IL2RB	3560	hgsc.bcm.edu	37	22	37531436	37531436	+	Silent	SNP	G	G	A	rs228953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37531436G>A	ENST00000216223.5	-	8	948	c.750C>T	c.(748-750)ggC>ggT	p.G250G	AL022314.1_ENST00000516333.1_RNA	NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	250					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	CCCCGCTGAGGCCCACGAGGA	0.577													G|||	2059	0.411142	0.413	0.428	5008	,	,		13117	0.3929		0.4235	False		,,,				2504	0.4029				p.G250G		Atlas-SNP	.											.	IL2RB	44	.	0			c.C750T						PASS	.	G		1790,2616	527.1+/-372.1	358,1074,771	108.0	107.0	107.0		750	2.9	0.1	22	dbSNP_79	107	3715,4885	530.6+/-381.8	806,2103,1391	no	coding-synonymous	IL2RB	NM_000878.2		1164,3177,2162	AA,AG,GG		43.1977,40.6264,42.3266		250/552	37531436	5505,7501	2203	4300	6503	SO:0001819	synonymous_variant	3560	exon8			GCTGAGGCCCACG	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"""Interleukins and interleukin receptors"", ""CD molecules"""	6009	protein-coding gene	gene with protein product		146710	"""interleukin 15 receptor, beta"""	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.750C>T	22.37:g.37531436G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_000878	B2R765	Silent	SNP	ENST00000216223.5	37	CCDS13942.1	919	0.4207875457875458	186	0.3780487804878049	156	0.430939226519337	258	0.45104895104895104	319	0.420844327176781	G	4.119	0.020364	0.08006	0.406264	0.431977	ENSG00000100385	ENST00000447922	.	.	.	3.96	2.94	0.34122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.199999999996649E-5	.	.	.	.	.	.	T	0.49986	-0.8880	3	.	.	.	-7.8657	6.7992	0.23742	0.1273:0.0:0.8727:0.0	rs228953;rs2228142;rs17845770;rs17858730;rs228953	.	.	.	S	5	.	.	P	-	1	0	IL2RB	35861382	0.000000	0.05858	0.062000	0.19696	0.005000	0.04900	0.230000	0.17852	2.211000	0.71520	0.549000	0.68633	CCT	G|0.585;A|0.415	0.415	strong		0.577	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1		
AGMAT	79814	hgsc.bcm.edu	37	1	15909744	15909744	+	Missense_Mutation	SNP	C	C	T	rs11580170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15909744C>T	ENST00000375826.3	-	2	561	c.419G>A	c.(418-420)cGa>cAa	p.R140Q	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	140			R -> Q (in dbSNP:rs11580170). {ECO:0000269|PubMed:11804860}.		agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTTGAATTCGCCGGCAGCT	0.527													C|||	1364	0.272364	0.5492	0.2133	5008	,	,		18278	0.0565		0.2326	False		,,,				2504	0.2035				p.R140Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G419A						PASS	.	C	GLN/ARG	2311,2095	603.0+/-390.0	608,1095,500	64.0	65.0	65.0		419	1.2	0.4	1	dbSNP_120	65	2130,6470	365.7+/-334.0	252,1626,2422	yes	missense	AGMAT	NM_024758.4	43	860,2721,2922	TT,TC,CC		24.7674,47.5488,34.1458	benign	140/353	15909744	4441,8565	2203	4300	6503	SO:0001583	missense	79814	exon2			TGAATTCGCCGGC	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.419G>A	1.37:g.15909744C>T	ENSP00000364986:p.Arg140Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	575	0.2632783882783883	260	0.5284552845528455	99	0.27348066298342544	37	0.06468531468531469	179	0.23614775725593667	C	8.173	0.792103	0.16258	0.524512	0.247674	ENSG00000116771	ENST00000375826	D	0.83992	-1.79	5.17	1.23	0.21249	Ureohydrolase domain (1);	0.437097	0.21674	N	0.070839	T	0.00012	0.0000	N	0.20445	0.575	0.53005	P	3.100000000000325E-5	B	0.16166	0.016	B	0.22880	0.042	T	0.41520	-0.9504	9	0.12430	T	0.62	-1.7129	8.4855	0.33069	0.3127:0.5585:0.0:0.1288	rs11580170;rs59956736;rs11580170	140	Q9BSE5	SPEB_HUMAN	Q	140	ENSP00000364986:R140Q	ENSP00000364986:R140Q	R	-	2	0	AGMAT	15782331	0.113000	0.22115	0.431000	0.26735	0.563000	0.35712	0.542000	0.23222	0.280000	0.22209	-0.457000	0.05445	CGA	C|0.690;T|0.310	0.310	strong		0.527	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
TNKS	8658	hgsc.bcm.edu	37	8	9584176	9584176	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:9584176T>C	ENST00000310430.6	+	13	1973	c.1947T>C	c.(1945-1947)gaT>gaC	p.D649D	TNKS_ENST00000518281.1_Silent_p.D412D	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	649					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		GTACTTCTGATGTTGATTATC	0.373																																					p.D649D		Atlas-SNP	.											.	TNKS	198	.	0			c.T1947C						PASS	.						257.0	262.0	260.0					8																	9584176		2203	4300	6503	SO:0001819	synonymous_variant	8658	exon13			TTCTGATGTTGAT	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.1947T>C	8.37:g.9584176T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			.	.	none		0.373	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
SDHA	6389	hgsc.bcm.edu	37	5	256455	256455	+	Missense_Mutation	SNP	C	C	G	rs1126697		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:256455C>G	ENST00000264932.6	+	15	2030	c.1915C>G	c.(1915-1917)Ctg>Gtg	p.L639V	SDHA_ENST00000504309.1_Missense_Mutation_p.L558V|SDHA_ENST00000507522.1_Intron|SDHA_ENST00000510361.1_Missense_Mutation_p.L591V	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	639					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)	CAAGGTCACTCTGGAATATAG	0.418									Familial Paragangliomas																												p.L639V		Atlas-SNP	.											SDHA,NS,adenocarcinoma,0,1	SDHA	80	1	0			c.C1915G						scavenged	.						92.0	103.0	99.0					5																	256455		2203	4300	6503	SO:0001583	missense	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	GTCACTCTGGAAT	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.1915C>G	5.37:g.256455C>G	ENSP00000264932:p.Leu639Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	2	0.0192308	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	4.275|4.275	0.050102|0.050102	0.08243|0.08243	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361|ENST00000515815	D;D;D|.	0.82344|.	-1.6;-1.6;-1.6|.	4.12|4.12	-1.06|-1.06	0.10002|0.10002	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);|.	0.000000|.	0.64402|.	U|.	0.000014|.	T|T	0.53899|0.53899	0.1825|0.1825	L|L	0.50333|0.50333	1.59|1.59	0.50467|0.50467	D|D	0.999871|0.999871	B;B;D;B|.	0.57257|.	0.432;0.049;0.979;0.072|.	B;B;D;B|.	0.71414|.	0.344;0.085;0.973;0.063|.	T|T	0.47799|0.47799	-0.9089|-0.9089	10|5	0.72032|.	D|.	0.01|.	.|.	7.982|7.982	0.30190|0.30190	0.0:0.2524:0.0:0.7476|0.0:0.2524:0.0:0.7476	rs1126697;rs3181866;rs17414511|rs1126697;rs3181866;rs17414511	591;233;558;639|.	E9PBJ5;B3KYA5;D6RFM5;P31040|.	.;.;.;DHSA_HUMAN|.	V|C	639;494;558;591|121	ENSP00000264932:L639V;ENSP00000426514:L558V;ENSP00000427703:L591V|.	ENSP00000264932:L639V|.	L|S	+|+	1|2	2|0	SDHA|SDHA	309455|309455	0.152000|0.152000	0.22762|0.22762	0.492000|0.492000	0.27490|0.27490	0.237000|0.237000	0.25408|0.25408	0.546000|0.546000	0.23284|0.23284	-0.096000|-0.096000	0.12329|0.12329	-0.680000|-0.680000	0.03767|0.03767	CTG|TCT	C|0.998;G|0.002	0.002	weak		0.418	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
OR9K2	441639	hgsc.bcm.edu	37	12	55523860	55523860	+	Missense_Mutation	SNP	A	A	C	rs7305779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523860A>C	ENST00000305377.5	+	1	396	c.308A>C	c.(307-309)gAa>gCa	p.E103A		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	103			E -> A (in dbSNP:rs7305779).			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(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TCTGTTATTGAACCCAAGGCT	0.423													C|||	1523	0.304113	0.4085	0.2421	5008	,	,		21118	0.1141		0.334	False		,,,				2504	0.3722				p.E103A		Atlas-SNP	.											.	OR9K2	63	.	0			c.A308C						PASS	.	C	ALA/GLU	1703,2703	652.6+/-399.4	308,1087,808	150.0	150.0	150.0		308	5.0	1.0	12	dbSNP_116	150	2777,5823	678.6+/-403.5	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	107	764,2952,2787	CC,CA,AA		32.2907,38.6518,34.4456	benign	103/336	55523860	4480,8526	2203	4300	6503	SO:0001583	missense	441639	exon1			TTATTGAACCCAA	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.308A>C	12.37:g.55523860A>C	ENSP00000307598:p.Glu103Ala	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	624	0.2857142857142857	200	0.4065040650406504	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	C	0.294	-0.977862	0.02197	0.386518	0.322907	ENSG00000170605	ENST00000305377	T	0.00892	5.57	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	N	0.000123	T	0.00012	0.0000	N	0.00135	-2.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	9	0.17832	T	0.49	-6.9223	6.3141	0.21180	0.1599:0.695:0.0:0.1451	rs7305779;rs52807355;rs60412666;rs7305779	103	Q8NGE7	OR9K2_HUMAN	A	103	ENSP00000307598:E103A	ENSP00000307598:E103A	E	+	2	0	OR9K2	53810127	0.000000	0.05858	0.995000	0.50966	0.896000	0.52359	0.353000	0.20130	1.482000	0.48325	-0.127000	0.14921	GAA	A|0.677;C|0.323	0.323	strong		0.423	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
EXOSC10	5394	hgsc.bcm.edu	37	1	11159823	11159823	+	Silent	SNP	T	T	C	rs12133922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11159823T>C	ENST00000376936.4	-	1	115	c.66A>G	c.(64-66)ggA>ggG	p.G22G	EXOSC10_ENST00000544779.1_Silent_p.G22G|RP4-635E18.6_ENST00000447600.1_RNA|RP4-635E18.6_ENST00000435388.1_RNA|EXOSC10_ENST00000304457.7_Silent_p.G22G	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	22					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G22G(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		GCACCATCTCTCCGTCGGATT	0.677													T|||	563	0.11242	0.1384	0.072	5008	,	,		13359	0.1577		0.0258	False		,,,				2504	0.1483				p.G22G	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											EXOSC10,NS,lymphoid_neoplasm,0,1	EXOSC10	59	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A66G						scavenged	.	T	,	493,3913	211.8+/-231.9	27,439,1737	41.0	46.0	44.0		66,66	-2.5	0.0	1	dbSNP_120	44	199,8401	82.3+/-144.9	5,189,4106	no	coding-synonymous,coding-synonymous	EXOSC10	NM_001001998.1,NM_002685.2	,	32,628,5843	CC,CT,TT		2.314,11.1893,5.3206	,	22/886,22/861	11159823	692,12314	2203	4300	6503	SO:0001819	synonymous_variant	5394	exon1			CATCTCTCCGTCG	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.66A>G	1.37:g.11159823T>C		Somatic	124	2	0.016129		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Silent	SNP	ENST00000376936.4	37	CCDS30584.1																																																																																			T|0.931;C|0.069	0.069	strong		0.677	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
NDUFB1	4707	hgsc.bcm.edu	37	14	92588002	92588002	+	5'UTR	SNP	T	T	G	rs3818263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:92588002T>G	ENST00000553514.1	-	0	66				NDUFB1_ENST00000556555.1_5'UTR|NDUFB1_ENST00000605997.1_5'UTR|NDUFB1_ENST00000555441.1_5'Flank|CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000329559.3_Silent_p.V40V			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						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)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		CCTCAGCGCCTACAGCGACCC	0.711													G|||	2703	0.539736	0.5514	0.379	5008	,	,		10980	0.8552		0.334	False		,,,				2504	0.5245				p.V40V		Atlas-SNP	.											NDUFB1,rectum,carcinoma,0,1	NDUFB1	5	1	0			c.A120C						PASS	.	G		2232,2174		573,1086,544	33.0	39.0	37.0		120	-7.0	0.0	14	dbSNP_107	37	2915,5681		489,1937,1872	no	coding-synonymous	NDUFB1	NM_004545.3		1062,3023,2416	GG,GT,TT		33.9111,49.3418,39.5862		40/106	92588002	5147,7855	2203	4298	6501	SO:0001623	5_prime_UTR_variant	4707	exon1			AGCGCCTACAGCG	BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"""Mitochondrial respiratory chain complex / Complex I"""	7695	protein-coding gene	gene with protein product	"""complex I MNLL subunit"""	603837	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"""			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000553514.1:c.-140A>C	14.37:g.92588002T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_004545	A0AV68	Silent	SNP	ENST00000553514.1	37																																																																																				T|0.520;G|0.480	0.480	strong		0.711	NDUFB1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412116.2	NM_004545	
ZNF664	144348	hgsc.bcm.edu	37	12	124496864	124496864	+	Missense_Mutation	SNP	T	T	G	rs80197353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124496864T>G	ENST00000539644.1	+	6	2003	c.173T>G	c.(172-174)gTc>gGc	p.V58G	ZNF664_ENST00000337815.4_Missense_Mutation_p.V58G|ZNF664_ENST00000392404.3_Missense_Mutation_p.V58G|ZNF664_ENST00000538932.2_Missense_Mutation_p.V58G|FAM101A_ENST00000545615.1_Intron			Q8N3J9	ZN664_HUMAN	zinc finger protein 664	58					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)|large_intestine(5)|lung(6)|skin(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		GGAGAGAAGGTCTATAAATGT	0.373													T|||	255	0.0509185	0.0333	0.0447	5008	,	,		21967	0.0		0.0984	False		,,,				2504	0.0828				p.V58G		Atlas-SNP	.											.	ZNF664	27	.	0			c.T173G						PASS	.	T	GLY/VAL,,GLY/VAL	212,4194		0,212,1991	92.0	101.0	98.0		173,,173	3.2	1.0	12	dbSNP_131	98	827,7773		0,827,3473	yes	missense,intron,missense	ZNF664,ZNF664-FAM101A	NM_001204298.1,NM_001204299.1,NM_152437.2	109,,109	0,1039,5464	GG,GT,TT		9.6163,4.8116,7.9886	benign,,benign	58/262,,58/262	124496864	1039,11967	2203	4300	6503	SO:0001583	missense	144348	exon5			AGAAGGTCTATAA		CCDS9257.1	12q24.31	2013-05-10			ENSG00000179195	ENSG00000179195		"""Zinc fingers, C2H2-type"""	25406	protein-coding gene	gene with protein product			"""zinc finger protein 176"""	ZNF176		12477932	Standard	NM_001204298		Approved	ZFOC1, DKFZp761B128	uc001uga.3	Q8N3J9	OTTHUMG00000168596	ENST00000539644.1:c.173T>G	12.37:g.124496864T>G	ENSP00000441405:p.Val58Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	175	53	0.302857	NM_152437	B3KP97|Q15914|Q3ZCQ7	Missense_Mutation	SNP	ENST00000539644.1	37	CCDS9257.1	107	0.04899267399267399	14	0.028455284552845527	18	0.049723756906077346	0	0.0	75	0.09894459102902374	T	15.37	2.814650	0.50527	0.048116	0.096163	ENSG00000179195	ENST00000539644;ENST00000392404;ENST00000538932;ENST00000337815	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.4	3.25	0.37280	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36628	N	0.002500	T	0.00384	0.0012	L	0.33668	1.02	0.54753	D	0.999987	P	0.40083	0.702	P	0.44623	0.455	T	0.28299	-1.0048	9	.	.	.	-24.1678	6.119	0.20142	0.0:0.1965:0.0:0.8035	.	58	Q8N3J9	ZN664_HUMAN	G	58	ENSP00000441405:V58G;ENSP00000376205:V58G;ENSP00000440645:V58G;ENSP00000337320:V58G	.	V	+	2	0	ZNF664	123062817	0.989000	0.36119	0.994000	0.49952	0.992000	0.81027	2.596000	0.46205	1.007000	0.39238	0.533000	0.62120	GTC	T|0.928;G|0.072	0.072	strong		0.373	ZNF664-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400365.1	NM_152437	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652929	46652929	+	Silent	SNP	G	G	A	rs6008365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46652929G>A	ENST00000253255.5	-	1	6290	c.6291C>T	c.(6289-6291)tcC>tcT	p.S2097S		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2097					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AGAAATACACGGACACAACAA	0.483													G|||	1213	0.242212	0.6604	0.1297	5008	,	,		21491	0.002		0.16	False		,,,				2504	0.089				p.S2097S		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C6291T						PASS	.	G		2567,1839	627.1+/-394.8	748,1071,384	42.0	42.0	42.0		6291	-3.4	0.0	22	dbSNP_114	42	1257,7343	249.0+/-276.5	88,1081,3131	no	coding-synonymous	PKDREJ	NM_006071.1		836,2152,3515	AA,AG,GG		14.6163,41.7385,29.4018		2097/2254	46652929	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			ATACACGGACACA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6291C>T	22.37:g.46652929G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.739;A|0.261	0.261	strong		0.483	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TTN	7273	hgsc.bcm.edu	37	2	179453429	179453429	+	Missense_Mutation	SNP	G	G	A	rs72646850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179453429G>A	ENST00000591111.1	-	254	58324	c.58100C>T	c.(58099-58101)aCa>aTa	p.T19367I	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T21008I|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T18440I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12135I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12068I|TTN_ENST00000460472.2_Missense_Mutation_p.T11943I|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19367	Fibronectin type-III 40. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> 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)			GACCCATCGTGTTGAATGCTT	0.428													G|||	29	0.00579073	0.0008	0.0159	5008	,	,		20616	0.0		0.0169	False		,,,				2504	0.0				p.T21008I		Atlas-SNP	.											.	TTN	18412	.	0			c.C63023T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	12,3802		0,12,1895	162.0	152.0	155.0		36404,36203,55319,35828	-6.5	0.0	2	dbSNP_130	155	134,8108		2,130,3989	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	2,142,5884	AA,AG,GG		1.6258,0.3146,1.211	benign,benign,benign,benign	12135/27119,12068/27052,18440/33424,11943/26927	179453429	146,11910	1907	4121	6028	SO:0001583	missense	7273	exon304			CATCGTGTTGAAT	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.58100C>T	2.37:g.179453429G>A	ENSP00000465570:p.Thr19367Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	208	119	0.572115	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		21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	9.129	1.011021	0.19277	0.003146	0.016258	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.16	-6.48	0.01896	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19765	0.0475	N	0.10874	0.06	0.09310	N	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	0.08764	-1.0706	9	0.87932	D	0	.	19.6396	0.95753	0.9305:0.0:0.0695:0.0	.	11943;12068;12135;19367	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18440;11943;12135;12068;11941	ENSP00000343764:T18440I;ENSP00000434586:T11943I;ENSP00000340554:T12135I;ENSP00000352154:T12068I	ENSP00000340554:T12135I	T	-	2	0	TTN	179161675	0.000000	0.05858	0.000000	0.03702	0.925000	0.55904	1.233000	0.32648	-1.316000	0.02295	-0.312000	0.09012	ACA	G|0.988;A|0.012	0.012	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ST5	6764	hgsc.bcm.edu	37	11	8751889	8751889	+	Missense_Mutation	SNP	C	C	G	rs3794153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8751889C>G	ENST00000534127.1	-	6	1333	c.948G>C	c.(946-948)aaG>aaC	p.K316N	ST5_ENST00000357665.1_Missense_Mutation_p.K316N|ST5_ENST00000530438.1_Intron|ST5_ENST00000313726.6_Missense_Mutation_p.K316N|ST5_ENST00000526757.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	316			K -> N (in dbSNP:rs3794153). {ECO:0000269|PubMed:15489334}.		positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		AGGTTCCAGTCTTCCTTTTCC	0.692													C|||	1403	0.280152	0.0159	0.4539	5008	,	,		14399	0.3472		0.4354	False		,,,				2504	0.2853				p.K316N		Atlas-SNP	.											.	ST5	85	.	0			c.G948C						PASS	.	C	ASN/LYS,,ASN/LYS	398,3988		31,336,1826	34.0	39.0	37.0		948,,948	6.2	1.0	11	dbSNP_107	37	3765,4817		842,2081,1368	yes	missense,intron,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	94,,94	873,2417,3194	GG,GC,CC		43.8709,9.0743,32.1021	probably-damaging,,probably-damaging	316/1138,,316/1138	8751889	4163,8805	2193	4291	6484	SO:0001583	missense	6764	exon6			TCCAGTCTTCCTT	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.948G>C	11.37:g.8751889C>G	ENSP00000433528:p.Lys316Asn	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	699	0.32005494505494503	13	0.026422764227642278	132	0.36464088397790057	230	0.4020979020979021	324	0.42744063324538256	C	26.5	4.744853	0.89663	0.090743	0.438709	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.10005	2.92;2.92;2.92	6.17	6.17	0.99709	.	0.096519	0.64402	D	0.000001	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.999999863828	D	0.71674	0.998	P	0.59115	0.852	T	0.43605	-0.9381	9	0.72032	D	0.01	-17.847	20.8794	0.99867	0.0:1.0:0.0:0.0	rs3794153;rs17251393;rs17853684;rs59980123;rs3794153	316	P78524	ST5_HUMAN	N	316	ENSP00000433528:K316N;ENSP00000319678:K316N;ENSP00000350294:K316N	ENSP00000319678:K316N	K	-	3	2	ST5	8708465	1.000000	0.71417	0.996000	0.52242	0.827000	0.46813	2.756000	0.47549	2.941000	0.99782	0.655000	0.94253	AAG	C|0.673;G|0.327	0.327	strong		0.692	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
GOLGB1	2804	hgsc.bcm.edu	37	3	121416623	121416623	+	Missense_Mutation	SNP	G	G	C	rs3732407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121416623G>C	ENST00000340645.5	-	13	2857	c.2732C>G	c.(2731-2733)aCt>aGt	p.T911S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.T916S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	911			T -> S (in dbSNP:rs3732407). {ECO:0000269|PubMed:18487259}.		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)		CATTTTCTCAGTCATACTAAA	0.383													G|||	528	0.105431	0.0121	0.147	5008	,	,		20713	0.0476		0.2435	False		,,,				2504	0.1196				p.T916S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C2747G						PASS	.	G	SER/THR	181,4225	116.7+/-154.6	3,175,2025	143.0	148.0	146.0		2732	4.5	1.0	3	dbSNP_107	146	2073,6525	359.6+/-331.6	263,1547,2489	yes	missense	GOLGB1	NM_004487.3	58	266,1722,4514	CC,CG,GG		24.1103,4.108,17.3331	benign	911/3260	121416623	2254,10750	2203	4299	6502	SO:0001583	missense	2804	exon13			TTCTCAGTCATAC	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.2732C>G	3.37:g.121416623G>C	ENSP00000341848:p.Thr911Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	217	78	0.359447	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	303|303	0.13873626373626374|0.13873626373626374	10|10	0.02032520325203252|0.02032520325203252	70|70	0.19337016574585636|0.19337016574585636	34|34	0.05944055944055944|0.05944055944055944	189|189	0.24934036939313983|0.24934036939313983	G|G	7.435|7.435	0.639547|0.639547	0.14386|0.14386	0.04108|0.04108	0.241103|0.241103	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.13089	.|3.16;3.16;2.62	5.35|5.35	4.48|4.48	0.54585|0.54585	.|.	.|0.198851	.|0.35495	.|N	.|0.003174	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13043|0.13043	0.29|0.29	0.43545|0.43545	P|P	0.004153999999999991|0.004153999999999991	.|B;B;B;B	.|0.15141	.|0.012;0.005;0.012;0.002	.|B;B;B;B	.|0.19946	.|0.027;0.013;0.027;0.012	T|T	0.42481|0.42481	-0.9449|-0.9449	4|9	.|0.09843	.|T	.|0.71	.|.	12.0937|12.0937	0.53742|0.53742	0.0827:0.0:0.9173:0.0|0.0827:0.0:0.9173:0.0	rs3732407;rs17549959;rs52791658;rs3732407|rs3732407;rs17549959;rs52791658;rs3732407	.|836;875;916;911	.|F1T0J2;E7EU81;E7EP74;Q14789	.|.;.;.;GOGB1_HUMAN	V|S	782|911;916;875;723	.|ENSP00000341848:T911S;ENSP00000377275:T916S;ENSP00000418231:T875S	.|ENSP00000341848:T911S	L|T	-|-	1|2	2|0	GOLGB1|GOLGB1	122899313|122899313	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.999000|0.999000	0.98932|0.98932	3.941000|3.941000	0.56607|0.56607	1.493000|1.493000	0.48517|0.48517	0.655000|0.655000	0.94253|0.94253	CTG|ACT	G|0.843;C|0.157	0.157	strong		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
MAP3K1	4214	hgsc.bcm.edu	37	5	56177443	56177443	+	Missense_Mutation	SNP	G	G	A	rs702689	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:56177443G>A	ENST00000399503.3	+	14	2416	c.2416G>A	c.(2416-2418)Gat>Aat	p.D806N		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	806			D -> N (in dbSNP:rs702689).		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)		GCAGTCCATTGATAATTCCCA	0.363													G|||	2386	0.476438	0.4622	0.4914	5008	,	,		19052	0.2431		0.7117	False		,,,				2504	0.4836				p.D806N		Atlas-SNP	.											.	MAP3K1	355	.	0			c.G2416A						PASS	.	G	ASN/ASP	1844,1884		456,932,476	105.0	95.0	98.0		2416	5.6	1.0	5	dbSNP_86	98	5908,2288		2133,1642,323	yes	missense	MAP3K1	NM_005921.1	23	2589,2574,799	AA,AG,GG		27.9161,49.4635,34.9883	probably-damaging	806/1513	56177443	7752,4172	1864	4098	5962	SO:0001583	missense	4214	exon14			TCCATTGATAATT	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.2416G>A	5.37:g.56177443G>A	ENSP00000382423:p.Asp806Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	1096	0.5018315018315018	234	0.47560975609756095	191	0.5276243093922652	139	0.243006993006993	532	0.7018469656992085	G	13.63	2.295264	0.40594	0.494635	0.720839	ENSG00000095015	ENST00000399503	T	0.48201	0.82	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.41236	1.265	0.18873	P	0.9999853616	D	0.76494	0.999	D	0.63488	0.915	T	0.36335	-0.9752	9	0.24483	T	0.36	.	19.8805	0.96895	0.0:0.0:1.0:0.0	rs702689;rs2229884;rs52796136;rs59564733;rs702689	806	Q13233	M3K1_HUMAN	N	806	ENSP00000382423:D806N	ENSP00000382423:D806N	D	+	1	0	MAP3K1	56213200	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.102000	0.89548	2.778000	0.95560	0.655000	0.94253	GAT	G|0.472;A|0.528	0.528	strong		0.363	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
TBX6	6911	hgsc.bcm.edu	37	16	30097630	30097630	+	Silent	SNP	C	C	T	rs2289292	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	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	
TULP2	7288	hgsc.bcm.edu	37	19	49398405	49398405	+	Missense_Mutation	SNP	C	C	T	rs34378208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49398405C>T	ENST00000221399.3	-	6	508	c.364G>A	c.(364-366)Ggt>Agt	p.G122S		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	122			G -> S (in dbSNP:rs34378208).		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)		GACTGGAGACCGAGATTCCTG	0.542													C|||	260	0.0519169	0.0113	0.0648	5008	,	,		19540	0.002		0.0805	False		,,,				2504	0.1196				p.G122S		Atlas-SNP	.											.	TULP2	60	.	0			c.G364A						PASS	.	C	SER/GLY	87,4319	73.1+/-111.1	2,83,2118	64.0	62.0	63.0		364	-3.8	0.0	19	dbSNP_126	63	688,7912	170.1+/-221.3	25,638,3637	yes	missense	TULP2	NM_003323.2	56	27,721,5755	TT,TC,CC		8.0,1.9746,5.9588	benign	122/521	49398405	775,12231	2203	4300	6503	SO:0001583	missense	7288	exon6			GGAGACCGAGATT	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.364G>A	19.37:g.49398405C>T	ENSP00000221399:p.Gly122Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	99	0.04532967032967033	5	0.01016260162601626	27	0.07458563535911603	1	0.0017482517482517483	66	0.0870712401055409	C	10.91	1.485510	0.26686	0.019746	0.08	ENSG00000104804	ENST00000221399;ENST00000518572;ENST00000522945;ENST00000520977	D;T;T;T	0.83755	-1.76;2.11;1.26;0.68	4.92	-3.78	0.04333	.	4.406720	0.00567	N	0.000298	T	0.05364	0.0142	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.12156	0.007	T	0.30909	-0.9962	10	0.19147	T	0.46	11.6829	2.3847	0.04363	0.1423:0.2474:0.4186:0.1917	rs34378208	122	O00295	TULP2_HUMAN	S	122;76;119;103	ENSP00000221399:G122S;ENSP00000428420:G76S;ENSP00000430040:G119S;ENSP00000428535:G103S	ENSP00000221399:G122S	G	-	1	0	TULP2	54090217	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.132000	0.00590	-0.814000	0.04352	-0.311000	0.09066	GGT	C|0.945;T|0.055	0.055	strong		0.542	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
F5	2153	hgsc.bcm.edu	37	1	169513583	169513583	+	Silent	SNP	G	G	T	rs6037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169513583G>T	ENST00000367797.3	-	12	2127	c.1926C>A	c.(1924-1926)acC>acA	p.T642T	F5_ENST00000367796.3_Silent_p.T647T	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	642	F5/8 type A 2.|Plastocyanin-like 4.				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)	TGGGGAAGAGGGTCAAGGTGT	0.478													N|||	252	0.0503195	0.0053	0.1009	5008	,	,		19493	0.0298		0.0736	False		,,,				2504	0.0726				p.T642T		Atlas-SNP	.											.	F5	301	.	0			c.C1926A						PASS	.	G		57,4349	54.9+/-90.9	0,57,2146	98.0	87.0	91.0		1926	-1.6	1.0	1	dbSNP_52	91	659,7941	167.0+/-218.8	23,613,3664	yes	coding-synonymous	F5	NM_000130.4		23,670,5810	TT,TG,GG		7.6628,1.2937,5.5052		642/2225	169513583	716,12290	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon12			GAAGAGGGTCAAG	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.1926C>A	1.37:g.169513583G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	146	53	0.363014	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.946;T|0.054	0.054	strong		0.478	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ADAM33	80332	hgsc.bcm.edu	37	20	3651765	3651765	+	Missense_Mutation	SNP	C	C	T	rs3918396	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3651765C>T	ENST00000356518.2	-	19	2369	c.2128G>A	c.(2128-2130)Gtc>Atc	p.V710I	ADAM33_ENST00000379861.4_Missense_Mutation_p.V710I|ADAM33_ENST00000350009.2_Missense_Mutation_p.V684I|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	710			V -> I (in dbSNP:rs3918396). {ECO:0000269|Ref.4}.		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						GGCAGCAGGACGCTGAGGAGC	0.677													C|||	241	0.048123	0.0023	0.0418	5008	,	,		18411	0.0179		0.0835	False		,,,				2504	0.1094				p.V710I		Atlas-SNP	.											.	ADAM33	76	.	0			c.G2128A						PASS	.	C	ILE/VAL,ILE/VAL	90,4312		0,90,2111	25.0	29.0	28.0		2128,2050	3.5	0.9	20	dbSNP_108	28	757,7837		38,681,3578	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	29,29	38,771,5689	TT,TC,CC		8.8085,2.0445,6.5174	benign,benign	710/814,684/788	3651765	847,12149	2201	4297	6498	SO:0001583	missense	80332	exon19			GCAGGACGCTGAG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.2128G>A	20.37:g.3651765C>T	ENSP00000348912:p.Val710Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	105	0.04807692307692308	4	0.008130081300813009	26	0.0718232044198895	9	0.015734265734265736	66	0.0870712401055409	C	1.089	-0.664660	0.03428	0.020445	0.088085	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.01505	4.83;4.83;4.82	5.82	3.45	0.39498	.	.	.	.	.	T	0.00073	0.0002	L	0.28556	0.865	0.80722	P	0.0	B;B;B	0.24920	0.114;0.069;0.069	B;B;B	0.16289	0.015;0.007;0.007	T	0.28522	-1.0041	8	0.02654	T	1	.	11.8344	0.52314	0.562:0.438:0.0:0.0	rs3918396	684;710;710	Q9BZ11-2;Q9BZ11;A2A2L3	.;ADA33_HUMAN;.	I	710;710;684;590	ENSP00000348912:V710I;ENSP00000369190:V710I;ENSP00000322550:V684I	ENSP00000322550:V684I	V	-	1	0	ADAM33	3599765	0.011000	0.17503	0.900000	0.35374	0.490000	0.33462	1.267000	0.33050	1.041000	0.40125	-0.397000	0.06425	GTC	C|0.949;T|0.051	0.051	strong		0.677	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
DNAI2	64446	hgsc.bcm.edu	37	17	72278021	72278021	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72278021A>G	ENST00000311014.6	+	2	132	c.65A>G	c.(64-66)gAc>gGc	p.D22G	DNAI2_ENST00000582036.1_Missense_Mutation_p.D22G|DNAI2_ENST00000307504.5_5'UTR|DNAI2_ENST00000446837.2_Missense_Mutation_p.D22G|DNAI2_ENST00000579490.1_Missense_Mutation_p.D79G			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	22					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						AATTTCTCGGACCGCCAGGCC	0.622									Kartagener syndrome																												p.D22G		Atlas-SNP	.											DNAI2,NS,carcinoma,-1,3	DNAI2	102	3	0			c.A65G						scavenged	.						144.0	121.0	129.0					17																	72278021		2203	4300	6503	SO:0001583	missense	64446	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TCTCGGACCGCCA	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.65A>G	17.37:g.72278021A>G	ENSP00000308312:p.Asp22Gly	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	101	3	0.029703	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	37	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.801970	0.70682	.	.	ENSG00000171595	ENST00000311014;ENST00000446837	T;T	0.70045	-0.45;-0.45	5.22	5.22	0.72569	.	0.048188	0.85682	D	0.000000	T	0.82135	0.4971	M	0.86178	2.8	0.80722	D	1	D	0.71674	0.998	D	0.64776	0.929	D	0.84840	0.0807	10	0.56958	D	0.05	-68.7399	15.323	0.74139	1.0:0.0:0.0:0.0	.	22	Q9GZS0	DNAI2_HUMAN	G	22	ENSP00000308312:D22G;ENSP00000400252:D22G	ENSP00000308312:D22G	D	+	2	0	DNAI2	69789616	1.000000	0.71417	0.996000	0.52242	0.957000	0.61999	8.058000	0.89460	2.205000	0.71048	0.524000	0.50904	GAC	.	.	none		0.622	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
MUC20	200958	hgsc.bcm.edu	37	3	195453205	195453205	+	Silent	SNP	G	G	A	rs9870815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195453205G>A	ENST00000447234.2	+	2	1857	c.1731G>A	c.(1729-1731)tcG>tcA	p.S577S	MUC20_ENST00000320736.6_Silent_p.S406S|MUC20_ENST00000445522.2_Silent_p.S542S|MUC20_ENST00000436408.1_Silent_p.S577S	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	577	Involved in oligomerization.				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)		ACAGCCCCTCGGAAGCCGCCC	0.592																																					p.S406S		Atlas-SNP	.											.	MUC20	84	.	0			c.G1218A						PASS	.	G	,	75,3983		0,75,1954	62.0	60.0	61.0		1113,1218	-9.1	0.0	3	dbSNP_119	61	945,7457		0,945,3256	no	coding-synonymous,coding-synonymous	MUC20	NM_001098516.1,NM_152673.2	,	0,1020,5210	AA,AG,GG		11.2473,1.8482,8.1862	,	371/504,406/539	195453205	1020,11440	2029	4201	6230	SO:0001819	synonymous_variant	200958	exon3			CCCCTCGGAAGCC	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.1731G>A	3.37:g.195453205G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37																																																																																				G|0.938;A|0.062	0.062	strong		0.592	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482271	54482271	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:54482271T>C	ENST00000317802.7	-	1	1138	c.1018A>G	c.(1018-1020)Att>Gtt	p.I340V	ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	340					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						TTCCTATGAATGAAGGACTGG	0.498																																					p.I340V		Atlas-SNP	.											.	TSPYL6	54	.	0			c.A1018G						PASS	.						74.0	79.0	77.0					2																	54482271		2124	4267	6391	SO:0001583	missense	388951	exon1			TATGAATGAAGGA	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.1018A>G	2.37:g.54482271T>C	ENSP00000417919:p.Ile340Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	T	7.246	0.602182	0.13939	.	.	ENSG00000178021	ENST00000317802	T	0.28666	1.6	1.52	0.306	0.15806	.	.	.	.	.	T	0.16938	0.0407	N	0.05177	-0.1	0.09310	N	1	P	0.35192	0.489	P	0.45232	0.474	T	0.36432	-0.9748	9	0.12430	T	0.62	.	5.7092	0.17925	0.0:0.0:0.3027:0.6972	.	340	Q8N831	TSYL6_HUMAN	V	340	ENSP00000417919:I340V	ENSP00000417919:I340V	I	-	1	0	TSPYL6	54335775	0.000000	0.05858	0.006000	0.13384	0.349000	0.29174	-0.527000	0.06200	0.071000	0.16664	0.383000	0.25322	ATT	.	.	none		0.498	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
LOX	4015	hgsc.bcm.edu	37	5	121413208	121413208	+	Missense_Mutation	SNP	C	C	T	rs1800449	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:121413208C>T	ENST00000231004.4	-	1	772	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	LOX_ENST00000513319.1_5'Flank	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	158			R -> Q (in dbSNP:rs1800449). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8100215}.		blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		GCTGGGCGGCCGCAGGTTACT	0.592													T|||	785	0.156749	0.1437	0.1599	5008	,	,		14108	0.1875		0.162	False		,,,				2504	0.135				p.R158Q		Atlas-SNP	.											LOX,NS,carcinoma,0,1	LOX	29	1	0			c.G473A						PASS	.	T	GLN/ARG	784,3610		81,622,1494	40.0	49.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	473	2.4	0.4	5	dbSNP_89	46	1494,7104		148,1198,2953	yes	missense	LOX	NM_002317.5	43	229,1820,4447	TT,TC,CC		17.3761,17.8425,17.5339	benign	158/418	121413208	2278,10714	2197	4299	6496	SO:0001583	missense	4015	exon1			GGCGGCCGCAGGT		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.473G>A	5.37:g.121413208C>T	ENSP00000231004:p.Arg158Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	37	CCDS4129.1	363	0.1662087912087912	73	0.1483739837398374	62	0.1712707182320442	113	0.19755244755244755	115	0.1517150395778364	T	2.703	-0.270433	0.05716	0.178425	0.173761	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.22134	1.97	4.3	2.41	0.29592	.	0.596299	0.16360	N	0.217810	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36187	-0.9758	9	0.09338	T	0.73	.	9.8413	0.40999	0.0:0.7856:0.0:0.2144	rs1800449;rs1800449	158	P28300	LYOX_HUMAN	Q	158;118	ENSP00000231004:R158Q	ENSP00000231004:R158Q	R	-	2	0	LOX	121441107	0.000000	0.05858	0.397000	0.26308	0.054000	0.15201	-0.034000	0.12225	-0.042000	0.13535	-0.893000	0.02921	CGG	C|0.827;T|0.173	0.173	strong		0.592	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2		
TTC21A	199223	hgsc.bcm.edu	37	3	39178437	39178437	+	Missense_Mutation	SNP	G	G	T	rs35934336	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:39178437G>T	ENST00000431162.2	+	24	3298	c.3164G>T	c.(3163-3165)cGc>cTc	p.R1055L	TTC21A_ENST00000440121.1_Missense_Mutation_p.R1007L|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000301819.6_Missense_Mutation_p.R1056L			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1055			R -> L (in dbSNP:rs35934336). {ECO:0000269|PubMed:14702039}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AACAAGGCACGCAAGGACAGC	0.547													G|||	100	0.0199681	0.0023	0.0173	5008	,	,		21162	0.0		0.0606	False		,,,				2504	0.0245				p.R1055L		Atlas-SNP	.											.	TTC21A	96	.	0			c.G3164T						PASS	.	G	LEU/ARG,LEU/ARG	54,4152		0,54,2049	110.0	115.0	113.0		3020,3164	4.8	1.0	3	dbSNP_126	113	484,7964		17,450,3757	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	102,102	17,504,5806	TT,TG,GG		5.7292,1.2839,4.2516	probably-damaging,probably-damaging	1007/1273,1055/1321	39178437	538,12116	2103	4224	6327	SO:0001583	missense	199223	exon24			AGGCACGCAAGGA	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.3164G>T	3.37:g.39178437G>T	ENSP00000398211:p.Arg1055Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	60	0.027472527472527472	3	0.006097560975609756	7	0.019337016574585635	0	0.0	50	0.06596306068601583	G	21.7	4.191567	0.78902	0.012839	0.057292	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.28895	1.59;1.59;1.59	4.85	4.85	0.62838	Tetratricopeptide-like helical (1);	0.090927	0.40469	N	0.001085	T	0.10078	0.0247	M	0.90082	3.085	0.50632	D	0.999889	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.997	T	0.50482	-0.8823	10	0.13470	T	0.59	-17.788	14.9103	0.70752	0.0:0.0:1.0:0.0	rs35934336;rs62242336	1007;1056;1055	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	L	1056;1038;1055;1007	ENSP00000301819:R1056L;ENSP00000398211:R1055L;ENSP00000410882:R1007L	ENSP00000301819:R1056L	R	+	2	0	TTC21A	39153441	1.000000	0.71417	0.978000	0.43139	0.444000	0.32077	9.405000	0.97313	2.237000	0.73441	0.462000	0.41574	CGC	G|0.960;T|0.040	0.040	strong		0.547	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
MVB12B	89853	hgsc.bcm.edu	37	9	129102840	129102840	+	Silent	SNP	G	G	A	rs1888156	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:129102840G>A	ENST00000361171.3	+	2	216	c.135G>A	c.(133-135)acG>acA	p.T45T	MVB12B_ENST00000436593.3_Silent_p.T30T|MVB12B_ENST00000545391.1_Silent_p.T45T	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	45					protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										TGCCAGAAACGTCAATGGATC	0.478													G|||	1577	0.314896	0.3858	0.3026	5008	,	,		21217	0.2897		0.2903	False		,,,				2504	0.2791				p.T45T		Atlas-SNP	.											.	.	.	.	0			c.G135A						PASS	.	G	,	1566,2840	491.0+/-362.0	267,1032,904	107.0	100.0	103.0		135,135	-3.0	0.0	9	dbSNP_92	103	2762,5838	439.3+/-359.2	447,1868,1985	no	coding-synonymous,coding-synonymous	FAM125B	NM_001011703.2,NM_033446.2	,	714,2900,2889	AA,AG,GG		32.1163,35.5424,33.2769	,	45/222,45/320	129102840	4328,8678	2203	4300	6503	SO:0001819	synonymous_variant	89853	exon2			AGAAACGTCAATG	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 28"", ""family with sequence similarity 125, member B"""	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.135G>A	9.37:g.129102840G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_001011703	Q8N6S7	Silent	SNP	ENST00000361171.3	37	CCDS35142.1																																																																																			G|0.676;A|0.324	0.324	strong		0.478	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525	
NLRP7	199713	hgsc.bcm.edu	37	19	55451258	55451258	+	Missense_Mutation	SNP	T	T	C	rs77812009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451258T>C	ENST00000590030.1	-	3	969	c.929A>G	c.(928-930)cAg>cGg	p.Q310R	NLRP7_ENST00000340844.2_Missense_Mutation_p.Q310R|NLRP7_ENST00000588756.1_Missense_Mutation_p.Q310R|NLRP7_ENST00000446217.1_Missense_Mutation_p.Q338R|NLRP7_ENST00000328092.5_Missense_Mutation_p.Q310R|NLRP7_ENST00000592784.1_Missense_Mutation_p.Q310R|NLRP7_ENST00000448121.2_Missense_Mutation_p.Q310R			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	310	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CGCCAGGAGCTGGAGGTCCCT	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16817	0.0		0.0219	False		,,,				2504	0.0				p.Q310R		Atlas-SNP	.											NLRP7_ENST00000328092,NS,lymphoid_neoplasm,+1,2	NLRP7	411	2	0			c.A929G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	3,4403	6.2+/-15.9	0,3,2200	38.0	38.0	38.0		929,929,929	-3.5	0.0	19	dbSNP_131	38	136,8464	59.8+/-121.6	1,134,4165	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	43,43,43	1,137,6365	CC,CT,TT		1.5814,0.0681,1.0687	benign,benign,benign	310/1038,310/1010,310/981	55451258	139,12867	2203	4300	6503	SO:0001583	missense	199713	exon4			AGGAGCTGGAGGT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.929A>G	19.37:g.55451258T>C	ENSP00000465520:p.Gln310Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	T	0.005	-2.144416	0.00332	6.81E-4	0.015814	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	1.77	-3.54	0.04653	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.30293	0.0760	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12156	0.007;0.007;0.002	T	0.37596	-0.9699	9	0.06099	T	0.92	.	3.6467	0.08187	0.1766:0.364:0.0:0.4594	.	338;310;310	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	R	310;310;310;338	ENSP00000329568:Q310R;ENSP00000409137:Q310R;ENSP00000339491:Q310R;ENSP00000414273:Q338R	ENSP00000329568:Q310R	Q	-	2	0	NLRP7	60143070	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.617000	0.24359	-1.039000	0.03275	-1.457000	0.01029	CAG	T|0.989;C|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
IKBKAP	8518	hgsc.bcm.edu	37	9	111653574	111653574	+	Silent	SNP	C	C	G	rs1063110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:111653574C>G	ENST00000374647.5	-	28	3376	c.3069G>C	c.(3067-3069)ctG>ctC	p.L1023L	IKBKAP_ENST00000467959.1_5'Flank|IKBKAP_ENST00000537196.1_Silent_p.L674L	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1023					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						TGCCACATGTCAGAAAGGCTG	0.562													C|||	1580	0.315495	0.0477	0.4553	5008	,	,		16868	0.4762		0.4523	False		,,,				2504	0.272				p.L1023L		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G3069C						PASS	.	C		494,3912	227.5+/-242.7	36,422,1745	89.0	84.0	86.0		3069	3.9	1.0	9	dbSNP_86	86	3914,4686	546.6+/-385.0	907,2100,1293	no	coding-synonymous	IKBKAP	NM_003640.3		943,2522,3038	GG,GC,CC		45.5116,11.212,33.892		1023/1333	111653574	4408,8598	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon28			ACATGTCAGAAAG	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.3069G>C	9.37:g.111653574C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			G|0.357;C|0.643	0.357	strong		0.562	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
MYADML2	255275	hgsc.bcm.edu	37	17	79899283	79899283	+	Missense_Mutation	SNP	C	C	T	rs118129884	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79899283C>T	ENST00000409745.2	-	3	689	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	AC137723.5_ENST00000415556.1_RNA|MYADML2_ENST00000330655.3_Missense_Mutation_p.R112Q	NM_001145113.2	NP_001138585.2	A6NDP7	MADL2_HUMAN	myeloid-associated differentiation marker-like 2	112	MARVEL 1. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(1)	1						ACACTCCCGCCGGGCAAAGTA	0.692													C|||	154	0.0307508	0.0023	0.0504	5008	,	,		15236	0.0089		0.0785	False		,,,				2504	0.0286				p.R112Q		Atlas-SNP	.											.	MYADML2	11	.	0			c.G335A						PASS	.						4.0	8.0	7.0					17																	79899283		635	1482	2117	SO:0001583	missense	255275	exon3			TCCCGCCGGGCAA	AC137723, BC029306	CCDS45815.1	17q25.3	2008-10-15			ENSG00000185105	ENSG00000185105			34548	protein-coding gene	gene with protein product							Standard	NM_001145113		Approved	LOC255275	uc010wvf.1	A6NDP7	OTTHUMG00000154388	ENST00000409745.2:c.335G>A	17.37:g.79899283C>T	ENSP00000386702:p.Arg112Gln	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_001145113		Missense_Mutation	SNP	ENST00000409745.2	37	CCDS45815.1	78	0.03571428571428571	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	58	0.07651715039577836	C	0.014	-1.597740	0.00857	.	.	ENSG00000185105	ENST00000409745;ENST00000330655	T;T	0.25250	1.81;1.81	4.95	1.91	0.25777	Marvel (1);MARVEL-like domain (1);	0.364427	0.29342	N	0.012429	T	0.00384	0.0012	N	0.03608	-0.345	0.22213	N	0.999288	B	0.06786	0.001	B	0.04013	0.001	T	0.33548	-0.9864	10	0.02654	T	1	-1.4418	4.3983	0.11374	0.0:0.4852:0.1577:0.3571	.	112	A6NDP7	MADL2_HUMAN	Q	112	ENSP00000386702:R112Q;ENSP00000327718:R112Q	ENSP00000327718:R112Q	R	-	2	0	MYADML2	77492574	0.532000	0.26346	0.868000	0.34077	0.043000	0.13939	0.982000	0.29539	0.297000	0.22615	-0.254000	0.11334	CGG	C|0.964;T|0.036	0.036	strong		0.692	MYADML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335008.2	XR_041347	
C5AR2	27202	hgsc.bcm.edu	37	19	47844383	47844383	+	Silent	SNP	G	G	T	rs373920189		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47844383G>T	ENST00000595464.1	+	2	545	c.327G>T	c.(325-327)gcG>gcT	p.A109A	C5AR2_ENST00000257267.2_Silent_p.A109A|C5AR2_ENST00000600626.1_Silent_p.A109A	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	109					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of interleukin-8 secretion (GO:2000482)	apical part of cell (GO:0045177)|basal plasma membrane (GO:0009925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)										GCTGTCGGGCGCTGCCCTCCA	0.647																																					p.A109A		Atlas-SNP	.											.	.	.	.	0			c.G327T						PASS	.						96.0	91.0	93.0					19																	47844383		2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TCGGGCGCTGCCC	AB038237	CCDS12699.1	19q13.33	2013-01-28	2013-01-28	2013-01-28		ENSG00000134830		"""GPCR / Class A : Complement component receptors"""	4527	protein-coding gene	gene with protein product		609949	"""G protein-coupled receptor 77"""	GPR77		11165367	Standard	NM_018485		Approved	C5L2	uc010ela.1	Q9P296		ENST00000595464.1:c.327G>T	19.37:g.47844383G>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			.	.	alt		0.647	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485	
AQP7	364	hgsc.bcm.edu	37	9	33385241	33385241	+	3'UTR	SNP	C	C	A	rs62542743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33385241C>A	ENST00000537089.1	-	0	1191				AQP7_ENST00000377425.4_Intron			O14520	AQP7_HUMAN	aquaporin 7						excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TAGATAGGCACCCAGAAGTGG	0.602													c|||	106	0.0211661	0.0015	0.0288	5008	,	,		17850	0.0248		0.0398	False		,,,				2504	0.0194				p.G264V		Atlas-SNP	.											.	AQP7	58	.	0			c.G791T	GRCh37	CM023765	AQP7	M	rs62542743	PASS	.	C	VAL/GLY	51,4355	50.2+/-85.5	0,51,2152	76.0	77.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	791	4.3	1.0	9	dbSNP_129	77	420,8180	125.5+/-184.1	10,400,3890	no	missense	AQP7	NM_001170.1	109	10,451,6042	AA,AC,CC		4.8837,1.1575,3.6214	probably-damaging	264/343	33385241	471,12535	2203	4300	6503	SO:0001624	3_prime_UTR_variant	364	exon8			TAGGCACCCAGAA	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.*375G>T	9.37:g.33385241C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		56	0.02564102564102564	0	0.0	12	0.03314917127071823	14	0.024475524475524476	30	0.0395778364116095	c	17.74	3.463323	0.63513	0.011575	0.048837	ENSG00000165269	ENST00000379507;ENST00000297988	T;T	0.58652	0.32;0.32	4.27	4.27	0.50696	Aquaporin-like (2);	0.115830	0.64402	D	0.000015	T	0.54240	0.1846	H	0.99211	4.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81949	-0.0699	10	0.87932	D	0	-7.358	12.1166	0.53868	0.0:1.0:0.0:0.0	rs62542743	264	O14520	AQP7_HUMAN	V	263;264	ENSP00000368821:G263V;ENSP00000297988:G264V	ENSP00000297988:G264V	G	-	2	0	AQP7	33375241	1.000000	0.71417	0.959000	0.39883	0.437000	0.31866	7.278000	0.78587	2.235000	0.73313	0.537000	0.68136	GGT	C|0.964;A|0.036	0.036	strong		0.602	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
DPP7	29952	hgsc.bcm.edu	37	9	140006202	140006202	+	Silent	SNP	G	G	A	rs13631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	108	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	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	
DGKH	160851	hgsc.bcm.edu	37	13	42793479	42793479	+	Silent	SNP	G	G	A	rs180870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:42793479G>A	ENST00000337343.4	+	27	3348	c.3327G>A	c.(3325-3327)gaG>gaA	p.E1109E	DGKH_ENST00000540693.1_Silent_p.E1109E|DGKH_ENST00000379274.2_Silent_p.E973E|DGKH_ENST00000261491.5_Silent_p.E1109E|DGKH_ENST00000536612.1_Silent_p.E973E|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Silent_p.E864E	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1109					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)		ACCCAAATGAGGATGAGGTAT	0.363													G|||	3139	0.626797	0.5976	0.634	5008	,	,		17423	0.7341		0.6879	False		,,,				2504	0.4877				p.E1109E		Atlas-SNP	.											.	DGKH	106	.	0			c.G3327A						PASS	.	G	,,,,	2711,1695	653.5+/-399.6	836,1039,328	130.0	137.0	135.0		3327,2919,2919,3327,3327	1.0	1.0	13	dbSNP_79	135	5877,2723	680.7+/-403.7	2021,1835,444	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	,,,,	2857,2874,772	AA,AG,GG		31.6628,38.4703,33.9689	,,,,	1109/1165,973/1101,973/1085,1109/1165,1109/1221	42793479	8588,4418	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon28			AAATGAGGATGAG	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.3327G>A	13.37:g.42793479G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			G|0.337;A|0.663	0.663	strong		0.363	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
GAPDH	2597	hgsc.bcm.edu	37	12	6647109	6647109	+	Silent	SNP	T	T	C	rs1803621	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:6647109T>C	ENST00000229239.5	+	8	1551	c.885T>C	c.(883-885)ttT>ttC	p.F295F	RP5-940J5.9_ENST00000602946.1_RNA|GAPDH_ENST00000396858.1_Silent_p.F253F|GAPDH_ENST00000396859.1_Silent_p.F295F|GAPDH_ENST00000396856.1_Silent_p.F220F|GAPDH_ENST00000396861.1_Silent_p.F295F	NM_002046.4	NP_002037.2	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase	295					carbohydrate metabolic process (GO:0005975)|cellular response to interferon-gamma (GO:0071346)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of translation (GO:0017148)|neuron apoptotic process (GO:0051402)|peptidyl-cysteine S-trans-nitrosylation (GO:0035606)|protein stabilization (GO:0050821)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GAIT complex (GO:0097452)|lipid particle (GO:0005811)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|identical protein binding (GO:0042802)|microtubule binding (GO:0008017)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|peptidyl-cysteine S-nitrosylase activity (GO:0035605)			central_nervous_system(1)|cervix(1)|endometrium(1)|lung(4)	7						CCTCCACCTTTGACGCTGGGG	0.587											OREG0021628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2077	0.414736	0.5666	0.3228	5008	,	,		20164	0.5486		0.2217	False		,,,				2504	0.3354				p.F295F		Atlas-SNP	.											.	GAPDH	20	.	0			c.T885C						PASS	.	C		2048,2350		493,1062,644	45.0	51.0	49.0		885	-5.3	0.9	12	dbSNP_89	49	1757,6837		184,1389,2724	no	coding-synonymous	GAPDH	NM_002046.3		677,2451,3368	CC,CT,TT		20.4445,46.5666,29.2873		295/336	6647109	3805,9187	2199	4297	6496	SO:0001819	synonymous_variant	2597	exon8			CACCTTTGACGCT	AF261085	CCDS8549.1, CCDS58201.1	12p13.31	2012-10-02		2005-05-06	ENSG00000111640	ENSG00000111640	1.2.1.12		4141	protein-coding gene	gene with protein product		138400		GAPD		3170585	Standard	NM_002046		Approved		uc001qop.2	P04406	OTTHUMG00000137379	ENST00000229239.5:c.885T>C	12.37:g.6647109T>C		Somatic	24	0	0	635	WXS	Illumina HiSeq	Phase_I	21	16	0.761905	NM_002046	E7EUT4|P00354|Q53X65	Silent	SNP	ENST00000229239.5	37	CCDS8549.1																																																																																			T|0.686;C|0.314	0.314	strong		0.587	GAPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268059.1	NM_002046	
CCDC125	202243	hgsc.bcm.edu	37	5	68616331	68616331	+	Missense_Mutation	SNP	C	C	T	rs10471774	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:68616331C>T	ENST00000396496.2	-	2	144	c.37G>A	c.(37-39)Gtg>Atg	p.V13M	CCDC125_ENST00000511257.1_De_novo_Start_OutOfFrame|CCDC125_ENST00000396499.1_Missense_Mutation_p.V13M|CCDC125_ENST00000383374.2_Missense_Mutation_p.V13M|CCDC125_ENST00000460090.1_5'UTR			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	94	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	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	
TOX3	27324	hgsc.bcm.edu	37	16	52473263	52473263	+	Silent	SNP	A	A	G	rs9925256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:52473263A>G	ENST00000219746.9	-	7	1889	c.1605T>C	c.(1603-1605)ccT>ccC	p.P535P	TOX3_ENST00000407228.3_Silent_p.P530P	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	535	Gln-rich.				apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)	p.P535P(1)		NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GAGAGGCGACAGGGGAGTGCT	0.607													G|||	2452	0.489617	0.7648	0.3977	5008	,	,		16094	0.2679		0.4473	False		,,,				2504	0.455				p.P535P		Atlas-SNP	.											TOX3,NS,carcinoma,0,1	TOX3	121	1	1	Substitution - coding silent(1)	stomach(1)	c.T1605C						scavenged	.	G	,	3033,1091		1138,757,167	20.0	22.0	21.0		1605,1590	-12.0	0.0	16	dbSNP_119	21	3986,4480		920,2146,1167	no	coding-synonymous,coding-synonymous	TOX3	NM_001080430.2,NM_001146188.1	,	2058,2903,1334	GG,GA,AA		47.0824,26.4549,44.2494	,	535/577,530/572	52473263	7019,5571	2062	4233	6295	SO:0001819	synonymous_variant	27324	exon7			GGCGACAGGGGAG	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.1605T>C	16.37:g.52473263A>G		Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001080430	B4DRD0|B5MCW4	Silent	SNP	ENST00000219746.9	37	CCDS54009.1																																																																																			A|0.542;G|0.458	0.458	strong		0.607	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
OVGP1	5016	hgsc.bcm.edu	37	1	111957517	111957517	+	Missense_Mutation	SNP	T	T	C	rs3767609|rs201350653|rs549398942	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:111957517T>C	ENST00000369732.3	-	11	1661	c.1606A>G	c.(1606-1608)Agt>Ggt	p.S536G		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	536			S -> G (in dbSNP:rs3767609).		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)		GACTGATGACTCACAGGGGTC	0.547													T|||	1503	0.30012	0.4092	0.2291	5008	,	,		16183	0.2044		0.2972	False		,,,				2504	0.3047				p.S536G		Atlas-SNP	.											.	OVGP1	177	.	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.A1606G						PASS	.	T	GLY/SER	1138,3170		242,654,1258	58.0	69.0	66.0		1606	-4.5	0.0	1	dbSNP_107	66	2424,6110		368,1688,2211	yes	missense	OVGP1	NM_002557.3	56	610,2342,3469	CC,CT,TT		28.404,26.416,27.7371	benign	536/679	111957517	3562,9280	2154	4267	6421	SO:0001583	missense	5016	exon11			GATGACTCACAGG	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.1606A>G	1.37:g.111957517T>C	ENSP00000358747:p.Ser536Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	90	25	0.277778	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	T	6.657	0.489649	0.12702	0.26416	0.28404	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.02787	4.16	2.23	-4.46	0.03536	.	.	.	.	.	T	0.00524	0.0017	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.44982	-0.9292	8	0.31617	T	0.26	0.2049	3.9657	0.09431	0.0:0.2687:0.3546:0.3767	rs3767609;rs3767609	536;600	Q12889;Q59HH5	OVGP1_HUMAN;.	G	536;600;344	ENSP00000358747:S536G	ENSP00000358743:S600G	S	-	1	0	OVGP1	111759040	0.017000	0.18338	0.000000	0.03702	0.168000	0.22595	0.634000	0.24614	-1.729000	0.01364	0.254000	0.18369	AGT	T|0.776;C|0.224	0.224	strong		0.547	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
LRRK1	79705	hgsc.bcm.edu	37	15	101598314	101598314	+	Silent	SNP	C	C	T	rs11853661	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:101598314C>T	ENST00000388948.3	+	29	5006	c.4647C>T	c.(4645-4647)acC>acT	p.T1549T	LRRK1_ENST00000284395.5_Silent_p.T1546T|RP11-505E24.2_ENST00000559857.1_RNA	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)			AGGAGTACACCGTGGTGTTTT	0.572													C|||	1552	0.309904	0.2821	0.2795	5008	,	,		20576	0.1329		0.4374	False		,,,				2504	0.4202				p.T1549T		Atlas-SNP	.											.	LRRK1	310	.	0			c.C4647T						PASS	.	C		1132,2774		169,794,990	65.0	64.0	65.0		4647	-2.2	1.0	15	dbSNP_120	65	3723,4543		854,2015,1264	no	coding-synonymous	LRRK1	NM_024652.3		1023,2809,2254	TT,TC,CC		45.0399,28.9811,39.8866		1549/2016	101598314	4855,7317	1953	4133	6086	SO:0001819	synonymous_variant	79705	exon29			GTACACCGTGGTG	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.4647C>T	15.37:g.101598314C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.644;T|0.356	0.356	strong		0.572	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
CTAG2	30848	hgsc.bcm.edu	37	X	153881525	153881525	+	Missense_Mutation	SNP	G	G	C	rs17328091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153881525G>C	ENST00000247306.4	-	1	328	c.265C>G	c.(265-267)Cag>Gag	p.Q89E	CTAG2_ENST00000369585.3_Missense_Mutation_p.Q89E	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	89			Q -> E (in dbSNP:rs17328091). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17899192, ECO:0000269|PubMed:9626360}.			centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-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)					GGATACAACTGAAGCAGGCGG	0.682													g|||	1923	0.509404	0.6634	0.3069	3775	,	,		6030	0.1796		0.2604	False		,,,				2504	0.3988				p.Q89E		Atlas-SNP	.											.	CTAG2	88	.	0			c.C265G						PASS	.	G	GLU/GLN,GLU/GLN	3117,713		1081,480,475,69,95	40.0	39.0	39.0		265,265	-3.3	0.0	X	dbSNP_123	39	2554,4171		366,1121,701,941,1168	yes	missense,missense	CTAG2	NM_020994.3,NM_172377.3	29,29	1447,1601,1176,1010,1263	CC,CG,C,GG,G		37.9777,18.6162,46.2719	benign,benign	89/211,89/181	153881525	5671,4884	2200	4297	6497	SO:0001583	missense	30848	exon1			ACAACTGAAGCAG	AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"""CTL-recognized antigen on melanoma"", ""LAGE-1a protein"", ""cancer/testis antigen family 6, member 2a"", ""cancer/testis antigen family 6, member 2b"""	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.265C>G	X.37:g.153881525G>C	ENSP00000247306:p.Gln89Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_020994	O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Missense_Mutation	SNP	ENST00000247306.4	37	CCDS14759.1	750	0.45207956600361665	229	0.8357664233576643	84	0.28378378378378377	58	0.116	141	0.22100313479623823	g	0.001	-3.347120	0.00016	0.813838	0.379777	ENSG00000126890	ENST00000247306;ENST00000369585;ENST00000454505	T;T	0.27256	1.68;1.68	1.65	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B	0.24618	0.107;0.087	B;B	0.16722	0.016;0.01	T	0.39014	-0.9634	8	0.02654	T	1	.	1.7181	0.02905	0.2303:0.3703:0.2625:0.1369	rs17328091;rs17855366	89;89	O75638;O75638-2	CTAG2_HUMAN;.	E	89;89;31	ENSP00000247306:Q89E;ENSP00000358598:Q89E	ENSP00000247306:Q89E	Q	-	1	0	CTAG2	153534719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.469000	0.06648	-3.244000	0.00206	-1.390000	0.01156	CAG	0|0.004;C|0.526	0.526	strong		0.682	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061176.1	NM_020994	
CAMK2G	818	hgsc.bcm.edu	37	10	75632760	75632760	+	Silent	SNP	C	C	T	rs2675671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:75632760C>T	ENST00000351293.3	-	2	204	c.147G>A	c.(145-147)aaG>aaA	p.K49K	CAMK2G_ENST00000423381.1_Silent_p.K49K|CAMK2G_ENST00000322635.3_Silent_p.K49K|CAMK2G_ENST00000394762.2_Silent_p.K49K|CAMK2G_ENST00000322680.3_Silent_p.K49K|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000372765.1_Silent_p.K49K|CAMK2G_ENST00000444854.2_Silent_p.K49K|CAMK2G_ENST00000305762.7_Silent_p.K49K	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	49	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	GGGCAGACAACTTCTTGGTAT	0.547													C|||	1424	0.284345	0.1936	0.3386	5008	,	,		18209	0.1121		0.5785	False		,,,				2504	0.2434				p.K49K		Atlas-SNP	.											CAMK2G_ENST00000322680,colon,carcinoma,0,2	CAMK2G	79	2	0			c.G147A						PASS	.	C	,,,,,	1173,3233	411.5+/-335.8	154,865,1184	261.0	238.0	246.0		147,147,147,147,147,147	4.1	1.0	10	dbSNP_100	246	4866,3734	617.6+/-396.7	1356,2154,790	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2G	NM_001204492.1,NM_001222.3,NM_172169.2,NM_172170.4,NM_172171.2,NM_172173.2	,,,,,	1510,3019,1974	TT,TC,CC		43.4186,26.6228,46.4324	,,,,,	49/540,49/496,49/528,49/519,49/557,49/505	75632760	6039,6967	2203	4300	6503	SO:0001819	synonymous_variant	818	exon2			AGACAACTTCTTG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.147G>A	10.37:g.75632760C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Silent	SNP	ENST00000351293.3	37	CCDS7336.1																																																																																			C|0.601;T|0.399	0.399	strong		0.547	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
ERGIC2	51290	hgsc.bcm.edu	37	12	29521193	29521193	+	Silent	SNP	A	A	G	rs12831730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:29521193A>G	ENST00000360150.4	-	4	318	c.243T>C	c.(241-243)acT>acC	p.T81T		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	81					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					TCATGGCAACAGTAATATCTA	0.299													A|||	735	0.146765	0.1301	0.1182	5008	,	,		15589	0.1895		0.164	False		,,,				2504	0.1278				p.T81T		Atlas-SNP	.											.	ERGIC2	29	.	0			c.T243C						PASS	.	A		503,3107		36,431,1338	63.0	61.0	62.0		243	3.0	1.0	12	dbSNP_121	62	1224,6908		91,1042,2933	no	coding-synonymous	ERGIC2	NM_016570.2		127,1473,4271	GG,GA,AA		15.0516,13.9335,14.7079		81/378	29521193	1727,10015	1805	4066	5871	SO:0001819	synonymous_variant	51290	exon4			GGCAACAGTAATA	AF216751	CCDS41765.1	12p11.22	2006-02-08							30208	protein-coding gene	gene with protein product		612236				11445006, 12932305	Standard	NM_016570		Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.243T>C	12.37:g.29521193A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	112	0.982456	NM_016570	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Silent	SNP	ENST00000360150.4	37	CCDS41765.1																																																																																			A|0.833;G|0.167	0.167	strong		0.299	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403489.1	NM_016570	
FHDC1	85462	hgsc.bcm.edu	37	4	153886104	153886104	+	Silent	SNP	G	G	A	rs2018007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:153886104G>A	ENST00000511601.1	+	9	1265	c.1077G>A	c.(1075-1077)ttG>ttA	p.L359L	FHDC1_ENST00000260008.3_Silent_p.L359L			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	359	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CAGAAAAATTGCATCATGTTC	0.303													G|||	113	0.0225639	0.0749	0.0086	5008	,	,		18165	0.0		0.005	False		,,,				2504	0.0031				p.L359L		Atlas-SNP	.											.	FHDC1	102	.	0			c.G1077A						PASS	.	G		277,4129	152.2+/-185.9	13,251,1939	75.0	81.0	79.0		1077	0.9	0.0	4	dbSNP_92	79	37,8557	24.6+/-71.5	1,35,4261	no	coding-synonymous	FHDC1	NM_033393.2		14,286,6200	AA,AG,GG		0.4305,6.2869,2.4154		359/1144	153886104	314,12686	2203	4297	6500	SO:0001819	synonymous_variant	85462	exon8			AAAATTGCATCAT	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.1077G>A	4.37:g.153886104G>A		Somatic	383	1	0.00261097		WXS	Illumina HiSeq	Phase_I	330	166	0.50303	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			G|0.973;A|0.027	0.027	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
ATP6V0A2	23545	hgsc.bcm.edu	37	12	124209332	124209332	+	Silent	SNP	T	T	C	rs1139789	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124209332T>C	ENST00000330342.3	+	4	674	c.426T>C	c.(424-426)aaT>aaC	p.N142N		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	142					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TGAAACGCAATGTTGAGGTAC	0.383													C|||	3761	0.750998	0.7027	0.7723	5008	,	,		14701	0.9474		0.6282	False		,,,				2504	0.7249				p.N142N		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.T426C						PASS	.	C		2994,1412	462.3+/-353.2	1034,926,243	120.0	119.0	119.0		426	-7.5	0.0	12	dbSNP_86	119	5416,3184	482.8+/-371.0	1723,1970,607	no	coding-synonymous	ATP6V0A2	NM_012463.3		2757,2896,850	CC,CT,TT		37.0233,32.0472,35.3375		142/857	124209332	8410,4596	2203	4300	6503	SO:0001819	synonymous_variant	23545	exon4			ACGCAATGTTGAG	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.426T>C	12.37:g.124209332T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	NM_012463	A8K026|Q6NUM0	Silent	SNP	ENST00000330342.3	37	CCDS9254.1																																																																																			T|0.317;G|0.037	.	strong		0.383	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
MXD1	4084	hgsc.bcm.edu	37	2	70162534	70162534	+	Silent	SNP	T	T	G	rs2228183	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	120	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	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	
KDM2B	84678	hgsc.bcm.edu	37	12	121877738	121877738	+	Missense_Mutation	SNP	C	C	T	rs200642027		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121877738C>T	ENST00000377071.4	-	22	3823	c.3751G>A	c.(3751-3753)Gtc>Atc	p.V1251I	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Missense_Mutation_p.V1182I|KDM2B_ENST00000542973.1_Missense_Mutation_p.V619I	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1251					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TGGTCGGTGACGTGGTTACAG	0.607																																					p.V1251I		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3751A						PASS	.	C	ILE/VAL,ILE/VAL	0,4368		0,0,2184	125.0	148.0	140.0		3544,3751	3.9	0.6	12		140	4,8542		0,4,4269	yes	missense,missense	KDM2B	NM_001005366.1,NM_032590.4	29,29	0,4,6453	TT,TC,CC		0.0468,0.0,0.031	benign,benign	1182/1266,1251/1337	121877738	4,12910	2184	4273	6457	SO:0001583	missense	84678	exon22			CGGTGACGTGGTT	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3751G>A	12.37:g.121877738C>T	ENSP00000366271:p.Val1251Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.154362	0.38021	0.0	4.68E-4	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.01172	5.23;5.23;5.23	5.73	3.88	0.44766	.	0.145937	0.30575	N	0.009338	T	0.00468	0.0015	N	0.01624	-0.795	0.80722	D	1	B;B;B;B	0.30114	0.103;0.001;0.269;0.037	B;B;B;B	0.15484	0.008;0.001;0.013;0.008	T	0.52343	-0.8588	10	0.02654	T	1	-15.9978	10.6917	0.45875	0.0:0.7916:0.0:0.2084	.	691;1251;1182;694	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	I	1241;619;1182;1251;694;1254	ENSP00000437821:V619I;ENSP00000366269:V1182I;ENSP00000366271:V1251I	ENSP00000261824:V1254I	V	-	1	0	KDM2B	120362121	1.000000	0.71417	0.613000	0.29037	0.983000	0.72400	1.995000	0.40767	0.742000	0.32697	0.655000	0.94253	GTC	.	.	weak		0.607	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605257	32605257	+	Missense_Mutation	SNP	C	C	A	rs1047989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32605257C>A	ENST00000343139.5	+	1	124	c.22C>A	c.(22-24)Ctg>Atg	p.L8M	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.L8M|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.L8M	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	8			M -> L (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*04:01 and allele DQA1*06:01; dbSNP:rs1047989).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAAAGCTCTGCTGCTGGGGGC	0.522													.|||	2363	0.471845	0.407	0.6196	5008	,	,		14810	0.4345		0.5358	False		,,,				2504	0.4274				p.L8M		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C22A						PASS	.	C	MET/LEU	1769,2637		383,1003,817	73.0	66.0	68.0		22	0.5	0.0	6	dbSNP_86	68	4719,3881		1369,1981,950	no	missense	HLA-DQA1	NM_002122.3	15	1752,2984,1767	AA,AC,CC		45.1279,40.1498,49.8847	benign	8/256	32605257	6488,6518	2203	4300	6503	SO:0001583	missense	3117	exon1			GCTCTGCTGCTGG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.22C>A	6.37:g.32605257C>A	ENSP00000339398:p.Leu8Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	1077	0.49313186813186816	180	0.36585365853658536	214	0.5911602209944752	287	0.5017482517482518	396	0.5224274406332454	.	0.536	-0.855524	0.02630	0.401498	0.548721	ENSG00000196735	ENST00000422863;ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	T;T;T;T;T	0.18174	2.23;4.59;4.59;4.26;4.59	4.15	0.462	0.16695	.	0.387707	0.24497	U	0.038020	T	0.01222	0.0040	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.18013	0.025;0.0	B;B	0.17979	0.02;0.005	T	0.45948	-0.9226	9	0.21014	T	0.42	.	3.4423	0.07468	0.5769:0.2049:0.2182:0.0	rs1047989;rs2308821;rs3176020;rs9272430;rs12722037;rs16870362;rs35187591	14;8	Q59F33;G4XQK2	.;.	M	8	ENSP00000405797:L8M;ENSP00000339398:L8M;ENSP00000378767:L8M;ENSP00000437302:L8M;ENSP00000364087:L8M	ENSP00000339398:L8M	L	+	1	2	HLA-DQA1	32713235	0.222000	0.23652	0.005000	0.12908	0.168000	0.22595	0.027000	0.13621	-0.059000	0.13154	-0.396000	0.06452	CTG	C|0.493;A|0.507	0.507	strong		0.522	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
YTHDC2	64848	hgsc.bcm.edu	37	5	112917278	112917278	+	Silent	SNP	T	T	G	rs11748794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	116	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	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	
WNK2	65268	hgsc.bcm.edu	37	9	96055063	96055063	+	Silent	SNP	C	C	T	rs41278286	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:96055063C>T	ENST00000297954.4	+	23	5427	c.5427C>T	c.(5425-5427)gaC>gaT	p.D1809D	WNK2_ENST00000427277.2_Silent_p.D1384D|WNK2_ENST00000356055.3_Silent_p.D136D|WNK2_ENST00000349097.3_Silent_p.D1421D|WNK2_ENST00000395475.2_3'UTR|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						scavenged	.	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	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	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	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33391270	33391270	+	Silent	SNP	T	T	C	rs587780476|rs142359891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33391270T>C	ENST00000418600.2	+	2	185	c.84T>C	c.(82-84)tcT>tcC	p.S28S	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.S28S	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	28					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)			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						GGGGACCCTCTATGCACCGAA	0.527													T|||	10	0.00199681	0.0	0.0	5008	,	,		20532	0.0		0.006	False		,,,				2504	0.0041				p.S28S		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T84C						PASS	.	T		16,4390	23.3+/-48.9	0,16,2187	255.0	222.0	233.0		84	3.7	1.0	6	dbSNP_134	233	101,8499	55.2+/-116.2	0,101,4199	no	coding-synonymous	SYNGAP1	NM_006772.2		0,117,6386	CC,CT,TT		1.1744,0.3631,0.8996		28/1344	33391270	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon2			ACCCTCTATGCAC	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.84T>C	6.37:g.33391270T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			T|0.993;C|0.007	0.007	strong		0.527	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
CTRC	11330	hgsc.bcm.edu	37	1	15767036	15767036	+	Silent	SNP	C	C	T	rs497078	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	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	
SLC22A1	6580	hgsc.bcm.edu	37	6	160575837	160575837	+	Missense_Mutation	SNP	G	G	A	rs34059508	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160575837G>A	ENST00000366963.4	+	9	1540	c.1393G>A	c.(1393-1395)Gga>Aga	p.G465R	SLC22A1_ENST00000324965.4_Intron|SLC22A1_ENST00000457470.2_Intron	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	465			G -> R (reduction of the localization to the basolateral membrane. No MPP uptake; when associated with V-408; dbSNP:rs34059508). {ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039}.		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)	p.G465*(1)	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)	CAGGAACCTCGGAGTGATGGT	0.438													G|||	33	0.00658946	0.0	0.0187	5008	,	,		22706	0.0		0.0199	False		,,,				2504	0.0				p.G465R		Atlas-SNP	.											.	SLC22A1	69	.	1	Substitution - Nonsense(1)	lung(1)	c.G1393A	GRCh37	CM035895	SLC22A1	M	rs34059508	PASS	.	G	ARG/GLY,	15,4391	22.3+/-47.3	0,15,2188	181.0	156.0	165.0		1393,	5.4	0.1	6	dbSNP_126	165	224,8376	93.5+/-155.5	3,218,4079	yes	missense,intron	SLC22A1	NM_003057.2,NM_153187.1	125,	3,233,6267	AA,AG,GG		2.6047,0.3404,1.8376	probably-damaging,	465/555,	160575837	239,12767	2203	4300	6503	SO:0001583	missense	6580	exon9			AACCTCGGAGTGA	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.1393G>A	6.37:g.160575837G>A	ENSP00000355930:p.Gly465Arg	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	157	68	0.433121	NM_003057	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	18	0.008241758241758242	0	0.0	7	0.019337016574585635	0	0.0	11	0.014511873350923483	G	17.11	3.305767	0.60305	0.003404	0.026047	ENSG00000175003	ENST00000366963	T	0.78481	-1.18	5.43	5.43	0.79202	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.125820	0.52532	D	0.000061	D	0.92328	0.7566	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.94979	0.8124	10	0.72032	D	0.01	.	16.1783	0.81884	0.0:0.0:1.0:0.0	rs34059508;rs45476695;rs57829971	465	O15245	S22A1_HUMAN	R	465	ENSP00000355930:G465R	ENSP00000355930:G465R	G	+	1	0	SLC22A1	160495827	1.000000	0.71417	0.051000	0.19133	0.641000	0.38312	4.194000	0.58393	2.523000	0.85059	0.655000	0.94253	GGA	A|0.014;C|0.000;G|0.986	0.014	strong		0.438	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
NDST3	9348	hgsc.bcm.edu	37	4	119161795	119161795	+	Silent	SNP	G	G	A	rs617430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:119161795G>A	ENST00000296499.5	+	11	2638	c.2235G>A	c.(2233-2235)ccG>ccA	p.P745P		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	745	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.P745P(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						GTTTGGTCCCGGGGTGGTATG	0.488													G|||	1244	0.248403	0.0454	0.3588	5008	,	,		15669	0.2083		0.3688	False		,,,				2504	0.362				p.P745P		Atlas-SNP	.											NDST3,NS,carcinoma,0,1	NDST3	107	1	1	Substitution - coding silent(1)	prostate(1)	c.G2235A						PASS	.	G		420,3986	205.8+/-227.6	30,360,1813	85.0	80.0	82.0		2235	-11.0	0.4	4	dbSNP_83	82	3443,5157	506.3+/-376.6	683,2077,1540	no	coding-synonymous	NDST3	NM_004784.2		713,2437,3353	AA,AG,GG		40.0349,9.5325,29.7017		745/874	119161795	3863,9143	2203	4300	6503	SO:0001819	synonymous_variant	9348	exon11			GGTCCCGGGGTGG	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2235G>A	4.37:g.119161795G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	37	CCDS3708.1																																																																																			G|0.732;A|0.268	0.268	strong		0.488	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
GALNT4	8693	hgsc.bcm.edu	37	12	89916811	89916811	+	Missense_Mutation	SNP	C	C	T	rs2230283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:89916811C>T	ENST00000529983.2	-	1	1772	c.1516G>A	c.(1516-1518)Gta>Ata	p.V506I	POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549035.1_Intron|GALNT4_ENST00000413530.1_Missense_Mutation_p.V334I|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.V503I	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	71	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	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	
MUC7	4589	hgsc.bcm.edu	37	4	71347185	71347185	+	Missense_Mutation	SNP	T	T	C	rs79807294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71347185T>C	ENST00000304887.5	+	3	914	c.724T>C	c.(724-726)Tct>Cct	p.S242P	MUC7_ENST00000413702.1_Missense_Mutation_p.S242P|MUC7_ENST00000456088.1_Missense_Mutation_p.S242P	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	242	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)			ACCCACACCTTCTGCAACTAC	0.592																																					p.S242P		Atlas-SNP	.											MUC7,right_upper_lobe,carcinoma,0,4	MUC7	91	4	0			c.T724C						scavenged	.						422.0	341.0	368.0					4																	71347185		2203	4300	6503	SO:0001583	missense	4589	exon4			ACACCTTCTGCAA	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.724T>C	4.37:g.71347185T>C	ENSP00000302021:p.Ser242Pro	Somatic	291	11	0.0378007		WXS	Illumina HiSeq	Phase_I	194	33	0.170103	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	9.595	1.127046	0.20959	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.52754	0.65;0.65;0.65	1.88	-3.76	0.04359	.	.	.	.	.	T	0.26048	0.0635	N	0.24115	0.695	0.09310	N	1	B	0.24823	0.112	B	0.17722	0.019	T	0.17837	-1.0356	8	.	.	.	0.6471	6.6904	0.23167	0.7198:0.0:0.0:0.2802	.	242	Q8TAX7	MUC7_HUMAN	P	242	ENSP00000407422:S242P;ENSP00000400585:S242P;ENSP00000302021:S242P	.	S	+	1	0	MUC7	71381774	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.151000	0.01289	-0.798000	0.04444	-0.438000	0.05819	TCT	T|0.993;C|0.007	0.007	strong		0.592	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
MAP1S	55201	hgsc.bcm.edu	37	19	17837090	17837090	+	Silent	SNP	C	C	T	rs12975100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17837090C>T	ENST00000324096.4	+	5	1048	c.897C>T	c.(895-897)ccC>ccT	p.P299P	MAP1S_ENST00000544059.2_Silent_p.P273P|MAP1S_ENST00000597681.1_Intron|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	299	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						ACAGCCTCCCCGGCCTCAACA	0.692													C|||	693	0.138379	0.0182	0.1614	5008	,	,		13392	0.0149		0.2843	False		,,,				2504	0.2618				p.P299P		Atlas-SNP	.											.	MAP1S	74	.	0			c.C897T						PASS	.	C		248,4150		10,228,1961	15.0	14.0	14.0		897	-8.5	0.2	19	dbSNP_121	14	2492,6088		396,1700,2194	no	coding-synonymous	MAP1S	NM_018174.4		406,1928,4155	TT,TC,CC		29.0443,5.6389,21.1127		299/1060	17837090	2740,10238	2199	4290	6489	SO:0001819	synonymous_variant	55201	exon5			CCTCCCCGGCCTC	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.897C>T	19.37:g.17837090C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	37	CCDS32954.1																																																																																			C|0.836;T|0.164	0.164	strong		0.692	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133963499	133963499	+	Missense_Mutation	SNP	C	C	T	rs117391524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:133963499C>T	ENST00000298622.4	+	15	2099	c.1961C>T	c.(1960-1962)gCg>gTg	p.A654V	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	654						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)		ATTGTGGTTGCGGAGCTGATG	0.617													C|||	208	0.0415335	0.003	0.085	5008	,	,		9632	0.0		0.1014	False		,,,				2504	0.044				p.A654V		Atlas-SNP	.											JAKMIP3,brain,glioma,0,1	JAKMIP3	69	1	0			c.C1961T						PASS	.		VAL/ALA	58,4306	52.3+/-87.9	1,56,2125	135.0	86.0	103.0		1961	2.9	0.4	10	dbSNP_132	103	774,7798	181.8+/-230.4	28,718,3540	yes	missense	JAKMIP3	NM_001105521.2	64	29,774,5665	TT,TC,CC		9.0294,1.3291,6.4317	benign	654/845	133963499	832,12104	2182	4286	6468	SO:0001583	missense	282973	exon15			TGGTTGCGGAGCT	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.1961C>T	10.37:g.133963499C>T	ENSP00000298622:p.Ala654Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	120	0.054945054945054944	3	0.006097560975609756	39	0.10773480662983426	0	0.0	78	0.10290237467018469	C	9.478	1.097276	0.20552	0.013291	0.090294	ENSG00000188385	ENST00000298622	T	0.22539	1.95	3.84	2.88	0.33553	.	.	.	.	.	T	0.00300	0.0009	L	0.34521	1.04	0.09310	N	1	B;B	0.33022	0.394;0.072	B;B	0.25506	0.061;0.024	T	0.11060	-1.0603	9	0.30854	T	0.27	.	12.5549	0.56248	0.167:0.833:0.0:0.0	.	91;654	Q5VZ66-2;Q5VZ66	.;JKIP3_HUMAN	V	654	ENSP00000298622:A654V	ENSP00000298622:A654V	A	+	2	0	JAKMIP3	133813489	0.013000	0.17824	0.362000	0.25862	0.324000	0.28378	2.608000	0.46308	1.697000	0.51169	0.299000	0.19835	GCG	C|0.940;T|0.060	0.060	strong		0.617	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249552	3249552	+	Missense_Mutation	SNP	C	C	T	rs4391795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	15	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	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	
OR51B5	282763	hgsc.bcm.edu	37	11	5364295	5364295	+	Missense_Mutation	SNP	C	C	T	rs12273630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364295C>T	ENST00000300773.2	-	1	514	c.460G>A	c.(460-462)Gtt>Att	p.V154I	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	154			V -> I (in dbSNP:rs12273630).		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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGGGAACAACGGATACAAAT	0.438													C|||	487	0.0972444	0.3026	0.0476	5008	,	,		19117	0.0		0.0467	False		,,,				2504	0.0072				p.V154I		Atlas-SNP	.											.	OR51B5	60	.	0			c.G460A						PASS	.	C	ILE/VAL	1218,3184	414.4+/-336.8	162,894,1145	53.0	59.0	57.0		460	-1.3	0.0	11	dbSNP_120	57	453,8141	135.1+/-192.4	13,427,3857	yes	missense	OR51B5	NM_001005567.2	29	175,1321,5002	TT,TC,CC		5.2711,27.6692,12.8578	benign	154/313	5364295	1671,11325	2201	4297	6498	SO:0001583	missense	282763	exon5			GAACAACGGATAC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.460G>A	11.37:g.5364295C>T	ENSP00000300773:p.Val154Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	134	0.27235772357723576	20	0.055248618784530384	0	0.0	34	0.044854881266490766	C	0.678	-0.799441	0.02841	0.276692	0.052711	ENSG00000242180	ENST00000300773	T	0.37411	1.2	4.76	-1.28	0.09318	GPCR, rhodopsin-like superfamily (1);	0.194438	0.24818	N	0.035344	T	0.00012	0.0000	N	0.01789	-0.72	0.80722	P	0.0	B	0.16166	0.016	B	0.15870	0.014	T	0.32402	-0.9908	9	0.02654	T	1	.	5.2403	0.15467	0.0:0.4688:0.239:0.2922	rs12273630;rs52831752;rs59964283;rs12273630	154	Q9H339	O51B5_HUMAN	I	154	ENSP00000300773:V154I	ENSP00000300773:V154I	V	-	1	0	OR51B5	5320871	0.000000	0.05858	0.002000	0.10522	0.868000	0.49771	-3.516000	0.00445	-0.111000	0.12001	0.650000	0.86243	GTT	C|0.888;T|0.112	0.112	strong		0.438	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
DNAH9	1770	hgsc.bcm.edu	37	17	11532835	11532835	+	Silent	SNP	A	A	G	rs9895535	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:11532835A>G	ENST00000262442.4	+	7	1520	c.1452A>G	c.(1450-1452)gaA>gaG	p.E484E	DNAH9_ENST00000454412.2_Silent_p.E484E	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	484	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)		AAATGCATGAAGAATTTCAAG	0.542													G|||	1967	0.392772	0.7761	0.2334	5008	,	,		15250	0.131		0.3161	False		,,,				2504	0.3364				p.E484E		Atlas-SNP	.											.	DNAH9	695	.	0			c.A1452G						PASS	.	G		3135,1271	433.5+/-343.6	1137,861,205	117.0	110.0	112.0		1452	-6.0	0.0	17	dbSNP_119	112	2607,5993	688.5+/-404.3	405,1797,2098	no	coding-synonymous	DNAH9	NM_001372.3		1542,2658,2303	GG,GA,AA		30.314,28.847,44.1489		484/4487	11532835	5742,7264	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon7			GCATGAAGAATTT	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.1452A>G	17.37:g.11532835A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			A|0.589;G|0.411	0.411	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
TECPR2	9895	hgsc.bcm.edu	37	14	102916966	102916966	+	Missense_Mutation	SNP	C	C	A	rs139247564		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:102916966C>A	ENST00000359520.7	+	15	3612	c.3386C>A	c.(3385-3387)tCt>tAt	p.S1129Y	TECPR2_ENST00000558678.1_Missense_Mutation_p.S1129Y	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1129					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GTGTTGGCTTCTGCAGCTCCC	0.498																																					p.S1129Y		Atlas-SNP	.											.	TECPR2	114	.	0			c.C3386A						PASS	.						104.0	83.0	90.0					14																	102916966		2203	4300	6503	SO:0001583	missense	9895	exon15			TGGCTTCTGCAGC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3386C>A	14.37:g.102916966C>A	ENSP00000352510:p.Ser1129Tyr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	170	72	0.423529	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493237	0.84962	.	.	ENSG00000196663	ENST00000359520	T	0.20598	2.06	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.20207	-1.0282	10	0.87932	D	0	.	19.3784	0.94521	0.0:1.0:0.0:0.0	.	312;1129;1129	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	Y	1129	ENSP00000352510:S1129Y	ENSP00000352510:S1129Y	S	+	2	0	TECPR2	101986719	1.000000	0.71417	0.172000	0.22920	0.842000	0.47809	6.757000	0.74924	2.585000	0.87301	0.655000	0.94253	TCT	C|0.999;A|0.001	0.001	weak		0.498	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
UGGT2	55757	hgsc.bcm.edu	37	13	96638636	96638636	+	Missense_Mutation	SNP	A	A	C	rs816142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:96638636A>C	ENST00000376747.3	-	9	1052	c.982T>G	c.(982-984)Tcc>Gcc	p.S328A	UGGT2_ENST00000376714.3_3'UTR|UGGT2_ENST00000397618.3_Missense_Mutation_p.S328A|UGGT2_ENST00000467305.1_5'UTR	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	328			S -> A (in dbSNP:rs816142). {ECO:0000269|PubMed:10694380, ECO:0000269|PubMed:15489334}.		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						AATTTAATGGAATCATAAACT	0.303													C|||	4215	0.841653	0.7814	0.7781	5008	,	,		15128	0.9276		0.8728	False		,,,				2504	0.8476				p.S328A		Atlas-SNP	.											.	UGGT2	127	.	0			c.T982G						PASS	.	C	ALA/SER	3553,853	330.7+/-301.6	1419,715,69	80.0	81.0	80.0		982	5.5	1.0	13	dbSNP_86	80	7521,1067	223.7+/-260.4	3279,963,52	yes	missense	UGGT2	NM_020121.3	99	4698,1678,121	CC,CA,AA		12.4243,19.36,14.7761	benign	328/1517	96638636	11074,1920	2203	4294	6497	SO:0001583	missense	55757	exon9			TAATGGAATCATA	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.982T>G	13.37:g.96638636A>C	ENSP00000365938:p.Ser328Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	1872	0.8571428571428571	384	0.7804878048780488	302	0.8342541436464088	529	0.9248251748251748	657	0.866754617414248	C	5.414	0.261525	0.10239	0.8064	0.875757	ENSG00000102595	ENST00000376747;ENST00000397618	T;T	0.12255	2.7;2.7	5.54	5.54	0.83059	.	0.223530	0.47852	N	0.000213	T	0.00012	0.0000	N	0.00226	-1.805	0.09310	P	1.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.38457	-0.9660	9	0.02654	T	1	-0.5589	14.8728	0.70471	0.1452:0.8548:0.0:0.0	rs816142;rs57901148;rs816142	328;328	E7EMU6;Q9NYU1	.;UGGG2_HUMAN	A	328	ENSP00000365938:S328A;ENSP00000380743:S328A	ENSP00000365938:S328A	S	-	1	0	UGGT2	95436637	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.920000	0.40025	1.329000	0.45376	-0.121000	0.15023	TCC	T|0.000;C|0.856;A|0.143	0.856	strong		0.303	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
SRMS	6725	hgsc.bcm.edu	37	20	62173927	62173927	+	Missense_Mutation	SNP	G	G	A	rs378483|rs386816161	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62173927G>A	ENST00000217188.1	-	4	693	c.653C>T	c.(652-654)cCg>cTg	p.P218L		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	218			P -> L (in dbSNP:rs378483).		peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.P218L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GTCCTGCCTCGGGGCCTTCTG	0.697													G|||	747	0.149161	0.438	0.0749	5008	,	,		15261	0.0238		0.0606	False		,,,				2504	0.0317				p.P218L		Atlas-SNP	.											SRMS,NS,lymphoid_neoplasm,0,1	SRMS	48	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C653T						scavenged	.	G	LEU/PRO	1335,3063		274,787,1138	32.0	34.0	33.0		653	-8.5	0.0	20	dbSNP_80	33	335,8261		8,319,3971	no	missense	SRMS	NM_080823.2	98	282,1106,5109	AA,AG,GG		3.8972,30.3547,12.8521	benign	218/489	62173927	1670,11324	2199	4298	6497	SO:0001583	missense	6725	exon4			TGCCTCGGGGCCT		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.653C>T	20.37:g.62173927G>A	ENSP00000217188:p.Pro218Leu	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	309	0.14148351648351648	220	0.44715447154471544	24	0.06629834254143646	18	0.03146853146853147	47	0.06200527704485488	G	10.88	1.475066	0.26511	0.303547	0.038972	ENSG00000125508	ENST00000217188	T	0.76578	-1.03	4.47	-8.54	0.00912	Protein kinase-like domain (1);SH2 motif (1);	0.887861	0.09553	N	0.786625	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.09377	0.004	T	0.22243	-1.0222	9	0.35671	T	0.21	.	2.2127	0.03952	0.4352:0.0925:0.2866:0.1858	rs378483;rs1757737	218	Q9H3Y6	SRMS_HUMAN	L	218	ENSP00000217188:P218L	ENSP00000217188:P218L	P	-	2	0	SRMS	61644371	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.815000	0.04481	-1.674000	0.01461	-1.036000	0.02392	CCG	G|0.845;A|0.155	0.155	strong		0.697	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
FBN3	84467	hgsc.bcm.edu	37	19	8176945	8176945	+	Missense_Mutation	SNP	T	T	C	rs4804063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8176945T>C	ENST00000600128.1	-	31	4291	c.3877A>G	c.(3877-3879)Agt>Ggt	p.S1293G	FBN3_ENST00000601739.1_Missense_Mutation_p.S1293G|FBN3_ENST00000270509.2_Missense_Mutation_p.S1293G			Q75N90	FBN3_HUMAN	fibrillin 3	1293	EGF-like 19; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		S -> G (in dbSNP:rs4804063).|S -> N (in dbSNP:rs4804063).			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						GAGGCGTGACTGTCACAGTTG	0.572													T|||	1541	0.307708	0.2814	0.2522	5008	,	,		12565	0.369		0.175	False		,,,				2504	0.456				p.S1293G		Atlas-SNP	.											.	FBN3	300	.	0			c.A3877G						PASS	.	T	GLY/SER	1200,3206	418.3+/-338.2	165,870,1168	162.0	133.0	142.0		3877	-5.6	0.0	19	dbSNP_111	142	1480,7120	280.9+/-294.7	137,1206,2957	yes	missense	FBN3	NM_032447.3	56	302,2076,4125	CC,CT,TT		17.2093,27.2356,20.6059	benign	1293/2810	8176945	2680,10326	2203	4300	6503	SO:0001583	missense	84467	exon30			CGTGACTGTCACA		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.3877A>G	19.37:g.8176945T>C	ENSP00000470498:p.Ser1293Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	45	0.375	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	563	0.25778388278388276	125	0.2540650406504065	90	0.24861878453038674	209	0.36538461538461536	139	0.18337730870712401	T	8.850	0.944307	0.18356	0.272356	0.172093	ENSG00000142449	ENST00000270509	D	0.88201	-2.35	4.34	-5.58	0.02512	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.518583	0.20895	U	0.083753	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09840	-1.0656	9	0.23302	T	0.38	.	7.9098	0.29785	0.0:0.3184:0.4344:0.2472	rs4804063;rs52819503;rs60677672;rs4804063	1293	Q75N90	FBN3_HUMAN	G	1293	ENSP00000270509:S1293G	ENSP00000270509:S1293G	S	-	1	0	FBN3	8082945	0.002000	0.14202	0.001000	0.08648	0.261000	0.26267	-0.077000	0.11394	-1.174000	0.02754	0.402000	0.26972	AGT	C|0.236;N|0.000	0.236	strong		0.572	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ANO10	55129	hgsc.bcm.edu	37	3	43602803	43602803	+	Missense_Mutation	SNP	C	C	T	rs3772165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:43602803C>T	ENST00000292246.3	-	9	1555	c.1385G>A	c.(1384-1386)cGg>cAg	p.R462Q	ANO10_ENST00000396091.3_Missense_Mutation_p.R396Q|ANO10_ENST00000350459.4_Missense_Mutation_p.R272Q|ANO10_ENST00000451430.2_Missense_Mutation_p.R351Q|ANO10_ENST00000414522.2_Missense_Mutation_p.R462Q	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	152	0	0		WXS	Illumina HiSeq	Phase_I	174	109	0.626437	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	
ZNF229	7772	hgsc.bcm.edu	37	19	44933947	44933947	+	Missense_Mutation	SNP	G	G	A	rs12151338	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44933947G>A	ENST00000588931.1	-	6	1442	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000291187.4_Missense_Mutation_p.R331C|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	337			R -> C (in dbSNP:rs12151338).		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)				GGGTGGTTACGTATGTGCGTG	0.498													G|||	1441	0.28774	0.028	0.2651	5008	,	,		19954	0.3343		0.3678	False		,,,				2504	0.5245				p.R337C		Atlas-SNP	.											ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	0			c.C1009T						PASS	.	G	CYS/ARG	295,3621		15,265,1678	66.0	64.0	65.0		1009	0.6	0.0	19	dbSNP_120	65	2916,5400		520,1876,1762	yes	missense	ZNF229	NM_014518.2	180	535,2141,3440	AA,AG,GG		35.0649,7.5332,26.2508	possibly-damaging	337/826	44933947	3211,9021	1958	4158	6116	SO:0001583	missense	7772	exon6			GGTTACGTATGTG	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.1009C>T	19.37:g.44933947G>A	ENSP00000466519:p.Arg337Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	576	0.26373626373626374	12	0.024390243902439025	97	0.26795580110497236	185	0.32342657342657344	282	0.3720316622691293	G	8.511	0.866580	0.17250	0.075332	0.350649	ENSG00000167383	ENST00000291187	.	.	.	3.16	0.592	0.17471	.	.	.	.	.	T	0.00012	0.0000	M	0.69523	2.12	0.80722	P	0.0	P	0.40970	0.734	B	0.38921	0.285	T	0.36625	-0.9740	7	0.38643	T	0.18	.	9.6208	0.39721	0.0:0.5592:0.4408:0.0	rs12151338;rs17281928;rs60383343;rs12151338	337	Q9UJW7	ZN229_HUMAN	C	337	.	ENSP00000291187:R337C	R	-	1	0	ZNF229	49625787	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-3.507000	0.00448	0.609000	0.30018	0.609000	0.83330	CGT	G|0.732;A|0.268	0.268	strong		0.498	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
H6PD	9563	hgsc.bcm.edu	37	1	9324670	9324670	+	Silent	SNP	A	A	G	rs9434743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9324670A>G	ENST00000377403.2	+	5	2420	c.2118A>G	c.(2116-2118)tcA>tcG	p.S706S	H6PD_ENST00000602477.1_Silent_p.S717S	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	706	6-phosphogluconolactonase.				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)		TCCCACAGTCACCCACTGGCC	0.662													G|||	2014	0.402157	0.5106	0.428	5008	,	,		16647	0.1538		0.4016	False		,,,				2504	0.4939				p.S706S		Atlas-SNP	.											.	H6PD	71	.	0			c.A2118G						PASS	.	G		2176,2230	582.1+/-385.5	534,1108,561	52.0	51.0	51.0		2118	-8.6	0.0	1	dbSNP_119	51	3336,5262	630.5+/-398.4	637,2062,1600	no	coding-synonymous	H6PD	NM_004285.3		1171,3170,2161	GG,GA,AA		38.7997,49.3872,42.387		706/792	9324670	5512,7492	2203	4299	6502	SO:0001819	synonymous_variant	9563	exon5			ACAGTCACCCACT	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.2118A>G	1.37:g.9324670A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			A|0.603;G|0.397	0.397	strong		0.662	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720851	135720851	+	Missense_Mutation	SNP	G	G	T	rs6779903	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:135720851G>T	ENST00000264977.3	+	2	1128	c.511G>T	c.(511-513)Gcc>Tcc	p.A171S	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	171			A -> S (in dbSNP:rs6779903).		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						CGATGGGAACGCCCCATCCTT	0.423													G|||	1731	0.345647	0.5537	0.281	5008	,	,		17100	0.1964		0.2823	False		,,,				2504	0.3292				p.A171S		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.G511T						PASS	.	G	,SER/ALA	2231,2175	591.1+/-387.5	570,1091,542	74.0	79.0	77.0		,511	0.1	0.5	3	dbSNP_116	77	2364,6236	394.2+/-344.6	313,1738,2249	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,99	883,2829,2791	TT,TG,GG		27.4884,49.3645,35.3298	,benign	,171/1151	135720851	4595,8411	2203	4300	6503	SO:0001583	missense	5523	exon2			GGGAACGCCCCAT	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.511G>T	3.37:g.135720851G>T	ENSP00000264977:p.Ala171Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	748	0.3424908424908425	278	0.5650406504065041	111	0.30662983425414364	133	0.23251748251748253	226	0.29815303430079154	G	0.001	-2.910977	0.00056	0.506355	0.274884	ENSG00000073711	ENST00000264977	T	0.05258	3.47	5.55	0.0664	0.14361	.	0.420852	0.26000	N	0.026941	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	0.22626	-1.0211	9	0.09590	T	0.72	.	8.5274	0.33313	0.1218:0.0:0.3925:0.4856	rs6779903;rs52800757;rs61128780;rs6779903	171	Q06190	P2R3A_HUMAN	S	171	ENSP00000264977:A171S	ENSP00000264977:A171S	A	+	1	0	PPP2R3A	137203541	0.567000	0.26626	0.471000	0.27229	0.086000	0.17979	1.057000	0.30492	0.060000	0.16281	-1.072000	0.02254	GCC	G|0.660;T|0.340	0.340	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
DNAH3	55567	hgsc.bcm.edu	37	16	20998720	20998720	+	Silent	SNP	G	G	A	rs111770788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:20998720G>A	ENST00000261383.3	-	47	6932	c.6933C>T	c.(6931-6933)ttC>ttT	p.F2311F	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2311					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)		GACGATCATAGAAGACCCGAT	0.428													G|||	44	0.00878594	0.0008	0.0202	5008	,	,		20953	0.0		0.0239	False		,,,				2504	0.0051				p.F2311F		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C6933T						PASS	.	G		43,4359	45.3+/-79.5	0,43,2158	112.0	108.0	109.0		6933	3.7	1.0	16	dbSNP_132	109	353,8247	117.6+/-177.1	6,341,3953	no	coding-synonymous	DNAH3	NM_017539.1		6,384,6111	AA,AG,GG		4.1047,0.9768,3.0457		2311/4117	20998720	396,12606	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon47			ATCATAGAAGACC	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.6933C>T	16.37:g.20998720G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.976;A|0.024	0.024	strong		0.428	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
MERTK	10461	hgsc.bcm.edu	37	2	112754943	112754943	+	Silent	SNP	C	C	T	rs386649211|rs3811634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:112754943C>T	ENST00000295408.4	+	10	1751	c.1494C>T	c.(1492-1494)aaC>aaT	p.N498N	MERTK_ENST00000409780.1_Silent_p.N322N|MERTK_ENST00000421804.2_Silent_p.N498N			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	498			N -> S (in dbSNP:rs35858762). {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						CGCCTGGCAACGCAGATCCTG	0.448													C|||	954	0.190495	0.1036	0.1888	5008	,	,		17965	0.1696		0.2873	False		,,,				2504	0.2311				p.N498N		Atlas-SNP	.											MERTK,colon,carcinoma,0,1	MERTK	112	1	0			c.C1494T						PASS	.	C		656,3750	275.7+/-272.7	43,570,1590	195.0	187.0	190.0		1494	1.4	0.0	2	dbSNP_107	190	2591,6009	420.1+/-353.3	389,1813,2098	no	coding-synonymous	MERTK	NM_006343.2		432,2383,3688	TT,TC,CC		30.1279,14.8888,24.9654		498/1000	112754943	3247,9759	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon10			TGGCAACGCAGAT	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.1494C>T	2.37:g.112754943C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1	384	0.17582417582417584	43	0.08739837398373984	80	0.22099447513812154	69	0.12062937062937062	192	0.2532981530343008	C	6.769	0.510703	0.12883	0.148888	0.301279	ENSG00000153208	ENST00000393237	.	.	.	5.87	1.35	0.21983	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.15809	-1.0424	4	0.72032	D	0.01	-18.0861	9.3383	0.38065	0.0:0.6864:0.0:0.3136	rs3811634;rs58464178;rs3811634	.	.	.	C	142	.	ENSP00000376929:R142C	R	+	1	0	MERTK	112471414	0.000000	0.05858	0.003000	0.11579	0.881000	0.50899	-0.329000	0.07935	0.254000	0.21573	0.655000	0.94253	CGC	C|0.776;T|0.224	0.224	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
NUP62	23636	hgsc.bcm.edu	37	19	50412417	50412417	+	Silent	SNP	G	G	A	rs999583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50412417G>A	ENST00000596217.1	-	2	2535	c.648C>T	c.(646-648)agC>agT	p.S216S	NUP62_ENST00000597029.1_Silent_p.S216S|NUP62_ENST00000422090.2_Silent_p.S216S|NUP62_ENST00000597723.1_Silent_p.S216S|NUP62_ENST00000413454.1_Silent_p.S216S|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Silent_p.S216S|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	216	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				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)		TGGGCCCAGTGCTGGTGATGG	0.652													A|||	4309	0.860423	0.9221	0.8473	5008	,	,		16527	0.9544		0.7783	False		,,,				2504	0.774				p.S216S		Atlas-SNP	.											.	NUP62	50	.	0			c.C648T						PASS	.	A	,,,,,	3985,421	206.2+/-227.9	1804,377,22	83.0	78.0	80.0		648,648,648,648,648,	2.9	0.2	19	dbSNP_86	80	6518,2082	361.0+/-332.2	2459,1600,241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	,,,,,	4263,1977,263	AA,AG,GG		24.2093,9.5552,19.245	,,,,,	216/523,216/523,216/523,216/523,216/523,	50412417	10503,2503	2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			CCCAGTGCTGGTG	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.648C>T	19.37:g.50412417G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			G|0.175;A|0.825	0.825	strong		0.652	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
REPIN1	29803	hgsc.bcm.edu	37	7	150068620	150068620	+	Missense_Mutation	SNP	C	C	T	rs17173703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150068620C>T	ENST00000425389.2	+	1	368	c.290C>T	c.(289-291)gCc>gTc	p.A97V	REPIN1_ENST00000540729.1_Missense_Mutation_p.A97V|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000397281.2_Missense_Mutation_p.A97V|REPIN1_ENST00000489432.2_Missense_Mutation_p.A154V|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000444957.1_Missense_Mutation_p.A97V|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	97			A -> V (in dbSNP:rs17173703).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TTTCGCCATGCCCCCTTCTTA	0.687													C|||	1164	0.232428	0.0227	0.1527	5008	,	,		14808	0.3988		0.2793	False		,,,				2504	0.3528				p.A154V		Atlas-SNP	.											.	REPIN1	74	.	0			c.C461T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	212,4040		8,196,1922	20.0	23.0	22.0		461,290,290,290	3.6	1.0	7	dbSNP_123	22	2231,6223		284,1663,2280	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	64,64,64,64	292,1859,4202	TT,TC,CC		26.3899,4.9859,19.2271	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	154/625,97/568,97/568,97/568	150068620	2443,10263	2126	4227	6353	SO:0001583	missense	29803	exon3			GCCATGCCCCCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.290C>T	7.37:g.150068620C>T	ENSP00000388287:p.Ala97Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	C	16.32	3.091429	0.55968	0.049859	0.263899	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.52754	0.65;2.45;2.45;2.45;2.45;2.45;2.45;2.45	5.54	3.63	0.41609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.33306	P	0.43454800000000005	P;P	0.38745	0.645;0.645	P;B	0.46975	0.533;0.405	T	0.46693	-0.9173	8	0.48119	T	0.1	-8.9286	7.3226	0.26536	0.0:0.6246:0.2862:0.0892	rs17173703	154;97	C9J3L7;Q9BWE0	.;REPI1_HUMAN	V	97;97;97;97;154;156;157;154;97	ENSP00000428562:A97V;ENSP00000445016:A97V;ENSP00000380451:A97V;ENSP00000407714:A97V;ENSP00000417291:A154V;ENSP00000419789:A156V;ENSP00000419872:A157V;ENSP00000388287:A97V	ENSP00000380451:A97V	A	+	2	0	REPIN1	149699553	0.814000	0.29104	0.999000	0.59377	0.982000	0.71751	0.878000	0.28126	1.340000	0.45581	0.462000	0.41574	GCC	C|0.765;T|0.235	0.235	strong		0.687	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
SETDB2	83852	hgsc.bcm.edu	37	13	50057097	50057097	+	Splice_Site	SNP	G	G	A	rs2057413	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50057097G>A	ENST00000317257.8	+	10	2242	c.1417G>A	c.(1417-1419)Gtg>Atg	p.V473M	SETDB2_ENST00000354234.4_Splice_Site_p.V461M|SETDB2_ENST00000258672.5_Splice_Site_p.V461M	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	473	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		V -> M (in dbSNP:rs2057413). {ECO:0000269|PubMed:12754510, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		GGAGCTTACTGTGTAAGTAAC	0.363													A|||	4110	0.820687	0.9675	0.7839	5008	,	,		16789	0.873		0.6909	False		,,,				2504	0.728				p.V473M		Atlas-SNP	.											.	SETDB2	48	.	0			c.G1417A						PASS	.	A	MET/VAL,MET/VAL	4109,297	160.7+/-193.0	1920,269,14	38.0	39.0	39.0		1381,1417	-0.8	0.0	13	dbSNP_94	39	6035,2565	414.1+/-351.3	2141,1753,406	yes	missense-near-splice,missense-near-splice	SETDB2	NM_001160308.1,NM_031915.2	21,21	4061,2022,420	AA,AG,GG		29.8256,6.7408,22.0052	benign,benign	461/708,473/720	50057097	10144,2862	2203	4300	6503	SO:0001630	splice_region_variant	83852	exon10			CTTACTGTGTAAG	AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"""Chromatin-modifying enzymes / K-methyltransferases"""	20263	protein-coding gene	gene with protein product		607865	"""chromosome 13 open reading frame 4"""	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.1418+1G>A	13.37:g.50057097G>A		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_031915	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Missense_Mutation	SNP	ENST00000317257.8	37	CCDS9417.1	1785	0.8173076923076923	469	0.9532520325203252	288	0.7955801104972375	496	0.8671328671328671	532	0.7018469656992085	A	2.655	-0.281056	0.05642	0.932592	0.701744	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	D;D;T	0.86769	-2.17;-2.15;1.13	5.1	-0.814	0.10846	SET domain (3);	1.077320	0.06935	N	0.811684	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.09377	0.002;0.003;0.004;0.001	T	0.40251	-0.9573	9	0.45353	T	0.12	.	5.8109	0.18465	0.4901:0.2622:0.2477:0.0	rs2057413;rs52807581;rs60193538;rs2057413	473;461;473;191	Q96T68-3;Q96T68-2;Q96T68;Q59FW0	.;.;SETB2_HUMAN;.	M	461;473;461	ENSP00000346175:V461M;ENSP00000326477:V473M;ENSP00000258672:V461M	ENSP00000258672:V461M	V	+	1	0	SETDB2	48955098	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.045000	0.12003	-0.236000	0.09753	-0.254000	0.11334	GTG	G|0.195;A|0.805	0.805	strong		0.363	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915	Missense_Mutation
TEX33	339669	hgsc.bcm.edu	37	22	37387257	37387257	+	Missense_Mutation	SNP	T	T	C	rs9610624	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37387257T>C	ENST00000405091.2	-	7	1057	c.806A>G	c.(805-807)tAt>tGt	p.Y269C	TEX33_ENST00000381821.1_Missense_Mutation_p.Y269C|TEX33_ENST00000402860.3_Missense_Mutation_p.Y184C			O43247	TEX33_HUMAN	testis expressed 33	269																	GTTTTCTCCATATTTCTCTTC	0.438													T|||	585	0.116813	0.1369	0.1801	5008	,	,		21699	0.0813		0.0885	False		,,,				2504	0.1104				p.Y269C		Atlas-SNP	.											.	TEX33	25	.	0			c.A806G						PASS	.	T	CYS/TYR,CYS/TYR	661,3745	281.6+/-276.1	52,557,1594	181.0	174.0	176.0		806,551	0.9	0.1	22	dbSNP_119	176	671,7929	168.4+/-220.0	28,615,3657	yes	missense,missense	C22orf33	NM_001163857.1,NM_178552.3	194,194	80,1172,5251	CC,CT,TT		7.8023,15.0023,10.2414	probably-damaging,probably-damaging	269/281,184/196	37387257	1332,11674	2203	4300	6503	SO:0001583	missense	339669	exon6			TCTCCATATTTCT	BC042635	CCDS13937.1, CCDS54524.1	22q12.3	2013-10-11	2012-02-16	2012-02-16	ENSG00000185264	ENSG00000185264			28568	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 33"""	C22orf33		22332119	Standard	NM_178552		Approved	MGC35206, EAN57	uc003aqf.3	O43247	OTTHUMG00000150531	ENST00000405091.2:c.806A>G	22.37:g.37387257T>C	ENSP00000386118:p.Tyr269Cys	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	228	122	0.535088	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Missense_Mutation	SNP	ENST00000405091.2	37	CCDS54524.1	229|229	0.10485347985347986|0.10485347985347986	68|68	0.13821138211382114|0.13821138211382114	56|56	0.15469613259668508|0.15469613259668508	39|39	0.06818181818181818|0.06818181818181818	66|66	0.0870712401055409|0.0870712401055409	T|T	10.31|10.31	1.315712|1.315712	0.23908|0.23908	0.150023|0.150023	0.078023|0.078023	ENSG00000185264|ENSG00000185264	ENST00000442538|ENST00000402860;ENST00000405091;ENST00000381821	.|.	.|.	.|.	4.43|4.43	0.878|0.878	0.19150|0.19150	.|.	.|1.510860	.|0.04364	.|N	.|0.357914	T|T	0.00210|0.00210	0.0006|0.0006	L|L	0.27053|0.27053	0.805|0.805	0.49798|0.49798	P|P	1.7800000000001148E-4|1.7800000000001148E-4	.|D	.|0.61697	.|0.99	.|P	.|0.50192	.|0.634	T|T	0.08371|0.08371	-1.0725|-1.0725	4|8	.|0.59425	.|D	.|0.04	2.9586|2.9586	8.6414|8.6414	0.33978|0.33978	0.7144:0.0:0.0:0.2856|0.7144:0.0:0.0:0.2856	rs9610624;rs52812150;rs58780254;rs9610624|rs9610624;rs52812150;rs58780254;rs9610624	.|269	.|O43247	.|EAN57_HUMAN	M|C	127|184;269;269	.|.	.|ENSP00000371243:Y269C	I|Y	-|-	3|2	3|0	C22orf33|C22orf33	35717203|35717203	0.022000|0.022000	0.18835|0.18835	0.062000|0.062000	0.19696|0.19696	0.175000|0.175000	0.22909|0.22909	0.127000|0.127000	0.15790|0.15790	-0.141000|-0.141000	0.11374|0.11374	0.460000|0.460000	0.39030|0.39030	ATA|TAT	T|0.899;C|0.101	0.101	strong		0.438	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	
PCDH12	51294	hgsc.bcm.edu	37	5	141334921	141334921	+	Silent	SNP	C	C	T	rs2434322	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141334921C>T	ENST00000231484.3	-	1	3706	c.2496G>A	c.(2494-2496)caG>caA	p.Q832Q	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	832					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGTGCTCCCTGGTTGCCTT	0.622													C|||	614	0.122604	0.0166	0.072	5008	,	,		19046	0.2688		0.1173	False		,,,				2504	0.1564				p.Q832Q		Atlas-SNP	.											.	PCDH12	133	.	0			c.G2496A						PASS	.	C		193,4213	122.5+/-159.9	7,179,2017	70.0	66.0	67.0		2496	4.2	1.0	5	dbSNP_100	67	969,7631	211.4+/-252.0	65,839,3396	yes	coding-synonymous	PCDH12	NM_016580.2		72,1018,5413	TT,TC,CC		11.2674,4.3804,8.9343		832/1185	141334921	1162,11844	2203	4300	6503	SO:0001819	synonymous_variant	51294	exon1			TGCTCCCTGGTTG	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2496G>A	5.37:g.141334921C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																			C|0.889;T|0.111	0.111	strong		0.622	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
LRP1	4035	hgsc.bcm.edu	37	12	57592067	57592067	+	Silent	SNP	G	G	A	rs143423493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57592067G>A	ENST00000243077.3	+	59	9877	c.9411G>A	c.(9409-9411)acG>acA	p.T3137T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3137					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTATCGGACGGTGCTGGTCA	0.637													G|||	11	0.00219649	0.0008	0.0014	5008	,	,		21534	0.0		0.006	False		,,,				2504	0.0031				p.T3137T		Atlas-SNP	.											LRP1,colon,carcinoma,+2,1	LRP1	428	1	0			c.G9411A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	78.0	79.0	78.0		9411	-6.1	0.7	12	dbSNP_134	78	36,8564	25.1+/-72.6	0,36,4264	no	coding-synonymous	LRP1	NM_002332.2		0,37,6466	AA,AG,GG		0.4186,0.0227,0.2845		3137/4545	57592067	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon59			TCGGACGGTGCTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.9411G>A	12.37:g.57592067G>A		Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			G|0.996;A|0.004	0.004	strong		0.637	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
SSTR3	6753	hgsc.bcm.edu	37	22	37603051	37603051	+	Silent	SNP	C	C	T	rs229569	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	34	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	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		
PARP4	143	hgsc.bcm.edu	37	13	25016092	25016092	+	Silent	SNP	C	C	T	rs55888616	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25016092C>T	ENST00000381989.3	-	30	3663	c.3558G>A	c.(3556-3558)tcG>tcA	p.S1186S		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1186					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)		CAGGAAAAGGCGACTCATTCT	0.408													c|||	1926	0.384585	0.4834	0.3473	5008	,	,		24558	0.3601		0.4115	False		,,,				2504	0.2751				p.S1186S		Atlas-SNP	.											.	PARP4	142	.	0			c.G3558A						PASS	.						40.0	43.0	42.0					13																	25016092		2203	4299	6502	SO:0001819	synonymous_variant	143	exon30			AAAAGGCGACTCA	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.3558G>A	13.37:g.25016092C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	29	27	0.931035	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.673;T|0.327	0.327	strong		0.408	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
ACOT11	26027	hgsc.bcm.edu	37	1	55060254	55060254	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55060254G>A	ENST00000371316.3	+	6	579	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Missense_Mutation_p.R166Q	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	166					fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						ATCACGCCGCGGACAGAAGAG	0.627																																					p.R166Q	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											ACOT11_ENST00000371316,bladder,carcinoma,+1,2	ACOT11	105	2	0			c.G497A						scavenged	.						45.0	42.0	43.0					1																	55060254		2203	4300	6503	SO:0001583	missense	26027	exon6			CGCCGCGGACAGA	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	18156	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 14"""	606803	"""thioesterase, adipose associated"""	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.497G>A	1.37:g.55060254G>A	ENSP00000360366:p.Arg166Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	157	3	0.0191083	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	37	CCDS592.1	.	.	.	.	.	.	.	.	.	.	G	7.785	0.710417	0.15239	.	.	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.40225	1.04;1.04	4.93	-2.29	0.06805	.	0.802457	0.11900	N	0.518734	T	0.12390	0.0301	N	0.02181	-0.65	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.06405	0.002;0.002	T	0.30504	-0.9976	10	0.12430	T	0.62	-19.0339	4.4492	0.11612	0.3963:0.0:0.278:0.3257	.	166;166	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	Q	166	ENSP00000340260:R166Q;ENSP00000360366:R166Q	ENSP00000340260:R166Q	R	+	2	0	ACOT11	54832842	0.000000	0.05858	0.019000	0.16419	0.610000	0.37248	-0.093000	0.11111	-0.276000	0.09206	0.561000	0.74099	CGG	.	.	none		0.627	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
C20orf194	25943	hgsc.bcm.edu	37	20	3285126	3285126	+	Silent	SNP	A	A	T	rs2254916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3285126A>T	ENST00000252032.9	-	21	1810	c.1743T>A	c.(1741-1743)atT>atA	p.I581I	C20orf194_ENST00000453730.2_Silent_p.I319I|C20orf194_ENST00000498079.1_5'UTR	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	581										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GATCCTTGGAAATGATGATAC	0.438													a|||	1279	0.255391	0.1823	0.3184	5008	,	,		21848	0.3492		0.2505	False		,,,				2504	0.2178				p.I581I		Atlas-SNP	.											.	C20orf194	83	.	0			c.T1743A						PASS	.			651,3161		49,553,1304	117.0	108.0	111.0		1743	2.0	1.0	20	dbSNP_100	111	2196,6052		278,1640,2206	no	coding-synonymous	C20orf194	NM_001009984.1		327,2193,3510	TT,TA,AA		26.6246,17.0776,23.607		581/1178	3285126	2847,9213	1906	4124	6030	SO:0001819	synonymous_variant	25943	exon21			CTTGGAAATGATG	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.1743T>A	20.37:g.3285126A>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Silent	SNP	ENST00000252032.9	37	CCDS42851.1																																																																																			A|0.732;T|0.268	0.268	strong		0.438	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
CNR1	1268	hgsc.bcm.edu	37	6	88854166	88854166	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88854166C>T	ENST00000537554.1	-	2	4390	c.828G>A	c.(826-828)ctG>ctA	p.L276L	CNR1_ENST00000549890.1_Silent_p.L276L|CNR1_ENST00000549716.1_Silent_p.L215L|CNR1_ENST00000369501.2_Silent_p.L276L|CNR1_ENST00000535130.1_Silent_p.L276L|CNR1_ENST00000468898.1_Silent_p.L243L|CNR1_ENST00000369499.2_Silent_p.L276L|CNR1_ENST00000428600.2_Silent_p.L276L|CNR1_ENST00000362094.5_3'UTR	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	276					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TCCAGAACATCAGGTAGGTTT	0.512																																					p.L276L		Atlas-SNP	.											.	CNR1	91	.	0			c.G828A						PASS	.						83.0	72.0	76.0					6																	88854166		2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			GAACATCAGGTAG	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"""GPCR / Class A : Cannabinoid receptors"""	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.828G>A	6.37:g.88854166C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																			.	.	none		0.512	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2		
ADSSL1	122622	hgsc.bcm.edu	37	14	105211221	105211221	+	Silent	SNP	C	C	T	rs12432802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105211221C>T	ENST00000330877.2	+	11	1231	c.1146C>T	c.(1144-1146)aaC>aaT	p.N382N	ADSSL1_ENST00000556623.1_5'Flank|ADSSL1_ENST00000554657.1_3'UTR|ADSSL1_ENST00000555674.1_5'Flank|ADSSL1_ENST00000332972.5_Silent_p.N425N	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	65	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	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		
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Silent_p.K393K|WDR41_ENST00000414719.2_Silent_p.K194K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118.0	121.0	120.0		1344	-0.2	1.0	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1344A>G	5.37:g.76728996T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	201	101	0.502488	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
RFX5	5993	hgsc.bcm.edu	37	1	151315287	151315287	+	Missense_Mutation	SNP	G	G	C	rs2233854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000478564.1_5'Flank|RFX5_ENST00000452671.2_Missense_Mutation_p.P409R|RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452513.2_Missense_Mutation_p.P369R	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	87	0	0		WXS	Illumina HiSeq	Phase_I	115	71	0.617391	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	
OR10X1	128367	hgsc.bcm.edu	37	1	158549511	158549511	+	Missense_Mutation	SNP	A	A	G	rs863363	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158549511A>G	ENST00000368150.1	-	1	178	c.179T>C	c.(178-180)aTc>aCc	p.I60T		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	60			I -> T (in dbSNP:rs863363).			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(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					ACCCATGATGATCAGATTACC	0.458													G|||	2595	0.518171	0.6324	0.4164	5008	,	,		20990	0.5853		0.4732	False		,,,				2504	0.4131				p.I60T		Atlas-SNP	.											.	OR10X1	96	.	0			c.T179C						PASS	.	G	THR/ILE	2726,1680	510.6+/-367.6	824,1078,301	127.0	123.0	124.0		179	3.2	0.3	1	dbSNP_86	124	3829,4771	612.1+/-395.9	876,2077,1347	yes	missense	OR10X1	NM_001004477.1	89	1700,3155,1648	GG,GA,AA		44.5233,38.1298,49.6002	benign	60/327	158549511	6555,6451	2203	4300	6503	SO:0001583	missense	128367	exon1			ATGATGATCAGAT	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.179T>C	1.37:g.158549511A>G	ENSP00000357132:p.Ile60Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	134	45	0.335821	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	1194	0.5467032967032966	318	0.6463414634146342	151	0.4171270718232044	355	0.6206293706293706	370	0.48812664907651715	G	0.010	-1.774832	0.00640	0.618702	0.445233	ENSG00000186400	ENST00000368150	T	0.01139	5.28	5.13	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	1.012140	0.07936	N	0.978378	T	0.00241	0.0007	N	0.12831	0.26	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	9	0.10377	T	0.69	.	4.2448	0.10667	0.3305:0.1617:0.5077:0.0	rs863363;rs17684795;rs52797051;rs59753391;rs863363	60	Q8NGY0	O10X1_HUMAN	T	60	ENSP00000357132:I60T	ENSP00000357132:I60T	I	-	2	0	OR10X1	156816135	0.000000	0.05858	0.254000	0.24359	0.204000	0.24138	-0.149000	0.10204	0.296000	0.22592	-0.128000	0.14901	ATC	A|0.470;G|0.529	0.529	strong		0.458	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
FRY	10129	hgsc.bcm.edu	37	13	32776603	32776603	+	Silent	SNP	T	T	C	rs2428249	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	95	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	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	
SGOL2	151246	hgsc.bcm.edu	37	2	201437214	201437214	+	Silent	SNP	A	A	G	rs17532679	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:201437214A>G	ENST00000357799.4	+	7	2243	c.2145A>G	c.(2143-2145)aaA>aaG	p.K715K		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)	715					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)		p.K715K(1)		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						TTAGGCAGAAAGTAAATCGGA	0.338													A|||	620	0.123802	0.0711	0.1138	5008	,	,		18421	0.0794		0.2207	False		,,,				2504	0.1483				p.K715K		Atlas-SNP	.											SGOL2,NS,carcinoma,0,1	SGOL2	126	1	1	Substitution - coding silent(1)	stomach(1)	c.A2145G						PASS	.	A	,,	353,3271		16,321,1475	58.0	52.0	54.0		2145,2145,2145	-0.0	0.1	2	dbSNP_123	54	1629,6511		156,1317,2597	no	coding-synonymous,coding-synonymous,coding-synonymous	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	,,	172,1638,4072	GG,GA,AA		20.0123,9.7406,16.848	,,	715/1261,715/1262,715/1266	201437214	1982,9782	1812	4070	5882	SO:0001819	synonymous_variant	151246	exon7			GCAGAAAGTAAAT	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.2145A>G	2.37:g.201437214A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																			A|0.865;G|0.135	0.135	strong		0.338	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11420773C>T	ENST00000279573.7	-	3	545	c.410G>A	c.(409-411)cGt>cAt	p.R137H	PRB3_ENST00000538488.1_Intron|PRB3_ENST00000381842.3_Missense_Mutation_p.R137H|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	137	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			R -> H (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCCGGACGAGGCGGGGG	0.642																																					p.R137H		Atlas-SNP	.											PRB3,NS,carcinoma,0,2	PRB3	84	2	0			c.G410A						scavenged	.						26.0	28.0	27.0					12																	11420773		1477	3379	4856	SO:0001583	missense	5544	exon3			CCCGGACGAGGCG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.410G>A	12.37:g.11420773C>T	ENSP00000279573:p.Arg137His	Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	37	5	0.135135	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.697568	0.00725	.	.	ENSG00000197870	ENST00000381842	T	0.04917	3.53	0.707	-1.41	0.08941	.	21.670500	0.01603	N	0.022149	T	0.05547	0.0146	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38650	-0.9651	9	0.41790	T	0.15	.	4.061	0.09839	0.0:0.1851:0.2048:0.6101	.	137	Q04118	PRB3_HUMAN	H	137	ENSP00000371264:R137H	ENSP00000279573:R137H	R	-	2	0	PRB3	11312040	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.782000	0.04643	-2.300000	0.00658	-1.404000	0.01136	CGT	C|0.998;T|0.002	0.002	weak		0.642	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
WDR81	124997	hgsc.bcm.edu	37	17	1636945	1636945	+	Silent	SNP	C	C	T	rs146469235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1636945C>T	ENST00000409644.1	+	7	4614	c.4614C>T	c.(4612-4614)acC>acT	p.T1538T	WDR81_ENST00000437219.2_Silent_p.T335T|WDR81_ENST00000446363.1_Silent_p.T177T|WDR81_ENST00000309182.5_Silent_p.T487T|WDR81_ENST00000419248.1_Silent_p.T311T|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000545662.1_Silent_p.T169T	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1538					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)		TGCCCGGCACCGGGCCCGAGT	0.682													C|||	70	0.0139776	0.0015	0.0259	5008	,	,		15736	0.001		0.0338	False		,,,				2504	0.0153				p.T1538T		Atlas-SNP	.											.	WDR81	180	.	0			c.C4614T						PASS	.	C	,,,	18,4386		1,16,2185	28.0	33.0	31.0		1005,4614,933,1461	-3.9	0.0	17	dbSNP_134	31	255,8327		7,241,4043	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	8,257,6228	TT,TC,CC		2.9713,0.4087,2.1023	,,,	335/739,1538/1942,311/715,487/891	1636945	273,12713	2202	4291	6493	SO:0001819	synonymous_variant	124997	exon7			CGGCACCGGGCCC	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.4614C>T	17.37:g.1636945C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.981;T|0.019	0.019	strong		0.682	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
VWA3A	146177	hgsc.bcm.edu	37	16	22155629	22155629	+	Missense_Mutation	SNP	A	A	G	rs9937453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:22155629A>G	ENST00000389398.5	+	26	2750	c.2654A>G	c.(2653-2655)aAc>aGc	p.N885S	VWA3A_ENST00000563755.1_5'Flank|VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	885				N -> S (in Ref. 5; AAH38400). {ECO:0000305}.		extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		ATGGGTCCCAACTGCACTCAT	0.433													A|||	1862	0.371805	0.5318	0.1542	5008	,	,		19171	0.5982		0.16	False		,,,				2504	0.2945				p.N885S		Atlas-SNP	.											VWA3A_ENST00000389398,NS,carcinoma,-1,2	VWA3A	115	2	0			c.A2654G						PASS	.	A	SER/ASN	1748,2264		396,956,654	75.0	77.0	76.0		2654	-1.4	0.7	16	dbSNP_119	76	1431,6933		135,1161,2886	yes	missense	VWA3A	NM_173615.3	46	531,2117,3540	GG,GA,AA		17.109,43.5693,25.6868	benign	885/1185	22155629	3179,9197	2006	4182	6188	SO:0001583	missense	146177	exon26			GTCCCAACTGCAC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2654A>G	16.37:g.22155629A>G	ENSP00000374049:p.Asn885Ser	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	229	105	0.458515	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	788	0.3608058608058608	279	0.5670731707317073	53	0.1464088397790055	332	0.5804195804195804	124	0.16358839050131926	A	9.133	1.011929	0.19277	0.435693	0.17109	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.11930	2.73	5.05	-1.42	0.08913	.	1.091720	0.06781	N	0.785336	T	0.00012	0.0000	L	0.28192	0.835	0.09310	P	0.999999418883	B	0.13145	0.007	B	0.04013	0.001	T	0.43605	-0.9381	9	0.11485	T	0.65	.	9.7499	0.40470	0.539:0.0:0.461:0.0	rs9937453;rs52819722;rs61173829;rs9937453	885	A6NCI4	VWA3A_HUMAN	S	885;508	ENSP00000374049:N885S	ENSP00000299840:N508S	N	+	2	0	VWA3A	22063130	0.027000	0.19231	0.684000	0.30055	0.693000	0.40251	0.517000	0.22832	-0.488000	0.06726	-0.376000	0.06991	AAC	A|0.627;G|0.373	0.373	strong		0.433	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
FAT1	2195	hgsc.bcm.edu	37	4	187542316	187542316	+	Silent	SNP	T	T	C	rs2099854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187542316T>C	ENST00000441802.2	-	10	5633	c.5424A>G	c.(5422-5424)gtA>gtG	p.V1808V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1808	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CAATGTGATATACAAGCAAAG	0.403										HNSCC(5;0.00058)			T|||	343	0.0684904	0.003	0.1499	5008	,	,		22440	0.1806		0.0338	False		,,,				2504	0.0194				p.V1808V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A5424G						PASS	.	T		40,3880		0,40,1920	82.0	80.0	81.0		5424	-5.7	0.9	4	dbSNP_96	81	255,8057		4,247,3905	no	coding-synonymous	FAT1	NM_005245.3		4,287,5825	CC,CT,TT		3.0679,1.0204,2.4117		1808/4589	187542316	295,11937	1960	4156	6116	SO:0001819	synonymous_variant	2195	exon10			GTGATATACAAGC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5424A>G	4.37:g.187542316T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.923;C|0.077	0.077	strong		0.403	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
COL6A3	1293	hgsc.bcm.edu	37	2	238253065	238253065	+	Silent	SNP	C	C	T	rs2291795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238253065C>T	ENST00000295550.4	-	36	8048	c.7596G>A	c.(7594-7596)aaG>aaA	p.K2532K	COL6A3_ENST00000347401.3_Silent_p.K2331K|COL6A3_ENST00000409809.1_Silent_p.K2326K|COL6A3_ENST00000472056.1_Silent_p.K1925K|COL6A3_ENST00000353578.4_Silent_p.K2326K|COL6A3_ENST00000346358.4_Silent_p.K2332K	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2532	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)		CATCTGAGAGCTTGAGCACAG	0.537													C|||	775	0.154752	0.1747	0.1182	5008	,	,		21761	0.1865		0.0944	False		,,,				2504	0.183				p.K2532K		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7596A						PASS	.	C	,,	716,3690	296.4+/-284.2	62,592,1549	162.0	159.0	160.0		7596,5775,6978	4.0	1.0	2	dbSNP_100	160	989,7611	213.8+/-253.6	61,867,3372	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	123,1459,4921	TT,TC,CC		11.5,16.2506,13.1093	,,	2532/3178,1925/2571,2326/2972	238253065	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			TGAGAGCTTGAGC	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.7596G>A	2.37:g.238253065C>T		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.865;T|0.135	0.135	strong		0.537	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145015877	145015877	+	Missense_Mutation	SNP	G	G	T	rs77741369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145015877G>T	ENST00000530740.1	-	3	462	c.424C>A	c.(424-426)Ctt>Att	p.L142I	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.L142I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.L71I|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.L71I|RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.L71I|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.L142I			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	5					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)		AAGTCTCGAAGAGCCTGGGTC	0.438			T	PDGFRB	MPD																																p.L142I		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,0,2	PDE4DIP	817	2	0			c.C424A						scavenged	.	G	ILE/LEU,ILE/LEU	351,4055		0,351,1852	501.0	587.0	558.0		211,424	5.3	1.0	1	dbSNP_131	558	2135,6465		0,2135,2165	yes	missense,missense	PDE4DIP	NM_001198832.1,NM_022359.5	5,5	0,2486,4017	TT,TG,GG		24.8256,7.9664,19.1143	,	71/2241,142/311	145015877	2486,10520	2203	4300	6503	SO:0001583	missense	9659	exon3			CTCGAAGAGCCTG	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	ENST00000530740.1:c.424C>A	1.37:g.145015877G>T	ENSP00000435654:p.Leu142Ile	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	222	35	0.157658	NM_022359	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	ENST00000530740.1	37		419	0.19184981684981686	18	0.036585365853658534	88	0.2430939226519337	49	0.08566433566433566	264	0.3482849604221636	G	19.22	3.784896	0.70222	0.079664	0.248256	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	5.26	5.26	0.73747	.	.	.	.	.	T	0.42017	0.1184	M	0.74467	2.265	0.80722	D	1	D;B;P	0.53619	0.961;0.445;0.931	P;B;P	0.53224	0.721;0.282;0.699	T	0.26573	-1.0099	9	0.42905	T	0.14	.	14.2417	0.65961	0.0:0.0:1.0:0.0	.	71;142;71	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	I	71;142;142;71;142;72;71;71	ENSP00000327209:L71I;ENSP00000435654:L142I;ENSP00000358366:L142I;ENSP00000358354:L142I;ENSP00000435616:L72I	ENSP00000327209:L71I	L	-	1	0	PDE4DIP	143727234	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.501000	0.60393	2.727000	0.93392	0.655000	0.94253	CTT	G|0.821;T|0.179	0.179	strong		0.438	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
ZNF589	51385	hgsc.bcm.edu	37	3	48309828	48309828	+	Missense_Mutation	SNP	C	C	G	rs11718329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48309828C>G	ENST00000354698.3	+	4	719	c.647C>G	c.(646-648)aCg>aGg	p.T216R	ZNF589_ENST00000412564.1_Intron|ZNF589_ENST00000427617.2_Intron|ZNF589_ENST00000440261.2_Intron	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	216			T -> R (in dbSNP:rs11718329). {ECO:0000269|PubMed:10029171, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGAGCAGTCACGTTTGGGGAG	0.473													G|||	1281	0.255791	0.3336	0.2219	5008	,	,		20430	0.124		0.2913	False		,,,				2504	0.274				p.T216R	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											.	ZNF589	20	.	0			c.C647G						PASS	.	G	ARG/THR	1304,2808		228,848,980	65.0	71.0	69.0		647	-2.7	0.0	3	dbSNP_120	69	2615,5801		422,1771,2015	yes	missense	ZNF589	NM_016089.2	71	650,2619,2995	GG,GC,CC		31.0718,31.7121,31.2819	probably-damaging	216/365	48309828	3919,8609	2056	4208	6264	SO:0001583	missense	51385	exon4			CAGTCACGTTTGG	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"""Zinc fingers, C2H2-type"", ""-"""	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	ENST00000354698.3:c.647C>G	3.37:g.48309828C>G	ENSP00000346729:p.Thr216Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	110	68	0.618182	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	37	CCDS43085.1	508	0.2326007326007326	140	0.2845528455284553	88	0.2430939226519337	64	0.11188811188811189	216	0.2849604221635884	G	0.012	-1.656907	0.00779	0.317121	0.310718	ENSG00000164048	ENST00000354698;ENST00000296437	T	0.06294	3.32	1.35	-2.69	0.06022	.	.	.	.	.	T	0.00012	0.0000	N	0.17764	0.52	0.53005	P	3.500000000000725E-5	B;B	0.30104	0.268;0.0	B;B	0.21360	0.034;0.0	T	0.45425	-0.9262	8	0.19590	T	0.45	.	0.105	0.00051	0.2658:0.1676:0.2423:0.3244	rs11718329;rs17845084;rs17857868;rs52834072;rs11718329	213;216	Q86UQ0-2;Q86UQ0	.;ZN589_HUMAN	R	216;213	ENSP00000346729:T216R	ENSP00000296437:T213R	T	+	2	0	ZNF589	48284832	0.001000	0.12720	0.000000	0.03702	0.363000	0.29612	-0.710000	0.05024	-2.576000	0.00465	-1.508000	0.00951	ACG	C|0.735;G|0.265	0.265	strong		0.473	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089	
GSTA2	2939	hgsc.bcm.edu	37	6	52615415	52615415	+	Missense_Mutation	SNP	T	T	G	rs6577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:52615415T>G	ENST00000493422.1	-	7	784	c.629A>C	c.(628-630)gAg>gCg	p.E210A		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	210			E -> A (in dbSNP:rs6577). {ECO:0000269|PubMed:11668220, ECO:0000269|PubMed:1329668, ECO:0000269|PubMed:1497629}.		epithelial cell differentiation (GO:0030855)|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)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)	p.E210A(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	TAAAGATTTCTCATCCATGGG	0.423													.|||	1326	0.264776	0.6967	0.0951	5008	,	,		18235	0.1825		0.0616	False		,,,				2504	0.0951				p.E210A		Atlas-SNP	.											GSTA2,NS,carcinoma,0,1	GSTA2	33	1	1	Substitution - Missense(1)	stomach(1)	c.A629C						PASS	.	G	ALA/GLU	2648,1758		805,1038,360	125.0	127.0	126.0		629	-0.1	0.0	6	dbSNP_52	126	491,8109		24,443,3833	no	missense	GSTA2	NM_000846.4	107	829,1481,4193	GG,GT,TT		5.7093,39.9001,24.135	benign	210/223	52615415	3139,9867	2203	4300	6503	SO:0001583	missense	2939	exon7			GATTTCTCATCCA	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4627	protein-coding gene	gene with protein product		138360	"""glutathione S-transferase A2"""	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.629A>C	6.37:g.52615415T>G	ENSP00000420168:p.Glu210Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	522	0.23901098901098902	343	0.6971544715447154	34	0.09392265193370165	96	0.16783216783216784	49	0.06464379947229551	N	2.795	-0.250392	0.05867	0.600999	0.057093	ENSG00000244067	ENST00000493422	T	0.11821	2.74	2.32	-0.126	0.13515	Glutathione S-transferase, C-terminal-like (1);	0.422288	0.21606	N	0.071873	T	0.02083	0.0065	L	0.28344	0.845	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47947	-0.9077	9	0.18710	T	0.47	.	5.1576	0.15044	0.0:0.133:0.1938:0.6733	rs6577;rs769234;rs1051972;rs1052135;rs2257319;rs3175125;rs52833466;rs57487028;rs6577	210	P09210	GSTA2_HUMAN	A	210	ENSP00000420168:E210A	ENSP00000420168:E210A	E	-	2	0	GSTA2	52723374	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-0.890000	0.04140	-0.196000	0.10366	-0.703000	0.03666	GAG	T|0.753;G|0.247	0.247	strong		0.423	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846	
TEAD1	7003	hgsc.bcm.edu	37	11	12903443	12903443	+	Splice_Site	SNP	C	C	T	rs2304733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:12903443C>T	ENST00000526600.1	+	3	448	c.225C>T	c.(223-225)gaC>gaT	p.D75D	TEAD1_ENST00000527636.1_Splice_Site_p.D171D|TEAD1_ENST00000361905.4_Splice_Site_p.D156D|TEAD1_ENST00000361985.2_Splice_Site_p.D171D|TEAD1_ENST00000334310.6_Splice_Site_p.D160D|TEAD1_ENST00000527575.1_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	120	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	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
SVIL	6840	hgsc.bcm.edu	37	10	29840164	29840164	+	Silent	SNP	A	A	G	rs3740002	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29840164A>G	ENST00000355867.4	-	6	941	c.189T>C	c.(187-189)tcT>tcC	p.S63S	SVIL_ENST00000375398.2_Silent_p.S63S|SVIL_ENST00000375400.3_Silent_p.S63S	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	63	Interaction with MYLK. {ECO:0000250}.				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)				GAGAAGAATCAGAAGTTTCCT	0.453													A|||	1277	0.254992	0.2337	0.245	5008	,	,		21044	0.3462		0.2376	False		,,,				2504	0.2147				p.S63S		Atlas-SNP	.											.	SVIL	226	.	0			c.T189C						PASS	.	A	,	1160,3246	398.8+/-331.0	153,854,1196	55.0	46.0	49.0		189,189	-4.9	0.4	10	dbSNP_107	49	2233,6367	362.0+/-332.6	287,1659,2354	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	440,2513,3550	GG,GA,AA		25.9651,26.3277,26.088	,	63/1789,63/2215	29840164	3393,9613	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			AGAATCAGAAGTT	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.189T>C	10.37:g.29840164A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.744;G|0.256	0.256	strong		0.453	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
MAML2	84441	hgsc.bcm.edu	37	11	95825404	95825404	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:95825404C>T	ENST00000524717.1	-	2	3075	c.1791G>A	c.(1789-1791)caG>caA	p.Q597Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	597					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)				gctgctgctgctgctgctgct	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q597Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,1	MAML2	94	1	0			c.G1791A						scavenged	.						25.0	32.0	29.0					11																	95825404		2096	4109	6205	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	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.1791G>A	11.37:g.95825404C>T		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	87	9	0.103448	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	none		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
OR1A1	8383	hgsc.bcm.edu	37	17	3119767	3119767	+	Missense_Mutation	SNP	C	C	T	rs769427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3119767C>T	ENST00000304094.1	+	1	853	c.853C>T	c.(853-855)Cct>Tct	p.P285S		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	285			P -> S (in dbSNP:rs769427). {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.P285S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						AATGTTAAATCCTTTCATCTA	0.468													C|||	1714	0.342252	0.3343	0.33	5008	,	,		20427	0.1438		0.492	False		,,,				2504	0.4121				p.P285S		Atlas-SNP	.											OR1A1,NS,carcinoma,0,1	OR1A1	54	1	1	Substitution - Missense(1)	stomach(1)	c.C853T						PASS	.	C	SER/PRO	1601,2805	494.8+/-363.1	280,1041,882	127.0	119.0	122.0		853	4.1	1.0	17	dbSNP_86	122	4240,4360	571.6+/-389.6	1053,2134,1113	yes	missense	OR1A1	NM_014565.2	74	1333,3175,1995	TT,TC,CC		49.3023,36.3368,44.91	possibly-damaging	285/310	3119767	5841,7165	2203	4300	6503	SO:0001583	missense	8383	exon1			TTAAATCCTTTCA	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.853C>T	17.37:g.3119767C>T	ENSP00000305207:p.Pro285Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	37	CCDS11022.1	741	0.3392857142857143	176	0.35772357723577236	115	0.31767955801104975	81	0.14160839160839161	369	0.4868073878627968	C	20.4	3.976185	0.74360	0.363368	0.493023	ENSG00000172146	ENST00000304094	T	0.63417	-0.04	5.05	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000106	T	0.00012	0.0000	H	0.95187	3.635	0.24492	P	0.99429051	D	0.61697	0.99	P	0.47299	0.543	T	0.30387	-0.9980	9	0.87932	D	0	.	13.6842	0.62506	0.1558:0.8442:0.0:0.0	rs769427;rs17762753;rs57027071;rs769427	285	Q9P1Q5	OR1A1_HUMAN	S	285	ENSP00000305207:P285S	ENSP00000305207:P285S	P	+	1	0	OR1A1	3066517	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.333000	0.65917	1.350000	0.45770	0.511000	0.50034	CCT	C|0.608;T|0.392	0.392	strong		0.468	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565	
RALY	22913	hgsc.bcm.edu	37	20	32664926	32664926	+	Missense_Mutation	SNP	G	G	A	rs2281209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:32664926G>A	ENST00000246194.3	+	8	1253	c.751G>A	c.(751-753)Ggc>Agc	p.G251S	RALY_ENST00000375114.3_Missense_Mutation_p.G235S	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	251	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.		G -> S (in dbSNP:rs2281209).		mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G250_G251delGG(1)		kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						cggtggcggtggcagcagcCG	0.701													G|||	245	0.0489217	0.0015	0.0173	5008	,	,		10783	0.0962		0.0577	False		,,,				2504	0.0777				p.G251S		Atlas-SNP	.											.	RALY	44	.	1	Deletion - In frame(1)	prostate(1)	c.G751A						PASS	.	G	SER/GLY,SER/GLY	48,4170		0,48,2061	8.0	9.0	9.0		703,751	-3.1	0.0	20	dbSNP_100	9	423,7927		8,407,3760	yes	missense,missense	RALY	NM_007367.3,NM_016732.2	56,56	8,455,5821	AA,AG,GG		5.0659,1.138,3.7476	benign,benign	235/291,251/307	32664926	471,12097	2109	4175	6284	SO:0001583	missense	22913	exon8			GGCGGTGGCAGCA	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.751G>A	20.37:g.32664926G>A	ENSP00000246194:p.Gly251Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Missense_Mutation	SNP	ENST00000246194.3	37	CCDS13230.1	110	0.05036630036630037	5	0.01016260162601626	7	0.019337016574585635	50	0.08741258741258741	48	0.0633245382585752	G	10.99	1.507084	0.27036	0.01138	0.050659	ENSG00000125970	ENST00000375114;ENST00000246194;ENST00000442805	D;D;D	0.87966	-2.15;-2.32;-2.15	4.43	-3.06	0.05379	.	0.873151	0.10124	N	0.713074	T	0.11324	0.0276	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.002	T	0.40924	-0.9537	9	0.28530	T	0.3	-0.8129	11.1383	0.48388	0.2895:0.0:0.7105:0.0	rs2281209	235;251	Q9UKM9-2;Q9UKM9	.;RALY_HUMAN	S	235;251;235	ENSP00000364255:G235S;ENSP00000246194:G251S;ENSP00000415973:G235S	ENSP00000246194:G251S	G	+	1	0	RALY	32128587	0.827000	0.29292	0.001000	0.08648	0.004000	0.04260	1.825000	0.39081	-0.415000	0.07484	-1.628000	0.00784	GGC	G|0.949;C|0.000;A|0.050	0.050	strong		0.701	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
GPC1	2817	hgsc.bcm.edu	37	2	241405485	241405485	+	Silent	SNP	C	C	T	rs2228330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241405485C>T	ENST00000264039.2	+	9	1703	c.1455C>T	c.(1453-1455)ggC>ggT	p.G485G	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	485					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)		GTGACGACGGCAGCGGCTCGG	0.682													c|||	727	0.145168	0.1755	0.134	5008	,	,		15348	0.0149		0.2107	False		,,,				2504	0.1789				p.G485G		Atlas-SNP	.											.	GPC1	32	.	0			c.C1455T						PASS	.			758,3630		79,600,1515	18.0	23.0	21.0		1455	2.8	1.0	2	dbSNP_98	21	1940,6622		215,1510,2556	no	coding-synonymous	GPC1	NM_002081.2		294,2110,4071	TT,TC,CC		22.6583,17.2744,20.834		485/559	241405485	2698,10252	2194	4281	6475	SO:0001819	synonymous_variant	2817	exon9			CGACGGCAGCGGC	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.1455C>T	2.37:g.241405485C>T		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	299	0.13690476190476192	85	0.17276422764227642	52	0.143646408839779	6	0.01048951048951049	156	0.20580474934036938	c	7.291	0.611022	0.14066	0.172744	0.226583	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.69	2.77	0.32553	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.6614	10.396	0.44201	0.0:0.5342:0.4658:0.0	rs2228330;rs10183272;rs2228330	.	.	.	X	525;237	.	.	Q	+	1	0	GPC1	241054158	0.134000	0.22483	0.982000	0.44146	0.770000	0.43624	0.518000	0.22847	0.610000	0.30035	0.443000	0.29094	CAG	C|0.832;T|0.168	0.168	strong		0.682	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969085	49969085	+	Silent	SNP	C	C	T	rs10853810	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49969085C>T	ENST00000293350.4	+	13	1822	c.1659C>T	c.(1657-1659)aaC>aaT	p.N553N	ALDH16A1_ENST00000540132.1_Silent_p.N390N|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000455361.2_Silent_p.N502N|ALDH16A1_ENST00000433981.2_Silent_p.N388N	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	553						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGTCTGGCAACCTCCATGGCT	0.657													C|||	1048	0.209265	0.3427	0.2277	5008	,	,		15702	0.005		0.335	False		,,,				2504	0.0971				p.N553N		Atlas-SNP	.											ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	1	0			c.C1659T						scavenged	.	C	,	1393,3013	451.2+/-349.6	220,953,1030	40.0	42.0	41.0		1506,1659	-4.2	0.3	19	dbSNP_120	41	3014,5586	460.2+/-365.1	526,1962,1812	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	746,2915,2842	TT,TC,CC		35.0465,31.616,33.8844	,	502/752,553/803	49969085	4407,8599	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon13			TGGCAACCTCCAT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1659C>T	19.37:g.49969085C>T		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.695;T|0.305	0.305	strong		0.657	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
MCM3AP	8888	hgsc.bcm.edu	37	21	47704896	47704896	+	Missense_Mutation	SNP	G	G	A	rs9975588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47704896G>A	ENST00000397708.1	-	2	559	c.305C>T	c.(304-306)tCa>tTa	p.S102L	YBEY_ENST00000397701.4_5'Flank|YBEY_ENST00000339195.6_5'Flank|MCM3AP_ENST00000291688.1_Missense_Mutation_p.S102L|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397694.1_5'Flank|YBEY_ENST00000397692.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	102	FG-repeats.		S -> L (in dbSNP:rs9975588). {ECO:0000269|PubMed:15489334, 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)					CAGCACAGATGAACTTGAAGG	0.473													G|||	1245	0.248602	0.1982	0.232	5008	,	,		18278	0.1488		0.4085	False		,,,				2504	0.2669				p.S102L		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C305T	GRCh37	CM065300	MCM3AP	M	rs9975588	PASS	.	G	LEU/SER	940,3466	357.1+/-313.8	91,758,1354	75.0	74.0	75.0		305	4.6	1.0	21	dbSNP_119	75	3371,5229	500.2+/-375.2	664,2043,1593	yes	missense	MCM3AP	NM_003906.3	145	755,2801,2947	AA,AG,GG		39.1977,21.3345,33.1462	probably-damaging	102/1981	47704896	4311,8695	2203	4300	6503	SO:0001583	missense	8888	exon1			ACAGATGAACTTG	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.305C>T	21.37:g.47704896G>A	ENSP00000380820:p.Ser102Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	578	0.26465201465201466	102	0.2073170731707317	101	0.27900552486187846	72	0.1258741258741259	303	0.3997361477572559	G	18.71	3.682683	0.68157	0.213345	0.391977	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.19250	2.16;2.16	5.47	4.59	0.56863	.	0.290888	0.31612	N	0.007357	T	0.00012	0.0000	L	0.29908	0.895	0.33270	P	0.439095	P	0.44816	0.844	B	0.39904	0.313	T	0.47799	-0.9089	9	0.66056	D	0.02	-13.7559	12.4261	0.55548	0.0815:0.0:0.9185:0.0	rs9975588;rs17176138;rs52809897;rs60025591;rs9975588	102	O60318	MCM3A_HUMAN	L	102	ENSP00000380820:S102L;ENSP00000291688:S102L	ENSP00000291688:S102L	S	-	2	0	MCM3AP	46529324	0.887000	0.30362	0.992000	0.48379	0.974000	0.67602	4.224000	0.58593	2.561000	0.86390	0.561000	0.74099	TCA	G|0.707;A|0.293	0.293	strong		0.473	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
RFPL3	10738	hgsc.bcm.edu	37	22	32754232	32754232	+	Silent	SNP	C	C	T	rs57606003|rs386820741	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32754232C>T	ENST00000249007.4	+	1	379	c.174C>T	c.(172-174)acC>acT	p.T58T	RFPL3_ENST00000397468.1_Silent_p.T29T|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Silent_p.T29T	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	58							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GTGGATGCACCGTCTGCCTCA	0.542													c|||	724	0.144569	0.0265	0.0893	5008	,	,		19377	0.4583		0.0408	False		,,,				2504	0.1268				p.T58T		Atlas-SNP	.											.	RFPL3	91	.	0			c.C174T						PASS	.	C	,	165,4241	98.0+/-136.7	6,153,2044	119.0	113.0	115.0		174,87	-0.3	0.0	22	dbSNP_129	115	453,8147	130.0+/-188.0	11,431,3858	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	17,584,5902	TT,TC,CC		5.2674,3.7449,4.7517	,	58/318,29/289	32754232	618,12388	2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			ATGCACCGTCTGC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.174C>T	22.37:g.32754232C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	223	100	0.44843	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			C|0.923;T|0.077	0.077	strong		0.542	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
EYS	346007	hgsc.bcm.edu	37	6	65149185	65149185	+	Missense_Mutation	SNP	T	T	A	rs9353806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:65149185T>A	ENST00000370621.3	-	27	6231	c.5705A>T	c.(5704-5706)aAt>aTt	p.N1902I	EYS_ENST00000503581.1_Missense_Mutation_p.N1902I|EYS_ENST00000370616.2_Missense_Mutation_p.N1902I			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1902	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		N -> I (in dbSNP:rs9353806). {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)			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						ATTTTGTGGATTTAAAGCCAC	0.328													T|||	1459	0.291334	0.1793	0.2997	5008	,	,		14982	0.4593		0.2833	False		,,,				2504	0.272				p.N1902I		Atlas-SNP	.											.	EYS	527	.	0			c.A5705T						PASS	.						66.0	60.0	62.0					6																	65149185		692	1588	2280	SO:0001583	missense	346007	exon27			TGTGGATTTAAAG		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.5705A>T	6.37:g.65149185T>A	ENSP00000359655:p.Asn1902Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	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		683	0.31272893772893773	101	0.20528455284552846	117	0.32320441988950277	247	0.4318181818181818	218	0.287598944591029	T	12.83	2.057027	0.36277	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.68025	-0.3;-0.3;-0.3	4.33	-1.38	0.09027	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.20659	0.0497	N	0.08118	0	0.80722	P	0.0	P;P	0.45011	0.848;0.531	B;B	0.41174	0.349;0.118	T	0.03673	-1.1014	8	0.30078	T	0.28	.	4.7675	0.13139	0.0:0.1692:0.3058:0.525	rs9353806;rs52802069;rs9353806	1902;1902	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	I	1902	ENSP00000424243:N1902I;ENSP00000359655:N1902I;ENSP00000359650:N1902I	ENSP00000359650:N1902I	N	-	2	0	EYS	65205906	0.344000	0.24827	0.803000	0.32268	0.390000	0.30446	0.360000	0.20250	0.086000	0.17137	0.482000	0.46254	AAT	T|0.686;A|0.314	0.314	strong		0.328	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
DNAJB13	374407	hgsc.bcm.edu	37	11	73681135	73681135	+	Missense_Mutation	SNP	G	G	A	rs72982975	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:73681135G>A	ENST00000339764.1	+	8	1678	c.927G>A	c.(925-927)atG>atA	p.M309I	DNAJB13_ENST00000543947.1_Missense_Mutation_p.M134I|DNAJB13_ENST00000537753.1_Missense_Mutation_p.M134I|RP11-167N4.2_ENST00000537019.1_RNA	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	309					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					AGAAGCAGATGCTGCGCCAGG	0.622													g|||	1119	0.223442	0.1929	0.3473	5008	,	,		18231	0.1637		0.2575	False		,,,				2504	0.2035				p.M309I		Atlas-SNP	.											.	DNAJB13	28	.	0			c.G927A						PASS	.	G	ILE/MET	879,3521	342.8+/-307.3	76,727,1397	117.0	108.0	111.0		927	4.6	1.0	11	dbSNP_130	111	2234,6352	378.8+/-339.0	280,1674,2339	yes	missense	DNAJB13	NM_153614.2	10	356,2401,3736	AA,AG,GG		26.0191,19.9773,23.972	benign	309/317	73681135	3113,9873	2200	4293	6493	SO:0001583	missense	374407	exon8			GCAGATGCTGCGC	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.927G>A	11.37:g.73681135G>A	ENSP00000344431:p.Met309Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_153614	B3LEP4|Q8IZW5	Missense_Mutation	SNP	ENST00000339764.1	37	CCDS8227.1	521|521	0.23855311355311357|0.23855311355311357	104|104	0.21138211382113822|0.21138211382113822	118|118	0.3259668508287293|0.3259668508287293	94|94	0.16433566433566432|0.16433566433566432	205|205	0.2704485488126649|0.2704485488126649	G|G	16.13|16.13	3.036820|3.036820	0.54896|0.54896	0.199773|0.199773	0.260191|0.260191	ENSG00000187726|ENSG00000187726	ENST00000542350|ENST00000339764;ENST00000537753;ENST00000543947	.|T;T;T	.|0.39229	.|1.09;1.09;1.09	5.54|5.54	4.59|4.59	0.56863|0.56863	.|HSP40/DnaJ peptide-binding (1);	.|0.115848	.|0.64402	.|D	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02708|0.02708	-0.52|-0.52	0.31243|0.31243	P|P	0.6949609999999999|0.6949609999999999	.|B	.|0.10296	.|0.003	.|B	.|0.16722	.|0.016	T|T	0.30851|0.30851	-0.9964|-0.9964	4|9	.|0.23891	.|T	.|0.37	.|.	13.1925|13.1925	0.59719|0.59719	0.0:0.2743:0.7257:0.0|0.0:0.2743:0.7257:0.0	.|.	.|309	.|P59910	.|DJB13_HUMAN	T|I	210|309;134;134	.|ENSP00000344431:M309I;ENSP00000439711:M134I;ENSP00000438576:M134I	.|ENSP00000344431:M309I	A|M	+|+	1|3	0|0	DNAJB13|DNAJB13	73358783|73358783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	2.898000|2.898000	0.48672|0.48672	2.619000|2.619000	0.88677|0.88677	0.644000|0.644000	0.83932|0.83932	GCT|ATG	G|0.759;A|0.241	0.241	strong		0.622	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
OR2M3	127062	hgsc.bcm.edu	37	1	248366702	248366702	+	Silent	SNP	G	G	A	rs4916112	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248366702G>A	ENST00000456743.1	+	1	371	c.333G>A	c.(331-333)gaG>gaA	p.E111E		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	111						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)			TTGGCTCTGAGTGCTTTCTTT	0.448													A|||	2419	0.483027	0.3306	0.5072	5008	,	,		19244	0.4325		0.6083	False		,,,				2504	0.5951				p.E111E		Atlas-SNP	.											.	OR2M3	116	.	0			c.G333A						PASS	.	A		1684,2722	654.9+/-399.8	294,1096,813	247.0	253.0	251.0		333	-0.2	0.0	1	dbSNP_111	251	5311,3289	491.9+/-373.2	1639,2033,628	no	coding-synonymous	OR2M3	NM_001004689.1		1933,3129,1441	AA,AG,GG		38.2442,38.2206,46.2171		111/313	248366702	6995,6011	2203	4300	6503	SO:0001819	synonymous_variant	127062	exon1			CTCTGAGTGCTTT		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.333G>A	1.37:g.248366702G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_001004689	B9EH06|Q6IEY0	Silent	SNP	ENST00000456743.1	37	CCDS31107.1																																																																																			G|0.470;A|0.530	0.530	strong		0.448	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
FBLN1	2192	hgsc.bcm.edu	37	22	45937149	45937149	+	Silent	SNP	C	C	T	rs9682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45937149C>T	ENST00000327858.6	+	9	1058	c.963C>T	c.(961-963)atC>atT	p.I321I	FBLN1_ENST00000402984.3_Silent_p.I359I|FBLN1_ENST00000348697.2_Silent_p.I321I|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000442170.2_Silent_p.I321I|FBLN1_ENST00000340923.5_Silent_p.I321I|FBLN1_ENST00000262722.7_Silent_p.I321I	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	321	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CGTGCCCTATCGGGCATACAT	0.542													C|||	1313	0.262181	0.2171	0.2637	5008	,	,		18136	0.1825		0.4294	False		,,,				2504	0.2321				p.I321I		Atlas-SNP	.											.	FBLN1	143	.	0			c.C963T						PASS	.	C	,,,	1091,3315	394.7+/-329.4	129,833,1241	143.0	118.0	127.0		963,963,963,963	-10.6	0.0	22	dbSNP_52	127	3601,4999	522.2+/-380.1	717,2167,1416	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FBLN1	NM_001996.3,NM_006485.3,NM_006486.2,NM_006487.2	,,,	846,3000,2657	TT,TC,CC		41.8721,24.7617,36.0757	,,,	321/684,321/602,321/704,321/567	45937149	4692,8314	2203	4300	6503	SO:0001819	synonymous_variant	2192	exon9			CCCTATCGGGCAT		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.963C>T	22.37:g.45937149C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	186	87	0.467742	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	37	CCDS14067.1																																																																																			C|0.673;T|0.327	0.327	strong		0.542	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	
INCENP	3619	hgsc.bcm.edu	37	11	61908440	61908440	+	Missense_Mutation	SNP	T	T	C	rs2277283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:61908440T>C	ENST00000394818.3	+	10	1719	c.1517T>C	c.(1516-1518)aTg>aCg	p.M506T	INCENP_ENST00000278849.4_Missense_Mutation_p.M506T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	506			M -> T (in dbSNP:rs2277283).		chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CAGATGCTCATGACCCCGACC	0.642													T|||	853	0.170327	0.1498	0.1916	5008	,	,		19216	0.0744		0.3002	False		,,,				2504	0.1483				p.M506T		Atlas-SNP	.											.	INCENP	122	.	0			c.T1517C						PASS	.	T	THR/MET,THR/MET	777,3627	310.8+/-291.8	67,643,1492	77.0	76.0	77.0		1517,1517	5.5	1.0	11	dbSNP_100	77	2670,5928	428.7+/-356.0	422,1826,2051	yes	missense,missense	INCENP	NM_001040694.1,NM_020238.2	81,81	489,2469,3543	CC,CT,TT		31.0537,17.6431,26.5113	probably-damaging,probably-damaging	506/919,506/915	61908440	3447,9555	2202	4299	6501	SO:0001583	missense	3619	exon10			TGCTCATGACCCC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1517T>C	11.37:g.61908440T>C	ENSP00000378295:p.Met506Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	440	0.20146520146520147	79	0.16056910569105692	79	0.21823204419889503	39	0.06818181818181818	243	0.32058047493403696	T	15.33	2.802715	0.50315	0.176431	0.310537	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.39997	1.05;1.05	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	L	0.57536	1.79	0.21184	P	0.9997604	P;D;D	0.76494	0.568;0.999;0.998	P;D;D	0.77557	0.472;0.99;0.977	T	0.16364	-1.0405	9	0.35671	T	0.21	.	13.5006	0.61452	0.0:0.0:0.0:1.0	rs2277283;rs17707972	506;506;506	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	T	506	ENSP00000378295:M506T;ENSP00000278849:M506T	ENSP00000278849:M506T	M	+	2	0	INCENP	61665016	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.826000	0.75298	2.081000	0.62600	0.533000	0.62120	ATG	T|0.764;C|0.236;A|0.000	0.236	strong		0.642	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
KIF26A	26153	hgsc.bcm.edu	37	14	104642524	104642524	+	Silent	SNP	C	C	T	rs78184481	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104642524C>T	ENST00000423312.2	+	12	3399	c.3399C>T	c.(3397-3399)ttC>ttT	p.F1133F	KIF26A_ENST00000315264.7_Silent_p.F994F	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1133					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)		AGCCCCGCTTCAGCCCCGACT	0.706													C|||	105	0.0209665	0.0045	0.0346	5008	,	,		13789	0.0		0.0577	False		,,,				2504	0.0174				p.F1133F		Atlas-SNP	.											.	KIF26A	84	.	0			c.C3399T						PASS	.	C		39,3513		0,39,1737	5.0	7.0	6.0		3399	2.8	0.2	14	dbSNP_132	6	445,7313		19,407,3453	no	coding-synonymous	KIF26A	NM_015656.1		19,446,5190	TT,TC,CC		5.736,1.098,4.2794		1133/1883	104642524	484,10826	1776	3879	5655	SO:0001819	synonymous_variant	26153	exon12			CCGCTTCAGCCCC	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.3399C>T	14.37:g.104642524C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.971;T|0.029	0.029	strong		0.706	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
HAGHL	84264	hgsc.bcm.edu	37	16	778024	778024	+	Silent	SNP	T	T	C	rs1406814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:778024T>C	ENST00000341413.4	+	3	446	c.165T>C	c.(163-165)caT>caC	p.H55H	HAGHL_ENST00000561546.1_Silent_p.H55H|HAGHL_ENST00000389703.3_Silent_p.H55H|CCDC78_ENST00000293889.6_5'Flank|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564537.1_Silent_p.H55H|HAGHL_ENST00000564545.1_Intron|HAGHL_ENST00000549114.1_Silent_p.H55H			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	55							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				CCACCCACCATCACTGGTGAG	0.721													t|||	2574	0.513978	0.5862	0.4928	5008	,	,		8072	0.7579		0.2425	False		,,,				2504	0.4591				p.H55H	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											HAGHL,NS,carcinoma,0,1	HAGHL	18	1	0			c.T165C						PASS	.			2208,2150		571,1066,542	22.0	29.0	27.0		165	-1.6	1.0	16	dbSNP_88	27	1792,6782		199,1394,2694	no	coding-synonymous	HAGHL	NM_032304.2		770,2460,3236	CC,CT,TT		20.9004,49.3346,30.931		55/283	778024	4000,8932	2179	4287	6466	SO:0001819	synonymous_variant	84264	exon2			CCACCATCACTGG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.165T>C	16.37:g.778024T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				T|0.616;C|0.384	0.384	strong		0.721	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
HDAC9	9734	hgsc.bcm.edu	37	7	18705964	18705964	+	Silent	SNP	C	C	T	rs35691757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:18705964C>T	ENST00000432645.2	+	11	1587	c.1587C>T	c.(1585-1587)agC>agT	p.S529S	HDAC9_ENST00000456174.2_Silent_p.S501S|HDAC9_ENST00000406451.4_Silent_p.S529S|HDAC9_ENST00000428307.2_Silent_p.S485S|HDAC9_ENST00000405010.3_Silent_p.S529S|HDAC9_ENST00000441542.2_Silent_p.S532S|HDAC9_ENST00000417496.2_Silent_p.S527S|HDAC9_ENST00000406072.1_Silent_p.S516S|HDAC9_ENST00000401921.1_Silent_p.S488S|HDAC9_ENST00000524023.1_Silent_p.S452S	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	529					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)	GCACTAGGAGCGACAGCAGTG	0.557											OREG0017877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	138	0.0275559	0.0053	0.1484	5008	,	,		17985	0.0		0.0219	False		,,,				2504	0.0061				p.S532S		Atlas-SNP	.											HDAC9_ENST00000417496,colon,carcinoma,+2,5	HDAC9	560	5	0			c.C1596T						PASS	.	C	,,,,,,,,	34,4088		0,34,2027	94.0	107.0	103.0		1581,1455,1464,1356,1503,1587,1587,1587,1596	1.6	1.0	7	dbSNP_126	103	211,8199		4,203,3998	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_001204144.1,NM_001204145.1,NM_001204146.1,NM_001204147.1,NM_001204148.1,NM_014707.1,NM_058176.2,NM_178423.1,NM_178425.2	,,,,,,,,	4,237,6025	TT,TC,CC		2.5089,0.8248,1.955	,,,,,,,,	527/589,485/547,488/550,452/514,501/563,529/591,529/1012,529/1067,532/1070	18705964	245,12287	2061	4205	6266	SO:0001819	synonymous_variant	9734	exon11			TAGGAGCGACAGC	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.1587C>T	7.37:g.18705964C>T		Somatic	77	0	0	727	WXS	Illumina HiSeq	Phase_I	137	88	0.642336	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			C|0.972;T|0.028	0.028	strong		0.557	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52888048	52888048	+	Silent	SNP	G	G	A	rs324124	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52888048G>A	ENST00000422689.2	+	4	1230	c.1215G>A	c.(1213-1215)gaG>gaA	p.E405E		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	405					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						ACACGGGAGAGCAACCTTACA	0.403													G|||	772	0.154153	0.2526	0.1124	5008	,	,		20761	0.1468		0.1421	False		,,,				2504	0.0706				p.E405E		Atlas-SNP	.											.	ZNF880	45	.	0			c.G1215A						PASS	.						69.0	63.0	65.0					19																	52888048		1568	3582	5150	SO:0001819	synonymous_variant	400713	exon4			GGGAGAGCAACCT	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.1215G>A	19.37:g.52888048G>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			G|0.865;A|0.135	0.135	strong		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
HPS5	11234	hgsc.bcm.edu	37	11	18327684	18327684	+	Silent	SNP	G	G	T	rs1140047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18327684G>T	ENST00000349215.3	-	7	1099	c.822C>A	c.(820-822)ctC>ctA	p.L274L	HPS5_ENST00000438420.2_Silent_p.L160L|HPS5_ENST00000531848.1_Silent_p.L160L|HPS5_ENST00000396253.3_Silent_p.L160L	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	274					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ATCGTTACCTGAGAGTAATCA	0.398									Hermansky-Pudlak syndrome				T|||	4030	0.804712	0.7852	0.7536	5008	,	,		18638	0.9722		0.7107	False		,,,				2504	0.7914				p.L274L		Atlas-SNP	.											.	HPS5	70	.	0			c.C822A						PASS	.	T	,,	3367,1031	381.4+/-324.0	1287,793,119	78.0	77.0	77.0		480,822,480	1.8	0.9	11	dbSNP_86	77	5881,2705	433.5+/-357.4	2021,1839,433	no	coding-synonymous,coding-synonymous,coding-synonymous	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	,,	3308,2632,552	TT,TG,GG		31.5048,23.4425,28.7739	,,	160/1016,274/1130,160/1016	18327684	9248,3736	2199	4293	6492	SO:0001819	synonymous_variant	11234	exon7	Familial Cancer Database	HPS, HPS1-8	TTACCTGAGAGTA	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.822C>A	11.37:g.18327684G>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																			G|0.215;T|0.590	0.590	strong		0.398	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
KRT3	3850	hgsc.bcm.edu	37	12	53189428	53189428	+	Silent	SNP	C	C	A	rs148531142|rs184322044		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53189428C>A	ENST00000417996.2	-	1	473	c.399G>T	c.(397-399)ggG>ggT	p.G133G	KRT3_ENST00000309505.3_Silent_p.G133G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	133	Gly-rich.|Head.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						agccaccagcccctccaaagc	0.632																																					p.G133G		Atlas-SNP	.											.	KRT3	65	.	0			c.G399T						PASS	.						141.0	187.0	172.0					12																	53189428		2177	4259	6436	SO:0001819	synonymous_variant	3850	exon1			ACCAGCCCCTCCA		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.399G>T	12.37:g.53189428C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	12	0.137931	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																			C|0.888;A|0.112	0.112	strong		0.632	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
ZNF519	162655	hgsc.bcm.edu	37	18	14106039	14106039	+	Missense_Mutation	SNP	T	T	C	rs62086326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:14106039T>C	ENST00000590202.1	-	3	652	c.500A>G	c.(499-501)aAt>aGt	p.N167S	ZNF519_ENST00000589203.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	167				N -> D (in Ref. 2; AAH24227). {ECO:0000305}.	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						TTTACTAATATTTGAGTCATG	0.259													T|||	967	0.193091	0.0136	0.281	5008	,	,		17985	0.2381		0.2525	False		,,,				2504	0.2658				p.N167S		Atlas-SNP	.											.	ZNF519	53	.	0			c.A500G						PASS	.	T	SER/ASN	213,4087		9,195,1946	24.0	26.0	25.0		500	0.3	0.0	18	dbSNP_129	25	2065,6437		285,1495,2471	yes	missense	ZNF519	NM_145287.3	46	294,1690,4417	CC,CT,TT		24.2884,4.9535,17.7941	benign	167/541	14106039	2278,10524	2150	4251	6401	SO:0001583	missense	162655	exon3			CTAATATTTGAGT	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.500A>G	18.37:g.14106039T>C	ENSP00000464872:p.Asn167Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	64	42	0.65625	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	450	0.20604395604395603	12	0.024390243902439025	103	0.2845303867403315	142	0.24825174825174826	193	0.2546174142480211	T	0.005	-2.137334	0.00335	0.049535	0.242884	ENSG00000175322	ENST00000309305	.	.	.	0.328	0.328	0.15918	.	.	.	.	.	T	0.00012	0.0000	N	0.05199	-0.095	0.80722	P	0.0	B	0.30526	0.283	B	0.29176	0.099	T	0.38436	-0.9661	7	0.08381	T	0.77	.	5.0724	0.14613	0.0:2.0E-4:0.0:0.9998	rs62086326	167	Q8TB69	ZN519_HUMAN	S	167	.	ENSP00000307908:N167S	N	-	2	0	ZNF519	14096039	0.000000	0.05858	0.010000	0.14722	0.252000	0.25951	-1.143000	0.03200	0.367000	0.24454	0.076000	0.15429	AAT	T|0.799;C|0.201	0.201	strong		0.259	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
PRDM1	639	hgsc.bcm.edu	37	6	106554343	106554343	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106554343T>A	ENST00000369096.4	+	6	2105	c.1871T>A	c.(1870-1872)gTa>gAa	p.V624E	PRDM1_ENST00000369091.2_Missense_Mutation_p.V588E|PRDM1_ENST00000369089.3_Missense_Mutation_p.V490E	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	624					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CACTACCTGGTACACACGGGA	0.512			"""D, N, Mis, F, S"""		DLBCL																																p.V624E		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.T1871A						PASS	.						116.0	96.0	103.0					6																	106554343		2203	4300	6503	SO:0001583	missense	639	exon6			ACCTGGTACACAC		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1871T>A	6.37:g.106554343T>A	ENSP00000358092:p.Val624Glu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	13	0.22807	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	T	25.0	4.589481	0.86851	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	T;T;T	0.07688	3.17;3.17;3.17	5.55	5.55	0.83447	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.052469	0.85682	D	0.000000	T	0.14700	0.0355	L	0.50993	1.605	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.994;0.998	T	0.00613	-1.1644	10	0.87932	D	0	-13.8246	12.4582	0.55716	0.0:0.0:0.1492:0.8508	.	490;624	Q86WM7;O75626	.;PRDM1_HUMAN	E	588;624;587;490	ENSP00000358087:V588E;ENSP00000358092:V624E;ENSP00000358085:V490E	ENSP00000358085:V490E	V	+	2	0	PRDM1	106661036	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.180000	0.71981	2.118000	0.64928	0.533000	0.62120	GTA	.	.	none		0.512	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
ABCF2	10061	hgsc.bcm.edu	37	7	150912750	150912750	+	Silent	SNP	G	G	T	rs12538823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150912750G>T	ENST00000287844.2	-	13	1579	c.1470C>A	c.(1468-1470)atC>atA	p.I490I	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.I490I	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	490	ABC transporter 2. {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)		CCTTCTCCTTGATCTCTGGGT	0.488													G|||	250	0.0499201	0.0197	0.1138	5008	,	,		20679	0.0159		0.0775	False		,,,				2504	0.0521				p.I490I		Atlas-SNP	.											.	ABCF2	54	.	0			c.C1470A						PASS	.	G	,	154,4252	105.2+/-143.6	0,154,2049	245.0	209.0	221.0		1470,1470	3.8	1.0	7	dbSNP_120	221	822,7778	191.4+/-237.6	45,732,3523	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	45,886,5572	TT,TG,GG		9.5581,3.4952,7.5042	,	490/635,490/624	150912750	976,12030	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon13			CTCCTTGATCTCT	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.1470C>A	7.37:g.150912750G>T		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.939;T|0.061	0.061	strong		0.488	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
THUMPD3	25917	hgsc.bcm.edu	37	3	9425944	9425944	+	Silent	SNP	G	G	C	rs1046788	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9425944G>C	ENST00000345094.3	+	9	1618	c.1284G>C	c.(1282-1284)cgG>cgC	p.R428R	SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000515662.2_Silent_p.R428R|SETD5-AS1_ENST00000521609.1_RNA|SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000520629.1_RNA|THUMPD3_ENST00000452837.2_Silent_p.R428R	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	428						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		CTTGCCTACGGGAGATGAGCC	0.428													g|||	531	0.10603	0.0348	0.2248	5008	,	,		17980	0.0615		0.1879	False		,,,				2504	0.0798				p.R428R		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G1284C						PASS	.		,	268,4138	150.3+/-184.3	5,258,1940	202.0	209.0	207.0		1284,1284	-3.0	0.1	3	dbSNP_86	207	1276,7324	254.7+/-279.9	85,1106,3109	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	90,1364,5049	CC,CG,GG		14.8372,6.0826,11.8714	,	428/508,428/508	9425944	1544,11462	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon9			CCTACGGGAGATG	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1284G>C	3.37:g.9425944G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1	290	0.13278388278388278	23	0.046747967479674794	82	0.2265193370165746	43	0.07517482517482517	142	0.18733509234828497	G	7.498	0.652120	0.14580	0.060826	0.148372	ENSG00000134077	ENST00000416603	.	.	.	5.66	-3.01	0.05463	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999956	.	.	.	.	.	.	T	0.31641	-0.9936	3	.	.	.	-8.8946	5.1373	0.14941	0.3653:0.0:0.4284:0.2063	rs1046788;rs3172463;rs1046788	.	.	.	R	199	.	.	G	+	1	0	THUMPD3	9400944	0.156000	0.22821	0.056000	0.19401	0.937000	0.57800	0.545000	0.23268	-0.398000	0.07679	-0.188000	0.12872	GGA	G|0.878;C|0.122	0.122	strong		0.428	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
PNP	4860	hgsc.bcm.edu	37	14	20940515	20940515	+	Silent	SNP	C	C	T	rs1049562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	124	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	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	
FOLH1	2346	hgsc.bcm.edu	37	11	49221885	49221885	+	Silent	SNP	T	T	A	rs202680	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:49221885T>A	ENST00000256999.2	-	3	593	c.333A>T	c.(331-333)gcA>gcT	p.A111A	FOLH1_ENST00000340334.7_Silent_p.A96A|FOLH1_ENST00000533034.1_Silent_p.A96A|FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000356696.3_Silent_p.A111A	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	111					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	CATCATAATGTGCTAGCTCAA	0.353													A|||	2078	0.414936	0.6354	0.3156	5008	,	,		15587	0.3165		0.2753	False		,,,				2504	0.4325				p.A111A		Atlas-SNP	.											.	FOLH1	141	.	0			c.A333T						PASS	.	A	,,,,	2359,2039	528.2+/-372.3	663,1033,503	65.0	67.0	66.0		333,288,288,,333	-0.8	1.0	11	dbSNP_79	66	2297,6299	686.0+/-404.1	332,1633,2333	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	,,,,	995,2666,2836	AA,AT,TT		26.7217,46.362,35.8319	,,,,	111/720,96/736,96/705,,111/751	49221885	4656,8338	2199	4298	6497	SO:0001819	synonymous_variant	2346	exon3			ATAATGTGCTAGC	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.333A>T	11.37:g.49221885T>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	ENST00000256999.2	37	CCDS7946.1																																																																																			T|0.646;A|0.354	0.354	strong		0.353	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
CLIP2	7461	hgsc.bcm.edu	37	7	73753250	73753250	+	Silent	SNP	T	T	C	rs539518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:73753250T>C	ENST00000395060.1	+	2	594	c.594T>C	c.(592-594)acT>acC	p.T198T	CLIP2_ENST00000223398.6_Silent_p.T198T|CLIP2_ENST00000361545.5_Silent_p.T198T			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	198						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						CCGTGAAGACTGGCAACGAGT	0.662													C|||	2712	0.541534	0.3464	0.5778	5008	,	,		14448	0.494		0.7584	False		,,,				2504	0.6053				p.T198T		Atlas-SNP	.											.	CLIP2	134	.	0			c.T594C						PASS	.	C	,	1728,2558		371,986,786	33.0	33.0	33.0		594,594	-8.8	0.7	7	dbSNP_83	33	6246,2146		2395,1456,345	no	coding-synonymous,coding-synonymous	CLIP2	NM_003388.4,NM_032421.2	,	2766,2442,1131	CC,CT,TT		25.572,40.3173,37.1036	,	198/1047,198/1012	73753250	7974,4704	2143	4196	6339	SO:0001819	synonymous_variant	7461	exon3			GAAGACTGGCAAC	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.594T>C	7.37:g.73753250T>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	37	CCDS5569.1																																																																																			T|0.406;C|0.594	0.594	strong		0.662	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
CLCNKA	1187	hgsc.bcm.edu	37	1	16354590	16354590	+	Missense_Mutation	SNP	A	A	T	rs12126269	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16354590A>T	ENST00000331433.4	+	10	963	c.944A>T	c.(943-945)tAc>tTc	p.Y315F	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.Y315F|CLCNKA_ENST00000439316.2_Missense_Mutation_p.Y272F|CLCNKA_ENST00000420078.1_Missense_Mutation_p.Y315F			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	315			Y -> F (in dbSNP:rs12126269). {ECO:0000269|PubMed:15489334}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	ACCAATCGGTACAGCTCCAAA	0.562													T|||	774	0.154553	0.1014	0.196	5008	,	,		16650	0.2123		0.1879	False		,,,				2504	0.1033				p.Y315F		Atlas-SNP	.											.	CLCNKA	56	.	0			c.A944T						PASS	.	T	PHE/TYR,PHE/TYR	587,3817	771.2+/-413.8	35,517,1650	160.0	124.0	136.0		944,944	2.2	0.1	1	dbSNP_120	136	1855,6745	729.7+/-406.7	221,1413,2666	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	22,22	256,1930,4316	TT,TA,AA		21.5698,13.3288,18.7788	benign,benign	315/687,315/688	16354590	2442,10562	2202	4300	6502	SO:0001583	missense	1187	exon10			ATCGGTACAGCTC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.944A>T	1.37:g.16354590A>T	ENSP00000332771:p.Tyr315Phe	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	167	92	0.550898	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	398	0.18223443223443223	52	0.10569105691056911	70	0.19337016574585636	131	0.229020979020979	145	0.19129287598944592	T	0.587	-0.834613	0.02713	0.133288	0.215698	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.84370	-1.77;-1.77;-1.84;-1.77	3.3	2.18	0.27775	Chloride channel, core (2);	1.288350	0.05059	N	0.479536	T	0.00039	0.0001	N	0.01438	-0.865	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	0.09509	-1.0671	9	0.09843	T	0.71	.	4.9674	0.14098	0.1662:0.0997:0.0:0.7342	rs12126269;rs17846434;rs17857433;rs17859483;rs12126269	272;315;315	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	F	315;315;272;315	ENSP00000364844:Y315F;ENSP00000410353:Y315F;ENSP00000414445:Y272F;ENSP00000332771:Y315F	ENSP00000332771:Y315F	Y	+	2	0	CLCNKA	16227177	0.015000	0.18098	0.115000	0.21578	0.382000	0.30200	1.906000	0.39887	0.451000	0.26802	-0.827000	0.03088	TAC	A|0.809;T|0.191	0.191	strong		0.562	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
SPECC1	92521	hgsc.bcm.edu	37	17	20217375	20217375	+	Silent	SNP	G	G	A	rs75296798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:20217375G>A	ENST00000261503.5	+	15	3255	c.3204G>A	c.(3202-3204)acG>acA	p.T1068T	SPECC1_ENST00000536879.1_Silent_p.T408T|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395530.2_Silent_p.T987T|SPECC1_ENST00000395527.4_Silent_p.T1068T	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	1068					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		ACTTTGAGACGTAACCCTGGA	0.587													g|||	186	0.0371406	0.0045	0.0836	5008	,	,		19090	0.0		0.1024	False		,,,				2504	0.0194				p.T1068T		Atlas-SNP	.											.	SPECC1	100	.	0			c.G3204A						PASS	.	A	,	101,4305	79.3+/-117.8	2,97,2104	76.0	62.0	67.0		3204,2961	-6.7	0.1	17	dbSNP_132	67	1037,7563	219.4+/-257.5	71,895,3334	no	coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_001033555.2	,	73,992,5438	AA,AG,GG		12.0581,2.2923,8.7498	,	1068/1069,987/988	20217375	1138,11868	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon15			TGAGACGTAACCC	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.3204G>A	17.37:g.20217375G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			G|0.923;A|0.077	0.077	strong		0.587	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
SSR1	6745	hgsc.bcm.edu	37	6	7310259	7310259	+	Missense_Mutation	SNP	A	A	G	rs10004	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7310259A>G	ENST00000244763.4	-	2	169	c.83T>C	c.(82-84)tTg>tCg	p.L28S	SSR1_ENST00000534851.1_Missense_Mutation_p.L28S|SSR1_ENST00000462112.1_Missense_Mutation_p.L28S|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000474597.1_Missense_Mutation_p.L28S|SSR1_ENST00000397511.2_Missense_Mutation_p.L28S|SSR1_ENST00000489567.1_Missense_Mutation_p.L28S|SSR1_ENST00000479365.1_Missense_Mutation_p.L28S	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	28			L -> S (in dbSNP:rs10004). {ECO:0000269|PubMed:8050590, ECO:0000269|Ref.6}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.L28S(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					CACTGCTAACAAGCCTAATGA	0.363													G|||	1474	0.294329	0.5144	0.1542	5008	,	,		17650	0.2609		0.2455	False		,,,				2504	0.181				p.L28S		Atlas-SNP	.											SSR1,NS,carcinoma,0,1	SSR1	21	1	1	Substitution - Missense(1)	lung(1)	c.T83C						PASS	.	G	SER/LEU	2004,2402	613.7+/-392.2	439,1126,638	124.0	121.0	122.0		83	3.0	0.0	6	dbSNP_52	122	2258,6342	707.5+/-405.6	305,1648,2347	yes	missense	SSR1	NM_003144.3	145	744,2774,2985	GG,GA,AA		26.2558,45.4834,32.7695	benign	28/287	7310259	4262,8744	2203	4300	6503	SO:0001583	missense	6745	exon2			GCTAACAAGCCTA		CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783			11323	protein-coding gene	gene with protein product	"""translocon-associated protein alpha"""	600868					Standard	NM_001292008		Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.83T>C	6.37:g.7310259A>G	ENSP00000244763:p.Leu28Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	642	0.29395604395604397	241	0.4898373983739837	65	0.17955801104972377	144	0.2517482517482518	192	0.2532981530343008	G	8.517	0.867893	0.17250	0.454834	0.262558	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000462112	T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93	3.91	3.04	0.35103	.	0.456420	0.21293	N	0.076926	T	0.10252	0.0251	N	0.20986	0.625	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	0.17379	-1.0371	9	0.20519	T	0.43	.	7.6038	0.28091	0.3016:0.0:0.6984:0.0	rs10004;rs1139088;rs3203131;rs7746261;rs11552673;rs17295574;rs52829480;rs58553065;rs7746261	28;28;28	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	S	28	ENSP00000418617:L28S;ENSP00000244763:L28S;ENSP00000380647:L28S;ENSP00000443020:L28S;ENSP00000420730:L28S;ENSP00000417911:L28S;ENSP00000417290:L28S	ENSP00000244763:L28S	L	-	2	0	SSR1	7255258	0.995000	0.38212	0.028000	0.17463	0.602000	0.36980	3.670000	0.54569	0.625000	0.30304	-0.748000	0.03510	TTG	T|0.123;G|0.260	0.260	strong		0.363	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2		
TNRC18	84629	hgsc.bcm.edu	37	7	5353061	5353061	+	Silent	SNP	C	C	T	rs188607046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5353061C>T	ENST00000430969.1	-	27	7809	c.7461G>A	c.(7459-7461)ccG>ccA	p.P2487P	TNRC18_ENST00000399537.4_Silent_p.P2487P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2487							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCCCCGCCCCCGGATCCTCCC	0.692													C|||	290	0.0579073	0.0545	0.1167	5008	,	,		11447	0.0575		0.0378	False		,,,				2504	0.0419				p.P2487P		Atlas-SNP	.											.	TNRC18	311	.	0			c.G7461A						PASS	.	C		137,2991		5,127,1432	10.0	11.0	11.0		7461	-9.8	0.0	7		11	287,6859		9,269,3295	no	coding-synonymous	TNRC18	NM_001080495.2		14,396,4727	TT,TC,CC		4.0162,4.3798,4.1269		2487/2969	5353061	424,9850	1564	3573	5137	SO:0001819	synonymous_variant	84629	exon27			CGCCCCCGGATCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7461G>A	7.37:g.5353061C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	201	146	0.726368	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1	134	0.06135531135531135	37	0.07520325203252033	36	0.09944751381215469	28	0.04895104895104895	33	0.04353562005277045	t	0.068	-1.209017	0.01568	0.043798	0.040162	ENSG00000182095	ENST00000328270	.	.	.	4.89	-9.77	0.00500	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.09443	-1.0674	3	.	.	.	.	1.8474	0.03162	0.2028:0.3835:0.136:0.2777	.	.	.	.	R	301	.	.	G	-	1	0	TNRC18	5319587	0.000000	0.05858	0.000000	0.03702	0.163000	0.22366	-6.100000	0.00081	-2.886000	0.00317	-1.195000	0.01675	GGG	C|0.942;T|0.058	0.058	strong		0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SLCO1C1	53919	hgsc.bcm.edu	37	12	20885931	20885931	+	Silent	SNP	A	A	G	rs16923154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:20885931A>G	ENST00000266509.2	+	10	1643	c.1275A>G	c.(1273-1275)gcA>gcG	p.A425A	SLCO1C1_ENST00000545102.1_Silent_p.A307A|SLCO1C1_ENST00000540354.1_Silent_p.A376A|SLCO1C1_ENST00000381552.1_Silent_p.A425A|SLCO1C1_ENST00000545604.1_Silent_p.A425A	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	425					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.A425A(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	GTGGAGCTGCAAAACTCTACT	0.448													A|||	394	0.0786741	0.0522	0.0288	5008	,	,		15838	0.1855		0.0865	False		,,,				2504	0.0317				p.A425A		Atlas-SNP	.											SLCO1C1,NS,carcinoma,0,1	SLCO1C1	216	1	1	Substitution - coding silent(1)	stomach(1)	c.A1275G						scavenged	.	A	,,,	239,4167	139.6+/-175.2	5,229,1969	202.0	179.0	187.0		921,1128,1275,1275	1.3	1.0	12	dbSNP_123	187	678,7922	170.3+/-221.5	31,616,3653	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	36,845,5622	GG,GA,AA		7.8837,5.4244,7.0506	,,,	307/613,376/664,425/731,425/713	20885931	917,12089	2203	4300	6503	SO:0001819	synonymous_variant	53919	exon10			AGCTGCAAAACTC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1275A>G	12.37:g.20885931A>G		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			A|0.919;G|0.081	0.081	strong		0.448	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831628	7831628	+	Missense_Mutation	SNP	G	G	A	rs2277998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7831628G>A	ENST00000327325.5	+	5	989	c.871G>A	c.(871-873)Gac>Aac	p.D291N	CLEC4M_ENST00000334806.5_Missense_Mutation_p.D240N|CLEC4M_ENST00000248228.4_Missense_Mutation_p.D269N|CLEC4M_ENST00000595496.1_Missense_Mutation_p.D155N|CLEC4M_ENST00000596707.1_Missense_Mutation_p.D224N|CLEC4M_ENST00000597522.1_Missense_Mutation_p.D199N|CLEC4M_ENST00000394122.2_Missense_Mutation_p.D279N|CLEC4M_ENST00000359059.5_Missense_Mutation_p.D224N|CLEC4M_ENST00000357361.2_Missense_Mutation_p.D291N|CLEC4M_ENST00000596363.1_Missense_Mutation_p.D263N	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						PASS	.	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	107	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	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	
ACTN2	88	hgsc.bcm.edu	37	1	236908053	236908053	+	Silent	SNP	C	C	T	rs34827377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236908053C>T	ENST00000366578.4	+	12	1549	c.1383C>T	c.(1381-1383)atC>atT	p.I461I	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000546208.1_5'UTR|ACTN2_ENST00000542672.1_Silent_p.I461I	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	461					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)			TGGAGCAGATCGCAGCCATCG	0.652													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18183	0.0		0.003	False		,,,				2504	0.0				p.I461I		Atlas-SNP	.											.	ACTN2	191	.	0			c.C1383T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	61.0	52.0	55.0		1383	-9.9	0.1	1	dbSNP_126	55	16,8584	11.9+/-42.8	0,16,4284	yes	coding-synonymous	ACTN2	NM_001103.2		0,17,6486	TT,TC,CC		0.186,0.0227,0.1307		461/895	236908053	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	88	exon12			GCAGATCGCAGCC	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.1383C>T	1.37:g.236908053C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
CCDC129	223075	hgsc.bcm.edu	37	7	31594508	31594508	+	Silent	SNP	C	C	T	rs2286711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:31594508C>T	ENST00000407970.3	+	4	287	c.249C>T	c.(247-249)gaC>gaT	p.D83D	CCDC129_ENST00000319386.3_Silent_p.D83D|CCDC129_ENST00000451887.2_Silent_p.D109D|CCDC129_ENST00000409210.1_5'UTR|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	115	0	0		WXS	Illumina HiSeq	Phase_I	154	111	0.720779	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	
NLRX1	79671	hgsc.bcm.edu	37	11	119043656	119043656	+	Missense_Mutation	SNP	C	C	T	rs643423	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119043656C>T	ENST00000409109.1	+	4	774	c.187C>T	c.(187-189)Ccc>Tcc	p.P63S	NLRX1_ENST00000409991.1_Missense_Mutation_p.P63S|NLRX1_ENST00000409265.4_Missense_Mutation_p.P63S|NLRX1_ENST00000292199.2_Missense_Mutation_p.P63S|NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000525863.1_Missense_Mutation_p.P63S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	63			P -> S (in dbSNP:rs643423). {ECO:0000269|PubMed:12766759, ECO:0000269|PubMed:14702039}.		innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CGCTCCCCCACCCGGGAGGCA	0.632													T|||	3417	0.682308	0.6936	0.402	5008	,	,		16229	0.8829		0.5497	False		,,,				2504	0.7955				p.P63S		Atlas-SNP	.											.	NLRX1	128	.	0			c.C187T						PASS	.	T	SER/PRO,SER/PRO	2863,1537	486.0+/-360.5	927,1009,264	72.0	71.0	72.0		187,187	-4.8	0.0	11	dbSNP_83	72	4487,4103	563.2+/-388.1	1169,2149,977	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	74,74	2096,3158,1241	TT,TC,CC		47.7648,34.9318,43.418	benign,benign	63/976,63/922	119043656	7350,5640	2200	4295	6495	SO:0001583	missense	79671	exon4			CCCCCACCCGGGA	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.187C>T	11.37:g.119043656C>T	ENSP00000387334:p.Pro63Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	1387	0.63507326007326	319	0.6483739837398373	162	0.44751381215469616	496	0.8671328671328671	410	0.5408970976253298	T	0.040	-1.287510	0.01387	0.650682	0.522352	ENSG00000160703	ENST00000454811;ENST00000449394;ENST00000422249;ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T;T;T;T	0.69806	1.67;1.67;1.67;-0.3;-0.3;-0.43;-0.3;-0.43	5.4	-4.75	0.03239	.	1.123620	0.06731	N	0.776696	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.12013	0.005;0.0	B;B	0.06405	0.002;0.0	T	0.32161	-0.9917	9	0.06099	T	0.92	.	11.9448	0.52922	0.0:0.6535:0.1091:0.2373	rs643423;rs59337253;rs643423	63;63	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	63	ENSP00000400268:P63S;ENSP00000402801:P63S;ENSP00000402381:P63S;ENSP00000386851:P63S;ENSP00000292199:P63S;ENSP00000386858:P63S;ENSP00000387334:P63S;ENSP00000433442:P63S	ENSP00000292199:P63S	P	+	1	0	NLRX1	118548866	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.208000	0.01229	-1.172000	0.02762	-1.177000	0.01723	CCC	C|0.405;T|0.595	0.595	strong		0.632	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
F9	2158	hgsc.bcm.edu	37	X	138633280	138633280	+	Missense_Mutation	SNP	A	A	G	rs6048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:138633280A>G	ENST00000218099.2	+	6	587	c.580A>G	c.(580-582)Act>Gct	p.T194A	F9_ENST00000394090.2_Missense_Mutation_p.T156A	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	194			T -> A (in dbSNP:rs6048). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2994716, ECO:0000269|PubMed:3857619, ECO:0000269|PubMed:6329734}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	CCGTGCTGAGACTGTTTTTCC	0.373													A|||	550	0.145695	0.1036	0.1037	3775	,	,		14937	0.001		0.2237	False		,,,				2504	0.1176				p.T194A		Atlas-SNP	.											.	F9	107	.	0			c.A580G						PASS	.	A	ALA/THR	474,3361		17,377,63,1238,508	119.0	104.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	580	1.2	0.0	X	dbSNP_52	109	2007,4721		228,1013,538,1187,1334	yes	missense	F9	NM_000133.3	58	245,1390,601,2425,1842	GG,GA,G,AA,A		29.8306,12.3598,23.4876	benign	194/462	138633280	2481,8082	2203	4300	6503	SO:0001583	missense	2158	exon6			GCTGAGACTGTTT	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.580A>G	X.37:g.138633280A>G	ENSP00000218099:p.Thr194Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Missense_Mutation	SNP	ENST00000218099.2	37	CCDS14666.1	261	0.15732368896925858	32	0.06694560669456066	31	0.09281437125748503	0	0.0	115	0.18138801261829654	A	0.020	-1.437526	0.01098	0.123598	0.298306	ENSG00000101981	ENST00000218099;ENST00000394090	D;D	0.94417	-3.42;-3.42	4.94	1.21	0.21127	.	1.193210	0.05709	N	0.595504	T	0.00039	0.0001	L	0.60455	1.87	0.80722	P	0.0	B;B	0.12013	0.005;0.0	B;B	0.12837	0.008;0.003	T	0.12889	-1.0530	9	0.15499	T	0.54	.	3.6323	0.08137	0.5672:0.0:0.2742:0.1586	rs6048;rs3181844;rs52802349;rs59606308;rs6048	156;194	Q5FBE1;P00740	.;FA9_HUMAN	A	194;156	ENSP00000218099:T194A;ENSP00000377650:T156A	ENSP00000218099:T194A	T	+	1	0	F9	138460946	0.001000	0.12720	0.008000	0.14137	0.151000	0.21798	0.477000	0.22196	-0.118000	0.11851	0.430000	0.28490	ACT	A|0.797;0|0.004	.	strong		0.373	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1		
ZNF512B	57473	hgsc.bcm.edu	37	20	62598815	62598815	+	Silent	SNP	C	C	T	rs817330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	105	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	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	
OR4C46	119749	hgsc.bcm.edu	37	11	51515460	51515460	+	Missense_Mutation	SNP	C	C	T	rs11246606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:51515460C>T	ENST00000328188.1	+	1	179	c.179C>T	c.(178-180)tCc>tTc	p.S60F		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						ATGTACCTTTCCCTGGCCTAT	0.463													.|||	1194	0.238419	0.2375	0.2003	5008	,	,		17485	0.2272		0.1561	False		,,,				2504	0.363				p.S60F		Atlas-SNP	.											.	OR4C46	96	.	0			c.C179T						PASS	.	T	PHE/SER	943,3459		101,741,1359	236.0	227.0	230.0		179	2.6	0.9	11	dbSNP_120	230	1421,7171		124,1173,2999	no	missense	OR4C46	NM_001004703.1	155	225,1914,4358	TT,TC,CC		16.5386,21.4221,18.193	benign	60/310	51515460	2364,10630	2201	4296	6497	SO:0001583	missense	119749	exon1			ACCTTTCCCTGGC		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.179C>T	11.37:g.51515460C>T	ENSP00000329056:p.Ser60Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	354	0.1620879120879121	78	0.15853658536585366	53	0.1464088397790055	124	0.21678321678321677	99	0.13060686015831136	.	0.007	-1.951416	0.00470	0.214221	0.165386	ENSG00000185926	ENST00000328188	T	0.00792	5.69	2.63	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	N	0.000419	T	0.00012	0.0000	N	0.00000	-4.73	0.40897	P	0.01587700000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.40905	-0.9538	9	0.02654	T	1	.	6.1158	0.20126	0.0:0.1373:0.0:0.8627	rs11246606	60	A6NHA9	O4C46_HUMAN	F	60	ENSP00000329056:S60F	ENSP00000329056:S60F	S	+	2	0	OR4C46	51372036	0.935000	0.31712	0.862000	0.33874	0.014000	0.08584	4.214000	0.58527	0.272000	0.22027	-1.611000	0.00801	TCC	C|0.823;T|0.177	0.177	strong		0.463	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497961	32497961	+	Missense_Mutation	SNP	T	T	G	rs1064587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32497961T>G	ENST00000374975.3	-	1	103	c.41A>C	c.(40-42)aAg>aCg	p.K14T		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						CACTGTCAGCTTTGCCATGTA	0.587																																					p.K14T		Atlas-SNP	.											HLA-DRB5,colon,carcinoma,-1,2	HLA-DRB5	31	2	0			c.A41C						scavenged	.	A	THR/LYS	2754,1588		1124,506,541	54.0	60.0	58.0		41	-0.8	0.0	6	dbSNP_86	58	5681,2851		2479,723,1064	no	missense	HLA-DRB5	NM_002125.3	78	3603,1229,1605	GG,GT,TT		33.4154,36.573,34.4803	benign	14/267	32497961	8435,4439	2171	4266	6437	SO:0001583	missense	3127	exon1			GTCAGCTTTGCCA		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.41A>C	6.37:g.32497961T>G	ENSP00000364114:p.Lys14Thr	Somatic	115	8	0.0695652		WXS	Illumina HiSeq	Phase_I	84	77	0.916667	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	10.82	1.457039	0.26161	0.63427	0.665846	ENSG00000198502	ENST00000374975	T	0.00241	8.46	4.54	-0.77	0.11005	MHC classes I/II-like antigen recognition protein (1);	0.968061	0.08500	N	0.936540	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	0.36480	-0.9746	9	0.72032	D	0.01	.	0.2598	0.00217	0.2711:0.1456:0.285:0.2982	.	14	Q30154	DRB5_HUMAN	T	14	ENSP00000364114:K14T	ENSP00000364114:K14T	K	-	2	0	HLA-DRB5	32605939	0.121000	0.22262	0.001000	0.08648	0.000000	0.00434	0.591000	0.23969	-0.062000	0.13088	-1.634000	0.00779	AAG	G|0.051;C|0.542;A|0.407	0.051	strong		0.587	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
PALM	5064	hgsc.bcm.edu	37	19	746712	746712	+	Silent	SNP	C	C	T	rs10421265	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:746712C>T	ENST00000338448.5	+	9	1108	c.1062C>T	c.(1060-1062)gcC>gcT	p.A354A	PALM_ENST00000593172.1_3'UTR|PALM_ENST00000264560.7_Silent_p.A310A	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	30	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	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	
GREB1	9687	hgsc.bcm.edu	37	2	11758536	11758536	+	Missense_Mutation	SNP	C	C	A	rs61741332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11758536C>A	ENST00000381486.2	+	22	3835	c.3535C>A	c.(3535-3537)Ccc>Acc	p.P1179T	GREB1_ENST00000234142.5_Missense_Mutation_p.P1179T|GREB1_ENST00000396123.1_Missense_Mutation_p.P177T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1179	Ser-rich.					integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAAACAGAGGCCCCGGGCAAG	0.721													C|||	32	0.00638978	0.0008	0.0159	5008	,	,		14493	0.001		0.0159	False		,,,				2504	0.0031				p.P1179T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C3535A						PASS	.	C	THR/PRO	17,3853		0,17,1918	9.0	12.0	11.0		3535	1.9	0.0	2	dbSNP_129	11	145,8019		3,139,3940	no	missense	GREB1	NM_014668.3	38	3,156,5858	AA,AC,CC		1.7761,0.4393,1.3462	benign	1179/1950	11758536	162,11872	1935	4082	6017	SO:0001583	missense	9687	exon22			CAGAGGCCCCGGG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.3535C>A	2.37:g.11758536C>A	ENSP00000370896:p.Pro1179Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	12	0.0158311345646438	C	9.915	1.210717	0.22289	0.004393	0.017761	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.21543	3.34;3.34;2.0	4.84	1.93	0.25924	.	2.089630	0.01658	N	0.024926	T	0.04998	0.0134	N	0.03608	-0.345	0.09310	N	1	B	0.22211	0.066	B	0.23419	0.046	T	0.24083	-1.0170	10	0.22109	T	0.4	-25.9697	5.8172	0.18500	0.1667:0.6621:0.0:0.1712	rs61741332	1179	Q4ZG55	GREB1_HUMAN	T	1179;1179;177	ENSP00000370896:P1179T;ENSP00000234142:P1179T;ENSP00000379429:P177T	ENSP00000234142:P1179T	P	+	1	0	GREB1	11675987	0.036000	0.19791	0.000000	0.03702	0.357000	0.29423	1.934000	0.40163	0.084000	0.17077	0.643000	0.83706	CCC	C|0.989;A|0.011	0.011	strong		0.721	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
SP8	221833	hgsc.bcm.edu	37	7	20824956	20824956	+	Silent	SNP	C	C	G	rs201180283		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20824956C>G	ENST00000361443.4	-	3	663	c.426G>C	c.(424-426)ggG>ggC	p.G142G	SP8_ENST00000418710.2_Silent_p.G160G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	142					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						cgccgccgcccccgccgccgc	0.741																																					p.G160G		Atlas-SNP	.											.	SP8	43	.	0			c.G480C						PASS	.						2.0	2.0	2.0					7																	20824956		542	1367	1909	SO:0001819	synonymous_variant	221833	exon2			GCCGCCCCCGCCG		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.426G>C	7.37:g.20824956C>G		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	weak		0.741	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
LPIN1	23175	hgsc.bcm.edu	37	2	11911761	11911761	+	Silent	SNP	C	C	T	rs11538448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11911761C>T	ENST00000256720.2	+	4	645	c.552C>T	c.(550-552)atC>atT	p.I184I	LPIN1_ENST00000396098.1_Silent_p.I190I|LPIN1_ENST00000396099.1_Silent_p.I190I|LPIN1_ENST00000449576.2_Silent_p.I233I|LPIN1_ENST00000425416.2_Silent_p.I190I	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	184					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TGTTCCCCATCGAGATGAGCT	0.493													C|||	254	0.0507188	0.0061	0.0692	5008	,	,		18791	0.001		0.1382	False		,,,				2504	0.0593				p.I233I		Atlas-SNP	.											.	LPIN1	99	.	0			c.C699T						PASS	.	C		123,4283	84.8+/-123.5	0,123,2080	57.0	41.0	46.0		552	-9.1	1.0	2	dbSNP_120	46	1208,7392	234.4+/-267.4	83,1042,3175	no	coding-synonymous	LPIN1	NM_145693.1		83,1165,5255	TT,TC,CC		14.0465,2.7916,10.2337		184/891	11911761	1331,11675	2203	4300	6503	SO:0001819	synonymous_variant	23175	exon5			CCCCATCGAGATG	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.552C>T	2.37:g.11911761C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			C|0.912;T|0.088	0.088	strong		0.493	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
JRK	8629	hgsc.bcm.edu	37	8	143746701	143746701	+	RNA	SNP	A	A	G	rs3802232	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143746701A>G	ENST00000507178.2	-	0	1109							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ccacccaggcattcccctggg	0.567													G|||	2639	0.526957	0.7179	0.3213	5008	,	,		18708	0.5188		0.3907	False		,,,				2504	0.5634				p.N259N		Atlas-SNP	.											.	.	.	.	0			c.T777C						PASS	.	G	,	1645,1183		507,631,276	14.0	17.0	16.0		777,777	-1.2	0.0	8	dbSNP_107	16	2041,3571		395,1251,1160	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	902,1882,1436	GG,GA,AA		36.3685,41.8317,43.673	,	259/557,259/569	143746701	3686,4754	1414	2806	4220			8629	exon2			CCAGGCATTCCCC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746701A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.479;G|0.521	0.521	strong		0.567	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
POM121L12	285877	hgsc.bcm.edu	37	7	53103370	53103370	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:53103370C>T	ENST00000408890.4	+	1	22	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	2										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CAGCCATGGGCGCTGCAGCTC	0.701																																					p.G2G		Atlas-SNP	.											.	POM121L12	146	.	0			c.C6T						PASS	.																																			SO:0001819	synonymous_variant	285877	exon1			CATGGGCGCTGCA		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.6C>T	7.37:g.53103370C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	53	0.736111	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			.	.	none		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
FAM149A	25854	hgsc.bcm.edu	37	4	187078866	187078866	+	Missense_Mutation	SNP	C	C	T	rs2276922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187078866C>T	ENST00000356371.5	+	8	1595	c.1595C>T	c.(1594-1596)cCg>cTg	p.P532L	FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000227065.4_Missense_Mutation_p.P241L|FAM149A_ENST00000502970.1_Missense_Mutation_p.P241L|FAM149A_ENST00000503432.1_Missense_Mutation_p.P241L|FAM149A_ENST00000514153.1_Missense_Mutation_p.P241L|FAM149A_ENST00000389354.5_Missense_Mutation_p.P241L			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	532			P -> L (in dbSNP:rs2276922).							breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CGTCTGAACCCGCCCCAGGTC	0.597													C|||	1333	0.266174	0.4554	0.2003	5008	,	,		17440	0.0972		0.2614	False		,,,				2504	0.2362				p.P241L		Atlas-SNP	.											FAM149A,right_upper_lobe,carcinoma,-1,1	FAM149A	52	1	0			c.C722T						PASS	.	C	LEU/PRO,LEU/PRO	1857,2549	536.7+/-374.5	387,1083,733	53.0	53.0	53.0		722,722	2.9	0.0	4	dbSNP_100	53	2214,6386	376.0+/-338.0	283,1648,2369	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	98,98	670,2731,3102	TT,TC,CC		25.7442,42.1471,31.3009	probably-damaging,probably-damaging	241/483,241/483	187078866	4071,8935	2203	4300	6503	SO:0001583	missense	25854	exon7			TGAACCCGCCCCA	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1595C>T	4.37:g.187078866C>T	ENSP00000348732:p.Pro532Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		562	0.2573260073260073	229	0.4654471544715447	87	0.24033149171270718	48	0.08391608391608392	198	0.2612137203166227	C	12.17	1.857297	0.32791	0.421471	0.257442	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.13089	2.68;2.62;2.68;2.68;2.68;2.68	5.6	2.89	0.33648	.	0.229225	0.38436	N	0.001690	T	0.00012	0.0000	L	0.48362	1.52	0.54753	P	1.3000000000040757E-5	B;B;P	0.38788	0.333;0.399;0.647	B;B;B	0.26517	0.061;0.045;0.07	T	0.47686	-0.9098	9	0.59425	D	0.04	-9.1334	8.5296	0.33326	0.0:0.7451:0.0:0.2549	rs2276922;rs52822013;rs58499361;rs2276922	532;532;241	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	L	241;532;241;241;241;241	ENSP00000426835:P241L;ENSP00000348732:P532L;ENSP00000227065:P241L;ENSP00000427155:P241L;ENSP00000424380:P241L;ENSP00000374005:P241L	ENSP00000227065:P241L	P	+	2	0	FAM149A	187315860	0.009000	0.17119	0.005000	0.12908	0.002000	0.02628	0.968000	0.29357	0.304000	0.22809	-0.272000	0.10252	CCG	C|0.713;T|0.287	0.287	strong		0.597	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71376999	71376999	+	Missense_Mutation	SNP	G	G	A	rs6574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71376999G>A	ENST00000244230.2	+	11	2252	c.1900G>A	c.(1900-1902)Gaa>Aaa	p.E634K		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	634			E -> K (in dbSNP:rs6574).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						ATTGCAGGATGAAGGTAAAGA	0.318													G|||	1429	0.285343	0.1838	0.3905	5008	,	,		17497	0.2649		0.2942	False		,,,				2504	0.3599				p.E634K		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G1900A						PASS	.	G	LYS/GLU	834,3572	321.8+/-297.3	82,670,1451	138.0	144.0	142.0		1900	5.8	1.0	2	dbSNP_52	142	2537,6059	412.1+/-350.7	394,1749,2155	yes	missense	MPHOSPH10	NM_005791.2	56	476,2419,3606	AA,AG,GG		29.5137,18.9287,25.9268	possibly-damaging	634/682	71376999	3371,9631	2203	4298	6501	SO:0001583	missense	10199	exon11			CAGGATGAAGGTA	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1900G>A	2.37:g.71376999G>A	ENSP00000244230:p.Glu634Lys	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	288	126	0.4375	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	626	0.2866300366300366	101	0.20528455284552846	134	0.3701657458563536	175	0.30594405594405594	216	0.2849604221635884	G	21.4	4.150114	0.78001	0.189287	0.295137	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.13307	2.6;2.6	5.85	5.85	0.93711	.	0.111229	0.64402	D	0.000010	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.99999884409	D	0.54964	0.969	P	0.58077	0.832	T	0.52873	-0.8517	9	0.12103	T	0.63	.	18.0364	0.89305	0.0:0.0:1.0:0.0	rs6574;rs357743;rs1129261;rs3177500;rs3186969;rs11549403;rs17429514;rs52821931;rs58145471;rs6574	634	O00566	MPP10_HUMAN	K	634;494	ENSP00000244230:E634K;ENSP00000393034:E494K	ENSP00000244230:E634K	E	+	1	0	MPHOSPH10	71230507	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.869000	0.92326	2.941000	0.99782	0.655000	0.94253	GAA	G|0.736;T|0.001	.	strong		0.318	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
DCDC2	51473	hgsc.bcm.edu	37	6	24302046	24302046	+	Missense_Mutation	SNP	G	G	C	rs33914824	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24302046G>C	ENST00000378454.3	-	4	755	c.454C>G	c.(454-456)Cca>Gca	p.P152A		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	152	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		P -> A (in dbSNP:rs33914824).		cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				CGAGAAGCTGGGTTTATGAGG	0.438													G|||	189	0.0377396	0.0356	0.0317	5008	,	,		18602	0.0129		0.0358	False		,,,				2504	0.0726				p.P152A		Atlas-SNP	.											.	DCDC2	53	.	0			c.C454G						PASS	.	G	ALA/PRO,ALA/PRO	159,4247	110.4+/-148.6	5,149,2049	116.0	114.0	115.0		454,454	5.9	0.9	6	dbSNP_126	115	361,8239	120.2+/-179.5	9,343,3948	yes	missense,missense	DCDC2	NM_001195610.1,NM_016356.3	27,27	14,492,5997	CC,CG,GG		4.1977,3.6087,3.9982	probably-damaging,probably-damaging	152/477,152/477	24302046	520,12486	2203	4300	6503	SO:0001583	missense	51473	exon5			AAGCTGGGTTTAT	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.454C>G	6.37:g.24302046G>C	ENSP00000367715:p.Pro152Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	71	0.03250915750915751	18	0.036585365853658534	12	0.03314917127071823	12	0.02097902097902098	29	0.03825857519788918	G	27.0	4.793825	0.90453	0.036087	0.041977	ENSG00000146038	ENST00000378454	D	0.93659	-3.26	5.87	5.87	0.94306	Doublecortin domain (4);	0.050337	0.85682	D	0.000000	D	0.95316	0.8480	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.92661	0.6141	10	0.30854	T	0.27	-15.9632	20.5827	0.99408	0.0:0.0:1.0:0.0	rs33914824	152	Q9UHG0	DCDC2_HUMAN	A	152	ENSP00000367715:P152A	ENSP00000367715:P152A	P	-	1	0	DCDC2	24410025	1.000000	0.71417	0.893000	0.35052	0.998000	0.95712	5.795000	0.69074	2.941000	0.99782	0.655000	0.94253	CCA	G|0.959;C|0.041	0.041	strong		0.438	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
KMT2C	58508	hgsc.bcm.edu	37	7	151859683	151859683	+	Missense_Mutation	SNP	G	G	A	rs74483926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:151859683G>A	ENST00000262189.6	-	43	11197	c.10979C>T	c.(10978-10980)tCg>tTg	p.S3660L	KMT2C_ENST00000355193.2_Missense_Mutation_p.S3660L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3660					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)										TGGTTCCACCGACTCTTGGTC	0.512													G|||	290	0.0579073	0.003	0.0216	5008	,	,		16329	0.1478		0.0408	False		,,,				2504	0.0828				p.S3660L		Atlas-SNP	.											.	MLL3	1564	.	0			c.C10979T						PASS	.	G	LEU/SER	40,4366	43.8+/-77.6	0,40,2163	110.0	113.0	112.0		10979	1.7	0.0	7	dbSNP_131	112	329,8271	115.3+/-175.2	8,313,3979	yes	missense	MLL3	NM_170606.2	145	8,353,6142	AA,AG,GG		3.8256,0.9079,2.8372	benign	3660/4912	151859683	369,12637	2203	4300	6503	SO:0001583	missense	58508	exon43			TCCACCGACTCTT	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.10979C>T	7.37:g.151859683G>A	ENSP00000262189:p.Ser3660Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	144	0.06593406593406594	5	0.01016260162601626	6	0.016574585635359115	97	0.16958041958041958	36	0.047493403693931395	G	9.435	1.086440	0.20390	0.009079	0.038256	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877	D;D;D	0.89123	-1.77;-1.8;-2.47	5.51	1.72	0.24424	.	1.114660	0.07039	N	0.829852	T	0.01092	0.0036	L	0.47716	1.5	0.58432	P	2.9999999999752447E-6	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.30822	-0.9965	9	0.20046	T	0.44	.	10.6226	0.45489	0.2616:0.0:0.7384:0.0	.	3660;2721;3660	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	L	3660;3660;246	ENSP00000262189:S3660L;ENSP00000347325:S3660L;ENSP00000410411:S246L	ENSP00000262189:S3660L	S	-	2	0	MLL3	151490616	0.010000	0.17322	0.000000	0.03702	0.000000	0.00434	1.887000	0.39698	0.037000	0.15575	-0.827000	0.03088	TCG	G|0.962;A|0.038	0.038	strong		0.512	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
NBPF10	100132406	hgsc.bcm.edu	37	1	145297661	145297661	+	Missense_Mutation	SNP	C	C	A	rs4068083	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145297661C>A	ENST00000342960.5	+	4	571	c.536C>A	c.(535-537)gCt>gAt	p.A179D	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	179	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.A179D(2)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTTGAGGAGGCTGAGAAAGTA	0.433																																					p.A179D		Atlas-SNP	.											NBPF10,NS,carcinoma,0,2	NBPF10	221	2	2	Substitution - Missense(2)	kidney(2)	c.C536A						scavenged	.						30.0	25.0	26.0					1																	145297661		692	1591	2283	SO:0001583	missense	100132406	exon4			AGGAGGCTGAGAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.536C>A	1.37:g.145297661C>A	ENSP00000345684:p.Ala179Asp	Somatic	103	4	0.038835		WXS	Illumina HiSeq	Phase_I	43	8	0.186047	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	0.030	-1.338203	0.01287	.	.	ENSG00000163386	ENST00000369339;ENST00000448873;ENST00000342960	T	0.03004	4.08	0.837	-1.67	0.08238	.	.	.	.	.	T	0.00440	0.0014	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.49204	-0.8964	7	0.05620	T	0.96	.	0.0757	0.00026	0.283:0.2521:0.2163:0.2486	rs4068083	.	.	.	D	179;104;179	ENSP00000345684:A179D	ENSP00000345684:A179D	A	+	2	0	NBPF10	144009018	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.906000	0.04071	-1.916000	0.01075	-1.492000	0.00969	GCT	C|0.583;A|0.417	0.417	strong		0.433	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
USP15	9958	hgsc.bcm.edu	37	12	62696599	62696599	+	Silent	SNP	C	C	T	rs11174420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:62696599C>T	ENST00000280377.5	+	3	304	c.246C>T	c.(244-246)caC>caT	p.H82H	USP15_ENST00000393654.3_Silent_p.H82H|USP15_ENST00000312635.6_Silent_p.H82H|USP15_ENST00000353364.3_Silent_p.H82H|USP15_ENST00000550632.1_3'UTR	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	82	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				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)		TTAAGGAACACCTTATTGATG	0.363													T|||	1595	0.31849	0.4849	0.2392	5008	,	,		16503	0.1528		0.3082	False		,,,				2504	0.3313				p.H82H	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.C246T						PASS	.	T		2023,2383	611.5+/-391.8	469,1085,649	141.0	137.0	138.0		246	2.1	1.0	12	dbSNP_120	138	2637,5963	686.7+/-404.1	399,1839,2062	no	coding-synonymous	USP15	NM_006313.1		868,2924,2711	TT,TC,CC		30.6628,45.9147,35.8296		82/953	62696599	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	9958	exon3			GGAACACCTTATT	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.246C>T	12.37:g.62696599C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1	647	0.29624542124542125	235	0.47764227642276424	95	0.26243093922651933	96	0.16783216783216784	221	0.29155672823219	T	9.131	1.011384	0.19277	0.459147	0.306628	ENSG00000135655	ENST00000549237	.	.	.	5.72	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48080	-0.9066	3	.	.	.	-16.2145	9.3407	0.38079	0.0:0.2693:0.0:0.7307	rs11174420;rs61396060;rs11174420	.	.	.	I	78	.	.	T	+	2	0	USP15	60982866	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	1.279000	0.33191	-0.090000	0.12462	-0.381000	0.06696	ACC	C|0.662;T|0.338	0.338	strong		0.363	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
TNFRSF10B	8795	hgsc.bcm.edu	37	8	22900701	22900701	+	Missense_Mutation	SNP	G	G	A	rs1047266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:22900701G>A	ENST00000276431.4	-	2	484	c.200C>T	c.(199-201)gCg>gTg	p.A67V	TNFRSF10B_ENST00000519910.1_5'UTR|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.A67V|TNFRSF10B_ENST00000542226.1_Intron	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	67			A -> V (in dbSNP:rs1047266). {ECO:0000269|PubMed:10072170, ECO:0000269|PubMed:9285725, ECO:0000269|PubMed:9325248, ECO:0000269|PubMed:9373179, ECO:0000269|PubMed:9430227, ECO:0000269|Ref.11}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)			NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		TTGTGGGGCCGCTCTCTGCTG	0.572													G|||	500	0.0998403	0.0038	0.1542	5008	,	,		18677	0.2867		0.0616	False		,,,				2504	0.0378				p.A67V	GBM(94;1064 1342 1839 21060 42553)	Atlas-SNP	.											.	TNFRSF10B	34	.	0			c.C200T						PASS	.	G	VAL/ALA,VAL/ALA	79,4327	69.8+/-107.6	0,79,2124	123.0	103.0	110.0		200,200	2.6	0.0	8	dbSNP_86	110	601,7999	158.9+/-212.3	30,541,3729	yes	missense,missense	TNFRSF10B	NM_003842.4,NM_147187.2	64,64	30,620,5853	AA,AG,GG		6.9884,1.793,5.2284	possibly-damaging,possibly-damaging	67/441,67/412	22900701	680,12326	2203	4300	6503	SO:0001583	missense	8795	exon2			GGGGCCGCTCTCT	AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.200C>T	8.37:g.22900701G>A	ENSP00000276431:p.Ala67Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_147187	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	274	0.12545787545787546	1	0.0020325203252032522	57	0.1574585635359116	166	0.2902097902097902	50	0.06596306068601583	g	11.04	1.521897	0.27211	0.01793	0.069884	ENSG00000120889	ENST00000276431;ENST00000347739	D;D	0.85629	-1.8;-2.01	2.57	2.57	0.30868	.	7739.340000	0.00357	U	0.000023	T	0.00039	0.0001	N	0.11789	0.175	0.45025	P	0.0019559999999999578	D;D	0.89917	1.0;1.0	D;D	0.72625	0.951;0.978	T	0.60717	-0.7208	9	0.02654	T	1	.	8.7945	0.34872	0.0:0.0:1.0:0.0	rs1047266;rs3187298;rs52805544;rs61593150;rs1047266	67;67	O14763;O14763-2	TR10B_HUMAN;.	V	67	ENSP00000276431:A67V;ENSP00000317859:A67V	ENSP00000276431:A67V	A	-	2	0	TNFRSF10B	22956646	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.116000	0.10724	1.744000	0.51775	0.563000	0.77884	GCG	G|0.919;A|0.081	0.081	strong		0.572	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187	
SREK1IP1	285672	hgsc.bcm.edu	37	5	64020316	64020316	+	Missense_Mutation	SNP	T	T	G	rs80170948	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:64020316T>G	ENST00000513458.4	-	5	530	c.363A>C	c.(361-363)aaA>aaC	p.K121N		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	121	Lys-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						atttactctttttttcttttt	0.299													T|||	72	0.014377	0.0015	0.0202	5008	,	,		17285	0.0		0.0487	False		,,,				2504	0.0072				p.K121N		Atlas-SNP	.											.	SREK1IP1	28	.	0			c.A363C						PASS	.	T	ASN/LYS	33,4327		0,33,2147	41.0	35.0	37.0		363	3.0	1.0	5	dbSNP_132	37	329,8225		7,315,3955	yes	missense	SREK1IP1	NM_173829.3	94	7,348,6102	GG,GT,TT		3.8462,0.7569,2.8032	benign	121/156	64020316	362,12552	2180	4277	6457	SO:0001583	missense	285672	exon5			ACTCTTTTTTTCT	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"""p18 splicing regulatory protein"""		"""SFRS12-interacting protein 1"""	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.363A>C	5.37:g.64020316T>G	ENSP00000427401:p.Lys121Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_173829	Q32NC8	Missense_Mutation	SNP	ENST00000513458.4	37	CCDS34171.1	46	0.021062271062271064	0	0.0	9	0.024861878453038673	0	0.0	37	0.048812664907651716	T	13.49	2.254241	0.39896	0.007569	0.038462	ENSG00000153006	ENST00000513458	.	.	.	5.42	3.05	0.35203	.	0.092655	0.64402	D	0.000001	T	0.11239	0.0274	L	0.47716	1.5	0.39389	D	0.966385	B	0.26635	0.155	B	0.23716	0.048	T	0.07731	-1.0757	9	0.40728	T	0.16	0.212	6.9507	0.24544	0.0:0.1814:0.0:0.8186	.	121	Q8N9Q2	SR1IP_HUMAN	N	121	.	ENSP00000427401:K121N	K	-	3	2	SREK1IP1	64056072	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.793000	0.26944	0.386000	0.24997	0.533000	0.62120	AAA	T|0.972;G|0.028	0.028	strong		0.299	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184566	72184566	+	Missense_Mutation	SNP	C	C	T	rs35370634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	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	
CNTN5	53942	hgsc.bcm.edu	37	11	99690376	99690376	+	Nonsense_Mutation	SNP	C	C	T	rs12292659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:99690376C>T	ENST00000524871.1	+	4	447	c.157C>T	c.(157-159)Cga>Tga	p.R53*	CNTN5_ENST00000527185.1_Nonsense_Mutation_p.R53*|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000279463.3_Nonsense_Mutation_p.R53*|CNTN5_ENST00000528682.1_Nonsense_Mutation_p.R53*	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	53					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AACCAGACCACGATACAGCAG	0.428																																					p.R53X		Atlas-SNP	.											.	CNTN5	324	.	0			c.C157T						PASS	.	C	stop/ARG,	827,2987		0,827,1080	115.0	115.0	115.0		157,	3.0	0.9	11	dbSNP_120	115	2016,6260		0,2016,2122	yes	stop-gained,intron	CNTN5	NM_014361.3,NM_175566.2	,	0,2843,3202	TT,TC,CC		24.3596,21.6833,23.5153	,	53/1101,	99690376	2843,9247	1907	4138	6045	SO:0001587	stop_gained	53942	exon3			AGACCACGATACA	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.157C>T	11.37:g.99690376C>T	ENSP00000435637:p.Arg53*	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	102	35	0.343137	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Nonsense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.456071	0.84209	0.216833	0.243596	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	.	.	.	5.06	2.96	0.34315	.	0.104565	0.37483	N	0.002068	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0077	0.47644	0.1446:0.7156:0.1398:0.0	rs12292659;rs12292659	.	.	.	X	53	.	ENSP00000279463:R53X	R	+	1	2	CNTN5	99195586	0.798000	0.28890	0.915000	0.36163	0.672000	0.39443	1.290000	0.33319	1.385000	0.46445	0.650000	0.86243	CGA	C|0.822;T|0.178	0.178	strong		0.428	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
PKD1L1	168507	hgsc.bcm.edu	37	7	47968927	47968927	+	Missense_Mutation	SNP	C	C	A	rs2686817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:47968927C>A	ENST00000289672.2	-	7	984	c.934G>T	c.(934-936)Gtt>Ttt	p.V312F		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	312			V -> F (in dbSNP:rs2686817).		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						GCCATATGAACACGGAATCCC	0.498													C|||	2428	0.484824	0.5136	0.5072	5008	,	,		19692	0.5089		0.505	False		,,,				2504	0.3845				p.V312F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G934T						PASS	.	C	PHE/VAL	2182,2224	586.2+/-386.4	556,1070,577	156.0	162.0	160.0		934	2.0	0.0	7	dbSNP_100	160	4220,4380	571.8+/-389.6	1029,2162,1109	yes	missense	PKD1L1	NM_138295.3	50	1585,3232,1686	AA,AC,CC		49.0698,49.5234,49.2234	probably-damaging	312/2850	47968927	6402,6604	2203	4300	6503	SO:0001583	missense	168507	exon7			TATGAACACGGAA	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.934G>T	7.37:g.47968927C>A	ENSP00000289672:p.Val312Phe	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	249	249	1	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	1075	0.49221611721611724	230	0.46747967479674796	174	0.48066298342541436	279	0.48776223776223776	392	0.5171503957783641	C	13.77	2.335500	0.41398	0.495234	0.490698	ENSG00000158683	ENST00000289672	T	0.42131	0.98	3.97	2.03	0.26663	.	3.865810	0.00589	N	0.000357	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.42882	-0.9425	9	0.87932	D	0	-11.5068	5.4202	0.16396	0.0:0.68:0.2049:0.1151	rs2686817;rs2686817	312	Q8TDX9	PK1L1_HUMAN	F	312	ENSP00000289672:V312F	ENSP00000289672:V312F	V	-	1	0	PKD1L1	47935452	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.448000	0.21726	0.395000	0.25257	0.579000	0.79373	GTT	C|0.513;A|0.487	0.487	strong		0.498	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
TPRX1	284355	hgsc.bcm.edu	37	19	48305626	48305626	+	Silent	SNP	T	T	C	rs62130757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48305626T>C	ENST00000322175.3	-	2	797	c.642A>G	c.(640-642)ccA>ccG	p.P214P	TPRX1_ENST00000543508.1_Silent_p.P204P|TPRX1_ENST00000535759.1_Silent_p.P311P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	214	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		ggcctgagattgggcctgaga	0.672													T|||	691	0.137979	0.1808	0.0908	5008	,	,		12921	0.1984		0.0547	False		,,,				2504	0.137				p.P214P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.A642G						PASS	.	T		443,3269		25,393,1438	12.0	10.0	11.0		642	0.4	0.0	19	dbSNP_129	11	352,6916		8,336,3290	no	coding-synonymous	TPRX1	NM_198479.2		33,729,4728	CC,CT,TT		4.8431,11.9343,7.2404		214/412	48305626	795,10185	1856	3634	5490	SO:0001819	synonymous_variant	284355	exon2			TGAGATTGGGCCT		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.642A>G	19.37:g.48305626T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			T|0.887;C|0.113	0.113	strong		0.672	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
CRTAC1	55118	hgsc.bcm.edu	37	10	99655648	99655648	+	Silent	SNP	G	G	T	rs577537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99655648G>T	ENST00000370597.3	-	10	1666	c.1311C>A	c.(1309-1311)ggC>ggA	p.G437G	CRTAC1_ENST00000370591.2_Silent_p.G437G|CRTAC1_ENST00000298819.4_Silent_p.G437G	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	437						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)		GCACCTGATTGCCCCGGAAGA	0.622													G|||	170	0.0339457	0.034	0.0375	5008	,	,		17944	0.0		0.0726	False		,,,				2504	0.0266				p.G437G		Atlas-SNP	.											.	CRTAC1	86	.	0			c.C1311A						PASS	.	G	,	206,4200	128.2+/-165.1	6,194,2003	89.0	76.0	81.0		1311,1311	-1.0	0.9	10	dbSNP_83	81	536,8064	148.5+/-203.7	19,498,3783	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	25,692,5786	TT,TG,GG		6.2326,4.6754,5.7051	,	437/646,437/662	99655648	742,12264	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon10			CTGATTGCCCCGG	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.1311C>A	10.37:g.99655648G>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			G|0.950;T|0.050	0.050	strong		0.622	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64612845C>T	ENST00000344113.4	+	84	15755	c.15543C>T	c.(15541-15543)atC>atT	p.I5181I	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.I1815I|SYNE2_ENST00000357395.3_Silent_p.I1566I|SYNE2_ENST00000394768.2_Silent_p.I1566I|SYNE2_ENST00000554584.1_Silent_p.I5098I|SYNE2_ENST00000358025.3_Silent_p.I5181I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5181					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.I5181I(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAATACAGATCTTGAACAACT	0.353													T|||	2213	0.441893	0.5726	0.3977	5008	,	,		17561	0.504		0.3469	False		,,,				2504	0.3303				p.I5181I		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	prostate(1)	c.C15543T						scavenged	.	T	,	2373,2033	561.1+/-380.6	642,1089,472	59.0	65.0	63.0		15543,15543	-1.2	0.8	14	dbSNP_120	63	2918,5682	668.0+/-402.5	502,1914,1884	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1144,3003,2356	TT,TC,CC		33.9302,46.1416,40.6812	,	5181/6886,5181/6908	64612845	5291,7715	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon84			ACAGATCTTGAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15543C>T	14.37:g.64612845C>T		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.567;T|0.433	0.433	strong		0.353	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
XYLT2	64132	hgsc.bcm.edu	37	17	48431021	48431021	+	Missense_Mutation	SNP	G	G	A	rs113835371	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48431021G>A	ENST00000017003.2	+	2	215	c.166G>A	c.(166-168)Gac>Aac	p.D56N	XYLT2_ENST00000507602.1_Missense_Mutation_p.D56N	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	56			D -> N. {ECO:0000269|PubMed:16571645}.		chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					ACGGCCACTGGACCCTGGCGA	0.622													G|||	28	0.00559105	0.0	0.0216	5008	,	,		17247	0.0		0.0099	False		,,,				2504	0.0031				p.D56N		Atlas-SNP	.											.	XYLT2	51	.	0			c.G166A	GRCh37	CM064362	XYLT2	M	rs113835371	PASS	.	G	ASN/ASP	16,4378		0,16,2181	14.0	13.0	14.0		166	4.4	1.0	17	dbSNP_132	14	118,8466		1,116,4175	yes	missense	XYLT2	NM_022167.2	23	1,132,6356	AA,AG,GG		1.3747,0.3641,1.0325	benign	56/866	48431021	134,12844	2197	4292	6489	SO:0001583	missense	64132	exon2			CCACTGGACCCTG	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.166G>A	17.37:g.48431021G>A	ENSP00000017003:p.Asp56Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	21	0.009615384615384616	0	0.0	11	0.03038674033149171	0	0.0	10	0.013192612137203167	G	14.87	2.663214	0.47572	0.003641	0.013747	ENSG00000015532	ENST00000017003;ENST00000509778;ENST00000507602	T;T;T	0.64438	3.63;-0.1;3.08	4.38	4.38	0.52667	.	0.157923	0.56097	D	0.000030	T	0.17152	0.0412	N	0.03608	-0.345	0.46849	D	0.999224	B	0.12013	0.005	B	0.14023	0.01	T	0.09840	-1.0656	10	0.31617	T	0.26	-26.3183	15.2929	0.73879	0.0:0.0:1.0:0.0	.	56	Q9H1B5	XYLT2_HUMAN	N	56;41;56	ENSP00000017003:D56N;ENSP00000425511:D41N;ENSP00000426501:D56N	ENSP00000017003:D56N	D	+	1	0	XYLT2	45786020	1.000000	0.71417	0.995000	0.50966	0.772000	0.43724	6.544000	0.73878	2.286000	0.76751	0.313000	0.20887	GAC	G|0.991;A|0.009	0.009	strong		0.622	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
OR4N2	390429	hgsc.bcm.edu	37	14	20295834	20295834	+	Missense_Mutation	SNP	T	T	C	rs2801164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	225	0	0		WXS	Illumina HiSeq	Phase_I	244	45	0.184426	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		
KCNMB3	27094	hgsc.bcm.edu	37	3	178968660	178968660	+	Missense_Mutation	SNP	T	T	C	rs1170672	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:178968660T>C	ENST00000314235.5	-	2	642	c.131A>G	c.(130-132)gAt>gGt	p.D44G	KCNMB3_ENST00000497599.1_Missense_Mutation_p.D42G|KCNMB3_ENST00000392685.2_Missense_Mutation_p.D40G|KCNMB3_ENST00000349697.2_Missense_Mutation_p.D42G|KCNMB3_ENST00000485523.1_Missense_Mutation_p.D22G	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	44			D -> G (in dbSNP:rs1170672).		action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	CTTGTGCACATCTAGTGGGTC	0.542													T|||	347	0.0692891	0.0408	0.0375	5008	,	,		18388	0.005		0.0954	False		,,,				2504	0.1697				p.D44G		Atlas-SNP	.											.	KCNMB3	46	.	0			c.A131G						PASS	.	T	GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP,GLY/ASP	233,4173	137.3+/-173.1	6,221,1976	124.0	112.0	116.0		125,131,125,65,119	2.3	0.0	3	dbSNP_87	116	991,7609	214.5+/-254.1	63,865,3372	yes	missense,missense,missense,missense,missense	KCNMB3	NM_001163677.1,NM_014407.3,NM_171828.1,NM_171829.2,NM_171830.1	94,94,94,94,94	69,1086,5348	CC,CT,TT		11.5233,5.2882,9.411	benign,benign,benign,benign,benign	42/174,44/280,42/278,22/258,40/276	178968660	1224,11782	2203	4300	6503	SO:0001583	missense	27094	exon2			TGCACATCTAGTG	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.131A>G	3.37:g.178968660T>C	ENSP00000319370:p.Asp44Gly	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	205	85	0.414634	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000314235.5	37	CCDS3226.1	120	0.054945054945054944	35	0.07113821138211382	12	0.03314917127071823	3	0.005244755244755245	70	0.09234828496042216	T	14.90	2.672063	0.47781	0.052882	0.115233	ENSG00000171121	ENST00000497599;ENST00000392685;ENST00000349697;ENST00000314235;ENST00000485523	T;T;T;T;T	0.20738	2.05;2.74;2.77;2.81;2.77	6.07	2.34	0.29019	.	1.479250	0.03645	N	0.240197	T	0.00241	0.0007	N	0.24115	0.695	0.09310	N	1	B;B;P;P;P	0.42248	0.006;0.041;0.628;0.774;0.665	B;B;B;B;B	0.40066	0.004;0.066;0.318;0.318;0.169	T	0.19353	-1.0308	10	0.66056	D	0.02	-8.1794	7.3861	0.26882	0.0:0.0714:0.2725:0.6561	rs1170672;rs17565640;rs57414713;rs1170672	42;42;22;40;44	E9PER5;Q9NPA1-2;Q9NPA1-4;Q9NPA1-3;Q9NPA1	.;.;.;.;KCMB3_HUMAN	G	42;40;42;44;22	ENSP00000417091:D42G;ENSP00000376451:D40G;ENSP00000327866:D42G;ENSP00000319370:D44G;ENSP00000418536:D22G	ENSP00000319370:D44G	D	-	2	0	KCNMB3	180451354	0.029000	0.19370	0.004000	0.12327	0.007000	0.05969	1.097000	0.30988	0.169000	0.19679	0.528000	0.53228	GAT	T|0.918;C|0.082	0.082	strong		0.542	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
EIF4E	1977	hgsc.bcm.edu	37	4	99808254	99808254	+	Silent	SNP	G	G	A	rs62323192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:99808254G>A	ENST00000450253.2	-	5	1899	c.375C>T	c.(373-375)gaC>gaT	p.D125D	EIF4E_ENST00000505992.1_Silent_p.D125D|EIF4E_ENST00000280892.6_Silent_p.D145D|EIF4E_ENST00000504432.1_Silent_p.D153D	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	125					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)	p.D125D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		AGCGATCGAGGTCACTTCGTC	0.383													G|||	548	0.109425	0.0144	0.1455	5008	,	,		21025	0.001		0.2734	False		,,,				2504	0.1554				p.D145D		Atlas-SNP	.											EIF4E,NS,carcinoma,0,1	EIF4E	18	1	1	Substitution - coding silent(1)	prostate(1)	c.C435T						PASS	.	G	,,	230,4176	136.1+/-172.1	7,216,1980	239.0	207.0	218.0		435,375,375	4.1	1.0	4	dbSNP_129	218	2472,6128	406.4+/-348.8	344,1784,2172	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4E	NM_001130678.1,NM_001130679.1,NM_001968.3	,,	351,2000,4152	AA,AG,GG		28.7442,5.2202,20.775	,,	145/238,125/249,125/218	99808254	2702,10304	2203	4300	6503	SO:0001819	synonymous_variant	1977	exon5			ATCGAGGTCACTT	M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.375C>T	4.37:g.99808254G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	164	86	0.52439	NM_001130678	B7Z6V1|D6RCQ6|Q96E95	Silent	SNP	ENST00000450253.2	37	CCDS34031.1	271	0.12408424908424909	9	0.018292682926829267	54	0.14917127071823205	1	0.0017482517482517483	207	0.27308707124010556	G	10.27	1.303728	0.23736	0.052202	0.287442	ENSG00000151247	ENST00000511644	.	.	.	5.85	4.14	0.48551	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16129	-1.0413	3	.	.	.	-16.6535	9.8967	0.41322	0.2072:0.0:0.7928:0.0	rs62323192	.	.	.	S	122	.	.	P	-	1	0	EIF4E	100027277	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.700000	0.61803	0.823000	0.34589	0.557000	0.71058	CCT	G|0.819;A|0.181	0.181	strong		0.383	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1	NM_001968	
MS4A14	84689	hgsc.bcm.edu	37	11	60184277	60184277	+	Missense_Mutation	SNP	A	A	C	rs73481226	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60184277A>C	ENST00000300187.6	+	5	2113	c.1836A>C	c.(1834-1836)caA>caC	p.Q612H	MS4A14_ENST00000395005.2_Missense_Mutation_p.Q595H|MS4A14_ENST00000531787.1_Missense_Mutation_p.Q500H|MS4A14_ENST00000531783.1_Missense_Mutation_p.Q645H	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	78	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	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		
SERPINF2	5345	hgsc.bcm.edu	37	17	1657653	1657653	+	Missense_Mutation	SNP	G	G	A	rs1057335	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	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	
MRS2	57380	hgsc.bcm.edu	37	6	24418348	24418348	+	Silent	SNP	G	G	A	rs2793422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24418348G>A	ENST00000378386.3	+	8	966	c.873G>A	c.(871-873)gaG>gaA	p.E291E	MRS2_ENST00000443868.2_Silent_p.E294E|MRS2_ENST00000543597.1_De_novo_Start_InFrame|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.E241E|MRS2_ENST00000378353.1_Silent_p.E291E|MRS2_ENST00000274747.7_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	291						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						ATGCAGAAGAGATGGAGTTGC	0.388													G|||	1143	0.228235	0.0923	0.2464	5008	,	,		14391	0.2272		0.3618	False		,,,				2504	0.2628				p.E291E		Atlas-SNP	.											.	MRS2	31	.	0			c.G873A						PASS	.	G		592,3814	261.6+/-264.4	44,504,1655	146.0	132.0	137.0		873	4.3	1.0	6	dbSNP_100	137	3334,5266	497.0+/-374.4	649,2036,1615	no	coding-synonymous	MRS2	NM_020662.2		693,2540,3270	AA,AG,GG		38.7674,13.4362,30.1861		291/444	24418348	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon8			AGAAGAGATGGAG	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.873G>A	6.37:g.24418348G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1	505	0.23122710622710624	33	0.06707317073170732	96	0.26519337016574585	111	0.19405594405594406	265	0.3496042216358839	G	10.03	1.237670	0.22711	0.134362	0.387674	ENSG00000124532	ENST00000446191	.	.	.	6.06	4.3	0.51218	.	.	.	.	.	T	0.39436	0.1078	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.32322	-0.9911	3	.	.	.	-21.2535	10.6715	0.45762	0.2184:0.0:0.7816:0.0	rs2793422;rs3736797;rs17305417;rs61074641;rs2793422	.	.	.	K	110	.	.	R	+	2	0	MRS2	24526327	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.113000	0.57851	0.910000	0.36722	-0.245000	0.11935	AGA	G|0.730;A|0.270	0.270	strong		0.388	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
GRID2	2895	hgsc.bcm.edu	37	4	94344042	94344042	+	Missense_Mutation	SNP	G	G	A	rs10034345	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:94344042G>A	ENST00000282020.4	+	10	1726	c.1468G>A	c.(1468-1470)Gta>Ata	p.V490I	GRID2_ENST00000510992.1_Missense_Mutation_p.V395I	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	490			V -> I (in dbSNP:rs10034345).		cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CGAAATTTACGTAGCACCGGA	0.403													G|||	535	0.106829	0.1823	0.0605	5008	,	,		17501	0.0159		0.0815	False		,,,				2504	0.1575				p.V490I		Atlas-SNP	.											.	GRID2	233	.	0			c.G1468A						PASS	.	G	ILE/VAL	693,3713	291.8+/-281.7	47,599,1557	119.0	120.0	120.0		1468	4.4	1.0	4	dbSNP_119	120	575,8025	153.6+/-207.9	23,529,3748	yes	missense	GRID2	NM_001510.2	29	70,1128,5305	AA,AG,GG		6.686,15.7286,9.7493	possibly-damaging	490/1008	94344042	1268,11738	2203	4300	6503	SO:0001583	missense	2895	exon10			ATTTACGTAGCAC	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.1468G>A	4.37:g.94344042G>A	ENSP00000282020:p.Val490Ile	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	161	0.07371794871794872	65	0.13211382113821138	23	0.06353591160220995	0	0.0	73	0.09630606860158311	G	16.99	3.273252	0.59649	0.157286	0.06686	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.10960	2.82;2.82	5.23	4.37	0.52481	Extracellular solute-binding protein, family 3 (1);Glutamate receptor, L-glutamate/glycine-binding (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	N	0.11756	0.17	0.19775	P	0.9999567534	B;B	0.31318	0.319;0.319	B;B	0.20577	0.03;0.03	T	0.38887	-0.9640	9	0.56958	D	0.05	.	15.7467	0.77949	0.0:0.137:0.863:0.0	rs10034345;rs52796027;rs10034345	395;490	E9PH24;O43424	.;GRID2_HUMAN	I	490;395	ENSP00000282020:V490I;ENSP00000421257:V395I	ENSP00000282020:V490I	V	+	1	0	GRID2	94563065	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.931000	0.63469	1.177000	0.42855	0.650000	0.86243	GTA	G|0.911;A|0.089	0.089	strong		0.403	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
JMJD4	65094	hgsc.bcm.edu	37	1	227922918	227922918	+	Missense_Mutation	SNP	A	A	C	rs2295994	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:227922918A>C	ENST00000366758.3	-	1	194	c.195T>G	c.(193-195)gaT>gaG	p.D65E	JMJD4_ENST00000485807.1_5'Flank|SNAP47_ENST00000366759.4_5'UTR|SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Missense_Mutation_p.D65E|SNAP47_ENST00000315781.5_5'UTR	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	65			D -> E (in dbSNP:rs2295994).							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)				CGCCGGGGACATCGACCCCCA	0.711													A|||	2080	0.415335	0.4682	0.4914	5008	,	,		12997	0.3671		0.3976	False		,,,				2504	0.3579				p.D65E		Atlas-SNP	.											.	JMJD4	28	.	0			c.T195G						PASS	.	A	GLU/ASP,GLU/ASP,	1536,2512		358,820,846	5.0	6.0	6.0		195,195,	-9.0	0.0	1	dbSNP_100	6	3051,5001		653,1745,1628	no	missense,missense,utr-5	JMJD4,SNAP47	NM_001161465.1,NM_023007.2,NM_053052.3	45,45,	1011,2565,2474	CC,CA,AA		37.8912,37.9447,37.9091	benign,benign,	65/448,65/464,	227922918	4587,7513	2024	4026	6050	SO:0001583	missense	65094	exon1			GGGGACATCGACC	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.195T>G	1.37:g.227922918A>C	ENSP00000355720:p.Asp65Glu	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	16	5	0.3125	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Missense_Mutation	SNP	ENST00000366758.3	37	CCDS1561.1	902|902	0.413003663003663|0.413003663003663	222|222	0.45121951219512196|0.45121951219512196	164|164	0.4530386740331492|0.4530386740331492	213|213	0.3723776223776224|0.3723776223776224	303|303	0.3997361477572559|0.3997361477572559	A|A	5.356|5.356	0.250977|0.250977	0.10130|0.10130	0.379447|0.379447	0.378912|0.378912	ENSG00000081692|ENSG00000081692	ENST00000366758|ENST00000438896	T|.	0.13196|.	2.61|.	4.48|4.48	-8.96|-8.96	0.00761|0.00761	.|.	1.594540|.	0.03876|.	N|.	0.276375|.	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|.	0.06786|.	0.001;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.41342|0.41342	-0.9514|-0.9514	9|4	0.02654|.	T|.	1|.	0.1735|0.1735	4.3941|4.3941	0.11355|0.11355	0.1274:0.3193:0.4422:0.1111|0.1274:0.3193:0.4422:0.1111	rs2295994;rs17619699;rs61644370;rs2295994|rs2295994;rs17619699;rs61644370;rs2295994	65;65|.	Q9H9V9-2;Q9H9V9|.	.;JMJD4_HUMAN|.	E|R	65|58	ENSP00000355720:D65E|.	ENSP00000355720:D65E|.	D|M	-|-	3|2	2|0	JMJD4|JMJD4	225989541|225989541	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.942000|-1.942000	0.01541|0.01541	-1.884000|-1.884000	0.01119|0.01119	-0.436000|-0.436000	0.05848|0.05848	GAT|ATG	A|0.590;C|0.410	0.410	strong		0.711	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
SCFD2	152579	hgsc.bcm.edu	37	4	54011526	54011526	+	Missense_Mutation	SNP	A	A	G	rs7675987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:54011526A>G	ENST00000401642.3	-	5	1668	c.1535T>C	c.(1534-1536)tTg>tCg	p.L512S	SCFD2_ENST00000388940.4_Missense_Mutation_p.L512S	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	512			L -> S (in dbSNP:rs7675987).		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)			CAAAGGTGACAATCCAGATTC	0.403													A|||	1266	0.252796	0.1906	0.2781	5008	,	,		20849	0.2143		0.3907	False		,,,				2504	0.2168				p.L512S		Atlas-SNP	.											.	SCFD2	78	.	0			c.T1535C						PASS	.	A	SER/LEU	942,3464	358.9+/-314.6	111,720,1372	146.0	130.0	135.0		1535	4.8	0.9	4	dbSNP_116	135	3162,5438	479.6+/-370.2	598,1966,1736	yes	missense	SCFD2	NM_152540.3	145	709,2686,3108	GG,GA,AA		36.7674,21.3799,31.5547	probably-damaging	512/685	54011526	4104,8902	2203	4300	6503	SO:0001583	missense	152579	exon5			GGTGACAATCCAG	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.1535T>C	4.37:g.54011526A>G	ENSP00000384182:p.Leu512Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	599	0.2742673992673993	92	0.18699186991869918	102	0.281767955801105	102	0.17832167832167833	303	0.3997361477572559	A	12.45	1.942212	0.34283	0.213799	0.367674	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.80393	-1.37;-1.32	4.81	4.81	0.61882	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	M	0.61703	1.905	0.27248	P	0.9589737	D;D	0.89917	0.999;1.0	D;D	0.72982	0.976;0.979	T	0.26052	-1.0114	9	0.22109	T	0.4	.	10.8679	0.46866	0.9232:0.0:0.0768:0.0	rs7675987;rs17703439;rs52828053;rs60150787;rs7675987	512;512	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	S	512	ENSP00000384182:L512S;ENSP00000373592:L512S	ENSP00000373592:L512S	L	-	2	0	SCFD2	53706283	0.558000	0.26554	0.914000	0.36105	0.160000	0.22226	2.669000	0.46825	2.142000	0.66516	0.460000	0.39030	TTG	A|0.710;G|0.290	0.290	strong		0.403	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324333	39324333	+	Missense_Mutation	SNP	T	T	A	rs12953139	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39324333T>A	ENST00000391356.2	-	1	91	c.92A>T	c.(91-93)cAg>cTg	p.Q31L		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	31					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCAGGTGGTCTGGCAGCAGCT	0.637																																					p.Q31L		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,0,1	KRTAP4-3	40	1	0			c.A92T						scavenged	.						29.0	32.0	31.0					17																	39324333		2195	4293	6488	SO:0001583	missense	85290	exon1			GTGGTCTGGCAGC	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.92A>T	17.37:g.39324333T>A	ENSP00000375151:p.Gln31Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	16	0.132231	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	8.661	0.900435	0.17686	.	.	ENSG00000196156	ENST00000391356	T	0.01629	4.72	5.15	0.112	0.14623	.	.	.	.	.	T	0.03608	0.0103	M	0.85373	2.75	0.80722	P	0.0	B	0.34181	0.44	B	0.38378	0.272	T	0.11131	-1.0600	8	0.35671	T	0.21	.	3.821	0.08836	0.1588:0.2591:0.0:0.5822	.	31	Q9BYR4	KRA43_HUMAN	L	31	ENSP00000375151:Q31L	ENSP00000375151:Q31L	Q	-	2	0	KRTAP4-3	36577859	0.006000	0.16342	0.208000	0.23602	0.204000	0.24138	0.129000	0.15830	0.020000	0.15106	0.533000	0.62120	CAG	A|0.046;T|0.954	0.046	strong		0.637	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
E2F8	79733	hgsc.bcm.edu	37	11	19251826	19251826	+	Silent	SNP	G	G	A	rs11821023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:19251826G>A	ENST00000527884.1	-	9	1552	c.1320C>T	c.(1318-1320)ctC>ctT	p.L440L	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Silent_p.L440L	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	440					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|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 corepressor activity (GO:0003714)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AAATAGCTGCGAGCTGAGCCA	0.383													G|||	519	0.103634	0.1142	0.0519	5008	,	,		18875	0.1687		0.0915	False		,,,				2504	0.0716				p.L440L		Atlas-SNP	.											.	E2F8	84	.	0			c.C1320T						PASS	.	G		568,3830	253.4+/-259.3	36,496,1667	110.0	107.0	108.0		1320	-6.6	0.3	11	dbSNP_120	108	820,7766	191.4+/-237.6	40,740,3513	no	coding-synonymous	E2F8	NM_024680.2		76,1236,5180	AA,AG,GG		9.5504,12.915,10.6901		440/868	19251826	1388,11596	2199	4293	6492	SO:0001819	synonymous_variant	79733	exon9			AGCTGCGAGCTGA		CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1320C>T	11.37:g.19251826G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_001256372	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Silent	SNP	ENST00000527884.1	37	CCDS7849.1																																																																																			G|0.897;A|0.103	0.103	strong		0.383	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047105	46047105	+	Missense_Mutation	SNP	T	T	C	rs200504844		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46047105T>C	ENST00000397911.3	+	1	66	c.17T>C	c.(16-18)aTg>aCg	p.M6T	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_3'UTR	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	6						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCGTCCACCATGTCCATCCGC	0.642													T|||	1	0.000199681	0.0	0.0	5008	,	,		16835	0.0		0.001	False		,,,				2504	0.0				p.M6T		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T17C						PASS	.	T	,THR/MET	0,4406		0,0,2203	73.0	85.0	81.0		,17	-1.0	0.9	21		81	8,8592	5.7+/-21.5	0,8,4292	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,81	0,8,6495	CC,CT,TT		0.093,0.0,0.0615	,benign	,6/293	46047105	8,12998	2203	4300	6503	SO:0001583	missense	386676	exon1			CCACCATGTCCAT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.17T>C	21.37:g.46047105T>C	ENSP00000381009:p.Met6Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	.	.	.	.	.	.	.	.	.	.	t	3.359	-0.130818	0.06753	0.0	9.3E-4	ENSG00000221837	ENST00000397911	T	0.13196	2.61	3.67	-0.997	0.10215	.	.	.	.	.	T	0.09158	0.0226	L	0.41573	1.285	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.39440	-0.9614	9	0.66056	D	0.02	.	0.7715	0.01024	0.16:0.2466:0.1626:0.4307	.	6	P60411	KR109_HUMAN	T	6	ENSP00000381009:M6T	ENSP00000381009:M6T	M	+	2	0	KRTAP10-9	44871533	0.058000	0.20735	0.903000	0.35520	0.008000	0.06430	0.077000	0.14738	0.001000	0.14605	-0.408000	0.06270	ATG	T|0.999;C|0.001	0.001	weak		0.642	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
PARP4	143	hgsc.bcm.edu	37	13	25009441	25009441	+	Missense_Mutation	SNP	C	C	G	rs13428	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25009441C>G	ENST00000381989.3	-	31	3943	c.3838G>C	c.(3838-3840)Ggt>Cgt	p.G1280R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1280			G -> R (in dbSNP:rs13428). {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)	p.G1280R(1)		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)		TTTTCCACACCTCCACGTTCC	0.388													c|||	1929	0.385184	0.4849	0.3473	5008	,	,		20026	0.3601		0.4125	False		,,,				2504	0.2751				p.G1280R		Atlas-SNP	.											PARP4,NS,carcinoma,0,1	PARP4	142	1	1	Substitution - Missense(1)	stomach(1)	c.G3838C						PASS	.	C	ARG/GLY	2076,2330	570.7+/-382.9	472,1132,599	92.0	98.0	96.0		3838	-1.3	0.0	13	dbSNP_52	96	3204,5396	483.7+/-371.2	594,2016,1690	no	missense	PARP4	NM_006437.3	125	1066,3148,2289	GG,GC,CC		37.2558,47.1176,40.5966	benign	1280/1725	25009441	5280,7726	2203	4300	6503	SO:0001583	missense	143	exon31			CCACACCTCCACG	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.3838G>C	13.37:g.25009441C>G	ENSP00000371419:p.Gly1280Arg	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	843	0.385989010989011	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	315	0.4155672823218997	c	3.922	-0.017936	0.07681	0.471176	0.372558	ENSG00000102699	ENST00000381989	T	0.01665	4.7	1.95	-1.34	0.09143	.	1.603710	0.04481	U	0.377866	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.28324	0.207	B	0.21917	0.037	T	0.33033	-0.9884	9	0.34782	T	0.22	0.2916	5.0283	0.14396	0.2244:0.3332:0.4424:0.0	rs13428;rs3190395;rs3742174;rs11557034;rs52831662;rs13428	1280	Q9UKK3	PARP4_HUMAN	R	1280	ENSP00000371419:G1280R	ENSP00000371419:G1280R	G	-	1	0	PARP4	23907441	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.178000	0.03093	-0.420000	0.07427	-0.802000	0.03209	GGT	G|0.405;C|0.595;A|0.000	0.405	strong		0.388	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
GTF2F1	2962	hgsc.bcm.edu	37	19	6392908	6392908	+	Missense_Mutation	SNP	T	T	C	rs140541374		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392908T>C	ENST00000394456.5	-	2	483	c.19A>G	c.(19-21)Agc>Ggc	p.S7G	CTB-180A7.6_ENST00000599584.1_RNA|GTF2F1_ENST00000429701.2_5'Flank	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|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)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						TTCTGGCTGCTAGGGCCCTGC	0.597											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		16539	0.0		0.001	False		,,,				2504	0.0				p.S7G		Atlas-SNP	.											.	GTF2F1	39	.	0			c.A19G						PASS	.						135.0	136.0	136.0					19																	6392908		2203	4300	6503	SO:0001583	missense	2962	exon2			GGCTGCTAGGGCC		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.19A>G	19.37:g.6392908T>C	ENSP00000377969:p.Ser7Gly	Somatic	70	0	0	633	WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.77	1.737992	0.30774	.	.	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.49720	0.77	5.07	-2.96	0.05547	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.26593	0.0650	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.02512	-1.1148	10	0.46703	T	0.11	-8.1482	12.3718	0.55260	0.0:0.1636:0.0:0.8364	.	7	P35269	T2FA_HUMAN	G	7	ENSP00000377969:S7G	ENSP00000377969:S7G	S	-	1	0	GTF2F1	6343908	0.999000	0.42202	0.929000	0.37066	0.680000	0.39746	0.351000	0.20096	-0.625000	0.05604	-0.353000	0.07706	AGC	T|0.999;C|0.001	0.001	strong		0.597	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
HLA-B	3106	hgsc.bcm.edu	37	6	31323254	31323254	+	Silent	SNP	G	G	C	rs61759952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31323254G>C	ENST00000412585.2	-	4	763	c.735C>G	c.(733-735)ggC>ggG	p.G245G		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	245	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						TTTGGTCCTCGCCATCCCGCT	0.602									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	309	0.0617013	0.0507	0.0591	5008	,	,		21808	0.119		0.0487	False		,,,				2504	0.0327				p.G245G		Atlas-SNP	.											.	HLA-B	54	.	0			c.C735G						PASS	.						105.0	93.0	97.0					6																	31323254		2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GTCCTCGCCATCC	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.735C>G	6.37:g.31323254G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	154	39	0.253247	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.992;C|0.008;A|0.000	0.008	strong		0.602	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TMEM86B	255043	hgsc.bcm.edu	37	19	55739689	55739689	+	Silent	SNP	G	G	A	rs10413828	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55739689G>A	ENST00000327042.4	-	2	690	c.168C>T	c.(166-168)ccC>ccT	p.P56P	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	56					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		GGCAGAGGACGGGCAGGCACT	0.652													G|||	2167	0.432708	0.3222	0.4582	5008	,	,		17485	0.5992		0.4175	False		,,,				2504	0.408				p.P56P		Atlas-SNP	.											.	TMEM86B	12	.	0			c.C168T						PASS	.	G		1323,3079		187,949,1065	56.0	49.0	51.0		168	-10.0	0.0	19	dbSNP_119	51	3319,5279		632,2055,1612	no	coding-synonymous	TMEM86B	NM_173804.4		819,3004,2677	AA,AG,GG		38.602,30.0545,35.7077		56/227	55739689	4642,8358	2201	4299	6500	SO:0001819	synonymous_variant	255043	exon2			GAGGACGGGCAGG	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.168C>T	19.37:g.55739689G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			G|0.620;A|0.380	0.380	strong		0.652	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
CYP2D6	1565	hgsc.bcm.edu	37	22	42524795	42524795	+	Silent	SNP	A	A	G	rs28371713	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42524795A>G	ENST00000360608.5	-	4	771	c.657T>C	c.(655-657)ttT>ttC	p.F219F	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Silent_p.F219F|CYP2D6_ENST00000359033.4_Silent_p.F168F	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	219					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)	CCTCGCGCAGAAAGCCCGACT	0.667																																					p.F219F		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.T657C						PASS	.						34.0	28.0	30.0					22																	42524795		2199	4299	6498	SO:0001819	synonymous_variant	1565	exon4			GCGCAGAAAGCCC	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.657T>C	22.37:g.42524795A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	144	31	0.215278	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																			A|0.625;G|0.375	0.375	strong		0.667	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
PHF20	51230	hgsc.bcm.edu	37	20	34502107	34502107	+	Missense_Mutation	SNP	G	G	A	rs17431878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34502107G>A	ENST00000374012.3	+	12	1942	c.1813G>A	c.(1813-1815)Gtg>Atg	p.V605M	PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	605			V -> M (in dbSNP:rs17431878). {ECO:0000269|PubMed:15489334}.		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CAAAGGGAAAGTGAAAGCATT	0.478													G|||	530	0.105831	0.0726	0.1153	5008	,	,		19635	0.0863		0.1034	False		,,,				2504	0.1667				p.V605M		Atlas-SNP	.											.	PHF20	94	.	0			c.G1813A						PASS	.	G	MET/VAL	329,4077	173.7+/-203.5	7,315,1881	82.0	75.0	78.0		1813	3.2	1.0	20	dbSNP_123	78	903,7697	201.0+/-244.6	44,815,3441	yes	missense	PHF20	NM_016436.4	21	51,1130,5322	AA,AG,GG		10.5,7.4671,9.4726	benign	605/1013	34502107	1232,11774	2203	4300	6503	SO:0001583	missense	51230	exon12			GGGAAAGTGAAAG	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1813G>A	20.37:g.34502107G>A	ENSP00000363124:p.Val605Met	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	191	0.08745421245421245	29	0.05894308943089431	46	0.1270718232044199	41	0.07167832167832168	75	0.09894459102902374	G	8.860	0.946747	0.18356	0.074671	0.105	ENSG00000025293	ENST00000374012	T	0.32023	1.47	5.17	3.18	0.36537	.	1.525570	0.03373	N	0.199239	T	0.00210	0.0006	N	0.08118	0	0.09310	P	0.99999280361	B	0.26400	0.148	B	0.21151	0.033	T	0.13495	-1.0507	9	0.48119	T	0.1	.	8.4562	0.32901	0.0:0.13:0.5102:0.3598	rs17431878;rs52794293;rs17431878	605	Q9BVI0	PHF20_HUMAN	M	605	ENSP00000363124:V605M	ENSP00000363124:V605M	V	+	1	0	PHF20	33965521	0.993000	0.37304	0.990000	0.47175	0.533000	0.34776	1.275000	0.33144	0.694000	0.31654	0.643000	0.83706	GTG	G|0.905;A|0.095	0.095	strong		0.478	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
RP1L1	94137	hgsc.bcm.edu	37	8	10467653	10467653	+	Missense_Mutation	SNP	C	C	T	rs386722180|rs73201156		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10467653C>T	ENST00000382483.3	-	4	4178	c.3955G>A	c.(3955-3957)Gcg>Acg	p.A1319T		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1335	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		G -> A (in allele RP1L1-3; dbSNP:rs4840501). {ECO:0000269|PubMed:16421571}.		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)		aactgcaccgcctcttcttgc	0.468																																					p.A1319T		Atlas-SNP	.											.	RP1L1	453	.	0			c.G3955A						PASS	.						135.0	134.0	134.0					8																	10467653		1957	4134	6091	SO:0001583	missense	94137	exon4			GCACCGCCTCTTC	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.3955G>A	8.37:g.10467653C>T	ENSP00000371923:p.Ala1319Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	48	0.6	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	2.930	-0.221157	0.06061	.	.	ENSG00000183638	ENST00000382483	T	0.04551	3.6	2.13	0.0636	0.14349	.	2.034630	0.02921	U	0.137998	T	0.04634	0.0126	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.42882	-0.9425	10	0.54805	T	0.06	.	6.003	0.19531	0.0:0.5526:0.0:0.4474	.	1319	A6NKC6	.	T	1319	ENSP00000371923:A1319T	ENSP00000371923:A1319T	A	-	1	0	RP1L1	10505063	0.001000	0.12720	0.000000	0.03702	0.032000	0.12392	0.705000	0.25675	-0.151000	0.11176	0.313000	0.20887	GCG	.	.	strong		0.468	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
CSRNP3	80034	hgsc.bcm.edu	37	2	166535918	166535918	+	Silent	SNP	C	C	T	rs777346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:166535918C>T	ENST00000342316.4	+	5	1685	c.1413C>T	c.(1411-1413)acC>acT	p.T471T	CSRNP3_ENST00000409420.1_Silent_p.T503T|CSRNP3_ENST00000314499.7_Silent_p.T471T	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	87	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	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	
OR1A1	8383	hgsc.bcm.edu	37	17	3119673	3119673	+	Silent	SNP	A	A	G	rs769426	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3119673A>G	ENST00000304094.1	+	1	759	c.759A>G	c.(757-759)acA>acG	p.T253T		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	253						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(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						ATTATGGTACAGTCATGGGCA	0.488													A|||	646	0.128994	0.1021	0.1643	5008	,	,		21057	0.004		0.2803	False		,,,				2504	0.1135				p.T253T		Atlas-SNP	.											OR1A1,NS,carcinoma,+1,1	OR1A1	54	1	0			c.A759G						PASS	.	A		556,3850	247.8+/-255.9	40,476,1687	159.0	136.0	143.0		759	-0.0	1.0	17	dbSNP_86	143	2533,6067	413.8+/-351.3	387,1759,2154	yes	coding-synonymous	OR1A1	NM_014565.2		427,2235,3841	GG,GA,AA		29.4535,12.6192,23.7506		253/310	3119673	3089,9917	2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			TGGTACAGTCATG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.759A>G	17.37:g.3119673A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	37	CCDS11022.1																																																																																			A|0.801;G|0.199	0.199	strong		0.488	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565	
CNDP1	84735	hgsc.bcm.edu	37	18	72228154	72228154	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72228154A>C	ENST00000358821.3	+	4	595	c.367A>C	c.(367-369)Acg>Ccg	p.T123P	CNDP1_ENST00000582365.1_Missense_Mutation_p.T80P|RP11-231E4.3_ENST00000583702.1_RNA|CNDP1_ENST00000585136.1_Intron	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	123						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)		GAGCGATCCCACGAAAGGCAC	0.577																																					p.T123P	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											CNDP1,NS,carcinoma,-1,1	CNDP1	98	1	0			c.A367C						PASS	.						124.0	121.0	122.0					18																	72228154		2203	4300	6503	SO:0001583	missense	84735	exon4			GATCCCACGAAAG		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.367A>C	18.37:g.72228154A>C	ENSP00000351682:p.Thr123Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	34	0.300885	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	.	.	.	.	.	.	.	.	.	.	A	8.474	0.858173	0.17178	.	.	ENSG00000150656	ENST00000358821	T	0.14893	2.47	4.93	-2.86	0.05717	.	0.808128	0.11858	N	0.522700	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B	0.18610	0.029	B	0.23716	0.048	T	0.33727	-0.9857	10	0.51188	T	0.08	-4.9001	7.9888	0.30229	0.3867:0.4619:0.1513:0.0	.	123	Q96KN2	CNDP1_HUMAN	P	123	ENSP00000351682:T123P	ENSP00000351682:T123P	T	+	1	0	CNDP1	70379134	0.000000	0.05858	0.002000	0.10522	0.128000	0.20619	-0.201000	0.09464	-0.375000	0.07955	0.533000	0.62120	ACG	.	.	none		0.577	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
FGD4	121512	hgsc.bcm.edu	37	12	32764184	32764184	+	Silent	SNP	G	G	A	rs10844253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:32764184G>A	ENST00000427716.2	+	10	1729	c.1305G>A	c.(1303-1305)cgG>cgA	p.R435R	FGD4_ENST00000534526.2_Silent_p.R572R|FGD4_ENST00000546442.1_Silent_p.R342R|FGD4_ENST00000531134.1_Silent_p.R520R|FGD4_ENST00000381025.3_Silent_p.R187R|FGD4_ENST00000525053.1_Silent_p.R547R|FGD4_ENST00000266482.3_Silent_p.R187R	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	435	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|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)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|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)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TAGCTGCTCGGAACACTTCAG	0.368													G|||	1328	0.265176	0.2027	0.2781	5008	,	,		18003	0.1657		0.3161	False		,,,				2504	0.3906				p.R435R		Atlas-SNP	.											FGD4,NS,carcinoma,+2,1	FGD4	86	1	0			c.G1305A						PASS	.	G		1049,3357	381.1+/-324.0	131,787,1285	95.0	98.0	97.0		1305	1.1	1.0	12	dbSNP_120	97	2691,5909	429.1+/-356.1	445,1801,2054	no	coding-synonymous	FGD4	NM_139241.2		576,2588,3339	AA,AG,GG		31.2907,23.8084,28.756		435/767	32764184	3740,9266	2203	4300	6503	SO:0001819	synonymous_variant	121512	exon10			TGCTCGGAACACT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1305G>A	12.37:g.32764184G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			G|0.731;A|0.269	0.269	strong		0.368	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
KCNK4	50801	hgsc.bcm.edu	37	11	64066999	64066999	+	Missense_Mutation	SNP	C	C	T	rs953778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64066999C>T	ENST00000539216.1	+	6	1343	c.983C>T	c.(982-984)cCg>cTg	p.P328L	RP11-783K16.10_ENST00000539086.1_RNA|KCNK4_ENST00000538767.1_Silent_p.A212A|KCNK4_ENST00000394525.2_Missense_Mutation_p.P328L|TEX40_ENST00000539943.1_5'Flank|TEX40_ENST00000328404.6_5'Flank|KCNK4_ENST00000422670.2_Missense_Mutation_p.P328L			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	25	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	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	
CARD17	440068	hgsc.bcm.edu	37	11	104971257	104971257	+	Missense_Mutation	SNP	G	G	A	rs12806837	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:104971257G>A	ENST00000375707.1	-	2	273	c.257C>T	c.(256-258)aCg>aTg	p.T86M	CASP1_ENST00000593315.1_Intron|CASP1_ENST00000598974.1_Intron|CASP1_ENST00000594519.1_Intron|CARD16_ENST00000525374.1_Intron|CASP1_ENST00000415981.2_Intron	NM_001007232.1	NP_001007233.1	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	86	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	6						GAGTCCCAGCGTCCCTGCCAG	0.488													.|||	512	0.102236	0.143	0.2233	5008	,	,		20238	0.006		0.0815	False		,,,				2504	0.0818				p.T86M		Atlas-SNP	.											.	CARD17	15	.	0			c.C257T						PASS	.	G	MET/THR	601,3803		31,539,1632	122.0	106.0	111.0		257	-2.5	0.0	11	dbSNP_121	111	694,7904		29,636,3634	no	missense	CARD17	NM_001007232.1	81	60,1175,5266	AA,AG,GG		8.0716,13.6467,9.96		86/111	104971257	1295,11707	2202	4299	6501	SO:0001583	missense	440068	exon2			CCCAGCGTCCCTG		CCDS31662.1	11q22.3	2009-01-13				ENSG00000255221			33827	protein-coding gene	gene with protein product	"""Inhibitory CARD"""	609490				15383541	Standard	NM_001007232		Approved	INCA	uc001pir.1	Q5XLA6		ENST00000375707.1:c.257C>T	11.37:g.104971257G>A	ENSP00000364859:p.Thr86Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001007232		Missense_Mutation	SNP	ENST00000375707.1	37	CCDS31662.1	216	0.0989010989010989	81	0.16463414634146342	75	0.20718232044198895	2	0.0034965034965034965	58	0.07651715039577836	.	6.103	0.387223	0.11581	0.136467	0.080716	ENSG00000255221	ENST00000375707	T	0.20881	2.04	2.69	-2.47	0.06442	DEATH-like (2);Caspase Recruitment (3);	.	.	.	.	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	P	0.38617	0.64	B	0.29598	0.104	T	0.12167	-1.0558	8	0.40728	T	0.16	.	2.9218	0.05771	0.4783:0.0:0.2414:0.2803	rs12806837	86	Q5XLA6	CAR17_HUMAN	M	86	ENSP00000364859:T86M	ENSP00000364859:T86M	T	-	2	0	CARD17	104476467	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.712000	0.01885	-0.752000	0.04728	0.511000	0.50034	ACG	G|0.903;A|0.097	0.097	strong		0.488	CARD17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388181.1	NM_001007232	
RNF122	79845	hgsc.bcm.edu	37	8	33416189	33416189	+	Silent	SNP	G	G	A	rs3735950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:33416189G>A	ENST00000256257.1	-	2	527	c.126C>T	c.(124-126)ttC>ttT	p.F42F		NM_024787.2	NP_079063.2	Q9H9V4	RN122_HUMAN	ring finger protein 122	42						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)		TGCCTGTGCCGAAGATGACCA	0.542													G|||	2488	0.496805	0.6165	0.4496	5008	,	,		19679	0.381		0.5606	False		,,,				2504	0.4223				p.F42F		Atlas-SNP	.											.	RNF122	17	.	0			c.C126T						PASS	.	G		2639,1767	644.8+/-398.1	793,1053,357	123.0	106.0	111.0		126	-6.9	0.7	8	dbSNP_107	111	4837,3763	616.0+/-396.5	1351,2135,814	no	coding-synonymous	RNF122	NM_024787.2		2144,3188,1171	AA,AG,GG		43.7558,40.1044,42.5188		42/156	33416189	7476,5530	2203	4300	6503	SO:0001819	synonymous_variant	79845	exon2			TGTGCCGAAGATG	AK022588	CCDS6091.1	8p12	2013-01-09			ENSG00000133874	ENSG00000133874		"""RING-type (C3HC4) zinc fingers"""	21147	protein-coding gene	gene with protein product							Standard	NM_024787		Approved	FLJ12526	uc003xjo.1	Q9H9V4	OTTHUMG00000163960	ENST00000256257.1:c.126C>T	8.37:g.33416189G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_024787	Q52LK3	Silent	SNP	ENST00000256257.1	37	CCDS6091.1																																																																																			G|0.454;A|0.546	0.546	strong		0.542	RNF122-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376562.1	NM_024787	
ABCF2	10061	hgsc.bcm.edu	37	7	150920891	150920891	+	Silent	SNP	G	G	A	rs41273648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150920891G>A	ENST00000287844.2	-	5	704	c.595C>T	c.(595-597)Ctg>Ttg	p.L199L	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.L199L	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	199	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)		TCGGCATCCAGCTCCTCCAGG	0.602													G|||	37	0.00738818	0.0015	0.0115	5008	,	,		19099	0.0		0.0209	False		,,,				2504	0.0061				p.L199L		Atlas-SNP	.											.	ABCF2	54	.	0			c.C595T						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	41.0	36.0	38.0		595,595	2.2	1.0	7	dbSNP_127	38	238,8362	96.8+/-158.5	6,226,4068	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	6,247,6250	AA,AG,GG		2.7674,0.4766,1.9914	,	199/635,199/624	150920891	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon5			CATCCAGCTCCTC	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.595C>T	7.37:g.150920891G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.985;A|0.015	0.015	strong		0.602	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
MUC6	4588	hgsc.bcm.edu	37	11	1029320	1029320	+	Missense_Mutation	SNP	C	C	T	rs11604757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	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	
DNAH5	1767	hgsc.bcm.edu	37	5	13811775	13811775	+	Missense_Mutation	SNP	T	T	C	rs10078391	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13811775T>C	ENST00000265104.4	-	44	7492	c.7388A>G	c.(7387-7389)cAa>cGa	p.Q2463R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2463			Q -> R (in dbSNP:rs10078391).		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)					AATCAGGCCTTGAAGCATGTT	0.413									Kartagener syndrome				T|||	1313	0.262181	0.1884	0.1758	5008	,	,		11862	0.5585		0.2147	False		,,,				2504	0.1667				p.Q2463R		Atlas-SNP	.											DNAH5,right_upper_lobe,carcinoma,-1,1	DNAH5	868	1	0			c.A7388G						scavenged	.	T	ARG/GLN	888,3518	344.9+/-308.3	101,686,1416	94.0	93.0	93.0		7388	5.8	0.5	5	dbSNP_119	93	1761,6839	320.9+/-314.9	172,1417,2711	yes	missense	DNAH5	NM_001369.2	43	273,2103,4127	CC,CT,TT		20.4767,20.1543,20.3675	possibly-damaging	2463/4625	13811775	2649,10357	2203	4300	6503	SO:0001583	missense	1767	exon44	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGCCTTGAAGCA	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.7388A>G	5.37:g.13811775T>C	ENSP00000265104:p.Gln2463Arg	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	622	0.2847985347985348	99	0.20121951219512196	63	0.17403314917127072	293	0.5122377622377622	167	0.22031662269129287	T	15.09	2.730316	0.48939	0.201543	0.204767	ENSG00000039139	ENST00000265104	T	0.25579	1.79	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.83603	2.65	0.09310	P	0.999999792992	B	0.32893	0.389	B	0.35039	0.194	T	0.46020	-0.9221	9	0.66056	D	0.02	.	16.1193	0.81336	0.0:0.0:0.0:1.0	rs10078391;rs52804450;rs10078391	2463	Q8TE73	DYH5_HUMAN	R	2463	ENSP00000265104:Q2463R	ENSP00000265104:Q2463R	Q	-	2	0	DNAH5	13864775	1.000000	0.71417	0.547000	0.28179	0.422000	0.31414	7.977000	0.88081	2.204000	0.70986	0.528000	0.53228	CAA	T|0.764;C|0.236	0.236	strong		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
MUC16	94025	hgsc.bcm.edu	37	19	9076728	9076728	+	Missense_Mutation	SNP	C	C	T	rs2591594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076728C>T	ENST00000397910.4	-	3	10921	c.10718G>A	c.(10717-10719)cGc>cAc	p.R3573H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3574	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						AGAAGTTGTGCGCCTCTCTGT	0.512													C|||	1243	0.248203	0.2005	0.2118	5008	,	,		21876	0.249		0.3121	False		,,,				2504	0.272				p.R3573H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,4	MUC16	4315	4	0			c.G10718A						PASS	.	C	HIS/ARG	892,3336		102,688,1324	179.0	177.0	178.0		10718	-2.8	0.0	19	dbSNP_100	178	2435,6017		349,1737,2140	yes	missense	MUC16	NM_024690.2	29	451,2425,3464	TT,TC,CC		28.8097,21.0974,26.2382	benign	3573/14508	9076728	3327,9353	2114	4226	6340	SO:0001583	missense	94025	exon3			GTTGTGCGCCTCT	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.10718G>A	19.37:g.9076728C>T	ENSP00000381008:p.Arg3573His	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	269	118	0.438662	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	551	0.2522893772893773	109	0.22154471544715448	88	0.2430939226519337	122	0.21328671328671328	232	0.30606860158311344	c	1.183	-0.637672	0.03557	0.210974	0.288097	ENSG00000181143	ENST00000397910	T	0.02916	4.11	1.49	-2.79	0.05841	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	8	0.87932	D	0	.	7.7924	0.29127	0.0:0.6856:0.0:0.3144	rs2591594;rs52835104;rs58009126;rs2591594	3573	B5ME49	.	H	3573	ENSP00000381008:R3573H	ENSP00000381008:R3573H	R	-	2	0	MUC16	8937728	0.008000	0.16893	0.000000	0.03702	0.003000	0.03518	-0.053000	0.11846	-1.341000	0.02225	-1.786000	0.00637	CGC	C|0.751;T|0.249	0.249	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PMEPA1	56937	hgsc.bcm.edu	37	20	56227532	56227532	+	Silent	SNP	T	T	C	rs6025699	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:56227532T>C	ENST00000341744.3	-	4	760	c.441A>G	c.(439-441)ccA>ccG	p.P147P	PMEPA1_ENST00000265626.4_Silent_p.P97P|PMEPA1_ENST00000347215.4_Silent_p.P112P|PMEPA1_ENST00000395814.1_Silent_p.P97P|PMEPA1_ENST00000395816.3_Silent_p.P97P	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	147					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)			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						AGATGGTGGGTGGCAGGTCGA	0.706													C|||	3346	0.668131	0.4334	0.6412	5008	,	,		14728	0.8363		0.7505	False		,,,				2504	0.7464				p.P147P		Atlas-SNP	.											PMEPA1,caecum,carcinoma,0,1	PMEPA1	29	1	0			c.A441G						scavenged	.	C	,,,	2100,2306	592.5+/-387.8	494,1112,597	34.0	36.0	35.0		441,336,291,291	-10.9	0.0	20	dbSNP_114	35	6567,2033	350.3+/-327.8	2492,1583,225	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PMEPA1	NM_020182.3,NM_199169.1,NM_199170.1,NM_199171.1	,,,	2986,2695,822	CC,CT,TT		23.6395,47.6623,33.3615	,,,	147/288,112/253,97/238,97/238	56227532	8667,4339	2203	4300	6503	SO:0001819	synonymous_variant	56937	exon4			GGTGGGTGGCAGG	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.441A>G	20.37:g.56227532T>C		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	37	CCDS13463.1																																																																																			C|0.670;G|0.000;T|0.330	0.670	strong		0.706	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182	
OR52K1	390036	hgsc.bcm.edu	37	11	4510285	4510285	+	Missense_Mutation	SNP	A	A	G	rs96489	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4510285A>G	ENST00000307632.3	+	1	177	c.155A>G	c.(154-156)cAg>cGg	p.Q52R		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	52			Q -> R (in dbSNP:rs96489). {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)	p.Q52R(1)		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)		TTCATTATCCAGGCTGATGCA	0.502													G|||	1923	0.383986	0.5477	0.2161	5008	,	,		21614	0.3194		0.2952	False		,,,				2504	0.4397				p.Q52R		Atlas-SNP	.											OR52K1,NS,carcinoma,+1,3	OR52K1	70	3	1	Substitution - Missense(1)	stomach(1)	c.A155G						PASS	.	G	ARG/GLN	2220,2182	584.5+/-386.0	552,1116,533	168.0	157.0	161.0		155	-1.9	0.0	11	dbSNP_79	161	2544,6052	692.0+/-404.6	392,1760,2146	yes	missense	OR52K1	NM_001005171.2	43	944,2876,2679	GG,GA,AA		29.5952,49.5684,36.6518	benign	52/315	4510285	4764,8234	2201	4298	6499	SO:0001583	missense	390036	exon1			TTATCCAGGCTGA	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.155A>G	11.37:g.4510285A>G	ENSP00000302422:p.Gln52Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_001005171	B9EH54|Q6IFK5	Missense_Mutation	SNP	ENST00000307632.3	37	CCDS31352.1	773	0.35393772893772896	270	0.5487804878048781	96	0.26519337016574585	200	0.34965034965034963	207	0.27308707124010556	G	0.001	-3.197733	0.00025	0.504316	0.295952	ENSG00000196778	ENST00000307632	T	0.02944	4.1	3.59	-1.92	0.07618	GPCR, rhodopsin-like superfamily (1);	1.211190	0.06110	N	0.666991	T	0.00012	0.0000	N	0.01219	-0.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37641	-0.9697	9	0.06365	T	0.9	.	7.2622	0.26209	0.6431:0.0:0.2236:0.1332	rs96489;rs865224;rs2004596;rs16913225;rs56631972;rs60402006;rs96489	52	Q8NGK4	O52K1_HUMAN	R	52	ENSP00000302422:Q52R	ENSP00000302422:Q52R	Q	+	2	0	OR52K1	4466861	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-6.840000	0.00052	-0.754000	0.04715	-1.221000	0.01599	CAG	A|0.625;G|0.375	0.375	strong		0.502	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171	
KANK4	163782	hgsc.bcm.edu	37	1	62739495	62739495	+	Silent	SNP	C	C	T	rs115190866	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62739495C>T	ENST00000371153.4	-	3	1659	c.1281G>A	c.(1279-1281)tcG>tcA	p.S427S	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	427						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						CCTTATCACACGACTCCCTGG	0.557													C|||	63	0.0125799	0.0023	0.0159	5008	,	,		21973	0.001		0.0348	False		,,,				2504	0.0133				p.S427S		Atlas-SNP	.											.	KANK4	135	.	0			c.G1281A						PASS	.	C		38,4368	43.1+/-76.7	1,36,2166	213.0	194.0	201.0		1281	-10.7	0.0	1	dbSNP_132	201	347,8253	117.9+/-177.5	11,325,3964	no	coding-synonymous	KANK4	NM_181712.4		12,361,6130	TT,TC,CC		4.0349,0.8625,2.9602		427/996	62739495	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			ATCACACGACTCC	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.1281G>A	1.37:g.62739495C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	37	CCDS620.1																																																																																			C|0.976;T|0.024	0.024	strong		0.557	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
SH2D3C	10044	hgsc.bcm.edu	37	9	130504070	130504070	+	Silent	SNP	G	G	A	rs514024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:130504070G>A	ENST00000314830.8	-	9	2198	c.2085C>T	c.(2083-2085)gcC>gcT	p.A695A	SH2D3C_ENST00000471939.1_5'Flank|SH2D3C_ENST00000373277.4_Silent_p.A538A|SH2D3C_ENST00000373276.3_Silent_p.A627A|SH2D3C_ENST00000420366.1_Silent_p.A537A|SH2D3C_ENST00000373274.3_Silent_p.A535A|SH2D3C_ENST00000429553.1_Silent_p.A341A	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	695	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCAGTACCTGGGCCATGTCCA	0.622													G|||	2663	0.531749	0.5711	0.5764	5008	,	,		13327	0.2847		0.6103	False		,,,				2504	0.6207				p.A695A		Atlas-SNP	.											SH2D3C_ENST00000314830,NS,carcinoma,0,2	SH2D3C	102	2	0			c.C2085T						PASS	.	G	,,,,,	2540,1866		757,1026,420	30.0	29.0	30.0		1023,1023,1611,1605,1614,2085	0.2	1.0	9	dbSNP_83	30	4947,3653		1435,2077,788	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH2D3C	NM_001142531.1,NM_001142532.1,NM_001142533.1,NM_001142534.1,NM_005489.2,NM_170600.2	,,,,,	2192,3103,1208	AA,AG,GG		42.4767,42.3513,42.4343	,,,,,	341/507,341/507,537/703,535/701,538/704,695/861	130504070	7487,5519	2203	4300	6503	SO:0001819	synonymous_variant	10044	exon9			TACCTGGGCCATG	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.2085C>T	9.37:g.130504070G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	135	132	0.977778	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Silent	SNP	ENST00000314830.8	37	CCDS6877.1																																																																																			G|0.444;A|0.556	0.556	strong		0.622	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489	
FAM167A	83648	hgsc.bcm.edu	37	8	11301601	11301601	+	Missense_Mutation	SNP	G	G	C	rs3021512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11301601G>C	ENST00000528897.1	-	2	939	c.320C>G	c.(319-321)aCt>aGt	p.T107S	FAM167A_ENST00000534308.1_Missense_Mutation_p.T107S|FAM167A_ENST00000531564.1_5'Flank|FAM167A_ENST00000284486.4_Missense_Mutation_p.T107S			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	107			T -> S (in dbSNP:rs3021512). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						CAGCTTGCCAGTGGACAGGGG	0.627													G|||	394	0.0786741	0.034	0.1124	5008	,	,		15628	0.0		0.2107	False		,,,				2504	0.0603				p.T107S		Atlas-SNP	.											.	FAM167A	21	.	0			c.C320G						PASS	.	G	SER/THR	236,3916		7,222,1847	50.0	55.0	53.0		320	2.5	0.0	8	dbSNP_101	53	1710,6754		177,1356,2699	yes	missense	FAM167A	NM_053279.2	58	184,1578,4546	CC,CG,GG		20.2032,5.684,15.4249	benign	107/215	11301601	1946,10670	2076	4232	6308	SO:0001583	missense	83648	exon2			TTGCCAGTGGACA		CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"""chromosome 8 open reading frame 13"""	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.320C>G	8.37:g.11301601G>C	ENSP00000436655:p.Thr107Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_053279	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	233	0.10668498168498168	18	0.036585365853658534	48	0.13259668508287292	0	0.0	167	0.22031662269129287	G	3.552	-0.091530	0.07053	0.05684	0.202032	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897	T;T;T	0.06933	3.24;3.24;3.24	5.42	2.55	0.30701	.	1.544380	0.03516	N	0.220302	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39165	-0.9627	9	0.05620	T	0.96	0.7646	7.0385	0.25006	0.1488:0.0:0.7113:0.1399	rs3021512	107	Q96KS9	F167A_HUMAN	S	107	ENSP00000284486:T107S;ENSP00000432232:T107S;ENSP00000436655:T107S	ENSP00000284486:T107S	T	-	2	0	FAM167A	11339011	0.993000	0.37304	0.000000	0.03702	0.004000	0.04260	3.705000	0.54823	0.661000	0.30985	0.655000	0.94253	ACT	G|0.854;C|0.146	0.146	strong		0.627	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1		
CBR3	874	hgsc.bcm.edu	37	21	37518706	37518706	+	Missense_Mutation	SNP	G	G	A	rs1056892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:37518706G>A	ENST00000290354.5	+	3	1011	c.730G>A	c.(730-732)Gtg>Atg	p.V244M	CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000427491.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	244			V -> M (increased catalytic activity; dbSNP:rs1056892). {ECO:0000269|Ref.5}.		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)	CATCAGGACTGTGGAGGAGGG	0.552													G|||	2139	0.427117	0.5098	0.2608	5008	,	,		19102	0.4048		0.3539	False		,,,				2504	0.5317				p.V244M		Atlas-SNP	.											.	CBR3	11	.	0			c.G730A	GRCh37	CM057648	CBR3	M	rs1056892	PASS	.	G	MET/VAL	2092,2314	573.1+/-383.5	503,1086,614	89.0	87.0	87.0		730	0.6	0.4	21	dbSNP_86	87	3094,5506	472.9+/-368.5	551,1992,1757	yes	missense	CBR3	NM_001236.3	21	1054,3078,2371	AA,AG,GG		35.9767,47.4807,39.8739	benign	244/278	37518706	5186,7820	2203	4300	6503	SO:0001583	missense	874	exon3			AGGACTGTGGAGG	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.730G>A	21.37:g.37518706G>A	ENSP00000290354:p.Val244Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001236	Q6FHP2	Missense_Mutation	SNP	ENST00000290354.5	37	CCDS13642.1	839	0.3841575091575092	229	0.4654471544715447	105	0.2900552486187845	232	0.40559440559440557	273	0.36015831134564646	G	13.78	2.340505	0.41498	0.474807	0.359767	ENSG00000159231	ENST00000290354	T	0.10477	2.87	4.8	0.552	0.17230	NAD(P)-binding domain (1);	0.272984	0.41823	D	0.000805	T	0.00012	0.0000	M	0.71920	2.185	0.37059	P	0.10204400000000002	P	0.38195	0.622	B	0.32149	0.141	T	0.48410	-0.9038	9	0.56958	D	0.05	-3.09	11.3336	0.49490	0.0859:0.65:0.2641:0.0	rs1056892;rs3171445;rs52816011;rs58776388;rs1056892	244	O75828	CBR3_HUMAN	M	244	ENSP00000290354:V244M	ENSP00000290354:V244M	V	+	1	0	CBR3	36440576	0.854000	0.29725	0.415000	0.26534	0.926000	0.56050	2.055000	0.41345	0.567000	0.29293	0.655000	0.94253	GTG	G|0.606;A|0.394	0.394	strong		0.552	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
STYXL1	51657	hgsc.bcm.edu	37	7	75634687	75634687	+	Silent	SNP	G	G	A	rs1044484	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:75634687G>A	ENST00000248600.1	-	6	831	c.489C>T	c.(487-489)atC>atT	p.I163I	STYXL1_ENST00000359697.3_Silent_p.I163I|STYXL1_ENST00000340062.5_Silent_p.I67I|STYXL1_ENST00000431581.1_Silent_p.I163I|STYXL1_ENST00000451157.1_Silent_p.I163I|STYXL1_ENST00000360591.3_3'UTR	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	163	Tyrosine-protein phosphatase.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						TCCCTGGCACGATTTCAATGG	0.473													g|||	257	0.0513179	0.0053	0.1052	5008	,	,		13912	0.001		0.1551	False		,,,				2504	0.0204				p.I163I		Atlas-SNP	.											.	STYXL1	35	.	0			c.C489T						PASS	.	G		137,4269	97.6+/-136.3	3,131,2069	124.0	112.0	116.0		489	-2.4	0.0	7	dbSNP_86	116	1438,7162	277.4+/-292.8	112,1214,2974	no	coding-synonymous	STYXL1	NM_016086.2		115,1345,5043	AA,AG,GG		16.7209,3.1094,12.1098		163/314	75634687	1575,11431	2203	4300	6503	SO:0001819	synonymous_variant	51657	exon6			TGGCACGATTTCA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	18165	protein-coding gene	gene with protein product			"""dual specificity phosphatase 24 (putative)"""	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.489C>T	7.37:g.75634687G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Silent	SNP	ENST00000248600.1	37	CCDS5580.1																																																																																			G|0.900;A|0.100	0.100	strong		0.473	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	
CRB2	286204	hgsc.bcm.edu	37	9	126128211	126128211	+	Missense_Mutation	SNP	T	T	C	rs1105223	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:126128211T>C	ENST00000373631.3	+	3	435	c.434T>C	c.(433-435)aTg>aCg	p.M145T	CRB2_ENST00000359999.3_Missense_Mutation_p.M145T|CRB2_ENST00000373629.2_5'Flank	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	145			M -> T (in dbSNP:rs1105223). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15851977}.		cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						ACCTGCGAGATGGAGGTGGAC	0.701													C|||	1880	0.375399	0.3714	0.3516	5008	,	,		12632	0.4107		0.3817	False		,,,				2504	0.3548				p.M145T		Atlas-SNP	.											.	CRB2	86	.	0			c.T434C						PASS	.	C	THR/MET	1547,2827		286,975,926	31.0	25.0	27.0		434	-0.6	0.0	9	dbSNP_86	27	3286,5276		654,1978,1649	yes	missense	CRB2	NM_173689.5	81	940,2953,2575	CC,CT,TT		38.3789,35.3681,37.3609	benign	145/1286	126128211	4833,8103	2187	4281	6468	SO:0001583	missense	286204	exon3			GCGAGATGGAGGT	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.434T>C	9.37:g.126128211T>C	ENSP00000362734:p.Met145Thr	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	809	0.37042124542124544	161	0.32723577235772355	143	0.39502762430939226	209	0.36538461538461536	296	0.39050131926121373	C	0.180	-1.062689	0.01950	0.353681	0.383789	ENSG00000148204	ENST00000359999;ENST00000373631	T;T	0.79352	-1.26;-1.26	4.79	-0.624	0.11552	.	1.567310	0.03926	N	0.284455	T	0.00012	0.0000	N	0.00661	-1.28	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04961	-1.0915	9	0.07482	T	0.82	.	3.6393	0.08161	0.2787:0.3057:0.0:0.4156	rs1105223;rs60781662;rs1105223	145;145	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	T	145	ENSP00000353092:M145T;ENSP00000362734:M145T	ENSP00000353092:M145T	M	+	2	0	CRB2	125168032	0.000000	0.05858	0.002000	0.10522	0.239000	0.25481	-0.472000	0.06623	-0.849000	0.04158	-0.380000	0.06706	ATG	T|0.636;C|0.364	0.364	strong		0.701	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
PRPF8	10594	hgsc.bcm.edu	37	17	1580929	1580929	+	Silent	SNP	G	G	C	rs11078565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	58	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	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		
OR52N2	390077	hgsc.bcm.edu	37	11	5842384	5842384	+	Missense_Mutation	SNP	C	C	G	rs62621415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5842384C>G	ENST00000317037.2	+	1	841	c.819C>G	c.(817-819)aaC>aaG	p.N273K	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	273						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)		ATATCCCAAACCACATACACA	0.428													C|||	203	0.0405351	0.0741	0.0259	5008	,	,		21672	0.001		0.0467	False		,,,				2504	0.0399				p.N273K		Atlas-SNP	.											.	OR52N2	58	.	0			c.C819G						PASS	.	C	LYS/ASN	338,4064	178.0+/-206.8	9,320,1872	191.0	157.0	169.0		819	2.6	0.1	11	dbSNP_129	169	576,8016	154.8+/-208.9	16,544,3736	yes	missense	OR52N2	NM_001005174.1	94	25,864,5608	GG,GC,CC		6.7039,7.6783,7.034	benign	273/322	5842384	914,12080	2201	4296	6497	SO:0001583	missense	390077	exon1			CCCAAACCACATA	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.819C>G	11.37:g.5842384C>G	ENSP00000322801:p.Asn273Lys	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	199	87	0.437186	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	82	0.037545787545787544	37	0.07520325203252033	12	0.03314917127071823	0	0.0	33	0.04353562005277045	C	0	-2.582695	0.00129	0.076783	0.067039	ENSG00000180988	ENST00000317037	T	0.00058	8.79	6.09	2.64	0.31445	GPCR, rhodopsin-like superfamily (1);	0.108660	0.41605	D	0.000857	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	N	1	B	0.13594	0.008	B	0.19946	0.027	T	0.10894	-1.0610	10	0.09338	T	0.73	.	3.572	0.07921	0.2805:0.4303:0.0:0.2892	rs62621415	273	Q8NGI0	O52N2_HUMAN	K	273	ENSP00000322801:N273K	ENSP00000322801:N273K	N	+	3	2	OR52N2	5798960	0.000000	0.05858	0.052000	0.19188	0.037000	0.13140	-3.145000	0.00584	0.604000	0.29930	0.643000	0.83706	AAC	C|0.939;G|0.061	0.061	strong		0.428	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
MST1L	11223	hgsc.bcm.edu	37	1	17085373	17085373	+	RNA	SNP	C	C	T	rs2092130		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17085373C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.G440R(1)|p.G397R(1)									TGGCTATCCCCATCTGGGTCT	0.602																																					p.G440R		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	2	Substitution - Missense(2)	kidney(2)	c.G1318A						scavenged	.																																					11223	exon10			TATCCCCATCTGG	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.17085373C>T		Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	380	16	0.0421053	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	3.164	-0.171433	0.06421	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.699669	0.12362	N	0.475555	T	0.21761	0.0524	.	.	.	.	.	.	B	0.16166	0.016	B	0.17979	0.02	T	0.23940	-1.0174	5	.	.	.	.	3.5811	0.07954	2.0E-4:0.4998:0.4998:2.0E-4	rs2092130;rs2095110;rs4567270;rs9701105	440	Q2TV78-2	.	R	397;440;440	.	.	G	-	1	0	MST1P9	16957960	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	1.482000	0.35486	-0.000000	0.14550	0.000000	0.15137	GGG	C|1.000;|0.000	.	weak		0.602	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
FAT4	79633	hgsc.bcm.edu	37	4	126240510	126240510	+	Silent	SNP	T	T	C	rs2940779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:126240510T>C	ENST00000394329.3	+	1	2957	c.2944T>C	c.(2944-2946)Tta>Cta	p.L982L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	982	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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						TAGTGTCATCTTAACAGTTTA	0.443													C|||	3611	0.721046	0.9251	0.7291	5008	,	,		20548	0.4603		0.7127	False		,,,				2504	0.7168				p.L982L		Atlas-SNP	.											.	FAT4	1752	.	0			c.T2944C						PASS	.	C		3480,428		1553,374,27	97.0	95.0	96.0		2944	0.1	0.3	4	dbSNP_101	96	5860,2426		2053,1754,336	no	coding-synonymous	FAT4	NM_024582.4		3606,2128,363	CC,CT,TT		29.2783,10.9519,23.405		982/4982	126240510	9340,2854	1954	4143	6097	SO:0001819	synonymous_variant	79633	exon1			GTCATCTTAACAG	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.2944T>C	4.37:g.126240510T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			T|0.291;C|0.709	0.709	strong		0.443	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
RADIL	55698	hgsc.bcm.edu	37	7	4874420	4874420	+	Missense_Mutation	SNP	G	G	C	rs2292498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4874420G>C	ENST00000399583.3	-	4	1421	c.1234C>G	c.(1234-1236)Cac>Gac	p.H412D	RADIL_ENST00000538469.1_Missense_Mutation_p.H172D|RADIL_ENST00000536091.1_Missense_Mutation_p.H412D	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	34	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	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	
CENPC	1060	hgsc.bcm.edu	37	4	68380070	68380070	+	Missense_Mutation	SNP	C	C	T	rs1056787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:68380070C>T	ENST00000273853.6	-	8	1416	c.1166G>A	c.(1165-1167)gGt>gAt	p.G389D		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	389			G -> D (in dbSNP:rs1056787). {ECO:0000269|PubMed:1339310}.		chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										TACTGTTTCACCTATCAAAGC	0.338													C|||	124	0.0247604	0.0045	0.0519	5008	,	,		18799	0.0		0.0755	False		,,,				2504	0.0061				p.G389D		Atlas-SNP	.											.	CENPC1	66	.	0			c.G1166A						PASS	.	C	ASP/GLY	66,3552		0,66,1743	79.0	66.0	70.0		1166	2.2	0.1	4	dbSNP_86	70	737,7421		25,687,3367	yes	missense	CENPC1	NM_001812.2	94	25,753,5110	TT,TC,CC		9.0341,1.8242,6.819	benign	389/944	68380070	803,10973	1809	4079	5888	SO:0001583	missense	1060	exon8			GTTTCACCTATCA	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1166G>A	4.37:g.68380070C>T	ENSP00000273853:p.Gly389Asp	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	37	CCDS47063.1	83	0.038003663003663	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	61	0.08047493403693931	C	3.004	-0.205492	0.06180	0.018242	0.090341	ENSG00000145241	ENST00000273853	.	.	.	4.63	2.17	0.27698	.	1.062250	0.07311	N	0.875940	T	0.00496	0.0016	N	0.04203	-0.255	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27088	-1.0084	8	0.02654	T	1	-1.2622	4.4653	0.11685	0.0:0.1071:0.1984:0.6945	rs1056787;rs3197406;rs17624860;rs52834666;rs60270492;rs1056787	389;389	Q8IW27;Q03188	.;CENPC_HUMAN	D	389	.	ENSP00000273853:G389D	G	-	2	0	CENPC1	68062665	0.331000	0.24713	0.056000	0.19401	0.083000	0.17756	0.306000	0.19279	0.370000	0.24538	-0.471000	0.05019	GGT	C|0.973;T|0.027	0.027	strong		0.338	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2		
SNX29	92017	hgsc.bcm.edu	37	16	12162969	12162969	+	Silent	SNP	A	A	G	rs1641843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:12162969A>G	ENST00000566228.1	+	10	1368	c.1299A>G	c.(1297-1299)ccA>ccG	p.P433P	SNX29_ENST00000323433.4_Silent_p.P48P|SNX29_ENST00000306030.3_Silent_p.P48P	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	433						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.P48P(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						ACGTTCTCCCAGATCCTGGAC	0.463													g|||	3050	0.609026	0.8116	0.5014	5008	,	,		18048	0.5258		0.4632	False		,,,				2504	0.6472				p.P433P		Atlas-SNP	.											SNX29_ENST00000306030,NS,carcinoma,0,1	SNX29	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A1299G						PASS	.			2767,971		1036,695,138	89.0	97.0	95.0		144	-10.7	0.0	16	dbSNP_89	95	3365,4857		689,1987,1435	no	coding-synonymous	SNX29	NM_001080530.2		1725,2682,1573	GG,GA,AA		40.9268,25.9765,48.7291		48/429	12162969	6132,5828	1869	4111	5980	SO:0001819	synonymous_variant	92017	exon10			TCTCCCAGATCCT	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.1299A>G	16.37:g.12162969A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			A|0.468;G|0.532	0.532	strong		0.463	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
DMXL1	1657	hgsc.bcm.edu	37	5	118454599	118454599	+	Missense_Mutation	SNP	T	T	C	rs200933738		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:118454599T>C	ENST00000311085.8	+	8	913	c.833T>C	c.(832-834)cTa>cCa	p.L278P	DMXL1_ENST00000539542.1_Missense_Mutation_p.L278P	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	278										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)		GATTGTTTGCTATACGGAGGT	0.363																																					p.L278P		Atlas-SNP	.											.	DMXL1	268	.	0			c.T833C						PASS	.	T	PRO/LEU	0,4404		0,0,2202	158.0	151.0	154.0		833	5.4	0.4	5		154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DMXL1	NM_005509.4	98	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	278/3028	118454599	3,13001	2202	4300	6502	SO:0001583	missense	1657	exon8			GTTTGCTATACGG	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.833T>C	5.37:g.118454599T>C	ENSP00000309690:p.Leu278Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.770171	0.49680	0.0	3.49E-4	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.28069	1.63;2.67;2.67	5.38	5.38	0.77491	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000002	T	0.56001	0.1956	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.72338	0.977;0.931	T	0.60905	-0.7170	10	0.72032	D	0.01	-1.619	15.3913	0.74747	0.0:0.0:0.0:1.0	.	278;278	F5H269;Q9Y485	.;DMXL1_HUMAN	P	278	ENSP00000427692:L278P;ENSP00000309690:L278P;ENSP00000439479:L278P	ENSP00000309690:L278P	L	+	2	0	DMXL1	118482498	0.940000	0.31905	0.396000	0.26296	0.137000	0.21094	5.757000	0.68766	2.046000	0.60703	0.533000	0.62120	CTA	T|0.999;C|0.001	0.001	weak		0.363	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
LY75	4065	hgsc.bcm.edu	37	2	160661704	160661704	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160661704C>T	ENST00000263636.4	-	35	5047	c.5020G>A	c.(5020-5022)Gtt>Att	p.V1674I	LY75-CD302_ENST00000505052.1_Intron|LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1674					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)		AGTGTGGCAACTATGATAGCT	0.423																																					p.V1674I		Atlas-SNP	.											.	LY75	151	.	0			c.G5020A						PASS	.						107.0	98.0	101.0					2																	160661704		2203	4300	6503	SO:0001583	missense	4065	exon35			TGGCAACTATGAT	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.5020G>A	2.37:g.160661704C>T	ENSP00000263636:p.Val1674Ile	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	16	0.161616	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	8.786	0.929415	0.18131	.	.	ENSG00000054219	ENST00000263636	T	0.08634	3.07	5.38	-5.11	0.02901	.	1.327090	0.05825	N	0.616489	T	0.02970	0.0088	N	0.08118	0	0.24881	N	0.992224	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	10	0.12766	T	0.61	.	2.3409	0.04260	0.3665:0.2775:0.066:0.29	.	1674	O60449	LY75_HUMAN	I	1674	ENSP00000263636:V1674I	ENSP00000263636:V1674I	V	-	1	0	LY75	160369950	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.555000	0.05999	-0.516000	0.06470	-2.451000	0.00208	GTT	.	.	none		0.423	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
FRYL	285527	hgsc.bcm.edu	37	4	48542671	48542671	+	Silent	SNP	G	G	A	rs373260615		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:48542671G>A	ENST00000503238.1	-	43	5993	c.5994C>T	c.(5992-5994)aaC>aaT	p.N1998N	FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000537810.1_Silent_p.N1998N|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.N1998N			O94915	FRYL_HUMAN	FRY-like	1998					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TGGCCATCAAGTTGGTAGGCT	0.423																																					p.N1998N		Atlas-SNP	.											.	FRYL	242	.	0			c.C5994T						PASS	.	G		0,3846		0,0,1923	79.0	78.0	79.0		5994	5.3	1.0	4		79	2,8232		0,2,4115	no	coding-synonymous	FRYL	NM_015030.1		0,2,6038	AA,AG,GG		0.0243,0.0,0.0166		1998/3014	48542671	2,12078	1923	4117	6040	SO:0001819	synonymous_variant	285527	exon46			CATCAAGTTGGTA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.5994C>T	4.37:g.48542671G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	G	2.279	-0.365058	0.05103	0.0	2.43E-4	ENSG00000075539	ENST00000514617	.	.	.	6.16	5.33	0.75918	.	.	.	.	.	T	0.62696	0.2449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61594	-0.7031	4	.	.	.	.	10.6144	0.45441	0.1986:0.0:0.8014:0.0	.	.	.	.	F	868	.	.	L	-	1	0	FRYL	48237428	1.000000	0.71417	0.978000	0.43139	0.571000	0.35966	3.050000	0.49877	1.628000	0.50416	0.650000	0.86243	CTT	.	.	weak		0.423	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
PANK1	53354	hgsc.bcm.edu	37	10	91404448	91404448	+	Silent	SNP	C	C	G	rs11185826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:91404448C>G	ENST00000307534.4	-	1	767	c.612G>C	c.(610-612)ctG>ctC	p.L204L	RP11-80H5.2_ENST00000451733.1_RNA|PANK1_ENST00000371774.2_5'Flank|RP11-80H5.2_ENST00000454174.1_RNA|RP11-80H5.6_ENST00000428166.1_lincRNA|PANK1_ENST00000322191.6_5'Flank|PANK1_ENST00000488482.1_5'Flank|PANK1_ENST00000342512.3_5'Flank	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	204					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						GCTGCGGCTGCAGCTCCGGCA	0.716													G|||	1807	0.360823	0.4766	0.2233	5008	,	,		10422	0.2986		0.2604	False		,,,				2504	0.4693				p.L204L		Atlas-SNP	.											.	PANK1	35	.	0			c.G612C						PASS	.	G		1436,2386		274,888,749	3.0	4.0	4.0		612	-2.9	1.0	10	dbSNP_120	4	1672,6224		207,1258,2483	no	coding-synonymous	PANK1	NM_148977.2		481,2146,3232	GG,GC,CC		21.1753,37.572,26.5233		204/599	91404448	3108,8610	1911	3948	5859	SO:0001819	synonymous_variant	53354	exon1			CGGCTGCAGCTCC	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.612G>C	10.37:g.91404448C>G		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			C|0.693;G|0.307	0.307	strong		0.716	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
PKDREJ	10343	hgsc.bcm.edu	37	22	46654323	46654323	+	Silent	SNP	G	G	A	rs6007740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46654323G>A	ENST00000253255.5	-	1	4896	c.4897C>T	c.(4897-4899)Ctg>Ttg	p.L1633L		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1633					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AAGCCTGACAGGAGTATAATT	0.393													A|||	1205	0.240615	0.6626	0.1297	5008	,	,		20164	0.001		0.16	False		,,,				2504	0.0787				p.L1633L		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C4897T						PASS	.	A		2581,1825	523.8+/-371.2	757,1067,379	78.0	77.0	77.0		4897	-9.9	0.0	22	dbSNP_114	77	1253,7347	758.3+/-407.5	88,1077,3135	no	coding-synonymous	PKDREJ	NM_006071.1		845,2144,3514	AA,AG,GG		14.5698,41.4208,29.4787		1633/2254	46654323	3834,9172	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			CTGACAGGAGTAT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4897C>T	22.37:g.46654323G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.736;A|0.264	0.264	strong		0.393	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
COL15A1	1306	hgsc.bcm.edu	37	9	101778272	101778272	+	Missense_Mutation	SNP	A	A	C	rs35250850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	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	
VAV3	10451	hgsc.bcm.edu	37	1	108417534	108417534	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:108417534C>T	ENST00000370056.4	-	2	584	c.310G>A	c.(310-312)Gac>Aac	p.D104N	VAV3_ENST00000371846.4_Missense_Mutation_p.D39N|VAV3_ENST00000527011.1_Missense_Mutation_p.D104N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	104	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|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)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TTTCCAAAGTCACGAACATCA	0.353																																					p.D104N		Atlas-SNP	.											.	VAV3	176	.	0			c.G310A						PASS	.						78.0	74.0	76.0					1																	108417534		2203	4300	6503	SO:0001583	missense	10451	exon2			CAAAGTCACGAAC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.310G>A	1.37:g.108417534C>T	ENSP00000359073:p.Asp104Asn	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	190	92	0.484211	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.850961	0.91277	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.41758	0.99;0.99;0.99	6.08	6.08	0.98989	Calponin homology domain (5);	0.229124	0.43416	D	0.000580	T	0.40423	0.1116	N	0.20328	0.56	0.58432	D	0.99999	B;B;D	0.54397	0.004;0.272;0.966	B;B;D	0.70487	0.023;0.322;0.969	T	0.09773	-1.0659	10	0.22706	T	0.39	.	19.2273	0.93822	0.0:1.0:0.0:0.0	.	104;104;104	B7ZLR1;E9PQ97;Q9UKW4	.;.;VAV3_HUMAN	N	104;104;39	ENSP00000359073:D104N;ENSP00000432540:D104N;ENSP00000360912:D39N	ENSP00000359073:D104N	D	-	1	0	VAV3	108219057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.302000	0.78861	2.894000	0.99253	0.655000	0.94253	GAC	.	.	none		0.353	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999922	46999922	+	Missense_Mutation	SNP	G	G	T	rs4926046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:46999922G>T	ENST00000374317.1	+	3	1315	c.1042G>T	c.(1042-1044)Gtg>Ttg	p.V348L	GPRIN2_ENST00000374314.4_Missense_Mutation_p.V348L	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	348										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CTGCAAGGCTGTGGCCACCAG	0.672																																					p.V348L		Atlas-SNP	.											GPRIN2,colon,carcinoma,0,1	GPRIN2	94	1	0			c.G1042T						scavenged	.						51.0	53.0	52.0					10																	46999922		2203	4300	6503	SO:0001583	missense	9721	exon3			AAGGCTGTGGCCA	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1042G>T	10.37:g.46999922G>T	ENSP00000363436:p.Val348Leu	Somatic	79	2	0.0253165		WXS	Illumina HiSeq	Phase_I	72	16	0.222222	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	799	0.3658424908424908	95	0.19308943089430894	136	0.3756906077348066	287	0.5017482517482518	281	0.370712401055409	G	20.7	4.034376	0.75617	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.30981	1.51;1.51	4.85	4.85	0.62838	.	0.000000	0.38111	N	0.001808	T	0.00012	0.0000	M	0.77103	2.36	0.53688	D	0.999976	D	0.76494	0.999	D	0.80764	0.994	T	0.49978	-0.8881	10	0.87932	D	0	-18.1542	15.8316	0.78757	0.0:0.0:1.0:0.0	rs4926046	348	O60269	GRIN2_HUMAN	L	348	ENSP00000363436:V348L;ENSP00000363433:V348L	ENSP00000363433:V348L	V	+	1	0	GPRIN2	46419928	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	4.918000	0.63376	2.415000	0.81967	0.313000	0.20887	GTG	G|0.634;T|0.366	0.366	strong		0.672	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
TGM2	7052	hgsc.bcm.edu	37	20	36766591	36766591	+	Silent	SNP	G	G	A	rs140171902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36766591G>A	ENST00000361475.2	-	10	1712	c.1539C>T	c.(1537-1539)acC>acT	p.T513T	TGM2_ENST00000536724.1_Silent_p.T453T|TGM2_ENST00000536701.1_Silent_p.T432T	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	513					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TGTAGCTGACGGTGCGGGCAC	0.577													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17458	0.0		0.001	False		,,,				2504	0.0				p.T513T		Atlas-SNP	.											.	TGM2	88	.	0			c.C1539T						PASS	.	G	,	0,4406		0,0,2203	93.0	70.0	78.0		1539,1539	-7.9	0.8	20	dbSNP_134	78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	513/688,513/549	36766591	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	7052	exon10			GCTGACGGTGCGG	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1539C>T	20.37:g.36766591G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
KIF18A	81930	hgsc.bcm.edu	37	11	28057957	28057957	+	Missense_Mutation	SNP	T	T	C	rs10458896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:28057957T>C	ENST00000263181.6	-	14	2493	c.2203A>G	c.(2203-2205)Atc>Gtc	p.I735V		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	735			I -> V (in dbSNP:rs10458896). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15878648}.		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 metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TTTGAGCTGATAGCCTGAAAA	0.363													T|||	1990	0.397364	0.6384	0.2046	5008	,	,		17315	0.4762		0.2962	False		,,,				2504	0.2311				p.I735V		Atlas-SNP	.											.	KIF18A	92	.	0			c.A2203G						PASS	.	T	VAL/ILE	2631,1773	642.2+/-397.6	781,1069,352	140.0	139.0	140.0		2203	0.2	0.0	11	dbSNP_119	140	2507,6089	410.1+/-350.0	352,1803,2143	yes	missense	KIF18A	NM_031217.3	29	1133,2872,2495	CC,CT,TT		29.1647,40.2589,39.5231	benign	735/899	28057957	5138,7862	2202	4298	6500	SO:0001583	missense	81930	exon14			AGCTGATAGCCTG	AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2203A>G	11.37:g.28057957T>C	ENSP00000263181:p.Ile735Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Missense_Mutation	SNP	ENST00000263181.6	37	CCDS7867.1	874	0.4001831501831502	306	0.6219512195121951	88	0.2430939226519337	264	0.46153846153846156	216	0.2849604221635884	T	0.008	-1.916505	0.00503	0.597411	0.291647	ENSG00000121621	ENST00000263181	T	0.70516	-0.49	5.3	0.187	0.15109	.	1.461270	0.04163	N	0.323394	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40646	-0.9552	9	0.08179	T	0.78	.	8.3793	0.32461	0.0:0.3327:0.0:0.6673	rs10458896;rs17846441;rs17859490;rs52792047;rs60178096;rs10458896	735	Q8NI77	KI18A_HUMAN	V	735	ENSP00000263181:I735V	ENSP00000263181:I735V	I	-	1	0	KIF18A	28014533	0.000000	0.05858	0.000000	0.03702	0.454000	0.32378	-0.358000	0.07641	-0.144000	0.11314	-0.408000	0.06270	ATC	C|0.398;N|0.000	0.398	strong		0.363	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110489620	110489620	+	Silent	SNP	A	A	T	rs1783148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:110489620A>T	ENST00000378402.5	+	53	9188	c.9084A>T	c.(9082-9084)acA>acT	p.T3028T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3028					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)			GACCAGCCACATATAAGTACA	0.378										HNSCC(38;0.096)			A|||	2135	0.426318	0.3828	0.5187	5008	,	,		19204	0.3284		0.337	False		,,,				2504	0.6125				p.T3028T		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A9084T						PASS	.	A		1421,2329		289,843,743	63.0	58.0	60.0		9084	-5.7	0.5	8	dbSNP_89	60	3000,5224		571,1858,1683	no	coding-synonymous	PKHD1L1	NM_177531.4		860,2701,2426	TT,TA,AA		36.4786,37.8933,36.9217		3028/4244	110489620	4421,7553	1875	4112	5987	SO:0001819	synonymous_variant	93035	exon53			AGCCACATATAAG	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.9084A>T	8.37:g.110489620A>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			A|0.634;T|0.366	0.366	strong		0.378	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
FAM83H	286077	hgsc.bcm.edu	37	8	144810346	144810346	+	Missense_Mutation	SNP	C	C	A	rs144418186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144810346C>A	ENST00000388913.3	-	5	1410	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	429					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TGCCGCGACACCTGCCGCGCG	0.682													C|||	21	0.00419329	0.0	0.013	5008	,	,		6410	0.0		0.008	False		,,,				2504	0.0041				p.V429L		Atlas-SNP	.											.	FAM83H	68	.	0			c.G1285T						PASS	.	C	LEU/VAL	8,4120		0,8,2056	15.0	24.0	21.0		1285	4.0	1.0	8	dbSNP_134	21	137,8219		2,133,4043	yes	missense	FAM83H	NM_198488.3	32	2,141,6099	AA,AC,CC		1.6395,0.1938,1.1615	possibly-damaging	429/1180	144810346	145,12339	2064	4178	6242	SO:0001583	missense	286077	exon5			GCGACACCTGCCG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1285G>T	8.37:g.144810346C>A	ENSP00000373565:p.Val429Leu	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	c	8.338	0.828008	0.16749	0.001938	0.016395	ENSG00000180921	ENST00000388913	T	0.15017	2.46	4.96	4.02	0.46733	.	0.947136	0.08665	N	0.911838	T	0.05731	0.0150	L	0.27053	0.805	0.25299	N	0.9893	B	0.31581	0.329	B	0.25987	0.065	T	0.11372	-1.0590	10	0.21014	T	0.42	.	10.4754	0.44661	0.361:0.639:0.0:0.0	.	429	Q6ZRV2	FA83H_HUMAN	L	429	ENSP00000373565:V429L	ENSP00000373565:V429L	V	-	1	0	FAM83H	144882334	0.976000	0.34144	0.995000	0.50966	0.035000	0.12851	2.070000	0.41491	2.277000	0.76020	0.555000	0.69702	GTG	C|0.991;A|0.009	0.009	strong		0.682	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
PROC	5624	hgsc.bcm.edu	37	2	128186156	128186156	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128186156G>A	ENST00000234071.3	+	9	1107	c.1020G>A	c.(1018-1020)acG>acA	p.T340T	PROC_ENST00000453608.2_Silent_p.T395T|PROC_ENST00000409048.1_Silent_p.T374T|PROC_ENST00000422777.3_Silent_p.T340T	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	340	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> M (in THPH3; Vermont-2). {ECO:0000269|PubMed:8292730, ECO:0000269|PubMed:9798967}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.T340T(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCCTCGTGACGGGCTGGGGCT	0.632																																					p.T340T		Atlas-SNP	.											.	PROC	31	.	1	Substitution - coding silent(1)	lung(1)	c.G1020A						PASS	.						85.0	99.0	94.0					2																	128186156		2203	4300	6503	SO:0001819	synonymous_variant	5624	exon9			CGTGACGGGCTGG	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"""Endogenous ligands"""	9451	protein-coding gene	gene with protein product	"""prepro-protein C"""	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.1020G>A	2.37:g.128186156G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	37	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142460	0.01728	.	.	ENSG00000115718	ENST00000402125	.	.	.	5.23	-10.5	0.00291	.	.	.	.	.	T	0.32224	0.0822	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41016	-0.9532	4	.	.	.	.	1.6144	0.02700	0.4409:0.2044:0.1371:0.2175	.	.	.	.	Q	115	.	.	R	+	2	0	PROC	127902626	0.000000	0.05858	0.263000	0.24496	0.026000	0.11368	-5.090000	0.00152	-2.914000	0.00307	-1.036000	0.02392	CGG	.	.	none		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
PROM1	8842	hgsc.bcm.edu	37	4	16020162	16020162	+	Splice_Site	SNP	C	C	T	rs2286455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:16020162C>T	ENST00000510224.1	-	9	1034	c.786G>A	c.(784-786)gcG>gcA	p.A262A	PROM1_ENST00000508167.1_Splice_Site_p.A253A|PROM1_ENST00000539194.1_Splice_Site_p.A262A|PROM1_ENST00000505450.1_Splice_Site_p.A253A|PROM1_ENST00000543373.1_Splice_Site_p.A253A|PROM1_ENST00000447510.2_Splice_Site_p.A262A|PROM1_ENST00000540805.1_Splice_Site_p.A262A|PROM1_ENST00000502943.1_5'UTR			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	153	0	0		WXS	Illumina HiSeq	Phase_I	172	79	0.459302	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
OR7C1	26664	hgsc.bcm.edu	37	19	14910654	14910654	+	Missense_Mutation	SNP	T	T	C	rs17230134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14910654T>C	ENST00000248073.2	-	1	369	c.295A>G	c.(295-297)Agt>Ggt	p.S99G	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	99			S -> G (in dbSNP:rs17230134).		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						AAAATCTGACTGAGACAGCCT	0.448													T|||	996	0.198882	0.326	0.2176	5008	,	,		21511	0.0486		0.2157	False		,,,				2504	0.1513				p.S99G		Atlas-SNP	.											.	OR7C1	58	.	0			c.A295G						PASS	.	T	GLY/SER	1402,3004	685.8+/-404.6	215,972,1016	68.0	67.0	68.0		295	-1.0	0.0	19	dbSNP_123	68	1743,6857	736.1+/-407.0	174,1395,2731	yes	missense	OR7C1	NM_198944.1	56	389,2367,3747	CC,CT,TT		20.2674,31.8202,24.1811	possibly-damaging	99/321	14910654	3145,9861	2203	4300	6503	SO:0001583	missense	26664	exon1			TCTGACTGAGACA	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.295A>G	19.37:g.14910654T>C	ENSP00000248073:p.Ser99Gly	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	426	0.19505494505494506	159	0.3231707317073171	79	0.21823204419889503	18	0.03146853146853147	170	0.22427440633245382	c	8.672	0.903003	0.17760	0.318202	0.202674	ENSG00000127530	ENST00000248073	T	0.03004	4.08	3.54	-0.988	0.10245	GPCR, rhodopsin-like superfamily (1);	1.124590	0.07101	U	0.840387	T	0.00012	0.0000	M	0.61703	1.905	0.80722	P	0.0	B	0.28552	0.215	B	0.26614	0.071	T	0.43877	-0.9364	9	0.87932	D	0	.	8.1555	0.31167	0.0:0.3568:0.0:0.6432	rs17230134;rs52830580;rs17230134	99	O76099	OR7C1_HUMAN	G	99	ENSP00000248073:S99G	ENSP00000248073:S99G	S	-	1	0	OR7C1	14771654	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-5.089000	0.00152	-0.149000	0.11215	-1.652000	0.00757	AGT	T|0.783;C|0.217	0.217	strong		0.448	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
ROBO3	64221	hgsc.bcm.edu	37	11	124742365	124742365	+	Missense_Mutation	SNP	G	G	A	rs3862618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124742365G>A	ENST00000397801.1	+	8	1439	c.1247G>A	c.(1246-1248)cGt>cAt	p.R416H	ROBO3_ENST00000538940.1_Missense_Mutation_p.R394H	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	416	Ig-like C2-type 4.		R -> H (in dbSNP:rs3862618).		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)		GCGGTGCAGCGTGGGGATGCT	0.602													G|||	645	0.128794	0.0053	0.1023	5008	,	,		18425	0.2698		0.1252	False		,,,				2504	0.1728				p.R416H		Atlas-SNP	.											.	ROBO3	199	.	0			c.G1247A						PASS	.	G	HIS/ARG	93,4145		1,91,2027	68.0	70.0	70.0		1247	3.8	1.0	11	dbSNP_108	70	932,7564		58,816,3374	yes	missense	ROBO3	NM_022370.3	29	59,907,5401	AA,AG,GG		10.9699,2.1944,8.0493	benign	416/1387	124742365	1025,11709	2119	4248	6367	SO:0001583	missense	64221	exon8			TGCAGCGTGGGGA	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.1247G>A	11.37:g.124742365G>A	ENSP00000380903:p.Arg416His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_022370		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	295	0.13507326007326007	6	0.012195121951219513	30	0.08287292817679558	166	0.2902097902097902	93	0.12269129287598944	G	11.06	1.527304	0.27299	0.021944	0.109699	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.75154	-0.91;-0.91	5.7	3.8	0.43715	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.456093	0.18418	N	0.141833	T	0.00012	0.0000	M	0.69185	2.1	0.20638	P	0.999870763	P	0.40931	0.733	B	0.42214	0.38	T	0.07195	-1.0785	9	0.62326	D	0.03	.	5.1705	0.15108	0.0789:0.2467:0.5502:0.1242	rs3862618;rs52800435;rs3862618	416	Q96MS0	ROBO3_HUMAN	H	416;394	ENSP00000380903:R416H;ENSP00000441797:R394H	ENSP00000380903:R416H	R	+	2	0	ROBO3	124247575	0.819000	0.29175	0.994000	0.49952	0.379000	0.30106	1.130000	0.31393	0.728000	0.32382	-0.126000	0.14955	CGT	G|0.872;A|0.128	0.128	strong		0.602	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	
WDR90	197335	hgsc.bcm.edu	37	16	715990	715990	+	Missense_Mutation	SNP	G	G	A	rs7190775	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:715990G>A	ENST00000293879.4	+	36	4475	c.4475G>A	c.(4474-4476)cGc>cAc	p.R1492H	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Missense_Mutation_p.R1494H|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Missense_Mutation_p.R91H|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	30	29	0.966667	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	
TRIM10	10107	hgsc.bcm.edu	37	6	30128442	30128442	+	Missense_Mutation	SNP	C	C	T	rs12212092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30128442C>T	ENST00000449742.2	-	1	269	c.194G>A	c.(193-195)cGt>cAt	p.R65H	TRIM10_ENST00000376704.3_Missense_Mutation_p.R65H|TRIM15_ENST00000376694.4_5'Flank	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	65			R -> H (in dbSNP:rs12212092).		erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						GCTCCCAGGACGGAAGGGTTC	0.612													C|||	455	0.0908546	0.2254	0.0677	5008	,	,		20638	0.002		0.0954	False		,,,				2504	0.0123				p.R65H		Atlas-SNP	.											.	TRIM10	65	.	0			c.G194A						PASS	.	C	HIS/ARG,HIS/ARG	928,3478	354.9+/-312.8	102,724,1377	158.0	166.0	163.0		194,194	2.6	0.6	6	dbSNP_120	163	591,8009	157.3+/-211.0	23,545,3732	yes	missense,missense	TRIM10	NM_006778.3,NM_052828.2	29,29	125,1269,5109	TT,TC,CC		6.8721,21.0622,11.6792	benign,benign	65/482,65/396	30128442	1519,11487	2203	4300	6503	SO:0001583	missense	10107	exon1			CCAGGACGGAAGG	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.194G>A	6.37:g.30128442C>T	ENSP00000397073:p.Arg65His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	58	0.411348	NM_052828	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	37	CCDS34375.1	197	0.0902014652014652	107	0.21747967479674796	25	0.06906077348066299	3	0.005244755244755245	62	0.08179419525065963	C	6.115	0.389391	0.11581	0.210622	0.068721	ENSG00000204613	ENST00000449742;ENST00000376704;ENST00000376706	D;D	0.84223	-1.82;-1.82	5.37	2.61	0.31194	Zinc finger, RING/FYVE/PHD-type (1);	0.241027	0.29972	N	0.010731	T	0.60495	0.2273	L	0.37850	1.14	0.53688	P	2.999999999997449E-5	B;B	0.15719	0.014;0.011	B;B	0.12156	0.003;0.007	T	0.51764	-0.8664	9	0.49607	T	0.09	.	4.6385	0.12536	0.1569:0.5851:0.0:0.258	rs12212092;rs17188092;rs52799461;rs56746532;rs12212092	65;65	Q9UDY6;Q9UDY6-2	TRI10_HUMAN;.	H	65	ENSP00000397073:R65H;ENSP00000365894:R65H	ENSP00000365894:R65H	R	-	2	0	TRIM10	30236421	0.000000	0.05858	0.582000	0.28627	0.212000	0.24457	-0.827000	0.04424	0.776000	0.33473	0.549000	0.68633	CGT	C|0.895;T|0.105	0.105	strong		0.612	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
MVB12B	89853	hgsc.bcm.edu	37	9	129143435	129143435	+	Silent	SNP	A	A	G	rs2286889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:129143435A>G	ENST00000361171.3	+	3	378	c.297A>G	c.(295-297)tcA>tcG	p.S99S	MVB12B_ENST00000436593.3_Silent_p.S84S|MVB12B_ENST00000535766.1_Silent_p.S92S|MVB12B_ENST00000545391.1_Silent_p.S99S	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	99	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										TCACAAGATCATTTTCCAAAG	0.403													A|||	649	0.129593	0.0053	0.1427	5008	,	,		21125	0.2639		0.1113	False		,,,				2504	0.1687				p.S99S		Atlas-SNP	.											.	.	.	.	0			c.A297G						PASS	.	A	,	99,4307	79.3+/-117.8	2,95,2106	104.0	96.0	99.0		297,297	1.5	1.0	9	dbSNP_100	99	956,7644	209.1+/-250.4	52,852,3396	no	coding-synonymous,coding-synonymous	FAM125B	NM_001011703.2,NM_033446.2	,	54,947,5502	GG,GA,AA		11.1163,2.2469,8.1116	,	99/222,99/320	129143435	1055,11951	2203	4300	6503	SO:0001819	synonymous_variant	89853	exon3			AAGATCATTTTCC	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 28"", ""family with sequence similarity 125, member B"""	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.297A>G	9.37:g.129143435A>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_001011703	Q8N6S7	Silent	SNP	ENST00000361171.3	37	CCDS35142.1																																																																																			A|0.895;G|0.105	0.105	strong		0.403	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084435	31084435	+	Intron	SNP	G	G	A	rs1062470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31084435G>A	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.Y319Y|PSORS1C1_ENST00000467107.1_3'UTR	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	21	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	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	
ALDH1L2	160428	hgsc.bcm.edu	37	12	105433523	105433523	+	Silent	SNP	T	T	A	rs4964317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:105433523T>A	ENST00000258494.9	-	17	2153	c.2013A>T	c.(2011-2013)ggA>ggT	p.G671G	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	671	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						TAGGAGTGGATCCAGTGAAAC	0.383													A|||	1555	0.310503	0.1596	0.2622	5008	,	,		19147	0.2619		0.3748	False		,,,				2504	0.5327				p.G671G		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.A2013T						PASS	.	A		858,3548	745.0+/-411.6	74,710,1419	173.0	158.0	163.0		2013	-10.3	0.1	12	dbSNP_111	163	3279,5321	647.4+/-400.4	623,2033,1644	no	coding-synonymous	ALDH1L2	NM_001034173.3		697,2743,3063	AA,AT,TT		38.1279,19.4734,31.8084		671/924	105433523	4137,8869	2203	4300	6503	SO:0001819	synonymous_variant	160428	exon17			AGTGGATCCAGTG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2013A>T	12.37:g.105433523T>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Silent	SNP	ENST00000258494.9	37	CCDS31891.1																																																																																			T|0.687;A|0.313	0.313	strong		0.383	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609806	32609806	+	Missense_Mutation	SNP	C	C	T	rs707952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609806C>T	ENST00000343139.5	+	3	491	c.389C>T	c.(388-390)aCc>aTc	p.T130I	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.T130I|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.T130I	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	129	Alpha-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)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAGCCCAACACCCTCATTTGT	0.507													.|||	937	0.187101	0.2209	0.2392	5008	,	,		18850	0.12		0.2286	False		,,,				2504	0.1309				p.T130I		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C389T						PASS	.	C	ILE/THR	680,2342		130,420,961	156.0	115.0	130.0		389	2.1	1.0	6	dbSNP_86	130	1340,4078		191,958,1560	yes	missense	HLA-DQA1	NM_002122.3	89	321,1378,2521	TT,TC,CC		24.7324,22.5017,23.9336	benign	130/256	32609806	2020,6420	1511	2709	4220	SO:0001583	missense	3117	exon3			CCAACACCCTCAT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.389C>T	6.37:g.32609806C>T	ENSP00000339398:p.Thr130Ile	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	180	101	0.561111	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	444|444	0.2032967032967033|0.2032967032967033	103|103	0.20934959349593496|0.20934959349593496	96|96	0.26519337016574585|0.26519337016574585	87|87	0.1520979020979021|0.1520979020979021	158|158	0.20844327176781002|0.20844327176781002	.|.	7.950|7.950	0.744573|0.744573	0.15710|0.15710	0.225017|0.225017	0.247324|0.247324	ENSG00000196735|ENSG00000196735	ENST00000486548|ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	.|T;T;T;T	.|0.00646	.|6.0;6.0;6.0;6.0	4.1|4.1	2.07|2.07	0.26955|0.26955	.|.	.|0.503713	.|0.18451	.|N	.|0.140840	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.49640|0.49640	1.575|1.575	0.34178|0.34178	P|P	0.32944399999999996|0.32944399999999996	.|B;B	.|0.14012	.|0.009;0.001	.|B;B	.|0.16722	.|0.016;0.016	T|T	0.41124|0.41124	-0.9526|-0.9526	4|9	.|0.26408	.|T	.|0.33	.|.	4.8377|4.8377	0.13473|0.13473	0.0:0.5171:0.0:0.4829|0.0:0.5171:0.0:0.4829	rs707952;rs2308879;rs3176021;rs9272745;rs16870410;rs707952|rs707952;rs2308879;rs3176021;rs9272745;rs16870410;rs707952	.|136;130	.|Q59F33;G4XQK2	.|.;.	S|I	103|130	.|ENSP00000339398:T130I;ENSP00000378767:T130I;ENSP00000437302:T130I;ENSP00000364087:T130I	.|ENSP00000339398:T130I	P|T	+|+	1|2	0|0	HLA-DQA1|HLA-DQA1	32717784|32717784	0.879000|0.879000	0.30193|0.30193	0.999000|0.999000	0.59377|0.59377	0.311000|0.311000	0.27955|0.27955	0.300000|0.300000	0.19156|0.19156	0.410000|0.410000	0.25675|0.25675	0.655000|0.655000	0.94253|0.94253	CCC|ACC	C|0.785;T|0.215	0.215	strong		0.507	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
COQ6	51004	hgsc.bcm.edu	37	14	74428445	74428445	+	Missense_Mutation	SNP	G	G	A	rs8500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74428445G>A	ENST00000334571.2	+	11	1256	c.1216G>A	c.(1216-1218)Gtg>Atg	p.V406M	COQ6_ENST00000394026.4_Missense_Mutation_p.V381M|ENTPD5_ENST00000557325.1_Intron|COQ6_ENST00000554920.1_Intron|COQ6_ENST00000238709.4_Missense_Mutation_p.V331M	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	406			V -> M (in dbSNP:rs8500). {ECO:0000269|Ref.4}.		small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|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)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TTCAGGTTCCGTGAGCCACCT	0.438													A|||	1730	0.345447	0.1868	0.4251	5008	,	,		20118	0.1984		0.4821	False		,,,				2504	0.5143				p.V406M		Atlas-SNP	.											.	COQ6	27	.	0			c.G1216A						PASS	.	A	MET/VAL,MET/VAL	940,3466	736.9+/-410.8	109,722,1372	136.0	132.0	133.0		1216,991	4.1	1.0	14	dbSNP_52	133	4061,4539	594.4+/-393.3	951,2159,1190	yes	missense,missense	COQ6	NM_182476.2,NM_182480.2	21,21	1060,2881,2562	AA,AG,GG		47.2209,21.3345,38.4515	benign,benign	406/469,331/394	74428445	5001,8005	2203	4300	6503	SO:0001583	missense	51004	exon11			GGTTCCGTGAGCC	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.1216G>A	14.37:g.74428445G>A	ENSP00000333946:p.Val406Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	37	CCDS9823.1	745	0.3411172161172161	89	0.18089430894308944	161	0.4447513812154696	129	0.22552447552447552	366	0.48284960422163586	A	8.409	0.843656	0.16963	0.213345	0.472209	ENSG00000119723	ENST00000394026;ENST00000555376;ENST00000238709;ENST00000334571;ENST00000556299	T;T;T	0.51574	0.7;0.7;0.7	5.34	4.14	0.48551	Monooxygenase, FAD-binding (1);	0.168630	0.64402	N	0.000003	T	0.00012	0.0000	N	0.12569	0.235	0.09310	P	0.9999999999998209	B;B;B;B	0.15719	0.014;0.003;0.012;0.008	B;B;B;B	0.20184	0.013;0.006;0.016;0.028	T	0.46233	-0.9206	9	0.31617	T	0.26	-10.2637	6.8788	0.24160	0.7218:0.0:0.0763:0.2019	rs8500;rs1139778;rs2074929;rs3179799;rs3203830;rs52834700;rs60262625;rs8500	381;406;331;331	B7Z3K8;Q9Y2Z9;G3XA86;Q86U30	.;COQ6_HUMAN;.;.	M	381;331;331;406;94	ENSP00000377594:V381M;ENSP00000238709:V331M;ENSP00000333946:V406M	ENSP00000238709:V331M	V	+	1	0	COQ6	73498198	0.993000	0.37304	0.997000	0.53966	0.777000	0.43975	2.062000	0.41413	1.049000	0.40321	-0.254000	0.11334	GTG	G|0.641;A|0.359	0.359	strong		0.438	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
FAM126A	84668	hgsc.bcm.edu	37	7	23030692	23030692	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23030692C>T	ENST00000432176.2	-	2	271	c.39G>A	c.(37-39)ttG>ttA	p.L13L	FAM126A_ENST00000409923.1_Silent_p.L13L|FAM126A_ENST00000409763.1_Silent_p.L13L	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	13					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TAAACTCTGACAACCATTCCT	0.308																																					p.L13L		Atlas-SNP	.											.	FAM126A	53	.	0			c.G39A						PASS	.						107.0	108.0	108.0					7																	23030692		2203	4294	6497	SO:0001819	synonymous_variant	84668	exon2			CTCTGACAACCAT	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.39G>A	7.37:g.23030692C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	139	106	0.76259	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1																																																																																			.	.	none		0.308	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
ZADH2	284273	hgsc.bcm.edu	37	18	72913920	72913920	+	Silent	SNP	C	C	T	rs61910717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72913920C>T	ENST00000322342.3	-	2	874	c.585G>A	c.(583-585)aaG>aaA	p.K195K	ZADH2_ENST00000537114.2_Silent_p.K72K	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	195						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		GGCACTTTGCCTTCTTTGAAA	0.478													C|||	127	0.0253594	0.003	0.0202	5008	,	,		21275	0.0		0.0358	False		,,,				2504	0.0746				p.K195K		Atlas-SNP	.											.	ZADH2	25	.	0			c.G585A						PASS	.	C		38,4368	41.6+/-74.8	0,38,2165	177.0	189.0	185.0		585	2.3	0.6	18	dbSNP_129	185	317,8283	111.0+/-171.3	5,307,3988	no	coding-synonymous	ZADH2	NM_175907.4		5,345,6153	TT,TC,CC		3.686,0.8625,2.7295		195/378	72913920	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	284273	exon2			CTTTGCCTTCTTT	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.585G>A	18.37:g.72913920C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	59	0.702381	NM_175907	A8KA15|B4DZ91	Silent	SNP	ENST00000322342.3	37	CCDS12008.1																																																																																			C|0.973;T|0.027	0.027	strong		0.478	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907	
STK40	83931	hgsc.bcm.edu	37	1	36820927	36820927	+	Silent	SNP	G	G	A	rs11263875	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:36820927G>A	ENST00000373129.3	-	6	856	c.450C>T	c.(448-450)agC>agT	p.S150S	STK40_ENST00000359297.2_Silent_p.S150S|STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373130.3_Silent_p.S155S|STK40_ENST00000373132.3_Silent_p.S150S	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CGGTCTTATCGCTGAAGTCAT	0.537													G|||	423	0.0844649	0.0514	0.098	5008	,	,		25098	0.0407		0.1163	False		,,,				2504	0.1319				p.S150S		Atlas-SNP	.											.	STK40	53	.	0			c.C450T						PASS	.	G		268,4138	152.5+/-186.2	12,244,1947	300.0	260.0	273.0		450	-3.3	1.0	1	dbSNP_120	273	1045,7555	221.7+/-259.0	65,915,3320	no	coding-synonymous	STK40	NM_032017.1		77,1159,5267	AA,AG,GG		12.1512,6.0826,10.0953		150/436	36820927	1313,11693	2203	4300	6503	SO:0001819	synonymous_variant	83931	exon6			CTTATCGCTGAAG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.450C>T	1.37:g.36820927G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	145	142	0.97931	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	37	CCDS407.1																																																																																			G|0.907;A|0.093	0.093	strong		0.537	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
DOCK8	81704	hgsc.bcm.edu	37	9	377111	377111	+	Silent	SNP	G	G	C	rs10814431	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:377111G>C	ENST00000453981.1	+	20	2452	c.2340G>C	c.(2338-2340)ctG>ctC	p.L780L	DOCK8_ENST00000469391.1_Silent_p.L712L|DOCK8_ENST00000382331.1_Silent_p.L82L|DOCK8_ENST00000432829.2_Silent_p.L712L|DOCK8_ENST00000382329.1_Silent_p.L247L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	780					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)		TCATCTGCCTGAACTCCTCCC	0.612													G|||	1145	0.228634	0.3094	0.2262	5008	,	,		18085	0.0794		0.2505	False		,,,				2504	0.2526				p.L780L		Atlas-SNP	.											.	DOCK8	401	.	0			c.G2340C						PASS	.	G	,,	1271,3135	430.1+/-342.5	177,917,1109	59.0	42.0	48.0		2136,2136,2340	-11.2	0.7	9	dbSNP_120	48	2196,6404	371.0+/-336.1	275,1646,2379	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	452,2563,3488	CC,CG,GG		25.5349,28.847,26.6569	,,	712/2000,712/2032,780/2100	377111	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon20			CTGCCTGAACTCC	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.2340G>C	9.37:g.377111G>C		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			G|0.749;C|0.251	0.251	strong		0.612	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
SYNE1	23345	hgsc.bcm.edu	37	6	152534768	152534768	+	Silent	SNP	C	C	T	rs34891041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152534768C>T	ENST00000367255.5	-	123	23074	c.22473G>A	c.(22471-22473)ttG>ttA	p.L7491L	SYNE1_ENST00000341594.5_Silent_p.L7103L|SYNE1_ENST00000356820.4_Silent_p.L2015L|SYNE1_ENST00000423061.1_Silent_p.L7420L|SYNE1_ENST00000265368.4_Silent_p.L7491L|SYNE1_ENST00000448038.1_Silent_p.L7420L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7491					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)		TCTGCTGTTCCAAAAGGTGCT	0.393										HNSCC(10;0.0054)			C|||	103	0.0205671	0.0378	0.0173	5008	,	,		18365	0.0129		0.0249	False		,,,				2504	0.0031				p.L7491L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G22473A						PASS	.	C	,	193,4213	122.1+/-159.5	5,183,2015	294.0	289.0	290.0		22260,22473	4.6	1.0	6	dbSNP_126	290	233,8367	95.2+/-157.0	3,227,4070	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	8,410,6085	TT,TC,CC		2.7093,4.3804,3.2754	,	7420/8750,7491/8798	152534768	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon123			CTGTTCCAAAAGG	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.22473G>A	6.37:g.152534768C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	243	133	0.547325	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|0.969;T|0.031	0.031	strong		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TUBA1B	10376	hgsc.bcm.edu	37	12	49522578	49522578	+	Silent	SNP	T	T	C	rs1057725|rs11267025	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49522578T>C	ENST00000336023.5	-	4	613	c.519A>G	c.(517-519)ccA>ccG	p.P173P	RP11-386G11.10_ENST00000551496.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000547387.1_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	191	0	0		WXS	Illumina HiSeq	Phase_I	156	55	0.352564	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	
IGFN1	91156	hgsc.bcm.edu	37	1	201168499	201168499	+	Silent	SNP	G	G	A	rs1534057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201168499G>A	ENST00000335211.4	+	6	535	c.405G>A	c.(403-405)ccG>ccA	p.P135P	IGFN1_ENST00000451870.2_Silent_p.P135P|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	135						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						ACAGGGAACCGCAGGAAGGTA	0.547													G|||	994	0.198482	0.1498	0.2075	5008	,	,		20083	0.256		0.1501	False		,,,				2504	0.2485				p.P135P		Atlas-SNP	.											.	IGFN1	220	.	0			c.G405A						PASS	.	G		184,1200		10,164,518	117.0	117.0	117.0		405	-3.7	0.7	1	dbSNP_88	117	457,2725		32,393,1166	no	coding-synonymous	IGFN1	NM_001164586.1		42,557,1684	AA,AG,GG		14.362,13.2948,14.0385		135/3709	201168499	641,3925	692	1591	2283	SO:0001819	synonymous_variant	91156	exon6			GGAACCGCAGGAA	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.405G>A	1.37:g.201168499G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	133	86	0.646617	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																			G|0.819;A|0.181	0.181	strong		0.547	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
BANP	54971	hgsc.bcm.edu	37	16	88105725	88105725	+	Silent	SNP	G	G	A	rs8050209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88105725G>A	ENST00000393207.1	+	13	1616	c.1395G>A	c.(1393-1395)gcG>gcA	p.A465A	BANP_ENST00000393208.2_Silent_p.A437A|BANP_ENST00000355022.4_Silent_p.A415A|BANP_ENST00000355163.5_Silent_p.A443A|BANP_ENST00000479780.2_Silent_p.A412A|BANP_ENST00000286122.7_Silent_p.A465A|BANP_ENST00000538234.1_Silent_p.A454A|BANP_ENST00000481948.1_3'UTR	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	465					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		ACCCCGCGGCGGCGGGCGTGG	0.706													g|||	2278	0.454872	0.525	0.3804	5008	,	,		14347	0.3016		0.5388	False		,,,				2504	0.4847				p.A465A		Atlas-SNP	.											.	BANP	67	.	0			c.G1395A						PASS	.	A	,,,,,,	2401,1967		708,985,491	13.0	14.0	14.0		1353,1329,1236,1362,1395,1245,1311	-11.6	0.0	16	dbSNP_116	14	4625,3925		1296,2033,946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	2004,3018,1437	AA,AG,GG		45.9064,45.0321,45.6108	,,,,,,	451/506,443/498,412/467,454/509,465/520,415/470,437/492	88105725	7026,5892	2184	4275	6459	SO:0001819	synonymous_variant	54971	exon13			CGCGGCGGCGGGC	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1395G>A	16.37:g.88105725G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_001173543	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			G|0.524;A|0.476	0.476	strong		0.706	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
CARD10	29775	hgsc.bcm.edu	37	22	37915100	37915100	+	Silent	SNP	A	A	G	rs7287804	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37915100A>G	ENST00000403299.1	-	2	324	c.108T>C	c.(106-108)caT>caC	p.H36H	CARD10_ENST00000251973.5_Silent_p.H36H			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	36	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GAGCCAGCCGATGCCGGACGC	0.736													G|||	564	0.11262	0.2973	0.072	5008	,	,		10615	0.0476		0.0487	False		,,,				2504	0.0245				p.H36H		Atlas-SNP	.											.	CARD10	55	.	0			c.T108C						PASS	.	G		1112,3172		141,830,1171	13.0	14.0	13.0		108	2.9	1.0	22	dbSNP_116	13	399,8047		6,387,3830	no	coding-synonymous	CARD10	NM_014550.3		147,1217,5001	GG,GA,AA		4.7241,25.957,11.8696		36/1033	37915100	1511,11219	2142	4223	6365	SO:0001819	synonymous_variant	29775	exon1			CAGCCGATGCCGG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.108T>C	22.37:g.37915100A>G		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.879;G|0.121	0.121	strong		0.736	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
DDIT3	1649	hgsc.bcm.edu	37	12	57911160	57911160	+	Silent	SNP	G	G	A	rs697221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57911160G>A	ENST00000346473.3	-	3	209	c.30C>T	c.(28-30)ttC>ttT	p.F10F	DDIT3_ENST00000552740.1_Silent_p.F33F|DDIT3_ENST00000547303.1_Silent_p.F10F|MIR616_ENST00000385293.1_RNA|DDIT3_ENST00000551116.1_Silent_p.F33F	NM_001195057.1|NM_004083.5	NP_001181986.1|NP_004074.2	P35638	DDIT3_HUMAN	DNA-damage-inducible transcript 3	10	Interaction with TRIB3.|N-terminal.			FGTLS -> SDTV (in Ref. 1; AAB22646). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|blood vessel maturation (GO:0001955)|cell cycle arrest (GO:0007050)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of determination of dorsal identity (GO:2000016)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|regulation of transcription, DNA-templated (GO:0006355)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to starvation (GO:0042594)|response to unfolded protein (GO:0006986)|Wnt signaling pathway (GO:0016055)	late endosome (GO:0005770)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)		EWSR1/DDIT3(45)|FUS/DDIT3(631)	central_nervous_system(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)	16						ACAGTGTCCCGAAGGAGAAAG	0.522			T	FUS	liposarcoma								G|||	1009	0.201478	0.2421	0.1398	5008	,	,		21716	0.245		0.175	False		,,,				2504	0.1728				p.F33F	GBM(112;1383 1547 7626 23045 28770)	Atlas-SNP	.		Dom	yes		12	12q13.1-q13.2	1649	DNA-damage-inducible transcript 3		M	.	DDIT3	29	.	0			c.C99T						PASS	.	G	,,,,,	975,3431	366.1+/-317.7	106,763,1334	64.0	59.0	60.0		99,99,99,99,30,30	-7.6	0.7	12	dbSNP_86	60	1233,7367	248.2+/-276.0	87,1059,3154	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDIT3	NM_001195053.1,NM_001195054.1,NM_001195055.1,NM_001195056.1,NM_001195057.1,NM_004083.5	,,,,,	193,1822,4488	AA,AG,GG		14.3372,22.1289,16.9768	,,,,,	33/193,33/193,33/193,33/193,10/170,10/170	57911160	2208,10798	2203	4300	6503	SO:0001819	synonymous_variant	1649	exon3			TGTCCCGAAGGAG	BC003637	CCDS8943.1, CCDS55838.1	12q13.1-q13.2	2008-02-05				ENSG00000175197			2726	protein-coding gene	gene with protein product	"""C/EBP zeta"""	126337				1990262	Standard	NM_001195053		Approved	CHOP10, GADD153, CHOP	uc021qzk.1	P35638		ENST00000346473.3:c.30C>T	12.37:g.57911160G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001195054	F8VS99	Silent	SNP	ENST00000346473.3	37	CCDS8943.1																																																																																			G|0.811;A|0.189	0.189	strong		0.522	DDIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407137.1	NM_004083	
TAB2	23118	hgsc.bcm.edu	37	6	149700491	149700491	+	Silent	SNP	G	G	A	rs3734296	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:149700491G>A	ENST00000367456.1	+	4	2017	c.1440G>A	c.(1438-1440)gtG>gtA	p.V480V	TAB2_ENST00000536230.1_Silent_p.V448V|TAB2_ENST00000286332.5_Silent_p.V480V|TAB2_ENST00000392282.1_Silent_p.V480V|TAB2_ENST00000538427.1_Silent_p.V480V			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	480					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|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)|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 protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|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)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						CACCAGGGGTGGTGTCCCCTA	0.453													G|||	1092	0.218051	0.0552	0.2507	5008	,	,		18785	0.5496		0.0944	False		,,,				2504	0.2004				p.V480V		Atlas-SNP	.											.	TAB2	55	.	0			c.G1440A						PASS	.	G		277,4129	156.3+/-189.4	8,261,1934	91.0	87.0	89.0		1440	-4.4	0.2	6	dbSNP_107	89	909,7691	202.7+/-245.9	53,803,3444	no	coding-synonymous	TAB2	NM_015093.4		61,1064,5378	AA,AG,GG		10.5698,6.2869,9.1189		480/694	149700491	1186,11820	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGGGGTGGTGTCC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.1440G>A	6.37:g.149700491G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	47	0.618421	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			G|0.856;A|0.144	0.144	strong		0.453	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
TOPBP1	11073	hgsc.bcm.edu	37	3	133368362	133368362	+	Missense_Mutation	SNP	T	T	G	rs3192149	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133368362T>G	ENST00000260810.5	-	10	1500	c.1369A>C	c.(1369-1371)Aag>Cag	p.K457Q	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	457				K -> Q (in Ref. 1; BAA34202 and 2; BAA13389). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTTTCAGGCTTATGTGAAACT	0.383								Other conserved DNA damage response genes					G|||	3485	0.695887	0.7905	0.6398	5008	,	,		18413	0.625		0.7724	False		,,,				2504	0.6022				p.K457Q	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A1369C						PASS	.	G	GLN/LYS	2902,788		1141,620,84	165.0	155.0	158.0		1369	4.8	0.9	3	dbSNP_105	158	6273,1909		2416,1441,234	yes	missense	TOPBP1	NM_007027.3	53	3557,2061,318	GG,GT,TT		23.3317,21.355,22.7173	benign	457/1523	133368362	9175,2697	1845	4091	5936	SO:0001583	missense	11073	exon10			CAGGCTTATGTGA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.1369A>C	3.37:g.133368362T>G	ENSP00000260810:p.Lys457Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	203	203	1	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	1558	0.7133699633699634	384	0.7804878048780488	226	0.6243093922651933	364	0.6363636363636364	584	0.7704485488126649	G	2.916	-0.224167	0.06061	0.78645	0.766683	ENSG00000163781	ENST00000260810	T	0.11712	2.75	5.72	4.84	0.62591	.	0.483083	0.23775	N	0.044697	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19943	-1.0290	9	0.09843	T	0.71	.	15.3445	0.74324	0.0:0.0:0.7446:0.2554	rs3192149;rs16840574;rs52800635;rs58841240;rs3192149	457	Q92547	TOPB1_HUMAN	Q	457	ENSP00000260810:K457Q	ENSP00000260810:K457Q	K	-	1	0	TOPBP1	134851052	0.993000	0.37304	0.921000	0.36526	0.784000	0.44337	3.153000	0.50685	0.777000	0.33496	-0.127000	0.14921	AAG	T|0.283;G|0.717	0.717	strong		0.383	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
BCORL1	63035	hgsc.bcm.edu	37	X	129147373	129147373	+	Missense_Mutation	SNP	G	G	A	rs5932715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:129147373G>A	ENST00000218147.7	+	4	822	c.625G>A	c.(625-627)Ggt>Agt	p.G209S	BCORL1_ENST00000303743.5_Missense_Mutation_p.G209S|BCORL1_ENST00000359304.2_Missense_Mutation_p.G209S|BCORL1_ENST00000540052.1_Missense_Mutation_p.G209S			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	209	Pro-rich.		G -> S (in dbSNP:rs5932715).		chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CCCTGCTCCCGGTTCGGCCTC	0.612													G|||	98	0.0259603	0.0023	0.0231	3775	,	,		13002	0.0		0.0716	False		,,,				2504	0.0072				p.G209S		Atlas-SNP	.											.	BCORL1	213	.	0			c.G625A						PASS	.	G	SER/GLY	54,3781		2,38,12,1592,559	131.0	120.0	124.0		625	2.7	0.5	X	dbSNP_114	124	691,6037		25,448,193,1955,1679	yes	missense	BCORL1	NM_021946.4	56	27,486,205,3547,2238	AA,AG,A,GG,G		10.2705,1.4081,7.0529	benign	209/1712	129147373	745,9818	2203	4300	6503	SO:0001583	missense	63035	exon3			GCTCCCGGTTCGG	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.625G>A	X.37:g.129147373G>A	ENSP00000218147:p.Gly209Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	37	CCDS14616.1	69	0.04159132007233273	1	0.0020325203252032522	5	0.014044943820224719	0	0.0	47	0.06420765027322405	G	0.037	-1.301551	0.01353	0.014081	0.102705	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052	T;T;T;T	0.37752	1.18;1.54;1.18;1.18	4.72	2.71	0.32032	.	0.410734	0.17757	N	0.163038	T	0.00356	0.0011	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	0.14282	-1.0478	8	.	.	.	-2.8823	1.3641	0.02197	0.2237:0.1629:0.4453:0.1681	rs5932715	209;209	Q5H9F3-2;Q5H9F3	.;BCORL_HUMAN	S	209	ENSP00000218147:G209S;ENSP00000307541:G209S;ENSP00000352253:G209S;ENSP00000437775:G209S	.	G	+	1	0	BCORL1	128975054	0.507000	0.26146	0.454000	0.27019	0.119000	0.20118	1.922000	0.40045	0.603000	0.29913	0.436000	0.28706	GGT	G|0.944;A|0.056	0.056	strong		0.612	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946	
WWC2	80014	hgsc.bcm.edu	37	4	184192278	184192278	+	Missense_Mutation	SNP	G	G	T	rs11734376	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184192278G>T	ENST00000403733.3	+	16	2645	c.2446G>T	c.(2446-2448)Gtt>Ttt	p.V816F	WWC2_ENST00000513834.1_Missense_Mutation_p.V767F|WWC2_ENST00000504005.1_Missense_Mutation_p.V498F|WWC2_ENST00000448232.2_Missense_Mutation_p.V816F	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	816			V -> F (in dbSNP:rs11734376). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TTCCAGTGAGGTTTTCACTCT	0.363													G|||	319	0.0636981	0.0083	0.1052	5008	,	,		15336	0.0		0.1431	False		,,,				2504	0.093				p.V816F		Atlas-SNP	.											.	WWC2	78	.	0			c.G2446T						PASS	.	G	PHE/VAL	138,4268	94.8+/-133.5	1,136,2066	48.0	46.0	47.0		2446	-2.0	1.0	4	dbSNP_120	47	1320,7280	251.2+/-277.8	112,1096,3092	yes	missense	WWC2	NM_024949.5	50	113,1232,5158	TT,TG,GG		15.3488,3.1321,11.2102	benign	816/1193	184192278	1458,11548	2203	4300	6503	SO:0001583	missense	80014	exon16			AGTGAGGTTTTCA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2446G>T	4.37:g.184192278G>T	ENSP00000384222:p.Val816Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	155	0.07097069597069597	6	0.012195121951219513	50	0.13812154696132597	0	0.0	99	0.13060686015831136	G	5.020	0.189364	0.09547	0.031321	0.153488	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.52	-2.0	0.07433	C2 calcium/lipid-binding domain, CaLB (1);	0.638313	0.15838	N	0.242183	T	0.00109	0.0003	L	0.31926	0.97	0.31401	P	0.6767179999999999	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.08055	0.003;0.002;0.002	T	0.24368	-1.0162	9	0.09338	T	0.73	-1.9517	6.7782	0.23630	0.4971:0.0:0.3839:0.119	rs11734376;rs17846520;rs17859593;rs52823830;rs57873564;rs11734376	816;816;767	Q6AWC2-6;Q6AWC2;Q6AWC2-4	.;WWC2_HUMAN;.	F	816;767;816;498	ENSP00000384222:V816F;ENSP00000425054:V767F;ENSP00000398577:V816F;ENSP00000427569:V498F	ENSP00000384222:V816F	V	+	1	0	WWC2	184429272	0.792000	0.28813	0.985000	0.45067	0.848000	0.48234	0.175000	0.16762	-0.093000	0.12396	-0.253000	0.11424	GTT	G|0.902;T|0.098	0.098	strong		0.363	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
TMEM132C	92293	hgsc.bcm.edu	37	12	128900005	128900005	+	Missense_Mutation	SNP	G	G	A	rs1683723	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:128900005G>A	ENST00000435159.2	+	2	814	c.814G>A	c.(814-816)Gtc>Atc	p.V272I		NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	272			V -> I (in dbSNP:rs1683723).			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						GATCGGCACCGTCGGCCTTTA	0.637													G|||	2556	0.510383	0.2526	0.5908	5008	,	,		18038	0.5992		0.4622	False		,,,				2504	0.7597				p.V272I		Atlas-SNP	.											TMEM132C_ENST00000435159,colon,carcinoma,-2,1	TMEM132C	142	1	0			c.G814A						scavenged	.	G	ILE/VAL	405,979		62,281,349	62.0	70.0	67.0		814	4.2	0.0	12	dbSNP_89	67	1484,1698		346,792,453	yes	missense	TMEM132C	NM_001136103.2	29	408,1073,802	AA,AG,GG		46.6373,29.263,41.371	benign	272/1109	128900005	1889,2677	692	1591	2283	SO:0001583	missense	92293	exon2			GGCACCGTCGGCC	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.814G>A	12.37:g.128900005G>A	ENSP00000410852:p.Val272Ile	Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		1031	0.47206959706959706	128	0.2601626016260163	204	0.56353591160221	343	0.5996503496503497	356	0.46965699208443273	G	0.055	-1.237788	0.01493	0.29263	0.466373	ENSG00000181234	ENST00000435159	T	0.11495	2.77	5.08	4.18	0.49190	.	.	.	.	.	T	0.00012	0.0000	N	0.20357	0.565	0.53688	P	2.8000000000028002E-5	B	0.32543	0.375	B	0.24394	0.053	T	0.12528	-1.0544	8	0.17369	T	0.5	.	8.0732	0.30701	0.3101:0.0:0.6899:0.0	rs1683723;rs17797133;rs52813618;rs58190173;rs1683723	272	Q8N3T6	T132C_HUMAN	I	272	ENSP00000410852:V272I	ENSP00000410852:V272I	V	+	1	0	TMEM132C	127465958	0.789000	0.28775	0.014000	0.15608	0.024000	0.10985	1.105000	0.31086	1.239000	0.43787	0.650000	0.86243	GTC	G|0.536;A|0.464	0.464	strong		0.637	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
CAPN13	92291	hgsc.bcm.edu	37	2	30976058	30976058	+	Silent	SNP	C	C	T	rs2926304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:30976058C>T	ENST00000295055.8	-	10	1124	c.948G>A	c.(946-948)tcG>tcA	p.S316S	CAPN13_ENST00000534090.2_Silent_p.S316S	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	316	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.S316S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AATCTTGACACGACATCCTGT	0.473													T|||	1922	0.383786	0.1475	0.4928	5008	,	,		21621	0.5109		0.4085	False		,,,				2504	0.4693				p.S316S		Atlas-SNP	.											CAPN13,NS,carcinoma,0,1	CAPN13	70	1	1	Substitution - coding silent(1)	stomach(1)	c.G948A						PASS	.	T		664,3172		56,552,1310	151.0	135.0	140.0		948	-2.4	1.0	2	dbSNP_101	140	3303,4941		657,1989,1476	no	coding-synonymous	CAPN13	NM_144575.2		713,2541,2786	TT,TC,CC		40.0655,17.3097,32.8394		316/670	30976058	3967,8113	1918	4122	6040	SO:0001819	synonymous_variant	92291	exon10			TTGACACGACATC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.948G>A	2.37:g.30976058C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	37	CCDS46252.1																																																																																			C|0.617;N|0.000	.	strong		0.473	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
KRT76	51350	hgsc.bcm.edu	37	12	53162528	53162528	+	Missense_Mutation	SNP	G	G	A	rs2280480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53162528G>A	ENST00000332411.2	-	9	1939	c.1886C>T	c.(1885-1887)aCg>aTg	p.T629M		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	629	Tail.		T -> M (in dbSNP:rs2280480).		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						GCTTGAGCTCGTGGTCTGGGA	0.542													G|||	831	0.165935	0.0401	0.2795	5008	,	,		17508	0.1538		0.2644	False		,,,				2504	0.1667				p.T629M		Atlas-SNP	.											.	KRT76	72	.	0			c.C1886T						PASS	.	G	MET/THR	279,4127	156.6+/-189.7	8,263,1932	163.0	161.0	161.0		1886	2.2	1.0	12	dbSNP_100	161	2334,6266	390.9+/-343.5	308,1718,2274	yes	missense	KRT76	NM_015848.4	81	316,1981,4206	AA,AG,GG		27.1395,6.3323,20.0907	probably-damaging	629/639	53162528	2613,10393	2203	4300	6503	SO:0001583	missense	51350	exon9			GAGCTCGTGGTCT	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.1886C>T	12.37:g.53162528G>A	ENSP00000330101:p.Thr629Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	400	0.18315018315018314	32	0.06504065040650407	90	0.24861878453038674	86	0.15034965034965034	192	0.2532981530343008	g	9.686	1.150608	0.21371	0.063323	0.271395	ENSG00000185069	ENST00000332411	D	0.83837	-1.77	4.14	2.21	0.28008	.	0.639211	0.13003	N	0.421514	T	0.00012	0.0000	N	0.08118	0	0.29465	P	0.857477	D	0.54047	0.964	B	0.37422	0.249	T	0.04153	-1.0973	9	0.87932	D	0	.	12.4355	0.55596	0.0:0.4951:0.5049:0.0	rs2280480;rs17370790;rs52796754;rs59105661;rs2280480	629	Q01546	K22O_HUMAN	M	629	ENSP00000330101:T629M	ENSP00000330101:T629M	T	-	2	0	KRT76	51448795	0.998000	0.40836	0.989000	0.46669	0.439000	0.31926	0.746000	0.26275	0.446000	0.26666	-0.181000	0.13052	ACG	G|0.811;A|0.189	0.189	strong		0.542	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
UTP20	27340	hgsc.bcm.edu	37	12	101732655	101732655	+	Silent	SNP	C	C	T	rs56265469	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:101732655C>T	ENST00000261637.4	+	31	4107	c.3933C>T	c.(3931-3933)agC>agT	p.S1311S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1311					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AGTATCTCAGCAAAACCACAA	0.328													C|||	1285	0.256589	0.1536	0.317	5008	,	,		17124	0.375		0.2376	False		,,,				2504	0.2505				p.S1311S		Atlas-SNP	.											.	UTP20	222	.	0			c.C3933T						PASS	.	C		768,3638	310.2+/-291.5	64,640,1499	95.0	94.0	95.0		3933	4.4	1.0	12	dbSNP_129	95	2074,6522	356.5+/-330.3	268,1538,2492	no	coding-synonymous	UTP20	NM_014503.2		332,2178,3991	TT,TC,CC		24.1275,17.4308,21.8582		1311/2786	101732655	2842,10160	2203	4298	6501	SO:0001819	synonymous_variant	27340	exon31			TCTCAGCAAAACC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.3933C>T	12.37:g.101732655C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.766;T|0.234	0.234	strong		0.328	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
BCLAF1	9774	hgsc.bcm.edu	37	6	136589431	136589431	+	Missense_Mutation	SNP	C	C	T	rs150210620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:136589431C>T	ENST00000531224.1	-	10	2518	c.2266G>A	c.(2266-2268)Gca>Aca	p.A756T	BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527536.1_Missense_Mutation_p.A756T|BCLAF1_ENST00000530767.1_Missense_Mutation_p.A583T|BCLAF1_ENST00000527759.1_Missense_Mutation_p.A754T|BCLAF1_ENST00000353331.4_Missense_Mutation_p.A754T|BCLAF1_ENST00000392348.2_Missense_Mutation_p.A754T|BCLAF1_ENST00000031135.9_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	756	Poly-Ser.				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)		GAAGGTGATGCTGAAGAGGAT	0.343																																					p.A756T	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.G2266A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	6,4400	4.2+/-10.8	0,6,2197	129.0	113.0	118.0		2260,1747,2266	3.0	1.0	6	dbSNP_134	118	39,8561	11.2+/-40.8	0,39,4261	yes	missense,missense,missense	BCLAF1	NM_001077440.1,NM_001077441.1,NM_014739.2	58,58,58	0,45,6458	TT,TC,CC		0.4535,0.1362,0.346	possibly-damaging,possibly-damaging,possibly-damaging	754/870,583/748,756/921	136589431	45,12961	2203	4300	6503	SO:0001583	missense	9774	exon10			GTGATGCTGAAGA	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.2266G>A	6.37:g.136589431C>T	ENSP00000435210:p.Ala756Thr	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	146	21	0.143836	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.549504	0.27652	0.001362	0.004535	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54	4.87	2.96	0.34315	.	0.352858	0.24240	N	0.040278	T	0.02119	0.0066	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.16396	0.0;0.017;0.0;0.0;0.0	B;B;B;B;B	0.12156	0.0;0.007;0.0;0.0;0.0	T	0.34527	-0.9825	10	0.37606	T	0.19	-8.6063	3.5805	0.07950	0.135:0.4505:0.3176:0.0969	.	754;84;754;756;583	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	T	756;754;756;583;754;754	ENSP00000435210:A756T;ENSP00000229446:A754T;ENSP00000435441:A756T;ENSP00000436501:A583T;ENSP00000434826:A754T;ENSP00000376159:A754T	ENSP00000229446:A754T	A	-	1	0	BCLAF1	136631124	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.285000	0.43487	2.431000	0.82371	0.484000	0.47621	GCA	C|0.996;T|0.004	0.004	strong		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
GATA6	2627	hgsc.bcm.edu	37	18	19762989	19762989	+	Silent	SNP	A	A	G	rs117646477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:19762989A>G	ENST00000269216.3	+	6	1882	c.1605A>G	c.(1603-1605)caA>caG	p.Q535Q	RNU6-702P_ENST00000364982.1_RNA|GATA6_ENST00000581694.1_Silent_p.Q535Q	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	535					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			CCACAACACAACCTACAGCCT	0.393													A|||	3	0.000599042	0.0	0.0	5008	,	,		15678	0.0		0.002	False		,,,				2504	0.001				p.Q535Q	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.A1605G						PASS	.	A		0,4406		0,0,2203	104.0	92.0	96.0		1605	2.4	1.0	18	dbSNP_133	96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GATA6	NM_005257.3		0,4,6499	GG,GA,AA		0.0465,0.0,0.0308		535/596	19762989	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2627	exon6			AACACAACCTACA	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"""GATA zinc finger domain containing"""	4174	protein-coding gene	gene with protein product		601656	"""GATA-binding protein 6"""			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1605A>G	18.37:g.19762989A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	160	97	0.60625	NM_005257	B0YJ17|P78327	Silent	SNP	ENST00000269216.3	37	CCDS11872.1																																																																																			A|0.999;G|0.001	0.001	strong		0.393	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257	
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16852206	16852206	+	Silent	SNP	A	A	C	rs35062843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:16852206A>C	ENST00000261652.2	-	3	303	c.291T>G	c.(289-291)ccT>ccG	p.P97P	TNFRSF13B_ENST00000581616.2_5'UTR|TNFRSF13B_ENST00000437538.2_Silent_p.P51P|TNFRSF13B_ENST00000583789.1_Silent_p.P51P|TNFRSF13B_ENST00000579315.1_Silent_p.P97P	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	97					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						CACATTGCTTAGGGTGCTGTC	0.537									IgA Deficiency, Selective				A|||	243	0.0485224	0.0265	0.0533	5008	,	,		21074	0.0089		0.0408	False		,,,				2504	0.1237				p.P97P		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.T291G						PASS	.	A		115,4291	87.8+/-126.4	2,111,2090	163.0	144.0	150.0		291	-2.4	0.8	17	dbSNP_126	150	296,8304	108.6+/-169.2	6,284,4010	no	coding-synonymous	TNFRSF13B	NM_012452.2		8,395,6100	CC,CA,AA		3.4419,2.6101,3.1601		97/294	16852206	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	23495	exon3	Familial Cancer Database	IGAD1, IGAD2	TTGCTTAGGGTGC	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.291T>G	17.37:g.16852206A>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	84	0.531646	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Silent	SNP	ENST00000261652.2	37	CCDS11181.1																																																																																			A|0.968;C|0.032	0.032	strong		0.537	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
GABRA6	2559	hgsc.bcm.edu	37	5	161117243	161117243	+	Missense_Mutation	SNP	A	A	G	rs76773579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:161117243A>G	ENST00000274545.5	+	7	1143	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	GABRA6_ENST00000523217.1_Missense_Mutation_p.Q227R|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	237					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|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)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		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)	TTCCACTTGCAAAGGAAGATG	0.393										TCGA Ovarian(5;0.080)			A|||	4	0.000798722	0.0	0.0014	5008	,	,		19724	0.0		0.002	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.											.	GABRA6	139	.	0			c.A710G						PASS	.	A	ARG/GLN	1,4405	2.1+/-5.4	0,1,2202	152.0	135.0	141.0		710	5.3	1.0	5	dbSNP_131	141	35,8565	24.6+/-71.5	0,35,4265	yes	missense	GABRA6	NM_000811.2	43	0,36,6467	GG,GA,AA		0.407,0.0227,0.2768	benign	237/454	161117243	36,12970	2203	4300	6503	SO:0001583	missense	2559	exon7			ACTTGCAAAGGAA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.710A>G	5.37:g.161117243A>G	ENSP00000274545:p.Gln237Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	A|A	14.82|14.82	2.648356|2.648356	0.47258|0.47258	2.27E-4|2.27E-4	0.00407|0.00407	ENSG00000145863|ENSG00000145863	ENST00000520000|ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	.|T;T;T;T	.|0.75589	.|-0.95;-0.95;-0.95;-0.95	5.31|5.31	5.31|5.31	0.75309|0.75309	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.053501	.|0.85682	.|D	.|0.000000	T|T	0.57257|0.57257	0.2041|0.2041	N|N	0.04959|0.04959	-0.14|-0.14	0.47778|0.47778	D|D	0.999516|0.999516	.|B	.|0.20052	.|0.041	.|B	.|0.25405	.|0.06	T|T	0.55547|0.55547	-0.8124|-0.8124	5|10	.|0.39692	.|T	.|0.17	.|.	15.2733|15.2733	0.73723|0.73723	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|237	.|Q16445	.|GBRA6_HUMAN	E|R	177|237;227;184;157	.|ENSP00000274545:Q237R;ENSP00000430527:Q227R;ENSP00000430212:Q184R;ENSP00000427989:Q157R	.|ENSP00000274545:Q237R	K|Q	+|+	1|2	0|0	GABRA6|GABRA6	161049821|161049821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.423000|7.423000	0.80229|0.80229	2.016000|2.016000	0.59253|0.59253	0.533000|0.533000	0.62120|0.62120	AAA|CAA	A|0.997;G|0.003	0.003	strong		0.393	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
AOX1	316	hgsc.bcm.edu	37	2	201534389	201534389	+	Missense_Mutation	SNP	A	A	G	rs3731722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:201534389A>G	ENST00000374700.2	+	34	4131	c.3890A>G	c.(3889-3891)cAt>cGt	p.H1297R	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1297			H -> R (increases homodimerization and turnover number with phenanthridine as substrate; nearly no effect on kinetic parameters with benzaldehyde, phtalazine and chloroquinazolinone as substrate; dbSNP:rs3731722). {ECO:0000269|PubMed:22279051}.		inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.H1297R(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	AGAGGCCTGCATGGACCCTTG	0.512													A|||	422	0.0842652	0.0386	0.1571	5008	,	,		15871	0.0942		0.0706	False		,,,				2504	0.0982				p.H1297R		Atlas-SNP	.											AOX1,NS,carcinoma,0,1	AOX1	152	1	1	Substitution - Missense(1)	stomach(1)	c.A3890G						PASS	.	A	ARG/HIS	209,4197	129.0+/-165.8	6,197,2000	175.0	169.0	171.0		3890	-11.0	0.0	2	dbSNP_107	171	507,8093	144.7+/-200.5	17,473,3810	yes	missense	AOX1	NM_001159.3	29	23,670,5810	GG,GA,AA		5.8953,4.7435,5.5052	benign	1297/1339	201534389	716,12290	2203	4300	6503	SO:0001583	missense	316	exon34			GCCTGCATGGACC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3890A>G	2.37:g.201534389A>G	ENSP00000363832:p.His1297Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	182	0.08333333333333333	21	0.042682926829268296	58	0.16022099447513813	50	0.08741258741258741	53	0.06992084432717678	A	8.328	0.825775	0.16749	0.047435	0.058953	ENSG00000138356	ENST00000374700;ENST00000260930;ENST00000439380	T;T;T	0.62105	0.05;0.05;0.05	5.51	-11.0	0.00169	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (2);	2.740490	0.00775	N	0.001232	T	0.00178	0.0005	N	0.17631	0.505	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03354	-1.1045	9	0.27082	T	0.32	2.8876	7.2554	0.26173	0.0675:0.4952:0.365:0.0723	rs3731722;rs52800969;rs3731722	1297	Q06278	ADO_HUMAN	R	1297;161;137	ENSP00000363832:H1297R;ENSP00000260930:H161R;ENSP00000413326:H137R	ENSP00000260930:H161R	H	+	2	0	AOX1	201242634	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.587000	0.00902	-3.490000	0.00153	-1.440000	0.01072	CAT	A|0.937;G|0.063	0.063	strong		0.512	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
VPS8	23355	hgsc.bcm.edu	37	3	184766301	184766301	+	Missense_Mutation	SNP	T	T	C	rs3821750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184766301T>C	ENST00000437079.3	+	47	4262	c.4091T>C	c.(4090-4092)aTc>aCc	p.I1364T	VPS8_ENST00000436792.2_Missense_Mutation_p.I1362T|VPS8_ENST00000287546.4_Missense_Mutation_p.I1364T|VPS8_ENST00000446204.2_Missense_Mutation_p.I1272T	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1364			I -> T (in dbSNP:rs3821750).				zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			CCACAGCAAATCCAAGCATTT	0.423													T|||	934	0.186502	0.4062	0.1398	5008	,	,		22053	0.0536		0.1421	False		,,,				2504	0.1053				p.I1364T		Atlas-SNP	.											.	VPS8	109	.	0			c.T4091C						PASS	.	T	THR/ILE,THR/ILE	1352,2380		241,870,755	150.0	150.0	150.0		4091,4085	4.9	1.0	3	dbSNP_107	150	1247,6993		97,1053,2970	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	89,89	338,1923,3725	CC,CT,TT		15.1335,36.2272,21.709	benign,benign	1364/1429,1362/1427	184766301	2599,9373	1866	4120	5986	SO:0001583	missense	23355	exon46			AGCAAATCCAAGC	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.4091T>C	3.37:g.184766301T>C	ENSP00000397879:p.Ile1364Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	364	0.16666666666666666	179	0.3638211382113821	53	0.1464088397790055	21	0.03671328671328671	111	0.14643799472295516	T	13.54	2.266996	0.40095	0.362272	0.151335	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	6.08	4.89	0.63831	.	0.532223	0.20583	N	0.089495	T	0.00012	0.0000	N	0.08118	0	0.43211	P	0.004927000000000015	B;B;B	0.15719	0.0;0.014;0.0	B;B;B	0.19391	0.0;0.025;0.0	T	0.45527	-0.9255	9	0.09338	T	0.73	-12.5221	8.0611	0.30633	0.0:0.1578:0.0:0.8422	rs3821750;rs58124847;rs3821750	1364;1272;1362	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	T	1364;1364;1362;1272	ENSP00000287546:I1364T;ENSP00000397879:I1364T;ENSP00000404704:I1362T;ENSP00000405483:I1272T	ENSP00000287546:I1364T	I	+	2	0	VPS8	186248995	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.538000	0.36094	1.079000	0.41038	0.533000	0.62120	ATC	T|0.818;C|0.182	0.182	strong		0.423	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
APC	324	hgsc.bcm.edu	37	5	112177171	112177171	+	Silent	SNP	G	G	A	rs465899|rs587779801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112177171G>A	ENST00000457016.1	+	16	6260	c.5880G>A	c.(5878-5880)ccG>ccA	p.P1960P	APC_ENST00000508376.2_Silent_p.P1960P|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.P1960P			P25054	APC_HUMAN	adenomatous polyposis coli	1960	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAATACTCCGGTTTGCTTTT	0.398		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	3338	0.666534	0.5212	0.7161	5008	,	,		20489	0.8165		0.5994	False		,,,				2504	0.7423				p.P1960P	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G5880A						PASS	.	A	,,	2328,2076	560.3+/-380.4	623,1082,497	66.0	64.0	65.0	http://omim.org/entry/114500	5880,5880,5826	-3.7	1.0	5	dbSNP_80	65	5303,3295	486.2+/-371.8	1668,1967,664	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2291,3049,1161	AA,AG,GG		38.3229,47.139,41.309	,,	1960/2844,1960/2844,1942/2826	112177171	7631,5371	2202	4299	6501	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TACTCCGGTTTGC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5880G>A	5.37:g.112177171G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	139	0.985816	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.332;A|0.668	0.668	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
HELB	92797	hgsc.bcm.edu	37	12	66731864	66731864	+	Silent	SNP	C	C	A	rs1168329	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:66731864C>A	ENST00000247815.4	+	13	3305	c.3246C>A	c.(3244-3246)acC>acA	p.T1082T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1082					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)		TCAAGCCCACCGATAATCAAG	0.343													A|||	2686	0.536342	0.5953	0.6282	5008	,	,		15529	0.5585		0.4235	False		,,,				2504	0.4847				p.T1082T		Atlas-SNP	.											.	HELB	90	.	0			c.C3246A						PASS	.	A		2477,1929	546.4+/-377.0	721,1035,447	68.0	71.0	70.0		3246	-1.6	0.0	12	dbSNP_87	70	3721,4879	617.7+/-396.7	811,2099,1390	no	coding-synonymous	HELB	NM_033647.2		1532,3134,1837	AA,AC,CC		43.2674,43.7812,47.6549		1082/1088	66731864	6198,6808	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon13			GCCCACCGATAAT	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.3246C>A	12.37:g.66731864C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			C|0.503;A|0.497	0.497	strong		0.343	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
DAPL1	92196	hgsc.bcm.edu	37	2	159672252	159672252	+	Silent	SNP	G	G	A	rs61740878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:159672252G>A	ENST00000309950.3	+	4	299	c.243G>A	c.(241-243)gcG>gcA	p.A81A	DAPL1_ENST00000409042.1_Intron	NM_001017920.2	NP_001017920.2	A0PJW8	DAPL1_HUMAN	death associated protein-like 1	81					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)					prostate(1)	1						TGCACATGGCGCATCAAAAAC	0.388													G|||	513	0.102436	0.0061	0.1556	5008	,	,		18301	0.0764		0.1541	False		,,,				2504	0.1687				p.A81A		Atlas-SNP	.											.	DAPL1	11	.	0			c.G243A						PASS	.	G		143,4263	101.2+/-139.8	2,139,2062	137.0	131.0	133.0		243	1.5	1.0	2	dbSNP_129	133	1515,7085	286.7+/-297.9	139,1237,2924	no	coding-synonymous	DAPL1	NM_001017920.2		141,1376,4986	AA,AG,GG		17.6163,3.2456,12.748		81/108	159672252	1658,11348	2203	4300	6503	SO:0001819	synonymous_variant	92196	exon4			CATGGCGCATCAA		CCDS33307.1	2q24	2007-06-26			ENSG00000163331	ENSG00000163331			21490	protein-coding gene	gene with protein product							Standard	NM_001017920		Approved		uc002uaf.3	A0PJW8	OTTHUMG00000153970	ENST00000309950.3:c.243G>A	2.37:g.159672252G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_001017920	A0PJW9|B9EIK6	Silent	SNP	ENST00000309950.3	37	CCDS33307.1																																																																																			G|0.880;A|0.120	0.120	strong		0.388	DAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333265.1	NM_001017920	
C11orf24	53838	hgsc.bcm.edu	37	11	68029887	68029887	+	Silent	SNP	G	G	A	rs78911714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:68029887G>A	ENST00000304271.6	-	4	978	c.576C>T	c.(574-576)ctC>ctT	p.L192L	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	192						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						GCACTTGTGCGAGGGCTGTGC	0.622													G|||	113	0.0225639	0.0068	0.0	5008	,	,		19285	0.0704		0.002	False		,,,				2504	0.0317				p.L192L	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C576T						PASS	.	G		25,4375	31.7+/-61.6	0,25,2175	71.0	66.0	68.0		576	-7.0	0.0	11	dbSNP_132	68	12,8576	9.1+/-34.3	0,12,4282	no	coding-synonymous	C11orf24	NM_022338.3		0,37,6457	AA,AG,GG		0.1397,0.5682,0.2849		192/450	68029887	37,12951	2200	4294	6494	SO:0001819	synonymous_variant	53838	exon4			TTGTGCGAGGGCT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.576C>T	11.37:g.68029887G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	236	123	0.521186	NM_022338	Q9H2K4	Silent	SNP	ENST00000304271.6	37	CCDS8180.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
MBTPS2	51360	hgsc.bcm.edu	37	X	21861434	21861434	+	Silent	SNP	A	A	G	rs3213451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:21861434A>G	ENST00000379484.5	+	2	321	c.222A>G	c.(220-222)caA>caG	p.Q74Q	MBTPS2_ENST00000465888.1_3'UTR|MBTPS2_ENST00000365779.2_Silent_p.Q74Q	NM_015884.3	NP_056968.1	O43462	MBTP2_HUMAN	membrane-bound transcription factor peptidase, site 2	74					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(3)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24						TGCTTTACCAATGGTATTCTT	0.398													A|||	1728	0.457748	0.3722	0.4193	3775	,	,		13554	0.4117		0.2992	False		,,,				2504	0.2342				p.Q74Q		Atlas-SNP	.											.	MBTPS2	52	.	0			c.A222G						PASS	.	A		1787,2048		349,813,276,470,295	170.0	178.0	175.0		222	-3.5	0.9	X	dbSNP_106	175	2621,4107		377,1144,723,907,1149	no	coding-synonymous	MBTPS2	NM_015884.3		726,1957,999,1377,1444	GG,GA,G,AA,A		38.9566,46.5971,41.7306		74/520	21861434	4408,6155	2203	4300	6503	SO:0001819	synonymous_variant	51360	exon2			TTACCAATGGTAT	AF019612	CCDS14201.1	Xp22.12-p22.11	2014-02-03	2005-08-17		ENSG00000012174	ENSG00000012174			15455	protein-coding gene	gene with protein product		300294	"""membrane-bound transcription factor protease, site 2"", ""keratosis follicularis spinulosa decalvans"""	KFSD		9847074, 9659902, 20672378	Standard	NM_015884		Approved	S2P	uc004dae.3	O43462	OTTHUMG00000021237	ENST00000379484.5:c.222A>G	X.37:g.21861434A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_015884	Q9UM70|Q9UMD3	Silent	SNP	ENST00000379484.5	37	CCDS14201.1																																																																																			A|0.567;G|0.433	0.433	strong		0.398	MBTPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056026.1		
RNF175	285533	hgsc.bcm.edu	37	4	154631587	154631587	+	Missense_Mutation	SNP	C	C	G	rs1337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	72	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	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	
OR4N2	390429	hgsc.bcm.edu	37	14	20296010	20296010	+	Missense_Mutation	SNP	G	G	C	rs17114261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	275	0	0		WXS	Illumina HiSeq	Phase_I	348	61	0.175287	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		
COL6A1	1291	hgsc.bcm.edu	37	21	47423509	47423509	+	Missense_Mutation	SNP	C	C	T	rs71336107|rs13051496	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47423509C>T	ENST00000361866.3	+	35	2783	c.2669C>T	c.(2668-2670)tCg>tTg	p.S890L	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	890	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		S -> L (in dbSNP:rs13051496). {ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:16130093}.		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)		GAGCGGGCGTCGCTGCAGTTC	0.677													C|||	545	0.108826	0.0424	0.1196	5008	,	,		14971	0.0615		0.2604	False		,,,				2504	0.0838				p.S890L		Atlas-SNP	.											COL6A1,NS,carcinoma,0,1	COL6A1	101	1	0			c.C2669T						PASS	.	C	LEU/SER	246,4160		9,228,1966	29.0	30.0	29.0		2669	4.0	0.0	21	dbSNP_121	29	1859,6739		209,1441,2649	yes	missense	COL6A1	NM_001848.2	145	218,1669,4615	TT,TC,CC		21.6213,5.5833,16.1873	possibly-damaging	890/1029	47423509	2105,10899	2203	4299	6502	SO:0001583	missense	1291	exon35			GGGCGTCGCTGCA	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.2669C>T	21.37:g.47423509C>T	ENSP00000355180:p.Ser890Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	326	0.14926739926739926	32	0.06504065040650407	49	0.13535911602209943	41	0.07167832167832168	204	0.2691292875989446	C	10.83	1.462082	0.26248	0.055833	0.216213	ENSG00000142156	ENST00000361866	T	0.79352	-1.26	4.94	4.03	0.46877	von Willebrand factor, type A (3);	0.392531	0.22699	N	0.056720	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.25441	0.126	B	0.22753	0.041	T	0.05068	-1.0908	9	0.30854	T	0.27	-11.2045	11.892	0.52635	0.4862:0.5138:0.0:0.0	rs13051496	890	P12109	CO6A1_HUMAN	L	890	ENSP00000355180:S890L	ENSP00000355180:S890L	S	+	2	0	COL6A1	46247937	0.996000	0.38824	0.003000	0.11579	0.134000	0.20937	3.945000	0.56637	1.035000	0.39972	0.530000	0.56133	TCG	C|0.849;T|0.151	0.151	strong		0.677	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
NEIL3	55247	hgsc.bcm.edu	37	4	178262784	178262784	+	Missense_Mutation	SNP	A	A	G	rs34193982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	42	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	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	
SERPINA10	51156	hgsc.bcm.edu	37	14	94756450	94756450	+	Missense_Mutation	SNP	T	T	A	rs2232700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:94756450T>A	ENST00000393096.1	-	2	946	c.481A>T	c.(481-483)Aca>Tca	p.T161S	SERPINA10_ENST00000554723.1_Missense_Mutation_p.T201S|SERPINA10_ENST00000261994.4_Missense_Mutation_p.T161S|SERPINA10_ENST00000554173.1_Missense_Mutation_p.T161S	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	161			T -> S (in dbSNP:rs2232700). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CTCCCCTGTGTGAGGCCCAGT	0.517													T|||	1436	0.286741	0.2511	0.134	5008	,	,		18152	0.6042		0.166	False		,,,				2504	0.2403				p.T161S		Atlas-SNP	.											.	SERPINA10	83	.	0			c.A481T						PASS	.	T	SER/THR,SER/THR	993,3413	359.6+/-314.9	110,773,1320	61.0	67.0	65.0		481,481	-9.9	0.0	14	dbSNP_98	65	1413,7187	269.3+/-288.3	125,1163,3012	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	58,58	235,1936,4332	AA,AT,TT		16.4302,22.5374,18.4992	benign,benign	161/445,161/445	94756450	2406,10600	2203	4300	6503	SO:0001583	missense	51156	exon2			CCTGTGTGAGGCC	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.481A>T	14.37:g.94756450T>A	ENSP00000376809:p.Thr161Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	648	0.2967032967032967	130	0.26422764227642276	51	0.1408839779005525	340	0.5944055944055944	127	0.16754617414248021	T	0.270	-0.993593	0.02145	0.225374	0.164302	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.97	-9.94	0.00449	Serpin domain (3);	1.698980	0.03320	N	0.191763	T	0.00012	0.0000	N	0.01824	-0.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.07177	-1.0786	9	0.06891	T	0.86	.	3.7892	0.08713	0.2143:0.1744:0.0749:0.5364	rs2232700;rs52837981;rs2232700	161	Q9UK55	ZPI_HUMAN	S	201;161;161;161	ENSP00000450896:T201S;ENSP00000376809:T161S;ENSP00000261994:T161S;ENSP00000450971:T161S	ENSP00000261994:T161S	T	-	1	0	SERPINA10	93826203	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-1.741000	0.01837	-1.939000	0.01044	-0.736000	0.03550	ACA	T|0.775;N|0.000	.	strong		0.517	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
DDX60	55601	hgsc.bcm.edu	37	4	169227551	169227551	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169227551T>C	ENST00000393743.3	-	5	876	c.585A>G	c.(583-585)agA>agG	p.R195R		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	195					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		AAATCTGGTGTCTGTACATGC	0.378																																					p.R195R		Atlas-SNP	.											.	DDX60	304	.	0			c.A585G						PASS	.						59.0	59.0	59.0					4																	169227551		2203	4300	6503	SO:0001819	synonymous_variant	55601	exon5			CTGGTGTCTGTAC	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.585A>G	4.37:g.169227551T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	38	4	0.105263	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																			.	.	none		0.378	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
ASAP1	50807	hgsc.bcm.edu	37	8	131124559	131124559	+	Missense_Mutation	SNP	T	T	C	rs966185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:131124559T>C	ENST00000518721.1	-	24	2409	c.2182A>G	c.(2182-2184)Atc>Gtc	p.I728V	ASAP1_ENST00000357668.1_Missense_Mutation_p.I728V	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	728			I -> V (in dbSNP:rs966185).		cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.I728V(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TCTTTCTTGATAGGGCTTGGC	0.562													T|||	2376	0.474441	0.2247	0.3689	5008	,	,		19924	0.7153		0.4642	False		,,,				2504	0.6493				p.I728V		Atlas-SNP	.											ASAP1,NS,carcinoma,0,1	ASAP1	133	1	1	Substitution - Missense(1)	stomach(1)	c.A2182G						PASS	.	T	VAL/ILE	1233,3173	425.1+/-340.7	152,929,1122	76.0	78.0	77.0		2182	-0.5	0.0	8	dbSNP_86	77	3952,4648	551.4+/-385.9	899,2154,1247	yes	missense	ASAP1	NM_018482.2	29	1051,3083,2369	CC,CT,TT		45.9535,27.9846,39.8662	benign	728/1130	131124559	5185,7821	2203	4300	6503	SO:0001583	missense	50807	exon24			TCTTGATAGGGCT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2720	protein-coding gene	gene with protein product	"""centaurin, beta 4"""	605953	"""development and differentiation enhancing factor 1"""	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.2182A>G	8.37:g.131124559T>C	ENSP00000429900:p.Ile728Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	86	0.977273	NM_018482	B2RNV3	Missense_Mutation	SNP	ENST00000518721.1	37	CCDS6362.1	1023|1023	0.4684065934065934|0.4684065934065934	123|123	0.25|0.25	134|134	0.3701657458563536|0.3701657458563536	406|406	0.7097902097902098|0.7097902097902098	360|360	0.47493403693931396|0.47493403693931396	T|T	5.890|5.890	0.348337|0.348337	0.11126|0.11126	0.279846|0.279846	0.459535|0.459535	ENSG00000153317|ENSG00000153317	ENST00000343135;ENST00000357668;ENST00000518721|ENST00000524124;ENST00000519483	T;T|.	0.05382|.	3.45;3.45|.	5.96|5.96	-0.54|-0.54	0.11861|0.11861	.|.	0.357617|.	0.33217|.	N|.	0.005154|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.20986|0.20986	0.625|0.625	0.28757|0.28757	P|P	0.9011277|0.9011277	B;B;B|.	0.11235|.	0.002;0.002;0.004|.	B;B;B|.	0.09377|.	0.002;0.002;0.004|.	T|T	0.34700|0.34700	-0.9818|-0.9818	9|4	0.08179|.	T|.	0.78|.	.|.	9.8396|9.8396	0.40991|0.40991	0.0:0.3617:0.0:0.6383|0.0:0.3617:0.0:0.6383	rs966185;rs1143252;rs17281610;rs52815528;rs59807099;rs966185|rs966185;rs1143252;rs17281610;rs52815528;rs59807099;rs966185	728;728;731|.	B2RNV3;Q9ULH1;Q9ULH1-2|.	.;ASAP1_HUMAN;.|.	V|C	731;728;728|548;141	ENSP00000350297:I728V;ENSP00000429900:I728V|.	ENSP00000344591:I731V|.	I|Y	-|-	1|2	0|0	ASAP1|ASAP1	131193741|131193741	0.302000|0.302000	0.24454|0.24454	0.034000|0.034000	0.17996|0.17996	0.989000|0.989000	0.77384|0.77384	0.633000|0.633000	0.24598|0.24598	-0.300000|-0.300000	0.08895|0.08895	0.533000|0.533000	0.62120|0.62120	ATC|TAT	T|0.556;C|0.444	0.444	strong		0.562	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688388	26688388	+	Silent	SNP	A	A	C	rs35377445	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26688388A>C	ENST00000248933.6	+	2	206	c.111A>C	c.(109-111)ggA>ggC	p.G37G	SEZ6L_ENST00000360929.3_Silent_p.G37G|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000529632.2_Silent_p.G37G|SEZ6L_ENST00000343706.4_Silent_p.G37G|SEZ6L_ENST00000404234.3_Silent_p.G37G|SEZ6L_ENST00000403121.1_5'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	37					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TTCCCGAGGGAGATGCTAGCC	0.572													A|||	217	0.0433307	0.0129	0.0793	5008	,	,		18827	0.001		0.1233	False		,,,				2504	0.0204				p.G37G		Atlas-SNP	.											SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	0			c.A111C						PASS	.	A	,,,,,	127,4279	92.0+/-130.7	2,123,2078	46.0	37.0	40.0		111,111,111,111,111,111	2.4	0.9	22	dbSNP_126	40	1029,7571	213.8+/-253.6	61,907,3332	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	63,1030,5410	CC,CA,AA		11.9651,2.8824,8.8882	,,,,,	37/1024,37/1014,37/1012,37/950,37/949,37/1025	26688388	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			CGAGGGAGATGCT	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.111A>C	22.37:g.26688388A>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	57	21	0.368421	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			A|0.919;C|0.081	0.081	strong		0.572	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
PYGL	5836	hgsc.bcm.edu	37	14	51376774	51376774	+	Silent	SNP	G	G	A	rs15669	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:51376774G>A	ENST00000216392.7	-	17	2348	c.2016C>T	c.(2014-2016)acC>acT	p.T672T	PYGL_ENST00000532462.1_Silent_p.T672T|PYGL_ENST00000544180.2_Silent_p.T638T|RP11-218E20.5_ENST00000557343.1_RNA	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	672					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)	CCGAGGCTTCGGTGCCTGCAG	0.478													G|||	1115	0.222644	0.4697	0.1225	5008	,	,		20002	0.121		0.1312	False		,,,				2504	0.1585				p.T672T		Atlas-SNP	.											.	PYGL	77	.	0			c.C2016T						PASS	.	G	,	1769,2637	525.2+/-371.5	333,1103,767	137.0	127.0	130.0		1914,2016	-11.2	0.2	14	dbSNP_52	130	1078,7522	226.9+/-262.5	62,954,3284	no	coding-synonymous,coding-synonymous	PYGL	NM_001163940.1,NM_002863.4	,	395,2057,4051	AA,AG,GG		12.5349,40.1498,21.8899	,	638/814,672/848	51376774	2847,10159	2203	4300	6503	SO:0001819	synonymous_variant	5836	exon17			GGCTTCGGTGCCT		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.2016C>T	14.37:g.51376774G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Silent	SNP	ENST00000216392.7	37	CCDS32080.1																																																																																			G|0.787;A|0.213	0.213	strong		0.478	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
COL17A1	1308	hgsc.bcm.edu	37	10	105793750	105793750	+	Missense_Mutation	SNP	T	T	C	rs17116350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	183	4	0.0218579		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	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	
OR52E2	119678	hgsc.bcm.edu	37	11	5080844	5080844	+	Missense_Mutation	SNP	T	T	C	rs16909440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	64	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	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	
HEXDC	284004	hgsc.bcm.edu	37	17	80391684	80391684	+	Missense_Mutation	SNP	A	A	G	rs4789773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	207	104	0.502415	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	
RCN3	57333	hgsc.bcm.edu	37	19	50045979	50045979	+	Missense_Mutation	SNP	C	C	A	rs146159696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50045979C>A	ENST00000270645.3	+	6	1296	c.849C>A	c.(847-849)aaC>aaA	p.N283K		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	283	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		TGGAAGCCAACCACCTGCTGC	0.667													C|||	26	0.00519169	0.0008	0.0115	5008	,	,		15800	0.0		0.0169	False		,,,				2504	0.0				p.N283K		Atlas-SNP	.											.	RCN3	28	.	0			c.C849A						PASS	.	C	LYS/ASN	20,4372		0,20,2176	29.0	28.0	29.0		849	-0.2	1.0	19	dbSNP_134	29	123,8469		2,119,4175	yes	missense	RCN3	NM_020650.2	94	2,139,6351	AA,AC,CC		1.4316,0.4554,1.1014	benign	283/329	50045979	143,12841	2196	4296	6492	SO:0001583	missense	57333	exon6			AGCCAACCACCTG	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"""EF-hand domain containing"""	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.849C>A	19.37:g.50045979C>A	ENSP00000270645:p.Asn283Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_020650	Q9HBZ8	Missense_Mutation	SNP	ENST00000270645.3	37	CCDS12771.1	17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	4.932	0.173104	0.09391	0.004554	0.014316	ENSG00000142552	ENST00000270645	T	0.78246	-1.16	5.07	-0.163	0.13363	EF-hand-like domain (1);	0.194036	0.44483	D	0.000459	T	0.21881	0.0527	N	0.01003	-1.06	0.33463	D	0.585258	B	0.11235	0.004	B	0.11329	0.006	T	0.42032	-0.9475	10	0.02654	T	1	-44.8359	4.2842	0.10846	0.2256:0.4201:0.0:0.3543	.	283	Q96D15	RCN3_HUMAN	K	283	ENSP00000270645:N283K	ENSP00000270645:N283K	N	+	3	2	RCN3	54737791	0.994000	0.37717	1.000000	0.80357	0.824000	0.46624	0.395000	0.20850	0.175000	0.19841	-0.236000	0.12185	AAC	C|0.990;A|0.010	0.010	strong		0.667	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650	
SCN10A	6336	hgsc.bcm.edu	37	3	38793989	38793989	+	Silent	SNP	G	G	A	rs7617919	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38793989G>A	ENST00000449082.2	-	11	1475	c.1476C>T	c.(1474-1476)ctC>ctT	p.L492L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	492					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)			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)	TTCCAGAGGCGAGGCCTAGAA	0.552													G|||	1040	0.207668	0.0787	0.1052	5008	,	,		18386	0.373		0.2495	False		,,,				2504	0.2413				p.L492L		Atlas-SNP	.											.	SCN10A	359	.	0			c.C1476T						PASS	.	G		471,3935		26,419,1758	23.0	25.0	25.0		1476	-5.6	0.0	3	dbSNP_116	25	2169,6429		280,1609,2410	no	coding-synonymous	SCN10A	NM_006514.2		306,2028,4168	AA,AG,GG		25.2268,10.69,20.3014		492/1957	38793989	2640,10364	2203	4299	6502	SO:0001819	synonymous_variant	6336	exon11			AGAGGCGAGGCCT	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.1476C>T	3.37:g.38793989G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	89	31	0.348315	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.780;A|0.220	0.220	strong		0.552	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
MET	4233	hgsc.bcm.edu	37	7	116435768	116435768	+	Silent	SNP	C	C	T	rs41736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	123	1	0.00813008	1473	WXS	Illumina HiSeq	Phase_I	123	122	0.99187	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		
MAST2	23139	hgsc.bcm.edu	37	1	46496709	46496709	+	Silent	SNP	A	A	G	rs925524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:46496709A>G	ENST00000361297.2	+	23	3022	c.2739A>G	c.(2737-2739)tcA>tcG	p.S913S	MAST2_ENST00000372009.2_Silent_p.S843S	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)					TGTCTGAGTCATCCCACACAG	0.637													G|||	3225	0.64397	0.5794	0.6297	5008	,	,		17286	0.6984		0.7396	False		,,,				2504	0.5869				p.S913S		Atlas-SNP	.											.	MAST2	136	.	0			c.A2739G						PASS	.	G		2578,1510		827,924,293	30.0	33.0	32.0		2739	-9.2	0.1	1	dbSNP_92	32	6013,2353		2162,1689,332	no	coding-synonymous	MAST2	NM_015112.2		2989,2613,625	GG,GA,AA		28.1257,36.9374,31.0181		913/1799	46496709	8591,3863	2044	4183	6227	SO:0001819	synonymous_variant	23139	exon23			TGAGTCATCCCAC	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.2739A>G	1.37:g.46496709A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			A|0.307;C|0.013	.	strong		0.637	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
RGSL1	353299	hgsc.bcm.edu	37	1	182496829	182496829	+	Missense_Mutation	SNP	A	A	G	rs7535533	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:182496829A>G	ENST00000294854.8	+	11	2067	c.2047A>G	c.(2047-2049)Ata>Gta	p.I683V	RGSL1_ENST00000542961.1_Missense_Mutation_p.I718V|RGSL1_ENST00000456971.2_3'UTR	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	683	RGS.			I -> V (in Ref. 6; BC121032/BC121033). {ECO:0000305}.	termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						GAAGATCAGTATAGAGACCAA	0.418													A|||	1563	0.312101	0.1914	0.2435	5008	,	,		20402	0.4315		0.3877	False		,,,				2504	0.3231				p.I683V	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											.	RGSL1	111	.	0			c.A2047G						PASS	.	A	VAL/ILE	306,1078		39,228,425	98.0	84.0	88.0		2047	0.7	0.0	1	dbSNP_116	88	1180,2002		213,754,624	yes	missense	RGSL1	NM_001137669.1	29	252,982,1049	GG,GA,AA		37.0836,22.1098,32.5449	benign	683/1077	182496829	1486,3080	692	1591	2283	SO:0001583	missense	353299	exon11			ATCAGTATAGAGA	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.2047A>G	1.37:g.182496829A>G	ENSP00000457748:p.Ile683Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	188	116	0.617021	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Missense_Mutation	SNP	ENST00000294854.8	37	CCDS58049.1																																																																																			A|0.661;G|0.339	0.339	strong		0.418	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
IGFN1	91156	hgsc.bcm.edu	37	1	201183363	201183363	+	Silent	SNP	C	C	T	rs2282415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201183363C>T	ENST00000335211.4	+	13	8917	c.8787C>T	c.(8785-8787)gcC>gcT	p.A2929A	IGFN1_ENST00000451870.2_Silent_p.A472A|IGFN1_ENST00000295591.8_Silent_p.A89A	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	39	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	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	
AOAH	313	hgsc.bcm.edu	37	7	36763672	36763672	+	Missense_Mutation	SNP	C	C	T	rs2228410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:36763672C>T	ENST00000258749.5	-	1	481	c.82G>A	c.(82-84)Gat>Aat	p.D28N	AOAH_ENST00000535891.1_Missense_Mutation_p.D28N|AOAH_ENST00000431169.1_Missense_Mutation_p.D28N	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	28			D -> N (in dbSNP:rs11976480). {ECO:0000269|PubMed:12690205, ECO:0000269|Ref.6}.		inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						GACTGGTCATCGTTGGCTGGA	0.502													C|||	1758	0.351038	0.1293	0.4294	5008	,	,		17607	0.5248		0.3569	False		,,,				2504	0.41				p.D28N		Atlas-SNP	.											.	AOAH	79	.	0			c.G82A	GRCh37	CM064972	AOAH	M	rs11976480	PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	668,3738	282.8+/-276.7	52,564,1587	56.0	60.0	58.0		82,82,82	-0.6	0.0	7	dbSNP_120	58	2805,5795	444.1+/-360.6	447,1911,1942	yes	missense,missense,missense	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	23,23,23	499,2475,3529	TT,TC,CC		32.6163,15.1611,26.7031	benign,benign,benign	28/689,28/544,28/576	36763672	3473,9533	2203	4300	6503	SO:0001583	missense	313	exon1			GGTCATCGTTGGC	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.82G>A	7.37:g.36763672C>T	ENSP00000258749:p.Asp28Asn	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	61	41	0.672131	NM_001177507	A4D1Y5|B7Z490|Q53F13	Missense_Mutation	SNP	ENST00000258749.5	37	CCDS5448.1	771	0.35302197802197804	63	0.12804878048780488	136	0.3756906077348066	294	0.513986013986014	278	0.36675461741424803	C	5.549	0.286216	0.10513	0.151611	0.326163	ENSG00000136250	ENST00000535891;ENST00000258749;ENST00000431169;ENST00000544647;ENST00000435386	T;T;T;T	0.77620	1.63;-1.07;-1.11;0.66	4.18	-0.577	0.11727	.	3.465610	0.00944	N	0.002871	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.18968	0.0;0.032;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.29792	-1.0000	8	0.23891	T	0.37	-9.38	5.0497	0.14501	0.0:0.4354:0.1664:0.3982	rs11976480;rs52827163;rs58377668;rs11976480	28;28;28	B7Z490;C9J8T1;P28039	.;.;AOAH_HUMAN	N	28	ENSP00000441101:D28N;ENSP00000258749:D28N;ENSP00000405683:D28N;ENSP00000416051:D28N	ENSP00000258749:D28N	D	-	1	0	AOAH	36730197	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.187000	0.09656	-0.447000	0.07138	-2.449000	0.00209	GAT	C|0.697;T|0.303	0.303	strong		0.502	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
KIF2C	11004	hgsc.bcm.edu	37	1	45218895	45218895	+	Silent	SNP	A	A	T	rs3795713	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45218895A>T	ENST00000372224.4	+	6	644	c.531A>T	c.(529-531)cgA>cgT	p.R177R	KIF2C_ENST00000372222.3_Silent_p.R64R|KIF2C_ENST00000372217.1_Silent_p.R123R|KIF2C_ENST00000372218.4_Intron|KIF2C_ENST00000493027.1_Intron	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	177	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)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|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)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					ATTCCATCCGAGGCAGCTCTT	0.532													a|||	1435	0.286542	0.4818	0.2781	5008	,	,		22360	0.2857		0.1392	False		,,,				2504	0.181				p.R177R		Atlas-SNP	.											KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	0			c.A531T						PASS	.	A		1963,2443	554.2+/-379.0	456,1051,696	171.0	148.0	156.0		531	1.6	0.9	1	dbSNP_107	156	1457,7143	277.9+/-293.1	130,1197,2973	no	coding-synonymous	KIF2C	NM_006845.3		586,2248,3669	TT,TA,AA		16.9419,44.5529,26.2956		177/726	45218895	3420,9586	2203	4300	6503	SO:0001819	synonymous_variant	11004	exon6			CATCCGAGGCAGC	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.531A>T	1.37:g.45218895A>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Silent	SNP	ENST00000372224.4	37	CCDS512.1																																																																																			A|0.741;T|0.259	0.259	strong		0.532	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
UGT2B11	10720	hgsc.bcm.edu	37	4	70071216	70071216	+	Missense_Mutation	SNP	G	G	A	rs138927896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:70071216G>A	ENST00000446444.1	-	4	1080	c.1072C>T	c.(1072-1074)Ccc>Tcc	p.P358S	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	358					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						TCATTCTGGGGTATCCACTTG	0.378													.|||	64	0.0127796	0.0	0.036	5008	,	,		15776	0.0		0.0378	False		,,,				2504	0.001				p.P358S		Atlas-SNP	.											.	UGT2B11	92	.	0			c.C1072T						PASS	.	G	SER/PRO	28,4378		1,26,2176	120.0	118.0	119.0		1072	1.1	0.4	4	dbSNP_134	119	252,8342		3,246,4048	no	missense	UGT2B11	NM_001073.1	74	4,272,6224	AA,AG,GG		2.9323,0.6355,2.1538	probably-damaging	358/530	70071216	280,12720	2203	4297	6500	SO:0001583	missense	10720	exon4			TCTGGGGTATCCA	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.1072C>T	4.37:g.70071216G>A	ENSP00000387683:p.Pro358Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	36	0.016483516483516484	0	0.0	14	0.03867403314917127	0	0.0	22	0.029023746701846966	-	15.02	2.708352	0.48517	0.006355	0.029323	ENSG00000213759	ENST00000446444	D	0.82711	-1.64	2.02	1.14	0.20703	.	0.000000	0.64402	U	0.000001	T	0.76919	0.4055	H	0.94925	3.6	0.24740	N	0.993047	D	0.89917	1.0	D	0.97110	1.0	T	0.75858	-0.3169	10	0.87932	D	0	.	6.4817	0.22067	0.168:0.0:0.832:0.0	.	358	O75310	UDB11_HUMAN	S	358	ENSP00000387683:P358S	ENSP00000387683:P358S	P	-	1	0	UGT2B11	70105805	1.000000	0.71417	0.365000	0.25901	0.187000	0.23431	6.137000	0.71710	0.189000	0.20188	0.184000	0.17185	CCC	.	.	weak		0.378	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24458162	24458162	+	Missense_Mutation	SNP	G	G	C	rs2273946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24458162G>C	ENST00000335125.6	+	1	132	c.6G>C	c.(4-6)caG>caC	p.Q2H	DHRS4L2_ENST00000382755.4_5'Flank|DHRS4L2_ENST00000545240.1_Missense_Mutation_p.Q2H|DHRS4L2_ENST00000558753.1_Missense_Mutation_p.Q2H|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Missense_Mutation_p.Q2H|DHRS4L2_ENST00000397071.1_Missense_Mutation_p.Q2H|DHRS4L2_ENST00000534993.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	0						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		GATCCATGCAGATGGCCAGGC	0.657													N|||	3375	0.673922	0.969	0.4928	5008	,	,		17501	0.8571		0.338	False		,,,				2504	0.5603				p.Q2H		Atlas-SNP	.											.	DHRS4L2	29	.	0			c.G6C						PASS	.	C	,,,HIS/GLN	3792,608	264.1+/-265.8	1657,478,65	56.0	51.0	52.0		,,,6	-5.1	0.0	14	dbSNP_100	52	2915,5685	667.2+/-402.4	513,1889,1898	yes	intron,intron,intron,missense	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,24	2170,2367,1963	CC,CG,GG		33.8953,13.8182,48.4077	,,,	,,,2/233	24458162	6707,6293	2200	4300	6500	SO:0001583	missense	317749	exon1			CATGCAGATGGCC		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.6G>C	14.37:g.24458162G>C	ENSP00000334801:p.Gln2His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_198083	Q3YLD4	Missense_Mutation	SNP	ENST00000335125.6	37	CCDS9606.2	1378	0.6309523809523809	462	0.9390243902439024	172	0.47513812154696133	495	0.8653846153846154	249	0.32849604221635886	C	0.007	-1.945070	0.00479	0.861818	0.338953	ENSG00000187630	ENST00000397071;ENST00000335125;ENST00000537912;ENST00000545240	T;D;T;T	0.82526	1.76;-1.62;1.92;2.54	2.83	-5.08	0.02929	.	1.104000	0.07136	N	0.846448	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	T	0.27502	-1.0072	7	0.16420	T	0.52	.	2.5528	0.04753	0.1055:0.1365:0.361:0.397	rs2273946;rs17693039	.	.	.	H	2	ENSP00000380261:Q2H;ENSP00000334801:Q2H;ENSP00000439942:Q2H;ENSP00000437883:Q2H	ENSP00000334801:Q2H	Q	+	3	2	DHRS4L2	23528002	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.089000	0.03376	-1.254000	0.02485	-3.348000	0.00042	CAG	G|0.452;C|0.548	0.548	strong		0.657	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
OR56A4	120793	hgsc.bcm.edu	37	11	6023640	6023640	+	Missense_Mutation	SNP	T	T	C	rs11040249	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	110	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	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	
PCDH15	65217	hgsc.bcm.edu	37	10	55755491	55755491	+	Missense_Mutation	SNP	C	C	T	rs2135720	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:55755491C>T	ENST00000320301.6	-	21	3180	c.2786G>A	c.(2785-2787)cGa>cAa	p.R929Q	PCDH15_ENST00000395430.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.R936Q|PCDH15_ENST00000395438.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000395433.1_Missense_Mutation_p.R907Q|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.R929Q|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.R540Q|PCDH15_ENST00000373955.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000437009.1_Missense_Mutation_p.R858Q|PCDH15_ENST00000395432.2_Missense_Mutation_p.R892Q|PCDH15_ENST00000414778.1_Missense_Mutation_p.R934Q|PCDH15_ENST00000373965.2_Missense_Mutation_p.R936Q	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	929	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs2135720). {ECO:0000269|PubMed:11487575, 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)				TTTGTATATTCGTTTACTAAA	0.403										HNSCC(58;0.16)			c|||	1579	0.315296	0.2368	0.1859	5008	,	,		18799	0.495		0.1988	False		,,,				2504	0.4479				p.R934Q		Atlas-SNP	.											PCDH15_ENST00000417177,NS,carcinoma,-1,4	PCDH15	1715	4	0			c.G2801A						scavenged	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1027,3379	379.2+/-323.2	116,795,1292	125.0	111.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2801,2786,2573,2786,2675,2720,2822,2786,2801,2786,2720,2786	3.0	0.9	10	dbSNP_96	116	1719,6881	313.0+/-311.1	160,1399,2741	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	43,43,43,43,43,43,43,43,43,43,43,43	276,2194,4033	TT,TC,CC		19.9884,23.3091,21.1133	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	934/1963,929/1958,858/1887,929/1953,892/1916,907/1936,941/1791,929/1540,934/1683,929/1678,907/1933,929/1956	55755491	2746,10260	2203	4300	6503	SO:0001583	missense	65217	exon22			TATATTCGTTTAC	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.2786G>A	10.37:g.55755491C>T	ENSP00000322604:p.Arg929Gln	Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	646	0.2957875457875458	119	0.241869918699187	64	0.17679558011049723	307	0.5367132867132867	156	0.20580474934036938	C	5.539	0.284333	0.10513	0.233091	0.199884	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T	0.60672	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;0.17	5.93	2.97	0.34412	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.04297	-0.235	0.45883	P	0.0012689999999999646	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.30664	0.109;0.067;0.067;0.011;0.289;0.067;0.109;0.01;0.032;0.032;0.067;0.067;0.014;0.067	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.24848	0.028;0.018;0.018;0.008;0.056;0.018;0.028;0.005;0.008;0.008;0.018;0.018;0.01;0.018	T	0.46105	-0.9215	8	0.16896	T	0.51	.	7.6818	0.28518	0.0:0.5239:0.3189:0.1572	rs2135720;rs61298453;rs2135720	907;929;929;934;858;892;929;929;936;936;929;934;929;929	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	Q	936;934;929;929;540;936;892;929;907;929;929;934;858;929	ENSP00000363076:R936Q;ENSP00000410304:R934Q;ENSP00000378826:R929Q;ENSP00000386693:R540Q;ENSP00000378832:R936Q;ENSP00000378820:R892Q;ENSP00000354950:R929Q;ENSP00000378821:R907Q;ENSP00000322604:R929Q;ENSP00000378818:R929Q;ENSP00000412628:R858Q;ENSP00000363066:R929Q	ENSP00000322604:R929Q	R	-	2	0	PCDH15	55425497	0.002000	0.14202	0.929000	0.37066	0.126000	0.20510	0.539000	0.23175	1.512000	0.48834	-0.136000	0.14681	CGA	C|0.754;T|0.246	0.246	strong		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
NSD1	64324	hgsc.bcm.edu	37	5	176639105	176639105	+	Silent	SNP	T	T	C	rs28932181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176639105T>C	ENST00000439151.2	+	5	3750	c.3705T>C	c.(3703-3705)aaT>aaC	p.N1235N	NSD1_ENST00000361032.4_Silent_p.N1132N|NSD1_ENST00000354179.4_Silent_p.N966N|NSD1_ENST00000347982.4_Silent_p.N966N	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1235					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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;0.198)	Kidney(146;0.235)		CACGGTTAAATGTTTGTGATA	0.478			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			T|||	529	0.105631	0.2534	0.0706	5008	,	,		17833	0.0179		0.0537	False		,,,				2504	0.0746				p.N1235N		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T3705C						PASS	.	T	,	1055,3351	387.0+/-326.3	118,819,1266	62.0	63.0	63.0		3705,2898	2.1	1.0	5	dbSNP_125	63	428,8172	131.2+/-189.0	5,418,3877	no	coding-synonymous,coding-synonymous	NSD1	NM_022455.4,NM_172349.2	,	123,1237,5143	CC,CT,TT		4.9767,23.9446,11.4024	,	1235/2697,966/2428	176639105	1483,11523	2203	4300	6503	SO:0001819	synonymous_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GTTAAATGTTTGT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3705T>C	5.37:g.176639105T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			T|0.896;C|0.104	0.104	strong		0.478	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
RHBDD3	25807	hgsc.bcm.edu	37	22	29656389	29656389	+	Silent	SNP	G	G	T	rs2231398	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:29656389G>T	ENST00000216085.7	-	6	1333	c.909C>A	c.(907-909)gcC>gcA	p.A303A	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	303					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						CAAGAAGCGAGGCCTGGATGC	0.667													G|||	858	0.171326	0.1006	0.245	5008	,	,		17314	0.0397		0.3608	False		,,,				2504	0.1554				p.A303A		Atlas-SNP	.											.	RHBDD3	17	.	0			c.C909A						PASS	.	G		631,3775		46,539,1618	24.0	23.0	23.0		909	0.6	1.0	22	dbSNP_98	23	3246,5352		622,2002,1675	no	coding-synonymous	RHBDD3	NM_012265.1		668,2541,3293	TT,TG,GG		37.753,14.3214,29.8139		303/387	29656389	3877,9127	2203	4299	6502	SO:0001819	synonymous_variant	25807	exon6			AAGCGAGGCCTGG	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.909C>A	22.37:g.29656389G>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_012265	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	37	CCDS13850.1																																																																																			G|0.749;T|0.251	0.251	strong		0.667	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265	
CBLN2	147381	hgsc.bcm.edu	37	18	70209321	70209321	+	Silent	SNP	C	C	A	rs7237888	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:70209321C>A	ENST00000269503.4	-	3	848	c.75G>T	c.(73-75)ccG>ccT	p.P25P	CBLN2_ENST00000585159.1_Silent_p.P25P|CBLN2_ENST00000583651.1_Intron|CBLN2_ENST00000584764.1_Intron|CBLN2_ENST00000581073.1_Intron	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	25					positive regulation of synapse assembly (GO:0051965)	extracellular space (GO:0005615)				endometrium(2)|lung(15)	17		Esophageal squamous(42;0.131)				CGCAgccgcccggctcgcgca	0.786													C|||	2820	0.563099	0.1868	0.8573	5008	,	,		7947	0.381		0.9304	False		,,,				2504	0.6728				p.P25P		Atlas-SNP	.											CBLN2,right_upper_lobe,carcinoma,-1,1	CBLN2	41	1	0			c.G75T						scavenged	.	C		1660,2420		328,1004,708	5.0	7.0	6.0		75	-0.8	1.0	18	dbSNP_116	6	7475,487		3530,415,36	no	coding-synonymous	CBLN2	NM_182511.3		3858,1419,744	AA,AC,CC		6.1166,40.6863,24.1405		25/225	70209321	9135,2907	2040	3981	6021	SO:0001819	synonymous_variant	147381	exon3			GCCGCCCGGCTCG	BC035789	CCDS11999.1	18q22.3	2007-11-19			ENSG00000141668	ENSG00000141668			1544	protein-coding gene	gene with protein product		600433				7877445	Standard	NM_182511		Approved		uc002lkv.2	Q8IUK8	OTTHUMG00000132825	ENST00000269503.4:c.75G>T	18.37:g.70209321C>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_182511	Q53Z56	Silent	SNP	ENST00000269503.4	37	CCDS11999.1																																																																																			C|0.390;A|0.610	0.610	strong		0.786	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511	
MS4A13	503497	hgsc.bcm.edu	37	11	60296879	60296879	+	Silent	SNP	C	C	T	rs11230364	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60296879C>T	ENST00000378186.2	+	6	671	c.348C>T	c.(346-348)taC>taT	p.Y116Y	MS4A13_ENST00000378185.2_Silent_p.Y76Y|MS4A13_ENST00000437058.2_Silent_p.Y57Y|MS4A13_ENST00000527948.1_Intron	NM_001012417.2	NP_001012417.2	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	123						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						TGTTCTTCTACGGTTTGGAAT	0.353													C|||	539	0.107628	0.0613	0.098	5008	,	,		15834	0.129		0.0825	False		,,,				2504	0.181				p.Y116Y		Atlas-SNP	.											.	MS4A13	27	.	0			c.C348T						PASS	.	C	,	294,4112	161.1+/-193.3	11,272,1920	199.0	197.0	198.0		348,228	1.5	0.0	11	dbSNP_120	198	770,7828	181.9+/-230.5	25,720,3554	no	coding-synonymous,coding-synonymous	MS4A13	NM_001012417.2,NM_001100909.1	,	36,992,5474	TT,TC,CC		8.9556,6.6727,8.1821	,	116/153,76/113	60296879	1064,11940	2203	4299	6502	SO:0001819	synonymous_variant	503497	exon6			CTTCTACGGTTTG	AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000378186.2:c.348C>T	11.37:g.60296879C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_001012417	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Silent	SNP	ENST00000378186.2	37	CCDS31571.1																																																																																			C|0.906;T|0.094	0.094	strong		0.353	MS4A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395408.1	NM_001012417	
SCUBE1	80274	hgsc.bcm.edu	37	22	43623395	43623395	+	Missense_Mutation	SNP	C	C	G	rs129415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43623395C>G	ENST00000360835.4	-	10	1318	c.1192G>C	c.(1192-1194)Ggg>Cgg	p.G398R		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	398	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		G -> R (in dbSNP:rs129415). {ECO:0000269|PubMed:12270931}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CAATCCTTCCCGTTCCAGTGG	0.662													G|||	3689	0.736621	0.9297	0.6527	5008	,	,		17589	0.5377		0.7237	False		,,,				2504	0.7536				p.G398R		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G1192C						PASS	.	G	ARG/GLY	3974,430	200.1+/-223.5	1790,394,18	56.0	48.0	51.0		1192	-7.0	0.4	22	dbSNP_78	51	6064,2536	401.9+/-347.3	2163,1738,399	no	missense	SCUBE1	NM_173050.3	125	3953,2132,417	GG,GC,CC		29.4884,9.7639,22.8084	benign	398/989	43623395	10038,2966	2202	4300	6502	SO:0001583	missense	80274	exon10			CCTTCCCGTTCCA		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1192G>C	22.37:g.43623395C>G	ENSP00000354080:p.Gly398Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	43	0.955556	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	1527	0.6991758241758241	446	0.9065040650406504	237	0.6546961325966851	295	0.5157342657342657	549	0.7242744063324539	G	6.861	0.528224	0.13127	0.902361	0.705116	ENSG00000159307	ENST00000360835	D	0.89343	-2.5	3.91	-7.04	0.01578	EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.240064	0.39210	N	0.001422	T	0.00012	0.0000	L	0.39692	1.235	0.09310	P	0.99999999084931	B	0.02656	0.0	B	0.13407	0.009	T	0.35624	-0.9781	9	0.10902	T	0.67	.	11.0482	0.47872	0.0:0.1634:0.1214:0.7152	rs129415;rs59848162;rs129415	398	Q8IWY4	SCUB1_HUMAN	R	398	ENSP00000354080:G398R	ENSP00000354080:G398R	G	-	1	0	SCUBE1	41953339	1.000000	0.71417	0.411000	0.26484	0.398000	0.30690	2.953000	0.49105	-1.366000	0.02155	-1.511000	0.00944	GGG	C|0.262;G|0.738	0.738	strong		0.662	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
NOTCH4	4855	hgsc.bcm.edu	37	6	32189032	32189032	+	Silent	SNP	T	T	C	rs415929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	88	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	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		
LRP5L	91355	hgsc.bcm.edu	37	22	25753321	25753321	+	Silent	SNP	G	G	A	rs9624807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:25753321G>A	ENST00000402785.2	-	2	435	c.339C>T	c.(337-339)cgC>cgT	p.R113R	LRP5L_ENST00000444995.3_Silent_p.R113R|LRP5L_ENST00000402859.2_Silent_p.R113R			A4QPB2	LRP5L_HUMAN	low density lipoprotein receptor-related protein 5-like	113					canonical Wnt signaling pathway (GO:0060070)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)		Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	6						TGACCAGCACGCGCAGCTCCT	0.597													G|||	409	0.0816693	0.1301	0.0663	5008	,	,		16078	0.001		0.1133	False		,,,				2504	0.0777				p.R113R		Atlas-SNP	.											.	LRP5L	23	.	0			c.C339T						PASS	.	G	,	599,3803	261.6+/-264.4	43,513,1645	116.0	99.0	105.0		339,339	-0.2	0.1	22	dbSNP_119	105	970,7630	210.4+/-251.3	66,838,3396	no	coding-synonymous,coding-synonymous	LRP5L	NM_001135772.1,NM_182492.2	,	109,1351,5041	AA,AG,GG		11.2791,13.6075,12.0674	,	113/253,113/253	25753321	1569,11433	2201	4300	6501	SO:0001819	synonymous_variant	91355	exon4			CAGCACGCGCAGC	AL137651	CCDS33626.1	22q11.23	2013-05-30			ENSG00000100068	ENSG00000100068			25323	protein-coding gene	gene with protein product							Standard	NM_182492		Approved	DKFZp434O0213	uc011ajz.2	A4QPB2	OTTHUMG00000150900	ENST00000402785.2:c.339C>T	22.37:g.25753321G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_001135772	B0QYF3|B0QYF4|B2RPI5	Silent	SNP	ENST00000402785.2	37	CCDS33626.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	LRP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320477.2	NM_182492	
LNX2	222484	hgsc.bcm.edu	37	13	28143229	28143229	+	Missense_Mutation	SNP	A	A	G	rs8002697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:28143229A>G	ENST00000316334.3	-	3	721	c.592T>C	c.(592-594)Tcc>Ccc	p.S198P		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	198			S -> P (in dbSNP:rs8002697).		protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CTCCATGTGGAAAGAGACGCT	0.542													G|||	2653	0.529752	0.6762	0.3818	5008	,	,		15405	0.4613		0.5736	False		,,,				2504	0.4622				p.S198P		Atlas-SNP	.											.	LNX2	70	.	0			c.T592C						PASS	.	G	PRO/SER	2936,1470	473.1+/-356.6	972,992,239	202.0	193.0	196.0		592	3.0	0.0	13	dbSNP_116	196	4732,3868	542.8+/-384.3	1283,2166,851	yes	missense	LNX2	NM_153371.3	74	2255,3158,1090	GG,GA,AA		44.9767,33.3636,41.0426	benign	198/691	28143229	7668,5338	2203	4300	6503	SO:0001583	missense	222484	exon3			ATGTGGAAAGAGA	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"""RING-type (C3HC4) zinc fingers"""	20421	protein-coding gene	gene with protein product		609733	"""PDZ domain containing ring finger 1"""	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.592T>C	13.37:g.28143229A>G	ENSP00000325929:p.Ser198Pro	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	1155	0.5288461538461539	323	0.6565040650406504	155	0.4281767955801105	253	0.4423076923076923	424	0.5593667546174143	G	1.725	-0.495664	0.04291	0.666364	0.550233	ENSG00000139517	ENST00000316334	T	0.05996	3.36	5.74	3.03	0.35002	.	0.204155	0.52532	N	0.000061	T	0.00012	0.0000	N	0.00504	-1.425	0.52501	P	4.499999999996174E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.09952	-1.0651	9	0.15952	T	0.53	.	10.5605	0.45142	0.2652:0.0:0.7348:0.0	rs8002697;rs61064382;rs8002697	198	Q8N448	LNX2_HUMAN	P	198	ENSP00000325929:S198P	ENSP00000325929:S198P	S	-	1	0	LNX2	27041229	1.000000	0.71417	0.004000	0.12327	0.001000	0.01503	1.916000	0.39986	0.141000	0.18875	-1.951000	0.00486	TCC	A|0.434;G|0.566	0.566	strong		0.542	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2		
EPG5	57724	hgsc.bcm.edu	37	18	43523997	43523997	+	Missense_Mutation	SNP	T	T	C	rs61734402	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43523997T>C	ENST00000282041.5	-	8	1800	c.1766A>G	c.(1765-1767)cAg>cGg	p.Q589R		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	589					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						AAGAAGATGCTGAAAGAGTTC	0.398													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		20382	0.0		0.0129	False		,,,				2504	0.0				p.Q589R		Atlas-SNP	.											.	EPG5	199	.	0			c.A1766G						PASS	.	T	ARG/GLN	10,3706		0,10,1848	150.0	134.0	139.0		1766	5.2	0.9	18	dbSNP_129	139	147,8069		1,145,3962	yes	missense	EPG5	NM_020964.2	43	1,155,5810	CC,CT,TT		1.7892,0.2691,1.3158	benign	589/2580	43523997	157,11775	1858	4108	5966	SO:0001583	missense	57724	exon8			AGATGCTGAAAGA	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.1766A>G	18.37:g.43523997T>C	ENSP00000282041:p.Gln589Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	9.853	1.194070	0.22037	0.002691	0.017892	ENSG00000152223	ENST00000282041	T	0.09817	2.94	5.25	5.25	0.73442	.	0.170822	0.38720	N	0.001587	T	0.04998	0.0134	L	0.40543	1.245	0.29097	N	0.881736	P;B	0.34724	0.465;0.4	B;B	0.34242	0.178;0.085	T	0.08868	-1.0701	10	0.22109	T	0.4	-10.7121	15.1999	0.73126	0.0:0.0:0.0:1.0	.	589;589	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	589	ENSP00000282041:Q589R	ENSP00000282041:Q589R	Q	-	2	0	EPG5	41777995	1.000000	0.71417	0.894000	0.35097	0.212000	0.24457	4.972000	0.63756	1.991000	0.58162	0.374000	0.22700	CAG	T|0.994;C|0.006	0.006	strong		0.398	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
CAMSAP3	57662	hgsc.bcm.edu	37	19	7675369	7675369	+	Silent	SNP	C	C	T	rs62113420	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7675369C>T	ENST00000160298.4	+	6	869	c.768C>T	c.(766-768)tgC>tgT	p.C256C	CAMSAP3_ENST00000446248.2_Silent_p.C283C	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	256	CH.				epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						CAGAGGTGTGCTTGAAGGACC	0.632													C|||	371	0.0740815	0.0862	0.0994	5008	,	,		14322	0.002		0.161	False		,,,				2504	0.0245				p.C283C		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C849T						PASS	.	C	,	310,3818		16,278,1770	87.0	96.0	93.0		849,768	4.3	1.0	19	dbSNP_129	93	1141,7251		65,1011,3120	no	coding-synonymous,coding-synonymous	CAMSAP3	NM_001080429.2,NM_020902.1	,	81,1289,4890	TT,TC,CC		13.5963,7.5097,11.5895	,	283/1277,256/1250	7675369	1451,11069	2064	4196	6260	SO:0001819	synonymous_variant	57662	exon8			GGTGTGCTTGAAG	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 80"""	612685	"""KIAA1543"""	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.768C>T	19.37:g.7675369C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																			C|0.897;T|0.103	0.103	strong		0.632	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
NPAP1	23742	hgsc.bcm.edu	37	15	24921771	24921771	+	Missense_Mutation	SNP	G	G	C	rs1563102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:24921771G>C	ENST00000329468.2	+	1	1231	c.757G>C	c.(757-759)Gga>Cga	p.G253R		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	253			G -> R (in dbSNP:rs1563102). {ECO:0000269|PubMed:10783265}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCGGCATCTTGGAAAGCCTGA	0.637													G|||	1370	0.273562	0.0129	0.3516	5008	,	,		15590	0.4673		0.325	False		,,,				2504	0.318				p.G253R		Atlas-SNP	.											C15orf2,NS,carcinoma,0,2	.	.	2	0			c.G757C						PASS	.	G	ARG/GLY	276,4128		13,250,1939	33.0	36.0	35.0		757	-4.1	0.0	15	dbSNP_88	35	2643,5955		405,1833,2061	yes	missense	C15orf2	NM_018958.2	125	418,2083,4000	CC,CG,GG		30.7397,6.267,22.4504	possibly-damaging	253/1157	24921771	2919,10083	2202	4299	6501	SO:0001583	missense	23742	exon1			CATCTTGGAAAGC	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.757G>C	15.37:g.24921771G>C	ENSP00000333735:p.Gly253Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	638	0.29212454212454214	10	0.02032520325203252	125	0.3453038674033149	276	0.4825174825174825	227	0.2994722955145119	.	11.44	1.639244	0.29157	0.06267	0.307397	ENSG00000185823	ENST00000329468	T	0.10477	2.87	2.07	-4.13	0.03904	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.45594	0.862	P	0.51101	0.659	T	0.23655	-1.0182	8	0.10111	T	0.7	.	5.3948	0.16263	0.0:0.4581:0.2796:0.2623	rs1563102;rs3784245;rs1563102	253	Q9NZP6	CO002_HUMAN	R	253	ENSP00000333735:G253R	ENSP00000333735:G253R	G	+	1	0	C15orf2	22472864	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.085000	0.03390	-1.084000	0.03092	0.436000	0.28706	GGA	G|0.744;C|0.256	0.256	strong		0.637	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
SGSM2	9905	hgsc.bcm.edu	37	17	2268311	2268311	+	Missense_Mutation	SNP	G	G	A	rs2248821	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2268311G>A	ENST00000426855.2	+	10	1296	c.1121G>A	c.(1120-1122)cGg>cAg	p.R374Q	SGSM2_ENST00000574563.1_Missense_Mutation_p.R374Q|SGSM2_ENST00000268989.3_Missense_Mutation_p.R374Q	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	374			R -> Q (in dbSNP:rs2248821). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17509819}.		late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CTGCTGCCTCGGGGACAGCTA	0.642													G|||	2824	0.563898	0.5393	0.3444	5008	,	,		18172	0.7619		0.4274	False		,,,				2504	0.6892				p.R374Q		Atlas-SNP	.											.	SGSM2	60	.	0			c.G1121A						PASS	.	G	GLN/ARG,GLN/ARG	2357,2049	582.9+/-385.7	631,1095,477	32.0	35.0	34.0		1121,1121	2.5	0.8	17	dbSNP_100	34	3950,4650	530.2+/-381.7	900,2150,1250	yes	missense,missense	SGSM2	NM_001098509.1,NM_014853.2	43,43	1531,3245,1727	AA,AG,GG		45.9302,46.5048,48.493	benign,benign	374/1007,374/1052	2268311	6307,6699	2203	4300	6503	SO:0001583	missense	9905	exon10			TGCCTCGGGGACA	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1121G>A	17.37:g.2268311G>A	ENSP00000415107:p.Arg374Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Missense_Mutation	SNP	ENST00000426855.2	37	CCDS45570.1	1152	0.5274725274725275	254	0.516260162601626	139	0.3839779005524862	426	0.7447552447552448	333	0.4393139841688654	G	19.03	3.748905	0.69533	0.534952	0.459302	ENSG00000141258	ENST00000268989;ENST00000426855	T;T	0.28895	1.59;1.59	5.52	2.47	0.30058	.	0.057886	0.64402	N	0.000001	T	0.00012	0.0000	L	0.50333	1.59	0.19775	P	0.9999556456	B;B;B	0.20052	0.041;0.029;0.002	B;B;B	0.20184	0.028;0.009;0.002	T	0.18681	-1.0329	9	0.54805	T	0.06	-7.7074	10.2336	0.43268	0.2152:0.0:0.7848:0.0	rs2248821;rs17857179;rs58247251;rs2248821	374;374;374	O43147-5;O43147;O43147-2	.;SGSM2_HUMAN;.	Q	374	ENSP00000268989:R374Q;ENSP00000415107:R374Q	ENSP00000268989:R374Q	R	+	2	0	SGSM2	2215061	0.983000	0.35010	0.831000	0.32960	0.997000	0.91878	2.258000	0.43249	0.303000	0.22785	0.655000	0.94253	CGG	G|0.492;A|0.508	0.508	strong		0.642	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
ZNF500	26048	hgsc.bcm.edu	37	16	4802386	4802386	+	Silent	SNP	G	G	T	rs3747602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4802386G>T	ENST00000219478.6	-	6	1733	c.1434C>A	c.(1432-1434)gcC>gcA	p.A478A	RP11-127I20.7_ENST00000588099.1_RNA|ZNF500_ENST00000591026.1_5'UTR|ZNF500_ENST00000545009.1_Intron			O60304	ZN500_HUMAN	zinc finger protein 500	478					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)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						ATCAGGCTTTGGCACCGGGGC	0.637													G|||	2574	0.513978	0.3646	0.5403	5008	,	,		16426	0.6607		0.6163	False		,,,				2504	0.4407				p.A478A		Atlas-SNP	.											.	ZNF500	45	.	0			c.C1434A						PASS	.	G		1872,2282		468,936,673	7.0	6.0	6.0		1434	2.6	0.0	16	dbSNP_107	6	5199,2945		1789,1621,662	no	coding-synonymous	ZNF500	NM_021646.1		2257,2557,1335	TT,TG,GG		36.1616,45.065,42.5028		478/481	4802386	7071,5227	2077	4072	6149	SO:0001819	synonymous_variant	26048	exon6			GGCTTTGGCACCG	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.1434C>A	16.37:g.4802386G>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Silent	SNP	ENST00000219478.6	37	CCDS32383.1																																																																																			G|0.445;T|0.555	0.555	strong		0.637	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
KIF26B	55083	hgsc.bcm.edu	37	1	245704130	245704130	+	Missense_Mutation	SNP	G	G	C	rs61754898	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	207	3	0.0144928		WXS	Illumina HiSeq	Phase_I	185	81	0.437838	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	
THOC1	9984	hgsc.bcm.edu	37	18	264030	264030	+	Silent	SNP	A	A	G	rs371643145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264030A>G	ENST00000261600.6	-	4	259	c.252T>C	c.(250-252)acT>acC	p.T84T	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	84					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				ACTTACCTTCAGTTACTCCCC	0.353																																					p.T84T		Atlas-SNP	.											.	THOC1	43	.	0			c.T252C						PASS	.	A		0,3698		0,0,1849	86.0	73.0	77.0		252	1.0	1.0	18		77	5,8177		0,5,4086	no	coding-synonymous	THOC1	NM_005131.2		0,5,5935	GG,GA,AA		0.0611,0.0,0.0421		84/658	264030	5,11875	1849	4091	5940	SO:0001819	synonymous_variant	9984	exon4			ACCTTCAGTTACT	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"""THO complex subunits"""	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.252T>C	18.37:g.264030A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	182	61	0.335165	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.353	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131	
DDRGK1	65992	hgsc.bcm.edu	37	20	3171337	3171337	+	Missense_Mutation	SNP	C	C	T	rs11591	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3171337C>T	ENST00000354488.3	-	9	964	c.907G>A	c.(907-909)Gcc>Acc	p.A303T	DDRGK1_ENST00000496781.1_5'UTR	NM_023935.1	NP_076424.1	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1	303			A -> T (in dbSNP:rs11591). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum (GO:0005783)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7						CGGCCCCAGGCGATGAGGGAG	0.637													C|||	351	0.0700879	0.0061	0.0994	5008	,	,		17224	0.001		0.1968	False		,,,				2504	0.0767				p.A303T		Atlas-SNP	.											.	DDRGK1	21	.	0			c.G907A						PASS	.	C	THR/ALA	181,4225	115.9+/-153.8	7,167,2029	47.0	55.0	52.0		907	-2.3	0.9	20	dbSNP_52	52	1581,7019	294.3+/-301.8	140,1301,2859	yes	missense	DDRGK1	NM_023935.1	58	147,1468,4888	TT,TC,CC		18.3837,4.108,13.5476	benign	303/315	3171337	1762,11244	2203	4300	6503	SO:0001583	missense	65992	exon9			CCCAGGCGATGAG	AL121891	CCDS13050.1	20p13	2011-08-18	2008-10-03	2008-10-03	ENSG00000198171	ENSG00000198171			16110	protein-coding gene	gene with protein product	"""Dashurin"""		"""chromosome 20 open reading frame 116"""	C20orf116		20036718, 20228063, 21494687	Standard	NM_023935		Approved	dJ1187M17.3	uc002wic.3	Q96HY6	OTTHUMG00000031732	ENST00000354488.3:c.907G>A	20.37:g.3171337C>T	ENSP00000346483:p.Ala303Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_023935	A6NIU5|C9JSZ5|Q9BW47	Missense_Mutation	SNP	ENST00000354488.3	37	CCDS13050.1	190	0.08699633699633699	7	0.014227642276422764	42	0.11602209944751381	0	0.0	141	0.18601583113456466	C	9.251	1.040633	0.19669	0.04108	0.183837	ENSG00000198171	ENST00000354488;ENST00000380213	T	0.43688	0.94	4.98	-2.27	0.06846	.	0.347908	0.30869	N	0.008703	T	0.00039	0.0001	N	0.08118	0	0.09310	P	0.99999999739718	B	0.11235	0.004	B	0.08055	0.003	T	0.17018	-1.0383	9	0.31617	T	0.26	-0.4349	3.4261	0.07412	0.4458:0.2276:0.0:0.3266	rs11591;rs3171338;rs17256431;rs17845142;rs17857945;rs59952895;rs11591	303	Q96HY6	DDRGK_HUMAN	T	303;302	ENSP00000346483:A303T	ENSP00000346483:A303T	A	-	1	0	DDRGK1	3119337	1.000000	0.71417	0.942000	0.38095	0.997000	0.91878	1.072000	0.30678	-0.223000	0.09943	0.561000	0.74099	GCC	C|0.885;T|0.115	0.115	strong		0.637	DDRGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077709.2	NM_023935	
ADH7	131	hgsc.bcm.edu	37	4	100341861	100341861	+	Silent	SNP	C	C	T	rs971074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:100341861C>T	ENST00000209665.4	-	6	930	c.690G>A	c.(688-690)agG>agA	p.R230R	ADH7_ENST00000476959.1_Silent_p.R238R|ADH7_ENST00000482593.1_Silent_p.R161R|ADH7_ENST00000437033.2_Silent_p.R218R	NM_000673.4	NP_000664.2	P40394	ADH7_HUMAN	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	230					ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|extracellular negative regulation of signal transduction (GO:1900116)|fatty acid omega-oxidation (GO:0010430)|oxidation-reduction process (GO:0055114)|response to bacterium (GO:0009617)|response to ethanol (GO:0045471)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular region (GO:0005576)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|aldehyde oxidase activity (GO:0004031)|ethanol binding (GO:0035276)|receptor antagonist activity (GO:0048019)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)	19				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)		TCCCAATGATCCTAGATGCAC	0.517													C|||	600	0.119808	0.1422	0.1268	5008	,	,		19050	0.12		0.1183	False		,,,				2504	0.0859				p.R238R		Atlas-SNP	.											.	ADH7	76	.	0			c.G714A						PASS	.	C	,	747,3659	306.9+/-289.7	68,611,1524	151.0	130.0	137.0	http://www.ncbi.nlm.nih.gov/pubmed?term	690,714	1.1	0.2	4	dbSNP_86	137	1042,7558	221.3+/-258.8	74,894,3332	yes	coding-synonymous,coding-synonymous	ADH7	NM_000673.4,NM_001166504.1	,	142,1505,4856	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	12.1163,16.9542,13.7552	,	230/387,238/395	100341861	1789,11217	2203	4300	6503	SO:0001819	synonymous_variant	131	exon6			AATGATCCTAGAT	X76342	CCDS34034.1, CCDS54781.1	4q23-q24	2008-02-05			ENSG00000196344	ENSG00000196344	1.1.1.1	"""Alcohol dehydrogenases"""	256	protein-coding gene	gene with protein product		600086				8195208	Standard	NM_000673		Approved	ADH-4	uc021xqj.1	P40394	OTTHUMG00000159318	ENST00000209665.4:c.690G>A	4.37:g.100341861C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_001166504	A2RRB6|A8MVN9|B2R760|B4DWV6|Q13713	Silent	SNP	ENST00000209665.4	37	CCDS34034.1																																																																																			C|0.862;T|0.138	0.138	strong		0.517	ADH7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000673	
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	3'UTR	SNP	T	T	C	rs8392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1350709T>C	ENST00000400137.4	-	0	534				SDCBP2-AS1_ENST00000609470.1_RNA|SDCBP2-AS1_ENST00000446423.1_RNA|SDCBP2-AS1_ENST00000609285.1_RNA|FKBP1A_ENST00000381724.3_3'UTR|FKBP1A_ENST00000460490.1_5'UTR	NM_000801.4	NP_000792.1	P62942	FKB1A_HUMAN	FK506 binding protein 1A, 12kDa						'de novo' protein folding (GO:0006458)|amyloid fibril formation (GO:1990000)|calcium ion transmembrane transport (GO:0070588)|chaperone-mediated protein folding (GO:0061077)|extracellular fibril organization (GO:0043206)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of amyloid precursor protein catabolic process (GO:1902991)|regulation of immune response (GO:0050776)|regulation of protein localization (GO:0032880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|SMAD protein complex assembly (GO:0007183)|T cell activation (GO:0042110)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|terminal cisterna (GO:0014802)|Z disc (GO:0030018)	activin binding (GO:0048185)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|macrolide binding (GO:0005527)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|type I transforming growth factor beta receptor binding (GO:0034713)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	GATCCCTCCATGGCAGATCTG	0.502													T|||	1719	0.343251	0.5129	0.3458	5008	,	,		19072	0.0883		0.4155	False		,,,				2504	0.3006				p.P86P		Atlas-SNP	.											.	FKBP1A	6	.	0			c.A258G						PASS	.																																			SO:0001624	3_prime_UTR_variant	2280	exon4			CCTCCATGGCAGA	M92423	CCDS13014.1, CCDS74688.1	20p13	2013-03-20	2002-08-29		ENSG00000088832	ENSG00000088832			3711	protein-coding gene	gene with protein product	"""calstabin 1"""	186945	"""FK506-binding protein 1A (12kD)"""	FKBP1		1930186	Standard	NM_000801		Approved	FKBP-12, FKBP12, PKC12, PPIASE, FKBP12C	uc002wey.3	P62942	OTTHUMG00000031666	ENST00000400137.4:c.*44A>G	20.37:g.1350709T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001199786	D3DVW6|P20071|Q4VC47|Q6FGD9|Q6LEU3|Q9H103|Q9H566	Silent	SNP	ENST00000400137.4	37	CCDS13014.1																																																																																			T|0.408;G|0.125;C|0.192;A|0.276	0.192	strong		0.502	FKBP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077534.2		
SLC7A13	157724	hgsc.bcm.edu	37	8	87241847	87241847	+	Silent	SNP	G	G	A	rs7814198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:87241847G>A	ENST00000297524.3	-	1	763	c.660C>T	c.(658-660)ggC>ggT	p.G220G	SLC7A13_ENST00000520624.1_Intron|SLC7A13_ENST00000419776.2_Splice_Site	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	63	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	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	
ZNF337	26152	hgsc.bcm.edu	37	20	25666737	25666737	+	Missense_Mutation	SNP	C	C	T	rs926487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25666737C>T	ENST00000376436.1	-	2	588	c.49G>A	c.(49-51)Gtc>Atc	p.V17I	ZNF337_ENST00000538750.1_Missense_Mutation_p.V17I|ZNF337_ENST00000481610.1_5'UTR|ZNF337_ENST00000252979.5_Missense_Mutation_p.V17I			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	17	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> I (in dbSNP:rs926487).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TCCACAGTGACATCCCCAAAT	0.552													C|||	832	0.166134	0.4478	0.0821	5008	,	,		20528	0.0734		0.0606	False		,,,				2504	0.0491				p.V17I		Atlas-SNP	.											.	ZNF337	65	.	0			c.G49A						PASS	.	C	ILE/VAL	1674,2732		305,1064,834	113.0	111.0	112.0		49	1.0	0.0	20	dbSNP_86	112	408,8192		7,394,3899	yes	missense	ZNF337	NM_015655.2	29	312,1458,4733	TT,TC,CC		4.7442,37.9936,16.008	probably-damaging	17/752	25666737	2082,10924	2203	4300	6503	SO:0001583	missense	26152	exon3			CAGTGACATCCCC		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.49G>A	20.37:g.25666737C>T	ENSP00000365619:p.Val17Ile	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	37	CCDS13174.1	315	0.14423076923076922	203	0.41260162601626016	32	0.08839779005524862	34	0.05944055944055944	46	0.06068601583113457	.	15.97	2.989929	0.54041	0.379936	0.047442	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.08720	3.06;3.06;3.06	2.02	1.05	0.20165	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	D;D	0.56968	0.978;0.978	D;D	0.63793	0.918;0.918	T	0.44862	-0.9300	8	0.87932	D	0	.	6.0643	0.19854	0.0:0.8238:0.0:0.1762	rs926487;rs52820675;rs926487	17;17	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	I	17	ENSP00000365619:V17I;ENSP00000252979:V17I;ENSP00000442181:V17I	ENSP00000252979:V17I	V	-	1	0	ZNF337	25614737	0.403000	0.25319	0.009000	0.14445	0.959000	0.62525	1.441000	0.35035	0.074000	0.16767	0.461000	0.40582	GTC	C|0.838;T|0.162	0.162	strong		0.552	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
PRR5	55615	hgsc.bcm.edu	37	22	45075738	45075738	+	Missense_Mutation	SNP	T	T	C	rs763213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45075738T>C	ENST00000403581.1	+	2	668	c.59T>C	c.(58-60)aTg>aCg	p.M20T	PRR5_ENST00000006251.7_Intron	NM_001198721.1	NP_001185650.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	0	Interaction with RICTOR.				cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		CCGGAAAAGATGCCGGCGCAG	0.607													C|||	3525	0.703874	0.8805	0.755	5008	,	,		14917	0.6161		0.6292	False		,,,				2504	0.5961				p.M20T		Atlas-SNP	.											.	PRR5	75	.	0			c.T59C						PASS	.	C	,,,THR/MET,	1490,262		636,218,22	11.0	11.0	11.0		,,,59,	0.4	0.0	22	dbSNP_86	11	2531,1445		808,915,265	yes	intron,intron,intron,missense,intron	PRR5	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3	,,,81,	1444,1133,287	CC,CT,TT		36.3431,14.9543,29.801	,,,,	,,,20/412,	45075738	4021,1707	876	1988	2864	SO:0001583	missense	55615	exon2			AAAAGATGCCGGC	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000403581.1:c.59T>C	22.37:g.45075738T>C	ENSP00000384848:p.Met20Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000403581.1	37	CCDS56232.1	1526	0.6987179487179487	421	0.8556910569105691	251	0.6933701657458563	371	0.6486013986013986	483	0.637203166226913	C	0.265	-0.996854	0.02145	0.850457	0.636569	ENSG00000186654	ENST00000403581	T	0.29142	1.58	0.361	0.361	0.16107	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10019	-1.0648	6	0.87932	D	0	.	.	.	.	rs763213;rs57612953;rs763213	20	B1AHF6	.	T	20	ENSP00000384848:M20T	ENSP00000384848:M20T	M	+	2	0	PRR5	43454402	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.189000	0.09629	-0.476000	0.06842	-0.473000	0.04963	ATG	T|0.308;C|0.692	0.692	strong		0.607	PRR5-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318199.1	NM_001017528	
MED16	10025	hgsc.bcm.edu	37	19	871987	871987	+	Silent	SNP	G	G	A	rs78047294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:871987G>A	ENST00000589119.1	-	11	2036	c.2037C>T	c.(2035-2037)acC>acT	p.T679T	MED16_ENST00000606828.1_5'Flank|MED16_ENST00000325464.1_Silent_p.T679T|MED16_ENST00000395808.3_Silent_p.T679T|MED16_ENST00000269814.4_Intron|MED16_ENST00000312090.6_Silent_p.T679T			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	679					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		GGGTATCCGAGGTGGCCGTAT	0.662													-|||	867	0.173123	0.2821	0.1744	5008	,	,		7668	0.0228		0.2346	False		,,,				2504	0.1166				p.T679T		Atlas-SNP	.											.	MED16	61	.	0			c.C2037T						PASS	.			1094,3248	383.0+/-324.7	152,790,1229	53.0	44.0	47.0		2037	0.1	1.0	19	dbSNP_131	47	2068,6486	353.4+/-329.1	242,1584,2451	no	coding-synonymous	MED16	NM_005481.2		394,2374,3680	AA,AG,GG		24.1758,25.1958,24.5192		679/878	871987	3162,9734	2171	4277	6448	SO:0001819	synonymous_variant	10025	exon12			ATCCGAGGTGGCC	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2037C>T	19.37:g.871987G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.771;A|0.229	0.229	strong		0.662	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
MGAM	8972	hgsc.bcm.edu	37	7	141759676	141759676	+	Silent	SNP	T	T	C	rs62477620	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	216	210	0.972222	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		
NID2	22795	hgsc.bcm.edu	37	14	52478315	52478315	+	Silent	SNP	A	A	G	rs1051069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52478315A>G	ENST00000216286.5	-	17	3506	c.3507T>C	c.(3505-3507)gcT>gcC	p.A1169A	NID2_ENST00000541773.1_Silent_p.A1068A	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1169					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)					GTTCCAGACCAGCACGGCTGA	0.498													N|||	3458	0.690495	0.7859	0.745	5008	,	,		19929	0.7738		0.5378	False		,,,				2504	0.5941				p.A1169A		Atlas-SNP	.											NID2,NS,carcinoma,-1,1	NID2	201	1	0			c.T3507C						PASS	.	G		3311,1095	394.4+/-329.3	1248,815,140	150.0	123.0	132.0		3507	-0.7	0.0	14	dbSNP_86	132	4660,3940	550.8+/-385.8	1281,2098,921	no	coding-synonymous	NID2	NM_007361.3		2529,2913,1061	GG,GA,AA		45.814,24.8525,38.7129		1169/1376	52478315	7971,5035	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon17			CAGACCAGCACGG	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.3507T>C	14.37:g.52478315A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1	1479	0.6771978021978022	386	0.7845528455284553	260	0.7182320441988951	438	0.7657342657342657	395	0.521108179419525	G	0.851	-0.738684	0.03111	0.751475	0.54186	ENSG00000087303	ENST00000556572	.	.	.	5.92	-0.731	0.11151	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.25847	-1.0120	3	.	.	.	.	5.6379	0.17546	0.176:0.4591:0.2713:0.0937	rs1051069;rs3191452;rs17831519;rs17846144;rs17859152;rs59260357;rs1051069	.	.	.	R	438	.	.	W	-	1	0	NID2	51548065	0.015000	0.18098	0.000000	0.03702	0.058000	0.15608	-0.734000	0.04893	-0.721000	0.04929	-0.812000	0.03155	TGG	A|0.354;G|0.646	0.646	strong		0.498	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:64612858C>A	ENST00000344113.4	+	84	15768	c.15556C>A	c.(15556-15558)Ctg>Atg	p.L5186M	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1820M|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1571M|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1571M|SYNE2_ENST00000554584.1_Missense_Mutation_p.L5103M|SYNE2_ENST00000358025.3_Missense_Mutation_p.L5186M	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5186			L -> M (in dbSNP:rs10151658). {ECO:0000269|PubMed:12118075, ECO:0000269|PubMed:14702039}.		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.L5186M(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAACAACTGGCTGGAAGCACA	0.383													A|||	3164	0.631789	0.9168	0.513	5008	,	,		17217	0.6429		0.4553	False		,,,				2504	0.501				p.L5186M		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - Missense(1)	prostate(1)	c.C15556A						scavenged	.	A	MET/LEU,MET/LEU	3745,661	281.4+/-275.9	1603,539,61	68.0	73.0	71.0		15556,15556	-2.1	1.0	14	dbSNP_119	71	3771,4829	614.9+/-396.3	832,2107,1361	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	15,15	2435,2646,1422	AA,AC,CC		43.8488,15.0023,42.2113	benign,benign	5186/6886,5186/6908	64612858	7516,5490	2203	4300	6503	SO:0001583	missense	23224	exon84			AACTGGCTGGAAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15556C>A	14.37:g.64612858C>A	ENSP00000341781:p.Leu5186Met	Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	1340	0.6135531135531136	448	0.9105691056910569	184	0.5082872928176796	368	0.6433566433566433	340	0.44854881266490765	A	2.298	-0.360858	0.05103	0.849977	0.438488	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;3.78;0.71	5.63	-2.1	0.07210	.	0.647372	0.14331	N	0.326332	T	0.00012	0.0000	N	0.05510	-0.035	0.09310	P	0.9999999999999748	B;B;B;B	0.18310	0.002;0.027;0.002;0.006	B;B;B;B	0.17098	0.01;0.017;0.01;0.012	T	0.27020	-1.0086	9	0.15952	T	0.53	.	12.0809	0.53669	0.1859:0.6107:0.0:0.2034	rs10151658;rs17179138;rs58728365;rs10151658	1571;5103;5186;5186	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	M	5186;1571;5186;5103;5109;1820;1571	ENSP00000350719:L5186M;ENSP00000349969:L1571M;ENSP00000341781:L5186M;ENSP00000452570:L5103M;ENSP00000450831:L1820M;ENSP00000378249:L1571M	ENSP00000261678:L5109M	L	+	1	2	SYNE2	63682611	0.060000	0.20803	0.953000	0.39169	0.324000	0.28378	-0.595000	0.05727	-1.072000	0.03141	-1.140000	0.01884	CTG	C|0.386;A|0.614	0.614	strong		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
UGT1A7	54577	hgsc.bcm.edu	37	2	234590616	234590616	+	Silent	SNP	C	C	A	rs7577677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234590616C>A	ENST00000373426.3	+	1	33	c.33C>A	c.(31-33)ccC>ccA	p.P11P	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	11					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GCCTCCTTCCCCTATATGTGT	0.547											OREG0003832	type=REGULATORY REGION|Gene=UGT1A7|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1489	0.297324	0.2481	0.2637	5008	,	,		18471	0.1964		0.3598	False		,,,				2504	0.4274				p.P11P		Atlas-SNP	.											.	UGT1A7	74	.	0			c.C33A						PASS	.	C	,,,	1205,3201	420.8+/-339.2	179,847,1177	135.0	129.0	131.0		,,33,	-3.0	0.0	2	dbSNP_116	131	3332,5268	496.3+/-374.3	653,2026,1621	no	intron,intron,coding-synonymous,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A9	NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2	,,,	832,2873,2798	AA,AC,CC		38.7442,27.3491,34.8839	,,,	,,11/531,	234590616	4537,8469	2203	4300	6503	SO:0001819	synonymous_variant	54577	exon1			CCTTCCCCTATAT	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.33C>A	2.37:g.234590616C>A		Somatic	84	0	0	2374	WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_019077	B8K293|O00473	Silent	SNP	ENST00000373426.3	37	CCDS2506.1																																																																																			C|0.686;A|0.314	0.314	strong		0.547	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
PAK2	5062	hgsc.bcm.edu	37	3	196530022	196530022	+	Silent	SNP	C	C	T	rs115224945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196530022C>T	ENST00000327134.3	+	4	745	c.423C>T	c.(421-423)agC>agT	p.S141S		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	141					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		AATATCTGAGCTTTACTCCTC	0.418																																					p.S141S		Atlas-SNP	.											PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	0			c.C423T						scavenged	.						85.0	79.0	81.0					3																	196530022		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			TCTGAGCTTTACT	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.423C>T	3.37:g.196530022C>T		Somatic	46	2	0.0434783		WXS	Illumina HiSeq	Phase_I	92	13	0.141304	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			C|0.986;T|0.015	0.015	strong		0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R			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	38	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	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	
PTPLAD1	51495	hgsc.bcm.edu	37	15	65856653	65856653	+	Silent	SNP	G	G	A	rs11539008	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65856653G>A	ENST00000261875.5	+	7	799	c.633G>A	c.(631-633)acG>acA	p.T211T	PTPLAD1_ENST00000568793.1_Silent_p.T186T|PTPLAD1_ENST00000565299.1_Silent_p.T249T|PTPLAD1_ENST00000562901.1_Silent_p.T94T|PTPLAD1_ENST00000569894.1_Silent_p.T94T|PTPLAD1_ENST00000566074.1_Silent_p.T94T|PTPLAD1_ENST00000566511.1_Silent_p.T94T|PTPLAD1_ENST00000442729.2_Silent_p.T156T	NM_016395.2	NP_057479.2	Q9P035	HACD3_HUMAN	protein tyrosine phosphatase-like A domain containing 1	211					activation of JUN kinase activity (GO:0007257)|fatty acid biosynthetic process (GO:0006633)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|positive regulation of GTPase activity (GO:0043547)|Rac protein signal transduction (GO:0016601)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)	GTPase activator activity (GO:0005096)|lyase activity (GO:0016829)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|pancreas(1)	5						GAGTCACTACGTCACCGGTGC	0.443													G|||	554	0.110623	0.093	0.1484	5008	,	,		20223	0.0774		0.17	False		,,,				2504	0.0808				p.T211T		Atlas-SNP	.											.	PTPLAD1	23	.	0			c.G633A						PASS	.	G		417,3503		20,377,1563	148.0	140.0	143.0		633	-4.4	0.0	15	dbSNP_120	143	1557,6735		153,1251,2742	no	coding-synonymous	PTPLAD1	NM_016395.2		173,1628,4305	AA,AG,GG		18.7771,10.6378,16.1644		211/363	65856653	1974,10238	1960	4146	6106	SO:0001819	synonymous_variant	51495	exon7			CACTACGTCACCG		CCDS45282.1	15q22.2	2005-11-11				ENSG00000074696			24175	protein-coding gene	gene with protein product		615940				10747961, 11042152	Standard	NM_016395		Approved	B-ind1, HSPC121	uc002apc.3	Q9P035		ENST00000261875.5:c.633G>A	15.37:g.65856653G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_016395	A0PJA1|B4DRF4|Q280Z3|Q6PD63|Q8IUI5|Q8NC86|Q8NCB1|Q96T12|Q9NQA7	Silent	SNP	ENST00000261875.5	37	CCDS45282.1																																																																																			G|0.872;A|0.128	0.128	strong		0.443	PTPLAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419739.1	NM_016395	
SLC12A9	56996	hgsc.bcm.edu	37	7	100463492	100463492	+	Silent	SNP	G	G	A	rs34433055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100463492G>A	ENST00000354161.3	+	14	2135	c.2010G>A	c.(2008-2010)cgG>cgA	p.R670R	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	670					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTCCTCCCCGGGCTCCTGGGA	0.667													G|||	26	0.00519169	0.0008	0.0043	5008	,	,		14655	0.0		0.0159	False		,,,				2504	0.0061				p.R670R		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2010A						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	30.0	36.0	34.0		2010	3.3	1.0	7	dbSNP_126	34	132,8466	64.9+/-127.2	1,130,4168	no	coding-synonymous	SLC12A9	NM_020246.2		1,143,6358	AA,AG,GG		1.5352,0.2951,1.115		670/915	100463492	145,12859	2203	4299	6502	SO:0001819	synonymous_variant	56996	exon14			TCCCCGGGCTCCT	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.2010G>A	7.37:g.100463492G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			G|0.991;A|0.009	0.009	strong		0.667	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
CMYA5	202333	hgsc.bcm.edu	37	5	79041057	79041057	+	Missense_Mutation	SNP	A	A	G	rs12514461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79041057A>G	ENST00000446378.2	+	4	10778	c.10747A>G	c.(10747-10749)Aaa>Gaa	p.K3583E		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3583	B-box coiled-coil; BBC.		K -> E (in dbSNP:rs12514461). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		AAACTGTAGTAAAAATGAGAA	0.353													A|||	499	0.0996406	0.0393	0.1744	5008	,	,		18473	0.0833		0.1252	False		,,,				2504	0.1186				p.K3583E		Atlas-SNP	.											.	CMYA5	643	.	0			c.A10747G						PASS	.	A	GLU/LYS	176,3482		8,160,1661	30.0	30.0	30.0		10747	5.4	1.0	5	dbSNP_120	30	903,7257		57,789,3234	yes	missense	CMYA5	NM_153610.3	56	65,949,4895	GG,GA,AA		11.0662,4.8114,9.1301	benign	3583/4070	79041057	1079,10739	1829	4080	5909	SO:0001583	missense	202333	exon4			TGTAGTAAAAATG	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.10747A>G	5.37:g.79041057A>G	ENSP00000394770:p.Lys3583Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	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	222	0.10164835164835165	20	0.04065040650406504	58	0.16022099447513813	45	0.07867132867132867	99	0.13060686015831136	A	14.25	2.478239	0.44044	0.048114	0.110662	ENSG00000164309	ENST00000446378	T	0.26518	1.73	5.43	5.43	0.79202	.	0.000000	0.53938	D	0.000044	T	0.00144	0.0004	L	0.61036	1.89	0.28591	P	0.9096466	D	0.57899	0.981	P	0.53490	0.727	T	0.13202	-1.0518	9	0.59425	D	0.04	.	8.2949	0.31980	0.8513:0.0:0.1487:0.0	rs12514461;rs52825873;rs58659811;rs12514461	3583	Q8N3K9	CMYA5_HUMAN	E	3583	ENSP00000394770:K3583E	ENSP00000394770:K3583E	K	+	1	0	CMYA5	79076813	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.280000	0.58959	2.179000	0.69175	0.533000	0.62120	AAA	A|0.904;G|0.096	0.096	strong		0.353	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
OPA1	4976	hgsc.bcm.edu	37	3	193374964	193374964	+	Silent	SNP	T	T	C	rs9851685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:193374964T>C	ENST00000392438.3	+	21	2343	c.2109T>C	c.(2107-2109)gcT>gcC	p.A703A	OPA1_ENST00000361150.2_Silent_p.A704A|OPA1_ENST00000361908.3_Silent_p.A740A|OPA1_ENST00000361715.2_Silent_p.A722A|OPA1_ENST00000361510.2_Silent_p.A758A|OPA1_ENST00000361828.2_Silent_p.A721A	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	703					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)		TTAAAGAGGCTGTTAAGGAAG	0.388													C|||	2336	0.466454	0.5862	0.4697	5008	,	,		16355	0.3571		0.4563	False		,,,				2504	0.4254				p.A758A		Atlas-SNP	.											.	OPA1	79	.	0			c.T2274C						PASS	.	C	,,,,,,,	2475,1931	547.6+/-377.3	693,1089,421	100.0	104.0	102.0		2109,2001,2055,2112,2163,2166,2220,2274	0.1	1.0	3	dbSNP_119	102	3991,4609	599.5+/-394.1	907,2177,1216	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	,,,,,,,	1600,3266,1637	CC,CT,TT		46.407,43.8266,49.7155	,,,,,,,	703/961,667/925,685/943,704/962,721/979,722/980,740/998,758/1016	193374964	6466,6540	2203	4300	6503	SO:0001819	synonymous_variant	4976	exon23			AGAGGCTGTTAAG	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.2109T>C	3.37:g.193374964T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_130837	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			T|0.517;C|0.483	0.483	strong		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
FLG	2312	hgsc.bcm.edu	37	1	152280736	152280736	+	Missense_Mutation	SNP	T	T	C	rs66977240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280736T>C	ENST00000368799.1	-	3	6661	c.6626A>G	c.(6625-6627)cAt>cGt	p.H2209R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2209	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)			TTCATGATGATGCGACCCTGA	0.562									Ichthyosis																												p.H2209R		Atlas-SNP	.											.	FLG	900	.	0			c.A6626G						PASS	.						397.0	353.0	368.0					1																	152280736		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGATGATGCGACC	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.6626A>G	1.37:g.152280736T>C	ENSP00000357789:p.His2209Arg	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	374	72	0.192513	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	1.757	-0.487824	0.04352	.	.	ENSG00000143631	ENST00000368799	T	0.02890	4.12	1.98	-0.241	0.13043	.	.	.	.	.	T	0.00300	0.0009	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34279	-0.9835	9	0.09843	T	0.71	.	5.4443	0.16527	0.0:0.4996:0.0:0.5004	.	2209	P20930	FILA_HUMAN	R	2209	ENSP00000357789:H2209R	ENSP00000357789:H2209R	H	-	2	0	FLG	150547360	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.263000	0.00136	-0.710000	0.05001	-1.436000	0.01078	CAT	T|0.865;C|0.135	0.135	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727265	25727265	+	Silent	SNP	C	C	T	rs4712960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	83	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	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	
CYB5D1	124637	hgsc.bcm.edu	37	17	7761512	7761512	+	Missense_Mutation	SNP	C	C	A	rs12453250	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7761512C>A	ENST00000332439.4	+	1	212	c.60C>A	c.(58-60)ttC>ttA	p.F20L	LSMD1_ENST00000575208.1_5'Flank|LSMD1_ENST00000335155.5_5'Flank|LSMD1_ENST00000570555.1_Intron|LSMD1_ENST00000575071.1_5'Flank|LSMD1_ENST00000576384.1_5'Flank|CYB5D1_ENST00000571846.1_Missense_Mutation_p.F20L|CYB5D1_ENST00000570446.1_Missense_Mutation_p.F20L|LSMD1_ENST00000333775.5_5'Flank|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000575771.1_5'Flank	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	20	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.		F -> L (in dbSNP:rs12453250).				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)				GTCGCTATTTCACGCCGGCGG	0.582											OREG0024147	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1284	0.25639	0.3472	0.2867	5008	,	,		17307	0.2728		0.0934	False		,,,				2504	0.2628				p.F20L		Atlas-SNP	.											.	CYB5D1	16	.	0			c.C60A						PASS	.	C	LEU/PHE	1332,3074	443.7+/-347.1	202,928,1073	77.0	82.0	80.0		60	1.3	1.0	17	dbSNP_120	80	958,7642	210.0+/-251.0	47,864,3389	yes	missense	CYB5D1	NM_144607.4	22	249,1792,4462	AA,AC,CC		11.1395,30.2315,17.6073	probably-damaging	20/229	7761512	2290,10716	2203	4300	6503	SO:0001583	missense	124637	exon1			CTATTTCACGCCG	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.60C>A	17.37:g.7761512C>A	ENSP00000331479:p.Phe20Leu	Somatic	76	0	0	644	WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_144607	D3DTQ8|Q96DM7	Missense_Mutation	SNP	ENST00000332439.4	37	CCDS11123.1	407	0.18635531135531136	130	0.26422764227642276	85	0.23480662983425415	132	0.23076923076923078	60	0.079155672823219	C	18.52	3.640753	0.67244	0.302315	0.111395	ENSG00000182224	ENST00000332439;ENST00000541486	D	0.82081	-1.57	5.41	1.28	0.21552	Cytochrome b5 (4);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.39326	1.205	0.40772	P	0.016907000000000005	P;D	0.54047	0.945;0.964	P;P	0.51297	0.641;0.665	T	0.02766	-1.1113	9	0.62326	D	0.03	-4.3159	9.3842	0.38333	0.0:0.7044:0.0:0.2956	rs12453250;rs61658971;rs12453250	20;20	Q6P9G0-2;Q6P9G0	.;CB5D1_HUMAN	L	20	ENSP00000331479:F20L	ENSP00000331479:F20L	F	+	3	2	CYB5D1	7702237	1.000000	0.71417	0.996000	0.52242	0.926000	0.56050	1.582000	0.36568	0.139000	0.18822	0.561000	0.74099	TTC	C|0.814;A|0.186	0.186	strong		0.582	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607	
EMC1	23065	hgsc.bcm.edu	37	1	19566881	19566881	+	Silent	SNP	C	C	T	rs12084825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19566881C>T	ENST00000477853.1	-	7	738	c.696G>A	c.(694-696)gaG>gaA	p.E232E	EMC1_ENST00000375208.3_Silent_p.E210E|EMC1_ENST00000375199.3_Silent_p.E232E|RP1-43E13.2_ENST00000437898.1_RNA	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	119	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	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	
SH3BP2	6452	hgsc.bcm.edu	37	4	2822467	2822467	+	Silent	SNP	G	G	T	rs231402	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2822467G>T	ENST00000356331.5	+	2	384	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SH3BP2_ENST00000452765.2_Silent_p.L41L|SH3BP2_ENST00000511747.1_Silent_p.L41L|SH3BP2_ENST00000435136.2_Silent_p.L41L|SH3BP2_ENST00000389838.2_Silent_p.L41L|SH3BP2_ENST00000503393.2_Silent_p.L98L|SH3BP2_ENST00000442312.2_Silent_p.L69L	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	41	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GTACCCAGCTGCAGCTGCTGA	0.612									Cherubism				G|||	1863	0.372005	0.1097	0.487	5008	,	,		21198	0.4603		0.4324	False		,,,				2504	0.4918				p.L98L		Atlas-SNP	.											.	SH3BP2	43	.	0			c.G294T						PASS	.	G	,,,	714,3692	297.0+/-284.5	64,586,1553	46.0	46.0	46.0		123,207,294,123	4.3	1.0	4	dbSNP_79	46	3834,4764	537.9+/-383.3	879,2076,1344	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	943,2662,2897	TT,TG,GG		44.5918,16.2052,34.9739	,,,	41/562,69/590,98/619,41/562	2822467	4548,8456	2203	4299	6502	SO:0001819	synonymous_variant	6452	exon2	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCAGCTGCAGCTG	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.123G>T	4.37:g.2822467G>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			G|0.647;T|0.353	0.353	strong		0.612	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
THSD7A	221981	hgsc.bcm.edu	37	7	11509561	11509561	+	Missense_Mutation	SNP	G	G	C	rs2285744	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:11509561G>C	ENST00000423059.4	-	9	2564	c.2313C>G	c.(2311-2313)gaC>gaG	p.D771E	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	771	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.		D -> E (in dbSNP:rs2285744).		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCACAATACAGTCCTTCTTAC	0.448										HNSCC(18;0.044)			G|||	1396	0.278754	0.1195	0.2435	5008	,	,		17089	0.2252		0.4125	False		,,,				2504	0.4366				p.D771E		Atlas-SNP	.											.	THSD7A	219	.	0			c.C2313G						PASS	.	G	GLU/ASP	604,3212		60,484,1364	64.0	56.0	59.0		2313	3.7	1.0	7	dbSNP_100	59	3576,4686		762,2052,1317	yes	missense	THSD7A	NM_015204.2	45	822,2536,2681	CC,CG,GG		43.2825,15.8281,34.6084	probably-damaging	771/1658	11509561	4180,7898	1908	4131	6039	SO:0001583	missense	221981	exon9			AATACAGTCCTTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2313C>G	7.37:g.11509561G>C	ENSP00000406482:p.Asp771Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	115	71	0.617391	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	600	0.27472527472527475	71	0.1443089430894309	102	0.281767955801105	123	0.21503496503496503	304	0.40105540897097625	G	21.5	4.156823	0.78114	0.158281	0.432825	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.20332	2.08	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.90595	3.13	0.19775	P	0.9999597667	D	0.89917	1.0	D	0.91635	0.999	T	0.45234	-0.9275	9	0.23302	T	0.38	.	8.8978	0.35476	0.2856:0.0:0.7144:0.0	rs2285744;rs17631276;rs52802345;rs2285744	771	Q9UPZ6	THS7A_HUMAN	E	771	ENSP00000406482:D771E	ENSP00000262042:D771E	D	-	3	2	THSD7A	11476086	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.051000	0.41307	0.801000	0.34066	0.650000	0.86243	GAC	G|0.719;C|0.281	0.281	strong		0.448	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
MED16	10025	hgsc.bcm.edu	37	19	875389	875389	+	Silent	SNP	G	G	A	rs11546307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:875389G>A	ENST00000589119.1	-	9	1625	c.1626C>T	c.(1624-1626)acC>acT	p.T542T	MED16_ENST00000606828.1_Intron|MED16_ENST00000325464.1_Silent_p.T542T|MED16_ENST00000395808.3_Silent_p.T542T|MED16_ENST00000269814.4_Silent_p.T542T|MED16_ENST00000312090.6_Silent_p.T542T			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	542					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		CGCACACGCGGGTCACCGTGC	0.647													G|||	914	0.182508	0.2935	0.1916	5008	,	,		10002	0.0179		0.2555	False		,,,				2504	0.1207				p.T542T		Atlas-SNP	.											.	MED16	61	.	0			c.C1626T						PASS	.	G		1213,3191	416.3+/-337.5	171,871,1160	63.0	57.0	59.0		1626	-5.5	0.7	19	dbSNP_120	59	2170,6428	369.7+/-335.6	272,1626,2401	no	coding-synonymous	MED16	NM_005481.2		443,2497,3561	AA,AG,GG		25.2384,27.5431,26.0191		542/878	875389	3383,9619	2202	4299	6501	SO:0001819	synonymous_variant	10025	exon10			CACGCGGGTCACC	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1626C>T	19.37:g.875389G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.765;A|0.235	0.235	strong		0.647	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
C8orf74	203076	hgsc.bcm.edu	37	8	10532249	10532249	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10532249C>T	ENST00000304519.5	+	2	171	c.142C>T	c.(142-144)Ctc>Ttc	p.L48F	RP1L1_ENST00000329335.3_Intron|C8orf74_ENST00000524025.1_3'UTR	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	48										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		GCTGGACACCCTCTACGAGAG	0.582																																					p.L48F		Atlas-SNP	.											C8orf74,NS,carcinoma,-2,2	C8orf74	28	2	0			c.C142T						scavenged	.						57.0	65.0	62.0					8																	10532249		2019	4196	6215	SO:0001583	missense	203076	exon2			GACACCCTCTACG	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.142C>T	8.37:g.10532249C>T	ENSP00000307129:p.Leu48Phe	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	111	2	0.018018	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	37	CCDS47800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.72|15.72	2.917123|2.917123	0.52546|0.52546	.|.	.|.	ENSG00000171060|ENSG00000171060	ENST00000304519|ENST00000521818	T|.	0.32515|.	1.45|.	5.06|5.06	3.22|3.22	0.36961|0.36961	.|.	0.251997|.	0.28560|.	N|.	0.014901|.	T|T	0.39410|0.39410	0.1077|0.1077	L|L	0.48642|0.48642	1.525|1.525	0.27092|0.27092	N|N	0.96283|0.96283	P|.	0.44044|.	0.825|.	B|.	0.43103|.	0.408|.	T|T	0.24404|0.24404	-1.0161|-1.0161	10|5	0.39692|.	T|.	0.17|.	.|.	7.2592|7.2592	0.26193|0.26193	0.1715:0.7374:0.0:0.0911|0.1715:0.7374:0.0:0.0911	.|.	48|.	Q6P047|.	CH074_HUMAN|.	F|L	48|46	ENSP00000307129:L48F|.	ENSP00000307129:L48F|.	L|P	+|+	1|2	0|0	C8orf74|C8orf74	10569659|10569659	0.000000|0.000000	0.05858|0.05858	0.952000|0.952000	0.39060|0.39060	0.666000|0.666000	0.39218|0.39218	-0.145000|-0.145000	0.10265|0.10265	1.098000|1.098000	0.41479|0.41479	0.430000|0.430000	0.28490|0.28490	CTC|CCT	.	.	none		0.582	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
COL19A1	1310	hgsc.bcm.edu	37	6	70854818	70854818	+	Silent	SNP	G	G	A	rs34837646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:70854818G>A	ENST00000322773.4	+	25	1791	c.1689G>A	c.(1687-1689)ccG>ccA	p.P563P	COL19A1_ENST00000393344.1_Silent_p.P185P	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	563	Triple-helical region 3 (COL3).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						AGGGAGATCCGGGTGGGATCA	0.502													G|||	218	0.0435304	0.0053	0.0476	5008	,	,		17183	0.001		0.1153	False		,,,				2504	0.0624				p.P563P		Atlas-SNP	.											.	COL19A1	232	.	0			c.G1689A						PASS	.	G		70,4328		0,70,2129	28.0	31.0	30.0		1689	-3.9	1.0	6	dbSNP_126	30	821,7759		38,745,3507	no	coding-synonymous	COL19A1	NM_001858.4		38,815,5636	AA,AG,GG		9.5688,1.5916,6.8655		563/1143	70854818	891,12087	2199	4290	6489	SO:0001819	synonymous_variant	1310	exon25			AGATCCGGGTGGG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1689G>A	6.37:g.70854818G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																			G|0.939;A|0.061	0.061	strong		0.502	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
FAT4	79633	hgsc.bcm.edu	37	4	126241871	126241871	+	Silent	SNP	C	C	T	rs2710555	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:126241871C>T	ENST00000394329.3	+	1	4318	c.4305C>T	c.(4303-4305)atC>atT	p.I1435I		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1435	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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						ACATTCCCATCGGTACATCTG	0.423													T|||	3562	0.711262	0.8979	0.7277	5008	,	,		20357	0.4474		0.7127	False		,,,				2504	0.7178				p.I1435I		Atlas-SNP	.											.	FAT4	1752	.	0			c.C4305T						PASS	.	T		3255,535		1393,469,33	152.0	139.0	143.0		4305	1.1	1.0	4	dbSNP_100	143	5826,2422		2035,1756,333	no	coding-synonymous	FAT4	NM_024582.4		3428,2225,366	TT,TC,CC		29.3647,14.1161,24.5639		1435/4982	126241871	9081,2957	1895	4124	6019	SO:0001819	synonymous_variant	79633	exon1			TCCCATCGGTACA	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.4305C>T	4.37:g.126241871C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			C|0.301;T|0.699	0.699	strong		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CACNA1S	779	hgsc.bcm.edu	37	1	201047111	201047111	+	Silent	SNP	A	A	G	rs9427714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201047111A>G	ENST00000362061.3	-	11	1741	c.1515T>C	c.(1513-1515)tgT>tgC	p.C505C	CACNA1S_ENST00000367338.3_Silent_p.C505C	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	505					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)	GGATACCGCTACACACCACGA	0.572													G|||	636	0.126997	0.028	0.2032	5008	,	,		19464	0.001		0.34	False		,,,				2504	0.1176				p.C505C		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T1515C						PASS	.	G		346,4060	794.9+/-415.3	18,310,1875	116.0	92.0	100.0		1515	4.8	1.0	1	dbSNP_119	100	3252,5348	648.8+/-400.5	652,1948,1700	no	coding-synonymous	CACNA1S	NM_000069.2		670,2258,3575	GG,GA,AA		37.814,7.8529,27.6642		505/1874	201047111	3598,9408	2203	4300	6503	SO:0001819	synonymous_variant	779	exon11			ACCGCTACACACC	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.1515T>C	1.37:g.201047111A>G		Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			A|0.768;G|0.232	0.232	strong		0.572	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
DTX3L	151636	hgsc.bcm.edu	37	3	122290579	122290579	+	Silent	SNP	C	C	T	rs2036342	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:122290579C>T	ENST00000296161.4	+	5	2397	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A	DTX3L_ENST00000383661.3_Silent_p.A224A	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	736					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		AGCTGAAAGCCAAAGGAATTG	0.368													C|||	1720	0.34345	0.2731	0.2622	5008	,	,		19773	0.4355		0.3211	False		,,,				2504	0.4243				p.A736A		Atlas-SNP	.											.	DTX3L	59	.	0			c.C2208T						PASS	.	C		1296,3110	437.6+/-345.0	181,934,1088	103.0	97.0	99.0		2208	-10.5	0.0	3	dbSNP_94	99	2699,5901	430.0+/-356.4	439,1821,2040	no	coding-synonymous	DTX3L	NM_138287.3		620,2755,3128	TT,TC,CC		31.3837,29.4144,30.7166		736/741	122290579	3995,9011	2203	4300	6503	SO:0001819	synonymous_variant	151636	exon5			GAAAGCCAAAGGA		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.2208C>T	3.37:g.122290579C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Silent	SNP	ENST00000296161.4	37	CCDS3015.1																																																																																			C|0.681;T|0.319	0.319	strong		0.368	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
HLA-B	3106	hgsc.bcm.edu	37	6	31324595	31324595	+	Silent	SNP	C	C	G	rs1050543|rs281864598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324595C>G	ENST00000412585.2	-	2	241	c.213G>C	c.(211-213)ccG>ccC	p.P71P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	71	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						ACGGCGCCCGCGGCTCCTCTC	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2476	0.494409	0.4902	0.4539	5008	,	,		8006	0.5417		0.3718	False		,,,				2504	0.6063				p.P71P		Atlas-SNP	.											.	HLA-B	54	.	0			c.G213C						PASS	.	C		1038,3194		276,486,1354	35.0	35.0	35.0		213	0.2	0.6	6	dbSNP_134	35	1583,6613		422,739,2937	no	coding-synonymous	HLA-B	NM_005514.6		698,1225,4291	GG,GC,CC		19.3143,24.5274,21.0895		71/363	31324595	2621,9807	2116	4098	6214	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CGCCCGCGGCTCC	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.213G>C	6.37:g.31324595C>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.381;C|0.619	0.381	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ALMS1	7840	hgsc.bcm.edu	37	2	73828538	73828538	+	Missense_Mutation	SNP	G	G	A	rs1052161	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73828538G>A	ENST00000264448.6	+	19	12197	c.12086G>A	c.(12085-12087)aGg>aAg	p.R4029K	ALMS1_ENST00000409009.1_Missense_Mutation_p.R3987K|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4029				R -> K (in Ref. 1; CAD10391 and 3; BAA20786). {ECO:0000305}.	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						GACCTACTGAGGCCATTTGTG	0.592													A|||	2916	0.582268	0.2466	0.7061	5008	,	,		18466	0.7599		0.6561	False		,,,				2504	0.6892				p.R4029K		Atlas-SNP	.											.	ALMS1	384	.	0			c.G12086A						PASS	.	A	LYS/ARG	1498,2904	618.6+/-393.2	281,936,984	29.0	34.0	32.0		12086	-6.3	0.0	2	dbSNP_86	32	5479,3121	457.4+/-364.3	1739,2001,560	yes	missense	ALMS1	NM_015120.4	26	2020,2937,1544	AA,AG,GG		36.2907,34.03,46.339	benign	4029/4168	73828538	6977,6025	2201	4300	6501	SO:0001583	missense	7840	exon19			TACTGAGGCCATT	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.12086G>A	2.37:g.73828538G>A	ENSP00000264448:p.Arg4029Lys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	1272	0.5824175824175825	124	0.25203252032520324	252	0.6961325966850829	410	0.7167832167832168	486	0.6411609498680739	A	2.887	-0.230570	0.05983	0.3403	0.637093	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.05319	3.46;3.46	5.17	-6.29	0.02013	.	1.180180	0.06066	N	0.659294	T	0.00012	0.0000	N	0.01874	-0.695	0.48452	P	3.429999999999822E-4	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.38265	-0.9669	9	0.02654	T	1	.	12.9421	0.58350	0.2574:0.0992:0.6434:0.0	rs1052161;rs1320373;rs3192572;rs17266496;rs17848874;rs52825392;rs56597987;rs60369267;rs1052161	3987;4029	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	K	3987;4029	ENSP00000386627:R3987K;ENSP00000264448:R4029K	ENSP00000264448:R4029K	R	+	2	0	ALMS1	73682046	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.799000	0.01746	-2.132000	0.00814	-0.361000	0.07541	AGG	G|0.424;N|0.000	.	strong		0.592	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
VSX1	30813	hgsc.bcm.edu	37	20	25060143	25060143	+	Missense_Mutation	SNP	G	G	C	rs140122268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25060143G>C	ENST00000376709.4	-	2	695	c.432C>G	c.(430-432)gaC>gaG	p.D144E	VSX1_ENST00000429762.3_Missense_Mutation_p.D144E|VSX1_ENST00000376707.3_Missense_Mutation_p.D144E|VSX1_ENST00000451258.1_Missense_Mutation_p.D144E|VSX1_ENST00000444511.2_Missense_Mutation_p.D144E|VSX1_ENST00000424574.1_Missense_Mutation_p.D144E	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	144	Asp/Glu-rich (acidic).		D -> E (in PPCD1 and KTCN1; dbSNP:rs140122268). {ECO:0000269|PubMed:11978762, ECO:0000269|PubMed:15623752}.		neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						CAGACTGGCTGTCCTCATCTG	0.502													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19019	0.001		0.005	False		,,,				2504	0.0031				p.D144E		Atlas-SNP	.											.	VSX1	20	.	0			c.C432G	GRCh37	CM020983	VSX1	M	rs140122268	PASS	.	G	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	59.0	46.0	50.0		432,432	1.8	0.9	20	dbSNP_134	50	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense	VSX1	NM_014588.4,NM_199425.1	45,45	0,35,6468	CC,CG,GG		0.3605,0.0908,0.2691	possibly-damaging,possibly-damaging	144/366,144/240	25060143	35,12971	2203	4300	6503	SO:0001583	missense	30813	exon2			CTGGCTGTCCTCA	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.432C>G	20.37:g.25060143G>C	ENSP00000365899:p.Asp144Glu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_014588	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	11.20	1.568006	0.28003	9.08E-4	0.003605	ENSG00000100987	ENST00000429762;ENST00000444511;ENST00000424574;ENST00000451258;ENST00000376709;ENST00000376707	D;D;D;D;D;D	0.92965	-2.89;-3.14;-2.88;-2.99;-2.99;-3.05	5.01	1.75	0.24633	.	0.158273	0.56097	N	0.000035	D	0.85124	0.5625	L	0.47716	1.5	0.80722	D	1	B;B;B;B	0.29136	0.234;0.027;0.122;0.023	B;B;B;B	0.35859	0.212;0.013;0.16;0.016	T	0.80099	-0.1524	10	0.44086	T	0.13	.	9.0206	0.36198	0.0:0.1814:0.5437:0.2748	.	144;144;144;144	Q9NZR4-7;Q9NZR4-8;Q9NZR4-2;Q9NZR4	.;.;.;VSX1_HUMAN	E	144	ENSP00000401690:D144E;ENSP00000387720:D144E;ENSP00000399496:D144E;ENSP00000389654:D144E;ENSP00000365899:D144E;ENSP00000365897:D144E	ENSP00000365897:D144E	D	-	3	2	VSX1	25008143	1.000000	0.71417	0.933000	0.37362	0.545000	0.35147	0.397000	0.20883	0.188000	0.20168	0.462000	0.41574	GAC	G|0.997;C|0.003	0.003	strong		0.502	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
TSPYL4	23270	hgsc.bcm.edu	37	6	116574977	116574977	+	Missense_Mutation	SNP	A	A	C	rs187133419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116574977A>C	ENST00000420283.1	-	1	284	c.195T>G	c.(193-195)gaT>gaG	p.D65E	DSE_ENST00000540275.1_5'Flank|RP3-486I3.7_ENST00000448740.2_lincRNA	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	65					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)		AGTCGACAGGATCCTGGGATG	0.667													A|||	8	0.00159744	0.0	0.0086	5008	,	,		15829	0.0		0.002	False		,,,				2504	0.0				p.D65E		Atlas-SNP	.											.	TSPYL4	18	.	0			c.T195G						PASS	.	A	GLU/ASP	3,4039		0,3,2018	19.0	22.0	21.0		195	-7.5	0.0	6		21	36,8334		0,36,4149	yes	missense	TSPYL4	NM_021648.4	45	0,39,6167	CC,CA,AA		0.4301,0.0742,0.3142	possibly-damaging	65/415	116574977	39,12373	2021	4185	6206	SO:0001583	missense	23270	exon1			GACAGGATCCTGG		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.195T>G	6.37:g.116574977A>C	ENSP00000410943:p.Asp65Glu	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.13	1.264700	0.23136	7.42E-4	0.004301	ENSG00000187189	ENST00000420283	T	0.18810	2.19	3.75	-7.5	0.01351	.	.	.	.	.	T	0.03220	0.0094	M	0.63843	1.955	0.09310	N	1	B	0.15930	0.015	B	0.15052	0.012	T	0.43718	-0.9374	9	0.02654	T	1	-2.0876	2.3433	0.04265	0.1299:0.3779:0.1165:0.3757	.	65	Q9UJ04	TSYL4_HUMAN	E	65	ENSP00000410943:D65E	ENSP00000410943:D65E	D	-	3	2	TSPYL4	116681670	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.061000	0.11693	-1.631000	0.01543	-0.648000	0.03929	GAT	A|0.998;C|0.002	0.002	strong		0.667	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
CHD9	80205	hgsc.bcm.edu	37	16	53283966	53283966	+	Silent	SNP	G	G	A	rs8052283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53283966G>A	ENST00000398510.3	+	16	3936	c.3849G>A	c.(3847-3849)caG>caA	p.Q1283Q	CHD9_ENST00000566029.1_Silent_p.Q1283Q|CHD9_ENST00000447540.1_Silent_p.Q1283Q|Y_RNA_ENST00000391280.1_RNA|CHD9_ENST00000564845.1_Silent_p.Q1283Q			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1283	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GGAATCCTCAGAATGATCTTC	0.318													A|||	1526	0.304712	0.3699	0.1902	5008	,	,		14840	0.247		0.2962	False		,,,				2504	0.3661				p.Q1283Q		Atlas-SNP	.											.	CHD9	203	.	0			c.G3849A						PASS	.	A		1220,2424		199,822,801	73.0	70.0	71.0		3849	2.0	1.0	16	dbSNP_116	71	2559,5583		401,1757,1913	no	coding-synonymous	CHD9	NM_025134.4		600,2579,2714	AA,AG,GG		31.4296,33.4797,32.0635		1283/2882	53283966	3779,8007	1822	4071	5893	SO:0001819	synonymous_variant	80205	exon17			TCCTCAGAATGAT	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.3849G>A	16.37:g.53283966G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																				G|0.692;A|0.308	0.308	strong		0.318	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
MRTO4	51154	hgsc.bcm.edu	37	1	19585207	19585207	+	Silent	SNP	G	G	A	rs2294939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:19585207G>A	ENST00000330263.4	+	8	900	c.603G>A	c.(601-603)aaG>aaA	p.K201K		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	201					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K201K(2)		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)		CTGAATTCAAGGTGACCATCA	0.478													.|||	547	0.109225	0.087	0.0908	5008	,	,		19401	0.1012		0.1262	False		,,,				2504	0.1431				p.K201K	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											MRTO4,colon,carcinoma,0,2	MRTO4	17	2	2	Substitution - coding silent(2)	large_intestine(1)|stomach(1)	c.G603A						PASS	.	G		455,3951	215.8+/-234.7	22,411,1770	110.0	107.0	108.0		603	-2.8	1.0	1	dbSNP_100	108	1239,7361	248.3+/-276.0	102,1035,3163	no	coding-synonymous	MRTO4	NM_016183.3		124,1446,4933	AA,AG,GG		14.407,10.3268,13.0248		201/240	19585207	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon8			ATTCAAGGTGACC	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.603G>A	1.37:g.19585207G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			G|1.000;|0.000	.	weak		0.478	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
ZNF436	80818	hgsc.bcm.edu	37	1	23689083	23689083	+	Silent	SNP	G	G	A	rs3795308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23689083G>A	ENST00000314011.4	-	4	928	c.792C>T	c.(790-792)caC>caT	p.H264H	ZNF436_ENST00000374608.3_Silent_p.H264H	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	264					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H264H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		GCTGAGCTAGGTGAGAGCTCC	0.512													G|||	607	0.121206	0.0151	0.1066	5008	,	,		21344	0.1776		0.0656	False		,,,				2504	0.274				p.H264H		Atlas-SNP	.											ZNF436,NS,carcinoma,0,1	ZNF436	49	1	1	Substitution - coding silent(1)	stomach(1)	c.C792T						PASS	.	G	,	117,4289	87.8+/-126.4	2,113,2088	101.0	107.0	105.0		792,792	3.9	1.0	1	dbSNP_107	105	635,7965	163.8+/-216.2	19,597,3684	no	coding-synonymous,coding-synonymous	ZNF436	NM_001077195.1,NM_030634.2	,	21,710,5772	AA,AG,GG		7.3837,2.6555,5.7819	,	264/471,264/471	23689083	752,12254	2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			AGCTAGGTGAGAG	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"""Zinc fingers, C2H2-type"", ""-"""	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.792C>T	1.37:g.23689083G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	37	CCDS233.1																																																																																			G|0.921;A|0.079	0.079	strong		0.512	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634	
OR11L1	391189	hgsc.bcm.edu	37	1	248004296	248004296	+	Silent	SNP	A	A	G	rs6681483	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248004296A>G	ENST00000355784.2	-	1	958	c.903T>C	c.(901-903)gtT>gtC	p.V301V		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	301						extracellular vesicular exosome (GO:0070062)|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)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TGACCTTTCTAACAGCTTCTT	0.383													A|||	746	0.148962	0.3616	0.1282	5008	,	,		22844	0.004		0.1014	False		,,,				2504	0.0746				p.V301V		Atlas-SNP	.											OR11L1,right_lower_lobe,carcinoma,-2,1	OR11L1	108	1	0			c.T903C						PASS	.	A		1483,2923	476.3+/-357.6	239,1005,959	91.0	86.0	88.0		903	0.1	0.4	1	dbSNP_116	88	1023,7577	219.2+/-257.4	61,901,3338	no	coding-synonymous	OR11L1	NM_001001959.1		300,1906,4297	GG,GA,AA		11.8953,33.6586,19.268		301/323	248004296	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	391189	exon1			CTTTCTAACAGCT	AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"""GPCR / Class A : Olfactory receptors"""	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.903T>C	1.37:g.248004296A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001001959		Silent	SNP	ENST00000355784.2	37	CCDS31098.1																																																																																			A|0.825;G|0.175	0.175	strong		0.383	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959	
CD300E	342510	hgsc.bcm.edu	37	17	72610089	72610089	+	Missense_Mutation	SNP	C	C	T	rs1878061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72610089C>T	ENST00000328630.3	-	3	512	c.472G>A	c.(472-474)Ggg>Agg	p.G158R	CD300E_ENST00000426295.2_Missense_Mutation_p.G199R|CD300E_ENST00000392619.1_Missense_Mutation_p.G185R			Q496F6	CLM2_HUMAN	CD300e molecule	158			G -> R (in dbSNP:rs1878061). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G158R(1)		breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						AACACCTCCCCGGTGCTGAGG	0.607													C|||	1102	0.220048	0.0953	0.2622	5008	,	,		17883	0.0794		0.4135	False		,,,				2504	0.3047				p.G158R		Atlas-SNP	.											CD300E,NS,carcinoma,0,1	CD300E	70	1	1	Substitution - Missense(1)	stomach(1)	c.G472A						PASS	.	C	ARG/GLY	695,3711	290.4+/-280.9	53,589,1561	114.0	92.0	100.0		472	-5.8	0.0	17	dbSNP_92	100	3457,5143	505.1+/-376.3	719,2019,1562	yes	missense	CD300E	NM_181449.2	125	772,2608,3123	TT,TC,CC		40.1977,15.7739,31.9237	possibly-damaging	158/206	72610089	4152,8854	2203	4300	6503	SO:0001583	missense	342510	exon3			CCTCCCCGGTGCT	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	28874	protein-coding gene	gene with protein product		609801	"""CD300 antigen like family member E"", ""CD300e antigen"""	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.472G>A	17.37:g.72610089C>T	ENSP00000329942:p.Gly158Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	519	0.23763736263736263	51	0.10365853658536585	110	0.30386740331491713	45	0.07867132867132867	313	0.4129287598944591	C	0.198	-1.047342	0.01981	0.157739	0.401977	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630	T;T;T	0.03607	3.88;3.87;3.91	2.88	-5.75	0.02384	.	4.595650	0.00674	U	0.000640	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.44659	0.84	B	0.33568	0.166	T	0.50381	-0.8835	9	0.16896	T	0.51	.	2.733	0.05232	0.112:0.1222:0.3353:0.4304	rs1878061;rs17555132;rs52818238;rs58718257;rs1878061	158	Q496F6	CLM2_HUMAN	R	185;199;158	ENSP00000376395:G185R;ENSP00000416642:G199R;ENSP00000329942:G158R	ENSP00000329942:G158R	G	-	1	0	CD300E	70121684	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.366000	0.01078	-2.914000	0.00307	-0.474000	0.04947	GGG	C|0.728;N|0.000	.	strong		0.607	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
HCN2	610	hgsc.bcm.edu	37	19	603832	603832	+	Silent	SNP	C	C	T	rs56180027	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:603832C>T	ENST00000251287.2	+	2	974	c.921C>T	c.(919-921)atC>atT	p.I307I		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	307					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		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)		TCTTCCTTATCGTGGAGAAGG	0.582													c|||	406	0.0810703	0.0068	0.2478	5008	,	,		13714	0.0367		0.1083	False		,,,				2504	0.0808				p.I307I	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C921T						PASS	.	C		97,4301		0,97,2102	134.0	102.0	113.0		921	0.5	1.0	19	dbSNP_129	113	903,7695		45,813,3441	no	coding-synonymous	HCN2	NM_001194.3		45,910,5543	TT,TC,CC		10.5024,2.2055,7.6947		307/890	603832	1000,11996	2199	4299	6498	SO:0001819	synonymous_variant	610	exon2			CCTTATCGTGGAG	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.921C>T	19.37:g.603832C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.922;T|0.078	0.078	strong		0.582	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
MSGN1	343930	hgsc.bcm.edu	37	2	17998095	17998095	+	Missense_Mutation	SNP	C	C	T	rs35858730	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	84	84	1	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	
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs3745115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22848028G>C	ENST00000456783.2	+	4	1801	c.1557G>C	c.(1555-1557)aaG>aaC	p.K519N	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	519					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.K519N(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ACATTGCAAAGATTTCCAAAT	0.323													N|||	980	0.195687	0.354	0.1268	5008	,	,		20410	0.1667		0.1302	False		,,,				2504	0.1278				p.K519N		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G1557C						scavenged	.						18.0	18.0	18.0					19																	22848028		1781	4025	5806	SO:0001583	missense	57615	exon4			TGCAAAGATTTCC	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1557G>C	19.37:g.22848028G>C	ENSP00000413660:p.Lys519Asn	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	476	145	0.304622	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.565994	0.00134	.	.	ENSG00000229676	ENST00000456783	T	0.07688	3.17	1.03	-2.06	0.07298	.	.	.	.	.	T	0.02156	0.0067	N	0.03000	-0.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	8	0.07482	T	0.82	.	0.2809	0.00244	0.2469:0.289:0.2459:0.2181	rs3745115;rs7259827;rs59664756	519	Q9P255	ZN492_HUMAN	N	519	ENSP00000413660:K519N	ENSP00000413660:K519N	K	+	3	2	ZNF492	22639868	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-0.195000	0.09546	-1.287000	0.02381	-1.858000	0.00562	AAG	G|0.500;C|0.500	0.500	weak		0.323	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
FAM3D	131177	hgsc.bcm.edu	37	3	58639418	58639418	+	Missense_Mutation	SNP	C	C	T	rs13097314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58639418C>T	ENST00000358781.2	-	3	414	c.104G>A	c.(103-105)cGt>cAt	p.R35H		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	35					negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)			large_intestine(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		GCGTGGCAGACGGATGGTTTT	0.572													C|||	13	0.00259585	0.0008	0.0014	5008	,	,		22521	0.0		0.0109	False		,,,				2504	0.0				p.R35H		Atlas-SNP	.											FAM3D,colon,carcinoma,-1,1	FAM3D	29	1	0			c.G104A						PASS	.	C	HIS/ARG	9,4397	15.5+/-35.6	0,9,2194	132.0	128.0	129.0		104	3.4	1.0	3	dbSNP_121	129	79,8521	45.8+/-104.6	1,77,4222	yes	missense	FAM3D	NM_138805.2	29	1,86,6416	TT,TC,CC		0.9186,0.2043,0.6766	possibly-damaging	35/225	58639418	88,12918	2203	4300	6503	SO:0001583	missense	131177	exon3			GGCAGACGGATGG	AF494381	CCDS2893.1	3p21.1	2008-07-18			ENSG00000198643	ENSG00000198643			18665	protein-coding gene	gene with protein product		608619				12160727	Standard	NM_138805		Approved	EF7, OIT1	uc003dkq.3	Q96BQ1	OTTHUMG00000159148	ENST00000358781.2:c.104G>A	3.37:g.58639418C>T	ENSP00000351632:p.Arg35His	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_138805	Q547G2	Missense_Mutation	SNP	ENST00000358781.2	37	CCDS2893.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	16.58	3.163527	0.57476	0.002043	0.009186	ENSG00000198643	ENST00000358781;ENST00000483787;ENST00000498347	T;T;T	0.53857	0.6;1.85;1.44	4.26	3.38	0.38709	.	0.262588	0.30920	N	0.008602	T	0.41190	0.1148	L	0.54323	1.7	0.33744	D	0.619856	D	0.63046	0.992	P	0.49047	0.599	T	0.55611	-0.8114	10	0.13470	T	0.59	-5.3718	9.7791	0.40637	0.2049:0.795:0.0:0.0	rs13097314	35	Q96BQ1	FAM3D_HUMAN	H	35	ENSP00000351632:R35H;ENSP00000417099:R35H;ENSP00000418982:R35H	ENSP00000351632:R35H	R	-	2	0	FAM3D	58614458	0.956000	0.32656	0.971000	0.41717	0.801000	0.45260	1.522000	0.35921	1.156000	0.42514	0.435000	0.28638	CGT	C|0.994;T|0.006	0.006	strong		0.572	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805	
MUC16	94025	hgsc.bcm.edu	37	19	9077803	9077803	+	Missense_Mutation	SNP	T	T	C	rs2591597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9077803T>C	ENST00000397910.4	-	3	9846	c.9643A>G	c.(9643-9645)Agc>Ggc	p.S3215G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3216	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						GGGCTGATGCTGGGTTCCTTG	0.478													C|||	1244	0.248403	0.2005	0.2118	5008	,	,		19215	0.249		0.3121	False		,,,				2504	0.273				p.S3215G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A9643G						PASS	.	C	GLY/SER	813,3071		96,621,1225	143.0	139.0	140.0		9643	0.8	0.0	19	dbSNP_100	140	2385,5895		346,1693,2101	yes	missense	MUC16	NM_024690.2	56	442,2314,3326	CC,CT,TT		28.8043,20.932,26.2907	benign	3215/14508	9077803	3198,8966	1942	4140	6082	SO:0001583	missense	94025	exon3			TGATGCTGGGTTC	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.9643A>G	19.37:g.9077803T>C	ENSP00000381008:p.Ser3215Gly	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	189	90	0.47619	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	553	0.2532051282051282	109	0.22154471544715448	88	0.2430939226519337	124	0.21678321678321677	232	0.30606860158311344	c	2.692	-0.272980	0.05716	0.20932	0.288043	ENSG00000181143	ENST00000397910	T	0.02606	4.23	1.86	0.813	0.18749	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.09377	0.004	T	0.47071	-0.9145	8	0.87932	D	0	.	5.6327	0.17520	0.0:0.1705:0.0:0.8295	rs2591597;rs52795507;rs59466788;rs2591597	3215	B5ME49	.	G	3215	ENSP00000381008:S3215G	ENSP00000381008:S3215G	S	-	1	0	MUC16	8938803	0.003000	0.15002	0.002000	0.10522	0.012000	0.07955	-0.572000	0.05881	-0.165000	0.10908	-2.028000	0.00425	AGC	T|0.751;C|0.249	0.249	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116060427	116060427	+	Missense_Mutation	SNP	G	G	C	rs2781806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:116060427G>C	ENST00000304129.4	-	14	1594	c.1565C>G	c.(1564-1566)aCc>aGc	p.T522S	AFAP1L2_ENST00000369271.3_Missense_Mutation_p.T522S|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.T575S|AFAP1L2_ENST00000491814.1_5'UTR			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	522			T -> S (in dbSNP:rs2781806).		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)		TGCAACAGGGGTGGCTTCCTC	0.582													G|||	237	0.0473243	0.0976	0.0274	5008	,	,		19209	0.0		0.0239	False		,,,				2504	0.0665				p.T522S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1565G						PASS	.	G	SER/THR,SER/THR	348,4058	181.9+/-209.8	19,310,1874	108.0	100.0	103.0		1565,1565	2.9	0.0	10	dbSNP_100	103	241,8359	96.6+/-158.3	6,229,4065	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	58,58	25,539,5939	CC,CG,GG		2.8023,7.8983,4.5287	benign,benign	522/819,522/815	116060427	589,12417	2203	4300	6503	SO:0001583	missense	84632	exon14			ACAGGGGTGGCTT	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.1565C>G	10.37:g.116060427G>C	ENSP00000303042:p.Thr522Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	83	0.038003663003663	54	0.10975609756097561	12	0.03314917127071823	0	0.0	17	0.022427440633245383	G	8.804	0.933576	0.18206	0.078983	0.028023	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.14640	2.5;2.5;2.49	5.76	2.92	0.33932	.	1.232620	0.05157	N	0.497043	T	0.00178	0.0005	L	0.31664	0.95	0.09310	N	1	B;B;B;B;B;B;B	0.14438	0.003;0.01;0.002;0.003;0.004;0.0;0.0	B;B;B;B;B;B;B	0.17098	0.006;0.017;0.003;0.007;0.006;0.002;0.001	T	0.39901	-0.9591	10	0.10377	T	0.69	-1.3422	2.8866	0.05663	0.1501:0.1225:0.547:0.1805	rs2781806;rs58103503	575;88;576;44;550;522;522	F5GZE1;B7Z363;B7Z2Q0;Q8N4X5-3;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;.;.;AF1L2_HUMAN	S	522;522;549;575	ENSP00000358276:T522S;ENSP00000303042:T522S;ENSP00000444511:T575S	ENSP00000303042:T522S	T	-	2	0	AFAP1L2	116050417	0.006000	0.16342	0.039000	0.18376	0.509000	0.34042	0.973000	0.29422	0.360000	0.24265	-0.137000	0.14449	ACC	G|0.949;C|0.051	0.051	strong		0.582	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
PRND	23627	hgsc.bcm.edu	37	20	4705718	4705718	+	Missense_Mutation	SNP	C	C	T	rs2245220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4705718C>T	ENST00000305817.2	+	2	592	c.521C>T	c.(520-522)aCg>aTg	p.T174M		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	174			T -> M (common polymorphism; dbSNP:rs2245220). {ECO:0000269|PubMed:10525406, ECO:0000269|PubMed:10825657, ECO:0000269|PubMed:11702213, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						ATCTGGCTCACGGTGAAATAA	0.577													T|||	2480	0.495208	0.6702	0.3646	5008	,	,		19250	0.253		0.4871	False		,,,				2504	0.6094				p.T174M		Atlas-SNP	.											PRND,caecum,carcinoma,0,1	PRND	34	1	0			c.C521T	GRCh37	CM014824	PRND	M	rs2245220	PASS	.	T	MET/THR	2798,1608		897,1004,302	22.0	21.0	21.0		521	2.2	0.0	20	dbSNP_100	21	4200,4392		1030,2140,1126	yes	missense	PRND	NM_012409.2	81	1927,3144,1428	TT,TC,CC		48.8827,36.4957,46.1609	benign	174/177	4705718	6998,6000	2203	4296	6499	SO:0001583	missense	23627	exon2			GGCTCACGGTGAA	AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.521C>T	20.37:g.4705718C>T	ENSP00000306900:p.Thr174Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_012409	A7U7M5|Q9H311|Q9H312|Q9NTM4	Missense_Mutation	SNP	ENST00000305817.2	37	CCDS13081.1	1004	0.4597069597069597	345	0.7012195121951219	140	0.3867403314917127	151	0.263986013986014	368	0.48548812664907653	T	8.922	0.961269	0.18583	0.635043	0.488827	ENSG00000171864	ENST00000305817	D	0.88664	-2.41	4.7	2.23	0.28157	Prion/Doppel protein, beta-ribbon domain (1);	0.787074	0.11050	N	0.605177	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	0.43766	-0.9371	9	0.38643	T	0.18	-13.5917	3.7704	0.08639	0.0:0.2044:0.1882:0.6074	rs2245220;rs17736407;rs17846360;rs17859396;rs52805311;rs61599564;rs2245220	174	Q9UKY0	PRND_HUMAN	M	174	ENSP00000306900:T174M	ENSP00000306900:T174M	T	+	2	0	PRND	4653718	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.864000	0.27926	0.253000	0.21552	-0.381000	0.06696	ACG	C|0.492;T|0.508	0.508	strong		0.577	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409	
CD5L	922	hgsc.bcm.edu	37	1	157804260	157804260	+	Missense_Mutation	SNP	G	G	A	rs141546266	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:157804260G>A	ENST00000368174.4	-	4	751	c.655C>T	c.(655-657)Cct>Tct	p.P219S	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	219	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GGCCCAGAAGGGCAATCCTGA	0.512													G|||	49	0.00978435	0.0008	0.0288	5008	,	,		20409	0.0		0.0139	False		,,,				2504	0.0143				p.P219S		Atlas-SNP	.											.	CD5L	112	.	0			c.C655T						PASS	.	G	SER/PRO	15,4391	22.3+/-47.3	0,15,2188	58.0	50.0	53.0		655	3.0	0.1	1	dbSNP_134	53	149,8451	72.0+/-134.6	3,143,4154	yes	missense	CD5L	NM_005894.2	74	3,158,6342	AA,AG,GG		1.7326,0.3404,1.261	benign	219/348	157804260	164,12842	2203	4300	6503	SO:0001583	missense	922	exon4			CAGAAGGGCAATC	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"""apoptosis inhibitor 6"", ""CD5 antigen-like (scavenger receptor cysteine rich family)"""	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.655C>T	1.37:g.157804260G>A	ENSP00000357156:p.Pro219Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	90	63	0.7	NM_005894	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	26	0.011904761904761904	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	12	0.0158311345646438	G	10.88	1.474753	0.26511	0.003404	0.017326	ENSG00000073754	ENST00000368174	T	0.34667	1.35	4.97	3.05	0.35203	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.703291	0.12473	N	0.465820	T	0.06096	0.0158	N	0.20357	0.565	0.19575	N	0.999962	B	0.24132	0.098	B	0.26310	0.068	T	0.41106	-0.9527	10	0.09843	T	0.71	.	3.4578	0.07522	0.0922:0.171:0.5602:0.1766	.	219	O43866	CD5L_HUMAN	S	219	ENSP00000357156:P219S	ENSP00000357156:P219S	P	-	1	0	CD5L	156070884	0.000000	0.05858	0.125000	0.21846	0.528000	0.34623	0.008000	0.13197	0.648000	0.30732	0.655000	0.94253	CCT	G|0.987;A|0.013	0.013	strong		0.512	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894	
OR11A1	26531	hgsc.bcm.edu	37	6	29394926	29394926	+	Missense_Mutation	SNP	C	C	T	rs9257857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29394926C>T	ENST00000377149.1	-	5	965	c.493G>A	c.(493-495)Gcc>Acc	p.A165T	OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377148.1_Missense_Mutation_p.A165T|OR11A1_ENST00000377147.2_Missense_Mutation_p.A165T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	165			A -> T (in allele 6M1-18*02; dbSNP:rs9257857). {ECO:0000269|PubMed:14574404, 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)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CTCAGCTGGGCCACCAGGGCC	0.577													C|||	590	0.117812	0.0507	0.1888	5008	,	,		19249	0.0794		0.1471	False		,,,				2504	0.1677				p.A165T		Atlas-SNP	.											.	OR11A1	30	.	0			c.G493A						PASS	.	C	THR/ALA	171,2847		6,159,1344	47.0	51.0	49.0		493	0.7	0.0	6	dbSNP_118	49	819,4599		50,719,1940	yes	missense	OR11A1	NM_013937.2	58	56,878,3284	TT,TC,CC		15.1163,5.666,11.7354	benign	165/316	29394926	990,7446	1509	2709	4218	SO:0001583	missense	26531	exon1			GCTGGGCCACCAG		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"""GPCR / Class A : Olfactory receptors"""	8176	protein-coding gene	gene with protein product			"""olfactory receptor, family 11, subfamily A, member 2"""	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.493G>A	6.37:g.29394926C>T	ENSP00000366354:p.Ala165Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	253	0.11584249084249085	29	0.05894308943089431	68	0.1878453038674033	37	0.06468531468531469	119	0.15699208443271767	C	9.637	1.137993	0.21123	0.05666	0.151163	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.08102	3.13;3.13;3.13	3.78	0.719	0.18208	GPCR, rhodopsin-like superfamily (1);	1.539180	0.04523	N	0.384881	T	0.01730	0.0055	L	0.33339	1.005	0.80722	P	0.0	B	0.19200	0.034	B	0.19666	0.026	T	0.44483	-0.9325	9	0.10902	T	0.67	-6.1585	6.1726	0.20427	0.4864:0.4183:0.0:0.0953	rs9257857;rs17183988;rs9257857	165	Q9GZK7	O11A1_HUMAN	T	165	ENSP00000366353:A165T;ENSP00000366354:A165T;ENSP00000366352:A165T	ENSP00000366352:A165T	A	-	1	0	OR11A1	29502905	0.000000	0.05858	0.031000	0.17742	0.837000	0.47467	-0.220000	0.09215	-0.075000	0.12798	0.405000	0.27470	GCC	C|0.879;T|0.121	0.121	strong		0.577	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1		
TRIM22	10346	hgsc.bcm.edu	37	11	5730343	5730343	+	Missense_Mutation	SNP	G	G	A	rs12364019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5730343G>A	ENST00000379965.3	+	8	1239	c.962G>A	c.(961-963)aGa>aAa	p.R321K	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	321	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> K (in dbSNP:rs12364019).		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)			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)		GTGGATCAGAGACAAGTGAAA	0.418													G|||	58	0.0115815	0.0008	0.0144	5008	,	,		20306	0.0		0.0308	False		,,,				2504	0.0164				p.R321K	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G962A						PASS	.	G	LYS/ARG,LYS/ARG	16,3874		0,16,1929	148.0	139.0	142.0		950,962	2.8	0.7	11	dbSNP_120	142	338,7968		9,320,3824	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	26,26	9,336,5753	AA,AG,GG		4.0693,0.4113,2.9026	probably-damaging,probably-damaging	317/495,321/499	5730343	354,11842	1945	4153	6098	SO:0001583	missense	10346	exon8			ATCAGAGACAAGT	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.962G>A	11.37:g.5730343G>A	ENSP00000369299:p.Arg321Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	32	0.014652014652014652	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	24	0.0316622691292876	G	20.4	3.976912	0.74360	0.004113	0.040693	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000454828;ENST00000455293	T;T	0.59638	2.71;0.25	3.72	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.34658	0.0905	L	0.43152	1.355	0.23411	N	0.997739	D;D;D	0.89917	0.99;1.0;0.999	D;D;D	0.83275	0.979;0.991;0.996	T	0.38178	-0.9673	9	0.87932	D	0	.	9.9749	0.41777	0.1096:0.0:0.8904:0.0	rs12364019;rs52821696;rs12364019	243;317;321	F8WAP8;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	K	321;132;289;243	ENSP00000369299:R321K;ENSP00000393250:R289K	ENSP00000369299:R321K	R	+	2	0	TRIM22	5686919	0.118000	0.22208	0.678000	0.29963	0.381000	0.30169	0.558000	0.23469	0.825000	0.34637	0.460000	0.39030	AGA	G|0.976;A|0.024	0.024	strong		0.418	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
OR4C15	81309	hgsc.bcm.edu	37	11	55322298	55322298	+	Silent	SNP	C	C	T	rs8181485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55322298C>T	ENST00000314644.2	+	1	516	c.516C>T	c.(514-516)gcC>gcT	p.A172A		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	118						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						CAGCCATGGCCTATGATCGTT	0.502										HNSCC(20;0.049)			c|||	908	0.18131	0.0787	0.1744	5008	,	,		19755	0.2331		0.1004	False		,,,				2504	0.3548				p.A172A		Atlas-SNP	.											.	OR4C15	145	.	0			c.C516T						PASS	.	C		412,3990	202.8+/-225.5	23,366,1812	130.0	116.0	121.0		516	4.2	1.0	11	dbSNP_117	121	932,7660	205.4+/-247.8	57,818,3421	no	coding-synonymous	OR4C15	NM_001001920.1		80,1184,5233	TT,TC,CC		10.8473,9.3594,10.3432		172/371	55322298	1344,11650	2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			CATGGCCTATGAT	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.516C>T	11.37:g.55322298C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	37	CCDS31501.1																																																																																			C|0.884;T|0.116	0.116	strong		0.502	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
PSG11	5680	hgsc.bcm.edu	37	19	43519362	43519362	+	Silent	SNP	C	C	T	rs11083680	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43519362C>T	ENST00000401740.1	-	4	973	c.870G>A	c.(868-870)caG>caA	p.Q290Q	PSG11_ENST00000403486.1_Silent_p.Q168Q|PSG11_ENST00000320078.7_Silent_p.Q290Q|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_Silent_p.Q168Q			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	299	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				TTGGAGTAATCTGAGGGATAA	0.458													.|||	3243	0.647564	0.6551	0.4986	5008	,	,		20620	0.9871		0.4751	False		,,,				2504	0.5706				p.Q290Q		Atlas-SNP	.											PSG11,right_lower_lobe,carcinoma,-2,1	PSG11	57	1	0			c.G870A						scavenged	.	T	,,	2884,1514	479.9+/-358.7	986,912,301	163.0	162.0	162.0		504,870,504	-0.8	0.0	19	dbSNP_120	162	3875,4719	606.8+/-395.2	915,2045,1337	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	,,	1901,2957,1638	TT,TC,CC		45.0896,34.4247,47.9757	,,	168/214,290/336,168/214	43519362	6759,6233	2199	4297	6496	SO:0001819	synonymous_variant	5680	exon4			AGTAATCTGAGGG	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.870G>A	19.37:g.43519362C>T		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000401740.1	37	CCDS12614.2																																																																																			C|0.424;T|0.576	0.576	strong		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
MPZL2	10205	hgsc.bcm.edu	37	11	118134830	118134830	+	Silent	SNP	G	G	A	rs36040758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:118134830G>A	ENST00000278937.2	-	1	167	c.39C>T	c.(37-39)ctC>ctT	p.L13L	MPZL2_ENST00000438295.2_Silent_p.L13L|MPZL2_ENST00000525647.1_5'UTR	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	13					anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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;3.04e-05)		GTATGCCAAGGAGAAGAAGCA	0.547													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		17565	0.0		0.005	False		,,,				2504	0.001				p.L13L		Atlas-SNP	.											.	MPZL2	20	.	0			c.C39T						PASS	.	G	,	9,4391	15.5+/-35.6	0,9,2191	81.0	75.0	77.0		39,39	-1.1	0.1	11	dbSNP_126	77	74,8518	44.0+/-102.2	0,74,4222	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	0,83,6413	AA,AG,GG		0.8613,0.2045,0.6389	,	13/216,13/216	118134830	83,12909	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon1			GCCAAGGAGAAGA	AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"""Immunoglobulin superfamily / V-set domain containing"""	3496	protein-coding gene	gene with protein product		604873	"""epithelial V-like antigen 1"""	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.39C>T	11.37:g.118134830G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			G|0.993;A|0.007	0.007	strong		0.547	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797	
ATP6V1B1	525	hgsc.bcm.edu	37	2	71163086	71163086	+	Start_Codon_SNP	SNP	T	T	C	rs11681642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71163086T>C	ENST00000234396.4	+	1	75	c.2T>C	c.(1-3)aTg>aCg	p.M1T	ATP6V1B1_ENST00000412314.1_Start_Codon_SNP_p.M1T	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	1					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						GACTGCTCCATGGCCATGGAG	0.627													T|||	1847	0.36881	0.3714	0.2939	5008	,	,		12582	0.3591		0.4473	False		,,,				2504	0.3476				p.M1T		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.T2C						PASS	.	T	THR/MET	1644,2762	490.4+/-361.8	288,1068,847	33.0	36.0	35.0		2	4.9	1.0	2	dbSNP_120	35	3754,4846	526.3+/-380.9	834,2086,1380	yes	missense	ATP6V1B1	NM_001692.3	81	1122,3154,2227	CC,CT,TT		43.6512,37.3128,41.5039	benign	1/514	71163086	5398,7608	2203	4300	6503	SO:0001582	initiator_codon_variant	525	exon1			GCTCCATGGCCAT	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.2T>C	2.37:g.71163086T>C	ENSP00000234396:p.Met1Thr	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	177	84	0.474576	NM_001692	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	861	0.3942307692307692	195	0.39634146341463417	112	0.30939226519337015	207	0.3618881118881119	347	0.4577836411609499	T	13.49	2.251676	0.39797	0.373128	0.436512	ENSG00000116039	ENST00000234396;ENST00000412314	D;D	0.82433	-1.61;-1.61	4.9	4.9	0.64082	.	0.000000	0.48286	D	0.000193	T	0.00012	0.0000	.	.	.	0.53688	P	2.4000000000024002E-5	P;P	0.44090	0.826;0.826	B;P	0.49047	0.405;0.599	T	0.07790	-1.0754	8	0.87932	D	0	-11.1772	12.4999	0.55950	0.0:0.0:0.0:1.0	rs11681642;rs52824699;rs11681642	1;1	C9JL73;P15313	.;VATB1_HUMAN	T	1	ENSP00000234396:M1T;ENSP00000388353:M1T	ENSP00000234396:M1T	M	+	2	0	ATP6V1B1	71016594	1.000000	0.71417	0.996000	0.52242	0.238000	0.25445	2.696000	0.47052	1.834000	0.53371	0.482000	0.46254	ATG	T|0.602;C|0.398	0.398	strong		0.627	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692	Missense_Mutation
COL1A2	1278	hgsc.bcm.edu	37	7	94030899	94030899	+	Silent	SNP	T	T	C	rs1800222|rs74315131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	126	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	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	
ALS2CL	259173	hgsc.bcm.edu	37	3	46717175	46717175	+	Splice_Site	SNP	C	C	T	rs142971127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46717175C>T	ENST00000318962.4	-	20	2271	c.2188G>A	c.(2188-2190)Ggt>Agt	p.G730S	ALS2CL_ENST00000383742.3_Splice_Site_p.G77S|ALS2CL_ENST00000415953.1_Splice_Site_p.G730S	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	730					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCAGCAGACCCCTGTGAGTC	0.577													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20439	0.0		0.0089	False		,,,				2504	0.001				p.G730S		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2188A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	9,4397	15.5+/-35.6	0,9,2194	81.0	76.0	78.0		2188,2188,229	4.7	1.0	3	dbSNP_134	78	89,8511	49.4+/-109.1	1,87,4212	yes	missense-near-splice,missense-near-splice,missense-near-splice	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	56,56,56	1,96,6406	TT,TC,CC		1.0349,0.2043,0.7535	probably-damaging,probably-damaging,probably-damaging	730/954,730/954,77/301	46717175	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	259173	exon20			GCAGACCCCTGTG	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2187-1G>A	3.37:g.46717175C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	12.27	1.886260	0.33348	0.002043	0.010349	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.30182	1.54;1.54;1.54	4.66	4.66	0.58398	.	0.195229	0.35970	N	0.002863	T	0.31638	0.0803	L	0.60455	1.87	0.45541	D	0.998496	D	0.62365	0.991	P	0.55785	0.784	T	0.06643	-1.0815	10	0.10377	T	0.69	.	13.236	0.59969	0.0:1.0:0.0:0.0	.	730	Q60I27	AL2CL_HUMAN	S	730;730;77	ENSP00000313670:G730S;ENSP00000413223:G730S;ENSP00000373248:G77S	ENSP00000313670:G730S	G	-	1	0	ALS2CL	46692179	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	1.715000	0.37971	2.592000	0.87571	0.561000	0.74099	GGT	C|0.993;T|0.007	0.007	strong		0.577	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	Missense_Mutation
ANKRD18A	253650	hgsc.bcm.edu	37	9	38615698	38615698	+	Missense_Mutation	SNP	C	C	T	rs1832313	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	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		
FAM71B	153745	hgsc.bcm.edu	37	5	156590355	156590355	+	Silent	SNP	A	A	G	rs31220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	70	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	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	
CLCNKA	1187	hgsc.bcm.edu	37	1	16356289	16356289	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16356289A>G	ENST00000331433.4	+	13	1310	c.1291A>G	c.(1291-1293)Atc>Gtc	p.I431V	CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.I431V|CLCNKA_ENST00000439316.2_Missense_Mutation_p.I388V|CLCNKA_ENST00000420078.1_Missense_Mutation_p.I431V			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	431					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GCCCATCTTTATCCTTGGTGA	0.582																																					p.I431V		Atlas-SNP	.											CLCNKA,NS,lymphoid_neoplasm,0,1	CLCNKA	56	1	0			c.A1291G						scavenged	.						214.0	184.0	194.0					1																	16356289		2203	4300	6503	SO:0001583	missense	1187	exon13			ATCTTTATCCTTG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1291A>G	1.37:g.16356289A>G	ENSP00000332771:p.Ile431Val	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	241	7	0.0290456	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	.	.	.	.	.	.	.	.	.	.	A	2.427	-0.331836	0.05314	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04	3.45	0.904	0.19302	Chloride channel, core (2);	0.278938	0.37095	N	0.002253	T	0.76314	0.3970	N	0.02181	-0.65	0.29219	N	0.874061	B;B;B;B	0.22746	0.074;0.001;0.002;0.002	B;B;B;B	0.36666	0.23;0.005;0.007;0.007	T	0.68420	-0.5413	10	0.02654	T	1	.	6.5441	0.22397	0.6624:0.0:0.3376:0.0	.	167;388;431;431	B4DE56;E7EPH6;Q5T5Q4;P51800	.;.;.;CLCKA_HUMAN	V	431;431;388;431	ENSP00000364844:I431V;ENSP00000410353:I431V;ENSP00000414445:I388V;ENSP00000332771:I431V	ENSP00000332771:I431V	I	+	1	0	CLCNKA	16228876	0.000000	0.05858	0.004000	0.12327	0.661000	0.39034	-1.293000	0.02770	0.059000	0.16252	0.260000	0.18958	ATC	.	.	none		0.582	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
PIGT	51604	hgsc.bcm.edu	37	20	44054349	44054349	+	Silent	SNP	T	T	C	rs707577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44054349T>C	ENST00000279036.6	+	12	1700	c.1620T>C	c.(1618-1620)taT>taC	p.Y540Y	PIGT_ENST00000279035.9_Silent_p.Y438Y|PIGT_ENST00000372689.5_Silent_p.Y473Y|PIGT_ENST00000535404.1_Silent_p.Y385Y|PIGT_ENST00000543458.2_Silent_p.Y484Y|PIGT_ENST00000545755.1_Silent_p.Y278Y|PIGT_ENST00000341555.5_Silent_p.Y346Y	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	540					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				CCGTGTGCTATGGCTCCTTCT	0.637													t|||	3554	0.709665	0.8169	0.7061	5008	,	,		14966	0.5466		0.7505	False		,,,				2504	0.6933				p.Y540Y		Atlas-SNP	.											PIGT_ENST00000279036,NS,carcinoma,0,2	PIGT	85	2	0			c.T1620C						PASS	.	T	,,,	3523,883	740.8+/-411.2	1407,709,87	70.0	46.0	54.0		1452,1419,1314,1620	-7.7	0.3	20	dbSNP_86	54	6545,2055	718.9+/-406.2	2510,1525,265	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIGT	NM_001184728.1,NM_001184729.1,NM_001184730.1,NM_015937.4	,,,	3917,2234,352	CC,CT,TT		23.8953,20.0409,22.5896	,,,	484/523,473/512,438/477,540/579	44054349	10068,2938	2203	4300	6503	SO:0001819	synonymous_variant	51604	exon12			GTGCTATGGCTCC		CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"""Phosphatidylinositol glycan anchor biosynthesis"""	14938	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610272	"""phosphatidylinositol glycan, class T"""			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.1620T>C	20.37:g.44054349T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_015937	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Silent	SNP	ENST00000279036.6	37	CCDS13353.1																																																																																			T|0.259;C|0.741	0.741	strong		0.637	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937	
KRT6A	3853	hgsc.bcm.edu	37	12	52886490	52886490	+	Silent	SNP	A	A	G	rs711317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52886490A>G	ENST00000330722.6	-	1	551	c.483T>C	c.(481-483)gcT>gcC	p.A161A		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	161	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.A161A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACGCTCCTCAGCCCGCACCC	0.597													A|||	2249	0.449081	0.1331	0.6023	5008	,	,		18611	0.6319		0.6044	False		,,,				2504	0.4192				p.A161A		Atlas-SNP	.											KRT6A,NS,carcinoma,0,1	KRT6A	89	1	1	Substitution - coding silent(1)	prostate(1)	c.T483C						PASS	.	A		868,3538	339.9+/-306.0	77,714,1412	169.0	155.0	160.0		483	-10.6	0.3	12	dbSNP_86	160	5019,3581	627.2+/-397.9	1467,2085,748	no	coding-synonymous	KRT6A	NM_005554.3		1544,2799,2160	GG,GA,AA		41.6395,19.7004,45.2637		161/565	52886490	5887,7119	2203	4300	6503	SO:0001819	synonymous_variant	3853	exon1			CTCCTCAGCCCGC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.483T>C	12.37:g.52886490A>G		Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	278	138	0.496403	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			A|0.452;G|0.547	0.547	strong		0.597	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
P2RY12	64805	hgsc.bcm.edu	37	3	151056616	151056616	+	Silent	SNP	G	G	A	rs6785930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:151056616G>A	ENST00000302632.3	-	3	317	c.18C>T	c.(16-18)aaC>aaT	p.N6N	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	6					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	CAGAGGTGAGGTTGTCGACGG	0.458													G|||	1211	0.241813	0.1672	0.2781	5008	,	,		17210	0.2113		0.3151	False		,,,				2504	0.273				p.N6N		Atlas-SNP	.											P2RY12,NS,malignant_melanoma,-1,1	P2RY12	36	1	0			c.C18T						PASS	.	G	,,	836,3570	333.1+/-302.8	80,676,1447	72.0	68.0	69.0		18,,18	4.1	0.9	3	dbSNP_116	69	2721,5879	433.3+/-357.4	427,1867,2006	no	coding-synonymous,intron,coding-synonymous	P2RY12,MED12L	NM_022788.3,NM_053002.4,NM_176876.1	,,	507,2543,3453	AA,AG,GG		31.6395,18.9741,27.3489	,,	6/343,,6/343	151056616	3557,9449	2203	4300	6503	SO:0001819	synonymous_variant	64805	exon3			GGTGAGGTTGTCG	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.18C>T	3.37:g.151056616G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_022788	D3DNJ5|Q546J7	Silent	SNP	ENST00000302632.3	37	CCDS3159.1																																																																																			G|0.736;A|0.264	0.264	strong		0.458	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1		
WASF3	10810	hgsc.bcm.edu	37	13	27250823	27250823	+	Silent	SNP	T	T	C	rs3764108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:27250823T>C	ENST00000335327.5	+	7	856	c.678T>C	c.(676-678)caT>caC	p.H226H	WASF3_ENST00000361042.4_Intron	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	226					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		GTGTGTACCATGGAGCGTCTT	0.512													C|||	1635	0.326478	0.466	0.2666	5008	,	,		17792	0.1081		0.3161	False		,,,				2504	0.4162				p.H226H		Atlas-SNP	.											.	WASF3	68	.	0			c.T678C						PASS	.	C		2000,2406	614.5+/-392.4	479,1042,682	172.0	161.0	165.0		678	-0.2	1.0	13	dbSNP_107	165	2736,5864	680.9+/-403.7	424,1888,1988	no	coding-synonymous	WASF3	NM_006646.5		903,2930,2670	CC,CT,TT		31.814,45.3926,36.414		226/503	27250823	4736,8270	2203	4300	6503	SO:0001819	synonymous_variant	10810	exon7			GTACCATGGAGCG	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.678T>C	13.37:g.27250823T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_006646	O94974|Q86VQ2	Silent	SNP	ENST00000335327.5	37	CCDS9318.1																																																																																			T|0.660;C|0.340	0.340	strong		0.512	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1		
OR6B2	389090	hgsc.bcm.edu	37	2	240969312	240969312	+	Missense_Mutation	SNP	A	A	G	rs10187574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240969312A>G	ENST00000402971.2	-	1	594	c.535T>C	c.(535-537)Tgt>Cgt	p.C179R		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	179			C -> R (in dbSNP:rs10187574).			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(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		GAAATGTCACAGAAGAAGTGG	0.527													A|||	1381	0.275759	0.1558	0.2896	5008	,	,		23316	0.4583		0.3509	False		,,,				2504	0.1626				p.C179R		Atlas-SNP	.											.	OR6B2	30	.	0			c.T535C						PASS	.						31.0	33.0	32.0					2																	240969312		1911	4108	6019	SO:0001583	missense	389090	exon1			TGTCACAGAAGAA		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"""GPCR / Class A : Olfactory receptors"""	15041	protein-coding gene	gene with protein product			"""olfactory receptor, family 6, subfamily B, member 2 pseudogene"""	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.535T>C	2.37:g.240969312A>G	ENSP00000384563:p.Cys179Arg	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	248	208	0.83871	NM_001005853	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	37	CCDS46559.1	717	0.3282967032967033	74	0.15040650406504066	111	0.30662983425414364	246	0.43006993006993005	286	0.37730870712401055	A	17.27	3.348132	0.61183	.	.	ENSG00000182083	ENST00000402971	T	0.62498	0.02	4.36	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000098	T	0.00012	0.0000	H	0.99074	4.42	0.09310	P	0.9999999587148	D	0.89917	1.0	D	0.97110	1.0	T	0.13045	-1.0524	9	0.87932	D	0	.	11.8219	0.52242	1.0:0.0:0.0:0.0	rs10187574;rs60097153	179	Q6IFH4	OR6B2_HUMAN	R	179	ENSP00000384563:C179R	ENSP00000384563:C179R	C	-	1	0	OR6B2	240617985	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	8.092000	0.89530	1.938000	0.56188	0.482000	0.46254	TGT	A|0.703;G|0.297	0.297	strong		0.527	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610504	38610504	+	Silent	SNP	G	G	A	rs59185302	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:38610504G>A	ENST00000222345.6	+	9	3359	c.2850G>A	c.(2848-2850)gaG>gaA	p.E950E		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	950					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ACATAAGGGAGATAGTGCAGA	0.532													G|||	711	0.141973	0.2224	0.1455	5008	,	,		19812	0.0893		0.1342	False		,,,				2504	0.093				p.E950E		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.G2850A						PASS	.	G		783,3621		85,613,1504	25.0	27.0	26.0		2850	-5.9	0.4	19	dbSNP_129	26	1113,7485		87,939,3273	no	coding-synonymous	SIPA1L3	NM_015073.1		172,1552,4777	AA,AG,GG		12.9449,17.7793,14.5824		950/1782	38610504	1896,11106	2202	4299	6501	SO:0001819	synonymous_variant	23094	exon9			AAGGGAGATAGTG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2850G>A	19.37:g.38610504G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																			G|0.866;A|0.134	0.134	strong		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
MYO7A	4647	hgsc.bcm.edu	37	11	76922946	76922946	+	Silent	SNP	G	G	A	rs11237123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76922946G>A	ENST00000409709.3	+	46	6590	c.6318G>A	c.(6316-6318)aaG>aaA	p.K2106K	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.K2057K|MYO7A_ENST00000458637.2_Silent_p.K2068K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2106	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TCATCTTCAAGTGGCCCACCT	0.562													G|||	980	0.195687	0.3994	0.147	5008	,	,		15615	0.0635		0.2227	False		,,,				2504	0.0634				p.K2106K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6318A						PASS	.	G	,	1490,2892		279,932,980	57.0	60.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6318,6204	4.6	1.0	11	dbSNP_120	59	1705,6857		175,1355,2751	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	454,2287,3731	AA,AG,GG		19.9136,34.0027,24.6833	,	2106/2216,2068/2176	76922946	3195,9749	2191	4281	6472	SO:0001819	synonymous_variant	4647	exon46			CTTCAAGTGGCCC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6318G>A	11.37:g.76922946G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	22	0.305556	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.785;A|0.215	0.215	strong		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
FAT1	2195	hgsc.bcm.edu	37	4	187510280	187510280	+	Silent	SNP	G	G	A	rs3775307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187510280G>A	ENST00000441802.2	-	27	13442	c.13233C>T	c.(13231-13233)ccC>ccT	p.P4411P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4411					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTGAGTACAGGGGTGTCTGCT	0.517										HNSCC(5;0.00058)			G|||	276	0.0551118	0.0023	0.1023	5008	,	,		18712	0.1587		0.0328	False		,,,				2504	0.0092				p.P4411P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C13233T						PASS	.	G		31,4047		0,31,2008	201.0	198.0	199.0		13233	0.3	1.0	4	dbSNP_107	199	250,8140		3,244,3948	no	coding-synonymous	FAT1	NM_005245.3		3,275,5956	AA,AG,GG		2.9797,0.7602,2.2538		4411/4589	187510280	281,12187	2039	4195	6234	SO:0001819	synonymous_variant	2195	exon27			GTACAGGGGTGTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13233C>T	4.37:g.187510280G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1	162	0.07417582417582418	2	0.0040650406504065045	22	0.06077348066298342	109	0.19055944055944055	29	0.03825857519788918	G	6.987	0.552195	0.13374	0.007602	0.029797	ENSG00000083857	ENST00000512772;ENST00000507105	T;T	0.63913	-0.07;-0.07	5.37	0.336	0.15958	.	0.052622	0.85682	D	0.000000	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09684	-1.0663	6	0.66056	D	0.02	.	6.7536	0.23501	0.1987:0.3605:0.4408:0.0	rs3775307;rs17692347;rs60346763;rs3775307	.	.	.	S	191;179	ENSP00000424157:P191S;ENSP00000423801:P179S	ENSP00000423801:P179S	P	-	1	0	FAT1	187747274	0.988000	0.35896	0.997000	0.53966	0.864000	0.49448	0.229000	0.17833	0.101000	0.17610	0.455000	0.32223	CCT	G|0.920;A|0.080	0.080	strong		0.517	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PADI3	51702	hgsc.bcm.edu	37	1	17597655	17597655	+	Silent	SNP	C	C	T	rs2293916	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17597655C>T	ENST00000375460.3	+	9	1069	c.1029C>T	c.(1027-1029)cgC>cgT	p.R343R		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	343					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		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;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CCGAGAACCGCAACGACCGCT	0.612													C|||	500	0.0998403	0.0144	0.098	5008	,	,		18339	0.1012		0.1083	False		,,,				2504	0.2065				p.R343R		Atlas-SNP	.											.	PADI3	81	.	0			c.C1029T						PASS	.	C		137,4269	97.1+/-135.8	3,131,2069	41.0	38.0	39.0		1029	2.3	1.0	1	dbSNP_100	39	953,7647	203.0+/-246.1	53,847,3400	no	coding-synonymous	PADI3	NM_016233.2		56,978,5469	TT,TC,CC		11.0814,3.1094,8.3807		343/665	17597655	1090,11916	2203	4300	6503	SO:0001819	synonymous_variant	51702	exon9			GAACCGCAACGAC	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1029C>T	1.37:g.17597655C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_016233	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	37	CCDS179.1																																																																																			C|0.923;T|0.077	0.077	strong		0.612	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
TNFSF13B	10673	hgsc.bcm.edu	37	13	108955609	108955609	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:108955609A>G	ENST00000375887.4	+	4	668	c.490A>G	c.(490-492)Aca>Gca	p.T164A	TNFSF13B_ENST00000542136.1_Intron|TNFSF13B_ENST00000430559.1_Missense_Mutation_p.T145A|RNA5SP39_ENST00000411245.1_RNA|TNFSF13B_ENST00000479435.1_3'UTR	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	164					B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	AGGATCTTACACATTTGTTCC	0.343																																					p.T164A		Atlas-SNP	.											.	TNFSF13B	25	.	0			c.A490G						PASS	.						52.0	54.0	53.0					13																	108955609		2199	4298	6497	SO:0001583	missense	10673	exon4			TCTTACACATTTG	AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11929	protein-coding gene	gene with protein product		603969		TNFSF20		10331498, 10359578	Standard	NM_006573		Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.490A>G	13.37:g.108955609A>G	ENSP00000365048:p.Thr164Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	46	11	0.23913	NM_006573	E0ADT7|Q6FHD6|Q7Z5J2	Missense_Mutation	SNP	ENST00000375887.4	37	CCDS9509.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141866	0.57044	.	.	ENSG00000102524	ENST00000430559;ENST00000375887	T;T	0.31769	1.48;1.48	5.95	5.95	0.96441	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.101283	0.64402	D	0.000003	T	0.27629	0.0679	L	0.39898	1.24	0.80722	D	1	B;B	0.34399	0.452;0.299	B;B	0.36719	0.231;0.164	T	0.09079	-1.0691	10	0.62326	D	0.03	-22.6206	9.8726	0.41185	0.9173:0.0:0.0827:0.0	.	145;164	Q9Y275-2;Q9Y275	.;TN13B_HUMAN	A	145;164	ENSP00000389540:T145A;ENSP00000365048:T164A	ENSP00000365048:T164A	T	+	1	0	TNFSF13B	107753610	1.000000	0.71417	0.987000	0.45799	0.977000	0.68977	7.198000	0.77823	2.281000	0.76405	0.528000	0.53228	ACA	.	.	none		0.343	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045739.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155241572	155241572	+	Missense_Mutation	SNP	G	G	A	rs11935573	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	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	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360144	71360144	+	Missense_Mutation	SNP	A	A	C	rs10199088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71360144A>C	ENST00000244230.2	+	2	558	c.206A>C	c.(205-207)gAa>gCa	p.E69A	MCEE_ENST00000244217.5_5'Flank|MPHOSPH10_ENST00000468427.1_3'UTR|MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.E69A	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	69			E -> A (in dbSNP:rs10199088).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CTTGTGATAGAAAATTTTGAT	0.318													C|||	1784	0.35623	0.4259	0.4049	5008	,	,		19377	0.2738		0.2982	False		,,,				2504	0.3722				p.E69A		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.A206C						PASS	.	C	ALA/GLU	1656,2750	625.0+/-394.4	301,1054,848	37.0	39.0	38.0		206	-3.0	0.0	2	dbSNP_119	38	2571,6029	666.7+/-402.4	405,1761,2134	no	missense	MPHOSPH10	NM_005791.2	107	706,2815,2982	CC,CA,AA		29.8953,37.5851,32.5004	benign	69/682	71360144	4227,8779	2203	4300	6503	SO:0001583	missense	10199	exon2			TGATAGAAAATTT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.206A>C	2.37:g.71360144A>C	ENSP00000244230:p.Glu69Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	754	0.34523809523809523	215	0.4369918699186992	140	0.3867403314917127	180	0.3146853146853147	219	0.28891820580474936	C	9.061	0.994481	0.19043	0.375851	0.298953	ENSG00000124383	ENST00000244230	T	0.12039	2.72	4.47	-3.03	0.05429	.	0.648090	0.16397	N	0.216201	T	0.00012	0.0000	M	0.62088	1.915	0.58432	P	2.9999999999752447E-6	B	0.16166	0.016	B	0.12837	0.008	T	0.43491	-0.9388	9	0.46703	T	0.11	.	6.9292	0.24432	0.4658:0.385:0.1492:0.0	rs10199088;rs52833288;rs10199088	69	O00566	MPP10_HUMAN	A	69	ENSP00000244230:E69A	ENSP00000244230:E69A	E	+	2	0	MPHOSPH10	71213652	0.994000	0.37717	0.000000	0.03702	0.561000	0.35649	3.299000	0.51826	-1.020000	0.03354	-1.558000	0.00888	GAA	A|0.666;C|0.334	0.334	strong		0.318	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
MTMR6	9107	hgsc.bcm.edu	37	13	25831883	25831883	+	Silent	SNP	G	G	A	rs9511729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:25831883G>A	ENST00000381801.5	-	8	1721	c.960C>T	c.(958-960)ttC>ttT	p.F320F	MTMR6_ENST00000482345.1_5'Flank|MTMR6_ENST00000540661.1_Silent_p.F320F	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	320	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		CTTTGGCCAAGAAGATTGCAG	0.423													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		15120	0.0		0.0139	False		,,,				2504	0.002				p.F320F		Atlas-SNP	.											.	MTMR6	75	.	0			c.C960T						PASS	.	G		8,4398	12.9+/-30.5	0,8,2195	69.0	67.0	67.0		960	4.7	1.0	13	dbSNP_119	67	116,8484	60.6+/-122.4	1,114,4185	no	coding-synonymous	MTMR6	NM_004685.3		1,122,6380	AA,AG,GG		1.3488,0.1816,0.9534		320/622	25831883	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	9107	exon8			GGCCAAGAAGATT	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.960C>T	13.37:g.25831883G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	19	0.678571	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	37	CCDS9313.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685	
PKHD1	5314	hgsc.bcm.edu	37	6	51771044	51771044	+	Silent	SNP	G	G	A	rs140065359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:51771044G>A	ENST00000371117.3	-	41	7052	c.6777C>T	c.(6775-6777)ttC>ttT	p.F2259F	PKHD1_ENST00000340994.4_Silent_p.F2259F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2259					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)	p.F2259L(2)		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)					AAATATTGTAGAATACATTAC	0.438													G|||	11	0.00219649	0.0	0.0014	5008	,	,		17456	0.0		0.0099	False		,,,				2504	0.0				p.F2259F		Atlas-SNP	.											PKHD1_ENST00000340994,NS,carcinoma,0,2	PKHD1	927	2	2	Substitution - Missense(2)	lung(2)	c.C6777T						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	80.0	79.0	79.0		6777,6777	3.7	1.0	6	dbSNP_134	79	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,53,6450	AA,AG,GG		0.5814,0.0681,0.4075	,	2259/4075,2259/3397	51771044	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon41			ATTGTAGAATACA	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.6777C>T	6.37:g.51771044G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.996;A|0.004	0.004	strong		0.438	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DACT1	51339	hgsc.bcm.edu	37	14	59105188	59105188	+	Silent	SNP	C	C	T	rs2003021	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:59105188C>T	ENST00000335867.4	+	1	292	c.268C>T	c.(268-270)Ctg>Ttg	p.L90L	DACT1_ENST00000555845.1_Intron|DACT1_ENST00000541264.2_5'Flank|DACT1_ENST00000556859.1_Intron|DACT1_ENST00000395153.3_Silent_p.L90L			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	8	0	0		WXS	Illumina HiSeq	Phase_I	15	15	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	
COPG1	22820	hgsc.bcm.edu	37	3	128976451	128976451	+	Missense_Mutation	SNP	C	C	G	rs62266876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:128976451C>G	ENST00000314797.6	+	9	822	c.718C>G	c.(718-720)Ctg>Gtg	p.L240V		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	240					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										CAGCAAGCAGCTGGAAGAGGA	0.552													C|||	259	0.0517173	0.0477	0.0908	5008	,	,		21874	0.0079		0.0726	False		,,,				2504	0.0532				p.L240V		Atlas-SNP	.											.	.	.	.	0			c.C718G						PASS	.	C	VAL/LEU	206,4200	127.0+/-164.0	6,194,2003	187.0	186.0	186.0		718	4.3	1.0	3	dbSNP_129	186	852,7748	194.2+/-239.7	43,766,3491	yes	missense	COPG	NM_016128.3	32	49,960,5494	GG,GC,CC		9.907,4.6754,8.1347	benign	240/875	128976451	1058,11948	2203	4300	6503	SO:0001583	missense	22820	exon9			AAGCAGCTGGAAG	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.718C>G	3.37:g.128976451C>G	ENSP00000325002:p.Leu240Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	152	55	0.361842	NM_016128	A8K6M8|B3KMF6|Q54AC4	Missense_Mutation	SNP	ENST00000314797.6	37	CCDS33851.1	117	0.05357142857142857	25	0.0508130081300813	36	0.09944751381215469	5	0.008741258741258742	51	0.06728232189973615	C	13.91	2.378373	0.42207	0.046754	0.09907	ENSG00000181789	ENST00000314797	T	0.24538	1.85	5.19	4.31	0.51392	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.52532	D	0.000071	T	0.01454	0.0047	M	0.71920	2.185	0.38766	D	0.954443	D	0.57257	0.979	D	0.71414	0.973	T	0.01105	-1.1450	10	0.56958	D	0.05	-5.5733	7.0285	0.24954	0.0:0.8134:0.0:0.1866	rs62266876	240	Q9Y678	COPG_HUMAN	V	240	ENSP00000325002:L240V	ENSP00000325002:L240V	L	+	1	2	COPG	130459141	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.526000	0.45607	2.433000	0.82419	0.585000	0.79938	CTG	C|0.924;G|0.076	0.076	strong		0.552	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
CACNA1S	779	hgsc.bcm.edu	37	1	201060865	201060865	+	Silent	SNP	G	G	A	rs2296383	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	135	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	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	
GNAS	2778	hgsc.bcm.edu	37	20	57478807	57478807	+	Silent	SNP	C	C	T	rs7121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:57478807C>T	ENST00000371085.3	+	5	817	c.393C>T	c.(391-393)atC>atT	p.I131I	GNAS_ENST00000371100.4_Silent_p.I774I|GNAS_ENST00000354359.7_Silent_p.I132I|GNAS_ENST00000371102.4_Silent_p.I760I|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Silent_p.I116I|GNAS_ENST00000371095.3_Silent_p.I117I|GNAS_ENST00000306090.10_Silent_p.I117I	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	131					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|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)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			TGGACTACATCCTGAGTGTGA	0.557			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)			T|||	3227	0.644369	0.8139	0.6124	5008	,	,		18620	0.6716		0.4742	False		,,,				2504	0.5849				p.I774I	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	GNAS	867	.	0			c.C2322T	GRCh37	CM023931	GNAS	M	rs7121	PASS	.	T	,,,,,,	3298,1108	398.3+/-330.8	1234,830,139	247.0	224.0	232.0		393,396,348,,,2322,351	-9.2	0.2	20	dbSNP_52	232	4238,4362	582.0+/-391.3	1060,2118,1122	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous,coding-synonymous	GNAS	NM_000516.4,NM_001077488.2,NM_001077489.2,NM_001077490.1,NM_016592.2,NM_080425.2,NM_080426.2	,,,,,,	2294,2948,1261	TT,TC,CC		49.2791,25.1475,42.0575	,,,,,,	131/395,132/396,116/380,,,774/1038,117/381	57478807	7536,5470	2203	4300	6503	SO:0001819	synonymous_variant	2778	exon5			CTACATCCTGAGT	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.393C>T	20.37:g.57478807C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000371085.3	37	CCDS13472.1	1341	0.614010989010989	407	0.8272357723577236	227	0.6270718232044199	366	0.6398601398601399	341	0.449868073878628	T	10.08	1.252619	0.22880	0.748525	0.492791	ENSG00000087460	ENST00000450130	.	.	.	5.81	-9.18	0.00688	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999101873	.	.	.	.	.	.	T	0.04400	-1.0954	3	.	.	.	.	21.0308	0.99944	0.0914:0.759:0.0:0.1496	rs7121;rs1053389;rs3171206;rs3730167;rs17829840;rs61041002;rs7121	.	.	.	S	146	.	.	P	+	1	0	GNAS	56912202	0.382000	0.25148	0.173000	0.22940	0.924000	0.55760	-0.313000	0.08103	-2.651000	0.00424	-1.760000	0.00671	CCT	C|0.395;T|0.605	0.605	strong		0.557	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516	
HADHB	3032	hgsc.bcm.edu	37	2	26502875	26502875	+	Silent	SNP	T	T	C	rs1056389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26502875T>C	ENST00000317799.5	+	10	929	c.825T>C	c.(823-825)gtT>gtC	p.V275V	HADHB_ENST00000405867.3_Silent_p.V152V|HADHB_ENST00000545822.1_Silent_p.V253V|HADHB_ENST00000537713.1_Silent_p.V260V|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	275					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGATACAGTTACCAAAGATA	0.363													T|||	729	0.145567	0.0303	0.1585	5008	,	,		15976	0.1458		0.2087	False		,,,				2504	0.227				p.V275V		Atlas-SNP	.											.	HADHB	50	.	0			c.T825C						PASS	.	T		272,4134	152.5+/-186.2	9,254,1940	87.0	80.0	82.0		825	1.6	1.0	2	dbSNP_86	82	1861,6739	332.8+/-320.3	204,1453,2643	no	coding-synonymous	HADHB	NM_000183.2		213,1707,4583	CC,CT,TT		21.6395,6.1734,16.4001		275/475	26502875	2133,10873	2203	4300	6503	SO:0001819	synonymous_variant	3032	exon10			TACAGTTACCAAA		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.825T>C	2.37:g.26502875T>C		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																			T|0.834;C|0.166	0.166	strong		0.363	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701799	8701799	+	Missense_Mutation	SNP	G	G	T	rs17854013	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8701799G>T	ENST00000329805.4	-	1	868	c.640C>A	c.(640-642)Cct>Act	p.P214T		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	214				P -> T (in Ref. 3; AAH40487). {ECO:0000305}.		integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						TTCCCCCCAGGAAGCAAGGGG	0.567													G|||	1345	0.26857	0.2398	0.2147	5008	,	,		16754	0.4256		0.1889	False		,,,				2504	0.2658				p.P214T		Atlas-SNP	.											.	MFSD6L	46	.	0			c.C640A						PASS	.	G	THR/PRO	950,3456	358.6+/-314.5	117,716,1370	69.0	76.0	74.0		640	3.9	0.6	17	dbSNP_123	74	1648,6952	303.6+/-306.5	152,1344,2804	yes	missense	MFSD6L	NM_152599.3	38	269,2060,4174	TT,TG,GG		19.1628,21.5615,19.9754	benign	214/587	8701799	2598,10408	2203	4300	6503	SO:0001583	missense	162387	exon1			CCCCAGGAAGCAA	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.640C>A	17.37:g.8701799G>T	ENSP00000330051:p.Pro214Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_152599	Q6YL34|Q8NA76	Missense_Mutation	SNP	ENST00000329805.4	37	CCDS11146.1	575	0.2632783882783883	102	0.2073170731707317	80	0.22099447513812154	253	0.4423076923076923	140	0.18469656992084432	G	8.956	0.969329	0.18659	0.215615	0.191628	ENSG00000185156	ENST00000329805	T	0.43688	0.94	4.86	3.89	0.44902	.	0.464570	0.19760	N	0.106692	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	1.0000000000287557E-6	P	0.49307	0.922	P	0.49012	0.598	T	0.39099	-0.9630	9	0.11182	T	0.66	-27.0946	12.0746	0.53636	0.0:0.2203:0.7797:0.0	rs17854013	214	Q8IWD5	MFS6L_HUMAN	T	214	ENSP00000330051:P214T	ENSP00000330051:P214T	P	-	1	0	MFSD6L	8642524	0.002000	0.14202	0.560000	0.28344	0.070000	0.16714	1.414000	0.34736	1.257000	0.44085	0.655000	0.94253	CCT	G|0.783;T|0.217	0.217	strong		0.567	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
TBC1D2	55357	hgsc.bcm.edu	37	9	100995758	100995758	+	Missense_Mutation	SNP	G	G	T	rs879368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:100995758G>T	ENST00000375064.1	-	4	759	c.721C>A	c.(721-723)Cca>Aca	p.P241T	TBC1D2_ENST00000342112.5_Missense_Mutation_p.P23T|TBC1D2_ENST00000375066.5_Missense_Mutation_p.P241T	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	241			P -> T (in dbSNP:rs879368). {ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CCACTCTGTGGAGAATCTTCC	0.602													G|||	1055	0.210663	0.1687	0.2507	5008	,	,		20031	0.1627		0.2744	False		,,,				2504	0.2229				p.P241T		Atlas-SNP	.											.	TBC1D2	70	.	0			c.C721A						PASS	.	G	THR/PRO	785,3621	318.0+/-295.4	79,627,1497	158.0	142.0	147.0		721	0.8	0.0	9	dbSNP_86	147	2261,6339	381.8+/-340.2	287,1687,2326	yes	missense	TBC1D2	NM_018421.3	38	366,2314,3823	TT,TG,GG		26.2907,17.8166,23.42	benign	241/918	100995758	3046,9960	2203	4300	6503	SO:0001583	missense	55357	exon4			TCTGTGGAGAATC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.721C>A	9.37:g.100995758G>T	ENSP00000364205:p.Pro241Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		494	0.2261904761904762	79	0.16056910569105692	100	0.27624309392265195	93	0.16258741258741258	222	0.2928759894459103	G	5.827	0.336876	0.11013	0.178166	0.262907	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112	T;T;T	0.15603	2.41;3.15;2.41	4.88	0.842	0.18927	.	0.473238	0.20036	N	0.100610	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;P	0.34724	0.335;0.465	B;B	0.31101	0.058;0.124	T	0.45425	-0.9262	9	0.18276	T	0.48	.	4.9031	0.13784	0.2703:0.1646:0.5651:0.0	rs879368;rs52794052;rs58612705;rs879368	241;241	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	T	241;241;23	ENSP00000364205:P241T;ENSP00000364207:P241T;ENSP00000341567:P23T	ENSP00000341567:P23T	P	-	1	0	TBC1D2	100035579	0.000000	0.05858	0.000000	0.03702	0.981000	0.71138	-0.811000	0.04500	-0.011000	0.14247	0.655000	0.94253	CCA	G|0.769;T|0.231	0.231	strong		0.602	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
RSBN1	54665	hgsc.bcm.edu	37	1	114354942	114354942	+	Silent	SNP	T	T	G	rs3789604	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	scavenged	.	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	18	1	0.0555556		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	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	
ZNF718	255403	hgsc.bcm.edu	37	4	155411	155411	+	lincRNA	SNP	A	A	T	rs142742436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:155411A>T	ENST00000510175.1	+	0	846							Q3SXZ3	ZN718_HUMAN	zinc finger protein 718						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		AACCCTTCTCATGCGAAGAAT	0.383													A|||	20	0.00399361	0.0	0.0014	5008	,	,		20733	0.0		0.0189	False		,,,				2504	0.0				p.S312S		Atlas-SNP	.											.	.	.	.	0			c.A936T						PASS	.	A		8,4220		0,8,2106	30.0	34.0	33.0		747	-0.9	0.0	4	dbSNP_134	33	95,8429		3,89,4170	no	coding-synonymous	ZNF718	NM_001039127.3		3,97,6276	TT,TA,AA		1.1145,0.1892,0.8077		249/416	155411	103,12649	2114	4262	6376			255403	exon4			CTTCTCATGCGAA	AK096662	CCDS75078.1, CCDS75079.1	4p16.3	2011-05-24			ENSG00000250312	ENSG00000250312		"""Zinc fingers, C2H2-type"""	26889	protein-coding gene	gene with protein product							Standard	XM_005278364		Approved	FLJ90036	uc003fzt.4	Q3SXZ3	OTTHUMG00000159873		4.37:g.155411A>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_001039127	Q3SXZ4|Q3SXZ5	Silent	SNP	ENST00000510175.1	37																																																																																				A|0.992;T|0.008	0.008	strong		0.383	ZNF718-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000357865.3	NM_001039127	
TNRC18	84629	hgsc.bcm.edu	37	7	5347749	5347749	+	Silent	SNP	G	G	A	rs9639976	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5347749G>A	ENST00000430969.1	-	30	9243	c.8895C>T	c.(8893-8895)ccC>ccT	p.P2965P	TNRC18_ENST00000399537.4_Silent_p.P2965P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2965							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		AGCAGAGCACGGGCACGCCGT	0.682													G|||	646	0.128994	0.0552	0.17	5008	,	,		14507	0.1151		0.2565	False		,,,				2504	0.0828				p.P2965P		Atlas-SNP	.											.	TNRC18	311	.	0			c.C8895T						PASS	.	G		313,3739		24,265,1737	21.0	24.0	23.0		8895	-9.2	1.0	7	dbSNP_119	23	2092,6130		286,1520,2305	no	coding-synonymous	TNRC18	NM_001080495.2		310,1785,4042	AA,AG,GG		25.4439,7.7246,19.5943		2965/2969	5347749	2405,9869	2026	4111	6137	SO:0001819	synonymous_variant	84629	exon30			GAGCACGGGCACG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8895C>T	7.37:g.5347749G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	160	116	0.725	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.833;A|0.167	0.167	strong		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
GRID2IP	392862	hgsc.bcm.edu	37	7	6547902	6547902	+	Missense_Mutation	SNP	G	G	A	rs112305062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6547902G>A	ENST00000457091.2	-	13	2257	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	GRID2IP_ENST00000452113.1_Missense_Mutation_p.P562L|GRID2IP_ENST00000435185.1_Missense_Mutation_p.P569L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	753	Pro-rich.				long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GGGGCTGAGCGGGGGTGGGGG	0.657													G|||	401	0.0800719	0.0098	0.196	5008	,	,		4499	0.0685		0.1054	False		,,,				2504	0.0787				p.P753L		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C2258T						PASS	.						6.0	6.0	6.0					7																	6547902		684	1570	2254	SO:0001583	missense	392862	exon13			CTGAGCGGGGGTG		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.2258C>T	7.37:g.6547902G>A	ENSP00000397351:p.Pro753Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	173	128	0.739884	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	210	0.09615384615384616	19	0.03861788617886179	78	0.2154696132596685	37	0.06468531468531469	76	0.10026385224274406	g	15.29	2.789692	0.50102	.	.	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.57107	0.46;0.45;0.42	3.75	3.75	0.43078	.	0.000000	0.85682	U	0.000000	T	0.00073	0.0002	L	0.61218	1.895	0.09310	P	0.99999281359	D	0.89917	1.0	D	0.74023	0.982	T	0.02885	-1.1098	9	0.54805	T	0.06	.	13.4078	0.60924	0.0:0.0:1.0:0.0	.	753	A4D2P6	GRD2I_HUMAN	L	562;569;753	ENSP00000397887:P562L;ENSP00000408364:P569L;ENSP00000397351:P753L	ENSP00000408364:P569L	P	-	2	0	GRID2IP	6514427	1.000000	0.71417	0.614000	0.29051	0.845000	0.48019	5.766000	0.68843	1.814000	0.52955	0.558000	0.71614	CCG	G|0.908;A|0.092	0.092	strong		0.657	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
PLIN4	729359	hgsc.bcm.edu	37	19	4512669	4512669	+	Missense_Mutation	SNP	T	T	C	rs55901236	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	60	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	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	
DGKG	1608	hgsc.bcm.edu	37	3	186006618	186006618	+	Missense_Mutation	SNP	G	G	C	rs1004588	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186006618G>C	ENST00000265022.3	-	6	964	c.425C>G	c.(424-426)aCc>aGc	p.T142S	DGKG_ENST00000344484.4_Missense_Mutation_p.T142S|DGKG_ENST00000382164.4_Missense_Mutation_p.T142S|DGKG_ENST00000544847.1_Missense_Mutation_p.T142S	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	142			T -> S (in dbSNP:rs1004588). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TTCCAGGGGGGTCGCAGCCAC	0.522													G|||	2599	0.51897	0.4387	0.5101	5008	,	,		16155	0.6081		0.5318	False		,,,				2504	0.5286				p.T142S		Atlas-SNP	.											.	DGKG	98	.	0			c.C425G						PASS	.	G	SER/THR,SER/THR,SER/THR	1929,2477	539.3+/-375.2	420,1089,694	123.0	137.0	132.0		425,425,425	2.2	0.0	3	dbSNP_86	132	4447,4153	580.4+/-391.1	1167,2113,1020	yes	missense,missense,missense	DGKG	NM_001080744.1,NM_001080745.1,NM_001346.2	58,58,58	1587,3202,1714	CC,CG,GG		48.2907,43.7812,49.0235	benign,benign,benign	142/767,142/753,142/792	186006618	6376,6630	2203	4300	6503	SO:0001583	missense	1608	exon6			AGGGGGGTCGCAG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.425C>G	3.37:g.186006618G>C	ENSP00000265022:p.Thr142Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	1183	0.5416666666666666	243	0.49390243902439024	173	0.47790055248618785	358	0.6258741258741258	409	0.5395778364116095	G	3.558	-0.090221	0.07053	0.437812	0.517093	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.87	2.16	0.27623	.	0.961737	0.08649	N	0.914365	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.09022	0.002;0.001;0.0;0.001	B;B;B;B	0.13407	0.006;0.009;0.003;0.004	T	0.46076	-0.9217	9	0.05620	T	0.96	.	5.3794	0.16183	0.3513:0.1326:0.5161:0.0	rs1004588;rs2228941;rs52831315;rs57454656;rs1004588	142;142;142;142	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	S	142;142;142;142;145	ENSP00000265022:T142S;ENSP00000339777:T142S;ENSP00000371599:T142S;ENSP00000440507:T142S	ENSP00000265022:T142S	T	-	2	0	DGKG	187489312	.	.	0.000000	0.03702	0.002000	0.02628	.	.	0.191000	0.20236	-0.137000	0.14449	ACC	G|0.460;C|0.540	0.540	strong		0.522	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		
KIF17	57576	hgsc.bcm.edu	37	1	21011346	21011346	+	Silent	SNP	A	A	G	rs12028811	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:21011346A>G	ENST00000247986.2	-	10	2497	c.2187T>C	c.(2185-2187)acT>acC	p.T729T	KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000375044.1_Silent_p.T629T|KIF17_ENST00000400463.3_Silent_p.T729T			Q9P2E2	KIF17_HUMAN	kinesin family member 17	729					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		GCGGGTCATCAGTCAGCACTG	0.697													G|||	1129	0.225439	0.3116	0.1455	5008	,	,		16866	0.3353		0.0855	False		,,,				2504	0.1963				p.T729T		Atlas-SNP	.											KIF17,caecum,carcinoma,-1,1	KIF17	130	1	0			c.T2187C						scavenged	.	G	,	1193,3201		170,853,1174	53.0	43.0	46.0		2187,2187	-7.8	0.0	1	dbSNP_120	46	755,7827		35,685,3571	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	205,1538,4745	GG,GA,AA		8.7975,27.1507,15.0123	,	729/1029,729/1030	21011346	1948,11028	2197	4291	6488	SO:0001819	synonymous_variant	57576	exon10			GTCATCAGTCAGC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.2187T>C	1.37:g.21011346A>G		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			A|0.831;G|0.169	0.169	strong		0.697	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
KANK4	163782	hgsc.bcm.edu	37	1	62740264	62740264	+	Missense_Mutation	SNP	T	T	C	rs41309173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62740264T>C	ENST00000371153.4	-	3	890	c.512A>G	c.(511-513)cAc>cGc	p.H171R	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	171						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						AGCCCTGCTGTGCAGCAGCGT	0.637													T|||	70	0.0139776	0.0076	0.0159	5008	,	,		18100	0.001		0.0348	False		,,,				2504	0.0133				p.H171R		Atlas-SNP	.											.	KANK4	135	.	0			c.A512G						PASS	.	T	ARG/HIS	52,4352	50.2+/-85.5	1,50,2151	26.0	29.0	28.0		512	1.6	0.0	1	dbSNP_127	28	343,8255	111.4+/-171.7	11,321,3967	yes	missense	KANK4	NM_181712.4	29	12,371,6118	CC,CT,TT		3.9893,1.1807,3.038	benign	171/996	62740264	395,12607	2202	4299	6501	SO:0001583	missense	163782	exon3			CTGCTGTGCAGCA	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.512A>G	1.37:g.62740264T>C	ENSP00000360195:p.His171Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	33	0.01510989010989011	3	0.006097560975609756	8	0.022099447513812154	0	0.0	22	0.029023746701846966	T	4.124	0.021294	0.08006	0.011807	0.039893	ENSG00000132854	ENST00000371153	T	0.75821	-0.97	5.41	1.58	0.23477	.	0.214742	0.23573	N	0.046728	T	0.24851	0.0603	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29610	-1.0006	10	0.07813	T	0.8	0.0206	14.9532	0.71091	0.0:0.0:0.5734:0.4265	rs41309173	171	Q5T7N3	KANK4_HUMAN	R	171	ENSP00000360195:H171R	ENSP00000360195:H171R	H	-	2	0	KANK4	62512852	0.853000	0.29707	0.009000	0.14445	0.025000	0.11179	1.083000	0.30815	0.012000	0.14892	-0.460000	0.05396	CAC	T|0.978;C|0.022	0.022	strong		0.637	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435721	7435721	+	Missense_Mutation	SNP	C	C	T	rs6850206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:7435721C>T	ENST00000319098.4	-	1	979	c.886G>A	c.(886-888)Gtg>Atg	p.V296M	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	296	Saposin B-type 3. {ECO:0000255|PROSITE- ProRule:PRU00415}.		V -> M (in dbSNP:rs6850206).		sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						TTCATGCACACCTCACAGGTC	0.587													C|||	647	0.129193	0.1044	0.1383	5008	,	,		20561	0.0764		0.1948	False		,,,				2504	0.1431				p.V296M		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G886A						PASS	.	C	MET/VAL,	547,3769		33,481,1644	55.0	60.0	58.0		886,	0.7	0.5	4	dbSNP_116	58	1659,6879		161,1337,2771	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	21,	194,1818,4415	TT,TC,CC		19.4308,12.6738,17.162	possibly-damaging,	296/522,	7435721	2206,10648	2158	4269	6427	SO:0001583	missense	768239	exon1			TGCACACCTCACA	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.886G>A	4.37:g.7435721C>T	ENSP00000317445:p.Val296Met	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	34	0.666667	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	285	0.1304945054945055	53	0.10772357723577236	53	0.1464088397790055	33	0.057692307692307696	146	0.19261213720316622	C	10.15	1.271609	0.23221	0.126738	0.194308	ENSG00000178597	ENST00000319098	D	0.85411	-1.98	3.8	0.671	0.17929	Saposin-like (2);Saposin-like type B, 1 (1);Saposin B (2);	0.339732	0.29924	N	0.010851	T	0.00784	0.0026	L	0.56340	1.77	0.35994	P	0.16310100000000005	D	0.76494	0.999	D	0.72338	0.977	T	0.44205	-0.9343	9	0.48119	T	0.1	-1.1881	11.0437	0.47846	0.0:0.4309:0.5691:0.0	rs6850206;rs60725764;rs6850206	296	Q6NUJ1	SAPL1_HUMAN	M	296	ENSP00000317445:V296M	ENSP00000317445:V296M	V	-	1	0	PSAPL1	7486622	0.031000	0.19500	0.520000	0.27837	0.033000	0.12548	0.050000	0.14120	0.356000	0.24157	-0.305000	0.09177	GTG	C|0.871;T|0.129	0.129	strong		0.587	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
UBQLN3	50613	hgsc.bcm.edu	37	11	5529152	5529152	+	Missense_Mutation	SNP	A	A	G	rs2234455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5529152A>G	ENST00000311659.4	-	2	1784	c.1637T>C	c.(1636-1638)aTg>aCg	p.M546T	HBE1_ENST00000380237.1_5'Flank|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_5'Flank	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	546			M -> T (in dbSNP:rs2234455).							NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAGGCAAGGCATGAACCAGAG	0.577													A|||	580	0.115815	0.0098	0.2363	5008	,	,		20349	0.0933		0.2127	False		,,,				2504	0.0971				p.M546T	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											UBQLN3,NS,carcinoma,+1,1	UBQLN3	107	1	0			c.T1637C						PASS	.	A	THR/MET	175,4227	112.9+/-151.0	4,167,2030	56.0	51.0	52.0		1637	2.7	1.0	11	dbSNP_98	52	1584,7010	291.6+/-300.4	158,1268,2871	yes	missense	UBQLN3	NM_017481.2	81	162,1435,4901	GG,GA,AA		18.4315,3.9755,13.5349	benign	546/656	5529152	1759,11237	2201	4297	6498	SO:0001583	missense	50613	exon2			CAAGGCATGAACC	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1637T>C	11.37:g.5529152A>G	ENSP00000347997:p.Met546Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	303	0.13873626373626374	11	0.022357723577235773	76	0.20994475138121546	52	0.09090909090909091	164	0.21635883905013192	A	0.011	-1.731286	0.00687	0.039755	0.184315	ENSG00000175520	ENST00000311659	T	0.34275	1.37	5.02	2.65	0.31530	.	0.544265	0.16946	N	0.193082	T	0.00012	0.0000	L	0.28694	0.88	0.43342	P	0.0046040000000000525	B	0.29716	0.255	B	0.21360	0.034	T	0.25984	-1.0116	9	0.39692	T	0.17	-30.8581	2.0753	0.03623	0.5861:0.1666:0.0872:0.1601	rs2234455;rs17370907;rs52800429;rs2234455	546	Q9H347	UBQL3_HUMAN	T	546	ENSP00000347997:M546T	ENSP00000347997:M546T	M	-	2	0	UBQLN3	5485728	0.879000	0.30193	0.990000	0.47175	0.974000	0.67602	1.668000	0.37481	0.457000	0.26962	0.533000	0.62120	ATG	A|0.867;G|0.133	0.133	strong		0.577	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481	
TMEM92	162461	hgsc.bcm.edu	37	17	48356260	48356260	+	Missense_Mutation	SNP	G	G	C	rs6504642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48356260G>C	ENST00000300433.3	+	5	379	c.269G>C	c.(268-270)aGc>aCc	p.S90T	TMEM92_ENST00000511882.1_3'UTR|RP11-893F2.9_ENST00000508851.1_RNA|TMEM92_ENST00000507382.1_Missense_Mutation_p.S90T	NM_001168215.1	NP_001161687.1	Q6UXU6	TMM92_HUMAN	transmembrane protein 92	90	Pro-rich.		S -> N (in dbSNP:rs6504642).|S -> T (in dbSNP:rs6504642). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(1)	7						GAGCCAGACAGCCCAGTGGAT	0.602													C|||	2721	0.543331	0.4871	0.5677	5008	,	,		17393	0.5982		0.5467	False		,,,				2504	0.5419				p.S90T		Atlas-SNP	.											.	TMEM92	13	.	0			c.G269C						PASS	.	C	THR/SER,THR/SER	2690,1716		946,798,459	73.0	83.0	80.0		269,269	-0.1	0.0	17	dbSNP_116	80	5068,3532		1609,1850,841	yes	missense,missense	TMEM92	NM_001168215.1,NM_153229.2	58,58	2555,2648,1300	CC,CG,GG		41.0698,38.9469,40.3506	benign,benign	90/160,90/160	48356260	7758,5248	2203	4300	6503	SO:0001583	missense	162461	exon4			CAGACAGCCCAGT		CCDS11562.1	17q21.33	2005-12-13							26579	protein-coding gene	gene with protein product						12975309	Standard	NM_153229		Approved	FLJ33318	uc002iqn.2	Q6UXU6		ENST00000300433.3:c.269G>C	17.37:g.48356260G>C	ENSP00000300433:p.Ser90Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_153229	Q8NBF0	Missense_Mutation	SNP	ENST00000300433.3	37	CCDS11562.1	1407	0.6442307692307693	325	0.6605691056910569	215	0.5939226519337016	418	0.7307692307692307	449	0.5923482849604221	C	0.089	-1.170336	0.01660	0.610531	0.589302	ENSG00000167105	ENST00000300433;ENST00000507382	T;T	0.05258	3.47;3.47	4.38	-0.12	0.13539	.	1.726280	0.03668	N	0.243598	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	0.33369	-0.9871	9	0.02654	T	1	0.2952	6.2699	0.20949	0.0:0.3756:0.4451:0.1793	rs6504642;rs17846666;rs17859763;rs61418340	90	Q6UXU6	TMM92_HUMAN	T	90	ENSP00000300433:S90T;ENSP00000425144:S90T	ENSP00000300433:S90T	S	+	2	0	TMEM92	45711259	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.745000	0.04834	-0.394000	0.07727	-0.357000	0.07601	AGC	A|0.014;C|0.601;G|0.385	0.601	strong		0.602	TMEM92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367053.2	NM_153229	
IP6K3	117283	hgsc.bcm.edu	37	6	33703089	33703089	+	Silent	SNP	C	C	T	rs623813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33703089C>T	ENST00000293756.4	-	2	491	c.165G>A	c.(163-165)ccG>ccA	p.P55P	IP6K3_ENST00000451316.1_Silent_p.P55P	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	55					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						TCATGGCCAGCGGCAGGGATT	0.617													C|||	390	0.0778754	0.0734	0.098	5008	,	,		18105	0.0218		0.1551	False		,,,				2504	0.0481				p.P55P		Atlas-SNP	.											.	IP6K3	52	.	0			c.G165A						PASS	.	C	,	399,4007	186.0+/-213.0	20,359,1824	53.0	38.0	43.0		165,165	-10.9	0.3	6	dbSNP_83	43	1354,7246	251.1+/-277.7	124,1106,3070	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	144,1465,4894	TT,TC,CC		15.7442,9.0558,13.4784	,	55/411,55/411	33703089	1753,11253	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon3			GGCCAGCGGCAGG	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.165G>A	6.37:g.33703089C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			C|0.889;T|0.111	0.111	strong		0.617	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
SSTR3	6753	hgsc.bcm.edu	37	22	37603744	37603744	+	Silent	SNP	C	C	T	rs86583	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	78	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	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		
MUC4	4585	hgsc.bcm.edu	37	3	195506990	195506990	+	Missense_Mutation	SNP	C	C	G	rs200783894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506990C>G	ENST00000463781.3	-	2	11920	c.11461G>C	c.(11461-11463)Gac>Cac	p.D3821H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3821H	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)		GGGGTGGTGTCACCTGTGGAT	0.587													.|||	203	0.0405351	0.0537	0.0476	5008	,	,		9160	0.0188		0.0368	False		,,,				2504	0.044				p.D3821H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G11461C						scavenged	.						4.0	4.0	4.0					3																	195506990		522	1378	1900	SO:0001583	missense	4585	exon2			TGGTGTCACCTGT	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.11461G>C	3.37:g.195506990C>G	ENSP00000417498:p.Asp3821His	Somatic	42	3	0.0714286		WXS	Illumina HiSeq	Phase_I	81	12	0.148148	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	.	.	.	.	.	.	.	.	.	.	c	3.752	-0.051387	0.07407	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35048	1.4;1.33	.	.	.	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.09310	N	1	B	0.26876	0.162	B	0.09377	0.004	T	0.18935	-1.0321	7	.	.	.	.	2.6646	0.05037	0.0:0.5037:0.0:0.4962	rs3107751;rs28520424	3693	E7ESK3	.	H	3821	ENSP00000417498:D3821H;ENSP00000420243:D3821H	.	D	-	1	0	MUC4	196991769	0.001000	0.12720	0.109000	0.21407	0.109000	0.19521	-0.170000	0.09897	0.064000	0.16427	0.064000	0.15345	GAC	C|0.746;G|0.253	0.253	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203463	140203463	+	Silent	SNP	C	C	A	rs142924665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140203463C>A	ENST00000529859.1	+	1	2103	c.2103C>A	c.(2101-2103)atC>atA	p.I701I	PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Silent_p.I701I|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Silent_p.I701I	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	701					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)			ACCTGATCATCGCCATCTGTG	0.692													.|||	2	0.000399361	0.0	0.0	5008	,	,		16849	0.0		0.002	False		,,,				2504	0.0				p.I701I		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C2103A						PASS	.	C	,,,,,,	4,4402	8.1+/-20.4	0,4,2199	63.0	62.0	62.0		,,,,2103,,2103	2.2	1.0	5	dbSNP_134	62	35,8561	23.4+/-69.3	0,35,4263	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	,,,,,,	0,39,6462	AA,AC,CC		0.4072,0.0908,0.3	,,,,,,	,,,,701/937,,701/817	140203463	39,12963	2203	4298	6501	SO:0001819	synonymous_variant	56143	exon1			GATCATCGCCATC	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.2103C>A	5.37:g.140203463C>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.997;A|0.003	0.003	strong		0.692	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
UBAP2	55833	hgsc.bcm.edu	37	9	33941759	33941759	+	Missense_Mutation	SNP	T	T	C	rs307658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:33941759T>C	ENST00000379238.1	-	16	1934	c.1817A>G	c.(1816-1818)aAt>aGt	p.N606S	UBAP2_ENST00000379239.4_Missense_Mutation_p.N339S|UBAP2_ENST00000360802.1_Missense_Mutation_p.N606S|UBAP2_ENST00000539807.1_Missense_Mutation_p.N361S|UBAP2_ENST00000449054.1_Missense_Mutation_p.N606S|UBAP2_ENST00000418786.2_Missense_Mutation_p.N553S|UBAP2_ENST00000379225.1_Missense_Mutation_p.N239S					ubiquitin associated protein 2									p.N606S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ACTAGCAGAATTCAGTGATGA	0.448													C|||	1857	0.370807	0.5083	0.268	5008	,	,		18167	0.1726		0.3837	False		,,,				2504	0.4489				p.N606S		Atlas-SNP	.											UBAP2,NS,carcinoma,0,1	UBAP2	82	1	1	Substitution - Missense(1)	stomach(1)	c.A1817G						PASS	.	C	SER/ASN	2060,2346	607.3+/-390.9	478,1104,621	174.0	159.0	164.0		1817	5.8	1.0	9	dbSNP_79	164	3291,5309	646.8+/-400.3	648,1995,1657	yes	missense	UBAP2	NM_018449.2	46	1126,3099,2278	CC,CT,TT		38.2674,46.7544,41.1425	benign	606/1120	33941759	5351,7655	2203	4300	6503	SO:0001583	missense	55833	exon16			GCAGAATTCAGTG	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.1817A>G	9.37:g.33941759T>C	ENSP00000368540:p.Asn606Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	778	0.35622710622710624	248	0.5040650406504065	106	0.292817679558011	114	0.1993006993006993	310	0.40897097625329815	C	1.094	-0.663234	0.03428	0.467544	0.382674	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379239;ENST00000539807;ENST00000418786;ENST00000379225	T;T;T;T;T;T;T	0.20738	2.79;2.79;2.79;2.58;2.59;2.28;2.05	5.76	5.76	0.90799	.	0.521330	0.23587	N	0.046596	T	0.00012	0.0000	N	0.01015	-1.05	0.58432	P	4.000000000004E-6	B;B;B;B;B;B;B;B	0.17038	0.0;0.006;0.0;0.0;0.0;0.001;0.003;0.02	B;B;B;B;B;B;B;B	0.06405	0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.002	T	0.41124	-0.9526	9	0.02654	T	1	-4.2248	12.9291	0.58276	0.0:0.866:0.0:0.134	rs307658;rs601694;rs1626808;rs52833981;rs60695207;rs307658	553;531;361;339;515;239;531;606	E7EWG4;F5H4D5;F5H2U4;A6NCA8;F5H2C8;A2A306;B4DH66;Q5T6F2	.;.;.;.;.;.;.;UBAP2_HUMAN	S	606;606;606;515;339;361;553;239	ENSP00000368540:N606S;ENSP00000416932:N606S;ENSP00000354039:N606S;ENSP00000368541:N339S;ENSP00000439329:N361S;ENSP00000404436:N553S;ENSP00000368527:N239S	ENSP00000354039:N606S	N	-	2	0	UBAP2	33931759	1.000000	0.71417	1.000000	0.80357	0.356000	0.29392	2.117000	0.41939	1.449000	0.47699	-0.119000	0.15052	AAT	T|0.617;C|0.383	0.383	strong		0.448	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	54	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	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	
THADA	63892	hgsc.bcm.edu	37	2	43804229	43804229	+	Silent	SNP	T	T	C	rs13021894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:43804229T>C	ENST00000405006.4	-	10	1320	c.969A>G	c.(967-969)ggA>ggG	p.G323G	THADA_ENST00000402360.2_Silent_p.G323G|THADA_ENST00000404790.1_Silent_p.G323G|THADA_ENST00000403856.1_Silent_p.G323G|THADA_ENST00000415080.2_Silent_p.G33G|THADA_ENST00000405975.2_Silent_p.G323G|THADA_ENST00000330266.7_Silent_p.G33G	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	323										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)				GACCCATGCTTCCGTTCTGCC	0.498											OREG0014580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1890	0.377396	0.5136	0.245	5008	,	,		19120	0.2659		0.341	False		,,,				2504	0.4397				p.G323G		Atlas-SNP	.											.	THADA	131	.	0			c.A969G						PASS	.	C	,	1817,2129		433,951,589	61.0	64.0	63.0		969,969	1.4	1.0	2	dbSNP_121	63	2830,5506		480,1870,1818	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	913,2821,2407	CC,CT,TT		33.9491,46.0466,37.8359	,	323/1954,323/1954	43804229	4647,7635	1973	4168	6141	SO:0001819	synonymous_variant	63892	exon10			CATGCTTCCGTTC	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.969A>G	2.37:g.43804229T>C		Somatic	122	0	0	919	WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1																																																																																			T|0.636;C|0.364	0.364	strong		0.498	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
USP6NL	9712	hgsc.bcm.edu	37	10	11505175	11505175	+	Silent	SNP	A	A	G	rs3740204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:11505175A>G	ENST00000609104.1	-	15	2146	c.1752T>C	c.(1750-1752)ccT>ccC	p.P584P	USP6NL_ENST00000277575.5_Silent_p.P601P|USP6NL_ENST00000379237.2_Silent_p.P607P	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	584					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						TTCTCGGGCTAGGAGGGTAAA	0.567													G|||	2501	0.499401	0.5772	0.2997	5008	,	,		18328	0.7351		0.3042	False		,,,				2504	0.4939				p.P601P		Atlas-SNP	.											.	USP6NL	57	.	0			c.T1803C						PASS	.	G	,	2008,1898		504,1000,449	47.0	49.0	48.0		1803,1752	-1.2	0.0	10	dbSNP_107	48	2613,5693		402,1809,1942	no	coding-synonymous,coding-synonymous	USP6NL	NM_001080491.2,NM_014688.2	,	906,2809,2391	GG,GA,AA		31.4592,48.5919,37.8398	,	601/846,584/829	11505175	4621,7591	1953	4153	6106	SO:0001819	synonymous_variant	9712	exon14			CGGGCTAGGAGGG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1752T>C	10.37:g.11505175A>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Silent	SNP	ENST00000609104.1	37	CCDS53492.1																																																																																			A|0.502;G|0.498	0.498	strong		0.567	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
LPCAT1	79888	hgsc.bcm.edu	37	5	1467004	1467004	+	Splice_Site	SNP	A	A	G	rs35452723	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	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
FPR1	2357	hgsc.bcm.edu	37	19	52249947	52249947	+	Missense_Mutation	SNP	C	C	G	rs2070745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52249947C>G	ENST00000595042.1	-	3	442	c.301G>C	c.(301-303)Gtc>Ctc	p.V101L	FPR1_ENST00000304748.4_Missense_Mutation_p.V101L	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	101			V -> L (in dbSNP:rs2070745). {ECO:0000269|PubMed:2161213, ECO:0000269|PubMed:2176894}.		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.V101L(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)	ATGGTAAAGACGAATTTGCAC	0.532													T|||	1972	0.39377	0.3086	0.4986	5008	,	,		22085	0.4861		0.3718	False		,,,				2504	0.362				p.V101L		Atlas-SNP	.											FPR1,colon,carcinoma,0,2	FPR1	64	2	1	Substitution - Missense(1)	stomach(1)	c.G301C	GRCh37	CM074876	FPR1	M	rs2070745	PASS	.	T	LEU/VAL,LEU/VAL	1389,3017		220,949,1034	135.0	104.0	114.0		301,301	-2.0	0.0	19	dbSNP_96	114	3075,5525		534,2007,1759	yes	missense,missense	FPR1	NM_001193306.1,NM_002029.3	32,32	754,2956,2793	GG,GC,CC		35.7558,31.5252,34.3226	benign,benign	101/351,101/351	52249947	4464,8542	2203	4300	6503	SO:0001583	missense	2357	exon3			TAAAGACGAATTT	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.301G>C	19.37:g.52249947C>G	ENSP00000471493:p.Val101Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001193306	Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	854	0.391025641025641	128	0.2601626016260163	167	0.4613259668508287	270	0.47202797202797203	289	0.3812664907651715	.	0.026	-1.368558	0.01225	0.315252	0.357558	ENSG00000171051	ENST00000304748	T	0.36699	1.24	3.66	-2.04	0.07343	GPCR, rhodopsin-like superfamily (1);	0.146450	0.44097	D	0.000486	T	0.00012	0.0000	L	0.59912	1.85	0.80722	P	0.0	B	0.06786	0.001	B	0.18871	0.023	T	0.46735	-0.9170	9	0.19147	T	0.46	.	3.4324	0.07433	0.2884:0.3276:0.0:0.3839	rs2070745;rs17717709;rs52831811;rs2070745	101	P21462	FPR1_HUMAN	L	101	ENSP00000302707:V101L	ENSP00000302707:V101L	V	-	1	0	FPR1	56941759	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.065000	0.14466	-0.599000	0.05798	-0.254000	0.11334	GTC	C|0.644;G|0.356	0.356	strong		0.532	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029	
EIF5B	9669	hgsc.bcm.edu	37	2	99978048	99978048	+	Silent	SNP	G	G	A	rs12233086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	209	0	0		WXS	Illumina HiSeq	Phase_I	173	77	0.445087	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	
DAAM1	23002	hgsc.bcm.edu	37	14	59789727	59789727	+	Silent	SNP	G	G	A	rs8022614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:59789727G>A	ENST00000395125.1	+	5	581	c.558G>A	c.(556-558)aaG>aaA	p.K186K	DAAM1_ENST00000351081.1_Silent_p.K186K|DAAM1_ENST00000360909.3_Silent_p.K186K	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	186	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)		GCTGTATAAAGGCGTTAATGA	0.438													G|||	1685	0.336462	0.0787	0.2406	5008	,	,		20067	0.5883		0.3936	False		,,,				2504	0.4346				p.K186K		Atlas-SNP	.											.	DAAM1	95	.	0			c.G558A						PASS	.	G		526,3880	230.7+/-244.8	38,450,1715	109.0	101.0	104.0		558	3.9	1.0	14	dbSNP_116	104	3354,5246	490.0+/-372.8	668,2018,1614	no	coding-synonymous	DAAM1	NM_014992.1		706,2468,3329	AA,AG,GG		39.0,11.9383,29.8324		186/1079	59789727	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			TATAAAGGCGTTA	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.558G>A	14.37:g.59789727G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.684;A|0.316	0.316	strong		0.438	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
MAGEC1	9947	hgsc.bcm.edu	37	X	140994407	140994407	+	Missense_Mutation	SNP	C	C	G	rs62611965	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:140994407C>G	ENST00000285879.4	+	4	1503	c.1217C>G	c.(1216-1218)tCt>tGt	p.S406C	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	406										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)					TTTCCCCAGTCTCCTCTCCAG	0.478										HNSCC(15;0.026)			-|||	283	0.0749669	0.0393	0.0533	3775	,	,		13424	0.0337		0.0577	False		,,,				2504	0.1043				p.S406C		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C1217G						PASS	.	C	CYS/SER	188,3647		10,136,32,1486,539	118.0	130.0	126.0		1217		0.0	X	dbSNP_129	126	633,6088		21,429,162,1978,1703	no	missense	MAGEC1	NM_005462.4	112	31,565,194,3464,2242	GG,GC,G,CC,C		9.4182,4.9022,7.7776	probably-damaging	406/1143	140994407	821,9735	2203	4293	6496	SO:0001583	missense	9947	exon4			CCCAGTCTCCTCT	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.1217C>G	X.37:g.140994407C>G	ENSP00000285879:p.Ser406Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	100	0.917431	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	107	0.0644966847498493	19	0.03991596638655462	11	0.03197674418604651	10	0.017793594306049824	33	0.045205479452054796	c	4.098	0.016180	0.07959	0.049022	0.094182	ENSG00000155495	ENST00000285879	T	0.02606	4.23	.	.	.	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.32593	P	0.52694	D	0.62365	0.991	P	0.52710	0.707	T	0.51568	-0.8689	7	0.72032	D	0.01	.	5.9409	0.19192	0.0:0.9994:0.0:6.0E-4	rs62611965	406	O60732	MAGC1_HUMAN	C	406	ENSP00000285879:S406C	ENSP00000285879:S406C	S	+	2	0	MAGEC1	140822073	0.007000	0.16637	0.041000	0.18516	0.041000	0.13682	-0.137000	0.10389	0.148000	0.19059	0.150000	0.16122	TCT	C|0.933;G|0.067	0.067	strong		0.478	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239253224	239253224	+	Missense_Mutation	SNP	A	A	T	rs58277463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239253224A>T	ENST00000373327.4	+	9	1468	c.1246A>T	c.(1246-1248)Aca>Tca	p.T416S	TRAF3IP1_ENST00000391993.3_Intron|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.T416S	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	416	DISC1-interaction domain.		T -> S (in dbSNP:rs58277463).		cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		GCCCAACCCCACAGAGAAGCA	0.468													A|||	767	0.153155	0.3283	0.0821	5008	,	,		18983	0.0992		0.0586	False		,,,				2504	0.1196				p.T416S		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.A1246T						PASS	.	A	,SER/THR	1124,3282	404.0+/-332.9	156,812,1235	93.0	95.0	94.0		,1246	3.1	0.0	2	dbSNP_129	94	340,8260	116.8+/-176.5	3,334,3963	yes	intron,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	,58	159,1146,5198	TT,TA,AA		3.9535,25.5107,11.2563	,	,416/692	239253224	1464,11542	2203	4300	6503	SO:0001583	missense	26146	exon9			AACCCCACAGAGA	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.1246A>T	2.37:g.239253224A>T	ENSP00000362424:p.Thr416Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	294	0.1346153846153846	150	0.3048780487804878	38	0.10497237569060773	64	0.11188811188811189	42	0.055408970976253295	A	8.813	0.935747	0.18206	0.255107	0.039535	ENSG00000204104	ENST00000373327;ENST00000391994	T;T	0.13420	2.62;2.59	4.93	3.11	0.35812	.	0.447478	0.21374	N	0.075596	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.14805	0.011	B	0.16722	0.016	T	0.46289	-0.9202	9	0.09084	T	0.74	-4.9865	8.3354	0.32211	0.1904:0.0:0.8096:0.0	rs58277463;rs61752233	416	Q8TDR0	MIPT3_HUMAN	S	416	ENSP00000362424:T416S;ENSP00000375852:T416S	ENSP00000362424:T416S	T	+	1	0	TRAF3IP1	238917963	0.000000	0.05858	0.011000	0.14972	0.060000	0.15804	0.089000	0.15002	1.063000	0.40649	-0.146000	0.13790	ACA	A|0.882;T|0.118	0.118	strong		0.468	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
CSNK2B	1460	hgsc.bcm.edu	37	6	31635710	31635710	+	Silent	SNP	T	T	C	rs14365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31635710T>C	ENST00000375882.2	+	3	294	c.138T>C	c.(136-138)taT>taC	p.Y46Y	LY6G5B_ENST00000409525.1_5'Flank|CSNK2B_ENST00000375865.2_Silent_p.Y46Y|CSNK2B_ENST00000375866.2_Silent_p.Y46Y|GPANK1_ENST00000375895.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_Silent_p.Y46Y|GPANK1_ENST00000375893.2_5'Flank|GPANK1_ENST00000375906.1_5'Flank|GPANK1_ENST00000375896.4_5'Flank|GPANK1_ENST00000375900.4_5'Flank|LY6G5B_ENST00000375864.4_5'Flank|CSNK2B_ENST00000375885.4_Silent_p.Y65Y	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	60	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	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	
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24424367G>A	ENST00000313250.5	+	2	455	c.252G>A	c.(250-252)acG>acA	p.T84T	DHRS4_ENST00000543741.2_Silent_p.T84T|DHRS4_ENST00000397075.3_Silent_p.T84T|DHRS4_ENST00000559632.1_Silent_p.T84T|DHRS4_ENST00000382761.3_Silent_p.T66T|DHRS4_ENST00000421831.1_Silent_p.T66T|DHRS4_ENST00000558263.1_Silent_p.T84T|DHRS4_ENST00000558581.1_Silent_p.T84T|DHRS4_ENST00000397074.3_Silent_p.T84T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_Silent_p.T66T|DHRS4_ENST00000397073.2_Silent_p.T66T	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	84					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	TGAGCGTGACGGGCACCGTGT	0.682													.|||	1006	0.200879	0.5998	0.1095	5008	,	,		15536	0.0099		0.0785	False		,,,				2504	0.0491				p.T84T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G252A						PASS	.	G		2291,2115		588,1115,500	37.0	41.0	39.0		252	-6.6	0.3	14	dbSNP_120	39	612,7988		6,600,3694	no	coding-synonymous	DHRS4	NM_021004.2		594,1715,4194	AA,AG,GG		7.1163,48.0027,22.3205		84/279	24424367	2903,10103	2203	4300	6503	SO:0001819	synonymous_variant	10901	exon2			CGTGACGGGCACC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.252G>A	14.37:g.24424367G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	245	115	0.469388	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			G|0.796;A|0.204	0.204	strong		0.682	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
GSX1	219409	hgsc.bcm.edu	37	13	28367061	28367061	+	Silent	SNP	A	A	G	rs1231058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:28367061A>G	ENST00000302945.2	+	1	282	c.234A>G	c.(232-234)ctA>ctG	p.L78L		NM_145657.1	NP_663632.1	Q9H4S2	GSX1_HUMAN	GS homeobox 1	78					adenohypophysis development (GO:0021984)|hypothalamus development (GO:0021854)|neuron fate commitment (GO:0048663)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spinal cord association neuron differentiation (GO:0021527)	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 (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		cgcTGCCTCTACTCAAGGCTT	0.751													G|||	4592	0.916933	0.9834	0.8732	5008	,	,		10675	0.997		0.7972	False		,,,				2504	0.8988				p.L78L		Atlas-SNP	.											.	GSX1	20	.	0			c.A234G						PASS	.	G		3048,136		1461,126,5	2.0	3.0	3.0		234	1.1	1.0	13	dbSNP_87	3	5457,1143		2229,999,72	no	coding-synonymous	GSX1	NM_145657.1		3690,1125,77	GG,GA,AA		17.3182,4.2714,13.0724		78/265	28367061	8505,1279	1592	3300	4892	SO:0001819	synonymous_variant	219409	exon1			GCCTCTACTCAAG	AB044157	CCDS9326.1	13q12.2	2012-03-09		2007-07-26	ENSG00000169840	ENSG00000169840		"""Homeoboxes / ANTP class : HOXL subclass"""	20374	protein-coding gene	gene with protein product				GSH1			Standard	NM_145657		Approved	Gsh-1	uc001urr.1	Q9H4S2	OTTHUMG00000016637	ENST00000302945.2:c.234A>G	13.37:g.28367061A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_145657	Q9UD62	Silent	SNP	ENST00000302945.2	37	CCDS9326.1																																																																																			A|0.104;G|0.896	0.896	strong		0.751	GSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044309.2	NM_145657	
ZNF469	84627	hgsc.bcm.edu	37	16	88502482	88502482	+	Silent	SNP	C	C	T	rs3812953	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88502482C>T	ENST00000437464.1	+	2	8520	c.8520C>T	c.(8518-8520)cgC>cgT	p.R2840R	ZNF469_ENST00000565624.1_Silent_p.R2868R	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2840					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(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CAGGCGGTCGCTTGACTAGAA	0.602													C|||	2354	0.470048	0.3457	0.5231	5008	,	,		15669	0.4514		0.4682	False		,,,				2504	0.6217				p.R2840R		Atlas-SNP	.											ZNF469,NS,carcinoma,0,1	ZNF469	121	1	0			c.C8520T						PASS	.						12.0	16.0	15.0					16																	88502482		692	1587	2279	SO:0001819	synonymous_variant	84627	exon2			CGGTCGCTTGACT	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8520C>T	16.37:g.88502482C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			C|0.551;T|0.449	0.449	strong		0.602	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MGAT5B	146664	hgsc.bcm.edu	37	17	74944151	74944151	+	Silent	SNP	C	C	T	rs71384132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74944151C>T	ENST00000569840.2	+	17	2737	c.2163C>T	c.(2161-2163)agC>agT	p.S721S	RP11-87G24.3_ENST00000564292.1_RNA|MGAT5B_ENST00000301618.4_Silent_p.S719S|MGAT5B_ENST00000428789.2_Silent_p.S730S	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	721					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCCTGAACAGCCAGGACGCCT	0.662													C|||	344	0.0686901	0.0454	0.0922	5008	,	,		12821	0.0		0.1034	False		,,,				2504	0.1186				p.S730S		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C2190T						PASS	.	C	,,	246,4160	139.6+/-175.2	6,234,1963	33.0	30.0	31.0		2163,2157,2190	3.9	1.0	17	dbSNP_130	31	1017,7583	209.8+/-250.9	62,893,3345	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	68,1127,5308	TT,TC,CC		11.8256,5.5833,9.7109	,,	721/793,719/791,730/802	74944151	1263,11743	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon15			GAACAGCCAGGAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.2163C>T	17.37:g.74944151C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	15	0.306122	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.913;T|0.087	0.087	strong		0.662	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
NRROS	375387	hgsc.bcm.edu	37	3	196388099	196388099	+	Missense_Mutation	SNP	G	G	C	rs62623661	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	233	70	0.300429	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	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6889973	6889973	+	Silent	SNP	A	A	G	rs4239328	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:6889973A>G	ENST00000383472.4	+	13	1727	c.1623A>G	c.(1621-1623)ccA>ccG	p.P541P	ARHGAP28_ENST00000262227.3_Silent_p.P489P|ARHGAP28_ENST00000314319.3_Silent_p.P382P|ARHGAP28_ENST00000419673.2_Silent_p.P382P|ARHGAP28_ENST00000400091.2_Silent_p.P541P|ARHGAP28_ENST00000532996.1_Silent_p.P364P|ARHGAP28_ENST00000531294.1_Silent_p.P377P|ARHGAP28_ENST00000418986.1_Silent_p.P382P			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	541	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TGATGGCACCAAACCTTTTCT	0.403													A|||	2809	0.560903	0.5545	0.5331	5008	,	,		21051	0.6052		0.5736	False		,,,				2504	0.5307				p.P382P		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A1146G						PASS	.	A		2503,1903	628.0+/-395.0	689,1125,389	146.0	142.0	143.0		1146	-1.0	1.0	18	dbSNP_111	143	4919,3681	621.9+/-397.2	1384,2151,765	no	coding-synonymous	ARHGAP28	NM_001010000.2		2073,3276,1154	GG,GA,AA		42.8023,43.1911,42.934		382/571	6889973	7422,5584	2203	4300	6503	SO:0001819	synonymous_variant	79822	exon12			GGCACCAAACCTT	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1623A>G	18.37:g.6889973A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Silent	SNP	ENST00000383472.4	37																																																																																				A|0.424;G|0.576	0.576	strong		0.403	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
IGF2R	3482	hgsc.bcm.edu	37	6	160464289	160464289	+	Silent	SNP	G	G	A	rs894817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:160464289G>A	ENST00000356956.1	+	12	1738	c.1590G>A	c.(1588-1590)ggG>ggA	p.G530G		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	530					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AGGCACGAGGGTGTCCCGAGG	0.493													G|||	2122	0.423722	0.2784	0.3516	5008	,	,		18930	0.748		0.3181	False		,,,				2504	0.4458				p.G530G		Atlas-SNP	.											.	IGF2R	251	.	0			c.G1590A						PASS	.	G		1232,3174	425.7+/-340.9	159,914,1130	137.0	127.0	130.0		1590	3.6	0.5	6	dbSNP_86	130	2632,5968	426.4+/-355.3	416,1800,2084	no	coding-synonymous	IGF2R	NM_000876.2		575,2714,3214	AA,AG,GG		30.6047,27.9619,29.7094		530/2492	160464289	3864,9142	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon12			ACGAGGGTGTCCC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1590G>A	6.37:g.160464289G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	38	0.655172	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			G|0.650;A|0.350	0.350	strong		0.493	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
ZNF217	7764	hgsc.bcm.edu	37	20	52193088	52193088	+	Missense_Mutation	SNP	C	C	T	rs6063966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:52193088C>T	ENST00000371471.2	-	4	2640	c.2215G>A	c.(2215-2217)Gtt>Att	p.V739I	ZNF217_ENST00000302342.3_Missense_Mutation_p.V739I|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	739			V -> I (in dbSNP:rs6063966).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.V739I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TTTTTATGAACGTCAGGATTG	0.438													C|||	785	0.156749	0.2602	0.1066	5008	,	,		19555	0.0833		0.1203	False		,,,				2504	0.1656				p.V739I		Atlas-SNP	.											ZNF217,NS,carcinoma,0,1	ZNF217	227	1	1	Substitution - Missense(1)	stomach(1)	c.G2215A						scavenged	.	C	ILE/VAL	931,3475	356.4+/-313.5	107,717,1379	75.0	77.0	76.0		2215	-9.8	0.0	20	dbSNP_114	76	1060,7540	224.1+/-260.6	59,942,3299	yes	missense	ZNF217	NM_006526.2	29	166,1659,4678	TT,TC,CC		12.3256,21.1303,15.3083	benign	739/1049	52193088	1991,11015	2203	4300	6503	SO:0001583	missense	7764	exon3			TATGAACGTCAGG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2215G>A	20.37:g.52193088C>T	ENSP00000360526:p.Val739Ile	Somatic	93	2	0.0215054		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	296	0.13553113553113552	138	0.2804878048780488	41	0.1132596685082873	33	0.057692307692307696	84	0.11081794195250659	C	3.852	-0.031630	0.07543	0.211303	0.123256	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.09445	2.98;2.98	5.45	-9.83	0.00482	.	2.230010	0.01570	N	0.020552	T	0.00012	0.0000	N	0.03967	-0.31	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.36089	-0.9762	9	0.11182	T	0.66	-0.48	4.7667	0.13135	0.0985:0.4318:0.2022:0.2675	rs6063966;rs16998239;rs60939286;rs6063966	739	O75362	ZN217_HUMAN	I	739	ENSP00000360526:V739I;ENSP00000304308:V739I	ENSP00000304308:V739I	V	-	1	0	ZNF217	51626495	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.738000	0.04871	-2.542000	0.00485	-0.300000	0.09419	GTT	C|0.859;T|0.141	0.141	strong		0.438	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
KIF19	124602	hgsc.bcm.edu	37	17	72349040	72349040	+	Silent	SNP	C	C	T	rs9897137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:72349040C>T	ENST00000389916.4	+	15	2199	c.2061C>T	c.(2059-2061)agC>agT	p.S687S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	687					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						AGACATTGAGCTCTGATGCCC	0.632													C|||	1558	0.311102	0.7519	0.232	5008	,	,		18662	0.0813		0.1819	False		,,,				2504	0.1411				p.S687S		Atlas-SNP	.											.	KIF19	102	.	0			c.C2061T						PASS	.	C		2557,1485		817,923,281	94.0	101.0	99.0		2061	-2.5	0.0	17	dbSNP_119	99	1457,6917		123,1211,2853	no	coding-synonymous	KIF19	NM_153209.3		940,2134,3134	TT,TC,CC		17.3991,36.7392,32.3293		687/999	72349040	4014,8402	2021	4187	6208	SO:0001819	synonymous_variant	124602	exon15			ATTGAGCTCTGAT	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.2061C>T	17.37:g.72349040C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.737;T|0.263	0.263	strong		0.632	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
PKP3	11187	hgsc.bcm.edu	37	11	404317	404317	+	Silent	SNP	C	C	T	rs1134578	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:404317C>T	ENST00000331563.2	+	12	2428	c.2352C>T	c.(2350-2352)ttC>ttT	p.F784F		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	784					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)		ACCGTGACTTCCGGGCGGTAC	0.667													c|||	2261	0.451478	0.3147	0.5893	5008	,	,		17904	0.3542		0.5586	False		,,,				2504	0.5286				p.F784F		Atlas-SNP	.											.	PKP3	36	.	0			c.C2352T						PASS	.	C		1609,2781	490.6+/-361.9	294,1021,880	64.0	60.0	61.0		2352	3.4	1.0	11	dbSNP_86	61	4798,3776	611.5+/-395.8	1350,2098,839	no	coding-synonymous	PKP3	NM_007183.2		1644,3119,1719	TT,TC,CC		44.0401,36.6515,49.4215		784/798	404317	6407,6557	2195	4287	6482	SO:0001819	synonymous_variant	11187	exon12			TGACTTCCGGGCG	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.2352C>T	11.37:g.404317C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_007183	F8J390|Q53EX8	Silent	SNP	ENST00000331563.2	37	CCDS7695.1	956	0.43772893772893773	139	0.28252032520325204	201	0.5552486187845304	200	0.34965034965034963	416	0.5488126649076517	c	8.024	0.760279	0.15914	0.366515	0.559599	ENSG00000184363	ENST00000525642	.	.	.	4.28	3.36	0.38483	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50056	-0.8872	3	.	.	.	-26.8957	9.5666	0.39402	0.0:0.827:0.0:0.173	rs1134578;rs3088021;rs3196808;rs11545916;rs12420261;rs17348549;rs17844819;rs17857527;rs56710170;rs1134578	.	.	.	F	44	.	.	S	+	2	0	PKP3	394317	1.000000	0.71417	1.000000	0.80357	0.535000	0.34838	2.547000	0.45786	0.931000	0.37242	0.313000	0.20887	TCC	C|0.528;T|0.472	0.472	strong		0.667	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183	
TNIP1	10318	hgsc.bcm.edu	37	5	150410219	150410219	+	3'UTR	SNP	C	C	A	rs2233311	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150410219C>A	ENST00000389378.2	-	0	2554				TNIP1_ENST00000523338.1_Missense_Mutation_p.R631I|TNIP1_ENST00000522226.1_3'UTR|TNIP1_ENST00000518977.1_Missense_Mutation_p.R631I|TNIP1_ENST00000524280.1_3'UTR|TNIP1_ENST00000520931.1_3'UTR|TNIP1_ENST00000521591.1_3'UTR|TNIP1_ENST00000315050.7_3'UTR|TNIP1_ENST00000521423.1_5'Flank	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						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)			TCTTGGCAATCTGAGATCAGC	0.517													C|||	535	0.106829	0.0673	0.0634	5008	,	,		18524	0.1726		0.0944	False		,,,				2504	0.136				p.R631I		Atlas-SNP	.											.	TNIP1	51	.	0			c.G1892T						PASS	.	C		95,1289		3,89,600	68.0	63.0	65.0			4.8	1.0	5	dbSNP_98	65	372,2810		24,324,1243	no	utr-3	TNIP1	NM_006058.3		27,413,1843	AA,AC,CC		11.6908,6.8642,10.2278			150410219	467,4099	692	1591	2283	SO:0001624	3_prime_UTR_variant	10318	exon18			GGCAATCTGAGAT	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.*55G>T	5.37:g.150410219C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001252393	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	236	0.10805860805860806	51	0.10365853658536585	22	0.06077348066298342	87	0.1520979020979021	76	0.10026385224274406	C	12.73	2.025598	0.35701	0.068642	0.116908	ENSG00000145901	ENST00000523338;ENST00000518977	T;T	0.11821	2.74;2.74	5.62	4.75	0.60458	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999980101	P;P	0.35628	0.513;0.513	B;B	0.36989	0.238;0.181	T	0.20739	-1.0266	7	0.49607	T	0.09	.	12.5228	0.56069	0.0:0.8324:0.1676:0.0	rs2233311;rs60477588;rs2233311	521;631	A4F1X7;A4F1W9	.;.	I	631	ENSP00000428243:R631I;ENSP00000430971:R631I	ENSP00000430971:R631I	R	-	2	0	TNIP1	150390412	0.996000	0.38824	0.959000	0.39883	0.222000	0.24845	3.585000	0.53943	1.353000	0.45828	0.448000	0.29417	AGA	G|0.000;C|0.890;A|0.109	0.109	strong		0.517	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
PAPLN	89932	hgsc.bcm.edu	37	14	73735366	73735366	+	Missense_Mutation	SNP	C	C	T	rs4903104	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73735366C>T	ENST00000554301.1	+	25	3765	c.3602C>T	c.(3601-3603)aCg>aTg	p.T1201M	PAPLN_ENST00000427855.1_Missense_Mutation_p.T1201M|PAPLN_ENST00000555445.1_Missense_Mutation_p.T1185M|PAPLN_ENST00000381166.3_Intron|PAPLN_ENST00000340738.5_Missense_Mutation_p.T1174M			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	1201	Ig-like C2-type 3.		T -> M (in dbSNP:rs4903104). {ECO:0000269|PubMed:12975309}.			basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GGCTCCTACACGTGCAGTGCC	0.612													C|||	576	0.115016	0.0159	0.0937	5008	,	,		20430	0.1121		0.1909	False		,,,				2504	0.1892				p.T1174M		Atlas-SNP	.											.	PAPLN	180	.	0			c.C3521T						PASS	.	C	MET/THR	200,4206	125.3+/-162.5	8,184,2011	62.0	49.0	54.0		3521	5.0	1.0	14	dbSNP_111	54	1627,6973	300.4+/-304.9	147,1333,2820	yes	missense	PAPLN	NM_173462.3	81	155,1517,4831	TT,TC,CC		18.9186,4.5393,14.0474	probably-damaging	1174/1252	73735366	1827,11179	2203	4300	6503	SO:0001583	missense	89932	exon25			CCTACACGTGCAG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.3602C>T	14.37:g.73735366C>T	ENSP00000451803:p.Thr1201Met	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		262	0.11996336996336997	7	0.014227642276422764	42	0.11602209944751381	77	0.1346153846153846	136	0.17941952506596306	C	24.7	4.565487	0.86439	0.045393	0.189186	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.01	5.01	0.66863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00178	0.0005	M	0.80746	2.51	0.09310	P	1.0	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	T	0.00380	-1.1776	8	0.87932	D	0	.	18.5068	0.90900	0.0:1.0:0.0:0.0	rs4903104;rs17182258;rs52812969;rs59890020;rs4903104	1185;1201;400;1174	O95428-5;O95428;O95428-2;O95428-6	.;PPN_HUMAN;.;.	M	1174;1201;1201;1185	ENSP00000345395:T1174M;ENSP00000403403:T1201M;ENSP00000451803:T1201M;ENSP00000451729:T1185M	ENSP00000345395:T1174M	T	+	2	0	PAPLN	72805119	1.000000	0.71417	0.965000	0.40720	0.946000	0.59487	4.802000	0.62539	2.585000	0.87301	0.655000	0.94253	ACG	C|0.871;T|0.129	0.129	strong		0.612	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
SLFN14	342618	hgsc.bcm.edu	37	17	33876083	33876083	+	Silent	SNP	G	G	A	rs1001441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33876083G>A	ENST00000415846.3	-	4	1949	c.1914C>T	c.(1912-1914)acC>acT	p.T638T		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	638							ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						CTTGGCAGGTGGTTTGTTGGC	0.433													G|||	950	0.189696	0.2231	0.1902	5008	,	,		21612	0.2976		0.0954	False		,,,				2504	0.1299				p.T638T		Atlas-SNP	.											.	SLFN14	43	.	0			c.C1914T						PASS	.	G		291,1093		29,233,430	76.0	64.0	68.0		1914	-0.2	0.0	17	dbSNP_86	68	276,2906		11,254,1326	no	coding-synonymous	SLFN14	NM_001129820.1		40,487,1756	AA,AG,GG		8.6738,21.026,12.4179		638/913	33876083	567,3999	692	1591	2283	SO:0001819	synonymous_variant	342618	exon4			GCAGGTGGTTTGT		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.1914C>T	17.37:g.33876083G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_001129820	B2RTW9	Silent	SNP	ENST00000415846.3	37	CCDS45650.1																																																																																			G|0.790;A|0.210	0.210	strong		0.433	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
CACNA1H	8912	hgsc.bcm.edu	37	16	1256127	1256127	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1256127C>T	ENST00000348261.5	+	12	2875	c.2627C>T	c.(2626-2628)gCg>gTg	p.A876V	CACNA1H_ENST00000565831.1_Missense_Mutation_p.A876V|CACNA1H_ENST00000358590.4_Missense_Mutation_p.A876V|RP11-616M22.3_ENST00000564700.1_RNA	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	876					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)	GTGGGGCAGGCGGACGGTGGC	0.701																																					p.A876V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2627T						PASS	.																																			SO:0001583	missense	8912	exon12			GGCAGGCGGACGG	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.2627C>T	16.37:g.1256127C>T	ENSP00000334198:p.Ala876Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	12	0.244898	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607711	0.66558	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98419	-4.92;-4.92	3.96	3.96	0.45880	Ion transport (1);	0.416444	0.21210	N	0.078324	D	0.97782	0.9272	L	0.39467	1.215	0.37503	D	0.91685	D;D	0.69078	0.997;0.989	P;P	0.61658	0.892;0.805	D	0.99229	1.0881	10	0.46703	T	0.11	.	15.1886	0.73025	0.0:1.0:0.0:0.0	.	876;876	O95180-2;O95180	.;CAC1H_HUMAN	V	876	ENSP00000334198:A876V;ENSP00000351401:A876V	ENSP00000334198:A876V	A	+	2	0	CACNA1H	1196128	1.000000	0.71417	0.943000	0.38184	0.404000	0.30871	4.442000	0.59988	2.050000	0.60909	0.561000	0.74099	GCG	.	.	none		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ADRB2	154	hgsc.bcm.edu	37	5	148207447	148207447	+	Silent	SNP	G	G	C	rs1042719	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148207447G>C	ENST00000305988.4	+	1	1292	c.1053G>C	c.(1051-1053)ggG>ggC	p.G351G		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	351					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	AGGCCTATGGGAATGGCTACT	0.522													G|||	1874	0.374201	0.3533	0.3516	5008	,	,		18458	0.4772		0.2793	False		,,,				2504	0.41				p.G351G		Atlas-SNP	.											.	ADRB2	42	.	0			c.G1053C						PASS	.	G		1554,2852	486.7+/-360.7	281,992,930	55.0	57.0	56.0		1053	3.9	1.0	5	dbSNP_86	56	2468,6132	407.0+/-349.0	350,1768,2182	no	coding-synonymous	ADRB2	NM_000024.5		631,2760,3112	CC,CG,GG		28.6977,35.2701,30.9242		351/414	148207447	4022,8984	2203	4300	6503	SO:0001819	synonymous_variant	154	exon1			CTATGGGAATGGC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.1053G>C	5.37:g.148207447G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			G|0.668;C|0.332	0.332	strong		0.522	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
SEC16B	89866	hgsc.bcm.edu	37	1	177905469	177905469	+	Missense_Mutation	SNP	C	C	A	rs7522194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177905469C>A	ENST00000308284.6	-	20	2624	c.2535G>T	c.(2533-2535)caG>caT	p.Q845H	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	845			Q -> H (in dbSNP:rs7522194). {ECO:0000269|PubMed:17974005}.		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						CATCAGGAGGCTGGGAAGTTT	0.463													C|||	977	0.195088	0.1006	0.2349	5008	,	,		22653	0.1716		0.2624	False		,,,				2504	0.2495				p.Q845H		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2535T						PASS	.	C	HIS/GLN	487,3513		27,433,1540	143.0	138.0	140.0		2535	3.0	0.0	1	dbSNP_116	140	1944,6436		233,1478,2479	yes	missense	SEC16B	NM_033127.2	24	260,1911,4019	AA,AC,CC		23.1981,12.175,19.6365	possibly-damaging	845/1061	177905469	2431,9949	2000	4190	6190	SO:0001583	missense	89866	exon20			AGGAGGCTGGGAA	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.2535G>T	1.37:g.177905469C>A	ENSP00000308339:p.Gln845His	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	247	92	0.37247	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	440	0.20146520146520147	48	0.0975609756097561	84	0.23204419889502761	113	0.19755244755244755	195	0.25725593667546176	C	10.30	1.311719	0.23821	0.12175	0.231981	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.15139	2.45	4.88	2.97	0.34412	.	0.682824	0.14155	N	0.337745	T	0.00012	0.0000	M	0.67953	2.075	0.58432	P	1.999999999946489E-6	D;P;P;P	0.67145	0.996;0.93;0.93;0.93	P;P;P;P	0.56700	0.804;0.459;0.459;0.459	T	0.22382	-1.0218	9	0.11485	T	0.65	-1.0168	7.9554	0.30040	0.0:0.8101:0.0:0.1899	rs7522194;rs52799069;rs58699701;rs7522194	400;846;845;542	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	H	845;529;560	ENSP00000308339:Q845H	ENSP00000239472:Q560H	Q	-	3	2	AL359075.1	176172092	0.034000	0.19679	0.005000	0.12908	0.055000	0.15305	1.251000	0.32862	0.744000	0.32741	0.655000	0.94253	CAG	C|0.807;A|0.193	0.193	strong		0.463	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
OR51B2	79345	hgsc.bcm.edu	37	11	5345128	5345128	+	Missense_Mutation	SNP	G	G	A	rs10837814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5345128G>A	ENST00000328813.2	-	1	454	c.400C>T	c.(400-402)Ctc>Ttc	p.L134F	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2	134			L -> F (in dbSNP:rs10837814). {ECO:0000269|PubMed:10220430, ECO:0000269|PubMed:12213199}.			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)		GTATTGGTGAGAATGGAAGCA	0.413													G|||	2221	0.44349	0.3427	0.4582	5008	,	,		23625	0.3224		0.6074	False		,,,				2504	0.5256				p.L134F		Atlas-SNP	.											.	OR51B2	69	.	0			c.C400T						PASS	.	G	PHE/LEU	1624,2778	499.6+/-364.5	291,1042,868	103.0	97.0	99.0		400	3.3	0.4	11	dbSNP_120	99	5263,3331	644.1+/-400.0	1588,2087,622	yes	missense	OR51B2	NM_033180.4	22	1879,3129,1490	AA,AG,GG		38.7596,36.8923,47.0068	probably-damaging	134/313	5345128	6887,6109	2201	4297	6498	SO:0001583	missense	79345	exon1			TGGTGAGAATGGA	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.400C>T	11.37:g.5345128G>A	ENSP00000327540:p.Leu134Phe	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_033180	Q96RD4	Missense_Mutation	SNP	ENST00000328813.2	37	CCDS31377.1	986	0.45146520146520147	150	0.3048780487804878	180	0.4972375690607735	185	0.32342657342657344	471	0.6213720316622692	G	11.84	1.760017	0.31137	0.368923	0.612404	ENSG00000184881	ENST00000328813	T	0.23147	1.92	4.28	3.35	0.38373	GPCR, rhodopsin-like superfamily (1);	0.520005	0.14291	U	0.328903	T	0.00012	0.0000	M	0.88570	2.965	0.33813	P	0.371911	D	0.62365	0.991	D	0.63793	0.918	T	0.43829	-0.9367	9	0.72032	D	0.01	.	12.2225	0.54441	0.0:0.0:0.8281:0.1719	rs10837814;rs52818543;rs60930558;rs10837814	134	Q9Y5P1	O51B2_HUMAN	F	134	ENSP00000327540:L134F	ENSP00000327540:L134F	L	-	1	0	OR51B2	5301704	0.169000	0.23002	0.435000	0.26784	0.065000	0.16274	0.525000	0.22956	1.009000	0.39289	0.644000	0.83932	CTC	G|0.512;A|0.488	0.488	strong		0.413	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	NM_033180	
HHAT	55733	hgsc.bcm.edu	37	1	210577831	210577831	+	Silent	SNP	C	C	T	rs34772809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:210577831C>T	ENST00000367010.1	+	6	719	c.492C>T	c.(490-492)aaC>aaT	p.N164N	HHAT_ENST00000545154.1_Silent_p.N165N|HHAT_ENST00000413764.2_Silent_p.N164N|HHAT_ENST00000545781.1_Silent_p.N101N|HHAT_ENST00000537898.1_Silent_p.N99N|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000261458.3_Silent_p.N164N|HHAT_ENST00000391905.3_Silent_p.N164N|HHAT_ENST00000308852.6_Silent_p.N119N	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	164					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)			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)		AGACAGAAAACGAGTACTACC	0.552													c|||	406	0.0810703	0.0348	0.111	5008	,	,		19835	0.002		0.1789	False		,,,				2504	0.1033				p.N165N		Atlas-SNP	.											.	HHAT	66	.	0			c.C495T						PASS	.	T	,,,,,	240,4166	140.0+/-175.5	6,228,1969	98.0	78.0	85.0		492,,492,495,297,492	-3.7	0.0	1	dbSNP_126	85	1599,7001	296.6+/-303.0	161,1277,2862	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HHAT	NM_001122834.2,NM_001170564.1,NM_001170580.1,NM_001170587.1,NM_001170588.1,NM_018194.4	,,,,,	167,1505,4831	TT,TC,CC		18.593,5.4471,14.1396	,,,,,	164/494,,164/494,165/495,99/429,164/494	210577831	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	55733	exon5			AGAAAACGAGTAC	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.492C>T	1.37:g.210577831C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Silent	SNP	ENST00000367010.1	37	CCDS1495.1																																																																																			C|0.875;T|0.125	0.125	strong		0.552	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
MEGF10	84466	hgsc.bcm.edu	37	5	126792974	126792974	+	Silent	SNP	T	T	A	rs3812052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:126792974T>A	ENST00000274473.6	+	26	3654	c.3387T>A	c.(3385-3387)ggT>ggA	p.G1129G	MEGF10_ENST00000503335.2_Silent_p.G1129G	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	1129	Necessary for formation of large intracellular vacuoles.|Ser-rich.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGGACAGTGGTGGTagcagca	0.517													C|||	1893	0.377995	0.1604	0.4712	5008	,	,		19136	0.3026		0.6372	False		,,,				2504	0.4172				p.G1129G		Atlas-SNP	.											.	MEGF10	152	.	0			c.T3387A						PASS	.	C		1060,3346		137,786,1280	95.0	79.0	84.0		3387	2.8	0.9	5	dbSNP_107	84	5357,3243		1657,2043,600	no	coding-synonymous	MEGF10	NM_032446.2		1794,2829,1880	AA,AT,TT		37.7093,24.0581,49.3388		1129/1141	126792974	6417,6589	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon26			CAGTGGTGGTAGC	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3387T>A	5.37:g.126792974T>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			T|0.531;A|0.469	0.469	strong		0.517	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
RNF213	57674	hgsc.bcm.edu	37	17	78319963	78319963	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78319963A>G	ENST00000582970.1	+	29	7971	c.7828A>G	c.(7828-7830)Aac>Gac	p.N2610D	RNF213_ENST00000508628.2_Missense_Mutation_p.N2659D|RNF213_ENST00000336301.6_Missense_Mutation_p.N683D	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2610					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)			CCTAGATGAAAACGGGACTCG	0.522																																					p.N2610D		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,-2,2	RNF213	766	2	0			c.A7828G						scavenged	.						82.0	84.0	83.0					17																	78319963		2203	4300	6503	SO:0001583	missense	57674	exon29			GATGAAAACGGGA	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.7828A>G	17.37:g.78319963A>G	ENSP00000464087:p.Asn2610Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	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	.	.	.	.	.	.	.	.	.	.	A	3.700	-0.061829	0.07317	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.37584	1.19	5.77	-6.91	0.01649	.	2.549210	0.01121	N	0.005794	T	0.17959	0.0431	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27226	-1.0080	10	0.09084	T	0.74	.	10.3049	0.43674	0.6391:0.1114:0.2495:0.0	.	683	Q63HN8	RN213_HUMAN	D	2610;2659;683	ENSP00000338218:N683D	ENSP00000338218:N683D	N	+	1	0	RNF213	75934558	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.331000	0.01110	-0.935000	0.03728	-0.408000	0.06270	AAC	.	.	none		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568687	33568687	+	Silent	SNP	T	T	A	rs7032174	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	57	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	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	
DFNB31	25861	hgsc.bcm.edu	37	9	117166246	117166246	+	Missense_Mutation	SNP	A	A	G	rs2274159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	47	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	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	
MON2	23041	hgsc.bcm.edu	37	12	62959137	62959137	+	Missense_Mutation	SNP	A	A	G	rs11174549	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:62959137A>G	ENST00000393632.2	+	27	4544	c.4153A>G	c.(4153-4155)Att>Gtt	p.I1385V	MON2_ENST00000552738.1_Missense_Mutation_p.I1362V|MON2_ENST00000393630.3_Missense_Mutation_p.I1386V|MON2_ENST00000280379.6_Missense_Mutation_p.I1386V|MON2_ENST00000546600.1_Missense_Mutation_p.I1385V|MON2_ENST00000393629.2_Missense_Mutation_p.I1385V	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1385					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AACAAAGCACATTGCAAATGC	0.323													A|||	291	0.058107	0.0386	0.0476	5008	,	,		17704	0.0585		0.1183	False		,,,				2504	0.0297				p.I1385V		Atlas-SNP	.											.	MON2	160	.	0			c.A4153G						PASS	.	A	VAL/ILE	239,4167	138.8+/-174.5	5,229,1969	111.0	110.0	110.0		4153	5.8	1.0	12	dbSNP_120	110	953,7647	209.8+/-250.9	59,835,3406	yes	missense	MON2	NM_015026.2	29	64,1064,5375	GG,GA,AA		11.0814,5.4244,9.165	benign	1385/1718	62959137	1192,11814	2203	4300	6503	SO:0001583	missense	23041	exon27			AAGCACATTGCAA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4153A>G	12.37:g.62959137A>G	ENSP00000377252:p.Ile1385Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	170	0.07783882783882784	19	0.03861788617886179	19	0.052486187845303865	37	0.06468531468531469	95	0.12532981530343007	A	11.89	1.774762	0.31411	0.054244	0.110814	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.55052	0.55;0.54;0.55;0.55;0.58;0.57	5.76	5.76	0.90799	.	0.058459	0.64402	D	0.000001	T	0.00300	0.0009	N	0.03608	-0.345	0.18873	P	0.9999817629	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.002;0.004;0.004;0.001	T	0.07009	-1.0795	8	.	.	.	-21.6838	16.3695	0.83350	1.0:0.0:0.0:0.0	rs11174549;rs56625845;rs57809371;rs11174549	1385;1362;1385;260;1385	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	V	1385;1386;1386;1385;1362;1385	ENSP00000377252:I1385V;ENSP00000377250:I1386V;ENSP00000280379:I1386V;ENSP00000447407:I1385V;ENSP00000449215:I1362V;ENSP00000377249:I1385V	.	I	+	1	0	MON2	61245404	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.131000	0.71670	2.315000	0.78130	0.533000	0.62120	ATT	A|0.924;G|0.076	0.076	strong		0.323	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
LAMA4	3910	hgsc.bcm.edu	37	6	112480041	112480041	+	Silent	SNP	A	A	G	rs3752577	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:112480041A>G	ENST00000230538.7	-	14	2107	c.1710T>C	c.(1708-1710)agT>agC	p.S570S	LAMA4_ENST00000522006.1_Silent_p.S563S|RP1-142L7.5_ENST00000425503.1_RNA|LAMA4_ENST00000389463.4_Silent_p.S563S|RP1-142L7.5_ENST00000585373.1_RNA|LAMA4_ENST00000424408.2_Silent_p.S563S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	570	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CTTGTAGTTCACTTTTGGCTC	0.323													A|||	457	0.091254	0.028	0.1225	5008	,	,		17123	0.13		0.1034	False		,,,				2504	0.1022				p.S570S		Atlas-SNP	.											.	LAMA4	227	.	0			c.T1710C						PASS	.	A	,,	195,4211	122.5+/-159.9	5,185,2013	192.0	168.0	176.0		1710,1689,1689	-0.3	0.9	6	dbSNP_107	176	758,7842	181.9+/-230.5	35,688,3577	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	40,873,5590	GG,GA,AA		8.814,4.4258,7.3274	,,	570/1824,563/1817,563/1817	112480041	953,12053	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon14			TAGTTCACTTTTG		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.1710T>C	6.37:g.112480041A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			A|0.915;G|0.085	0.085	strong		0.323	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
PRTG	283659	hgsc.bcm.edu	37	15	55912875	55912875	+	Missense_Mutation	SNP	T	T	A	rs1438914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	103	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	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	
TNRC18	84629	hgsc.bcm.edu	37	7	5396866	5396866	+	Missense_Mutation	SNP	C	C	G	rs200950320		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5396866C>G	ENST00000430969.1	-	16	5223	c.4875G>C	c.(4873-4875)caG>caC	p.Q1625H	TNRC18_ENST00000399537.4_Missense_Mutation_p.Q1625H	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1625							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGCTTGCCAACTGCTCCTGGT	0.498																																					p.Q1625H		Atlas-SNP	.											.	TNRC18	311	.	0			c.G4875C						PASS	.	C	HIS/GLN	0,4034		0,0,2017	48.0	48.0	48.0		4875	3.4	0.9	7		48	1,8387		0,1,4193	yes	missense	TNRC18	NM_001080495.2	24	0,1,6210	GG,GC,CC		0.0119,0.0,0.0081	probably-damaging	1625/2969	5396866	1,12421	2017	4194	6211	SO:0001583	missense	84629	exon16			TGCCAACTGCTCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4875G>C	7.37:g.5396866C>G	ENSP00000395538:p.Gln1625His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	124	47	0.379032	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	c	11.99	1.803262	0.31869	0.0	1.19E-4	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.55052	2.34;2.4;0.54	5.25	3.37	0.38596	.	0.000000	0.37483	N	0.002071	T	0.61123	0.2322	L	0.47016	1.485	0.39858	D	0.973332	D;D	0.71674	0.997;0.998	D;D	0.79784	0.993;0.956	T	0.61441	-0.7062	10	0.66056	D	0.02	.	7.4435	0.27198	0.0:0.7123:0.0:0.2877	.	680;1625	A8MSW5;O15417	.;TNC18_HUMAN	H	1625;1625;680;115	ENSP00000382452:Q1625H;ENSP00000395538:Q1625H;ENSP00000395990:Q115H	ENSP00000382452:Q1625H	Q	-	3	2	TNRC18	5363392	0.999000	0.42202	0.878000	0.34440	0.983000	0.72400	1.017000	0.29989	0.550000	0.28991	0.561000	0.74099	CAG	.	.	weak		0.498	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
USH2A	7399	hgsc.bcm.edu	37	1	215848935	215848935	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:215848935C>T	ENST00000307340.3	-	63	12704	c.12318G>A	c.(12316-12318)ggG>ggA	p.G4106G	USH2A_ENST00000366943.2_Silent_p.G4106G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4106	Fibronectin type-III 26. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|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)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTCCAGGAACCCGTCACTGA	0.473										HNSCC(13;0.011)																											p.G4106G		Atlas-SNP	.											USH2A,NS,carcinoma,-2,1	USH2A	1168	1	0			c.G12318A						scavenged	.						68.0	65.0	66.0					1																	215848935		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			CAGGAACCCGTCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.12318G>A	1.37:g.215848935C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			.	.	none		0.473	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SNAP47	116841	hgsc.bcm.edu	37	1	227935444	227935444	+	Missense_Mutation	SNP	A	A	G	rs2236359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:227935444A>G	ENST00000366759.4	+	2	556	c.142A>G	c.(142-144)Agg>Ggg	p.R48G	SNAP47-AS1_ENST00000413347.2_RNA|SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_Missense_Mutation_p.R48G	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	48			R -> G (in dbSNP:rs2236359).		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						ACAGATGAGCAGGGATGTCTG	0.572													A|||	2100	0.419329	0.4826	0.4928	5008	,	,		20212	0.3651		0.3996	False		,,,				2504	0.3579				p.R48G		Atlas-SNP	.											.	SNAP47	42	.	0			c.A142G						PASS	.	A	GLY/ARG	1937,2469	549.3+/-377.7	427,1083,693	83.0	67.0	72.0		142	1.7	0.6	1	dbSNP_98	72	3550,5050	515.5+/-378.6	722,2106,1472	yes	missense	SNAP47	NM_053052.3	125	1149,3189,2165	GG,GA,AA		41.2791,43.9628,42.1882	benign	48/465	227935444	5487,7519	2203	4300	6503	SO:0001583	missense	116841	exon2			ATGAGCAGGGATG	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.142A>G	1.37:g.227935444A>G	ENSP00000355721:p.Arg48Gly	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	219	112	0.511416	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	918|918	0.42032967032967034|0.42032967032967034	231|231	0.4695121951219512|0.4695121951219512	168|168	0.46408839779005523|0.46408839779005523	214|214	0.3741258741258741|0.3741258741258741	305|305	0.4023746701846966|0.4023746701846966	A|A	6.376|6.376	0.437453|0.437453	0.12104|0.12104	0.439628|0.439628	0.412791|0.412791	ENSG00000143740|ENSG00000143740	ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.16897	.|2.31;2.31	4.08|4.08	1.67|1.67	0.24075|0.24075	.|.	.|0.767945	.|0.12787	.|N	.|0.439145	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.40237|0.40237	P|P	0.022087999999999997|0.022087999999999997	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.06405	.|0.002;0.002	T|T	0.44390|0.44390	-0.9331|-0.9331	4|9	.|0.35671	.|T	.|0.21	-14.59|-14.59	4.557|4.557	0.12141|0.12141	0.7309:0.0:0.0991:0.17|0.7309:0.0:0.0991:0.17	rs2236359;rs3183672;rs17555295;rs52818129;rs61005345;rs2236359|rs2236359;rs3183672;rs17555295;rs52818129;rs61005345;rs2236359	.|48;48	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	R|G	39|48	.|ENSP00000355721:R48G;ENSP00000314157:R48G	.|ENSP00000314157:R48G	Q|R	+|+	2|1	0|2	SNAP47|SNAP47	226002067|226002067	1.000000|1.000000	0.71417|0.71417	0.568000|0.568000	0.28447|0.28447	0.240000|0.240000	0.25518|0.25518	2.485000|2.485000	0.45250|0.45250	0.139000|0.139000	0.18822|0.18822	0.482000|0.482000	0.46254|0.46254	CAG|AGG	A|0.578;G|0.422	0.422	strong		0.572	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462787	21462787	+	Silent	SNP	G	G	A	rs427233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:21462787G>A	ENST00000281523.2	-	8	1625	c.1107C>T	c.(1105-1107)tcC>tcT	p.S369S		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	369						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						GAGGAAGCGCGGAAGTCTGGA	0.562													A|||	4586	0.915735	0.9818	0.9352	5008	,	,		10685	0.999		0.8141	False		,,,				2504	0.8313				p.S369S		Atlas-SNP	.											.	ZNF385D	93	.	0			c.C1107T						PASS	.	A		4207,199	125.3+/-162.5	2008,191,4	60.0	58.0	59.0		1107	-11.7	0.1	3	dbSNP_80	59	7142,1458	277.9+/-293.1	2965,1212,123	no	coding-synonymous	ZNF385D	NM_024697.2		4973,1403,127	AA,AG,GG		16.9535,4.5166,12.7403		369/396	21462787	11349,1657	2203	4300	6503	SO:0001819	synonymous_variant	79750	exon8			AAGCGCGGAAGTC	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.1107C>T	3.37:g.21462787G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_024697		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																			G|0.116;A|0.884	0.884	strong		0.562	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
BST1	683	hgsc.bcm.edu	37	4	15713446	15713446	+	Silent	SNP	C	C	T	rs2302463	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15713446C>T	ENST00000265016.4	+	4	663	c.468C>T	c.(466-468)tcC>tcT	p.S156S	BST1_ENST00000382346.3_Silent_p.S171S	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	156					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.S156S(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						ATTACCAATCCTGCCCTACAT	0.393													C|||	420	0.0838658	0.0703	0.0288	5008	,	,		21378	0.1895		0.0199	False		,,,				2504	0.0982				p.S156S		Atlas-SNP	.											BST1,NS,carcinoma,0,1	BST1	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C468T						PASS	.	C		358,4048	183.3+/-210.9	12,334,1857	144.0	139.0	141.0		468	1.9	1.0	4	dbSNP_100	141	233,8367	95.4+/-157.2	1,231,4068	no	coding-synonymous	BST1	NM_004334.2		13,565,5925	TT,TC,CC		2.7093,8.1253,4.5441		156/319	15713446	591,12415	2203	4300	6503	SO:0001819	synonymous_variant	683	exon4			CCAATCCTGCCCT	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.468C>T	4.37:g.15713446C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Silent	SNP	ENST00000265016.4	37	CCDS3416.1	165	0.07554945054945054	27	0.054878048780487805	12	0.03314917127071823	111	0.19405594405594406	15	0.01978891820580475	C	5.214	0.224934	0.09916	0.081253	0.027093	ENSG00000109743	ENST00000505785	.	.	.	5.64	1.87	0.25490	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999761068	.	.	.	.	.	.	T	0.17198	-1.0377	3	.	.	.	-19.4162	2.0425	0.03553	0.1628:0.5085:0.1575:0.1713	rs2302463;rs11548108;rs2302463	.	.	.	L	52	.	.	P	+	2	0	BST1	15322544	0.998000	0.40836	0.963000	0.40424	0.492000	0.33523	0.227000	0.17795	0.278000	0.22164	-0.126000	0.14955	CCT	C|0.946;T|0.054	0.054	strong		0.393	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
SUPT5H	6829	hgsc.bcm.edu	37	19	39955533	39955533	+	Silent	SNP	G	G	A	rs2304217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39955533G>A	ENST00000599117.1	+	12	1087	c.720G>A	c.(718-720)gaG>gaA	p.E240E	SUPT5H_ENST00000359191.6_Silent_p.E236E|SUPT5H_ENST00000598725.1_Silent_p.E240E|SUPT5H_ENST00000432763.2_Silent_p.E240E|SUPT5H_ENST00000402194.2_Silent_p.E236E			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	240	Interaction with SUPT4H1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGCCATTGAGGGGGTGGGCA	0.577													G|||	687	0.137181	0.1619	0.1254	5008	,	,		17964	0.1111		0.171	False		,,,				2504	0.1043				p.E240E		Atlas-SNP	.											.	SUPT5H	119	.	0			c.G720A						PASS	.	G	,,,	715,3691	295.9+/-283.9	59,597,1547	97.0	83.0	88.0		720,720,708,720	2.3	1.0	19	dbSNP_100	88	1462,7138	278.2+/-293.3	130,1202,2968	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SUPT5H	NM_001111020.2,NM_001130824.1,NM_001130825.1,NM_003169.3	,,,	189,1799,4515	AA,AG,GG		17.0,16.2279,16.7384	,,,	240/1088,240/1088,236/1084,240/1088	39955533	2177,10829	2203	4300	6503	SO:0001819	synonymous_variant	6829	exon10			CATTGAGGGGGTG	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.720G>A	19.37:g.39955533G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_003169	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																			G|0.846;A|0.154	0.154	strong		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
TEX14	56155	hgsc.bcm.edu	37	17	56676368	56676368	+	Missense_Mutation	SNP	T	T	C	rs389389	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56676368T>C	ENST00000240361.8	-	14	2441	c.2356A>G	c.(2356-2358)Aat>Gat	p.N786D	TEX14_ENST00000349033.5_Missense_Mutation_p.N780D|TEX14_ENST00000389934.3_Missense_Mutation_p.N780D			Q8IWB6	TEX14_HUMAN	testis expressed 14	786					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGTAGGCATTTGTAAACTCT	0.473													T|||	449	0.0896565	0.0356	0.1282	5008	,	,		20816	0.0		0.2286	False		,,,				2504	0.0849				p.N786D		Atlas-SNP	.											.	TEX14	343	.	0			c.A2356G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	250,4156	144.2+/-179.2	10,230,1963	154.0	142.0	146.0		2356,2338,2338	-3.6	0.0	17	dbSNP_80	146	1851,6749	332.9+/-320.3	195,1461,2644	yes	missense,missense,missense	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	23,23,23	205,1691,4607	CC,CT,TT		21.5233,5.6741,16.1541	benign,benign,benign	786/1498,780/1452,780/1492	56676368	2101,10905	2203	4300	6503	SO:0001583	missense	56155	exon14			AGGCATTTGTAAA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2356A>G	17.37:g.56676368T>C	ENSP00000240361:p.Asn786Asp	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	147	80	0.544218	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	240	0.10989010989010989	22	0.044715447154471545	57	0.1574585635359116	0	0.0	161	0.21240105540897097	T	8.000	0.755293	0.15846	0.056741	0.215233	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78246	-1.16;-1.16;-1.13	5.63	-3.63	0.04529	.	0.669699	0.15016	N	0.285245	T	0.00073	0.0002	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.003	T	0.04481	-1.0948	9	0.26408	T	0.33	-1.4549	7.0204	0.24910	0.0:0.3313:0.2115:0.4572	rs389389;rs389389	786;780;780	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	D	786;780;780	ENSP00000240361:N786D;ENSP00000374584:N780D;ENSP00000268910:N780D	ENSP00000240361:N786D	N	-	1	0	TEX14	54031367	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.600000	0.05693	-1.256000	0.02478	-1.139000	0.01908	AAT	T|0.866;C|0.134	0.134	strong		0.473	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
KIAA1549	57670	hgsc.bcm.edu	37	7	138603282	138603282	+	Missense_Mutation	SNP	T	T	C	rs59985563	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:138603282T>C	ENST00000422774.1	-	2	1138	c.1090A>G	c.(1090-1092)Act>Gct	p.T364A	KIAA1549_ENST00000242365.4_Missense_Mutation_p.T314A|KIAA1549_ENST00000440172.1_Missense_Mutation_p.T364A			Q9HCM3	K1549_HUMAN	KIAA1549	364						integral component of membrane (GO:0016021)		p.T364A(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GCAAGAGGAGTTGAAAGCAAT	0.478			O	BRAF	pilocytic astrocytoma																																p.T364A	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,colon,carcinoma,0,3	KIAA1549	314	3	1	Substitution - Missense(1)	stomach(1)	c.A1090G						PASS	.	T	ALA/THR,ALA/THR	2043,2269		496,1051,609	167.0	178.0	174.0		1090,1090	-2.7	0.0	7	dbSNP_129	174	1555,6951		151,1253,2849	yes	missense,missense	KIAA1549	NM_001164665.1,NM_020910.2	58,58	647,2304,3458	CC,CT,TT		18.2812,47.3794,28.0699	benign,benign	364/1951,364/1935	138603282	3598,9220	2156	4253	6409	SO:0001583	missense	57670	exon2			GAGGAGTTGAAAG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1090A>G	7.37:g.138603282T>C	ENSP00000416040:p.Thr364Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	546	0.25	269	0.5467479674796748	58	0.16022099447513813	79	0.1381118881118881	140	0.18469656992084432	T	10.23	1.292535	0.23564	0.473794	0.182812	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.24151	1.87;1.88;1.88	4.84	-2.67	0.06059	.	0.915639	0.09251	N	0.827865	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.11235	0.002;0.004	B;B	0.11329	0.003;0.006	T	0.47995	-0.9073	9	0.13853	T	0.58	.	3.9485	0.09358	0.2749:0.2382:0.0:0.4869	rs59985563;rs61995725	364;364	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	A	364;314;364	ENSP00000406661:T364A;ENSP00000242365:T314A;ENSP00000416040:T364A	ENSP00000242365:T314A	T	-	1	0	KIAA1549	138253822	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.444000	0.02403	-0.209000	0.10156	0.528000	0.53228	ACT	T|0.760;C|0.240	0.240	strong		0.478	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
SURF6	6838	hgsc.bcm.edu	37	9	136199503	136199503	+	Missense_Mutation	SNP	G	G	A	rs886090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136199503G>A	ENST00000372022.4	-	4	752	c.487C>T	c.(487-489)Cgg>Tgg	p.R163W	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	163			R -> W (in dbSNP:rs886090).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		TCTTTCGCCCGCAGCTCCTTT	0.687													G|||	1417	0.282947	0.0386	0.3501	5008	,	,		15157	0.3075		0.3569	False		,,,				2504	0.4642				p.R163W		Atlas-SNP	.											.	SURF6	32	.	0			c.C487T						PASS	.	G	TRP/ARG	372,4034	184.3+/-211.7	20,332,1851	106.0	109.0	108.0		487	1.0	0.1	9	dbSNP_86	108	3018,5582	457.2+/-364.3	543,1932,1825	yes	missense	SURF6	NM_006753.4	101	563,2264,3676	AA,AG,GG		35.093,8.443,26.0649	probably-damaging	163/362	136199503	3390,9616	2203	4300	6503	SO:0001583	missense	6838	exon4			TCGCCCGCAGCTC	AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.487C>T	9.37:g.136199503G>A	ENSP00000361092:p.Arg163Trp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_006753	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	590	0.27014652014652013	31	0.06300813008130081	122	0.3370165745856354	160	0.27972027972027974	277	0.3654353562005277	G	10.01	1.233467	0.22626	0.08443	0.35093	ENSG00000148296	ENST00000372022	T	0.15718	2.4	4.42	1.02	0.19986	.	0.655439	0.14812	N	0.296982	T	0.00012	0.0000	L	0.56769	1.78	0.46149	P	0.0011010000000000186	D	0.76494	0.999	D	0.63033	0.91	T	0.42241	-0.9463	9	0.66056	D	0.02	-1.4527	6.6473	0.22943	0.1205:0.0:0.4417:0.4377	rs886090;rs17293245;rs58674881;rs886090	163	O75683	SURF6_HUMAN	W	163	ENSP00000361092:R163W	ENSP00000361092:R163W	R	-	1	2	SURF6	135189324	0.028000	0.19301	0.112000	0.21494	0.571000	0.35966	0.524000	0.22940	0.029000	0.15352	0.467000	0.42956	CGG	G|0.745;A|0.255	0.255	strong		0.687	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
PLCE1	51196	hgsc.bcm.edu	37	10	96076495	96076495	+	Silent	SNP	C	C	G	rs942676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:96076495C>G	ENST00000371380.3	+	28	6559	c.6324C>G	c.(6322-6324)gtC>gtG	p.V2108V	NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371375.1_Silent_p.V1800V|PLCE1_ENST00000260766.3_Silent_p.V2108V|RP11-76P2.4_ENST00000609123.1_RNA|PLCE1_ENST00000371385.3_Silent_p.V1800V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2108	Ras-associating 1. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GCAGGATTGTCTTAAAAACCC	0.453													C|||	436	0.0870607	0.0053	0.1873	5008	,	,		15639	0.003		0.1571	False		,,,				2504	0.1411				p.V2108V		Atlas-SNP	.											.	PLCE1	543	.	0			c.C6324G						PASS	.	C	,	108,3688		3,102,1793	71.0	72.0	71.0		5400,6324	2.3	1.0	10	dbSNP_86	71	1319,6897		108,1103,2897	no	coding-synonymous,coding-synonymous	PLCE1	NM_001165979.1,NM_016341.3	,	111,1205,4690	GG,GC,CC		16.054,2.8451,11.8798	,	1800/1995,2108/2303	96076495	1427,10585	1898	4108	6006	SO:0001819	synonymous_variant	51196	exon29			GATTGTCTTAAAA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6324C>G	10.37:g.96076495C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			C|0.924;G|0.076	0.076	strong		0.453	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
SI	6476	hgsc.bcm.edu	37	3	164773057	164773057	+	Silent	SNP	G	G	A	rs9290257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	65	45	0.692308	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	
SCEL	8796	hgsc.bcm.edu	37	13	78216915	78216915	+	Silent	SNP	C	C	T	rs2813739	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:78216915C>T	ENST00000349847.3	+	32	2106	c.2022C>T	c.(2020-2022)caC>caT	p.H674H	SCEL_ENST00000377246.3_Silent_p.H654H|SCEL_ENST00000535157.1_Silent_p.H632H	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	674	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AGACAATACACTGTGAACCTT	0.318													C|||	755	0.150759	0.1626	0.1556	5008	,	,		16708	0.1409		0.1252	False		,,,				2504	0.1677				p.H674H		Atlas-SNP	.											.	SCEL	85	.	0			c.C2022T						PASS	.	C	,,	750,3656	304.4+/-288.4	65,620,1518	106.0	106.0	106.0		1896,1962,2022	1.9	1.0	13	dbSNP_100	106	1240,7356	246.5+/-274.9	104,1032,3162	no	coding-synonymous,coding-synonymous,coding-synonymous	SCEL	NM_001160706.1,NM_003843.3,NM_144777.2	,,	169,1652,4680	TT,TC,CC		14.4253,17.0222,15.3053	,,	632/647,654/669,674/689	78216915	1990,11012	2203	4298	6501	SO:0001819	synonymous_variant	8796	exon32			AATACACTGTGAA	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.2022C>T	13.37:g.78216915C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Silent	SNP	ENST00000349847.3	37	CCDS9459.1																																																																																			C|0.851;T|0.149	0.149	strong		0.318	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
DNAH10	196385	hgsc.bcm.edu	37	12	124274474	124274474	+	Splice_Site	SNP	A	A	G	rs10846559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124274474A>G	ENST00000409039.3	+	11	1463	c.1438A>G	c.(1438-1440)Att>Gtt	p.I480V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	480	Stem. {ECO:0000250}.		I -> V (in dbSNP:rs10846559). {ECO:0000269|PubMed:14702039}.		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GATTGGACAGATTTTGGAGGA	0.443													G|||	4196	0.837859	0.8775	0.7738	5008	,	,		18865	0.998		0.7127	False		,,,				2504	0.7935				p.I480V		Atlas-SNP	.											.	DNAH10	888	.	0			c.A1438G						PASS	.	G	VAL/ILE	3743,663	281.1+/-275.7	1587,569,47	71.0	75.0	74.0		1438	5.2	1.0	12	dbSNP_120	74	5759,2841	447.5+/-361.5	1955,1849,496	yes	missense-near-splice	DNAH10	NM_207437.3	29	3542,2418,543	GG,GA,AA		33.0349,15.0477,26.9414	benign	480/4472	124274474	9502,3504	2203	4300	6503	SO:0001630	splice_region_variant	196385	exon11			GGACAGATTTTGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1438-1A>G	12.37:g.124274474A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	1809	0.8282967032967034	421	0.8556910569105691	283	0.7817679558011049	571	0.9982517482517482	534	0.7044854881266491	G	0.183	-1.060517	0.01950	0.849523	0.669651	ENSG00000197653	ENST00000409039	T	0.55052	0.54	5.2	5.2	0.72013	Dynein heavy chain, domain-1 (1);	0.410436	0.20194	N	0.097259	T	0.00012	0.0000	N	0.00185	-1.9	0.50313	P	1.3900000000000023E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	8	.	.	.	.	12.3487	0.55136	0.079:0.0:0.921:0.0	rs10846559;rs58161138;rs10846559	480	Q8IVF4	DYH10_HUMAN	V	480	ENSP00000386770:I480V	.	I	+	1	0	DNAH10	122840427	1.000000	0.71417	0.973000	0.42090	0.431000	0.31685	3.354000	0.52254	1.222000	0.43521	-0.222000	0.12452	ATT	A|0.235;G|0.765	0.765	strong		0.443	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation
TEK	7010	hgsc.bcm.edu	37	9	27205021	27205021	+	Silent	SNP	G	G	A	rs542913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	155	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	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		
SSC5D	284297	hgsc.bcm.edu	37	19	56029621	56029621	+	Silent	SNP	A	A	C	rs202012508		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56029621A>C	ENST00000389623.6	+	14	4001	c.3978A>C	c.(3976-3978)acA>acC	p.T1326T		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1326	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						ctcaccccACAACTCCTGACC	0.597																																					p.T1326T		Atlas-SNP	.											.	SSC5D	65	.	0			c.A3978C						PASS	.						332.0	320.0	323.0					19																	56029621		692	1591	2283	SO:0001819	synonymous_variant	284297	exon14			CCCCACAACTCCT		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.3978A>C	19.37:g.56029621A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	6	0.09375	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			.	.	weak		0.597	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
FLNB	2317	hgsc.bcm.edu	37	3	58109162	58109162	+	Missense_Mutation	SNP	G	G	A	rs1131356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58109162G>A	ENST00000295956.4	+	21	3634	c.3469G>A	c.(3469-3471)Gac>Aac	p.D1157N	FLNB_ENST00000490882.1_Missense_Mutation_p.D1157N|FLNB_ENST00000429972.2_Missense_Mutation_p.D1157N|FLNB_ENST00000493452.1_Missense_Mutation_p.D988N|FLNB_ENST00000419752.2_Missense_Mutation_p.D988N|FLNB_ENST00000358537.3_Missense_Mutation_p.D1157N|FLNB_ENST00000357272.4_Missense_Mutation_p.D1157N|FLNB_ENST00000348383.5_Missense_Mutation_p.D1157N	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1157	Interaction with FBLP1.		D -> N (in dbSNP:rs1131356). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		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)		CCTTAGCGTCGACTGCTCGGA	0.582													G|||	2735	0.546126	0.4758	0.4726	5008	,	,		16378	0.9187		0.2803	False		,,,				2504	0.5828				p.D1157N		Atlas-SNP	.											.	FLNB	430	.	0			c.G3469A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1813,2593	529.0+/-372.6	370,1073,760	64.0	72.0	69.0		3469,3469,3469,3469	5.1	0.9	3	dbSNP_86	69	2097,6503	360.6+/-332.0	263,1571,2466	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	23,23,23,23	633,2644,3226	AA,AG,GG		24.3837,41.1484,30.063	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1157/2634,1157/2592,1157/2579,1157/2603	58109162	3910,9096	2203	4300	6503	SO:0001583	missense	2317	exon21			AGCGTCGACTGCT	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.3469G>A	3.37:g.58109162G>A	ENSP00000295956:p.Asp1157Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	81	23	0.283951	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1105	0.5059523809523809	232	0.4715447154471545	145	0.4005524861878453	521	0.9108391608391608	207	0.27308707124010556	G	18.92	3.725331	0.68959	0.411484	0.243837	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.95	5.08	0.68730	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	0.9999999382633	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.987;1.0;1.0	D;D;D;P;D;D	0.91635	0.985;0.918;0.998;0.863;0.999;0.999	T	0.39251	-0.9623	9	0.54805	T	0.06	.	15.2231	0.73330	0.0672:0.0:0.9328:0.0	rs1131356;rs17058842;rs56425027;rs58310728;rs1131356	1157;1157;988;988;1157;1157	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	N	1157;1157;1157;1157;1157;1157;988;988	ENSP00000295956:D1157N;ENSP00000420213:D1157N;ENSP00000351339:D1157N;ENSP00000415599:D1157N;ENSP00000232447:D1157N;ENSP00000349819:D1157N;ENSP00000418510:D988N;ENSP00000414532:D988N	ENSP00000295956:D1157N	D	+	1	0	FLNB	58084202	1.000000	0.71417	0.888000	0.34837	0.016000	0.09150	9.869000	0.99810	1.537000	0.49254	0.563000	0.77884	GAC	G|0.596;A|0.404	0.404	strong		0.582	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
DTX2	113878	hgsc.bcm.edu	37	7	76131644	76131644	+	Silent	SNP	C	C	T	rs141587206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:76131644C>T	ENST00000324432.5	+	9	1770	c.1260C>T	c.(1258-1260)tcC>tcT	p.S420S	DTX2_ENST00000446600.1_Silent_p.S329S|DTX2_ENST00000430490.2_Silent_p.S420S|DTX2_ENST00000307569.8_Silent_p.S373S|DTX2_ENST00000446820.2_Silent_p.S373S|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	107	0	0		WXS	Illumina HiSeq	Phase_I	133	5	0.037594	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		
ZNF318	24149	hgsc.bcm.edu	37	6	43307861	43307861	+	Missense_Mutation	SNP	G	G	A	rs10948072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43307861G>A	ENST00000361428.2	-	10	3952	c.3875C>T	c.(3874-3876)aCc>aTc	p.T1292I	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1292	Lys-rich.		T -> I (in dbSNP:rs10948072).		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)			GATACTTGGGGTCACCAATGA	0.393													G|||	764	0.152556	0.3041	0.1888	5008	,	,		20470	0.0446		0.1093	False		,,,				2504	0.0777				p.T1292I		Atlas-SNP	.											.	ZNF318	175	.	0			c.C3875T						PASS	.	G	ILE/THR	1282,3124	436.4+/-344.6	191,900,1112	186.0	191.0	189.0		3875	0.9	0.0	6	dbSNP_120	189	854,7746	194.7+/-240.0	37,780,3483	yes	missense	ZNF318	NM_014345.2	89	228,1680,4595	AA,AG,GG		9.9302,29.0967,16.4232	benign	1292/2280	43307861	2136,10870	2203	4300	6503	SO:0001583	missense	24149	exon10			CTTGGGGTCACCA	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.3875C>T	6.37:g.43307861G>A	ENSP00000354964:p.Thr1292Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	37	CCDS4895.2	311	0.1423992673992674	132	0.2682926829268293	69	0.19060773480662985	26	0.045454545454545456	84	0.11081794195250659	G	0.768	-0.766795	0.02974	0.290967	0.099302	ENSG00000171467	ENST00000361428	T	0.44881	0.91	5.69	0.91	0.19337	.	0.809119	0.10709	N	0.643131	T	0.08582	0.0213	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.23655	-1.0182	9	0.40728	T	0.16	3.6527	4.7197	0.12912	0.3861:0.0:0.4759:0.138	rs10948072;rs52834978;rs60042958;rs10948072	1292	Q5VUA4	ZN318_HUMAN	I	1292	ENSP00000354964:T1292I	ENSP00000354964:T1292I	T	-	2	0	ZNF318	43415839	0.000000	0.05858	0.001000	0.08648	0.261000	0.26267	0.098000	0.15189	-0.118000	0.11851	0.655000	0.94253	ACC	G|0.847;A|0.153	0.153	strong		0.393	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
CCDC57	284001	hgsc.bcm.edu	37	17	80146154	80146154	+	Silent	SNP	G	G	C	rs201504809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80146154G>C	ENST00000389641.4	-	7	1029	c.993C>G	c.(991-993)ctC>ctG	p.L331L	CCDC57_ENST00000392347.1_Silent_p.L331L|CCDC57_ENST00000392343.3_Silent_p.L331L			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	331										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			CTGCCCTGCGGAGCTGCGCCT	0.667													G|||	5	0.000998403	0.0	0.0	5008	,	,		16916	0.0		0.005	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											.	CCDC57	102	.	0			c.C993G						PASS	.	G		0,4394		0,0,2197	22.0	25.0	24.0		993	-1.5	0.9	17		24	28,8552		0,28,4262	no	coding-synonymous	CCDC57	NM_198082.2		0,28,6459	CC,CG,GG		0.3263,0.0,0.2158		331/916	80146154	28,12946	2197	4290	6487	SO:0001819	synonymous_variant	284001	exon7			CCTGCGGAGCTGC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.993C>G	17.37:g.80146154G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.994;C|0.006	0.006	weak		0.667	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
COPZ1	22818	hgsc.bcm.edu	37	12	54734289	54734289	+	Intron	SNP	A	A	G	rs11170877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:54734289A>G	ENST00000262061.2	+	2	55				COPZ1_ENST00000416254.2_Intron|RP11-968A15.8_ENST00000553061.1_RNA|COPZ1_ENST00000549116.1_Intron|COPZ1_ENST00000548753.1_Intron|COPZ1_ENST00000552218.1_Intron|COPZ1_ENST00000551779.1_Intron|COPZ1_ENST00000455864.2_Intron|COPZ1_ENST00000549043.1_Start_Codon_SNP_p.M1V|COPZ1_ENST00000552362.1_Intron|COPZ1_ENST00000553231.1_Intron|COPZ1_ENST00000548281.1_Intron	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						ACCAGTGGTGATGGGAGGCTT	0.488													G|||	1008	0.201278	0.2413	0.2349	5008	,	,		18652	0.2222		0.1252	False		,,,				2504	0.18				p.M1V		Atlas-SNP	.											.	COPZ1	10	.	0			c.A1G						PASS	.	G		1016,3390	728.6+/-410.0	136,744,1323	149.0	123.0	132.0			2.5	0.0	12	dbSNP_120	132	958,7642	775.2+/-407.7	58,842,3400	no	intron	COPZ1	NM_016057.1		194,1586,4723	GG,GA,AA		11.1395,23.0595,15.1776			54734289	1974,11032	2203	4300	6503	SO:0001627	intron_variant	22818	exon2			GTGGTGATGGGAG	AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"""coatomer protein complex, subunit zeta"""	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.19-42A>G	12.37:g.54734289A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_001271736	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	37	CCDS8877.1	371	0.16987179487179488	80	0.16260162601626016	76	0.20994475138121546	126	0.2202797202797203	89	0.11741424802110818	G	7.333	0.619402	0.14129	0.230595	0.111395	ENSG00000111481	ENST00000549043;ENST00000550713	.	.	.	4.35	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10800	-1.0614	6	0.87932	D	0	.	4.024	0.09678	0.1994:0.0:0.6156:0.185	rs11170877;rs58661926;rs11170877	1	F8VWL5	.	V	1	.	ENSP00000449270:M1V	M	+	1	0	COPZ1	53020556	0.000000	0.05858	0.000000	0.03702	0.252000	0.25951	0.266000	0.18534	0.206000	0.20587	-0.213000	0.12676	ATG	A|0.825;G|0.175	0.175	strong		0.488	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057	
RFX4	5992	hgsc.bcm.edu	37	12	107090201	107090201	+	Silent	SNP	T	T	C	rs10778502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:107090201T>C	ENST00000392842.1	+	8	1224	c.810T>C	c.(808-810)acT>acC	p.T270T	RFX4_ENST00000229387.5_Silent_p.T176T|RFX4_ENST00000357881.4_Silent_p.T279T|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	270					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TGATGCCCACTGTGCTGCAGG	0.537													C|||	2012	0.401757	0.5393	0.3588	5008	,	,		15716	0.2956		0.3748	False		,,,				2504	0.3834				p.T279T		Atlas-SNP	.											.	RFX4	218	.	0			c.T837C						PASS	.	C	,,	2251,2155	581.6+/-385.4	581,1089,533	129.0	107.0	114.0		837,528,810	-10.9	0.3	12	dbSNP_120	114	3345,5255	643.5+/-399.9	641,2063,1596	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	1222,3152,2129	CC,CT,TT		38.8953,48.9106,43.0263	,,	279/745,176/642,270/736	107090201	5596,7410	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon8			GCCCACTGTGCTG	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.810T>C	12.37:g.107090201T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			T|0.585;C|0.415	0.415	strong		0.537	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
FAM101A	144347	hgsc.bcm.edu	37	12	124798801	124798801	+	Silent	SNP	C	C	T	rs12318072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124798801C>T	ENST00000389727.3	+	3	381	c.381C>T	c.(379-381)ccC>ccT	p.P127P	FAM101A_ENST00000338359.4_Silent_p.P46P|FAM101A_ENST00000546355.1_Silent_p.P46P|FAM101A_ENST00000324038.3_Silent_p.P46P			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	127										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		TCTATGCGCCCGTACCCACCG	0.632													C|||	1749	0.349241	0.4592	0.3444	5008	,	,		18625	0.4117		0.159	False		,,,				2504	0.3354				p.P46P		Atlas-SNP	.											FAM101A,NS,carcinoma,0,2	FAM101A	10	2	0			c.C138T						scavenged	.	C	,	1861,2545	537.1+/-374.7	402,1057,744	86.0	75.0	79.0		138,138	-9.4	0.0	12	dbSNP_120	79	1478,7122	280.1+/-294.3	134,1210,2956	no	coding-synonymous,coding-synonymous	FAM101A,ZNF664-FAM101A	NM_001204299.1,NM_181709.4	,	536,2267,3700	TT,TC,CC		17.186,42.2379,25.6728	,	46/136,46/136	124798801	3339,9667	2203	4300	6503	SO:0001819	synonymous_variant	144347	exon3			TGCGCCCGTACCC		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.381C>T	12.37:g.124798801C>T		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	133	72	0.541353	NM_181709	A5D8T5	Silent	SNP	ENST00000389727.3	37																																																																																				C|0.714;T|0.286	0.286	strong		0.632	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709	
FOXD4	2298	hgsc.bcm.edu	37	9	117268	117268	+	Silent	SNP	C	C	T	rs144487093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:117268C>T	ENST00000382500.2	-	1	1149	c.852G>A	c.(850-852)gcG>gcA	p.A284A		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	284	Pro-rich.				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)		TCGCCAGGTCCGCGCCTTCTG	0.697													.|||	88	0.0175719	0.0023	0.0389	5008	,	,		16796	0.0		0.0487	False		,,,				2504	0.0092				p.A284A		Atlas-SNP	.											.	FOXD4	75	.	0			c.G852A						PASS	.	C		26,3522		0,26,1748	18.0	25.0	23.0		852	-0.9	0.0	9	dbSNP_134	23	299,6839		4,291,3274	no	coding-synonymous	FOXD4	NM_207305.3		4,317,5022	TT,TC,CC		4.1888,0.7328,3.0414		284/440	117268	325,10361	1774	3569	5343	SO:0001819	synonymous_variant	2298	exon1			CAGGTCCGCGCCT	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.852G>A	9.37:g.117268C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			C|0.973;T|0.027	0.027	strong		0.697	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
MUC13	56667	hgsc.bcm.edu	37	3	124646837	124646837	+	Splice_Site	SNP	G	G	A	rs4679394	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124646837G>A	ENST00000311075.3	-	2	91	c.53C>T	c.(52-54)gCc>gTc	p.A18V	MUC13_ENST00000497378.1_5'UTR	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	18			A -> V (in dbSNP:rs4679394).		cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						TTGGTTGGTGGCTGGAGGAAC	0.398													G|||	532	0.10623	0.0159	0.2003	5008	,	,		20177	0.0298		0.1511	False		,,,				2504	0.1943				p.A18V		Atlas-SNP	.											.	MUC13	57	.	0			c.C53T						PASS	.	G	VAL/ALA	155,4251	106.5+/-144.9	4,147,2052	95.0	82.0	87.0		53	-0.4	0.0	3	dbSNP_111	87	1335,7265	261.2+/-283.7	102,1131,3067	yes	missense-near-splice	MUC13	NM_033049.3	64	106,1278,5119	AA,AG,GG		15.5233,3.5179,11.4563	possibly-damaging	18/512	124646837	1490,11516	2203	4300	6503	SO:0001630	splice_region_variant	56667	exon2			TTGGTGGCTGGAG	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.53-1C>T	3.37:g.124646837G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	37		205	0.09386446886446886	7	0.014227642276422764	74	0.20441988950276244	14	0.024475524475524476	110	0.14511873350923482	G	11.13	1.548071	0.27652	0.035179	0.155233	ENSG00000173702	ENST00000311075	T	0.17370	2.28	3.51	-0.446	0.12238	.	2.119150	0.02138	N	0.056900	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.43094	0.799	B	0.36092	0.217	T	0.18366	-1.0339	9	0.66056	D	0.02	.	3.4876	0.07625	0.3494:0.1974:0.4532:0.0	rs4679394;rs52807645;rs58071710;rs4679394	18	Q9H3R2	MUC13_HUMAN	V	18	ENSP00000312235:A18V	ENSP00000312235:A18V	A	-	2	0	MUC13	126129527	0.004000	0.15560	0.000000	0.03702	0.084000	0.17831	0.130000	0.15850	-0.111000	0.12001	0.655000	0.94253	GCC	G|0.895;A|0.105	0.105	strong		0.398	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049	Missense_Mutation
CLEC12B	387837	hgsc.bcm.edu	37	12	10163375	10163375	+	Missense_Mutation	SNP	C	C	A	rs1359082	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:10163375C>A	ENST00000338896.5	+	1	145	c.17C>A	c.(16-18)aCc>aAc	p.T6N	CLEC1B_ENST00000428126.2_Intron|CLEC12B_ENST00000396502.1_Missense_Mutation_p.T6N	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	6			T -> N (in dbSNP:rs1359082). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						GAAGAAGTGACCTACGCGACA	0.403													C|||	1565	0.3125	0.3896	0.3775	5008	,	,		20689	0.1538		0.4245	False		,,,				2504	0.2106				p.T6N		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C17A						PASS	.	C	ASN/THR,ASN/THR	1647,2759	495.3+/-363.2	309,1029,865	60.0	57.0	58.0		17,17	4.9	1.0	12	dbSNP_88	58	3306,5294	485.9+/-371.7	643,2020,1637	yes	missense,missense	CLEC12B	NM_001129998.1,NM_205852.2	65,65	952,3049,2502	AA,AC,CC		38.4419,37.3808,38.0824	probably-damaging,probably-damaging	6/277,6/233	10163375	4953,8053	2203	4300	6503	SO:0001583	missense	387837	exon1			AAGTGACCTACGC	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"""C-type lectin domain containing"""	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.17C>A	12.37:g.10163375C>A	ENSP00000344563:p.Thr6Asn	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	37	CCDS44830.1	742	0.33974358974358976	192	0.3902439024390244	139	0.3839779005524862	84	0.14685314685314685	327	0.4313984168865435	C	18.07	3.542762	0.65198	0.373808	0.384419	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.02158	4.42;4.73	4.88	4.88	0.63580	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	M	0.69823	2.125	0.25333	P	0.9890114	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	T	0.52510	-0.8566	9	0.66056	D	0.02	.	14.2691	0.66140	0.0:1.0:0.0:0.0	rs1359082;rs60399276	6;6;6	Q2HXU8;Q2HXU8-2;F5H4H7	CL12B_HUMAN;.;.	N	6	ENSP00000379759:T6N;ENSP00000344563:T6N	ENSP00000344563:T6N	T	+	2	0	CLEC12B	10054642	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	1.818000	0.39012	2.652000	0.90054	0.561000	0.74099	ACC	C|0.642;A|0.358	0.358	strong		0.403	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
SRMS	6725	hgsc.bcm.edu	37	20	62173925	62173925	+	Silent	SNP	T	T	G	rs404613|rs386816161	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62173925T>G	ENST00000217188.1	-	4	695	c.655A>C	c.(655-657)Agg>Cgg	p.R219R		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	219					peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R219R(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			ACGTCCTGCCTCGGGGCCTTC	0.692													G|||	1839	0.367212	0.9516	0.1254	5008	,	,		15383	0.0327		0.0686	False		,,,				2504	0.4008				p.R219R		Atlas-SNP	.											SRMS,NS,lymphoid_neoplasm,0,1	SRMS	48	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A655C						PASS	.	G		3387,1011		1379,629,191	33.0	37.0	36.0		655	1.4	0.0	20	dbSNP_80	36	436,8160		14,408,3876	yes	coding-synonymous	SRMS	NM_080823.2		1393,1037,4067	GG,GT,TT		5.0721,22.9877,29.4213		219/489	62173925	3823,9171	2199	4298	6497	SO:0001819	synonymous_variant	6725	exon4			CCTGCCTCGGGGC		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.655A>C	20.37:g.62173925T>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_080823		Silent	SNP	ENST00000217188.1	37	CCDS13525.1																																																																																			T|0.680;G|0.320	0.320	strong		0.692	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
PCED1B	91523	hgsc.bcm.edu	37	12	47471439	47471439	+	5'Flank	SNP	G	G	A	rs2269828	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:47471439G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000550413.1_Silent_p.P449P|AMIGO2_ENST00000429635.1_Silent_p.P449P|AMIGO2_ENST00000266581.4_Silent_p.P449P|AMIGO2_ENST00000321382.3_Silent_p.P449P			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										CATCACTAGCGGGGCCAGGAC	0.507													G|||	1110	0.221645	0.1346	0.2882	5008	,	,		21472	0.124		0.3211	False		,,,				2504	0.2904				p.P449P		Atlas-SNP	.											.	AMIGO2	50	.	0			c.C1347T						PASS	.	G	,	756,3650	310.5+/-291.6	61,634,1508	153.0	156.0	155.0		1347,1347	-9.6	0.0	12	dbSNP_100	155	2788,5812	443.1+/-360.3	444,1900,1956	no	coding-synonymous,coding-synonymous	AMIGO2	NM_001143668.1,NM_181847.4	,	505,2534,3464	AA,AG,GG		32.4186,17.1584,27.249	,	449/523,449/523	47471439	3544,9462	2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			ACTAGCGGGGCCA	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		12.37:g.47471439G>A	Exception_encountered	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	266	263	0.988722	NM_181847	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.750;A|0.250	0.250	strong		0.507	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
PIGQ	9091	hgsc.bcm.edu	37	16	624713	624713	+	Silent	SNP	C	C	T	rs4984669	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:624713C>T	ENST00000026218.5	+	2	727	c.639C>T	c.(637-639)tgC>tgT	p.C213C	PIGQ_ENST00000470411.2_Silent_p.C213C|PIGQ_ENST00000409527.2_Silent_p.C213C|PIGQ_ENST00000321878.5_Silent_p.C213C	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	213					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GACCCATTTGCCTGCTGTTGG	0.677													C|||	2687	0.536542	0.5053	0.4914	5008	,	,		15783	0.6349		0.4264	False		,,,				2504	0.6227				p.C213C		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	0			c.C639T						PASS	.	C	,	2117,2261		529,1059,601	14.0	17.0	16.0		639,639	0.1	0.8	16	dbSNP_111	16	3466,5116		733,2000,1558	no	coding-synonymous,coding-synonymous	PIGQ	NM_004204.3,NM_148920.1	,	1262,3059,2159	TT,TC,CC		40.3869,48.3554,43.0787	,	213/582,213/761	624713	5583,7377	2189	4291	6480	SO:0001819	synonymous_variant	9091	exon2			CATTTGCCTGCTG	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.639C>T	16.37:g.624713C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			C|0.521;T|0.479	0.479	strong		0.677	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
ZNF302	55900	hgsc.bcm.edu	37	19	35175775	35175775	+	Missense_Mutation	SNP	C	C	T	rs11543232	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35175775C>T	ENST00000446502.2	+	6	1173	c.965C>T	c.(964-966)aCt>aTt	p.T322I	ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000505242.1_Missense_Mutation_p.T278I|ZNF302_ENST00000457781.2_Missense_Mutation_p.T278I|ZNF302_ENST00000423823.2_Missense_Mutation_p.T278I			Q9NR11	ZN302_HUMAN	zinc finger protein 302	357					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)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CATCAGAGCACTCACACGGGA	0.423													C|||	1255	0.250599	0.1369	0.2075	5008	,	,		21906	0.3006		0.3767	False		,,,				2504	0.2536				p.T278I		Atlas-SNP	.											.	ZNF302	27	.	0			c.C833T						PASS	.	C	ILE/THR,ILE/THR	817,3589	324.0+/-298.4	80,657,1466	91.0	90.0	90.0		833,833	1.0	1.0	19	dbSNP_120	90	3087,5513	471.9+/-368.2	544,1999,1757	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	89,89	624,2656,3223	TT,TC,CC		35.8953,18.5429,30.0169	benign,benign	278/400,278/400	35175775	3904,9102	2203	4300	6503	SO:0001583	missense	55900	exon5			AGAGCACTCACAC	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.965C>T	19.37:g.35175775C>T	ENSP00000396379:p.Thr322Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		615	0.2815934065934066	74	0.15040650406504066	83	0.2292817679558011	174	0.3041958041958042	284	0.37467018469656993	C	1.640	-0.516644	0.04200	0.185429	0.358953	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.19532	2.66;2.66;2.66;2.14	0.967	0.967	0.19674	.	.	.	.	.	T	0.00012	0.0000	N	0.12471	0.22	0.45607	P	0.0014539999999999553	D;B	0.71674	0.998;0.034	D;B	0.79784	0.993;0.017	T	0.25082	-1.0142	8	0.02654	T	1	.	3.2227	0.06721	0.0:0.7107:0.0:0.2893	rs11543232;rs12971555;rs52834410	322;278	E7EVR1;Q9NR11-2	.;.	I	278;278;278;322	ENSP00000391067:T278I;ENSP00000421028:T278I;ENSP00000405219:T278I;ENSP00000396379:T322I	ENSP00000405219:T278I	T	+	2	0	ZNF302	39867615	0.096000	0.21769	0.998000	0.56505	0.974000	0.67602	0.177000	0.16801	0.822000	0.34565	0.467000	0.42956	ACT	C|0.704;T|0.296	0.296	strong		0.423	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
FAM172A	83989	hgsc.bcm.edu	37	5	93159971	93159971	+	Silent	SNP	T	T	C	rs141777861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:93159971T>C	ENST00000395965.3	-	8	931	c.789A>G	c.(787-789)gaA>gaG	p.E263E	FAM172A_ENST00000505869.1_Silent_p.E153E|FAM172A_ENST00000509163.1_Silent_p.E217E|FAM172A_ENST00000509739.1_Silent_p.E116E	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	263						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						GAGAACCATTTTCCTATAAGG	0.343													T|||	42	0.00838658	0.0	0.0086	5008	,	,		11615	0.0		0.0199	False		,,,				2504	0.0164				p.E263E		Atlas-SNP	.											.	FAM172A	38	.	0			c.A789G						PASS	.	T	,,	28,4378	32.6+/-62.9	0,28,2175	102.0	100.0	101.0		651,459,789	2.3	1.0	5	dbSNP_134	101	195,8405	84.2+/-146.7	3,189,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM172A	NM_001163417.1,NM_001163418.1,NM_032042.5	,,	3,217,6283	CC,CT,TT		2.2674,0.6355,1.7146	,,	217/371,153/307,263/417	93159971	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	83989	exon8			ACCATTTTCCTAT		CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391			25365	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 21"""	C5orf21		11230166	Standard	NM_032042		Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.789A>G	5.37:g.93159971T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Silent	SNP	ENST00000395965.3	37	CCDS4069.1																																																																																			T|0.986;C|0.015	0.015	strong		0.343	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042	
PIGT	51604	hgsc.bcm.edu	37	20	44052992	44052992	+	Silent	SNP	G	G	A	rs13217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44052992G>A	ENST00000279036.6	+	10	1451	c.1371G>A	c.(1369-1371)acG>acA	p.T457T	PIGT_ENST00000279035.9_Silent_p.T355T|PIGT_ENST00000372689.5_Silent_p.T390T|PIGT_ENST00000535404.1_Silent_p.T302T|PIGT_ENST00000543458.2_Silent_p.T401T|PIGT_ENST00000545755.1_Silent_p.T195T|PIGT_ENST00000341555.5_Silent_p.T263T	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	457					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)	p.T457T(1)		breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				CCGAGTACACGCCAGATCCTA	0.582													G|||	1375	0.274561	0.0628	0.3199	5008	,	,		19965	0.2411		0.5129	False		,,,				2504	0.318				p.T457T		Atlas-SNP	.											PIGT_ENST00000279036,caecum,carcinoma,0,3	PIGT	85	3	1	Substitution - coding silent(1)	stomach(1)	c.G1371A						PASS	.	G	,,,	640,3766	272.8+/-271.0	50,540,1613	82.0	76.0	78.0		1203,1170,1065,1371	-7.4	0.8	20	dbSNP_52	78	4441,4159	587.6+/-392.2	1138,2165,997	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIGT	NM_001184728.1,NM_001184729.1,NM_001184730.1,NM_015937.4	,,,	1188,2705,2610	AA,AG,GG		48.3605,14.5256,39.0666	,,,	401/523,390/512,355/477,457/579	44052992	5081,7925	2203	4300	6503	SO:0001819	synonymous_variant	51604	exon10			GTACACGCCAGAT		CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"""Phosphatidylinositol glycan anchor biosynthesis"""	14938	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610272	"""phosphatidylinositol glycan, class T"""			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.1371G>A	20.37:g.44052992G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	71	0.972603	NM_015937	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Silent	SNP	ENST00000279036.6	37	CCDS13353.1																																																																																			G|0.654;A|0.346	0.346	strong		0.582	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937	
ANKS4B	257629	hgsc.bcm.edu	37	16	21261302	21261302	+	Missense_Mutation	SNP	G	G	A	rs539999603		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21261302G>A	ENST00000311620.5	+	2	488	c.415G>A	c.(415-417)Gct>Act	p.A139T		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	139					response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		GAAGGAGCAGGCTCAGAAGAA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		21059	0.0		0.0	False		,,,				2504	0.001				p.A139T		Atlas-SNP	.											.	ANKS4B	43	.	0			c.G415A						PASS	.						49.0	50.0	50.0					16																	21261302		2088	4223	6311	SO:0001583	missense	257629	exon2			GAGCAGGCTCAGA	AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	26795	protein-coding gene	gene with protein product		609901					Standard	NM_145865		Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.415G>A	16.37:g.21261302G>A	ENSP00000308772:p.Ala139Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_145865		Missense_Mutation	SNP	ENST00000311620.5	37	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609379	0.87258	.	.	ENSG00000175311	ENST00000311620	T	0.51071	0.72	5.77	4.81	0.61882	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.69169	0.3081	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.73946	-0.3822	10	0.66056	D	0.02	-10.602	15.2442	0.73493	0.0:0.0:0.8584:0.1416	.	139	Q8N8V4	ANS4B_HUMAN	T	139	ENSP00000308772:A139T	ENSP00000308772:A139T	A	+	1	0	ANKS4B	21168803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.776000	0.99001	1.422000	0.47177	-0.282000	0.10007	GCT	.	.	none		0.542	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865	
CUL9	23113	hgsc.bcm.edu	37	6	43152573	43152573	+	Silent	SNP	A	A	G	rs9472022	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43152573A>G	ENST00000252050.4	+	2	609	c.525A>G	c.(523-525)ttA>ttG	p.L175L	CUL9_ENST00000372647.2_Silent_p.L175L|CUL9_ENST00000354495.3_Silent_p.L175L	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	175					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						TGCACATGTTATGCAATCCTG	0.587													G|||	1768	0.353035	0.6248	0.2795	5008	,	,		18745	0.375		0.1223	False		,,,				2504	0.2526				p.L175L		Atlas-SNP	.											.	CUL9	248	.	0			c.A525G						PASS	.	G		2463,1943	536.2+/-374.4	693,1077,433	40.0	42.0	41.0		525	2.9	1.0	6	dbSNP_119	41	1325,7273	733.6+/-406.9	102,1121,3076	no	coding-synonymous	CUL9	NM_015089.2		795,2198,3509	GG,GA,AA		15.4106,44.099,29.1295		175/2518	43152573	3788,9216	2203	4299	6502	SO:0001819	synonymous_variant	23113	exon2			CATGTTATGCAAT	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.525A>G	6.37:g.43152573A>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			A|0.711;G|0.289	0.289	strong		0.587	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
C14orf159	80017	hgsc.bcm.edu	37	14	91681784	91681784	+	Missense_Mutation	SNP	G	G	A	rs115874122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91681784G>A	ENST00000523771.1	+	13	2188	c.1585G>A	c.(1585-1587)Gca>Aca	p.A529T	C14orf159_ENST00000521077.2_Missense_Mutation_p.A494T|C14orf159_ENST00000428926.2_Missense_Mutation_p.A529T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A529T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A534T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A534T|C14orf159_ENST00000256324.10_Missense_Mutation_p.A534T|C14orf159_ENST00000525393.2_Missense_Mutation_p.A405T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A529T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A477T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	529						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)		CCTGGCCTGCGCACTCTACAT	0.542													G|||	20	0.00399361	0.0	0.0245	5008	,	,		17334	0.001		0.001	False		,,,				2504	0.001				p.A534T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1600A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	132.0	118.0	123.0		1585,1585,1600,1429,1585	1.3	0.0	14	dbSNP_132	123	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	58,58,58,58,58	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign,benign,benign,benign,benign	529/617,529/617,534/622,477/565,529/617	91681784	13,12993	2203	4300	6503	SO:0001583	missense	80017	exon13			GCCTGCGCACTCT	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.1585G>A	14.37:g.91681784G>A	ENSP00000429655:p.Ala529Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	10	0.004578754578754579	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	0	0.0	G	9.610	1.130943	0.21041	4.54E-4	0.001279	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06	5.34	1.28	0.21552	.	0.240499	0.41097	N	0.000955	T	0.07728	0.0194	M	0.62088	1.915	0.09310	N	1	B;P;B;B;B	0.43662	0.202;0.814;0.168;0.41;0.168	B;B;B;B;B	0.34931	0.034;0.192;0.02;0.033;0.02	T	0.14615	-1.0466	10	0.54805	T	0.06	.	4.7277	0.12948	0.2495:0.0:0.5999:0.1506	.	529;405;477;534;494	Q7Z3D6;Q8NB88;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.	T	477;534;494;534;529;405;529;529;529;534	ENSP00000429453:A477T;ENSP00000256324:A534T;ENSP00000430137:A494T;ENSP00000428263:A534T;ENSP00000428974:A529T;ENSP00000435459:A405T;ENSP00000404343:A529T;ENSP00000427953:A529T;ENSP00000429655:A529T;ENSP00000404196:A534T	ENSP00000256324:A534T	A	+	1	0	C14orf159	90751537	0.408000	0.25360	0.014000	0.15608	0.002000	0.02628	2.292000	0.43549	0.265000	0.21872	-0.136000	0.14681	GCA	G|0.998;A|0.002	0.002	strong		0.542	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
ALPP	250	hgsc.bcm.edu	37	2	233245982	233245982	+	Missense_Mutation	SNP	G	G	A	rs143205011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:233245982G>A	ENST00000392027.2	+	10	1483	c.1214G>A	c.(1213-1215)cGg>cAg	p.R405Q	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	405					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)		GGCAAGGCCCGGGACAGGAAG	0.637													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19588	0.0		0.001	False		,,,				2504	0.002				p.R405Q		Atlas-SNP	.											.	ALPP	53	.	0			c.G1214A						PASS	.	A	GLN/ARG	3,4395		0,3,2196	24.0	30.0	28.0		1214	-4.7	0.0	2	dbSNP_134	28	41,8505		0,41,4232	no	missense	ALPP	NM_001632.3	43	0,44,6428	AA,AG,GG		0.4798,0.0682,0.3399	benign	405/536	233245982	44,12900	2199	4273	6472	SO:0001583	missense	250	exon10			AGGCCCGGGACAG	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.1214G>A	2.37:g.233245982G>A	ENSP00000375881:p.Arg405Gln	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	393	121	0.307888	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	g	1.358	-0.589485	0.03799	6.82E-4	0.004798	ENSG00000163283	ENST00000392027	D	0.96491	-4.03	2.35	-4.69	0.03299	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	2.308210	0.01558	N	0.019990	D	0.85084	0.5616	N	0.02368	-0.58	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.81695	-0.0816	10	0.13108	T	0.6	.	0.4192	0.00453	0.392:0.1279:0.2136:0.2665	.	405	P05187	PPB1_HUMAN	Q	405	ENSP00000375881:R405Q	ENSP00000375881:R405Q	R	+	2	0	ALPP	232954226	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-6.351000	0.00069	-3.004000	0.00275	-3.289000	0.00047	CGG	G|0.999;A|0.001	0.001	strong		0.637	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
PRRT3	285368	hgsc.bcm.edu	37	3	9991163	9991163	+	Missense_Mutation	SNP	A	A	G	rs55847610	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9991163A>G	ENST00000412055.1	-	2	766	c.637T>C	c.(637-639)Tcc>Ccc	p.S213P	PRRT3-AS1_ENST00000431558.1_RNA|PRRT3_ENST00000411976.2_Missense_Mutation_p.S213P	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	31	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	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	
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57840547A>G	ENST00000321545.4	+	4	2062	c.1717A>G	c.(1717-1719)Atg>Gtg	p.M573V		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	573			M -> V (in dbSNP:rs10410649).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAGACCTTTTATGACTGCACA	0.413													A|||	989	0.197484	0.3169	0.1816	5008	,	,		20065	0.0317		0.2843	False		,,,				2504	0.1288				p.M573V		Atlas-SNP	.											.	ZNF543	61	.	0			c.A1717G						PASS	.	A	VAL/MET	1351,3055	450.6+/-349.4	200,951,1052	87.0	81.0	84.0		1717	-2.8	0.0	19	dbSNP_119	84	2352,6248	393.0+/-344.2	323,1706,2271	yes	missense	ZNF543	NM_213598.3	21	523,2657,3323	GG,GA,AA		27.3488,30.6627,28.4715	benign	573/601	57840547	3703,9303	2203	4300	6503	SO:0001583	missense	125919	exon4			CCTTTTATGACTG	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1717A>G	19.37:g.57840547A>G	ENSP00000322545:p.Met573Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	466	0.21336996336996336	152	0.3089430894308943	79	0.21823204419889503	18	0.03146853146853147	217	0.2862796833773087	A	4.434	0.080299	0.08533	0.306627	0.273488	ENSG00000178229	ENST00000321545	T	0.05513	3.43	2.45	-2.81	0.05805	.	.	.	.	.	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	0.47573	-0.9107	8	0.52906	T	0.07	.	5.4467	0.16539	0.323:0.4652:0.2119:0.0	rs10410649;rs52820047;rs10410649	573	Q08ER8	ZN543_HUMAN	V	573	ENSP00000322545:M573V	ENSP00000322545:M573V	M	+	1	0	ZNF543	62532359	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.653000	0.05360	-0.852000	0.04141	0.379000	0.24179	ATG	A|0.737;G|0.263	0.263	strong		0.413	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
SPACA3	124912	hgsc.bcm.edu	37	17	31323886	31323886	+	Silent	SNP	C	C	T	rs200596990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:31323886C>T	ENST00000269053.3	+	3	439	c.369C>T	c.(367-369)agC>agT	p.S123S	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Silent_p.S54S|SPACA3_ENST00000394638.1_Silent_p.S20S	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	123					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			ATTTCACAAGCGGTTTCAACG	0.582																																					p.S123S		Atlas-SNP	.											SPACA3,NS,carcinoma,+1,1	SPACA3	35	1	0			c.C369T						PASS	.	C		0,4406		0,0,2203	104.0	92.0	96.0		369	0.9	1.0	17		96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	SPACA3	NM_173847.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		123/216	31323886	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	124912	exon3			CACAAGCGGTTTC	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"""cancer/testis antigen 54"", ""sperm lyzozyme-like acrosomal protein 1"""	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.369C>T	17.37:g.31323886C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_173847	Q7Z4Y5	Silent	SNP	ENST00000269053.3	37	CCDS11275.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847	
RORA	6095	hgsc.bcm.edu	37	15	60803741	60803741	+	Silent	SNP	C	C	T	rs61740274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:60803741C>T	ENST00000335670.6	-	5	604	c.504G>A	c.(502-504)caG>caA	p.Q168Q	RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000560004.1_5'UTR|RP11-219B17.1_ENST00000559902.1_RNA|RP11-219B17.1_ENST00000501579.2_RNA|RORA_ENST00000449337.2_Silent_p.Q113Q|RORA_ENST00000309157.4_Silent_p.Q193Q|RP11-219B17.1_ENST00000558235.1_RNA|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000261523.5_Silent_p.Q201Q	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	168	Hinge.|Poly-Gln.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|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 cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						GGTCGCGCTGCTGCTGCTGCA	0.542													C|||	219	0.04373	0.0363	0.0634	5008	,	,		18969	0.0		0.0865	False		,,,				2504	0.0409				p.Q201Q		Atlas-SNP	.											.	RORA	114	.	0			c.G603A						PASS	.	C	,,,	225,4181	133.7+/-170.0	4,217,1982	97.0	77.0	84.0		579,603,504,339	5.0	1.0	15	dbSNP_129	84	888,7712	199.0+/-243.2	56,776,3468	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RORA	NM_002943.3,NM_134260.2,NM_134261.2,NM_134262.2	,,,	60,993,5450	TT,TC,CC		10.3256,5.1067,8.5576	,,,	193/549,201/557,168/524,113/469	60803741	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	6095	exon6			GCGCTGCTGCTGC	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"""Nuclear hormone receptors"""	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.504G>A	15.37:g.60803741C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	140	80	0.571429	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Silent	SNP	ENST00000335670.6	37	CCDS10177.1																																																																																			C|0.924;T|0.076	0.076	strong		0.542	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		
PRDM15	63977	hgsc.bcm.edu	37	21	43230669	43230669	+	Silent	SNP	C	C	T	rs146699277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43230669C>T	ENST00000269844.3	-	28	3701	c.3591G>A	c.(3589-3591)acG>acA	p.T1197T	PRDM15_ENST00000398548.1_Silent_p.T868T|PRDM15_ENST00000447207.2_Silent_p.T831T|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000422911.1_Silent_p.T888T|PRDM15_ENST00000538201.1_Silent_p.T851T	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						ACACGGAGCACGTCCACTGCT	0.582													c|||	9	0.00179712	0.0008	0.0043	5008	,	,		20936	0.0		0.003	False		,,,				2504	0.002				p.T1197T		Atlas-SNP	.											.	PRDM15	110	.	0			c.G3591A						PASS	.		,	0,4406		0,0,2203	134.0	78.0	97.0		2604,3591	-4.3	1.0	21	dbSNP_134	97	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	,	868/1179,1197/1508	43230669	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon28			GGAGCACGTCCAC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3591G>A	21.37:g.43230669C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
CLPP	8192	hgsc.bcm.edu	37	19	6368688	6368688	+	Silent	SNP	G	G	A	rs112620134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6368688G>A	ENST00000245816.4	+	6	924	c.801G>A	c.(799-801)gcG>gcA	p.A267A	CLPP_ENST00000596605.1_3'UTR|CLPP_ENST00000596149.1_Silent_p.A180A	NM_006012.2	NP_006003.1	Q16740	CLPP_HUMAN	caseinolytic mitochondrial matrix peptidase proteolytic subunit	267					protein homooligomerization (GO:0051260)|proteolysis involved in cellular protein catabolic process (GO:0051603)	endopeptidase Clp complex (GO:0009368)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|ovary(2)	6						TAGAAGCAGCGCCGGCAGCAG	0.637													G|||	27	0.00539137	0.0061	0.0043	5008	,	,		15983	0.0		0.0129	False		,,,				2504	0.0031				p.A267A		Atlas-SNP	.											.	CLPP	15	.	0			c.G801A						PASS	.	G		28,4364		0,28,2168	24.0	18.0	20.0		801	-7.9	0.0	19	dbSNP_132	20	92,8500		1,90,4205	no	coding-synonymous	CLPP	NM_006012.2		1,118,6373	AA,AG,GG		1.0708,0.6375,0.9242		267/278	6368688	120,12864	2196	4296	6492	SO:0001819	synonymous_variant	8192	exon6			AGCAGCGCCGGCA	Z50853	CCDS12162.1	19p13.3	2013-09-12	2013-09-12		ENSG00000125656	ENSG00000125656		"""ATPases / AAA-type"""	2084	protein-coding gene	gene with protein product	"""ATP-dependent protease ClpAP (E. coli), proteolytic subunit, human"""	601119	"""ClpP (caseinolytic protease, ATP-dependent, proteolytic subunit, E. coli) homolog"", ""ClpP caseinolytic protease, ATP-dependent, proteolytic subunit homolog (E. coli)"", ""ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)"""			8543061, 23360988	Standard	NM_006012		Approved		uc002mem.1	Q16740	OTTHUMG00000180779	ENST00000245816.4:c.801G>A	19.37:g.6368688G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_006012	B2R4W5	Silent	SNP	ENST00000245816.4	37	CCDS12162.1																																																																																			G|0.994;A|0.006	0.006	strong		0.637	CLPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452984.1	NM_006012	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33581306	33581306	+	Silent	SNP	G	G	A	rs2281380	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:33581306G>A	ENST00000321505.4	+	6	3156	c.2976G>A	c.(2974-2976)acG>acA	p.T992T	KIAA1549L_ENST00000265654.5_Silent_p.T998T|KIAA1549L_ENST00000389726.3_Silent_p.T998T			Q6ZVL6	K154L_HUMAN	KIAA1549-like	992						integral component of membrane (GO:0016021)											TTGTGAGCACGTCCAATGCCT	0.582													G|||	1948	0.388978	0.469	0.3213	5008	,	,		22143	0.3264		0.3887	False		,,,				2504	0.3937				p.T992T		Atlas-SNP	.											.	.	.	.	0			c.G2976A						PASS	.	G		1926,2268		480,966,651	83.0	80.0	81.0		2976	-5.2	1.0	11	dbSNP_100	81	3268,5198		645,1978,1610	no	coding-synonymous	C11orf41	NM_012194.2		1125,2944,2261	AA,AG,GG		38.6015,45.9227,41.0269		992/1850	33581306	5194,7466	2097	4233	6330	SO:0001819	synonymous_variant	25758	exon6			GAGCACGTCCAAT	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.2976G>A	11.37:g.33581306G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	846	0.3873626373626374	227	0.4613821138211382	126	0.34806629834254144	188	0.32867132867132864	305	0.4023746701846966	G	7.557	0.663994	0.14710	0.459227	0.386015	ENSG00000110427	ENST00000526400	.	.	.	5.42	-5.21	0.02815	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999989427	.	.	.	.	.	.	T	0.44697	-0.9311	3	.	.	.	-8.4917	5.8334	0.18593	0.6112:0.1336:0.1659:0.0893	rs2281380;rs59777290;rs2281380	.	.	.	H	390	.	.	R	+	2	0	C11orf41	33537882	0.018000	0.18449	0.951000	0.38953	0.712000	0.41017	-0.872000	0.04219	-0.823000	0.04301	0.573000	0.79308	CGT	G|0.613;A|0.387	0.387	strong		0.582	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386118	56386118	+	Silent	SNP	A	A	G	rs2680689	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56386118A>G	ENST00000343736.4	-	22	4678	c.4515T>C	c.(4513-4515)gaT>gaC	p.D1505D	BZRAP1_ENST00000355701.3_Silent_p.D1505D|BZRAP1_ENST00000268893.6_Silent_p.D1445D			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1505						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCTCCTGCTCATCCTCCGAAT	0.652													G|||	1422	0.283946	0.3086	0.2738	5008	,	,		16907	0.25		0.332	False		,,,				2504	0.2434				p.D1505D		Atlas-SNP	.											BZRAP1_ENST00000355701,NS,carcinoma,0,4	BZRAP1	287	4	0			c.T4515C						scavenged	.	G	,	1294,3082		192,910,1086	19.0	21.0	20.0		4515,4335	-9.7	0.2	17	dbSNP_100	20	2545,6013		413,1719,2147	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	605,2629,3233	GG,GA,AA		29.7383,29.5704,29.6815	,	1505/1858,1445/1798	56386118	3839,9095	2188	4279	6467	SO:0001819	synonymous_variant	9256	exon22			CTGCTCATCCTCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4515T>C	17.37:g.56386118A>G		Somatic	69	2	0.0289855		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			A|0.709;G|0.291	0.291	strong		0.652	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
CENPM	79019	hgsc.bcm.edu	37	22	42336172	42336172	+	Intron	SNP	G	G	A	rs5758511	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42336172G>A	ENST00000215980.5	-	6	490				CENPM_ENST00000407253.3_Intron|CENPM_ENST00000402420.1_Intron|CENPM_ENST00000402338.1_Intron|CENPM_ENST00000404067.1_Intron|CENPM_ENST00000472374.2_Nonsense_Mutation_p.R3*	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M						mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						tcccacactcggcccatgcac	0.562													G|||	1198	0.239217	0.0265	0.2147	5008	,	,		17200	0.5575		0.2664	False		,,,				2504	0.1881				p.R3X		Atlas-SNP	.											.	CENPM	8	.	0			c.C7T						PASS	.	G	,stop/ARG,	182,2954		5,172,1391	58.0	52.0	54.0		,7,	0.8	0.0	22	dbSNP_114	54	2020,5138		291,1438,1850	yes	intron,stop-gained,intron	CENPM	NM_001002876.1,NM_001110215.1,NM_024053.3	,,	296,1610,3241	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	28.2202,5.8036,21.3911	,,	,3/59,	42336172	2202,8092	1568	3579	5147	SO:0001627	intron_variant	79019	exon1			ACACTCGGCCCAT	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.403-972C>T	22.37:g.42336172G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_001110215	A7LM22|B1AHQ9|Q6I9W3	Nonsense_Mutation	SNP	ENST00000215980.5	37	CCDS14025.1	582	0.2664835164835165	16	0.032520325203252036	73	0.20165745856353592	289	0.5052447552447552	204	0.2691292875989446	G	11.61	1.690609	0.29962	0.058036	0.282202	ENSG00000100162	ENST00000472374	.	.	.	1.82	0.783	0.18572	.	.	.	.	.	.	.	.	.	.	.	0.52099	P	5.500000000002725E-5	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.15	0.10234	0.2157:0.0:0.7843:0.0	rs5758511;rs61341024;rs5758511	.	.	.	X	3	.	ENSP00000430624:R3X	R	-	1	2	CENPM	40666118	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	-0.136000	0.10405	0.337000	0.23665	0.407000	0.27541	CGA	G|0.752;A|0.248	0.248	strong		0.562	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	
ADAM10	102	hgsc.bcm.edu	37	15	58957371	58957371	+	Missense_Mutation	SNP	C	C	G	rs61751103	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:58957371C>G	ENST00000260408.3	-	5	953	c.510G>C	c.(508-510)caG>caC	p.Q170H	ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000558733.1_5'UTR|ADAM10_ENST00000396140.2_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	170			Q -> H (in AD18; associated with disease susceptibility; significantly attenuates alpha-secretase activity of the enzyme; shifts APP processing toward beta- secretase-mediated cleavage resulting in enhanced beta-amyloid plaque load and reactive gliosis). {ECO:0000269|PubMed:19608551}.		cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		CACAGCCCCCCTGAGGACCGT	0.363													C|||	6	0.00119808	0.0	0.0043	5008	,	,		17409	0.0		0.003	False		,,,				2504	0.0				p.Q170H		Atlas-SNP	.											.	ADAM10	59	.	0			c.G510C						PASS	.	C	HIS/GLN	0,4384		0,0,2192	128.0	125.0	126.0		510	2.7	1.0	15	dbSNP_129	126	5,8579	4.3+/-15.6	0,5,4287	yes	missense	ADAM10	NM_001110.2	24	0,5,6479	GG,GC,CC		0.0582,0.0,0.0386	benign	170/749	58957371	5,12963	2192	4292	6484	SO:0001583	missense	102	exon5			GCCCCCCTGAGGA	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.510G>C	15.37:g.58957371C>G	ENSP00000260408:p.Gln170His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001110	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	37	CCDS10167.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	14.63	2.593548	0.46214	0.0	5.82E-4	ENSG00000137845	ENST00000260408;ENST00000439637	T;T	0.78816	1.82;-1.21	5.6	2.68	0.31781	.	0.159589	0.53938	D	0.000041	T	0.62405	0.2425	N	0.25647	0.755	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.55483	-0.8134	10	0.37606	T	0.19	-32.7843	8.6056	0.33771	0.0:0.6984:0.0:0.3016	rs61751103	170;170	A0AV88;O14672	.;ADA10_HUMAN	H	170;117	ENSP00000260408:Q170H;ENSP00000391930:Q117H	ENSP00000260408:Q170H	Q	-	3	2	ADAM10	56744663	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	0.640000	0.24705	0.835000	0.34877	0.650000	0.86243	CAG	C|1.000;G|0.000	0.000	strong		0.363	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110	
OR2A5	393046	hgsc.bcm.edu	37	7	143748257	143748257	+	Missense_Mutation	SNP	G	G	A	rs6464574	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	110	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	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		
HS6ST1	9394	hgsc.bcm.edu	37	2	129075939	129075939	+	Nonsense_Mutation	SNP	T	T	A	rs202247387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	61	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	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	
MST1L	11223	hgsc.bcm.edu	37	1	17085865	17085865	+	RNA	SNP	A	A	G	rs1057378		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17085865A>G	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.L319P(2)|p.L309P(2)									TGAGCCGTCGAGGTTCCAGCA	0.667																																					p.L319P		Atlas-SNP	.											Q13209_HUMAN,right_upper_lobe,carcinoma,0,8	.	.	8	4	Substitution - Missense(4)	prostate(4)	c.T956C						scavenged	.																																					11223	exon8			CCGTCGAGGTTCC	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.17085865A>G		Somatic	164	5	0.0304878		WXS	Illumina HiSeq	Phase_I	155	15	0.0967742	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	0.025	-1.380835	0.01204	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.000000	0.41823	N	0.000801	T	0.13243	0.0321	.	.	.	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.28202	-1.0051	6	0.02654	T	1	.	2.6652	0.05046	0.5:0.0:0.5:0.0	rs1057378;rs2092131;rs2446557;rs3206761;rs3982165;rs4052564;rs57482948	319	Q2TV78-2	.	P	309;319;319	.	ENSP00000439273:L319P	L	-	2	0	MST1P9	16958452	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	4.768000	0.62293	-0.000000	0.14550	0.000000	0.15137	CTC	A|1.000;|0.000	.	weak		0.667	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
GXYLT1	283464	hgsc.bcm.edu	37	12	42481617	42481617	+	Missense_Mutation	SNP	G	G	C	rs75740340		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:42481617G>C	ENST00000398675.3	-	8	1526	c.1294C>G	c.(1294-1296)Cgt>Ggt	p.R432G	GXYLT1_ENST00000280876.6_Missense_Mutation_p.R401G	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	432					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						CTGGCATAACGATCTCTTACA	0.328																																					p.R432G		Atlas-SNP	.											Q8IXV1_HUMAN,NS,carcinoma,+1,2	GXYLT1	47	2	0			c.C1294G						scavenged	.						105.0	93.0	97.0					12																	42481617		1836	4080	5916	SO:0001583	missense	283464	exon8			CATAACGATCTCT	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.1294C>G	12.37:g.42481617G>C	ENSP00000381666:p.Arg432Gly	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	104	3	0.0288462	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	37	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.647203	0.00792	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	.	.	.	4.9	2.75	0.32379	.	0.707951	0.13008	N	0.421091	T	0.29093	0.0723	L	0.29908	0.895	0.09310	N	1	B;B	0.24721	0.043;0.11	B;B	0.27608	0.068;0.081	T	0.18209	-1.0344	9	0.25751	T	0.34	-7.8089	7.8107	0.29230	0.1594:0.0:0.6532:0.1874	.	401;432	Q4G148-2;Q4G148	.;GXLT1_HUMAN	G	432;401	.	ENSP00000280876:R401G	R	-	1	0	GXYLT1	40767884	0.003000	0.15002	0.006000	0.13384	0.029000	0.11900	0.908000	0.28545	1.214000	0.43395	-0.119000	0.15052	CGT	G|0.998;C|0.002	0.002	weak		0.328	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
IQGAP3	128239	hgsc.bcm.edu	37	1	156499969	156499969	+	Silent	SNP	T	T	C	rs386635735|rs1171566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	72	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	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	
SNX16	64089	hgsc.bcm.edu	37	8	82727569	82727569	+	Silent	SNP	T	T	C	rs16909651	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:82727569T>C	ENST00000345957.4	-	5	950	c.672A>G	c.(670-672)gaA>gaG	p.E224E	SNX16_ENST00000396330.2_Silent_p.E224E|RP13-923O23.6_ENST00000524337.1_RNA|SNX16_ENST00000353788.4_Silent_p.E195E	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	88	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	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	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16535487	16535487	+	Missense_Mutation	SNP	G	G	C	rs143314517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16535487G>C	ENST00000270747.3	-	2	199	c.63C>G	c.(61-63)caC>caG	p.H21Q	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	21					regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		CTACAGGGTGGTGGGCAGTGC	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17289	0.0		0.0119	False		,,,				2504	0.0				p.H21Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C63G						PASS	.	G	GLN/HIS	9,4395		0,9,2193	17.0	19.0	18.0		63	1.0	0.0	1	dbSNP_134	18	114,8482		0,114,4184	no	missense	ARHGEF19	NM_153213.3	24	0,123,6377	CC,CG,GG		1.3262,0.2044,0.9462	benign	21/803	16535487	123,12877	2202	4298	6500	SO:0001583	missense	128272	exon2			AGGGTGGTGGGCA	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.63C>G	1.37:g.16535487G>C	ENSP00000270747:p.His21Gln	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.788	0.329777	0.10956	0.002044	0.013262	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.39592	1.07;1.07	5.12	1.02	0.19986	.	0.844696	0.10118	N	0.713769	T	0.16471	0.0396	N	0.14661	0.345	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.19516	-1.0303	10	0.52906	T	0.07	.	3.3172	0.07038	0.3042:0.0:0.5128:0.1829	.	21	Q8IW93	ARHGJ_HUMAN	Q	21	ENSP00000270747:H21Q;ENSP00000396001:H21Q	ENSP00000270747:H21Q	H	-	3	2	ARHGEF19	16408074	0.761000	0.28439	0.015000	0.15790	0.010000	0.07245	0.817000	0.27281	-0.076000	0.12775	0.462000	0.41574	CAC	G|0.993;C|0.007	0.007	strong		0.642	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
CTDP1	9150	hgsc.bcm.edu	37	18	77478011	77478011	+	Silent	SNP	C	C	T	rs35456241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:77478011C>T	ENST00000299543.7	+	10	2559	c.2412C>T	c.(2410-2412)tcC>tcT	p.S804S	CTDP1_ENST00000075430.7_Silent_p.S804S	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	804					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)		AGCCCTCTTCCTTCAGGTACG	0.647													C|||	293	0.0585064	0.0197	0.0303	5008	,	,		14405	0.0377		0.0318	False		,,,				2504	0.18				p.S804S		Atlas-SNP	.											.	CTDP1	67	.	0			c.C2412T						PASS	.	C	,,	101,4305		0,101,2102	22.0	27.0	26.0		2055,2412,2412	1.1	1.0	18	dbSNP_126	26	426,8172		17,392,3890	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	17,493,5992	TT,TC,CC		4.9546,2.2923,4.0526	,,	685/843,804/962,804/868	77478011	527,12477	2203	4299	6502	SO:0001819	synonymous_variant	9150	exon10			CTCTTCCTTCAGG	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.2412C>T	18.37:g.77478011C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			C|0.967;T|0.033	0.033	strong		0.647	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
NES	10763	hgsc.bcm.edu	37	1	156640933	156640933	+	Missense_Mutation	SNP	C	C	T	rs2365718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156640933C>T	ENST00000368223.3	-	4	3179	c.3047G>A	c.(3046-3048)aGc>aAc	p.S1016N		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1016	Tail.		S -> N (in dbSNP:rs2365718). {ECO:0000269|PubMed:1478958}.		brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCTCAGGGCTCTCTGGGTG	0.632													C|||	366	0.0730831	0.2171	0.036	5008	,	,		15575	0.0089		0.006	False		,,,				2504	0.0399				p.S1016N		Atlas-SNP	.											.	NES	196	.	0			c.G3047A						PASS	.	C	ASN/SER	913,3493	349.5+/-310.4	87,739,1377	142.0	158.0	153.0		3047	0.8	0.2	1	dbSNP_100	153	69,8531	41.7+/-99.0	0,69,4231	yes	missense	NES	NM_006617.1	46	87,808,5608	TT,TC,CC		0.8023,20.7217,7.5504	possibly-damaging	1016/1622	156640933	982,12024	2203	4300	6503	SO:0001583	missense	10763	exon4			TCAGGGCTCTCTG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3047G>A	1.37:g.156640933C>T	ENSP00000357206:p.Ser1016Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	124	0.056776556776556776	104	0.21138211382113822	11	0.03038674033149171	6	0.01048951048951049	3	0.00395778364116095	C	14.18	2.458809	0.43634	0.207217	0.008023	ENSG00000132688	ENST00000368223	D	0.89343	-2.5	5.35	0.766	0.18476	.	0.564159	0.14978	N	0.287443	T	0.80037	0.4550	M	0.63843	1.955	0.80722	P	0.0	P	0.40476	0.718	B	0.41860	0.368	T	0.72054	-0.4406	9	0.54805	T	0.06	.	8.4863	0.33074	0.3951:0.3473:0.2576:0.0	rs2365718;rs59519571;rs2365718	1016	P48681	NEST_HUMAN	N	1016	ENSP00000357206:S1016N	ENSP00000357206:S1016N	S	-	2	0	NES	154907557	0.000000	0.05858	0.187000	0.23214	0.428000	0.31595	-0.574000	0.05868	0.167000	0.19631	0.563000	0.77884	AGC	C|0.928;T|0.072	0.072	strong		0.632	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
MSGN1	343930	hgsc.bcm.edu	37	2	17998025	17998025	+	Missense_Mutation	SNP	A	A	T	rs34069439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	62	57	0.919355	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	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37488689	37488689	+	Missense_Mutation	SNP	G	G	C	rs1209750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:37488689G>C	ENST00000602533.1	+	30	2682	c.2583G>C	c.(2581-2583)aaG>aaC	p.K861N	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.K861N|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.K980N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	917					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						AACAAAAGAAGGTTGAAGAAA	0.274													.|||	2415	0.482228	0.671	0.5029	5008	,	,		15886	0.3244		0.5875	False		,,,				2504	0.2669				p.K861N		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G2583C						PASS	.	C	ASN/LYS	2319,1241		752,815,213	88.0	79.0	81.0		2583	-1.7	0.0	10	dbSNP_87	81	4648,3468		1323,2002,733	yes	missense	ANKRD30A	NM_052997.2	94	2075,2817,946	CC,CG,GG		42.7304,34.8596,40.3306	benign	861/1342	37488689	6967,4709	1780	4058	5838	SO:0001583	missense	91074	exon30			AAAGAAGGTTGAA	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.2583G>C	10.37:g.37488689G>C	ENSP00000473551:p.Lys861Asn	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	186	108	0.580645	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		1139	0.5215201465201466	324	0.6585365853658537	196	0.5414364640883977	167	0.291958041958042	452	0.5963060686015831	N	0.022	-1.408058	0.01155	0.651404	0.572696	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05580	3.42;3.42	0.868	-1.74	0.08056	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.28324	0.207	B	0.18561	0.022	T	0.42275	-0.9461	8	0.27082	T	0.32	.	4.0495	0.09788	0.2908:0.3384:0.3708:0.0	rs1209750;rs1782096;rs16906089;rs17606786;rs52817964;rs1209750	917	Q9BXX3	AN30A_HUMAN	N	861;980	ENSP00000354432:K861N;ENSP00000363792:K980N	ENSP00000354432:K861N	K	+	3	2	ANKRD30A	37528695	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.926000	0.03988	-3.843000	0.00100	-2.001000	0.00444	AAG	A|0.002;C|0.510;G|0.489	0.510	strong		0.274	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
RPL5	6125	hgsc.bcm.edu	37	1	93303114	93303114	+	Missense_Mutation	SNP	A	A	G	rs11540832	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:93303114A>G	ENST00000370321.3	+	6	719	c.629A>G	c.(628-630)tAc>tGc	p.Y210C	SNORA66_ENST00000515986.1_RNA|SNORD21_ENST00000383953.1_RNA	NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	210			Y -> C (in dbSNP:rs11540832). {ECO:0000269|PubMed:15489334}.		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 large subunit biogenesis (GO:0042273)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		TACATGCGCTACTTAATGGAA	0.388													A|||	11	0.00219649	0.0008	0.0029	5008	,	,		21318	0.0		0.007	False		,,,				2504	0.001				p.Y210C		Atlas-SNP	.											.	RPL5	38	.	0			c.A629G						PASS	.	A	CYS/TYR	7,4399	9.9+/-24.2	0,7,2196	39.0	37.0	38.0		629	5.2	1.0	1	dbSNP_120	38	66,8524	37.4+/-92.8	0,66,4229	yes	missense	RPL5	NM_000969.3	194	0,73,6425	GG,GA,AA		0.7683,0.1589,0.5617	benign	210/298	93303114	73,12923	2203	4295	6498	SO:0001583	missense	6125	exon6			TGCGCTACTTAAT	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"""L ribosomal proteins"""	10360	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 135"""	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.629A>G	1.37:g.93303114A>G	ENSP00000359345:p.Tyr210Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_000969	Q32LZ3|Q53HH6|Q9H3F4	Missense_Mutation	SNP	ENST00000370321.3	37	CCDS741.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	11.16	1.556840	0.27827	0.001589	0.007683	ENSG00000122406	ENST00000432788;ENST00000370321	T	0.42513	0.97	5.2	5.2	0.72013	.	0.264502	0.38959	N	0.001510	T	0.26122	0.0637	M	0.63843	1.955	0.80722	D	1	B;B	0.13594	0.008;0.008	B;B	0.15870	0.014;0.014	T	0.20706	-1.0267	10	0.54805	T	0.06	.	10.5895	0.45302	0.8563:0.0:0.0:0.1437	rs11540832;rs52827912;rs11540832	210;210	A2RUM7;P46777	.;RL5_HUMAN	C	160;210	ENSP00000359345:Y210C	ENSP00000359345:Y210C	Y	+	2	0	RPL5	93075702	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	3.663000	0.54518	2.080000	0.62538	0.533000	0.62120	TAC	A|0.995;G|0.005	0.005	strong		0.388	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969	
UQCC3	790955	hgsc.bcm.edu	37	11	62439569	62439569	+	Missense_Mutation	SNP	G	G	A	rs13941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:62439569G>A	ENST00000531323.1	+	3	808	c.265G>A	c.(265-267)Ggc>Agc	p.G89S	C11orf48_ENST00000354588.3_5'Flank|C11orf48_ENST00000431002.2_5'Flank|C11orf83_ENST00000377953.3_Missense_Mutation_p.G89S|C11orf48_ENST00000532208.1_5'Flank			Q6UW78	CK083_HUMAN		89				G -> S (in Ref. 1; AAQ89294 and 3; AAH90057). {ECO:0000305}.		extracellular region (GO:0005576)		p.G89S(1)		cervix(1)|lung(1)|prostate(1)	3						AGGCGGCGCCGGCGGGAGGTC	0.682													G|||	3753	0.749401	0.584	0.7522	5008	,	,		15513	0.9385		0.7296	False		,,,				2504	0.7965				p.G89S		Atlas-SNP	.											C11orf83,NS,carcinoma,0,2	C11orf83	13	2	1	Substitution - Missense(1)	prostate(1)	c.G265A						PASS	.	G	SER/GLY	2713,1609		851,1011,299	16.0	26.0	23.0		265	-3.4	0.0	11	dbSNP_52	23	5998,2498		2155,1688,405	yes	missense	C11orf83	NM_001085372.2	56	3006,2699,704	AA,AG,GG		29.4021,37.2281,32.0409	possibly-damaging	89/94	62439569	8711,4107	2161	4248	6409	SO:0001583	missense	790955	exon2			GGCGCCGGCGGGA																												ENST00000531323.1:c.265G>A	11.37:g.62439569G>A	ENSP00000432692:p.Gly89Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	72	0.972973	NM_001085372	Q5FVD5	Missense_Mutation	SNP	ENST00000531323.1	37	CCDS41658.1	1601	0.733058608058608	265	0.5386178861788617	252	0.6961325966850829	532	0.9300699300699301	552	0.7282321899736148	G	9.952	1.220343	0.22457	0.627719	0.705979	ENSG00000204922	ENST00000531323;ENST00000377953	.	.	.	3.14	-3.42	0.04825	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.22983	0.078	B	0.15484	0.013	T	0.20806	-1.0264	6	0.34782	T	0.22	-11.1992	8.551	0.33451	0.642:0.0:0.358:0.0	rs13941;rs3195442;rs13941	89	Q6UW78	CK083_HUMAN	S	89	.	ENSP00000367189:G89S	G	+	1	0	C11orf83	62196145	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.297000	0.19101	-0.828000	0.04273	-0.367000	0.07326	GGC	G|0.263;A|0.737	0.737	strong		0.682	C11orf83-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394992.2		
CUL7	9820	hgsc.bcm.edu	37	6	43020188	43020188	+	Silent	SNP	G	G	A	rs4711738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43020188G>A	ENST00000265348.3	-	2	424	c.339C>T	c.(337-339)gaC>gaT	p.D113D	CUL7_ENST00000535468.1_Silent_p.D165D			Q14999	CUL7_HUMAN	cullin 7	113					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)			GGGACTTCACGTCGGTTTCCA	0.612													A|||	1413	0.282149	0.5613	0.2205	5008	,	,		19600	0.2054		0.0905	False		,,,				2504	0.2249				p.D165D		Atlas-SNP	.											.	CUL7	133	.	0			c.C495T						PASS	.	A	,	2133,2273	597.5+/-388.9	504,1125,574	91.0	78.0	83.0		495,339	-9.3	0.0	6	dbSNP_111	83	790,7810	783.7+/-407.6	37,716,3547	no	coding-synonymous,coding-synonymous	CUL7	NM_001168370.1,NM_014780.4	,	541,1841,4121	AA,AG,GG		9.186,48.4113,22.4742	,	165/1783,113/1699	43020188	2923,10083	2203	4300	6503	SO:0001819	synonymous_variant	9820	exon2			CTTCACGTCGGTT	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.339C>T	6.37:g.43020188G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	41	0.66129	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																			G|0.755;A|0.245	0.245	strong		0.612	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
PELP1	27043	hgsc.bcm.edu	37	17	4577950	4577950	+	Silent	SNP	C	C	A	rs8081507	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:4577950C>A	ENST00000574876.1	-	13	1454	c.1437G>T	c.(1435-1437)cgG>cgT	p.R479R	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000301396.4_Silent_p.R623R|PELP1_ENST00000269230.7_Silent_p.R477R|PELP1_ENST00000572293.1_Silent_p.R529R|PELP1_ENST00000436683.2_Silent_p.R332R			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	479					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						CAGGGCTCCCCCGCGGGCTAC	0.582													C|||	240	0.0479233	0.0484	0.0749	5008	,	,		16277	0.0		0.0567	False		,,,				2504	0.0685				p.R479R		Atlas-SNP	.											.	PELP1	102	.	0			c.G1437T						PASS	.	C		180,3740		4,172,1784	29.0	31.0	30.0		1437	2.0	1.0	17	dbSNP_116	30	482,7832		16,450,3691	no	coding-synonymous	PELP1	NM_014389.2		20,622,5475	AA,AC,CC		5.7975,4.5918,5.4111		479/1131	4577950	662,11572	1960	4157	6117	SO:0001819	synonymous_variant	27043	exon13			GCTCCCCCGCGGG		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.1437G>T	17.37:g.4577950C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			C|0.939;A|0.061	0.061	strong		0.582	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
ASPHD2	57168	hgsc.bcm.edu	37	22	26829914	26829914	+	Silent	SNP	T	T	C	rs3747128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26829914T>C	ENST00000215906.5	+	2	771	c.333T>C	c.(331-333)ccT>ccC	p.P111P		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	111					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						GCCAGTCCCCTGAGTGCGTGC	0.647													C|||	324	0.0646965	0.0439	0.0591	5008	,	,		19562	0.0169		0.1382	False		,,,				2504	0.0706				p.P111P		Atlas-SNP	.											.	ASPHD2	42	.	0			c.T333C						PASS	.	C		309,4097	793.6+/-415.2	8,293,1902	59.0	49.0	52.0		333	-4.1	1.0	22	dbSNP_107	52	1442,7158	747.7+/-407.3	129,1184,2987	no	coding-synonymous	ASPHD2	NM_020437.4		137,1477,4889	CC,CT,TT		16.7674,7.0132,13.463		111/370	26829914	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	57168	exon2			GTCCCCTGAGTGC	AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.333T>C	22.37:g.26829914T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Silent	SNP	ENST00000215906.5	37	CCDS13834.2																																																																																			T|0.890;C|0.110	0.110	strong		0.647	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
RP1	6101	hgsc.bcm.edu	37	8	55541226	55541226	+	Missense_Mutation	SNP	G	G	A	rs35084330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55541226G>A	ENST00000220676.1	+	4	4932	c.4784G>A	c.(4783-4785)cGg>cAg	p.R1595Q		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1595			R -> Q (in dbSNP:rs35084330). {ECO:0000269|PubMed:10484783, ECO:0000269|PubMed:11095597}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TCAGACTATCGGCCTGACAGT	0.398													G|||	121	0.0241613	0.0673	0.0231	5008	,	,		17908	0.0		0.0099	False		,,,				2504	0.0061				p.R1595Q	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G4784A						PASS	.	G	GLN/ARG	296,4110	162.5+/-194.5	9,278,1916	64.0	62.0	63.0		4784	3.0	0.0	8	dbSNP_126	63	141,8459	69.7+/-132.2	0,141,4159	yes	missense	RP1	NM_006269.1	43	9,419,6075	AA,AG,GG		1.6395,6.7181,3.36	probably-damaging	1595/2157	55541226	437,12569	2203	4300	6503	SO:0001583	missense	6101	exon4			ACTATCGGCCTGA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4784G>A	8.37:g.55541226G>A	ENSP00000220676:p.Arg1595Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	60	0.027472527472527472	40	0.08130081300813008	15	0.04143646408839779	0	0.0	5	0.006596306068601583	G	13.24	2.176960	0.38413	0.067181	0.016395	ENSG00000104237	ENST00000220676	T	0.68181	-0.31	5.74	2.96	0.34315	.	0.388763	0.22090	N	0.064773	T	0.10895	0.0266	M	0.66939	2.045	0.20764	N	0.999858	D	0.63880	0.993	P	0.48227	0.571	T	0.25363	-1.0134	10	0.87932	D	0	-0.3854	11.1721	0.48577	0.0649:0.241:0.6941:0.0	rs35084330	1595	P56715	RP1_HUMAN	Q	1595	ENSP00000220676:R1595Q	ENSP00000220676:R1595Q	R	+	2	0	RP1	55703779	0.986000	0.35501	0.001000	0.08648	0.144000	0.21451	2.623000	0.46435	0.335000	0.23614	-0.136000	0.14681	CGG	G|0.969;A|0.031	0.031	strong		0.398	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:95496882C>T	ENST00000317968.4	+	5	543	c.407C>T	c.(406-408)tCt>tTt	p.S136F	PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.S14F|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000450793.1_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	136			S -> F (in dbSNP:rs2452600). {ECO:0000269|PubMed:14702039}.		regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		GGTTCTGTGTCTTCACCAAAA	0.527													C|||	1125	0.224641	0.1051	0.2378	5008	,	,		19873	0.378		0.3121	False		,,,				2504	0.1288				p.S136F		Atlas-SNP	.											.	PDLIM5	76	.	0			c.C407T						PASS	.	C	,,,PHE/SER	594,3812	261.9+/-264.6	38,518,1647	296.0	259.0	271.0		,,,407	4.4	1.0	4	dbSNP_100	271	2668,5932	429.7+/-356.3	434,1800,2066	yes	intron,intron,intron,missense	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,155	472,2318,3713	TT,TC,CC		31.0233,13.4816,25.0807	,,,possibly-damaging	,,,136/597	95496882	3262,9744	2203	4300	6503	SO:0001583	missense	10611	exon5			CTGTGTCTTCACC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.407C>T	4.37:g.95496882C>T	ENSP00000321746:p.Ser136Phe	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	601	0.2751831501831502	43	0.08739837398373984	84	0.23204419889502761	242	0.4230769230769231	232	0.30606860158311344	C	20.8	4.042342	0.75732	0.134816	0.310233	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.61627	0.58;0.09	5.25	4.39	0.52855	.	0.343767	0.28865	N	0.013899	T	0.00012	0.0000	L	0.44542	1.39	0.28580	P	0.9101637	P	0.49961	0.93	B	0.42214	0.38	T	0.45086	-0.9285	9	0.56958	D	0.05	.	13.5979	0.62002	0.0:0.9248:0.0:0.0752	rs2452600;rs3792659;rs52807888;rs56704997;rs2452600	136	Q96HC4	PDLI5_HUMAN	F	136;14	ENSP00000321746:S136F;ENSP00000442187:S14F	ENSP00000321746:S136F	S	+	2	0	PDLIM5	95715905	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.262000	0.43285	2.590000	0.87494	0.655000	0.94253	TCT	C|0.737;T|0.263	0.263	strong		0.527	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
P2RX7	5027	hgsc.bcm.edu	37	12	121615131	121615131	+	Missense_Mutation	SNP	C	C	G	rs2230911	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121615131C>G	ENST00000546057.1	+	11	1213	c.1070C>G	c.(1069-1071)aCt>aGt	p.T357S	P2RX7_ENST00000535250.1_Missense_Mutation_p.T267S|P2RX7_ENST00000541446.1_Missense_Mutation_p.T68S|P2RX7_ENST00000328963.5_Missense_Mutation_p.T187S|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	357			T -> S (in dbSNP:rs2230911). {ECO:0000269|PubMed:14702039}.		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)					CTCATCGACACTTACTCCAGT	0.502													C|||	826	0.164936	0.1589	0.2622	5008	,	,		19005	0.1677		0.0785	False		,,,				2504	0.1902				p.T357S		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1070G	GRCh37	CM060405	P2RX7	M	rs2230911	PASS	.	C	SER/THR	695,3711	291.5+/-281.6	57,581,1565	122.0	108.0	113.0		1070	4.8	1.0	12	dbSNP_98	113	635,7965	163.5+/-216.0	29,577,3694	yes	missense	P2RX7	NM_002562.5	58	86,1158,5259	GG,GC,CC		7.3837,15.7739,10.226	possibly-damaging	357/596	121615131	1330,11676	2203	4300	6503	SO:0001583	missense	5027	exon11			TCGACACTTACTC	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.1070C>G	12.37:g.121615131C>G	ENSP00000442349:p.Thr357Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	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	314	0.14377289377289376	79	0.16056910569105692	85	0.23480662983425415	95	0.1660839160839161	55	0.07255936675461741	C	16.20	3.055762	0.55325	0.157739	0.073837	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.04156	3.69;3.69;3.69;3.69	5.69	4.8	0.61643	.	0.000000	0.51477	D	0.000087	T	0.00012	0.0000	M	0.78456	2.415	0.31019	P	0.718307	B;B;B;P	0.45531	0.314;0.084;0.169;0.86	B;B;B;B	0.43052	0.027;0.037;0.029;0.406	T	0.50825	-0.8782	9	0.23302	T	0.38	.	12.16	0.54099	0.0:0.9185:0.0:0.0815	rs2230911;rs6489795;rs52828044;rs58737639;rs2230911	187;68;267;357	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	S	357;187;267;68	ENSP00000442349:T357S;ENSP00000330696:T187S;ENSP00000442572:T267S;ENSP00000437471:T68S	ENSP00000330696:T187S	T	+	2	0	P2RX7	120099514	0.892000	0.30473	0.989000	0.46669	0.952000	0.60782	1.802000	0.38853	2.699000	0.92147	0.591000	0.81541	ACT	C|0.885;G|0.115	0.115	strong		0.502	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ZNF492	57615	hgsc.bcm.edu	37	19	22847084	22847084	+	Missense_Mutation	SNP	G	G	T	rs139985933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:22847084G>T	ENST00000456783.2	+	4	857	c.613G>T	c.(613-615)Gcc>Tcc	p.A205S	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	205					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.A205S(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				GTGTGGAAAAGCCTTTAACCG	0.388													N|||	1056	0.210863	0.3994	0.1311	5008	,	,		16784	0.1736		0.1362	False		,,,				2504	0.1278				p.A205S		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G613T						scavenged	.						10.0	14.0	13.0					19																	22847084		1817	4100	5917	SO:0001583	missense	57615	exon4			GGAAAAGCCTTTA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.613G>T	19.37:g.22847084G>T	ENSP00000413660:p.Ala205Ser	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	205	68	0.331707	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	372	0.17032967032967034	149	0.30284552845528456	48	0.13259668508287292	91	0.1590909090909091	84	0.11081794195250659	.	11.77	1.736335	0.30774	.	.	ENSG00000229676	ENST00000456783	T	0.00856	5.61	1.3	-2.61	0.06171	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.20304	0.555	0.49915	P	1.6799999999994597E-4	D	0.76494	0.999	D	0.79784	0.993	T	0.54180	-0.8332	8	0.56958	D	0.05	.	2.3465	0.04272	0.374:0.0:0.3942:0.2319	.	205	Q9P255	ZN492_HUMAN	S	205	ENSP00000413660:A205S	ENSP00000413660:A205S	A	+	1	0	ZNF492	22638924	0.000000	0.05858	0.012000	0.15200	0.018000	0.09664	-0.253000	0.08794	-0.480000	0.06803	-0.798000	0.03219	GCC	G|0.500;T|0.500	0.500	strong		0.388	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
FLVCR1	28982	hgsc.bcm.edu	37	1	213031948	213031948	+	Missense_Mutation	SNP	G	G	C	rs11120047	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:213031948G>C	ENST00000366971.4	+	1	352	c.154G>C	c.(154-156)Gcc>Ccc	p.A52P	FLVCR1-AS1_ENST00000356684.3_lincRNA	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	52			A -> P (in dbSNP:rs11120047). {ECO:0000269|PubMed:15489334}.		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)		GGTGAATGGGGCCCCCCGGGA	0.716													G|||	2226	0.444489	0.2269	0.3084	5008	,	,		12077	0.5476		0.5646	False		,,,				2504	0.6053				p.A52P	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.G154C						PASS	.	G	PRO/ALA	992,2868		199,594,1137	3.0	6.0	5.0		154	3.2	0.0	1	dbSNP_120	5	3551,4103		951,1649,1227	yes	missense	FLVCR1	NM_014053.3	27	1150,2243,2364	CC,CG,GG		46.394,25.6995,39.4563	benign	52/556	213031948	4543,6971	1930	3827	5757	SO:0001583	missense	28982	exon1			AATGGGGCCCCCC	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.154G>C	1.37:g.213031948G>C	ENSP00000355938:p.Ala52Pro	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	34	29	0.852941	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	37	CCDS1510.1	986	0.45146520146520147	129	0.2621951219512195	129	0.356353591160221	315	0.5506993006993007	413	0.5448548812664907	G	13.29	2.193274	0.38707	0.256995	0.46394	ENSG00000162769	ENST00000366971	D	0.83250	-1.7	5.04	3.17	0.36434	.	1.238010	0.05829	N	0.617282	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22604	0.072	B	0.23018	0.043	T	0.38845	-0.9642	9	0.30078	T	0.28	-10.6878	10.1458	0.42762	0.1646:0.0:0.8354:0.0	rs11120047;rs17846435;rs17859484;rs56728027;rs11120047	52	Q9Y5Y0	FLVC1_HUMAN	P	52	ENSP00000355938:A52P	ENSP00000355938:A52P	A	+	1	0	FLVCR1	211098571	1.000000	0.71417	0.002000	0.10522	0.010000	0.07245	5.238000	0.65366	0.534000	0.28695	-0.253000	0.11424	GCC	G|0.542;C|0.458	0.458	strong		0.716	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	
ZNF486	90649	hgsc.bcm.edu	37	19	20308207	20308207	+	Missense_Mutation	SNP	A	A	T	rs148497901	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:20308207A>T	ENST00000335117.8	+	4	745	c.688A>T	c.(688-690)Ata>Tta	p.I230L	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	230					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						TACACATAAGATAACTCATAC	0.363													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		19318	0.0		0.0249	False		,,,				2504	0.001				p.I230L		Atlas-SNP	.											.	ZNF486	74	.	0			c.A688T						PASS	.	A	LEU/ILE	16,4292		0,16,2138	40.0	43.0	42.0		688	0.8	0.0	19	dbSNP_134	42	187,8375		6,175,4100	no	missense	ZNF486	NM_052852.2	5	6,191,6238	TT,TA,AA		2.1841,0.3714,1.5773	benign	230/464	20308207	203,12667	2154	4281	6435	SO:0001583	missense	90649	exon4			CATAAGATAACTC	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.688A>T	19.37:g.20308207A>T	ENSP00000335042:p.Ile230Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	27	0.75	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	24	0.01098901098901099	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	19	0.025065963060686015	a	9.789	1.177288	0.21787	0.003714	0.021841	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.18016	2.24	0.814	0.814	0.18756	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02267	0.0070	N	0.01076	-1.035	0.19575	N	0.999961	B	0.32467	0.372	B	0.42959	0.403	T	0.36311	-0.9753	9	0.66056	D	0.02	.	5.4337	0.16469	1.0:0.0:0.0:0.0	.	230	Q96H40	ZN486_HUMAN	L	269;230	ENSP00000335042:I230L	ENSP00000335042:I230L	I	+	1	0	ZNF486	20169207	0.000000	0.05858	0.037000	0.18230	0.036000	0.12997	-0.471000	0.06631	0.158000	0.19367	0.156000	0.16432	ATA	A|0.986;T|0.014	0.014	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
ABCA12	26154	hgsc.bcm.edu	37	2	215854156	215854156	+	Silent	SNP	C	C	T	rs71428357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:215854156C>T	ENST00000272895.7	-	26	3945	c.3726G>A	c.(3724-3726)ccG>ccA	p.P1242P	ABCA12_ENST00000389661.4_Silent_p.P924P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1242					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)		CATCCTGAACCGGGGAGGTGT	0.418													C|||	360	0.071885	0.0968	0.1888	5008	,	,		12269	0.001		0.0567	False		,,,				2504	0.044				p.P1242P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.G3726A						PASS	.	C	,	427,3979	208.2+/-229.3	24,379,1800	111.0	111.0	111.0		2772,3726	-9.2	1.0	2	dbSNP_130	111	512,8088	145.4+/-201.1	18,476,3806	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	42,855,5606	TT,TC,CC		5.9535,9.6913,7.2197	,	924/2278,1242/2596	215854156	939,12067	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon26			CTGAACCGGGGAG	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.3726G>A	2.37:g.215854156C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			C|0.925;T|0.075	0.075	strong		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
BPIFC	254240	hgsc.bcm.edu	37	22	32808078	32808078	+	IGR	SNP	G	G	A	rs11545749	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32808078G>A	ENST00000397452.1	-	0	2091				RTCB_ENST00000451746.2_Silent_p.I22I|RTCB_ENST00000216038.5_Silent_p.I22I			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C							extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										AGCCCTTCTTGATCCTCCAGC	0.577													G|||	290	0.0579073	0.1188	0.0303	5008	,	,		16916	0.0139		0.0527	False		,,,				2504	0.046				p.I22I		Atlas-SNP	.											.	C22orf28	43	.	0			c.C66T						PASS	.	G		478,3928	224.3+/-240.5	33,412,1758	106.0	106.0	106.0		66	5.0	1.0	22	dbSNP_120	106	372,8228	122.2+/-181.2	15,342,3943	no	coding-synonymous	C22orf28	NM_014306.4		48,754,5701	AA,AG,GG		4.3256,10.8488,6.5354		22/506	32808078	850,12156	2203	4300	6503	SO:0001628	intergenic_variant	51493	exon1			CTTCTTGATCCTC	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273		22.37:g.32808078G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_014306	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																			G|0.934;A|0.066	0.066	strong		0.577	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
SLFN5	162394	hgsc.bcm.edu	37	17	33592591	33592591	+	Missense_Mutation	SNP	C	C	T	rs11651240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33592591C>T	ENST00000299977.4	+	5	2508	c.2360C>T	c.(2359-2361)cCg>cTg	p.P787L	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	787			P -> L (in dbSNP:rs11651240). {ECO:0000269|PubMed:14702039}.		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)		GGTTATTCTCCGAAGGATATT	0.408													C|||	1054	0.210463	0.0703	0.2594	5008	,	,		23096	0.0744		0.4751	False		,,,				2504	0.2331				p.P787L		Atlas-SNP	.											.	SLFN5	92	.	0			c.C2360T						PASS	.	C	LEU/PRO	547,3859	247.8+/-255.9	35,477,1691	126.0	120.0	122.0		2360	2.3	0.1	17	dbSNP_120	122	3903,4697	547.6+/-385.2	884,2135,1281	yes	missense	SLFN5	NM_144975.3	98	919,2612,2972	TT,TC,CC		45.3837,12.4149,34.215	benign	787/892	33592591	4450,8556	2203	4300	6503	SO:0001583	missense	162394	exon5			ATTCTCCGAAGGA	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.2360C>T	17.37:g.33592591C>T	ENSP00000299977:p.Pro787Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	547	0.25045787545787546	35	0.07113821138211382	107	0.2955801104972376	48	0.08391608391608392	357	0.470976253298153	c	13.72	2.322746	0.41096	0.124149	0.453837	ENSG00000166750	ENST00000299977	D	0.82984	-1.67	3.28	2.29	0.28610	.	0.225673	0.22687	N	0.056868	T	0.00012	0.0000	M	0.75085	2.285	0.52501	P	4.099999999995774E-5	D	0.52996	0.957	B	0.34242	0.178	T	0.30765	-0.9967	9	0.59425	D	0.04	.	6.4697	0.22001	0.0:0.8595:0.0:0.1405	rs11651240;rs17548033;rs52816228;rs61114948;rs11651240	787	Q08AF3	SLFN5_HUMAN	L	787	ENSP00000299977:P787L	ENSP00000299977:P787L	P	+	2	0	SLFN5	30616704	0.000000	0.05858	0.149000	0.22428	0.417000	0.31264	0.314000	0.19432	0.710000	0.31997	0.655000	0.94253	CCG	C|0.710;T|0.290	0.290	strong		0.408	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
VPS13A	23230	hgsc.bcm.edu	37	9	79917864	79917864	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:79917864A>G	ENST00000360280.3	+	34	4106	c.3846A>G	c.(3844-3846)gtA>gtG	p.V1282V	VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000357409.5_Silent_p.V1282V|VPS13A_ENST00000376636.3_Silent_p.V1243V|VPS13A_ENST00000376634.4_Silent_p.V1282V	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1282					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ACCAGGAAGTACTGGATCTAC	0.338																																					p.V1282V		Atlas-SNP	.											VPS13A_ENST00000376634,NS,carcinoma,+2,3	VPS13A	735	3	0			c.A3846G						scavenged	.						118.0	115.0	116.0					9																	79917864		2203	4300	6503	SO:0001819	synonymous_variant	23230	exon34			GGAAGTACTGGAT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3846A>G	9.37:g.79917864A>G		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	121	3	0.0247934	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			.	.	none		0.338	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
BFSP1	631	hgsc.bcm.edu	37	20	17479617	17479617	+	Silent	SNP	G	G	A	rs11537702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:17479617G>A	ENST00000377873.3	-	6	843	c.804C>T	c.(802-804)aaC>aaT	p.N268N	BFSP1_ENST00000377868.2_Silent_p.N143N|BFSP1_ENST00000536626.1_Silent_p.N129N|BFSP1_ENST00000544874.1_Silent_p.N129N	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	268	Coil 2.|Rod.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CAATCTGCTCGTTATAAAGCT	0.507													G|||	113	0.0225639	0.003	0.0346	5008	,	,		20099	0.0		0.0696	False		,,,				2504	0.0153				p.N268N		Atlas-SNP	.											.	BFSP1	55	.	0			c.C804T						PASS	.	G	,	62,4344	59.3+/-96.0	2,58,2143	149.0	135.0	140.0		429,804	-12.1	0.0	20	dbSNP_120	140	677,7923	169.3+/-220.7	32,613,3655	no	coding-synonymous,coding-synonymous	BFSP1	NM_001161705.1,NM_001195.3	,	34,671,5798	AA,AG,GG		7.8721,1.4072,5.682	,	143/541,268/666	17479617	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	631	exon6			CTGCTCGTTATAA	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.804C>T	20.37:g.17479617G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																			G|0.955;A|0.045	0.045	strong		0.507	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
OR1D5	8386	hgsc.bcm.edu	37	17	2966273	2966273	+	Missense_Mutation	SNP	G	G	A	rs2676567	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2966273G>A	ENST00000575751.1	-	1	628	c.629C>T	c.(628-630)cCc>cTc	p.P210L		NM_014566.1	NP_055381.1	P58170	OR1D5_HUMAN	olfactory receptor, family 1, subfamily D, member 5	210					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|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(1)|lung(10)	11						GAACCCTAAGGGGGTGAGGAA	0.493													g|||	1358	0.271166	0.3843	0.2968	5008	,	,		30243	0.0228		0.331	False		,,,				2504	0.2945				p.P210L		Atlas-SNP	.											.	OR1D5	33	.	0			c.C629T						PASS	.						60.0	72.0	68.0					17																	2966273		2170	4290	6460	SO:0001583	missense	8386	exon1			CCTAAGGGGGTGA	AF087923	CCDS58499.1	17p13.3	2012-10-09			ENSG00000262628	ENSG00000262628		"""GPCR / Class A : Olfactory receptors"""	8186	protein-coding gene	gene with protein product						10673334	Standard	NM_014566		Approved	OR17-31	uc021tns.1	P58170	OTTHUMG00000177676	ENST00000575751.1:c.629C>T	17.37:g.2966273G>A	ENSP00000459028:p.Pro210Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	285	74	0.259649	NM_014566	Q96RA6	Missense_Mutation	SNP	ENST00000575751.1	37	CCDS58499.1																																																																																			G|0.645;A|0.355	0.355	strong		0.493	OR1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438410.2	NM_014566	
LRRC8B	23507	hgsc.bcm.edu	37	1	90048248	90048248	+	Silent	SNP	C	C	T	rs12130207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:90048248C>T	ENST00000330947.2	+	5	399	c.39C>T	c.(37-39)gcC>gcT	p.A13A	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.A13A|LRRC8B_ENST00000439853.1_Silent_p.A13A	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	13					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		TAGCAGATGCCCAGTCATCTT	0.463													C|||	738	0.147364	0.1573	0.1873	5008	,	,		21834	0.0407		0.2177	False		,,,				2504	0.1431				p.A13A		Atlas-SNP	.											LRRC8B,NS,neuroblastoma,+2,1	LRRC8B	49	1	0			c.C39T						scavenged	.	C	,	692,3714	289.2+/-280.3	58,576,1569	146.0	137.0	140.0		39,39	3.5	1.0	1	dbSNP_120	140	1808,6792	325.9+/-317.1	195,1418,2687	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	253,1994,4256	TT,TC,CC		21.0233,15.7059,19.2219	,	13/804,13/804	90048248	2500,10506	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			AGATGCCCAGTCA	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.39C>T	1.37:g.90048248C>T		Somatic	155	2	0.0129032		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			C|0.814;T|0.186	0.186	strong		0.463	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
NBEAL1	65065	hgsc.bcm.edu	37	2	204073435	204073435	+	Missense_Mutation	SNP	G	G	A	rs182855092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204073435G>A	ENST00000449802.1	+	51	7828	c.7495G>A	c.(7495-7497)Ggc>Agc	p.G2499S		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2499										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						ACTGAGTGTCGGCATCAGCAC	0.393													G|||	12	0.00239617	0.0008	0.0029	5008	,	,		18561	0.0		0.0089	False		,,,				2504	0.0				p.G2499S		Atlas-SNP	.											NBEAL1_ENST00000449802,NS,carcinoma,0,2	NBEAL1	266	2	0			c.G7495A						PASS	.	G	SER/GLY	11,3773		0,11,1881	118.0	107.0	111.0		7495	4.2	0.2	2		111	63,8201		0,63,4069	yes	missense	NBEAL1	NM_001114132.1	56	0,74,5950	AA,AG,GG		0.7623,0.2907,0.6142	benign	2499/2695	204073435	74,11974	1892	4132	6024	SO:0001583	missense	65065	exon51			AGTGTCGGCATCA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7495G>A	2.37:g.204073435G>A	ENSP00000399903:p.Gly2499Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	12.53	1.964359	0.34659	0.002907	0.007623	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.56275	0.47;0.47	5.95	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.436558	0.29699	N	0.011432	T	0.17450	0.0419	N	0.02103	-0.685	0.22511	N	0.999033	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.006	T	0.11941	-1.0567	10	0.34782	T	0.22	.	7.7682	0.28993	0.1365:0.0:0.7329:0.1306	.	2499;2488	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	S	2499;2430;514	ENSP00000399903:G2499S;ENSP00000388466:G514S	ENSP00000344985:G2430S	G	+	1	0	NBEAL1	203781680	0.097000	0.21791	0.157000	0.22605	0.707000	0.40811	0.907000	0.28531	0.858000	0.35431	-0.244000	0.11960	GGC	G|0.995;A|0.005	0.005	strong		0.393	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
COL18A1	80781	hgsc.bcm.edu	37	21	46909426	46909426	+	Silent	SNP	G	G	A	rs61731167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46909426G>A	ENST00000359759.4	+	18	3216	c.3195G>A	c.(3193-3195)ccG>ccA	p.P1065P	COL18A1_ENST00000400337.2_Silent_p.P650P|COL18A1_ENST00000355480.5_Silent_p.P830P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1065	Triple-helical region 4 (COL4).				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)		CTGGGCTGCCGGGGGCGAAGG	0.701													g|||	230	0.0459265	0.0219	0.0288	5008	,	,		11637	0.005		0.0755	False		,,,				2504	0.1022				p.P830P		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2490A						PASS	.	A	,	94,3850		1,92,1879	14.0	18.0	16.0		2490,1950	-7.5	0.0	21	dbSNP_129	16	458,7796		9,440,3678	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	10,532,5557	AA,AG,GG		5.5488,2.3834,4.5253	,	830/1520,650/1340	46909426	552,11646	1972	4127	6099	SO:0001819	synonymous_variant	80781	exon18			GCTGCCGGGGGCG		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.3195G>A	21.37:g.46909426G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				G|0.956;A|0.044	0.044	strong		0.701	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
UCP1	7350	hgsc.bcm.edu	37	4	141489068	141489068	+	Missense_Mutation	SNP	C	C	T	rs45539933	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:141489068C>T	ENST00000262999.3	-	2	265	c.190G>A	c.(190-192)Gct>Act	p.A64T		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	64			A -> T (in dbSNP:rs45539933). {ECO:0000269|PubMed:12756473}.		brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)	oxidative phosphorylation uncoupler activity (GO:0017077)	p.A64T(1)		NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					TTTACCACAGCGGTGATTGTT	0.537													T|||	430	0.0858626	0.0832	0.0879	5008	,	,		16446	0.0645		0.0765	False		,,,				2504	0.1196				p.A64T		Atlas-SNP	.											UCP1,NS,carcinoma,0,1	UCP1	33	1	1	Substitution - Missense(1)	stomach(1)	c.G190A	GRCh37	CM031390	UCP1	M	rs45539933	PASS	.	T	THR/ALA	299,4107	799.3+/-415.5	9,281,1913	92.0	96.0	95.0		190	5.5	0.1	4	dbSNP_127	95	641,7959	790.7+/-407.6	17,607,3676	yes	missense	UCP1	NM_021833.4	58	26,888,5589	TT,TC,CC		7.4535,6.7862,7.2274	benign	64/308	141489068	940,12066	2203	4300	6503	SO:0001583	missense	7350	exon2			CCACAGCGGTGAT	X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"""Solute carriers"""	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.190G>A	4.37:g.141489068C>T	ENSP00000262999:p.Ala64Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_021833	Q13218|Q4KMZ3|Q68G66	Missense_Mutation	SNP	ENST00000262999.3	37	CCDS3753.1	190	0.08699633699633699	50	0.1016260162601626	33	0.09116022099447514	47	0.08216783216783216	60	0.079155672823219	T	1.398	-0.578927	0.03854	0.067862	0.074535	ENSG00000109424	ENST00000262999	T	0.78246	-1.16	5.51	5.51	0.81932	Mitochondrial carrier domain (2);	0.049674	0.85682	N	0.000000	T	0.01092	0.0036	N	0.00197	-1.87	0.46823	P	7.810000000000317E-4	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.24476	-1.0159	9	0.02654	T	1	.	9.7753	0.40614	0.0:0.0821:0.0:0.9179	rs45539933	64;64	Q4KMT7;P25874	.;UCP1_HUMAN	T	64	ENSP00000262999:A64T	ENSP00000262999:A64T	A	-	1	0	UCP1	141708518	1.000000	0.71417	0.067000	0.19924	0.206000	0.24218	3.926000	0.56491	0.933000	0.37291	-0.254000	0.11334	GCT	C|0.920;T|0.080	0.080	strong		0.537	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1		
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242757820G>A	ENST00000391969.2	+	5	1612	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	NEU4_ENST00000407683.1_Missense_Mutation_p.G301R|NEU4_ENST00000404257.1_Missense_Mutation_p.G313R|NEU4_ENST00000405370.1_Missense_Mutation_p.G301R|NEU4_ENST00000325935.6_Missense_Mutation_p.G314R	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	301	Pro-rich.		G -> R (in dbSNP:rs11545301). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14962670, ECO:0000269|PubMed:15498874}.		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)		AGTGGGCCCCGGGAGTCCCCT	0.701													G|||	1213	0.242212	0.2988	0.2176	5008	,	,		13537	0.1002		0.2783	False		,,,				2504	0.2924				p.G314R		Atlas-SNP	.											.	NEU4	39	.	0			c.G940A						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1158,3026		168,822,1102	9.0	12.0	11.0		940,901,901,901,937	-3.2	0.0	2	dbSNP_120	11	2335,5971		357,1621,2175	yes	missense,missense,missense,missense,missense	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	125,125,125,125,125	525,2443,3277	AA,AG,GG		28.1122,27.6769,27.9664	benign,benign,benign,benign,benign	314/498,301/485,301/485,301/485,313/497	242757820	3493,8997	2092	4153	6245	SO:0001583	missense	129807	exon4			GGCCCCGGGAGTC	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.901G>A	2.37:g.242757820G>A	ENSP00000375830:p.Gly301Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	37	CCDS54442.1	531	0.24313186813186813	153	0.31097560975609756	92	0.2541436464088398	62	0.10839160839160839	224	0.2955145118733509	G	1.760	-0.486996	0.04352	0.276769	0.281122	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000404257;ENST00000391969;ENST00000325935	T;T;T;T;T	0.75367	-0.92;-0.92;-0.93;-0.92;-0.93	3.37	-3.25	0.05079	Neuraminidase (1);	1.630680	0.03917	N	0.282864	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.03566	-1.1024	9	0.09084	T	0.74	-3.816	5.0178	0.14345	0.4482:0.0:0.4064:0.1453	rs11545301	313;313;301	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	R	301;301;311;313;301;314	ENSP00000385402:G301R;ENSP00000384804:G301R;ENSP00000385149:G313R;ENSP00000375830:G301R;ENSP00000320318:G314R	ENSP00000320318:G314R	G	+	1	0	NEU4	242406493	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.972000	0.03802	-0.372000	0.07992	-0.529000	0.04317	GGG	G|0.725;A|0.275	0.275	strong		0.701	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
POM121	9883	hgsc.bcm.edu	37	7	72413243	72413243	+	Missense_Mutation	SNP	A	A	C	rs437678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72413243A>C	ENST00000434423.2	+	11	2711	c.2711A>C	c.(2710-2712)cAc>cCc	p.H904P	POM121_ENST00000446813.1_Missense_Mutation_p.H639P|POM121_ENST00000358357.3_Missense_Mutation_p.H639P|POM121_ENST00000257622.4_Missense_Mutation_p.H639P|POM121_ENST00000395270.1_Missense_Mutation_p.H639P			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	904	Pore side. {ECO:0000255}.|Thr-rich.			H -> P (in Ref. 3; BAB14097). {ECO:0000305}.	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.H639P(6)		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)				CAGTCCCTGCACACTGCCGTG	0.647																																					p.H639P		Atlas-SNP	.											POM121_ENST00000395270,NS,carcinoma,0,6	POM121	131	6	6	Substitution - Missense(6)	prostate(6)	c.A1916C						scavenged	.						88.0	107.0	101.0					7																	72413243		2117	4262	6379	SO:0001583	missense	9883	exon11			CCCTGCACACTGC	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.2711A>C	7.37:g.72413243A>C	ENSP00000405562:p.His904Pro	Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	248	5	0.0201613	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	C	0.003	-2.495477	0.00159	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.04454	3.62;3.62;3.62;3.62;3.87	1.77	1.77	0.24775	.	0.328471	0.18142	N	0.150374	T	0.00815	0.0027	N	0.00063	-2.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41124	-0.9526	9	0.02654	T	1	.	7.4894	0.27452	0.2589:0.7411:0.0:0.0	.	639;904	A8MXF9;Q96HA1	.;P121A_HUMAN	P	639;639;639;639;904	ENSP00000393020:H639P;ENSP00000257622:H639P;ENSP00000378687:H639P;ENSP00000351124:H639P;ENSP00000405562:H904P	ENSP00000257622:H639P	H	+	2	0	POM121	72051179	0.000000	0.05858	0.008000	0.14137	0.223000	0.24884	0.580000	0.23803	0.325000	0.23359	-1.203000	0.01651	CAC	A|0.500;C|0.500	0.500	strong		0.647	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
LRRTM1	347730	hgsc.bcm.edu	37	2	80530062	80530062	+	Missense_Mutation	SNP	T	T	C	rs76300062	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:80530062T>C	ENST00000295057.3	-	2	1539	c.883A>G	c.(883-885)Atc>Gtc	p.I295V	CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.I295V|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000541047.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	295					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CGGGGCTCGATGTAGGTGAGG	0.622										HNSCC(69;0.2)			T|||	115	0.0229633	0.0061	0.0144	5008	,	,		18209	0.0397		0.0358	False		,,,				2504	0.0215				p.I295V		Atlas-SNP	.											.	LRRTM1	251	.	0			c.A883G						PASS	.	T	,,VAL/ILE	37,4369	41.6+/-74.8	0,37,2166	57.0	57.0	57.0		,,883	-8.1	0.3	2	dbSNP_131	57	193,8407	84.8+/-147.2	0,193,4107	yes	intron,intron,missense	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,29	0,230,6273	CC,CT,TT		2.2442,0.8398,1.7684	,,benign	,,295/523	80530062	230,12776	2203	4300	6503	SO:0001583	missense	347730	exon2			GCTCGATGTAGGT	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.883A>G	2.37:g.80530062T>C	ENSP00000295057:p.Ile295Val	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	162	86	0.530864	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	64	0.029304029304029304	2	0.0040650406504065045	9	0.024861878453038673	25	0.043706293706293704	28	0.036939313984168866	T	0.873	-0.731247	0.03135	0.008398	0.022442	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.62498	0.02;0.02	5.26	-8.12	0.01078	.	0.308918	0.30901	N	0.008659	T	0.09949	0.0244	N	0.16602	0.42	0.36834	D	0.88705	B	0.06786	0.001	B	0.10450	0.005	T	0.12372	-1.0550	9	.	.	.	.	11.4996	0.50430	0.0:0.5628:0.1164:0.3207	.	295	Q86UE6	LRRT1_HUMAN	V	295	ENSP00000295057:I295V;ENSP00000386646:I295V	.	I	-	1	0	LRRTM1	80383573	0.984000	0.35163	0.299000	0.25016	0.957000	0.61999	0.178000	0.16820	-2.019000	0.00942	-0.899000	0.02877	ATC	T|0.979;C|0.021	0.021	strong		0.622	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
PSCA	8000	hgsc.bcm.edu	37	8	143763490	143763490	+	Silent	SNP	T	T	C	rs2978982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:143763490T>C	ENST00000301258.4	+	3	368	c.285T>C	c.(283-285)gcT>gcC	p.A95A		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	104	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AGCCGGCTGCTGCCATCCTTG	0.662													C|||	2030	0.405351	0.3676	0.5072	5008	,	,		15544	0.3413		0.4473	False		,,,				2504	0.407				p.A95A		Atlas-SNP	.											.	PSCA	9	.	0			c.T285C						PASS	.	C		1728,2590		364,1000,795	31.0	36.0	34.0		285	-4.0	0.0	8	dbSNP_101	34	3823,4711		882,2059,1326	no	coding-synonymous	PSCA	NM_005672.4		1246,3059,2121	CC,CT,TT		44.7973,40.0185,43.1917		95/115	143763490	5551,7301	2159	4267	6426	SO:0001819	synonymous_variant	8000	exon3			GGCTGCTGCCATC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.285T>C	8.37:g.143763490T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	37	CCDS47925.2																																																																																			T|0.576;C|0.424	0.424	strong		0.662	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
SYNE3	161176	hgsc.bcm.edu	37	14	95912388	95912388	+	Missense_Mutation	SNP	G	G	A	rs61749972	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95912388G>A	ENST00000334258.5	-	8	1504	c.1490C>T	c.(1489-1491)aCg>aTg	p.T497M	SYNE3_ENST00000553340.1_Missense_Mutation_p.T497M|SYNE3_ENST00000557275.1_Missense_Mutation_p.T497M|SYNE3_ENST00000554873.1_Missense_Mutation_p.T254M	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	497					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						CTGCAGCATCGTCAGCAGCTC	0.587													G|||	294	0.0587061	0.0424	0.0605	5008	,	,		20204	0.002		0.0895	False		,,,				2504	0.1063				p.T497M		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1490T						PASS	.	G	MET/THR	252,4154	145.7+/-180.5	7,238,1958	115.0	118.0	117.0		1490	3.1	0.5	14	dbSNP_129	117	733,7867	178.5+/-227.8	30,673,3597	yes	missense	C14orf49	NM_152592.3	81	37,911,5555	AA,AG,GG		8.5233,5.7195,7.5734	benign	497/976	95912388	985,12021	2203	4300	6503	SO:0001583	missense	161176	exon8			AGCATCGTCAGCA	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.1490C>T	14.37:g.95912388G>A	ENSP00000334308:p.Thr497Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	121	0.0554029304029304	25	0.0508130081300813	28	0.07734806629834254	1	0.0017482517482517483	67	0.08839050131926121	G	13.20	2.166674	0.38217	0.057195	0.085233	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.14266	3.53;2.52;3.52;2.93	5.31	3.12	0.35913	.	0.586050	0.14224	N	0.333221	T	0.00356	0.0011	L	0.50919	1.6	0.09310	N	1	P;P;P	0.39352	0.669;0.521;0.54	B;B;B	0.27500	0.08;0.08;0.036	T	0.33599	-0.9862	10	0.40728	T	0.16	-9.8178	4.6667	0.12670	0.2707:0.1827:0.5466:0.0	rs61749972	497;497;497	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	M	497;254;497;497	ENSP00000334308:T497M;ENSP00000452154:T254M;ENSP00000450562:T497M;ENSP00000450774:T497M	ENSP00000334308:T497M	T	-	2	0	C14orf49	94982141	0.303000	0.24463	0.527000	0.27925	0.492000	0.33523	0.954000	0.29175	1.239000	0.43787	0.561000	0.74099	ACG	G|0.929;A|0.071	0.071	strong		0.587	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
FNDC3A	22862	hgsc.bcm.edu	37	13	49776080	49776080	+	Silent	SNP	A	A	G	rs9316430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:49776080A>G	ENST00000492622.2	+	24	3437	c.3132A>G	c.(3130-3132)aaA>aaG	p.K1044K	FNDC3A_ENST00000398316.3_Silent_p.K988K|FNDC3A_ENST00000541916.1_Silent_p.K1044K	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1044	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CTACTCCAAAATCTGTCCCAG	0.323													A|||	358	0.0714856	0.0552	0.0288	5008	,	,		16507	0.0754		0.0487	False		,,,				2504	0.1431				p.K1044K		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3132G						PASS	.	A	,	175,4231	112.9+/-151.0	4,167,2032	73.0	75.0	75.0		3132,2964	6.2	1.0	13	dbSNP_119	75	385,8215	122.7+/-181.7	3,379,3918	no	coding-synonymous,coding-synonymous	FNDC3A	NM_001079673.1,NM_014923.3	,	7,546,5950	GG,GA,AA		4.4767,3.9719,4.3057	,	1044/1199,988/1143	49776080	560,12446	2203	4300	6503	SO:0001819	synonymous_variant	22862	exon24			TCCAAAATCTGTC	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3132A>G	13.37:g.49776080A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	37	CCDS41886.1																																																																																			A|0.949;G|0.051	0.051	strong		0.323	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
INMT	11185	hgsc.bcm.edu	37	7	30795288	30795288	+	Missense_Mutation	SNP	A	A	G	rs2302339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:30795288A>G	ENST00000013222.5	+	3	629	c.613A>G	c.(613-615)Atg>Gtg	p.M205V	INMT_ENST00000409539.1_Missense_Mutation_p.M204V|INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Intron	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	205			M -> V (in dbSNP:rs2302339). {ECO:0000269|PubMed:10552930}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CCCGTCCTACATGGTGGGGAA	0.597													A|||	1234	0.246406	0.1293	0.245	5008	,	,		20761	0.1677		0.3499	False		,,,				2504	0.3804				p.M205V		Atlas-SNP	.											INMT,brain,glioma,0,1	INMT	38	1	0			c.A613G						PASS	.	A	VAL/MET,VAL/MET	679,3727	287.2+/-279.2	53,573,1577	101.0	88.0	92.0		610,613	1.3	0.8	7	dbSNP_100	92	2834,5766	447.4+/-361.5	473,1888,1939	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	21,21	526,2461,3516	GG,GA,AA		32.9535,15.4108,27.0106	possibly-damaging,possibly-damaging	204/263,205/264	30795288	3513,9493	2203	4300	6503	SO:0001583	missense	11185	exon3			TCCTACATGGTGG		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.613A>G	7.37:g.30795288A>G	ENSP00000013222:p.Met205Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	63	0.7	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	513	0.2348901098901099	59	0.11991869918699187	93	0.2569060773480663	90	0.15734265734265734	271	0.3575197889182058	A	10.32	1.317284	0.23908	0.154108	0.329535	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.08896	3.04;3.04	3.67	1.28	0.21552	.	0.231263	0.32473	N	0.006058	T	0.00012	0.0000	L	0.48986	1.54	0.46609	P	8.709999999999551E-4	P;P	0.38195	0.622;0.622	B;B	0.40066	0.318;0.2	T	0.45977	-0.9224	9	0.13108	T	0.6	-20.8625	6.598	0.22685	0.7998:0.0:0.2002:0.0	rs2302339;rs61115369;rs2302339	204;205	B8ZZ69;O95050	.;INMT_HUMAN	V	205;204	ENSP00000013222:M205V;ENSP00000386961:M204V	ENSP00000013222:M205V	M	+	1	0	INMT	30761813	0.653000	0.27358	0.819000	0.32651	0.420000	0.31355	0.540000	0.23191	0.137000	0.18759	0.459000	0.35465	ATG	A|0.750;G|0.250	0.250	strong		0.597	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
SLC2A4	6517	hgsc.bcm.edu	37	17	7188459	7188459	+	Missense_Mutation	SNP	C	C	T	rs8192702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7188459C>T	ENST00000317370.8	+	9	1341	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V	SLC2A4_ENST00000571308.1_Missense_Mutation_p.A358V|SLC2A4_ENST00000424875.2_Missense_Mutation_p.A348V|RP1-4G17.2_ENST00000576271.1_RNA	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	358			A -> V (in dbSNP:rs8192702).		amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CTGGGCCTGGCGGGCATGTGT	0.662													C|||	8	0.00159744	0.0	0.0	5008	,	,		17560	0.0		0.007	False		,,,				2504	0.001				p.A358V		Atlas-SNP	.											.	SLC2A4	44	.	0			c.C1073T						PASS	.	C	VAL/ALA	5,4401		1,3,2199	34.0	36.0	35.0		1073	5.9	1.0	17	dbSNP_117	35	61,8539		0,61,4239	yes	missense	SLC2A4	NM_001042.2	64	1,64,6438	TT,TC,CC		0.7093,0.1135,0.5075	benign	358/510	7188459	66,12940	2203	4300	6503	SO:0001583	missense	6517	exon9			GCCTGGCGGGCAT	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1073C>T	17.37:g.7188459C>T	ENSP00000320935:p.Ala358Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	15.10	2.733429	0.48939	0.001135	0.007093	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.80480	0.35;-1.38	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.209191	0.41712	D	0.000827	T	0.65709	0.2717	L	0.37800	1.135	0.36892	D	0.889926	B;B	0.31351	0.175;0.32	B;B	0.29524	0.103;0.024	T	0.72437	-0.4294	10	0.41790	T	0.15	.	13.4065	0.60915	0.0:0.8425:0.1575:0.0	rs8192702	358;348	P14672;F5H081	GTR4_HUMAN;.	V	358;348	ENSP00000320935:A358V;ENSP00000396887:A348V	ENSP00000320935:A358V	A	+	2	0	SLC2A4	7129183	0.040000	0.19996	0.983000	0.44433	0.909000	0.53808	0.267000	0.18552	2.813000	0.96785	0.561000	0.74099	GCG	C|0.996;T|0.004	0.004	strong		0.662	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
NUP54	53371	hgsc.bcm.edu	37	4	77057501	77057501	+	Silent	SNP	A	A	G	rs11558468	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77057501A>G	ENST00000264883.3	-	4	500	c.360T>C	c.(358-360)acT>acC	p.T120T	NUP54_ENST00000458189.2_Intron|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000514987.1_Silent_p.T72T|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	120	9 X 2 AA repeats of F-G.				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 targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GAGCACTCGCAGTATTTATCA	0.433													A|||	776	0.154952	0.0567	0.1282	5008	,	,		16678	0.3512		0.1312	False		,,,				2504	0.1288				p.T120T		Atlas-SNP	.											.	NUP54	48	.	0			c.T360C						PASS	.	A		308,4098	166.2+/-197.5	15,278,1910	92.0	94.0	93.0		360	3.2	1.0	4	dbSNP_120	93	1299,7301	257.3+/-281.4	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	GG,GA,AA		15.1047,6.9905,12.3558		120/508	77057501	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon4			ACTCGCAGTATTT	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.360T>C	4.37:g.77057501A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.433	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
TFCP2L1	29842	hgsc.bcm.edu	37	2	121981950	121981950	+	Silent	SNP	A	A	G	rs11890430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:121981950A>G	ENST00000263707.5	-	15	1504	c.1407T>C	c.(1405-1407)gaT>gaC	p.D469D		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	469					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.D469D(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					TGTGGTAGCCATCATTGCTCT	0.522													G|||	1822	0.363818	0.441	0.2997	5008	,	,		21888	0.2639		0.3101	False		,,,				2504	0.4632				p.D469D		Atlas-SNP	.											TFCP2L1,NS,carcinoma,0,1	TFCP2L1	54	1	1	Substitution - coding silent(1)	stomach(1)	c.T1407C						PASS	.	G		1816,2590	638.1+/-396.9	381,1054,768	96.0	80.0	86.0		1407	-4.7	0.9	2	dbSNP_120	86	2531,6069	692.0+/-404.6	370,1791,2139	no	coding-synonymous	TFCP2L1	NM_014553.2		751,2845,2907	GG,GA,AA		29.4302,41.2165,33.423		469/480	121981950	4347,8659	2203	4300	6503	SO:0001819	synonymous_variant	29842	exon15			GTAGCCATCATTG	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1407T>C	2.37:g.121981950A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_014553	Q4ZG43	Silent	SNP	ENST00000263707.5	37	CCDS2134.1																																																																																			A|0.666;G|0.334	0.334	strong		0.522	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553	
SALL4	57167	hgsc.bcm.edu	37	20	50407502	50407502	+	Missense_Mutation	SNP	A	A	C	rs6126344	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50407502A>C	ENST00000217086.4	-	2	1631	c.1520T>G	c.(1519-1521)cTg>cGg	p.L507R	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	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	37	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	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		
WDR66	144406	hgsc.bcm.edu	37	12	122372176	122372176	+	Silent	SNP	C	C	T	rs78614343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122372176C>T	ENST00000288912.4	+	5	1766	c.912C>T	c.(910-912)tgC>tgT	p.C304C	WDR66_ENST00000397454.2_Silent_p.C304C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	304							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)		TTATCTCCTGCCTCTGCGTCA	0.542													C|||	244	0.048722	0.056	0.0403	5008	,	,		17609	0.0496		0.0457	False		,,,				2504	0.047				p.C304C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,caecum,carcinoma,0,1	WDR66	143	1	0			c.C912T						PASS	.	C	,	222,3828		6,210,1809	73.0	75.0	74.0		912,912	4.0	1.0	12	dbSNP_131	74	381,7967		14,353,3807	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	20,563,5616	TT,TC,CC		4.564,5.4815,4.8637	,	304/942,304/1150	122372176	603,11795	2025	4174	6199	SO:0001819	synonymous_variant	144406	exon5			CTCCTGCCTCTGC	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.912C>T	12.37:g.122372176C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.951;T|0.049	0.049	strong		0.542	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
STIL	6491	hgsc.bcm.edu	37	1	47746678	47746678	+	Silent	SNP	G	G	C	rs10789505	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:47746678G>C	ENST00000360380.3	-	13	1815	c.1452C>G	c.(1450-1452)tcC>tcG	p.S484S	STIL_ENST00000243182.6_Silent_p.S484S|STIL_ENST00000396221.2_Silent_p.S484S|STIL_ENST00000371877.3_Silent_p.S484S|STIL_ENST00000337817.5_Silent_p.S484S	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	484					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)				TTCCTCTCAAGGAAGGCTCTC	0.438													G|||	1162	0.232029	0.3911	0.0677	5008	,	,		17252	0.3095		0.0905	False		,,,				2504	0.1994				p.S484S		Atlas-SNP	.											.	STIL	91	.	0			c.C1452G						PASS	.	G	,	1488,2918	477.4+/-357.9	243,1002,958	124.0	118.0	120.0		1452,1452	-3.3	0.0	1	dbSNP_120	120	658,7942	167.5+/-219.3	21,616,3663	no	coding-synonymous,coding-synonymous	STIL	NM_001048166.1,NM_003035.2	,	264,1618,4621	CC,CG,GG		7.6512,33.7721,16.5001	,	484/1289,484/1288	47746678	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	6491	exon12			TCTCAAGGAAGGC	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.1452C>G	1.37:g.47746678G>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	161	69	0.428571	NM_003035	Q5T0C5|Q68CN9	Silent	SNP	ENST00000360380.3	37	CCDS548.1	474	0.21703296703296704	203	0.41260162601626016	29	0.08011049723756906	178	0.3111888111888112	64	0.08443271767810026	G	2.296	-0.361387	0.05103	0.337721	0.076512	ENSG00000123473	ENST00000436811	.	.	.	5.14	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47058	-0.9146	3	.	.	.	-3.396	1.0397	0.01556	0.3133:0.0919:0.2388:0.3561	rs10789505;rs10789505	.	.	.	V	18	.	.	L	-	1	0	STIL	47519265	0.001000	0.12720	0.001000	0.08648	0.594000	0.36715	0.169000	0.16641	-0.453000	0.07076	0.655000	0.94253	CTT	G|0.817;C|0.183	0.183	strong		0.438	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035	
SCARF1	8578	hgsc.bcm.edu	37	17	1538669	1538669	+	Missense_Mutation	SNP	C	C	T	rs36108564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1538669C>T	ENST00000263071.4	-	11	1925	c.1876G>A	c.(1876-1878)Ggt>Agt	p.G626S	SCARF1_ENST00000348987.3_Missense_Mutation_p.G540S|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	626	Gly-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCTCAGGACCCGACTGCGCC	0.677													C|||	275	0.0549121	0.0076	0.1167	5008	,	,		14353	0.0079		0.1392	False		,,,				2504	0.0368				p.G626S		Atlas-SNP	.											.	SCARF1	46	.	0			c.G1876A						PASS	.	C	SER/GLY,,SER/GLY	131,4275	90.2+/-128.9	0,131,2072	26.0	30.0	29.0		1876,,1618	1.5	0.3	17	dbSNP_126	29	1204,7396	232.8+/-266.3	80,1044,3176	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	56,,56	80,1175,5248	TT,TC,CC		14.0,2.9732,10.2645	benign,,benign	626/831,,540/745	1538669	1335,11671	2203	4300	6503	SO:0001583	missense	8578	exon11			CAGGACCCGACTG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1876G>A	17.37:g.1538669C>T	ENSP00000263071:p.Gly626Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	165	0.07554945054945054	3	0.006097560975609756	51	0.1408839779005525	4	0.006993006993006993	107	0.14116094986807387	C	8.573	0.880576	0.17467	0.029732	0.14	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.36520	1.25;1.25	5.21	1.48	0.22813	.	0.771440	0.11051	N	0.605086	T	0.00241	0.0007	L	0.47716	1.5	0.80722	P	0.0	B;B	0.19583	0.037;0.027	B;B	0.15484	0.013;0.012	T	0.14035	-1.0487	9	0.22706	T	0.39	-4.2449	10.3537	0.43952	0.0:0.4454:0.403:0.1516	rs36108564	540;626	Q14162-2;Q14162	.;SREC_HUMAN	S	626;540	ENSP00000263071:G626S;ENSP00000323964:G540S	ENSP00000263071:G626S	G	-	1	0	SCARF1	1485419	0.000000	0.05858	0.327000	0.25402	0.015000	0.08874	0.444000	0.21661	0.477000	0.27464	0.555000	0.69702	GGT	C|0.913;T|0.087	0.087	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
FILIP1L	11259	hgsc.bcm.edu	37	3	99643176	99643176	+	Missense_Mutation	SNP	C	C	T	rs793440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:99643176C>T	ENST00000354552.3	-	4	973	c.503G>A	c.(502-504)cGt>cAt	p.R168H	FILIP1L_ENST00000398326.2_Missense_Mutation_p.R168H|CMSS1_ENST00000496116.1_Intron|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000331335.5_Missense_Mutation_p.R168H	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	168			R -> H (in dbSNP:rs793440). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GGTTTGCCTACGGGATTTTTC	0.373													T|||	1269	0.253395	0.1558	0.3545	5008	,	,		19145	0.1954		0.3111	False		,,,				2504	0.3139				p.R168H		Atlas-SNP	.											.	FILIP1L	154	.	0			c.G503A						PASS	.	T	HIS/ARG,,HIS/ARG	713,2967		61,591,1188	248.0	227.0	233.0		503,,503	5.5	0.9	3	dbSNP_86	233	2720,5448		463,1794,1827	yes	missense,intron,missense	FILIP1L,C3orf26	NM_001042459.1,NM_032359.3,NM_182909.2	29,,29	524,2385,3015	TT,TC,CC		33.3007,19.375,28.9754	benign,,benign	168/1134,,168/1136	99643176	3433,8415	1840	4084	5924	SO:0001583	missense	11259	exon4			TGCCTACGGGATT		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.503G>A	3.37:g.99643176C>T	ENSP00000346560:p.Arg168His	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	328	327	0.996951	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	37	CCDS43117.1	527	0.2413003663003663	80	0.16260162601626016	120	0.3314917127071823	80	0.13986013986013987	247	0.3258575197889182	T	4.956	0.177581	0.09443	0.19375	0.333007	ENSG00000168386	ENST00000354552;ENST00000331335;ENST00000398326	T;T;T	0.41400	1.0;1.0;1.0	5.5	5.5	0.81552	Cortactin-binding protein-2, N-terminal (1);	0.277746	0.25073	N	0.033358	T	0.00012	0.0000	N	0.00030	-2.605	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38112	-0.9676	9	0.02654	T	1	-5.2185	11.5161	0.50522	0.0:0.0703:0.0:0.9297	rs793440;rs1680276;rs17379418;rs52794044;rs60414686;rs793440	168;168	Q4L180-2;Q4L180	.;FIL1L_HUMAN	H	168	ENSP00000346560:R168H;ENSP00000327880:R168H;ENSP00000381371:R168H	ENSP00000327880:R168H	R	-	2	0	FILIP1L	101125866	1.000000	0.71417	0.927000	0.36925	0.478000	0.33099	5.664000	0.68045	0.931000	0.37242	-0.352000	0.07741	CGT	C|0.763;T|0.237	0.237	strong		0.373	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
PLD4	122618	hgsc.bcm.edu	37	14	105393556	105393556	+	Missense_Mutation	SNP	G	G	C	rs2841280	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105393556G>C	ENST00000392593.4	+	2	247	c.79G>C	c.(79-81)Gag>Cag	p.E27Q	PLD4_ENST00000540372.1_Missense_Mutation_p.E34Q	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	27			E -> Q (in dbSNP:rs2841280).		glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|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)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			GTGGGACAGAGAGGCTGGCAC	0.657													G|||	2063	0.411941	0.2201	0.4813	5008	,	,		16805	0.5982		0.4692	False		,,,				2504	0.3712				p.E27Q		Atlas-SNP	.											.	PLD4	46	.	0			c.G79C						PASS	.	G	GLN/GLU	832,2894		111,610,1142	7.0	9.0	8.0		79	1.2	0.0	14	dbSNP_100	8	3591,4533		883,1825,1354	no	missense	PLD4	NM_138790.2	29	994,2435,2496	CC,CG,GG		44.2024,22.3296,37.3249	benign	27/507	105393556	4423,7427	1863	4062	5925	SO:0001583	missense	122618	exon2			GACAGAGAGGCTG		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 175"""	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.79G>C	14.37:g.105393556G>C	ENSP00000376372:p.Glu27Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_138790	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	37	CCDS9995.2	982	0.44963369963369965	104	0.21138211382113822	160	0.4419889502762431	358	0.6258741258741258	360	0.47493403693931396	G	3.851	-0.031823	0.07543	0.223296	0.442024	ENSG00000166428	ENST00000540372;ENST00000392593;ENST00000557573	T;T;T	0.24723	1.93;1.93;1.84	3.23	1.17	0.20885	.	2.738770	0.02964	U	0.143486	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B;B	0.26483	0.15;0.092	B;B	0.17098	0.017;0.007	T	0.42361	-0.9456	9	0.15066	T	0.55	-6.5022	9.5387	0.39237	0.0:0.416:0.584:0.0	rs2841280;rs11543933;rs2841280	34;27	F5H2B5;Q96BZ4	.;PLD4_HUMAN	Q	34;27;27	ENSP00000438677:E34Q;ENSP00000376372:E27Q;ENSP00000451278:E27Q	ENSP00000376372:E27Q	E	+	1	0	PLD4	104464601	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.448000	0.06820	0.115000	0.18071	0.511000	0.50034	GAG	G|0.554;C|0.446	0.446	strong		0.657	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790	
HIPK2	28996	hgsc.bcm.edu	37	7	139415775	139415775	+	Silent	SNP	G	G	C	rs7456421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	161	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	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	
MARCH1	55016	hgsc.bcm.edu	37	4	165118796	165118796	+	Intron	SNP	G	G	A	rs2288674	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:165118796G>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						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)			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)				GTTGTCCAGGGCAAGTTCTTT	0.517													G|||	1477	0.294928	0.118	0.3141	5008	,	,		16046	0.2133		0.4732	False		,,,				2504	0.4213				p.A23V		Atlas-SNP	.											.	ANP32C	59	.	0			c.C68T						PASS	.	G	,VAL/ALA	742,3664	301.0+/-286.6	71,600,1532	140.0	140.0	140.0		,68	-0.9	0.0	4	dbSNP_100	140	4245,4355	570.1+/-389.3	1048,2149,1103	no	intron,missense	ANP32C,MARCH1	NM_001166373.1,NM_012403.1	,64	1119,2749,2635	AA,AG,GG		49.3605,16.8407,38.3438	,benign	,23/235	165118796	4987,8019	2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TCCAGGGCAAGTT	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.113-85982C>T	4.37:g.165118796G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	128	72	0.5625	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			G|0.673;A|0.327	0.327	strong		0.517	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
EIF4G1	1981	hgsc.bcm.edu	37	3	184046470	184046470	+	Silent	SNP	C	C	T	rs2230571	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184046470C>T	ENST00000346169.2	+	27	4276	c.4005C>T	c.(4003-4005)caC>caT	p.H1335H	SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000435046.2_Silent_p.H1139H|EIF4G1_ENST00000319274.6_Silent_p.H1335H|EIF4G1_ENST00000411531.1_Silent_p.H1296H|EIF4G1_ENST00000427845.1_Silent_p.H1249H|EIF4G1_ENST00000392537.2_Silent_p.H1248H|EIF4G1_ENST00000342981.4_Silent_p.H1336H|EIF4G1_ENST00000414031.1_Silent_p.H1295H|EIF4G1_ENST00000382330.3_Silent_p.H1342H|EIF4G1_ENST00000352767.3_Silent_p.H1342H|EIF4G1_ENST00000441154.1_Silent_p.H1172H|EIF4G1_ENST00000350481.5_Silent_p.H1171H|EIF4G1_ENST00000434061.2_Silent_p.H1140H|EIF4G1_ENST00000424196.1_Silent_p.H1342H|EIF2B5_ENST00000444495.1_Intron	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	84	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	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	
ITM2C	81618	hgsc.bcm.edu	37	2	231738263	231738263	+	Silent	SNP	C	C	T	rs2289234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231738263C>T	ENST00000326427.6	+	2	378	c.252C>T	c.(250-252)ttC>ttT	p.F84F	ITM2C_ENST00000335005.6_Intron|ITM2C_ENST00000409704.2_Silent_p.F22F|ITM2C_ENST00000326407.6_Silent_p.F84F|ITM2C_ENST00000492029.1_3'UTR	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	84					negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		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;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GATACTTCTTCCTTGCGCAGG	0.622													C|||	2553	0.509784	0.2277	0.5331	5008	,	,		20020	0.8155		0.504	False		,,,				2504	0.5654				p.F84F		Atlas-SNP	.											.	ITM2C	17	.	0			c.C252T						PASS	.	C	,,	1099,3307	384.2+/-325.2	138,823,1242	96.0	66.0	76.0		,252,252	2.9	1.0	2	dbSNP_100	76	4159,4441	553.8+/-386.4	1025,2109,1166	no	intron,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1163,2932,2408	TT,TC,CC		48.3605,24.9433,40.4275	,,	,84/231,84/268	231738263	5258,7748	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon2			CTTCTTCCTTGCG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.252C>T	2.37:g.231738263C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			C|0.546;T|0.454	0.454	strong		0.622	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
CALCOCO1	57658	hgsc.bcm.edu	37	12	54109733	54109733	+	Silent	SNP	A	A	G	rs3741658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:54109733A>G	ENST00000550804.1	-	9	1164	c.1104T>C	c.(1102-1104)agT>agC	p.S368S	CALCOCO1_ENST00000548263.1_Silent_p.S368S|CALCOCO1_ENST00000262059.4_Silent_p.S368S|CALCOCO1_ENST00000430117.2_Silent_p.S283S			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	368	Poly-Ala.				intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						CTGCTGCTGCACTGGCCAACT	0.627													G|||	2105	0.420327	0.4213	0.3674	5008	,	,		18170	0.5288		0.3042	False		,,,				2504	0.4642				p.S368S		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.T1104C						PASS	.	G	,	1805,2601	640.0+/-397.2	370,1065,768	47.0	50.0	49.0		849,1104	-2.7	0.6	12	dbSNP_107	49	2267,6333	706.9+/-405.6	301,1665,2334	no	coding-synonymous,coding-synonymous	CALCOCO1	NM_001143682.1,NM_020898.2	,	671,2730,3102	GG,GA,AA		26.3605,40.9669,31.3086	,	283/607,368/692	54109733	4072,8934	2203	4300	6503	SO:0001819	synonymous_variant	57658	exon9			TGCTGCACTGGCC	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"""coiled-coil leucine zipper coactivator 1"", ""inorganic pyrophosphatase activator"""					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.1104T>C	12.37:g.54109733A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Silent	SNP	ENST00000550804.1	37	CCDS8864.1																																																																																			A|0.644;G|0.356	0.356	strong		0.627	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898	
NUP37	79023	hgsc.bcm.edu	37	12	102494849	102494849	+	Silent	SNP	T	T	C	rs17438178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000251074.1_Silent_p.R105R|NUP37_ENST00000543021.1_5'UTR			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|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)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29.0	31.0	31.0		315	0.3	1.0	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"""WD repeat domain containing"""	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.315A>G	12.37:g.102494849T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057	
PAPL	390928	hgsc.bcm.edu	37	19	39591829	39591829	+	Missense_Mutation	SNP	G	G	T	rs117752516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39591829G>T	ENST00000331256.5	+	9	1229	c.955G>T	c.(955-957)Gat>Tat	p.D319Y	PAPL_ENST00000594229.1_Missense_Mutation_p.R277S	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		319						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CGGGTTGGAGGATCTTTTCTA	0.587													G|||	41	0.0081869	0.0008	0.0072	5008	,	,		14701	0.0		0.0179	False		,,,				2504	0.0174				p.D319Y		Atlas-SNP	.											.	.	.	.	0			c.G955T						PASS	.	G	TYR/ASP	22,4384	29.9+/-59.1	0,22,2181	59.0	52.0	55.0		955	5.7	1.0	19	dbSNP_132	55	159,8441	74.8+/-137.4	0,159,4141	yes	missense	PAPL	NM_001004318.2	160	0,181,6322	TT,TG,GG		1.8488,0.4993,1.3917	possibly-damaging	319/439	39591829	181,12825	2203	4300	6503	SO:0001583	missense	0	exon9			TTGGAGGATCTTT																												ENST00000331256.5:c.955G>T	19.37:g.39591829G>T	ENSP00000327557:p.Asp319Tyr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_001004318	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	37	CCDS33018.1	20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	G	17.67	3.446113	0.63178	0.004993	0.018488	ENSG00000183760	ENST00000331256	D	0.85556	-2.0	5.71	5.71	0.89125	Metallophosphoesterase domain (1);	0.050469	0.85682	D	0.000000	D	0.87497	0.6192	M	0.84219	2.685	0.49213	D	0.999765	D	0.67145	0.996	D	0.69307	0.963	D	0.89212	0.3565	10	0.54805	T	0.06	-24.1155	17.3422	0.87299	0.0:0.0:1.0:0.0	.	319	Q6ZNF0	PAPL_HUMAN	Y	319	ENSP00000327557:D319Y	ENSP00000327557:D319Y	D	+	1	0	AC011443.1	44283669	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	4.138000	0.58017	2.684000	0.91462	0.655000	0.94253	GAT	G|0.988;T|0.012	0.012	strong		0.587	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
SELP	6403	hgsc.bcm.edu	37	1	169562904	169562904	+	Silent	SNP	C	C	T	rs6128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169562904C>T	ENST00000263686.6	-	14	2383	c.2346G>A	c.(2344-2346)acG>acA	p.T782T	SELP_ENST00000367794.2_Silent_p.T720T|SELP_ENST00000367788.2_Silent_p.T720T|SELP_ENST00000367793.2_Silent_p.T720T|SELP_ENST00000367786.2_Silent_p.T720T|SELP_ENST00000367791.2_Silent_p.T596T|SELP_ENST00000367792.2_Silent_p.T598T|SELP_ENST00000458599.2_Silent_p.T598T	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						PASS	.	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	74	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607758	84607758	+	Silent	SNP	T	T	A	rs10867826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	319	0	0		WXS	Illumina HiSeq	Phase_I	324	168	0.518519	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	
FAM71E2	284418	hgsc.bcm.edu	37	19	55870478	55870478	+	Silent	SNP	C	C	T	rs79366553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55870478C>T	ENST00000424985.3	-	9	1951	c.1758G>A	c.(1756-1758)ccG>ccA	p.P586P	CTD-2105E13.6_ENST00000591954.3_Missense_Mutation_p.R136Q	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	586										NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						CCACCGGCTCCGGTTTCCCTC	0.622													c|||	261	0.0521166	0.0711	0.0836	5008	,	,		15825	0.0		0.0845	False		,,,				2504	0.0245				p.P586P		Atlas-SNP	.											.	FAM71E2	41	.	0			c.G1758A						PASS	.	C		119,1265		4,111,577	16.0	15.0	15.0		1758	-7.8	0.0	19	dbSNP_132	15	249,2933		13,223,1355	no	coding-synonymous	FAM71E2	NM_001145402.1		17,334,1932	TT,TC,CC		7.8253,8.5983,8.0596		586/923	55870478	368,4198	692	1591	2283	SO:0001819	synonymous_variant	284418	exon9			CGGCTCCGGTTTC	AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.1758G>A	19.37:g.55870478C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_001145402	Q8ND99	Silent	SNP	ENST00000424985.3	37																																																																																				C|0.934;T|0.066	0.066	strong		0.622	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
CXorf56	63932	hgsc.bcm.edu	37	X	118678364	118678364	+	Silent	SNP	G	G	A	rs5910611	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:118678364G>A	ENST00000371594.4	-	4	453	c.375C>T	c.(373-375)ggC>ggT	p.G125G	CXorf56_ENST00000536133.1_Silent_p.G111G|CXorf56_ENST00000320339.4_Silent_p.G76G|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	51	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	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	
PER1	5187	hgsc.bcm.edu	37	17	8053085	8053085	+	Silent	SNP	T	T	G	rs3027178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8053085T>G	ENST00000317276.4	-	5	876	c.639A>C	c.(637-639)acA>acC	p.T213T	PER1_ENST00000354903.5_Silent_p.T197T|PER1_ENST00000581082.1_Silent_p.T213T	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	213	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|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)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.T213T(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGTTCTGAAGTGTGTACTCAG	0.597			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					T|||	1436	0.286741	0.267	0.4553	5008	,	,		20009	0.2738		0.2922	False		,,,				2504	0.2014				p.T213T		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	PER1,NS,carcinoma,0,1	PER1	104	1	1	Substitution - coding silent(1)	stomach(1)	c.A639C						scavenged	.	T		1133,3273	404.0+/-332.9	147,839,1217	194.0	188.0	190.0		639	-11.1	0.0	17	dbSNP_102	190	2636,5964	424.1+/-354.6	396,1844,2060	no	coding-synonymous	PER1	NM_002616.2		543,2683,3277	GG,GT,TT		30.6512,25.7149,28.9789		213/1291	8053085	3769,9237	2203	4300	6503	SO:0001819	synonymous_variant	5187	exon5			CTGAAGTGTGTAC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.639A>C	17.37:g.8053085T>G		Somatic	13	1	0.0769231		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			T|0.699;G|0.301	0.301	strong		0.597	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
ABCB5	340273	hgsc.bcm.edu	37	7	20768013	20768013	+	Silent	SNP	G	G	A	rs10254317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20768013G>A	ENST00000404938.2	+	23	3454	c.2802G>A	c.(2800-2802)gcG>gcA	p.A934A	ABCB5_ENST00000258738.6_Silent_p.A489A	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	934	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						TTGCCTATGCGGCAGGGTTTC	0.423													A|||	2985	0.596046	0.789	0.67	5008	,	,		17944	0.6905		0.4294	False		,,,				2504	0.3569				p.A934A		Atlas-SNP	.											ABCB5,colon,carcinoma,+1,1	ABCB5	357	1	0			c.G2802A						PASS	.	A	,	3197,1209	421.9+/-339.5	1158,881,164	128.0	128.0	128.0		2802,1467	-1.1	0.1	7	dbSNP_119	128	3592,5008	627.3+/-398.0	744,2104,1452	no	coding-synonymous,coding-synonymous	ABCB5	NM_001163941.1,NM_178559.5	,	1902,2985,1616	AA,AG,GG		41.7674,27.4399,47.801	,	934/1258,489/813	20768013	6789,6217	2203	4300	6503	SO:0001819	synonymous_variant	340273	exon23			CTATGCGGCAGGG	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.2802G>A	7.37:g.20768013G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			G|0.421;A|0.579	0.579	strong		0.423	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
C9orf135	138255	hgsc.bcm.edu	37	9	72472831	72472831	+	Silent	SNP	C	C	T	rs10780682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:72472831C>T	ENST00000377197.3	+	4	474	c.387C>T	c.(385-387)acC>acT	p.T129T	C9orf135_ENST00000527647.1_Silent_p.T129T|C9orf135_ENST00000466872.2_3'UTR	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135	129						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TTAGGGTCACCGGATTGCCTG	0.403													c|||	1355	0.270567	0.0938	0.2925	5008	,	,		19323	0.4067		0.331	False		,,,				2504	0.2914				p.T129T		Atlas-SNP	.											.	C9orf135	25	.	0			c.C387T						PASS	.	T		620,3786	268.3+/-268.4	52,516,1635	108.0	99.0	102.0		387	-0.0	1.0	9	dbSNP_120	102	2875,5725	450.6+/-362.4	469,1937,1894	no	coding-synonymous	C9orf135	NM_001010940.1		521,2453,3529	TT,TC,CC		33.4302,14.0717,26.8722		129/230	72472831	3495,9511	2203	4300	6503	SO:0001819	synonymous_variant	138255	exon4			GGTCACCGGATTG		CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.387C>T	9.37:g.72472831C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_001010940	A7E2U4|B2RN61	Silent	SNP	ENST00000377197.3	37	CCDS35041.1	631	0.2889194139194139	42	0.08536585365853659	112	0.30939226519337015	209	0.36538461538461536	268	0.35356200527704484	c	0.127	-1.118773	0.01785	0.140717	0.334302	ENSG00000204711	ENST00000480564	.	.	.	5.2	-0.0103	0.13997	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999979904	.	.	.	.	.	.	T	0.44452	-0.9327	3	.	.	.	-10.0596	4.5019	0.11869	0.1462:0.1956:0.0:0.6582	rs10780682;rs17518953;rs56592328;rs10780682	.	.	.	W	103	.	.	R	+	1	2	C9orf135	71662651	0.991000	0.36638	0.986000	0.45419	0.004000	0.04260	0.095000	0.15127	-0.170000	0.10816	-1.120000	0.02017	CGG	C|0.722;T|0.278	0.278	strong		0.403	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56763328	56763328	+	Silent	SNP	T	T	C	rs1565377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56763328T>C	ENST00000296315.3	-	10	1719	c.1551A>G	c.(1549-1551)ggA>ggG	p.G517G	ARHGEF3_ENST00000497267.1_Silent_p.G488G|ARHGEF3_ENST00000338458.4_Silent_p.G549G|ARHGEF3_ENST00000496106.1_Silent_p.G523G|ARHGEF3_ENST00000413728.2_Silent_p.G523G	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	517					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)		GCCTGCTGTTTCCACAGGAAG	0.512													C|||	3648	0.728435	0.8722	0.6585	5008	,	,		21966	0.8542		0.4245	False		,,,				2504	0.7669				p.G549G		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.A1647G						PASS	.	C	,,	3589,817	316.3+/-294.6	1466,657,80	211.0	158.0	176.0		1647,1569,1551	2.1	1.0	3	dbSNP_88	176	3605,4995	619.9+/-397.0	730,2145,1425	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF3	NM_001128615.1,NM_001128616.1,NM_019555.2	,,	2196,2802,1505	CC,CT,TT		41.9186,18.5429,44.6871	,,	549/559,523/533,517/527	56763328	7194,5812	2203	4300	6503	SO:0001819	synonymous_variant	50650	exon13			GCTGTTTCCACAG	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.1551A>G	3.37:g.56763328T>C		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	210	208	0.990476	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			T|0.391;C|0.609	0.609	strong		0.512	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
SYTL2	54843	hgsc.bcm.edu	37	11	85445365	85445365	+	Missense_Mutation	SNP	G	G	C	rs74718633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:85445365G>C	ENST00000528231.1	-	6	1281	c.1004C>G	c.(1003-1005)tCt>tGt	p.S335C	SYTL2_ENST00000316356.4_Missense_Mutation_p.S336C|SYTL2_ENST00000527523.1_Missense_Mutation_p.S287C|SYTL2_ENST00000389960.4_Missense_Mutation_p.S335C|SYTL2_ENST00000524452.1_Missense_Mutation_p.S335C	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	335					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)		CTTCACTGCAGAGAATCTCAC	0.443													G|||	19	0.00379393	0.0008	0.0058	5008	,	,		19642	0.0		0.0139	False		,,,				2504	0.0				p.S336C		Atlas-SNP	.											.	SYTL2	231	.	0			c.C1007G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	10,4396	16.8+/-37.8	0,10,2193	104.0	107.0	106.0		1004,1007,1004	5.2	1.0	11	dbSNP_131	106	113,8485	61.0+/-122.8	1,111,4187	yes	missense,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	112,112,112	1,121,6380	CC,CG,GG		1.3143,0.227,0.9459	,,	335/935,336/936,335/911	85445365	123,12881	2203	4299	6502	SO:0001583	missense	54843	exon6			ACTGCAGAGAATC	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.1004C>G	11.37:g.85445365G>C	ENSP00000431701:p.Ser335Cys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	20.5	4.002879	0.74932	0.00227	0.013143	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.59083	0.29;0.69;0.62;0.49;0.29	6.06	5.15	0.70609	.	.	.	.	.	T	0.67011	0.2848	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.999;0.999;0.994;1.0	T	0.71836	-0.4472	8	.	.	.	.	14.79	0.69833	0.0694:0.0:0.9306:0.0	.	287;335;335;336;193	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	C	335;336;335;287;335	ENSP00000374610:S335C;ENSP00000318803:S336C;ENSP00000431701:S335C;ENSP00000434010:S287C;ENSP00000435238:S335C	.	S	-	2	0	SYTL2	85123013	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.541000	0.73865	1.567000	0.49668	0.650000	0.86243	TCT	G|0.993;C|0.007	0.007	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
MUC20	200958	hgsc.bcm.edu	37	3	195453406	195453406	+	Silent	SNP	G	G	C	rs3210209	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195453406G>C	ENST00000447234.2	+	2	2058	c.1932G>C	c.(1930-1932)acG>acC	p.T644T	MUC20_ENST00000320736.6_Silent_p.T473T|MUC20_ENST00000445522.2_Silent_p.T609T|MUC20_ENST00000436408.1_Silent_p.T644T	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						scavenged	.						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	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	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	
SPATA3	130560	hgsc.bcm.edu	37	2	231861057	231861057	+	Missense_Mutation	SNP	C	C	T	rs72362780		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231861057C>T	ENST00000452881.1	+	1	217	c.109C>T	c.(109-111)Cca>Tca	p.P37S	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Missense_Mutation_p.P37S|SPATA3_ENST00000455816.1_Missense_Mutation_p.P37S|SPATA3_ENST00000424440.1_Missense_Mutation_p.P37S			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	37										endometrium(2)|lung(1)	3						TGAATCCACACCACAGCAGCC	0.577																																					p.P37S		Atlas-SNP	.											SPATA3,NS,carcinoma,-2,4	SPATA3	52	4	0			c.C109T						scavenged	.						132.0	138.0	137.0					2																	231861057		692	1590	2282	SO:0001583	missense	130560	exon1			TCCACACCACAGC	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.109C>T	2.37:g.231861057C>T	ENSP00000388895:p.Pro37Ser	Somatic	66	2	0.030303		WXS	Illumina HiSeq	Phase_I	47	8	0.170213	NM_139073	Q86WX5|Q8N9Y6	Missense_Mutation	SNP	ENST00000452881.1	37	CCDS2481.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829371	0.32329	.	.	ENSG00000173699	ENST00000424440;ENST00000452881;ENST00000433428;ENST00000455816;ENST00000355662;ENST00000440792	.	.	.	3.0	-0.25	0.13007	.	0.940554	0.08697	N	0.907107	T	0.19248	0.0462	N	0.12746	0.255	0.09310	N	1	.	.	.	.	.	.	T	0.27673	-1.0067	7	0.72032	D	0.01	0.139	2.334	0.04242	0.2359:0.4502:0.0:0.3139	.	.	.	.	S	37;37;37;37;37;3	.	ENSP00000347884:P37S	P	+	1	0	SPATA3	231569301	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.302000	0.08221	-0.061000	0.13110	-0.367000	0.07326	CCA	.	.	none		0.577	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
OR11H12	440153	hgsc.bcm.edu	37	14	19377859	19377859	+	Missense_Mutation	SNP	T	T	C	rs61969156	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:19377859T>C	ENST00000550708.1	+	1	338	c.266T>C	c.(265-267)gTc>gCc	p.V89A		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	89						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)		ATATGGTATGTCTCTTCTACA	0.413																																					p.V89A		Atlas-SNP	.											OR11H12,NS,carcinoma,0,2	OR11H12	58	2	0			c.T266C						scavenged	.						20.0	24.0	23.0					14																	19377859		1471	3234	4705	SO:0001583	missense	440153	exon1			GGTATGTCTCTTC		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.266T>C	14.37:g.19377859T>C	ENSP00000449002:p.Val89Ala	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	190	46	0.242105	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	t	8.138	0.784491	0.16189	.	.	ENSG00000257115	ENST00000550708	T	0.00418	7.49	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37715	N	0.001976	T	0.00300	0.0009	L	0.47190	1.495	0.23107	N	0.998281	P	0.42409	0.779	B	0.40636	0.335	T	0.51702	-0.8672	9	0.41790	T	0.15	.	5.5303	0.16980	0.0:1.0E-4:0.0:0.9999	.	89	B2RN74	O11HC_HUMAN	A	89	ENSP00000449002:V89A	ENSP00000449002:V89A	V	+	2	0	CR383656.1	18447859	0.000000	0.05858	0.997000	0.53966	0.305000	0.27757	-0.341000	0.07811	0.518000	0.28383	0.055000	0.15244	GTC	.	.	weak		0.413	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
PIGQ	9091	hgsc.bcm.edu	37	16	633354	633354	+	Missense_Mutation	SNP	G	G	A	rs112194445|rs710925|rs71391136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:633354G>A	ENST00000026218.5	+	10	2091	c.2003G>A	c.(2002-2004)tGt>tAt	p.C668Y	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	668			C -> R (in dbSNP:rs710924).|C -> Y (in dbSNP:rs710925).		C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CCCACCCTGTGTACCCAGGTC	0.692													G|||	2655	0.530152	0.4735	0.4885	5008	,	,		16792	0.6369		0.4324	False		,,,				2504	0.6268				p.C668Y		Atlas-SNP	.											PIGQ,NS,carcinoma,+1,1	PIGQ	43	1	0			c.G2003A						PASS	.	G	,TYR/CYS	1962,2438		485,992,723	45.0	52.0	50.0		,2003	-5.5	0.0	16	dbSNP_86	50	3355,5241		722,1911,1665	yes	utr-3,missense	PIGQ	NM_004204.3,NM_148920.1	,194	1207,2903,2388	AA,AG,GG		39.0298,44.5909,40.9126	,benign	,668/761	633354	5317,7679	2200	4298	6498	SO:0001583	missense	9091	exon10			CCCTGTGTACCCA	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.2003G>A	16.37:g.633354G>A	ENSP00000026218:p.Cys668Tyr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	1044	0.47802197802197804	237	0.4817073170731707	169	0.46685082872928174	328	0.5734265734265734	310	0.40897097625329815	G	5.669	0.308075	0.10733	0.445909	0.390298	ENSG00000007541	ENST00000026218	T	0.22945	1.93	2.73	-5.47	0.02600	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.15473	0.013;0.0	B;B	0.17433	0.018;0.003	T	0.46275	-0.9203	7	.	.	.	.	1.9037	0.03273	0.1828:0.292:0.3795:0.1457	rs710925;rs58256275;rs710925	238;668	B3KRR7;Q9BRB3	.;PIGQ_HUMAN	Y	668	ENSP00000026218:C668Y	.	C	+	2	0	PIGQ	573355	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.644000	0.24766	-1.690000	0.01432	-0.481000	0.04817	TGT	G|0.544;A|0.456	0.456	strong		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
HMGCS1	3157	hgsc.bcm.edu	37	5	43294192	43294192	+	Silent	SNP	C	C	T	rs56257144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:43294192C>T	ENST00000325110.6	-	8	1355	c.1149G>A	c.(1147-1149)ctG>ctA	p.L383L	HMGCS1_ENST00000433297.2_Silent_p.L383L	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	383					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						TAAGAGAGTACAGAGTGGCAG	0.448													C|||	304	0.0607029	0.0227	0.0663	5008	,	,		19438	0.002		0.1173	False		,,,				2504	0.1104				p.L383L		Atlas-SNP	.											.	HMGCS1	33	.	0			c.G1149A						PASS	.	C	,	166,4240	110.8+/-149.0	2,162,2039	132.0	115.0	120.0		1149,1149	-3.8	0.6	5	dbSNP_129	120	1058,7542	224.3+/-260.7	61,936,3303	no	coding-synonymous,coding-synonymous	HMGCS1	NM_001098272.1,NM_002130.6	,	63,1098,5342	TT,TC,CC		12.3023,3.7676,9.411	,	383/521,383/521	43294192	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	3157	exon8			AGAGTACAGAGTG		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"""3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"""	142940	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"""	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.1149G>A	5.37:g.43294192C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	41	0.359649	NM_001098272	B2RDL8	Silent	SNP	ENST00000325110.6	37	CCDS34154.1																																																																																			C|0.913;T|0.087	0.087	strong		0.448	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1		
SLC8A3	6547	hgsc.bcm.edu	37	14	70634546	70634546	+	Silent	SNP	C	C	T	rs7161524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:70634546C>T	ENST00000381269.2	-	2	1347	c.594G>A	c.(592-594)aaG>aaA	p.K198K	SLC8A3_ENST00000357887.3_Silent_p.K198K|SLC8A3_ENST00000534137.1_Silent_p.K198K|SLC8A3_ENST00000356921.2_Silent_p.K198K|SLC8A3_ENST00000528359.1_Silent_p.K198K	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	198					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CTCGTAGATGCTTGATCTTGC	0.493													C|||	713	0.142372	0.202	0.1124	5008	,	,		21617	0.0089		0.2068	False		,,,				2504	0.1544				p.K198K		Atlas-SNP	.											.	SLC8A3	234	.	0			c.G594A						PASS	.	C	,,,	830,3576	328.3+/-300.5	80,670,1453	86.0	77.0	80.0		594,594,594,594	3.8	1.0	14	dbSNP_116	80	1594,7006	297.0+/-303.2	169,1256,2875	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC8A3	NM_033262.3,NM_058240.2,NM_182932.1,NM_183002.1	,,,	249,1926,4328	TT,TC,CC		18.5349,18.8379,18.6376	,,,	198/926,198/925,198/922,198/928	70634546	2424,10582	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon2			TAGATGCTTGATC	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.594G>A	14.37:g.70634546C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			C|0.830;T|0.170	0.170	strong		0.493	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
QRFP	347148	hgsc.bcm.edu	37	9	133769169	133769169	+	Silent	SNP	G	G	A	rs3847193	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133769169G>A	ENST00000343079.1	-	1	56	c.57C>T	c.(55-57)ttC>ttT	p.F19F		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		CCAGTAGAGGGAAGCAGGCGC	0.637													A|||	1786	0.356629	0.7436	0.2939	5008	,	,		19043	0.0714		0.2475	False		,,,				2504	0.2843				p.F19F		Atlas-SNP	.											.	QRFP	14	.	0			c.C57T						PASS	.	A		2880,1526		958,964,281	42.0	49.0	47.0		57	-0.2	0.9	9	dbSNP_108	47	2249,6351		298,1653,2349	no	coding-synonymous	QRFP	NM_198180.1		1256,2617,2630	AA,AG,GG		26.1512,34.6346,39.4356		19/137	133769169	5129,7877	2203	4300	6503	SO:0001819	synonymous_variant	347148	exon1			TAGAGGGAAGCAG	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"""Endogenous ligands"""	29982	protein-coding gene	gene with protein product	"""prepro-QRFP"""	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.57C>T	9.37:g.133769169G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_198180		Silent	SNP	ENST00000343079.1	37	CCDS6936.1																																																																																			G|0.629;A|0.371	0.371	strong		0.637	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
FCER2	2208	hgsc.bcm.edu	37	19	7755056	7755056	+	Silent	SNP	G	G	A	rs2228138	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:7755056G>A	ENST00000346664.5	-	10	929	c.717C>T	c.(715-717)caC>caT	p.H239H	FCER2_ENST00000360067.4_Silent_p.H238H|FCER2_ENST00000597921.1_Silent_p.H239H	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)	239	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						TGTAGTCCACGTGGCTCCCAT	0.592													g|||	1995	0.398363	0.6029	0.2176	5008	,	,		15752	0.3403		0.2843	False		,,,				2504	0.4274				p.H239H		Atlas-SNP	.											FCER2,colon,carcinoma,0,1	FCER2	19	1	0			c.C717T						PASS	.		,,	2382,2024	613.1+/-392.1	638,1106,459	87.0	81.0	83.0		714,717,717	-4.9	0.0	19	dbSNP_98	83	2462,6138	406.2+/-348.7	342,1778,2180	no	coding-synonymous,coding-synonymous,coding-synonymous	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	,,	980,2884,2639	AA,AG,GG		28.6279,45.9374,37.2443	,,	238/321,239/322,239/322	7755056	4844,8162	2203	4300	6503	SO:0001819	synonymous_variant	2208	exon10			GTCCACGTGGCTC	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.717C>T	19.37:g.7755056G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_002002		Silent	SNP	ENST00000346664.5	37	CCDS12184.1																																																																																			G|0.634;A|0.366	0.366	strong		0.592	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
BIN1	274	hgsc.bcm.edu	37	2	127809840	127809840	+	Silent	SNP	C	C	A	rs61748155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127809840C>A	ENST00000316724.5	-	15	1773	c.1362G>T	c.(1360-1362)ggG>ggT	p.G454G	BIN1_ENST00000409400.1_Intron|BIN1_ENST00000346226.3_Silent_p.G379G|BIN1_ENST00000357970.3_Silent_p.G411G|BIN1_ENST00000351659.3_Silent_p.G367G|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000393041.3_Silent_p.G336G	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	454					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGGGCAGGCCCCGGCTCGG	0.692													C|||	73	0.0145767	0.0	0.0144	5008	,	,		14417	0.0		0.0159	False		,,,				2504	0.0481				p.G454G		Atlas-SNP	.											BIN1,brain,glioma,0,1	BIN1	85	1	0			c.G1362T						scavenged	.	C	,,,,,,,,,	14,4288		0,14,2137	9.0	12.0	11.0		,1362,1233,1101,,1137,,1008,,	3.8	1.0	2	dbSNP_129	11	149,8367		1,147,4110	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,intron,intron	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	1,161,6247	AA,AC,CC		1.7496,0.3254,1.2716	,,,,,,,,,	,454/594,411/551,367/507,,379/519,,336/476,,	127809840	163,12655	2151	4258	6409	SO:0001819	synonymous_variant	274	exon15			GGCAGGCCCCGGC	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1362G>T	2.37:g.127809840C>A		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.990;A|0.010	0.010	strong		0.692	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
FCGBP	8857	hgsc.bcm.edu	37	19	40392631	40392631	+	Missense_Mutation	SNP	G	G	A	rs80068592	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40392631G>A	ENST00000221347.6	-	16	7880	c.7873C>T	c.(7873-7875)Ccc>Tcc	p.P2625S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2625	VWFD 6. {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)			GGAGAGTCGGGCACCACCTCC	0.642													G|||	1353	0.270168	0.1808	0.4121	5008	,	,		18489	0.2093		0.3569	False		,,,				2504	0.2638				p.P2625S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C7873T						PASS	.						14.0	17.0	16.0					19																	40392631		2165	4278	6443	SO:0001583	missense	8857	exon16			AGTCGGGCACCAC	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.7873C>T	19.37:g.40392631G>A	ENSP00000221347:p.Pro2625Ser	Somatic	395	1	0.00253165		WXS	Illumina HiSeq	Phase_I	280	110	0.392857	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.277	0.608327	0.14002	.	.	ENSG00000090920	ENST00000221347	T	0.18657	2.2	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.27731	0.0682	M	0.71920	2.185	0.37706	P	0.07559199999999999	P	0.41131	0.739	P	0.48304	0.573	T	0.29761	-1.0001	8	0.02654	T	1	.	12.5273	0.56093	0.0:0.0:1.0:0.0	.	2625	Q9Y6R7	FCGBP_HUMAN	S	2625	ENSP00000221347:P2625S	ENSP00000221347:P2625S	P	-	1	0	FCGBP	45084471	0.034000	0.19679	0.110000	0.21437	0.008000	0.06430	0.899000	0.28417	1.495000	0.48549	0.298000	0.19748	CCC	G|0.772;A|0.228	0.228	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
EPM2A	7957	hgsc.bcm.edu	37	6	146007332	146007332	+	Silent	SNP	C	C	T	rs35230590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:146007332C>T	ENST00000367519.3	-	2	927	c.402G>A	c.(400-402)ggG>ggA	p.G134G	EPM2A_ENST00000496228.1_5'UTR	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	134					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		CATTGGTGTGCCCAGTGGCCT	0.418													C|||	611	0.122005	0.0008	0.3314	5008	,	,		17112	0.0089		0.2266	False		,,,				2504	0.1462				p.G134G		Atlas-SNP	.											.	EPM2A	21	.	0			c.G402A						PASS	.	C	,	204,4202	126.1+/-163.2	7,190,2006	175.0	150.0	159.0		402,402	3.8	1.0	6	dbSNP_126	159	2127,6473	367.5+/-334.7	256,1615,2429	no	coding-synonymous,coding-synonymous	EPM2A	NM_001018041.1,NM_005670.3	,	263,1805,4435	TT,TC,CC		24.7326,4.63,17.9225	,	134/318,134/332	146007332	2331,10675	2203	4300	6503	SO:0001819	synonymous_variant	7957	exon2			GGTGTGCCCAGTG	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3413	protein-coding gene	gene with protein product		607566	"""epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"""			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.402G>A	6.37:g.146007332C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_005670	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Silent	SNP	ENST00000367519.3	37	CCDS5206.1	309	0.14148351648351648	1	0.0020325203252032522	129	0.356353591160221	2	0.0034965034965034965	177	0.23350923482849603	C	9.721	1.159735	0.21454	0.0463	0.247326	ENSG00000112425	ENST00000450221;ENST00000435470	D;D	0.96554	-3.06;-4.05	5.6	3.81	0.43845	.	0.000000	0.85682	D	0.000000	D	0.95589	0.8566	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	D	0.95635	0.8693	6	0.66056	D	0.02	-32.4686	10.7796	0.46369	0.0:0.7916:0.0:0.2084	rs35230590;rs61748671	.	.	.	D	34;54	ENSP00000414900:G34D;ENSP00000405913:G54D	ENSP00000405913:G54D	G	-	2	0	EPM2A	146049025	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.678000	0.25277	1.357000	0.45904	0.491000	0.48974	GGC	C|0.823;T|0.177	0.177	strong		0.418	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1		
CEP68	23177	hgsc.bcm.edu	37	2	65298839	65298839	+	Silent	SNP	A	A	G	rs17849707	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:65298839A>G	ENST00000377990.2	+	3	812	c.609A>G	c.(607-609)acA>acG	p.T203T	CEP68_ENST00000546106.1_Silent_p.T203T|CEP68_ENST00000260569.4_Silent_p.T203T|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000497039.1_3'UTR|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	203					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTTCCTCCACAGGCAGCAGTC	0.632													A|||	1239	0.247404	0.1475	0.2738	5008	,	,		19795	0.3304		0.2256	False		,,,				2504	0.3006				p.T203T		Atlas-SNP	.											.	CEP68	69	.	0			c.A609G						PASS	.	A		780,3626	314.1+/-293.5	70,640,1493	49.0	49.0	49.0		609	-12.0	0.0	2	dbSNP_123	49	2010,6590	350.0+/-327.7	251,1508,2541	no	coding-synonymous	CEP68	NM_015147.2		321,2148,4034	GG,GA,AA		23.3721,17.7031,21.4516		203/758	65298839	2790,10216	2203	4300	6503	SO:0001819	synonymous_variant	23177	exon3			CTCCACAGGCAGC	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.609A>G	2.37:g.65298839A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																			A|0.773;G|0.227	0.227	strong		0.632	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
P4HB	5034	hgsc.bcm.edu	37	17	79818260	79818260	+	Silent	SNP	G	G	T	rs11558886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79818260G>T	ENST00000331483.4	-	1	310	c.88C>A	c.(88-90)Cgg>Agg	p.R30R	P4HB_ENST00000472244.1_5'Flank|P4HB_ENST00000439918.2_Silent_p.R30R|P4HB_ENST00000576390.1_Silent_p.R30R	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	30	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)	p.R30R(1)		NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			TTGCTTTTCCGCAGCACCAGG	0.736													G|||	520	0.103834	0.0083	0.2262	5008	,	,		8175	0.1042		0.175	False		,,,				2504	0.0726				p.R30R	Colon(49;444 983 1296 7887 42561)	Atlas-SNP	.											P4HB,NS,NS,0,1	P4HB	43	1	1	Substitution - coding silent(1)	NS(1)	c.C88A						PASS	.	G		114,3550		3,108,1721	7.0	8.0	8.0		88	-1.7	0.0	17	dbSNP_120	8	1119,5993		74,971,2511	no	coding-synonymous	P4HB	NM_000918.3		77,1079,4232	TT,TG,GG		15.734,3.1114,11.4421		30/509	79818260	1233,9543	1832	3556	5388	SO:0001819	synonymous_variant	5034	exon1			TTTTCCGCAGCAC	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"""Protein disulfide isomerases"""	8548	protein-coding gene	gene with protein product	"""protein disulfide isomerase-associated 1"", ""protein disulfide isomerase family A, member 1"", ""collagen prolyl 4-hydroxylase beta"""	176790	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"""	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.88C>A	17.37:g.79818260G>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Silent	SNP	ENST00000331483.4	37	CCDS11787.1																																																																																			G|0.867;T|0.133	0.133	strong		0.736	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111504479	111504479	+	Missense_Mutation	SNP	C	C	T	rs7703522	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:111504479C>T	ENST00000261486.5	-	22	2165	c.1889G>A	c.(1888-1890)cGt>cAt	p.R630H	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	630						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)		ATCCGAAGAACGGGTCACCGG	0.393													C|||	4291	0.856829	0.9206	0.7839	5008	,	,		21165	0.998		0.6551	False		,,,				2504	0.8845				p.R630H		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.G1889A						PASS	.	C	HIS/ARG	3314,456		1461,392,32	97.0	95.0	96.0		1889	3.8	0.7	5	dbSNP_116	96	5272,2956		1677,1918,519	yes	missense	EPB41L4A	NM_022140.3	29	3138,2310,551	TT,TC,CC		35.9261,12.0955,28.4381	probably-damaging	630/687	111504479	8586,3412	1885	4114	5999	SO:0001583	missense	64097	exon22			GAAGAACGGGTCA	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.1889G>A	5.37:g.111504479C>T	ENSP00000261486:p.Arg630His	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	1785	0.8173076923076923	444	0.9024390243902439	269	0.7430939226519337	571	0.9982517482517482	501	0.6609498680738787	C	15.04	2.716645	0.48622	0.879045	0.640739	ENSG00000129595	ENST00000261486	D	0.83163	-1.69	5.54	3.77	0.43336	.	0.000000	0.52532	U	0.000066	T	0.00012	0.0000	L	0.29908	0.895	0.27998	P	0.9354066	D	0.89917	1.0	D	0.83275	0.996	T	0.38329	-0.9666	9	0.59425	D	0.04	.	10.7231	0.46052	0.0:0.8445:0.0:0.1555	rs7703522;rs17319585;rs52825715;rs60560740;rs7703522	630	Q9HCS5	E41LA_HUMAN	H	630	ENSP00000261486:R630H	ENSP00000261486:R630H	R	-	2	0	EPB41L4A	111532378	0.996000	0.38824	0.728000	0.30774	0.089000	0.18198	3.282000	0.51693	0.704000	0.31869	-0.229000	0.12294	CGT	C|0.141;T|0.859	0.859	strong		0.393	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
BCHE	590	hgsc.bcm.edu	37	3	165491280	165491280	+	Missense_Mutation	SNP	C	C	T	rs1803274	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:165491280C>T	ENST00000264381.3	-	4	1865	c.1699G>A	c.(1699-1701)Gca>Aca	p.A567T	BCHE_ENST00000540653.1_Missense_Mutation_p.A29T	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	567			A -> T (in BChE deficiency; allele K variant; with reduced enzyme activity; dbSNP:rs1803274). {ECO:0000269|PubMed:11928765, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7634491, ECO:0000269|PubMed:9191541}.		cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TCCCATTCTGCTTCATCAATA	0.303													C|||	794	0.158546	0.1725	0.1225	5008	,	,		13648	0.1339		0.1859	False		,,,				2504	0.1626				p.A567T		Atlas-SNP	.											.	BCHE	136	.	0			c.G1699A	GRCh37	CM920127	BCHE	M	rs1803274	PASS	.	C	THR/ALA	835,3569	327.2+/-299.9	84,667,1451	91.0	85.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1699	4.1	1.0	3	dbSNP_89	87	1735,6863	309.8+/-309.6	171,1393,2735	yes	missense	BCHE	NM_000055.2	58	255,2060,4186	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	20.1791,18.96,19.7662	benign	567/603	165491280	2570,10432	2202	4299	6501	SO:0001583	missense	590	exon4			ATTCTGCTTCATC	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"""cholinesterase 1"", ""cholinesterase (serum) 2"""	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1699G>A	3.37:g.165491280C>T	ENSP00000264381:p.Ala567Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	48	0.4	NM_000055	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	351	0.16071428571428573	69	0.1402439024390244	47	0.1298342541436464	93	0.16258741258741258	142	0.18733509234828497	C	15.90	2.969877	0.53614	0.1896	0.201791	ENSG00000114200	ENST00000264381;ENST00000479451;ENST00000540653	T;T;T	0.77620	-0.18;-1.1;-1.11	5.03	4.14	0.48551	Acetylcholinesterase, tetramerisation (2);	0.339910	0.27433	N	0.019382	T	0.00210	0.0006	L	0.61218	1.895	0.37967	P	0.06682699999999997	B	0.06786	0.001	B	0.15052	0.012	T	0.24083	-1.0170	9	0.52906	T	0.07	.	11.9722	0.53069	0.0:0.9138:0.0:0.0862	rs1803274;rs3773869;rs17713328;rs17846898;rs52816414;rs60242395;rs1803274	567	P06276	CHLE_HUMAN	T	567;97;29	ENSP00000264381:A567T;ENSP00000418325:A97T;ENSP00000443583:A29T	ENSP00000264381:A567T	A	-	1	0	BCHE	166973974	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.872000	0.63050	1.206000	0.43276	0.650000	0.86243	GCA	C|0.822;T|0.178	0.178	strong		0.303	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1		
RFPL3	10738	hgsc.bcm.edu	37	22	32754230	32754230	+	Missense_Mutation	SNP	A	A	G	rs386820741|rs57676160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32754230A>G	ENST00000249007.4	+	1	377	c.172A>G	c.(172-174)Acc>Gcc	p.T58A	RFPL3_ENST00000397468.1_Missense_Mutation_p.T29A|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.T29A	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	58							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GTGTGGATGCACCGTCTGCCT	0.537													a|||	737	0.147165	0.0295	0.0951	5008	,	,		19161	0.4603		0.0427	False		,,,				2504	0.1278				p.T58A		Atlas-SNP	.											.	RFPL3	91	.	0			c.A172G						PASS	.	A	ALA/THR,ALA/THR	175,4231	102.5+/-141.1	9,157,2037	121.0	114.0	116.0		172,85	-1.2	0.0	22	dbSNP_129	116	459,8141	132.0+/-189.7	11,437,3852	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	58,58	20,594,5889	GG,GA,AA		5.3372,3.9719,4.8747	benign,benign	58/318,29/289	32754230	634,12372	2203	4300	6503	SO:0001583	missense	10738	exon1			GGATGCACCGTCT	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.172A>G	22.37:g.32754230A>G	ENSP00000249007:p.Thr58Ala	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	220	99	0.45	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	316	0.1446886446886447	8	0.016260162601626018	34	0.09392265193370165	243	0.42482517482517484	31	0.040897097625329816	A	0.006	-2.102065	0.00360	0.039719	0.053372	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	D;D;D	0.94650	-3.48;-3.48;-3.48	0.622	-1.24	0.09435	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	.	.	.	.	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	0.38243	-0.9670	7	0.06365	T	0.9	.	.	.	.	rs57676160;rs61729171	58	O75679	RFPL3_HUMAN	A	29;58;29	ENSP00000380609:T29A;ENSP00000249007:T58A;ENSP00000371520:T29A	ENSP00000249007:T58A	T	+	1	0	RFPL3	31084230	0.994000	0.37717	0.000000	0.03702	0.021000	0.10359	0.834000	0.27518	-2.719000	0.00389	-2.809000	0.00112	ACC	A|0.920;G|0.080	0.080	strong		0.537	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
TMEM55A	55529	hgsc.bcm.edu	37	8	92033502	92033502	+	Silent	SNP	T	T	C	rs34503257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:92033502T>C	ENST00000285419.3	-	2	551	c.237A>G	c.(235-237)acA>acG	p.T79T	GS1-251I9.3_ENST00000517920.1_RNA	NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	79						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			CATTGCAAACTGTGCACTTAA	0.378													T|||	466	0.0930511	0.1868	0.0418	5008	,	,		17831	0.0516		0.0726	False		,,,				2504	0.0665				p.T79T		Atlas-SNP	.											.	TMEM55A	34	.	0			c.A237G						PASS	.	T		694,3712	289.5+/-280.5	53,588,1562	110.0	100.0	103.0		237	-10.7	0.1	8	dbSNP_126	103	797,7803	187.9+/-235.0	34,729,3537	no	coding-synonymous	TMEM55A	NM_018710.2		87,1317,5099	CC,CT,TT		9.2674,15.7512,11.4639		79/258	92033502	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	55529	exon2			GCAAACTGTGCAC	BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.237A>G	8.37:g.92033502T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_018710	B2R9H4|Q68CU2	Silent	SNP	ENST00000285419.3	37	CCDS6252.1																																																																																			T|0.896;C|0.104	0.104	strong		0.378	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376778.1	NM_018710	
SFXN1	94081	hgsc.bcm.edu	37	5	174936102	174936102	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:174936102G>T	ENST00000321442.5	+	3	486	c.232G>T	c.(232-234)Gct>Tct	p.A78S	SFXN1_ENST00000502393.1_Missense_Mutation_p.A78S	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	78					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)			CTATGATTCAGCTTTTCATCC	0.393																																					p.A78S		Atlas-SNP	.											.	SFXN1	23	.	0			c.G232T						PASS	.						204.0	192.0	196.0					5																	174936102		2203	4300	6503	SO:0001583	missense	94081	exon3			GATTCAGCTTTTC	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.232G>T	5.37:g.174936102G>T	ENSP00000316905:p.Ala78Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	204	9	0.0441176	NM_022754	B3KPW3|D3DQN2|Q9HA53	Missense_Mutation	SNP	ENST00000321442.5	37	CCDS4394.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923734	0.92319	.	.	ENSG00000164466	ENST00000507017;ENST00000321442;ENST00000506963	T;T;T	0.36157	1.27;1.27;1.27	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	T	0.57277	-0.7839	10	0.39692	T	0.17	-21.0535	17.8038	0.88596	0.0:0.0:1.0:0.0	.	78;78	D6RFI0;Q9H9B4	.;SFXN1_HUMAN	S	78	ENSP00000420961:A78S;ENSP00000316905:A78S;ENSP00000421467:A78S	ENSP00000316905:A78S	A	+	1	0	SFXN1	174868708	1.000000	0.71417	0.048000	0.18961	0.968000	0.65278	9.731000	0.98807	2.444000	0.82710	0.555000	0.69702	GCT	.	.	none		0.393	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754	
ADAM21	8747	hgsc.bcm.edu	37	14	70924812	70924812	+	Missense_Mutation	SNP	C	C	T	rs370238293		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:70924812C>T	ENST00000603540.1	+	2	854	c.596C>T	c.(595-597)tCt>tTt	p.S199F	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.S199F	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	199					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAACCAAAATCTGCTGGTGAC	0.448																																					p.S199F		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,6	ADAM21	181	6	0			c.C596T						scavenged	.						74.0	76.0	75.0					14																	70924812		2203	4300	6503	SO:0001583	missense	8747	exon2			CAAAATCTGCTGG	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.596C>T	14.37:g.70924812C>T	ENSP00000474385:p.Ser199Phe	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	186	2	0.0107527	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	9.262	1.043355	0.19748	.	.	ENSG00000139985	ENST00000267499	T	0.01215	5.16	3.49	3.49	0.39957	.	0.378699	0.19013	U	0.125029	T	0.02230	0.0069	M	0.68593	2.085	0.26948	N	0.966098	B	0.32876	0.388	B	0.37422	0.249	T	0.24764	-1.0151	10	0.40728	T	0.16	.	10.6601	0.45698	0.0:1.0:0.0:0.0	.	199	Q9UKJ8	ADA21_HUMAN	F	199	ENSP00000267499:S199F	ENSP00000267499:S199F	S	+	2	0	ADAM21	69994565	0.001000	0.12720	0.813000	0.32504	0.022000	0.10575	0.380000	0.20602	1.947000	0.56498	0.557000	0.71058	TCT	.	.	weak		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
SPATA33	124045	hgsc.bcm.edu	37	16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	rs13329897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000550102.1_5'Flank|CHMP1A_ENST00000397901.3_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000253475.5_5'Flank|SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L|SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	45			S -> L (in dbSNP:rs13329897).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACAGGGAGTCGGAGAAGCCT	0.612													C|||	37	0.00738818	0.0	0.013	5008	,	,		13663	0.0		0.0249	False		,,,				2504	0.0031				p.S46L		Atlas-SNP	.											.	C16orf55	6	.	0			c.C137T						PASS	.		LEU/SER	24,4370	29.9+/-59.1	0,24,2173	34.0	38.0	37.0		134	-1.5	0.0	16	dbSNP_121	37	174,8426	79.5+/-142.1	2,170,4128	yes	missense	C16orf55	NM_153025.1	145	2,194,6301	TT,TC,CC		2.0233,0.5462,1.5238	possibly-damaging	45/140	89724755	198,12796	2197	4300	6497	SO:0001583	missense	124045	exon2			GGGAGTCGGAGAA	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"""chromosome 16 open reading frame 55"""	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.134C>T	16.37:g.89724755C>T	ENSP00000301031:p.Ser45Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_001271910	A8WFL2|B4DZN8	Missense_Mutation	SNP	ENST00000301031.4	37	CCDS10983.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	6.839	0.524082	0.13066	0.005462	0.020233	ENSG00000167523	ENST00000301031;ENST00000457689	T	0.40225	1.04	1.95	-1.52	0.08637	.	.	.	.	.	T	0.11665	0.0284	L	0.27053	0.805	0.09310	N	1	B;B;B	0.22851	0.004;0.076;0.008	B;B;B	0.08055	0.001;0.003;0.001	T	0.12426	-1.0548	9	0.36615	T	0.2	.	2.8748	0.05628	0.0:0.4326:0.2424:0.325	rs13329897;rs52799200;rs13329897	46;59;45	B4DZN8;Q86XC3;Q96N06	.;.;CP055_HUMAN	L	45;46	ENSP00000301031:S45L	ENSP00000301031:S45L	S	+	2	0	C16orf55	88252256	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.868000	0.04236	-0.356000	0.08187	-2.290000	0.00267	TCG	C|0.987;T|0.013	0.013	strong		0.612	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025	
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662251	35662251	+	Missense_Mutation	SNP	T	T	C	rs2297879	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35662251T>C	ENST00000378387.3	-	8	1034	c.917A>G	c.(916-918)cAt>cGt	p.H306R	ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.H270R|ARHGEF39_ENST00000343259.3_Silent_p.S186S	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	306	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		H -> R (in dbSNP:rs2297879).		positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										TAGCTTCTCATGAGGGAAGGA	0.527													T|||	1531	0.305711	0.0628	0.3545	5008	,	,		20777	0.503		0.325	False		,,,				2504	0.3763				p.H306R		Atlas-SNP	.											.	.	.	.	0			c.A917G						PASS	.	T	ARG/HIS	531,3875	240.9+/-251.5	36,459,1708	112.0	98.0	103.0		917	2.4	0.2	9	dbSNP_100	103	2729,5871	436.5+/-358.3	426,1877,1997	yes	missense	C9orf100	NM_032818.2	29	462,2336,3705	CC,CT,TT		31.7326,12.0517,25.0654	benign	306/336	35662251	3260,9746	2203	4300	6503	SO:0001583	missense	84904	exon8			TTCTCATGAGGGA	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.917A>G	9.37:g.35662251T>C	ENSP00000367638:p.His306Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	37	CCDS6584.2	724	0.3315018315018315	49	0.09959349593495935	136	0.3756906077348066	285	0.4982517482517482	254	0.33509234828496043	T	5.983	0.365374	0.11352	0.120517	0.317326	ENSG00000137135	ENST00000378387;ENST00000378395	T;T	0.41065	1.01;1.01	5.97	2.39	0.29439	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.34399	P	0.304968	B	0.02656	0.0	B	0.01281	0.0	T	0.47971	-0.9075	8	0.13853	T	0.58	-7.3161	7.5244	0.27647	0.0:0.2434:0.0:0.7566	rs2297879;rs58265228;rs2297879	306	Q8N4T4	CI100_HUMAN	R	306;270	ENSP00000367638:H306R;ENSP00000367648:H270R	ENSP00000367638:H306R	H	-	2	0	C9orf100	35652251	0.163000	0.22920	0.163000	0.22734	0.974000	0.67602	0.418000	0.21230	0.169000	0.19679	-0.250000	0.11733	CAT	T|0.720;C|0.280	0.280	strong		0.527	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
PADI6	353238	hgsc.bcm.edu	37	1	17707601	17707601	+	RNA	SNP	T	T	C	rs6669650	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17707601T>C	ENST00000434762.2	+	0	545							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		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;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	ATTGCAACCCTGCTGATGTGG	0.498													T|||	812	0.162141	0.1029	0.1196	5008	,	,		19632	0.2788		0.1292	False		,,,				2504	0.1861				p.P165P		Atlas-SNP	.											.	PADI6	51	.	0			c.T495C						PASS	.	T		361,3521		13,335,1593	75.0	79.0	78.0		495	-2.6	0.0	1	dbSNP_116	78	1351,6935		132,1087,2924	no	coding-synonymous	PADI6	NM_207421.3		145,1422,4517	CC,CT,TT		16.3046,9.2993,14.0697		165/695	17707601	1712,10456	1941	4143	6084			353238	exon5			CAACCCTGCTGAT	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17707601T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				T|0.832;C|0.168	0.168	strong		0.498	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
OR52N1	79473	hgsc.bcm.edu	37	11	5809746	5809746	+	Missense_Mutation	SNP	C	C	T	rs10742787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5809746C>T	ENST00000317078.1	-	1	300	c.301G>A	c.(301-303)Gcc>Acc	p.A101T	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	101			A -> T (in dbSNP:rs10742787).			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)		AACATCTGGGCGAGGCAGGCT	0.507													C|||	1612	0.321885	0.4584	0.2738	5008	,	,		24308	0.2004		0.332	False		,,,				2504	0.2863				p.A101T		Atlas-SNP	.											.	OR52N1	70	.	0			c.G301A						PASS	.	C	THR/ALA	1899,2503	544.9+/-376.7	400,1099,702	150.0	138.0	142.0		301	1.5	0.7	11	dbSNP_120	142	2639,5953	424.9+/-354.8	396,1847,2053	yes	missense	OR52N1	NM_001001913.1	58	796,2946,2755	TT,TC,CC		30.7146,43.1395,34.9238	benign	101/321	5809746	4538,8456	2201	4296	6497	SO:0001583	missense	79473	exon1			TCTGGGCGAGGCA	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.301G>A	11.37:g.5809746C>T	ENSP00000322823:p.Ala101Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	37	CCDS31398.1	668	0.3058608058608059	218	0.44308943089430897	94	0.2596685082872928	109	0.19055944055944055	247	0.3258575197889182	C	0.012	-1.671662	0.00758	0.431395	0.307146	ENSG00000181001	ENST00000317078	T	0.03004	4.08	4.59	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.426972	0.19690	N	0.108285	T	0.00012	0.0000	N	0.10972	0.075	0.54753	P	1.8999999999991246E-5	B	0.06786	0.001	B	0.08055	0.003	T	0.43940	-0.9360	9	0.02654	T	1	.	3.9046	0.09177	0.1428:0.577:0.1179:0.1623	rs10742787;rs59383013;rs10742787	101	Q8NH53	O52N1_HUMAN	T	101	ENSP00000322823:A101T	ENSP00000322823:A101T	A	-	1	0	OR52N1	5766322	0.000000	0.05858	0.731000	0.30826	0.146000	0.21551	-2.069000	0.01381	-0.010000	0.14271	-0.921000	0.02739	GCC	C|0.675;T|0.325	0.325	strong		0.507	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145904	42145904	+	Missense_Mutation	SNP	G	G	A	rs188061762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42145904G>A	ENST00000320955.6	-	58	10083	c.9856C>T	c.(9856-9858)Ccg>Tcg	p.P3286S	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3286					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)		AGGCCCCCCGGAGCTGCAGGA	0.672													G|||	6	0.00119808	0.0	0.0014	5008	,	,		16632	0.0		0.004	False		,,,				2504	0.001				p.P3251S		Atlas-SNP	.											SPTBN5,NS,carcinoma,0,1	SPTBN5	171	1	0			c.C9751T						PASS	.	G	SER/PRO	6,3876		0,6,1935	18.0	23.0	21.0		9751	3.8	0.0	15		21	81,8161		1,79,4041	yes	missense	SPTBN5	NM_016642.2	74	1,85,5976	AA,AG,GG		0.9828,0.1546,0.7176	benign	3251/3640	42145904	87,12037	1941	4121	6062	SO:0001583	missense	51332	exon58			CCCCCGGAGCTGC	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.9856C>T	15.37:g.42145904G>A	ENSP00000317790:p.Pro3286Ser	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	.	8.908	0.957895	0.18507	0.001546	0.009828	ENSG00000137877	ENST00000320955	T	0.46063	0.88	4.74	3.82	0.43975	.	0.690860	0.13222	N	0.404301	T	0.12390	0.0301	N	0.01576	-0.805	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.16364	-1.0405	10	0.28530	T	0.3	.	9.6181	0.39704	0.1684:0.0:0.8316:0.0	.	3286	Q9NRC6	SPTN5_HUMAN	S	3286	ENSP00000317790:P3286S	ENSP00000317790:P3286S	P	-	1	0	SPTBN5	39933196	0.004000	0.15560	0.022000	0.16811	0.031000	0.12232	1.464000	0.35288	1.126000	0.42016	0.313000	0.20887	CCG	G|0.997;A|0.003	0.003	strong		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
WDR18	57418	hgsc.bcm.edu	37	19	990281	990281	+	Missense_Mutation	SNP	G	G	A	rs2158367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:990281G>A	ENST00000251289.5	+	4	537	c.514G>A	c.(514-516)Gcg>Acg	p.A172T	WDR18_ENST00000591997.1_3'UTR|WDR18_ENST00000587001.2_Missense_Mutation_p.A172T	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	172			A -> T (in dbSNP:rs2158367). {ECO:0000269|PubMed:15489334}.		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)		GTCTCACCACGCGCTCCCCAT	0.731													.|||	4459	0.890375	0.9977	0.7651	5008	,	,		13729	0.7679		0.9553	False		,,,				2504	0.8937				p.A172T		Atlas-SNP	.											.	WDR18	20	.	0			c.G514A						PASS	.		THR/ALA	4329,51		2139,51,0	21.0	22.0	22.0		514	4.1	1.0	19	dbSNP_96	22	8054,534		3780,494,20	yes	missense	WDR18	NM_024100.3	58	5919,545,20	AA,AG,GG		6.218,1.1644,4.5111	benign	172/433	990281	12383,585	2190	4294	6484	SO:0001583	missense	57418	exon4			CACCACGCGCTCC		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.514G>A	19.37:g.990281G>A	ENSP00000251289:p.Ala172Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	1917	0.8777472527472527	490	0.9959349593495935	290	0.8011049723756906	416	0.7272727272727273	721	0.9511873350923483	A	8.087	0.773690	0.16051	0.988356	0.93782	ENSG00000065268	ENST00000251289	T	0.16073	2.37	4.12	4.12	0.48240	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.174679	0.49916	N	0.000126	T	0.00012	0.0000	N	0.00980	-1.08	0.53005	P	3.900000000001125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.10111	T	0.7	.	8.8655	0.35282	0.9095:0.0:0.0905:0.0	rs2158367;rs17855342;rs17855361;rs59027907;rs2158367	172	Q9BV38	WDR18_HUMAN	T	172	ENSP00000251289:A172T	ENSP00000251289:A172T	A	+	1	0	WDR18	941281	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	4.081000	0.57627	0.643000	0.30638	-0.376000	0.06991	GCG	G|0.082;A|0.918	0.918	strong		0.731	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
NLRP7	199713	hgsc.bcm.edu	37	19	55451613	55451613	+	Missense_Mutation	SNP	T	T	G	rs104895529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451613T>G	ENST00000590030.1	-	3	614	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	NLRP7_ENST00000340844.2_Missense_Mutation_p.M192L|NLRP7_ENST00000588756.1_Missense_Mutation_p.M192L|NLRP7_ENST00000446217.1_Missense_Mutation_p.M220L|NLRP7_ENST00000328092.5_Missense_Mutation_p.M192L|NLRP7_ENST00000592784.1_Missense_Mutation_p.M192L|NLRP7_ENST00000448121.2_Missense_Mutation_p.M192L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	192	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CAGTCCAGCATACACTTTTTG	0.582													.|||	4	0.000798722	0.0	0.0	5008	,	,		19202	0.0		0.003	False		,,,				2504	0.001				p.M192L		Atlas-SNP	.											.	NLRP7	411	.	0			c.A574C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	3,4403	6.2+/-15.9	0,3,2200	124.0	122.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574,574,574	-0.6	0.0	19	dbSNP_132	122	36,8564	25.1+/-72.6	1,34,4265	yes	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	15,15,15	1,37,6465	GG,GT,TT		0.4186,0.0681,0.2999	benign,benign,benign	192/1038,192/1010,192/981	55451613	39,12967	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGCATACACTT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.574A>C	19.37:g.55451613T>G	ENSP00000465520:p.Met192Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.712	1.157458	0.21454	6.81E-4	0.004186	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	1.88	-0.548	0.11833	NACHT nucleoside triphosphatase (1);	0.000000	0.38837	N	0.001543	T	0.68393	0.2996	L	0.41632	1.29	0.09310	N	1	B;B;B;B	0.34147	0.438;0.438;0.438;0.384	B;B;B;B	0.40782	0.34;0.34;0.34;0.23	T	0.59423	-0.7457	10	0.49607	T	0.09	.	0.1778	0.00120	0.2414:0.1591:0.2466:0.3529	.	220;192;192;192	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	L	192;192;192;220	ENSP00000329568:M192L;ENSP00000409137:M192L;ENSP00000339491:M192L;ENSP00000414273:M220L	ENSP00000329568:M192L	M	-	1	0	NLRP7	60143425	0.008000	0.16893	0.016000	0.15963	0.144000	0.21451	0.142000	0.16096	-0.222000	0.09958	0.379000	0.24179	ATG	T|0.998;G|0.002	0.002	strong		0.582	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
HSPH1	10808	hgsc.bcm.edu	37	13	31729729	31729729	+	Silent	SNP	A	A	G	rs1047086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:31729729A>G	ENST00000320027.5	-	3	572	c.228T>C	c.(226-228)aaT>aaC	p.N76N	HSPH1_ENST00000380405.4_Silent_p.N76N|HSPH1_ENST00000380406.5_Silent_p.N76N|HSPH1_ENST00000429785.2_5'UTR|HSPH1_ENST00000445273.2_Silent_p.N78N	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	76					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TGAAGGGGTCATTGAATGCTC	0.338													A|||	1131	0.225839	0.2451	0.2723	5008	,	,		16489	0.0109		0.4642	False		,,,				2504	0.1431				p.N76N		Atlas-SNP	.											.	HSPH1	65	.	0			c.T228C						PASS	.	A		1261,3145	430.8+/-342.7	171,919,1113	118.0	116.0	117.0		228	3.3	0.9	13	dbSNP_86	117	4063,4537	557.6+/-387.1	952,2159,1189	no	coding-synonymous	HSPH1	NM_006644.2		1123,3078,2302	GG,GA,AA		47.2442,28.6201,40.935		76/859	31729729	5324,7682	2203	4300	6503	SO:0001819	synonymous_variant	10808	exon3			GGGGTCATTGAAT	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.228T>C	13.37:g.31729729A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Silent	SNP	ENST00000320027.5	37	CCDS9340.1																																																																																			A|0.651;G|0.349	0.349	strong		0.338	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
ABCF2	10061	hgsc.bcm.edu	37	7	150912786	150912786	+	Silent	SNP	T	T	C	rs7786151	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150912786T>C	ENST00000287844.2	-	13	1543	c.1434A>G	c.(1432-1434)tcA>tcG	p.S478S	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.S478S	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	478	ABC transporter 2. {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)		ACTCCAAAGGTGAGAGATCTA	0.468													C|||	436	0.0870607	0.1573	0.1196	5008	,	,		21058	0.0159		0.0775	False		,,,				2504	0.0521				p.S478S		Atlas-SNP	.											.	ABCF2	54	.	0			c.A1434G						PASS	.	C	,	640,3766	766.9+/-413.5	46,548,1609	154.0	135.0	141.0		1434,1434	-10.0	0.3	7	dbSNP_116	141	835,7765	781.0+/-407.6	47,741,3512	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	93,1289,5121	CC,CT,TT		9.7093,14.5256,11.3409	,	478/635,478/624	150912786	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon13			CAAAGGTGAGAGA	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.1434A>G	7.37:g.150912786T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			T|0.901;C|0.099	0.099	strong		0.468	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
PLB1	151056	hgsc.bcm.edu	37	2	28865760	28865760	+	Silent	SNP	T	T	C	rs2272387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:28865760T>C	ENST00000327757.5	+	58	4254	c.4210T>C	c.(4210-4212)Ttg>Ctg	p.L1404L	PLB1_ENST00000422425.2_Silent_p.L1393L|PLB1_ENST00000541605.1_Silent_p.L369L|AC074011.2_ENST00000431376.1_RNA	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1404	Necessary for membrane localization. {ECO:0000250}.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GAACAGCCGATTGCTCCCAGA	0.617													C|||	1940	0.38738	0.4962	0.2637	5008	,	,		16583	0.3591		0.4125	False		,,,				2504	0.3313				p.L1404L		Atlas-SNP	.											.	PLB1	255	.	0			c.T4210C						PASS	.	C	,	2160,2246		501,1158,544	37.0	35.0	35.0		4177,4210	2.8	0.0	2	dbSNP_100	35	3329,5271		657,2015,1628	no	coding-synonymous,coding-synonymous	PLB1	NM_001170585.1,NM_153021.4	,	1158,3173,2172	CC,CT,TT		38.7093,49.0241,42.2036	,	1393/1448,1404/1459	28865760	5489,7517	2203	4300	6503	SO:0001819	synonymous_variant	151056	exon58			AGCCGATTGCTCC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.4210T>C	2.37:g.28865760T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	876	0.4010989010989011	253	0.5142276422764228	104	0.287292817679558	193	0.3374125874125874	326	0.43007915567282323	C	4.832	0.154611	0.09236	0.490241	0.387093	ENSG00000163803	ENST00000436775	.	.	.	5.7	2.85	0.33270	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.46762	-0.9168	3	.	.	.	-0.39	2.6537	0.05005	0.1504:0.5432:0.1454:0.1611	rs2272387;rs2272387	.	.	.	T	106	.	.	I	+	2	0	PLB1	28719264	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.364000	0.07583	0.053000	0.16036	-0.119000	0.15052	ATT	T|0.595;C|0.405	0.405	strong		0.617	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
ITM2C	81618	hgsc.bcm.edu	37	2	231738269	231738269	+	Silent	SNP	G	G	A	rs2289233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231738269G>A	ENST00000326427.6	+	2	384	c.258G>A	c.(256-258)gcG>gcA	p.A86A	ITM2C_ENST00000335005.6_Intron|ITM2C_ENST00000409704.2_Silent_p.A24A|ITM2C_ENST00000326407.6_Silent_p.A86A|ITM2C_ENST00000492029.1_3'UTR	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	86					negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		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;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TCTTCCTTGCGCAGGTGAGGG	0.617													G|||	2551	0.509385	0.2277	0.5331	5008	,	,		19946	0.8135		0.504	False		,,,				2504	0.5654				p.A86A		Atlas-SNP	.											.	ITM2C	17	.	0			c.G258A						PASS	.	G	,,	1101,3305	384.4+/-325.3	139,823,1241	88.0	61.0	70.0		,258,258	-5.2	0.8	2	dbSNP_100	70	4165,4435	553.2+/-386.3	1027,2111,1162	no	intron,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1166,2934,2403	AA,AG,GG		48.4302,24.9887,40.489	,,	,86/231,86/268	231738269	5266,7740	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon2			CCTTGCGCAGGTG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.258G>A	2.37:g.231738269G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			G|0.534;A|0.466	0.466	strong		0.617	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
PRSS50	29122	hgsc.bcm.edu	37	3	46784532	46784532	+	Intron	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46784532C>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Silent_p.E108E			Q9UI38	TSP50_HUMAN	protease, serine, 50						proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						ACACCTCAGCCTCCTGCAGCT	0.577																																					p.E108E	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.G324A						PASS	.						61.0	69.0	66.0					3																	46784532		2133	4258	6391	SO:0001627	intron_variant	377047	exon3			CTCAGCCTCCTGC	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.541+5582G>A	3.37:g.46784532C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_199183		Silent	SNP	ENST00000460241.1	37	CCDS2745.1																																																																																			.	.	none		0.577	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	88	31	0.352273	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	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209634	84209634	+	Silent	SNP	C	C	G	rs2288019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84209634C>G	ENST00000378553.5	+	11	1918	c.1794C>G	c.(1792-1794)ctC>ctG	p.L598L	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	598					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)	p.L598L(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TGGAAAACCTCCCCACAGACA	0.468											OREG0023983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2663	0.531749	0.5159	0.5245	5008	,	,		18997	0.5268		0.504	False		,,,				2504	0.592				p.L598L		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,1	DNAAF1	81	1	1	Substitution - coding silent(1)	stomach(1)	c.C1794G						PASS	.	G		2265,2135	577.8+/-384.5	609,1047,544	81.0	72.0	75.0		1794	-3.8	0.0	16	dbSNP_100	75	4374,4226	571.9+/-389.6	1130,2114,1056	no	coding-synonymous	DNAAF1	NM_178452.4		1739,3161,1600	GG,GC,CC		49.1395,48.5227,48.9308		598/726	84209634	6639,6361	2200	4300	6500	SO:0001819	synonymous_variant	123872	exon11			AAACCTCCCCACA	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.1794C>G	16.37:g.84209634C>G		Somatic	110	0	0	1227	WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	37	CCDS10943.2																																																																																			C|0.475;G|0.525	0.525	strong		0.468	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
SEZ6L	23544	hgsc.bcm.edu	37	22	26702015	26702015	+	Silent	SNP	A	A	C	rs1210894	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26702015A>C	ENST00000248933.6	+	6	1514	c.1419A>C	c.(1417-1419)acA>acC	p.T473T	SEZ6L_ENST00000360929.3_Silent_p.T473T|SEZ6L_ENST00000402979.1_Silent_p.T246T|SEZ6L_ENST00000529632.2_Silent_p.T473T|SEZ6L_ENST00000343706.4_Silent_p.T473T|SEZ6L_ENST00000404234.3_Silent_p.T473T|SEZ6L_ENST00000403121.1_Silent_p.T246T			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	473	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.T473T(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CTGAAAACACAAATGGGAGCC	0.557													C|||	1817	0.362819	0.6611	0.3386	5008	,	,		15893	0.1042		0.4433	False		,,,				2504	0.1605				p.T473T		Atlas-SNP	.											SEZ6L,NS,carcinoma,0,1	SEZ6L	174	1	1	Substitution - coding silent(1)	stomach(1)	c.A1419C						PASS	.	C	,,,,,	2748,1658	506.6+/-366.4	852,1044,307	75.0	69.0	71.0		1419,1419,1419,1419,1419,1419	3.6	0.6	22	dbSNP_87	71	3722,4878	618.1+/-396.7	831,2060,1409	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	1683,3104,1716	CC,CA,AA		43.2791,37.6305,49.7463	,,,,,	473/1024,473/1014,473/1012,473/950,473/949,473/1025	26702015	6470,6536	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon6			AAACACAAATGGG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1419A>C	22.37:g.26702015A>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			A|0.555;C|0.445	0.445	strong		0.557	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
FUT5	2527	hgsc.bcm.edu	37	19	5867191	5867191	+	Silent	SNP	G	G	A	rs10412834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5867191G>A	ENST00000588525.1	-	2	633	c.546C>T	c.(544-546)taC>taT	p.Y182Y	FUT5_ENST00000252675.5_Silent_p.Y182Y	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	182					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						CCAGCCAGCCGTAGGGCGTGA	0.662													G|||	452	0.0902556	0.0764	0.1124	5008	,	,		13354	0.0109		0.1531	False		,,,				2504	0.1104				p.Y182Y		Atlas-SNP	.											.	FUT5	29	.	0			c.C546T						PASS	.	G		370,3984		11,348,1818	26.0	23.0	24.0		546	-1.2	1.0	19	dbSNP_119	24	1225,7311		92,1041,3135	no	coding-synonymous	FUT5	NM_002034.2		103,1389,4953	AA,AG,GG		14.351,8.4979,12.3739		182/375	5867191	1595,11295	2177	4268	6445	SO:0001819	synonymous_variant	2527	exon2			CCAGCCGTAGGGC		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.546C>T	19.37:g.5867191G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_002034	A8K4X2	Silent	SNP	ENST00000588525.1	37	CCDS12154.1																																																																																			G|0.912;A|0.088	0.088	strong		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
ZNF835	90485	hgsc.bcm.edu	37	19	57175484	57175484	+	Silent	SNP	A	A	G	rs7250003	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57175484A>G	ENST00000537055.2	-	2	1314	c.1083T>C	c.(1081-1083)ccT>ccC	p.P361P		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	361					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.P383P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						GGCAGGGGTAAGGCCGCTCTC	0.682													.|||	2374	0.474042	0.6679	0.4078	5008	,	,		16463	0.4732		0.3151	False		,,,				2504	0.4233				p.P361P		Atlas-SNP	.											ZNF835,NS,carcinoma,0,2	ZNF835	106	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1083C						PASS	.	G		2885,1519		962,961,279	21.0	21.0	21.0		1083	-2.0	0.0	19	dbSNP_116	21	2566,6026		394,1778,2124	no	coding-synonymous	ZNF835	NM_001005850.2		1356,2739,2403	GG,GA,AA		29.865,34.4914,41.9437		361/538	57175484	5451,7545	2202	4296	6498	SO:0001819	synonymous_variant	90485	exon2			GGGGTAAGGCCGC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1083T>C	19.37:g.57175484A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			A|0.575;G|0.425	0.425	strong		0.682	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626820	43626820	+	Missense_Mutation	SNP	G	G	C	rs138779714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	16	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	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	
CELSR1	9620	hgsc.bcm.edu	37	22	46761497	46761497	+	Missense_Mutation	SNP	C	C	G	rs12165943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46761497C>G	ENST00000262738.3	-	31	8389	c.8390G>C	c.(8389-8391)tGc>tCc	p.C2797S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2797			C -> S (in dbSNP:rs12165943).		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)		GGGATCCTTGCAGCTCCTGGG	0.637													G|||	1525	0.304513	0.848	0.1715	5008	,	,		12450	0.003		0.2187	False		,,,				2504	0.0634				p.C2797S		Atlas-SNP	.											.	CELSR1	242	.	0			c.G8390C						PASS	.	G	SER/CYS	3221,1131		1203,815,158	22.0	24.0	23.0		8390	1.9	0.0	22	dbSNP_120	23	1720,6856		159,1402,2727	yes	missense	CELSR1	NM_014246.1	112	1362,2217,2885	GG,GC,CC		20.056,25.9881,38.2194	benign	2797/3015	46761497	4941,7987	2176	4288	6464	SO:0001583	missense	9620	exon31			TCCTTGCAGCTCC	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.8390G>C	22.37:g.46761497C>G	ENSP00000262738:p.Cys2797Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	641	0.2934981684981685	410	0.8333333333333334	72	0.19889502762430938	1	0.0017482517482517483	158	0.20844327176781002	G	0.007	-1.966069	0.00461	0.740119	0.20056	ENSG00000075275	ENST00000262738	T	0.65178	-0.14	4.23	1.89	0.25635	.	1.869630	0.03427	N	0.207180	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.39251	-0.9623	9	0.08837	T	0.75	.	12.3882	0.55345	0.0:0.4886:0.5114:0.0	rs12165943;rs12165943	2797	Q9NYQ6	CELR1_HUMAN	S	2797	ENSP00000262738:C2797S	ENSP00000262738:C2797S	C	-	2	0	CELSR1	45140161	0.046000	0.20272	0.029000	0.17559	0.005000	0.04900	0.107000	0.15375	0.357000	0.24183	-0.647000	0.03941	TGC	C|0.641;G|0.359	0.359	strong		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
ACSM6	142827	hgsc.bcm.edu	37	10	96971638	96971638	+	Silent	SNP	G	G	A	rs75252129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:96971638G>A	ENST00000394005.3	+	5	768	c.759G>A	c.(757-759)cgG>cgA	p.R253R	C10orf129_ENST00000430183.1_Silent_p.R98R|C10orf129_ENST00000341686.3_Silent_p.R253R			Q6P461	ACSM6_HUMAN		253					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.R253R(1)|p.R98R(1)		breast(1)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TCTTTAGACGGTGGATGGATC	0.473													G|||	179	0.0357428	0.0008	0.0576	5008	,	,		20742	0.0		0.1044	False		,,,				2504	0.0337				p.R253R		Atlas-SNP	.											C10orf129_ENST00000341686,NS,carcinoma,0,2	C10orf129	52	2	2	Substitution - coding silent(2)	pancreas(2)	c.G759A						PASS	.	G		91,4315	75.7+/-113.9	0,91,2112	126.0	111.0	116.0		759	0.8	0.1	10	dbSNP_132	116	925,7675	204.9+/-247.5	48,829,3423	no	coding-synonymous	C10orf129	NM_207321.2		48,920,5535	AA,AG,GG		10.7558,2.0654,7.8118		253/481	96971638	1016,11990	2203	4300	6503	SO:0001819	synonymous_variant	142827	exon6			TAGACGGTGGATG																												ENST00000394005.3:c.759G>A	10.37:g.96971638G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_207321	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Silent	SNP	ENST00000394005.3	37	CCDS7440.2																																																																																			G|0.931;A|0.069	0.069	strong		0.473	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2		
TBX2	6909	hgsc.bcm.edu	37	17	59480547	59480547	+	Silent	SNP	C	C	T	rs140013823		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59480547C>T	ENST00000240328.3	+	3	1070	c.789C>T	c.(787-789)gtC>gtT	p.V263V	RP11-332H18.5_ENST00000585765.1_RNA|RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	263					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						TCATCGCCGTCACTGCCTACC	0.637													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.V263V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C789T						PASS	.	C		0,4406		0,0,2203	90.0	76.0	81.0		789	4.8	1.0	17	dbSNP_134	81	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TBX2	NM_005994.3		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		263/713	59480547	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6909	exon3			CGCCGTCACTGCC	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.789C>T	17.37:g.59480547C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	37	CCDS11627.2																																																																																			C|0.999;T|0.001	0.001	strong		0.637	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994	
ITPR3	3710	hgsc.bcm.edu	37	6	33641379	33641379	+	Silent	SNP	T	T	C	rs1803831	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33641379T>C	ENST00000374316.5	+	24	4000	c.2940T>C	c.(2938-2940)aaT>aaC	p.N980N	ITPR3_ENST00000605930.1_Silent_p.N980N			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	980					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)	TCATCCTCAATGTCCGCCTGG	0.557													T|||	2379	0.47504	0.3086	0.4813	5008	,	,		21094	0.5268		0.505	False		,,,				2504	0.6115				p.N980N		Atlas-SNP	.											.	ITPR3	409	.	0			c.T2940C						PASS	.	T		1442,2964	467.6+/-354.9	244,954,1005	282.0	242.0	256.0		2940	-10.4	0.3	6	dbSNP_89	256	4517,4083	594.2+/-393.3	1169,2179,952	no	coding-synonymous	ITPR3	NM_002224.3		1413,3133,1957	CC,CT,TT		47.4767,32.7281,45.8173		980/2672	33641379	5959,7047	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon23			CCTCAATGTCCGC	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.2940T>C	6.37:g.33641379T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	227	121	0.53304	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			A|0.000;C|0.461;T|0.538	0.461	strong		0.557	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
KANK1	23189	hgsc.bcm.edu	37	9	712137	712137	+	Silent	SNP	G	G	C	rs912175	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:712137G>C	ENST00000382303.1	+	7	2023	c.1371G>C	c.(1369-1371)ctG>ctC	p.L457L	KANK1_ENST00000382293.3_Silent_p.L299L|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Silent_p.L457L	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	457	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.L299L(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AAATTGAGCTGCAACAGCAGA	0.463													G|||	918	0.183307	0.1823	0.2968	5008	,	,		21835	0.1925		0.2107	False		,,,				2504	0.0665				p.L457L		Atlas-SNP	.											KANK1,NS,carcinoma,0,1	KANK1	231	1	1	Substitution - coding silent(1)	stomach(1)	c.G1371C						PASS	.	G	,	793,3613	318.2+/-295.5	83,627,1493	95.0	92.0	93.0		1371,897	2.6	1.0	9	dbSNP_86	93	1891,6709	334.5+/-321.0	227,1437,2636	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	310,2064,4129	CC,CG,GG		21.9884,17.9982,20.6366	,	457/1353,299/1195	712137	2684,10322	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon7			TGAGCTGCAACAG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1371G>C	9.37:g.712137G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			G|0.771;C|0.229	0.229	strong		0.463	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
CHML	1122	hgsc.bcm.edu	37	1	241798443	241798443	+	Missense_Mutation	SNP	G	G	A	rs41269377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:241798443G>A	ENST00000366553.1	-	1	789	c.626C>T	c.(625-627)gCc>gTc	p.A209V	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)	209					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)			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)			TGGTTCATCGGCCTTATCTTC	0.348													G|||	98	0.0195687	0.0136	0.0173	5008	,	,		19467	0.0		0.0249	False		,,,				2504	0.044				p.A209V		Atlas-SNP	.											.	CHML	82	.	0			c.C626T						PASS	.	G	VAL/ALA,	82,4324	70.3+/-108.2	0,82,2121	199.0	201.0	200.0		626,	0.7	0.0	1	dbSNP_127	200	200,8398	87.1+/-149.5	2,196,4101	yes	missense,intron	CHML,OPN3	NM_001821.3,NM_014322.2	64,	2,278,6222	AA,AG,GG		2.3261,1.8611,2.1686	benign,	209/657,	241798443	282,12722	2203	4299	6502	SO:0001583	missense	1122	exon1			TCATCGGCCTTAT	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.626C>T	1.37:g.241798443G>A	ENSP00000355511:p.Ala209Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	34	0.015567765567765568	7	0.014227642276422764	10	0.027624309392265192	0	0.0	17	0.022427440633245383	G	1.202	-0.632223	0.03584	0.018611	0.023261	ENSG00000203668	ENST00000366553	T	0.60299	0.2	4.67	0.66	0.17868	.	1.059620	0.07295	U	0.873097	T	0.14056	0.0340	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.18871	0.023	T	0.14144	-1.0483	9	0.15499	T	0.54	0.5364	3.7952	0.08737	0.3306:0.2065:0.4629:0.0	rs41269377;rs61736557	209	P26374	RAE2_HUMAN	V	209	ENSP00000355511:A209V	ENSP00000355511:A209V	A	-	2	0	CHML	239865066	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.340000	0.02650	0.281000	0.22233	0.650000	0.86243	GCC	G|0.980;A|0.020	0.020	strong		0.348	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
ZNF695	57116	hgsc.bcm.edu	37	1	247162658	247162658	+	Missense_Mutation	SNP	C	C	T	rs2642973	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247162658C>T	ENST00000339986.7	-	3	398	c.251G>A	c.(250-252)aGa>aAa	p.R84K	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Missense_Mutation_p.R84K	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	84	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		R -> K (in dbSNP:rs2642973). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACCTGAGTGTCTGGCTGTCTT	0.473													T|||	4162	0.83107	0.8268	0.9265	5008	,	,		16357	0.9742		0.833	False		,,,				2504	0.6196				p.R84K		Atlas-SNP	.											.	ZNF695	55	.	0			c.G251A						PASS	.	T	LYS/ARG,LYS/ARG	3377,713		1397,583,65	113.0	116.0	115.0		251,251	0.2	0.1	1	dbSNP_100	115	7048,1426		2939,1170,128	yes	missense,missense	ZNF695	NM_001204221.1,NM_020394.4	26,26	4336,1753,193	TT,TC,CC		16.8279,17.4328,17.0248	benign,benign	84/173,84/516	247162658	10425,2139	2045	4237	6282	SO:0001583	missense	57116	exon3			GAGTGTCTGGCTG		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.251G>A	1.37:g.247162658C>T	ENSP00000341236:p.Arg84Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	1949	0.8923992673992674	417	0.8475609756097561	331	0.914364640883978	560	0.9790209790209791	641	0.8456464379947229	T	0.008	-1.927999	0.00493	0.825672	0.831721	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.06768	5.79;3.26	0.149	0.149	0.14863	Krueppel-associated box (1);	.	.	.	.	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	0.06405	0.0;0.002;0.0	T	0.45760	-0.9239	7	0.02654	T	1	.	.	.	.	rs2642973;rs4384271;rs4971297;rs6426196;rs17856691;rs17857244;rs17857446;rs52817797;rs60461496;rs2642973	84;72;84	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	K	84	ENSP00000429736:R84K;ENSP00000341236:R84K	ENSP00000428213:R72K	R	-	2	0	ZNF695	245229281	0.254000	0.23992	0.098000	0.21074	0.099000	0.18886	-0.944000	0.03913	-1.257000	0.02475	-1.297000	0.01338	AGA	C|0.133;T|0.867	0.867	strong		0.473	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
PRPF18	8559	hgsc.bcm.edu	37	10	13653653	13653653	+	Silent	SNP	A	A	G	rs1135102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13653653A>G	ENST00000378572.3	+	6	709	c.549A>G	c.(547-549)aaA>aaG	p.K183K		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	183					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						ATGATCATAAAGACATGGACA	0.393													A|||	1835	0.366414	0.4644	0.487	5008	,	,		18703	0.0615		0.4632	False		,,,				2504	0.363				p.K183K		Atlas-SNP	.											.	PRPF18	32	.	0			c.A549G						PASS	.	A		2101,2305	575.3+/-384.0	524,1053,626	138.0	128.0	131.0		549	0.9	1.0	10	dbSNP_86	131	4057,4543	558.4+/-387.2	941,2175,1184	no	coding-synonymous	PRPF18	NM_003675.3		1465,3228,1810	GG,GA,AA		47.1744,47.685,47.3474		183/343	13653653	6158,6848	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon6			TCATAAAGACATG	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.549A>G	10.37:g.13653653A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			A|0.659;G|0.341	0.341	strong		0.393	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
CPA1	1357	hgsc.bcm.edu	37	7	130023539	130023539	+	Silent	SNP	C	C	T	rs12706927	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	93	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	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	
SYNE1	23345	hgsc.bcm.edu	37	6	152469204	152469204	+	Missense_Mutation	SNP	G	G	A	rs141716975	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152469204G>A	ENST00000367255.5	-	137	25553	c.24952C>T	c.(24952-24954)Ctc>Ttc	p.L8318F	SYNE1_ENST00000539504.1_Missense_Mutation_p.L473F|SYNE1_ENST00000341594.5_Missense_Mutation_p.L7930F|SYNE1_ENST00000354674.4_Missense_Mutation_p.L473F|SYNE1_ENST00000356820.4_Missense_Mutation_p.L2842F|SYNE1_ENST00000423061.1_Missense_Mutation_p.L8247F|SYNE1_ENST00000265368.4_Missense_Mutation_p.L8318F|SYNE1_ENST00000448038.1_Missense_Mutation_p.L8247F|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8318					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)		GCTCCCCGGAGGTAGAAATCT	0.502										HNSCC(10;0.0054)			G|||	11	0.00219649	0.0008	0.0029	5008	,	,		18884	0.0		0.003	False		,,,				2504	0.0051				p.L8318F		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C24952T						PASS	.	G	PHE/LEU,PHE/LEU	3,4403	8.1+/-20.4	0,3,2200	56.0	58.0	58.0		24739,24952	3.5	1.0	6	dbSNP_134	58	48,8552	31.2+/-83.2	0,48,4252	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	22,22	0,51,6452	AA,AG,GG		0.5581,0.0681,0.3921	probably-damaging,probably-damaging	8247/8750,8318/8798	152469204	51,12955	2203	4300	6503	SO:0001583	missense	23345	exon137			CCCGGAGGTAGAA	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.24952C>T	6.37:g.152469204G>A	ENSP00000356224:p.Leu8318Phe	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	12.15	1.853073	0.32699	6.81E-4	0.005581	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.56941	0.53;4.57;1.43;0.58;0.43;0.58;0.64;2.55;1.65;4.66	5.34	3.45	0.39498	.	0.138648	0.32736	N	0.005705	T	0.44582	0.1300	M	0.75264	2.295	0.31624	N	0.649914	P;P;P;P;P	0.51537	0.911;0.911;0.946;0.911;0.715	B;B;P;B;B	0.48921	0.391;0.391;0.595;0.391;0.342	T	0.47289	-0.9129	10	0.54805	T	0.06	.	9.784	0.40664	0.0731:0.0:0.7873:0.1396	.	8318;8318;8247;8247;520	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	F	8318;473;964;8247;8318;8247;7930;2842;480;475;1240;473	ENSP00000356224:L8318F;ENSP00000441052:L473F;ENSP00000356226:L964F;ENSP00000396024:L8247F;ENSP00000265368:L8318F;ENSP00000390975:L8247F;ENSP00000341887:L7930F;ENSP00000349276:L2842F;ENSP00000356220:L1240F;ENSP00000346701:L473F	ENSP00000265368:L8318F	L	-	1	0	SYNE1	152510897	1.000000	0.71417	0.998000	0.56505	0.013000	0.08279	6.968000	0.76086	1.269000	0.44280	-0.140000	0.14226	CTC	G|0.997;A|0.003	0.003	strong		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PFKP	5214	hgsc.bcm.edu	37	10	3155353	3155353	+	Silent	SNP	C	C	T	rs3816699	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:3155353C>T	ENST00000381125.4	+	12	1273	c.1197C>T	c.(1195-1197)atC>atT	p.I399I	PFKP_ENST00000381075.2_Silent_p.I391I	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	399	N-terminal catalytic PFK domain 1.				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)		GACTTGCCATCAAGCTGCCGG	0.597													C|||	616	0.123003	0.152	0.1888	5008	,	,		18819	0.0536		0.162	False		,,,				2504	0.0685				p.I399I		Atlas-SNP	.											.	PFKP	182	.	0			c.C1197T						PASS	.	C	,	675,3731	279.3+/-274.7	62,551,1590	87.0	74.0	78.0		1173,1197	-0.7	0.9	10	dbSNP_107	78	1427,7173	269.8+/-288.6	109,1209,2982	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	171,1760,4572	TT,TC,CC		16.593,15.32,16.1618	,	391/777,399/785	3155353	2102,10904	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon12			TGCCATCAAGCTG	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.1197C>T	10.37:g.3155353C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.848;T|0.152	0.152	strong		0.597	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
SPATA7	55812	hgsc.bcm.edu	37	14	88852166	88852166	+	Missense_Mutation	SNP	G	G	A	rs4904448	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:88852166G>A	ENST00000393545.4	+	1	293	c.4G>A	c.(4-6)Gat>Aat	p.D2N	SPATA7_ENST00000554102.1_3'UTR|SPATA7_ENST00000045347.7_Missense_Mutation_p.D2N|SPATA7_ENST00000556553.1_Missense_Mutation_p.D2N|SPATA7_ENST00000356583.5_Missense_Mutation_p.D2N	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	2			D -> N (in dbSNP:rs4904448).		response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						ACTAAGCATGGATGGCAGCCG	0.701													G|||	951	0.189896	0.034	0.2608	5008	,	,		15263	0.0446		0.4443	False		,,,				2504	0.2382				p.D2N		Atlas-SNP	.											SPATA7,NS,carcinoma,0,1	SPATA7	58	1	0			c.G4A						PASS	.	G	ASN/ASP,ASN/ASP	466,3930		30,406,1762	23.0	23.0	23.0		4,4	2.2	1.0	14	dbSNP_111	23	3358,5222		661,2036,1593	yes	missense,missense	SPATA7	NM_001040428.3,NM_018418.4	23,23	691,2442,3355	AA,AG,GG		39.1375,10.6005,29.4698	possibly-damaging,possibly-damaging	2/568,2/600	88852166	3824,9152	2198	4290	6488	SO:0001583	missense	55812	exon1			AGCATGGATGGCA	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.4G>A	14.37:g.88852166G>A	ENSP00000377176:p.Asp2Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	37	CCDS9883.1	467	0.21382783882783882	17	0.034552845528455285	98	0.27071823204419887	29	0.050699300699300696	323	0.4261213720316623	G	13.05	2.122744	0.37436	0.106005	0.391375	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000555401;ENST00000553885;ENST00000045347	T;T;T;T;T;T	0.52754	1.1;1.31;1.1;1.81;0.65;1.21	4.25	2.23	0.28157	.	1.092970	0.07011	N	0.825115	T	0.00012	0.0000	L	0.51422	1.61	0.36438	P	0.13467099999999999	B;P	0.46142	0.015;0.873	B;B	0.42361	0.018;0.385	T	0.38373	-0.9664	9	0.52906	T	0.07	0.0185	6.4031	0.21650	0.2546:0.0:0.7454:0.0	rs4904448;rs17808075;rs56439463;rs59975682;rs4904448	2;2	Q9P0W8-2;Q9P0W8	.;SPAT7_HUMAN	N	2	ENSP00000451128:D2N;ENSP00000377176:D2N;ENSP00000348991:D2N;ENSP00000452435:D2N;ENSP00000450606:D2N;ENSP00000045347:D2N	ENSP00000045347:D2N	D	+	1	0	SPATA7	87921919	0.988000	0.35896	0.989000	0.46669	0.974000	0.67602	0.243000	0.18106	0.436000	0.26393	0.655000	0.94253	GAT	G|0.775;A|0.225	0.225	strong		0.701	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1		
CDPF1	150383	hgsc.bcm.edu	37	22	46644168	46644168	+	Missense_Mutation	SNP	A	A	G	rs9627281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46644168A>G	ENST00000314567.3	-	2	437	c.14T>C	c.(13-15)gTa>gCa	p.V5A	CDPF1_ENST00000404744.1_Missense_Mutation_p.V5A|CDPF1_ENST00000404583.1_Missense_Mutation_p.V5A|CDPF1_ENST00000475605.1_Intron	NM_207327.4	NP_997210.3	Q6NVV7	CDPF1_HUMAN	cysteine-rich, DPF motif domain containing 1	5			V -> A (in dbSNP:rs9627281).														ACGGCACTCTACATGGGACGC	0.547													G|||	1398	0.279153	0.7602	0.1686	5008	,	,		19465	0.001		0.1938	False		,,,				2504	0.0818				p.V5A		Atlas-SNP	.											.	.	.	.	0			c.T14C						PASS	.	G	ALA/VAL	3035,1371	450.4+/-349.3	1051,933,219	73.0	56.0	62.0		14	0.4	0.0	22	dbSNP_119	62	1571,7029	742.3+/-407.2	135,1301,2864	yes	missense	C22orf40	NM_207327.4	64	1186,2234,3083	GG,GA,AA		18.2674,31.1167,35.4144	benign	5/124	46644168	4606,8400	2203	4300	6503	SO:0001583	missense	150383	exon2			CACTCTACATGGG		CCDS33670.1	22q13.31	2012-07-18	2012-07-18	2012-07-18	ENSG00000205643	ENSG00000205643			33710	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 40"""	C22orf40			Standard	NM_207327		Approved	LOC150383	uc003bhe.3	Q6NVV7	OTTHUMG00000030672	ENST00000314567.3:c.14T>C	22.37:g.46644168A>G	ENSP00000325301:p.Val5Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_207327	A6NCA1|A9IU12|A9IU16|Q3ZCR8	Missense_Mutation	SNP	ENST00000314567.3	37	CCDS33670.1	566	0.2591575091575092	358	0.7276422764227642	69	0.19060773480662985	0	0.0	139	0.18337730870712401	G	0.220	-1.029070	0.02045	0.688833	0.182674	ENSG00000205643	ENST00000404583;ENST00000314567;ENST00000404744	T;T;T	0.28895	1.69;1.72;1.59	5.02	0.371	0.16168	.	1.182090	0.06046	N	0.655683	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	0.43861	-0.9365	9	0.02654	T	1	.	1.6123	0.02696	0.1825:0.3076:0.3521:0.1578	rs9627281	5;5;5	Q6NVV7;F6RAJ7;F6UL18	CV040_HUMAN;.;.	A	5	ENSP00000384451:V5A;ENSP00000325301:V5A;ENSP00000385460:V5A	ENSP00000325301:V5A	V	-	2	0	C22orf40	45022832	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.533000	0.23082	0.288000	0.22398	-0.119000	0.15052	GTA	A|0.682;G|0.318	0.318	strong		0.547	CDPF1-001	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075560.4	NM_207327	
KRTAP15-1	254950	hgsc.bcm.edu	37	21	31812772	31812772	+	Missense_Mutation	SNP	C	C	A	rs2832873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:31812772C>A	ENST00000334067.3	+	1	176	c.127C>A	c.(127-129)Ctg>Atg	p.L43M		NM_181623.1	NP_853654.1	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	43			L -> M (in dbSNP:rs2832873). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			intermediate filament (GO:0005882)				kidney(1)|large_intestine(3)|lung(6)|skin(1)	11						TACCTGCCAACTGGGCTCCTC	0.488													C|||	2775	0.554113	0.6543	0.6427	5008	,	,		19927	0.2788		0.5736	False		,,,				2504	0.6196				p.L43M		Atlas-SNP	.											KRTAP15-1,rectum,carcinoma,-2,1	KRTAP15-1	35	1	0			c.C127A						PASS	.	C	MET/LEU	2839,1567	669.0+/-402.1	900,1039,264	85.0	85.0	85.0		127	0.8	1.0	21	dbSNP_100	85	5043,3557	630.1+/-398.3	1483,2077,740	yes	missense	KRTAP15-1	NM_181623.1	15	2383,3116,1004	AA,AC,CC		41.3605,35.5651,39.3972	possibly-damaging	43/138	31812772	7882,5124	2203	4300	6503	SO:0001583	missense	254950	exon1			TGCCAACTGGGCT	AP001708	CCDS13593.1	21q22.1	2008-05-21			ENSG00000186970	ENSG00000186970		"""Keratin associated proteins"""	18927	protein-coding gene	gene with protein product						12359730	Standard	NM_181623		Approved	KAP15.1	uc002yod.3	Q3LI76	OTTHUMG00000057784	ENST00000334067.3:c.127C>A	21.37:g.31812772C>A	ENSP00000334866:p.Leu43Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_181623	Q2M3F4	Missense_Mutation	SNP	ENST00000334067.3	37	CCDS13593.1	1153	0.5279304029304029	329	0.6686991869918699	234	0.6464088397790055	170	0.2972027972027972	420	0.554089709762533	C	12.58	1.980915	0.34942	0.644349	0.586395	ENSG00000186970	ENST00000334067	T	0.03635	3.86	4.79	0.826	0.18829	.	1.886810	0.02903	N	0.135621	T	0.00012	0.0000	M	0.76170	2.325	0.54753	P	1.399999999995849E-5	P	0.52842	0.956	P	0.49799	0.622	T	0.43925	-0.9361	9	0.59425	D	0.04	0.1574	3.5753	0.07932	0.1394:0.3289:0.4302:0.1015	rs2832873;rs17596869;rs52830193;rs57673787;rs2832873	43	Q3LI76	KR151_HUMAN	M	43	ENSP00000334866:L43M	ENSP00000334866:L43M	L	+	1	2	KRTAP15-1	30734643	0.917000	0.31117	0.961000	0.40146	0.252000	0.25951	0.037000	0.13840	0.140000	0.18849	0.655000	0.94253	CTG	C|0.432;A|0.568	0.568	strong		0.488	KRTAP15-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128236.1		
CPNE1	8904	hgsc.bcm.edu	37	20	34219496	34219496	+	Missense_Mutation	SNP	T	T	C	rs6579255	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34219496T>C	ENST00000317619.3	-	10	1026	c.632A>G	c.(631-633)cAa>cGa	p.Q211R	CPNE1_ENST00000397445.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000397442.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000397443.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000352393.4_Missense_Mutation_p.Q211R|CPNE1_ENST00000317677.5_Missense_Mutation_p.Q216R|CPNE1_ENST00000397446.1_Missense_Mutation_p.Q211R			Q99829	CPNE1_HUMAN	copine I	211	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.		Q -> R (in dbSNP:rs6579255).		lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			ATCGGAGCATTGCACCTGAGG	0.562													C|||	1362	0.271965	0.4244	0.1844	5008	,	,		20547	0.1359		0.1899	False		,,,				2504	0.3528				p.Q216R		Atlas-SNP	.											.	CPNE1	44	.	0			c.A647G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1738,2668	647.5+/-398.6	333,1072,798	68.0	50.0	56.0		632,647,632,632,632,632	4.5	1.0	20	dbSNP_116	56	1639,6961	741.0+/-407.1	172,1295,2833	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	43,43,43,43,43,43	505,2367,3631	CC,CT,TT		19.0581,39.4462,25.9649	benign,benign,benign,benign,benign,benign	211/537,216/543,211/538,211/538,211/538,211/538	34219496	3377,9629	2203	4300	6503	SO:0001583	missense	8904	exon8			GAGCATTGCACCT	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.632A>G	20.37:g.34219496T>C	ENSP00000326126:p.Gln211Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	482	0.2206959706959707	195	0.39634146341463417	78	0.2154696132596685	63	0.11013986013986014	146	0.19261213720316622	C	11.35	1.612918	0.28712	0.394462	0.190581	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570;ENST00000412056;ENST00000414664;ENST00000416778;ENST00000439806	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.43	4.46	0.54185	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.839098	0.10589	N	0.657022	T	0.00012	0.0000	N	0.16307	0.4	0.50632	P	1.1200000000000099E-4	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;0.002;0.001;0.001;0.001	T	0.37820	-0.9689	9	0.15952	T	0.53	-17.6282	6.5162	0.22248	0.0:0.6028:0.0:0.3972	rs6579255;rs11543241;rs52798653;rs57435970;rs6579255	216;211;211;211;191	B0QZ18;E7ENH5;A6PVH9;Q99829;Q59EI4	.;.;.;CPNE1_HUMAN;.	R	211;216;211;211;211;211;211;211;187;187;211;187;211	ENSP00000336945:Q211R;ENSP00000317257:Q216R;ENSP00000326126:Q211R;ENSP00000380588:Q211R;ENSP00000380587:Q211R;ENSP00000380585:Q211R;ENSP00000380584:Q211R;ENSP00000415597:Q211R;ENSP00000390626:Q187R;ENSP00000416962:Q187R;ENSP00000404355:Q211R;ENSP00000389662:Q187R;ENSP00000387434:Q211R	ENSP00000326126:Q211R	Q	-	2	0	CPNE1	33682910	0.761000	0.28439	1.000000	0.80357	0.952000	0.60782	1.628000	0.37060	0.812000	0.34326	-0.119000	0.15052	CAA	T|0.753;C|0.247	0.247	strong		0.562	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
APOL3	80833	hgsc.bcm.edu	37	22	36537500	36537500	+	Silent	SNP	A	A	T	rs132618	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36537500A>T	ENST00000349314.2	-	3	994	c.957T>A	c.(955-957)ggT>ggA	p.G319G	APOL3_ENST00000424878.2_Silent_p.G119G|APOL3_ENST00000361710.2_Silent_p.G119G|APOL3_ENST00000397287.2_Silent_p.G119G|APOL3_ENST00000397293.2_Silent_p.G248G|APOL3_ENST00000487423.1_5'Flank	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	319					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)	p.G248G(1)		endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						CTGCTTGACCACCACTTCCAG	0.592													A|||	1816	0.36262	0.0651	0.3847	5008	,	,		19846	0.3502		0.496	False		,,,				2504	0.6247				p.G319G		Atlas-SNP	.											APOL3,NS,carcinoma,0,1	APOL3	60	1	1	Substitution - coding silent(1)	stomach(1)	c.T957A						PASS	.	A	,,	573,3833	255.5+/-260.7	40,493,1670	56.0	52.0	53.0		957,357,357	-3.5	0.0	22	dbSNP_78	53	4175,4425	567.5+/-388.9	1014,2147,1139	no	coding-synonymous,coding-synonymous,coding-synonymous	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	,,	1054,2640,2809	TT,TA,AA		48.5465,13.005,36.5062	,,	319/403,119/203,119/203	36537500	4748,8258	2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			TTGACCACCACTT	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.957T>A	22.37:g.36537500A>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	37	CCDS13922.1																																																																																			A|0.630;T|0.370	0.370	strong		0.592	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:152226570A>G	ENST00000243347.3	+	4	506	c.431A>G	c.(430-432)cAa>cGa	p.Q144R	RN7SL124P_ENST00000498656.2_RNA|MIR4773-1_ENST00000585225.1_RNA	NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	144	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.		Q -> R (in dbSNP:rs1046668). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1730767}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	GATCCAAAGCAAATTTTTAAA	0.383													G|||	887	0.177117	0.3033	0.1138	5008	,	,		17071	0.1329		0.1382	False		,,,				2504	0.137				p.Q144R		Atlas-SNP	.											.	TNFAIP6	98	.	0			c.A431G						PASS	.	G	ARG/GLN	1301,3105	695.6+/-406.0	199,903,1101	112.0	113.0	113.0		431	3.5	1.0	2	dbSNP_86	113	1188,7412	763.4+/-407.6	77,1034,3189	yes	missense	TNFAIP6	NM_007115.3	43	276,1937,4290	GG,GA,AA		13.814,29.5279,19.1373	benign	144/278	152226570	2489,10517	2203	4300	6503	SO:0001583	missense	7130	exon4			CAAAGCAAATTTT		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.431A>G	2.37:g.152226570A>G	ENSP00000243347:p.Gln144Arg	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	33	21	0.636364	NM_007115	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	389	0.17811355311355312	144	0.2926829268292683	39	0.10773480662983426	96	0.16783216783216784	110	0.14511873350923482	G	0.071	-1.201428	0.01581	0.295279	0.13814	ENSG00000123610	ENST00000243347	T	0.28255	1.62	5.27	3.46	0.39613	CUB (5);	0.247185	0.38436	N	0.001692	T	0.00012	0.0000	N	0.05383	-0.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41342	-0.9514	9	0.42905	T	0.14	.	5.9954	0.19491	0.2722:0.1359:0.592:0.0	rs1046668;rs3186656;rs17411793;rs56445941;rs61444688;rs1046668	144	P98066	TSG6_HUMAN	R	144	ENSP00000243347:Q144R	ENSP00000243347:Q144R	Q	+	2	0	TNFAIP6	151934816	0.990000	0.36364	0.963000	0.40424	0.230000	0.25150	1.071000	0.30666	0.225000	0.20959	-0.227000	0.12334	CAA	A|0.810;G|0.190	0.190	strong		0.383	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115	
PKD1L2	114780	hgsc.bcm.edu	37	16	81209325	81209325	+	RNA	SNP	G	G	A	rs145948343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81209325G>A	ENST00000527937.1	-	0	349				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA			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						TGATGGGAGGGCAGGTTCAGG	0.547													G|||	2	0.000399361	0.0	0.0	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0				p.A823V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2468T						PASS	.	G	VAL/ALA,VAL/ALA	1,4073		0,1,2036	85.0	87.0	86.0		2468,2468	-0.1	0.9	16	dbSNP_134	86	4,8360		0,4,4178	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	64,64	0,5,6214	AA,AG,GG		0.0478,0.0245,0.0402	benign,benign	823/992,823/2460	81209325	5,12433	2037	4182	6219			114780	exon15			GGGAGGGCAGGTT	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.81209325G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	10.51	1.369906	0.24771	2.45E-4	4.78E-4	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.70631	-0.5;-0.5;2.14	4.82	-0.11	0.13580	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.500926	0.19769	N	0.106485	T	0.44307	0.1287	.	.	.	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.08973	-1.0696	9	0.18710	T	0.47	-8.2539	2.0758	0.03623	0.225:0.1363:0.4838:0.1549	.	79;823;823	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	V	138;823;79	ENSP00000436309:A138V;ENSP00000337397:A823V;ENSP00000432818:A79V	ENSP00000337397:A823V	A	-	2	0	PKD1L2	79766826	0.386000	0.25180	0.907000	0.35723	0.962000	0.63368	-0.022000	0.12480	0.331000	0.23511	-0.611000	0.04053	GCC	G|0.999;A|0.001	0.001	strong		0.547	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
TMEM244	253582	hgsc.bcm.edu	37	6	130152520	130152520	+	Missense_Mutation	SNP	A	A	C	rs7776426	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:130152520A>C	ENST00000368143.1	-	5	413	c.331T>G	c.(331-333)Ttc>Gtc	p.F111V	TMEM244_ENST00000438392.1_Missense_Mutation_p.F111V	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	111			F -> V (in dbSNP:rs7776426).			integral component of membrane (GO:0016021)											GTCAAGGGGAATTCCAACATA	0.308													A|||	1215	0.242612	0.1823	0.245	5008	,	,		17149	0.1359		0.4583	False		,,,				2504	0.2106				p.F111V		Atlas-SNP	.											.	.	.	.	0			c.T331G						PASS	.	A	VAL/PHE	1105,3299	393.1+/-328.7	146,813,1243	65.0	63.0	64.0		331	3.3	0.9	6	dbSNP_116	64	4096,4504	559.5+/-387.4	1003,2090,1207	yes	missense	C6orf191	NM_001010876.1	50	1149,2903,2450	CC,CA,AA		47.6279,25.0908,39.9954	benign	111/129	130152520	5201,7803	2202	4300	6502	SO:0001583	missense	253582	exon5			AGGGGAATTCCAA		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.331T>G	6.37:g.130152520A>C	ENSP00000357125:p.Phe111Val	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	159	70	0.440252	NM_001010876		Missense_Mutation	SNP	ENST00000368143.1	37	CCDS34536.1	605	0.27701465201465203	92	0.18699186991869918	98	0.27071823204419887	73	0.12762237762237763	342	0.45118733509234826	A	16.85	3.235466	0.58886	0.250908	0.476279	ENSG00000203756	ENST00000368143;ENST00000438392	T;T	0.34667	1.35;1.35	4.5	3.31	0.37934	.	0.067056	0.64402	U	0.000012	T	0.24275	0.0588	L	0.55481	1.735	0.32129	P	0.587021	P	0.46912	0.886	P	0.47573	0.55	T	0.07083	-1.0791	9	0.54805	T	0.06	-16.8847	9.7114	0.40247	0.8444:0.0:0.0:0.1556	rs7776426;rs17395737;rs52808693;rs58635664;rs7776426	111	Q5VVB8	CF191_HUMAN	V	111	ENSP00000357125:F111V;ENSP00000403755:F111V	ENSP00000357125:F111V	F	-	1	0	C6orf191	130194213	1.000000	0.71417	0.935000	0.37517	0.865000	0.49528	2.021000	0.41020	0.664000	0.31047	0.455000	0.32223	TTC	A|0.663;C|0.337	0.337	strong		0.308	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
PTGER4	5734	hgsc.bcm.edu	37	5	40681254	40681254	+	Silent	SNP	C	C	T	rs2228058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:40681254C>T	ENST00000302472.3	+	2	1183	c.159C>T	c.(157-159)acC>acT	p.T53T	PTGER4_ENST00000514343.1_3'UTR	NM_000958.2	NP_000949.1	P35408	PE2R4_HUMAN	prostaglandin E receptor 4 (subtype EP4)	53					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|bone development (GO:0060348)|cellular response to mechanical stimulus (GO:0071260)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|JNK cascade (GO:0007254)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of eosinophil extravasation (GO:2000420)|negative regulation of inflammatory response (GO:0050728)|negative regulation of integrin activation (GO:0033624)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|regulation of ossification (GO:0030278)|regulation of stress fiber assembly (GO:0051492)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|T-helper cell differentiation (GO:0042093)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(3)|liver(1)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23					Dinoprostone(DB00917)|Misoprostol(DB00929)	AGGAGACGACCTTCTACACGC	0.612											OREG0016588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	292	0.0583067	0.112	0.0562	5008	,	,		19308	0.0		0.0696	False		,,,				2504	0.0358				p.T53T		Atlas-SNP	.											.	PTGER4	49	.	0			c.C159T						PASS	.	C		459,3947	217.1+/-235.6	27,405,1771	75.0	64.0	68.0		159	2.6	1.0	5	dbSNP_98	68	638,7962	162.7+/-215.4	20,598,3682	no	coding-synonymous	PTGER4	NM_000958.2		47,1003,5453	TT,TC,CC		7.4186,10.4176,8.4346		53/489	40681254	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	5734	exon2			GACGACCTTCTAC	L28175	CCDS3930.1	5p13.1	2012-08-08			ENSG00000171522	ENSG00000171522		"""GPCR / Class A : Prostanoid receptors"""	9596	protein-coding gene	gene with protein product		601586				7759114, 8661119	Standard	NM_000958		Approved	EP4	uc003jlz.3	P35408	OTTHUMG00000094769	ENST00000302472.3:c.159C>T	5.37:g.40681254C>T		Somatic	103	0	0	895	WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_000958	Q3MJ87	Silent	SNP	ENST00000302472.3	37	CCDS3930.1																																																																																			C|0.924;T|0.076	0.076	strong		0.612	PTGER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211578.2	NM_000958	
CRYGD	1421	hgsc.bcm.edu	37	2	208989037	208989037	+	Silent	SNP	A	A	G	rs2242074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:208989037A>G	ENST00000264376.4	-	2	78	c.51T>C	c.(49-51)taT>taC	p.Y17Y		NM_006891.3	NP_008822.2	P07320	CRGD_HUMAN	crystallin, gamma D	17	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				cellular response to reactive oxygen species (GO:0034614)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		TGCTGCATTCATAGTGGCGGC	0.647													G|||	3229	0.644768	0.739	0.5014	5008	,	,		15187	0.6319		0.5338	False		,,,				2504	0.7464				p.Y17Y		Atlas-SNP	.											.	CRYGD	18	.	0			c.T51C						PASS	.	G		2955,1319		1105,745,287	11.0	12.0	12.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	51	-3.7	0.4	2	dbSNP_98	12	4354,4096		1216,1922,1087	no	coding-synonymous	CRYGD	NM_006891.3		2321,2667,1374	GG,GA,AA		48.4734,30.861,42.5574		17/175	208989037	7309,5415	2137	4225	6362	SO:0001819	synonymous_variant	1421	exon2			GCATTCATAGTGG		CCDS2378.1	2q33.3	2013-02-14			ENSG00000118231	ENSG00000118231			2411	protein-coding gene	gene with protein product		123690		CRYG4			Standard	NM_006891		Approved		uc002vcn.4	P07320	OTTHUMG00000132944	ENST00000264376.4:c.51T>C	2.37:g.208989037A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	44	0.382609	NM_006891	Q17RF7|Q53R51|Q99681	Silent	SNP	ENST00000264376.4	37	CCDS2378.1																																																																																			A|0.398;G|0.602	0.602	strong		0.647	CRYGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256476.2	NM_006891	
HTR6	3362	hgsc.bcm.edu	37	1	19992513	19992513	+	Silent	SNP	C	C	T	rs1805054	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67	0	0		WXS	Illumina HiSeq	Phase_I	108	68	0.62963	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	
KALRN	8997	hgsc.bcm.edu	37	3	124048764	124048764	+	Silent	SNP	C	C	T	rs2276740	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124048764C>T	ENST00000240874.3	+	8	1492	c.1335C>T	c.(1333-1335)tcC>tcT	p.S445S	KALRN_ENST00000360013.3_Silent_p.S445S|KALRN_ENST00000460856.1_Silent_p.S445S	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	445					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GTCTGCCATCCGAGATGCAAG	0.577													C|||	605	0.120807	0.1611	0.0951	5008	,	,		17215	0.1488		0.0825	False		,,,				2504	0.0951				p.S445S		Atlas-SNP	.											.	KALRN	556	.	0			c.C1335T						PASS	.	C	,	639,3767	276.6+/-273.2	48,543,1612	137.0	111.0	120.0		1335,1335	-7.5	0.2	3	dbSNP_100	120	691,7909	172.5+/-223.2	38,615,3647	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	86,1158,5259	TT,TC,CC		8.0349,14.503,10.226	,	445/2987,445/1664	124048764	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon8			GCCATCCGAGATG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1335C>T	3.37:g.124048764C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	259	0.11858974358974358	75	0.1524390243902439	39	0.10773480662983426	88	0.15384615384615385	57	0.07519788918205805	C	5.149	0.213145	0.09757	0.14503	0.080349	ENSG00000160145	ENST00000354186	.	.	.	5.0	-7.46	0.01369	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.09310	P	0.9999999999999927	.	.	.	.	.	.	T	0.27400	-1.0075	3	.	.	.	.	15.2128	0.73238	0.0998:0.101:0.0:0.7992	rs2276740;rs2276740	.	.	.	L	423	.	.	P	+	2	0	KALRN	125531454	0.000000	0.05858	0.212000	0.23672	0.672000	0.39443	-5.326000	0.00131	-1.551000	0.01706	-0.751000	0.03497	CCG	C|0.888;T|0.112	0.112	strong		0.577	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
PLXNC1	10154	hgsc.bcm.edu	37	12	94543506	94543506	+	Silent	SNP	C	C	T	rs2230754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:94543506C>T	ENST00000258526.4	+	1	1008	c.759C>T	c.(757-759)taC>taT	p.Y253Y		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	253	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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						CCTACAACTACACGAGCGGCG	0.682													C|||	2261	0.451478	0.5204	0.4654	5008	,	,		15562	0.4831		0.34	False		,,,				2504	0.4305				p.Y253Y		Atlas-SNP	.											PLXNC1,rectum,carcinoma,0,1	PLXNC1	135	1	0			c.C759T						PASS	.	C		1851,2441		433,985,728	31.0	36.0	34.0		759	4.1	1.0	12	dbSNP_98	34	3103,5439		592,1919,1760	no	coding-synonymous	PLXNC1	NM_005761.2		1025,2904,2488	TT,TC,CC		36.3264,43.1267,38.6006		253/1569	94543506	4954,7880	2146	4271	6417	SO:0001819	synonymous_variant	10154	exon1			CAACTACACGAGC	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.759C>T	12.37:g.94543506C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.560;T|0.440	0.440	strong		0.682	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
MYO10	4651	hgsc.bcm.edu	37	5	16701796	16701796	+	Missense_Mutation	SNP	A	A	G	rs112696559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16701796A>G	ENST00000513610.1	-	25	3162	c.2708T>C	c.(2707-2709)aTg>aCg	p.M903T	MYO10_ENST00000427430.2_Missense_Mutation_p.M260T|MYO10_ENST00000274203.9_Missense_Mutation_p.M260T|MYO10_ENST00000505695.1_Missense_Mutation_p.M242T|MYO10_ENST00000515803.1_Missense_Mutation_p.M242T|MYO10_ENST00000512061.1_5'Flank	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	903	Mediates antiparallel dimerization.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTGCTCCTTCATGCGCTGCAG	0.587													A|||	28	0.00559105	0.0	0.0029	5008	,	,		18003	0.0		0.0129	False		,,,				2504	0.0133				p.M903T		Atlas-SNP	.											.	MYO10	198	.	0			c.T2708C						PASS	.	A	THR/MET	6,4234		0,6,2114	40.0	44.0	43.0		2708	3.8	1.0	5	dbSNP_132	43	79,8425		2,75,4175	yes	missense	MYO10	NM_012334.2	81	2,81,6289	GG,GA,AA		0.929,0.1415,0.667	benign	903/2059	16701796	85,12659	2120	4252	6372	SO:0001583	missense	4651	exon25			TCCTTCATGCGCT	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2708T>C	5.37:g.16701796A>G	ENSP00000421280:p.Met903Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	A	9.654	1.142336	0.21205	0.001415	0.00929	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.03982	3.74;3.74;3.74;3.74;3.74	5.0	3.82	0.43975	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.29659	N	0.843378	B;B	0.17667	0.01;0.023	B;B	0.11329	0.004;0.006	T	0.40289	-0.9571	9	0.19147	T	0.46	.	7.2935	0.26380	0.7044:0.1512:0.0:0.1444	.	544;903	Q69YP8;Q9HD67	.;MYO10_HUMAN	T	903;242;260;242;260	ENSP00000421280:M903T;ENSP00000425051:M242T;ENSP00000274203:M260T;ENSP00000421170:M242T;ENSP00000391106:M260T	ENSP00000274203:M260T	M	-	2	0	MYO10	16754796	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.753000	0.55180	0.733000	0.32492	-0.460000	0.05396	ATG	A|0.994;G|0.006;T|0.000	0.006	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
OR2A25	392138	hgsc.bcm.edu	37	7	143771536	143771536	+	Missense_Mutation	SNP	G	G	A	rs6951485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	114	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	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		
C15orf53	400359	hgsc.bcm.edu	37	15	38988815	38988815	+	Missense_Mutation	SNP	C	C	G	rs7165988	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	80	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	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	
FAM71E2	284418	hgsc.bcm.edu	37	19	55872591	55872591	+	Missense_Mutation	SNP	C	C	T	rs2124920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55872591C>T	ENST00000424985.3	-	5	798	c.605G>A	c.(604-606)cGc>cAc	p.R202H	CTD-2105E13.6_ENST00000591954.3_5'Flank	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	202										NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						CGGAAAGTTGCGCTCAGCAAC	0.652													T|||	648	0.129393	0.2973	0.1182	5008	,	,		15731	0.0357		0.0934	False		,,,				2504	0.044				p.R202H		Atlas-SNP	.											.	FAM71E2	41	.	0			c.G605A						PASS	.	T	HIS/ARG	395,989		53,289,350	34.0	37.0	36.0		605	0.0	0.0	19	dbSNP_96	36	273,2909		15,243,1333	yes	missense	FAM71E2	NM_001145402.1	29	68,532,1683	TT,TC,CC		8.5795,28.5405,14.6299	benign	202/923	55872591	668,3898	692	1591	2283	SO:0001583	missense	284418	exon5			AAGTTGCGCTCAG	AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.605G>A	19.37:g.55872591C>T	ENSP00000398617:p.Arg202His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001145402	Q8ND99	Missense_Mutation	SNP	ENST00000424985.3	37		285	0.1304945054945055	145	0.29471544715447157	46	0.1270718232044199	20	0.03496503496503497	74	0.09762532981530343	t	4.277	0.050486	0.08243	0.285405	0.085795	ENSG00000180043	ENST00000424985	T	0.12774	2.65	2.4	0.0349	0.14185	.	.	.	.	.	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	0.47420	-0.9119	8	0.37606	T	0.19	.	4.9702	0.14111	0.0:0.2005:0.3708:0.4288	rs2124920;rs60805576;rs2124920	202	Q8N5Q1	F71E2_HUMAN	H	202	ENSP00000398617:R202H	ENSP00000398617:R202H	R	-	2	0	FAM71E2	60564403	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.699000	0.05087	-0.170000	0.10816	-1.766000	0.00665	CGC	C|0.859;T|0.141	0.141	strong		0.652	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
AKR1C4	1109	hgsc.bcm.edu	37	10	5242164	5242164	+	Silent	SNP	A	A	G	rs17306779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	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	
KDM6B	23135	hgsc.bcm.edu	37	17	7749972	7749972	+	Missense_Mutation	SNP	G	G	T	rs148641957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7749972G>T	ENST00000448097.2	+	8	956	c.625G>T	c.(625-627)Gtg>Ttg	p.V209L	KDM6B_ENST00000254846.5_Missense_Mutation_p.V209L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	209	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						GGTGCAGCCTGTGCCTCCTGC	0.607													G|||	10	0.00199681	0.0	0.0058	5008	,	,		9853	0.0		0.006	False		,,,				2504	0.0				p.V209L		Atlas-SNP	.											.	KDM6B	95	.	0			c.G625T						PASS	.	G	LEU/VAL	6,4400	11.4+/-27.6	0,6,2197	53.0	60.0	58.0		625	1.4	1.0	17	dbSNP_134	58	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KDM6B	NM_001080424.1	32	0,40,6463	TT,TG,GG		0.3953,0.1362,0.3076	benign	209/1683	7749972	40,12966	2203	4300	6503	SO:0001583	missense	23135	exon8			CAGCCTGTGCCTC	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.625G>T	17.37:g.7749972G>T	ENSP00000412513:p.Val209Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	10.41	1.342148	0.24339	0.001362	0.003953	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.06933	3.24;3.24	5.14	1.42	0.22433	.	0.725657	0.12197	N	0.490623	T	0.02380	0.0073	N	0.08118	0	0.23440	N	0.997671	B	0.06786	0.001	B	0.06405	0.002	T	0.47275	-0.9130	10	0.19147	T	0.46	-1.9231	4.5059	0.11887	0.3322:0.1581:0.5097:0.0	.	209	O15054-1	.	L	209	ENSP00000254846:V209L;ENSP00000412513:V209L	ENSP00000254846:V209L	V	+	1	0	KDM6B	7690697	0.994000	0.37717	0.996000	0.52242	0.991000	0.79684	0.849000	0.27723	0.108000	0.17862	0.561000	0.74099	GTG	G|0.997;T|0.003	0.003	strong		0.607	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
CCDC116	164592	hgsc.bcm.edu	37	22	21991072	21991072	+	Missense_Mutation	SNP	T	T	C	rs861852	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21991072T>C	ENST00000292779.3	+	5	1716	c.1555T>C	c.(1555-1557)Tgc>Cgc	p.C519R		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	0										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CACCTCCCACTGCAGCACAGA	0.662													C|||	1490	0.297524	0.5688	0.1643	5008	,	,		15536	0.122		0.2485	False		,,,				2504	0.2566				p.C519R		Atlas-SNP	.											.	CCDC116	56	.	0			c.T1555C						PASS	.	C	ARG/CYS	2284,2122	564.4+/-381.4	589,1106,508	45.0	53.0	51.0		1555	-0.6	0.0	22	dbSNP_86	51	1947,6653	706.5+/-405.5	224,1499,2577	yes	missense	CCDC116	NM_152612.2	180	813,2605,3085	CC,CT,TT		22.6395,48.1616,32.5311	benign	519/614	21991072	4231,8775	2203	4300	6503	SO:0001583	missense	164592	exon5			TCCCACTGCAGCA	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.1555T>C	22.37:g.21991072T>C	ENSP00000292779:p.Cys519Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	618	0.28296703296703296	283	0.5752032520325203	64	0.17679558011049723	71	0.12412587412587413	200	0.2638522427440633	C	0.926	-0.714148	0.03206	0.518384	0.226395	ENSG00000161180	ENST00000292779	T	0.10668	2.85	3.13	-0.564	0.11774	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	7	0.27785	T	0.31	.	4.7009	0.12827	0.5302:0.3543:0.0:0.1155	rs861852;rs1647701	519	Q8IYX3-2	.	R	519	ENSP00000292779:C519R	ENSP00000292779:C519R	C	+	1	0	CCDC116	20321072	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.074000	0.14662	-0.265000	0.09352	-0.320000	0.08662	TGC	T|0.681;C|0.319	0.319	strong		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
FBXO36	130888	hgsc.bcm.edu	37	2	230861519	230861519	+	Missense_Mutation	SNP	G	G	T	rs1035834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:230861519G>T	ENST00000283946.3	+	3	276	c.258G>T	c.(256-258)ttG>ttT	p.L86F	FBXO36_ENST00000373652.3_Missense_Mutation_p.L55F|FBXO36_ENST00000409992.1_Intron	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	196	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	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	
FLG	2312	hgsc.bcm.edu	37	1	152276889	152276889	+	Silent	SNP	A	A	G	rs3126067	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276889A>G	ENST00000368799.1	-	3	10508	c.10473T>C	c.(10471-10473)aaT>aaC	p.N3491N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3491	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)			ATTGTTCGTCATTACGAGTTT	0.577									Ichthyosis				a|||	2617	0.522564	0.7912	0.4553	5008	,	,		19155	0.6498		0.1511	False		,,,				2504	0.4581				p.N3491N		Atlas-SNP	.											.	FLG	900	.	0			c.T10473C						PASS	.	G		3036,1370	690.8+/-405.3	1065,906,232	295.0	287.0	289.0		10473	0.8	0.0	1	dbSNP_103	289	1298,7296	256.5+/-280.9	126,1046,3125	no	coding-synonymous	FLG	NM_002016.1		1191,1952,3357	GG,GA,AA		15.1036,31.094,33.3385		3491/4062	152276889	4334,8666	2203	4297	6500	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTCGTCATTACGA	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.10473T>C	1.37:g.152276889A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	213	124	0.58216	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.637;G|0.363	0.363	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SLC5A1	6523	hgsc.bcm.edu	37	22	32487700	32487700	+	Missense_Mutation	SNP	G	G	A	rs17683430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32487700G>A	ENST00000266088.4	+	11	1481	c.1231G>A	c.(1231-1233)Gcc>Acc	p.A411T	SLC5A1_ENST00000543737.1_Missense_Mutation_p.A284T	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	411			A -> T (in dbSNP:rs17683430).		carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	GGACATCTACGCCAAGGTCCG	0.537													A|||	111	0.0221645	0.003	0.0259	5008	,	,		13181	0.0		0.0606	False		,,,				2504	0.0286				p.A411T		Atlas-SNP	.											.	SLC5A1	80	.	0			c.G1231A	GRCh37	CM961335	SLC5A1	M	rs17683430	PASS	.	A	THR/ALA	61,4345	820.8+/-416.4	0,61,2142	127.0	107.0	114.0		1231	5.9	1.0	22	dbSNP_123	114	602,7998	792.5+/-407.5	20,562,3718	yes	missense	SLC5A1	NM_000343.3	58	20,623,5860	AA,AG,GG		7.0,1.3845,5.0976	benign	411/665	32487700	663,12343	2203	4300	6503	SO:0001583	missense	6523	exon11			ATCTACGCCAAGG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.1231G>A	22.37:g.32487700G>A	ENSP00000266088:p.Ala411Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	37	CCDS13902.1	68	0.031135531135531136	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	55	0.07255936675461741	A	8.026	0.760781	0.15914	0.013845	0.07	ENSG00000100170	ENST00000266088;ENST00000543737	D;D	0.87887	-2.31;-2.31	5.94	5.94	0.96194	.	0.044291	0.85682	N	0.000000	T	0.11410	0.0278	N	0.00630	-1.315	0.20196	N	0.999928	B	0.02656	0.0	B	0.04013	0.001	T	0.27905	-1.0060	10	0.06236	T	0.91	.	11.4898	0.50375	0.9303:0.0:0.0697:0.0	rs17683430;rs52804782;rs17683430	411	P13866	SC5A1_HUMAN	T	411;284	ENSP00000266088:A411T;ENSP00000444898:A284T	ENSP00000266088:A411T	A	+	1	0	SLC5A1	30817700	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	4.270000	0.58896	1.075000	0.40932	-0.269000	0.10298	GCC	G|0.955;A|0.045	0.045	strong		0.537	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
OR2A25	392138	hgsc.bcm.edu	37	7	143771937	143771937	+	Missense_Mutation	SNP	G	G	C	rs2961135	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	156	0	0		WXS	Illumina HiSeq	Phase_I	181	74	0.40884	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		
A4GNT	51146	hgsc.bcm.edu	37	3	137843476	137843476	+	Missense_Mutation	SNP	G	G	T	rs2246945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:137843476G>T	ENST00000236709.3	-	3	854	c.653C>A	c.(652-654)gCc>gAc	p.A218D		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	218			A -> D (in dbSNP:rs2246945). {ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						GCCCCAAATGGCTGAATTATA	0.478													T|||	3274	0.653754	0.6384	0.7233	5008	,	,		19232	0.6389		0.672	False		,,,				2504	0.6217				p.A218D		Atlas-SNP	.											.	A4GNT	42	.	0			c.C653A						PASS	.	T	ASP/ALA	2835,1571	481.4+/-359.1	915,1005,283	82.0	91.0	88.0		653	-1.8	0.0	3	dbSNP_100	88	5756,2844	444.8+/-360.8	1916,1924,460	yes	missense	A4GNT	NM_016161.2	126	2831,2929,743	TT,TG,GG		33.0698,35.6559,33.9459	benign	218/341	137843476	8591,4415	2203	4300	6503	SO:0001583	missense	51146	exon3			CAAATGGCTGAAT	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.653C>A	3.37:g.137843476G>T	ENSP00000236709:p.Ala218Asp	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_016161	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	ENST00000236709.3	37	CCDS3097.1	1468	0.6721611721611722	337	0.6849593495934959	251	0.6933701657458563	373	0.6520979020979021	507	0.6688654353562006	T	0.784	-0.761128	0.02996	0.643441	0.669302	ENSG00000118017	ENST00000236709	T	0.78707	-1.2	5.0	-1.83	0.07833	Alpha 1,4-glycosyltransferase domain (1);	1.049160	0.07444	N	0.897822	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40459	-0.9562	9	0.07482	T	0.82	-14.1816	10.3806	0.44110	0.0:0.114:0.6092:0.2767	rs2246945;rs2246945	218	Q9UNA3	A4GCT_HUMAN	D	218	ENSP00000236709:A218D	ENSP00000236709:A218D	A	-	2	0	A4GNT	139326166	0.000000	0.05858	0.010000	0.14722	0.802000	0.45316	-0.385000	0.07379	-1.055000	0.03209	-0.362000	0.07510	GCC	G|0.339;T|0.661	0.661	strong		0.478	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	
ANKK1	255239	hgsc.bcm.edu	37	11	113268059	113268059	+	Missense_Mutation	SNP	G	G	A	rs11604671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:113268059G>A	ENST00000303941.3	+	6	1046	c.952G>A	c.(952-954)Ggg>Agg	p.G318R		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	318			G -> R (in dbSNP:rs11604671). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GCGCCAGCCCGGGGAGGTGAG	0.607													C|||	1133	0.226238	0.0393	0.3026	5008	,	,		19688	0.0625		0.501	False		,,,				2504	0.3108				p.G318R		Atlas-SNP	.											.	ANKK1	83	.	0			c.G952A						PASS	.	C	ARG/GLY	514,3762		27,460,1651	39.0	46.0	44.0		952	0.5	0.0	11	dbSNP_120	44	4269,4221		1103,2063,1079	yes	missense	ANKK1	NM_178510.1	125	1130,2523,2730	AA,AG,GG		49.7173,12.0206,37.4667	benign	318/766	113268059	4783,7983	2138	4245	6383	SO:0001583	missense	255239	exon6			CAGCCCGGGGAGG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.952G>A	11.37:g.113268059G>A	ENSP00000306678:p.Gly318Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	562	0.2573260073260073	29	0.05894308943089431	129	0.356353591160221	33	0.057692307692307696	371	0.4894459102902375	C	12.15	1.851560	0.32699	0.120206	0.502827	ENSG00000170209	ENST00000303941	T	0.73897	-0.79	4.58	0.519	0.17035	.	2.280460	0.02431	N	0.083550	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	0.31447	-0.9943	9	0.14252	T	0.57	0.0976	2.5272	0.04694	0.1373:0.4149:0.2897:0.158	rs11604671;rs17600946;rs11604671	318	Q8NFD2	ANKK1_HUMAN	R	318	ENSP00000306678:G318R	ENSP00000306678:G318R	G	+	1	0	ANKK1	112773269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.959000	0.01518	-0.309000	0.08779	-0.920000	0.02741	GGG	G|0.718;A|0.282	0.282	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
TTLL13P	440307	hgsc.bcm.edu	37	15	90800408	90800408	+	Silent	SNP	C	C	G	rs2063742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90800408C>G	ENST00000561573.1	+	5	720	c.456C>G	c.(454-456)gtC>gtG	p.V152V	TTLL13_ENST00000438251.1_Silent_p.V248V|TTLL13_ENST00000339615.5_Silent_p.V248V																							ATATGCGAGTCTACGTCCTGA	0.502													C|||	1894	0.378195	0.112	0.4179	5008	,	,		19477	0.6925		0.2644	False		,,,				2504	0.5031				p.V248V		Atlas-SNP	.											.	TTLL13	44	.	0			c.C744G						PASS	.	C		661,3737	281.9+/-276.2	55,551,1593	110.0	97.0	101.0		744	4.0	1.0	15	dbSNP_94	101	2239,6357	378.9+/-339.1	275,1689,2334	no	coding-synonymous	TTLL13	NM_001029964.2		330,2240,3927	GG,GC,CC		26.047,15.0296,22.318		248/460	90800408	2900,10094	2199	4298	6497	SO:0001819	synonymous_variant	440307	exon7			GCGAGTCTACGTC																												ENST00000561573.1:c.456C>G	15.37:g.90800408C>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_001029964		Silent	SNP	ENST00000561573.1	37																																																																																				C|0.716;G|0.284	0.284	strong		0.502	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1		
SMARCA5	8467	hgsc.bcm.edu	37	4	144442611	144442611	+	Silent	SNP	T	T	C	rs11100790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:144442611T>C	ENST00000283131.3	+	3	744	c.282T>C	c.(280-282)taT>taC	p.Y94Y		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	94					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GATTCGAGTATTTATTAAAGC	0.353													T|||	1463	0.292133	0.2247	0.2594	5008	,	,		16713	0.6052		0.2078	False		,,,				2504	0.1708				p.Y94Y		Atlas-SNP	.											.	SMARCA5	73	.	0			c.T282C						PASS	.	T		963,3443	357.9+/-314.1	100,763,1340	54.0	59.0	58.0		282	5.6	1.0	4	dbSNP_120	58	1655,6945	304.8+/-307.1	163,1329,2808	no	coding-synonymous	SMARCA5	NM_003601.3		263,2092,4148	CC,CT,TT		19.2442,21.8566,20.1292		94/1053	144442611	2618,10388	2203	4300	6503	SO:0001819	synonymous_variant	8467	exon3			CGAGTATTTATTA	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.282T>C	4.37:g.144442611T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_003601		Silent	SNP	ENST00000283131.3	37	CCDS3761.1																																																																																			A|0.000;C|0.252;T|0.748	0.252	strong		0.353	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
OR10X1	128367	hgsc.bcm.edu	37	1	158549492	158549492	+	Nonsense_Mutation	SNP	C	C	T	rs863362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158549492C>T	ENST00000368150.1	-	1	197	c.198G>A	c.(196-198)tgG>tgA	p.W66*		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	66						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(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					ACCTGTCCACCCAAGTTAGAC	0.478													C|||	2516	0.502396	0.5741	0.4135	5008	,	,		20922	0.5853		0.4732	False		,,,				2504	0.4131				p.W66X		Atlas-SNP	.											.	OR10X1	96	.	0			c.G198A	GRCh37	CM035844	OR10X1	M	rs863362	PASS	.	C	stop/TRP	2499,1907	627.1+/-394.8	679,1141,383	126.0	121.0	123.0		198	4.2	1.0	1	dbSNP_86	123	3826,4774	538.8+/-383.5	876,2074,1350	yes	stop-gained	OR10X1	NM_001004477.1		1555,3215,1733	TT,TC,CC		44.4884,43.2819,48.6314		66/327	158549492	6325,6681	2203	4300	6503	SO:0001587	stop_gained	128367	exon1			GTCCACCCAAGTT	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.198G>A	1.37:g.158549492C>T	ENSP00000357132:p.Trp66*	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	142	45	0.316901	NM_001004477	Q6IFR8	Nonsense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	1168	0.5347985347985348	292	0.5934959349593496	151	0.4171270718232044	355	0.6206293706293706	370	0.48812664907651715	C	14.65	2.598003	0.46318	0.567181	0.444884	ENSG00000186400	ENST00000368150	.	.	.	5.13	4.18	0.49190	.	0.153354	0.31221	N	0.008035	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	13.0701	0.59057	0.0:0.8393:0.1607:0.0	rs863362;rs17633629;rs52794442;rs58574723;rs863362	.	.	.	X	66	.	ENSP00000357132:W66X	W	-	3	0	OR10X1	156816116	0.000000	0.05858	0.956000	0.39512	0.514000	0.34195	-0.039000	0.12124	2.648000	0.89879	0.650000	0.86243	TGG	C|0.488;N|0.000	.	strong		0.478	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
UGDH	7358	hgsc.bcm.edu	37	4	39510264	39510264	+	Silent	SNP	A	A	G	rs1129052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:39510264A>G	ENST00000316423.6	-	7	1170	c.828T>C	c.(826-828)tgT>tgC	p.C276C	UGDH_ENST00000507089.1_Silent_p.C179C|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000506179.1_Silent_p.C276C|UGDH_ENST00000501493.2_Silent_p.C209C	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	276					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						CCTTTTGGAAACAGCTCCCAC	0.353													G|||	1485	0.296526	0.5212	0.1657	5008	,	,		16561	0.4067		0.1044	False		,,,				2504	0.1697				p.C276C		Atlas-SNP	.											.	UGDH	52	.	0			c.T828C						PASS	.	G	,,	2031,2375	606.2+/-390.7	465,1101,637	68.0	72.0	71.0		627,537,828	2.5	1.0	4	dbSNP_86	71	850,7750	779.6+/-407.7	37,776,3487	no	coding-synonymous,coding-synonymous,coding-synonymous	UGDH	NM_001184700.1,NM_001184701.1,NM_003359.3	,,	502,1877,4124	GG,GA,AA		9.8837,46.0962,22.1513	,,	209/428,179/398,276/495	39510264	2881,10125	2203	4300	6503	SO:0001819	synonymous_variant	7358	exon7			TTGGAAACAGCTC	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.828T>C	4.37:g.39510264A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	37	CCDS3455.1																																																																																			A|0.746;G|0.254	0.254	strong		0.353	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
ART4	420	hgsc.bcm.edu	37	12	14982352	14982352	+	Missense_Mutation	SNP	G	G	C	rs3088190	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	86	0	0		WXS	Illumina HiSeq	Phase_I	113	46	0.40708	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	
C12orf43	64897	hgsc.bcm.edu	37	12	121454148	121454148	+	Missense_Mutation	SNP	C	C	T	rs11537857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121454148C>T	ENST00000288757.3	-	1	152	c.130G>A	c.(130-132)Ggg>Agg	p.G44R	C12orf43_ENST00000536407.2_Missense_Mutation_p.G44R|C12orf43_ENST00000366211.2_5'UTR|C12orf43_ENST00000537817.1_Missense_Mutation_p.G14R|C12orf43_ENST00000539736.1_Missense_Mutation_p.G44R|C12orf43_ENST00000445832.3_Missense_Mutation_p.G14R	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	44			G -> R (in dbSNP:rs16950706).							cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTTGGCTTCCCTGCCACGTGC	0.627													C|||	170	0.0339457	0.0045	0.049	5008	,	,		14707	0.005		0.0606	False		,,,				2504	0.0654				p.G44R		Atlas-SNP	.											.	C12orf43	30	.	0			c.G130A						PASS	.	C	ARG/GLY	52,4354	48.9+/-83.8	2,48,2153	33.0	35.0	34.0		130	2.2	0.0	12	dbSNP_123	34	474,8126	134.1+/-191.5	16,442,3842	yes	missense	C12orf43	NM_022895.1	125	18,490,5995	TT,TC,CC		5.5116,1.1802,4.0443	benign	44/263	121454148	526,12480	2203	4300	6503	SO:0001583	missense	64897	exon1			GCTTCCCTGCCAC	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.130G>A	12.37:g.121454148C>T	ENSP00000288757:p.Gly44Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	75|75	0.034340659340659344|0.034340659340659344	5|5	0.01016260162601626|0.01016260162601626	21|21	0.058011049723756904|0.058011049723756904	1|1	0.0017482517482517483|0.0017482517482517483	48|48	0.0633245382585752|0.0633245382585752	C|C	13.11|13.11	2.140389|2.140389	0.37825|0.37825	0.011802|0.011802	0.055116|0.055116	ENSG00000157895|ENSG00000157895	ENST00000445832;ENST00000288757;ENST00000537817;ENST00000539736;ENST00000538296|ENST00000536407	T;T;T;T;T|.	0.44083|.	0.96;0.99;0.93;0.99;0.94|.	5.06|5.06	2.16|2.16	0.27623|0.27623	.|.	1.154110|.	0.06168|.	N|.	0.677205|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.08118|0.08118	0|0	0.47123|0.47123	P|P	6.730000000000347E-4|6.730000000000347E-4	B;B;B;B|.	0.27416|.	0.069;0.178;0.02;0.034|.	B;B;B;B|.	0.23419|.	0.046;0.037;0.046;0.014|.	T|T	0.20438|0.20438	-1.0275|-1.0275	9|4	0.15499|.	T|.	0.54|.	-7.2169|-7.2169	7.8635|7.8635	0.29524|0.29524	0.0:0.6737:0.2379:0.0884|0.0:0.6737:0.2379:0.0884	rs16950706;rs16950706|rs16950706;rs16950706	44;14;44;44|.	G5EA44;F5H7W8;B4DWJ9;Q96C57|.	.;.;.;CL043_HUMAN|.	R|K	14;44;14;44;14|48	ENSP00000409788:G14R;ENSP00000288757:G44R;ENSP00000442224:G14R;ENSP00000437803:G44R;ENSP00000442041:G14R|.	ENSP00000288757:G44R|.	G|R	-|-	1|2	0|0	C12orf43|C12orf43	119938531|119938531	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.340000|0.340000	0.19892|0.19892	0.368000|0.368000	0.24481|0.24481	0.650000|0.650000	0.86243|0.86243	GGG|AGG	T|0.040;C|0.960	0.040	strong		0.627	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
RAB11FIP2	22841	hgsc.bcm.edu	37	10	119774598	119774598	+	Missense_Mutation	SNP	T	T	A	rs58533443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:119774598T>A	ENST00000355624.3	-	4	1728	c.1289A>T	c.(1288-1290)aAt>aTt	p.N430I	RAB11FIP2_ENST00000476207.1_5'UTR|RP11-354M20.3_ENST00000451610.2_RNA|RAB11FIP2_ENST00000369199.3_Missense_Mutation_p.N450I|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	80	0	0		WXS	Illumina HiSeq	Phase_I	96	25	0.260417	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	
AMOT	154796	hgsc.bcm.edu	37	X	112053138	112053138	+	Silent	SNP	C	C	T	rs57201849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:112053138C>T	ENST00000524145.1	-	5	1688	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	AMOT_ENST00000371958.1_Silent_p.S306S|AMOT_ENST00000371959.3_Silent_p.S538S|AMOT_ENST00000304758.1_Silent_p.S129S|AMOT_ENST00000371962.1_Silent_p.S306S			Q4VCS5	AMOT_HUMAN	angiomotin	538					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						CAAAGAGCTGCGAGATGGTTT	0.458													C|||	85	0.0225166	0.062	0.0043	3775	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.S538S		Atlas-SNP	.											.	AMOT	204	.	0			c.G1614A						PASS	.	C	,	221,3614		4,173,40,1455,531	254.0	220.0	231.0		1614,387	-0.6	1.0	X	dbSNP_129	231	4,6724		0,4,0,2424,1872	no	coding-synonymous,coding-synonymous	AMOT	NM_001113490.1,NM_133265.2	,	4,177,40,3879,2403	TT,TC,T,CC,C		0.0595,5.7627,2.1301	,	538/1085,129/676	112053138	225,10338	2203	4300	6503	SO:0001819	synonymous_variant	154796	exon4			GAGCTGCGAGATG	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.1614G>A	X.37:g.112053138C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Silent	SNP	ENST00000524145.1	37	CCDS48154.1																																																																																			C|0.980;T|0.020	0.020	strong		0.458	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
STK31	56164	hgsc.bcm.edu	37	7	23775454	23775454	+	Missense_Mutation	SNP	G	G	A	rs10264952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23775454G>A	ENST00000355870.3	+	7	900	c.781G>A	c.(781-783)Gag>Aag	p.E261K	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.E238K|STK31_ENST00000354639.3_Missense_Mutation_p.E238K|STK31_ENST00000433467.2_Missense_Mutation_p.E261K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	261			E -> K (in dbSNP:rs10264952). {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						GCACTTAAGTGAGAAAATGAC	0.413													g|||	423	0.0844649	0.0582	0.1196	5008	,	,		18454	0.0308		0.173	False		,,,				2504	0.0593				p.E261K		Atlas-SNP	.											.	STK31	175	.	0			c.G781A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	353,4053	181.9+/-209.8	14,325,1864	72.0	74.0	73.0		712,781,712	5.2	0.9	7	dbSNP_119	73	1622,6978	300.4+/-304.9	133,1356,2811	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	56,56,56	147,1681,4675	AA,AG,GG		18.8605,8.0118,15.1853	benign,benign,benign	238/997,261/1020,238/997	23775454	1975,11031	2203	4300	6503	SO:0001583	missense	56164	exon7			TTAAGTGAGAAAA	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.781G>A	7.37:g.23775454G>A	ENSP00000348132:p.Glu261Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	85	56	0.658824	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	232	0.10622710622710622	32	0.06504065040650407	55	0.15193370165745856	15	0.026223776223776224	130	0.17150395778364116	g	9.806	1.181881	0.21787	0.080118	0.188605	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.16	5.16	0.70880	.	0.412070	0.25302	N	0.031648	T	0.00012	0.0000	N	0.08118	0	0.38838	P	0.044008999999999965	B;B	0.21520	0.002;0.057	B;B	0.20767	0.001;0.031	T	0.23297	-1.0192	9	0.36615	T	0.2	-3.9172	10.0315	0.42103	0.0927:0.0:0.9073:0.0	rs10264952;rs52803859;rs57441640;rs10264952	261;261	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	261;261;238;238	ENSP00000348132:E261K;ENSP00000411852:E261K;ENSP00000346660:E238K;ENSP00000406146:E238K	ENSP00000346660:E238K	E	+	1	0	STK31	23741979	1.000000	0.71417	0.933000	0.37362	0.064000	0.16182	4.713000	0.61895	2.557000	0.86248	0.467000	0.42956	GAG	G|0.873;A|0.127	0.127	strong		0.413	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:15733454A>C	ENST00000265016.4	+	9	1138	c.943A>C	c.(943-945)Agg>Cgg	p.R315R	BST1_ENST00000382346.3_Silent_p.R330R	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	315					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.R315R(2)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						GCTGGCTTCCAGGACTCAACT	0.493													G|||	931	0.185903	0.115	0.0951	5008	,	,		16685	0.502		0.0308	False		,,,				2504	0.18				p.R315R		Atlas-SNP	.											BST1,colon,carcinoma,0,3	BST1	30	3	2	Substitution - coding silent(2)	stomach(1)|central_nervous_system(1)	c.A943C						PASS	.	G		506,3900		26,454,1723	55.0	52.0	53.0		943	4.0	0.0	4	dbSNP_86	53	260,8340		3,254,4043	no	coding-synonymous	BST1	NM_004334.2		29,708,5766	CC,CA,AA		3.0233,11.4843,5.8896		315/319	15733454	766,12240	2203	4300	6503	SO:0001819	synonymous_variant	683	exon9			GCTTCCAGGACTC	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.943A>C	4.37:g.15733454A>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Silent	SNP	ENST00000265016.4	37	CCDS3416.1																																																																																			A|0.883;C|0.117	0.117	strong		0.493	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
ITPR3	3710	hgsc.bcm.edu	37	6	33636907	33636907	+	Silent	SNP	C	C	T	rs2077163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33636907C>T	ENST00000374316.5	+	19	3223	c.2163C>T	c.(2161-2163)caC>caT	p.H721H	ITPR3_ENST00000605930.1_Silent_p.H721H			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	721					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)	GCAACGCCCACGACGAGAATG	0.607													C|||	2458	0.490815	0.3707	0.4827	5008	,	,		17767	0.5238		0.504	False		,,,				2504	0.6115				p.H721H		Atlas-SNP	.											.	ITPR3	409	.	0			c.C2163T						PASS	.	C		1707,2699	513.1+/-368.2	332,1043,828	86.0	81.0	82.0		2163	1.7	1.0	6	dbSNP_96	82	4528,4072	594.4+/-393.3	1177,2174,949	no	coding-synonymous	ITPR3	NM_002224.3		1509,3217,1777	TT,TC,CC		47.3488,38.7426,47.9394		721/2672	33636907	6235,6771	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon18			CGCCCACGACGAG	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.2163C>T	6.37:g.33636907C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.521;T|0.479	0.479	strong		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
UGGT1	56886	hgsc.bcm.edu	37	2	128934400	128934400	+	Silent	SNP	T	T	C	rs2290111	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128934400T>C	ENST00000259253.6	+	32	3599	c.3552T>C	c.(3550-3552)acT>acC	p.T1184T	UGGT1_ENST00000375990.3_Silent_p.T1160T	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1184					'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						ACGATGGCACTGATTCTCCCC	0.418													C|||	3327	0.664337	0.9622	0.5418	5008	,	,		22234	0.4127		0.5855	False		,,,				2504	0.6892				p.T1184T		Atlas-SNP	.											.	UGGT1	126	.	0			c.T3552C						PASS	.	C		3992,414	204.1+/-226.4	1809,374,20	184.0	175.0	178.0		3552	0.2	0.9	2	dbSNP_100	178	5104,3496	511.4+/-377.7	1512,2080,708	no	coding-synonymous	UGGT1	NM_020120.3		3321,2454,728	CC,CT,TT		40.6512,9.3963,30.063		1184/1556	128934400	9096,3910	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon32			TGGCACTGATTCT	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.3552T>C	2.37:g.128934400T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			T|0.323;C|0.677	0.677	strong		0.418	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
OR4K13	390433	hgsc.bcm.edu	37	14	20502120	20502120	+	Silent	SNP	C	C	T	rs17277032	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20502120C>T	ENST00000315693.2	-	1	799	c.798G>A	c.(796-798)tcG>tcA	p.S266S	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	266						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(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTTTATCTACCGAGTATCTGC	0.383													C|||	1332	0.265974	0.0877	0.3444	5008	,	,		18724	0.255		0.507	False		,,,				2504	0.2147				p.S266S		Atlas-SNP	.											.	OR4K13	68	.	0			c.G798A						PASS	.	C		782,3624		75,632,1496	61.0	61.0	61.0		798	1.0	0.2	14	dbSNP_123	61	4289,4311		1076,2137,1087	no	coding-synonymous	OR4K13	NM_001004714.1		1151,2769,2583	TT,TC,CC		49.8721,17.7485,38.9897		266/305	20502120	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	390433	exon1			ATCTACCGAGTAT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"""GPCR / Class A : Olfactory receptors"""	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.798G>A	14.37:g.20502120C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_001004714	Q6IF13	Silent	SNP	ENST00000315693.2	37	CCDS32028.1																																																																																			C|0.636;T|0.364	0.364	strong		0.383	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1		
MUC16	94025	hgsc.bcm.edu	37	19	9072313	9072313	+	Missense_Mutation	SNP	A	A	G	rs2121133	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9072313A>G	ENST00000397910.4	-	3	15336	c.15133T>C	c.(15133-15135)Tcc>Ccc	p.S5045P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5047	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						GCAGGTGAGGACAGAAAGGAA	0.478													A|||	1054	0.210463	0.0628	0.2046	5008	,	,		20061	0.249		0.3101	False		,,,				2504	0.272				p.S5045P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T15133C						PASS	.		PRO/SER	401,3505		23,355,1575	83.0	80.0	81.0		15133	-3.2	0.0	19	dbSNP_96	81	2393,5903		341,1711,2096	yes	missense	MUC16	NM_024690.2	74	364,2066,3671	GG,GA,AA		28.8452,10.2663,22.8979	benign	5045/14508	9072313	2794,9408	1953	4148	6101	SO:0001583	missense	94025	exon3			GTGAGGACAGAAA	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.15133T>C	19.37:g.9072313A>G	ENSP00000381008:p.Ser5045Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	488	0.22344322344322345	47	0.09552845528455285	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	a	4.940	0.174556	0.09391	0.102663	0.288452	ENSG00000181143	ENST00000397910	T	0.29142	1.58	1.59	-3.18	0.05186	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	.	.	.	B	0.09022	0.002	B	0.04013	0.001	T	0.40251	-0.9573	8	0.87932	D	0	.	3.207	0.06670	0.4598:0.2227:0.3175:0.0	rs2121133;rs2121133	5045	B5ME49	.	P	5045	ENSP00000381008:S5045P	ENSP00000381008:S5045P	S	-	1	0	MUC16	8933313	0.004000	0.15560	0.000000	0.03702	0.265000	0.26407	0.008000	0.13197	-1.081000	0.03105	0.234000	0.17832	TCC	A|0.771;G|0.229	0.229	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
L3HYPDH	112849	hgsc.bcm.edu	37	14	59939804	59939804	+	Missense_Mutation	SNP	G	G	A	rs1046701	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:59939804G>A	ENST00000247194.4	-	5	1057	c.944C>T	c.(943-945)gCg>gTg	p.A315V	L3HYPDH_ENST00000543619.1_5'UTR	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	315			A -> V (in dbSNP:rs1046701).		metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	ACCACATTTCGCTTCCTGAAA	0.373													g|||	160	0.0319489	0.0318	0.0375	5008	,	,		19147	0.0198		0.0596	False		,,,				2504	0.0123				p.A315V		Atlas-SNP	.											.	.	.	.	0			c.C944T						PASS	.	G	VAL/ALA	143,4263	100.3+/-138.9	2,139,2062	140.0	133.0	135.0		944	3.2	1.0	14	dbSNP_86	135	465,8135	137.6+/-194.5	14,437,3849	yes	missense	C14orf149	NM_144581.1	64	16,576,5911	AA,AG,GG		5.407,3.2456,4.6748	benign	315/355	59939804	608,12398	2203	4300	6503	SO:0001583	missense	112849	exon5			CATTTCGCTTCCT	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"""trans-L-3-hydroxyproline dehydratase"""	614811	"""chromosome 14 open reading frame 149"""	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.944C>T	14.37:g.59939804G>A	ENSP00000247194:p.Ala315Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_144581	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	37	CCDS9739.1	85	0.03891941391941392	15	0.03048780487804878	15	0.04143646408839779	10	0.017482517482517484	45	0.059366754617414245	g	9.240	1.038049	0.19669	0.032456	0.05407	ENSG00000126790	ENST00000247194	T	0.16196	2.36	4.99	3.17	0.36434	.	0.349133	0.32952	N	0.005457	T	0.01061	0.0035	N	0.17474	0.49	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.17992	-1.0351	10	0.56958	D	0.05	.	11.1206	0.48287	0.1515:0.0:0.8485:0.0	rs1046701;rs3168924;rs1046701	315	Q96EM0	PRCM_HUMAN	V	315	ENSP00000247194:A315V	ENSP00000247194:A315V	A	-	2	0	C14orf149	59009557	0.987000	0.35691	0.998000	0.56505	0.440000	0.31957	2.385000	0.44371	0.504000	0.28082	-0.824000	0.03097	GCG	G|0.960;A|0.040	0.040	strong		0.373	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	
ZNF805	390980	hgsc.bcm.edu	37	19	57760057	57760057	+	Missense_Mutation	SNP	G	G	A	rs3746231	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57760057G>A	ENST00000414468.2	+	3	242	c.242G>A	c.(241-243)gGc>gAc	p.G81D	ZNF805_ENST00000535550.1_5'UTR|ZNF805_ENST00000354309.4_5'UTR	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	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)			breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						CTCTCCCAAGGCACCTGTCCA	0.577													.|||	1836	0.366613	0.2489	0.4496	5008	,	,		19467	0.1687		0.5746	False		,,,				2504	0.4571				p.G81D		Atlas-SNP	.											.	ZNF805	30	.	0			c.G242A						PASS	.	G	ASP/GLY,	383,1001		52,279,361	59.0	54.0	56.0		242,	2.5	0.0	19	dbSNP_107	56	1646,1536		429,788,374	no	missense,utr-5	ZNF805	NM_001023563.3,NM_001145078.1	94,	481,1067,735	AA,AG,GG		48.2715,27.6734,44.4371	benign,	81/628,	57760057	2029,2537	692	1591	2283	SO:0001583	missense	390980	exon3			CCCAAGGCACCTG	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.242G>A	19.37:g.57760057G>A	ENSP00000412999:p.Gly81Asp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	792	0.3626373626373626	114	0.23170731707317074	166	0.4585635359116022	100	0.17482517482517482	412	0.5435356200527705	G	2.919	-0.223725	0.06061	0.276734	0.517285	ENSG00000204524	ENST00000414468	T	0.21191	2.02	4.67	2.54	0.30619	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	L	0.31420	0.93	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.42799	-0.9430	8	0.23891	T	0.37	.	8.8209	0.35025	0.2708:0.0:0.7292:0.0	rs3746231;rs60834144;rs3746231	81	Q5CZA5	ZN805_HUMAN	D	81	ENSP00000412999:G81D	ENSP00000412999:G81D	G	+	2	0	ZNF805	62451869	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	0.190000	0.17057	0.214000	0.20742	-0.797000	0.03246	GGC	G|0.643;A|0.357	0.357	strong		0.577	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
GALM	130589	hgsc.bcm.edu	37	2	38916970	38916970	+	Missense_Mutation	SNP	A	A	T	rs6741892	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:38916970A>T	ENST00000272252.5	+	4	820	c.568A>T	c.(568-570)Aat>Tat	p.N190Y	GALM_ENST00000410063.1_Intron	NM_138801.2	NP_620156.1	Q96C23	GALM_HUMAN	galactose mutarotase (aldose 1-epimerase)	190			N -> Y (in dbSNP:rs6741892).		galactose metabolic process (GO:0006012)|glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldose 1-epimerase activity (GO:0004034)|carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	14		all_hematologic(82;0.248)				CCCAAATataaatgaccatga	0.368													T|||	919	0.183506	0.2542	0.1023	5008	,	,		17622	0.1915		0.0746	False		,,,				2504	0.2495				p.N190Y		Atlas-SNP	.											.	GALM	20	.	0			c.A568T						PASS	.	T	TYR/ASN	1027,3379	726.9+/-409.8	115,797,1291	95.0	92.0	93.0	http://www.ncbi.nlm.nih.gov/pubmed?term	568	4.8	1.0	2	dbSNP_116	93	683,7917	788.1+/-407.6	28,627,3645	yes	missense	GALM	NM_138801.2	143	143,1424,4936	TT,TA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	7.9419,23.3091,13.1478	benign	190/343	38916970	1710,11296	2203	4300	6503	SO:0001583	missense	130589	exon4			AATATAAATGACC		CCDS1797.1	2p22.3	2008-02-05			ENSG00000143891	ENSG00000143891			24063	protein-coding gene	gene with protein product	"""aldose 1 epimerase"""	608883				12753898	Standard	NM_138801		Approved		uc002rqy.3	Q96C23	OTTHUMG00000102077	ENST00000272252.5:c.568A>T	2.37:g.38916970A>T	ENSP00000272252:p.Asn190Tyr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_138801	Q53RY1|Q8NIA2|V9HWA8	Missense_Mutation	SNP	ENST00000272252.5	37	CCDS1797.1	330	0.1510989010989011	121	0.2459349593495935	34	0.09392265193370165	111	0.19405594405594406	64	0.08443271767810026	T	4.140	0.024364	0.08054	0.233091	0.079419	ENSG00000143891	ENST00000272252;ENST00000434934	T;T	0.43294	0.95;0.95	4.8	4.8	0.61643	Glycoside hydrolase-type carbohydrate-binding, subgroup (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00980	-1.08	0.09310	P	0.9999999999999701	B	0.02656	0.0	B	0.01281	0.0	T	0.26360	-1.0105	9	0.09843	T	0.71	-6.837	9.3927	0.38383	0.1594:0.0:0.0:0.8406	rs6741892;rs52825962;rs6741892	190	Q96C23	GALM_HUMAN	Y	190;70	ENSP00000272252:N190Y;ENSP00000399473:N70Y	ENSP00000272252:N190Y	N	+	1	0	GALM	38770474	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	2.568000	0.45965	0.931000	0.37242	-0.265000	0.10407	AAT	A|0.849;T|0.151	0.151	strong		0.368	GALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219891.2	NM_138801	
COLEC12	81035	hgsc.bcm.edu	37	18	334742	334742	+	Splice_Site	SNP	C	C	T	rs17857498|rs2305027	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	90	0	0		WXS	Illumina HiSeq	Phase_I	94	26	0.276596	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
IL17RB	55540	hgsc.bcm.edu	37	3	53886912	53886912	+	Silent	SNP	C	C	T	rs3733075	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:53886912C>T	ENST00000288167.3	+	5	378	c.369C>T	c.(367-369)taC>taT	p.Y123Y		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	123					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				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)		CATTTTCCTACATCGGCTTCC	0.413													C|||	2150	0.429313	0.4281	0.3228	5008	,	,		21206	0.5913		0.3449	False		,,,				2504	0.4264				p.Y123Y		Atlas-SNP	.											.	IL17RB	27	.	0			c.C369T						PASS	.	C		1780,2626	526.2+/-371.8	345,1090,768	119.0	100.0	107.0		369	0.2	0.1	3	dbSNP_107	107	2828,5772	446.1+/-361.2	448,1932,1920	no	coding-synonymous	IL17RB	NM_018725.3		793,3022,2688	TT,TC,CC		32.8837,40.3995,35.4298		123/503	53886912	4608,8398	2203	4300	6503	SO:0001819	synonymous_variant	55540	exon5			TTCCTACATCGGC	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"""Interleukins and interleukin receptors"""	18015	protein-coding gene	gene with protein product		605458	"""interleukin 17B receptor"""	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.369C>T	3.37:g.53886912C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	197	72	0.365482	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Silent	SNP	ENST00000288167.3	37	CCDS2874.1																																																																																			C|0.603;T|0.397	0.397	strong		0.413	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	
SLITRK6	84189	hgsc.bcm.edu	37	13	86370571	86370571	+	Missense_Mutation	SNP	G	G	A	rs12863734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:86370571G>A	ENST00000400286.2	-	2	671	c.73C>T	c.(73-75)Ctc>Ttc	p.L25F		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	25			L -> F (in dbSNP:rs12863734).		adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		CTGGATGAGAGCACTGGAGTT	0.393													A|||	61	0.0121805	0.028	0.0187	5008	,	,		18501	0.0		0.0099	False		,,,				2504	0.001				p.L25F		Atlas-SNP	.											.	SLITRK6	150	.	0			c.C73T						PASS	.	A	PHE/LEU	86,3674		0,86,1794	68.0	65.0	66.0		73	0.9	0.1	13	dbSNP_121	66	146,8078		1,144,3967	yes	missense	SLITRK6	NM_032229.2	22	1,230,5761	AA,AG,GG		1.7753,2.2872,1.9359	benign	25/842	86370571	232,11752	1880	4112	5992	SO:0001583	missense	84189	exon2			ATGAGAGCACTGG	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.73C>T	13.37:g.86370571G>A	ENSP00000383143:p.Leu25Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	35	0.016025641025641024	19	0.03861788617886179	8	0.022099447513812154	0	0.0	8	0.010554089709762533	A	4.456	0.084442	0.08583	0.022872	0.017753	ENSG00000184564	ENST00000400286	T	0.59224	0.28	6.17	0.876	0.19138	.	0.653705	0.15341	N	0.267500	T	0.12092	0.0294	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10200	-1.0640	10	0.49607	T	0.09	0.0871	4.6406	0.12546	0.2161:0.1326:0.5211:0.1302	rs12863734;rs52806014;rs12863734	25	Q9H5Y7	SLIK6_HUMAN	F	25	ENSP00000383143:L25F	ENSP00000383143:L25F	L	-	1	0	SLITRK6	85268572	0.004000	0.15560	0.102000	0.21198	0.009000	0.06853	-0.016000	0.12613	-0.027000	0.13873	-0.254000	0.11334	CTC	G|0.982;A|0.018	0.018	strong		0.393	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
OR52I1	390037	hgsc.bcm.edu	37	11	4615857	4615857	+	Missense_Mutation	SNP	G	G	A	rs62622512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4615857G>A	ENST00000530443.2	+	1	589	c.589G>A	c.(589-591)Gtg>Atg	p.V197M	OR52I1_ENST00000450052.2_Missense_Mutation_p.V221M	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	197						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(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCTGACCCCGTGCCCAGCAG	0.488													G|||	106	0.0211661	0.0023	0.0418	5008	,	,		21906	0.0		0.0517	False		,,,				2504	0.0225				p.V197M		Atlas-SNP	.											.	OR52I1	29	.	0			c.G589A						PASS	.	G	MET/VAL	55,4347	52.3+/-87.9	2,51,2148	177.0	169.0	172.0		589	2.6	1.0	11	dbSNP_129	172	518,8078	147.3+/-202.7	20,478,3800	no	missense	OR52I1	NM_001005169.1	21	22,529,5948	AA,AG,GG		6.0261,1.2494,4.4084	benign	197/325	4615857	573,12425	2201	4298	6499	SO:0001583	missense	390037	exon1			GACCCCGTGCCCA	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.589G>A	11.37:g.4615857G>A	ENSP00000436453:p.Val197Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	124	70	0.564516	NM_001005169	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	64	0.029304029304029304	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	39	0.051451187335092345	G	5.986	0.365892	0.11352	0.012494	0.060261	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.37752	1.18;1.18	4.96	2.57	0.30868	GPCR, rhodopsin-like superfamily (1);	0.372474	0.22806	N	0.055419	T	0.01320	0.0043	N	0.02539	-0.55	0.20638	N	0.999876	B	0.06786	0.001	B	0.04013	0.001	T	0.05162	-1.0902	9	0.56958	D	0.05	-6.5379	5.4857	0.16749	0.7603:0.0:0.0861:0.1536	rs62622512	197	Q8NGK6	O52I1_HUMAN	M	221;197	ENSP00000409094:V221M;ENSP00000436453:V197M	ENSP00000409094:V221M	V	+	1	0	OR52I1	4572433	0.000000	0.05858	0.997000	0.53966	0.928000	0.56348	-0.140000	0.10342	0.441000	0.26529	-0.351000	0.07748	GTG	G|0.956;A|0.044	0.044	strong		0.488	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
ASIC2	40	hgsc.bcm.edu	37	17	32483237	32483237	+	Silent	SNP	A	A	G	rs2228990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:32483237A>G	ENST00000359872.6	-	1	1076	c.315T>C	c.(313-315)aaT>aaC	p.N105N		NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	105					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GGTACAGGTCATTGGTGGTGA	0.612													A|||	1363	0.272165	0.1876	0.3674	5008	,	,		18957	0.3552		0.2018	False		,,,				2504	0.3057				p.N105N		Atlas-SNP	.											.	.	.	.	0			c.T315C						PASS	.	A		786,3588		76,634,1477	73.0	82.0	79.0		315	-4.2	1.0	17	dbSNP_98	79	1650,6926		157,1336,2795	no	coding-synonymous	ACCN1	NM_001094.4		233,1970,4272	GG,GA,AA		19.2397,17.9698,18.8108		105/513	32483237	2436,10514	2187	4288	6475	SO:0001819	synonymous_variant	40	exon1			CAGGTCATTGGTG	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.315T>C	17.37:g.32483237A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001094	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																			A|0.761;G|0.239	0.239	strong		0.612	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
LAMA1	284217	hgsc.bcm.edu	37	18	7010233	7010233	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:7010233C>T	ENST00000389658.3	-	26	3932	c.3839G>A	c.(3838-3840)gGa>gAa	p.G1280E		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1280	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				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)				CTGTCTCACTCCATTCTCTGG	0.443																																					p.G1280E		Atlas-SNP	.											.	LAMA1	458	.	0			c.G3839A						PASS	.						193.0	164.0	174.0					18																	7010233		2203	4300	6503	SO:0001583	missense	284217	exon26			CTCACTCCATTCT	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.3839G>A	18.37:g.7010233C>T	ENSP00000374309:p.Gly1280Glu	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	254	52	0.204724	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516908	0.64634	.	.	ENSG00000101680	ENST00000389658	T	0.31247	1.5	5.57	5.57	0.84162	Laminin B type IV (2);Laminin B, subgroup (1);	0.059894	0.64402	D	0.000003	T	0.55561	0.1928	M	0.64080	1.96	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.51926	-0.8643	10	0.48119	T	0.1	.	19.5479	0.95307	0.0:1.0:0.0:0.0	.	1280	P25391	LAMA1_HUMAN	E	1280	ENSP00000374309:G1280E	ENSP00000374309:G1280E	G	-	2	0	LAMA1	7000233	0.987000	0.35691	0.982000	0.44146	0.385000	0.30292	5.643000	0.67895	2.632000	0.89209	0.579000	0.79373	GGA	.	.	none		0.443	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DNAH2	146754	hgsc.bcm.edu	37	17	7735063	7735063	+	Missense_Mutation	SNP	T	T	G	rs57985356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7735063T>G	ENST00000572933.1	+	82	14156	c.12696T>G	c.(12694-12696)ttT>ttG	p.F4232L	DNAH2_ENST00000389173.2_Missense_Mutation_p.F4232L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4232					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)				ATTGCATCTTTGATGCCCATG	0.498													T|||	755	0.150759	0.0045	0.268	5008	,	,		20127	0.2837		0.0626	False		,,,				2504	0.2188				p.F4232L		Atlas-SNP	.											.	DNAH2	498	.	0			c.T12696G						PASS	.	T	LEU/PHE	122,4284	89.7+/-128.4	3,116,2084	164.0	140.0	148.0		12696	4.3	1.0	17	dbSNP_129	148	728,7872	177.0+/-226.7	29,670,3601	yes	missense	DNAH2	NM_020877.2	22	32,786,5685	GG,GT,TT		8.4651,2.769,6.5354	benign	4232/4428	7735063	850,12156	2203	4300	6503	SO:0001583	missense	146754	exon81			CATCTTTGATGCC	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.12696T>G	17.37:g.7735063T>G	ENSP00000458355:p.Phe4232Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	262	0.11996336996336997	5	0.01016260162601626	76	0.20994475138121546	137	0.2395104895104895	44	0.05804749340369393	T	9.971	1.225367	0.22457	0.02769	0.084651	ENSG00000183914	ENST00000389173	T	0.07908	3.15	5.37	4.27	0.50696	Dynein heavy chain (1);	0.127433	0.53938	D	0.000041	T	0.00012	0.0000	L	0.28458	0.855	0.09310	P	1.0	B	0.10296	0.003	B	0.14023	0.01	T	0.47249	-0.9132	8	.	.	.	.	9.7193	0.40293	0.0:0.086:0.0:0.914	rs57985356;rs61747293	4232	Q9P225	DYH2_HUMAN	L	4232	ENSP00000373825:F4232L	.	F	+	3	2	DNAH2	7675788	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.018000	0.40991	1.038000	0.40049	0.533000	0.62120	TTT	T|0.921;G|0.079	0.079	strong		0.498	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
PCLO	27445	hgsc.bcm.edu	37	7	82544987	82544987	+	Silent	SNP	A	A	G	rs17156844	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:82544987A>G	ENST00000333891.9	-	7	12652	c.12315T>C	c.(12313-12315)caT>caC	p.H4105H	PCLO_ENST00000423517.2_Silent_p.H4105H|PCLO_ENST00000437081.1_Silent_p.H825H	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						TCACATAACTATGCAATCTAG	0.453													A|||	2137	0.426717	0.5023	0.4986	5008	,	,		20097	0.5466		0.2028	False		,,,				2504	0.3804				p.H4105H		Atlas-SNP	.											.	PCLO	1506	.	0			c.T12315C						PASS	.	A	,	1540,2230		305,930,650	58.0	53.0	55.0		12315,12315	-0.8	1.0	7	dbSNP_123	55	1814,6384		213,1388,2498	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	518,2318,3148	GG,GA,AA		22.1273,40.8488,28.0247	,	4105/4936,4105/5143	82544987	3354,8614	1885	4099	5984	SO:0001819	synonymous_variant	27445	exon7			ATAACTATGCAAT	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.12315T>C	7.37:g.82544987A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_014510		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			A|0.591;G|0.409	0.409	strong		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
EXD3	54932	hgsc.bcm.edu	37	9	140267490	140267490	+	Missense_Mutation	SNP	G	G	A	rs143312119	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140267490G>A	ENST00000340951.4	-	5	524	c.329C>T	c.(328-330)gCg>gTg	p.A110V	EXD3_ENST00000475006.1_5'UTR|EXD3_ENST00000342129.4_5'UTR|EXD3_ENST00000479452.1_Missense_Mutation_p.A110V	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0	Pro-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GACTTTGACCGCTCGGGCCTG	0.647													G|||	64	0.0127796	0.003	0.0173	5008	,	,		16501	0.0		0.0358	False		,,,				2504	0.0123				p.A110V		Atlas-SNP	.											.	EXD3	86	.	0			c.C329T						PASS	.	G	VAL/ALA	21,4163		0,21,2071	45.0	54.0	51.0		329	0.3	0.0	9	dbSNP_134	51	232,8194		6,220,3987	yes	missense	EXD3	NM_017820.3	64	6,241,6058	AA,AG,GG		2.7534,0.5019,2.0063	benign	110/877	140267490	253,12357	2092	4213	6305	SO:0001583	missense	54932	exon5			TTGACCGCTCGGG		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.329C>T	9.37:g.140267490G>A	ENSP00000340474:p.Ala110Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	29	0.013278388278388278	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	25	0.032981530343007916	G	10.38	1.335343	0.24253	0.005019	0.027534	ENSG00000187609	ENST00000340951;ENST00000479452	T;T	0.55052	0.54;1.08	4.38	0.277	0.15668	.	0.177719	0.48286	N	0.000188	T	0.16811	0.0404	L	0.49640	1.575	0.19775	N	0.999951	P;D	0.58620	0.858;0.983	B;B	0.39660	0.109;0.306	T	0.19516	-1.0303	10	0.51188	T	0.08	.	6.9062	0.24311	0.5134:0.0:0.4866:0.0	.	110;110	Q8N9H8-4;Q8N9H8	.;MUT7_HUMAN	V	110	ENSP00000340474:A110V;ENSP00000431859:A110V	ENSP00000340474:A110V	A	-	2	0	EXD3	139387311	0.000000	0.05858	0.012000	0.15200	0.083000	0.17756	0.162000	0.16501	-0.014000	0.14175	0.313000	0.20887	GCG	G|0.982;A|0.018	0.018	strong		0.647	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
COL9A2	1298	hgsc.bcm.edu	37	1	40773123	40773123	+	Missense_Mutation	SNP	G	G	C	rs2228567	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:40773123G>C	ENST00000372748.3	-	19	1099	c.1003C>G	c.(1003-1005)Cta>Gta	p.L335V	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	335	Triple-helical region 3 (COL3).		L -> V (in dbSNP:rs2228567). {ECO:0000269|PubMed:11565064}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	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)	p.L335V(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-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;2.08e-17)			CTTACCGCTAGGCCCTGGTGG	0.597													g|||	424	0.0846645	0.0514	0.0836	5008	,	,		16140	0.1052		0.0974	False		,,,				2504	0.0961				p.L335V		Atlas-SNP	.											COL9A2,NS,lymphoid_neoplasm,0,1	COL9A2	63	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1003G						scavenged	.		VAL/LEU	325,4081		9,307,1887	33.0	35.0	35.0		1003	3.0	1.0	1	dbSNP_98	35	974,7626		55,864,3381	yes	missense	COL9A2	NM_001852.3	32	64,1171,5268	CC,CG,GG		11.3256,7.3763,9.9877	possibly-damaging	335/690	40773123	1299,11707	2203	4300	6503	SO:0001583	missense	1298	exon19			CCGCTAGGCCCTG	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1003C>G	1.37:g.40773123G>C	ENSP00000361834:p.Leu335Val	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	37	CCDS450.1	185	0.08470695970695971	32	0.06504065040650407	25	0.06906077348066299	50	0.08741258741258741	78	0.10290237467018469	.	11.73	1.724854	0.30593	0.073763	0.113256	ENSG00000049089	ENST00000372748	D	0.93547	-3.24	5.92	3.0	0.34707	.	0.389541	0.26765	N	0.022605	T	0.16514	0.0397	N	0.21617	0.685	0.34033	P	0.34592599999999996	P	0.43938	0.822	P	0.47626	0.552	T	0.65005	-0.6273	9	0.25106	T	0.35	.	8.2411	0.31660	0.2528:0.0:0.7472:0.0	rs2228567;rs12722877	335	Q14055	CO9A2_HUMAN	V	335	ENSP00000361834:L335V	ENSP00000361834:L335V	L	-	1	2	COL9A2	40545710	0.984000	0.35163	0.997000	0.53966	0.237000	0.25408	0.345000	0.19979	0.829000	0.34733	0.639000	0.83563	CTA	G|0.909;C|0.091	0.091	strong		0.597	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	
EIF2B5	8893	hgsc.bcm.edu	37	3	183861243	183861243	+	Missense_Mutation	SNP	A	A	G	rs843358	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183861243A>G	ENST00000273783.3	+	13	1881	c.1759A>G	c.(1759-1761)Ata>Gta	p.I587V	EIF2B5_ENST00000444495.1_Missense_Mutation_p.I587V	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	587	W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.		I -> V (in dbSNP:rs843358). {ECO:0000269|PubMed:11704758, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8688466, ECO:0000269|Ref.3}.		astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|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)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|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)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			TGCCTATAACATAAGTCTAAA	0.527													A|||	1953	0.389976	0.3268	0.3646	5008	,	,		19751	0.5288		0.3042	False		,,,				2504	0.4387				p.I587V		Atlas-SNP	.											.	EIF2B5	62	.	0			c.A1759G						PASS	.	A	VAL/ILE	1441,2965	468.1+/-355.0	254,933,1016	95.0	85.0	88.0		1759	5.7	1.0	3	dbSNP_86	88	2827,5773	446.5+/-361.3	452,1923,1925	yes	missense	EIF2B5	NM_003907.2	29	706,2856,2941	GG,GA,AA		32.8721,32.7054,32.8156	benign	587/722	183861243	4268,8738	2203	4300	6503	SO:0001583	missense	8893	exon13			TATAACATAAGTC	U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"""eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"""			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.1759A>G	3.37:g.183861243A>G	ENSP00000273783:p.Ile587Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	132	73	0.55303	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	811	0.37133699633699635	164	0.3333333333333333	122	0.3370165745856354	303	0.5297202797202797	222	0.2928759894459103	a	12.60	1.988085	0.35036	0.327054	0.328721	ENSG00000145191	ENST00000273783;ENST00000444495	D;D	0.81908	-1.55;-1.55	5.72	5.72	0.89469	eIF4-gamma/eIF5/eIF2-epsilon (1);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.43923	1.385	0.09310	P	0.99999874126	P;B	0.37352	0.591;0.264	B;B	0.33392	0.163;0.076	T	0.36792	-0.9733	9	0.02654	T	1	.	16.0146	0.80427	1.0:0.0:0.0:0.0	rs843358;rs1709671;rs3816863;rs11540445;rs17851047;rs52797406;rs58049539;rs843358	587;587	E9PC74;Q13144	.;EI2BE_HUMAN	V	587	ENSP00000273783:I587V;ENSP00000409142:I587V	ENSP00000273783:I587V	I	+	1	0	EIF2B5	185343937	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.214000	0.65236	2.183000	0.69458	0.379000	0.24179	ATA	T|0.002;G|0.345	0.345	strong		0.527	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331419	55331419	+	Missense_Mutation	SNP	C	C	T	rs143886704	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55331419C>T	ENST00000391728.4	+	4	640	c.607C>T	c.(607-609)Ccc>Tcc	p.P203S	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.P203S|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.P108S|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.P203S|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.P203S|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.P203S	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	203			P -> S (in dbSNP:rs2273731).		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TACTCACACCCCCTATCAGTT	0.517													c|||	1118	0.223243	0.1362	0.2824	5008	,	,		13667	0.1617		0.4284	False		,,,				2504	0.1513				p.P203S		Atlas-SNP	.											KIR3DL1_ENST00000402254,NS,neuroblastoma,0,2	KIR3DL1	174	2	0			c.C607T						PASS	.	C	SER/PRO	729,3637		118,493,1572	150.0	128.0	136.0		607	-2.9	0.0	19	dbSNP_100	136	3261,5035		995,1271,1882	no	missense	KIR3DL1	NM_013289.2	74	1113,1764,3454	TT,TC,CC		39.3081,16.6972,31.5116		203/445	55331419	3990,8672	2183	4148	6331	SO:0001583	missense	3811	exon4			CACACCCCCTATC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.607C>T	19.37:g.55331419C>T	ENSP00000375608:p.Pro203Ser	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	126	46	0.365079	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	560	0.2564102564102564	67	0.13617886178861788	98	0.27071823204419887	86	0.15034965034965034	309	0.4076517150395778	-	5.868	0.344314	0.11126	0.166972	0.393081	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T;T	0.00873	5.59;5.59;5.59;5.59;5.59;5.59	1.44	-2.88	0.05682	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.928050	0.04022	N	0.299910	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P;B;P	0.44139	0.46;0.827;0.041;0.626	B;B;B;B	0.38985	0.058;0.287;0.03;0.036	T	0.28490	-1.0042	9	0.59425	D	0.04	.	1.9712	0.03406	0.2616:0.3423:0.0:0.3961	rs2273731;rs12971727	203;108;203;203	Q15702;Q14946;F6QF33;P43629	.;.;.;KI3L1_HUMAN	S	203;203;203;181;203;203;108	ENSP00000384528:P203S;ENSP00000443350:P203S;ENSP00000442355:P203S;ENSP00000375608:P203S;ENSP00000326868:P203S;ENSP00000350901:P108S	ENSP00000326868:P203S	P	+	1	0	KIR3DL1	60023231	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.035000	0.13797	-0.710000	0.05001	0.184000	0.17185	CCC	C|0.250;T|0.750	0.750	weak		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
ADNP2	22850	hgsc.bcm.edu	37	18	77895192	77895192	+	Silent	SNP	G	G	A	rs3744878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:77895192G>A	ENST00000262198.4	+	4	2351	c.1896G>A	c.(1894-1896)gcG>gcA	p.A632A		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	632					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|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(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GAGGCCTTGCGACTGTCGCTC	0.632													G|||	549	0.109625	0.1241	0.1254	5008	,	,		18997	0.0337		0.16	False		,,,				2504	0.1053				p.A632A		Atlas-SNP	.											.	ADNP2	102	.	0			c.G1896A						PASS	.	G		519,3887	236.5+/-248.6	33,453,1717	74.0	72.0	72.0		1896	-9.7	0.0	18	dbSNP_107	72	1405,7195	272.3+/-290.0	126,1153,3021	no	coding-synonymous	ADNP2	NM_014913.3		159,1606,4738	AA,AG,GG		16.3372,11.7794,14.7932		632/1132	77895192	1924,11082	2203	4300	6503	SO:0001819	synonymous_variant	22850	exon4			CCTTGCGACTGTC	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.1896G>A	18.37:g.77895192G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																			G|0.871;A|0.129	0.129	strong		0.632	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
FAT1	2195	hgsc.bcm.edu	37	4	187539217	187539217	+	Silent	SNP	G	G	A	rs3733405	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187539217G>A	ENST00000441802.2	-	10	8732	c.8523C>T	c.(8521-8523)aaC>aaT	p.N2841N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2841	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAACTTGGCCGTTGGTTCCTG	0.428										HNSCC(5;0.00058)			G|||	344	0.0686901	0.003	0.1499	5008	,	,		20252	0.1796		0.0358	False		,,,				2504	0.0194				p.N2841N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8523T						PASS	.	G		39,3851		0,39,1906	113.0	105.0	107.0		8523	-8.4	0.5	4	dbSNP_107	107	256,8062		4,248,3907	no	coding-synonymous	FAT1	NM_005245.3		4,287,5813	AA,AG,GG		3.0777,1.0026,2.4164		2841/4589	187539217	295,11913	1945	4159	6104	SO:0001819	synonymous_variant	2195	exon10			TTGGCCGTTGGTT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8523C>T	4.37:g.187539217G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	49	0.382812	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.923;A|0.077	0.077	strong		0.428	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
IFNAR2	3455	hgsc.bcm.edu	37	21	34614250	34614250	+	Missense_Mutation	SNP	T	T	C	rs2229207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34614250T>C	ENST00000342136.4	+	2	349	c.23T>C	c.(22-24)tTc>tCc	p.F8S	IFNAR2_ENST00000342101.3_Missense_Mutation_p.F8S|IFNAR2_ENST00000404220.3_Missense_Mutation_p.F8S|IFNAR2_ENST00000382264.3_Missense_Mutation_p.F8S|IFNAR2_ENST00000382241.3_Missense_Mutation_p.F8S|IFNAR2_ENST00000420068.1_3'UTR|IFNAR2_ENST00000413881.1_Intron			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	8			F -> S (associated with susceptibility to HVB infection; lower cell surface levels; lower induction of MHC class 1 expression by INF-alpha; dbSNP:rs2229207). {ECO:0000269|PubMed:16757563, ECO:0000269|Ref.6}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|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)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	CAGAATGCCTTCATCTTCAGA	0.378													T|||	594	0.11861	0.0809	0.147	5008	,	,		20723	0.1706		0.0736	False		,,,				2504	0.1421				p.F8S		Atlas-SNP	.											.	IFNAR2	44	.	0			c.T23C	GRCh37	CM066573	IFNAR2	M	rs2229207	PASS	.	T	SER/PHE,SER/PHE,SER/PHE	333,4073	174.8+/-204.3	13,307,1883	192.0	172.0	179.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	23,23,23	-4.9	0.0	21	dbSNP_98	179	670,7930	168.0+/-219.6	32,606,3662	yes	missense,missense,missense	IFNAR2	NM_000874.3,NM_207584.1,NM_207585.1	155,155,155	45,913,5545	CC,CT,TT		7.7907,7.5579,7.7118	benign,benign,benign	8/332,8/332,8/516	34614250	1003,12003	2203	4300	6503	SO:0001583	missense	3455	exon2			ATGCCTTCATCTT		CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110		"""Interferons"""	5433	protein-coding gene	gene with protein product		602376		IFNABR		8181059	Standard	NM_207585		Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.23T>C	21.37:g.34614250T>C	ENSP00000343957:p.Phe8Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_207585	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	Missense_Mutation	SNP	ENST00000342136.4	37	CCDS13621.1	258	0.11813186813186813	40	0.08130081300813008	54	0.14917127071823205	110	0.19230769230769232	54	0.0712401055408971	T	9.507	1.104641	0.20632	0.075579	0.077907	ENSG00000159110	ENST00000382264;ENST00000404220;ENST00000382241;ENST00000342136;ENST00000342101;ENST00000447980	T;T;T;T;T;T	0.30981	1.92;1.92;1.93;1.93;1.94;1.51	4.51	-4.95	0.03048	.	3.265270	0.00827	N	0.001627	T	0.00012	0.0000	N	0.01505	-0.83	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.26677	-1.0096	9	0.54805	T	0.06	.	7.617	0.28163	0.0:0.232:0.1365:0.6315	rs2229207;rs4986956;rs17860176;rs52830005;rs59670283;rs4986956	8;8;8	P48551-3;P48551;P48551-2	.;INAR2_HUMAN;.	S	8;8;8;8;8;32	ENSP00000371699:F8S;ENSP00000384309:F8S;ENSP00000371676:F8S;ENSP00000343957:F8S;ENSP00000343289:F8S;ENSP00000402311:F32S	ENSP00000343289:F8S	F	+	2	0	IFNAR2	33536120	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.407000	0.02488	-0.897000	0.03910	-1.145000	0.01858	TTC	T|0.904;C|0.096	0.096	strong		0.378	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139825.1		
OR9K2	441639	hgsc.bcm.edu	37	12	55524314	55524314	+	Silent	SNP	T	T	C	rs7137261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55524314T>C	ENST00000305377.5	+	1	850	c.762T>C	c.(760-762)caT>caC	p.H254H		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	254						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(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TAAAGATACATTCTACTGAGG	0.383													C|||	1523	0.304113	0.4085	0.2421	5008	,	,		18723	0.1141		0.334	False		,,,				2504	0.3722				p.H254H		Atlas-SNP	.											.	OR9K2	63	.	0			c.T762C						PASS	.	C		1703,2703	652.8+/-399.5	308,1087,808	130.0	118.0	122.0		762	-1.6	0.0	12	dbSNP_116	122	2777,5823	678.6+/-403.5	456,1865,1979	no	coding-synonymous	OR9K2	NM_001005243.1		764,2952,2787	CC,CT,TT		32.2907,38.6518,34.4456		254/336	55524314	4480,8526	2203	4300	6503	SO:0001819	synonymous_variant	441639	exon1			GATACATTCTACT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.762T>C	12.37:g.55524314T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_001005243	B9EH19|Q6IFD6	Silent	SNP	ENST00000305377.5	37	CCDS31814.1																																																																																			T|0.674;C|0.326	0.326	strong		0.383	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
SUN1	23353	hgsc.bcm.edu	37	7	881668	881668	+	Missense_Mutation	SNP	C	C	T	rs6461378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:881668C>T	ENST00000405266.1	+	3	376	c.352C>T	c.(352-354)Cac>Tac	p.H118Y	SUN1_ENST00000456758.2_Missense_Mutation_p.H176Y|SUN1_ENST00000452783.2_Missense_Mutation_p.H118Y|SUN1_ENST00000457378.2_Missense_Mutation_p.H139Y|SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000401592.1_Missense_Mutation_p.H118Y|SUN1_ENST00000389574.3_Missense_Mutation_p.H68Y|SUN1_ENST00000425407.2_Missense_Mutation_p.H68Y|SUN1_ENST00000403868.1_Missense_Mutation_p.H118Y			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	118	LMNA-binding.		H -> Y (in dbSNP:rs6461378). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9872452}.		cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGGCGTCAGCCACGGCGGCAC	0.517													C|||	2669	0.532947	0.6233	0.4438	5008	,	,		19433	0.6399		0.4324	False		,,,				2504	0.4673				p.H139Y		Atlas-SNP	.											.	SUN1	157	.	0			c.C415T						PASS	.	C	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS	2346,1818		679,988,415	81.0	84.0	83.0		352,352,415,352,202	5.6	1.0	7	dbSNP_116	83	3641,4787		780,2081,1353	yes	missense,missense,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	83,83,83,83,83	1459,3069,1768	TT,TC,CC		43.2012,43.6599,47.5461	benign,benign,benign,benign,benign	118/786,118/683,139/279,118/258,68/703	881668	5987,6605	2082	4214	6296	SO:0001583	missense	23353	exon5			GTCAGCCACGGCG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.352C>T	7.37:g.881668C>T	ENSP00000384116:p.His118Tyr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	116	84	0.724138	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		1153	0.5279304029304029	315	0.6402439024390244	151	0.4171270718232044	363	0.6346153846153846	324	0.42744063324538256	C	10.65	1.410311	0.25465	0.563401	0.432012	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000439679;ENST00000457598;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;T;T;T;T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7	5.56	5.56	0.83823	.	0.647730	0.15176	N	0.276357	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	1.0	P;P;P;P;P	0.51449	0.917;0.945;0.608;0.666;0.898	B;P;B;B;B	0.47827	0.212;0.558;0.175;0.311;0.354	T	0.42137	-0.9469	9	0.23302	T	0.38	-11.7323	19.1101	0.93313	0.0:1.0:0.0:0.0	rs6461378;rs10334882;rs11555973;rs52823062;rs57703989;rs6461378	118;118;139;68;118	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	Y	176;68;139;118;118;118;118;118;118;118;118;68;93	ENSP00000388743:H176Y;ENSP00000374225:H68Y;ENSP00000395952:H139Y;ENSP00000413439:H118Y;ENSP00000388430:H118Y;ENSP00000413188:H118Y;ENSP00000404965:H118Y;ENSP00000384116:H118Y;ENSP00000384015:H118Y;ENSP00000383947:H118Y;ENSP00000392309:H68Y;ENSP00000392595:H93Y	ENSP00000297445:H118Y	H	+	1	0	SUN1	848194	1.000000	0.71417	0.960000	0.40013	0.026000	0.11368	5.379000	0.66196	2.610000	0.88304	0.655000	0.94253	CAC	C|0.476;T|0.524	0.524	strong		0.517	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
BMP2	650	hgsc.bcm.edu	37	20	6759706	6759706	+	Silent	SNP	C	C	T	rs13037675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:6759706C>T	ENST00000378827.4	+	3	2380	c.1161C>T	c.(1159-1161)gaC>gaT	p.D387D		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	387			D -> G (in dbSNP:rs11545591).		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						ACTATCAGGACATGGTTGTGG	0.348													C|||	226	0.0451278	0.0386	0.1225	5008	,	,		12726	0.0		0.0706	False		,,,				2504	0.0194				p.D387D		Atlas-SNP	.											.	BMP2	45	.	0			c.C1161T						PASS	.	C		215,4191	131.0+/-167.6	7,201,1995	67.0	65.0	65.0		1161	4.6	1.0	20	dbSNP_121	65	577,8023	154.0+/-208.3	19,539,3742	no	coding-synonymous	BMP2	NM_001200.2		26,740,5737	TT,TC,CC		6.7093,4.8797,6.0895		387/397	6759706	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	650	exon3			TCAGGACATGGTT		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.1161C>T	20.37:g.6759706C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_001200		Silent	SNP	ENST00000378827.4	37	CCDS13099.1																																																																																			C|0.943;T|0.057	0.057	strong		0.348	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
RP1L1	94137	hgsc.bcm.edu	37	8	10470148	10470148	+	Missense_Mutation	SNP	G	G	A	rs74400517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	40	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	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		
GRHL3	57822	hgsc.bcm.edu	37	1	24658063	24658063	+	Missense_Mutation	SNP	C	C	G	rs2486668	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24658063C>G	ENST00000350501.5	+	2	292	c.165C>G	c.(163-165)gaC>gaG	p.D55E	GRHL3_ENST00000530984.1_3'UTR|GRHL3_ENST00000236255.4_Missense_Mutation_p.D60E|GRHL3_ENST00000361548.4_Missense_Mutation_p.D55E|GRHL3_ENST00000356046.2_Missense_Mutation_p.D9E|GRHL3_ENST00000342072.4_5'UTR	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						scavenged	.	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	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	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	
RRP12	23223	hgsc.bcm.edu	37	10	99126513	99126513	+	Silent	SNP	C	C	T	rs45527941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000414986.1_Silent_p.Q1006Q|RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000315563.6_Silent_p.Q967Q|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1067	Glu-rich.					integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CACCTTTGCCCTGGGCGGGct	0.672													C|||	128	0.0255591	0.0038	0.0548	5008	,	,		15272	0.0		0.0716	False		,,,				2504	0.0133				p.Q1067Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3201A						PASS	.	C	,	58,4348	56.2+/-92.4	0,58,2145	70.0	82.0	78.0		3018,3201	4.8	1.0	10	dbSNP_127	78	501,8099	143.6+/-199.6	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	17,525,5961	TT,TC,CC		5.8256,1.3164,4.298	,	1006/1237,1067/1298	99126513	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			TTTGCCCTGGGCG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3201G>A	10.37:g.99126513C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.962;T|0.038	0.038	strong		0.672	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
IGDCC3	9543	hgsc.bcm.edu	37	15	65621441	65621441	+	Missense_Mutation	SNP	C	C	A	rs12907128	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65621441C>A	ENST00000327987.4	-	14	2502	c.2251G>T	c.(2251-2253)Gtg>Ttg	p.V751L	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	751			V -> L (in dbSNP:rs12907128). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9922388}.		neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AGTGGCAGCACGGAGAGCTGG	0.706													C|||	3078	0.614617	0.3744	0.4841	5008	,	,		15867	0.8482		0.5974	False		,,,				2504	0.8088				p.V751L		Atlas-SNP	.											IGDCC3,NS,carcinoma,0,1	IGDCC3	82	1	0			c.G2251T						PASS	.	C	LEU/VAL	1879,2519		420,1039,740	14.0	18.0	17.0		2251	-5.2	0.0	15	dbSNP_121	17	4960,3636		1438,2084,776	yes	missense	IGDCC3	NM_004884.3	32	1858,3123,1516	AA,AC,CC		42.2987,42.724,47.368	benign	751/815	65621441	6839,6155	2199	4298	6497	SO:0001583	missense	9543	exon14			GCAGCACGGAGAG	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2251G>T	15.37:g.65621441C>A	ENSP00000332773:p.Val751Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	37	CCDS10205.1	1281	0.5865384615384616	174	0.35365853658536583	183	0.505524861878453	473	0.8269230769230769	451	0.5949868073878628	C	10.92	1.488150	0.26686	0.42724	0.577013	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.64618	-0.11	5.69	-5.23	0.02798	.	0.954563	0.08665	N	0.911846	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.39210	-0.9625	9	0.22706	T	0.39	-4.3374	0.4385	0.00483	0.3463:0.2056:0.1194:0.3287	rs12907128;rs17854187;rs60161490;rs12907128	751	Q8IVU1	IGDC3_HUMAN	L	751;574	ENSP00000332773:V751L	ENSP00000332773:V751L	V	-	1	0	IGDCC3	63408494	0.638000	0.27225	0.000000	0.03702	0.005000	0.04900	-0.442000	0.06871	-0.789000	0.04498	-1.181000	0.01715	GTG	C|0.461;A|0.539	0.539	strong		0.706	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
OSBPL5	114879	hgsc.bcm.edu	37	11	3141744	3141744	+	Silent	SNP	C	C	T	rs34950527	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:3141744C>T	ENST00000263650.7	-	6	672	c.513G>A	c.(511-513)ctG>ctA	p.L171L	OSBPL5_ENST00000389989.3_Intron|OSBPL5_ENST00000525498.1_Intron|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000348039.5_Intron	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	171	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CGCAGCAGTGCAGCAGCACCG	0.642													T|||	611	0.122005	0.1558	0.1297	5008	,	,		17968	0.0258		0.1451	False		,,,				2504	0.1462				p.L171L		Atlas-SNP	.											OSBPL5,NS,carcinoma,0,1	OSBPL5	78	1	0			c.G513A						PASS	.	T	,,	673,3731	761.0+/-413.0	46,581,1575	74.0	64.0	67.0		,513,	2.4	1.0	11	dbSNP_126	67	1076,7520	768.1+/-407.6	79,918,3301	no	intron,coding-synonymous,intron	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	,,	125,1499,4876	TT,TC,CC		12.5174,15.2816,13.4538	,,	,171/880,	3141744	1749,11251	2202	4298	6500	SO:0001819	synonymous_variant	114879	exon6			GCAGTGCAGCAGC	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.513G>A	11.37:g.3141744C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																			C|0.870;T|0.130	0.130	strong		0.642	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
DDOST	1650	hgsc.bcm.edu	37	1	20980799	20980799	+	Silent	SNP	G	G	A	rs34189097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20980799G>A	ENST00000375048.3	-	7	867	c.762C>T	c.(760-762)cgC>cgT	p.R254R	DDOST_ENST00000602624.2_Silent_p.R237R|PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000415136.2_Silent_p.R217R	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	254					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-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;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TGAAGATGACGCGGGCATTGT	0.602													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17003	0.0		0.0	False		,,,				2504	0.001				p.R254R		Atlas-SNP	.											DDOST,caecum,carcinoma,-1,1	DDOST	30	1	0			c.C762T						PASS	.	G		1,4391		0,1,2195	50.0	42.0	45.0		762	-2.0	1.0	1	dbSNP_126	45	9,8553		0,9,4272	no	coding-synonymous	DDOST	NM_005216.4		0,10,6467	AA,AG,GG		0.1051,0.0228,0.0772		254/457	20980799	10,12944	2196	4281	6477	SO:0001819	synonymous_variant	1650	exon7			GATGACGCGGGCA	D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.762C>T	1.37:g.20980799G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	31	0.292453	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
SBDS	51119	hgsc.bcm.edu	37	7	66459256	66459256	+	Silent	SNP	T	T	C	rs1061695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:66459256T>C	ENST00000246868.2	-	2	384	c.201A>G	c.(199-201)aaA>aaG	p.K67K	TYW1_ENST00000359626.5_5'Flank	NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	67			K -> E (in SDS). {ECO:0000269|PubMed:12496757}.		bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						GATCTTCCTTTTTGGCAACCT	0.433			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome				T|||	252	0.0503195	0.0098	0.1023	5008	,	,		18219	0.0079		0.1262	False		,,,				2504	0.0337				p.K67K		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.A201G						PASS	.	T		112,4294	86.8+/-125.4	0,112,2091	150.0	129.0	136.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	201	2.0	1.0	7	dbSNP_86	136	955,7645	206.2+/-248.4	58,839,3403	no	coding-synonymous	SBDS	NM_016038.2		58,951,5494	CC,CT,TT		11.1047,2.542,8.2039		67/251	66459256	1067,11939	2203	4300	6503	SO:0001819	synonymous_variant	51119	exon2	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	TTCCTTTTTGGCA	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.201A>G	7.37:g.66459256T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_016038	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	37	CCDS5537.1																																																																																			T|0.923;C|0.077	0.077	strong		0.433	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	
SLIT3	6586	hgsc.bcm.edu	37	5	168176517	168176517	+	Silent	SNP	A	A	G	rs2304035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:168176517A>G	ENST00000519560.1	-	19	2516	c.2097T>C	c.(2095-2097)atT>atC	p.I699I	SLIT3_ENST00000332966.8_Silent_p.I699I|SLIT3_ENST00000404867.3_Silent_p.I699I	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	699	LRRCT 3.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTGGATGGGAATCTCCTTGA	0.582													A|||	2504	0.5	0.5787	0.5533	5008	,	,		19809	0.496		0.3797	False		,,,				2504	0.4836				p.I699I	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.T2097C						PASS	.	A		2425,1981	617.7+/-393.0	688,1049,466	101.0	98.0	99.0		2097	-10.0	0.7	5	dbSNP_100	99	3174,5426	481.3+/-370.6	599,1976,1725	yes	coding-synonymous	SLIT3	NM_003062.2		1287,3025,2191	GG,GA,AA		36.907,44.9614,43.0494		699/1524	168176517	5599,7407	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon19			GATGGGAATCTCC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2097T>C	5.37:g.168176517A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			A|0.541;G|0.459	0.459	strong		0.582	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
DNM2	1785	hgsc.bcm.edu	37	19	10939884	10939884	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10939884T>C	ENST00000355667.6	+	19	2311	c.2231T>C	c.(2230-2232)gTg>gCg	p.V744A	DNM2_ENST00000408974.4_Missense_Mutation_p.V740A|DNM2_ENST00000359692.6_Missense_Mutation_p.V740A|DNM2_ENST00000585892.1_Missense_Mutation_p.V744A|DNM2_ENST00000389253.4_Missense_Mutation_p.V744A|DNM2_ENST00000314646.5_Missense_Mutation_p.V744A	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	744	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)			ACCAGCACTGTGTCCACGCCT	0.637			"""F, N, Splice, Mis, O"""		ETP ALL																																p.V744A		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T2231C						PASS	.						86.0	64.0	71.0					19																	10939884		2203	4300	6503	SO:0001583	missense	1785	exon19			GCACTGTGTCCAC		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.2231T>C	19.37:g.10939884T>C	ENSP00000347890:p.Val744Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254187	0.22965	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	D;D;D;D	0.92911	-3.13;-3.06;-3.12;-3.12	4.83	4.83	0.62350	GTPase effector domain, GED (1);	0.361801	0.25241	N	0.032084	D	0.87485	0.6189	L	0.42245	1.32	0.37324	D	0.909672	B;B;B;B;B;B;B	0.14012	0.009;0.004;0.005;0.002;0.002;0.0;0.002	B;B;B;B;B;B;B	0.15052	0.005;0.012;0.009;0.005;0.008;0.005;0.003	D	0.85541	0.1215	10	0.59425	D	0.04	.	8.187	0.31346	0.0:0.0927:0.0:0.9073	.	338;744;473;740;740;744;744	Q8N1K8;F5H4R9;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;.;DYN2_HUMAN;.	A	740;740;744;744;744;351	ENSP00000386192:V740A;ENSP00000352721:V744A;ENSP00000373905:V744A;ENSP00000313164:V744A	ENSP00000313164:V744A	V	+	2	0	DNM2	10800884	0.996000	0.38824	0.990000	0.47175	0.005000	0.04900	5.022000	0.64078	1.808000	0.52836	0.377000	0.23210	GTG	.	.	none		0.637	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
CPNE1	8904	hgsc.bcm.edu	37	20	34220755	34220755	+	Missense_Mutation	SNP	C	C	T	rs11543244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34220755C>T	ENST00000317619.3	-	4	485	c.91G>A	c.(91-93)Gtc>Atc	p.V31I	CPNE1_ENST00000397445.1_Missense_Mutation_p.V31I|CPNE1_ENST00000397442.1_Missense_Mutation_p.V31I|RP1-309K20.6_ENST00000541176.2_3'UTR|CPNE1_ENST00000397443.1_Missense_Mutation_p.V31I|CPNE1_ENST00000352393.4_Missense_Mutation_p.V31I|CPNE1_ENST00000317677.5_Missense_Mutation_p.V36I|CPNE1_ENST00000397446.1_Missense_Mutation_p.V31I			Q99829	CPNE1_HUMAN	copine I	31	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGTAAAAGGACGCAGAGTGGG	0.552													C|||	397	0.0792732	0.0658	0.0259	5008	,	,		20843	0.0516		0.0517	False		,,,				2504	0.1922				p.V36I		Atlas-SNP	.											.	CPNE1	44	.	0			c.G106A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	280,4126	157.4+/-190.3	11,258,1934	161.0	153.0	156.0		91,106,91,91,91,91	4.7	1.0	20	dbSNP_120	156	419,8181	130.2+/-188.1	14,391,3895	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	29,29,29,29,29,29	25,649,5829	TT,TC,CC		4.8721,6.355,5.3744	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	31/537,36/543,31/538,31/538,31/538,31/538	34220755	699,12307	2203	4300	6503	SO:0001583	missense	8904	exon2			AAAGGACGCAGAG	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.91G>A	20.37:g.34220755C>T	ENSP00000326126:p.Val31Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	121	0.0554029304029304	43	0.08739837398373984	13	0.03591160220994475	22	0.038461538461538464	43	0.05672823218997362	C	24.6	4.550870	0.86127	0.06355	0.048721	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570;ENST00000412056;ENST00000414664;ENST00000416778;ENST00000439806;ENST00000420363;ENST00000434795;ENST00000440240;ENST00000458038;ENST00000437100;ENST00000414711;ENST00000435747	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.66	4.66	0.58398	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000002	T	0.05823	0.0152	M	0.71920	2.185	0.22629	P	0.99891048	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0	D;D;D;D;D	0.85130	0.936;0.936;0.936;0.924;0.997	T	0.41752	-0.9491	9	0.62326	D	0.03	-2.1566	15.7329	0.77819	0.0:0.8631:0.1369:0.0	rs11543244;rs52809749;rs11543244	36;31;31;31;35	B0QZ18;E7ENH5;A6PVH9;Q99829;Q59EI4	.;.;.;CPNE1_HUMAN;.	I	31;36;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31	ENSP00000336945:V31I;ENSP00000317257:V36I;ENSP00000326126:V31I;ENSP00000380588:V31I;ENSP00000380587:V31I;ENSP00000380585:V31I;ENSP00000380584:V31I;ENSP00000415597:V31I;ENSP00000390626:V31I;ENSP00000416962:V31I;ENSP00000404355:V31I;ENSP00000389662:V31I;ENSP00000387434:V31I;ENSP00000401915:V31I;ENSP00000409794:V31I;ENSP00000397638:V31I;ENSP00000390141:V31I;ENSP00000391483:V31I;ENSP00000409955:V31I;ENSP00000412806:V31I	ENSP00000326126:V31I	V	-	1	0	CPNE1	33684169	0.991000	0.36638	0.984000	0.44739	0.969000	0.65631	3.784000	0.55416	2.665000	0.90641	0.637000	0.83480	GTC	T|0.057;C|0.943	0.057	strong		0.552	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
PKD1	5310	hgsc.bcm.edu	37	16	2165395	2165395	+	Missense_Mutation	SNP	G	G	A	rs138575342		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2165395G>A	ENST00000262304.4	-	10	2289	c.2081C>T	c.(2080-2082)cCc>cTc	p.P694L	PKD1_ENST00000423118.1_Missense_Mutation_p.P694L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	694					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						CTGCGCGGGGGGCCCCGCGGG	0.682																																					p.P694L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	1	0			c.C2081T						scavenged	.						3.0	5.0	4.0					16																	2165395		1659	3504	5163	SO:0001583	missense	5310	exon10			GCGGGGGGCCCCG	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.2081C>T	16.37:g.2165395G>A	ENSP00000262304:p.Pro694Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	21	0.3	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.606219	0.46527	.	.	ENSG00000008710	ENST00000262304;ENST00000423118	T;T	0.37915	1.17;1.17	5.17	5.17	0.71159	Polycystin cation channel (1);	0.333966	0.29587	N	0.011721	T	0.57725	0.2073	M	0.76002	2.32	0.52099	D	0.999947	D;D	0.89917	1.0;1.0	D;D	0.79108	0.984;0.992	T	0.61202	-0.7110	10	0.72032	D	0.01	.	10.8459	0.46743	0.0877:0.0:0.9123:0.0	.	694;694	P98161-3;P98161	.;PKD1_HUMAN	L	694	ENSP00000262304:P694L;ENSP00000399501:P694L	ENSP00000262304:P694L	P	-	2	0	PKD1	2105396	0.999000	0.42202	0.746000	0.31095	0.102000	0.19082	4.544000	0.60691	2.384000	0.81235	0.557000	0.71058	CCC	.	.	weak		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
ENTPD3	956	hgsc.bcm.edu	37	3	40468896	40468896	+	Missense_Mutation	SNP	C	C	T	rs1047855	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:40468896C>T	ENST00000301825.3	+	11	1605	c.1487C>T	c.(1486-1488)gCg>gTg	p.A496V	ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3_ENST00000456402.1_Missense_Mutation_p.A496V|ENTPD3-AS1_ENST00000452768.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	496			A -> V (in dbSNP:rs1047855). {ECO:0000269|PubMed:9676430}.		nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TTCTTCACAGCGGCAGCCTTG	0.537													C|||	1392	0.277955	0.0378	0.2867	5008	,	,		21086	0.4881		0.2883	False		,,,				2504	0.3691				p.A496V		Atlas-SNP	.											ENTPD3,NS,carcinoma,-1,1	ENTPD3	48	1	0			c.C1487T						scavenged	.	C	VAL/ALA	376,4030	191.9+/-217.4	23,330,1850	118.0	102.0	107.0		1487	-1.6	0.0	3	dbSNP_86	107	2551,6049	416.3+/-352.1	397,1757,2146	yes	missense	ENTPD3	NM_001248.2	64	420,2087,3996	TT,TC,CC		29.6628,8.5338,22.505	benign	496/530	40468896	2927,10079	2203	4300	6503	SO:0001583	missense	956	exon11			TCACAGCGGCAGC	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.1487C>T	3.37:g.40468896C>T	ENSP00000301825:p.Ala496Val	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	180	123	0.683333	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	622	0.2847985347985348	30	0.06097560975609756	117	0.32320441988950277	255	0.4458041958041958	220	0.29023746701846964	C	3.599	-0.081966	0.07141	0.085338	0.296628	ENSG00000168032	ENST00000301825;ENST00000456402	T;T	0.09817	2.94;2.94	5.18	-1.64	0.08318	.	0.634926	0.15141	N	0.278298	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.43877	-0.9364	9	0.16896	T	0.51	-0.097	5.6082	0.17391	0.0:0.403:0.266:0.331	rs1047855;rs3733166;rs52835170;rs58911447;rs1047855	496	O75355	ENTP3_HUMAN	V	496	ENSP00000301825:A496V;ENSP00000401565:A496V	ENSP00000301825:A496V	A	+	2	0	ENTPD3	40443900	0.014000	0.17966	0.000000	0.03702	0.167000	0.22549	0.238000	0.18004	-0.395000	0.07715	-0.140000	0.14226	GCG	C|0.754;T|0.246	0.246	strong		0.537	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
UEVLD	55293	hgsc.bcm.edu	37	11	18555901	18555901	+	Silent	SNP	C	C	G	rs56151250	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18555901C>G	ENST00000396197.3	-	11	1252	c.1224G>C	c.(1222-1224)gtG>gtC	p.V408V	UEVLD_ENST00000320750.6_Intron|UEVLD_ENST00000535484.1_Intron|UEVLD_ENST00000379387.4_Silent_p.V386V|UEVLD_ENST00000543987.1_Intron|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000540666.1_5'UTR	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						ATACAGAATGCACTTTCTTCT	0.313													C|||	1262	0.251997	0.0469	0.2363	5008	,	,		17778	0.4415		0.1958	False		,,,				2504	0.4029				p.V408V		Atlas-SNP	.											.	UEVLD	58	.	0			c.G1224C						PASS	.	C	,	255,3441		7,241,1600	109.0	95.0	99.0		1224,	-3.6	1.0	11	dbSNP_129	99	1263,6899		116,1031,2934	no	coding-synonymous,intron	UEVLD	NM_001040697.1,NM_018314.3	,	123,1272,4534	GG,GC,CC		15.4741,6.8994,12.8015	,	408/472,	18555901	1518,10340	1848	4081	5929	SO:0001819	synonymous_variant	55293	exon11			AGAATGCACTTTC	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1224G>C	11.37:g.18555901C>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_001040697		Silent	SNP	ENST00000396197.3	37	CCDS41624.1																																																																																			C|0.794;G|0.206	0.206	strong		0.313	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
CPZ	8532	hgsc.bcm.edu	37	4	8603117	8603117	+	Missense_Mutation	SNP	A	A	T	rs35993494	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:8603117A>T	ENST00000360986.4	+	3	563	c.389A>T	c.(388-390)cAg>cTg	p.Q130L	CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000315782.6_Missense_Mutation_p.Q119L|CPZ_ENST00000506287.1_3'UTR|CPZ_ENST00000429646.2_5'Flank	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	130	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		Q -> L (in dbSNP:rs35993494).		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						GAGGTCTGCCAGCCCGCCTTC	0.682													A|||	506	0.101038	0.0408	0.0749	5008	,	,		16996	0.0446		0.162	False		,,,				2504	0.1963				p.Q130L		Atlas-SNP	.											.	CPZ	95	.	0			c.A389T						PASS	.	A	LEU/GLN,,LEU/GLN	321,4077		9,303,1887	24.0	28.0	27.0		389,,356	0.8	1.0	4	dbSNP_126	27	1571,7021		157,1257,2882	yes	missense,utr-5,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	113,,113	166,1560,4769	TT,TA,AA		18.2845,7.2988,14.5651	benign,,benign	130/653,,119/642	8603117	1892,11098	2199	4296	6495	SO:0001583	missense	8532	exon3			TCTGCCAGCCCGC	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.389A>T	4.37:g.8603117A>T	ENSP00000354255:p.Gln130Leu	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	196	0.08974358974358974	20	0.04065040650406504	29	0.08011049723756906	22	0.038461538461538464	125	0.16490765171503957	A	5.045	0.193960	0.09599	0.072988	0.182845	ENSG00000109625	ENST00000360986;ENST00000315782	T;T	0.75821	-0.97;-0.97	3.41	0.837	0.18896	Frizzled domain (5);	0.788238	0.11423	N	0.565573	T	0.00109	0.0003	N	0.05441	-0.05	0.24497	P	0.99427309	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.05194	-1.0900	9	0.02654	T	1	-21.0897	4.2433	0.10660	0.3522:0.0:0.1083:0.5395	rs35993494;rs61734028	119;130	Q66K79-2;Q66K79	.;CBPZ_HUMAN	L	130;119	ENSP00000354255:Q130L;ENSP00000315074:Q119L	ENSP00000315074:Q119L	Q	+	2	0	CPZ	8654017	0.176000	0.23096	0.977000	0.42913	0.179000	0.23085	0.639000	0.24690	-0.007000	0.14345	0.459000	0.35465	CAG	A|0.884;T|0.116	0.116	strong		0.682	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
TBCD	6904	hgsc.bcm.edu	37	17	80899349	80899349	+	Missense_Mutation	SNP	T	T	C	rs2292969	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80899349T>C	ENST00000355528.4	+	38	3684	c.3554T>C	c.(3553-3555)cTg>cCg	p.L1185P	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.L1223P	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1185			L -> P (in dbSNP:rs2292969).		'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			AGGCCCCAGCTGGTGCCCCAG	0.622													T|||	23	0.00459265	0.0	0.0058	5008	,	,		18723	0.002		0.0089	False		,,,				2504	0.0082				p.L1185P		Atlas-SNP	.											.	TBCD	94	.	0			c.T3554C						PASS	.	T	PRO/LEU	6,4162		0,6,2078	44.0	58.0	53.0		3554	5.0	1.0	17	dbSNP_100	53	48,8376		1,46,4165	yes	missense	TBCD	NM_005993.4	98	1,52,6243	CC,CT,TT		0.5698,0.144,0.4288	probably-damaging	1185/1193	80899349	54,12538	2084	4212	6296	SO:0001583	missense	6904	exon38			CCCAGCTGGTGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3554T>C	17.37:g.80899349T>C	ENSP00000347719:p.Leu1185Pro	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	2|2	0.0034965034965034965|0.0034965034965034965	5|5	0.006596306068601583|0.006596306068601583	T|T	13.78|13.78	2.340685|2.340685	0.41498|0.41498	0.00144|0.00144	0.005698|0.005698	ENSG00000141556|ENSG00000141556	ENST00000355528;ENST00000539345|ENST00000334614	T|.	0.22336|.	1.96|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.369474	.|0.21711	.|N	.|0.070272	T|T	0.65481|0.65481	0.2695|0.2695	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	B|.	0.26744|.	0.158|.	B|.	0.26202|.	0.067|.	T|T	0.70096|0.70096	-0.4966|-0.4966	8|6	.|.	.|.	.|.	.|.	11.3315|11.3315	0.49479|0.49479	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2292969;rs2292969|rs2292969;rs2292969	1185|.	Q9BTW9|.	TBCD_HUMAN|.	P|R	1185;177|973	ENSP00000347719:L1185P|.	.|.	L|W	+|+	2|1	0|0	TBCD|TBCD	78492638|78492638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	3.885000|3.885000	0.56182|0.56182	2.015000|2.015000	0.59207|0.59207	0.460000|0.460000	0.39030|0.39030	CTG|TGG	T|0.994;C|0.006	0.006	strong		0.622	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745129	135745129	+	Missense_Mutation	SNP	G	G	A	rs16831235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:135745129G>A	ENST00000375845.3	-	7	1343	c.1313C>T	c.(1312-1314)aCt>aTt	p.T438I	MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.T325I|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.T455I	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	180	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	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	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39914748	39914748	+	Missense_Mutation	SNP	G	G	A	rs31726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39914748G>A	ENST00000409794.3	+	19	3825	c.2975G>A	c.(2974-2976)aGa>aAa	p.R992K	PLEKHG2_ENST00000409797.2_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R933K|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R963K	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	992			R -> K (in dbSNP:rs31726). {ECO:0000269|PubMed:14702039, 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)			CCTGAGCATAGAAGTCACATG	0.562													G|||	2884	0.575879	0.6702	0.4798	5008	,	,		19876	0.5962		0.4911	False		,,,				2504	0.5828				p.R992K		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G2975A						PASS	.	G	LYS/ARG	2855,1551	669.7+/-402.2	926,1003,274	141.0	140.0	140.0		2975	0.4	0.0	19	dbSNP_76	140	3942,4658	548.4+/-385.4	933,2076,1291	yes	missense	PLEKHG2	NM_022835.2	26	1859,3079,1565	AA,AG,GG		45.8372,35.202,47.7395	benign	992/1387	39914748	6797,6209	2203	4300	6503	SO:0001583	missense	64857	exon19			AGCATAGAAGTCA	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.2975G>A	19.37:g.39914748G>A	ENSP00000386733:p.Arg992Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	1168|1168	0.5347985347985348|0.5347985347985348	318|318	0.6463414634146342|0.6463414634146342	173|173	0.47790055248618785|0.47790055248618785	313|313	0.5472027972027972|0.5472027972027972	364|364	0.48021108179419525|0.48021108179419525	G|G	12.08|12.08	1.830209|1.830209	0.32329|0.32329	0.64798|0.64798	0.458372|0.458372	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.71461	.|-0.43;-0.48;-0.57	3.82|3.82	0.404|0.404	0.16355|0.16355	.|.	.|0.460484	.|0.18621	.|N	.|0.135848	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.34521|0.34521	1.04|1.04	0.51233|0.51233	P|P	8.699999999994823E-5|8.699999999994823E-5	.|B;B;B	.|0.11235	.|0.004;0.001;0.002	.|B;B;B	.|0.13407	.|0.009;0.002;0.007	T|T	0.45687|0.45687	-0.9244|-0.9244	4|8	.|.	.|.	.|.	.|.	5.8143|5.8143	0.18484|0.18484	0.1091:0.3853:0.5057:0.0|0.1091:0.3853:0.5057:0.0	rs31726;rs550284;rs3746078;rs17856424;rs58173412;rs31726|rs31726;rs550284;rs3746078;rs17856424;rs58173412;rs31726	.|963;992;933	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	K|K	860|992;963;933	.|ENSP00000386733:R992K;ENSP00000392906:R963K;ENSP00000408857:R933K	.|.	E|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44606588|44606588	0.002000|0.002000	0.14202|0.14202	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	0.589000|0.589000	0.23939|0.23939	0.200000|0.200000	0.20447|0.20447	-0.274000|-0.274000	0.10170|0.10170	GAA|AGA	G|0.463;A|0.537	0.537	strong		0.562	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
ODC1	4953	hgsc.bcm.edu	37	2	10580967	10580967	+	Silent	SNP	G	G	A	rs1049500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10580967G>A	ENST00000234111.4	-	12	1779	c.1269C>T	c.(1267-1269)ccC>ccT	p.P423P	ODC1_ENST00000405333.1_Silent_p.P423P	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	423					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	GTGGGAAGTCGGGGTTCTGGA	0.517													G|||	1363	0.272165	0.3018	0.1254	5008	,	,		17561	0.5694		0.0547	False		,,,				2504	0.2536				p.P423P		Atlas-SNP	.											.	ODC1	40	.	0			c.C1269T						PASS	.	G		1058,3348	388.9+/-327.1	130,798,1275	93.0	92.0	92.0		1269	-8.9	0.0	2	dbSNP_86	92	326,8274	113.5+/-173.5	6,314,3980	no	coding-synonymous	ODC1	NM_002539.1		136,1112,5255	AA,AG,GG		3.7907,24.0127,10.6412		423/462	10580967	1384,11622	2203	4300	6503	SO:0001819	synonymous_variant	4953	exon12			GAAGTCGGGGTTC		CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1269C>T	2.37:g.10580967G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_002539	Q53TU3|Q6LDS9	Silent	SNP	ENST00000234111.4	37	CCDS1672.1																																																																																			G|0.827;A|0.173	0.173	strong		0.517	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2		
KRT40	125115	hgsc.bcm.edu	37	17	39137387	39137387	+	Missense_Mutation	SNP	C	C	T	rs2010027	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67	30	0.447761	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	
ZFHX3	463	hgsc.bcm.edu	37	16	72832135	72832135	+	Silent	SNP	T	T	A	rs740178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72832135T>A	ENST00000268489.5	-	9	5118	c.4446A>T	c.(4444-4446)gcA>gcT	p.A1482A	ZFHX3_ENST00000397992.5_Silent_p.A568A	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1482					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)				TATGGTCCTCTGCCAGAGTGG	0.537													A|||	4438	0.886182	0.9917	0.8343	5008	,	,		18728	0.9603		0.7952	False		,,,				2504	0.7975				p.A1482A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A4446T						PASS	.	A	,	4219,177	114.6+/-152.6	2023,173,2	117.0	121.0	119.0		1704,4446	-11.6	0.2	16	dbSNP_86	119	6890,1710	309.7+/-309.5	2773,1344,183	no	coding-synonymous,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	4796,1517,185	AA,AT,TT		19.8837,4.0264,14.5199	,	568/2790,1482/3704	72832135	11109,1887	2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			GTCCTCTGCCAGA	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.4446A>T	16.37:g.72832135T>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			T|0.159;A|0.841	0.841	strong		0.537	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
DIP2A	23181	hgsc.bcm.edu	37	21	47985655	47985655	+	Silent	SNP	C	C	T	rs2248636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47985655C>T	ENST00000417564.2	+	36	4215	c.4194C>T	c.(4192-4194)acC>acT	p.T1398T	DIP2A_ENST00000318711.7_Silent_p.T1399T|DIP2A_ENST00000400274.1_Silent_p.T1394T|DIP2A_ENST00000479654.1_3'UTR			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1398					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)		ACAATGCCACCGGGTACTACA	0.572													C|||	601	0.120008	0.0363	0.0634	5008	,	,		16886	0.3254		0.0815	False		,,,				2504	0.1012				p.T1398T		Atlas-SNP	.											.	DIP2A	332	.	0			c.C4194T						PASS	.	C	,	198,3842		7,184,1829	45.0	47.0	46.0		4182,4194	-10.9	0.4	21	dbSNP_100	46	565,7805		16,533,3636	no	coding-synonymous,coding-synonymous	DIP2A	NM_001146116.1,NM_015151.3	,	23,717,5465	TT,TC,CC		6.7503,4.901,6.1483	,	1394/1568,1398/1572	47985655	763,11647	2020	4185	6205	SO:0001819	synonymous_variant	23181	exon36			TGCCACCGGGTAC	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.4194C>T	21.37:g.47985655C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			C|0.861;T|0.139	0.139	strong		0.572	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
INMT	11185	hgsc.bcm.edu	37	7	30791848	30791848	+	Missense_Mutation	SNP	G	G	A	rs4723010	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:30791848G>A	ENST00000013222.5	+	1	98	c.82G>A	c.(82-84)Gat>Aat	p.D28N	INMT_ENST00000409539.1_Missense_Mutation_p.D28N|INMT_ENST00000484180.1_Intron|INMT-FAM188B_ENST00000458257.1_Missense_Mutation_p.D28N	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	28			D -> N (in dbSNP:rs4723010). {ECO:0000269|PubMed:15489334}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CTACAGCTTCGATGGCAGCCC	0.567													G|||	1296	0.258786	0.2784	0.3314	5008	,	,		19963	0.0367		0.3936	False		,,,				2504	0.271				p.D28N		Atlas-SNP	.											.	INMT	38	.	0			c.G82A						PASS	.	G	ASN/ASP,ASN/ASP	1249,3157	428.9+/-342.0	184,881,1138	118.0	112.0	114.0		82,82	-2.4	0.0	7	dbSNP_111	114	3384,5216	501.6+/-375.5	681,2022,1597	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	23,23	865,2903,2735	AA,AG,GG		39.3488,28.3477,35.622	benign,benign	28/263,28/264	30791848	4633,8373	2203	4300	6503	SO:0001583	missense	11185	exon1			AGCTTCGATGGCA		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.82G>A	7.37:g.30791848G>A	ENSP00000013222:p.Asp28Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001199219	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	561	0.25686813186813184	126	0.25609756097560976	122	0.3370165745856354	15	0.026223776223776224	298	0.39313984168865435	G	5.964	0.361850	0.11296	0.283477	0.393488	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.09163	3.01;3.01	3.28	-2.41	0.06562	.	1.281540	0.05467	N	0.552416	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.009	T	0.48703	-0.9012	9	0.15499	T	0.54	0.7645	1.7368	0.02944	0.2776:0.1371:0.4455:0.1398	rs4723010;rs17780446;rs4723010	28;28	B8ZZ69;O95050	.;INMT_HUMAN	N	28	ENSP00000013222:D28N;ENSP00000386961:D28N	ENSP00000013222:D28N	D	+	1	0	INMT	30758373	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.185000	0.09684	-0.566000	0.06054	-0.140000	0.14226	GAT	G|0.696;A|0.304	0.304	strong		0.567	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
FLG	2312	hgsc.bcm.edu	37	1	152283283	152283283	+	Missense_Mutation	SNP	C	C	T	rs11586631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152283283C>T	ENST00000368799.1	-	3	4114	c.4079G>A	c.(4078-4080)cGc>cAc	p.R1360H	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1360	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)			CTGCTGGTGGCGGGATCCATG	0.537									Ichthyosis				C|||	1441	0.28774	0.0144	0.389	5008	,	,		20885	0.5823		0.1421	False		,,,				2504	0.4315				p.R1360H		Atlas-SNP	.											.	FLG	900	.	0			c.G4079A						PASS	.	C	HIS/ARG	163,4243	109.1+/-147.4	2,159,2042	375.0	355.0	362.0		4079	-7.6	0.0	1	dbSNP_120	362	1237,7359	248.6+/-276.2	97,1043,3158	no	missense	FLG	NM_002016.1	29	99,1202,5200	TT,TC,CC		14.3904,3.6995,10.7676	benign	1360/4062	152283283	1400,11602	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGGCGGGATC	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.4079G>A	1.37:g.152283283C>T	ENSP00000357789:p.Arg1360His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	158	92	0.582278	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	505	0.23122710622710624	7	0.014227642276422764	104	0.287292817679558	300	0.5244755244755245	94	0.12401055408970976	C	11.44	1.640902	0.29157	0.036995	0.143904	ENSG00000143631	ENST00000368799	T	0.01474	4.85	3.78	-7.56	0.01322	.	.	.	.	.	T	0.00300	0.0009	L	0.29908	0.895	0.80722	P	0.0	B	0.33288	0.406	B	0.24155	0.051	T	0.49194	-0.8965	8	0.15066	T	0.55	.	1.3944	0.02257	0.1228:0.3039:0.2443:0.329	rs11586631	1360	P20930	FILA_HUMAN	H	1360	ENSP00000357789:R1360H	ENSP00000357789:R1360H	R	-	2	0	FLG	150549907	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-6.306000	0.00071	-1.837000	0.01189	-0.300000	0.09419	CGC	C|0.851;T|0.149	0.149	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC16	94025	hgsc.bcm.edu	37	19	9075635	9075635	+	Silent	SNP	G	G	A	rs2547070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9075635G>A	ENST00000397910.4	-	3	12014	c.11811C>T	c.(11809-11811)tcC>tcT	p.S3937S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3938	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						TGTCTGTGGTGGACTCAGAAG	0.493													G|||	1054	0.210463	0.0628	0.2046	5008	,	,		20997	0.249		0.3101	False		,,,				2504	0.272				p.S3937S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11811T						PASS	.	G		403,3505		23,357,1574	69.0	65.0	66.0		11811	-0.2	0.0	19	dbSNP_100	66	2385,5881		341,1703,2089	no	coding-synonymous	MUC16	NM_024690.2		364,2060,3663	AA,AG,GG		28.8531,10.3122,22.9013		3937/14508	9075635	2788,9386	1954	4133	6087	SO:0001819	synonymous_variant	94025	exon3			TGTGGTGGACTCA	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.11811C>T	19.37:g.9075635G>A		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	237	127	0.535865	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.788;A|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PIF1	80119	hgsc.bcm.edu	37	15	65108504	65108504	+	Missense_Mutation	SNP	A	A	T	rs17802279	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65108504A>T	ENST00000268043.4	-	13	2013	c.1919T>A	c.(1918-1920)aTc>aAc	p.I640N	PIF1_ENST00000559239.1_Missense_Mutation_p.I640N|PIF1_ENST00000333425.6_Intron					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GGCTCAGAGGATTGGGTCCAT	0.587													T|||	1387	0.276957	0.2587	0.2608	5008	,	,		16924	0.1101		0.4891	False		,,,				2504	0.2669				p.I640N		Atlas-SNP	.											.	PIF1	43	.	0			c.T1919A						PASS	.	T	ASN/ILE	1355,3049	692.3+/-405.5	188,979,1035	113.0	99.0	103.0		1919	3.3	0.4	15	dbSNP_123	103	3983,4615	600.4+/-394.2	934,2115,1250	yes	missense	PIF1	NM_025049.2	149	1122,3094,2285	TT,TA,AA		46.3247,30.7675,41.0552	benign	640/642	65108504	5338,7664	2202	4299	6501	SO:0001583	missense	80119	exon13			CAGAGGATTGGGT	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1919T>A	15.37:g.65108504A>T	ENSP00000268043:p.Ile640Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	664	0.304029304029304	141	0.2865853658536585	107	0.2955801104972376	48	0.08391608391608392	368	0.48548812664907653	T	0.222	-1.028031	0.02045	0.307675	0.463247	ENSG00000140451	ENST00000268043	T	0.63580	-0.05	5.66	3.27	0.37495	.	.	.	.	.	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	0.44817	-0.9303	8	0.02654	T	1	.	2.6979	0.05140	0.1466:0.0805:0.1532:0.6198	rs17802279;rs17802279	640	Q9H611	PIF1_HUMAN	N	640	ENSP00000268043:I640N	ENSP00000268043:I640N	I	-	2	0	PIF1	62895557	0.947000	0.32204	0.431000	0.26735	0.605000	0.37080	0.543000	0.23237	0.070000	0.16634	-0.257000	0.10917	ATC	A|0.627;N|0.001	.	strong		0.587	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124634	26124634	+	Silent	SNP	C	C	T	rs4645	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26124634C>T	ENST00000602637.1	+	1	204	c.174C>T	c.(172-174)taC>taT	p.Y58Y	HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.Y58Y|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	58						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						TGTTAGAGTACCTGACCGCCG	0.667													C|||	402	0.0802716	0.0076	0.1066	5008	,	,		16130	0.0139		0.2127	False		,,,				2504	0.092				p.Y58Y		Atlas-SNP	.											HIST1H2AC,NS,carcinoma,+1,1	HIST1H2AC	29	1	0			c.C174T						PASS	.	C		208,4198		8,192,2003	53.0	54.0	54.0		174	3.0	1.0	6	dbSNP_52	54	1863,6737		201,1461,2638	no	coding-synonymous	HIST1H2AC	NM_003512.3		209,1653,4641	TT,TC,CC		21.6628,4.7208,15.9234		58/131	26124634	2071,10935	2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			AGAGTACCTGACC	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.174C>T	6.37:g.26124634C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			C|0.857;T|0.143	0.143	strong		0.667	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
TTC38	55020	hgsc.bcm.edu	37	22	46685380	46685380	+	Silent	SNP	C	C	T	rs11705624	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46685380C>T	ENST00000381031.3	+	12	1240	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	TTC38_ENST00000445282.2_Silent_p.D330D	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	388						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						AGGCTGAGGACGGGAACCCTG	0.692													C|||	204	0.0407348	0.0083	0.0576	5008	,	,		14688	0.001		0.1193	False		,,,				2504	0.0327				p.D388D		Atlas-SNP	.											.	TTC38	40	.	0			c.C1164T						PASS	.	C		82,4088		1,80,2004	28.0	36.0	33.0		1164	-6.7	0.0	22	dbSNP_120	33	867,7541		48,771,3385	no	coding-synonymous	TTC38	NM_017931.2		49,851,5389	TT,TC,CC		10.3116,1.9664,7.5449		388/470	46685380	949,11629	2085	4204	6289	SO:0001819	synonymous_variant	55020	exon12			TGAGGACGGGAAC		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.1164C>T	22.37:g.46685380C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_017931	Q8WV27|Q9NWP8	Silent	SNP	ENST00000381031.3	37	CCDS43030.1																																																																																			C|0.932;T|0.068	0.068	strong		0.692	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
TOPBP1	11073	hgsc.bcm.edu	37	3	133327457	133327457	+	Silent	SNP	T	T	C	rs1051772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:133327457T>C	ENST00000260810.5	-	27	4478	c.4347A>G	c.(4345-4347)tcA>tcG	p.S1449S		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1449	BRCT 8. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TATTAACTCCTGAGTCATCTG	0.393								Other conserved DNA damage response genes					T|||	466	0.0930511	0.1694	0.0706	5008	,	,		18764	0.0506		0.1044	False		,,,				2504	0.0378				p.S1449S	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A4347G						PASS	.	T		557,3143		40,477,1333	122.0	111.0	114.0		4347	-10.9	0.4	3	dbSNP_86	114	786,7420		29,728,3346	no	coding-synonymous	TOPBP1	NM_007027.3		69,1205,4679	CC,CT,TT		9.5784,15.0541,11.28		1449/1523	133327457	1343,10563	1850	4103	5953	SO:0001819	synonymous_variant	11073	exon27			AACTCCTGAGTCA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4347A>G	3.37:g.133327457T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	148	87	0.587838	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			T|0.900;C|0.100	0.100	strong		0.393	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
OXCT2	64064	hgsc.bcm.edu	37	1	40235448	40235448	+	Missense_Mutation	SNP	C	C	T	rs150795467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:40235448C>T	ENST00000327582.5	-	1	1572	c.1480G>A	c.(1480-1482)Gac>Aac	p.D494N	BMP8B_ENST00000397360.2_Intron|BMP8B_ENST00000372827.3_Intron	NM_022120.1	NP_071403.1	Q9BYC2	SCOT2_HUMAN	3-oxoacid CoA transferase 2	494					ketone body catabolic process (GO:0046952)	mitochondrion (GO:0005739)|motile cilium (GO:0031514)	3-oxoacid CoA-transferase activity (GO:0008260)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|pancreas(1)|upper_aerodigestive_tract(1)	6	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Succinic acid(DB00139)	TTTTTGATGTCGTCCACCGTC	0.632																																					p.D494N		Atlas-SNP	.											.	OXCT2	12	.	0			c.G1480A						PASS	.						41.0	40.0	40.0					1																	40235448		2203	4299	6502	SO:0001583	missense	64064	exon1			TGATGTCGTCCAC	AB050193	CCDS445.1	1p34	2008-02-05			ENSG00000198754	ENSG00000198754			18606	protein-coding gene	gene with protein product		610289				11214971, 11756565	Standard	NM_022120		Approved	FKSG25, FLJ00030, SCOT-T	uc001ceb.1	Q9BYC2	OTTHUMG00000009249	ENST00000327582.5:c.1480G>A	1.37:g.40235448C>T	ENSP00000361914:p.Asp494Asn	Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	449	88	0.195991	NM_022120	B2RBB4|Q5QPK4|Q8NHR1|Q9H1I4	Missense_Mutation	SNP	ENST00000327582.5	37	CCDS445.1	.	.	.	.	.	.	.	.	.	.	c	14.42	2.530386	0.45073	.	.	ENSG00000198754	ENST00000327582	D	0.93247	-3.19	2.51	2.51	0.30379	3-oxoacid CoA-transferase, subunit B (1);	0.052044	0.64402	U	0.000001	D	0.94202	0.8139	.	.	.	0.37421	P	0.086372	D;D	0.60575	0.988;0.988	P;P	0.55785	0.784;0.71	D	0.95837	0.8863	8	0.62326	D	0.03	.	11.1506	0.48455	0.0:1.0:0.0:0.0	.	494;494	B3KS89;Q9BYC2	.;SCOT2_HUMAN	N	494	ENSP00000361914:D494N	ENSP00000361914:D494N	D	-	1	0	OXCT2	40008035	0.937000	0.31787	0.010000	0.14722	0.096000	0.18686	3.036000	0.49767	1.698000	0.51180	0.556000	0.70494	GAC	C|0.800;T|0.200	0.200	strong		0.632	OXCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025656.1	NM_022120	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_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	73	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	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	
NAV3	89795	hgsc.bcm.edu	37	12	78530979	78530979	+	Silent	SNP	G	G	A	rs1852464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:78530979G>A	ENST00000397909.2	+	19	4637	c.4464G>A	c.(4462-4464)caG>caA	p.Q1488Q	NAV3_ENST00000536525.2_Silent_p.Q1488Q|NAV3_ENST00000266692.7_Silent_p.Q1311Q|NAV3_ENST00000228327.6_Silent_p.Q1488Q			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1488	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ATTTGTCTCAGTTTAACCTTC	0.448										HNSCC(70;0.22)			A|||	3066	0.61222	0.7814	0.6052	5008	,	,		18043	0.5565		0.5954	False		,,,				2504	0.4632				p.Q1488Q		Atlas-SNP	.											.	NAV3	506	.	0			c.G4464A						PASS	.	A		2813,915		1060,693,111	116.0	111.0	113.0		4464	-7.3	0.5	12	dbSNP_92	113	5083,3119		1602,1879,620	no	coding-synonymous	NAV3	NM_014903.4		2662,2572,731	AA,AG,GG		38.0273,24.544,33.8139		1488/2364	78530979	7896,4034	1864	4101	5965	SO:0001819	synonymous_variant	89795	exon19			GTCTCAGTTTAAC	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.4464G>A	12.37:g.78530979G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		1349	0.6176739926739927	387	0.7865853658536586	219	0.6049723756906077	287	0.5017482517482518	456	0.6015831134564644	A	0.442	-0.897977	0.02472	0.75456	0.619727	ENSG00000067798	ENST00000552895	.	.	.	5.76	-7.26	0.01466	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999991572	.	.	.	.	.	.	T	0.01874	-1.1256	3	.	.	.	-8.1447	19.4193	0.94713	0.1488:0.0:0.8512:0.0	rs1852464;rs17823355;rs60768267;rs1852464	.	.	.	I	383	.	.	V	+	1	0	NAV3	77055110	1.000000	0.71417	0.459000	0.27081	0.093000	0.18481	0.745000	0.26259	-2.031000	0.00928	-2.095000	0.00367	GTT	G|0.382;A|0.618	0.618	strong		0.448	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
ALG11	440138	hgsc.bcm.edu	37	13	52598799	52598799	+	Silent	SNP	G	G	A	rs61958802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52598799G>A	ENST00000521508.1	+	3	938	c.933G>A	c.(931-933)ccG>ccA	p.P311P	ALG11_ENST00000523764.1_Intron|ALG11_ENST00000519151.1_3'UTR|UTP14C_ENST00000521776.2_5'Flank	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		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;2.44e-08)		AGTTTAGGCCGGAAAAGAATC	0.433													g|||	151	0.0301518	0.0068	0.0231	5008	,	,		20807	0.0079		0.0388	False		,,,				2504	0.0808				p.P311P		Atlas-SNP	.											.	ALG11	39	.	0			c.G933A						PASS	.	A		73,4333	65.8+/-103.3	1,71,2131	80.0	77.0	78.0		933	-9.9	0.8	13	dbSNP_129	78	398,8202	127.7+/-186.0	9,380,3911	no	coding-synonymous	ALG11	NM_001004127.2		10,451,6042	AA,AG,GG		4.6279,1.6568,3.6214		311/493	52598799	471,12535	2203	4300	6503	SO:0001819	synonymous_variant	440138	exon3			TAGGCCGGAAAAG	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.933G>A	13.37:g.52598799G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	81	0.632812	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Silent	SNP	ENST00000521508.1	37	CCDS31977.1																																																																																			G|0.967;A|0.033	0.033	strong		0.433	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
FREM1	158326	hgsc.bcm.edu	37	9	14816829	14816829	+	Missense_Mutation	SNP	G	G	C	rs7041710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:14816829G>C	ENST00000380880.3	-	15	3370	c.2587C>G	c.(2587-2589)Ctc>Gtc	p.L863V	FREM1_ENST00000422223.2_Missense_Mutation_p.L863V|FREM1_ENST00000380881.4_Missense_Mutation_p.L864V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	863			L -> V (in dbSNP:rs7041710). {ECO:0000269|PubMed:15878328}.		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)		acctccaagagtaggtcatcc	0.418													G|||	668	0.133387	0.1687	0.0793	5008	,	,		19534	0.1498		0.0984	False		,,,				2504	0.1431				p.L863V		Atlas-SNP	.											.	FREM1	261	.	0			c.C2587G						PASS	.	G	VAL/LEU	529,3217		48,433,1392	67.0	70.0	69.0		2587	-4.4	0.0	9	dbSNP_116	69	999,7191		54,891,3150	yes	missense	FREM1	NM_144966.5	32	102,1324,4542	CC,CG,GG		12.1978,14.1217,12.8016	benign	863/2180	14816829	1528,10408	1873	4095	5968	SO:0001583	missense	158326	exon16			CCAAGAGTAGGTC	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.2587C>G	9.37:g.14816829G>C	ENSP00000370262:p.Leu863Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	297	0.13598901098901098	86	0.17479674796747968	38	0.10497237569060773	88	0.15384615384615385	85	0.11213720316622691	G	1.582	-0.531394	0.04112	0.141217	0.121978	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.26518	1.73;1.73;1.73	5.65	-4.39	0.03611	.	1.807960	0.01944	N	0.042162	T	0.00039	0.0001	N	0.03324	-0.35	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.22312	-1.0220	9	0.28530	T	0.3	4.8189	7.0784	0.25217	0.3052:0.4779:0.217:0.0	rs7041710;rs7041710	863	Q5H8C1	FREM1_HUMAN	V	864;863;863	ENSP00000370263:L864V;ENSP00000412940:L863V;ENSP00000370262:L863V	ENSP00000370257:L866V	L	-	1	0	FREM1	14806829	0.000000	0.05858	0.001000	0.08648	0.370000	0.29829	-0.610000	0.05629	-1.049000	0.03234	-0.175000	0.13238	CTC	G|0.856;C|0.144	0.144	strong		0.418	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
TTN	7273	hgsc.bcm.edu	37	2	179611809	179611809	+	Intron	SNP	A	A	G	rs397517815|rs569499266		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611809A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.Y5106Y|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGGTGTGGAATATCGCTCTA	0.498																																					p.Y5106Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15318C						PASS	.																																			SO:0001627	intron_variant	7273	exon46			TGTGGAATATCGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5161T>C	2.37:g.179611809A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	164	12	0.0731707	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KRT38	8687	hgsc.bcm.edu	37	17	39595484	39595484	+	Nonsense_Mutation	SNP	G	G	A	rs148768443	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39595484G>A	ENST00000246646.3	-	3	702	c.703C>T	c.(703-705)Cag>Tag	p.Q235*		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	235	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.Q235*(2)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				AGGGAGAGCTGCTCCTCCTTC	0.667																																					p.Q235X		Atlas-SNP	.											KRT38,NS,carcinoma,0,7	KRT38	63	7	2	Substitution - Nonsense(2)	breast(1)|central_nervous_system(1)	c.C703T						PASS	.						58.0	53.0	54.0					17																	39595484		2203	4298	6501	SO:0001587	stop_gained	8687	exon3			AGAGCTGCTCCTC	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.703C>T	17.37:g.39595484G>A	ENSP00000246646:p.Gln235*	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	90	9	0.1	NM_006771	A2RRM5|Q6A164	Nonsense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.158641	0.57368	.	.	ENSG00000171360	ENST00000246646	.	.	.	4.31	1.01	0.19927	.	0.526305	0.15723	N	0.247837	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.0787	0.30731	0.0815:0.0:0.5477:0.3708	.	.	.	.	X	235	.	ENSP00000246646:Q235X	Q	-	1	0	KRT38	36849010	0.779000	0.28652	0.994000	0.49952	0.627000	0.37826	0.894000	0.28350	1.013000	0.39391	0.484000	0.47621	CAG	G|0.975;A|0.025	0.025	strong		0.667	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
POTEG	404785	hgsc.bcm.edu	37	14	19553556	19553556	+	Missense_Mutation	SNP	G	G	A	rs79489020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:19553556G>A	ENST00000409832.3	+	1	192	c.140G>A	c.(139-141)gGa>gAa	p.G47E		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	47										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						GGCACTTCTGGAGACCACGAC	0.597																																					p.G47E		Atlas-SNP	.											POTEG,NS,malignant_melanoma,+1,1	POTEG	118	1	0			c.G140A						PASS	.	G	GLU/GLY	380,3110		1,378,1366	56.0	79.0	71.0		140		0.0	14	dbSNP_134	71	219,6919		0,219,3350	no	missense	POTEG	NM_001005356.2	98	1,597,4716	AA,AG,GG		3.0681,10.8883,5.6361	probably-damaging	47/509	19553556	599,10029	1745	3569	5314	SO:0001583	missense	404785	exon1			CTTCTGGAGACCA		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.140G>A	14.37:g.19553556G>A	ENSP00000386971:p.Gly47Glu	Somatic	712	1	0.00140449		WXS	Illumina HiSeq	Phase_I	636	92	0.144654	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	107	0.04899267399267399	47	0.09552845528455285	4	0.011049723756906077	29	0.050699300699300696	27	0.03562005277044855	g	9.648	1.140782	0.21205	0.108883	0.030681	ENSG00000222036	ENST00000409832	T	0.50001	0.76	.	.	.	.	.	.	.	.	T	0.01661	0.0053	L	0.43152	1.355	0.09310	N	1	D	0.89917	1.0	D	0.76071	0.987	T	0.01464	-1.1348	7	0.62326	D	0.03	.	.	.	.	.	47	Q6S5H5	POTEG_HUMAN	E	47	ENSP00000386971:G47E	ENSP00000386971:G47E	G	+	2	0	POTEG	18623556	0.001000	0.12720	0.028000	0.17463	0.028000	0.11728	-1.547000	0.02186	0.162000	0.19483	0.165000	0.16767	GGA	G|0.968;A|0.032	0.032	strong		0.597	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
OR5H1	26341	hgsc.bcm.edu	37	3	97852229	97852229	+	Missense_Mutation	SNP	T	T	A	rs9849637	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:97852229T>A	ENST00000354565.2	+	1	688	c.688T>A	c.(688-690)Tct>Act	p.S230T	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	230			S -> T (in dbSNP:rs9849637).			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						AAAAAAGAAATCTGATAAAGG	0.378													T|||	1183	0.236222	0.466	0.0937	5008	,	,		18820	0.131		0.1571	False		,,,				2504	0.2168				p.S230T		Atlas-SNP	.											.	OR5H1	71	.	0			c.T688A						PASS	.	T	THR/SER	1830,2576	520.2+/-370.2	391,1048,764	78.0	86.0	83.0		688	3.6	0.2	3	dbSNP_119	83	1335,7263	259.9+/-283.0	97,1141,3061	yes	missense	OR5H1	NM_001005338.1	58	488,2189,3825	AA,AT,TT		15.5269,41.5343,24.3387	possibly-damaging	230/314	97852229	3165,9839	2203	4299	6502	SO:0001583	missense	26341	exon1			AAGAAATCTGATA	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.688T>A	3.37:g.97852229T>A	ENSP00000346575:p.Ser230Thr	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	235	126	0.53617	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	444	0.2032967032967033	220	0.44715447154471544	34	0.09392265193370165	66	0.11538461538461539	124	0.16358839050131926	T	9.373	1.071102	0.20147	0.415343	0.155269	ENSG00000231192	ENST00000354565	T	0.00325	8.1	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000293	T	0.00012	0.0000	M	0.84156	2.68	0.53688	P	2.5000000000052758E-5	D	0.89917	1.0	D	0.91635	0.999	T	0.30446	-0.9978	9	0.66056	D	0.02	.	10.1009	0.42504	0.0:0.0:0.0:1.0	rs9849637;rs52822700;rs9849637	230	A6NKK0	OR5H1_HUMAN	T	230	ENSP00000346575:S230T	ENSP00000346575:S230T	S	+	1	0	OR5H1	99334919	0.027000	0.19231	0.212000	0.23672	0.003000	0.03518	0.961000	0.29267	1.481000	0.48307	0.164000	0.16699	TCT	T|0.779;A|0.221	0.221	strong		0.378	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
FBXO7	25793	hgsc.bcm.edu	37	22	32887150	32887150	+	Silent	SNP	C	C	T	rs9726	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32887150C>T	ENST00000266087.7	+	6	1276	c.949C>T	c.(949-951)Ctg>Ttg	p.L317L	FBXO7_ENST00000382058.3_Silent_p.L238L|FBXO7_ENST00000397426.1_Silent_p.L203L	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	317	Important for dimerization and interaction with PSMF1.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.L317L(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTATCCTCTTCTGGCTTTTAC	0.338													C|||	2442	0.48762	0.4039	0.5663	5008	,	,		17651	0.6925		0.3748	False		,,,				2504	0.4499				p.L317L		Atlas-SNP	.											FBXO7_ENST00000266087,NS,carcinoma,0,1	FBXO7	131	1	1	Substitution - coding silent(1)	stomach(1)	c.C949T						PASS	.	C	,	1640,2766	501.8+/-365.1	309,1022,872	73.0	75.0	75.0		712,949	2.4	1.0	22	dbSNP_52	75	3201,5399	482.5+/-370.9	571,2059,1670	no	coding-synonymous,coding-synonymous	FBXO7	NM_001033024.1,NM_012179.3	,	880,3081,2542	TT,TC,CC		37.2209,37.222,37.2213	,	238/444,317/523	32887150	4841,8165	2203	4300	6503	SO:0001819	synonymous_variant	25793	exon6			CCTCTTCTGGCTT	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"""F-boxes /  ""other"""", ""Parkinson disease"""	13586	protein-coding gene	gene with protein product		605648	"""F-box only protein 7"""			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.949C>T	22.37:g.32887150C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	37	CCDS13907.1																																																																																			C|0.583;T|0.417	0.417	strong		0.338	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
GART	2618	hgsc.bcm.edu	37	21	34883618	34883618	+	Missense_Mutation	SNP	T	T	C	rs8971	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34883618T>C	ENST00000381831.3	-	17	2518	c.2255A>G	c.(2254-2256)gAt>gGt	p.D752G	GART_ENST00000543717.1_Missense_Mutation_p.D304G|GART_ENST00000381815.4_Missense_Mutation_p.D752G|GART_ENST00000381839.3_Missense_Mutation_p.D752G	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	162	0	0		WXS	Illumina HiSeq	Phase_I	174	67	0.385057	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	
PDIK1L	149420	hgsc.bcm.edu	37	1	26448447	26448447	+	Silent	SNP	A	A	G	rs17257107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:26448447A>G	ENST00000374271.4	+	4	692	c.405A>G	c.(403-405)aaA>aaG	p.K135K	PDIK1L_ENST00000374269.1_Silent_p.K135K	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	135	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)		TGTCCAGGAAACCCAATCGTA	0.433													A|||	587	0.117212	0.1929	0.1052	5008	,	,		15996	0.0159		0.1789	False		,,,				2504	0.0644				p.K135K		Atlas-SNP	.											.	PDIK1L	19	.	0			c.A405G						PASS	.	A		895,3511	344.9+/-308.3	81,733,1389	114.0	117.0	116.0		405	4.8	1.0	1	dbSNP_123	116	1535,7065	289.4+/-299.3	136,1263,2901	no	coding-synonymous	PDIK1L	NM_152835.4		217,1996,4290	GG,GA,AA		17.8488,20.3132,18.6837		135/342	26448447	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	149420	exon3			CAGGAAACCCAAT	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.405A>G	1.37:g.26448447A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Silent	SNP	ENST00000374271.4	37	CCDS274.1																																																																																			A|0.835;G|0.165	0.165	strong		0.433	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835	
PLEKHA7	144100	hgsc.bcm.edu	37	11	16837788	16837788	+	Silent	SNP	G	G	A	rs217750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:16837788G>A	ENST00000355661.3	-	12	1900	c.1890C>T	c.(1888-1890)cgC>cgT	p.R630R	PLEKHA7_ENST00000448080.2_Silent_p.R630R|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Silent_p.R630R			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	630	Interaction with CTNND1.				epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						AGGGCATGGAGCGTCGGTCCA	0.557													G|||	566	0.113019	0.2466	0.0735	5008	,	,		19217	0.0		0.17	False		,,,				2504	0.0184				p.R630R		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.C1890T						PASS	.	G		985,3415	368.1+/-318.5	109,767,1324	104.0	87.0	93.0		1890	4.8	1.0	11	dbSNP_79	93	1265,7323	251.2+/-277.8	71,1123,3100	no	coding-synonymous	PLEKHA7	NM_175058.4		180,1890,4424	AA,AG,GG		14.7299,22.3864,17.3237		630/1122	16837788	2250,10738	2200	4294	6494	SO:0001819	synonymous_variant	144100	exon12			CATGGAGCGTCGG	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.1890C>T	11.37:g.16837788G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	37	CCDS31434.1	262	0.11996336996336997	105	0.21341463414634146	22	0.06077348066298342	0	0.0	135	0.17810026385224276	G	10.56	1.384486	0.25031	0.223864	0.147299	ENSG00000166689	ENST00000530489	.	.	.	5.67	4.75	0.60458	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.01725	-1.1287	3	.	.	.	-18.1367	13.7276	0.62767	0.0748:0.0:0.9252:0.0	rs217750;rs217750	.	.	.	V	261	.	.	A	-	2	0	PLEKHA7	16794364	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.547000	0.36190	1.364000	0.46038	0.563000	0.77884	GCT	G|0.854;A|0.146	0.146	strong		0.557	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
IPO5	3843	hgsc.bcm.edu	37	13	98645253	98645253	+	Silent	SNP	A	A	G	rs626716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:98645253A>G	ENST00000490680.1	+	7	842	c.777A>G	c.(775-777)ctA>ctG	p.L259L	IPO5_ENST00000539640.1_Silent_p.L134L|IPO5_ENST00000261574.5_Silent_p.L277L			O00410	IPO5_HUMAN	importin 5	259					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						AAGCAACTCTACAGCTAAGTC	0.348													A|||	718	0.143371	0.1142	0.0303	5008	,	,		20955	0.3155		0.0457	False		,,,				2504	0.1861				p.L277L		Atlas-SNP	.											.	IPO5	90	.	0			c.A831G						PASS	.	A		436,3970	211.8+/-231.9	27,382,1794	116.0	110.0	112.0		831	-5.2	0.9	13	dbSNP_83	112	343,8257	117.0+/-176.6	4,335,3961	no	coding-synonymous	IPO5	NM_002271.4		31,717,5755	GG,GA,AA		3.9884,9.8956,5.9895		277/1116	98645253	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	3843	exon10			AACTCTACAGCTA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.777A>G	13.37:g.98645253A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	37		270	0.12362637362637363	59	0.11991869918699187	14	0.03867403314917127	163	0.28496503496503495	34	0.044854881266490766	A	10.48	1.362466	0.24684	0.098956	0.039884	ENSG00000065150	ENST00000469360	.	.	.	6.17	-5.19	0.02832	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26224	-1.0109	3	.	.	.	-25.4394	10.7192	0.46030	0.4233:0.099:0.4777:0.0	rs626716;rs2230410;rs17301628;rs626716	.	.	.	C	261	.	.	Y	+	2	0	IPO5	97443254	0.985000	0.35326	0.902000	0.35471	0.988000	0.76386	0.264000	0.18497	-0.754000	0.04715	0.533000	0.62120	TAC	A|0.901;G|0.099	0.099	strong		0.348	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
KDM4C	23081	hgsc.bcm.edu	37	9	6986464	6986464	+	Missense_Mutation	SNP	G	G	C	rs35826653	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:6986464G>C	ENST00000381309.3	+	11	2040	c.1475G>C	c.(1474-1476)aGt>aCt	p.S492T	KDM4C_ENST00000442236.2_Missense_Mutation_p.S311T|KDM4C_ENST00000381306.3_Missense_Mutation_p.S492T|KDM4C_ENST00000536108.1_Missense_Mutation_p.S311T|KDM4C_ENST00000543771.1_Missense_Mutation_p.S492T|KDM4C_ENST00000428870.2_Missense_Mutation_p.S179T|KDM4C_ENST00000535193.1_Missense_Mutation_p.S514T	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	492			S -> T (in dbSNP:rs35826653). {ECO:0000269|PubMed:10987278, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9872452}.		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						CCATTGTCTAGTGGCTATGAG	0.433													G|||	155	0.0309505	0.0038	0.0403	5008	,	,		21408	0.001		0.1064	False		,,,				2504	0.0143				p.S514T		Atlas-SNP	.											.	KDM4C	186	.	0			c.G1541C						PASS	.	G	THR/SER,THR/SER,THR/SER,THR/SER	102,4304	80.9+/-119.3	0,102,2101	127.0	114.0	119.0		1475,1475,1541,1475	-0.1	0.0	9	dbSNP_126	119	1126,7474	234.3+/-267.3	66,994,3240	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	58,58,58,58	66,1096,5341	CC,CG,GG		13.093,2.315,9.4418	benign,benign,benign,benign	492/1048,492/814,514/836,492/1057	6986464	1228,11778	2203	4300	6503	SO:0001583	missense	23081	exon11			TGTCTAGTGGCTA	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.1475G>C	9.37:g.6986464G>C	ENSP00000370710:p.Ser492Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	105	0.04807692307692308	5	0.01016260162601626	15	0.04143646408839779	1	0.0017482517482517483	84	0.11081794195250659	G	6.416	0.444839	0.12164	0.02315	0.13093	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.3	-0.0835	0.13694	.	2.711160	0.00937	N	0.002785	T	0.00300	0.0009	L	0.36672	1.1	0.80722	P	0.0	B;B;B;B;B	0.26547	0.094;0.152;0.095;0.002;0.01	B;B;B;B;B	0.21917	0.016;0.036;0.037;0.001;0.005	T	0.03017	-1.1082	9	0.11485	T	0.65	-33.3234	2.7012	0.05149	0.2011:0.3382:0.3434:0.1173	rs35826653;rs61752862	311;492;514;492;492	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	T	514;492;492;492;311;311;179	ENSP00000442382:S514T;ENSP00000445427:S492T;ENSP00000370710:S492T;ENSP00000370707:S492T;ENSP00000409353:S311T;ENSP00000440656:S311T;ENSP00000405739:S179T	ENSP00000370707:S492T	S	+	2	0	KDM4C	6976464	0.000000	0.05858	0.004000	0.12327	0.067000	0.16453	-0.339000	0.07832	0.327000	0.23409	0.655000	0.94253	AGT	G|0.923;C|0.077	0.077	strong		0.433	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
WDFY3	23001	hgsc.bcm.edu	37	4	85630087	85630087	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:85630087C>T	ENST00000295888.4	-	53	8599	c.8192G>A	c.(8191-8193)tGg>tAg	p.W2731*	WDFY3_ENST00000322366.6_Nonsense_Mutation_p.W2714*	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2731	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGCAAGGATCCAGGGGAAGAC	0.368																																					p.W2731X		Atlas-SNP	.											WDFY3,NS,carcinoma,+1,1	WDFY3	314	1	0			c.G8192A						scavenged	.						92.0	94.0	93.0					4																	85630087		2203	4300	6503	SO:0001587	stop_gained	23001	exon53			AGGATCCAGGGGA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.8192G>A	4.37:g.85630087C>T	ENSP00000295888:p.Trp2731*	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	202	3	0.0148515	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Nonsense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	35	5.486361	0.96323	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1918	0.93669	0.0:1.0:0.0:0.0	.	.	.	.	X	2714;2731;334	.	ENSP00000295888:W2731X	W	-	2	0	WDFY3	85849111	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.545000	0.82128	2.768000	0.95171	0.650000	0.86243	TGG	.	.	none		0.368	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
FLG	2312	hgsc.bcm.edu	37	1	152280788	152280788	+	Missense_Mutation	SNP	T	T	G	rs66954353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280788T>G	ENST00000368799.1	-	3	6609	c.6574A>C	c.(6574-6576)Aaa>Caa	p.K2192Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2192	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)			TCATATGTTTTTCTGCTTGCA	0.532									Ichthyosis																												p.K2192Q		Atlas-SNP	.											.	FLG	900	.	0			c.A6574C						PASS	.	G	GLN/LYS	1049,3357		0,1049,1154	476.0	402.0	427.0		6574	2.0	0.0	1	dbSNP_130	427	819,7781		4,811,3485	yes	missense	FLG	NM_002016.1	53	4,1860,4639	GG,GT,TT		9.5233,23.8084,14.3626	benign	2192/4062	152280788	1868,11138	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGTTTTTCTGCT	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.6574A>C	1.37:g.152280788T>G	ENSP00000357789:p.Lys2192Gln	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	358	125	0.349162	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	5.601	0.295698	0.10622	0.238084	0.095233	ENSG00000143631	ENST00000368799	T	0.01725	4.67	2.99	1.99	0.26369	.	.	.	.	.	T	0.00144	0.0004	N	0.00146	-1.995	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13548	-1.0505	8	0.15066	T	0.55	.	5.49	0.16771	0.0:0.2239:0.546:0.2301	.	2192	P20930	FILA_HUMAN	Q	2192	ENSP00000357789:K2192Q	ENSP00000357789:K2192Q	K	-	1	0	FLG	150547412	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.245000	0.18142	-0.043000	0.13513	-0.332000	0.08345	AAA	T|0.500;G|0.500	0.500	strong		0.532	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37438725	37438725	+	Missense_Mutation	SNP	C	C	G	rs200260827	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:37438725C>G	ENST00000602533.1	+	11	1524	c.1425C>G	c.(1423-1425)aaC>aaG	p.N475K	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.N475K|ANKRD30A_ENST00000374660.1_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						PASS	.						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	182	0	0		WXS	Illumina HiSeq	Phase_I	197	18	0.0913706	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	
NDUFB10	4716	hgsc.bcm.edu	37	16	2009697	2009697	+	Silent	SNP	C	C	T	rs2302175	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2009697C>T	ENST00000268668.6	+	1	189	c.72C>T	c.(70-72)atC>atT	p.I24I	SNORA10_ENST00000384084.1_RNA|NDUFB10_ENST00000543683.2_Silent_p.I24I|RPL3L_ENST00000566484.1_5'Flank|NDUFB10_ENST00000569148.1_Silent_p.I24I	NM_004548.2	NP_004539.1	O96000	NDUBA_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa	24					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)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			lung(1)|urinary_tract(1)	2						CCAATCCCATCGTCTACATGA	0.701													C|||	602	0.120208	0.1528	0.0375	5008	,	,		12015	0.3075		0.0239	False		,,,				2504	0.0409				p.I24I		Atlas-SNP	.											.	NDUFB10	17	.	0			c.C72T						PASS	.	C		683,3715	282.8+/-276.7	54,575,1570	64.0	60.0	61.0		72	2.7	0.4	16	dbSNP_100	61	168,8432	77.5+/-140.1	2,164,4134	no	coding-synonymous	NDUFB10	NM_004548.2		56,739,5704	TT,TC,CC		1.9535,15.5298,6.5472		24/173	2009697	851,12147	2199	4300	6499	SO:0001819	synonymous_variant	4716	exon1			TCCCATCGTCTAC	AF044954	CCDS10451.1	16p13.3	2011-07-04	2002-08-29		ENSG00000140990	ENSG00000140990		"""Mitochondrial respiratory chain complex / Complex I"""	7696	protein-coding gene	gene with protein product	"""complex I PDSW subunit"""	603843	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)"""			9763677, 9878551	Standard	NM_004548		Approved	PDSW	uc002cni.2	O96000	OTTHUMG00000128709	ENST00000268668.6:c.72C>T	16.37:g.2009697C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_004548	Q96II6	Silent	SNP	ENST00000268668.6	37	CCDS10451.1																																																																																			C|0.906;T|0.094	0.094	strong		0.701	NDUFB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250614.2	NM_004548	
SHROOM2	357	hgsc.bcm.edu	37	X	9863112	9863112	+	Silent	SNP	A	A	G	rs6530341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:9863112A>G	ENST00000380913.3	+	4	1254	c.1164A>G	c.(1162-1164)ccA>ccG	p.P388P		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	388					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				CGGGCTGCCCACAGGAGGCCC	0.677													A|||	786	0.208212	0.1672	0.1974	3775	,	,		10580	0.2669		0.0905	False		,,,				2504	0.0695				p.P388P		Atlas-SNP	.											.	SHROOM2	139	.	0			c.A1164G						PASS	.	A		865,2957		89,557,130,984,432	19.0	16.0	17.0		1164	-8.6	0.0	X	dbSNP_116	17	928,5788		49,587,243,1791,1619	no	coding-synonymous	SHROOM2	NM_001649.2		138,1144,373,2775,2051	GG,GA,G,AA,A		13.8177,22.6321,17.0146		388/1617	9863112	1793,8745	2192	4289	6481	SO:0001819	synonymous_variant	357	exon4			CTGCCCACAGGAG	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1164A>G	X.37:g.9863112A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																			A|0.805;0|0.004	.	strong		0.677	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
HIVEP2	3097	hgsc.bcm.edu	37	6	143081035	143081035	+	Silent	SNP	A	A	G	rs9496457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:143081035A>G	ENST00000367604.1	-	8	7029	c.6390T>C	c.(6388-6390)tcT>tcC	p.S2130S	HIVEP2_ENST00000367603.2_Silent_p.S2130S|HIVEP2_ENST00000012134.2_Silent_p.S2130S			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	2130	10 X 4 AA tandem repeats of S-P-[RGMKC]- [RK].|Arg-rich.				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)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CTCTTCTAGGAGAGAGGTCTC	0.468													A|||	582	0.116214	0.1664	0.1182	5008	,	,		21507	0.005		0.1889	False		,,,				2504	0.0869				p.S2130S	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.T6390C						PASS	.	A		555,3269		46,463,1403	172.0	162.0	165.0		6390	-0.1	1.0	6	dbSNP_119	165	1628,6602		165,1298,2652	no	coding-synonymous	HIVEP2	NM_006734.3		211,1761,4055	GG,GA,AA		19.7813,14.5136,18.1102		2130/2447	143081035	2183,9871	1912	4115	6027	SO:0001819	synonymous_variant	3097	exon9			TCTAGGAGAGAGG	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.6390T>C	6.37:g.143081035A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	158	85	0.537975	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																			A|0.844;G|0.156	0.156	strong		0.468	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
ADAM15	8751	hgsc.bcm.edu	37	1	155033308	155033308	+	Splice_Site	SNP	G	G	A	rs11589479	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:155033308G>A	ENST00000356955.2	+	19	2378	c.2277G>A	c.(2275-2277)aaG>aaA	p.K759K	ADAM15_ENST00000449910.2_Splice_Site_p.K759K|ADAM15_ENST00000271836.6_Splice_Site_p.K759K|ADAM15_ENST00000355956.2_Splice_Site_p.K759K|EFNA3_ENST00000556931.1_5'Flank|EFNA3_ENST00000505139.1_5'Flank|ADAM15_ENST00000360674.4_Intron|ADAM15_ENST00000531455.1_Splice_Site_p.K769K|EFNA4_ENST00000359751.4_5'Flank|EFNA4_ENST00000427683.2_5'Flank|EFNA4_ENST00000368409.3_5'Flank|ADAM15_ENST00000368412.3_Intron|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000359280.4_Splice_Site_p.K759K|ADAM15_ENST00000368413.1_Splice_Site_p.K465K|ADAM15_ENST00000368410.2_Splice_Site_p.K465K	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	759					angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	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)			GAGGCACTAAGGTGAGTCCTG	0.627													G|||	376	0.0750799	0.0045	0.0951	5008	,	,		18530	0.0089		0.1819	False		,,,				2504	0.1145				p.K769K		Atlas-SNP	.											.	ADAM15	92	.	0			c.G2307A						PASS	.	G	,,,,,	141,4265	93.4+/-132.2	1,139,2063	56.0	57.0	57.0		2277,,2277,2277,2277,2277	4.8	1.0	1	dbSNP_120	57	1456,7144	267.9+/-287.5	118,1220,2962	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ADAM15	NM_003815.3,NM_207191.1,NM_207194.1,NM_207195.1,NM_207196.1,NM_207197.1	,,,,,	119,1359,5025	AA,AG,GG		16.9302,3.2002,12.2789	,,,,,	759/815,,759/840,759/839,759/863,759/864	155033308	1597,11409	2203	4300	6503	SO:0001630	splice_region_variant	8751	exon19			CACTAAGGTGAGT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.2277+1G>A	1.37:g.155033308G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Silent	SNP	ENST00000356955.2	37	CCDS1087.1																																																																																			G|0.889;A|0.111	0.111	strong		0.627	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	Silent
ZNF778	197320	hgsc.bcm.edu	37	16	89294798	89294798	+	Missense_Mutation	SNP	A	A	G	rs118093429	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89294798A>G	ENST00000433976.2	+	6	2350	c.2018A>G	c.(2017-2019)tAt>tGt	p.Y673C	ZNF778_ENST00000306502.6_Missense_Mutation_p.Y631C|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	673					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(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CAGAAACCCTATAAATGTAAG	0.393													a|||	207	0.0413339	0.003	0.036	5008	,	,		23978	0.0694		0.0278	False		,,,				2504	0.0818				p.Y701C		Atlas-SNP	.											.	ZNF778	67	.	0			c.A2102G						PASS	.	A	CYS/TYR,CYS/TYR	25,4303		0,25,2139	43.0	46.0	45.0		2102,2018	-0.2	0.0	16	dbSNP_132	45	301,8265		3,295,3985	yes	missense,missense	ZNF778	NM_001201407.1,NM_182531.3	194,194	3,320,6124	GG,GA,AA		3.5139,0.5776,2.5283	probably-damaging,probably-damaging	701/758,673/730	89294798	326,12568	2164	4283	6447	SO:0001583	missense	197320	exon7			AACCCTATAAATG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.2018A>G	16.37:g.89294798A>G	ENSP00000405289:p.Tyr673Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001201407	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	37	CCDS45550.1	79	0.036172161172161175	0	0.0	14	0.03867403314917127	42	0.07342657342657342	23	0.030343007915567283	A	11.58	1.682042	0.29872	0.005776	0.035139	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.25414	1.8;1.8	1.21	-0.189	0.13260	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03390	0.0098	M	0.79123	2.44	0.22081	N	0.999371	D;D	0.69078	0.997;0.994	P;P	0.55965	0.764;0.788	T	0.04650	-1.0936	9	0.87932	D	0	.	2.0904	0.03655	0.4072:0.2975:0.0:0.2953	.	631;673	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	C	673;631	ENSP00000405289:Y673C;ENSP00000305203:Y631C	ENSP00000305203:Y631C	Y	+	2	0	ZNF778	87822299	0.000000	0.05858	0.005000	0.12908	0.157000	0.22087	0.004000	0.13106	-0.061000	0.13110	0.378000	0.23410	TAT	A|0.964;G|0.036	0.036	strong		0.393	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
F5	2153	hgsc.bcm.edu	37	1	169521853	169521853	+	Missense_Mutation	SNP	A	A	G	rs6033	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:169521853A>G	ENST00000367797.3	-	8	1439	c.1238T>C	c.(1237-1239)aTg>aCg	p.M413T	F5_ENST00000546081.1_Missense_Mutation_p.M276T|F5_ENST00000367796.3_Missense_Mutation_p.M413T	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	413	F5/8 type A 2.|Plastocyanin-like 3.		M -> T (in dbSNP:rs6033). {ECO:0000269|PubMed:10391209, 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)	ATCTTCTTTCATATTGGGATT	0.358													A|||	251	0.0501198	0.0053	0.098	5008	,	,		15429	0.0298		0.0726	False		,,,				2504	0.0746				p.M413T		Atlas-SNP	.											F5,larynx,carcinoma,-1,1	F5	301	1	0			c.T1238C	GRCh37	CM045144	F5	M	rs6033	PASS	.	A	THR/MET	59,4347	56.2+/-92.4	2,55,2146	157.0	156.0	157.0		1238	-10.6	0.0	1	dbSNP_52	157	674,7926	169.1+/-220.5	25,624,3651	yes	missense	F5	NM_000130.4	81	27,679,5797	GG,GA,AA		7.8372,1.3391,5.6359	benign	413/2225	169521853	733,12273	2203	4300	6503	SO:0001583	missense	2153	exon8			TCTTTCATATTGG	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.1238T>C	1.37:g.169521853A>G	ENSP00000356771:p.Met413Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	254	85	0.334646	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	115	0.052655677655677656	6	0.012195121951219513	35	0.09668508287292818	16	0.027972027972027972	58	0.07651715039577836	A	5.504	0.277936	0.10403	0.013391	0.078372	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98914	-5.23;-5.23;-5.23	5.74	-10.6	0.00265	Cupredoxin (2);	1.658480	0.02698	N	0.111473	D	0.86581	0.5967	N	0.20685	0.6	0.22305	N	0.99922	B	0.14012	0.009	B	0.11329	0.006	D	0.87803	0.2626	9	0.19147	T	0.46	0.7786	1.37	0.02209	0.1931:0.3401:0.2141:0.2527	rs6033;rs17520687;rs60762156;rs6033	413	P12259	FA5_HUMAN	T	413;413;276	ENSP00000356771:M413T;ENSP00000356770:M413T;ENSP00000439664:M276T	ENSP00000356770:M413T	M	-	2	0	F5	167788477	0.000000	0.05858	0.000000	0.03702	0.505000	0.33919	-0.365000	0.07573	-1.926000	0.01061	0.533000	0.62120	ATG	A|0.946;G|0.054	0.054	strong		0.358	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
BTNL2	56244	hgsc.bcm.edu	37	6	32363955	32363955	+	Silent	SNP	T	T	C	rs2076529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32363955T>C	ENST00000374993.1	-	5	938	c.939A>G	c.(937-939)gtA>gtG	p.V313V	BTNL2_ENST00000374995.3_Silent_p.V219V|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000429232.2_Silent_p.V220V|BTNL2_ENST00000414363.1_Silent_p.V103V|BTNL2_ENST00000454136.3_Silent_p.V313V|BTNL2_ENST00000540315.1_Silent_p.V103V|BTNL2_ENST00000544175.1_Silent_p.V36V	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	313	Ig-like V-type 3.					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						CACTCACCAGTACAGTCCTCC	0.562													c|||	1888	0.376997	0.3268	0.4784	5008	,	,		19952	0.2728		0.4364	False		,,,				2504	0.4192				p.V313V		Atlas-SNP	.											.	BTNL2	50	.	0			c.A939G						PASS	.			970,2052		155,660,696	159.0	106.0	125.0	http://www.ncbi.nlm.nih.gov/pubmed?term	939	-5.6	0.0	6	dbSNP_96	125	2334,3084		490,1354,865	no	coding-synonymous	BTNL2	NM_019602.1		645,2014,1561	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	43.0786,32.0979,39.1469		313/456	32363955	3304,5136	1511	2709	4220	SO:0001819	synonymous_variant	56244	exon5			CACCAGTACAGTC	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.939A>G	6.37:g.32363955T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	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|0.636;C|0.364	0.364	strong		0.562	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
MOCOS	55034	hgsc.bcm.edu	37	18	33831189	33831189	+	Missense_Mutation	SNP	C	C	A	rs594445	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	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		
PNP	4860	hgsc.bcm.edu	37	14	20940606	20940606	+	Missense_Mutation	SNP	G	G	A	rs1049564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	86	0	0		WXS	Illumina HiSeq	Phase_I	86	55	0.639535	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	
NANOS3	342977	hgsc.bcm.edu	37	19	13988416	13988416	+	Silent	SNP	A	A	G	rs2016163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13988416A>G	ENST00000397555.2	+	2	297	c.297A>G	c.(295-297)acA>acG	p.T99T	MIR181C_ENST00000384881.1_RNA|MIR181D_ENST00000384853.1_RNA|NANOS3_ENST00000339133.5_Silent_p.T118T|NANOS3_ENST00000591727.1_Intron	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	51	0	0		WXS	Illumina HiSeq	Phase_I	50	48	0.96	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	
SHROOM3	57619	hgsc.bcm.edu	37	4	77675505	77675505	+	Missense_Mutation	SNP	C	C	T	rs3733242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:77675505C>T	ENST00000296043.6	+	7	4822	c.3869C>T	c.(3868-3870)cCg>cTg	p.P1290L	RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1290			P -> L (in dbSNP:rs3733242). {ECO:0000269|PubMed:10819331, ECO:0000269|Ref.1}.		actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GAGATGCTGCCGCTCTTCCAC	0.547													T|||	2651	0.529353	0.6604	0.4438	5008	,	,		21022	0.5655		0.3907	False		,,,				2504	0.5184				p.P1290L		Atlas-SNP	.											.	SHROOM3	134	.	0			c.C3869T						PASS	.	T	LEU/PRO	2722,1684	510.1+/-367.4	845,1032,326	154.0	150.0	151.0		3869	-1.6	0.0	4	dbSNP_107	151	3505,5095	633.0+/-398.7	723,2059,1518	yes	missense	SHROOM3	NM_020859.3	98	1568,3091,1844	TT,TC,CC		40.7558,38.2206,47.8779	benign	1290/1997	77675505	6227,6779	2203	4300	6503	SO:0001583	missense	57619	exon7			TGCTGCCGCTCTT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.3869C>T	4.37:g.77675505C>T	ENSP00000296043:p.Pro1290Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	1120	0.5128205128205128	358	0.7276422764227642	160	0.4419889502762431	305	0.5332167832167832	297	0.391820580474934	T	2.086	-0.409578	0.04799	0.617794	0.407558	ENSG00000138771	ENST00000296043	T	0.18174	2.23	5.16	-1.61	0.08399	.	1.575460	0.04026	N	0.300504	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	0.33803	-0.9854	9	0.20046	T	0.44	3.0917	7.4316	0.27131	0.0:0.5528:0.1652:0.2821	rs3733242;rs52791336;rs56694465;rs3733242	1290	Q8TF72	SHRM3_HUMAN	L	1290	ENSP00000296043:P1290L	ENSP00000296043:P1290L	P	+	2	0	SHROOM3	77894529	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.675000	0.05227	-0.404000	0.07610	-0.269000	0.10298	CCG	C|0.508;T|0.492	0.492	strong		0.547	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
FRRS1	391059	hgsc.bcm.edu	37	1	100203648	100203648	+	Silent	SNP	C	C	T	rs7537296	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:100203648C>T	ENST00000414213.1	-	7	1354	c.753G>A	c.(751-753)caG>caA	p.Q251Q	FRRS1_ENST00000287474.5_Silent_p.Q251Q			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	251	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					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)		CAACCATCCACTGATCATGAG	0.483													c|||	2796	0.558307	0.9402	0.4928	5008	,	,		19702	0.3909		0.3082	False		,,,				2504	0.5184				p.Q251Q		Atlas-SNP	.											.	FRRS1	50	.	0			c.G753A						PASS	.	T		3680,726	757.7+/-412.7	1536,608,59	109.0	113.0	112.0		753	-1.3	0.5	1	dbSNP_116	112	2915,5685	454.1+/-363.4	505,1905,1890	yes	coding-synonymous	FRRS1	NM_001013660.2		2041,2513,1949	TT,TC,CC		33.8953,16.4775,49.2926		251/627	100203648	6595,6411	2203	4300	6503	SO:0001819	synonymous_variant	391059	exon7			CATCCACTGATCA	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.753G>A	1.37:g.100203648C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	37																																																																																				C|0.486;T|0.514	0.514	strong		0.483	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
LMOD2	442721	hgsc.bcm.edu	37	7	123301940	123301940	+	Silent	SNP	A	A	G	rs7809453	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	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		
KALRN	8997	hgsc.bcm.edu	37	3	124157798	124157798	+	Silent	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124157798C>A	ENST00000240874.3	+	18	3263	c.3106C>A	c.(3106-3108)Cga>Aga	p.R1036R	KALRN_ENST00000360013.3_Silent_p.R1036R|KALRN_ENST00000460856.1_Silent_p.R1027R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1036					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1036*(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GTGTGGTGGACGAGATAAGCT	0.468																																					p.R1036R		Atlas-SNP	.											KALRN_ENST00000360013,caecum,carcinoma,0,2	KALRN	556	2	2	Substitution - Nonsense(2)	large_intestine(2)	c.C3106A						PASS	.						197.0	186.0	190.0					3																	124157798		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon18			GGTGGACGAGATA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3106C>A	3.37:g.124157798C>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292179	0.23564	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.54	3.54	0.40534	.	.	.	.	.	T	0.72011	0.3408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71182	-0.4668	4	.	.	.	.	16.5605	0.84565	0.1516:0.8484:0.0:0.0	.	.	.	.	E	1004	.	.	D	+	3	2	KALRN	125640488	0.957000	0.32711	1.000000	0.80357	0.997000	0.91878	1.191000	0.32138	0.683000	0.31428	0.655000	0.94253	GAC	.	.	none		0.468	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
PIEZO1	9780	hgsc.bcm.edu	37	16	88789709	88789709	+	Missense_Mutation	SNP	C	C	T	rs191656121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88789709C>T	ENST00000301015.9	-	32	4609	c.4363G>A	c.(4363-4365)Gcc>Acc	p.A1455T	RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1455					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						ACCGCCTGGGCGTTGGTCACC	0.701													C|||	6	0.00119808	0.0	0.0	5008	,	,		13017	0.001		0.001	False		,,,				2504	0.0041				p.A1455T		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G4363A						PASS	.						22.0	27.0	25.0					16																	88789709		691	1585	2276	SO:0001583	missense	9780	exon32			CCTGGGCGTTGGT	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.4363G>A	16.37:g.88789709C>T	ENSP00000301015:p.Ala1455Thr	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	2|2	0.002638522427440633|0.002638522427440633	C|C	20.1|20.1	3.934414|3.934414	0.73442|0.73442	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000301015|ENST00000451779	T|.	0.73047|.	-0.71|.	5.1|5.1	4.09|4.09	0.47781|0.47781	.|.	0.200054|.	0.41396|.	D|.	0.000890|.	T|T	0.57519|0.57519	0.2059|0.2059	L|L	0.48362|0.48362	1.52|1.52	0.80722|0.80722	D|D	1|1	B|.	0.31859|.	0.343|.	B|.	0.21546|.	0.035|.	T|T	0.53308|0.53308	-0.8457|-0.8457	10|5	0.13853|.	T|.	0.58|.	-40.0355|-40.0355	9.4442|9.4442	0.38688|0.38688	0.0:0.7677:0.1478:0.0845|0.0:0.7677:0.1478:0.0845	.|.	1455|.	Q92508|.	PIEZ1_HUMAN|.	T|H	1455|1400	ENSP00000301015:A1455T|.	ENSP00000301015:A1455T|.	A|R	-|-	1|2	0|0	FAM38A|FAM38A	87317210|87317210	0.558000|0.558000	0.26554|0.26554	0.801000|0.801000	0.32222|0.32222	0.978000|0.978000	0.69477|0.69477	1.004000|1.004000	0.29822|0.29822	2.545000|2.545000	0.85829|0.85829	0.561000|0.561000	0.74099|0.74099	GCC|CGC	C|0.999;T|0.001	0.001	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
SPTBN5	51332	hgsc.bcm.edu	37	15	42143118	42143118	+	Missense_Mutation	SNP	T	T	C	rs78489122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42143118T>C	ENST00000320955.6	-	66	11082	c.10855A>G	c.(10855-10857)Atc>Gtc	p.I3619V	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3619	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GCAAACAGGATCTCTGCCCCA	0.672													T|||	65	0.0129792	0.0008	0.0288	5008	,	,		16168	0.0		0.0398	False		,,,				2504	0.0041				p.I3584V		Atlas-SNP	.											.	SPTBN5	171	.	0			c.A10750G						PASS	.	T	VAL/ILE	50,4282		0,50,2116	24.0	30.0	28.0		10750	0.9	0.0	15	dbSNP_131	28	426,8116		13,400,3858	yes	missense	SPTBN5	NM_016642.2	29	13,450,5974	CC,CT,TT		4.9871,1.1542,3.6974	benign	3584/3640	42143118	476,12398	2166	4271	6437	SO:0001583	missense	51332	exon66			ACAGGATCTCTGC	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.10855A>G	15.37:g.42143118T>C	ENSP00000317790:p.Ile3619Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		37	0.01694139194139194	0	0.0	11	0.03038674033149171	0	0.0	26	0.03430079155672823	.	1.533	-0.543941	0.04024	0.011542	0.049871	ENSG00000137877	ENST00000320955	T	0.30448	1.53	3.27	0.876	0.19138	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	1.049830	0.07578	N	0.919741	T	0.02848	0.0085	L	0.36672	1.1	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.27297	-1.0078	10	0.20046	T	0.44	.	0.867	0.01206	0.1865:0.1174:0.2202:0.476	.	3619	Q9NRC6	SPTN5_HUMAN	V	3619	ENSP00000317790:I3619V	ENSP00000317790:I3619V	I	-	1	0	SPTBN5	39930410	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.284000	0.08422	0.169000	0.19679	0.459000	0.35465	ATC	T|0.980;C|0.020	0.020	strong		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
CRELD2	79174	hgsc.bcm.edu	37	22	50320943	50320943	+	Silent	SNP	C	C	T	rs1608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50320943C>T	ENST00000328268.4	+	10	1124	c.1050C>T	c.(1048-1050)cgC>cgT	p.R350R	CRELD2_ENST00000403427.3_Silent_p.R322R|CRELD2_ENST00000404488.3_Silent_p.R399R|CRELD2_ENST00000407217.3_Silent_p.R318R	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	350						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TGCCCTCCCGCGAAGACCTGT	0.557													C|||	689	0.13758	0.2474	0.0476	5008	,	,		15225	0.0486		0.0795	False		,,,				2504	0.2045				p.R399R		Atlas-SNP	.											.	CRELD2	57	.	0			c.C1197T						PASS	.	C	,	860,3542	334.9+/-303.7	81,698,1422	126.0	128.0	128.0		1197,1050	-7.6	0.0	22	dbSNP_36	128	768,7828	181.9+/-230.5	33,702,3563	no	coding-synonymous,coding-synonymous	CRELD2	NM_001135101.1,NM_024324.3	,	114,1400,4985	TT,TC,CC		8.9344,19.5366,12.525	,	399/403,350/354	50320943	1628,11370	2201	4298	6499	SO:0001819	synonymous_variant	79174	exon11			CTCCCGCGAAGAC	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.1050C>T	22.37:g.50320943C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Silent	SNP	ENST00000328268.4	37	CCDS14082.1																																																																																			C|0.875;T|0.125	0.125	strong		0.557	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
PIEZO1	9780	hgsc.bcm.edu	37	16	88783100	88783100	+	Missense_Mutation	SNP	T	T	C	rs1803382	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88783100T>C	ENST00000301015.9	-	47	7039	c.6793A>G	c.(6793-6795)Atc>Gtc	p.I2265V	PIEZO1_ENST00000327397.7_Missense_Mutation_p.I133V|RP5-1142A6.9_ENST00000564984.1_RNA|MIR4722_ENST00000578292.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2265					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						GCCGTGACGATGTCCTCAGGG	0.647													T|||	993	0.198283	0.1029	0.1902	5008	,	,		19929	0.0913		0.326	False		,,,				2504	0.3119				p.I2265V		Atlas-SNP	.											.	PIEZO1	79	.	0			c.A6793G						PASS	.	T	VAL/ILE	186,1198		13,160,519	45.0	49.0	48.0		6793	2.3	1.0	16	dbSNP_89	48	1027,2145		150,727,709	yes	missense	PIEZO1	NM_001142864.2	29	163,887,1228	CC,CT,TT		32.377,13.4393,26.6242	probably-damaging	2265/2522	88783100	1213,3343	692	1586	2278	SO:0001583	missense	9780	exon47			TGACGATGTCCTC	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.6793A>G	16.37:g.88783100T>C	ENSP00000301015:p.Ile2265Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	416|416	0.19047619047619047|0.19047619047619047	55|55	0.11178861788617886|0.11178861788617886	82|82	0.2265193370165746|0.2265193370165746	48|48	0.08391608391608392|0.08391608391608392	231|231	0.30474934036939316|0.30474934036939316	T|T	12.61|12.61	1.988341|1.988341	0.35036|0.35036	0.134393|0.134393	0.32377|0.32377	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015;ENST00000327397	.|T;T	.|0.72394	.|-0.65;-0.65	4.67|4.67	2.32|2.32	0.28847|0.28847	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25485|0.25485	0.75|0.75	0.24021|0.24021	P|P	0.99614979|0.99614979	.|B;D;D	.|0.65815	.|0.288;0.995;0.995	.|P;D;D	.|0.79108	.|0.578;0.992;0.992	T|T	0.09885|0.09885	-1.0654|-1.0654	4|9	.|0.24483	.|T	.|0.36	-37.9372|-37.9372	10.6074|10.6074	0.45402|0.45402	0.0:0.0:0.3085:0.6915|0.0:0.0:0.3085:0.6915	rs1803382;rs58765949;rs1803382|rs1803382;rs58765949;rs1803382	.|2265;133;133	.|Q92508;E7EUT2;Q96HU3	.|PIEZ1_HUMAN;.;.	R|V	2210|2265;133	.|ENSP00000301015:I2265V;ENSP00000333704:I133V	.|ENSP00000301015:I2265V	H|I	-|-	2|1	0|0	FAM38A|FAM38A	87310601|87310601	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.910000|0.910000	0.53928|0.53928	5.680000|5.680000	0.68168|0.68168	0.144000|0.144000	0.18951|0.18951	0.460000|0.460000	0.39030|0.39030	CAT|ATC	T|0.811;C|0.189	0.189	strong		0.647	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
GC	2638	hgsc.bcm.edu	37	4	72618334	72618334	+	Missense_Mutation	SNP	A	A	C	rs7041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:72618334A>C	ENST00000273951.8	-	11	1639	c.1296T>G	c.(1294-1296)gaT>gaG	p.D432E	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Missense_Mutation_p.D451E|GC_ENST00000513476.1_Missense_Mutation_p.D432E	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	432	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.		D -> E (in allele GC*1S; dbSNP:rs7041). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2416779, ECO:0000269|PubMed:7505619, ECO:0000269|PubMed:8325650, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)	p.D432E(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	TGGGTGTGGCATCAGGCAATT	0.398													A|||	1911	0.381589	0.0938	0.5375	5008	,	,		18676	0.2996		0.5835	False		,,,				2504	0.5368				p.D451E		Atlas-SNP	.											GC,NS,carcinoma,0,1	GC	132	1	1	Substitution - Missense(1)	stomach(1)	c.T1353G	GRCh37	CM931251	GC	M	rs7041	PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP	765,3641	310.8+/-291.8	74,617,1512	179.0	152.0	161.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1296,1296,1353	-10.0	0.0	4	dbSNP_52	161	4808,3792	614.1+/-396.2	1334,2140,826	yes	missense,missense,missense	GC	NM_000583.3,NM_001204306.1,NM_001204307.1	45,45,45	1408,2757,2338	CC,CA,AA		44.093,17.3627,42.8495	benign,benign,benign	432/475,432/475,451/494	72618334	5573,7433	2203	4300	6503	SO:0001583	missense	2638	exon12			TGTGGCATCAGGC	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.1296T>G	4.37:g.72618334A>C	ENSP00000273951:p.Asp432Glu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Missense_Mutation	SNP	ENST00000273951.8	37	CCDS3550.1	843	0.385989010989011	47	0.09552845528455285	190	0.5248618784530387	164	0.2867132867132867	442	0.58311345646438	A	7.855	0.724733	0.15439	0.173627	0.55907	ENSG00000145321	ENST00000273951;ENST00000504199;ENST00000513476	T;T;T	0.18338	2.22;2.22;2.22	5.33	-10.0	0.00425	.	0.659026	0.16073	N	0.230909	T	0.00012	0.0000	L	0.35723	1.085	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43523	-0.9386	9	0.20519	T	0.43	.	6.1018	0.20051	0.313:0.1039:0.4813:0.1017	rs7041;rs222037;rs1047213;rs3172682;rs3737551;rs52808188;rs60269151;rs7041	451;432	D6RAK8;D6RF35	.;.	E	432;451;432	ENSP00000273951:D432E;ENSP00000421725:D451E;ENSP00000426683:D432E	ENSP00000273951:D432E	D	-	3	2	GC	72837198	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.805000	0.00362	-1.287000	0.02381	-1.055000	0.02315	GAT	A|0.597;C|0.403	0.403	strong		0.398	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2		
ANGPTL7	10218	hgsc.bcm.edu	37	1	11255008	11255008	+	Silent	SNP	T	T	C	rs2076658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11255008T>C	ENST00000376819.3	+	5	1208	c.969T>C	c.(967-969)taT>taC	p.Y323Y	MTOR_ENST00000361445.4_Intron|ANGPTL7_ENST00000476934.1_3'UTR	NM_021146.2	NP_066969.1	O43827	ANGL7_HUMAN	angiopoietin-like 7	323	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)		p.Y323Y(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)		TCACCTGGTATGGCTGGCATG	0.537													C|||	493	0.0984425	0.1316	0.072	5008	,	,		20379	0.0853		0.0249	False		,,,				2504	0.1616				p.Y323Y		Atlas-SNP	.											ANGPTL7,NS,carcinoma,0,1	ANGPTL7	23	1	1	Substitution - coding silent(1)	stomach(1)	c.T969C						PASS	.	C	,	453,3953	784.8+/-414.7	24,405,1774	116.0	95.0	102.0		,969	-8.7	0.2	1	dbSNP_96	102	211,8389	810.1+/-407.1	6,199,4095	no	intron,coding-synonymous	MTOR,ANGPTL7	NM_004958.3,NM_021146.2	,	30,604,5869	CC,CT,TT		2.4535,10.2814,5.1053	,	,323/347	11255008	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	10218	exon5			CTGGTATGGCTGG	Y16132	CCDS128.1	1p36	2013-02-06			ENSG00000171819	ENSG00000171819		"""Fibrinogen C domain containing"""	24078	protein-coding gene	gene with protein product						9727400, 11682471	Standard	NM_021146		Approved	CDT6, AngX	uc001ase.4	O43827	OTTHUMG00000002002	ENST00000376819.3:c.969T>C	1.37:g.11255008T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	53	0.407692	NM_021146	B2R9B2|F1T0A6|Q4ZGK4	Silent	SNP	ENST00000376819.3	37	CCDS128.1																																																																																			T|0.937;C|0.063	0.063	strong		0.537	ANGPTL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005564.1	NM_021146	
HPS1	3257	hgsc.bcm.edu	37	10	100195130	100195130	+	Silent	SNP	G	G	A	rs11539873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100195130G>A	ENST00000325103.6	-	5	530	c.297C>T	c.(295-297)acC>acT	p.T99T	HPS1_ENST00000338546.5_Silent_p.T99T|HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Silent_p.T99T	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	99					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		CCTCGCTCTCGGTGTGGTCAC	0.577									Hermansky-Pudlak syndrome				G|||	320	0.0638978	0.0045	0.0634	5008	,	,		18959	0.1508		0.0795	False		,,,				2504	0.0389				p.T99T		Atlas-SNP	.											.	HPS1	65	.	0			c.C297T						PASS	.	G	,	56,4350	52.9+/-88.7	1,54,2148	112.0	101.0	105.0		297,297	-10.6	0.0	10	dbSNP_120	105	512,8088	145.6+/-201.3	15,482,3803	no	coding-synonymous,coding-synonymous	HPS1	NM_000195.3,NM_182639.2	,	16,536,5951	AA,AG,GG		5.9535,1.271,4.3672	,	99/701,99/325	100195130	568,12438	2203	4300	6503	SO:0001819	synonymous_variant	3257	exon5	Familial Cancer Database	HPS, HPS1-8	GCTCTCGGTGTGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.297C>T	10.37:g.100195130G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																			G|0.942;A|0.058	0.058	strong		0.577	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
MRPS9	64965	hgsc.bcm.edu	37	2	105713697	105713697	+	Silent	SNP	A	A	G	rs15567	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	59	0	0		WXS	Illumina HiSeq	Phase_I	58	19	0.327586	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	
DYTN	391475	hgsc.bcm.edu	37	2	207564537	207564537	+	Silent	SNP	C	C	T	rs113447424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564537C>T	ENST00000452335.2	-	7	749	c.633G>A	c.(631-633)ccG>ccA	p.P211P	Y_RNA_ENST00000384589.1_RNA|DYTN_ENST00000477734.1_5'UTR	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	211						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GGTGGCAGGTCGGGAGCCACA	0.532													C|||	16	0.00319489	0.0076	0.0058	5008	,	,		16997	0.0		0.002	False		,,,				2504	0.0				p.P211P		Atlas-SNP	.											DYTN,medulla,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	DYTN	168	1	0			c.G633A						scavenged	.	C		46,3908		1,44,1932	70.0	76.0	74.0		633	-11.8	0.0	2	dbSNP_132	74	52,8280		0,52,4114	no	coding-synonymous	DYTN	NM_001093730.1		1,96,6046	TT,TC,CC		0.6241,1.1634,0.7977		211/579	207564537	98,12188	1977	4166	6143	SO:0001819	synonymous_variant	391475	exon7			GCAGGTCGGGAGC	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.633G>A	2.37:g.207564537C>T		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_001093730		Silent	SNP	ENST00000452335.2	37	CCDS46502.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
R3HDML	140902	hgsc.bcm.edu	37	20	42973935	42973935	+	Silent	SNP	T	T	C	rs11697359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:42973935T>C	ENST00000217043.2	+	4	718	c.546T>C	c.(544-546)tgT>tgC	p.C182C	Y_RNA_ENST00000364493.1_RNA|RP5-881L22.5_ENST00000438702.1_RNA	NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	182	SCP.					extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			GGCTGGGCTGTGCCATCCACA	0.582													C|||	327	0.0652955	0.0348	0.1037	5008	,	,		15835	0.0		0.1461	False		,,,				2504	0.0634				p.C182C		Atlas-SNP	.											R3HDML,NS,carcinoma,0,1	R3HDML	33	1	0			c.T546C						PASS	.	C		222,4184	806.0+/-415.8	4,214,1985	145.0	124.0	131.0		546	-5.3	0.9	20	dbSNP_120	131	1184,7416	763.0+/-407.6	71,1042,3187	no	coding-synonymous	R3HDML	NM_178491.2		75,1256,5172	CC,CT,TT		13.7674,5.0386,10.8104		182/254	42973935	1406,11600	2203	4300	6503	SO:0001819	synonymous_variant	140902	exon4			GGGCTGTGCCATC	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.546T>C	20.37:g.42973935T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	NM_178491		Silent	SNP	ENST00000217043.2	37	CCDS13329.1																																																																																			T|0.901;C|0.099	0.099	strong		0.582	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
KIR3DL3	115653	hgsc.bcm.edu	37	19	55247306	55247306	+	Silent	SNP	A	A	G	rs62132702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55247306A>G	ENST00000291860.1	+	7	1092	c.1074A>G	c.(1072-1074)caA>caG	p.Q358Q	KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_5'Flank|KIR2DL3_ENST00000342376.3_5'Flank|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	358						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TAATGGACCAAGAGCCTGCAG	0.517													.|||	374	0.0746805	0.0068	0.0576	5008	,	,		12655	0.1121		0.1252	False		,,,				2504	0.0879				p.Q358Q		Atlas-SNP	.											KIR3DL3,NS,carcinoma,0,2	KIR3DL3	46	2	0			c.A1074G						PASS	.	A		90,3832		26,38,1897	67.0	79.0	75.0		1074	0.9	0.0	19	dbSNP_129	75	1078,6770		320,438,3166	no	coding-synonymous	KIR3DL3	NM_153443.3		346,476,5063	GG,GA,AA		13.736,2.2947,9.9235		358/411	55247306	1168,10602	1961	3924	5885	SO:0001819	synonymous_variant	115653	exon7			GGACCAAGAGCCT	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.1074A>G	19.37:g.55247306A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	52	33	0.634615	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Silent	SNP	ENST00000291860.1	37	CCDS12903.1																																																																																			.	.	weak		0.517	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
DTX1	1840	hgsc.bcm.edu	37	12	113532617	113532617	+	Silent	SNP	A	A	G	rs12427377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:113532617A>G	ENST00000257600.3	+	6	1754	c.1251A>G	c.(1249-1251)cgA>cgG	p.R417R	DTX1_ENST00000547974.1_3'UTR	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	417					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						GCATGGAGCGACTGGTCACAG	0.672													G|||	324	0.0646965	0.0401	0.0879	5008	,	,		14354	0.0		0.1521	False		,,,				2504	0.0583				p.R417R		Atlas-SNP	.											DTX1,NS,carcinoma,0,1	DTX1	83	1	0			c.A1251G						PASS	.	G		271,4135	780.3+/-414.4	8,255,1940	40.0	37.0	38.0		1251	-4.8	0.9	12	dbSNP_120	38	1261,7339	739.1+/-407.1	94,1073,3133	no	coding-synonymous	DTX1	NM_004416.2		102,1328,5073	GG,GA,AA		14.6628,6.1507,11.7792		417/621	113532617	1532,11474	2203	4300	6503	SO:0001819	synonymous_variant	1840	exon6			GGAGCGACTGGTC	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.1251A>G	12.37:g.113532617A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			A|0.898;G|0.102	0.102	strong		0.672	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
KCNK17	89822	hgsc.bcm.edu	37	6	39267230	39267230	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:39267230G>A	ENST00000373231.4	-	5	1204	c.972C>T	c.(970-972)caC>caT	p.H324H	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	324					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)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						aGCCTGCAGCGTGAGCAGAAG	0.547																																					p.H324H		Atlas-SNP	.											.	KCNK17	61	.	0			c.C972T						PASS	.						68.0	60.0	63.0					6																	39267230		2203	4300	6503	SO:0001819	synonymous_variant	89822	exon5			TGCAGCGTGAGCA	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.972C>T	6.37:g.39267230G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Silent	SNP	ENST00000373231.4	37	CCDS4842.1																																																																																			.	.	none		0.547	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
HEXDC	284004	hgsc.bcm.edu	37	17	80393704	80393704	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80393704T>C	ENST00000327949.9	+	5	598	c.587T>C	c.(586-588)gTg>gCg	p.V196A	HEXDC_ENST00000337014.6_Missense_Mutation_p.V196A|HEXDC_ENST00000577944.1_Missense_Mutation_p.V196A			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	196					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)			ACACCCCTGGTGTGGGACGAC	0.682																																					p.V196A		Atlas-SNP	.											.	HEXDC	43	.	0			c.T587C						PASS	.						50.0	60.0	57.0					17																	80393704		2060	4155	6215	SO:0001583	missense	284004	exon6			CCCTGGTGTGGGA	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.587T>C	17.37:g.80393704T>C	ENSP00000332634:p.Val196Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	37		.	.	.	.	.	.	.	.	.	.	T	10.28	1.306572	0.23736	.	.	ENSG00000169660	ENST00000337014;ENST00000327949	D;D	0.95821	-3.82;-3.82	5.72	4.65	0.58169	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.286925	0.43110	N	0.000601	D	0.87474	0.6186	N	0.05592	-0.015	0.36187	D	0.849809	B;B	0.22276	0.027;0.067	B;B	0.20955	0.026;0.032	D	0.83518	0.0084	10	0.30854	T	0.27	-18.7938	8.2399	0.31654	0.0:0.152:0.0:0.848	.	196;196	Q8WVB3;Q8WVB3-2	HEXDC_HUMAN;.	A	196	ENSP00000337854:V196A;ENSP00000332634:V196A	ENSP00000332634:V196A	V	+	2	0	HEXDC	77986993	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	4.183000	0.58317	0.995000	0.38917	-0.376000	0.06991	GTG	.	.	none		0.682	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620	
NUDT7	283927	hgsc.bcm.edu	37	16	77769834	77769834	+	Missense_Mutation	SNP	G	G	A	rs308925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:77769834G>A	ENST00000268533.5	+	3	368	c.299G>A	c.(298-300)cGt>cAt	p.R100H	NUDT7_ENST00000437314.3_Intron|NUDT7_ENST00000568787.1_Missense_Mutation_p.R100H|NUDT7_ENST00000564085.1_Missense_Mutation_p.R100H|NUDT7_ENST00000563839.1_Intron	NM_001105663.2	NP_001099133.1	P0C024	NUDT7_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 7	100	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.		R -> H (in dbSNP:rs308925).		acetyl-CoA catabolic process (GO:0046356)|brown fat cell differentiation (GO:0050873)|coenzyme A catabolic process (GO:0015938)|nucleoside diphosphate metabolic process (GO:0009132)	peroxisome (GO:0005777)	acetyl-CoA hydrolase activity (GO:0003986)|hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides (GO:0016818)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|receptor binding (GO:0005102)|snoRNA binding (GO:0030515)			breast(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|skin(1)	18						GTGGGTCTCCGTCCTCACCAA	0.572													G|||	1164	0.232428	0.1157	0.2075	5008	,	,		15914	0.2778		0.2336	False		,,,				2504	0.3599				p.R100H		Atlas-SNP	.											.	NUDT7	47	.	0			c.G299A						PASS	.	G	HIS/ARG	473,3621		30,413,1604	113.0	120.0	118.0		299	-3.4	0.0	16	dbSNP_79	118	1410,6976		117,1176,2900	yes	missense	NUDT7	NM_001105663.2	29	147,1589,4504	AA,AG,GG		16.8137,11.5535,15.0881	benign	100/239	77769834	1883,10597	2047	4193	6240	SO:0001583	missense	283927	exon3			GTCTCCGTCCTCA	AA227330	CCDS42195.1, CCDS58480.1, CCDS58479.1, CCDS73916.1	16q23.1	2007-06-15				ENSG00000140876		"""Nudix motif containing"""	8054	protein-coding gene	gene with protein product		609231				11415433	Standard	NM_001105663		Approved		uc010chd.3	P0C024		ENST00000268533.5:c.299G>A	16.37:g.77769834G>A	ENSP00000268533:p.Arg100His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_001243657	B4DLE5|H3BUB8	Missense_Mutation	SNP	ENST00000268533.5	37	CCDS42195.1	481	0.22023809523809523	62	0.12601626016260162	70	0.19337016574585636	167	0.291958041958042	182	0.24010554089709762	G	6.335	0.429953	0.11987	0.115535	0.168137	ENSG00000140876	ENST00000268533	T	0.08807	3.05	5.72	-3.44	0.04796	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	1.158930	0.06024	N	0.651727	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.48490	-0.9031	9	0.23302	T	0.38	0.1902	13.0348	0.58864	0.4973:0.0:0.5027:0.0	rs308925;rs17773575;rs52819583;rs59180982;rs308925	100	P0C024	NUDT7_HUMAN	H	100	ENSP00000268533:R100H	ENSP00000268533:R100H	R	+	2	0	NUDT7	76327335	0.000000	0.05858	0.021000	0.16686	0.161000	0.22273	-2.239000	0.01198	-1.072000	0.03141	-0.133000	0.14855	CGT	G|0.801;N|0.001	.	strong		0.572	NUDT7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433873.1		
OR7C1	26664	hgsc.bcm.edu	37	19	14910210	14910210	+	Missense_Mutation	SNP	C	C	G	rs73004304	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	85	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	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		
CACNA2D1	781	hgsc.bcm.edu	37	7	81588636	81588636	+	Silent	SNP	G	G	A	rs1229502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:81588636G>A	ENST00000356253.5	-	38	3405	c.3150C>T	c.(3148-3150)ccC>ccT	p.P1050P	CACNA2D1_ENST00000356860.3_Silent_p.P1038P|CACNA2D1_ENST00000535308.1_Silent_p.P250P			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	1050					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.P1038P(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTCGGTATCTGGGTTGCTTAA	0.358													G|||	1115	0.222644	0.1127	0.255	5008	,	,		18274	0.2371		0.3042	False		,,,				2504	0.2495				p.P1038P		Atlas-SNP	.											CACNA2D1,NS,carcinoma,0,1	CACNA2D1	191	1	1	Substitution - coding silent(1)	stomach(1)	c.C3114T						PASS	.	G		608,3798	262.8+/-265.1	49,510,1644	114.0	104.0	107.0		3114	3.1	1.0	7	dbSNP_87	107	2712,5888	432.7+/-357.2	484,1744,2072	no	coding-synonymous	CACNA2D1	NM_000722.2		533,2254,3716	AA,AG,GG		31.5349,13.7994,25.5267		1038/1092	81588636	3320,9686	2203	4300	6503	SO:0001819	synonymous_variant	781	exon38			GTATCTGGGTTGC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.3150C>T	7.37:g.81588636G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																				G|0.750;A|0.250	0.250	strong		0.358	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
PPP1R15B	84919	hgsc.bcm.edu	37	1	204379452	204379452	+	Missense_Mutation	SNP	T	T	C	rs2089891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:204379452T>C	ENST00000367188.4	-	1	1467	c.1088A>G	c.(1087-1089)gAa>gGa	p.E363G	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	363			E -> G (in dbSNP:rs2089891).		ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			TTCTATTTTTTCTTCAGTGGA	0.458													T|||	232	0.0463259	0.0575	0.0346	5008	,	,		19036	0.0		0.0924	False		,,,				2504	0.0399				p.E363G		Atlas-SNP	.											.	PPP1R15B	67	.	0			c.A1088G						PASS	.	T	GLY/GLU	237,4169	122.5+/-159.9	6,225,1972	67.0	74.0	72.0		1088	-0.1	0.0	1	dbSNP_96	72	636,7962	147.4+/-202.8	21,594,3684	yes	missense	PPP1R15B	NM_032833.3	98	27,819,5656	CC,CT,TT		7.3971,5.379,6.7133	benign	363/714	204379452	873,12131	2203	4299	6502	SO:0001583	missense	84919	exon1			ATTTTTTCTTCAG	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14951	protein-coding gene	gene with protein product		613257	"""protein phosphatase 1, regulatory (inhibitor) subunit 15B"""			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1088A>G	1.37:g.204379452T>C	ENSP00000356156:p.Glu363Gly	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Missense_Mutation	SNP	ENST00000367188.4	37	CCDS1445.1	104	0.047619047619047616	23	0.046747967479674794	18	0.049723756906077346	0	0.0	63	0.08311345646437995	T	11.83	1.754641	0.31046	0.05379	0.073971	ENSG00000158615	ENST00000367188;ENST00000543650	T	0.19938	2.11	5.1	-0.117	0.13551	Protein phosphatase 1, regulatory subunit 15B, N-terminal (1);	0.928117	0.09135	N	0.843835	T	0.00784	0.0026	L	0.47716	1.5	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.28808	-1.0032	10	0.36615	T	0.2	-4.4508	4.0526	0.09801	0.0:0.2886:0.1781:0.5334	rs2089891;rs17475029;rs52826289;rs2089891	363	Q5SWA1	PR15B_HUMAN	G	363;273	ENSP00000356156:E363G	ENSP00000356156:E363G	E	-	2	0	PPP1R15B	202646075	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	0.043000	0.13971	0.007000	0.14760	-0.264000	0.10439	GAA	T|0.945;C|0.055	0.055	strong		0.458	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833	
KRT40	125115	hgsc.bcm.edu	37	17	39135214	39135214	+	Silent	SNP	T	T	C	rs8068970	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	74	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	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	
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281007A>G	ENST00000368799.1	-	3	6390	c.6355T>C	c.(6355-6357)Tat>Cat	p.Y2119H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2119	Ser-rich.		Y -> H (in dbSNP:rs7512553).		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)			GCCTGATCATAATGGGATCCT	0.572									Ichthyosis				-|||	1641	0.327676	0.3843	0.3357	5008	,	,		29956	0.4355		0.1282	False		,,,				2504	0.3395				p.Y2119H		Atlas-SNP	.											FLG,brain,glioma,+2,1	FLG	900	1	0			c.T6355C						PASS	.	G	HIS/TYR	1451,2955		0,1451,752	349.0	263.0	292.0		6355	1.3	0.0	1	dbSNP_116	292	1089,7511		0,1089,3211	yes	missense	FLG	NM_002016.1	83	0,2540,3963	GG,GA,AA		12.6628,32.9324,19.5294	benign	2119/4062	152281007	2540,10466	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCATAATGGGA	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.6355T>C	1.37:g.152281007A>G	ENSP00000357789:p.Tyr2119His	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	423	175	0.413712	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	4.212	0.038141	0.08148	0.329324	0.126628	ENSG00000143631	ENST00000368799	T	0.02345	4.33	3.26	1.28	0.21552	.	.	.	.	.	T	0.00178	0.0005	N	0.00049	-2.42	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	9	0.14656	T	0.56	.	3.5172	0.07728	0.2299:0.0:0.5769:0.1931	.	2119	P20930	FILA_HUMAN	H	2119	ENSP00000357789:Y2119H	ENSP00000357789:Y2119H	Y	-	1	0	FLG	150547631	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.121000	0.15667	-0.057000	0.13199	-3.035000	0.00072	TAT	A|0.030;G|0.970	0.970	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SEC16B	89866	hgsc.bcm.edu	37	1	177902387	177902387	+	Missense_Mutation	SNP	C	C	A	rs61745560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177902387C>A	ENST00000308284.6	-	22	2874	c.2785G>T	c.(2785-2787)Gct>Tct	p.A929S	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	929				A -> S (in Ref. 4; CAI46016). {ECO:0000305}.	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						TCGTCTCCAGCGGGGGATGCG	0.592													A|||	1139	0.227436	0.2655	0.2608	5008	,	,		17935	0.1052		0.2604	False		,,,				2504	0.2444				p.A929S		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2785T						PASS	.	A	SER/ALA	1116,2828		153,810,1009	29.0	35.0	33.0		2785	2.7	0.3	1	dbSNP_129	33	1952,6404		231,1490,2457	yes	missense	SEC16B	NM_033127.2	99	384,2300,3466	AA,AC,CC		23.3605,28.2961,24.9431	benign	929/1061	177902387	3068,9232	1972	4178	6150	SO:0001583	missense	89866	exon22			CTCCAGCGGGGGA	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.2785G>T	1.37:g.177902387C>A	ENSP00000308339:p.Ala929Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	484	0.2216117216117216	114	0.23170731707317074	95	0.26243093922651933	73	0.12762237762237763	202	0.26649076517150394	A	9.107	1.005487	0.19199	0.282961	0.233605	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.13089	2.62	5.19	2.68	0.31781	.	0.478491	0.19860	N	0.104444	T	0.00012	0.0000	N	0.00325	-1.645	0.49483	P	2.0299999999995322E-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	0.43360	-0.9396	9	0.10636	T	0.68	-11.2487	4.9398	0.13960	0.4842:0.1644:0.0:0.3515	rs61745560	484;930;929;626	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	S	929;613;644	ENSP00000308339:A929S	ENSP00000239472:A644S	A	-	1	0	AL359075.1	176169010	0.563000	0.26594	0.314000	0.25224	0.002000	0.02628	0.987000	0.29603	0.287000	0.22375	-0.256000	0.11100	GCT	C|0.774;A|0.226	0.226	strong		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
MUC4	4585	hgsc.bcm.edu	37	3	195506569	195506569	+	Missense_Mutation	SNP	A	A	G	rs201891747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195506569A>G	ENST00000463781.3	-	2	12341	c.11882T>C	c.(11881-11883)gTa>gCa	p.V3961A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3961A	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)		ACCTGTGGATACTGAGGAAGT	0.592													.|||	988	0.197284	0.1755	0.2075	5008	,	,		8418	0.0804		0.336	False		,,,				2504	0.1973				p.V3961A		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.T11882C						scavenged	.						17.0	11.0	13.0					3																	195506569		677	1513	2190	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	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.11882T>C	3.37:g.195506569A>G	ENSP00000417498:p.Val3961Ala	Somatic	38	28	0.736842		WXS	Illumina HiSeq	Phase_I	27	19	0.703704	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	.	.	.	.	.	.	.	.	.	.	a	0.974	-0.699236	0.03279	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.36;1.3	.	.	.	.	.	.	.	.	T	0.16642	0.0400	N	0.19112	0.55	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.18935	-1.0321	7	.	.	.	6.9246	3.9397	0.09321	0.6657:0.0:0.3343:0.0	.	3833	E7ESK3	.	A	3961	ENSP00000417498:V3961A;ENSP00000420243:V3961A	.	V	-	2	0	MUC4	196991348	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	-4.523000	0.00221	-2.036000	0.00922	-2.094000	0.00368	GTA	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC16	94025	hgsc.bcm.edu	37	19	9083124	9083124	+	Silent	SNP	G	G	A	rs12608495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9083124G>A	ENST00000397910.4	-	1	8894	c.8691C>T	c.(8689-8691)gtC>gtT	p.V2897V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2898	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)		p.V2897V(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						CCAAACTTGGGACCTCAGAAA	0.512													G|||	696	0.138978	0.0174	0.1527	5008	,	,		21125	0.0496		0.3042	False		,,,				2504	0.2157				p.V2897V		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	stomach(2)	c.C8691T						PASS	.	G		270,3522		12,246,1638	77.0	70.0	72.0		8691	-0.9	0.0	19	dbSNP_120	72	2507,5739		381,1745,1997	no	coding-synonymous	MUC16	NM_024690.2		393,1991,3635	AA,AG,GG		30.4026,7.1203,23.0686		2897/14508	9083124	2777,9261	1896	4123	6019	SO:0001819	synonymous_variant	94025	exon1			ACTTGGGACCTCA	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.8691C>T	19.37:g.9083124G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.840;A|0.160	0.160	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CACNA1H	8912	hgsc.bcm.edu	37	16	1270349	1270349	+	Silent	SNP	T	T	C	rs4247094	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1270349T>C	ENST00000348261.5	+	35	6665	c.6417T>C	c.(6415-6417)gaT>gaC	p.D2139D	CACNA1H_ENST00000565831.1_Silent_p.D2133D|CACNA1H_ENST00000358590.4_Silent_p.D2133D	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2139					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)	ACAGCGTGGATGCTCAGGGCT	0.761													C|||	4577	0.913938	0.9312	0.8401	5008	,	,		11184	0.999		0.827	False		,,,				2504	0.9448				p.D2139D		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T6417C						PASS	.	C	,	3072,276		1409,254,11	7.0	9.0	8.0		6399,6417	-5.8	0.0	16	dbSNP_111	8	6099,1221		2546,1007,107	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	3955,1261,118	CC,CT,TT		16.6803,8.2437,14.0326	,	2133/2348,2139/2354	1270349	9171,1497	1674	3660	5334	SO:0001819	synonymous_variant	8912	exon35			CGTGGATGCTCAG	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.6417T>C	16.37:g.1270349T>C		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			T|0.102;C|0.898	0.898	strong		0.761	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
G6PC2	57818	hgsc.bcm.edu	37	2	169764176	169764176	+	Missense_Mutation	SNP	G	G	C	rs492594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:169764176G>C	ENST00000375363.3	+	5	747	c.655G>C	c.(655-657)Gtt>Ctt	p.V219L	G6PC2_ENST00000429379.2_3'UTR|G6PC2_ENST00000461586.1_3'UTR|SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000421979.1_3'UTR	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	219			V -> L (in dbSNP:rs492594).		carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.V219L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						CCTGTTTGCAGTTGGCTTTTA	0.527													C|||	2321	0.463458	0.3101	0.5634	5008	,	,		21028	0.4335		0.4443	False		,,,				2504	0.6503				p.V219L		Atlas-SNP	.											G6PC2,NS,carcinoma,0,1	G6PC2	44	1	1	Substitution - Missense(1)	stomach(1)	c.G655C						PASS	.	C	,LEU/VAL	1416,2990	685.6+/-404.6	221,974,1008	216.0	171.0	186.0		,655	3.1	0.9	2	dbSNP_83	186	3923,4677	605.1+/-394.9	899,2125,1276	yes	utr-3,missense	G6PC2	NM_001081686.1,NM_021176.2	,32	1120,3099,2284	CC,CG,GG		45.6163,32.138,41.0503	,benign	,219/356	169764176	5339,7667	2203	4300	6503	SO:0001583	missense	57818	exon5			TTTGCAGTTGGCT	AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"""islet specific glucose 6 phosphatase catalytic subunit related protein"""	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.655G>C	2.37:g.169764176G>C	ENSP00000364512:p.Val219Leu	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	255	254	0.996078	NM_021176	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	ENST00000375363.3	37	CCDS2230.1	958	0.43864468864468864	166	0.33739837398373984	204	0.56353591160221	249	0.4353146853146853	339	0.4472295514511873	C	2.235	-0.375122	0.05034	0.32138	0.456163	ENSG00000152254	ENST00000375363	T	0.74315	-0.83	5.86	3.06	0.35304	.	0.500214	0.19206	N	0.120047	T	0.00012	0.0000	N	0.01656	-0.775	0.09310	P	0.9999999999999954	B	0.02656	0.0	B	0.01281	0.0	T	0.43814	-0.9368	9	0.02654	T	1	-19.5491	5.6207	0.17455	0.1171:0.6455:0.1129:0.1245	rs492594;rs3732032;rs52825832;rs492594	219	Q9NQR9	G6PC2_HUMAN	L	219	ENSP00000364512:V219L	ENSP00000364512:V219L	V	+	1	0	G6PC2	169472422	0.973000	0.33851	0.882000	0.34594	0.655000	0.38815	2.141000	0.42168	0.398000	0.25338	-0.824000	0.03097	GTT	G|0.584;C|0.416	0.416	strong		0.527	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176	
KLK4	9622	hgsc.bcm.edu	37	19	51412668	51412668	+	Missense_Mutation	SNP	A	A	C	rs1654551	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51412668A>C	ENST00000324041.1	-	2	63	c.64T>G	c.(64-66)Tcg>Gcg	p.S22A	KLK4_ENST00000597441.1_5'Flank|KLK4_ENST00000431178.2_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						PASS	.	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	100	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228547901	228547901	+	Intron	SNP	C	C	T	rs12035900	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228547901C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000284548.11_Silent_p.D6436D|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Silent_p.D3555D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AAGACGGAGACGCCTTTGTGA	0.637													C|||	1496	0.298722	0.1142	0.3112	5008	,	,		18726	0.2669		0.328	False		,,,				2504	0.5419				p.D6436D		Atlas-SNP	.											OBSCN_ENST00000284548,NS,carcinoma,0,1	OBSCN	2142	1	0			c.C19308T						scavenged	.	C	,	699,3671		53,593,1539	51.0	63.0	59.0		,19308	-3.8	0.0	1	dbSNP_120	59	2582,5992		417,1748,2122	yes	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	470,2341,3661	TT,TC,CC		30.1143,15.9954,25.3477	,	,6436/6621	228547901	3281,9663	2185	4287	6472	SO:0001627	intron_variant	84033	exon81			CGGAGACGCCTTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2376C>T	1.37:g.228547901C>T		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	54	33	0.611111	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.727;T|0.273	0.273	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KIAA0368	23392	hgsc.bcm.edu	37	9	114195587	114195587	+	Silent	SNP	G	G	A	rs2297530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:114195587G>A	ENST00000338205.5	-	7	993	c.774C>T	c.(772-774)caC>caT	p.H258H	KIAA0368_ENST00000259335.4_Silent_p.H436H			Q5VYK3	ECM29_HUMAN	KIAA0368	264					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CAATCACCAAGTGGAGAACAG	0.443													G|||	430	0.0858626	0.0023	0.0807	5008	,	,		19782	0.1984		0.0666	False		,,,				2504	0.1063				p.H436H		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C1308T						PASS	.	G		58,3850		0,58,1896	113.0	108.0	109.0		1308	2.6	1.0	9	dbSNP_100	109	464,7826		17,430,3698	no	coding-synonymous	KIAA0368	NM_001080398.1		17,488,5594	AA,AG,GG		5.5971,1.4841,4.2794		436/2018	114195587	522,11676	1954	4145	6099	SO:0001819	synonymous_variant	23392	exon9			CACCAAGTGGAGA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.774C>T	9.37:g.114195587G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				G|0.908;A|0.092	0.092	strong		0.443	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
FANCD2	2177	hgsc.bcm.edu	37	3	10085536	10085536	+	Silent	SNP	A	A	G	rs34046352	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10085536A>G	ENST00000419585.1	+	14	1283	c.1122A>G	c.(1120-1122)gtA>gtG	p.V374V	FANCD2_ENST00000287647.3_Silent_p.V374V|FANCD2_ENST00000383807.1_Silent_p.V374V|FANCD2_ENST00000383806.1_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	69	0	0		WXS	Illumina HiSeq	Phase_I	115	37	0.321739	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		
LCA5	167691	hgsc.bcm.edu	37	6	80228535	80228535	+	Missense_Mutation	SNP	T	T	G	rs34068461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:80228535T>G	ENST00000392959.1	-	3	688	c.77A>C	c.(76-78)gAt>gCt	p.D26A	LCA5_ENST00000467898.3_Missense_Mutation_p.D26A|LCA5_ENST00000369846.4_Missense_Mutation_p.D26A	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	26			D -> A (in dbSNP:rs34068461).		intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		CGTTTCAAAATCAGATAAGTA	0.418													T|||	867	0.173123	0.0741	0.2334	5008	,	,		17933	0.2192		0.173	False		,,,				2504	0.2168				p.D26A		Atlas-SNP	.											.	LCA5	71	.	0			c.A77C						PASS	.	T	ALA/ASP,ALA/ASP	338,4068	178.0+/-206.8	12,314,1877	301.0	284.0	290.0		77,77	4.1	0.9	6	dbSNP_126	290	1559,7041	294.2+/-301.7	129,1301,2870	yes	missense,missense	LCA5	NM_001122769.2,NM_181714.3	126,126	141,1615,4747	GG,GT,TT		18.1279,7.6714,14.5856	probably-damaging,probably-damaging	26/698,26/698	80228535	1897,11109	2203	4300	6503	SO:0001583	missense	167691	exon2			TCAAAATCAGATA		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.77A>C	6.37:g.80228535T>G	ENSP00000376686:p.Asp26Ala	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	207	105	0.507246	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	376	0.17216117216117216	43	0.08739837398373984	84	0.23204419889502761	129	0.22552447552447552	120	0.158311345646438	T	17.17	3.320429	0.60634	0.076714	0.181279	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.62788	-0.0;-0.0	5.28	4.09	0.47781	.	0.662303	0.14761	N	0.299945	T	0.42494	0.1205	L	0.59436	1.845	0.29152	P	0.87834	B;B	0.20671	0.004;0.047	B;B	0.23419	0.01;0.046	T	0.43410	-0.9393	9	0.62326	D	0.03	-2.4209	10.295	0.43618	0.0:0.0:0.1657:0.8343	rs34068461	26;26	B4DRL2;Q86VQ0	.;LCA5_HUMAN	A	26	ENSP00000358861:D26A;ENSP00000376686:D26A	ENSP00000358861:D26A	D	-	2	0	LCA5	80285254	0.997000	0.39634	0.864000	0.33941	0.599000	0.36880	2.917000	0.48821	0.986000	0.38683	0.533000	0.62120	GAT	T|0.843;G|0.157	0.157	strong		0.418	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
KRT27	342574	hgsc.bcm.edu	37	17	38935876	38935876	+	Missense_Mutation	SNP	C	C	T	rs17558532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38935876C>T	ENST00000301656.3	-	5	890	c.850G>A	c.(850-852)Gcc>Acc	p.A284T	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)				TGCAGCGAGGCGCTCTGGAAC	0.627													C|||	808	0.161342	0.1611	0.1571	5008	,	,		13962	0.0625		0.1849	False		,,,				2504	0.2423				p.A284T		Atlas-SNP	.											.	KRT27	41	.	0			c.G850A						PASS	.	C	THR/ALA	763,3643	310.2+/-291.5	70,623,1510	39.0	37.0	38.0		850	5.5	1.0	17	dbSNP_123	38	1469,7131	279.3+/-293.9	127,1215,2958	yes	missense	KRT27	NM_181537.3	58	197,1838,4468	TT,TC,CC		17.0814,17.3173,17.1613	benign	284/460	38935876	2232,10774	2203	4300	6503	SO:0001583	missense	342574	exon5			GCGAGGCGCTCTG	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.850G>A	17.37:g.38935876C>T	ENSP00000301656:p.Ala284Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	297	0.13598901098901098	63	0.12804878048780488	60	0.16574585635359115	31	0.05419580419580419	143	0.18865435356200527	C	23.3	4.403329	0.83230	0.173173	0.170814	ENSG00000171446	ENST00000301656	D	0.89196	-2.48	5.52	5.52	0.82312	Filament (1);	0.000000	0.64402	D	0.000015	T	0.00524	0.0017	L	0.31476	0.935	0.20563	P	0.999887189	P	0.35872	0.525	B	0.34180	0.177	T	0.37384	-0.9708	9	0.51188	T	0.08	.	18.7774	0.91916	0.0:1.0:0.0:0.0	rs17558532;rs17558532	284	Q7Z3Y8	K1C27_HUMAN	T	284	ENSP00000301656:A284T	ENSP00000301656:A284T	A	-	1	0	KRT27	36189402	0.011000	0.17503	0.998000	0.56505	0.903000	0.53119	2.482000	0.45224	2.754000	0.94517	0.591000	0.81541	GCC	C|0.849;T|0.151	0.151	strong		0.627	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882673	143882673	+	Missense_Mutation	SNP	C	C	T	rs201010806	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143882673C>T	ENST00000486333.1	+	1	2115	c.2077C>T	c.(2077-2079)Ctt>Ttt	p.L693F		NM_198495.2	NP_940897.2	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4	693	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(1)|ovary(2)	3						TGGCCCTGGCCTTATTCCTCC	0.488																																					p.L693F		Atlas-SNP	.											CTAGE4,NS,carcinoma,0,1	CTAGE4	10	1	0			c.C2077T						scavenged	.						3.0	4.0	4.0					7																	143882673		116	650	766	SO:0001583	missense	100128553	exon1			CCTGGCCTTATTC	AF338232	CCDS55176.1	7q35	2009-10-15			ENSG00000225932	ENSG00000225932			24772	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 4"""	608910				12839582, 11149944	Standard	NM_198495		Approved	FLJ43692, cTAGE-4	uc010lpc.3	Q8IX94	OTTHUMG00000157997	ENST00000486333.1:c.2077C>T	7.37:g.143882673C>T	ENSP00000419539:p.Leu693Phe	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	200	92	0.46	NM_198495	A8K871|O95046	Missense_Mutation	SNP	ENST00000486333.1	37	CCDS55176.1	.	.	.	.	.	.	.	.	.	.	.	0.639	-0.814097	0.02798	.	.	ENSG00000225932	ENST00000486333	T	0.05447	3.44	.	.	.	.	.	.	.	.	T	0.00666	0.0022	N	0.00016	-2.855	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36625	-0.9740	7	0.02654	T	1	.	.	.	.	.	693	Q8IX94	CTGE4_HUMAN	F	693	ENSP00000419539:L693F	ENSP00000419539:L693F	L	+	1	0	CTAGE4	143513606	0.830000	0.29337	0.003000	0.11579	0.003000	0.03518	0.348000	0.20031	-1.497000	0.01826	-1.514000	0.00941	CTT	.	.	weak		0.488	CTAGE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349970.1	NM_198495	
ZNF302	55900	hgsc.bcm.edu	37	19	35175208	35175208	+	Missense_Mutation	SNP	A	A	G	rs2290652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35175208A>G	ENST00000446502.2	+	6	606	c.398A>G	c.(397-399)tAt>tGt	p.Y133C	ZNF302_ENST00000509528.1_Missense_Mutation_p.M21V|ZNF302_ENST00000507959.1_3'UTR|ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000505242.1_Missense_Mutation_p.Y89C|ZNF302_ENST00000457781.2_Missense_Mutation_p.Y89C|ZNF302_ENST00000423823.2_Missense_Mutation_p.Y89C			Q9NR11	ZN302_HUMAN	zinc finger protein 302	73					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)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AAGGATATTTATGATGAAGAT	0.289													A|||	1255	0.250599	0.1369	0.2075	5008	,	,		15422	0.3006		0.3767	False		,,,				2504	0.2536				p.Y89C		Atlas-SNP	.											.	ZNF302	27	.	0			c.A266G						PASS	.	A	CYS/TYR,CYS/TYR	726,3476		68,590,1443	47.0	51.0	50.0		266,266	1.0	0.7	19	dbSNP_100	50	3012,5452		533,1946,1753	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	194,194	601,2536,3196	GG,GA,AA		35.586,17.2775,29.5121	probably-damaging,probably-damaging	89/400,89/400	35175208	3738,8928	2101	4232	6333	SO:0001583	missense	55900	exon5			ATATTTATGATGA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.398A>G	19.37:g.35175208A>G	ENSP00000396379:p.Tyr133Cys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	197	110	0.558376	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		615	0.2815934065934066	74	0.15040650406504066	83	0.2292817679558011	174	0.3041958041958042	284	0.37467018469656993	A	10.21	1.288432	0.23478	0.172775	0.35586	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000446502	T;T;T;T;T	0.04654	3.59;3.59;6.05;3.59;3.58	0.967	0.967	0.19674	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41825	P	0.009959999999999969	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	T	0.48410	-0.9038	7	0.45353	T	0.12	.	4.1694	0.10322	1.0:0.0:0.0:0.0	rs2290652;rs17649399;rs52790156;rs60043199;rs2290652	133;89	E7EVR1;Q9NR11-2	.;.	C	89;89;89;89;133	ENSP00000391067:Y89C;ENSP00000421028:Y89C;ENSP00000421696:Y89C;ENSP00000405219:Y89C;ENSP00000396379:Y133C	ENSP00000405219:Y89C	Y	+	2	0	ZNF302	39867048	0.989000	0.36119	0.678000	0.29963	0.054000	0.15201	0.223000	0.17719	0.686000	0.31488	0.383000	0.25322	TAT	A|0.726;G|0.274	0.274	strong		0.289	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
DRICH1	51233	hgsc.bcm.edu	37	22	23974200	23974200	+	Missense_Mutation	SNP	A	A	G	rs3827318	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23974200A>G	ENST00000317749.5	-	1	308	c.11T>C	c.(10-12)aTa>aCa	p.I4T	KB-1572G7.3_ENST00000390329.3_RNA	NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		4			I -> T (in dbSNP:rs3827318).							endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						ACAGGTCAGTATATTCCCCAT	0.547													A|||	822	0.164137	0.1785	0.1383	5008	,	,		17295	0.2371		0.1133	False		,,,				2504	0.1401				p.I4T		Atlas-SNP	.											.	C22orf43	18	.	0			c.T11C						PASS	.	A	THR/ILE	666,3202		59,548,1327	66.0	65.0	65.0		11	0.1	0.0	22	dbSNP_107	65	935,7319		55,825,3247	yes	missense	C22orf43	NM_016449.3	89	114,1373,4574	GG,GA,AA		11.3278,17.2182,13.2074	probably-damaging	4/230	23974200	1601,10521	1934	4127	6061	SO:0001583	missense	51233	exon1			GTCAGTATATTCC																												ENST00000317749.5:c.11T>C	22.37:g.23974200A>G	ENSP00000316137:p.Ile4Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	Missense_Mutation	SNP	ENST00000317749.5	37	CCDS42985.1	350	0.16025641025641027	80	0.16260162601626016	47	0.1298342541436464	124	0.21678321678321677	99	0.13060686015831136	a	2.546	-0.305118	0.05495	0.172182	0.113278	ENSG00000189269	ENST00000317749	T	0.29917	1.55	0.14	0.14	0.14804	.	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	P	0.47106	0.89	P	0.52554	0.702	T	0.07028	-1.0794	7	0.09084	T	0.74	.	.	.	.	rs3827318;rs17002925;rs52826285;rs58693816;rs3827318	4	Q6PGQ1	CV043_HUMAN	T	4	ENSP00000316137:I4T	ENSP00000316137:I4T	I	-	2	0	C22orf43	22304200	0.021000	0.18746	0.018000	0.16275	0.018000	0.09664	0.238000	0.18004	0.157000	0.19338	0.155000	0.16302	ATA	A|0.842;G|0.156	0.156	strong		0.547	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2		
MICA	100507436	hgsc.bcm.edu	37	6	31379115	31379115	+	Missense_Mutation	SNP	G	G	A	rs1131896	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31379115G>A	ENST00000449934.2	+	3	646	c.592G>A	c.(592-594)Ggc>Agc	p.G198S	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)				TCTAGAATCCGGCGTAGTCCT	0.537													g|||	1730	0.345447	0.2852	0.3501	5008	,	,		20682	0.4216		0.2823	False		,,,				2504	0.41				p.G198S		Atlas-SNP	.											.	MICA	21	.	0			c.G592A						PASS	.	G	SER/GLY	379,1005		53,273,366	97.0	86.0	89.0		592	-2.8	0.0	6	dbSNP_86	89	805,2377		100,605,886	yes	missense	MICA	NM_001177519.1	56	153,878,1252	AA,AG,GG		25.2986,27.3844,25.9308	benign	198/333	31379115	1184,3382	692	1591	2283	SO:0001583	missense	100507436	exon3			GAATCCGGCGTAG	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.592G>A	6.37:g.31379115G>A	ENSP00000413079:p.Gly198Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	672	0.3076923076923077	143	0.29065040650406504	112	0.30939226519337015	228	0.3986013986013986	189	0.24934036939313983	N	6.785	0.513740	0.12944	0.273844	0.252986	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934	T	0.00995	5.46	1.41	-2.82	0.05787	.	3.067170	0.01197	N	0.007461	T	0.00412	0.0013	M	0.67625	2.065	0.80722	P	0.0	B;P	0.34837	0.435;0.472	B;B	0.28553	0.036;0.091	T	0.41161	-0.9524	9	0.62326	D	0.03	.	0.6695	0.00856	0.1927:0.1761:0.3847:0.2464	rs1131896;rs2523494;rs3819266;rs17884174;rs56738748;rs1131896	60;198	Q5SS58;Q96QC4	.;.	S	60;198;155;198	ENSP00000413079:G198S	ENSP00000365394:G198S	G	+	1	0	MICA	31487094	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.607000	0.05648	-1.451000	0.01933	-1.206000	0.01644	GGC	G|0.689;A|0.311	0.311	strong		0.537	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
ZDHHC7	55625	hgsc.bcm.edu	37	16	85015541	85015541	+	Silent	SNP	G	G	A	rs16975086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:85015541G>A	ENST00000313732.4	-	4	727	c.375C>T	c.(373-375)ccC>ccT	p.P125P	ZDHHC7_ENST00000569488.1_Intron|ZDHHC7_ENST00000564466.1_Silent_p.P162P	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	125					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						TGACTTCCCCGGGCTTCAGCT	0.517													G|||	668	0.133387	0.0083	0.304	5008	,	,		16621	0.1508		0.1571	False		,,,				2504	0.1391				p.P162P		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.C486T						PASS	.	G	,	166,4232	110.8+/-149.0	2,162,2035	145.0	154.0	151.0		486,375	-10.7	0.0	16	dbSNP_123	151	1470,7130	281.8+/-295.3	126,1218,2956	no	coding-synonymous,coding-synonymous	ZDHHC7	NM_001145548.1,NM_017740.2	,	128,1380,4991	AA,AG,GG		17.093,3.7744,12.5866	,	162/346,125/309	85015541	1636,11362	2199	4300	6499	SO:0001819	synonymous_variant	55625	exon5			TTCCCCGGGCTTC	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.375C>T	16.37:g.85015541G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	201	99	0.492537	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Silent	SNP	ENST00000313732.4	37	CCDS10950.1																																																																																			G|0.870;A|0.129	0.129	strong		0.517	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
ZNF354A	6940	hgsc.bcm.edu	37	5	178140090	178140090	+	Silent	SNP	C	C	T	rs1132336	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178140090C>T	ENST00000335815.2	-	5	986	c.789G>A	c.(787-789)acG>acA	p.T263T		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	263					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|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.T263T(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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;0.185)		CTCCAGTATGCGTTATTTGAT	0.353													C|||	1318	0.263179	0.09	0.2464	5008	,	,		19499	0.3333		0.2813	False		,,,				2504	0.4182				p.T263T		Atlas-SNP	.											ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.G789A						PASS	.	C		570,3836	251.5+/-258.2	38,494,1671	98.0	98.0	98.0		789	-5.9	0.9	5	dbSNP_86	98	2355,6245	392.0+/-343.8	322,1711,2267	no	coding-synonymous	ZNF354A	NM_005649.2		360,2205,3938	TT,TC,CC		27.3837,12.9369,22.4896		263/606	178140090	2925,10081	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			AGTATGCGTTATT	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.789G>A	5.37:g.178140090C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.762;T|0.238	0.238	strong		0.353	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
MMP2	4313	hgsc.bcm.edu	37	16	55536763	55536763	+	Silent	SNP	C	C	G	rs11541998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000437642.2_Silent_p.P564P|MMP2_ENST00000570308.1_Silent_p.P538P	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	54	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	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		
CCDC138	165055	hgsc.bcm.edu	37	2	109408159	109408159	+	Missense_Mutation	SNP	G	G	T	rs35794776	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:109408159G>T	ENST00000295124.4	+	4	355	c.295G>T	c.(295-297)Gat>Tat	p.D99Y	CCDC138_ENST00000470608.1_Intron|CCDC138_ENST00000412964.2_Missense_Mutation_p.D99Y	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	99			D -> Y (in dbSNP:rs35794776).							endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TTCTTTCCATGATTTGAAGAA	0.289													G|||	361	0.0720847	0.0582	0.0663	5008	,	,		15869	0.0317		0.0527	False		,,,				2504	0.1564				p.D99Y		Atlas-SNP	.											.	CCDC138	49	.	0			c.G295T						PASS	.	G	TYR/ASP	232,4164	130.2+/-166.9	7,218,1973	85.0	102.0	96.0		295	1.9	1.0	2	dbSNP_126	96	503,8053	140.5+/-197.0	17,469,3792	yes	missense	CCDC138	NM_144978.1	160	24,687,5765	TT,TG,GG		5.8789,5.2775,5.6748	benign	99/666	109408159	735,12217	2198	4278	6476	SO:0001583	missense	165055	exon4			TTCCATGATTTGA	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.295G>T	2.37:g.109408159G>T	ENSP00000295124:p.Asp99Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	119	0.05448717948717949	31	0.06300813008130081	23	0.06353591160220995	26	0.045454545454545456	39	0.051451187335092345	G	9.969	1.225072	0.22457	0.052775	0.058789	ENSG00000163006	ENST00000412964;ENST00000295124	D;D	0.90900	-2.75;-2.75	5.77	1.94	0.25998	.	0.572646	0.16856	N	0.196758	T	0.48021	0.1477	L	0.57536	1.79	0.31858	N	0.621322	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.004	T	0.70270	-0.4918	10	0.56958	D	0.05	0.065	3.7033	0.08391	0.1459:0.1312:0.5869:0.136	rs35794776	99;99	Q96M89-2;Q96M89	.;CC138_HUMAN	Y	99	ENSP00000411800:D99Y;ENSP00000295124:D99Y	ENSP00000295124:D99Y	D	+	1	0	CCDC138	108774591	1.000000	0.71417	0.968000	0.41197	0.490000	0.33462	1.379000	0.34340	0.076000	0.16826	-0.152000	0.13540	GAT	G|0.942;T|0.058	0.058	strong		0.289	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
OPRD1	4985	hgsc.bcm.edu	37	1	29189597	29189597	+	Silent	SNP	C	C	T	rs2234918	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	63	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	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	
HTR3C	170572	hgsc.bcm.edu	37	3	183777328	183777328	+	Silent	SNP	C	C	T	rs138181384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183777328C>T	ENST00000318351.1	+	7	859	c.825C>T	c.(823-825)agC>agT	p.S275S		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	275					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)			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)	CAGCAGAGAGCGAGAATCGTG	0.547													C|||	3	0.000599042	0.0	0.0	5008	,	,		17250	0.002		0.001	False		,,,				2504	0.0				p.S275S		Atlas-SNP	.											.	HTR3C	65	.	0			c.C825T						PASS	.	C		0,4406		0,0,2203	150.0	133.0	139.0		825	-3.0	0.0	3	dbSNP_134	139	5,8595		0,5,4295	no	coding-synonymous	HTR3C	NM_130770.2		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		275/448	183777328	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	170572	exon7			AGAGAGCGAGAAT	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.825C>T	3.37:g.183777328C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	134	44	0.328358	NM_130770	A2RRR5	Silent	SNP	ENST00000318351.1	37	CCDS3250.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
SAMM50	25813	hgsc.bcm.edu	37	22	44360335	44360335	+	Missense_Mutation	SNP	G	G	A	rs143095808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:44360335G>A	ENST00000350028.4	+	3	293	c.136G>A	c.(136-138)Gtt>Att	p.V46I	SAMM50_ENST00000493161.1_3'UTR|SAMM50_ENST00000396202.3_De_novo_Start_InFrame	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	46					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)				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)				CTTTTAGGTGGTTGTTCAACA	0.368													g|||	4	0.000798722	0.0	0.0014	5008	,	,		21680	0.001		0.002	False		,,,				2504	0.0				p.V46I		Atlas-SNP	.											.	SAMM50	30	.	0			c.G136A						PASS	.	C	ILE/VAL	5,4401	9.9+/-24.2	0,5,2198	202.0	178.0	186.0		136	3.9	1.0	22	dbSNP_134	186	47,8553	29.6+/-80.5	1,45,4254	yes	missense	SAMM50	NM_015380.4	29	1,50,6452	AA,AG,GG		0.5465,0.1135,0.3998	benign	46/470	44360335	52,12954	2203	4300	6503	SO:0001583	missense	25813	exon3			TAGGTGGTTGTTC	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.136G>A	22.37:g.44360335G>A	ENSP00000345445:p.Val46Ile	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	221	87	0.393665	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Missense_Mutation	SNP	ENST00000350028.4	37	CCDS14055.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	g	11.48	1.650498	0.29336	0.001135	0.005465	ENSG00000100347	ENST00000350028	T	0.44881	0.91	4.87	3.86	0.44501	.	0.133087	0.49305	D	0.000145	T	0.26340	0.0643	L	0.32530	0.975	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.10474	-1.0628	10	0.54805	T	0.06	-20.1534	14.7239	0.69329	0.0:0.1459:0.8541:0.0	.	46	Q9Y512	SAM50_HUMAN	I	46	ENSP00000345445:V46I	ENSP00000345445:V46I	V	+	1	0	SAMM50	42691668	1.000000	0.71417	0.995000	0.50966	0.719000	0.41307	5.509000	0.67012	1.182000	0.42928	-0.215000	0.12644	GTT	G|0.997;A|0.003	0.003	strong		0.368	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
PLXNB2	23654	hgsc.bcm.edu	37	22	50728062	50728062	+	Missense_Mutation	SNP	T	T	C	rs28379706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50728062T>C	ENST00000449103.1	-	3	1092	c.952A>G	c.(952-954)Aag>Gag	p.K318E	PLXNB2_ENST00000359337.4_Missense_Mutation_p.K318E			O15031	PLXB2_HUMAN	plexin B2	318	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		K -> E (in dbSNP:rs28379706).		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)		GCGTGCACCTTGTCCAGCGGG	0.647													C|||	2274	0.454073	0.6982	0.2666	5008	,	,		14681	0.5734		0.3996	False		,,,				2504	0.1902				p.K318E		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A952G						PASS	.	C	GLU/LYS	2384,1518		750,884,317	43.0	51.0	49.0		952	-1.3	0.0	22	dbSNP_125	49	3140,5180		628,1884,1648	yes	missense	PLXNB2	NM_012401.3	56	1378,2768,1965	CC,CT,TT		37.7404,38.9031,45.1972	benign	318/1839	50728062	5524,6698	1951	4160	6111	SO:0001583	missense	23654	exon3			GCACCTTGTCCAG		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.952A>G	22.37:g.50728062T>C	ENSP00000409171:p.Lys318Glu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	1049	0.4803113553113553	323	0.6565040650406504	99	0.27348066298342544	323	0.5646853146853147	304	0.40105540897097625	C	0.005	-2.194844	0.00299	0.610969	0.377404	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000414275;ENST00000432455	T;T;T	0.04156	3.69;3.69;3.69	4.75	-1.27	0.09347	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.992853	0.08183	N	0.985111	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.34825	-0.9813	9	0.02654	T	1	.	6.7594	0.23532	0.0:0.3825:0.3364:0.2812	rs28379706;rs58514877	318	O15031	PLXB2_HUMAN	E	318	ENSP00000409171:K318E;ENSP00000352288:K318E;ENSP00000392620:K318E	ENSP00000352288:K318E	K	-	1	0	PLXNB2	49070189	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.279000	0.08479	-0.271000	0.09272	-0.215000	0.12644	AAG	T|0.543;C|0.457	0.457	strong		0.647	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
ZNF880	400713	hgsc.bcm.edu	37	19	52887603	52887603	+	Missense_Mutation	SNP	G	G	A	rs78052167|rs148392772	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	40	0	0		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	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	
CELSR1	9620	hgsc.bcm.edu	37	22	46786315	46786315	+	Missense_Mutation	SNP	T	T	C	rs4044210	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	65	0	0	941	WXS	Illumina HiSeq	Phase_I	47	19	0.404255	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	
EPS8L1	54869	hgsc.bcm.edu	37	19	55598724	55598724	+	Missense_Mutation	SNP	A	A	G	rs1054940	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55598724A>G	ENST00000201647.6	+	19	2062	c.2006A>G	c.(2005-2007)aAg>aGg	p.K669R	EPS8L1_ENST00000245618.5_Missense_Mutation_p.K542R|EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000540810.1_Missense_Mutation_p.K605R|EPS8L1_ENST00000588359.1_Missense_Mutation_p.K355R	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	669			K -> R (in dbSNP:rs1054940). {ECO:0000269|PubMed:12620401, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15498874}.		positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TCGCTGCAGAAGGAGGAGCTG	0.731													A|||	2342	0.467652	0.3419	0.4597	5008	,	,		13706	0.4514		0.506	False		,,,				2504	0.6207				p.K669R	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											EPS8L1_ENST00000245618,NS,carcinoma,0,2	EPS8L1	122	2	0			c.A2006G						PASS	.	A	ARG/LYS,ARG/LYS	1592,2812		310,972,920	26.0	28.0	27.0		1625,2006	4.0	1.0	19	dbSNP_86	27	4241,4353		1078,2085,1134	yes	missense,missense	EPS8L1	NM_017729.3,NM_133180.2	26,26	1388,3057,2054	GG,GA,AA		49.3484,36.149,44.8761	probably-damaging,probably-damaging	542/597,669/724	55598724	5833,7165	2202	4297	6499	SO:0001583	missense	54869	exon19			TGCAGAAGGAGGA	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.2006A>G	19.37:g.55598724A>G	ENSP00000201647:p.Lys669Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	983	0.4500915750915751	171	0.3475609756097561	170	0.4696132596685083	260	0.45454545454545453	382	0.503957783641161	A	27.8	4.868341	0.91587	0.36149	0.493484	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.25250	1.81;1.81;1.81	4.02	4.02	0.46733	.	0.121108	0.53938	D	0.000057	T	0.00012	0.0000	L	0.54908	1.71	0.09310	P	0.99999486196	D;D;P	0.89917	1.0;0.991;0.863	D;D;P	0.87578	0.998;0.927;0.73	T	0.50440	-0.8828	9	0.34782	T	0.22	-35.624	11.4935	0.50394	1.0:0.0:0.0:0.0	rs1054940;rs3195458;rs58630253;rs1054940	448;542;669	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	R	669;605;542;355	ENSP00000201647:K669R;ENSP00000437541:K605R;ENSP00000245618:K542R	ENSP00000201647:K669R	K	+	2	0	EPS8L1	60290536	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.360000	0.66086	1.768000	0.52137	0.260000	0.18958	AAG	A|0.559;G|0.441	0.441	strong		0.731	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
MUC20	200958	hgsc.bcm.edu	37	3	195452987	195452987	+	Missense_Mutation	SNP	G	G	A	rs9866681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195452987G>A	ENST00000447234.2	+	2	1639	c.1513G>A	c.(1513-1515)Gcc>Acc	p.A505T	MUC20_ENST00000320736.6_Missense_Mutation_p.A334T|MUC20_ENST00000445522.2_Missense_Mutation_p.A470T|MUC20_ENST00000436408.1_Missense_Mutation_p.A505T	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	316	0	0		WXS	Illumina HiSeq	Phase_I	397	106	0.267003	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	
GAL3ST2	64090	hgsc.bcm.edu	37	2	242743357	242743357	+	Missense_Mutation	SNP	G	G	A	rs78253117	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242743357G>A	ENST00000192314.6	+	4	1104	c.973G>A	c.(973-975)Ggc>Agc	p.G325S	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	325					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)		CCTGCAGGACGGCGGCGCGCT	0.751													G|||	155	0.0309505	0.0567	0.0346	5008	,	,		10848	0.0		0.0547	False		,,,				2504	0.001				p.G325S		Atlas-SNP	.											.	GAL3ST2	34	.	0			c.G973A						PASS	.	G	SER/GLY	211,4005		2,207,1899	5.0	6.0	6.0		973	-1.0	0.0	2	dbSNP_131	6	356,7918		10,336,3791	no	missense	GAL3ST2	NM_022134.2	56	12,543,5690	AA,AG,GG		4.3026,5.0047,4.5396	benign	325/399	242743357	567,11923	2108	4137	6245	SO:0001583	missense	64090	exon4			CAGGACGGCGGCG	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.973G>A	2.37:g.242743357G>A	ENSP00000192314:p.Gly325Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_022134	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	81	0.03708791208791209	24	0.04878048780487805	17	0.04696132596685083	0	0.0	40	0.052770448548812667	G	3.119	-0.181019	0.06380	0.050047	0.043026	ENSG00000154252	ENST00000192314	T	0.16457	2.34	0.502	-0.981	0.10269	.	1.160310	0.06213	N	0.685334	T	0.02267	0.0070	L	0.52573	1.65	0.09310	N	1	P	0.44139	0.827	P	0.44946	0.465	T	0.14144	-1.0483	10	0.09843	T	0.71	-8.6016	3.8916	0.09120	0.0:0.2197:0.4151:0.3651	.	325	Q9H3Q3	G3ST2_HUMAN	S	325	ENSP00000192314:G325S	ENSP00000192314:G325S	G	+	1	0	GAL3ST2	242392030	0.001000	0.12720	0.002000	0.10522	0.032000	0.12392	-0.154000	0.10130	-0.465000	0.06953	0.313000	0.20887	GGC	G|0.962;A|0.038	0.038	strong		0.751	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
VWA5B1	127731	hgsc.bcm.edu	37	1	20680718	20680718	+	Missense_Mutation	SNP	G	G	A	rs2072751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20680718G>A	ENST00000375079.2	+	22	3821	c.3625G>A	c.(3625-3627)Gag>Aag	p.E1209K	VWA5B1_ENST00000289815.8_Missense_Mutation_p.E1178K	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	1209						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						TGAGAATCTCGAGTTCAATAT	0.607													G|||	1149	0.229433	0.208	0.1801	5008	,	,		17189	0.2887		0.2237	False		,,,				2504	0.2382				p.E1204K		Atlas-SNP	.											.	VWA5B1	44	.	0			c.G3610A						PASS	.						7.0	11.0	10.0					1																	20680718		690	1588	2278	SO:0001583	missense	127731	exon22			AATCTCGAGTTCA	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.3625G>A	1.37:g.20680718G>A	ENSP00000364220:p.Glu1209Lys	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		507	0.23214285714285715	84	0.17073170731707318	75	0.20718232044198895	189	0.3304195804195804	159	0.20976253298153033	G	9.915	1.210621	0.22289	.	.	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375079	T;T	0.33438	1.41;1.41	5.58	4.67	0.58626	.	0.128661	0.53938	N	0.000059	T	0.00012	0.0000	N	0.20685	0.6	0.09310	P	0.9999999999999991	P;B;D	0.65815	0.94;0.016;0.995	B;B;P	0.49332	0.187;0.016;0.607	T	0.44003	-0.9356	9	0.22706	T	0.39	-6.2611	11.7748	0.51979	0.0726:0.1247:0.8026:0.0	rs2072751;rs59623880;rs2072751	1209;1179;1204	Q5TIE3;Q5TIE3-5;Q5TIE3-2	VW5B1_HUMAN;.;.	K	1209;1178;1209	ENSP00000289815:E1178K;ENSP00000364220:E1209K	ENSP00000289815:E1178K	E	+	1	0	VWA5B1	20553305	1.000000	0.71417	0.892000	0.35008	0.362000	0.29581	4.651000	0.61447	0.737000	0.32582	-1.688000	0.00730	GAG	G|0.772;A|0.228	0.228	strong		0.607	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
HPS4	89781	hgsc.bcm.edu	37	22	26860269	26860269	+	Missense_Mutation	SNP	G	G	C	rs2014410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26860269G>C	ENST00000398145.2	-	11	1943	c.1327C>G	c.(1327-1329)Ctc>Gtc	p.L443V	HPS4_ENST00000398141.1_Missense_Mutation_p.L456V|HPS4_ENST00000336873.5_Missense_Mutation_p.L443V|HPS4_ENST00000493455.2_5'Flank|HPS4_ENST00000402105.3_Missense_Mutation_p.L438V	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	443			L -> V (in dbSNP:rs2014410). {ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						TGGTCTTCGAGCTGCTCTTGG	0.622									Hermansky-Pudlak syndrome				G|||	1774	0.354233	0.2927	0.2536	5008	,	,		18410	0.3026		0.3817	False		,,,				2504	0.5337				p.L443V		Atlas-SNP	.											.	HPS4	123	.	0			c.C1327G						PASS	.	G	VAL/LEU,VAL/LEU	1381,3025	453.6+/-350.4	215,951,1037	94.0	90.0	91.0		1327,1312	-3.8	0.0	22	dbSNP_92	91	3536,5064	513.8+/-378.2	701,2134,1465	yes	missense,missense	HPS4	NM_022081.4,NM_152841.1	32,32	916,3085,2502	CC,CG,GG		41.1163,31.3436,37.8056	benign,benign	443/709,438/704	26860269	4917,8089	2203	4300	6503	SO:0001583	missense	89781	exon11	Familial Cancer Database	HPS, HPS1-8	CTTCGAGCTGCTC		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.1327C>G	22.37:g.26860269G>C	ENSP00000381213:p.Leu443Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	37	CCDS13835.1	735	0.33653846153846156	156	0.3170731707317073	94	0.2596685082872928	185	0.32342657342657344	300	0.39577836411609496	G	3.661	-0.069509	0.07228	0.313436	0.411163	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873;ENST00000312736;ENST00000422379	T;T;T;T;T	0.56275	1.46;1.46;1.46;1.46;0.47	4.83	-3.76	0.04359	.	2.135670	0.01490	N	0.017037	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B;B;B;P;B	0.37276	0.187;0.187;0.187;0.589;0.187	B;B;B;B;B	0.27796	0.037;0.037;0.037;0.083;0.037	T	0.16808	-1.0390	9	0.18710	T	0.47	5.0752	10.0843	0.42408	0.6724:0.0:0.3276:0.0	rs2014410;rs17401332;rs2014410	443;443;443;456;438	Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;HPS4_HUMAN;.;.;.	V	443;456;438;443;461;461	ENSP00000381213:L443V;ENSP00000381210:L456V;ENSP00000384185:L438V;ENSP00000338457:L443V;ENSP00000415081:L461V	ENSP00000325840:L461V	L	-	1	0	HPS4	25190269	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.433000	0.06948	-0.455000	0.07054	-1.202000	0.01658	CTC	G|0.640;C|0.360	0.360	strong		0.622	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081	
RSBN1	54665	hgsc.bcm.edu	37	1	114354654	114354654	+	Silent	SNP	T	T	C	rs3195954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	12	0	0		WXS	Illumina HiSeq	Phase_I	29	9	0.310345	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	
PAPL	390928	hgsc.bcm.edu	37	19	39592138	39592138	+	Silent	SNP	C	C	T	rs1313617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	40	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	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		
MPC1	51660	hgsc.bcm.edu	37	6	166779464	166779464	+	Silent	SNP	G	G	A	rs12205572	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:166779464G>A	ENST00000360961.6	-	4	424	c.303C>T	c.(301-303)caC>caT	p.H101H	MPC1_ENST00000487218.1_5'UTR|MPC1_ENST00000341756.6_Silent_p.H101H	NM_001270879.1|NM_016098.3	NP_001257808.1|NP_057182.1	Q9Y5U8	MPC1_HUMAN	mitochondrial pyruvate carrier 1	101					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	pyruvate transmembrane transporter activity (GO:0050833)										CTGCTTACTCGTGTTTGATAA	0.463													G|||	160	0.0319489	0.0023	0.0375	5008	,	,		19560	0.0		0.0606	False		,,,				2504	0.0716				p.H58H		Atlas-SNP	.											.	.	.	.	0			c.C174T						PASS	.	G		44,4362	46.7+/-81.2	0,44,2159	87.0	80.0	82.0		303	-3.1	0.0	6	dbSNP_120	82	504,8096	144.0+/-200.0	12,480,3808	yes	coding-synonymous	BRP44L	NM_016098.2		12,524,5967	AA,AG,GG		5.8605,0.9986,4.2134		101/110	166779464	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	51660	exon4			TTACTCGTGTTTG	AF125101	CCDS5293.1, CCDS75547.1	6q27	2012-08-01	2012-07-30	2012-07-30	ENSG00000060762	ENSG00000060762			21606	protein-coding gene	gene with protein product		614738	"""brain protein 44-like"""	BRP44L		22628558	Standard	NM_016098		Approved	dJ68L15.3, CGI-129	uc031sra.1	Q9Y5U8	OTTHUMG00000015999	ENST00000360961.6:c.303C>T	6.37:g.166779464G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_001270879	B2R5I7|Q5TI66|Q9HB67|Q9UQN4	Silent	SNP	ENST00000360961.6	37	CCDS5293.1																																																																																			G|0.962;A|0.038	0.038	strong		0.463	MPC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043052.1	NM_016098	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523528	42523528	+	Missense_Mutation	SNP	C	C	T	rs1058172	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:42523528C>T	ENST00000360608.5	-	7	1208	c.1094G>A	c.(1093-1095)cGc>cAc	p.R365H	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.R365H|CYP2D6_ENST00000359033.4_Missense_Mutation_p.R314H	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						PASS	.						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	123	0	0		WXS	Illumina HiSeq	Phase_I	252	119	0.472222	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		
OR52E4	390081	hgsc.bcm.edu	37	11	5906205	5906205	+	Missense_Mutation	SNP	G	G	A	rs4757987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5906205G>A	ENST00000316987.2	+	1	705	c.683G>A	c.(682-684)cGc>cAc	p.R228H		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	228			R -> H (in dbSNP:rs4757987).			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)		GCTGTTTTTCGCCTTCCCTCT	0.388													G|||	2115	0.422324	0.4894	0.3516	5008	,	,		21841	0.4613		0.3907	False		,,,				2504	0.3742				p.R228H		Atlas-SNP	.											.	OR52E4	65	.	0			c.G683A						PASS	.	G	HIS/ARG	2083,2319	572.5+/-383.3	497,1089,615	300.0	257.0	272.0		683	0.1	0.0	11	dbSNP_111	272	3142,5450	477.4+/-369.6	585,1972,1739	yes	missense	OR52E4	NM_001005165.1	29	1082,3061,2354	AA,AG,GG		36.5689,47.3194,40.2109	benign	228/313	5906205	5225,7769	2201	4296	6497	SO:0001583	missense	390081	exon1			TTTTTCGCCTTCC	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.683G>A	11.37:g.5906205G>A	ENSP00000321426:p.Arg228His	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	209	92	0.440191	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	944	0.43223443223443225	240	0.4878048780487805	131	0.36187845303867405	265	0.4632867132867133	308	0.40633245382585753	G	6.342	0.431134	0.12045	0.473194	0.365689	ENSG00000180974	ENST00000316987	T	0.00262	8.4	5.15	0.0472	0.14280	GPCR, rhodopsin-like superfamily (1);	0.135165	0.32190	N	0.006445	T	0.00012	0.0000	L	0.52759	1.655	0.80722	P	0.0	B	0.10296	0.003	B	0.15484	0.013	T	0.06499	-1.0823	9	0.18276	T	0.48	.	9.6342	0.39798	0.3688:0.0:0.6312:0.0	rs4757987	228	Q8NGH9	O52E4_HUMAN	H	228	ENSP00000321426:R228H	ENSP00000321426:R228H	R	+	2	0	OR52E4	5862781	0.000000	0.05858	0.023000	0.16930	0.756000	0.42949	-1.394000	0.02518	0.078000	0.16900	-0.149000	0.13747	CGC	G|0.588;A|0.412	0.412	strong		0.388	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987363	154987363	+	Missense_Mutation	SNP	G	G	T	rs145349387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:154987363G>T	ENST00000368426.3	+	3	364	c.227G>T	c.(226-228)gGt>gTt	p.G76V	ZBTB7B_ENST00000292176.2_Missense_Mutation_p.G76V|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.G110V|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.G76V	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	76	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GGGGCCGGGGGTAGCGGGACG	0.622													G|||	7	0.00139776	0.0	0.0101	5008	,	,		15973	0.0		0.0	False		,,,				2504	0.0				p.G110V		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.G329T						PASS	.	G	VAL/GLY	0,4406		0,0,2203	33.0	39.0	37.0		227	3.7	0.9	1	dbSNP_134	37	14,8586	8.4+/-32.0	0,14,4286	yes	missense	ZBTB7B	NM_015872.2	109	0,14,6489	TT,TG,GG		0.1628,0.0,0.1076	benign	76/540	154987363	14,12992	2203	4300	6503	SO:0001583	missense	51043	exon4			CCGGGGGTAGCGG	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.227G>T	1.37:g.154987363G>T	ENSP00000357411:p.Gly76Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	77	30	0.38961	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	37	CCDS1081.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	8.561	0.877867	0.17395	0.0	0.001628	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.10099	2.96;2.96;2.91;2.96	3.66	3.66	0.41972	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.847359	0.09620	N	0.777684	T	0.10380	0.0254	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.76071	0.987;0.966;0.987	T	0.24905	-1.0147	10	0.39692	T	0.17	.	10.7167	0.46017	0.0:0.0:1.0:0.0	.	76;76;110	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	V	76;76;110;76	ENSP00000438647:G76V;ENSP00000357411:G76V;ENSP00000406286:G110V;ENSP00000292176:G76V	ENSP00000292176:G76V	G	+	2	0	ZBTB7B	153253987	0.978000	0.34361	0.893000	0.35052	0.005000	0.04900	0.651000	0.24873	1.867000	0.54127	0.455000	0.32223	GGT	G|0.999;T|0.001	0.001	strong		0.622	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
CR1	1378	hgsc.bcm.edu	37	1	207755284	207755284	+	Silent	SNP	C	C	T	rs199697417		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:207755284C>T	ENST00000367049.4	+	32	5238	c.5238C>T	c.(5236-5238)tcC>tcT	p.S1746S	RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000400960.2_Silent_p.S1296S|CR1_ENST00000367051.1_Silent_p.S1296S|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367052.1_Silent_p.S1296S|CR1_ENST00000367053.1_Silent_p.S1296S	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1296	Sushi 27. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						AGGGCAGTTCCGTTAGTCATT	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		19670	0.001		0.0	False		,,,				2504	0.0				p.S1746S		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,+1,2	CR1	354	2	0			c.C5238T						scavenged	.						208.0	211.0	210.0					1																	207755284		1971	4157	6128	SO:0001819	synonymous_variant	1378	exon32			CAGTTCCGTTAGT	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.5238C>T	1.37:g.207755284C>T		Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	368	4	0.0108696	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1																																																																																			C|0.999;T|0.001	0.001	strong		0.448	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
OR52N2	390077	hgsc.bcm.edu	37	11	5841926	5841926	+	Missense_Mutation	SNP	G	G	A	rs73394377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5841926G>A	ENST00000317037.2	+	1	383	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	121						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)		CATGCTCATGGCCCTGGACCG	0.542													G|||	204	0.0407348	0.0749	0.0259	5008	,	,		22638	0.001		0.0467	False		,,,				2504	0.0399				p.A121T		Atlas-SNP	.											.	OR52N2	58	.	0			c.G361A						PASS	.	G	THR/ALA	338,4064	178.0+/-206.8	9,320,1872	159.0	129.0	140.0		361	5.9	1.0	11	dbSNP_130	140	576,8016	154.8+/-208.9	16,544,3736	yes	missense	OR52N2	NM_001005174.1	58	25,864,5608	AA,AG,GG		6.7039,7.6783,7.034	probably-damaging	121/322	5841926	914,12080	2201	4296	6497	SO:0001583	missense	390077	exon1			CTCATGGCCCTGG	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.361G>A	11.37:g.5841926G>A	ENSP00000322801:p.Ala121Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_001005174	Q6IFF9	Missense_Mutation	SNP	ENST00000317037.2	37	CCDS31399.1	82	0.037545787545787544	37	0.07520325203252033	12	0.03314917127071823	0	0.0	33	0.04353562005277045	G	33	5.228929	0.95173	0.076783	0.067039	ENSG00000180988	ENST00000317037	T	0.54071	0.59	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.24236	0.0587	H	0.97611	4.04	0.48830	D	0.999714	D	0.63046	0.992	P	0.62184	0.899	T	0.73733	-0.3890	10	0.87932	D	0	.	18.8574	0.92259	0.0:0.0:1.0:0.0	.	121	Q8NGI0	O52N2_HUMAN	T	121	ENSP00000322801:A121T	ENSP00000322801:A121T	A	+	1	0	OR52N2	5798502	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.504000	0.73704	2.801000	0.96364	0.655000	0.94253	GCC	G|0.939;A|0.061	0.061	strong		0.542	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1	NM_001005174	
SESTD1	91404	hgsc.bcm.edu	37	2	180047908	180047908	+	Silent	SNP	T	T	C	rs6757681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:180047908T>C	ENST00000428443.3	-	3	379	c.63A>G	c.(61-63)aaA>aaG	p.K21K	SESTD1_ENST00000486468.1_5'UTR	NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	21	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|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)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCCGTCTGTCTTTTCCTCCTA	0.328													C|||	4305	0.859625	0.8411	0.8314	5008	,	,		16742	0.9077		0.7873	False		,,,				2504	0.9294				p.K21K		Atlas-SNP	.											.	SESTD1	66	.	0			c.A63G						PASS	.	C		3691,715	276.0+/-272.9	1550,591,62	85.0	83.0	83.0		63	2.5	1.0	2	dbSNP_116	83	6601,1999	319.9+/-314.4	2550,1501,249	no	coding-synonymous	SESTD1	NM_178123.4		4100,2092,311	CC,CT,TT		23.2442,16.2279,20.8673		21/697	180047908	10292,2714	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon3			TCTGTCTTTTCCT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.63A>G	2.37:g.180047908T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.191;C|0.809	0.809	strong		0.328	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595375	140595375	+	Silent	SNP	C	C	T	rs2910331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140595375C>T	ENST00000341948.4	+	1	1867	c.1680C>T	c.(1678-1680)ttC>ttT	p.F560F		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	560	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)			ACTCGCCCTTCGTGCTGTACC	0.721													C|||	879	0.175519	0.2716	0.1398	5008	,	,		16235	0.0933		0.161	False		,,,				2504	0.1708				p.F560F		Atlas-SNP	.											PCDHB13,NS,carcinoma,0,1	PCDHB13	142	1	0			c.C1680T						PASS	.						20.0	23.0	22.0					5																	140595375		2200	4291	6491	SO:0001819	synonymous_variant	56123	exon1			GCCCTTCGTGCTG	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.1680C>T	5.37:g.140595375C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			.	.	weak		0.721	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
ASTN2	23245	hgsc.bcm.edu	37	9	119739015	119739015	+	Silent	SNP	G	G	A	rs10983437	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000373996.3_Silent_p.H547H|ASTN2_ENST00000361477.3_5'UTR			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	49	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	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	
FAM135A	57579	hgsc.bcm.edu	37	6	71236216	71236216	+	Silent	SNP	C	C	T	rs7740873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000457062.2_Silent_p.N930N|FAM135A_ENST00000505868.1_Silent_p.N1143N|FAM135A_ENST00000370479.3_Silent_p.N930N|FAM135A_ENST00000505769.1_Silent_p.N723N	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	141	0	0		WXS	Illumina HiSeq	Phase_I	150	59	0.393333	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	
DDX58	23586	hgsc.bcm.edu	37	9	32481339	32481339	+	Splice_Site	SNP	C	C	T	rs61752945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32481339C>T	ENST00000379883.2	-	11	1794	c.1637G>A	c.(1636-1638)cGg>cAg	p.R546Q	DDX58_ENST00000545044.1_Splice_Site_p.R343Q|DDX58_ENST00000542096.1_Splice_Site_p.R475Q|DDX58_ENST00000379868.1_Splice_Site_p.R343Q|DDX58_ENST00000379882.1_Splice_Site_p.R501Q	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	546	Interaction with ZC3HAV1.				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 defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GGAACGTACCCGCAAATGTGA	0.443													C|||	57	0.0113818	0.0204	0.0101	5008	,	,		17585	0.0		0.0089	False		,,,				2504	0.0143				p.R546Q		Atlas-SNP	.											DDX58,colon,carcinoma,-1,1	DDX58	82	1	0			c.G1637A						scavenged	.	C	GLN/ARG	83,4323	70.3+/-108.2	1,81,2121	139.0	117.0	124.0		1637	3.9	1.0	9	dbSNP_129	124	113,8487	59.8+/-121.6	1,111,4188	yes	missense-near-splice	DDX58	NM_014314.3	43	2,192,6309	TT,TC,CC		1.314,1.8838,1.507	probably-damaging	546/926	32481339	196,12810	2203	4300	6503	SO:0001630	splice_region_variant	23586	exon11			CGTACCCGCAAAT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.1638+1G>A	9.37:g.32481339C>T		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	21	0.009615384615384616	11	0.022357723577235773	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	24.3	4.511527	0.85389	0.018838	0.01314	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	4.77	3.87	0.44632	.	0.000000	0.64402	D	0.000002	T	0.59810	0.2221	M	0.88775	2.98	0.45284	D	0.998289	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.995;0.952;0.985	T	0.70561	-0.4838	10	0.30078	T	0.28	-5.8222	12.4045	0.55432	0.0:0.915:0.0:0.085	rs61752945	343;501;475;546	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	Q	501;546;343;475;343	ENSP00000369212:R501Q;ENSP00000369213:R546Q;ENSP00000369197:R343Q;ENSP00000442160:R475Q;ENSP00000443055:R343Q	ENSP00000369197:R343Q	R	-	2	0	DDX58	32471339	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.447000	0.44917	1.308000	0.44962	0.655000	0.94253	CGG	C|0.987;T|0.013	0.013	strong		0.443	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	Missense_Mutation
TICRR	90381	hgsc.bcm.edu	37	15	90169192	90169192	+	Silent	SNP	C	C	T	rs75843552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90169192C>T	ENST00000268138.7	+	21	5607	c.5502C>T	c.(5500-5502)gcC>gcT	p.A1834A	TICRR_ENST00000560985.1_Silent_p.A1833A|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1834					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CCAGCTGTGCCGTGCGGAGCT	0.622													C|||	24	0.00479233	0.0023	0.0072	5008	,	,		15174	0.0		0.0149	False		,,,				2504	0.001				p.A1834A		Atlas-SNP	.											.	.	.	.	0			c.C5502T						PASS	.	C		13,4387	20.2+/-43.8	0,13,2187	42.0	46.0	45.0		5502	-9.4	0.0	15	dbSNP_132	45	156,8442	74.5+/-137.1	0,156,4143	no	coding-synonymous	C15orf42	NM_152259.3		0,169,6330	TT,TC,CC		1.8144,0.2955,1.3002		1834/1911	90169192	169,12829	2200	4299	6499	SO:0001819	synonymous_variant	90381	exon21			CTGTGCCGTGCGG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.5502C>T	15.37:g.90169192C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			C|0.990;T|0.010	0.010	strong		0.622	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
MRPS9	64965	hgsc.bcm.edu	37	2	105705507	105705507	+	Silent	SNP	C	C	T	rs11538198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	48	0	0		WXS	Illumina HiSeq	Phase_I	14	4	0.285714	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	
SOX7	83595	hgsc.bcm.edu	37	8	10583506	10583506	+	Silent	SNP	A	A	G	rs4841432	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10583506A>G	ENST00000304501.1	-	2	987	c.909T>C	c.(907-909)ctT>ctC	p.L303L	SOX7_ENST00000554914.1_Silent_p.L355L|SOX7_ENST00000553390.1_Silent_p.L355L	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	303	Sox C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00849}.				endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		GAGGCGGGGAAAGCTGGCCCA	0.607													G|||	2167	0.432708	0.8389	0.3833	5008	,	,		15982	0.1359		0.3777	False		,,,				2504	0.2812				p.L303L		Atlas-SNP	.											.	SOX7	50	.	0			c.T909C						PASS	.	G		3254,1152	404.9+/-333.3	1195,864,144	41.0	43.0	42.0		909	2.6	1.0	8	dbSNP_111	42	3167,5433	653.2+/-401.0	568,2031,1701	no	coding-synonymous	SOX7	NM_031439.2		1763,2895,1845	GG,GA,AA		36.8256,26.1462,49.3695		303/389	10583506	6421,6585	2203	4300	6503	SO:0001819	synonymous_variant	83595	exon2			CGGGGAAAGCTGG	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.909T>C	8.37:g.10583506A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_031439	B4DKV0|Q53YD0	Silent	SNP	ENST00000304501.1	37	CCDS5977.1																																																																																			A|0.526;G|0.474	0.474	strong		0.607	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487265	32487265	+	Missense_Mutation	SNP	C	C	G	rs139485758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32487265C>G	ENST00000374975.3	-	3	596	c.534G>C	c.(532-534)caG>caC	p.Q178H		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5									p.Q178H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						AGTCTCCATTCTGAATCAGGC	0.552													C|||	836	0.166933	0.2224	0.1326	5008	,	,		15097	0.1667		0.1531	False		,,,				2504	0.1309				p.Q178H		Atlas-SNP	.											HLA-DRB5,NS,NS,0,1	HLA-DRB5	31	1	1	Substitution - Missense(1)	NS(1)	c.G534C						scavenged	.						61.0	68.0	65.0					6																	32487265		1933	3889	5822	SO:0001583	missense	3127	exon3			TCCATTCTGAATC		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.534G>C	6.37:g.32487265C>G	ENSP00000364114:p.Gln178His	Somatic	150	7	0.0466667		WXS	Illumina HiSeq	Phase_I	153	15	0.0980392	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	2.451	-0.326294	0.05350	.	.	ENSG00000198502	ENST00000374975	T	0.14391	2.51	4.6	-9.19	0.00685	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.115120	0.06656	N	0.763651	T	0.02193	0.0068	L	0.35487	1.065	0.80722	P	0.0	B;B	0.19445	0.036;0.003	B;B	0.33690	0.168;0.014	T	0.35871	-0.9771	9	0.35671	T	0.21	.	1.7649	0.03000	0.2235:0.402:0.1926:0.1818	.	105;178	Q29973;Q30154	.;DRB5_HUMAN	H	178	ENSP00000364114:Q178H	ENSP00000364114:Q178H	Q	-	3	2	HLA-DRB5	32595243	0.000000	0.05858	0.000000	0.03702	0.495000	0.33615	-4.437000	0.00234	-3.808000	0.00104	-0.273000	0.10243	CAG	A|0.003;C|0.930;G|0.067	0.067	strong		0.552	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
C11orf24	53838	hgsc.bcm.edu	37	11	68030015	68030015	+	Missense_Mutation	SNP	C	C	T	rs901827	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:68030015C>T	ENST00000304271.6	-	4	850	c.448G>A	c.(448-450)Gca>Aca	p.A150T	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'UTR	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	150			A -> T (in dbSNP:rs901827).			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						CTGGAGGCTGCAGTCGTGGGA	0.642													C|||	1755	0.350439	0.3359	0.2911	5008	,	,		17897	0.4127		0.4473	False		,,,				2504	0.2485				p.A150T	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.G448A						PASS	.	C	THR/ALA	1520,2880	475.7+/-357.4	252,1016,932	39.0	39.0	39.0		448	-1.7	0.0	11	dbSNP_86	39	3732,4856	524.7+/-380.6	816,2100,1378	yes	missense	C11orf24	NM_022338.3	58	1068,3116,2310	TT,TC,CC		43.456,34.5455,40.4373	benign	150/450	68030015	5252,7736	2200	4294	6494	SO:0001583	missense	53838	exon4			AGGCTGCAGTCGT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.448G>A	11.37:g.68030015C>T	ENSP00000307264:p.Ala150Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	863	0.39514652014652013	195	0.39634146341463417	98	0.27071823204419887	239	0.4178321678321678	331	0.4366754617414248	C	3.202	-0.163472	0.06502	0.345455	0.43456	ENSG00000171067	ENST00000304271	T	0.33865	1.39	3.24	-1.71	0.08133	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.11329	0.006	T	0.42085	-0.9472	8	0.02654	T	1	.	9.1596	0.37014	0.0:0.3205:0.5829:0.0965	rs901827;rs3187860;rs3802747;rs17415819;rs52836565;rs57250660;rs901827	150	Q96F05	CK024_HUMAN	T	150	ENSP00000307264:A150T	ENSP00000307264:A150T	A	-	1	0	C11orf24	67786591	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-0.761000	0.04670	-0.515000	0.04445	GCA	C|0.589;A|0.002	.	strong		0.642	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
SH2D4B	387694	hgsc.bcm.edu	37	10	82369219	82369219	+	Missense_Mutation	SNP	T	T	A	rs17107368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:82369219T>A	ENST00000470604.2	+	6	894	c.894T>A	c.(892-894)gaT>gaA	p.D298E	SH2D4B_ENST00000372150.3_3'UTR|SH2D4B_ENST00000313455.4_Missense_Mutation_p.D251E|SH2D4B_ENST00000339284.2_Missense_Mutation_p.D299E			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	298										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			TCTCCAGAGATGTCATCGTCC	0.597													T|||	751	0.14996	0.0242	0.1239	5008	,	,		14881	0.3442		0.171	False		,,,				2504	0.1166				p.D299E		Atlas-SNP	.											SH2D4B,colon,carcinoma,+2,1	SH2D4B	44	1	0			c.T897A						PASS	.	T	GLU/ASP,GLU/ASP	235,4171	137.7+/-173.5	7,221,1975	76.0	73.0	74.0		753,897	-6.9	0.9	10	dbSNP_123	74	1463,7137	278.7+/-293.6	142,1179,2979	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	45,45	149,1400,4954	AA,AT,TT		17.0116,5.3336,13.0555	benign,benign	251/310,299/358	82369219	1698,11308	2203	4300	6503	SO:0001583	missense	387694	exon6			CAGAGATGTCATC		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.894T>A	10.37:g.82369219T>A	ENSP00000417953:p.Asp298Glu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		413	0.1891025641025641	18	0.036585365853658534	43	0.11878453038674033	219	0.38286713286713286	133	0.17546174142480211	T	4.624	0.116020	0.08831	0.053336	0.170116	ENSG00000178217	ENST00000339284;ENST00000470604;ENST00000313455	T;T;T	0.08193	3.12;3.12;3.12	5.32	-6.92	0.01644	.	0.496191	0.21175	N	0.078911	T	0.00012	0.0000	N	0.00666	-1.275	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.002;0.001	T	0.28996	-1.0026	9	0.02654	T	1	-5.2867	1.4482	0.02369	0.1492:0.1968:0.3315:0.3224	rs17107368;rs52818132;rs17107368	298;251;299	Q5SQS7;Q5SQS7-3;Q5SQS7-2	SH24B_HUMAN;.;.	E	299;298;251	ENSP00000345295:D299E;ENSP00000417953:D298E;ENSP00000314242:D251E	ENSP00000314242:D251E	D	+	3	2	SH2D4B	82359199	0.007000	0.16637	0.901000	0.35422	0.780000	0.44128	-0.914000	0.04038	-0.527000	0.06374	-0.400000	0.06385	GAT	T|0.847;A|0.153	0.153	strong		0.597	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
EDNRA	1909	hgsc.bcm.edu	37	4	148461073	148461073	+	Silent	SNP	G	G	A	rs5334	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:148461073G>A	ENST00000324300.5	+	6	1520	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	EDNRA_ENST00000511804.1_Silent_p.E110E|EDNRA_ENST00000358556.4_Silent_p.E226E|EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_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						PASS	.	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	115	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	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		
USP10	9100	hgsc.bcm.edu	37	16	84778697	84778697	+	Missense_Mutation	SNP	G	G	C	rs1812061	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84778697G>C	ENST00000219473.7	+	4	723	c.610G>C	c.(610-612)Gtt>Ctt	p.V204L	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Missense_Mutation_p.V208L	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	204			V -> L (in dbSNP:rs1812061). {ECO:0000269|PubMed:15489334}.		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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GCCCCCGTCAGTTACGCCCAG	0.552													G|||	1406	0.280751	0.2337	0.121	5008	,	,		17449	0.4107		0.1531	False		,,,				2504	0.455				p.V208L		Atlas-SNP	.											.	USP10	51	.	0			c.G622C						PASS	.	G	LEU/VAL	831,3131		80,671,1230	29.0	29.0	29.0		610	5.2	0.0	16	dbSNP_92	29	1174,7140		85,1004,3068	no	missense	USP10	NM_005153.2	32	165,1675,4298	CC,CG,GG		14.1208,20.9743,16.3327	benign	204/799	84778697	2005,10271	1981	4157	6138	SO:0001583	missense	9100	exon5			CCGTCAGTTACGC	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.610G>C	16.37:g.84778697G>C	ENSP00000219473:p.Val204Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	528	0.24175824175824176	114	0.23170731707317074	48	0.13259668508287292	256	0.44755244755244755	110	0.14511873350923482	G	9.251	1.040870	0.19669	0.209743	0.141208	ENSG00000103194	ENST00000219473	T	0.06687	3.27	5.17	5.17	0.71159	.	1.756670	0.03339	N	0.194567	T	0.00012	0.0000	N	0.22421	0.69	0.52099	P	5.999999999994898E-5	B;B	0.20261	0.043;0.025	B;B	0.24541	0.054;0.024	T	0.47636	-0.9102	9	0.31617	T	0.26	-8.596	15.8288	0.78736	0.0:0.0:1.0:0.0	rs1812061;rs17849289;rs1812061	208;204	Q14694-3;Q14694	.;UBP10_HUMAN	L	204	ENSP00000219473:V204L	ENSP00000219473:V204L	V	+	1	0	USP10	83336198	0.426000	0.25506	0.007000	0.13788	0.173000	0.22820	2.140000	0.42159	2.403000	0.81681	0.491000	0.48974	GTT	G|0.896;C|0.104	0.104	strong		0.552	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
EEA1	8411	hgsc.bcm.edu	37	12	93258665	93258665	+	Silent	SNP	A	A	G	rs17194451	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:93258665A>G	ENST00000322349.8	-	3	480	c.216T>C	c.(214-216)caT>caC	p.H72H	EEA1_ENST00000547833.1_5'UTR	NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	72					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						ACTCTCCTCCATGACCTGAGT	0.373													A|||	855	0.170727	0.1876	0.1599	5008	,	,		17058	0.0218		0.3191	False		,,,				2504	0.1564				p.H72H		Atlas-SNP	.											.	EEA1	104	.	0			c.T216C						PASS	.	A		928,3478	356.1+/-313.4	111,706,1386	119.0	105.0	110.0		216	0.3	1.0	12	dbSNP_123	110	2657,5943	427.4+/-355.6	414,1829,2057	no	coding-synonymous	EEA1	NM_003566.3		525,2535,3443	GG,GA,AA		30.8953,21.0622,27.5642		72/1412	93258665	3585,9421	2203	4300	6503	SO:0001819	synonymous_variant	8411	exon3			TCCTCCATGACCT	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.216T>C	12.37:g.93258665A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	37	CCDS31874.1																																																																																			A|0.756;G|0.244	0.244	strong		0.373	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
JAG2	3714	hgsc.bcm.edu	37	14	105615514	105615514	+	Silent	SNP	G	G	A	rs368778866		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105615514G>A	ENST00000331782.3	-	13	2149	c.1746C>T	c.(1744-1746)gcC>gcT	p.A582A	JAG2_ENST00000347004.2_Silent_p.A544A	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	582	EGF-like 10; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		CACCTCTGCAGGCCCCGCCAG	0.657																																					p.A582A		Atlas-SNP	.											.	JAG2	69	.	0			c.C1746T						PASS	.	G	,	0,4400		0,0,2200	43.0	50.0	47.0		1746,1632	1.0	1.0	14		47	2,8578		0,2,4288	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,	582/1239,544/1201	105615514	2,12978	2200	4290	6490	SO:0001819	synonymous_variant	3714	exon13			TCTGCAGGCCCCG	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.1746C>T	14.37:g.105615514G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			.	.	weak		0.657	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609855	32609855	+	Silent	SNP	A	A	C	rs1048173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609855A>C	ENST00000343139.5	+	3	540	c.438A>C	c.(436-438)acA>acC	p.T146T	HLA-DQA1_ENST00000374949.2_Silent_p.T146T|HLA-DQA1_ENST00000395363.1_Silent_p.T146T	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	145	Alpha-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)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TCAACATCACATGGCTGAGCA	0.498													.|||	1380	0.275559	0.1596	0.3545	5008	,	,		15254	0.3046		0.2952	False		,,,				2504	0.3262				p.T146T		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A438C						PASS	.						142.0	95.0	112.0					6																	32609855		1509	2704	4213	SO:0001819	synonymous_variant	3117	exon3			CATCACATGGCTG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.438A>C	6.37:g.32609855A>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	113	36	0.318584	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	606	0.2774725274725275	69	0.1402439024390244	115	0.31767955801104975	194	0.33916083916083917	228	0.3007915567282322	.	0.051	-1.249330	0.01469	.	.	ENSG00000196735	ENST00000486548	.	.	.	4.1	-8.2	0.01045	.	.	.	.	.	T	0.27629	0.0679	.	.	.	0.20873	P	0.99983088	.	.	.	.	.	.	T	0.30179	-0.9987	3	.	.	.	.	15.2303	0.73383	0.1426:0.1982:0.6591:0.0	rs1048173;rs2308881;rs3188168;rs9272747;rs16870416	.	.	.	P	119	.	.	H	+	2	0	HLA-DQA1	32717833	0.004000	0.15560	0.017000	0.16124	0.074000	0.17049	-2.279000	0.01159	-2.762000	0.00369	-1.063000	0.02288	CAT	A|0.726;C|0.274	0.274	strong		0.498	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
NIPSNAP3A	25934	hgsc.bcm.edu	37	9	107515214	107515214	+	Missense_Mutation	SNP	G	G	A	rs2274870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:107515214G>A	ENST00000374767.4	+	3	404	c.299G>A	c.(298-300)cGg>cAg	p.R100Q		NM_015469.1	NP_056284.1	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A (C. elegans)	100			R -> Q (in dbSNP:rs2274870). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	8						ACTGAAGTTCGGAAAGCCTTG	0.343													G|||	3193	0.63758	0.7648	0.7118	5008	,	,		17454	0.5228		0.6173	False		,,,				2504	0.5521				p.R100Q		Atlas-SNP	.											.	NIPSNAP3A	18	.	0			c.G299A						PASS	.	G	GLN/ARG	3317,1089	719.0+/-408.9	1244,829,130	87.0	84.0	85.0		299	1.3	1.0	9	dbSNP_100	85	5471,3129	655.9+/-401.3	1772,1927,601	yes	missense	NIPSNAP3A	NM_015469.1	43	3016,2756,731	AA,AG,GG		36.3837,24.7163,32.4312		100/248	107515214	8788,4218	2203	4300	6503	SO:0001583	missense	25934	exon3			AAGTTCGGAAAGC	BC005935	CCDS6760.1	9q31.3	2003-11-27			ENSG00000136783	ENSG00000136783			23619	protein-coding gene	gene with protein product		608871				12477932	Standard	NM_015469		Approved	DKFZp564D177, FLJ13953, HSPC299, MGC14553		Q9UFN0	OTTHUMG00000020413	ENST00000374767.4:c.299G>A	9.37:g.107515214G>A	ENSP00000363899:p.Arg100Gln	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_015469	A6NM55|Q5VX32|Q9BRV7|Q9H843|Q9P083	Missense_Mutation	SNP	ENST00000374767.4	37	CCDS6760.1	1409	0.6451465201465202	378	0.7682926829268293	250	0.6906077348066298	317	0.5541958041958042	464	0.6121372031662269	G	21.6	4.179941	0.78564	0.752837	0.636163	ENSG00000136783	ENST00000374767	T	0.67698	-0.28	5.4	1.26	0.21427	Dimeric alpha-beta barrel (1);	0.054700	0.64402	N	0.000001	T	0.00012	0.0000	M	0.92317	3.295	0.28152	P	0.929344	P;P	0.52061	0.95;0.95	P;B	0.51615	0.675;0.43	T	0.42447	-0.9451	9	0.48119	T	0.1	.	6.5591	0.22476	0.2114:0.0:0.6626:0.126	rs2274870;rs60079462;rs2274870	100;100	B4DW81;Q9UFN0	.;NPS3A_HUMAN	Q	100	ENSP00000363899:R100Q	ENSP00000363899:R100Q	R	+	2	0	NIPSNAP3A	106555035	0.970000	0.33590	0.989000	0.46669	0.986000	0.74619	0.876000	0.28092	0.243000	0.21327	0.655000	0.94253	CGG	G|0.331;A|0.669	0.669	strong		0.343	NIPSNAP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053484.1	NM_015469	
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	Somatic	165	5	0.030303		WXS	Illumina HiSeq	Phase_I	202	5	0.0247525	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
HELB	92797	hgsc.bcm.edu	37	12	66725202	66725202	+	Missense_Mutation	SNP	C	C	T	rs1168312	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:66725202C>T	ENST00000247815.4	+	12	2998	c.2939C>T	c.(2938-2940)aCa>aTa	p.T980I		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	980			T -> I (in dbSNP:rs1168312). {ECO:0000269|PubMed:14702039}.		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)		GGACCCAGCACACCGTCAGCA	0.547													C|||	870	0.173722	0.0832	0.2262	5008	,	,		17646	0.2252		0.17	False		,,,				2504	0.2096				p.T980I		Atlas-SNP	.											.	HELB	90	.	0			c.C2939T						PASS	.	C	ILE/THR	448,3958	216.1+/-234.9	20,408,1775	82.0	65.0	71.0		2939	0.4	0.0	12	dbSNP_87	71	1627,6973	301.0+/-305.2	165,1297,2838	yes	missense	HELB	NM_033647.2	89	185,1705,4613	TT,TC,CC		18.9186,10.168,15.9542	possibly-damaging	980/1088	66725202	2075,10931	2203	4300	6503	SO:0001583	missense	92797	exon12			CCAGCACACCGTC	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.2939C>T	12.37:g.66725202C>T	ENSP00000247815:p.Thr980Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	368	0.1684981684981685	46	0.09349593495934959	59	0.16298342541436464	128	0.22377622377622378	135	0.17810026385224276	C	11.67	1.708033	0.30322	0.10168	0.189186	ENSG00000127311	ENST00000247815	T	0.13089	2.62	5.37	0.373	0.16178	.	1.822040	0.02726	N	0.114571	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.44241	0.829	B	0.41571	0.36	T	0.21211	-1.0252	8	.	.	.	0.2645	4.6677	0.12673	0.1401:0.5487:0.0:0.3112	rs1168312;rs1691824;rs17245677;rs61013182;rs1168312	980	Q8NG08	HELB_HUMAN	I	980	ENSP00000247815:T980I	.	T	+	2	0	HELB	65011469	0.002000	0.14202	0.000000	0.03702	0.069000	0.16628	0.502000	0.22594	-0.215000	0.10063	-0.258000	0.10820	ACA	C|0.844;T|0.156	0.156	strong		0.547	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1255773	1255773	+	Silent	SNP	C	C	T	rs7116614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1255773C>T	ENST00000529681.1	+	21	2551	c.2493C>T	c.(2491-2493)tgC>tgT	p.C831C	MUC5B_ENST00000447027.1_Silent_p.C834C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	831	TIL 3.				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)		GCACACACTGCGTGTCCGGCT	0.667													c|||	1700	0.339457	0.2095	0.33	5008	,	,		11037	0.5982		0.2883	False		,,,				2504	0.3078				p.C831C		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C2493T						PASS	.			812,3458		79,654,1402	25.0	30.0	28.0		2493	-8.2	0.0	11	dbSNP_116	28	2440,6004		386,1668,2168	no	coding-synonymous	MUC5B	NM_002458.2		465,2322,3570	TT,TC,CC		28.8963,19.0164,25.5781		831/5763	1255773	3252,9462	2135	4222	6357	SO:0001819	synonymous_variant	727897	exon21			ACACTGCGTGTCC	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.2493C>T	11.37:g.1255773C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.647;T|0.353	0.353	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
INPP5B	3633	hgsc.bcm.edu	37	1	38411445	38411445	+	Silent	SNP	G	G	A	rs871524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38411445G>A	ENST00000373026.1	-	2	135	c.135C>T	c.(133-135)caC>caT	p.H45H	INPP5B_ENST00000373024.3_Silent_p.H45H|INPP5B_ENST00000373021.1_Silent_p.H45H|INPP5B_ENST00000373023.2_Silent_p.H45H			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	45	PH.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CCTGGCCGCCGTGCTCCAGGC	0.652													G|||	1011	0.201877	0.0431	0.2262	5008	,	,		15761	0.2401		0.3181	False		,,,				2504	0.2403				p.H45H		Atlas-SNP	.											.	INPP5B	76	.	0			c.C135T						PASS	.	G		351,3805		17,317,1744	54.0	65.0	62.0		135	-8.0	0.0	1	dbSNP_86	62	2590,5800		388,1814,1993	no	coding-synonymous	INPP5B	NM_005540.2		405,2131,3737	AA,AG,GG		30.8701,8.4456,23.4417		45/914	38411445	2941,9605	2078	4195	6273	SO:0001819	synonymous_variant	3633	exon3			GCCGCCGTGCTCC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.135C>T	1.37:g.38411445G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37																																																																																				G|0.734;A|0.266	0.266	strong		0.652	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
KLHL25	64410	hgsc.bcm.edu	37	15	86312681	86312681	+	Silent	SNP	G	G	A	rs11073537	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:86312681G>A	ENST00000337975.5	-	2	635	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	KLHL25_ENST00000536947.1_Silent_p.L121L|MIR1276_ENST00000408707.1_RNA|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	64	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	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	
NEUROG1	4762	hgsc.bcm.edu	37	5	134870913	134870913	+	Silent	SNP	G	G	A	rs8192559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:134870913G>A	ENST00000314744.4	-	1	726	c.468C>T	c.(466-468)ccC>ccT	p.P156P		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	156					cell fate commitment (GO:0045165)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of exit from mitosis (GO:0031536)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perikaryon (GO:0043204)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			endometrium(1)|liver(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CACCGCCTCCGGGCAGCCCTT	0.706													G|||	162	0.0323482	0.0053	0.0807	5008	,	,		11444	0.0		0.0825	False		,,,				2504	0.0164				p.P156P		Atlas-SNP	.											.	NEUROG1	18	.	0			c.C468T						PASS	.	G		97,4291		3,91,2100	21.0	24.0	23.0		468	0.3	1.0	5	dbSNP_117	23	785,7791		23,739,3526	no	coding-synonymous	NEUROG1	NM_006161.2		26,830,5626	AA,AG,GG		9.1535,2.2106,6.8035		156/238	134870913	882,12082	2194	4288	6482	SO:0001819	synonymous_variant	4762	exon1			GCCTCCGGGCAGC	U63842	CCDS4187.1	5q23-q31	2013-05-21			ENSG00000181965	ENSG00000181965		"""Basic helix-loop-helix proteins"""	7764	protein-coding gene	gene with protein product	"""neurogenic differentiation 3"""	601726		NEUROD3		9119405	Standard	NM_006161		Approved	AKA, Math4C, ngn1, bHLHa6	uc003lax.3	Q92886	OTTHUMG00000129138	ENST00000314744.4:c.468C>T	5.37:g.134870913G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	46	0.613333	NM_006161	Q5U0Q9|Q96HE1	Silent	SNP	ENST00000314744.4	37	CCDS4187.1																																																																																			G|0.941;A|0.059	0.059	strong		0.706	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161	
MLIP	90523	hgsc.bcm.edu	37	6	53883843	53883843	+	Missense_Mutation	SNP	G	G	A	rs17625497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:53883843G>A	ENST00000274897.5	+	1	130	c.17G>A	c.(16-18)cGt>cAt	p.R6H	MLIP_ENST00000370877.2_Missense_Mutation_p.R6H|MLIP_ENST00000509997.1_Missense_Mutation_p.R6H|MLIP_ENST00000514921.1_Missense_Mutation_p.R6H	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	6	Interaction with LMNA.		R -> H (in dbSNP:rs17625497).			nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						CTTGAAAAGCGTGAAAAAAGA	0.353													G|||	987	0.197085	0.1702	0.3991	5008	,	,		18877	0.0575		0.2853	False		,,,				2504	0.1431				p.R6H		Atlas-SNP	.											.	MLIP	84	.	0			c.G17A						PASS	.	G	HIS/ARG	804,3602	314.9+/-293.9	66,672,1465	60.0	64.0	62.0		17	3.5	1.0	6	dbSNP_123	62	2418,6182	396.8+/-345.5	321,1776,2203	yes	missense	MLIP	NM_138569.2	29	387,2448,3668	AA,AG,GG		28.1163,18.2478,24.7732		6/459	53883843	3222,9784	2203	4300	6503	SO:0001583	missense	90523	exon1			AAAAGCGTGAAAA	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.17G>A	6.37:g.53883843G>A	ENSP00000274897:p.Arg6His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	74	0.973684	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Missense_Mutation	SNP	ENST00000274897.5	37	CCDS4954.1	468	0.21428571428571427	72	0.14634146341463414	141	0.38950276243093923	41	0.07167832167832168	214	0.28232189973614774	G	4.650	0.120805	0.08881	0.182478	0.281163	ENSG00000146147	ENST00000274897;ENST00000514921;ENST00000370877;ENST00000509997	T;T;T;T	0.24538	2.21;1.86;1.85;1.86	5.9	3.46	0.39613	.	1.095070	0.06929	N	0.810852	T	0.01489	0.0048	N	0.00436	-1.5	0.09310	P	0.999999999963233	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43097	-0.9412	9	0.02654	T	1	-9.0E-4	7.5222	0.27635	0.8049:0.0:0.0689:0.1262	rs17625497;rs56485234;rs60544912;rs17625497	6;6	Q5VWP3;D6RE05	MLIP_HUMAN;.	H	6	ENSP00000274897:R6H;ENSP00000425142:R6H;ENSP00000359914:R6H;ENSP00000427584:R6H	ENSP00000274897:R6H	R	+	2	0	MLIP	53991802	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.751000	0.55165	0.454000	0.26884	-0.295000	0.09555	CGT	G|0.784;A|0.216	0.216	strong		0.353	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
GLRX5	51218	hgsc.bcm.edu	37	14	96010424	96010424	+	Missense_Mutation	SNP	G	G	A	rs11628901	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:96010424G>A	ENST00000331334.4	+	2	933	c.436G>A	c.(436-438)Gcc>Acc	p.A146T	GLRX5_ENST00000553672.1_3'UTR	NM_016417.2	NP_057501.2	Q86SX6	GLRX5_HUMAN	glutaredoxin 5	146			A -> T (in dbSNP:rs11628901). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16110529}.		cell redox homeostasis (GO:0045454)|hemopoiesis (GO:0030097)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|protein disulfide oxidoreductase activity (GO:0015035)			large_intestine(1)|lung(1)	2		all_cancers(154;0.135)		Epithelial(152;0.133)|COAD - Colon adenocarcinoma(157;0.21)|all cancers(159;0.212)		GATCCACTCCGCCCTTTTAGA	0.527													G|||	416	0.0830671	0.0431	0.1153	5008	,	,		16548	0.0218		0.1362	False		,,,				2504	0.1227				p.A146T		Atlas-SNP	.											.	GLRX5	7	.	0			c.G436A						PASS	.	G	THR/ALA	255,4151	146.5+/-181.1	10,235,1958	45.0	48.0	47.0		436	4.1	1.0	14	dbSNP_120	47	1261,7339	250.7+/-277.5	84,1093,3123	yes	missense	GLRX5	NM_016417.2	58	94,1328,5081	AA,AG,GG		14.6628,5.7876,11.6562	benign	146/158	96010424	1516,11490	2203	4300	6503	SO:0001583	missense	51218	exon2			CACTCCGCCCTTT	AF113691	CCDS9936.1	14q32.2	2007-08-16	2007-08-16	2005-11-11		ENSG00000182512			20134	protein-coding gene	gene with protein product		609588	"""chromosome 14 open reading frame 87"", ""glutaredoxin 5 homolog (S. cerevisiae)"""	C14orf87			Standard	NM_016417		Approved	PR01238, GRX5	uc001yem.1	Q86SX6		ENST00000331334.4:c.436G>A	14.37:g.96010424G>A	ENSP00000328570:p.Ala146Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_016417	Q0X088|Q3YML0|Q86WY3|Q8IZ54	Missense_Mutation	SNP	ENST00000331334.4	37	CCDS9936.1	174	0.07967032967032966	23	0.046747967479674794	34	0.09392265193370165	14	0.024475524475524476	103	0.1358839050131926	G	19.41	3.822386	0.71028	0.057876	0.146628	ENSG00000182512	ENST00000331334	T	0.36157	1.27	5.02	4.11	0.48088	Thioredoxin-like fold (1);	0.160491	0.56097	D	0.000037	T	0.00109	0.0003	L	0.41824	1.3	0.09310	P	0.9999999495891	P	0.45768	0.866	B	0.27715	0.082	T	0.11084	-1.0602	9	0.38643	T	0.18	-7.2558	12.8273	0.57726	0.0801:0.0:0.9199:0.0	rs11628901;rs17092662;rs17852142	146	Q86SX6	GLRX5_HUMAN	T	146	ENSP00000328570:A146T	ENSP00000328570:A146T	A	+	1	0	GLRX5	95080177	1.000000	0.71417	0.989000	0.46669	0.931000	0.56810	7.191000	0.77763	1.079000	0.41038	0.491000	0.48974	GCC	G|0.897;A|0.103	0.103	strong		0.527	GLRX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414550.1		
ZNF418	147686	hgsc.bcm.edu	37	19	58437773	58437773	+	Silent	SNP	T	T	C	rs184676943	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58437773T>C	ENST00000396147.1	-	4	2067	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000599852.1_Silent_p.E507E|ZNF418_ENST00000425570.3_Silent_p.E613E|ZNF418_ENST00000595830.1_Silent_p.E592E	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	83	0	0		WXS	Illumina HiSeq	Phase_I	48	8	0.166667	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	
CAMTA1	23261	hgsc.bcm.edu	37	1	7723534	7723534	+	Silent	SNP	G	G	A	rs3737907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:7723534G>A	ENST00000303635.7	+	9	1134	c.927G>A	c.(925-927)tcG>tcA	p.S309S	CAMTA1_ENST00000439411.2_Silent_p.S309S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		ATGACGTGTCGGAGGGCAAGC	0.637			T	WWTR1	epitheliod hemangioendothelioma								G|||	766	0.152955	0.1793	0.2493	5008	,	,		17481	0.2411		0.0626	False		,,,				2504	0.0511				p.S309S		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	CAMTA1,NS,carcinoma,+1,1	CAMTA1	226	1	0			c.G927A						PASS	.	G		597,3809	263.1+/-265.3	36,525,1642	103.0	102.0	103.0		927	-9.8	0.1	1	dbSNP_107	103	581,8019	156.0+/-209.9	17,547,3736	no	coding-synonymous	CAMTA1	NM_015215.2		53,1072,5378	AA,AG,GG		6.7558,13.5497,9.0574		309/1674	7723534	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			CGTGTCGGAGGGC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.927G>A	1.37:g.7723534G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																			G|0.883;A|0.117	0.117	strong		0.637	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
PRDM10	56980	hgsc.bcm.edu	37	11	129801043	129801043	+	Silent	SNP	C	C	T	rs2277033	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:129801043C>T	ENST00000360871.3	-	11	1629	c.1398G>A	c.(1396-1398)caG>caA	p.Q466Q	PRDM10_ENST00000526082.1_Silent_p.Q380Q|PRDM10_ENST00000528746.1_Silent_p.Q440Q|PRDM10_ENST00000423662.2_Silent_p.Q380Q|PRDM10_ENST00000358825.5_Silent_p.Q466Q|PRDM10_ENST00000304538.6_Silent_p.Q380Q	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		ACTGGGTTTCCTGTGGCAGCT	0.547													T|||	3215	0.641973	0.8691	0.513	5008	,	,		17483	0.7758		0.4294	False		,,,				2504	0.5072				p.Q466Q		Atlas-SNP	.											.	PRDM10	120	.	0			c.G1398A						PASS	.	T	,,,	3583,819	326.4+/-299.6	1464,655,82	197.0	194.0	195.0		1398,1398,1140,1140	1.8	0.8	11	dbSNP_100	195	3732,4862	617.3+/-396.6	793,2146,1358	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	2257,2801,1440	TT,TC,CC		43.4256,18.6052,43.7135	,,,	466/1161,466/1157,380/1062,380/1024	129801043	7315,5681	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon11			GGTTTCCTGTGGC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.1398G>A	11.37:g.129801043C>T		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	182	181	0.994505	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			C|0.395;T|0.605	0.605	strong		0.547	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
OR2B6	26212	hgsc.bcm.edu	37	6	27925827	27925827	+	Missense_Mutation	SNP	A	A	G	rs9380030	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27925827A>G	ENST00000244623.1	+	1	809	c.809A>G	c.(808-810)cAa>cGa	p.Q270R		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	270			Q -> R (in dbSNP:rs9380030).			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						TCCAAGGACCAAGGAAAGATG	0.448													G|||	299	0.0597045	0.0265	0.111	5008	,	,		18046	0.0843		0.0119	False		,,,				2504	0.092				p.Q270R		Atlas-SNP	.											.	OR2B6	48	.	0			c.A809G						PASS	.	G	ARG/GLN	98,4308		1,96,2106	127.0	121.0	123.0		809	1.0	0.2	6	dbSNP_119	123	228,8372		3,222,4075	yes	missense	OR2B6	NM_012367.1	43	4,318,6181	GG,GA,AA		2.6512,2.2242,2.5065	benign	270/314	27925827	326,12680	2203	4300	6503	SO:0001583	missense	26212	exon1			AGGACCAAGGAAA	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.809A>G	6.37:g.27925827A>G	ENSP00000244623:p.Gln270Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_012367	O43883|Q6IF89|Q9H5B0	Missense_Mutation	SNP	ENST00000244623.1	37	CCDS4642.1	112	0.05128205128205128	14	0.028455284552845527	39	0.10773480662983426	52	0.09090909090909091	7	0.009234828496042216	N	1.036	-0.680462	0.03353	0.022242	0.026512	ENSG00000124657	ENST00000244623	T	0.00152	8.66	3.82	0.993	0.19825	GPCR, rhodopsin-like superfamily (1);	0.268063	0.18063	N	0.152865	T	0.00039	0.0001	N	0.20401	0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.00800	-1.1561	9	0.24483	T	0.36	.	7.2274	0.26022	0.4104:0.0:0.5896:0.0	rs9380030;rs56478767;rs60575097;rs9380030	270	P58173	OR2B6_HUMAN	R	270	ENSP00000244623:Q270R	ENSP00000244623:Q270R	Q	+	2	0	OR2B6	28033806	0.000000	0.05858	0.200000	0.23457	0.162000	0.22319	-1.783000	0.01770	-0.180000	0.10637	-1.950000	0.00486	CAA	A|0.962;G|0.038	0.038	strong		0.448	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1		
FANCD2	2177	hgsc.bcm.edu	37	3	10138069	10138069	+	Silent	SNP	T	T	G	rs2272125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10138069T>G	ENST00000419585.1	+	42	4259	c.4098T>G	c.(4096-4098)ctT>ctG	p.L1366L	FANCD2OS_ENST00000524279.1_Intron|FANCD2OS_ENST00000436517.1_5'Flank|FANCD2_ENST00000287647.3_Silent_p.L1366L|FANCD2_ENST00000383807.1_Silent_p.L1366L|FANCD2_ENST00000383806.1_3'UTR			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	61	0	0		WXS	Illumina HiSeq	Phase_I	93	34	0.365591	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		
RNPEP	6051	hgsc.bcm.edu	37	1	201969082	201969082	+	Silent	SNP	G	G	A	rs1130790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201969082G>A	ENST00000295640.4	+	6	1186	c.1143G>A	c.(1141-1143)caG>caA	p.Q381Q	RNPEP_ENST00000367286.3_Silent_p.Q342Q|RNPEP_ENST00000471105.1_3'UTR|RP11-465N4.4_ENST00000419190.1_RNA|RP11-465N4.4_ENST00000415582.1_RNA	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	381					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.Q381Q(1)		breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TGCTGCGTCAGCACATGGACA	0.577											OREG0014093	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1545	0.308506	0.1558	0.438	5008	,	,		18265	0.3978		0.4284	False		,,,				2504	0.2076				p.Q381Q	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											RNPEP,NS,carcinoma,0,2	RNPEP	39	2	1	Substitution - coding silent(1)	stomach(1)	c.G1143A						PASS	.	G		802,3604	320.2+/-296.5	72,658,1473	96.0	83.0	87.0		1143	4.3	1.0	1	dbSNP_86	87	3723,4877	529.8+/-381.7	795,2133,1372	no	coding-synonymous	RNPEP	NM_020216.3		867,2791,2845	AA,AG,GG		43.2907,18.2025,34.7916		381/651	201969082	4525,8481	2203	4300	6503	SO:0001819	synonymous_variant	6051	exon6			GCGTCAGCACATG	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.1143G>A	1.37:g.201969082G>A		Somatic	95	0	0	2125	WXS	Illumina HiSeq	Phase_I	168	70	0.416667	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Silent	SNP	ENST00000295640.4	37	CCDS1418.1																																																																																			G|0.652;A|0.348	0.348	strong		0.577	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216	
C16orf71	146562	hgsc.bcm.edu	37	16	4790204	4790204	+	Missense_Mutation	SNP	C	C	G	rs61731839	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:4790204C>G	ENST00000299320.5	+	4	805	c.327C>G	c.(325-327)aaC>aaG	p.N109K	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.N123K	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	109										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCAGACAGAACACAAGGACAA	0.517													C|||	65	0.0129792	0.0038	0.0115	5008	,	,		16618	0.0		0.0417	False		,,,				2504	0.0102				p.N109K		Atlas-SNP	.											.	C16orf71	46	.	0			c.C327G						PASS	.	C	LYS/ASN	31,4363	37.6+/-69.7	2,27,2168	103.0	103.0	103.0		327	-8.1	0.0	16	dbSNP_129	103	402,8198	127.8+/-186.1	4,394,3902	yes	missense	C16orf71	NM_139170.2	94	6,421,6070	GG,GC,CC		4.6744,0.7055,3.3323	possibly-damaging	109/521	4790204	433,12561	2197	4300	6497	SO:0001583	missense	146562	exon4			ACAGAACACAAGG	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.327C>G	16.37:g.4790204C>G	ENSP00000299320:p.Asn109Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	50	32	0.64	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	43	0.019688644688644688	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	37	0.048812664907651716	C	0.145	-1.097910	0.01843	0.007055	0.046744	ENSG00000166246	ENST00000299320	T	0.12984	2.63	4.05	-8.09	0.01090	.	2.450670	0.02220	N	0.063935	T	0.01061	0.0035	L	0.40543	1.245	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.39396	-0.9616	10	0.08381	T	0.77	0.2266	1.2497	0.01980	0.1817:0.1455:0.2207:0.4521	rs61731839	109	Q8IYS4	CP071_HUMAN	K	109	ENSP00000299320:N109K	ENSP00000299320:N109K	N	+	3	2	C16orf71	4730205	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.012000	0.00314	-2.896000	0.00313	-0.718000	0.03613	AAC	C|0.973;G|0.027	0.027	strong		0.517	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
LMO2	4005	hgsc.bcm.edu	37	11	33886294	33886294	+	Silent	SNP	A	A	G	rs2038602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:33886294A>G	ENST00000395833.3	-	2	540	c.111T>C	c.(109-111)atT>atC	p.I37I	LMO2_ENST00000257818.2_Silent_p.I106I	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	37	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|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)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						AGCGGTCCCCAATGTTCTGCT	0.652			T	TRD@	T-ALL								G|||	2175	0.434305	0.5847	0.2839	5008	,	,		19179	0.4067		0.4185	False		,,,				2504	0.3824				p.I106I		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	.	LMO2	21	.	0			c.T318C						PASS	.	G	,,	2446,1958	546.4+/-377.0	674,1098,430	62.0	53.0	56.0		111,111,318	-4.5	0.9	11	dbSNP_94	56	3551,5045	623.2+/-397.4	762,2027,1509	no	coding-synonymous,coding-synonymous,coding-synonymous	LMO2	NM_001142315.1,NM_001142316.1,NM_005574.3	,,	1436,3125,1939	GG,GA,AA		41.3099,44.4596,46.1308	,,	37/159,37/159,106/228	33886294	5997,7003	2202	4298	6500	SO:0001819	synonymous_variant	4005	exon5			GTCCCCAATGTTC	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.111T>C	11.37:g.33886294A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_005574	Q9HD58	Silent	SNP	ENST00000395833.3	37	CCDS44567.1																																																																																			A|0.546;G|0.454	0.454	strong		0.652	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
FBN3	84467	hgsc.bcm.edu	37	19	8191184	8191184	+	Missense_Mutation	SNP	C	C	T	rs35025963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8191184C>T	ENST00000600128.1	-	21	3016	c.2602G>A	c.(2602-2604)Gat>Aat	p.D868N	FBN3_ENST00000601739.1_Missense_Mutation_p.D868N|FBN3_ENST00000270509.2_Missense_Mutation_p.D868N			Q75N90	FBN3_HUMAN	fibrillin 3	868			D -> N (in dbSNP:rs35025963).			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						CAGTTACCATCGCAGGTGACA	0.647													C|||	1500	0.299521	0.0938	0.3228	5008	,	,		15630	0.379		0.2823	False		,,,				2504	0.4969				p.D868N		Atlas-SNP	.											.	FBN3	300	.	0			c.G2602A						PASS	.	C	ASN/ASP	563,3837		50,463,1687	41.0	40.0	41.0		2602	0.8	0.0	19	dbSNP_126	41	2368,6198		334,1700,2249	yes	missense	FBN3	NM_032447.3	23	384,2163,3936	TT,TC,CC		27.6442,12.7955,22.6053	benign	868/2810	8191184	2931,10035	2200	4283	6483	SO:0001583	missense	84467	exon20			TACCATCGCAGGT		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.2602G>A	19.37:g.8191184C>T	ENSP00000470498:p.Asp868Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	615	0.2815934065934066	60	0.12195121951219512	118	0.3259668508287293	214	0.3741258741258741	223	0.2941952506596306	c	8.987	0.976745	0.18812	0.127955	0.276442	ENSG00000142449	ENST00000270509	D	0.90844	-2.74	3.05	0.768	0.18487	Matrix fibril-associated (2);	0.187814	0.45126	U	0.000389	T	0.00012	0.0000	N	0.20401	0.57	0.42668	P	0.006492999999999971	B	0.25048	0.117	B	0.17098	0.017	T	0.08680	-1.0710	9	0.31617	T	0.26	.	5.0229	0.14370	0.1654:0.6381:0.0:0.1965	rs35025963;rs62123265	868	Q75N90	FBN3_HUMAN	N	868	ENSP00000270509:D868N	ENSP00000270509:D868N	D	-	1	0	FBN3	8097184	1.000000	0.71417	0.028000	0.17463	0.010000	0.07245	2.090000	0.41682	0.130000	0.18549	0.555000	0.69702	GAT	C|0.760;T|0.240	0.240	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
SEC14L6	730005	hgsc.bcm.edu	37	22	30927975	30927975	+	Missense_Mutation	SNP	C	C	T	rs5749118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:30927975C>T	ENST00000402034.2	-	6	433	c.434G>A	c.(433-435)aGg>aAg	p.R145K		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	145	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						TTTCTCCACCCTCTTCCCCAG	0.607													T|||	4409	0.880391	0.8729	0.7911	5008	,	,		19984	0.999		0.8082	False		,,,				2504	0.9059				p.R145K		Atlas-SNP	.											.	SEC14L6	6	.	0			c.G434A						PASS	.																																			SO:0001583	missense	730005	exon6			TCCACCCTCTTCC		CCDS54518.1	22q12.2	2011-05-06			ENSG00000214491	ENSG00000214491			40047	protein-coding gene	gene with protein product							Standard	NM_001193336		Approved		uc021wnu.1	B5MCN3	OTTHUMG00000151267	ENST00000402034.2:c.434G>A	22.37:g.30927975C>T	ENSP00000385695:p.Arg145Lys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001193336		Missense_Mutation	SNP	ENST00000402034.2	37	CCDS54518.1	1903	0.8713369963369964	424	0.8617886178861789	303	0.8370165745856354	569	0.9947552447552448	607	0.8007915567282322	.	1.798	-0.477785	0.04414	.	.	ENSG00000214491	ENST00000402034	T	0.74106	-0.81	3.21	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	N	0.02412	-0.56	0.09310	P	0.999999999389428	.	.	.	.	.	.	T	0.35126	-0.9801	6	0.10377	T	0.69	-1.5081	6.792	0.23705	0.0:0.3043:0.0:0.6957	rs5749118;rs6518699;rs52797912;rs59166374;rs5749118	.	.	.	K	145	ENSP00000385695:R145K	ENSP00000385695:R145K	R	-	2	0	SEC14L6	29257975	0.954000	0.32549	0.870000	0.34147	0.172000	0.22775	1.446000	0.35090	0.019000	0.15079	-0.665000	0.03846	AGG	C|0.135;T|0.865	0.865	strong		0.607	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
ARHGAP28	79822	hgsc.bcm.edu	37	18	6890434	6890434	+	Silent	SNP	A	A	G	rs1116757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:6890434A>G	ENST00000383472.4	+	14	1844	c.1740A>G	c.(1738-1740)ccA>ccG	p.P580P	ARHGAP28_ENST00000262227.3_Silent_p.P528P|ARHGAP28_ENST00000314319.3_Silent_p.P421P|ARHGAP28_ENST00000419673.2_Silent_p.P421P|ARHGAP28_ENST00000400091.2_Silent_p.P580P|ARHGAP28_ENST00000532996.1_Silent_p.P403P|ARHGAP28_ENST00000531294.1_Silent_p.P416P|ARHGAP28_ENST00000418986.1_Silent_p.P421P			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	580					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TCCAGGTTCCATCTTTCTTAA	0.458													G|||	2820	0.563099	0.5719	0.5331	5008	,	,		19204	0.6052		0.5686	False		,,,				2504	0.5235				p.P421P		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A1263G						PASS	.	G		2530,1876	540.2+/-375.5	711,1108,384	76.0	74.0	74.0		1263	-7.3	0.4	18	dbSNP_86	74	4832,3768	532.5+/-382.2	1327,2178,795	no	coding-synonymous	ARHGAP28	NM_001010000.2		2038,3286,1179	GG,GA,AA		43.814,42.5783,43.3954		421/571	6890434	7362,5644	2203	4300	6503	SO:0001819	synonymous_variant	79822	exon13			GGTTCCATCTTTC	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1740A>G	18.37:g.6890434A>G		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	323	186	0.575851	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Silent	SNP	ENST00000383472.4	37																																																																																				A|0.426;G|0.574	0.574	strong		0.458	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
MGAM	8972	hgsc.bcm.edu	37	7	141752213	141752213	+	Silent	SNP	C	C	A	rs386718585|rs2961085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141752213C>A	ENST00000549489.2	+	25	3020	c.2925C>A	c.(2923-2925)gcC>gcA	p.A975A	MGAM_ENST00000475668.2_Silent_p.A975A	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	975	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				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.A975A(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)	GTGCTTCTGCCGAAAACTGCA	0.448													a|||	1517	0.302915	0.3994	0.4654	5008	,	,		18950	0.0298		0.3966	False		,,,				2504	0.2423				p.A975A		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,0,4	MGAM	767	4	1	Substitution - coding silent(1)	stomach(1)	c.C2925A						PASS	.	A		1370,2540		267,836,852	76.0	70.0	72.0		2925	-1.3	0.0	7	dbSNP_101	72	3099,5187		591,1917,1635	no	coding-synonymous	MGAM	NM_004668.2		858,2753,2487	AA,AC,CC		37.4004,35.0384,36.6432		975/1858	141752213	4469,7727	1955	4143	6098	SO:0001819	synonymous_variant	8972	exon25			TTCTGCCGAAAAC	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.2925C>A	7.37:g.141752213C>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|0.723;A|0.277	0.277	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
HK2	3099	hgsc.bcm.edu	37	2	75101454	75101454	+	Silent	SNP	T	T	C	rs2229622	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	231	0	0		WXS	Illumina HiSeq	Phase_I	207	108	0.521739	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	
HSPB9	94086	hgsc.bcm.edu	37	17	40274873	40274873	+	Missense_Mutation	SNP	A	A	C	rs1122326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40274873A>C	ENST00000355067.3	+	1	118	c.5A>C	c.(4-6)cAg>cCg	p.Q2P	KAT2A_ENST00000225916.5_5'Flank|CTD-2132N18.3_ENST00000592574.1_Intron	NM_033194.2	NP_149971.1	Q9BQS6	HSPB9_HUMAN	heat shock protein, alpha-crystallin-related, B9	2			Q -> P (in dbSNP:rs1122326).		response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	4		all_cancers(22;0.00064)|Breast(137;0.00104)|all_epithelial(22;0.00866)		BRCA - Breast invasive adenocarcinoma(366;0.124)		ACTCGGATGCAGAGAGTCGGT	0.667													A|||	1675	0.334465	0.6876	0.1916	5008	,	,		17291	0.1657		0.2326	False		,,,				2504	0.2372				p.Q2P		Atlas-SNP	.											.	HSPB9	11	.	0			c.A5C						PASS	.	A	PRO/GLN	2639,1767	619.6+/-393.4	815,1009,379	33.0	35.0	34.0		5	2.5	1.0	17	dbSNP_86	34	1919,6681	322.8+/-315.7	226,1467,2607	yes	missense	HSPB9	NM_033194.2	76	1041,2476,2986	CC,CA,AA		22.314,40.1044,35.0454	possibly-damaging	2/160	40274873	4558,8448	2203	4300	6503	SO:0001583	missense	94086	exon1			GGATGCAGAGAGT	AJ302068	CCDS11418.1	17q21	2011-09-02			ENSG00000197723	ENSG00000260325		"""Heat shock proteins / HSPB"""	30589	protein-coding gene	gene with protein product	"""cancer/testis antigen 51"""	608344				11470154, 12820654	Standard	NM_033194		Approved	CT51	uc002hyy.2	Q9BQS6	OTTHUMG00000133500	ENST00000355067.3:c.5A>C	17.37:g.40274873A>C	ENSP00000347178:p.Gln2Pro	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_033194	B3KSG6|Q52LB4	Missense_Mutation	SNP	ENST00000355067.3	37	CCDS11418.1	664	0.304029304029304	337	0.6849593495934959	76	0.20994475138121546	77	0.1346153846153846	174	0.22955145118733508	A	14.37	2.513722	0.44763	0.598956	0.22314	ENSG00000197723	ENST00000355067	D	0.89270	-2.49	3.55	2.47	0.30058	.	0.335739	0.26560	U	0.023700	T	0.00012	0.0000	L	0.34521	1.04	0.34383	P	0.306724	D	0.58620	0.983	P	0.56474	0.799	T	0.48536	-0.9027	9	0.87932	D	0	-8.0531	7.0866	0.25261	0.893:0.0:0.107:0.0	rs1122326;rs2285656;rs52821681;rs57608717;rs1122326	2	Q9BQS6	HSPB9_HUMAN	P	2	ENSP00000347178:Q2P	ENSP00000347178:Q2P	Q	+	2	0	HSPB9	37528399	0.211000	0.23529	0.970000	0.41538	0.037000	0.13140	0.039000	0.13884	0.749000	0.32854	0.379000	0.24179	CAG	A|0.661;C|0.339	0.339	strong		0.667	HSPB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257438.1	NM_033194	
KCNK12	56660	hgsc.bcm.edu	37	2	47748388	47748388	+	Silent	SNP	G	G	A	rs115862926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:47748388G>A	ENST00000327876.4	-	2	1558	c.951C>T	c.(949-951)tgC>tgT	p.C317C	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	317						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCGCGCGCAGCAGCGGCAGC	0.697													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11033	0.0		0.001	False		,,,				2504	0.001				p.C317C		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C951T						PASS	.	G		5,4319		0,5,2157	13.0	15.0	14.0		951	3.4	1.0	2	dbSNP_132	14	15,8443		0,15,4214	no	coding-synonymous	KCNK12	NM_022055.1		0,20,6371	AA,AG,GG		0.1773,0.1156,0.1565		317/431	47748388	20,12762	2162	4229	6391	SO:0001819	synonymous_variant	56660	exon2			CGCGCAGCAGCGG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.951C>T	2.37:g.47748388G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	19	12	0.631579	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
CLCNKB	1188	hgsc.bcm.edu	37	1	16377999	16377999	+	Silent	SNP	C	C	T	rs6650118|rs386628877	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16377999C>T	ENST00000375679.4	+	13	1365	c.1254C>T	c.(1252-1254)acC>acT	p.T418T	CLCNKB_ENST00000375667.3_Silent_p.T249T	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	418					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		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;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TGGCCACCACCATCCCCATGC	0.597													C|||	490	0.0978435	0.2133	0.0677	5008	,	,		18910	0.0099		0.0984	False		,,,				2504	0.0532				p.T418T		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1254T						PASS	.	C	,	868,3538		105,658,1440	208.0	196.0	200.0		1254,747	-4.5	0.9	1	dbSNP_116	200	840,7760		54,732,3514	no	coding-synonymous,coding-synonymous	CLCNKB	NM_000085.3,NM_001165945.1	,	159,1390,4954	TT,TC,CC		9.7674,19.7004,13.1324	,	418/688,249/519	16377999	1708,11298	2203	4300	6503	SO:0001819	synonymous_variant	1188	exon13			CACCACCATCCCC	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1254C>T	1.37:g.16377999C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	228	99	0.434211	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	CCDS168.1																																																																																			C|0.884;T|0.116	0.116	strong		0.597	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461185	141461185	+	Silent	SNP	A	A	G	rs3735802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461185A>G	ENST00000438773.2	-	2	421	c.288T>C	c.(286-288)ttT>ttC	p.F96F	TRAPPC9_ENST00000389327.3_Silent_p.F96F|TRAPPC9_ENST00000389328.4_Silent_p.F194F	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	36	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	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	
ITPR2	3709	hgsc.bcm.edu	37	12	26749831	26749831	+	Silent	SNP	G	G	A	rs2230377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:26749831G>A	ENST00000381340.3	-	31	4655	c.4239C>T	c.(4237-4239)gaC>gaT	p.D1413D		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1413					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGATGCAGTCGTCATGGGTCA	0.458													G|||	898	0.179313	0.0938	0.1599	5008	,	,		18276	0.0476		0.3579	False		,,,				2504	0.2607				p.D1413D		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4239T						PASS	.	G		521,3579		37,447,1566	82.0	82.0	82.0		4239	-5.6	1.0	12	dbSNP_98	82	2873,5519		500,1873,1823	no	coding-synonymous	ITPR2	NM_002223.2		537,2320,3389	AA,AG,GG		34.235,12.7073,27.1694		1413/2702	26749831	3394,9098	2050	4196	6246	SO:0001819	synonymous_variant	3709	exon31			GCAGTCGTCATGG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4239C>T	12.37:g.26749831G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.780;A|0.220	0.220	strong		0.458	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ATP13A5	344905	hgsc.bcm.edu	37	3	192994543	192994543	+	Missense_Mutation	SNP	A	A	G	rs2271791	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:192994543A>G	ENST00000342358.4	-	29	3509	c.3392T>C	c.(3391-3393)gTa>gCa	p.V1131A	ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	1131			V -> A (in dbSNP:rs2271791). {ECO:0000269|PubMed:12975309}.			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)		CTTTACCTCTACAAAGAAAGC	0.368													A|||	1664	0.332268	0.1067	0.438	5008	,	,		15486	0.3621		0.4881	False		,,,				2504	0.3712				p.V1131A		Atlas-SNP	.											.	ATP13A5	171	.	0			c.T3392C						PASS	.	A	ALA/VAL	763,3643	310.0+/-291.3	69,625,1509	50.0	49.0	50.0		3392	5.4	1.0	3	dbSNP_100	50	4037,4563	553.8+/-386.4	959,2119,1222	yes	missense	ATP13A5	NM_198505.2	64	1028,2744,2731	GG,GA,AA		46.9419,17.3173,36.906	benign	1131/1219	192994543	4800,8206	2203	4300	6503	SO:0001583	missense	344905	exon29			ACCTCTACAAAGA	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.3392T>C	3.37:g.192994543A>G	ENSP00000341942:p.Val1131Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	171	66	0.385965	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	790	0.3617216117216117	67	0.13617886178861788	148	0.4088397790055249	198	0.34615384615384615	377	0.4973614775725594	A	14.41	2.527006	0.44969	0.173173	0.469419	ENSG00000187527	ENST00000342358	T	0.52295	0.67	5.43	5.43	0.79202	.	0.176189	0.39475	N	0.001341	T	0.00012	0.0000	N	0.24115	0.695	0.26652	P	0.972075	B	0.10296	0.003	B	0.12837	0.008	T	0.44620	-0.9316	9	0.27785	T	0.31	-14.6911	13.7429	0.62857	1.0:0.0:0.0:0.0	rs2271791;rs17355334;rs52835209;rs56782554;rs2271791	1131	Q4VNC0	AT135_HUMAN	A	1131	ENSP00000341942:V1131A	ENSP00000341942:V1131A	V	-	2	0	ATP13A5	194477237	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.102000	0.50291	2.194000	0.70268	0.533000	0.62120	GTA	A|0.649;G|0.351	0.351	strong		0.368	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
LGALS9	3965	hgsc.bcm.edu	37	17	25970633	25970633	+	Missense_Mutation	SNP	G	G	A	rs361497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:25970633G>A	ENST00000395473.2	+	5	1995	c.527G>A	c.(526-528)gGg>gAg	p.G176E	LGALS9_ENST00000413914.2_Missense_Mutation_p.G119E|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000310394.5_Intron|LGALS9_ENST00000302228.5_Intron	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	176					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		AGGCCCAGGGGGCGCAGACAA	0.617													G|||	1145	0.228634	0.1241	0.3069	5008	,	,		17913	0.25		0.2425	False		,,,				2504	0.2781				p.G176E	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.G527A						PASS	.	G	,GLU/GLY	695,3711		67,561,1575	25.0	25.0	25.0		,527	2.5	0.9	17	dbSNP_79	25	2100,6492		289,1522,2485	no	intron,missense	LGALS9	NM_002308.3,NM_009587.2	,98	356,2083,4060	AA,AG,GG		24.4413,15.7739,21.5033	,probably-damaging	,176/356	25970633	2795,10203	2203	4296	6499	SO:0001583	missense	3965	exon5			CCAGGGGGCGCAG	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.527G>A	17.37:g.25970633G>A	ENSP00000378856:p.Gly176Glu	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	318	149	0.468553	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	497	0.22756410256410256	64	0.13008130081300814	109	0.3011049723756906	149	0.26048951048951047	175	0.23087071240105542	G	14.66	2.600487	0.46423	0.157739	0.244413	ENSG00000168961	ENST00000395473;ENST00000413914	T;T	0.16196	3.9;2.36	3.53	2.55	0.30701	.	0.096582	0.40064	N	0.001182	T	0.00012	0.0000	L	0.27053	0.805	0.44018	P	0.003269999999999995	P;B	0.44734	0.842;0.391	B;B	0.38378	0.272;0.104	T	0.47302	-0.9128	9	0.20046	T	0.44	.	6.1273	0.20186	0.1384:0.0:0.8616:0.0	rs361497;rs4795834;rs17399022;rs61705051	119;176	B4DWP7;O00182	.;LEG9_HUMAN	E	176;119	ENSP00000378856:G176E;ENSP00000393695:G119E	ENSP00000378856:G176E	G	+	2	0	LGALS9	22994760	0.169000	0.23002	0.855000	0.33649	0.658000	0.38924	1.469000	0.35343	1.988000	0.58038	0.586000	0.80456	GGG	G|0.833;A|0.167	0.167	strong		0.617	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
ERCC6	2074	hgsc.bcm.edu	37	10	50678317	50678317	+	Missense_Mutation	SNP	C	C	G	rs4253211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:50678317C>G	ENST00000355832.5	-	18	3767	c.3689G>C	c.(3688-3690)cGt>cCt	p.R1230P	ERCC6_ENST00000542458.1_Missense_Mutation_p.R600P|ERCC6_ENST00000465653.1_5'UTR|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1230			R -> P (in dbSNP:rs4253211). {ECO:0000269|Ref.3}.		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.R1230P(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						CTTCTGGTAACGCCTTTTCTT	0.413								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	238	0.047524	0.0076	0.0274	5008	,	,		20047	0.0804		0.0915	False		,,,				2504	0.0368				p.K1230T		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	1	Substitution - Missense(1)	stomach(1)	c.A3689C						PASS	.	C	PRO/ARG	92,4314	76.8+/-115.0	0,92,2111	368.0	347.0	354.0		3689	-7.1	0.0	10	dbSNP_111	354	827,7773	191.3+/-237.5	46,735,3519	yes	missense	ERCC6	NM_000124.2	103	46,827,5630	GG,GC,CC		9.6163,2.0881,7.066	benign	1230/1494	50678317	919,12087	2203	4300	6503	SO:0001583	missense	2074	exon18			TGGTAACGCCTTT	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.3689G>C	10.37:g.50678317C>G	ENSP00000348089:p.Arg1230Pro	Somatic	356	1	0.00280899		WXS	Illumina HiSeq	Phase_I	367	159	0.433242	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	140	0.0641025641025641	5	0.01016260162601626	11	0.03038674033149171	58	0.10139860139860139	66	0.0870712401055409	C	9.193	1.026462	0.19512	0.020881	0.096163	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83419	-1.72;-1.46	5.41	-7.13	0.01532	.	.	.	.	.	T	0.07007	0.0178	M	0.62016	1.91	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.37033	-0.9723	8	0.35671	T	0.21	-2.4611	5.033	0.14419	0.0753:0.6027:0.1507:0.1713	rs4253211;rs17783841;rs52816732;rs56589667;rs4253211	1230;607	Q03468;Q59FF6	ERCC6_HUMAN;.	P	1230;607;600	ENSP00000348089:R1230P;ENSP00000445134:R600P	ENSP00000348089:R1230P	R	-	2	0	ERCC6	50348323	0.000000	0.05858	0.004000	0.12327	0.601000	0.36947	-0.548000	0.06048	-1.579000	0.01646	-0.229000	0.12294	CGT	C|0.930;G|0.070	0.070	strong		0.413	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
TIAM2	26230	hgsc.bcm.edu	37	6	155485554	155485554	+	Silent	SNP	G	G	A	rs1032141	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:155485554G>A	ENST00000461783.3	+	10	3307	c.2034G>A	c.(2032-2034)caG>caA	p.Q678Q	TIAM2_ENST00000528391.2_5'UTR|TIAM2_ENST00000360366.4_Silent_p.Q678Q|TIAM2_ENST00000367174.2_Silent_p.Q30Q|TIAM2_ENST00000318981.5_Silent_p.Q678Q|TIAM2_ENST00000456877.2_5'UTR|TIAM2_ENST00000529824.2_Silent_p.Q678Q|TIAM2_ENST00000456144.1_Silent_p.Q678Q			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	678					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)		TTAAGATCCAGCAATGGGAGC	0.388													G|||	2860	0.571086	0.3608	0.7464	5008	,	,		17640	0.5605		0.6093	False		,,,				2504	0.7025				p.Q678Q		Atlas-SNP	.											.	TIAM2	161	.	0			c.G2034A						PASS	.	G		1926,2480	534.2+/-373.9	413,1100,690	50.0	55.0	53.0		2034	5.3	1.0	6	dbSNP_86	53	5351,3249	641.9+/-399.7	1657,2037,606	no	coding-synonymous	TIAM2	NM_012454.3		2070,3137,1296	AA,AG,GG		37.7791,43.7131,44.0489		678/1702	155485554	7277,5729	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon7			GATCCAGCAATGG		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.2034G>A	6.37:g.155485554G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			G|0.435;A|0.565	0.565	strong		0.388	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
CHSY1	22856	hgsc.bcm.edu	37	15	101717888	101717888	+	Missense_Mutation	SNP	C	C	T	rs62621399	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	106	57	0.537736	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	
PRRG2	5639	hgsc.bcm.edu	37	19	50091763	50091763	+	Missense_Mutation	SNP	G	G	A	rs117225796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50091763G>A	ENST00000246794.5	+	5	480	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	PRRG2_ENST00000596700.1_Intron	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	104						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		GGGCGTGGACGAGTGGATGTG	0.607													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17535	0.0		0.0089	False		,,,				2504	0.0051				p.R104Q		Atlas-SNP	.											.	PRRG2	13	.	0			c.G311A						PASS	.	G	GLN/ARG	4,4398		0,4,2197	35.0	29.0	31.0		311	2.4	0.2	19	dbSNP_132	31	68,8532		0,68,4232	yes	missense	PRRG2	NM_000951.2	43	0,72,6429	AA,AG,GG		0.7907,0.0909,0.5538	benign	104/203	50091763	72,12930	2201	4300	6501	SO:0001583	missense	5639	exon5			GTGGACGAGTGGA		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.311G>A	19.37:g.50091763G>A	ENSP00000246794:p.Arg104Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_000951	Q6IBF8	Missense_Mutation	SNP	ENST00000246794.5	37	CCDS12773.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	10.82	1.459638	0.26248	9.09E-4	0.007907	ENSG00000126460	ENST00000246794;ENST00000543867	D	0.99773	-6.72	5.62	2.36	0.29203	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.544550	0.17501	N	0.171991	D	0.98061	0.9361	L	0.50333	1.59	0.09310	N	1	B;B	0.20052	0.028;0.041	B;B	0.13407	0.009;0.002	D	0.97650	1.0154	10	0.23302	T	0.38	-7.5056	6.9565	0.24574	0.276:0.0:0.724:0.0	.	81;104	F5GZ13;O14669	.;TMG2_HUMAN	Q	104;81	ENSP00000246794:R104Q	ENSP00000246794:R104Q	R	+	2	0	PRRG2	54783575	0.740000	0.28207	0.163000	0.22734	0.416000	0.31233	1.066000	0.30604	0.738000	0.32606	0.563000	0.77884	CGA	G|0.995;A|0.005	0.005	strong		0.607	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181537	128181537	+	Silent	SNP	C	C	T	rs2953129	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:128181537C>T	ENST00000469083.1	-	2	3109	c.552G>A	c.(550-552)tcG>tcA	p.S184S	DNAJB8_ENST00000319153.3_Silent_p.S184S|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	184	Ser-rich.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		TCTCGGTGGACGACATCACCG	0.627													C|||	995	0.198682	0.0136	0.2291	5008	,	,		16918	0.4008		0.2008	False		,,,				2504	0.2168				p.S184S		Atlas-SNP	.											.	DNAJB8	34	.	0			c.G552A						PASS	.	C		220,4186	131.8+/-168.3	7,206,1990	115.0	100.0	105.0		552	-1.9	0.9	3	dbSNP_101	105	1612,6988	300.5+/-305.0	169,1274,2857	no	coding-synonymous	DNAJB8	NM_153330.2		176,1480,4847	TT,TC,CC		18.7442,4.9932,14.0858		184/233	128181537	1832,11174	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			GGTGGACGACATC		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.552G>A	3.37:g.128181537C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			C|0.820;T|0.180	0.180	strong		0.627	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
OR51B6	390058	hgsc.bcm.edu	37	11	5373006	5373006	+	Missense_Mutation	SNP	T	T	C	rs7483122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373006T>C	ENST00000380219.1	+	1	269	c.269T>C	c.(268-270)aTt>aCt	p.I90T	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	90			I -> T (in dbSNP:rs7483122). {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)			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)		CACAGGGAGATTGGCCATGGA	0.468													T|||	1172	0.234026	0.3275	0.2349	5008	,	,		22609	0.0863		0.2644	False		,,,				2504	0.228				p.I90T		Atlas-SNP	.											.	OR51B6	53	.	0			c.T269C						PASS	.	T	THR/ILE	1298,3104	441.6+/-346.4	177,944,1080	131.0	123.0	126.0		269	5.0	1.0	11	dbSNP_116	126	2268,6326	382.1+/-340.3	310,1648,2339	yes	missense	OR51B6	NM_001004750.1	89	487,2592,3419	CC,CT,TT		26.3905,29.4866,27.4392	benign	90/313	5373006	3566,9430	2201	4297	6498	SO:0001583	missense	390058	exon1			GGGAGATTGGCCA		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.269T>C	11.37:g.5373006T>C	ENSP00000369568:p.Ile90Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	473	0.21657509157509158	160	0.3252032520325203	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	T	13.29	2.191954	0.38707	0.294866	0.263905	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00605	6.27	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000053	T	0.00012	0.0000	H	0.96889	3.9	0.22947	P	0.99852053	B	0.34290	0.447	B	0.34242	0.178	T	0.14839	-1.0458	9	0.66056	D	0.02	.	13.6838	0.62504	0.0:0.0:0.0:1.0	rs7483122;rs52804602;rs59784769;rs7483122	90	Q9H340	O51B6_HUMAN	T	89;90	ENSP00000369568:I90T	ENSP00000369568:I90T	I	+	2	0	OR51B6	5329582	1.000000	0.71417	0.955000	0.39395	0.480000	0.33159	4.774000	0.62339	2.103000	0.63969	0.374000	0.22700	ATT	T|0.768;C|0.232	0.232	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
NCAM2	4685	hgsc.bcm.edu	37	21	22746187	22746187	+	Missense_Mutation	SNP	T	T	C	rs232518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:22746187T>C	ENST00000400546.1	+	9	1298	c.1049T>C	c.(1048-1050)cTg>cCg	p.L350P	NCAM2_ENST00000284894.7_Missense_Mutation_p.L208P|NCAM2_ENST00000535285.1_Missense_Mutation_p.L375P	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	350	Ig-like C2-type 4.		L -> P (in dbSNP:rs232518). {ECO:0000269|PubMed:9226371}.		axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AAACAGAGCCTGGACGGCCGT	0.408													C|||	1952	0.389776	0.3782	0.2939	5008	,	,		16709	0.5804		0.3539	False		,,,				2504	0.3139				p.L350P		Atlas-SNP	.											.	NCAM2	220	.	0			c.T1049C						PASS	.	C	PRO/LEU	1402,2394		248,906,744	108.0	101.0	104.0		1049	4.5	1.0	21	dbSNP_79	104	2886,5338		504,1878,1730	yes	missense	NCAM2	NM_004540.3	98	752,2784,2474	CC,CT,TT		35.0924,36.9336,35.6739	benign	350/838	22746187	4288,7732	1898	4112	6010	SO:0001583	missense	4685	exon9			AGAGCCTGGACGG		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1049T>C	21.37:g.22746187T>C	ENSP00000383392:p.Leu350Pro	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	868	0.3974358974358974	179	0.3638211382113821	112	0.30939226519337015	302	0.527972027972028	275	0.3627968337730871	C	10.94	1.491592	0.26774	0.369336	0.350924	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.64803	1.5;1.5;-0.12	5.43	4.54	0.55810	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.238190	0.44688	N	0.000432	T	0.00012	0.0000	N	0.04655	-0.195	0.30244	P	0.7947569999999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46789	-0.9166	9	0.30854	T	0.27	-3.5509	6.1798	0.20465	0.1491:0.6938:0.0:0.1571	rs232518;rs17203863;rs59322715;rs232518	375;350	B7Z841;O15394	.;NCAM2_HUMAN	P	350;208;375	ENSP00000383392:L350P;ENSP00000284894:L208P;ENSP00000441887:L375P	ENSP00000284894:L208P	L	+	2	0	NCAM2	21668058	0.994000	0.37717	0.984000	0.44739	0.776000	0.43924	1.490000	0.35573	0.679000	0.31345	-0.133000	0.14855	CTG	C|0.391;N|0.000	0.391	strong		0.408	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
ELL2	22936	hgsc.bcm.edu	37	5	95234392	95234392	+	Silent	SNP	A	A	C	rs3777202	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	273	0	0		WXS	Illumina HiSeq	Phase_I	254	105	0.413386	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	
ZNF845	91664	hgsc.bcm.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	62	0	0		WXS	Illumina HiSeq	Phase_I	77	3	0.038961	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	
ZBBX	79740	hgsc.bcm.edu	37	3	167034814	167034814	+	Silent	SNP	T	T	C	rs13068132	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167034814T>C	ENST00000392766.2	-	14	1513	c.1173A>G	c.(1171-1173)ctA>ctG	p.L391L	ZBBX_ENST00000469220.1_5'UTR|ZBBX_ENST00000455345.2_Silent_p.L391L|ZBBX_ENST00000392767.2_Silent_p.L391L|ZBBX_ENST00000307529.5_Silent_p.L391L|ZBBX_ENST00000392764.1_Silent_p.L362L	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	189	0	0		WXS	Illumina HiSeq	Phase_I	216	108	0.5	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	
KIAA0020	9933	hgsc.bcm.edu	37	9	2838470	2838470	+	Missense_Mutation	SNP	C	C	T	rs10968457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:2838470C>T	ENST00000397885.2	-	2	244	c.38G>A	c.(37-39)aGt>aAt	p.S13N		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	13			S -> N (in dbSNP:rs10968457). {ECO:0000269|PubMed:15489334}.			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)		TGTCTTTGTACTCTTTCCTGT	0.388													C|||	193	0.0385383	0.0189	0.0533	5008	,	,		19686	0.0536		0.0437	False		,,,				2504	0.0337				p.S13N		Atlas-SNP	.											.	KIAA0020	56	.	0			c.G38A						PASS	.	C	ASN/SER	96,3590		0,96,1747	221.0	193.0	202.0		38	-1.5	0.5	9	dbSNP_120	202	337,7865		4,329,3768	yes	missense	KIAA0020	NM_014878.4	46	4,425,5515	TT,TC,CC		4.1088,2.6044,3.6423	benign	13/649	2838470	433,11455	1843	4101	5944	SO:0001583	missense	9933	exon2			TTTGTACTCTTTC	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.38G>A	9.37:g.2838470C>T	ENSP00000380982:p.Ser13Asn	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	88	0.040293040293040296	4	0.008130081300813009	14	0.03867403314917127	39	0.06818181818181818	31	0.040897097625329816	C	1.958	-0.439506	0.04636	0.026044	0.041088	ENSG00000080608	ENST00000397885	D	0.86366	-2.11	4.59	-1.52	0.08637	.	0.899626	0.09690	N	0.768538	T	0.18299	0.0439	N	0.12182	0.205	0.21020	N	0.999805	B	0.02656	0.0	B	0.01281	0.0	T	0.21793	-1.0235	10	0.10377	T	0.69	-27.9913	10.2478	0.43352	0.0:0.4909:0.0:0.5091	rs10968457;rs52813097;rs10968457	13	Q15397	K0020_HUMAN	N	13	ENSP00000380982:S13N	ENSP00000380982:S13N	S	-	2	0	KIAA0020	2828470	0.032000	0.19561	0.452000	0.26994	0.585000	0.36419	0.029000	0.13666	-0.419000	0.07439	-0.749000	0.03505	AGT	C|0.958;T|0.042	0.042	strong		0.388	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
URB2	9816	hgsc.bcm.edu	37	1	229772693	229772693	+	Missense_Mutation	SNP	T	T	G	rs3811473	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229772693T>G	ENST00000258243.2	+	4	2469	c.2333T>G	c.(2332-2334)gTc>gGc	p.V778G		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	778			V -> G (in dbSNP:rs3811473).			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						GCCCAGGAAGTCTCAATAGAT	0.443													G|||	2864	0.571885	0.4796	0.5432	5008	,	,		21764	0.7649		0.5189	False		,,,				2504	0.5726				p.V778G		Atlas-SNP	.											.	URB2	152	.	0			c.T2333G						PASS	.	G	GLY/VAL	2223,2183	583.2+/-385.8	559,1105,539	79.0	81.0	80.0		2333	-2.1	0.0	1	dbSNP_107	80	4410,4190	569.7+/-389.2	1104,2202,994	yes	missense	URB2	NM_014777.2	109	1663,3307,1533	GG,GT,TT		48.7209,49.5461,49.0005	benign	778/1525	229772693	6633,6373	2203	4300	6503	SO:0001583	missense	9816	exon4			AGGAAGTCTCAAT	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.2333T>G	1.37:g.229772693T>G	ENSP00000258243:p.Val778Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	1297	0.5938644688644689	244	0.4959349593495935	202	0.5580110497237569	461	0.8059440559440559	390	0.5145118733509235	G	2.280	-0.365044	0.05103	0.504539	0.512791	ENSG00000135763	ENST00000258243	T	0.28255	1.62	5.32	-2.13	0.07144	.	0.944668	0.08900	N	0.877421	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	0.25293	-1.0136	8	.	.	.	0.0525	3.4003	0.07321	0.1362:0.4288:0.1573:0.2777	rs3811473;rs56801351;rs3811473	778	Q14146	URB2_HUMAN	G	778	ENSP00000258243:V778G	.	V	+	2	0	URB2	227839316	0.000000	0.05858	0.000000	0.03702	0.428000	0.31595	-0.568000	0.05909	-0.911000	0.03843	-0.195000	0.12781	GTC	T|0.464;G|0.536	0.536	strong		0.443	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036950	33036950	+	Silent	SNP	C	C	T	rs386699855|rs2308931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33036950C>T	ENST00000419277.1	-	4	603	c.474G>A	c.(472-474)ctG>ctA	p.L158L	HLA-DPA1_ENST00000428995.1_Silent_p.L158L|HLA-DPA1_ENST00000463066.1_5'UTR	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						CCTCAGTGACCAGCTCCCCGT	0.567													C|||	980	0.195687	0.239	0.2147	5008	,	,		18947	0.1319		0.1183	False		,,,				2504	0.2689				p.L158L		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G474A						PASS	.	C	,,	526,2492		50,426,1033	166.0	189.0	181.0		474,474,474	0.4	0.0	6	dbSNP_121	181	537,4879		26,485,2197	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	76,911,3230	TT,TC,CC		9.9151,17.4288,12.6037	,,	158/261,158/261,158/261	33036950	1063,7371	1509	2708	4217	SO:0001819	synonymous_variant	3113	exon3			AGTGACCAGCTCC	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.474G>A	6.37:g.33036950C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	294	0.1346153846153846	94	0.1910569105691057	58	0.16022099447513813	72	0.1258741258741259	70	0.09234828496042216	C	1.623	-0.520905	0.04171	0.174288	0.099151	ENSG00000231389	ENST00000437811	.	.	.	3.4	0.388	0.16264	.	.	.	.	.	T	0.19087	0.0458	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.13045	-1.0524	3	.	.	.	.	5.6131	0.17416	0.0:0.423:0.0:0.577	rs2308931;rs11551424	.	.	.	S	26	.	.	G	-	1	0	HLA-DPA1	33144928	0.000000	0.05858	0.011000	0.14972	0.406000	0.30931	-1.401000	0.02502	0.178000	0.19917	0.643000	0.83706	GGT	C|0.869;T|0.131	0.131	strong		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
GAK	2580	hgsc.bcm.edu	37	4	860192	860192	+	Silent	SNP	A	A	G	rs1064207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:860192A>G	ENST00000314167.4	-	22	3113	c.3003T>C	c.(3001-3003)agT>agC	p.S1001S	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.S922S	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1001					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)		GGGGCGGAGCACTGTGGGCAG	0.632													G|||	3269	0.652756	0.5772	0.585	5008	,	,		16289	0.6567		0.6252	False		,,,				2504	0.8272				p.S1001S		Atlas-SNP	.											.	GAK	104	.	0			c.T3003C						PASS	.	G		2687,1719	514.5+/-368.7	821,1045,337	78.0	75.0	76.0		3003	-4.8	0.8	4	dbSNP_86	76	5440,3160	479.4+/-370.1	1745,1950,605	no	coding-synonymous	GAK	NM_005255.2		2566,2995,942	GG,GA,AA		36.7442,39.015,37.5135		1001/1312	860192	8127,4879	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon22			CGGAGCACTGTGG	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.3003T>C	4.37:g.860192A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	1308|1308	0.5989010989010989|0.5989010989010989	265|265	0.5386178861788617|0.5386178861788617	208|208	0.574585635359116|0.574585635359116	361|361	0.6311188811188811|0.6311188811188811	474|474	0.6253298153034301|0.6253298153034301	G|G	1.579|1.579	-0.532196|-0.532196	0.04112|0.04112	0.60985|0.60985	0.632558|0.632558	ENSG00000178950|ENSG00000178950	ENST00000510799|ENST00000511980	.|.	.|.	.|.	5.24|5.24	-4.8|-4.8	0.03190|0.03190	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999555762|0.99999555762	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.11591|0.11591	-1.0581|-1.0581	3|3	.|.	.|.	.|.	-34.3133|-34.3133	15.233|15.233	0.73407|0.73407	0.6304:0.0:0.3696:0.0|0.6304:0.0:0.3696:0.0	rs1064207;rs60937528;rs1064207|rs1064207;rs60937528;rs1064207	.|.	.|.	.|.	R|A	121|113	.|.	.|.	C|V	-|-	1|2	0|0	GAK|GAK	850192|850192	0.032000|0.032000	0.19561|0.19561	0.765000|0.765000	0.31456|0.31456	0.005000|0.005000	0.04900|0.04900	-1.084000|-1.084000	0.03393|0.03393	-1.390000|-1.390000	0.02087|0.02087	-2.599000|-2.599000	0.00162|0.00162	TGC|GTG	A|0.389;G|0.611	0.611	strong		0.632	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ITPR1	3708	hgsc.bcm.edu	37	3	4856234	4856234	+	Silent	SNP	G	G	A	rs901854	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:4856234G>A	ENST00000443694.2	+	55	7644	c.7644G>A	c.(7642-7644)aaG>aaA	p.K2548K	AC018816.3_ENST00000489771.1_Intron|ITPR1_ENST00000357086.4_Silent_p.K2515K|ITPR1_ENST00000302640.8_Silent_p.K2548K|ITPR1_ENST00000456211.2_Silent_p.K2500K|ITPR1_ENST00000544951.1_Silent_p.K526K|ITPR1_ENST00000463980.1_3'UTR|AC018816.3_ENST00000449914.1_Intron|AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000423119.2_Silent_p.K2515K|ITPR1_ENST00000354582.6_Silent_p.K2548K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2563					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TACTCAGGAAGCCGTCCAAAG	0.567													G|||	2942	0.58746	0.5295	0.5346	5008	,	,		14907	0.7202		0.5885	False		,,,				2504	0.5654				p.K2548K		Atlas-SNP	.											.	ITPR1	659	.	0			c.G7644A						PASS	.	G	,,	2310,1668		686,938,365	54.0	57.0	56.0		7545,7644,7500	3.1	1.0	3	dbSNP_86	56	4999,3297		1517,1965,666	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	,,	2203,2903,1031	AA,AG,GG		39.742,41.9306,40.4514	,,	2515/2711,2548/2744,2500/2696	4856234	7309,4965	1989	4148	6137	SO:0001819	synonymous_variant	3708	exon57			CAGGAAGCCGTCC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7644G>A	3.37:g.4856234G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			G|0.382;A|0.618	0.618	strong		0.567	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
A2ML1	144568	hgsc.bcm.edu	37	12	9013755	9013755	+	Missense_Mutation	SNP	C	C	T	rs1860967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:9013755C>T	ENST00000299698.7	+	28	3544	c.3364C>T	c.(3364-3366)Cgg>Tgg	p.R1122W	A2ML1_ENST00000539547.1_Missense_Mutation_p.R631W	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						TCAGGGTCTACGGTGTCTCAA	0.438													C|||	2165	0.432308	0.1067	0.5231	5008	,	,		-128	0.7857		0.3867	False		,,,				2504	0.4908				p.R1122W		Atlas-SNP	.											A2ML1,NS,lymphoid_neoplasm,-2,1	A2ML1	199	1	0			c.C3364T						PASS	.	C	TRP/ARG	598,3340		53,492,1424	136.0	137.0	137.0		3364	0.4	0.3	12	dbSNP_92	137	3096,5212		579,1938,1637	yes	missense	A2ML1	NM_144670.3	101	632,2430,3061	TT,TC,CC		37.2653,15.1854,30.165	possibly-damaging	1122/1455	9013755	3694,8552	1969	4154	6123	SO:0001583	missense	144568	exon28			GGTCTACGGTGTC	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3364C>T	12.37:g.9013755C>T	ENSP00000299698:p.Arg1122Trp	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	150	75	0.5	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	1003	0.4592490842490842	62	0.12601626016260162	178	0.49171270718232046	465	0.8129370629370629	298	0.39313984168865435	C	7.164	0.586213	0.13749	0.151854	0.372653	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.37915	1.17;1.17;1.17	3.56	0.387	0.16259	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	1.110230	0.06791	N	0.787057	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.49090	0.919	P	0.49140	0.601	T	0.36187	-0.9758	9	0.37606	T	0.19	.	2.615	0.04901	0.4748:0.2729:0.1551:0.0972	rs1860967;rs17729723;rs56907838;rs1860967	1122	A8K2U0	A2ML1_HUMAN	W	1122;1122;672;631	ENSP00000299698:R1122W;ENSP00000443174:R672W;ENSP00000438292:R631W	ENSP00000299698:R1122W	R	+	1	2	A2ML1	8905022	0.000000	0.05858	0.310000	0.25168	0.419000	0.31324	-0.361000	0.07612	0.072000	0.16694	0.563000	0.77884	CGG	C|0.568;T|0.432	0.432	strong		0.438	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
PNPLA7	375775	hgsc.bcm.edu	37	9	140356721	140356721	+	Silent	SNP	C	C	T	rs78453847	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140356721C>T	ENST00000277531.4	-	30	3666	c.3480G>A	c.(3478-3480)gaG>gaA	p.E1160E	NSMF_ENST00000371474.3_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000371473.3_5'Flank|PNPLA7_ENST00000371457.1_Silent_p.E766E|NSMF_ENST00000371475.3_5'Flank|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000437259.1_5'Flank|NSMF_ENST00000392812.4_5'Flank|PNPLA7_ENST00000406427.1_Silent_p.E1185E|NSMF_ENST00000371472.2_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1160					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)		TCTTCACCACCTCCAGCTGCC	0.627													C|||	37	0.00738818	0.0023	0.0072	5008	,	,		15711	0.0		0.0249	False		,,,				2504	0.0041				p.E1185E		Atlas-SNP	.											.	PNPLA7	124	.	0			c.G3555A						PASS	.	C	,	15,4391	21.2+/-45.6	0,15,2188	64.0	62.0	62.0		3555,3480	3.5	0.9	9	dbSNP_131	62	179,8417	79.5+/-142.1	2,175,4121	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	2,190,6309	TT,TC,CC		2.0824,0.3404,1.4921	,	1185/1343,1160/1318	140356721	194,12808	2203	4298	6501	SO:0001819	synonymous_variant	375775	exon31			CACCACCTCCAGC	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.3480G>A	9.37:g.140356721C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			C|0.987;T|0.013	0.013	strong		0.627	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
SASH1	23328	hgsc.bcm.edu	37	6	148792617	148792617	+	Silent	SNP	A	A	G	rs1883625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:148792617A>G	ENST00000367467.3	+	6	967	c.492A>G	c.(490-492)ggA>ggG	p.G164G		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	164					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)		ACCAGAAAGGAATAATGAGAC	0.368													A|||	1088	0.217252	0.4017	0.0965	5008	,	,		16207	0.1389		0.1402	False		,,,				2504	0.2137				p.G164G		Atlas-SNP	.											.	SASH1	123	.	0			c.A492G						PASS	.	A		1511,2895	476.4+/-357.6	250,1011,942	58.0	57.0	58.0		492	3.3	1.0	6	dbSNP_92	58	1022,7578	213.5+/-253.4	56,910,3334	no	coding-synonymous	SASH1	NM_015278.3		306,1921,4276	GG,GA,AA		11.8837,34.2941,19.4756		164/1248	148792617	2533,10473	2203	4300	6503	SO:0001819	synonymous_variant	23328	exon6			GAAAGGAATAATG	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.492A>G	6.37:g.148792617A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	207	107	0.516908	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																			A|0.811;G|0.189	0.189	strong		0.368	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
MAP3K1	4214	hgsc.bcm.edu	37	5	56161787	56161787	+	Silent	SNP	G	G	A	rs832575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:56161787G>A	ENST00000399503.3	+	6	1284	c.1284G>A	c.(1282-1284)acG>acA	p.T428T		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	428	Poly-Ser.				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)		GTACTTCTACGTCTAGTTCAG	0.343													A|||	4028	0.804313	0.7663	0.7219	5008	,	,		19245	0.7183		0.8678	False		,,,				2504	0.9376				p.T428T		Atlas-SNP	.											.	MAP3K1	355	.	0			c.G1284A						PASS	.	A		2975,753		1190,595,79	86.0	82.0	83.0		1284	2.1	1.0	5	dbSNP_86	83	7198,1000		3163,872,64	no	coding-synonymous	MAP3K1	NM_005921.1		4353,1467,143	AA,AG,GG		12.1981,20.1985,14.699		428/1513	56161787	10173,1753	1864	4099	5963	SO:0001819	synonymous_variant	4214	exon6			TTCTACGTCTAGT	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.1284G>A	5.37:g.56161787G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	129	73	0.565891	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			G|0.196;A|0.803	0.803	strong		0.343	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
PLEC	5339	hgsc.bcm.edu	37	8	144995964	144995964	+	Silent	SNP	G	G	A	rs35139934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144995964G>A	ENST00000322810.4	-	32	8605	c.8436C>T	c.(8434-8436)ggC>ggT	p.G2812G	PLEC_ENST00000527096.1_Silent_p.G2698G|PLEC_ENST00000436759.2_Silent_p.G2702G|PLEC_ENST00000354958.2_Silent_p.G2653G|PLEC_ENST00000345136.3_Silent_p.G2675G|PLEC_ENST00000354589.3_Silent_p.G2675G|PLEC_ENST00000356346.3_Silent_p.G2661G|PLEC_ENST00000398774.2_Silent_p.G2643G|PLEC_ENST00000357649.2_Silent_p.G2679G	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2812	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						CCGTGGTGTGGCCCTGCGCCA	0.672													G|||	138	0.0275559	0.0061	0.0461	5008	,	,		17074	0.004		0.0676	False		,,,				2504	0.0266				p.G2812G		Atlas-SNP	.											.	PLEC	1144	.	0			c.C8436T						PASS	.	G	,,,,,,,	50,4262		0,50,2106	27.0	30.0	29.0		8106,7983,7959,8436,7929,8025,8037,8025	1.4	0.8	8	dbSNP_126	29	656,7850		31,594,3628	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	,,,,,,,	31,644,5734	AA,AG,GG		7.7122,1.1596,5.5079	,,,,,,,	2702/4575,2661/4534,2653/4526,2812/4685,2643/4516,2675/4548,2679/4552,2675/4548	144995964	706,12112	2156	4253	6409	SO:0001819	synonymous_variant	5339	exon32			GGTGTGGCCCTGC	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.8436C>T	8.37:g.144995964G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.948;A|0.052	0.052	strong		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
MACC1	346389	hgsc.bcm.edu	37	7	20198440	20198440	+	Missense_Mutation	SNP	G	G	A	rs975263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20198440G>A	ENST00000400331.5	-	5	1852	c.1544C>T	c.(1543-1545)tCg>tTg	p.S515L	MACC1_ENST00000589011.1_Missense_Mutation_p.S515L|MACC1_ENST00000332878.4_Missense_Mutation_p.S515L	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	515			S -> L (in dbSNP:rs975263). {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						TGGCAGATTCGAGAGTCTTTT	0.393													G|||	2131	0.425519	0.2799	0.3256	5008	,	,		19058	0.7837		0.2445	False		,,,				2504	0.5102				p.S515L		Atlas-SNP	.											.	MACC1	99	.	0			c.C1544T						PASS	.	G	LEU/SER	1276,3130	421.5+/-339.4	186,904,1113	103.0	111.0	108.0		1544	5.1	0.0	7	dbSNP_86	108	2048,6552	352.5+/-328.7	274,1500,2526	yes	missense	MACC1	NM_182762.3	145	460,2404,3639	AA,AG,GG		23.814,28.9605,25.5574	benign	515/853	20198440	3324,9682	2203	4300	6503	SO:0001583	missense	346389	exon5			AGATTCGAGAGTC		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.1544C>T	7.37:g.20198440G>A	ENSP00000383185:p.Ser515Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	126	44	0.349206	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	920	0.42124542124542125	173	0.3516260162601626	107	0.2955801104972376	455	0.7954545454545454	185	0.24406332453825857	G	1.747	-0.490207	0.04322	0.289605	0.23814	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.10668	2.85;2.85	5.93	5.05	0.67936	.	0.587313	0.19435	N	0.114325	T	0.00012	0.0000	M	0.72894	2.215	0.80722	P	0.0	B	0.15719	0.014	B	0.08055	0.003	T	0.26985	-1.0087	9	0.08599	T	0.76	-2.993	9.7127	0.40256	0.1959:0.0:0.8041:0.0	rs975263;rs52813696;rs58060920;rs975263	515	Q6ZN28	MACC1_HUMAN	L	515	ENSP00000383185:S515L;ENSP00000328410:S515L	ENSP00000328410:S515L	S	-	2	0	MACC1	20164965	0.076000	0.21285	0.010000	0.14722	0.895000	0.52256	2.152000	0.42272	1.510000	0.48803	0.655000	0.94253	TCG	G|0.652;N|0.000	.	strong		0.393	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	
PCSK5	5125	hgsc.bcm.edu	37	9	78910241	78910241	+	Missense_Mutation	SNP	A	A	C	rs2842480	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:78910241A>C	ENST00000545128.1	+	26	3774	c.3236A>C	c.(3235-3237)gAa>gCa	p.E1079A		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1079	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						TACAGTGAGGAAGTGGAATGC	0.408													A|||	1156	0.230831	0.4039	0.2104	5008	,	,		20277	0.0804		0.2406	False		,,,				2504	0.1564				p.E1079A		Atlas-SNP	.											.	PCSK5	329	.	0			c.A3236C						PASS	.	A	ALA/GLU	645,1107		129,387,360	53.0	48.0	49.0		3236	1.8	0.0	9	dbSNP_100	49	877,3105		95,687,1209	yes	missense	PCSK5	NM_001190482.1	107	224,1074,1569	CC,CA,AA		22.0241,36.8151,26.5434		1079/1861	78910241	1522,4212	876	1991	2867	SO:0001583	missense	5125	exon26			GTGAGGAAGTGGA		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.3236A>C	9.37:g.78910241A>C	ENSP00000446280:p.Glu1079Ala	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	495	0.22664835164835165	184	0.37398373983739835	88	0.2430939226519337	49	0.08566433566433566	174	0.22955145118733508	A	0.467	-0.886413	0.02511	0.368151	0.220241	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.30182	1.54;1.55	5.7	1.79	0.24919	.	0.462757	0.24915	N	0.034587	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	.	.	.	.	.	.	T	0.45877	-0.9231	7	0.14252	T	0.57	-2.7265	8.3655	0.32385	0.7304:0.0:0.2696:0.0	rs2842480;rs58068564;rs2842480	.	.	.	A	1079;782;752	ENSP00000446280:E1079A;ENSP00000411654:E752A	ENSP00000365945:E782A	E	+	2	0	PCSK5	78100061	0.980000	0.34600	0.002000	0.10522	0.011000	0.07611	1.947000	0.40293	0.036000	0.15547	0.533000	0.62120	GAA	A|0.770;C|0.230	0.230	strong		0.408	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CRAMP1L	57585	hgsc.bcm.edu	37	16	1682281	1682281	+	Silent	SNP	A	A	G	rs3169425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1682281A>G	ENST00000397412.3	+	4	708	c.609A>G	c.(607-609)gcA>gcG	p.A203A	LA16c-431H6.6_ENST00000454337.1_Missense_Mutation_p.K8E|CRAMP1L_ENST00000436138.3_Silent_p.A200A|CRAMP1L_ENST00000293925.5_Silent_p.A203A			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	203	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GCAAGCCAGCAAGCATGGTGA	0.468													G|||	2273	0.453874	0.6838	0.3386	5008	,	,		19935	0.5605		0.173	False		,,,				2504	0.4039				p.A203A		Atlas-SNP	.											CRAMP1L,NS,carcinoma,+1,2	CRAMP1L	60	2	0			c.A609G						PASS	.	G		2453,1791		693,1067,362	44.0	51.0	49.0		609	-10.8	0.0	16	dbSNP_105	49	1490,6980		150,1190,2895	no	coding-synonymous	CRAMP1L	NM_020825.3		843,2257,3257	GG,GA,AA		17.5915,42.2008,31.0131		203/1270	1682281	3943,8771	2122	4235	6357	SO:0001819	synonymous_variant	57585	exon3			GCCAGCAAGCATG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.609A>G	16.37:g.1682281A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	94	31	0.329787	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			A|0.586;G|0.414	0.414	strong		0.468	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
MYH7	4625	hgsc.bcm.edu	37	14	23899027	23899027	+	Silent	SNP	C	C	T	rs735711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23899027C>T	ENST00000355349.3	-	12	1257	c.1095G>A	c.(1093-1095)aaG>aaA	p.K365K		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	365	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|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)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GCTGCTTCAGCTTGAACTTCA	0.542													c|||	399	0.0796725	0.1362	0.0706	5008	,	,		17780	0.001		0.1402	False		,,,				2504	0.0286				p.K365K		Atlas-SNP	.											.	MYH7	349	.	0			c.G1095A						PASS	.			635,3771	273.1+/-271.2	50,535,1618	98.0	89.0	92.0		1095	-5.8	1.0	14	dbSNP_86	92	1301,7299	258.1+/-281.9	109,1083,3108	no	coding-synonymous	MYH7	NM_000257.2		159,1618,4726	TT,TC,CC		15.1279,14.4122,14.8854		365/1936	23899027	1936,11070	2203	4300	6503	SO:0001819	synonymous_variant	4625	exon12			CTTCAGCTTGAAC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1095G>A	14.37:g.23899027C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																			T|0.131;G|0.000;C|0.869	0.131	strong		0.542	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
OR2H2	7932	hgsc.bcm.edu	37	6	29555864	29555864	+	Missense_Mutation	SNP	C	C	T	rs1233387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29555864C>T	ENST00000383640.2	+	1	182	c.143C>T	c.(142-144)gCg>gTg	p.A48V	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	48			A -> V (in dbSNP:rs1233387). {ECO:0000269|PubMed:10880742, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14983052}.		defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	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)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						CTGCTGTCTGCGCTGGACCCC	0.527													T|||	1718	0.343051	0.2685	0.3559	5008	,	,		21347	0.4831		0.2555	False		,,,				2504	0.3804				p.A48V		Atlas-SNP	.											OR2H2,NS,carcinoma,0,1	OR2H2	29	1	0			c.C143T						PASS	.	T	VAL/ALA	786,2236		100,586,825	231.0	198.0	210.0		143	2.0	0.0	6	dbSNP_87	210	1371,4047		178,1015,1516	yes	missense	OR2H2	NM_007160.3	64	278,1601,2341	TT,TC,CC		25.3045,26.0093,25.5569	benign	48/313	29555864	2157,6283	1511	2709	4220	SO:0001583	missense	7932	exon1			TGTCTGCGCTGGA		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"""GPCR / Class A : Olfactory receptors"""	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.143C>T	6.37:g.29555864C>T	ENSP00000373136:p.Ala48Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Missense_Mutation	SNP	ENST00000383640.2	37	CCDS34365.1	688	0.315018315018315	125	0.2540650406504065	109	0.3011049723756906	272	0.4755244755244755	182	0.24010554089709762	T	5.424	0.263305	0.10294	0.260093	0.253045	ENSG00000204657	ENST00000383640	T	0.01076	5.37	4.44	1.96	0.26148	GPCR, rhodopsin-like superfamily (1);	0.908400	0.09070	N	0.853071	T	0.00210	0.0006	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35895	-0.9770	9	0.17832	T	0.49	.	0.8099	0.01091	0.1659:0.293:0.1712:0.3699	rs1233387;rs1233387	48	O95918	OR2H2_HUMAN	V	48	ENSP00000373136:A48V	ENSP00000373136:A48V	A	+	2	0	OR2H2	29663843	0.000000	0.05858	0.001000	0.08648	0.987000	0.75469	-1.347000	0.02632	-0.043000	0.13513	-0.352000	0.07741	GCG	C|0.722;T|0.278	0.278	strong		0.527	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2		
MYRIP	25924	hgsc.bcm.edu	37	3	40286017	40286017	+	Silent	SNP	T	T	C	rs4618168	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:40286017T>C	ENST00000302541.6	+	13	2523	c.2181T>C	c.(2179-2181)agT>agC	p.S727S	MYRIP_ENST00000396217.3_Silent_p.S638S|MYRIP_ENST00000539167.1_Silent_p.S540S|MYRIP_ENST00000425621.1_Silent_p.S662S|MYRIP_ENST00000444716.1_Silent_p.S727S|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	727	Actin-binding.				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)		GCATCCACAGTGGCACTGATG	0.582													C|||	3248	0.648562	0.7965	0.4712	5008	,	,		17394	0.7629		0.4254	False		,,,				2504	0.6861				p.S727S		Atlas-SNP	.											.	MYRIP	98	.	0			c.T2181C						PASS	.	C		3259,1147	406.6+/-333.9	1212,835,156	64.0	61.0	62.0		2181	-5.1	0.8	3	dbSNP_111	62	3823,4777	611.0+/-395.8	882,2059,1359	no	coding-synonymous	MYRIP	NM_015460.2		2094,2894,1515	CC,CT,TT		44.4535,26.0327,45.5482		727/860	40286017	7082,5924	2203	4300	6503	SO:0001819	synonymous_variant	25924	exon13			CCACAGTGGCACT	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.2181T>C	3.37:g.40286017T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	230	228	0.991304	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			T|0.418;C|0.582	0.582	strong		0.582	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
KRT16	3868	hgsc.bcm.edu	37	17	39767731	39767731	+	Missense_Mutation	SNP	G	G	A	rs148173278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39767731G>A	ENST00000301653.4	-	3	701	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	213	Coil 1B.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				ACAGTCTGCCGCAGGGCCAGT	0.637													g|||	10	0.00199681	0.0076	0.0	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R213W		Atlas-SNP	.											.	KRT16	45	.	0			c.C637T						PASS	.	G	TRP/ARG	34,4372	38.4+/-70.7	0,34,2169	47.0	48.0	48.0		637	0.3	1.0	17	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT16	NM_005557.3	101	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	213/474	39767731	35,12971	2203	4300	6503	SO:0001583	missense	3868	exon3			TCTGCCGCAGGGC	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.637C>T	17.37:g.39767731G>A	ENSP00000301653:p.Arg213Trp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.20	3.329471	0.60743	0.007717	1.16E-4	ENSG00000186832	ENST00000301653	D	0.92099	-2.97	4.84	0.345	0.16011	Filament (1);	0.000000	0.47852	D	0.000203	D	0.95567	0.8559	H	0.98199	4.17	0.50171	D	0.999858	D	0.89917	1.0	D	0.85130	0.997	D	0.93019	0.6438	10	0.87932	D	0	.	6.7407	0.23435	0.141:0.0:0.6081:0.251	.	213	P08779	K1C16_HUMAN	W	213	ENSP00000301653:R213W	ENSP00000301653:R213W	R	-	1	2	KRT16	37021257	1.000000	0.71417	0.999000	0.59377	0.584000	0.36387	2.574000	0.46016	0.338000	0.23692	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.637	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
L1TD1	54596	hgsc.bcm.edu	37	1	62675664	62675664	+	Silent	SNP	G	G	A	rs200931139|rs532563709		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62675664G>A	ENST00000498273.1	+	4	1513	c.1218G>A	c.(1216-1218)gaG>gaA	p.E406E	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	406	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						Tggaggaggaggaggaagagc	0.547																																					p.E406E		Atlas-SNP	.											.	L1TD1	114	.	0			c.G1218A						PASS	.						36.0	40.0	39.0					1																	62675664		2200	4298	6498	SO:0001819	synonymous_variant	54596	exon5			GGAGGAGGAGGAA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1218G>A	1.37:g.62675664G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	15	0.192308	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			.	.	weak		0.547	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
CLEC4C	170482	hgsc.bcm.edu	37	12	7894056	7894056	+	Missense_Mutation	SNP	G	G	A	rs73056605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	101	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	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	
ITM2C	81618	hgsc.bcm.edu	37	2	231738168	231738168	+	Missense_Mutation	SNP	G	G	A	rs2289235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231738168G>A	ENST00000326427.6	+	2	283	c.157G>A	c.(157-159)Ggc>Agc	p.G53S	ITM2C_ENST00000335005.6_Intron|ITM2C_ENST00000409704.2_5'UTR|ITM2C_ENST00000326407.6_Missense_Mutation_p.G53S|ITM2C_ENST00000492029.1_3'UTR	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	53			G -> S (in dbSNP:rs2289235). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.7}.		negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		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;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		CAAGAGGGGGGGCTCAGTGGG	0.617													G|||	2557	0.510583	0.233	0.5303	5008	,	,		17865	0.8135		0.503	False		,,,				2504	0.5675				p.G53S		Atlas-SNP	.											.	ITM2C	17	.	0			c.G157A						PASS	.	G	,SER/GLY,SER/GLY	1122,3284	397.2+/-330.3	143,836,1224	87.0	68.0	74.0		,157,157	-2.6	0.7	2	dbSNP_100	74	4152,4448	563.2+/-388.1	1020,2112,1168	yes	intron,missense,missense	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,56,56	1163,2948,2392	AA,AG,GG		48.2791,25.4653,40.5505	,benign,benign	,53/231,53/268	231738168	5274,7732	2203	4300	6503	SO:0001583	missense	81618	exon2			AGGGGGGGCTCAG	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.157G>A	2.37:g.231738168G>A	ENSP00000322730:p.Gly53Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Missense_Mutation	SNP	ENST00000326427.6	37	CCDS2479.1	1175	0.538003663003663	139	0.28252032520325204	177	0.4889502762430939	471	0.8234265734265734	388	0.5118733509234829	G	0.012	-1.673453	0.00758	0.254653	0.482791	ENSG00000135916	ENST00000457215;ENST00000326427;ENST00000326407	T;T;T	0.28255	1.62;2.01;2.03	4.85	-2.61	0.06171	.	0.677726	0.14983	N	0.287104	T	0.00012	0.0000	N	0.05124	-0.11	0.53688	P	2.6999999999999247E-5	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.36578	-0.9742	9	0.02654	T	1	-29.8811	4.6856	0.12755	0.5479:0.0:0.2897:0.1624	rs2289235;rs17849577;rs17852294;rs61461656;rs2289235	53;53	Q9NQX7-3;Q9NQX7	.;ITM2C_HUMAN	S	53	ENSP00000390655:G53S;ENSP00000322730:G53S;ENSP00000322100:G53S	ENSP00000322100:G53S	G	+	1	0	ITM2C	231446412	0.611000	0.26992	0.739000	0.30968	0.006000	0.05464	0.093000	0.15086	-0.144000	0.11314	-0.783000	0.03347	GGC	G|0.531;A|0.469	0.469	strong		0.617	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
MED22	6837	hgsc.bcm.edu	37	9	136208442	136208442	+	Silent	SNP	C	C	T	rs78711238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136208442C>T	ENST00000491289.1	-	5	1097	c.516G>A	c.(514-516)gcG>gcA	p.A172A	MED22_ENST00000476080.1_3'UTR|MED22_ENST00000471524.1_5'Flank|MED22_ENST00000344469.5_3'UTR|MED22_ENST00000343730.5_Silent_p.A172A			Q15528	MED22_HUMAN	mediator complex subunit 22	172						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		GCTCCGGGGACGCCAGCAGAG	0.677													C|||	37	0.00738818	0.0038	0.0043	5008	,	,		15768	0.0		0.0258	False		,,,				2504	0.0031				p.A172A		Atlas-SNP	.											.	MED22	13	.	0			c.G516A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	32.0	35.0	34.0		516,	-5.3	0.4	9	dbSNP_133	34	122,8478	62.1+/-124.0	1,120,4179	no	coding-synonymous,utr-3	MED22	NM_133640.3,NM_181491.1	,	1,145,6357	TT,TC,CC		1.4186,0.5674,1.1302	,	172/201,	136208442	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	6837	exon5			CGGGGACGCCAGC		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"""surfeit 5"""	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.516G>A	9.37:g.136208442C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Silent	SNP	ENST00000491289.1	37	CCDS6963.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640	
STK31	56164	hgsc.bcm.edu	37	7	23811795	23811795	+	Missense_Mutation	SNP	T	T	G	rs10263079	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23811795T>G	ENST00000355870.3	+	15	1982	c.1863T>G	c.(1861-1863)aaT>aaG	p.N621K	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Missense_Mutation_p.N598K|STK31_ENST00000354639.3_Missense_Mutation_p.N598K|STK31_ENST00000433467.2_Missense_Mutation_p.N621K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	621			N -> K (in dbSNP:rs10263079). {ECO:0000269|PubMed:17344846}.	NKS -> KKI (in Ref. 1; AAK31978). {ECO:0000305}.		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						AATATTTAAATAAGAGTCCCA	0.289													T|||	484	0.0966454	0.0454	0.1297	5008	,	,		16803	0.0575		0.2117	False		,,,				2504	0.0644				p.N621K		Atlas-SNP	.											.	STK31	175	.	0			c.T1863G						PASS	.	T	LYS/ASN,LYS/ASN,LYS/ASN	305,4097	154.4+/-187.8	14,277,1910	42.0	44.0	43.0		1794,1863,1794	1.5	1.0	7	dbSNP_119	43	1823,6755	318.2+/-313.6	179,1465,2645	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	94,94,94	193,1742,4555	GG,GT,TT		21.252,6.9287,16.3945	possibly-damaging,possibly-damaging,possibly-damaging	598/997,621/1020,598/997	23811795	2128,10852	2201	4289	6490	SO:0001583	missense	56164	exon15			TTTAAATAAGAGT	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.1863T>G	7.37:g.23811795T>G	ENSP00000348132:p.Asn621Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	156	100	0.641026	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	284	0.13003663003663005	28	0.056910569105691054	61	0.1685082872928177	31	0.05419580419580419	164	0.21635883905013192	T	17.51	3.408289	0.62399	0.069287	0.21252	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.70045	-0.45;1.29;-0.44;-0.44	5.19	1.51	0.23008	.	0.121725	0.53938	D	0.000050	T	0.00073	0.0002	M	0.64997	1.995	0.29422	P	0.860491	P;P	0.52842	0.956;0.956	P;P	0.45071	0.468;0.468	T	0.03259	-1.1055	9	0.51188	T	0.08	-16.6838	8.6987	0.34312	0.0:0.2245:0.0:0.7755	rs10263079;rs10263079	621;621	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	621;621;598;598	ENSP00000348132:N621K;ENSP00000411852:N621K;ENSP00000346660:N598K;ENSP00000406146:N598K	ENSP00000346660:N598K	N	+	3	2	STK31	23778320	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	1.330000	0.33781	0.024000	0.15214	-0.379000	0.06801	AAT	T|0.843;G|0.157	0.157	strong		0.289	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180473	57180473	+	Missense_Mutation	SNP	C	C	A	rs6823339	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57180473C>A	ENST00000504228.1	+	6	910	c.805C>A	c.(805-807)Ctc>Atc	p.L269I	KIAA1211_ENST00000264229.6_Missense_Mutation_p.L269I|KIAA1211_ENST00000541073.1_Missense_Mutation_p.L262I			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	51	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	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	
ATXN1	6310	hgsc.bcm.edu	37	6	16327918	16327918	+	Missense_Mutation	SNP	C	C	A	rs28555263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:16327918C>A	ENST00000244769.4	-	8	1560	c.624G>T	c.(622-624)caG>caT	p.Q208H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q208H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	208	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gatgctgatgctgctgctgct	0.662													C|||	649	0.129593	0.1437	0.1153	5008	,	,		12912	0.2044		0.0318	False		,,,				2504	0.1442				p.Q208H		Atlas-SNP	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	0			c.G624T						PASS	.						5.0	8.0	7.0					6																	16327918		1579	3505	5084	SO:0001583	missense	6310	exon7			CTGATGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.624G>T	6.37:g.16327918C>A	ENSP00000244769:p.Gln208His	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	6	0.171429	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	5.901	0.350402	0.11182	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56103	0.48;0.48	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	P	0.39520	0.676	B	0.36030	0.216	T	0.18493	-1.0335	8	0.13108	T	0.6	.	.	.	.	rs28555263	208	P54253	ATX1_HUMAN	H	208	ENSP00000244769:Q208H;ENSP00000416360:Q208H	ENSP00000244769:Q208H	Q	-	3	2	ATXN1	16435897	0.129000	0.22400	0.018000	0.16275	0.062000	0.15995	1.183000	0.32041	0.132000	0.18615	0.134000	0.15878	CAG	C|0.500;A|0.500	0.500	weak		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
C2orf49	79074	hgsc.bcm.edu	37	2	105959592	105959592	+	Missense_Mutation	SNP	G	G	A	rs28930676	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:105959592G>A	ENST00000258457.2	+	3	783	c.554G>A	c.(553-555)gGc>gAc	p.G185D	C2orf49_ENST00000410049.1_Missense_Mutation_p.G143D|C2orf49_ENST00000437250.2_Missense_Mutation_p.G181D			Q9BVC5	ASHWN_HUMAN	chromosome 2 open reading frame 49	185			G -> D (in dbSNP:rs28930676). {ECO:0000269|PubMed:14702039}.		embryonic morphogenesis (GO:0048598)	tRNA-splicing ligase complex (GO:0072669)				endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6						AGTCCTTCAGGCCCTGTGAAG	0.443													G|||	254	0.0507188	0.0779	0.0403	5008	,	,		19627	0.0218		0.0417	False		,,,				2504	0.0603				p.G185D		Atlas-SNP	.											.	C2orf49	19	.	0			c.G554A						PASS	.	G	ASP/GLY	332,4074	175.1+/-204.6	13,306,1884	101.0	98.0	99.0		554	3.7	0.0	2	dbSNP_125	99	383,8217	124.3+/-183.0	6,371,3923	yes	missense	C2orf49	NM_024093.1	94	19,677,5807	AA,AG,GG		4.4535,7.5352,5.4975	possibly-damaging	185/233	105959592	715,12291	2203	4300	6503	SO:0001583	missense	79074	exon3			CTTCAGGCCCTGT	BC001310	CCDS2068.1, CCDS74550.1	2q12.2	2009-04-22			ENSG00000135974	ENSG00000135974			28772	protein-coding gene	gene with protein product	"""ashwin"""					12477932	Standard	NM_001286537		Approved	MGC5509, asw	uc002tcs.1	Q9BVC5	OTTHUMG00000130808	ENST00000258457.2:c.554G>A	2.37:g.105959592G>A	ENSP00000258457:p.Gly185Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_024093	B3KXN3|B4E2G9	Missense_Mutation	SNP	ENST00000258457.2	37	CCDS2068.1	99	0.04532967032967033	42	0.08536585365853659	16	0.04419889502762431	13	0.022727272727272728	28	0.036939313984168866	G	9.424	1.083802	0.20309	0.075352	0.044535	ENSG00000135974	ENST00000258457;ENST00000437250;ENST00000410049	T;T;T	0.42900	1.01;0.96;0.96	5.62	3.7	0.42460	.	0.574981	0.19713	N	0.107762	T	0.01156	0.0038	L	0.50333	1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.05484	-1.0882	10	0.30854	T	0.27	-1.8511	2.9627	0.05897	0.1123:0.3477:0.4049:0.1351	rs28930676;rs28930676	181;185	B4E2G9;Q9BVC5	.;ASHWN_HUMAN	D	185;181;143	ENSP00000258457:G185D;ENSP00000400208:G181D;ENSP00000386361:G143D	ENSP00000258457:G185D	G	+	2	0	C2orf49	105326024	0.010000	0.17322	0.005000	0.12908	0.908000	0.53690	1.075000	0.30716	1.272000	0.44329	0.650000	0.86243	GGC	G|0.949;A|0.051	0.051	strong		0.443	C2orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253353.2	NM_024093	
SGTA	6449	hgsc.bcm.edu	37	19	2762585	2762585	+	Silent	SNP	A	A	C	rs2302491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2762585A>C	ENST00000221566.2	-	7	716	c.555T>G	c.(553-555)gcT>gcG	p.A185A		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	185					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		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)		CCAGCTCCAGAGCCTTCTTGT	0.637													C|||	2394	0.478035	0.6513	0.2478	5008	,	,		16066	0.6647		0.2356	False		,,,				2504	0.4642				p.A185A		Atlas-SNP	.											.	SGTA	19	.	0			c.T555G						PASS	.	C		2421,1985	557.1+/-379.7	673,1075,455	135.0	128.0	131.0		555	0.8	0.4	19	dbSNP_100	131	1953,6647	724.8+/-406.5	226,1501,2573	no	coding-synonymous	SGTA	NM_003021.3		899,2576,3028	CC,CA,AA		22.7093,45.0522,33.6306		185/314	2762585	4374,8632	2203	4300	6503	SO:0001819	synonymous_variant	6449	exon7			CTCCAGAGCCTTC	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.555T>G	19.37:g.2762585A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	39	0.378641	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Silent	SNP	ENST00000221566.2	37	CCDS12094.1																																																																																			A|0.635;C|0.365	0.365	strong		0.637	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021	
ARRDC2	27106	hgsc.bcm.edu	37	19	18123738	18123738	+	Missense_Mutation	SNP	T	T	C	rs7259041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18123738T>C	ENST00000222250.4	+	8	1330	c.1187T>C	c.(1186-1188)cTc>cCc	p.L396P	ARRDC2_ENST00000379656.3_Missense_Mutation_p.L391P	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	396			L -> P (in dbSNP:rs7259041). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						CCAAACCCACTCTTGGGGGAC	0.532													C|||	1558	0.311102	0.4947	0.1772	5008	,	,		19326	0.2837		0.2545	False		,,,				2504	0.2444				p.L396P		Atlas-SNP	.											.	ARRDC2	60	.	0			c.T1187C						PASS	.	C	PRO/LEU,PRO/LEU	2000,2406	615.6+/-392.6	454,1092,657	63.0	58.0	60.0		1172,1187	2.9	0.4	19	dbSNP_116	60	1976,6624	723.4+/-406.5	245,1486,2569	yes	missense,missense	ARRDC2	NM_001025604.1,NM_015683.1	98,98	699,2578,3226	CC,CT,TT		22.9767,45.3926,30.5705	benign,benign	391/403,396/408	18123738	3976,9030	2203	4300	6503	SO:0001583	missense	27106	exon8			ACCCACTCTTGGG		CCDS12370.1, CCDS32956.1	19p13.12	2008-02-05				ENSG00000105643			25225	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015683		Approved	CLONE24945, PP2703	uc002nhv.3	Q8TBH0		ENST00000222250.4:c.1187T>C	19.37:g.18123738T>C	ENSP00000222250:p.Leu396Pro	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Missense_Mutation	SNP	ENST00000222250.4	37	CCDS12370.1	650	0.2976190476190476	236	0.4796747967479675	74	0.20441988950276244	140	0.24475524475524477	200	0.2638522427440633	C	0.003	-2.488262	0.00161	0.453926	0.229767	ENSG00000105643	ENST00000379656;ENST00000222250	T;T	0.16324	2.35;2.35	2.93	2.93	0.34026	.	0.125947	0.56097	N	0.000035	T	0.00012	0.0000	N	0.00182	-1.905	0.43808	P	0.0036399999999999766	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45425	-0.9262	9	0.06099	T	0.92	-20.7914	8.2902	0.31952	0.0:0.8828:0.0:0.1172	rs7259041;rs11558478;rs17856672;rs52816962;rs7259041	396;391	Q8TBH0;Q8TBH0-2	ARRD2_HUMAN;.	P	391;396	ENSP00000368977:L391P;ENSP00000222250:L396P	ENSP00000222250:L396P	L	+	2	0	ARRDC2	17984738	0.330000	0.24705	0.412000	0.26496	0.062000	0.15995	3.653000	0.54446	0.834000	0.34852	-0.320000	0.08662	CTC	T|0.697;C|0.303	0.303	strong		0.532	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045858	76045858	+	Silent	SNP	G	G	A	rs2287016	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	75	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	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	
CBX2	84733	hgsc.bcm.edu	37	17	77758691	77758691	+	Silent	SNP	G	G	A	rs3751957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:77758691G>A	ENST00000310942.4	+	5	1553	c.1449G>A	c.(1447-1449)ccG>ccA	p.P483P		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	483					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GACAGAACCCGTCAGTGTCCG	0.637													g|||	2119	0.423123	0.6694	0.3458	5008	,	,		16653	0.4058		0.2087	False		,,,				2504	0.3834				p.P483P		Atlas-SNP	.											CBX2,mucosal,malignant_melanoma,+2,1	CBX2	50	1	0			c.G1449A						PASS	.	A		2594,1812	634.6+/-396.2	771,1052,380	59.0	53.0	55.0		1449	-3.2	0.0	17	dbSNP_107	55	2071,6529	358.1+/-331.0	263,1545,2492	no	coding-synonymous	CBX2	NM_005189.2		1034,2597,2872	AA,AG,GG		24.0814,41.1257,35.8681		483/533	77758691	4665,8341	2203	4300	6503	SO:0001819	synonymous_variant	84733	exon5			GAACCCGTCAGTG	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.1449G>A	17.37:g.77758691G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			G|0.630;A|0.370	0.370	strong		0.637	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
SLC25A43	203427	hgsc.bcm.edu	37	X	118587003	118587003	+	Missense_Mutation	SNP	C	C	T	rs3810755	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:118587003C>T	ENST00000217909.7	+	5	1345	c.1001C>T	c.(1000-1002)cCg>cTg	p.P334L	SLC25A43_ENST00000488158.1_3'UTR|SLC25A43_ENST00000336249.7_3'UTR	NM_145305.2	NP_660348.2	Q8WUT9	S2543_HUMAN	solute carrier family 25, member 43	334			P -> L (in dbSNP:rs3810755). {ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	9						ACGAGAAAACCGAAGCCTAAA	0.408													T|||	2144	0.567947	0.4478	0.3919	3775	,	,		14788	0.4077		0.4334	False		,,,				2504	0.4427				p.P334L		Atlas-SNP	.											.	SLC25A43	29	.	0			c.C1001T						PASS	.	T	LEU/PRO	2295,1540		601,752,341,279,230	79.0	82.0	81.0		1001	5.2	0.3	X	dbSNP_107	81	3899,2828		822,1197,1058,409,813	yes	missense	SLC25A43	NM_145305.2	98	1423,1949,1399,688,1043	TT,TC,T,CC,C		42.0395,40.1565,41.3558	benign	334/342	118587003	6194,4368	2203	4299	6502	SO:0001583	missense	203427	exon5			GAAAACCGAAGCC	BC019584	CCDS14577.1	Xq24	2013-05-22			ENSG00000077713	ENSG00000077713		"""Solute carriers"""	30557	protein-coding gene	gene with protein product		300641				16949250	Standard	NM_145305		Approved		uc004erd.3	Q8WUT9	OTTHUMG00000022272	ENST00000217909.7:c.1001C>T	X.37:g.118587003C>T	ENSP00000217909:p.Pro334Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_145305	O75854|Q8N9L5	Missense_Mutation	SNP	ENST00000217909.7	37	CCDS14577.1	906	0.546112115732369	156	0.42857142857142855	97	0.35661764705882354	145	0.3419811320754717	222	0.40217391304347827	T	4.463	0.085769	0.08583	0.598435	0.579605	ENSG00000077713	ENST00000217909;ENST00000326714	T	0.76316	-1.01	5.24	5.24	0.73138	.	.	.	.	.	T	0.00012	0.0000	N	0.00436	-1.5	0.28831	P	0.897126	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	8	0.06757	T	0.87	0.016	9.5806	0.39486	0.0:0.0832:0.0:0.9168	rs3810755;rs17842216;rs17855482;rs52793991;rs56481507;rs56752420;rs3810755	334	Q8WUT9	S2543_HUMAN	L	334;282	ENSP00000217909:P334L	ENSP00000217909:P334L	P	+	2	0	SLC25A43	118471031	0.914000	0.31030	0.338000	0.25549	0.930000	0.56654	3.893000	0.56243	0.653000	0.30826	-0.314000	0.08810	CCG	0|0.015;T|0.551	0.551	strong		0.408	SLC25A43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058028.1	NM_145305	
AES	166	hgsc.bcm.edu	37	19	3062857	3062857	+	5'Flank	SNP	T	T	C	rs11539938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3062857T>C	ENST00000327141.4	-	0	0				AES_ENST00000592330.1_5'Flank|AES_ENST00000221561.8_Silent_p.L23L|AES_ENST00000586839.1_5'Flank	NM_001130.5|NM_198970.1	NP_001121.2|NP_945321.1	Q08117	AES_HUMAN	amino-terminal enhancer of split						multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of gene expression (GO:0010629)|negative regulation of protein binding (GO:0032091)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of anoikis (GO:2000210)|response to interleukin-1 (GO:0070555)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			lung(8)	8		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)		tgctgagccttagtttccttt	0.607													C|||	1930	0.385383	0.2103	0.438	5008	,	,		8565	0.5169		0.4026	False		,,,				2504	0.4315				p.L23L	Pancreas(11;265 407 11814 26840 35326)	Atlas-SNP	.											.	AES	14	.	0			c.A69G						PASS	.	C		608,2046		73,462,792	55.0	46.0	49.0		69	0.5	0.1	19	dbSNP_120	49	1943,2675		389,1165,755	no	coding-synonymous	AES	NM_198969.1		462,1627,1547	CC,CT,TT		42.0745,22.9088,35.0798		23/265	3062857	2551,4721	1327	2309	3636	SO:0001631	upstream_gene_variant	166	exon1			GAGCCTTAGTTTC	AK094591	CCDS12101.1, CCDS12102.1	19p13.3	2008-02-05							307	protein-coding gene	gene with protein product		600188				8365415	Standard	NM_001130		Approved	GRG5, TLE5	uc002lwx.1	Q08117			19.37:g.3062857T>C	Exception_encountered	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_198969	B2RBL0|Q12808|Q14CJ1|Q96TG9|Q9UDY9	Silent	SNP	ENST00000327141.4	37	CCDS12102.1																																																																																			T|0.607;C|0.393	0.393	strong		0.607	AES-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452154.1	NM_198969	
NEIL3	55247	hgsc.bcm.edu	37	4	178231152	178231152	+	Silent	SNP	C	C	A	rs10013040	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	89	0	0		WXS	Illumina HiSeq	Phase_I	107	65	0.607477	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	
FOXA3	3171	hgsc.bcm.edu	37	19	46375779	46375779	+	Silent	SNP	C	C	T	rs16980091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46375779C>T	ENST00000302177.2	+	2	713	c.516C>T	c.(514-516)aaC>aaT	p.N172N		NM_004497.2	NP_004488.2	P55318	FOXA3_HUMAN	forkhead box A3	172					cell differentiation (GO:0030154)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|chromatin modification (GO:0016568)|endocrine pancreas development (GO:0031018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	13		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)		TGTCTTTCAACGACTGCTTCG	0.562													C|||	1153	0.230232	0.3147	0.1138	5008	,	,		14151	0.369		0.1133	False		,,,				2504	0.1759				p.N172N		Atlas-SNP	.											.	FOXA3	19	.	0			c.C516T						PASS	.	C		1196,3210	417.8+/-338.1	158,880,1165	69.0	66.0	67.0		516	-0.0	1.0	19	dbSNP_123	67	860,7740	195.6+/-240.8	56,748,3496	no	coding-synonymous	FOXA3	NM_004497.2		214,1628,4661	TT,TC,CC		10.0,27.1448,15.8081		172/351	46375779	2056,10950	2203	4300	6503	SO:0001819	synonymous_variant	3171	exon2			TTTCAACGACTGC	L12141	CCDS12677.1	19q13.32	2014-09-11		2002-09-20	ENSG00000170608	ENSG00000170608		"""Forkhead boxes"""	5023	protein-coding gene	gene with protein product		602295	"""hepatocyte nuclear factor 3, gamma"""	HNF3G		9119385	Standard	NM_004497		Approved		uc002pdr.3	P55318	OTTHUMG00000182484	ENST00000302177.2:c.516C>T	19.37:g.46375779C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_004497	A9LYI5|Q53F16|Q9UMW9	Silent	SNP	ENST00000302177.2	37	CCDS12677.1																																																																																			C|0.807;T|0.193	0.193	strong		0.562	FOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461682.1		
TAF1	6872	hgsc.bcm.edu	37	X	70597546	70597546	+	Missense_Mutation	SNP	C	C	G	rs28382158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:70597546C>G	ENST00000373790.4	+	6	856	c.805C>G	c.(805-807)Ctg>Gtg	p.L269V	TAF1_ENST00000449580.1_Missense_Mutation_p.L269V|TAF1_ENST00000276072.3_Missense_Mutation_p.L290V|TAF1_ENST00000423759.1_Missense_Mutation_p.L290V	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	269	Protein kinase 1.		L -> V (in dbSNP:rs28382158). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|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)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GCACCGTGAGCTGATACAGGA	0.507													C|||	167	0.0442384	0.0015	0.196	3775	,	,		14839	0.0		0.005	False		,,,				2504	0.0245				p.L290V		Atlas-SNP	.											.	TAF1	439	.	0			c.C868G						PASS	.	C	VAL/LEU,VAL/LEU	10,3825		0,10,0,1622,571	156.0	117.0	130.0		868,805	5.3	1.0	X	dbSNP_125	130	67,6661		1,44,21,2383,1851	yes	missense,missense	TAF1	NM_004606.3,NM_138923.2	32,32	1,54,21,4005,2422	GG,GC,G,CC,C		0.9958,0.2608,0.729	benign,benign	290/1894,269/1873	70597546	77,10486	2203	4300	6503	SO:0001583	missense	6872	exon6			CGTGAGCTGATAC		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.805C>G	X.37:g.70597546C>G	ENSP00000362895:p.Leu269Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	63	0.0379746835443038	2	0.0040650406504065045	33	0.10576923076923077	0	0.0	3	0.00395778364116095	.	8.424	0.847002	0.17034	0.002608	0.009958	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.08458	3.1;3.15;3.15;3.09	5.35	5.35	0.76521	.	0.297103	0.32785	N	0.005657	T	0.00144	0.0004	N	0.25647	0.755	0.35219	P	0.22418800000000005	B;B	0.12013	0.001;0.005	B;B	0.15484	0.002;0.013	T	0.26916	-1.0089	9	0.29301	T	0.29	.	6.583	0.22605	0.1589:0.7012:0.0:0.1399	rs28382158	269;290	P21675;P21675-2	TAF1_HUMAN;.	V	269;269;290;290	ENSP00000362895:L269V;ENSP00000389000:L269V;ENSP00000406549:L290V;ENSP00000276072:L290V	ENSP00000276072:L290V	L	+	1	2	TAF1	70514271	0.998000	0.40836	0.991000	0.47740	0.922000	0.55478	1.887000	0.39698	2.377000	0.81083	0.468000	0.43344	CTG	C|0.961;0|0.018	.	strong		0.507	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
FAT1	2195	hgsc.bcm.edu	37	4	187542736	187542736	+	Silent	SNP	T	T	C	rs35753072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187542736T>C	ENST00000441802.2	-	10	5213	c.5004A>G	c.(5002-5004)acA>acG	p.T1668T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1668	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATTCTTTTGATGTAAACTTCG	0.398										HNSCC(5;0.00058)			T|||	342	0.0682907	0.003	0.1499	5008	,	,		19850	0.1796		0.0338	False		,,,				2504	0.0194				p.T1668T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A5004G						PASS	.	T		39,3709		0,39,1835	99.0	95.0	96.0		5004	-4.3	0.9	4	dbSNP_126	96	253,7975		4,245,3865	no	coding-synonymous	FAT1	NM_005245.3		4,284,5700	CC,CT,TT		3.0749,1.0406,2.4382		1668/4589	187542736	292,11684	1874	4114	5988	SO:0001819	synonymous_variant	2195	exon10			TTTTGATGTAAAC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5004A>G	4.37:g.187542736T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.926;C|0.074	0.074	strong		0.398	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
MUC16	94025	hgsc.bcm.edu	37	19	9065510	9065510	+	Silent	SNP	G	G	A	rs1867692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9065510G>A	ENST00000397910.4	-	3	22139	c.21936C>T	c.(21934-21936)ttC>ttT	p.F7312F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7314	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						GGGAAGTAGGGAACTTAATGA	0.453													N|||	906	0.180911	0.2458	0.1196	5008	,	,		22237	0.2679		0.0895	False		,,,				2504	0.1411				p.F7312F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C21936T						PASS	.	G		844,3010		94,656,1177	143.0	138.0	140.0		21936	-0.8	0.0	19	dbSNP_92	140	642,7584		27,588,3498	no	coding-synonymous	MUC16	NM_024690.2		121,1244,4675	AA,AG,GG		7.8045,21.8993,12.3013		7312/14508	9065510	1486,10594	1927	4113	6040	SO:0001819	synonymous_variant	94025	exon3			AGTAGGGAACTTA	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.21936C>T	19.37:g.9065510G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.825;A|0.175	0.175	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRT6C	286887	hgsc.bcm.edu	37	12	52863621	52863621	+	Silent	SNP	T	T	G	rs382367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52863621T>G	ENST00000252250.6	-	7	1304	c.1257A>C	c.(1255-1257)gcA>gcC	p.A419A		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	419	Coil 2.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		CATCCTTGAGTGCCATCTCCC	0.587													G|||	2434	0.486022	0.2617	0.611	5008	,	,		21154	0.6369		0.6074	False		,,,				2504	0.4202				p.A419A		Atlas-SNP	.											.	KRT6C	55	.	0			c.A1257C						PASS	.	G		1274,3132	684.6+/-404.4	196,882,1125	81.0	62.0	68.0		1257	-0.8	1.0	12	dbSNP_80	68	4944,3654	501.5+/-375.5	1473,1998,828	no	coding-synonymous	KRT6C	NM_173086.4		1669,2880,1953	GG,GT,TT		42.4983,28.9151,47.8161		419/565	52863621	6218,6786	2203	4299	6502	SO:0001819	synonymous_variant	286887	exon7			CTTGAGTGCCATC	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1257A>C	12.37:g.52863621T>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			T|0.451;G|0.549	0.549	strong		0.587	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605295	32605295	+	Silent	SNP	C	C	T	rs1129735	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32605295C>T	ENST00000343139.5	+	1	162	c.60C>T	c.(58-60)ccC>ccT	p.P20P	HLA-DQA1_ENST00000374949.2_Silent_p.P20P|HLA-DQA1_ENST00000395363.1_Silent_p.P20P	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	20					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGAGCCCCTGTGGAGGTG	0.512													.|||	1659	0.33127	0.2057	0.3963	5008	,	,		15856	0.4087		0.337	False		,,,				2504	0.3691				p.P20P		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C60T						PASS	.	T		980,3426		113,754,1336	76.0	68.0	71.0		60	-0.0	0.0	6	dbSNP_118	71	2968,5632		519,1930,1851	no	coding-synonymous	HLA-DQA1	NM_002122.3		632,2684,3187	TT,TC,CC		34.5116,22.2424,30.3552		20/256	32605295	3948,9058	2203	4300	6503	SO:0001819	synonymous_variant	3117	exon1			GAGCCCCTGTGGA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.60C>T	6.37:g.32605295C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	91	71	0.78022	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			C|0.693;T|0.307	0.307	strong		0.512	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
SLC25A6	293	hgsc.bcm.edu	37	X	1508324	1508324	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:1508324G>A	ENST00000381401.5	-	2	1122	c.408C>T	c.(406-408)ttC>ttT	p.F136F	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	136					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)	GGGTTCTGGCGAAATCCAGCG	0.652													g|||	1617	0.322883	0.4856	0.3256	5008	,	,		17263	0.1062		0.2724	False		,,,				2504	0.3763				p.F136F		Atlas-SNP	.											.	SLC25A6	27	.	0			c.C408T						PASS	.	G		1974,2432		461,1052,690	110.0	118.0	115.0		408	-1.4	0.4	X	dbSNP_134	115	2176,6416		278,1620,2398	no	coding-synonymous	SLC25A6	NM_001636.3		739,2672,3088	AA,AG,GG		25.3259,44.8025,31.928		136/299	1508324	4150,8848	2203	4296	6499	SO:0001819	synonymous_variant	293	exon2			TCTGGCGAAATCC	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.408C>T	X.37:g.1508324G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	98	29	0.295918	NM_001636	Q96C49	Silent	SNP	ENST00000381401.5	37	CCDS14114.1																																																																																			G|0.691;A|0.309	0.309	strong		0.652	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636	
HLA-B	3106	hgsc.bcm.edu	37	6	31324603	31324603	+	Missense_Mutation	SNP	C	C	T	rs9266178|rs200186034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31324603C>T	ENST00000412585.2	-	2	233	c.205G>A	c.(205-207)Gag>Aag	p.E69K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	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						CGCGGCTCCTCTCTCGGACTC	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2428	0.484824	0.4644	0.5058	5008	,	,		7573	0.4256		0.4354	False		,,,				2504	0.6094				p.E69K		Atlas-SNP	.											.	HLA-B	54	.	0			c.G205A						PASS	.						34.0	34.0	34.0					6																	31324603		2066	4050	6116	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GCTCCTCTCTCGG	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.205G>A	6.37:g.31324603C>T	ENSP00000399168:p.Glu69Lys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	367	0.16804029304029305	64	0.13008130081300814	56	0.15469613259668508	115	0.20104895104895104	132	0.1741424802110818	N	1.204	-0.631712	0.03584	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00009	9.48;9.48	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);	4.848800	0.01913	U	0.040001	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B;B;P	0.41673	0.0;0.0;0.759	B;B;P	0.50136	0.0;0.0;0.632	T	0.54662	-0.8260	9	0.02654	T	1	.	7.8979	0.29717	0.1052:0.3562:0.0:0.5386	rs9266178	69;69;44	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	K	69;80	ENSP00000399168:E69K;ENSP00000405931:E80K	ENSP00000399168:E69K	E	-	1	0	HLA-B	31432582	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.600000	0.00210	-3.012000	0.00272	-0.833000	0.03075	GAG	C|0.719;T|0.281	0.281	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SCUBE1	80274	hgsc.bcm.edu	37	22	43610106	43610106	+	Silent	SNP	C	C	T	rs34893532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43610106C>T	ENST00000360835.4	-	16	2169	c.2043G>A	c.(2041-2043)tcG>tcA	p.S681S	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	681					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CTCCACATTCCGACACGTTGC	0.652													C|||	341	0.0680911	0.1089	0.0865	5008	,	,		11075	0.0		0.1054	False		,,,				2504	0.0317				p.S681S		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G2043A						PASS	.			476,3930	213.1+/-232.8	26,424,1753	42.0	33.0	36.0		2043	-7.8	0.0	22	dbSNP_126	36	958,7642	200.2+/-244.0	67,824,3409	no	coding-synonymous	SCUBE1	NM_173050.3		93,1248,5162	TT,TC,CC		11.1395,10.8034,11.0257		681/989	43610106	1434,11572	2203	4300	6503	SO:0001819	synonymous_variant	80274	exon16			ACATTCCGACACG		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2043G>A	22.37:g.43610106C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																			C|0.901;T|0.099	0.099	strong		0.652	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
WDR90	197335	hgsc.bcm.edu	37	16	709001	709001	+	Missense_Mutation	SNP	C	C	A	rs4984906	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:709001C>A	ENST00000293879.4	+	24	3001	c.3001C>A	c.(3001-3003)Cct>Act	p.P1001T	WDR90_ENST00000549091.1_Missense_Mutation_p.P1001T|LA16c-349E10.1_ENST00000573609.1_RNA			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	88	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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	
DNAH5	1767	hgsc.bcm.edu	37	5	13902220	13902220	+	Missense_Mutation	SNP	T	T	C	rs1530498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13902220T>C	ENST00000265104.4	-	13	1776	c.1672A>G	c.(1672-1674)Aca>Gca	p.T558A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	558	Stem. {ECO:0000250}.		T -> A (in dbSNP:rs1530498).		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)					TTTGCAAATGTAACATCCATG	0.294									Kartagener syndrome				T|||	1945	0.388379	0.1483	0.4251	5008	,	,		16928	0.7579		0.3996	False		,,,				2504	0.2945				p.T558A		Atlas-SNP	.											.	DNAH5	868	.	0			c.A1672G						PASS	.	T	ALA/THR	831,3573	319.9+/-296.3	78,675,1449	50.0	44.0	46.0		1672	2.6	0.8	5	dbSNP_88	46	3481,5103	491.7+/-373.2	730,2021,1541	yes	missense	DNAH5	NM_001369.2	58	808,2696,2990	CC,CT,TT		40.5522,18.8692,33.1999	benign	558/4625	13902220	4312,8676	2202	4292	6494	SO:0001583	missense	1767	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAATGTAACATC	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.1672A>G	5.37:g.13902220T>C	ENSP00000265104:p.Thr558Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	996	0.45604395604395603	76	0.15447154471544716	161	0.4447513812154696	442	0.7727272727272727	317	0.4182058047493404	T	5.215	0.225193	0.09916	0.188692	0.405522	ENSG00000039139	ENST00000265104	T	0.52295	0.67	4.94	2.56	0.30785	Dynein heavy chain, domain-1 (1);	0.161948	0.53938	N	0.000059	T	0.00012	0.0000	L	0.58669	1.825	0.21604	P	0.999628715	B	0.09022	0.002	B	0.16722	0.016	T	0.44298	-0.9337	9	0.06365	T	0.9	.	8.8615	0.35261	0.0:0.1533:0.0:0.8467	rs1530498;rs17276273;rs52824180;rs61580738;rs1530498	558	Q8TE73	DYH5_HUMAN	A	558	ENSP00000265104:T558A	ENSP00000265104:T558A	T	-	1	0	DNAH5	13955220	0.989000	0.36119	0.822000	0.32727	0.988000	0.76386	1.739000	0.38217	0.338000	0.23692	0.533000	0.62120	ACA	T|0.601;C|0.399	0.399	strong		0.294	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
EP300	2033	hgsc.bcm.edu	37	22	41574383	41574383	+	Missense_Mutation	SNP	A	A	C	rs1046088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:41574383A>C	ENST00000263253.7	+	31	7887	c.6668A>C	c.(6667-6669)cAg>cCg	p.Q2223P	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2223	Interaction with NCOA2.		Q -> P (in dbSNP:rs1046088). {ECO:0000269|PubMed:7523245}.		apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|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 type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CCACCACAGCAGCAGCAGCGG	0.577			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	57	0.0113818	0.0015	0.0173	5008	,	,		21238	0.0		0.0388	False		,,,				2504	0.0041				p.Q2223P		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A6668C						PASS	.	A	PRO/GLN	25,4381	32.6+/-62.9	0,25,2178	60.0	60.0	60.0		6668	3.3	1.0	22	dbSNP_86	60	312,8288	111.4+/-171.7	5,302,3993	yes	missense	EP300	NM_001429.3	76	5,327,6171	CC,CA,AA		3.6279,0.5674,2.5911	benign	2223/2415	41574383	337,12669	2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	CACAGCAGCAGCA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6668A>C	22.37:g.41574383A>C	ENSP00000263253:p.Gln2223Pro	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	42	0.019230769230769232	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	33	0.04353562005277045	A	7.129	0.579572	0.13686	0.005674	0.036279	ENSG00000100393	ENST00000263253	D	0.84944	-1.92	5.5	3.27	0.37495	.	0.532986	0.15322	N	0.268513	T	0.45337	0.1337	N	0.22421	0.69	0.39836	D	0.973045	B	0.02656	0.0	B	0.01281	0.0	T	0.58561	-0.7615	10	0.27082	T	0.32	.	12.1846	0.54231	0.7172:0.2828:0.0:0.0	rs1046088;rs60456996;rs1046088	2223	Q09472	EP300_HUMAN	P	2223	ENSP00000263253:Q2223P	ENSP00000263253:Q2223P	Q	+	2	0	EP300	39904329	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.250000	0.58772	0.920000	0.36970	0.533000	0.62120	CAG	A|0.977;C|0.023	0.023	strong		0.577	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
AMOT	154796	hgsc.bcm.edu	37	X	112024157	112024157	+	Silent	SNP	G	G	T	rs2286063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:112024157G>T	ENST00000524145.1	-	10	2504	c.2430C>A	c.(2428-2430)atC>atA	p.I810I	AMOT_ENST00000371958.1_Silent_p.I578I|AMOT_ENST00000371959.3_Silent_p.I810I|AMOT_ENST00000304758.1_Silent_p.I401I|AMOT_ENST00000371962.1_Silent_p.I578I|MIR4329_ENST00000582643.1_RNA			Q4VCS5	AMOT_HUMAN	angiomotin	810					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						TTTCTTCCATGATGGGGGAGC	0.512													G|||	593	0.157086	0.1293	0.1513	3775	,	,		13133	0.1171		0.0378	False		,,,				2504	0.1646				p.I810I		Atlas-SNP	.											.	AMOT	204	.	0			c.C2430A						PASS	.	G	,	540,3295		28,395,89,1209,482	129.0	117.0	121.0		2430,1203	3.9	1.0	X	dbSNP_100	121	363,6365		8,255,92,2165,1780	no	coding-synonymous,coding-synonymous	AMOT	NM_001113490.1,NM_133265.2	,	36,650,181,3374,2262	TT,TG,T,GG,G		5.3954,14.0808,8.5487	,	810/1085,401/676	112024157	903,9660	2203	4300	6503	SO:0001819	synonymous_variant	154796	exon9			TTCCATGATGGGG	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.2430C>A	X.37:g.112024157G>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Silent	SNP	ENST00000524145.1	37	CCDS48154.1																																																																																			G|0.899;T|0.101	0.101	strong		0.512	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
LZTS3	9762	hgsc.bcm.edu	37	20	3147468	3147468	+	Silent	SNP	G	G	A	rs17853865	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:3147468G>A	ENST00000329152.3	-	1	1739	c.342C>T	c.(340-342)aaC>aaT	p.N114N	LZTS3_ENST00000360342.3_Silent_p.N114N|LZTS3_ENST00000337576.5_Silent_p.N114N			O60299	LZTS3_HUMAN		114						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											TGCCAACCACGTTGCCACAGA	0.647													G|||	700	0.139776	0.062	0.2003	5008	,	,		16794	0.0208		0.2256	False		,,,				2504	0.2362				p.N114N		Atlas-SNP	.											ProSAPiP1,NS,carcinoma,0,1	.	.	1	0			c.C342T						PASS	.	G		422,3984	209.2+/-230.0	21,380,1802	81.0	64.0	69.0		342	0.9	1.0	20	dbSNP_123	69	2030,6570	354.0+/-329.3	236,1558,2506	no	coding-synonymous	ProSAPiP1	NM_014731.2		257,1938,4308	AA,AG,GG		23.6047,9.5778,18.8528		114/674	3147468	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	0	exon1			AACCACGTTGCCA																												ENST00000329152.3:c.342C>T	20.37:g.3147468G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	Silent	SNP	ENST00000329152.3	37	CCDS13049.1																																																																																			G|0.830;A|0.170	0.170	strong		0.647	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
BPI	671	hgsc.bcm.edu	37	20	36940314	36940314	+	Missense_Mutation	SNP	C	C	T	rs5743509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36940314C>T	ENST00000262865.4	+	5	676	c.587C>T	c.(586-588)gCg>gTg	p.A196V	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	196			A -> V (in dbSNP:rs5743509).		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				ATTGAGTCTGCGCTTCGAAAC	0.507													C|||	257	0.0513179	0.0219	0.0346	5008	,	,		18767	0.0526		0.0447	False		,,,				2504	0.1084				p.A196V		Atlas-SNP	.											BPI,NS,carcinoma,-1,1	BPI	67	1	0			c.C587T						PASS	.	C	VAL/ALA	87,4319	72.5+/-110.5	0,87,2116	95.0	84.0	88.0		587	0.5	0.0	20	dbSNP_114	88	474,8126	139.0+/-195.8	9,456,3835	yes	missense	BPI	NM_001725.2	64	9,543,5951	TT,TC,CC		5.5116,1.9746,4.3134	possibly-damaging	196/488	36940314	561,12445	2203	4300	6503	SO:0001583	missense	671	exon5			AGTCTGCGCTTCG	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.587C>T	20.37:g.36940314C>T	ENSP00000262865:p.Ala196Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	102	0.046703296703296704	28	0.056910569105691054	14	0.03867403314917127	21	0.03671328671328671	39	0.051451187335092345	C	8.347	0.829967	0.16749	0.019746	0.055116	ENSG00000101425	ENST00000262865	T	0.05258	3.47	3.49	0.462	0.16695	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.401930	0.04517	N	0.383938	T	0.00608	0.0020	M	0.65975	2.015	0.09310	N	1	P	0.42692	0.787	B	0.21546	0.035	T	0.43032	-0.9416	10	0.30078	T	0.28	-0.4186	3.6591	0.08232	0.0:0.5552:0.2087:0.2362	rs5743509;rs17701056;rs52825707;rs57291884;rs5743509	196	P17213	BPI_HUMAN	V	196	ENSP00000262865:A196V	ENSP00000262865:A196V	A	+	2	0	BPI	36373728	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.297000	0.08276	0.138000	0.18790	0.505000	0.49811	GCG	C|0.953;T|0.047	0.047	strong		0.507	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
SEC23A	10484	hgsc.bcm.edu	37	14	39517925	39517925	+	Silent	SNP	T	T	C	rs11556216	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:39517925T>C	ENST00000307712.6	-	15	2185	c.1668A>G	c.(1666-1668)aaA>aaG	p.K556K	SEC23A_ENST00000536508.1_Silent_p.K430K|SEC23A_ENST00000545328.2_Silent_p.K527K|SEC23A_ENST00000537403.1_Silent_p.K354K	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	556					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ATTCTCCAAATTTCTGACACT	0.299													T|||	1241	0.247804	0.0673	0.281	5008	,	,		15501	0.3065		0.3509	False		,,,				2504	0.3016				p.K556K		Atlas-SNP	.											.	SEC23A	73	.	0			c.A1668G						PASS	.	T		506,3900	222.3+/-239.2	25,456,1722	55.0	62.0	60.0		1668	1.9	1.0	14	dbSNP_121	60	2946,5654	450.2+/-362.3	535,1876,1889	no	coding-synonymous	SEC23A	NM_006364.2		560,2332,3611	CC,CT,TT		34.2558,11.4843,26.5416		556/766	39517925	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	10484	exon15			TCCAAATTTCTGA	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"""Sec23 (S. cerevisiae) homolog A"""			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1668A>G	14.37:g.39517925T>C		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_006364	B2R5P4|B3KXI2|Q8NE16	Silent	SNP	ENST00000307712.6	37	CCDS9668.1																																																																																			T|0.741;C|0.259	0.259	strong		0.299	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2		
ITGA2	3673	hgsc.bcm.edu	37	5	52351876	52351876	+	Silent	SNP	A	A	G	rs3212523	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52351876A>G	ENST00000296585.5	+	9	1136	c.993A>G	c.(991-993)gcA>gcG	p.A331A		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	331	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)				AAATAAAAGCAATCGCTAGTA	0.353													A|||	490	0.0978435	0.1717	0.0605	5008	,	,		14554	0.0327		0.0895	False		,,,				2504	0.1002				p.A331A		Atlas-SNP	.											.	ITGA2	211	.	0			c.A993G						PASS	.	A		680,3722	264.4+/-266.0	50,580,1571	47.0	53.0	51.0		993	2.0	1.0	5	dbSNP_106	51	814,7780	185.7+/-233.4	37,740,3520	no	coding-synonymous	ITGA2	NM_002203.3		87,1320,5091	GG,GA,AA		9.4717,15.4475,11.4958		331/1182	52351876	1494,11502	2201	4297	6498	SO:0001819	synonymous_variant	3673	exon9			AAAAGCAATCGCT		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.993A>G	5.37:g.52351876A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			A|0.897;G|0.103	0.103	strong		0.353	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
C1orf123	54987	hgsc.bcm.edu	37	1	53681699	53681699	+	Silent	SNP	T	T	G	rs1134688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:53681699T>G	ENST00000294360.4	-	7	410	c.369A>C	c.(367-369)tcA>tcC	p.S123S	RP5-1024G6.2_ENST00000452466.1_RNA|C1orf123_ENST00000470385.1_5'UTR	NM_017887.1	NP_060357.1	Q9NWV4	CA123_HUMAN	chromosome 1 open reading frame 123	123						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|pancreas(2)|skin(1)	6						AGGCTGTCCCTGACTCCACAC	0.517													T|||	500	0.0998403	0.0227	0.1542	5008	,	,		19147	0.0813		0.2078	False		,,,				2504	0.0736				p.S123S		Atlas-SNP	.											.	C1orf123	9	.	0			c.A369C						PASS	.	T		240,4166	140.8+/-176.2	7,226,1970	142.0	131.0	135.0		369	-11.4	0.4	1	dbSNP_86	135	1933,6667	341.2+/-323.9	208,1517,2575	no	coding-synonymous	C1orf123	NM_017887.1		215,1743,4545	GG,GT,TT		22.4767,5.4471,16.7077		123/161	53681699	2173,10833	2203	4300	6503	SO:0001819	synonymous_variant	54987	exon7			TGTCCCTGACTCC	BC010908	CCDS576.1	1p32.3	2011-02-18			ENSG00000162384	ENSG00000162384			26059	protein-coding gene	gene with protein product						12477932	Standard	NM_017887		Approved	FLJ20580	uc001cvd.3	Q9NWV4	OTTHUMG00000008940	ENST00000294360.4:c.369A>C	1.37:g.53681699T>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_017887		Silent	SNP	ENST00000294360.4	37	CCDS576.1	280	0.1282051282051282	14	0.028455284552845527	68	0.1878453038674033	53	0.09265734265734266	145	0.19129287598944592	T	7.846	0.722953	0.15439	0.054471	0.224767	ENSG00000162384	ENST00000371480	.	.	.	5.7	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.28522	-1.0041	4	0.59425	D	0.04	-2.5814	7.3621	0.26752	0.0716:0.093:0.2523:0.5831	rs1134688;rs2297665;rs3196986;rs17369346	.	.	.	P	103	.	ENSP00000360535:Q103P	Q	-	2	0	C1orf123	53454287	0.000000	0.05858	0.433000	0.26760	0.044000	0.14063	-2.547000	0.00931	-2.135000	0.00811	-0.993000	0.02533	CAG	T|0.843;G|0.157	0.157	strong		0.517	C1orf123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024751.1	NM_017887	
AHCTF1	25909	hgsc.bcm.edu	37	1	247048834	247048834	+	Missense_Mutation	SNP	T	T	C	rs2642990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247048834T>C	ENST00000391829.2	-	21	2744	c.2621A>G	c.(2620-2622)aAc>aGc	p.N874S	AHCTF1_ENST00000326225.3_Missense_Mutation_p.N883S|AHCTF1_ENST00000366508.1_Missense_Mutation_p.N909S|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	874	Necessary for cytoplasmic localization. {ECO:0000250}.		N -> S (in dbSNP:rs2642990).		cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GATAACATCGTTACCACTGGA	0.368													C|||	3414	0.681709	0.9803	0.6311	5008	,	,		18418	0.622		0.5159	False		,,,				2504	0.546				p.N883S	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A2648G						PASS	.	C	SER/ASN	3934,472	207.5+/-228.8	1781,372,50	63.0	77.0	73.0		2648	-0.7	0.0	1	dbSNP_100	73	4262,4336	573.5+/-389.9	1080,2102,1117	yes	missense	AHCTF1	NM_015446.4	46	2861,2474,1167	CC,CT,TT		49.5697,10.7127,36.9732	benign	883/2276	247048834	8196,4808	2203	4299	6502	SO:0001583	missense	25909	exon21			ACATCGTTACCAC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.2621A>G	1.37:g.247048834T>C	ENSP00000375705:p.Asn874Ser	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	264	261	0.988636	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		1392	0.6373626373626373	452	0.9186991869918699	214	0.5911602209944752	349	0.6101398601398601	377	0.4973614775725594	C	0.233	-1.019547	0.02078	0.892873	0.495697	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.39997	1.05;1.05;1.05	5.01	-0.677	0.11357	.	0.677862	0.15449	N	0.261774	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	0.04013	0.001;0.001	T	0.32107	-0.9919	9	0.02654	T	1	-0.0791	7.2244	0.26007	0.0:0.5506:0.1071:0.3423	rs2642990;rs60462085;rs2642990	909;874	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	S	909;883;874	ENSP00000355464:N909S;ENSP00000355465:N883S;ENSP00000375705:N874S	ENSP00000355465:N883S	N	-	2	0	AHCTF1	245115457	0.009000	0.17119	0.002000	0.10522	0.713000	0.41058	0.390000	0.20768	-0.289000	0.09038	-0.213000	0.12676	AAC	T|0.364;C|0.636	0.636	strong		0.368	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8431131	8431131	+	Missense_Mutation	SNP	C	C	G	rs547981454		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8431131C>G	ENST00000301455.2	+	3	646	c.475C>G	c.(475-477)Cct>Gct	p.P159A	ANGPTL4_ENST00000393962.2_Missense_Mutation_p.P159A|ANGPTL4_ENST00000541807.1_5'UTR	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	159					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						GGTGGCCAAGCCTGCCCGAAG	0.652																																					p.P159A		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C475G						PASS	.						83.0	85.0	84.0					19																	8431131		2203	4300	6503	SO:0001583	missense	51129	exon3			GCCAAGCCTGCCC	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.475C>G	19.37:g.8431131C>G	ENSP00000301455:p.Pro159Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_001039667	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834379	0.16820	.	.	ENSG00000167772	ENST00000301455;ENST00000393962	T;T	0.54866	0.71;0.55	4.09	-1.04	0.10068	.	613.611000	0.00166	N	0.000000	T	0.28167	0.0695	N	0.08118	0	0.09310	N	0.999992	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.06463	-1.0825	10	0.25106	T	0.35	.	0.667	0.00852	0.1966:0.3829:0.1774:0.2431	.	159;159	A8MY84;Q9BY76	.;ANGL4_HUMAN	A	159	ENSP00000301455:P159A;ENSP00000377534:P159A	ENSP00000301455:P159A	P	+	1	0	ANGPTL4	8337131	0.001000	0.12720	0.004000	0.12327	0.796000	0.44982	-0.456000	0.06754	-0.190000	0.10465	0.655000	0.94253	CCT	.	.	none		0.652	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
GRB7	2886	hgsc.bcm.edu	37	17	37898909	37898909	+	Silent	SNP	A	A	C	rs36079893	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:37898909A>C	ENST00000309156.4	+	3	503	c.246A>C	c.(244-246)ccA>ccC	p.P82P	GRB7_ENST00000309185.3_Silent_p.P82P|GRB7_ENST00000445327.2_Silent_p.P105P|GRB7_ENST00000394211.3_Silent_p.P82P|GRB7_ENST00000578702.1_3'UTR|GRB7_ENST00000394204.1_Silent_p.P82P|GRB7_ENST00000394209.2_Silent_p.P82P	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	82					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CACAGAGCCCAATTCTCGGGG	0.652													C|||	606	0.121006	0.3026	0.072	5008	,	,		16347	0.006		0.0537	False		,,,				2504	0.0982				p.P105P		Atlas-SNP	.											.	GRB7	48	.	0			c.A315C						PASS	.	C	,,,	1127,3277		147,833,1222	53.0	62.0	59.0		246,315,246,246	5.3	1.0	17	dbSNP_126	59	474,8126		14,446,3840	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRB7	NM_001030002.2,NM_001242442.1,NM_001242443.1,NM_005310.3	,,,	161,1279,5062	CC,CA,AA		5.5116,25.5904,12.3116	,,,	82/533,105/556,82/533,82/533	37898909	1601,11403	2202	4300	6502	SO:0001819	synonymous_variant	2886	exon3			GAGCCCAATTCTC	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.246A>C	17.37:g.37898909A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001242442	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Silent	SNP	ENST00000309156.4	37	CCDS11345.1																																																																																			A|0.887;C|0.113	0.113	strong		0.652	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310	
SNX13	23161	hgsc.bcm.edu	37	7	17854532	17854532	+	Silent	SNP	G	G	T	rs2723501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:17854532G>T	ENST00000409389.1	-	20	2194	c.2022C>A	c.(2020-2022)ccC>ccA	p.P674P	SNX13_ENST00000428135.3_Silent_p.P663P|SNX13_ENST00000496855.1_5'UTR			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	674	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					GAGCTAAAGCGGGGGATGCCT	0.383													T|||	3494	0.697684	0.8661	0.5807	5008	,	,		12907	0.7192		0.5239	False		,,,				2504	0.7096				p.P663P		Atlas-SNP	.											.	SNX13	113	.	0			c.C1989A						PASS	.	T		2905,807		1147,611,98	82.0	73.0	76.0		1989	-4.5	1.0	7	dbSNP_100	76	4355,3819		1168,2019,900	no	coding-synonymous	SNX13	NM_015132.4		2315,2630,998	TT,TG,GG		46.7213,21.7403,38.9197		663/958	17854532	7260,4626	1856	4087	5943	SO:0001819	synonymous_variant	23161	exon20			TAAAGCGGGGGAT	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.2022C>A	7.37:g.17854532G>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000409389.1	37																																																																																				G|0.331;T|0.669	0.669	strong		0.383	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
ZNF454	285676	hgsc.bcm.edu	37	5	178391902	178391902	+	Missense_Mutation	SNP	A	A	C	rs12719860	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
GAPDH	2597	hgsc.bcm.edu	37	12	6646320	6646320	+	Silent	SNP	T	T	C	rs1065691	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:6646320T>C	ENST00000229239.5	+	6	1047	c.381T>C	c.(379-381)gaT>gaC	p.D127D	RP5-940J5.9_ENST00000602946.1_RNA|GAPDH_ENST00000396858.1_Silent_p.D85D|GAPDH_ENST00000396859.1_Silent_p.D127D|GAPDH_ENST00000396856.1_Silent_p.D52D|GAPDH_ENST00000396861.1_Silent_p.D127D	NM_002046.4	NP_002037.2	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase	127	Interaction with WARS.				carbohydrate metabolic process (GO:0005975)|cellular response to interferon-gamma (GO:0071346)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of translation (GO:0017148)|neuron apoptotic process (GO:0051402)|peptidyl-cysteine S-trans-nitrosylation (GO:0035606)|protein stabilization (GO:0050821)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GAIT complex (GO:0097452)|lipid particle (GO:0005811)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|identical protein binding (GO:0042802)|microtubule binding (GO:0008017)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|peptidyl-cysteine S-nitrosylase activity (GO:0035605)			central_nervous_system(1)|cervix(1)|endometrium(1)|lung(4)	7						CCTCTGCTGATGCCCCCATGT	0.567													C|||	2028	0.404952	0.5651	0.3112	5008	,	,		19477	0.5188		0.2217	False		,,,				2504	0.3262				p.D127D		Atlas-SNP	.											.	GAPDH	20	.	0			c.T381C						PASS	.	C		2078,2328	603.9+/-390.2	498,1082,623	46.0	48.0	47.0		381	1.3	1.0	12	dbSNP_86	47	1755,6845	735.2+/-406.9	182,1391,2727	no	coding-synonymous	GAPDH	NM_002046.3		680,2473,3350	CC,CT,TT		20.407,47.163,29.471		127/336	6646320	3833,9173	2203	4300	6503	SO:0001819	synonymous_variant	2597	exon6			TGCTGATGCCCCC	AF261085	CCDS8549.1, CCDS58201.1	12p13.31	2012-10-02		2005-05-06	ENSG00000111640	ENSG00000111640	1.2.1.12		4141	protein-coding gene	gene with protein product		138400		GAPD		3170585	Standard	NM_002046		Approved		uc001qop.2	P04406	OTTHUMG00000137379	ENST00000229239.5:c.381T>C	12.37:g.6646320T>C		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_002046	E7EUT4|P00354|Q53X65	Silent	SNP	ENST00000229239.5	37	CCDS8549.1																																																																																			T|0.687;C|0.313	0.313	strong		0.567	GAPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268059.1	NM_002046	
C15orf56	644809	hgsc.bcm.edu	37	15	40544617	40544617	+	Missense_Mutation	SNP	G	G	A	rs55863440	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40544617G>A	ENST00000319503.3	-	2	376	c.355C>T	c.(355-357)Cca>Tca	p.P119S	PAK6_ENST00000260404.4_Intron|C15orf56_ENST00000559727.1_3'UTR|PAK6_ENST00000441369.1_Intron|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000560346.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000453867.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	119			P -> S (in dbSNP:rs55863440).							lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CAAGCAGGTGGAGAGAAAGAG	0.736													G|||	791	0.157947	0.0499	0.1988	5008	,	,		11428	0.0873		0.3052	False		,,,				2504	0.1963				p.P119S		Atlas-SNP	.											.	C15orf56	3	.	0			c.C355T						PASS	.	G	,,,SER/PRO	417,3971		19,379,1796	17.0	21.0	20.0		,,,355	-3.0	0.0	15	dbSNP_129	20	2822,5768		478,1866,1951	yes	intron,intron,intron,missense	PAK6,C15orf56	NM_001128628.1,NM_001128629.1,NM_020168.4,NM_001039905.1	,,,74	497,2245,3747	AA,AG,GG		32.8522,9.5032,24.9576	,,,benign	,,,119/162	40544617	3239,9739	2194	4295	6489	SO:0001583	missense	644809	exon2			CAGGTGGAGAGAA		CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.355C>T	15.37:g.40544617G>A	ENSP00000315794:p.Pro119Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001039905		Missense_Mutation	SNP	ENST00000319503.3	37	CCDS32197.1	384	0.17582417582417584	30	0.06097560975609756	85	0.23480662983425415	40	0.06993006993006994	229	0.3021108179419525	G	12.42	1.932278	0.34096	0.095032	0.328522	ENSG00000176753	ENST00000319503	T	0.32272	1.46	4.2	-3.04	0.05412	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22414	0.069	B	0.21360	0.034	T	0.43669	-0.9377	8	0.87932	D	0	.	3.0052	0.06026	0.18:0.4429:0.2494:0.1276	rs55863440	119	Q8N910	CO056_HUMAN	S	119	ENSP00000315794:P119S	ENSP00000315794:P119S	P	-	1	0	C15orf56	38331909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.857000	0.04286	-0.735000	0.04837	-1.134000	0.01955	CCA	G|0.812;A|0.188	0.188	strong		0.736	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905	
WFIKKN1	117166	hgsc.bcm.edu	37	16	681280	681280	+	Silent	SNP	G	G	T	rs4984905	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:681280G>T	ENST00000319070.2	+	1	349	c.27G>T	c.(25-27)ccG>ccT	p.P9P		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	9					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CACTCCTGCCGCTCCTGCTCC	0.741													g|||	1569	0.313299	0.0825	0.3833	5008	,	,		10832	0.62		0.2485	False		,,,				2504	0.3262				p.P9P		Atlas-SNP	.											.	WFIKKN1	30	.	0			c.G27T						PASS	.			455,3849		22,411,1719	9.0	10.0	10.0		27	-3.1	0.0	16	dbSNP_111	10	1798,6714		183,1432,2641	no	coding-synonymous	WFIKKN1	NM_053284.2		205,1843,4360	TT,TG,GG		21.1231,10.5716,17.5796		9/549	681280	2253,10563	2152	4256	6408	SO:0001819	synonymous_variant	117166	exon1			CCTGCCGCTCCTG	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30912	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20A"""	608021	"""chromosome 16 open reading frame 12"""	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.27G>T	16.37:g.681280G>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			G|0.669;T|0.331	0.331	strong		0.741	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
NFATC2	4773	hgsc.bcm.edu	37	20	50092193	50092193	+	Missense_Mutation	SNP	T	T	C	rs12479626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50092193T>C	ENST00000396009.3	-	4	1556	c.1337A>G	c.(1336-1338)cAt>cGt	p.H446R	NFATC2_ENST00000610033.1_Missense_Mutation_p.H227R|NFATC2_ENST00000609507.1_Missense_Mutation_p.H227R|NFATC2_ENST00000414705.1_Missense_Mutation_p.H426R|NFATC2_ENST00000609943.1_Missense_Mutation_p.H426R|NFATC2_ENST00000371564.3_Missense_Mutation_p.H446R	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	446	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.		H -> R (in dbSNP:rs12479626).		B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	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 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)	p.H446R(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CATGTAGCCATGGAGCTGGTG	0.502													T|||	65	0.0129792	0.0023	0.0274	5008	,	,		17874	0.0387		0.0	False		,,,				2504	0.0041				p.H446R		Atlas-SNP	.											NFATC2,NS,carcinoma,0,1	NFATC2	112	1	1	Substitution - Missense(1)	stomach(1)	c.A1337G						scavenged	.	T	ARG/HIS,ARG/HIS,ARG/HIS	5,4401	8.1+/-20.4	0,5,2198	65.0	60.0	61.0		1277,1337,1337	5.4	1.0	20	dbSNP_120	61	8,8592	7.1+/-27.0	0,8,4292	yes	missense,missense,missense	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	29,29,29	0,13,6490	CC,CT,TT		0.093,0.1135,0.1	benign,benign,benign	426/902,446/922,446/926	50092193	13,12993	2203	4300	6503	SO:0001583	missense	4773	exon4			TAGCCATGGAGCT	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1337A>G	20.37:g.50092193T>C	ENSP00000379330:p.His446Arg	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	34	0.015567765567765568	3	0.006097560975609756	3	0.008287292817679558	28	0.04895104895104895	0	0.0	T	23.5	4.419816	0.83559	0.001135	9.3E-4	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.42900	0.96;0.96;0.96	5.44	5.44	0.79542	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.048788	0.85682	D	0.000000	T	0.04907	0.0132	N	0.08118	0	0.58432	D	0.999991	B;P;B;B	0.51351	0.114;0.944;0.068;0.068	B;P;B;B	0.44394	0.032;0.448;0.058;0.032	T	0.02691	-1.1123	10	0.29301	T	0.29	-19.6058	15.5154	0.75818	0.0:0.0:0.0:1.0	rs12479626;rs52802474;rs12479626	426;426;446;446	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	R	446;446;227;426	ENSP00000360619:H446R;ENSP00000379330:H446R;ENSP00000396471:H426R	ENSP00000360619:H446R	H	-	2	0	NFATC2	49525600	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	6.153000	0.71819	2.063000	0.61619	0.528000	0.53228	CAT	T|0.992;C|0.008	0.008	strong		0.502	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
DNAH6	1768	hgsc.bcm.edu	37	2	84848596	84848596	+	Missense_Mutation	SNP	G	G	A	rs61733547	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:84848596G>A	ENST00000237449.6	+	25	4000	c.3992G>A	c.(3991-3993)cGt>cAt	p.R1331H	DNAH6_ENST00000389394.3_Missense_Mutation_p.R1331H|DNAH6_ENST00000398278.2_Missense_Mutation_p.R1331H			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1331	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(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						ATGTGGTGCCGTGATTTGACT	0.343													G|||	90	0.0179712	0.0008	0.0288	5008	,	,		20917	0.0		0.0557	False		,,,				2504	0.0133				p.R1331H		Atlas-SNP	.											.	DNAH6	194	.	0			c.G3992A						PASS	.	G	HIS/ARG	15,1369		0,15,677	109.0	94.0	98.0		3992	4.1	1.0	2	dbSNP_129	98	181,3001		4,173,1414	yes	missense	DNAH6	NM_001370.1	29	4,188,2091	AA,AG,GG		5.6882,1.0838,4.2926	possibly-damaging	1331/4159	84848596	196,4370	692	1591	2283	SO:0001583	missense	1768	exon26			GGTGCCGTGATTT	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.3992G>A	2.37:g.84848596G>A	ENSP00000237449:p.Arg1331His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	58	0.026556776556776556	0	0.0	14	0.03867403314917127	0	0.0	44	0.05804749340369393	G	18.27	3.588064	0.66105	0.010838	0.056882	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.58797	0.31;0.31;0.31	5.02	4.13	0.48395	.	.	.	.	.	T	0.08802	0.0218	L	0.58354	1.805	0.29575	N	0.84958	P	0.41546	0.754	B	0.30179	0.112	T	0.27606	-1.0069	9	0.45353	T	0.12	.	11.769	0.51947	0.0878:0.0:0.9122:0.0	rs61733547	1331	Q9C0G6	DYH6_HUMAN	H	1331	ENSP00000374045:R1331H;ENSP00000381326:R1331H;ENSP00000237449:R1331H	ENSP00000237449:R1331H	R	+	2	0	DNAH6	84702107	1.000000	0.71417	0.956000	0.39512	0.867000	0.49689	4.676000	0.61627	2.326000	0.78906	0.563000	0.77884	CGT	G|0.971;A|0.029	0.029	strong		0.343	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
IGSF1	3547	hgsc.bcm.edu	37	X	130410965	130410965	+	Silent	SNP	A	A	G	rs4830219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:130410965A>G	ENST00000361420.3	-	14	2635	c.2556T>C	c.(2554-2556)taT>taC	p.Y852Y	IGSF1_ENST00000370903.3_Silent_p.Y857Y|IGSF1_ENST00000467244.1_5'UTR|IGSF1_ENST00000370910.1_Silent_p.Y843Y|IGSF1_ENST00000370904.1_Silent_p.Y843Y			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	852	Ig-like C2-type 8.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						TAGAAAAGTCATAATATCGGC	0.567													A|||	920	0.243709	0.3253	0.2406	3775	,	,		12325	0.002		0.2525	False		,,,				2504	0.0685				p.Y857Y		Atlas-SNP	.											.	IGSF1	231	.	0			c.T2571C						PASS	.	A	,,	1675,2160		318,787,252,527,319	153.0	154.0	154.0		2571,2529,2556	-2.5	1.0	X	dbSNP_111	154	2336,4392		295,1082,664,1051,1208	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF1	NM_001170961.1,NM_001170962.1,NM_001555.4	,,	613,1869,916,1578,1527	GG,GA,G,AA,A		34.7206,43.6767,37.9722	,,	857/1342,843/1328,852/1337	130410965	4011,6552	2203	4300	6503	SO:0001819	synonymous_variant	3547	exon14			AAAGTCATAATAT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.2556T>C	X.37:g.130410965A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001170961	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	37	CCDS14629.1																																																																																			A|0.663;0|0.005	.	strong		0.567	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
PRICKLE1	144165	hgsc.bcm.edu	37	12	42854208	42854208	+	Silent	SNP	A	A	G	rs3747563|rs111643910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:42854208A>G	ENST00000455697.1	-	8	2184	c.1899T>C	c.(1897-1899)ttT>ttC	p.F633F	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Silent_p.F633F|PRICKLE1_ENST00000552240.1_Silent_p.F633F|PRICKLE1_ENST00000445766.2_Silent_p.F633F|PRICKLE1_ENST00000548696.1_Silent_p.F633F	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	633					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CATCATCAGAAAACTTGACCT	0.488													A|||	1355	0.270567	0.1634	0.3847	5008	,	,		18152	0.256		0.3678	False		,,,				2504	0.2495				p.F633F		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.T1899C						PASS	.	A	,,,	887,3519		115,657,1431	99.0	94.0	96.0		1899,1899,1899,1899	-4.5	0.5	12	dbSNP_107	96	3013,5587		588,1837,1875	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	703,2494,3306	GG,GA,AA		35.0349,20.1316,29.9862	,,,	633/832,633/832,633/832,633/832	42854208	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon8			ATCAGAAAACTTG	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1899T>C	12.37:g.42854208A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			A|0.686;G|0.314	0.314	strong		0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
CDC5L	988	hgsc.bcm.edu	37	6	44371714	44371714	+	Silent	SNP	C	C	T	rs6934058	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44371714C>T	ENST00000371477.3	+	6	1007	c.708C>T	c.(706-708)gaC>gaT	p.D236D		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	236	Nuclear localization signal. {ECO:0000255}.				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)			AAGCTCTTGACGCAGATTTCA	0.398													c|||	1485	0.296526	0.2201	0.1571	5008	,	,		14421	0.6111		0.0934	False		,,,				2504	0.3834				p.D236D		Atlas-SNP	.											.	CDC5L	86	.	0			c.C708T						PASS	.	T		932,3474	350.8+/-311.0	89,754,1360	67.0	70.0	69.0		708	1.0	1.0	6	dbSNP_116	69	745,7855	179.0+/-228.3	31,683,3586	no	coding-synonymous	CDC5L	NM_001253.2		120,1437,4946	TT,TC,CC		8.6628,21.153,12.894		236/803	44371714	1677,11329	2203	4300	6503	SO:0001819	synonymous_variant	988	exon6			TCTTGACGCAGAT	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.708C>T	6.37:g.44371714C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_001253	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			C|0.795;T|0.205	0.205	strong		0.398	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
KIF26A	26153	hgsc.bcm.edu	37	14	104633227	104633227	+	Silent	SNP	A	A	C	rs76304797	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104633227A>C	ENST00000423312.2	+	5	955	c.955A>C	c.(955-957)Agg>Cgg	p.R319R	KIF26A_ENST00000315264.7_Silent_p.R180R	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	319					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)		GGCCTCCAAGAGGAAGAAGCC	0.697													c|||	114	0.0227636	0.0023	0.036	5008	,	,		13321	0.0		0.0586	False		,,,				2504	0.0276				p.R319R		Atlas-SNP	.											.	KIF26A	84	.	0			c.A955C						PASS	.			43,3959		0,43,1958	7.0	11.0	10.0		955	3.1	1.0	14	dbSNP_132	10	503,7777		18,467,3655	no	coding-synonymous	KIF26A	NM_015656.1		18,510,5613	CC,CA,AA		6.0749,1.0745,4.4455		319/1883	104633227	546,11736	2001	4140	6141	SO:0001819	synonymous_variant	26153	exon5			TCCAAGAGGAAGA	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.955A>C	14.37:g.104633227A>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			A|0.973;C|0.027	0.027	strong		0.697	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
KIAA1467	57613	hgsc.bcm.edu	37	12	13208552	13208552	+	Silent	SNP	C	C	T	rs4763924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:13208552C>T	ENST00000197268.8	+	2	225	c.105C>T	c.(103-105)gaC>gaT	p.D35D		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	35						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		AGAGCGAAGACGATCTGGTGC	0.512													C|||	1642	0.327875	0.3903	0.2752	5008	,	,		20666	0.4901		0.17	False		,,,				2504	0.2761				p.D35D		Atlas-SNP	.											.	KIAA1467	78	.	0			c.C105T						PASS	.	C		1557,2849	490.8+/-361.9	270,1017,916	80.0	80.0	80.0		105	-2.3	0.9	12	dbSNP_111	80	1223,7377	247.2+/-275.4	106,1011,3183	no	coding-synonymous	KIAA1467	NM_020853.1		376,2028,4099	TT,TC,CC		14.2209,35.3382,21.3748		35/623	13208552	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	57613	exon2			CGAAGACGATCTG	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.105C>T	12.37:g.13208552C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_020853	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Silent	SNP	ENST00000197268.8	37	CCDS31750.1																																																																																			C|0.738;T|0.262	0.262	strong		0.512	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853	
AHRR	57491	hgsc.bcm.edu	37	5	434546	434546	+	Missense_Mutation	SNP	C	C	T	rs61757546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:434546C>T	ENST00000505113.1	+	11	1747	c.1703C>T	c.(1702-1704)gCc>gTc	p.A568V	AHRR_ENST00000512529.1_Missense_Mutation_p.A414V|AHRR_ENST00000506456.1_Missense_Mutation_p.A424V|AHRR_ENST00000316418.5_Missense_Mutation_p.A586V	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	568	Needed for transcriptional repression. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			AGCCACCCAGCCACCTTCCCT	0.637													C|||	16	0.00319489	0.0	0.0029	5008	,	,		16396	0.0		0.0129	False		,,,				2504	0.001				p.A586V		Atlas-SNP	.											.	AHRR	67	.	0			c.C1757T						PASS	.	C	VAL/ALA,VAL/ALA	2,4254		0,2,2126	51.0	58.0	56.0		1703,1757	-2.3	0.0	5	dbSNP_129	56	40,8438		0,40,4199	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	64,64	0,42,6325	TT,TC,CC		0.4718,0.047,0.3298	benign,benign	568/702,586/720	434546	42,12692	2128	4239	6367	SO:0001583	missense	57491	exon12			ACCCAGCCACCTT	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1703C>T	5.37:g.434546C>T	ENSP00000424601:p.Ala568Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	0.008	-1.892504	0.00522	4.7E-4	0.004718	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.20069	2.44;2.43;2.11;2.1	4.43	-2.29	0.06805	.	0.629100	0.15903	N	0.238965	T	0.03095	0.0091	N	0.01168	-0.975	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	0.39860	-0.9593	10	0.09590	T	0.72	.	5.5855	0.17272	0.1478:0.4627:0.0:0.3895	rs61757546	424;568;586	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	V	568;586;414;424	ENSP00000424601:A568V;ENSP00000323816:A586V;ENSP00000424880:A414V;ENSP00000426932:A424V	ENSP00000323816:A586V	A	+	2	0	AHRR	487546	0.000000	0.05858	0.000000	0.03702	0.179000	0.23085	0.002000	0.13061	-0.364000	0.08088	-0.263000	0.10527	GCC	C|0.996;T|0.004	0.004	strong		0.637	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
HFE	3077	hgsc.bcm.edu	37	6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	rs1800562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000352392.4_Intron|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000461397.1_Missense_Mutation_p.C268Y	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	152	0	0		WXS	Illumina HiSeq	Phase_I	138	77	0.557971	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		
MUC16	94025	hgsc.bcm.edu	37	19	9005674	9005674	+	Silent	SNP	G	G	A	rs4804091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9005674G>A	ENST00000397910.4	-	46	39935	c.39732C>T	c.(39730-39732)gaC>gaT	p.D13244D	MUC16_ENST00000380951.5_5'Flank	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13246	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						GGATTTTGGGGTCAGGGCGGT	0.582													N|||	1104	0.220447	0.1528	0.2939	5008	,	,		18886	0.2212		0.2793	False		,,,				2504	0.1984				p.D13244D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C39732T						PASS	.	A		796,3300		77,642,1329	98.0	93.0	95.0		39732	-0.4	0.0	19	dbSNP_111	95	2503,5855		346,1811,2022	no	coding-synonymous	MUC16	NM_024690.2		423,2453,3351	AA,AG,GG		29.9474,19.4336,26.4895		13244/14508	9005674	3299,9155	2048	4179	6227	SO:0001819	synonymous_variant	94025	exon46			TTTGGGGTCAGGG	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.39732C>T	19.37:g.9005674G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	121	118	0.975207	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	506	0.2316849816849817	62	0.12601626016260162	102	0.281767955801105	141	0.2465034965034965	201	0.26517150395778366	.	2.958	-0.215194	0.06101	0.194336	0.299474	ENSG00000181143	ENST00000542240	.	.	.	3.31	-0.436	0.12275	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.38499	-0.9658	3	.	.	.	-15.3585	3.311	0.07016	0.2474:0.0:0.5502:0.2024	rs4804091	.	.	.	I	84	.	.	T	-	2	0	MUC16	8866674	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.480000	0.06559	-0.105000	0.12132	-0.372000	0.07161	ACC	G|0.754;A|0.246	0.246	strong		0.582	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRRK2	120892	hgsc.bcm.edu	37	12	40757330	40757330	+	Silent	SNP	A	A	G	rs33962975	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:40757330A>G	ENST00000298910.7	+	48	7213	c.7155A>G	c.(7153-7155)ggA>ggG	p.G2385G		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2385			G -> R (associated with Parkinson disease; under conditions of oxidative stress the variant protein is more toxic and is associated with a higher rate of apoptosis; dbSNP:rs34778348). {ECO:0000269|PubMed:16172858}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AACTCTGTGGACTAATAGACT	0.373													A|||	280	0.0559105	0.0257	0.0908	5008	,	,		15127	0.0139		0.1491	False		,,,				2504	0.0194				p.G2385G		Atlas-SNP	.											LRRK2_ENST00000298910,NS,carcinoma,+2,2	LRRK2	763	2	0			c.A7155G						scavenged	.	A		199,4207	123.3+/-160.7	0,199,2004	116.0	118.0	117.0		7155	2.9	0.6	12	dbSNP_126	117	1184,7416	239.7+/-270.7	74,1036,3190	no	coding-synonymous	LRRK2	NM_198578.3		74,1235,5194	GG,GA,AA		13.7674,4.5166,10.6336		2385/2528	40757330	1383,11623	2203	4300	6503	SO:0001819	synonymous_variant	120892	exon48			CTGTGGACTAATA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.7155A>G	12.37:g.40757330A>G		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			A|0.901;G|0.099	0.099	strong		0.373	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
HELQ	113510	hgsc.bcm.edu	37	4	84370091	84370091	+	Silent	SNP	A	A	G	rs13141136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:84370091A>G	ENST00000295488.3	-	3	1198	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	HELQ_ENST00000510985.1_Silent_p.L346L	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	346	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ACAGAATTCAATGTTAAACAA	0.318								Other identified genes with known or suspected DNA repair function					A|||	2076	0.414537	0.1059	0.5245	5008	,	,		16998	0.6766		0.3787	False		,,,				2504	0.5204				p.L346L		Atlas-SNP	.											.	HELQ	95	.	0			c.T1036C						PASS	.	A		687,3715	266.2+/-267.1	54,579,1568	37.0	37.0	37.0		1036	-6.4	0.3	4	dbSNP_121	37	3504,5090	492.3+/-373.3	712,2080,1505	no	coding-synonymous	HELQ	NM_133636.2		766,2659,3073	GG,GA,AA		40.7726,15.6065,32.2484		346/1102	84370091	4191,8805	2201	4297	6498	SO:0001819	synonymous_variant	113510	exon3			AATTCAATGTTAA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1036T>C	4.37:g.84370091A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.654;G|0.346	0.346	strong		0.318	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42135988	42135988	+	Silent	SNP	C	C	T	rs1672466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42135988C>T	ENST00000452633.1	+	12	1210	c.858C>T	c.(856-858)gaC>gaT	p.D286D	JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.D517D|JMJD7-PLA2G4B_ENST00000342159.4_Silent_p.D517D|PLA2G4B_ENST00000542534.2_Silent_p.D517D|PLA2G4B_ENST00000458483.1_Silent_p.D286D			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	286	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		TGCAGCTGGACGGAGACCTGC	0.672													c|||	3783	0.755391	0.5756	0.8228	5008	,	,		17543	0.879		0.8171	False		,,,				2504	0.7597				p.D517D		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.C1551T						PASS	.	C	,,	2751,1655		858,1035,310	38.0	40.0	39.0		858,1551,1551	-2.6	0.0	15	dbSNP_89	39	6982,1618		2839,1304,157	no	coding-synonymous,coding-synonymous,coding-synonymous	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	,,	3697,2339,467	TT,TC,CC		18.814,37.5624,25.1653	,,	286/782,517/894,517/1013	42135988	9733,3273	2203	4300	6503	SO:0001819	synonymous_variant	8681	exon16			GCTGGACGGAGAC	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.858C>T	15.37:g.42135988C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Silent	SNP	ENST00000452633.1	37	CCDS45241.1																																																																																			C|0.245;T|0.755	0.755	strong		0.672	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
NYNRIN	57523	hgsc.bcm.edu	37	14	24883887	24883887	+	Missense_Mutation	SNP	G	G	A	rs8017377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24883887G>A	ENST00000382554.3	+	9	3250	c.2932G>A	c.(2932-2934)Gct>Act	p.A978T	NYNRIN_ENST00000554505.1_3'UTR	NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	978			A -> T (in dbSNP:rs8017377).		DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GAGTGATGACGCTGACTCTGG	0.557													G|||	1224	0.244409	0.1218	0.255	5008	,	,		20580	0.0496		0.4811	False		,,,				2504	0.3599				p.A978T		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G2932A						PASS	.	G	THR/ALA	691,3709	274.6+/-272.0	68,555,1577	52.0	58.0	56.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2932	-9.1	0.0	14	dbSNP_116	56	3981,4583	539.9+/-383.7	948,2085,1249	yes	missense	NYNRIN	NM_025081.2	58	1016,2640,2826	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.4853,15.7045,36.0383	benign	978/1899	24883887	4672,8292	2200	4282	6482	SO:0001583	missense	57523	exon9			GATGACGCTGACT	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.2932G>A	14.37:g.24883887G>A	ENSP00000371994:p.Ala978Thr	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	536	0.2454212454212454	60	0.12195121951219512	97	0.26795580110497236	31	0.05419580419580419	348	0.45910290237467016	G	10.03	1.239423	0.22711	0.157045	0.464853	ENSG00000205978	ENST00000382554	T	0.11169	2.8	4.54	-9.08	0.00720	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.47699	-0.9097	8	0.32370	T	0.25	.	0.3875	0.00405	0.375:0.1851:0.1579:0.2819	rs8017377;rs17795076;rs58497689;rs8017377	978	Q9P2P1	NYNRI_HUMAN	T	978	ENSP00000371994:A978T	ENSP00000371994:A978T	A	+	1	0	NYNRIN	23953727	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.409000	0.07160	-1.685000	0.01441	-1.824000	0.00597	GCT	G|0.753;A|0.247	0.247	strong		0.557	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
APC	324	hgsc.bcm.edu	37	5	112164561	112164561	+	Silent	SNP	G	G	A	rs351771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112164561G>A	ENST00000457016.1	+	14	2015	c.1635G>A	c.(1633-1635)gcG>gcA	p.A545A	APC_ENST00000508376.2_Silent_p.A545A|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.R41Q|APC_ENST00000257430.4_Silent_p.A545A			P25054	APC_HUMAN	adenomatous polyposis coli	545	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGGTTATTGCGAGTGTTTTGA	0.313		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	3336	0.666134	0.5166	0.7161	5008	,	,		17820	0.8165		0.5994	False		,,,				2504	0.7464				p.A545A	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G1635A						PASS	.	A	,,	2321,2083	570.8+/-382.9	619,1083,500	101.0	105.0	104.0	http://omim.org/entry/114500	1635,1635,1581	4.5	1.0	5	dbSNP_79	104	5305,3295	491.5+/-373.1	1671,1963,666	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2290,3046,1166	AA,AG,GG		38.314,47.2979,41.3565	,,	545/2844,545/2844,527/2826	112164561	7626,5378	2202	4300	6502	SO:0001819	synonymous_variant	324	exon15	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TATTGCGAGTGTT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1635G>A	5.37:g.112164561G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.388;A|0.612	0.612	strong		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
HLA-A	3105	hgsc.bcm.edu	37	6	29911306	29911306	+	Missense_Mutation	SNP	C	C	T	rs9391665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29911306C>T	ENST00000396634.1	+	5	946	c.605C>T	c.(604-606)aCg>aTg	p.T202M	HLA-A_ENST00000376806.5_Missense_Mutation_p.T202M|HLA-A_ENST00000376809.5_Missense_Mutation_p.T202M|HLA-A_ENST00000376802.2_Missense_Mutation_p.T202M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	202	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)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGGAAGGAGACGCTGCAGCGC	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.T202M		Atlas-SNP	.											HLA-A,NS,adenoma,0,2	HLA-A	89	2	0			c.C605T						scavenged	.						48.0	42.0	44.0					6																	29911306		1509	2706	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGAGACGCTGCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.605C>T	6.37:g.29911306C>T	ENSP00000379873:p.Thr202Met	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	122	22	0.180328	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	308	0.14102564102564102	84	0.17073170731707318	56	0.15469613259668508	56	0.0979020979020979	112	0.14775725593667546	.	3.947	-0.013107	0.07727	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00848	5.62;5.62;5.62;5.62	3.54	1.66	0.24008	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	1.297700	0.06193	U	0.681759	T	0.01976	0.0062	M	0.83953	2.67	0.80722	P	0.0	D;B;D;B;D;B;B	0.89917	0.998;0.013;1.0;0.025;1.0;0.008;0.025	D;B;D;B;D;B;B	0.91635	0.99;0.025;0.999;0.053;0.999;0.014;0.053	T	0.43147	-0.9409	9	0.87932	D	0	.	3.0431	0.06145	0.2126:0.5463:0.0:0.2411	rs9391665	81;202;202;202;202;202;202	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	M	202	ENSP00000379873:T202M;ENSP00000366002:T202M;ENSP00000366005:T202M;ENSP00000365998:T202M	ENSP00000365998:T202M	T	+	2	0	HLA-A	30019285	0.000000	0.05858	0.241000	0.24154	0.380000	0.30137	-2.455000	0.01003	0.798000	0.33994	0.485000	0.47835	ACG	C|0.855;T|0.145	0.145	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
NUDT12	83594	hgsc.bcm.edu	37	5	102894673	102894673	+	Missense_Mutation	SNP	T	T	C	rs34468716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:102894673T>C	ENST00000230792.2	-	3	799	c.703A>G	c.(703-705)Att>Gtt	p.I235V	NUDT12_ENST00000507423.1_Missense_Mutation_p.I217V|NUDT12_ENST00000515407.1_5'Flank	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	235			I -> V (in dbSNP:rs34468716).		NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TCAGCAGCAATAGGATCTATA	0.393													T|||	238	0.047524	0.0598	0.0476	5008	,	,		18404	0.0		0.1093	False		,,,				2504	0.0164				p.I235V		Atlas-SNP	.											.	NUDT12	27	.	0			c.A703G						PASS	.	T	VAL/ILE	328,4076	174.1+/-203.8	18,292,1892	80.0	80.0	80.0		703	-2.0	0.0	5	dbSNP_126	80	916,7684	203.7+/-246.6	51,814,3435	yes	missense	NUDT12	NM_031438.2	29	69,1106,5327	CC,CT,TT		10.6512,7.4478,9.5663	benign	235/463	102894673	1244,11760	2202	4300	6502	SO:0001583	missense	83594	exon3			CAGCAATAGGATC	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.703A>G	5.37:g.102894673T>C	ENSP00000230792:p.Ile235Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_031438	B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	37	CCDS4096.1	119	0.05448717948717949	29	0.05894308943089431	15	0.04143646408839779	0	0.0	75	0.09894459102902374	T	2.171	-0.389925	0.04932	0.074478	0.106512	ENSG00000112874	ENST00000230792;ENST00000507423	T;T	0.28895	1.59;1.59	5.55	-1.98	0.07480	NADH pyrophosphatase-like, N-terminal (1);	0.763219	0.13347	N	0.394714	T	0.00271	0.0008	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.19095	-1.0316	9	0.24483	T	0.36	0.2325	15.6774	0.77338	0.0:0.6833:0.0:0.3167	rs34468716	217;235	E7EM93;Q9BQG2	.;NUD12_HUMAN	V	235;217	ENSP00000230792:I235V;ENSP00000424521:I217V	ENSP00000230792:I235V	I	-	1	0	NUDT12	102922572	0.000000	0.05858	0.007000	0.13788	0.989000	0.77384	0.211000	0.17474	-0.249000	0.09569	0.528000	0.53228	ATT	T|0.915;C|0.085	0.085	strong		0.393	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	
OR2T8	343172	hgsc.bcm.edu	37	1	248084440	248084440	+	Missense_Mutation	SNP	T	T	G	rs111379878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:248084440T>G	ENST00000319968.4	+	1	121	c.121T>G	c.(121-123)Tcc>Gcc	p.S41A		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S41A(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GTTTGGCAATTCCCTCATGAT	0.502													T|||	184	0.0367412	0.059	0.0274	5008	,	,		14500	0.0109		0.0249	False		,,,				2504	0.0521				p.S41A		Atlas-SNP	.											OR2T8,NS,other,0,1	OR2T8	67	1	1	Substitution - Missense(1)	pancreas(1)	c.T121G						scavenged	.						63.0	57.0	59.0					1																	248084440		2202	4280	6482	SO:0001583	missense	343172	exon1			GGCAATTCCCTCA		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.121T>G	1.37:g.248084440T>G	ENSP00000326225:p.Ser41Ala	Somatic	414	5	0.0120773		WXS	Illumina HiSeq	Phase_I	402	5	0.0124378	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	29	0.013278388278388278	20	0.04065040650406504	5	0.013812154696132596	0	0.0	4	0.005277044854881266	N	3.205	-0.162862	0.06502	.	.	ENSG00000177462	ENST00000319968	T	0.00012	9.33	3.65	-0.565	0.11771	GPCR, rhodopsin-like superfamily (1);	0.792834	0.10272	N	0.694616	T	0.00012	0.0000	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13953	-1.0490	10	0.06891	T	0.86	.	0.9955	0.01465	0.2883:0.2491:0.3226:0.14	.	41	A6NH00	OR2T8_HUMAN	A	41	ENSP00000326225:S41A	ENSP00000326225:S41A	S	+	1	0	OR2T8	246151063	0.000000	0.05858	0.060000	0.19600	0.299000	0.27559	-3.158000	0.00579	-0.030000	0.13804	-0.186000	0.12905	TCC	T|0.988;G|0.012	0.012	strong		0.502	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
SCN7A	6332	hgsc.bcm.edu	37	2	167262169	167262169	+	Missense_Mutation	SNP	T	T	C	rs35344714	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	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		
BAGE2	85319	hgsc.bcm.edu	37	21	11049596	11049596	+	RNA	SNP	C	C	T	rs28571918	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11049596C>T	ENST00000470054.1	-	0	512							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								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)		GGCTGTCGCACACTGCACAGT	0.373																																					p.C102Y		Atlas-SNP	.											.	.	.	.	0			c.G305A						PASS	.						86.0	66.0	72.0					21																	11049596		692	1591	2283			85318	exon4			GTCGCACACTGCA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049596C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	327	41	0.125382	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				C|0.571;T|0.429	0.429	strong		0.373	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
MASP1	5648	hgsc.bcm.edu	37	3	186954324	186954324	+	Intron	SNP	G	G	A	rs3774268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186954324G>A	ENST00000337774.5	-	10	1693				MASP1_ENST00000392472.2_Silent_p.S332S|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000296280.6_Silent_p.S445S	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)						complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TCTTGACCAGGCTTGGCAGGG	0.587													G|||	760	0.151757	0.202	0.1311	5008	,	,		19267	0.1319		0.1531	False		,,,				2504	0.1176				p.S445S		Atlas-SNP	.											.	MASP1	240	.	0			c.C1335T						PASS	.	G	,	835,3571	327.2+/-299.9	77,681,1445	90.0	92.0	91.0		,1335	5.2	1.0	3	dbSNP_107	91	1177,7423	236.8+/-268.9	85,1007,3208	no	intron,coding-synonymous	MASP1	NM_001879.5,NM_139125.3	,	162,1688,4653	AA,AG,GG		13.686,18.9514,15.4698	,	,445/729	186954324	2012,10994	2203	4300	6503	SO:0001627	intron_variant	5648	exon11			GACCAGGCTTGGC	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1303+4944C>T	3.37:g.186954324G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																			G|0.853;A|0.147	0.147	strong		0.587	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
DDX55	57696	hgsc.bcm.edu	37	12	124086736	124086736	+	Missense_Mutation	SNP	T	T	G	rs141195308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124086736T>G	ENST00000238146.4	+	1	91	c.41T>G	c.(40-42)gTg>gGg	p.V14G	DDX55_ENST00000538744.1_Missense_Mutation_p.V14G	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	14						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		TCGCTGCCTGTGCCGCTGCAC	0.706													T|||	6	0.00119808	0.0	0.0029	5008	,	,		15400	0.0		0.004	False		,,,				2504	0.0				p.V14G		Atlas-SNP	.											DDX55,NS,lymphoid_neoplasm,0,1	DDX55	51	1	0			c.T41G						scavenged	.	T	GLY/VAL	3,4375		0,3,2186	12.0	13.0	13.0		41	3.9	0.3	12	dbSNP_134	13	25,8541		0,25,4258	yes	missense	DDX55	NM_020936.1	109	0,28,6444	GG,GT,TT		0.2919,0.0685,0.2163	benign	14/601	124086736	28,12916	2189	4283	6472	SO:0001583	missense	57696	exon1			TGCCTGTGCCGCT	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.41T>G	12.37:g.124086736T>G	ENSP00000238146:p.Val14Gly	Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	8	0.003663003663003663	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	3	0.00395778364116095	T	8.130	0.782942	0.16189	6.85E-4	0.002919	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	T;T	0.04234	3.95;3.67	5.03	3.89	0.44902	RNA helicase, DEAD-box type, Q motif (1);	0.578293	0.17416	N	0.175019	T	0.04679	0.0127	M	0.72894	2.215	0.80722	D	1	B	0.25850	0.136	B	0.19391	0.025	T	0.16600	-1.0397	10	0.22109	T	0.4	-20.8964	9.5249	0.39158	0.0:0.0796:0.0:0.9204	.	14	Q8NHQ9	DDX55_HUMAN	G	14	ENSP00000238146:V14G;ENSP00000443114:V14G	ENSP00000238146:V14G	V	+	2	0	DDX55	122652689	0.995000	0.38212	0.349000	0.25694	0.004000	0.04260	2.926000	0.48892	0.941000	0.37499	0.533000	0.62120	GTG	T|0.998;G|0.002	0.002	strong		0.706	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
GLTSCR1	29998	hgsc.bcm.edu	37	19	48183748	48183748	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48183748G>A	ENST00000396720.3	+	6	1515	c.1321G>A	c.(1321-1323)Ggg>Agg	p.G441R	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	441										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)		gcagccccccggggcccTGAG	0.687																																					p.G441R		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G1321A						PASS	.						12.0	17.0	16.0					19																	48183748		1779	3787	5566	SO:0001583	missense	29998	exon6			CCCCCCGGGGCCC	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.1321G>A	19.37:g.48183748G>A	ENSP00000379946:p.Gly441Arg	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	6.411	0.443896	0.12164	.	.	ENSG00000063169	ENST00000396720	T	0.33216	1.42	3.93	3.93	0.45458	.	.	.	.	.	T	0.25419	0.0618	N	0.14661	0.345	0.32728	N	0.50933	D	0.62365	0.991	P	0.52856	0.711	T	0.05989	-1.0852	9	0.16420	T	0.52	.	11.3225	0.49430	0.0:0.0:1.0:0.0	.	441	Q9NZM4	GSCR1_HUMAN	R	441	ENSP00000379946:G441R	ENSP00000379946:G441R	G	+	1	0	GLTSCR1	52875560	0.914000	0.31030	0.859000	0.33776	0.345000	0.29048	2.650000	0.46665	2.018000	0.59344	0.491000	0.48974	GGG	.	.	none		0.687	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
ARMC9	80210	hgsc.bcm.edu	37	2	232196564	232196564	+	Silent	SNP	C	C	T	rs1669083	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:232196564C>T	ENST00000349938.4	+	20	2027	c.1833C>T	c.(1831-1833)ctC>ctT	p.L611L	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	611						extracellular vesicular exosome (GO:0070062)		p.L611L(2)		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)		AGCCCCAGCTCGGAGAACTCT	0.542													C|||	1314	0.26238	0.211	0.3084	5008	,	,		20373	0.2212		0.3241	False		,,,				2504	0.2781				p.L611L		Atlas-SNP	.											ARMC9_ENST00000359743,NS,carcinoma,0,2	ARMC9	129	2	2	Substitution - coding silent(2)	stomach(2)	c.C1833T						PASS	.	C		957,3449	360.9+/-315.4	99,759,1345	72.0	71.0	71.0		1833	-11.3	0.7	2	dbSNP_89	71	2655,5945	425.9+/-355.1	429,1797,2074	no	coding-synonymous	ARMC9	NM_025139.3		528,2556,3419	TT,TC,CC		30.8721,21.7204,27.7718		611/666	232196564	3612,9394	2203	4300	6503	SO:0001819	synonymous_variant	80210	exon20			CCAGCTCGGAGAA	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.1833C>T	2.37:g.232196564C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	45	0.365854	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Silent	SNP	ENST00000349938.4	37	CCDS2484.1																																																																																			C|0.721;T|0.279	0.279	strong		0.542	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
RGS9BP	388531	hgsc.bcm.edu	37	19	33167865	33167865	+	Silent	SNP	G	G	A	rs150936907	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:33167865G>A	ENST00000334176.3	+	1	1553	c.696G>A	c.(694-696)gcG>gcA	p.A232A	ANKRD27_ENST00000306065.4_5'Flank|ANKRD27_ENST00000587352.1_5'Flank	NM_207391.2	NP_997274.2	Q6ZS82	R9BP_HUMAN	regulator of G protein signaling 9 binding protein	232					detection of light stimulus involved in visual perception (GO:0050908)|negative regulation of signal transduction (GO:0009968)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	integral component of membrane (GO:0016021)				central_nervous_system(1)|lung(2)	3	Esophageal squamous(110;0.137)					TGTGCGTGGCGAAGCTGAGCT	0.706													G|||	38	0.00758786	0.0	0.0014	5008	,	,		11561	0.0		0.0219	False		,,,				2504	0.0153				p.A232A		Atlas-SNP	.											RGS9BP,caecum,carcinoma,+1,1	RGS9BP	9	1	0			c.G696A						PASS	.	G		10,3894		0,10,1942	6.0	8.0	7.0		696	-3.5	1.0	19	dbSNP_134	7	142,7678		0,142,3768	no	coding-synonymous	RGS9BP	NM_207391.2		0,152,5710	AA,AG,GG		1.8159,0.2561,1.2965		232/236	33167865	152,11572	1952	3910	5862	SO:0001819	synonymous_variant	388531	exon1			CGTGGCGAAGCTG	AW302149	CCDS12424.1	19q13.11	2008-02-05	2007-08-14			ENSG00000186326			30304	protein-coding gene	gene with protein product		607814	"""regulator of G protein signalling 9 binding protein"""			12119397, 8889548	Standard	NM_207391		Approved	FLJ45744, PERRS, R9AP, RGS9	uc002ntp.1	Q6ZS82		ENST00000334176.3:c.696G>A	19.37:g.33167865G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_207391	Q6ZVJ6	Silent	SNP	ENST00000334176.3	37	CCDS12424.1																																																																																			G|0.990;A|0.010	0.010	strong		0.706	RGS9BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450337.1	NM_207391	
MICA	100507436	hgsc.bcm.edu	37	6	31378956	31378956	+	Missense_Mutation	SNP	C	C	G	rs1051790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31378956C>G	ENST00000449934.2	+	3	487	c.433C>G	c.(433-435)Ctg>Gtg	p.L145V	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)				CTCCCAAAACCTGGAGACTGA	0.522													c|||	1093	0.218251	0.2723	0.2118	5008	,	,		20699	0.122		0.1948	False		,,,				2504	0.273				p.L145V		Atlas-SNP	.											.	MICA	21	.	0			c.C433G						PASS	.	C	VAL/LEU	338,1046		43,252,397	68.0	60.0	63.0		433	1.9	0.0	6	dbSNP_86	63	489,2693		39,411,1141	yes	missense	MICA	NM_001177519.1	32	82,663,1538	GG,GC,CC		15.3677,24.422,18.1121	probably-damaging	145/333	31378956	827,3739	692	1591	2283	SO:0001583	missense	100507436	exon3			CAAAACCTGGAGA	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.433C>G	6.37:g.31378956C>G	ENSP00000413079:p.Leu145Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	414	0.18956043956043955	138	0.2804878048780488	66	0.18232044198895028	93	0.16258741258741258	117	0.15435356200527706	N	7.509	0.654194	0.14580	0.24422	0.153677	ENSG00000204520	ENST00000364810;ENST00000449934	T	0.00700	5.82	1.94	1.94	0.25998	.	0.504913	0.14706	N	0.303268	T	0.01695	0.0054	M	0.85859	2.78	0.80722	P	0.0	D	0.76494	0.999	D	0.85130	0.997	T	0.40059	-0.9583	9	0.59425	D	0.04	.	5.7228	0.17996	0.3182:0.6818:0.0:0.0	rs1051790;rs3819271;rs17883141;rs1051790	145	Q96QC4	.	V	145	ENSP00000413079:L145V	ENSP00000365394:L145V	L	+	1	2	MICA	31486935	0.000000	0.05858	0.004000	0.12327	0.030000	0.12068	-0.198000	0.09505	1.130000	0.42092	0.306000	0.20318	CTG	C|0.812;G|0.188	0.188	strong		0.522	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464736	39464736	+	Missense_Mutation	SNP	C	C	G	rs2074284	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39464736C>G	ENST00000391352.1	-	1	769	c.770G>C	c.(769-771)aGt>aCt	p.S257T		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	257	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						CTCTGAGCAACTTGGCTCACA	0.607													G|||	1605	0.320487	0.4818	0.1974	5008	,	,		22646	0.371		0.2634	False		,,,				2504	0.1963				p.S257T		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.G770C						PASS	.																																			SO:0001583	missense	100505753	exon1			GAGCAACTTGGCT	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.770G>C	17.37:g.39464736C>G	ENSP00000375147:p.Ser257Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	717	0.3282967032967033	229	0.4654471544715447	79	0.21823204419889503	206	0.36013986013986016	203	0.2678100263852243	G	3.035	-0.198720	0.06219	.	.	ENSG00000212657	ENST00000391352	T	0.01787	4.64	5.1	4.13	0.48395	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.51482	P	7.599999999996498E-5	.	.	.	.	.	.	T	0.19160	-1.0314	6	0.23891	T	0.37	.	3.6587	0.08230	0.0883:0.1689:0.5671:0.1757	rs2074284;rs2074284	.	.	.	T	257	ENSP00000375147:S257T	ENSP00000375147:S257T	S	-	2	0	KRTAP16-1	36718262	0.176000	0.23096	0.878000	0.34440	0.005000	0.04900	1.025000	0.30090	1.527000	0.49086	-0.120000	0.15030	AGT	C|0.672;G|0.328	0.328	strong		0.607	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
SRMS	6725	hgsc.bcm.edu	37	20	62172269	62172269	+	Missense_Mutation	SNP	C	C	A	rs310654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62172269C>A	ENST00000217188.1	-	8	1409	c.1369G>T	c.(1369-1371)Gtg>Ttg	p.V457L		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	457	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> L (in dbSNP:rs310654). {ECO:0000269|PubMed:17344846}.		peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			AGCATGAGCACGTAGACCTCC	0.692													C|||	801	0.159944	0.4758	0.0793	5008	,	,		16427	0.0238		0.0606	False		,,,				2504	0.0327				p.V457L		Atlas-SNP	.											.	SRMS	48	.	0			c.G1369T						PASS	.	C	LEU/VAL	1733,2671	506.2+/-366.3	337,1059,806	79.0	79.0	79.0		1369	-4.5	0.0	20	dbSNP_79	79	436,8162	131.5+/-189.3	8,420,3871	yes	missense	SRMS	NM_080823.2	32	345,1479,4677	AA,AC,CC		5.0709,39.3506,16.682	benign	457/489	62172269	2169,10833	2202	4299	6501	SO:0001583	missense	6725	exon8			TGAGCACGTAGAC		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1369G>T	20.37:g.62172269C>A	ENSP00000217188:p.Val457Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	326	0.14926739926739926	237	0.4817073170731707	24	0.06629834254143646	18	0.03146853146853147	47	0.06200527704485488	C	7.992	0.753556	0.15778	0.393506	0.050709	ENSG00000125508	ENST00000217188	T	0.10860	2.83	4.96	-4.53	0.03462	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	2.105440	0.02316	N	0.072531	T	0.00012	0.0000	N	0.02111	-0.68	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.47114	-0.9142	9	0.72032	D	0.01	.	7.8857	0.29648	0.1131:0.2898:0.0:0.5971	rs310654;rs311538;rs1757732;rs61110786;rs310654	457	Q9H3Y6	SRMS_HUMAN	L	457	ENSP00000217188:V457L	ENSP00000217188:V457L	V	-	1	0	SRMS	61642713	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-4.265000	0.00263	-1.399000	0.02063	-0.136000	0.14681	GTG	C|0.822;A|0.178	0.178	strong		0.692	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
PRRT4	401399	hgsc.bcm.edu	37	7	127999459	127999459	+	Missense_Mutation	SNP	G	G	A	rs145413607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:127999459G>A	ENST00000446477.2	-	3	900	c.587C>T	c.(586-588)aCg>aTg	p.T196M	PRRT4_ENST00000435512.1_Missense_Mutation_p.T196M|PRRT4_ENST00000535159.1_Missense_Mutation_p.T196M|PRRT4_ENST00000489835.2_Missense_Mutation_p.T196M	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	196						integral component of membrane (GO:0016021)		p.T196M(1)		endometrium(4)|prostate(1)	5						CAGGGGCAGCGTTCGATGCCC	0.652													G|||	28	0.00559105	0.0	0.0072	5008	,	,		16449	0.0		0.0199	False		,,,				2504	0.0031				p.T196M		Atlas-SNP	.											PRRT4,NS,carcinoma,0,1	PRRT4	31	1	1	Substitution - Missense(1)	endometrium(1)	c.C587T						PASS	.	G	MET/THR,MET/THR	5,1379		0,5,687	19.0	23.0	22.0		587,587	2.8	0.9	7	dbSNP_134	22	55,3127		2,51,1538	yes	missense,missense	PRRT4	NM_001174164.1,NM_001114726.2	81,81	2,56,2225	AA,AG,GG		1.7285,0.3613,1.3141	benign,benign	196/900,196/430	127999459	60,4506	692	1591	2283	SO:0001583	missense	401399	exon3			GGCAGCGTTCGAT	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.587C>T	7.37:g.127999459G>A	ENSP00000415026:p.Thr196Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	9.816	1.184515	0.21870	0.003613	0.017285	ENSG00000224940	ENST00000489835;ENST00000446477;ENST00000535159;ENST00000435512;ENST00000489517;ENST00000464607;ENST00000495931	.	.	.	4.97	2.78	0.32641	.	.	.	.	.	T	0.08537	0.0212	N	0.08118	0	0.09310	N	1	B;B	0.32893	0.077;0.389	B;B	0.23716	0.01;0.048	T	0.09250	-1.0683	8	0.87932	D	0	-13.8848	7.9713	0.30130	0.2241:0.0:0.7759:0.0	.	196;196	C9JH25;C9JH25-2	PRRT4_HUMAN;.	M	196	.	ENSP00000410779:T196M	T	-	2	0	PRRT4	127786695	0.137000	0.22531	0.873000	0.34254	0.521000	0.34408	1.775000	0.38584	1.115000	0.41800	0.585000	0.79938	ACG	G|0.991;A|0.009	0.009	strong		0.652	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
MTUS1	57509	hgsc.bcm.edu	37	8	17541999	17541999	+	Silent	SNP	T	T	C	rs2979792	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:17541999T>C	ENST00000262102.6	-	7	2900	c.2676A>G	c.(2674-2676)acA>acG	p.T892T	MTUS1_ENST00000544260.1_Silent_p.T37T|MTUS1_ENST00000381861.3_Silent_p.T139T|MTUS1_ENST00000297488.6_Silent_p.T58T|MIR548V_ENST00000584165.1_RNA|MTUS1_ENST00000381869.3_Silent_p.T838T|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000519263.1_Silent_p.T838T	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	892					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)		CATCGGGAGCTGTCTGTGGCT	0.413													C|||	1267	0.252995	0.0711	0.2752	5008	,	,		20314	0.374		0.4135	False		,,,				2504	0.1933				p.T892T		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2676G						PASS	.	C	,,,,	488,3352		32,424,1464	232.0	228.0	229.0		2676,2514,417,111,174	-5.9	0.5	8	dbSNP_101	229	3103,5153		578,1947,1603	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	,,,,	610,2371,3067	CC,CT,TT		37.5848,12.7083,29.6875	,,,,	892/1271,838/1217,139/518,37/416,58/437	17541999	3591,8505	1920	4128	6048	SO:0001819	synonymous_variant	57509	exon7			GGGAGCTGTCTGT	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.2676A>G	8.37:g.17541999T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			T|0.699;C|0.301	0.301	strong		0.413	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
CXCL1	2919	hgsc.bcm.edu	37	4	74735244	74735244	+	Silent	SNP	A	A	G	rs2071425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:74735244A>G	ENST00000395761.3	+	1	124	c.57A>G	c.(55-57)gcA>gcG	p.A19A	CXCL1_ENST00000509101.1_3'UTR	NM_001511.3	NP_001502.1	P09341	GROA_HUMAN	chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)	19					actin cytoskeleton organization (GO:0030036)|cell chemotaxis (GO:0060326)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|enzyme activator activity (GO:0008047)|receptor binding (GO:0005102)			lung(2)	2	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TGCGAGTGGCACTGCTGCTCC	0.751													A|||	1893	0.377995	0.5469	0.4265	5008	,	,		11021	0.3859		0.1819	False		,,,				2504	0.3088				p.A19A		Atlas-SNP	.											.	CXCL1	6	.	0			c.A57G						PASS	.	A		1581,2363		323,935,714	6.0	10.0	9.0		57	-2.3	0.0	4	dbSNP_96	9	1543,6721		156,1231,2745	no	coding-synonymous	CXCL1	NM_001511.2		479,2166,3459	GG,GA,AA		18.6713,40.0862,25.5898		19/108	74735244	3124,9084	1972	4132	6104	SO:0001819	synonymous_variant	2919	exon1			AGTGGCACTGCTG	J03561	CCDS47074.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163739		"""Endogenous ligands"""	4602	protein-coding gene	gene with protein product		155730	"""GRO1 oncogene (melanoma growth stimulating activity, alpha)"", ""fibroblast secretory protein"""	MGSA, GRO1, FSP		2217207	Standard	NM_001511		Approved	SCYB1, GROa, MGSA-a, NAP-3	uc003hhh.3	P09341		ENST00000395761.3:c.57A>G	4.37:g.74735244A>G		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_001511	Q9UCR7	Silent	SNP	ENST00000395761.3	37	CCDS47074.1																																																																																			A|0.668;G|0.332	0.332	strong		0.751	CXCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362734.1		
LMNA	4000	hgsc.bcm.edu	37	1	156107534	156107534	+	Splice_Site	SNP	C	C	T	rs4641	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156107534C>T	ENST00000368300.4	+	10	1910	c.1698C>T	c.(1696-1698)caC>caT	p.H566H	LMNA_ENST00000361308.4_Silent_p.H566H|LMNA_ENST00000473598.2_Splice_Site_p.H467H|LMNA_ENST00000368297.1_Silent_p.H485H|LMNA_ENST00000368299.3_Splice_Site_p.H566H|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000347559.2_Intron|LMNA_ENST00000392353.3_Silent_p.H485H|LMNA_ENST00000368301.2_Silent_p.H566H|LMNA_ENST00000448611.2_Splice_Site_p.H454H	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	566	Tail.				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)					ATCACCACCACGTGAGTGGTA	0.642									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	1103	0.220248	0.0658	0.3012	5008	,	,		13360	0.2738		0.2247	False		,,,				2504	0.3119				p.H566H		Atlas-SNP	.											.	LMNA	31	.	0			c.C1698T	GRCh37	CM003892	LMNA	M	rs4641	PASS	.	C	,,	367,3797		20,327,1735	30.0	24.0	26.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1698,1698,	-3.2	0.9	1	dbSNP_52	26	2046,6038		296,1454,2292	yes	coding-synonymous,coding-synonymous-near-splice,intron	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	316,1781,4027	TT,TC,CC		25.3093,8.8136,19.7012	,,	566/573,566/665,	156107534	2413,9835	2082	4042	6124	SO:0001630	splice_region_variant	4000	exon10	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CCACCACGTGAGT	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.1698+1C>T	1.37:g.156107534C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	30	0.652174	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			C|0.808;T|0.192	0.192	strong		0.642	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Silent
PPP1R21	129285	hgsc.bcm.edu	37	2	48681868	48681868	+	Silent	SNP	C	C	G	rs76587580	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48681868C>G	ENST00000294952.8	+	3	418	c.261C>G	c.(259-261)ggC>ggG	p.G87G	PPP1R21_ENST00000281394.4_Silent_p.G87G|PPP1R21_ENST00000449090.2_Silent_p.G87G	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	87						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						AACCACGAGGCAAGAAAAACA	0.433													C|||	153	0.0305511	0.0023	0.0476	5008	,	,		18857	0.0		0.1103	False		,,,				2504	0.0061				p.G87G		Atlas-SNP	.											.	PPP1R21	47	.	0			c.C261G						PASS	.	C	,,	108,4298	83.4+/-121.9	3,102,2098	91.0	83.0	86.0		261,261,261	5.6	1.0	2	dbSNP_132	86	894,7706	200.0+/-243.9	49,796,3455	no	coding-synonymous,coding-synonymous,coding-synonymous	KLRAQ1	NM_001135629.2,NM_001193475.1,NM_152994.4	,,	52,898,5553	GG,GC,CC		10.3953,2.4512,7.7041	,,	87/781,87/739,87/770	48681868	1002,12004	2203	4300	6503	SO:0001819	synonymous_variant	129285	exon3			ACGAGGCAAGAAA	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30595	protein-coding gene	gene with protein product			"""coiled-coil domain containing 128"", ""KLRAQ motif containing 1"""	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.261C>G	2.37:g.48681868C>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	199	87	0.437186	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			C|0.931;G|0.069	0.069	strong		0.433	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994	
CD248	57124	hgsc.bcm.edu	37	11	66083782	66083782	+	Silent	SNP	G	G	A	rs3741368	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:66083782G>A	ENST00000311330.3	-	1	733	c.717C>T	c.(715-717)aaC>aaT	p.N239N	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	239					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						CGCAGCCCCCGTTGTCAGGGC	0.682													G|||	1279	0.255391	0.0378	0.5303	5008	,	,		17523	0.2272		0.4463	False		,,,				2504	0.1871				p.N239N		Atlas-SNP	.											CD248,NS,carcinoma,0,1	CD248	69	1	0			c.C717T						PASS	.	G		443,3957		27,389,1784	28.0	38.0	35.0		717	0.1	1.0	11	dbSNP_107	35	3830,4754		857,2116,1319	no	coding-synonymous	CD248	NM_020404.2		884,2505,3103	AA,AG,GG		44.6179,10.0682,32.9097		239/758	66083782	4273,8711	2200	4292	6492	SO:0001819	synonymous_variant	57124	exon1			GCCCCCGTTGTCA	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.717C>T	11.37:g.66083782G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																			G|0.702;A|0.298	0.298	strong		0.682	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404	
DDX1	1653	hgsc.bcm.edu	37	2	15735648	15735648	+	Silent	SNP	T	T	C	rs2302929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:15735648T>C	ENST00000381341.2	+	4	492	c.103T>C	c.(103-105)Ttg>Ctg	p.L35L	DDX1_ENST00000233084.3_Silent_p.L35L			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	35	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		ATCTATCCCATTGATCTTAGG	0.383													T|||	876	0.17492	0.0333	0.1354	5008	,	,		18132	0.371		0.164	False		,,,				2504	0.2035				p.L35L		Atlas-SNP	.											.	DDX1	70	.	0			c.T103C						PASS	.	T		272,4134	154.0+/-187.5	8,256,1939	130.0	122.0	125.0		103	-5.1	0.0	2	dbSNP_100	125	1624,6976	301.6+/-305.5	162,1300,2838	no	coding-synonymous	DDX1	NM_004939.1		170,1556,4777	CC,CT,TT		18.8837,6.1734,14.5779		35/741	15735648	1896,11110	2203	4300	6503	SO:0001819	synonymous_variant	1653	exon3			ATCCCATTGATCT	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.103T>C	2.37:g.15735648T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	37	CCDS1686.1																																																																																			T|0.830;C|0.170	0.170	strong		0.383	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939	
SPINK8	646424	hgsc.bcm.edu	37	3	48360992	48360992	+	Missense_Mutation	SNP	T	T	G	rs11718350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48360992T>G	ENST00000434006.1	-	3	233	c.234A>C	c.(232-234)aaA>aaC	p.K78N		NM_001080525.1	NP_001073994.1	P0C7L1	ISK8_HUMAN	serine peptidase inhibitor, Kazal type 8 (putative)	78	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		K -> N (in dbSNP:rs11718350).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CTTACAGAATTTTGGAGCACA	0.428													T|||	844	0.16853	0.0318	0.1772	5008	,	,		21625	0.123		0.2843	False		,,,				2504	0.2751				p.K78N		Atlas-SNP	.											.	SPINK8	5	.	0			c.A234C						PASS	.	T	ASN/LYS	229,3597		9,211,1693	127.0	126.0	126.0		234	2.4	0.4	3	dbSNP_120	126	2501,5759		396,1709,2025	yes	missense	SPINK8	NM_001080525.1	94	405,1920,3718	GG,GT,TT		30.2785,5.9854,22.5881	possibly-damaging	78/98	48360992	2730,9356	1913	4130	6043	SO:0001583	missense	646424	exon3			CAGAATTTTGGAG		CCDS46822.1	3p21.31	2011-08-31			ENSG00000229453	ENSG00000229453		"""Serine peptidase inhibitors, Kazal type"""	33160	protein-coding gene	gene with protein product						16930550	Standard	NM_001080525		Approved		uc003csq.1	P0C7L1	OTTHUMG00000156832	ENST00000434006.1:c.234A>C	3.37:g.48360992T>G	ENSP00000407497:p.Lys78Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	137	81	0.591241	NM_001080525		Missense_Mutation	SNP	ENST00000434006.1	37	CCDS46822.1	363	0.1662087912087912	18	0.036585365853658534	70	0.19337016574585636	63	0.11013986013986014	212	0.2796833773087071	T	12.28	1.889555	0.33348	0.059854	0.302785	ENSG00000229453	ENST00000434006	T	0.75154	-0.91	3.58	2.39	0.29439	Proteinase inhibitor I1, Kazal (2);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	P	0.43826	0.818	B	0.39617	0.305	T	0.06356	-1.0831	7	0.20519	T	0.43	.	6.9836	0.24715	0.0:0.0:0.2345:0.7655	rs11718350;rs11718350	78	P0C7L1	ISK8_HUMAN	N	78	ENSP00000407497:K78N	ENSP00000407497:K78N	K	-	3	2	SPINK8	48335996	0.002000	0.14202	0.359000	0.25824	0.346000	0.29079	0.234000	0.17930	0.729000	0.32403	0.528000	0.53228	AAA	T|0.820;G|0.180	0.180	strong		0.428	SPINK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346123.1	NM_001080525	
DMRT3	58524	hgsc.bcm.edu	37	9	990840	990840	+	Silent	SNP	C	C	T	rs7021244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:990840C>T	ENST00000190165.2	+	2	1292	c.1254C>T	c.(1252-1254)gtC>gtT	p.V418V		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	418					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CTACCAGCGTCTTCAGAAGCT	0.547													C|||	929	0.185503	0.0113	0.1758	5008	,	,		19419	0.2312		0.2167	False		,,,				2504	0.3487				p.V418V		Atlas-SNP	.											DMRT3,NS,carcinoma,+2,2	DMRT3	83	2	0			c.C1254T						scavenged	.	C		218,4188	130.6+/-167.2	5,208,1990	85.0	66.0	73.0		1254	5.2	1.0	9	dbSNP_116	73	1914,6686	339.0+/-323.0	227,1460,2613	no	coding-synonymous	DMRT3	NM_021240.2		232,1668,4603	TT,TC,CC		22.2558,4.9478,16.3924		418/473	990840	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	58524	exon2			CAGCGTCTTCAGA	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1254C>T	9.37:g.990840C>T		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Silent	SNP	ENST00000190165.2	37	CCDS6443.1																																																																																			C|0.827;N|0.000	.	strong		0.547	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
CCDC77	84318	hgsc.bcm.edu	37	12	520947	520947	+	Missense_Mutation	SNP	A	A	C	rs4980895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:520947A>C	ENST00000239830.4	+	4	252	c.73A>C	c.(73-75)Agt>Cgt	p.S25R	CCDC77_ENST00000412006.2_5'UTR|CCDC77_ENST00000540180.1_5'UTR|CCDC77_ENST00000422000.1_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	55	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	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	
ATAD3B	83858	hgsc.bcm.edu	37	1	1431060	1431060	+	Missense_Mutation	SNP	T	T	C	rs9792997		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1431060T>C	ENST00000308647.7	+	16	1926	c.1810T>C	c.(1810-1812)Tac>Cac	p.Y604H		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	604						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	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)		GGACCCCTCCTACCCCTGCCT	0.682																																					p.Y604H		Atlas-SNP	.											ATAD3B,rectum,carcinoma,0,1	ATAD3B	68	1	0			c.T1810C						scavenged	.						33.0	35.0	34.0					1																	1431060		2202	4298	6500	SO:0001583	missense	83858	exon16			CCCTCCTACCCCT	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1810T>C	1.37:g.1431060T>C	ENSP00000311766:p.Tyr604His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	134	6	0.0447761	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	t	0.011	-1.733306	0.00687	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.94457	-3.43	1.2	-2.41	0.06562	.	9.894780	0.04442	U	0.371029	D	0.84065	0.5390	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.73350	-0.4010	10	0.17832	T	0.49	.	2.7341	0.05235	0.0:0.3111:0.2569:0.4319	rs9792997	558;604	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	H	438;604	ENSP00000311766:Y604H	ENSP00000311766:Y604H	Y	+	1	0	ATAD3B	1420923	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.763000	0.01802	-1.174000	0.02754	-1.140000	0.01884	TAC	.	.	weak		0.682	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:7091569C>T	ENST00000299481.4	+	11	3374	c.3028C>T	c.(3028-3030)Ctt>Ttt	p.L1010F		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1010			L -> F (in dbSNP:rs17280682). {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)		CTCCTCTGCTCTTATCTGCAA	0.358													C|||	481	0.0960463	0.0666	0.1297	5008	,	,		19436	0.0169		0.2147	False		,,,				2504	0.0716				p.L1010F		Atlas-SNP	.											.	NLRP14	187	.	0			c.C3028T						PASS	.	C	PHE/LEU	368,4034	189.9+/-215.9	10,348,1843	108.0	103.0	105.0		3028	4.1	0.1	11	dbSNP_123	105	1848,6744	330.3+/-319.2	205,1438,2653	yes	missense	NLRP14	NM_176822.3	22	215,1786,4496	TT,TC,CC		21.5084,8.3598,17.054	probably-damaging	1010/1094	7091569	2216,10778	2201	4296	6497	SO:0001583	missense	338323	exon11			TCTGCTCTTATCT	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.3028C>T	11.37:g.7091569C>T	ENSP00000299481:p.Leu1010Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	246	0.11263736263736264	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	161	0.21240105540897097	C	14.57	2.575489	0.45902	0.083598	0.215084	ENSG00000158077	ENST00000299481	T	0.61859	0.07	4.13	4.13	0.48395	.	0.000000	0.37095	N	0.002246	T	0.00073	0.0002	M	0.74881	2.28	0.47547	P	5.450000000000177E-4	P	0.40197	0.706	B	0.43838	0.433	T	0.07539	-1.0767	9	0.51188	T	0.08	.	12.1948	0.54290	0.0:1.0:0.0:0.0	rs17280682;rs58608223;rs17280682	1010	Q86W24	NAL14_HUMAN	F	1010	ENSP00000299481:L1010F	ENSP00000299481:L1010F	L	+	1	0	NLRP14	7048145	0.901000	0.30685	0.091000	0.20842	0.027000	0.11550	2.377000	0.44300	2.602000	0.87976	0.557000	0.71058	CTT	C|0.850;T|0.150	0.150	strong		0.358	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
SNAI3	333929	hgsc.bcm.edu	37	16	88744949	88744949	+	Silent	SNP	G	G	T	rs139375690	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88744949G>T	ENST00000332281.5	-	3	872	c.786C>A	c.(784-786)gcC>gcA	p.A262A	SNAI3-AS1_ENST00000563261.1_RNA	NM_178310.3	NP_840101.1	Q3KNW1	SNAI3_HUMAN	snail family zinc finger 3	262					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	copper ion binding (GO:0005507)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(1)|kidney(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(80;0.048)		GGTACTTCTTGGCGTCTGAGT	0.662													G|||	21	0.00419329	0.0	0.0029	5008	,	,		16584	0.0		0.0089	False		,,,				2504	0.0102				p.A262A	Colon(27;366 710 19748 23199 27567)	Atlas-SNP	.											.	SNAI3	23	.	0			c.C786A						PASS	.	G		1,4395	2.1+/-5.4	0,1,2197	72.0	57.0	62.0		786	3.1	0.5	16	dbSNP_134	62	35,8565	23.4+/-69.3	0,35,4265	no	coding-synonymous	SNAI3	NM_178310.3		0,36,6462	TT,TG,GG		0.407,0.0227,0.277		262/293	88744949	36,12960	2198	4300	6498	SO:0001819	synonymous_variant	333929	exon3			CTTCTTGGCGTCT	BC041461	CCDS32505.1	16q24.3	2013-05-23	2013-05-23			ENSG00000185669		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	18411	protein-coding gene	gene with protein product		612741	"""zinc finger protein 293"", ""snail homolog 3 (Drosophila)"""	ZNF293		12579345	Standard	NM_178310		Approved	SMUC, Zfp293	uc002flj.3	Q3KNW1		ENST00000332281.5:c.786C>A	16.37:g.88744949G>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_178310	Q86SU5	Silent	SNP	ENST00000332281.5	37	CCDS32505.1																																																																																			G|0.997;T|0.003	0.003	strong		0.662	SNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422582.1		
XPNPEP2	7512	hgsc.bcm.edu	37	X	128880614	128880614	+	Silent	SNP	T	T	C	rs3747343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	128	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	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	
SDK2	54549	hgsc.bcm.edu	37	17	71410891	71410891	+	Silent	SNP	C	C	T	rs12386051	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	45	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	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	
RBMX	27316	hgsc.bcm.edu	37	X	135956586	135956586	+	Silent	SNP	T	T	C	rs150079822		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:135956586T>C	ENST00000320676.7	-	9	1045	c.891A>G	c.(889-891)acA>acG	p.T297T	RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000565438.1_Silent_p.T169T|RBMX_ENST00000570135.1_Silent_p.T162T	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	297					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)			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)					GGGGCCCTCGTGTAGGTGGAG	0.453																																					p.T297T		Atlas-SNP	.											.	RBMX	149	.	0			c.A891G						PASS	.						82.0	77.0	79.0					X																	135956586		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon9			CCCTCGTGTAGGT		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.891A>G	X.37:g.135956586T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	28	0.297872	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Silent	SNP	ENST00000320676.7	37	CCDS14661.1																																																																																			T|0.500;C|0.500	0.500	weak		0.453	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
ANKRD44	91526	hgsc.bcm.edu	37	2	197946392	197946392	+	Silent	SNP	C	C	T	rs35272229	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:197946392C>T	ENST00000328737.2	-	15	1516	c.1440G>A	c.(1438-1440)gaG>gaA	p.E480E	ANKRD44_ENST00000477852.1_5'Flank|ANKRD44_ENST00000337207.5_Silent_p.E480E|ANKRD44_ENST00000282272.8_Silent_p.E497E|ANKRD44_ENST00000450567.1_Silent_p.E480E|ANKRD44_ENST00000409153.1_Silent_p.E505E|ANKRD44_ENST00000539527.1_Silent_p.E433E			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	106	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	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	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68264867	68264867	+	Silent	SNP	A	A	G	rs12891164	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:68264867A>G	ENST00000347230.4	-	11	2250	c.2112T>C	c.(2110-2112)ccT>ccC	p.P704P	ZFYVE26_ENST00000555452.1_Silent_p.P704P	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	704					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)		GCTTCTCAGGAGGGCTGCGGC	0.522													G|||	3862	0.771166	0.7186	0.7695	5008	,	,		18652	0.9722		0.6223	False		,,,				2504	0.7894				p.P704P		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T2112C						PASS	.	G		3007,1399	454.9+/-350.8	1029,949,225	52.0	55.0	54.0		2112	2.1	0.0	14	dbSNP_121	54	5517,3083	468.7+/-367.4	1791,1935,574	no	coding-synonymous	ZFYVE26	NM_015346.3		2820,2884,799	GG,GA,AA		35.8488,31.7522,34.461		704/2540	68264867	8524,4482	2203	4300	6503	SO:0001819	synonymous_variant	23503	exon11			CTCAGGAGGGCTG	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.2112T>C	14.37:g.68264867A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	37	CCDS9788.1																																																																																			A|0.303;G|0.697	0.697	strong		0.522	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
FAM209B	388799	hgsc.bcm.edu	37	20	55111371	55111371	+	Silent	SNP	G	G	A	rs2296130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:55111371G>A	ENST00000371325.1	+	2	489	c.393G>A	c.(391-393)caG>caA	p.Q131Q		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	131						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											CCGAAGTGCAGAATCTTAAAG	0.398													G|||	1873	0.374002	0.5461	0.3473	5008	,	,		20008	0.0466		0.4483	False		,,,				2504	0.4213				p.Q131Q		Atlas-SNP	.											.	.	.	.	0			c.G393A						PASS	.	G		2376,2030	612.7+/-392.0	639,1098,466	99.0	99.0	99.0		393	1.5	0.2	20	dbSNP_100	99	3934,4666	549.6+/-385.6	869,2196,1235	no	coding-synonymous	C20orf107	NM_001013646.2		1508,3294,1701	AA,AG,GG		45.7442,46.0735,48.5161		131/172	55111371	6310,6696	2203	4300	6503	SO:0001819	synonymous_variant	388799	exon2			AGTGCAGAATCTT	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.393G>A	20.37:g.55111371G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			G|0.585;A|0.415	0.415	strong		0.398	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
HK2	3099	hgsc.bcm.edu	37	2	75099477	75099477	+	Missense_Mutation	SNP	A	A	T	rs2229621	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	162	0	0		WXS	Illumina HiSeq	Phase_I	191	89	0.465969	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	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104280	26104280	+	Silent	SNP	T	T	C	rs2229768	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	77	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	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	
RCBTB1	55213	hgsc.bcm.edu	37	13	50123622	50123622	+	Silent	SNP	G	G	C	rs3751384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50123622G>C	ENST00000378302.2	-	9	1277	c.1017C>G	c.(1015-1017)ccC>ccG	p.P339P	RCBTB1_ENST00000258646.3_Silent_p.P339P|RCBTB1_ENST00000546015.1_Silent_p.P339P	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	339					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		ACGAGACGGCGGGAGTGGCAA	0.597													G|||	2380	0.47524	0.2632	0.6441	5008	,	,		15536	0.5149		0.6441	False		,,,				2504	0.4274				p.P339P		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C1017G						PASS	.	G		1401,3005	458.2+/-351.9	217,967,1019	67.0	53.0	58.0		1017	-10.1	0.1	13	dbSNP_107	58	5809,2791	675.5+/-403.2	1987,1835,478	no	coding-synonymous	RCBTB1	NM_018191.3		2204,2802,1497	CC,CG,GG		32.4535,31.7975,44.564		339/532	50123622	7210,5796	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon9			GACGGCGGGAGTG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1017C>G	13.37:g.50123622G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			G|0.453;C|0.547	0.547	strong		0.597	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
NUGGC	389643	hgsc.bcm.edu	37	8	27898580	27898580	+	Silent	SNP	T	T	C	rs17058502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:27898580T>C	ENST00000413272.2	-	13	1741	c.1599A>G	c.(1597-1599)agA>agG	p.R533R	NUGGC_ENST00000341513.6_Silent_p.R533R	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	533					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)										CCAAGCATGCTCTGAGGATGC	0.562													C|||	555	0.110823	0.174	0.1052	5008	,	,		18994	0.0516		0.1213	False		,,,				2504	0.0798				p.R533R		Atlas-SNP	.											.	.	.	.	0			c.A1599G						PASS	.	C		606,3486		42,522,1482	49.0	49.0	49.0		1599	0.3	0.0	8	dbSNP_123	49	934,7488		54,826,3331	no	coding-synonymous	C8orf80	NM_001010906.1		96,1348,4813	CC,CT,TT		11.09,14.8094,12.3062		533/797	27898580	1540,10974	2046	4211	6257	SO:0001819	synonymous_variant	389643	exon13			GCATGCTCTGAGG	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.1599A>G	8.37:g.27898580T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			T|0.884;C|0.116	0.116	strong		0.562	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
KRT8	3856	hgsc.bcm.edu	37	12	53294381	53294381	+	Silent	SNP	T	T	C	rs8608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:53294381T>C	ENST00000552551.1	-	5	1113	c.681A>G	c.(679-681)ctA>ctG	p.L227L	KRT8_ENST00000552150.1_Silent_p.L255L|KRT8_ENST00000293308.6_Silent_p.L227L|KRT8_ENST00000546897.1_Silent_p.L227L			P05787	K2C8_HUMAN	keratin 8	227	Coil 1B.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	CCTCTTCATATAGCTGCCTGA	0.582													C|||	2842	0.567492	0.3986	0.6182	5008	,	,		18626	0.6042		0.5318	False		,,,				2504	0.7587				p.L255L		Atlas-SNP	.											.	KRT8	41	.	0			c.A765G						PASS	.	C		1920,2486	626.3+/-394.7	423,1074,706	112.0	110.0	111.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	681	1.5	1.0	12	dbSNP_52	111	4399,4201	569.6+/-389.2	1144,2111,1045	no	coding-synonymous	KRT8	NM_002273.3		1567,3185,1751	CC,CT,TT		48.8488,43.5769,48.5853		227/484	53294381	6319,6687	2203	4300	6503	SO:0001819	synonymous_variant	3856	exon5			TTCATATAGCTGC	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.681A>G	12.37:g.53294381T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Silent	SNP	ENST00000552551.1	37	CCDS8841.1																																																																																			T|0.483;C|0.517	0.517	strong		0.582	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
FAM214B	80256	hgsc.bcm.edu	37	9	35107765	35107765	+	Silent	SNP	C	C	A	rs13287211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35107765C>A	ENST00000378561.1	-	2	3562	c.507G>T	c.(505-507)ggG>ggT	p.G169G	FAM214B_ENST00000488109.2_Silent_p.G169G|FAM214B_ENST00000605244.1_Silent_p.G169G|FAM214B_ENST00000322813.5_Silent_p.G169G|FAM214B_ENST00000603301.1_Silent_p.G169G|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000378554.2_Silent_p.G169G|FAM214B_ENST00000378566.1_Intron|FAM214B_ENST00000378557.1_Silent_p.G169G			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	169						nucleus (GO:0005634)											CCCCCAGGGACCCCTGTCCCC	0.627													C|||	937	0.187101	0.0197	0.4424	5008	,	,		16091	0.003		0.3936	False		,,,				2504	0.2096				p.G169G		Atlas-SNP	.											.	.	.	.	0			c.G507T						PASS	.	C		319,4069		15,289,1890	33.0	42.0	39.0		507	3.0	1.0	9	dbSNP_121	39	3388,5212		670,2048,1582	no	coding-synonymous	KIAA1539	NM_025182.2		685,2337,3472	AA,AC,CC		39.3953,7.2698,28.5417		169/539	35107765	3707,9281	2194	4300	6494	SO:0001819	synonymous_variant	80256	exon3			CAGGGACCCCTGT	AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"""KIAA1539"""	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.507G>T	9.37:g.35107765C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_025182	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Silent	SNP	ENST00000378561.1	37	CCDS6578.1																																																																																			C|0.718;A|0.282	0.282	strong		0.627	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182	
ANKLE2	23141	hgsc.bcm.edu	37	12	133331364	133331364	+	Silent	SNP	G	G	A	rs34152718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133331364G>A	ENST00000357997.5	-	2	626	c.537C>T	c.(535-537)ccC>ccT	p.P179P	ANKLE2_ENST00000337516.5_Silent_p.P179P|ANKLE2_ENST00000539605.1_Silent_p.P117P	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	179					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		TGTCACTAGGGGGCACCGAGC	0.557													G|||	172	0.034345	0.0	0.0461	5008	,	,		16904	0.0804		0.0437	False		,,,				2504	0.0153				p.P179P		Atlas-SNP	.											.	ANKLE2	76	.	0			c.C537T						PASS	.	G		24,3894		0,24,1935	68.0	70.0	69.0		537	-2.8	0.0	12	dbSNP_126	69	380,7898		15,350,3774	no	coding-synonymous	ANKLE2	NM_015114.1		15,374,5709	AA,AG,GG		4.5905,0.6126,3.3126		179/939	133331364	404,11792	1959	4139	6098	SO:0001819	synonymous_variant	23141	exon2			ACTAGGGGGCACC	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.537C>T	12.37:g.133331364G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Silent	SNP	ENST00000357997.5	37	CCDS41869.1																																																																																			G|0.957;A|0.043	0.043	strong		0.557	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
MYH9	4627	hgsc.bcm.edu	37	22	36681272	36681272	+	Missense_Mutation	SNP	T	T	C	rs141440715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36681272T>C	ENST00000216181.5	-	38	5608	c.5378A>G	c.(5377-5379)aAg>aGg	p.K1793R	MYH9_ENST00000475726.1_5'UTR	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1793					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						CTCCTGCAGCTTGACCTTAAG	0.587			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.K1793R		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A5378G						PASS	.	T	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	144.0	115.0	125.0		5378	5.0	1.0	22	dbSNP_134	125	3,8597	3.7+/-12.6	0,3,4297	yes	missense	MYH9	NM_002473.4	26	0,4,6499	CC,CT,TT		0.0349,0.0227,0.0308	benign	1793/1961	36681272	4,13002	2203	4300	6503	SO:0001583	missense	4627	exon38	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	TGCAGCTTGACCT		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.5378A>G	22.37:g.36681272T>C	ENSP00000216181:p.Lys1793Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.011097	0.54361	2.27E-4	3.49E-4	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.75154	-0.91	5.03	5.03	0.67393	Myosin tail (1);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	N	0.25647	0.755	0.80722	D	1	B	0.24651	0.108	B	0.31016	0.123	T	0.56001	-0.8051	10	0.02654	T	1	.	14.7562	0.69567	0.0:0.0:0.0:1.0	.	1793	P35579	MYH9_HUMAN	R	1215;395;1793	ENSP00000216181:K1793R	ENSP00000216181:K1793R	K	-	2	0	MYH9	35011218	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	1.879000	0.54435	0.455000	0.32223	AAG	T|1.000;C|0.000	0.000	strong		0.587	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
SLC25A48	153328	hgsc.bcm.edu	37	5	135178142	135178142	+	Silent	SNP	A	A	G	rs6596270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:135178142A>G	ENST00000420621.1	+	2	256	c.84A>G	c.(82-84)acA>acG	p.T28T	SLC25A48_ENST00000274513.5_Silent_p.T28T|SLC25A48_ENST00000433282.2_5'UTR|SLC25A48_ENST00000412661.2_Silent_p.T28T|SLC25A48_ENST00000425402.1_Silent_p.T28T			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	28					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CTCTGGACACAGTCAAGGTAC	0.507													G|||	691	0.137979	0.208	0.1225	5008	,	,		17766	0.0099		0.2117	False		,,,				2504	0.1104				p.T28T		Atlas-SNP	.											.	SLC25A48	37	.	0			c.A84G						PASS	.	G		740,3508		73,594,1457	132.0	143.0	140.0		84	-1.4	1.0	5	dbSNP_116	140	1786,6722		184,1418,2652	no	coding-synonymous	SLC25A48	NM_145282.4		257,2012,4109	GG,GA,AA		20.992,17.42,19.8024		28/158	135178142	2526,10230	2124	4254	6378	SO:0001819	synonymous_variant	153328	exon2			GGACACAGTCAAG		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"""Solute carriers"""	30451	protein-coding gene	gene with protein product	"""HCC-down-regulated mitochondrial carrier protein"""					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.84A>G	5.37:g.135178142A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_145282	Q8TAV9	Silent	SNP	ENST00000420621.1	37																																																																																				A|0.820;G|0.180	0.180	strong		0.507	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188383	32188383	+	Missense_Mutation	SNP	T	T	C	rs422951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	39	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	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		
ADGB	79747	hgsc.bcm.edu	37	6	147067093	147067093	+	Silent	SNP	C	C	T	rs9647637	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:147067093C>T	ENST00000397944.3	+	26	3289	c.3213C>T	c.(3211-3213)ggC>ggT	p.G1071G	ADGB_ENST00000367493.3_Silent_p.G490G	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	1071					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						CATTTACAGGCGACACATATG	0.423													c|||	804	0.160543	0.0242	0.1542	5008	,	,		13903	0.1954		0.2634	False		,,,				2504	0.2076				p.G1071G		Atlas-SNP	.											C6orf103_ENST00000367493,caecum,carcinoma,+2,2	ADGB	93	2	0			c.C3213T						PASS	.	C		87,1297		3,81,608	85.0	83.0	83.0		3213	-3.5	0.1	6	dbSNP_119	83	894,2288		125,644,822	no	coding-synonymous	C6orf103	NM_024694.3		128,725,1430	TT,TC,CC		28.0955,6.2861,21.4849		1071/1668	147067093	981,3585	692	1591	2283	SO:0001819	synonymous_variant	79747	exon26			TACAGGCGACACA	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.3213C>T	6.37:g.147067093C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				C|0.826;T|0.174	0.174	strong		0.423	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
AZIN1	51582	hgsc.bcm.edu	37	8	103851052	103851052	+	Silent	SNP	T	T	C	rs1062048	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:103851052T>C	ENST00000337198.5	-	5	1532	c.369A>G	c.(367-369)gcA>gcG	p.A123A	AZIN1_ENST00000522311.1_5'UTR|AZIN1_ENST00000347770.4_Silent_p.A123A	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	123					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			CAACTTTTGCTGCATACTTTA	0.353													T|||	1001	0.19988	0.0628	0.1599	5008	,	,		21040	0.1488		0.2634	False		,,,				2504	0.4008				p.A123A		Atlas-SNP	.											.	AZIN1	26	.	0			c.A369G						PASS	.	T	,	406,4000	199.8+/-223.2	17,372,1814	148.0	132.0	137.0		369,369	5.4	1.0	8	dbSNP_86	137	2250,6350	381.2+/-339.9	289,1672,2339	no	coding-synonymous,coding-synonymous	AZIN1	NM_015878.4,NM_148174.2	,	306,2044,4153	CC,CT,TT		26.1628,9.2147,20.4213	,	123/449,123/449	103851052	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	51582	exon6			TTTTGCTGCATAC	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"""ornithine decarboxylase 1-like"""	607909	"""ornithine decarboxylase antizyme inhibitor"""	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.369A>G	8.37:g.103851052T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Silent	SNP	ENST00000337198.5	37	CCDS6295.1																																																																																			T|0.804;C|0.196	0.196	strong		0.353	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1		
OGDH	4967	hgsc.bcm.edu	37	7	44715599	44715599	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44715599A>T	ENST00000222673.5	+	9	1099	c.1057A>T	c.(1057-1059)Atg>Ttg	p.M353L	OGDH_ENST00000443864.2_Missense_Mutation_p.M353L|OGDH_ENST00000449767.1_Missense_Mutation_p.M349L|OGDH_ENST00000543843.1_Missense_Mutation_p.M304L|OGDH_ENST00000439616.2_Missense_Mutation_p.M203L|OGDH_ENST00000444676.1_Missense_Mutation_p.M368L|OGDH_ENST00000447398.1_Missense_Mutation_p.M364L	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	353					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CCACCTGGGCATGTATCACCG	0.547																																					p.M353L		Atlas-SNP	.											.	OGDH	145	.	0			c.A1057T						PASS	.						111.0	98.0	102.0					7																	44715599		2203	4300	6503	SO:0001583	missense	4967	exon9			CTGGGCATGTATC	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.1057A>T	7.37:g.44715599A>T	ENSP00000222673:p.Met353Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	130	85	0.653846	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392130	0.62066	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95724	-3.79;2.71;-3.79;-3.79;-3.79;-3.79;-3.79	5.14	5.14	0.70334	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.93582	0.7951	L	0.52905	1.665	0.58432	D	0.99999	B;B;B;B;B;B;B	0.18310	0.004;0.004;0.002;0.002;0.002;0.002;0.027	B;B;B;B;B;B;B	0.24006	0.029;0.02;0.029;0.029;0.02;0.029;0.05	D	0.91106	0.4918	10	0.37606	T	0.19	-47.9559	14.9242	0.70862	1.0:0.0:0.0:0.0	.	148;203;349;364;255;353;353	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	L	203;353;349;364;368;353;304	ENSP00000398576:M203L;ENSP00000388084:M353L;ENSP00000392878:M349L;ENSP00000388183:M364L;ENSP00000414662:M368L;ENSP00000222673:M353L;ENSP00000443821:M304L	ENSP00000222673:M353L	M	+	1	0	OGDH	44682124	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.043000	0.93799	2.063000	0.61619	0.379000	0.24179	ATG	.	.	none		0.547	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
PRODH2	58510	hgsc.bcm.edu	37	19	36302921	36302921	+	Silent	SNP	T	T	C	rs12462360	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36302921T>C	ENST00000301175.3	-	5	785	c.768A>G	c.(766-768)ccA>ccG	p.P256P		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	256					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGGAGGCTCCTGGCCTTCTGA	0.662													T|||	1162	0.232029	0.1377	0.2752	5008	,	,		18544	0.3194		0.2664	False		,,,				2504	0.2035				p.P256P		Atlas-SNP	.											.	PRODH2	68	.	0			c.A768G						PASS	.	T		650,3756	278.1+/-274.1	53,544,1606	53.0	49.0	50.0		768	-9.7	0.0	19	dbSNP_120	50	2297,6303	386.0+/-341.7	305,1687,2308	no	coding-synonymous	PRODH2	NM_021232.1		358,2231,3914	CC,CT,TT		26.7093,14.7526,22.6588		256/537	36302921	2947,10059	2203	4300	6503	SO:0001819	synonymous_variant	58510	exon5			GGCTCCTGGCCTT	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.768A>G	19.37:g.36302921T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_021232		Silent	SNP	ENST00000301175.3	37	CCDS12478.1																																																																																			T|0.771;C|0.229	0.229	strong		0.662	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
TMED8	283578	hgsc.bcm.edu	37	14	77810133	77810133	+	Missense_Mutation	SNP	C	C	T	rs142882254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77810133C>T	ENST00000216468.7	-	4	416	c.361G>A	c.(361-363)Gac>Aac	p.D121N		NM_213601.1	NP_998766.1	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain containing 8	121					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)	15			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ATAACGATGTCCCCAGACCTC	0.438													C|||	5	0.000998403	0.0	0.0	5008	,	,		19285	0.0		0.005	False		,,,				2504	0.0				p.D121N		Atlas-SNP	.											.	TMED8	27	.	0			c.G361A						PASS	.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	143.0	136.0	138.0		361	6.0	1.0	14	dbSNP_134	138	33,8567	22.2+/-67.0	0,33,4267	yes	missense	TMED8	NM_213601.1	23	0,35,6468	TT,TC,CC		0.3837,0.0454,0.2691	probably-damaging	121/326	77810133	35,12971	2203	4300	6503	SO:0001583	missense	283578	exon4			CGATGTCCCCAGA	AK095650	CCDS32125.1	14q24.3	2005-08-26	2005-08-26	2005-01-07		ENSG00000100580			18633	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member B"", ""transmembrane emp24 domain containing 8"""	FAM15B			Standard	NM_213601		Approved		uc001xto.1	Q6PL24		ENST00000216468.7:c.361G>A	14.37:g.77810133C>T	ENSP00000216468:p.Asp121Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_213601	B3KTI6|Q3MJB0|Q9P1V9	Missense_Mutation	SNP	ENST00000216468.7	37	CCDS32125.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	29.0	4.971209	0.92919	4.54E-4	0.003837	ENSG00000100580	ENST00000216468	T	0.29142	1.58	5.98	5.98	0.97165	.	0.051631	0.85682	D	0.000000	T	0.39682	0.1087	L	0.34521	1.04	0.52099	D	0.999945	D	0.89917	1.0	D	0.83275	0.996	T	0.10359	-1.0633	10	0.36615	T	0.2	-2.0029	20.4293	0.99080	0.0:1.0:0.0:0.0	.	121	Q6PL24	TMED8_HUMAN	N	121	ENSP00000216468:D121N	ENSP00000216468:D121N	D	-	1	0	TMED8	76879886	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	5.026000	0.64103	2.833000	0.97629	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.438	TMED8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414100.1	NM_213601	
MYO16	23026	hgsc.bcm.edu	37	13	109661359	109661359	+	Missense_Mutation	SNP	C	C	G	rs3825491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:109661359C>G	ENST00000357550.2	+	21	2532	c.2491C>G	c.(2491-2493)Cct>Gct	p.P831A	MYO16_ENST00000251041.5_Missense_Mutation_p.P831A|MYO16_ENST00000457511.2_Missense_Mutation_p.P343A|MYO16_ENST00000356711.2_Missense_Mutation_p.P831A	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)			AGCATATTCTCCTGGTAACCA	0.363													C|||	2271	0.453474	0.3139	0.4452	5008	,	,		20533	0.6627		0.3777	False		,,,				2504	0.5102				p.P853A		Atlas-SNP	.											.	MYO16	285	.	0			c.C2557G						PASS	.	C	ALA/PRO,ALA/PRO	1496,2910	477.4+/-357.9	249,998,956	104.0	104.0	104.0		2557,2491	5.7	1.0	13	dbSNP_107	104	3231,5369	486.3+/-371.9	608,2015,1677	yes	missense,missense	MYO16	NM_001198950.1,NM_015011.1	27,27	857,3013,2633	GG,GC,CC		37.5698,33.9537,36.3448	possibly-damaging,possibly-damaging	853/1881,831/1859	109661359	4727,8279	2203	4300	6503	SO:0001583	missense	23026	exon22			TATTCTCCTGGTA		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.2491C>G	13.37:g.109661359C>G	ENSP00000350160:p.Pro831Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	956	0.43772893772893773	134	0.27235772357723576	163	0.45027624309392267	357	0.6241258741258742	302	0.39841688654353563	C	12.91	2.079127	0.36662	0.339537	0.375698	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.180058	0.26522	U	0.023911	T	0.00012	0.0000	L	0.37466	1.105	0.20563	P	0.999888754	P;P;D	0.55172	0.787;0.528;0.97	B;B;P	0.55824	0.302;0.234;0.785	T	0.50808	-0.8784	8	.	.	.	.	19.1034	0.93283	0.0:1.0:0.0:0.0	rs3825491;rs52808554;rs3825491	343;831;831	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	A	831;831;831;831;619;343	ENSP00000349145:P831A;ENSP00000350160:P831A;ENSP00000251041:P831A;ENSP00000401633:P343A	.	P	+	1	0	MYO16	108459360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.690000	0.61731	2.824000	0.97209	0.655000	0.94253	CCT	C|0.610;G|0.390	0.390	strong		0.363	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
KIAA1468	57614	hgsc.bcm.edu	37	18	59936142	59936142	+	Silent	SNP	C	C	T	rs17645999	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	142	0	0		WXS	Illumina HiSeq	Phase_I	164	161	0.981707	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	
DDX60L	91351	hgsc.bcm.edu	37	4	169343044	169343044	+	Missense_Mutation	SNP	A	A	G	rs61740705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169343044A>G	ENST00000511577.1	-	17	2508	c.2261T>C	c.(2260-2262)gTg>gCg	p.V754A	DDX60L_ENST00000505890.1_Missense_Mutation_p.V754A|DDX60L_ENST00000260184.7_Missense_Mutation_p.V754A			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	754	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CTTATCTACCACATCCAGGAG	0.468													A|||	497	0.0992412	0.0113	0.0893	5008	,	,		20966	0.0129		0.2177	False		,,,				2504	0.1922				p.V754A		Atlas-SNP	.											.	DDX60L	116	.	0			c.T2261C						PASS	.	A	ALA/VAL	169,4237	112.1+/-150.2	5,159,2039	159.0	152.0	154.0		2261	4.0	0.6	4	dbSNP_129	154	1676,6924	307.4+/-308.4	155,1366,2779	yes	missense	DDX60L	NM_001012967.1	64	160,1525,4818	GG,GA,AA		19.4884,3.8357,14.1858	benign	754/1707	169343044	1845,11161	2203	4300	6503	SO:0001583	missense	91351	exon17			TCTACCACATCCA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2261T>C	4.37:g.169343044A>G	ENSP00000422423:p.Val754Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		225	0.10302197802197802	10	0.02032520325203252	40	0.11049723756906077	8	0.013986013986013986	167	0.22031662269129287	A	11.32	1.604186	0.28534	0.038357	0.194884	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.31769	2.57;2.57;1.48;1.48	3.96	3.96	0.45880	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.225469	0.21645	U	0.071266	T	0.00012	0.0000	N	0.05230	-0.09	0.46260	P	0.0010430000000000161	P;B;P	0.39601	0.68;0.195;0.68	P;B;P	0.47941	0.562;0.164;0.562	T	0.29912	-0.9996	9	0.27785	T	0.31	.	8.5222	0.33282	0.9019:0.0:0.0981:0.0	.	754;754;754	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	A	754;754;754;482	ENSP00000260184:V754A;ENSP00000422423:V754A;ENSP00000422202:V754A;ENSP00000421026:V482A	ENSP00000260184:V754A	V	-	2	0	DDX60L	169579619	0.998000	0.40836	0.567000	0.28434	0.590000	0.36582	2.887000	0.48586	1.430000	0.47334	0.383000	0.25322	GTG	A|0.878;G|0.122	0.122	strong		0.468	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
CEP68	23177	hgsc.bcm.edu	37	2	65296798	65296798	+	Missense_Mutation	SNP	G	G	A	rs7572857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:65296798G>A	ENST00000377990.2	+	2	423	c.220G>A	c.(220-222)Ggc>Agc	p.G74S	CEP68_ENST00000546106.1_Missense_Mutation_p.G74S|CEP68_ENST00000260569.4_Missense_Mutation_p.G74S|CEP68_ENST00000537589.1_Intron|RAB1A_ENST00000494188.1_5'Flank	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	74			G -> S (in dbSNP:rs7572857). {ECO:0000269|PubMed:15489334}.		centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.G74S(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TGACCCTGGCGGCCCCTCTAG	0.647													G|||	578	0.115415	0.0076	0.1239	5008	,	,		16521	0.0913		0.171	False		,,,				2504	0.2229				p.G74S		Atlas-SNP	.											CEP68,NS,carcinoma,0,1	CEP68	69	1	1	Substitution - Missense(1)	prostate(1)	c.G220A						PASS	.	G	SER/GLY	170,4236	105.2+/-143.6	3,164,2036	33.0	38.0	36.0		220	-5.9	0.0	2	dbSNP_116	36	1514,7086	270.2+/-288.9	142,1230,2928	yes	missense	CEP68	NM_015147.2	56	145,1394,4964	AA,AG,GG		17.6047,3.8584,12.9479	benign	74/758	65296798	1684,11322	2203	4300	6503	SO:0001583	missense	23177	exon2			CCTGGCGGCCCCT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.220G>A	2.37:g.65296798G>A	ENSP00000367229:p.Gly74Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	244	0.11172161172161173	2	0.0040650406504065045	53	0.1464088397790055	55	0.09615384615384616	134	0.17678100263852242	G	4.206	0.036901	0.08148	0.038584	0.176047	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.19105	2.17;2.17;2.17	3.83	-5.92	0.02261	.	0.556823	0.15431	N	0.262729	T	0.00012	0.0000	N	0.03608	-0.345	0.53005	P	4.0000000000040004E-5	B;B;B;B;B	0.21520	0.057;0.057;0.014;0.003;0.057	B;B;B;B;B	0.14578	0.007;0.004;0.004;0.003;0.011	T	0.32561	-0.9902	9	0.11794	T	0.64	.	4.7843	0.13217	0.5233:0.0:0.1875:0.2891	rs7572857;rs17849706;rs17849872;rs52812658;rs60638735;rs7572857	62;74;74;74;74	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	S	74;74;74;62	ENSP00000367229:G74S;ENSP00000438306:G74S;ENSP00000260569:G74S	ENSP00000260569:G74S	G	+	1	0	CEP68	65150302	0.000000	0.05858	0.003000	0.11579	0.077000	0.17291	-1.258000	0.02863	-1.411000	0.02032	-1.012000	0.02466	GGC	G|0.877;A|0.122	0.122	strong		0.647	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
PTPRB	5787	hgsc.bcm.edu	37	12	71016340	71016340	+	Missense_Mutation	SNP	C	C	T	rs7298147	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:71016340C>T	ENST00000550358.1	-	3	563	c.538G>A	c.(538-540)Ggc>Agc	p.G180S	PTPRB_ENST00000551525.1_Missense_Mutation_p.G179S|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.G180S			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	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)			AATACCAGGCCATCTGGAACT	0.493													T|||	99	0.0197684	0.0061	0.0216	5008	,	,		17317	0.0		0.0507	False		,,,				2504	0.0256				p.G180S		Atlas-SNP	.											.	PTPRB	676	.	0			c.G538A						PASS	.	T	SER/GLY	46,3704		0,46,1829	54.0	58.0	57.0		538	2.0	0.0	12	dbSNP_116	57	590,7634		22,546,3544	yes	missense	PTPRB	NM_001109754.2	56	22,592,5373	TT,TC,CC		7.1741,1.2267,5.3115	benign	180/2216	71016340	636,11338	1875	4112	5987	SO:0001583	missense	5787	exon3			CCAGGCCATCTGG	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	ENST00000550358.1:c.538G>A	12.37:g.71016340C>T	ENSP00000448058:p.Gly180Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000550358.1	37		54	0.024725274725274724	8	0.016260162601626018	8	0.022099447513812154	0	0.0	38	0.05013192612137203	T	1.822	-0.472110	0.04445	0.012267	0.071741	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.03889	4.27;4.28;3.77	5.72	2.04	0.26737	.	.	.	.	.	T	0.00178	0.0005	N	0.01874	-0.695	0.09310	N	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	0.47156	-0.9139	9	0.06891	T	0.86	.	5.7236	0.18000	0.0:0.2148:0.1408:0.6444	rs7298147;rs7298147	180;179;180;180	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	S	180;180;180;179	ENSP00000334928:G180S;ENSP00000448058:G180S;ENSP00000448349:G179S	ENSP00000334928:G180S	G	-	1	0	PTPRB	69302607	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	0.393000	0.20817	0.112000	0.17975	-0.254000	0.11334	GGC	C|0.970;T|0.030	0.030	strong		0.493	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1		
SPATA3	130560	hgsc.bcm.edu	37	2	231861059	231861059	+	Silent	SNP	A	A	T	rs72362780		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231861059A>T	ENST00000452881.1	+	1	219	c.111A>T	c.(109-111)ccA>ccT	p.P37P	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Silent_p.P37P|SPATA3_ENST00000455816.1_Silent_p.P37P|SPATA3_ENST00000424440.1_Silent_p.P37P			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	37										endometrium(2)|lung(1)	3						AATCCACACCACAGCAGCCTA	0.572																																					p.P37P		Atlas-SNP	.											SPATA3,NS,carcinoma,0,4	SPATA3	52	4	0			c.A111T						scavenged	.						127.0	133.0	131.0					2																	231861059		692	1591	2283	SO:0001819	synonymous_variant	130560	exon1			CACACCACAGCAG	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.111A>T	2.37:g.231861059A>T		Somatic	67	4	0.0597015		WXS	Illumina HiSeq	Phase_I	47	9	0.191489	NM_139073	Q86WX5|Q8N9Y6	Silent	SNP	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	none		0.572	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
PCSK5	5125	hgsc.bcm.edu	37	9	78910273	78910273	+	Missense_Mutation	SNP	G	G	A	rs2643325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:78910273G>A	ENST00000545128.1	+	26	3806	c.3268G>A	c.(3268-3270)Ggc>Agc	p.G1090S		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1090	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						TAGTAACTGTGGCAGCTGTGA	0.458													G|||	1156	0.230831	0.4039	0.2104	5008	,	,		19073	0.0804		0.2406	False		,,,				2504	0.1564				p.G1090S		Atlas-SNP	.											.	PCSK5	329	.	0			c.G3268A						PASS	.	G	SER/GLY	645,1107		129,387,360	59.0	53.0	55.0		3268	2.6	0.9	9	dbSNP_100	55	878,3104		95,688,1208	yes	missense	PCSK5	NM_001190482.1	56	224,1075,1568	AA,AG,GG		22.0492,36.8151,26.5609		1090/1861	78910273	1523,4211	876	1991	2867	SO:0001583	missense	5125	exon26			AACTGTGGCAGCT		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.3268G>A	9.37:g.78910273G>A	ENSP00000446280:p.Gly1090Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	495	0.22664835164835165	184	0.37398373983739835	88	0.2430939226519337	49	0.08566433566433566	174	0.22955145118733508	G	11.16	1.555625	0.27739	0.368151	0.220492	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.27890	1.64;1.64	5.7	2.62	0.31277	.	0.432040	0.24813	N	0.035390	T	0.00012	0.0000	N	0.16903	0.455	0.37170	P	0.09701800000000005	.	.	.	.	.	.	T	0.42258	-0.9462	7	0.08381	T	0.77	-24.4976	1.1709	0.01825	0.2612:0.1505:0.4331:0.1553	rs2643325;rs60104490	.	.	.	S	1090;793;763	ENSP00000446280:G1090S;ENSP00000411654:G763S	ENSP00000365945:G793S	G	+	1	0	PCSK5	78100093	0.069000	0.21087	0.912000	0.35992	0.905000	0.53344	0.725000	0.25970	0.688000	0.31529	0.655000	0.94253	GGC	G|0.769;A|0.231	0.231	strong		0.458	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NAT2	10	hgsc.bcm.edu	37	8	18258103	18258103	+	Missense_Mutation	SNP	G	G	A	rs1799930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:18258103G>A	ENST00000286479.3	+	2	697	c.590G>A	c.(589-591)cGa>cAa	p.R197Q	NAT2_ENST00000520116.1_Missense_Mutation_p.R67Q	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	197			R -> Q (in allele NAT2*5E, allele NAT2*6A, allele NAT2*6B, allele NAT2*6C, allele NAT2*6D and allele NAT2*14D; a slow acetylator; dbSNP:rs1799930). {ECO:0000269|PubMed:1381364, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16416399, ECO:0000269|Ref.14, ECO:0000269|Ref.8}.		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	CTTGAACCTCGAACAATTGAA	0.363									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				G|||	1327	0.264976	0.2375	0.1715	5008	,	,		18802	0.256		0.2823	False		,,,				2504	0.3599				p.R197Q		Atlas-SNP	.											.	NAT2	34	.	0			c.G590A	GRCh37	CM910270	NAT2	M	rs1799930	PASS	.	G	GLN/ARG	1171,3235	388.6+/-327.0	169,833,1201	87.0	93.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	590	2.5	1.0	8	dbSNP_89	91	2497,6103	403.0+/-347.6	356,1785,2159	yes	missense	NAT2	NM_000015.2	43	525,2618,3360	AA,AG,GG		29.0349,26.5774,28.2024	probably-damaging	197/291	18258103	3668,9338	2203	4300	6503	SO:0001583	missense	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	AACCTCGAACAAT	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.590G>A	8.37:g.18258103G>A	ENSP00000286479:p.Arg197Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Missense_Mutation	SNP	ENST00000286479.3	37	CCDS6008.1	535	0.24496336996336995	130	0.26422764227642276	65	0.17955801104972377	129	0.22552447552447552	211	0.2783641160949868	G	13.33	2.204474	0.38905	0.265774	0.290349	ENSG00000156006	ENST00000286479;ENST00000520116	T;T	0.02140	4.43;4.43	2.51	2.51	0.30379	.	0.074179	0.53938	D	0.000041	T	0.00012	0.0000	M	0.76328	2.33	0.23010	P	0.99843819	D	0.89917	1.0	D	0.78314	0.991	T	0.44050	-0.9353	9	0.51188	T	0.08	.	8.6215	0.33864	0.0:0.0:1.0:0.0	rs1799930;rs4646269;rs17517027;rs17856496;rs60190029;rs1799930	197	A4Z6T7	.	Q	197;67	ENSP00000286479:R197Q;ENSP00000428416:R67Q	ENSP00000286479:R197Q	R	+	2	0	NAT2	18302383	0.068000	0.21057	0.990000	0.47175	0.021000	0.10359	1.291000	0.33330	1.706000	0.51276	0.436000	0.28706	CGA	G|0.742;A|0.258	0.258	strong		0.363	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
NEK10	152110	hgsc.bcm.edu	37	3	27332177	27332177	+	Silent	SNP	T	T	C	rs674303	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	95	0	0		WXS	Illumina HiSeq	Phase_I	114	35	0.307018	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	
CAPN11	11131	hgsc.bcm.edu	37	6	44151490	44151490	+	Missense_Mutation	SNP	G	G	A	rs7761137	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44151490G>A	ENST00000398776.1	+	22	2221	c.2183G>A	c.(2182-2184)aGc>aAc	p.S728N	CAPN11_ENST00000542245.1_Missense_Mutation_p.S728N	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	728	Domain IV.		S -> N (in dbSNP:rs7761137).		proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ATTTGCTTGAGCCTGGAACAG	0.567													A|||	1369	0.273363	0.5862	0.232	5008	,	,		17118	0.0099		0.2256	False		,,,				2504	0.2004				p.S728N		Atlas-SNP	.											.	CAPN11	66	.	0			c.G2183A						PASS	.	A	ASN/SER	1943,1935		483,977,479	59.0	60.0	60.0		2183	1.8	0.0	6	dbSNP_116	60	1934,6366		222,1490,2438	yes	missense	CAPN11	NM_007058.3	46	705,2467,2917	AA,AG,GG		23.3012,49.8969,31.8361	benign	728/740	44151490	3877,8301	1939	4150	6089	SO:0001583	missense	11131	exon22			GCTTGAGCCTGGA	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.2183G>A	6.37:g.44151490G>A	ENSP00000381758:p.Ser728Asn	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	532	0.24358974358974358	274	0.556910569105691	88	0.2430939226519337	2	0.0034965034965034965	168	0.22163588390501318	A	2.406	-0.336407	0.05278	0.501031	0.233012	ENSG00000137225	ENST00000398776;ENST00000542245	T;T	0.29917	1.55;1.55	4.28	1.82	0.25136	EF-hand-like domain (1);	0.750513	0.11867	N	0.521786	T	0.02342	0.0072	N	0.02685	-0.53	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	9	0.02654	T	1	.	4.4802	0.11764	0.6492:0.1676:0.1833:0.0	rs7761137;rs61438246;rs7761137	728	Q9UMQ6	CAN11_HUMAN	N	728	ENSP00000381758:S728N;ENSP00000441078:S728N	ENSP00000381758:S728N	S	+	2	0	CAPN11	44259468	0.894000	0.30519	0.000000	0.03702	0.644000	0.38419	0.549000	0.23329	0.082000	0.17018	-0.321000	0.08615	AGC	G|0.721;A|0.279	0.279	strong		0.567	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
NACAD	23148	hgsc.bcm.edu	37	7	45120248	45120248	+	Silent	SNP	G	G	A	rs1132130	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:45120248G>A	ENST00000490531.2	-	7	4684	c.4665C>T	c.(4663-4665)aaC>aaT	p.N1555N		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1555					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CCATGATGGCGTTGACGATGT	0.622													G|||	539	0.107628	0.0166	0.1657	5008	,	,		20196	0.1081		0.173	False		,,,				2504	0.1217				p.N1555N		Atlas-SNP	.											.	NACAD	44	.	0			c.C4665T						PASS	.	G		49,1335		0,49,643	191.0	195.0	194.0		4665	-4.9	1.0	7	dbSNP_86	194	595,2587		48,499,1044	no	coding-synonymous	NACAD	NM_001146334.1		48,548,1687	AA,AG,GG		18.6989,3.5405,14.1042		1555/1563	45120248	644,3922	692	1591	2283	SO:0001819	synonymous_variant	23148	exon7			GATGGCGTTGACG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.4665C>T	7.37:g.45120248G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	283	77	0.272085	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			G|0.875;C|0.000;A|0.124	0.124	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
MIOX	55586	hgsc.bcm.edu	37	22	50928026	50928026	+	Silent	SNP	G	G	A	rs2232885	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50928026G>A	ENST00000216075.6	+	9	776	c.702G>A	c.(700-702)ctG>ctA	p.L234L	MIOX_ENST00000395732.3_Silent_p.L234L|MIOX_ENST00000395733.3_Intron	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	234					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|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)		ACCAGCAGCTGTGCAGCCAGC	0.662													g|||	989	0.197484	0.1225	0.2176	5008	,	,		8343	0.3125		0.2137	False		,,,				2504	0.1493				p.L234L		Atlas-SNP	.											.	MIOX	21	.	0			c.G702A						PASS	.	G		654,3740		49,556,1592	24.0	25.0	24.0		702	3.0	1.0	22	dbSNP_98	24	1859,6725		207,1445,2640	no	coding-synonymous	MIOX	NM_017584.5		256,2001,4232	AA,AG,GG		21.6566,14.8839,19.3635		234/286	50928026	2513,10465	2197	4292	6489	SO:0001819	synonymous_variant	55586	exon9			GCAGCTGTGCAGC	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.702G>A	22.37:g.50928026G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1																																																																																			G|0.798;A|0.202	0.202	strong		0.662	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
TRIM51	84767	hgsc.bcm.edu	37	11	55653617	55653617	+	Missense_Mutation	SNP	A	A	C	rs144396749	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55653617A>C	ENST00000449290.2	+	3	522	c.430A>C	c.(430-432)Atg>Ctg	p.M144L	TRIM51_ENST00000244891.3_Start_Codon_SNP_p.M1L	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	144						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										CCTAAAAAAAATGCAGTCTTT	0.403													N|||	44	0.00878594	0.0008	0.0173	5008	,	,		16943	0.0		0.0298	False		,,,				2504	0.001				p.M144L		Atlas-SNP	.											.	.	.	.	0			c.A430C						PASS	.	A	LEU/MET	30,4372		0,30,2171	51.0	53.0	52.0		430		0.0	11	dbSNP_134	52	376,8216		9,358,3929	no	missense	SPRYD5	NM_032681.3	15	9,388,6100	CC,CA,AA		4.3762,0.6815,3.1245	possibly-damaging	144/453	55653617	406,12588	2201	4296	6497	SO:0001583	missense	84767	exon3			AAAAAAATGCAGT	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.430A>C	11.37:g.55653617A>C	ENSP00000395086:p.Met144Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	138	75	0.543478	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		26	0.011904761904761904	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	19	0.025065963060686015	.	5.218	0.225717	0.09916	0.006815	0.043762	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.50001	0.76;0.78	.	.	.	.	.	.	.	.	T	0.15046	0.0363	M	0.71581	2.175	0.80722	D	1	B	0.14805	0.011	B	0.21151	0.033	T	0.15665	-1.0429	7	0.37606	T	0.19	.	.	.	.	.	144	Q9BSJ1	SPRY5_HUMAN	L	144;1	ENSP00000395086:M144L;ENSP00000244891:M1L	ENSP00000244891:M1L	M	+	1	0	SPRYD5	55410193	0.002000	0.14202	0.019000	0.16419	0.091000	0.18340	-0.667000	0.05274	0.415000	0.25817	0.128000	0.15822	ATG	A|0.984;C|0.016	0.016	strong		0.403	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
GP6	51206	hgsc.bcm.edu	37	19	55539049	55539049	+	Silent	SNP	C	C	T	rs5030705	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55539049C>T	ENST00000417454.1	-	4	534	c.507G>A	c.(505-507)acG>acA	p.T169T	CTC-550B14.7_ENST00000586961.1_RNA|GP6_ENST00000310373.3_Silent_p.T169T|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.T169T|CTC-550B14.6_ENST00000585492.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	169	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		CGGCGGTCACCGTGATGATGG	0.587													C|||	430	0.0858626	0.0151	0.1354	5008	,	,		15104	0.0308		0.2376	False		,,,				2504	0.047				p.T169T		Atlas-SNP	.											.	GP6	55	.	0			c.G507A						PASS	.	C	,	168,3808		6,156,1826	60.0	66.0	64.0		507,507	-8.0	0.0	19	dbSNP_113	64	1697,6651		179,1339,2656	no	coding-synonymous,coding-synonymous	GP6	NM_001083899.1,NM_016363.4	,	185,1495,4482	TT,TC,CC		20.3282,4.2254,15.1331	,	169/621,169/340	55539049	1865,10459	1988	4174	6162	SO:0001819	synonymous_variant	51206	exon4			GGTCACCGTGATG	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.507G>A	19.37:g.55539049C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_016363	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			C|0.847;T|0.153	0.153	strong		0.587	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
ITGA2	3673	hgsc.bcm.edu	37	5	52379277	52379277	+	Silent	SNP	C	C	T	rs2303122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	67	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	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	
ANKRD16	54522	hgsc.bcm.edu	37	10	5929962	5929962	+	Missense_Mutation	SNP	G	G	C	rs2296136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5929962G>C	ENST00000380094.5	-	2	926	c.383C>G	c.(382-384)gCc>gGc	p.A128G	FBXO18_ENST00000397269.3_5'Flank|ANKRD16_ENST00000191063.8_Missense_Mutation_p.A128G|FBXO18_ENST00000362091.4_5'Flank|ANKRD16_ENST00000380092.4_Missense_Mutation_p.A128G	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	128			A -> G (in dbSNP:rs2296136).					p.A128G(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						GAGTGGATTGGCGCCATGTTC	0.547													G|||	303	0.0605032	0.0008	0.0346	5008	,	,		15276	0.1429		0.0368	False		,,,				2504	0.0992				p.A128G		Atlas-SNP	.											ANKRD16,NS,carcinoma,0,1	ANKRD16	32	1	1	Substitution - Missense(1)	stomach(1)	c.C383G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	44,4362	46.7+/-81.2	0,44,2159	142.0	139.0	140.0		383,383,383	2.9	0.1	10	dbSNP_100	140	300,8300	109.0+/-169.6	1,298,4001	yes	missense,missense,missense	ANKRD16	NM_001009941.2,NM_001009943.2,NM_019046.2	60,60,60	1,342,6160	CC,CG,GG		3.4884,0.9986,2.6449	probably-damaging,probably-damaging,probably-damaging	128/362,128/305,128/362	5929962	344,12662	2203	4300	6503	SO:0001583	missense	54522	exon2			GGATTGGCGCCAT	AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"""Ankyrin repeat domain containing"""	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.383C>G	10.37:g.5929962G>C	ENSP00000369436:p.Ala128Gly	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_001009943	A6NEF0|F8WEI4|Q9NT01	Missense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	111	0.050824175824175824	1	0.0020325203252032522	11	0.03038674033149171	68	0.11888111888111888	31	0.040897097625329816	G	19.12	3.766762	0.69878	0.009986	0.034884	ENSG00000134461	ENST00000380094;ENST00000380092;ENST00000191063	T;T;T	0.76578	1.77;1.77;-1.03	4.85	2.94	0.34122	Ankyrin repeat-containing domain (4);	0.053190	0.85682	N	0.000000	T	0.08758	0.0217	M	0.79614	2.46	0.52099	D	0.999947	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.998	T	0.52786	-0.8529	10	0.62326	D	0.03	-13.0387	9.1617	0.37028	0.0778:0.0:0.7757:0.1466	rs2296136;rs52827967;rs2296136	128;128;128	Q6P6B7;C9JP28;F8WEI4	ANR16_HUMAN;.;.	G	128	ENSP00000369436:A128G;ENSP00000369434:A128G;ENSP00000352361:A128G	ENSP00000352361:A128G	A	-	2	0	ANKRD16	5969968	1.000000	0.71417	0.118000	0.21660	0.829000	0.46940	7.554000	0.82212	0.554000	0.29061	0.558000	0.71614	GCC	G|0.965;C|0.035	0.035	strong		0.547	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138	
PIK3R1	5295	hgsc.bcm.edu	37	5	67522722	67522722	+	Silent	SNP	C	C	T	rs706713	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:67522722C>T	ENST00000521381.1	+	2	835	c.219C>T	c.(217-219)taC>taT	p.Y73Y	PIK3R1_ENST00000274335.5_Silent_p.Y73Y|PIK3R1_ENST00000521657.1_Silent_p.Y73Y|PIK3R1_ENST00000396611.1_Silent_p.Y73Y	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	73	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CGGGAACTTACGTAGAATATA	0.498			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)			T|||	2100	0.419329	0.4425	0.3602	5008	,	,		16257	0.6746		0.2455	False		,,,				2504	0.3456				p.Y73Y		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	PIK3R1	869	.	1	Whole gene deletion(1)	large_intestine(1)	c.C219T						PASS	.	T		1803,2603	606.6+/-390.8	360,1083,760	45.0	56.0	53.0		219	-9.6	0.2	5	dbSNP_86	53	2012,6588	713.3+/-405.9	256,1500,2544	no	coding-synonymous	PIK3R1	NM_181523.2		616,2583,3304	TT,TC,CC		23.3953,40.9215,29.3326		73/725	67522722	3815,9191	2203	4300	6503	SO:0001819	synonymous_variant	5295	exon2			AACTTACGTAGAA	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.219C>T	5.37:g.67522722C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																			C|0.633;T|0.367	0.367	strong		0.498	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
GZMB	3002	hgsc.bcm.edu	37	14	25101548	25101548	+	Silent	SNP	G	G	A	rs1126639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:25101548G>A	ENST00000216341.4	-	3	427	c.321C>T	c.(319-321)aaC>aaT	p.N107N	RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000526004.1_Intron|GZMB_ENST00000415355.3_Silent_p.N95N|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Silent_p.N141N			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	107	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.N107N(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GCATGATGTCGTTGGAGAAGT	0.542													G|||	1514	0.302316	0.3775	0.2118	5008	,	,		17994	0.2867		0.2475	False		,,,				2504	0.3374				p.N107N		Atlas-SNP	.											GZMB_ENST00000382542,brain,glioma,0,3	GZMB	73	3	1	Substitution - coding silent(1)	stomach(1)	c.C321T						PASS	.						130.0	147.0	142.0					14																	25101548		2203	4297	6500	SO:0001819	synonymous_variant	3002	exon3			GATGTCGTTGGAG	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.321C>T	14.37:g.25101548G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	127	116	0.913386	NM_004131	Q8N1D2|Q9UCC1	Silent	SNP	ENST00000216341.4	37	CCDS9633.1																																																																																			G|0.721;A|0.279	0.279	strong		0.542	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
OR51B6	390058	hgsc.bcm.edu	37	11	5373104	5373104	+	Missense_Mutation	SNP	A	A	G	rs5006889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373104A>G	ENST00000380219.1	+	1	367	c.367A>G	c.(367-369)Acc>Gcc	p.T123A	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	123			T -> A (in dbSNP:rs5006889).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	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)		CTGTTTCATTACCATCCGCAG	0.483													G|||	1170	0.233626	0.326	0.2349	5008	,	,		22992	0.0863		0.2644	False		,,,				2504	0.228				p.T123A		Atlas-SNP	.											.	OR51B6	53	.	0			c.A367G						PASS	.	G	ALA/THR	1247,3155	699.6+/-406.5	173,901,1127	136.0	125.0	129.0		367	5.0	1.0	11	dbSNP_113	129	2238,6356	707.6+/-405.6	309,1620,2368	yes	missense	OR51B6	NM_001004750.1	58	482,2521,3495	GG,GA,AA		26.0414,28.328,26.8159	benign	123/313	5373104	3485,9511	2201	4297	6498	SO:0001583	missense	390058	exon1			TTCATTACCATCC		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.367A>G	11.37:g.5373104A>G	ENSP00000369568:p.Thr123Ala	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	164	59	0.359756	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	G	0.018	-1.478016	0.01035	0.28328	0.260414	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.24723	1.84	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	N	0.000063	T	0.00012	0.0000	N	0.00001	-3.785	0.39348	P	0.03429300000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.43637	-0.9379	9	0.02654	T	1	.	12.5381	0.56152	0.0813:0.0:0.9187:0.0	rs5006889;rs5006889	123	Q9H340	O51B6_HUMAN	A	122;123	ENSP00000369568:T123A	ENSP00000369568:T123A	T	+	1	0	OR51B6	5329680	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	5.415000	0.66411	1.352000	0.45808	-0.374000	0.07098	ACC	A|0.761;G|0.239	0.239	strong		0.483	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20864342	20864342	+	Missense_Mutation	SNP	C	C	A	rs36010656	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:20864342C>A	ENST00000266509.2	+	5	795	c.427C>A	c.(427-429)Cct>Act	p.P143T	SLCO1C1_ENST00000545102.1_Missense_Mutation_p.P25T|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.P143T|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.P143T|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.P143T	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	143					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	GAGATATTCTCCTTCCTCCAA	0.353													C|||	106	0.0211661	0.003	0.0519	5008	,	,		19517	0.0		0.0596	False		,,,				2504	0.0061				p.P143T		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C427A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO,THR/PRO	42,4364	47.5+/-82.1	1,40,2162	137.0	130.0	132.0		73,427,427,427	-0.1	0.0	12	dbSNP_126	132	475,8125	138.6+/-195.4	9,457,3834	yes	missense,missense,missense,missense	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	38,38,38,38	10,497,5996	AA,AC,CC		5.5233,0.9532,3.9751	benign,benign,benign,benign	25/613,143/664,143/731,143/713	20864342	517,12489	2203	4300	6503	SO:0001583	missense	53919	exon5			TATTCTCCTTCCT	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.427C>A	12.37:g.20864342C>A	ENSP00000266509:p.Pro143Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	69	0.03159340659340659	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	48	0.0633245382585752	C	7.596	0.671858	0.14776	0.009532	0.055233	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	4.08	-0.113	0.13568	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.021380	0.07801	N	0.956482	T	0.01592	0.0051	N	0.11673	0.155	0.19575	N	0.999961	B;B;B;B	0.21753	0.011;0.045;0.06;0.022	B;B;B;B	0.25405	0.018;0.028;0.06;0.06	T	0.20472	-1.0274	10	0.07030	T	0.85	.	4.4394	0.11566	0.0:0.3193:0.1758:0.5049	rs36010656	25;143;143;143	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	T	143;143;143;143;25	ENSP00000444149:P143T;ENSP00000438665:P143T;ENSP00000266509:P143T;ENSP00000370964:P143T;ENSP00000444527:P25T	ENSP00000266509:P143T	P	+	1	0	SLCO1C1	20755609	0.507000	0.26146	0.012000	0.15200	0.814000	0.46013	0.001000	0.13038	-0.239000	0.09710	-0.345000	0.07892	CCT	C|0.961;A|0.039	0.039	strong		0.353	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
PYGB	5834	hgsc.bcm.edu	37	20	25275621	25275621	+	Intron	SNP	T	T	C	rs73598373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25275621T>C	ENST00000216962.4	+	19	2422				PYGB_ENST00000471359.1_Intron|ABHD12_ENST00000376542.3_Silent_p.S401S	NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain						carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						ACACCAGCTCTGACCACATGC	0.502											OREG0025844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	279	0.0557109	0.0817	0.0476	5008	,	,		19172	0.0665		0.0537	False		,,,				2504	0.0174				p.S401S		Atlas-SNP	.											.	ABHD12	46	.	0			c.A1203G						PASS	.	T	,	315,4091	169.1+/-199.8	8,299,1896	145.0	141.0	142.0		,1203	-3.7	0.0	20	dbSNP_130	142	367,8233	121.8+/-180.9	6,355,3939	no	intron,coding-synonymous	PYGB,ABHD12	NM_002862.3,NM_015600.4	,	14,654,5835	CC,CT,TT		4.2674,7.1493,5.2437	,	,401/405	25275621	682,12324	2203	4300	6503	SO:0001627	intron_variant	26090	exon13			CAGCTCTGACCAC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.2313-619T>C	20.37:g.25275621T>C		Somatic	92	0	0	777	WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_015600	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			T|0.945;C|0.055	0.055	strong		0.502	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487174	32487174	+	Missense_Mutation	SNP	C	C	G	rs112872773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32487174C>G	ENST00000374975.3	-	3	687	c.625G>C	c.(625-627)Gtg>Ctg	p.V209L		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						GGGCTCGTCACGCTTGGGTGC	0.498													C|||	573	0.114417	0.0454	0.2104	5008	,	,		12481	0.121		0.16	False		,,,				2504	0.0859				p.V209L		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G625C						PASS	.	C	LEU/VAL	203,3581		25,153,1714	73.0	83.0	80.0		625	-3.6	0.0	6	dbSNP_132	80	1085,6435		126,833,2801	no	missense	HLA-DRB5	NM_002125.3	32	151,986,4515	GG,GC,CC		14.4282,5.3647,11.3942	benign	209/267	32487174	1288,10016	1892	3760	5652	SO:0001583	missense	3127	exon3			TCGTCACGCTTGG		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.625G>C	6.37:g.32487174C>G	ENSP00000364114:p.Val209Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	89	0.609589	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	0.979	-0.697691	0.03279	0.053647	0.144282	ENSG00000198502	ENST00000374975	T	0.01629	4.72	4.36	-3.57	0.04612	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.816604	0.11096	N	0.600213	T	0.00073	0.0002	N	0.00008	-3.11	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.38950	-0.9637	9	0.14656	T	0.56	.	1.4755	0.02425	0.3123:0.2462:0.3234:0.118	.	136;209	Q29973;Q30154	.;DRB5_HUMAN	L	209	ENSP00000364114:V209L	ENSP00000364114:V209L	V	-	1	0	HLA-DRB5	32595152	0.507000	0.26146	0.000000	0.03702	0.022000	0.10575	0.581000	0.23819	-0.961000	0.03609	-0.321000	0.08615	GTG	C|0.859;G|0.120;T|0.021	0.120	strong		0.498	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
PPFIA1	8500	hgsc.bcm.edu	37	11	70200529	70200529	+	Silent	SNP	C	C	T	rs17853270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70200529C>T	ENST00000253925.7	+	17	2501	c.2286C>T	c.(2284-2286)gtC>gtT	p.V762V	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Silent_p.V762V	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	762					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGCACACCGTCAGCCACGAGG	0.552													C|||	655	0.130791	0.2194	0.2003	5008	,	,		16140	0.0407		0.1223	False		,,,				2504	0.0634				p.V762V		Atlas-SNP	.											.	PPFIA1	114	.	0			c.C2286T						PASS	.	C	,	870,3530	334.9+/-303.7	88,694,1418	45.0	40.0	42.0		2286,2286	2.4	1.0	11	dbSNP_123	42	1038,7550	220.2+/-258.0	65,908,3321	no	coding-synonymous,coding-synonymous	PPFIA1	NM_003626.2,NM_177423.1	,	153,1602,4739	TT,TC,CC		12.0866,19.7727,14.6905	,	762/1203,762/1186	70200529	1908,11080	2200	4294	6494	SO:0001819	synonymous_variant	8500	exon17			CACCGTCAGCCAC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2286C>T	11.37:g.70200529C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Silent	SNP	ENST00000253925.7	37	CCDS31627.1	289|289	0.13232600732600733|0.13232600732600733	108|108	0.21951219512195122|0.21951219512195122	62|62	0.1712707182320442|0.1712707182320442	27|27	0.0472027972027972|0.0472027972027972	92|92	0.12137203166226913|0.12137203166226913	C|C	10.55|10.55	1.380523|1.380523	0.24944|0.24944	0.197727|0.197727	0.120866|0.120866	ENSG00000131626|ENSG00000131626	ENST00000530798|ENST00000528750	.|.	.|.	.|.	5.36|5.36	2.36|2.36	0.29203|0.29203	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999256|0.9999999999999256	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.20472	.|-1.0274	.|3	.|.	.|.	.|.	.|.	4.0275|4.0275	0.09693|0.09693	0.1192:0.4429:0.3422:0.0956|0.1192:0.4429:0.3422:0.0956	rs17853270|rs17853270	.|.	.|.	.|.	X|L	155|205	.|.	.|.	Q|S	+|+	1|2	0|0	PPFIA1|PPFIA1	69878177|69878177	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.859000|0.859000	0.49053|0.49053	2.049000|2.049000	0.41288|0.41288	1.281000|1.281000	0.44480|0.44480	0.561000|0.561000	0.74099|0.74099	CAG|TCA	C|0.855;T|0.145	0.145	strong		0.552	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
SMARCA4	6597	hgsc.bcm.edu	37	19	11170839	11170839	+	Silent	SNP	T	T	C	rs7275	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11170839T>C	ENST00000429416.3	+	35	5168	c.4887T>C	c.(4885-4887)gaT>gaC	p.D1629D	SMARCA4_ENST00000358026.2_Silent_p.D1661D|SMARCA4_ENST00000589677.1_Silent_p.D1598D|SMARCA4_ENST00000590574.1_Silent_p.D1596D|SMARCA4_ENST00000444061.3_Silent_p.D1595D|SMARCA4_ENST00000413806.3_Silent_p.D1599D|SMARCA4_ENST00000541122.2_Silent_p.D1599D|SMARCA4_ENST00000344626.4_Silent_p.D1629D|SMARCA4_ENST00000450717.3_Silent_p.D1598D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1629					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)				TGAGTGACGATGACAGTGAGG	0.687			"""F, N, Mis"""		NSCLC								C|||	1251	0.2498	0.3094	0.1715	5008	,	,		14726	0.0724		0.2942	False		,,,				2504	0.362				p.D1661D		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,caecum,carcinoma,0,2	SMARCA4	502	2	1	Unknown(1)	lung(1)	c.T4983C						PASS	.	C	,,,,,,	1060,2890		143,774,1058	26.0	31.0	29.0		4887,4797,4794,4788,4785,4983,4887	-5.1	0.0	19	dbSNP_52	29	1961,5729		253,1455,2137	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	,,,,,,	396,2229,3195	CC,CT,TT		25.5007,26.8354,25.9536	,,,,,,	1629/1648,1599/1618,1598/1617,1596/1615,1595/1614,1661/1680,1629/1648	11170839	3021,8619	1975	3845	5820	SO:0001819	synonymous_variant	6597	exon35			TGACGATGACAGT	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.4887T>C	19.37:g.11170839T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_001128849	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			T|0.776;C|0.224	0.224	strong		0.687	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
DNA2	1763	hgsc.bcm.edu	37	10	70191631	70191631	+	Silent	SNP	C	C	T	rs61855090	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:70191631C>T	ENST00000358410.3	-	13	2021	c.1971G>A	c.(1969-1971)acG>acA	p.T657T	DNA2_ENST00000399179.2_Silent_p.T657T|DNA2_ENST00000399180.2_Silent_p.T743T	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	75	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	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		
DCPS	28960	hgsc.bcm.edu	37	11	126174038	126174038	+	Silent	SNP	C	C	T	rs3740915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	39	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	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	
SULT2B1	6820	hgsc.bcm.edu	37	19	49079246	49079246	+	Silent	SNP	C	C	T	rs2544794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:49079246C>T	ENST00000201586.2	+	2	298	c.120C>T	c.(118-120)ccC>ccT	p.P40P	SULT2B1_ENST00000323090.4_Silent_p.P25P	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	40					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		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;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		TCCCCTTCCCCGTCGGCCTGT	0.587													C|||	652	0.130192	0.23	0.1023	5008	,	,		14059	0.003		0.1481	False		,,,				2504	0.1278				p.P40P		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C120T						PASS	.	C	,	1010,3396	373.7+/-320.9	119,772,1312	150.0	117.0	128.0		75,120	-5.5	0.0	19	dbSNP_100	128	1396,7204	271.1+/-289.3	125,1146,3029	no	coding-synonymous,coding-synonymous	SULT2B1	NM_004605.2,NM_177973.1	,	244,1918,4341	TT,TC,CC		16.2326,22.9233,18.4992	,	25/351,40/366	49079246	2406,10600	2203	4300	6503	SO:0001819	synonymous_variant	6820	exon2			CTTCCCCGTCGGC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.120C>T	19.37:g.49079246C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_177973	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																			C|0.852;T|0.148	0.148	strong		0.587	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
KIF19	124602	hgsc.bcm.edu	37	17	72349067	72349067	+	Silent	SNP	C	C	T	rs2280108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	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	
TRIM63	84676	hgsc.bcm.edu	37	1	26385003	26385003	+	Missense_Mutation	SNP	T	T	C	rs2275950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	130	0	0		WXS	Illumina HiSeq	Phase_I	172	172	1	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	
PRRT3	285368	hgsc.bcm.edu	37	3	9990800	9990800	+	Missense_Mutation	SNP	G	G	C	rs59465469	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9990800G>C	ENST00000412055.1	-	2	1129	c.1000C>G	c.(1000-1002)Cgg>Ggg	p.R334G	PRRT3-AS1_ENST00000431558.1_RNA|PRRT3_ENST00000411976.2_Missense_Mutation_p.R334G	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	34	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	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	
FNDC4	64838	hgsc.bcm.edu	37	2	27716823	27716823	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:27716823C>T	ENST00000264703.3	-	4	819	c.428G>A	c.(427-429)cGg>cAg	p.R143Q	GCKR_ENST00000424318.2_5'Flank|GCKR_ENST00000264717.2_5'Flank	NM_022823.2	NP_073734.1	Q9H6D8	FNDC4_HUMAN	fibronectin type III domain containing 4	143						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|prostate(1)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TGAAGGTAGCCGGTCAGAACC	0.562																																					p.R143Q		Atlas-SNP	.											FNDC4,NS,carcinoma,-1,1	FNDC4	21	1	0			c.G428A						PASS	.						75.0	81.0	79.0					2																	27716823		2203	4300	6503	SO:0001583	missense	64838	exon4			GGTAGCCGGTCAG	AK026015	CCDS1756.1	2p23.3	2013-02-11			ENSG00000115226	ENSG00000115226		"""Fibronectin type III domain containing"""	20239	protein-coding gene	gene with protein product		611905				12384288	Standard	NM_022823		Approved	FLJ22362, FRCP1	uc002rkx.3	Q9H6D8	OTTHUMG00000097787	ENST00000264703.3:c.428G>A	2.37:g.27716823C>T	ENSP00000264703:p.Arg143Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	24	0.315789	NM_022823	D6W560	Missense_Mutation	SNP	ENST00000264703.3	37	CCDS1756.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129221	0.37533	.	.	ENSG00000115226	ENST00000264703	T	0.07444	3.19	5.46	3.68	0.42216	.	0.057087	0.64402	D	0.000002	T	0.04092	0.0114	N	0.24115	0.695	0.44660	D	0.997647	P	0.41710	0.76	B	0.26770	0.073	T	0.54200	-0.8329	10	0.28530	T	0.3	-10.0669	8.5567	0.33485	0.0:0.7609:0.0:0.2391	.	143	Q9H6D8	FNDC4_HUMAN	Q	143	ENSP00000264703:R143Q	ENSP00000264703:R143Q	R	-	2	0	FNDC4	27570327	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.017000	0.40981	0.682000	0.31407	-0.244000	0.11960	CGG	.	.	none		0.562	FNDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215031.1	NM_022823	
RIC3	79608	hgsc.bcm.edu	37	11	8159892	8159892	+	Silent	SNP	G	G	T	rs10839976	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8159892G>T	ENST00000309737.6	-	3	353	c.354C>A	c.(352-354)ctC>ctA	p.L118L	RIC3_ENST00000539720.1_Silent_p.L69L|RIC3_ENST00000425599.2_Silent_p.L118L|RIC3_ENST00000335425.7_Intron|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000343202.4_Silent_p.L118L			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	118					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCCCCTTTGAGAGCTGAGAAT	0.433													G|||	1520	0.303514	0.2799	0.3444	5008	,	,		16372	0.4196		0.2197	False		,,,				2504	0.273				p.L118L		Atlas-SNP	.											.	RIC3	42	.	0			c.C354A						PASS	.	G	,,,	1189,3213	415.7+/-337.3	155,879,1167	203.0	196.0	198.0		,354,354,354	-1.8	1.0	11	dbSNP_120	198	2007,6585	351.5+/-328.3	234,1539,2523	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,,,	389,2418,3690	TT,TG,GG		23.3589,27.0104,24.596	,,,	,118/370,118/289,118/369	8159892	3196,9798	2201	4296	6497	SO:0001819	synonymous_variant	79608	exon3			CTTTGAGAGCTGA		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.354C>A	11.37:g.8159892G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Silent	SNP	ENST00000309737.6	37	CCDS55742.1																																																																																			G|0.727;T|0.273	0.273	strong		0.433	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037557	33037557	+	Silent	SNP	C	C	T	rs1042177	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33037557C>T	ENST00000419277.1	-	3	336	c.207G>A	c.(205-207)aaG>aaA	p.K69K	HLA-DPA1_ENST00000428995.1_Silent_p.K69K|HLA-DPA1_ENST00000463066.1_5'UTR	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	116	0	0		WXS	Illumina HiSeq	Phase_I	131	47	0.358779	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	
ZGRF1	55345	hgsc.bcm.edu	37	4	113539969	113539969	+	Missense_Mutation	SNP	T	T	C	rs7696816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:113539969T>C	ENST00000505019.1	-	6	1354	c.1229A>G	c.(1228-1230)aAt>aGt	p.N410S	C4orf21_ENST00000309071.5_Missense_Mutation_p.N410S|C4orf21_ENST00000445203.2_Missense_Mutation_p.N379S	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		410			N -> S (in dbSNP:rs7696816).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ACTGCTTTCATTGAATGAAGG	0.333													T|||	2092	0.417732	0.3003	0.5086	5008	,	,		20068	0.4117		0.4284	False		,,,				2504	0.5072				p.N410S		Atlas-SNP	.											.	C4orf21	223	.	0			c.A1229G						PASS	.	T	SER/ASN	1433,2973	455.5+/-351.0	234,965,1004	89.0	89.0	89.0		1229	-0.2	0.0	4	dbSNP_116	89	3647,4953	521.4+/-379.9	755,2137,1408	yes	missense	C4orf21	NM_018392.4	46	989,3102,2412	CC,CT,TT		42.407,32.5238,39.0589	benign	410/2105	113539969	5080,7926	2203	4300	6503	SO:0001583	missense	55345	exon6			CTTTCATTGAATG																												ENST00000505019.1:c.1229A>G	4.37:g.113539969T>C	ENSP00000424737:p.Asn410Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		905	0.4143772893772894	153	0.31097560975609756	181	0.5	245	0.42832167832167833	326	0.43007915567282323	T	0.008	-1.932518	0.00488	0.325238	0.42407	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	T;T;T	0.81163	-1.46;2.03;1.62	5.05	-0.147	0.13428	.	1.081160	0.07099	N	0.840098	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	0.30592	-0.9973	9	0.02654	T	1	1.4592	1.4742	0.02422	0.1541:0.4062:0.2096:0.2301	rs7696816;rs52796218;rs56876657;rs7696816	410;410	Q86YA3;G5EA02	CD021_HUMAN;.	S	410;410;379	ENSP00000424737:N410S;ENSP00000309095:N410S;ENSP00000390505:N379S	ENSP00000309095:N410S	N	-	2	0	C4orf21	113759418	0.000000	0.05858	0.011000	0.14972	0.022000	0.10575	-1.654000	0.01984	0.149000	0.19098	-1.022000	0.02435	AAT	T|0.598;C|0.402	0.402	strong		0.333	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
FOXN2	3344	hgsc.bcm.edu	37	2	48573875	48573875	+	Silent	SNP	A	A	G	rs35742253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48573875A>G	ENST00000340553.3	+	3	783	c.522A>G	c.(520-522)gaA>gaG	p.E174E		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	174					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			AGAAAGTGGAAAGAAGCCATG	0.418													A|||	16	0.00319489	0.0008	0.0072	5008	,	,		16893	0.0		0.0099	False		,,,				2504	0.0				p.E174E		Atlas-SNP	.											.	FOXN2	39	.	0			c.A522G						PASS	.	A		13,4363		1,11,2176	52.0	54.0	53.0		522	2.9	1.0	2	dbSNP_126	53	91,8483		0,91,4196	no	coding-synonymous	FOXN2	NM_002158.3		1,102,6372	GG,GA,AA		1.0613,0.2971,0.8031		174/432	48573875	104,12846	2188	4287	6475	SO:0001819	synonymous_variant	3344	exon3			AGTGGAAAGAAGC		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"""Forkhead boxes"""	5281	protein-coding gene	gene with protein product		143089	"""human T-cell leukemia virus enhancer factor"""	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.522A>G	2.37:g.48573875A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_002158	Q15769|Q6P4Q2	Silent	SNP	ENST00000340553.3	37	CCDS1838.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158	
XKR8	55113	hgsc.bcm.edu	37	1	28290132	28290132	+	Silent	SNP	T	T	C	rs61743136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:28290132T>C	ENST00000373884.5	+	2	1026	c.418T>C	c.(418-420)Ttg>Ctg	p.L140L		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	140					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		CGAGACCTTCTTGGAGACGGC	0.632													T|||	40	0.00798722	0.0129	0.0101	5008	,	,		17747	0.0		0.0159	False		,,,				2504	0.0				p.L140L		Atlas-SNP	.											.	XKR8	15	.	0			c.T418C						PASS	.	T		79,4327	64.7+/-102.0	1,77,2125	29.0	25.0	27.0		418	-3.5	0.9	1	dbSNP_129	27	90,8510	47.2+/-106.3	0,90,4210	no	coding-synonymous	XKR8	NM_018053.2		1,167,6335	CC,CT,TT		1.0465,1.793,1.2994		140/396	28290132	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			ACCTTCTTGGAGA	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.418T>C	1.37:g.28290132T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			T|0.987;C|0.013	0.013	strong		0.632	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65209867	65209867	+	Missense_Mutation	SNP	C	C	T	rs229649	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:65209867C>T	ENST00000394691.1	+	17	3253	c.3106C>T	c.(3106-3108)Cgg>Tgg	p.R1036W	PLEKHG3_ENST00000484731.2_Missense_Mutation_p.R541W|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.R980W|PLEKHG3_ENST00000471182.2_Missense_Mutation_p.R569W|PLEKHG3_ENST00000492928.1_Intron			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	1036			R -> W (in dbSNP:rs229649). {ECO:0000269|PubMed:15489334}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GCCCTCCGCCCGGAGCCCCCT	0.687													C|||	416	0.0830671	0.1596	0.0634	5008	,	,		14831	0.002		0.0805	False		,,,				2504	0.0798				p.R980W		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C2938T						PASS	.	C	TRP/ARG	618,3788	250.9+/-257.8	42,534,1627	54.0	64.0	61.0		2938	3.8	0.0	14	dbSNP_79	61	777,7819	176.2+/-226.1	41,695,3562	yes	missense	PLEKHG3	NM_015549.1	101	83,1229,5189	TT,TC,CC		9.0391,14.0263,10.7291	probably-damaging	980/1164	65209867	1395,11607	2203	4298	6501	SO:0001583	missense	26030	exon15			TCCGCCCGGAGCC	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.3106C>T	14.37:g.65209867C>T	ENSP00000378183:p.Arg1036Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Missense_Mutation	SNP	ENST00000394691.1	37		159	0.07280219780219781	72	0.14634146341463414	28	0.07734806629834254	1	0.0017482517482517483	58	0.07651715039577836	C	13.90	2.373988	0.42105	0.140263	0.090391	ENSG00000126822	ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731	T;T;T;T	0.65178	0.31;-0.14;1.19;1.2	5.66	3.81	0.43845	.	0.314051	0.25055	N	0.033482	T	0.01156	0.0038	M	0.69823	2.125	0.80722	P	0.0	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.73380	0.95;0.971;0.956;0.98	T	0.41574	-0.9501	9	0.62326	D	0.03	.	12.9469	0.58376	0.4224:0.5776:0.0:0.0	rs229649;rs1695766;rs17846643;rs17859738	569;541;1036;980	A1L390-2;G3V311;A1L390;A1L390-3	.;.;PKHG3_HUMAN;.	W	980;1036;569;541	ENSP00000247226:R980W;ENSP00000378183:R1036W;ENSP00000450945:R569W;ENSP00000450973:R541W	ENSP00000247226:R980W	R	+	1	2	PLEKHG3	64279620	0.001000	0.12720	0.034000	0.17996	0.043000	0.13939	0.092000	0.15066	0.711000	0.32018	0.655000	0.94253	CGG	C|0.906;T|0.094	0.094	strong		0.687	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
ANO7	50636	hgsc.bcm.edu	37	2	242135180	242135180	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242135180C>T	ENST00000274979.8	+	4	494	c.391C>T	c.(391-393)Cgg>Tgg	p.R131W	ANO7_ENST00000402430.3_Missense_Mutation_p.R130W|ANO7_ENST00000402530.3_Missense_Mutation_p.R130W	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	131					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						CAGTGCCGCCCGGGACAGAAC	0.597																																					p.R131W		Atlas-SNP	.											ANO7,caecum,carcinoma,-1,1	ANO7	136	1	0			c.C391T						scavenged	.						95.0	84.0	88.0					2																	242135180		2203	4300	6503	SO:0001583	missense	50636	exon4			GCCGCCCGGGACA	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.391C>T	2.37:g.242135180C>T	ENSP00000274979:p.Arg131Trp	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	3	0.03125	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.442073	0.43326	.	.	ENSG00000146205	ENST00000274979;ENST00000402530;ENST00000402430	T;T;T	0.68479	-0.33;0.75;-0.33	2.58	-3.97	0.04094	.	.	.	.	.	T	0.67268	0.2875	L	0.47716	1.5	0.09310	N	1	D;D	0.76494	0.997;0.999	P;P	0.60609	0.543;0.877	T	0.60870	-0.7177	9	0.72032	D	0.01	.	6.3197	0.21211	0.4821:0.3587:0.1592:0.0	.	131;130	Q6IWH7;Q6IWH7-2	ANO7_HUMAN;.	W	131;130;130	ENSP00000274979:R131W;ENSP00000383985:R130W;ENSP00000385418:R130W	ENSP00000274979:R131W	R	+	1	2	ANO7	241783853	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	-0.522000	0.06237	-0.489000	0.06716	-0.518000	0.04402	CGG	.	.	none		0.597	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98691137	98691137	+	Missense_Mutation	SNP	T	T	C	rs2274654	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:98691137T>C	ENST00000288985.7	+	11	2080	c.1775T>C	c.(1774-1776)gTc>gCc	p.V592A	ERCC6L2_ENST00000437817.1_Missense_Mutation_p.V403A|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	592	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		V -> A (in dbSNP:rs2274654).		DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										ATTTGCCTTGTCTCTACAATG	0.284													T|||	1137	0.227037	0.1936	0.2637	5008	,	,		15669	0.2639		0.1332	False		,,,				2504	0.3047				p.V592A		Atlas-SNP	.											.	.	.	.	0			c.T1775C						PASS	.	T	ALA/VAL	793,3613	314.7+/-293.7	73,647,1483	97.0	90.0	93.0		1775	5.1	1.0	9	dbSNP_100	93	1316,7284	257.5+/-281.5	89,1138,3073	yes	missense	C9orf102	NM_001010895.2	64	162,1785,4556	CC,CT,TT		15.3023,17.9982,16.2156	probably-damaging	592/713	98691137	2109,10897	2203	4300	6503	SO:0001583	missense	375748	exon11			GCCTTGTCTCTAC	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1775T>C	9.37:g.98691137T>C	ENSP00000288985:p.Val592Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	439	0.20100732600732601	86	0.17479674796747968	95	0.26243093922651933	152	0.26573426573426573	106	0.13984168865435356	T	23.1	4.377977	0.82682	0.179982	0.153023	ENSG00000182150	ENST00000405401;ENST00000288985;ENST00000437817;ENST00000426805	T;T;T	0.81078	-1.45;-1.45;-1.45	5.09	5.09	0.68999	Helicase, C-terminal (3);	0.000000	0.47455	D	0.000234	T	0.00039	0.0001	L	0.39147	1.195	0.09310	P	1.0	D;D;D	0.76494	0.993;0.996;0.999	P;D;D	0.70487	0.84;0.946;0.969	T	0.00647	-1.1628	9	0.87932	D	0	-14.9419	15.019	0.71613	0.0:0.0:0.0:1.0	rs2274654;rs52819942;rs58407137;rs2274654	403;274;592	Q5T890-2;F2Z2R4;Q5T890	.;.;RAD26_HUMAN	A	274;592;403;79	ENSP00000288985:V592A;ENSP00000416286:V403A;ENSP00000395345:V79A	ENSP00000288985:V592A	V	+	2	0	C9orf102	97730958	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.229000	0.78088	2.142000	0.66516	0.477000	0.44152	GTC	T|0.816;C|0.184	0.184	strong		0.284	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	
HLA-B	3106	hgsc.bcm.edu	37	6	31322911	31322911	+	Missense_Mutation	SNP	C	C	T	rs1051488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31322911C>T	ENST00000412585.2	-	5	1013	c.985G>A	c.(985-987)Gct>Act	p.A329T		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.A329T(3)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CACATCACAGCAGCGACCACA	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	2689	0.536941	0.6573	0.4971	5008	,	,		20334	0.5556		0.3827	False		,,,				2504	0.5419				p.A329T		Atlas-SNP	.											HLA-B,NS,carcinoma,0,7	HLA-B	54	7	3	Substitution - Missense(3)	kidney(3)	c.G985A						PASS	.	C	THR/ALA	1738,1284		487,764,260	102.0	101.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	985	1.7	0.1	6	dbSNP_86	101	1925,3493		353,1219,1137	yes	missense	HLA-B	NM_005514.6	58	840,1983,1397	TT,TC,CC		35.5297,42.4884,43.4005		329/363	31322911	3663,4777	1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	TCACAGCAGCGAC	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.985G>A	6.37:g.31322911C>T	ENSP00000399168:p.Ala329Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1030	0.4716117216117216	286	0.5813008130081301	179	0.494475138121547	297	0.5192307692307693	268	0.35356200527704484	N	8.411	0.844238	0.16963	0.575116	0.355297	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00631	6.09	3.73	1.67	0.24075	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.32481	-0.9905	7	0.48119	T	0.1	.	8.1384	0.31069	0.43:0.57:0.0:0.0	rs1051488;rs2308519;rs3178024;rs3191873;rs3819280;rs3873389;rs3957102;rs7768625;rs9266122;rs17199390;rs17417354;rs17840057;rs17845375;rs17858229;rs52797228;rs61195158	329	P01889	1B07_HUMAN	T	329;208	ENSP00000399168:A329T	ENSP00000399168:A329T	A	-	1	0	HLA-B	31430890	0.000000	0.05858	0.111000	0.21465	0.015000	0.08874	-0.118000	0.10692	0.660000	0.30964	0.448000	0.29417	GCT	T|0.451;G|0.000;C|0.549	0.451	strong		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
DCHS1	8642	hgsc.bcm.edu	37	11	6655433	6655433	+	Silent	SNP	G	G	A	rs997263	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6655433G>A	ENST00000299441.3	-	3	2313	c.1902C>T	c.(1900-1902)caC>caT	p.H634H	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	634	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATCACCGCTGTGGGCATCAA	0.592													G|||	1735	0.346446	0.2572	0.3631	5008	,	,		21138	0.4296		0.3777	False		,,,				2504	0.3374				p.H634H		Atlas-SNP	.											.	DCHS1	277	.	0			c.C1902T						PASS	.	G		1277,3125	434.1+/-343.8	202,873,1126	99.0	97.0	97.0		1902	1.7	1.0	11	dbSNP_86	97	3238,5354	487.5+/-372.1	598,2042,1656	no	coding-synonymous	DCHS1	NM_003737.2		800,2915,2782	AA,AG,GG		37.6862,29.0095,34.7468		634/3299	6655433	4515,8479	2201	4296	6497	SO:0001819	synonymous_variant	8642	exon3			ACCGCTGTGGGCA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.1902C>T	11.37:g.6655433G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			G|0.642;A|0.358	0.358	strong		0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
NARFL	64428	hgsc.bcm.edu	37	16	784765	784765	+	Silent	SNP	C	C	T	rs9928077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:784765C>T	ENST00000251588.2	-	5	562	c.546G>A	c.(544-546)gcG>gcA	p.A182A	NARFL_ENST00000301694.5_Missense_Mutation_p.R138H|NARFL_ENST00000568545.1_Silent_p.A80A|HAGHL_ENST00000569604.1_3'UTR|NARFL_ENST00000562862.1_5'Flank|NARFL_ENST00000540986.1_Silent_p.A80A	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	182					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCAGGGGCAGCGCCTGTCTGC	0.597													C|||	1886	0.376597	0.149	0.464	5008	,	,		17362	0.6736		0.2406	False		,,,				2504	0.456				p.A182A		Atlas-SNP	.											NARFL,NS,carcinoma,0,1	NARFL	31	1	0			c.G546A						PASS	.	C		560,3840	246.8+/-255.3	31,498,1671	73.0	82.0	79.0		546	3.8	1.0	16	dbSNP_119	79	1831,6769	329.0+/-318.6	201,1429,2670	no	coding-synonymous	NARFL	NM_022493.1		232,1927,4341	TT,TC,CC		21.2907,12.7273,18.3923		182/477	784765	2391,10609	2200	4300	6500	SO:0001819	synonymous_variant	64428	exon5			GGGCAGCGCCTGT	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.546G>A	16.37:g.784765C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1	820	0.37545787545787546	71	0.1443089430894309	149	0.4116022099447514	398	0.6958041958041958	202	0.26649076517150394	C	10.53	1.375962	0.24857	0.127273	0.212907	ENSG00000103245	ENST00000301694	T	0.30448	1.53	4.79	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46927	P	7.420000000000204E-4	P	0.42078	0.77	B	0.33750	0.169	T	0.14420	-1.0473	7	0.46703	T	0.11	-20.9669	9.771	0.40589	0.0801:0.1424:0.7775:0.0	rs9928077;rs9928077	138	B4DEE7	.	H	138	ENSP00000301694:R138H	ENSP00000301694:R138H	R	-	2	0	NARFL	724766	0.999000	0.42202	0.983000	0.44433	0.135000	0.20990	1.588000	0.36633	1.020000	0.39573	-0.299000	0.09455	CGC	C|0.740;T|0.260	0.260	strong		0.597	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
SCN10A	6336	hgsc.bcm.edu	37	3	38764998	38764998	+	Missense_Mutation	SNP	A	A	G	rs12632942	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38764998A>G	ENST00000449082.2	-	18	3274	c.3275T>C	c.(3274-3276)cTa>cCa	p.L1092P		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1092			L -> P (in dbSNP:rs12632942).		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)			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)	ctcaggatctAGGCAGTCCAC	0.612													G|||	1100	0.219649	0.121	0.121	5008	,	,		19013	0.376		0.2465	False		,,,				2504	0.2342				p.L1092P		Atlas-SNP	.											.	SCN10A	359	.	0			c.T3275C						PASS	.	G	PRO/LEU	625,3781	767.2+/-413.5	47,531,1625	77.0	65.0	69.0		3275	-0.5	0.0	3	dbSNP_120	69	2236,6364	705.7+/-405.5	288,1660,2352	yes	missense	SCN10A	NM_006514.2	98	335,2191,3977	GG,GA,AA		26.0,14.1852,21.9975	benign	1092/1957	38764998	2861,10145	2203	4300	6503	SO:0001583	missense	6336	exon18			GGATCTAGGCAGT	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.3275T>C	3.37:g.38764998A>G	ENSP00000390600:p.Leu1092Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	518	0.23717948717948717	53	0.10772357723577236	48	0.13259668508287292	237	0.4143356643356643	180	0.23746701846965698	G	7.645	0.681641	0.14907	0.141852	0.26	ENSG00000185313	ENST00000449082	D	0.83419	-1.72	4.65	-0.53	0.11898	Sodium ion transport-associated (1);	0.254741	0.39544	N	0.001332	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30736	-0.9968	9	0.19147	T	0.46	.	11.785	0.52037	0.2804:0.0:0.7196:0.0	rs12632942;rs52795271;rs61060144;rs12632942	1092	Q9Y5Y9	SCNAA_HUMAN	P	1092	ENSP00000390600:L1092P	ENSP00000390600:L1092P	L	-	2	0	SCN10A	38740002	0.004000	0.15560	0.010000	0.14722	0.896000	0.52359	0.034000	0.13776	-0.637000	0.05516	-0.227000	0.12334	CTA	A|0.777;G|0.223	0.223	strong		0.612	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
NTN3	4917	hgsc.bcm.edu	37	16	2522536	2522536	+	Silent	SNP	T	T	C	rs148996457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2522536T>C	ENST00000293973.1	+	1	1037	c.834T>C	c.(832-834)caT>caC	p.H278H	TBC1D24_ENST00000293970.5_5'Flank|TBC1D24_ENST00000567020.1_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	278	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(2)|lung(3)|prostate(1)	7						ACTGTCGGCATGGCACCGAGG	0.687																																					p.H278H		Atlas-SNP	.											.	NTN3	28	.	0			c.T834C						PASS	.	T		0,4370		0,0,2185	26.0	26.0	26.0		834	-6.5	0.7	16	dbSNP_134	26	3,8559		0,3,4278	no	coding-synonymous	NTN3	NM_006181.2		0,3,6463	CC,CT,TT		0.035,0.0,0.0232		278/581	2522536	3,12929	2185	4281	6466	SO:0001819	synonymous_variant	4917	exon1			TCGGCATGGCACC	U86759	CCDS10469.1	16p13.3	2013-03-01	2008-10-29	2008-10-29	ENSG00000162068	ENSG00000162068		"""Netrins"""	8030	protein-coding gene	gene with protein product	"""Netrin-3"""	602349	"""netrin 2 (chicken)-like"", ""netrin 2-like (chicken)"""	NTN2L		9143507, 10366627	Standard	NM_006181		Approved		uc002cqj.3	O00634	OTTHUMG00000128867	ENST00000293973.1:c.834T>C	16.37:g.2522536T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_006181		Silent	SNP	ENST00000293973.1	37	CCDS10469.1																																																																																			T|1.000;C|0.000	0.000	weak		0.687	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181	
KRT40	125115	hgsc.bcm.edu	37	17	39140221	39140221	+	Missense_Mutation	SNP	C	C	T	rs1510068	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	132	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	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	
GPC1	2817	hgsc.bcm.edu	37	2	241405483	241405483	+	Missense_Mutation	SNP	G	G	A	rs61737165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241405483G>A	ENST00000264039.2	+	9	1701	c.1453G>A	c.(1453-1455)Ggc>Agc	p.G485S	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	485					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)		AGGTGACGACGGCAGCGGCTC	0.677													g|||	64	0.0127796	0.034	0.0043	5008	,	,		15467	0.0		0.0129	False		,,,				2504	0.0031				p.G485S		Atlas-SNP	.											.	GPC1	32	.	0			c.G1453A						PASS	.		SER/GLY	100,4286		0,100,2093	18.0	22.0	21.0		1453	1.2	1.0	2	dbSNP_129	21	94,8470		0,94,4188	no	missense	GPC1	NM_002081.2	56	0,194,6281	AA,AG,GG		1.0976,2.28,1.4981	benign	485/559	241405483	194,12756	2193	4282	6475	SO:0001583	missense	2817	exon9			GACGACGGCAGCG	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.1453G>A	2.37:g.241405483G>A	ENSP00000264039:p.Gly485Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	26|26	0.011904761904761904|0.011904761904761904	13|13	0.026422764227642278|0.026422764227642278	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	g|g	8.927|8.927	0.962540|0.962540	0.18583|0.18583	0.0228|0.0228	0.010976|0.010976	ENSG00000063660|ENSG00000063660	ENST00000264039|ENST00000420138;ENST00000455111	T|.	0.48522|.	0.81|.	3.69|3.69	1.16|1.16	0.20824|0.20824	.|.	0.850231|.	0.10534|.	N|.	0.663449|.	T|T	0.06962|0.06962	0.0177|0.0177	N|N	0.16862|0.16862	0.45|0.45	0.24072|0.24072	N|N	0.995973|0.995973	B|.	0.13145|.	0.007|.	B|.	0.08055|.	0.003|.	T|T	0.19353|0.19353	-1.0308|-1.0308	10|5	0.07644|.	T|.	0.81|.	-24.6586|-24.6586	4.6843|4.6843	0.12750|0.12750	0.5324:0.0:0.4676:0.0|0.5324:0.0:0.4676:0.0	rs61737165|rs61737165	485|.	P35052|.	GPC1_HUMAN|.	S|Q	485|524;236	ENSP00000264039:G485S|.	ENSP00000264039:G485S|.	G|R	+|+	1|2	0|0	GPC1|GPC1	241054156|241054156	0.005000|0.005000	0.15991|0.15991	0.976000|0.976000	0.42696|0.42696	0.851000|0.851000	0.48451|0.48451	0.805000|0.805000	0.27112|0.27112	0.605000|0.605000	0.29947|0.29947	0.443000|0.443000	0.29094|0.29094	GGC|CGG	G|0.987;A|0.013	0.013	strong		0.677	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
FNBP1	23048	hgsc.bcm.edu	37	9	132720770	132720770	+	Splice_Site	SNP	A	A	G	rs17519205	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:132720770A>G	ENST00000446176.2	-	5	594	c.408T>C	c.(406-408)tcT>tcC	p.S136S	FNBP1_ENST00000420781.1_Splice_Site_p.S136S|FNBP1_ENST00000355681.3_Splice_Site_p.S136S	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	136	F-BAR domain.|Interaction with microtubules. {ECO:0000250}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		GTTCACTTACAGATTCAAGCT	0.448			T	MLL	AML								a|||	455	0.0908546	0.0522	0.1484	5008	,	,		17917	0.0813		0.0845	False		,,,				2504	0.1186				p.S136S		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	.	FNBP1	51	.	0			c.T408C						PASS	.	A		241,3555		12,217,1669	76.0	69.0	71.0		408	-10.9	0.0	9	dbSNP_123	71	773,7479		42,689,3395	yes	coding-synonymous-near-splice	FNBP1	NM_015033.2		54,906,5064	GG,GA,AA		9.3674,6.3488,8.4163		136/618	132720770	1014,11034	1898	4126	6024	SO:0001630	splice_region_variant	23048	exon5			ACTTACAGATTCA	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.408+1T>C	9.37:g.132720770A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	89	35	0.393258	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Silent	SNP	ENST00000446176.2	37	CCDS48040.1	177	0.08104395604395605	23	0.046747967479674794	48	0.13259668508287292	45	0.07867132867132867	61	0.08047493403693931	a	0.027	-1.366030	0.01235	0.063488	0.093674	ENSG00000187239	ENST00000449089	.	.	.	5.44	-10.9	0.00192	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999999215	.	.	.	.	.	.	T	0.06991	-1.0796	3	.	.	.	-7.194	1.2775	0.02033	0.3215:0.1651:0.3333:0.1801	rs17519205;rs56425656;rs60110438;rs17519205	.	.	.	P	98	.	.	L	-	2	0	FNBP1	131760591	0.000000	0.05858	0.020000	0.16555	0.235000	0.25334	-2.358000	0.01085	-3.464000	0.00158	-2.894000	0.00094	CTA	A|0.916;G|0.084	0.084	strong		0.448	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2		Silent
MCMBP	79892	hgsc.bcm.edu	37	10	121586882	121586882	+	IGR	SNP	A	A	G	rs3188055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:121586882A>G	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Missense_Mutation_p.N997D|INPP5F_ENST00000369080.3_Missense_Mutation_p.N387D	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.N997D(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TCAAGTTTCAAATGAAACCCA	0.448													A|||	1347	0.26897	0.2678	0.2824	5008	,	,		21231	0.1796		0.337	False		,,,				2504	0.2832				p.N997D		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - Missense(1)	stomach(1)	c.A2989G						PASS	.	A	ASP/ASN	1164,3242	408.9+/-334.8	153,858,1192	108.0	102.0	104.0		2989	1.9	0.0	10	dbSNP_105	104	2849,5751	449.3+/-362.1	488,1873,1939	yes	missense	INPP5F	NM_014937.3	23	641,2731,3131	GG,GA,AA		33.1279,26.4185,30.855	benign	997/1133	121586882	4013,8993	2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			GTTTCAAATGAAA	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121586882A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	37	CCDS7617.1	627	0.28708791208791207	159	0.3231707317073171	112	0.30939226519337015	103	0.18006993006993008	253	0.3337730870712401	A	0.257	-1.002580	0.02128	0.264185	0.331279	ENSG00000198825	ENST00000361976;ENST00000369080	T;T	0.43688	1.18;0.94	5.62	1.93	0.25924	.	0.840743	0.10898	N	0.621975	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.33394	-0.9870	9	0.34782	T	0.22	-5.5089	5.6696	0.17715	0.7097:0.1435:0.1467:0.0	rs3188055;rs3824829;rs56742122;rs3188055	387;997	Q5W135;Q9Y2H2	.;SAC2_HUMAN	D	997;387	ENSP00000354519:N997D;ENSP00000358076:N387D	ENSP00000354519:N997D	N	+	1	0	INPP5F	121576872	0.000000	0.05858	0.007000	0.13788	0.011000	0.07611	1.099000	0.31013	0.141000	0.18875	0.533000	0.62120	AAT	A|0.705;G|0.295	0.295	strong		0.448	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
MUC5B	727897	hgsc.bcm.edu	37	11	1274209	1274209	+	Splice_Site	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1274209G>T	ENST00000529681.1	+	33	15274	c.15216G>T	c.(15214-15216)gaG>gaT	p.E5072D	MUC5B_ENST00000447027.1_Splice_Site_p.E5075D	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5072					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)		ATGAGTGCGAGTGTGAGTGCG	0.642																																					p.E5072D		Atlas-SNP	.											.	MUC5B	473	.	0			c.G15216T						PASS	.						53.0	59.0	57.0					11																	1274209		2132	4227	6359	SO:0001630	splice_region_variant	727897	exon33			GTGCGAGTGTGAG	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.15217+1G>T	11.37:g.1274209G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295134	0.23564	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.15487	2.42;2.61	4.64	-4.49	0.03504	.	.	.	.	.	T	0.09949	0.0244	L	0.28274	0.84	0.20873	N	0.999838	P;P	0.43094	0.799;0.799	B;B	0.36845	0.234;0.234	T	0.20672	-1.0268	9	0.87932	D	0	.	9.6818	0.40074	0.7156:0.0:0.1642:0.1202	.	5394;5075	A7Y9J9;E9PBJ0	.;.	D	5072;5075;5016;4771	ENSP00000436812:E5072D;ENSP00000415793:E5075D	ENSP00000343037:E5016D	E	+	3	2	MUC5B	1230785	0.001000	0.12720	0.574000	0.28523	0.561000	0.35649	-2.094000	0.01351	-0.851000	0.04147	-0.258000	0.10820	GAG	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Missense_Mutation
COL11A2	1302	hgsc.bcm.edu	37	6	33153528	33153528	+	Missense_Mutation	SNP	C	C	T	rs9277934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33153528C>T	ENST00000341947.2	-	6	1053	c.826G>A	c.(826-828)Gag>Aag	p.E276K	COL11A2_ENST00000374714.1_Intron|COL11A2_ENST00000357486.1_Missense_Mutation_p.E276K|COL11A2_ENST00000395197.1_Missense_Mutation_p.E276K|COL11A2_ENST00000374713.1_Intron|COL11A2_ENST00000374712.1_Missense_Mutation_p.E276K|COL11A2_ENST00000374708.4_Intron|COL11A2_ENST00000361917.1_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	59	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	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			
FLG	2312	hgsc.bcm.edu	37	1	152281523	152281523	+	Missense_Mutation	SNP	A	A	C	rs80059102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152281523A>C	ENST00000368799.1	-	3	5874	c.5839T>G	c.(5839-5841)Tgg>Ggg	p.W1947G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1947	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)			GACTGCTCCCAAGCAGATCCA	0.572									Ichthyosis																												p.W1947G		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.T5839G						scavenged	.						253.0	240.0	245.0					1																	152281523		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCCCAAGCAGA	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.5839T>G	1.37:g.152281523A>C	ENSP00000357789:p.Trp1947Gly	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	412	138	0.334951	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	0.932	-0.712374	0.03206	.	.	ENSG00000143631	ENST00000368799	T	0.01613	4.73	2.54	0.616	0.17613	.	.	.	.	.	T	0.00412	0.0013	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41627	-0.9498	9	0.20519	T	0.43	.	5.0022	0.14269	0.3067:0.0:0.6933:0.0	.	1947	P20930	FILA_HUMAN	G	1947	ENSP00000357789:W1947G	ENSP00000357789:W1947G	W	-	1	0	FLG	150548147	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.553000	0.06012	0.161000	0.19458	-0.219000	0.12488	TGG	A|0.917;C|0.081;G|0.002	0.081	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BRD1	23774	hgsc.bcm.edu	37	22	50217300	50217300	+	Silent	SNP	G	G	A	rs374070979		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217300G>A	ENST00000216267.8	-	1	1152	c.666C>T	c.(664-666)gaC>gaT	p.D222D	BRD1_ENST00000404034.1_Silent_p.D222D|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.D222D|BRD1_ENST00000457780.2_Silent_p.D222D	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	222					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACACTCCCCGTCCATGCAGA	0.612																																					p.D222D		Atlas-SNP	.											.	BRD1	144	.	0			c.C666T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	62.0	49.0	53.0		666	-4.3	1.0	22		53	0,8600		0,0,4300	no	coding-synonymous	BRD1	NM_014577.1		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		222/1059	50217300	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTCCCCGTCCATG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.666C>T	22.37:g.50217300G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			.	.	weak		0.612	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
DOCK8	81704	hgsc.bcm.edu	37	9	368030	368030	+	Silent	SNP	T	T	C	rs10972587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:368030T>C	ENST00000453981.1	+	15	1804	c.1692T>C	c.(1690-1692)taT>taC	p.Y564Y	DOCK8_ENST00000469391.1_Silent_p.Y496Y|DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000432829.2_Silent_p.Y496Y|DOCK8_ENST00000382329.1_5'UTR			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	564	DHR-1.				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)		ACCTTCTCTATGTCTACCCAC	0.373													T|||	652	0.130192	0.4138	0.0663	5008	,	,		21192	0.001		0.0318	False		,,,				2504	0.0266				p.Y564Y		Atlas-SNP	.											.	DOCK8	401	.	0			c.T1692C						PASS	.	T	,,	1584,2822	493.4+/-362.7	300,984,919	89.0	84.0	85.0		1488,1488,1692	-2.0	1.0	9	dbSNP_120	85	344,8256	117.9+/-177.5	7,330,3963	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	307,1314,4882	CC,CT,TT		4.0,35.951,14.8239	,,	496/2000,496/2032,564/2100	368030	1928,11078	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon15			TCTCTATGTCTAC	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.1692T>C	9.37:g.368030T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			T|0.862;C|0.138	0.138	strong		0.373	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
CDH23	64072	hgsc.bcm.edu	37	10	73569749	73569749	+	Silent	SNP	C	C	T	rs11000009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:73569749C>T	ENST00000224721.6	+	60	8915	c.8910C>T	c.(8908-8910)ccC>ccT	p.P2970P	CDH23_ENST00000398788.3_Silent_p.P725P|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2965	Cadherin 27. {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						ACGAGATCCCCGACCGTGTGC	0.587													C|||	405	0.0808706	0.09	0.072	5008	,	,		21487	0.0079		0.1213	False		,,,				2504	0.1084				p.P2965P		Atlas-SNP	.											.	CDH23	365	.	0			c.C8895T						PASS	.	C	,,	395,3841		15,365,1738	99.0	100.0	99.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2175,2175,8895	-11.6	0.4	10	dbSNP_120	99	1074,7354		74,926,3214	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	,,	89,1291,4952	TT,TC,CC		12.7432,9.3248,11.5998	,,	725/1115,725/1080,2965/3355	73569749	1469,11195	2118	4214	6332	SO:0001819	synonymous_variant	64072	exon59			GATCCCCGACCGT	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.8910C>T	10.37:g.73569749C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.909;T|0.091	0.091	strong		0.587	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
TTLL12	23170	hgsc.bcm.edu	37	22	43579049	43579049	+	Missense_Mutation	SNP	T	T	C	rs13058467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43579049T>C	ENST00000216129.6	-	2	347	c.284A>G	c.(283-285)aAc>aGc	p.N95S		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	95			N -> S (in dbSNP:rs13058467).		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)				GCACAGCTCGTTCCCCGGGTT	0.632													C|||	249	0.0497204	0.0522	0.0692	5008	,	,		18526	0.001		0.0974	False		,,,				2504	0.0337				p.N95S		Atlas-SNP	.											.	TTLL12	50	.	0			c.A284G						PASS	.	C	SER/ASN	320,4086	797.0+/-415.4	12,296,1895	132.0	122.0	126.0		284	0.1	0.0	22	dbSNP_121	126	930,7670	776.5+/-407.7	55,820,3425	yes	missense	TTLL12	NM_015140.3	46	67,1116,5320	CC,CT,TT		10.814,7.2628,9.6109	benign	95/645	43579049	1250,11756	2203	4300	6503	SO:0001583	missense	23170	exon2			AGCTCGTTCCCCG	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.284A>G	22.37:g.43579049T>C	ENSP00000216129:p.Asn95Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	132	0.06043956043956044	33	0.06707317073170732	29	0.08011049723756906	0	0.0	70	0.09234828496042216	C	0.107	-1.143970	0.01728	0.072628	0.10814	ENSG00000100304	ENST00000216129;ENST00000357017;ENST00000423379	T	0.06608	3.28	5.08	0.0633	0.14348	.	0.876012	0.09812	N	0.752737	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47381	-0.9122	9	0.10111	T	0.7	-9.0748	0.8509	0.01172	0.1548:0.2013:0.3024:0.3415	rs13058467;rs58544459;rs13058467	95;95	B1AH89;Q14166	.;TTL12_HUMAN	S	95	ENSP00000216129:N95S	ENSP00000216129:N95S	N	-	2	0	TTLL12	41908993	0.000000	0.05858	0.001000	0.08648	0.450000	0.32258	0.178000	0.16820	0.177000	0.19895	-0.119000	0.15052	AAC	T|0.917;C|0.083	0.083	strong		0.632	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276659T>C	ENST00000368799.1	-	3	10738	c.10703A>G	c.(10702-10704)cAg>cGg	p.Q3568R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	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)			TGACTGCTCCTGAGCAGATCC	0.567									Ichthyosis				t|||	1035	0.206669	0.2133	0.1916	5008	,	,		18266	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A10703G						scavenged	.						148.0	201.0	183.0					1																	152276659		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCTCCTGAGCAG	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.10703A>G	1.37:g.152276659T>C	ENSP00000357789:p.Gln3568Arg	Somatic	205	2	0.0097561		WXS	Illumina HiSeq	Phase_I	197	20	0.101523	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	3.885	-0.025135	0.07589	.	.	ENSG00000143631	ENST00000368799	T	0.01647	4.71	3.16	-6.33	0.01988	.	.	.	.	.	T	0.00210	0.0006	N	0.04508	-0.205	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.45948	-0.9226	9	0.15066	T	0.55	.	1.2756	0.02030	0.1435:0.216:0.1461:0.4945	rs7532285;rs56765845;rs7532285	3568	P20930	FILA_HUMAN	R	3568	ENSP00000357789:Q3568R	ENSP00000357789:Q3568R	Q	-	2	0	FLG	150543283	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.180000	0.03088	-1.526000	0.01760	-1.734000	0.00692	CAG	T|0.993;C|0.007	0.007	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LRFN3	79414	hgsc.bcm.edu	37	19	36435564	36435564	+	Silent	SNP	G	G	A	rs2293756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36435564G>A	ENST00000588831.1	+	4	2584	c.1530G>A	c.(1528-1530)acG>acA	p.T510T	AF038458.3_ENST00000592518.1_lincRNA|LRFN3_ENST00000246529.3_Silent_p.T510T			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	510	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCACGGCCACGCGGCCTGTGG	0.711													A|||	421	0.0840655	0.1808	0.0749	5008	,	,		12088	0.1151		0.002	False		,,,				2504	0.0123				p.T510T		Atlas-SNP	.											.	LRFN3	43	.	0			c.G1530A						PASS	.	A		600,3792		36,528,1632	12.0	13.0	13.0		1530	-10.1	0.1	19	dbSNP_100	13	40,8522		1,38,4242	no	coding-synonymous	LRFN3	NM_024509.1		37,566,5874	AA,AG,GG		0.4672,13.6612,4.9406		510/629	36435564	640,12314	2196	4281	6477	SO:0001819	synonymous_variant	79414	exon3			GGCCACGCGGCCT	BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28370	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 1"""	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.1530G>A	19.37:g.36435564G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	4	0.4	NM_024509	Q6UY10	Silent	SNP	ENST00000588831.1	37	CCDS12483.1																																																																																			G|0.934;A|0.066	0.066	strong		0.711	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509	
MLXIP	22877	hgsc.bcm.edu	37	12	122618131	122618131	+	Silent	SNP	A	A	G	rs36045144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122618131A>G	ENST00000319080.7	+	9	1461	c.1329A>G	c.(1327-1329)ccA>ccG	p.P443P	MLXIP_ENST00000538698.1_Silent_p.P50P|MLXIP_ENST00000377037.2_Silent_p.P33P					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	41	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	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	
KCNQ5	56479	hgsc.bcm.edu	37	6	73904448	73904448	+	Missense_Mutation	SNP	G	G	A	rs148543637		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:73904448G>A	ENST00000370398.1	+	14	2219	c.2110G>A	c.(2110-2112)Gcg>Acg	p.A704T	KCNQ5_ENST00000355635.3_Missense_Mutation_p.A705T|KCNQ5_ENST00000355194.4_Missense_Mutation_p.A704T|KCNQ5_ENST00000414165.2_Missense_Mutation_p.A594T|KCNQ5_ENST00000342056.2_Missense_Mutation_p.A723T|KCNQ5_ENST00000403813.2_Missense_Mutation_p.A695T|KCNQ5_ENST00000402622.2_Missense_Mutation_p.A714T	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	704					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GACTTTCTACGCGCTTAGCCC	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		21573	0.0		0.001	False		,,,				2504	0.0				p.A723T	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											KCNQ5,colon,carcinoma,-1,3	KCNQ5	153	3	0			c.G2167A						scavenged	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	131.0	130.0	131.0		2083,2140,2167,1780,2110	4.4	0.9	6	dbSNP_134	131	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	KCNQ5	NM_001160130.1,NM_001160132.1,NM_001160133.1,NM_001160134.1,NM_019842.3	58,58,58,58,58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	695/924,714/943,723/952,594/823,704/933	73904448	2,13004	2203	4300	6503	SO:0001583	missense	56479	exon15			TTCTACGCGCTTA	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2110G>A	6.37:g.73904448G>A	ENSP00000359425:p.Ala704Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	97	2	0.0206186	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.516190	0.44763	0.0	2.33E-4	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99594	-5.86;-5.87;-5.87;-5.85;-5.88;-5.91;-6.25	5.32	4.45	0.53987	.	0.140270	0.48286	N	0.000184	D	0.98988	0.9655	L	0.56769	1.78	0.24669	N	0.993427	D;P;P;P;D	0.76494	0.999;0.584;0.947;0.865;0.99	P;B;B;B;P	0.61658	0.892;0.118;0.282;0.2;0.664	D	0.98220	1.0477	10	0.30078	T	0.28	.	13.8597	0.63552	0.074:0.0:0.9259:0.0	.	594;714;723;695;704	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	T	723;723;704;704;714;705;695;594	ENSP00000345055:A723T;ENSP00000347326:A704T;ENSP00000359425:A704T;ENSP00000385501:A714T;ENSP00000347853:A705T;ENSP00000384453:A695T;ENSP00000409861:A594T	ENSP00000345055:A723T	A	+	1	0	KCNQ5	73961169	1.000000	0.71417	0.922000	0.36590	0.992000	0.81027	2.770000	0.47662	1.233000	0.43693	0.561000	0.74099	GCG	G|1.000;A|0.000	0.000	weak		0.488	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
HEXB	3074	hgsc.bcm.edu	37	5	73992881	73992881	+	Missense_Mutation	SNP	A	A	G	rs10805890	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	56	0	0		WXS	Illumina HiSeq	Phase_I	63	41	0.650794	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	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713598	32713598	+	Missense_Mutation	SNP	T	T	C	rs138296677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32713598T>C	ENST00000374940.3	+	3	464	c.362T>C	c.(361-363)tTt>tCt	p.F121S		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	121	Alpha-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)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	TTTTCCAAGTTTCCTGTGACG	0.512													T|||	352	0.0702875	0.0961	0.0677	5008	,	,		25198	0.0873		0.0507	False		,,,				2504	0.0399				p.F121S		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.T362C						PASS	.						179.0	140.0	154.0					6																	32713598		1511	2709	4220	SO:0001583	missense	3118	exon3			CCAAGTTTCCTGT		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.362T>C	6.37:g.32713598T>C	ENSP00000364076:p.Phe121Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	262	33	0.125954	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.802170	0.00075	.	.	ENSG00000237541	ENST00000374940	T	0.00572	6.49	3.06	-0.236	0.13067	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.726686	0.12656	N	0.450006	T	0.00039	0.0001	N	0.00308	-1.67	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24119	-1.0169	10	0.02654	T	1	.	0.5152	0.00602	0.1938:0.3561:0.1905:0.2596	.	121	P01906	DQA2_HUMAN	S	121	ENSP00000364076:F121S	ENSP00000364076:F121S	F	+	2	0	HLA-DQA2	32821576	0.000000	0.05858	0.837000	0.33122	0.054000	0.15201	0.039000	0.13884	0.145000	0.18977	-1.188000	0.01700	TTT	T|0.978;C|0.022	0.022	strong		0.512	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
COBLL1	22837	hgsc.bcm.edu	37	2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	rs74459242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000194871.6_Missense_Mutation_p.V393M|COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M|COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000491126.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	365						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GTCTCATCCACGCTCATGGAT	0.458													C|||	63	0.0125799	0.0023	0.0202	5008	,	,		16844	0.0		0.0368	False		,,,				2504	0.0092				p.V327M		Atlas-SNP	.											.	COBLL1	122	.	0			c.G979A						PASS	.	C	MET/VAL	34,4372	40.0+/-72.8	0,34,2169	77.0	83.0	81.0		979	1.4	0.5	2	dbSNP_132	81	421,8179	130.5+/-188.4	13,395,3892	yes	missense	COBLL1	NM_014900.3	21	13,429,6061	TT,TC,CC		4.8953,0.7717,3.4984	probably-damaging	327/1167	165578602	455,12551	2203	4300	6503	SO:0001583	missense	22837	exon6			CATCCACGCTCAT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1093G>A	2.37:g.165578602C>T	ENSP00000376478:p.Val365Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.89	2.073757	0.36566	0.007717	0.048953	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.93076	-3.16	6.17	1.37	0.22104	Cordon-bleu domain (1);	0.602245	0.17823	N	0.160815	T	0.75428	0.3848	L	0.47716	1.5	0.21553	N	0.999649	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.982;0.982;0.968	T	0.76080	-0.3090	10	0.52906	T	0.07	-0.5122	2.5206	0.04679	0.1029:0.3543:0.2961:0.2466	.	365;393;365	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	M	327;327;365;365;393	ENSP00000194871:V393M	ENSP00000194871:V393M	V	-	1	0	COBLL1	165286848	0.099000	0.21834	0.503000	0.27626	0.406000	0.30931	0.134000	0.15932	0.180000	0.19960	0.655000	0.94253	GTG	C|0.971;T|0.029	0.029	strong		0.458	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
PSMD6	9861	hgsc.bcm.edu	37	3	63996577	63996577	+	Silent	SNP	C	C	A	rs373997221		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:63996577C>A	ENST00000295901.4	-	7	1190	c.1050G>T	c.(1048-1050)gtG>gtT	p.V350V	PSMD6_ENST00000492933.1_Silent_p.V403V|PSMD6_ENST00000394431.2_Silent_p.V312V|PSMD6_ENST00000482510.1_Silent_p.V311V|RP11-245J9.5_ENST00000607115.1_lincRNA|RP11-245J9.4_ENST00000462717.1_RNA|PSMD6-AS2_ENST00000472046.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	350	PCI.				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)|ATP catabolic process (GO:0006200)|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)|proteolysis (GO:0006508)|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)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		CTATTTCATTCACTTTATCTA	0.338																																					p.V403V		Atlas-SNP	.											.	PSMD6	30	.	0			c.G1209T						PASS	.	C		0,4404		0,0,2202	78.0	82.0	81.0		1050	0.2	1.0	3		81	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PSMD6	NM_014814.1		0,1,6500	AA,AC,CC		0.0116,0.0,0.0077		350/390	63996577	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	9861	exon8			TTCATTCACTTTA	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"""Proteasome (prosome, macropain) subunits"""	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.1050G>T	3.37:g.63996577C>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	116	40	0.344828	NM_001271779	A8K2E0|E9PHI9|Q6UV22	Silent	SNP	ENST00000295901.4	37	CCDS2901.1																																																																																			.	.	weak		0.338	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814	
PTCH2	8643	hgsc.bcm.edu	37	1	45293752	45293752	+	Silent	SNP	T	T	C	rs2295997	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:45293752T>C	ENST00000372192.3	-	14	1951	c.1821A>G	c.(1819-1821)gaA>gaG	p.E607E	PTCH2_ENST00000447098.2_Silent_p.E607E	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	607					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GGCTGCTGGCTTCACAGTGGG	0.622									Basal Cell Nevus syndrome				T|||	1065	0.21266	0.2156	0.2522	5008	,	,		19432	0.2897		0.1412	False		,,,				2504	0.1748				p.E607E		Atlas-SNP	.											.	PTCH2	96	.	0			c.A1821G						PASS	.	T	,	887,3519	340.5+/-306.2	82,723,1398	83.0	90.0	88.0		1821,1821	2.4	1.0	1	dbSNP_100	88	1447,7153	276.5+/-292.4	131,1185,2984	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	213,1908,4382	CC,CT,TT		16.8256,20.1316,17.9456	,	607/1147,607/1204	45293752	2334,10672	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon14	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	GCTGGCTTCACAG	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.1821A>G	1.37:g.45293752T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			T|0.813;C|0.187	0.187	strong		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
ZBTB16	7704	hgsc.bcm.edu	37	11	114121182	114121182	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:114121182T>A	ENST00000335953.4	+	7	2307	c.1927T>A	c.(1927-1929)Tcc>Acc	p.S643T	RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000392996.2_Missense_Mutation_p.S643T|ZBTB16_ENST00000535379.1_3'UTR	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	643					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		CCCCAGCCTCTCCTCCATGCA	0.602																																					p.S643T		Atlas-SNP	.											ZBTB16_ENST00000335953,NS,carcinoma,0,1	ZBTB16	101	1	0			c.T1927A						scavenged	.						76.0	68.0	71.0					11																	114121182		2201	4296	6497	SO:0001583	missense	7704	exon7			AGCCTCTCCTCCA	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1927T>A	11.37:g.114121182T>A	ENSP00000338157:p.Ser643Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	38	2	0.0526316	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	t	18.33	3.599781	0.66332	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.62232	0.04;0.04	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.066981	0.64402	D	0.000008	T	0.47040	0.1424	N	0.14661	0.345	0.45272	D	0.998277	P	0.38767	0.646	B	0.36464	0.225	T	0.54925	-0.8220	10	0.59425	D	0.04	-13.3009	15.4492	0.75259	0.0:0.0:0.0:1.0	.	643	Q05516	ZBT16_HUMAN	T	643;643;520	ENSP00000338157:S643T;ENSP00000376721:S643T	ENSP00000309507:S520T	S	+	1	0	ZBTB16	113626392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.924000	0.63418	2.047000	0.60756	0.358000	0.22013	TCC	.	.	none		0.602	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006	
TAP2	6891	hgsc.bcm.edu	37	6	32797809	32797809	+	Missense_Mutation	SNP	C	C	T	rs2228396	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32797809C>T	ENST00000452392.2	-	10	1866	c.1693G>A	c.(1693-1695)Gct>Act	p.A565T	TAP2_ENST00000374897.2_Missense_Mutation_p.A565T|TAP2_ENST00000374899.4_Missense_Mutation_p.A565T|TAP2_ENST00000485701.1_5'Flank			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)	AGCCCATAAGCAATGTTGTTC	0.552													C|||	399	0.0796725	0.0923	0.1081	5008	,	,		19997	0.0923		0.0865	False		,,,				2504	0.0225				p.A565T		Atlas-SNP	.											.	TAP2	98	.	0			c.G1693A	GRCh37	CM941307	TAP2	M	rs2228396	PASS	.	C	THR/ALA,THR/ALA	368,2654		29,310,1172	124.0	128.0	127.0		1693,1693	1.5	0.0	6	dbSNP_98	127	460,4958		17,426,2266	yes	missense,missense	TAP2	NM_000544.3,NM_018833.2	58,58	46,736,3438	TT,TC,CC		8.4902,12.1774,9.8104	benign,benign	565/704,565/654	32797809	828,7612	1511	2709	4220	SO:0001583	missense	6891	exon10			CATAAGCAATGTT	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.1693G>A	6.37:g.32797809C>T	ENSP00000391806:p.Ala565Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		214	0.09798534798534798	62	0.12601626016260162	34	0.09392265193370165	48	0.08391608391608392	70	0.09234828496042216	C	14.39	2.522422	0.44866	0.121774	0.084902	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.90732	-2.72;-2.72;-2.72	5.33	1.47	0.22746	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.362459	0.23668	N	0.045755	T	0.68824	0.3043	L	0.28344	0.845	0.37487	D	0.916232	B;B;B;B	0.32918	0.264;0.39;0.39;0.39	B;B;B;B	0.30646	0.118;0.062;0.062;0.062	T	0.55685	-0.8102	9	0.32370	T	0.25	-28.5102	6.9703	0.24644	0.0:0.5109:0.0:0.4891	rs2228396;rs17885149;rs2228396	565;566;565;565	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	T	565	ENSP00000364034:A565T;ENSP00000364032:A565T;ENSP00000391806:A565T	ENSP00000364032:A565T	A	-	1	0	XXbac-BPG246D15.9;TAP2	32905787	0.000000	0.05858	0.025000	0.17156	0.989000	0.77384	-0.507000	0.06352	0.212000	0.20703	0.501000	0.49751	GCT	C|0.911;T|0.089	0.089	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	
GRHL3	57822	hgsc.bcm.edu	37	1	24690676	24690676	+	Splice_Site	SNP	G	G	A	rs6694170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24690676G>A	ENST00000350501.5	+	16	1823	c.1696G>A	c.(1696-1698)Gaa>Aaa	p.E566K	STPG1_ENST00000337248.4_Intron|STPG1_ENST00000374409.1_Intron|STPG1_ENST00000468303.1_Intron|STPG1_ENST00000003583.8_Intron|STPG1_ENST00000440416.1_Intron	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	566					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)		TTCTTCCAGGGAAACTTCTCT	0.502													G|||	66	0.0131789	0.0008	0.0173	5008	,	,		20881	0.0		0.0477	False		,,,				2504	0.0051				p.E566K		Atlas-SNP	.											.	GRHL3	69	.	0			c.G1696A						PASS	.																																			SO:0001630	splice_region_variant	57822	exon16			TCCAGGGAAACTT	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.1695-1G>A	1.37:g.24690676G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_198174	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	39	0.017857142857142856	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	33	0.04353562005277045	G	12.34	1.909853	0.33721	.	.	ENSG00000158055	ENST00000350501	T	0.09445	2.98	2.94	1.88	0.25563	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.35822	-0.9773	7	0.87932	D	0	-8.581	6.4548	0.21924	0.0:0.0:0.7101:0.2899	rs6694170;rs52802544;rs6694170	.	.	.	K	566	ENSP00000288955:E566K	ENSP00000288955:E566K	E	+	1	0	GRHL3	24563263	0.000000	0.05858	0.007000	0.13788	0.085000	0.17905	-0.057000	0.11768	1.644000	0.50603	0.467000	0.42956	GAA	G|0.977;A|0.023	0.023	strong		0.502	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	Missense_Mutation
SENP3	26168	hgsc.bcm.edu	37	17	7468277	7468277	+	Splice_Site	SNP	C	C	T	rs35596387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7468277C>T	ENST00000429205.2	+	4	1006	c.957C>T	c.(955-957)agC>agT	p.S319S	SENP3_ENST00000321337.7_Splice_Site_p.S319S|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	319						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)				TTCCACCAGGCATCTTGGACG	0.532													C|||	125	0.0249601	0.0	0.0086	5008	,	,		19654	0.0		0.0388	False		,,,				2504	0.0818				p.S319S		Atlas-SNP	.											.	SENP3	18	.	0			c.C957T						PASS	.	C		21,3889		0,21,1934	53.0	56.0	55.0		957	4.5	1.0	17	dbSNP_126	55	266,8028		7,252,3888	yes	coding-synonymous-near-splice	SENP3	NM_015670.5		7,273,5822	TT,TC,CC		3.2071,0.5371,2.3517		319/575	7468277	287,11917	1955	4147	6102	SO:0001630	splice_region_variant	26168	exon4			ACCAGGCATCTTG	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.956-1C>T	17.37:g.7468277C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				C|0.976;T|0.024	0.024	strong		0.532	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Silent
KRT37	8688	hgsc.bcm.edu	37	17	39578424	39578424	+	Missense_Mutation	SNP	G	G	T	rs2071607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39578424G>T	ENST00000225550.3	-	5	916	c.917C>A	c.(916-918)gCc>gAc	p.A306D	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	306	Coil 2.|Rod.		A -> D (in dbSNP:rs2071607).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GCAGGACATGGCCTGCAGGCT	0.617													G|||	864	0.172524	0.0348	0.1268	5008	,	,		21797	0.3224		0.1759	False		,,,				2504	0.2331				p.A306D		Atlas-SNP	.											.	KRT37	61	.	0			c.C917A						PASS	.	G	ASP/ALA	245,4161		8,229,1966	140.0	106.0	118.0		917	-1.3	0.8	17	dbSNP_96	118	1520,7080		120,1280,2900	no	missense	KRT37	NM_003770.4	126	128,1509,4866	TT,TG,GG		17.6744,5.5606,13.5707	benign	306/450	39578424	1765,11241	2203	4300	6503	SO:0001583	missense	8688	exon5			GACATGGCCTGCA	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.917C>A	17.37:g.39578424G>T	ENSP00000225550:p.Ala306Asp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	381	0.17445054945054944	21	0.042682926829268296	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	13.24	2.177273	0.38413	0.055606	0.176744	ENSG00000108417	ENST00000225550	D	0.90385	-2.66	4.83	-1.33	0.09172	Filament (1);	0.509712	0.16338	N	0.218833	T	0.00012	0.0000	M	0.62723	1.935	0.58432	P	4.000000000004E-6	B	0.13145	0.007	B	0.16289	0.015	T	0.15263	-1.0443	9	0.54805	T	0.06	.	3.5228	0.07748	0.3042:0.0:0.2986:0.3972	rs2071607	306	O76014	KRT37_HUMAN	D	306	ENSP00000225550:A306D	ENSP00000225550:A306D	A	-	2	0	KRT37	36831950	0.000000	0.05858	0.752000	0.31206	0.999000	0.98932	0.732000	0.26072	0.077000	0.16863	0.655000	0.94253	GCC	G|0.854;T|0.146	0.146	strong		0.617	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
PRR12	57479	hgsc.bcm.edu	37	19	50098423	50098423	+	Silent	SNP	G	G	A	rs12462756	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50098423G>A	ENST00000418929.2	+	4	843	c.831G>A	c.(829-831)ccG>ccA	p.P277P		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GCCCACCGCCGCCTGAGCGGG	0.706													G|||	1493	0.298123	0.4962	0.2594	5008	,	,		7581	0.1855		0.17	False		,,,				2504	0.3057				p.P277P		Atlas-SNP	.											.	PRR12	157	.	0			c.G831A						PASS	.	G		1275,2067		250,775,646	7.0	8.0	8.0		831	-5.6	0.2	19	dbSNP_120	8	1150,6072		104,942,2565	no	coding-synonymous	PRR12	NM_020719.1		354,1717,3211	AA,AG,GG		15.9236,38.1508,22.9553		277/2037	50098423	2425,8139	1671	3611	5282	SO:0001819	synonymous_variant	57479	exon4			ACCGCCGCCTGAG	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.831G>A	19.37:g.50098423G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	80	47	0.5875	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			G|0.749;A|0.251	0.251	strong		0.706	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
SLC39A4	55630	hgsc.bcm.edu	37	8	145641564	145641564	+	Missense_Mutation	SNP	T	T	G	rs2280839	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145641564T>G	ENST00000276833.5	-	1	332	c.29A>C	c.(28-30)gAa>gCa	p.E10A	SLC39A4_ENST00000301305.3_Intron|SLC39A4_ENST00000531013.1_5'Flank	NM_001280557.1|NM_017767.2	NP_001267486.1|NP_060237	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	0					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)			AGGGCCTGTTTCCCTTTCAAG	0.662													T|||	2174	0.434105	0.4561	0.4135	5008	,	,		15139	0.38		0.5268	False		,,,				2504	0.3793				p.E10A		Atlas-SNP	.											.	SLC39A4	54	.	0			c.A29C						PASS	.	T	ALA/GLU,	1914,2120		462,990,565	27.0	34.0	32.0		29,	-3.1	0.0	8	dbSNP_100	32	4429,3911		1205,2019,946	yes	missense,intron	SLC39A4	NM_017767.2,NM_130849.2	107,	1667,3009,1511	GG,GT,TT		46.8945,47.4467,48.7393	,	10/623,	145641564	6343,6031	2017	4170	6187	SO:0001583	missense	55630	exon1			CCTGTTTCCCTTT	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		ENST00000276833.5:c.29A>C	8.37:g.145641564T>G	ENSP00000276833:p.Glu10Ala	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_017767	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000276833.5	37	CCDS43782.1	1061	0.4858058608058608	242	0.491869918699187	166	0.4585635359116022	238	0.4160839160839161	415	0.5474934036939314	T	13.03	2.114534	0.37339	0.474467	0.531055	ENSG00000147804	ENST00000276833	T	0.61627	0.09	3.0	-3.1	0.05315	.	.	.	.	.	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	0.45396	-0.9264	8	0.87932	D	0	.	5.3	0.15773	0.0:0.5884:0.1949:0.2167	rs2280839;rs61327800;rs2280839	10	A6NDY5	.	A	10	ENSP00000276833:E10A	ENSP00000276833:E10A	E	-	2	0	SLC39A4	145612372	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.695000	0.05109	-0.557000	0.06126	0.254000	0.18369	GAA	T|0.522;G|0.478	0.478	strong		0.662	SLC39A4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382687.2		
ZCCHC6	79670	hgsc.bcm.edu	37	9	88959938	88959938	+	Silent	SNP	C	C	T	rs791323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:88959938C>T	ENST00000375963.3	-	5	1123	c.951G>A	c.(949-951)ctG>ctA	p.L317L	ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375948.1_5'Flank|ZCCHC6_ENST00000375947.1_Silent_p.L150L|ZCCHC6_ENST00000375960.2_Silent_p.L317L|ZCCHC6_ENST00000375961.2_Silent_p.L317L	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	317					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						GTTTAATTTCCAGCCTCTGTT	0.383													T|||	3102	0.619409	0.8253	0.5288	5008	,	,		19149	0.5308		0.5447	False		,,,				2504	0.5736				p.L317L		Atlas-SNP	.											ZCCHC6,colon,carcinoma,0,1	ZCCHC6	105	1	0			c.G951A						PASS	.	T	,,	3447,959	362.6+/-316.2	1346,755,102	143.0	130.0	134.0		951,951,951	2.7	1.0	9	dbSNP_86	134	4670,3930	548.2+/-385.3	1249,2172,879	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC6	NM_001185059.1,NM_001185074.1,NM_024617.3	,,	2595,2927,981	TT,TC,CC		45.6977,21.7658,37.5903	,,	317/1496,317/1260,317/1496	88959938	8117,4889	2203	4300	6503	SO:0001819	synonymous_variant	79670	exon5			AATTTCCAGCCTC	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.951G>A	9.37:g.88959938C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Silent	SNP	ENST00000375963.3	37	CCDS35057.1																																																																																			C|0.379;N|0.000	.	strong		0.383	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
OR1D5	8386	hgsc.bcm.edu	37	17	2966308	2966308	+	Silent	SNP	C	C	T	rs2855605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2966308C>T	ENST00000575751.1	-	1	593	c.594G>A	c.(592-594)gcG>gcA	p.A198A		NM_014566.1	NP_055381.1	P58170	OR1D5_HUMAN	olfactory receptor, family 1, subfamily D, member 5	198					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|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(1)|lung(10)	11						TGGCAATCAACGCTGTGTGAA	0.522																																					p.A198A		Atlas-SNP	.											.	OR1D5	33	.	0			c.G594A						PASS	.	C		1585,2787		45,1495,646	97.0	104.0	102.0		594	1.1	0.0	17	dbSNP_100	102	2957,5637		2,2953,1342	no	coding-synonymous	OR1D5	NM_014566.1		47,4448,1988	TT,TC,CC		34.4077,36.2534,35.0301		198/313	2966308	4542,8424	2186	4297	6483	SO:0001819	synonymous_variant	8386	exon1			AATCAACGCTGTG	AF087923	CCDS58499.1	17p13.3	2012-10-09			ENSG00000262628	ENSG00000262628		"""GPCR / Class A : Olfactory receptors"""	8186	protein-coding gene	gene with protein product						10673334	Standard	NM_014566		Approved	OR17-31	uc021tns.1	P58170	OTTHUMG00000177676	ENST00000575751.1:c.594G>A	17.37:g.2966308C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	273	73	0.267399	NM_014566	Q96RA6	Silent	SNP	ENST00000575751.1	37	CCDS58499.1																																																																																			C|0.826;T|0.174	0.174	strong		0.522	OR1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438410.2	NM_014566	
RING1	6015	hgsc.bcm.edu	37	6	33179689	33179689	+	Silent	SNP	C	C	T	rs2854028	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33179689C>T	ENST00000374656.4	+	6	1237	c.1029C>T	c.(1027-1029)gaC>gaT	p.D343D	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	343	Gly-rich.|Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|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)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						GAGGAGGTGACGGTCCTGAGG	0.667													C|||	876	0.17492	0.0272	0.2219	5008	,	,		11671	0.1488		0.2147	False		,,,				2504	0.3272				p.D343D		Atlas-SNP	.											.	RING1	40	.	0			c.C1029T						PASS	.	C		259,4137		11,237,1950	21.0	25.0	24.0		1029	-3.6	0.8	6	dbSNP_100	24	2034,6556		229,1576,2490	yes	coding-synonymous	RING1	NM_002931.3		240,1813,4440	TT,TC,CC		23.6787,5.8917,17.6575		343/407	33179689	2293,10693	2198	4295	6493	SO:0001819	synonymous_variant	6015	exon6			AGGTGACGGTCCT		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"""RING-type (C3HC4) zinc fingers"""	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.1029C>T	6.37:g.33179689C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Silent	SNP	ENST00000374656.4	37	CCDS34424.1																																																																																			C|0.842;T|0.158	0.158	strong		0.667	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2		
PCDHB10	56126	hgsc.bcm.edu	37	5	140572763	140572763	+	Missense_Mutation	SNP	C	C	G	rs2907323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	130	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	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	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807523	18807523	+	Silent	SNP	G	G	A	rs377259272		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:18807523G>A	ENST00000400664.1	+	1	100	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	16						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)		TGGATATGCAGCTGACCGGCA	0.592																																					p.Q16Q		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G48A						PASS	.	G		1,4111		0,1,2055	51.0	57.0	55.0		48	4.9	1.0	1		55	0,8434		0,0,4217	no	coding-synonymous	KLHDC7A	NM_152375.2		0,1,6272	AA,AG,GG		0.0,0.0243,0.0080		16/778	18807523	1,12545	2056	4217	6273	SO:0001819	synonymous_variant	127707	exon1			TATGCAGCTGACC	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.48G>A	1.37:g.18807523G>A		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	218	113	0.518349	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			.	.	none		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
TATDN2	9797	hgsc.bcm.edu	37	3	10312507	10312507	+	Silent	SNP	A	A	G	rs2075353	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:10312507A>G	ENST00000287652.4	+	4	2692	c.1641A>G	c.(1639-1641)ctA>ctG	p.L547L	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.L547L	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	547					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						CAGATTGCCTATGGGAGGAGC	0.478													A|||	560	0.111821	0.0113	0.0576	5008	,	,		19167	0.2857		0.1034	False		,,,				2504	0.1155				p.L547L		Atlas-SNP	.											.	TATDN2	59	.	0			c.A1641G						PASS	.	A		122,4284	89.2+/-127.9	2,118,2083	107.0	112.0	110.0		1641	-5.2	0.8	3	dbSNP_96	110	816,7784	185.2+/-233.0	31,754,3515	no	coding-synonymous	TATDN2	NM_014760.3		33,872,5598	GG,GA,AA		9.4884,2.769,7.2121		547/762	10312507	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			TTGCCTATGGGAG	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.1641A>G	3.37:g.10312507A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			A|0.910;G|0.090	0.090	strong		0.478	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
TMEM52	339456	hgsc.bcm.edu	37	1	1849529	1849529	+	Missense_Mutation	SNP	A	A	G	rs28640257	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1849529A>G	ENST00000310991.3	-	5	429	c.422T>C	c.(421-423)aTg>aCg	p.M141T	TMEM52_ENST00000378602.3_Missense_Mutation_p.M126T	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	141			M -> T (in dbSNP:rs28640257). {ECO:0000269|PubMed:12975309}.|M -> V (in dbSNP:rs4459050).			integral component of membrane (GO:0016021)		p.M141T(1)		NS(1)|prostate(1)|stomach(1)	3	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGGAGGAGCCATGGAGTCCAG	0.627													A|||	1763	0.352037	0.053	0.5072	5008	,	,		19495	0.4623		0.4901	False		,,,				2504	0.3906				p.M141T		Atlas-SNP	.											TMEM52,NS,carcinoma,0,2	TMEM52	21	2	1	Substitution - Missense(1)	stomach(1)	c.T422C						PASS	.	A	THR/MET	532,3874		39,454,1710	90.0	88.0	89.0		422	0.2	0.0	1	dbSNP_125	89	4288,4312		1092,2104,1104	no	missense	TMEM52	NM_178545.3	81	1131,2558,2814	GG,GA,AA		49.8605,12.0744,37.0598	benign	141/210	1849529	4820,8186	2203	4300	6503	SO:0001583	missense	339456	exon5			GGAGCCATGGAGT	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.422T>C	1.37:g.1849529A>G	ENSP00000311122:p.Met141Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_178545	Q4VXS6|Q6UX25	Missense_Mutation	SNP	ENST00000310991.3	37	CCDS35.1	846	0.3873626373626374	32	0.06504065040650407	183	0.505524861878453	258	0.45104895104895104	373	0.4920844327176781	.	3.602	-0.081358	0.07141	0.120744	0.498605	ENSG00000178821	ENST00000378602;ENST00000310991	T;T	0.31510	1.49;1.49	3.84	0.201	0.15186	.	0.206931	0.29515	N	0.011934	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14438	0.002;0.01	B;B	0.12837	0.002;0.008	T	0.47209	-0.9135	9	0.16420	T	0.52	-5.174	3.3609	0.07186	0.6178:0.0:0.2079:0.1743	rs28640257	141;126	Q8NDY8;Q8NDY8-2	TMM52_HUMAN;.	T	126;141	ENSP00000367865:M126T;ENSP00000311122:M141T	ENSP00000311122:M141T	M	-	2	0	TMEM52	1839389	0.000000	0.05858	0.018000	0.16275	0.849000	0.48306	0.105000	0.15333	0.143000	0.18926	0.459000	0.35465	ATG	A|0.613;G|0.387;T|0.000	0.387	strong		0.627	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545	
SEC16B	89866	hgsc.bcm.edu	37	1	177902725	177902725	+	Missense_Mutation	SNP	C	C	T	rs3813649	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177902725C>T	ENST00000308284.6	-	21	2707	c.2618G>A	c.(2617-2619)aGt>aAt	p.S873N	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	873			S -> N (in dbSNP:rs3813649). {ECO:0000269|PubMed:17974005}.		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						CTTGGCTGAACTGGCGGAACT	0.478													T|||	1098	0.219249	0.2352	0.2594	5008	,	,		19789	0.1052		0.2604	False		,,,				2504	0.2444				p.S873N		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2618A						PASS	.	T	ASN/SER	985,2803		117,751,1026	74.0	73.0	74.0		2618	-10.2	0.0	1	dbSNP_107	74	1950,6310		237,1476,2417	yes	missense	SEC16B	NM_033127.2	46	354,2227,3443	TT,TC,CC		23.6077,26.0032,24.3609	benign	873/1061	177902725	2935,9113	1894	4130	6024	SO:0001583	missense	89866	exon21			GCTGAACTGGCGG	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.2618G>A	1.37:g.177902725C>T	ENSP00000308339:p.Ser873Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	141	48	0.340426	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	450	0.20604395604395603	96	0.1951219512195122	90	0.24861878453038674	71	0.12412587412587413	193	0.2546174142480211	T	3.674	-0.066930	0.07273	0.260032	0.236077	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.14022	2.54	5.11	-10.2	0.00374	.	3.603110	0.00508	N	0.000175	T	0.00012	0.0000	N	0.08118	0	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	0.25433	-1.0132	9	0.15952	T	0.53	15.6611	2.8549	0.05569	0.1716:0.1967:0.404:0.2277	rs3813649;rs52834956;rs3813649	428;874;873;570	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	N	873;557;588	ENSP00000308339:S873N	ENSP00000239472:S588N	S	-	2	0	AL359075.1	176169348	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.654000	0.01984	-4.241000	0.00062	-3.232000	0.00051	AGT	C|0.799;T|0.201	0.201	strong		0.478	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
TARBP1	6894	hgsc.bcm.edu	37	1	234603386	234603386	+	Silent	SNP	G	G	T	rs270502	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:234603386G>T	ENST00000040877.1	-	4	1109	c.1110C>A	c.(1108-1110)ctC>ctA	p.L370L		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	370					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)			ATGGGTGAAAGAGCCAACATC	0.348													G|||	624	0.124601	0.1044	0.1427	5008	,	,		21554	0.0		0.3141	False		,,,				2504	0.0726				p.L370L		Atlas-SNP	.											.	TARBP1	111	.	0			c.C1110A						PASS	.	G		628,3778	267.1+/-267.6	41,546,1616	65.0	65.0	65.0		1110	4.2	1.0	1	dbSNP_79	65	2569,6031	413.7+/-351.2	388,1793,2119	no	coding-synonymous	TARBP1	NM_005646.3		429,2339,3735	TT,TG,GG		29.8721,14.2533,24.581		370/1622	234603386	3197,9809	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon4			GTGAAAGAGCCAA		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.1110C>A	1.37:g.234603386G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	126	72	0.571429	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			G|0.791;T|0.209	0.209	strong		0.348	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
WDR59	79726	hgsc.bcm.edu	37	16	75018874	75018874	+	Silent	SNP	G	G	A	rs12448858	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:75018874G>A	ENST00000262144.6	-	1	172	c.42C>T	c.(40-42)ttC>ttT	p.F14F	WDR59_ENST00000562331.1_Intron	NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	14										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						GGGAGTCACGGAACTCTACAA	0.731													A|||	600	0.119808	0.3351	0.0764	5008	,	,		12715	0.001		0.0616	False		,,,				2504	0.0419				p.F14F		Atlas-SNP	.											.	WDR59	66	.	0			c.C42T						PASS	.	A		1097,3283		149,799,1242	67.0	52.0	57.0		42	0.2	1.0	16	dbSNP_120	57	510,8086		24,462,3812	no	coding-synonymous	WDR59	NM_030581.3		173,1261,5054	AA,AG,GG		5.933,25.0457,12.3844		14/975	75018874	1607,11369	2190	4298	6488	SO:0001819	synonymous_variant	79726	exon1			GTCACGGAACTCT	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.42C>T	16.37:g.75018874G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	37	CCDS32488.1																																																																																			G|0.886;A|0.114	0.114	strong		0.731	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
FREM2	341640	hgsc.bcm.edu	37	13	39263023	39263023	+	Silent	SNP	C	C	T	rs12874397	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	44	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	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	
OR52E6	390078	hgsc.bcm.edu	37	11	5862653	5862653	+	Missense_Mutation	SNP	T	T	C	rs4357719	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5862653T>C	ENST00000329322.5	-	1	474	c.475A>G	c.(475-477)Att>Gtt	p.I159V	TRIM5_ENST00000380027.1_Intron|OR52E6_ENST00000379946.2_Missense_Mutation_p.I163V	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	159			I -> V (in dbSNP:rs4357719).			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(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCAGTGGAATGACCATGTAC	0.498													t|||	1924	0.384185	0.3782	0.3184	5008	,	,		20596	0.4593		0.3728	False		,,,				2504	0.3732				p.I159V		Atlas-SNP	.											.	OR52E6	70	.	0			c.A475G						PASS	.	C	VAL/ILE	1615,2787	499.3+/-364.4	291,1033,877	170.0	157.0	162.0		475	-6.9	0.0	11	dbSNP_111	162	3009,5583	464.3+/-366.2	533,1943,1820	yes	missense	OR52E6	NM_001005167.1	29	824,2976,2697	CC,CT,TT		35.0209,36.6879,35.5857	benign	159/314	5862653	4624,8370	2201	4296	6497	SO:0001583	missense	390078	exon1			GTGGAATGACCAT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.475A>G	11.37:g.5862653T>C	ENSP00000328878:p.Ile159Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	879	0.4024725274725275	201	0.40853658536585363	120	0.3314917127071823	264	0.46153846153846156	294	0.38786279683377306	t	0.012	-1.651578	0.00785	0.366879	0.350209	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.37584	1.19;1.19	3.45	-6.91	0.01649	GPCR, rhodopsin-like superfamily (1);	1.903210	0.02623	N	0.103478	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.23190	-1.0195	9	0.30854	T	0.27	.	0.8012	0.01075	0.1831:0.2466:0.2267:0.3437	rs4357719;rs59781833;rs4357719	159	Q96RD3	O52E6_HUMAN	V	159;163	ENSP00000328878:I159V;ENSP00000369279:I163V	ENSP00000328878:I159V	I	-	1	0	OR52E6	5819229	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-12.782000	0.00001	-3.731000	0.00114	-2.248000	0.00284	ATT	T|0.605;C|0.395	0.395	strong		0.498	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
OR8H3	390152	hgsc.bcm.edu	37	11	55889987	55889987	+	Missense_Mutation	SNP	C	C	A	rs7107077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55889987C>A	ENST00000313472.3	+	1	139	c.139C>A	c.(139-141)Cta>Ata	p.L47I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	47			L -> I (in dbSNP:rs7107077).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L47L(1)		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)					TGTGGGGATGCTATTGATAAT	0.453													A|||	316	0.063099	0.1906	0.0447	5008	,	,		20197	0.001		0.0308	False		,,,				2504	0.001				p.L47I		Atlas-SNP	.											OR8H3,caecum,carcinoma,0,1	OR8H3	92	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C139A						PASS	.	A	ILE/LEU	627,3775		68,491,1642	302.0	304.0	303.0		139	3.4	0.4	11	dbSNP_116	303	337,8255		9,319,3968	no	missense	OR8H3	NM_001005201.1	5	77,810,5610	AA,AC,CC		3.9223,14.2435,7.4188	benign	47/313	55889987	964,12030	2201	4296	6497	SO:0001583	missense	390152	exon1			GGGATGCTATTGA	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.139C>A	11.37:g.55889987C>A	ENSP00000323928:p.Leu47Ile	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	156	62	0.397436	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	107	0.04899267399267399	70	0.14227642276422764	18	0.049723756906077346	1	0.0017482517482517483	18	0.023746701846965697	A	0	-2.823779	0.00071	0.142435	0.039223	ENSG00000181761	ENST00000313472	T	0.00378	7.66	3.44	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.204125	0.35179	N	0.003382	T	0.00012	0.0000	N	0.00405	-1.535	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10497	-1.0627	9	0.02654	T	1	.	5.5115	0.16884	0.5681:0.3353:0.0966:0.0	rs7107077;rs7112617	47	Q8N146	OR8H3_HUMAN	I	47	ENSP00000323928:L47I	ENSP00000323928:L47I	L	+	1	2	OR8H3	55646563	0.033000	0.19621	0.401000	0.26359	0.041000	0.13682	0.065000	0.14466	0.334000	0.23590	-1.536000	0.00914	CTA	C|0.950;A|0.050	0.050	strong		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
ABCA13	154664	hgsc.bcm.edu	37	7	48506642	48506642	+	Splice_Site	SNP	A	A	G	rs4917153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:48506642A>G	ENST00000435803.1	+	44	12929	c.12905A>G	c.(12904-12906)cAg>cGg	p.Q4302R	ABCA13_ENST00000544596.1_Intron	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4302			Q -> R (in dbSNP:rs4917153).		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						AACCCACGCCAGTAAGTGTCA	0.473													A|||	1155	0.230631	0.3525	0.2594	5008	,	,		16407	0.2163		0.1491	False		,,,				2504	0.1442				p.Q4302R		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A12905G						PASS	.	A	ARG/GLN	1137,2767		154,829,969	106.0	109.0	108.0		12905	-4.2	0.0	7	dbSNP_111	108	1004,7328		53,898,3215	yes	missense-near-splice	ABCA13	NM_152701.3	43	207,1727,4184	GG,GA,AA		12.0499,29.124,17.4975	benign	4302/5059	48506642	2141,10095	1952	4166	6118	SO:0001630	splice_region_variant	154664	exon44			CACGCCAGTAAGT	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.12905+1A>G	7.37:g.48506642A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	139	43	0.309353	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	493	0.22573260073260074	156	0.3170731707317073	91	0.2513812154696133	128	0.22377622377622378	118	0.15567282321899736	A	6.840	0.524274	0.13066	0.29124	0.120499	ENSG00000179869	ENST00000435803	D	0.85258	-1.96	5.29	-4.24	0.03777	.	2.536950	0.02036	N	0.048937	T	0.00012	0.0000	N	0.04508	-0.205	0.20975	P	0.999813732	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.06625	-1.0816	9	0.14656	T	0.56	.	4.4949	0.11831	0.5493:0.166:0.0:0.2847	rs4917153;rs10359028;rs52807126;rs60526568;rs4917153	2004;4302	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	R	4302	ENSP00000411096:Q4302R	ENSP00000411096:Q4302R	Q	+	2	0	ABCA13	48477188	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-1.436000	0.02421	-0.497000	0.06641	-0.339000	0.08088	CAG	A|0.777;G|0.223	0.223	strong		0.473	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	Missense_Mutation
FCRL6	343413	hgsc.bcm.edu	37	1	159785370	159785370	+	Silent	SNP	T	T	C	rs4301626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:159785370T>C	ENST00000368106.3	+	10	1225	c.1224T>C	c.(1222-1224)agT>agC	p.S408S	FCRL6_ENST00000321935.6_Nonstop_Mutation_p.*414R|FCRL6_ENST00000392235.3_Nonstop_Mutation_p.*312R|FCRL6_ENST00000339348.5_Nonstop_Mutation_p.*398R	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	408						external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.S408S(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					TGCAGCCCAGTGAGGTTTCAT	0.507													.|||	960	0.191693	0.4402	0.1499	5008	,	,		21238	0.1567		0.0616	False		,,,				2504	0.0552				p.S408S		Atlas-SNP	.											FCRL6,NS,carcinoma,0,1	FCRL6	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T1224C						PASS	.	T		1752,2654	523.1+/-371.0	357,1038,808	126.0	125.0	125.0		1224	-5.0	0.0	1	dbSNP_111	125	525,8075	147.7+/-203.1	13,499,3788	no	coding-synonymous	FCRL6	NM_001004310.2		370,1537,4596	CC,CT,TT		6.1047,39.764,17.5073		408/435	159785370	2277,10729	2203	4300	6503	SO:0001819	synonymous_variant	343413	exon10			GCCCAGTGAGGTT	AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.1224T>C	1.37:g.159785370T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	127	42	0.330709	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Silent	SNP	ENST00000368106.3	37	CCDS30912.1	385	0.1762820512820513	196	0.3983739837398374	47	0.1298342541436464	105	0.18356643356643357	37	0.048812664907651716	T	4.474	0.087809	0.08583	0.39764	0.061047	ENSG00000181036	ENST00000321935;ENST00000339348;ENST00000392235	.	.	.	3.87	-5.04	0.02964	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.2691	0.00229	0.2818:0.1849:0.2881:0.2452	rs4301626;rs57602564;rs4301626	.	.	.	R	414;398;312	.	.	X	+	1	0	FCRL6	158051994	0.000000	0.05858	0.000000	0.03702	0.155000	0.21991	-0.351000	0.07711	-1.064000	0.03172	0.402000	0.26972	TGA	T|0.814;C|0.186	0.186	strong		0.507	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310	
SIM2	6493	hgsc.bcm.edu	37	21	38117308	38117308	+	Missense_Mutation	SNP	C	C	A	rs2073601	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	77	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	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	
MOCS2	4338	hgsc.bcm.edu	37	5	52398005	52398005	+	Missense_Mutation	SNP	T	T	C	rs2233213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:52398005T>C	ENST00000396954.3	-	4	825	c.148A>G	c.(148-150)Act>Gct	p.T50A	MOCS2_ENST00000584946.1_Intron|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000510818.2_3'UTR|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000361377.4_3'UTR	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				TTCTCGGCAGTAAAGTTTATA	0.358													T|||	182	0.0363419	0.0151	0.0548	5008	,	,		16945	0.0665		0.0368	False		,,,				2504	0.0204				p.T50A		Atlas-SNP	.											.	MOCS2	28	.	0			c.A148G						PASS	.	T	ALA/THR,	94,4312	77.3+/-115.6	0,94,2109	88.0	83.0	85.0		148,	6.0	0.4	5	dbSNP_98	85	323,8277	113.9+/-173.9	6,311,3983	yes	missense,utr-3	MOCS2	NM_004531.3,NM_176806.2	58,	6,405,6092	CC,CT,TT		3.7558,2.1335,3.2062	possibly-damaging,	50/189,	52398005	417,12589	2203	4300	6503	SO:0001583	missense	4338	exon4			CGGCAGTAAAGTT	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.148A>G	5.37:g.52398005T>C	ENSP00000380157:p.Thr50Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_004531		Missense_Mutation	SNP	ENST00000396954.3	37	CCDS3958.1	105	0.04807692307692308	6	0.012195121951219513	20	0.055248618784530384	51	0.08916083916083917	28	0.036939313984168866	T	13.89	2.370873	0.42003	0.021335	0.037558	ENSG00000164172	ENST00000396954;ENST00000527216	T	0.22336	1.96	6.03	6.03	0.97812	.	0.168870	0.52532	D	0.000065	T	0.01454	0.0047	M	0.85099	2.735	0.80722	D	1	P	0.38535	0.635	B	0.39935	0.314	T	0.00350	-1.1797	10	0.49607	T	0.09	-9.8708	16.5724	0.84622	0.0:0.0:0.0:1.0	rs2233213;rs2233213	50	O96007	MOC2B_HUMAN	A	50	ENSP00000380157:T50A	ENSP00000380157:T50A	T	-	1	0	MOCS2	52433762	1.000000	0.71417	0.355000	0.25773	0.041000	0.13682	4.542000	0.60677	2.313000	0.78055	0.455000	0.32223	ACT	T|0.960;C|0.040	0.040	strong		0.358	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418	
PRRC2B	84726	hgsc.bcm.edu	37	9	134350231	134350231	+	Silent	SNP	C	C	T	rs17458486	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134350231C>T	ENST00000357304.4	+	15	2770	c.2715C>T	c.(2713-2715)aaC>aaT	p.N905N	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	905							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GGGACAAGAACGGGAGCCCCA	0.647													C|||	243	0.0485224	0.0083	0.1383	5008	,	,		15009	0.0556		0.0577	False		,,,				2504	0.0225				p.N905N		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C2715T						PASS	.	C		74,3820		1,72,1874	12.0	14.0	13.0		2715	-9.4	0.3	9	dbSNP_123	13	373,7881		13,347,3767	no	coding-synonymous	PRRC2B	NM_013318.3		14,419,5641	TT,TC,CC		4.519,1.9004,3.6796		905/2230	134350231	447,11701	1947	4127	6074	SO:0001819	synonymous_variant	84726	exon15			CAAGAACGGGAGC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.2715C>T	9.37:g.134350231C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1																																																																																			C|0.945;T|0.055	0.055	strong		0.647	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CCT6B	10693	hgsc.bcm.edu	37	17	33286664	33286664	+	Missense_Mutation	SNP	A	A	G	rs2230552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:33286664A>G	ENST00000314144.5	-	2	258	c.143T>C	c.(142-144)gTt>gCt	p.V48A	CCT6B_ENST00000436961.3_Missense_Mutation_p.V48A|CCT6B_ENST00000421975.3_Missense_Mutation_p.V48A|ZNF830_ENST00000361952.3_5'Flank	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	48			V -> A (in dbSNP:rs2230552). {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)				TGCACCAGAAACAAGCCTGTT	0.443													A|||	1457	0.290935	0.1225	0.2968	5008	,	,		18889	0.5278		0.2018	False		,,,				2504	0.362				p.V48A		Atlas-SNP	.											.	CCT6B	63	.	0			c.T143C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	547,3859	246.2+/-254.9	27,493,1683	116.0	101.0	106.0		143,143,143	4.3	1.0	17	dbSNP_98	106	1829,6771	326.4+/-317.4	196,1437,2667	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	64,64,64	223,1930,4350	GG,GA,AA		21.2674,12.4149,18.2685	probably-damaging,probably-damaging,probably-damaging	48/494,48/486,48/531	33286664	2376,10630	2203	4300	6503	SO:0001583	missense	10693	exon2			CCAGAAACAAGCC	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.143T>C	17.37:g.33286664A>G	ENSP00000327191:p.Val48Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	635	0.2907509157509158	62	0.12601626016260162	103	0.2845303867403315	322	0.5629370629370629	148	0.19525065963060687	A	23.1	4.379366	0.82682	0.124149	0.212674	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.80566	-1.39;-1.39;-1.39	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.99415	4.555	0.09310	P	0.999999893117	D;D;D	0.76494	0.996;0.998;0.999	D;D;D	0.72982	0.973;0.973;0.979	T	0.20306	-1.0279	9	0.87932	D	0	-19.3143	11.7011	0.51571	1.0:0.0:0.0:0.0	rs2230552;rs11658803;rs17845802;rs17855522;rs17858764;rs52817302;rs59421844;rs11658803	48;48;48	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	A	48	ENSP00000398044:V48A;ENSP00000327191:V48A;ENSP00000400917:V48A	ENSP00000327191:V48A	V	-	2	0	CCT6B	30310777	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.208000	0.89748	1.909000	0.55274	0.455000	0.32223	GTT	T|0.130;G|0.183	0.183	strong		0.443	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_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						PASS	.						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	110	0	0		WXS	Illumina HiSeq	Phase_I	65	20	0.307692	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	
GPR37L1	9283	hgsc.bcm.edu	37	1	202092332	202092332	+	Missense_Mutation	SNP	C	C	G	rs3795594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202092332C>G	ENST00000367282.5	+	1	347	c.241C>G	c.(241-243)Ccc>Gcc	p.P81A		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	81			P -> A (in dbSNP:rs3795594).		negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						GCCAACCAAGCCCTTGGTGGC	0.662													C|||	1118	0.223243	0.3094	0.2579	5008	,	,		18392	0.3423		0.0606	False		,,,				2504	0.1268				p.P81A		Atlas-SNP	.											.	GPR37L1	33	.	0			c.C241G						PASS	.	C	ALA/PRO	1230,3176	413.5+/-336.5	176,878,1149	41.0	40.0	41.0		241	-0.7	0.0	1	dbSNP_107	41	530,8070	144.5+/-200.4	15,500,3785	yes	missense	GPR37L1	NM_004767.3	27	191,1378,4934	GG,GC,CC		6.1628,27.9165,13.5322	benign	81/482	202092332	1760,11246	2203	4300	6503	SO:0001583	missense	9283	exon1			ACCAAGCCCTTGG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.241C>G	1.37:g.202092332C>G	ENSP00000356251:p.Pro81Ala	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	67	22	0.328358	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Missense_Mutation	SNP	ENST00000367282.5	37	CCDS1420.1	519	0.23763736263736263	152	0.3089430894308943	92	0.2541436464088398	230	0.4020979020979021	45	0.059366754617414245	C	10.51	1.370807	0.24771	0.279165	0.061628	ENSG00000170075	ENST00000367282	T	0.78924	-1.22	5.13	-0.693	0.11298	.	1.034510	0.07643	N	0.930710	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19549	-1.0302	9	0.51188	T	0.08	-8.5546	3.9173	0.09228	0.2601:0.2784:0.3819:0.0796	rs3795594;rs3795594	81	O60883	ETBR2_HUMAN	A	81	ENSP00000356251:P81A	ENSP00000356251:P81A	P	+	1	0	GPR37L1	200358955	0.000000	0.05858	0.002000	0.10522	0.984000	0.73092	-0.977000	0.03782	0.123000	0.18342	0.462000	0.41574	CCC	C|0.829;G|0.171	0.171	strong		0.662	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767	
CHRD	8646	hgsc.bcm.edu	37	3	184099342	184099342	+	Silent	SNP	G	G	C	rs3749228	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184099342G>C	ENST00000204604.1	+	4	687	c.441G>C	c.(439-441)ccG>ccC	p.P147P	CHRD_ENST00000450923.1_Silent_p.P147P|CHRD_ENST00000348986.3_Silent_p.P147P|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000545352.1_5'Flank|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	147					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)			CGCGGGACCCGGAGCATCGCA	0.706													G|||	562	0.11222	0.1626	0.1268	5008	,	,		12428	0.1022		0.0676	False		,,,				2504	0.09				p.P147P		Atlas-SNP	.											.	CHRD	149	.	0			c.G441C						PASS	.	G		446,3866		30,386,1740	10.0	16.0	14.0		441	-6.9	0.9	3	dbSNP_107	14	448,8076		16,416,3830	no	coding-synonymous	CHRD	NM_003741.2		46,802,5570	CC,CG,GG		5.2557,10.3432,6.9648		147/956	184099342	894,11942	2156	4262	6418	SO:0001819	synonymous_variant	8646	exon4			GGACCCGGAGCAT	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.441G>C	3.37:g.184099342G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	90	88	0.977778	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			G|0.904;C|0.096	0.096	strong		0.706	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
COLGALT2	23127	hgsc.bcm.edu	37	1	183920191	183920191	+	Silent	SNP	T	T	G	rs16861794	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:183920191T>G	ENST00000361927.4	-	8	1457	c.1086A>C	c.(1084-1086)acA>acC	p.T362T	COLGALT2_ENST00000546159.1_Silent_p.T362T|COLGALT2_ENST00000367520.3_Silent_p.T99T	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	362					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GTTCATACAGTGTGCGCAGCA	0.453													T|||	199	0.0397364	0.0363	0.0159	5008	,	,		17756	0.0635		0.0308	False		,,,				2504	0.046				p.T362T		Atlas-SNP	.											GLT25D2,NS,carcinoma,0,1	.	.	1	0			c.A1086C						scavenged	.	T		196,4210	120.8+/-158.4	4,188,2011	271.0	258.0	262.0		1086	-7.9	0.9	1	dbSNP_123	262	258,8342	100.6+/-161.9	4,250,4046	no	coding-synonymous	GLT25D2	NM_015101.2		8,438,6057	GG,GT,TT		3.0,4.4485,3.4907		362/627	183920191	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	23127	exon8			ATACAGTGTGCGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 17"", ""glycosyltransferase 25 domain containing 2"""	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.1086A>C	1.37:g.183920191T>G		Somatic	149	4	0.0268456		WXS	Illumina HiSeq	Phase_I	200	78	0.39	NM_015101	O60327|Q9BZR0	Silent	SNP	ENST00000361927.4	37	CCDS1360.1																																																																																			T|0.954;G|0.046	0.046	strong		0.453	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101	
WDR90	197335	hgsc.bcm.edu	37	16	711712	711712	+	Silent	SNP	C	C	T	rs3177415	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	75	0	0		WXS	Illumina HiSeq	Phase_I	112	109	0.973214	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	
DOCK2	1794	hgsc.bcm.edu	37	5	169267839	169267839	+	Missense_Mutation	SNP	C	C	T	rs200070944		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169267839C>T	ENST00000256935.8	+	27	2862	c.2782C>T	c.(2782-2784)Cgg>Tgg	p.R928W	DOCK2_ENST00000520908.1_Missense_Mutation_p.R420W|DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	928					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACCATGGGCCGGGATCACAT	0.458																																					p.R928W		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2782T						PASS	.						126.0	108.0	114.0					5																	169267839		2203	4300	6503	SO:0001583	missense	1794	exon27			ATGGGCCGGGATC	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.2782C>T	5.37:g.169267839C>T	ENSP00000256935:p.Arg928Trp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527368	0.64860	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628	T;T	0.69306	-0.39;-0.39	5.28	5.28	0.74379	.	0.120890	0.56097	D	0.000022	T	0.70518	0.3233	M	0.71036	2.16	0.80722	D	1	D;D	0.65815	0.995;0.959	P;B	0.49387	0.609;0.245	T	0.73202	-0.4057	10	0.49607	T	0.09	.	11.5168	0.50526	0.1792:0.8208:0.0:0.0	.	420;928	E7ERW7;Q92608	.;DOCK2_HUMAN	W	928;309;420;132	ENSP00000256935:R928W;ENSP00000429283:R420W	ENSP00000256935:R928W	R	+	1	2	DOCK2	169200417	0.994000	0.37717	1.000000	0.80357	0.778000	0.44026	3.353000	0.52247	2.460000	0.83146	0.585000	0.79938	CGG	C|0.999;A|0.001	.	alt		0.458	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:46760481C>G	ENST00000262738.3	-	33	8706	c.8707G>C	c.(8707-8709)Gag>Cag	p.E2903Q		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2903			E -> Q (in dbSNP:rs9615351).		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)		GGGGGGTACTCTCCACGGTGA	0.687													C|||	1203	0.240216	0.5492	0.1816	5008	,	,		16369	0.005		0.2455	False		,,,				2504	0.1012				p.E2903Q		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	1	0			c.G8707C						PASS	.	C	GLN/GLU	2305,2093	560.8+/-380.6	594,1117,488	31.0	36.0	34.0		8707	-1.8	0.0	22	dbSNP_119	34	2074,6516	337.7+/-322.4	228,1618,2449	yes	missense	CELSR1	NM_014246.1	29	822,2735,2937	GG,GC,CC		24.1444,47.5898,33.7157	possibly-damaging	2903/3015	46760481	4379,8609	2199	4295	6494	SO:0001583	missense	9620	exon33			GGTACTCTCCACG	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.8707G>C	22.37:g.46760481C>G	ENSP00000262738:p.Glu2903Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	515	0.2358058608058608	265	0.5386178861788617	73	0.20165745856353592	1	0.0017482517482517483	176	0.23218997361477572	C	11.43	1.635840	0.29068	0.524102	0.241444	ENSG00000075275	ENST00000262738	T	0.70516	-0.49	3.64	-1.76	0.08006	.	0.482328	0.14430	U	0.320053	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	P	0.39665	0.682	B	0.38428	0.273	T	0.43065	-0.9414	9	0.21540	T	0.41	.	2.3608	0.04307	0.1521:0.5191:0.1482:0.1806	rs9615351;rs60150914	2903	Q9NYQ6	CELR1_HUMAN	Q	2903	ENSP00000262738:E2903Q	ENSP00000262738:E2903Q	E	-	1	0	CELSR1	45139145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.527000	0.22987	-0.226000	0.09899	-0.251000	0.11542	GAG	C|0.700;G|0.300	0.300	strong		0.687	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
C2orf54	79919	hgsc.bcm.edu	37	2	241830969	241830969	+	Silent	SNP	G	G	A	rs10171067	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241830969G>A	ENST00000388934.4	-	2	884	c.726C>T	c.(724-726)agC>agT	p.S242S	C2orf54_ENST00000402775.2_Silent_p.S74S|C2orf54_ENST00000307486.8_Silent_p.S93S	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	68	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	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	
UNC13A	23025	hgsc.bcm.edu	37	19	17743622	17743622	+	Missense_Mutation	SNP	C	C	A	rs75595663	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17743622C>A	ENST00000519716.2	-	28	3396	c.3397G>T	c.(3397-3399)Gcc>Tcc	p.A1133S	UNC13A_ENST00000552293.1_Missense_Mutation_p.A1133S|UNC13A_ENST00000550896.1_Missense_Mutation_p.A1131S|UNC13A_ENST00000551649.1_Missense_Mutation_p.A1133S|UNC13A_ENST00000252773.7_Missense_Mutation_p.A1133S|UNC13A_ENST00000428389.2_Missense_Mutation_p.A1221S	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	126	0	0		WXS	Illumina HiSeq	Phase_I	134	73	0.544776	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	
GALT	2592	hgsc.bcm.edu	37	9	34649442	34649442	+	Missense_Mutation	SNP	A	A	G	rs2070074	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34649442A>G	ENST00000378842.3	+	10	982	c.940A>G	c.(940-942)Aac>Gac	p.N314D	GALT_ENST00000488412.2_3'UTR|GALT_ENST00000556278.1_Intron|IL11RA_ENST00000555003.1_5'Flank|IL11RA_ENST00000441545.2_5'Flank|GALT_ENST00000450095.2_Missense_Mutation_p.N205D	NM_000155.3	NP_000146.2	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase	314			N -> D (in Duarte; exists in two different types, D-1 with normal or increased activity and D-2 with an activity reduced to about 35-45% of normal; dbSNP:rs2070074). {ECO:0000269|PubMed:11754113, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18956253, ECO:0000269|PubMed:2011574, ECO:0000269|PubMed:23022339, ECO:0000269|PubMed:7550229, ECO:0000269|Ref.4}.		carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)|UDP-glucose catabolic process (GO:0006258)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	UDP-glucose:hexose-1-phosphate uridylyltransferase activity (GO:0008108)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(2)|lung(5)|upper_aerodigestive_tract(1)	16	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GGCCAACTGGAACCATTGGCA	0.552									Galactosemia				G|||	365	0.0728834	0.0151	0.0576	5008	,	,		18730	0.0188		0.1024	False		,,,				2504	0.1871				p.N314D		Atlas-SNP	.											.	GALT	29	.	0			c.A940G	GRCh37	CM940804	GALT	M	rs2070074	PASS	.	G	ASP/ASN	127,4279	814.5+/-416.2	1,125,2077	99.0	97.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	940	4.4	1.0	9	dbSNP_96	98	803,7797	782.2+/-407.6	38,727,3535	yes	missense	GALT	NM_000155.2	23	39,852,5612	GG,GA,AA		9.3372,2.8824,7.1505	benign	314/380	34649442	930,12076	2203	4300	6503	SO:0001583	missense	2592	exon10	Familial Cancer Database	Galactose-1-Phosphate Uridyltransferase Deficiency	AACTGGAACCATT	M60091	CCDS6565.1, CCDS59122.1	9p13	2013-01-08			ENSG00000213930	ENSG00000213930	2.7.7.12		4135	protein-coding gene	gene with protein product		606999					Standard	NM_000155		Approved		uc003zve.4	P07902	OTTHUMG00000019836	ENST00000378842.3:c.940A>G	9.37:g.34649442A>G	ENSP00000368119:p.Asn314Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_000155	B4E097|E7ET32|Q14355|Q14356|Q14357|Q14358|Q14359|Q14360|Q14361|Q14363|Q14364|Q14365|Q14369|Q14370|Q14371|Q14372|Q14373|Q14374|Q14375|Q14377|Q14378|Q14380|Q14381|Q14382|Q14383|Q14384|Q14385|Q14386|Q14387|Q14389|Q16766|Q53XK1|Q5VZ81|Q96BY1	Missense_Mutation	SNP	ENST00000378842.3	37	CCDS6565.1	119	0.05448717948717949	8	0.016260162601626018	23	0.06353591160220995	9	0.015734265734265736	79	0.10422163588390501	G	5.939	0.357315	0.11239	0.028824	0.093372	ENSG00000213930	ENST00000450095;ENST00000378842	D;D	0.99089	-5.41;-5.41	5.3	4.4	0.53042	Histidine triad motif (1);Galactose-1-phosphate uridyl transferase, C-terminal (1);Histidine triad-like motif (1);	0.363282	0.26560	N	0.023682	T	0.34164	0.0888	N	0.01454	-0.855	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.75068	-0.3448	10	0.02654	T	1	-8.4461	7.8294	0.29334	0.3139:0.0:0.6861:0.0	rs2070074;rs17845454;rs17858327;rs57246392;rs2070074	205;314	E7ET32;P07902	.;GALT_HUMAN	D	205;314	ENSP00000401956:N205D;ENSP00000368119:N314D	ENSP00000368119:N314D	N	+	1	0	GALT	34639442	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	1.578000	0.36525	1.256000	0.44068	-0.227000	0.12334	AAC	A|0.934;G|0.066	0.066	strong		0.552	GALT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052231.1	NM_000155	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43891639	43891639	+	Silent	SNP	G	G	A	rs200586830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	519	1	0.00192678		WXS	Illumina HiSeq	Phase_I	715	102	0.142657	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		
UGT1A10	54575	hgsc.bcm.edu	37	2	234545932	234545932	+	Missense_Mutation	SNP	C	C	T	rs45574333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234545932C>T	ENST00000344644.5	+	1	833	c.764C>T	c.(763-765)aCg>aTg	p.T255M	UGT1A10_ENST00000373445.1_Missense_Mutation_p.T255M|UGT1A1_ENST00000373450.4_Intron	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	255					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	TTGTTGCGAACGGACTTTGTT	0.433																																					p.T255M		Atlas-SNP	.											.	UGT1A10	71	.	0			c.C764T						PASS	.	C	MET/THR,	1,4405	2.1+/-5.4	0,1,2202	254.0	253.0	253.0		764,	1.5	0.5	2	dbSNP_127	253	11,8589	8.4+/-32.0	0,11,4289	no	missense,intron	UGT1A10,UGT1A8	NM_019075.2,NM_019076.4	81,	0,12,6491	TT,TC,CC		0.1279,0.0227,0.0923	,	255/531,	234545932	12,12994	2203	4300	6503	SO:0001583	missense	54575	exon1			TGCGAACGGACTT	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.764C>T	2.37:g.234545932C>T	ENSP00000343838:p.Thr255Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	153	71	0.464052	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	37	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	C	7.102	0.574235	0.13623	2.27E-4	0.001279	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.67345	-0.26;-0.26	3.52	1.53	0.23141	.	.	.	.	.	T	0.69726	0.3143	M	0.84433	2.695	0.09310	N	1	B;B	0.34147	0.234;0.438	B;B	0.42163	0.269;0.378	T	0.63418	-0.6642	9	0.51188	T	0.08	.	3.4103	0.07356	0.3801:0.3993:0.1324:0.0881	rs45574333	255;255	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	M	255	ENSP00000343838:T255M;ENSP00000362544:T255M	ENSP00000343838:T255M	T	+	2	0	UGT1A10	234210671	0.000000	0.05858	0.532000	0.27989	0.802000	0.45316	-2.845000	0.00735	0.254000	0.21573	0.405000	0.27470	ACG	C|0.999;T|0.001	0.001	strong		0.433	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
OR5AC2	81050	hgsc.bcm.edu	37	3	97806616	97806616	+	Missense_Mutation	SNP	G	G	A	rs4518168	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:97806616G>A	ENST00000358642.2	+	1	600	c.600G>A	c.(598-600)atG>atA	p.M200I		NM_054106.1	NP_473447.1	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC, member 2	200			M -> I (in dbSNP:rs4518168). {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)			endometrium(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	28						ACGCACTAATGATATTTATTT	0.289													G|||	2621	0.523363	0.5416	0.5461	5008	,	,		21366	0.4454		0.505	False		,,,				2504	0.5818				p.M200I		Atlas-SNP	.											.	OR5AC2	64	.	0			c.G600A						PASS	.	G	ILE/MET	2308,2098	579.2+/-384.9	600,1108,495	42.0	45.0	44.0		600	1.5	0.0	3	dbSNP_111	44	4408,4190	572.3+/-389.7	1163,2082,1054	yes	missense	OR5AC2	NM_054106.1	10	1763,3190,1549	AA,AG,GG		48.7323,47.6169,48.3544	benign	200/310	97806616	6716,6288	2203	4299	6502	SO:0001583	missense	81050	exon1			ACTAATGATATTT	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.600G>A	3.37:g.97806616G>A	ENSP00000351466:p.Met200Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_054106		Missense_Mutation	SNP	ENST00000358642.2	37	CCDS33796.1	1109	0.5077838827838828	276	0.5609756097560976	191	0.5276243093922652	254	0.44405594405594406	388	0.5118733509234829	G	7.949	0.744366	0.15710	0.523831	0.512677	ENSG00000196578	ENST00000358642	T	0.36157	1.27	4.51	1.48	0.22813	GPCR, rhodopsin-like superfamily (1);	2.028390	0.03140	N	0.166479	T	0.00012	0.0000	L	0.31371	0.925	0.80722	P	0.0	B	0.02656	0.0	B	0.14023	0.01	T	0.47249	-0.9132	9	0.38643	T	0.18	-10.6871	3.4285	0.07420	0.2307:0.0:0.5748:0.1945	rs4518168;rs52813836;rs58429769;rs4518168	200	Q9NZP5	O5AC2_HUMAN	I	200	ENSP00000351466:M200I	ENSP00000351466:M200I	M	+	3	0	OR5AC2	99289306	0.000000	0.05858	0.001000	0.08648	0.162000	0.22319	0.308000	0.19314	0.107000	0.17824	-0.555000	0.04198	ATG	G|0.491;A|0.509	0.509	strong		0.289	OR5AC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359116.1		
KRT39	390792	hgsc.bcm.edu	37	17	39119942	39119942	+	Silent	SNP	G	G	A	rs17843020	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39119942G>A	ENST00000355612.2	-	3	680	c.645C>T	c.(643-645)gaC>gaT	p.D215D	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	215	Coil 1B.|Rod.					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)				GTGCCTCTAGGTCGGCCTTGC	0.493													G|||	541	0.108027	0.0303	0.1484	5008	,	,		18447	0.0327		0.1581	False		,,,				2504	0.2106				p.D215D		Atlas-SNP	.											KRT39,caecum,carcinoma,-2,1	KRT39	53	1	0			c.C645T						scavenged	.	G		179,4227	115.9+/-153.8	5,169,2029	188.0	169.0	176.0		645	2.4	1.0	17	dbSNP_123	176	1346,7246	262.8+/-284.6	107,1132,3057	no	coding-synonymous	KRT39	NM_213656.3		112,1301,5086	AA,AG,GG		15.6657,4.0626,11.7326		215/492	39119942	1525,11473	2203	4296	6499	SO:0001819	synonymous_variant	390792	exon3			CTCTAGGTCGGCC	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.645C>T	17.37:g.39119942G>A		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_213656	B2RXK6|Q6IFU6	Silent	SNP	ENST00000355612.2	37	CCDS11382.1																																																																																			G|0.894;A|0.106	0.106	strong		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
CTAGE1	64693	hgsc.bcm.edu	37	18	19995731	19995731	+	5'Flank	SNP	T	T	C	rs9946136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:19995731T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.I682V			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)					CCTCTTCTTATGAACGGGCCC	0.522													T|||	937	0.187101	0.2481	0.1787	5008	,	,		15959	0.0387		0.2346	False		,,,				2504	0.2147				p.I682V		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A2044G						PASS	.	T	VAL/ILE	1107,3269		155,797,1236	79.0	88.0	85.0		2044	0.6	0.0	18	dbSNP_119	85	1994,6562		248,1498,2532	yes	missense	CTAGE1	NM_172241.2	29	403,2295,3768	CC,CT,TT		23.3053,25.2971,23.9793	benign	682/746	19995731	3101,9831	2188	4278	6466	SO:0001631	upstream_gene_variant	64693	exon1			TTCTTATGAACGG	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.19995731T>C	Exception_encountered	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		392	0.1794871794871795	115	0.23373983739837398	73	0.20165745856353592	25	0.043706293706293704	179	0.23614775725593667	T	3.003	-0.205701	0.06180	0.252971	0.233053	ENSG00000212710	ENST00000391403	T	0.07444	3.19	0.614	0.614	0.17603	.	.	.	.	.	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47886	-0.9082	6	.	.	.	.	.	.	.	rs9946136;rs16966941;rs59362725;rs9946136	682	Q96RT6	CTGE2_HUMAN	V	682	ENSP00000375220:I682V	.	I	-	1	0	CTAGE1	18249729	0.266000	0.24112	0.013000	0.15412	0.009000	0.06853	0.319000	0.19522	0.486000	0.27676	0.248000	0.18094	ATA	T|0.813;C|0.187	0.187	strong		0.522	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
FFAR3	2865	hgsc.bcm.edu	37	19	35850560	35850560	+	Silent	SNP	G	G	A	rs375946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:35850560G>A	ENST00000327809.4	+	2	969	c.768G>A	c.(766-768)gcG>gcA	p.A256A	FFAR3_ENST00000594310.1_Silent_p.A256A	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	256			A -> V (in dbSNP:rs424715). {ECO:0000269|PubMed:19630535}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|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 glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			AAAGCCCGGCGTGGAGGATCT	0.587																																					p.A256A	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											.	FFAR3	40	.	0			c.G768A						PASS	.	G		362,4040		0,362,1839	336.0	242.0	274.0		768	-10.3	0.0	19	dbSNP_131	274	1808,6788		29,1750,2519	no	coding-synonymous	FFAR3	NM_005304.3		29,2112,4358	AA,AG,GG		21.033,8.2235,16.6949		256/347	35850560	2170,10828	2201	4298	6499	SO:0001819	synonymous_variant	2865	exon2			CCCGGCGTGGAGG	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.768G>A	19.37:g.35850560G>A		Somatic	1058	1	0.00094518		WXS	Illumina HiSeq	Phase_I	870	581	0.667816	NM_005304	B2RWM8|Q14CM7	Silent	SNP	ENST00000327809.4	37	CCDS12459.1																																																																																			G|0.838;A|0.162	0.162	strong		0.587	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
OR4K17	390436	hgsc.bcm.edu	37	14	20586432	20586432	+	Silent	SNP	C	C	T	rs9323534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	158	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	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		
LIG1	3978	hgsc.bcm.edu	37	19	48621036	48621036	+	Silent	SNP	C	C	G	rs13436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48621036C>G	ENST00000263274.7	-	26	2861	c.2442G>C	c.(2440-2442)gcG>gcC	p.A814A	LIG1_ENST00000427526.2_Silent_p.A783A|CTC-453G23.5_ENST00000596563.1_RNA|CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000536218.1_Silent_p.A746A	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	814					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|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)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	GCAGCACCAGCGCCTGCAGTG	0.602								Nucleotide excision repair (NER)					G|||	2727	0.544529	0.5424	0.4236	5008	,	,		16249	0.748		0.4632	False		,,,				2504	0.5072				p.A814A		Atlas-SNP	.											.	LIG1	151	.	0			c.G2442C						PASS	.	G		2403,2003	533.6+/-373.7	669,1065,469	31.0	28.0	29.0		2442	4.4	1.0	19	dbSNP_52	29	3573,5027	602.0+/-394.4	747,2079,1474	no	coding-synonymous	LIG1	NM_000234.1		1416,3144,1943	GG,GC,CC		41.5465,45.4607,45.948		814/920	48621036	5976,7030	2203	4300	6503	SO:0001819	synonymous_variant	3978	exon26			CACCAGCGCCTGC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2442G>C	19.37:g.48621036C>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	158	155	0.981013	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																			C|0.503;G|0.497	0.497	strong		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
PRRC2B	84726	hgsc.bcm.edu	37	9	134358108	134358108	+	Silent	SNP	A	A	G	rs2275498	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134358108A>G	ENST00000357304.4	+	21	5242	c.5187A>G	c.(5185-5187)caA>caG	p.Q1729Q	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.Q1035Q|PRRC2B_ENST00000405995.1_Silent_p.Q1035Q|SNORD62A_ENST00000428514.1_RNA	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1729							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						ATTCAGAACAAGGCTCTGGAC	0.532													A|||	417	0.0832668	0.1172	0.1585	5008	,	,		18010	0.0595		0.0696	False		,,,				2504	0.0225				p.Q1729Q		Atlas-SNP	.											.	PRRC2B	266	.	0			c.A5187G						PASS	.	A		403,3503		16,371,1566	26.0	29.0	28.0		5187	3.9	1.0	9	dbSNP_100	28	457,7825		14,429,3698	no	coding-synonymous	PRRC2B	NM_013318.3		30,800,5264	GG,GA,AA		5.518,10.3175,7.0561		1729/2230	134358108	860,11328	1953	4141	6094	SO:0001819	synonymous_variant	84726	exon21			AGAACAAGGCTCT	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5187A>G	9.37:g.134358108A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	205	0.09386446886446886	72	0.14634146341463414	44	0.12154696132596685	36	0.06293706293706294	53	0.06992084432717678	A	8.016	0.758553	0.15846	0.103175	0.05518	ENSG00000130723	ENST00000451855	.	.	.	5.03	3.86	0.44501	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00172	-1.1958	4	.	.	.	-9.462	6.6264	0.22833	0.6851:0.1609:0.0:0.154	rs2275498;rs61075035;rs2275498	.	.	.	G	462	.	.	R	+	1	2	PRRC2B	133347929	0.991000	0.36638	0.998000	0.56505	0.979000	0.70002	0.446000	0.21694	0.730000	0.32425	0.459000	0.35465	AGG	A|0.900;G|0.100	0.100	strong		0.532	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
UNC13A	23025	hgsc.bcm.edu	37	19	17728572	17728572	+	Silent	SNP	C	C	T	rs56174023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17728572C>T	ENST00000519716.2	-	41	4496	c.4497G>A	c.(4495-4497)tcG>tcA	p.S1499S	UNC13A_ENST00000552293.1_Silent_p.S1474S|UNC13A_ENST00000550896.1_Silent_p.S1472S|UNC13A_ENST00000551649.1_Silent_p.S1499S|UNC13A_ENST00000252773.7_Silent_p.S1499S|UNC13A_ENST00000428389.2_Silent_p.S1587S	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	67	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	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	
CTBS	1486	hgsc.bcm.edu	37	1	85039955	85039955	+	Silent	SNP	G	G	A	rs2303307	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:85039955G>A	ENST00000370630.5	-	1	192	c.144C>T	c.(142-144)ctC>ctT	p.L48L	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	48					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		TCGGGCGGCAGAGCTCAGGCT	0.687													G|||	1373	0.274161	0.2595	0.2464	5008	,	,		8005	0.2302		0.2475	False		,,,				2504	0.3865				p.L48L		Atlas-SNP	.											CTBS,rectum,carcinoma,0,1	CTBS	24	1	0			c.C144T						PASS	.	G		1086,3252		157,772,1240	8.0	8.0	8.0		144	3.0	1.0	1	dbSNP_100	8	2129,6387		294,1541,2423	no	coding-synonymous	CTBS	NM_004388.2		451,2313,3663	AA,AG,GG		25.0,25.0346,25.0117		48/386	85039955	3215,9639	2169	4258	6427	SO:0001819	synonymous_variant	1486	exon1			GCGGCAGAGCTCA	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.144C>T	1.37:g.85039955G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_004388	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																			G|0.741;A|0.259	0.259	strong		0.687	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
FBXL16	146330	hgsc.bcm.edu	37	16	746914	746914	+	Silent	SNP	G	G	A	rs4984915	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:746914G>A	ENST00000397621.1	-	2	823	c.492C>T	c.(490-492)gcC>gcT	p.A164A	FBXL16_ENST00000562563.1_5'Flank|FBXL16_ENST00000324361.5_Silent_p.A164A|FBXL16_ENST00000562585.1_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	68	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	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	
APCDD1L	164284	hgsc.bcm.edu	37	20	57045765	57045765	+	Missense_Mutation	SNP	A	A	G	rs3946003	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:57045765A>G	ENST00000371149.3	-	2	318	c.88T>C	c.(88-90)Tgc>Cgc	p.C30R	APCDD1L_ENST00000439429.1_Missense_Mutation_p.C41R	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	30			C -> R (in dbSNP:rs3946003).			integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			CAGCGCAGGCAGCTGCCCCCG	0.662													G|||	2308	0.460863	0.618	0.4265	5008	,	,		13648	0.3998		0.3688	False		,,,				2504	0.4305				p.C30R		Atlas-SNP	.											.	APCDD1L	48	.	0			c.T88C						PASS	.	G	ARG/CYS	2249,1989		639,971,509	24.0	21.0	22.0		88	1.8	0.0	20	dbSNP_108	22	2836,5450		534,1768,1841	yes	missense	APCDD1L	NM_153360.1	180	1173,2739,2350	GG,GA,AA		34.2264,46.9325,40.602	benign	30/502	57045765	5085,7439	2119	4143	6262	SO:0001583	missense	164284	exon2			GCAGGCAGCTGCC	AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.88T>C	20.37:g.57045765A>G	ENSP00000360191:p.Cys30Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_153360		Missense_Mutation	SNP	ENST00000371149.3	37	CCDS13467.1	968	0.4432234432234432	297	0.6036585365853658	161	0.4447513812154696	231	0.40384615384615385	279	0.36807387862796836	G	0.016	-1.528342	0.00959	0.530675	0.342264	ENSG00000198768	ENST00000371149;ENST00000439429;ENST00000425773	T;T;T	0.28895	2.66;2.65;1.59	4.88	1.78	0.24846	.	1.184280	0.06181	N	0.679412	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	0.45498	-0.9257	9	0.02654	T	1	-1.6941	3.6523	0.08208	0.3072:0.0:0.3177:0.3751	rs3946003;rs59320716	41;30	F5H6V6;Q8NCL9	.;APCDL_HUMAN	R	30;41;41	ENSP00000360191:C30R;ENSP00000413261:C41R;ENSP00000396856:C41R	ENSP00000360191:C30R	C	-	1	0	APCDD1L	56479171	0.187000	0.23238	0.001000	0.08648	0.047000	0.14425	0.784000	0.26816	-0.034000	0.13713	-0.119000	0.15052	TGC	A|0.555;G|0.445	0.445	strong		0.662	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
ANKRD44	91526	hgsc.bcm.edu	37	2	197990741	197990741	+	Missense_Mutation	SNP	A	A	C	rs35338671	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000282272.8_Missense_Mutation_p.I86M|ANKRD44_ENST00000409919.1_Missense_Mutation_p.I94M|ANKRD44_ENST00000450567.1_Missense_Mutation_p.I69M|ANKRD44_ENST00000409153.1_Missense_Mutation_p.I94M|ANKRD44_ENST00000539527.1_Missense_Mutation_p.I22M			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	142	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	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	
MUC2	4583	hgsc.bcm.edu	37	11	1092884	1092884	+	Missense_Mutation	SNP	C	C	T	rs201415503		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1092884C>T	ENST00000441003.2	+	30	4730	c.4703C>T	c.(4702-4704)aCg>aTg	p.T1568M	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1569M|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1569M(2)|p.T1568M(2)		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)	ACCACCACCACGGTGacccca	0.637																																					p.T1568M		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	4	Substitution - Missense(4)	large_intestine(2)|skin(2)	c.C4703T						PASS	.						129.0	172.0	157.0					11																	1092884		1964	3669	5633	SO:0001583	missense	4583	exon30			CCACCACGGTGAC	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.4703C>T	11.37:g.1092884C>T	ENSP00000415183:p.Thr1568Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	6	0.117647	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.409	-0.335727	0.05278	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14893	2.5;2.47	1.63	0.367	0.16140	.	25.055600	0.00797	U	0.001394	T	0.21841	0.0526	.	.	.	0.09310	N	1	D	0.76494	0.999	P	0.48425	0.577	T	0.35301	-0.9794	9	0.45353	T	0.12	.	8.9064	0.35526	0.0:0.7681:0.2319:0.0	.	1568	E7EUV1	.	M	1568;1569	ENSP00000415183:T1568M;ENSP00000351956:T1569M	ENSP00000351956:T1569M	T	+	2	0	MUC2	1082884	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.878000	0.28126	0.945000	0.37605	0.121000	0.15741	ACG	.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
C22orf42	150297	hgsc.bcm.edu	37	22	32545762	32545762	+	Silent	SNP	C	C	T	rs45494991	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32545762C>T	ENST00000382097.3	-	8	732	c.660G>A	c.(658-660)aaG>aaA	p.K220K	C22orf42_ENST00000490640.1_5'UTR	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	220										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						CATATCTCTCCTTTGCCTGCA	0.343													c|||	116	0.0231629	0.003	0.0274	5008	,	,		11913	0.0		0.0666	False		,,,				2504	0.0266				p.K220K		Atlas-SNP	.											.	C22orf42	37	.	0			c.G660A						PASS	.	C		58,4334		1,56,2139	31.0	32.0	32.0		660		0.0	22	dbSNP_127	32	572,8024		20,532,3746	no	coding-synonymous	C22orf42	NM_001010859.1		21,588,5885	TT,TC,CC		6.6543,1.3206,4.8506		220/252	32545762	630,12358	2196	4298	6494	SO:0001819	synonymous_variant	150297	exon8			TCTCTCCTTTGCC	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.660G>A	22.37:g.32545762C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_001010859	A4QPH5	Silent	SNP	ENST00000382097.3	37	CCDS33639.1																																																																																			C|0.950;G|0.000;T|0.049	0.049	strong		0.343	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
CTNNA3	29119	hgsc.bcm.edu	37	10	68040325	68040325	+	Missense_Mutation	SNP	C	C	T	rs4548513	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:68040325C>T	ENST00000433211.2	-	13	1961	c.1787G>A	c.(1786-1788)aGc>aAc	p.S596N	CTNNA3_ENST00000373744.4_Missense_Mutation_p.S596N	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						ATTCAATGAGCTTTTGCTTAA	0.328													T|||	2429	0.485024	0.7269	0.4121	5008	,	,		17605	0.4187		0.3748	False		,,,				2504	0.3916				p.S596N		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G1787A	GRCh37	CM074765	CTNNA3	M	rs4548513	PASS	.	T	ASN/SER,ASN/SER	2954,1452	454.7+/-350.8	1007,940,256	135.0	129.0	131.0		1787,1787	3.2	0.6	10	dbSNP_111	131	3114,5486	647.5+/-400.4	561,1992,1747	yes	missense,missense	CTNNA3	NM_001127384.1,NM_013266.2	46,46	1568,2932,2003	TT,TC,CC		36.2093,32.9551,46.6554	benign,benign	596/896,596/896	68040325	6068,6938	2203	4300	6503	SO:0001583	missense	29119	exon13			AATGAGCTTTTGC	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1787G>A	10.37:g.68040325C>T	ENSP00000389714:p.Ser596Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	1032	0.4725274725274725	353	0.717479674796748	154	0.425414364640884	243	0.42482517482517484	282	0.3720316622691293	T	0.019	-1.454724	0.01071	0.670449	0.362093	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.36157	1.27;1.27	5.54	3.16	0.36331	.	0.101185	0.42294	N	0.000735	T	0.00012	0.0000	N	0.00325	-1.645	0.23943	P	0.99639428	B	0.02656	0.0	B	0.04013	0.001	T	0.44112	-0.9349	9	0.02654	T	1	-13.3321	7.5116	0.27577	0.0:0.2511:0.0:0.7489	rs4548513;rs52832156;rs59069553;rs4548513	596	Q9UI47	CTNA3_HUMAN	N	596	ENSP00000389714:S596N;ENSP00000362849:S596N	ENSP00000362849:S596N	S	-	2	0	CTNNA3	67710331	0.992000	0.36948	0.635000	0.29338	0.424000	0.31475	0.882000	0.28186	0.069000	0.16605	-0.254000	0.11334	AGC	C|0.526;N|0.000	.	strong		0.328	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50682865	50682865	+	Silent	SNP	G	G	A	rs5771270	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50682865G>A	ENST00000248846.5	-	1	128	c.24C>T	c.(22-24)ttC>ttT	p.F8F	TUBGCP6_ENST00000439308.2_Silent_p.F8F|HDAC10_ENST00000498366.1_5'Flank|MAPK12_ENST00000497036.1_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	37	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	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	
CYP2E1	1571	hgsc.bcm.edu	37	10	135347315	135347315	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:135347315C>T	ENST00000463117.2	+	8	1153	c.881C>T	c.(880-882)gCc>gTc	p.A294V	SPRN_ENST00000541506.1_Intron|CYP2E1_ENST00000252945.3_Missense_Mutation_p.A294V			P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E, polypeptide 1	294					drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organonitrogen compound (GO:0010243)|response to ozone (GO:0010193)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|triglyceride metabolic process (GO:0006641)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|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, 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)			NS(1)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(7)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		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;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Aldesleukin(DB00041)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminophylline(DB01223)|Amitriptyline(DB00321)|Antipyrine(DB01435)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupropion(DB01156)|Caffeine(DB00201)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Citalopram(DB00215)|Clevidipine(DB04920)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonazepam(DB01068)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Dacarbazine(DB00851)|Dalfampridine(DB06637)|Dapsone(DB00250)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Disulfiram(DB00822)|Econazole(DB01127)|Enflurane(DB00228)|Enfuvirtide(DB00109)|Estrone(DB00655)|Ethanol(DB00898)|Ethanolamine Oleate(DB06689)|Ethosuximide(DB00593)|Etoposide(DB00773)|Etoricoxib(DB01628)|Felbamate(DB00949)|Fingolimod(DB08868)|Flunitrazepam(DB01544)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluvoxamine(DB00176)|Folic Acid(DB00158)|Fomepizole(DB01213)|Glucosamine(DB01296)|Halothane(DB01159)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imipramine(DB00458)|Isoflurane(DB00753)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Itraconazole(DB01167)|Menadione(DB00170)|Meprobamate(DB00371)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Mexiletine(DB00379)|Miconazole(DB01110)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nitrazepam(DB01595)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Orphenadrine(DB01173)|Oxaliplatin(DB00526)|Paramethadione(DB00617)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Pimozide(DB01100)|Proguanil(DB01131)|Propofol(DB00818)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rufinamide(DB06201)|S-Adenosylmethionine(DB00118)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulfadiazine(DB00359)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiopental(DB00599)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Ursodeoxycholic acid(DB01586)|Zafirlukast(DB00549)|Zopiclone(DB01198)	GTGACTGTGGCCGACCTGTTC	0.532									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.A294V		Atlas-SNP	.											CYP2E1,NS,carcinoma,-1,1	CYP2E1	69	1	0			c.C881T						scavenged	.						187.0	161.0	170.0					10																	135347315		2203	4300	6503	SO:0001583	missense	1571	exon6	Familial Cancer Database	incl.: Familial Head and Neck Cancer	CTGTGGCCGACCT	J02843	CCDS7686.1	10q26.3	2013-05-03	2003-01-14	2002-09-13	ENSG00000130649	ENSG00000130649		"""Cytochrome P450s"""	2631	protein-coding gene	gene with protein product		124040	"""cytochrome P450, subfamily IIE (ethanol-inducible), polypeptide 1"""	CYP2E			Standard	NM_000773		Approved		uc001lnj.1	P05181	OTTHUMG00000019322	ENST00000463117.2:c.881C>T	10.37:g.135347315C>T	ENSP00000440689:p.Ala294Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	2	0.0206186	NM_000773	Q5VZD5|Q6NWT9|Q9UK47	Missense_Mutation	SNP	ENST00000463117.2	37	CCDS7686.1	.	.	.	.	.	.	.	.	.	.	C	7.637	0.680127	0.14907	.	.	ENSG00000130649	ENST00000463117;ENST00000252945;ENST00000421586;ENST00000418356	T;T;T;T	0.78816	5.15;5.15;2.77;-1.21	3.96	2.04	0.26737	.	0.294229	0.32041	N	0.006673	T	0.69895	0.3162	N	0.20845	0.615	0.09310	N	1	D;D	0.76494	0.999;0.979	P;P	0.60345	0.873;0.57	T	0.58233	-0.7672	10	0.25751	T	0.34	.	4.2041	0.10480	0.0:0.5977:0.1929:0.2094	.	190;294	Q59EW1;P05181	.;CP2E1_HUMAN	V	294;294;207;157	ENSP00000440689:A294V;ENSP00000252945:A294V;ENSP00000412754:A207V;ENSP00000397299:A157V	ENSP00000252945:A294V	A	+	2	0	CYP2E1	135197305	0.007000	0.16637	0.001000	0.08648	0.111000	0.19643	1.905000	0.39878	0.615000	0.30124	0.597000	0.82753	GCC	.	.	none		0.532	CYP2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051161.2	NM_000773	
COL23A1	91522	hgsc.bcm.edu	37	5	177683377	177683377	+	Missense_Mutation	SNP	T	T	C	rs890802	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:177683377T>C	ENST00000390654.3	-	15	1216	c.859A>G	c.(859-861)Acg>Gcg	p.T287A	COL23A1_ENST00000407622.1_Missense_Mutation_p.T251A	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	287	Collagen-like 2.|Gly-rich.		T -> A (in dbSNP:rs890802).		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	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)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GCTCCATCCGTGCCTCGGTGG	0.662													T|||	2613	0.521765	0.5953	0.5764	5008	,	,		12516	0.4335		0.493	False		,,,				2504	0.5041				p.T287A		Atlas-SNP	.											COL23A1,NS,carcinoma,0,1	COL23A1	47	1	0			c.A859G						PASS	.	T	ALA/THR	2322,1680		698,926,377	21.0	25.0	23.0		859	-8.8	0.0	5	dbSNP_86	23	4243,4095		1074,2095,1000	yes	missense	COL23A1	NM_173465.3	58	1772,3021,1377	CC,CT,TT		49.1125,41.979,46.799	benign	287/541	177683377	6565,5775	2001	4169	6170	SO:0001583	missense	91522	exon15			CATCCGTGCCTCG	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"""Collagens"""	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.859A>G	5.37:g.177683377T>C	ENSP00000375069:p.Thr287Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_173465	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	1114	0.51007326007326	286	0.5813008130081301	214	0.5911602209944752	242	0.4230769230769231	372	0.49076517150395776	T	1.832	-0.469521	0.04445	0.58021	0.508875	ENSG00000050767	ENST00000390654;ENST00000407622	D;D	0.82711	-1.64;-1.64	4.42	-8.84	0.00803	.	1.390520	0.04941	N	0.458564	T	0.00012	0.0000	N	0.04320	-0.23	0.80722	P	0.0	B	0.17852	0.024	B	0.18871	0.023	T	0.04115	-1.0976	9	0.08599	T	0.76	6.3691	6.5388	0.22369	0.0948:0.1434:0.0941:0.6677	rs890802;rs17578614;rs59984753;rs890802	287	Q86Y22	CONA1_HUMAN	A	287;251	ENSP00000375069:T287A;ENSP00000385092:T251A	ENSP00000375069:T287A	T	-	1	0	COL23A1	177615983	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.929000	0.00689	-2.538000	0.00487	-1.614000	0.00798	ACG	T|0.491;C|0.509	0.509	strong		0.662	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	
SLC5A1	6523	hgsc.bcm.edu	37	22	32445946	32445946	+	Missense_Mutation	SNP	A	A	G	rs17683011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32445946A>G	ENST00000266088.4	+	2	402	c.152A>G	c.(151-153)aAt>aGt	p.N51S		NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	51			N -> S (in dbSNP:rs17683011).		carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)			NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TTTTCCACCAATCGTGGGACT	0.468													A|||	106	0.0211661	0.003	0.0259	5008	,	,		20492	0.0		0.0606	False		,,,				2504	0.0235				p.N51S		Atlas-SNP	.											SLC5A1,NS,carcinoma,+1,1	SLC5A1	80	1	0			c.A152G	GRCh37	CM961319	SLC5A1	M	rs17683011	scavenged	.	A	SER/ASN	61,4345	58.1+/-94.6	0,61,2142	254.0	236.0	242.0		152	3.4	0.9	22	dbSNP_123	242	603,7997	158.0+/-211.6	20,563,3717	yes	missense	SLC5A1	NM_000343.3	46	20,624,5859	GG,GA,AA		7.0116,1.3845,5.1053	benign	51/665	32445946	664,12342	2203	4300	6503	SO:0001583	missense	6523	exon2			CCACCAATCGTGG		CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.152A>G	22.37:g.32445946A>G	ENSP00000266088:p.Asn51Ser	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Missense_Mutation	SNP	ENST00000266088.4	37	CCDS13902.1	68	0.031135531135531136	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	55	0.07255936675461741	A	8.959	0.970188	0.18659	0.013845	0.070116	ENSG00000100170	ENST00000266088	D	0.85484	-1.99	5.55	3.4	0.38934	.	0.131624	0.64402	N	0.000002	T	0.21550	0.0519	L	0.37897	1.145	0.58432	D	0.999999	B	0.25719	0.132	B	0.24006	0.05	T	0.47636	-0.9102	10	0.22706	T	0.39	.	7.6157	0.28156	0.8247:0.0:0.1753:0.0	rs17683011;rs52836243;rs17683011	51	P13866	SC5A1_HUMAN	S	51	ENSP00000266088:N51S	ENSP00000266088:N51S	N	+	2	0	SLC5A1	30775946	1.000000	0.71417	0.884000	0.34674	0.599000	0.36880	4.086000	0.57664	0.935000	0.37341	0.450000	0.29827	AAT	A|0.956;G|0.044	0.044	strong		0.468	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
IDH1	3417	hgsc.bcm.edu	37	2	209108317	209108317	+	Missense_Mutation	SNP	C	C	T	rs34218846	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209108317C>T	ENST00000415913.1	-	6	913	c.532G>A	c.(532-534)Gtt>Att	p.V178I	IDH1_ENST00000345146.2_Missense_Mutation_p.V178I|IDH1_ENST00000446179.1_Missense_Mutation_p.V178I	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	178			V -> I (in dbSNP:rs34218846).		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.V178I(8)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		CCCATGGCAACACCACCACCT	0.418			Mis		gliobastoma								C|||	247	0.0493211	0.0893	0.0447	5008	,	,		18161	0.0069		0.0477	False		,,,				2504	0.044				p.V178I	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	IDH1,colon,carcinoma,0,9	IDH1	6310	9	8	Substitution - Missense(8)	thyroid(8)	c.G532A						PASS	.	C	ILE/VAL	356,4050	182.6+/-210.3	12,332,1859	69.0	65.0	66.0		532	5.5	1.0	2	dbSNP_126	66	457,8143	137.1+/-194.1	7,443,3850	yes	missense	IDH1	NM_005896.2	29	19,775,5709	TT,TC,CC		5.314,8.0799,6.251	possibly-damaging	178/415	209108317	813,12193	2203	4300	6503	SO:0001583	missense	3417	exon6			TGGCAACACCACC		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.532G>A	2.37:g.209108317C>T	ENSP00000390265:p.Val178Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	90	0.04120879120879121	38	0.07723577235772358	16	0.04419889502762431	2	0.0034965034965034965	34	0.044854881266490766	C	20.3	3.968029	0.74131	0.080799	0.05314	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.77229	-1.08;-1.08;-1.08	5.52	5.52	0.82312	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.54863	1.705	0.80722	D	1	D	0.63046	0.992	D	0.74674	0.984	T	0.66701	-0.5857	10	0.44086	T	0.13	-13.6312	19.7971	0.96490	0.0:1.0:0.0:0.0	rs34218846	178	O75874	IDHC_HUMAN	I	178	ENSP00000260985:V178I;ENSP00000410513:V178I;ENSP00000390265:V178I	ENSP00000260985:V178I	V	-	1	0	IDH1	208816562	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.126000	0.71635	2.762000	0.94881	0.484000	0.47621	GTT	C|0.946;T|0.054	0.054	strong		0.418	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
FAM154B	283726	hgsc.bcm.edu	37	15	82574879	82574879	+	Missense_Mutation	SNP	T	T	C	rs11630197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:82574879T>C	ENST00000339465.5	+	3	742	c.673T>C	c.(673-675)Tgg>Cgg	p.W225R	FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Missense_Mutation_p.W210R	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	225			W -> R (in dbSNP:rs11630197).							autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TTTTCAACCATGGGAAATCCC	0.458													T|||	1176	0.234824	0.146	0.17	5008	,	,		20570	0.1647		0.2873	False		,,,				2504	0.4192				p.W225R		Atlas-SNP	.											.	FAM154B	50	.	0			c.T673C						PASS	.	T	ARG/TRP	737,3669	302.4+/-287.4	73,591,1539	87.0	86.0	86.0		673	3.9	0.8	15	dbSNP_120	86	2199,6401	375.3+/-337.7	291,1617,2392	no	missense	FAM154B	NM_001008226.1	101	364,2208,3931	CC,CT,TT		25.5698,16.7272,22.5742	probably-damaging	225/399	82574879	2936,10070	2203	4300	6503	SO:0001583	missense	283726	exon3			CAACCATGGGAAA	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.673T>C	15.37:g.82574879T>C	ENSP00000340445:p.Trp225Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_001008226	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	454	0.2078754578754579	59	0.11991869918699187	70	0.19337016574585636	98	0.17132867132867133	227	0.2994722955145119	T	17.60	3.429838	0.62844	0.167272	0.255698	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.19250	2.16;2.16	3.9	3.9	0.45041	.	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.83953	2.67	0.20489	P	0.999892806	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.26883	-1.0090	9	0.26408	T	0.33	-9.3148	13.1531	0.59500	0.0:0.0:0.0:1.0	rs11630197;rs52815083;rs11630197	210;225	B4E2M2;Q658L1	.;F154B_HUMAN	R	225;210	ENSP00000340445:W225R;ENSP00000403743:W210R	ENSP00000340445:W225R	W	+	1	0	FAM154B	80361934	1.000000	0.71417	0.817000	0.32601	0.817000	0.46193	6.255000	0.72466	1.751000	0.51876	0.438000	0.28831	TGG	T|0.779;C|0.221	0.221	strong		0.458	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	
RGS3	5998	hgsc.bcm.edu	37	9	116356373	116356373	+	Intron	SNP	G	G	C	rs12350531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:116356373G>C	ENST00000374140.2	+	23	3289				RGS3_ENST00000394646.3_Intron|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000462403.1_Silent_p.L58L	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|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)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGCTCCTCCTGTCTGAGTCCC	0.622													G|||	3717	0.742212	0.6853	0.7637	5008	,	,		14959	0.879		0.6978	False		,,,				2504	0.7086				p.L58L		Atlas-SNP	.											RGS3_ENST00000462403,NS,carcinoma,0,1	RGS3	251	1	0			c.G174C						PASS	.	G	,,,,	3020,1384		1052,916,234	73.0	82.0	79.0		,,,,174	4.5	1.0	9	dbSNP_120	79	5863,2733		2000,1863,435	no	intron,intron,intron,intron,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,	3052,2779,669	CC,CG,GG		31.7939,31.426,31.6692	,,,,	,,,,58/312	116356373	8883,4117	2202	4298	6500	SO:0001627	intron_variant	5998	exon1			CCTCCTGTCTGAG	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-337G>C	9.37:g.116356373G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	181	90	0.497238	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																			G|0.295;C|0.705	0.705	strong		0.622	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129955	175129955	+	Missense_Mutation	SNP	G	G	T	rs386636937|rs3208835|rs57794404|rs71563271		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:175129955G>T	ENST00000423313.1	-	4	731	c.195C>A	c.(193-195)aaC>aaA	p.N65K	KIAA0040_ENST00000545251.2_Missense_Mutation_p.N65K|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Missense_Mutation_p.N65K	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcttgttcttctCTG	0.522																																					p.N65K		Atlas-SNP	.											.	KIAA0040	2	.	0			c.C195A						PASS	.						65.0	53.0	56.0					1																	175129955		692	1591	2283	SO:0001583	missense	9674	exon3			CTTCTTGTTCTTC	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.195C>A	1.37:g.175129955G>T	ENSP00000462172:p.Asn65Lys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	23	0.239583	NM_001162895	A8K9H6|Q2NKQ0	Missense_Mutation	SNP	ENST00000423313.1	37																																																																																				T|0.500;G|0.500	0.500	strong		0.522	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ASMTL	8623	hgsc.bcm.edu	37	X	1546842	1546842	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:1546842A>G	ENST00000381317.3	-	7	714	c.682T>C	c.(682-684)Tcc>Ccc	p.S228P	ASMTL_ENST00000381333.4_Missense_Mutation_p.S212P|ASMTL_ENST00000463763.1_5'UTR|ASMTL_ENST00000416733.2_Missense_Mutation_p.S152P|ASMTL_ENST00000534940.1_Missense_Mutation_p.S170P	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	228				S -> P (in Ref. 2; BAG63287). {ECO:0000305}.		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)				GCCGGGATGGAGTCGTGCTTG	0.667													a|||	457	0.091254	0.0643	0.0908	5008	,	,		15206	0.0972		0.164	False		,,,				2504	0.047				p.S228P		Atlas-SNP	.											.	ASMTL	56	.	0			c.T682C						PASS	.	A	PRO/SER,PRO/SER,PRO/SER	266,3720		13,240,1740	46.0	55.0	52.0		508,634,682	-0.7	0.0	X	dbSNP_134	52	1340,6900		123,1094,2903	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	74,74,74	136,1334,4643	GG,GA,AA		16.2621,6.6734,13.1359	benign,benign,benign	170/564,212/606,228/622	1546842	1606,10620	1993	4120	6113	SO:0001583	missense	8623	exon7			GGATGGAGTCGTG	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.682T>C	X.37:g.1546842A>G	ENSP00000370718:p.Ser228Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	249	0.11401098901098901	44	0.08943089430894309	33	0.09116022099447514	64	0.11188811188811189	108	0.1424802110817942	a	9.813	1.183635	0.21870	0.066734	0.162621	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	1.99	-0.697	0.11284	.	0.789628	0.11208	U	0.587967	T	0.00384	0.0012	L	0.55481	1.735	0.09310	N	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.73708	0.923;0.981;0.915	T	0.00931	-1.1510	10	0.41790	T	0.15	.	5.94	0.19187	0.7342:0.0:0.2658:0.0	.	152;212;228	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	P	152;170;212;228	ENSP00000410578:S152P;ENSP00000446410:S170P;ENSP00000370734:S212P;ENSP00000370718:S228P	ENSP00000370718:S228P	S	-	1	0	ASMTL	1506842	0.996000	0.38824	0.006000	0.13384	0.033000	0.12548	0.313000	0.19415	-0.139000	0.11414	0.230000	0.17803	TCC	A|0.867;G|0.133	0.133	strong		0.667	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
TMEM47	83604	hgsc.bcm.edu	37	X	34674970	34674970	+	Silent	SNP	C	C	G	rs5928617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:34674970C>G	ENST00000275954.3	-	1	435	c.177G>C	c.(175-177)cgG>cgC	p.R59R		NM_031442.3	NP_113630.1	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	59						cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGGCGGGTTTCCGGCAGGACT	0.701													c|||	1579	0.418278	0.2693	0.2767	3775	,	,		7571	0.4871		0.1839	False		,,,				2504	0.363				p.R59R		Atlas-SNP	.											.	TMEM47	45	.	0			c.G177C						PASS	.			1082,2667		151,638,142,824,381	20.0	16.0	18.0		177	2.9	1.0	X	dbSNP_114	18	1592,4993		154,842,442,1395,1361	no	coding-synonymous	TMEM47	NM_031442.3		305,1480,584,2219,1742	GG,GC,G,CC,C		24.1762,28.861,25.8757		59/182	34674970	2674,7660	2136	4194	6330	SO:0001819	synonymous_variant	83604	exon1			GGGTTTCCGGCAG	AK090917	CCDS14235.1	Xp11.4	2008-02-05	2005-03-21	2005-03-21	ENSG00000147027	ENSG00000147027			18515	protein-coding gene	gene with protein product		300698	"""transmembrane 4 superfamily member 10"""	TM4SF10		11472633	Standard	NM_031442		Approved	BCMP1, DKFZP761J17121, DKFZp564E153	uc004ddh.3	Q9BQJ4	OTTHUMG00000021343	ENST00000275954.3:c.177G>C	X.37:g.34674970C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_031442	Q5JR44	Silent	SNP	ENST00000275954.3	37	CCDS14235.1																																																																																			C|0.689;G|0.311	0.311	strong		0.701	TMEM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056209.1	NM_031442	
RNF130	55819	hgsc.bcm.edu	37	5	179498658	179498658	+	Silent	SNP	G	G	T	rs3828698	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:179498658G>T	ENST00000261947.4	-	1	443	c.45C>A	c.(43-45)ctC>ctA	p.L15L	RNF130_ENST00000521389.1_Silent_p.L15L|RNF130_ENST00000522208.2_Silent_p.L15L	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGCAGGGCGAgcgcggcga	0.766													G|||	2231	0.445487	0.1233	0.4784	5008	,	,		5381	0.63		0.4573	False		,,,				2504	0.6554				p.L15L	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.C45A						PASS	.	G		632,3212		116,400,1406	4.0	5.0	5.0		45	-0.6	1.0	5	dbSNP_107	5	3378,4540		839,1700,1420	no	coding-synonymous	RNF130	NM_018434.4		955,2100,2826	TT,TG,GG		42.6623,16.4412,34.0928		15/420	179498658	4010,7752	1922	3959	5881	SO:0001819	synonymous_variant	55819	exon1			CAGGGCGAGCGCG	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"""RING-type (C3HC4) zinc fingers"""	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.45C>A	5.37:g.179498658G>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	22	7	0.318182	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				G|0.550;T|0.450	0.450	strong		0.766	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	
HRG	3273	hgsc.bcm.edu	37	3	186395436	186395436	+	Missense_Mutation	SNP	C	C	T	rs1042445	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:186395436C>T	ENST00000232003.4	+	7	1422	c.1342C>T	c.(1342-1344)Cgt>Tgt	p.R448C		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	448	His/Pro-rich (HRR).		R -> C (in dbSNP:rs1042445).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TAAAGGACCCCGTCCCTTCCA	0.567													C|||	1368	0.273163	0.2428	0.2752	5008	,	,		17691	0.2847		0.2455	False		,,,				2504	0.3292				p.R448C		Atlas-SNP	.											.	HRG	81	.	0			c.C1342T						PASS	.	C	CYS/ARG	1101,3305	396.5+/-330.1	140,821,1242	79.0	76.0	77.0		1342	2.3	0.0	3	dbSNP_86	77	1955,6645	344.0+/-325.1	202,1551,2547	yes	missense	HRG	NM_000412.2	180	342,2372,3789	TT,TC,CC		22.7326,24.9887,23.4968	benign	448/526	186395436	3056,9950	2203	4300	6503	SO:0001583	missense	3273	exon7			GGACCCCGTCCCT		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1342C>T	3.37:g.186395436C>T	ENSP00000232003:p.Arg448Cys	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	173	99	0.572254	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	588	0.2692307692307692	137	0.2784552845528455	96	0.26519337016574585	165	0.28846153846153844	190	0.25065963060686014	C	2.396	-0.338783	0.05243	0.249887	0.227326	ENSG00000113905	ENST00000232003	T	0.11277	2.79	4.94	2.35	0.29111	.	0.755923	0.11783	N	0.529939	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.46884	-0.9159	9	0.38643	T	0.18	-1.9829	6.7873	0.23679	0.0:0.197:0.0:0.803	rs1042445;rs3181923;rs52832999;rs60599328;rs1042445	448	P04196	HRG_HUMAN	C	448	ENSP00000232003:R448C	ENSP00000232003:R448C	R	+	1	0	HRG	187878130	0.000000	0.05858	0.037000	0.18230	0.001000	0.01503	-0.431000	0.06965	0.430000	0.26230	-0.474000	0.04947	CGT	C|0.750;T|0.250	0.250	strong		0.567	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
MMS19	64210	hgsc.bcm.edu	37	10	99220707	99220707	+	Missense_Mutation	SNP	C	C	T	rs3740526	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99220707C>T	ENST00000438925.2	-	24	2704	c.2369G>A	c.(2368-2370)gGc>gAc	p.G790D	MMS19_ENST00000327277.7_3'UTR|MMS19_ENST00000327238.10_Missense_Mutation_p.G692D|MMS19_ENST00000355839.6_Missense_Mutation_p.G747D|MMS19_ENST00000370782.2_Missense_Mutation_p.G790D	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	790			G -> D (in dbSNP:rs3740526). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)	p.G790D(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		GGGCCCAGAGCCCAGGCCAGC	0.498								Direct reversal of damage					C|||	1653	0.330072	0.1793	0.4063	5008	,	,		18602	0.375		0.4503	False		,,,				2504	0.3098				p.G790D		Atlas-SNP	.											MMS19,NS,carcinoma,0,1	MMS19	36	1	1	Substitution - Missense(1)	stomach(1)	c.G2369A						scavenged	.	C	ASP/GLY	889,3513		81,727,1393	33.0	32.0	32.0		2369	3.6	0.6	10	dbSNP_107	32	3552,5030		740,2072,1479	yes	missense	MMS19	NM_022362.4	94	821,2799,2872	TT,TC,CC		41.389,20.1954,34.2036	benign	790/1031	99220707	4441,8543	2201	4291	6492	SO:0001583	missense	64210	exon24			CCAGAGCCCAGGC	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2369G>A	10.37:g.99220707C>T	ENSP00000412698:p.Gly790Asp	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	819|819	0.375|0.375	96|96	0.1951219512195122|0.1951219512195122	157|157	0.43370165745856354|0.43370165745856354	220|220	0.38461538461538464|0.38461538461538464	346|346	0.45646437994722955|0.45646437994722955	C|C	12.25|12.25	1.880974|1.880974	0.33255|0.33255	0.201954|0.201954	0.41389|0.41389	ENSG00000155229|ENSG00000155229	ENST00000434538|ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000355839	.|T;T;T;T	.|0.64991	.|1.62;1.62;-0.13;1.62	5.66|5.66	3.64|3.64	0.41730|0.41730	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.491931	.|0.23435	.|N	.|0.048216	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B;B;B;B	.|0.24426	.|0.103;0.061;0.0;0.054	.|B;B;B;B	.|0.23419	.|0.029;0.046;0.004;0.013	T|T	0.43750|0.43750	-0.9372|-0.9372	4|9	.|0.12430	.|T	.|0.62	.|.	4.9046|4.9046	0.13791|0.13791	0.1374:0.4075:0.3757:0.0794|0.1374:0.4075:0.3757:0.0794	rs3740526;rs52816448;rs57965173;rs3740526|rs3740526;rs52816448;rs57965173;rs3740526	.|692;747;790;747	.|Q96T76-5;F8W9Y2;Q96T76;B4E2I3	.|.;.;MMS19_HUMAN;.	T|D	365|790;790;692;769;747	.|ENSP00000412698:G790D;ENSP00000359818:G790D;ENSP00000320059:G692D;ENSP00000348097:G747D	.|ENSP00000320059:G692D	A|G	-|-	1|2	0|0	MMS19|MMS19	99210697|99210697	0.656000|0.656000	0.27385|0.27385	0.647000|0.647000	0.29507|0.29507	0.947000|0.947000	0.59692|0.59692	1.234000|1.234000	0.32660|0.32660	1.336000|1.336000	0.45506|0.45506	0.484000|0.484000	0.47621|0.47621	GCT|GGC	C|0.642;T|0.358	0.358	strong		0.498	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
KRT74	121391	hgsc.bcm.edu	37	12	52967436	52967436	+	Silent	SNP	G	G	A	rs11836189	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52967436G>A	ENST00000305620.2	-	1	173	c.126C>T	c.(124-126)ggC>ggT	p.G42G	KRT74_ENST00000549343.1_Silent_p.G42G	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	42	Gly-rich.|Head.				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)		CAAAGCCAGCGCCAGCCCCTC	0.592													A|||	1001	0.19988	0.3699	0.1153	5008	,	,		18856	0.129		0.1541	False		,,,				2504	0.1503				p.G42G		Atlas-SNP	.											.	KRT74	67	.	0			c.C126T						PASS	.	A		1344,3062	693.6+/-405.7	214,916,1073	52.0	56.0	54.0		126	-0.1	0.0	12	dbSNP_120	54	1104,7496	768.1+/-407.6	58,988,3254	no	coding-synonymous	KRT74	NM_175053.3		272,1904,4327	AA,AG,GG		12.8372,30.5039,18.8221		42/530	52967436	2448,10558	2203	4300	6503	SO:0001819	synonymous_variant	121391	exon1			GCCAGCGCCAGCC	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.126C>T	12.37:g.52967436G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_175053	B5MD61|Q86Y45	Silent	SNP	ENST00000305620.2	37	CCDS8832.1																																																																																			G|0.809;A|0.191	0.191	strong		0.592	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
ZNF805	390980	hgsc.bcm.edu	37	19	57760018	57760018	+	Missense_Mutation	SNP	G	G	A	rs2014572	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57760018G>A	ENST00000414468.2	+	3	203	c.203G>A	c.(202-204)gGg>gAg	p.G68E	ZNF805_ENST00000535550.1_5'UTR|ZNF805_ENST00000354309.4_5'UTR	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	68	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		G -> E (in dbSNP:rs2014572).		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)|kidney(3)|lung(1)|stomach(1)	9						CTAGAGCATGGGCAGGAGCCA	0.542													.|||	1845	0.368411	0.2481	0.4496	5008	,	,		20344	0.1815		0.5746	False		,,,				2504	0.454				p.G68E		Atlas-SNP	.											.	ZNF805	30	.	0			c.G203A						PASS	.	A	GLU/GLY,	382,1002		52,278,362	70.0	63.0	65.0	http://www.ncbi.nlm.nih.gov/pubmed?term	203,	0.0	0.0	19	dbSNP_92	65	1648,1534		430,788,373	yes	missense,utr-5	ZNF805	NM_001023563.3,NM_001145078.1	98,	482,1066,735	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	48.2087,27.6012,44.459	benign,	68/628,	57760018	2030,2536	692	1591	2283	SO:0001583	missense	390980	exon3			AGCATGGGCAGGA	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.203G>A	19.37:g.57760018G>A	ENSP00000412999:p.Gly68Glu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001023563	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	852	0.3901098901098901	129	0.2621951219512195	175	0.48342541436464087	115	0.20104895104895104	433	0.5712401055408971	A	11.87	1.767179	0.31320	0.276012	0.517913	ENSG00000204524	ENST00000414468	T	0.00892	5.57	4.67	-0.00356	0.14025	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.58432	P	1.999999999946489E-6	P	0.39665	0.682	B	0.32864	0.154	T	0.00304	-1.1832	8	0.26408	T	0.33	.	10.9728	0.47448	0.2482:0.0:0.7518:0.0	rs2014572;rs3746232;rs52814311;rs60463144;rs2014572	68	Q5CZA5	ZN805_HUMAN	E	68	ENSP00000412999:G68E	ENSP00000412999:G68E	G	+	2	0	ZNF805	62451830	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.261000	0.18442	-0.048000	0.13401	-1.004000	0.02495	GGG	G|0.625;A|0.375	0.375	strong		0.542	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237751	239237751	+	Missense_Mutation	SNP	A	A	G	rs3769110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239237751A>G	ENST00000373327.4	+	5	905	c.683A>G	c.(682-684)aAc>aGc	p.N228S	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.N228S|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.N228S	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	228	Abolishes microtubules-binding when missing.|Arg-rich.|DISC1-interaction domain.		N -> S (in dbSNP:rs3769110). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		aggccagacaacgagcgacag	0.562													G|||	767	0.153155	0.3283	0.0821	5008	,	,		16420	0.0992		0.0586	False		,,,				2504	0.1196				p.N228S		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.A683G						PASS	.	G	SER/ASN,SER/ASN	975,3195		118,739,1228	67.0	65.0	65.0		683,683	-0.8	0.0	2	dbSNP_107	65	298,7934		1,296,3819	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	46,46	119,1035,5047	GG,GA,AA		3.62,23.3813,10.2645	benign,benign	228/626,228/692	239237751	1273,11129	2085	4116	6201	SO:0001583	missense	26146	exon5			CAGACAACGAGCG	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.683A>G	2.37:g.239237751A>G	ENSP00000362424:p.Asn228Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	294	0.1346153846153846	150	0.3048780487804878	38	0.10497237569060773	64	0.11188811188811189	42	0.055408970976253295	G	0.849	-0.739218	0.03088	0.233813	0.0362	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.13307	2.6;2.6;2.6	3.52	-0.824	0.10812	.	0.505809	0.19541	N	0.111788	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45498	-0.9257	9	0.07325	T	0.83	0.2404	4.9772	0.14146	0.3375:0.2666:0.3958:0.0	rs3769110;rs17846567;rs17859648;rs52817459;rs59175460;rs3769110	228;228	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	S	228	ENSP00000375851:N228S;ENSP00000362424:N228S;ENSP00000375852:N228S	ENSP00000362424:N228S	N	+	2	0	TRAF3IP1	238902490	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.242000	0.18087	-0.513000	0.06496	-0.119000	0.15052	AAC	A|0.850;G|0.150	0.150	strong		0.562	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
PSG4	5672	hgsc.bcm.edu	37	19	43699336	43699336	+	Missense_Mutation	SNP	T	T	C	rs1058718	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43699336T>C	ENST00000405312.3	-	4	1036	c.799A>G	c.(799-801)Aag>Gag	p.K267E	PSG4_ENST00000433626.2_Missense_Mutation_p.K174E|PSG4_ENST00000244295.9_Intron	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	267	Ig-like C2-type 2.		K -> E (in dbSNP:rs1058718). {ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:2783133, ECO:0000269|PubMed:7794280}.		female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				GTGTAGTTCTTACTCTTAGGT	0.453													C|||	3897	0.778155	0.8782	0.6239	5008	,	,		20698	0.9196		0.6332	False		,,,				2504	0.7556				p.Y267D		Atlas-SNP	.											.	PSG4	129	.	0			c.T799G						PASS	.	C	GLU/LYS,	3472,932		1533,406,263	194.0	221.0	212.0		799,	0.4	0.0	19	dbSNP_86	212	4922,3662		1751,1420,1121	no	missense,intron	PSG4	NM_002780.3,NM_213633.1	56,	3284,1826,1384	CC,CT,TT		42.6608,21.1626,35.3711	,	267/420,	43699336	8394,4594	2202	4292	6494	SO:0001583	missense	5672	exon4			AGTTCTTACTCTT		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.799A>G	19.37:g.43699336T>C	ENSP00000384770:p.Lys267Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	1499	0.6863553113553114	376	0.7642276422764228	199	0.5497237569060773	505	0.8828671328671329	419	0.5527704485488126	c	1.976	-0.435342	0.04669	0.788374	0.573392	ENSG00000243137	ENST00000405312;ENST00000433626	T;T	0.08984	3.03;3.03	1.55	0.359	0.16088	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.03281	-0.365	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05582	-1.0876	8	0.17832	T	0.49	.	3.7266	0.08477	0.0:0.2787:0.4428:0.2786	rs1058718;rs3175734;rs3859473;rs16976140;rs17846620;rs17859710;rs58532735	174;267	E7EX79;Q00888	.;PSG4_HUMAN	E	267;174	ENSP00000384770:K267E;ENSP00000387864:K174E	ENSP00000384770:K267E	K	-	1	0	PSG4	48391176	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.111000	0.01333	-0.465000	0.06953	-2.373000	0.00235	AAG	T|0.323;C|0.677	0.677	strong		0.453	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
GBP3	2635	hgsc.bcm.edu	37	1	89475093	89475093	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:89475093T>C	ENST00000370481.4	-	9	1667	c.1447A>G	c.(1447-1449)Aag>Gag	p.K483E		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0	Sufficient for membrane association.				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)		TCCTTTTCCTTTTCTGTGAGA	0.348																																					p.K483E		Atlas-SNP	.											GBP3,NS,carcinoma,0,1	GBP3	53	1	0			c.A1447G						scavenged	.						141.0	128.0	132.0					1																	89475093		2203	4300	6503	SO:0001583	missense	2635	exon9			TTTCCTTTTCTGT	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.1447A>G	1.37:g.89475093T>C	ENSP00000359512:p.Lys483Glu	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	247	5	0.0202429	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	T	9.340	1.062852	0.19987	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000445969	T;T	0.02236	4.38;4.38	3.9	3.9	0.45041	Guanylate-binding protein, C-terminal (3);	0.182680	0.48286	D	0.000196	T	0.02455	0.0075	M	0.91561	3.22	0.24394	N	0.994734	B;B	0.21821	0.049;0.061	B;B	0.26614	0.042;0.071	T	0.23368	-1.0190	10	0.38643	T	0.18	.	10.9883	0.47534	0.0:0.0:0.0:1.0	.	349;483	F6X827;Q9H0R5	.;GBP3_HUMAN	E	451;483;63	ENSP00000359512:K483E;ENSP00000415087:K63E	ENSP00000359512:K483E	K	-	1	0	GBP3	89247681	0.874000	0.30092	1.000000	0.80357	0.475000	0.33008	2.037000	0.41174	1.764000	0.52075	0.496000	0.49642	AAG	.	.	none		0.348	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
FLG	2312	hgsc.bcm.edu	37	1	152282267	152282267	+	Missense_Mutation	SNP	G	G	A	rs12405278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152282267G>A	ENST00000368799.1	-	3	5130	c.5095C>T	c.(5095-5097)Cgc>Tgc	p.R1699C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1699	Ser-rich.		R -> C (in dbSNP:rs12405278).		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)			TCTTGTCTGCGCCCAGTGCCT	0.572									Ichthyosis				g|||	1441	0.28774	0.0121	0.3905	5008	,	,		20090	0.5843		0.1421	False		,,,				2504	0.4315				p.R1699C		Atlas-SNP	.											FLG,colon,carcinoma,+1,1	FLG	900	1	0			c.C5095T						PASS	.	C	CYS/ARG	161,4245	108.2+/-146.6	2,157,2044	256.0	259.0	258.0		5095	1.8	0.0	1	dbSNP_120	258	1240,7360	249.0+/-276.5	97,1046,3157	yes	missense	FLG	NM_002016.1	180	99,1203,5201	AA,AG,GG		14.4186,3.6541,10.772	probably-damaging	1699/4062	152282267	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTGCGCCCAGT	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.5095C>T	1.37:g.152282267G>A	ENSP00000357789:p.Arg1699Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	151	94	0.622517	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	573	0.2623626373626374	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	111	0.14643799472295516	g	3.096	-0.185843	0.06340	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.04275	3.66	2.69	1.76	0.24704	.	.	.	.	.	T	0.05823	0.0152	L	0.54323	1.7	0.80722	P	0.0	D	0.76494	0.999	D	0.63192	0.912	T	0.21484	-1.0244	8	0.54805	T	0.06	.	7.611	0.28131	0.0:0.2659:0.7341:0.0	rs56401605;rs58569216	1699	P20930	FILA_HUMAN	C	1699	ENSP00000357789:R1699C	ENSP00000357789:R1699C	R	-	1	0	FLG	150548891	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.137000	0.15995	0.482000	0.27582	-0.672000	0.03802	CGC	G|0.811;A|0.189	0.189	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ASTN1	460	hgsc.bcm.edu	37	1	177001896	177001896	+	Silent	SNP	C	C	G	rs2076069	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177001896C>G	ENST00000367654.3	-	3	772	c.561G>C	c.(559-561)ccG>ccC	p.P187P	ASTN1_ENST00000367657.3_Silent_p.P187P|ASTN1_ENST00000424564.2_Silent_p.P187P|ASTN1_ENST00000361833.2_Silent_p.P187P|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	187					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCTGGGGCTGCGGGACCCGGC	0.612													G|||	751	0.14996	0.0272	0.2118	5008	,	,		17437	0.2599		0.1471	False		,,,				2504	0.1616				p.P187P		Atlas-SNP	.											.	ASTN1	314	.	0			c.G561C						PASS	.	G	,	228,4178	789.4+/-415.0	3,222,1978	38.0	39.0	38.0		561,561	-1.3	0.9	1	dbSNP_96	38	1418,7182	736.8+/-407.0	119,1180,3001	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	122,1402,4979	GG,GC,CC		16.4884,5.1748,12.6557	,	187/1295,187/1217	177001896	1646,11360	2203	4300	6503	SO:0001819	synonymous_variant	460	exon3			GGGCTGCGGGACC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.561G>C	1.37:g.177001896C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	33	0.717391	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				C|0.864;G|0.136	0.136	strong		0.612	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
GTF2F1	2962	hgsc.bcm.edu	37	19	6392910	6392910	+	Missense_Mutation	SNP	G	G	A	rs150462935		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392910G>A	ENST00000394456.5	-	2	481	c.17C>T	c.(16-18)cCt>cTt	p.P6L	CTB-180A7.6_ENST00000599584.1_RNA|GTF2F1_ENST00000429701.2_5'Flank	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	6					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|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)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						CTGGCTGCTAGGGCCCTGCGG	0.602											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16382	0.0		0.001	False		,,,				2504	0.0				p.P6L		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C17T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	134.0	135.0	134.0		17	5.1	1.0	19	dbSNP_134	134	4,8596	1.2+/-3.3	0,4,4296	yes	missense	GTF2F1	NM_002096.2	98	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	6/518	6392910	4,13002	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGCTAGGGCCCT		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.17C>T	19.37:g.6392910G>A	ENSP00000377969:p.Pro6Leu	Somatic	71	0	0	633	WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.23	3.063678	0.55432	0.0	4.65E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.46451	0.87	5.07	5.07	0.68467	.	0.397846	0.25529	N	0.030059	T	0.26521	0.0648	N	0.08118	0	0.80722	D	1	B	0.21225	0.053	B	0.16289	0.015	T	0.10177	-1.0641	10	0.72032	D	0.01	-21.0264	15.4688	0.75426	0.0:0.0:1.0:0.0	.	6	P35269	T2FA_HUMAN	L	6	ENSP00000377969:P6L	ENSP00000377969:P6L	P	-	2	0	GTF2F1	6343910	1.000000	0.71417	0.997000	0.53966	0.751000	0.42716	2.686000	0.46968	2.629000	0.89072	0.591000	0.81541	CCT	G|0.999;A|0.001	0.001	strong		0.602	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
NFKBIA	4792	hgsc.bcm.edu	37	14	35872926	35872926	+	Silent	SNP	G	G	A	rs1050851	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:35872926G>A	ENST00000216797.5	-	2	407	c.306C>T	c.(304-306)gcC>gcT	p.A102A	NFKBIA_ENST00000557389.1_Silent_p.A12A|NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557140.1_Silent_p.A102A	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	102					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)	AGTTGAGGAAGGCCAGGTCTC	0.572													G|||	509	0.101637	0.0204	0.1383	5008	,	,		15077	0.0188		0.2217	False		,,,				2504	0.1472				p.A102A		Atlas-SNP	.											.	NFKBIA	28	.	0			c.C306T						PASS	.	G		262,4144	146.9+/-181.5	7,248,1948	81.0	67.0	72.0		306	-0.2	1.0	14	dbSNP_86	72	1959,6641	342.6+/-324.5	224,1511,2565	no	coding-synonymous	NFKBIA	NM_020529.2		231,1759,4513	AA,AG,GG		22.7791,5.9464,17.0767		102/318	35872926	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	4792	exon2			GAGGAAGGCCAGG		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.306C>T	14.37:g.35872926G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_020529	B2R8L6	Silent	SNP	ENST00000216797.5	37	CCDS9656.1																																																																																			G|0.849;A|0.151	0.151	strong		0.572	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:2526746A>G	ENST00000378412.3	-	16	1714	c.1553T>C	c.(1552-1554)aTg>aCg	p.M518T	MMEL1_ENST00000502556.1_Missense_Mutation_p.M361T|MMEL1_ENST00000288709.6_Missense_Mutation_p.M509T			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	518			M -> T (in dbSNP:rs3748816). {ECO:0000269|PubMed:15489334}.			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)		GCGCCTGTTCATCTCCTCCAG	0.647													G|||	2711	0.541334	0.7284	0.487	5008	,	,		15245	0.5407		0.332	False		,,,				2504	0.5429				p.M518T		Atlas-SNP	.											.	MMEL1	64	.	0			c.T1553C						PASS	.	G	THR/MET	3002,1404	459.8+/-352.4	1022,958,223	70.0	66.0	67.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1553	-5.5	0.0	1	dbSNP_107	67	2892,5708	671.0+/-402.8	487,1918,1895	yes	missense	MMEL1	NM_033467.3	81	1509,2876,2118	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.6279,31.8656,45.3175	benign	518/780	2526746	5894,7112	2203	4300	6503	SO:0001583	missense	79258	exon16			CTGTTCATCTCCT	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.1553T>C	1.37:g.2526746A>G	ENSP00000367668:p.Met518Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	1043	0.4775641025641026	347	0.7052845528455285	165	0.4558011049723757	278	0.486013986013986	253	0.3337730870712401	G	0	-2.755514	0.00085	0.681344	0.336279	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	D;D;D	0.81579	-1.51;-1.51;-1.51	4.89	-5.48	0.02592	.	1.727810	0.02496	N	0.089927	T	0.00012	0.0000	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.08381	T	0.77	-0.0773	2.1612	0.03825	0.1136:0.2449:0.3589:0.2826	rs3748816;rs61663127;rs3748816	518	Q495T6	MMEL1_HUMAN	T	361;509;518;361	ENSP00000288709:M509T;ENSP00000367668:M518T;ENSP00000422492:M361T	ENSP00000288709:M509T	M	-	2	0	MMEL1	2516606	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.199000	0.00561	-1.671000	0.01466	-2.367000	0.00236	ATG	A|0.529;G|0.471	0.471	strong		0.647	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
EPB41L3	23136	hgsc.bcm.edu	37	18	5423422	5423422	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:5423422G>A	ENST00000341928.2	-	11	1634	c.1294C>T	c.(1294-1296)Cgc>Tgc	p.R432C	EPB41L3_ENST00000342933.3_Missense_Mutation_p.R432C|EPB41L3_ENST00000400111.3_Missense_Mutation_p.R432C|EPB41L3_ENST00000540638.2_Missense_Mutation_p.R432C|EPB41L3_ENST00000544123.1_Missense_Mutation_p.R432C|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	432	Hydrophilic.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.R432C(2)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CTGGATGAGCGTTCAAAGTAA	0.483																																					p.R432C		Atlas-SNP	.											EPB41L3,colon,carcinoma,0,2	EPB41L3	222	2	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C1294T						scavenged	.						194.0	148.0	164.0					18																	5423422		2203	4300	6503	SO:0001583	missense	23136	exon11			ATGAGCGTTCAAA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1294C>T	18.37:g.5423422G>A	ENSP00000343158:p.Arg432Cys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	203	3	0.0147783	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747670	0.89663	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.96619	-4.07;-4.07;-4.07;-4.07	6.08	6.08	0.98989	FERM adjacent (FA) (1);	0.000000	0.85682	D	0.000000	D	0.98814	0.9600	H	0.94886	3.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.999;0.998;1.0	D	0.98997	1.0810	10	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	432;323;432;432	F5GX05;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	C	432;323;432;323;432;432	ENSP00000343158:R432C;ENSP00000441174:R432C;ENSP00000341138:R432C;ENSP00000382981:R432C	ENSP00000343158:R432C	R	-	1	0	EPB41L3	5413422	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	7.837000	0.86796	2.894000	0.99253	0.591000	0.81541	CGC	.	.	none		0.483	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
ARNT2	9915	hgsc.bcm.edu	37	15	80884025	80884025	+	Missense_Mutation	SNP	G	G	A	rs4072568	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:80884025G>A	ENST00000303329.4	+	18	2200	c.2035G>A	c.(2035-2037)Ggt>Agt	p.G679S	ARNT2_ENST00000533983.1_Missense_Mutation_p.G668S|ARNT2_ENST00000527771.1_Missense_Mutation_p.G668S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	679			G -> S (in dbSNP:rs4072568). {ECO:0000269|PubMed:9205841}.		central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			CCAGCAGCCCGGTCAGACTGA	0.637													G|||	561	0.112021	0.1377	0.1066	5008	,	,		18357	0.003		0.166	False		,,,				2504	0.138				p.G679S		Atlas-SNP	.											ARNT2,NS,carcinoma,-1,1	ARNT2	88	1	0			c.G2035A						PASS	.	G	SER/GLY	602,3804	263.8+/-265.7	33,536,1634	111.0	107.0	108.0		2035	1.7	1.0	15	dbSNP_108	108	1684,6916	309.4+/-309.4	182,1320,2798	yes	missense	ARNT2	NM_014862.3	56	215,1856,4432	AA,AG,GG		19.5814,13.6632,17.5765	benign	679/718	80884025	2286,10720	2203	4300	6503	SO:0001583	missense	9915	exon18			CAGCCCGGTCAGA	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.2035G>A	15.37:g.80884025G>A	ENSP00000307479:p.Gly679Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	239	0.10943223443223443	72	0.14634146341463414	45	0.12430939226519337	0	0.0	122	0.16094986807387862	G	10.84	1.462974	0.26248	0.136632	0.195814	ENSG00000172379	ENST00000360062;ENST00000303329	T	0.03920	3.76	5.07	1.74	0.24563	.	0.276124	0.39274	N	0.001420	T	0.00012	0.0000	N	0.02011	-0.69	0.35400	P	0.20852800000000005	B	0.06786	0.001	B	0.06405	0.002	T	0.46992	-0.9151	9	0.11794	T	0.64	.	6.8547	0.24034	0.4281:0.0:0.5719:0.0	rs4072568;rs17608916;rs52827902;rs56876472;rs4072568	679	Q9HBZ2	ARNT2_HUMAN	S	668;679	ENSP00000307479:G679S	ENSP00000307479:G679S	G	+	1	0	ARNT2	78671080	1.000000	0.71417	0.976000	0.42696	0.991000	0.79684	2.649000	0.46656	0.533000	0.28675	0.313000	0.20887	GGT	G|0.856;A|0.144	0.144	strong		0.637	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
AP4B1	10717	hgsc.bcm.edu	37	1	114443899	114443899	+	Silent	SNP	G	G	A	rs17464525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:114443899G>A	ENST00000369569.1	-	4	856	c.576C>T	c.(574-576)ggC>ggT	p.G192G	AP4B1_ENST00000369566.3_Intron|AP4B1_ENST00000369567.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000256658.4_Silent_p.G192G	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	240	0	0		WXS	Illumina HiSeq	Phase_I	236	108	0.457627	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	
CLCC1	23155	hgsc.bcm.edu	37	1	109486196	109486196	+	Silent	SNP	A	A	G	rs338466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:109486196A>G	ENST00000369971.2	-	6	732	c.603T>C	c.(601-603)acT>acC	p.T201T	AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369970.3_Silent_p.T151T|CLCC1_ENST00000356970.2_Silent_p.T201T|CLCC1_ENST00000348264.2_Intron|CLCC1_ENST00000482889.1_5'UTR|CLCC1_ENST00000369969.2_Intron|CLCC1_ENST00000369976.1_Silent_p.T201T|CLCC1_ENST00000369968.2_Intron|CLCC1_ENST00000302500.4_Intron|CLCC1_ENST00000415331.1_Silent_p.T151T	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	201						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		TCCACAGCTCAGTAGCCACTA	0.393													G|||	2696	0.538339	0.7579	0.5101	5008	,	,		19123	0.3958		0.5219	False		,,,				2504	0.4254				p.T201T		Atlas-SNP	.											.	CLCC1	55	.	0			c.T603C						PASS	.	G	,	3198,1208	419.6+/-338.7	1169,860,174	93.0	99.0	97.0		603,453	-8.9	0.4	1	dbSNP_79	97	4538,4062	558.9+/-387.3	1185,2168,947	no	coding-synonymous,coding-synonymous	CLCC1	NM_001048210.1,NM_015127.3	,	2354,3028,1121	GG,GA,AA		47.2326,27.4172,40.5198	,	201/552,151/502	109486196	7736,5270	2203	4300	6503	SO:0001819	synonymous_variant	23155	exon6			CAGCTCAGTAGCC	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"""Mid1-related chloride channel (yeast)"""					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.603T>C	1.37:g.109486196A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Silent	SNP	ENST00000369971.2	37	CCDS41362.1																																																																																			A|0.429;G|0.571	0.571	strong		0.393	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
TAF5L	27097	hgsc.bcm.edu	37	1	229738170	229738170	+	Silent	SNP	T	T	G	rs3753886	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229738170T>G	ENST00000366676.1	-	3	743	c.744A>C	c.(742-744)cgA>cgC	p.R248R	TAF5L_ENST00000366675.3_Silent_p.R248R|TAF5L_ENST00000258281.2_Silent_p.R248R			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	248					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CATCCTTGACTCGCTTAATGC	0.552													G|||	2873	0.573682	0.4887	0.5447	5008	,	,		19925	0.7639		0.5179	False		,,,				2504	0.5706				p.R248R		Atlas-SNP	.											.	TAF5L	76	.	0			c.A744C						PASS	.	G	,	2246,2160	581.4+/-385.4	571,1104,528	91.0	90.0	90.0		744,744	-11.6	0.0	1	dbSNP_107	90	4407,4193	569.8+/-389.2	1100,2207,993	no	coding-synonymous,coding-synonymous	TAF5L	NM_001025247.1,NM_014409.3	,	1671,3311,1521	GG,GT,TT		48.7558,49.0241,48.8467	,	248/326,248/590	229738170	6653,6353	2203	4300	6503	SO:0001819	synonymous_variant	27097	exon4			CTTGACTCGCTTA	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"""WD repeat domain containing"""	17304	protein-coding gene	gene with protein product	"""PCAF associated factor 65 beta"""		"""TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.744A>C	1.37:g.229738170T>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001025247	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			T|0.456;G|0.544	0.544	strong		0.552	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	
LPCAT3	10162	hgsc.bcm.edu	37	12	7090193	7090193	+	Missense_Mutation	SNP	A	A	G	rs1984564	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	121	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	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	
CHD5	26038	hgsc.bcm.edu	37	1	6188596	6188596	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6188596G>A	ENST00000262450.3	-	24	3792	c.3693C>T	c.(3691-3693)gcC>gcT	p.A1231A	CHD5_ENST00000378021.1_Silent_p.A88A	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TTGCACTGGCGGCCAAGTTCC	0.627																																					p.A1231A		Atlas-SNP	.											.	CHD5	267	.	0			c.C3693T						PASS	.						59.0	62.0	61.0					1																	6188596		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon24			ACTGGCGGCCAAG	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.3693C>T	1.37:g.6188596G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			.	.	none		0.627	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128839405	128839405	+	Silent	SNP	C	C	T	rs78856194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:128839405C>T	ENST00000310343.9	-	22	5660	c.5661G>A	c.(5659-5661)caG>caA	p.Q1887Q	ARHGAP32_ENST00000392657.3_Silent_p.Q1538Q|ARHGAP32_ENST00000527272.1_Silent_p.Q1538Q|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1887	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						ACTCACAGAACTGCCTATGGC	0.562													C|||	74	0.0147764	0.0015	0.0173	5008	,	,		19902	0.0		0.0537	False		,,,				2504	0.0061				p.Q1887Q		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.G5661A						PASS	.	C	,	42,4360	46.0+/-80.4	0,42,2159	86.0	80.0	82.0		5661,4614	-11.7	0.0	11	dbSNP_132	82	356,8238	119.5+/-178.9	9,338,3950	yes	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	9,380,6109	TT,TC,CC		4.1424,0.9541,3.0625	,	1887/2088,1538/1739	128839405	398,12598	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon22			ACAGAACTGCCTA	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.5661G>A	11.37:g.128839405C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
SON	6651	hgsc.bcm.edu	37	21	34926043	34926043	+	Missense_Mutation	SNP	G	G	A	rs61743204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34926043G>A	ENST00000356577.4	+	3	4981	c.4506G>A	c.(4504-4506)atG>atA	p.M1502I	SON_ENST00000300278.4_Missense_Mutation_p.M1502I|SON_ENST00000381679.4_Missense_Mutation_p.M1502I|SON_ENST00000290239.6_Missense_Mutation_p.M1502I|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1502					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						AGATTGGCATGCAGGAGATTG	0.388													G|||	769	0.153554	0.118	0.1816	5008	,	,		23665	0.2351		0.1054	False		,,,				2504	0.1472				p.M1502I		Atlas-SNP	.											.	SON	343	.	0			c.G4506A						PASS	.	G	ILE/MET,ILE/MET	540,3864	240.9+/-251.5	35,470,1697	47.0	44.0	45.0		4506,4506	2.0	1.0	21	dbSNP_129	45	759,7841	181.3+/-230.0	41,677,3582	yes	missense,missense	SON	NM_032195.1,NM_138927.1	10,10	76,1147,5279	AA,AG,GG		8.8256,12.2616,9.9892	benign,benign	1502/2304,1502/2427	34926043	1299,11705	2202	4300	6502	SO:0001583	missense	6651	exon3			TGGCATGCAGGAG	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.4506G>A	21.37:g.34926043G>A	ENSP00000348984:p.Met1502Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	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	335|335	0.1533882783882784|0.1533882783882784	61|61	0.12398373983739837|0.12398373983739837	49|49	0.13535911602209943|0.13535911602209943	142|142	0.24825174825174826|0.24825174825174826	83|83	0.10949868073878628|0.10949868073878628	G|G	0.099|0.099	-1.155417|-1.155417	0.01700|0.01700	0.122616|0.122616	0.088256|0.088256	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.10960	.|3.03;3.02;3.0;2.82	5.03|5.03	2.02|2.02	0.26589|0.26589	.|.	.|0.501171	.|0.20410	.|N	.|0.092872	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.39007|0.39007	P|P	0.04052800000000001|0.04052800000000001	.|B;B;B;B;B	.|0.06786	.|0.0;0.0;0.0;0.0;0.001	.|B;B;B;B;B	.|0.09377	.|0.001;0.0;0.001;0.001;0.004	T|T	0.44862|0.44862	-0.9300|-0.9300	4|9	.|0.05620	.|T	.|0.96	.|.	5.6576|5.6576	0.17650|0.17650	0.0916:0.0:0.5638:0.3445|0.0916:0.0:0.5638:0.3445	rs61743204|rs61743204	.|1502;1502;1183;1502;1502	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	Y|I	497|1502	.|ENSP00000348984:M1502I;ENSP00000290239:M1502I;ENSP00000300278:M1502I;ENSP00000371095:M1502I	.|ENSP00000290239:M1502I	C|M	+|+	2|3	0|0	SON|SON	33847913|33847913	0.063000|0.063000	0.20901|0.20901	0.972000|0.972000	0.41901|0.41901	0.016000|0.016000	0.09150|0.09150	-0.191000|-0.191000	0.09601|0.09601	0.804000|0.804000	0.34136|0.34136	0.591000|0.591000	0.81541|0.81541	TGC|ATG	G|0.884;A|0.116	0.116	strong		0.388	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
DTL	51514	hgsc.bcm.edu	37	1	212276276	212276276	+	Silent	SNP	A	A	G	rs17853180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:212276276A>G	ENST00000366991.4	+	15	2501	c.2187A>G	c.(2185-2187)gaA>gaG	p.E729E	DTL_ENST00000475419.1_3'UTR|DTL_ENST00000542077.1_Silent_p.E687E	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	729					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.E729E(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		ACTCAACAGAATTATAGAttc	0.423													A|||	421	0.0840655	0.0023	0.0965	5008	,	,		17710	0.1806		0.0696	False		,,,				2504	0.1012				p.E729E		Atlas-SNP	.											DTL,NS,carcinoma,+2,2	DTL	52	2	1	Substitution - coding silent(1)	stomach(1)	c.A2187G						PASS	.	A		46,4360	48.2+/-83.0	0,46,2157	59.0	58.0	58.0		2187	-3.1	0.4	1	dbSNP_123	58	473,8125	138.3+/-195.1	16,441,3842	no	coding-synonymous	DTL	NM_016448.2		16,487,5999	GG,GA,AA		5.5013,1.044,3.9911		729/731	212276276	519,12485	2203	4299	6502	SO:0001819	synonymous_variant	51514	exon15			AACAGAATTATAG	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.2187A>G	1.37:g.212276276A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Silent	SNP	ENST00000366991.4	37	CCDS1502.1																																																																																			A|0.946;G|0.054	0.054	strong		0.423	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	
MEP1A	4224	hgsc.bcm.edu	37	6	46806809	46806809	+	Missense_Mutation	SNP	C	C	T	rs1804211	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	129	126	0.976744	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	
ZNF521	25925	hgsc.bcm.edu	37	18	22804942	22804942	+	Silent	SNP	C	C	T	rs187705938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:22804942C>T	ENST00000361524.3	-	4	3088	c.2940G>A	c.(2938-2940)acG>acA	p.T980T	ZNF521_ENST00000538137.2_Silent_p.T980T|ZNF521_ENST00000584787.1_Silent_p.T760T|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	980					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)					TCTTACTATGCGTGACTTTGT	0.468			T	PAX5	ALL								C|||	2	0.000399361	0.0	0.0	5008	,	,		21326	0.0		0.002	False		,,,				2504	0.0				p.T980T		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,NS,carcinoma,-1,1	ZNF521	269	1	0			c.G2940A						PASS	.	C		0,4406		0,0,2203	69.0	67.0	68.0		2940	-11.9	0.2	18		68	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ZNF521	NM_015461.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		980/1312	22804942	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			ACTATGCGTGACT	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.2940G>A	18.37:g.22804942C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	28	0.345679	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
PDIA6	10130	hgsc.bcm.edu	37	2	10929938	10929938	+	Silent	SNP	G	G	A	rs138712410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10929938G>A	ENST00000272227.3	-	8	924	c.777C>T	c.(775-777)tcC>tcT	p.S259S	PDIA6_ENST00000540494.1_Silent_p.S256S|PDIA6_ENST00000381611.4_Silent_p.S264S|PDIA6_ENST00000404824.2_Silent_p.S307S|PDIA6_ENST00000404371.2_Silent_p.S311S	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	259	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		ACACGATGTCGGATCTTGTCC	0.458													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		14648	0.0		0.008	False		,,,				2504	0.0276				p.S259S	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,NS,carcinoma,0,1	PDIA6	31	1	0			c.C777T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	85.0	83.0	84.0		777	-11.3	0.0	2	dbSNP_134	84	68,8532	41.7+/-99.0	0,68,4232	no	coding-synonymous	PDIA6	NM_005742.2		0,71,6432	AA,AG,GG		0.7907,0.0681,0.5459		259/441	10929938	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon8			GATGTCGGATCTT	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.777C>T	2.37:g.10929938G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
BGN	633	hgsc.bcm.edu	37	X	152771509	152771509	+	Silent	SNP	C	C	T	rs1126499	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:152771509C>T	ENST00000331595.4	+	4	726	c.540C>T	c.(538-540)agC>agT	p.S180S	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	180					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|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)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGTGTTCAGCGGGCTCCGGA	0.607													C|||	1266	0.335364	0.0726	0.2853	3775	,	,		11034	0.3016		0.3767	False		,,,				2504	0.2955				p.S180S		Atlas-SNP	.											.	BGN	44	.	0			c.C540T						PASS	.	C		628,3207		40,453,95,1139,476	50.0	46.0	47.0		540	-9.4	0.5	X	dbSNP_86	47	3135,3593		508,1207,912,713,960	no	coding-synonymous	BGN	NM_001711.4		548,1660,1007,1852,1436	TT,TC,T,CC,C		46.5963,16.3755,35.6243		180/369	152771509	3763,6800	2203	4300	6503	SO:0001819	synonymous_variant	633	exon4			GTTCAGCGGGCTC	AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.540C>T	X.37:g.152771509C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_001711	D3DWU3|P13247	Silent	SNP	ENST00000331595.4	37	CCDS14721.1																																																																																			C|0.658;T|0.342	0.342	strong		0.607	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711	
FAM198A	729085	hgsc.bcm.edu	37	3	43074434	43074434	+	Missense_Mutation	SNP	C	C	T	rs2936817	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:43074434C>T	ENST00000430121.2	+	2	774	c.679C>T	c.(679-681)Cat>Tat	p.H227Y	KRBOX1_ENST00000443313.1_Intron	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	227			H -> Y (in dbSNP:rs2936817). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)				endometrium(1)	1						CTCAGGAGCTCATCAGTGGCC	0.597													C|||	2197	0.438698	0.3419	0.5331	5008	,	,		20734	0.6518		0.4066	False		,,,				2504	0.316				p.H227Y		Atlas-SNP	.											.	FAM198A	23	.	0			c.C679T						PASS	.	C	TYR/HIS	454,930		72,310,310	20.0	24.0	23.0		679	-0.8	0.0	3	dbSNP_101	23	1295,1887		270,755,566	yes	missense	FAM198A	NM_001129908.2	83	342,1065,876	TT,TC,CC		40.6977,32.8035,38.3049	benign	227/576	43074434	1749,2817	692	1591	2283	SO:0001583	missense	729085	exon2			GGAGCTCATCAGT	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.679C>T	3.37:g.43074434C>T	ENSP00000407301:p.His227Tyr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	52	0.626506	NM_001129908	B3KR48	Missense_Mutation	SNP	ENST00000430121.2	37	CCDS46808.1	1034	0.4734432234432234	184	0.37398373983739835	190	0.5248618784530387	359	0.6276223776223776	301	0.3970976253298153	C	11.00	1.509802	0.27036	0.328035	0.406977	ENSG00000144649	ENST00000430121	T	0.30182	1.54	4.88	-0.785	0.10950	.	1.499980	0.04146	N	0.320400	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.38863	0.65	B	0.34242	0.178	T	0.40869	-0.9540	8	.	.	.	-9.0853	1.5116	0.02497	0.2799:0.4081:0.1372:0.1749	rs2936817;rs3732855;rs57615568;rs2936817	227	Q9UFP1	F198A_HUMAN	Y	227	ENSP00000407301:H227Y	.	H	+	1	0	FAM198A	43049438	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.050000	0.14120	-0.058000	0.13177	-0.218000	0.12543	CAT	C|0.535;T|0.465	0.465	strong		0.597	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
TBXAS1	6916	hgsc.bcm.edu	37	7	139715641	139715641	+	Missense_Mutation	SNP	G	G	A	rs8192868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:139715641G>A	ENST00000336425.5	+	15	1734	c.1345G>A	c.(1345-1347)Gag>Aag	p.E449K	TBXAS1_ENST00000458722.1_Missense_Mutation_p.E495K|TBXAS1_ENST00000425687.1_Missense_Mutation_p.E382K|TBXAS1_ENST00000414508.2_Missense_Mutation_p.E450K|TBXAS1_ENST00000448866.1_Missense_Mutation_p.E449K|TBXAS1_ENST00000436047.2_Missense_Mutation_p.E450K|TBXAS1_ENST00000411653.1_Missense_Mutation_p.E449K|TBXAS1_ENST00000263552.6_Missense_Mutation_p.E450K|TBXAS1_ENST00000416849.2_Missense_Mutation_p.E496K|TBXAS1_ENST00000462275.1_3'UTR			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	449			E -> K (in allele CYP5A1*7). {ECO:0000269|PubMed:11465543, ECO:0000269|PubMed:12721789}.		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)	GCCAAGCCCGGAGACCTTCAA	0.597													G|||	42	0.00838658	0.0	0.0043	5008	,	,		16479	0.0069		0.0179	False		,,,				2504	0.0143				p.E496K		Atlas-SNP	.											.	TBXAS1	121	.	0			c.G1486A	GRCh37	CM054135	TBXAS1	M	rs8192868	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	18,4388	24.3+/-50.5	0,18,2185	54.0	53.0	53.0		1348,1348,1486,1144,1348	3.6	0.0	7	dbSNP_117	53	195,8405	84.8+/-147.2	2,191,4107	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	56,56,56,56,56	2,209,6292	AA,AG,GG		2.2674,0.4085,1.6377	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	450/535,450/535,496/581,382/467,450/461	139715641	213,12793	2203	4300	6503	SO:0001583	missense	6916	exon12			AGCCCGGAGACCT	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.1345G>A	7.37:g.139715641G>A	ENSP00000338087:p.Glu449Lys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	30	11	0.366667	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		22	0.010073260073260074	0	0.0	1	0.0027624309392265192	7	0.012237762237762238	14	0.018469656992084433	G	11.87	1.767361	0.31320	0.004085	0.022674	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71;-0.71	4.52	3.64	0.41730	.	0.362911	0.29185	N	0.012887	T	0.68439	0.3001	M	0.68317	2.08	0.80722	D	1	B;D;P;D;P;P;P	0.63880	0.437;0.993;0.943;0.965;0.951;0.89;0.89	B;D;P;P;D;P;P	0.65773	0.406;0.934;0.823;0.842;0.938;0.714;0.714	T	0.76545	-0.2920	10	0.62326	D	0.03	.	12.2798	0.54757	0.0:0.3271:0.6729:0.0	rs8192868;rs58749746;rs8192868	430;496;401;382;450;450;449	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	K	382;450;449;496;450;450;449;495;449	ENSP00000388736:E382K;ENSP00000263552:E450K;ENSP00000338087:E449K;ENSP00000389414:E496K;ENSP00000392361:E450K;ENSP00000392702:E450K;ENSP00000402536:E449K;ENSP00000411274:E495K;ENSP00000411326:E449K	ENSP00000263552:E450K	E	+	1	0	TBXAS1	139362110	1.000000	0.71417	0.046000	0.18839	0.017000	0.09413	3.271000	0.51608	0.902000	0.36520	-0.371000	0.07208	GAG	G|0.985;A|0.015	0.015	strong		0.597	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
FAM205A	259308	hgsc.bcm.edu	37	9	34729392	34729392	+	Silent	SNP	A	A	G	rs12337278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34729392A>G	ENST00000378788.3	-	1	72	c.33T>C	c.(31-33)gtT>gtC	p.V11V		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	11						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						AGGGATATCCAACTTCCCACA	0.413													A|||	530	0.105831	0.3336	0.0375	5008	,	,		21145	0.0109		0.0189	False		,,,				2504	0.0337				p.V11V		Atlas-SNP	.											.	FAM205A	45	.	0			c.T33C						PASS	.	A		398,986		56,286,350	110.0	96.0	100.0		33	-8.2	0.0	9	dbSNP_120	100	63,3119		2,59,1530	yes	coding-synonymous	FAM205A	NM_001141917.1		58,345,1880	GG,GA,AA		1.9799,28.7572,10.0964		11/1336	34729392	461,4105	692	1591	2283	SO:0001819	synonymous_variant	259308	exon1			ATATCCAACTTCC		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.33T>C	9.37:g.34729392A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			A|0.915;G|0.085	0.085	strong		0.413	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
ARNT	405	hgsc.bcm.edu	37	1	150808889	150808889	+	Silent	SNP	C	C	G	rs2228099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:150808889C>G	ENST00000358595.5	-	7	767	c.567G>C	c.(565-567)gtG>gtC	p.V189V	ARNT_ENST00000468970.1_5'UTR|ARNT_ENST00000354396.2_Silent_p.V189V|ARNT_ENST00000505755.1_Silent_p.V174V|ARNT_ENST00000515192.1_Silent_p.V180V	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	189	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|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 protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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 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)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.V189V(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	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;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGGAGTCAGACACATACACCA	0.463			T	ETV6	AML								G|||	2359	0.471046	0.5174	0.4625	5008	,	,		16795	0.4018		0.3926	False		,,,				2504	0.5665				p.V189V		Atlas-SNP	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	ARNT,NS,carcinoma,0,1	ARNT	68	1	1	Substitution - coding silent(1)	stomach(1)	c.G567C						PASS	.	G	,,	2239,2167	583.2+/-385.8	564,1111,528	102.0	85.0	91.0		522,567,522	1.0	1.0	1	dbSNP_98	91	3164,5436	654.2+/-401.1	597,1970,1733	no	coding-synonymous,coding-synonymous,coding-synonymous	ARNT	NM_001197325.1,NM_001668.3,NM_178427.2	,,	1161,3081,2261	GG,GC,CC		36.7907,49.1829,41.5424	,,	174/774,189/790,174/775	150808889	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	405	exon7			GTCAGACACATAC	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.567G>C	1.37:g.150808889C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	143	51	0.356643	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Silent	SNP	ENST00000358595.5	37	CCDS970.1																																																																																			C|0.562;G|0.438	0.438	strong		0.463	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
ANK1	286	hgsc.bcm.edu	37	8	41559609	41559609	+	Silent	SNP	G	G	A	rs2304880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:41559609G>A	ENST00000347528.4	-	21	2432	c.2349C>T	c.(2347-2349)acC>acT	p.T783T	ANK1_ENST00000396945.1_Silent_p.T783T|ANK1_ENST00000352337.4_Silent_p.T783T|ANK1_ENST00000396942.1_Silent_p.T783T|ANK1_ENST00000265709.8_Silent_p.T816T|ANK1_ENST00000289734.7_Silent_p.T783T|ANK1_ENST00000379758.2_Silent_p.T783T	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	783	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGAGCACGTCGGTGACAGAAA	0.607											OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	905	0.180711	0.0159	0.2954	5008	,	,		18368	0.0794		0.2843	False		,,,				2504	0.32				p.T816T		Atlas-SNP	.											.	ANK1	497	.	0			c.C2448T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	122.0	110.0	114.0		2349,2448,2349,2349,2349	-3.0	0.7	8	dbSNP_100	114	2302,6298	387.0+/-342.0	319,1664,2317	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	326,1900,4277	AA,AG,GG		26.7674,5.6741,19.6217	,,,,	783/1881,816/1898,783/1857,783/1882,783/1720	41559609	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	286	exon21			CACGTCGGTGACA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2349C>T	8.37:g.41559609G>A		Somatic	58	0	0	902	WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	370	0.16941391941391942	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	222	0.2928759894459103	G	1.954	-0.440462	0.04636	0.056741	0.267674	ENSG00000029534	ENST00000520299	.	.	.	5.96	-2.95	0.05564	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.0165	0.06061	0.0902:0.1696:0.3084:0.4317	rs2304880;rs2304880	.	.	.	X	97	.	.	R	-	1	2	ANK1	41678766	0.006000	0.16342	0.704000	0.30370	0.001000	0.01503	-1.166000	0.03129	-0.110000	0.12022	-0.885000	0.02943	CGA	G|0.820;A|0.180	0.180	strong		0.607	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
FAT3	120114	hgsc.bcm.edu	37	11	92623877	92623877	+	Silent	SNP	G	G	A	rs12277422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:92623877G>A	ENST00000298047.6	+	27	13385	c.13368G>A	c.(13366-13368)ccG>ccA	p.P4456P	FAT3_ENST00000525166.1_Silent_p.P4306P|FAT3_ENST00000489716.1_3'UTR|FAT3_ENST00000409404.2_Silent_p.P4424P|FAT3_ENST00000533797.1_Silent_p.P759P			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	79	0	0		WXS	Illumina HiSeq	Phase_I	68	24	0.352941	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	
CDT1	81620	hgsc.bcm.edu	37	16	88870967	88870967	+	Silent	SNP	T	T	C	rs475667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88870967T>C	ENST00000301019.4	+	2	862	c.243T>C	c.(241-243)agT>agC	p.S81S		NM_030928.3	NP_112190.2			chromatin licensing and DNA replication factor 1											central_nervous_system(1)|endometrium(2)|kidney(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CCAGCCCCAGTACCCCCGAGG	0.642													T|||	656	0.13099	0.1846	0.1268	5008	,	,		12894	0.1419		0.0805	False		,,,				2504	0.1022				p.S81S	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.T243C						PASS	.	T		733,3663	290.1+/-280.8	52,629,1517	35.0	40.0	38.0		243	-5.8	0.0	16	dbSNP_83	38	679,7917	167.7+/-219.4	25,629,3644	no	coding-synonymous	CDT1	NM_030928.3		77,1258,5161	CC,CT,TT		7.899,16.6742,10.8682		81/547	88870967	1412,11580	2198	4298	6496	SO:0001819	synonymous_variant	81620	exon2			CCCCAGTACCCCC	AF070552	CCDS32510.1	16q24.3	2014-08-12			ENSG00000167513	ENSG00000167513			24576	protein-coding gene	gene with protein product		605525				11896191, 11555648	Standard	NM_030928		Approved	DUP, RIS2	uc002flu.3	Q9H211	OTTHUMG00000173467	ENST00000301019.4:c.243T>C	16.37:g.88870967T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_030928		Silent	SNP	ENST00000301019.4	37	CCDS32510.1																																																																																			T|0.874;C|0.126	0.126	strong		0.642	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928	
GPAM	57678	hgsc.bcm.edu	37	10	113920465	113920465	+	Silent	SNP	G	G	A	rs2277207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:113920465G>A	ENST00000348367.4	-	16	1853	c.1656C>T	c.(1654-1656)aaC>aaT	p.N552N	GPAM_ENST00000423155.1_Silent_p.N552N|GPAM_ENST00000369425.1_Silent_p.N552N			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	552					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		AAAACTCATCGTTCCTGCTAG	0.453													G|||	2772	0.553514	0.528	0.4553	5008	,	,		19398	0.6002		0.5437	False		,,,				2504	0.6196				p.N552N	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.C1656T						PASS	.	G		2218,2188	590.7+/-387.4	553,1112,538	153.0	126.0	135.0		1656	-12.1	0.0	10	dbSNP_100	135	5045,3555	630.2+/-398.3	1498,2049,753	no	coding-synonymous	GPAM	NM_020918.4		2051,3161,1291	AA,AG,GG		41.3372,49.6596,44.1565		552/829	113920465	7263,5743	2203	4300	6503	SO:0001819	synonymous_variant	57678	exon16			CTCATCGTTCCTG	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1656C>T	10.37:g.113920465G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	197	74	0.375635	NM_001244949	Q5VW51|Q86TA3	Silent	SNP	ENST00000348367.4	37	CCDS7570.1																																																																																			G|0.445;A|0.555	0.555	strong		0.453	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
PAXBP1	94104	hgsc.bcm.edu	37	21	34132288	34132288	+	Silent	SNP	G	G	A	rs149224793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34132288G>A	ENST00000331923.4	-	6	1182	c.993C>T	c.(991-993)ccC>ccT	p.P331P	PAXBP1_ENST00000290178.4_Silent_p.P331P|PAXBP1_ENST00000472588.1_5'UTR	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	331					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCACTTCTGCGGGTTGACTGG	0.373													G|||	3	0.000599042	0.0	0.0014	5008	,	,		18563	0.0		0.002	False		,,,				2504	0.0				p.P331P		Atlas-SNP	.											.	.	.	.	0			c.C993T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	100.0	103.0	102.0		993,993	0.4	0.2	21	dbSNP_134	102	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous,coding-synonymous	GCFC1	NM_013329.3,NM_016631.3	,	0,26,6477	AA,AG,GG		0.2907,0.0227,0.1999	,	331/816,331/918	34132288	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	94104	exon6			TTCTGCGGGTTGA	AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.993C>T	21.37:g.34132288G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_013329	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	
MUC20	200958	hgsc.bcm.edu	37	3	195453412	195453412	+	Silent	SNP	C	C	T	rs1063306	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195453412C>T	ENST00000447234.2	+	2	2064	c.1938C>T	c.(1936-1938)gcC>gcT	p.A646A	MUC20_ENST00000320736.6_Silent_p.A475A|MUC20_ENST00000445522.2_Silent_p.A611A|MUC20_ENST00000436408.1_Silent_p.A646A	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	80	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	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	
MYH7	4625	hgsc.bcm.edu	37	14	23892888	23892888	+	Silent	SNP	A	A	G	rs7157716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:23892888A>G	ENST00000355349.3	-	24	3129	c.2967T>C	c.(2965-2967)atT>atC	p.I989I		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	989					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|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)	p.I989I(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCAGCTTGGCAATGATCTCAT	0.542													G|||	1885	0.376398	0.7458	0.2334	5008	,	,		18292	0.1667		0.3111	False		,,,				2504	0.2618				p.I989I		Atlas-SNP	.											MYH7,NS,carcinoma,0,1	MYH7	349	1	1	Substitution - coding silent(1)	stomach(1)	c.T2967C						PASS	.	G		3086,1320	444.3+/-347.3	1092,902,209	156.0	149.0	152.0		2967	-6.3	0.6	14	dbSNP_116	152	2828,5772	675.9+/-403.2	475,1878,1947	no	coding-synonymous	MYH7	NM_000257.2		1567,2780,2156	GG,GA,AA		32.8837,29.9591,45.4713		989/1936	23892888	5914,7092	2203	4300	6503	SO:0001819	synonymous_variant	4625	exon24			CTTGGCAATGATC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2967T>C	14.37:g.23892888A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	195	94	0.482051	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																			A|0.583;G|0.416	0.416	strong		0.542	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
ACACB	32	hgsc.bcm.edu	37	12	109629457	109629457	+	Silent	SNP	C	C	T	rs7135947	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109629457C>T	ENST00000338432.7	+	14	2303	c.2184C>T	c.(2182-2184)ggC>ggT	p.G728G	ACACB_ENST00000377854.5_Silent_p.G728G|ACACB_ENST00000377848.3_Silent_p.G728G			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	728	Biotin carboxylation.				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)	CCATCCGAGGCGACTTTAGGA	0.493													C|||	1910	0.38139	0.2231	0.5677	5008	,	,		21807	0.2589		0.5666	False		,,,				2504	0.3988				p.G728G		Atlas-SNP	.											.	ACACB	330	.	0			c.C2184T						PASS	.	C		1173,3233	413.3+/-336.4	155,863,1185	174.0	157.0	163.0		2184	-10.7	0.0	12	dbSNP_116	163	4615,3985	600.8+/-394.3	1245,2125,930	no	coding-synonymous	ACACB	NM_001093.3		1400,2988,2115	TT,TC,CC		46.3372,26.6228,44.5025		728/2459	109629457	5788,7218	2203	4300	6503	SO:0001819	synonymous_variant	32	exon13			CCGAGGCGACTTT	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.2184C>T	12.37:g.109629457C>T		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	206	202	0.980583	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.587;T|0.413	0.413	strong		0.493	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
TJP3	27134	hgsc.bcm.edu	37	19	3740658	3740658	+	Silent	SNP	T	T	G	rs10416362	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3740658T>G	ENST00000541714.2	+	14	2202	c.1740T>G	c.(1738-1740)ctT>ctG	p.L580L	TJP3_ENST00000539908.2_Silent_p.L544L|TJP3_ENST00000589378.1_Silent_p.L589L|TJP3_ENST00000382008.3_Silent_p.L594L|TJP3_ENST00000262968.9_Silent_p.L613L|TJP3_ENST00000587686.1_Silent_p.L599L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	580	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCGGGGTCTTCGTCGAGGAG	0.692													T|||	2761	0.551318	0.5121	0.5865	5008	,	,		11836	0.5228		0.5099	False		,,,				2504	0.6513				p.L589L		Atlas-SNP	.											TJP3,NS,carcinoma,0,1	TJP3	79	1	0			c.T1767G						PASS	.	T		2313,2089		631,1051,519	15.0	18.0	17.0		1839	-9.7	0.0	19	dbSNP_119	17	4479,4113		1202,2075,1019	no	coding-synonymous	TJP3	NM_014428.1		1833,3126,1538	GG,GT,TT		47.8701,47.4557,47.7297		613/953	3740658	6792,6202	2201	4296	6497	SO:0001819	synonymous_variant	27134	exon14			GGGTCTTCGTCGA	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.1740T>G	19.37:g.3740658T>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			T|0.478;G|0.522	0.522	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33564123	33564123	+	Silent	SNP	T	T	C	rs2076623	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:33564123T>C	ENST00000321505.4	+	1	303	c.123T>C	c.(121-123)ggT>ggC	p.G41G	KIAA1549L_ENST00000265654.5_Silent_p.G41G|KIAA1549L_ENST00000389726.3_Silent_p.G41G			Q6ZVL6	K154L_HUMAN	KIAA1549-like	41						integral component of membrane (GO:0016021)											ATTCAGCAGGTTCATCCACAC	0.547													C|||	3490	0.696885	0.8918	0.6095	5008	,	,		18348	0.6617		0.6153	False		,,,				2504	0.6155				p.G41G		Atlas-SNP	.											.	.	.	.	0			c.T123C						PASS	.	C		3342,560		1431,480,40	96.0	97.0	97.0		123	1.9	0.0	11	dbSNP_96	97	5307,2989		1688,1931,529	no	coding-synonymous	C11orf41	NM_012194.2		3119,2411,569	CC,CT,TT		36.0294,14.3516,29.0949		41/1850	33564123	8649,3549	1951	4148	6099	SO:0001819	synonymous_variant	25758	exon1			AGCAGGTTCATCC	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.123T>C	11.37:g.33564123T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																			T|0.300;C|0.700	0.700	strong		0.547	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
ALPK3	57538	hgsc.bcm.edu	37	15	85401680	85401680	+	Silent	SNP	C	C	T	rs35931910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:85401680C>T	ENST00000258888.5	+	6	4484	c.4317C>T	c.(4315-4317)gaC>gaT	p.D1439D		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1439					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)			CGGCAGGAGACCTGGGCCCCA	0.682													C|||	287	0.0573083	0.0666	0.0807	5008	,	,		15929	0.0675		0.0606	False		,,,				2504	0.0143				p.D1439D		Atlas-SNP	.											.	ALPK3	289	.	0			c.C4317T						PASS	.	C		282,4050		13,256,1897	13.0	16.0	15.0		4317	3.2	0.0	15	dbSNP_126	15	534,7938		26,482,3728	no	coding-synonymous	ALPK3	NM_020778.4		39,738,5625	TT,TC,CC		6.3031,6.5097,6.373		1439/1908	85401680	816,11988	2166	4236	6402	SO:0001819	synonymous_variant	57538	exon6			AGGAGACCTGGGC	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.4317C>T	15.37:g.85401680C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			C|0.934;T|0.066	0.066	strong		0.682	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
MUC16	94025	hgsc.bcm.edu	37	19	9082514	9082514	+	Missense_Mutation	SNP	C	C	A	rs17000871	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9082514C>A	ENST00000397910.4	-	1	9504	c.9301G>T	c.(9301-9303)Gca>Tca	p.A3101S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3102	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						TCTTCTTCTGCAATGGTCTGG	0.483													c|||	863	0.172324	0.2496	0.1167	5008	,	,		17683	0.2292		0.0855	False		,,,				2504	0.138				p.A3101S		Atlas-SNP	.											.	MUC16	4315	.	0			c.G9301T						PASS	.	T	SER/ALA	843,3065		125,593,1236	267.0	276.0	273.0		9301	-1.1	0.0	19	dbSNP_123	273	635,7667		26,583,3542	yes	missense	MUC16	NM_024690.2	99	151,1176,4778	AA,AC,CC		7.6488,21.5711,12.1048	benign	3101/14508	9082514	1478,10732	1954	4151	6105	SO:0001583	missense	94025	exon1			CTTCTGCAATGGT	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.9301G>T	19.37:g.9082514C>A	ENSP00000381008:p.Ala3101Ser	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	252	124	0.492063	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	359	0.16437728937728938	106	0.21544715447154472	39	0.10773480662983426	146	0.25524475524475526	68	0.08970976253298153	t	0.394	-0.922017	0.02396	0.215711	0.076488	ENSG00000181143	ENST00000397910	T	0.02631	4.22	0.541	-1.08	0.09936	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.18166	0.026	B	0.15052	0.012	T	0.49762	-0.8905	7	0.87932	D	0	.	.	.	.	rs17000871;rs52804859;rs59318309;rs17000871	3101	B5ME49	.	S	3101	ENSP00000381008:A3101S	ENSP00000381008:A3101S	A	-	1	0	MUC16	8943514	0.019000	0.18553	0.001000	0.08648	0.005000	0.04900	-0.707000	0.05041	-2.646000	0.00426	-2.410000	0.00221	GCA	A|0.158;C|0.841;T|0.000	0.158	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs2672150		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:132021684C>A	ENST00000356920.5	+	15	2750	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	886	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCGGGAACTGCCTGACTACCT	0.592																																					p.P886T		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.C2656A						scavenged	.						46.0	47.0	47.0					2																	132021684		2203	4281	6484	SO:0001583	missense	445582	exon15			GAACTGCCTGACT	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.2656C>A	2.37:g.132021684C>A	ENSP00000439189:p.Pro886Thr	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	234	7	0.0299145	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	3.880	-0.026136	0.07589	.	.	ENSG00000188219	ENST00000356920	T	0.04360	3.64	.	.	.	.	.	.	.	.	T	0.00241	0.0007	N	0.00000	-5.39	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59606	-0.7423	8	0.02654	T	1	.	4.0636	0.09849	0.6406:0.3593:1.0E-4:0.0	.	886	Q6S8J3	POTEE_HUMAN	T	886	ENSP00000439189:P886T	ENSP00000439189:P886T	P	+	1	0	AC131180.1	131738154	1.000000	0.71417	0.081000	0.20488	0.082000	0.17680	4.531000	0.60602	-2.143000	0.00803	-2.210000	0.00300	CCT	.	.	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
ITGA11	22801	hgsc.bcm.edu	37	15	68643629	68643629	+	Silent	SNP	G	G	A	rs377301043		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:68643629G>A	ENST00000315757.7	-	8	947	c.861C>T	c.(859-861)agC>agT	p.S287S	ITGA11_ENST00000423218.2_Silent_p.S287S|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	287	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|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)	p.S287S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TGTCTCTTTCGCTTTGCTGGA	0.552																																					p.S287S		Atlas-SNP	.											ITGA11,NS,carcinoma,0,1	ITGA11	110	1	1	Substitution - coding silent(1)	endometrium(1)	c.C861T						scavenged	.	G		2,4138		0,2,2068	131.0	136.0	134.0		861	-0.5	1.0	15		134	0,8418		0,0,4209	no	coding-synonymous	ITGA11	NM_001004439.1		0,2,6277	AA,AG,GG		0.0,0.0483,0.0159		287/1189	68643629	2,12556	2070	4209	6279	SO:0001819	synonymous_variant	22801	exon8			TCTTTCGCTTTGC	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.861C>T	15.37:g.68643629G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	143	3	0.020979	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			.	.	weak		0.552	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
ZNF805	390980	hgsc.bcm.edu	37	19	57765432	57765432	+	Silent	SNP	A	A	G	rs8100154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:57765432A>G	ENST00000414468.2	+	4	1245	c.1245A>G	c.(1243-1245)aaA>aaG	p.K415K	ZNF805_ENST00000535550.1_Silent_p.K282K|ZNF805_ENST00000354309.4_Silent_p.K282K	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	415					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)|kidney(3)|lung(1)|stomach(1)	9						CCTACCTCAAAAGGCACCAGC	0.527													.|||	1838	0.367013	0.2466	0.4481	5008	,	,		19761	0.1776		0.5746	False		,,,				2504	0.454				p.K415K		Atlas-SNP	.											.	ZNF805	30	.	0			c.A1245G						PASS	.						34.0	35.0	35.0					19																	57765432		692	1591	2283	SO:0001819	synonymous_variant	390980	exon4			CCTCAAAAGGCAC	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.1245A>G	19.37:g.57765432A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_001023563	B4DNM5	Silent	SNP	ENST00000414468.2	37	CCDS46207.1																																																																																			A|0.594;G|0.406	0.406	strong		0.527	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
KRT33A	3883	hgsc.bcm.edu	37	17	39503163	39503163	+	Missense_Mutation	SNP	G	G	A	rs12937519	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39503163G>A	ENST00000007735.3	-	5	853	c.809C>T	c.(808-810)gCg>gTg	p.A270V		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	270	Coil 2.|Rod.		A -> V (in dbSNP:rs12937519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.			extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				GATGATCTCCGCCTGGTAGGA	0.592													g|||	1477	0.294928	0.3918	0.1902	5008	,	,		19991	0.37		0.2644	False		,,,				2504	0.1922				p.A270V		Atlas-SNP	.											KRT33A,colon,carcinoma,0,1	KRT33A	53	1	0			c.C809T						PASS	.	A	VAL/ALA	1640,2766	501.5+/-365.0	322,996,885	106.0	95.0	99.0		809	3.3	0.9	17	dbSNP_121	99	2338,6262	390.3+/-343.2	294,1750,2256	no	missense	KRT33A	NM_004138.2	64	616,2746,3141	AA,AG,GG		27.186,37.222,30.5859	benign	270/405	39503163	3978,9028	2203	4300	6503	SO:0001583	missense	3883	exon5			ATCTCCGCCTGGT	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6450	protein-coding gene	gene with protein product	"""hard keratin type I 3I"""	602761	"""keratin, hair, acidic, 3A"""	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.809C>T	17.37:g.39503163G>A	ENSP00000007735:p.Ala270Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	37	CCDS11388.1	668	0.3058608058608059	183	0.3719512195121951	74	0.20441988950276244	207	0.3618881118881119	204	0.2691292875989446	g	16.59	3.166855	0.57476	0.37222	0.27186	ENSG00000006059	ENST00000007735	D	0.88896	-2.44	4.27	3.3	0.37823	Filament (1);	0.198950	0.35970	N	0.002873	T	0.00012	0.0000	L	0.38175	1.15	0.38439	P	0.053339000000000025	B	0.24768	0.111	B	0.25405	0.06	T	0.06232	-1.0838	9	0.72032	D	0.01	.	11.7875	0.52051	0.0863:0.0:0.9137:0.0	rs12937519	270	O76009	KT33A_HUMAN	V	270	ENSP00000007735:A270V	ENSP00000007735:A270V	A	-	2	0	KRT33A	36756689	0.000000	0.05858	0.928000	0.36995	0.991000	0.79684	0.595000	0.24029	1.147000	0.42369	-0.213000	0.12676	GCG	G|0.333;A|0.667	0.667	weak		0.592	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138	
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:124525483C>T	ENST00000517956.1	-	6	797	c.606G>A	c.(604-606)acG>acA	p.T202T	FBXO32_ENST00000443022.2_Intron	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	202					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTGGAGAATCGTCTCCATCC	0.557													C|||	1019	0.203474	0.1808	0.1772	5008	,	,		17984	0.4673		0.0895	False		,,,				2504	0.0982				p.T202T		Atlas-SNP	.											.	FBXO32	39	.	0			c.G606A						PASS	.	C	,,	784,3622	317.4+/-295.1	66,652,1485	129.0	106.0	114.0		,606,171	-9.0	0.3	8	dbSNP_107	114	802,7798	186.7+/-234.1	43,716,3541	no	intron,coding-synonymous,coding-synonymous	FBXO32	NM_001242463.1,NM_058229.3,NM_148177.2	,,	109,1368,5026	TT,TC,CC		9.3256,17.7939,12.1944	,,	,202/356,57/211	124525483	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	114907	exon6			GAGAATCGTCTCC	AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"""F-boxes /  ""other"""""	16731	protein-coding gene	gene with protein product		606604	"""F-box only protein 32"""			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.606G>A	8.37:g.124525483C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_058229	A4KYM0	Silent	SNP	ENST00000517956.1	37	CCDS6345.1																																																																																			C|0.843;T|0.157	0.157	strong		0.557	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1		
MUC16	94025	hgsc.bcm.edu	37	19	9059307	9059307	+	Missense_Mutation	SNP	C	C	T	rs12461695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9059307C>T	ENST00000397910.4	-	3	28342	c.28139G>A	c.(28138-28140)gGt>gAt	p.G9380D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9382	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						GGTAAAGGTACCCTGCGAGGT	0.507													C|||	731	0.145966	0.0855	0.1787	5008	,	,		20436	0.2669		0.0865	False		,,,				2504	0.1411				p.G9380D		Atlas-SNP	.											MUC16_ENST00000397910,right_upper_lobe,carcinoma,-1,2	MUC16	4315	2	0			c.G28139A						PASS	.	C	ASP/GLY	381,3593		23,335,1629	140.0	139.0	140.0		28139	0.1	0.0	19	dbSNP_120	140	638,7666		25,588,3539	yes	missense	MUC16	NM_024690.2	94	48,923,5168	TT,TC,CC		7.683,9.5873,8.2994	possibly-damaging	9380/14508	9059307	1019,11259	1987	4152	6139	SO:0001583	missense	94025	exon3			AAGGTACCCTGCG	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.28139G>A	19.37:g.9059307C>T	ENSP00000381008:p.Gly9380Asp	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	333	0.15247252747252749	38	0.07723577235772358	56	0.15469613259668508	169	0.29545454545454547	70	0.09234828496042216	c	4.216	0.038924	0.08148	0.095873	0.07683	ENSG00000181143	ENST00000397910	T	0.24538	1.85	1.94	0.0918	0.14469	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	.	.	.	P	0.35456	0.502	B	0.38428	0.273	T	0.41610	-0.9499	8	0.87932	D	0	.	3.6378	0.08155	0.0:0.5627:0.0:0.4373	rs12461695	9380	B5ME49	.	D	9380	ENSP00000381008:G9380D	ENSP00000381008:G9380D	G	-	2	0	MUC16	8920307	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-2.733000	0.00803	0.046000	0.15833	0.306000	0.20318	GGT	C|0.861;T|0.139	0.139	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TST	7263	hgsc.bcm.edu	37	22	37407194	37407194	+	Silent	SNP	G	G	A	rs4764	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:37407194G>A	ENST00000403892.3	-	2	1502	c.768C>T	c.(766-768)caC>caT	p.H256H	TST_ENST00000249042.3_Silent_p.H256H|Y_RNA_ENST00000516603.1_RNA	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	256	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						CCAAGGCCACGTGGCAGGCGG	0.642													g|||	87	0.0173722	0.0023	0.0259	5008	,	,		17050	0.0		0.0636	False		,,,				2504	0.002				p.H256H		Atlas-SNP	.											.	TST	22	.	0			c.C768T						PASS	.	G		39,4367	40.0+/-72.8	0,39,2164	47.0	38.0	41.0		768	0.6	0.4	22	dbSNP_52	41	457,8141	132.0+/-189.7	14,429,3856	no	coding-synonymous	TST	NM_003312.4		14,468,6020	AA,AG,GG		5.3152,0.8852,3.8142		256/298	37407194	496,12508	2203	4299	6502	SO:0001819	synonymous_variant	7263	exon3			GGCCACGTGGCAG	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.768C>T	22.37:g.37407194G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	138	82	0.594203	NM_003312	B3KRM1|Q6IB06	Silent	SNP	ENST00000403892.3	37	CCDS13938.1																																																																																			G|0.966;A|0.034	0.034	strong		0.642	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1		
MAP2K3	5606	hgsc.bcm.edu	37	17	21203941	21203941	+	Missense_Mutation	SNP	G	G	A	rs2305873	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:21203941G>A	ENST00000342679.4	+	4	499	c.250G>A	c.(250-252)Gcc>Acc	p.A84T	MAP2K3_ENST00000316920.6_Missense_Mutation_p.A55T|MAP2K3_ENST00000361818.5_Missense_Mutation_p.A55T	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	84	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs2305873). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|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)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GGTGCGGCACGCCCAGAGCGG	0.627																																					p.A84T		Atlas-SNP	.											MAP2K3_ENST00000316920,NS,carcinoma,0,4	MAP2K3	135	4	0			c.G250A						PASS	.						50.0	46.0	47.0					17																	21203941		2203	4299	6502	SO:0001583	missense	5606	exon4			CGGCACGCCCAGA	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.250G>A	17.37:g.21203941G>A	ENSP00000345083:p.Ala84Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	575	0.2632783882783883	155	0.3150406504065041	86	0.23756906077348067	149	0.26048951048951047	185	0.24406332453825857	G	17.94	3.511568	0.64522	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;T	0.65732	-0.17;-0.17;-0.17	5.47	5.47	0.80525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.077419	0.50627	D	0.000110	T	0.00012	0.0000	N	0.04746	-0.17	0.45648	D	0.998578	P	0.45827	0.867	B	0.40702	0.338	T	0.24764	-1.0151	10	0.22109	T	0.4	-41.8517	19.3291	0.94278	0.0:0.0:1.0:0.0	rs2305873	84	P46734	MP2K3_HUMAN	T	84;55;55;55;88	ENSP00000345083:A84T;ENSP00000355081:A55T;ENSP00000434068:A55T	ENSP00000319139:A88T	A	+	1	0	MAP2K3	21144534	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	4.059000	0.57470	2.582000	0.87167	0.655000	0.94253	GCC	G|0.751;A|0.249	0.249	strong		0.627	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
NMT1	4836	hgsc.bcm.edu	37	17	43176804	43176804	+	Silent	SNP	C	C	T	rs2239923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	242	0	0	914	WXS	Illumina HiSeq	Phase_I	212	83	0.391509	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	
GPR111	222611	hgsc.bcm.edu	37	6	47649265	47649265	+	Missense_Mutation	SNP	T	T	A	rs17541107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:47649265T>A	ENST00000296862.1	+	6	970	c.970T>A	c.(970-972)Ttg>Atg	p.L324M	GPR111_ENST00000398742.2_Missense_Mutation_p.L256M|GPR111_ENST00000507065.1_Missense_Mutation_p.L256M			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	324					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						TGGGAGAGTGTTGATCAGCAG	0.418													T|||	1991	0.397564	0.236	0.5331	5008	,	,		22240	0.6915		0.3678	False		,,,				2504	0.2474				p.L256M		Atlas-SNP	.											.	GPR111	123	.	0			c.T766A						PASS	.	T	MET/LEU	1062,2724		134,794,965	154.0	144.0	147.0		766	-6.7	0.0	6	dbSNP_123	147	2868,5372		508,1852,1760	yes	missense	GPR111	NM_153839.6	15	642,2646,2725	AA,AT,TT		34.8058,28.0507,32.6792	possibly-damaging	256/643	47649265	3930,8096	1893	4120	6013	SO:0001583	missense	222611	exon7			AGAGTGTTGATCA	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.970T>A	6.37:g.47649265T>A	ENSP00000296862:p.Leu324Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		969	0.44368131868131866	110	0.22357723577235772	172	0.47513812154696133	401	0.701048951048951	286	0.37730870712401055	T	13.60	2.286730	0.40494	0.280507	0.348058	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.44881	0.91;0.91;0.91	5.37	-6.69	0.01772	.	0.636305	0.13081	N	0.415293	T	0.33411	0.0862	M	0.74881	2.28	0.80722	P	0.0	D;P	0.55800	0.973;0.954	P;P	0.56823	0.807;0.646	T	0.32188	-0.9916	9	0.38643	T	0.18	.	9.618	0.39704	0.0852:0.7102:0.0927:0.1119	rs17541107;rs52808586;rs61436836;rs17541107	256;324	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	M	256;324;256	ENSP00000422934:L256M;ENSP00000296862:L324M;ENSP00000381727:L256M	ENSP00000296862:L324M	L	+	1	2	GPR111	47757224	0.000000	0.05858	0.000000	0.03702	0.822000	0.46500	-1.302000	0.02746	-1.925000	0.01063	-0.472000	0.04984	TTG	T|0.577;A|0.423	0.423	strong		0.418	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
CMTM2	146225	hgsc.bcm.edu	37	16	66613725	66613725	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:66613725G>A	ENST00000268595.2	+	1	366	c.215G>A	c.(214-216)cGg>cAg	p.R72Q	RP11-403P17.2_ENST00000568430.1_RNA|CMTM2_ENST00000379486.2_Missense_Mutation_p.R72Q	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	72					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		CGCCGCTACCGGTGGGAATTA	0.562																																					p.R72Q		Atlas-SNP	.											.	CMTM2	33	.	0			c.G215A						PASS	.						48.0	52.0	51.0					16																	66613725		2201	4300	6501	SO:0001583	missense	146225	exon1			GCTACCGGTGGGA	BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"""chemokine-like factor super family 2"", ""chemokine-like factor superfamily 2"""	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.215G>A	16.37:g.66613725G>A	ENSP00000268595:p.Arg72Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_001199317	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781718	0.70222	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.49139	0.79;1.37	4.51	-7.19	0.01500	.	1.889910	0.02580	N	0.098726	T	0.26955	0.0660	L	0.36672	1.1	0.09310	N	1	P;B	0.38167	0.621;0.447	B;B	0.27608	0.081;0.045	T	0.21415	-1.0246	10	0.28530	T	0.3	1.8102	4.3444	0.11126	0.2588:0.0:0.2537:0.4874	.	72;72	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	Q	72	ENSP00000368800:R72Q;ENSP00000268595:R72Q	ENSP00000268595:R72Q	R	+	2	0	CMTM2	65171226	0.001000	0.12720	0.000000	0.03702	0.848000	0.48234	-1.284000	0.02793	-1.329000	0.02258	0.561000	0.74099	CGG	.	.	none		0.562	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1		
HIVEP3	59269	hgsc.bcm.edu	37	1	41976217	41976217	+	Missense_Mutation	SNP	G	G	A	rs72669005	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41976217G>A	ENST00000372583.1	-	9	8011	c.7126C>T	c.(7126-7128)Ccc>Tcc	p.P2376S	HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Missense_Mutation_p.P2375S|HIVEP3_ENST00000247584.5_Missense_Mutation_p.P2376S|HIVEP3_ENST00000429157.2_Missense_Mutation_p.P2375S	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2376				P -> S (in Ref. 1; AAK01082). {ECO:0000305}.	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)				CTGGTCCTGGGTTCCCCGGAG	0.687													G|||	496	0.0990415	0.2277	0.0648	5008	,	,		13605	0.004		0.0288	False		,,,				2504	0.1196				p.P2376S		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C7126T						PASS	.	G	SER/PRO,SER/PRO	790,3594		71,648,1473	23.0	23.0	23.0		7123,7126	4.3	1.0	1	dbSNP_130	23	426,8166		8,410,3878	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	74,74	79,1058,5351	AA,AG,GG		4.9581,18.0201,9.3711	probably-damaging,probably-damaging	2375/2406,2376/2407	41976217	1216,11760	2192	4296	6488	SO:0001583	missense	59269	exon9			TCCTGGGTTCCCC	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.7126C>T	1.37:g.41976217G>A	ENSP00000361664:p.Pro2376Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	146	0.06684981684981685	102	0.2073170731707317	22	0.06077348066298342	1	0.0017482517482517483	21	0.027704485488126648	G	16.05	3.013199	0.54468	0.180201	0.049581	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.06218	3.35;3.33;3.33;3.35	5.27	4.33	0.51752	.	0.000000	0.40908	D	0.000990	T	0.00012	0.0000	N	0.24115	0.695	0.31508	N	0.663996	P;P	0.46142	0.873;0.799	B;B	0.42282	0.382;0.212	T	0.32666	-0.9898	10	0.46703	T	0.11	-12.859	13.2296	0.59936	0.0:0.3043:0.6957:0.0	.	2375;2376	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	S	2375;2376;2376;2375	ENSP00000361665:P2375S;ENSP00000361664:P2376S;ENSP00000247584:P2376S;ENSP00000410828:P2375S	ENSP00000247584:P2376S	P	-	1	0	HIVEP3	41748804	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	2.132000	0.42083	1.398000	0.46701	0.561000	0.74099	CCC	G|0.910;A|0.090	0.090	strong		0.687	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1268064C>T	ENST00000529681.1	+	31	10012	c.9954C>T	c.(9952-9954)gcC>gcT	p.A3318A	MUC5B_ENST00000447027.1_Silent_p.A3321A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3318	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)		GCTTCACAGCCACCCCCTCCT	0.652													c|||	1636	0.326677	0.2156	0.3256	5008	,	,		19867	0.5387		0.2853	False		,,,				2504	0.3016				p.A3318A		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C9954T						PASS	.						15.0	28.0	24.0					11																	1268064		1776	4009	5785	SO:0001819	synonymous_variant	727897	exon31			CACAGCCACCCCC	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.9954C>T	11.37:g.1268064C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	181	64	0.353591	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	3.753	-0.051234	0.07407	.	.	ENSG00000117983	ENST00000538459	.	.	.	3.18	0.963	0.19649	.	.	.	.	.	T	0.15392	0.0371	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.38908	-0.9639	4	0.02654	T	1	.	6.2137	0.20644	0.3708:0.4477:0.1814:0.0	.	.	.	.	Y	201	.	ENSP00000442622:H201Y	H	+	1	0	MUC5B	1224640	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.998000	0.03701	-0.041000	0.13558	0.305000	0.20034	CAC	C|0.846;T|0.154	0.154	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
DCAKD	79877	hgsc.bcm.edu	37	17	43111688	43111688	+	Silent	SNP	G	G	A	rs9900173	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:43111688G>A	ENST00000452796.2	-	2	438	c.183C>T	c.(181-183)aaC>aaT	p.N61N	DCAKD_ENST00000588499.1_Silent_p.N61N|DCAKD_ENST00000342350.5_Silent_p.N61N|DCAKD_ENST00000310604.4_Silent_p.N61N|DCAKD_ENST00000588295.1_5'UTR			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	79	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	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	
CLIP4	79745	hgsc.bcm.edu	37	2	29383256	29383256	+	Missense_Mutation	SNP	G	G	T	rs3100246	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000404424.1_Missense_Mutation_p.R486L|CLIP4_ENST00000401605.1_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	81	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	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	
LECT2	3950	hgsc.bcm.edu	37	5	135287029	135287029	+	Missense_Mutation	SNP	T	T	C	rs31517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:135287029T>C	ENST00000274507.1	-	3	372	c.172A>G	c.(172-174)Atc>Gtc	p.I58V	LECT2_ENST00000471827.1_5'UTR|LECT2_ENST00000514447.2_Missense_Mutation_p.I58V|LECT2_ENST00000522943.1_Missense_Mutation_p.I58V|FBXL21_ENST00000467490.1_RNA|LECT2_ENST00000512872.1_5'UTR	NM_002302.2	NP_002293.2	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2	58			I -> V (in dbSNP:rs31517). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15372022, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9524238, ECO:0000269|PubMed:9545637, ECO:0000269|PubMed:9832057}.		chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.I58V(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GAGCACAAGATGTCCACACCC	0.468													t|||	3187	0.636382	0.5484	0.696	5008	,	,		20018	0.6478		0.6412	False		,,,				2504	0.6963				p.I58V		Atlas-SNP	.											LECT2,NS,carcinoma,0,2	LECT2	24	2	1	Substitution - Missense(1)	prostate(1)	c.A172G						PASS	.	C	VAL/ILE	2550,1856	634.2+/-396.2	733,1084,386	124.0	109.0	114.0		172	3.3	0.5	5	dbSNP_76	114	5472,3128	656.8+/-401.4	1758,1956,586	yes	missense	LECT2	NM_002302.2	29	2491,3040,972	CC,CT,TT		36.3721,42.1244,38.3208	benign	58/152	135287029	8022,4984	2203	4300	6503	SO:0001583	missense	3950	exon3			ACAAGATGTCCAC	AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000274507.1:c.172A>G	5.37:g.135287029T>C	ENSP00000274507:p.Ile58Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_002302	B2RA90|O14565|Q52M49	Missense_Mutation	SNP	ENST00000274507.1	37	CCDS4190.1	1369	0.6268315018315018	276	0.5609756097560976	242	0.6685082872928176	362	0.6328671328671329	489	0.6451187335092349	t	6.245	0.413265	0.11812	0.578756	0.636279	ENSG00000145826	ENST00000522943;ENST00000274507;ENST00000514447	T;T;T	0.53640	0.61;0.61;0.61	6.07	3.33	0.38152	Peptidase M23 (1);	0.294138	0.38548	N	0.001660	T	0.00012	0.0000	N	0.02225	-0.63	0.50632	P	1.1200000000000099E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.48352	-0.9043	9	0.02654	T	1	-7.2743	12.6058	0.56523	0.0:0.7792:0.0:0.2208	rs31517;rs52790489;rs59733851;rs31517	58	O14960	LECT2_HUMAN	V	58	ENSP00000429618:I58V;ENSP00000274507:I58V;ENSP00000421123:I58V	ENSP00000274507:I58V	I	-	1	0	LECT2	135314928	0.257000	0.24022	0.459000	0.27081	0.177000	0.22998	0.461000	0.21940	-0.028000	0.13850	-1.820000	0.00599	ATC	T|0.380;C|0.620	0.620	strong		0.468	LECT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251209.1	NM_002302	
GZMB	3002	hgsc.bcm.edu	37	14	25101629	25101629	+	Silent	SNP	T	T	C	rs10909625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:25101629T>C	ENST00000216341.4	-	3	346	c.240A>G	c.(238-240)aaA>aaG	p.K80K	RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000526004.1_Intron|GZMB_ENST00000415355.3_Silent_p.K68K|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Silent_p.K114K			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	80	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.K80K(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GCTCCTGTTCTTTGATATTGT	0.517													C|||	1515	0.302516	0.379	0.2118	5008	,	,		16974	0.2867		0.2475	False		,,,				2504	0.3364				p.K80K		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - coding silent(1)	stomach(1)	c.A240G						PASS	.						93.0	106.0	102.0					14																	25101629		2203	4300	6503	SO:0001819	synonymous_variant	3002	exon3			CTGTTCTTTGATA	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.240A>G	14.37:g.25101629T>C		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_004131	Q8N1D2|Q9UCC1	Silent	SNP	ENST00000216341.4	37	CCDS9633.1																																																																																			T|0.742;C|0.258	0.258	strong		0.517	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
TAS2R42	353164	hgsc.bcm.edu	37	12	11338957	11338957	+	Missense_Mutation	SNP	A	A	G	rs5020531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:11338957A>G	ENST00000334266.1	-	1	586	c.587T>C	c.(586-588)tTc>tCc	p.F196S		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	196			F -> S (in dbSNP:rs5020531). {ECO:0000269|PubMed:16541075}.		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)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			GGAGGTCAGGAACAGAGAAAA	0.373													G|||	2708	0.540735	0.1596	0.6167	5008	,	,		16958	0.7569		0.6521	False		,,,				2504	0.6646				p.F196S	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.T587C						PASS	.	G	SER/PHE	962,3430		116,730,1350	46.0	50.0	49.0		587	1.6	0.0	12	dbSNP_113	49	5138,3456		1564,2010,723	yes	missense	TAS2R42	NM_181429.1	155	1680,2740,2073	GG,GA,AA		40.2141,21.9035,46.9737	benign	196/315	11338957	6100,6886	2196	4297	6493	SO:0001583	missense	353164	exon1			GTCAGGAACAGAG	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.587T>C	12.37:g.11338957A>G	ENSP00000334050:p.Phe196Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	1242	0.5686813186813187	91	0.18495934959349594	232	0.6408839779005525	426	0.7447552447552448	493	0.6503957783641161	G	0.006	-2.057232	0.00390	0.219035	0.597859	ENSG00000186136	ENST00000334266	T	0.36878	1.23	3.46	1.59	0.23543	GPCR, rhodopsin-like superfamily (1);	0.446550	0.21287	N	0.077046	T	0.00012	0.0000	N	0.00268	-1.735	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40270	-0.9572	9	0.02654	T	1	.	7.4037	0.26979	0.1092:0.177:0.7138:0.0	rs5020531	196	Q7RTR8	T2R42_HUMAN	S	196	ENSP00000334050:F196S	ENSP00000334050:F196S	F	-	2	0	TAS2R42	11230224	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.141000	0.10327	0.019000	0.15079	-2.610000	0.00160	TTC	A|0.479;G|0.521	0.521	strong		0.373	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
PTPRQ	374462	hgsc.bcm.edu	37	12	80935345	80935345	+	Missense_Mutation	SNP	T	T	C	rs6539524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	57	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	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	
MUSK	4593	hgsc.bcm.edu	37	9	113538122	113538122	+	Missense_Mutation	SNP	G	G	A	rs2274419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:113538122G>A	ENST00000374448.4	+	10	1373	c.1239G>A	c.(1237-1239)atG>atA	p.M413I	MUSK_ENST00000374438.1_Missense_Mutation_p.G5R|MUSK_ENST00000189978.5_Missense_Mutation_p.M413I|MUSK_ENST00000416899.2_Missense_Mutation_p.M413I	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	413	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		M -> I (in dbSNP:rs2274419). {ECO:0000269|PubMed:17344846}.		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						GGCTGGTAATGGAAGAGAAGA	0.468													G|||	503	0.100439	0.0045	0.0389	5008	,	,		17692	0.1895		0.1252	False		,,,				2504	0.1564				p.M413I		Atlas-SNP	.											.	MUSK	112	.	0			c.G1239A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET	83,3709		0,83,1813	84.0	85.0	85.0		1005,975,1239	1.1	0.9	9	dbSNP_100	85	1094,7152		73,948,3102	yes	missense,missense,missense	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	10,10,10	73,1031,4915	AA,AG,GG		13.267,2.1888,9.7774	benign,benign,benign	335/784,325/774,413/870	113538122	1177,10861	1896	4123	6019	SO:0001583	missense	4593	exon9			GGTAATGGAAGAG	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.1239G>A	9.37:g.113538122G>A	ENSP00000363571:p.Met413Ile	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	224|224	0.10256410256410256|0.10256410256410256	3|3	0.006097560975609756|0.006097560975609756	14|14	0.03867403314917127|0.03867403314917127	119|119	0.20804195804195805|0.20804195804195805	88|88	0.11609498680738786|0.11609498680738786	G|G	5.688|5.688	0.311434|0.311434	0.10789|0.10789	0.021888|0.021888	0.13267|0.13267	ENSG00000030304|ENSG00000030304	ENST00000374441;ENST00000374438|ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	D|T	0.84442|0.71817	-1.85|-0.6	5.43|5.43	1.08|1.08	0.20341|0.20341	.|Frizzled domain (2);	.|0.533746	.|0.23008	.|N	.|0.052987	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.04229|0.04229	-1.0967|-1.0967	6|9	0.87932|0.10377	D|T	0|0.69	.|.	7.3856|7.3856	0.26880|0.26880	0.2043:0.139:0.6568:0.0|0.2043:0.139:0.6568:0.0	rs2274419;rs52816297;rs56547888;rs59906813;rs2274419|rs2274419;rs52816297;rs56547888;rs59906813;rs2274419	.|413	.|O15146	.|MUSK_HUMAN	R|I	5|419;413;413;335;335;419	ENSP00000363561:G5R|ENSP00000363571:M413I	ENSP00000363561:G5R|ENSP00000189978:M419I	G|M	+|+	1|3	0|0	MUSK|MUSK	112577943|112577943	1.000000|1.000000	0.71417|0.71417	0.924000|0.924000	0.36721|0.36721	0.605000|0.605000	0.37080|0.37080	0.809000|0.809000	0.27168|0.27168	0.259000|0.259000	0.21709|0.21709	0.655000|0.655000	0.94253|0.94253	GGA|ATG	G|0.885;A|0.115	0.115	strong		0.468	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027234	103027234	+	Missense_Mutation	SNP	A	A	G	rs17301750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:103027234A>G	ENST00000375735.2	+	26	4006	c.3862A>G	c.(3862-3864)Act>Gct	p.T1288A	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.T1288A|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	1288	Stem. {ECO:0000250}.		T -> A (in dbSNP:rs17301750).		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)		CCAAAGTCGAACTATGAAGCT	0.358													A|||	382	0.076278	0.0023	0.0922	5008	,	,		15673	0.0923		0.1233	False		,,,				2504	0.1002				p.T1288A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A3862G						PASS	.	A	ALA/THR,ALA/THR	97,3585		2,93,1746	96.0	95.0	95.0		3862,3862	4.1	1.0	11	dbSNP_123	95	944,7242		58,828,3207	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	58,58	60,921,4953	GG,GA,AA		11.5319,2.6344,8.7715	benign,benign	1288/4315,1288/4308	103027234	1041,10827	1841	4093	5934	SO:0001583	missense	79659	exon26			AGTCGAACTATGA	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.3862A>G	11.37:g.103027234A>G	ENSP00000364887:p.Thr1288Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	190	0.08699633699633699	3	0.006097560975609756	33	0.09116022099447514	50	0.08741258741258741	104	0.13720316622691292	A	6.130	0.392124	0.11581	0.026344	0.115319	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.60424	0.19;0.19	5.27	4.1	0.47936	Dynein heavy chain, domain-2 (1);	0.981166	0.08306	N	0.966220	T	0.00524	0.0017	L	0.54323	1.7	0.38246	P	0.05853600000000003	B;B	0.11235	0.004;0.004	B;B	0.16722	0.016;0.014	T	0.18681	-1.0329	9	0.08599	T	0.76	.	11.2807	0.49192	0.8632:0.0:0.0:0.1368	rs17301750;rs52791460;rs17301750	1288;1288	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	1288	ENSP00000364887:T1288A;ENSP00000381167:T1288A	ENSP00000364887:T1288A	T	+	1	0	DYNC2H1	102532444	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	4.416000	0.59815	0.796000	0.33947	0.460000	0.39030	ACT	A|0.912;G|0.088	0.088	strong		0.358	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
SYMPK	8189	hgsc.bcm.edu	37	19	46327053	46327053	+	Silent	SNP	C	C	T	rs7251942	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:46327053C>T	ENST00000245934.7	-	19	2815	c.2571G>A	c.(2569-2571)acG>acA	p.T857T	SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	857					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GCAGACATCTCGTGACCAGTG	0.587													C|||	862	0.172125	0.1929	0.072	5008	,	,		16962	0.3512		0.0825	False		,,,				2504	0.1227				p.T857T		Atlas-SNP	.											.	SYMPK	104	.	0			c.G2571A						PASS	.	C		776,3630	315.8+/-294.3	71,634,1498	93.0	81.0	85.0		2571	-7.9	0.0	19	dbSNP_116	85	685,7915	171.3+/-222.3	30,625,3645	no	coding-synonymous	SYMPK	NM_004819.2		101,1259,5143	TT,TC,CC		7.9651,17.6123,11.2333		857/1275	46327053	1461,11545	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon19			ACATCTCGTGACC	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.2571G>A	19.37:g.46327053C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			C|0.852;T|0.148	0.148	strong		0.587	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
DISC1	27185	hgsc.bcm.edu	37	1	231954101	231954101	+	Missense_Mutation	SNP	C	C	T	rs6675281	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:231954101C>T	ENST00000602281.1	+	9	1872	c.1819C>T	c.(1819-1821)Ctc>Ttc	p.L607F	DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000539444.1_Silent_p.T572T|DISC1_ENST00000366633.3_Missense_Mutation_p.L607F|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.L607F|DISC1_ENST00000602873.1_3'UTR|DISC1_ENST00000439617.2_Missense_Mutation_p.L607F|DISC1_ENST00000366636.4_Missense_Mutation_p.L607F	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	607	Interaction with ATF4 and ATF5.|Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.		L -> F (associated with susceptibility to schizoaffective disorder; dbSNP:rs6675281). {ECO:0000269|PubMed:15386212}.		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)				GGCTAAAGACCTCACCGAGGA	0.483													C|||	480	0.0958466	0.1884	0.0821	5008	,	,		20772	0.003		0.1243	False		,,,				2504	0.047				p.L639F		Atlas-SNP	.											.	DISC1	207	.	0			c.C1915T	GRCh37	CM042974	DISC1	M	rs6675281	PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,,,,,,PHE/LEU	781,3625	314.7+/-293.7	53,675,1475	107.0	108.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1819,1819,1915,1819,1819,1453,1819,1819,1819,1716,,,,,1819	4.3	1.0	1	dbSNP_116	107	1218,7382	246.0+/-274.6	86,1046,3168	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,coding-synonymous,intron,intron,utr-3,utr-3,missense	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	22,22,22,22,22,22,22,22,22,,,,,,22	139,1721,4643	TT,TC,CC		14.1628,17.7258,15.3698	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,,,,probably-damaging	607/833,607/679,639/887,607/804,607/756,485/733,607/696,607/682,607/663,572/580,,,,,607/855	231954101	1999,11007	2203	4300	6503	SO:0001583	missense	27185	exon10			AAAGACCTCACCG	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.1819C>T	1.37:g.231954101C>T	ENSP00000473425:p.Leu607Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001164537	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	204	0.09340659340659341	84	0.17073170731707318	29	0.08011049723756906	0	0.0	91	0.12005277044854881	C	20.8	4.051022	0.75960	0.177258	0.141628	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000366633	T;T;T;T	0.24151	2.01;1.88;1.87;2.03	5.23	4.32	0.51571	.	0.178636	0.36591	N	0.002514	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.994;1.0;0.994;1.0;0.986;0.994;1.0;1.0;1.0;0.994;1.0;0.986;1.0	D;P;D;P;D;P;P;D;D;D;P;D;P;D	0.91635	0.999;0.799;0.999;0.683;0.999;0.799;0.683;0.999;0.999;0.999;0.683;0.999;0.683;0.999	T	0.04915	-1.0918	8	0.87932	D	0	-8.5446	11.9831	0.53131	0.0:0.9205:0.0:0.0795	rs6675281;rs52801396;rs59116826;rs6675281	639;485;639;607;607;485;607;607;607;607;607;607;607;607	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;F5H1F1;C4P0A4;A6NLH2;C4P0B6;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	F	607;607;607;639;485;607;607	ENSP00000403888:L607F;ENSP00000355596:L607F;ENSP00000443996:L607F;ENSP00000355593:L607F	ENSP00000355593:L607F	L	+	1	0	DISC1	230020724	1.000000	0.71417	0.977000	0.42913	0.978000	0.69477	3.306000	0.51881	1.425000	0.47237	0.591000	0.81541	CTC	C|0.877;T|0.123	0.123	strong		0.483	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137852	32137852	+	Silent	SNP	C	C	G	rs3759297	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	72	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	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	
SUPT5H	6829	hgsc.bcm.edu	37	19	39944082	39944082	+	Silent	SNP	C	C	T	rs1130180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39944082C>T	ENST00000599117.1	+	4	529	c.162C>T	c.(160-162)taC>taT	p.Y54Y	SUPT5H_ENST00000359191.6_Silent_p.Y54Y|SUPT5H_ENST00000598725.1_Silent_p.Y54Y|SUPT5H_ENST00000432763.2_Silent_p.Y54Y|SUPT5H_ENST00000402194.2_Silent_p.Y54Y			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	54	Glu-rich.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			aggaggaatacgatgaggaag	0.567													C|||	3120	0.623003	0.7655	0.5159	5008	,	,		15177	0.5675		0.5606	False		,,,				2504	0.6278				p.Y54Y		Atlas-SNP	.											.	SUPT5H	119	.	0			c.C162T						PASS	.	C	,,,	3219,1183		1174,871,156	56.0	50.0	52.0		162,162,162,162	-4.9	0.9	19	dbSNP_86	52	4462,4132		1194,2074,1029	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SUPT5H	NM_001111020.2,NM_001130824.1,NM_001130825.1,NM_003169.3	,,,	2368,2945,1185	TT,TC,CC		48.0801,26.8741,40.8972	,,,	54/1088,54/1088,54/1084,54/1088	39944082	7681,5315	2201	4297	6498	SO:0001819	synonymous_variant	6829	exon3			GGAATACGATGAG	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.162C>T	19.37:g.39944082C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_001130825	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																			C|0.402;T|0.598	0.598	strong		0.567	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
STKLD1	169436	hgsc.bcm.edu	37	9	136268084	136268084	+	Missense_Mutation	SNP	A	A	G	rs3124747	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	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		
TTLL13P	440307	hgsc.bcm.edu	37	15	90800449	90800449	+	Missense_Mutation	SNP	C	C	T	rs2063743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:90800449C>T	ENST00000561573.1	+	5	761	c.497C>T	c.(496-498)aCa>aTa	p.T166I	TTLL13_ENST00000438251.1_Missense_Mutation_p.T262I|TTLL13_ENST00000339615.5_Missense_Mutation_p.T262I																							CGGATCTTCACATATGAGGAG	0.537													T|||	1889	0.377196	0.1074	0.4193	5008	,	,		18043	0.6925		0.2644	False		,,,				2504	0.5031				p.T262I		Atlas-SNP	.											.	TTLL13	44	.	0			c.C785T						PASS	.	T	ILE/THR	647,3751	765.2+/-413.3	51,545,1603	103.0	92.0	96.0		785	5.9	1.0	15	dbSNP_94	96	2239,6357	709.6+/-405.7	275,1689,2334	yes	missense	TTLL13	NM_001029964.2	89	326,2234,3937	TT,TC,CC		26.047,14.7112,22.2103	benign	262/460	90800449	2886,10108	2199	4298	6497	SO:0001583	missense	440307	exon7			TCTTCACATATGA																												ENST00000561573.1:c.497C>T	15.37:g.90800449C>T	ENSP00000456615:p.Thr166Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001029964		Missense_Mutation	SNP	ENST00000561573.1	37		759	0.3475274725274725	60	0.12195121951219512	132	0.36464088397790057	369	0.6451048951048951	198	0.2612137203166227	T	14.49	2.550254	0.45383	0.147112	0.26047	ENSG00000213471	ENST00000438251;ENST00000339615	T;T	0.04706	3.57;3.57	5.89	5.89	0.94794	.	0.204155	0.43747	N	0.000532	T	0.00012	0.0000	N	0.00296	-1.695	0.48395	P	3.549999999999942E-4	B	0.06786	0.001	B	0.13407	0.009	T	0.19614	-1.0300	9	0.56958	D	0.05	.	11.4177	0.49962	0.0:0.0702:0.0:0.9298	rs2063743;rs17689407;rs2063743	262	A6NNM8-2	.	I	262	ENSP00000413362:T262I;ENSP00000345294:T262I	ENSP00000345294:T262I	T	+	2	0	TTLL13	88601453	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	5.862000	0.69560	1.059000	0.40554	-0.269000	0.10298	ACA	C|0.720;T|0.280	0.280	strong		0.537	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1		
TAF1A	9015	hgsc.bcm.edu	37	1	222732051	222732051	+	Missense_Mutation	SNP	C	C	T	rs143557200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222732051C>T	ENST00000352967.4	-	11	1492	c.1304G>A	c.(1303-1305)cGg>cAg	p.R435Q	TAF1A_ENST00000391882.1_Missense_Mutation_p.R321Q|TAF1A_ENST00000350027.4_Missense_Mutation_p.R435Q|TAF1A_ENST00000366890.1_Missense_Mutation_p.R321Q	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	435					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)		TCTCTTCATCCGCTTAATTTT	0.303													C|||	20	0.00399361	0.0	0.0144	5008	,	,		12618	0.0		0.007	False		,,,				2504	0.0031				p.R435Q		Atlas-SNP	.											TAF1A,NS,carcinoma,0,1	TAF1A	35	1	0			c.G1304A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4400	4.2+/-10.8	0,2,2199	82.0	84.0	83.0		1304,1304,962	-3.5	0.8	1	dbSNP_134	83	72,8498	40.8+/-97.7	1,70,4214	yes	missense,missense,missense	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	43,43,43	1,72,6413	TT,TC,CC		0.8401,0.0454,0.5705	benign,benign,benign	435/451,435/451,321/337	222732051	74,12898	2201	4285	6486	SO:0001583	missense	9015	exon11			TTCATCCGCTTAA	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.1304G>A	1.37:g.222732051C>T	ENSP00000327072:p.Arg435Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Missense_Mutation	SNP	ENST00000352967.4	37	CCDS1531.1	10	0.004578754578754579	0	0.0	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	10.77	1.444536	0.25987	4.54E-4	0.008401	ENSG00000143498	ENST00000366890;ENST00000350027;ENST00000352967;ENST00000391882	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.34	-3.51	0.04696	.	0.878450	0.10066	N	0.720352	T	0.16214	0.0390	N	0.21583	0.68	0.38468	D	0.947394	B	0.15141	0.012	B	0.10450	0.005	T	0.21965	-1.0230	10	0.18276	T	0.48	-18.2737	7.0687	0.25167	0.0:0.2261:0.1415:0.6324	.	435	Q15573	TAF1A_HUMAN	Q	321;435;435;321	ENSP00000355856:R321Q;ENSP00000339976:R435Q;ENSP00000327072:R435Q;ENSP00000375754:R321Q	ENSP00000339976:R435Q	R	-	2	0	TAF1A	220798674	0.035000	0.19736	0.844000	0.33320	0.826000	0.46750	-1.046000	0.03525	-0.257000	0.09459	-0.345000	0.07892	CGG	C|0.994;T|0.006	0.006	strong		0.303	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
LIG1	3978	hgsc.bcm.edu	37	19	48664687	48664687	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48664687C>T	ENST00000263274.7	-	4	604	c.185G>A	c.(184-186)cGg>cAg	p.R62Q	LIG1_ENST00000427526.2_Missense_Mutation_p.R32Q|LIG1_ENST00000599165.1_Intron|LIG1_ENST00000536218.1_Missense_Mutation_p.R62Q	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	62			R -> W (in dbSNP:rs3730863). {ECO:0000269|Ref.2}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|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)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	GCCCAGGACCCGGGCCGCCTT	0.602								Nucleotide excision repair (NER)																													p.R62Q		Atlas-SNP	.											.	LIG1	151	.	0			c.G185A						PASS	.						124.0	120.0	121.0					19																	48664687		2203	4300	6503	SO:0001583	missense	3978	exon4			AGGACCCGGGCCG		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.185G>A	19.37:g.48664687C>T	ENSP00000263274:p.Arg62Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063708	0.36373	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218;ENST00000542460	T;T;T;T	0.58652	0.45;0.32;0.46;1.98	4.62	-1.03	0.10102	.	0.681137	0.14004	N	0.347948	T	0.39545	0.1082	L	0.39397	1.21	0.20975	N	0.999815	B;B;B	0.18013	0.008;0.025;0.008	B;B;B	0.09377	0.001;0.004;0.001	T	0.25710	-1.0124	10	0.12766	T	0.61	-5.9785	7.7073	0.28657	0.0:0.5183:0.0:0.4817	.	32;62;62	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	Q	62;94;32;62;62	ENSP00000263274:R62Q;ENSP00000442841:R32Q;ENSP00000441531:R62Q;ENSP00000445928:R62Q	ENSP00000263274:R62Q	R	-	2	0	LIG1	53356499	0.489000	0.26004	0.781000	0.31783	0.827000	0.46813	-0.049000	0.11924	-0.188000	0.10499	-0.369000	0.07265	CGG	.	.	none		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
SEC31B	25956	hgsc.bcm.edu	37	10	102269206	102269206	+	Missense_Mutation	SNP	A	A	G	rs3763695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:102269206A>G	ENST00000370345.3	-	4	363	c.266T>C	c.(265-267)gTt>gCt	p.V89A	SEC31B_ENST00000370329.5_Missense_Mutation_p.V89A|NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000557395.1_Intron|SEC31B_ENST00000451524.1_Missense_Mutation_p.V89A|SEC31B_ENST00000535773.1_Intron	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	89			V -> A (in dbSNP:rs3763695). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCCGCCGCCAACAATAACCCC	0.522											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	928	0.185304	0.1997	0.1844	5008	,	,		16965	0.1319		0.1909	False		,,,				2504	0.2157				p.V89A		Atlas-SNP	.											.	SEC31B	84	.	0			c.T266C						PASS	.	G	ALA/VAL	856,3550	742.3+/-411.4	86,684,1433	47.0	51.0	50.0		266	5.4	1.0	10	dbSNP_107	50	1889,6711	727.5+/-406.6	216,1457,2627	yes	missense	SEC31B	NM_015490.3	64	302,2141,4060	GG,GA,AA		21.9651,19.4281,21.1056	benign	89/1180	102269206	2745,10261	2203	4300	6503	SO:0001583	missense	25956	exon4			CCGCCAACAATAA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.266T>C	10.37:g.102269206A>G	ENSP00000359370:p.Val89Ala	Somatic	59	0	0	1365	WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	395	0.18086080586080586	71	0.1443089430894309	71	0.19613259668508287	94	0.16433566433566432	159	0.20976253298153033	G	9.995	1.231922	0.22626	0.194281	0.219651	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.24908	1.83;1.83;1.83	5.36	5.36	0.76844	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.216027	0.45126	N	0.000397	T	0.00012	0.0000	N	0.00507	-1.42	0.09310	P	1.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.29882	-0.9997	9	0.07325	T	0.83	-5.3373	7.5007	0.27516	0.2557:0.0:0.7443:0.0	rs3763695;rs59707262;rs3763695	89;89;89;89	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	A	89	ENSP00000359370:V89A;ENSP00000391178:V89A;ENSP00000359354:V89A	ENSP00000359354:V89A	V	-	2	0	SEC31B	102259196	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.183000	0.65065	1.419000	0.47118	-0.213000	0.12676	GTT	A|0.809;G|0.191	0.191	strong		0.522	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PLXNA1	5361	hgsc.bcm.edu	37	3	126708453	126708453	+	Silent	SNP	T	T	C	rs6773789	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:126708453T>C	ENST00000393409.2	+	1	1017	c.1017T>C	c.(1015-1017)acT>acC	p.T339T	PLXNA1_ENST00000251772.4_Silent_p.T316T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	339	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TGCTGTTCACTGTGTTCGCCC	0.637													C|||	2368	0.472843	0.7088	0.353	5008	,	,		19836	0.4236		0.339	False		,,,				2504	0.4274				p.T339T		Atlas-SNP	.											PLXNA1,NS,carcinoma,0,1	PLXNA1	185	1	0			c.T1017C						scavenged	.	C		2860,1546	484.2+/-360.0	904,1052,247	71.0	72.0	72.0		1017	-3.8	0.8	3	dbSNP_116	72	2722,5878	679.7+/-403.6	438,1846,2016	no	coding-synonymous	PLXNA1	NM_032242.3		1342,2898,2263	CC,CT,TT		31.6512,35.0885,42.9187		339/1897	126708453	5582,7424	2203	4300	6503	SO:0001819	synonymous_variant	5361	exon1			GTTCACTGTGTTC	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1017T>C	3.37:g.126708453T>C		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	124	73	0.58871	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			T|0.567;C|0.433	0.433	strong		0.637	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
PRDM8	56978	hgsc.bcm.edu	37	4	81123378	81123378	+	Silent	SNP	C	C	T	rs142234659	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:81123378C>T	ENST00000504452.1	+	8	1601	c.762C>T	c.(760-762)agC>agT	p.S254S	PRDM8_ENST00000415738.2_Silent_p.S254S|PRDM8_ENST00000339711.4_Silent_p.S254S			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	254	Gly-rich.|Ser-rich.				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)	p.S254S(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GCGGCAGCAGCGCGAAGCCAT	0.677											OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	145	0.0289537	0.003	0.0533	5008	,	,		10280	0.0		0.0984	False		,,,				2504	0.0051				p.S254S		Atlas-SNP	.											PRDM8,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PRDM8	44	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C762T						scavenged	.	C	,	43,3207		0,43,1582	18.0	26.0	23.0		762,762	3.7	0.4	4	dbSNP_134	23	513,6883		11,491,3196	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	11,534,4778	TT,TC,CC		6.9362,1.3231,5.2226	,	254/690,254/690	81123378	556,10090	1625	3698	5323	SO:0001819	synonymous_variant	56978	exon4			CAGCAGCGCGAAG	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.762C>T	4.37:g.81123378C>T		Somatic	74	1	0.0135135	1203	WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			C|0.950;T|0.050	0.050	strong		0.677	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
RASSF8	11228	hgsc.bcm.edu	37	12	26220591	26220591	+	Silent	SNP	C	C	T	rs34873759	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:26220591C>T	ENST00000405154.2	+	4	1282	c.1083C>T	c.(1081-1083)acC>acT	p.T361T	RASSF8_ENST00000542865.1_Silent_p.T361T|RASSF8_ENST00000282884.9_Silent_p.T361T|RASSF8_ENST00000381352.3_Silent_p.T361T|RASSF8_ENST00000541490.1_Silent_p.T361T	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	361					signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					CAAAAGTTACCGTTTTGCCAG	0.443													C|||	87	0.0173722	0.031	0.013	5008	,	,		19814	0.0069		0.0189	False		,,,				2504	0.0112				p.T361T		Atlas-SNP	.											.	RASSF8	56	.	0			c.C1083T						PASS	.	C	,,,	89,4317	74.1+/-112.3	0,89,2114	112.0	106.0	108.0		1083,1083,1083,1083	-6.9	0.0	12	dbSNP_126	108	116,8484	61.3+/-123.2	4,108,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RASSF8	NM_001164746.1,NM_001164747.1,NM_001164748.1,NM_007211.4	,,,	4,197,6302	TT,TC,CC		1.3488,2.02,1.5762	,,,	361/420,361/420,361/420,361/393	26220591	205,12801	2203	4300	6503	SO:0001819	synonymous_variant	11228	exon5			AGTTACCGTTTTG	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"""chromosome 12 open reading frame 2"""	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.1083C>T	12.37:g.26220591C>T		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	229	102	0.445415	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Silent	SNP	ENST00000405154.2	37	CCDS53765.1																																																																																			C|0.985;T|0.015	0.015	strong		0.443	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211	
PDXDC1	23042	hgsc.bcm.edu	37	16	15102639	15102639	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15102639G>A	ENST00000396410.4	+	7	680	c.583G>A	c.(583-585)Ggc>Agc	p.G195S	PDXDC1_ENST00000447912.2_Missense_Mutation_p.G104S|PDXDC1_ENST00000455313.2_Intron|PDXDC1_ENST00000535621.2_Missense_Mutation_p.G195S|MIR1972-1_ENST00000459337.1_RNA|PDXDC1_ENST00000450288.2_Missense_Mutation_p.G167S|PDXDC1_ENST00000569715.1_Missense_Mutation_p.G168S|PDXDC1_ENST00000563679.1_Missense_Mutation_p.G213S|PDXDC1_ENST00000325823.7_Missense_Mutation_p.G180S	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	195					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)	p.G195S(1)		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						CCTGCAGCTCGGCTTGCCCTT	0.463																																					p.G195S		Atlas-SNP	.											PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	1	Substitution - Missense(1)	endometrium(1)	c.G583A						scavenged	.						340.0	283.0	302.0					16																	15102639		2197	4300	6497	SO:0001583	missense	23042	exon7			CAGCTCGGCTTGC	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.583G>A	16.37:g.15102639G>A	ENSP00000379691:p.Gly195Ser	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	372	4	0.0107527	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139547	0.77775	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288	T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05	5.8	4.85	0.62838	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.046591	0.85682	N	0.000000	T	0.73377	0.3579	M	0.81942	2.565	0.80722	D	1	P;D;P;P;P;P	0.59767	0.903;0.986;0.866;0.802;0.903;0.943	P;P;P;B;P;P	0.53266	0.722;0.639;0.518;0.397;0.722;0.722	T	0.76900	-0.2788	10	0.49607	T	0.09	-25.4334	14.291	0.66278	0.0716:0.0:0.9284:0.0	.	167;104;180;195;167;195	E7EPL4;E7EMH5;B4DHL7;Q86XE2;B4DR55;Q6P996	.;.;.;.;.;PDXD1_HUMAN	S	180;104;195;195;167	ENSP00000322807:G180S;ENSP00000400310:G104S;ENSP00000437835:G195S;ENSP00000379691:G195S;ENSP00000391147:G167S	ENSP00000322807:G180S	G	+	1	0	PDXDC1	15010140	1.000000	0.71417	0.996000	0.52242	0.903000	0.53119	7.177000	0.77650	1.462000	0.47948	0.650000	0.86243	GGC	.	.	none		0.463	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
DYSF	8291	hgsc.bcm.edu	37	2	71778829	71778829	+	Silent	SNP	G	G	A	rs35984374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71778829G>A	ENST00000258104.3	+	19	2008	c.1731G>A	c.(1729-1731)gcG>gcA	p.A577A	DYSF_ENST00000409582.3_Silent_p.A594A|DYSF_ENST00000429174.2_Silent_p.A577A|DYSF_ENST00000409744.1_Silent_p.A564A|DYSF_ENST00000410020.3_Silent_p.A595A|DYSF_ENST00000409366.1_Silent_p.A578A|DYSF_ENST00000413539.2_Silent_p.A608A|DYSF_ENST00000394120.2_Silent_p.A578A|DYSF_ENST00000409762.1_Silent_p.A594A|DYSF_ENST00000410041.1_Silent_p.A595A|DYSF_ENST00000409651.1_Silent_p.A609A	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	577					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						ACCTTCCTGCGGATGACATCC	0.652													G|||	30	0.00599042	0.0008	0.0058	5008	,	,		15341	0.0		0.0249	False		,,,				2504	0.0				p.A609A		Atlas-SNP	.											.	DYSF	536	.	0			c.G1827A						PASS	.	G	,,,,,,,,,,,,,	17,4389	23.3+/-48.9	1,15,2187	73.0	61.0	65.0		1734,1689,1689,1731,1824,1782,1782,1827,1734,1692,1785,1692,1785,1731	-10.9	0.0	2	dbSNP_126	65	168,8432	76.9+/-139.5	1,166,4133	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	,,,,,,,,,,,,,	2,181,6320	AA,AG,GG		1.9535,0.3858,1.4224	,,,,,,,,,,,,,	578/2082,563/2067,563/2088,577/2102,608/2112,594/2098,594/2119,609/2113,578/2103,564/2089,595/2099,564/2068,595/2120,577/2081	71778829	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon20			TCCTGCGGATGAC	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.1731G>A	2.37:g.71778829G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	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																																																																																			G|0.987;A|0.013	0.013	strong		0.652	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
CPO	130749	hgsc.bcm.edu	37	2	207827220	207827220	+	Missense_Mutation	SNP	G	G	A	rs62617140	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207827220G>A	ENST00000272852.3	+	7	705	c.659G>A	c.(658-660)aGc>aAc	p.S220N		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	220						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		GCTGTTGCCAGCTTCATAGAG	0.433													G|||	103	0.0205671	0.0008	0.0274	5008	,	,		21599	0.001		0.0716	False		,,,				2504	0.0102				p.S220N		Atlas-SNP	.											.	CPO	42	.	0			c.G659A						PASS	.	G	ASN/SER	62,4344	58.1+/-94.6	0,62,2141	206.0	196.0	199.0		659	3.7	0.3	2	dbSNP_129	199	408,8192	129.3+/-187.4	9,390,3901	yes	missense	CPO	NM_173077.2	46	9,452,6042	AA,AG,GG		4.7442,1.4072,3.6137	benign	220/375	207827220	470,12536	2203	4300	6503	SO:0001583	missense	130749	exon7			TTGCCAGCTTCAT		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.659G>A	2.37:g.207827220G>A	ENSP00000272852:p.Ser220Asn	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_173077	Q2M277|Q7RTW7	Missense_Mutation	SNP	ENST00000272852.3	37	CCDS2372.1	61	0.027930402930402932	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	53	0.06992084432717678	G	0.429	-0.904539	0.02453	0.014072	0.047442	ENSG00000144410	ENST00000272852	T	0.27720	1.65	5.5	3.72	0.42706	Peptidase M14, carboxypeptidase A (2);	0.443249	0.28665	N	0.014547	T	0.00815	0.0027	N	0.03000	-0.44	0.22050	N	0.99939	B	0.12630	0.006	B	0.10450	0.005	T	0.22452	-1.0216	10	0.23302	T	0.38	.	7.3163	0.26503	0.2513:0.0:0.7487:0.0	rs62617140	220	Q8IVL8	CBPO_HUMAN	N	220	ENSP00000272852:S220N	ENSP00000272852:S220N	S	+	2	0	CPO	207535465	0.286000	0.24305	0.292000	0.24919	0.419000	0.31324	2.790000	0.47821	0.893000	0.36288	0.555000	0.69702	AGC	G|0.965;A|0.035	0.035	strong		0.433	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
ERAP1	51752	hgsc.bcm.edu	37	5	96127833	96127833	+	Silent	SNP	G	G	A	rs3213809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:96127833G>A	ENST00000443439.2	-	8	1317	c.1251C>T	c.(1249-1251)caC>caT	p.H417H	ERAP1_ENST00000296754.3_Silent_p.H417H	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	417					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)		TAGACACAGGGTGTGAGGAAT	0.363													G|||	485	0.096845	0.0144	0.2507	5008	,	,		18650	0.0268		0.1481	False		,,,				2504	0.1186				p.H417H		Atlas-SNP	.											.	ERAP1	59	.	0			c.C1251T						PASS	.	G	,,	141,4265	98.0+/-136.7	1,139,2063	138.0	135.0	136.0		1251,1251,1251	4.8	1.0	5	dbSNP_106	136	1240,7360	248.6+/-276.2	72,1096,3132	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	73,1235,5195	AA,AG,GG		14.4186,3.2002,10.6182	,,	417/942,417/942,417/949	96127833	1381,11625	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon8			CACAGGGTGTGAG	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.1251C>T	5.37:g.96127833G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			G|0.905;A|0.095	0.095	strong		0.363	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
C4orf45	152940	hgsc.bcm.edu	37	4	159894391	159894391	+	Missense_Mutation	SNP	G	G	A	rs17037864	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:159894391G>A	ENST00000434826.2	-	2	221	c.137C>T	c.(136-138)gCg>gTg	p.A46V	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	46			A -> V (in dbSNP:rs17037864).							large_intestine(2)|lung(3)	5						TTTTTCTAACGCCAGATGCTG	0.378													G|||	774	0.154553	0.0	0.0591	5008	,	,		15858	0.3333		0.1322	False		,,,				2504	0.2699				p.A46V		Atlas-SNP	.											.	C4orf45	8	.	0			c.C137T						PASS	.	G	VAL/ALA	105,3549		1,103,1723	90.0	78.0	82.0		137	-4.9	0.0	4	dbSNP_123	82	998,7172		57,884,3144	yes	missense	C4orf45	NM_152543.2	64	58,987,4867	AA,AG,GG		12.2154,2.8736,9.3285	benign	46/187	159894391	1103,10721	1827	4085	5912	SO:0001583	missense	152940	exon2			TCTAACGCCAGAT		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.137C>T	4.37:g.159894391G>A	ENSP00000412215:p.Ala46Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_152543	A8MPU3|C9J0T8	Missense_Mutation	SNP	ENST00000434826.2	37	CCDS47156.1	322	0.14743589743589744	0	0.0	28	0.07734806629834254	192	0.3356643356643357	102	0.1345646437994723	G	3.724	-0.056991	0.07317	0.028736	0.122154	ENSG00000164123	ENST00000434826	T	0.15139	2.45	5.73	-4.88	0.03113	.	1.086240	0.06999	N	0.823032	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	B	0.14012	0.009	B	0.08055	0.003	T	0.48091	-0.9065	8	.	.	.	-0.2266	7.1752	0.25740	0.3933:0.0:0.4927:0.114	rs17037864;rs59308484;rs17037864	46	Q96LM5	CD045_HUMAN	V	46	ENSP00000412215:A46V	.	A	-	2	0	C4orf45	160113841	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.894000	0.04123	-0.952000	0.03649	-0.345000	0.07892	GCG	G|0.843;A|0.157	0.157	strong		0.378	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543	
TNK2	10188	hgsc.bcm.edu	37	3	195594950	195594950	+	Missense_Mutation	SNP	G	G	A	rs56260729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:195594950G>A	ENST00000333602.6	-	12	2791	c.2174C>T	c.(2173-2175)cCg>cTg	p.P725L	TNK2_ENST00000428187.1_Missense_Mutation_p.P757L|TNK2_ENST00000392400.1_Missense_Mutation_p.P725L|TNK2_ENST00000381916.2_Missense_Mutation_p.P803L	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	725	Pro-rich.		P -> L (in dbSNP:rs56260729). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.	Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	AGAGGGGGCCGGGGAGCCGGC	0.716													g|||	620	0.123802	0.0166	0.2349	5008	,	,		12164	0.0367		0.2366	False		,,,				2504	0.1636				p.P803L		Atlas-SNP	.											.	TNK2	246	.	0			c.C2408T						PASS	.		LEU/PRO,LEU/PRO	187,4111		7,173,1969	8.0	11.0	10.0		2408,2174	1.4	0.0	3	dbSNP_129	10	1796,6674		195,1406,2634	yes	missense,missense	TNK2	NM_001010938.1,NM_005781.4	98,98	202,1579,4603	AA,AG,GG		21.2043,4.3509,15.531	benign,benign	803/1087,725/1039	195594950	1983,10785	2149	4235	6384	SO:0001583	missense	10188	exon13			GGGGCCGGGGAGC	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2174C>T	3.37:g.195594950G>A	ENSP00000329425:p.Pro725Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	275	0.1259157509157509	12	0.024390243902439025	63	0.17403314917127072	20	0.03496503496503497	180	0.23746701846965698	G	0.221	-1.028459	0.02045	0.043509	0.212043	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000416152;ENST00000428187;ENST00000392400	T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73	5.04	1.38	0.22167	.	0.708126	0.13524	N	0.381455	T	0.00012	0.0000	N	0.00583	-1.355	0.44123	P	0.0030970000000000164	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.43782	-0.9370	9	0.02654	T	1	.	8.5498	0.33444	0.788:0.0:0.212:0.0	rs56260729;rs61749507	725;803;757;250	Q07912;Q07912-3;C9J1X3;B3KXJ4	ACK1_HUMAN;.;.;.	L	725;803;292;757;725	ENSP00000329425:P725L;ENSP00000371341:P803L;ENSP00000398614:P292L;ENSP00000392546:P757L;ENSP00000376201:P725L	ENSP00000329425:P725L	P	-	2	0	TNK2	197079347	0.147000	0.22687	0.006000	0.13384	0.002000	0.02628	1.514000	0.35834	0.008000	0.14787	-1.292000	0.01352	CCG	G|0.858;A|0.142	0.142	strong		0.716	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
HLA-G	3135	hgsc.bcm.edu	37	6	29797436	29797436	+	Silent	SNP	T	T	C	rs74547057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29797436T>C	ENST00000360323.6	+	4	885	c.861T>C	c.(859-861)caT>caC	p.H287H	HLA-G_ENST00000428701.1_Silent_p.H287H|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Silent_p.H195H|HLA-G_ENST00000376828.2_Silent_p.H292H			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	287	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.H287H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						ATGTGCAGCATGAGGGGCTGC	0.577																																					p.H287H		Atlas-SNP	.											HLA-G,NS,carcinoma,0,1	HLA-G	90	1	1	Substitution - coding silent(1)	prostate(1)	c.T861C						scavenged	.						55.0	57.0	56.0					6																	29797436		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			GCAGCATGAGGGG		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.861T>C	6.37:g.29797436T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	15	0.174419	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			T|0.985;C|0.015	0.015	strong		0.577	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
CMSS1	84319	hgsc.bcm.edu	37	3	99886662	99886662	+	Missense_Mutation	SNP	G	G	A	rs11537816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:99886662G>A	ENST00000421999.2	+	6	642	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	CMSS1_ENST00000489081.1_Missense_Mutation_p.V148I	NM_032359.3	NP_115735.2	Q9BQ75	CMS1_HUMAN	cms1 ribosomal small subunit homolog (yeast)	166			V -> I (in dbSNP:rs11537816).				poly(A) RNA binding (GO:0044822)										CAGCTCGGCCGTCCGAGCCCT	0.418													A|||	602	0.120208	0.0242	0.2233	5008	,	,		16980	0.0417		0.162	False		,,,				2504	0.2147				p.V166I		Atlas-SNP	.											.	.	.	.	0			c.G496A						PASS	.	A	ILE/VAL,ILE/VAL	203,4203	808.0+/-415.9	7,189,2007	133.0	138.0	137.0		442,496	-8.8	0.1	3	dbSNP_120	137	1526,7074	747.1+/-407.3	135,1256,2909	yes	missense,missense	C3orf26	NM_001167924.1,NM_032359.3	29,29	142,1445,4916	AA,AG,GG		17.7442,4.6074,13.2939	benign,benign	148/262,166/280	99886662	1729,11277	2203	4300	6503	SO:0001583	missense	84319	exon6			TCGGCCGTCCGAG		CCDS2935.1, CCDS54618.1	3q12.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000184220	ENSG00000184220			28666	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 26"""	C3orf26		12477932	Standard	NM_032359		Approved	MGC4308	uc003dtl.3	Q9BQ75	OTTHUMG00000159054	ENST00000421999.2:c.496G>A	3.37:g.99886662G>A	ENSP00000410396:p.Val166Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	103	65	0.631068	NM_032359	A8K5S7|B4DUM1|E9PHS3	Missense_Mutation	SNP	ENST00000421999.2	37	CCDS2935.1	235|235	0.10760073260073261|0.10760073260073261	21|21	0.042682926829268296|0.042682926829268296	67|67	0.1850828729281768|0.1850828729281768	18|18	0.03146853146853147|0.03146853146853147	129|129	0.17018469656992086|0.17018469656992086	A|A	11.24|11.24	1.581789|1.581789	0.28180|0.28180	0.046074|0.046074	0.177442|0.177442	ENSG00000184220|ENSG00000184220	ENST00000497345|ENST00000421999;ENST00000489081;ENST00000478909	.|T;T;T	.|0.31769	.|1.48;1.48;1.48	5.62|5.62	-8.83|-8.83	0.00806|0.00806	.|DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	.|0.617522	.|0.17485	.|N	.|0.172544	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11789|0.11789	0.175|0.175	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.12630	.|0.006	.|B	.|0.06405	.|0.002	T|T	0.23368|0.23368	-1.0190|-1.0190	4|8	.|.	.|.	.|.	.|.	14.5932|14.5932	0.68386|0.68386	0.1416:0.2756:0.5828:0.0|0.1416:0.2756:0.5828:0.0	rs11537816;rs11537816|rs11537816;rs11537816	.|166	.|Q9BQ75	.|CC026_HUMAN	H|I	74|166;148;122	.|ENSP00000410396:V166I;ENSP00000419161:V148I;ENSP00000417293:V122I	.|.	R|V	+|+	2|1	0|0	C3orf26|C3orf26	101369352|101369352	0.000000|0.000000	0.05858|0.05858	0.082000|0.082000	0.20525|0.20525	0.663000|0.663000	0.39108|0.39108	-0.461000|-0.461000	0.06712|0.06712	-1.984000|-1.984000	0.00985|0.00985	-1.760000|-1.760000	0.00671|0.00671	CGT|GTC	G|0.873;A|0.127	0.127	strong		0.418	CMSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353060.1	NM_032359	
CRB2	286204	hgsc.bcm.edu	37	9	126128253	126128253	+	Missense_Mutation	SNP	G	G	C	rs1105222	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:126128253G>C	ENST00000373631.3	+	3	477	c.476G>C	c.(475-477)gGc>gCc	p.G159A	CRB2_ENST00000359999.3_Missense_Mutation_p.G159A|CRB2_ENST00000373629.2_5'Flank	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	159	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		G -> A (in dbSNP:rs1105222). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15851977}.		cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CTGCACGGGGGCTCGTGCCTG	0.706													G|||	1582	0.315895	0.1989	0.3314	5008	,	,		12014	0.3889		0.3728	False		,,,				2504	0.3292				p.G159A		Atlas-SNP	.											CRB2,NS,carcinoma,0,1	CRB2	86	1	0			c.G476C						PASS	.	G	ALA/GLY	906,3482		99,708,1387	30.0	25.0	27.0		476	4.8	1.0	9	dbSNP_86	27	3118,5442		590,1938,1752	no	missense	CRB2	NM_173689.5	60	689,2646,3139	CC,CG,GG		36.4252,20.6472,31.0782	probably-damaging	159/1286	126128253	4024,8924	2194	4280	6474	SO:0001583	missense	286204	exon3			ACGGGGGCTCGTG	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.476G>C	9.37:g.126128253G>C	ENSP00000362734:p.Gly159Ala	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	706	0.3232600732600733	90	0.18292682926829268	134	0.3701657458563536	192	0.3356643356643357	290	0.38258575197889183	G	15.71	2.914538	0.52546	0.206472	0.364252	ENSG00000148204	ENST00000359999;ENST00000373631	D;D	0.96300	-3.97;-3.97	4.79	4.79	0.61399	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.47093	D	0.000256	T	0.00012	0.0000	L	0.28740	0.885	0.09310	P	1.0	P;P	0.41784	0.61;0.762	B;P	0.46253	0.397;0.509	T	0.01557	-1.1325	9	0.11485	T	0.65	.	11.2646	0.49104	0.0:0.1854:0.8146:0.0	rs1105222;rs1105222	159;159	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	A	159	ENSP00000353092:G159A;ENSP00000362734:G159A	ENSP00000353092:G159A	G	+	2	0	CRB2	125168074	0.953000	0.32496	1.000000	0.80357	0.786000	0.44442	1.278000	0.33179	2.186000	0.69663	0.448000	0.29417	GGC	G|0.691;C|0.309	0.309	strong		0.706	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
SLC2A14	144195	hgsc.bcm.edu	37	12	7985318	7985318	+	Splice_Site	SNP	C	C	A	rs10846018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7985318C>A	ENST00000543909.1	-	8	939	c.180G>T	c.(178-180)acG>acT	p.T60T	SLC2A14_ENST00000539924.1_Splice_Site_p.T75T|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000396589.2_Splice_Site_p.T60T|SLC2A14_ENST00000431042.2_Splice_Site_p.T37T|SLC2A14_ENST00000542546.1_Splice_Site_p.R5L|SLC2A14_ENST00000340749.5_Splice_Site_p.T37T|SLC2A14_ENST00000535295.1_Splice_Site_p.R5L			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	60					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)		TGGCACTCACCGTCTCAGGAG	0.478											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	55	0.0109824	0.0015	0.0144	5008	,	,		-128	0.0		0.0398	False		,,,				2504	0.0031				p.T60T		Atlas-SNP	.											.	SLC2A14	78	.	0			c.G180T						PASS	.	C		40,4366	43.8+/-77.6	0,40,2163	96.0	92.0	93.0		180	0.5	0.4	12	dbSNP_120	93	276,8324	104.6+/-165.6	4,268,4028	yes	coding-synonymous-near-splice	SLC2A14	NM_153449.2		4,308,6191	AA,AC,CC		3.2093,0.9079,2.4296		60/521	7985318	316,12690	2203	4300	6503	SO:0001630	splice_region_variant	144195	exon4			ACTCACCGTCTCA	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.180+1G>T	12.37:g.7985318C>A		Somatic	97	0	0	645	WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1	42	0.019230769230769232	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	34	0.044854881266490766	C	14.99	2.701667	0.48307	0.009079	0.032093	ENSG00000173262	ENST00000535295;ENST00000542546	D;D	0.83837	-1.77;-1.77	2.59	0.538	0.17150	.	.	.	.	.	T	0.69187	0.3083	.	.	.	0.53688	D	0.999972	D	0.64830	0.994	D	0.68943	0.961	T	0.77040	-0.2735	7	.	.	.	.	8.4863	0.33074	0.0:0.7381:0.0:0.2619	rs10846018;rs10846018	5	B7Z844	.	L	5	ENSP00000440492:R5L;ENSP00000443903:R5L	.	R	-	2	0	SLC2A14	7876585	0.256000	0.24012	0.446000	0.26920	0.094000	0.18550	0.809000	0.27168	-0.343000	0.08351	-1.641000	0.00772	CGG	C|0.979;A|0.021	0.021	strong		0.478	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	Silent
ZPBP2	124626	hgsc.bcm.edu	37	17	38031674	38031674	+	Silent	SNP	C	C	T	rs10852935	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38031674C>T	ENST00000348931.4	+	7	1067	c.876C>T	c.(874-876)tgC>tgT	p.C292C	ZPBP2_ENST00000377940.3_Silent_p.C270C|ZPBP2_ENST00000584588.1_Silent_p.C219C	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	292					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)		p.C292C(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACAGTAATTGCGCTAGCTGTT	0.358													C|||	1453	0.290136	0.1135	0.3415	5008	,	,		15697	0.2827		0.4722	False		,,,				2504	0.3129				p.C292C		Atlas-SNP	.											ZPBP2,colon,carcinoma,0,2	ZPBP2	33	2	1	Substitution - coding silent(1)	stomach(1)	c.C876T						PASS	.	C	,	652,3754	276.9+/-273.4	46,560,1597	57.0	52.0	54.0		810,876	-9.6	0.6	17	dbSNP_120	54	3869,4731	535.7+/-382.9	859,2151,1290	no	coding-synonymous,coding-synonymous	ZPBP2	NM_198844.2,NM_199321.2	,	905,2711,2887	TT,TC,CC		44.9884,14.798,34.7609	,	270/317,292/339	38031674	4521,8485	2203	4300	6503	SO:0001819	synonymous_variant	124626	exon7			TAATTGCGCTAGC	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.876C>T	17.37:g.38031674C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			C|0.654;T|0.346	0.346	strong		0.358	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
HOXD12	3238	hgsc.bcm.edu	37	2	176964904	176964904	+	Silent	SNP	G	G	A	rs847151	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	82	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	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	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42281719	42281719	+	Silent	SNP	G	G	A	rs1668579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42281719G>A	ENST00000399518.3	-	15	2103	c.1617C>T	c.(1615-1617)ggC>ggT	p.G539G	PLA2G4E_ENST00000413860.2_Silent_p.G510G|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	527	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)		ACTTCTGCAGGCCCACCTCGT	0.632											OREG0023079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2122	0.423722	0.6861	0.2291	5008	,	,		17989	0.2927		0.2803	False		,,,				2504	0.4898				p.G539G		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C1617T						PASS	.	G		2548,1826		772,1004,411	32.0	38.0	36.0		1617	1.2	1.0	15	dbSNP_89	36	2258,6326		303,1652,2337	no	coding-synonymous	PLA2G4E	NM_001206670.1		1075,2656,2748	AA,AG,GG		26.3048,41.7467,37.0891		539/869	42281719	4806,8152	2187	4292	6479	SO:0001819	synonymous_variant	123745	exon15			CTGCAGGCCCACC		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.1617C>T	15.37:g.42281719G>A		Somatic	45	0	0	907	WXS	Illumina HiSeq	Phase_I	59	55	0.932203	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																			G|0.630;A|0.370	0.370	strong		0.632	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
MRPS9	64965	hgsc.bcm.edu	37	2	105665808	105665808	+	Splice_Site	SNP	C	C	T	rs11538197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	96	0	0		WXS	Illumina HiSeq	Phase_I	69	45	0.652174	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
RPS16	6217	hgsc.bcm.edu	37	19	39926509	39926509	+	Silent	SNP	A	A	C	rs17628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39926509A>C	ENST00000251453.3	-	1	79	c.27T>G	c.(25-27)tcT>tcG	p.S9S	RPS16_ENST00000339471.4_Silent_p.S9S|RPS16_ENST00000601655.1_Silent_p.S9S|RPS16_ENST00000599539.1_Silent_p.S9S	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	9					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)			AGACCTGCACAGACTGCAGCG	0.662													C|||	2561	0.511382	0.7126	0.379	5008	,	,		14095	0.5506		0.3827	False		,,,				2504	0.4254				p.S9S		Atlas-SNP	.											.	RPS16	12	.	0			c.T27G						PASS	.	C		2833,1571	490.8+/-361.9	909,1015,278	47.0	47.0	47.0		27	-12.1	0.3	19	dbSNP_63	47	2925,5675	667.8+/-402.5	491,1943,1866	yes	coding-synonymous	RPS16	NM_001020.4		1400,2958,2144	CC,CA,AA		34.0116,35.6721,44.2787		9/147	39926509	5758,7246	2202	4300	6502	SO:0001819	synonymous_variant	6217	exon1			CTGCACAGACTGC	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.27T>G	19.37:g.39926509A>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_001020	B2RDD5|P17008	Silent	SNP	ENST00000251453.3	37	CCDS12535.1																																																																																			A|0.550;C|0.450	0.450	strong		0.662	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020	
PRSS37	136242	hgsc.bcm.edu	37	7	141537735	141537735	+	Missense_Mutation	SNP	T	T	G	rs12669721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:141537735T>G	ENST00000350549.3	-	3	726	c.355A>C	c.(355-357)Acc>Ccc	p.T119P	PRSS37_ENST00000438520.1_Missense_Mutation_p.T119P	NM_001008270.2|NM_001171951.1	NP_001008271.2|NP_001165422.1	A4D1T9	PRS37_HUMAN	protease, serine, 37	119	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> P (in dbSNP:rs12669721).		binding of sperm to zona pellucida (GO:0007339)|cell migration (GO:0016477)|protein maturation (GO:0051604)	extracellular region (GO:0005576)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(3)	15						GTGGCGAGGGTAAGGGGCTGG	0.547													G|||	2651	0.529353	0.3464	0.5764	5008	,	,		20788	0.755		0.4642	False		,,,				2504	0.5777				p.T119P		Atlas-SNP	.											PRSS37,NS,adenoma,0,1	PRSS37	42	1	0			c.A355C						scavenged	.	G	PRO/THR,PRO/THR	1655,2751	657.7+/-400.3	335,985,883	207.0	171.0	183.0		355,355	-6.7	0.0	7	dbSNP_120	183	4139,4461	589.8+/-392.6	981,2177,1142	yes	missense,missense	PRSS37	NM_001008270.2,NM_001171951.1	38,38	1316,3162,2025	GG,GT,TT		48.1279,37.5624,44.5487	benign,benign	119/236,119/235	141537735	5794,7212	2203	4300	6503	SO:0001583	missense	136242	exon3			CGAGGGTAAGGGG		CCDS34764.1	7q34	2010-05-07			ENSG00000165076	ENSG00000165076		"""Serine peptidases / Serine peptidases"""	29211	protein-coding gene	gene with protein product							Standard	NM_001008270		Approved		uc003vws.2	A4D1T9	OTTHUMG00000157174	ENST00000350549.3:c.355A>C	7.37:g.141537735T>G	ENSP00000297767:p.Thr119Pro	Somatic	184	7	0.0380435		WXS	Illumina HiSeq	Phase_I	194	93	0.479381	NM_001171951	B2RPB5	Missense_Mutation	SNP	ENST00000350549.3	37	CCDS34764.1	1185	0.5425824175824175	198	0.4024390243902439	203	0.5607734806629834	436	0.7622377622377622	348	0.45910290237467016	G	0.453	-0.892662	0.02491	0.375624	0.481279	ENSG00000165076	ENST00000350549;ENST00000438520	T;T	0.41065	1.01;1.01	5.45	-6.72	0.01755	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.083900	0.07029	N	0.828117	T	0.00012	0.0000	N	0.00560	-1.38	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34551	-0.9824	9	0.10111	T	0.7	.	4.1826	0.10383	0.1821:0.4397:0.2215:0.1567	rs12669721;rs52815952;rs60731623;rs12669721	119;119	B7ZMK3;A4D1T9	.;PRS37_HUMAN	P	119	ENSP00000297767:T119P;ENSP00000414461:T119P	ENSP00000297767:T119P	T	-	1	0	PRSS37	141184204	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.125000	0.03257	-1.543000	0.01723	-0.770000	0.03390	ACC	T|0.509;G|0.491	0.491	strong		0.547	PRSS37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347763.1	NM_001008270	
ARPP21	10777	hgsc.bcm.edu	37	3	35780947	35780947	+	Missense_Mutation	SNP	G	G	A	rs151173813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:35780947G>A	ENST00000187397.4	+	17	2239	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T	ARPP21_ENST00000337271.5_Missense_Mutation_p.A576T|ARPP21_ENST00000417925.1_Missense_Mutation_p.A596T|ARPP21_ENST00000444190.1_Missense_Mutation_p.A576T|ARPP21_ENST00000458225.1_Missense_Mutation_p.A596T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	595	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.A595T(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						CTATGTAATCGCCTCTACAGG	0.627													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15714	0.0		0.003	False		,,,				2504	0.002				p.A596T		Atlas-SNP	.											ARPP21,NS,NS,0,1	ARPP21	153	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1786A						PASS	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	58.0	59.0	58.0		1783	4.1	0.4	3	dbSNP_134	58	37,8563	25.7+/-73.6	0,37,4263	yes	missense	ARPP21	NM_016300.4	58	0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076	benign	595/813	35780947	40,12966	2203	4300	6503	SO:0001583	missense	10777	exon16			GTAATCGCCTCTA	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1783G>A	3.37:g.35780947G>A	ENSP00000187397:p.Ala595Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	135	76	0.562963	NM_001267619	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	11.71	1.719677	0.30503	6.81E-4	0.004302	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.96	4.14	0.48551	.	0.068903	0.56097	N	0.000036	T	0.19127	0.0459	L	0.31476	0.935	0.31779	N	0.631164	B;B;B;B	0.32543	0.067;0.375;0.011;0.067	B;B;B;B	0.28385	0.023;0.089;0.006;0.023	T	0.19418	-1.0306	10	0.12103	T	0.63	-7.922	10.8408	0.46715	0.1502:0.0:0.8498:0.0	.	596;118;595;576	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	T	596;576;576;595;596	ENSP00000414351:A596T;ENSP00000337792:A576T;ENSP00000405276:A576T;ENSP00000187397:A595T;ENSP00000412326:A596T	ENSP00000187397:A595T	A	+	1	0	ARPP21	35755951	1.000000	0.71417	0.406000	0.26421	0.573000	0.36030	4.374000	0.59543	1.499000	0.48617	0.655000	0.94253	GCC	G|0.997;A|0.003	0.003	strong		0.627	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399	
GPLD1	2822	hgsc.bcm.edu	37	6	24489652	24489652	+	Missense_Mutation	SNP	C	C	T	rs1126617	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:24489652C>T	ENST00000230036.1	-	1	198	c.88G>A	c.(88-90)Gta>Ata	p.V30I	GPLD1_ENST00000474784.1_5'UTR	NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	30			V -> I (in dbSNP:rs1126617). {ECO:0000269|PubMed:11072085, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		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						CCTATTTCTACGTGTGTTGAA	0.463													C|||	1345	0.26857	0.3139	0.2089	5008	,	,		23090	0.1667		0.332	False		,,,				2504	0.2894				p.V30I		Atlas-SNP	.											.	GPLD1	91	.	0			c.G88A						PASS	.	C	ILE/VAL,ILE/VAL	1367,3039	453.2+/-350.3	210,947,1046	131.0	107.0	115.0		88,88	-6.8	0.1	6	dbSNP_86	115	2890,5710	452.1+/-362.9	465,1960,1875	yes	missense,missense	GPLD1	NM_001503.2,NM_177483.1	29,29	675,2907,2921	TT,TC,CC		33.6047,31.0259,32.731	benign,benign	30/841,30/177	24489652	4257,8749	2203	4300	6503	SO:0001583	missense	2822	exon1			TTTCTACGTGTGT	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.88G>A	6.37:g.24489652C>T	ENSP00000230036:p.Val30Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	606	0.2774725274725275	147	0.29878048780487804	93	0.2569060773480663	108	0.1888111888111888	258	0.3403693931398417	C	0.006	-2.052583	0.00394	0.310259	0.336047	ENSG00000112293	ENST00000230036;ENST00000378243	T	0.38722	1.12	4.89	-6.76	0.01732	.	0.560584	0.17082	N	0.187745	T	0.03651	0.0104	N	0.01751	-0.74	0.80722	P	0.0	B;B	0.13594	0.004;0.008	B;B	0.14023	0.002;0.01	T	0.24440	-1.0160	9	0.02654	T	1	-2.006	14.647	0.68767	0.0:0.3288:0.0:0.6712	rs1126617;rs1804164;rs2235500;rs3181755;rs17374253;rs17404904;rs59497448;rs1126617	30;30	P80108-2;P80108	.;PHLD_HUMAN	I	30	ENSP00000230036:V30I	ENSP00000230036:V30I	V	-	1	0	GPLD1	24597631	0.004000	0.15560	0.147000	0.22382	0.007000	0.05969	-0.977000	0.03782	-1.433000	0.01977	-0.991000	0.02546	GTA	C|0.700;T|0.299	0.299	strong		0.463	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209864	84209864	+	Missense_Mutation	SNP	G	G	C	rs2288023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:84209864G>C	ENST00000378553.5	+	11	2148	c.2024G>C	c.(2023-2025)aGt>aCt	p.S675T	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	675			S -> T (in dbSNP:rs2288023). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						CTCACTTCCAGTGGAGACAGG	0.627													G|||	1340	0.267572	0.0613	0.4063	5008	,	,		17997	0.376		0.3439	False		,,,				2504	0.2577				p.S675T		Atlas-SNP	.											DNAAF1,rectum,carcinoma,0,1	DNAAF1	81	1	0			c.G2024C						PASS	.	G	THR/SER	491,3909	225.2+/-241.2	32,427,1741	46.0	42.0	43.0		2024	-1.7	0.0	16	dbSNP_100	43	3062,5538	457.8+/-364.4	561,1940,1799	yes	missense	DNAAF1	NM_178452.4	58	593,2367,3540	CC,CG,GG		35.6047,11.1591,27.3308	benign	675/726	84209864	3553,9447	2200	4300	6500	SO:0001583	missense	123872	exon11			CTTCCAGTGGAGA	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.2024G>C	16.37:g.84209864G>C	ENSP00000367815:p.Ser675Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	659	0.3017399267399267	36	0.07317073170731707	125	0.3453038674033149	237	0.4143356643356643	261	0.34432717678100266	G	9.612	1.131548	0.21041	0.111591	0.356047	ENSG00000154099	ENST00000378553	T	0.32023	1.47	4.34	-1.74	0.08056	.	1.806150	0.03273	N	0.185064	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	2.9999999999752447E-6	B;B	0.20988	0.05;0.021	B;B	0.20184	0.028;0.008	T	0.42666	-0.9438	9	0.15066	T	0.55	0.1543	5.967	0.19330	0.2144:0.5194:0.2662:0.0	rs2288023;rs17845738;rs17858688;rs2288023	439;675	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	T	675	ENSP00000367815:S675T	ENSP00000367815:S675T	S	+	2	0	DNAAF1	82767365	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.037000	0.12164	-0.128000	0.11641	0.563000	0.77884	AGT	G|0.706;C|0.294	0.294	strong		0.627	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	118	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	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	
FAT1	2195	hgsc.bcm.edu	37	4	187540635	187540635	+	Missense_Mutation	SNP	T	T	G	rs77834784	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187540635T>G	ENST00000441802.2	-	10	7314	c.7105A>C	c.(7105-7107)Acg>Ccg	p.T2369P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2369	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTGCTCAGCGTGGGCATACCA	0.502										HNSCC(5;0.00058)			G|||	336	0.0670927	0.003	0.1499	5008	,	,		20820	0.1736		0.0338	False		,,,				2504	0.0194				p.T2369P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,colon,carcinoma,0,2	FAT1	500	2	0			c.A7105C						scavenged	.	G	PRO/THR	38,4224		0,38,2093	92.0	94.0	94.0		7105	1.2	0.0	4	dbSNP_131	94	250,8226		4,242,3992	yes	missense	FAT1	NM_005245.3	38	4,280,6085	GG,GT,TT		2.9495,0.8916,2.261	benign	2369/4589	187540635	288,12450	2131	4238	6369	SO:0001583	missense	2195	exon10			TCAGCGTGGGCAT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7105A>C	4.37:g.187540635T>G	ENSP00000406229:p.Thr2369Pro	Somatic	120	2	0.0166667		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	187	0.08562271062271062	3	0.006097560975609756	40	0.11049723756906077	113	0.19755244755244755	31	0.040897097625329816	G	0	-2.850445	0.00066	0.008916	0.029495	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.42900	0.96	5.14	1.24	0.21308	Cadherin (4);Cadherin-like (1);	0.420019	0.27668	N	0.018357	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33497	-0.9866	9	0.02654	T	1	.	7.34	0.26632	0.0631:0.3383:0.482:0.1166	.	2369	Q14517	FAT1_HUMAN	P	2369;2371	ENSP00000406229:T2369P	ENSP00000260147:T2371P	T	-	1	0	FAT1	187777629	0.936000	0.31750	0.004000	0.12327	0.030000	0.12068	1.372000	0.34261	-0.109000	0.12044	-0.127000	0.14921	ACG	T|0.926;G|0.074	0.074	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CCDC65	85478	hgsc.bcm.edu	37	12	49312540	49312540	+	Missense_Mutation	SNP	C	C	T	rs78877829	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49312540C>T	ENST00000320516.4	+	6	1068	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Missense_Mutation_p.R294C	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	294										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						CCGGTATATCCGTAATGACAA	0.458													C|||	89	0.0177716	0.0023	0.0274	5008	,	,		19284	0.0		0.0567	False		,,,				2504	0.0102				p.R294C		Atlas-SNP	.											.	CCDC65	41	.	0			c.C880T						PASS	.	C	CYS/ARG	48,4358	48.2+/-83.0	0,48,2155	111.0	102.0	105.0		880	4.7	1.0	12	dbSNP_131	105	477,8123	140.3+/-196.8	14,449,3837	yes	missense	CCDC65	NM_033124.4	180	14,497,5992	TT,TC,CC		5.5465,1.0894,4.0366	probably-damaging	294/485	49312540	525,12481	2203	4300	6503	SO:0001583	missense	85478	exon6			TATATCCGTAATG		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.880C>T	12.37:g.49312540C>T	ENSP00000312706:p.Arg294Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	66	0.03021978021978022	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	51	0.06728232189973615	C	18.72	3.684596	0.68157	0.010894	0.055465	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	T;T;T	0.51071	1.34;0.72;1.35	4.72	4.72	0.59763	.	0.337418	0.30920	N	0.008603	T	0.14657	0.0354	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.69824	0.966	T	0.49399	-0.8944	10	0.59425	D	0.04	-7.8024	16.9918	0.86356	0.0:1.0:0.0:0.0	.	294	Q8IXS2	CCD65_HUMAN	C	294;191;294	ENSP00000266984:R294C;ENSP00000446569:R191C;ENSP00000312706:R294C	ENSP00000266984:R294C	R	+	1	0	CCDC65	47598807	0.989000	0.36119	0.985000	0.45067	0.508000	0.34012	2.687000	0.46976	2.630000	0.89119	0.655000	0.94253	CGT	C|0.965;T|0.035	0.035	strong		0.458	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
NLRP5	126206	hgsc.bcm.edu	37	19	56549510	56549510	+	Missense_Mutation	SNP	T	T	C	rs16986899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56549510T>C	ENST00000390649.3	+	10	2735	c.2735T>C	c.(2734-2736)aTg>aCg	p.M912T		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	912			M -> T (in dbSNP:rs16986899). {ECO:0000269|PubMed:11925379}.		cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.M912T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGGGAGTAATGCCTCTCAGT	0.532													C|||	1327	0.264976	0.4486	0.1398	5008	,	,		21362	0.3006		0.1889	False		,,,				2504	0.1472				p.M912T		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - Missense(1)	stomach(1)	c.T2735C						PASS	.	C	THR/MET	1623,2587		320,983,802	132.0	134.0	133.0		2735	-3.1	0.0	19	dbSNP_123	133	1407,7041		129,1149,2946	yes	missense	NLRP5	NM_153447.4	81	449,2132,3748	CC,CT,TT		16.6548,38.5511,23.9374	benign	912/1201	56549510	3030,9628	2105	4224	6329	SO:0001583	missense	126206	exon10			GAGTAATGCCTCT	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2735T>C	19.37:g.56549510T>C	ENSP00000375063:p.Met912Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	73	0.561538	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	580	0.26556776556776557	208	0.42276422764227645	57	0.1574585635359116	178	0.3111888111888112	137	0.18073878627968337	C	0.711	-0.787261	0.02907	0.385511	0.166548	ENSG00000171487	ENST00000390649	T	0.51817	0.69	3.59	-3.09	0.05331	.	1.126530	0.06995	N	0.822221	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40739	-0.9547	9	0.34782	T	0.22	.	2.2949	0.04147	0.2037:0.4503:0.2034:0.1426	rs16986899;rs52814735;rs60032233;rs16986899	912	P59047	NALP5_HUMAN	T	912	ENSP00000375063:M912T	ENSP00000375063:M912T	M	+	2	0	NLRP5	61241322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.013000	0.12678	-1.137000	0.02888	-1.292000	0.01352	ATG	T|0.731;C|0.269	0.269	strong		0.532	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
LEPROTL1	23484	hgsc.bcm.edu	37	8	29961951	29961951	+	Silent	SNP	C	C	T	rs11557703	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:29961951C>T	ENST00000321250.8	+	3	343	c.228C>T	c.(226-228)ggC>ggT	p.G76G	LEPROTL1_ENST00000518192.1_Silent_p.G99G|LEPROTL1_ENST00000523116.1_Silent_p.G76G|LEPROTL1_ENST00000442880.2_Silent_p.G76G|LEPROTL1_ENST00000518001.1_Silent_p.G15G	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						scavenged	.	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	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	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		
PPP2R5C	5527	hgsc.bcm.edu	37	14	102384272	102384272	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:102384272C>T	ENST00000334743.5	+	13	1479	c.1431C>T	c.(1429-1431)gaC>gaT	p.D477D	PPP2R5C_ENST00000328724.5_Intron|PPP2R5C_ENST00000350249.3_Intron|PPP2R5C_ENST00000422945.2_Silent_p.D508D	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	477					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CAGTGAAGGACGAGGCTCATC	0.473																																					p.D508D		Atlas-SNP	.											PPP2R5C,NS,carcinoma,0,1	PPP2R5C	74	1	0			c.C1524T						scavenged	.						141.0	120.0	127.0					14																	102384272		2203	4300	6503	SO:0001819	synonymous_variant	5527	exon15			GAAGGACGAGGCT	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9311	protein-coding gene	gene with protein product		601645	"""protein phosphatase 2, regulatory subunit B (B56), gamma isoform"", ""protein phosphatase 2, regulatory subunit B', gamma isoform"""			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1431C>T	14.37:g.102384272C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	3	0.0306122	NM_001161725	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Silent	SNP	ENST00000334743.5	37	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	9.065	0.995545	0.19043	.	.	ENSG00000078304	ENST00000555237	.	.	.	5.83	0.0993	0.14502	.	.	.	.	.	T	0.54615	0.1869	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	.	8.1725	0.31262	0.4604:0.1607:0.3789:0.0	.	.	.	.	M	102	.	.	T	+	2	0	PPP2R5C	101454025	0.982000	0.34865	0.861000	0.33841	0.850000	0.48378	0.336000	0.19823	-0.186000	0.10533	0.555000	0.69702	ACG	.	.	none		0.473	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	
TFIP11	24144	hgsc.bcm.edu	37	22	26899695	26899695	+	Silent	SNP	G	G	A	rs74334826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26899695G>A	ENST00000407690.1	-	7	868	c.585C>T	c.(583-585)tcC>tcT	p.S195S	TFIP11_ENST00000405938.1_Silent_p.S195S|TFIP11_ENST00000407148.1_Silent_p.S195S|TFIP11_ENST00000496523.1_5'UTR|TFIP11_ENST00000407431.1_Silent_p.S195S	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	195	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						TGGTGCGCTCGGATCCATAAG	0.483													G|||	22	0.00439297	0.0008	0.0072	5008	,	,		19610	0.0		0.0149	False		,,,				2504	0.001				p.S195S		Atlas-SNP	.											.	TFIP11	72	.	0			c.C585T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	154.0	135.0	141.0		585,585	-11.4	0.0	22	dbSNP_132	141	143,8457	71.3+/-133.9	0,143,4157	no	coding-synonymous,coding-synonymous	TFIP11	NM_001008697.1,NM_012143.2	,	0,155,6348	AA,AG,GG		1.6628,0.2724,1.1918	,	195/838,195/838	26899695	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	24144	exon8			GCGCTCGGATCCA	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"""G patch domain containing"""	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.585C>T	22.37:g.26899695G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	0.332	-0.955568	0.02267	0.002724	0.016628	ENSG00000100109	ENST00000450493	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.17789	0.0427	.	.	.	0.51012	D	0.999905	.	.	.	.	.	.	T	0.45542	-0.9254	4	.	.	.	-16.0333	1.8375	0.03143	0.1951:0.1397:0.2425:0.4227	.	.	.	.	L	32	.	.	P	-	2	0	TFIP11	25229695	0.000000	0.05858	0.008000	0.14137	0.031000	0.12232	-7.970000	0.00027	-3.591000	0.00136	-0.867000	0.03001	CCG	G|0.991;A|0.009	0.009	strong		0.483	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697	
VSX2	338917	hgsc.bcm.edu	37	14	74727367	74727367	+	Silent	SNP	G	G	A	rs60106203|rs62006815	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74727367G>A	ENST00000261980.2	+	5	921	c.831G>A	c.(829-831)ctG>ctA	p.L277L		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	277					cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		GCCAGGCCCTGCCCAAGCTCG	0.627													G|||	98	0.0195687	0.0023	0.0202	5008	,	,		16869	0.0		0.0447	False		,,,				2504	0.0368				p.L277L		Atlas-SNP	.											.	VSX2	32	.	0			c.G831A						PASS	.	G		35,4351		0,35,2158	15.0	17.0	16.0		831	4.9	1.0	14	dbSNP_129	16	395,8197		8,379,3909	no	coding-synonymous	VSX2	NM_182894.2		8,414,6067	AA,AG,GG		4.5973,0.798,3.3133		277/362	74727367	430,12548	2193	4296	6489	SO:0001819	synonymous_variant	338917	exon5			GGCCCTGCCCAAG	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"""Homeoboxes / PRD class"""	1975	protein-coding gene	gene with protein product		142993	"""C elegans ceh-10 homeo domain-containing homolog"", ""ceh-10 homeo domain containing homolog (C. elegans)"", ""ceh-10 homeodomain containing homolog (C. elegans)"""	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.831G>A	14.37:g.74727367G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_182894	A1A4X6	Silent	SNP	ENST00000261980.2	37	CCDS9827.1																																																																																			G|0.975;A|0.025	0.025	strong		0.627	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894	
OR52M1	119772	hgsc.bcm.edu	37	11	4566711	4566711	+	Silent	SNP	C	C	T	rs2709182	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:4566711C>T	ENST00000360213.1	+	1	291	c.291C>T	c.(289-291)gaC>gaT	p.D97D		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	97						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(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGGCCTGGACGCCTGCTTGG	0.512													T|||	2190	0.4373	0.5174	0.3444	5008	,	,		21627	0.2639		0.492	False		,,,				2504	0.5174				p.D97D		Atlas-SNP	.											.	OR52M1	53	.	0			c.C291T						PASS	.	T		2223,2179	585.3+/-386.2	556,1111,534	164.0	148.0	153.0		291	4.7	1.0	11	dbSNP_100	153	4454,4142	565.0+/-388.4	1154,2146,998	no	coding-synonymous	OR52M1	NM_001004137.1		1710,3257,1532	TT,TC,CC		48.1852,49.5002,48.6306		97/318	4566711	6677,6321	2201	4298	6499	SO:0001819	synonymous_variant	119772	exon1			CCTGGACGCCTGC	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.291C>T	11.37:g.4566711C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_001004137		Silent	SNP	ENST00000360213.1	37	CCDS31353.1																																																																																			C|0.520;T|0.480	0.480	strong		0.512	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
KRT82	3888	hgsc.bcm.edu	37	12	52788928	52788928	+	Missense_Mutation	SNP	G	G	A	rs2658658	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52788928G>A	ENST00000257974.2	-	9	1450	c.1373C>T	c.(1372-1374)aCg>aTg	p.T458M	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	458	Tail.		T -> M (in dbSNP:rs2658658).			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GAGGACAGGCGTGCTGACCCC	0.642													G|||	1696	0.338658	0.3374	0.3746	5008	,	,		20091	0.0645		0.4702	False		,,,				2504	0.4622				p.T458M		Atlas-SNP	.											.	KRT82	45	.	0			c.C1373T						PASS	.	G	MET/THR	1604,2802	494.1+/-362.9	305,994,904	52.0	45.0	47.0		1373	3.8	0.7	12	dbSNP_100	47	4105,4495	557.3+/-387.0	979,2147,1174	yes	missense	KRT82	NM_033033.3	81	1284,3141,2078	AA,AG,GG		47.7326,36.4049,43.8951	probably-damaging	458/514	52788928	5709,7297	2203	4300	6503	SO:0001583	missense	3888	exon9			ACAGGCGTGCTGA	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1373C>T	12.37:g.52788928G>A	ENSP00000257974:p.Thr458Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	697	0.3191391941391941	170	0.34552845528455284	142	0.39226519337016574	32	0.055944055944055944	353	0.4656992084432718	G	10.42	1.344757	0.24426	0.364049	0.477326	ENSG00000161850	ENST00000257974	D	0.82711	-1.64	4.73	3.84	0.44239	.	0.181657	0.26967	N	0.021583	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	D	0.76494	0.999	P	0.59221	0.854	T	0.36962	-0.9726	9	0.72032	D	0.01	.	7.9321	0.29907	0.191:0.0:0.809:0.0	rs2658658;rs3741733;rs17715642;rs52836177;rs57500516;rs2658658	458	Q9NSB4	KRT82_HUMAN	M	458	ENSP00000257974:T458M	ENSP00000257974:T458M	T	-	2	0	KRT82	51075195	0.030000	0.19436	0.696000	0.30242	0.028000	0.11728	2.017000	0.40981	1.137000	0.42214	-0.215000	0.12644	ACG	G|0.611;A|0.389	0.389	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
WDR66	144406	hgsc.bcm.edu	37	12	122404946	122404946	+	Missense_Mutation	SNP	C	C	T	rs146415200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122404946C>T	ENST00000288912.4	+	16	3432	c.2578C>T	c.(2578-2580)Cgc>Tgc	p.R860C	WDR66_ENST00000545752.1_3'UTR|WDR66_ENST00000397454.2_Missense_Mutation_p.R860C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	860							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)		GCTACAGAAACGCTACTTGGT	0.483													C|||	13	0.00259585	0.0	0.0043	5008	,	,		14206	0.001		0.007	False		,,,				2504	0.002				p.R860C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,NS,carcinoma,-1,1	WDR66	143	1	0			c.C2578T						PASS	.	C	CYS/ARG,CYS/ARG	8,3860		0,8,1926	110.0	111.0	111.0		2578,2578	4.6	1.0	12	dbSNP_134	111	69,8201		1,67,4067	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	180,180	1,75,5993	TT,TC,CC		0.8343,0.2068,0.6344	possibly-damaging,possibly-damaging	860/942,860/1150	122404946	77,12061	1934	4135	6069	SO:0001583	missense	144406	exon16			CAGAAACGCTACT	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.2578C>T	12.37:g.122404946C>T	ENSP00000288912:p.Arg860Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	14.97	2.695530	0.48202	0.002068	0.008343	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.56776	0.44;1.19	4.61	4.61	0.57282	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.385177	0.27415	N	0.019473	T	0.49304	0.1549	M	0.78916	2.43	0.42205	D	0.991785	P	0.52316	0.952	P	0.44561	0.453	T	0.64592	-0.6371	10	0.66056	D	0.02	.	13.2823	0.60222	0.0:0.8409:0.1591:0.0	.	860	Q8TBY9	WDR66_HUMAN	C	860	ENSP00000288912:R860C;ENSP00000380595:R860C	ENSP00000288912:R860C	R	+	1	0	WDR66	120889329	0.923000	0.31300	0.999000	0.59377	0.216000	0.24613	1.620000	0.36976	2.124000	0.65301	0.551000	0.68910	CGC	C|0.995;T|0.005	0.005	strong		0.483	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
SMOX	54498	hgsc.bcm.edu	37	20	4163302	4163302	+	Silent	SNP	A	A	G	rs1051904	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4163302A>G	ENST00000305958.4	+	5	1401	c.1176A>G	c.(1174-1176)gcA>gcG	p.A392A	SMOX_ENST00000379460.2_Silent_p.A392A|SMOX_ENST00000278795.3_Silent_p.A339A|SMOX_ENST00000346595.2_Intron|SMOX_ENST00000339123.6_Silent_p.A339A	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	392					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)	AGGACGAAGCAGAGAGCCACA	0.597													G|||	2551	0.509385	0.4448	0.6023	5008	,	,		17731	0.4345		0.67	False		,,,				2504	0.4427				p.A392A		Atlas-SNP	.											.	SMOX	119	.	0			c.A1176G						PASS	.	G	,,,	2170,2236	592.6+/-387.8	525,1120,558	128.0	115.0	120.0		1176,1017,,1017	-11.0	0.1	20	dbSNP_86	120	5753,2847	448.1+/-361.7	1941,1871,488	yes	coding-synonymous,coding-synonymous,intron,coding-synonymous	SMOX	NM_175839.1,NM_175840.1,NM_175841.1,NM_175842.1	,,,	2466,2991,1046	GG,GA,AA		33.1047,49.251,39.082	,,,	392/556,339/503,,339/533	4163302	7923,5083	2203	4300	6503	SO:0001819	synonymous_variant	54498	exon5			CGAAGCAGAGAGC	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.1176A>G	20.37:g.4163302A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	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																																																																																			A|0.432;G|0.568	0.568	strong		0.597	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842	
RFPL3	10738	hgsc.bcm.edu	37	22	32754306	32754306	+	Missense_Mutation	SNP	T	T	C	rs16987625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32754306T>C	ENST00000249007.4	+	1	453	c.248T>C	c.(247-249)aTg>aCg	p.M83T	RFPL3_ENST00000397468.1_Missense_Mutation_p.M54T|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.M54T	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	83			M -> T (in dbSNP:rs16987625).				zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGCTGTTCCATGGTCTCTCAG	0.532													t|||	730	0.145767	0.0303	0.0908	5008	,	,		19526	0.4583		0.0408	False		,,,				2504	0.1268				p.M83T		Atlas-SNP	.											.	RFPL3	91	.	0			c.T248C						PASS	.	T	THR/MET,THR/MET	203,4203	127.0+/-164.0	9,185,2009	130.0	121.0	124.0		248,161	-1.7	0.0	22	dbSNP_123	124	474,8126	139.5+/-196.2	11,452,3837	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	81,81	20,637,5846	CC,CT,TT		5.5116,4.6074,5.2053	benign,benign	83/318,54/289	32754306	677,12329	2203	4300	6503	SO:0001583	missense	10738	exon1			GTTCCATGGTCTC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.248T>C	22.37:g.32754306T>C	ENSP00000249007:p.Met83Thr	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	208	104	0.5	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	341	0.15613553113553114	10	0.02032520325203252	37	0.10220994475138122	260	0.45454545454545453	34	0.044854881266490766	T	0.005	-2.141191	0.00332	0.046074	0.055116	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.21932	1.98;1.98;1.98	0.851	-1.7	0.08159	Zinc finger, RING/FYVE/PHD-type (1);RDM domain, Ret finger protein-like (1);	.	.	.	.	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	8	0.20519	T	0.43	.	2.4356	0.04482	0.2332:0.2312:0.0:0.5355	rs16987625;rs52810165;rs56897624;rs16987625	83	O75679	RFPL3_HUMAN	T	54;83;54	ENSP00000380609:M54T;ENSP00000249007:M83T;ENSP00000371520:M54T	ENSP00000249007:M83T	M	+	2	0	RFPL3	31084306	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.115000	0.10741	-2.354000	0.00614	-1.366000	0.01203	ATG	T|0.910;C|0.090	0.090	strong		0.532	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
PDXDC1	23042	hgsc.bcm.edu	37	16	15127249	15127249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15127249A>G	ENST00000396410.4	+	19	1902	c.1805A>G	c.(1804-1806)aAc>aGc	p.N602S	PDXDC1_ENST00000447912.2_Missense_Mutation_p.N511S|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Missense_Mutation_p.N574S|PDXDC1_ENST00000569715.1_Missense_Mutation_p.N575S|PDXDC1_ENST00000563679.1_Missense_Mutation_p.N620S|PDXDC1_ENST00000325823.7_Missense_Mutation_p.N587S	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	602					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						ATAGAGGAGAACTCGAGGGTC	0.572																																					p.N602S		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A1805G						PASS	.						120.0	112.0	115.0					16																	15127249		2197	4300	6497	SO:0001583	missense	23042	exon19			AGGAGAACTCGAG	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.1805A>G	16.37:g.15127249A>G	ENSP00000379691:p.Asn602Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	A	9.764	1.170997	0.21621	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.83	5.83	0.93111	.	0.077261	0.85682	D	0.000000	T	0.54806	0.1881	N	0.17631	0.505	0.80722	D	1	B;B;B;B	0.26400	0.021;0.148;0.021;0.037	B;B;B;B	0.23574	0.029;0.047;0.029;0.029	T	0.52902	-0.8513	10	0.12103	T	0.63	-25.0955	15.3837	0.74681	1.0:0.0:0.0:0.0	.	574;511;574;602	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	S	587;511;602;574	ENSP00000322807:N587S;ENSP00000400310:N511S;ENSP00000379691:N602S;ENSP00000391147:N574S	ENSP00000322807:N587S	N	+	2	0	PDXDC1	15034750	1.000000	0.71417	0.994000	0.49952	0.218000	0.24690	4.530000	0.60595	2.231000	0.72958	0.459000	0.35465	AAC	.	.	none		0.572	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
ZNF623	9831	hgsc.bcm.edu	37	8	144732450	144732450	+	Silent	SNP	G	G	A	rs3750204	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144732450G>A	ENST00000501748.2	+	1	497	c.408G>A	c.(406-408)tcG>tcA	p.S136S	ZNF623_ENST00000458270.2_Silent_p.S96S|ZNF623_ENST00000526926.1_Silent_p.S96S	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	136					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.S136S(1)		endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CGTTTAATTCGGACCTAGTTA	0.483													g|||	1545	0.308506	0.3563	0.3141	5008	,	,		23243	0.3651		0.2266	False		,,,				2504	0.2658				p.S136S		Atlas-SNP	.											ZNF623,NS,carcinoma,0,1	ZNF623	63	1	1	Substitution - coding silent(1)	stomach(1)	c.G408A						PASS	.	A	,	1402,3004	458.6+/-352.0	204,994,1005	115.0	103.0	107.0		288,408	-8.0	0.0	8	dbSNP_107	107	1917,6683	340.0+/-323.4	220,1477,2603	no	coding-synonymous,coding-synonymous	ZNF623	NM_001082480.1,NM_014789.3	,	424,2471,3608	AA,AG,GG		22.2907,31.8202,25.519	,	96/497,136/537	144732450	3319,9687	2203	4300	6503	SO:0001819	synonymous_variant	9831	exon1			TAATTCGGACCTA	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.408G>A	8.37:g.144732450G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_014789	A4FU80|B4DGP3|E7ENV5	Silent	SNP	ENST00000501748.2	37	CCDS34957.1																																																																																			G|0.722;A|0.278	0.278	strong		0.483	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
SETD5	55209	hgsc.bcm.edu	37	3	9517369	9517369	+	Missense_Mutation	SNP	C	C	T	rs11542009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:9517369C>T	ENST00000406341.1	+	22	4113	c.3923C>T	c.(3922-3924)aCa>aTa	p.T1308I	SETD5_ENST00000402466.1_Missense_Mutation_p.T1210I|SETD5_ENST00000407969.1_Missense_Mutation_p.T1327I|SETD5_ENST00000402198.1_Missense_Mutation_p.T1308I|SETD5_ENST00000302463.6_Missense_Mutation_p.T1210I			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1308	Ser-rich.		T -> I (in dbSNP:rs11542009).							NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CCTGTGTCCACAGACTCGTTG	0.567													C|||	197	0.0393371	0.0098	0.0533	5008	,	,		18375	0.001		0.0875	False		,,,				2504	0.0593				p.T1308I		Atlas-SNP	.											.	SETD5	210	.	0			c.C3923T						PASS	.	C	ILE/THR	104,3712		1,102,1805	44.0	44.0	44.0		3923	5.2	1.0	3	dbSNP_120	44	904,7346		48,808,3269	yes	missense	SETD5	NM_001080517.1	89	49,910,5074	TT,TC,CC		10.9576,2.7254,8.3541	possibly-damaging	1308/1443	9517369	1008,11058	1908	4125	6033	SO:0001583	missense	55209	exon23			TGTCCACAGACTC	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.3923C>T	3.37:g.9517369C>T	ENSP00000383939:p.Thr1308Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	99	0.04532967032967033	6	0.012195121951219513	23	0.06353591160220995	1	0.0017482517482517483	69	0.09102902374670185	C	16.85	3.236147	0.58886	0.027254	0.109576	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.93307	-2.86;-3.2;-2.86;-2.85;-3.2	5.23	5.23	0.72850	.	0.163740	0.42964	D	0.000636	T	0.17874	0.0429	N	0.19112	0.55	0.36809	D	0.885795	P;P	0.48294	0.908;0.689	P;B	0.46543	0.52;0.242	T	0.66697	-0.5858	10	0.41790	T	0.15	-11.7016	12.5086	0.55995	0.0:0.9233:0.0:0.0767	rs11542009	1210;1308	Q9C0A6-3;Q9C0A6	.;SETD5_HUMAN	I	1308;1210;1308;1327;1210	ENSP00000385852:T1308I;ENSP00000384429:T1210I;ENSP00000383939:T1308I;ENSP00000384114:T1327I;ENSP00000302028:T1210I	ENSP00000302028:T1210I	T	+	2	0	SETD5	9492369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.376000	0.52417	2.586000	0.87340	0.591000	0.81541	ACA	T|0.068;G|0.000;C|0.932	0.068	strong		0.567	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
CC2D1B	200014	hgsc.bcm.edu	37	1	52828384	52828384	+	Missense_Mutation	SNP	A	A	G	rs11555349	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:52828384A>G	ENST00000371586.2	-	3	242	c.104T>C	c.(103-105)aTg>aCg	p.M35T	CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000460261.1_5'Flank|CC2D1B_ENST00000284376.3_Missense_Mutation_p.M35T	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	35			M -> T (in dbSNP:rs11555349).			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)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						GCCCAGCAGCATGTCCTCAGG	0.577													A|||	362	0.0722843	0.1369	0.0418	5008	,	,		20658	0.003		0.0507	False		,,,				2504	0.1002				p.M35T		Atlas-SNP	.											.	CC2D1B	73	.	0			c.T104C						PASS	.	A	THR/MET	523,3883	239.6+/-250.7	26,471,1706	143.0	142.0	143.0		104	4.8	1.0	1	dbSNP_120	143	466,8134	138.4+/-195.2	12,442,3846	yes	missense	CC2D1B	NM_032449.2	81	38,913,5552	GG,GA,AA		5.4186,11.8702,7.6042	benign	35/859	52828384	989,12017	2203	4300	6503	SO:0001583	missense	200014	exon3			AGCAGCATGTCCT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.104T>C	1.37:g.52828384A>G	ENSP00000360642:p.Met35Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	134	0.06135531135531135	78	0.15853658536585366	14	0.03867403314917127	1	0.0017482517482517483	41	0.05408970976253298	A	14.90	2.673409	0.47781	0.118702	0.054186	ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371575	T;T	0.22945	1.93;1.93	4.85	4.85	0.62838	.	0.204155	0.47455	D	0.000235	T	0.00109	0.0003	M	0.62723	1.935	0.09310	P	1.0	P	0.36282	0.546	B	0.26770	0.073	T	0.10730	-1.0617	9	0.72032	D	0.01	-9.6858	11.9234	0.52806	1.0:0.0:0.0:0.0	rs11555349;rs60350082	35	Q5T0F9	C2D1B_HUMAN	T	35	ENSP00000360642:M35T;ENSP00000284376:M35T	ENSP00000284376:M35T	M	-	2	0	CC2D1B	52600972	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.201000	0.65163	2.028000	0.59812	0.533000	0.62120	ATG	A|0.928;G|0.072	0.072	strong		0.577	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
VWA3A	146177	hgsc.bcm.edu	37	16	22157582	22157582	+	Missense_Mutation	SNP	C	C	A	rs61744122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:22157582C>A	ENST00000389398.5	+	27	2852	c.2756C>A	c.(2755-2757)aCg>aAg	p.T919K	VWA3A_ENST00000563755.1_5'Flank|VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	919						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		ATCCAGTGGACGCCCAGGGAG	0.567													C|||	130	0.0259585	0.0015	0.0259	5008	,	,		18179	0.0		0.0417	False		,,,				2504	0.0695				p.T919K		Atlas-SNP	.											.	VWA3A	115	.	0			c.C2756A						PASS	.	C	LYS/THR	25,4175		0,25,2075	79.0	82.0	81.0		2756	2.8	0.8	16	dbSNP_129	81	318,8154		9,300,3927	yes	missense	VWA3A	NM_173615.3	78	9,325,6002	AA,AC,CC		3.7535,0.5952,2.7068	benign	919/1185	22157582	343,12329	2100	4236	6336	SO:0001583	missense	146177	exon27			AGTGGACGCCCAG	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2756C>A	16.37:g.22157582C>A	ENSP00000374049:p.Thr919Lys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	48	0.02197802197802198	0	0.0	9	0.024861878453038673	0	0.0	39	0.051451187335092345	C	10.05	1.244947	0.22796	0.005952	0.037535	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.12147	2.71	5.11	2.85	0.33270	.	0.404912	0.26457	N	0.024266	T	0.01254	0.0041	L	0.55103	1.725	0.54753	D	0.999985	P	0.45957	0.869	B	0.35240	0.198	T	0.34800	-0.9814	10	0.13853	T	0.58	.	5.6832	0.17788	0.3098:0.5911:0.0:0.0991	rs61744122	919	A6NCI4	VWA3A_HUMAN	K	919;542	ENSP00000374049:T919K	ENSP00000299840:T542K	T	+	2	0	VWA3A	22065083	0.812000	0.29077	0.843000	0.33291	0.274000	0.26718	1.557000	0.36299	1.265000	0.44215	0.655000	0.94253	ACG	C|0.974;A|0.026	0.026	strong		0.567	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
VSTM1	284415	hgsc.bcm.edu	37	19	54545186	54545186	+	Silent	SNP	C	C	T	rs73058793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54545186C>T	ENST00000338372.2	-	7	712	c.537G>A	c.(535-537)ccG>ccA	p.P179P	VSTM1_ENST00000425006.2_3'UTR|VSTM1_ENST00000376626.1_Silent_p.P148P|VSTM1_ENST00000366170.2_Silent_p.P91P	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	179					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CCTCCTGCTCCGGAAGTTTGG	0.493													C|||	907	0.18111	0.1384	0.2896	5008	,	,		17447	0.0645		0.331	False		,,,				2504	0.1278				p.P179P		Atlas-SNP	.											.	VSTM1	30	.	0			c.G537A						PASS	.	C		745,3661	304.1+/-288.3	66,613,1524	55.0	56.0	55.0		537	-6.1	0.0	19	dbSNP_130	55	2663,5937	426.5+/-355.3	400,1863,2037	no	coding-synonymous	VSTM1	NM_198481.3		466,2476,3561	TT,TC,CC		30.9651,16.9088,26.2033		179/237	54545186	3408,9598	2203	4300	6503	SO:0001819	synonymous_variant	284415	exon7			CTGCTCCGGAAGT	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.537G>A	19.37:g.54545186C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	37	CCDS12872.1																																																																																			C|0.755;T|0.245	0.245	strong		0.493	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	
OR2S2	56656	hgsc.bcm.edu	37	9	35958047	35958047	+	Missense_Mutation	SNP	T	T	C	rs2233558	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:35958047T>C	ENST00000341959.2	-	1	104	c.49A>G	c.(49-51)Agg>Ggg	p.R17G		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	17			R -> G (in dbSNP:rs2233558).		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(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GCAGAGAGCCTCAGGAGAACG	0.537													C|||	1729	0.345248	0.4939	0.2968	5008	,	,		21441	0.2996		0.2793	False		,,,				2504	0.2935				p.R17G	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.A49G						PASS	.	C	GLY/ARG	2032,2374	599.7+/-389.3	448,1136,619	49.0	48.0	48.0		49	4.1	1.0	9	dbSNP_98	48	2830,5770	665.2+/-402.2	508,1814,1978	yes	missense	OR2S2	NM_019897.2	125	956,2950,2597	CC,CT,TT		32.907,46.1189,37.3827	benign	17/320	35958047	4862,8144	2203	4300	6503	SO:0001583	missense	56656	exon1			AGAGCCTCAGGAG	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.49A>G	9.37:g.35958047T>C	ENSP00000344040:p.Arg17Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	760	0.34798534798534797	262	0.532520325203252	124	0.3425414364640884	164	0.2867132867132867	210	0.2770448548812665	C	1.590	-0.529238	0.04112	0.461189	0.32907	ENSG00000122718	ENST00000341959	T	0.00198	8.57	4.07	4.07	0.47477	.	0.000000	0.49916	N	0.000121	T	0.00012	0.0000	N	0.00007	-3.175	0.41380	P	0.012454999999999994	B	0.02656	0.0	B	0.01281	0.0	T	0.17531	-1.0366	9	0.02654	T	1	.	10.395	0.44196	0.0:0.9022:0.0:0.0978	rs2233558;rs3739615;rs2233558	17	Q9NQN1	OR2S1_HUMAN	G	17	ENSP00000344040:R17G	ENSP00000344040:R17G	R	-	1	2	OR2S2	35948047	0.841000	0.29509	0.988000	0.46212	0.430000	0.31655	2.444000	0.44890	1.308000	0.44962	-0.119000	0.15052	AGG	T|0.637;C|0.363	0.363	strong		0.537	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
TRIM15	89870	hgsc.bcm.edu	37	6	30131546	30131546	+	Missense_Mutation	SNP	A	A	G	rs17194460	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30131546A>G	ENST00000376694.4	+	1	554	c.85A>G	c.(85-87)Att>Gtt	p.I29V	TRIM10_ENST00000449742.2_5'Flank|TRIM10_ENST00000376704.3_5'Flank|TRIM15_ENST00000376688.1_Missense_Mutation_p.I29V	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	29			I -> V (in dbSNP:rs17194460). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:8304341, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						TGCGGTGACCATTCCCTGTGG	0.667													G|||	1195	0.238618	0.0787	0.1383	5008	,	,		16933	0.3929		0.2038	False		,,,				2504	0.4029				p.I29V		Atlas-SNP	.											.	TRIM15	34	.	0			c.A85G						PASS	.	G	VAL/ILE	283,2737		11,261,1238	62.0	54.0	57.0		85	0.2	0.0	6	dbSNP_123	57	1008,4410		96,816,1797	yes	missense	TRIM15	NM_033229.2	29	107,1077,3035	GG,GA,AA		18.6047,9.3709,15.2998	benign	29/466	30131546	1291,7147	1510	2709	4219	SO:0001583	missense	89870	exon1			GTGACCATTCCCT	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.85A>G	6.37:g.30131546A>G	ENSP00000365884:p.Ile29Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Missense_Mutation	SNP	ENST00000376694.4	37	CCDS4677.1	450	0.20604395604395603	34	0.06910569105691057	59	0.16298342541436464	203	0.3548951048951049	154	0.20316622691292877	G	2.296	-0.361285	0.05103	0.093709	0.186047	ENSG00000204610	ENST00000376694;ENST00000376688	T;T	0.17370	2.28;2.28	4.63	0.228	0.15364	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	1.605840	0.03977	N	0.292689	T	0.02533	0.0077	N	0.20328	0.56	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39418	-0.9615	9	0.25106	T	0.35	.	0.9083	0.01289	0.1768:0.2678:0.2831:0.2723	rs17194460;rs58384720	29	Q9C019	TRI15_HUMAN	V	29	ENSP00000365884:I29V;ENSP00000365878:I29V	ENSP00000365878:I29V	I	+	1	0	TRIM15	30239525	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.785000	0.04628	-0.096000	0.12329	-0.380000	0.06706	ATT	A|0.829;G|0.171	0.171	strong		0.667	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
WASL	8976	hgsc.bcm.edu	37	7	123388732	123388732	+	Silent	SNP	G	G	A	rs1054706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	39	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	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	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609192	32609192	+	Missense_Mutation	SNP	A	A	G	rs1142323	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32609192A>G	ENST00000343139.5	+	2	290	c.188A>G	c.(187-189)gAg>gGg	p.E63G	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.E63G|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.E63G	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	63	Alpha-1.		G -> E (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06, allele DQA1*01:07, allele DQA1*02:01, allele DQA1*03:01, allele DQA1*03:02 and allele DQA1*03:03; dbSNP:rs1142323).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GTGGACCTGGAGAGGAAGGAG	0.517													.|||	1419	0.283347	0.3275	0.3487	5008	,	,		13238	0.246		0.3002	False		,,,				2504	0.1984				p.E63G		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A188G						PASS	.	A	GLY/GLU	1153,3243		338,477,1383	112.0	96.0	101.0		188	1.4	0.0	6	dbSNP_86	101	2081,6451		569,943,2754	no	missense	HLA-DQA1	NM_002122.3	98	907,1420,4137	GG,GA,AA		24.3905,26.2284,25.0155	benign	63/256	32609192	3234,9694	2198	4266	6464	SO:0001583	missense	3117	exon2			ACCTGGAGAGGAA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.188A>G	6.37:g.32609192A>G	ENSP00000339398:p.Glu63Gly	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	30	25	0.833333	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	645|645	0.29532967032967034|0.29532967032967034	162|162	0.32926829268292684|0.32926829268292684	134|134	0.3701657458563536|0.3701657458563536	133|133	0.23251748251748253|0.23251748251748253	216|216	0.2849604221635884|0.2849604221635884	.|.	0.083|0.083	-1.179542|-1.179542	0.01633|0.01633	0.262284|0.262284	0.243905|0.243905	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.00808|.	5.67;5.67;5.67;5.67|.	3.84|3.84	1.4|1.4	0.22301|0.22301	.|.	0.860258|.	0.10150|.	U|.	0.709694|.	T|T	0.18676|0.18676	0.0448|0.0448	N|N	0.25825|0.25825	0.765|0.765	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.13145|.	0.007;0.001|.	B;B|.	0.14023|.	0.01;0.002|.	T|T	0.09975|0.09975	-1.0650|-1.0650	9|4	0.25751|.	T|.	0.34|.	.|.	9.286|9.286	0.37758|0.37758	0.8976:0.0:0.1024:0.0|0.8976:0.0:0.1024:0.0	rs1142323;rs3205985;rs9272691;rs12722053;rs17840125;rs36219700|rs1142323;rs3205985;rs9272691;rs12722053;rs17840125;rs36219700	69;63|.	Q59F33;G4XQK2|.	.;.|.	G|G	63|36	ENSP00000339398:E63G;ENSP00000378767:E63G;ENSP00000437302:E63G;ENSP00000364087:E63G|.	ENSP00000339398:E63G|.	E|R	+|+	2|1	0|2	HLA-DQA1|HLA-DQA1	32717170|32717170	0.011000|0.011000	0.17503|0.17503	0.013000|0.013000	0.15412|0.15412	0.002000|0.002000	0.02628|0.02628	0.495000|0.495000	0.22483|0.22483	0.191000|0.191000	0.20236|0.20236	-1.271000|-1.271000	0.01417|0.01417	GAG|AGA	A|0.709;G|0.291	0.291	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
MAP2K3	5606	hgsc.bcm.edu	37	17	21207834	21207834	+	Missense_Mutation	SNP	C	C	T	rs58609466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:21207834C>T	ENST00000342679.4	+	8	914	c.665C>T	c.(664-666)aCg>aTg	p.T222M	MAP2K3_ENST00000316920.6_Missense_Mutation_p.T193M|MAP2K3_ENST00000361818.5_Missense_Mutation_p.T193M	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	222	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|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)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GTGGCCAAGACGATGGATGCC	0.592																																					p.T222M		Atlas-SNP	.											MAP2K3_ENST00000316920,NS,haematopoietic_neoplasm,-1,3	MAP2K3	135	3	0			c.C665T						PASS	.						238.0	173.0	195.0					17																	21207834		2203	4300	6503	SO:0001583	missense	5606	exon8			CCAAGACGATGGA	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.665C>T	17.37:g.21207834C>T	ENSP00000345083:p.Thr222Met	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	243	116	0.477366	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	656	0.30036630036630035	185	0.37601626016260165	93	0.2569060773480663	167	0.291958041958042	211	0.2783641160949868	C	26.4	4.735409	0.89482	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.68025	-0.3;-0.3	4.87	4.87	0.63330	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	0.64402	D	0.000001	T	0.00012	0.0000	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00920	-1.1514	10	0.72032	D	0.01	-22.3871	18.0327	0.89290	0.0:1.0:0.0:0.0	rs58609466	222	P46734	MP2K3_HUMAN	M	222;193;193;226	ENSP00000345083:T222M;ENSP00000355081:T193M	ENSP00000319139:T226M	T	+	2	0	MAP2K3	21148427	1.000000	0.71417	0.971000	0.41717	0.990000	0.78478	7.677000	0.84024	2.242000	0.73789	0.563000	0.77884	ACG	C|0.733;T|0.267	0.267	strong		0.592	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
OPA1	4976	hgsc.bcm.edu	37	3	193334991	193334991	+	Missense_Mutation	SNP	G	G	A	rs7624750	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:193334991G>A	ENST00000392438.3	+	4	707	c.473G>A	c.(472-474)aGt>aAt	p.S158N	OPA1_ENST00000361150.2_Intron|OPA1_ENST00000361908.3_Missense_Mutation_p.S158N|OPA1-AS1_ENST00000444085.1_RNA|OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361715.2_Intron|OPA1-AS1_ENST00000433105.1_RNA|OPA1_ENST00000361510.2_Missense_Mutation_p.S158N|OPA1_ENST00000361828.2_Missense_Mutation_p.S158N	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	158			S -> N (in dbSNP:rs7624750). {ECO:0000269|PubMed:11440988, ECO:0000269|PubMed:11440989, ECO:0000269|PubMed:12036970, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15948788, ECO:0000269|PubMed:16617242, ECO:0000269|PubMed:9628581}.		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)		GCCCTTCCTAGTTCAGAAGAC	0.338													A|||	2344	0.468051	0.5847	0.4683	5008	,	,		16978	0.3681		0.4573	False		,,,				2504	0.4243				p.S158N		Atlas-SNP	.											OPA1,NS,carcinoma,0,1	OPA1	79	1	0			c.G473A						PASS	.	A	ASN/SER,,,,ASN/SER,,ASN/SER,ASN/SER	2474,1930	539.4+/-375.3	696,1082,424	57.0	62.0	60.0		473,,,,473,,473,473	3.6	1.0	3	dbSNP_116	60	3988,4610	596.8+/-393.7	906,2176,1217	yes	missense,intron,intron,intron,missense,intron,missense,missense	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	46,,,,46,,46,46	1602,3258,1641	AA,AG,GG		46.3829,43.8238,49.7	benign,,,,benign,,benign,benign	158/961,,,,158/979,,158/998,158/1016	193334991	6462,6540	2202	4299	6501	SO:0001583	missense	4976	exon4			TTCCTAGTTCAGA	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.473G>A	3.37:g.193334991G>A	ENSP00000376233:p.Ser158Asn	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	276	152	0.550725	NM_130836	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	997|997	0.4565018315018315|0.4565018315018315	297|297	0.6036585365853658|0.6036585365853658	157|157	0.43370165745856354|0.43370165745856354	194|194	0.33916083916083917|0.33916083916083917	349|349	0.4604221635883905|0.4604221635883905	A|A	5.124|5.124	0.208417|0.208417	0.09757|0.09757	0.561762|0.561762	0.463829|0.463829	ENSG00000198836|ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361828;ENST00000419435;ENST00000392436|ENST00000434811	D;D;D;D;T;T|.	0.92965|.	-3.1;-3.14;-3.14;-3.13;1.97;-0.86|.	6.05|6.05	3.64|3.64	0.41730|0.41730	.|.	0.424265|.	0.28766|.	N|.	0.014207|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	P|P	0.999999999863361|0.999999999863361	B;B;B;B|.	0.06786|.	0.0;0.0;0.001;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.001;0.0|.	T|T	0.44907|0.44907	-0.9297|-0.9297	9|4	0.16420|.	T|.	0.52|.	-8.8622|-8.8622	6.4094|6.4094	0.21682|0.21682	0.7267:0.1327:0.1406:0.0|0.7267:0.1327:0.1406:0.0	rs7624750;rs52806158;rs58655170;rs7624750|rs7624750;rs52806158;rs58655170;rs7624750	158;158;158;158|.	O60313;E5KLJ6;E5KLJ7;E5KLJ5|.	OPA1_HUMAN;.;.;.|.	N|I	158;158;158;158;34;158|58	ENSP00000354681:S158N;ENSP00000376233:S158N;ENSP00000355324:S158N;ENSP00000354429:S158N;ENSP00000399877:S34N;ENSP00000376231:S158N|.	ENSP00000355324:S158N|.	S|V	+|+	2|1	0|0	OPA1|OPA1	194817685|194817685	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	3.435000|3.435000	0.52849|0.52849	0.166000|0.166000	0.19597|0.19597	-0.269000|-0.269000	0.10298|0.10298	AGT|GTT	G|0.517;A|0.483	0.483	strong		0.338	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
SCUBE1	80274	hgsc.bcm.edu	37	22	43610207	43610207	+	Missense_Mutation	SNP	A	A	G	rs138993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43610207A>G	ENST00000360835.4	-	16	2068	c.1942T>C	c.(1942-1944)Tca>Cca	p.S648P	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	648			S -> P (in dbSNP:rs138993). {ECO:0000269|PubMed:12270931}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GGCATACATGACACACACTGG	0.642													G|||	2176	0.434505	0.3797	0.5865	5008	,	,		14946	0.0784		0.6789	False		,,,				2504	0.5164				p.S648P		Atlas-SNP	.											SCUBE1,NS,carcinoma,0,1	SCUBE1	105	1	0			c.T1942C						PASS	.		PRO/SER	1954,2452	620.6+/-393.6	448,1058,697	79.0	59.0	66.0		1942	3.8	1.0	22	dbSNP_78	66	5931,2669	428.4+/-355.9	2033,1865,402	yes	missense	SCUBE1	NM_173050.3	74	2481,2923,1099	GG,GA,AA		31.0349,44.3486,39.3741	benign	648/989	43610207	7885,5121	2203	4300	6503	SO:0001583	missense	80274	exon16			TACATGACACACA		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1942T>C	22.37:g.43610207A>G	ENSP00000354080:p.Ser648Pro	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	952	0.4358974358974359	185	0.37601626016260165	219	0.6049723756906077	55	0.09615384615384616	493	0.6503957783641161	g	1.626	-0.520336	0.04171	0.443486	0.689651	ENSG00000159307	ENST00000360835;ENST00000381243	T	0.12255	2.7	3.81	3.81	0.43845	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.160270	0.56097	N	0.000023	T	0.00012	0.0000	N	0.01003	-1.06	0.09310	P	0.9999999999999984	B	0.02656	0.0	B	0.01281	0.0	T	0.25152	-1.0140	9	0.07813	T	0.8	.	11.924	0.52808	0.0866:0.0:0.9134:0.0	rs138993;rs60843257;rs138993	648	Q8IWY4	SCUB1_HUMAN	P	648;278	ENSP00000354080:S648P	ENSP00000354080:S648P	S	-	1	0	SCUBE1	41940151	1.000000	0.71417	0.976000	0.42696	0.167000	0.22549	4.576000	0.60915	0.958000	0.37956	-0.246000	0.11932	TCA	A|0.489;G|0.511	0.511	strong		0.642	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
FAM187B	148109	hgsc.bcm.edu	37	19	35718891	35718891	+	Nonsense_Mutation	SNP	C	C	T	rs35001809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	128	49	0.382812	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	
CRACR2A	84766	hgsc.bcm.edu	37	12	3724583	3724583	+	Missense_Mutation	SNP	T	T	C	rs11062745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:3724583T>C	ENST00000440314.2	-	20	2607	c.2134A>G	c.(2134-2136)Aca>Gca	p.T712A		NM_001144958.1	NP_001138430.1	Q9BSW2	EFC4B_HUMAN		0					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)			TCTCTCACTGTGTCTTCTTGC	0.557													T|||	452	0.0902556	0.0393	0.1023	5008	,	,		19250	0.0347		0.163	False		,,,				2504	0.1329				p.T712A		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.A2134G						PASS	.	T	ALA/THR	70,1314		3,64,625	276.0	217.0	235.0		2134	4.6	0.9	12	dbSNP_120	235	487,2695		36,415,1140	yes	missense	EFCAB4B	NM_001144958.1	58	39,479,1765	CC,CT,TT		15.3048,5.0578,12.1989	benign	712/732	3724583	557,4009	692	1591	2283	SO:0001583	missense	84766	exon20			TCACTGTGTCTTC																												ENST00000440314.2:c.2134A>G	12.37:g.3724583T>C	ENSP00000409382:p.Thr712Ala	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	184	93	0.505435	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	37	CCDS44803.1	191	0.08745421245421245	10	0.02032520325203252	42	0.11602209944751381	12	0.02097902097902098	127	0.16754617414248021	T	7.189	0.591211	0.13812	0.050578	0.153048	ENSG00000130038	ENST00000440314	T	0.61040	0.14	4.56	4.56	0.56223	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999999956	B	0.32507	0.373	B	0.32289	0.143	T	0.06789	-1.0807	7	0.09843	T	0.71	.	10.2464	0.43343	0.0:0.0:0.0:1.0	rs11062745;rs17697498;rs58756036;rs11062745	712	Q9BSW2-2	.	A	712	ENSP00000409382:T712A	ENSP00000409382:T712A	T	-	1	0	EFCAB4B	3594844	0.997000	0.39634	0.945000	0.38365	0.804000	0.45430	2.427000	0.44740	1.905000	0.55150	0.533000	0.62120	ACA	T|0.925;C|0.075	0.075	strong		0.557	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2		
MOG	4340	hgsc.bcm.edu	37	6	29634003	29634003	+	Missense_Mutation	SNP	G	G	C	rs2857766	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29634003G>C	ENST00000376917.3	+	3	740	c.511G>C	c.(511-513)Gtt>Ctt	p.V171L	MOG_ENST00000490427.1_Missense_Mutation_p.V55L|MOG_ENST00000533330.2_3'UTR|MOG_ENST00000483013.1_Missense_Mutation_p.V55L|MOG_ENST00000376888.2_Missense_Mutation_p.V55L|MOG_ENST00000431798.2_Missense_Mutation_p.V171L|MOG_ENST00000396704.3_Missense_Mutation_p.V171L|MOG_ENST00000416766.2_Intron|MOG_ENST00000376898.3_Missense_Mutation_p.V171L|MOG_ENST00000396701.2_Missense_Mutation_p.V171L|MOG_ENST00000376902.3_3'UTR|MOG_ENST00000376894.4_Missense_Mutation_p.V171L|MOG_ENST00000494692.1_Missense_Mutation_p.V171L|MOG_ENST00000376891.4_Missense_Mutation_p.V171L	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	171			V -> L (in dbSNP:rs2857766). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:8530032}.		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						GCAGATCACTGTTGGCCTCAT	0.547													G|||	904	0.180511	0.1203	0.1902	5008	,	,		19031	0.2788		0.2425	False		,,,				2504	0.09				p.V171L		Atlas-SNP	.											.	MOG	47	.	0			c.G511C						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	368,2654		20,328,1163	253.0	222.0	233.0		511,511,163,511,511,511,511,511,163	0.6	0.3	6	dbSNP_100	233	1233,4185		143,947,1619	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	MOG	NM_001008228.2,NM_001008229.2,NM_001170418.1,NM_002433.4,NM_206809.3,NM_206810.3,NM_206811.3,NM_206812.3,NM_206814.5	32,32,32,32,32,32,32,32,32	163,1275,2782	CC,CG,GG		22.7575,12.1774,18.9692	benign,benign,benign,benign,benign,benign,benign,benign,benign	171/225,171/207,55/109,171/253,171/248,171/214,171/230,171/209,55/132	29634003	1601,6839	1511	2709	4220	SO:0001583	missense	4340	exon3			ATCACTGTTGGCC		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.511G>C	6.37:g.29634003G>C	ENSP00000366115:p.Val171Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_001008229	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	Missense_Mutation	SNP	ENST00000376917.3	37	CCDS34370.1	460	0.21062271062271062	59	0.11991869918699187	67	0.1850828729281768	143	0.25	191	0.2519788918205805	G	10.26	1.300214	0.23650	0.121774	0.227575	ENSG00000204655	ENST00000376917;ENST00000376888;ENST00000376894;ENST00000483013;ENST00000490427;ENST00000376891;ENST00000376898;ENST00000431798;ENST00000396701;ENST00000494692;ENST00000396704	T;T;T;T;T;T;T;T;T;T;T	0.37752	3.5;1.29;3.5;1.21;1.18;3.52;3.56;3.55;3.52;3.5;3.51	5.71	0.628	0.17681	.	0.326843	0.22794	N	0.055580	T	0.11410	0.0278	L	0.46157	1.445	0.58432	P	5.999999999950489E-6	B;B;B;B;B;B;B;P;B;B;B;B	0.35656	0.002;0.011;0.002;0.113;0.214;0.002;0.225;0.514;0.004;0.113;0.001;0.011	B;B;B;B;B;B;B;B;B;B;B;B	0.31946	0.004;0.011;0.019;0.072;0.138;0.024;0.048;0.11;0.012;0.066;0.003;0.005	T	0.05566	-1.0877	9	0.51188	T	0.08	.	5.4211	0.16400	0.2439:0.2752:0.4809:0.0	rs2857766;rs6910436;rs2857766	55;55;101;171;171;171;171;171;171;171;55;171	E9PG44;E9PGF0;B7Z2X8;F8W9D5;Q16653-2;Q16653-3;Q16653-6;Q16653-7;Q16653;Q16653-5;Q16653-4;Q5SUK5	.;.;.;.;.;.;.;.;MOG_HUMAN;.;.;.	L	171;55;171;55;55;171;171;171;171;171;171	ENSP00000366115:V171L;ENSP00000366085:V55L;ENSP00000366091:V171L;ENSP00000418090:V55L;ENSP00000420350:V55L;ENSP00000366088:V171L;ENSP00000366095:V171L;ENSP00000410866:V171L;ENSP00000379929:V171L;ENSP00000417405:V171L;ENSP00000379932:V171L	ENSP00000366085:V55L	V	+	1	0	MOG	29741982	0.144000	0.22641	0.295000	0.24960	0.218000	0.24690	0.286000	0.18902	0.343000	0.23821	0.655000	0.94253	GTT	G|0.810;C|0.190	0.190	strong		0.547	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433	
SCN11A	11280	hgsc.bcm.edu	37	3	38936134	38936134	+	Missense_Mutation	SNP	C	C	T	rs33985936	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38936134C>T	ENST00000302328.3	-	15	2923	c.2725G>A	c.(2725-2727)Gtc>Atc	p.V909I	SCN11A_ENST00000456224.3_Missense_Mutation_p.V909I|SCN11A_ENST00000444237.2_Missense_Mutation_p.V909I|SCN11A_ENST00000450244.1_Missense_Mutation_p.V909I	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	909			V -> I (in dbSNP:rs33985936).		cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCATGCCTGACGCCCAGGGTC	0.507													C|||	769	0.153554	0.0749	0.2248	5008	,	,		20781	0.12		0.2376	False		,,,				2504	0.1575				p.V909I		Atlas-SNP	.											.	SCN11A	296	.	0			c.G2725A						PASS	.	C	ILE/VAL	553,3853	249.3+/-256.8	30,493,1680	137.0	130.0	132.0		2725	-9.1	0.0	3	dbSNP_126	132	2108,6492	363.0+/-333.0	272,1564,2464	yes	missense	SCN11A	NM_014139.2	29	302,2057,4144	TT,TC,CC		24.5116,12.5511,20.4598	benign	909/1792	38936134	2661,10345	2203	4300	6503	SO:0001583	missense	11280	exon15			GCCTGACGCCCAG	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2725G>A	3.37:g.38936134C>T	ENSP00000307599:p.Val909Ile	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	241	154	0.639004	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	362	0.16575091575091574	41	0.08333333333333333	78	0.2154696132596685	62	0.10839160839160839	181	0.23878627968337732	C	6.773	0.511621	0.12944	0.125511	0.245116	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.53	-9.06	0.00727	Sodium ion transport-associated (1);	3.067170	0.00864	N	0.001956	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.05649	-1.0872	9	0.24483	T	0.36	.	9.7812	0.40649	0.0:0.6478:0.1818:0.1704	rs33985936;rs59878058	909	Q9UI33	SCNBA_HUMAN	I	909	ENSP00000307599:V909I;ENSP00000400945:V909I;ENSP00000416757:V909I;ENSP00000408028:V909I	ENSP00000307599:V909I	V	-	1	0	SCN11A	38911138	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.830000	0.00744	-1.817000	0.01219	-1.027000	0.02421	GTC	C|0.801;T|0.199	0.199	strong		0.507	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
ERICH1	157697	hgsc.bcm.edu	37	8	623906	623906	+	Missense_Mutation	SNP	C	C	T	rs118014343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:623906C>T	ENST00000262109.7	-	4	523	c.446G>A	c.(445-447)cGa>cAa	p.R149Q	ERICH1_ENST00000522706.1_Missense_Mutation_p.R55Q|ERICH1_ENST00000518277.1_5'UTR	NM_207332.1	NP_997215.1	Q86X53	ERIC1_HUMAN	glutamate-rich 1	149										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)	20		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		TGTGTGCTGTCGCTGAGATTT	0.353													c|||	45	0.00898562	0.0008	0.0101	5008	,	,		19959	0.0		0.0328	False		,,,				2504	0.0041				p.R149Q		Atlas-SNP	.											.	ERICH1	50	.	0			c.G446A						PASS	.	T	GLN/ARG	28,4378		0,28,2175	68.0	79.0	75.0		446	1.1	0.0	8	dbSNP_132	75	234,8366		6,222,4072	yes	missense	ERICH1	NM_207332.1	43	6,250,6247	TT,TC,CC		2.7209,0.6355,2.0145	benign	149/444	623906	262,12744	2203	4300	6503	SO:0001583	missense	157697	exon4			TGCTGTCGCTGAG		CCDS5955.1	8p23.3	2005-09-01			ENSG00000104714	ENSG00000104714			27234	protein-coding gene	gene with protein product							Standard	NM_207332		Approved		uc003wph.3	Q86X53	OTTHUMG00000129163	ENST00000262109.7:c.446G>A	8.37:g.623906C>T	ENSP00000262109:p.Arg149Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_207332	A8K2J9|Q9P063	Missense_Mutation	SNP	ENST00000262109.7	37	CCDS5955.1	28	0.01282051282051282	0	0.0	3	0.008287292817679558	0	0.0	25	0.032981530343007916	c	2.320	-0.355933	0.05138	0.006355	0.027209	ENSG00000104714	ENST00000543819;ENST00000522706;ENST00000262109	T;T	0.30182	1.54;1.56	5.98	1.06	0.20224	.	0.519305	0.20585	N	0.089450	T	0.04634	0.0126	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.002	T	0.26087	-1.0113	10	0.10636	T	0.68	-0.6134	4.1113	0.10060	0.0693:0.2391:0.3133:0.3782	.	149;149;55	B4DMI5;Q86X53;E5RHA3	.;ERIC1_HUMAN;.	Q	149;55;149	ENSP00000428635:R55Q;ENSP00000262109:R149Q	ENSP00000262109:R149Q	R	-	2	0	ERICH1	613906	0.564000	0.26602	0.002000	0.10522	0.006000	0.05464	-0.113000	0.10774	-0.082000	0.12640	-2.129000	0.00344	CGA	C|0.982;T|0.018	0.018	strong		0.353	ERICH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251228.3	NM_207332	
GAB2	9846	hgsc.bcm.edu	37	11	77936166	77936166	+	Silent	SNP	A	A	G	rs1385600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77936166A>G	ENST00000361507.4	-	5	1375	c.1290T>C	c.(1288-1290)gtT>gtC	p.V430V	GAB2_ENST00000340149.2_Silent_p.V392V|GAB2_ENST00000526030.1_5'Flank	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	61	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	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	
TNRC6A	27327	hgsc.bcm.edu	37	16	24834233	24834233	+	Silent	SNP	C	C	T	rs2303085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24834233C>T	ENST00000395799.3	+	24	5541	c.5412C>T	c.(5410-5412)caC>caT	p.H1804H	TNRC6A_ENST00000432286.2_Silent_p.H282H|TNRC6A_ENST00000315183.7_Silent_p.H1755H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1804	RRM.|Sufficient for interaction with AGO2.				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)	p.H1804H(1)		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)		GCATGCAGCACGGCCCGCTGA	0.557													c|||	1106	0.220847	0.1626	0.2637	5008	,	,		22656	0.4038		0.166	False		,,,				2504	0.137				p.H1804H		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	1	Substitution - coding silent(1)	stomach(1)	c.C5412T						PASS	.	C		692,3702	289.5+/-280.5	45,602,1550	124.0	101.0	109.0		5412	1.9	1.0	16	dbSNP_100	109	1175,7425	239.4+/-270.5	78,1019,3203	no	coding-synonymous	TNRC6A	NM_014494.2		123,1621,4753	TT,TC,CC		13.6628,15.7487,14.3682		1804/1963	24834233	1867,11127	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon24			GCAGCACGGCCCG	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.5412C>T	16.37:g.24834233C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2	506	0.2316849816849817	63	0.12804878048780488	80	0.22099447513812154	230	0.4020979020979021	133	0.17546174142480211	c	9.384	1.073739	0.20147	0.157487	0.136628	ENSG00000090905	ENST00000450465	.	.	.	5.27	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44787	-0.9305	3	.	.	.	-6.083	7.3864	0.26884	0.0:0.4108:0.0:0.5892	rs2303085;rs57489138;rs2303085	.	.	.	W	695	.	.	R	+	1	2	TNRC6A	24741734	0.979000	0.34478	1.000000	0.80357	0.993000	0.82548	0.189000	0.17037	0.338000	0.23692	-0.310000	0.09108	CGG	C|0.816;T|0.184	0.184	strong		0.557	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
SDK1	221935	hgsc.bcm.edu	37	7	4172006	4172006	+	Silent	SNP	C	C	T	rs13224870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:4172006C>T	ENST00000404826.2	+	28	4318	c.4179C>T	c.(4177-4179)tcC>tcT	p.S1393S	SDK1_ENST00000389531.3_Silent_p.S1393S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1393	Fibronectin type-III 8. {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)		GACTCACCTCCGTGCGGATAG	0.622													C|||	1226	0.244808	0.1067	0.3084	5008	,	,		17826	0.0992		0.3907	False		,,,				2504	0.3865				p.S1393S		Atlas-SNP	.											SDK1,NS,malignant_melanoma,+1,1	SDK1	361	1	0			c.C4179T						PASS	.	C		624,3782	262.5+/-264.9	43,538,1622	56.0	45.0	49.0		4179	-10.9	0.0	7	dbSNP_121	49	3494,5106	503.6+/-376.0	720,2054,1526	no	coding-synonymous	SDK1	NM_152744.3		763,2592,3148	TT,TC,CC		40.6279,14.1625,31.6623		1393/2214	4172006	4118,8888	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon28			CACCTCCGTGCGG	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.4179C>T	7.37:g.4172006C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	78	49	0.628205	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.720;T|0.280	0.280	strong		0.622	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
FAM198A	729085	hgsc.bcm.edu	37	3	43073761	43073761	+	Silent	SNP	G	G	A	rs658958	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:43073761G>A	ENST00000430121.2	+	2	101	c.6G>A	c.(4-6)gcG>gcA	p.A2A	KRBOX1_ENST00000418093.2_3'UTR|KRBOX1_ENST00000443313.1_Intron	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	2						extracellular region (GO:0005576)				endometrium(1)	1						TCTCTCAGGCGTCTTGGCTCC	0.527													G|||	2195	0.438299	0.3404	0.5331	5008	,	,		20480	0.6518		0.4066	False		,,,				2504	0.316				p.A2A		Atlas-SNP	.											FAM198A_ENST00000430121,caecum,carcinoma,0,1	FAM198A	23	1	0			c.G6A						PASS	.	G		454,930		72,310,310	27.0	26.0	27.0		6	-5.3	0.8	3	dbSNP_83	27	1298,1884		269,760,562	no	coding-synonymous	FAM198A	NM_001129908.2		341,1070,872	AA,AG,GG		40.792,32.8035,38.3706		2/576	43073761	1752,2814	692	1591	2283	SO:0001819	synonymous_variant	729085	exon2			TCAGGCGTCTTGG	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.6G>A	3.37:g.43073761G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			G|0.533;A|0.467	0.467	strong		0.527	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42368614	42368614	+	Missense_Mutation	SNP	A	A	G	rs200348657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:42368614A>G	ENST00000377601.2	+	1	312	c.200A>G	c.(199-201)cAc>cGc	p.H67R	RP11-216M21.7_ENST00000450520.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2	67										large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						GACAAGCAGCACAGGTAGCGG	0.741																																					p.H67R		Atlas-SNP	.											ANKRD20A2,NS,carcinoma,0,1	ANKRD20A2	9	1	0			c.A200G						scavenged	.						10.0	10.0	10.0					9																	42368614		2122	4050	6172	SO:0001583	missense	441430	exon1			AGCAGCACAGGTA		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641	ENST00000377601.2:c.200A>G	9.37:g.42368614A>G	ENSP00000366826:p.His67Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	160	18	0.1125	NM_001012421		Missense_Mutation	SNP	ENST00000377601.2	37	CCDS35028.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.941398	0.34283	.	.	ENSG00000183148	ENST00000377601	T	0.52057	0.68	1.23	1.23	0.21249	Ankyrin repeat-containing domain (8);	.	.	.	.	T	0.39253	0.1071	N	0.10664	0.02	0.09310	N	1	P;P	0.44877	0.845;0.65	P;P	0.59288	0.855;0.537	T	0.18023	-1.0350	9	0.46703	T	0.11	.	4.7373	0.12995	1.0:0.0:0.0:0.0	.	67;67	Q5CZ79;Q5SQ80	AN20B_HUMAN;A20A2_HUMAN	R	67	ENSP00000366826:H67R	ENSP00000366826:H67R	H	+	2	0	ANKRD20A2	42358610	0.240000	0.23847	0.163000	0.22734	0.016000	0.09150	0.524000	0.22940	0.836000	0.34901	0.102000	0.15555	CAC	A|0.500;G|0.500	0.500	weak		0.741	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129794.1	NM_001012421	
RNF186	54546	hgsc.bcm.edu	37	1	20141528	20141528	+	Missense_Mutation	SNP	C	C	T	rs1541185	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20141528C>T	ENST00000375121.2	-	1	243	c.67G>A	c.(67-69)Gct>Act	p.A23T	RP11-91K11.2_ENST00000454736.1_RNA	NM_019062.1	NP_061935.1	Q9NXI6	RN186_HUMAN	ring finger protein 186	23			A -> T (in dbSNP:rs1541185).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			kidney(1)|lung(3)|urinary_tract(1)	5		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;7.77e-05)|Kidney(64;0.000162)|GBM - Glioblastoma multiforme(114;0.00036)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGGGCCACAGCGGTGGTGGTT	0.647													C|||	1445	0.288538	0.2511	0.3761	5008	,	,		17996	0.3323		0.2416	False		,,,				2504	0.2802				p.A23T		Atlas-SNP	.											.	RNF186	14	.	0			c.G67A						PASS	.	C	THR/ALA	998,3408		108,782,1313	43.0	48.0	47.0		67	-5.3	0.0	1	dbSNP_88	47	2077,6523		230,1617,2453	yes	missense	RNF186	NM_019062.1	58	338,2399,3766	TT,TC,CC		24.1512,22.6509,23.6429	possibly-damaging	23/228	20141528	3075,9931	2203	4300	6503	SO:0001583	missense	54546	exon1			CCACAGCGGTGGT		CCDS199.1	1p36.13	2008-02-05			ENSG00000178828	ENSG00000178828		"""RING-type (C3HC4) zinc fingers"""	25978	protein-coding gene	gene with protein product	"""hypothetical protein FLJ20225"""					12477932	Standard	NM_019062		Approved	FLJ20225	uc001bcr.3	Q9NXI6	OTTHUMG00000002709	ENST00000375121.2:c.67G>A	1.37:g.20141528C>T	ENSP00000364263:p.Ala23Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	209	105	0.502392	NM_019062	Q53GE0	Missense_Mutation	SNP	ENST00000375121.2	37	CCDS199.1	659	0.3017399267399267	129	0.2621951219512195	142	0.39226519337016574	200	0.34965034965034963	188	0.24802110817941952	C	17.26	3.343486	0.61073	0.226509	0.241512	ENSG00000178828	ENST00000375121	T	0.30714	1.52	5.51	-5.27	0.02763	.	0.864179	0.09858	N	0.746555	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.31817	0.341	B	0.19148	0.024	T	0.37753	-0.9692	9	0.56958	D	0.05	0.1393	9.0371	0.36293	0.0:0.3286:0.1038:0.5676	rs1541185;rs52827467;rs58741288;rs1541185	23	Q9NXI6	RN186_HUMAN	T	23	ENSP00000364263:A23T	ENSP00000364263:A23T	A	-	1	0	RNF186	20014115	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.405000	0.07196	-0.859000	0.04105	-0.291000	0.09656	GCT	C|0.735;T|0.265	0.265	strong		0.647	RNF186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007694.1	NM_019062	
OR4Q3	441669	hgsc.bcm.edu	37	14	20216066	20216066	+	Silent	SNP	G	G	A	rs141710392	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20216066G>A	ENST00000331723.1	+	1	480	c.480G>A	c.(478-480)caG>caA	p.Q160Q		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	160						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(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CTATCATGCAGGTCATACTAG	0.507													G|||	38	0.00758786	0.0008	0.0159	5008	,	,		29950	0.0		0.0239	False		,,,				2504	0.002				p.Q160Q		Atlas-SNP	.											.	OR4Q3	117	.	0			c.G480A						PASS	.			12,4394		0,12,2191	111.0	107.0	109.0		480	4.1	0.9	14	dbSNP_134	109	175,8425		0,175,4125	no	coding-synonymous	OR4Q3	NM_172194.1		0,187,6316	AA,AG,GG		2.0349,0.2724,1.4378		160/314	20216066	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	441669	exon1			CATGCAGGTCATA	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.480G>A	14.37:g.20216066G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	142	33	0.232394	NM_172194	Q6IEX4	Silent	SNP	ENST00000331723.1	37	CCDS32020.1																																																																																			A|0.016;G|0.984	0.016	strong		0.507	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
ASPN	54829	hgsc.bcm.edu	37	9	95237024	95237024	+	Missense_Mutation	SNP	C	C	A	rs113747060|rs71362392|rs111419727|rs3078372|rs397838876|rs376433743|rs557103556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:95237024C>A	ENST00000375544.3	-	2	399	c.156G>T	c.(154-156)gaG>gaT	p.E52D	ASPN_ENST00000375543.1_Missense_Mutation_p.E52D|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000395538.3_Missense_Mutation_p.E52D|ASPN_ENST00000450139.2_Missense_Mutation_p.E24D	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	52	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						GAGAGTTGTCCtcatcatcat	0.398																																					p.E52D		Atlas-SNP	.											.	ASPN	52	.	0			c.G156T						PASS	.						114.0	105.0	108.0					9																	95237024		2203	4300	6503	SO:0001583	missense	54829	exon2			GTTGTCCTCATCA	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.156G>T	9.37:g.95237024C>A	ENSP00000364694:p.Glu52Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	5	0.0458716	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	37		.	.	.	.	.	.	.	.	.	.	C	4.117	0.019984	0.08006	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538;ENST00000450139	T;T;T	0.54279	0.58;1.1;1.1	5.02	-4.61	0.03380	.	1.173110	0.06296	N	0.700091	T	0.14270	0.0345	N	0.00268	-1.735	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25467	-1.0131	10	0.12766	T	0.61	.	7.4765	0.27378	0.3957:0.2175:0.3868:0.0	.	52;52	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	D	52;52;52;24	ENSP00000364694:E52D;ENSP00000364693:E52D;ENSP00000378909:E52D	ENSP00000364693:E52D	E	-	3	2	ASPN	94276845	0.675000	0.27558	0.000000	0.03702	0.005000	0.04900	-0.788000	0.04614	-1.088000	0.03077	-0.867000	0.03001	GAG	.	.	alt		0.398	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
PDZD8	118987	hgsc.bcm.edu	37	10	119134707	119134707	+	Missense_Mutation	SNP	G	G	A	rs78645354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:119134707G>A	ENST00000334464.5	-	1	271	c.32C>T	c.(31-33)gCc>gTc	p.A11V		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	11					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		ACCCAGCACGGCCGACGCCAG	0.751													G|||	109	0.0217652	0.0015	0.0331	5008	,	,		7188	0.0		0.0547	False		,,,				2504	0.0297				p.A11V		Atlas-SNP	.											.	PDZD8	85	.	0			c.C32T						PASS	.	G	VAL/ALA	62,3966		1,60,1953	9.0	7.0	7.0		32	4.2	1.0	10	dbSNP_131	7	519,7551		6,507,3522	yes	missense	PDZD8	NM_173791.3	64	7,567,5475	AA,AG,GG		6.4312,1.5392,4.8024	benign	11/1155	119134707	581,11517	2014	4035	6049	SO:0001583	missense	118987	exon1			AGCACGGCCGACG	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.32C>T	10.37:g.119134707G>A	ENSP00000334642:p.Ala11Val	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	58	0.026556776556776556	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	43	0.05672823218997362	G	13.58	2.279590	0.40294	0.015392	0.064312	ENSG00000165650	ENST00000334464	D	0.88975	-2.45	4.17	4.17	0.49024	.	0.070775	0.53938	D	0.000041	T	0.42944	0.1225	L	0.29908	0.895	0.41950	D	0.990653	B	0.26081	0.141	B	0.28553	0.091	T	0.68292	-0.5447	10	0.27785	T	0.31	-3.7617	16.3354	0.83059	0.0:0.0:1.0:0.0	.	11	Q8NEN9	PDZD8_HUMAN	V	11	ENSP00000334642:A11V	ENSP00000334642:A11V	A	-	2	0	PDZD8	119124697	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.376000	0.59556	2.171000	0.68590	0.306000	0.20318	GCC	G|0.972;A|0.028	0.028	strong		0.751	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
SGSM2	9905	hgsc.bcm.edu	37	17	2275734	2275734	+	Silent	SNP	C	C	G	rs3213712	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:2275734C>G	ENST00000426855.2	+	14	1780	c.1605C>G	c.(1603-1605)tcC>tcG	p.S535S	SGSM2_ENST00000574563.1_Silent_p.S535S|RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000268989.3_Silent_p.S580S	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	535					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CGGGGGCCTCCGCGGGCCTCA	0.687													C|||	1288	0.257188	0.5507	0.1124	5008	,	,		12916	0.1478		0.0954	False		,,,				2504	0.2423				p.S580S		Atlas-SNP	.											SGSM2,colon,carcinoma,0,1	SGSM2	60	1	0			c.C1740G						PASS	.	C	,	1915,2437		438,1039,699	9.0	13.0	12.0		1605,1740	-11.4	0.0	17	dbSNP_106	12	721,7807		34,653,3577	no	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	472,1692,4276	GG,GC,CC		8.4545,44.0028,20.4658	,	535/1007,580/1052	2275734	2636,10244	2176	4264	6440	SO:0001819	synonymous_variant	9905	exon15			GGCCTCCGCGGGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1605C>G	17.37:g.2275734C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																			C|0.810;G|0.190	0.190	strong		0.687	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
EFNA1	1942	hgsc.bcm.edu	37	1	155106227	155106227	+	Missense_Mutation	SNP	A	A	T	rs4745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:155106227A>T	ENST00000368407.3	+	4	994	c.476A>T	c.(475-477)gAc>gTc	p.D159V	SLC50A1_ENST00000368404.4_5'Flank|EFNA1_ENST00000469878.1_3'UTR|SLC50A1_ENST00000484157.1_5'Flank|SLC50A1_ENST00000368401.5_5'Flank|EFNA1_ENST00000368406.2_Missense_Mutation_p.D137V|SLC50A1_ENST00000303343.8_5'Flank	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	159			D -> V (in dbSNP:rs4745). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2233719, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			CAGGCCCATGACAATCCACAG	0.547													A|||	1602	0.319888	0.152	0.3141	5008	,	,		21251	0.1964		0.5209	False		,,,				2504	0.4714				p.D159V		Atlas-SNP	.											.	EFNA1	10	.	0			c.A476T						PASS	.	A	VAL/ASP,VAL/ASP	766,3640	311.4+/-292.0	67,632,1504	126.0	120.0	122.0		476,410	-0.3	0.8	1	dbSNP_52	122	4547,4053	595.4+/-393.5	1194,2159,947	yes	missense,missense	EFNA1	NM_004428.2,NM_182685.1	152,152	1261,2791,2451	TT,TA,AA		47.1279,17.3854,40.8504	benign,benign	159/206,137/184	155106227	5313,7693	2203	4300	6503	SO:0001583	missense	1942	exon4			CCCATGACAATCC		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"""Ephrins"""	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.476A>T	1.37:g.155106227A>T	ENSP00000357392:p.Asp159Val	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	185	183	0.989189	NM_004428	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	37	CCDS1091.1	668	0.3058608058608059	65	0.13211382113821138	140	0.3867403314917127	82	0.14335664335664336	381	0.5026385224274407	A	10.66	1.411824	0.25465	0.173854	0.528721	ENSG00000169242	ENST00000368407;ENST00000368406	D;D	0.93307	-3.2;-3.16	5.64	-0.259	0.12971	.	0.994739	0.08165	N	0.987808	T	0.64713	0.2623	N	0.03608	-0.345	0.24654	P	0.99350447	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48703	-0.9012	9	0.27082	T	0.32	-8.7206	3.6358	0.08148	0.293:0.4243:0.0:0.2827	rs4745;rs1126731;rs3181946;rs4255378;rs11545253;rs17855562;rs52820739;rs58483156;rs4745	137;159	P20827-2;P20827	.;EFNA1_HUMAN	V	159;137	ENSP00000357392:D159V;ENSP00000357391:D137V	ENSP00000357391:D137V	D	+	2	0	EFNA1	153372851	0.002000	0.14202	0.784000	0.31847	0.699000	0.40488	-0.443000	0.06862	-0.223000	0.09943	-0.396000	0.06452	GAC	A|0.640;T|0.360	0.360	strong		0.547	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428	
SPINK5	11005	hgsc.bcm.edu	37	5	147498019	147498019	+	Missense_Mutation	SNP	G	G	A	rs3777134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:147498019G>A	ENST00000256084.7	+	23	2174	c.2132G>A	c.(2131-2133)cGg>cAg	p.R711Q	SPINK5_ENST00000398454.1_Missense_Mutation_p.R711Q|SPINK5_ENST00000359874.3_Missense_Mutation_p.R711Q	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	711	Kazal-like 11. {ECO:0000255|PROSITE- ProRule:PRU00798}.		R -> Q (in dbSNP:rs3777134). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:16374478}.		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.R711Q(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)			GCTGAGTATCGGGAACAAATG	0.408													G|||	2446	0.488419	0.3139	0.634	5008	,	,		18442	0.4821		0.5924	False		,,,				2504	0.5204				p.R711Q		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - Missense(1)	stomach(1)	c.G2132A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	1456,2366		270,916,725	133.0	132.0	132.0		2132,2132,2132	3.0	0.1	5	dbSNP_107	132	5070,3154		1538,1994,580	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	43,43,43	1808,2910,1305	AA,AG,GG		38.3512,38.0952,45.8243	benign,benign,benign	711/1095,711/917,711/1065	147498019	6526,5520	1911	4112	6023	SO:0001583	missense	11005	exon23			AGTATCGGGAACA	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.2132G>A	5.37:g.147498019G>A	ENSP00000256084:p.Arg711Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	1078	0.4935897435897436	177	0.3597560975609756	213	0.5883977900552486	262	0.458041958041958	426	0.5620052770448549	G	8.108	0.778056	0.16120	0.380952	0.616488	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.06768	3.26;3.26;3.26;3.26	5.75	2.99	0.34606	Proteinase inhibitor I1, Kazal (1);	0.687092	0.12200	N	0.490350	T	0.00012	0.0000	L	0.31526	0.94	0.80722	P	0.0	P;B;P	0.36495	0.474;0.219;0.556	B;B;B	0.29524	0.052;0.016;0.103	T	0.06110	-1.0845	9	0.17369	T	0.5	-0.1409	8.5873	0.33666	0.2532:0.0:0.7468:0.0	rs3777134;rs17637605;rs52793936;rs61224732;rs3777134	711;711;711	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	Q	711;711;692;711	ENSP00000381472:R711Q;ENSP00000352936:R711Q;ENSP00000421519:R692Q;ENSP00000256084:R711Q	ENSP00000256084:R711Q	R	+	2	0	SPINK5	147478212	0.001000	0.12720	0.148000	0.22405	0.010000	0.07245	0.440000	0.21592	0.907000	0.36646	-0.140000	0.14226	CGG	G|0.493;N|0.000	.	strong		0.408	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702725	27702725	+	Missense_Mutation	SNP	A	A	G	rs6482626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:27702725A>G	ENST00000438700.3	-	1	572	c.455T>C	c.(454-456)cTg>cCg	p.L152P		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						GCCGGTGCCCAGCGCGGCTGT	0.672													A|||	994	0.198482	0.3805	0.2853	5008	,	,		12858	0.0129		0.2137	False		,,,				2504	0.0665				p.L152P		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T455C						PASS	.	A	PRO/LEU	1561,2845	463.0+/-353.4	279,1003,921	62.0	71.0	68.0		455	3.6	0.0	10	dbSNP_116	68	1921,6679	319.3+/-314.1	234,1453,2613	yes	missense	PTCHD3	NM_001034842.3	98	513,2456,3534	GG,GA,AA		22.3372,35.429,26.7723	probably-damaging	152/768	27702725	3482,9524	2203	4300	6503	SO:0001583	missense	374308	exon1			GTGCCCAGCGCGG	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.455T>C	10.37:g.27702725A>G	ENSP00000417658:p.Leu152Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	437	0.2000915750915751	176	0.35772357723577236	90	0.24861878453038674	10	0.017482517482517484	161	0.21240105540897097	A	16.00	2.997444	0.54147	0.35429	0.223372	ENSG00000182077	ENST00000438700	D	0.91351	-2.83	3.62	3.62	0.41486	.	0.165305	0.41938	N	0.000787	T	0.00012	0.0000	M	0.68952	2.095	0.20403	P	0.9999007308	D	0.76494	0.999	D	0.70935	0.971	T	0.00000	-1.3717	9	0.87932	D	0	-16.4668	10.9518	0.47334	1.0:0.0:0.0:0.0	rs6482626;rs17388746;rs57918946;rs6482626	152	Q3KNS1	PTHD3_HUMAN	P	152	ENSP00000417658:L152P	ENSP00000417658:L152P	L	-	2	0	PTCHD3	27742731	0.990000	0.36364	0.011000	0.14972	0.015000	0.08874	4.227000	0.58612	1.528000	0.49103	0.454000	0.30748	CTG	A|0.769;G|0.231	0.231	strong		0.672	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
MARK3	4140	hgsc.bcm.edu	37	14	103941454	103941454	+	Silent	SNP	G	G	A	rs56126530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:103941454G>A	ENST00000429436.2	+	13	1899	c.1389G>A	c.(1387-1389)aaG>aaA	p.K463K	MARK3_ENST00000216288.7_Silent_p.K447K|MARK3_ENST00000303622.9_Silent_p.K463K|MARK3_ENST00000335102.5_Silent_p.K486K|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000553942.1_Silent_p.K463K|MARK3_ENST00000416682.2_Silent_p.K486K|MARK3_ENST00000440884.3_Silent_p.K384K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	463						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			TTGGAGGAAAGGGAATTGCTC	0.488													G|||	20	0.00399361	0.0	0.0029	5008	,	,		18604	0.001		0.0169	False		,,,				2504	0.0				p.K463K		Atlas-SNP	.											.	MARK3	86	.	0			c.G1389A						PASS	.	G	,,,,	3,3887		0,3,1942	78.0	77.0	77.0		1389,1389,1341,1152,1389	3.9	1.0	14	dbSNP_129	77	95,8197		2,91,4053	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	,,,,	2,94,5995	AA,AG,GG		1.1457,0.0771,0.8045	,,,,	463/754,463/745,447/714,384/660,463/730	103941454	98,12084	1945	4146	6091	SO:0001819	synonymous_variant	4140	exon13			AGGAAAGGGAATT	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.1389G>A	14.37:g.103941454G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Silent	SNP	ENST00000429436.2	37	CCDS45165.1	18	0.008241758241758242	0	0.0	0	0.0	1	0.0017482517482517483	17	0.022427440633245383	G	9.682	1.149478	0.21288	7.71E-4	0.011457	ENSG00000075413	ENST00000554627	.	.	.	5.78	3.91	0.45181	.	.	.	.	.	T	0.31040	0.0784	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25882	-1.0119	4	.	.	.	.	3.6647	0.08252	0.2736:0.0:0.5486:0.1777	rs56126530	.	.	.	K	215	.	.	R	+	2	0	MARK3	103011207	1.000000	0.71417	0.960000	0.40013	0.953000	0.61014	1.561000	0.36342	0.744000	0.32741	0.655000	0.94253	AGG	G|0.989;A|0.011	0.011	strong		0.488	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
OR52B6	340980	hgsc.bcm.edu	37	11	5602615	5602615	+	Missense_Mutation	SNP	A	A	G	rs2341434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5602615A>G	ENST00000345043.2	+	1	509	c.509A>G	c.(508-510)cAc>cGc	p.H170R	AC015691.13_ENST00000394793.2_RNA|HBG2_ENST00000380259.2_Intron	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	170			H -> R (in dbSNP:rs2341434).			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)		GCCCTGAGCCACAGCTTCATC	0.493													G|||	3589	0.716653	0.7413	0.67	5008	,	,		25430	0.9802		0.4761	False		,,,				2504	0.6922				p.H170R		Atlas-SNP	.											.	OR52B6	37	.	0			c.A509G						PASS	.	G	ARG/HIS	3065,1337	411.5+/-335.8	1072,921,208	191.0	202.0	198.0		509	5.2	0.2	11	dbSNP_100	198	4020,4572	582.5+/-391.4	930,2160,1206	yes	missense	OR52B6	NM_001005162.2	29	2002,3081,1414	GG,GA,AA		46.7877,30.3726,45.4748	benign	170/336	5602615	7085,5909	2201	4296	6497	SO:0001583	missense	340980	exon1			TGAGCCACAGCTT	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.509A>G	11.37:g.5602615A>G	ENSP00000341581:p.His170Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	1500	0.6868131868131868	355	0.7215447154471545	228	0.6298342541436464	557	0.9737762237762237	360	0.47493403693931396	G	0.006	-2.090174	0.00367	0.696274	0.467877	ENSG00000187747	ENST00000345043	T	0.36340	1.26	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.181100	0.26496	N	0.024042	T	0.00012	0.0000	N	0.00002	-3.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40289	-0.9571	9	0.02654	T	1	.	9.9359	0.41550	0.1637:0.0:0.8363:0.0	rs2341434;rs16933210;rs60514876;rs2341434	170	Q8NGF0	O52B6_HUMAN	R	170	ENSP00000341581:H170R	ENSP00000341581:H170R	H	+	2	0	OR52B6	5559191	0.745000	0.28261	0.154000	0.22540	0.023000	0.10783	1.843000	0.39259	1.413000	0.46997	-0.128000	0.14901	CAC	A|0.331;G|0.669	0.669	strong		0.493	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
HECTD1	25831	hgsc.bcm.edu	37	14	31647448	31647448	+	Silent	SNP	G	G	A	rs34666986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:31647448G>A	ENST00000399332.1	-	3	641	c.153C>T	c.(151-153)cgC>cgT	p.R51R	HECTD1_ENST00000553700.1_Silent_p.R51R	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	51					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GTAAGAAAGTGCGAGGAGGAC	0.333													G|||	327	0.0652955	0.0023	0.0735	5008	,	,		16513	0.0317		0.1541	False		,,,				2504	0.0879				p.R51R		Atlas-SNP	.											.	HECTD1	159	.	0			c.C153T						PASS	.	G		67,3629		2,63,1783	60.0	56.0	57.0		153	-6.6	0.9	14	dbSNP_126	57	981,7191		67,847,3172	no	coding-synonymous	HECTD1	NM_015382.2		69,910,4955	AA,AG,GG		12.0044,1.8128,8.8305		51/2611	31647448	1048,10820	1848	4086	5934	SO:0001819	synonymous_variant	25831	exon3			GAAAGTGCGAGGA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.153C>T	14.37:g.31647448G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			G|0.910;A|0.090	0.090	strong		0.333	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
SPEG	10290	hgsc.bcm.edu	37	2	220353013	220353013	+	Silent	SNP	G	G	A	rs875098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:220353013G>A	ENST00000312358.7	+	32	7971	c.7839G>A	c.(7837-7839)ccG>ccA	p.P2613P	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2613	Ig-like 9.				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)		GCCCTGCACCGCACATCTCCT	0.642													G|||	1434	0.286342	0.2905	0.2709	5008	,	,		19669	0.1468		0.2724	False		,,,				2504	0.4499				p.P2613P		Atlas-SNP	.											.	SPEG	272	.	0			c.G7839A						PASS	.	G		1078,3026		146,786,1120	43.0	46.0	45.0		7839	1.3	1.0	2	dbSNP_86	45	2129,6277		274,1581,2348	no	coding-synonymous	SPEG	NM_005876.4		420,2367,3468	AA,AG,GG		25.3271,26.2671,25.6355		2613/3268	220353013	3207,9303	2052	4203	6255	SO:0001819	synonymous_variant	10290	exon32			TGCACCGCACATC	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.7839G>A	2.37:g.220353013G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.747;A|0.253	0.253	strong		0.642	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
LZTR1	8216	hgsc.bcm.edu	37	22	21347150	21347150	+	Missense_Mutation	SNP	C	C	T	rs375451574		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21347150C>T	ENST00000215739.8	+	11	1576	c.1217C>T	c.(1216-1218)aCg>aTg	p.T406M	LZTR1_ENST00000389355.3_Missense_Mutation_p.T387M|LZTR1_ENST00000479606.1_3'UTR	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	406					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T406M(1)		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)			TTCGGGGGCACGGTGGACAAC	0.642																																					p.T406M		Atlas-SNP	.											LZTR1,NS,carcinoma,0,1	LZTR1	99	1	1	Substitution - Missense(1)	endometrium(1)	c.C1217T						scavenged	.	C	MET/THR	1,4399	2.1+/-5.4	0,1,2199	57.0	47.0	50.0		1217	5.0	1.0	22		50	0,8600		0,0,4300	no	missense	LZTR1	NM_006767.3	81	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	406/841	21347150	1,12999	2200	4300	6500	SO:0001583	missense	8216	exon11			GGGGCACGGTGGA	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.1217C>T	22.37:g.21347150C>T	ENSP00000215739:p.Thr406Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	37	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.945781	0.92593	2.27E-4	0.0	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	T;T	0.28666	1.6;1.6	4.98	4.98	0.66077	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.55497	0.1924	M	0.79123	2.44	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.968;0.995;0.968;0.96	T	0.58255	-0.7668	10	0.59425	D	0.04	-37.6876	13.6201	0.62132	0.0:1.0:0.0:0.0	.	387;365;406;365	B7Z3T9;Q6ZSY0;Q8N653;F5GXU8	.;.;LZTR1_HUMAN;.	M	365;406;387	ENSP00000215739:T406M;ENSP00000374006:T387M	ENSP00000215739:T406M	T	+	2	0	LZTR1	19677150	1.000000	0.71417	0.963000	0.40424	0.987000	0.75469	7.554000	0.82212	2.582000	0.87167	0.655000	0.94253	ACG	.	.	weak		0.642	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
IPO11	51194	hgsc.bcm.edu	37	5	61847073	61847073	+	Silent	SNP	G	G	C	rs32170	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:61847073G>C	ENST00000325324.6	+	26	2539	c.2370G>C	c.(2368-2370)acG>acC	p.T790T	IPO11_ENST00000409296.3_Silent_p.T830T	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	790					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		TGATGTCCACGTATCTTGGAG	0.343													G|||	430	0.0858626	0.1021	0.0562	5008	,	,		12896	0.1349		0.0785	False		,,,				2504	0.0419				p.T830T		Atlas-SNP	.											.	IPO11	76	.	0			c.G2490C						PASS	.	G	,	527,3879	240.6+/-251.3	28,471,1704	197.0	185.0	189.0		2490,2370	-10.0	0.0	5	dbSNP_76	189	620,7978	160.5+/-213.6	23,574,3702	no	coding-synonymous,coding-synonymous	IPO11	NM_001134779.1,NM_016338.4	,	51,1045,5406	CC,CG,GG		7.211,11.961,8.8204	,	830/1016,790/976	61847073	1147,11857	2203	4299	6502	SO:0001819	synonymous_variant	51194	exon26			GTCCACGTATCTT	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.2370G>C	5.37:g.61847073G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_001134779	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Silent	SNP	ENST00000325324.6	37	CCDS34167.1	197	0.0902014652014652	44	0.08943089430894309	21	0.058011049723756904	72	0.1258741258741259	60	0.079155672823219	G	5.757	0.324142	0.10900	0.11961	0.07211	ENSG00000086200	ENST00000511713	.	.	.	4.98	-9.96	0.00443	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.09310	P	0.9999999834138	.	.	.	.	.	.	T	0.12837	-1.0532	3	.	.	.	.	9.0813	0.36554	0.0951:0.0644:0.5166:0.324	rs32170;rs1307433;rs32170	.	.	.	P	55	.	.	R	+	2	0	IPO11	61882830	0.002000	0.14202	0.035000	0.18076	0.975000	0.68041	-1.337000	0.02657	-4.680000	0.00036	-0.886000	0.02939	CGT	G|0.912;C|0.088	0.088	strong		0.343	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338	
TRIOBP	11078	hgsc.bcm.edu	37	22	38121013	38121013	+	Missense_Mutation	SNP	C	C	G	rs41302575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38121013C>G	ENST00000406386.3	+	7	2705	c.2450C>G	c.(2449-2451)aCt>aGt	p.T817S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	817			T -> S (in dbSNP:rs41302575).		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)					AACCCCAGAACTTGTATTCAA	0.502													C|||	289	0.0577077	0.0862	0.0389	5008	,	,		21712	0.001		0.0368	False		,,,				2504	0.1125				p.T817S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C2450G						PASS	.	C	SER/THR	317,3657		18,281,1688	156.0	165.0	162.0		2450	3.7	0.0	22	dbSNP_127	162	372,7960		4,364,3798	yes	missense	TRIOBP	NM_001039141.2	58	22,645,5486	GG,GC,CC		4.4647,7.9768,5.5989	benign	817/2366	38121013	689,11617	1987	4166	6153	SO:0001583	missense	11078	exon7			CCAGAACTTGTAT	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.2450C>G	22.37:g.38121013C>G	ENSP00000384312:p.Thr817Ser	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	149	68	0.456376	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	84	0.038461538461538464	39	0.07926829268292683	16	0.04419889502762431	0	0.0	29	0.03825857519788918	C	13.52	2.261086	0.39995	0.079768	0.044647	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19669	2.13	3.71	3.71	0.42584	.	.	.	.	.	T	0.00496	0.0016	N	0.25201	0.72	0.28764	P	0.9007214	P	0.43024	0.798	B	0.28916	0.096	T	0.09997	-1.0649	8	0.09590	T	0.72	.	11.1608	0.48514	0.0:1.0:0.0:0.0	rs41302575	817	Q9H2D6	TARA_HUMAN	S	817	ENSP00000384312:T817S	ENSP00000384312:T817S	T	+	2	0	TRIOBP	36450959	0.000000	0.05858	0.022000	0.16811	0.751000	0.42716	-0.071000	0.11505	2.072000	0.62099	0.460000	0.39030	ACT	C|0.959;G|0.041	0.041	strong		0.502	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
VWA3B	200403	hgsc.bcm.edu	37	2	98797660	98797660	+	Silent	SNP	C	C	T	rs375244468		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:98797660C>T	ENST00000477737.1	+	9	1500	c.1296C>T	c.(1294-1296)tcC>tcT	p.S432S	VWA3B_ENST00000435344.1_Silent_p.S432S|VWA3B_ENST00000451075.2_Silent_p.S282S	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	432										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						AGAATGAGTCCGTGCAGACCA	0.592																																					p.S432S		Atlas-SNP	.											.	VWA3B	138	.	0			c.C1296T						PASS	.	C		0,4068		0,0,2034	87.0	90.0	89.0		1296	-2.5	0.1	2		89	1,8365		0,1,4182	no	coding-synonymous	VWA3B	NM_144992.4		0,1,6216	TT,TC,CC		0.012,0.0,0.0080		432/1295	98797660	1,12433	2034	4183	6217	SO:0001819	synonymous_variant	200403	exon9			TGAGTCCGTGCAG	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.1296C>T	2.37:g.98797660C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	168	68	0.404762	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			.	.	weak		0.592	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
CR1	1378	hgsc.bcm.edu	37	1	207782707	207782707	+	Missense_Mutation	SNP	A	A	G	rs17259045	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:207782707A>G	ENST00000367049.4	+	37	5969	c.5969A>G	c.(5968-5970)aAt>aGt	p.N1990S	RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000400960.2_Missense_Mutation_p.N1540S|CR1_ENST00000367051.1_Missense_Mutation_p.N1540S|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367052.1_Missense_Mutation_p.N1540S|CR1_ENST00000367053.1_Missense_Mutation_p.N1540S	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	133	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	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	
TUBB8	347688	hgsc.bcm.edu	37	10	94026	94026	+	Silent	SNP	G	G	A	rs10904032	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:94026G>A	ENST00000309812.4	-	4	368	c.306C>T	c.(304-306)gcC>gcT	p.A102A	TUBB8_ENST00000332708.5_Missense_Mutation_p.P66L|TUBB8_ENST00000447903.2_Silent_p.A30A|TUBB8_ENST00000413237.3_5'UTR	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	209	0	0		WXS	Illumina HiSeq	Phase_I	162	61	0.376543	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	
MUC6	4588	hgsc.bcm.edu	37	11	1026048	1026048	+	Silent	SNP	G	G	A	rs55965773	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1026048G>A	ENST00000421673.2	-	21	2690	c.2640C>T	c.(2638-2640)gaC>gaT	p.D880D		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	880	VWFD 3. {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)	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)		AGCGCTGGCCGTCGAAGGTGA	0.677													g|||	419	0.0836661	0.0182	0.1254	5008	,	,		18109	0.0198		0.1839	False		,,,				2504	0.1053				p.D880D		Atlas-SNP	.											.	MUC6	408	.	0			c.C2640T						PASS	.	G		147,4171		2,143,2014	41.0	48.0	45.0		2640	-7.8	0.6	11	dbSNP_129	45	1573,6901		148,1277,2812	no	coding-synonymous	MUC6	NM_005961.2		150,1420,4826	AA,AG,GG		18.5627,3.4044,13.4459		880/2440	1026048	1720,11072	2159	4237	6396	SO:0001819	synonymous_variant	4588	exon21			CTGGCCGTCGAAG	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.2640C>T	11.37:g.1026048G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.902;A|0.098	0.098	strong		0.677	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
RPE65	6121	hgsc.bcm.edu	37	1	68895516	68895516	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:68895516C>T	ENST00000262340.5	-	14	1598	c.1545G>A	c.(1543-1545)cgG>cgA	p.R515R		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	515			R -> W (in RP20; this mutation has been found in compound heterozygosity in LCA2). {ECO:0000269|PubMed:15557452}.		cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						CCACTTCAGCCCGGGCAACTT	0.448																																					p.R515R		Atlas-SNP	.											RPE65,NS,carcinoma,-2,1	RPE65	87	1	0			c.G1545A						scavenged	.						88.0	82.0	84.0					1																	68895516		2203	4300	6503	SO:0001819	synonymous_variant	6121	exon14			TTCAGCCCGGGCA	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1545G>A	1.37:g.68895516C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	3	0.0283019	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			.	.	none		0.448	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
SBNO2	22904	hgsc.bcm.edu	37	19	1122201	1122201	+	Silent	SNP	G	G	A	rs62131221	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	68	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	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	
OR4Q3	441669	hgsc.bcm.edu	37	14	20215989	20215989	+	Missense_Mutation	SNP	A	A	G	rs17210864	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20215989A>G	ENST00000331723.1	+	1	403	c.403A>G	c.(403-405)Aca>Gca	p.T135A		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	135			T -> A (in dbSNP:rs17210864).			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(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCGCTACCTTACAGTCATGAA	0.493													A|||	549	0.109625	0.0885	0.0764	5008	,	,		30995	0.0079		0.1481	False		,,,				2504	0.227				p.T135A		Atlas-SNP	.											.	OR4Q3	117	.	0			c.A403G						PASS	.		ALA/THR	475,3931		8,459,1736	121.0	123.0	122.0		403	3.2	0.1	14	dbSNP_123	122	1437,7163		36,1365,2899	no	missense	OR4Q3	NM_172194.1	58	44,1824,4635	GG,GA,AA		16.7093,10.7808,14.7009	benign	135/314	20215989	1912,11094	2203	4300	6503	SO:0001583	missense	441669	exon1			TACCTTACAGTCA	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.403A>G	14.37:g.20215989A>G	ENSP00000330049:p.Thr135Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	157	46	0.292994	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	37	CCDS32020.1	187	0.08562271062271062	31	0.06300813008130081	33	0.09116022099447514	5	0.008741258741258742	118	0.15567282321899736	.	4.346	0.063601	0.08388	0.107808	0.167093	ENSG00000182652	ENST00000331723	T	0.00388	7.59	4.36	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.359276	0.19822	U	0.105292	T	0.00012	0.0000	N	0.25332	0.735	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.51426	-0.8707	10	0.59425	D	0.04	.	4.5362	0.12032	0.6998:0.1965:0.1037:0.0	rs17210864;rs52817214;rs17210864	135	Q8NH05	OR4Q3_HUMAN	A	135	ENSP00000330049:T135A	ENSP00000330049:T135A	T	+	1	0	OR4Q3	19285829	0.000000	0.05858	0.108000	0.21378	0.045000	0.14185	-0.357000	0.07651	0.707000	0.31934	0.333000	0.21579	ACA	A|0.904;G|0.096	0.096	strong		0.493	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
LACTB2	51110	hgsc.bcm.edu	37	8	71550832	71550832	+	Silent	SNP	T	T	C	rs7830986	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:71550832T>C	ENST00000276590.4	-	6	810	c.774A>G	c.(772-774)aaA>aaG	p.K258K	RP11-382J12.1_ENST00000518553.1_Intron|LACTB2_ENST00000517601.1_5'UTR|LACTB2_ENST00000522447.1_Silent_p.K258K|RP11-382J12.1_ENST00000499227.2_Intron	NM_016027.2	NP_057111.1	Q53H82	LACB2_HUMAN	lactamase, beta 2	258						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|prostate(1)	10	Breast(64;0.0716)		Epithelial(68;0.00319)|all cancers(69;0.0175)|OV - Ovarian serous cystadenocarcinoma(28;0.0628)|BRCA - Breast invasive adenocarcinoma(89;0.166)			AGAGATTATGTTTAGCCATTT	0.234													T|||	847	0.169129	0.4009	0.1499	5008	,	,		15985	0.0159		0.0934	False		,,,				2504	0.1053				p.K258K		Atlas-SNP	.											.	LACTB2	26	.	0			c.A774G						PASS	.	T		1319,2997		194,931,1033	25.0	31.0	29.0		774	2.6	0.0	8	dbSNP_116	29	820,7686		50,720,3483	no	coding-synonymous	LACTB2	NM_016027.2		244,1651,4516	CC,CT,TT		9.6403,30.5607,16.6823		258/289	71550832	2139,10683	2158	4253	6411	SO:0001819	synonymous_variant	51110	exon6			ATTATGTTTAGCC	AF151841	CCDS6208.1	8q13.3	2005-10-14			ENSG00000147592	ENSG00000147592			18512	protein-coding gene	gene with protein product							Standard	NM_016027		Approved	CGI-83	uc003xyp.3	Q53H82	OTTHUMG00000164430	ENST00000276590.4:c.774A>G	8.37:g.71550832T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	94	31	0.329787	NM_016027	A8K2D6|Q9Y392	Silent	SNP	ENST00000276590.4	37	CCDS6208.1																																																																																			T|0.840;C|0.160	0.160	strong		0.234	LACTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378748.1	NM_016027	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629764	32629764	+	Missense_Mutation	SNP	C	C	T	rs1130398	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32629764C>T	ENST00000399082.3	-	2	415	c.371G>A	c.(370-372)aGc>aAc	p.S124N	HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.S214N			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	214	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|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)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GGTGATGGGGCTCTGGAGGCT	0.537									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1981	0.395567	0.3154	0.5476	5008	,	,		17107	0.4782		0.3946	False		,,,				2504	0.3119				p.S214N	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G641A						PASS	.	T	ASN/SER	1305,3089		211,883,1103	54.0	59.0	57.0		641	1.6	0.9	6	dbSNP_86	57	3090,5502		594,1902,1800	yes	missense	HLA-DQB1	NM_002123.4	46	805,2785,2903	TT,TC,CC		35.9637,29.6996,33.8441	benign	214/262	32629764	4395,8591	2197	4296	6493	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	ATGGGGCTCTGGA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.371G>A	6.37:g.32629764C>T	ENSP00000382032:p.Ser124Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		930	0.4258241758241758	152	0.3089430894308943	190	0.5248618784530387	283	0.49475524475524474	305	0.4023746701846966	.	5.911	0.352128	0.11182	0.296996	0.359637	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09	4.52	1.62	0.23740	.	0.726356	0.13327	N	0.396223	T	0.00784	0.0026	.	.	.	0.52099	P	5.999999999994898E-5	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	0.45977	-0.9224	8	0.59425	D	0.04	.	3.5408	0.07811	0.0:0.4996:0.1955:0.3049	rs1130398;rs3189185;rs9273924;rs12722372;rs17412846;rs28724254;rs34909169	214;179;214;214	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	N	124;214;214;214;214	ENSP00000382032:S124N;ENSP00000382029:S214N;ENSP00000364080:S214N;ENSP00000407332:S214N;ENSP00000382034:S214N	ENSP00000364080:S214N	S	-	2	0	HLA-DQB1	32737742	0.000000	0.05858	0.933000	0.37362	0.413000	0.31143	-0.126000	0.10563	0.319000	0.23209	-0.642000	0.03964	AGC	T|0.416;C|0.584	0.416	strong		0.537	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
CNN2	1265	hgsc.bcm.edu	37	19	1036444	1036444	+	Silent	SNP	G	G	A	rs930231	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:1036444G>A	ENST00000263097.4	+	6	900	c.537G>A	c.(535-537)tcG>tcA	p.S179S	CNN2_ENST00000562958.2_Silent_p.S200S|CNN2_ENST00000348419.3_Silent_p.S140S|CNN2_ENST00000565096.2_Silent_p.S168S|AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000606983.1_3'UTR	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	179					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)		CCAGCCAGTCGGGCATGACTG	0.592													G|||	851	0.169928	0.0439	0.3646	5008	,	,		17922	0.0496		0.3002	False		,,,				2504	0.1922				p.S179S		Atlas-SNP	.											.	CNN2	26	.	0			c.G537A						PASS	.	G	,	401,4005	196.4+/-220.7	19,363,1821	65.0	61.0	62.0		537,420	-8.4	0.8	19	dbSNP_86	62	2734,5866	433.9+/-357.6	444,1846,2010	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	463,2209,3831	AA,AG,GG		31.7907,9.1012,24.1043	,	179/310,140/271	1036444	3135,9871	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			CCAGTCGGGCATG	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.537G>A	19.37:g.1036444G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			G|0.770;C|0.000;A|0.230	0.230	strong		0.592	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
FAM161B	145483	hgsc.bcm.edu	37	14	74413129	74413129	+	Silent	SNP	C	C	G	rs7146634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74413129C>G	ENST00000534936.1	-	2	339	c.234G>C	c.(232-234)ggG>ggC	p.G78G	FAM161B_ENST00000286544.3_Silent_p.G141G			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	78										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						GACACCATCTCCCTTTCTGCT	0.478													G|||	1301	0.259784	0.3003	0.3429	5008	,	,		20403	0.0506		0.4056	False		,,,				2504	0.2117				p.G141G		Atlas-SNP	.											.	FAM161B	67	.	0			c.G423C						PASS	.	G		1345,3061	694.1+/-405.8	198,949,1056	197.0	188.0	191.0		423	-0.5	0.0	14	dbSNP_116	191	3561,5039	628.9+/-398.2	730,2101,1469	no	coding-synonymous	FAM161B	NM_152445.2		928,3050,2525	GG,GC,CC		41.407,30.5266,37.7211		141/711	74413129	4906,8100	2203	4300	6503	SO:0001819	synonymous_variant	145483	exon2			CCATCTCCCTTTC	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.234G>C	14.37:g.74413129C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_152445	B7Z882|J3KNA2	Silent	SNP	ENST00000534936.1	37																																																																																				C|0.648;G|0.352	0.352	strong		0.478	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
WNK1	65125	hgsc.bcm.edu	37	12	863152	863152	+	Missense_Mutation	SNP	G	G	A	rs11554421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:863152G>A	ENST00000315939.6	+	1	1064	c.421G>A	c.(421-423)Gcc>Acc	p.A141T	WNK1_ENST00000535572.1_Missense_Mutation_p.A141T|WNK1_ENST00000447667.2_Missense_Mutation_p.A141T|WNK1_ENST00000530271.2_Missense_Mutation_p.A141T|WNK1_ENST00000537687.1_Missense_Mutation_p.A141T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	141			A -> T (in dbSNP:rs11554421). {ECO:0000269|PubMed:17344846}.		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)			TCCAGCCGCTGCCGCCCCTGG	0.721													G|||	373	0.0744808	0.0166	0.0533	5008	,	,		14639	0.0665		0.1322	False		,,,				2504	0.1166				p.A141T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G421A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	107,4097		5,97,2000	7.0	9.0	8.0		421,421,421,421	4.3	0.1	12	dbSNP_120	8	896,7406		40,816,3295	no	missense,missense,missense,missense	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	58,58,58,58	45,913,5295	AA,AG,GG		10.7926,2.5452,8.0202	probably-damaging,probably-damaging,probably-damaging,probably-damaging	141/2643,141/2135,141/2383,141/2635	863152	1003,11503	2102	4151	6253	SO:0001583	missense	65125	exon1			GCCGCTGCCGCCC	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.421G>A	12.37:g.863152G>A	ENSP00000313059:p.Ala141Thr	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	38	28	0.736842	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	154	0.07051282051282051	9	0.018292682926829267	17	0.04696132596685083	26	0.045454545454545456	102	0.1345646437994723	G	11.44	1.639840	0.29157	0.025452	0.107926	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.71698	-0.48;-0.45;-0.45;-0.59;-0.46	4.35	4.35	0.52113	.	0.000000	0.43919	D	0.000516	T	0.00967	0.0032	L	0.47716	1.5	0.42902	P	0.005767999999999995	B;B;B	0.24721	0.11;0.067;0.041	B;B;B	0.14578	0.011;0.005;0.011	T	0.32508	-0.9904	9	0.49607	T	0.09	-11.1421	6.9599	0.24591	0.0883:0.0:0.7378:0.1739	rs11554421;rs11554421	141;141;141	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	T	141	ENSP00000441972:A141T;ENSP00000313059:A141T;ENSP00000444465:A141T;ENSP00000392542:A141T;ENSP00000433548:A141T	ENSP00000313059:A141T	A	+	1	0	WNK1	733413	0.770000	0.28543	0.079000	0.20413	0.448000	0.32197	2.054000	0.41335	2.264000	0.75181	0.561000	0.74099	GCC	G|0.938;A|0.062	0.062	strong		0.721	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
SCNN1D	6339	hgsc.bcm.edu	37	1	1226889	1226889	+	Missense_Mutation	SNP	G	G	A	rs609805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1226889G>A	ENST00000338555.2	+	15	2960	c.1816G>A	c.(1816-1818)Ggg>Agg	p.G606R	SCNN1D_ENST00000400928.3_Missense_Mutation_p.G606R|SCNN1D_ENST00000325425.8_Missense_Mutation_p.G672R|SCNN1D_ENST00000379116.5_Missense_Mutation_p.G770R			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	606			G -> R (in dbSNP:rs609805). {ECO:0000269|PubMed:14702039}.		ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	GGAGCCCAGCGGGCCTCATCT	0.687													G|||	550	0.109824	0.1467	0.0836	5008	,	,		15573	0.1478		0.0378	False		,,,				2504	0.1135				p.G770R		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G2308A						PASS	.	G	ARG/GLY	443,3895		16,411,1742	14.0	18.0	17.0		2308	-5.4	0.0	1	dbSNP_83	17	239,8279		6,227,4026	yes	missense	SCNN1D	NM_001130413.3	125	22,638,5768	AA,AG,GG		2.8058,10.2121,5.3049	benign	770/803	1226889	682,12174	2169	4259	6428	SO:0001583	missense	6339	exon18			CCCAGCGGGCCTC	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.1816G>A	1.37:g.1226889G>A	ENSP00000339504:p.Gly606Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		226	0.10347985347985347	83	0.16869918699186992	40	0.11049723756906077	76	0.13286713286713286	27	0.03562005277044855	G	7.126	0.578837	0.13686	0.102121	0.028058	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928	T;T;T;T	0.69806	-0.43;-0.34;-0.38;-0.34	2.72	-5.43	0.02632	.	3.111310	0.01956	N	0.042969	T	0.00144	0.0004	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.18461	0.002;0.007;0.028	B;B;B	0.08055	0.001;0.001;0.003	T	0.03555	-1.1025	9	0.17832	T	0.49	.	0.585	0.00718	0.2229:0.1426:0.236:0.3985	rs609805	428;606;770	B1AMF2;P51172;A6NNF7	.;SCNND_HUMAN;.	R	637;770;606;672;606	ENSP00000368411:G770R;ENSP00000339504:G606R;ENSP00000321594:G672R;ENSP00000383717:G606R	ENSP00000321594:G672R	G	+	1	0	SCNN1D	1216752	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.943000	0.00682	-1.836000	0.01190	-0.350000	0.07774	GGG	G|0.929;A|0.071	0.071	strong		0.687	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
ANKRD50	57182	hgsc.bcm.edu	37	4	125591687	125591687	+	Silent	SNP	A	A	G	rs3733471	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:125591687A>G	ENST00000504087.1	-	4	3782	c.2745T>C	c.(2743-2745)aaT>aaC	p.N915N	ANKRD50_ENST00000515641.1_Silent_p.N736N	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	915										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CCCGCAGTGCATTTCTTCCAT	0.408													G|||	1439	0.28734	0.3933	0.2233	5008	,	,		23630	0.2629		0.2107	False		,,,				2504	0.2935				p.N915N		Atlas-SNP	.											.	ANKRD50	136	.	0			c.T2745C						PASS	.	G	,	1571,2835	667.9+/-401.9	259,1053,891	100.0	97.0	98.0		2208,2745	-6.2	0.1	4	dbSNP_107	98	1803,6797	732.6+/-406.8	203,1397,2700	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	462,2450,3591	GG,GA,AA		20.9651,35.6559,25.9419	,	736/1251,915/1430	125591687	3374,9632	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			CAGTGCATTTCTT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2745T>C	4.37:g.125591687A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	194	81	0.417526	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			A|0.742;G|0.258	0.258	strong		0.408	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
FAT1	2195	hgsc.bcm.edu	37	4	187538330	187538330	+	Silent	SNP	G	G	A	rs1280099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:187538330G>A	ENST00000441802.2	-	11	9113	c.8904C>T	c.(8902-8904)gcC>gcT	p.A2968A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2968	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAGTTTCAACGGCAAACTGTC	0.348										HNSCC(5;0.00058)			A|||	2084	0.416134	0.5424	0.4683	5008	,	,		17635	0.2808		0.4662	False		,,,				2504	0.2965				p.A2968A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8904T						PASS	.	A		1961,1693		534,893,400	122.0	110.0	113.0		8904	0.3	0.9	4	dbSNP_87	113	3659,4507		820,2019,1244	no	coding-synonymous	FAT1	NM_005245.3		1354,2912,1644	AA,AG,GG		44.8077,46.3328,47.5465		2968/4589	187538330	5620,6200	1827	4083	5910	SO:0001819	synonymous_variant	2195	exon11			TTCAACGGCAAAC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8904C>T	4.37:g.187538330G>A		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.546;A|0.453	0.453	strong		0.348	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
LAMA5	3911	hgsc.bcm.edu	37	20	60899206	60899206	+	Missense_Mutation	SNP	C	C	T	rs2427283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60899206C>T	ENST00000252999.3	-	43	5764	c.5698G>A	c.(5698-5700)Gtg>Atg	p.V1900M		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1900	Laminin EGF-like 17. {ECO:0000255|PROSITE-ProRule:PRU00460}.		V -> M (in dbSNP:rs2427283). {ECO:0000269|PubMed:11821406}.		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)	p.V1900M(1)		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)			CTGCTGCTCACGAAGCCAGCC	0.662													.|||	3319	0.66274	0.5416	0.7061	5008	,	,		16749	0.7907		0.667	False		,,,				2504	0.6595				p.V1900M		Atlas-SNP	.											LAMA5,NS,carcinoma,0,1	LAMA5	268	1	1	Substitution - Missense(1)	stomach(1)	c.G5698A						PASS	.	C	MET/VAL	2384,2004		649,1086,459	28.0	31.0	30.0		5698	2.0	0.0	20	dbSNP_100	30	5993,2561		2109,1775,393	yes	missense	LAMA5	NM_005560.3	21	2758,2861,852	TT,TC,CC		29.9392,45.67,35.2728	probably-damaging	1900/3696	60899206	8377,4565	2194	4277	6471	SO:0001583	missense	3911	exon43			TGCTCACGAAGCC	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.5698G>A	20.37:g.60899206C>T	ENSP00000252999:p.Val1900Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1478	0.6767399267399268	255	0.5182926829268293	254	0.7016574585635359	455	0.7954545454545454	514	0.6781002638522428	C	10.02	1.236089	0.22626	0.5433	0.700608	ENSG00000130702	ENST00000252999	T	0.62498	0.02	4.22	1.99	0.26369	EGF-like, laminin (4);	0.390864	0.25225	U	0.032219	T	0.00012	0.0000	L	0.59967	1.855	0.58432	P	1.0000000000287557E-6	P	0.44627	0.839	B	0.36719	0.231	T	0.33701	-0.9858	9	0.44086	T	0.13	.	5.8577	0.18728	0.0:0.526:0.3043:0.1697	rs2427283;rs57380273;rs2427283	1900	O15230	LAMA5_HUMAN	M	1900	ENSP00000252999:V1900M	ENSP00000252999:V1900M	V	-	1	0	LAMA5	60332601	0.237000	0.23815	0.017000	0.16124	0.121000	0.20230	0.486000	0.22340	0.699000	0.31761	0.478000	0.44815	GTG	C|0.350;T|0.650	0.650	strong		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SLC22A7	10864	hgsc.bcm.edu	37	6	43270151	43270151	+	Splice_Site	SNP	C	C	T	rs2270860	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	25	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	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
KIAA1024	23251	hgsc.bcm.edu	37	15	79749447	79749447	+	Missense_Mutation	SNP	G	G	T	rs11634652	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79749447G>T	ENST00000305428.3	+	2	1033	c.958G>T	c.(958-960)Gtt>Ttt	p.V320F		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	320			V -> F (in dbSNP:rs11634652).			integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						GTATTCCCCGGTTCCTGACAA	0.522													G|||	670	0.133786	0.3321	0.049	5008	,	,		18437	0.0823		0.0636	False		,,,				2504	0.0511				p.V320F		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G958T						PASS	.	G	PHE/VAL	1225,3167	425.3+/-340.8	180,865,1151	127.0	135.0	132.0		958	-1.6	0.0	15	dbSNP_120	132	523,8063	146.5+/-202.0	14,495,3784	yes	missense	KIAA1024	NM_015206.2	50	194,1360,4935	TT,TG,GG		6.0913,27.8916,13.4689	benign	320/917	79749447	1748,11230	2196	4293	6489	SO:0001583	missense	23251	exon2			TCCCCGGTTCCTG	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.958G>T	15.37:g.79749447G>T	ENSP00000307461:p.Val320Phe	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	285	0.1304945054945055	167	0.3394308943089431	23	0.06353591160220995	46	0.08041958041958042	49	0.06464379947229551	G	10.64	1.407212	0.25378	0.278916	0.060913	ENSG00000169330	ENST00000305428	T	0.32515	1.45	5.01	-1.58	0.08479	.	0.611918	0.15992	N	0.234776	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.29085	0.232	B	0.24701	0.055	T	0.46133	-0.9213	8	.	.	.	.	6.2025	0.20583	0.4768:0.1324:0.3908:0.0	rs11634652;rs52819290;rs56800743;rs11634652	320	Q9UPX6	K1024_HUMAN	F	320	ENSP00000307461:V320F	.	V	+	1	0	KIAA1024	77536502	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	0.248000	0.18198	-0.097000	0.12307	0.591000	0.81541	GTT	G|0.866;T|0.134	0.134	strong		0.522	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
TRIO	7204	hgsc.bcm.edu	37	5	14498727	14498727	+	Silent	SNP	G	G	A	rs26107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:14498727G>A	ENST00000344204.4	+	53	8334	c.8310G>A	c.(8308-8310)tcG>tcA	p.S2770S	TRIO_ENST00000344135.5_Silent_p.S269S|TRIO_ENST00000537187.1_Silent_p.S2594S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2770	Ig-like C2-type.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CAGCCTCATCGTCGGCCAGCC	0.577													G|||	560	0.111821	0.0537	0.2089	5008	,	,		22675	0.13		0.0934	False		,,,				2504	0.1217				p.S2770S		Atlas-SNP	.											.	TRIO	305	.	0			c.G8310A						PASS	.	G		242,4164	139.2+/-174.8	5,232,1966	188.0	158.0	168.0		8310	-10.6	0.0	5	dbSNP_76	168	1034,7566	221.0+/-258.6	77,880,3343	no	coding-synonymous	TRIO	NM_007118.2		82,1112,5309	AA,AG,GG		12.0233,5.4925,9.8109		2770/3098	14498727	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon53			CTCATCGTCGGCC	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.8310G>A	5.37:g.14498727G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.894;N|0.000	.	strong		0.577	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
WFS1	7466	hgsc.bcm.edu	37	4	6302830	6302830	+	Silent	SNP	C	C	T	rs71539646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:6302830C>T	ENST00000226760.1	+	8	1478	c.1308C>T	c.(1306-1308)acC>acT	p.T436T	WFS1_ENST00000503569.1_Silent_p.T436T	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	436					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		CTGTCATCACCGGCTTCTTTA	0.622													c|||	21	0.00419329	0.0	0.0058	5008	,	,		21550	0.003		0.0099	False		,,,				2504	0.0041				p.T436T		Atlas-SNP	.											.	WFS1	71	.	0			c.C1308T						PASS	.		,	7,4399	11.4+/-27.6	0,7,2196	118.0	118.0	118.0		1308,1308	1.6	0.0	4	dbSNP_130	118	104,8496	56.0+/-117.1	0,104,4196	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	0,111,6392	TT,TC,CC		1.2093,0.1589,0.8535	,	436/891,436/891	6302830	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			CATCACCGGCTTC	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.1308C>T	4.37:g.6302830C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			C|0.994;T|0.006	0.006	strong		0.622	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
RCBTB1	55213	hgsc.bcm.edu	37	13	50126382	50126382	+	Silent	SNP	G	G	A	rs2274278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:50126382G>A	ENST00000378302.2	-	7	903	c.643C>T	c.(643-645)Ctg>Ttg	p.L215L	RCBTB1_ENST00000258646.3_Silent_p.L215L|RCBTB1_ENST00000546015.1_Silent_p.L215L	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	215					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		TTGTTTCCCAGGCCCAGCTGA	0.517													A|||	4302	0.859026	0.8911	0.8732	5008	,	,		17924	0.8889		0.8241	False		,,,				2504	0.8108				p.L215L		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C643T						PASS	.	A		3950,456		1773,404,26	67.0	45.0	52.0		643	0.3	1.0	13	dbSNP_100	52	7172,1428		2977,1218,105	no	coding-synonymous	RCBTB1	NM_018191.3		4750,1622,131	AA,AG,GG		16.6047,10.3495,14.4856		215/532	50126382	11122,1884	2203	4300	6503	SO:0001819	synonymous_variant	55213	exon7			TTCCCAGGCCCAG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.643C>T	13.37:g.50126382G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			G|0.139;A|0.861	0.861	strong		0.517	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
CFTR	1080	hgsc.bcm.edu	37	7	117235055	117235055	+	Silent	SNP	T	T	G	rs397508396|rs1042077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	141	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	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	
ZZZ3	26009	hgsc.bcm.edu	37	1	78098403	78098403	+	Missense_Mutation	SNP	T	T	C	rs34535037	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:78098403T>C	ENST00000370801.3	-	5	1112	c.637A>G	c.(637-639)Ata>Gta	p.I213V	ZZZ3_ENST00000370798.1_Intron|ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	213					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						TCACAGTTTATAACAGCTGAA	0.418													T|||	127	0.0253594	0.0015	0.049	5008	,	,		22914	0.0248		0.0219	False		,,,				2504	0.045				p.I213V		Atlas-SNP	.											.	ZZZ3	80	.	0			c.A637G						PASS	.	T	VAL/ILE	19,4387	25.3+/-52.1	0,19,2184	113.0	110.0	111.0		637	0.4	1.0	1	dbSNP_126	111	140,8460	68.7+/-131.2	1,138,4161	yes	missense	ZZZ3	NM_015534.4	29	1,157,6345	CC,CT,TT		1.6279,0.4312,1.2225	benign	213/904	78098403	159,12847	2203	4300	6503	SO:0001583	missense	26009	exon5			AGTTTATAACAGC	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.637A>G	1.37:g.78098403T>C	ENSP00000359837:p.Ile213Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	37	CCDS677.1	42	0.019230769230769232	1	0.0020325203252032522	10	0.027624309392265192	13	0.022727272727272728	18	0.023746701846965697	T	3.784	-0.045131	0.07452	0.004312	0.016279	ENSG00000036549	ENST00000370801	.	.	.	5.49	0.375	0.16188	.	0.481200	0.23983	N	0.042651	T	0.12475	0.0303	N	0.22421	0.69	0.49389	D	0.999784	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.08289	-1.0729	8	.	.	.	.	1.7365	0.02943	0.1194:0.3162:0.2148:0.3496	rs34535037	213;213;213	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	V	213	.	.	I	-	1	0	ZZZ3	77870991	0.942000	0.31987	0.999000	0.59377	0.989000	0.77384	0.288000	0.18939	0.455000	0.26910	0.528000	0.53228	ATA	T|0.984;C|0.016	0.016	strong		0.418	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577650	90577650	+	RNA	SNP	T	T	G	rs200433993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:90577650T>G	ENST00000551025.1	+	0	6078									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)		AAATACGACGTGCAACACCAT	0.443													T|||	5	0.000998403	0.0	0.0	5008	,	,		21746	0.0		0.005	False		,,,				2504	0.0				p.R1547R	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											CASP8AP2,caecum,carcinoma,+2,1	CASP8AP2	108	1	0			c.T4641G						PASS	.	T	,,	5,3875		0,5,1935	142.0	128.0	133.0		4641,4641,4641	4.3	1.0	6		133	22,8250		0,22,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	0,27,6049	GG,GT,TT		0.266,0.1289,0.2222	,,	1547/1967,1547/1967,1547/1967	90577650	27,12125	1940	4136	6076			9994	exon8			ACGACGTGCAACA	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.90577650T>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	37	0.385417	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				T|0.996;G|0.004	0.004	strong		0.443	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
AVPI1	60370	hgsc.bcm.edu	37	10	99439673	99439673	+	Splice_Site	SNP	C	C	G	rs3818780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	45	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	.	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
ATRNL1	26033	hgsc.bcm.edu	37	10	117486763	117486763	+	Silent	SNP	G	G	T	rs2254619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:117486763G>T	ENST00000355044.3	+	27	3927	c.3801G>T	c.(3799-3801)ctG>ctT	p.L1267L	ATRNL1_ENST00000303745.7_Silent_p.L60L|ATRNL1_ENST00000423111.2_Silent_p.L318L	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	18	0	0		WXS	Illumina HiSeq	Phase_I	25	25	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	
REV1	51455	hgsc.bcm.edu	37	2	100058870	100058870	+	Missense_Mutation	SNP	C	C	T	rs3087403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	110	0	0		WXS	Illumina HiSeq	Phase_I	144	59	0.409722	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	
OR4N2	390429	hgsc.bcm.edu	37	14	20296004	20296004	+	Missense_Mutation	SNP	C	C	T	rs2318279	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	267	0	0		WXS	Illumina HiSeq	Phase_I	348	62	0.178161	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		
ZNF100	163227	hgsc.bcm.edu	37	19	21910621	21910621	+	Silent	SNP	A	A	G	rs11556742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:21910621A>G	ENST00000358296.6	-	5	691	c.493T>C	c.(493-495)Tta>Cta	p.L165L	ZNF100_ENST00000305570.6_Silent_p.L101L	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	165					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						CACTGGTTTAATTTGTTATCA	0.313													N|||	92	0.0183706	0.0023	0.0576	5008	,	,		16971	0.0		0.0249	False		,,,				2504	0.0245				p.L165L		Atlas-SNP	.											.	ZNF100	62	.	0			c.T493C						PASS	.	A		16,4080		0,16,2032	168.0	169.0	169.0		493	1.4	0.0	19	dbSNP_120	169	178,8286		1,176,4055	no	coding-synonymous	ZNF100	NM_173531.3		1,192,6087	GG,GA,AA		2.103,0.3906,1.5446		165/543	21910621	194,12366	2048	4232	6280	SO:0001819	synonymous_variant	163227	exon5			GGTTTAATTTGTT	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.493T>C	19.37:g.21910621A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			A|0.980;G|0.020	0.020	strong		0.313	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
TRPM1	4308	hgsc.bcm.edu	37	15	31294702	31294702	+	Missense_Mutation	SNP	G	G	T	rs61734298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:31294702G>T	ENST00000256552.6	-	28	4348	c.4201C>A	c.(4201-4203)Cca>Aca	p.P1401T	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.P1418T|TRPM1_ENST00000397795.2_Missense_Mutation_p.P1379T	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)		TTTAAACTTGGGGAAATAGTT	0.353													G|||	89	0.0177716	0.0045	0.0216	5008	,	,		22427	0.0		0.0268	False		,,,				2504	0.0419				p.P1418T		Atlas-SNP	.											.	TRPM1	183	.	0			c.C4252A						PASS	.	G	THR/PRO	28,3676		0,28,1824	173.0	160.0	164.0		4135	0.5	0.0	15	dbSNP_129	164	333,7843		9,315,3764	yes	missense	TRPM1	NM_002420.4	38	9,343,5588	TT,TG,GG		4.0729,0.7559,3.0387	benign	1379/1604	31294702	361,11519	1852	4088	5940	SO:0001583	missense	4308	exon27			AACTTGGGGAAAT	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.4201C>A	15.37:g.31294702G>T	ENSP00000256552:p.Pro1401Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	35	0.016025641025641024	3	0.006097560975609756	8	0.022099447513812154	0	0.0	24	0.0316622691292876	G	2.051	-0.417829	0.04766	0.007559	0.040729	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.49720	0.79;0.77;0.8	4.68	0.513	0.17000	.	4.558330	0.00465	N	0.000106	T	0.10208	0.0250	N	0.14661	0.345	0.09310	N	1	B;B	0.18968	0.032;0.019	B;B	0.25614	0.062;0.028	T	0.18304	-1.0341	10	0.37606	T	0.19	-0.012	8.7758	0.34760	0.3244:0.0:0.6756:0.0	.	1373;1379	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	T	1379;1418;1401;1379	ENSP00000380897:P1379T;ENSP00000437849:P1418T;ENSP00000256552:P1401T	ENSP00000256552:P1401T	P	-	1	0	TRPM1	29081994	0.306000	0.24490	0.000000	0.03702	0.065000	0.16274	0.904000	0.28491	-0.186000	0.10533	-0.145000	0.13849	CCA	G|0.977;T|0.023	0.023	strong		0.353	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
TMTC4	84899	hgsc.bcm.edu	37	13	101287340	101287340	+	Missense_Mutation	SNP	C	C	T	rs946837	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:101287340C>T	ENST00000376234.3	-	10	1444	c.1255G>A	c.(1255-1257)Gtt>Att	p.V419I	TMTC4_ENST00000342624.5_Missense_Mutation_p.V438I|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Missense_Mutation_p.V308I	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	419			V -> I (in dbSNP:rs946837).			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)					CAGTACCCAACGCTGGGGAGG	0.532													.|||	1950	0.389377	0.3805	0.245	5008	,	,		18621	0.6052		0.3022	False		,,,				2504	0.3712				p.V438I		Atlas-SNP	.											TMTC4,caecum,carcinoma,0,1	TMTC4	103	1	0			c.G1312A						PASS	.	C	ILE/VAL,ILE/VAL	1575,2831	491.7+/-362.2	274,1027,902	79.0	73.0	75.0		1255,1312	2.4	0.0	13	dbSNP_86	75	2561,6039	416.8+/-352.2	387,1787,2126	yes	missense,missense	TMTC4	NM_001079669.1,NM_032813.2	29,29	661,2814,3028	TT,TC,CC		29.7791,35.7467,31.8007	benign,benign	419/742,438/761	101287340	4136,8870	2203	4300	6503	SO:0001583	missense	84899	exon11			ACCCAACGCTGGG		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.1255G>A	13.37:g.101287340C>T	ENSP00000365408:p.Val419Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	837	0.38324175824175827	200	0.4065040650406504	82	0.2265193370165746	330	0.5769230769230769	225	0.29683377308707126	C	0.773	-0.765192	0.02996	0.357467	0.297791	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.51071	0.72;0.72;0.72	5.5	2.4	0.29515	.	0.364899	0.31415	N	0.007686	T	0.00012	0.0000	N	0.17723	0.515	0.80722	P	0.0	B;B;B;B	0.12013	0.002;0.001;0.0;0.005	B;B;B;B	0.12837	0.005;0.008;0.002;0.002	T	0.45145	-0.9281	9	0.10377	T	0.69	.	8.9018	0.35499	0.0:0.6428:0.0:0.3572	rs946837;rs17613595;rs52804855;rs61344452;rs946837	308;419;419;438	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	I	419;438;308	ENSP00000365408:V419I;ENSP00000343871:V438I;ENSP00000365409:V308I	ENSP00000365409:V308I	V	-	1	0	TMTC4	100085341	0.022000	0.18835	0.004000	0.12327	0.099000	0.18886	1.160000	0.31761	0.697000	0.31718	-0.251000	0.11542	GTT	C|0.645;N|0.001	.	strong		0.532	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
PGLYRP4	57115	hgsc.bcm.edu	37	1	153313044	153313044	+	Missense_Mutation	SNP	C	C	T	rs12063091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:153313044C>T	ENST00000359650.5	-	7	701	c.637G>A	c.(637-639)Gtt>Att	p.V213I	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.V209I	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	213			V -> I (in dbSNP:rs12063091). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.V213I(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CGTGGGACAACGCCGGGGCAA	0.592													c|||	295	0.0589058	0.1536	0.0389	5008	,	,		13931	0.0		0.0398	False		,,,				2504	0.0256				p.V213I		Atlas-SNP	.											PGLYRP4,NS,carcinoma,0,1	PGLYRP4	45	1	1	Substitution - Missense(1)	prostate(1)	c.G637A						scavenged	.	C	ILE/VAL	580,3826	255.2+/-260.5	29,522,1652	46.0	45.0	45.0		637	-0.3	0.0	1	dbSNP_120	45	515,8085	145.7+/-201.4	9,497,3794	yes	missense	PGLYRP4	NM_020393.2	29	38,1019,5446	TT,TC,CC		5.9884,13.1639,8.4192	benign	213/374	153313044	1095,11911	2203	4300	6503	SO:0001583	missense	57115	exon7			GGACAACGCCGGG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.637G>A	1.37:g.153313044C>T	ENSP00000352672:p.Val213Ile	Somatic	28	1	0.0357143		WXS	Illumina HiSeq	Phase_I	42	25	0.595238	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	126	0.057692307692307696	87	0.17682926829268292	13	0.03591160220994475	0	0.0	26	0.03430079155672823	c	0	-2.799602	0.00076	0.131639	0.059884	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.14640	2.49;2.49	3.64	-0.273	0.12915	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (2);	0.338684	0.23220	N	0.050576	T	0.00440	0.0014	N	0.00053	-2.39	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.39057	-0.9632	9	0.02654	T	1	-25.9949	6.3688	0.21469	0.0:0.3413:0.0:0.6587	rs12063091;rs12063091	209;213	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	I	209;213	ENSP00000357728:V209I;ENSP00000352672:V213I	ENSP00000352672:V213I	V	-	1	0	PGLYRP4	151579668	0.012000	0.17670	0.013000	0.15412	0.016000	0.09150	0.482000	0.22276	-0.183000	0.10585	-1.149000	0.01842	GTT	C|0.923;T|0.077	0.077	strong		0.592	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
SCN11A	11280	hgsc.bcm.edu	37	3	38888764	38888764	+	Silent	SNP	G	G	A	rs62244134	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38888764G>A	ENST00000302328.3	-	26	4995	c.4797C>T	c.(4795-4797)taC>taT	p.Y1599Y	SCN11A_ENST00000456224.3_Silent_p.Y1561Y|SCN11A_ENST00000450244.1_Silent_p.Y1599Y	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1599					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCACAGCAATGTACATGTTGA	0.403													G|||	289	0.0577077	0.0348	0.0663	5008	,	,		22909	0.003		0.1153	False		,,,				2504	0.0798				p.Y1599Y		Atlas-SNP	.											.	SCN11A	296	.	0			c.C4797T						PASS	.	G		275,4131	154.8+/-188.1	5,265,1933	124.0	123.0	123.0		4797	-4.1	0.9	3	dbSNP_129	123	1033,7567	220.2+/-258.0	61,911,3328	no	coding-synonymous	SCN11A	NM_014139.2		66,1176,5261	AA,AG,GG		12.0116,6.2415,10.0569		1599/1792	38888764	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	11280	exon26			AGCAATGTACATG	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4797C>T	3.37:g.38888764G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	CCDS33737.1																																																																																			G|0.911;A|0.089	0.089	strong		0.403	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
ANLN	54443	hgsc.bcm.edu	37	7	36445856	36445856	+	Missense_Mutation	SNP	G	G	A	rs386712160|rs197367	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:36445856G>A	ENST00000265748.2	+	4	775	c.554G>A	c.(553-555)aGa>aAa	p.R185K	ANLN_ENST00000396068.2_Missense_Mutation_p.R185K	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	185	Nuclear localization.		R -> K (in dbSNP:rs197367). {ECO:0000269|PubMed:10931866, ECO:0000269|PubMed:16964243}.		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						TCCCCTCCCAGACCTCTGCTT	0.468													A|||	3108	0.620607	0.4145	0.6254	5008	,	,		18730	0.7153		0.6262	False		,,,				2504	0.7924				p.R185K		Atlas-SNP	.											.	ANLN	101	.	0			c.G554A						PASS	.	A	LYS/ARG	1906,2500		500,906,797	75.0	76.0	76.0		554	3.6	0.0	7	dbSNP_79	76	5105,3495		1706,1693,901	yes	missense	ANLN	NM_018685.2	26	2206,2599,1698	AA,AG,GG		40.6395,43.2592,46.0941	benign	185/1125	36445856	7011,5995	2203	4300	6503	SO:0001583	missense	54443	exon4			CTCCCAGACCTCT	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.554G>A	7.37:g.36445856G>A	ENSP00000265748:p.Arg185Lys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	145	41	0.282759	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	37	CCDS5447.1	1352	0.6190476190476191	203	0.41260162601626016	225	0.6215469613259669	432	0.7552447552447552	492	0.6490765171503958	A	0.134	-1.109485	0.01813	0.432592	0.593605	ENSG00000011426	ENST00000265748;ENST00000396068;ENST00000424865	T;T;T	0.24151	4.08;4.08;1.87	5.95	3.61	0.41365	.	0.393945	0.29145	N	0.013017	T	0.00012	0.0000	N	0.00092	-2.175	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	0.42430	-0.9452	9	0.02654	T	1	-10.7367	9.6729	0.40023	0.8051:0.0:0.1949:0.0	rs62873663	185;185;185	A8K5D9;Q9NQW6-2;Q9NQW6	.;.;ANLN_HUMAN	K	185;185;163	ENSP00000265748:R185K;ENSP00000379380:R185K;ENSP00000404979:R163K	ENSP00000265748:R185K	R	+	2	0	ANLN	36412381	0.966000	0.33281	0.022000	0.16811	0.180000	0.23129	1.913000	0.39956	0.171000	0.19730	-0.269000	0.10298	AGA	G|0.431;A|0.569	0.569	strong		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
CEP250	11190	hgsc.bcm.edu	37	20	34089718	34089718	+	Silent	SNP	G	G	T	rs2274238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34089718G>T	ENST00000397527.1	+	29	4665	c.3945G>T	c.(3943-3945)ctG>ctT	p.L1315L	CEP250_ENST00000342580.4_Silent_p.L1259L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1315	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AATCTGAGCTGATGGAACTAC	0.498													G|||	362	0.0722843	0.0643	0.0692	5008	,	,		22156	0.0794		0.0239	False		,,,				2504	0.1278				p.L1315L		Atlas-SNP	.											.	CEP250	141	.	0			c.G3945T						PASS	.	G		247,4159	142.7+/-177.9	10,227,1966	81.0	79.0	79.0		3945	4.1	1.0	20	dbSNP_100	79	169,8431	78.4+/-141.0	4,161,4135	no	coding-synonymous	CEP250	NM_007186.3		14,388,6101	TT,TG,GG		1.9651,5.606,3.1985		1315/2443	34089718	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	11190	exon29			TGAGCTGATGGAA	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.3945G>T	20.37:g.34089718G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			G|0.953;T|0.047	0.047	strong		0.498	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
GOT2	2806	hgsc.bcm.edu	37	16	58768129	58768129	+	Missense_Mutation	SNP	C	C	A	rs11558171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:58768129C>A	ENST00000245206.5	-	1	132	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	GOT2_ENST00000564400.1_5'UTR|GOT2_ENST00000434819.2_Missense_Mutation_p.A2S	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	2			A -> S (in dbSNP:rs11558171).		2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	TGCAGCAGGGCCATGGTGGAC	0.706											OREG0023844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	217	0.0433307	0.0045	0.0432	5008	,	,		13779	0.0		0.1203	False		,,,				2504	0.0613				p.A2S		Atlas-SNP	.											GOT2,NS,carcinoma,0,1	GOT2	42	1	0			c.G4T						PASS	.	C	SER/ALA	96,4034		0,96,1969	6.0	7.0	7.0		4	4.9	1.0	16	dbSNP_120	7	931,7311		34,863,3224	no	missense	GOT2	NM_002080.2	99	34,959,5193	AA,AC,CC		11.2958,2.3245,8.301	benign	2/431	58768129	1027,11345	2065	4121	6186	SO:0001583	missense	2806	exon1			GCAGGGCCATGGT		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.4G>T	16.37:g.58768129C>A	ENSP00000245206:p.Ala2Ser	Somatic	10	0	0	1033	WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	CCDS10801.1	116	0.05311355311355311	7	0.014227642276422764	17	0.04696132596685083	0	0.0	92	0.12137203166226913	C	17.68	3.449346	0.63178	0.023245	0.112958	ENSG00000125166	ENST00000245206;ENST00000434819;ENST00000425685	T;T	0.20463	2.14;2.07	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	L	0.36672	1.1	0.38751	D	0.954117	D;D	0.58970	0.984;0.984	D;D	0.65443	0.935;0.935	T	0.00414	-1.1754	9	.	.	.	0.0015	13.5501	0.61728	0.0:1.0:0.0:0.0	rs11558171	2;2	E7ERW2;P00505	.;AATM_HUMAN	S	2	ENSP00000245206:A2S;ENSP00000394100:A2S	.	A	-	1	0	GOT2	57325630	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.168000	0.50801	2.558000	0.86282	0.563000	0.77884	GCC	C|0.946;A|0.054	0.054	strong		0.706	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
CSTL1	128817	hgsc.bcm.edu	37	20	23424638	23424638	+	Missense_Mutation	SNP	C	C	T	rs3746737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23424638C>T	ENST00000246020.2	+	2	307	c.287C>T	c.(286-288)aCg>aTg	p.T96M	CSTL1_ENST00000347397.1_Missense_Mutation_p.T96M			Q9H114	CST1L_HUMAN	cystatin-like 1	96			T -> M (in dbSNP:rs3746737).			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.T96M(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					AGGAATGACACGAGCAATTCT	0.468													C|||	638	0.127396	0.0378	0.1542	5008	,	,		20391	0.2996		0.0795	False		,,,				2504	0.1012				p.T96M		Atlas-SNP	.											CSTL1,NS,carcinoma,0,1	CSTL1	30	1	1	Substitution - Missense(1)	stomach(1)	c.C287T						PASS	.	C	MET/THR	189,4217	118.4+/-156.1	4,181,2018	137.0	116.0	123.0		287	-7.8	0.0	20	dbSNP_107	123	695,7905	171.9+/-222.7	33,629,3638	yes	missense	CSTL1	NM_138283.1	81	37,810,5656	TT,TC,CC		8.0814,4.2896,6.7969	probably-damaging	96/146	23424638	884,12122	2203	4300	6503	SO:0001583	missense	128817	exon3			ATGACACGAGCAA	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.287C>T	20.37:g.23424638C>T	ENSP00000246020:p.Thr96Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_138283	Q17RA8|Q64FF7	Missense_Mutation	SNP	ENST00000246020.2	37	CCDS13153.1	291	0.13324175824175824	20	0.04065040650406504	53	0.1464088397790055	160	0.27972027972027974	58	0.07651715039577836	C	7.460	0.644517	0.14451	0.042896	0.080814	ENSG00000125823	ENST00000347397;ENST00000246020	T;T	0.27104	1.69;1.69	3.92	-7.84	0.01196	Proteinase inhibitor I25, cystatin (2);	2.031310	0.02546	N	0.095146	T	0.00012	0.0000	M	0.74258	2.255	0.80722	P	0.0	P	0.42649	0.786	B	0.37833	0.259	T	0.13255	-1.0516	9	0.48119	T	0.1	-9.4384	3.2703	0.06879	0.2021:0.1623:0.4632:0.1724	rs3746737;rs17830517;rs52797059;rs58774540;rs3746737	96	Q9H114	CST1L_HUMAN	M	96	ENSP00000344907:T96M;ENSP00000246020:T96M	ENSP00000246020:T96M	T	+	2	0	CSTL1	23372638	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.916000	0.01576	-1.909000	0.01085	-1.018000	0.02450	ACG	C|0.903;T|0.097	0.097	strong		0.468	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
NCS1	23413	hgsc.bcm.edu	37	9	132988709	132988709	+	Silent	SNP	T	T	G	rs2277200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:132988709T>G	ENST00000372398.3	+	7	602	c.516T>G	c.(514-516)ggT>ggG	p.G172G	NCS1_ENST00000458469.1_Silent_p.G154G	NM_014286.3	NP_055101.2	P62166	NCS1_HUMAN	neuronal calcium sensor 1	172	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion transmembrane transport (GO:0070588)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of exocytosis (GO:0045921)|regulation of neuron projection development (GO:0010975)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|voltage-gated calcium channel activity (GO:0005245)	p.G172G(1)		large_intestine(1)|lung(4)|stomach(1)	6						TCCAGGAGGGTTCCAAGGCAG	0.642													g|||	1566	0.3127	0.4667	0.4683	5008	,	,		17391	0.1379		0.3091	False		,,,				2504	0.1779				p.G172G	Melanoma(30;182 1162 22581 33240)	Atlas-SNP	.											NCS1,colon,carcinoma,0,2	NCS1	18	2	1	Substitution - coding silent(1)	stomach(1)	c.T516G						PASS	.		,	1877,2529	625.1+/-394.5	361,1155,687	51.0	44.0	47.0		462,516	-4.5	0.9	9	dbSNP_100	47	2873,5727	668.0+/-402.5	478,1917,1905	no	coding-synonymous,coding-synonymous	NCS1	NM_001128826.1,NM_014286.3	,	839,3072,2592	GG,GT,TT		33.407,42.601,36.5216	,	154/173,172/191	132988709	4750,8256	2203	4300	6503	SO:0001819	synonymous_variant	23413	exon7			GGAGGGTTCCAAG	AF186409	CCDS6932.1	9q34.11	2013-01-10	2010-01-27	2010-01-27	ENSG00000107130	ENSG00000107130		"""EF-hand domain containing"""	3953	protein-coding gene	gene with protein product		603315	"""frequenin (Drosophila) homolog"", ""frequenin homolog (Drosophila)"""	FREQ		11092894	Standard	NM_014286		Approved	NCS-1	uc004bzi.2	P62166	OTTHUMG00000020801	ENST00000372398.3:c.516T>G	9.37:g.132988709T>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_014286	E9PAY3|P36610|Q9UK26	Silent	SNP	ENST00000372398.3	37	CCDS6932.1																																																																																			T|0.646;G|0.354	0.354	strong		0.642	NCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054637.1	NM_014286	
ROBO4	54538	hgsc.bcm.edu	37	11	124767067	124767067	+	Missense_Mutation	SNP	T	T	C	rs59648931	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124767067T>C	ENST00000306534.3	-	2	646	c.161A>G	c.(160-162)cAa>cGa	p.Q54R	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Intron	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	104	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	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	
SKA3	221150	hgsc.bcm.edu	37	13	21735998	21735998	+	Missense_Mutation	SNP	T	T	C	rs17345690	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21735998T>C	ENST00000314759.5	-	5	884	c.760A>G	c.(760-762)Aca>Gca	p.T254A	SKA3_ENST00000400018.3_Missense_Mutation_p.T254A	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	254			T -> A (in dbSNP:rs17345690). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.T254A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CTGGATTCTGTATCTATGGCC	0.368													T|||	491	0.0980431	0.0666	0.0735	5008	,	,		16660	0.0972		0.1362	False		,,,				2504	0.1196				p.T254A		Atlas-SNP	.											SKA3,NS,carcinoma,0,1	SKA3	76	1	1	Substitution - Missense(1)	stomach(1)	c.A760G						PASS	.	T	ALA/THR,ALA/THR	343,4063	178.0+/-206.8	13,317,1873	134.0	136.0	135.0		760,760	1.3	0.0	13	dbSNP_123	135	1184,7416	239.0+/-270.3	71,1042,3187	yes	missense,missense	SKA3	NM_001166017.1,NM_145061.5	58,58	84,1359,5060	CC,CT,TT		13.7674,7.7848,11.7407	benign,benign	254/389,254/413	21735998	1527,11479	2203	4300	6503	SO:0001583	missense	221150	exon5			ATTCTGTATCTAT	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.760A>G	13.37:g.21735998T>C	ENSP00000319417:p.Thr254Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	249	0.11401098901098901	46	0.09349593495934959	30	0.08287292817679558	60	0.1048951048951049	113	0.14907651715039577	T	11.04	1.523280	0.27299	0.077848	0.137674	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.22945	1.93;1.93	4.99	1.32	0.21799	.	0.796448	0.11947	N	0.514052	T	0.00073	0.0002	L	0.56769	1.78	0.80722	P	0.0	B;B	0.20671	0.017;0.047	B;B	0.17979	0.02;0.02	T	0.31586	-0.9938	9	0.02654	T	1	-1.4902	1.4913	0.02457	0.1775:0.0953:0.1855:0.5418	rs17345690;rs17851040;rs52826626;rs17345690	254;254	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	A	254	ENSP00000319417:T254A;ENSP00000382896:T254A	ENSP00000319417:T254A	T	-	1	0	SKA3	20633998	0.001000	0.12720	0.030000	0.17652	0.059000	0.15707	0.091000	0.15046	0.436000	0.26393	0.482000	0.46254	ACA	T|0.886;C|0.114	0.114	strong		0.368	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
TBP	6908	hgsc.bcm.edu	37	6	170871067	170871067	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:170871067G>A	ENST00000392092.2	+	3	522	c.243G>A	c.(241-243)caG>caA	p.Q81Q	TBP_ENST00000230354.6_Silent_p.Q81Q|TBP_ENST00000540980.1_Silent_p.Q61Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	81	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)	p.Q81Q(1)		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	0.587																																					p.Q81Q		Atlas-SNP	.											TBP,NS,carcinoma,0,1	TBP	58	1	1	Substitution - coding silent(1)	kidney(1)	c.G243A						PASS	.						11.0	17.0	15.0					6																	170871067		1946	3814	5760	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.243G>A	6.37:g.170871067G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	7	0.179487	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			.	.	none		0.587	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
AQP4	361	hgsc.bcm.edu	37	18	24442392	24442392	+	Silent	SNP	C	C	A	rs35248760	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:24442392C>A	ENST00000383168.4	-	2	329	c.201G>T	c.(199-201)ccG>ccT	p.P67P	AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000578701.1_RNA|AQP4_ENST00000440832.3_Silent_p.P45P|AQP4_ENST00000581374.1_Silent_p.P45P|AQP4_ENST00000583022.1_5'Flank|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000582605.1_RNA	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4	67					carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					CCATGTCGACCGGTAAAGGCT	0.512													C|||	221	0.0441294	0.0068	0.1009	5008	,	,		21652	0.001		0.1223	False		,,,				2504	0.0184				p.P67P		Atlas-SNP	.											.	AQP4	27	.	0			c.G201T						PASS	.	C	,	122,4284	92.0+/-130.7	2,118,2083	180.0	162.0	168.0		201,135	-8.5	0.9	18	dbSNP_126	168	1050,7550	222.3+/-259.4	65,920,3315	no	coding-synonymous,coding-synonymous	AQP4	NM_001650.4,NM_004028.3	,	67,1038,5398	AA,AC,CC		12.2093,2.769,9.0112	,	67/324,45/302	24442392	1172,11834	2203	4300	6503	SO:0001819	synonymous_variant	361	exon2			GTCGACCGGTAAA	U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"""Ion channels / Aquaporins"""	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955	ENST00000383168.4:c.201G>T	18.37:g.24442392C>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	149	56	0.375839	NM_001650	P78564	Silent	SNP	ENST00000383168.4	37	CCDS11889.1																																																																																			C|0.914;A|0.086	0.086	strong		0.512	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254914.2	NM_001650, NM_004028	
DDX60L	91351	hgsc.bcm.edu	37	4	169382991	169382991	+	Silent	SNP	C	C	A	rs17612630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169382991C>A	ENST00000511577.1	-	5	712	c.465G>T	c.(463-465)acG>acT	p.T155T	DDX60L_ENST00000505890.1_Silent_p.T155T|DDX60L_ENST00000260184.7_Silent_p.T155T			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	155							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TAAAAAGGTACGTTTGTAAAT	0.368													c|||	402	0.0802716	0.0098	0.0648	5008	,	,		19306	0.0109		0.1948	False		,,,				2504	0.1401				p.T155T		Atlas-SNP	.											DDX60L,caecum,carcinoma,-1,1	DDX60L	116	1	0			c.G465T						PASS	.	C		123,3577		4,115,1731	59.0	53.0	55.0		465	-5.2	0.0	4	dbSNP_123	55	1461,6719		128,1205,2757	no	coding-synonymous	DDX60L	NM_001012967.1		132,1320,4488	AA,AC,CC		17.8606,3.3243,13.3333		155/1707	169382991	1584,10296	1850	4090	5940	SO:0001819	synonymous_variant	91351	exon5			AAGGTACGTTTGT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.465G>T	4.37:g.169382991C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.904;A|0.096	0.096	strong		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
OR5D16	390144	hgsc.bcm.edu	37	11	55606693	55606693	+	Missense_Mutation	SNP	G	G	A	rs6591700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55606693G>A	ENST00000378396.1	+	1	466	c.466G>A	c.(466-468)Gca>Aca	p.A156T		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	156			A -> T (in dbSNP:rs6591700).			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)				ATGGGGAGTCGCATGTTCCCT	0.453													-|||	571	0.114018	0.2761	0.0879	5008	,	,		19409	0.0		0.1302	False		,,,				2504	0.0143				p.A156T		Atlas-SNP	.											.	OR5D16	94	.	0			c.G466A						PASS	.	G	THR/ALA	1149,3253		167,815,1219	147.0	132.0	137.0		466	-2.2	0.0	11	dbSNP_116	137	1196,7396		88,1020,3188	yes	missense	OR5D16	NM_001005496.1	58	255,1835,4407	AA,AG,GG		13.9199,26.1018,18.0468	benign	156/329	55606693	2345,10649	2201	4296	6497	SO:0001583	missense	390144	exon1			GGAGTCGCATGTT	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.466G>A	11.37:g.55606693G>A	ENSP00000367649:p.Ala156Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	275	0.1259157509157509	139	0.28252032520325204	34	0.09392265193370165	2	0.0034965034965034965	100	0.13192612137203166	.	10.19	1.282917	0.23392	0.261018	0.139199	ENSG00000205029	ENST00000378396	T	0.38401	1.14	4.47	-2.16	0.07080	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.20304	0.555	0.80722	P	0.0	B	0.22604	0.072	B	0.21546	0.035	T	0.39603	-0.9606	8	0.37606	T	0.19	1.0901	6.6069	0.22729	0.4761:0.1226:0.4014:0.0	rs6591700;rs52793346;rs57898201;rs6591700	156	Q8NGK9	OR5DG_HUMAN	T	156	ENSP00000367649:A156T	ENSP00000367649:A156T	A	+	1	0	OR5D16	55363269	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.639000	0.00865	-0.358000	0.08162	-0.352000	0.07741	GCA	G|0.841;A|0.159	0.159	strong		0.453	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
PANX1	24145	hgsc.bcm.edu	37	11	93862493	93862493	+	Missense_Mutation	SNP	A	A	C	rs1138800	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:93862493A>C	ENST00000227638.3	+	1	400	c.15A>C	c.(13-15)caA>caC	p.Q5H	PANX1_ENST00000436171.2_Missense_Mutation_p.Q5H	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	5			Q -> H (in dbSNP:rs1138800). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15028292, ECO:0000269|PubMed:16303743, ECO:0000269|Ref.1}.		calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	CCATCGCTCAACTGGCCACGG	0.657													C|||	3497	0.698283	0.8608	0.7723	5008	,	,		15311	0.6171		0.6203	False		,,,				2504	0.59				p.Q5H		Atlas-SNP	.											PANX1,NS,carcinoma,+2,1	PANX1	38	1	0			c.A15C						PASS	.	C	HIS/GLN	3607,795	316.1+/-294.4	1477,653,71	39.0	37.0	38.0		15	3.3	1.0	11	dbSNP_86	38	5502,3094	469.9+/-367.7	1766,1970,562	yes	missense	PANX1	NM_015368.3	24	3243,2623,633	CC,CA,AA		35.9935,18.06,29.92	benign	5/427	93862493	9109,3889	2201	4298	6499	SO:0001583	missense	24145	exon1			CGCTCAACTGGCC	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.15A>C	11.37:g.93862493A>C	ENSP00000227638:p.Gln5His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	1554	0.7115384615384616	437	0.8882113821138211	268	0.7403314917127072	384	0.6713286713286714	465	0.6134564643799473	C	5.433	0.265015	0.10294	0.8194	0.640065	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.27402	1.67;1.67	4.21	3.3	0.37823	.	0.225864	0.43579	N	0.000546	T	0.00012	0.0000	N	0.00210	-1.845	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34030	-0.9845	9	0.02654	T	1	-18.9619	4.9587	0.14056	0.1705:0.6531:0.0:0.1765	rs1138800;rs1802493;rs3202841;rs16912510;rs59720163;rs1138800	5;5	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	H	5	ENSP00000227638:Q5H;ENSP00000411461:Q5H	ENSP00000227638:Q5H	Q	+	3	2	PANX1	93502141	0.830000	0.29337	1.000000	0.80357	0.977000	0.68977	0.217000	0.17603	0.442000	0.26555	-0.323000	0.08544	CAA	A|0.289;C|0.711	0.711	strong		0.657	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
OPN1LW	5956	hgsc.bcm.edu	37	X	153418541	153418541	+	Missense_Mutation	SNP	T	T	G	rs949431	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153418541T>G	ENST00000369951.4	+	3	598	c.538T>G	c.(538-540)Tct>Gct	p.S180A	OPN1LW_ENST00000463296.1_3'UTR	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	180			S -> A (in 38% of the population; dbSNP:rs949431). {ECO:0000269|PubMed:1557123}.		phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGGATCTGGTCTGCTGTGTG	0.572													T|||	632	0.167417	0.0386	0.219	3775	,	,		13412	0.1121		0.2147	False		,,,				2504	0.1022				p.S180A		Atlas-SNP	.											.	OPN1LW	87	.	0			c.T538G	GRCh37	CM045803	OPN1LW	M	rs949431	PASS	.						248.0	147.0	183.0					X																	153418541		2171	3980	6151	SO:0001583	missense	5956	exon3			ATCTGGTCTGCTG	Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"""GPCR / Class A : Opsin receptors"""	9936	protein-coding gene	gene with protein product	"""cone dystrophy 5 (X-linked)"""	300822	"""color blindness, protan"", ""red cone photoreceptor pigment"""	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.538T>G	X.37:g.153418541T>G	ENSP00000358967:p.Ser180Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	195	194	0.994872	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.677614	0.00751	.	.	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.38887	1.11;1.11	4.57	-2.02	0.07388	GPCR, rhodopsin-like superfamily (1);	0.466822	0.23684	N	0.045597	T	0.16471	0.0396	N	0.10945	0.07	0.18873	N	0.999985	B	0.09022	0.002	B	0.12837	0.008	T	0.33548	-0.9864	10	0.02654	T	1	.	9.812	0.40828	0.0:0.1173:0.3112:0.5715	.	180	P04000	OPSR_HUMAN	A	180;43	ENSP00000358967:S180A;ENSP00000402493:S43A	ENSP00000358967:S180A	S	+	1	0	OPN1LW	153071735	0.004000	0.15560	0.824000	0.32777	0.110000	0.19582	-1.702000	0.01901	-0.414000	0.07495	-0.464000	0.05259	TCT	T|0.257;G|0.743	0.743	strong		0.572	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
HHAT	55733	hgsc.bcm.edu	37	1	210577901	210577901	+	Missense_Mutation	SNP	T	T	C	rs34228541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:210577901T>C	ENST00000367010.1	+	6	789	c.562T>C	c.(562-564)Tgc>Cgc	p.C188R	HHAT_ENST00000545154.1_Missense_Mutation_p.C189R|HHAT_ENST00000413764.2_Missense_Mutation_p.C188R|HHAT_ENST00000545781.1_Missense_Mutation_p.C125R|HHAT_ENST00000537898.1_Missense_Mutation_p.C123R|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000261458.3_Missense_Mutation_p.C188R|HHAT_ENST00000391905.3_Missense_Mutation_p.C188R|HHAT_ENST00000308852.6_Missense_Mutation_p.C143R	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	188			C -> R (in dbSNP:rs34228541). {ECO:0000269|PubMed:14702039}.		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)			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)		CCTGGAGCTCTGCTGGCAGCA	0.527													T|||	405	0.0808706	0.034	0.111	5008	,	,		20164	0.002		0.1789	False		,,,				2504	0.1033				p.C189R		Atlas-SNP	.											HHAT,NS,carcinoma,-2,1	HHAT	66	1	0			c.T565C						scavenged	.	T	ARG/CYS,,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	239,4167	139.6+/-175.2	6,227,1970	101.0	88.0	92.0		562,,562,565,367,562	5.5	1.0	1	dbSNP_126	92	1603,6997	297.3+/-303.3	163,1277,2860	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	180,,180,180,180,180	169,1504,4830	CC,CT,TT		18.6395,5.4244,14.1627	probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging	188/494,,188/494,189/495,123/429,188/494	210577901	1842,11164	2203	4300	6503	SO:0001583	missense	55733	exon5			GAGCTCTGCTGGC	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.562T>C	1.37:g.210577901T>C	ENSP00000355977:p.Cys188Arg	Somatic	68	2	0.0294118		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	37	CCDS1495.1	202	0.0924908424908425	23	0.046747967479674794	40	0.11049723756906077	0	0.0	139	0.18337730870712401	T	24.0	4.487403	0.84854	0.054244	0.186395	ENSG00000054392	ENST00000413764;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	T;T;T;T;T;T;T;T;T	0.25749	2.01;2.0;2.1;1.97;2.02;2.01;2.05;2.01;1.78	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.80183	2.485	0.09310	P	0.999999999893868	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;1.0	T	0.00728	-1.1591	9	0.34782	T	0.22	-39.1205	15.3723	0.74573	0.0:0.0:0.0:1.0	rs34228541	143;189;123;188	B7Z2U8;F5H444;B7Z5I1;Q5VTY9	.;.;.;HHAT_HUMAN	R	188;189;123;188;125;188;143;188;60	ENSP00000416845:C188R;ENSP00000438468:C189R;ENSP00000442625:C123R;ENSP00000375773:C188R;ENSP00000439229:C125R;ENSP00000261458:C188R;ENSP00000308628:C143R;ENSP00000355977:C188R;ENSP00000413399:C60R	ENSP00000261458:C188R	C	+	1	0	HHAT	208644524	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	7.100000	0.76989	2.107000	0.64212	0.482000	0.46254	TGC	T|0.874;C|0.126	0.126	strong		0.527	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
MYO9A	4649	hgsc.bcm.edu	37	15	72172883	72172883	+	Missense_Mutation	SNP	G	G	C	rs2306575	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72172883G>C	ENST00000356056.5	-	29	5887	c.5415C>G	c.(5413-5415)caC>caG	p.H1805Q	MYO9A_ENST00000564571.1_Missense_Mutation_p.H1805Q|MYO9A_ENST00000444904.1_Missense_Mutation_p.H1786Q|MYO9A_ENST00000424560.1_Missense_Mutation_p.H1876Q	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1805	Tail.		H -> Q (in dbSNP:rs2306575).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GAGGTGTTGGGTGATATGCAG	0.408													G|||	260	0.0519169	0.0	0.0216	5008	,	,		20256	0.1736		0.0229	False		,,,				2504	0.0481				p.H1805Q		Atlas-SNP	.											.	MYO9A	203	.	0			c.C5415G						PASS	.	G	GLN/HIS	26,4372	30.8+/-60.4	0,26,2173	70.0	72.0	71.0		5415	-5.0	0.8	15	dbSNP_100	71	223,8371	91.1+/-153.3	2,219,4076	yes	missense	MYO9A	NM_006901.2	24	2,245,6249	CC,CG,GG		2.5948,0.5912,1.9166	probably-damaging	1805/2549	72172883	249,12743	2199	4297	6496	SO:0001583	missense	4649	exon29			TGTTGGGTGATAT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5415C>G	15.37:g.72172883G>C	ENSP00000348349:p.His1805Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	151	0.06913919413919414	0	0.0	7	0.019337016574585635	123	0.21503496503496503	21	0.027704485488126648	G	8.463	0.855868	0.17106	0.005912	0.025948	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83673	-1.73;-1.75;-1.73	5.5	-4.97	0.03029	.	.	.	.	.	T	0.00073	0.0002	L	0.57536	1.79	0.43683	P	0.0038759999999999906	B;B	0.22146	0.0;0.065	B;B	0.13407	0.003;0.009	T	0.13442	-1.0509	8	0.11485	T	0.65	.	2.4801	0.04585	0.3209:0.2246:0.3598:0.0948	rs2306575	1876;1805	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	Q	1805;1876;1786	ENSP00000348349:H1805Q;ENSP00000399162:H1876Q;ENSP00000398250:H1786Q	ENSP00000348349:H1805Q	H	-	3	2	MYO9A	69959937	0.984000	0.35163	0.769000	0.31535	0.607000	0.37147	0.019000	0.13444	-0.988000	0.03489	-0.378000	0.06908	CAC	G|0.965;C|0.035	0.035	strong		0.408	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152280900T>G	ENST00000368799.1	-	3	6497	c.6462A>C	c.(6460-6462)caA>caC	p.Q2154H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2154	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)			CCGATTGCTCTTGGTGGGACC	0.592									Ichthyosis				-|||	1722	0.34385	0.3843	0.3487	5008	,	,		25148	0.4444		0.1541	False		,,,				2504	0.3773				p.Q2154H		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.A6462C						scavenged	.						380.0	322.0	342.0					1																	152280900		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCTCTTGGTGG	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.6462A>C	1.37:g.152280900T>G	ENSP00000357789:p.Gln2154His	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	328	110	0.335366	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	2.361	-0.346581	0.05208	.	.	ENSG00000143631	ENST00000368799	T	0.03524	3.9	2.59	-5.18	0.02840	.	.	.	.	.	T	0.00178	0.0005	N	0.00074	-2.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49943	-0.8885	9	0.38643	T	0.18	.	0.1659	0.00108	0.2732:0.2266:0.1592:0.341	.	2154	P20930	FILA_HUMAN	H	2154	ENSP00000357789:Q2154H	ENSP00000357789:Q2154H	Q	-	3	2	FLG	150547524	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.334000	0.00508	-3.813000	0.00104	-2.053000	0.00404	CAA	T|0.872;G|0.128	0.128	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TIMM50	92609	hgsc.bcm.edu	37	19	39971432	39971432	+	5'Flank	SNP	G	G	C	rs2304220	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39971432G>C	ENST00000607714.1	+	0	0				TIMM50_ENST00000544017.1_5'Flank|TIMM50_ENST00000599794.1_5'Flank|TIMM50_ENST00000314349.4_Missense_Mutation_p.S83T			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)						cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	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;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ATTGGCTGTAGCTCCGGCCCG	0.701													G|||	707	0.141174	0.1626	0.1268	5008	,	,		14516	0.1121		0.173	False		,,,				2504	0.1196				p.S83T		Atlas-SNP	.											.	TIMM50	37	.	0			c.G248C						PASS	.	G	THR/SER	677,3715		57,563,1576	14.0	17.0	16.0		248	2.3	0.0	19	dbSNP_100	16	1415,7163		125,1165,2999	yes	missense	TIMM50	NM_001001563.1	58	182,1728,4575	CC,CG,GG		16.4957,15.4144,16.1295	benign	83/457	39971432	2092,10878	2196	4289	6485	SO:0001631	upstream_gene_variant	92609	exon1			GCTGTAGCTCCGG	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	23656	protein-coding gene	gene with protein product		607381	"""translocase of inner mitochondrial membrane 50 homolog (yeast)"""			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8			19.37:g.39971432G>C	Exception_encountered	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Missense_Mutation	SNP	ENST00000607714.1	37		280	0.1282051282051282	60	0.12195121951219512	42	0.11602209944751381	49	0.08566433566433566	129	0.17018469656992086	G	13.33	2.205918	0.39003	0.154144	0.164957	ENSG00000105197	ENST00000314349	.	.	.	4.57	2.29	0.28610	.	0.606995	0.15867	N	0.240740	T	0.00073	0.0002	.	.	.	0.53688	P	2.999999999997449E-5	B	0.22146	0.065	B	0.24848	0.056	T	0.10776	-1.0615	6	.	.	.	-0.7841	5.7869	0.18338	0.1055:0.1974:0.6971:0.0	rs2304220	83	Q3ZCQ8-2	.	T	83	.	.	S	+	2	0	TIMM50	44663272	0.012000	0.17670	0.003000	0.11579	0.064000	0.16182	1.700000	0.37815	1.291000	0.44653	0.462000	0.41574	AGC	G|0.869;C|0.131	0.131	strong		0.701	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563	
DNAH9	1770	hgsc.bcm.edu	37	17	11672607	11672607	+	Missense_Mutation	SNP	G	G	T	rs61744697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:11672607G>T	ENST00000262442.4	+	38	7581	c.7513G>T	c.(7513-7515)Gtg>Ttg	p.V2505L	DNAH9_ENST00000454412.2_Missense_Mutation_p.V2505L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2505	AAA 3. {ECO:0000250}.			V -> L (in Ref. 1; AAF69004). {ECO:0000305}.	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)		GGTGAAAAACGTGCCATTCAA	0.627													G|||	353	0.0704872	0.0061	0.0908	5008	,	,		18763	0.0387		0.1561	False		,,,				2504	0.0879				p.V2505L		Atlas-SNP	.											.	DNAH9	695	.	0			c.G7513T						PASS	.	G	LEU/VAL	129,4277	91.6+/-130.3	4,121,2078	61.0	53.0	56.0		7513	4.4	1.0	17	dbSNP_129	56	1268,7332	250.4+/-277.3	91,1086,3123	yes	missense	DNAH9	NM_001372.3	32	95,1207,5201	TT,TG,GG		14.7442,2.9278,10.7412	possibly-damaging	2505/4487	11672607	1397,11609	2203	4300	6503	SO:0001583	missense	1770	exon38			AAAAACGTGCCAT	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.7513G>T	17.37:g.11672607G>T	ENSP00000262442:p.Val2505Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	172	0.07875457875457875	5	0.01016260162601626	38	0.10497237569060773	13	0.022727272727272728	116	0.15303430079155672	G	27.6	4.842872	0.91197	0.029278	0.147442	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.46063	0.88;0.88	5.41	4.42	0.53409	ATPase, AAA+ type, core (1);	0.072443	0.53938	D	0.000045	T	0.00412	0.0013	L	0.50847	1.595	0.09310	P	1.0	D	0.56521	0.976	P	0.60173	0.87	T	0.00740	-1.1586	9	0.37606	T	0.19	.	15.0436	0.71811	0.0722:0.0:0.9278:0.0	rs61744697	2505	Q9NYC9	DYH9_HUMAN	L	2505;2505;1087	ENSP00000262442:V2505L;ENSP00000414874:V2505L	ENSP00000262442:V2505L	V	+	1	0	DNAH9	11613332	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	6.624000	0.74243	2.696000	0.92011	0.655000	0.94253	GTG	G|0.901;T|0.099	0.099	strong		0.627	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351343	134351343	+	Missense_Mutation	SNP	C	C	T	rs11243403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134351343C>T	ENST00000357304.4	+	15	3882	c.3827C>T	c.(3826-3828)gCg>gTg	p.A1276V	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1276				A -> V (in Ref. 5; CAH18678). {ECO:0000305}.			poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GACAGCCGCGCGGAGGACAAG	0.572											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1681	0.335663	0.3707	0.3228	5008	,	,		17060	0.1161		0.5586	False		,,,				2504	0.2945				p.A1276V		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C3827T						PASS	.	C	VAL/ALA	1653,2295		349,955,670	43.0	49.0	47.0		3827	0.8	0.0	9	dbSNP_120	47	4883,3429		1416,2051,689	yes	missense	PRRC2B	NM_013318.3	64	1765,3006,1359	TT,TC,CC		41.2536,41.8693,46.6884	benign	1276/2230	134351343	6536,5724	1974	4156	6130	SO:0001583	missense	84726	exon15			GCCGCGCGGAGGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3827C>T	9.37:g.134351343C>T	ENSP00000349856:p.Ala1276Val	Somatic	53	0	0	1610	WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	789	0.36126373626373626	176	0.35772357723577236	135	0.3729281767955801	63	0.11013986013986014	415	0.5474934036939314	C	1.360	-0.588965	0.03799	0.418693	0.587464	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.01871	4.59	5.66	0.799	0.18667	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.54753	P	1.399999999995849E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04128	-1.0975	8	0.29301	T	0.29	.	5.3177	0.15864	0.0:0.3088:0.1429:0.5483	rs11243403;rs60709203;rs11243403	9;1276	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	V	1276;572	ENSP00000349856:A1276V	ENSP00000349856:A1276V	A	+	2	0	PRRC2B	133341164	0.020000	0.18652	0.003000	0.11579	0.019000	0.09904	0.735000	0.26115	-0.091000	0.12440	-0.302000	0.09304	GCG	C|0.636;T|0.364	0.364	strong		0.572	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLC20A1	6574	hgsc.bcm.edu	37	2	113404708	113404708	+	Silent	SNP	G	G	A	rs4849091	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113404708G>A	ENST00000272542.3	+	2	842	c.303G>A	c.(301-303)ctG>ctA	p.L101L	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	101					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						CTCAAGGGCTGCTGATGGCCG	0.483													G|||	1806	0.360623	0.1573	0.4481	5008	,	,		18952	0.2202		0.5497	False		,,,				2504	0.5235				p.L101L		Atlas-SNP	.											SLC20A1,NS,carcinoma,+2,1	SLC20A1	59	1	0			c.G303A						PASS	.	G		922,3484	355.1+/-312.9	104,714,1385	166.0	145.0	152.0		303	5.5	0.7	2	dbSNP_111	152	4807,3793	613.7+/-396.1	1328,2151,821	no	coding-synonymous	SLC20A1	NM_005415.4		1432,2865,2206	AA,AG,GG		44.1047,20.926,44.0489		101/680	113404708	5729,7277	2203	4300	6503	SO:0001819	synonymous_variant	6574	exon2			AGGGCTGCTGATG		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"""Solute carriers"""	10946	protein-coding gene	gene with protein product	"""gibbon ape leukemia virus receptor 1"""	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.303G>A	2.37:g.113404708G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_005415	Q08344|Q6DHX8|Q9UQ82	Silent	SNP	ENST00000272542.3	37	CCDS2099.1																																																																																			G|0.602;A|0.398	0.398	strong		0.483	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415	
TTN	7273	hgsc.bcm.edu	37	2	179395067	179395067	+	Silent	SNP	C	C	G	rs56207956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179395067C>G	ENST00000591111.1	-	308	101576	c.101352G>C	c.(101350-101352)ggG>ggC	p.G33784G	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Silent_p.G35425G|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000342992.6_Silent_p.G32857G|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN_ENST00000342175.6_Silent_p.G26552G|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000359218.5_Silent_p.G26485G|TTN_ENST00000460472.2_Silent_p.G26360G			Q8WZ42	TITIN_HUMAN	titin	33784	Ig-like 149.				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)			TATCCTGCAACCCAGTAACAA	0.423													C|||	255	0.0509185	0.0726	0.0692	5008	,	,		16703	0.0		0.0875	False		,,,				2504	0.0235				p.G35425G		Atlas-SNP	.											.	TTN	18412	.	0			c.G106275C						PASS	.	C	,,,	278,3364		9,260,1552	154.0	140.0	144.0		79080,98571,79455,79656	2.2	1.0	2	dbSNP_129	144	714,7454		36,642,3406	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	45,902,4958	GG,GC,CC		8.7414,7.6332,8.3997	,,,	26360/26927,32857/33424,26485/27052,26552/27119	179395067	992,10818	1821	4084	5905	SO:0001819	synonymous_variant	7273	exon358			CTGCAACCCAGTA	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.101352G>C	2.37:g.179395067C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	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|0.940;G|0.060	0.060	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RSPH4A	345895	hgsc.bcm.edu	37	6	116950734	116950734	+	Missense_Mutation	SNP	G	G	A	rs6927567	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	45	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	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	
C20orf173	140873	hgsc.bcm.edu	37	20	34116307	34116307	+	Silent	SNP	C	C	T	rs35756561	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:34116307C>T	ENST00000246199.2	-	3	674	c.396G>A	c.(394-396)gtG>gtA	p.V132V	C20orf173_ENST00000374345.4_Silent_p.V185V|C20orf173_ENST00000444723.1_Silent_p.V185V|RP3-477O4.5_ENST00000422009.1_RNA			Q96LM9	CT173_HUMAN	chromosome 20 open reading frame 173	132										haematopoietic_and_lymphoid_tissue(1)|skin(1)	2						CTGAAGTCCACACCAGGTCAG	0.557													C|||	307	0.0613019	0.0076	0.0591	5008	,	,		18973	0.0784		0.0318	False		,,,				2504	0.1483				p.V185V		Atlas-SNP	.											.	C20orf173	19	.	0			c.G555A						PASS	.	C		16,1368		0,16,676	132.0	112.0	118.0		555	-6.7	0.0	20	dbSNP_126	118	85,3097		1,83,1507	no	coding-synonymous	C20orf173	NM_001145350.1		1,99,2183	TT,TC,CC		2.6713,1.1561,2.212		185/203	34116307	101,4465	692	1591	2283	SO:0001819	synonymous_variant	140873	exon4			AGTCCACACCAGG	AL121586	CCDS46594.1	20q11.22	2012-10-30			ENSG00000125975	ENSG00000125975			16166	protein-coding gene	gene with protein product							Standard	NM_001145350		Approved	dJ477O4.4	uc010zvf.1	Q96LM9	OTTHUMG00000032340	ENST00000246199.2:c.396G>A	20.37:g.34116307C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	219	110	0.502283	NM_001145350	A6PVJ1|Q2M293|Q5JWS4|Q9H449	Silent	SNP	ENST00000246199.2	37																																																																																				C|0.963;T|0.037	0.037	strong		0.557	C20orf173-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078874.6	NM_001145350	
TTN	7273	hgsc.bcm.edu	37	2	179633644	179633644	+	Silent	SNP	G	G	C	rs4894045	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179633644G>C	ENST00000591111.1	-	38	9143	c.8919C>G	c.(8917-8919)tcC>tcG	p.S2973S	TTN_ENST00000589042.1_Silent_p.S2973S|TTN_ENST00000360870.5_Silent_p.S2973S|TTN_ENST00000342992.6_Silent_p.S2973S|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.S2927S|TTN_ENST00000359218.5_Silent_p.S2927S|TTN_ENST00000460472.2_Silent_p.S2927S			Q8WZ42	TITIN_HUMAN	titin	13303	Ig-like 17.				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)			CTTTCAGCATGGAAGTAATCA	0.368													G|||	434	0.0866613	0.0756	0.1542	5008	,	,		22539	0.0208		0.0348	False		,,,				2504	0.1748				p.S2973S		Atlas-SNP	.											.	TTN	18412	.	0			c.C8919G						PASS	.	G	,,,,	320,4086	170.5+/-200.9	8,304,1891	105.0	99.0	101.0		8781,8919,8919,8781,8781	1.0	1.0	2	dbSNP_111	101	185,8415	82.9+/-145.4	3,179,4118	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	11,483,6009	CC,CG,GG		2.1512,7.2628,3.8828	,,,,	2927/26927,2973/33424,2973/5605,2927/27052,2927/27119	179633644	505,12501	2203	4300	6503	SO:0001819	synonymous_variant	7273	exon38			CAGCATGGAAGTA	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.8919C>G	2.37:g.179633644G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	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|0.957;C|0.043	0.043	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PEAR1	375033	hgsc.bcm.edu	37	1	156879580	156879580	+	Silent	SNP	C	C	T	rs3737224	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156879580C>T	ENST00000338302.3	+	13	1674	c.1449C>T	c.(1447-1449)ccC>ccT	p.P483P	PEAR1_ENST00000292357.7_Silent_p.P483P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	483					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTGCCCACCCGGAACCTGGG	0.622													C|||	885	0.176717	0.1589	0.1037	5008	,	,		17946	0.3145		0.1024	False		,,,				2504	0.1871				p.P483P		Atlas-SNP	.											.	PEAR1	118	.	0			c.C1449T						PASS	.	C		687,3719	286.9+/-279.0	57,573,1573	51.0	49.0	50.0		1449	-2.0	0.9	1	dbSNP_107	50	891,7709	199.2+/-243.3	50,791,3459	no	coding-synonymous	PEAR1	NM_001080471.1		107,1364,5032	TT,TC,CC		10.3605,15.5924,12.1329		483/1038	156879580	1578,11428	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon12			CCCACCCGGAACC	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1449C>T	1.37:g.156879580C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.847;T|0.153	0.153	strong		0.622	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
FOXRED2	80020	hgsc.bcm.edu	37	22	36886112	36886112	+	Silent	SNP	G	G	A	rs34949308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36886112G>A	ENST00000397224.4	-	9	2091	c.1998C>T	c.(1996-1998)tcC>tcT	p.S666S	FOXRED2_ENST00000397223.4_Silent_p.S666S|FOXRED2_ENST00000366463.3_Silent_p.S218S|FOXRED2_ENST00000216187.6_Silent_p.S666S	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	666					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GAGCCAGGGGGGAACCTAGTG	0.642													G|||	40	0.00798722	0.0	0.0	5008	,	,		18397	0.0		0.0099	False		,,,				2504	0.0307				p.S666S		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C1998T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	33.0	37.0	36.0		1998,1998	-4.8	0.0	22	dbSNP_126	36	123,8477	61.0+/-122.8	1,121,4178	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	1,133,6369	AA,AG,GG		1.4302,0.2724,1.038	,	666/685,666/685	36886112	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			CAGGGGGGAACCT	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1998C>T	22.37:g.36886112G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			G|0.991;A|0.009	0.009	strong		0.642	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
CCP110	9738	hgsc.bcm.edu	37	16	19553950	19553950	+	Silent	SNP	A	A	C	rs72767539	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19553950A>C	ENST00000381396.5	+	7	2482	c.2235A>C	c.(2233-2235)acA>acC	p.T745T	CCP110_ENST00000396208.2_Silent_p.T745T|CCP110_ENST00000396212.2_Silent_p.T745T	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	745					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						TAGGTTTCACAAATTCTGCCA	0.363													A|||	68	0.0135783	0.0008	0.0259	5008	,	,		19059	0.001		0.0457	False		,,,				2504	0.002				p.T745T		Atlas-SNP	.											.	CCP110	57	.	0			c.A2235C						PASS	.	A	,	31,4363	36.0+/-67.5	0,31,2166	89.0	87.0	87.0		2235,2235	0.4	1.0	16	dbSNP_130	87	370,8230	119.9+/-179.2	10,350,3940	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	10,381,6106	CC,CA,AA		4.3023,0.7055,3.086	,	745/1013,745/992	19553950	401,12593	2197	4300	6497	SO:0001819	synonymous_variant	9738	exon7			TTTCACAAATTCT	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.2235A>C	16.37:g.19553950A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			A|0.973;C|0.027	0.027	strong		0.363	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
SERPINA10	51156	hgsc.bcm.edu	37	14	94756794	94756794	+	Missense_Mutation	SNP	T	T	C	rs941590	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:94756794T>C	ENST00000393096.1	-	2	602	c.137A>G	c.(136-138)aAg>aGg	p.K46R	SERPINA10_ENST00000554723.1_Missense_Mutation_p.K86R|SERPINA10_ENST00000261994.4_Missense_Mutation_p.K46R|SERPINA10_ENST00000554173.1_Missense_Mutation_p.K46R	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	46			K -> R (in dbSNP:rs941590). {ECO:0000269|PubMed:12975309, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CTCTTCCTCCTTGGGAGCCTG	0.632													C|||	3145	0.627995	0.8956	0.4899	5008	,	,		18316	0.6558		0.3618	False		,,,				2504	0.6094				p.K46R		Atlas-SNP	.											.	SERPINA10	83	.	0			c.A137G						PASS	.	C	ARG/LYS,ARG/LYS	3559,847	325.9+/-299.3	1434,691,78	37.0	37.0	37.0		137,137	-0.5	0.0	14	dbSNP_86	37	3376,5224	634.7+/-398.9	676,2024,1600	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	26,26	2110,2715,1678	CC,CT,TT		39.2558,19.2238,46.6785	benign,benign	46/445,46/445	94756794	6935,6071	2203	4300	6503	SO:0001583	missense	51156	exon2			TCCTCCTTGGGAG	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"""Serine (or cysteine) peptidase inhibitors"""	15996	protein-coding gene	gene with protein product		605271	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"""			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.137A>G	14.37:g.94756794T>C	ENSP00000376809:p.Lys46Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	1253	0.5737179487179487	442	0.8983739837398373	160	0.4419889502762431	375	0.6555944055944056	276	0.3641160949868074	C	5.090	0.202249	0.09652	0.807762	0.392558	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.85411	-1.98;-1.94;-1.94;-1.94	3.61	-0.49	0.12049	Serpin domain (1);	2.313430	0.02100	N	0.053885	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	0.41998	-0.9477	9	0.15952	T	0.53	.	1.4765	0.02427	0.1477:0.1207:0.2369:0.4946	rs941590;rs17783896;rs52814027;rs56859162;rs941590	46	Q9UK55	ZPI_HUMAN	R	86;46;46;46	ENSP00000450896:K86R;ENSP00000376809:K46R;ENSP00000261994:K46R;ENSP00000450971:K46R	ENSP00000261994:K46R	K	-	2	0	SERPINA10	93826547	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	-3.317000	0.00514	-0.739000	0.04809	-0.642000	0.03964	AAG	T|0.428;C|0.572	0.572	strong		0.632	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186	
BBOX1	8424	hgsc.bcm.edu	37	11	27148847	27148847	+	Silent	SNP	G	G	A	rs77035197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:27148847G>A	ENST00000529202.1	+	8	1350	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	RP11-1L12.3_ENST00000526061.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA|RP11-1L12.3_ENST00000530430.1_RNA|BBOX1_ENST00000263182.3_Silent_p.V337V|BBOX1_ENST00000528583.1_Silent_p.V337V|BBOX1_ENST00000525090.1_Silent_p.V337V			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	337					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	TAGGTGATGTGATTACTTTTG	0.398													G|||	104	0.0207668	0.0008	0.0375	5008	,	,		18591	0.0		0.0507	False		,,,				2504	0.0266				p.V337V		Atlas-SNP	.											.	BBOX1	46	.	0			c.G1011A						PASS	.	G		26,4378	32.6+/-62.9	0,26,2176	104.0	93.0	96.0		1011	4.0	1.0	11	dbSNP_132	96	366,8232	121.1+/-180.3	9,348,3942	no	coding-synonymous	BBOX1	NM_003986.2		9,374,6118	AA,AG,GG		4.2568,0.5904,3.0149		337/388	27148847	392,12610	2202	4299	6501	SO:0001819	synonymous_variant	8424	exon9			TGATGTGATTACT	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.1011G>A	11.37:g.27148847G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			G|0.968;A|0.032	0.032	strong		0.398	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986	
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:149806388C>T	ENST00000435030.1	+	9	1118	c.750C>T	c.(748-750)gaC>gaT	p.D250D	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.D18D|KIF5C_ENST00000414838.2_Silent_p.D155D			O60282	KIF5C_HUMAN	kinesin family member 5C	250	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CTGTTCTTGACGAAGCTAAAA	0.443													C|||	654	0.130591	0.3086	0.0965	5008	,	,		18947	0.0159		0.0924	False		,,,				2504	0.0716				p.D250D		Atlas-SNP	.											.	KIF5C	166	.	0			c.C750T						PASS	.	C		997,2855		141,715,1070	105.0	102.0	103.0		461	-7.3	0.3	2	dbSNP_129	103	701,7595		36,629,3483	no	coding-synonymous	KIF5C	NM_004522.1		177,1344,4553	TT,TC,CC		8.4499,25.8827,13.9776		250/958	149806388	1698,10450	1926	4148	6074	SO:0001819	synonymous_variant	3800	exon9			TCTTGACGAAGCT	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.750C>T	2.37:g.149806388C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				C|0.884;T|0.116	0.116	strong		0.443	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
REPIN1	29803	hgsc.bcm.edu	37	7	150068605	150068605	+	Missense_Mutation	SNP	G	G	A	rs17173702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150068605G>A	ENST00000425389.2	+	1	353	c.275G>A	c.(274-276)cGt>cAt	p.R92H	REPIN1_ENST00000540729.1_Missense_Mutation_p.R92H|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000397281.2_Missense_Mutation_p.R92H|REPIN1_ENST00000489432.2_Missense_Mutation_p.R149H|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000444957.1_Missense_Mutation_p.R92H|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	92			R -> H (in dbSNP:rs17173702).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGTGTGGCCGTCGCTTTCGC	0.672													G|||	1164	0.232428	0.0227	0.1527	5008	,	,		14905	0.3988		0.2793	False		,,,				2504	0.3528				p.R149H		Atlas-SNP	.											.	REPIN1	74	.	0			c.G446A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	217,4035		8,201,1917	20.0	23.0	22.0		446,275,275,275	3.6	0.0	7	dbSNP_123	22	2270,6180		287,1696,2242	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	29,29,29,29	295,1897,4159	AA,AG,GG		26.8639,5.1035,19.5796	probably-damaging,probably-damaging,probably-damaging,probably-damaging	149/625,92/568,92/568,92/568	150068605	2487,10215	2126	4225	6351	SO:0001583	missense	29803	exon3			GTGGCCGTCGCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.275G>A	7.37:g.150068605G>A	ENSP00000388287:p.Arg92His	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	G	10.69	1.420773	0.25639	0.051035	0.268639	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.55588	0.51;2.37;2.37;2.37;2.37;2.37;2.37;2.37	5.54	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.47511	P	5.600000000000049E-4	B;B	0.17268	0.021;0.021	B;B	0.15052	0.012;0.012	T	0.34725	-0.9817	8	0.87932	D	0	-6.7004	4.7515	0.13063	0.1912:0.1804:0.6283:0.0	rs17173702	149;92	C9J3L7;Q9BWE0	.;REPI1_HUMAN	H	92;92;92;92;149;151;152;149;92	ENSP00000428562:R92H;ENSP00000445016:R92H;ENSP00000380451:R92H;ENSP00000407714:R92H;ENSP00000417291:R149H;ENSP00000419789:R151H;ENSP00000419872:R152H;ENSP00000388287:R92H	ENSP00000380451:R92H	R	+	2	0	REPIN1	149699538	0.000000	0.05858	0.014000	0.15608	0.772000	0.43724	0.281000	0.18810	1.305000	0.44909	0.462000	0.41574	CGT	G|0.761;C|0.000;A|0.238	0.238	strong		0.672	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
RECQL5	9400	hgsc.bcm.edu	37	17	73624466	73624466	+	Silent	SNP	G	G	A	rs140010427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73624466G>A	ENST00000317905.5	-	18	2796	c.2637C>T	c.(2635-2637)gtC>gtT	p.V879V	RECQL5_ENST00000423245.2_Silent_p.V852V|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	879					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)			CCTCAGCTACGACGGAGGGCT	0.637								Other identified genes with known or suspected DNA repair function					G|||	16	0.00319489	0.0008	0.0	5008	,	,		17331	0.0149		0.0	False		,,,				2504	0.0				p.V879V		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2637T						PASS	.	G		0,4128		0,0,2064	60.0	71.0	67.0		2637	3.0	0.0	17	dbSNP_134	67	6,8362		0,6,4178	no	coding-synonymous	RECQL5	NM_004259.6		0,6,6242	AA,AG,GG		0.0717,0.0,0.048		879/992	73624466	6,12490	2064	4184	6248	SO:0001819	synonymous_variant	9400	exon18			AGCTACGACGGAG	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.2637C>T	17.37:g.73624466G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
SVIL	6840	hgsc.bcm.edu	37	10	29770551	29770551	+	Missense_Mutation	SNP	A	A	G	rs11007612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:29770551A>G	ENST00000355867.4	-	28	5814	c.5062T>C	c.(5062-5064)Tcg>Ccg	p.S1688P	PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.S602P|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000538146.1_Missense_Mutation_p.S480P|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375398.2_Missense_Mutation_p.S1688P|SVIL_ENST00000375400.3_Missense_Mutation_p.S1262P	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1688			S -> P (in dbSNP:rs11007612).		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)				TTCTCATTCGATCTCTTCAGT	0.517													G|||	253	0.0505192	0.0371	0.0533	5008	,	,		16228	0.001		0.1362	False		,,,				2504	0.0297				p.S1688P		Atlas-SNP	.											SVIL,NS,carcinoma,+1,1	SVIL	226	1	0			c.T5062C						scavenged	.	G	PRO/SER,PRO/SER	223,4183	806.3+/-415.8	0,223,1980	197.0	218.0	211.0		3784,5062	3.3	0.1	10	dbSNP_120	211	1131,7469	767.0+/-407.6	81,969,3250	yes	missense,missense	SVIL	NM_003174.3,NM_021738.2	74,74	81,1192,5230	GG,GA,AA		13.1512,5.0613,10.4106	benign,benign	1262/1789,1688/2215	29770551	1354,11652	2203	4300	6503	SO:0001583	missense	6840	exon28			CATTCGATCTCTT	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.5062T>C	10.37:g.29770551A>G	ENSP00000348128:p.Ser1688Pro	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	144	79	0.548611	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	148	0.06776556776556776	17	0.034552845528455285	25	0.06906077348066299	0	0.0	106	0.13984168865435356	G	0.022	-1.418037	0.01136	0.050613	0.131512	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.27	3.35	0.38373	.	0.168540	0.52532	N	0.000062	T	0.00039	0.0001	N	0.02916	-0.46	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.0;0.002;0.0	T	0.38200	-0.9672	9	0.09338	T	0.73	-6.3887	9.3137	0.37921	0.0814:0.1543:0.7642:0.0	rs11007612;rs17756635;rs52797377;rs11007612	602;480;1262;1688	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	P	1262;1688;1688;602;642;480	ENSP00000364549:S1262P;ENSP00000364547:S1688P;ENSP00000348128:S1688P;ENSP00000445472:S602P;ENSP00000440343:S480P	ENSP00000348128:S1688P	S	-	1	0	SVIL	29810557	1.000000	0.71417	0.112000	0.21494	0.161000	0.22273	4.520000	0.60524	0.440000	0.26502	-0.215000	0.12644	TCG	A|0.915;G|0.085	0.085	strong		0.517	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
HPSE2	60495	hgsc.bcm.edu	37	10	100219374	100219374	+	Missense_Mutation	SNP	T	T	A	rs10883100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100219374T>A	ENST00000370552.3	-	12	1795	c.1736A>T	c.(1735-1737)tAt>tTt	p.Y579F	HPSE2_ENST00000404542.1_Missense_Mutation_p.Y467F|HPSE2_ENST00000370546.1_3'UTR|HPSE2_ENST00000370549.1_Missense_Mutation_p.Y521F	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	579			Y -> F (in dbSNP:rs10883100). {ECO:0000269|PubMed:11027606, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CTTGACCACATAAAAGCCCAT	0.597													T|||	2657	0.530551	0.6233	0.5346	5008	,	,		17494	0.5119		0.5099	False		,,,				2504	0.4427				p.Y579F		Atlas-SNP	.											HPSE2,NS,carcinoma,0,1	HPSE2	203	1	0			c.A1736T						scavenged	.	T	PHE/TYR,PHE/TYR,,PHE/TYR	2738,1668	654.7+/-399.8	851,1036,316	71.0	70.0	70.0		1562,1400,,1736	5.3	1.0	10	dbSNP_120	70	4185,4415	567.2+/-388.8	1027,2131,1142	yes	missense,missense,utr-3,missense	HPSE2	NM_001166244.1,NM_001166245.1,NM_001166246.1,NM_021828.4	22,22,,22	1878,3167,1458	AA,AT,TT		48.6628,37.8575,46.7707	benign,benign,,benign	521/535,467/481,,579/593	100219374	6923,6083	2203	4300	6503	SO:0001583	missense	60495	exon12			ACCACATAAAAGC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1736A>T	10.37:g.100219374T>A	ENSP00000359583:p.Tyr579Phe	Somatic	75	2	0.0266667		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_021828	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	1186	0.543040293040293	309	0.6280487804878049	195	0.5386740331491713	300	0.5244755244755245	382	0.503957783641161	T	13.65	2.301038	0.40694	0.621425	0.486628	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000404542	T;T;T	0.41758	0.99;1.0;1.0	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	N	0.17674	0.51	0.09310	P	0.9999999693858	D;D;B	0.67145	0.996;0.996;0.001	D;D;B	0.73380	0.98;0.98;0.003	T	0.04103	-1.0977	9	0.02654	T	1	-6.674	15.2788	0.73764	0.0:0.0:0.0:1.0	rs10883100;rs52819603;rs60701436;rs10883100	467;521;579	Q8WWQ2-4;Q8WWQ2-3;Q8WWQ2	.;.;HPSE2_HUMAN	F	579;521;467	ENSP00000359583:Y579F;ENSP00000359580:Y521F;ENSP00000384384:Y467F	ENSP00000359580:Y521F	Y	-	2	0	HPSE2	100209364	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.564000	0.82326	2.013000	0.59113	0.528000	0.53228	TAT	A|0.539;N|0.000	0.539	strong		0.597	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
WDR90	197335	hgsc.bcm.edu	37	16	705795	705795	+	Silent	SNP	C	C	T	rs12599798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:705795C>T	ENST00000293879.4	+	17	1872	c.1872C>T	c.(1870-1872)agC>agT	p.S624S	WDR90_ENST00000549091.1_Silent_p.S624S|LA16c-349E10.1_ENST00000573609.1_RNA			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	40	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609913	84609913	+	Silent	SNP	C	C	T	rs12341627	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	82	0	0		WXS	Illumina HiSeq	Phase_I	78	24	0.307692	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	
ABCA13	154664	hgsc.bcm.edu	37	7	48314798	48314798	+	Silent	SNP	G	G	T	rs13233225	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:48314798G>T	ENST00000435803.1	+	17	5559	c.5535G>T	c.(5533-5535)ggG>ggT	p.G1845G		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1845					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						ATGTCCATGGGCTCATGTCTT	0.443													G|||	1084	0.216454	0.261	0.2147	5008	,	,		18298	0.0119		0.3926	False		,,,				2504	0.1871				p.G1845G		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G5535T						PASS	.	G		1098,2664		166,766,949	60.0	59.0	59.0		5535	2.6	0.0	7	dbSNP_121	59	2908,5328		509,1890,1719	no	coding-synonymous	ABCA13	NM_152701.3		675,2656,2668	TT,TG,GG		35.3084,29.1866,33.3889		1845/5059	48314798	4006,7992	1881	4118	5999	SO:0001819	synonymous_variant	154664	exon17			CCATGGGCTCATG	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.5535G>T	7.37:g.48314798G>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	183	181	0.989071	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.750;T|0.250	0.250	strong		0.443	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
DOCK8	81704	hgsc.bcm.edu	37	9	271638	271638	+	Missense_Mutation	SNP	C	C	T	rs506121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:271638C>T	ENST00000453981.1	+	2	177	c.65C>T	c.(64-66)gCg>gTg	p.A22V	DOCK8_ENST00000469391.1_5'Flank|DOCK8_ENST00000432829.2_5'UTR|RP11-59O6.3_ENST00000429661.1_RNA			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	22				A -> V (in Ref. 1; BAE45254). {ECO:0000305}.	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)		TATTCTTCAGCGGAAATAAGG	0.348													C|||	1541	0.307708	0.2776	0.2767	5008	,	,		21157	0.375		0.341	False		,,,				2504	0.2669				p.A22V		Atlas-SNP	.											.	DOCK8	401	.	0			c.C65T						PASS	.	C	VAL/ALA	405,979		72,261,359	148.0	120.0	128.0		65	4.1	1.0	9	dbSNP_83	128	1051,2131		168,715,708	yes	missense	DOCK8	NM_203447.3	64	240,976,1067	TT,TC,CC		33.0295,29.263,31.8879	possibly-damaging	22/2100	271638	1456,3110	692	1591	2283	SO:0001583	missense	81704	exon2			CTTCAGCGGAAAT	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.65C>T	9.37:g.271638C>T	ENSP00000408464:p.Ala22Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	683	0.31272893772893773	121	0.2459349593495935	102	0.281767955801105	216	0.3776223776223776	244	0.32189973614775724	C	15.91	2.971367	0.53614	0.29263	0.330295	ENSG00000107099	ENST00000453981;ENST00000287364	T	0.18174	2.23	5.88	4.05	0.47172	.	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.09310	P	0.9999999999999373	B	0.06786	0.001	B	0.01281	0.0	T	0.41270	-0.9518	8	0.72032	D	0.01	.	10.1042	0.42524	0.0:0.8454:0.0:0.1546	rs506121;rs52809292;rs56483158;rs56808348;rs506121	22	Q8NF50	DOCK8_HUMAN	V	22	ENSP00000408464:A22V	ENSP00000287364:A22V	A	+	2	0	DOCK8	261638	0.975000	0.34042	0.974000	0.42286	0.974000	0.67602	1.418000	0.34782	0.839000	0.34971	0.557000	0.71058	GCG	C|0.688;T|0.312	0.312	strong		0.348	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
COL27A1	85301	hgsc.bcm.edu	37	9	116931737	116931737	+	Silent	SNP	C	C	T	rs2808771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:116931737C>T	ENST00000356083.3	+	3	2293	c.1902C>T	c.(1900-1902)ggC>ggT	p.G634G		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	634	Collagen-like 1.|Pro-rich.|Triple-helical region.				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						GAGACTGTGGCTTGCCGGTAA	0.607													T|||	1078	0.215256	0.295	0.183	5008	,	,		16987	0.1339		0.2992	False		,,,				2504	0.1278				p.G634G		Atlas-SNP	.											.	COL27A1	200	.	0			c.C1902T						PASS	.	T		1340,3066		210,920,1073	41.0	43.0	42.0		1902	-0.9	0.9	9	dbSNP_100	42	2400,6196		329,1742,2227	no	coding-synonymous	COL27A1	NM_032888.2		539,2662,3300	TT,TC,CC		27.92,30.4131,28.7648		634/1861	116931737	3740,9262	2203	4298	6501	SO:0001819	synonymous_variant	85301	exon3			CTGTGGCTTGCCG	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.1902C>T	9.37:g.116931737C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			C|0.745;T|0.255	0.255	strong		0.607	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
HIVEP3	59269	hgsc.bcm.edu	37	1	42045747	42045747	+	Silent	SNP	T	T	C	rs35730380	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:42045747T>C	ENST00000372583.1	-	4	5607	c.4722A>G	c.(4720-4722)tcA>tcG	p.S1574S	HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Silent_p.S1574S|HIVEP3_ENST00000247584.5_Silent_p.S1574S|HIVEP3_ENST00000429157.2_Silent_p.S1574S	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1574					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)				AGGACGTTTCTGACAGAGGCA	0.537													T|||	229	0.0457268	0.0083	0.1124	5008	,	,		20084	0.003		0.0398	False		,,,				2504	0.0992				p.S1574S		Atlas-SNP	.											.	HIVEP3	235	.	0			c.A4722G						PASS	.	T	,	85,4321	72.5+/-110.5	0,85,2118	131.0	119.0	123.0		4722,4722	4.3	1.0	1	dbSNP_126	123	471,8129	138.4+/-195.2	11,449,3840	no	coding-synonymous,coding-synonymous	HIVEP3	NM_001127714.2,NM_024503.4	,	11,534,5958	CC,CT,TT		5.4767,1.9292,4.275	,	1574/2406,1574/2407	42045747	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			CGTTTCTGACAGA	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.4722A>G	1.37:g.42045747T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	33	0.611111	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			T|0.958;C|0.042	0.042	strong		0.537	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
CCDC105	126402	hgsc.bcm.edu	37	19	15133803	15133803	+	Missense_Mutation	SNP	G	G	A	rs116923487	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:15133803G>A	ENST00000292574.3	+	7	1454	c.1372G>A	c.(1372-1374)Ggc>Agc	p.G458S		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	458						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						TGAGGTGGACGGCAACGTGGT	0.662													g|||	166	0.033147	0.059	0.013	5008	,	,		14890	0.0129		0.0129	False		,,,				2504	0.0542				p.G458S		Atlas-SNP	.											.	CCDC105	53	.	0			c.G1372A						PASS	.		SER/GLY	195,4209	115.4+/-153.4	3,189,2010	47.0	34.0	39.0		1372	-7.8	0.0	19	dbSNP_132	39	120,8480	59.8+/-121.6	3,114,4183	yes	missense	CCDC105	NM_173482.2	56	6,303,6193	AA,AG,GG		1.3953,4.4278,2.4223	benign	458/500	15133803	315,12689	2202	4300	6502	SO:0001583	missense	126402	exon7			GTGGACGGCAACG	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.1372G>A	19.37:g.15133803G>A	ENSP00000292574:p.Gly458Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	57	0.0260989010989011	37	0.07520325203252033	5	0.013812154696132596	6	0.01048951048951049	9	0.011873350923482849	g	3.705	-0.060730	0.07317	0.044278	0.013953	ENSG00000160994	ENST00000292574	T	0.02258	4.37	4.12	-7.77	0.01227	.	0.972282	0.08413	N	0.949564	T	0.00039	0.0001	N	0.03608	-0.345	0.09310	N	1	B	0.28801	0.223	B	0.19666	0.026	T	0.43245	-0.9403	10	0.05620	T	0.96	-2.1966	2.7869	0.05376	0.124:0.4011:0.2608:0.214	.	458	Q8IYK2	CC105_HUMAN	S	458	ENSP00000292574:G458S	ENSP00000292574:G458S	G	+	1	0	CCDC105	14994803	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.492000	0.02300	-1.967000	0.01008	-2.121000	0.00349	GGC	G|0.976;A|0.024	0.024	strong		0.662	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
FANCL	55120	hgsc.bcm.edu	37	2	58388696	58388696	+	Silent	SNP	A	A	G	rs848291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:58388696A>G	ENST00000233741.4	-	12	1017	c.981T>C	c.(979-981)tcT>tcC	p.S327S	FANCL_ENST00000403676.1_Silent_p.S210S|FANCL_ENST00000403295.3_Silent_p.S299S|FANCL_ENST00000402135.3_Silent_p.S332S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	327					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						GTCCACACTGAGAATTATCAC	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	3538	0.70647	0.947	0.6412	5008	,	,		19414	0.5883		0.6173	False		,,,				2504	0.6411				p.S332S		Atlas-SNP	.											.	FANCL	35	.	0			c.T996C						PASS	.	G	,	3966,438	207.5+/-228.8	1797,372,33	99.0	102.0	101.0		996,981	-0.5	0.0	2	dbSNP_86	101	5190,3410	501.6+/-375.5	1567,2056,677	no	coding-synonymous,coding-synonymous	FANCL	NM_001114636.1,NM_018062.3	,	3364,2428,710	GG,GA,AA		39.6512,9.9455,29.5909	,	332/381,327/376	58388696	9156,3848	2202	4300	6502	SO:0001819	synonymous_variant	55120	exon12	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ACACTGAGAATTA	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"""Zinc fingers, PHD-type"", ""Fanconi anemia, complementation groups"""	20748	protein-coding gene	gene with protein product		608111	"""PHD finger protein 9"""	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.981T>C	2.37:g.58388696A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_001114636	Q6GU60	Silent	SNP	ENST00000233741.4	37	CCDS1860.1																																																																																			A|0.313;G|0.687	0.687	strong		0.313	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062	
OR9K2	441639	hgsc.bcm.edu	37	12	55523685	55523685	+	Missense_Mutation	SNP	C	C	T	rs12303066	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523685C>T	ENST00000305377.5	+	1	221	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	45			R -> C (in dbSNP:rs12303066).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R45S(1)		NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CTTCAGGGTACGCCCAGAGCT	0.453													-|||	1523	0.304113	0.4085	0.2421	5008	,	,		17414	0.1141		0.334	False		,,,				2504	0.3722				p.R45C		Atlas-SNP	.											OR9K2,NS,carcinoma,0,2	OR9K2	63	2	1	Substitution - Missense(1)	prostate(1)	c.C133T						PASS	.	C	CYS/ARG	1703,2703	513.6+/-368.4	308,1087,808	177.0	166.0	170.0		133	-3.9	0.0	12	dbSNP_120	170	2777,5823	441.0+/-359.7	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	180	764,2952,2787	TT,TC,CC		32.2907,38.6518,34.4456	benign	45/336	55523685	4480,8526	2203	4300	6503	SO:0001583	missense	441639	exon1			AGGGTACGCCCAG	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.133C>T	12.37:g.55523685C>T	ENSP00000307598:p.Arg45Cys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	624	0.2857142857142857	200	0.4065040650406504	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	C	8.501	0.864300	0.17250	0.386518	0.322907	ENSG00000170605	ENST00000305377	T	0.01084	5.36	4.98	-3.9	0.04181	.	1.019550	0.07834	N	0.961843	T	0.00012	0.0000	L	0.38692	1.165	0.80722	P	0.0	B	0.15930	0.015	B	0.13407	0.009	T	0.36915	-0.9728	9	0.56958	D	0.05	6.1352	2.3085	0.04180	0.3837:0.1609:0.3173:0.1381	rs12303066;rs52808341;rs61113706;rs12303066	45	Q8NGE7	OR9K2_HUMAN	C	45	ENSP00000307598:R45C	ENSP00000307598:R45C	R	+	1	0	OR9K2	53809952	0.000000	0.05858	0.000000	0.03702	0.643000	0.38383	-1.903000	0.01594	-0.457000	0.07033	-0.766000	0.03442	CGC	C|0.679;T|0.321	0.321	strong		0.453	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
SERPINA5	5104	hgsc.bcm.edu	37	14	95058462	95058462	+	Silent	SNP	A	A	C	rs6116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:95058462A>C	ENST00000554866.1	+	5	1221	c.1107A>C	c.(1105-1107)atA>atC	p.I369I	SERPINA5_ENST00000554276.1_Silent_p.I369I|RP11-986E7.7_ENST00000553947.1_Missense_Mutation_p.Y23S|SERPINA5_ENST00000553780.1_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	79	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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	
ADAM12	8038	hgsc.bcm.edu	37	10	127753478	127753478	+	Silent	SNP	G	G	A	rs1278279	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127753478G>A	ENST00000368679.4	-	14	1824	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	ADAM12_ENST00000368676.4_Silent_p.N505N|ADAM12_ENST00000467145.1_5'UTR	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	505	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GCAGGTACACGTTGGCTGGGC	0.607													G|||	1516	0.302716	0.3775	0.4294	5008	,	,		19629	0.1647		0.2406	False		,,,				2504	0.318				p.N505N		Atlas-SNP	.											.	ADAM12	388	.	0			c.C1515T						PASS	.	G	,	1498,2908	465.7+/-354.3	249,1000,954	107.0	84.0	92.0		1515,1515	-2.3	1.0	10	dbSNP_87	92	1809,6791	321.5+/-315.1	174,1461,2665	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	423,2461,3619	AA,AG,GG		21.0349,33.9991,25.4267	,	505/910,505/739	127753478	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	8038	exon14			GTACACGTTGGCT	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.1515C>T	10.37:g.127753478G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			G|0.726;A|0.274	0.274	strong		0.607	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
TNFRSF1A	7132	hgsc.bcm.edu	37	12	6450945	6450945	+	Silent	SNP	T	T	C	rs767455	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:6450945T>C	ENST00000162749.2	-	1	335	c.36A>G	c.(34-36)ccA>ccG	p.P12P	TNFRSF1A_ENST00000366159.4_Silent_p.P12P|RN7SL391P_ENST00000582559.1_RNA|TNFRSF1A_ENST00000540022.1_Silent_p.P12P	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	12					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						GTCTCACCAGTGGCAGCAGCA	0.687													T|||	1510	0.301518	0.3631	0.3012	5008	,	,		16699	0.122		0.4294	False		,,,				2504	0.272				p.P12P		Atlas-SNP	.											TNFRSF1A,NS,carcinoma,0,1	TNFRSF1A	39	1	0			c.A36G						PASS	.	T		1579,2827	479.0+/-358.4	283,1013,907	52.0	48.0	50.0		36	-0.3	1.0	12	dbSNP_86	50	3677,4923	505.5+/-376.4	796,2085,1419	no	coding-synonymous	TNFRSF1A	NM_001065.3		1079,3098,2326	CC,CT,TT		42.7558,35.8375,40.4121		12/456	6450945	5256,7750	2203	4300	6503	SO:0001819	synonymous_variant	7132	exon1			CACCAGTGGCAGC	M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11916	protein-coding gene	gene with protein product		191190		TNFR1		1655358, 2158863	Standard	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.36A>G	12.37:g.6450945T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001065	A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Silent	SNP	ENST00000162749.2	37	CCDS8542.1																																																																																			T|0.619;C|0.381	0.381	strong		0.687	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1	NM_001065	
GPR144	347088	hgsc.bcm.edu	37	9	127228596	127228596	+	Silent	SNP	A	A	G	rs4838184	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127228596A>G	ENST00000334810.1	+	11	1851	c.1851A>G	c.(1849-1851)acA>acG	p.T617T				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	617	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)			central_nervous_system(1)|endometrium(3)	4						GGGCCACCACAGGCTGCTCCG	0.602													G|||	3757	0.7502	0.7322	0.7954	5008	,	,		15815	0.8135		0.6451	False		,,,				2504	0.7853				p.T617T		Atlas-SNP	.											.	GPR144	33	.	0			c.A1851G						PASS	.						29.0	32.0	31.0					9																	127228596		692	1591	2283	SO:0001819	synonymous_variant	347088	exon11			CACCACAGGCTGC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1851A>G	9.37:g.127228596A>G		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	199	103	0.517588	NM_001161808	Q86SL4|Q8NH12	Silent	SNP	ENST00000334810.1	37	CCDS48016.1	1603	0.7339743589743589	358	0.7276422764227642	270	0.7458563535911602	483	0.8444055944055944	492	0.6490765171503958	G	0.499	-0.871711	0.02570	.	.	ENSG00000180264	ENST00000439837	.	.	.	5.46	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999595964	.	.	.	.	.	.	T	0.30563	-0.9974	4	0.46703	T	0.11	.	0.9339	0.01340	0.3033:0.233:0.2847:0.179	rs4838184;rs60375364	.	.	.	G	339	.	ENSP00000405734:R339G	R	+	1	2	GPR144	126268417	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	-3.960000	0.00325	-3.361000	0.00179	-2.497000	0.00192	AGG	A|0.273;G|0.727	0.727	strong		0.602	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
UGT2B11	10720	hgsc.bcm.edu	37	4	70066376	70066376	+	Missense_Mutation	SNP	C	C	G	rs144149579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	92	0	0		WXS	Illumina HiSeq	Phase_I	87	8	0.091954	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	
AMBN	258	hgsc.bcm.edu	37	4	71469604	71469604	+	Missense_Mutation	SNP	C	C	T	rs7439186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:71469604C>T	ENST00000322937.6	+	12	867	c.764C>T	c.(763-765)gCc>gTc	p.A255V	AMBN_ENST00000449493.2_Missense_Mutation_p.A240V	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	255			A -> V (in dbSNP:rs7439186).		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)			AATGCCCCTGCCAGACTTGGC	0.383													C|||	598	0.119409	0.1475	0.0735	5008	,	,		19832	0.1498		0.0646	False		,,,				2504	0.1391				p.A255V		Atlas-SNP	.											.	AMBN	73	.	0			c.C764T						PASS	.	C	VAL/ALA	587,3819	259.8+/-263.3	38,511,1654	90.0	86.0	88.0		764	-0.8	0.7	4	dbSNP_116	88	620,7980	162.3+/-215.1	22,576,3702	yes	missense	AMBN	NM_016519.5	64	60,1087,5356	TT,TC,CC		7.2093,13.3227,9.2803	probably-damaging	255/448	71469604	1207,11799	2203	4300	6503	SO:0001583	missense	258	exon12			CCCCTGCCAGACT	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.764C>T	4.37:g.71469604C>T	ENSP00000313809:p.Ala255Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	37	CCDS3543.1	242	0.1108058608058608	81	0.16463414634146342	28	0.07734806629834254	86	0.15034965034965034	47	0.06200527704485488	C	18.73	3.685563	0.68157	0.133227	0.072093	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.36878	1.23;1.23	5.72	-0.765	0.11023	.	0.769688	0.11950	N	0.513769	T	0.00241	0.0007	M	0.62723	1.935	0.35590	P	0.193017	P	0.46859	0.885	P	0.51324	0.666	T	0.32561	-0.9902	9	0.87932	D	0	0.6651	13.4708	0.61281	0.0:0.2714:0.6561:0.0725	rs7439186;rs52837214;rs7439186	255	Q9NP70	AMBN_HUMAN	V	255;254;240	ENSP00000313809:A255V;ENSP00000391234:A240V	ENSP00000313809:A255V	A	+	2	0	AMBN	71504193	0.006000	0.16342	0.735000	0.30896	0.968000	0.65278	-0.898000	0.04105	-0.438000	0.07232	-0.282000	0.10007	GCC	C|0.897;T|0.103	0.103	strong		0.383	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
PPP3CA	5530	hgsc.bcm.edu	37	4	101984390	101984390	+	Splice_Site	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:101984390T>C	ENST00000394854.3	-	9	1763	c.1080A>G	c.(1078-1080)aaA>aaG	p.K360K	PPP3CA_ENST00000512215.1_Splice_Site_p.K128K|PPP3CA_ENST00000323055.6_Intron|PPP3CA_ENST00000507176.1_Splice_Site_p.K262K|PPP3CA_ENST00000523694.2_Splice_Site_p.K293K|PPP3CA_ENST00000394853.4_Splice_Site_p.K360K	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	360					calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		ACAACATACCTTTTTCCCCAA	0.383																																					p.K360K		Atlas-SNP	.											.	PPP3CA	51	.	0			c.A1080G						PASS	.						86.0	86.0	86.0					4																	101984390		2203	4300	6503	SO:0001630	splice_region_variant	5530	exon9			CATACCTTTTTCC		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9314	protein-coding gene	gene with protein product	"""calcineurin A alpha"", ""protein phosphatase 2B, catalytic subunit, alpha isoform"""	114105	"""protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"""	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.1081+1A>G	4.37:g.101984390T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	26	0.209677	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Silent	SNP	ENST00000394854.3	37	CCDS34037.1																																																																																			.	.	none		0.383	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944	Silent
ZNF90	7643	hgsc.bcm.edu	37	19	20228941	20228941	+	Missense_Mutation	SNP	A	A	G	rs61998186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:20228941A>G	ENST00000418063.2	+	4	690	c.578A>G	c.(577-579)aAa>aGa	p.K193R	ZNF90_ENST00000474284.1_Intron	NM_007138.1	NP_009069.1	Q03938	ZNF90_HUMAN	zinc finger protein 90	193					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)|lung(2)|ovary(1)|skin(1)	5						ACACATAAGAAAATTCATACT	0.383													a|||	614	0.122604	0.0076	0.1873	5008	,	,		20447	0.3393		0.0885	False		,,,				2504	0.044				p.K193R		Atlas-SNP	.											ZNF90_ENST00000418063,NS,carcinoma,-1,2	ZNF90	93	2	0			c.A578G						PASS	.	A	ARG/LYS	24,1360		0,24,668	27.0	25.0	26.0		578	1.2	0.1	19	dbSNP_129	26	300,2882		14,272,1305	no	missense	ZNF90	NM_007138.1	26	14,296,1973	GG,GA,AA		9.428,1.7341,7.0959	benign	193/602	20228941	324,4242	692	1591	2283	SO:0001583	missense	7643	exon4			ATAAGAAAATTCA	M61870	CCDS46028.1	19p12	2013-01-08	2006-02-01		ENSG00000213988	ENSG00000213988		"""Zinc fingers, C2H2-type"", ""-"""	13165	protein-coding gene	gene with protein product		603973	"""zinc finger protein 90 (HTF9)"""			8467795	Standard	NM_007138		Approved	HTF9	uc002nor.2	Q03938	OTTHUMG00000158057	ENST00000418063.2:c.578A>G	19.37:g.20228941A>G	ENSP00000410466:p.Lys193Arg	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_007138	B9EH87	Missense_Mutation	SNP	ENST00000418063.2	37	CCDS46028.1	314	0.14377289377289376	7	0.014227642276422764	56	0.15469613259668508	184	0.32167832167832167	67	0.08839050131926121	A	0.017	-1.495373	0.01009	0.017341	0.09428	ENSG00000213988	ENST00000418063	T	0.12984	2.63	1.18	1.18	0.20946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.02697	-0.525	0.58432	P	4.000000000004E-6	B	0.26512	0.151	B	0.30716	0.119	T	0.48293	-0.9048	7	.	.	.	.	2.9598	0.05889	0.701:0.0:0.299:0.0	rs61998186	193	Q03938	ZNF90_HUMAN	R	193	ENSP00000410466:K193R	.	K	+	2	0	ZNF90	20089941	0.000000	0.05858	0.075000	0.20258	0.075000	0.17131	-0.704000	0.05058	0.251000	0.21505	0.248000	0.18094	AAA	A|0.869;G|0.131	0.131	strong		0.383	ZNF90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350101.1	NM_007138	
GSG1L	146395	hgsc.bcm.edu	37	16	27974487	27974487	+	Silent	SNP	T	T	C	rs2051743	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:27974487T>C	ENST00000447459.2	-	2	471	c.387A>G	c.(385-387)gcA>gcG	p.A129A	GSG1L_ENST00000395724.3_Silent_p.A129A|GSG1L_ENST00000380898.2_5'UTR	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	90	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	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	
TRIM48	79097	hgsc.bcm.edu	37	11	55032462	55032462	+	Missense_Mutation	SNP	T	T	C	rs79623326	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:55032462T>C	ENST00000417545.2	+	2	217	c.131T>C	c.(130-132)aTa>aCa	p.I44T		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	28						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CCGGTCACCATAGACTGTGGG	0.468																																					p.I44T		Atlas-SNP	.											TRIM48_ENST00000417545,NS,haematopoietic_neoplasm,0,2	TRIM48	149	2	0			c.T131C						scavenged	.						94.0	96.0	95.0					11																	55032462		2192	4260	6452	SO:0001583	missense	79097	exon2			TCACCATAGACTG	AF521869	CCDS7947.2	11q12	2013-01-09	2011-01-25		ENSG00000150244	ENSG00000150244		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19021	protein-coding gene	gene with protein product			"""tripartite motif-containing 48"""				Standard	NM_024114		Approved	RNF101	uc010rid.2	Q8IWZ4	OTTHUMG00000157011	ENST00000417545.2:c.131T>C	11.37:g.55032462T>C	ENSP00000402414:p.Ile44Thr	Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	211	17	0.0805687	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	.	.	.	.	.	.	.	.	.	.	t	10.21	1.288335	0.23478	.	.	ENSG00000150244	ENST00000417545	T	0.12672	2.66	0.596	0.596	0.17496	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.08403	0.0209	N	0.16130	0.375	0.21719	N	0.999571	B	0.27700	0.186	B	0.33121	0.158	T	0.37267	-0.9713	9	0.56958	D	0.05	.	5.56	0.17137	0.0:1.0E-4:0.0:0.9999	.	28	Q8IWZ4	TRI48_HUMAN	T	44	ENSP00000402414:I44T	ENSP00000402414:I44T	I	+	2	0	TRIM48	54789038	0.000000	0.05858	0.178000	0.23040	0.225000	0.24961	0.461000	0.21940	0.526000	0.28541	0.338000	0.21704	ATA	T|0.994;C|0.006	0.006	strong		0.468	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1		
NOTCH4	4855	hgsc.bcm.edu	37	6	32188640	32188640	+	Missense_Mutation	SNP	T	T	C	rs71556915|rs520692	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	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		
SLC6A5	9152	hgsc.bcm.edu	37	11	20623007	20623007	+	Silent	SNP	C	C	T	rs7109418	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:20623007C>T	ENST00000525748.1	+	2	609	c.336C>T	c.(334-336)tcC>tcT	p.S112S		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	112					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)	CCGGGAGCTCCGGGCCCGGCA	0.682													C|||	953	0.190296	0.2534	0.1556	5008	,	,		15026	0.005		0.2853	False		,,,				2504	0.2229				p.S112S		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C336T						PASS	.	C		1102,3298		131,840,1229	26.0	29.0	28.0		336	-5.6	0.0	11	dbSNP_116	28	2356,6238		332,1692,2273	no	coding-synonymous	SLC6A5	NM_004211.3		463,2532,3502	TT,TC,CC		27.4145,25.0455,26.6123		112/798	20623007	3458,9536	2200	4297	6497	SO:0001819	synonymous_variant	9152	exon2			GAGCTCCGGGCCC	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.336C>T	11.37:g.20623007C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|0.774;T|0.226	0.226	strong		0.682	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
NCOR2	9612	hgsc.bcm.edu	37	12	124856830	124856830	+	Missense_Mutation	SNP	C	C	T	rs142292731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124856830C>T	ENST00000405201.1	-	20	2545	c.2545G>A	c.(2545-2547)Gag>Aag	p.E849K	NCOR2_ENST00000404121.2_Missense_Mutation_p.E402K|NCOR2_ENST00000397355.1_Missense_Mutation_p.E832K|NCOR2_ENST00000356219.3_Missense_Mutation_p.E849K|NCOR2_ENST00000429285.2_Missense_Mutation_p.E831K|NCOR2_ENST00000404621.1_Missense_Mutation_p.E831K			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	849					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)		GCCAGCTCCTCAGCCGCGGGG	0.701													C|||	21	0.00419329	0.0	0.0101	5008	,	,		10880	0.0		0.0129	False		,,,				2504	0.001				p.E849K		Atlas-SNP	.											.	NCOR2	475	.	0			c.G2545A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	15,3945		0,15,1965	19.0	23.0	22.0		2491,2491,2545	0.7	0.0	12	dbSNP_134	22	226,8042		3,220,3911	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	56,56,56	3,235,5876	TT,TC,CC		2.7334,0.3788,1.9709	benign,benign,benign	831/2459,831/2505,849/2515	124856830	241,11987	1980	4134	6114	SO:0001583	missense	9612	exon22			GCTCCTCAGCCGC	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.2545G>A	12.37:g.124856830C>T	ENSP00000384018:p.Glu849Lys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	10.89	1.477039	0.26511	0.003788	0.027334	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	4.77	0.655	0.17839	.	0.491076	0.15915	N	0.238404	T	0.05273	0.0140	N	0.22421	0.69	0.09310	N	0.99999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.17868	-1.0355	10	0.27785	T	0.31	-1.4997	4.0561	0.09818	0.2308:0.4004:0.2913:0.0776	.	831;832;849	C9J0Q5;C9J239;C9JFD3	.;.;.	K	849;831;849;832;848;402;831;849	ENSP00000384018:E849K;ENSP00000384202:E831K;ENSP00000348551:E849K;ENSP00000380513:E832K;ENSP00000385618:E402K;ENSP00000400281:E831K;ENSP00000402808:E849K	ENSP00000348551:E849K	E	-	1	0	NCOR2	123422783	0.527000	0.26306	0.001000	0.08648	0.004000	0.04260	2.329000	0.43876	-0.171000	0.10797	-0.310000	0.09108	GAG	C|0.988;T|0.012	0.012	strong		0.701	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
COQ6	51004	hgsc.bcm.edu	37	14	74424938	74424938	+	Silent	SNP	T	T	C	rs3180946	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74424938T>C	ENST00000334571.2	+	5	610	c.570T>C	c.(568-570)caT>caC	p.H190H	COQ6_ENST00000394026.4_Silent_p.H165H|ENTPD5_ENST00000557325.1_3'UTR|COQ6_ENST00000554920.1_Intron|COQ6_ENST00000238709.4_Silent_p.H115H	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	190					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|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)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		CTTGGGTTCATATTACCCTAG	0.473													T|||	926	0.184904	0.0325	0.3199	5008	,	,		19445	0.0496		0.4026	False		,,,				2504	0.2106				p.H190H		Atlas-SNP	.											.	COQ6	27	.	0			c.T570C						PASS	.	T	,	386,4020	194.3+/-219.2	17,352,1834	109.0	97.0	101.0		570,345	-4.1	0.9	14	dbSNP_105	101	3555,5045	517.7+/-379.1	726,2103,1471	no	coding-synonymous,coding-synonymous	COQ6	NM_182476.2,NM_182480.2	,	743,2455,3305	CC,CT,TT		41.3372,8.7608,30.3014	,	190/469,115/394	74424938	3941,9065	2203	4300	6503	SO:0001819	synonymous_variant	51004	exon5			GGTTCATATTACC	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.570T>C	14.37:g.74424938T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	37	CCDS9823.1																																																																																			T|0.737;C|0.263	0.263	strong		0.473	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
EVPL	2125	hgsc.bcm.edu	37	17	74014634	74014634	+	Missense_Mutation	SNP	G	G	T	rs7218767	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:74014634G>T	ENST00000301607.3	-	12	1585	c.1332C>A	c.(1330-1332)gaC>gaA	p.D444E	EVPL_ENST00000586740.1_Missense_Mutation_p.D444E	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	444	Globular 1.			D -> E (in Ref. 1; AAC64662 and 2; AAD00186). {ECO:0000305}.	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						AGGCGTGCGGGTCAGTGTTAT	0.672													G|||	463	0.0924521	0.2095	0.0634	5008	,	,		14611	0.0744		0.0338	False		,,,				2504	0.0337				p.D444E		Atlas-SNP	.											EVPL,NS,carcinoma,0,1	EVPL	155	1	0			c.C1332A						scavenged	.	G	GLU/ASP	762,3644		67,628,1508	22.0	25.0	24.0		1332	3.1	0.7	17	dbSNP_116	24	283,8317		3,277,4020	yes	missense	EVPL	NM_001988.2	45	70,905,5528	TT,TG,GG		3.2907,17.2946,8.0348	probably-damaging	444/2034	74014634	1045,11961	2203	4300	6503	SO:0001583	missense	2125	exon12			GTGCGGGTCAGTG	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.1332C>A	17.37:g.74014634G>T	ENSP00000301607:p.Asp444Glu	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	194	0.08882783882783883	110	0.22357723577235772	16	0.04419889502762431	42	0.07342657342657342	26	0.03430079155672823	G	11.20	1.569434	0.28003	0.172946	0.032907	ENSG00000167880	ENST00000301607	T	0.65916	-0.18	5.12	3.07	0.35406	.	0.417816	0.27397	N	0.019559	T	0.00039	0.0001	L	0.47716	1.5	0.34435	P	0.30100899999999997	P;P	0.40909	0.732;0.682	B;B	0.33568	0.166;0.115	T	0.06162	-1.0842	9	0.33940	T	0.23	-27.5202	8.3565	0.32333	0.1459:0.1289:0.7252:0.0	rs7218767	444;444	B7ZLH8;Q92817	.;EVPL_HUMAN	E	444	ENSP00000301607:D444E	ENSP00000301607:D444E	D	-	3	2	EVPL	71526229	1.000000	0.71417	0.741000	0.31004	0.041000	0.13682	2.139000	0.42149	1.304000	0.44892	0.561000	0.74099	GAC	G|0.921;T|0.079	0.079	strong		0.672	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
FCGBP	8857	hgsc.bcm.edu	37	19	40360928	40360928	+	Silent	SNP	G	G	A	rs1053686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:40360928G>A	ENST00000221347.6	-	33	15487	c.15480C>T	c.(15478-15480)cgC>cgT	p.R5160R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5160	Cys-rich.|TIL 12.					extracellular vesicular exosome (GO:0070062)		p.R5160R(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)			AAAGCAGGAAGCGGTCGTCGC	0.622													G|||	590	0.117812	0.1271	0.1988	5008	,	,		16856	0.0387		0.1431	False		,,,				2504	0.1033				p.R5160R		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C15480T						PASS	.	G		689,3717	290.1+/-280.8	58,573,1572	68.0	65.0	66.0		15480	1.4	1.0	19	dbSNP_86	66	1357,7243	265.3+/-286.1	110,1137,3053	no	coding-synonymous	FCGBP	NM_003890.2		168,1710,4625	AA,AG,GG		15.7791,15.6378,15.7312		5160/5406	40360928	2046,10960	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon33			CAGGAAGCGGTCG	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.15480C>T	19.37:g.40360928G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.865;N|0.000	.	strong		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PROKR2	128674	hgsc.bcm.edu	37	20	5283376	5283376	+	Silent	SNP	G	G	A	rs3746684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:5283376G>A	ENST00000217270.3	-	2	464	c.465C>T	c.(463-465)ctC>ctT	p.L155L	PROKR2_ENST00000546004.1_Silent_p.L155L	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	155					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						GAACGATGGCGAGATATCTGG	0.488										HNSCC(71;0.22)			G|||	2236	0.446486	0.4675	0.4222	5008	,	,		22221	0.504		0.3738	False		,,,				2504	0.4509				p.L155L		Atlas-SNP	.											.	PROKR2	90	.	0			c.C465T						PASS	.	G		2014,2392	549.6+/-377.8	467,1080,656	71.0	78.0	75.0		465	-10.6	0.0	20	dbSNP_107	75	3309,5291	487.4+/-372.1	633,2043,1624	no	coding-synonymous	PROKR2	NM_144773.2		1100,3123,2280	AA,AG,GG		38.4767,45.7104,40.9273		155/385	5283376	5323,7683	2203	4300	6503	SO:0001819	synonymous_variant	128674	exon2			GATGGCGAGATAT	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"""GPCR / Class A : Prokineticin receptors"""	15836	protein-coding gene	gene with protein product		607123	"""G protein-coupled receptor 73-like 1"", ""Kallmann syndrome 3 (autosomal dominant)"""	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.465C>T	20.37:g.5283376G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Silent	SNP	ENST00000217270.3	37	CCDS13089.1																																																																																			G|0.578;A|0.422	0.422	strong		0.488	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
C11orf80	79703	hgsc.bcm.edu	37	11	66610645	66610645	+	Silent	SNP	G	G	C	rs7570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:66610645G>C	ENST00000360962.4	+	17	1981	c.1974G>C	c.(1972-1974)gtG>gtC	p.V658V	C11orf80_ENST00000525449.2_Silent_p.V466V|RCE1_ENST00000525356.1_5'Flank|RCE1_ENST00000309657.3_5'Flank|C11orf80_ENST00000346672.4_Silent_p.V467V|C11orf80_ENST00000527634.1_Silent_p.V441V|C11orf80_ENST00000532565.2_Silent_p.V440V|C11orf80_ENST00000540737.1_Silent_p.V492V|RCE1_ENST00000524506.1_5'Flank	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	658										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						CGCAGGACGTGCTGTGGCTGC	0.716													G|||	973	0.194289	0.2345	0.196	5008	,	,		10884	0.1508		0.2674	False		,,,				2504	0.1084				p.V658V		Atlas-SNP	.											.	C11orf80	31	.	0			c.G1974C						PASS	.	G		865,3057		93,679,1189	15.0	20.0	19.0		1974	-1.8	0.0	11	dbSNP_52	19	2101,6169		276,1549,2310	yes	coding-synonymous	C11orf80	NM_024650.3		369,2228,3499	CC,CG,GG		25.4051,22.0551,24.3274		658/678	66610645	2966,9226	1961	4135	6096	SO:0001819	synonymous_variant	79703	exon17			GGACGTGCTGTGG			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.1974G>C	11.37:g.66610645G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_024650	Q9H677	Silent	SNP	ENST00000360962.4	37	CCDS53664.1																																																																																			G|0.787;C|0.213	0.213	strong		0.716	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650	
WFDC8	90199	hgsc.bcm.edu	37	20	44184498	44184498	+	Missense_Mutation	SNP	A	A	G	rs2272955	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44184498A>G	ENST00000357199.4	-	4	365	c.287T>C	c.(286-288)aTg>aCg	p.M96T	WFDC8_ENST00000289953.2_Missense_Mutation_p.M96T	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	96	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		M -> T (in dbSNP:rs2272955).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.M96T(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				CACAGGTAGCATGCAGGGTTC	0.458													A|||	518	0.103435	0.1694	0.0634	5008	,	,		21266	0.1716		0.0567	False		,,,				2504	0.0204				p.M96T		Atlas-SNP	.											WFDC8,NS,carcinoma,0,1	WFDC8	28	1	1	Substitution - Missense(1)	stomach(1)	c.T287C						PASS	.	A	THR/MET,THR/MET	715,3691	295.3+/-283.6	60,595,1548	87.0	80.0	82.0		287,287	-3.8	0.0	20	dbSNP_100	82	507,8093	144.7+/-200.5	12,483,3805	yes	missense,missense	WFDC8	NM_130896.2,NM_181510.2	81,81	72,1078,5353	GG,GA,AA		5.8953,16.2279,9.3957	benign,benign	96/242,96/242	44184498	1222,11784	2203	4300	6503	SO:0001583	missense	90199	exon4			GGTAGCATGCAGG	AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"""WAP four-disulfide core domain containing"""	16163	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 170"""	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.287T>C	20.37:g.44184498A>G	ENSP00000361735:p.Met96Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_181510	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	37	CCDS13361.1	266	0.12179487179487179	92	0.18699186991869918	27	0.07458563535911603	105	0.18356643356643357	42	0.055408970976253295	A	0.030	-1.343661	0.01277	0.162279	0.058953	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.56275	0.47;0.47	4.26	-3.81	0.04294	Proteinase inhibitor I2, Kunitz metazoa (6);	1.987250	0.02150	N	0.057931	T	0.00039	0.0001	N	0.16833	0.445	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.12811	-1.0533	9	0.06891	T	0.86	.	10.2379	0.43294	0.5409:0.0:0.4591:0.0	rs2272955;rs52829198;rs59271448;rs2272955	96	Q8IUA0	WFDC8_HUMAN	T	96	ENSP00000361735:M96T;ENSP00000289953:M96T	ENSP00000289953:M96T	M	-	2	0	WFDC8	43617912	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.787000	0.04510	-0.755000	0.03482	ATG	A|0.897;G|0.103	0.103	strong		0.458	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1		
SCN4A	6329	hgsc.bcm.edu	37	17	62049749	62049749	+	Missense_Mutation	SNP	C	C	T	rs41280110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62049749C>T	ENST00000435607.1	-	2	431	c.355G>A	c.(355-357)Gta>Ata	p.V119I	SCN4A_ENST00000578147.1_Missense_Mutation_p.V119I|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	119					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CGCCTGACTACGCTGAAGGGG	0.607													C|||	6	0.00119808	0.0	0.0	5008	,	,		21598	0.0		0.004	False		,,,				2504	0.002				p.V119I		Atlas-SNP	.											SCN4A,NS,carcinoma,+1,1	SCN4A	205	1	0			c.G355A						PASS	.	C	ILE/VAL	2,4316		0,2,2157	66.0	72.0	70.0		355	-1.0	0.1	17	dbSNP_127	70	36,8498		0,36,4231	yes	missense	SCN4A	NM_000334.4	29	0,38,6388	TT,TC,CC		0.4218,0.0463,0.2957	benign	119/1837	62049749	38,12814	2159	4267	6426	SO:0001583	missense	6329	exon2			TGACTACGCTGAA	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.355G>A	17.37:g.62049749C>T	ENSP00000396320:p.Val119Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	146	85	0.582192	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	3.276	-0.148162	0.06627	4.63E-4	0.004218	ENSG00000007314	ENST00000435607	D	0.95918	-3.85	4.23	-0.98	0.10272	.	1.351180	0.04536	N	0.387199	D	0.82296	0.5006	N	0.00801	-1.175	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74624	-0.3603	10	0.33141	T	0.24	.	2.0281	0.03523	0.1273:0.1785:0.4109:0.2833	rs41280110	119	P35499	SCN4A_HUMAN	I	119	ENSP00000396320:V119I	ENSP00000396320:V119I	V	-	1	0	SCN4A	59403481	0.000000	0.05858	0.116000	0.21606	0.196000	0.23810	-0.152000	0.10159	-0.405000	0.07599	-2.222000	0.00295	GTA	C|0.998;T|0.002	0.002	strong		0.607	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
HJURP	55355	hgsc.bcm.edu	37	2	234758500	234758500	+	Silent	SNP	G	G	A	rs529963	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234758500G>A	ENST00000411486.2	-	4	311	c.246C>T	c.(244-246)tcC>tcT	p.S82S	HJURP_ENST00000432087.1_Intron|HJURP_ENST00000441687.1_Intron	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	82					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GCTTCATGGAGGAGTCCTCCA	0.522													G|||	903	0.180312	0.2776	0.1412	5008	,	,		17025	0.1448		0.174	False		,,,				2504	0.1196				p.S82S		Atlas-SNP	.											.	HJURP	72	.	0			c.C246T						PASS	.	G		1080,3164		148,784,1190	26.0	21.0	23.0		246	0.5	0.0	2	dbSNP_83	23	1316,6948		111,1094,2927	no	coding-synonymous	HJURP	NM_018410.3		259,1878,4117	AA,AG,GG		15.9245,25.4477,19.1557		82/749	234758500	2396,10112	2122	4132	6254	SO:0001819	synonymous_variant	55355	exon4			CATGGAGGAGTCC		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.246C>T	2.37:g.234758500G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Silent	SNP	ENST00000411486.2	37	CCDS33406.1																																																																																			G|0.792;A|0.208	0.208	strong		0.522	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
LAMA5	3911	hgsc.bcm.edu	37	20	60897487	60897487	+	Missense_Mutation	SNP	C	C	T	rs2274934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60897487C>T	ENST00000252999.3	-	47	6250	c.6184G>A	c.(6184-6186)Gat>Aat	p.D2062N		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2062	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.		D -> N (in dbSNP:rs2274934). {ECO:0000269|PubMed:11821406, ECO:0000269|PubMed:9628581}.		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)			CCGCAGCCATCGAAACCAAAA	0.672													.|||	2393	0.477835	0.0976	0.5159	5008	,	,		11156	0.747		0.5547	False		,,,				2504	0.6084				p.D2062N		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6184A						PASS	.	C	ASN/ASP	647,3647		65,517,1565	9.0	12.0	11.0		6184	2.8	0.1	20	dbSNP_100	11	4883,3619		1464,1955,832	no	missense	LAMA5	NM_005560.3	23	1529,2472,2397	TT,TC,CC		42.5665,15.0675,43.2166	possibly-damaging	2062/3696	60897487	5530,7266	2147	4251	6398	SO:0001583	missense	3911	exon47			AGCCATCGAAACC	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.6184G>A	20.37:g.60897487C>T	ENSP00000252999:p.Asp2062Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	1118	0.5119047619047619	64	0.13008130081300814	184	0.5082872928176796	441	0.7709790209790209	429	0.5659630606860159	c	10.33	1.319163	0.23994	0.150675	0.574335	ENSG00000130702	ENST00000252999	T	0.32023	1.47	3.82	2.83	0.33086	EGF-like, laminin (4);	0.605183	0.16797	U	0.199131	T	0.00012	0.0000	N	0.25094	0.71	0.09310	P	1.0	B	0.25563	0.129	B	0.18871	0.023	T	0.17806	-1.0357	9	0.22706	T	0.39	.	7.0499	0.25067	0.0:0.7291:0.1768:0.0942	rs2274934;rs2274934	2062	O15230	LAMA5_HUMAN	N	2062	ENSP00000252999:D2062N	ENSP00000252999:D2062N	D	-	1	0	LAMA5	60330882	0.025000	0.19082	0.068000	0.19968	0.008000	0.06430	0.835000	0.27531	0.768000	0.33290	0.485000	0.47835	GAT	C|0.463;T|0.537	0.537	strong		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CCDC74B	91409	hgsc.bcm.edu	37	2	130898813	130898813	+	Missense_Mutation	SNP	G	G	A	rs142452531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:130898813G>A	ENST00000310463.6	-	4	738	c.601C>T	c.(601-603)Ccc>Tcc	p.P201S	CCDC74B_ENST00000409128.1_Missense_Mutation_p.P177S|CCDC74B_ENST00000409943.3_Missense_Mutation_p.P135S|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000392984.3_Missense_Mutation_p.P303S	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	201										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					GCCTTCTGGGGGACGTCAGCT	0.592																																					p.P201S		Atlas-SNP	.											CCDC74B,NS,carcinoma,+2,2	CCDC74B	27	2	0			c.C601T						scavenged	.						165.0	115.0	132.0					2																	130898813		2201	4264	6465	SO:0001583	missense	91409	exon4			TCTGGGGGACGTC		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.601C>T	2.37:g.130898813G>A	ENSP00000308873:p.Pro201Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	136	23	0.169118	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	37	CCDS2155.1	114	0.0521978021978022	3	0.006097560975609756	31	0.0856353591160221	5	0.008741258741258742	75	0.09894459102902374	.	0.008	-1.866645	0.00547	.	.	ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984;ENST00000409488;ENST00000409128	T;T;T;T	0.44881	1.9;1.93;1.87;0.91	2.39	1.48	0.22813	.	0.638174	0.12247	U	0.485969	T	0.00875	0.0029	M	0.62723	1.935	0.09310	N	1	P;B;B	0.50710	0.938;0.009;0.264	B;B;B	0.38156	0.266;0.015;0.05	T	0.02560	-1.1141	10	0.30854	T	0.27	-0.2433	4.9656	0.14089	0.1864:0.0:0.8136:0.0	.	303;135;201	E7ESC5;Q96LY2-2;Q96LY2	.;.;CC74B_HUMAN	S	135;201;303;139;177	ENSP00000386294:P135S;ENSP00000308873:P201S;ENSP00000376710:P303S;ENSP00000386644:P177S	ENSP00000308873:P201S	P	-	1	0	CCDC74B	130615283	0.000000	0.05858	0.044000	0.18714	0.014000	0.08584	0.104000	0.15313	0.333000	0.23563	0.298000	0.19748	CCC	G|0.700;A|0.300	0.300	strong		0.592	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
MUC16	94025	hgsc.bcm.edu	37	19	9060541	9060541	+	Missense_Mutation	SNP	C	C	T	rs11882256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9060541C>T	ENST00000397910.4	-	3	27108	c.26905G>A	c.(26905-26907)Gtg>Atg	p.V8969M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8971	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						GAGGTGACCACTGGAGATGTC	0.473													t|||	1962	0.391773	0.3427	0.4712	5008	,	,		22676	0.5933		0.2525	False		,,,				2504	0.3374				p.V8969M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G26905A						PASS	.	C	MET/VAL	1278,2694		198,882,906	208.0	194.0	199.0		26905	-5.2	0.0	19	dbSNP_120	199	2173,6167		270,1633,2267	yes	missense	MUC16	NM_024690.2	21	468,2515,3173	TT,TC,CC		26.0552,32.1752,28.0296	probably-damaging	8969/14508	9060541	3451,8861	1986	4170	6156	SO:0001583	missense	94025	exon3			TGACCACTGGAGA	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.26905G>A	19.37:g.9060541C>T	ENSP00000381008:p.Val8969Met	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	230	110	0.478261	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	877	0.4015567765567766	156	0.3170731707317073	152	0.4198895027624309	374	0.6538461538461539	195	0.25725593667546176	t	2.257	-0.370133	0.05069	0.321752	0.260552	ENSG00000181143	ENST00000397910	T	0.20881	2.04	2.62	-5.24	0.02789	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	.	.	.	B	0.06786	0.001	B	0.06405	0.002	T	0.39121	-0.9629	8	0.87932	D	0	.	3.1852	0.06598	0.1063:0.4194:0.3199:0.1545	rs11882256;rs52832468;rs59005440;rs11882256	8969	B5ME49	.	M	8969	ENSP00000381008:V8969M	ENSP00000381008:V8969M	V	-	1	0	MUC16	8921541	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-7.589000	0.00033	-3.677000	0.00122	-0.871000	0.02989	GTG	C|0.615;T|0.385	0.385	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ERICH6	131831	hgsc.bcm.edu	37	3	150398311	150398311	+	Missense_Mutation	SNP	C	C	A	rs144597450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:150398311C>A	ENST00000295910.6	-	9	1107	c.1055G>T	c.(1054-1056)cGa>cTa	p.R352L	FAM194A_ENST00000491361.1_Missense_Mutation_p.R206L	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						TCTGGCCATTCGTTGCTCCTG	0.383													C|||	20	0.00399361	0.0008	0.0014	5008	,	,		18752	0.0		0.0089	False		,,,				2504	0.0092				p.R352L		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1055T						PASS	.	C	LEU/ARG	17,4389	23.3+/-48.9	0,17,2186	203.0	181.0	189.0		1055	-0.5	0.3	3	dbSNP_134	189	155,8445	73.8+/-136.5	0,155,4145	yes	missense	FAM194A	NM_152394.3	102	0,172,6331	AA,AC,CC		1.8023,0.3858,1.3225	benign	352/664	150398311	172,12834	2203	4300	6503	SO:0001583	missense	131831	exon9			GCCATTCGTTGCT																												ENST00000295910.6:c.1055G>T	3.37:g.150398311C>A	ENSP00000295910:p.Arg352Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	C	6.981	0.551108	0.13374	0.003858	0.018023	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14144	2.73;2.53	4.93	-0.458	0.12182	.	0.483859	0.19089	N	0.123014	T	0.03053	0.0090	N	0.22421	0.69	0.20638	N	0.999872	B	0.13594	0.008	B	0.13407	0.009	T	0.26292	-1.0107	10	0.42905	T	0.14	-6.1936	2.7584	0.05299	0.321:0.1879:0.0:0.491	.	352	Q7L0X2	F194A_HUMAN	L	352;206;310	ENSP00000295910:R352L;ENSP00000419366:R206L	ENSP00000295910:R352L	R	-	2	0	FAM194A	151881001	0.994000	0.37717	0.258000	0.24420	0.019000	0.09904	0.567000	0.23608	-0.140000	0.11394	-0.471000	0.05019	CGA	C|0.990;A|0.010	0.010	strong		0.383	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
IL1RL2	8808	hgsc.bcm.edu	37	2	102851708	102851708	+	Missense_Mutation	SNP	T	T	C	rs2302612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:102851708T>C	ENST00000264257.2	+	11	1775	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P	IL1RL2_ENST00000441515.2_Missense_Mutation_p.L432P|IL1RL2_ENST00000539491.1_Missense_Mutation_p.L550P|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	550			L -> P (in dbSNP:rs2302612). {ECO:0000269|Ref.3}.	PPVQLLQHTPCY -> LRSTCRSTHLCTA (in Ref. 2). {ECO:0000305}.	cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						GTCCAGCTGCTGCAGCACACA	0.577											OREG0014848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1592	0.317891	0.5356	0.4496	5008	,	,		20642	0.2857		0.1889	False		,,,				2504	0.0961				p.L550P		Atlas-SNP	.											IL1RL2_ENST00000441515,NS,carcinoma,-1,2	IL1RL2	118	2	0			c.T1649C						PASS	.	C	PRO/LEU	2167,2239	588.8+/-387.0	550,1067,586	58.0	54.0	55.0		1649	1.0	0.2	2	dbSNP_100	55	1642,6958	739.0+/-407.1	173,1296,2831	yes	missense	IL1RL2	NM_003854.2	98	723,2363,3417	CC,CT,TT		19.093,49.1829,29.2865	benign	550/576	102851708	3809,9197	2203	4300	6503	SO:0001583	missense	8808	exon11			AGCTGCTGCAGCA	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1649T>C	2.37:g.102851708T>C	ENSP00000264257:p.Leu550Pro	Somatic	78	0	0	1369	WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	689	0.31547619047619047	263	0.5345528455284553	137	0.3784530386740331	152	0.26573426573426573	137	0.18073878627968337	C	9.673	1.147281	0.21288	0.491829	0.19093	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.04809	3.83;3.55;3.83	4.81	1.03	0.20045	.	1.599210	0.03353	N	0.196412	T	0.00012	0.0000	N	0.19112	0.55	0.54753	P	1.3000000000040757E-5	B;B	0.13145	0.003;0.007	B;B	0.09377	0.002;0.004	T	0.46610	-0.9179	9	0.40728	T	0.16	.	9.2098	0.37311	0.0:0.3158:0.0:0.6842	rs2302612;rs59675966;rs2302612	432;550	A4FU63;Q9HB29	.;ILRL2_HUMAN	P	550;432;550	ENSP00000264257:L550P;ENSP00000413348:L432P;ENSP00000442184:L550P	ENSP00000264257:L550P	L	+	2	0	IL1RL2	102218140	0.000000	0.05858	0.166000	0.22797	0.017000	0.09413	0.048000	0.14078	0.084000	0.17077	-1.364000	0.01208	CTG	T|0.699;C|0.301	0.301	strong		0.577	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
DNHD1	144132	hgsc.bcm.edu	37	11	6579106	6579106	+	Missense_Mutation	SNP	C	C	A	rs11040920	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	35	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	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	
NTSR1	4923	hgsc.bcm.edu	37	20	61386231	61386231	+	Silent	SNP	C	C	T	rs6010685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:61386231C>T	ENST00000370501.3	+	2	1280	c.909C>T	c.(907-909)cgC>cgT	p.R303R		NM_002531.2	NP_002522.2	P30989	NTR1_HUMAN	neurotensin receptor 1 (high affinity)	303					adult locomotory behavior (GO:0008344)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			ACGGCGTGCGCGTCCTACGTA	0.687													c|||	319	0.0636981	0.1142	0.0202	5008	,	,		16835	0.0198		0.0616	False		,,,				2504	0.0736				p.R303R	GBM(37;400 780 6403 19663 35669)	Atlas-SNP	.											NTSR1,NS,malignant_melanoma,+1,1	NTSR1	59	1	0			c.C909T						PASS	.			474,3920	211.2+/-231.4	25,424,1748	38.0	30.0	33.0		909	-4.5	0.0	20	dbSNP_114	33	441,8147	129.8+/-187.9	6,429,3859	no	coding-synonymous	NTSR1	NM_002531.2		31,853,5607	TT,TC,CC		5.1351,10.7874,7.0482		303/419	61386231	915,12067	2197	4294	6491	SO:0001819	synonymous_variant	4923	exon2			CGTGCGCGTCCTA		CCDS13502.1	20q13	2012-08-08			ENSG00000101188	ENSG00000101188		"""GPCR / Class A : Neurotensin receptors"""	8039	protein-coding gene	gene with protein product		162651				8075503	Standard	NM_002531		Approved	NTR	uc002ydf.3	P30989	OTTHUMG00000032932	ENST00000370501.3:c.909C>T	20.37:g.61386231C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_002531	Q9H4H1|Q9H4T5	Silent	SNP	ENST00000370501.3	37	CCDS13502.1																																																																																			C|0.934;T|0.066	0.066	strong		0.687	NTSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080061.1		
MET	4233	hgsc.bcm.edu	37	7	116436097	116436097	+	Silent	SNP	G	G	A	rs41737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	126	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	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		
CLEC17A	388512	hgsc.bcm.edu	37	19	14705574	14705574	+	Missense_Mutation	SNP	T	T	C	rs78269670	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14705574T>C	ENST00000417570.1	+	7	403	c.365T>C	c.(364-366)cTg>cCg	p.L122P	CLEC17A_ENST00000547437.1_Missense_Mutation_p.L122P|CLEC17A_ENST00000397439.2_Missense_Mutation_p.L105P	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	60	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	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	
CCDC186	55088	hgsc.bcm.edu	37	10	115910928	115910928	+	Missense_Mutation	SNP	G	G	T	rs7095762	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:115910928G>T	ENST00000369287.3	-	4	1077	c.811C>A	c.(811-813)Caa>Aaa	p.Q271K		NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		271			Q -> K (in dbSNP:rs7095762). {ECO:0000269|PubMed:14996095, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		GCTATTAGTTGATCTCTGGAA	0.328													T|||	1038	0.207268	0.3434	0.2349	5008	,	,		16833	0.0585		0.2505	False		,,,				2504	0.1125				p.Q271K		Atlas-SNP	.											.	C10orf118	70	.	0			c.C811A						PASS	.	T	LYS/GLN	1397,3009	686.3+/-404.7	210,977,1016	198.0	173.0	181.0		811	4.8	1.0	10	dbSNP_116	181	2021,6579	720.7+/-406.3	246,1529,2525	yes	missense	C10orf118	NM_018017.2	53	456,2506,3541	TT,TG,GG		23.5,31.7068,26.2802	benign	271/899	115910928	3418,9588	2203	4300	6503	SO:0001583	missense	55088	exon4			TTAGTTGATCTCT																												ENST00000369287.3:c.811C>A	10.37:g.115910928G>T	ENSP00000358293:p.Gln271Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	459	0.21016483516483517	152	0.3089430894308943	92	0.2541436464088398	34	0.05944055944055944	181	0.23878627968337732	T	0.970	-0.700333	0.03279	0.317068	0.235	ENSG00000165813	ENST00000369287;ENST00000430353	T	0.35605	1.3	5.94	4.8	0.61643	.	0.096473	0.64402	N	0.000001	T	0.00012	0.0000	N	0.02802	-0.49	0.09310	P	0.9999999999999921	B	0.02656	0.0	B	0.01281	0.0	T	0.37009	-0.9724	9	0.02654	T	1	.	11.9902	0.53171	0.0:0.0:0.2861:0.7139	rs7095762;rs52832101;rs57533496;rs7095762	271	Q7Z3E2	CJ118_HUMAN	K	271;377	ENSP00000358293:Q271K	ENSP00000358293:Q271K	Q	-	1	0	C10orf118	115900918	1.000000	0.71417	0.984000	0.44739	0.247000	0.25773	4.641000	0.61375	0.496000	0.27904	-0.270000	0.10280	CAA	G|0.758;T|0.242	0.242	strong		0.328	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
FAM20A	54757	hgsc.bcm.edu	37	17	66596463	66596463	+	Silent	SNP	C	C	T	rs986099	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:66596463C>T	ENST00000592554.1	-	1	1067	c.345G>A	c.(343-345)tcG>tcA	p.S115S		NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	115					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)					TGGCCAGGAGCGAGTCCTCGG	0.716													c|||	849	0.169529	0.0961	0.2522	5008	,	,		12777	0.2748		0.163	False		,,,				2504	0.1084				p.S115S		Atlas-SNP	.											.	FAM20A	35	.	0			c.G345A						PASS	.			375,3867		18,339,1764	5.0	8.0	7.0		345	1.2	1.0	17	dbSNP_86	7	1255,7133		85,1085,3024	no	coding-synonymous	FAM20A	NM_017565.3		103,1424,4788	TT,TC,CC		14.9619,8.8402,12.9058		115/542	66596463	1630,11000	2121	4194	6315	SO:0001819	synonymous_variant	54757	exon1			CAGGAGCGAGTCC	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.345G>A	17.37:g.66596463C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_017565	B2RN47|B2RN49|Q9UF95	Silent	SNP	ENST00000592554.1	37	CCDS11679.1																																																																																			C|0.816;T|0.184	0.184	strong		0.716	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
NTN4	59277	hgsc.bcm.edu	37	12	96131895	96131895	+	Missense_Mutation	SNP	A	A	G	rs17288108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:96131895A>G	ENST00000343702.4	-	3	1061	c.613T>C	c.(613-615)Tac>Cac	p.Y205H	NTN4_ENST00000553059.1_Missense_Mutation_p.Y205H|NTN4_ENST00000344911.4_Missense_Mutation_p.Y168H|NTN4_ENST00000552603.1_5'UTR|NTN4_ENST00000538383.1_Missense_Mutation_p.Y168H	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	95	0	0		WXS	Illumina HiSeq	Phase_I	102	65	0.637255	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	
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	137	0	0		WXS	Illumina HiSeq	Phase_I	136	45	0.330882	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	
PKD1L1	168507	hgsc.bcm.edu	37	7	47913580	47913580	+	Silent	SNP	G	G	A	rs73105162|rs386712932	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:47913580G>A	ENST00000289672.2	-	24	3863	c.3813C>T	c.(3811-3813)ggC>ggT	p.G1271G		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1271	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						TGGAGCCTTTGCCATCTGTGA	0.527													G|||	1524	0.304313	0.4455	0.3357	5008	,	,		17834	0.0962		0.2932	False		,,,				2504	0.317				p.G1271G		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3813T						PASS	.	G		1835,2571	523.1+/-371.0	381,1073,749	111.0	93.0	99.0		3813	-4.4	0.0	7	dbSNP_130	99	2413,6187	370.5+/-335.9	343,1727,2230	no	coding-synonymous	PKD1L1	NM_138295.3		724,2800,2979	AA,AG,GG		28.0581,41.6478,32.6618		1271/2850	47913580	4248,8758	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon24			GCCTTTGCCATCT	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.3813C>T	7.37:g.47913580G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	157	108	0.687898	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.699;A|0.301	0.301	strong		0.527	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
VPS8	23355	hgsc.bcm.edu	37	3	184700426	184700426	+	Missense_Mutation	SNP	C	C	T	rs11555405	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:184700426C>T	ENST00000437079.3	+	41	3664	c.3493C>T	c.(3493-3495)Cac>Tac	p.H1165Y	VPS8_ENST00000436792.2_Missense_Mutation_p.H1163Y|VPS8_ENST00000287546.4_Missense_Mutation_p.H1165Y|VPS8_ENST00000446204.2_Missense_Mutation_p.H1073Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1165			H -> Y (in dbSNP:rs11555405). {ECO:0000269|PubMed:17974005}.				zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TCCTCATCTACACTCTGAAGG	0.398													C|||	1432	0.285942	0.0174	0.3285	5008	,	,		16904	0.506		0.2883	False		,,,				2504	0.3896				p.H1165Y		Atlas-SNP	.											.	VPS8	109	.	0			c.C3493T						PASS	.	C	TYR/HIS,TYR/HIS	184,3598		2,180,1709	77.0	68.0	71.0		3493,3487	5.1	0.0	3	dbSNP_120	71	2082,6166		255,1572,2297	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	83,83	257,1752,4006	TT,TC,CC		25.2425,4.8652,18.8362	benign,benign	1165/1429,1163/1427	184700426	2266,9764	1891	4124	6015	SO:0001583	missense	23355	exon40			CATCTACACTCTG	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3493C>T	3.37:g.184700426C>T	ENSP00000397879:p.His1165Tyr	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	258	127	0.492248	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	659	0.3017399267399267	11	0.022357723577235773	127	0.35082872928176795	290	0.506993006993007	231	0.30474934036939316	C	4.147	0.025712	0.08054	0.048652	0.252425	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	6.05	5.09	0.68999	.	0.413977	0.28983	N	0.013505	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.15870	0.0;0.014;0.0	T	0.41413	-0.9510	9	0.02654	T	1	-17.2505	9.2184	0.37362	0.0:0.824:0.0:0.176	rs11555405;rs13095607;rs52814306;rs61568357;rs11555405	1165;1073;1163	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	Y	1165;1165;1163;1073	ENSP00000287546:H1165Y;ENSP00000397879:H1165Y;ENSP00000404704:H1163Y;ENSP00000405483:H1073Y	ENSP00000287546:H1165Y	H	+	1	0	VPS8	186183120	0.000000	0.05858	0.008000	0.14137	0.700000	0.40528	0.339000	0.19875	1.408000	0.46895	0.650000	0.86243	CAC	C|0.726;T|0.274	0.274	strong		0.398	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
AASDH	132949	hgsc.bcm.edu	37	4	57237683	57237683	+	Silent	SNP	G	G	A	rs6554354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:57237683G>A	ENST00000205214.6	-	5	975	c.795C>T	c.(793-795)tcC>tcT	p.S265S	AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000451613.1_Silent_p.S265S|AASDH_ENST00000510762.1_Intron|AASDH_ENST00000602986.1_Silent_p.S112S|AASDH_ENST00000513376.1_Silent_p.S165S|AASDH_ENST00000502617.1_Silent_p.S265S	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	69	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	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	
RLBP1	6017	hgsc.bcm.edu	37	15	89753546	89753546	+	Silent	SNP	G	G	C	rs144615495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:89753546G>C	ENST00000268125.5	-	9	1363	c.924C>G	c.(922-924)ccC>ccG	p.P308P		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	308					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	CTTGGGCCTGGGGGCCAAAGA	0.562													G|||	2	0.000399361	0.0	0.0	5008	,	,		20947	0.0		0.002	False		,,,				2504	0.0				p.P308P		Atlas-SNP	.											.	RLBP1	34	.	0			c.C924G						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	94.0	92.0	93.0		924	-0.9	0.1	15	dbSNP_134	93	15,8583	11.2+/-40.8	0,15,4284	no	coding-synonymous	RLBP1	NM_000326.4		0,16,6483	CC,CG,GG		0.1745,0.0227,0.1231		308/318	89753546	16,12982	2200	4299	6499	SO:0001819	synonymous_variant	6017	exon9			GGCCTGGGGGCCA	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.924C>G	15.37:g.89753546G>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_000326	B2R667	Silent	SNP	ENST00000268125.5	37	CCDS32324.1																																																																																			G|0.999;C|0.001	0.001	strong		0.562	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
ASMTL	8623	hgsc.bcm.edu	37	X	1537953	1537953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:1537953C>T	ENST00000381317.3	-	10	1332	c.1300G>A	c.(1300-1302)Ggc>Agc	p.G434S	ASMTL_ENST00000381333.4_Missense_Mutation_p.G418S|ASMTL_ENST00000416733.2_Missense_Mutation_p.G358S|ASMTL_ENST00000534940.1_Missense_Mutation_p.G376S	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	434	ASMT-like.			G -> S (in Ref. 2; BAG63287). {ECO:0000305}.		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)				TTCGTCATGCCGTGCATGGCC	0.672													c|||	600	0.119808	0.1256	0.1023	5008	,	,		15106	0.0972		0.1869	False		,,,				2504	0.0787				p.G434S		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1300A						PASS	.		SER/GLY,SER/GLY,SER/GLY	596,3652		41,514,1569	37.0	50.0	46.0		1126,1252,1300	-3.8	0.0	X	dbSNP_134	46	1369,7073		125,1119,2977	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	56,56,56	166,1633,4546	TT,TC,CC		16.2165,14.0301,15.4846	benign,benign,benign	376/564,418/606,434/622	1537953	1965,10725	2124	4221	6345	SO:0001583	missense	8623	exon10			TCATGCCGTGCAT	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.1300G>A	X.37:g.1537953C>T	ENSP00000370718:p.Gly434Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	309	0.14148351648351648	76	0.15447154471544716	37	0.10220994475138122	63	0.11013986013986014	133	0.17546174142480211	c	1.729	-0.494575	0.04322	0.140301	0.162165	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	1.88	-3.76	0.04359	O-methyltransferase, family 2 (1);	0.325338	0.30901	N	0.008641	T	0.00012	0.0000	N	0.13235	0.315	0.09310	N	1	B;B;B	0.14805	0.011;0.009;0.011	B;B;B	0.18871	0.023;0.011;0.019	T	0.26360	-1.0105	10	0.10636	T	0.68	.	3.4151	0.07373	0.264:0.2992:0.0:0.4368	.	358;418;434	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	S	358;376;418;434	ENSP00000410578:G358S;ENSP00000446410:G376S;ENSP00000370734:G418S;ENSP00000370718:G434S	ENSP00000370718:G434S	G	-	1	0	ASMTL	1497953	0.996000	0.38824	0.036000	0.18154	0.045000	0.14185	0.139000	0.16036	-1.731000	0.01360	-1.717000	0.00709	GGC	C|0.858;T|0.142	0.142	strong		0.672	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152277055C>G	ENST00000368799.1	-	3	10342	c.10307G>C	c.(10306-10308)gGa>gCa	p.G3436A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3436	Ser-rich.		G -> A (in dbSNP:rs2065955).		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)			CCCCGGGTGTCCACGAATGGT	0.597									Ichthyosis				C|||	2575	0.514177	0.7882	0.4481	5008	,	,		18425	0.6349		0.1481	False		,,,				2504	0.4427				p.G3436A		Atlas-SNP	.											.	FLG	900	.	0			c.G10307C						PASS	.	C	ALA/GLY	3017,1389	686.4+/-404.7	1050,917,236	295.0	296.0	295.0		10307	-1.1	0.0	1	dbSNP_94	295	1294,7306	254.0+/-279.5	122,1050,3128	no	missense	FLG	NM_002016.1	60	1172,1967,3364	GG,GC,CC		15.0465,31.5252,33.1462	possibly-damaging	3436/4062	152277055	4311,8695	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGGTGTCCACGAA	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.10307G>C	1.37:g.152277055C>G	ENSP00000357789:p.Gly3436Ala	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	177	93	0.525424	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	949	0.43452380952380953	355	0.7215447154471545	137	0.3784530386740331	342	0.5979020979020979	115	0.1517150395778364	C	3.831	-0.035729	0.07497	0.684748	0.150465	ENSG00000143631	ENST00000368799	T	0.07114	3.22	3.31	-1.14	0.09741	.	.	.	.	.	T	0.04634	0.0126	L	0.57536	1.79	0.80722	P	0.0	P	0.46327	0.876	P	0.54312	0.748	T	0.23261	-1.0193	8	0.18710	T	0.47	-3.9699	3.0433	0.06145	0.1908:0.4576:0.0:0.3516	rs56734521	3436	P20930	FILA_HUMAN	A	3436	ENSP00000357789:G3436A	ENSP00000357789:G3436A	G	-	2	0	FLG	150543679	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.597000	0.05713	-0.563000	0.06078	-0.396000	0.06452	GGA	C|0.615;G|0.385	0.385	strong		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PSG4	5672	hgsc.bcm.edu	37	19	43702342	43702342	+	Silent	SNP	C	C	T	rs9789333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43702342C>T	ENST00000405312.3	-	3	753	c.516G>A	c.(514-516)gcG>gcA	p.A172A	PSG4_ENST00000433626.2_Intron|PSG4_ENST00000244295.9_Silent_p.A172A	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	172	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CGGCTGGAGTCGCAGGATCAC	0.527													C|||	2257	0.450679	0.2383	0.3631	5008	,	,		13137	0.8591		0.2445	False		,,,				2504	0.591				p.V172V		Atlas-SNP	.											.	PSG4	129	.	0			c.G516A						PASS	.	C	,	943,3311		251,441,1435	152.0	173.0	166.0		516,516	0.9	0.0	19	dbSNP_119	166	2158,6388		382,1394,2497	yes	coding-synonymous,coding-synonymous	PSG4	NM_002780.3,NM_213633.1	,	633,1835,3932	TT,TC,CC		25.2516,22.1674,24.2266	,	172/420,172/327	43702342	3101,9699	2127	4273	6400	SO:0001819	synonymous_variant	5672	exon3			TGGAGTCGCAGGA		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.516G>A	19.37:g.43702342C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1																																																																																			C|0.597;T|0.403	0.403	strong		0.527	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
PPFIA1	8500	hgsc.bcm.edu	37	11	70189892	70189892	+	Missense_Mutation	SNP	A	A	G	rs146858711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70189892A>G	ENST00000253925.7	+	15	2040	c.1825A>G	c.(1825-1827)Act>Gct	p.T609A	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.T609A	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	609					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGACAGGGACACTCTCCTCAG	0.557													A|||	7	0.00139776	0.0	0.0	5008	,	,		17819	0.0		0.007	False		,,,				2504	0.0				p.T609A		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A1825G						PASS	.	A	ALA/THR,ALA/THR	1,4399	2.1+/-5.4	0,1,2199	139.0	95.0	110.0		1825,1825	1.7	0.7	11	dbSNP_134	110	13,8575	9.8+/-36.6	0,13,4281	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	58,58	0,14,6480	GG,GA,AA		0.1514,0.0227,0.1078	benign,benign	609/1203,609/1186	70189892	14,12974	2200	4294	6494	SO:0001583	missense	8500	exon15			AGGGACACTCTCC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.1825A>G	11.37:g.70189892A>G	ENSP00000253925:p.Thr609Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	9.790	1.177733	0.21787	2.27E-4	0.001514	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950	T;T	0.23950	1.88;1.88	5.3	1.66	0.24008	.	0.134893	0.49305	N	0.000153	T	0.17789	0.0427	M	0.72118	2.19	0.42471	D	0.992829	B;B	0.15473	0.001;0.013	B;B	0.17979	0.009;0.02	T	0.04041	-1.0982	10	0.37606	T	0.19	.	6.1866	0.20500	0.7209:0.1362:0.1429:0.0	.	609;609	Q13136;Q13136-2	LIPA1_HUMAN;.	A	609;609;96	ENSP00000253925:T609A;ENSP00000374198:T609A	ENSP00000253925:T609A	T	+	1	0	PPFIA1	69867540	1.000000	0.71417	0.739000	0.30968	0.957000	0.61999	2.204000	0.42761	0.033000	0.15463	0.459000	0.35465	ACT	A|0.998;G|0.002	0.002	strong		0.557	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
MUC16	94025	hgsc.bcm.edu	37	19	9075737	9075737	+	Silent	SNP	T	T	C	rs2547071	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9075737T>C	ENST00000397910.4	-	3	11912	c.11709A>G	c.(11707-11709)gtA>gtG	p.V3903V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3904	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						GGGTCCTTAATACACTGGAGG	0.453													T|||	2284	0.45607	0.4652	0.4265	5008	,	,		21982	0.5169		0.4314	False		,,,				2504	0.4274				p.V3903V		Atlas-SNP	.											.	MUC16	4315	.	0			c.A11709G						PASS	.	T		1783,2059		422,939,560	87.0	79.0	82.0		11709	1.6	0.0	19	dbSNP_100	82	3400,4868		696,2008,1430	no	coding-synonymous	MUC16	NM_024690.2		1118,2947,1990	CC,CT,TT		41.1224,46.4081,42.7993		3903/14508	9075737	5183,6927	1921	4134	6055	SO:0001819	synonymous_variant	94025	exon3			CCTTAATACACTG	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.11709A>G	19.37:g.9075737T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.560;C|0.440	0.440	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRIM50	135892	hgsc.bcm.edu	37	7	72738638	72738638	+	Missense_Mutation	SNP	C	C	T	rs138877207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72738638C>T	ENST00000333149.2	-	2	348	c.148G>A	c.(148-150)Gag>Aag	p.E50K	TRIM50_ENST00000453152.1_Missense_Mutation_p.E50K|TRIM50_ENST00000493498.1_5'UTR	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	50						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						CAGCGCAGCTCGGCATCCAGG	0.667											OREG0018105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0015	0.0	5008	,	,		15859	0.0		0.0	False		,,,				2504	0.0				p.E50K		Atlas-SNP	.											.	TRIM50	78	.	0			c.G148A						PASS	.						52.0	52.0	52.0					7																	72738638		2203	4300	6503	SO:0001583	missense	135892	exon2			GCAGCTCGGCATC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19017	protein-coding gene	gene with protein product		612548	"""tripartite motif-containing 50A"", ""tripartite motif-containing 50"""	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.148G>A	7.37:g.72738638C>T	ENSP00000327994:p.Glu50Lys	Somatic	156	0	0	1139	WXS	Illumina HiSeq	Phase_I	150	82	0.546667	NM_178125	Q86XT3	Missense_Mutation	SNP	ENST00000333149.2	37	CCDS34654.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.430	-0.903959	0.02453	.	.	ENSG00000146755	ENST00000333149;ENST00000453152	T;T	0.08546	3.08;3.08	3.94	-0.221	0.13126	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.408805	0.22937	N	0.053826	T	0.04003	0.0112	N	0.19112	0.55	0.18873	N	0.999982	B;B	0.20780	0.038;0.048	B;B	0.16289	0.009;0.015	T	0.39375	-0.9617	10	0.25106	T	0.35	.	4.0294	0.09701	0.0:0.4312:0.2394:0.3294	.	50;50	Q86XT4-2;Q86XT4	.;TRI50_HUMAN	K	50	ENSP00000327994:E50K;ENSP00000413875:E50K	ENSP00000327994:E50K	E	-	1	0	TRIM50	72376574	0.702000	0.27816	0.244000	0.24202	0.021000	0.10359	1.858000	0.39408	0.127000	0.18452	-1.166000	0.01754	GAG	A|0.000;C|1.000;T|0.000	0.000	strong		0.667	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125	
ASTL	431705	hgsc.bcm.edu	37	2	96795714	96795714	+	Silent	SNP	G	G	A	rs749459	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:96795714G>A	ENST00000342380.2	-	8	722	c.723C>T	c.(721-723)ctC>ctT	p.L241L		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						GGCTGAAGGCGAGCCTGGAAC	0.657													G|||	1897	0.378794	0.2784	0.4712	5008	,	,		16671	0.5952		0.3569	False		,,,				2504	0.2485				p.L241L		Atlas-SNP	.											.	ASTL	59	.	0			c.C723T						PASS	.	G		1301,3105	440.0+/-345.9	184,933,1086	61.0	67.0	65.0		723	-2.8	1.0	2	dbSNP_86	65	3125,5475	476.1+/-369.3	557,2011,1732	no	coding-synonymous	ASTL	NM_001002036.3		741,2944,2818	AA,AG,GG		36.3372,29.5279,34.0304		241/432	96795714	4426,8580	2203	4300	6503	SO:0001819	synonymous_variant	431705	exon8			GAAGGCGAGCCTG	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.723C>T	2.37:g.96795714G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001002036		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																			G|0.639;A|0.361	0.361	strong		0.657	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
OR13G1	441933	hgsc.bcm.edu	37	1	247835674	247835674	+	Missense_Mutation	SNP	G	G	A	rs28446289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247835674G>A	ENST00000359688.2	-	1	691	c.670C>T	c.(670-672)Cgt>Tgt	p.R224C	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	224			R -> C (in dbSNP:rs28446289).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	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)			GTGCGGATACGGAGAATAGCA	0.428													G|||	1657	0.330871	0.2958	0.2392	5008	,	,		24096	0.3839		0.3519	False		,,,				2504	0.3671				p.R224C		Atlas-SNP	.											.	OR13G1	78	.	0			c.C670T						PASS	.	G	CYS/ARG	1312,3094	441.4+/-346.4	188,936,1079	119.0	106.0	111.0		670	1.1	0.0	1	dbSNP_125	111	3098,5502	474.1+/-368.8	562,1974,1764	yes	missense	OR13G1	NM_001005487.1	180	750,2910,2843	AA,AG,GG		36.0233,29.7776,33.9074	possibly-damaging	224/308	247835674	4410,8596	2203	4300	6503	SO:0001583	missense	441933	exon1			GGATACGGAGAAT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.670C>T	1.37:g.247835674G>A	ENSP00000352717:p.Arg224Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	682	0.31227106227106227	138	0.2804878048780488	88	0.2430939226519337	191	0.3339160839160839	265	0.3496042216358839	G	7.576	0.667780	0.14710	0.297776	0.360233	ENSG00000197437	ENST00000359688	T	0.00267	8.38	4.2	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	0.317710	0.22947	N	0.053716	T	0.00012	0.0000	M	0.87180	2.865	0.80722	P	0.0	B	0.24823	0.112	B	0.24269	0.052	T	0.43734	-0.9373	9	0.72032	D	0.01	-8.4764	6.3931	0.21597	0.0908:0.0:0.5911:0.3181	rs28446289;rs58765113;rs28446289	224	Q8NGZ3	O13G1_HUMAN	C	224	ENSP00000352717:R224C	ENSP00000352717:R224C	R	-	1	0	OR13G1	245902297	0.000000	0.05858	0.001000	0.08648	0.335000	0.28730	0.339000	0.19875	0.122000	0.18314	0.563000	0.77884	CGT	G|0.665;A|0.335	0.335	strong		0.428	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
OR51B6	390058	hgsc.bcm.edu	37	11	5373129	5373129	+	Missense_Mutation	SNP	C	C	T	rs5006887	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5373129C>T	ENST00000380219.1	+	1	392	c.392C>T	c.(391-393)aCc>aTc	p.T131I	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	131			T -> I (in dbSNP:rs5006887). {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)			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)		TTAAGATATACCTCTATCCTG	0.463													C|||	1173	0.234225	0.326	0.2349	5008	,	,		23502	0.0863		0.2644	False		,,,				2504	0.2311				p.T131I		Atlas-SNP	.											.	OR51B6	53	.	0			c.C392T						PASS	.	C	ILE/THR	1240,3162	424.2+/-340.4	174,892,1135	128.0	116.0	120.0		392	4.1	0.7	11	dbSNP_113	120	2214,6380	370.8+/-336.0	308,1598,2391	yes	missense	OR51B6	NM_001004750.1	89	482,2490,3526	TT,TC,CC		25.7622,28.169,26.5774	benign	131/313	5373129	3454,9542	2201	4297	6498	SO:0001583	missense	390058	exon1			GATATACCTCTAT		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.392C>T	11.37:g.5373129C>T	ENSP00000369568:p.Thr131Ile	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	177	58	0.327684	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	C	6.898	0.535295	0.13188	0.28169	0.257622	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.19938	2.11	5.01	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.238996	0.29444	N	0.012131	T	0.00012	0.0000	M	0.87097	2.86	0.80722	P	0.0	B	0.23442	0.085	B	0.20955	0.032	T	0.17107	-1.0380	9	0.66056	D	0.02	.	13.5332	0.61633	0.0:0.7017:0.2983:0.0	rs5006887;rs5006887	131	Q9H340	O51B6_HUMAN	I	130;131	ENSP00000369568:T131I	ENSP00000369568:T131I	T	+	2	0	OR51B6	5329705	0.000000	0.05858	0.714000	0.30535	0.382000	0.30200	-0.232000	0.09055	1.315000	0.45114	0.455000	0.32223	ACC	C|0.760;T|0.240	0.240	strong		0.463	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
IKBKAP	8518	hgsc.bcm.edu	37	9	111659483	111659483	+	Missense_Mutation	SNP	T	T	G	rs2230793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	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		
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:152276660G>C	ENST00000368799.1	-	3	10737	c.10702C>G	c.(10702-10704)Cag>Gag	p.Q3568E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	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)			GACTGCTCCTGAGCAGATCCA	0.572									Ichthyosis				G|||	1035	0.206669	0.2133	0.1916	5008	,	,		17873	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568E		Atlas-SNP	.											FLG,NS,carcinoma,+2,1	FLG	900	1	0			c.C10702G						scavenged	.						149.0	201.0	183.0					1																	152276660		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCCTGAGCAGA	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.10702C>G	1.37:g.152276660G>C	ENSP00000357789:p.Gln3568Glu	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	200	21	0.105	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	3.450	-0.112146	0.06881	.	.	ENSG00000143631	ENST00000368799	T	0.01629	4.72	3.16	1.14	0.20703	.	.	.	.	.	T	0.00412	0.0013	L	0.44542	1.39	0.09310	N	1	P	0.41080	0.737	B	0.36504	0.226	T	0.32402	-0.9908	9	0.02654	T	1	.	3.1883	0.06608	0.1468:0.0:0.5899:0.2633	rs7540123;rs57866496;rs7540123	3568	P20930	FILA_HUMAN	E	3568	ENSP00000357789:Q3568E	ENSP00000357789:Q3568E	Q	-	1	0	FLG	150543284	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	1.365000	0.34182	0.608000	0.30000	0.398000	0.26397	CAG	G|0.995;C|0.005	0.005	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
RP1L1	94137	hgsc.bcm.edu	37	8	10469233	10469233	+	Missense_Mutation	SNP	A	A	G	rs35602868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:10469233A>G	ENST00000382483.3	-	4	2598	c.2375T>C	c.(2374-2376)cTg>cCg	p.L792P		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	792			L -> P (in dbSNP:rs35602868). {ECO:0000269|PubMed:12724644}.		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)		CTCTTCCCCCAGGCTGGCAGC	0.692													A|||	1577	0.314896	0.3525	0.3602	5008	,	,		15992	0.0218		0.5567	False		,,,				2504	0.2853				p.L792P		Atlas-SNP	.											.	RP1L1	453	.	0			c.T2375C						PASS	.	A	PRO/LEU	1358,2534		220,918,808	53.0	58.0	57.0		2375	-0.8	0.0	8	dbSNP_126	57	4444,3826		1223,1998,914	yes	missense	RP1L1	NM_178857.5	98	1443,2916,1722	GG,GA,AA		46.2636,34.8921,47.706	probably-damaging	792/2401	10469233	5802,6360	1946	4135	6081	SO:0001583	missense	94137	exon4			TCCCCCAGGCTGG	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.2375T>C	8.37:g.10469233A>G	ENSP00000371923:p.Leu792Pro	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	721	0.3301282051282051	167	0.3394308943089431	138	0.3812154696132597	13	0.022727272727272728	403	0.5316622691292876	A	12.25	1.881182	0.33255	0.348921	0.537364	ENSG00000183638	ENST00000382483	T	0.07908	3.15	5.11	-0.8	0.10897	.	2.282260	0.02877	U	0.132403	T	0.00012	0.0000	N	0.19112	0.55	0.53688	P	2.6999999999999247E-5	P	0.38827	0.649	B	0.36186	0.219	T	0.41088	-0.9528	9	0.33940	T	0.23	-2.9284	5.5366	0.17016	0.4338:0.1325:0.0:0.4337	rs35602868	792	A6NKC6	.	P	792	ENSP00000371923:L792P	ENSP00000371923:L792P	L	-	2	0	RP1L1	10506643	0.000000	0.05858	0.018000	0.16275	0.014000	0.08584	-0.052000	0.11865	0.226000	0.20979	-0.695000	0.03696	CTG	A|0.605;G|0.395	0.395	strong		0.692	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
LILRB2	10288	hgsc.bcm.edu	37	19	54784130	54784130	+	Missense_Mutation	SNP	T	T	C	rs383369	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:54784130T>C	ENST00000391749.4	-	3	330	c.59A>G	c.(58-60)cAc>cGc	p.H20R	LILRB2_ENST00000434421.1_Intron|LILRB2_ENST00000314446.5_Missense_Mutation_p.H20R|LILRB2_ENST00000471216.1_5'UTR|LILRB2_ENST00000391746.1_Missense_Mutation_p.H20R|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000391748.1_Missense_Mutation_p.H20R	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	20			H -> R (in dbSNP:rs383369).		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)			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)		TGTCTGCACGTGGGTCCTGGG	0.627													.|||	1172	0.234026	0.0643	0.232	5008	,	,		17863	0.6012		0.172	False		,,,				2504	0.1503				p.H20R		Atlas-SNP	.											.	LILRB2	94	.	0			c.A59G						PASS	.	T	ARG/HIS,ARG/HIS	391,4015	194.7+/-219.5	10,371,1822	78.0	81.0	80.0		59,59	-2.9	0.0	19	dbSNP_80	80	1558,7042	291.5+/-300.3	156,1246,2898	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	29,29	166,1617,4720	CC,CT,TT		18.1163,8.8743,14.9854	benign,benign	20/598,20/599	54784130	1949,11057	2203	4300	6503	SO:0001583	missense	10288	exon3			TGCACGTGGGTCC	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.59A>G	19.37:g.54784130T>C	ENSP00000375629:p.His20Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	686	0.3141025641025641	33	0.06707317073170732	90	0.24861878453038674	426	0.7447552447552448	137	0.18073878627968337	T	1.895	-0.454535	0.04540	0.088743	0.181163	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746	T;T;T;T	0.00479	7.26;7.26;7.23;7.12	2.24	-2.9	0.05648	.	3.954810	0.00885	N	0.002178	T	0.00012	0.0000	N	0.25426	0.745	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.12837	0.008;0.001;0.002	T	0.05451	-1.0884	9	0.09590	T	0.72	.	3.6436	0.08176	0.0:0.1749:0.483:0.3421	rs383369;rs11544409;rs17842601;rs60581242;rs383369	20;37;20	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	R	20	ENSP00000375628:H20R;ENSP00000319960:H20R;ENSP00000375629:H20R;ENSP00000375626:H20R	ENSP00000319960:H20R	H	-	2	0	LILRB2	59475942	0.000000	0.05858	0.000000	0.03702	0.468000	0.32798	-5.356000	0.00129	-0.340000	0.08388	0.240000	0.17902	CAC	A|0.001;C|0.191	0.191	strong		0.627	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
PSMD12	5718	hgsc.bcm.edu	37	17	65362552	65362552	+	Silent	SNP	T	T	A	rs11079691	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:65362552T>A	ENST00000356126.3	-	1	191	c.84A>T	c.(82-84)ctA>ctT	p.L28L	PSMD12_ENST00000581618.1_5'UTR|PSMD12_ENST00000357146.4_Silent_p.L28L	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	28					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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CACACTCGGGTAGGCGCTGAT	0.701													T|||	1084	0.216454	0.2595	0.1859	5008	,	,		13937	0.1696		0.2644	False		,,,				2504	0.1789				p.L28L		Atlas-SNP	.											PSMD12,NS,carcinoma,0,2	PSMD12	32	2	0			c.A84T						PASS	.	T	,	1198,3208	393.7+/-329.0	167,864,1172	41.0	32.0	35.0		84,84	3.5	1.0	17	dbSNP_120	35	2064,6534	340.7+/-323.7	260,1544,2495	no	coding-synonymous,coding-synonymous	PSMD12	NM_002816.3,NM_174871.2	,	427,2408,3667	AA,AT,TT		24.0056,27.1902,25.0846	,	28/457,28/437	65362552	3262,9742	2203	4299	6502	SO:0001819	synonymous_variant	5718	exon1			CTCGGGTAGGCGC	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"""Proteasome (prosome, macropain) subunits"""	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.84A>T	17.37:g.65362552T>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_174871	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	37	CCDS11669.1																																																																																			T|0.752;A|0.248	0.248	strong		0.701	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
ABCB8	11194	hgsc.bcm.edu	37	7	150733025	150733025	+	Silent	SNP	T	T	A	rs2303926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150733025T>A	ENST00000297504.6	+	8	1101	c.1035T>A	c.(1033-1035)cgT>cgA	p.R345R	ABCB8_ENST00000477092.1_Silent_p.R328R|ABCB8_ENST00000542328.1_Silent_p.R240R|ABCB8_ENST00000356058.4_Silent_p.R365R|ABCB8_ENST00000498578.1_Silent_p.R328R|ABCB8_ENST00000477719.1_Silent_p.R328R|ABCB8_ENST00000358849.4_Silent_p.R328R			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	345	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGACTGTGCGTGCCTTCGCCA	0.622													T|||	1505	0.300519	0.3306	0.219	5008	,	,		19863	0.2778		0.2863	False		,,,				2504	0.3558				p.R328R		Atlas-SNP	.											ABCB8,rectum,carcinoma,+1,2	ABCB8	65	2	0			c.T984A						PASS	.	T		1335,3071	445.7+/-347.8	195,945,1063	80.0	65.0	70.0		984	-10.0	0.3	7	dbSNP_100	70	2803,5797	442.7+/-360.2	480,1843,1977	no	coding-synonymous	ABCB8	NM_007188.3		675,2788,3040	AA,AT,TT		32.593,30.2996,31.8161		328/719	150733025	4138,8868	2203	4300	6503	SO:0001819	synonymous_variant	11194	exon7			TGTGCGTGCCTTC	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1035T>A	7.37:g.150733025T>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Silent	SNP	ENST00000297504.6	37		632	0.2893772893772894	175	0.3556910569105691	80	0.22099447513812154	157	0.2744755244755245	220	0.29023746701846964	T	3.131	-0.178409	0.06380	0.302996	0.32593	ENSG00000197150	ENST00000491920	.	.	.	5.34	-9.97	0.00440	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998351	.	.	.	.	.	.	T	0.27502	-1.0072	3	.	.	.	1.4811	5.0431	0.14469	0.176:0.0819:0.5759:0.1662	rs2303926;rs11553419;rs17448656;rs60135809	.	.	.	S	61	.	.	C	+	1	0	ABCB8	150363958	0.097000	0.21791	0.277000	0.24703	0.177000	0.22998	-0.630000	0.05502	-2.005000	0.00959	-2.213000	0.00299	TGC	T|0.697;A|0.303	0.303	strong		0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
BEND7	222389	hgsc.bcm.edu	37	10	13534851	13534851	+	Silent	SNP	A	A	G	rs2251555	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13534851A>G	ENST00000396900.2	-	5	596	c.597T>C	c.(595-597)ccT>ccC	p.P199P	BEND7_ENST00000341083.3_Silent_p.P147P|BEND7_ENST00000378605.3_Silent_p.P160P|BEND7_ENST00000396898.2_Silent_p.P212P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	199						extracellular vesicular exosome (GO:0070062)		p.P147P(1)|p.P160P(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GGGAAATTGGAGGTTGTTGTC	0.413													G|||	2407	0.480631	0.4887	0.5533	5008	,	,		19988	0.3403		0.5378	False		,,,				2504	0.5041				p.P160P		Atlas-SNP	.											BEND7_ENST00000378605,colon,carcinoma,0,4	BEND7	85	4	2	Substitution - coding silent(2)	stomach(2)	c.T480C						PASS	.	G	,	2261,2143	543.9+/-376.4	580,1101,521	71.0	73.0	73.0		480,441	4.5	1.0	10	dbSNP_100	73	4934,3666	513.7+/-378.2	1412,2110,778	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	1992,3211,1299	GG,GA,AA		42.6279,48.6603,44.6709	,	160/375,147/469	13534851	7195,5809	2202	4300	6502	SO:0001819	synonymous_variant	222389	exon4			AATTGGAGGTTGT	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.597T>C	10.37:g.13534851A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				A|0.476;G|0.524	0.524	strong		0.413	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
TEX14	56155	hgsc.bcm.edu	37	17	56659018	56659018	+	Missense_Mutation	SNP	C	C	T	rs6503870	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:56659018C>T	ENST00000240361.8	-	20	3348	c.3263G>A	c.(3262-3264)gGt>gAt	p.G1088D	TEX14_ENST00000349033.5_Intron|TEX14_ENST00000389934.3_Missense_Mutation_p.G1082D			Q8IWB6	TEX14_HUMAN	testis expressed 14	1088					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAAATATTCACCGTCTGGAGT	0.368													T|||	3042	0.607428	0.7489	0.4337	5008	,	,		18256	0.4812		0.6332	False		,,,				2504	0.6431				p.G1088D		Atlas-SNP	.											.	TEX14	343	.	0			c.G3263A						PASS	.	T	ASP/GLY,,ASP/GLY	3127,1279	433.5+/-343.6	1115,897,191	93.0	92.0	92.0		3263,,3245	-1.6	0.1	17	dbSNP_116	92	5365,3235	486.7+/-371.9	1688,1989,623	yes	missense,intron,missense	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	94,,94	2803,2886,814	TT,TC,CC		37.6163,29.0286,34.7071	benign,,benign	1088/1498,,1082/1492	56659018	8492,4514	2203	4300	6503	SO:0001583	missense	56155	exon20			TATTCACCGTCTG	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.3263G>A	17.37:g.56659018C>T	ENSP00000240361:p.Gly1088Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	1305	0.5975274725274725	382	0.7764227642276422	168	0.46408839779005523	275	0.4807692307692308	480	0.633245382585752	T	0.196	-1.049129	0.01981	0.709714	0.623837	ENSG00000121101	ENST00000240361;ENST00000389934	T;T	0.78364	-1.17;-1.17	5.34	-1.65	0.08291	.	1.098750	0.06862	N	0.799290	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	0.43988	-0.9357	9	0.05525	T	0.97	0.6288	1.2323	0.01946	0.1247:0.248:0.212:0.4153	rs6503870;rs17822783;rs52791468;rs60747821;rs6503870	1088;1082	Q8IWB6;Q8IWB6-2	TEX14_HUMAN;.	D	1088;1082	ENSP00000240361:G1088D;ENSP00000374584:G1082D	ENSP00000240361:G1088D	G	-	2	0	TEX14	54014017	0.236000	0.23804	0.057000	0.19452	0.672000	0.39443	0.439000	0.21575	-0.208000	0.10171	-2.009000	0.00441	GGT	C|0.367;N|0.000	.	strong		0.368	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
FAM8A1	51439	hgsc.bcm.edu	37	6	17608511	17608511	+	Nonsense_Mutation	SNP	C	C	T	rs200041366		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:17608511C>T	ENST00000259963.3	+	5	1238	c.1183C>T	c.(1183-1185)Cga>Tga	p.R395*		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	395	RDD.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			TCAGCATAATCGAACAGCTTA	0.383																																					p.R395X		Atlas-SNP	.											FAM8A1,lower_third,carcinoma,-1,1	FAM8A1	26	1	0			c.C1183T						scavenged	.						109.0	104.0	106.0					6																	17608511		2203	4300	6503	SO:0001587	stop_gained	51439	exon5			CATAATCGAACAG	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.1183C>T	6.37:g.17608511C>T	ENSP00000259963:p.Arg395*	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	137	6	0.0437956	NM_016255	B2R725	Nonsense_Mutation	SNP	ENST00000259963.3	37	CCDS4540.1	.	.	.	.	.	.	.	.	.	.	C	36	5.927702	0.97110	.	.	ENSG00000137414	ENST00000542476;ENST00000259963	.	.	.	5.63	4.76	0.60689	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0172	8.5079	0.33199	0.2528:0.6721:0.0:0.0751	.	.	.	.	X	145;395	.	ENSP00000259963:R395X	R	+	1	2	FAM8A1	17716490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.235000	0.51328	1.373000	0.46208	0.557000	0.71058	CGA	.	.	weak		0.383	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1		
UGT1A5	54579	hgsc.bcm.edu	37	2	234622429	234622429	+	Silent	SNP	T	T	C	rs2012734	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234622429T>C	ENST00000373414.3	+	1	792	c.792T>C	c.(790-792)gaT>gaC	p.D264D	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Silent_p.D264D|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609637.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	264						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		TTGTGATGGATTACCCCAGGC	0.517													C|||	2895	0.578075	0.8162	0.5303	5008	,	,		17643	0.3512		0.4443	False		,,,				2504	0.6616				p.D264D		Atlas-SNP	.											.	UGT1A5	66	.	0			c.T792C						PASS	.	C	,,,,,,	3104,1302		1198,708,297	119.0	133.0	128.0		,,,,792,,	-2.1	0.7	2	dbSNP_92	128	3635,4957		947,1741,1608	no	intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9	NM_001072.3,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_021027.2,NM_205862.1	,,,,,,	2145,2449,1905	CC,CT,TT		42.3068,29.5506,48.1536	,,,,,,	,,,,264/535,,	234622429	6739,6259	2203	4296	6499	SO:0001819	synonymous_variant	54579	exon1			GATGGATTACCCC	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"""UDP glucuronosyltransferases"""	12537	other	complex locus constituent		606430	"""UDP glycosyltransferase 1 family, polypeptide A5"""			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.792T>C	2.37:g.234622429T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_019078	B8K294	Silent	SNP	ENST00000373414.3	37	CCDS33404.1																																																																																			.	.	weak		0.517	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078	
KRT72	140807	hgsc.bcm.edu	37	12	52994896	52994896	+	Missense_Mutation	SNP	A	A	G	rs56207115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:52994896A>G	ENST00000537672.2	-	1	351	c.341T>C	c.(340-342)aTg>aCg	p.M114T	KRT72_ENST00000293745.2_Missense_Mutation_p.M114T|KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000354310.4_Missense_Mutation_p.M114T|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	114	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)		CTCGGGGTCCATCTCCACGTT	0.657													A|||	402	0.0802716	0.1982	0.0576	5008	,	,		16016	0.0218		0.0477	False		,,,				2504	0.0307				p.M114T		Atlas-SNP	.											.	KRT72	70	.	0			c.T341C						PASS	.	A	THR/MET,THR/MET,THR/MET	726,3680	300.4+/-286.3	74,578,1551	96.0	89.0	91.0		341,341,341	4.5	1.0	12	dbSNP_129	91	427,8173	132.3+/-190.0	11,405,3884	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	81,81,81	85,983,5435	GG,GA,AA		4.9651,16.4775,8.8651	benign,benign,benign	114/512,114/470,114/512	52994896	1153,11853	2203	4300	6503	SO:0001583	missense	140807	exon1			GGGTCCATCTCCA	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.341T>C	12.37:g.52994896A>G	ENSP00000441160:p.Met114Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	164|164	0.07509157509157509|0.07509157509157509	90|90	0.18292682926829268|0.18292682926829268	26|26	0.0718232044198895|0.0718232044198895	14|14	0.024475524475524476|0.024475524475524476	34|34	0.044854881266490766|0.044854881266490766	A|A	16.44|16.44	3.123859|3.123859	0.56613|0.56613	0.164775|0.164775	0.049651|0.049651	ENSG00000170486|ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310|ENST00000549979	T;T;T|.	0.74947|.	-0.89;-0.89;-0.89|.	4.49|4.49	4.49|4.49	0.54785|0.54785	.|.	0.180263|.	0.26627|.	N|.	0.023324|.	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.08118|0.08118	0|0	0.09310|0.09310	P|P	1.0|1.0	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.15484|.	0.0;0.013|.	T|T	0.11446|0.11446	-1.0587|-1.0587	9|4	0.87932|.	D|.	0|.	.|.	14.8433|14.8433	0.70240|0.70240	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs56207115;rs61747191|rs56207115;rs61747191	114;114|.	B4DEI8;Q14CN4|.	.;K2C72_HUMAN|.	T|R	114|100	ENSP00000441160:M114T;ENSP00000293745:M114T;ENSP00000346269:M114T|.	ENSP00000293745:M114T|.	M|W	-|-	2|1	0|0	KRT72|KRT72	51281163|51281163	0.974000|0.974000	0.33945|0.33945	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	9.084000|9.084000	0.94076|0.94076	2.244000|2.244000	0.73946|0.73946	0.459000|0.459000	0.35465|0.35465	ATG|TGG	A|0.918;G|0.082	0.082	strong		0.657	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
MUC16	94025	hgsc.bcm.edu	37	19	9076163	9076163	+	Silent	SNP	C	C	T	rs2547073	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9076163C>T	ENST00000397910.4	-	3	11486	c.11283G>A	c.(11281-11283)caG>caA	p.Q3761Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3762	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						AAGTGAGTTCCTGGGGAGTTG	0.527													T|||	1243	0.248203	0.2005	0.2118	5008	,	,		21334	0.249		0.3121	False		,,,				2504	0.272				p.Q3761Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.G11283A						PASS	.	T		849,3241		97,655,1293	123.0	123.0	123.0		11283	0.9	0.0	19	dbSNP_100	123	2418,5966		346,1726,2120	no	coding-synonymous	MUC16	NM_024690.2		443,2381,3413	TT,TC,CC		28.8406,20.7579,26.1905		3761/14508	9076163	3267,9207	2045	4192	6237	SO:0001819	synonymous_variant	94025	exon3			GAGTTCCTGGGGA	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.11283G>A	19.37:g.9076163C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.745;T|0.255	0.255	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NPHP3	27031	hgsc.bcm.edu	37	3	132441143	132441143	+	Silent	SNP	C	C	G	rs192633696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132441143C>G	ENST00000337331.5	-	1	143	c.57G>C	c.(55-57)acG>acC	p.T19T	NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000343113.4_Silent_p.T19T|NPHP3_ENST00000326682.8_Silent_p.T19T|NPHP3-AS1_ENST00000489343.1_RNA|NPHP3_ENST00000383282.2_Silent_p.T19T	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	19					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						CCGCCCCGTACGTGTCCTCGA	0.721													c|||	46	0.0091853	0.0008	0.0202	5008	,	,		6716	0.001		0.0179	False		,,,				2504	0.0123				p.T19T		Atlas-SNP	.											.	NPHP3	110	.	0			c.G57C						PASS	.			13,3561		0,13,1774	10.0	12.0	12.0		57	0.6	1.0	3		12	120,7108		3,114,3497	no	coding-synonymous	NPHP3	NM_153240.4		3,127,5271	GG,GC,CC		1.6602,0.3637,1.2313		19/1331	132441143	133,10669	1787	3614	5401	SO:0001819	synonymous_variant	27031	exon1			CCCGTACGTGTCC	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.57G>C	3.37:g.132441143C>G		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	37	CCDS3078.1																																																																																			C|0.991;G|0.009	0.009	strong		0.721	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
TFE3	7030	hgsc.bcm.edu	37	X	48888074	48888074	+	Silent	SNP	T	T	C	rs3027472|rs199492429	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:48888074T>C	ENST00000315869.7	-	10	1582	c.1323A>G	c.(1321-1323)gtA>gtG	p.V441V	TFE3_ENST00000487451.1_5'Flank	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	441					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GAGTGGGAGGTACTGGCAGGC	0.582			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""								T|||	873	0.231258	0.0204	0.2363	3775	,	,		11253	0.0546		0.4185	False		,,,				2504	0.2106				p.V441V		Atlas-SNP	.		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3	93	.	0			c.A1323G						PASS	.	T		306,3528		12,230,52,1390,518	47.0	43.0	44.0		1323	-5.1	0.4	X	dbSNP_102	44	3549,3179		693,1178,985,557,887	no	coding-synonymous	TFE3	NM_006521.4		705,1408,1037,1947,1405	CC,CT,C,TT,T		47.2503,7.9812,36.4988		441/576	48888074	3855,6707	2202	4300	6502	SO:0001819	synonymous_variant	7030	exon10			GGGAGGTACTGGC	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1323A>G	X.37:g.48888074T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Silent	SNP	ENST00000315869.7	37	CCDS14315.3																																																																																			T|0.674;C|0.326	0.326	strong		0.582	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521	
HLA-DRA	3122	hgsc.bcm.edu	37	6	32411035	32411035	+	Splice_Site	SNP	A	A	C	rs61117681|rs8084	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32411035A>C	ENST00000374982.5	+	3	401		c.e3-1		HLA-DRA_ENST00000395388.2_Silent_p.I134I			P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|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)|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)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|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 protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						TCTGTTTCATAGACAAGTTCA	0.527									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of				a|||	3141	0.627196	0.5961	0.6744	5008	,	,		21375	0.6756		0.5865	False		,,,				2504	0.6278				p.I134I		Atlas-SNP	.											HLA-DRA,colon,carcinoma,0,1	HLA-DRA	34	1	0			c.A402C						PASS	.	C		1728,1294		473,782,256	137.0	108.0	118.0		402	-9.7	0.1	6	dbSNP_52	118	3084,2334		868,1348,493	no	coding-synonymous	HLA-DRA	NM_019111.4		1341,2130,749	CC,CA,AA		43.0786,42.8193,42.9858		134/255	32411035	4812,3628	1511	2709	4220	SO:0001630	splice_region_variant	3122	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;	TTTCATAGACAAG		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000374982.5:c.329-1A>C	6.37:g.32411035A>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_019111	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Silent	SNP	ENST00000374982.5	37		1329	0.6085164835164835	284	0.5772357723577236	233	0.643646408839779	384	0.6713286713286714	428	0.5646437994722955	a	0.008	-1.924142	0.00493	0.571807	0.569214	ENSG00000204287	ENST00000374982	.	.	.	5.59	-9.66	0.00534	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999732924	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7745	0.23613	0.1597:0.1508:0.074:0.6155	rs8084;rs1050014;rs3175098;rs9268660;rs17353511;rs57826480;rs8084	.	.	.	.	-1	.	.	.	+	.	.	HLA-DRA	32519013	0.001000	0.12720	0.060000	0.19600	0.158000	0.22134	-3.492000	0.00453	-2.686000	0.00406	-1.712000	0.00714	.	A|0.404;C|0.596	0.596	strong		0.527	HLA-DRA-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000076587.3	NM_019111	Intron
SPATA21	374955	hgsc.bcm.edu	37	1	16748432	16748432	+	Silent	SNP	C	C	T	rs114456729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	109	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	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	
IRG1	730249	hgsc.bcm.edu	37	13	77532094	77532094	+	Missense_Mutation	SNP	A	A	T	rs147055675	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:77532094A>T	ENST00000377462.1	+	5	1482	c.1420A>T	c.(1420-1422)Aat>Tat	p.N474Y	IRG1_ENST00000449753.1_Missense_Mutation_p.N474Y	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	474					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)										TCCAGCATGTAATAATTCTAT	0.408													A|||	7	0.00139776	0.0	0.0	5008	,	,		20349	0.0		0.007	False		,,,				2504	0.0				p.N470Y		Atlas-SNP	.											.	IRG1	1	.	0			c.A1408T						PASS	.																																			SO:0001583	missense	730249	exon4			GCATGTAATAATT		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.1420A>T	13.37:g.77532094A>T	ENSP00000366682:p.Asn474Tyr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_001258406		Missense_Mutation	SNP	ENST00000377462.1	37	CCDS58299.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	11.74	1.730187	0.30684	.	.	ENSG00000102794	ENST00000377462;ENST00000449753	.	.	.	5.1	-2.03	0.07365	.	1.271430	0.05367	N	0.534703	T	0.11793	0.0287	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.15492	-1.0435	7	0.54805	T	0.06	0.0475	1.3455	0.02162	0.4322:0.2769:0.1571:0.1337	.	.	.	.	Y	474	.	ENSP00000366682:N474Y	N	+	1	0	IRG1	76430095	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.415000	0.21181	-0.462000	0.06984	-0.316000	0.08728	AAT	A|0.998;T|0.002	0.002	strong		0.408	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
APIP	51074	hgsc.bcm.edu	37	11	34916657	34916657	+	Splice_Site	SNP	C	C	T	rs61734605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:34916657C>T	ENST00000395787.3	-	2	272	c.58G>A	c.(58-60)Gac>Aac	p.D20N	APIP_ENST00000527830.1_Intron|APIP_ENST00000278359.5_Splice_Site_p.D37N	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)			TGCTCCTTGTCCTTAAAAAGA	0.373													C|||	574	0.114617	0.0204	0.1643	5008	,	,		20546	0.0		0.328	False		,,,				2504	0.1053				p.D20N		Atlas-SNP	.											.	APIP	21	.	0			c.G58A						PASS	.	C	ASN/ASP	366,4038	182.9+/-210.6	13,340,1849	81.0	77.0	78.0		58	5.2	1.0	11	dbSNP_129	78	2877,5719	449.3+/-362.1	467,1943,1888	yes	missense-near-splice	APIP	NM_015957.2	23	480,2283,3737	TT,TC,CC		33.4691,8.3106,24.9462	benign	20/243	34916657	3243,9757	2202	4298	6500	SO:0001630	splice_region_variant	51074	exon2			CCTTGTCCTTAAA	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.58-1G>A	11.37:g.34916657C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_015957		Missense_Mutation	SNP	ENST00000395787.3	37	CCDS7895.1	334	0.15293040293040294	12	0.024390243902439025	63	0.17403314917127072	0	0.0	259	0.341688654353562	C	18.64	3.668045	0.67814	0.083106	0.334691	ENSG00000149089	ENST00000278359;ENST00000395787	T;T	0.30714	1.52;1.82	5.17	5.17	0.71159	Class II aldolase/adducin, N-terminal (1);	0.159136	0.56097	D	0.000037	T	0.00012	0.0000	L	0.37850	1.14	0.09310	P	0.99999778761	B	0.31752	0.338	B	0.28709	0.093	T	0.43829	-0.9367	9	0.40728	T	0.16	-24.48	18.6546	0.91448	0.0:1.0:0.0:0.0	rs61734605	20	Q96GX9	MTNB_HUMAN	N	37;20	ENSP00000278359:D37N;ENSP00000379133:D20N	ENSP00000278359:D37N	D	-	1	0	APIP	34873233	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.770000	0.74990	2.417000	0.82017	0.563000	0.77884	GAC	C|0.778;T|0.222	0.222	strong		0.373	APIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389864.1	NM_015957	Missense_Mutation
TBC1D29	26083	hgsc.bcm.edu	37	17	28887134	28887134	+	Splice_Site	SNP	G	G	A	rs111780165	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:28887134G>A	ENST00000580161.1	+	3	2509		c.e3-1		TBC1D29_ENST00000579181.1_Splice_Site|RP11-218M11.6_ENST00000582125.1_RNA|TBC1D29_ENST00000584297.1_Splice_Site			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29								Rab GTPase activator activity (GO:0005097)			breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				CCTCCCATCAGGACAAGGAAG	0.597													.|||	112	0.0223642	0.0008	0.0231	5008	,	,		20343	0.0		0.0636	False		,,,				2504	0.0317				.		Atlas-SNP	.											.	TBC1D29	19	.	0			c.13-1G>A						PASS	.	G		77,4329		2,73,2128	45.0	41.0	42.0			-0.3	0.0	17	dbSNP_132	42	544,8056		13,518,3769	no	splice-3	TBC1D29	NM_015594.2		15,591,5897	AA,AG,GG		6.3256,1.7476,4.7747			28887134	621,12385	2203	4300	6503	SO:0001630	splice_region_variant	26083	exon2			CCATCAGGACAAG	BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.13-1G>A	17.37:g.28887134G>A		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	248	119	0.479839	NM_015594		Splice_Site	SNP	ENST00000580161.1	37	CCDS32606.1	63	0.028846153846153848	0	0.0	11	0.03038674033149171	0	0.0	52	0.06860158311345646	N	0.030	-1.341601	0.01277	0.017476	0.063256	ENSG00000197689	ENST00000329040;ENST00000378698	.	.	.	0.15	-0.299	0.12808	.	.	.	.	.	.	.	.	.	.	.	0.20074	N	0.999932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	-1	.	.	.	+	.	.	TBC1D29	25911260	0.793000	0.28825	0.004000	0.12327	0.004000	0.04260	0.807000	0.27140	-1.143000	0.02866	-1.137000	0.01932	.	G|0.962;A|0.038	0.038	strong		0.597	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443632.1	NM_015594	Intron
ELL2	22936	hgsc.bcm.edu	37	5	95234377	95234377	+	Silent	SNP	C	C	T	rs3777203	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	261	0	0		WXS	Illumina HiSeq	Phase_I	246	101	0.410569	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	
MC1R	4157	hgsc.bcm.edu	37	16	89986117	89986117	+	Missense_Mutation	SNP	C	C	T	rs1805007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89986117C>T	ENST00000555147.1	+	1	1831	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C	RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank|RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Missense_Mutation_p.R151C|TUBB3_ENST00000556922.1_Missense_Mutation_p.R151C	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	151			R -> C (associated with red hair and light skin of type I; binds to alpha-MSH but cannot be stimulated to produce cAMP; dbSNP:rs1805007). {ECO:0000269|PubMed:10101176, ECO:0000269|PubMed:12473109, ECO:0000269|PubMed:16463023, ECO:0000269|PubMed:17952075, ECO:0000269|PubMed:9302268, ECO:0000269|PubMed:9571181, ECO:0000269|Ref.12}.		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)		CTACGCACTGCGCTACCACAG	0.622									Melanoma, Familial Clustering of				C|||	93	0.0185703	0.003	0.0159	5008	,	,		16906	0.001		0.0716	False		,,,				2504	0.0051				p.R151C		Atlas-SNP	.											.	MC1R	20	.	0			c.C451T	GRCh37	CM981238	MC1R	M	rs1805007	PASS	.	C	CYS/ARG	75,4321	62.9+/-100.1	1,73,2124	73.0	76.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	451	4.8	1.0	16	dbSNP_89	75	655,7945	163.8+/-216.2	20,615,3665	yes	missense	MC1R	NM_002386.3	180	21,688,5789	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.6163,1.7061,5.6171		151/318	89986117	730,12266	2198	4300	6498	SO:0001583	missense	4157	exon1	Familial Cancer Database		GCACTGCGCTACC		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.451C>T	16.37:g.89986117C>T	ENSP00000451605:p.Arg151Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	66	0.03021978021978022	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	57	0.07519788918205805	C	32	5.184949	0.94885	0.017061	0.076163	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.43294	0.95;0.95;0.95	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.369626	0.19399	U	0.115208	T	0.16727	0.0402	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.68754	-0.5325	9	.	.	.	.	16.8525	0.85998	0.0:1.0:0.0:0.0	rs1805007;rs3212380;rs17719568;rs56569770;rs1805007	151	Q01726	MSHR_HUMAN	C	151	ENSP00000451760:R151C;ENSP00000451560:R151C;ENSP00000451605:R151C	.	R	+	1	0	MC1R;RP11-566K11.2	88513618	1.000000	0.71417	0.992000	0.48379	0.900000	0.52787	4.592000	0.61027	2.234000	0.73211	0.455000	0.32223	CGC	C|0.960;T|0.040	0.040	strong		0.622	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
SLC16A9	220963	hgsc.bcm.edu	37	10	61414011	61414011	+	Missense_Mutation	SNP	G	G	T	rs2242206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61414011G>T	ENST00000395348.3	-	5	1409	c.773C>A	c.(772-774)aCa>aAa	p.T258K	SLC16A9_ENST00000395347.1_Missense_Mutation_p.T258K	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	258			T -> K (in dbSNP:rs2242206).		urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						GTGTGTCACTGTGGGGTTTTT	0.398													G|||	1728	0.345048	0.0696	0.3847	5008	,	,		19641	0.5804		0.2664	False		,,,				2504	0.5276				p.T258K		Atlas-SNP	.											.	SLC16A9	58	.	0			c.C773A						PASS	.	G	LYS/THR	468,3938	219.1+/-236.9	23,422,1758	226.0	214.0	218.0		773	2.0	0.0	10	dbSNP_98	218	2235,6365	379.4+/-339.3	307,1621,2372	yes	missense	SLC16A9	NM_194298.2	78	330,2043,4130	TT,TG,GG		25.9884,10.6219,20.7827	benign	258/510	61414011	2703,10303	2203	4300	6503	SO:0001583	missense	220963	exon5			GTCACTGTGGGGT	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.773C>A	10.37:g.61414011G>T	ENSP00000378757:p.Thr258Lys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	158	60	0.379747	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	714	0.3269230769230769	48	0.0975609756097561	113	0.31215469613259667	342	0.5979020979020979	211	0.2783641160949868	G	0.004	-2.322151	0.00232	0.106219	0.259884	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.04119	3.7;3.7	5.02	2.0	0.26442	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.506790	0.03439	N	0.209031	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.25007	0.116	B	0.22152	0.038	T	0.37384	-0.9708	9	0.05959	T	0.93	.	3.3426	0.07124	0.2824:0.0:0.4133:0.3043	rs2242206;rs52832507;rs61451304;rs2242206	258	Q7RTY1	MOT9_HUMAN	K	258	ENSP00000378757:T258K;ENSP00000378756:T258K	ENSP00000378756:T258K	T	-	2	0	SLC16A9	61084017	0.001000	0.12720	0.002000	0.10522	0.105000	0.19272	1.236000	0.32683	0.470000	0.27294	0.591000	0.81541	ACA	G|0.740;T|0.260	0.260	strong		0.398	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298	
GSTO1	9446	hgsc.bcm.edu	37	10	106022789	106022789	+	Missense_Mutation	SNP	C	C	A	rs4925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:106022789C>A	ENST00000369713.5	+	4	613	c.419C>A	c.(418-420)gCt>gAt	p.A140D	GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000539281.1_Missense_Mutation_p.A112D|GSTO1_ENST00000369710.4_Intron	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	57	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	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	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864591	131864591	+	Silent	SNP	T	T	C	rs3734989	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:131864591T>C	ENST00000359827.3	-	20	4691	c.3729A>G	c.(3727-3729)gcA>gcG	p.A1243A	PLXNA4_ENST00000321063.4_Silent_p.A1243A			Q9HCM2	PLXA4_HUMAN	plexin A4	1243					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CGCCAGCCACTGCGATGCTGA	0.632													C|||	3918	0.782348	0.9803	0.7305	5008	,	,		17133	0.6329		0.6133	False		,,,				2504	0.8793				p.A1243A		Atlas-SNP	.											PLXNA4_ENST00000359827,rectum,carcinoma,0,2	PLXNA4	873	2	0			c.A3729G						scavenged	.	C		4025,351		1855,315,18	15.0	20.0	18.0		3729	-9.8	0.1	7	dbSNP_107	18	5269,3299		1650,1969,665	no	coding-synonymous	PLXNA4	NM_020911.1		3505,2284,683	CC,CT,TT		38.5037,8.021,28.1984		1243/1895	131864591	9294,3650	2188	4284	6472	SO:0001819	synonymous_variant	91584	exon20			AGCCACTGCGATG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3729A>G	7.37:g.131864591T>C		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			T|0.270;C|0.730	0.730	strong		0.632	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	98	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	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	
UBE2NL	389898	hgsc.bcm.edu	37	X	142967468	142967468	+	Nonsense_Mutation	SNP	T	T	G	rs237520	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:142967468T>G	ENST00000370494.1	+	1	296	c.266T>G	c.(265-267)tTa>tGa	p.L89*		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	89						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)			breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					AGAATAAGTTTAGATATTTTG	0.408													T|||	2331	0.617483	0.4766	0.4409	3775	,	,		14337	0.501		0.4911	False		,,,				2504	0.4049				p.L89X		Atlas-SNP	.											.	UBE2NL	46	.	0			c.T266G						PASS	.	T	stop/LEU	2511,1324		695,750,371,187,200	82.0	76.0	78.0		266	1.1	1.0	X	dbSNP_79	78	4533,2195		1122,1035,1254,271,618	yes	stop-gained	UBE2NL	NM_001012989.1		1817,1785,1625,458,818	GG,GT,G,TT,T		32.6249,34.5241,33.3144		89/154	142967468	7044,3519	2203	4300	6503	SO:0001587	stop_gained	389898	exon1			TAAGTTTAGATAT			Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"""Ubiquitin-conjugating enzymes E2"""	31710	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2N-like"""			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.266T>G	X.37:g.142967468T>G	ENSP00000359525:p.Leu89*	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001012989	E9KL27	Nonsense_Mutation	SNP	ENST00000370494.1	37	CCDS35420.1	1034	0.6232670283303194	162	0.4602272727272727	113	0.424812030075188	190	0.45893719806763283	260	0.4961832061068702	T	8.482	0.860042	0.17178	0.654759	0.673751	ENSG00000102069	ENST00000370494	.	.	.	1.06	1.06	0.20224	.	0.000000	0.34828	U	0.003653	.	.	.	.	.	.	0.09310	P	0.9999999999999988	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0255	6.0546	0.19804	0.0:0.0:0.0:1.0	rs237520;rs665277;rs16994781;rs237520	.	.	.	X	89	.	ENSP00000359525:L89X	L	+	2	0	UBE2NL	142795134	1.000000	0.71417	0.981000	0.43875	0.009000	0.06853	5.490000	0.66881	0.695000	0.31675	0.151000	0.16131	TTA	0|0.003;G|0.651	0.651	strong		0.408	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989	
STK4	6789	hgsc.bcm.edu	37	20	43629135	43629135	+	Missense_Mutation	SNP	G	G	A	rs17420378	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:43629135G>A	ENST00000372806.3	+	8	1029	c.934G>A	c.(934-936)Gtg>Atg	p.V312M	STK4_ENST00000372801.1_Missense_Mutation_p.V312M|STK4_ENST00000499879.2_Missense_Mutation_p.V257M|STK4_ENST00000396731.4_Missense_Mutation_p.V312M	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	312			V -> M (in dbSNP:rs17420378). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7665586}.		apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				GCAGCGGGAAGTGGACCAGGA	0.478													G|||	849	0.169529	0.1286	0.1585	5008	,	,		19370	0.0119		0.3221	False		,,,				2504	0.2382				p.V312M	GBM(187;1039 2137 11798 21916 33213)	Atlas-SNP	.											.	STK4	84	.	0			c.G934A						PASS	.	G	MET/VAL	674,3732	286.3+/-278.7	50,574,1579	67.0	56.0	60.0		934	4.9	1.0	20	dbSNP_123	60	2684,5916	429.5+/-356.2	424,1836,2040	yes	missense	STK4	NM_006282.2	21	474,2410,3619	AA,AG,GG		31.2093,15.2973,25.8189	benign	312/488	43629135	3358,9648	2203	4300	6503	SO:0001583	missense	6789	exon8			CGGGAAGTGGACC		CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109			11408	protein-coding gene	gene with protein product	"""mammalian sterile 20-like 1"", ""yeast Ste20-like"", ""kinase responsive to stress 2"""	604965				8816758, 9545236, 11517310	Standard	NM_006282		Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.934G>A	20.37:g.43629135G>A	ENSP00000361892:p.Val312Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_006282	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	Missense_Mutation	SNP	ENST00000372806.3	37	CCDS13341.1	388	0.17765567765567766	80	0.16260162601626016	61	0.1685082872928177	6	0.01048951048951049	241	0.3179419525065963	G	14.67	2.604203	0.46423	0.152973	0.312093	ENSG00000101109	ENST00000372806;ENST00000396731;ENST00000372801;ENST00000499879	T;T;T;T	0.72394	-0.63;-0.65;-0.65;0.38	5.88	4.88	0.63580	Protein kinase-like domain (1);	0.269791	0.38005	N	0.001842	T	0.00012	0.0000	L	0.40543	1.245	0.29640	P	0.844813	B;B;B;B	0.13145	0.004;0.007;0.0;0.001	B;B;B;B	0.19666	0.012;0.026;0.004;0.007	T	0.05484	-1.0882	9	0.48119	T	0.1	.	17.4899	0.87700	0.0:0.175:0.825:0.0	rs17420378;rs17420378	257;312;312;312	F5H5B4;Q13043-2;A0PJ51;Q13043	.;.;.;STK4_HUMAN	M	312;312;312;257	ENSP00000361892:V312M;ENSP00000379957:V312M;ENSP00000361887:V312M;ENSP00000443514:V257M	ENSP00000361887:V312M	V	+	1	0	STK4	43062549	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.710000	0.47169	2.782000	0.95742	0.655000	0.94253	GTG	G|0.783;A|0.217	0.217	strong		0.478	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080401.4	NM_006282	
FKBP15	23307	hgsc.bcm.edu	37	9	115933885	115933885	+	Silent	SNP	A	A	C	rs1128118	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115933885A>C	ENST00000238256.3	-	24	2751	c.2634T>G	c.(2632-2634)gcT>gcG	p.A878A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	878					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						CAGATGCAGCAGCTTCAACCC	0.458													A|||	417	0.0832668	0.112	0.0403	5008	,	,		16027	0.0387		0.0477	False		,,,				2504	0.1575				p.A878A		Atlas-SNP	.											.	FKBP15	128	.	0			c.T2634G						PASS	.	A		431,3379		14,403,1488	78.0	84.0	82.0		2634	-2.8	0.0	9	dbSNP_86	82	520,7738		15,490,3624	no	coding-synonymous	FKBP15	NM_015258.1		29,893,5112	CC,CA,AA		6.2969,11.3123,7.8803		878/1220	115933885	951,11117	1905	4129	6034	SO:0001819	synonymous_variant	23307	exon24			TGCAGCAGCTTCA	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.2634T>G	9.37:g.115933885A>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			A|0.938;C|0.062	0.062	strong		0.458	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
COLEC12	81035	hgsc.bcm.edu	37	18	334994	334994	+	Missense_Mutation	SNP	A	A	G	rs2305025	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						scavenged	.	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	30	1	0.0333333		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	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		
MICALCL	84953	hgsc.bcm.edu	37	11	12315915	12315915	+	Missense_Mutation	SNP	A	A	G	rs1493954	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:12315915A>G	ENST00000256186.2	+	3	1228	c.937A>G	c.(937-939)Agc>Ggc	p.S313G		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	313			S -> G (in dbSNP:rs1493954). {ECO:0000269|PubMed:14702039}.		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)		TCGCTCATTCAGCCTTCGGAA	0.572													A|||	2659	0.53095	0.618	0.4755	5008	,	,		17570	0.6786		0.3429	False		,,,				2504	0.4939				p.S313G		Atlas-SNP	.											.	MICALCL	59	.	0			c.A937G						PASS	.	A	GLY/SER	2129,1777		601,927,425	87.0	97.0	94.0		937	5.4	0.1	11	dbSNP_88	94	2779,5495		490,1799,1848	yes	missense	MICALCL	NM_032867.2	56	1091,2726,2273	GG,GA,AA		33.5871,45.4941,40.2956	benign	313/696	12315915	4908,7272	1953	4137	6090	SO:0001583	missense	84953	exon3			TCATTCAGCCTTC	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.937A>G	11.37:g.12315915A>G	ENSP00000256186:p.Ser313Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	1080	0.4945054945054945	284	0.5772357723577236	154	0.425414364640884	381	0.666083916083916	261	0.34432717678100266	A	9.494	1.101419	0.20632	0.545059	0.335871	ENSG00000133808	ENST00000256186	T	0.37915	1.17	5.41	5.41	0.78517	.	0.217809	0.32640	N	0.005834	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.22851	0.076	B	0.20384	0.029	T	0.35500	-0.9786	9	0.22109	T	0.4	.	11.8195	0.52230	1.0:0.0:0.0:0.0	rs1493954;rs56583837;rs57257051;rs1493954	313	Q6ZW33	MICLK_HUMAN	G	313	ENSP00000256186:S313G	ENSP00000256186:S313G	S	+	1	0	MICALCL	12272491	0.750000	0.28316	0.132000	0.22025	0.076000	0.17211	3.504000	0.53347	2.049000	0.60858	0.455000	0.32223	AGC	A|0.511;C|0.004	.	strong		0.572	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
PEAR1	375033	hgsc.bcm.edu	37	1	156877797	156877797	+	Silent	SNP	C	C	A	rs77235035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156877797C>A	ENST00000338302.3	+	9	1081	c.856C>A	c.(856-858)Cga>Aga	p.R286R	PEAR1_ENST00000292357.7_Silent_p.R286R			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	286	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTCTGTGACCGATTCACTGG	0.692													C|||	1140	0.227636	0.2383	0.1931	5008	,	,		12560	0.3502		0.1223	False		,,,				2504	0.2198				p.R286R		Atlas-SNP	.											PEAR1,NS,carcinoma,0,2	PEAR1	118	2	0			c.C856A						PASS	.	C		972,3404		115,742,1331	13.0	14.0	14.0		856	3.6	1.0	1	dbSNP_131	14	1050,7512		71,908,3302	no	coding-synonymous	PEAR1	NM_001080471.1		186,1650,4633	AA,AC,CC		12.2635,22.2121,15.6284		286/1038	156877797	2022,10916	2188	4281	6469	SO:0001819	synonymous_variant	375033	exon8			TGTGACCGATTCA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.856C>A	1.37:g.156877797C>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	202	72	0.356436	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.810;A|0.190	0.190	strong		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
PKD1L2	114780	hgsc.bcm.edu	37	16	81241100	81241100	+	RNA	SNP	G	G	C	rs386792899|rs11150370	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	52	0	0		WXS	Illumina HiSeq	Phase_I	49	11	0.22449	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		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:12921137T>A	ENST00000240189.2	+	4	1015	c.928T>A	c.(928-930)Ttg>Atg	p.L310M		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	310			L -> M (in dbSNP:rs17039283).		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)					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)		AGAAGAGGACTTGAAGTGTCT	0.493																																					p.L310M		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	0			c.T928A						scavenged	.						132.0	134.0	133.0					1																	12921137		2202	4297	6499	SO:0001583	missense	65122	exon4			GAGGACTTGAAGT		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.928T>A	1.37:g.12921137T>A	ENSP00000240189:p.Leu310Met	Somatic	103	2	0.0194175		WXS	Illumina HiSeq	Phase_I	131	6	0.0458015	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	G	2.970	-0.212708	0.06140	.	.	ENSG00000120952	ENST00000240189	T	0.01076	5.37	0.824	-1.65	0.08291	.	0.471727	0.17963	N	0.156117	T	0.00936	0.0031	N	0.25825	0.765	0.09310	N	1	B	0.06786	0.001	B	0.21360	0.034	T	0.44742	-0.9308	10	0.38643	T	0.18	.	5.2047	0.15285	0.0:0.0:0.2907:0.7093	rs17039283	310	O60811	PRAM2_HUMAN	M	310	ENSP00000240189:L310M	ENSP00000240189:L310M	L	+	1	2	PRAMEF2	12843724	0.011000	0.17503	0.001000	0.08648	0.011000	0.07611	-0.072000	0.11486	-1.430000	0.01985	-1.205000	0.01647	TTG	T|1.000;|0.000	.	weak		0.493	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
GLI3	2737	hgsc.bcm.edu	37	7	42079765	42079765	+	Silent	SNP	G	G	A	rs35961850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:42079765G>A	ENST00000395925.3	-	7	984	c.900C>T	c.(898-900)tcC>tcT	p.S300S	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	300					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						AGCTATGATCGGAGAGTGGTG	0.488									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	192	0.0383387	0.025	0.0389	5008	,	,		18920	0.0		0.1133	False		,,,				2504	0.0184				p.S300S		Atlas-SNP	.											.	GLI3	312	.	0			c.C900T						PASS	.	G		138,4268	98.9+/-137.6	3,132,2068	211.0	186.0	195.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	900	-0.9	1.0	7	dbSNP_126	195	818,7782	189.7+/-236.4	38,742,3520	no	coding-synonymous	GLI3	NM_000168.5		41,874,5588	AA,AG,GG		9.5116,3.1321,7.3505		300/1581	42079765	956,12050	2203	4300	6503	SO:0001819	synonymous_variant	2737	exon7	Familial Cancer Database	;	ATGATCGGAGAGT		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.900C>T	7.37:g.42079765G>A		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	326	205	0.628834	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.931;A|0.069	0.069	strong		0.488	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
L1TD1	54596	hgsc.bcm.edu	37	1	62675892	62675892	+	Silent	SNP	A	A	G	rs2481694|rs386631746	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:62675892A>G	ENST00000498273.1	+	4	1741	c.1446A>G	c.(1444-1446)gaA>gaG	p.E482E	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	482	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						AGGAGGAAGAAGAAGGAAAGA	0.398													G|||	2542	0.507588	0.5166	0.6254	5008	,	,		21834	0.251		0.6481	False		,,,				2504	0.5317				p.E482E		Atlas-SNP	.											.	L1TD1	114	.	0			c.A1446G						PASS	.	G	,	2369,2037	556.1+/-379.4	633,1103,467	62.0	62.0	62.0		1446,1446	-3.6	0.0	1	dbSNP_100	62	5648,2952	456.8+/-364.2	1859,1930,511	yes	coding-synonymous,coding-synonymous	L1TD1	NM_001164835.1,NM_019079.4	,	2492,3033,978	GG,GA,AA		34.3256,46.2324,38.3592	,	482/866,482/866	62675892	8017,4989	2203	4300	6503	SO:0001819	synonymous_variant	54596	exon5			GGAAGAAGAAGGA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1446A>G	1.37:g.62675892A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			A|0.412;G|0.588	0.588	strong		0.398	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
FARP2	9855	hgsc.bcm.edu	37	2	242380734	242380734	+	Missense_Mutation	SNP	G	G	A	rs146443541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242380734G>A	ENST00000264042.3	+	13	1344	c.1174G>A	c.(1174-1176)Gag>Aag	p.E392K	FARP2_ENST00000373287.4_Missense_Mutation_p.E392K|FARP2_ENST00000545004.1_Missense_Mutation_p.E392K	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	392					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)		CTCATTCCCCGAGGGATTGAG	0.473													G|||	6	0.00119808	0.0	0.0	5008	,	,		17915	0.0		0.005	False		,,,				2504	0.001				p.E392K		Atlas-SNP	.											.	FARP2	92	.	0			c.G1174A						PASS	.	G	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	104.0	98.0	100.0		1174	5.3	0.5	2	dbSNP_134	100	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FARP2	NM_014808.2	56	0,21,6482	AA,AG,GG		0.2209,0.0454,0.1615	benign	392/1055	242380734	21,12985	2203	4300	6503	SO:0001583	missense	9855	exon13			TTCCCCGAGGGAT	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.1174G>A	2.37:g.242380734G>A	ENSP00000264042:p.Glu392Lys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	12.87	2.068509	0.36470	4.54E-4	0.002209	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	T;T;T;D	0.81739	-0.88;-1.46;-1.46;-1.53	5.28	5.28	0.74379	.	0.652894	0.15957	N	0.236471	T	0.64605	0.2613	L	0.34521	1.04	0.47153	D	0.999336	P;P;P	0.52577	0.954;0.907;0.76	B;B;B	0.39840	0.311;0.246;0.091	T	0.68179	-0.5477	10	0.09843	T	0.71	.	18.9095	0.92477	0.0:0.0:1.0:0.0	.	392;392;392	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	K	392;392;392;79	ENSP00000264042:E392K;ENSP00000443876:E392K;ENSP00000362384:E392K;ENSP00000412772:E79K	ENSP00000264042:E392K	E	+	1	0	FARP2	242029407	1.000000	0.71417	0.484000	0.27391	0.024000	0.10985	8.223000	0.89779	2.472000	0.83506	0.655000	0.94253	GAG	G|0.999;A|0.001	0.001	strong		0.473	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
KIAA0100	9703	hgsc.bcm.edu	37	17	26961735	26961735	+	Missense_Mutation	SNP	G	G	A	rs118181996		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26961735G>A	ENST00000528896.2	-	16	2944	c.2870C>T	c.(2869-2871)aCa>aTa	p.T957I	RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.T814I|KIAA0100_ENST00000389003.3_Missense_Mutation_p.T814I|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	957						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GCGCATGGGTGTGTTGCCATA	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		19628	0.0		0.001	False		,,,				2504	0.0				p.T957I		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C2870T						PASS	.	G	ILE/THR	0,4406		0,0,2203	113.0	112.0	113.0		2870	5.9	1.0	17	dbSNP_132	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0100	NM_014680.3	89	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	957/2236	26961735	3,13003	2203	4300	6503	SO:0001583	missense	9703	exon16			ATGGGTGTGTTGC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2870C>T	17.37:g.26961735G>A	ENSP00000436773:p.Thr957Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	22	0.305556	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.4	4.139429	0.77775	0.0	3.49E-4	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.25085	1.83;1.82	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	L	0.47716	1.5	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.04537	-1.0944	10	0.25106	T	0.35	.	20.2651	0.98459	0.0:0.0:1.0:0.0	.	957	Q14667	K0100_HUMAN	I	957;927;957;814	ENSP00000436773:T957I;ENSP00000446443:T814I	ENSP00000005905:T957I	T	-	2	0	KIAA0100	23985862	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.328000	0.79160	2.796000	0.96246	0.563000	0.77884	ACA	G|0.999;A|0.001	0.001	strong		0.527	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
LRR1	122769	hgsc.bcm.edu	37	14	50074122	50074122	+	Missense_Mutation	SNP	T	T	A	rs17121605	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:50074122T>A	ENST00000298288.6	+	3	611	c.287T>A	c.(286-288)aTt>aAt	p.I96N	LRR1_ENST00000557531.1_3'UTR|LRR1_ENST00000318317.4_Intron	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	96			I -> N (in dbSNP:rs17121605).		protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						ATTCAGGCCATTTCCAGCAGT	0.363													A|||	943	0.188299	0.323	0.317	5008	,	,		17181	0.0268		0.2296	False		,,,				2504	0.0389				p.I96N		Atlas-SNP	.											.	LRR1	35	.	0			c.T287A						PASS	.	A	ASN/ILE,	1338,3064		204,930,1067	60.0	69.0	66.0		287,	4.4	1.0	14	dbSNP_123	66	1870,6728		219,1432,2648	yes	missense,intron	LRR1	NM_152329.3,NM_203467.1	149,	423,2362,3715	AA,AT,TT		21.7492,30.3953,24.6769	benign,	96/415,	50074122	3208,9792	2201	4299	6500	SO:0001583	missense	122769	exon3			AGGCCATTTCCAG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"""LRR-repeat protein 1"""	609193	"""peptidylprolyl isomerase (cyclophilin)-like 5"""	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.287T>A	14.37:g.50074122T>A	ENSP00000298288:p.Ile96Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	37	CCDS9686.1	432|432	0.1978021978021978|0.1978021978021978	134|134	0.27235772357723576|0.27235772357723576	107|107	0.2955801104972376|0.2955801104972376	27|27	0.0472027972027972|0.0472027972027972	164|164	0.21635883905013192|0.21635883905013192	A|A	2.002|2.002	-0.429268|-0.429268	0.04701|0.04701	0.303953|0.303953	0.217492|0.217492	ENSG00000165501|ENSG00000165501	ENST00000361579|ENST00000298288	.|T	.|0.37411	.|1.2	5.58|5.58	4.43|4.43	0.53597|0.53597	.|.	.|0.197635	.|0.56097	.|N	.|0.000028	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00413|0.00413	-1.525|-1.525	0.09310|0.09310	P|P	0.9999999999998432|0.9999999999998432	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.37478|0.37478	-0.9704|-0.9704	5|9	0.18710|0.07325	T|T	0.47|0.83	-8.4979|-8.4979	7.8858|7.8858	0.29648|0.29648	0.8097:0.0:0.0668:0.1235|0.8097:0.0:0.0668:0.1235	rs17121605;rs56802702;rs17121605|rs17121605;rs56802702;rs17121605	.|96	.|Q96L50	.|LLR1_HUMAN	Q|N	118|96	.|ENSP00000298288:I96N	ENSP00000354839:H118Q|ENSP00000298288:I96N	H|I	+|+	3|2	2|0	LRR1|LRR1	49143872|49143872	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.966000|0.966000	0.64601|0.64601	3.432000|3.432000	0.52824|0.52824	0.494000|0.494000	0.27859|0.27859	-0.263000|-0.263000	0.10527|0.10527	CAT|ATT	T|0.789;A|0.211	0.211	strong		0.363	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467	
OR51B5	282763	hgsc.bcm.edu	37	11	5364431	5364431	+	Silent	SNP	G	G	A	rs58233587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46.0	45.0	46.0		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
CCDC38	120935	hgsc.bcm.edu	37	12	96284650	96284650	+	Silent	SNP	A	A	G	rs6538681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:96284650A>G	ENST00000344280.3	-	9	1388	c.831T>C	c.(829-831)gcT>gcC	p.A277A	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	277										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTGAAAGGACAGCTGTCCTCC	0.443													G|||	3778	0.754393	0.9145	0.536	5008	,	,		21217	0.745		0.7058	False		,,,				2504	0.7526				p.A277A		Atlas-SNP	.											.	CCDC38	45	.	0			c.T831C						PASS	.	G		3874,532	244.3+/-253.7	1705,464,34	87.0	80.0	82.0		831	-5.0	0.0	12	dbSNP_116	82	6036,2564	418.2+/-352.7	2111,1814,375	no	coding-synonymous	CCDC38	NM_182496.2		3816,2278,409	GG,GA,AA		29.814,12.0744,23.8044		277/564	96284650	9910,3096	2203	4300	6503	SO:0001819	synonymous_variant	120935	exon9			AAGGACAGCTGTC	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.831T>C	12.37:g.96284650A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_182496	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																			A|0.248;G|0.752	0.752	strong		0.443	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
TTN	7273	hgsc.bcm.edu	37	2	179611884	179611884	+	Intron	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611884T>C	ENST00000591111.1	-	46	10585				TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.L5081L|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATATCTCTCTAGAGTCTCTC	0.552																																					p.L5081L		Atlas-SNP	.											.	TTN	18412	.	0			c.A15243G						PASS	.						63.0	72.0	69.0					2																	179611884		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TCTCTCTAGAGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5236A>G	2.37:g.179611884T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	165	17	0.10303	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.552	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PLCG2	5336	hgsc.bcm.edu	37	16	81929527	81929527	+	Silent	SNP	C	C	G	rs13333716	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81929527C>G	ENST00000359376.3	+	13	1402	c.1188C>G	c.(1186-1188)acC>acG	p.T396T		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	396	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						CCTTTGTTACCTCGAGGTCAG	0.547													C|||	224	0.0447284	0.0749	0.0403	5008	,	,		19718	0.002		0.0696	False		,,,				2504	0.0256				p.T396T		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1188G						PASS	.	C		300,3886		11,278,1804	170.0	180.0	177.0		1188	3.0	1.0	16	dbSNP_121	177	619,7837		19,581,3628	no	coding-synonymous	PLCG2	NM_002661.3		30,859,5432	GG,GC,CC		7.3202,7.1667,7.2694		396/1266	81929527	919,11723	2093	4228	6321	SO:0001819	synonymous_variant	5336	exon13			TGTTACCTCGAGG		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.1188C>G	16.37:g.81929527C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.936;G|0.064	0.064	strong		0.547	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
KCNQ4	9132	hgsc.bcm.edu	37	1	41300690	41300690	+	Silent	SNP	G	G	A	rs55964611	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41300690G>A	ENST00000347132.5	+	12	1747	c.1665G>A	c.(1663-1665)ccG>ccA	p.P555P	KCNQ4_ENST00000509682.2_Silent_p.P501P|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	555	A-domain (Tetramerization).				inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CACTGCGACCGTACGACGTGA	0.577													G|||	60	0.0119808	0.0061	0.0159	5008	,	,		19777	0.0		0.0358	False		,,,				2504	0.0051				p.P555P		Atlas-SNP	.											KCNQ4,colon,carcinoma,+1,1	KCNQ4	58	1	0			c.G1665A						PASS	.	G	,	61,4345	58.7+/-95.3	0,61,2142	126.0	111.0	116.0		1665,1503	-10.2	0.1	1	dbSNP_129	116	339,8261	116.8+/-176.5	5,329,3966	no	coding-synonymous,coding-synonymous	KCNQ4	NM_004700.3,NM_172163.2	,	5,390,6108	AA,AG,GG		3.9419,1.3845,3.0755	,	555/696,501/642	41300690	400,12606	2203	4300	6503	SO:0001819	synonymous_variant	9132	exon12			GCGACCGTACGAC	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1665G>A	1.37:g.41300690G>A		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	213	117	0.549296	NM_004700	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	35	0.016025641025641024	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	27	0.03562005277044855	G	7.173	0.587968	0.13812	0.013845	0.039419	ENSG00000117013	ENST00000443478	.	.	.	5.12	-10.2	0.00374	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46205	-0.9208	4	.	.	.	-16.1176	3.1599	0.06516	0.2055:0.2654:0.3752:0.1539	rs55964611;rs61745209	.	.	.	I	416	.	.	V	+	1	0	KCNQ4	41073277	0.000000	0.05858	0.129000	0.21949	0.974000	0.67602	-5.980000	0.00087	-3.636000	0.00128	-1.535000	0.00915	GTA	G|0.974;A|0.026	0.026	strong		0.577	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
CDH17	1015	hgsc.bcm.edu	37	8	95158382	95158382	+	Silent	SNP	C	C	T	rs1131830	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:95158382C>T	ENST00000027335.3	-	15	2065	c.1941G>A	c.(1939-1941)ttG>ttA	p.L647L	CDH17_ENST00000441892.2_Silent_p.L433L|CDH17_ENST00000450165.2_Silent_p.L647L	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	647	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)			ACACAGAGCTCAAGGAAGACC	0.443													C|||	2161	0.43151	0.2678	0.3761	5008	,	,		18107	0.5327		0.5457	False		,,,				2504	0.4703				p.L647L		Atlas-SNP	.											.	CDH17	119	.	0			c.G1941A						PASS	.	C	,	1319,3087	443.1+/-346.9	185,949,1069	85.0	78.0	81.0		1941,1941	5.9	0.1	8	dbSNP_86	81	4604,3996	599.3+/-394.1	1238,2128,934	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	1423,3077,2003	TT,TC,CC		46.4651,29.9365,45.5405	,	647/833,647/833	95158382	5923,7083	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon15			AGAGCTCAAGGAA	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.1941G>A	8.37:g.95158382C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			T|0.375;G|0.108;C|0.432;A|0.085	0.375	strong		0.443	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
DISP2	85455	hgsc.bcm.edu	37	15	40656141	40656141	+	Silent	SNP	T	T	C	rs12443160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40656141T>C	ENST00000267889.3	+	2	522	c.435T>C	c.(433-435)caT>caC	p.H145H		NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	145					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		TGCAGCACCATGTGGTCAGCG	0.657													T|||	1245	0.248602	0.1036	0.3213	5008	,	,		14594	0.5337		0.0895	False		,,,				2504	0.2628				p.H145H		Atlas-SNP	.											.	DISP2	86	.	0			c.T435C						PASS	.	T		468,3938		26,416,1761	31.0	34.0	33.0		435	-7.3	0.7	15	dbSNP_120	33	707,7889		22,663,3613	no	coding-synonymous	DISP2	NM_033510.1		48,1079,5374	CC,CT,TT		8.2248,10.6219,9.0371		145/1402	40656141	1175,11827	2203	4298	6501	SO:0001819	synonymous_variant	85455	exon2			GCACCATGTGGTC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.435T>C	15.37:g.40656141T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			T|0.861;C|0.139	0.139	strong		0.657	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
FAM118A	55007	hgsc.bcm.edu	37	22	45723854	45723854	+	Silent	SNP	C	C	G	rs9615108	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45723854C>G	ENST00000216214.3	+	5	1266	c.432C>G	c.(430-432)gtC>gtG	p.V144V	FAM118A_ENST00000405673.1_Silent_p.V144V|FAM118A_ENST00000441876.2_Silent_p.V144V|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	144						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)		GCGCCATGGTCCTGACCACCA	0.597													C|||	1569	0.313299	0.0371	0.5014	5008	,	,		18201	0.3006		0.5905	False		,,,				2504	0.2812				p.V144V		Atlas-SNP	.											.	FAM118A	32	.	0			c.C432G						PASS	.	C	,	546,3860	246.5+/-255.1	36,474,1693	52.0	43.0	46.0		432,432	-7.5	0.9	22	dbSNP_119	46	5192,3408	636.3+/-399.1	1559,2074,667	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	1595,2548,2360	GG,GC,CC		39.6279,12.3922,44.1181	,	144/358,144/358	45723854	5738,7268	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon4			CATGGTCCTGACC	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.432C>G	22.37:g.45723854C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			C|0.590;G|0.410	0.410	strong		0.597	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
CFAP69	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:89906609C>T	ENST00000389297.4	+	11	1367	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N	C7orf63_ENST00000316089.8_Silent_p.N372N|C7orf63_ENST00000497910.1_Silent_p.N354N	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	97	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	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		
COL6A2	1292	hgsc.bcm.edu	37	21	47545823	47545823	+	Silent	SNP	G	G	A	rs13052956	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47545823G>A	ENST00000300527.4	+	26	2198	c.2094G>A	c.(2092-2094)gcG>gcA	p.A698A	COL6A2_ENST00000409416.1_Silent_p.A698A|COL6A2_ENST00000397763.1_Silent_p.A698A|COL6A2_ENST00000310645.5_Silent_p.A698A|COL6A2_ENST00000357838.4_Silent_p.A698A	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	698	Nonhelical region.|VWFA 2. {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)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		AGTGGATTGCGGGCGGCACCT	0.607													G|||	1974	0.394169	0.208	0.6398	5008	,	,		14604	0.4306		0.5109	False		,,,				2504	0.3139				p.A698A		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2094A						PASS	.	G	,,	1065,3341	387.2+/-326.4	148,769,1286	76.0	69.0	72.0		2094,2094,2094	-8.4	0.0	21	dbSNP_121	72	4303,4297	576.5+/-390.4	1047,2209,1044	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	1195,2978,2330	AA,AG,GG		49.9651,24.1716,41.2733	,,	698/1020,698/919,698/829	47545823	5368,7638	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			GATTGCGGGCGGC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2094G>A	21.37:g.47545823G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	153	150	0.980392	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			G|0.578;A|0.422	0.422	strong		0.607	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
MKI67	4288	hgsc.bcm.edu	37	10	129904560	129904560	+	Silent	SNP	C	C	T	rs2853346	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:129904560C>T	ENST00000368654.3	-	13	5919	c.5544G>A	c.(5542-5544)acG>acA	p.T1848T	MKI67_ENST00000368653.3_Silent_p.T1488T	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1848	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)				TCTCATCAGTCGTGGGGTTAT	0.488													C|||	1440	0.28754	0.236	0.219	5008	,	,		19486	0.3819		0.2992	False		,,,				2504	0.2965				p.T1848T		Atlas-SNP	.											MKI67,NS,adenocarcinoma,-1,1	MKI67	363	1	0			c.G5544A						PASS	.	C	,	1107,3299	398.1+/-330.7	134,839,1230	225.0	226.0	225.0		4464,5544	-1.6	0.0	10	dbSNP_100	225	2503,6097	410.9+/-350.3	359,1785,2156	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	493,2624,3386	TT,TC,CC		29.1047,25.1248,27.7564	,	1488/2897,1848/3257	129904560	3610,9396	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			ATCAGTCGTGGGG	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.5544G>A	10.37:g.129904560C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	257	111	0.431907	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			T|0.226;G|0.139;C|0.578;A|0.056	0.226	strong		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ETV3L	440695	hgsc.bcm.edu	37	1	157062739	157062739	+	Missense_Mutation	SNP	C	C	G	rs12136960	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67	0	0		WXS	Illumina HiSeq	Phase_I	105	68	0.647619	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	
MBD1	4152	hgsc.bcm.edu	37	18	47801800	47801800	+	Intron	SNP	G	G	A	rs140690	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:47801800G>A	ENST00000591416.1	-	8	1224				MBD1_ENST00000269471.5_Intron|MBD1_ENST00000585595.1_Silent_p.R269R|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000398488.1_Intron|MBD1_ENST00000398495.2_Silent_p.R269R|MBD1_ENST00000269468.5_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000457839.2_Silent_p.R269R|MBD1_ENST00000398493.1_Intron|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000353909.3_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000591535.1_Intron|MBD1_ENST00000424334.2_Silent_p.R295R|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000339998.6_Intron			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1						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						GGCGACGCAGGCGGTGAGCAA	0.622													G|||	1019	0.203474	0.1051	0.1873	5008	,	,		17450	0.123		0.3956	False		,,,				2504	0.2331				p.R269R		Atlas-SNP	.											MBD1_ENST00000457839,NS,carcinoma,0,1	MBD1	228	1	0			c.C807T						PASS	.	G	,,,,,,,,,,,,,	286,1460		21,244,608	14.0	14.0	14.0		,807,807,,807,,,,,,,,,	-1.5	0.9	18	dbSNP_78	14	1479,2495		281,917,789	no	intron,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron	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	,,,,,,,,,,,,,	302,1161,1397	AA,AG,GG		37.2169,16.3803,30.8566	,,,,,,,,,,,,,	,269/631,269/630,,269/575,,,,,,,,,	47801800	1765,3955	873	1987	2860	SO:0001627	intron_variant	4152	exon9			ACGCAGGCGGTGA	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.792+169C>T	18.37:g.47801800G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			G|0.782;A|0.218	0.218	strong		0.622	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
PRRC2B	84726	hgsc.bcm.edu	37	9	134371165	134371165	+	Silent	SNP	C	C	T	rs41296113	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134371165C>T	ENST00000357304.4	+	31	6649	c.6594C>T	c.(6592-6594)gcC>gcT	p.A2198A	PRRC2B_ENST00000372249.1_Missense_Mutation_p.P268L|PRRC2B_ENST00000458550.1_Silent_p.A1504A|PRRC2B_ENST00000465931.1_3'UTR|PRRC2B_ENST00000405995.1_Silent_p.A1504A	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	2198							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCCTGGGAGCCGTGAAGCTGC	0.547													C|||	296	0.0591054	0.0492	0.1412	5008	,	,		18174	0.0526		0.0577	False		,,,				2504	0.0225				p.A2198A		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C6594T						PASS	.	C		191,3711		2,187,1762	45.0	50.0	48.0		6594	1.6	1.0	9	dbSNP_127	48	390,7898		11,368,3765	no	coding-synonymous	PRRC2B	NM_013318.3		13,555,5527	TT,TC,CC		4.7056,4.8949,4.7662		2198/2230	134371165	581,11609	1951	4144	6095	SO:0001819	synonymous_variant	84726	exon31			GGGAGCCGTGAAG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.6594C>T	9.37:g.134371165C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	141	0.06456043956043957	29	0.05894308943089431	39	0.10773480662983426	30	0.05244755244755245	43	0.05672823218997362	C	19.23	3.786569	0.70337	0.048949	0.047056	ENSG00000130723	ENST00000372249	.	.	.	4.75	1.56	0.23342	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.28068	N	0.93271	.	.	.	.	.	.	T	0.08806	-1.0704	5	0.87932	D	0	-16.5039	4.0105	0.09621	0.177:0.4296:0.0:0.3935	rs41296113;rs61742042	.	.	.	L	268	.	ENSP00000361323:P268L	P	+	2	0	PRRC2B	133360986	0.958000	0.32768	0.998000	0.56505	0.995000	0.86356	-0.042000	0.12063	0.161000	0.19458	0.557000	0.71058	CCG	C|0.936;T|0.064	0.064	strong		0.547	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TMC2	117532	hgsc.bcm.edu	37	20	2575543	2575543	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:2575543C>T	ENST00000358864.1	+	9	1021	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	336					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						GCTGAGGTACCGGCTGCCTAT	0.517																																					p.R336W		Atlas-SNP	.											TMC2,NS,carcinoma,0,1	TMC2	121	1	0			c.C1006T						scavenged	.						127.0	100.0	109.0					20																	2575543		2203	4300	6503	SO:0001583	missense	117532	exon9			AGGTACCGGCTGC	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.1006C>T	20.37:g.2575543C>T	ENSP00000351732:p.Arg336Trp	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	247	3	0.0121457	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549299	0.65311	.	.	ENSG00000149488	ENST00000358864	T	0.50813	0.73	5.36	0.135	0.14775	.	0.000000	0.85682	D	0.000000	T	0.70465	0.3227	M	0.89478	3.035	0.54753	D	0.999987	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.991;0.999;0.997	T	0.76702	-0.2862	10	0.87932	D	0	-23.6014	14.1015	0.65059	0.4488:0.5512:0.0:0.0	.	167;168;336;336	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	W	336	ENSP00000351732:R336W	ENSP00000351732:R336W	R	+	1	2	TMC2	2523543	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.836000	0.39191	0.107000	0.17824	-1.028000	0.02416	CGG	.	.	none		0.517	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
NRG1	3084	hgsc.bcm.edu	37	8	32505633	32505633	+	Intron	SNP	G	G	C	rs35641374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:32505633G>C	ENST00000405005.3	+	5	502				NRG1_ENST00000287845.5_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520502.2_Missense_Mutation_p.V133L|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000521670.1_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TGCCTCAGCTGTGTGGGTGTC	0.502													G|||	151	0.0301518	0.0401	0.0245	5008	,	,		18191	0.0		0.0179	False		,,,				2504	0.0644				p.V133L		Atlas-SNP	.											.	NRG1	260	.	0			c.G397C						PASS	.	G	,,,,,,,,,,,,LEU/VAL,,,	108,4298	84.8+/-123.5	2,104,2097	136.0	120.0	125.0		,,,,,,,,,,,,397,,,	4.3	1.0	8	dbSNP_126	125	160,8440	75.7+/-138.4	0,160,4140	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron	NRG1	NM_001159995.1,NM_001159999.1,NM_001160001.1,NM_001160002.1,NM_001160004.1,NM_001160005.1,NM_001160007.1,NM_001160008.1,NM_004495.3,NM_013956.3,NM_013957.3,NM_013958.3,NM_013959.3,NM_013960.3,NM_013962.2,NM_013964.3	,,,,,,,,,,,,32,,,	2,264,6237	CC,CG,GG		1.8605,2.4512,2.0606	,,,,,,,,,,,,,,,	,,,,,,,,,,,,133/297,,,	32505633	268,12738	2203	4300	6503	SO:0001627	intron_variant	3084	exon1			TCAGCTGTGTGGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31230G>C	8.37:g.32505633G>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_013959	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	47	0.02152014652014652	25	0.0508130081300813	11	0.03038674033149171	0	0.0	11	0.014511873350923483	G	12.29	1.893835	0.33442	0.024512	0.018605	ENSG00000157168	ENST00000520502;ENST00000523041	.	.	.	6.07	4.26	0.50523	.	.	.	.	.	T	0.09818	0.0241	L	0.27053	0.805	0.80722	D	1	B;B	0.18610	0.029;0.012	B;B	0.17979	0.02;0.014	T	0.05305	-1.0893	8	0.34782	T	0.22	.	10.1211	0.42621	0.1604:0.0:0.8396:0.0	rs35641374	133;133	Q53F54;Q02297-10	.;.	L	133;93	.	ENSP00000433289:V133L	V	+	1	0	NRG1	32625175	0.999000	0.42202	0.996000	0.52242	0.945000	0.59286	1.799000	0.38824	1.550000	0.49438	0.655000	0.94253	GTG	G|0.976;C|0.024	0.024	strong		0.502	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
RAI14	26064	hgsc.bcm.edu	37	5	34807928	34807928	+	Silent	SNP	C	C	T	rs6895634	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:34807928C>T	ENST00000265109.3	+	6	632	c.345C>T	c.(343-345)gtC>gtT	p.V115V	RAI14_ENST00000515799.1_Silent_p.V118V|RAI14_ENST00000428746.2_Silent_p.V115V|RAI14_ENST00000397449.1_Silent_p.V108V|RAI14_ENST00000503673.1_Silent_p.V115V|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000512629.1_Silent_p.V115V|RAI14_ENST00000506376.1_Silent_p.V107V	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	139	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	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	
